PeakID (cmd=annotatePeaks.pl ../MergedChipseq.bed hg38 -m knownResults/known5.motif)	Chr	Start	End	Strand	Peak Score	Focus Ratio/Region Size	Annotation	Detailed Annotation	Distance to TSS	Nearest PromoterID	Entrez ID	Nearest Unigene	Nearest Refseq	Nearest Ensembl	Gene Name	Gene Alias	Gene Description	Gene Type	CpG%	GC%	ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer Distance From Peak(sequence,strand,conservation)
chunk0013_450_1	chr1	173918372	173918571	+	0	NA	Intergenic	L2a|LINE|L2	-1093	NM_000488	462	Hs.75599	NM_000488	ENSG00000117601	SERPINC1	AT3|AT3D|ATIII|ATIII-R2|ATIII-T1|ATIII-T2|THPH7	serpin family C member 1	protein-coding	0.015075	0.460000	80(CAGCAGACACTGTTCT,-,0.00),81(AGCAGACACTGTTCTT,+,0.00)
chunk0147_447_1	chr4	187919966	187920317	+	0	NA	Intergenic	Intergenic	-75630	NM_174900	132625	Hs.335787	NM_174900	ENSG00000179059	ZFP42	REX-1|REX1|ZNF754|zfp-42	ZFP42 zinc finger protein	protein-coding	0.008547	0.372159	
chunk0178_362_1	chr7	39238816	39239127	+	0	NA	intron (NM_007252, intron 5 of 10)	L1ME3|LINE|L1	167375	NR_046711	100861520	Hs.571292	NR_046711	ENSG00000224122	POU6F2-AS1	-	POU6F2 antisense RNA 1	ncRNA	0.009646	0.365385	
chunk0088_208_1	chr18	48061609	48062427	+	0	NA	intron (NM_001039360, intron 1 of 2)	intron (NM_001039360, intron 1 of 2)	75291	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.008557	0.440781	385(GGGCACACAGTGTACC,-,0.00),386(GGCACACAGTGTACCT,+,0.00)
chunk0005_384_1	chr1	61975778	61976502	+	0	NA	intron (NM_176877, intron 27 of 42)	intron (NM_176877, intron 27 of 42)	-102646	NR_036058	100422902		NR_036058	ENSG00000263908	MIR3116-1	-	microRNA 3116-1	ncRNA	0.008287	0.431724	
chunk0192_105_1	chr8	61666528	61666910	+	0	NA	intron (NM_032467, intron 4 of 4)	intron (NM_032467, intron 4 of 4)	23130	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.002618	0.336815	
chunk0111_416_1	chr20	34759364	34759663	+	0	NA	intron (NM_014071, intron 5 of 14)	L1ME4b|LINE|L1	55169	NM_021202	58476	Hs.516994	NM_021202	ENSG00000078804	TP53INP2	C20orf110|DOR|PIG-U|PIGU|PINH|dJ1181N3.1	tumor protein p53 inducible nuclear protein 2	protein-coding	0.000000	0.323333	
chunk0205_66_1	chr9	106672510	106672871	+	0	NA	intron (NR_104145, intron 5 of 6)	intron (NR_104145, intron 5 of 6)	56632	NR_104145	100996590	Hs.147110	NR_104145	ENSG00000234323	LINC01505	-	long intergenic non-protein coding RNA 1505	ncRNA	0.008310	0.381215	
chunk0101_290_1	chr2	134396803	134397039	+	0	NA	intron (NM_002410, intron 10 of 15)	intron (NM_002410, intron 10 of 15)	142662	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.000000	0.535865	
chunk0175_42_1	chr7	1070539	1071022	+	0	NA	intron (NM_032350, intron 2 of 4)	(CACACA)n|Simple_repeat|Simple_repeat	15505	NM_138445	115330	Hs.585007	NM_138445	ENSG00000164849	GPR146	PGR8	G protein-coupled receptor 146	protein-coding	0.086957	0.576446	
chunk0059_186_1	chr14	32667784	32668238	+	0	NA	intron (NM_004274, intron 7 of 13)	intron (NM_004274, intron 7 of 13)	-271242	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.004405	0.362637	
chunk0022_57_1	chr10	8350377	8350649	+	0	NA	Intergenic	Intergenic	-82208	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.007353	0.362637	172(CAGCACGCTGTGTACT,-,0.00),173(AGCACGCTGTGTACTT,+,0.00)
chunk0210_176_1	chrX	79149611	79150070	+	0	NA	Intergenic	Intergenic	-21132	NM_032553	84636	Hs.326713	NM_032553	ENSG00000147138	GPR174	FKSG79|GPCR17|LYPSR3	G protein-coupled receptor 174	protein-coding	0.002179	0.350000	
chunk0210_167_1	chrX	78009048	78009468	+	0	NA	exon (NM_001282224, exon 7 of 22)	exon (NM_001282224, exon 7 of 22)	-39620	NM_001029891	441531	Hs.632822	NM_001029891	ENSG00000226784	PGAM4	PGAM-B|PGAM1|PGAM3|dJ1000K24.1	phosphoglycerate mutase family member 4	protein-coding	0.011905	0.368171	
chunk0196_236_1	chr8	108225296	108225560	+	0	NA	intron (NM_001568, intron 7 of 12)	Charlie1|DNA|hAT-Charlie	23302	NM_001568	3646	Hs.405590	NM_001568	ENSG00000104408	EIF3E	EIF3-P48|EIF3S6|INT6|eIF3-p46	eukaryotic translation initiation factor 3 subunit E	protein-coding	0.003788	0.392453	
chunk0003_231_1	chr1	35718515	35718753	+	0	NA	intron (NM_152374, intron 1 of 1)	intron (NM_152374, intron 1 of 1)	555	NM_152374	127703	Hs.112023	NM_152374	ENSG00000142686	C1orf216	-	chromosome 1 open reading frame 216	protein-coding	0.084034	0.694561	
chunk0032_83_1	chr11	2890488	2891073	+	0	NA	intron (NM_001302862, intron 2 of 2).2	intron (NM_001302862, intron 2 of 2).2	-5015	NM_000076	1028	Hs.106070	NM_000076	ENSG00000129757	CDKN1C	BWCR|BWS|KIP2|WBS|p57|p57Kip2	cyclin dependent kinase inhibitor 1C	protein-coding	0.035897	0.679181	306(CAGGACAGGCTGTTCT,-,0.00),307(AGGACAGGCTGTTCTT,+,0.00)
chunk0110_329_1	chr20	19120601	19120953	+	0	NA	Intergenic	Intergenic	-91869	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.011364	0.371105	
chunk0154_430_1	chr5	89473127	89473487	+	0	NA	Intergenic	Intergenic	543413	NR_037433	100500825		NR_037433	ENSG00000264342	MIR3660	mir-3660	microRNA 3660	ncRNA	0.005556	0.390582	
chunk0009_7_1	chr1	99850086	99850465	+	0	NA	promoter-TSS (NM_000646)	promoter-TSS (NM_000646)	191	NM_000642	178	Hs.904	NM_000028	ENSG00000162688	AGL	GDE	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	protein-coding	0.100264	0.689474	
chunk0172_10_1	chr6	132675977	132676318	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-30144	NM_138327	134864	Hs.375030	NM_138327	ENSG00000146399	TAAR1	TA1|TAR1|TRAR1	trace amine associated receptor 1	protein-coding	0.000000	0.301170	
chunk0166_253_1	chr6	47483912	47484541	+	0	NA	intron (NM_012120, intron 1 of 17)	intron (NM_012120, intron 1 of 17)	6437	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.001590	0.330159	325(GAGACCATGCTGTACT,-,0.00),326(AGACCATGCTGTACTC,+,0.00)
chunk0092_48_1	chr19	19606027	19606340	+	0	NA	intron (NR_038198, intron 1 of 7)	MLT1E1A|LTR|ERVL-MaLR	12733	NR_038198	80714	Hs.466257	NM_025245	ENSG00000105717	PBX4	-	PBX homeobox 4	protein-coding	0.000000	0.484076	
chunk0151_158_1	chr5	49656984	49658353	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	783732	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.018262	0.402920	
chunk0157_176_1	chr5	118413300	118413819	+	0	NA	intron (NR_104610, intron 9 of 9)	L1MA9|LINE|L1	130985	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.001927	0.246154	297(AAGAACACAAAGTACA,-,0.00),298(AGAACACAAAGTACAC,+,0.00)
chunk0110_208_1	chr20	15170946	15171168	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	-25801	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.022523	0.488789	
chunk0145_45_1	chr4	144705991	144706294	+	0	NA	intron (NM_022475, intron 4 of 12)	intron (NM_022475, intron 4 of 12)	-60123	NR_037595	646576	Hs.632595	NR_037595	ENSG00000248890	HHIP-AS1	-	HHIP antisense RNA 1	ncRNA	0.009901	0.404605	
chunk0017_239_1	chr1	208292767	208293537	+	0	NA	Intergenic	Intergenic	-48832	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.005195	0.395590	544(GGTACTCCCTGTGCAC,+,0.00)
chunk0010_312_1	chr1	118055922	118056174	+	0	NA	intron (NM_206996, intron 18 of 48)	L1MEd|LINE|L1	126299	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.003968	0.296443	
chunk0212_416_1	chrX	152101383	152101717	+	0	NA	Intergenic	L1MD2|LINE|L1	16389	NM_021049	4104	Hs.18048	NM_021049		MAGEA5	CT1.5|MAGE5|MAGEA4	MAGE family member A5	protein-coding	0.008982	0.316418	
chunk0021_42_1	chr10	899135	899685	+	0	NA	intron (NM_015155, intron 1 of 17)	intron (NM_015155, intron 1 of 17)	32295	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.001818	0.344828	
chunk0165_217_1	chr6	35092979	35093217	+	0	NA	Intergenic	Intergenic	48312	NM_001093728									0.021008	0.489540	
chunk0194_178_1	chr8	85126757	85127399	+	0	NA	intron (NM_033402, intron 9 of 18)	intron (NM_033402, intron 9 of 18)	19990	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.001558	0.321928	
chunk0049_82_1	chr12	90677371	90677819	+	0	NA	Intergenic	Intergenic	-240428	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.013393	0.338530	
chunk0191_348_1	chr8	56395200	56396061	+	0	NA	Intergenic	Intergenic	-4920	NR_103832	442388	Hs.632065	NM_001145251	ENSG00000253542	SDR16C6P	SDR16C6	short chain dehydrogenase/reductase family 16C member 6, pseudogene	pseudo	0.004646	0.365429	541(AAGTACATCAAGTGCT,-,0.00),542(AGTACATCAAGTGCTC,+,0.00)
chunk0175_365_1	chr6	167880752	167881454	+	0	NA	intron (NM_001207008, intron 6 of 31)	L1M5|LINE|L1	53468	NM_001291964	4301	Hs.614974	NM_005936	ENSG00000130396	AFDN	AF6|MLL-AF6|MLLT4|l-afadin	afadin, adherens junction formation factor	protein-coding	0.000000	0.320057	
chunk0047_403_1	chr12	75819625	75819975	+	0	NA	Intergenic	Intergenic	211976	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.008571	0.424501	
chunk0185_315_1	chr7	131400809	131401599	+	0	NA	intron (NM_001145354, intron 7 of 18)	intron (NM_001145354, intron 7 of 18)	73368	NM_013255	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.000000	0.345133	268(AAGGACAAGAAGTTCC,-,0.00),269(AGGACAAGAAGTTCCT,+,0.00)
chunk0051_330_1	chr12	120142222	120142696	+	0	NA	intron (NM_006836, intron 44 of 57)	intron (NM_006836, intron 44 of 57)	13040	NR_039719	100616179		NR_039719	ENSG00000266704	MIR4498	mir-4498	microRNA 4498	ncRNA	0.027426	0.541053	158(AAGAACACAATGTCCC,-,0.00),159(AGAACACAATGTCCCT,+,0.00)
chunk0149_187_1	chr5	21340304	21340558	+	0	NA	Intergenic	Intergenic	-119049	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.007874	0.329412	
chunk0033_216_1	chr11	17238531	17238763	+	0	NA	Intergenic	Intergenic	-38092	NM_005013	4925	Hs.654599	NM_005013	ENSG00000070081	NUCB2	HEL-S-109|NEFA	nucleobindin 2	protein-coding	0.008621	0.429185	
chunk0036_146_1	chr11	62179896	62180587	+	0	NA	Intergenic	L1PA13|LINE|L1	-9997	NM_006552	10648	Hs.202686	NM_006552	ENSG00000168515	SCGB1D1	LIPA|LPHA|LPNA	secretoglobin family 1D member 1	protein-coding	0.013025	0.397399	
chunk0147_22_1	chr4	171308665	171309047	+	0	NA	Intergenic	L1MC3|LINE|L1	122672	NR_106730	102466953		NR_106730	ENSG00000278502	MIR6082	hsa-mir-6082	microRNA 6082	ncRNA	0.000000	0.355091	
chunk0182_63_1	chr7	92064534	92065004	+	0	NA	intron (NM_147185, intron 24 of 49)	intron (NM_147185, intron 24 of 49)	69757	NM_000786	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.004255	0.343949	
chunk0138_458_1	chr4	47672042	47672397	+	0	NA	intron (NM_001278585, intron 8 of 19)	L2a|LINE|L2	19550	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.008451	0.373596	172(TGGAACATCATGTACA,-,0.00),173(GGAACATCATGTACAC,+,0.00)
chunk0131_250_1	chr3	149539470	149539711	+	0	NA	intron (NM_015472, intron 4 of 6)	intron (NM_015472, intron 4 of 6)	65009	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.004149	0.471074	
chunk0200_399_1	chr9	27184976	27185550	+	0	NA	intron (NM_001290077, intron 7 of 21)	intron (NM_001290077, intron 7 of 21)	76122	NM_001290077	7010	Hs.89640	NM_000459	ENSG00000120156	TEK	CD202B|GLC3E|TIE-2|TIE2|VMCM|VMCM1	TEK receptor tyrosine kinase	protein-coding	0.008711	0.405217	
chunk0123_211_1	chr3	44988435	44988677	+	0	NA	intron (NR_023353, intron 1 of 6)	MER58A|DNA|hAT-Charlie	12307	NM_015004	23016	Hs.719958	NM_015004	ENSG00000075914	EXOSC7	EAP1|RRP42|Rrp42p|hRrp42p|p8	exosome component 7	protein-coding	0.000000	0.411523	
chunk0121_203_1	chr3	21491748	21491947	+	0	NA	intron (NM_024697, intron 4 of 7)	intron (NM_024697, intron 4 of 7)	-50942	NR_046731	100874216	Hs.661720	NR_046731	ENSG00000225542	ZNF385D-AS1	-	ZNF385D antisense RNA 1	ncRNA	0.005025	0.345000	
chunk0040_33_1	chr11	110348640	110349860	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-52538	NM_001260493	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.004918	0.438165	
chunk0198_422_1	chr8	143055426	143056438	+	0	NA	Intergenic	Intergenic	15570	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.019763	0.372162	
chunk0042_93_1	chr12	2752674	2752961	+	0	NA	Intergenic	CpG	18852	NR_033958	283440	Hs.448720	NR_033958	ENSG00000256150	ITFG2-AS1	-	ITFG2 antisense RNA 1	ncRNA	0.073171	0.687500	
chunk0056_63_1	chr13	78379413	78379757	+	0	NA	intron (NR_047001, intron 3 of 5)	intron (NR_047001, intron 3 of 5)	223975	NM_006237	5457	Hs.654522	NM_006237	ENSG00000152192	POU4F1	BRN3A|Oct-T1|RDC-1|brn-3A	POU class 4 homeobox 1	protein-coding	0.011628	0.339130	
chunk0153_391_1	chr5	75274447	75275094	+	0	NA	Intergenic	Intergenic	-37892	NM_001164443	256006	Hs.482533	NM_001164443	ENSG00000145700	ANKRD31	-	ankyrin repeat domain 31	protein-coding	0.007728	0.429012	
chunk0066_192_1	chr15	33214174	33214555	+	0	NA	Intergenic	Intergenic	-19631	NM_001277313	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.007874	0.329843	188(AAGACTTCCTGTTCTT,+,0.00)
chunk0109_278_1	chr20	8116222	8116477	+	0	NA	Intergenic	Intergenic	-15916	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.011765	0.437500	
chunk0197_255_1	chr8	123441114	123441895	+	0	NA	3' UTR (NM_001283027, exon 7 of 7)	3' UTR (NM_001283027, exon 7 of 7)	24779	NM_001283024	55093	Hs.18029	NM_018024	ENSG00000156795	WDYHV1	C8orf32	WDYHV motif containing 1	protein-coding	0.012804	0.384910	
chunk0211_342_1	chrX	124911756	124911998	+	0	NA	intron (NM_001163278, intron 1 of 31)	intron (NM_001163278, intron 1 of 31)	51940	NM_001163279	10178	Hs.23796	NM_014253	ENSG00000009694	TENM1	ODZ1|ODZ3|TEN-M1|TNM|TNM1|ten-1	teneurin transmembrane protein 1	protein-coding	0.012397	0.353909	
chunk0054_124_1	chr13	43335909	43336146	+	0	NA	intron (NM_001127615, intron 9 of 16)	intron (NM_001127615, intron 9 of 16)	-112825	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.000000	0.357143	
chunk0195_36_1	chr8	93239817	93240702	+	0	NA	Intergenic	Intergenic	-73409	NM_001242668									0.004520	0.442438	268(TTGTACATAATGTTCT,-,0.00),269(TGTACATAATGTTCTC,+,0.00),683(TAGGACAGAGTGTGAT,-,0.00),684(AGGACAGAGTGTGATT,+,0.00)
chunk0126_141_1	chr3	76418575	76418787	+	0	NA	Intergenic	MER57F|LTR|ERV1	-621462	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.014151	0.314554	
chunk0103_102_1	chr2	161308513	161308738	+	0	NA	intron (NM_005805, intron 1 of 11)	CpG	350	NM_005805	10213	Hs.740477	NM_005805	ENSG00000115233	PSMD14	PAD1|POH1|RPN11	proteasome 26S subunit, non-ATPase 14	protein-coding	0.075556	0.676991	
chunk0064_154_1	chr14	91822051	91822283	+	0	NA	intron (NM_001128596, intron 1 of 11)	L1ME2|LINE|L1	14359	NM_152332	123036	Hs.510262	NM_152332	ENSG00000165929	TC2N	C14orf47|C2CD1|MTAC2D1|Tac2-N	tandem C2 domains, nuclear	protein-coding	0.000000	0.313305	
chunk0133_42_1	chr3	166177661	166178157	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-340444	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.004032	0.334004	
chunk0086_33_1	chr18	12589250	12589949	+	0	NA	intron (NM_001128627, intron 2 of 15)	intron (NM_001128627, intron 2 of 15)	67133	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.004292	0.411429	
chunk0016_271_1	chr1	200473966	200474581	+	0	NA	Intergenic	Intergenic	-64215	NM_001281293	23528	Hs.59757	NM_012482	ENSG00000162702	ZNF281	ZBP-99|ZNP-99	zinc finger protein 281	protein-coding	0.017886	0.443182	
chunk0047_416_1	chr12	76003017	76003679	+	0	NA	Intergenic	Intergenic	28428	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.003021	0.408748	
chunk0102_114_1	chr2	144596275	144596474	+	0	NA	Intergenic	Intergenic	-71593	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.015075	0.465000	
chunk0038_295_1	chr11	90363705	90364228	+	0	NA	intron (NR_104190, intron 1 of 6)	MLT1J2|LTR|ERVL-MaLR	112734	NR_104190	101929222	Hs.616763	NR_104190	ENSG00000261645	DISC1FP1	Boymaw	DISC1 fusion partner 1	ncRNA	0.001912	0.396947	
chunk0124_115_1	chr3	53995041	53995336	+	0	NA	Intergenic	Intergenic	-103226	NM_021237	58515	Hs.58471	NM_021237	ENSG00000113811	SELENOK	HSPC030|HSPC297|SELK	selenoprotein K	protein-coding	0.013559	0.493243	100(TGGTACAGGGTGTTCC,-,0.00),101(GGTACAGGGTGTTCCT,+,0.00)
chunk0027_439_1	chr10	81068445	81068672	+	0	NA	Intergenic	Intergenic	527739	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.013216	0.486842	
chunk0212_403_1	chrX	151484919	151485274	+	0	NA	Intergenic	Intergenic	-78439	NM_173493	139135	Hs.160594	NM_173493	ENSG00000166049	PASD1	CT63|CT64|OXTES1	PAS domain containing repressor 1	protein-coding	0.002817	0.328652	
chunk0094_380_1	chr2	9947266	9947600	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4230	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.005988	0.402985	
chunk0125_100_1	chr3	65483705	65483904	+	0	NA	intron (NM_015520, intron 3 of 24)	intron (NM_015520, intron 3 of 24)	-410012	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.005025	0.415000	
chunk0032_25_1	chr11	827657	827921	+	0	NA	promoter-TSS (NM_173584)	promoter-TSS (NM_173584)	-471	NM_001286606	283229	Hs.660936	NM_173584	ENSG00000177685	CRACR2B	EFCAB4A	calcium release activated channel regulator 2B	protein-coding	0.037879	0.641509	
chunk0119_404_1	chr22	49390358	49390706	+	0	NA	Intergenic	L1M4a2|LINE|L1	152934	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.028736	0.444126	
chunk0152_33_1	chr5	56859035	56859525	+	0	NA	intron (NM_005921, intron 2 of 19)	intron (NM_005921, intron 2 of 19)	44207	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.004082	0.303462	
chunk0120_408_1	chr3	12655333	12655868	+	0	NA	intron (NM_002880, intron 1 of 16)	L1MB4|LINE|L1	8601	NM_002880	5894	Hs.159130	NM_002880	ENSG00000132155	RAF1	CMD1NN|CRAF|NS5|Raf-1|c-Raf	Raf-1 proto-oncogene, serine/threonine kinase	protein-coding	0.003738	0.393657	
chunk0093_137_1	chr19	46300679	46301406	+	0	NA	intron (NM_152796, intron 1 of 11)	intron (NM_152796, intron 1 of 11)	-2557	NM_152794	64344	Hs.420830	NM_022462	ENSG00000124440	HIF3A	HIF-3A|HIF3-alpha-1|IPAS|MOP7|PASD7|bHLHe17	hypoxia inducible factor 3 subunit alpha	protein-coding	0.012380	0.590659	382(CAGGACGGAATGTCCT,-,0.00),383(AGGACGGAATGTCCTC,+,0.00)
chunk0121_216_1	chr3	21753239	21753657	+	0	NA	Intergenic	Intergenic	-2124	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.000000	0.343675	
chunk0139_145_1	chr4	53576692	53577287	+	0	NA	intron (NM_001126328, intron 1 of 10)	intron (NM_001126328, intron 1 of 10)	14597	NM_001126328	84708	Hs.518760	NM_032622	ENSG00000072201	LNX1	LNX|MPDZ|PDZRN2	ligand of numb-protein X 1	protein-coding	0.003361	0.367450	
chunk0151_396_1	chr5	55435436	55435823	+	0	NA	intron (NR_103485, intron 5 of 6)	intron (NR_103485, intron 5 of 6)	73297	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.010336	0.396907	
chunk0023_250_1	chr10	27340976	27341464	+	0	NA	Intergenic	Intergenic	73148	NM_001034842	374308	Hs.631832	NM_001034842	ENSG00000182077	PTCHD3	PTR	patched domain containing 3	protein-coding	0.006148	0.351738	
chunk0068_372_1	chr15	58222005	58222321	+	0	NA	Intergenic	Intergenic	83954	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.009494	0.318612	
chunk0028_387_1	chr10	92934512	92935047	+	0	NA	intron (NM_019053, intron 11 of 21)	intron (NM_019053, intron 11 of 21)	86311	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.001869	0.291045	
chunk0206_48_1	chr9	117491376	117491981	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-76639	NM_014010	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.009917	0.392739	
chunk0031_211_1	chr10	125905340	125905983	+	0	NA	intron (NM_145235, intron 1 of 10)	intron (NM_145235, intron 1 of 10)	9122	NM_145235	92565	Hs.352591	NM_145235	ENSG00000203780	FANK1	HSD13	fibronectin type III and ankyrin repeat domains 1	protein-coding	0.001555	0.381988	
chunk0033_203_1	chr11	16918504	16918961	+	0	NA	intron (NM_175058, intron 3 of 22)	MER113A|DNA|hAT-Charlie	95684	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.006565	0.406114	
chunk0122_420_1	chr3	39013642	39013883	+	0	NA	Intergenic	Intergenic	-38224	NM_020839	57599	Hs.109778	NM_020839	ENSG00000114742	WDR48	P80|SPG60|UAF1	WD repeat domain 48	protein-coding	0.004149	0.396694	
chunk0141_239_1	chr4	84966140	84966346	+	0	NA	promoter-TSS (NR_015359)	promoter-TSS (NR_015359)	148	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.174757	0.840580	
chunk0005_252_1	chr1	59699007	59699412	+	0	NA	non-coding (NR_103473, exon 17 of 17)	non-coding (NR_103473, exon 17 of 17)	34087	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.004938	0.312808	
chunk0201_114_1	chr9	35258477	35259167	+	0	NA	intron (NM_006377, intron 6 of 38)	intron (NM_006377, intron 6 of 38)	96830	NM_006377	10497	Hs.493791	NM_006377	ENSG00000198722	UNC13B	MUNC13|UNC13|Unc13h2	unc-13 homolog B	protein-coding	0.002899	0.416787	372(AGGAGCAGGATGTTCT,-,0.00),373(GGAGCAGGATGTTCTG,+,0.00)
chunk0114_347_1	chr21	17819314	17819920	+	0	NA	promoter-TSS (NM_001100421)	promoter-TSS (NM_001100421)	-231	NM_001100420	54149	Hs.293811	NM_017447	ENSG00000154642	C21orf91	C21orf14|C21orf38|CSSG1|EURL|YG81	chromosome 21 open reading frame 91	protein-coding	0.085809	0.611203	
chunk0210_417_1	chrX	100980650	100981095	+	0	NA	intron (NM_001162491, intron 3 of 7)	L1MA3|LINE|L1	11164	NR_103708	392509	Hs.147237	NM_001162491	ENSG00000174225	ARL13A	ARL13|dJ341D10.2	ADP ribosylation factor like GTPase 13A	protein-coding	0.008989	0.547085	319(GTAACACAATGTTCTC,+,0.00)
chunk0156_185_1	chr5	107855151	107855484	+	0	NA	Intergenic	LTR40b|LTR|ERVL	-184422	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.003003	0.434132	
chunk0082_223_1	chr17	57215234	57215803	+	0	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-41052	NM_138962	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.015817	0.408772	309(CAGAACAGCGTGTACC,-,0.00),310(AGAACAGCGTGTACCT,+,0.00)
chunk0001_236_1	chr1	8258912	8259907	+	0	NA	Intergenic	Intergenic	50737	NR_125998	102724539	Hs.516816	NR_125998	ENSG00000227634	LINC01714	-	long intergenic non-protein coding RNA 1714	ncRNA	0.013065	0.421687	
chunk0099_235_1	chr2	96638130	96638606	+	0	NA	promoter-TSS (NM_001115016)	promoter-TSS (NM_001115016)	11	NM_001115016	55683	Hs.516341	NM_017991	ENSG00000114982	KANSL3	KIAA1310|NSL3|Rcd1	KAT8 regulatory NSL complex subunit 3	protein-coding	0.121849	0.698113	
chunk0185_12_1	chr7	123844193	123844639	+	0	NA	promoter-TSS (NM_012269)	promoter-TSS (NM_012269)	-753	NM_012269	23553	Hs.28673	NM_012269	ENSG00000106302	HYAL4	CSHY|HYAL-4	hyaluronidase 4	protein-coding	0.017937	0.498881	
chunk0144_181_1	chr4	133310179	133310531	+	0	NA	Intergenic	L1MA9|LINE|L1	161065	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.011364	0.441926	
chunk0156_223_1	chr5	108237529	108238444	+	0	NA	intron (NM_001163315, intron 4 of 8)	intron (NM_001163315, intron 4 of 8)	144112	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.005464	0.346070	322(GAGTACATAAAGTACT,-,0.00),323(AGTACATAAAGTACTG,+,0.00)
chunk0198_288_1	chr8	135623329	135623535	+	0	NA	intron (NM_006558, intron 7 of 8)	MIRb|SINE|MIR	165967	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.014563	0.352657	
chunk0161_128_1	chr5	168269316	168269536	+	0	NA	Intergenic	Intergenic	-22634	NM_001161662	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.050000	0.651584	
chunk0111_403_1	chr20	34310455	34310882	+	0	NA	intron (NM_001161766, intron 1 of 9)	L1ME4b|LINE|L1	1134	NM_001161766	191	Hs.388004	NM_000687	ENSG00000101444	AHCY	SAHH|adoHcyase	adenosylhomocysteinase	protein-coding	0.021077	0.418224	
chunk0082_185_1	chr17	56422100	56422303	+	0	NA	intron (NM_153228, intron 7 of 16)	intron (NM_153228, intron 7 of 16)	-171498	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.004926	0.313725	
chunk0035_292_1	chr11	46936577	46936801	+	0	NA	promoter-TSS (NM_001278222)	promoter-TSS (NM_001278222)	0	NM_024113	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.062500	0.604444	
chunk0071_100_1	chr15	81008433	81008862	+	0	NA	Intergenic	MIRc|SINE|MIR	7693	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.004662	0.402326	
chunk0111_166_1	chr20	25227028	25227319	+	0	NA	TTS (NM_001247)	TTS (NM_001247)	-20897	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.024055	0.578767	
chunk0096_290_1	chr2	32427629	32428623	+	0	NA	intron (NM_016252, intron 10 of 73)	L1M4a1|LINE|L1	71098	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.006036	0.395980	
chunk0136_117_1	chr4	3461417	3461893	+	0	NA	Intergenic	Intergenic	-1651	NM_001164673	285489	Hs.122110	NM_173660	ENSG00000175920	DOK7	C4orf25|CMS10|CMS1B|FADS3	docking protein 7	protein-coding	0.031513	0.656184	
chunk0007_422_1	chr1	86353665	86353992	+	0	NA	intron (NM_001007022, intron 16 of 17)	intron (NM_001007022, intron 16 of 17)	3859	NR_107010	102465842		NR_107010	ENSG00000278281	MIR7856	hsa-mir-7856	microRNA 7856	ncRNA	0.015291	0.475610	
chunk0157_417_1	chr5	124655805	124656472	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	88974	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.010495	0.405689	
chunk0085_266_1	chr18	7690120	7690825	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	123156	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.000000	0.338527	381(AGGGACAGTGTGTCTT,-,0.00),382(GGGACAGTGTGTCTTA,+,0.00)
chunk0022_134_1	chr10	11825851	11826280	+	0	NA	intron (NM_153256, intron 1 of 3)	L1MB5|LINE|L1	2667	NM_153256	254427	Hs.435775	NM_153256	ENSG00000148426	PROSER2	C10orf47	proline and serine rich 2	protein-coding	0.030303	0.418605	
chunk0037_10_1	chr11	68963932	68964179	+	0	NA	Intergenic	Intergenic	16931	NM_198923	116512	Hs.527802	NM_198923	ENSG00000172938	MRGPRD	MRGD|TGR7	MAS related GPR family member D	protein-coding	0.004049	0.564516	
chunk0085_277_1	chr18	7871031	7871318	+	0	NA	intron (NM_001105244, intron 2 of 32)	intron (NM_001105244, intron 2 of 32)	303858	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.003484	0.395833	108(GTGGACATGCTGTTCC,-,0.00),109(TGGACATGCTGTTCCT,+,0.00)
chunk0075_216_1	chr16	52720800	52721610	+	0	NA	Intergenic	Intergenic	-114230	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.009877	0.434032	
chunk0105_193_1	chr2	187596764	187597504	+	0	NA	Intergenic	Intergenic	-42642	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.001351	0.304993	303(GAAAACATTCTGTTCT,-,0.00),304(AAAACATTCTGTTCTG,+,0.00)
chunk0133_247_1	chr3	171613411	171614144	+	0	NA	intron (NM_001130081, intron 23 of 25)	intron (NM_001130081, intron 23 of 25)	-153369	NM_001161563	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.004093	0.410082	
chunk0002_29_1	chr1	12463996	12464198	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-43149	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.014851	0.443350	
chunk0114_265_1	chr21	16204278	16204484	+	0	NA	intron (NR_027791, intron 1 of 5)	intron (NR_027791, intron 1 of 5)	10002	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.009709	0.299517	
chunk0064_58_1	chr14	89955126	89955515	+	0	NA	promoter-TSS (NM_001284269)	promoter-TSS (NM_001284269)	-543	NM_145231	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.030848	0.443590	
chunk0107_419_1	chr2	224565370	224565781	+	0	NA	intron (NM_003590, intron 1 of 15)	Tigger2|DNA|TcMar-Tigger	4250	NM_001257198	8452	Hs.372286	NM_003590	ENSG00000036257	CUL3	CUL-3|PHA2E	cullin 3	protein-coding	0.007299	0.424757	
chunk0079_23_1	chr17	9731146	9731431	+	0	NA	Intergenic	Intergenic	60009	NM_001105571	201140	Hs.61684	NM_001105571	ENSG00000184544	DHRS7C	SDR32C2	dehydrogenase/reductase 7C	protein-coding	0.007018	0.506993	
chunk0195_97_1	chr8	94435315	94435687	+	0	NA	intron (NM_001205262, intron 3 of 3)	intron (NM_001205262, intron 3 of 3)	1451	NM_001256141	100861412	Hs.30561	NM_001256141	ENSG00000265817	FSBP	-	fibrinogen silencer binding protein	protein-coding	0.000000	0.319035	
chunk0176_357_1	chr7	18109910	18110398	+	0	NA	intron (NM_001204144, intron 1 of 12)	MARNA|DNA|TcMar-Mariner	17155	NR_031635	100302140		NR_031635	ENSG00000221393	MIR1302-6	MIRN1302-6|hsa-mir-1302-6	microRNA 1302-6	ncRNA	0.002049	0.380368	
chunk0109_334_1	chr20	9345650	9345906	+	0	NA	intron (NM_001172646, intron 6 of 37)	intron (NM_001172646, intron 6 of 37)	37978	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.000000	0.264591	
chunk0131_444_1	chr3	154022993	154023505	+	0	NA	Intergenic	Intergenic	-97754	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.001953	0.335283	
chunk0155_136_1	chr5	93557334	93557752	+	0	NA	intron (NR_021490, intron 2 of 5)	Tigger1|DNA|TcMar-Tigger	13800	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.002392	0.334129	
chunk0004_433_1	chr1	52928061	52928343	+	0	NA	promoter-TSS (NR_039971)	promoter-TSS (NR_039971)	-472	NR_039971									0.042553	0.537102	142(CTGCACTTACTGTGCT,-,0.00),143(TGCACTTACTGTGCTC,+,0.00)
chunk0143_97_1	chr4	108477738	108478018	+	0	NA	Intergenic	Intergenic	142579	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.007143	0.423488	
chunk0085_205_1	chr18	6605437	6605856	+	0	NA	Intergenic	Intergenic	94230	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.009547	0.409524	
chunk0191_342_1	chr8	56060099	56060596	+	0	NA	Intergenic	Intergenic	13554	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.010060	0.457831	
chunk0172_394_1	chr6	139679203	139679463	+	0	NA	Intergenic	L1ME3D|LINE|L1	-91740	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.003846	0.268199	
chunk0194_172_1	chr8	84893752	84894700	+	0	NA	intron (NM_001100393, intron 8 of 8)	intron (NM_001100393, intron 8 of 8)	188299	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002110	0.389884	
chunk0065_307_1	chr14	102949444	102950211	+	0	NA	exon (NM_006035, exon 26 of 37)	exon (NM_006035, exon 26 of 37)	27171	NM_030943	81693	Hs.534494	NM_030943	ENSG00000166126	AMN	PRO1028|amnionless	amnion associated transmembrane protein	protein-coding	0.036506	0.541667	244(AGGAACACACCGTCCT,-,0.00),245(GGAACACACCGTCCTT,+,0.00)
chunk0083_67_1	chr17	64081942	64082748	+	0	NA	intron (NM_001433, intron 2 of 21)	intron (NM_001433, intron 2 of 21)	47797	NM_001433	2081	Hs.133982	NM_001433	ENSG00000178607	ERN1	IRE1|IRE1P|IRE1a|hIRE1p	endoplasmic reticulum to nucleus signaling 1	protein-coding	0.007444	0.420074	
chunk0039_407_1	chr11	107486608	107487202	+	0	NA	Intergenic	L1ME4b|LINE|L1	-29059	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.008418	0.294118	
chunk0159_11_1	chr5	136123222	136123804	+	0	NA	Intergenic	Intergenic	-9332	NM_005903	4090	Hs.167700	NM_005903	ENSG00000113658	SMAD5	DWFC|JV5-1|MADH5	SMAD family member 5	protein-coding	0.001718	0.384220	
chunk0011_48_1	chr1	143248122	143248339	+	0	NA	Intergenic	Intergenic	174362	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.064516	0.385321	
chunk0135_64_1	chr3	185796534	185797063	+	0	NA	intron (NM_001007225, intron 2 of 14)	intron (NM_001007225, intron 2 of 14)	24333	NM_001291875	10644	Hs.35354	NM_006548	ENSG00000073792	IGF2BP2	IMP-2|IMP2|VICKZ2	insulin like growth factor 2 mRNA binding protein 2	protein-coding	0.009452	0.405660	
chunk0026_264_1	chr10	66921898	66922097	+	0	NA	intron (NR_111911, intron 3 of 6)	intron (NR_111911, intron 3 of 6)	-4037	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.000000	0.260000	
chunk0007_282_1	chr1	83792211	83792433	+	0	NA	intron (NR_119375, intron 1 of 2)	intron (NR_119375, intron 1 of 2)	68224	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.004505	0.412556	
chunk0116_29_1	chr21	33292550	33293282	+	0	NA	intron (NM_000628, intron 6 of 6)	ERV3-16A3_I-int|LTR|ERVL	26556	NM_000628	3588	Hs.654593	NM_000628	ENSG00000243646	IL10RB	CDW210B|CRF2-4|CRFB4|D21S58|D21S66|IL-10R2	interleukin 10 receptor subunit beta	protein-coding	0.019126	0.540246	
chunk0021_313_1	chr1	245060399	245060872	+	0	NA	intron (NM_032328, intron 4 of 7)	intron (NM_032328, intron 4 of 7)	-89766	NR_111907	101928068	Hs.134857	NR_111907		LOC101928068	-	uncharacterized LOC101928068	ncRNA	0.006342	0.377637	96(AAGAACACATTGTTTT,-,0.00),97(AGAACACATTGTTTTT,+,0.00)
chunk0023_301_1	chr10	28818329	28818996	+	0	NA	Intergenic	Intergenic	-22612	NR_038374	100507605	Hs.119207	NR_038374	ENSG00000235824	LINC00837	-	long intergenic non-protein coding RNA 837	ncRNA	0.011994	0.417665	139(CAGGACAGTTAGTTCC,-,0.00),140(AGGACAGTTAGTTCCT,+,0.00)
chunk0060_394_1	chr14	52934814	52935044	+	0	NA	intron (NM_001134999, intron 2 of 15)	Tigger6a|DNA|TcMar-Tigger	16168	NM_006832	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.000000	0.385281	
chunk0030_335_1	chr10	118356676	118357058	+	0	NA	promoter-TSS (NR_108045)	promoter-TSS (NR_108045)	-241	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.005236	0.464752	
chunk0206_447_1	chr9	128067048	128067601	+	0	NA	promoter-TSS (NM_197956)	promoter-TSS (NM_197956)	-4	NM_197956	203245	Hs.373606	NM_197956	ENSG00000171169	NAIF1	C9orf90|bA379C10.2	nuclear apoptosis inducing factor 1	protein-coding	0.057866	0.574007	
chunk0051_293_1	chr12	118357200	118357893	+	0	NA	intron (NM_016281, intron 1 of 20)	intron (NM_016281, intron 1 of 20)	15399	NM_016281	51347	Hs.644420	NM_016281	ENSG00000135090	TAOK3	DPK|JIK|MAP3K18|hKFC-A	TAO kinase 3	protein-coding	0.008658	0.334294	
chunk0168_180_1	chr6	84484339	84484541	+	0	NA	Intergenic	L1PB3|LINE|L1	-9511	NR_132100	105377880	Hs.171384	NR_132100	ENSG00000231776	LINC01611	TCONS_l2_00025430	long intergenic non-protein coding RNA 1611	ncRNA	0.014851	0.354680	
chunk0191_220_1	chr8	52588172	52588416	+	0	NA	Intergenic	L1MEf|LINE|L1	-22833	NM_207413	389658	Hs.527111	NM_207413	ENSG00000196711	ALKAL1	AUGA|AUGB|FAM150A|UNQ9433	ALK and LTK ligand 1	protein-coding	0.012295	0.322449	
chunk0137_183_1	chr4	17544720	17545180	+	0	NA	Intergenic	L2a|LINE|L2	29785	NM_001079827	645104	Hs.631526	NM_001079827	ENSG00000249581	CLRN2	-	clarin 2	protein-coding	0.004348	0.427332	
chunk0198_428_1	chr8	143150564	143150911	+	0	NA	Intergenic	Intergenic	9303	NM_002347	4062	Hs.159590	NM_002347	ENSG00000176956	LY6H	NMLY6	lymphocyte antigen 6 family member H	protein-coding	0.023055	0.462644	
chunk0201_271_1	chr9	38633847	38634388	+	0	NA	Intergenic	L1MD2|LINE|L1	13029	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.014787	0.420664	
chunk0184_349_1	chr7	120763364	120763591	+	0	NA	Intergenic	L1M1|LINE|L1	94646	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.000000	0.521930	
chunk0111_105_1	chr20	23635075	23635748	+	0	NA	intron (NM_001288614, intron 1 of 3)	intron (NM_001288614, intron 1 of 3)	2637	NM_001288614	1471	Hs.304682	NM_000099	ENSG00000101439	CST3	ARMD11|HEL-S-2	cystatin C	protein-coding	0.017831	0.531157	318(AGGGACAGCACGTTCT,-,0.00),319(GGGACAGCACGTTCTG,+,0.00)
chunk0192_416_1	chr8	69496822	69497184	+	0	NA	intron (NM_015170, intron 2 of 22)	intron (NM_015170, intron 2 of 22)	4210	NM_001128206	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.011050	0.426997	312(TAAAACAGAATGTTCT,-,0.00),313(AAAACAGAATGTTCTT,+,0.00)
chunk0181_179_1	chr7	83058177	83058571	+	0	NA	intron (NM_014510, intron 3 of 19)	intron (NM_014510, intron 3 of 19)	104507	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.000000	0.311392	
chunk0133_306_1	chr3	172297941	172298770	+	0	NA	intron (NM_022763, intron 8 of 25)	intron (NM_022763, intron 8 of 25)	150101	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.007238	0.330120	
chunk0128_91_1	chr3	105792321	105792723	+	0	NA	intron (NM_170662, intron 3 of 18)	intron (NM_170662, intron 3 of 18)	76521	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.009950	0.473945	201(TGGGACAGCGTGTACT,-,0.00),202(GGGACAGCGTGTACTT,+,0.00)
chunk0198_354_1	chr8	140511695	140511925	+	0	NA	promoter-TSS (NR_040712)	promoter-TSS (NR_040712)	-172	NR_040712	54108	Hs.279704	NM_017444	ENSG00000104472	CHRAC1	CHARC1|CHARC15|CHRAC-1|CHRAC-15|CHRAC15|YCL1	chromatin accessibility complex subunit 1	protein-coding	0.165217	0.770563	
chunk0137_225_1	chr4	20036866	20037383	+	0	NA	Intergenic	Intergenic	-214781	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.005803	0.310811	173(CTGCACTCTCTGTTCC,-,0.00),174(TGCACTCTCTGTTCCT,+,0.00)
chunk0146_327_1	chr4	165709935	165710729	+	0	NA	intron (NR_121676, intron 3 of 5)	intron (NR_121676, intron 3 of 5)	25693	NR_121676	101928151	Hs.639858	NR_121676	ENSG00000249500	LINC01179	-	long intergenic non-protein coding RNA 1179	ncRNA	0.003778	0.388679	
chunk0199_70_1	chr9	2381721	2382437	+	0	NA	Intergenic	Intergenic	223623	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.013966	0.410042	345(ATGAACATGATGTTCT,-,0.00),346(TGAACATGATGTTCTG,+,0.00)
chunk0065_86_1	chr15	23690380	23690705	+	0	NA	Intergenic	Intergenic	-3239	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.015385	0.539877	
chunk0034_344_1	chr11	35761938	35762352	+	0	NA	intron (NM_017583, intron 4 of 4)	intron (NM_017583, intron 4 of 4)	99393	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.002415	0.436145	
chunk0158_144_1	chr5	127406421	127406765	+	0	NA	intron (NM_001308121, intron 8 of 13)	intron (NM_001308121, intron 8 of 13)	-111016	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.008721	0.481159	
chunk0165_343_1	chr6	37891463	37891923	+	0	NA	intron (NM_021943, intron 1 of 5)	L1M4|LINE|L1	72162	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.013043	0.431670	
chunk0206_22_1	chr9	115944670	115944969	+	0	NA	Intergenic	Intergenic	-19721	NR_024032	58483	Hs.23367	NR_024032	ENSG00000204148	LINC00474	C9orf27|EST-YD1	long intergenic non-protein coding RNA 474	ncRNA	0.013378	0.463333	
chunk0101_333_1	chr2	136105062	136105328	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	11048	NM_001008540	7852	Hs.593413	NM_003467	ENSG00000121966	CXCR4	CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS	C-X-C motif chemokine receptor 4	protein-coding	0.011278	0.426966	121(ATCACAGAGTGTGCTT,+,0.00)
chunk0094_442_1	chr2	11452810	11453185	+	0	NA	intron (NM_198256, intron 3 of 6)	intron (NM_198256, intron 3 of 6)	13180	NM_198256	1876	Hs.603093	NM_198256	ENSG00000169016	E2F6	E2F-6	E2F transcription factor 6	protein-coding	0.000000	0.337766	168(GAGGTCACTATGTACT,-,0.00),169(AGGTCACTATGTACTT,+,0.00)
chunk0114_38_1	chr21	8239078	8239303	+	0	NA	intron (NR_003287, intron 1 of 2)	AluSx3|SINE|Alu	-10315	NR_106782	102465433		NR_106782	ENSG00000275950	MIR6724-1	MIR6724|hsa-mir-6724|hsa-mir-6724-1	microRNA 6724-1	ncRNA	0.017778	0.446903	
chunk0056_326_1	chr13	91151735	91152317	+	0	NA	intron (NR_047004, intron 2 of 3)	intron (NR_047004, intron 2 of 3)	59672	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.001718	0.332762	359(GAGGACTTGCTGTCCT,-,0.00),360(AGGACTTGCTGTCCTC,+,0.00),517(CAGAGCATCCTGTACC,-,0.00),518(AGAGCATCCTGTACCT,+,0.00)
chunk0077_74_1	chr16	77178678	77179027	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-12067	NM_001286640	22879	Hs.513743	NM_014940	ENSG00000103111	MON1B	HSRG1|SAND2|SRG1	MON1 homolog B, secretory trafficking associated	protein-coding	0.011461	0.288571	
chunk0008_93_1	chr1	90924146	90924809	+	0	NA	intron (NM_016620, intron 2 of 3)	intron (NM_016620, intron 2 of 3)	97031	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.007541	0.308735	
chunk0088_202_1	chr18	47930101	47930943	+	0	NA	promoter-TSS (NM_005901)	promoter-TSS (NM_005901)	77	NM_005901	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.123515	0.776987	
chunk0169_355_1	chr6	106681331	106681837	+	0	NA	Intergenic	Intergenic	52018	NM_018292	55278	Hs.406917	NM_018292	ENSG00000130348	QRSL1	GatA	glutaminyl-tRNA amidotransferase subunit QRSL1	protein-coding	0.007905	0.337278	
chunk0190_176_1	chr8	32834851	32835083	+	0	NA	Intergenic	Intergenic	113134	NM_001159996	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.008621	0.442060	72(GATACAGAGTGTACCC,+,0.00)
chunk0099_95_1	chr2	85537552	85538139	+	0	NA	non-coding (NR_038942, exon 1 of 1)	non-coding (NR_038942, exon 1 of 1)	1041	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.034072	0.537415	
chunk0010_318_1	chr1	118100943	118101325	+	0	NA	intron (NM_206996, intron 5 of 48)	AluJr|SINE|Alu	84091	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.000000	0.428198	
chunk0209_415_1	chrX	56817181	56817768	+	0	NA	TTS (NR_015367)	TTS (NR_015367)	-79890	NR_002308	442454	Hs.663220	NR_002308		UQCRBP1	-	ubiquinol-cytochrome c reductase binding protein pseudogene 1	pseudo	0.008518	0.335034	316(GGTGACATCCTGTTCT,-,0.00),317(GTGACATCCTGTTCTT,+,0.00)
chunk0016_114_1	chr1	196026488	196026729	+	0	NA	Intergenic	LTR78|LTR|ERV1	555873	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.008299	0.466942	
chunk0154_3_1	chr5	76496131	76496750	+	0	NA	intron (NM_006633, intron 2 of 35)	MLT1F2|LTR|ERVL-MaLR	-50969	NM_001285460	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.008078	0.425806	364(GAGTACAGTCTGTCCC,-,0.00),365(AGTACAGTCTGTCCCC,+,0.00)
chunk0013_244_1	chr1	169676029	169676331	+	0	NA	Intergenic	Intergenic	32676	NR_029467	6402	Hs.728756	NM_000655	ENSG00000188404	SELL	CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1	selectin L	protein-coding	0.006623	0.458746	
chunk0112_348_1	chr20	45204528	45204727	+	0	NA	Intergenic	L1M1|LINE|L1	-2370	NM_003007	6406	Hs.1968	NM_003007	ENSG00000124233	SEMG1	CT103|SEMG|SGI|dJ172H20.2	semenogelin 1	protein-coding	0.010050	0.470000	41(AGGAACTATGTGTTCC,-,0.00),42(GGAACTATGTGTTCCT,+,0.00)
chunk0038_1_1	chr11	80658962	80659294	+	0	NA	Intergenic	Intergenic	103675	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003012	0.354354	
chunk0085_84_1	chr18	2331601	2331967	+	0	NA	Intergenic	Intergenic	239719	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.013661	0.389646	
chunk0110_202_1	chr20	14888208	14888568	+	0	NA	intron (NR_037841, intron 1 of 2)	intron (NR_037841, intron 1 of 2)	41130	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.002778	0.490305	
chunk0120_389_1	chr3	12356130	12356694	+	0	NA	intron (NM_015869, intron 1 of 6)	intron (NM_015869, intron 1 of 6)	4910	NM_015869	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.010638	0.355752	240(GAGTACACAGTGTTTT,-,0.00),241(AGTACACAGTGTTTTA,+,0.00)
chunk0133_28_1	chr3	165836336	165836598	+	0	NA	intron (NM_000055, intron 1 of 3)	intron (NM_000055, intron 1 of 3)	998	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.235741	
chunk0189_257_1	chr8	25220544	25220743	+	0	NA	intron (NM_024940, intron 1 of 51)	AluSx1|SINE|Alu	35871	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.030151	0.540000	
chunk0035_298_1	chr11	46988236	46988597	+	0	NA	intron (NR_103472, intron 2 of 7)	L1MA1|LINE|L1	51727	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.002770	0.383978	
chunk0143_36_1	chr4	106898473	106898956	+	0	NA	Intergenic	Intergenic	137582	NM_014421	27123	Hs.211869	NM_014421	ENSG00000155011	DKK2	DKK-2	dickkopf WNT signaling pathway inhibitor 2	protein-coding	0.006211	0.318182	
chunk0198_282_1	chr8	135562151	135562596	+	0	NA	intron (NM_006558, intron 5 of 8)	Tigger3|DNA|TcMar-Tigger	104908	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.011236	0.390135	288(AAGTACACTCTGTGAT,-,0.00)
chunk0161_122_1	chr5	167713169	167713809	+	0	NA	intron (NM_001122679, intron 2 of 28)	(CACATG)n|Simple_repeat|Simple_repeat	-41447	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.017188	0.441498	
chunk0061_119_1	chr14	58476234	58476760	+	0	NA	intron (NM_001244192, intron 20 of 31)	intron (NM_001244192, intron 20 of 31)	36816	NM_001244193	9786	Hs.232532	NM_014749	ENSG00000100578	KIAA0586	JBTS23|SRTD14|Talpid3	KIAA0586	protein-coding	0.003802	0.347249	
chunk0173_64_1	chr6	142421361	142421590	+	0	NA	intron (NM_020455, intron 22 of 25)	intron (NM_020455, intron 22 of 25)	119556	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.000000	0.282609	
chunk0184_6_1	chr7	111620584	111620880	+	0	NA	Intergenic	L1MB8|LINE|L1	-58215	NM_001244606	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.000000	0.299663	
chunk0123_174_1	chr3	44061785	44062235	+	0	NA	Intergenic	Intergenic	-52202	NR_029700	406929		NR_029700	ENSG00000207954	MIR138-1	MIRN138-1|mir-138-1	microRNA 138-1	ncRNA	0.015556	0.450111	
chunk0187_399_1	chr7	157861546	157862323	+	0	NA	intron (NR_038966, intron 3 of 3)	intron (NR_038966, intron 3 of 3)	7349	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.041184	0.597686	304(GAGGACTCTGTGTGCC,-,0.00),305(AGGACTCTGTGTGCCG,+,0.00),358(GAGGACTCTGTGTGCC,-,0.00),359(AGGACTCTGTGTGCCG,+,0.00),412(GAGGACTCTGTGTGCC,-,0.00),413(AGGACTCTGTGTGCCG,+,0.00),466(GAGGACTCTGTGTGCC,-,0.00),467(AGGACTCTGTGTGCCG,+,0.00),520(GAGGACTCTGTGTGCC,-,0.00),521(AGGACTCTGTGTGCCG,+,0.00),574(GAGGACTCTGTGTGCT,-,0.00),575(AGGACTCTGTGTGCTG,+,0.00)
chunk0034_401_1	chr11	37364145	37364348	+	0	NA	Intergenic	L1PB3|LINE|L1	-765967	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.009852	0.485294	
chunk0148_114_1	chr5	5136033	5136332	+	0	NA	intron (NR_109915, intron 1 of 3)	MER58A|DNA|hAT-Charlie	3872	NR_109915	101929176	Hs.208717	NR_109915		CTD-2297D10.2	-	uncharacterized LOC101929176	ncRNA	0.006689	0.400000	
chunk0074_379_1	chr16	34661110	34661343	+	0	NA	Intergenic	Intergenic	-501190	NR_038368									0.030043	0.350427	
chunk0049_47_1	chr12	89901362	89901763	+	0	NA	Intergenic	Intergenic	192607	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.002494	0.460199	242(AAGGACAGAGTGTTCC,-,0.00),243(AGGACAGAGTGTTCCT,+,0.00)
chunk0066_356_1	chr15	38243218	38243746	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-9369	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.011364	0.374291	105(ATCACAGACTGTACTT,+,0.00),373(AAAGACAGACTGTTCA,-,0.00),374(AAGACAGACTGTTCAA,+,0.00)
chunk0124_163_1	chr3	55028729	55028965	+	0	NA	intron (NM_018398, intron 35 of 37)	intron (NM_018398, intron 35 of 37)	-61759	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.016949	0.371308	
chunk0209_165_1	chrX	43407674	43408008	+	0	NA	Intergenic	Intergenic	230847	NR_110387	101927501	Hs.495998	NR_110387	ENSG00000224294	PINCR	-	p53-induced noncoding RNA	ncRNA	0.008982	0.492537	
chunk0031_53_1	chr10	122679965	122680691	+	0	NA	Intergenic	Intergenic	19494	NM_001010912	399814	Hs.363649	NM_001010912	ENSG00000183559	C10orf120	bA318C4.1	chromosome 10 open reading frame 120	protein-coding	0.005510	0.475928	
chunk0190_417_1	chr8	41175564	41175982	+	0	NA	Intergenic	LTR88b|LTR|Gypsy?	95370	NR_049801	100847068		NR_049801	ENSG00000263372	MIR548AO	-	microRNA 548ao	ncRNA	0.014354	0.539379	
chunk0126_49_1	chr3	74048915	74049218	+	0	NA	Intergenic	Intergenic	-424145	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.000000	0.351974	
chunk0164_270_1	chr6	23697828	23698248	+	0	NA	Intergenic	Intergenic	-428148	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.002381	0.399050	
chunk0163_61_1	chr6	8954385	8955059	+	0	NA	Intergenic	Intergenic	302513	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.005935	0.284444	
chunk0007_428_1	chr1	86595927	86596479	+	0	NA	Intergenic	Intergenic	-38073	NR_024604	9629	Hs.673847	NM_004921	ENSG00000153923	CLCA3P	CLCA3	chloride channel accessory 3, pseudogene	pseudo	0.007246	0.370705	
chunk0175_306_1	chr6	166556981	166557315	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	-47715	NR_031734	100302141		NR_031734	ENSG00000222958	MIR1913	MIRN1913|hsa-mir-1913	microRNA 1913	ncRNA	0.041916	0.602985	
chunk0015_360_1	chr1	190372099	190372673	+	0	NA	intron (NM_199051, intron 2 of 7)	intron (NM_199051, intron 2 of 7)	105243	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003484	0.443478	
chunk0021_28_1	chr10	652346	652762	+	0	NA	non-coding (NR_027151, exon 3 of 3)	non-coding (NR_027151, exon 3 of 3)	2477	NR_027152									0.031250	0.587530	305(AATAACACCATGTCCT,-,0.00),306(ATAACACCATGTCCTC,+,0.00)
chunk0188_131_1	chr8	9261910	9262561	+	0	NA	Intergenic	Intergenic	-62816	NR_040039	157273	Hs.650222	NR_040039	ENSG00000248538	LOC157273	-	uncharacterized LOC157273	ncRNA	0.006144	0.404908	
chunk0193_45_1	chr8	71835585	71835837	+	0	NA	Intergenic	Intergenic	-7412	NR_033652	100132891	Hs.137674	NR_033651	ENSG00000235531	MSC-AS1	-	MSC antisense RNA 1	ncRNA	0.003968	0.363636	
chunk0055_190_1	chr13	61665380	61665770	+	0	NA	Intergenic	LTR18B|LTR|ERVL	-250053	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.012821	0.485934	
chunk0023_444_1	chr10	32000143	32000563	+	0	NA	Intergenic	Intergenic	56090	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.014286	0.377672	232(AGCACTTCCAGTTCTG,+,0.00)
chunk0160_183_1	chr5	154159817	154160217	+	0	NA	Intergenic	L1ME3G|LINE|L1	-30718	NM_198321	55568	Hs.631797	NM_017540	ENSG00000164574	GALNT10	GALNACT10|PPGALNACT10|PPGANTASE10	polypeptide N-acetylgalactosaminyltransferase 10	protein-coding	0.010000	0.329177	
chunk0159_46_1	chr5	137192244	137193034	+	0	NA	intron (NM_004598, intron 3 of 10)	L2|LINE|L2	306690	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.007595	0.431100	
chunk0067_335_1	chr15	48393643	48393987	+	0	NA	Intergenic	Intergenic	61647	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.014535	0.530435	
chunk0197_93_1	chr8	119353176	119353540	+	0	NA	Intergenic	Intergenic	28187	NR_106755	102466162		NR_106755	ENSG00000276479	MIR548AZ	hsa-mir-548az	microRNA 548az	ncRNA	0.005495	0.328767	
chunk0184_251_1	chr7	117950663	117950887	+	0	NA	Intergenic	L2c|LINE|L2	-77268	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.013393	0.506667	
chunk0180_327_1	chr7	72636402	72636822	+	0	NA	intron (NM_001145440, intron 11 of 13)	L1ME3B|LINE|L1	-61291	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.004762	0.299287	
chunk0114_213_1	chr21	15586743	15587390	+	0	NA	Intergenic	LTR48B|LTR|ERV1	-142959	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.004637	0.408951	
chunk0037_394_1	chr11	79134663	79135233	+	0	NA	intron (NM_001098816, intron 4 of 33)	L1PB1|LINE|L1	267161	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.005263	0.362522	
chunk0204_159_1	chr9	95835455	95836026	+	0	NA	intron (NR_023390, intron 2 of 2)	L4_C_Mam|LINE|RTE-X	-39878	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.005254	0.403846	
chunk0160_225_1	chr5	155128746	155129815	+	0	NA	Intergenic	MIRb|SINE|MIR	115580	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.006548	0.421495	
chunk0087_237_1	chr18	36500869	36501068	+	0	NA	intron (NM_001281739, intron 3 of 23)	intron (NM_001281739, intron 3 of 23)	162450	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.015075	0.555000	
chunk0092_22_1	chr19	18769257	18769671	+	0	NA	intron (NM_001098482, intron 11 of 14)	intron (NM_001098482, intron 11 of 14)	21841	NM_000095	1311	Hs.1584	NM_000095	ENSG00000105664	COMP	EDM1|EPD1|MED|PSACH|THBS5|TSP5	cartilage oligomeric matrix protein	protein-coding	0.021739	0.602410	178(GGGCACAATGAGTCCT,-,0.00),179(GGCACAATGAGTCCTC,+,0.00)
chunk0074_79_1	chr16	21597593	21598171	+	0	NA	intron (NR_110930, intron 1 of 2)	intron (NR_110930, intron 1 of 2)	661	NM_001288660	51108	Hs.279583	NM_016025	ENSG00000197006	METTL9	CGI-81|DREV|DREV1|PAP1	methyltransferase like 9	protein-coding	0.012111	0.464594	
chunk0208_239_1	chrX	19981081	19981828	+	0	NA	Intergenic	L1MB7|LINE|L1	8325	NR_024440	729609	Hs.554726	NR_024440		LOC729609	-	uncharacterized LOC729609	ncRNA	0.005355	0.330214	
chunk0103_108_1	chr2	161367692	161368079	+	0	NA	exon (NM_005805, exon 5 of 12)	exon (NM_005805, exon 5 of 12)	-48224	NM_006593	10716	Hs.210862	NM_006593	ENSG00000136535	TBR1	IDDAS|TBR-1|TES-56	T-box brain transcription factor 1	protein-coding	0.010336	0.337629	205(AGGAACAGTGAGTACT,-,0.00),206(GGAACAGTGAGTACTT,+,0.00)
chunk0195_285_1	chr8	98519089	98519293	+	0	NA	intron (NM_006281, intron 10 of 10)	intron (NM_006281, intron 10 of 10)	92169	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.004902	0.360976	70(GAGAACAAGCAGTTCT,-,0.00),71(AGAACAAGCAGTTCTT,+,0.00)
chunk0006_342_1	chr1	72449880	72450146	+	0	NA	Intergenic	L1MA4|LINE|L1	-167419	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.003759	0.565543	
chunk0053_37_1	chr13	27323988	27324491	+	0	NA	Intergenic	L1MC1|LINE|L1	53912	NM_206827	387496	Hs.192131	NM_206827	ENSG00000122035	RASL11A	-	RAS like family 11 member A	protein-coding	0.000000	0.398810	
chunk0100_261_1	chr2	113239401	113239606	+	0	NA	non-coding (NR_047570, exon 3 of 3)	non-coding (NR_047570, exon 3 of 3)	3234	NR_015377	654433	Hs.656660	NR_015377	ENSG00000189223	PAX8-AS1	-	PAX8 antisense RNA 1	ncRNA	0.004878	0.543689	
chunk0192_403_1	chr8	68934873	68935360	+	0	NA	intron (NR_039986, intron 3 of 4)	intron (NR_039986, intron 3 of 4)	169074	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.006160	0.288934	
chunk0192_177_1	chr8	62860869	62861323	+	0	NA	intron (NR_130764, intron 4 of 6)	MER117|DNA|hAT-Charlie	-116765	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.006608	0.439560	
chunk0133_313_1	chr3	172369709	172369908	+	0	NA	intron (NM_022763, intron 23 of 25)	intron (NM_022763, intron 23 of 25)	78648	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.025126	0.465000	
chunk0072_183_1	chr15	94116075	94116506	+	0	NA	Intergenic	Intergenic	-8352	NR_120320	101927112	Hs.134687	NR_120320	ENSG00000259724	LINC01581	-	long intergenic non-protein coding RNA 1581	ncRNA	0.002320	0.273148	
chunk0175_87_1	chr7	2555361	2555837	+	0	NA	5' UTR (NM_152743, exon 1 of 14)	5' UTR (NM_152743, exon 1 of 14)	159	NM_152743	221927	Hs.520623	NM_152743	ENSG00000106009	BRAT1	BAAT1|C7orf27|NEDCAS|RMFSL	BRCA1 associated ATM activator 1	protein-coding	0.100840	0.733753	
chunk0034_8_1	chr11	25927713	25928526	+	0	NA	Intergenic	Intergenic	-261004	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.004920	0.318182	
chunk0068_378_1	chr15	58279379	58279663	+	0	NA	Intergenic	Intergenic	141312	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.007042	0.392982	
chunk0021_306_1	chr1	244840438	244840847	+	0	NA	intron (NM_001312872, intron 2 of 4)	intron (NM_001312872, intron 2 of 4)	5166	NR_132421	116228	Hs.411490	NM_198076	ENSG00000203667	COX20	FAM36A	cytochrome c oxidase assembly factor COX20	protein-coding	0.009780	0.400000	
chunk0010_131_1	chr1	114603851	114604185	+	0	NA	intron (NM_001256404, intron 11 of 20)	intron (NM_001256404, intron 11 of 20)	-22374	NM_005872	10286	Hs.22960	NM_005872	ENSG00000116752	BCAS2	DAM1|SPF27|Snt309	BCAS2 pre-mRNA processing factor	protein-coding	0.000000	0.376119	
chunk0149_14_1	chr5	15900468	15900922	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-34487	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.004405	0.307692	
chunk0018_327_1	chr1	221309671	221310234	+	0	NA	Intergenic	Intergenic	26344	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.001776	0.391844	
chunk0125_149_1	chr3	66358663	66359459	+	0	NA	intron (NR_028475, intron 6 of 9)	intron (NR_028475, intron 6 of 9)	138319	NR_028475	115286	Hs.379386	NM_173471	ENSG00000144741	SLC25A26	COXPD28|SAMC	solute carrier family 25 member 26	protein-coding	0.007538	0.367629	
chunk0203_267_1	chr9	88146567	88146766	+	0	NA	Intergenic	Intergenic	-11681	NM_001166137	645961	Hs.632070	NM_001166137		SPATA31C2	FAM75C2	SPATA31 subfamily C member 2	protein-coding	0.010050	0.360000	75(AGGAGCATCTTGTGCT,-,0.00)
chunk0072_225_1	chr15	95742962	95743396	+	0	NA	Intergenic	Intergenic	310086	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.004608	0.379310	
chunk0006_220_1	chr1	68397802	68398556	+	0	NA	Intergenic	L2b|LINE|L2	51780	NM_000329	6121	Hs.2133	NM_000329	ENSG00000116745	RPE65	BCO3|LCA2|RP20|mRPE65|p63|rd12|sRPE65	retinoid isomerohydrolase RPE65	protein-coding	0.003979	0.388079	
chunk0203_276_1	chr9	88604933	88605274	+	0	NA	Intergenic	Intergenic	47057	NM_001100111									0.008798	0.429825	219(CAGGTCACTATGTTCC,-,0.00),220(AGGTCACTATGTTCCC,+,0.00)
chunk0113_25_1	chr20	49662748	49663336	+	0	NA	intron (NM_004776, intron 1 of 8)	L1ME3A|LINE|L1	50842	NM_004776	9334	Hs.370487	NM_004776	ENSG00000158470	B4GALT5	B4Gal-T5|BETA4-GALT-IV|beta4Gal-T5|beta4GalT-V|gt-V	beta-1,4-galactosyltransferase 5	protein-coding	0.003401	0.344652	
chunk0106_28_1	chr2	195953719	195953959	+	0	NA	intron (NM_018897, intron 19 of 64)	intron (NM_018897, intron 19 of 64)	114973	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.004167	0.365145	
chunk0165_208_1	chr6	34810919	34811362	+	0	NA	intron (NM_017754, intron 1 of 20)	Tigger2b_Pri|DNA|TcMar-Tigger	19123	NM_017754	54887	Hs.700656	NM_017754	ENSG00000065060	UHRF1BP1	C6orf107|ICBP90|dJ349A12.1	UHRF1 binding protein 1	protein-coding	0.006772	0.326577	
chunk0099_314_1	chr2	99431659	99431952	+	0	NA	intron (NM_016316, intron 8 of 22)	intron (NM_016316, intron 8 of 22)	58213	NM_001037872	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.023891	0.551020	160(AGGGACACACTGTCCT,-,0.00),161(GGGACACACTGTCCTC,+,0.00)
chunk0075_220_1	chr16	52756551	52757254	+	0	NA	Intergenic	L2a|LINE|L2	-149927	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.002845	0.410511	372(GAGGGCAAAGTGTTCC,-,0.00)
chunk0120_176_1	chr3	6074048	6074568	+	0	NA	Intergenic	Intergenic	731141	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.005769	0.387716	
chunk0001_49_1	chr1	1857280	1857811	+	0	NA	intron (NM_002074, intron 1 of 11)	intron (NM_002074, intron 1 of 11)	33572	NM_002074	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.005650	0.479323	
chunk0029_95_1	chr10	97334641	97335083	+	0	NA	promoter-TSS (NM_012083)	promoter-TSS (NM_012083)	-161	NM_012083	23401	Hs.140720	NM_012083	ENSG00000181274	FRAT2	FRAT-2	FRAT regulator of WNT signaling pathway 2	protein-coding	0.128959	0.735892	
chunk0120_167_1	chr3	5750167	5750575	+	0	NA	Intergenic	Intergenic	-500116	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.004902	0.364303	263(TGGCACAAAATGTTCA,-,0.00),264(GGCACAAAATGTTCAT,+,0.00)
chunk0143_100_1	chr4	108480734	108481261	+	0	NA	Intergenic	Intergenic	139460	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.000000	0.392045	
chunk0012_42_1	chr1	155244541	155245162	+	0	NA	promoter-TSS (NM_001171811)	promoter-TSS (NM_001171811)	11	NM_001005742	2629	Hs.282997	NM_000157	ENSG00000177628	GBA	GBA1|GCB|GLUC	glucosylceramidase beta	protein-coding	0.069243	0.593248	
chunk0076_258_1	chr16	69290864	69291344	+	0	NA	intron (NM_006750, intron 5 of 6)	intron (NM_006750, intron 5 of 6)	-20280	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.000000	0.440748	200(GAGAACACAGTGTCAT,-,0.00),201(AGAACACAGTGTCATG,+,0.00)
chunk0139_429_1	chr4	64493562	64494007	+	0	NA	Intergenic	Intergenic	-84324	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.000000	0.338565	98(GGAGACACTTTGTTCC,-,0.00),99(GAGACACTTTGTTCCA,+,0.00)
chunk0190_389_1	chr8	40115542	40116140	+	0	NA	Intergenic	MER21C|LTR|ERVL	-37627	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.011706	0.383973	
chunk0193_53_1	chr8	72107458	72107771	+	0	NA	Intergenic	Intergenic	-32030	NM_007332	8989	Hs.716816	NM_007332	ENSG00000104321	TRPA1	ANKTM1|FEPS|FEPS1	transient receptor potential cation channel subfamily A member 1	protein-coding	0.006390	0.369427	
chunk0112_203_1	chr20	40441874	40442073	+	0	NA	Intergenic	MIR|SINE|MIR	247267	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.005025	0.410000	
chunk0024_442_1	chr10	46531610	46532095	+	0	NA	Intergenic	L1ME1|LINE|L1	24219	NM_014696	9721	Hs.523375	NM_014696	ENSG00000204175	GPRIN2	GRIN2|KIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding	0.006186	0.339506	
chunk0189_130_1	chr8	22442674	22443079	+	0	NA	intron (NM_001243974, intron 1 of 14)	Tigger15a|DNA|TcMar-Tigger	1906	NM_001243974	5533	Hs.731683	NM_005605	ENSG00000120910	PPP3CC	CALNA3|CNA3|PP2Bgamma	protein phosphatase 3 catalytic subunit gamma	protein-coding	0.012346	0.374384	
chunk0054_23_1	chr13	40665402	40665685	+	0	NA	intron (NM_002015, intron 1 of 2)	CpG	1054	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.109541	0.693662	
chunk0186_195_1	chr7	139731931	139732292	+	0	NA	intron (NM_001113239, intron 1 of 14)	intron (NM_001113239, intron 1 of 14)	45783	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.008310	0.400552	
chunk0075_342_1	chr16	55363917	55364298	+	0	NA	Intergenic	Intergenic	39548	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.010499	0.387435	169(AAGACATCTTGTTCCT,+,0.00)
chunk0134_35_1	chr3	175650858	175651212	+	0	NA	intron (NM_207015, intron 11 of 13)	MIRb|SINE|MIR	125298	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.008475	0.309859	
chunk0058_15_1	chr14	19171676	19172131	+	0	NA	Intergenic	L1M2|LINE|L1	-78566	NR_073459	414763	Hs.617315	NR_073459		BMS1P18	C14orf17|LINC00516	BMS1 pseudogene 18	pseudo	0.004396	0.300439	
chunk0192_280_1	chr8	66259593	66259897	+	0	NA	Intergenic	Intergenic	67631	NR_039979	100505659	Hs.529729	NR_039979	ENSG00000253138	LINC00967	-	long intergenic non-protein coding RNA 967	ncRNA	0.006579	0.531148	
chunk0046_228_1	chr12	60035955	60036715	+	0	NA	Intergenic	Intergenic	346998	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001316	0.345598	
chunk0052_195_1	chr13	24882773	24883092	+	0	NA	non-coding (NR_047595, exon 16 of 16)	non-coding (NR_047595, exon 16 of 16)	39957	NR_047595	55835	Hs.513379	NM_018451	ENSG00000151849	CENPJ	BM032|CENP-J|CPAP|LAP|LIP1|MCPH6|SASS4|SCKL4|Sas-4	centromere protein J	protein-coding	0.006270	0.362500	
chunk0147_134_1	chr4	174461599	174462173	+	0	NA	Intergenic	Intergenic	38091	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.005226	0.391304	
chunk0002_436_1	chr1	28153130	28153369	+	0	NA	intron (NM_001164722, intron 1 of 1)	intron (NM_001164722, intron 1 of 1)	23695	NM_001164723	5724	Hs.77542	NM_000952	ENSG00000169403	PTAFR	PAFR	platelet activating factor receptor	protein-coding	0.012552	0.466667	
chunk0045_250_1	chr12	49060555	49060926	+	0	NA	Intergenic	CpG	-5416	NM_003482	8085	Hs.731384	NM_003482	ENSG00000167548	KMT2D	AAD10|ALR|CAGL114|KABUK1|KMS|MLL2|MLL4|TNRC21	lysine methyltransferase 2D	protein-coding	0.097035	0.669355	
chunk0204_336_1	chr9	101366080	101366520	+	0	NA	intron (NM_001701, intron 3 of 3)	intron (NM_001701, intron 3 of 3)	17219	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.004545	0.371882	
chunk0046_309_1	chr12	62368899	62369098	+	0	NA	intron (NM_006313, intron 7 of 20)	L2a|LINE|L2	-97819	NM_001278472	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.005025	0.365000	38(TGGTACTGGTTGTTCT,-,0.00),39(GGTACTGGTTGTTCTT,+,0.00)
chunk0015_10_1	chr1	184085220	184085802	+	0	NA	Intergenic	L2a|LINE|L2	33860	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.001718	0.396226	448(GGGAACAGCAAGTGCA,-,0.00),449(GGAACAGCAAGTGCAA,+,0.00)
chunk0130_441_1	chr3	141245740	141245982	+	0	NA	intron (NM_152282, intron 3 of 7)	intron (NM_152282, intron 3 of 7)	14036	NM_001037172	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.012397	0.395062	
chunk0066_139_1	chr15	31335222	31335920	+	0	NA	intron (NM_001302461, intron 1 of 1).2	intron (NM_001302461, intron 1 of 1).2	8716	NM_001302461	51621	Hs.376443	NM_015995	ENSG00000169926	KLF13	BTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel like factor 13	protein-coding	0.012894	0.536481	
chunk0128_428_1	chr3	114928734	114929235	+	0	NA	intron (NM_001164343, intron 2 of 11)	L2b|LINE|L2	-28362	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.001996	0.358566	222(TGGTACAAGGTGTACT,-,0.00),223(GGTACAAGGTGTACTG,+,0.00)
chunk0181_386_1	chr7	89481627	89481915	+	0	NA	Intergenic	Intergenic	-637629	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.006944	0.387543	94(TGGAACACACTGTGCT,-,0.00),95(GGAACACACTGTGCTA,+,0.00)
chunk0078_267_1	chr17	7824453	7824654	+	0	NA	exon (NM_020877, exon 77 of 86)	exon (NM_020877, exon 77 of 86)	-15364	NM_001080424	23135	Hs.223678	NM_001080424	ENSG00000132510	KDM6B	JMJD3	lysine demethylase 6B	protein-coding	0.004975	0.579208	84(GACACTGGGTGTTCCT,+,0.00)
chunk0093_301_1	chr19	52923168	52923516	+	0	NA	Intergenic	Intergenic	-5411	NM_001310127	388559		NM_001310127	ENSG00000213793	ZNF888	-	zinc finger protein 888	protein-coding	0.054598	0.604585	
chunk0091_313_1	chr19	12991149	12991801	+	0	NA	Intergenic	Intergenic	-4295	NM_002501	4784	Hs.257970	NM_002501	ENSG00000008441	NFIX	CTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2	nuclear factor I X	protein-coding	0.015337	0.548239	
chunk0200_332_1	chr9	23829201	23829822	+	0	NA	Intergenic	Intergenic	-3446	NM_004432	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.009662	0.339228	
chunk0207_219_1	chr9	131650453	131650652	+	0	NA	intron (NM_198679, intron 2 of 23)	intron (NM_198679, intron 2 of 23)	59290	NM_198679	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.015075	0.530000	81(GTGGACATGATGTGCT,-,0.00),82(TGGACATGATGTGCTG,+,0.00)
chunk0032_411_1	chr11	11943653	11944034	+	0	NA	intron (NM_017944, intron 19 of 26)	intron (NM_017944, intron 19 of 26)	64796	NM_001018057	27122	Hs.292156	NM_013253	ENSG00000050165	DKK3	REIC|RIG	dickkopf WNT signaling pathway inhibitor 3	protein-coding	0.000000	0.335079	
chunk0106_306_1	chr2	204911446	204912040	+	0	NA	intron (NM_205863, intron 2 of 21)	intron (NM_205863, intron 2 of 21)	365950	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.003367	0.310924	
chunk0167_304_1	chr6	71404039	71404348	+	0	NA	promoter-TSS (NR_029504)	promoter-TSS (NR_029504)	-572	NR_029504	407029		NR_029504	ENSG00000207827	MIR30A	MIRN30A|mir-30a	microRNA 30a	ncRNA	0.009709	0.354839	
chunk0104_39_1	chr2	171112628	171112997	+	0	NA	intron (NM_001136554, intron 2 of 20)	L1M5|LINE|L1	-45839	NM_001136555	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.002710	0.297297	
chunk0117_153_1	chr22	19849613	19850422	+	0	NA	3' UTR (NM_024627, exon 3 of 3)	3' UTR (NM_024627, exon 3 of 3)	4831	NM_024627	79680	Hs.105642	NM_024627	ENSG00000215012	RTL10	BOP|C22orf29	retrotransposon Gag like 10	protein-coding	0.008653	0.518519	
chunk0128_354_1	chr3	112990855	112991154	+	0	NA	promoter-TSS (NM_138485)	promoter-TSS (NM_138485)	51	NM_014170	29083	Hs.127496	NM_014170	ENSG00000163607	GTPBP8	HSPC135	GTP binding protein 8 (putative)	protein-coding	0.076923	0.613333	
chunk0098_34_1	chr2	65944623	65944930	+	0	NA	Intergenic	Intergenic	413552	NR_039938	100616464		NR_039938	ENSG00000264525	MIR4778	-	microRNA 4778	ncRNA	0.003257	0.327922	
chunk0077_450_1	chr16	85867789	85868097	+	0	NA	Intergenic	MER83|LTR|ERV1	-31225	NM_002163	3394	Hs.137427	NM_002163	ENSG00000140968	IRF8	H-ICSBP|ICSBP|ICSBP1|IMD32A|IMD32B|IRF-8	interferon regulatory factor 8	protein-coding	0.022727	0.508091	
chunk0129_70_1	chr3	117677063	117677682	+	0	NA	Intergenic	Intergenic	755941	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.004847	0.337097	
chunk0187_111_1	chr7	148428569	148428768	+	0	NA	Intergenic	L1PA7|LINE|L1	-161897	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.005025	0.355000	
chunk0205_1_1	chr9	104765982	104766455	+	0	NA	intron (NR_130759, intron 1 of 4)	intron (NR_130759, intron 1 of 4)	2477	NR_130760	55335	Hs.429294	NM_018376	ENSG00000165028	NIPSNAP3B	FP944|NIPSNAP3|SNAP1	nipsnap homolog 3B	protein-coding	0.016913	0.358650	
chunk0122_416_1	chr3	38945458	38945850	+	0	NA	intron (NM_014139, intron 2 of 25)	LTR16A1|LTR|ERVL	4907	NM_014139	11280	Hs.591657	NM_014139	ENSG00000168356	SCN11A	FEPS3|HSAN7|NAV1.9|NaN|PN5|SCN12A|SNS-2	sodium voltage-gated channel alpha subunit 11	protein-coding	0.010204	0.496183	
chunk0177_161_1	chr7	23181789	23182157	+	0	NA	5' UTR (NM_007342, exon 1 of 7)	5' UTR (NM_007342, exon 1 of 7)	146	NM_007342	11097	Hs.408241	NM_007342	ENSG00000136243	NUP42	CG1|NLP-1|NLP_1|NUPL2|hCG1	nucleoporin 42	protein-coding	0.086957	0.607046	
chunk0198_91_1	chr8	130285611	130285977	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	10739	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.010929	0.356948	
chunk0011_57_1	chr1	143266217	143266556	+	0	NA	Intergenic	Intergenic	156206	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.058997	0.370588	
chunk0121_342_1	chr3	24551225	24551515	+	0	NA	Intergenic	Intergenic	-29935	NR_039955									0.003448	0.371134	
chunk0089_358_1	chr18	66874850	66875591	+	0	NA	Intergenic	Intergenic	-206364	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.004049	0.349057	345(AGGACAAAATGATCTT,+,0.00)
chunk0047_420_1	chr12	76096240	76096672	+	0	NA	Intergenic	Intergenic	-11423	NM_139207	4673	Hs.524599	NM_004537	ENSG00000187109	NAP1L1	NAP1|NAP1L|NRP	nucleosome assembly protein 1 like 1	protein-coding	0.004630	0.415704	
chunk0211_203_1	chrX	118066910	118067227	+	0	NA	intron (NM_001168301, intron 1 of 7)	Tigger3b|DNA|TcMar-Tigger	49797	NM_001168302	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.003155	0.352201	
chunk0200_274_1	chr9	22136527	22136845	+	0	NA	Intergenic	Intergenic	-127373	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.003145	0.319749	
chunk0073_239_1	chr16	11584012	11584295	+	0	NA	intron (NR_024320, intron 1 of 3)	intron (NR_024320, intron 1 of 3)	2220	NM_004862	9516	Hs.459940	NM_004862	ENSG00000189067	LITAF	PIG7|SIMPLE|TP53I7	lipopolysaccharide induced TNF factor	protein-coding	0.017668	0.426056	
chunk0031_45_1	chr10	122423959	122424478	+	0	NA	exon (NM_021622, exon 9 of 12)	exon (NM_021622, exon 9 of 12)	7253	NR_037506	100500866		NR_037506	ENSG00000265442	MIR3941	-	microRNA 3941	ncRNA	0.007707	0.319231	
chunk0110_217_1	chr20	15419663	15420416	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	223181	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.010624	0.385942	
chunk0012_247_1	chr1	161083480	161083853	+	0	NA	intron (NM_030916, intron 1 of 8)	intron (NM_030916, intron 1 of 8)	5929	NM_030916	81607	Hs.492490	NM_030916	ENSG00000143217	NECTIN4	EDSS1|LNIR|PRR4|PVRL4|nectin-4	nectin cell adhesion molecule 4	protein-coding	0.018767	0.644385	
chunk0124_172_1	chr3	55343675	55344299	+	0	NA	Intergenic	Intergenic	137411	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.000000	0.427200	150(CAGAACAAGCTGTTTC,-,0.00),151(AGAACAAGCTGTTTCT,+,0.00),315(CAGAACATTCTCTCCT,-,0.00),316(AGAACATTCTCTCCTT,+,0.00)
chunk0078_345_1	chr16	86256369	86256573	+	0	NA	intron (NR_104139, intron 3 of 5)	L1MDa|LINE|L1	29776	NR_104139	101154687	Hs.640512	NR_104139		LINC01081	TCONS00024764|TCONS_00024764	long intergenic non-protein coding RNA 1081	ncRNA	0.000000	0.502439	
chunk0164_187_1	chr6	22133191	22133720	+	0	NA	intron (NR_015410, intron 9 of 11)	MER77|LTR|ERVL	13738	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.011342	0.449057	299(TGGTACAGCATGATCC,-,0.00),300(GGTACAGCATGATCCA,+,0.00)
chunk0210_408_1	chrX	100658904	100659619	+	0	NA	intron (NM_014467, intron 3 of 10)	L3|LINE|CR1	15095	NM_014467	27286	Hs.306339	NM_014467	ENSG00000102359	SRPX2	BPP|CBPS|PMGX|RESDX|SRPUL	sushi repeat containing protein X-linked 2	protein-coding	0.008392	0.416201	
chunk0009_305_1	chr1	108051711	108051910	+	0	NA	Intergenic	Intergenic	-86887	NM_006113	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.015075	0.475000	107(AAGAGCAGCGAGTGCT,-,0.00)
chunk0033_220_1	chr11	17278412	17278647	+	0	NA	intron (NM_005013, intron 1 of 13)	intron (NM_005013, intron 1 of 13)	1790	NM_005013	4925	Hs.654599	NM_005013	ENSG00000070081	NUCB2	HEL-S-109|NEFA	nucleobindin 2	protein-coding	0.021277	0.423729	124(AGGTACATATTGTTCA,-,0.00),125(GGTACATATTGTTCAT,+,0.00)
chunk0122_403_1	chr3	38133111	38133764	+	0	NA	intron (NR_024024, intron 3 of 9)	intron (NR_024024, intron 3 of 9)	3805	NM_001130410	30	Hs.643487	NM_001607	ENSG00000060971	ACAA1	ACAA|PTHIO|THIO	acetyl-CoA acyltransferase 1	protein-coding	0.004594	0.457187	
chunk0113_83_1	chr20	50741268	50741467	+	0	NA	intron (NM_032521, intron 2 of 2)	L2a|LINE|L2	9823	NM_032521	84612	Hs.589848	NM_032521	ENSG00000124171	PARD6B	PAR6B	par-6 family cell polarity regulator beta	protein-coding	0.010050	0.440000	
chunk0177_411_1	chr7	27527358	27527671	+	0	NA	intron (NM_152740, intron 7 of 7)	intron (NM_152740, intron 7 of 7)	-88460	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.006390	0.423567	
chunk0122_166_1	chr3	32292174	32292470	+	0	NA	intron (NM_178868, intron 1 of 3)	intron (NM_178868, intron 1 of 3)	53643	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.013514	0.447811	
chunk0014_242_1	chr1	179970030	179970282	+	0	NA	intron (NM_014810, intron 1 of 37)	intron (NM_014810, intron 1 of 37)	15383	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.003968	0.387352	133(TGGGACATTGTGTTCT,-,0.00),134(GGGACATTGTGTTCTC,+,0.00)
chunk0122_177_1	chr3	32557770	32557989	+	0	NA	intron (NM_016141, intron 2 of 12)	intron (NM_016141, intron 2 of 12)	12995	NM_016141	51143	Hs.529495	NM_016141	ENSG00000144635	DYNC1LI1	DLC-A|DNCLI1|LIC1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding	0.009132	0.368182	
chunk0195_149_1	chr8	95269150	95269502	+	0	NA	promoter-TSS (NM_177965)	promoter-TSS (NM_177965)	-92	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.093750	0.643059	
chunk0183_381_1	chr7	109708754	109708954	+	0	NA	Intergenic	Intergenic	251359	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.015000	0.412935	
chunk0106_313_1	chr2	205181252	205181860	+	0	NA	intron (NM_205863, intron 13 of 21)	MER58A|DNA|hAT-Charlie	-500944	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.008224	0.390805	
chunk0079_124_1	chr17	12574462	12575188	+	0	NA	intron (NR_034144, intron 1 of 2)	L1ME4a|LINE|L1	24857	NR_034144	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.005510	0.342503	42(TGGGACATGATGTTTT,-,0.00),43(GGGACATGATGTTTTT,+,0.00)
chunk0212_420_1	chrX	152858047	152858354	+	0	NA	intron (NM_015922, intron 3 of 7)	L1MC5a|LINE|L1	27233	NM_001129765	50814	Hs.57698	NM_015922	ENSG00000147383	NSDHL	H105E3|SDR31E1|XAP104	NAD(P) dependent steroid dehydrogenase-like	protein-coding	0.006515	0.431818	156(TGGTACAAGGTGTGCC,-,0.00),157(GGTACAAGGTGTGCCT,+,0.00)
chunk0136_108_1	chr4	3183306	3183651	+	0	NA	intron (NM_002111, intron 37 of 66)	intron (NM_002111, intron 37 of 66)	-65562	NM_001042690	345222	Hs.442291	NM_001012982	ENSG00000188981	MSANTD1	C4orf44	Myb/SANT DNA binding domain containing 1	protein-coding	0.005797	0.453757	
chunk0033_342_1	chr11	22884061	22884406	+	0	NA	Intergenic	Intergenic	-23807	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.000000	0.291908	187(GAGGACACAGTGTTAC,-,0.00)
chunk0125_123_1	chr3	65830470	65831766	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-62698	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.004630	0.374711	
chunk0157_408_1	chr5	124420643	124420842	+	0	NA	intron (NR_125774, intron 3 of 5)	L1M3e|LINE|L1	17778	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005025	0.570000	
chunk0123_45_1	chr3	40939077	40939744	+	0	NA	Intergenic	Intergenic	-260041	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005997	0.446108	549(CTGAACAATGTGTACC,-,0.00),550(TGAACAATGTGTACCT,+,0.00)
chunk0190_402_1	chr8	40336744	40337157	+	0	NA	Intergenic	Intergenic	183482	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.007264	0.480676	
chunk0063_396_1	chr14	87473108	87473545	+	0	NA	Intergenic	Intergenic	519945	NM_001201401	2581	Hs.513439	NM_000153	ENSG00000054983	GALC	-	galactosylceramidase	protein-coding	0.004577	0.349315	166(AAGCACATGCTCTTCT,-,0.00),167(AGCACATGCTCTTCTT,+,0.00)
chunk0011_134_1	chr1	147219392	147219918	+	0	NA	intron (NM_001144830, intron 1 of 6)	L1MC|LINE|L1	5983	NM_001461	2330	Hs.642706	NM_001461	ENSG00000131781	FMO5	-	flavin containing dimethylaniline monoxygenase 5	protein-coding	0.007605	0.354839	
chunk0211_216_1	chrX	118411586	118411914	+	0	NA	intron (NM_019045, intron 12 of 19)	intron (NM_019045, intron 12 of 19)	25356	NR_031685	100302214		NR_031685	ENSG00000221463	MIR1277	MIRN1277|hsa-mir-1277	microRNA 1277	ncRNA	0.000000	0.355623	
chunk0022_22_1	chr10	7722102	7722546	+	0	NA	intron (NM_002216, intron 8 of 20)	intron (NM_002216, intron 8 of 20)	19051	NM_002216	3698	Hs.75285	NM_002216	ENSG00000151655	ITIH2	H2P|SHAP	inter-alpha-trypsin inhibitor heavy chain 2	protein-coding	0.020270	0.483146	
chunk0187_338_1	chr7	156820700	156820985	+	0	NA	intron (NM_022458, intron 4 of 16)	ERVL-B4-int|LTR|ERVL	72366	NM_022458	64327	Hs.209989	NM_022458	ENSG00000105983	LMBR1	ACHP|C7orf2|DIF14|LSS|PPD2|THYP|TPT|ZRS	limb development membrane protein 1	protein-coding	0.021053	0.573427	
chunk0053_128_1	chr13	29809080	29809714	+	0	NA	intron (NM_007106, intron 1 of 4)	L2c|LINE|L2	41286	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.003155	0.415748	
chunk0091_87_1	chr19	5577763	5578285	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-9990	NR_027064	257000	Hs.515575	NM_153375	ENSG00000223573	TINCR	LINC00036|NCRNA00036|PLAC2|onco-lncRNA-16	TINCR ubiquitin domain containing	ncRNA	0.032567	0.565966	
chunk0188_246_1	chr8	14329641	14329947	+	0	NA	intron (NM_139167, intron 2 of 7)	intron (NM_139167, intron 2 of 7)	523716	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.003268	0.345277	
chunk0007_91_1	chr1	78591117	78591607	+	0	NA	Intergenic	L1MC4|LINE|L1	-29020	NM_006820	10964	Hs.744918	NM_006820	ENSG00000137959	IFI44L	C1orf29|GS3686	interferon induced protein 44 like	protein-coding	0.004082	0.403259	219(CAGTACAATCTGTCCT,-,0.00),220(AGTACAATCTGTCCTC,+,0.00)
chunk0022_447_1	chr10	19879229	19879747	+	0	NA	intron (NM_032812, intron 1 of 13)	MIRb|SINE|MIR	63045	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.007722	0.356455	
chunk0041_153_1	chr11	125764513	125764793	+	0	NA	Intergenic	Intergenic	14166	NM_212555	399967	Hs.369185	NM_212555	ENSG00000196844	PATE2	C11orf38|PATE-M|UNQ3112	prostate and testis expressed 2	protein-coding	0.003571	0.466192	101(AAGAACAGTTTCTTCT,-,0.00)
chunk0074_186_1	chr16	24700749	24701327	+	0	NA	Intergenic	L3|LINE|CR1	-28690	NM_014494	27327	Hs.655057	NM_014494	ENSG00000090905	TNRC6A	CAGH26|FAME6|GW1|GW182|TNRC6	trinucleotide repeat containing adaptor 6A	protein-coding	0.013841	0.511226	306(AAGAACATTCAGTTCT,-,0.00),307(AGAACATTCAGTTCTG,+,0.00)
chunk0068_12_1	chr15	50576317	50576569	+	0	NA	intron (NM_001301212, intron 31 of 38)	intron (NM_001301212, intron 31 of 38)	-29738	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.003968	0.347826	
chunk0091_28_1	chr19	3429544	3430210	+	0	NA	intron (NM_205843, intron 3 of 10)	intron (NM_205843, intron 3 of 10)	50665	NM_001136503	284422	Hs.130714	NM_001136503	ENSG00000095932	SMIM24	C19orf77|HSPC323|MARDI	small integral membrane protein 24	protein-coding	0.027027	0.541229	284(TGCACGGGCTGTTCCC,+,0.00),306(GGGAACATCGTGGCCC,-,0.00),307(GGAACATCGTGGCCCT,+,0.00)
chunk0080_228_1	chr17	29806019	29806512	+	0	NA	intron (NM_033389, intron 1 of 14)	MIRc|SINE|MIR	-44833	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.004057	0.398785	374(CAGAACAGGTTGCTCC,-,0.00),375(AGAACAGGTTGCTCCT,+,0.00)
chunk0039_162_1	chr11	98972440	98972731	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-48391	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003436	0.349315	
chunk0140_195_1	chr4	70239465	70239840	+	0	NA	Intergenic	Intergenic	-2964	NM_005212	1448	Hs.54415	NM_005212	ENSG00000171209	CSN3	CNS10|CSN10|CSNK|KCA	casein kappa	protein-coding	0.000000	0.337766	
chunk0194_406_1	chr8	91207372	91208041	+	0	NA	intron (NM_001129890, intron 7 of 7)	intron (NM_001129890, intron 7 of 7)	-1788	NM_001282357	115111	Hs.354013	NM_052832	ENSG00000147606	SLC26A7	SUT2	solute carrier family 26 member 7	protein-coding	0.004484	0.413433	
chunk0147_57_1	chr4	172628093	172628425	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	60658	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.003012	0.294294	
chunk0120_417_1	chr3	12967764	12968016	+	0	NA	promoter-TSS (NM_014869)	promoter-TSS (NM_014869)	-192	NM_014869	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.123016	0.778656	
chunk0049_58_1	chr12	90112214	90112448	+	0	NA	Intergenic	Intergenic	403376	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.008547	0.472340	
chunk0168_266_1	chr6	89506911	89507589	+	0	NA	intron (NM_014942, intron 1 of 15)	intron (NM_014942, intron 1 of 15)	-55068	NM_001242811	22881	Hs.702213	NM_014942	ENSG00000135299	ANKRD6	-	ankyrin repeat domain 6	protein-coding	0.001475	0.354934	
chunk0035_239_1	chr11	46051990	46052508	+	0	NA	intron (NM_016621, intron 5 of 17)	MLT1K|LTR|ERVL-MaLR	69185	NM_001101802	51317	Hs.502458	NM_016621	ENSG00000135365	PHF21A	BHC80|BM-006	PHD finger protein 21A	protein-coding	0.000000	0.423892	
chunk0109_263_1	chr20	8026798	8027260	+	0	NA	Intergenic	L1M5|LINE|L1	-7200	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.006494	0.295896	
chunk0111_420_1	chr20	34825277	34825548	+	0	NA	intron (NM_014071, intron 1 of 14)	CpG	218	NM_001242539	23054	Hs.368971	NM_014071	ENSG00000198646	NCOA6	AIB3|ASC2|NRC|PRIP|RAP250|TRBP	nuclear receptor coactivator 6	protein-coding	0.177122	0.823529	
chunk0145_211_1	chr4	147991449	147992158	+	0	NA	intron (NM_024605, intron 18 of 22)	MER68B|LTR|ERVL	209208	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.011283	0.450704	
chunk0155_359_1	chr5	97243104	97243557	+	0	NA	Intergenic	Intergenic	-60029	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.002208	0.348018	
chunk0026_333_1	chr10	68384248	68384711	+	0	NA	intron (NR_103475, intron 8 of 18)	intron (NR_103475, intron 8 of 18)	22710	NM_017987	55680	Hs.653144	NM_017987	ENSG00000204130	RUFY2	RABIP4R|ZFYVE13	RUN and FYVE domain containing 2	protein-coding	0.006479	0.312500	
chunk0112_216_1	chr20	40654821	40655300	+	0	NA	Intergenic	CR1-L3A_Croc|LINE|CR1	34180	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.008351	0.464583	226(CAGAACACAATGTATC,-,0.00),227(AGAACACAATGTATCT,+,0.00)
chunk0193_174_1	chr8	74913468	74913948	+	0	NA	Intergenic	Intergenic	-70765	NM_031461	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.004167	0.361746	
chunk0188_375_1	chr8	18238455	18239080	+	0	NA	Intergenic	Intergenic	17099	NM_001160174	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.003200	0.375399	344(ATGAACACAGTGACCT,-,0.00),345(TGAACACAGTGACCTC,+,0.00)
chunk0071_285_1	chr15	85806977	85807424	+	0	NA	Intergenic	Intergenic	-12242	NM_022480	64410	Hs.498371	NM_022480	ENSG00000183655	KLHL25	ENC-2|ENC2	kelch like family member 25	protein-coding	0.011186	0.377232	
chunk0179_430_1	chr7	52022064	52022600	+	0	NA	Intergenic	Intergenic	-705514	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.001866	0.340782	247(TGGGACTCTATGTTCT,-,0.00),248(GGGACTCTATGTTCTC,+,0.00)
chunk0118_309_1	chr22	35070645	35071281	+	0	NA	intron (NM_001303508, intron 2 of 4)	MER58A|DNA|hAT-Charlie	4827	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.004717	0.494505	421(GGCACTCAAAGTCCTT,+,0.00)
chunk0082_200_1	chr17	56834862	56835102	+	0	NA	exon (NM_003647, exon 2 of 12)	exon (NM_003647, exon 2 of 12)	883	NM_003647	8526	Hs.239514	NM_003647	ENSG00000153933	DGKE	AHUS7|DAGK5|DAGK6|DGK|NPHS7	diacylglycerol kinase epsilon	protein-coding	0.095833	0.668050	
chunk0013_74_1	chr1	167544350	167545064	+	0	NA	intron (NM_003851, intron 3 of 3)	MIR|SINE|MIR	9112	NM_003851	8804	Hs.5710	NM_003851	ENSG00000143162	CREG1	CREG	cellular repressor of E1A stimulated genes 1	protein-coding	0.005602	0.443357	341(AGGCCAGTTTGTTCTC,+,0.00)
chunk0059_79_1	chr14	30610588	30611166	+	0	NA	intron (NM_001308097, intron 11 of 13)	MER58A|DNA|hAT-Charlie	-11377	NM_182835	23256	Hs.369168	NM_016106	ENSG00000092108	SCFD1	C14orf163|RA410|SLY1|SLY1P|STXBP1L2	sec1 family domain containing 1	protein-coding	0.008651	0.388601	
chunk0062_370_1	chr14	74084019	74084382	+	0	NA	promoter-TSS (NM_001024674)	promoter-TSS (NM_001024674)	293	NM_001278593	4329	Hs.293970	NM_005589	ENSG00000119711	ALDH6A1	MMSADHA|MMSDH	aldehyde dehydrogenase 6 family member A1	protein-coding	0.046832	0.626374	
chunk0168_205_1	chr6	85680043	85680351	+	0	NA	Intergenic	FLAM_C|SINE|Alu	-1464	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.009740	0.368932	
chunk0184_41_1	chr7	112211627	112211918	+	0	NA	intron (NM_021994, intron 1 of 11)	L2c|LINE|L2	5184	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.000000	0.380137	
chunk0125_36_1	chr3	62568285	62568484	+	0	NA	intron (NM_003716, intron 9 of 29)	MLT2B3|LTR|ERVL	-194869	NM_018008	55079	Hs.241523	NM_018008	ENSG00000153266	FEZF2	FEZ|FEZL|FKSG36|TOF|ZFP312|ZNF312	FEZ family zinc finger 2	protein-coding	0.020101	0.525000	
chunk0206_134_1	chr9	121062561	121062760	+	0	NA	Intergenic	Intergenic	-12384	NM_001735	727	Hs.494997	NM_001735	ENSG00000106804	C5	C5D|C5a|C5b|CPAMD4|ECLZB	complement C5	protein-coding	0.005025	0.365000	
chunk0127_255_1	chr3	97204634	97205034	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	-234759	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002500	0.296758	
chunk0111_280_1	chr20	31605480	31605679	+	0	NA	exon (NM_181353, exon 1 of 1)	exon (NM_181353, exon 1 of 1)	296	NM_181353	3397	Hs.504609	NM_002165	ENSG00000125968	ID1	ID|bHLHb24	inhibitor of DNA binding 1, HLH protein	protein-coding	0.085427	0.665000	
chunk0015_394_1	chr1	190784104	190784683	+	0	NA	intron (NR_033922, intron 2 of 4)	L1PA16|LINE|L1	159503	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.005181	0.343103	
chunk0172_279_1	chr6	137648537	137649238	+	0	NA	Intergenic	Intergenic	-16759	NR_125867	102723649	Hs.129235	NR_125867		LOC102723649	-	uncharacterized LOC102723649	ncRNA	0.005706	0.433048	256(AGAAACACTGTGTACT,-,0.00),257(GAAACACTGTGTACTT,+,0.00)
chunk0128_422_1	chr3	114892241	114892446	+	0	NA	intron (NM_001164343, intron 3 of 11)	intron (NM_001164343, intron 3 of 11)	8279	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.000000	0.368932	
chunk0193_211_1	chr8	76305270	76305668	+	0	NA	Intergenic	Intergenic	-101185	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.007538	0.328321	
chunk0191_203_1	chr8	52012968	52013499	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-114047	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.005650	0.385338	
chunk0067_214_1	chr15	45123037	45123247	+	0	NA	promoter-TSS (NM_001276265)	promoter-TSS (NM_001276265)	-99	NM_001276266	90527	Hs.356664	NM_144565	ENSG00000140254	DUOXA1	NIP|NUMBIP|mol	dual oxidase maturation factor 1	protein-coding	0.004762	0.473934	77(CAGCACAGAATGAGCC,-,0.00),78(AGCACAGAATGAGCCA,+,0.00)
chunk0006_216_1	chr1	68301619	68301911	+	0	NA	Intergenic	Intergenic	-69164	NM_024911	79971	Hs.647659	NM_024911	ENSG00000116729	WLS	C1orf139|EVI|GPR177|MRP|mig-14	Wnt ligand secretion mediator	protein-coding	0.003425	0.375427	
chunk0149_369_1	chr5	28104176	28104599	+	0	NA	Intergenic	Intergenic	632095	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.000000	0.273585	
chunk0174_46_1	chr6	154698832	154699203	+	0	NA	Intergenic	L1MEh|LINE|L1	-34361	NM_001286188	22828	Hs.591329	NM_014892	ENSG00000213079	SCAF8	RBM16	SR-related CTD associated factor 8	protein-coding	0.008086	0.379032	
chunk0124_178_1	chr3	55417115	55417758	+	0	NA	Intergenic	Intergenic	63962	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.006221	0.347826	
chunk0170_370_1	chr6	116922768	116923459	+	0	NA	exon (NM_173560, exon 14 of 19)	exon (NM_173560, exon 14 of 19)	45900	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.004342	0.335260	
chunk0010_307_1	chr1	117981267	117981466	+	0	NA	exon (NM_206996, exon 43 of 49)	exon (NM_206996, exon 43 of 49)	51617	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.000000	0.335000	
chunk0091_42_1	chr19	4118583	4119083	+	0	NA	intron (NM_030662, intron 1 of 10)	intron (NM_030662, intron 1 of 10)	5296	NM_030662	5605	Hs.465627	NM_030662	ENSG00000126934	MAP2K2	CFC4|MAPKK2|MEK2|MKK2|PRKMK2	mitogen-activated protein kinase kinase 2	protein-coding	0.012000	0.423154	
chunk0085_180_1	chr18	5659338	5659812	+	0	NA	Intergenic	L2a|LINE|L2	-30584	NM_001281535	23136	Hs.213394	NM_012307	ENSG00000082397	EPB41L3	4.1B|DAL-1|DAL1	erythrocyte membrane protein band 4.1 like 3	protein-coding	0.008439	0.444211	
chunk0131_137_1	chr3	145375049	145375335	+	0	NA	Intergenic	L1M1|LINE|L1	786303	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.000000	0.494774	
chunk0089_352_1	chr18	66320271	66320495	+	0	NA	Intergenic	Intergenic	283755	NM_021153	28513	Hs.42771	NM_021153	ENSG00000071991	CDH19	CDH7|CDH7L2	cadherin 19	protein-coding	0.004464	0.431111	
chunk0038_66_1	chr11	83025197	83025767	+	0	NA	intron (NM_001286060, intron 1 of 4)	intron (NM_001286060, intron 1 of 4)	9087	NM_001286059	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.003509	0.411559	
chunk0163_293_1	chr6	14092743	14093739	+	0	NA	Intergenic	Intergenic	-24015	NM_001251901	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.010040	0.398195	295(CGGTACAGAATGTTCC,-,0.00),296(GGTACAGAATGTTCCT,+,0.00)
chunk0163_4_1	chr6	7685292	7686120	+	0	NA	Intergenic	Intergenic	-41072	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.008454	0.367913	
chunk0077_244_1	chr16	80718655	80718927	+	0	NA	intron (NM_152342, intron 1 of 6)	intron (NM_152342, intron 1 of 6)	85487	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.014706	0.560440	
chunk0041_64_1	chr11	123486995	123487569	+	0	NA	Intergenic	L2c|LINE|L2	-38354	NM_020716	57476	Hs.144725	NM_020716	ENSG00000023171	GRAMD1B	LINC01059	GRAM domain containing 1B	protein-coding	0.010453	0.480000	379(GGGAACAAGATGTACA,-,0.00),380(GGAACAAGATGTACAT,+,0.00)
chunk0178_81_1	chr7	30466778	30467318	+	0	NA	intron (NM_006092, intron 1 of 13)	L1ME3G|LINE|L1	11729	NM_006092	10392	Hs.405153	NM_006092	ENSG00000106100	NOD1	CARD4|CLR7.1|NLRC1	nucleotide binding oligomerization domain containing 1	protein-coding	0.011111	0.426987	
chunk0076_252_1	chr16	69253742	69254151	+	0	NA	intron (NM_006750, intron 2 of 6)	intron (NM_006750, intron 2 of 6)	-57438	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.004890	0.378049	177(GTGAACATTCTGTGCC,-,0.00),178(TGAACATTCTGTGCCT,+,0.00)
chunk0088_343_1	chr18	51513788	51514063	+	0	NA	intron (NR_040074, intron 1 of 2)	intron (NR_040074, intron 1 of 2)	121883	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.003636	0.525362	
chunk0157_389_1	chr5	124090193	124090436	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	348206	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004115	0.377049	
chunk0125_425_1	chr3	72410830	72411561	+	0	NA	intron (NM_012234, intron 1 of 3)	intron (NM_012234, intron 1 of 3)	35428	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.005472	0.353825	
chunk0114_69_1	chr21	9119311	9119513	+	0	NA	intron (NR_038329, intron 2 of 2)	MER52A|LTR|ERV1	10349	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.029703	0.615764	
chunk0200_461_1	chr9	31890942	31891569	+	0	NA	Intergenic	Intergenic	-493348	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.001595	0.356688	336(CAATACAGACTGTTCT,-,0.00),337(AATACAGACTGTTCTC,+,0.00)
chunk0199_459_1	chr9	14203241	14203661	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	-22649	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.026190	0.456057	
chunk0107_387_1	chr2	223650128	223650365	+	0	NA	Intergenic	Intergenic	-47747	NM_003469	7857	Hs.516726	NM_003469	ENSG00000171951	SCG2	CHGC|EM66|SN|SgII	secretogranin II	protein-coding	0.016878	0.428571	90(CAGCTCACCGTGTCCC,-,0.00),91(AGCTCACCGTGTCCCC,+,0.00)
chunk0199_204_1	chr9	4914042	4914268	+	0	NA	Intergenic	L1MC3|LINE|L1	63858	NR_029836	406894		NR_029836	ENSG00000199065	MIR101-2	MIRN101-2|mir-101-2	microRNA 101-2	ncRNA	0.008850	0.387665	
chunk0181_94_1	chr7	80455537	80455736	+	0	NA	Intergenic	Intergenic	56290	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.010050	0.395000	
chunk0212_280_1	chrX	140457832	140458140	+	0	NA	Intergenic	L2a|LINE|L2	47074	NM_005634	6658	Hs.157429	NM_005634	ENSG00000134595	SOX3	GHDX|MRGH|PHP|PHPX|SOXB	SRY-box transcription factor 3	protein-coding	0.009740	0.404531	
chunk0037_360_1	chr11	78061065	78061430	+	0	NA	intron (NM_001203262, intron 1 of 2)	intron (NM_001203262, intron 1 of 2)	-2614	NM_003251	7069	Hs.591969	NM_003251	ENSG00000151365	THRSP	LPGP1|Lpgp|S14|SPOT14|THRP	thyroid hormone responsive	protein-coding	0.005479	0.513661	
chunk0068_363_1	chr15	58026803	58027289	+	0	NA	intron (NM_003888, intron 1 of 12)	L1PA4|LINE|L1	-12949	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.006173	0.535934	
chunk0036_231_1	chr11	64165948	64166248	+	0	NA	promoter-TSS (NM_014067)	promoter-TSS (NM_014067)	15	NM_014067	28992	Hs.602898	NM_014067	ENSG00000133315	MACROD1	LRP16	mono-ADP ribosylhydrolase 1	protein-coding	0.123333	0.700997	
chunk0104_104_1	chr2	172614635	172615189	+	0	NA	intron (NR_103731, intron 11 of 13)	Charlie22a|DNA|hAT-Charlie	58943	NM_001278549	5163	Hs.470633	NM_002610	ENSG00000152256	PDK1	-	pyruvate dehydrogenase kinase 1	protein-coding	0.009025	0.441441	
chunk0092_57_1	chr19	20052329	20052747	+	0	NA	Intergenic	Intergenic	-13070	NM_033196	91120	Hs.306298	NM_033196	ENSG00000197124	ZNF682	BC39498_3	zinc finger protein 682	protein-coding	0.031100	0.551313	
chunk0108_439_1	chr2	238060676	238060875	+	0	NA	promoter-TSS (NM_016510)	promoter-TSS (NM_016510)	-149	NM_016510	51540	Hs.731909	NM_016510	ENSG00000132330	SCLY	SCL|hSCL	selenocysteine lyase	protein-coding	0.120603	0.725000	
chunk0168_84_1	chr6	79866832	79867135	+	0	NA	Intergenic	L1ME4b|LINE|L1	-54737	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.000000	0.375000	169(AAGTGCAGTATGTCCT,-,0.00),170(AGTGCAGTATGTCCTC,+,0.00)
chunk0009_377_1	chr1	109947854	109948654	+	0	NA	Intergenic	Intergenic	-36511	NM_001242673	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.007500	0.390762	276(TAGTACAGTAAGTTCT,-,0.00),277(AGTACAGTAAGTTCTG,+,0.00)
chunk0210_389_1	chrX	97894683	97895139	+	0	NA	Intergenic	L1MA1|LINE|L1	-330376	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.004386	0.352298	
chunk0075_348_1	chr16	55504114	55504456	+	0	NA	intron (NM_001127891, intron 12 of 12)	MER102b|DNA|hAT-Charlie	-4716	NM_017839	54947	Hs.460857	NM_017839	ENSG00000087253	LPCAT2	AGPAT11|AYTL1|LysoPAFAT	lysophosphatidylcholine acyltransferase 2	protein-coding	0.002924	0.373178	
chunk0126_236_1	chr3	79126594	79126882	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-107279	NM_001145845	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.006944	0.411765	125(GGGAACAGTGTGTCAC,-,0.00),126(GGAACAGTGTGTCACT,+,0.00)
chunk0158_437_1	chr5	135549890	135550569	+	0	NA	Intergenic	Intergenic	-14280	NM_006161	4762	Hs.248149	NM_006161	ENSG00000181965	NEUROG1	AKA|Math4C|NEUROD3|bHLHa6|ngn1	neurogenin 1	protein-coding	0.005891	0.501471	
chunk0091_365_1	chr19	15495040	15495655	+	0	NA	Intergenic	L1MC5|LINE|L1	-13178	NM_173483	126410	Hs.156452	NM_173483	ENSG00000171954	CYP4F22	ARCI5|INLNE|LI3	cytochrome P450 family 4 subfamily F member 22	protein-coding	0.014634	0.441558	347(GGGAACATCTTGTTCA,-,0.00),348(GGAACATCTTGTTCAT,+,0.00)
chunk0010_86_1	chr1	113453553	113453902	+	0	NA	intron (NM_152900, intron 1 of 20)	intron (NM_152900, intron 1 of 20)	62874	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.002865	0.397143	
chunk0161_96_1	chr5	167345002	167345448	+	0	NA	intron (NM_001122679, intron 1 of 28)	intron (NM_001122679, intron 1 of 28)	60387	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.017937	0.458613	
chunk0110_343_1	chr20	19427608	19427891	+	0	NA	intron (NM_020689, intron 2 of 16)	intron (NM_020689, intron 2 of 16)	-143153	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.024735	0.552817	
chunk0153_119_1	chr5	68593329	68593596	+	0	NA	Intergenic	Intergenic	300894	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.007491	0.470149	138(TAGAACAGGCTGTTCA,-,0.00),139(AGAACAGGCTGTTCAA,+,0.00)
chunk0080_222_1	chr17	29723144	29723564	+	0	NA	intron (NM_001282129, intron 3 of 15)	intron (NM_001282129, intron 3 of 15)	38078	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.002381	0.358670	
chunk0089_284_1	chr18	63008906	63009146	+	0	NA	Intergenic	L1MC2|LINE|L1	293587	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.025000	0.402490	
chunk0200_111_1	chr9	16954047	16954463	+	0	NA	Intergenic	Intergenic	-83467	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.004808	0.381295	
chunk0092_134_1	chr19	27997595	27997983	+	0	NA	Intergenic	L1M2|LINE|L1	-203849	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.005155	0.251928	
chunk0060_360_1	chr14	52327143	52328136	+	0	NA	3' UTR (NM_000956, exon 2 of 2)	3' UTR (NM_000956, exon 2 of 2)	13341	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.007049	0.386318	
chunk0156_249_1	chr5	108842107	108842681	+	0	NA	3' UTR (NM_001308038, exon 8 of 8)	3' UTR (NM_001308038, exon 8 of 8)	-82212	NM_001308031	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.001742	0.311304	
chunk0166_321_1	chr6	49813475	49813977	+	0	NA	intron (NR_125839, intron 1 of 3)	MER67A|LTR|ERV1	2186	NR_125839	101927020	Hs.571168	NR_125839		LOC101927020	-	uncharacterized LOC101927020	ncRNA	0.005976	0.393638	
chunk0082_249_1	chr17	57480705	57481041	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	42724	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.002976	0.454006	
chunk0106_247_1	chr2	203336941	203337521	+	0	NA	intron (NM_001282932, intron 1 of 9)	L1MA9|LINE|L1	8992	NM_005759	10152	Hs.471156	NM_005759	ENSG00000138443	ABI2	ABI-2|ABI2B|AIP-1|AIP1|AblBP3|SSH3BP2|argBP1|argBPIA|argBPIB	abl interactor 2	protein-coding	0.005172	0.327022	
chunk0125_97_1	chr3	65408600	65408938	+	0	NA	intron (NM_015520, intron 12 of 24)	intron (NM_015520, intron 12 of 24)	-485047	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.008876	0.410029	
chunk0103_117_1	chr2	161617223	161617422	+	0	NA	Intergenic	MIR|SINE|MIR	-7013	NM_001178015	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.005025	0.365000	
chunk0187_332_1	chr7	156725086	156725383	+	0	NA	intron (NM_022458, intron 14 of 16)	intron (NM_022458, intron 14 of 16)	81433	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.013468	0.385906	
chunk0180_219_1	chr7	67141055	67141747	+	0	NA	intron (NM_018264, intron 13 of 15)	intron (NM_018264, intron 13 of 15)	-27004	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.007225	0.363636	410(AAGCACTGAGTGTTTC,-,0.00)
chunk0069_9_1	chr15	60136071	60136270	+	0	NA	Intergenic	Intergenic	131948	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.000000	0.500000	
chunk0053_122_1	chr13	29653475	29653908	+	0	NA	Intergenic	Intergenic	-58003	NM_003045	6541	Hs.14846	NM_003045	ENSG00000139514	SLC7A1	ATRC1|CAT-1|ERR|HCAT1|REC1L	solute carrier family 7 member 1	protein-coding	0.002309	0.354839	
chunk0012_306_1	chr1	162224718	162224965	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	67734	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.004049	0.491935	29(AGGACAAGTAGTGCCT,+,0.00)
chunk0172_360_1	chr6	139152278	139152662	+	0	NA	intron (NM_016217, intron 1 of 3)	intron (NM_016217, intron 1 of 3)	17358	NM_016217	51696	Hs.197644	NM_016217	ENSG00000112406	HECA	HDC|HDCL|HHDC|dJ225E12.1	hdc homolog, cell cycle regulator	protein-coding	0.002604	0.353247	
chunk0080_340_1	chr17	32696431	32696678	+	0	NA	intron (NM_015194, intron 16 of 21)	LTR106_Mam|LTR|LTR	180619	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.004049	0.358871	
chunk0051_61_1	chr12	112518564	112518936	+	0	NA	Intergenic	Intergenic	100018	NM_080601	5781	Hs.506852	NM_002834	ENSG00000179295	PTPN11	BPTP3|CFC|JMML|METCDS|NS1|PTP-1D|PTP2C|SH-PTP2|SH-PTP3|SHP2	protein tyrosine phosphatase non-receptor type 11	protein-coding	0.018817	0.415550	181(TGGAGCATTCTGTTCT,-,0.00),182(GGAGCATTCTGTTCTA,+,0.00)
chunk0149_270_1	chr5	24376250	24376782	+	0	NA	Intergenic	Intergenic	268460	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.005639	0.324578	
chunk0018_219_1	chr1	219555701	219556147	+	0	NA	Intergenic	Intergenic	372727	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.008969	0.384787	
chunk0074_294_1	chr16	29807556	29807907	+	0	NA	exon (NM_002383, exon 2 of 5)	exon (NM_002383, exon 2 of 5)	1194	NM_001042539	4150	Hs.23650	NM_002383	ENSG00000103495	MAZ	PUR1|Pur-1|SAF-1|SAF-2|SAF-3|ZF87|ZNF801|Zif87	MYC associated zinc finger protein	protein-coding	0.102564	0.678977	
chunk0056_310_1	chr13	91022695	91023295	+	0	NA	Intergenic	Intergenic	66622	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.001667	0.409318	341(GAGAGCAGGAAGTTCT,-,0.00),342(AGAGCAGGAAGTTCTT,+,0.00)
chunk0179_3_1	chr7	42327445	42328145	+	0	NA	Intergenic	Intergenic	-90776	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.010000	0.410842	
chunk0205_295_1	chr9	112012288	112012504	+	0	NA	Intergenic	Intergenic	80296	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.004630	0.511521	
chunk0026_290_1	chr10	67707274	67707592	+	0	NA	Intergenic	L2a|LINE|L2	-11242	NM_013266	29119	Hs.21375	NM_013266	ENSG00000183230	CTNNA3	ARVD13|VR22	catenin alpha 3	protein-coding	0.006289	0.388715	154(TTGCACTTGCTGTTCC,-,0.00),155(TGCACTTGCTGTTCCT,+,0.00)
chunk0055_414_1	chr13	74871777	74871976	+	0	NA	Intergenic	Intergenic	319033	NR_034025	338864	Hs.97408	NR_034024	ENSG00000236678	LINC00347	-	long intergenic non-protein coding RNA 347	ncRNA	0.000000	0.370000	
chunk0187_274_1	chr7	155317063	155317262	+	0	NA	Intergenic	Intergenic	19386	NM_005542	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.020101	0.620000	
chunk0045_301_1	chr12	50532647	50533348	+	0	NA	intron (NM_173602, intron 1 of 37)	intron (NM_173602, intron 1 of 37)	28012	NM_173602	57609	Hs.505516	NM_020849	ENSG00000066084	DIP2B	-	disco interacting protein 2 homolog B	protein-coding	0.004280	0.411681	
chunk0117_64_1	chr22	16915542	16916050	+	0	NA	Intergenic	Intergenic	88322	NR_003607	27437	Hs.143955	NR_003607	ENSG00000229027	HSFY1P1	CECR8|HSFYL1|HSFYP1|NCRNA00016	HSFY1 pseudogene 1	pseudo	0.007874	0.465619	
chunk0001_141_1	chr1	5809093	5809378	+	0	NA	Intergenic	Intergenic	53506	NR_039838	100616421		NR_039838	ENSG00000264101	MIR4689	mir-4689	microRNA 4689	ncRNA	0.007018	0.503497	
chunk0098_387_1	chr2	79489743	79490203	+	0	NA	Intergenic	Intergenic	10871	NR_110289	101927987	Hs.574704	NR_110289	ENSG00000229385	LOC101927987	-	uncharacterized LOC101927987	ncRNA	0.004348	0.394794	
chunk0059_260_1	chr14	35203836	35204416	+	0	NA	intron (NM_014672, intron 5 of 7)	intron (NM_014672, intron 5 of 7)	-74432	NM_001282234	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.006897	0.332186	264(AGGAACACTTTGTATT,-,0.00)
chunk0184_16_1	chr7	111793405	111793604	+	0	NA	intron (NM_014705, intron 30 of 51)	intron (NM_014705, intron 30 of 51)	-15001	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.000000	0.285000	
chunk0178_373_1	chr7	39744684	39744909	+	0	NA	intron (NR_026999, intron 1 of 11)	intron (NR_026999, intron 1 of 11)	11228	NR_026999	349114	Hs.414183	NM_198284		LINC00265	NCRNA00265	long intergenic non-protein coding RNA 265	ncRNA	0.008889	0.446903	
chunk0081_283_1	chr17	44269395	44269770	+	0	NA	Intergenic	MIR|SINE|MIR	-1448	NM_000342	6521	Hs.210751	NM_000342	ENSG00000004939	SLC4A1	AE1|BND3|CD233|CHC|DI|EMPB3|EPB3|FR|RTA1A|SAO|SPH4|SW|WD|WD1|WR	solute carrier family 4 member 1 (Diego blood group)	protein-coding	0.018667	0.555851	
chunk0186_2_1	chr7	135493239	135493741	+	0	NA	intron (NM_001008225, intron 1 of 10)	L2|LINE|L2	16637	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.001992	0.413519	
chunk0006_203_1	chr1	67686282	67686481	+	0	NA	exon (NM_001199741, exon 2 of 3)	exon (NM_001199741, exon 2 of 3)	1204	NM_001924	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.100503	0.660000	
chunk0192_420_1	chr8	69526875	69527164	+	0	NA	intron (NM_015170, intron 3 of 22)	intron (NM_015170, intron 3 of 22)	34226	NM_001128206	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.010381	0.393103	
chunk0028_169_1	chr10	87643239	87643461	+	0	NA	Intergenic	Intergenic	-16369	NM_001015880	9060	Hs.524491	NM_004670	ENSG00000198682	PAPSS2	ATPSK2|BCYM4|SK2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding	0.000000	0.345291	
chunk0052_2_1	chr13	18211972	18212254	+	0	NA	intron (NR_027278, intron 1 of 7)	HSATI|Satellite|Satellite	16816	NR_027278	26080	Hs.448583	NR_027278	ENSG00000279516	FAM230C	LINC00281|NCRNA00281	family with sequence similarity 230 member C	ncRNA	0.003546	0.314488	
chunk0037_279_1	chr11	75783618	75783987	+	0	NA	intron (NM_001253891, intron 1 of 6)	intron (NM_001253891, intron 1 of 6)	15069	NM_032564	84649	Hs.129798	NM_032564	ENSG00000062282	DGAT2	ARAT|GS1999FULL|HMFN1045	diacylglycerol O-acyltransferase 2	protein-coding	0.005420	0.556757	
chunk0014_248_1	chr1	180054011	180054363	+	0	NA	intron (NM_014810, intron 24 of 37)	intron (NM_014810, intron 24 of 37)	99414	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.008523	0.359773	
chunk0109_215_1	chr20	5696125	5696409	+	0	NA	Intergenic	Intergenic	-54120	NM_001303479	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.007042	0.410526	
chunk0116_436_1	chr21	43262425	43262840	+	0	NA	Intergenic	Intergenic	69407	NR_103713	100126693	Hs.473952	NR_103713		LINC00322	C21orf136|NCRNA00322	long intergenic non-protein coding RNA 322	ncRNA	0.002653	0.582011	
chunk0004_371_1	chr1	51654097	51654321	+	0	NA	intron (NR_036662, intron 2 of 22)	L1MC5|LINE|L1	37335	NM_148909	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.000000	0.422222	125(AAGAACATAGTGTCTA,-,0.00)
chunk0081_125_1	chr17	40332392	40332779	+	0	NA	intron (NM_001145302, intron 2 of 6)	intron (NM_001145302, intron 2 of 6)	-9434	NM_001024809	5914	Hs.654583	NM_000964	ENSG00000131759	RARA	NR1B1|RAR	retinoic acid receptor alpha	protein-coding	0.018088	0.659794	
chunk0210_402_1	chrX	98975858	98976314	+	0	NA	Intergenic	L1MD2|LINE|L1	963757	NR_024608	442459	Hs.706599	NM_001127438		XRCC6P5	-	X-ray repair cross complementing 6 pseudogene 5	pseudo	0.006579	0.297593	
chunk0071_97_1	chr15	80991100	80991451	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-1397	NR_126328	23184	Hs.578450	NM_015154	ENSG00000117899	MESD	BOCA|MESDC2	mesoderm development LRP chaperone	protein-coding	0.002849	0.440341	
chunk0208_292_1	chrX	22066324	22066644	+	0	NA	intron (NM_001282754, intron 3 of 20)	intron (NM_001282754, intron 3 of 20)	34040	NM_001282754	5251	Hs.495834	NM_000444	ENSG00000102174	PHEX	HPDR|HPDR1|HYP|HYP1|LXHR|PEX|XLH	phosphate regulating endopeptidase homolog X-linked	protein-coding	0.003125	0.451713	
chunk0194_115_1	chr8	83884645	83885659	+	0	NA	Intergenic	L1M5|LINE|L1	-298066	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002959	0.291626	
chunk0115_225_1	chr21	27154937	27155667	+	0	NA	Intergenic	Intergenic	-188182	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.005479	0.407661	
chunk0139_289_1	chr4	57320790	57321205	+	0	NA	Intergenic	Intergenic	-104875	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.012048	0.413462	
chunk0145_53_1	chr4	145065849	145066352	+	0	NA	intron (NM_001256711, intron 4 of 6)	intron (NM_001256711, intron 4 of 6)	-31904	NM_002940	6059	Hs.12013	NM_002940	ENSG00000164163	ABCE1	ABC38|OABP|RLI|RLI1|RNASEL1|RNASELI|RNS4I	ATP binding cassette subfamily E member 1	protein-coding	0.003976	0.357143	
chunk0012_28_1	chr1	155005679	155005931	+	0	NA	intron (NM_001256455, intron 1 of 2)	intron (NM_001256455, intron 1 of 2)	3175	NR_046206	51043	Hs.729279	NM_001252406	ENSG00000160685	ZBTB7B	CKROX|THPOK|ZBTB15|ZFP-67|ZFP67|ZNF857B|c-KROX|hcKROX	zinc finger and BTB domain containing 7B	protein-coding	0.039683	0.632411	
chunk0084_226_1	chr17	78408970	78409459	+	0	NA	intron (NR_110601, intron 6 of 8)	intron (NR_110601, intron 6 of 8)	30596	NR_111989	9489	Hs.654671	NM_024419	ENSG00000087157	PGS1	-	phosphatidylglycerophosphate synthase 1	protein-coding	0.020450	0.510204	
chunk0115_183_1	chr21	25942122	25942515	+	0	NA	intron (NM_001136016, intron 12 of 16)	MIRc|SINE|MIR	198072	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.022901	0.403553	
chunk0161_37_1	chr5	165831235	165831484	+	0	NA	Intergenic	L1MEf|LINE|L1	1095011	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.008032	0.364000	
chunk0185_378_1	chr7	133155289	133155580	+	0	NA	Intergenic	Intergenic	-73366	NM_017812	54927	Hs.655010	NM_017812	ENSG00000106554	CHCHD3	MICOS19|MINOS3|Mic19|PPP1R22	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding	0.006873	0.479452	
chunk0023_137_1	chr10	23989726	23990150	+	0	NA	intron (NM_001098500, intron 1 of 18)	MIRb|SINE|MIR	-218853	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.000000	0.390588	
chunk0190_408_1	chr8	40390816	40391126	+	0	NA	Intergenic	Intergenic	237503	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.006452	0.414791	
chunk0206_57_1	chr9	118209519	118209730	+	0	NA	Intergenic	Intergenic	505449	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.000000	0.490566	
chunk0136_102_1	chr4	2906422	2906706	+	0	NA	intron (NM_014189, intron 10 of 14)	intron (NM_014189, intron 10 of 14)	27673	NM_001120	10227	Hs.632581	NM_001120	ENSG00000109736	MFSD10	TETRAN|TETTRAN	major facilitator superfamily domain containing 10	protein-coding	0.017606	0.424561	
chunk0024_380_1	chr10	44673453	44674085	+	0	NA	Intergenic	Intergenic	-237547	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.004747	0.437599	
chunk0097_439_1	chr2	64084338	64085009	+	0	NA	Intergenic	Intergenic	59798	NM_020651	57162	Hs.7886	NM_020651	ENSG00000197329	PELI1	-	pellino E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.345238	
chunk0195_100_1	chr8	94446192	94446456	+	0	NA	intron (NM_001205262, intron 3 of 3)	intron (NM_001205262, intron 3 of 3)	-9372	NM_001205263	25788	Hs.30561	NM_006550	ENSG00000197275	RAD54B	RDH54	RAD54 homolog B	protein-coding	0.000000	0.373585	
chunk0070_188_1	chr15	71950753	71951412	+	0	NA	intron (NM_006901, intron 15 of 41)	intron (NM_006901, intron 15 of 41)	140534	NM_016346	10002	Hs.187354	NM_014249	ENSG00000278570	NR2E3	ESCS|PNR|RNR|RP37|rd7	nuclear receptor subfamily 2 group E member 3	protein-coding	0.006070	0.337879	
chunk0106_42_1	chr2	196231243	196231731	+	0	NA	intron (NM_020760, intron 21 of 28)	MER58A|DNA|hAT-Charlie	-28537	NR_110225	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.012295	0.433538	
chunk0033_348_1	chr11	22946475	22947157	+	0	NA	Intergenic	L1MCb|LINE|L1	-86390	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.001466	0.325037	
chunk0119_277_1	chr22	46060182	46060466	+	0	NA	Intergenic	Intergenic	-6180	NM_018280	55267	Hs.567529	NM_018280		PRR34	C22orf26	PRR34 long non-coding RNA	protein-coding	0.010563	0.287719	
chunk0053_281_1	chr13	33311978	33312576	+	0	NA	intron (NM_001243476, intron 5 of 17)	intron (NM_001243476, intron 5 of 17)	-26513	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.008361	0.380634	
chunk0019_73_1	chr1	224304643	224305269	+	0	NA	intron (NM_206840, intron 6 of 21)	intron (NM_206840, intron 6 of 21)	25233	NM_001243147	4931	Hs.497867	NM_002533	ENSG00000143748	NVL	NVL2	nuclear VCP like	protein-coding	0.003195	0.349282	
chunk0005_11_1	chr1	54088490	54088689	+	0	NA	intron (NM_153035, intron 3 of 4)	intron (NM_153035, intron 3 of 4)	34510	NR_039942	100616315		NR_039942	ENSG00000283749	MIR4781	mir-4781	microRNA 4781	ncRNA	0.015075	0.445000	
chunk0212_159_1	chrX	132304512	132305417	+	0	NA	intron (NR_110410, intron 2 of 2)	intron (NR_110410, intron 2 of 2)	-85484	NR_073150	57826	Hs.119889	NM_021183	ENSG00000123728	RAP2C	-	RAP2C, member of RAS oncogene family	protein-coding	0.002210	0.388521	
chunk0148_265_1	chr5	10457803	10458427	+	0	NA	intron (NM_031916, intron 3 of 4)	MER63A|DNA|hAT-Blackjack	16253	NM_001201466	83853	Hs.381089	NM_031916	ENSG00000145491	ROPN1L	ASP|RSPH11	rhophilin associated tail protein 1 like	protein-coding	0.027244	0.590400	
chunk0064_253_1	chr14	94570447	94570821	+	0	NA	TTS (NM_001289033)	TTS (NM_001289033)	9214	NM_001289033	5267	Hs.719893	NM_006215	ENSG00000100665	SERPINA4	KAL|KLST|KST|PI-4|PI4|kallistatin	serpin family A member 4	protein-coding	0.024064	0.573333	163(ATGGACACGGAGTTCC,-,0.00),164(TGGACACGGAGTTCCC,+,0.00),242(TAGCTCACCCTGTGCT,-,0.00),243(AGCTCACCCTGTGCTT,+,0.00)
chunk0013_445_1	chr1	173805959	173806158	+	0	NA	intron (NM_033319, intron 4 of 5)	MER58A|DNA|hAT-Charlie	18074	NM_001171182	91687	Hs.531856	NM_033319	ENSG00000120334	CENPL	C1orf155|CENP-L|dJ383J4.3	centromere protein L	protein-coding	0.000000	0.405000	
chunk0175_371_1	chr6	167906750	167907323	+	0	NA	intron (NM_001207008, intron 11 of 31)	intron (NM_001207008, intron 11 of 31)	69903	NM_001129895	100128124	Hs.448059	NM_001129895		HGC6.3	-	uncharacterized LOC100128124	protein-coding	0.019197	0.440767	261(GTGGACATAGTGTCCC,-,0.00),262(TGGACATAGTGTCCCC,+,0.00)
chunk0055_334_1	chr13	69028939	69029460	+	0	NA	Intergenic	Intergenic	-143874	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.001919	0.310345	
chunk0135_254_1	chr3	188947748	188948507	+	0	NA	promoter-TSS (NR_046873)	promoter-TSS (NR_046873)	-488	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.040843	0.588158	347(ATGCACTGGATGTGCT,-,0.00),348(TGCACTGGATGTGCTC,+,0.00),366(GGGAACAGAATGTACT,-,0.00),367(GGAACAGAATGTACTT,+,0.00)
chunk0037_130_1	chr11	73047500	73048107	+	0	NA	intron (NM_014824, intron 3 of 19)	intron (NM_014824, intron 3 of 19)	94295	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.001647	0.320724	
chunk0209_214_1	chrX	44690209	44690587	+	0	NA	Intergenic	Intergenic	-147423	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.002646	0.424802	149(GAGGACAAGCTGTGTC,-,0.00),150(AGGACAAGCTGTGTCT,+,0.00)
chunk0072_196_1	chr15	94400413	94400915	+	0	NA	intron (NM_018349, intron 15 of 21)	intron (NM_018349, intron 15 of 21)	44729	NM_001159644	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.015936	0.425447	307(AAGAACAAAGTGTCCC,-,0.00),308(AGAACAAAGTGTCCCC,+,0.00)
chunk0080_181_1	chr17	28808667	28809141	+	0	NA	intron (NM_001288635, intron 1 of 3)	intron (NM_001288635, intron 1 of 3)	3531	NM_001288634	55731	Hs.564533	NM_018182	ENSG00000173065	FAM222B	C17orf63	family with sequence similarity 222 member B	protein-coding	0.010549	0.442105	342(GAGAACATAGAGTCCT,-,0.00),343(AGAACATAGAGTCCTT,+,0.00)
chunk0056_430_1	chr13	95035574	95036152	+	0	NA	intron (NM_005845, intron 29 of 30)	intron (NM_005845, intron 29 of 30)	75822	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.005190	0.373057	
chunk0094_236_1	chr2	6998167	6998607	+	0	NA	intron (NM_014746, intron 3 of 8)	MIRc|SINE|MIR	79493	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.006818	0.394558	
chunk0130_142_1	chr3	132248839	132249038	+	0	NA	Intergenic	Intergenic	-68429	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.000000	0.435000	
chunk0208_427_1	chrX	29931910	29932748	+	0	NA	intron (NM_014271, intron 8 of 10)	intron (NM_014271, intron 8 of 10)	-283229	NM_002364	4113	Hs.113824	NM_002364	ENSG00000099399	MAGEB2	CT3.2|DAM6|MAGE-XP-2	MAGE family member B2	protein-coding	0.002387	0.362336	
chunk0033_104_1	chr11	14308125	14308324	+	0	NA	intron (NM_001177314, intron 1 of 5)	L1ME4b|LINE|L1	50261	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.005025	0.350000	
chunk0041_75_1	chr11	124086564	124086961	+	0	NA	Intergenic	Intergenic	-28642	NM_001130142	4013	Hs.152944	NM_014622	ENSG00000110002	VWA5A	BCSC-1|BCSC1|LOH11CR2A	von Willebrand factor A domain containing 5A	protein-coding	0.007557	0.412060	187(CAGAACACAGTGTACA,-,0.00),188(AGAACACAGTGTACAT,+,0.00)
chunk0098_156_1	chr2	70037878	70038493	+	0	NA	intron (NR_033872, intron 6 of 10)	intron (NR_033872, intron 6 of 10)	48830	NR_033872	400960	Hs.683864	NR_033872	ENSG00000179818	PCBP1-AS1	-	PCBP1 antisense RNA 1	ncRNA	0.000000	0.420455	
chunk0118_181_1	chr22	31131727	31132098	+	0	NA	intron (NM_001002837, intron 9 of 12)	intron (NM_001002837, intron 9 of 12)	8695	NM_015715	50487	Hs.149623	NM_015715	ENSG00000100078	PLA2G3	GIII-SPLA2|SPLA2III|sPLA2-III	phospholipase A2 group III	protein-coding	0.010782	0.532258	
chunk0032_112_1	chr11	3801980	3802548	+	0	NA	intron (NR_027017, intron 1 of 7)	intron (NR_027017, intron 1 of 7)	4305	NR_027017	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.005282	0.405975	157(GAGTACATTCAGTCCA,-,0.00)
chunk0160_196_1	chr5	154686305	154686553	+	0	NA	TTS (NR_031638)	TTS (NR_031638)	653	NR_031638	100302284		NR_031638	ENSG00000221552	MIR1303	MIRN1303|hsa-mir-1303	microRNA 1303	ncRNA	0.004032	0.405622	116(AAGTTCAATGTGTTCC,-,0.00),117(AGTTCAATGTGTTCCT,+,0.00)
chunk0132_129_1	chr3	156140052	156140569	+	0	NA	intron (NM_001308217, intron 1 of 12)	MLT1A0|LTR|ERVL-MaLR	-2652	NM_003471	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.005803	0.391892	
chunk0187_412_1	chr7	158188809	158189026	+	0	NA	intron (NM_001308268, intron 5 of 22)	intron (NM_001308268, intron 5 of 22)	334332	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.013825	0.532110	161(CAGGACATGCAGTACA,-,0.00),162(AGGACATGCAGTACAC,+,0.00)
chunk0019_12_1	chr1	223350664	223350878	+	0	NA	intron (NM_001037175, intron 2 of 5)	intron (NM_001037175, intron 2 of 5)	13431	NM_017982	55061	Hs.497841	NM_017982	ENSG00000143502	SUSD4	PRO222	sushi domain containing 4	protein-coding	0.004673	0.446512	
chunk0177_462_1	chr7	28661890	28662104	+	0	NA	intron (NM_182899, intron 4 of 9)	intron (NM_182899, intron 4 of 9)	-23984	NM_001011666	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.004673	0.465116	
chunk0026_32_1	chr10	60725070	60725639	+	0	NA	intron (NM_001204403, intron 1 of 43)	L1ME5|LINE|L1	8172	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.007030	0.412281	
chunk0017_287_1	chr1	210150115	210150537	+	0	NA	intron (NM_001146262, intron 6 of 8)	intron (NM_001146262, intron 6 of 8)	-82524	NM_019605	56256	Hs.600545	NM_019605	ENSG00000082497	SERTAD4	DJ667H12.2	SERTA domain containing 4	protein-coding	0.007109	0.489362	
chunk0150_328_1	chr5	38432919	38433150	+	0	NA	intron (NM_152403, intron 15 of 21)	intron (NM_152403, intron 15 of 21)	-12442	NM_182801	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.008658	0.482759	
chunk0164_192_1	chr6	22255008	22255207	+	0	NA	Intergenic	Intergenic	42394	NM_000948	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.010050	0.315000	
chunk0156_124_1	chr5	106529862	106530115	+	0	NA	Intergenic	Intergenic	481026	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.000000	0.303150	
chunk0137_424_1	chr4	28222799	28223133	+	0	NA	Intergenic	L2a|LINE|L2	-596616	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.002994	0.334328	204(TAAAACAGACTGTTCT,-,0.00),205(AAAACAGACTGTTCTC,+,0.00)
chunk0183_109_1	chr7	105316891	105317273	+	0	NA	intron (NM_182692, intron 2 of 15)	Charlie1a|DNA|hAT-Charlie	-18303	NM_001278273	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.002618	0.407311	
chunk0131_376_1	chr3	152211509	152212239	+	0	NA	Intergenic	Intergenic	-56594	NM_207292	4154	Hs.201858	NM_021038	ENSG00000152601	MBNL1	EXP|MBNL	muscleblind like splicing regulator 1	protein-coding	0.008219	0.370725	
chunk0197_322_1	chr8	125069737	125070200	+	0	NA	intron (NM_014846, intron 9 of 28)	intron (NM_014846, intron 9 of 28)	21851	NM_014846	9897	Hs.270043	NM_014846	ENSG00000164961	WASHC5	KIAA0196|RTSC|RTSC1|SPG8	WASH complex subunit 5	protein-coding	0.000000	0.392241	
chunk0100_207_1	chr2	111826332	111827624	+	0	NA	intron (NM_022662, intron 21 of 47)	L1ME1|LINE|L1	-55844	NR_039928	100616370		NR_039928	ENSG00000264793	MIR4771-1	-	microRNA 4771-1	ncRNA	0.016254	0.399845	
chunk0154_63_1	chr5	77328716	77329381	+	0	NA	exon (NM_001029853, exon 3 of 21)	exon (NM_001029853, exon 3 of 21)	118167	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.013534	0.399399	307(GAGCACACGGTGATCC,-,0.00),308(AGCACACGGTGATCCT,+,0.00)
chunk0111_159_1	chr20	25117230	25117468	+	0	NA	Intergenic	Intergenic	30644	NR_027093	284798	Hs.334934	NR_027091	ENSG00000230725	LOC284798	-	uncharacterized LOC284798	ncRNA	0.016807	0.543933	
chunk0203_201_1	chr9	86521090	86521475	+	0	NA	Intergenic	MER57-int|LTR|ERV1	-166795	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.010390	0.393782	
chunk0134_146_1	chr3	177628805	177629171	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	187067	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.008197	0.435967	
chunk0097_319_1	chr2	56902747	56903014	+	0	NA	Intergenic	LTR33|LTR|ERVL	-717110	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.003745	0.395522	
chunk0150_209_1	chr5	35168676	35168946	+	0	NA	intron (NM_000949, intron 1 of 9)	MamGypsy2-I|LTR|Gypsy	-50689	NM_001204318	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.007407	0.324723	222(AAGATCATCCTGTTCA,-,0.00),223(AGATCATCCTGTTCAT,+,0.00)
chunk0145_262_1	chr4	148953484	148953778	+	0	NA	Intergenic	Intergenic	-200664	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.000000	0.338983	169(AAGCACAGTCAGATCT,-,0.00)
chunk0058_275_1	chr14	26232989	26233538	+	0	NA	Intergenic	Intergenic	364491	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.003643	0.414545	217(TAGAACTCACTGTGCC,-,0.00),218(AGAACTCACTGTGCCC,+,0.00)
chunk0149_139_1	chr5	19930565	19931313	+	0	NA	intron (NM_001167667, intron 2 of 12)	intron (NM_001167667, intron 2 of 12)	-44667	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.009358	0.336449	
chunk0152_300_1	chr5	61637461	61637977	+	0	NA	promoter-TSS (NR_126525)	promoter-TSS (NR_126525)	-62	NM_173667									0.000000	0.415861	241(GAGAACACAATGCTCC,-,0.00),242(AGAACACAATGCTCCC,+,0.00)
chunk0197_240_1	chr8	123202419	123203180	+	0	NA	promoter-TSS (NR_024479)	promoter-TSS (NR_024479)	-56	NR_024479	100131726	Hs.660862	NR_024479	ENSG00000204949	FAM83A-AS1	HCCC11|HCCC11_v1|HCCC11_v2	FAM83A antisense RNA 1	ncRNA	0.013141	0.395013	
chunk0125_13_1	chr3	61931006	61931310	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	369589	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.016447	0.514754	
chunk0081_60_1	chr17	38732782	38732981	+	0	NA	intron (NM_001136498, intron 3 of 3)	intron (NM_001136498, intron 3 of 3)	2624	NM_001136498	284106	Hs.713595	NM_001136498	ENSG00000277972	CISD3	MiNT|Miner2	CDGSH iron sulfur domain 3	protein-coding	0.005025	0.465000	
chunk0085_404_1	chr18	10251028	10251324	+	0	NA	Intergenic	Intergenic	163194	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.010135	0.414141	
chunk0096_178_1	chr2	29763797	29764240	+	0	NA	intron (NM_004304, intron 1 of 28)	intron (NM_004304, intron 1 of 28)	157593	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.002257	0.515766	
chunk0141_90_1	chr4	78763272	78763797	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-12844	NM_017593	55589	Hs.146551	NM_017593	ENSG00000138756	BMP2K	BIKE|HRIHFB2017	BMP2 inducible kinase	protein-coding	0.001905	0.321293	
chunk0116_316_1	chr21	40734637	40735013	+	0	NA	intron (NR_073202, intron 1 of 32)	intron (NR_073202, intron 1 of 32)	-104058	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.010638	0.395225	
chunk0022_233_1	chr10	14090324	14090793	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	16274	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.023454	0.485106	
chunk0085_259_1	chr18	7635789	7636572	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	68864	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.002554	0.415816	
chunk0131_245_1	chr3	149492790	149493230	+	0	NA	intron (NM_004617, intron 3 of 4)	MIRb|SINE|MIR	18429	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.000000	0.353741	
chunk0105_294_1	chr2	189951752	189952119	+	0	NA	Intergenic	MER34A|LTR|ERV1	110794	NM_005259	2660	Hs.41565	NM_005259	ENSG00000138379	MSTN	GDF8|MSLHP	myostatin	protein-coding	0.002725	0.388587	92(AAGAACTCTGTGACCT,-,0.00)
chunk0129_116_1	chr3	119797810	119798499	+	0	NA	intron (NM_022002, intron 1 of 8)	L1MEg|LINE|L1	15444	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.010160	0.313043	
chunk0001_380_1	chr1	10489826	10490048	+	0	NA	intron (NM_004565, intron 1 of 8)	L1ME2|LINE|L1	14991	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.009009	0.443946	
chunk0201_206_1	chr9	37122018	37122299	+	0	NA	intron (NM_001289121, intron 1 of 8)	intron (NM_001289121, intron 1 of 8)	1560	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.010676	0.375887	
chunk0102_38_1	chr2	141873938	141874433	+	0	NA	intron (NM_018557, intron 1 of 90)	intron (NM_018557, intron 1 of 90)	257516	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.002020	0.272177	
chunk0072_424_1	chr15	101037463	101037662	+	0	NA	intron (NM_024652, intron 20 of 33)	L1MA4A|LINE|L1	118347	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.000000	0.595000	
chunk0005_325_1	chr1	61045127	61045327	+	0	NA	Intergenic	Intergenic	-32047	NM_001145511	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.000000	0.432836	110(CAGAACAGCCTGTGCC,-,0.00),111(AGAACAGCCTGTGCCC,+,0.00)
chunk0023_376_1	chr10	30365127	30365372	+	0	NA	non-coding (NR_120609, exon 10 of 12)	non-coding (NR_120609, exon 10 of 12)	3416	NR_106985	102466227		NR_106985	ENSG00000284277	MIR7162	hsa-mir-7162	microRNA 7162	ncRNA	0.008163	0.560976	
chunk0023_367_1	chr10	30114386	30114735	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-55001	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.002865	0.337143	
chunk0133_371_1	chr3	173747910	173748617	+	0	NA	intron (NM_014932, intron 3 of 6)	intron (NM_014932, intron 3 of 6)	172533	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.001414	0.395480	
chunk0070_197_1	chr15	72113695	72114054	+	0	NA	promoter-TSS (NM_001166340)	promoter-TSS (NM_001166340)	-384	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.005571	0.391667	
chunk0143_224_1	chr4	114100461	114100874	+	0	NA	Intergenic	Intergenic	-120945	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.007264	0.345411	312(GGGCCATTCTGTACTT,+,0.00)
chunk0196_380_1	chr8	115482245	115482853	+	0	NA	intron (NM_001282903, intron 5 of 6)	intron (NM_001282903, intron 5 of 6)	185463	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.001645	0.316913	299(GAGCACATTCTGTCCC,-,0.00),300(AGCACATTCTGTCCCA,+,0.00)
chunk0160_424_1	chr5	164374732	164375224	+	0	NA	Intergenic	Intergenic	92424	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.012195	0.371197	241(AAATACATTCTGTTCT,-,0.00),242(AATACATTCTGTTCTG,+,0.00)
chunk0117_75_1	chr22	17115918	17116474	+	0	NA	TTS (NM_001163079)	TTS (NM_001163079)	5127	NM_031890	27439	Hs.209577	NM_031890	ENSG00000183307	TMEM121B	CECR6	transmembrane protein 121B	protein-coding	0.010791	0.436266	
chunk0075_104_1	chr16	48546869	48547099	+	0	NA	intron (NM_153029, intron 5 of 6)	intron (NM_153029, intron 5 of 6)	63225	NM_153029	9683	Hs.511839	NM_153029	ENSG00000102921	N4BP1	-	NEDD4 binding protein 1	protein-coding	0.000000	0.411255	
chunk0135_382_1	chr3	191095788	191096211	+	0	NA	Intergenic	Charlie10a|DNA|hAT-Charlie	-116534	NM_198184	344901	Hs.526794	NM_198184	ENSG00000188729	OSTN	MUSCLIN	osteocrin	protein-coding	0.004728	0.410377	
chunk0114_271_1	chr21	16280433	16280831	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	86253	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.007538	0.411028	
chunk0048_316_1	chr12	83157799	83158079	+	0	NA	Intergenic	Intergenic	470784	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.007143	0.352313	
chunk0139_150_1	chr4	53644330	53645036	+	0	NA	Intergenic	Intergenic	-51218	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.008499	0.465347	
chunk0026_115_1	chr10	61965144	61965508	+	0	NA	intron (NM_032199, intron 3 of 9)	intron (NM_032199, intron 3 of 9)	64072	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.005495	0.347945	
chunk0205_110_1	chr9	107687783	107688176	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-198259	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.000000	0.416244	
chunk0162_197_1	chr6	3913242	3914022	+	0	NA	Intergenic	L1MC1|LINE|L1	64234	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.007692	0.384123	454(TGGAACAACTTGTCCA,-,0.00),455(GGAACAACTTGTCCAC,+,0.00)
chunk0023_245_1	chr10	27155052	27155292	+	0	NA	promoter-TSS (NM_139312)	promoter-TSS (NM_139312)	348	NM_001172303	84930	Hs.276905	NM_032844	ENSG00000120539	MASTL	GREATWALL|GW|GWL|MAST-L|THC2	microtubule associated serine/threonine kinase like	protein-coding	0.075000	0.609959	105(CAGAACTGTTTGTGCC,-,0.00),106(AGAACTGTTTGTGCCT,+,0.00)
chunk0107_156_1	chr2	215206858	215207577	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-68789	NM_173076	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.001391	0.337500	
chunk0166_154_1	chr6	45260647	45261110	+	0	NA	intron (NM_001261823, intron 2 of 9)	intron (NM_001261823, intron 2 of 9)	-63108	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.006479	0.355603	
chunk0042_454_1	chr12	12481605	12481808	+	0	NA	intron (NM_030640, intron 5 of 6)	intron (NM_030640, intron 5 of 6)	80808	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.004926	0.352941	
chunk0019_315_1	chr1	229085315	229085777	+	0	NA	Intergenic	L1MC2|LINE|L1	89255	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.006494	0.395248	147(AAGAACAGAATGTTCT,-,0.00),148(AGAACAGAATGTTCTG,+,0.00)
chunk0191_68_1	chr8	47147625	47148129	+	0	NA	Intergenic	L1PA16|LINE|L1	-41430	NR_037168	100287846	Hs.21550	NR_037168		LOC100287846	-	uncharacterized LOC100287846	ncRNA	0.007937	0.396040	248(AAGGACATGATGTACA,-,0.00),249(AGGACATGATGTACAA,+,0.00)
chunk0065_361_1	chr14	103834857	103835379	+	0	NA	intron (NM_015316, intron 1 of 16)	AluJb|SINE|Alu	12472	NM_015316	23368	Hs.709297	NM_015316	ENSG00000088808	PPP1R13B	ASPP1|p53BP2-like|p85	protein phosphatase 1 regulatory subunit 13B	protein-coding	0.007663	0.453155	272(AGGATCTGTCTGTACT,-,0.00),288(CTGTACAGCCTGTACT,-,0.00),289(TGTACAGCCTGTACTC,+,0.00)
chunk0184_33_1	chr7	112079753	112079958	+	0	NA	intron (NM_014705, intron 1 of 51)	L3|LINE|CR1	126552	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.000000	0.330097	
chunk0200_418_1	chr9	27571825	27572363	+	0	NA	intron (NM_145005, intron 1 of 4)	intron (NM_145005, intron 1 of 4)	1399	NM_018325	203228	Hs.493639	NM_018325	ENSG00000147894	C9orf72	ALSFTD|DENND9|DENNL72|FTDALS|FTDALS1	C9orf72-SMCR8 complex subunit	protein-coding	0.009294	0.423006	
chunk0108_319_1	chr2	235540908	235541468	+	0	NA	intron (NM_001037131, intron 1 of 17)	L1ME3D|LINE|L1	35437	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.016071	0.376114	
chunk0027_191_1	chr10	75605044	75605710	+	0	NA	intron (NM_001305581, intron 2 of 6)	intron (NM_001305581, intron 2 of 6)	-42132	NR_131178	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.009009	0.400300	278(GAAGACAGTCTGTTCC,-,0.00),279(AAGACAGTCTGTTCCA,+,0.00),495(TGGAACACTTTGATCT,-,0.00),496(GGAACACTTTGATCTG,+,0.00)
chunk0016_265_1	chr1	200338300	200338674	+	0	NA	Intergenic	Intergenic	35305	NR_040064	554279	Hs.434694	NR_040064	ENSG00000203721	LINC00862	C1orf98|SMIM16	long intergenic non-protein coding RNA 862	ncRNA	0.002674	0.389333	
chunk0102_206_1	chr2	148194785	148195372	+	0	NA	intron (NM_018328, intron 3 of 14)	MER58A|DNA|hAT-Charlie	-173474	NM_181742	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.000000	0.299320	
chunk0047_159_1	chr12	69840479	69841424	+	0	NA	intron (NM_182530, intron 1 of 24)	intron (NM_182530, intron 1 of 24)	15628	NM_182530	196446	Hs.253773	NM_182530	ENSG00000166268	MYRFL	C12orf15|C12orf28|bcm1377	myelin regulatory factor like	protein-coding	0.008466	0.428118	
chunk0201_38_1	chr9	33445193	33445643	+	0	NA	intron (NM_004925, intron 1 of 5)	intron (NM_004925, intron 1 of 5)	2215	NM_004925	360	Hs.234642	NM_004925	ENSG00000165272	AQP3	AQP-3|GIL	aquaporin 3 (Gill blood group)	protein-coding	0.013333	0.558758	
chunk0167_142_1	chr6	62400521	62401027	+	0	NA	Intergenic	L1MA3|LINE|L1	-114579	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.005929	0.445759	
chunk0190_101_1	chr8	30339609	30339809	+	0	NA	Intergenic	Intergenic	-44792	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.010000	0.472637	
chunk0005_46_1	chr1	54927522	54927901	+	0	NA	Intergenic	Intergenic	-40463	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.002639	0.410526	
chunk0051_286_1	chr12	118264032	118264650	+	0	NA	intron (NM_016281, intron 2 of 20)	L1ME1|LINE|L1	108604	NM_016281	51347	Hs.644420	NM_016281	ENSG00000135090	TAOK3	DPK|JIK|MAP3K18|hKFC-A	TAO kinase 3	protein-coding	0.001618	0.350565	
chunk0109_190_1	chr20	4949087	4949811	+	0	NA	intron (NM_005116, intron 2 of 16)	intron (NM_005116, intron 2 of 16)	52050	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.016575	0.417931	
chunk0106_135_1	chr2	199914695	199914923	+	0	NA	intron (NM_153689, intron 1 of 1)	L2a|LINE|L2	3553	NM_153689	205327	Hs.154494	NM_153689	ENSG00000178074	C2orf69	-	chromosome 2 open reading frame 69	protein-coding	0.000000	0.414847	
chunk0128_297_1	chr3	111285072	111285348	+	0	NA	Intergenic	Intergenic	213042	NM_001243288	25945	Hs.293917	NM_015480	ENSG00000177707	NECTIN3	CD113|CDW113|NECTIN-3|PPR3|PRR3|PVRL3|PVRR3	nectin cell adhesion molecule 3	protein-coding	0.000000	0.375451	
chunk0008_322_1	chr1	95286259	95286908	+	0	NA	Intergenic	Intergenic	52428	NR_103484	25950	Hs.483512	NM_015485	ENSG00000122481	RWDD3	RSUME	RWD domain containing 3	protein-coding	0.007704	0.389231	
chunk0172_130_1	chr6	135270794	135271100	+	0	NA	Intergenic	Intergenic	31787	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.009804	0.475570	
chunk0034_117_1	chr11	28110191	28110452	+	0	NA	5' UTR (NM_001297775, exon 2 of 7)	5' UTR (NM_001297775, exon 2 of 7)	2070	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.061303	0.591603	
chunk0158_317_1	chr5	132766923	132767560	+	0	NA	intron (NM_001098813, intron 1 of 9)	intron (NM_001098813, intron 1 of 9)	10134	NM_001300799	23176	Hs.522057	NM_015146	ENSG00000164402	SEPTIN8	SEP2|SEPT8	septin 8	protein-coding	0.007849	0.520376	
chunk0137_196_1	chr4	17914490	17914873	+	0	NA	intron (NM_001166139, intron 4 of 6)	intron (NM_001166139, intron 4 of 6)	103868	NR_073124	64151	Hs.567567	NM_022346	ENSG00000109805	NCAPG	CAPG|CHCG|NY-MEL-3|YCG1	non-SMC condensin I complex subunit G	protein-coding	0.002611	0.382812	
chunk0187_162_1	chr7	150651305	150651919	+	0	NA	Intergenic	L1PB1|LINE|L1	-18964	NM_001244072	474344	Hs.647105	NM_024711	ENSG00000133561	GIMAP6	IAN-2|IAN-6|IAN2|IAN6	GTPase, IMAP family member 6	protein-coding	0.008143	0.359350	
chunk0121_104_1	chr3	17070512	17071127	+	0	NA	intron (NM_001144382, intron 5 of 5)	intron (NM_001144382, intron 5 of 5)	137623	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.008130	0.459416	
chunk0194_290_1	chr8	87584961	87585596	+	0	NA	Intergenic	Intergenic	288790	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.015748	0.386792	
chunk0046_181_1	chr12	58745960	58746458	+	0	NA	intron (NR_120452, intron 1 of 7)	intron (NR_120452, intron 1 of 7)	35507	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.002008	0.356713	
chunk0054_223_1	chr13	45450313	45450587	+	0	NA	Intergenic	MER4C|LTR|ERV1	-14445	NM_031431	83548	Hs.507948	NM_031431	ENSG00000136152	COG3	SEC34	component of oligomeric golgi complex 3	protein-coding	0.003650	0.400000	
chunk0177_112_1	chr7	22142416	22142988	+	0	NA	intron (NM_012294, intron 20 of 25)	intron (NM_012294, intron 20 of 25)	-196778	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.005245	0.371728	
chunk0202_178_1	chr9	74284682	74285096	+	0	NA	Intergenic	Intergenic	-86642	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.016908	0.407229	
chunk0159_258_1	chr5	142097837	142098481	+	0	NA	Intergenic	Intergenic	-10600	NM_030571	80762	Hs.9788	NM_030571	ENSG00000131507	NDFIP1	N4WBP5	Nedd4 family interacting protein 1	protein-coding	0.017081	0.443411	321(TGGAACATTGTGTCCA,-,0.00),322(GGAACATTGTGTCCAA,+,0.00)
chunk0077_129_1	chr16	78504967	78505589	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	405865	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.016077	0.443018	
chunk0017_90_1	chr1	205758725	205759248	+	0	NA	Intergenic	L1ME3G|LINE|L1	-8742	NM_022731	64710	Hs.213061	NM_022731	ENSG00000069275	NUCKS1	JC7|NUCKS	nuclear casein kinase and cyclin dependent kinase substrate 1	protein-coding	0.013384	0.383588	252(TGGAACTGTATGTTCT,-,0.00),253(GGAACTGTATGTTCTT,+,0.00)
chunk0029_147_1	chr10	99394998	99395362	+	0	NA	TTS (NM_020348)	TTS (NM_020348)	35593	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.010989	0.471233	
chunk0060_130_1	chr14	44513231	44513563	+	0	NA	Intergenic	L1PA6|LINE|L1	-6101	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.012048	0.372372	223(AGGAACAGGTTGTTCA,-,0.00),224(GGAACAGGTTGTTCAG,+,0.00)
chunk0193_268_1	chr8	77156515	77156827	+	0	NA	Intergenic	L1MEd|LINE|L1	-155627	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.003205	0.293930	
chunk0092_364_1	chr19	35803809	35804008	+	0	NA	intron (NM_021232, intron 8 of 10)	intron (NM_021232, intron 8 of 10)	-5999	NR_104176	644050	Hs.651888	NR_104176	ENSG00000225872	LINC01529	-	long intergenic non-protein coding RNA 1529	ncRNA	0.020101	0.525000	
chunk0001_448_1	chr1	11808403	11808824	+	0	NA	intron (NM_001256959, intron 2 of 21)	L1MC5|LINE|L1	-2510	NM_005957	4524	Hs.214142	NM_005957	ENSG00000177000	MTHFR	-	methylenetetrahydrofolate reductase	protein-coding	0.002375	0.286730	
chunk0008_240_1	chr1	94236795	94237271	+	0	NA	intron (NM_004815, intron 1 of 22)	MIR|SINE|MIR	718	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.067227	0.574423	
chunk0138_385_1	chr4	42657203	42657672	+	0	NA	promoter-TSS (NM_001105529)	promoter-TSS (NM_001105529)	-332	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.063966	0.617021	
chunk0065_438_1	chr14	106521589	106521815	+	0	NA	Intergenic	Intergenic	39263	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.004425	0.400881	
chunk0054_185_1	chr13	44812286	44812719	+	0	NA	Intergenic	HAL1|LINE|L1	-2872	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.002309	0.343318	
chunk0078_5_1	chr17	245092	245422	+	0	NA	intron (NM_001190411, intron 6 of 8)	intron (NM_001190411, intron 6 of 8)	-58006	NR_104420	100506371		NR_104420		LINC02091	-	long intergenic non-protein coding RNA 2091	ncRNA	0.018182	0.501511	
chunk0039_338_1	chr11	104793045	104793643	+	0	NA	Intergenic	MER21C|LTR|ERVL	105326	NR_034063	100506742	Hs.476989	NM_001191016	ENSG00000204403	CASP12	CASP-12|CASP12P1	caspase 12 (gene/pseudogene)	protein-coding	0.001672	0.415693	
chunk0027_44_1	chr10	72735606	72736526	+	0	NA	intron (NR_073062, intron 3 of 9)	intron (NR_073062, intron 3 of 9)	15037	NR_039823	100616286		NR_039823	ENSG00000266719	MIR4676	-	microRNA 4676	ncRNA	0.002174	0.365907	
chunk0057_232_1	chr13	104389536	104390214	+	0	NA	Intergenic	LTR40a|LTR|ERVL	964675	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.007375	0.341679	
chunk0197_454_1	chr8	127870421	127870841	+	0	NA	intron (NR_003367, intron 1 of 8)	intron (NR_003367, intron 1 of 8)	74669	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.007143	0.456057	
chunk0050_319_1	chr12	107110367	107110808	+	0	NA	Intergenic	Intergenic	-16730	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.002268	0.402715	
chunk0197_209_1	chr8	122644867	122645404	+	0	NA	Intergenic	Intergenic	48971	NR_126348	104266958	Hs.575540	NR_126348	ENSG00000253819	LINC01151	-	long intergenic non-protein coding RNA 1151	ncRNA	0.009311	0.401487	88(GAGTACAGCAAGTTCA,-,0.00),89(AGTACAGCAAGTTCAG,+,0.00)
chunk0044_327_1	chr12	34277200	34277539	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	255088	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.008850	0.438235	
chunk0040_251_1	chr11	115452297	115452667	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	52041	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.008108	0.388140	
chunk0163_160_1	chr6	11067291	11067858	+	0	NA	intron (NR_038964, intron 3 of 4)	intron (NR_038964, intron 3 of 4)	22883	NR_038962	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.008818	0.457746	
chunk0115_78_1	chr21	22004950	22005149	+	0	NA	Intergenic	Intergenic	93410	NR_109959	101927843	Hs.652879	NR_109959	ENSG00000233215	LINC01687	-	long intergenic non-protein coding RNA 1687	ncRNA	0.005025	0.310000	
chunk0090_238_1	chr18	73768122	73768494	+	0	NA	Intergenic	Intergenic	379456	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.016129	0.528150	
chunk0152_349_1	chr5	62751465	62751664	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	172829	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.000000	0.475000	
chunk0123_273_1	chr3	46196246	46196730	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	11853	NM_001295	1230	Hs.301921	NM_001295	ENSG00000163823	CCR1	CD191|CKR-1|CKR1|CMKBR1|HM145|MIP1aR|SCYAR1	C-C motif chemokine receptor 1	protein-coding	0.012397	0.331959	
chunk0033_39_1	chr11	13052256	13052687	+	0	NA	Intergenic	Intergenic	43048	NM_001080521	644943	Hs.134650	NM_001080521	ENSG00000189431	RASSF10	-	Ras association domain family member 10	protein-coding	0.011601	0.479167	
chunk0137_352_1	chr4	25607380	25607902	+	0	NA	Intergenic	Intergenic	-48172	NM_006424	10568	Hs.479372	NM_006424	ENSG00000157765	SLC34A2	NAPI-3B|NAPI-IIb|NPTIIb	solute carrier family 34 member 2	protein-coding	0.013410	0.489484	251(AAGCACTTGATGTTCC,-,0.00),252(AGCACTTGATGTTCCA,+,0.00)
chunk0197_328_1	chr8	125129897	125130119	+	0	NA	intron (NM_173685, intron 3 of 7)	L1MC3|LINE|L1	38167	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.018018	0.349776	
chunk0086_349_1	chr18	25261955	25262236	+	0	NA	intron (NM_001308225, intron 2 of 6)	intron (NM_001308225, intron 2 of 6)	90155	NM_001308225	25925	Hs.116935	NM_015461	ENSG00000198795	ZNF521	EHZF|Evi3	zinc finger protein 521	protein-coding	0.003559	0.358156	108(AAGGACAGACAGTACA,-,0.00),109(AGGACAGACAGTACAA,+,0.00),118(AGTACAAGAAGTCCCT,+,0.00)
chunk0208_90_1	chrX	13495351	13495735	+	0	NA	Intergenic	Intergenic	-74032	NM_001167890	25975	Hs.12844	NM_015507	ENSG00000198759	EGFL6	MAEG|W80	EGF like domain multiple 6	protein-coding	0.000000	0.506494	193(AAAGACACTATGTTCT,-,0.00),194(AAGACACTATGTTCTG,+,0.00)
chunk0164_198_1	chr6	22444430	22444652	+	0	NA	Intergenic	Intergenic	-124908	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.009009	0.385650	
chunk0150_322_1	chr5	38167388	38168052	+	0	NA	Intergenic	Intergenic	-90689	NM_001205301	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.024096	0.529323	
chunk0159_384_1	chr5	146433721	146434124	+	0	NA	Intergenic	Intergenic	-13388	NM_001040006	10915	Hs.443465	NM_006706	ENSG00000113649	TCERG1	CA150|TAF2S|Urn1	transcription elongation regulator 1	protein-coding	0.002481	0.319307	
chunk0124_264_1	chr3	57205186	57205724	+	0	NA	Intergenic	L2a|LINE|L2	-5203	NM_003865	8820	Hs.171980	NM_003865	ENSG00000163666	HESX1	ANF|CPHD5|RPX	HESX homeobox 1	protein-coding	0.001859	0.474954	
chunk0057_374_1	chr13	109163125	109163356	+	0	NA	TTS (NR_047700)	TTS (NR_047700)	4063	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.012987	0.491379	43(CAGAACAGGCTGTGCT,-,0.00),44(AGAACAGGCTGTGCTC,+,0.00)
chunk0177_331_1	chr7	26404579	26405161	+	0	NA	intron (NR_015364, intron 1 of 4)	L2b|LINE|L2	1382	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.008591	0.447684	
chunk0102_265_1	chr2	149816979	149817286	+	0	NA	intron (NR_110240, intron 2 of 2)	intron (NR_110240, intron 2 of 2)	-229316	NM_015702	27249	Hs.5324	NM_015702	ENSG00000168288	MMADHC	C2orf25|CL25022|cblD	metabolism of cobalamin associated D	protein-coding	0.000000	0.334416	
chunk0183_140_1	chr7	105794591	105794909	+	0	NA	intron (NM_020725, intron 2 of 11)	intron (NM_020725, intron 2 of 11)	81835	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.006289	0.373041	
chunk0176_260_1	chr7	16313723	16314159	+	0	NA	intron (NM_001101417, intron 2 of 8)	L1MC1|LINE|L1	103455	NR_038947	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.002294	0.329519	
chunk0016_206_1	chr1	198777129	198777473	+	0	NA	Intergenic	Intergenic	81681	NR_029612	406955		NR_029612	ENSG00000207975	MIR181B1	MIRN181B1|mir-181b-1	microRNA 181b-1	ncRNA	0.000000	0.353623	
chunk0186_210_1	chr7	139902053	139902630	+	0	NA	intron (NM_001314028, intron 3 of 12)	L1MD2|LINE|L1	73188	NM_001061	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.006932	0.380623	
chunk0096_172_1	chr2	29694422	29695085	+	0	NA	intron (NM_004304, intron 3 of 28)	intron (NM_004304, intron 3 of 28)	226858	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.009050	0.463855	
chunk0051_426_1	chr12	122838837	122839302	+	0	NA	intron (NM_003959, intron 1 of 31)	intron (NM_003959, intron 1 of 31)	3631	NM_001303097	9026	Hs.524815	NM_003959	ENSG00000130787	HIP1R	HIP12|HIP3|ILWEQ	huntingtin interacting protein 1 related	protein-coding	0.010753	0.482833	
chunk0200_162_1	chr9	18817764	18818008	+	0	NA	intron (NM_001040272, intron 21 of 28)	intron (NM_001040272, intron 21 of 28)	215372	NM_153707	158297	Hs.731593	NM_153707	ENSG00000155875	SAXO1	C9orf138|FAM154A	stabilizer of axonemal microtubules 1	protein-coding	0.012295	0.518367	
chunk0022_390_1	chr10	17682605	17682855	+	0	NA	intron (NR_037774, intron 2 of 11)	L1ME1|LINE|L1	38605	NM_003473	8027	Hs.335391	NM_003473	ENSG00000136738	STAM	STAM-1|STAM1	signal transducing adaptor molecule	protein-coding	0.000000	0.346614	
chunk0155_7_1	chr5	90829980	90831024	+	0	NA	intron (NR_003149, intron 77 of 89)	intron (NR_003149, intron 77 of 89)	271702	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.005747	0.371292	97(CAGGACATTCTGTGCA,-,0.00),98(AGGACATTCTGTGCAT,+,0.00)
chunk0148_213_1	chr5	8660454	8660917	+	0	NA	Intergenic	L1MC4a|LINE|L1	-179047	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.006479	0.362069	
chunk0066_369_1	chr15	38454081	38454427	+	0	NA	intron (NM_173611, intron 1 of 7)	CpG	127	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.075145	0.645533	
chunk0150_240_1	chr5	36046226	36046528	+	0	NA	intron (NR_031764, intron 3 of 5)	L1MA3|LINE|L1	20544	NM_001168316	167127	Hs.348941	NM_174914	ENSG00000168671	UGT3A2	-	UDP glycosyltransferase family 3 member A2	protein-coding	0.009934	0.363036	
chunk0074_357_1	chr16	34049857	34050172	+	0	NA	Intergenic	Intergenic	110022	NR_038368									0.041270	0.468354	
chunk0204_177_1	chr9	96073538	96073984	+	0	NA	intron (NR_033838, intron 1 of 8)	MLT1I|LTR|ERVL-MaLR	7922	NR_033838	158435	Hs.652615	NR_033838		LOC158435	-	uncharacterized LOC158435	ncRNA	0.011211	0.467562	171(CAGAACTGCCAGTTCT,-,0.00),172(AGAACTGCCAGTTCTT,+,0.00)
chunk0204_166_1	chr9	95901541	95901996	+	0	NA	intron (NM_001010895, intron 3 of 13)	intron (NM_001010895, intron 3 of 13)	-25791	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.006593	0.355263	
chunk0178_199_1	chr7	34493783	34494038	+	0	NA	intron (NR_033665, intron 2 of 3)	L2b|LINE|L2	-164329	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.015686	0.410156	
chunk0141_427_1	chr4	88812433	88812660	+	0	NA	intron (NM_014883, intron 7 of 23)	L2b|LINE|L2	10815	NM_001265580	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.000000	0.447368	2(TGGCACATGAAGTCCC,-,0.00),3(GGCACATGAAGTCCCT,+,0.00),78(TTGTACATGTTGTTCT,-,0.00),79(TGTACATGTTGTTCTT,+,0.00)
chunk0058_98_1	chr14	21631101	21631461	+	0	NA	Intergenic	Intergenic	3659	NM_001005466	26534	Hs.554580	NM_001005466	ENSG00000255582	OR10G2	OR14-41	olfactory receptor family 10 subfamily G member 2	protein-coding	0.008333	0.382271	
chunk0129_405_1	chr3	126839100	126839447	+	0	NA	intron (NM_032343, intron 4 of 7)	L2c|LINE|L2	135053	NM_032343	84303	Hs.518119	NM_032343	ENSG00000159685	CHCHD6	CHCM1|MICOS25|Mic25|PPP1R23	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.005764	0.402299	
chunk0204_403_1	chr9	102639092	102639341	+	0	NA	intron (NR_103830, intron 3 of 4)	intron (NR_103830, intron 3 of 4)	119579	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.000000	0.344000	
chunk0002_303_1	chr1	23727330	23727944	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	-15729	NM_003198	6924	Hs.15535	NM_003198	ENSG00000011007	ELOA	SIII|SIII p110|TCEB3|TCEB3A	elongin A	protein-coding	0.014658	0.447154	
chunk0069_219_1	chr15	63613652	63614130	+	0	NA	intron (NM_003922, intron 76 of 77)	intron (NM_003922, intron 76 of 77)	-13064	NR_034080	100130855	Hs.631163	NR_034080	ENSG00000259248	USP3-AS1	-	USP3 antisense RNA 1	ncRNA	0.004184	0.419624	
chunk0182_3_1	chr7	90864745	90865108	+	0	NA	intron (NM_001287136, intron 5 of 13)	intron (NM_001287136, intron 5 of 13)	155110	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.002755	0.359890	
chunk0180_9_1	chr7	53195142	53195656	+	0	NA	Intergenic	Intergenic	159743	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.003891	0.316505	
chunk0179_310_1	chr7	50482108	50482605	+	0	NA	intron (NM_001082971, intron 9 of 14)	L1M5|LINE|L1	-31966	NM_001287494	63979	Hs.137516	NM_022116	ENSG00000132436	FIGNL1	-	fidgetin like 1	protein-coding	0.016097	0.383534	
chunk0169_222_1	chr6	104362741	104362966	+	0	NA	Intergenic	L2c|LINE|L2	497066	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.013333	0.398230	
chunk0040_6_1	chr11	108613960	108614480	+	0	NA	Intergenic	Intergenic	-20482	NM_001308019	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.005769	0.368522	
chunk0201_347_1	chr9	66699565	66699815	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-201039	NM_033160	26149	Hs.522147	NM_033160	ENSG00000274349	ZNF658	-	zinc finger protein 658	protein-coding	0.000000	0.442231	
chunk0114_114_1	chr21	9589578	9590204	+	0	NA	Intergenic	Intergenic	231170	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.004792	0.451356	
chunk0189_360_1	chr8	26999463	26999937	+	0	NA	Intergenic	LTR8A|LTR|ERV1	49263	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.006329	0.381053	
chunk0127_17_1	chr3	88178898	88179534	+	0	NA	Intergenic	L1ME2z|LINE|L1	-29350	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.003145	0.321821	
chunk0195_224_1	chr8	97266203	97266650	+	0	NA	intron (NR_125390, intron 2 of 2)	intron (NR_125390, intron 2 of 2)	11522	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.004474	0.462054	208(AGGGACTCAGTGTCCC,-,0.00),209(GGGACTCAGTGTCCCT,+,0.00),352(AGGGACAATCTGCCCT,-,0.00),353(GGGACAATCTGCCCTG,+,0.00)
chunk0029_18_1	chr10	95542294	95542928	+	0	NA	intron (NM_001290294, intron 1 of 31)	intron (NM_001290294, intron 1 of 31)	18809	NM_001290294	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.007886	0.442520	
chunk0003_35_1	chr1	30216643	30216865	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-179142	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.013514	0.421525	
chunk0107_392_1	chr2	223802868	223803255	+	0	NA	intron (NR_110905, intron 1 of 5)	intron (NR_110905, intron 1 of 5)	34541	NR_110905	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.000000	0.314433	
chunk0154_326_1	chr5	84877488	84877780	+	0	NA	Intergenic	L1PA13|LINE|L1	-492767	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.013699	0.426621	
chunk0016_38_1	chr1	193114785	193115183	+	0	NA	Intergenic	Intergenic	-6974	NM_024529	79577	Hs.378996	NM_024529	ENSG00000134371	CDC73	C1orf28|FIHP|HPTJT|HRPT1|HRPT2|HYX	cell division cycle 73	protein-coding	0.010050	0.290727	
chunk0055_278_1	chr13	64387100	64387762	+	0	NA	Intergenic	Intergenic	-543306	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.006042	0.351433	
chunk0045_189_1	chr12	47273500	47273829	+	0	NA	Intergenic	Intergenic	-57221	NR_026544	100233209	Hs.657722	NR_026544	ENSG00000247774	PCED1B-AS1	-	PCED1B antisense RNA 1	ncRNA	0.009119	0.409091	
chunk0038_126_1	chr11	83978932	83979328	+	0	NA	intron (NM_001142699, intron 12 of 27)	intron (NM_001142699, intron 12 of 27)	294150	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.002525	0.347607	
chunk0187_418_1	chr7	158377796	158378212	+	0	NA	intron (NM_130842, intron 1 of 21)	intron (NM_130842, intron 1 of 21)	154809	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.021635	0.551559	
chunk0120_337_1	chr3	10983006	10983286	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	-9588	NM_003042	6529	Hs.443874	NM_003042	ENSG00000157103	SLC6A1	GABATHG|GABATR|GAT1|MAE	solute carrier family 6 member 1	protein-coding	0.007143	0.320285	
chunk0169_340_1	chr6	106468781	106469520	+	0	NA	Intergenic	L2b|LINE|L2	-42705	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.005413	0.424324	
chunk0135_440_1	chr3	193997381	193997858	+	0	NA	intron (NR_033944, intron 1 of 2)	intron (NR_033944, intron 1 of 2)	-3381	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.014675	0.504184	336(TGGCACAGCGTGTCCT,-,0.00),337(GGCACAGCGTGTCCTC,+,0.00)
chunk0032_118_1	chr11	3970085	3970338	+	0	NA	intron (NM_001277961, intron 2 of 11)	intron (NM_001277961, intron 2 of 11)	114149	NR_039835	100616453		NR_039835	ENSG00000284525	MIR4687	-	microRNA 4687	ncRNA	0.007905	0.437008	91(CAGCACAAACTGTTCC,-,0.00),92(AGCACAAACTGTTCCG,+,0.00)
chunk0072_284_1	chr15	98369102	98369371	+	0	NA	Intergenic	Intergenic	145146	NM_182562	283777	Hs.668070	NM_182562	ENSG00000283597	FAM169B	-	family with sequence similarity 169 member B	protein-coding	0.007435	0.451852	
chunk0173_388_1	chr6	150139659	150139941	+	0	NA	Intergenic	Intergenic	-3252	NM_030949	81706	Hs.486798	NM_030949	ENSG00000198729	PPP1R14C	CPI17-like|KEPI|NY-BR-81	protein phosphatase 1 regulatory inhibitor subunit 14C	protein-coding	0.007092	0.346290	
chunk0136_344_1	chr3	195748802	195749038	+	0	NA	exon (NM_004532, exon 23 of 24)	exon (NM_004532, exon 23 of 24)	28038	NM_020790	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.029661	0.628692	
chunk0130_148_1	chr3	132273596	132274223	+	0	NA	Intergenic	Intergenic	-43458	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.003190	0.364650	434(CAGAACAGTGAGTTCA,-,0.00),435(AGAACAGTGAGTTCAT,+,0.00)
chunk0008_328_1	chr1	95370121	95371083	+	0	NA	Intergenic	Intergenic	-104135	NR_033966	440594	Hs.514123	NR_033966	ENSG00000233907	LINC01761	-	long intergenic non-protein coding RNA 1761	ncRNA	0.012474	0.441329	381(CTGATCAGAGTGTTCC,-,0.00),382(TGATCAGAGTGTTCCC,+,0.00),456(CTGCACATTCTGTTCT,-,0.00),457(TGCACATTCTGTTCTC,+,0.00)
chunk0075_39_1	chr16	47045453	47045731	+	0	NA	Intergenic	Intergenic	-71878	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.010791	0.437276	
chunk0019_363_1	chr1	229787948	229788378	+	0	NA	Intergenic	Intergenic	161947	NM_014777	9816	Hs.533628	NM_014777	ENSG00000135763	URB2	KIAA0133|NET10|NPA2	URB2 ribosome biogenesis homolog	protein-coding	0.018605	0.491879	
chunk0112_68_1	chr20	37759449	37760250	+	0	NA	intron (NM_030877, intron 5 of 15)	intron (NM_030877, intron 5 of 15)	65894	NM_030877	56259	Hs.472667	NM_030877	ENSG00000132792	CTNNBL1	C20orf33|NAP|P14L|PP8304|dJ633O20.1	catenin beta like 1	protein-coding	0.007491	0.402743	
chunk0039_274_1	chr11	102485336	102485565	+	0	NA	Intergenic	MER34-int|LTR|ERV1	-32406	NM_052932	114908	Hs.503709	NM_052932	ENSG00000152558	TMEM123	KCT3|PORIMIN|PORMIN	transmembrane protein 123	protein-coding	0.004367	0.382609	
chunk0026_163_1	chr10	63099528	63099727	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-33620	NM_001282405	29982	Hs.449628	NM_030759	ENSG00000148572	NRBF2	COPR|COPR1|COPR2|NRBF-2	nuclear receptor binding factor 2	protein-coding	0.000000	0.275000	
chunk0058_207_1	chr14	24920063	24920330	+	0	NA	intron (NM_014178, intron 2 of 5)	intron (NM_014178, intron 2 of 5)	128804	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.003745	0.343284	
chunk0024_49_1	chr10	33722148	33722505	+	0	NA	Intergenic	Intergenic	50354	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.008403	0.377095	
chunk0026_406_1	chr10	70192190	70192779	+	0	NA	Intergenic	Intergenic	-21955	NM_001142648	56681	Hs.499960	NM_020150	ENSG00000079332	SAR1A	SAR1|SARA1|Sara|masra2	secretion associated Ras related GTPase 1A	protein-coding	0.008489	0.396610	
chunk0066_270_1	chr15	34956801	34957196	+	0	NA	intron (NM_014691, intron 3 of 34)	intron (NM_014691, intron 3 of 34)	12796	NM_014691	9716	Hs.510958	NM_014691	ENSG00000021776	AQR	IBP160|fSAP164	aquarius intron-binding spliceosomal factor	protein-coding	0.007595	0.358586	
chunk0176_379_1	chr7	18593594	18594107	+	0	NA	intron (NM_178425, intron 4 of 24)	intron (NM_178425, intron 4 of 24)	84573	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.005848	0.416342	228(GTGTACAGCGTGTGCA,-,0.00),229(TGTACAGCGTGTGCAG,+,0.00)
chunk0164_356_1	chr6	25490044	25490357	+	0	NA	intron (NM_017640, intron 13 of 36)	intron (NM_017640, intron 13 of 36)	-162001	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.009585	0.544586	
chunk0100_346_1	chr2	117202102	117202885	+	0	NA	Intergenic	Intergenic	-612186	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.012771	0.371173	652(GTGGACAAACTGTACT,-,0.00),653(TGGACAAACTGTACTT,+,0.00)
chunk0204_416_1	chr9	102938326	102939222	+	0	NA	Intergenic	Intergenic	-56537	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.005580	0.282051	
chunk0136_401_1	chr3	197203861	197204272	+	0	NA	intron (NM_004087, intron 4 of 25)	intron (NM_004087, intron 4 of 25)	-19935	NM_001204388	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.007299	0.388350	
chunk0002_316_1	chr1	24129042	24129880	+	0	NA	intron (NM_021258, intron 4 of 6)	L2|LINE|L2	13824	NM_021258	58985	Hs.110915	NM_021258	ENSG00000142677	IL22RA1	CRF2-9|IL22R|IL22R1	interleukin 22 receptor subunit alpha 1	protein-coding	0.005967	0.445769	
chunk0015_257_1	chr1	188128510	188129084	+	0	NA	Intergenic	L1PA16|LINE|L1	685169	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008711	0.523478	
chunk0194_333_1	chr8	88963618	88964219	+	0	NA	Intergenic	Intergenic	-636430	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.000000	0.335548	289(GAATACAGCCTGTGCT,-,0.00),290(AATACAGCCTGTGCTT,+,0.00)
chunk0001_442_1	chr1	11731992	11732362	+	0	NA	Intergenic	MIR|SINE|MIR	-3908	NM_020350	57085	Hs.464438	NM_020350	ENSG00000177674	AGTRAP	ATRAP	angiotensin II receptor associated protein	protein-coding	0.027027	0.495957	247(AAGAACAGCGCGTGCC,-,0.00),248(AGAACAGCGCGTGCCA,+,0.00)
chunk0113_107_1	chr20	51160427	51161102	+	0	NA	Intergenic	Intergenic	-137626	NM_002237	3755	Hs.118695	NM_002237	ENSG00000026559	KCNG1	K13|KCNG|KV6.1|kH2	potassium voltage-gated channel modifier subfamily G member 1	protein-coding	0.010370	0.529586	
chunk0086_6_1	chr18	11976386	11977072	+	0	NA	Intergenic	Intergenic	-4699	NM_014214	3613	Hs.743311	NM_014214	ENSG00000141401	IMPA2	-	inositol monophosphatase 2	protein-coding	0.013120	0.526929	
chunk0181_157_1	chr7	82067657	82068456	+	0	NA	intron (NM_001302890, intron 7 of 10)	LTR41|LTR|ERVL	58879	NR_110077	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.002503	0.447500	
chunk0065_432_1	chr14	106325210	106325587	+	0	NA	Intergenic	Intergenic	37724	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.005305	0.370370	
chunk0017_24_1	chr1	204506871	204507125	+	0	NA	Intergenic	L1MA8|LINE|L1	-9381	NM_001278518	4194	Hs.497492	NM_002393	ENSG00000198625	MDM4	HDMX|MDMX|MRP1	MDM4 regulator of p53	protein-coding	0.027559	0.411765	91(CAGAACATGGTGTTAT,-,0.00)
chunk0159_252_1	chr5	141970270	141970661	+	0	NA	intron (NM_183401, intron 1 of 8)	intron (NM_183401, intron 1 of 8)	1318	NM_183401	9604	Hs.483616	NM_004290	ENSG00000013561	RNF14	ARA54|HFB30|HRIHFB2038|TRIAD2	ring finger protein 14	protein-coding	0.000000	0.408163	152(TGGGGCATGGTGTCCT,-,0.00),153(GGGGCATGGTGTCCTG,+,0.00)
chunk0099_434_1	chr2	102814118	102814507	+	0	NA	intron (NM_144632, intron 4 of 4)	intron (NM_144632, intron 4 of 4)	52281	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.007712	0.343590	
chunk0148_38_1	chr5	1130603	1130923	+	0	NA	Intergenic	Intergenic	-18706	NM_006598	10723	Hs.172613	NM_006598	ENSG00000113504	SLC12A7	KCC4	solute carrier family 12 member 7	protein-coding	0.025000	0.660436	
chunk0193_262_1	chr8	76986431	76987269	+	0	NA	intron (NM_001079867, intron 1 of 2)	L2c|LINE|L2	13438	NM_000318	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.004773	0.400477	
chunk0165_99_1	chr6	32272539	32272795	+	0	NA	Intergenic	L1PB1|LINE|L1	-48600	NM_004557	4855	Hs.436100	NM_004557	ENSG00000204301	NOTCH4	INT3	notch receptor 4	protein-coding	0.000000	0.408560	
chunk0095_395_1	chr2	24076167	24076397	+	0	NA	promoter-TSS (NM_001291328)	promoter-TSS (NM_001291328)	162	NM_016047	51639	Hs.177861	NM_016047	ENSG00000115128	SF3B6	CGI-110|HSPC175|Ht006|P14|SAP14|SAP14a|SF3B14|SF3B14a	splicing factor 3b subunit 6	protein-coding	0.100000	0.593074	
chunk0202_172_1	chr9	73857394	73857887	+	0	NA	Intergenic	Intergenic	-513891	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.012170	0.321862	302(AGAAGAAACTGTTCTT,+,0.00)
chunk0051_194_1	chr12	116293545	116294030	+	0	NA	Intergenic	Intergenic	-16601	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.012371	0.368313	
chunk0049_321_1	chr12	94648554	94649125	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	1723	NM_020698	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.008757	0.367133	
chunk0137_284_1	chr4	23874171	23874756	+	0	NA	intron (NM_013261, intron 2 of 12)	intron (NM_013261, intron 2 of 12)	15614	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.008547	0.397611	281(GGGAACACTGTGTCCT,-,0.00),282(GGAACACTGTGTCCTT,+,0.00)
chunk0146_9_1	chr4	154961147	154961537	+	0	NA	Intergenic	Intergenic	179837	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.002564	0.386189	
chunk0210_101_1	chrX	71587027	71587317	+	0	NA	intron (NM_052957, intron 2 of 12)	L2c|LINE|L2	9148	NM_052957	93953	Hs.135167	NM_052957	ENSG00000147174	GCNA	ACRC|NAAR1	germ cell nuclear acidic peptidase	protein-coding	0.006897	0.467354	129(AGGGACACTGTGTTCC,-,0.00),130(GGGACACTGTGTTCCC,+,0.00)
chunk0017_427_1	chr1	213196381	213196818	+	0	NA	intron (NM_001287220, intron 8 of 12)	L1PB1|LINE|L1	145366	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.004577	0.363014	
chunk0104_220_1	chr2	176383718	176384407	+	0	NA	Intergenic	Intergenic	114667	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.004354	0.373913	
chunk0121_39_1	chr3	15348443	15348877	+	0	NA	Intergenic	Intergenic	-7266	NM_001018009	9467	Hs.257761	NM_004844	ENSG00000131370	SH3BP5	SAB|SH3BP-5	SH3 domain binding protein 5	protein-coding	0.004608	0.377011	
chunk0183_52_1	chr7	104028094	104028301	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-38681	NM_173054	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.009662	0.427885	
chunk0151_21_1	chr5	41531716	41532503	+	0	NA	Intergenic	Intergenic	-21481	NM_001005473	345557	Hs.145404	NM_001005473	ENSG00000182836	PLCXD3	-	phosphatidylinositol specific phospholipase C X domain containing 3	protein-coding	0.003812	0.347716	
chunk0211_68_1	chrX	109934945	109935358	+	0	NA	Intergenic	Intergenic	64750	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.012107	0.451691	
chunk0042_240_1	chr12	6334800	6335125	+	0	NA	intron (NM_001065, intron 1 of 9)	L1ME3A|LINE|L1	7155	NM_001065	7132	Hs.279594	NM_001065	ENSG00000067182	TNFRSF1A	CD120a|FPF|TBP1|TNF-R|TNF-R-I|TNF-R55|TNFAR|TNFR1|TNFR55|TNFR60|p55|p55-R|p60	TNF receptor superfamily member 1A	protein-coding	0.021538	0.503067	
chunk0158_243_1	chr5	129854952	129855301	+	0	NA	Intergenic	MER135|DNA|DNA	-49704	NM_175856	337876	Hs.213137	NM_175856	ENSG00000198108	CHSY3	CHSY2|CSS3	chondroitin sulfate synthase 3	protein-coding	0.002865	0.354286	
chunk0140_210_1	chr4	70688171	70688512	+	0	NA	promoter-TSS (NM_020368)	promoter-TSS (NM_020368)	-138	NM_020368	57050	Hs.322901	NM_020368	ENSG00000132467	UTP3	CRL1|CRLZ1|SAS10	UTP3 small subunit processome component	protein-coding	0.085044	0.567251	
chunk0176_79_1	chr7	11450136	11450868	+	0	NA	intron (NM_015204, intron 11 of 26)	intron (NM_015204, intron 11 of 26)	381696	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.001366	0.332879	314(CAGCACAATCTGTACA,-,0.00),315(AGCACAATCTGTACAA,+,0.00)
chunk0160_352_1	chr5	160286838	160287257	+	0	NA	intron (NR_131769, intron 2 of 7)	intron (NR_131769, intron 2 of 7)	25553	NM_001308173	79616	Hs.14070	NM_024565	ENSG00000135083	CCNJL	-	cyclin J like	protein-coding	0.016706	0.464286	235(GAGGTCAGGCAGTTCT,-,0.00),236(AGGTCAGGCAGTTCTG,+,0.00)
chunk0032_331_1	chr11	10119057	10119486	+	0	NA	intron (NM_030962, intron 2 of 39)	intron (NM_030962, intron 2 of 39)	174936	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.002331	0.286047	186(TAGTACTTCCTGTTCC,-,0.00),187(AGTACTTCCTGTTCCG,+,0.00)
chunk0148_206_1	chr5	8547814	8548177	+	0	NA	Intergenic	Intergenic	87070	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.002755	0.489011	
chunk0040_349_1	chr11	118602681	118603078	+	0	NA	3' UTR (NM_001655, exon 10 of 10)	3' UTR (NM_001655, exon 10 of 10)	-3619	NM_015157	23187	Hs.504062	NM_015157	ENSG00000019144	PHLDB1	LL5A	pleckstrin homology like domain family B member 1	protein-coding	0.005038	0.296482	
chunk0200_412_1	chr9	27436220	27436755	+	0	NA	intron (NM_024761, intron 2 of 3)	L2b|LINE|L2	-87827	NM_020124	56832	Hs.591083	NM_020124	ENSG00000147896	IFNK	IFNT1|INFE1	interferon kappa	protein-coding	0.005607	0.371269	
chunk0189_279_1	chr8	25386556	25386915	+	0	NA	intron (NM_024940, intron 40 of 51)	intron (NM_024940, intron 40 of 51)	38305	NM_000825	2796	Hs.82963	NM_000825	ENSG00000147437	GNRH1	GNRH|GRH|LHRH|LNRH	gonadotropin releasing hormone 1	protein-coding	0.019499	0.422222	
chunk0152_251_1	chr5	60827116	60827992	+	0	NA	intron (NM_024930, intron 1 of 8)	intron (NM_024930, intron 1 of 8)	16720	NM_001297618	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.001142	0.361460	
chunk0086_251_1	chr18	23331076	23331828	+	0	NA	intron (NM_032933, intron 13 of 14)	intron (NM_032933, intron 13 of 14)	106509	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.030585	0.537849	
chunk0068_435_1	chr15	59587026	59587476	+	0	NA	Intergenic	Intergenic	-24532	NM_004751	9245	Hs.194710	NM_004751	ENSG00000140297	GCNT3	C2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding	0.004444	0.416851	
chunk0042_322_1	chr12	9273316	9273531	+	0	NA	Intergenic	Intergenic	-10234	NR_024374	642846	Hs.447869	NR_024374		LOC642846	-	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11-like	ncRNA	0.004651	0.333333	
chunk0122_336_1	chr3	37173763	37174417	+	0	NA	intron (NM_017724, intron 2 of 13)	intron (NM_017724, intron 2 of 13)	515	NM_006309	9209	Hs.740522	NM_006309	ENSG00000093167	LRRFIP2	HUFI-2	LRR binding FLII interacting protein 2	protein-coding	0.004587	0.320611	
chunk0016_213_1	chr1	198991595	198991876	+	0	NA	TTS (NR_110525)	TTS (NR_110525)	-24398	NR_126351	104266961	Hs.576501	NR_126351	ENSG00000235492	LINC01221	TCONS_00000366	long intergenic non-protein coding RNA 1221	ncRNA	0.000000	0.304965	
chunk0098_392_1	chr2	79655163	79655508	+	0	NA	intron (NM_004389, intron 2 of 17)	intron (NM_004389, intron 2 of 17)	-5976	NR_036231	100422888		NR_036231	ENSG00000266436	MIR4264	-	microRNA 4264	ncRNA	0.000000	0.315029	
chunk0013_143_1	chr1	168405893	168406171	+	0	NA	intron (NR_037851, intron 3 of 3)	MLT1J|LTR|ERVL-MaLR	16624	NR_037851	100505918	Hs.568494	NR_037851		LOC100505918	-	uncharacterized LOC100505918	ncRNA	0.003597	0.405018	152(AAGGACTTCCAGTTCT,-,0.00),153(AGGACTTCCAGTTCTG,+,0.00)
chunk0053_421_1	chr13	37349265	37349657	+	0	NA	Intergenic	L2a|LINE|L2	135323	NR_125762	103695431	Hs.550637	NR_125762	ENSG00000230390	LINC01048	-	long intergenic non-protein coding RNA 1048	ncRNA	0.002551	0.386768	
chunk0173_440_1	chr6	151452041	151452625	+	0	NA	promoter-TSS (NM_024573)	promoter-TSS (NM_024573)	75	NM_024573	79624	Hs.15929	NM_024573	ENSG00000146476	ARMT1	C6orf211	acidic residue methyltransferase 1	protein-coding	0.083904	0.617094	
chunk0103_344_1	chr2	168066055	168066681	+	0	NA	intron (NM_013233, intron 12 of 17)	L1ME2z|LINE|L1	-125224	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.006390	0.333333	
chunk0002_248_1	chr1	21032924	21033170	+	0	NA	intron (NM_001198801, intron 4 of 34)	intron (NM_001198801, intron 4 of 34)	-44615	NR_031657	100302155		NR_031657	ENSG00000221808	MIR1256	MIRN1256|hsa-mir-1256	microRNA 1256	ncRNA	0.004065	0.352227	
chunk0179_40_1	chr7	43261116	43261754	+	0	NA	intron (NM_015052, intron 3 of 29)	intron (NM_015052, intron 3 of 29)	110540	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.012539	0.461659	
chunk0144_309_1	chr4	138573797	138574172	+	0	NA	Intergenic	L1ME5|LINE|L1	264273	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.002667	0.345745	173(AGGTACAGAATGTTCT,-,0.00),174(GGTACAGAATGTTCTC,+,0.00)
chunk0097_227_1	chr2	52565848	52566276	+	0	NA	Intergenic	(AT)n|Simple_repeat|Simple_repeat	136553	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.007009	0.331002	
chunk0047_62_1	chr12	67519890	67520217	+	0	NA	promoter-TSS (NR_103861)	promoter-TSS (NR_103861)	-29	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.015291	0.509146	
chunk0031_262_1	chr10	127308136	127308769	+	0	NA	intron (NM_001290223, intron 29 of 51)	L1PA8|LINE|L1	-112294	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.009479	0.487382	
chunk0099_18_1	chr2	82919723	82920059	+	0	NA	Intergenic	Intergenic	63088	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.000000	0.281899	
chunk0012_371_1	chr1	163084313	163084912	+	0	NA	Intergenic	Intergenic	12707	NM_001113380	5999	Hs.386726	NM_005613	ENSG00000117152	RGS4	RGP4|SCZD9	regulator of G protein signaling 4	protein-coding	0.005008	0.380000	
chunk0161_281_1	chr5	172837515	172838006	+	0	NA	intron (NM_001031711, intron 1 of 9)	intron (NM_001031711, intron 1 of 9)	3540	NM_001031711	57222	Hs.509163	NM_020462	ENSG00000113719	ERGIC1	AMCN|ERGIC-32|ERGIC32|NET24	endoplasmic reticulum-golgi intermediate compartment 1	protein-coding	0.018330	0.536585	
chunk0198_121_1	chr8	131924501	131924739	+	0	NA	intron (NM_015137, intron 1 of 22)	intron (NM_015137, intron 1 of 22)	20511	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.000000	0.405858	99(CAGAACATCCTGTTTC,-,0.00),100(AGAACATCCTGTTTCC,+,0.00)
chunk0045_376_1	chr12	52130564	52130824	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	37125	NR_120440	26628	Hs.524431	NR_120438	ENSG00000257542	OR7E47P	OR7E141	olfactory receptor family 7 subfamily E member 47 pseudogene	pseudo	0.011538	0.394636	
chunk0036_35_1	chr11	58708503	58709028	+	0	NA	TTS (NM_201648)	TTS (NM_201648)	23209	NM_201648	10249	Hs.145384	NM_005838	ENSG00000149124	GLYAT	ACGNAT|CAT|GAT	glycine-N-acyltransferase	protein-coding	0.001905	0.410646	129(GAGGACACAGTGTTCA,-,0.00),130(AGGACACAGTGTTCAT,+,0.00)
chunk0045_367_1	chr12	52052477	52052688	+	0	NA	5' UTR (NM_002135, exon 2 of 8)	5' UTR (NM_002135, exon 2 of 8)	1180	NM_173157	3164	Hs.524430	NM_002135	ENSG00000123358	NR4A1	GFRP1|HMR|N10|NAK-1|NGFIB|NP10|NUR77|TR3	nuclear receptor subfamily 4 group A member 1	protein-coding	0.009479	0.556604	
chunk0144_228_1	chr4	134677162	134677666	+	0	NA	Intergenic	L1PA13|LINE|L1	-475666	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.001984	0.336634	
chunk0105_79_1	chr2	183904186	183904534	+	0	NA	Intergenic	MER90|LTR|ERV1	-474615	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.355301	
chunk0187_92_1	chr8	3691399	3691753	+	0	NA	intron (NM_033225, intron 7 of 69)	intron (NM_033225, intron 7 of 69)	-963125	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.008475	0.343662	
chunk0177_175_1	chr7	23334501	23334996	+	0	NA	intron (NM_006547, intron 10 of 14)	intron (NM_006547, intron 10 of 14)	35427	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.010101	0.417339	
chunk0142_191_1	chr4	96561918	96562477	+	0	NA	Intergenic	Intergenic	722109	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.000000	0.341071	
chunk0122_159_1	chr3	32216196	32216467	+	0	NA	Intergenic	Intergenic	-22348	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.018450	0.481618	
chunk0185_133_1	chr7	126908363	126908892	+	0	NA	intron (NR_028041, intron 2 of 10)	intron (NR_028041, intron 2 of 10)	149557	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.001890	0.343396	
chunk0178_138_1	chr7	32851042	32851801	+	0	NA	Intergenic	L1ME3D|LINE|L1	25119	NR_132360	102724668	Hs.636806	NR_132360		DPY19L1P2	THC1072510	DPY19L1 pseudogene 2	pseudo	0.001318	0.298684	
chunk0045_245_1	chr12	49022517	49022733	+	0	NA	exon (NM_003482, exon 51 of 54)	exon (NM_003482, exon 51 of 54)	-3779	NM_002733	5571	Hs.530862	NM_002733	ENSG00000181929	PRKAG1	AMPKG	protein kinase AMP-activated non-catalytic subunit gamma 1	protein-coding	0.037037	0.557604	
chunk0011_233_1	chr1	150487096	150487531	+	0	NA	promoter-TSS (NM_001271895)	promoter-TSS (NM_001271895)	-51	NM_001271896	80222	Hs.288974	NM_025150	ENSG00000143374	TARS2	COXPD21|TARSL1|thrRS	threonyl-tRNA synthetase 2, mitochondrial	protein-coding	0.041379	0.541284	
chunk0035_90_1	chr11	42048085	42048547	+	0	NA	Intergenic	Intergenic	205374	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.280778	
chunk0199_405_1	chr9	13487760	13488491	+	0	NA	Intergenic	Intergenic	-56796	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.012312	0.378415	375(AAGTACAGAGCGTACC,-,0.00),376(AGTACAGAGCGTACCT,+,0.00)
chunk0079_223_1	chr17	15122582	15123058	+	0	NA	Intergenic	Intergenic	-16633	NR_103559	94151	Hs.98684	NR_103559		CDRT8	-	CMT1A duplicated region transcript 8	ncRNA	0.006303	0.410901	
chunk0101_406_1	chr2	138941974	138942722	+	0	NA	Intergenic	L1PA6|LINE|L1	45024	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.006684	0.492657	
chunk0125_224_1	chr3	67733253	67733712	+	0	NA	intron (NR_109992, intron 3 of 6)	intron (NR_109992, intron 3 of 6)	78785	NR_109992	101927111	Hs.518057	NR_109992	ENSG00000241316	SUCLG2-AS1	-	SUCLG2 antisense RNA 1 (head to head)	ncRNA	0.002179	0.347826	
chunk0004_28_1	chr1	42392325	42392537	+	0	NA	intron (NM_173642, intron 1 of 4)	intron (NM_173642, intron 1 of 4)	11634	NM_173642	284716	Hs.420244	NM_173642	ENSG00000177181	RIMKLA	FAM80A|NAAGS|NAAGS-II	ribosomal modification protein rimK like family member A	protein-coding	0.004717	0.455399	
chunk0081_296_1	chr17	45093388	45093632	+	0	NA	intron (NM_021079, intron 3 of 11)	intron (NM_021079, intron 3 of 11)	20923	NR_106842	102465470		NR_106842	ENSG00000277249	MIR6784	hsa-mir-6784	microRNA 6784	ncRNA	0.008197	0.453061	166(AAGCACAGAATGTTCT,-,0.00),167(AGCACAGAATGTTCTT,+,0.00)
chunk0077_65_1	chr16	76858871	76860031	+	0	NA	Intergenic	L1PBa|LINE|L1	-9485	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.003448	0.322136	
chunk0045_80_1	chr12	45803839	45804136	+	0	NA	intron (NM_152641, intron 3 of 20)	Charlie7|DNA|hAT-Charlie	74150	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.010101	0.389262	
chunk0026_172_1	chr10	63269040	63269416	+	0	NA	promoter-TSS (NM_001282948)	promoter-TSS (NM_001282948)	-5	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.026596	0.480106	
chunk0041_409_1	chr11	133928668	133929024	+	0	NA	intron (NM_001277285, intron 12 of 19)	intron (NM_001277285, intron 12 of 19)	-27106	NR_024344	283174	Hs.504370	NM_001001873	ENSG00000280237	MIR4697HG	LINC00947	MIR4697 host gene	ncRNA	0.011236	0.512605	
chunk0077_445_1	chr16	85753627	85753826	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-2643	NM_206967	404550	Hs.461655	NM_206967	ENSG00000154102	C16orf74	-	chromosome 16 open reading frame 74	protein-coding	0.015075	0.510000	
chunk0066_187_1	chr15	33135353	33135711	+	0	NA	intron (NM_001277313, intron 4 of 20)	intron (NM_001277313, intron 4 of 20)	59201	NM_001277314	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.008380	0.470752	
chunk0019_372_1	chr1	229891288	229891497	+	0	NA	Intergenic	Intergenic	-166397	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.004785	0.376190	
chunk0194_264_1	chr8	86940805	86941102	+	0	NA	intron (NM_173538, intron 4 of 10)	Tigger3c|DNA|TcMar-Tigger	74505	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.010101	0.362416	
chunk0133_433_1	chr3	174936493	174937109	+	0	NA	intron (NM_207015, intron 1 of 13)	MER58A|DNA|hAT-Charlie	77480	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.008117	0.346840	
chunk0086_323_1	chr18	24397756	24398060	+	0	NA	promoter-TSS (NM_080597)	promoter-TSS (NM_080597)	-39	NM_080597	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.128289	0.750820	
chunk0152_323_1	chr5	62124384	62124769	+	0	NA	Intergenic	Intergenic	-181586	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.015584	0.520725	
chunk0205_126_1	chr9	107946277	107946710	+	0	NA	Intergenic	Intergenic	-456773	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.009238	0.435484	
chunk0092_390_1	chr19	36572356	36572558	+	0	NA	promoter-TSS (NR_110705)	promoter-TSS (NR_110705)	-613	NR_110705	101927599	Hs.515376	NR_110703	ENSG00000233527	ZNF529-AS1	-	ZNF529 antisense RNA 1	ncRNA	0.019802	0.477833	88(AAGAACACAGTGTTCA,-,0.00),89(AGAACACAGTGTTCAC,+,0.00)
chunk0095_457_1	chr2	25762712	25762911	+	0	NA	intron (NM_018263, intron 7 of 11)	L1MEd|LINE|L1	-89164	NM_001256303	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.000000	0.330000	
chunk0149_192_1	chr5	21420913	21421410	+	0	NA	Intergenic	Intergenic	-38319	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.008048	0.331325	152(AAGAACACAGTGCACC,-,0.00),153(AGAACACAGTGCACCT,+,0.00)
chunk0030_165_1	chr10	114057035	114057421	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	13181	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.010363	0.467700	219(AGGGACAACATGTCTT,-,0.00)
chunk0020_238_1	chr1	235818437	235819034	+	0	NA	intron (NM_001301365, intron 3 of 52)	intron (NM_001301365, intron 3 of 52)	34325	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.008375	0.416388	
chunk0105_379_1	chr2	192159952	192160596	+	0	NA	intron (NM_016192, intron 4 of 9)	intron (NM_016192, intron 4 of 9)	34659	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.003106	0.364341	
chunk0067_415_1	chr15	49645951	49646267	+	0	NA	TTS (NM_020234)	TTS (NM_020234)	25080	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.000000	0.454259	
chunk0193_273_1	chr8	77244508	77244980	+	0	NA	Intergenic	Intergenic	-205953	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.004237	0.401691	
chunk0090_299_1	chr18	75207562	75207916	+	0	NA	intron (NM_175907, intron 1 of 1)	intron (NM_175907, intron 1 of 1)	1609	NM_175907	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.019774	0.419718	217(AGGTACATTTTGTCCT,-,0.00),218(GGTACATTTTGTCCTT,+,0.00)
chunk0019_234_1	chr1	227374608	227374973	+	0	NA	Intergenic	L2b|LINE|L2	-56665	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.002740	0.450820	
chunk0073_287_1	chr16	13629726	13629938	+	0	NA	Intergenic	MamRep1527|LTR|LTR	-290325	NM_005236	2072	Hs.567265	NM_005236	ENSG00000175595	ERCC4	ERCC11|FANCQ|RAD1|XFEPS|XPF	ERCC excision repair 4, endonuclease catalytic subunit	protein-coding	0.004717	0.403756	
chunk0097_44_1	chr2	43131387	43131657	+	0	NA	Intergenic	Intergenic	-91979	NR_110585	102723854	Hs.570165	NR_110585	ENSG00000231826	LINC01819	-	long intergenic non-protein coding RNA 1819	ncRNA	0.025926	0.579336	194(GGGAACAGCCTGTTCC,-,0.00),195(GGAACAGCCTGTTCCT,+,0.00)
chunk0166_82_1	chr6	43681803	43682120	+	0	NA	intron (NM_018135, intron 1 of 5)	intron (NM_018135, intron 1 of 5)	5851	NM_001193343	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.015773	0.468553	
chunk0078_350_1	chr16	86545623	86546681	+	0	NA	intron (NR_027489, intron 6 of 8)	intron (NR_027489, intron 6 of 8)	9051	NM_001159380	64779	Hs.343627	NM_022764	ENSG00000103248	MTHFSD	-	methenyltetrahydrofolate synthetase domain containing	protein-coding	0.027410	0.534466	
chunk0135_75_1	chr3	185933787	185934006	+	0	NA	intron (NM_004593, intron 1 of 8)	intron (NM_004593, intron 1 of 8)	4240	NM_001243879	6434	Hs.533122	NM_004593	ENSG00000136527	TRA2B	Htra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B	transformer 2 beta homolog	protein-coding	0.000000	0.322727	
chunk0168_259_1	chr6	89148240	89148872	+	0	NA	intron (NM_001010853, intron 1 of 6)	intron (NM_001010853, intron 1 of 6)	2506	NM_001010853	135293	Hs.356247	NM_001010853	ENSG00000146281	PM20D2	ACY1L2	peptidase M20 domain containing 2	protein-coding	0.004747	0.358610	
chunk0129_54_1	chr3	117477282	117477741	+	0	NA	Intergenic	Intergenic	556080	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.013072	0.452174	
chunk0168_404_1	chr6	94874919	94875300	+	0	NA	Intergenic	Intergenic	702342	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.002625	0.348168	
chunk0209_71_1	chrX	38006471	38006670	+	0	NA	promoter-TSS (NM_001163335)	promoter-TSS (NM_001163335)	-12	NM_001163335	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.000000	0.390000	
chunk0117_382_1	chr21	45191484	45191791	+	0	NA	intron (NM_015834, intron 9 of 12)	L1M5|LINE|L1	96259	NM_133635	23275	Hs.592164	NM_015227	ENSG00000186866	POFUT2	C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding	0.000000	0.256494	
chunk0004_306_1	chr1	49063329	49063776	+	0	NA	intron (NM_032785, intron 4 of 13)	L2a|LINE|L2	-193859	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.006711	0.359375	
chunk0006_39_1	chr1	64349622	64349852	+	0	NA	Intergenic	Intergenic	-121056	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.021739	0.497835	
chunk0202_406_1	chr9	81473111	81473641	+	0	NA	Intergenic	Intergenic	216159	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.005660	0.423729	129(TAGGACACAAAGTGCT,-,0.00),130(AGGACACAAAGTGCTC,+,0.00)
chunk0127_328_1	chr3	100386667	100387006	+	0	NA	exon (NM_014820, exon 2 of 12)	exon (NM_014820, exon 2 of 12)	-14357	NM_001085451	348801	Hs.591294	NM_001085451	ENSG00000206535	LNP1	NP3	leukemia NUP98 fusion partner 1	protein-coding	0.000000	0.335294	
chunk0202_163_1	chr9	73774056	73774255	+	0	NA	Intergenic	Intergenic	-597376	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.000000	0.360000	
chunk0155_377_1	chr5	97896636	97896996	+	0	NA	Intergenic	L1MC3|LINE|L1	392120	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.013889	0.426593	266(GGGTACTAGGTGTGCT,-,0.00),267(GGTACTAGGTGTGCTT,+,0.00)
chunk0070_353_1	chr15	76034154	76034353	+	0	NA	Intergenic	MLT1L-int|LTR|ERVL-MaLR	-21809	NM_138573	145957	Hs.732438	NM_138573	ENSG00000169752	NRG4	HRG4	neuregulin 4	protein-coding	0.005025	0.385000	
chunk0111_62_1	chr20	22851728	22852401	+	0	NA	Intergenic	L1MA9|LINE|L1	-183356	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.004458	0.489614	
chunk0082_85_1	chr17	52384826	52385123	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-224957	NM_001082534	56934	Hs.463466	NM_020178	ENSG00000154975	CA10	CA-RPX|CARPX|HUCEP-15	carbonic anhydrase 10	protein-coding	0.013468	0.379195	
chunk0158_229_1	chr5	128973682	128974342	+	0	NA	intron (NM_001017372, intron 1 of 9)	intron (NM_001017372, intron 1 of 9)	8492	NM_001017372	28965	Hs.49765	NM_014031	ENSG00000113396	SLC27A6	ACSVL2|FACVL2|FATP6|VLCS-H1	solute carrier family 27 member 6	protein-coding	0.015152	0.422088	369(AGGGCCACAGTGTCCC,-,0.00),370(GGGCCACAGTGTCCCT,+,0.00)
chunk0204_280_1	chr9	98838453	98838760	+	0	NA	intron (NM_024642, intron 6 of 9)	intron (NM_024642, intron 6 of 9)	30907	NM_024642	79695	Hs.47099	NM_024642	ENSG00000119514	GALNT12	CRCS1|GalNAc-T12	polypeptide N-acetylgalactosaminyltransferase 12	protein-coding	0.013029	0.551948	
chunk0021_433_1	chr1	247677452	247677891	+	0	NA	Intergenic	Intergenic	-4630	NM_001005487	441933	Hs.553834	NM_001005487	ENSG00000197437	OR13G1	OR1-37	olfactory receptor family 13 subfamily G member 1	protein-coding	0.011390	0.377273	
chunk0115_358_1	chr21	29435993	29436572	+	0	NA	Intergenic	MER70C|LTR|ERVL	63781	NR_046564	100874322	Hs.326404	NR_046564		BACH1-IT2	-	BACH1 intronic transcript 2	ncRNA	0.013817	0.520690	
chunk0163_30_1	chr6	8206890	8207283	+	0	NA	Intergenic	Intergenic	-104491	NM_001135650	9521	Hs.602353	NM_004280	ENSG00000124802	EEF1E1	AIMP3|P18	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.020356	0.454315	146(GGGTTCAGGCTGTTCC,-,0.00),147(GGTTCAGGCTGTTCCT,+,0.00)
chunk0171_395_1	chr6	131173474	131174079	+	0	NA	intron (NM_016377, intron 5 of 7)	intron (NM_016377, intron 5 of 7)	38090	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.001653	0.341584	
chunk0028_392_1	chr10	92990295	92991040	+	0	NA	intron (NM_019053, intron 18 of 21)	L1PA10|LINE|L1	-70597	NM_183374	340665	Hs.369993	NM_183374	ENSG00000187553	CYP26C1	FFDD4	cytochrome P450 family 26 subfamily C member 1	protein-coding	0.005369	0.379357	
chunk0156_85_1	chr5	104362159	104362396	+	0	NA	Intergenic	MER57C1|LTR|ERV1	-737197	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.004219	0.378151	
chunk0058_212_1	chr14	24964512	24965091	+	0	NA	intron (NM_014178, intron 2 of 5)	intron (NM_014178, intron 2 of 5)	84199	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.003454	0.405172	
chunk0168_341_1	chr6	92887649	92888157	+	0	NA	Intergenic	Intergenic	531679	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.007874	0.432220	
chunk0102_69_1	chr2	142989040	142989710	+	0	NA	3' UTR (NM_001032998, exon 12 of 12)	3' UTR (NM_001032998, exon 12 of 12)	111749	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.008955	0.326379	
chunk0034_108_1	chr11	27856676	27857048	+	0	NA	Intergenic	MIR|SINE|MIR	-134804	NM_170731	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.000000	0.329759	
chunk0192_336_1	chr8	67452780	67452979	+	0	NA	intron (NM_020361, intron 8 of 10)	L2a|LINE|L2	-109202	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.015075	0.485000	
chunk0115_424_1	chr21	31659589	31659800	+	0	NA	promoter-TSS (NM_000454)	promoter-TSS (NM_000454)	72	NM_000454	6647	Hs.443914	NM_000454	ENSG00000142168	SOD1	ALS|ALS1|HEL-S-44|IPOA|SOD|hSod1|homodimer	superoxide dismutase 1	protein-coding	0.109005	0.655660	
chunk0129_120_1	chr3	119833931	119834521	+	0	NA	intron (NM_001146156, intron 10 of 10)	intron (NM_001146156, intron 10 of 10)	51516	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.010169	0.373942	
chunk0158_308_1	chr5	132409582	132409824	+	0	NA	Intergenic	Intergenic	-1070	NR_045116									0.008264	0.386831	
chunk0073_90_1	chr16	4171056	4171302	+	0	NA	Intergenic	Intergenic	-54994	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.008130	0.384615	60(AGTCACACAGTGTTCT,-,0.00),61(GTCACACAGTGTTCTT,+,0.00)
chunk0008_17_1	chr1	87449294	87449607	+	0	NA	Intergenic	Intergenic	-77795	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.015974	0.512739	
chunk0147_233_1	chr4	182230066	182230391	+	0	NA	Intergenic	Intergenic	-13203	NM_001080477	55714	Hs.130438	NM_001080477	ENSG00000218336	TENM3	MCOPCB9|ODZ3|TNM3|Ten-m3|ten-3	teneurin transmembrane protein 3	protein-coding	0.021538	0.463190	103(AAGAACACAGTGTACC,-,0.00),104(AGAACACAGTGTACCT,+,0.00)
chunk0004_313_1	chr1	49340628	49341148	+	0	NA	intron (NM_032785, intron 3 of 13)	MER41C|LTR|ERV1	83477	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.001923	0.374280	
chunk0202_413_1	chr9	81587576	81588632	+	0	NA	intron (NM_005077, intron 16 of 19)	intron (NM_005077, intron 16 of 19)	101431	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.021780	0.494797	707(AAGCACAGGGTGTACA,-,0.00),708(AGCACAGGGTGTACAG,+,0.00)
chunk0109_414_1	chr2	241006539	241006889	+	0	NA	intron (NM_001080437, intron 1 of 31)	L1MC4|LINE|L1	7876	NM_001080437	25992	Hs.471834	NM_001080437	ENSG00000162804	SNED1	IRE-BP1|SST3|Snep	sushi, nidogen and EGF like domains 1	protein-coding	0.005714	0.433048	
chunk0103_8_1	chr2	158907626	158907979	+	0	NA	Intergenic	Intergenic	-60832	NM_033394	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.005666	0.370056	
chunk0112_104_1	chr20	38300001	38300352	+	0	NA	Intergenic	MIR|SINE|MIR	-3974	NM_001725	671	Hs.529019	NM_001725	ENSG00000101425	BPI	BPIFD1|rBPI	bactericidal permeability increasing protein	protein-coding	0.014245	0.582386	
chunk0067_165_1	chr15	44060323	44060560	+	0	NA	intron (NM_001286491, intron 1 of 14)	Tigger15a|DNA|TcMar-Tigger	134005	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.004219	0.390756	
chunk0178_311_1	chr7	38104000	38104199	+	0	NA	Intergenic	L1MEg|LINE|L1	-74107	NM_032016	83930	Hs.309753	NM_032016	ENSG00000010270	STARD3NL	MENTHO	STARD3 N-terminal like	protein-coding	0.000000	0.340000	
chunk0116_242_1	chr21	38561654	38562093	+	0	NA	intron (NR_111949, intron 3 of 4)	intron (NR_111949, intron 3 of 4)	23072	NM_001243429	2078	Hs.473819	NM_004449	ENSG00000157554	ERG	erg-3|p55	ETS transcription factor ERG	protein-coding	0.004556	0.309091	
chunk0113_112_1	chr20	51376826	51377336	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	75896	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.013725	0.442270	373(CAAGACAAACTGTCCT,-,0.00),374(AAGACAAACTGTCCTT,+,0.00)
chunk0117_254_1	chr22	23415410	23415807	+	0	NA	Intergenic	Intergenic	-12996	NR_003950	150244	Hs.386693	NM_152509		ZDHHC8P1	ZDHHC8P	zinc finger DHHC-type containing 8 pseudogene 1	pseudo	0.027708	0.605528	
chunk0029_434_1	chr10	110052948	110053184	+	0	NA	intron (NM_016824, intron 1 of 14)	intron (NM_016824, intron 1 of 14)	-44685	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.000000	0.367089	
chunk0015_130_1	chr1	185534687	185535374	+	0	NA	Intergenic	Intergenic	93458	NR_110793	101929093	Hs.535227	NR_110793	ENSG00000228309	LINC01350	GS1-204I12.1	long intergenic non-protein coding RNA 1350	ncRNA	0.010189	0.366279	
chunk0163_286_1	chr6	13923485	13923990	+	0	NA	promoter-TSS (NM_001165034)	promoter-TSS (NM_001165034)	-709	NM_001165034	221687	Hs.111164	NM_152737	ENSG00000180537	RNF182	-	ring finger protein 182	protein-coding	0.005941	0.383399	198(AGGAACAAACTGTTTT,-,0.00),199(GGAACAAACTGTTTTC,+,0.00)
chunk0143_72_1	chr4	108072401	108072746	+	0	NA	intron (NM_016269, intron 8 of 11)	intron (NM_016269, intron 8 of 11)	82859	NM_001184705	3033	Hs.438289	NM_005327	ENSG00000138796	HADH	HAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHAD	hydroxyacyl-CoA dehydrogenase	protein-coding	0.011594	0.421965	
chunk0055_215_1	chr13	62241390	62241808	+	0	NA	intron (NR_125787, intron 3 of 3)	Tigger3b|DNA|TcMar-Tigger	29317	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.002392	0.279236	
chunk0175_433_1	chr6	169529836	169530345	+	0	NA	intron (NM_001202550, intron 21 of 21)	intron (NM_001202550, intron 21 of 21)	171973	NM_182552	253769	Hs.131903	NM_182552	ENSG00000184465	WDR27	-	WD repeat domain 27	protein-coding	0.009823	0.390196	
chunk0206_390_1	chr9	126985235	126985449	+	0	NA	intron (NM_001190729, intron 4 of 17)	MLT1H|LTR|ERVL-MaLR	23117	NM_001190728	9649	Hs.432842	NM_014636	ENSG00000136828	RALGPS1	RALGEF2|RALGPS1A	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.009346	0.409302	
chunk0123_262_1	chr3	45995843	45996093	+	0	NA	promoter-TSS (NM_024513)	promoter-TSS (NM_024513)	-144	NM_024513	79443	Hs.200227	NM_024513	ENSG00000163820	FYCO1	CATC2|CTRCT18|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding	0.072000	0.649402	
chunk0010_438_1	chr1	119974055	119974359	+	0	NA	intron (NM_024408, intron 5 of 33)	intron (NM_024408, intron 5 of 33)	-77683	NM_021794	11085	Hs.283011	NM_021794	ENSG00000134249	ADAM30	svph4	ADAM metallopeptidase domain 30	protein-coding	0.000000	0.403279	
chunk0124_333_1	chr3	58252516	58252993	+	0	NA	intron (NM_020676, intron 1 of 8)	intron (NM_020676, intron 1 of 8)	15222	NM_020676	57406	Hs.476454	NM_020676	ENSG00000163686	ABHD6	-	abhydrolase domain containing 6	protein-coding	0.000000	0.410042	286(GGGTACATAGAGTACT,-,0.00),287(GGTACATAGAGTACTC,+,0.00)
chunk0105_260_1	chr2	189149906	189150544	+	0	NA	intron (NM_000393, intron 1 of 53)	intron (NM_000393, intron 1 of 53)	-17114	NR_036076	100422908		NR_036076	ENSG00000264725	MIR3129	mir-3129	microRNA 3129	ncRNA	0.003135	0.338028	
chunk0032_175_1	chr11	5638368	5638692	+	0	NA	intron (NM_001003819, intron 10 of 13)	intron (NM_001003819, intron 10 of 13)	6275	NM_130390	53840	Hs.729048	NM_021616	ENSG00000258659	TRIM34	IFP1|RNF21	tripartite motif containing 34	protein-coding	0.003086	0.387692	
chunk0054_200_1	chr13	44967961	44968709	+	0	NA	intron (NM_012345, intron 5 of 9)	intron (NM_012345, intron 5 of 9)	21143	NM_012345	26747	Hs.525006	NM_012345	ENSG00000083635	NUFIP1	NUFIP|bA540M5.1	nuclear FMR1 interacting protein 1	protein-coding	0.005348	0.339119	
chunk0101_413_1	chr2	139159430	139160141	+	0	NA	Intergenic	Intergenic	262461	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005626	0.297753	
chunk0176_186_1	chr7	13875009	13875208	+	0	NA	Intergenic	L3|LINE|CR1	111406	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.005025	0.340000	
chunk0041_382_1	chr11	131949050	131949420	+	0	NA	intron (NM_001144058, intron 1 of 7)	L1MB1|LINE|L1	38417	NM_001144059	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.016216	0.380054	
chunk0143_13_1	chr4	105859375	105859878	+	0	NA	Intergenic	L2a|LINE|L2	-32454	NR_125927	101929529	Hs.603751	NR_125927	ENSG00000251175	LOC101929529	-	uncharacterized LOC101929529	ncRNA	0.001988	0.335317	
chunk0188_438_1	chr8	19198633	19199371	+	0	NA	intron (NR_038919, intron 3 of 4)	intron (NR_038919, intron 3 of 4)	46520	NR_038919	100128993	Hs.697742	NR_038919		LOC100128993	-	uncharacterized LOC100128993	ncRNA	0.008130	0.388363	
chunk0211_104_1	chrX	111151704	111152094	+	0	NA	intron (NM_001128168, intron 5 of 15)	MER44B|DNA|TcMar-Tigger	28822	NM_001128168	5063	Hs.593599	NM_002578	ENSG00000077264	PAK3	ARA|MRX30|MRX47|OPHN3|PAK-3|PAK3beta|bPAK|beta-PAK	p21 (RAC1) activated kinase 3	protein-coding	0.007692	0.378517	
chunk0200_173_1	chr9	19209239	19209598	+	0	NA	Intergenic	Intergenic	-21347	NM_017925	55667	Hs.249591	NM_017925	ENSG00000137145	DENND4C	C9orf55|C9orf55B|RAB10GEF|bA513M16.3	DENN domain containing 4C	protein-coding	0.011142	0.344444	
chunk0200_407_1	chr9	27349572	27349973	+	0	NA	intron (NM_024761, intron 3 of 3)	intron (NM_024761, intron 3 of 3)	-52633	NM_001161585	54586	Hs.163070	NM_020641	ENSG00000120160	EQTN	AFAF|C9orf11|SPACA8	equatorin	protein-coding	0.004988	0.427861	
chunk0132_65_1	chr3	155161121	155161446	+	0	NA	intron (NM_000902, intron 17 of 22)	intron (NM_000902, intron 17 of 22)	-79662	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.003077	0.368098	197(AGGTACACTCAGTCCT,-,0.00),198(GGTACACTCAGTCCTG,+,0.00)
chunk0173_75_1	chr6	142659619	142660259	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-22050	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.004687	0.333853	
chunk0170_256_1	chr6	113723151	113723698	+	0	NA	Intergenic	L2c|LINE|L2	-73349	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.012797	0.406934	
chunk0089_225_1	chr18	61545069	61545948	+	0	NA	intron (NM_031891, intron 9 of 10)	intron (NM_031891, intron 9 of 10)	54966	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.005688	0.422727	
chunk0127_240_1	chr3	96915503	96915812	+	0	NA	intron (NM_001080448, intron 2 of 17)	MIRb|SINE|MIR	101076	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.006472	0.329032	
chunk0101_115_1	chr2	126100448	126100891	+	0	NA	Intergenic	Intergenic	-555266	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.002257	0.351351	
chunk0040_16_1	chr11	108817652	108818159	+	0	NA	intron (NM_004398, intron 13 of 17)	L4_B_Mam|LINE|RTE-X	152880	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.013807	0.372047	
chunk0072_78_1	chr15	90556322	90556593	+	0	NA	intron (NM_001042574, intron 2 of 14)	Tigger12|DNA|TcMar-Tigger	26571	NM_001042574	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.014760	0.375000	
chunk0199_116_1	chr9	3434672	3434884	+	0	NA	intron (NM_001282116, intron 1 of 16)	Tigger3b|DNA|TcMar-Tigger	-39182	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.000000	0.413146	172(CATCACAGAGTGTTCT,-,0.00),173(ATCACAGAGTGTTCTT,+,0.00)
chunk0069_327_1	chr15	66089165	66089461	+	0	NA	intron (NM_032445, intron 5 of 22)	intron (NM_032445, intron 5 of 22)	49080	NR_036196	100422905		NR_036196	ENSG00000263512	MIR4311	-	microRNA 4311	ncRNA	0.016892	0.515152	21(AAGAACACGCTGGACT,-,0.00),22(AGAACACGCTGGACTT,+,0.00),159(CAGGACAGTGTGTACC,-,0.00),160(AGGACAGTGTGTACCG,+,0.00)
chunk0035_427_1	chr11	57277571	57278231	+	0	NA	Intergenic	Intergenic	-40448	NM_005161	187	Hs.438311	NM_005161	ENSG00000134817	APLNR	AGTRL1|APJ|APJR|HG11	apelin receptor	protein-coding	0.022727	0.482602	354(GAGAAGAGAATGTTCT,-,0.00),355(AGAAGAGAATGTTCTT,+,0.00)
chunk0051_160_1	chr12	115872714	115873276	+	0	NA	Intergenic	Intergenic	275659	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.007117	0.417407	
chunk0092_233_1	chr19	32478735	32479138	+	0	NA	intron (NM_001172774, intron 17 of 18)	L1ME4b|LINE|L1	72820	NM_207325	147991	Hs.194392	NM_207325	ENSG00000178904	DPY19L3	-	dpy-19 like C-mannosyltransferase 3	protein-coding	0.007444	0.403465	
chunk0009_241_1	chr1	106978429	106978904	+	0	NA	Intergenic	MER99|DNA|hAT?	-77979	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.006316	0.346639	
chunk0074_193_1	chr16	24893320	24893550	+	0	NA	intron (NM_052944, intron 9 of 15)	intron (NM_052944, intron 9 of 15)	47204	NM_052944	115584	Hs.164118	NM_052944	ENSG00000158865	SLC5A11	KST1|RKST1|SGLT6|SMIT2	solute carrier family 5 member 11	protein-coding	0.013043	0.441558	
chunk0127_322_1	chr3	100042612	100042811	+	0	NA	intron (NM_001042459, intron 1 of 4)	intron (NM_001042459, intron 1 of 4)	71802	NM_001042459	11259	Hs.104672	NM_014890	ENSG00000168386	FILIP1L	DOC-1|DOC1|GIP130|GIP90	filamin A interacting protein 1 like	protein-coding	0.005025	0.355000	
chunk0007_297_1	chr1	84143635	84144411	+	0	NA	promoter-TSS (NM_182948)	promoter-TSS (NM_182948)	-225	NM_001300916	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.001289	0.314028	332(GAGGACAGCTTGGCCT,-,0.00)
chunk0076_46_1	chr16	60158345	60158629	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	201276	NM_001282301	729159		NM_001282301		NPAP1L	-	nuclear pore associated protein 1 like	protein-coding	0.000000	0.392982	
chunk0047_336_1	chr12	74557062	74557453	+	0	NA	Intergenic	Intergenic	19486	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.005115	0.301020	183(GGAACAAAAAGTACTC,+,0.00)
chunk0104_216_1	chr2	176317203	176317728	+	0	NA	intron (NR_027850, intron 4 of 10)	HAL1|LINE|L1	48070	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.001905	0.387833	
chunk0081_55_1	chr17	38560798	38560997	+	0	NA	intron (NM_025248, intron 7 of 18)	MamRTE1|LINE|RTE-BovB	45033	NM_025248	80725	Hs.448872	NM_025248	ENSG00000277363	SRCIN1	P140|SNIP	SRC kinase signaling inhibitor 1	protein-coding	0.020101	0.600000	
chunk0048_248_1	chr12	81611301	81611603	+	0	NA	intron (NM_001220474, intron 2 of 30)	L1PA16|LINE|L1	-13081	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.016556	0.623762	
chunk0187_173_1	chr7	150903530	150904469	+	0	NA	Intergenic	Intergenic	51522	NM_001272072	26	Hs.647097	NM_001091	ENSG00000002726	AOC1	ABP|ABP1|DAO|DAO1|KAO	amine oxidase copper containing 1	protein-coding	0.018104	0.493617	
chunk0117_388_1	chr21	45364350	45364549	+	0	NA	Intergenic	Intergenic	-22459	NR_103811	388830	Hs.592162	NR_103811	ENSG00000237664	LINC00316	C21orf111|NCRNA00316|PRED59	long intergenic non-protein coding RNA 316	ncRNA	0.070352	0.655000	
chunk0187_407_1	chr7	158020993	158021281	+	0	NA	intron (NM_001308268, intron 11 of 22)	Plat_L3|LINE|CR1	166552	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.000000	0.366782	
chunk0094_141_1	chr2	4974065	4974264	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-317942	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.005025	0.535000	
chunk0152_41_1	chr5	57173895	57174179	+	0	NA	promoter-TSS (NM_001203246)	promoter-TSS (NM_001203246)	89	NM_022913	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.077465	0.610526	
chunk0195_72_1	chr8	93968816	93969015	+	0	NA	Intergenic	L1PA6|LINE|L1	51864	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.005025	0.430000	
chunk0131_189_1	chr3	148354920	148355133	+	0	NA	Intergenic	Intergenic	-342845	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.004695	0.392523	
chunk0091_371_1	chr19	15604578	15604949	+	0	NA	Intergenic	LTR57-int|LTR|ERVL	-10455	NM_007253	11283	Hs.268554	NM_007253	ENSG00000186526	CYP4F8	CPF8|CYPIVF8	cytochrome P450 family 4 subfamily F member 8	protein-coding	0.002695	0.252688	
chunk0032_107_1	chr11	3745274	3745525	+	0	NA	intron (NM_016320, intron 11 of 32)	intron (NM_016320, intron 11 of 32)	-52325	NM_001256235	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.015936	0.384921	
chunk0020_232_1	chr1	235714120	235714724	+	0	NA	intron (NM_001301365, intron 42 of 52)	L3|LINE|CR1	-63668	NM_001098721	2786	Hs.159711	NM_004485	ENSG00000168243	GNG4	-	G protein subunit gamma 4	protein-coding	0.003311	0.370248	
chunk0050_44_1	chr12	100630266	100630591	+	0	NA	Intergenic	Intergenic	36810	NM_001303131	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.000000	0.276074	
chunk0140_226_1	chr4	71067200	71067782	+	0	NA	Intergenic	Intergenic	73943	NM_000788	1633	Hs.709	NM_000788	ENSG00000156136	DCK	-	deoxycytidine kinase	protein-coding	0.003436	0.313894	
chunk0027_319_1	chr10	78174525	78174935	+	0	NA	Intergenic	Intergenic	-73895	NR_038985	100132987	Hs.55047	NR_038985	ENSG00000230417	LINC00856	-	long intergenic non-protein coding RNA 856	ncRNA	0.004878	0.447689	
chunk0163_426_1	chr6	17162043	17162510	+	0	NA	Intergenic	Intergenic	60018	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.008565	0.412393	
chunk0202_115_1	chr9	72763100	72763622	+	0	NA	intron (NM_138691, intron 12 of 23)	L2c|LINE|L2	110748	NR_121180	101927258	Hs.586433	NR_121120	ENSG00000236849	LINC01474	-	long intergenic non-protein coding RNA 1474	ncRNA	0.001916	0.367113	
chunk0063_383_1	chr14	86570488	86570725	+	0	NA	Intergenic	L1PBa|LINE|L1	-335172	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.000000	0.542017	
chunk0028_156_1	chr10	86915607	86916126	+	0	NA	intron (NM_004329, intron 8 of 12)	intron (NM_004329, intron 8 of 12)	41802	NM_024756	79812	Hs.524479	NM_024756	ENSG00000173269	MMRN2	EMILIN-3|EMILIN3|ENDOGLYX-1	multimerin 2	protein-coding	0.013487	0.361538	223(TGGAGCATAATGTTCT,-,0.00),224(GGAGCATAATGTTCTT,+,0.00)
chunk0126_448_1	chr3	87169195	87169537	+	0	NA	Intergenic	MIRb|SINE|MIR	56911	NR_039958	100616161		NR_039958	ENSG00000264119	MIR4795	-	microRNA 4795	ncRNA	0.005848	0.309038	
chunk0046_355_1	chr12	63010699	63011020	+	0	NA	Intergenic	LTR33C|LTR|ERVL	-75974	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.006231	0.503106	111(AAGGACATCCTGTTCC,-,0.00),112(AGGACATCCTGTTCCT,+,0.00)
chunk0037_257_1	chr11	75572741	75573163	+	0	NA	TTS (NM_001235)	TTS (NM_001235)	10896	NM_001235	871	Hs.596449	NM_001235	ENSG00000149257	SERPINH1	AsTP3|CBP1|CBP2|HSP47|OI10|PIG14|PPROM|RA-A47|SERPINH2|gp46	serpin family H member 1	protein-coding	0.018957	0.496454	
chunk0083_127_1	chr17	65239587	65239921	+	0	NA	Intergenic	MIR|SINE|MIR	102416	NM_003835	8787	Hs.664380	NM_003835	ENSG00000108370	RGS9	PERRS|RGS9L	regulator of G protein signaling 9	protein-coding	0.005988	0.483582	
chunk0144_222_1	chr4	134579351	134579639	+	0	NA	Intergenic	Intergenic	-377747	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.000000	0.287197	194(AGAAACACTCTGTGCT,-,0.00),195(GAAACACTCTGTGCTG,+,0.00)
chunk0044_219_1	chr12	31324758	31325541	+	0	NA	non-coding (NR_026806, exon 1 of 1)	non-coding (NR_026806, exon 1 of 1)	833	NR_026806	79857	Hs.534485	NM_024799	ENSG00000177340	FLJ13224	-	uncharacterized LOC79857	ncRNA	0.097063	0.626276	
chunk0054_351_1	chr13	49584612	49585090	+	0	NA	intron (NM_018191, intron 1 of 12)	intron (NM_018191, intron 1 of 12)	732	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.027197	0.425887	216(CAGAACACAGCGTGCT,-,0.00),217(AGAACACAGCGTGCTC,+,0.00)
chunk0050_227_1	chr12	104941364	104941944	+	0	NA	Intergenic	Intergenic	-12960	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.006897	0.325301	
chunk0107_339_1	chr2	221309960	221310186	+	0	NA	Intergenic	Intergenic	262285	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.013274	0.449339	
chunk0138_151_1	chr4	37297412	37298094	+	0	NA	intron (NM_001144990, intron 1 of 6)	L1MC4|LINE|L1	52685	NM_001144990	57495	Hs.4280	NM_001144990	ENSG00000174145	NWD2	KIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.002933	0.361640	
chunk0031_268_1	chr10	127797444	127797735	+	0	NA	Intergenic	Intergenic	60315	NM_207426	399823	Hs.449674	NM_207426	ENSG00000186766	FOXI2	-	forkhead box I2	protein-coding	0.000000	0.595890	
chunk0067_463_1	chr15	50470874	50471519	+	0	NA	intron (NM_001283049, intron 5 of 16)	MIR|SINE|MIR	46819	NM_005154	9101	Hs.443731	NM_005154	ENSG00000138592	USP8	HumORF8|PITA4|SPG59|UBPY	ubiquitin specific peptidase 8	protein-coding	0.009302	0.360681	
chunk0067_106_1	chr15	42306809	42307038	+	0	NA	intron (NM_001301409, intron 8 of 11)	intron (NM_001301409, intron 8 of 11)	32755	NM_198141	2595	Hs.730806	NM_198141	ENSG00000214013	GANC	-	glucosidase alpha, neutral C	protein-coding	0.004367	0.434783	
chunk0134_231_1	chr3	178895143	178895668	+	0	NA	Intergenic	L1ME1|LINE|L1	-35000	NR_126561	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.005714	0.338403	
chunk0011_390_1	chr1	153966865	153967504	+	0	NA	promoter-TSS (NM_130898)	promoter-TSS (NM_130898)	548	NM_014437	27173	Hs.7854	NM_014437	ENSG00000143570	SLC39A1	ZIP1|ZIRTL	solute carrier family 39 member 1	protein-coding	0.059468	0.510938	217(TGGGACATAATGTTCC,-,0.00),218(GGGACATAATGTTCCC,+,0.00)
chunk0115_284_1	chr21	28186519	28187125	+	0	NA	intron (NR_126012, intron 3 of 5)	MLT1D|LTR|ERVL-MaLR	41845	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.001650	0.349259	213(AAGTACAAACAGTTCT,-,0.00),214(AGTACAAACAGTTCTC,+,0.00),282(GAGGACAAGATGTTCC,-,0.00),283(AGGACAAGATGTTCCT,+,0.00)
chunk0150_17_1	chr5	30568975	30569224	+	0	NA	Intergenic	L2a|LINE|L2	-624556	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.008032	0.412000	
chunk0210_337_1	chrX	95463867	95464317	+	0	NA	Intergenic	MIRc|SINE|MIR	-400866	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.000000	0.337029	
chunk0144_340_1	chr4	139452944	139453544	+	0	NA	promoter-TSS (NM_031296)	promoter-TSS (NM_031296)	-563	NM_031296	83452	Hs.591679	NM_031296	ENSG00000172007	RAB33B	SMC2	RAB33B, member RAS oncogene family	protein-coding	0.050000	0.520799	
chunk0035_24_1	chr11	40368811	40369138	+	0	NA	intron (NM_020929, intron 2 of 4)	MIRb|SINE|MIR	-75844	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003058	0.341463	
chunk0087_443_1	chr18	42622982	42623714	+	0	NA	intron (NR_046174, intron 7 of 9)	intron (NR_046174, intron 7 of 9)	436680	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.004098	0.286494	
chunk0016_69_1	chr1	193658663	193659002	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	354087	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.002950	0.432353	207(AAGAACAGCATGTCCC,-,0.00),208(AGAACAGCATGTCCCC,+,0.00)
chunk0204_420_1	chr9	103025884	103026400	+	0	NA	Intergenic	Intergenic	30831	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.003876	0.342360	
chunk0113_331_1	chr20	58638002	58638485	+	0	NA	Intergenic	L2c|LINE|L2	3471	NR_125359	79160	Hs.280135	NR_125359	ENSG00000268941	LINC01711	-	long intergenic non-protein coding RNA 1711	ncRNA	0.037267	0.533058	
chunk0141_170_1	chr4	82500401	82501107	+	0	NA	intron (NM_001080506, intron 5 of 7)	intron (NM_001080506, intron 5 of 7)	61219	NM_001080506	441027	Hs.507676	NM_001080506	ENSG00000249242	TMEM150C	TTN3	transmembrane protein 150C	protein-coding	0.007082	0.393211	
chunk0183_27_1	chr7	103447544	103448149	+	0	NA	intron (NR_110141, intron 2 of 3)	MIR|SINE|MIR	-1669	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.009917	0.422442	
chunk0178_132_1	chr7	32513588	32514090	+	0	NA	intron (NM_015060, intron 1 of 15)	LTR5B|LTR|ERVK	18413	NM_015060	23080	Hs.128056	NM_015060	ENSG00000105778	AVL9	KIAA0241	AVL9 cell migration associated	protein-coding	0.017928	0.455268	
chunk0076_325_1	chr16	70702864	70703462	+	0	NA	intron (NM_018052, intron 14 of 18)	intron (NM_018052, intron 14 of 18)	-17112	NM_138383	92154	Hs.432387	NM_138383	ENSG00000132613	MTSS2	ABBA|ABBA-1|ABBA1|MTSS1L	MTSS I-BAR domain containing 2	protein-coding	0.015050	0.577629	
chunk0118_355_1	chr22	36268861	36269485	+	0	NA	Intergenic	L1P3|LINE|L1	16102	NM_003661	8542	Hs.114309	NM_003661	ENSG00000100342	APOL1	APO-L|APOL|APOL-I|FSGS4	apolipoprotein L1	protein-coding	0.012821	0.424000	243(GGTACATTGTGTCTTT,+,0.00),326(AGGAACACGTTGTTCA,-,0.00),327(GGAACACGTTGTTCAA,+,0.00),538(GGGACGGAGAGTTCTG,+,0.00)
chunk0101_32_1	chr2	121877342	121878046	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	122149	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.002841	0.354610	
chunk0206_233_1	chr9	123569438	123569673	+	0	NA	intron (NM_024820, intron 12 of 20)	intron (NM_024820, intron 12 of 20)	-83933	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.021277	0.461864	
chunk0172_257_1	chr6	137371047	137371370	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	123186	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.000000	0.385802	
chunk0176_294_1	chr7	16764294	16764658	+	0	NA	intron (NM_014399, intron 1 of 5)	intron (NM_014399, intron 1 of 5)	10750	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.008242	0.361644	186(CAACACACAGTGTGCT,-,0.00),187(AACACACAGTGTGCTC,+,0.00)
chunk0191_104_1	chr8	48074720	48075424	+	0	NA	Intergenic	Intergenic	66637	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.011364	0.453901	
chunk0154_310_1	chr5	83649766	83649965	+	0	NA	intron (NM_001884, intron 3 of 4)	intron (NM_001884, intron 3 of 4)	71212	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.000000	0.320000	
chunk0166_47_1	chr6	42528323	42528636	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-35543	NM_015255	23304	Hs.529925	NM_015255	ENSG00000024048	UBR2	C6orf133|bA49A4.1|dJ242G1.1|dJ392M17.3	ubiquitin protein ligase E3 component n-recognin 2	protein-coding	0.012780	0.391720	182(CATCACAGAGTGTTCT,-,0.00),183(ATCACAGAGTGTTCTT,+,0.00)
chunk0038_110_1	chr11	83727259	83727680	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	-45044	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.462085	
chunk0042_17_1	chr12	1252377	1252839	+	0	NA	intron (NR_027946, intron 13 of 18)	intron (NR_027946, intron 13 of 18)	224860	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.000000	0.352052	
chunk0145_273_1	chr4	149463561	149463814	+	0	NA	Intergenic	Intergenic	309392	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.000000	0.291339	146(ATGAACTCATTGTTCT,-,0.00),147(TGAACTCATTGTTCTT,+,0.00)
chunk0010_432_1	chr1	119785460	119785754	+	0	NA	Intergenic	Intergenic	-16675	NM_005518	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.013605	0.532203	
chunk0073_427_1	chr16	19123800	19124134	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	10035	NM_001034841	162073	Hs.530899	NM_001034841	ENSG00000205730	ITPRIPL2	-	ITPRIP like 2	protein-coding	0.005988	0.462687	
chunk0061_89_1	chr14	57171603	57171967	+	0	NA	Intergenic	Intergenic	-97103	NM_018229	55745	Hs.597349	NM_018229	ENSG00000053770	AP5M1	C14orf108|MUDENG|Mu5|MuD	adaptor related protein complex 5 subunit mu 1	protein-coding	0.005495	0.457534	
chunk0110_99_1	chr20	11496226	11496568	+	0	NA	Intergenic	Intergenic	-223014	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.005848	0.448980	
chunk0099_147_1	chr2	86675073	86675747	+	0	NA	intron (NM_001198954, intron 2 of 7)	intron (NM_001198954, intron 2 of 7)	-44881	NM_022780	64795	Hs.75277	NM_022780	ENSG00000153561	RMND5A	CTLH|GID2|GID2A|RMD5|p44CTLH	required for meiotic nuclear division 5 homolog A	protein-coding	0.004451	0.405926	
chunk0133_135_1	chr3	169173709	169173995	+	0	NA	intron (NM_001205194, intron 1 of 15)	L2b|LINE|L2	-26118	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.006993	0.386760	
chunk0163_194_1	chr6	11694065	11694362	+	0	NA	Intergenic	Intergenic	84834	NM_032744	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.013468	0.382550	
chunk0120_101_1	chr3	4467107	4467338	+	0	NA	promoter-TSS (NM_001164675)	promoter-TSS (NM_001164675)	60	NM_182760	285362	Hs.350475	NM_182760	ENSG00000144455	SUMF1	AAPA3037|FGE|UNQ3037	sulfatase modifying factor 1	protein-coding	0.069264	0.655172	
chunk0064_321_1	chr14	95971497	95971869	+	0	NA	Intergenic	Intergenic	-67641	NM_001282464	56967	Hs.6434	NM_020215	ENSG00000227051	C14orf132	C14orf88	chromosome 14 open reading frame 132	protein-coding	0.000000	0.469169	22(ATGAACATGCTGTTTC,-,0.00),23(TGAACATGCTGTTTCT,+,0.00)
chunk0117_440_1	chr21	46406617	46406819	+	0	NA	intron (NM_001315529, intron 27 of 46)	L1M5|LINE|L1	-52231	NM_206891	23181	Hs.189585	NM_015151	ENSG00000160305	DIP2A	C21orf106|DIP2	disco interacting protein 2 homolog A	protein-coding	0.000000	0.374384	
chunk0060_257_1	chr14	50146633	50147084	+	0	NA	intron (NM_006939, intron 14 of 22)	L1ME3Cz|LINE|L1	-30279	NM_024558	79609	Hs.558541	NM_024558	ENSG00000100483	VCPKMT	C14orf138|METTL21D|VCP-KMT	valosin containing protein lysine methyltransferase	protein-coding	0.006652	0.358407	
chunk0041_388_1	chr11	132704649	132705428	+	0	NA	intron (NM_001012393, intron 2 of 7)	intron (NM_001012393, intron 2 of 7)	238104	NM_002545	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.006418	0.410256	
chunk0004_247_1	chr1	47380772	47381132	+	0	NA	non-coding (NR_126355, exon 5 of 5)	non-coding (NR_126355, exon 5 of 5)	-35120	NM_012186	2301	Hs.112968	NM_012186	ENSG00000186790	FOXE3	AAT11|ASGD2|CTRCT34|FKHL12|FREAC8	forkhead box E3	protein-coding	0.002778	0.434903	
chunk0148_69_1	chr5	2183381	2183755	+	0	NA	Intergenic	Intergenic	128633	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.016043	0.504000	
chunk0080_355_1	chr17	32876027	32876292	+	0	NA	intron (NM_015194, intron 1 of 21)	intron (NM_015194, intron 1 of 21)	1014	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.026415	0.424812	
chunk0093_80_1	chr19	40805091	40805452	+	0	NA	intron (NM_053046, intron 2 of 5)	intron (NM_053046, intron 2 of 5)	5842	NM_053046	112398	Hs.515417	NM_017555	ENSG00000269858	EGLN2	EIT-6|EIT6|HIF-PH1|HIFPH1|HPH-1|HPH-3|PHD1	egl-9 family hypoxia inducible factor 2	protein-coding	0.013850	0.533149	
chunk0054_249_1	chr13	46168374	46168763	+	0	NA	intron (NM_002298, intron 1 of 15)	intron (NM_002298, intron 1 of 15)	13756	NM_002298	3936	Hs.381099	NM_002298	ENSG00000136167	LCP1	CP64|HEL-S-37|L-PLASTIN|LC64P|LPL|PLS2	lymphocyte cytosolic protein 1	protein-coding	0.017995	0.523077	
chunk0142_227_1	chr4	98283818	98284067	+	0	NA	intron (NM_001100427, intron 1 of 14)	intron (NM_001100427, intron 1 of 14)	22566	NM_001100426	5910	Hs.132858	NM_021159	ENSG00000138698	RAP1GDS1	GDS1|SmgGDS	Rap1 GTPase-GDP dissociation stimulator 1	protein-coding	0.008032	0.344000	123(AGGTACAGACAGTCCT,-,0.00),124(GGTACAGACAGTCCTT,+,0.00),212(AGGAAGAGCCTGTACT,-,0.00),213(GGAAGAGCCTGTACTT,+,0.00)
chunk0181_393_1	chr7	89686896	89687434	+	0	NA	Intergenic	Intergenic	-432235	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.003717	0.332096	
chunk0199_466_1	chr9	14304189	14304496	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	9704	NM_005596	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.006515	0.389610	
chunk0098_339_1	chr2	77191572	77192057	+	0	NA	intron (NM_001282924, intron 3 of 3)	L1PA10|LINE|L1	205849	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.002062	0.277778	
chunk0034_102_1	chr11	27675749	27676035	+	0	NA	non-coding (NR_033312, exon 6 of 9)	non-coding (NR_033312, exon 6 of 9)	-16243	NM_001143816	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.010490	0.487805	
chunk0174_384_1	chr6	165070002	165070416	+	0	NA	Intergenic	L1MC2|LINE|L1	239413	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.000000	0.291566	
chunk0004_42_1	chr1	42931783	42932034	+	0	NA	intron (NM_006516, intron 2 of 9)	intron (NM_006516, intron 2 of 9)	-27141	NR_033967	440584	Hs.260928	NR_033967	ENSG00000227533	SLC2A1-AS1	-	SLC2A1 antisense RNA 1	ncRNA	0.007968	0.539683	
chunk0028_398_1	chr10	93192879	93193477	+	0	NA	Intergenic	Intergenic	119288	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.001672	0.373957	
chunk0186_226_1	chr7	140418030	140418271	+	0	NA	intron (NM_001008749, intron 3 of 3)	intron (NM_001008749, intron 3 of 3)	14107	NM_001008749	401409	Hs.583545	NM_001008749	ENSG00000146955	RAB19	RAB19B	RAB19, member RAS oncogene family	protein-coding	0.000000	0.363636	
chunk0202_32_1	chr9	70607186	70607696	+	0	NA	intron (NM_024971, intron 19 of 25)	intron (NM_024971, intron 19 of 25)	-192784	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.009804	0.461840	
chunk0119_180_1	chr22	43955358	43955753	+	0	NA	5' UTR (NM_015380, exon 1 of 15)	5' UTR (NM_015380, exon 1 of 15)	174	NM_015380	25813	Hs.505824	NM_015380	ENSG00000100347	SAMM50	CGI-51|OMP85|SAM50|TOB55|TRG-3|YNL026W	SAMM50 sorting and assembly machinery component	protein-coding	0.096203	0.712121	
chunk0051_410_1	chr12	122152858	122153057	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	-14762	NM_152759	254050	Hs.374856	NM_152759	ENSG00000158113	LRRC43	-	leucine rich repeat containing 43	protein-coding	0.020101	0.530000	
chunk0058_218_1	chr14	25013616	25014275	+	0	NA	intron (NM_001304476, intron 1 of 6)	L1MC5|LINE|L1	35055	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.006070	0.353030	
chunk0142_44_1	chr4	91037807	91038508	+	0	NA	intron (NM_001145065, intron 9 of 10)	intron (NM_001145065, intron 9 of 10)	803126	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.001427	0.287749	378(AAGTACTGACTGTCCT,-,0.00),379(AGTACTGACTGTCCTT,+,0.00)
chunk0137_78_1	chr4	12957130	12957639	+	0	NA	Intergenic	MIR|SINE|MIR	526981	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.005894	0.384314	
chunk0066_14_1	chr15	27057934	27058387	+	0	NA	intron (NM_033223, intron 3 of 9)	intron (NM_033223, intron 3 of 9)	86878	NM_001270873	2567	Hs.569475	NM_033223	ENSG00000182256	GABRG3	-	gamma-aminobutyric acid type A receptor gamma3 subunit	protein-coding	0.024283	0.486784	
chunk0093_245_1	chr19	50861101	50861367	+	0	NA	TTS (NM_001648)	TTS (NM_001648)	6319	NM_001030048	354	Hs.171995	NM_001648	ENSG00000142515	KLK3	APS|KLK2A1|PSA|hK3	kallikrein related peptidase 3	protein-coding	0.018797	0.513109	
chunk0115_352_1	chr21	29305352	29305852	+	0	NA	intron (NR_027655, intron 1 of 7)	intron (NR_027655, intron 1 of 7)	398	NR_027655	571	Hs.154276	NM_001186	ENSG00000156273	BACH1	BACH-1|BTBD24	BTB domain and CNC homolog 1	protein-coding	0.002000	0.407186	
chunk0052_226_1	chr13	25499459	25499899	+	0	NA	intron (NM_001313741, intron 2 of 35)	intron (NM_001313741, intron 2 of 35)	30905	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.009091	0.401361	
chunk0121_68_1	chr3	15781912	15782519	+	0	NA	intron (NM_015199, intron 2 of 27)	L1MC1|LINE|L1	15969	NM_001195098	23243	Hs.335239	NM_015199	ENSG00000206560	ANKRD28	PITK|PPP1R65	ankyrin repeat domain 28	protein-coding	0.006590	0.338816	295(GAGAACAGAGTGTTCT,-,0.00),296(AGAACAGAGTGTTCTG,+,0.00)
chunk0040_41_1	chr11	110695512	110696051	+	0	NA	intron (NM_001258416, intron 1 of 15)	L1MB8|LINE|L1	16269	NM_001258415	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.007421	0.344444	
chunk0101_465_1	chr2	140529580	140529863	+	0	NA	intron (NM_018557, intron 47 of 90)	intron (NM_018557, intron 47 of 90)	56964	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.007067	0.411972	97(CAGAACTGCTAGTTCC,-,0.00),98(AGAACTGCTAGTTCCC,+,0.00),166(GGGAGCAGTCTGTACT,-,0.00),167(GGAGCAGTCTGTACTC,+,0.00)
chunk0063_21_1	chr14	76518851	76519288	+	0	NA	Intergenic	Intergenic	147722	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.009153	0.495434	
chunk0152_16_1	chr5	56357466	56357703	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	124185	NR_104664	102467147	Hs.650177	NR_104664	ENSG00000248727	LINC01948	-	long intergenic non-protein coding RNA 1948	ncRNA	0.000000	0.428571	77(TTGAACTGTGTGTTCT,-,0.00),78(TGAACTGTGTGTTCTA,+,0.00),96(AAGGACTGTATGTACT,-,0.00),97(AGGACTGTATGTACTG,+,0.00)
chunk0106_371_1	chr2	207233558	207234129	+	0	NA	intron (NR_110283, intron 3 of 3)	intron (NR_110283, intron 3 of 3)	20473	NR_110283	101927865	Hs.574609	NR_110283		MYOSLID-AS1	-	MYOSLID antisense RNA 1	ncRNA	0.005254	0.416084	
chunk0014_436_1	chr1	183664345	183664724	+	0	NA	intron (NM_001297670, intron 1 of 17)	MIRc|SINE|MIR	-11221	NM_203454	403314	Hs.97335	NM_203454	ENSG00000173627	APOBEC4	C1orf169	apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4	protein-coding	0.007916	0.321053	
chunk0059_357_1	chr14	37274596	37274874	+	0	NA	intron (NM_001195296, intron 8 of 14)	MIR|SINE|MIR	76822	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.007194	0.336918	
chunk0078_201_1	chr17	5299028	5299441	+	0	NA	intron (NM_001291581, intron 1 of 16)	L1MC3|LINE|L1	16971	NM_001291582	9135	Hs.584784	NM_004703	ENSG00000029725	RABEP1	RAB5EP|RABPT5	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.004843	0.403382	
chunk0093_376_1	chr19	56113783	56114230	+	0	NA	intron (NM_001002836, intron 1 of 2)	L1MB7|LINE|L1	7367	NM_001002836	126208	Hs.397153	NM_001002836	ENSG00000142409	ZNF787	TIP20	zinc finger protein 787	protein-coding	0.031320	0.508929	
chunk0039_77_1	chr11	97059867	97060130	+	0	NA	Intergenic	L1MA4A|LINE|L1	-553121	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.003802	0.511364	
chunk0116_248_1	chr21	38753168	38753951	+	0	NA	intron (NR_027065, intron 1 of 6)	intron (NR_027065, intron 1 of 6)	-1302	NR_027067	400866	Hs.278704	NM_001001789	ENSG00000223806	LINC00114	C21orf24|NCRNA00114	long intergenic non-protein coding RNA 114	ncRNA	0.008940	0.408163	416(AAGTACATAGTGTTTC,-,0.00),417(AGTACATAGTGTTTCC,+,0.00),440(GGGAACATTCTGTTCC,-,0.00),441(GGAACATTCTGTTCCC,+,0.00)
chunk0161_421_1	chr5	178304805	178305397	+	0	NA	intron (NM_173465, intron 3 of 28)	intron (NM_173465, intron 3 of 28)	-72279	NM_001278346	85007	Hs.248746	NM_153373	ENSG00000175309	PHYKPL	AGXT2L2|PHLU	5-phosphohydroxy-L-lysine phospho-lyase	protein-coding	0.018581	0.456998	
chunk0212_336_1	chrX	145066038	145066349	+	0	NA	Intergenic	MER74C|LTR|ERVL	-181394	NM_001009614	494118		NM_001009614	ENSG00000203923	SPANXN1	CT11.6	SPANX family member N1	protein-coding	0.009646	0.512821	100(GGGACAGTATGCACTC,+,0.00)
chunk0084_2_1	chr18	109100	109584	+	0	NA	non-coding (NR_033770, exon 1 of 5)	non-coding (NR_033770, exon 1 of 5)	277	NR_033770	727758	Hs.585843	NR_033770	ENSG00000263006	ROCK1P1	ROCK1P	Rho associated coiled-coil containing protein kinase 1 pseudogene 1	pseudo	0.010331	0.482474	
chunk0076_11_1	chr16	58684771	58685349	+	0	NA	promoter-TSS (NM_018231)	promoter-TSS (NM_018231)	-283	NM_018231	55238	Hs.10499	NM_018231	ENSG00000103042	SLC38A7	SNAT7	solute carrier family 38 member 7	protein-coding	0.036332	0.531952	
chunk0023_189_1	chr10	25018215	25018654	+	0	NA	intron (NM_024838, intron 1 of 2)	MER58A|DNA|hAT-Charlie	1855	NM_024838	79896	Hs.645274	NM_024838	ENSG00000185875	THNSL1	TSH1	threonine synthase like 1	protein-coding	0.006834	0.377273	
chunk0185_435_1	chr7	134887692	134887891	+	0	NA	intron (NM_033157, intron 3 of 14)	intron (NM_033157, intron 3 of 14)	-3609	NM_033139	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.020101	0.465000	
chunk0104_203_1	chr2	175829227	175829577	+	0	NA	Intergenic	L1ME1|LINE|L1	172943	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.000000	0.353276	
chunk0055_263_1	chr13	63554113	63554674	+	0	NA	Intergenic	Intergenic	-183042	NR_002171	283491	Hs.363054	NR_002171		OR7E156P	-	olfactory receptor family 7 subfamily E member 156 pseudogene	pseudo	0.001783	0.304270	
chunk0073_24_1	chr16	2331901	2332190	+	0	NA	intron (NM_001089, intron 1 of 32)	intron (NM_001089, intron 1 of 32)	8701	NM_001089	21	Hs.26630	NM_001089	ENSG00000167972	ABCA3	ABC-C|ABC3|EST111653|LBM180|SMDP3	ATP binding cassette subfamily A member 3	protein-coding	0.020761	0.448276	
chunk0086_16_1	chr18	12264892	12265269	+	0	NA	intron (NM_001279, intron 3 of 4)	intron (NM_001279, intron 3 of 4)	10719	NR_036468									0.005305	0.396825	
chunk0187_5_1	chr8	433506	433718	+	0	NA	intron (NM_183420, intron 4 of 9)	intron (NM_183420, intron 4 of 9)	26804	NM_012173	26260	Hs.438454	NM_012173	ENSG00000147364	FBXO25	FBX25	F-box protein 25	protein-coding	0.009434	0.403756	
chunk0197_456_1	chr8	127879445	127879890	+	0	NA	intron (NR_003367, intron 1 of 8)	MIR|SINE|MIR	69056	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.020225	0.497758	
chunk0162_90_1	chr6	2178844	2179399	+	0	NA	intron (NM_001500, intron 1 of 10)	intron (NM_001500, intron 1 of 10)	-3130	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.007207	0.321942	
chunk0160_30_1	chr5	149280737	149280952	+	0	NA	intron (NM_152406, intron 1 of 18)	intron (NM_152406, intron 1 of 18)	9006	NM_152406	134265	Hs.62930	NM_152406	ENSG00000157510	AFAP1L1	-	actin filament associated protein 1 like 1	protein-coding	0.004651	0.504630	
chunk0105_184_1	chr2	187541568	187542185	+	0	NA	intron (NM_001032281, intron 1 of 6)	L2|LINE|L2	12616	NM_006287	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.009724	0.386731	
chunk0198_270_1	chr8	135282417	135283042	+	0	NA	intron (NR_120396, intron 1 of 4)	L2a|LINE|L2	48598	NR_120396	286094	Hs.440978	NR_026706	ENSG00000254083	LINC01591	-	long intergenic non-protein coding RNA 1591	ncRNA	0.004800	0.396166	
chunk0088_112_1	chr18	45416063	45416635	+	0	NA	intron (NM_001242692, intron 1 of 20)	intron (NM_001242692, intron 1 of 20)	90687	NR_110899	101927980	Hs.591058	NR_110899		SLC14A2-AS1	-	SLC14A2 antisense RNA 1	ncRNA	0.012238	0.364747	
chunk0013_361_1	chr1	172373069	172373353	+	0	NA	intron (NM_015569, intron 17 of 20)	intron (NM_015569, intron 17 of 20)	-47477	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.003521	0.301754	
chunk0078_162_1	chr17	4235367	4236019	+	0	NA	intron (NR_047571, intron 2 of 23)	intron (NR_047571, intron 2 of 23)	28154	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.009202	0.369066	217(AGGTACACAAAGTACC,-,0.00),218(GGTACACAAAGTACCT,+,0.00)
chunk0057_245_1	chr13	104590269	104590611	+	0	NA	Intergenic	Intergenic	-875427	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.005848	0.370262	327(TAGAGCAGAGTGTGCC,-,0.00)
chunk0073_353_1	chr16	14969746	14970246	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-4739	NM_001285447	23042	Hs.370781	NM_015027	ENSG00000179889	PDXDC1	LP8165	pyridoxal dependent decarboxylase domain containing 1	protein-coding	0.006000	0.389222	
chunk0043_323_1	chr12	22415660	22416112	+	0	NA	Intergenic	Intergenic	-81172	NM_003034	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.006637	0.388521	
chunk0110_112_1	chr20	12102211	12102563	+	0	NA	Intergenic	Intergenic	184522	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.005682	0.334278	
chunk0051_424_1	chr12	122750181	122750380	+	0	NA	Intergenic	Intergenic	-2541	NM_003677	8562	Hs.22393	NM_003677	ENSG00000139726	DENR	DRP|DRP1|SMAP-3	density regulated re-initiation and release factor	protein-coding	0.020101	0.390000	
chunk0207_88_1	chrX	9463010	9463460	+	0	NA	promoter-TSS (NM_001139468)	promoter-TSS (NM_001139468)	-60	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.033333	0.521064	
chunk0016_459_1	chr1	204256560	204256904	+	0	NA	intron (NM_014935, intron 9 of 22)	intron (NM_014935, intron 9 of 22)	-42640	NM_198447	127845	Hs.532401	NM_198447	ENSG00000174567	GOLT1A	CGI-141|GOT1|HMFN1187|YMR292W|hGOT1b	golgi transport 1A	protein-coding	0.026163	0.594203	141(AGGCACAGAGCGTCCC,-,0.00),142(GGCACAGAGCGTCCCT,+,0.00)
chunk0124_266_1	chr3	57216814	57217385	+	0	NA	Intergenic	L1MC4|LINE|L1	-10638	NM_012096	26060	Hs.476415	NM_012096	ENSG00000157500	APPL1	APPL|DIP13alpha|MODY14	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1	protein-coding	0.003503	0.377622	256(AGGTACATCTTGTTCT,-,0.00),257(GGTACATCTTGTTCTT,+,0.00)
chunk0016_204_1	chr1	198699461	198699901	+	0	NA	exon (NM_002838, exon 5 of 33)	exon (NM_002838, exon 5 of 33)	60713	NM_080921	5788	Hs.654514	NM_002838	ENSG00000081237	PTPRC	B220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200	protein tyrosine phosphatase receptor type C	protein-coding	0.027273	0.430839	
chunk0164_282_1	chr6	24489428	24489992	+	0	NA	promoter-TSS (NM_001503)	promoter-TSS (NM_001503)	-88	NM_001503	2822	Hs.533291	NM_001503	ENSG00000112293	GPLD1	GPIPLD|GPIPLDM|PIGPLD|PIGPLD1|PLD	glycosylphosphatidylinositol specific phospholipase D1	protein-coding	0.012411	0.467257	
chunk0100_8_1	chr2	104685719	104686391	+	0	NA	Intergenic	Intergenic	71664	NR_038231	284998	Hs.410180	NR_038231	ENSG00000234177	LINC01114	PANCAT	long intergenic non-protein coding RNA 1114	ncRNA	0.013393	0.436850	
chunk0007_369_1	chr1	85200035	85200441	+	0	NA	intron (NM_032184, intron 1 of 6)	CpG	807	NM_032184	84144	Hs.533853	NM_032184	ENSG00000097096	SYDE2	-	synapse defective Rho GTPase homolog 2	protein-coding	0.049261	0.474201	
chunk0051_358_1	chr12	120899110	120899621	+	0	NA	intron (NM_139015, intron 1 of 10)	intron (NM_139015, intron 1 of 10)	4987	NM_139015	121665	Hs.507087	NM_139015	ENSG00000157837	SPPL3	IMP2|MDHV1887|PRO4332|PSH1|PSL4	signal peptide peptidase like 3	protein-coding	0.003914	0.343750	
chunk0207_27_1	chrX	3362933	3363351	+	0	NA	Intergenic	Intergenic	-16499	NM_015419	25878	Hs.369422	NM_015419	ENSG00000101825	MXRA5	-	matrix remodeling associated 5	protein-coding	0.011962	0.448687	199(GGGAACAGCATGTGCC,-,0.00),200(GGAACAGCATGTGCCG,+,0.00)
chunk0131_238_1	chr3	149376741	149377412	+	0	NA	promoter-TSS (NR_109810)	promoter-TSS (NR_109810)	-702	NR_109810	100874091	Hs.549633	NR_046650	ENSG00000240541	TM4SF1-AS1	-	TM4SF1 antisense RNA 1	ncRNA	0.013413	0.377976	
chunk0167_433_1	chr6	75815214	75815749	+	0	NA	intron (NM_001300899, intron 1 of 32)	L2|LINE|L2	66289	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.007477	0.389925	
chunk0138_430_1	chr4	45174945	45175335	+	0	NA	Intergenic	Tigger10|DNA|TcMar-Tigger	-448506	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.005128	0.301790	
chunk0010_129_1	chr1	114539081	114539517	+	0	NA	Intergenic	HAL1|LINE|L1	-28139	NM_033020	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.011468	0.421053	
chunk0055_62_1	chr13	52706252	52706674	+	0	NA	intron (NM_007015, intron 6 of 6)	MIRb|SINE|MIR	33349	NM_007015	11061	Hs.421391	NM_007015	ENSG00000136110	CNMD	BRICD3|CHM-I|CHM1|LECT1|MYETS1	chondromodulin	protein-coding	0.004739	0.347518	
chunk0072_30_1	chr16	695504	695971	+	0	NA	exon (NM_153350, exon 3 of 6)	exon (NM_153350, exon 3 of 6)	-5313	NM_032259	84219	Hs.459632	NM_032259	ENSG00000127580	WDR24	C16orf21|JFP7	WD repeat domain 24	protein-coding	0.100642	0.677350	
chunk0070_90_1	chr15	70284895	70285131	+	0	NA	Intergenic	Intergenic	-187096	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.004237	0.531646	
chunk0034_261_1	chr11	34422349	34422721	+	0	NA	Intergenic	Intergenic	-16390	NM_001752	847	Hs.502302	NM_001752	ENSG00000121691	CAT	-	catalase	protein-coding	0.008065	0.394102	
chunk0085_115_1	chr18	2916929	2917482	+	0	NA	3' UTR (NM_014646, exon 20 of 20)	3' UTR (NM_014646, exon 20 of 20)	29418	NR_026659	727896	Hs.673126	NR_026659		LOC727896	-	cysteine and histidine rich domain containing 1 pseudogene	pseudo	0.007233	0.368231	
chunk0118_291_1	chr22	34189407	34189730	+	0	NA	Intergenic	Intergenic	-269140	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.003096	0.429012	
chunk0176_43_1	chr7	10757024	10757343	+	0	NA	Intergenic	Intergenic	183003	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.006270	0.371875	
chunk0147_366_1	chr4	185865950	185866432	+	0	NA	intron (NM_021069, intron 1 of 20)	intron (NM_021069, intron 1 of 20)	-53935	NM_001145670	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.008299	0.407867	
chunk0147_377_1	chr4	186107161	186107442	+	0	NA	Intergenic	Intergenic	-37540	NM_015398	25854	Hs.744961	NM_015398	ENSG00000109794	FAM149A	MST119|MSTP119	family with sequence similarity 149 member A	protein-coding	0.000000	0.294326	
chunk0204_164_1	chr9	95899807	95900080	+	0	NA	intron (NM_001010895, intron 3 of 13)	MER2|DNA|TcMar-Tigger	-23966	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.003663	0.284672	
chunk0091_148_1	chr19	7398708	7399178	+	0	NA	intron (NM_015318, intron 1 of 20)	intron (NM_015318, intron 1 of 20)	3830	NM_015318	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.012766	0.420382	
chunk0062_75_1	chr14	67700076	67700308	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-1694	NM_152443	145226	Hs.415322	NM_152443	ENSG00000139988	RDH12	LCA13|RP53|SDR7C2	retinol dehydrogenase 12	protein-coding	0.004310	0.364807	
chunk0075_165_1	chr16	51740214	51740511	+	0	NA	Intergenic	Intergenic	-22157	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.003367	0.372483	
chunk0017_197_1	chr1	207510169	207510629	+	0	NA	intron (NM_000651, intron 3 of 46)	intron (NM_000651, intron 3 of 46)	14271	NM_000651	1378	Hs.334019	NM_000573	ENSG00000203710	CR1	C3BR|C4BR|CD35|KN	complement C3b/C4b receptor 1 (Knops blood group)	protein-coding	0.004348	0.338395	
chunk0195_226_1	chr8	97267223	97267844	+	0	NA	intron (NR_125390, intron 2 of 2)	L2c|LINE|L2	10415	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.000000	0.385852	
chunk0114_116_1	chr21	9622600	9622905	+	0	NA	Intergenic	Intergenic	198309	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.006557	0.450980	
chunk0084_100_1	chr17	75607504	75608068	+	0	NA	intron (NM_001309242, intron 20 of 62)	L1MB4|LINE|L1	19728	NM_001309242	80022	Hs.390817	NM_001080847	ENSG00000266714	MYO15B	MYO15BP	myosin XVB	protein-coding	0.019504	0.476106	
chunk0159_20_1	chr5	136375826	136376421	+	0	NA	Intergenic	Intergenic	-10647	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.008403	0.404362	105(AAGGACACTGTGTAAT,-,0.00)
chunk0140_72_1	chr4	67481800	67482012	+	0	NA	intron (NM_001812, intron 17 of 18)	L1PB1|LINE|L1	-59906	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.004717	0.370892	
chunk0160_286_1	chr5	157999447	157999865	+	0	NA	Intergenic	L1MC4|LINE|L1	-140481	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.004785	0.384248	217(GGGTACACAATGTCCA,-,0.00),218(GGTACACAATGTCCAT,+,0.00)
chunk0095_16_1	chr2	12160969	12161314	+	0	NA	intron (NR_110196, intron 2 of 5)	L1M4a2|LINE|L1	-37989	NR_037452	100500884		NR_037452	ENSG00000264089	MIR3681	-	microRNA 3681	ncRNA	0.000000	0.430636	
chunk0170_75_1	chr6	109814493	109814975	+	0	NA	intron (NM_014845, intron 22 of 22)	L1MC4|LINE|L1	-61518	NR_106988									0.002075	0.366460	173(AAGCTCAGAGTGTTCC,-,0.00),174(AGCTCAGAGTGTTCCA,+,0.00),271(TGGCACAAGATGTTCT,-,0.00),272(GGCACAAGATGTTCTA,+,0.00),287(AGGCTCATCATGTCCT,-,0.00),288(GGCTCATCATGTCCTT,+,0.00)
chunk0154_324_1	chr5	84443276	84443832	+	0	NA	Intergenic	L1MC2|LINE|L1	-58687	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.000000	0.321364	
chunk0140_13_1	chr4	65430492	65430691	+	0	NA	intron (NM_001281765, intron 5 of 17)	MIR|SINE|MIR	-239370	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.005025	0.330000	40(AGAAACATTATGTGCC,-,0.00),41(GAAACATTATGTGCCA,+,0.00)
chunk0059_423_1	chr14	38230728	38231062	+	0	NA	Intergenic	Intergenic	22896	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.002994	0.301493	
chunk0196_435_1	chr8	116485171	116485393	+	0	NA	Intergenic	Intergenic	-160223	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.009009	0.385650	
chunk0053_191_1	chr13	31612921	31613420	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-126372	NM_130806	122042	Hs.680763	NM_130806	ENSG00000133105	RXFP2	GPR106|GREAT|INSL3R|LGR8|LGR8.1|RXFPR2	relaxin family peptide receptor 2	protein-coding	0.000000	0.456000	305(AGGCACACTGTGTCCC,-,0.00),306(GGCACACTGTGTCCCA,+,0.00)
chunk0019_141_1	chr1	225714757	225715074	+	0	NA	Intergenic	Intergenic	-61772	NM_018212	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.003155	0.424528	
chunk0105_55_1	chr2	183244114	183244851	+	0	NA	Intergenic	L2b|LINE|L2	120127	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.002714	0.380759	
chunk0080_291_1	chr17	31467988	31468324	+	0	NA	intron (NM_032932, intron 3 of 14)	intron (NM_032932, intron 3 of 14)	-19845	NM_001303542	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.017857	0.563798	
chunk0049_387_1	chr12	96101298	96101603	+	0	NA	Intergenic	AluSz|SINE|Alu	-57930	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.013115	0.447712	
chunk0057_80_1	chr13	98463254	98463628	+	0	NA	intron (NM_003576, intron 7 of 10)	(AACAG)n|Simple_repeat|Simple_repeat	58684	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.010695	0.432000	
chunk0192_263_1	chr8	66009147	66009914	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-12026	NM_033105	85479	Hs.491885	NM_033105	ENSG00000147570	DNAJC5B	CSP-beta	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding	0.005215	0.432292	
chunk0100_401_1	chr2	119315564	119315836	+	0	NA	intron (NM_001017927, intron 5 of 6)	intron (NM_001017927, intron 5 of 6)	50982	NM_001017927	130355	Hs.99488	NM_001017927	ENSG00000186132	C2orf76	AIM29	chromosome 2 open reading frame 76	protein-coding	0.003676	0.362637	
chunk0052_13_1	chr13	20025546	20025998	+	0	NA	intron (NM_001190964, intron 8 of 25)	Tigger3a|DNA|TcMar-Tigger	66938	NM_001190965	7750	Hs.507433	NM_003453	ENSG00000121741	ZMYM2	FIM|MYM|RAMP|SCLL|ZNF198	zinc finger MYM-type containing 2	protein-coding	0.008850	0.379691	
chunk0074_400_1	chr16	35433250	35433484	+	0	NA	Intergenic	Intergenic	47229	NR_026980	146481	Hs.316564	NR_026980		FRG2DP	-	FSHD region gene 2 family member D, pseudogene	pseudo	0.004274	0.531915	
chunk0026_259_1	chr10	66812808	66813375	+	0	NA	intron (NM_001127384, intron 7 of 17)	intron (NM_001127384, intron 7 of 17)	-112943	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.001764	0.336268	245(AAGAACATAAAGTGCA,-,0.00),246(AGAACATAAAGTGCAG,+,0.00),319(AGGTACATCATGTTCA,-,0.00),320(GGTACATCATGTTCAG,+,0.00)
chunk0007_270_1	chr1	83511348	83511846	+	0	NA	Intergenic	Intergenic	348949	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.004016	0.352705	
chunk0114_103_1	chr21	9530868	9531260	+	0	NA	Intergenic	Intergenic	289997	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.022959	0.569975	
chunk0046_291_1	chr12	62138430	62138818	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	54215	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.005155	0.429306	170(CAGAACACACTGAACT,-,0.00),171(AGAACACACTGAACTG,+,0.00)
chunk0194_180_1	chr8	85146356	85147034	+	0	NA	TTS (NM_033402)	TTS (NM_033402)	-30689	NM_001083588	1875	Hs.445758	NM_001951	ENSG00000133740	E2F5	E2F-5	E2F transcription factor 5	protein-coding	0.000000	0.371134	
chunk0164_428_1	chr6	27472188	27472513	+	0	NA	5' UTR (NM_007149, exon 2 of 6)	5' UTR (NM_007149, exon 2 of 6)	768	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.027692	0.521472	
chunk0206_305_1	chr9	124792052	124792497	+	0	NA	intron (NM_182487, intron 2 of 7)	intron (NM_182487, intron 2 of 7)	-8600	NM_001282715	169611	Hs.357004	NM_182487	ENSG00000185585	OLFML2A	PRO34319	olfactomedin like 2A	protein-coding	0.011236	0.547085	118(TGGCACTACCTGTGCC,-,0.00),119(GGCACTACCTGTGCCC,+,0.00)
chunk0025_300_1	chr10	57411732	57411940	+	0	NA	Intergenic	Intergenic	-107277	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.000000	0.277512	
chunk0039_267_1	chr11	102364796	102365539	+	0	NA	intron (NM_001256166, intron 5 of 8)	L2a|LINE|L2	17793	NM_001256163	329	Hs.696238	NM_001166	ENSG00000110330	BIRC2	API1|HIAP2|Hiap-2|MIHB|RNF48|c-IAP1|cIAP1	baculoviral IAP repeat containing 2	protein-coding	0.004038	0.380376	
chunk0103_218_1	chr2	164009920	164010402	+	0	NA	Intergenic	Intergenic	-274158	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.006224	0.399586	
chunk0035_353_1	chr11	48453619	48453864	+	0	NA	Intergenic	L1PA7|LINE|L1	-35052	NM_001005512	403253	Hs.554532	NM_001005512	ENSG00000237388	OR4A47	OR11-113	olfactory receptor family 4 subfamily A member 47	protein-coding	0.004082	0.540650	
chunk0024_315_1	chr10	42769590	42770113	+	0	NA	Intergenic	MIRb|SINE|MIR	-12655	NM_014753	9790	Hs.10848	NM_014753	ENSG00000165733	BMS1	ACC|BMS1L	BMS1 ribosome biogenesis factor	protein-coding	0.024857	0.534351	110(CAGGACACCGAGTCCT,-,0.00),111(AGGACACCGAGTCCTT,+,0.00)
chunk0085_465_1	chr18	11851140	11851339	+	0	NA	promoter-TSS (NM_020412)	promoter-TSS (NM_020412)	-151	NM_020412	57132	Hs.656244	NM_020412	ENSG00000255112	CHMP1B	C10orf2|C18-ORF2|C18orf2|CHMP1.5|Vps46-2|Vps46B|hVps46-2	charged multivesicular body protein 1B	protein-coding	0.090452	0.585000	
chunk0008_456_1	chr1	99766462	99766785	+	0	NA	promoter-TSS (NM_001013660)	promoter-TSS (NM_001013660)	-830	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.027864	0.462963	
chunk0129_271_1	chr3	122745868	122746528	+	0	NA	intron (NM_024610, intron 6 of 7)	intron (NM_024610, intron 6 of 7)	47621	NM_024610	79663	Hs.29169	NM_024610	ENSG00000169087	HSPBAP1	PASS1	HSPB1 associated protein 1	protein-coding	0.004545	0.340393	
chunk0164_354_1	chr6	25478851	25479343	+	0	NA	intron (NM_017640, intron 11 of 36)	intron (NM_017640, intron 11 of 36)	-173104	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.002033	0.377282	275(AGAGACAGAATGTTCC,-,0.00),276(GAGACAGAATGTTCCC,+,0.00)
chunk0003_302_1	chr1	37563619	37564039	+	0	NA	intron (NM_003462, intron 5 of 5)	intron (NM_003462, intron 5 of 5)	6910	NM_003462	7802	Hs.406050	NM_003462	ENSG00000163879	DNALI1	P28|dJ423B22.5|hp28	dynein axonemal light intermediate chain 1	protein-coding	0.009524	0.475059	
chunk0075_415_1	chr16	57266018	57266599	+	0	NA	intron (NM_015993, intron 1 of 3)	intron (NM_015993, intron 1 of 3)	18364	NM_015993	51090	Hs.632215	NM_015993	ENSG00000102934	PLLP	PMLP|TM4SF11	plasmolipin	protein-coding	0.024096	0.544674	
chunk0106_148_1	chr2	200300234	200300604	+	0	NA	Intergenic	Intergenic	-5462	NM_001282743	26010	Hs.120323	NM_015535	ENSG00000196141	SPATS2L	DNAPTP6|SGNP	spermatogenesis associated serine rich 2 like	protein-coding	0.002703	0.398922	
chunk0028_82_1	chr10	83853528	83853925	+	0	NA	Intergenic	L1PA17|LINE|L1	-285703	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.005038	0.334171	
chunk0100_344_1	chr2	117178692	117179166	+	0	NA	Intergenic	MER92C|LTR|ERV1	-635750	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.004219	0.349474	274(AAGATCAGAGTGTTCC,-,0.00),275(AGATCAGAGTGTTCCA,+,0.00)
chunk0186_13_1	chr7	135678342	135678812	+	0	NA	Intergenic	Intergenic	16104	NM_001130929	647087	Hs.200022	NM_001130929	ENSG00000243317	STMP1	C7orf73|PL-5283	short transmembrane mitochondrial protein 1	protein-coding	0.006383	0.346072	
chunk0099_436_1	chr2	102976003	102976285	+	0	NA	Intergenic	Intergenic	214113	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.014184	0.466431	95(GTGTACTCTCTGTTCT,-,0.00),96(TGTACTCTCTGTTCTT,+,0.00)
chunk0186_72_1	chr7	137195867	137196640	+	0	NA	Intergenic	(TGTA)n|Simple_repeat|Simple_repeat	-31912	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.005175	0.335917	
chunk0168_172_1	chr6	83894827	83895439	+	0	NA	intron (NM_016230, intron 3 of 15)	intron (NM_016230, intron 3 of 15)	35482	NM_016230	51167	Hs.5741	NM_016230	ENSG00000065615	CYB5R4	NCB5OR|cb5/cb5R|dJ676J13.1	cytochrome b5 reductase 4	protein-coding	0.013072	0.473083	
chunk0128_187_1	chr3	107458832	107459264	+	0	NA	intron (NR_110039, intron 1 of 2)	intron (NR_110039, intron 1 of 2)	28118	NR_110039	101929607	Hs.252565	NR_110039	ENSG00000273125	LINC01990	-	long intergenic non-protein coding RNA 1990	ncRNA	0.000000	0.418014	243(CAGAACAGCATGGTCC,-,0.00),244(AGAACAGCATGGTCCT,+,0.00)
chunk0039_345_1	chr11	105449943	105450480	+	0	NA	Intergenic	L1M4a2|LINE|L1	-159862	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.003724	0.301115	350(TGGGACAGTGAGTGCT,-,0.00),351(GGGACAGTGAGTGCTC,+,0.00)
chunk0109_280_1	chr20	8121731	8121945	+	0	NA	Intergenic	Intergenic	-10427	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.004673	0.358140	
chunk0051_196_1	chr12	116298230	116298489	+	0	NA	Intergenic	Intergenic	-21173	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.003861	0.480769	
chunk0033_165_1	chr11	15662283	15662679	+	0	NA	intron (NM_001293172, intron 1 of 2)	L2a|LINE|L2	18596	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.002525	0.415617	
chunk0065_65_1	chr15	23039259	23039488	+	0	NA	intron (NM_001102610, intron 1 of 21)	CpG	300	NM_052903	114791	Hs.533898	NM_052903	ENSG00000275835	TUBGCP5	GCP5	tubulin gamma complex associated protein 5	protein-coding	0.122271	0.760870	
chunk0182_385_1	chr7	100141643	100142021	+	0	NA	Intergenic	Intergenic	-7075	NM_001008395	389541	Hs.406520	NM_001008395	ENSG00000188186	LAMTOR4	C7orf59	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4	protein-coding	0.010582	0.448549	
chunk0011_377_1	chr1	153751939	153752406	+	0	NA	intron (NM_023015, intron 7 of 29)	intron (NM_023015, intron 7 of 29)	-23120	NM_024330	11000	Hs.438723	NM_024330	ENSG00000143554	SLC27A3	ACSVL3|FATP3|VLCS-3	solute carrier family 27 member 3	protein-coding	0.004283	0.452991	247(TAGAACATGTTGTTCC,-,0.00),248(AGAACATGTTGTTCCT,+,0.00)
chunk0011_366_1	chr1	153360683	153360927	+	0	NA	exon (NM_002965, exon 3 of 3)	exon (NM_002965, exon 3 of 3)	2951	NM_002965	6280	Hs.112405	NM_002965	ENSG00000163220	S100A9	60B8AG|CAGB|CFAG|CGLB|L1AG|LIAG|MAC387|MIF|MRP14|NIF|P14	S100 calcium binding protein A9	protein-coding	0.036885	0.628571	
chunk0171_300_1	chr6	128601120	128601583	+	0	NA	Intergenic	Intergenic	-80677	NM_001291981	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.006479	0.385776	
chunk0085_32_1	chr18	519387	519635	+	0	NA	Intergenic	Intergenic	-18782	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.008065	0.417671	
chunk0061_328_1	chr14	63179502	63179930	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-24668	NM_020663	57381	Hs.656339	NM_020663	ENSG00000126785	RHOJ	ARHJ|RASL7B|TC10B|TCL	ras homolog family member J	protein-coding	0.011682	0.454545	
chunk0078_412_1	chr16	89153950	89154317	+	0	NA	exon (NM_001243279, exon 11 of 11)	exon (NM_001243279, exon 11 of 11)	-5087	NR_024347	283860	Hs.739138	NM_173617	ENSG00000180422	LINC00304	C16orf81|NCRNA00304	long intergenic non-protein coding RNA 304	ncRNA	0.049046	0.657609	
chunk0121_415_1	chr3	25739165	25739580	+	0	NA	intron (NM_001145295, intron 5 of 10)	MER58A|DNA|hAT-Charlie	44126	NM_001145293	55768	Hs.368960	NM_018297	ENSG00000151092	NGLY1	CDDG|CDG1V|PNG1|PNGase	N-glycanase 1	protein-coding	0.007229	0.314904	
chunk0178_429_1	chr7	41148623	41148942	+	0	NA	Intergenic	Intergenic	47178	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.003135	0.381250	
chunk0141_197_1	chr4	83962555	83962815	+	0	NA	Intergenic	LTR18A|LTR|ERVL	336484	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.011538	0.459770	
chunk0176_60_1	chr7	11214847	11215422	+	0	NA	Intergenic	Intergenic	241262	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.006957	0.380208	
chunk0130_433_1	chr3	140924412	140924927	+	0	NA	Intergenic	Intergenic	-17151	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.009709	0.470930	
chunk0061_209_1	chr14	60363312	60363636	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	114226	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.006173	0.412308	
chunk0162_287_1	chr6	6225842	6226230	+	0	NA	intron (NM_000129, intron 6 of 14)	intron (NM_000129, intron 6 of 14)	-56601	NR_107007	102466866		NR_107007	ENSG00000263572	MIR7853	hsa-mir-7853	microRNA 7853	ncRNA	0.002577	0.380463	
chunk0122_272_1	chr3	35508448	35508751	+	0	NA	Intergenic	L1MEd|LINE|L1	-114576	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.009901	0.391447	94(AAAAACAAAATGTCCT,-,0.00),95(AAAACAAAATGTCCTT,+,0.00)
chunk0014_147_1	chr1	178094188	178094705	+	0	NA	promoter-TSS (NR_027982)	promoter-TSS (NR_027982)	-453	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.110251	0.725869	
chunk0165_175_1	chr6	34338239	34338660	+	0	NA	intron (NM_006703, intron 2 of 4)	intron (NM_006703, intron 2 of 4)	54231	NM_006703	11165	Hs.188882	NM_006703	ENSG00000272325	NUDT3	DIPP|DIPP-1|DIPP1	nudix hydrolase 3	protein-coding	0.007126	0.419431	
chunk0148_204_1	chr5	8538576	8539375	+	0	NA	Intergenic	L1ME2z|LINE|L1	78050	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.010013	0.327500	
chunk0068_442_1	chr15	59669503	59669755	+	0	NA	intron (NM_004330, intron 7 of 9)	intron (NM_004330, intron 7 of 9)	-12091	NM_004492	2958	Hs.512934	NM_004492	ENSG00000140307	GTF2A2	HsT18745|T18745|TF2A2|TFIIA|TFIIA-12|TFIIA-gamma|TFIIAS	general transcription factor IIA subunit 2	protein-coding	0.003968	0.387352	
chunk0110_462_1	chr20	21550995	21551194	+	0	NA	Intergenic	Intergenic	-18930	NR_109880	101929625	Hs.542413	NR_109880		LINC01727	-	long intergenic non-protein coding RNA 1727	ncRNA	0.000000	0.305000	
chunk0070_287_1	chr15	74595115	74595647	+	0	NA	intron (NM_001307939, intron 8 of 8)	L2c|LINE|L2	-12991	NM_003992	1198	Hs.511790	NM_001292	ENSG00000179335	CLK3	PHCLK3|PHCLK3/152	CDC like kinase 3	protein-coding	0.007519	0.527205	
chunk0093_299_1	chr19	52723503	52723970	+	0	NA	intron (NM_030972, intron 3 of 6)	LTR5B|LTR|ERVK	6146	NM_030972	81856	Hs.143951	NM_030972	ENSG00000213020	ZNF611	-	zinc finger protein 611	protein-coding	0.012848	0.472222	
chunk0005_393_1	chr1	62286890	62287108	+	0	NA	intron (NM_181712, intron 1 of 9)	intron (NM_181712, intron 1 of 9)	32413	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.022936	0.561644	29(AAACACACCCAGTTCT,-,0.00)
chunk0190_273_1	chr8	37472352	37473115	+	0	NA	intron (NR_121620, intron 3 of 6)	intron (NR_121620, intron 3 of 6)	21180	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.017038	0.438482	
chunk0047_215_1	chr12	71664432	71664631	+	0	NA	promoter-TSS (NM_144982)	promoter-TSS (NM_144982)	-562	NM_144982	196441	Hs.245798	NM_144982	ENSG00000133858	ZFC3H1	CCDC131|CSRC2|PSRC2	zinc finger C3H1-type containing	protein-coding	0.035176	0.565000	
chunk0122_334_1	chr3	37144590	37145355	+	0	NA	intron (NM_017724, intron 3 of 13)	intron (NM_017724, intron 3 of 13)	29633	NM_006309	9209	Hs.740522	NM_006309	ENSG00000093167	LRRFIP2	HUFI-2	LRR binding FLII interacting protein 2	protein-coding	0.002614	0.312010	
chunk0045_299_1	chr12	50527186	50527385	+	0	NA	intron (NM_173602, intron 1 of 37)	intron (NM_173602, intron 1 of 37)	22300	NM_173602	57609	Hs.505516	NM_020849	ENSG00000066084	DIP2B	-	disco interacting protein 2 homolog B	protein-coding	0.010050	0.410000	
chunk0205_23_1	chr9	105278958	105279157	+	0	NA	intron (NM_001286730, intron 1 of 15)	intron (NM_001286730, intron 1 of 15)	34444	NM_001286730	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.020101	0.465000	45(CAGAACAAACTGTGCT,-,0.00),46(AGAACAAACTGTGCTG,+,0.00)
chunk0120_268_1	chr3	9226479	9226678	+	0	NA	intron (NM_001033117, intron 1 of 21)	Plat_L3|LINE|CR1	9683	NR_103443	100288831	Hs.694646	NR_103443	ENSG00000227929	SRGAP3-AS3	-	SRGAP3 antisense RNA 3	ncRNA	0.010050	0.450000	
chunk0025_251_1	chr10	54801128	54801455	+	0	NA	promoter-TSS (NM_001142767)	promoter-TSS (NM_001142767)	0	NM_001142771	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.024465	0.460366	
chunk0113_99_1	chr20	50931450	50931926	+	0	NA	promoter-TSS (NM_001282531)	promoter-TSS (NM_001282531)	-698	NM_001282531	23394	Hs.293736	NM_015339	ENSG00000101126	ADNP	ADNP1|HVDAS|MRD28	activity dependent neuroprotector homeobox	protein-coding	0.063025	0.664570	
chunk0159_94_1	chr5	138036203	138036531	+	0	NA	Intergenic	LTR78|LTR|ERV1	-3254	NM_001101801	51306	Hs.567453	NM_016603	ENSG00000031003	FAM13B	ARHGAP49|C5orf5|FAM13B1|KHCHP|N61	family with sequence similarity 13 member B	protein-coding	0.018293	0.519757	
chunk0059_31_1	chr14	29892202	29892646	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	35269	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.002252	0.361798	
chunk0070_427_1	chr15	78012560	78013173	+	0	NA	exon (NM_144572, exon 9 of 13)	exon (NM_144572, exon 9 of 13)	-18641	NR_026998	91450	Hs.406766	NR_026998		LOC91450	-	uncharacterized LOC91450	ncRNA	0.019576	0.478827	237(GGGAACATTTTGTGCT,-,0.00),238(GGAACATTTTGTGCTG,+,0.00)
chunk0165_107_1	chr6	32411969	32412379	+	0	NA	Intergenic	Intergenic	-5044	NM_001304561	56244	Hs.534471	NM_019602	ENSG00000204290	BTNL2	BTL-II|BTN7|HSBLMHC1|SS2	butyrophilin like 2	protein-coding	0.007317	0.418491	
chunk0094_372_1	chr2	9830485	9830684	+	0	NA	Intergenic	Intergenic	-12858	NM_005680	9014	Hs.584833	NM_005680	ENSG00000115750	TAF1B	MGC:9349|RAF1B|RAFI63|SL1|TAFI63	TATA-box binding protein associated factor, RNA polymerase I subunit B	protein-coding	0.010050	0.450000	
chunk0139_373_1	chr4	60802292	60802779	+	0	NA	Intergenic	Intergenic	-120084	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.342213	
chunk0013_432_1	chr1	173473918	173474361	+	0	NA	intron (NR_037845, intron 1 of 2)	Charlie8|DNA|hAT-Charlie	3016	NR_037845	100506023	Hs.731284	NR_037845		LOC100506023	-	uncharacterized LOC100506023	ncRNA	0.004515	0.409910	
chunk0146_27_1	chr4	155306042	155306364	+	0	NA	Intergenic	MIR3|SINE|MIR	-48013	NR_125937	102724776	Hs.61271	NR_125937	ENSG00000250910	LOC102724776	-	uncharacterized LOC102724776	ncRNA	0.006211	0.383901	204(AGGAACATCCTGTCTT,-,0.00),205(GGAACATCCTGTCTTT,+,0.00)
chunk0091_142_1	chr19	7179374	7180018	+	0	NA	intron (NM_001079817, intron 3 of 20)	MER58A|DNA|hAT-Charlie	110236	NM_001044387	79230	Hs.591380	NM_024341	ENSG00000130544	ZNF557	-	zinc finger protein 557	protein-coding	0.010870	0.462016	
chunk0135_256_1	chr3	189042563	189043293	+	0	NA	Intergenic	Intergenic	-95289	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.005479	0.414501	
chunk0072_194_1	chr15	94293836	94294035	+	0	NA	Intergenic	L1ME1|LINE|L1	-4266	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.005025	0.350000	
chunk0209_216_1	chrX	44714742	44715330	+	0	NA	Intergenic	Intergenic	-128967	NM_022076	63904	Hs.534478	NM_022076	ENSG00000189037	DUSP21	LMWDSP21	dual specificity phosphatase 21	protein-coding	0.003401	0.405772	
chunk0064_169_1	chr14	92308628	92309283	+	0	NA	Intergenic	Intergenic	-13626	NM_153648	123041	Hs.385530	NM_153646	ENSG00000140090	SLC24A4	AI2A5|NCKX4|SHEP6|SLC24A2	solute carrier family 24 member 4	protein-coding	0.015267	0.480183	
chunk0076_157_1	chr16	67323160	67323428	+	0	NA	intron (NM_001100915, intron 1 of 15)	L1M4|LINE|L1	3464	NM_001100915	146212	Hs.299127	NM_001100915	ENSG00000168676	KCTD19	-	potassium channel tetramerization domain containing 19	protein-coding	0.003731	0.382900	
chunk0055_336_1	chr13	69211229	69211636	+	0	NA	Intergenic	L1PA16|LINE|L1	-10914	NR_125752	103689913	Hs.585628	NR_125752	ENSG00000235221	LINC00383	LINC00401	long intergenic non-protein coding RNA 383	ncRNA	0.002457	0.321078	
chunk0171_6_1	chr6	119550049	119550343	+	0	NA	Intergenic	Intergenic	-58894	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.006803	0.437288	83(GGGAACACACAGCTCT,-,0.00),84(GGAACACACAGCTCTG,+,0.00)
chunk0098_154_1	chr2	69976659	69976944	+	0	NA	intron (NR_033872, intron 9 of 10)	intron (NR_033872, intron 9 of 10)	-14536	NM_152792	151516	Hs.516253	NM_152792	ENSG00000244617	ASPRV1	MUNO|SASP|SASPase|Taps	aspartic peptidase retroviral like 1	protein-coding	0.007018	0.527972	55(AGGCACAGAGTGTCCT,-,0.00),56(GGCACAGAGTGTCCTG,+,0.00),183(AGGAACAGAGTGCCCC,-,0.00),184(GGAACAGAGTGCCCCT,+,0.00)
chunk0128_14_1	chr3	103813972	103814482	+	0	NA	Intergenic	Intergenic	-290111	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.352250	
chunk0046_127_1	chr12	57426470	57426988	+	0	NA	Intergenic	Intergenic	-7956	NM_005538	3626	Hs.632722	NM_005538	ENSG00000175189	INHBC	IHBC	inhibin subunit beta C	protein-coding	0.007722	0.414258	482(CTGAACATCAAGTGCT,-,0.00),483(TGAACATCAAGTGCTG,+,0.00)
chunk0090_80_1	chr18	70428384	70428912	+	0	NA	Intergenic	Intergenic	-44057	NR_110764	101060542	Hs.586967	NR_110764	ENSG00000266278	LINC01910	-	long intergenic non-protein coding RNA 1910	ncRNA	0.013258	0.406427	
chunk0094_234_1	chr2	6977453	6977806	+	0	NA	intron (NM_014746, intron 2 of 8)	intron (NM_014746, intron 2 of 8)	-58947	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.014164	0.387006	
chunk0178_289_1	chr7	37511634	37512277	+	0	NA	Intergenic	Intergenic	-62629	NM_001206480	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.010886	0.478261	
chunk0127_89_1	chr3	89777574	89778563	+	0	NA	Intergenic	L1P4|LINE|L1	670544	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005056	0.345455	
chunk0083_355_1	chr17	70449514	70450433	+	0	NA	Intergenic	Intergenic	280438	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.004353	0.365217	42(AAGAACAGTGAGTCCA,-,0.00),43(AGAACAGTGAGTCCAA,+,0.00),143(AAGAACAAGATGTCCT,-,0.00),144(AGAACAAGATGTCCTG,+,0.00),558(AAGGACACTGAGTACC,-,0.00),559(AGGACACTGAGTACCT,+,0.00)
chunk0033_106_1	chr11	14359650	14359873	+	0	NA	promoter-TSS (NM_012250)	promoter-TSS (NM_012250)	-577	NM_012250	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.022422	0.495536	
chunk0081_379_1	chr17	48047009	48047302	+	0	NA	Intergenic	Intergenic	-1169	NM_003204	4779	Hs.514284	NM_003204	ENSG00000082641	NFE2L1	LCR-F1|NRF1|TCF11	nuclear factor, erythroid 2 like 1	protein-coding	0.017065	0.408163	
chunk0037_383_1	chr11	78576680	78576903	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	-1927	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.017937	0.450893	
chunk0084_149_1	chr17	76643553	76644292	+	0	NA	promoter-TSS (NM_001289107)	promoter-TSS (NM_001289107)	-84	NR_110309	55808	Hs.105352	NM_018414	ENSG00000070526	ST6GALNAC1	HSY11339|SIAT7A|ST6GalNAcI|STYI	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	protein-coding	0.010825	0.491892	
chunk0063_257_1	chr14	83096054	83096444	+	0	NA	Intergenic	Intergenic	-1473188	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.005128	0.340153	
chunk0121_113_1	chr3	17359406	17359820	+	0	NA	intron (NM_014744, intron 13 of 21)	intron (NM_014744, intron 13 of 21)	340407	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.002415	0.322892	
chunk0123_101_1	chr3	42224935	42225553	+	0	NA	3' UTR (NM_001042646, exon 16 of 16)	3' UTR (NM_001042646, exon 16 of 16)	38703	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.011327	0.400646	282(GTGACACCGTGTTCCA,+,0.00)
chunk0060_21_1	chr14	39669415	39669779	+	0	NA	Intergenic	Intergenic	-237097	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.005495	0.435616	
chunk0043_41_1	chr12	13375444	13376593	+	0	NA	intron (NR_036555, intron 2 of 2)	intron (NR_036555, intron 2 of 2)	727	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.003481	0.436522	
chunk0078_168_1	chr17	4310015	4310741	+	0	NA	intron (NM_003342, intron 1 of 5)	intron (NM_003342, intron 1 of 5)	-38484	NR_110982	103021295	Hs.741319	NR_110982		LOC103021295	-	uncharacterized LOC103021295	ncRNA	0.004132	0.394773	
chunk0131_374_1	chr3	152206532	152206829	+	0	NA	Intergenic	Intergenic	-61788	NM_207292	4154	Hs.201858	NM_021038	ENSG00000152601	MBNL1	EXP|MBNL	muscleblind like splicing regulator 1	protein-coding	0.000000	0.359060	249(AATACATGATGTGCTT,+,0.00)
chunk0192_215_1	chr8	65159861	65160383	+	0	NA	Intergenic	Intergenic	20218	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.011494	0.361377	
chunk0111_263_1	chr20	31060326	31060706	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-197148	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.013158	0.370079	
chunk0156_126_1	chr5	106639715	106640330	+	0	NA	Intergenic	Intergenic	370992	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.004878	0.358766	
chunk0014_18_1	chr1	174472166	174472381	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	24199	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.000000	0.462963	
chunk0088_118_1	chr18	45680359	45680704	+	0	NA	intron (NM_001242692, intron 20 of 20)	intron (NM_001242692, intron 20 of 20)	-43592	NM_001308279	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.005797	0.369942	
chunk0090_245_1	chr18	73881415	73881862	+	0	NA	Intergenic	MER72B|LTR|ERV1	266126	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.002237	0.448661	
chunk0162_24_1	chr6	880123	880737	+	0	NA	Intergenic	Intergenic	11932	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.009772	0.447154	
chunk0025_6_1	chr10	47183786	47184066	+	0	NA	Intergenic	Intergenic	-116298	NM_004962	2662	Hs.2171	NM_004962	ENSG00000266524	GDF10	BIP|BMP-3b|BMP3B	growth differentiation factor 10	protein-coding	0.014286	0.558719	101(AAGCACAGCCTCTCCC,-,0.00),102(AGCACAGCCTCTCCCT,+,0.00)
chunk0001_133_1	chr1	5551585	5551961	+	0	NA	Intergenic	Intergenic	-12298	NR_039612									0.010638	0.496021	
chunk0134_144_1	chr3	177618840	177619819	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	177408	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.010215	0.374490	
chunk0098_58_1	chr2	66802865	66803425	+	0	NA	Intergenic	Intergenic	-99918	NR_110264	101927577	Hs.380543	NR_110264	ENSG00000237179	LINC01797	-	long intergenic non-protein coding RNA 1797	ncRNA	0.010714	0.395722	223(ATGGACTTTGTGTCCT,-,0.00),224(TGGACTTTGTGTCCTA,+,0.00)
chunk0169_67_1	chr6	98979724	98980132	+	0	NA	Intergenic	Intergenic	-31922	NM_001278716	26235	Hs.536850	NM_012160	ENSG00000112234	FBXL4	FBL4|FBL5|MTDPS13	F-box and leucine rich repeat protein 4	protein-coding	0.007353	0.410758	83(CAGAACTTGTTGTACT,-,0.00),84(AGAACTTGTTGTACTC,+,0.00)
chunk0081_79_1	chr17	39319827	39320126	+	0	NA	intron (NM_001184906, intron 2 of 13)	intron (NM_001184906, intron 2 of 13)	81680	NM_032875	84961	Hs.462946	NM_032875	ENSG00000108306	FBXL20	Fbl2|Fbl20	F-box and leucine rich repeat protein 20	protein-coding	0.013378	0.390000	
chunk0206_377_1	chr9	126364170	126364422	+	0	NA	intron (NM_033446, intron 2 of 9)	intron (NM_033446, intron 2 of 9)	37452	NM_033446	89853	Hs.162659	NM_033446	ENSG00000196814	MVB12B	C9orf28|FAM125B	multivesicular body subunit 12B	protein-coding	0.019841	0.470356	
chunk0067_68_1	chr15	41244235	41244649	+	0	NA	intron (NM_007236, intron 2 of 6)	intron (NM_007236, intron 2 of 6)	13203	NM_007236	11261	Hs.406234	NM_007236	ENSG00000187446	CHP1	CHP|SLC9A1BP|SPAX9|Sid470p|p22|p24	calcineurin like EF-hand protein 1	protein-coding	0.002415	0.409639	243(TGGACAAAATGTTCAG,+,0.00)
chunk0136_98_1	chr4	2877309	2877677	+	0	NA	intron (NM_014190, intron 2 of 15)	L1ME3|LINE|L1	33343	NM_001286645	118	Hs.183706	NM_001119	ENSG00000087274	ADD1	ADDA	adducin 1	protein-coding	0.002717	0.365854	
chunk0131_232_1	chr3	149332134	149333154	+	0	NA	intron (NM_138786, intron 2 of 5)	MIRb|SINE|MIR	828	NM_001184723	116441	Hs.22026	NM_138786	ENSG00000163762	TM4SF18	L6D	transmembrane 4 L six family member 18	protein-coding	0.000980	0.339863	797(GAGAACATACTGTTTT,-,0.00),798(AGAACATACTGTTTTT,+,0.00)
chunk0070_24_1	chr15	69210624	69210889	+	0	NA	intron (NM_015554, intron 2 of 4)	MER58A|DNA|hAT-Charlie	50122	NM_015554	26035	Hs.183006	NM_015554	ENSG00000138604	GLCE	HSEPI	glucuronic acid epimerase	protein-coding	0.000000	0.383459	
chunk0114_405_1	chr20	63815352	63815789	+	0	NA	intron (NR_110081, intron 1 of 2)	intron (NR_110081, intron 1 of 2)	7494	NR_110081	101928604	Hs.676054	NR_110081		ZBTB46-AS1	-	ZBTB46 antisense RNA 1	ncRNA	0.004577	0.630137	
chunk0172_21_1	chr6	132931403	132932274	+	0	NA	Intergenic	Intergenic	-17510	NR_039664									0.006889	0.403670	
chunk0012_148_1	chr1	157701700	157702369	+	0	NA	Intergenic	Intergenic	-1177	NM_052939	115352	Hs.292449	NM_052939	ENSG00000160856	FCRL3	CD307c|FCRH3|IFGP3|IRTA3|SPAP2	Fc receptor like 3	protein-coding	0.004484	0.374627	598(TGAAACATCCTGTCCC,-,0.00),599(GAAACATCCTGTCCCT,+,0.00)
chunk0141_221_1	chr4	84652411	84652859	+	0	NA	Intergenic	Intergenic	69731	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.008929	0.394209	
chunk0054_1_1	chr13	40125805	40126070	+	0	NA	Intergenic	Intergenic	-55872	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.003774	0.466165	
chunk0145_337_1	chr4	150910173	150910412	+	0	NA	intron (NM_001199282, intron 9 of 56)	L1MB2|LINE|L1	104975	NM_001199282	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.012552	0.316667	
chunk0138_3_1	chr4	30237193	30237649	+	0	NA	Intergenic	Intergenic	-482987	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.004386	0.365427	
chunk0129_114_1	chr3	119792292	119792580	+	0	NA	intron (NM_022002, intron 1 of 8)	intron (NM_022002, intron 1 of 8)	9726	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.017361	0.595156	
chunk0115_410_1	chr21	30648963	30649283	+	0	NA	Intergenic	L1MC5a|LINE|L1	6259	NM_001128077	337985	Hs.580878	NM_001128077	ENSG00000206104	KRTAP20-3	KAP19D|KAP20.3|KRTAP19P4	keratin associated protein 20-3	protein-coding	0.006250	0.352025	
chunk0105_296_1	chr2	190069874	190070221	+	0	NA	Intergenic	Intergenic	-7318	NM_005259	2660	Hs.41565	NM_005259	ENSG00000138379	MSTN	GDF8|MSLHP	myostatin	protein-coding	0.005764	0.344828	
chunk0164_288_1	chr6	24585932	24586420	+	0	NA	intron (NM_001168374, intron 5 of 21)	MER4A|LTR|ERV1	-2949	NM_001252328	9856	Hs.26441	NM_014809	ENSG00000137261	KIAA0319	AAVR|DYLX2|DYX2|NMIG	KIAA0319	protein-coding	0.010246	0.425358	169(AAAAACAAGCTGTACC,-,0.00),170(AAAACAAGCTGTACCC,+,0.00)
chunk0090_376_1	chr18	77190863	77191442	+	0	NA	Intergenic	L1ME3G|LINE|L1	-58334	NM_001025100	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.003454	0.355172	
chunk0090_367_1	chr18	77084272	77084952	+	0	NA	intron (NM_001025101, intron 2 of 8)	MER65A|LTR|ERV1	48206	NM_001025101	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.013235	0.428781	
chunk0028_47_1	chr10	83192619	83193388	+	0	NA	Intergenic	Intergenic	-946426	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.009103	0.363636	
chunk0056_26_1	chr13	77281625	77282169	+	0	NA	intron (NM_015057, intron 3 of 82)	intron (NM_015057, intron 3 of 82)	45145	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.003676	0.308257	
chunk0116_314_1	chr21	40725889	40726428	+	0	NA	intron (NR_073202, intron 1 of 32)	HAL1|LINE|L1	-95391	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.009276	0.322222	
chunk0085_163_1	chr18	3722367	3722690	+	0	NA	intron (NM_001308390, intron 4 of 10)	LTR83|LTR|ERVL	118791	NR_119377	84777	Hs.659053	NM_032691		DLGAP1-AS2	-	DLGAP1 antisense RNA 2	ncRNA	0.012384	0.407407	
chunk0110_118_1	chr20	12737855	12738212	+	0	NA	Intergenic	Intergenic	198930	NR_109872	102606466	Hs.602196	NR_109872		LOC102606466	-	uncharacterized LOC102606466	ncRNA	0.005602	0.385475	209(GAGGACATTGTGTCTC,-,0.00),210(AGGACATTGTGTCTCC,+,0.00)
chunk0196_133_1	chr8	104070296	104070736	+	0	NA	intron (NM_001282881, intron 16 of 20)	intron (NM_001282881, intron 16 of 20)	-152819	NM_001282882	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.000000	0.285714	
chunk0059_125_1	chr14	31718476	31719145	+	0	NA	intron (NM_001201574, intron 1 of 5)	intron (NM_001201574, intron 1 of 5)	4241	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.007474	0.334328	
chunk0023_374_1	chr10	30242316	30242738	+	0	NA	Intergenic	L1M5|LINE|L1	30675	NR_120653	101929279	Hs.559153	NR_120653		LOC101929279	-	uncharacterized LOC101929279	ncRNA	0.004739	0.323877	
chunk0122_278_1	chr3	35549667	35550033	+	0	NA	Intergenic	Intergenic	-89324	NM_001267616	10777	Hs.475902	NM_016300	ENSG00000172995	ARPP21	ARPP-21|R3HDM3|RCS|TARPP	cAMP regulated phosphoprotein 21	protein-coding	0.005464	0.400545	
chunk0201_204_1	chr9	37102333	37102847	+	0	NA	Intergenic	Intergenic	-17882	NM_032226	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.005837	0.415534	
chunk0205_85_1	chr9	107285300	107285867	+	0	NA	intron (NM_001244713, intron 1 of 9)	intron (NM_001244713, intron 1 of 9)	814	NM_001244713	5887	Hs.521640	NM_002874	ENSG00000119318	RAD23B	HHR23B|HR23B|P58	RAD23 homolog B, nucleotide excision repair protein	protein-coding	0.017637	0.330986	
chunk0210_273_1	chrX	84532238	84532528	+	0	NA	Intergenic	L1MA1|LINE|L1	-29904	NM_144657	139324	Hs.559546	NM_144657	ENSG00000165259	HDX	CXorf43|D030011N01Rik	highly divergent homeobox	protein-coding	0.000000	0.357388	104(GGACACAGGTTGTTCC,-,0.00),105(GACACAGGTTGTTCCT,+,0.00)
chunk0072_426_1	chr15	101179574	101179794	+	0	NA	intron (NM_014918, intron 2 of 2)	intron (NM_014918, intron 2 of 2)	72248	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.050000	0.633484	
chunk0139_81_1	chr4	49313043	49313270	+	0	NA	Intergenic	Intergenic	326514	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.013216	0.346491	
chunk0030_68_1	chr10	112075950	112076230	+	0	NA	Intergenic	Intergenic	107689	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.003571	0.377224	
chunk0061_322_1	chr14	62972296	62972573	+	0	NA	intron (NM_172375, intron 6 of 9)	L1MC1|LINE|L1	72804	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.007220	0.359712	
chunk0071_210_1	chr15	84113142	84113341	+	0	NA	intron (NR_036652, intron 5 of 9)	intron (NR_036652, intron 5 of 9)	33054	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.000000	0.290000	
chunk0078_418_1	chr16	89300359	89300565	+	0	NA	intron (NR_045839, intron 5 of 9)	intron (NR_045839, intron 5 of 9)	-20671	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.038835	0.661836	101(GAGCACAGCCTGGCCC,-,0.00),102(AGCACAGCCTGGCCCC,+,0.00)
chunk0075_106_1	chr16	48667689	48668167	+	0	NA	Intergenic	L1PA6|LINE|L1	-57719	NM_153029	9683	Hs.511839	NM_153029	ENSG00000102921	N4BP1	-	NEDD4 binding protein 1	protein-coding	0.006276	0.494781	
chunk0143_226_1	chr4	114137578	114137777	+	0	NA	Intergenic	Intergenic	-157955	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.010050	0.335000	
chunk0053_44_1	chr13	27448455	27448692	+	0	NA	intron (NM_152912, intron 1 of 4)	intron (NM_152912, intron 1 of 4)	1616	NM_001166262	219402	Hs.534582	NM_152912	ENSG00000122033	MTIF3	IF3mt	mitochondrial translational initiation factor 3	protein-coding	0.012658	0.445378	98(GAGCACAAAGTGTACT,-,0.00),99(AGCACAAAGTGTACTC,+,0.00)
chunk0023_232_1	chr10	26810368	26811013	+	0	NA	intron (NM_001178116, intron 3 of 11)	MER58A|DNA|hAT-Charlie	50397	NM_001178123	10006	Hs.508148	NM_005470	ENSG00000136754	ABI1	ABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1	abl interactor 1	protein-coding	0.010853	0.360681	
chunk0157_273_1	chr5	120163491	120163785	+	0	NA	Intergenic	Intergenic	-300640	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.003401	0.305085	
chunk0085_413_1	chr18	10444606	10444871	+	0	NA	Intergenic	Intergenic	-9890	NM_153000	147495	Hs.293274	NM_153000	ENSG00000154856	APCDD1	B7323|DRAPC1|FP7019|HHS|HTS|HYPT1	APC down-regulated 1	protein-coding	0.011321	0.402256	
chunk0171_349_1	chr6	130199461	130199849	+	0	NA	intron (NM_001277185, intron 4 of 10)	intron (NM_001277185, intron 4 of 10)	16230	NM_001277185	154075	Hs.440508	NM_152552	ENSG00000164483	SAMD3	-	sterile alpha motif domain containing 3	protein-coding	0.005155	0.370180	
chunk0136_207_1	chr4	7103600	7103799	+	0	NA	promoter-TSS (NR_027441)	promoter-TSS (NR_027441)	-323	NR_027441	730971	Hs.591718	NR_027441		LINC02447	-	long intergenic non-protein coding RNA 2447	ncRNA	0.030151	0.575000	
chunk0147_305_1	chr4	184813424	184813742	+	0	NA	intron (NM_001286711, intron 1 of 19)	intron (NM_001286711, intron 1 of 19)	-1324	NM_001286708	2180	Hs.406678	NM_001995	ENSG00000151726	ACSL1	ACS1|FACL1|FACL2|LACS|LACS1|LACS2	acyl-CoA synthetase long chain family member 1	protein-coding	0.022013	0.426332	168(CATGACAGCATGTTCT,-,0.00),169(ATGACAGCATGTTCTA,+,0.00)
chunk0024_363_1	chr10	44149532	44149923	+	0	NA	Intergenic	L1PA4|LINE|L1	-143023	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.010230	0.390306	
chunk0174_179_1	chr6	159716068	159716659	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-10635	NM_152858	9589	Hs.446091	NM_004906	ENSG00000146457	WTAP	Mum2	WT1 associated protein	protein-coding	0.008460	0.454392	192(AAGAACTGGCAGTCCC,-,0.00),193(AGAACTGGCAGTCCCT,+,0.00)
chunk0166_156_1	chr6	45362331	45362585	+	0	NA	intron (NM_001024630, intron 2 of 8)	intron (NM_001024630, intron 2 of 8)	15593	NM_003599	8464	Hs.368325	NM_003599	ENSG00000196284	SUPT3H	SPT3|SPT3L	SPT3 homolog, SAGA and STAGA complex component	protein-coding	0.000000	0.329412	
chunk0005_230_1	chr1	59445021	59445567	+	0	NA	intron (NM_001244714, intron 3 of 13)	intron (NM_001244714, intron 3 of 13)	-70335	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.001832	0.436929	259(GGGCACATGCAGTTCT,-,0.00),260(GGCACATGCAGTTCTT,+,0.00)
chunk0042_456_1	chr12	12517743	12517990	+	0	NA	intron (NM_030640, intron 3 of 6)	intron (NM_030640, intron 3 of 6)	44648	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.008097	0.475806	
chunk0208_197_1	chrX	17541921	17542204	+	0	NA	intron (NM_001291867, intron 1 of 8)	intron (NM_001291867, intron 1 of 8)	17065	NR_046632	100873920	Hs.584577	NR_046632		NHS-AS1	-	NHS antisense RNA 1	ncRNA	0.003534	0.464789	
chunk0061_240_1	chr14	60761578	60761855	+	0	NA	intron (NM_002431, intron 1 of 7)	intron (NM_002431, intron 1 of 7)	26975	NM_002431	4331	Hs.509523	NM_002431	ENSG00000020426	MNAT1	CAP35|MAT1|RNF66|TFB3	MNAT1 component of CDK activating kinase	protein-coding	0.000000	0.298561	
chunk0048_314_1	chr12	83116707	83117189	+	0	NA	intron (NM_152588, intron 11 of 11)	L1PB1|LINE|L1	429793	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004149	0.372671	466(TTGAACAGGGTGTTCT,-,0.00),467(TGAACAGGGTGTTCTT,+,0.00)
chunk0087_199_1	chr18	35788874	35789076	+	0	NA	Intergenic	AluJb|SINE|Alu	115951	NR_029616	406963		NR_029616	ENSG00000207797	MIR187	MIRN187|miR-187|miRNA187	microRNA 187	ncRNA	0.014851	0.472906	
chunk0058_401_1	chr13	111626419	111626877	+	0	NA	Intergenic	Intergenic	-266730	NR_046992	101928616	Hs.528450	NR_046992		LINC00354	-	long intergenic non-protein coding RNA 354	ncRNA	0.026201	0.610022	162(CGGGACACTGAGTTCT,-,0.00),163(GGGACACTGAGTTCTC,+,0.00)
chunk0010_50_1	chr1	112905845	112906066	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-17395	NR_002796	246182	Hs.647691	NR_002796		AKR7A2P1	AFARP1	aldo-keto reductase family 7 member A2 pseudogene 1	pseudo	0.009050	0.427928	
chunk0003_308_1	chr1	37795294	37795570	+	0	NA	promoter-TSS (NM_152496)	promoter-TSS (NM_152496)	-56	NM_152496	149175	Hs.534562	NM_152496	ENSG00000185090	MANEAL	-	mannosidase endo-alpha like	protein-coding	0.050725	0.581227	
chunk0102_204_1	chr2	148162726	148163090	+	0	NA	intron (NM_018328, intron 2 of 14)	intron (NM_018328, intron 2 of 14)	-141304	NM_181742	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.000000	0.287671	188(GAGAACTTAATGTACC,-,0.00),189(AGAACTTAATGTACCA,+,0.00)
chunk0047_263_1	chr12	72847142	72847616	+	0	NA	Intergenic	Intergenic	-311811	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.004219	0.294737	
chunk0102_459_1	chr2	158619547	158619827	+	0	NA	intron (NM_001005476, intron 4 of 20)	MIRb|SINE|MIR	162807	NM_001005476	8502	Hs.407580	NM_003628	ENSG00000144283	PKP4	p0071	plakophilin 4	protein-coding	0.003571	0.416370	
chunk0018_88_1	chr1	217525926	217526676	+	0	NA	intron (NM_018040, intron 5 of 9)	intron (NM_018040, intron 5 of 9)	104801	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.004000	0.290280	354(CTGTACAGGCTGTTCT,-,0.00),355(TGTACAGGCTGTTCTC,+,0.00)
chunk0064_419_1	chr14	99605791	99605990	+	0	NA	Intergenic	L2a|LINE|L2	-1500	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.005025	0.600000	28(AGGAACAGCCAGTGCC,-,0.00),29(GGAACAGCCAGTGCCA,+,0.00)
chunk0053_227_1	chr13	32321111	32321478	+	0	NA	intron (NM_000059, intron 3 of 26)	L2c|LINE|L2	5814	NM_000059	675	Hs.34012	NM_000059	ENSG00000139618	BRCA2	BRCC2|BROVCA2|FACD|FAD|FAD1|FANCD|FANCD1|GLM3|PNCA2|XRCC11	BRCA2 DNA repair associated	protein-coding	0.008174	0.394022	
chunk0107_58_1	chr2	211556516	211556716	+	0	NA	intron (NM_001042599, intron 20 of 26)	L1PA12|LINE|L1	869744	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.005000	0.343284	
chunk0080_127_1	chr17	27271605	27271857	+	0	NA	Intergenic	Intergenic	22265	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.003968	0.367589	
chunk0167_135_1	chr6	62128216	62128555	+	0	NA	intron (NM_152688, intron 2 of 8)	intron (NM_152688, intron 2 of 8)	157810	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.000000	0.350000	150(AAGATCTTTGTGTTCC,-,0.00),151(AGATCTTTGTGTTCCT,+,0.00)
chunk0095_323_1	chr2	20599155	20599521	+	0	NA	Intergenic	Intergenic	-6790	NR_046836	100874343	Hs.591546	NR_046836	ENSG00000231948	HS1BP3-IT1	-	HS1BP3 intronic transcript 1	ncRNA	0.019126	0.588556	196(GGGTGCACGCTGTCCC,-,0.00)
chunk0200_5_1	chr9	14477740	14478524	+	0	NA	Intergenic	LTR85a|LTR|Gypsy?	-79149	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.005102	0.397452	
chunk0018_27_1	chr1	215546749	215547449	+	0	NA	Intergenic	Intergenic	-20293	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.001429	0.335235	
chunk0137_194_1	chr4	17866019	17867358	+	0	NA	intron (NM_153686, intron 6 of 6)	intron (NM_153686, intron 6 of 6)	55875	NR_073124	64151	Hs.567567	NM_022346	ENSG00000109805	NCAPG	CAPG|CHCG|NY-MEL-3|YCG1	non-SMC condensin I complex subunit G	protein-coding	0.007468	0.394030	
chunk0022_7_1	chr10	7202888	7203283	+	0	NA	intron (NM_001018039, intron 12 of 20)	intron (NM_001018039, intron 12 of 20)	-16301	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.005063	0.356061	
chunk0088_331_1	chr18	51030850	51031433	+	0	NA	intron (NM_005359, intron 1 of 11)	intron (NM_005359, intron 1 of 11)	928	NM_005359	4089	Hs.75862	NM_005359	ENSG00000141646	SMAD4	DPC4|JIP|MADH4|MYHRS	SMAD family member 4	protein-coding	0.027444	0.453767	383(TAGCACTGCATGTACT,-,0.00),384(AGCACTGCATGTACTG,+,0.00)
chunk0125_210_1	chr3	67487753	67488078	+	0	NA	intron (NM_001177599, intron 9 of 10)	L1ME4c|LINE|L1	166699	NM_001177599	8801	Hs.644919	NM_003848	ENSG00000172340	SUCLG2	G-SCS|GBETA|GTPSCS	succinate-CoA ligase GDP-forming beta subunit	protein-coding	0.003077	0.309816	
chunk0149_91_1	chr5	17998415	17998614	+	0	NA	Intergenic	L1MA7|LINE|L1	-611204	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.000000	0.290000	
chunk0025_349_1	chr10	58170710	58171178	+	0	NA	Intergenic	L1M5|LINE|L1	96990	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.000000	0.277186	
chunk0118_127_1	chr22	29679213	29679608	+	0	NA	intron (NM_181825, intron 14 of 15)	intron (NM_181825, intron 14 of 15)	-40945	NM_182527	164633	Hs.643608	NM_182527	ENSG00000100314	CABP7	CALN2	calcium binding protein 7	protein-coding	0.002532	0.446970	
chunk0180_27_1	chr7	53811713	53811929	+	0	NA	non-coding (NR_038371, exon 1 of 6)	non-coding (NR_038371, exon 1 of 6)	110	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.032407	0.635945	40(GGCCCACCGTGTGCTC,+,0.00)
chunk0110_331_1	chr20	19121360	19121968	+	0	NA	Intergenic	Intergenic	-90982	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.006579	0.403941	
chunk0168_178_1	chr6	84416118	84416503	+	0	NA	Intergenic	Intergenic	58619	NR_132100	105377880	Hs.171384	NR_132100	ENSG00000231776	LINC01611	TCONS_l2_00025430	long intergenic non-protein coding RNA 1611	ncRNA	0.005195	0.329016	
chunk0049_34_1	chr12	89757686	89758209	+	0	NA	Intergenic	L1PA16|LINE|L1	48992	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.001912	0.324427	
chunk0017_221_1	chr1	207964528	207964728	+	0	NA	Intergenic	Intergenic	-53290	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.020000	0.522388	
chunk0079_66_1	chr17	11274887	11275393	+	0	NA	intron (NM_001173461, intron 2 of 3)	intron (NM_001173461, intron 2 of 3)	33717	NM_207386	388336	Hs.592124	NM_175903	ENSG00000188803	SHISA6	-	shisa family member 6	protein-coding	0.011858	0.508876	217(TGGAACTCTGTGTTCT,-,0.00),218(GGAACTCTGTGTTCTA,+,0.00)
chunk0180_88_1	chr7	55045595	55045843	+	0	NA	intron (NM_201283, intron 1 of 9)	MIRb|SINE|MIR	26687	NM_005228	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.004032	0.429719	
chunk0153_17_1	chr5	66959262	66959525	+	0	NA	intron (NM_001290226, intron 1 of 26)	intron (NM_001290226, intron 1 of 26)	523	NM_001290226	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.011407	0.431818	
chunk0092_366_1	chr19	35919519	35919771	+	0	NA	Intergenic	L1ME3B|LINE|L1	-11336	NM_198125	7305	Hs.515369	NM_003332	ENSG00000011600	TYROBP	DAP12|KARAP|PLOSL|PLOSL1	TYRO protein tyrosine kinase binding protein	protein-coding	0.023810	0.462451	
chunk0031_101_1	chr10	124105672	124105902	+	0	NA	Intergenic	Intergenic	-12180	NM_001270764	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.017391	0.454545	
chunk0033_113_1	chr11	14449379	14449728	+	0	NA	Intergenic	Intergenic	50305	NM_016451	1315	Hs.339278	NM_016451	ENSG00000129083	COPB1	COPB	coatomer protein complex subunit beta 1	protein-coding	0.002865	0.417143	
chunk0092_377_1	chr19	36221581	36221889	+	0	NA	intron (NM_007145, intron 2 of 3)	L1MC5a|LINE|L1	-6651	NM_001042474	147929	Hs.596338	NM_152477	ENSG00000196357	ZNF565	-	zinc finger protein 565	protein-coding	0.000000	0.343042	
chunk0077_438_1	chr16	85615123	85615346	+	0	NA	intron (NM_001278184, intron 1 of 14)	CpG-10032	1998	NM_001278184	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.080717	0.691964	54(AGGCACAGGCTGTGCC,-,0.00),55(GGCACAGGCTGTGCCT,+,0.00)
chunk0073_197_1	chr16	9123761	9124265	+	0	NA	Intergenic	Intergenic	32333	NM_014117	29035	Hs.221497	NM_014117	ENSG00000182831	C16orf72	PRO0149	chromosome 16 open reading frame 72	protein-coding	0.011905	0.582178	
chunk0130_371_1	chr3	139329351	139329669	+	0	NA	Intergenic	Intergenic	-14509	NM_020191	56945	Hs.745001	NM_020191	ENSG00000175110	MRPS22	C3orf5|COXPD5|GIBT|GK002|MRP-S22|ODG7|RPMS22	mitochondrial ribosomal protein S22	protein-coding	0.066038	0.645768	
chunk0090_189_1	chr18	73034058	73034335	+	0	NA	Intergenic	L1MCa|LINE|L1	-166621	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.000000	0.388489	
chunk0065_129_1	chr15	24919463	24920161	+	0	NA	intron (NM_022808, intron 2 of 11)	MER31A|LTR|ERV1	-35111	NM_022804	8926	Hs.564847	NM_005678	ENSG00000273173	SNURF	-	SNRPN upstream reading frame	protein-coding	0.005731	0.416309	
chunk0170_409_1	chr6	117939999	117940646	+	0	NA	intron (NM_001029858, intron 1 of 7)	intron (NM_001029858, intron 1 of 7)	32796	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.006182	0.365741	
chunk0047_272_1	chr12	73053768	73054441	+	0	NA	Intergenic	Intergenic	-105086	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.002972	0.281899	
chunk0043_300_1	chr12	22050069	22050520	+	0	NA	intron (NM_018686, intron 1 of 7)	MIR|SINE|MIR	4118	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.011086	0.413717	
chunk0165_112_1	chr6	32853558	32854074	+	0	NA	promoter-TSS (NM_002800).4	promoter-TSS (NM_002800).4	155	NM_000593	6890	Hs.352018	NM_000593	ENSG00000168394	TAP1	ABC17|ABCB2|APT1|D6S114E|PSF-1|PSF1|RING4|TAP1*0102N|TAP1N	transporter 1, ATP binding cassette subfamily B member	protein-coding	0.069767	0.642166	219(AGGAACAGGCTGATCC,-,0.00),220(GGAACAGGCTGATCCT,+,0.00)
chunk0020_376_1	chr1	239876466	239877090	+	0	NA	intron (NM_000740, intron 4 of 4)	intron (NM_000740, intron 4 of 4)	23094	NR_046582	100873984	Hs.199475	NR_046582	ENSG00000234601	CHRM3-AS1	-	CHRM3 antisense RNA 1	ncRNA	0.003205	0.420800	
chunk0098_47_1	chr2	66490599	66491263	+	0	NA	intron (NM_002398, intron 7 of 12)	intron (NM_002398, intron 7 of 12)	-50601	NR_046625	100873998	Hs.734698	NR_046625	ENSG00000230749	MEIS1-AS2	MEIS1-AS1	MEIS1 antisense RNA 2	ncRNA	0.004518	0.390977	
chunk0116_95_1	chr21	35042167	35042479	+	0	NA	intron (NM_001754, intron 2 of 8)	intron (NM_001754, intron 2 of 8)	-2897	NR_026812	80215	Hs.672131	NM_025143		RUNX1-IT1	C21orf96	RUNX1 intronic transcript 1	ncRNA	0.003205	0.479233	
chunk0103_98_1	chr2	161222950	161223562	+	0	NA	TTS (NR_110593)	TTS (NR_110593)	-21483	NR_110164	100996579	Hs.660929	NR_110163	ENSG00000227403	LINC01806	-	long intergenic non-protein coding RNA 1806	ncRNA	0.001634	0.287113	
chunk0211_165_1	chrX	115030482	115030986	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-13090	NM_000640	3598	Hs.336046	NM_000640	ENSG00000123496	IL13RA2	CD213A2|CT19|IL-13R|IL13BP	interleukin 13 receptor subunit alpha 2	protein-coding	0.005952	0.441584	
chunk0203_418_1	chr9	90952246	90952572	+	0	NA	Intergenic	Intergenic	122723	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.009202	0.464832	
chunk0062_254_1	chr14	71575151	71575389	+	0	NA	intron (NM_001284245, intron 1 of 20)	intron (NM_001284245, intron 1 of 20)	-11011	NM_001284246	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.004202	0.464435	87(CGGAACTGACTGTCCC,-,0.00),88(GGAACTGACTGTCCCT,+,0.00)
chunk0163_358_1	chr6	15683765	15683992	+	0	NA	Intergenic	L2c|LINE|L2	-20820	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.000000	0.390351	
chunk0122_215_1	chr3	33441369	33441580	+	0	NA	Intergenic	Intergenic	-1069	NM_001128161	7342	Hs.729120	NM_014517	ENSG00000153560	UBP1	LBP-1B|LBP-1a|LBP1A|LBP1B	upstream binding protein 1	protein-coding	0.037915	0.466981	
chunk0047_334_1	chr12	74528153	74528696	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-9347	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.000000	0.338235	
chunk0152_395_1	chr5	64768622	64769118	+	0	NA	promoter-TSS (NM_173829)	promoter-TSS (NM_173829)	-48	NM_001297644	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.056452	0.513078	
chunk0175_142_1	chr7	3527469	3527730	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	226151	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.003831	0.564885	
chunk0086_395_1	chr18	26677861	26678533	+	0	NA	Intergenic	Intergenic	-20796	NM_001258222	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.004464	0.438336	246(GGGAACACTCTGTCTT,-,0.00),247(GGAACACTCTGTCTTA,+,0.00)
chunk0149_282_1	chr5	25125188	25125621	+	0	NA	Intergenic	L1MC4|LINE|L1	-284821	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.013857	0.384793	
chunk0097_421_1	chr2	63133626	63134218	+	0	NA	intron (NR_122106, intron 11 of 11)	L1MB3|LINE|L1	-14380	NR_036635	100169989	Hs.606147	NR_036635	ENSG00000242412	DBIL5P2	ELP1P	diazepam binding inhibitor-like 5 pseudogene 2	pseudo	0.005068	0.409781	
chunk0158_35_1	chr5	125602855	125603054	+	0	NA	TTS (NR_109887)	TTS (NR_109887)	109693	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.005025	0.410000	
chunk0095_6_1	chr2	11750936	11751190	+	0	NA	intron (NM_145693, intron 1 of 19)	intron (NM_145693, intron 1 of 19)	4467	NM_145693	23175	Hs.467740	NM_145693	ENSG00000134324	LPIN1	PAP1	lipin 1	protein-coding	0.019685	0.450980	53(AAGAACGTCCTGTCCT,-,0.00),54(AGAACGTCCTGTCCTT,+,0.00)
chunk0077_361_1	chr16	84108067	84108266	+	0	NA	intron (NM_003791, intron 1 of 22)	intron (NM_003791, intron 1 of 22)	8777	NM_003791	8720	Hs.75890	NM_003791	ENSG00000140943	MBTPS1	PCSK8|S1P|SEDKF|SKI-1	membrane bound transcription factor peptidase, site 1	protein-coding	0.010050	0.500000	
chunk0020_80_1	chr1	232717963	232718368	+	0	NA	Intergenic	LTR10C|LTR|ERV1	24550	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.004938	0.376847	
chunk0002_235_1	chr1	20341364	20342083	+	0	NA	intron (NM_001039500, intron 14 of 21)	L1ME4b|LINE|L1	50804	NM_001039500	127731	Hs.205178	NM_144623	ENSG00000158816	VWA5B1	-	von Willebrand factor A domain containing 5B1	protein-coding	0.004172	0.330556	416(CAGAACAGAAAGTCCA,-,0.00),417(AGAACAGAAAGTCCAT,+,0.00)
chunk0168_115_1	chr6	81746524	81747171	+	0	NA	3' UTR (NM_017633, exon 3 of 3)	3' UTR (NM_017633, exon 3 of 3)	5864	NM_017633	55603	Hs.10784	NM_017633	ENSG00000112773	TENT5A	C6orf37|FAM46A|OI18|XTP11	terminal nucleotidyltransferase 5A	protein-coding	0.007728	0.382716	418(GAGTACAGCCTGTTCT,-,0.00),419(AGTACAGCCTGTTCTA,+,0.00)
chunk0016_70_1	chr1	193663365	193663620	+	0	NA	Intergenic	Intergenic	358747	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.000000	0.335938	
chunk0079_295_1	chr17	17001939	17002193	+	0	NA	Intergenic	Intergenic	-29978	NM_012452	23495	Hs.158341	NM_012452	ENSG00000240505	TNFRSF13B	CD267|CVID|CVID2|IGAD2|RYZN|TACI|TNFRSF14B	TNF receptor superfamily member 13B	protein-coding	0.047244	0.662745	
chunk0017_353_1	chr1	211874644	211875156	+	0	NA	Intergenic	Intergenic	-44128	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.029297	0.582846	208(TAGGACTTAATGTTCC,-,0.00),209(AGGACTTAATGTTCCT,+,0.00)
chunk0191_113_1	chr8	48261509	48261785	+	0	NA	Intergenic	Intergenic	253212	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.010870	0.476534	
chunk0081_186_1	chr17	41773152	41773351	+	0	NA	intron (NM_021991, intron 1 of 14)	intron (NM_021991, intron 1 of 14)	13461	NM_021991	3728	Hs.514174	NM_002230	ENSG00000173801	JUP	CTNNG|DP3|DPIII|PDGB|PKGB	junction plakoglobin	protein-coding	0.015075	0.630000	
chunk0112_165_1	chr20	39835397	39835883	+	0	NA	Intergenic	Intergenic	-168821	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.010288	0.427105	176(AGGGACTGCCTGTGCC,-,0.00),177(GGGACTGCCTGTGCCC,+,0.00)
chunk0004_19_1	chr1	42190196	42190628	+	0	NA	intron (NM_014947, intron 9 of 12)	intron (NM_014947, intron 9 of 12)	-25688	NM_033553	2980	Hs.778	NM_033553	ENSG00000197273	GUCA2A	GCAP-I|GUCA2|STARA	guanylate cyclase activator 2A	protein-coding	0.006944	0.385681	
chunk0067_104_1	chr15	42286301	42286936	+	0	NA	intron (NM_001301409, intron 4 of 11)	intron (NM_001301409, intron 4 of 11)	12450	NM_198141	2595	Hs.730806	NM_198141	ENSG00000214013	GANC	-	glucosidase alpha, neutral C	protein-coding	0.006299	0.353774	
chunk0166_339_1	chr6	50929788	50930368	+	0	NA	Intergenic	Intergenic	111352	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.000000	0.296041	402(GAAAACTCTGTGTTCC,-,0.00)
chunk0059_400_1	chr14	37588114	37588626	+	0	NA	Intergenic	CpG	6750	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.085938	0.635478	
chunk0114_54_1	chr21	8759197	8759465	+	0	NA	Intergenic	Intergenic	-227668	NR_128711	103504731		NR_128711	ENSG00000264462	MIR3648-2	hsa-mir-3648-2	microRNA 3648-2	ncRNA	0.052239	0.646840	
chunk0045_238_1	chr12	48745773	48746378	+	0	NA	intron (NR_029448, intron 2 of 4)	L2a|LINE|L2	18640	NR_029449									0.003306	0.334983	
chunk0024_372_1	chr10	44395494	44395808	+	0	NA	Intergenic	Intergenic	-10554	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.009554	0.555556	59(AGGCCAGGATGTGCTT,+,0.00)
chunk0099_29_1	chr2	83380144	83380686	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	523612	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007380	0.388582	
chunk0178_145_1	chr7	33107850	33108182	+	0	NA	intron (NM_203288, intron 1 of 5)	MER57B2|LTR|ERV1	1374	NM_203288	6100	Hs.326805	NM_203288	ENSG00000164610	RP9	PAP-1|PAP1	RP9 pre-mRNA splicing factor	protein-coding	0.009036	0.423423	
chunk0190_268_1	chr8	37351015	37351466	+	0	NA	Intergenic	L1ME3F|LINE|L1	142673	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.004435	0.404867	
chunk0095_251_1	chr2	19354063	19354338	+	0	NA	intron (NM_145260, intron 1 of 2)	intron (NM_145260, intron 1 of 2)	4411	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.010909	0.460145	85(GGAAACTGCCTGTCCT,-,0.00),86(GAAACTGCCTGTCCTG,+,0.00)
chunk0189_158_1	chr8	23191603	23192172	+	0	NA	exon (NM_003844, exon 10 of 10)	exon (NM_003844, exon 10 of 10)	-27857	NM_003840	8793	Hs.213467	NM_003840	ENSG00000173530	TNFRSF10D	CD264|DCR2|TRAIL-R4|TRAILR4|TRUNDD	TNF receptor superfamily member 10d	protein-coding	0.012302	0.496491	
chunk0142_281_1	chr4	99922650	99922975	+	0	NA	TTS (NM_001278311)	TTS (NM_001278311)	23914	NM_001031723	79982	Hs.577426	NM_024920	ENSG00000164031	DNAJB14	EGNR9427|PRO34683	DnaJ heat shock protein family (Hsp40) member B14	protein-coding	0.006154	0.365031	
chunk0161_191_1	chr5	170236439	170236913	+	0	NA	intron (NM_001305395, intron 4 of 4)	L2c|LINE|L2	3669	NM_001305394	133874	Hs.519749	NM_001102609	ENSG00000234511	C5orf58	-	chromosome 5 open reading frame 58	protein-coding	0.002110	0.387368	
chunk0112_415_1	chr20	47304148	47304909	+	0	NA	intron (NM_001281769, intron 3 of 3)	intron (NM_001281769, intron 3 of 3)	-13974	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.005256	0.472441	
chunk0207_52_1	chrX	7132445	7132739	+	0	NA	intron (NM_001135565, intron 1 of 4)	intron (NM_001135565, intron 1 of 4)	-15268	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.003401	0.444068	
chunk0148_70_1	chr5	2231878	2232533	+	0	NA	Intergenic	Intergenic	79996	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.001527	0.346037	
chunk0149_354_1	chr5	27610619	27610865	+	0	NA	Intergenic	MIR|SINE|MIR	138450	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.004065	0.352227	
chunk0003_243_1	chr1	36161337	36162163	+	0	NA	intron (NM_001286365, intron 1 of 15)	intron (NM_001286365, intron 1 of 15)	-5697	NM_001270895	27095	Hs.523131	NM_014408	ENSG00000054116	TRAPPC3	BET3	trafficking protein particle complex 3	protein-coding	0.013317	0.492140	379(GGGGACATTGTGTCTC,-,0.00),380(GGGACATTGTGTCTCT,+,0.00)
chunk0209_348_1	chrX	53044966	53045258	+	0	NA	Intergenic	MER41G|LTR|ERV1	-4212	NM_018969	54328	Hs.193011	NM_018969	ENSG00000184194	GPR173	SREB3	G protein-coupled receptor 173	protein-coding	0.010274	0.433447	
chunk0044_453_1	chr12	42744485	42744954	+	0	NA	Intergenic	Intergenic	-98221	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.004264	0.442553	
chunk0010_445_1	chr1	120921759	120921969	+	0	NA	intron (NR_024511, intron 1 of 2)	AluSq|SINE|Alu	8647	NR_109754	728855	Hs.456578	NR_024510		LINC00623	CH17-118O6.2	long intergenic non-protein coding RNA 623	ncRNA	0.033333	0.431280	
chunk0062_382_1	chr14	74469661	74469877	+	0	NA	Intergenic	Intergenic	10435	NR_039858	100616211		NR_039858	ENSG00000283944	MIR4709	mir-4709	microRNA 4709	ncRNA	0.000000	0.442396	105(AAGAACACTGTGTTTT,-,0.00),106(AGAACACTGTGTTTTT,+,0.00)
chunk0149_428_1	chr5	29685970	29686492	+	0	NA	Intergenic	MLT1A0-int|LTR|ERVL-MaLR	-290255	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.001916	0.378585	
chunk0022_366_1	chr10	17442828	17443800	+	0	NA	intron (NM_001004470, intron 2 of 7)	intron (NM_001004470, intron 2 of 7)	10941	NM_001004470	338596	Hs.677766	NM_001004470	ENSG00000148488	ST8SIA6	SIA8F|SIAT8-F|SIAT8F|ST8SIA-VI|ST8SiaVI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding	0.006173	0.345324	707(AAGCACAGGTTGTGCC,-,0.00),708(AGCACAGGTTGTGCCC,+,0.00)
chunk0109_105_1	chr20	2368011	2368293	+	0	NA	Intergenic	HAL1|LINE|L1	-12756	NM_001254734	343641	Hs.452039	NM_198994	ENSG00000166948	TGM6	SCA35|TG6|TGM3L|TGY|dJ734P14.3	transglutaminase 6	protein-coding	0.000000	0.385159	
chunk0111_334_1	chr20	32851703	32852120	+	0	NA	Intergenic	Intergenic	32018	NM_012325	22919	Hs.472437	NM_012325	ENSG00000101367	MAPRE1	EB1	microtubule associated protein RP/EB family member 1	protein-coding	0.000000	0.392344	
chunk0163_196_1	chr6	11735173	11735720	+	0	NA	intron (NM_032744, intron 4 of 5)	intron (NM_032744, intron 4 of 5)	43601	NM_032744	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.007313	0.432482	
chunk0194_205_1	chr8	85864059	85864332	+	0	NA	Intergenic	Intergenic	-36253	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.000000	0.383212	146(GAGAACTGAAAGTACT,-,0.00),147(AGAACTGAAAGTACTC,+,0.00)
chunk0074_423_1	chr16	46386327	46386534	+	0	NA	Intergenic	Intergenic	182667	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.009662	0.322115	
chunk0092_7_1	chr19	18488964	18489250	+	0	NA	intron (NM_006532, intron 1 of 11)	intron (NM_006532, intron 1 of 11)	33020	NM_006532	8178	Hs.515260	NM_006532	ENSG00000105656	ELL	C19orf17|ELL1|MEN|PPP1R68	elongation factor for RNA polymerase II	protein-coding	0.027972	0.554007	
chunk0136_212_1	chr4	7376846	7377345	+	0	NA	intron (NM_020777, intron 1 of 26)	intron (NM_020777, intron 1 of 26)	57878	NM_001085382	768239	Hs.662523	NM_001085382	ENSG00000178597	PSAPL1	-	prosaposin like 1 (gene/pseudogene)	protein-coding	0.018036	0.470000	
chunk0038_85_1	chr11	83303150	83303724	+	0	NA	Intergenic	Intergenic	-17030	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.010453	0.446957	
chunk0114_120_1	chr21	9669554	9670097	+	0	NA	Intergenic	L2a|LINE|L2	151236	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.430147	295(GAGAACAGAAAGTCCT,-,0.00),296(AGAACAGAAAGTCCTG,+,0.00)
chunk0085_172_1	chr18	4849082	4849399	+	0	NA	Intergenic	LTR48B|LTR|ERV1	348016	NM_001145194	642597	Hs.437160	NM_001145194	ENSG00000231824	AKAIN1	C18orf42	A-kinase anchor inhibitor 1	protein-coding	0.000000	0.367925	126(AGGCACACTTTGTCCC,-,0.00),127(GGCACACTTTGTCCCA,+,0.00)
chunk0195_210_1	chr8	96963962	96964571	+	0	NA	intron (NR_125390, intron 2 of 2)	L1ME3A|LINE|L1	313682	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.004926	0.318033	
chunk0036_308_1	chr11	66071860	66072128	+	0	NA	intron (NM_018026, intron 1 of 23)	L1ME3E|LINE|L1	1641	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.007463	0.342007	
chunk0170_382_1	chr6	116969661	116969913	+	0	NA	Intergenic	Intergenic	92574	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.011905	0.383399	89(AAGGACAGTGAGTGCT,-,0.00),90(AGGACAGTGAGTGCTT,+,0.00)
chunk0188_445_1	chr8	19318637	19320069	+	0	NA	5' UTR (NM_022071, exon 2 of 10)	5' UTR (NM_022071, exon 2 of 10)	5377	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.006983	0.404047	
chunk0025_323_1	chr10	57759553	57760284	+	0	NA	Intergenic	L1PA15|LINE|L1	-455359	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.012312	0.382514	
chunk0133_142_1	chr3	169280093	169280709	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-132667	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.001623	0.366288	
chunk0186_224_1	chr7	140384891	140385175	+	0	NA	intron (NM_001287498, intron 1 of 13)	intron (NM_001287498, intron 1 of 13)	13517	NM_001287498	84255	Hs.446021	NM_032295	ENSG00000157800	SLC37A3	-	solute carrier family 37 member 3	protein-coding	0.000000	0.378947	
chunk0094_363_1	chr2	9640696	9640927	+	0	NA	Intergenic	L2c|LINE|L2	-9756	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.012987	0.504310	134(AGGAACAGCATGTACA,-,0.00),135(GGAACAGCATGTACAG,+,0.00)
chunk0165_462_1	chr6	41219396	41219629	+	0	NA	Intergenic	L1M2|LINE|L1	-1565	NR_027256	340206	Hs.93698	NR_027256	ENSG00000184106	TREML3P	TLT3|TREML3	triggering receptor expressed on myeloid cells like 3, pseudogene	pseudo	0.004292	0.316239	
chunk0139_362_1	chr4	60319039	60319821	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-603189	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.300128	
chunk0211_415_1	chrX	128947973	128948927	+	0	NA	Intergenic	Intergenic	575055	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.004193	0.385340	820(TGAGACACAGTGTTCT,-,0.00),821(GAGACACAGTGTTCTG,+,0.00)
chunk0200_201_1	chr9	20391146	20391616	+	0	NA	intron (NM_001286691, intron 5 of 10)	intron (NM_001286691, intron 5 of 10)	19857	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.002128	0.382166	
chunk0093_232_1	chr19	50600374	50600605	+	0	NA	Intergenic	L1MEd|LINE|L1	-4474	NR_004384	100126781	Hs.707968	NR_004384		SNAR-F	-	small NF90 (ILF3) associated RNA F	snRNA	0.008658	0.366379	80(TGGTACTTTGTGTTCT,-,0.00),81(GGTACTTTGTGTTCTT,+,0.00)
chunk0168_32_1	chr6	78061438	78062062	+	0	NA	Intergenic	ERVL47-int|LTR|ERVL	371094	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.004808	0.396800	
chunk0103_207_1	chr2	163780030	163780418	+	0	NA	Intergenic	Intergenic	-44221	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.012887	0.357326	
chunk0117_59_1	chr22	16352730	16352942	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	239974	NM_014406	150160	Hs.128342	NM_014406	ENSG00000198445	CCT8L2	CESK1	chaperonin containing TCP1 subunit 8 like 2	protein-coding	0.023585	0.417840	
chunk0008_89_1	chr1	90842750	90843274	+	0	NA	Intergenic	Intergenic	-125775	NM_020063	343472	Hs.451956	NM_020063	ENSG00000143032	BARHL2	-	BarH like homeobox 2	protein-coding	0.003817	0.413333	
chunk0069_381_1	chr15	67505679	67506223	+	0	NA	intron (NR_040051, intron 2 of 5)	MER67A|LTR|ERV1	15022	NR_040055	100506686	Hs.656245	NR_040051	ENSG00000259673	IQCH-AS1	-	IQCH antisense RNA 1	ncRNA	0.005515	0.381651	
chunk0007_14_1	chr1	77333542	77333815	+	0	NA	intron (NM_012093, intron 5 of 13)	MER58A|DNA|hAT-Charlie	51076	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.007326	0.430657	
chunk0087_138_1	chr18	33806939	33807204	+	0	NA	Intergenic	Intergenic	228494	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.000000	0.312030	
chunk0153_328_1	chr5	74073397	74074084	+	0	NA	Intergenic	L1M4b|LINE|L1	234585	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.010189	0.440407	
chunk0078_92_1	chr17	2049897	2050096	+	0	NA	promoter-TSS (NR_029674)	promoter-TSS (NR_029674)	12	NR_029674	406921		NR_029674	ENSG00000267200	MIR132	MIRN132|miRNA132|mir-132	microRNA 132	ncRNA	0.160804	0.775000	
chunk0204_190_1	chr9	96423498	96423706	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-5215	NM_153695	195828	Hs.494557	NM_153695	ENSG00000165244	ZNF367	AFF29|CDC14B|ZFF29	zinc finger protein 367	protein-coding	0.004808	0.478469	
chunk0212_334_1	chrX	144845610	144845914	+	0	NA	Intergenic	L2c|LINE|L2	-401825	NM_001009614	494118		NM_001009614	ENSG00000203923	SPANXN1	CT11.6	SPANX family member N1	protein-coding	0.006579	0.354098	
chunk0018_109_1	chr1	218283082	218283290	+	0	NA	Intergenic	Intergenic	-2101	NM_016052	51018	Hs.660109	NM_016052	ENSG00000067533	RRP15	CGI-115|KIAA0507	ribosomal RNA processing 15 homolog	protein-coding	0.000000	0.425837	54(TGGAACTCCTTGTTCC,-,0.00),55(GGAACTCCTTGTTCCA,+,0.00)
chunk0014_434_1	chr1	183629648	183630174	+	0	NA	intron (NM_005717, intron 3 of 3)	L1MB4|LINE|L1	6030	NM_005717	10092	Hs.518609	NM_005717	ENSG00000162704	ARPC5	ARC16|dJ127C7.3|p16-Arc	actin related protein 2/3 complex subunit 5	protein-coding	0.000000	0.314991	272(AAGGACTTTCTGTCCC,-,0.00),273(AGGACTTTCTGTCCCT,+,0.00)
chunk0126_133_1	chr3	76045266	76045874	+	0	NA	Intergenic	Intergenic	-259987	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.000000	0.376026	
chunk0167_371_1	chr6	73710611	73711508	+	0	NA	intron (NM_133493, intron 2 of 32)	MER58B|DNA|hAT-Charlie	-14928	NR_110889	101928489	Hs.660059	NR_110889	ENSG00000231652	LOC101928489	-	uncharacterized LOC101928489	ncRNA	0.004459	0.370824	
chunk0093_374_1	chr19	56091062	56091278	+	0	NA	intron (NM_001002836, intron 2 of 2)	HAL1ME|LINE|L1	24486	NR_110741	101928886	Hs.434652	NR_110741	ENSG00000267522	LINC01864	-	long intergenic non-protein coding RNA 1864	ncRNA	0.027778	0.391705	
chunk0171_323_1	chr6	129748123	129748322	+	0	NA	Intergenic	Intergenic	-37997	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.000000	0.355000	
chunk0055_159_1	chr13	60272375	60272582	+	0	NA	Intergenic	L2c|LINE|L2	-4374	NR_047022	100874169	Hs.171027	NR_047022		LINC00434	-	long intergenic non-protein coding RNA 434	ncRNA	0.014493	0.456731	
chunk0189_396_1	chr8	27490573	27491066	+	0	NA	promoter-TSS (NM_001979)	promoter-TSS (NM_001979)	-183	NM_001979	2053	Hs.212088	NM_001979	ENSG00000120915	EPHX2	ABHD20|CEH|SEH	epoxide hydrolase 2	protein-coding	0.028398	0.574899	
chunk0025_16_1	chr10	47701355	47701618	+	0	NA	intron (NR_027634, intron 2 of 6)	L1MC4a|LINE|L1	11786	NR_027634	439965	Hs.283521	NR_027634		SHLD2P3	FAM35B2|FAM35DP	shieldin complex subunit 2 pseudogene 3	pseudo	0.003802	0.344697	140(TGGAACACTATGTACT,-,0.00),141(GGAACACTATGTACTA,+,0.00),213(CAGGACATACTGTTAT,-,0.00),214(AGGACATACTGTTATG,+,0.00)
chunk0147_7_1	chr4	170527013	170527487	+	0	NA	Intergenic	L1MA10|LINE|L1	300659	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.000000	0.332632	
chunk0096_341_1	chr2	35592871	35593104	+	0	NA	Intergenic	Intergenic	121582	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.000000	0.324786	
chunk0088_107_1	chr18	45330200	45330399	+	0	NA	intron (NM_001242692, intron 1 of 20)	MamSINE1|SINE|tRNA-RTE	117317	NM_001242692	8170	Hs.710927	NM_007163	ENSG00000132874	SLC14A2	HUT2|UT-A2|UT2|UTA|UTR|hUT-A6	solute carrier family 14 member 2	protein-coding	0.000000	0.470000	
chunk0162_170_1	chr6	3664586	3665032	+	0	NA	Intergenic	Intergenic	87203	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.017937	0.456376	
chunk0150_89_1	chr5	32312755	32312974	+	0	NA	5' UTR (NM_001294343, exon 1 of 15)	5' UTR (NM_001294343, exon 1 of 15)	144	NM_001294343	54545	Hs.481836	NM_019061	ENSG00000150712	MTMR12	3-PAP|PIP3AP	myotubularin related protein 12	protein-coding	0.127854	0.740909	
chunk0210_268_1	chrX	84184750	84185277	+	0	NA	intron (NM_014496, intron 1 of 21)	intron (NM_014496, intron 1 of 21)	2922	NM_014496	27330	Hs.234478	NM_014496	ENSG00000072133	RPS6KA6	PP90RSK4|RSK-4|RSK4|S6K-alpha-6|p90RSK6	ribosomal protein S6 kinase A6	protein-coding	0.007590	0.378788	
chunk0045_374_1	chr12	52126188	52127281	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	33165	NR_120440	26628	Hs.524431	NR_120438	ENSG00000257542	OR7E47P	OR7E141	olfactory receptor family 7 subfamily E member 47 pseudogene	pseudo	0.016468	0.524680	96(AGGGAGAGGGTGTCCC,-,0.00),395(AGGGACAACCAGTTCC,-,0.00),396(GGGACAACCAGTTCCT,+,0.00),443(AGGGACAGCCAGTTCC,-,0.00),444(GGGACAGCCAGTTCCT,+,0.00),570(GGGAGAGTGTGTCCTT,+,0.00)
chunk0021_148_1	chr10	4280526	4280798	+	0	NA	Intergenic	Intergenic	-36750	NR_108040	100652988	Hs.433011	NR_108040		LINC00702	-	long intergenic non-protein coding RNA 702	ncRNA	0.007353	0.439560	
chunk0211_113_1	chrX	111846156	111846466	+	0	NA	intron (NM_012471, intron 6 of 10)	intron (NM_012471, intron 6 of 10)	-29740	NM_001195576	100329135	Hs.247868	NM_001195576	ENSG00000204025	TRPC5OS	TRPC5-AS1	TRPC5 opposite strand	protein-coding	0.009677	0.411576	145(TAGAACACTGAGTTCA,-,0.00),146(AGAACACTGAGTTCAG,+,0.00)
chunk0151_257_1	chr5	52218844	52219271	+	0	NA	Intergenic	Intergenic	-568883	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.004684	0.287383	
chunk0035_221_1	chr11	45160467	45160683	+	0	NA	intron (NM_001256696, intron 1 of 6)	L1ME3G|LINE|L1	13232	NM_001256696	56981	Hs.178715	NM_001256695	ENSG00000019485	PRDM11	PFM8	PR/SET domain 11	protein-coding	0.009259	0.373272	
chunk0054_66_1	chr13	42019788	42020358	+	0	NA	Intergenic	Intergenic	-19963	NM_001204504	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.003509	0.329247	
chunk0009_447_1	chr1	111565810	111566247	+	0	NA	Intergenic	L2c|LINE|L2	-2025	NM_001302680	57413	Hs.281342	NM_020683	ENSG00000121933	TMIGD3	AD026	transmembrane and immunoglobulin domain containing 3	protein-coding	0.011442	0.438356	
chunk0185_380_1	chr7	133185803	133186303	+	0	NA	Intergenic	L1MB4|LINE|L1	-67014	NM_021807	60412	Hs.321273	NM_021807	ENSG00000131558	EXOC4	SEC8|SEC8L1|Sec8p	exocyst complex component 4	protein-coding	0.000000	0.357285	
chunk0045_232_1	chr12	48364631	48364978	+	0	NA	Intergenic	Intergenic	-13558	NM_001172682	121274	Hs.23492	NM_152320	ENSG00000167528	ZNF641	-	zinc finger protein 641	protein-coding	0.000000	0.344828	
chunk0024_378_1	chr10	44656906	44657590	+	0	NA	Intergenic	L1MC|LINE|L1	-254068	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.002924	0.318248	
chunk0110_107_1	chr20	12030310	12030968	+	0	NA	Intergenic	Intergenic	112774	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.009119	0.415781	
chunk0070_170_1	chr15	71473816	71474306	+	0	NA	intron (NM_024817, intron 6 of 16)	intron (NM_024817, intron 6 of 16)	-73141	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.008163	0.482688	
chunk0101_259_1	chr2	133318048	133318658	+	0	NA	intron (NM_207481, intron 3 of 17)	intron (NM_207481, intron 3 of 17)	52158	NR_110294	101928161	Hs.661917	NR_110294	ENSG00000226953	NCKAP5-AS2	-	NCKAP5 antisense RNA 2	ncRNA	0.003279	0.391162	
chunk0103_275_1	chr2	165827123	165827622	+	0	NA	Intergenic	Intergenic	-33079	NM_004482	2591	Hs.170986	NM_004482	ENSG00000115339	GALNT3	GalNAc-T3|HFTC|HFTC1|HHS	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.006012	0.350000	
chunk0171_16_1	chr6	119916992	119917564	+	0	NA	Intergenic	Intergenic	-97901	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.001748	0.335079	
chunk0094_73_1	chr2	3504447	3505256	+	0	NA	intron (NM_001306077, intron 2 of 3)	intron (NM_001306077, intron 2 of 3)	12896	NM_001306077	55256	Hs.502773	NM_018269	ENSG00000182551	ADI1	APL1|ARD|Fe-ARD|HMFT1638|MTCBP1|Ni-ARD|SIPL|mtnD	acireductone dioxygenase 1	protein-coding	0.014833	0.393827	
chunk0143_210_1	chr4	113533800	113534017	+	0	NA	intron (NM_172114, intron 7 of 17)	intron (NM_172114, intron 7 of 17)	228019	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.009217	0.266055	
chunk0194_266_1	chr8	86994509	86994744	+	0	NA	intron (NM_173538, intron 4 of 10)	L1PA16|LINE|L1	128178	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.004255	0.508475	
chunk0144_67_1	chr4	127540844	127541163	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-91929	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.009404	0.403125	
chunk0200_350_1	chr9	24961550	24961749	+	0	NA	Intergenic	Intergenic	-415973	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.010050	0.330000	
chunk0041_256_1	chr11	129013820	129014576	+	0	NA	intron (NM_001142685, intron 10 of 21)	intron (NM_001142685, intron 10 of 21)	9995	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.006614	0.367239	
chunk0165_118_1	chr6	32909917	32910505	+	0	NA	Intergenic	Charlie7a|DNA|hAT-Charlie	16035	NR_037177	100294145	Hs.559456	NR_037177		LOC100294145	-	uncharacterized LOC100294145	ncRNA	0.005102	0.334465	
chunk0062_440_1	chr14	75420940	75421158	+	0	NA	Intergenic	Intergenic	-6757	NM_001135047	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.000000	0.356164	
chunk0146_140_1	chr4	159526159	159526634	+	0	NA	Intergenic	Intergenic	258550	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.014737	0.413866	221(TGGTACAGAAAGTGCT,-,0.00),222(GGTACAGAAAGTGCTG,+,0.00)
chunk0007_187_1	chr1	80768288	80768962	+	0	NA	Intergenic	Intergenic	127338	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.004451	0.317037	360(AAGTACAGTGAGTTCA,-,0.00),361(AGTACAGTGAGTTCAG,+,0.00)
chunk0181_11_1	chr7	77692153	77692362	+	0	NA	intron (NR_038361, intron 1 of 2)	intron (NR_038361, intron 1 of 2)	-4169	NM_198467	222194	Hs.72451	NM_198467	ENSG00000187257	RSBN1L	-	round spermatid basic protein 1 like	protein-coding	0.023923	0.428571	
chunk0074_283_1	chr16	29290964	29291163	+	0	NA	Intergenic	Intergenic	-11224	NR_002939	440352	Hs.658149	NR_002939		SNX29P2	RUNDC2C	sorting nexin 29 pseudogene 2	pseudo	0.050251	0.640000	
chunk0188_143_1	chr8	9592230	9592879	+	0	NA	intron (NM_003747, intron 2 of 26)	intron (NM_003747, intron 2 of 26)	36619	NM_003747	8658	Hs.370267	NM_003747	ENSG00000173273	TNKS	ARTD5|PARP-5a|PARP5A|PARPL|TIN1|TINF1|TNKS1|pART5	tankyrase	protein-coding	0.007704	0.346154	
chunk0057_189_1	chr13	102838255	102838670	+	0	NA	intron (NM_017693, intron 9 of 10)	intron (NM_017693, intron 9 of 10)	-7379	NM_000123	2073	Hs.258429	NM_000123	ENSG00000134899	ERCC5	COFS3|ERCC5-201|ERCM2|UVDR|XPG|XPGC	ERCC excision repair 5, endonuclease	protein-coding	0.002410	0.322115	
chunk0131_299_1	chr3	150620401	150620602	+	0	NA	intron (NM_016275, intron 1 of 5)	L2b|LINE|L2	17222	NM_016275	51714	Hs.369052	NM_016275	ENSG00000198843	SELENOT	SELT	selenoprotein T	protein-coding	0.014925	0.440594	
chunk0084_97_1	chr17	75557254	75557529	+	0	NA	intron (NM_001015002, intron 3 of 9)	intron (NM_001015002, intron 3 of 9)	-30667	NM_001309242	80022	Hs.390817	NM_001080847	ENSG00000266714	MYO15B	MYO15BP	myosin XVB	protein-coding	0.021818	0.619565	
chunk0077_432_1	chr16	85563668	85563912	+	0	NA	Intergenic	L3b|LINE|CR1	-47633	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.040984	0.620408	
chunk0108_281_1	chr2	234687901	234688217	+	0	NA	intron (NR_132376, intron 1 of 2)	intron (NR_132376, intron 1 of 2)	5391	NR_132376	106144537	Hs.580616	NR_132376	ENSG00000280744	LINC01173	-	long intergenic non-protein coding RNA 1173	ncRNA	0.009494	0.536278	
chunk0170_440_1	chr6	119108985	119109396	+	0	NA	intron (NM_001100411, intron 1 of 16)	intron (NM_001100411, intron 1 of 16)	-30543	NM_024581	79632	Hs.443789	NM_024581	ENSG00000111879	FAM184A	C6orf60	family with sequence similarity 184 member A	protein-coding	0.000000	0.344660	
chunk0018_52_1	chr1	216451725	216452337	+	0	NA	Intergenic	Intergenic	-28635	NM_007123	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.013072	0.398042	
chunk0019_236_1	chr1	227385116	227385811	+	0	NA	Intergenic	L1MC1|LINE|L1	-67338	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.007194	0.415230	
chunk0050_421_1	chr12	109963860	109964376	+	0	NA	intron (NM_001135214, intron 9 of 18)	intron (NM_001135214, intron 9 of 18)	32271	NM_057169	9815	Hs.434996	NM_014776	ENSG00000139436	GIT2	CAT-2|CAT2|PKL	GIT ArfGAP 2	protein-coding	0.003876	0.367505	
chunk0010_143_1	chr1	114865799	114866488	+	0	NA	intron (NR_104211, intron 8 of 32)	L1MC1|LINE|L1	11340	NR_104211	6847	Hs.112743	NM_003176	ENSG00000198765	SYCP1	CT8|HOM-TES-14|SCP-1|SCP1	synaptonemal complex protein 1	protein-coding	0.005806	0.360870	
chunk0107_82_1	chr2	212913750	212914193	+	0	NA	Intergenic	Intergenic	-12286	NR_039935	100616267		NR_039935	ENSG00000266354	MIR4776-1	mir-4776-1	microRNA 4776-1	ncRNA	0.013544	0.371622	
chunk0175_148_1	chr7	3670817	3671095	+	0	NA	intron (NM_152744, intron 4 of 44)	L2b|LINE|L2	369508	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.010791	0.401434	
chunk0112_113_1	chr20	38448178	38448877	+	0	NA	promoter-TSS (NR_002986)	promoter-TSS (NR_002986)	444	NR_002972	677821	Hs.741059	NR_002972	ENSG00000274309	SNORA71E	ACA39|SNORA39	small nucleolar RNA, H/ACA box 71E	snoRNA	0.005722	0.502857	
chunk0149_288_1	chr5	25357693	25357939	+	0	NA	Intergenic	L1MA2|LINE|L1	-517233	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.024390	0.510121	
chunk0006_415_1	chr1	76068657	76069435	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-5658	NM_152996	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.002571	0.379974	
chunk0191_165_1	chr8	50000535	50001315	+	0	NA	intron (NM_001287814, intron 1 of 16)	intron (NM_001287814, intron 1 of 16)	89146	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.006410	0.396927	
chunk0072_410_1	chr15	100897707	100898302	+	0	NA	intron (NM_000693, intron 7 of 12)	intron (NM_000693, intron 7 of 12)	18312	NM_000693	220	Hs.459538	NM_000693	ENSG00000184254	ALDH1A3	ALDH1A6|ALDH6|MCOP8|RALDH3	aldehyde dehydrogenase 1 family member A3	protein-coding	0.026891	0.588926	
chunk0202_404_1	chr9	81460347	81460848	+	0	NA	Intergenic	Intergenic	228938	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.001996	0.352590	
chunk0089_4_1	chr18	57359764	57360353	+	0	NA	exon (NM_015879, exon 4 of 4)	exon (NM_015879, exon 4 of 4)	7568	NM_015879	51046	Hs.23172	NM_015879	ENSG00000177511	ST8SIA3	SIAT8C|ST8SiaIII	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.010187	0.413559	
chunk0109_166_1	chr20	4029514	4029948	+	0	NA	Intergenic	L1MD2|LINE|L1	-14162	NM_001134338	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.009217	0.360920	
chunk0056_151_1	chr13	84015809	84016390	+	0	NA	Intergenic	(TTAT)n|Simple_repeat|Simple_repeat	-124503	NR_046871	100874128	Hs.578060	NR_046871		LINC00333	NCRNA00333	long intergenic non-protein coding RNA 333	ncRNA	0.005164	0.300687	
chunk0094_12_1	chr2	1037264	1037882	+	0	NA	intron (NM_018968, intron 1 of 16)	L1MB8|LINE|L1	86705	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.012945	0.444265	
chunk0202_259_1	chr9	76879104	76879737	+	0	NA	intron (NM_015225, intron 1 of 18)	L2a|LINE|L2	26667	NR_131751	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.004739	0.350158	
chunk0109_403_1	chr2	240409500	240410028	+	0	NA	Intergenic	L1M7|LINE|L1	-25934	NM_002081	2817	Hs.328232	NM_002081	ENSG00000063660	GPC1	glypican	glypican 1	protein-coding	0.011364	0.361059	
chunk0022_305_1	chr10	15710371	15710914	+	0	NA	intron (NM_001291494, intron 2 of 28)	intron (NM_001291494, intron 2 of 28)	9693	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.011050	0.463235	
chunk0137_160_1	chr4	16043832	16044704	+	0	NA	intron (NM_001145847, intron 2 of 26)	intron (NM_001145847, intron 2 of 26)	31850	NM_001145851	8842	Hs.614734	NM_006017	ENSG00000007062	PROM1	AC133|CD133|CORD12|MCDR2|MSTP061|PROML1|RP41|STGD4	prominin 1	protein-coding	0.010321	0.428408	
chunk0203_412_1	chr9	90920911	90921573	+	0	NA	Intergenic	Intergenic	93822	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.015106	0.567119	345(AGGGACACTGTGTTCC,-,0.00),346(GGGACACTGTGTTCCT,+,0.00)
chunk0089_293_1	chr18	63202371	63202753	+	0	NA	intron (NM_000633, intron 2 of 2)	intron (NM_000633, intron 2 of 2)	116818	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.007853	0.375979	
chunk0163_352_1	chr6	15569754	15569953	+	0	NA	intron (NM_001271667, intron 7 of 9)	L2b|LINE|L2	93205	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.015075	0.405000	
chunk0004_304_1	chr1	49025036	49025745	+	0	NA	intron (NM_032785, intron 5 of 13)	intron (NM_032785, intron 5 of 13)	-232021	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.004231	0.421127	381(ATAAACAGGATGTTCC,-,0.00)
chunk0067_39_1	chr15	40549503	40550217	+	0	NA	intron (NM_001289132, intron 3 of 3)	intron (NM_001289132, intron 3 of 3)	15197	NM_001289132	90416	Hs.654661	NM_052849	ENSG00000128891	CCDC32	C15orf57	coiled-coil domain containing 32	protein-coding	0.016807	0.520280	
chunk0168_406_1	chr6	94941443	94942002	+	0	NA	Intergenic	L1MA7|LINE|L1	635729	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.010733	0.339286	
chunk0128_270_1	chr3	110564799	110565205	+	0	NA	Intergenic	Intergenic	504957	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.000000	0.366093	
chunk0156_460_1	chr5	115054254	115054818	+	0	NA	Intergenic	Intergenic	115427	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.000000	0.458407	
chunk0084_425_1	chr17	82528528	82529000	+	0	NA	intron (NM_004514, intron 1 of 8)	intron (NM_004514, intron 1 of 8)	9046	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.025424	0.507400	
chunk0153_322_1	chr5	73823096	73823295	+	0	NA	intron (NM_001244364, intron 1 of 27)	MIRb|SINE|MIR	9677	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.015075	0.375000	
chunk0018_140_1	chr1	218646251	218646888	+	0	NA	intron (NR_031644, intron 3 of 6)	LTR40a|LTR|ERVL	203943	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.009419	0.410658	
chunk0065_50_1	chr15	22726067	22726429	+	0	NA	Intergenic	Intergenic	-31609	NR_040057	283683	Hs.534616	NR_040057	ENSG00000274253	LOC283683	-	uncharacterized LOC283683	ncRNA	0.000000	0.380165	
chunk0011_7_1	chr1	125173912	125174155	+	0	NA	Intergenic	Intergenic	3654921	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.061728	0.372951	
chunk0066_121_1	chr15	30991505	30991793	+	0	NA	promoter-TSS (NM_017762).2	promoter-TSS (NM_017762).2	-45	NM_017762	54893	Hs.30141	NM_017762	ENSG00000166912	MTMR10	-	myotubularin related protein 10	protein-coding	0.159722	0.792388	
chunk0178_443_1	chr7	41946934	41947426	+	0	NA	Intergenic	Intergenic	-244072	NM_002192	3624	Hs.28792	NM_002192	ENSG00000122641	INHBA	EDF|FRP	inhibin subunit beta A	protein-coding	0.008130	0.486815	
chunk0030_39_1	chr10	111579773	111580123	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	502916	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.002857	0.313390	
chunk0032_99_1	chr11	3697943	3698498	+	0	NA	intron (NM_016320, intron 25 of 32)	intron (NM_016320, intron 25 of 32)	-26836	NM_001303035	57053	Hs.732806	NM_020402	ENSG00000129749	CHRNA10	-	cholinergic receptor nicotinic alpha 10 subunit	protein-coding	0.001802	0.309353	
chunk0120_273_1	chr3	9352918	9353388	+	0	NA	Intergenic	Intergenic	-9880	NM_015453	25917	Hs.443081	NM_015453	ENSG00000134077	THUMPD3	-	THUMP domain containing 3	protein-coding	0.006383	0.486200	
chunk0202_341_1	chr9	79489471	79490313	+	0	NA	Intergenic	Intergenic	-81881	NM_001282749	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.008314	0.381969	504(AAGAACACACAGACCT,-,0.00),505(AGAACACACAGACCTT,+,0.00)
chunk0171_41_1	chr6	120841699	120842334	+	0	NA	Intergenic	Intergenic	492484	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.006299	0.402516	
chunk0192_334_1	chr8	67344599	67344932	+	0	NA	Intergenic	Intergenic	-1088	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.009009	0.371257	
chunk0043_251_1	chr12	20421401	20421912	+	0	NA	intron (NM_000921, intron 1 of 15)	intron (NM_000921, intron 1 of 15)	52411	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.003914	0.392578	320(GAGCACTCTGTGTTCC,-,0.00),321(AGCACTCTGTGTTCCT,+,0.00)
chunk0176_55_1	chr7	11192974	11193414	+	0	NA	Intergenic	MER61-int|LTR|ERV1	219322	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.029545	0.539683	
chunk0132_432_1	chr3	165034852	165035340	+	0	NA	intron (NM_001041, intron 22 of 47)	L2|LINE|L2	43399	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.002049	0.343558	
chunk0053_319_1	chr13	34201421	34201820	+	0	NA	Intergenic	L1MEg|LINE|L1	383551	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.002506	0.352500	
chunk0060_451_1	chr14	54895595	54895794	+	0	NA	intron (NM_001024024, intron 1 of 6)	intron (NM_001024024, intron 1 of 6)	7130	NM_001024024	2643	Hs.86724	NM_000161	ENSG00000131979	GCH1	DYT14|DYT5|DYT5a|GCH|GTP-CH-1|GTPCH1|HPABH4B	GTP cyclohydrolase 1	protein-coding	0.005025	0.390000	183(AAGGACAGCCAGTTCC,-,0.00),184(AGGACAGCCAGTTCCT,+,0.00)
chunk0181_46_1	chr7	79913146	79913391	+	0	NA	Intergenic	L1MC4|LINE|L1	-221556	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.000000	0.284553	190(AGTAACACCATGTTCC,-,0.00),191(GTAACACCATGTTCCT,+,0.00)
chunk0023_299_1	chr10	28797873	28798236	+	0	NA	intron (NR_120652, intron 2 of 3)	intron (NR_120652, intron 2 of 3)	-2004	NR_038374	100507605	Hs.119207	NR_038374	ENSG00000235824	LINC00837	-	long intergenic non-protein coding RNA 837	ncRNA	0.000000	0.398352	
chunk0139_368_1	chr4	60426545	60428126	+	0	NA	Intergenic	Intergenic	-495284	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.003795	0.322377	234(AGTACAGTCTGTCTAT,+,0.00)
chunk0004_441_1	chr1	53171974	53172517	+	0	NA	Intergenic	Intergenic	-24184	NM_000098	1376	Hs.713535	NM_000098	ENSG00000157184	CPT2	CPT1|CPTASE|IIAE4	carnitine palmitoyltransferase 2	protein-coding	0.011050	0.492647	262(GAGTACAGACTGCTCT,-,0.00),263(AGTACAGACTGCTCTC,+,0.00)
chunk0146_52_1	chr4	155676368	155676767	+	0	NA	intron (NM_000856, intron 3 of 10)	intron (NM_000856, intron 3 of 10)	8904	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.012531	0.367500	
chunk0073_221_1	chr16	10943621	10944045	+	0	NA	promoter-TSS (NM_001243403)	promoter-TSS (NM_001243403)	-655	NM_001243403	23274	Hs.35490	NM_015226	ENSG00000038532	CLEC16A	Gop-1|KIAA0350	C-type lectin domain containing 16A	protein-coding	0.007075	0.407059	223(AAGTACAAAATGTTCA,-,0.00),224(AGTACAAAATGTTCAG,+,0.00)
chunk0153_240_1	chr5	72274361	72274942	+	0	NA	intron (NM_001286748, intron 4 of 11)	Tigger3b|DNA|TcMar-Tigger	45606	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.008606	0.367698	
chunk0208_353_1	chrX	25458910	25459221	+	0	NA	Intergenic	Intergenic	-443117	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.003215	0.378205	
chunk0116_235_1	chr21	38262388	38262634	+	0	NA	intron (NM_002243, intron 2 of 3)	intron (NM_002243, intron 2 of 3)	5707	NM_170736	3772	Hs.411299	NM_002243	ENSG00000157551	KCNJ15	IRKK|KIR1.3|KIR4.2	potassium voltage-gated channel subfamily J member 15	protein-coding	0.004065	0.327935	
chunk0156_110_1	chr5	105530626	105531016	+	0	NA	Intergenic	LTR16|LTR|ERVL	431347	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.005128	0.404092	
chunk0203_162_1	chr9	85917706	85917905	+	0	NA	Intergenic	L1M5|LINE|L1	-23337	NM_024635	60560	Hs.436098	NM_021929	ENSG00000135040	NAA35	EGAP|MAK10|MAK10P|bA379P1.1	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding	0.020101	0.470000	
chunk0168_413_1	chr6	95234766	95235072	+	0	NA	Intergenic	L1MA3|LINE|L1	342532	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.006536	0.371336	
chunk0137_410_1	chr4	27897764	27898107	+	0	NA	Intergenic	Intergenic	680456	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.005831	0.316860	
chunk0185_448_1	chr7	135010585	135011036	+	0	NA	intron (NM_178563, intron 4 of 16)	L1ME3B|LINE|L1	24302	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.002217	0.309735	
chunk0051_78_1	chr12	113781699	113782237	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-8285	NR_110026	100506465	Hs.211461	NR_110025	ENSG00000249550	LINC01234	LCAL84|onco-lncRNA-32	long intergenic non-protein coding RNA 1234	ncRNA	0.007435	0.469388	
chunk0082_110_1	chr17	54832896	54833313	+	0	NA	Intergenic	L1ME3|LINE|L1	-67587	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.002398	0.318182	
chunk0161_44_1	chr5	165923952	165924189	+	0	NA	Intergenic	Intergenic	1002300	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.000000	0.315126	
chunk0192_272_1	chr8	66090847	66091577	+	0	NA	intron (NM_033105, intron 5 of 5)	L2b|LINE|L2	-35831	NM_184085	84675	Hs.85524	NM_033058	ENSG00000147573	TRIM55	MURF-2|RNF29|muRF2	tripartite motif containing 55	protein-coding	0.002740	0.428181	
chunk0191_415_1	chr8	57732290	57732709	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-245859	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.002387	0.347619	
chunk0180_140_1	chr7	56373440	56373639	+	0	NA	Intergenic	Intergenic	74836	NR_029420	650226	Hs.448401	NR_029420		LOC650226	-	ankyrin repeat domain 26 pseudogene	pseudo	0.065327	0.640000	
chunk0104_171_1	chr2	174535806	174536358	+	0	NA	Intergenic	L1ME3|LINE|L1	21990	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.014493	0.406872	
chunk0181_325_1	chr7	87906034	87906623	+	0	NA	intron (NM_006716, intron 11 of 11)	(T)n|Simple_repeat|Simple_repeat	-27923	NM_016351	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.005093	0.352542	210(TAGTACTGGTTGTTCC,-,0.00),211(AGTACTGGTTGTTCCT,+,0.00)
chunk0128_369_1	chr3	113271360	113271978	+	0	NA	intron (NM_001301861, intron 6 of 19)	Arthur1A|DNA|hAT-Tip100	59172	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.014563	0.478191	
chunk0029_436_1	chr10	110083867	110084135	+	0	NA	intron (NM_016824, intron 1 of 14)	intron (NM_016824, intron 1 of 14)	-75620	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.000000	0.345725	
chunk0117_256_1	chr22	23473214	23473555	+	0	NA	non-coding (NR_110539, exon 6 of 12)	non-coding (NR_110539, exon 6 of 12)	13596	NR_110539	388882	Hs.542766	NR_110539	ENSG00000178248	FAM230I	LINC01658	family with sequence similarity 230 member I	ncRNA	0.011730	0.441520	
chunk0043_6_1	chr12	12804201	12804509	+	0	NA	Intergenic	Intergenic	-8991	NM_201224	51202	Hs.719938	NM_016355	ENSG00000213782	DDX47	E4-DBP|HQ0256|MSTP162|RRP3	DEAD-box helicase 47	protein-coding	0.012987	0.430421	
chunk0097_281_1	chr2	55015469	55015843	+	0	NA	intron (NM_153828, intron 1 of 6)	L1ME4a|LINE|L1	-5322	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.002674	0.333333	222(TAGTACAGAATGTCCA,-,0.00),223(AGTACAGAATGTCCAG,+,0.00)
chunk0149_422_1	chr5	29521186	29521480	+	0	NA	Intergenic	Intergenic	-125357	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.006803	0.291525	
chunk0049_419_1	chr12	97568499	97569274	+	0	NA	Intergenic	Intergenic	5074	NR_029678	406926		NR_029678	ENSG00000207586	MIR135A2	MIRN135-2|MIRN135A2|mir-135a-2	microRNA 135a-2	ncRNA	0.009032	0.364691	
chunk0183_9_1	chr7	102862396	102862773	+	0	NA	intron (NM_145032, intron 16 of 19)	intron (NM_145032, intron 16 of 19)	-50313	NM_005824	10234	Hs.567412	NM_005824	ENSG00000128606	LRRC17	P37NB	leucine rich repeat containing 17	protein-coding	0.000000	0.298942	
chunk0078_407_1	chr16	88810854	88811351	+	0	NA	intron (NM_001030018, intron 2 of 4)	intron (NM_001030018, intron 2 of 4)	832	NM_000485	353	Hs.28914	NM_000485	ENSG00000198931	APRT	AMP|APRTD	adenine phosphoribosyltransferase	protein-coding	0.030181	0.634538	246(AGGAACACTCTGTTCT,-,0.00),247(GGAACACTCTGTTCTC,+,0.00)
chunk0209_342_1	chrX	51727758	51728041	+	0	NA	Intergenic	L1MCb|LINE|L1	-15486	NM_018094	23708	Hs.59523	NM_018094	ENSG00000189369	GSPT2	ERF3B|GST2	G1 to S phase transition 2	protein-coding	0.007067	0.281690	
chunk0111_278_1	chr20	31514402	31515224	+	0	NA	intron (NM_178580, intron 1 of 12)	CpG	403	NM_030789	81502	Hs.373741	NM_030789	ENSG00000101294	HM13	H13|IMP1|IMPAS|IMPAS-1|MSTP086|PSENL3|PSL3|SPP|SPPL1	histocompatibility minor 13	protein-coding	0.076642	0.642770	651(GGGCACTGATTGTTCT,-,0.00),652(GGCACTGATTGTTCTG,+,0.00)
chunk0101_341_1	chr2	137493169	137493420	+	0	NA	intron (NM_001316349, intron 15 of 27)	intron (NM_001316349, intron 15 of 27)	434638	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.003984	0.317460	
chunk0198_187_1	chr8	133449309	133449688	+	0	NA	Intergenic	Intergenic	122442	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.018470	0.523684	
chunk0139_431_1	chr4	64499889	64500221	+	0	NA	Intergenic	Intergenic	-90595	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.009036	0.330330	
chunk0161_227_1	chr5	171070521	171071329	+	0	NA	intron (NM_022897, intron 14 of 27)	L1ME4b|LINE|L1	209043	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.001238	0.330037	
chunk0025_41_1	chr10	49107121	49107363	+	0	NA	intron (NM_144984, intron 2 of 2)	MER67A|LTR|ERV1	8290	NM_001031746	196740	Hs.522928	NM_144984	ENSG00000165633	VSTM4	C10orf72	V-set and transmembrane domain containing 4	protein-coding	0.000000	0.502058	
chunk0124_180_1	chr3	55428159	55428556	+	0	NA	Intergenic	Intergenic	53041	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.007557	0.477387	
chunk0201_70_1	chr9	34125177	34125684	+	0	NA	intron (NM_015397, intron 1 of 8)	intron (NM_015397, intron 1 of 8)	1343	NM_015397	25853	Hs.493750	NM_015397	ENSG00000198876	DCAF12	CT102|KIAA1892|TCC52|WDR40A	DDB1 and CUL4 associated factor 12	protein-coding	0.009862	0.413386	
chunk0036_302_1	chr11	65927819	65928298	+	0	NA	Intergenic	L2a|LINE|L2	8801	NM_006442	10589	Hs.356742	NM_006442	ENSG00000175550	DRAP1	NC2-alpha	DR1 associated protein 1	protein-coding	0.016701	0.558333	
chunk0176_184_1	chr7	13872639	13873019	+	0	NA	Intergenic	Intergenic	113685	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.000000	0.380577	
chunk0170_388_1	chr6	117078552	117079101	+	0	NA	Intergenic	L2c|LINE|L2	-186732	NM_182645	245806	Hs.99324	NM_153453	ENSG00000170162	VGLL2	VGL2|VITO1	vestigial like family member 2	protein-coding	0.003643	0.354545	
chunk0136_218_1	chr4	7805607	7805965	+	0	NA	intron (NM_198595, intron 9 of 16)	L2b|LINE|L2	51696	NR_026892	84740	Hs.663029	NM_032654	ENSG00000272620	AFAP1-AS1	AFAP1-AS|AFAP1AS	AFAP1 antisense RNA 1	ncRNA	0.019553	0.493036	
chunk0096_259_1	chr2	31422867	31423420	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-8398	NM_000379	7498	Hs.250	NM_000379	ENSG00000158125	XDH	XAN1|XO|XOR	xanthine dehydrogenase	protein-coding	0.005425	0.370036	
chunk0015_383_1	chr1	190587893	190588633	+	0	NA	Intergenic	Intergenic	-36627	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.006757	0.317139	208(TAGAACATTCTGGTCT,-,0.00),209(AGAACATTCTGGTCTT,+,0.00)
chunk0123_337_1	chr3	47737221	47737526	+	0	NA	intron (NM_003074, intron 4 of 27)	AluJr|SINE|Alu	44542	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.006557	0.372549	
chunk0085_178_1	chr18	5392744	5393031	+	0	NA	3' UTR (NM_001281534, exon 20 of 20)	3' UTR (NM_001281534, exon 20 of 20)	-95834	NM_001243704	7541	Hs.592340	NM_003409	ENSG00000198081	ZBTB14	ZF5|ZFP-161|ZFP-5|ZFP161|ZNF478	zinc finger and BTB domain containing 14	protein-coding	0.010453	0.354167	
chunk0211_106_1	chrX	111205485	111205878	+	0	NA	intron (NM_001128168, intron 14 of 15)	intron (NM_001128168, intron 14 of 15)	64865	NM_014289	827	Hs.496593	NM_014289	ENSG00000077274	CAPN6	CANPX|CAPNX|CalpM|DJ914P14.1	calpain 6	protein-coding	0.002545	0.355330	
chunk0199_271_1	chr9	6395254	6395803	+	0	NA	Intergenic	Intergenic	-17623	NR_046386	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.001821	0.367273	
chunk0098_82_1	chr2	67477506	67477785	+	0	NA	Intergenic	MER131|DNA?|DNA?	80335	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.003584	0.417857	
chunk0002_95_1	chr1	14947313	14947832	+	0	NA	intron (NM_001017999, intron 1 of 7)	intron (NM_001017999, intron 1 of 7)	1653	NM_001017999	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.007707	0.548077	
chunk0164_91_1	chr6	20217471	20217670	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-5106	NR_073465	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.005025	0.380000	
chunk0094_315_1	chr2	8924176	8924776	+	0	NA	intron (NM_138799, intron 3 of 12)	intron (NM_138799, intron 3 of 12)	79271	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.005000	0.405990	
chunk0136_261_1	chr3	194311457	194311707	+	0	NA	intron (NR_024480, intron 1 of 2)	intron (NR_024480, intron 1 of 2)	1222	NR_024480	100131551	Hs.128066	NR_024480	ENSG00000214145	LINC00887	HEIRCC	long intergenic non-protein coding RNA 887	ncRNA	0.012000	0.454183	
chunk0180_381_1	chr7	74381520	74382023	+	0	NA	intron (NM_032421, intron 10 of 15)	L1ME4b|LINE|L1	-72019	NM_016328	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.007952	0.400794	
chunk0069_109_1	chr15	61660158	61660688	+	0	NA	Intergenic	Intergenic	400042	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.001887	0.386064	
chunk0172_396_1	chr6	139730701	139730920	+	0	NA	Intergenic	Intergenic	-40263	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.004566	0.368182	
chunk0109_336_1	chr20	9390224	9390824	+	0	NA	intron (NM_001172646, intron 15 of 37)	intron (NM_001172646, intron 15 of 37)	82724	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.005000	0.336106	116(GGAACAGAATCTCCTT,+,0.00),317(CAGTACAAGATGTCCA,-,0.00)
chunk0057_250_1	chr13	105043708	105043907	+	0	NA	Intergenic	Intergenic	-422060	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.000000	0.440000	
chunk0155_134_1	chr5	93530515	93530830	+	0	NA	intron (NR_109825, intron 5 of 8)	intron (NR_109825, intron 5 of 8)	40671	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.003175	0.386076	213(AGGCACAAAGAGTTCT,-,0.00),214(GGCACAAAGAGTTCTT,+,0.00)
chunk0075_171_1	chr16	51979441	51979806	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	94312	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.005479	0.431694	
chunk0126_73_1	chr3	74617057	74617510	+	0	NA	Intergenic	Intergenic	-96143	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002208	0.394273	
chunk0026_266_1	chr10	66979892	66980312	+	0	NA	intron (NM_178011, intron 2 of 2)	intron (NM_178011, intron 2 of 2)	32051	NR_111911	101928961	Hs.687014	NR_111911		LOC101928961	-	uncharacterized LOC101928961	ncRNA	0.002381	0.377672	354(GAGACCACTGTGTTCC,-,0.00),355(AGACCACTGTGTTCCT,+,0.00)
chunk0026_277_1	chr10	67240000	67240443	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	163189	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.002257	0.391892	
chunk0005_94_1	chr1	56414733	56415149	+	0	NA	Intergenic	Intergenic	164643	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.019231	0.486811	
chunk0191_335_1	chr8	56005196	56005465	+	0	NA	intron (NM_001111097, intron 12 of 12)	L1MB3|LINE|L1	68571	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.007435	0.511111	
chunk0110_83_1	chr20	11219618	11219817	+	0	NA	Intergenic	LTR37B|LTR|ERV1	53666	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.010050	0.360000	
chunk0061_93_1	chr14	57409499	57410008	+	0	NA	3' UTR (NM_001011713, exon 5 of 5)	3' UTR (NM_001011713, exon 5 of 5)	19200	NM_001011713	122830	Hs.165465	NM_001011713	ENSG00000139977	NAA30	C14orf35|MAK3|Mak3p|NAT12|NAT12P	N(alpha)-acetyltransferase 30, NatC catalytic subunit	protein-coding	0.009823	0.364706	
chunk0066_282_1	chr15	35235398	35236239	+	0	NA	Intergenic	Intergenic	-1508	NR_003144	723972	Hs.631698	NR_003144	ENSG00000259516	ANP32AP1	-	acidic nuclear phosphoprotein 32 family member A pseudogene 1	pseudo	0.001189	0.311164	
chunk0021_441_1	chr1	248239173	248239387	+	0	NA	exon (NM_017504, exon 1 of 1)	exon (NM_017504, exon 1 of 1)	351	NM_017504	26245	Hs.381309	NM_017504	ENSG00000171180	OR2M4	HSHTPCRX18|HTPCRX18|OR1-55|OST710|TPCR100	olfactory receptor family 2 subfamily M member 4	protein-coding	0.009346	0.465116	
chunk0126_12_1	chr3	73479958	73480157	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-5425	NM_001303141	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.000000	0.430000	
chunk0088_83_1	chr18	44789594	44790095	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	108946	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.011976	0.430279	
chunk0032_329_1	chr11	10109237	10109492	+	0	NA	intron (NM_030962, intron 2 of 39)	intron (NM_030962, intron 2 of 39)	184843	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.003922	0.320312	
chunk0003_437_1	chr1	41208707	41208923	+	0	NA	intron (NM_001172219, intron 1 of 14)	L1PA6|LINE|L1	33328	NM_001172218	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.004630	0.368664	
chunk0198_356_1	chr8	140699574	140699773	+	0	NA	intron (NM_001316342, intron 26 of 32)	intron (NM_001316342, intron 26 of 32)	32980	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.005025	0.365000	
chunk0147_241_1	chr4	182917891	182918090	+	0	NA	promoter-TSS (NM_001012732)	promoter-TSS (NM_001012732)	-513	NM_001921	1635	Hs.183850	NM_001921	ENSG00000129187	DCTD	-	dCMP deaminase	protein-coding	0.060302	0.635000	
chunk0132_312_1	chr3	160569668	160569998	+	0	NA	Intergenic	Intergenic	-4245	NM_002268	3840	Hs.467866	NM_002268	ENSG00000186432	KPNA4	IPOA3|QIP1|SRP3	karyopherin subunit alpha 4	protein-coding	0.003030	0.308157	
chunk0120_45_1	chr3	2862962	2863375	+	0	NA	intron (NM_001206955, intron 6 of 23)	intron (NM_001206955, intron 6 of 23)	-29047	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.009685	0.393720	
chunk0018_381_1	chr1	222286126	222286399	+	0	NA	Intergenic	LTR40c|LTR|ERVL	261840	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.010989	0.500000	
chunk0073_182_1	chr16	8955930	8956223	+	0	NA	intron (NM_003470, intron 1 of 30)	intron (NM_003470, intron 1 of 30)	7408	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.006826	0.472789	
chunk0192_414_1	chr8	69374572	69374919	+	0	NA	Intergenic	L1M4|LINE|L1	73499	NR_110433	100505739	Hs.127115	NR_110433		LINC01603	-	long intergenic non-protein coding RNA 1603	ncRNA	0.000000	0.293103	
chunk0030_342_1	chr10	118440952	118441164	+	0	NA	Intergenic	Intergenic	83950	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.000000	0.300469	
chunk0171_33_1	chr6	120501655	120501854	+	0	NA	Intergenic	L1M3|LINE|L1	486575	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.000000	0.335000	
chunk0133_304_1	chr3	172285346	172285565	+	0	NA	intron (NM_022763, intron 6 of 25)	intron (NM_022763, intron 6 of 25)	163001	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.018265	0.377273	
chunk0032_208_1	chr11	7457243	7457516	+	0	NA	intron (NR_103855, intron 3 of 4)	L2c|LINE|L2	8456	NR_103855	100506258	Hs.661614	NR_103855	ENSG00000251364	LOC100506258	-	uncharacterized LOC100506258	ncRNA	0.003663	0.459854	
chunk0143_195_1	chr4	112818984	112819444	+	0	NA	intron (NM_001127493, intron 1 of 46)	intron (NM_001127493, intron 1 of 46)	1131	NM_001127493	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.004348	0.373102	242(AAGAACAGATTGTTTA,-,0.00),243(AGAACAGATTGTTTAT,+,0.00)
chunk0121_171_1	chr3	19910717	19911318	+	0	NA	intron (NM_144715, intron 5 of 12)	L1M1|LINE|L1	23197	NM_144715	151651	Hs.733920	NM_144715	ENSG00000163576	EFHB	CFAP21	EF-hand domain family member B	protein-coding	0.003328	0.401993	
chunk0158_146_1	chr5	127435264	127435795	+	0	NA	intron (NM_032446, intron 17 of 25)	intron (NM_032446, intron 17 of 25)	-82080	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.011299	0.355263	
chunk0031_167_1	chr10	125416045	125416269	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-158214	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.004464	0.453333	
chunk0175_441_1	chr6	169934369	169934684	+	0	NA	Intergenic	CpG	-28097	NR_027434	100131532	Hs.703417	NR_027434		LOC100131532	-	uncharacterized LOC100131532	ncRNA	0.073016	0.623418	
chunk0031_176_1	chr10	125624822	125625117	+	0	NA	Intergenic	Intergenic	50598	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.013559	0.516892	
chunk0083_309_1	chr17	69465100	69465522	+	0	NA	intron (NM_002758, intron 1 of 11)	intron (NM_002758, intron 1 of 11)	50614	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.004739	0.375887	
chunk0195_2_1	chr8	92815590	92816198	+	0	NA	Intergenic	Intergenic	-29834	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.003289	0.377668	198(GAGAACTCACAGTACC,-,0.00)
chunk0182_458_1	chr7	102175826	102176294	+	0	NA	intron (NM_001202546, intron 9 of 21)	intron (NM_001202546, intron 9 of 21)	-109002	NM_020979	10603	Hs.489448	NM_020979	ENSG00000160999	SH2B2	APS	SH2B adaptor protein 2	protein-coding	0.034188	0.471215	181(CTGGACAGCCTGTGCC,-,0.00),182(TGGACAGCCTGTGCCT,+,0.00)
chunk0013_375_1	chr1	172512734	172512993	+	0	NA	Intergenic	Intergenic	-19486	NM_016227	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.000000	0.253846	
chunk0011_359_1	chr1	152996806	152997036	+	0	NA	Intergenic	Intergenic	-4826	NM_005416	6707	Hs.139322	NM_005416	ENSG00000163209	SPRR3	-	small proline rich protein 3	protein-coding	0.013043	0.532468	161(GAGAACAATCTGAGCC,-,0.00),162(AGAACAATCTGAGCCC,+,0.00)
chunk0056_324_1	chr13	91109947	91110192	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-20452	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.020408	0.459350	
chunk0064_392_1	chr14	99192028	99192778	+	0	NA	intron (NM_022898, intron 2 of 2)	intron (NM_022898, intron 2 of 2)	79310	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.036000	0.525965	
chunk0124_341_1	chr3	58356213	58356482	+	0	NA	intron (NM_001289101, intron 1 of 14)	intron (NM_001289101, intron 1 of 14)	23457	NM_001289101	54899	Hs.190544	NM_017771	ENSG00000168297	PXK	MONAKA|SLOB	PX domain containing serine/threonine kinase like	protein-coding	0.011152	0.548148	
chunk0013_246_1	chr1	169727345	169727553	+	0	NA	exon (NM_000450, exon 10 of 14)	exon (NM_000450, exon 10 of 14)	6630	NM_000450	6401	Hs.82848	NM_000450	ENSG00000007908	SELE	CD62E|ELAM|ELAM1|ESEL|LECAM2	selectin E	protein-coding	0.024038	0.545455	
chunk0186_100_1	chr7	137592314	137593006	+	0	NA	intron (NM_004717, intron 12 of 33)	intron (NM_004717, intron 12 of 33)	-248860	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.008671	0.411255	595(AGGTACACTGTGTGCT,-,0.00),596(GGTACACTGTGTGCTT,+,0.00)
chunk0029_316_1	chr10	104319186	104319589	+	0	NA	intron (NM_001272013, intron 1 of 1)	intron (NM_001272013, intron 1 of 1)	-3977	NR_120622	101927472	Hs.670333	NR_120622		ITPRIP-AS1	-	ITPRIP antisense RNA 1	ncRNA	0.019851	0.569307	219(AAGCACAAGATGTTCC,-,0.00),220(AGCACAAGATGTTCCA,+,0.00)
chunk0190_174_1	chr8	32641522	32641852	+	0	NA	intron (NM_013964, intron 5 of 11)	intron (NM_013964, intron 5 of 11)	-5045	NM_013959	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.006061	0.347432	118(AAGAACAAAATGTACC,-,0.00),119(AGAACAAAATGTACCA,+,0.00)
chunk0196_378_1	chr8	115452230	115452429	+	0	NA	intron (NM_001282903, intron 5 of 6)	intron (NM_001282903, intron 5 of 6)	215683	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.015075	0.410000	
chunk0165_411_1	chr6	39030683	39030950	+	0	NA	TTS (NM_001206927)	TTS (NM_001206927)	-17965	NM_002062	2740	Hs.351883	NM_002062	ENSG00000112164	GLP1R	GLP-1|GLP-1-R|GLP-1R	glucagon like peptide 1 receptor	protein-coding	0.007491	0.388060	
chunk0025_33_1	chr10	48755917	48756419	+	0	NA	intron (NM_020945, intron 12 of 61)	L1ME1|LINE|L1	70695	NM_020945	57705	Hs.287379	NM_020945	ENSG00000128815	WDFY4	C10orf64	WDFY family member 4	protein-coding	0.001992	0.298211	239(TAAACATAGTGTGCTT,+,0.00)
chunk0205_351_1	chr9	113418735	113419051	+	0	NA	intron (NM_152786, intron 3 of 13)	intron (NM_152786, intron 3 of 13)	-8144	NM_017443	54107	Hs.108112	NM_017443	ENSG00000148229	POLE3	CHARAC17|CHRAC17|CHRAC2|YBL1|p17	DNA polymerase epsilon 3, accessory subunit	protein-coding	0.012658	0.340694	
chunk0148_103_1	chr5	4407836	4408657	+	0	NA	Intergenic	Intergenic	-365235	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.012180	0.452555	
chunk0209_39_1	chrX	36322658	36323181	+	0	NA	intron (NM_001304548, intron 57 of 63)	intron (NM_001304548, intron 57 of 63)	117373	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.000000	0.320611	
chunk0052_100_1	chr13	22463949	22464210	+	0	NA	Intergenic	Intergenic	253794	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.000000	0.385496	
chunk0049_339_1	chr12	95003538	95003833	+	0	NA	promoter-TSS (NM_018838)	promoter-TSS (NM_018838)	28	NM_001258338	55967	Hs.506374	NM_018838	ENSG00000184752	NDUFA12	B17.2|DAP13|MC1DN23	NADH:ubiquinone oxidoreductase subunit A12	protein-coding	0.084746	0.638514	
chunk0190_53_1	chr8	29538170	29538439	+	0	NA	Intergenic	Intergenic	-187554	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.007435	0.459259	169(GGGAGAGGGTGTGCTT,+,0.00)
chunk0193_389_1	chr8	80379884	80380225	+	0	NA	Intergenic	Intergenic	-105565	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.002933	0.394737	227(GTGAACACTGTGTCCT,-,0.00),228(TGAACACTGTGTCCTC,+,0.00)
chunk0105_283_1	chr2	189803562	189803832	+	0	NA	intron (NM_001289408, intron 3 of 11)	intron (NM_001289408, intron 3 of 11)	-19326	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.011111	0.398524	162(TGGAACACACTGTATT,-,0.00),163(GGAACACACTGTATTT,+,0.00)
chunk0151_10_1	chr5	41156929	41157300	+	0	NA	intron (NM_001115131, intron 13 of 17)	intron (NM_001115131, intron 13 of 17)	56479	NM_000065	729	Hs.481992	NM_000065	ENSG00000039537	C6	-	complement C6	protein-coding	0.005391	0.327957	
chunk0185_141_1	chr7	127391861	127392149	+	0	NA	intron (NM_176814, intron 1 of 5)	CpG	719	NM_176814	168850	Hs.159006	NM_176814	ENSG00000048405	ZNF800	-	zinc finger protein 800	protein-coding	0.152778	0.778547	
chunk0172_158_1	chr6	135888185	135889045	+	0	NA	intron (NM_018945, intron 1 of 12)	intron (NM_018945, intron 1 of 12)	36919	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.003488	0.310105	
chunk0084_72_1	chr17	74804045	74804406	+	0	NA	intron (NM_017728, intron 8 of 9)	intron (NM_017728, intron 8 of 9)	27742	NM_017728	54868	Hs.370262	NM_017728	ENSG00000109066	TMEM104	-	transmembrane protein 104	protein-coding	0.016620	0.511050	
chunk0205_249_1	chr9	110206910	110207635	+	0	NA	intron (NM_001012993, intron 1 of 1)	intron (NM_001012993, intron 1 of 1)	861	NM_001012993	401546	Hs.125608	NM_001012993	ENSG00000188959	C9orf152	bA470J20.2	chromosome 9 open reading frame 152	protein-coding	0.011034	0.617080	
chunk0099_248_1	chr2	97844358	97844968	+	0	NA	intron (NM_015348, intron 5 of 40)	intron (NM_015348, intron 5 of 40)	110257	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.004918	0.381342	176(AATTACAGGCTGTTCC,-,0.00),177(ATTACAGGCTGTTCCA,+,0.00),333(AGGAACAAAATGTCCC,-,0.00),334(GGAACAAAATGTCCCA,+,0.00)
chunk0123_167_1	chr3	43738334	43738555	+	0	NA	Intergenic	Intergenic	47561	NM_016006	51099	Hs.19385	NM_016006	ENSG00000011198	ABHD5	CGI58|IECN2|NCIE2	abhydrolase domain containing 5	protein-coding	0.000000	0.495495	
chunk0123_176_1	chr3	44150939	44151716	+	0	NA	Intergenic	L1ME1|LINE|L1	37115	NR_029700	406929		NR_029700	ENSG00000207954	MIR138-1	MIRN138-1|mir-138-1	microRNA 138-1	ncRNA	0.006435	0.340617	
chunk0105_125_1	chr2	185551521	185551853	+	0	NA	Intergenic	Intergenic	-186941	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.003012	0.297297	
chunk0145_408_1	chr4	152782539	152782824	+	0	NA	intron (NM_001025595, intron 1 of 8)	intron (NM_001025595, intron 1 of 8)	2744	NM_001025595	27236	Hs.416089	NM_014447	ENSG00000164144	ARFIP1	HSU52521	ADP ribosylation factor interacting protein 1	protein-coding	0.003509	0.325175	
chunk0060_158_1	chr14	45195263	45195462	+	0	NA	intron (NM_001308133, intron 19 of 21)	intron (NM_001308133, intron 19 of 21)	58040	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.015075	0.355000	
chunk0159_230_1	chr5	141366273	141366996	+	0	NA	exon (NM_032054, exon 1 of 1)	exon (NM_032054, exon 1 of 1)	2303	NM_032054	56110	Hs.368160	NM_018918	ENSG00000253485	PCDHGA5	CDH-GAMMA-A5|ME3|PCDH-GAMMA-A5	protocadherin gamma subfamily A, 5	protein-coding	0.033195	0.487569	
chunk0165_161_1	chr6	33828113	33828823	+	0	NA	Intergenic	L2a|LINE|L2	-24452	NM_002418	4295	Hs.2813	NM_002418	ENSG00000096395	MLN	-	motilin	protein-coding	0.016901	0.556962	
chunk0084_13_1	chr17	73359758	73360494	+	0	NA	intron (NM_001144952, intron 39 of 44)	intron (NM_001144952, intron 39 of 44)	-48122	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.016304	0.565807	290(TAGAACAGCCTGTCCT,-,0.00),291(AGAACAGCCTGTCCTC,+,0.00)
chunk0004_148_1	chr1	45206435	45206818	+	0	NA	promoter-TSS (NM_020883)	promoter-TSS (NM_020883)	-48	NM_020883	57643	Hs.656613	NM_020883	ENSG00000162415	ZSWIM5	-	zinc finger SWIM-type containing 5	protein-coding	0.164491	0.768229	
chunk0119_115_1	chr22	42601849	42602246	+	0	NA	exon (NM_001278657, exon 3 of 9)	exon (NM_001278657, exon 3 of 9)	12915	NM_032311	84271	Hs.505802	NM_032311	ENSG00000100227	POLDIP3	PDIP3|PDIP46|SKAR	DNA polymerase delta interacting protein 3	protein-coding	0.012594	0.492462	
chunk0065_450_1	chr14	106553494	106553693	+	0	NA	Intergenic	L1P4|LINE|L1	71154	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.010050	0.395000	
chunk0191_71_1	chr8	47305597	47305858	+	0	NA	intron (NR_104581, intron 5 of 16)	intron (NR_104581, intron 5 of 16)	44849	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.003831	0.229008	
chunk0062_397_1	chr14	74846014	74846518	+	0	NA	Intergenic	MER135|DNA|DNA	17568	NM_001243007	283571	Hs.675293	NM_001080408	ENSG00000119608	PROX2	PROX-2	prospero homeobox 2	protein-coding	0.007937	0.409901	
chunk0096_180_1	chr2	29771918	29772607	+	0	NA	intron (NM_004304, intron 1 of 28)	HAL1|LINE|L1	149349	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.004354	0.421739	
chunk0142_128_1	chr4	94653022	94653584	+	0	NA	intron (NM_001256425, intron 8 of 11)	MIRc|SINE|MIR	104230	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.005338	0.385435	232(TTGAACATTCTGTACC,-,0.00),233(TGAACATTCTGTACCT,+,0.00)
chunk0128_139_1	chr3	106746955	106747541	+	0	NA	Intergenic	Intergenic	493390	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.003413	0.374787	
chunk0066_428_1	chr15	39629873	39630462	+	0	NA	intron (NM_152597, intron 10 of 11)	intron (NM_152597, intron 10 of 11)	49088	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.008489	0.381356	
chunk0124_259_1	chr3	56990514	56991059	+	0	NA	intron (NM_001128615, intron 2 of 12)	MIR|SINE|MIR	50746	NR_046572	100874200	Hs.549631	NR_046572	ENSG00000240198	ARHGEF3-AS1	-	ARHGEF3 antisense RNA 1	ncRNA	0.007339	0.441392	
chunk0016_103_1	chr1	195637557	195637879	+	0	NA	Intergenic	Intergenic	944763	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.015528	0.396285	
chunk0124_404_1	chr3	59957706	59958122	+	0	NA	intron (NM_001166243, intron 7 of 9)	intron (NM_001166243, intron 7 of 9)	659956	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.004808	0.364508	
chunk0072_330_1	chr15	99175077	99175345	+	0	NA	intron (NR_109947, intron 8 of 12)	intron (NR_109947, intron 8 of 12)	70131	NM_145728	23336	Hs.207106	NM_015286	ENSG00000182253	SYNM	DMN|SYN	synemin	protein-coding	0.014925	0.472119	
chunk0134_317_1	chr3	181755021	181755265	+	0	NA	Intergenic	MER53|DNA|hAT	43219	NM_003106	6657	Hs.518438	NM_003106	ENSG00000181449	SOX2	ANOP3|MCOPS3	SRY-box transcription factor 2	protein-coding	0.012295	0.318367	
chunk0006_335_1	chr1	72042240	72042814	+	0	NA	intron (NM_173808, intron 1 of 6)	LTR78|LTR|ERV1	-205515	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.006969	0.415652	
chunk0138_40_1	chr4	31281732	31282306	+	0	NA	Intergenic	L1MA7|LINE|L1	110875	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.001742	0.299130	
chunk0023_446_1	chr10	32048318	32048529	+	0	NA	intron (NM_004521, intron 2 of 25)	intron (NM_004521, intron 2 of 25)	8020	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.000000	0.330189	
chunk0090_301_1	chr18	75261380	75261757	+	0	NA	intron (NM_001308210, intron 1 of 1)	intron (NM_001308210, intron 1 of 1)	50039	NM_001308210	10194	Hs.284217	NM_005786	ENSG00000179981	TSHZ1	CAA|NY-CO-33|SDCCAG33|TSH1	teashirt zinc finger homeobox 1	protein-coding	0.010610	0.473545	
chunk0147_359_1	chr4	185721838	185722305	+	0	NA	intron (NM_001145672, intron 1 of 20)	intron (NM_001145672, intron 1 of 20)	53841	NM_001145673	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.008565	0.335470	251(TGGAACAAACAGTGCT,-,0.00),252(GGAACAAACAGTGCTT,+,0.00)
chunk0204_263_1	chr9	98175602	98176375	+	0	NA	intron (NM_052820, intron 1 of 11)	MIR|SINE|MIR	-3096	NM_003389	7464	Hs.113094	NM_003389	ENSG00000106789	CORO2A	CLIPINB|IR10|WDR2	coronin 2A	protein-coding	0.009056	0.439276	459(AAGCACAAAGTGTTCA,-,0.00),460(AGCACAAAGTGTTCAT,+,0.00)
chunk0129_265_1	chr3	122449221	122449639	+	0	NA	intron (NR_026698, intron 10 of 14)	intron (NR_026698, intron 10 of 14)	33224	NR_125405	102723582	Hs.675056	NR_125405	ENSG00000272758	LOC102723582	-	uncharacterized LOC102723582	ncRNA	0.009569	0.389021	
chunk0008_119_1	chr1	91725914	91726170	+	0	NA	intron (NR_036634, intron 8 of 17)	intron (NR_036634, intron 8 of 17)	160237	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.003906	0.389105	
chunk0162_239_1	chr6	4829045	4829621	+	0	NA	intron (NM_004824, intron 1 of 6)	L1MB4|LINE|L1	-6765	NM_001143970	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.003472	0.403813	
chunk0038_185_1	chr11	85878239	85878784	+	0	NA	intron (NM_173556, intron 3 of 11)	L1MD1|LINE|L1	23410	NM_001286159	220047	Hs.567774	NM_173556	ENSG00000150676	CCDC83	CT148|HSD9|KP-CoT-23	coiled-coil domain containing 83	protein-coding	0.003670	0.375458	
chunk0116_147_1	chr21	36420085	36420343	+	0	NA	Intergenic	Intergenic	34823	NM_005441	8208	Hs.75238	NM_005441	ENSG00000159259	CHAF1B	CAF-1|CAF-IP60|CAF1|CAF1A|CAF1P60|MPHOSPH7|MPP7	chromatin assembly factor 1 subunit B	protein-coding	0.027132	0.575290	130(GGGAACAGAGTGGCCT,-,0.00),131(GGAACAGAGTGGCCTT,+,0.00)
chunk0139_138_1	chr4	53511082	53511408	+	0	NA	intron (NM_001126328, intron 2 of 10)	intron (NM_001126328, intron 2 of 10)	11168	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.009202	0.428135	
chunk0154_385_1	chr5	88025509	88025819	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	243215	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.006452	0.389068	
chunk0155_57_1	chr5	91321413	91321801	+	0	NA	Intergenic	L1PB2|LINE|L1	-7205	NR_103548	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.005155	0.347044	
chunk0074_60_1	chr16	21033250	21033671	+	0	NA	intron (NM_017539, intron 36 of 61)	MIRb|SINE|MIR	-124917	NM_001301775	57146	Hs.258212	NM_020422	ENSG00000011638	TMEM159	-	transmembrane protein 159	protein-coding	0.007126	0.379147	
chunk0177_329_1	chr7	26388409	26389047	+	0	NA	Intergenic	Intergenic	-14760	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.014107	0.408451	
chunk0192_164_1	chr8	62507268	62507535	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	258459	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.007491	0.335821	
chunk0160_330_1	chr5	159856563	159857188	+	0	NA	intron (NR_109891, intron 2 of 2)	intron (NR_109891, intron 2 of 2)	14509	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.001600	0.364217	
chunk0129_347_1	chr3	124854096	124854510	+	0	NA	intron (NM_002213, intron 3 of 14)	L1MB7|LINE|L1	33002	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.002415	0.349398	
chunk0070_239_1	chr15	73057993	73058358	+	0	NA	intron (NM_002499, intron 1 of 28)	intron (NM_002499, intron 1 of 28)	5691	NM_002499	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.005479	0.357923	
chunk0146_381_1	chr4	168501180	168501761	+	0	NA	intron (NM_016081, intron 1 of 20)	intron (NM_016081, intron 1 of 20)	4404	NM_001166108	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.005164	0.434708	
chunk0203_274_1	chr9	88460732	88460975	+	0	NA	intron (NM_006717, intron 3 of 5)	MLT2B1|LTR|ERVL	72471	NM_006717	10927	Hs.146804	NM_006717	ENSG00000106723	SPIN1	SPIN|TDRD24	spindlin 1	protein-coding	0.004115	0.422131	
chunk0038_223_1	chr11	86898820	86899156	+	0	NA	intron (NR_120592, intron 2 of 2)	intron (NR_120592, intron 2 of 2)	-41034	NR_045004	8587	Hs.741959	NR_045004	ENSG00000255203	OR7E2P	OR11-6|OR7E143P|OR7E51P|OR7E52P|OR7F2P|OST245|hg94	olfactory receptor family 7 subfamily E member 2 pseudogene	pseudo	0.000000	0.498516	
chunk0210_211_1	chrX	81220830	81221448	+	0	NA	intron (NM_003022, intron 1 of 3)	L1M1|LINE|L1	-19197	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.004854	0.344103	
chunk0021_304_1	chr1	244834703	244835074	+	0	NA	promoter-TSS (NM_198076)	promoter-TSS (NM_198076)	-418	NM_001312871	116228	Hs.411490	NM_198076	ENSG00000203667	COX20	FAM36A	cytochrome c oxidase assembly factor COX20	protein-coding	0.078167	0.540323	
chunk0050_122_1	chr12	102070537	102071042	+	0	NA	Intergenic	Intergenic	-8665	NM_001301107	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.000000	0.308300	192(AGAAACTGAGTGTTCT,-,0.00),193(GAAACTGAGTGTTCTC,+,0.00)
chunk0005_386_1	chr1	61995903	61996409	+	0	NA	intron (NM_176877, intron 28 of 42)	intron (NM_176877, intron 28 of 42)	-82630	NR_036058	100422902		NR_036058	ENSG00000263908	MIR3116-1	-	microRNA 3116-1	ncRNA	0.001976	0.402367	
chunk0064_398_1	chr14	99357713	99358325	+	0	NA	Intergenic	Intergenic	-86306	NM_001282237	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.021242	0.499184	
chunk0059_184_1	chr14	32648366	32648897	+	0	NA	intron (NM_004274, intron 7 of 13)	intron (NM_004274, intron 7 of 13)	-290622	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.003766	0.362782	
chunk0002_147_1	chr1	17581998	17582454	+	0	NA	intron (NM_001011722, intron 1 of 26)	intron (NM_001011722, intron 1 of 26)	1673	NM_001011722	55160	Hs.443460	NM_018125	ENSG00000074964	ARHGEF10L	GrinchGEF	Rho guanine nucleotide exchange factor 10 like	protein-coding	0.006579	0.507659	
chunk0173_269_1	chr6	147285207	147285431	+	0	NA	intron (NM_001127715, intron 8 of 27)	intron (NM_001127715, intron 8 of 27)	-80705	NR_034115	729178	Hs.557608	NR_034115		STXBP5-AS1	-	STXBP5 antisense RNA 1	ncRNA	0.008929	0.328889	
chunk0186_149_1	chr7	139075744	139076463	+	0	NA	intron (NM_020119, intron 6 of 12)	intron (NM_020119, intron 6 of 12)	33616	NM_020119	56829	Hs.133512	NM_020119	ENSG00000105939	ZC3HAV1	ARTD13|FLB6421|PARP13|ZAP|ZC3H2|ZC3HDC2	zinc finger CCCH-type containing, antiviral 1	protein-coding	0.013908	0.411111	
chunk0182_452_1	chr7	101975633	101975881	+	0	NA	intron (NM_001202544, intron 2 of 21)	L1ME3G|LINE|L1	158155	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.024194	0.409639	
chunk0056_452_1	chr13	95232873	95233627	+	0	NA	intron (NM_001301830, intron 3 of 19)	MER2|DNA|TcMar-Tigger	68196	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.005305	0.357616	
chunk0196_234_1	chr8	107922123	107922361	+	0	NA	intron (NM_178565, intron 5 of 5)	L1PA13|LINE|L1	160961	NM_001282863	340419	Hs.444834	NM_178565	ENSG00000147655	RSPO2	CRISTIN2|HHRRD|TETAMS2	R-spondin 2	protein-coding	0.000000	0.393305	
chunk0063_360_1	chr14	85797117	85797806	+	0	NA	Intergenic	Intergenic	-137217	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.008708	0.344928	
chunk0206_241_1	chr9	123678082	123678968	+	0	NA	intron (NM_024820, intron 5 of 20)	intron (NM_024820, intron 5 of 20)	-192903	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.020316	0.446449	
chunk0037_152_1	chr11	73520377	73520671	+	0	NA	intron (NM_001286050, intron 1 of 8)	intron (NM_001286050, intron 1 of 8)	77665	NM_015159	23201	Hs.475334	NM_015159	ENSG00000054965	FAM168A	KIAA0280|TCRP1	family with sequence similarity 168 member A	protein-coding	0.003401	0.335593	
chunk0201_103_1	chr9	34956087	34956340	+	0	NA	Intergenic	L2c|LINE|L2	-1274	NM_001304333	23349	Hs.7989	NM_015297	ENSG00000122733	PHF24	-	PHD finger protein 24	protein-coding	0.015810	0.425197	
chunk0210_174_1	chrX	78746408	78746706	+	0	NA	Intergenic	Intergenic	-1152	NM_001278000	2846	Hs.522701	NM_005296	ENSG00000147145	LPAR4	GPR23|LPA4|P2RY9|P2Y5-LIKE|P2Y9	lysophosphatidic acid receptor 4	protein-coding	0.000000	0.444816	
chunk0144_127_1	chr4	129246809	129247234	+	0	NA	Intergenic	Intergenic	150894	NM_001099783	132321	Hs.567679	NM_173487	ENSG00000151470	C4orf33	-	chromosome 4 open reading frame 33	protein-coding	0.016471	0.368545	
chunk0083_222_1	chr17	67139742	67140307	+	0	NA	intron (NM_014877, intron 21 of 32)	intron (NM_014877, intron 21 of 32)	95488	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.005310	0.517668	
chunk0115_61_1	chr21	21459631	21460417	+	0	NA	intron (NM_004540, intron 12 of 17)	L1MA9|LINE|L1	277295	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.003817	0.297332	
chunk0150_119_1	chr5	32959550	32959968	+	0	NA	intron (NR_033832, intron 4 of 5)	intron (NR_033832, intron 4 of 5)	12316	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.007177	0.415274	
chunk0174_157_1	chr6	158142727	158143102	+	0	NA	intron (NM_032861, intron 8 of 16)	L2b|LINE|L2	25366	NR_073096	84947	Hs.154706	NM_032861	ENSG00000122335	SERAC1	-	serine active site containing 1	protein-coding	0.008000	0.462766	
chunk0107_253_1	chr2	217344810	217345321	+	0	NA	TTS (NR_133642)	TTS (NR_133642)	62332	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.007828	0.388672	
chunk0178_237_1	chr7	36053431	36054044	+	0	NA	Intergenic	HAL1M8|LINE|L1	-41573	NR_108089	101928618	Hs.561704	NR_108089	ENSG00000261184	LOC101928618	-	uncharacterized LOC101928618	ncRNA	0.004894	0.433225	265(CAGTTCAGTGTGTTCT,-,0.00),266(AGTTCAGTGTGTTCTT,+,0.00)
chunk0044_27_1	chr12	27279792	27280757	+	0	NA	intron (NM_015000, intron 1 of 13)	intron (NM_015000, intron 1 of 13)	36129	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.008290	0.371636	
chunk0109_62_1	chr20	1366617	1366824	+	0	NA	intron (NR_040047, intron 1 of 2)	L1ME4c|LINE|L1	26241	NR_106929	102465524		NR_106929	ENSG00000284436	MIR6869	hsa-mir-6869	microRNA 6869	ncRNA	0.004831	0.293269	
chunk0135_370_1	chr3	190785891	190786266	+	0	NA	Intergenic	Intergenic	76598	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.005333	0.353723	204(TGGGACACACTGTACC,-,0.00),205(GGGACACACTGTACCT,+,0.00)
chunk0129_206_1	chr3	121733232	121733587	+	0	NA	intron (NM_001256488, intron 1 of 20)	L1MC3|LINE|L1	16358	NM_001256488	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.008451	0.328652	
chunk0044_88_1	chr12	28276341	28276780	+	0	NA	intron (NM_018318, intron 2 of 11)	intron (NM_018318, intron 2 of 11)	19360	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.000000	0.325000	
chunk0077_131_1	chr16	78523624	78524319	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	424558	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.010072	0.400862	28(TGGTACAGTGTGTGCT,-,0.00),29(GGTACAGTGTGTGCTT,+,0.00)
chunk0083_340_1	chr17	70202692	70203305	+	0	NA	Intergenic	Intergenic	33463	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.003263	0.381107	377(TAGTACATTGTGTTCT,-,0.00),378(AGTACATTGTGTTCTA,+,0.00)
chunk0089_160_1	chr18	59086619	59087064	+	0	NA	Intergenic	Intergenic	51162	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.013483	0.448430	
chunk0168_290_1	chr6	91013548	91013806	+	0	NA	Intergenic	Intergenic	-426376	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.000000	0.366795	
chunk0156_1_1	chr5	101855387	101855895	+	0	NA	Intergenic	Intergenic	440908	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.284872	
chunk0189_451_1	chr8	28329175	28329374	+	0	NA	exon (NM_006228, exon 2 of 4)	exon (NM_006228, exon 2 of 4)	-9374	NM_001284244	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.005025	0.580000	
chunk0212_414_1	chrX	152100799	152101014	+	0	NA	Intergenic	L1MD2|LINE|L1	17033	NM_021049	4104	Hs.18048	NM_021049		MAGEA5	CT1.5|MAGE5|MAGEA4	MAGE family member A5	protein-coding	0.009302	0.356481	
chunk0119_413_1	chr22	49754658	49755102	+	0	NA	Intergenic	Intergenic	71020	NM_001304809	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.038288	0.638202	182(GGGCACAGCCTGTCTT,-,0.00),183(GGCACAGCCTGTCTTG,+,0.00)
chunk0066_288_1	chr15	35370452	35370950	+	0	NA	TTS (NM_080650)	TTS (NM_080650)	1663	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.004016	0.346693	
chunk0005_20_1	chr1	54302957	54303156	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	66613	NR_103541	619518	Hs.591438	NM_001034847	ENSG00000198711	SSBP3-AS1	C1orf191|MST128|MSTP128	SSBP3 antisense RNA 1	ncRNA	0.045226	0.490000	115(AAGTACACGCTGTACA,-,0.00),116(AGTACACGCTGTACAA,+,0.00)
chunk0047_164_1	chr12	69933023	69933296	+	0	NA	intron (NM_182530, intron 16 of 24)	intron (NM_182530, intron 16 of 24)	107836	NM_182530	196446	Hs.253773	NM_182530	ENSG00000166268	MYRFL	C12orf15|C12orf28|bcm1377	myelin regulatory factor like	protein-coding	0.010989	0.478102	
chunk0209_104_1	chrX	40141481	40141798	+	0	NA	intron (NM_001123383, intron 1 of 14)	intron (NM_001123383, intron 1 of 14)	35690	NM_001123383	54880	Hs.659681	NM_017745	ENSG00000183337	BCOR	ANOP2|MAA2|MCOPS2	BCL6 corepressor	protein-coding	0.009464	0.512579	
chunk0016_405_1	chr1	203268928	203269329	+	0	NA	Intergenic	Intergenic	-18024	NR_117097	100506775	Hs.443859	NR_117097	ENSG00000231507	LINC01353	-	long intergenic non-protein coding RNA 1353	ncRNA	0.009975	0.517413	
chunk0082_1_1	chr17	49635085	49635321	+	0	NA	intron (NM_001007228, intron 1 of 9)	intron (NM_001007228, intron 1 of 9)	42960	NM_001007228	8405	Hs.463382	NM_003563	ENSG00000121067	SPOP	BTBD32|TEF2	speckle type BTB/POZ protein	protein-coding	0.008475	0.337553	
chunk0078_399_1	chr16	88706386	88706638	+	0	NA	promoter-TSS (NM_001171815)	promoter-TSS (NM_001171815)	29	NM_001012762	348180	Hs.592074	NM_001012759	ENSG00000174177	CTU2	C16orf84|MFRG|NCS2|UPF0432	cytosolic thiouridylase subunit 2	protein-coding	0.162698	0.778656	
chunk0090_250_1	chr18	74197979	74198469	+	0	NA	Intergenic	Intergenic	49713	NM_014177	29090	Hs.532835	NM_014177	ENSG00000075336	TIMM21	C18orf55|HSPC154|TIM21	translocase of inner mitochondrial membrane 21	protein-coding	0.016327	0.615071	
chunk0051_225_1	chr12	116861743	116862297	+	0	NA	intron (NM_003806, intron 1 of 1)	L2c|LINE|L2	19407	NR_073189	8739	Hs.26605	NM_003806	ENSG00000135116	HRK	DP5|HARAKIRI	harakiri, BCL2 interacting protein	protein-coding	0.007220	0.454054	
chunk0030_348_1	chr10	118520788	118521032	+	0	NA	Intergenic	Intergenic	74738	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.008197	0.465306	
chunk0028_321_1	chr10	91891264	91891902	+	0	NA	Intergenic	Intergenic	17918	NM_152429	143282	Hs.466120	NM_152429	ENSG00000174721	FGFBP3	C10orf13|FGF-BP3	fibroblast growth factor binding protein 3	protein-coding	0.000000	0.424100	
chunk0036_144_1	chr11	62171330	62171660	+	0	NA	Intergenic	Intergenic	-18743	NM_006552	10648	Hs.202686	NM_006552	ENSG00000168515	SCGB1D1	LIPA|LPHA|LPNA	secretoglobin family 1D member 1	protein-coding	0.030303	0.429003	
chunk0032_202_1	chr11	7303107	7303309	+	0	NA	exon (NM_175733, exon 2 of 7)	exon (NM_175733, exon 2 of 7)	51258	NM_175733	143425	Hs.177193	NM_175733	ENSG00000170743	SYT9	-	synaptotagmin 9	protein-coding	0.024752	0.556650	
chunk0211_335_1	chrX	124209936	124210248	+	0	NA	Intergenic	Intergenic	-136190	NM_001114937	4068	Hs.349094	NM_002351	ENSG00000183918	SH2D1A	DSHP|EBVS|IMD5|LYP|MTCP1|SAP|SAP/SH2D1A|XLP|XLPD|XLPD1	SH2 domain containing 1A	protein-coding	0.009615	0.338658	
chunk0193_408_1	chr8	80620051	80620832	+	0	NA	Intergenic	Intergenic	134228	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.005122	0.383632	438(AAGTACAAGAAGTTCT,-,0.00),439(AGTACAAGAAGTTCTA,+,0.00)
chunk0020_137_1	chr1	233677739	233677970	+	0	NA	Intergenic	Intergenic	53702	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.017316	0.413793	145(TAGGACAGTGTGACCT,-,0.00),146(AGGACAGTGTGACCTT,+,0.00)
chunk0069_140_1	chr15	62209892	62210156	+	0	NA	Intergenic	MER9B|LTR|ERVK	-44741	NM_001007595	388125	Hs.144372	NM_001007595	ENSG00000205502	C2CD4B	FAM148B|NLF2	C2 calcium dependent domain containing 4B	protein-coding	0.018939	0.464151	105(AGGCACAGCCTGCTCC,-,0.00),106(GGCACAGCCTGCTCCT,+,0.00)
chunk0092_359_1	chr19	35565318	35565884	+	0	NA	Intergenic	L2a|LINE|L2	-1943	NM_000704	495	Hs.36992	NM_000704	ENSG00000105675	ATP4A	ATP6A	ATPase H+/K+ transporting subunit alpha	protein-coding	0.007067	0.514991	230(GGTACTTACAGTTCCT,+,0.00),345(CTGCACACTGTGTTCT,-,0.00),346(TGCACACTGTGTTCTG,+,0.00)
chunk0033_214_1	chr11	17196179	17196670	+	0	NA	Intergenic	L2|LINE|L2	-26617	NM_002645	5286	Hs.175343	NM_002645	ENSG00000011405	PIK3C2A	CPK|OCSKD|PI3-K-C2(ALPHA)|PI3-K-C2A|PI3K-C2-alpha|PI3K-C2alpha	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha	protein-coding	0.010183	0.376016	
chunk0116_18_1	chr21	32869035	32869598	+	0	NA	Intergenic	Intergenic	-55573	NM_019596	56245	Hs.517235	NM_019596	ENSG00000205929	C21orf62	B37|C21orf120|PRED81	chromosome 21 open reading frame 62	protein-coding	0.010657	0.487589	287(AGGGACACTTTGCCCC,-,0.00)
chunk0054_126_1	chr13	43456889	43457563	+	0	NA	intron (NR_120399, intron 2 of 3)	intron (NR_120399, intron 2 of 3)	8374	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.001484	0.342222	
chunk0007_192_1	chr1	81004905	81005173	+	0	NA	Intergenic	LTR16B|LTR|ERVL	363752	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.018657	0.486989	
chunk0103_15_1	chr2	158992883	158993496	+	0	NA	intron (NM_001145909, intron 1 of 26)	intron (NM_001145909, intron 1 of 26)	24555	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.013051	0.447883	
chunk0145_389_1	chr4	152094777	152096169	+	0	NA	Intergenic	FLAM_C|SINE|Alu	-5280	NR_121628	100996286	Hs.322462	NR_121627	ENSG00000245954	LINC02273	-	long intergenic non-protein coding RNA 2273	ncRNA	0.006466	0.500359	312(CAGAACACACAGTGCA,-,0.00),313(AGAACACACAGTGCAT,+,0.00)
chunk0138_326_1	chr4	41478574	41478775	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	117889	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.014925	0.425743	77(CAGGACTGTGTGTTCT,-,0.00),78(AGGACTGTGTGTTCTT,+,0.00)
chunk0129_38_1	chr3	117382072	117382580	+	0	NA	Intergenic	Intergenic	460895	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001969	0.383104	
chunk0168_76_1	chr6	79671583	79671803	+	0	NA	intron (NM_031469, intron 1 of 3)	intron (NM_031469, intron 1 of 3)	40410	NM_031469	83699	Hs.302772	NM_031469	ENSG00000198478	SH3BGRL2	-	SH3 domain binding glutamate rich protein like 2	protein-coding	0.013636	0.497738	81(CAGCACATGAAGTGCT,-,0.00),82(AGCACATGAAGTGCTC,+,0.00)
chunk0047_414_1	chr12	75991302	75991501	+	0	NA	Intergenic	Intergenic	40375	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.010050	0.445000	63(TAGTACATCGTGTACT,-,0.00),64(AGTACATCGTGTACTA,+,0.00)
chunk0102_116_1	chr2	144693661	144693951	+	0	NA	intron (NR_033870, intron 1 of 4)	L1ME4a|LINE|L1	25839	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.003448	0.302405	
chunk0069_52_1	chr15	60740495	60740761	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	59059	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.007519	0.400749	
chunk0057_301_1	chr13	106424868	106425115	+	0	NA	Intergenic	LTR107_Mam|LTR|LTR	48428	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.004049	0.423387	
chunk0072_293_1	chr15	98659879	98660513	+	0	NA	intron (NM_001291858, intron 1 of 20)	intron (NM_001291858, intron 1 of 20)	-8975	NR_126453	104472848	Hs.349049	NR_126453		IRAIN	IGF1R-AS	IGF1R antisense imprinted non-protein coding RNA	ncRNA	0.011041	0.433071	310(CAGTTCAGGCTGTACT,-,0.00),311(AGTTCAGGCTGTACTC,+,0.00)
chunk0009_233_1	chr1	106773233	106773590	+	0	NA	Intergenic	Intergenic	-283234	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.005602	0.555866	
chunk0092_241_1	chr19	32809112	32809377	+	0	NA	Intergenic	HAL1M8|LINE|L1	60533	NM_001243036	11136	Hs.743345	NM_014270	ENSG00000021488	SLC7A9	BAT1|CSNU3	solute carrier family 7 member 9	protein-coding	0.007547	0.533835	245(AGAGCTCTCTGTTCTC,+,0.00)
chunk0064_156_1	chr14	91829474	91829866	+	0	NA	intron (NM_001128596, intron 1 of 11)	L1MEd|LINE|L1	6856	NM_152332	123036	Hs.510262	NM_152332	ENSG00000165929	TC2N	C14orf47|C2CD1|MTAC2D1|Tac2-N	tandem C2 domains, nuclear	protein-coding	0.005102	0.333333	
chunk0072_4_1	chr16	221926	222221	+	0	NA	intron (NM_201412, intron 2 of 9)	intron (NM_201412, intron 2 of 9)	7377	NM_201412	55692	Hs.16803	NM_018032	ENSG00000007392	LUC7L	LUC7B1|Luc7|SR+89|hLuc7B1	LUC7 like	protein-coding	0.010169	0.398649	
chunk0067_348_1	chr15	48489315	48490018	+	0	NA	intron (NM_000138, intron 25 of 65)	intron (NM_000138, intron 25 of 65)	156122	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.018492	0.416193	205(CAGAACACCAAGTCCT,-,0.00),206(AGAACACCAAGTCCTT,+,0.00)
chunk0203_338_1	chr9	89771491	89772243	+	0	NA	Intergenic	Intergenic	132084	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.007979	0.504648	
chunk0179_151_1	chr7	46287539	46287892	+	0	NA	Intergenic	L1MA4|LINE|L1	-366443	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.002833	0.389831	
chunk0089_410_1	chr18	68606749	68607026	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	108229	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.007220	0.464029	
chunk0148_405_1	chr5	14884191	14884478	+	0	NA	Intergenic	Intergenic	-12556	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.006969	0.413194	
chunk0119_163_1	chr22	43225746	43226340	+	0	NA	intron (NM_173050, intron 10 of 21)	intron (NM_173050, intron 10 of 21)	-38912	NM_015140	23170	Hs.517670	NM_015140	ENSG00000100304	TTLL12	dJ526I14.2	tubulin tyrosine ligase like 12	protein-coding	0.015152	0.478992	250(AAGCACAGCAAGTCCT,-,0.00),251(AGCACAGCAAGTCCTT,+,0.00)
chunk0175_19_1	chr7	435570	436164	+	0	NA	Intergenic	MIRb|SINE|MIR	56442	NR_033960	442497	Hs.704269	NR_033960	ENSG00000249574	LOC442497	-	uncharacterized LOC442497	ncRNA	0.043771	0.573109	
chunk0108_128_1	chr2	229922096	229922321	+	0	NA	promoter-TSS (NM_001284216)	promoter-TSS (NM_001284216)	-199	NM_001284216	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.088889	0.681416	
chunk0026_84_1	chr10	61407696	61407966	+	0	NA	3' UTR (NM_178505, exon 6 of 6)	3' UTR (NM_178505, exon 6 of 6)	-44808	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.000000	0.405904	
chunk0119_406_1	chr22	49427064	49427263	+	0	NA	intron (NR_110522, intron 1 of 2)	intron (NR_110522, intron 1 of 2)	116303	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.020101	0.455000	
chunk0010_74_1	chr1	113241084	113241458	+	0	NA	Intergenic	Intergenic	-35018	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.002674	0.346667	
chunk0212_164_1	chrX	132425852	132426277	+	0	NA	intron (NM_133486, intron 1 of 8)	intron (NM_133486, intron 1 of 8)	-12456	NM_001170703	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.002353	0.356808	
chunk0160_4_1	chr5	148941125	148941509	+	0	NA	Intergenic	Intergenic	114724	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.002604	0.501299	140(AAGGACACCTAGTCCT,-,0.00),141(AGGACACCTAGTCCTC,+,0.00)
chunk0177_202_1	chr7	23888519	23888721	+	0	NA	Intergenic	Intergenic	178294	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.009901	0.339901	
chunk0061_255_1	chr14	61314542	61314906	+	0	NA	Intergenic	Intergenic	-6719	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.010989	0.479452	
chunk0149_121_1	chr5	19485915	19486330	+	0	NA	intron (NM_004934, intron 11 of 12)	L3|LINE|CR1	400150	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004819	0.317308	280(CAGTACAAAATGTACT,-,0.00),281(AGTACAAAATGTACTT,+,0.00)
chunk0151_394_1	chr5	55426168	55426483	+	0	NA	TTS (NM_015360)	TTS (NM_015360)	82601	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.009524	0.405063	
chunk0055_280_1	chr13	64416926	64417153	+	0	NA	Intergenic	Intergenic	-572914	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.004405	0.364035	
chunk0077_318_1	chr16	82148928	82149326	+	0	NA	intron (NM_005792, intron 4 of 4)	intron (NM_005792, intron 4 of 4)	21097	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.017588	0.433584	
chunk0098_253_1	chr2	75037791	75038277	+	0	NA	Intergenic	Intergenic	-52778	NR_049796	100846995		NR_049796	ENSG00000263909	MIR5000	-	microRNA 5000	ncRNA	0.000000	0.289528	
chunk0195_195_1	chr8	96843603	96844173	+	0	NA	intron (NM_016134, intron 3 of 7)	MER131|DNA?|DNA?	198661	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.005263	0.357268	326(AGTACAGGCTGTCATT,+,0.00)
chunk0048_18_1	chr12	77151953	77152423	+	0	NA	Intergenic	Intergenic	-86608	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.002128	0.297240	
chunk0013_307_1	chr1	171338714	171339275	+	0	NA	promoter-TSS (NR_002719)	promoter-TSS (NR_002719)	98	NR_002719	7151	Hs.661092	NR_002719		TOP1P1	-	DNA topoisomerase I pseudogene 1	pseudo	0.005348	0.343416	
chunk0094_133_1	chr2	4882591	4882923	+	0	NA	Intergenic	Intergenic	-226535	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.012048	0.375375	
chunk0173_370_1	chr6	149461610	149461919	+	0	NA	intron (NM_207360, intron 3 of 5)	L2a|LINE|L2	23248	NM_207360	340152	Hs.632618	NM_207360	ENSG00000178199	ZC3H12D	C6orf95|MCPIP4|TFL|dJ281H8.1|p34	zinc finger CCCH-type containing 12D	protein-coding	0.012945	0.441935	
chunk0139_132_1	chr4	53448583	53449325	+	0	NA	intron (NM_030917, intron 15 of 17)	L1MEd|LINE|L1	-51123	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.001348	0.325707	337(TTGAACAGTGTGTTCT,-,0.00),338(TGAACAGTGTGTTCTG,+,0.00)
chunk0081_357_1	chr17	47676375	47677036	+	0	NA	intron (NM_001276453, intron 15 of 20)	intron (NM_001276453, intron 15 of 20)	-18559	NM_014726	9755	Hs.94790	NM_014726	ENSG00000198933	TBKBP1	ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding	0.007564	0.383686	
chunk0027_96_1	chr10	73716295	73716692	+	0	NA	intron (NR_026592, intron 9 of 11)	intron (NR_026592, intron 9 of 11)	14021	NR_026592	729096	Hs.709171	NR_026592	ENSG00000271816	BMS1P4	BMS1LP4	BMS1 pseudogene 4	pseudo	0.002519	0.376884	113(CAGGTCAGAGAGTTCT,-,0.00),114(AGGTCAGAGAGTTCTC,+,0.00)
chunk0065_244_1	chr14	101408326	101408766	+	0	NA	promoter-TSS (NR_126006)	promoter-TSS (NR_126006)	-624	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.025000	0.478458	
chunk0145_402_1	chr4	152691291	152691648	+	0	NA	Intergenic	Intergenic	-11304	NM_152680	201799	Hs.518900	NM_152680	ENSG00000170006	TMEM154	-	transmembrane protein 154	protein-coding	0.005602	0.399441	106(CTGCACAGGCTGTCCT,-,0.00),107(TGCACAGGCTGTCCTT,+,0.00)
chunk0001_234_1	chr1	8189785	8190406	+	0	NA	Intergenic	Intergenic	-18577	NR_125998	102724539	Hs.516816	NR_125998	ENSG00000227634	LINC01714	-	long intergenic non-protein coding RNA 1714	ncRNA	0.012882	0.464630	
chunk0201_116_1	chr9	35271274	35271477	+	0	NA	intron (NM_006377, intron 7 of 38)	intron (NM_006377, intron 7 of 38)	109383	NM_006377	10497	Hs.493791	NM_006377	ENSG00000198722	UNC13B	MUNC13|UNC13|Unc13h2	unc-13 homolog B	protein-coding	0.004926	0.411765	
chunk0099_242_1	chr2	97201026	97201392	+	0	NA	intron (NM_001164315, intron 46 of 75)	intron (NM_001164315, intron 46 of 75)	-77508	NR_103732	100506076	Hs.732616	NR_103732		LOC100506076	-	uncharacterized LOC100506076	ncRNA	0.000000	0.340599	
chunk0021_19_1	chr10	494133	494473	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	147475	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.011765	0.480938	
chunk0172_152_1	chr6	135728544	135729088	+	0	NA	Intergenic	Intergenic	-122880	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.005515	0.365138	
chunk0111_164_1	chr20	25199997	25200699	+	0	NA	intron (NM_001114089, intron 1 of 13)	L1MB3|LINE|L1	-3456	NR_109994	101926889	Hs.585997	NR_109994		LOC101926889	-	uncharacterized LOC101926889	ncRNA	0.007123	0.349929	
chunk0075_214_1	chr16	52701339	52701630	+	0	NA	Intergenic	Intergenic	-94509	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.006873	0.332192	
chunk0159_393_1	chr5	147053206	147053405	+	0	NA	intron (NM_181677, intron 2 of 10)	(AACAA)n|Simple_repeat|Simple_repeat	2832	NM_181674	5521	Hs.627618	NM_181674	ENSG00000156475	PPP2R2B	B55BETA|PP2AB55BETA|PP2ABBETA|PP2APR55B|PP2APR55BETA|PR2AB55BETA|PR2ABBETA|PR2APR55BETA|PR52B|PR55-BETA|PR55BETA|SCA12	protein phosphatase 2 regulatory subunit Bbeta	protein-coding	0.010050	0.355000	
chunk0129_213_1	chr3	121799809	121800099	+	0	NA	intron (NM_001023570, intron 7 of 14)	LTR37B|LTR|ERV1	35125	NM_001023570	9657	Hs.604110	NM_001023570	ENSG00000173226	IQCB1	NPHP5|PIQ|SLSN5	IQ motif containing B1	protein-coding	0.003448	0.309278	
chunk0204_215_1	chr9	97108965	97109188	+	0	NA	Intergenic	L1ME3|LINE|L1	-27131	NR_002942	340508	Hs.680438	NR_002942	ENSG00000228376	GAS2L1P2	-	growth arrest specific 2 like 1 pseudogene 2	pseudo	0.004484	0.357143	
chunk0001_372_1	chr1	10155161	10155416	+	0	NA	intron (NM_001105562, intron 21 of 27)	intron (NM_001105562, intron 21 of 27)	-55418	NM_015074	23095	Hs.97858	NM_015074	ENSG00000054523	KIF1B	CMT2|CMT2A|CMT2A1|HMSNII|KLP|NBLST1	kinesin family member 1B	protein-coding	0.003922	0.449219	
chunk0013_86_1	chr1	167671731	167672261	+	0	NA	intron (NM_052862, intron 1 of 6)	L2a|LINE|L2	41759	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.005660	0.514124	
chunk0035_188_1	chr11	44191279	44191788	+	0	NA	intron (NM_001178083, intron 9 of 14)	intron (NM_001178083, intron 9 of 14)	95336	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.001965	0.447059	
chunk0099_320_1	chr2	99697413	99698176	+	0	NA	intron (NM_001025108, intron 10 of 23)	MIRc|SINE|MIR	-207776	NM_016316	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.001311	0.387435	
chunk0022_136_1	chr10	11831063	11831555	+	0	NA	intron (NM_153256, intron 1 of 3)	intron (NM_153256, intron 1 of 3)	7911	NM_153256	254427	Hs.435775	NM_153256	ENSG00000148426	PROSER2	C10orf47	proline and serine rich 2	protein-coding	0.004065	0.361055	
chunk0085_264_1	chr18	7687541	7687837	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	120373	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.010135	0.323232	
chunk0210_53_1	chrX	68933046	68933350	+	0	NA	Intergenic	MIR|SINE|MIR	104201	NM_004429	1947	Hs.144700	NM_004429	ENSG00000090776	EFNB1	CFND|CFNS|EFB1|EFL3|EPLG2|Elk-L|LERK2	ephrin B1	protein-coding	0.003289	0.377049	
chunk0206_359_1	chr9	125762857	125763165	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	14812	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.330097	
chunk0060_152_1	chr14	45097498	45097983	+	0	NA	intron (NM_017922, intron 4 of 13)	L1ME3G|LINE|L1	-13135	NR_003691	100113389	Hs.712501	NR_003691	ENSG00000239043	SNORD127	-	small nucleolar RNA, C/D box 127	snoRNA	0.002062	0.327160	
chunk0132_131_1	chr3	156171798	156172373	+	0	NA	intron (NM_003471, intron 1 of 13)	intron (NM_003471, intron 1 of 13)	29123	NM_003471	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.003478	0.383681	
chunk0184_457_1	chr7	123455848	123456141	+	0	NA	intron (NR_104244, intron 13 of 13)	intron (NR_104244, intron 13 of 13)	76954	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.006826	0.333333	
chunk0004_142_1	chr1	44986400	44986726	+	0	NA	5' UTR (NM_020365, exon 1 of 12)	5' UTR (NM_020365, exon 1 of 12)	159	NM_001166588	8891	Hs.533549	NM_020365	ENSG00000070785	EIF2B3	EIF-2B|EIF2Bgamma	eukaryotic translation initiation factor 2B subunit gamma	protein-coding	0.082822	0.657492	
chunk0205_200_1	chr9	109250979	109251518	+	0	NA	intron (NM_018424, intron 13 of 15)	intron (NM_018424, intron 13 of 15)	69716	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.012987	0.440741	202(ATGAGCACAGTGTGCT,-,0.00)
chunk0042_391_1	chr12	10925764	10926418	+	0	NA	intron (NM_001291314, intron 3 of 6).3	intron (NM_001291314, intron 3 of 6).3	-3145	NM_001110213	5555	Hs.408153	NM_005042	ENSG00000134551	PRH2	PRP-1/PRP-2|Pr|pr1/Pr2	proline rich protein HaeIII subfamily 2	protein-coding	0.001529	0.323664	
chunk0077_375_1	chr16	84595033	84595389	+	0	NA	intron (NM_021149, intron 2 of 3)	intron (NM_021149, intron 2 of 3)	22885	NM_021149	23406	Hs.289092	NM_021149	ENSG00000103187	COTL1	CLP	coactosin like F-actin binding protein 1	protein-coding	0.033708	0.507003	
chunk0090_137_1	chr18	72107644	72108086	+	0	NA	Intergenic	Intergenic	-325639	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.013575	0.367946	
chunk0123_408_1	chr3	49180164	49180621	+	0	NA	intron (NM_001080528, intron 2 of 3)	intron (NM_001080528, intron 2 of 3)	8807	NM_173546	200942	Hs.13781	NM_173546	ENSG00000185909	KLHDC8B	CHL	kelch domain containing 8B	protein-coding	0.000000	0.517467	
chunk0022_359_1	chr10	17220549	17220998	+	0	NA	intron (NR_108060, intron 1 of 3)	(A)n|Simple_repeat|Simple_repeat	6125	NR_108060	100507347	Hs.740502	NR_108060	ENSG00000229124	VIM-AS1	-	VIM antisense RNA 1	ncRNA	0.002227	0.326667	
chunk0145_167_1	chr4	147274224	147274534	+	0	NA	Intergenic	L1MA8|LINE|L1	70338	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.000000	0.540193	
chunk0202_205_1	chr9	75560655	75560943	+	0	NA	Intergenic	L1PA15|LINE|L1	-329845	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.006944	0.370242	
chunk0184_395_1	chr7	121666546	121666752	+	0	NA	Intergenic	Intergenic	-206456	NM_001206838	5803	Hs.489824	NM_002851	ENSG00000106278	PTPRZ1	HPTPZ|HPTPzeta|PTP-ZETA|PTP18|PTPRZ|PTPZ|R-PTP-zeta-2|RPTPB|RPTPbeta|phosphacan	protein tyrosine phosphatase receptor type Z1	protein-coding	0.000000	0.280193	148(GAGAACATGGTGTTTC,-,0.00),149(AGAACATGGTGTTTCT,+,0.00)
chunk0136_15_1	chr4	95034	95278	+	0	NA	Intergenic	MER61C|LTR|ERV1	-29320	NR_110528	255403	Hs.636638	NM_001039127	ENSG00000250312	ZNF718	-	zinc finger protein 718	protein-coding	0.008197	0.444898	
chunk0145_176_1	chr4	147518817	147519345	+	0	NA	intron (NM_001166055, intron 2 of 5)	intron (NM_001166055, intron 2 of 5)	38164	NM_001166055	1909	Hs.183713	NM_001957	ENSG00000151617	EDNRA	ET-A|ETA|ETA-R|ETAR|ETRA|MFDA|hET-AR	endothelin receptor type A	protein-coding	0.000000	0.387524	
chunk0157_45_1	chr5	115955527	115956060	+	0	NA	Intergenic	Intergenic	-6661	NM_173800	206338	Hs.98288	NM_173800	ENSG00000172901	LVRN	APQ|AQPEP|TAQPEP	laeverin	protein-coding	0.003752	0.402622	
chunk0164_297_1	chr6	24802916	24803567	+	0	NA	Intergenic	L2a|LINE|L2	-4345	NM_001282492	101928603	Hs.635133	NM_001282492	ENSG00000260286	ARMH2	C6orf229	armadillo like helical domain containing 2	protein-coding	0.007680	0.388037	366(TTGAACAAGGTGTACT,-,0.00),367(TGAACAAGGTGTACTT,+,0.00)
chunk0199_38_1	chr9	1050116	1050330	+	0	NA	promoter-TSS (NM_181872)	promoter-TSS (NM_181872)	-123	NM_006557	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.084112	0.627907	
chunk0023_56_1	chr10	21871100	21871326	+	0	NA	intron (NM_022365, intron 8 of 11)	L1ME2|LINE|L1	132508	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.008850	0.405286	
chunk0006_214_1	chr1	68078347	68078721	+	0	NA	intron (NR_040077, intron 3 of 9)	L1PA14|LINE|L1	-26903	NM_004675	9077	Hs.194695	NM_004675	ENSG00000162595	DIRAS3	ARHI|NOEY2	DIRAS family GTPase 3	protein-coding	0.008021	0.541333	
chunk0067_216_1	chr15	45139472	45140252	+	0	NA	intron (NM_017434, intron 13 of 34)	MIRb|SINE|MIR	9868	NM_175940	53905	Hs.272813	NM_017434	ENSG00000137857	DUOX1	LNOX1|NOXEF1|THOX1	dual oxidase 1	protein-coding	0.015385	0.517286	445(AGGAACAATCTGTGCT,-,0.00),446(GGAACAATCTGTGCTT,+,0.00)
chunk0206_136_1	chr9	121083389	121084049	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-4577	NM_007018	11064	Hs.653263	NM_007018	ENSG00000119397	CNTRL	CEP1|CEP110|FAN|bA165P4.1	centriolin	protein-coding	0.007576	0.349470	
chunk0044_109_1	chr12	28955976	28956175	+	0	NA	Intergenic	Intergenic	-192928	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.000000	0.370000	
chunk0015_396_1	chr1	190886687	190887272	+	0	NA	Intergenic	MLT1J2-int|LTR|ERVL-MaLR	262089	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.000000	0.368601	
chunk0100_102_1	chr2	108235473	108235955	+	0	NA	Intergenic	Intergenic	-11481	NM_001008743	442038		NM_001008743	ENSG00000196228	SULT1C3	ST1C3	sulfotransferase family 1C member 3	protein-coding	0.010373	0.366460	240(AGATACACAATGTTCT,-,0.00),241(GATACACAATGTTCTC,+,0.00)
chunk0014_95_1	chr1	176658005	176658204	+	0	NA	intron (NM_020318, intron 3 of 22)	intron (NM_020318, intron 3 of 22)	194933	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.380000	
chunk0165_83_1	chr6	31360311	31360552	+	0	NA	Intergenic	L1MD|LINE|L1	-3219	NM_005514	3106	Hs.77961	NM_005514	ENSG00000234745	HLA-B	AS|B-4901|HLAB	major histocompatibility complex, class I, B	protein-coding	0.000000	0.380165	
chunk0101_84_1	chr2	124048336	124049216	+	0	NA	intron (NM_130773, intron 1 of 23)	intron (NM_130773, intron 1 of 23)	23489	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.007955	0.367764	511(TTGGACACAGTGTCCT,-,0.00),512(TGGACACAGTGTCCTT,+,0.00)
chunk0030_203_1	chr10	114367697	114368141	+	0	NA	intron (NM_001001936, intron 1 of 18)	intron (NM_001001936, intron 1 of 18)	36859	NM_001287824	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.015766	0.442697	
chunk0210_45_1	chrX	68385302	68385511	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	48051	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.004785	0.404762	
chunk0001_363_1	chr1	10045982	10046220	+	0	NA	intron (NM_001105562, intron 1 of 27)	MLT1J|LTR|ERVL-MaLR	13118	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.008403	0.543933	
chunk0097_37_1	chr2	42787376	42787760	+	0	NA	intron (NM_012205, intron 2 of 9)	intron (NM_012205, intron 2 of 9)	5043	NM_012205	23498	Hs.368805	NM_012205	ENSG00000162882	HAAO	3-HAO|HAO|VCRL1|h3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding	0.007812	0.561039	
chunk0059_60_1	chr14	30186560	30186992	+	0	NA	Intergenic	Intergenic	-259083	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.006944	0.351039	61(AGGCACATGGTGAACT,-,0.00)
chunk0039_5_1	chr11	95068684	95068901	+	0	NA	non-coding (NR_103726, exon 2 of 2)	non-coding (NR_103726, exon 2 of 2)	1915	NR_103726	10929	Hs.476680	NM_032102	ENSG00000263465	SRSF8	DSM-1|SFRS2B|SRP46	serine and arginine rich splicing factor 8	protein-coding	0.009217	0.472477	
chunk0179_385_1	chr7	51295501	51295753	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	21191	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.003968	0.474308	
chunk0180_453_1	chr7	77479489	77479730	+	0	NA	Intergenic	Intergenic	-57847	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.004149	0.429752	
chunk0192_190_1	chr8	63329338	63329662	+	0	NA	Intergenic	MER124|DNA?|DNA?	-136349	NR_125825	102724612	Hs.97639	NR_125825	ENSG00000253894	LOC102724612	-	uncharacterized LOC102724612	ncRNA	0.006173	0.326154	
chunk0158_51_1	chr5	125964959	125965565	+	0	NA	Intergenic	Intergenic	-214315	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.011551	0.433278	
chunk0130_365_1	chr3	139140744	139141116	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	36745	NR_026783	60467	Hs.512673	NM_021812	ENSG00000232416	BPESC1	NCRNA00187	blepharophimosis, epicanthus inversus and ptosis candidate 1	ncRNA	0.002688	0.388740	24(CAGTACATTGTGTACA,-,0.00),25(AGTACATTGTGTACAC,+,0.00)
chunk0204_278_1	chr9	98807167	98807509	+	0	NA	promoter-TSS (NM_024642)	promoter-TSS (NM_024642)	-361	NM_024642	79695	Hs.47099	NM_024642	ENSG00000119514	GALNT12	CRCS1|GalNAc-T12	polypeptide N-acetylgalactosaminyltransferase 12	protein-coding	0.023392	0.489796	
chunk0148_120_1	chr5	5209051	5209411	+	0	NA	exon (NM_139056, exon 10 of 23)	exon (NM_139056, exon 10 of 23)	68901	NM_139056	170690	Hs.661915	NM_139056	ENSG00000145536	ADAMTS16	ADAMTS16s	ADAM metallopeptidase with thrombospondin type 1 motif 16	protein-coding	0.011111	0.418283	
chunk0052_123_1	chr13	23463237	23463592	+	0	NA	Intergenic	L1MC4|LINE|L1	-6098	NR_038995	100506697	Hs.50118	NR_038995	ENSG00000232977	LINC00327	NCRNA00327	long intergenic non-protein coding RNA 327	ncRNA	0.005634	0.382022	
chunk0186_123_1	chr7	138096266	138097124	+	0	NA	intron (NM_001190906, intron 3 of 7)	L2|LINE|L2	20263	NM_001190907	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.004662	0.420256	
chunk0155_22_1	chr5	90947644	90948011	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	366575	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.002725	0.364130	
chunk0126_372_1	chr3	84100841	84101508	+	0	NA	Intergenic	MER92A|LTR|ERV1	768401	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.007496	0.366766	
chunk0199_206_1	chr9	4931889	4932295	+	0	NA	Intergenic	L1MB4|LINE|L1	-53153	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.007389	0.341523	
chunk0027_128_1	chr10	74252262	74252614	+	0	NA	intron (NM_001123, intron 3 of 10)	intron (NM_001123, intron 3 of 10)	75949	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.002841	0.348442	
chunk0009_364_1	chr1	109808203	109808505	+	0	NA	Intergenic	Intergenic	-44332	NM_133181	79574	Hs.485352	NM_024526	ENSG00000198758	EPS8L3	EPS8R3	EPS8 like 3	protein-coding	0.009934	0.557756	
chunk0055_177_1	chr13	61128809	61129519	+	0	NA	Intergenic	Intergenic	70716	NR_036128	100422973		NR_036128	ENSG00000266663	MIR3169	-	microRNA 3169	ncRNA	0.002817	0.381153	
chunk0016_54_1	chr1	193283918	193284501	+	0	NA	Intergenic	(GTTT)n|Simple_repeat|Simple_repeat	-20536	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.008576	0.398973	
chunk0055_166_1	chr13	60493788	60494245	+	0	NA	intron (NM_030794, intron 7 of 13)	intron (NM_030794, intron 7 of 13)	96723	NM_001146070	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.002188	0.275109	
chunk0106_19_1	chr2	195658591	195658910	+	0	NA	intron (NM_020342, intron 1 of 9)	intron (NM_020342, intron 1 of 9)	1622	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.003135	0.356250	
chunk0104_106_1	chr2	172644942	172645271	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	89137	NM_001278549	5163	Hs.470633	NM_002610	ENSG00000152256	PDK1	-	pyruvate dehydrogenase kinase 1	protein-coding	0.006079	0.351515	
chunk0017_182_1	chr1	207307072	207307726	+	0	NA	Intergenic	HAL1|LINE|L1	-14073	NM_001300902	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.004587	0.343511	
chunk0088_411_1	chr18	54772133	54772453	+	0	NA	Intergenic	UCON65|Unknown|Unknown	-56184	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.000000	0.420561	
chunk0207_155_1	chr9	129885752	129886029	+	0	NA	Intergenic	CpG	16285	NR_106914	102466750		NR_106914	ENSG00000276124	MIR6855	hsa-mir-6855	microRNA 6855	ncRNA	0.075812	0.701439	
chunk0114_70_1	chr21	9126833	9127232	+	0	NA	intron (NR_038329, intron 2 of 2)	intron (NR_038329, intron 2 of 2)	2729	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.025063	0.475000	
chunk0005_179_1	chr1	58733416	58733878	+	0	NA	Intergenic	Intergenic	-33572	NM_001085487	114803	Hs.744921	NM_001085487	ENSG00000162601	MYSM1	2A-DUB|2ADUB|BMFS4	Myb like, SWIRM and MPN domains 1	protein-coding	0.017316	0.438445	
chunk0032_217_1	chr11	7538595	7539218	+	0	NA	intron (NM_003621, intron 1 of 23)	intron (NM_003621, intron 1 of 23)	25141	NM_003621	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.011236	0.455128	305(CAGAACAGCCTGATCT,-,0.00),306(AGAACAGCCTGATCTA,+,0.00)
chunk0134_308_1	chr3	180862545	180862965	+	0	NA	intron (NR_109986, intron 1 of 13)	L1MEc|LINE|L1	7423	NR_109986	101928882	Hs.734668	NR_109986	ENSG00000285336	LOC101928882	-	uncharacterized LOC101928882	ncRNA	0.007143	0.275534	
chunk0058_108_1	chr14	21856228	21856467	+	0	NA	Intergenic	L1PA17|LINE|L1	191264	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.008368	0.408333	184(GAGAACATTGTGTATT,-,0.00),185(AGAACATTGTGTATTT,+,0.00)
chunk0187_345_1	chr7	156984168	156984722	+	0	NA	Intergenic	Intergenic	24990	NM_001165255	3110	Hs.37035	NM_005515	ENSG00000130675	MNX1	HB9|HLXB9|HOXHB9|SCRA1	motor neuron and pancreas homeobox 1	protein-coding	0.012635	0.398198	266(AAGCACAGACTGTTCC,-,0.00),267(AGCACAGACTGTTCCA,+,0.00)
chunk0029_320_1	chr10	104345208	104345457	+	0	NA	Intergenic	Intergenic	-6839	NM_001272013	85450	Hs.523252	NM_033397	ENSG00000148841	ITPRIP	DANGER|KIAA1754|bA127L20|bA127L20.2	inositol 1,4,5-trisphosphate receptor interacting protein	protein-coding	0.004016	0.348000	
chunk0092_136_1	chr19	28116815	28117480	+	0	NA	Intergenic	Intergenic	-323207	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.003008	0.436937	336(AAGAACAGAGAGTTCC,-,0.00),337(AGAACAGAGAGTTCCT,+,0.00)
chunk0128_192_1	chr3	107520498	107520962	+	0	NA	Intergenic	MIRc|SINE|MIR	-2206	NM_001276286	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.010776	0.432258	256(AAGAACATTTTGTTCC,-,0.00),257(AGAACATTTTGTTCCT,+,0.00),361(GGTGCAGTCTGTACTC,+,0.00)
chunk0034_212_1	chr11	32597810	32598420	+	0	NA	intron (NM_001307929, intron 5 of 7)	intron (NM_001307929, intron 5 of 7)	14348	NM_001307929	10480	Hs.502244	NM_006360	ENSG00000149100	EIF3M	B5|GA17|PCID1|TANGO7|hfl-B5	eukaryotic translation initiation factor 3 subunit M	protein-coding	0.003279	0.338789	
chunk0176_423_1	chr7	19646365	19647068	+	0	NA	Intergenic	Intergenic	58720	NR_036101	100422967		NR_036101	ENSG00000265932	MIR3146	mir-3146	microRNA 3146	ncRNA	0.004267	0.343750	
chunk0089_286_1	chr18	63040842	63041068	+	0	NA	Intergenic	Intergenic	278425	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.008850	0.541850	
chunk0063_10_1	chr14	76195969	76196672	+	0	NA	intron (NM_017972, intron 8 of 8)	intron (NM_017972, intron 8 of 8)	41966	NR_110314	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.001422	0.379261	
chunk0015_158_1	chr1	186521518	186522438	+	0	NA	Intergenic	Intergenic	-60870	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.004348	0.357220	
chunk0096_205_1	chr2	30326123	30326358	+	0	NA	Intergenic	MIRb|SINE|MIR	-20406	NR_122048	285043	Hs.429119	NR_122048		LINC01936	-	long intergenic non-protein coding RNA 1936	ncRNA	0.008511	0.453390	125(ATGCACACAGTGCTCT,-,0.00)
chunk0134_229_1	chr3	178848951	178849179	+	0	NA	intron (NR_126561, intron 2 of 5)	intron (NR_126561, intron 2 of 5)	11340	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.008772	0.454148	
chunk0107_321_1	chr2	220198441	220199454	+	0	NA	Intergenic	Intergenic	-292382	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.008885	0.412229	531(AGACACAGGCAGTTCT,-,0.00),532(GACACAGGCAGTTCTG,+,0.00)
chunk0203_77_1	chr9	83833813	83834033	+	0	NA	Intergenic	Intergenic	-16086	NM_001135953	80318	Hs.522255	NM_025211	ENSG00000165113	GKAP1	FKSG21|GKAP42	G kinase anchoring protein 1	protein-coding	0.004545	0.389140	
chunk0167_247_1	chr6	67863447	67863836	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-191710	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.005141	0.317949	
chunk0088_161_1	chr18	46718546	46719096	+	0	NA	intron (NM_013305, intron 1 of 6)	intron (NM_013305, intron 1 of 6)	38348	NM_001307987	29906	Hs.465025	NM_013305	ENSG00000101638	ST8SIA5	SIAT8-E|SIAT8E|ST8SiaV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding	0.014545	0.439201	
chunk0169_291_1	chr6	105901636	105902139	+	0	NA	Intergenic	Intergenic	-184433	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.003976	0.363095	
chunk0167_365_1	chr6	73421720	73422083	+	0	NA	Intergenic	MER77B|LTR|ERVL	27339	NM_018665	55510	Hs.125507	NM_018665	ENSG00000080007	DDX43	CT13|HAGE	DEAD-box helicase 43	protein-coding	0.005510	0.439560	
chunk0097_96_1	chr2	45823659	45823982	+	0	NA	intron (NM_005400, intron 1 of 14)	intron (NM_005400, intron 1 of 14)	171916	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.012384	0.592593	
chunk0012_304_1	chr1	162206394	162206638	+	0	NA	intron (NM_001164757, intron 2 of 9)	MER58A|DNA|hAT-Charlie	49409	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.000000	0.387755	105(AGAGACAGTCTGTCCT,-,0.00),106(GAGACAGTCTGTCCTG,+,0.00)
chunk0113_208_1	chr20	53751880	53752084	+	0	NA	Intergenic	Intergenic	123727	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.004902	0.341463	
chunk0181_258_1	chr7	85806425	85806707	+	0	NA	Intergenic	Intergenic	-684635	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.452297	49(GGGAACAGTCTGTCAC,-,0.00),50(GGAACAGTCTGTCACA,+,0.00)
chunk0078_111_1	chr17	2549306	2549707	+	0	NA	Intergenic	Intergenic	-37600	NM_024086	79066	Hs.632237	NM_024086	ENSG00000127804	METTL16	METT10D	methyltransferase like 16	protein-coding	0.014963	0.517413	266(TAGAACAGAATGTCCT,-,0.00),267(AGAACAGAATGTCCTA,+,0.00)
chunk0140_285_1	chr4	72328213	72328513	+	0	NA	intron (NM_014243, intron 5 of 21)	intron (NM_014243, intron 5 of 21)	240436	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.006667	0.425249	164(CAGGACAATCTGACCT,-,0.00),165(AGGACAATCTGACCTG,+,0.00)
chunk0146_453_1	chr4	170090086	170090285	+	0	NA	promoter-TSS (NM_001286682)	promoter-TSS (NM_001286682)	36	NM_001286682	51166	Hs.529735	NM_016228	ENSG00000109576	AADAT	KAT2|KATII|KYAT2	aminoadipate aminotransferase	protein-coding	0.105528	0.705000	
chunk0091_19_1	chr19	3221368	3221567	+	0	NA	Intergenic	MIR|SINE|MIR	-3236	NM_021938	60680	Hs.655747	NM_021938	ENSG00000161082	CELF5	BRUNOL-5|BRUNOL5|CELF-5	CUGBP Elav-like family member 5	protein-coding	0.015075	0.560000	
chunk0074_296_1	chr16	29838052	29838262	+	0	NA	intron (NM_001293204, intron 6 of 13)	AluSx1|SINE|Alu	7642	NM_001293204	9961	Hs.632177	NM_005115	ENSG00000013364	MVP	LRP|VAULT1	major vault protein	protein-coding	0.019048	0.478673	
chunk0076_20_1	chr16	58809304	58809571	+	0	NA	Intergenic	L2|LINE|L2	-75080	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.007491	0.410448	
chunk0177_217_1	chr7	24143436	24143774	+	0	NA	Intergenic	Intergenic	-140583	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.008876	0.507375	
chunk0104_113_1	chr2	172860274	172860473	+	0	NA	intron (NM_001282899, intron 1 of 27)	intron (NM_001282899, intron 1 of 27)	335	NM_001282900	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.000000	0.365000	
chunk0113_329_1	chr20	58588750	58589235	+	0	NA	intron (NR_034147, intron 6 of 6)	L1ME4a|LINE|L1	-45780	NR_125359	79160	Hs.280135	NR_125359	ENSG00000268941	LINC01711	-	long intergenic non-protein coding RNA 1711	ncRNA	0.012371	0.351852	
chunk0191_214_1	chr8	52320973	52321293	+	0	NA	intron (NM_014682, intron 2 of 25)	L1ME3Cz|LINE|L1	88746	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.012500	0.426791	
chunk0132_375_1	chr3	162959302	162959914	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	343693	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.008170	0.404568	
chunk0089_30_1	chr18	57842148	57842419	+	0	NA	Intergenic	Intergenic	-39188	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.003690	0.363971	
chunk0038_200_1	chr11	86205883	86206259	+	0	NA	Intergenic	Intergenic	-38313	NM_001308007	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.005319	0.405836	
chunk0067_203_1	chr15	44907602	44908184	+	0	NA	Intergenic	Intergenic	-48809	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.003436	0.365352	
chunk0024_133_1	chr10	35004571	35005155	+	0	NA	Intergenic	L2b|LINE|L2	69467	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.011986	0.430769	
chunk0131_56_1	chr3	142786093	142786369	+	0	NA	intron (NM_003304, intron 6 of 11)	intron (NM_003304, intron 6 of 11)	61807	NM_003304	7220	Hs.250687	NM_003304	ENSG00000144935	TRPC1	HTRP-1|TRP1	transient receptor potential cation channel subfamily C member 1	protein-coding	0.003623	0.277978	
chunk0116_434_1	chr21	43188778	43189342	+	0	NA	Intergenic	Intergenic	20010	NM_001314050	102724652	Hs.184085	NM_001314050	ENSG00000276076	CRYAA2	CRYAA	crystallin alpha A2	protein-coding	0.026596	0.481416	403(CTGAACTTTCTGTACT,-,0.00),404(TGAACTTTCTGTACTC,+,0.00)
chunk0028_253_1	chr10	90580004	90580667	+	0	NA	Intergenic	MER54A|LTR|ERVL	-39530	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.003017	0.439759	
chunk0022_241_1	chr10	14259975	14260656	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	70552	NM_018027	55691	Hs.330463	NM_018027	ENSG00000151474	FRMD4A	CCAFCA|FRMD4|bA295P9.4	FERM domain containing 4A	protein-coding	0.007342	0.432551	642(AAGCACATTCTGATCT,-,0.00),643(AGCACATTCTGATCTT,+,0.00)
chunk0150_391_1	chr5	39656521	39657019	+	0	NA	Intergenic	L2a|LINE|L2	136339	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.000000	0.384770	
chunk0203_399_1	chr9	90579133	90579807	+	0	NA	intron (NR_034157, intron 1 of 5)	intron (NR_034157, intron 1 of 5)	3276	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.005935	0.392593	
chunk0196_363_1	chr8	115145242	115145759	+	0	NA	Intergenic	Intergenic	522512	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.007737	0.391892	
chunk0169_127_1	chr6	101083104	101083728	+	0	NA	Intergenic	Intergenic	-202044	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.009615	0.329600	
chunk0033_71_1	chr11	13736564	13736763	+	0	NA	Intergenic	Intergenic	68004	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.000000	0.460000	
chunk0072_61_1	chr16	1645868	1646542	+	0	NA	intron (NM_020825, intron 5 of 19)	L1MC3|LINE|L1	31565	NM_020825	57585	Hs.603676	NM_020825	ENSG00000007545	CRAMP1	CRAMP1L|HN1L|TCE4	cramped chromatin regulator homolog 1	protein-coding	0.020772	0.515556	
chunk0167_28_1	chr6	53829590	53829926	+	0	NA	intron (NM_018214, intron 1 of 13)	intron (NM_018214, intron 1 of 13)	34778	NM_018214	55227	Hs.606493	NM_018214	ENSG00000137269	LRRC1	LANO|dJ523E19.1	leucine rich repeat containing 1	protein-coding	0.011905	0.436202	183(GAGAACGGATTGTGCC,-,0.00),184(AGAACGGATTGTGCCC,+,0.00)
chunk0119_178_1	chr22	43734539	43734819	+	0	NA	intron (NM_198856, intron 5 of 29)	intron (NM_198856, intron 5 of 29)	77658	NM_022785	64800	Hs.658996	NM_022785	ENSG00000186976	EFCAB6	DJBP|HSCBCIP1|dJ185D5.1	EF-hand calcium binding domain 6	protein-coding	0.007143	0.323843	
chunk0189_383_1	chr8	27399935	27400395	+	0	NA	intron (NM_004103, intron 3 of 31)	MER103C|DNA|hAT-Charlie	-33205	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.002174	0.388286	
chunk0140_36_1	chr4	66356796	66357140	+	0	NA	Intergenic	L1PA16|LINE|L1	80144	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.000000	0.368116	
chunk0142_96_1	chr4	94298770	94299319	+	0	NA	3' UTR (NM_014485, exon 6 of 6)	3' UTR (NM_014485, exon 6 of 6)	43832	NM_014485	27306	Hs.128433	NM_014485	ENSG00000163106	HPGDS	GSTS|GSTS1|GSTS1-1|PGD2|PGDS	hematopoietic prostaglandin D synthase	protein-coding	0.007286	0.383636	
chunk0156_66_1	chr5	103485209	103485583	+	0	NA	Intergenic	Intergenic	56589	NR_104670	102467212	Hs.641885	NR_104670	ENSG00000248757	LINC02115	-	long intergenic non-protein coding RNA 2115	ncRNA	0.008021	0.397333	179(AGGTACTGATTGTGCC,-,0.00),180(GGTACTGATTGTGCCC,+,0.00)
chunk0167_87_1	chr6	56684964	56685440	+	0	NA	intron (NM_183380, intron 5 of 93)	L1PA17|LINE|L1	-42306	NM_015548	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.008403	0.379455	
chunk0049_398_1	chr12	96806334	96806656	+	0	NA	intron (NM_001306084, intron 63 of 67)	intron (NM_001306084, intron 63 of 67)	-100728	NM_001135177	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.012422	0.414861	
chunk0127_119_1	chr3	93470288	93470869	+	0	NA	Intergenic	SAR|Satellite|Satellite	503503	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.003945	0.244094	
chunk0160_61_1	chr5	149759782	149760390	+	0	NA	intron (NM_133263, intron 1 of 11)	intron (NM_133263, intron 1 of 11)	-11854	NM_001172699	133522	Hs.483816	NM_133263	ENSG00000155846	PPARGC1B	ERRL1|PERC|PGC-1(beta)|PGC1B	PPARG coactivator 1 beta	protein-coding	0.006579	0.543514	
chunk0069_88_1	chr15	61159838	61160467	+	0	NA	intron (NM_134261, intron 1 of 10)	MIRb|SINE|MIR	69151	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.009539	0.355556	
chunk0008_391_1	chr1	97230836	97231104	+	0	NA	intron (NM_000110, intron 19 of 22)	intron (NM_000110, intron 19 of 22)	135047	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.000000	0.427509	195(GAGGACACATAGTACT,-,0.00),196(AGGACACATAGTACTC,+,0.00)
chunk0144_470_1	chr4	142595272	142595891	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	250870	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.000000	0.353226	
chunk0193_417_1	chr8	80745565	80746310	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	128844	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.008054	0.336461	
chunk0201_120_1	chr9	35340053	35340490	+	0	NA	intron (NM_006377, intron 10 of 38)	intron (NM_006377, intron 10 of 38)	-66484	NR_003581	158381	Hs.575661	NR_003581	ENSG00000179766	ATP8B5P	FetA	ATPase phospholipid transporting 8B5, pseudogene	pseudo	0.002288	0.415525	
chunk0132_307_1	chr3	160378384	160378735	+	0	NA	intron (NM_001190242, intron 2 of 18)	L1MC4|LINE|L1	5207	NM_001190242	57560	Hs.478095	NM_020800	ENSG00000068885	IFT80	ATD2|SRTD2|WDR56	intraflagellar transport 80	protein-coding	0.000000	0.375000	203(TGGAACATCTTGTGCC,-,0.00),204(GGAACATCTTGTGCCA,+,0.00)
chunk0031_389_1	chr10	131113463	131114174	+	0	NA	intron (NM_174937, intron 9 of 11)	intron (NM_174937, intron 9 of 11)	18600	NR_120623	101927489	Hs.659317	NR_120623	ENSG00000230098	TCERG1L-AS1	-	TCERG1L antisense RNA 1	ncRNA	0.014065	0.490169	
chunk0191_171_1	chr8	50708174	50708560	+	0	NA	intron (NM_018967, intron 16 of 18)	intron (NM_018967, intron 16 of 18)	796588	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.005181	0.299742	
chunk0212_190_1	chrX	133972923	133973194	+	0	NA	intron (NM_001164617, intron 1 of 8)	L2|LINE|L2	12588	NM_004484	2719	Hs.644108	NM_004484	ENSG00000147257	GPC3	DGSX|GTR2-2|MXR7|OCI-5|SDYS|SGB|SGBS|SGBS1	glypican 3	protein-coding	0.007380	0.426471	
chunk0075_335_1	chr16	54848539	54848738	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	80140	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.000000	0.460000	
chunk0194_341_1	chr8	89079381	89079717	+	0	NA	Intergenic	L2b|LINE|L2	678162	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.000000	0.326409	198(TAGCACTGGGAGTTCC,-,0.00),199(AGCACTGGGAGTTCCA,+,0.00)
chunk0024_435_1	chr10	46128766	46129094	+	0	NA	intron (NR_126580, intron 5 of 6)	intron (NR_126580, intron 5 of 6)	19435	NR_126580	653268	Hs.447454	NM_001077685		AGAP7P	AGAP-7|AGAP7|CTGLF4|bA109G10.1	ArfGAP with GTPase domain, ankyrin repeat and PH domain 7, pseudogene	pseudo	0.012195	0.382979	
chunk0027_122_1	chr10	74189781	74190492	+	0	NA	intron (NM_001123, intron 1 of 10)	L1MB7|LINE|L1	13647	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.005626	0.380618	
chunk0174_393_1	chr6	165427709	165428355	+	0	NA	intron (NM_006661, intron 11 of 22)	intron (NM_006661, intron 11 of 22)	18431	NR_106988									0.003096	0.335394	
chunk0147_136_1	chr4	174520606	174521051	+	0	NA	intron (NM_001145816, intron 2 of 5)	intron (NM_001145816, intron 2 of 5)	2065	NM_001256301	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.002247	0.320628	204(TGGTACAATATGTTCC,-,0.00),205(GGTACAATATGTTCCT,+,0.00)
chunk0125_2_1	chr3	61644988	61645381	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	83615	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.002545	0.388325	
chunk0002_434_1	chr1	28090879	28091513	+	0	NA	Intergenic	L2a|LINE|L2	-2559	NM_001282560	2140	Hs.185774	NM_001990	ENSG00000158161	EYA3	-	EYA transcriptional coactivator and phosphatase 3	protein-coding	0.006309	0.440945	
chunk0181_384_1	chr7	89404638	89404979	+	0	NA	Intergenic	Intergenic	-609091	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.011730	0.441520	
chunk0158_231_1	chr5	129014337	129014671	+	0	NA	intron (NM_001017372, intron 4 of 9)	intron (NM_001017372, intron 4 of 9)	48984	NM_001017372	28965	Hs.49765	NM_014031	ENSG00000113396	SLC27A6	ACSVL2|FACVL2|FATP6|VLCS-H1	solute carrier family 27 member 6	protein-coding	0.005988	0.402985	
chunk0100_108_1	chr2	108358697	108358896	+	0	NA	Intergenic	L1PB|LINE|L1	-19169	NM_006588	27233	Hs.312644	NM_006588	ENSG00000198075	SULT1C4	SULT1C|SULT1C2	sulfotransferase family 1C member 4	protein-coding	0.005025	0.380000	
chunk0068_49_1	chr15	51494241	51495024	+	0	NA	intron (NM_015263, intron 19 of 42)	Charlie16a|DNA|hAT-Charlie	128138	NM_015263	23312	Hs.511386	NM_015263	ENSG00000104093	DMXL2	DFNA71|PEPNS|RC3	Dmx like 2	protein-coding	0.007663	0.355867	
chunk0106_304_1	chr2	204844051	204844328	+	0	NA	intron (NM_205863, intron 2 of 21)	intron (NM_205863, intron 2 of 21)	298396	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.007220	0.298561	
chunk0167_306_1	chr6	71463069	71463562	+	0	NA	Intergenic	L2a|LINE|L2	42288	NR_121615	102724000	Hs.145785	NR_121615		LINC01626	-	long intergenic non-protein coding RNA 1626	ncRNA	0.004057	0.340081	190(CTGAACAATGTGTACC,-,0.00),191(TGAACAATGTGTACCA,+,0.00)
chunk0007_139_1	chr1	79290886	79291591	+	0	NA	Intergenic	Intergenic	-284428	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.014184	0.422096	
chunk0154_151_1	chr5	79457332	79457649	+	0	NA	intron (NM_001277077, intron 1 of 5)	Tigger17a|DNA|TcMar-Tigger	56346	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.000000	0.396226	
chunk0140_425_1	chr4	76028331	76028779	+	0	NA	intron (NM_001130017, intron 1 of 9)	intron (NM_001130017, intron 1 of 9)	-5019	NM_001565	3627	Hs.632586	NM_001565	ENSG00000169245	CXCL10	C7|IFI10|INP10|IP-10|SCYB10|crg-2|gIP-10|mob-1	C-X-C motif chemokine ligand 10	protein-coding	0.013393	0.414254	143(AGGAACAGTCTGCCCT,-,0.00),144(GGAACAGTCTGCCCTG,+,0.00)
chunk0038_351_1	chr11	93189340	93190039	+	0	NA	intron (NM_152313, intron 1 of 10)	intron (NM_152313, intron 1 of 10)	7766	NM_001286139	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.004292	0.324286	
chunk0105_400_1	chr2	192577126	192577821	+	0	NA	Intergenic	Intergenic	-172372	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.001439	0.274425	
chunk0057_137_1	chr13	99831849	99832357	+	0	NA	intron (NR_120421, intron 1 of 4)	Mam_R4|LINE|Dong-R4	-103102	NR_120383	101927465	Hs.130690	NR_046525		CLYBL-AS1	-	CLYBL antisense RNA 1	ncRNA	0.011811	0.385069	290(CAGCACATTGTGTTCT,-,0.00),291(AGCACATTGTGTTCTT,+,0.00)
chunk0122_414_1	chr3	38518420	38518739	+	0	NA	intron (NM_001145464, intron 4 of 4)	intron (NM_001145464, intron 4 of 4)	22307	NM_001145464	9941	Hs.517897	NM_005107	ENSG00000157036	EXOG	ENDOGL1|ENDOGL2|ENGL|ENGL-a|ENGL-b|ENGLA|ENGLB	exo/endonuclease G	protein-coding	0.009404	0.387500	
chunk0036_437_1	chr11	68498464	68498673	+	0	NA	intron (NM_001164161, intron 1 of 23)	L1ME3A|LINE|L1	37850	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.004785	0.423810	
chunk0183_327_1	chr7	108158808	108159396	+	0	NA	intron (NM_001193582, intron 30 of 30)	intron (NM_001193582, intron 30 of 30)	-28746	NM_007356	22798	Hs.62022	NM_007356	ENSG00000091128	LAMB4	-	laminin subunit beta 4	protein-coding	0.001701	0.329372	
chunk0019_448_1	chr1	231336635	231336834	+	0	NA	exon (NM_175876, exon 1 of 1)	exon (NM_175876, exon 1 of 1)	1138	NM_175876	149371	Hs.356198	NM_175876	ENSG00000116903	EXOC8	EXO84|Exo84p|SEC84	exocyst complex component 8	protein-coding	0.015075	0.490000	
chunk0104_415_1	chr2	180787533	180788166	+	0	NA	intron (NR_104324, intron 3 of 4)	L1MD1|LINE|L1	95745	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.004739	0.315457	
chunk0123_402_1	chr3	48927734	48928087	+	0	NA	intron (NM_006321, intron 3 of 15)	intron (NM_006321, intron 3 of 15)	-8525	NM_001123040	646450	Hs.720727	NM_001123040	ENSG00000221883	ARIH2OS	C3orf71	ariadne RBR E3 ubiquitin protein ligase 2 opposite strand	ncRNA	0.000000	0.395480	
chunk0117_269_1	chr22	24011172	24011623	+	0	NA	promoter-TSS (NM_001201429)	promoter-TSS (NM_001201429)	27	NM_001199281	23523	Hs.517478	NM_012295	ENSG00000099991	CABIN1	CAIN|KB-318B8.7|PPP3IN	calcineurin binding protein 1	protein-coding	0.099778	0.707965	
chunk0163_183_1	chr6	11428371	11428628	+	0	NA	Intergenic	L2a|LINE|L2	-46151	NR_073131	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.003891	0.449612	
chunk0200_276_1	chr9	22257007	22257206	+	0	NA	Intergenic	L1PA16|LINE|L1	-189735	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.000000	0.550000	
chunk0176_125_1	chr7	12232582	12232972	+	0	NA	3' UTR (NM_018374, exon 9 of 9)	3' UTR (NM_018374, exon 9 of 9)	21555	NM_018374	54664	Hs.396358	NM_018374	ENSG00000106460	TMEM106B	HLD16	transmembrane protein 106B	protein-coding	0.000000	0.299233	
chunk0102_120_1	chr2	144872071	144872501	+	0	NA	intron (NR_033870, intron 2 of 4)	intron (NR_033870, intron 2 of 4)	204319	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.006977	0.392111	
chunk0129_69_1	chr3	117654382	117654716	+	0	NA	Intergenic	Intergenic	733118	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002994	0.355224	
chunk0013_131_1	chr1	168159251	168159604	+	0	NA	Intergenic	L1MA5A|LINE|L1	-19418	NM_152902	261726	Hs.209431	NM_152902	ENSG00000143155	TIPRL	TIP|TIP41|TIPRL1	TOR signaling pathway regulator	protein-coding	0.002833	0.370056	
chunk0089_426_1	chr18	69876318	69876720	+	0	NA	intron (NM_001303618, intron 3 of 5)	intron (NM_001303618, intron 3 of 5)	71334	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.009950	0.382134	
chunk0091_441_1	chr19	17138752	17139748	+	0	NA	intron (NM_004145, intron 2 of 39)	Tigger3a|DNA|TcMar-Tigger	63469	NM_004145	4650	Hs.123198	NM_004145	ENSG00000099331	MYO9B	CELIAC4|MYR5	myosin IXB	protein-coding	0.016064	0.485456	
chunk0071_2_1	chr15	78604244	78604849	+	0	NA	intron (NR_046313, intron 4 of 7)	intron (NR_046313, intron 4 of 7)	16749	NM_001166694	1136	Hs.89605	NM_000743	ENSG00000080644	CHRNA3	LNCR2|NACHRA3|PAOD2	cholinergic receptor nicotinic alpha 3 subunit	protein-coding	0.008264	0.496700	
chunk0176_283_1	chr7	16645815	16646200	+	0	NA	promoter-TSS (NM_014038)	promoter-TSS (NM_014038)	-127	NM_001159767	28969	Hs.487635	NM_014038	ENSG00000136261	BZW2	HSPC028|MST017|MSTP017	basic leucine zipper and W2 domains 2	protein-coding	0.064935	0.595855	
chunk0044_140_1	chr12	29561422	29561976	+	0	NA	intron (NM_001193451, intron 9 of 17)	intron (NM_001193451, intron 9 of 17)	-64013	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.007220	0.326126	254(TTGTACAATCTGTTCC,-,0.00),255(TGTACAATCTGTTCCA,+,0.00)
chunk0046_67_1	chr12	55939962	55940293	+	0	NA	exon (NM_201445, exon 11 of 25)	exon (NM_201445, exon 11 of 25)	8099	NM_201445	1606	Hs.524488	NM_001345	ENSG00000065357	DGKA	DAGK|DAGK1|DGK-alpha	diacylglycerol kinase alpha	protein-coding	0.006042	0.554217	
chunk0196_73_1	chr8	102528514	102528875	+	0	NA	Intergenic	(GTGCTGT)n|Simple_repeat|Simple_repeat	-22926	NM_024410	4956	Hs.159274	NM_024410	ENSG00000155087	ODF1	CT133|HSPB10|ODF|ODF2|ODF27|ODFP|ODFPG|ODFPGA|ODFPGB|RT7|SODF	outer dense fiber of sperm tails 1	protein-coding	0.060942	0.604972	
chunk0111_190_1	chr20	25498810	25499196	+	0	NA	intron (NM_025176, intron 8 of 23)	intron (NM_025176, intron 8 of 23)	86514	NM_025176	22981	Hs.631508	NM_025176	ENSG00000101004	NINL	NLP	ninein like	protein-coding	0.028497	0.542636	
chunk0096_266_1	chr2	31578412	31578790	+	0	NA	intron (NM_000348, intron 1 of 4)	intron (NM_000348, intron 1 of 4)	2370	NM_000348	6716	Hs.458345	NM_000348	ENSG00000277893	SRD5A2	-	steroid 5 alpha-reductase 2	protein-coding	0.005291	0.387863	
chunk0103_261_1	chr2	165540103	165540401	+	0	NA	intron (NM_001172173, intron 3 of 6)	X2_LINE|LINE|CR1	-32084	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.000000	0.387960	
chunk0052_97_1	chr13	22325186	22325385	+	0	NA	Intergenic	Intergenic	115000	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.000000	0.300000	
chunk0121_335_1	chr3	24470316	24470627	+	0	NA	intron (NM_001128176, intron 1 of 10)	MIR|SINE|MIR	-23616	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.012862	0.410256	
chunk0012_19_1	chr1	154911802	154912189	+	0	NA	Intergenic	Intergenic	25013	NM_006556	10654	Hs.30954	NM_006556	ENSG00000163344	PMVK	HUMPMKI|PMK|PMKA|PMKASE|POROK1	phosphomevalonate kinase	protein-coding	0.005168	0.525773	316(AGGAACAGCAAGTCCA,-,0.00),317(GGAACAGCAAGTCCAA,+,0.00)
chunk0185_236_1	chr7	129421534	129422257	+	0	NA	intron (NM_001130723, intron 12 of 16)	intron (NM_001130723, intron 12 of 16)	-12538	NM_001134336	57464	Hs.489988	NM_020704	ENSG00000128578	STRIP2	FAM40B|FAR11B	striatin interacting protein 2	protein-coding	0.004149	0.343923	
chunk0085_76_1	chr18	2070584	2070984	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	500719	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.015000	0.461347	156(TGGGTCATTCTGTTCC,-,0.00),157(GGGTCATTCTGTTCCA,+,0.00)
chunk0139_199_1	chr4	54784356	54784632	+	0	NA	Intergenic	Intergenic	126566	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.025362	0.509025	
chunk0199_347_1	chr9	11955605	11956234	+	0	NA	Intergenic	Intergenic	-737467	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.003180	0.358730	261(ATGACAAACTGTTCCT,+,0.00)
chunk0055_105_1	chr13	56527346	56527792	+	0	NA	Intergenic	Intergenic	-613349	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.000000	0.281879	259(GGGAACTTTATGTACT,-,0.00),260(GGAACTTTATGTACTT,+,0.00)
chunk0102_54_1	chr2	142754088	142754647	+	0	NA	Intergenic	Intergenic	-123259	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.001789	0.316071	
chunk0208_182_1	chrX	17036501	17036918	+	0	NA	intron (NM_004726, intron 5 of 17)	intron (NM_004726, intron 5 of 17)	90018	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.004796	0.440191	
chunk0080_67_1	chr17	21985243	21985484	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	292840	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.020747	0.433884	
chunk0070_298_1	chr15	74798243	74799023	+	0	NA	exon (NM_004383, exon 3 of 13)	exon (NM_004383, exon 3 of 13)	-9876	NR_039738	100616183		NR_039738	ENSG00000264386	MIR4513	-	microRNA 4513	ncRNA	0.029487	0.619718	
chunk0014_235_1	chr1	179894796	179895369	+	0	NA	intron (NM_001267578, intron 3 of 9)	intron (NM_001267578, intron 3 of 9)	13040	NM_015602	26092	Hs.496459	NM_015602	ENSG00000143337	TOR1AIP1	LAP1|LAP1B|LGMD2Y	torsin 1A interacting protein 1	protein-coding	0.005236	0.341463	
chunk0140_97_1	chr4	68349953	68350344	+	0	NA	promoter-TSS (NM_001031732)	promoter-TSS (NM_001031732)	-42	NM_001031732	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.076726	0.607143	
chunk0167_313_1	chr6	72040898	72041257	+	0	NA	intron (NM_014989, intron 2 of 33)	intron (NM_014989, intron 2 of 33)	154374	NM_014989	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.008357	0.352778	
chunk0138_310_1	chr4	41331051	41331775	+	0	NA	Intergenic	Intergenic	-28194	NM_001289124	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.004144	0.297931	
chunk0001_12_1	chr1	1013744	1013943	+	0	NA	intron (NM_005101, intron 1 of 1)	intron (NM_005101, intron 1 of 1)	376	NM_005101	9636	Hs.458485	NM_005101	ENSG00000187608	ISG15	G1P2|IFI15|IMD38|IP17|UCRP|hUCRP	ISG15 ubiquitin like modifier	protein-coding	0.030151	0.660000	
chunk0018_155_1	chr1	218817567	218818079	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	355965	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.011719	0.460039	
chunk0031_402_1	chr10	131758142	131758509	+	0	NA	Intergenic	Intergenic	31874	NR_038365	399827	Hs.523353	NM_001001677	ENSG00000189275	LINC01164	-	long intergenic non-protein coding RNA 1164	ncRNA	0.021798	0.489130	
chunk0115_293_1	chr21	28283456	28283970	+	0	NA	Intergenic	Intergenic	-55046	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.009728	0.396117	
chunk0179_26_1	chr7	42941494	42941762	+	0	NA	Intergenic	Intergenic	9288	NM_031903	64983	Hs.50252	NM_031903	ENSG00000106591	MRPL32	HSPC283|L32mt|MRP-L32|bMRP-59b	mitochondrial ribosomal protein L32	protein-coding	0.011194	0.524164	
chunk0044_52_1	chr12	27696006	27696840	+	0	NA	promoter-TSS (NM_001029874)	promoter-TSS (NM_001029874)	-72	NM_001029874	387849	Hs.269836	NM_001029874	ENSG00000174236	REP15	RAB15EP	RAB15 effector protein	protein-coding	0.008393	0.426347	
chunk0093_446_1	chr19	58407880	58408248	+	0	NA	promoter-TSS (NM_173548)	promoter-TSS (NM_173548)	-632	NM_173548	201514	Hs.439551	NM_173548	ENSG00000171574	ZNF584	-	zinc finger protein 584	protein-coding	0.051630	0.601626	
chunk0106_441_1	chr2	208867319	208867987	+	0	NA	Intergenic	L1MDb|LINE|L1	460823	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.001497	0.426009	
chunk0081_193_1	chr17	42171857	42172251	+	0	NA	intron (NM_012285, intron 6 of 16)	intron (NM_012285, intron 6 of 16)	9224	NM_012285	23415	Hs.304081	NM_012285	ENSG00000089558	KCNH4	BEC2|ELK1|Kv12.3	potassium voltage-gated channel subfamily H member 4	protein-coding	0.027919	0.554430	
chunk0052_425_1	chr12	131716483	131716875	+	0	NA	intron (NM_004592, intron 3 of 17)	MER58B|DNA|hAT-Charlie	5592	NM_001261411	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.007653	0.356234	
chunk0065_74_1	chr15	23529820	23530343	+	0	NA	Intergenic	HERV35I-int|LTR|ERV1	32050	NR_039731	100616275		NR_039731	ENSG00000265673	MIR4508	mir-4508	microRNA 4508	ncRNA	0.003824	0.337786	
chunk0079_126_1	chr17	12575374	12576051	+	0	NA	intron (NR_034144, intron 1 of 2)	L1ME4a|LINE|L1	25744	NR_034144	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.001477	0.259587	
chunk0038_249_1	chr11	87395916	87396446	+	0	NA	Intergenic	Intergenic	358337	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.003774	0.323917	
chunk0001_73_1	chr1	2465099	2465357	+	0	NA	Intergenic	Intergenic	-2231	NM_001303012	9651	Hs.170156	NM_014638	ENSG00000149527	PLCH2	PLC-L4|PLC-eta2|PLCL4|PLCeta2	phospholipase C eta 2	protein-coding	0.015504	0.625483	
chunk0101_266_1	chr2	133558625	133558921	+	0	NA	intron (NM_207481, intron 2 of 17)	intron (NM_207481, intron 2 of 17)	9687	NM_207363	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.006757	0.400673	269(TGGGACACACAGTGCT,-,0.00),270(GGGACACACAGTGCTG,+,0.00)
chunk0155_48_1	chr5	91188848	91189237	+	0	NA	Intergenic	Intergenic	125360	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.005141	0.356410	331(GAGAGCAACATGTTCT,-,0.00),332(AGAGCAACATGTTCTT,+,0.00)
chunk0101_277_1	chr2	133765741	133766100	+	0	NA	Intergenic	Intergenic	-197460	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.005571	0.463889	
chunk0199_265_1	chr9	6310105	6310411	+	0	NA	Intergenic	Intergenic	-18091	NM_001001874	89882	Hs.351815	NM_033516	ENSG00000170777	TPD52L3	D55|NYDSP25|hD55	TPD52 like 3	protein-coding	0.000000	0.423453	
chunk0087_81_1	chr18	32122072	32122547	+	0	NA	intron (NM_016271, intron 4 of 7)	intron (NM_016271, intron 4 of 7)	29703	NM_001191324	51444	Hs.302408	NM_016271	ENSG00000134758	RNF138	HSD-4|NARF|STRIN|hNARF	ring finger protein 138	protein-coding	0.010526	0.388655	
chunk0211_214_1	chrX	118345387	118345717	+	0	NA	promoter-TSS (NM_001184965)	promoter-TSS (NM_001184965)	-521	NM_001184965	54521	Hs.98510	NM_019045	ENSG00000131725	WDR44	RAB11BP|RPH11|SYM-4	WD repeat domain 44	protein-coding	0.045455	0.501511	
chunk0177_343_1	chr7	26515364	26515972	+	0	NA	Intergenic	Intergenic	23157	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.021382	0.530378	348(CTGCACAGCCTGCTCC,-,0.00),349(TGCACAGCCTGCTCCT,+,0.00)
chunk0141_188_1	chr4	83455871	83456256	+	0	NA	promoter-TSS (NM_133636)	promoter-TSS (NM_133636)	131	NM_001297767	51023	Hs.334772	NM_016067	ENSG00000163319	MRPS18C	CGI-134|MRP-S18-1|MRP-S18-c|MRPS18-1|S18mt-c|mrps18-c	mitochondrial ribosomal protein S18C	protein-coding	0.064935	0.549223	
chunk0063_394_1	chr14	87433983	87434476	+	0	NA	Intergenic	Intergenic	528451	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.002028	0.358300	
chunk0121_71_1	chr3	15897262	15897476	+	0	NA	Intergenic	Charlie15a|DNA|hAT-Charlie	23598	NR_030289	693148		NR_030289	ENSG00000207815	MIR563	MIRN563|hsa-mir-563	microRNA 563	ncRNA	0.004673	0.353488	
chunk0201_54_1	chr9	33878462	33879305	+	0	NA	intron (NM_017811, intron 1 of 4)	MER83|LTR|ERV1	55481	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.014235	0.471564	
chunk0137_61_1	chr4	11839822	11840190	+	0	NA	Intergenic	L2c|LINE|L2	-383445	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.000000	0.357724	
chunk0196_315_1	chr8	110657055	110657428	+	0	NA	Intergenic	L1PA17|LINE|L1	370192	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.005362	0.344920	
chunk0066_91_1	chr15	29753757	29753956	+	0	NA	intron (NM_175610, intron 8 of 26)	intron (NM_175610, intron 8 of 26)	67692	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.005025	0.325000	114(AAGAACACGTAGTACT,-,0.00),115(AGAACACGTAGTACTA,+,0.00)
chunk0166_34_1	chr6	42118379	42118862	+	0	NA	intron (NM_001164446, intron 2 of 4)	intron (NM_001164446, intron 2 of 4)	24357	NM_001164446	647024	Hs.444277	NM_001164446	ENSG00000188112	C6orf132	bA7K24.2	chromosome 6 open reading frame 132	protein-coding	0.014493	0.588843	
chunk0015_152_1	chr1	186424557	186424995	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-10385	NR_126002	102724919	Hs.576493	NR_126002	ENSG00000229739	LOC102724919	-	uncharacterized LOC102724919	ncRNA	0.004566	0.435080	210(GGGACTTGGAGTTCTT,+,0.00)
chunk0019_380_1	chr1	230015828	230016104	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-41823	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.010870	0.382671	168(AAGTACACTCTGTGCT,-,0.00),169(AGTACACTCTGTGCTG,+,0.00)
chunk0194_259_1	chr8	86784503	86784949	+	0	NA	Intergenic	Intergenic	-41051	NM_019098	54714	Hs.154433	NM_019098	ENSG00000170289	CNGB3	ACHM1	cyclic nucleotide gated channel beta 3	protein-coding	0.002242	0.297539	
chunk0194_404_1	chr8	91107683	91108427	+	0	NA	intron (NM_001129890, intron 1 of 7)	intron (NM_001129890, intron 1 of 7)	5436	NM_001129890	100130742	Hs.733070	NM_001129890	ENSG00000214954	LRRC69	-	leucine rich repeat containing 69	protein-coding	0.002688	0.366443	
chunk0134_302_1	chr3	180666550	180667133	+	0	NA	intron (NM_181426, intron 1 of 19)	L1MEh|LINE|L1	12654	NM_181426	339829	Hs.712820	NM_181426	ENSG00000284862	CCDC39	CILD14|FAP59	coiled-coil domain containing 39	protein-coding	0.003431	0.315068	
chunk0198_139_1	chr8	132768000	132768572	+	0	NA	Intergenic	Intergenic	-7072	NM_016018	51105	Hs.304362	NM_016018	ENSG00000129292	PHF20L1	CGI-72|TDRD20B|URLC1	PHD finger protein 20 like 1	protein-coding	0.006993	0.343805	
chunk0041_269_1	chr11	129118989	129119268	+	0	NA	intron (NM_001142685, intron 4 of 21)	intron (NM_001142685, intron 4 of 21)	73070	NM_001142685	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.007168	0.403571	
chunk0099_303_1	chr2	99155011	99155542	+	0	NA	promoter-TSS (NM_025244)	promoter-TSS (NM_025244)	202	NM_001204830	51601	Hs.719172	NM_015929	ENSG00000144182	LIPT1	LIPT1D	lipoyltransferase 1	protein-coding	0.071563	0.554511	
chunk0074_184_1	chr16	24540685	24541078	+	0	NA	intron (NM_006910, intron 1 of 17)	intron (NM_006910, intron 1 of 17)	1294	NM_018703	5930	Hs.188553	NM_006910	ENSG00000122257	RBBP6	MY038|P2P-R|PACT|RBQ-1|SNAMA	RB binding protein 6, ubiquitin ligase	protein-coding	0.025445	0.477157	
chunk0109_159_1	chr20	3969261	3969562	+	0	NA	intron (NM_001134337, intron 1 of 5)	L1MD1|LINE|L1	45996	NM_007219	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.006645	0.403974	
chunk0130_28_1	chr3	128848740	128849109	+	0	NA	Intergenic	Intergenic	22617	NR_034179	653712	Hs.653243	NR_034179	ENSG00000231305	LOC653712	-	intraflagellar transport 122 homolog (Chlamydomonas) pseudogene	pseudo	0.021680	0.478378	
chunk0076_94_1	chr16	64996575	64996991	+	0	NA	intron (NM_001797, intron 4 of 12)	L1PA16|LINE|L1	125354	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.009615	0.410072	
chunk0202_277_1	chr9	77158830	77159108	+	0	NA	Intergenic	Intergenic	-18476	NM_033305	23230	Hs.459790	NM_015186	ENSG00000197969	VPS13A	CHAC|CHOREIN	vacuolar protein sorting 13 homolog A	protein-coding	0.000000	0.387097	
chunk0077_307_1	chr16	81850193	81850655	+	0	NA	intron (NM_002661, intron 2 of 32)	intron (NM_002661, intron 2 of 32)	71166	NM_002661	5336	Hs.372303	NM_002661	ENSG00000197943	PLCG2	APLAID|FCAS3|PLC-IV|PLC-gamma-2	phospholipase C gamma 2	protein-coding	0.010823	0.395248	
chunk0117_370_1	chr21	45084411	45085232	+	0	NA	intron (NM_015834, intron 1 of 12)	intron (NM_015834, intron 1 of 12)	10243	NM_001160230	104	Hs.474018	NM_001112	ENSG00000197381	ADARB1	ADAR2|DRABA2|DRADA2|RED1	adenosine deaminase RNA specific B1	protein-coding	0.010962	0.459854	420(GGGCACAAGGTGTCCA,-,0.00),421(GGCACAAGGTGTCCAA,+,0.00)
chunk0010_244_1	chr1	116456280	116456656	+	0	NA	intron (NR_125973, intron 2 of 3)	L3|LINE|CR1	22358	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.007979	0.453581	202(CAGAACATTCTGTGTC,-,0.00),203(AGAACATTCTGTGTCC,+,0.00)
chunk0181_252_1	chr7	85763966	85764776	+	0	NA	Intergenic	Intergenic	-642440	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.006173	0.389642	447(ATGTACACAATGTGCA,-,0.00)
chunk0047_190_1	chr12	70810054	70810253	+	0	NA	intron (NM_002849, intron 2 of 13)	intron (NM_002849, intron 2 of 13)	-21223	NM_001207015	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.015075	0.390000	
chunk0159_157_1	chr5	139388279	139388759	+	0	NA	exon (NM_016459, exon 2 of 4)	exon (NM_016459, exon 2 of 4)	1397	NM_016459	51237	Hs.409563	NM_016459	ENSG00000170476	MZB1	MEDA-7|PACAP|pERp1	marginal zone B and B1 cell specific protein	protein-coding	0.016667	0.607069	
chunk0130_87_1	chr3	130761789	130761988	+	0	NA	Intergenic	L1MA3|LINE|L1	-15036	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.010050	0.500000	
chunk0112_214_1	chr20	40592798	40593223	+	0	NA	Intergenic	Intergenic	96230	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.004706	0.422535	
chunk0006_171_1	chr1	66704880	66705550	+	0	NA	intron (NM_032291, intron 18 of 24)	intron (NM_032291, intron 18 of 24)	-47242	NM_152665	200132	Hs.479226	NM_152665	ENSG00000152760	TCTEX1D1	-	Tctex1 domain containing 1	protein-coding	0.007463	0.359165	291(ATGGACTTTGTGTTCT,-,0.00),292(TGGACTTTGTGTTCTC,+,0.00)
chunk0052_36_1	chr13	20768986	20769481	+	0	NA	intron (NM_174928, intron 1 of 4)	L1M4c|LINE|L1	4685	NM_174928	221143	Hs.26674	NM_174928	ENSG00000150456	EEF1AKMT1	ESP13|N6AMT2	EEF1A lysine methyltransferase 1	protein-coding	0.004040	0.441532	
chunk0210_445_1	chrX	104913293	104913679	+	0	NA	intron (NM_017416, intron 2 of 10)	intron (NM_017416, intron 2 of 10)	307207	NM_031274	56157	Hs.567543	NM_031274	ENSG00000268629	TEX13A	-	testis expressed 13A	protein-coding	0.000000	0.408269	5(AGAAACACAGTGTTCA,-,0.00),6(GAAACACAGTGTTCAA,+,0.00)
chunk0009_348_1	chr1	109499722	109500339	+	0	NA	3' UTR (NM_182580, exon 3 of 3)	3' UTR (NM_182580, exon 3 of 3)	5951	NM_001134403	284613	Hs.514682	NM_182580	ENSG00000174151	CYB561D1	-	cytochrome b561 family member D1	protein-coding	0.004862	0.525890	
chunk0038_230_1	chr11	87000075	87000593	+	0	NA	non-coding (NR_038905, exon 3 of 3)	non-coding (NR_038905, exon 3 of 3)	-37510	NM_022918	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.000000	0.452794	
chunk0067_233_1	chr15	45435454	45435887	+	0	NA	Intergenic	Intergenic	2620	NR_030599	100126311		NR_030599	ENSG00000284386	MIR147B	MIRN147B|mir-147b	microRNA 147b	ncRNA	0.011547	0.405530	
chunk0031_438_1	chr10	132506728	132506975	+	0	NA	Intergenic	Intergenic	-30998	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.016194	0.524194	163(AAGGGCAGGATGTTCT,-,0.00),164(AGGGCAGGATGTTCTG,+,0.00)
chunk0206_113_1	chr9	120877555	120878183	+	0	NA	promoter-TSS (NM_001286843)	promoter-TSS (NM_001286843)	-541	NM_001286843	26147	Hs.460124	NM_015651	ENSG00000119403	PHF19	MTF2L1|PCL3|TDRD19B	PHD finger protein 19	protein-coding	0.035032	0.496025	329(GGGAACACACTGTACA,-,0.00),330(GGAACACACTGTACAC,+,0.00)
chunk0158_350_1	chr5	133494700	133495263	+	0	NA	intron (NM_015082, intron 3 of 15)	intron (NM_015082, intron 3 of 15)	-67275	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.019538	0.473404	
chunk0034_150_1	chr11	30167494	30168060	+	0	NA	Intergenic	Intergenic	-63239	NM_001018080	2488	Hs.36975	NM_000510	ENSG00000131808	FSHB	HH24	follicle stimulating hormone subunit beta	protein-coding	0.003534	0.361552	310(GAGTACAATCAGTCCT,-,0.00),311(AGTACAATCAGTCCTT,+,0.00)
chunk0042_353_1	chr12	10213516	10213976	+	0	NA	intron (NM_031412, intron 1 of 3)	intron (NM_031412, intron 1 of 3)	856	NM_031412	23710	Hs.524250	NM_031412	ENSG00000139112	GABARAPL1	APG8-LIKE|APG8L|ATG8|ATG8B|ATG8L|GEC1	GABA type A receptor associated protein like 1	protein-coding	0.039130	0.520607	
chunk0019_271_1	chr1	228445419	228445909	+	0	NA	Intergenic	Intergenic	12195	NM_033445	92815	Hs.26331	NM_033445	ENSG00000181218	HIST3H2A	-	histone cluster 3 H2A	protein-coding	0.034694	0.460285	
chunk0180_187_1	chr7	66099997	66100332	+	0	NA	Intergenic	Intergenic	-14654	NM_001040647	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.023881	0.574405	
chunk0147_165_1	chr4	176204859	176205483	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-9500	NM_144644	132851	Hs.481235	NM_144644	ENSG00000150628	SPATA4	SPEF1B|TSARG2	spermatogenesis associated 4	protein-coding	0.006410	0.489600	
chunk0103_289_1	chr2	166127969	166128168	+	0	NA	intron (NR_110260, intron 2 of 11)	(A)n|Simple_repeat|Simple_repeat	21064	NM_001202435	6323	Hs.22654	NM_006920	ENSG00000144285	SCN1A	EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI	sodium voltage-gated channel alpha subunit 1	protein-coding	0.015075	0.380000	
chunk0195_383_1	chr8	100176941	100177473	+	0	NA	intron (NM_003114, intron 3 of 18)	Tigger2|DNA|TcMar-Tigger	18872	NM_003114	6674	Hs.591866	NM_003114	ENSG00000104450	SPAG1	CILD28|CT140|HEL-S-268|HSD-3.8|SP75|TPIS	sperm associated antigen 1	protein-coding	0.003759	0.363977	
chunk0085_316_1	chr18	8331538	8331938	+	0	NA	intron (NM_001105244, intron 22 of 32)	intron (NM_001105244, intron 22 of 32)	35296	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.005000	0.401496	219(GAGTACAAAGAGTGCC,-,0.00)
chunk0075_377_1	chr16	56608057	56608570	+	0	NA	promoter-TSS (NM_005953)	promoter-TSS (NM_005953)	-253	NM_005953	4502	Hs.534330	NM_005953	ENSG00000125148	MT2A	MT-2|MT-II|MT2	metallothionein 2A	protein-coding	0.091618	0.640078	260(CGGTACACTGTGTCCT,-,0.00),261(GGTACACTGTGTCCTC,+,0.00)
chunk0115_300_1	chr21	28423286	28423745	+	0	NA	Intergenic	Intergenic	-115803	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.008715	0.363043	
chunk0075_366_1	chr16	56370797	56371186	+	0	NA	intron (NM_001144, intron 10 of 13)	intron (NM_001144, intron 10 of 13)	54547	NM_001144	267	Hs.295137	NM_001144	ENSG00000159461	AMFR	GP78|RNF45	autocrine motility factor receptor	protein-coding	0.010283	0.420513	117(AGGGACACGTTGTTCT,-,0.00),118(GGGACACGTTGTTCTG,+,0.00)
chunk0160_323_1	chr5	159416379	159416789	+	0	NA	Intergenic	Intergenic	49692	NR_027110	285627	Hs.552766	NR_027110	ENSG00000253298	LINC01845	-	long intergenic non-protein coding RNA 1845	ncRNA	0.014634	0.367397	
chunk0157_445_1	chr5	124906286	124906903	+	0	NA	Intergenic	Intergenic	-130237	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.009724	0.454693	
chunk0091_278_1	chr19	11639508	11639993	+	0	NA	Intergenic	CpG	27339	NR_002944	664709	Hs.534822	NR_002944		HNRNPA1P10	HNRPA1L-2	heterogeneous nuclear ribonucleoprotein A1 pseudogene 10	pseudo	0.061856	0.619342	
chunk0117_281_1	chr22	24270754	24271012	+	0	NA	promoter-TSS (NR_103546)	promoter-TSS (NR_103546)	66	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.112403	0.733591	
chunk0209_48_1	chrX	36843598	36844228	+	0	NA	Intergenic	L1ME3|LINE|L1	-164446	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.001587	0.286846	
chunk0097_256_1	chr2	54226619	54226818	+	0	NA	intron (NM_138448, intron 3 of 3)	intron (NM_138448, intron 3 of 3)	29554	NM_001003937	388951	Hs.620508	NM_001003937	ENSG00000178021	TSPYL6	-	TSPY like 6	protein-coding	0.000000	0.400000	
chunk0080_82_1	chr17	22521273	22521523	+	0	NA	Intergenic	Intergenic	-1713	NM_001190452	100462977	Hs.740185	NM_001190452	ENSG00000256618	MTRNR2L1	HN1	MT-RNR2 like 1	protein-coding	0.036000	0.474104	
chunk0134_338_1	chr3	182215506	182215985	+	0	NA	Intergenic	L2c|LINE|L2	263381	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.002088	0.433333	
chunk0159_185_1	chr5	140261352	140261778	+	0	NA	intron (NM_002622, intron 3 of 3)	intron (NM_002622, intron 3 of 3)	41539	NM_002622	5201	Hs.483564	NM_002622	ENSG00000113068	PFDN1	PDF|PFD1	prefoldin subunit 1	protein-coding	0.011737	0.405152	
chunk0031_361_1	chr10	130212721	130213306	+	0	NA	Intergenic	Intergenic	76638	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.015385	0.501706	
chunk0092_106_1	chr19	23403498	23403942	+	0	NA	non-coding (NR_126449, exon 3 of 5)	non-coding (NR_126449, exon 3 of 5)	-8160	NM_001300951	7644	Hs.58834	NM_003430	ENSG00000167232	ZNF91	HPF7|HTF10	zinc finger protein 91	protein-coding	0.011261	0.471910	
chunk0012_272_1	chr1	161807563	161807940	+	0	NA	intron (NM_007348, intron 7 of 15)	intron (NM_007348, intron 7 of 15)	41507	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.000000	0.333333	
chunk0130_62_1	chr3	129841029	129841309	+	0	NA	intron (NM_001128224, intron 1 of 5)	THE1D-int|LTR|ERVL-MaLR	39390	NM_001017395	23023	Hs.477547	NM_015008	ENSG00000172765	TMCC1	-	transmembrane and coiled-coil domain family 1	protein-coding	0.010714	0.434164	
chunk0054_258_1	chr13	46295031	46295552	+	0	NA	Intergenic	L1M5|LINE|L1	2553	NR_047493	100861554	Hs.90866	NR_047493	ENSG00000261097	LINC00563	-	long intergenic non-protein coding RNA 563	ncRNA	0.007678	0.365900	
chunk0121_366_1	chr3	24876979	24877465	+	0	NA	Intergenic	Intergenic	-297110	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.283368	
chunk0121_377_1	chr3	25079687	25080026	+	0	NA	Intergenic	L1ME2|LINE|L1	-94476	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.285294	
chunk0063_13_1	chr14	76226660	76227306	+	0	NA	Intergenic	Intergenic	72629	NR_110314	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.013932	0.479134	
chunk0096_235_1	chr2	30846406	30846681	+	0	NA	Intergenic	L2c|LINE|L2	-39098	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.003636	0.409420	
chunk0159_223_1	chr5	141014139	141014514	+	0	NA	Intergenic	Intergenic	-37050	NM_013340	29930	Hs.278950	NM_013340	ENSG00000171815	PCDHB1	PCDH-BETA1	protocadherin beta 1	protein-coding	0.000000	0.337766	
chunk0161_382_1	chr5	176837735	176837977	+	0	NA	intron (NM_133369, intron 1 of 14)	intron (NM_133369, intron 1 of 14)	27297	NM_133369	90249	Hs.33191	NM_133369	ENSG00000113763	UNC5A	UNC5H1	unc-5 netrin receptor A	protein-coding	0.049587	0.576132	
chunk0099_290_1	chr2	98775028	98775463	+	0	NA	Intergenic	Intergenic	-3347	NR_126337	101927070	Hs.469395	NR_126337		LINC02611	-	long intergenic non-protein coding RNA 2611	ncRNA	0.022989	0.571101	282(CTGAACACCAAGTCCT,-,0.00),283(TGAACACCAAGTCCTG,+,0.00)
chunk0139_117_1	chr4	52711233	52711483	+	0	NA	Intergenic	L2b|LINE|L2	-1096	NR_024031	57291	Hs.744077	NR_024031	ENSG00000226950	DANCR	AGU2|ANCR|KIAA0114|SNHG13|lncRNA-ANCR	differentiation antagonizing non-protein coding RNA	ncRNA	0.008000	0.458167	
chunk0059_40_1	chr14	29912405	29913122	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	14930	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.006974	0.325905	
chunk0113_238_1	chr20	54093486	54093781	+	0	NA	Intergenic	Intergenic	-22868	NM_003657	8537	Hs.400556	NM_003657	ENSG00000064787	BCAS1	AIBC1|NABC1	breast carcinoma amplified sequence 1	protein-coding	0.013559	0.442568	209(CAAAACACAGTGTCCT,-,0.00),210(AAAACACAGTGTCCTT,+,0.00)
chunk0095_426_1	chr2	24815212	24815948	+	0	NA	exon (NM_001199803, exon 4 of 7)	exon (NM_001199803, exon 4 of 7)	22118	NM_024322	79172	Hs.731569	NM_024322	ENSG00000138092	CENPO	CENP-O|ICEN-36|MCM21R	centromere protein O	protein-coding	0.012228	0.424695	470(CAGCACTTCCTGTTCA,-,0.00),471(AGCACTTCCTGTTCAG,+,0.00)
chunk0198_140_1	chr8	132772274	132772567	+	0	NA	Intergenic	Intergenic	-2938	NM_016018	51105	Hs.304362	NM_016018	ENSG00000129292	PHF20L1	CGI-72|TDRD20B|URLC1	PHD finger protein 20 like 1	protein-coding	0.003413	0.438776	125(TGGAACAGGGTGTGCT,-,0.00),126(GGAACAGGGTGTGCTG,+,0.00)
chunk0191_7_1	chr8	42460776	42461242	+	0	NA	intron (NM_006749, intron 4 of 10)	intron (NM_006749, intron 4 of 10)	40451	NM_001257180	6575	Hs.653173	NM_006749	ENSG00000168575	SLC20A2	GLVR-2|GLVR2|IBGC1|IBGC3|MLVAR|PIT-2|PIT2|RAM1|Ram-1	solute carrier family 20 member 2	protein-coding	0.012876	0.471092	
chunk0050_59_1	chr12	101182086	101182505	+	0	NA	intron (NM_145913, intron 9 of 14).2	(ATCTA)n|Simple_repeat|Simple_repeat	27943	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.004773	0.345238	
chunk0123_361_1	chr3	48236505	48237087	+	0	NA	Intergenic	LTR75|LTR|ERVL	-4310	NM_016089	51385	Hs.172602	NM_016089	ENSG00000164048	ZNF589	SZF1	zinc finger protein 589	protein-coding	0.006873	0.476844	
chunk0101_235_1	chr2	131231729	131231973	+	0	NA	intron (NM_001083538, intron 6 of 14)	intron (NM_001083538, intron 6 of 14)	13500	NM_001083538	445582	Hs.686146	NM_001004054	ENSG00000188219	POTEE	A26C1|A26C1A|CT104.2|POTE-2|POTE2|POTE2gamma	POTE ankyrin domain family member E	protein-coding	0.008197	0.338776	
chunk0114_12_1	chr21	6565761	6566049	+	0	NA	Intergenic	Intergenic	5172	NM_001314050	102724652	Hs.184085	NM_001314050	ENSG00000276076	CRYAA2	CRYAA	crystallin alpha A2	protein-coding	0.010417	0.564014	
chunk0056_186_1	chr13	85521524	85521925	+	0	NA	intron (NR_046989, intron 1 of 3)	intron (NR_046989, intron 1 of 3)	158121	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.007481	0.340796	
chunk0195_21_1	chr8	93116943	93117389	+	0	NA	Intergenic	Intergenic	49684	NM_001242668									0.013453	0.485459	254(TGGAACAAACTGTACT,-,0.00),255(GGAACAAACTGTACTA,+,0.00)
chunk0033_366_1	chr11	23127762	23128071	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	-267490	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.006472	0.306452	
chunk0170_191_1	chr6	112043028	112043322	+	0	NA	Intergenic	Intergenic	-10900	NR_125354	8838	Hs.558428	NM_003880	ENSG00000112761	CCN6	LIBC|PPAC|PPD|WISP-3|WISP3	cellular communication network factor 6	protein-coding	0.040816	0.494915	
chunk0182_186_1	chr7	95659693	95660289	+	0	NA	Intergenic	Intergenic	-63378	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.001678	0.371859	263(TGGTACAAAATGTACT,-,0.00),264(GGTACAAAATGTACTC,+,0.00)
chunk0092_113_1	chr19	23992203	23992619	+	0	NA	Intergenic	Intergenic	-40994	NM_001278661	9534	Hs.434406	NM_004876	ENSG00000213096	ZNF254	BMZF-5|HD-ZNF1|ZNF539|ZNF91L	zinc finger protein 254	protein-coding	0.012019	0.378897	
chunk0142_59_1	chr4	92231434	92231862	+	0	NA	Intergenic	LTR37B|LTR|ERV1	45654	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.002336	0.270396	
chunk0053_75_1	chr13	28394409	28394928	+	0	NA	intron (NM_001159920, intron 12 of 12)	MER115|DNA|hAT-Tip100	100460	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.007707	0.486538	
chunk0198_52_1	chr8	128507492	128507803	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	57032	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.006431	0.435897	143(AAGGACACAGTGTGCC,-,0.00),144(AGGACACAGTGTGCCT,+,0.00)
chunk0199_236_1	chr9	5400198	5400963	+	0	NA	intron (NM_018465, intron 3 of 5)	intron (NM_018465, intron 3 of 5)	37357	NM_018465	55848	Hs.584242	NM_018465	ENSG00000107020	PLGRKT	AD025|C9orf46|MDS030|PLG-RKT|Plg-R(KT)	plasminogen receptor with a C-terminal lysine	protein-coding	0.005229	0.314621	
chunk0064_309_1	chr14	95663580	95663839	+	0	NA	intron (NR_028288, intron 4 of 7)	intron (NR_028288, intron 4 of 7)	12531	NR_028288	27004	Hs.510368	NM_012468		TCL6	TNG1|TNG2	T cell leukemia/lymphoma 6	ncRNA	0.000000	0.403846	
chunk0036_92_1	chr11	60880672	60881329	+	0	NA	Intergenic	L2c|LINE|L2	13458	NM_207341	22917	Hs.172130	NM_207341	ENSG00000149506	ZP1	HEL163|OOMD|OOMD1	zona pellucida glycoprotein 1	protein-coding	0.012177	0.490881	315(TTGCACATCCTGTCCT,-,0.00),316(TGCACATCCTGTCCTC,+,0.00)
chunk0055_433_1	chr13	75456003	75456202	+	0	NA	intron (NM_001286659, intron 1 of 18)	FLAM_A|SINE|Alu	26066	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.000000	0.450000	
chunk0006_7_1	chr1	63859057	63859680	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	85349	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.006421	0.445513	
chunk0175_215_1	chr7	6104513	6104838	+	0	NA	promoter-TSS (NM_032172)	promoter-TSS (NM_032172)	-244	NM_032172	84132	Hs.31856	NM_032172	ENSG00000106346	USP42	-	ubiquitin specific peptidase 42	protein-coding	0.132308	0.711656	
chunk0108_256_1	chr2	234019941	234020849	+	0	NA	TTS (NM_024080)	TTS (NM_024080)	-30307	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.005507	0.434543	
chunk0185_265_1	chr7	130481494	130481715	+	0	NA	Intergenic	Intergenic	-4571	NM_001253901	4232	Hs.270978	NM_002402	ENSG00000106484	MEST	PEG1	mesoderm specific transcript	protein-coding	0.004525	0.387387	
chunk0120_129_1	chr3	4899608	4900089	+	0	NA	intron (NR_125914, intron 2 of 2)	MIRc|SINE|MIR	6653	NR_125914	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.016632	0.439834	221(CAGAACTCGCTGTTCC,-,0.00),222(AGAACTCGCTGTTCCT,+,0.00)
chunk0003_418_1	chr1	40712389	40712765	+	0	NA	intron (NM_001142590, intron 3 of 14)	intron (NM_001142590, intron 3 of 14)	3254	NM_001308115	4802	Hs.713051	NM_014223	ENSG00000066136	NFYC	CBF-C|CBFC|H1TF2A|HAP5|HSM|NF-YC	nuclear transcription factor Y subunit gamma	protein-coding	0.007979	0.374005	
chunk0169_253_1	chr6	105295987	105296277	+	0	NA	intron (NM_002726, intron 10 of 14)	L1ME4b|LINE|L1	106992	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.006897	0.329897	
chunk0165_367_1	chr6	38185755	38185966	+	0	NA	intron (NM_001099272, intron 10 of 10)	L1ME3B|LINE|L1	366329	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.028436	0.466981	
chunk0020_112_1	chr1	233221825	233222406	+	0	NA	intron (NM_014801, intron 10 of 33)	L2a|LINE|L2	73598	NM_014801	80003	Hs.370605	NM_014801	ENSG00000135749	PCNX2	PCNXL2	pecanex 2	protein-coding	0.008606	0.434708	
chunk0064_228_1	chr14	93901738	93902289	+	0	NA	Intergenic	MER87|LTR|ERV1	-16881	NM_138344	90050	Hs.525550	NM_138344	ENSG00000140067	FAM181A	C14orf152	family with sequence similarity 181 member A	protein-coding	0.018149	0.451087	234(AGGAACACTGTGGCCT,-,0.00),235(GGAACACTGTGGCCTG,+,0.00)
chunk0062_191_1	chr14	69786305	69786504	+	0	NA	intron (NM_003049, intron 1 of 4)	MIRb|SINE|MIR	10885	NM_003049	6554	Hs.952	NM_003049	ENSG00000100652	SLC10A1	NTCP	solute carrier family 10 member 1	protein-coding	0.005025	0.465000	
chunk0126_204_1	chr3	78630307	78631230	+	0	NA	intron (NM_133631, intron 23 of 28)	intron (NM_133631, intron 23 of 28)	388691	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.006501	0.345238	
chunk0122_142_1	chr3	31901314	31901724	+	0	NA	intron (NM_017784, intron 1 of 11)	L2b|LINE|L2	-80255	NM_001137674	344787	Hs.585139	NM_001137674	ENSG00000197385	ZNF860	-	zinc finger protein 860	protein-coding	0.007317	0.506083	
chunk0014_277_1	chr1	180516557	180516891	+	0	NA	Intergenic	Intergenic	-13837	NM_032360	84320	Hs.200051	NM_032360	ENSG00000230124	ACBD6	-	acyl-CoA binding domain containing 6	protein-coding	0.002994	0.289552	
chunk0138_296_1	chr4	41070960	41071178	+	0	NA	intron (NM_004307, intron 3 of 17)	intron (NM_004307, intron 3 of 17)	143549	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.000000	0.356164	
chunk0024_116_1	chr10	34773560	34773815	+	0	NA	intron (NM_019619, intron 1 of 24)	L1ME4c|LINE|L1	41638	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.011765	0.394531	229(AGGCACTTAATGTTCT,-,0.00),230(GGCACTTAATGTTCTT,+,0.00)
chunk0090_107_1	chr18	71136480	71136972	+	0	NA	Intergenic	Intergenic	442230	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.006098	0.393509	
chunk0123_438_1	chr3	50395073	50395361	+	0	NA	intron (NM_001005505, intron 3 of 37)	MIR3|SINE|MIR	29883	NR_111914	11068	Hs.149443	NM_007022	ENSG00000114395	CYB561D2	101F6|TSP10|XXcos-LUCA11.4	cytochrome b561 family member D2	protein-coding	0.017361	0.598616	
chunk0105_3_1	chr2	181613365	181613673	+	0	NA	intron (NR_027689, intron 1 of 10)	intron (NR_027689, intron 1 of 10)	43588	NM_001030313	375298	Hs.732358	NM_201548	ENSG00000188452	CERKL	RP26	ceramide kinase like	protein-coding	0.006494	0.368932	
chunk0153_90_1	chr5	68215251	68215713	+	0	NA	promoter-TSS (NM_181523)	promoter-TSS (NM_181523)	-274	NM_181523	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.106061	0.732181	
chunk0147_415_1	chr4	187135826	187136411	+	0	NA	Intergenic	Intergenic	369495	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.020513	0.455631	
chunk0127_197_1	chr3	96111264	96111626	+	0	NA	Intergenic	L1MB8|LINE|L1	-248519	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.002762	0.349862	
chunk0010_262_1	chr1	116717310	116717826	+	0	NA	Intergenic	L2|LINE|L2	23456	NM_001013643									0.005814	0.441006	
chunk0168_242_1	chr6	87923168	87923745	+	0	NA	Intergenic	Intergenic	-124333	NM_030960	81833	Hs.161241	NM_030960	ENSG00000118434	SPACA1	SAMP32	sperm acrosome associated 1	protein-coding	0.005199	0.415225	
chunk0058_311_1	chr14	27315612	27316197	+	0	NA	Intergenic	Intergenic	-296684	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.005128	0.354949	
chunk0028_291_1	chr10	91435299	91435665	+	0	NA	intron (NM_001284274, intron 2 of 21)	intron (NM_001284274, intron 2 of 21)	25197	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.008197	0.468665	
chunk0134_111_1	chr3	177062316	177062788	+	0	NA	intron (NM_024665, intron 3 of 15)	intron (NM_024665, intron 3 of 15)	134708	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.000000	0.342495	
chunk0048_404_1	chr12	88037790	88038256	+	0	NA	intron (NM_001009894, intron 1 of 6)	intron (NM_001009894, intron 1 of 6)	2532	NM_001009894	91298	Hs.591009	NM_001009894	ENSG00000133641	C12orf29	-	chromosome 12 open reading frame 29	protein-coding	0.004292	0.353319	
chunk0204_19_1	chr9	92062126	92062737	+	0	NA	intron (NM_006415, intron 6 of 14)	L1MD1|LINE|L1	53043	NM_001281303	10558	Hs.90458	NM_006415	ENSG00000090054	SPTLC1	HSAN1|HSN1|LBC1|LCB1|SPT1|SPTI	serine palmitoyltransferase long chain base subunit 1	protein-coding	0.003273	0.334967	
chunk0044_139_1	chr12	29552305	29552587	+	0	NA	intron (NM_001193451, intron 10 of 17)	MER33|DNA|hAT-Charlie	-54760	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.003546	0.335689	
chunk0100_132_1	chr2	108689235	108689676	+	0	NA	Intergenic	Intergenic	-30026	NM_006267	5903	Hs.199561	NM_006267	ENSG00000153201	RANBP2	ADANE|ANE1|IIAE3|NUP358|TRP1|TRP2	RAN binding protein 2	protein-coding	0.011338	0.472851	
chunk0161_254_1	chr5	171908323	171909115	+	0	NA	intron (NM_012300, intron 3 of 12)	intron (NM_012300, intron 3 of 12)	98154	NM_033644	23291	Hs.484138	NM_012300	ENSG00000072803	FBXW11	BTRC2|BTRCP2|FBW1B|FBXW1B|Fbw11|Hos	F-box and WD repeat domain containing 11	protein-coding	0.006313	0.398487	524(TAGAACACGGAGTCCT,-,0.00),525(AGAACACGGAGTCCTG,+,0.00)
chunk0146_187_1	chr4	161021142	161021674	+	0	NA	Intergenic	L1M2|LINE|L1	-1001325	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.001880	0.288931	345(AAGCACACACTGATCA,-,0.00),346(AGCACACACTGATCAT,+,0.00)
chunk0150_353_1	chr5	38682339	38682663	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	37772	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.006173	0.304615	
chunk0030_233_1	chr10	114928730	114929154	+	0	NA	Intergenic	Intergenic	-9251	NM_139169	142940	Hs.21187	NM_139169	ENSG00000165832	TRUB1	PUS4	TruB pseudouridine synthase family member 1	protein-coding	0.007075	0.388235	173(GAGGACATGCTGTCTC,-,0.00),174(AGGACATGCTGTCTCT,+,0.00)
chunk0039_146_1	chr11	98645506	98645934	+	0	NA	Intergenic	Intergenic	-375256	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.002336	0.305361	
chunk0078_229_1	chr17	6548560	6549052	+	0	NA	intron (NM_001165966, intron 1 of 18)	intron (NM_001165966, intron 1 of 18)	7751	NM_031220	83394	Hs.183983	NM_031220	ENSG00000091622	PITPNM3	ACKR6|CORD5|NIR1|RDGBA3	PITPNM family member 3	protein-coding	0.018293	0.537525	
chunk0095_194_1	chr2	18214613	18214942	+	0	NA	Intergenic	Intergenic	336120	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.000000	0.278788	138(GGGAACAGTTTGTGTC,-,0.00)
chunk0168_320_1	chr6	92421288	92421747	+	0	NA	Intergenic	L1PA5|LINE|L1	-731089	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.002179	0.497826	
chunk0178_212_1	chr7	35392249	35392664	+	0	NA	Intergenic	Intergenic	78601	NR_038864	401324	Hs.377034	NR_038864		LOC401324	-	uncharacterized LOC401324	ncRNA	0.002410	0.387019	
chunk0129_141_1	chr3	120441791	120442287	+	0	NA	intron (NM_007085, intron 2 of 10)	intron (NM_007085, intron 2 of 10)	9032	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.012097	0.424547	
chunk0188_262_1	chr8	14773207	14773608	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	80103	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.007481	0.368159	49(AAGAACATAATGGACT,-,0.00)
chunk0069_192_1	chr15	63282918	63283176	+	0	NA	intron (NM_001145646, intron 2 of 4)	intron (NM_001145646, intron 2 of 4)	5497	NM_031301	83464	Hs.511703	NM_031301	ENSG00000138613	APH1B	APH-1B|PRO1328|PSFL|TAAV688	aph-1 homolog B, gamma-secretase subunit	protein-coding	0.011628	0.312741	
chunk0082_325_1	chr17	59514332	59514810	+	0	NA	intron (NR_110813, intron 1 of 2)	LTR89|LTR|ERVL?	12286	NR_110813	101927728	Hs.569720	NR_110813	ENSG00000265313	LINC01476	-	long intergenic non-protein coding RNA 1476	ncRNA	0.010460	0.398747	355(AAGAACAAACTCTTCC,-,0.00)
chunk0043_194_1	chr12	19135536	19135770	+	0	NA	intron (NM_019012, intron 3 of 25)	intron (NM_019012, intron 3 of 25)	5961	NM_001256470	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.008547	0.340426	
chunk0211_7_1	chrX	107677024	107677316	+	0	NA	Intergenic	Intergenic	39311	NM_001015881	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.027397	0.511945	190(CAGAACATTTCGTTCT,-,0.00),191(AGAACATTTCGTTCTG,+,0.00)
chunk0144_321_1	chr4	138912304	138912552	+	0	NA	Intergenic	Intergenic	-103331	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.012097	0.361446	
chunk0185_38_1	chr7	124457291	124457647	+	0	NA	Intergenic	Intergenic	-105373	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.002809	0.352941	
chunk0203_317_1	chr9	89505712	89506117	+	0	NA	Intergenic	Intergenic	-26218	NM_001142287	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.012346	0.460591	246(AGACACAGACTGTTCT,-,0.00),247(GACACAGACTGTTCTC,+,0.00)
chunk0012_278_1	chr1	161884311	161884966	+	0	NA	intron (NM_007348, intron 14 of 15)	L2a|LINE|L2	118394	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.010687	0.291159	
chunk0113_374_1	chr20	59347238	59348091	+	0	NA	Intergenic	L1MC3|LINE|L1	47237	NM_207033	1908	Hs.1408	NM_000114	ENSG00000124205	EDN3	ET-3|ET3|HSCR4|PPET3|WS4B	endothelin 3	protein-coding	0.008206	0.425059	
chunk0204_441_1	chr9	104035614	104036050	+	0	NA	Intergenic	Intergenic	36123	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.004587	0.324943	
chunk0100_311_1	chr2	115909117	115909415	+	0	NA	Intergenic	Intergenic	747159	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.003356	0.401338	
chunk0133_263_1	chr3	171784926	171785198	+	0	NA	intron (NM_001130081, intron 1 of 25)	intron (NM_001130081, intron 1 of 25)	25432	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.007353	0.344322	
chunk0054_252_1	chr13	46213608	46214186	+	0	NA	intron (NM_001282460, intron 2 of 9)	Tigger17a|DNA|TcMar-Tigger	1954	NM_001282460	220416	Hs.267765	NM_001024609	ENSG00000173988	LRRC63	-	leucine rich repeat containing 63	protein-coding	0.001730	0.335060	
chunk0134_332_1	chr3	181913232	181913839	+	0	NA	Intergenic	Intergenic	-38829	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.004942	0.330592	
chunk0198_109_1	chr8	131319095	131319346	+	0	NA	Intergenic	L2a|LINE|L2	-278631	NM_001115	114	Hs.591859	NM_001115	ENSG00000155897	ADCY8	AC8|ADCY3|HBAC1	adenylate cyclase 8	protein-coding	0.015936	0.452381	
chunk0156_325_1	chr5	111515768	111516108	+	0	NA	intron (NR_040093, intron 1 of 6)	L1PA8|LINE|L1	-3341	NM_001308057	134429	Hs.93842	NM_139164	ENSG00000164211	STARD4	-	StAR related lipid transfer domain containing 4	protein-coding	0.002941	0.316716	
chunk0099_333_1	chr2	100000387	100000766	+	0	NA	intron (NM_001025108, intron 6 of 23)	intron (NM_001025108, intron 6 of 23)	105007	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.018470	0.373684	
chunk0058_132_1	chr14	22560917	22561479	+	0	NA	Intergenic	L2c|LINE|L2	28039	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.016014	0.417407	
chunk0003_162_1	chr1	33376986	33377358	+	0	NA	Intergenic	MIRb|SINE|MIR	-1579	NM_198040	1912	Hs.524271	NM_004427	ENSG00000134686	PHC2	EDR2|HPH2|PH2	polyhomeotic homolog 2	protein-coding	0.002688	0.455764	
chunk0008_353_1	chr1	96263514	96264080	+	0	NA	intron (NR_110693, intron 5 of 5)	L1M5|LINE|L1	110328	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.001767	0.306878	
chunk0077_337_1	chr16	82639395	82640002	+	0	NA	intron (NM_001220488, intron 2 of 14)	intron (NM_001220488, intron 2 of 14)	12904	NM_001220491	1012	Hs.654386	NM_001257	ENSG00000140945	CDH13	CDHH|P105	cadherin 13	protein-coding	0.011532	0.455592	
chunk0035_456_1	chr11	57791806	57792444	+	0	NA	intron (NM_001085461, intron 3 of 18)	intron (NM_001085461, intron 3 of 18)	30363	NM_001206883	1500	Hs.166011	NM_001331	ENSG00000198561	CTNND1	BCDS2|CAS|CTNND|P120CAS|P120CTN|p120|p120(CAS)|p120(CTN)	catenin delta 1	protein-coding	0.006270	0.442879	281(GGGAACAGTCTGTACC,-,0.00),282(GGAACAGTCTGTACCC,+,0.00)
chunk0069_356_1	chr15	66887144	66887343	+	0	NA	Intergenic	Intergenic	-178614	NM_005902	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.010050	0.545000	
chunk0147_113_1	chr4	174229691	174230205	+	0	NA	Intergenic	Intergenic	-9550	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.001946	0.359223	227(GGCACTCTTTGTTCAT,+,0.00)
chunk0113_232_1	chr20	54014046	54014665	+	0	NA	intron (NM_003657, intron 4 of 11)	intron (NM_003657, intron 4 of 11)	54130	NR_039913	100616225		NR_039913	ENSG00000265595	MIR4756	-	microRNA 4756	ncRNA	0.009693	0.383871	
chunk0065_273_1	chr14	101978512	101978904	+	0	NA	intron (NM_001376, intron 2 of 77)	L2a|LINE|L2	14180	NM_001376	1778	Hs.614080	NM_001376	ENSG00000197102	DYNC1H1	CMT2O|DHC1|DHC1a|DNCH1|DNCL|DNECL|DYHC|Dnchc1|HL-3|SMALED1|p22	dynein cytoplasmic 1 heavy chain 1	protein-coding	0.002551	0.386768	
chunk0170_227_1	chr6	113379184	113379713	+	0	NA	Intergenic	Intergenic	270627	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.003781	0.330189	
chunk0206_165_1	chr9	122088019	122088531	+	0	NA	intron (NM_194252, intron 1 of 3)	intron (NM_194252, intron 1 of 3)	5331	NM_001139442	158135	Hs.438937	NM_194252	ENSG00000175764	TTLL11	C9orf20|bA244O19.1	tubulin tyrosine ligase like 11	protein-coding	0.007812	0.489279	
chunk0019_464_1	chr1	231529961	231530207	+	0	NA	intron (NR_028398, intron 2 of 10)	MLT1F1|LTR|ERVL-MaLR	1431	NR_028398	100303453	Hs.13318	NR_028393	ENSG00000270106	TSNAX-DISC1	-	TSNAX-DISC1 readthrough (NMD candidate)	ncRNA	0.000000	0.469636	
chunk0014_84_1	chr1	176559448	176559947	+	0	NA	intron (NM_020318, intron 2 of 22)	intron (NM_020318, intron 2 of 22)	96526	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.008016	0.464000	57(GTGTACTCACTGTGCT,-,0.00),58(TGTACTCACTGTGCTT,+,0.00)
chunk0125_451_1	chr3	72957046	72957534	+	0	NA	exon (NM_001080393, exon 5 of 7)	exon (NM_001080393, exon 5 of 7)	-39678	NM_174907	151987	Hs.431092	NM_174907	ENSG00000163605	PPP4R2	PP4R2	protein phosphatase 4 regulatory subunit 2	protein-coding	0.014344	0.464213	213(GAGGACATGTTGTACC,-,0.00),214(AGGACATGTTGTACCC,+,0.00)
chunk0038_393_1	chr11	93643075	93643306	+	0	NA	Intergenic	Intergenic	-18460	NM_033395	85459	Hs.458418	NM_033395	ENSG00000166004	CEP295	KIAA1731	centrosomal protein 295	protein-coding	0.000000	0.293103	
chunk0067_390_1	chr15	49110484	49110746	+	0	NA	Intergenic	L1MA4A|LINE|L1	45042	NM_004236	9318	Hs.369614	NM_004236	ENSG00000166200	COPS2	ALIEN|CSN2|SGN2|TRIP15	COP9 signalosome subunit 2	protein-coding	0.000000	0.566540	
chunk0156_46_1	chr5	102957213	102957668	+	0	NA	intron (NM_000919, intron 11 of 24)	intron (NM_000919, intron 11 of 24)	91617	NM_001177306	5066	Hs.369430	NM_000919	ENSG00000145730	PAM	PAL|PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding	0.010989	0.412281	205(GAGCACATTGTGTATT,-,0.00)
chunk0185_206_1	chr7	128565417	128566011	+	0	NA	Intergenic	L1MD2|LINE|L1	-75527	NR_024368	402483	Hs.722350	NM_001039682		LINC01000	-	long intergenic non-protein coding RNA 1000	ncRNA	0.005051	0.368067	
chunk0154_193_1	chr5	80217150	80217443	+	0	NA	intron (NM_178276, intron 1 of 12)	intron (NM_178276, intron 1 of 12)	38786	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.010239	0.425170	
chunk0094_120_1	chr2	4533770	4534189	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	122243	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.004773	0.440476	201(CAGCACTGCGTGTCCT,-,0.00),202(AGCACTGCGTGTCCTT,+,0.00)
chunk0055_135_1	chr13	59470933	59471132	+	0	NA	Intergenic	L1MB1|LINE|L1	-541686	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.000000	0.315000	
chunk0015_210_1	chr1	187518406	187518988	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	75069	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006873	0.339623	
chunk0091_334_1	chr19	14110539	14110876	+	0	NA	intron (NM_002730, intron 1 of 9)	intron (NM_002730, intron 1 of 9)	-2317	NM_001304349	5566	Hs.631630	NM_002730	ENSG00000072062	PRKACA	PKACA|PPNAD4	protein kinase cAMP-activated catalytic subunit alpha	protein-coding	0.005935	0.464497	
chunk0072_41_1	chr16	1025273	1025744	+	0	NA	Intergenic	Intergenic	43700	NM_014587	30812	Hs.243678	NM_014587	ENSG00000005513	SOX8	-	SRY-box transcription factor 8	protein-coding	0.033970	0.684322	
chunk0014_205_1	chr1	179128468	179128956	+	0	NA	intron (NM_007314, intron 3 of 11)	AluJr4|SINE|Alu	14377	NM_001168239	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.010246	0.443763	
chunk0131_99_1	chr3	143729669	143730164	+	0	NA	intron (NM_173653, intron 4 of 15)	intron (NM_173653, intron 4 of 15)	118615	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.004040	0.405242	
chunk0009_342_1	chr1	109313017	109313329	+	0	NA	3' UTR (NM_001205228, exon 20 of 20)	3' UTR (NM_001205228, exon 20 of 20)	-6132	NM_001265613	343263	Hs.443402	NM_001010985	ENSG00000221986	MYBPHL	-	myosin binding protein H like	protein-coding	0.019231	0.466454	
chunk0170_44_1	chr6	109418267	109418505	+	0	NA	intron (NR_104429, intron 6 of 8)	L1MC5|LINE|L1	-22342	NM_003080	6610	Hs.55235	NM_003080	ENSG00000135587	SMPD2	ISC1|NSMASE|NSMASE1	sphingomyelin phosphodiesterase 2	protein-coding	0.004202	0.481172	
chunk0128_88_1	chr3	105671303	105671523	+	0	NA	intron (NM_170662, intron 17 of 18)	intron (NM_170662, intron 17 of 18)	197630	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.009091	0.343891	
chunk0031_432_1	chr10	132464209	132464459	+	0	NA	Intergenic	Intergenic	19124	NM_173541									0.036000	0.657371	
chunk0177_299_1	chr7	25940898	25941467	+	0	NA	Intergenic	MIR|SINE|MIR	8804	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.008787	0.417544	
chunk0127_221_1	chr3	96651142	96651501	+	0	NA	Intergenic	L1ME3A|LINE|L1	-163260	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002786	0.300000	
chunk0130_336_1	chr3	138431405	138431649	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-3046	NM_031913	83850	Hs.477711	NM_031913	ENSG00000158220	ESYT3	CHR3SYT|E-Syt3|FAM62C	extended synaptotagmin 3	protein-coding	0.016393	0.510204	
chunk0086_78_1	chr18	13291177	13291569	+	0	NA	intron (NM_181481, intron 1 of 5)	intron (NM_181481, intron 1 of 5)	13268	NM_181481	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.020408	0.483461	
chunk0001_70_1	chr1	2441790	2442176	+	0	NA	Intergenic	Intergenic	-25476	NM_001303012	9651	Hs.170156	NM_014638	ENSG00000149527	PLCH2	PLC-L4|PLC-eta2|PLCL4|PLCeta2	phospholipase C eta 2	protein-coding	0.031088	0.633075	
chunk0071_451_1	chr15	90174597	90174915	+	0	NA	Intergenic	Intergenic	-10164	NM_020210	10509	Hs.474935	NM_020210	ENSG00000185033	SEMA4B	SEMAC|SemC	semaphorin 4B	protein-coding	0.025157	0.551724	
chunk0091_272_1	chr19	11581111	11581377	+	0	NA	Intergenic	L2a|LINE|L2	-2258	NM_001111035	54	Hs.1211	NM_001611	ENSG00000102575	ACP5	HPAP|TRACP5a|TRACP5b|TRAP|TrATPase	acid phosphatase 5, tartrate resistant	protein-coding	0.011278	0.531835	244(TGGCACTTTCTGTTCT,-,0.00),245(GGCACTTTCTGTTCTC,+,0.00)
chunk0062_44_1	chr14	67252520	67253063	+	0	NA	intron (NM_022474, intron 1 of 14)	intron (NM_022474, intron 1 of 14)	11496	NM_001256550	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.003683	0.378676	
chunk0181_110_1	chr7	80634495	80634702	+	0	NA	intron (NM_001289911, intron 1 of 11)	intron (NM_001289911, intron 1 of 11)	-3918	NM_001001548	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.009662	0.370192	
chunk0190_445_1	chr8	41665652	41666673	+	0	NA	promoter-TSS (NM_020480)	promoter-TSS (NM_020480)	-876	NM_020478	286	Hs.654438	NM_000037	ENSG00000029534	ANK1	ANK|SPH1|SPH2	ankyrin 1	protein-coding	0.014691	0.486301	344(TAGATCAGGTTGTTCC,-,0.00),345(AGATCAGGTTGTTCCT,+,0.00)
chunk0037_226_1	chr11	74963707	74964005	+	0	NA	intron (NM_014752, intron 1 of 4)	L3|LINE|CR1	14609	NM_014752	9789	Hs.282700	NM_014752	ENSG00000118363	SPCS2	-	signal peptidase complex subunit 2	protein-coding	0.006711	0.294314	
chunk0152_78_1	chr5	58079005	58079366	+	0	NA	Intergenic	Intergenic	43156	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.002770	0.375691	222(AAGTACAGGTTGATCC,-,0.00),223(AGTACAGGTTGATCCT,+,0.00)
chunk0028_127_1	chr10	85008417	85009030	+	0	NA	Intergenic	Intergenic	190182	NR_120668	101929624	Hs.588831	NR_120667	ENSG00000237267	LINC01519	-	long intergenic non-protein coding RNA 1519	ncRNA	0.008157	0.405537	
chunk0115_349_1	chr21	29272072	29272674	+	0	NA	intron (NR_027072, intron 1 of 1)	Charlie7|DNA|hAT-Charlie	-26422	NM_001186	571	Hs.154276	NM_001186	ENSG00000156273	BACH1	BACH-1|BTBD24	BTB domain and CNC homolog 1	protein-coding	0.003322	0.369818	353(AAACACAGTCTGTCCT,-,0.00),354(AACACAGTCTGTCCTT,+,0.00)
chunk0200_35_1	chr9	15070515	15071160	+	0	NA	Intergenic	Intergenic	77510	NR_003920	389705	Hs.431257	NR_003920		LOC389705	-	histone PARylation factor 1 pseudogene	pseudo	0.003101	0.325077	
chunk0202_95_1	chr9	72315619	72316191	+	0	NA	TTS (NR_110953)	TTS (NR_110953)	10469	NR_110953	100507540	Hs.54957	NR_110952	ENSG00000225434	LINC01504	-	long intergenic non-protein coding RNA 1504	ncRNA	0.012238	0.476440	
chunk0083_156_1	chr17	65943091	65943426	+	0	NA	intron (NM_001302891, intron 16 of 24)	intron (NM_001302891, intron 16 of 24)	-116715	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.324405	
chunk0011_106_1	chr1	145996545	145996856	+	0	NA	promoter-TSS (NM_006472)	promoter-TSS (NM_006472)	-69	NM_006472	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.061093	0.612179	195(GTGGACACGGTGTGCT,-,0.00),196(TGGACACGGTGTGCTC,+,0.00)
chunk0171_160_1	chr6	124190299	124190749	+	0	NA	intron (NM_001300737, intron 2 of 7)	intron (NM_001300737, intron 2 of 7)	-92481	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.006667	0.328160	
chunk0092_415_1	chr19	37941977	37942491	+	0	NA	intron (NM_015073, intron 1 of 21)	L2a|LINE|L2	35013	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.017510	0.481553	
chunk0020_331_1	chr1	238415150	238415441	+	0	NA	Intergenic	L2a|LINE|L2	70722	NR_015407	339535	Hs.532047	NR_015407	ENSG00000215808	LINC01139	LINK-A|LINKA	long intergenic non-protein coding RNA 1139	ncRNA	0.000000	0.366438	
chunk0158_201_1	chr5	128046615	128046968	+	0	NA	intron (NR_015360, intron 2 of 2)	L1PA6|LINE|L1	36283	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.008499	0.378531	
chunk0100_138_1	chr2	108811671	108812068	+	0	NA	intron (NR_130121, intron 7 of 13)	L1PA17|LINE|L1	25119	NM_001303106	165055	Hs.362702	NM_144978	ENSG00000163006	CCDC138	-	coiled-coil domain containing 138	protein-coding	0.000000	0.334171	
chunk0106_334_1	chr2	206083587	206084331	+	0	NA	intron (NM_017759, intron 1 of 10)	intron (NM_017759, intron 1 of 10)	2223	NM_017759	54891	Hs.445036	NM_017759	ENSG00000114933	INO80D	-	INO80 complex subunit D	protein-coding	0.017473	0.413423	430(GGAAACATCCTGTCCC,-,0.00),431(GAAACATCCTGTCCCT,+,0.00)
chunk0167_336_1	chr6	72564249	72564703	+	0	NA	Intergenic	MIRb|SINE|MIR	-57367	NM_001160133	56479	Hs.445324	NM_019842	ENSG00000185760	KCNQ5	Kv7.5|MRD46	potassium voltage-gated channel subfamily Q member 5	protein-coding	0.002203	0.334066	
chunk0180_14_1	chr7	53230788	53231188	+	0	NA	Intergenic	L1MC5|LINE|L1	195332	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.002500	0.241895	
chunk0082_11_1	chr17	49821864	49822088	+	0	NA	intron (NM_007067, intron 11 of 14)	intron (NM_007067, intron 11 of 14)	-23934	NM_001242791	729220	Hs.434138	NM_001242791		FLJ45513	-	uncharacterized LOC729220	protein-coding	0.000000	0.386667	
chunk0161_440_1	chr5	178566972	178567419	+	0	NA	intron (NM_173465, intron 1 of 28)	L1MC4a|LINE|L1	23360	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.004474	0.410714	272(AAGCACACACAGTACC,-,0.00),273(AGCACACACAGTACCC,+,0.00)
chunk0168_248_1	chr6	88502460	88502863	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	36708	NR_110867	101928936	Hs.533080	NR_110867		LOC101928936	-	uncharacterized LOC101928936	ncRNA	0.009926	0.420792	
chunk0105_430_1	chr2	193474758	193475663	+	0	NA	Intergenic	Intergenic	725365	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.006630	0.415011	
chunk0142_256_1	chr4	99089003	99089284	+	0	NA	promoter-TSS (NM_000671)	promoter-TSS (NM_000671)	286	NR_037884	100507053	Hs.635084	NR_037884	ENSG00000246090	LOC100507053	-	uncharacterized LOC100507053	ncRNA	0.017794	0.500000	
chunk0137_41_1	chr4	11428843	11429382	+	0	NA	promoter-TSS (NM_005114)	promoter-TSS (NM_005114)	-199	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.087199	0.694444	
chunk0023_99_1	chr10	22702205	22703055	+	0	NA	intron (NM_005028, intron 1 of 9)	intron (NM_005028, intron 1 of 9)	11944	NM_005028	5305	Hs.57079	NM_005028	ENSG00000150867	PIP4K2A	PI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK	phosphatidylinositol-5-phosphate 4-kinase type 2 alpha	protein-coding	0.005882	0.391304	646(CTAAACACACTGTTCT,-,0.00),647(TAAACACACTGTTCTA,+,0.00)
chunk0010_268_1	chr1	117026255	117026905	+	0	NA	non-coding (NR_110786, exon 4 of 4)	non-coding (NR_110786, exon 4 of 4)	24830	NM_004258	9398	Hs.654598	NM_004258	ENSG00000134256	CD101	EWI-101|IGSF2|V7	CD101 molecule	protein-coding	0.012308	0.400922	
chunk0095_286_1	chr2	20127732	20128316	+	0	NA	Intergenic	AluSx|SINE|Alu	-75996	NM_014713	9741	Hs.467807	NM_014713	ENSG00000068697	LAPTM4A	HUMORF13|LAPTM4|MBNT|Mtrp	lysosomal protein transmembrane 4 alpha	protein-coding	0.006849	0.377778	
chunk0123_432_1	chr3	50238739	50239494	+	0	NA	intron (NM_001282618, intron 1 of 7)	intron (NM_001282618, intron 1 of 7)	2959	NM_002070	2771	Hs.77269	NM_002070	ENSG00000114353	GNAI2	GIP|GNAI2B|H_LUCA15.1|H_LUCA16.1	G protein subunit alpha i2	protein-coding	0.013245	0.562169	
chunk0153_24_1	chr5	67060876	67061211	+	0	NA	intron (NM_001290226, intron 2 of 26)	L1ME4a|LINE|L1	56423	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.005970	0.348214	
chunk0175_263_1	chr7	7395795	7396193	+	0	NA	intron (NM_001037763, intron 27 of 34)	intron (NM_001037763, intron 27 of 34)	139835	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.010050	0.395990	
chunk0043_426_1	chr12	25937115	25937366	+	0	NA	Intergenic	Intergenic	20345	NR_038227	100506451	Hs.560092	NR_038227		RASSF8-AS1	-	RASSF8 antisense RNA 1	ncRNA	0.000000	0.440476	
chunk0040_78_1	chr11	111353140	111353828	+	0	NA	3' UTR (NM_006235, exon 5 of 5)	3' UTR (NM_006235, exon 5 of 5)	5727	NR_039712	100616330		NR_039712	ENSG00000264032	MIR4491	mir-4491	microRNA 4491	ncRNA	0.010174	0.509434	247(ATGCACAGCCTGTTCC,-,0.00),248(TGCACAGCCTGTTCCC,+,0.00)
chunk0060_226_1	chr14	49460864	49461505	+	0	NA	Intergenic	Intergenic	125232	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.004680	0.334891	
chunk0029_264_1	chr10	103150374	103150610	+	0	NA	intron (NM_001134373, intron 2 of 17)	L1ME1|LINE|L1	42814	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.004237	0.299578	
chunk0209_447_1	chrX	65831081	65831715	+	0	NA	Intergenic	Intergenic	163754	NM_002444	4478	Hs.87752	NM_002444	ENSG00000147065	MSN	HEL70|IMD50	moesin	protein-coding	0.003155	0.461417	323(ATGGACGTTCTGTTCC,-,0.00),324(TGGACGTTCTGTTCCT,+,0.00)
chunk0094_54_1	chr2	3149901	3150226	+	0	NA	Intergenic	Intergenic	-24037	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.015385	0.432515	
chunk0078_302_1	chr17	8211213	8211420	+	0	NA	promoter-TSS (NM_001284526)	promoter-TSS (NM_001284526)	-690	NM_004217	9212	Hs.442658	NM_004217	ENSG00000178999	AURKB	AIK2|AIM-1|AIM1|ARK-2|ARK2|AurB|IPL1|PPP1R48|STK-1|STK12|STK5|aurkb-sv1|aurkb-sv2	aurora kinase B	protein-coding	0.014493	0.355769	
chunk0069_198_1	chr15	63403496	63404319	+	0	NA	intron (NR_120375, intron 4 of 6)	intron (NR_120375, intron 4 of 6)	13677	NR_120375	102723344	Hs.569500	NR_120375		LINC02568	-	long intergenic non-protein coding RNA 2568	ncRNA	0.017011	0.382282	335(TTGGACAGTTTGTTCA,-,0.00),336(TGGACAGTTTGTTCAG,+,0.00)
chunk0106_272_1	chr2	204000287	204000581	+	0	NA	Intergenic	Intergenic	63686	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.000000	0.342373	
chunk0081_151_1	chr17	40821374	40821974	+	0	NA	intron (NM_000421, intron 1 of 7)	intron (NM_000421, intron 1 of 7)	937	NM_000421	3858	Hs.99936	NM_000421	ENSG00000186395	KRT10	BCIE|BIE|CK10|EHK|K10|KPP	keratin 10	protein-coding	0.000000	0.347754	
chunk0011_113_1	chr1	146036970	146037199	+	0	NA	Intergenic	tRNA-Gly-GGA|tRNA|tRNA	15160	NR_104085	101954276		NR_104085	ENSG00000201558	RNVU1-6	RNU1-99|vU1.6	RNA, variant U1 small nuclear 6	snRNA	0.034934	0.452174	
chunk0172_226_1	chr6	137046903	137047516	+	0	NA	Intergenic	LTR50|LTR|ERVL	-2029	NM_001278723	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.009788	0.480456	311(AGGGACAGCTAGTTCT,-,0.00),312(GGGACAGCTAGTTCTA,+,0.00)
chunk0018_14_1	chr1	215164707	215164944	+	0	NA	intron (NM_001017424, intron 3 of 6)	L2b|LINE|L2	81608	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.008439	0.436975	60(AGGAACATTCTGTACT,-,0.00),61(GGAACATTCTGTACTT,+,0.00)
chunk0197_353_1	chr8	125566183	125566454	+	0	NA	Intergenic	L1MEd|LINE|L1	134109	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.003690	0.415441	
chunk0017_89_1	chr1	205749320	205749782	+	0	NA	intron (NM_022731, intron 1 of 6)	CpG	693	NM_022731	64710	Hs.213061	NM_022731	ENSG00000069275	NUCKS1	JC7|NUCKS	nuclear casein kinase and cyclin dependent kinase substrate 1	protein-coding	0.097403	0.749460	
chunk0196_70_1	chr8	102479963	102480222	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-67403	NM_001282873	51366	Hs.492445	NM_015902	ENSG00000104517	UBR5	DD5|EDD|EDD1|HYD	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.007722	0.423077	
chunk0115_6_1	chr21	20352255	20352591	+	0	NA	Intergenic	Intergenic	450685	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.000000	0.370920	140(AGGAACTAGGTGTGCA,-,0.00)
chunk0088_189_1	chr18	47562318	47562623	+	0	NA	Intergenic	MER33|DNA|hAT-Charlie	181974	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.000000	0.401961	
chunk0209_22_1	chrX	35570958	35571438	+	0	NA	Intergenic	Intergenic	-227144	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.002083	0.324324	
chunk0064_340_1	chr14	96574800	96575292	+	0	NA	Intergenic	MIRb|SINE|MIR	72181	NM_001293628	10914	Hs.253726	NM_032632	ENSG00000090060	PAPOLA	PAP|PAP-alpha	poly(A) polymerase alpha	protein-coding	0.008130	0.419878	
chunk0117_421_1	chr21	45931609	45931964	+	0	NA	intron (NM_001130141, intron 10 of 12)	intron (NM_001130141, intron 10 of 12)	-41184	NR_109931	101928796	Hs.130919	NR_109931		LOC101928796	-	uncharacterized LOC101928796	ncRNA	0.053521	0.539326	307(CGGGCCATGCTGTCCT,-,0.00),308(GGGCCATGCTGTCCTG,+,0.00),339(CGGGCCATGCTGTCCT,-,0.00),340(GGGCCATGCTGTCCTG,+,0.00)
chunk0021_263_1	chr1	243543785	243544121	+	0	NA	intron (NM_181690, intron 11 of 13)	intron (NM_181690, intron 11 of 13)	197777	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.002976	0.314540	
chunk0005_124_1	chr1	56797486	56797685	+	0	NA	intron (NM_001004303, intron 1 of 19)	intron (NM_001004303, intron 1 of 19)	22111	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.020101	0.545000	
chunk0061_170_1	chr14	59871107	59871599	+	0	NA	promoter-TSS (NM_021136)	promoter-TSS (NM_021136)	-514	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.014228	0.478702	
chunk0059_326_1	chr14	36771094	36771676	+	0	NA	intron (NM_030631, intron 3 of 9)	intron (NM_030631, intron 3 of 9)	113817	NM_006194	5083	Hs.132576	NM_006194	ENSG00000198807	PAX9	STHAG3	paired box 9	protein-coding	0.006873	0.353345	
chunk0138_55_1	chr4	31793311	31793800	+	0	NA	Intergenic	Intergenic	-203824	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.002045	0.342857	
chunk0080_47_1	chr17	21604507	21604973	+	0	NA	Intergenic	L1M4b|LINE|L1	-53062	NM_001113434	339263	Hs.514016	NM_001113434	ENSG00000212719	LINC02693	C17orf51	long intergenic non-protein coding RNA 2693	ncRNA	0.002146	0.331906	
chunk0095_30_1	chr2	12980220	12980730	+	0	NA	intron (NR_038434, intron 5 of 5)	intron (NR_038434, intron 5 of 5)	26538	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.005882	0.367906	251(CAGAACAGCAAGTGCC,-,0.00),252(AGAACAGCAAGTGCCA,+,0.00)
chunk0124_18_1	chr3	51780456	51780767	+	0	NA	Intergenic	Arthur1B|DNA|hAT-Tip100	-1424	NM_001143833	440956	Hs.444316	NM_001143833	ENSG00000214686	IQCF6	-	IQ motif containing F6	protein-coding	0.003215	0.320513	
chunk0052_257_1	chr12	123654268	123654523	+	0	NA	intron (NM_001271866, intron 7 of 10)	(GT)n|Simple_repeat|Simple_repeat	-16718	NM_001143850	79867	Hs.167165	NM_024809	ENSG00000168778	TCTN2	C12orf38|JBTS24|MKS8|TECT2	tectonic family member 2	protein-coding	0.007843	0.410156	
chunk0206_415_1	chr9	127485468	127485925	+	0	NA	intron (NM_001005373, intron 16 of 25)	intron (NM_001005373, intron 16 of 25)	33441	NM_001005374	90678	Hs.495188	NM_138361	ENSG00000148356	LRSAM1	CMT2P|RIFLE|TAL	leucine rich repeat and sterile alpha motif containing 1	protein-coding	0.013129	0.556769	
chunk0118_47_1	chr22	27888206	27888852	+	0	NA	intron (NM_001284277, intron 7 of 10)	intron (NM_001284277, intron 7 of 10)	30685	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.006192	0.417311	
chunk0103_429_1	chr2	169891492	169891932	+	0	NA	intron (NM_172070, intron 6 of 38)	intron (NM_172070, intron 6 of 38)	64204	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.004545	0.362812	
chunk0132_337_1	chr3	161233107	161233665	+	0	NA	intron (NM_015938, intron 4 of 15)	intron (NM_015938, intron 4 of 15)	12075	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.007168	0.322004	
chunk0064_222_1	chr14	93799460	93800244	+	0	NA	Intergenic	Intergenic	-11432	NM_178013	145270	Hs.432401	NM_178004	ENSG00000175785	PRIMA1	PRIMA	proline rich membrane anchor 1	protein-coding	0.011480	0.482803	
chunk0204_304_1	chr9	100148359	100148744	+	0	NA	intron (NM_014425, intron 3 of 16)	intron (NM_014425, intron 3 of 16)	49331	NM_014425	27130	Hs.558477	NM_014425	ENSG00000119509	INVS	INV|NPH2|NPHP2	inversin	protein-coding	0.000000	0.287565	
chunk0182_294_1	chr7	98326682	98327211	+	0	NA	intron (NM_018842, intron 3 of 13)	L1MC4|LINE|L1	45279	NM_015379	25798	Hs.567438	NM_015379	ENSG00000164713	BRI3	I3	brain protein I3	protein-coding	0.009452	0.428302	275(ATGAACACTGTGTGCT,-,0.00),276(TGAACACTGTGTGCTG,+,0.00)
chunk0083_398_1	chr17	71909884	71910607	+	0	NA	Intergenic	Intergenic	115734	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.006916	0.371547	327(GAGGACATTCAGTGCA,-,0.00),328(AGGACATTCAGTGCAC,+,0.00),353(ATGAACTCCGTGTTCC,-,0.00),354(TGAACTCCGTGTTCCT,+,0.00)
chunk0153_427_1	chr5	75864820	75865019	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-147431	NM_001099271	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.000000	0.465000	
chunk0164_219_1	chr6	22821583	22822168	+	0	NA	Intergenic	Intergenic	252426	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.001709	0.370307	286(TGGTACAGTGTGTGCC,-,0.00),287(GGTACAGTGTGTGCCA,+,0.00)
chunk0075_305_1	chr16	54388540	54388876	+	0	NA	Intergenic	L2a|LINE|L2	-102242	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.000000	0.424332	
chunk0155_68_1	chr5	91618392	91618656	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	-235192	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003788	0.407547	
chunk0024_405_1	chr10	45263470	45263790	+	0	NA	Intergenic	Intergenic	51978	NM_001004297	79290	Hs.532435	NM_001004297	ENSG00000256574	OR13A1	-	olfactory receptor family 13 subfamily A member 1	protein-coding	0.003125	0.542056	
chunk0002_404_1	chr1	27366804	27367470	+	0	NA	promoter-TSS (NM_004672)	promoter-TSS (NM_004672)	-271	NM_001297609	9064	Hs.194694	NM_004672	ENSG00000142733	MAP3K6	ASK2|MAPKKK6|MEKK6	mitogen-activated protein kinase kinase kinase 6	protein-coding	0.037538	0.610195	295(CGGAACAGCCTGTGCC,-,0.00),296(GGAACAGCCTGTGCCC,+,0.00)
chunk0186_257_1	chr7	141279283	141279695	+	0	NA	intron (NM_001195278, intron 2 of 3)	intron (NM_001195278, intron 2 of 3)	205257	NM_001195278	100507421	Hs.283851	NM_001195278	ENSG00000261115	TMEM178B	-	transmembrane protein 178B	protein-coding	0.004854	0.421308	
chunk0147_106_1	chr4	173672367	173672694	+	0	NA	Intergenic	Intergenic	142072	NR_003679	79804	Hs.61435	NR_003679	ENSG00000237125	HAND2-AS1	DEIN|NBLA00301|UPH	HAND2 antisense RNA 1	ncRNA	0.006116	0.454268	
chunk0112_377_1	chr20	46222707	46223206	+	0	NA	intron (NM_021248, intron 4 of 11)	intron (NM_021248, intron 4 of 11)	85542	NM_021248	64405	Hs.472861	NM_021248	ENSG00000149654	CDH22	C20orf25|dJ998H6.1	cadherin 22	protein-coding	0.024048	0.596000	196(AAGAACAGACTGTACC,-,0.00),197(AGAACAGACTGTACCT,+,0.00)
chunk0006_305_1	chr1	71366263	71366564	+	0	NA	Intergenic	Intergenic	285089	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.003322	0.291391	
chunk0081_385_1	chr17	48098188	48098473	+	0	NA	intron (NM_001127228, intron 1 of 4)	intron (NM_001127228, intron 1 of 4)	2868	NM_006807	10951	Hs.77254	NM_006807	ENSG00000108468	CBX1	CBX|HP1-BETA|HP1Hs-beta|HP1Hsbeta|M31|MOD1|p25beta	chromobox 1	protein-coding	0.007018	0.419580	
chunk0138_43_1	chr4	31391916	31392554	+	0	NA	Intergenic	Intergenic	221091	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.003135	0.322379	
chunk0040_424_1	chr11	121300189	121301548	+	0	NA	intron (NM_001024956, intron 1 of 4)	L1M4|LINE|L1	8000	NM_001024956	6309	Hs.287749	NM_006918	ENSG00000109929	SC5D	ERG3|S5DES|SC5DL	sterol-C5-desaturase	protein-coding	0.004415	0.393382	
chunk0207_270_1	chr9	132373325	132373524	+	0	NA	Intergenic	Intergenic	-18439	NM_015046	23064	Hs.460317	NM_015046	ENSG00000107290	SETX	ALS4|AOA2|SCAN2|SCAR1|Sen1|bA479K20.2	senataxin	protein-coding	0.005025	0.455000	
chunk0063_224_1	chr14	81561718	81562437	+	0	NA	Intergenic	Intergenic	-28216	NM_001244984	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.016690	0.425000	448(AGGAACAGAGAGACCT,-,0.00),449(GGAACAGAGAGACCTT,+,0.00)
chunk0197_221_1	chr8	122785846	122786222	+	0	NA	intron (NM_014943, intron 1 of 3)	intron (NM_014943, intron 1 of 3)	4372	NM_014943	22882	Hs.377090	NM_014943	ENSG00000178764	ZHX2	AFR1|RAF	zinc fingers and homeoboxes 2	protein-coding	0.007979	0.450928	
chunk0168_316_1	chr6	92258682	92259533	+	0	NA	Intergenic	Intergenic	-568679	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.003525	0.353286	
chunk0090_331_1	chr18	76154972	76155171	+	0	NA	Intergenic	Intergenic	32073	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.015075	0.515000	
chunk0042_197_1	chr12	5395438	5395809	+	0	NA	Intergenic	Intergenic	-36491	NM_001102654	4908	Hs.99171	NM_002527	ENSG00000185652	NTF3	HDNF|NGF-2|NGF2|NT-3|NT3	neurotrophin 3	protein-coding	0.002695	0.497312	
chunk0203_302_1	chr9	89312174	89312651	+	0	NA	TTS (NR_036108)	TTS (NR_036108)	187	NR_036108	100422936		NR_036108	ENSG00000265112	MIR3153	mir-3153	microRNA 3153	ncRNA	0.020964	0.426778	
chunk0022_415_1	chr10	18615590	18616030	+	0	NA	intron (NM_182543, intron 4 of 10)	intron (NM_182543, intron 4 of 10)	35827	NM_182543	221078	Hs.396175	NM_182543	ENSG00000241058	NSUN6	4933414E04Rik|ARL5B-AS1|NOPD1	NOP2/Sun RNA methyltransferase 6	protein-coding	0.009091	0.371882	
chunk0208_456_1	chrX	34382344	34382962	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-250323	NM_203408	158724	Hs.143268	NM_203408	ENSG00000185448	FAM47A	-	family with sequence similarity 47 member A	protein-coding	0.003236	0.399031	
chunk0162_454_1	chr5	180831468	180831914	+	0	NA	promoter-TSS (NR_045680)	promoter-TSS (NR_045680)	-73	NR_045680	100859930	Hs.655606	NR_045680	ENSG00000278970	HEIH	HCCAT2|LINC-HEIH|LINC00848|lncRNA-HEIH	hepatocellular carcinoma up-regulated EZH2-associated long non-coding RNA	ncRNA	0.087444	0.668904	
chunk0109_313_1	chr20	9072218	9072650	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	3380	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.000000	0.357968	
chunk0040_358_1	chr11	118790423	118791245	+	0	NA	intron (NM_004397, intron 1 of 13)	CpG	114	NM_001257191	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.090024	0.679222	94(CAATACAGCATGTCCC,-,0.00),95(AATACAGCATGTCCCT,+,0.00)
chunk0021_272_1	chr1	243940642	243941031	+	0	NA	intron (NR_033883, intron 1 of 11)	intron (NR_033883, intron 1 of 11)	23434	NR_033883	339529	Hs.209374	NR_033883	ENSG00000226828	LINC02774	-	long intergenic non-protein coding RNA 2774	ncRNA	0.015424	0.510256	
chunk0202_314_1	chr9	78227716	78227915	+	0	NA	Intergenic	L1MB8|LINE|L1	-8260	NM_032171	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.010050	0.310000	
chunk0162_209_1	chr6	4109386	4110004	+	0	NA	intron (NR_104464, intron 2 of 5)	intron (NR_104464, intron 2 of 5)	25773	NM_001166010	10455	Hs.15250	NM_006117	ENSG00000198721	ECI2	ACBD2|DRS-1|DRS1|HCA88|PECI|dJ1013A10.3	enoyl-CoA delta isomerase 2	protein-coding	0.006472	0.332795	302(AAGGACTAACTGTTCT,-,0.00),303(AGGACTAACTGTTCTT,+,0.00)
chunk0024_120_1	chr10	34854095	34854727	+	0	NA	Intergenic	Intergenic	38643	NR_108043	100505601	Hs.549790	NR_108043	ENSG00000226386	PARD3-AS1	-	PARD3 antisense RNA 1	ncRNA	0.009494	0.417062	366(CAGAACAGGCTGTCTA,-,0.00),367(AGAACAGGCTGTCTAC,+,0.00)
chunk0070_328_1	chr15	75532332	75532924	+	0	NA	intron (NM_002833, intron 1 of 12)	intron (NM_002833, intron 1 of 12)	46663	NM_002833	5780	Hs.445775	NM_002833	ENSG00000169410	PTPN9	MEG2|PTPMEG2	protein tyrosine phosphatase non-receptor type 9	protein-coding	0.005068	0.440135	
chunk0139_108_1	chr4	51910933	51911495	+	0	NA	intron (NM_001287755, intron 9 of 10)	intron (NM_001287755, intron 9 of 10)	67635	NM_001287755	23142	Hs.605388	NM_015115	ENSG00000109184	DCUN1D4	-	defective in cullin neddylation 1 domain containing 4	protein-coding	0.008897	0.367673	
chunk0115_323_1	chr21	28773384	28773785	+	0	NA	Intergenic	Intergenic	111789	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.002494	0.360697	
chunk0198_27_1	chr8	128157133	128157837	+	0	NA	Intergenic	Intergenic	7369	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.002841	0.392908	340(CAGAACAATTTGTTCT,-,0.00),341(AGAACAATTTGTTCTC,+,0.00)
chunk0074_63_1	chr16	21184323	21184812	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	-25126	NM_017539	55567	Hs.526500	NM_017539	ENSG00000158486	DNAH3	DNAHC3-B|DNAHC3B|HDHC8|HEL-36|HSADHC3	dynein axonemal heavy chain 3	protein-coding	0.008180	0.444898	95(AAGAACATGTTGACCT,-,0.00),96(AGAACATGTTGACCTT,+,0.00)
chunk0160_300_1	chr5	158694327	158694605	+	0	NA	Intergenic	L2c|LINE|L2	-284693	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.003597	0.448029	
chunk0201_435_1	chr9	70052551	70053358	+	0	NA	intron (NR_125850, intron 2 of 13)	intron (NR_125850, intron 2 of 13)	9373	NR_125850	256691	Hs.547172	NM_153267	ENSG00000165072	MAMDC2	-	MAM domain containing 2	protein-coding	0.001239	0.389851	
chunk0070_209_1	chr15	72210696	72211056	+	0	NA	intron (NM_001206798, intron 3 of 10)	intron (NM_001206798, intron 3 of 10)	-13081	NM_001012642	196996	Hs.596332	NM_001012642	ENSG00000175318	GRAMD2A	GRAMD2	GRAM domain containing 2A	protein-coding	0.002778	0.404432	
chunk0198_88_1	chr8	130255174	130255587	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	41153	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.002421	0.347826	
chunk0177_238_1	chr7	24701493	24702036	+	0	NA	intron (NM_004403, intron 9 of 9)	intron (NM_004403, intron 9 of 9)	55700	NM_001127453	1687	Hs.520708	NM_004403	ENSG00000105928	GSDME	DFNA5|ICERE-1	gasdermin E	protein-coding	0.003683	0.463235	
chunk0027_59_1	chr10	73076838	73077183	+	0	NA	intron (NM_000917, intron 1 of 14)	intron (NM_000917, intron 1 of 14)	19964	NM_001142595	5033	Hs.500047	NM_000917	ENSG00000122884	P4HA1	P4HA	prolyl 4-hydroxylase subunit alpha 1	protein-coding	0.011594	0.453757	
chunk0020_175_1	chr1	234531725	234531968	+	0	NA	promoter-TSS (NR_038426)	promoter-TSS (NR_038426)	-67	NR_038426	100506795	Hs.448989	NR_038426	ENSG00000231768	LINC01354	-	long intergenic non-protein coding RNA 1354	ncRNA	0.028807	0.504098	
chunk0211_366_1	chrX	126008792	126009152	+	0	NA	Intergenic	L1PREC2|LINE|L1	-100790	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.002778	0.362881	278(ATGAACTAAATGTCCC,-,0.00)
chunk0211_377_1	chrX	126791029	126791368	+	0	NA	Intergenic	L1MC3|LINE|L1	-28566	NM_001122716	100130613	Hs.130370	NM_001122716	ENSG00000183631	PRR32	CXorf64	proline rich 32	protein-coding	0.002950	0.335294	
chunk0166_181_1	chr6	46134129	46134588	+	0	NA	intron (NM_014936, intron 1 of 3)	intron (NM_014936, intron 1 of 3)	4394	NM_014936	22875	Hs.643497	NM_014936	ENSG00000001561	ENPP4	NPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding	0.004357	0.406522	
chunk0175_272_1	chr7	7529269	7529936	+	0	NA	intron (NM_001037763, intron 3 of 34)	intron (NM_001037763, intron 3 of 34)	6227	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.007496	0.449102	413(AGGAGCTGCCTGTCCC,-,0.00)
chunk0140_130_1	chr4	69106140	69106339	+	0	NA	intron (NM_001074, intron 3 of 5)	L1PA13|LINE|L1	9764	NM_001074	7364	Hs.654424	NM_001074	ENSG00000171234	UGT2B7	UDPGT 2B7|UDPGT 2B9|UDPGT2B7|UDPGTH2|UDPGTh-2|UGT2B9	UDP glucuronosyltransferase family 2 member B7	protein-coding	0.005025	0.390000	
chunk0101_314_1	chr2	135393217	135393581	+	0	NA	intron (NM_001286568, intron 2 of 20)	L1MEj|LINE|L1	137331	NM_001286569	84083	Hs.658422	NM_032143	ENSG00000121988	ZRANB3	4933425L19Rik|AH2	zinc finger RANBP2-type containing 3	protein-coding	0.005495	0.290411	
chunk0199_49_1	chr9	1599974	1600362	+	0	NA	Intergenic	Intergenic	-415051	NM_001289397	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.005155	0.370180	233(TGGAACAGGAAGTTCC,-,0.00),234(GGAACAGGAAGTTCCA,+,0.00)
chunk0095_160_1	chr2	17220588	17221035	+	0	NA	Intergenic	Intergenic	297628	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.006711	0.348214	
chunk0084_10_1	chr17	73335608	73335823	+	0	NA	3' UTR (NM_001144952, exon 45 of 45)	3' UTR (NM_001144952, exon 45 of 45)	-23711	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.009302	0.550926	
chunk0086_196_1	chr18	22198951	22199223	+	0	NA	intron (NM_005257, intron 6 of 6)	intron (NM_005257, intron 6 of 6)	29650	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.018382	0.531136	
chunk0047_142_1	chr12	69602545	69603218	+	0	NA	Intergenic	Intergenic	8281	NM_201550	376132	Hs.448708	NM_201550	ENSG00000198812	LRRC10	HRLRRP|LRRC10A	leucine rich repeat containing 10	protein-coding	0.002972	0.388724	
chunk0055_371_1	chr13	73057671	73058018	+	0	NA	promoter-TSS (NM_001730)	promoter-TSS (NM_001730)	-948	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.005764	0.347701	
chunk0151_72_1	chr5	42603477	42603928	+	0	NA	intron (NM_001242460, intron 1 of 7)	MER21A|LTR|ERVL	37838	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.002217	0.380531	
chunk0176_430_1	chr7	19805434	19805695	+	0	NA	Intergenic	Intergenic	-32783	NM_152774	256130	Hs.487670	NM_152774	ENSG00000173452	TMEM196	-	transmembrane protein 196	protein-coding	0.003831	0.332061	179(AGAACACACTGAACAT,+,0.00)
chunk0205_393_1	chr9	114456860	114457617	+	0	NA	intron (NM_015404, intron 3 of 11)	L1MC4a|LINE|L1	45977	NM_001083885	25861	Hs.93836	NM_015404	ENSG00000095397	WHRN	CIP98|DFNB31|PDZD7B|USH2D|WI	whirlin	protein-coding	0.002642	0.368074	
chunk0152_196_1	chr5	59917596	59917951	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-23979	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002817	0.233146	
chunk0102_435_1	chr2	157784117	157784761	+	0	NA	intron (NM_001111067, intron 3 of 10)	intron (NM_001111067, intron 3 of 10)	90672	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.017081	0.483721	
chunk0016_133_1	chr1	197027736	197027992	+	0	NA	Intergenic	L1MA9|LINE|L1	39403	NM_001994	2165	Hs.435782	NM_001994	ENSG00000143278	F13B	FXIIIB	coagulation factor XIII B chain	protein-coding	0.007812	0.307393	
chunk0124_434_1	chr3	61239797	61240312	+	0	NA	intron (NM_001166243, intron 1 of 9)	intron (NM_001166243, intron 1 of 9)	11405	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.001942	0.468992	
chunk0090_118_1	chr18	71640753	71640973	+	0	NA	Intergenic	LTR28B|LTR|ERV1	-61907	NR_038325	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.004545	0.502262	
chunk0130_159_1	chr3	132598105	132598817	+	0	NA	intron (NM_016557, intron 1 of 1)	L2b|LINE|L2	1224	NM_016557	51554	Hs.310512	NM_016557	ENSG00000129048	ACKR4	CC-CKR-11|CCBP2|CCR-11|CCR10|CCR11|CCRL1|CCX CKR|CCX-CKR|CKR-11|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding	0.008427	0.385694	578(AGGAACAGAATGAGCA,-,0.00)
chunk0110_376_1	chr20	19966793	19967503	+	0	NA	intron (NM_018993, intron 5 of 10)	intron (NM_018993, intron 5 of 10)	-50142	NM_016100	51126	Hs.368783	NM_016100	ENSG00000173418	NAA20	NAT3|NAT3P|NAT5|NAT5P|dJ1002M8.1	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding	0.001408	0.399437	
chunk0057_112_1	chr13	99190285	99190777	+	0	NA	Intergenic	Intergenic	-9894	NM_001144072	337867	Hs.508545	NM_177967	ENSG00000134882	UBAC2	PHGDHL1	UBA domain containing 2	protein-coding	0.012195	0.472617	122(ATGATCACACTGTTCT,-,0.00),123(TGATCACACTGTTCTG,+,0.00),164(AGGAACAAACTGTCTC,-,0.00),165(GGAACAAACTGTCTCA,+,0.00)
chunk0161_75_1	chr5	166848917	166849132	+	0	NA	Intergenic	Intergenic	77346	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.000000	0.379630	
chunk0026_95_1	chr10	61612480	61612679	+	0	NA	Intergenic	Intergenic	-50382	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.010050	0.440000	
chunk0192_148_1	chr8	62035422	62035829	+	0	NA	Intergenic	Intergenic	-213317	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.002457	0.375000	
chunk0174_223_1	chr6	160432114	160432545	+	0	NA	intron (NM_021977, intron 5 of 10)	intron (NM_021977, intron 5 of 10)	78795	NR_028093	80350	Hs.654503	NM_024492	ENSG00000213071	LPAL2	APOA2|APOAL|APOARGC|apo(a)rg-C	lipoprotein(a) like 2, pseudogene	pseudo	0.030162	0.451389	
chunk0107_127_1	chr2	214713306	214713816	+	0	NA	Intergenic	Intergenic	96150	NR_104212	580	Hs.591642	NM_000465	ENSG00000138376	BARD1	-	BRCA1 associated RING domain 1	protein-coding	0.009804	0.379648	
chunk0094_405_1	chr2	10427601	10427955	+	0	NA	TTS (NM_134421)	TTS (NM_134421)	19071	NR_028374	100302743	Hs.730525	NR_028374	ENSG00000206633	SNORA80B	ACA67B	small nucleolar RNA, H/ACA box 80B	snoRNA	0.048023	0.560563	160(TTGCACAGCCTGTTCT,-,0.00),161(TGCACAGCCTGTTCTT,+,0.00)
chunk0138_60_1	chr4	32066593	32067032	+	0	NA	intron (NR_125936, intron 1 of 2)	L1MEg|LINE|L1	69433	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.006834	0.300000	
chunk0136_429_1	chr3	197668008	197668324	+	0	NA	Intergenic	Intergenic	6410	NR_030627	100126321		NR_030627	ENSG00000284146	MIR922	MIRN922|hsa-mir-922	microRNA 922	ncRNA	0.012658	0.463722	
chunk0080_58_1	chr17	21863126	21863368	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	170724	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.033058	0.395062	
chunk0157_129_1	chr5	117290078	117290515	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-125216	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.011442	0.406393	
chunk0109_87_1	chr20	2087824	2088163	+	0	NA	Intergenic	Intergenic	-13889	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.002950	0.447059	128(GAGAACAAGCCGTACT,-,0.00),129(AGAACAAGCCGTACTG,+,0.00)
chunk0158_5_1	chr5	125176019	125176669	+	0	NA	intron (NR_109882, intron 4 of 5)	intron (NR_109882, intron 4 of 5)	139513	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.010769	0.416283	
chunk0174_185_1	chr6	159789735	159789934	+	0	NA	promoter-TSS (NM_001008897)	promoter-TSS (NM_001008897)	-131	NM_001008897	6950	Hs.363137	NM_030752	ENSG00000120438	TCP1	CCT-alpha|CCT1|CCTa|D6S230E|TCP-1-alpha	t-complex 1	protein-coding	0.060302	0.555000	
chunk0008_221_1	chr1	93908316	93908657	+	0	NA	intron (NM_002061, intron 1 of 6)	L1MA4A|LINE|L1	1112	NM_002061	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.005865	0.312865	
chunk0118_58_1	chr22	27952364	27953063	+	0	NA	intron (NR_026963, intron 2 of 4)	intron (NR_026963, intron 2 of 4)	-32101	NR_036169	100423034		NR_036169	ENSG00000264073	MIR3199-1	mir-3199-1	microRNA 3199-1	ncRNA	0.007153	0.344286	502(TGAACATTCAGTTCAC,+,0.00)
chunk0186_130_1	chr7	138247172	138247803	+	0	NA	Intergenic	LTR23|LTR|ERV1	123729	NR_039678	100616226		NR_039678	ENSG00000284028	MIR4468	-	microRNA 4468	ncRNA	0.006339	0.444620	
chunk0212_142_1	chrX	131819641	131820076	+	0	NA	intron (NR_026975, intron 2 of 12)	HAL1|LINE|L1	10785	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.004598	0.330275	
chunk0007_88_1	chr1	78516858	78517119	+	0	NA	intron (NM_001039585, intron 3 of 3)	intron (NM_001039585, intron 3 of 3)	25945	NM_000959	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.003831	0.393130	
chunk0049_228_1	chr12	93442045	93442281	+	0	NA	promoter-TSS (NM_003348)	promoter-TSS (NM_003348)	87	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.156780	0.776371	
chunk0189_195_1	chr8	23644897	23645200	+	0	NA	Intergenic	MIRb|SINE|MIR	37841	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.009901	0.414474	128(GAACACAGACTGTGCC,-,0.00),129(AACACAGACTGTGCCT,+,0.00)
chunk0110_245_1	chr20	16462590	16463094	+	0	NA	intron (NM_001199865, intron 12 of 24)	LTR9D|LTR|ERV1	110592	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.011905	0.449505	
chunk0144_253_1	chr4	136452704	136452903	+	0	NA	Intergenic	L1M3c|LINE|L1	-539123	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.005025	0.495000	
chunk0103_443_1	chr2	170098638	170099065	+	0	NA	Intergenic	L1MC4a|LINE|L1	-79294	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.004684	0.364486	
chunk0194_18_1	chr8	81591122	81591701	+	0	NA	Intergenic	MIRb|SINE|MIR	-60096	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.005181	0.375862	
chunk0171_286_1	chr6	128139616	128139950	+	0	NA	intron (NM_001291981, intron 7 of 32).2	intron (NM_001291981, intron 7 of 32).2	111918	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.002994	0.367164	
chunk0088_367_1	chr18	53771440	53772002	+	0	NA	Intergenic	Intergenic	-190662	NR_110800	101928167	Hs.382012	NR_110800	ENSG00000260433	LINC01917	-	long intergenic non-protein coding RNA 1917	ncRNA	0.000000	0.344583	112(AAGTTCATGCTGTGCC,-,0.00),113(AGTTCATGCTGTGCCT,+,0.00)
chunk0088_376_1	chr18	54205936	54206264	+	0	NA	intron (NM_003927, intron 1 of 6)	intron (NM_003927, intron 1 of 6)	16312	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.003049	0.355623	
chunk0007_27_1	chr1	77564404	77564764	+	0	NA	3' UTR (NM_001308237, exon 14 of 14)	3' UTR (NM_001308237, exon 14 of 14)	118074	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.000000	0.299169	167(AAGAACATACTGTATA,-,0.00)
chunk0091_263_1	chr19	11157882	11158226	+	0	NA	Intergenic	L1MB3|LINE|L1	-2242	NM_001317031	147841	Hs.381225	NM_182513	ENSG00000161888	SPC24	SPBC24	SPC24 component of NDC80 kinetochore complex	protein-coding	0.017442	0.469565	
chunk0052_130_1	chr13	23559228	23559611	+	0	NA	Intergenic	Intergenic	-10951	NM_148957	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.018277	0.416667	
chunk0074_40_1	chr16	20694937	20695426	+	0	NA	Intergenic	MIRb|SINE|MIR	-3925	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.008180	0.408163	
chunk0049_309_1	chr12	94574286	94574706	+	0	NA	intron (NM_001301036, intron 3 of 3)	intron (NM_001301036, intron 3 of 3)	-3144	NR_106998	102465834		NR_106998	ENSG00000283818	MIR7844	hsa-mir-7844	microRNA 7844	ncRNA	0.011905	0.415677	
chunk0012_215_1	chr1	160148203	160148406	+	0	NA	Intergenic	L2a|LINE|L2	-3258	NM_144699	480	Hs.662219	NM_144699	ENSG00000132681	ATP1A4	ATP1A1|ATP1AL2	ATPase Na+/K+ transporting subunit alpha 4	protein-coding	0.000000	0.450980	
chunk0137_300_1	chr4	24055686	24056032	+	0	NA	Intergenic	Intergenic	-165782	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.008671	0.469741	171(TGGGACATTCTGTTCC,-,0.00),172(GGGACATTCTGTTCCC,+,0.00)
chunk0168_303_1	chr6	91506418	91507007	+	0	NA	Intergenic	L1ME3|LINE|L1	-14948	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.010187	0.338983	
chunk0022_165_1	chr10	12631727	12632098	+	0	NA	intron (NM_020397, intron 2 of 9)	L2c|LINE|L2	21285	NR_039701	100616320		NR_039701	ENSG00000283699	MIR4481	-	microRNA 4481	ncRNA	0.024259	0.489247	
chunk0109_306_1	chr20	8834901	8835424	+	0	NA	intron (NM_182734, intron 32 of 32)	L2a|LINE|L2	3977	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.005736	0.423664	
chunk0155_104_1	chr5	92641160	92641894	+	0	NA	Intergenic	Intergenic	929816	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.012262	0.397279	
chunk0126_70_1	chr3	74564265	74565123	+	0	NA	Intergenic	Intergenic	-43554	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.003497	0.421420	443(AGGTTCATGGTGTTCT,-,0.00),444(GGTTCATGGTGTTCTT,+,0.00)
chunk0085_242_1	chr18	7174742	7174941	+	0	NA	Intergenic	Intergenic	-56298	NM_001105581	339291	Hs.647588	NM_001105581	ENSG00000206422	LRRC30	-	leucine rich repeat containing 30	protein-coding	0.010050	0.610000	
chunk0191_305_1	chr8	54916998	54917267	+	0	NA	Intergenic	Intergenic	-185325	NM_052898	114786	Hs.130197	NM_052898	ENSG00000206579	XKR4	XRG4	XK related 4	protein-coding	0.011152	0.559259	
chunk0061_90_1	chr14	57390389	57390624	+	0	NA	promoter-TSS (NM_001011713)	promoter-TSS (NM_001011713)	-47	NM_001011713	122830	Hs.165465	NM_001011713	ENSG00000139977	NAA30	C14orf35|MAK3|Mak3p|NAT12|NAT12P	N(alpha)-acetyltransferase 30, NatC catalytic subunit	protein-coding	0.072340	0.677966	
chunk0118_154_1	chr22	30290795	30291568	+	0	NA	TTS (NM_031937)	TTS (NM_031937)	-1554	NM_001037666	652968	Hs.444950	NM_001037666	ENSG00000239282	CASTOR1	GATSL3	cytosolic arginine sensor for mTORC1 subunit 1	protein-coding	0.016818	0.591731	257(CAGGACAGGATGTTCC,-,0.00),258(AGGACAGGATGTTCCA,+,0.00),433(AGGGACACCCTGTCCT,-,0.00),434(GGGACACCCTGTCCTT,+,0.00)
chunk0127_353_1	chr3	101070033	101070604	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-76828	NM_015429	25890	Hs.477015	NM_015429	ENSG00000154175	ABI3BP	NESHBP|TARSH	ABI family member 3 binding protein	protein-coding	0.007005	0.461538	373(GAGGACACGCTGCCCC,-,0.00),374(AGGACACGCTGCCCCT,+,0.00)
chunk0133_272_1	chr3	171967187	171967386	+	0	NA	Intergenic	Intergenic	-66546	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.015075	0.410000	
chunk0152_424_1	chr5	65901418	65901707	+	0	NA	Intergenic	Intergenic	-24992	NM_001253698	55914	Hs.591774	NM_018695	ENSG00000112851	ERBIN	ERBB2IP|HEL-S-78|LAP2	erbb2 interacting protein	protein-coding	0.003460	0.320690	
chunk0044_192_1	chr12	30531896	30532095	+	0	NA	Intergenic	Intergenic	145249	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.005025	0.405000	
chunk0088_80_1	chr18	44771886	44772493	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	91291	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.016474	0.496711	
chunk0039_51_1	chr11	96157044	96157529	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-184152	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.006186	0.434156	366(AGGAACAGCGAGTGCT,-,0.00),367(GGAACAGCGAGTGCTA,+,0.00)
chunk0003_173_1	chr1	33563664	33564080	+	0	NA	intron (NM_001281956, intron 53 of 70)	L2b|LINE|L2	91241	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.004808	0.422062	
chunk0135_281_1	chr3	189396766	189396965	+	0	NA	Intergenic	L1MC4|LINE|L1	-156271	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.010050	0.435000	39(AAGCACAAGATGATCC,-,0.00),40(AGCACAAGATGATCCT,+,0.00)
chunk0003_407_1	chr1	40120439	40120839	+	0	NA	Intergenic	Intergenic	-23169	NM_000310	5538	Hs.3873	NM_000310	ENSG00000131238	PPT1	CLN1|INCL|PPT	palmitoyl-protein thioesterase 1	protein-coding	0.002500	0.391521	64(GAGACATTCTGTACCC,+,0.00)
chunk0086_358_1	chr18	25931782	25932572	+	0	NA	Intergenic	Intergenic	158470	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.013924	0.381795	29(GAGGAGAGAGTGTTCT,-,0.00),30(AGGAGAGAGTGTTCTG,+,0.00)
chunk0152_358_1	chr5	63737004	63737858	+	0	NA	Intergenic	MLT2C2|LTR|ERVL	224861	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.005855	0.374269	
chunk0053_409_1	chr13	36906708	36907073	+	0	NA	intron (NM_001127217, intron 1 of 6)	L1MB4|LINE|L1	13382	NM_005905	4093	Hs.123119	NM_005905	ENSG00000120693	SMAD9	MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B	SMAD family member 9	protein-coding	0.002740	0.330601	223(AGGTACTCAATGTTCA,-,0.00),224(GGTACTCAATGTTCAT,+,0.00)
chunk0114_372_1	chr20	62922421	62923197	+	0	NA	intron (NM_022105, intron 1 of 5)	intron (NM_022105, intron 1 of 5)	3742	NM_001193370	11083	Hs.517172	NM_022105	ENSG00000101191	DIDO1	BYE1|C20orf158|DATF-1|DATF1|DIDO2|DIDO3|DIO-1|DIO1|dJ885L7.8	death inducer-obliterator 1	protein-coding	0.019330	0.508366	295(TGACACAGCCTGTGCT,-,0.00),296(GACACAGCCTGTGCTG,+,0.00),407(GGTGACATACTGTTCT,-,0.00),408(GTGACATACTGTTCTC,+,0.00)
chunk0085_320_1	chr18	8337166	8337529	+	0	NA	intron (NM_001105244, intron 22 of 32)	intron (NM_001105244, intron 22 of 32)	29687	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.002755	0.439560	
chunk0065_262_1	chr14	101811183	101811417	+	0	NA	intron (NM_178586, intron 1 of 12)	intron (NM_178586, intron 1 of 12)	1497	NM_002719	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.000000	0.395745	
chunk0163_395_1	chr6	16503147	16503658	+	0	NA	intron (NM_001128164, intron 5 of 7)	intron (NM_001128164, intron 5 of 7)	258088	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.005871	0.472656	238(GAGTACTGACTGTTCC,-,0.00),239(AGTACTGACTGTTCCC,+,0.00)
chunk0171_30_1	chr6	120391647	120392187	+	0	NA	Intergenic	Intergenic	376738	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.001852	0.319778	
chunk0150_197_1	chr5	34843710	34844203	+	0	NA	intron (NM_144725, intron 2 of 10)	L2c|LINE|L2	4792	NM_144725	153657	Hs.435742	NM_144725	ENSG00000205838	TTC23L	MC25-1	tetratricopeptide repeat domain 23 like	protein-coding	0.006085	0.406883	
chunk0086_424_1	chr18	27847353	27847878	+	0	NA	Intergenic	Intergenic	188970	NM_001308176	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.007619	0.372624	
chunk0025_286_1	chr10	56504499	56505013	+	0	NA	Intergenic	Intergenic	-143483	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.287379	
chunk0030_364_1	chr10	118753135	118753517	+	0	NA	intron (NM_153810, intron 1 of 8)	intron (NM_153810, intron 1 of 8)	1920	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.013089	0.389034	
chunk0005_85_1	chr1	56146469	56146937	+	0	NA	Intergenic	L3|LINE|CR1	432881	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.004274	0.424307	
chunk0145_432_1	chr4	153269490	153270028	+	0	NA	intron (NM_001302694, intron 1 of 2)	intron (NM_001302694, intron 1 of 2)	12400	NM_001302694	23321	Hs.435711	NM_015271	ENSG00000109654	TRIM2	CMT2R|RNF86	tripartite motif containing 2	protein-coding	0.009294	0.369202	
chunk0010_273_1	chr1	117268810	117269270	+	0	NA	Intergenic	Intergenic	-26426	NR_126408	104355292	Hs.576446	NR_126408	ENSG00000235202	LINC01525	lnc-MAN1A2-1	long intergenic non-protein coding RNA 1525	ncRNA	0.013043	0.479393	
chunk0001_204_1	chr1	7890435	7891232	+	0	NA	Intergenic	Intergenic	-37342	NM_021995	10911	Hs.715862	NM_006786	ENSG00000049247	UTS2	PRO1068|U-II|UCN2|UII	urotensin 2	protein-coding	0.005019	0.411028	
chunk0159_249_1	chr5	141963396	141963823	+	0	NA	Intergenic	(ATTC)n|Simple_repeat|Simple_repeat	-3228	NM_183399	9604	Hs.483616	NM_004290	ENSG00000013561	RNF14	ARA54|HFB30|HRIHFB2038|TRIAD2	ring finger protein 14	protein-coding	0.009368	0.378505	
chunk0175_278_1	chr7	7573580	7574335	+	0	NA	intron (NM_019005, intron 4 of 12)	intron (NM_019005, intron 4 of 12)	6972	NM_019005	54468	Hs.520215	NM_019005	ENSG00000164654	MIOS	MIO|Sea4|Yulink	meiosis regulator for oocyte development	protein-coding	0.010596	0.325397	
chunk0074_326_1	chr16	30898821	30899320	+	0	NA	intron (NM_001142544, intron 1 of 2)	Tigger3a|DNA|TcMar-Tigger	2463	NM_001330	1489	Hs.483811	NM_001330	ENSG00000150281	CTF1	CT-1|CT1	cardiotrophin 1	protein-coding	0.014028	0.442000	
chunk0045_99_1	chr12	46110082	46110281	+	0	NA	Intergenic	L1PBa|LINE|L1	-119563	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.010050	0.560000	
chunk0068_38_1	chr15	51205333	51205695	+	0	NA	Intergenic	Intergenic	-36676	NR_039863	100616369		NR_039863	ENSG00000266593	MIR4713	-	microRNA 4713	ncRNA	0.002762	0.471074	
chunk0157_50_1	chr5	116023973	116024614	+	0	NA	intron (NM_173800, intron 19 of 19)	intron (NM_173800, intron 19 of 19)	-27173	NM_001195581	644100	Hs.98288	NM_001195581	ENSG00000268223	ARL14EPL	-	ADP ribosylation factor like GTPase 14 effector protein like	protein-coding	0.007800	0.375389	
chunk0135_421_1	chr3	193592987	193593415	+	0	NA	promoter-TSS (NM_015560)	promoter-TSS (NM_015560)	57	NM_015560	4976	Hs.594504	NM_015560	ENSG00000198836	OPA1	BERHS|MGM1|MTDPS14|NPG|NTG|largeG	OPA1 mitochondrial dynamin like GTPase	protein-coding	0.093458	0.659674	
chunk0137_6_1	chr4	10530065	10531041	+	0	NA	intron (NM_052964, intron 12 of 18)	MamRep1527|LTR|LTR	-73145	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.015369	0.459570	335(AAGCACAGCTTGCCCT,-,0.00),336(AGCACAGCTTGCCCTG,+,0.00)
chunk0152_284_1	chr5	61464490	61464699	+	0	NA	intron (NM_020928, intron 1 of 13)	intron (NM_020928, intron 1 of 13)	132321	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.004785	0.509524	
chunk0128_140_1	chr3	106774655	106774943	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	465839	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.000000	0.294118	92(AGGAACTAGATGTCCT,-,0.00),93(GGAACTAGATGTCCTT,+,0.00)
chunk0121_7_1	chr3	14434688	14435174	+	0	NA	intron (NM_001134367, intron 2 of 14)	intron (NM_001134367, intron 2 of 14)	32355	NM_003043	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.020576	0.579055	
chunk0087_401_1	chr18	41910056	41910279	+	0	NA	Intergenic	Intergenic	-45031	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.008969	0.406250	
chunk0194_147_1	chr8	84507557	84507978	+	0	NA	intron (NM_001100392, intron 2 of 9)	intron (NM_001100392, intron 2 of 9)	-198160	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004751	0.379147	
chunk0178_98_1	chr7	30617396	30617682	+	0	NA	intron (NM_001316772, intron 10 of 16)	intron (NM_001316772, intron 10 of 16)	22646	NM_002047	2617	Hs.404321	NM_002047	ENSG00000106105	GARS	CMT2D|DSMAV|GlyRS|HMN5|SMAD1	glycyl-tRNA synthetase	protein-coding	0.006993	0.442509	
chunk0058_199_1	chr14	24630810	24631118	+	0	NA	TTS (NM_004131)	TTS (NM_004131)	3262	NM_004131	3002	Hs.1051	NM_004131	ENSG00000100453	GZMB	C11|CCPI|CGL-1|CGL1|CSP-B|CSPB|CTLA1|CTSGL1|HLP|SECT	granzyme B	protein-coding	0.009740	0.469256	
chunk0109_365_1	chr2	239311316	239311554	+	0	NA	intron (NM_006037, intron 2 of 26)	intron (NM_006037, intron 2 of 26)	5973	NR_036229	100423043		NR_036229	ENSG00000265215	MIR4269	-	microRNA 4269	ncRNA	0.058824	0.527197	
chunk0022_463_1	chr10	20446716	20447674	+	0	NA	Intergenic	Intergenic	-104775	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.003132	0.400417	
chunk0022_106_1	chr10	10101764	10101963	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	43141	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.010050	0.525000	
chunk0107_291_1	chr2	218444564	218445032	+	0	NA	intron (NM_007127, intron 19 of 19)	intron (NM_007127, intron 19 of 19)	25683	NM_007127	7429	Hs.654595	NM_007127	ENSG00000127831	VIL1	D2S1471|VIL	villin 1	protein-coding	0.010684	0.522388	
chunk0210_50_1	chrX	68719865	68720409	+	0	NA	intron (NM_001142504, intron 6 of 13)	L2c|LINE|L2	26497	NM_001142504	9754	Hs.95140	NM_014725	ENSG00000130052	STARD8	ARHGAP38|DLC3|STARTGAP3	StAR related lipid transfer domain containing 8	protein-coding	0.016544	0.554128	
chunk0029_290_1	chr10	103861338	103861645	+	0	NA	Intergenic	Intergenic	-6085	NM_014631	9644	Hs.678727	NM_014631	ENSG00000107957	SH3PXD2A	FISH|SH3MD1|TKS5	SH3 and PX domains 2A	protein-coding	0.006515	0.301948	
chunk0044_356_1	chr12	39089267	39089872	+	0	NA	Intergenic	Intergenic	-183951	NM_153634	144402	Hs.40910	NM_153634	ENSG00000139117	CPNE8	-	copine 8	protein-coding	0.008264	0.359736	
chunk0059_310_1	chr14	36302623	36302928	+	0	NA	intron (NM_001308110, intron 6 of 7)	intron (NM_001308110, intron 6 of 7)	17901	NM_001144891	51562	Hs.368647	NM_016586	ENSG00000151332	MBIP	-	MAP3K12 binding inhibitory protein 1	protein-coding	0.006557	0.346405	
chunk0071_383_1	chr15	89134966	89135224	+	0	NA	intron (NM_007011, intron 7 of 14)	intron (NM_007011, intron 7 of 14)	46945	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.000000	0.289575	
chunk0188_273_1	chr8	15276377	15276576	+	0	NA	Intergenic	L1MC1|LINE|L1	-38193	NM_139167	137868	Hs.545526	NM_139167	ENSG00000185053	SGCZ	ZSG1	sarcoglycan zeta	protein-coding	0.000000	0.310000	
chunk0191_377_1	chr8	56999243	56999458	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-5479	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.004651	0.384259	
chunk0132_101_1	chr3	155665153	155665718	+	0	NA	intron (NM_014996, intron 1 of 21)	intron (NM_014996, intron 1 of 21)	10881	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.007080	0.454064	
chunk0191_366_1	chr8	56940885	56941370	+	0	NA	Intergenic	Intergenic	52744	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.006186	0.413580	
chunk0008_197_1	chr1	93369567	93370046	+	0	NA	Intergenic	Intergenic	23885	NM_001938	1810	Hs.348418	NM_001938	ENSG00000117505	DR1	NC2|NC2-BETA|NC2B|NCB2	down-regulator of transcription 1	protein-coding	0.004175	0.314583	
chunk0205_230_1	chr9	109923424	109923718	+	0	NA	intron (NM_053016, intron 3 of 6)	intron (NM_053016, intron 3 of 6)	-125027	NM_001004065	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.013605	0.484746	
chunk0026_235_1	chr10	65794003	65794311	+	0	NA	Intergenic	MER57B1|LTR|ERV1	222732	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.003247	0.359223	
chunk0056_260_1	chr13	89946198	89946442	+	0	NA	Intergenic	L1MEf|LINE|L1	173397	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.020492	0.416327	
chunk0160_349_1	chr5	160161728	160162097	+	0	NA	Intergenic	L1M1|LINE|L1	-25455	NM_001130958	2172	Hs.519719	NM_001445	ENSG00000170231	FABP6	I-15P|I-BABP|I-BALB|I-BAP|ILBP|ILBP3|ILLBP	fatty acid binding protein 6	protein-coding	0.008130	0.413514	
chunk0040_352_1	chr11	118689903	118690304	+	0	NA	Intergenic	Intergenic	-10431	NM_007180	11181	Hs.129712	NM_007180	ENSG00000118094	TREH	TRE|TREA|TREHD	trehalase	protein-coding	0.047382	0.654229	
chunk0183_121_1	chr7	105461459	105461976	+	0	NA	intron (NM_019042, intron 14 of 15)	Tigger3c|DNA|TcMar-Tigger	60521	NM_019042	54517	Hs.520619	NM_019042	ENSG00000091127	PUS7	IDDABS	pseudouridine synthase 7	protein-coding	0.013540	0.430502	
chunk0021_278_1	chr1	244286119	244286730	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-66211	NM_001012970	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.016367	0.508170	299(AAGACCAGGCTGTACC,-,0.00),300(AGACCAGGCTGTACCA,+,0.00)
chunk0068_206_1	chr15	55004280	55004481	+	0	NA	Intergenic	Intergenic	192653	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.014925	0.514851	
chunk0057_331_1	chr13	106960150	106960665	+	0	NA	Intergenic	Intergenic	306527	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.003883	0.315891	
chunk0104_359_1	chr2	179961880	179962301	+	0	NA	intron (NM_020943, intron 13 of 19)	intron (NM_020943, intron 13 of 19)	44963	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.004751	0.324645	
chunk0177_374_1	chr7	26859294	26859526	+	0	NA	intron (NM_003930, intron 1 of 12)	intron (NM_003930, intron 1 of 12)	-1687	NM_001303468	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.000000	0.377682	
chunk0009_203_1	chr1	106064751	106065106	+	0	NA	Intergenic	Intergenic	-445993	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.000000	0.300562	195(TAGAACACACTGTATT,-,0.00),196(AGAACACACTGTATTG,+,0.00)
chunk0137_251_1	chr4	20682847	20683458	+	0	NA	Intergenic	Intergenic	-17261	NM_001258345	133015	Hs.479298	NM_145048	ENSG00000163138	PACRGL	C4orf28	parkin coregulated like	protein-coding	0.006547	0.498366	
chunk0171_426_1	chr6	131557027	131557296	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-16043	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.000000	0.329630	112(GGTACACAATGACCTC,+,0.00)
chunk0203_308_1	chr9	89386775	89387091	+	0	NA	intron (NM_006378, intron 14 of 17)	intron (NM_006378, intron 14 of 17)	68082	NM_001282690	79048	Hs.59804	NM_024077	ENSG00000187742	SECISBP2	SBP2	SECIS binding protein 2	protein-coding	0.028481	0.646688	
chunk0084_394_1	chr17	82113816	82114575	+	0	NA	intron (NM_198082, intron 16 of 16)	intron (NM_198082, intron 16 of 16)	-15965	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.025033	0.572368	339(AGGTACAGACTGTTCT,-,0.00),340(GGTACAGACTGTTCTT,+,0.00)
chunk0162_322_1	chr6	6750054	6750696	+	0	NA	Intergenic	Intergenic	-127549	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.020249	0.455677	307(AGGAACGCAGTGTTCC,-,0.00),308(GGAACGCAGTGTTCCT,+,0.00)
chunk0106_215_1	chr2	202494367	202494775	+	0	NA	intron (NM_001204, intron 3 of 12)	intron (NM_001204, intron 3 of 12)	118244	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.004902	0.396088	
chunk0148_435_1	chr4	189143225	189143490	+	0	NA	Intergenic	Intergenic	-516249	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.007547	0.398496	
chunk0203_229_1	chr9	87008339	87008908	+	0	NA	non-coding (NR_027471, exon 2 of 2)	non-coding (NR_027471, exon 2 of 2)	33503	NR_027471	440173	Hs.127361	NR_027471	ENSG00000269994	LOC440173	-	uncharacterized LOC440173	ncRNA	0.007030	0.421053	
chunk0154_357_1	chr5	87345991	87346201	+	0	NA	intron (NM_022650, intron 6 of 24)	intron (NM_022650, intron 6 of 24)	-22468	NR_130929	644285	Hs.709256	NR_130929		LOC644285	-	uncharacterized LOC644285	ncRNA	0.000000	0.308057	148(GAGAACACTAAGTCCT,-,0.00),149(AGAACACTAAGTCCTT,+,0.00)
chunk0150_221_1	chr5	35382801	35383000	+	0	NA	Intergenic	Intergenic	-152311	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.010050	0.475000	
chunk0027_256_1	chr10	77229706	77230058	+	0	NA	intron (NM_001014797, intron 3 of 28)	L1MB5|LINE|L1	89051	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.008523	0.365439	
chunk0119_436_1	chr22	50070150	50070540	+	0	NA	intron (NM_015166, intron 9 of 11)	intron (NM_015166, intron 9 of 11)	15007	NM_139202	23209	Hs.517729	NM_015166	ENSG00000100427	MLC1	LVM|MLC|VL	modulator of VRAC current 1	protein-coding	0.020513	0.601023	169(AGGTCTGCCTGTCCCT,+,0.00)
chunk0103_145_1	chr2	162154940	162155234	+	0	NA	intron (NR_110255, intron 1 of 3)	L1ME4b|LINE|L1	-2683	NM_002054	2641	Hs.516494	NM_002054	ENSG00000115263	GCG	GLP-1|GLP1|GLP2|GRPP	glucagon	protein-coding	0.003401	0.379661	
chunk0018_369_1	chr1	221941328	221941527	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-100761	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.010050	0.400000	
chunk0177_232_1	chr7	24573880	24574218	+	0	NA	intron (NM_001303037, intron 1 of 11)	CpG	703	NM_001303037	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.103550	0.699115	
chunk0180_369_1	chr7	74015430	74015983	+	0	NA	Intergenic	L2b|LINE|L2	-12083	NM_000501	2006	Hs.647061	NM_000501	ENSG00000049540	ELN	ADCL1|SVAS|WBS|WS	elastin	protein-coding	0.007233	0.422383	
chunk0072_349_1	chr15	99589632	99590288	+	0	NA	intron (NM_001130927, intron 1 of 9)	L1ME2|LINE|L1	24032	NM_005587	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.003049	0.305936	
chunk0136_289_1	chr3	194935590	194935906	+	0	NA	Intergenic	Intergenic	-158840	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.018987	0.429022	
chunk0162_240_1	chr6	4876783	4877328	+	0	NA	intron (NM_001143970, intron 1 of 6)	MLT1A0|LTR|ERVL-MaLR	-12937	NM_001143971	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.012844	0.432234	
chunk0014_180_1	chr1	178602703	178603127	+	0	NA	Intergenic	Intergenic	60119	NR_033186	400798	Hs.668085	NM_207467	ENSG00000213057	C1orf220	-	chromosome 1 open reading frame 220 (putative)	ncRNA	0.004717	0.385882	
chunk0141_456_1	chr4	89423744	89424267	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-115995	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.005736	0.332061	
chunk0109_42_1	chr20	739099	739369	+	0	NA	Intergenic	Intergenic	29350	NM_033409	113278	Hs.283865	NM_033409	ENSG00000101276	SLC52A3	BVVLS|BVVLS1|C20orf54|RFT2|RFVT3|bA371L19.1|hRFT2	solute carrier family 52 member 3	protein-coding	0.025926	0.568266	
chunk0013_337_1	chr1	171913471	171913840	+	0	NA	intron (NM_001136127, intron 1 of 19)	intron (NM_001136127, intron 1 of 19)	49463	NR_046845	100874284		NR_046845	ENSG00000233540	DNM3-IT1	-	DNM3 intronic transcript 1	ncRNA	0.005420	0.381081	
chunk0079_384_1	chr17	18542930	18543294	+	0	NA	intron (NR_036647, intron 16 of 16)	L2c|LINE|L2	-16266	NR_026809									0.013736	0.424658	
chunk0070_322_1	chr15	75454236	75454533	+	0	NA	intron (NM_001145357, intron 1 of 20)	CpG-8441	1399	NM_001145357	25942	Hs.513039	NM_015477	ENSG00000169375	SIN3A	WITKOS	SIN3 transcription regulator family member A	protein-coding	0.101010	0.714765	
chunk0139_102_1	chr4	51107136	51107624	+	0	NA	Intergenic	SAR|Satellite|Satellite	-735620	NM_001287757	23142	Hs.605388	NM_015115	ENSG00000109184	DCUN1D4	-	defective in cullin neddylation 1 domain containing 4	protein-coding	0.004515	0.247748	
chunk0125_383_1	chr3	71652772	71652971	+	0	NA	Intergenic	Intergenic	-68882	NM_032682	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.045226	0.475000	
chunk0012_263_1	chr1	161723416	161724205	+	0	NA	intron (NM_001002901, intron 5 of 7)	intron (NM_001002901, intron 5 of 7)	1157	NM_001288831	127943	Hs.517422	NM_001002901	ENSG00000162746	FCRLB	FCRL2|FCRLM2|FCRLY|FREB-2|FREB2|FcRY	Fc receptor like B	protein-coding	0.012674	0.511392	
chunk0133_278_1	chr3	172044884	172045316	+	0	NA	intron (NM_001135095, intron 1 of 25)	intron (NM_001135095, intron 1 of 25)	4546	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.002315	0.369515	
chunk0091_215_1	chr19	9803543	9803742	+	0	NA	Intergenic	LTR8A|LTR|ERV1	15461	NM_017703	54850	Hs.12439	NM_017703	ENSG00000127452	FBXL12	Fbl12	F-box and leucine rich repeat protein 12	protein-coding	0.020101	0.535000	
chunk0056_79_1	chr13	79567610	79567930	+	0	NA	intron (NR_125772, intron 1 of 2)	intron (NR_125772, intron 1 of 2)	1043	NR_125772	103724388	Hs.434862	NR_125772	ENSG00000227676	LINC01068	-	long intergenic non-protein coding RNA 1068	ncRNA	0.000000	0.358255	
chunk0061_24_1	chr14	55791352	55791592	+	0	NA	intron (NR_026796, intron 3 of 3)	intron (NR_026796, intron 3 of 3)	5202	NR_026797	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.000000	0.423237	
chunk0005_23_1	chr1	54370663	54370964	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	35582	NM_145716	23648	Hs.476706	NM_018070	ENSG00000157216	SSBP3	CSDP|SSDP|SSDP1	single stranded DNA binding protein 3	protein-coding	0.013289	0.483444	97(AGGCACTACATGTTCC,-,0.00),98(GGCACTACATGTTCCT,+,0.00)
chunk0068_213_1	chr15	55204311	55204936	+	0	NA	3' UTR (NM_004580, exon 6 of 6)	3' UTR (NM_004580, exon 6 of 6)	-7590	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.008000	0.380192	
chunk0037_210_1	chr11	74648364	74648824	+	0	NA	Intergenic	L2c|LINE|L2	55989	NR_046410	10714	Hs.82502	NM_006591	ENSG00000077514	POLD3	P66|P68|PPP1R128	DNA polymerase delta 3, accessory subunit	protein-coding	0.004348	0.444685	252(AAGCACAGACTGTTTA,-,0.00),253(AGCACAGACTGTTTAG,+,0.00)
chunk0102_133_1	chr2	145687605	145687804	+	0	NA	Intergenic	Intergenic	-899353	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.010050	0.430000	
chunk0199_141_1	chr9	4037925	4038300	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	114071	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.002667	0.353723	
chunk0016_435_1	chr1	203932067	203932404	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	70650	NM_001304464	6635	Hs.334612	NM_003094	ENSG00000182004	SNRPE	HYPT11|SME|Sm-E|snRNP-E	small nuclear ribonucleoprotein polypeptide E	protein-coding	0.005935	0.485207	
chunk0209_134_1	chrX	41526423	41526690	+	0	NA	intron (NM_003688, intron 25 of 26)	intron (NM_003688, intron 25 of 26)	79096	NM_022567	60506	Hs.302019	NM_022567	ENSG00000188937	NYX	CLRP|CSNB1|CSNB1A|CSNB4|NBM1	nyctalopin	protein-coding	0.003745	0.440299	
chunk0182_79_1	chr7	92528834	92529053	+	0	NA	promoter-TSS (NM_000466)	promoter-TSS (NM_000466)	170	NM_032120	84060	Hs.21590	NM_032120	ENSG00000127993	RBM48	C7orf64|HSPC304	RNA binding motif protein 48	protein-coding	0.073059	0.522727	
chunk0053_440_1	chr13	39335751	39335987	+	0	NA	Intergenic	Intergenic	267350	NM_005780	10186	Hs.507798	NM_005780	ENSG00000183722	LHFPL6	LHFP	LHFPL tetraspan subfamily member 6	protein-coding	0.004237	0.345992	
chunk0009_216_1	chr1	106321211	106321475	+	0	NA	Intergenic	Intergenic	-702408	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.000000	0.347170	40(CAGCACATTTTGTTCT,-,0.00),41(AGCACATTTTGTTCTA,+,0.00)
chunk0146_369_1	chr4	168308853	168309401	+	0	NA	intron (NM_017631, intron 3 of 37)	Tigger2|DNA|TcMar-Tigger	9680	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.005474	0.342441	231(TAGTACATACTGTACT,-,0.00),232(AGTACATACTGTACTA,+,0.00)
chunk0115_16_1	chr21	20438904	20439753	+	0	NA	Intergenic	L1PA10|LINE|L1	363780	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.004711	0.349412	
chunk0179_193_1	chr7	47226535	47227033	+	0	NA	Intergenic	Intergenic	355360	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.010040	0.454910	
chunk0104_241_1	chr2	176850106	176850431	+	0	NA	Intergenic	Intergenic	212514	NR_110599	102724224	Hs.663125	NR_110599	ENSG00000224577	LINC01117	-	long intergenic non-protein coding RNA 1117	ncRNA	0.000000	0.500000	
chunk0065_268_1	chr14	101867703	101868225	+	0	NA	intron (NM_178586, intron 2 of 12)	intron (NM_178586, intron 2 of 12)	58161	NM_002719	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.011494	0.405354	
chunk0015_226_1	chr1	187752422	187752968	+	0	NA	Intergenic	Intergenic	309067	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.005495	0.374771	
chunk0193_438_1	chr8	81029666	81030257	+	0	NA	intron (NM_018440, intron 3 of 8)	intron (NM_018440, intron 3 of 8)	82107	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.008460	0.403716	
chunk0152_352_1	chr5	63117007	63117460	+	0	NA	Intergenic	Intergenic	538498	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.000000	0.284141	
chunk0094_116_1	chr2	4460570	4460912	+	0	NA	Intergenic	Intergenic	195481	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.005848	0.279883	
chunk0184_183_1	chr7	116711434	116711898	+	0	NA	intron (NM_000245, intron 2 of 20)	intron (NM_000245, intron 2 of 20)	39261	NM_000245	4233	Hs.132966	NM_000245	ENSG00000105976	MET	AUTS9|DFNB97|HGFR|RCCP2|c-Met	MET proto-oncogene, receptor tyrosine kinase	protein-coding	0.004310	0.348387	
chunk0043_160_1	chr12	16738097	16738316	+	0	NA	Intergenic	Intergenic	-129992	NM_001001395	55885	Hs.504908	NM_018640	ENSG00000048540	LMO3	RBTN3|RBTNL2|RHOM3|Rhom-3	LIM domain only 3	protein-coding	0.004566	0.345455	
chunk0020_107_1	chr1	233025130	233025956	+	0	NA	intron (NM_014801, intron 25 of 33)	intron (NM_014801, intron 25 of 33)	74919	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.016949	0.444982	
chunk0137_349_1	chr4	25411120	25411577	+	0	NA	intron (NM_013367, intron 21 of 28)	intron (NM_013367, intron 21 of 28)	34122	NM_001286756	29945	Hs.152173	NM_013367	ENSG00000053900	ANAPC4	APC4	anaphase promoting complex subunit 4	protein-coding	0.006565	0.425764	
chunk0114_378_1	chr20	62980487	62980913	+	0	NA	Intergenic	Intergenic	26335	NM_080606	128408	Hs.551230	NM_080606	ENSG00000125533	BHLHE23	BETA4|BHLHB4|Beta3b|bA305P22.3	basic helix-loop-helix family member e23	protein-coding	0.023474	0.426230	229(AAGCACTGAGTGTTCC,-,0.00),230(AGCACTGAGTGTTCCC,+,0.00)
chunk0078_243_1	chr17	7012205	7012703	+	0	NA	promoter-TSS (NR_037716)	promoter-TSS (NR_037716)	37	NR_037717	100529209	Hs.511801	NR_037717	ENSG00000161939	RNASEK-C17orf49	BAP18|C17orf49	RNASEK-C17orf49 readthrough	ncRNA	0.064257	0.605210	
chunk0042_221_1	chr12	6215943	6216243	+	0	NA	intron (NM_001769, intron 1 of 7)	intron (NM_001769, intron 1 of 7)	15777	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.013333	0.581395	
chunk0111_148_1	chr20	25039682	25040241	+	0	NA	intron (NM_032501, intron 2 of 13)	intron (NM_032501, intron 2 of 13)	-7255	NM_001252676	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.010733	0.519643	
chunk0086_352_1	chr18	25712119	25712337	+	0	NA	Intergenic	Intergenic	-359978	NM_015461	25925	Hs.116935	NM_015461	ENSG00000198795	ZNF521	EHZF|Evi3	zinc finger protein 521	protein-coding	0.000000	0.438356	
chunk0044_198_1	chr12	30687593	30688033	+	0	NA	intron (NM_006390, intron 2 of 24)	intron (NM_006390, intron 2 of 24)	8182	NM_006390	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.004545	0.356009	
chunk0098_291_1	chr2	75890092	75890291	+	0	NA	Intergenic	L2c|LINE|L2	-179206	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.005025	0.360000	
chunk0087_344_1	chr18	40275367	40275764	+	0	NA	Intergenic	Intergenic	209279	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.314070	
chunk0190_129_1	chr8	30637046	30637463	+	0	NA	intron (NM_002095, intron 2 of 7)	intron (NM_002095, intron 2 of 7)	-1346	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.002398	0.332536	
chunk0165_189_1	chr6	34472278	34472662	+	0	NA	intron (NM_020804, intron 1 of 9)	intron (NM_020804, intron 1 of 9)	6409	NM_020804	29993	Hs.520087	NM_020804	ENSG00000124507	PACSIN1	SDPI	protein kinase C and casein kinase substrate in neurons 1	protein-coding	0.010417	0.361039	
chunk0196_204_1	chr8	106531560	106532117	+	0	NA	intron (NM_001198532, intron 2 of 15)	intron (NM_001198532, intron 2 of 15)	83914	NM_001198532	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.007181	0.360215	198(AGGTACGTGGTGTGCT,-,0.00)
chunk0171_194_1	chr6	125308082	125308601	+	0	NA	Intergenic	Intergenic	-6205	NM_016063	51020	Hs.32826	NM_016063	ENSG00000111906	HDDC2	C6orf74|CGI-130|NS5ATP2|dJ167O5.2	HD domain containing 2	protein-coding	0.011561	0.405769	
chunk0057_118_1	chr13	99340442	99341132	+	0	NA	intron (NM_001144072, intron 7 of 8)	intron (NM_001144072, intron 7 of 8)	-10633	NR_024013	100131561	Hs.721900	NR_024013		FKSG29	-	FKSG29	ncRNA	0.005797	0.374819	
chunk0049_340_1	chr12	95075500	95075921	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-2082	NM_001032287	7181	Hs.108301	NM_003297	ENSG00000120798	NR2C1	TR2	nuclear receptor subfamily 2 group C member 1	protein-coding	0.004751	0.364929	
chunk0192_142_1	chr8	62005922	62006648	+	0	NA	Intergenic	Intergenic	-242657	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.005510	0.407153	
chunk0201_133_1	chr9	35657759	35658040	+	0	NA	promoter-TSS (NM_001195217)	promoter-TSS (NM_001195217)	119	NR_003051	6023	Hs.587502	NR_003051	ENSG00000269900	RMRP	CHH|NME1|RMRPR|RRP2	RNA component of mitochondrial RNA processing endoribonuclease	ncRNA	0.081851	0.617021	
chunk0090_112_1	chr18	71364348	71364720	+	0	NA	Intergenic	Intergenic	214422	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.005376	0.281501	281(AAGTACAATGTGTACA,-,0.00),282(AGTACAATGTGTACAG,+,0.00)
chunk0003_92_1	chr1	31881736	31881944	+	0	NA	Intergenic	Intergenic	37818	NM_001195100	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.019231	0.507177	
chunk0180_270_1	chr7	69654396	69654781	+	0	NA	intron (NM_015570, intron 1 of 18)	MIR|SINE|MIR	55669	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.005195	0.411917	
chunk0072_6_1	chr16	267999	268287	+	0	NA	TTS (NM_001286486)	TTS (NM_001286486)	7800	NM_003834	8786	Hs.65756	NM_003834	ENSG00000076344	RGS11	RS11	regulator of G protein signaling 11	protein-coding	0.034722	0.515571	
chunk0039_231_1	chr11	101771682	101771937	+	0	NA	Intergenic	L2b|LINE|L2	-143206	NM_020802	57562	Hs.156352	NM_020802	ENSG00000110318	CEP126	KIAA1377	centrosomal protein 126	protein-coding	0.011765	0.449219	
chunk0125_21_1	chr3	62096990	62097853	+	0	NA	intron (NM_002841, intron 5 of 29)	intron (NM_002841, intron 5 of 29)	221526	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.015064	0.392361	310(CAGTTCAGGATGTTCT,-,0.00),311(AGTTCAGGATGTTCTG,+,0.00),686(TAGAACAAAGTGTGCA,-,0.00),687(AGAACAAAGTGTGCAT,+,0.00)
chunk0061_427_1	chr14	65243528	65244260	+	0	NA	Intergenic	L2a|LINE|L2	-21547	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.013661	0.491132	
chunk0155_39_1	chr5	91119467	91119783	+	0	NA	intron (NR_003149, intron 87 of 89)	intron (NR_003149, intron 87 of 89)	194777	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.003165	0.391167	
chunk0018_270_1	chr1	220541317	220541528	+	0	NA	intron (NM_001286128, intron 1 of 15)	L1M4c|LINE|L1	13239	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.014218	0.367925	
chunk0178_207_1	chr7	34814422	34814847	+	0	NA	intron (NM_001300935, intron 4 of 9)	L1PA6|LINE|L1	19697	NR_015356	404744	Hs.487951	NM_207283	ENSG00000197085	NPSR1-AS1	AAA1	NPSR1 antisense RNA 1	ncRNA	0.009412	0.525822	
chunk0159_351_1	chr5	144377081	144377693	+	0	NA	intron (NM_020768, intron 3 of 3)	MER102c|DNA|hAT-Charlie	206514	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.000000	0.409462	
chunk0073_89_1	chr16	4120210	4120409	+	0	NA	Intergenic	Intergenic	-4124	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.000000	0.485000	
chunk0112_305_1	chr20	44446028	44446431	+	0	NA	Intergenic	L2a|LINE|L2	4328	NR_109893	101927242	Hs.143307	NR_109893	ENSG00000168746	LINC01430	-	long intergenic non-protein coding RNA 1430	ncRNA	0.007444	0.490099	281(TGGAACATTCTGTCCT,-,0.00),282(GGAACATTCTGTCCTC,+,0.00)
chunk0006_377_1	chr1	74163098	74163757	+	0	NA	intron (NM_001105659, intron 3 of 7)	intron (NM_001105659, intron 3 of 7)	34760	NM_001105659	127255	Hs.644625	NM_145258	ENSG00000162620	LRRIQ3	LRRC44	leucine rich repeats and IQ motif containing 3	protein-coding	0.001517	0.298485	
chunk0149_219_1	chr5	22073447	22073731	+	0	NA	intron (NM_004061, intron 5 of 14)	intron (NM_004061, intron 5 of 14)	-68763	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.000000	0.315789	268(TAGCACAGTTTGTGCT,-,0.00),269(AGCACAGTTTGTGCTT,+,0.00)
chunk0049_222_1	chr12	93412303	93412790	+	0	NA	intron (NM_003348, intron 1 of 3)	LTR10C|LTR|ERV1	29704	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.016427	0.420082	
chunk0120_143_1	chr3	5179628	5180096	+	0	NA	3' UTR (NM_018184, exon 7 of 7)	3' UTR (NM_018184, exon 7 of 7)	-7812	NM_014674	9695	Hs.224616	NM_014674	ENSG00000134109	EDEM1	EDEM	ER degradation enhancing alpha-mannosidase like protein 1	protein-coding	0.004274	0.343284	
chunk0129_236_1	chr3	122004138	122004693	+	0	NA	intron (NM_175924, intron 3 of 6)	MIR|SINE|MIR	17865	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.010811	0.433453	
chunk0017_456_1	chr1	214460330	214460842	+	0	NA	intron (NM_005401, intron 2 of 18)	intron (NM_005401, intron 2 of 18)	91095	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.003906	0.463938	372(CAGCACAAGCAGTTCC,-,0.00),373(AGCACAAGCAGTTCCC,+,0.00)
chunk0029_76_1	chr10	96712114	96712470	+	0	NA	intron (NM_152309, intron 1 of 16)	Tigger10|DNA|TcMar-Tigger	8230	NM_152309	118788	Hs.310456	NM_152309	ENSG00000155629	PIK3AP1	BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.014045	0.425770	
chunk0040_284_1	chr11	116869571	116870262	+	0	NA	intron (NM_001281749, intron 13 of 23)	intron (NM_001281749, intron 13 of 23)	-32294	NM_000039	335	Hs.93194	NM_000039	ENSG00000118137	APOA1	apo(a)	apolipoprotein A1	protein-coding	0.007236	0.462428	
chunk0128_52_1	chr3	104816817	104817578	+	0	NA	Intergenic	Intergenic	-549516	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006570	0.355643	
chunk0056_379_1	chr13	93154549	93155159	+	0	NA	Intergenic	Intergenic	-71971	NM_005708	10082	Hs.444329	NM_005708	ENSG00000183098	GPC6	OMIMD1	glypican 6	protein-coding	0.001639	0.325696	
chunk0077_101_1	chr16	78122893	78123506	+	0	NA	intron (NM_016373, intron 4 of 8)	intron (NM_016373, intron 4 of 8)	23786	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.004894	0.340391	351(GGGAGCAGCCTGTTCT,-,0.00),352(GGAGCAGCCTGTTCTG,+,0.00)
chunk0022_113_1	chr10	10740999	10741291	+	0	NA	Intergenic	L1MA9|LINE|L1	53769	NR_027082	207107	Hs.31562	NR_027082	ENSG00000225383	SFTA1P	SFTPF	surfactant associated 1, pseudogene	pseudo	0.010274	0.368601	
chunk0212_148_1	chrX	131889097	131889372	+	0	NA	Intergenic	L1MD1|LINE|L1	-58591	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.000000	0.340580	
chunk0132_408_1	chr3	164281680	164282179	+	0	NA	Intergenic	L1M1|LINE|L1	-110373	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.002004	0.270000	
chunk0013_176_1	chr1	168907093	168907473	+	0	NA	intron (NR_104091, intron 4 of 4)	intron (NR_104091, intron 4 of 4)	120342	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.013158	0.401575	
chunk0092_214_1	chr19	31572857	31573454	+	0	NA	Intergenic	Intergenic	-15034	NM_001278575	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.023451	0.448161	
chunk0193_318_1	chr8	78553977	78554542	+	0	NA	intron (NR_125389, intron 2 of 2)	intron (NR_125389, intron 2 of 2)	4244	NR_125389	101927003	Hs.614849	NR_125389	ENSG00000254266	PKIA-AS1	-	PKIA antisense RNA 1	ncRNA	0.003540	0.376325	334(GGGAAGACACTGTTCT,-,0.00),335(GGAAGACACTGTTCTC,+,0.00)
chunk0031_375_1	chr10	130569291	130569536	+	0	NA	Intergenic	Intergenic	393255	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.012245	0.394309	
chunk0033_359_1	chr11	23063031	23063764	+	0	NA	Intergenic	Intergenic	-202971	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.000000	0.279292	
chunk0020_25_1	chr1	231848788	231849132	+	0	NA	intron (NM_001164541, intron 9 of 9)	intron (NM_001164541, intron 9 of 9)	-30443	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.005814	0.356522	249(TTGAACACTTTGTACC,-,0.00),250(TGAACACTTTGTACCT,+,0.00)
chunk0093_202_1	chr19	49497237	49497562	+	0	NA	promoter-TSS (NR_001285)	promoter-TSS (NR_001285)	-320	NR_001285	84546		NR_001285	ENSG00000200530	SNORD35B	RNU35B|U35B	small nucleolar RNA, C/D box 35B	snoRNA	0.033846	0.561350	
chunk0003_77_1	chr1	31413609	31413995	+	0	NA	promoter-TSS (NM_018565)	promoter-TSS (NM_018565)	-11	NM_018565	347735	Hs.270655	NM_018565	ENSG00000168528	SERINC2	FKSG84|PRO0899|TDE2|TDE2L	serine incorporator 2	protein-coding	0.093264	0.687339	
chunk0097_370_1	chr2	61015870	61016334	+	0	NA	intron (NM_144709, intron 1 of 17)	intron (NM_144709, intron 1 of 17)	-1575	NM_002618	5194	Hs.161377	NM_002618	ENSG00000162928	PEX13	NALD|PBD11A|PBD11B|ZWS	peroxisomal biogenesis factor 13	protein-coding	0.004310	0.313978	
chunk0032_56_1	chr11	1870622	1871039	+	0	NA	promoter-TSS (NM_001013255)	promoter-TSS (NM_001013255)	-39	NM_001013254	4046	Hs.56729	NM_002339	ENSG00000130592	LSP1	WP34|pp52	lymphocyte specific protein 1	protein-coding	0.057554	0.645933	
chunk0180_139_1	chr7	56371886	56372107	+	0	NA	Intergenic	Intergenic	76379	NR_029420	650226	Hs.448401	NR_029420		LOC650226	-	ankyrin repeat domain 26 pseudogene	pseudo	0.072398	0.711712	
chunk0143_396_1	chr4	123130548	123130814	+	0	NA	intron (NM_145207, intron 14 of 15)	L1ME1|LINE|L1	207611	NM_145207	166378	Hs.709648	NM_145207	ENSG00000145375	SPATA5	AFG2|EHLMRS|SPAF	spermatogenesis associated 5	protein-coding	0.011278	0.310861	
chunk0087_108_1	chr18	32566506	32567025	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	55102	NR_003558	441818	Hs.549773	NR_003558	ENSG00000260389	WBP11P1	HsT3017	WW domain binding protein 11 pseudogene 1	pseudo	0.007707	0.444231	
chunk0158_345_1	chr5	133289805	133290605	+	0	NA	intron (NM_015082, intron 6 of 15)	intron (NM_015082, intron 6 of 15)	137501	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.015000	0.526841	
chunk0034_145_1	chr11	29985852	29986405	+	0	NA	Intergenic	Intergenic	-3735	NR_132652	106456574	Hs.128812	NR_132652	ENSG00000261340	LINC01616	n341006	long intergenic non-protein coding RNA 1616	ncRNA	0.001808	0.359206	221(AAGAACATGCTGTTCT,-,0.00),222(AGAACATGCTGTTCTA,+,0.00)
chunk0061_292_1	chr14	61638949	61639455	+	0	NA	intron (NR_039985, intron 1 of 2)	Tigger2b_Pri|DNA|TcMar-Tigger	-56199	NM_001530	3091	Hs.597216	NM_001530	ENSG00000100644	HIF1A	HIF-1-alpha|HIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78	hypoxia inducible factor 1 subunit alpha	protein-coding	0.019763	0.362919	232(TAGTACATACTGTACT,-,0.00),233(AGTACATACTGTACTA,+,0.00)
chunk0018_139_1	chr1	218624716	218624964	+	0	NA	intron (NR_031644, intron 3 of 6)	intron (NR_031644, intron 3 of 6)	182214	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.004032	0.393574	
chunk0130_420_1	chr3	140765836	140766124	+	0	NA	Intergenic	Intergenic	87956	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.006944	0.387543	
chunk0042_182_1	chr12	4857423	4857983	+	0	NA	Intergenic	Intergenic	48527	NM_002235	3742	Hs.306190	NM_002235	ENSG00000130035	KCNA6	HBK2|KV1.6|PPP1R96	potassium voltage-gated channel subfamily A member 6	protein-coding	0.023214	0.490196	222(GGGAACACAGTGTTAC,-,0.00),223(GGAACACAGTGTTACC,+,0.00),355(AGGGACAGTCTCTTCT,-,0.00),356(GGGACAGTCTCTTCTC,+,0.00)
chunk0014_404_1	chr1	182990856	182991646	+	0	NA	Intergenic	Intergenic	-32209	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.007595	0.364096	
chunk0126_103_1	chr3	75021306	75021741	+	0	NA	Intergenic	Intergenic	-192953	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.000000	0.321101	
chunk0135_128_1	chr3	187218181	187218835	+	0	NA	3' UTR (NM_001879, exon 16 of 16)	3' UTR (NM_001879, exon 16 of 16)	-10879	NR_110052	101929106	Hs.640145	NR_110052	ENSG00000198491	LOC101929106	-	uncharacterized LOC101929106	ncRNA	0.000000	0.444275	
chunk0199_380_1	chr9	13070569	13071117	+	0	NA	Intergenic	L1MEc|LINE|L1	-98210	NR_132976	106635615		NR_132976		SNORD137	-	small nucleolar RNA, C/D box 137	snoRNA	0.005474	0.378871	
chunk0158_267_1	chr5	131260832	131261427	+	0	NA	Intergenic	Intergenic	-2880	NM_020240	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.001681	0.315436	252(TAGAACAACATGTTCC,-,0.00),253(AGAACAACATGTTCCT,+,0.00)
chunk0158_276_1	chr5	131530742	131531242	+	0	NA	intron (NM_016340, intron 6 of 27)	intron (NM_016340, intron 6 of 27)	104244	NM_001164386	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.004000	0.365269	
chunk0126_466_1	chr3	87694725	87695050	+	0	NA	Intergenic	Intergenic	-287689	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.006154	0.368098	
chunk0029_115_1	chr10	98169677	98169880	+	0	NA	intron (NM_001256621, intron 3 of 7)	intron (NM_001256621, intron 3 of 7)	35154	NM_138469	27291	Hs.419800	NM_014472	ENSG00000166024	R3HCC1L	C10orf28|GIDRP86|GIDRP88|PSORT	R3H domain and coiled-coil containing 1 like	protein-coding	0.004926	0.284314	
chunk0031_246_1	chr10	127044109	127044813	+	0	NA	intron (NM_001290223, intron 21 of 51)	intron (NM_001290223, intron 21 of 51)	139052	NM_001380	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.019886	0.480851	
chunk0195_152_1	chr8	95317293	95318084	+	0	NA	intron (NR_038208, intron 2 of 3)	intron (NR_038208, intron 2 of 3)	-48454	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.003793	0.386364	424(AGGGACATACTGTTTC,-,0.00),425(GGGACATACTGTTTCT,+,0.00)
chunk0016_315_1	chr1	201511946	201512437	+	0	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-4932	NM_004078	1465	Hs.108080	NM_004078	ENSG00000159176	CSRP1	CRP|CRP1|CSRP|CYRP|D1S181E|HEL-141|HEL-S-286	cysteine and glycine rich protein 1	protein-coding	0.010183	0.556911	
chunk0057_161_1	chr13	100734408	100734632	+	0	NA	intron (NR_047687, intron 1 of 7)	MER110|LTR|ERV1	26195	NR_047687	100885778	Hs.602949	NR_047687	ENSG00000233009	NALCN-AS1	-	NALCN antisense RNA 1	ncRNA	0.000000	0.377778	
chunk0048_277_1	chr12	82436287	82436654	+	0	NA	intron (NM_032230, intron 7 of 11)	intron (NM_032230, intron 7 of 11)	-77665	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.002725	0.355978	143(AGGCACAGACTGTTCA,-,0.00),144(GGCACAGACTGTTCAG,+,0.00)
chunk0169_58_1	chr6	98463144	98463343	+	0	NA	Intergenic	Intergenic	-371461	NM_005604	5454	Hs.182505	NM_005604	ENSG00000184486	POU3F2	BRN2|N-Oct3|OCT7|OTF-7|OTF7|POUF3|brn-2|oct-7	POU class 3 homeobox 2	protein-coding	0.015075	0.415000	
chunk0148_73_1	chr5	2445609	2446131	+	0	NA	Intergenic	L3|LINE|CR1	-133669	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.007663	0.403442	
chunk0017_391_1	chr1	212354683	212354896	+	0	NA	intron (NM_006243, intron 8 of 12)	Tigger3a|DNA|TcMar-Tigger	1971	NR_004389	692157	Hs.707958	NR_004389	ENSG00000201544	SNORA16B	U98b	small nucleolar RNA, H/ACA box 16B	snoRNA	0.009390	0.378505	196(AAGAACATCCTGTACA,-,0.00),197(AGAACATCCTGTACAG,+,0.00)
chunk0155_342_1	chr5	96981396	96981876	+	0	NA	intron (NM_175920, intron 2 of 17)	MamRep1879|DNA|hAT-Tip100?	23184	NM_175920	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.008333	0.361746	
chunk0019_265_1	chr1	228124716	228125201	+	0	NA	Intergenic	Intergenic	-15126	NM_001242839	2987	Hs.376933	NM_000858	ENSG00000143774	GUK1	GMK	guanylate kinase 1	protein-coding	0.008247	0.452675	
chunk0065_211_1	chr14	100193028	100193515	+	0	NA	Intergenic	CpG	-33596	NM_206918	123099	Hs.159643	NM_206918	ENSG00000168350	DEGS2	C14orf66|DES2|FADS8	delta 4-desaturase, sphingolipid 2	protein-coding	0.067762	0.655738	
chunk0106_190_1	chr2	201466309	201466809	+	0	NA	intron (NM_001206864, intron 3 of 11)	intron (NM_001206864, intron 3 of 11)	14890	NM_001206864	55437	Hs.652338	NM_018571	ENSG00000082146	STRADB	ALS2CR2|CALS-21|ILPIP|ILPIPA|PAPK|PRO1038	STE20 related adaptor beta	protein-coding	0.004000	0.355289	234(TTGGACAACTTGTTCT,-,0.00),235(TGGACAACTTGTTCTC,+,0.00)
chunk0172_195_1	chr6	136607227	136607426	+	0	NA	intron (NM_005923, intron 18 of 29)	intron (NM_005923, intron 18 of 29)	-21788	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.005025	0.295000	
chunk0147_171_1	chr4	176335793	176336031	+	0	NA	Intergenic	L1ME3B|LINE|L1	15973	NM_021928	60559	Hs.42194	NM_021928	ENSG00000129128	SPCS3	PRO3567|SPC22/23|SPC3|YLR066W	signal peptidase complex subunit 3	protein-coding	0.004202	0.351464	
chunk0008_188_1	chr1	93180088	93180485	+	0	NA	promoter-TSS (NM_001306076)	promoter-TSS (NM_001306076)	403	NM_001167830	50999	Hs.482873	NM_016040	ENSG00000117500	TMED5	CGI-100|p24g2|p28	transmembrane p24 trafficking protein 5	protein-coding	0.073048	0.638191	
chunk0113_446_1	chr20	62791314	62791589	+	0	NA	Intergenic	Intergenic	-5002	NM_018270	55257	Hs.443260	NM_018270	ENSG00000101189	MRGBP	C20orf20|Eaf7|MRG15BP|URCC4	MRG domain binding protein	protein-coding	0.047273	0.612319	
chunk0003_399_1	chr1	39957375	39957770	+	0	NA	intron (NR_109896, intron 2 of 11)	intron (NR_109896, intron 2 of 11)	2460	NR_109896	84879	Hs.655177	NM_032793	ENSG00000168389	MFSD2A	MCPH15|MFSD2|NLS1	major facilitator superfamily domain containing 2A	protein-coding	0.002532	0.545455	163(TGGCACACTGTGTTCC,-,0.00),164(GGCACACTGTGTTCCT,+,0.00)
chunk0095_293_1	chr2	20198026	20198238	+	0	NA	Intergenic	Intergenic	27034	NM_002997	6382	Hs.224607	NM_002997	ENSG00000115884	SDC1	CD138|SDC|SYND1|syndecan	syndecan 1	protein-coding	0.009434	0.600939	
chunk0198_155_1	chr8	133072912	133073339	+	0	NA	intron (NM_001045557, intron 1 of 7)	MIRb|SINE|MIR	-12767	NM_006748	6503	Hs.75367	NM_006748	ENSG00000155926	SLA	SLA1|SLAP	Src like adaptor	protein-coding	0.007026	0.341121	
chunk0075_241_1	chr16	53103327	53103695	+	0	NA	intron (NM_025134, intron 1 of 38)	MIRb|SINE|MIR	48478	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.005435	0.392954	
chunk0049_181_1	chr12	92547358	92547720	+	0	NA	Intergenic	Intergenic	-119391	NM_001025232	574016	Hs.551199	NM_001025232	ENSG00000205057	CLLU1OS	-	chronic lymphocytic leukemia up-regulated 1 opposite strand	protein-coding	0.008287	0.432507	
chunk0026_147_1	chr10	62381776	62382069	+	0	NA	intron (NM_199450, intron 2 of 4)	L2b|LINE|L2	-6795	NR_104162	283045		NR_104162		LOC283045	-	uncharacterized LOC283045	ncRNA	0.010239	0.431973	
chunk0036_338_1	chr11	66743250	66743523	+	0	NA	Intergenic	Intergenic	-1350	NM_001302084	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.018315	0.536496	
chunk0053_397_1	chr13	36323569	36323863	+	0	NA	intron (NM_015087, intron 5 of 8)	L4_A_Mam|LINE|RTE-X	-22715	NR_045180	100507135	Hs.631781	NR_045180	ENSG00000120664	SPART-AS1	C13orf43|SPG20-AS1|SPG20OS	SPART antisense RNA 1	ncRNA	0.010204	0.352542	
chunk0030_134_1	chr10	113475443	113475648	+	0	NA	Intergenic	Intergenic	-75286	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.009756	0.509709	
chunk0019_347_1	chr1	229485145	229485735	+	0	NA	intron (NM_018230, intron 11 of 25)	intron (NM_018230, intron 11 of 25)	22901	NM_018230	55746	Hs.12457	NM_018230	ENSG00000069248	NUP133	GAMOS8|NPHS18|hNUP133	nucleoporin 133	protein-coding	0.003390	0.373942	
chunk0192_19_1	chr8	58455555	58455843	+	0	NA	Intergenic	L2a|LINE|L2	44435	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.003472	0.384083	
chunk0060_195_1	chr14	47889739	47890176	+	0	NA	Intergenic	Intergenic	-94943	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.004577	0.388128	
chunk0023_217_1	chr10	25659406	25659605	+	0	NA	intron (NR_108067, intron 2 of 4)	L1MA2|LINE|L1	7793	NR_108068	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.000000	0.300000	
chunk0024_204_1	chr10	36423710	36424117	+	0	NA	Intergenic	Intergenic	645611	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.009828	0.382353	
chunk0020_83_1	chr1	232753945	232754194	+	0	NA	Intergenic	Intergenic	-11354	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.012048	0.324000	
chunk0108_370_1	chr2	236703423	236703790	+	0	NA	Intergenic	L2c|LINE|L2	133869	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.005450	0.432065	
chunk0002_205_1	chr1	19547908	19548107	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-48970	NR_033757	440574	Hs.466662	NM_001032363	ENSG00000173436	MICOS10	C1orf151|MINOS1|MIO10|Mic10	mitochondrial contact site and cristae organizing system subunit 10	protein-coding	0.005025	0.330000	
chunk0116_277_1	chr21	39763015	39763408	+	0	NA	intron (NM_001080444, intron 2 of 8)	intron (NM_001080444, intron 2 of 8)	17804	NM_001080444	150084	Hs.422120	NM_001080444	ENSG00000183067	IGSF5	GSF5|JAM4	immunoglobulin superfamily member 5	protein-coding	0.010178	0.459391	
chunk0091_190_1	chr19	8394760	8395124	+	0	NA	intron (NM_004218, intron 1 of 4)	AluSz|SINE|Alu	-4251	NR_038237	100507567	Hs.637720	NR_038237	ENSG00000269386	RAB11B-AS1	MIR4999HG	RAB11B antisense RNA 1	ncRNA	0.032967	0.545205	
chunk0016_73_1	chr1	193761972	193762695	+	0	NA	Intergenic	Intergenic	457588	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.005533	0.306630	
chunk0116_266_1	chr21	39163839	39164276	+	0	NA	Intergenic	LTR40a|LTR|ERVL	19457	NR_049728	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.000000	0.415525	
chunk0151_123_1	chr5	43787654	43787869	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	-184531	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.009302	0.504630	
chunk0166_228_1	chr6	46988421	46988622	+	0	NA	Intergenic	MIRb|SINE|MIR	-33583	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.000000	0.351485	
chunk0111_441_1	chr20	35302388	35302904	+	0	NA	TTS (NM_001184977)	TTS (NM_001184977)	-10224	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.007752	0.406190	
chunk0188_45_1	chr8	6677176	6677851	+	0	NA	intron (NR_125386, intron 1 of 4)	intron (NR_125386, intron 1 of 4)	30696	NR_125386	100507530	Hs.490892	NR_125386		MCPH1-AS1	-	MCPH1 antisense RNA 1	ncRNA	0.014815	0.446746	
chunk0030_57_1	chr10	111924435	111924642	+	0	NA	Intergenic	MIR|SINE|MIR	259241	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.004831	0.360577	118(TAGTACATGGTGTACT,-,0.00),119(AGTACATGGTGTACTT,+,0.00)
chunk0037_195_1	chr11	74312094	74312768	+	0	NA	promoter-TSS (NR_110031)	promoter-TSS (NR_110031)	-755	NM_182904	283208	Hs.660541	NM_182904	ENSG00000149380	P4HA3	-	prolyl 4-hydroxylase subunit alpha 3	protein-coding	0.007418	0.429630	
chunk0203_144_1	chr9	85577478	85577677	+	0	NA	intron (NM_001286715, intron 23 of 24)	intron (NM_001286715, intron 23 of 24)	164452	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.000000	0.420000	167(CTGAACAGAAAGTACT,-,0.00),168(TGAACAGAAAGTACTG,+,0.00)
chunk0067_134_1	chr15	42931719	42932049	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-11075	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.003030	0.359517	
chunk0006_136_1	chr1	66112821	66113534	+	0	NA	intron (NM_001037340, intron 1 of 14)	intron (NM_001037340, intron 1 of 14)	-62459	NR_123718	101927139	Hs.127908	NR_123718	ENSG00000227466	LOC101927139	-	uncharacterized LOC101927139	ncRNA	0.002805	0.345938	
chunk0059_430_1	chr14	38293549	38294168	+	0	NA	Intergenic	L1PB2|LINE|L1	-37488	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.000000	0.329032	
chunk0128_381_1	chr3	113523078	113523783	+	0	NA	Intergenic	MER89-int|LTR|ERV1	-8243	NM_144718	152185	Hs.477144	NM_144718	ENSG00000163611	SPICE1	CCDC52|SPICE	spindle and centriole associated protein 1	protein-coding	0.007092	0.393768	
chunk0201_363_1	chr9	68512815	68513321	+	0	NA	intron (NM_021965, intron 10 of 10)	intron (NM_021965, intron 10 of 10)	27799	NM_153237	169693	Hs.663056	NM_153237	ENSG00000181778	TMEM252	C9orf71	transmembrane protein 252	protein-coding	0.003953	0.335306	
chunk0145_312_1	chr4	150462675	150462957	+	0	NA	intron (NM_001199282, intron 44 of 56)	intron (NM_001199282, intron 44 of 56)	-119109	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.003546	0.240283	
chunk0016_12_1	chr1	192768423	192768803	+	0	NA	Intergenic	Intergenic	-40426	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.000000	0.412073	
chunk0045_329_1	chr12	51009079	51009281	+	0	NA	promoter-TSS (NM_001174130)	promoter-TSS (NM_001174130)	90	NM_001174130	4891	Hs.505545	NM_000617	ENSG00000110911	SLC11A2	AHMIO1|DCT1|DMT1|NRAMP2	solute carrier family 11 member 2	protein-coding	0.019802	0.453202	
chunk0038_386_1	chr11	93522394	93522819	+	0	NA	intron (NM_020179, intron 1 of 2)	intron (NM_020179, intron 1 of 2)	20774	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.016471	0.471831	
chunk0131_217_1	chr3	149161899	149162469	+	0	NA	TTS (NR_046371)	TTS (NR_046371)	32600	NM_001308258	84343	Hs.558314	NM_032383	ENSG00000163755	HPS3	BLOC2S1|SUTAL	HPS3 biogenesis of lysosomal organelles complex 2 subunit 1	protein-coding	0.003509	0.350263	304(AGGGACAGATTGTTCC,-,0.00),305(GGGACAGATTGTTCCA,+,0.00)
chunk0029_32_1	chr10	96072982	96073643	+	0	NA	intron (NR_038444, intron 2 of 5)	L1ME2|LINE|L1	-8913	NR_036113	100422892		NR_036113	ENSG00000266407	MIR3157	mir-3157	microRNA 3157	ncRNA	0.007564	0.368580	
chunk0077_408_1	chr16	84995834	84996070	+	0	NA	5' UTR (NM_017740, exon 2 of 8)	5' UTR (NM_017740, exon 2 of 8)	15583	NM_001145548	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.012712	0.354430	113(TTGAACATTTTGTGCC,-,0.00),114(TGAACATTTTGTGCCG,+,0.00),146(AGGTGCATACTGTCCT,-,0.00)
chunk0150_182_1	chr5	34521253	34521924	+	0	NA	Intergenic	Intergenic	-134740	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.022355	0.500000	
chunk0105_326_1	chr2	190979898	190980181	+	0	NA	intron (NM_007315, intron 19 of 24)	intron (NM_007315, intron 19 of 24)	34211	NM_139266	6772	Hs.642990	NM_007315	ENSG00000115415	STAT1	CANDF7|IMD31A|IMD31B|IMD31C|ISGF-3|STAT91	signal transducer and activator of transcription 1	protein-coding	0.014134	0.549296	
chunk0121_359_1	chr3	24829486	24829685	+	0	NA	Intergenic	CpG	-308150	NR_039955									0.065327	0.625000	
chunk0123_375_1	chr3	48609714	48609936	+	0	NA	promoter-TSS (NM_003365)	promoter-TSS (NM_003365)	-160	NM_003365	7384	Hs.119251	NM_003365	ENSG00000010256	UQCRC1	D3S3191|QCR1|UQCR1	ubiquinol-cytochrome c reductase core protein 1	protein-coding	0.085586	0.659193	
chunk0212_441_1	chrX	154988038	154988391	+	0	NA	intron (NM_000132, intron 4 of 25)	LTR65|LTR|ERV1	34509	NM_000132	2157	Hs.632836	NM_000132	ENSG00000185010	F8	AHF|DXS1253E|F8B|F8C|FVIII|HEMA	coagulation factor VIII	protein-coding	0.000000	0.378531	
chunk0159_124_1	chr5	138868898	138869641	+	0	NA	TTS (NM_015564)	TTS (NM_015564)	-5961	NM_001290312	1495	Hs.445981	NM_001903	ENSG00000044115	CTNNA1	CAP102|MDPT2	catenin alpha 1	protein-coding	0.004038	0.353495	
chunk0004_278_1	chr1	48450363	48450815	+	0	NA	intron (NM_019073, intron 3 of 12)	intron (NM_019073, intron 3 of 12)	21619	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.002212	0.344371	170(CTGAACAAGATGTTCA,-,0.00),171(TGAACAAGATGTTCAG,+,0.00)
chunk0174_85_1	chr6	156469860	156470398	+	0	NA	Intergenic	L1MA4A|LINE|L1	-307801	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.005576	0.343228	
chunk0138_423_1	chr4	45099881	45100368	+	0	NA	Intergenic	Intergenic	-373490	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.004107	0.321721	
chunk0014_341_1	chr1	182217842	182218399	+	0	NA	intron (NR_104175, intron 2 of 2)	intron (NR_104175, intron 2 of 2)	95941	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.008977	0.360215	248(AGGAGCATTGTGTCCT,-,0.00),249(GGAGCATTGTGTCCTG,+,0.00)
chunk0197_188_1	chr8	121426647	121427182	+	0	NA	Intergenic	Intergenic	-212432	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.005607	0.399254	
chunk0170_439_1	chr6	118943267	118943550	+	0	NA	Intergenic	L1M1|LINE|L1	-8246	NM_153255	254394	Hs.279008	NM_017696	ENSG00000111877	MCM9	C6orf61|MCMDC1|ODG4|dJ329L24.1|dJ329L24.3	minichromosome maintenance 9 homologous recombination repair factor	protein-coding	0.000000	0.299296	
chunk0107_67_1	chr2	212224088	212224612	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	202010	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.003817	0.304762	
chunk0011_171_1	chr1	147694577	147694776	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-24164	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.000000	0.355000	
chunk0177_56_1	chr7	21086685	21087159	+	0	NA	Intergenic	MLT1H1-int|LTR|ERVL-MaLR	251491	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.000000	0.406316	
chunk0013_417_1	chr1	173257847	173258156	+	0	NA	intron (NR_037845, intron 2 of 2)	MER77B|LTR|ERVL	-50688	NM_003326	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.006472	0.454839	
chunk0187_51_1	chr8	1766604	1767044	+	0	NA	intron (NM_018941, intron 1 of 2).2	intron (NM_018941, intron 1 of 2).2	3120	NM_018941	2055	Hs.127675	NM_018941	ENSG00000182372	CLN8	C8orf61|EPMR|TLCD6	CLN8 transmembrane ER and ERGIC protein	protein-coding	0.018182	0.546485	
chunk0002_84_1	chr1	14426768	14427221	+	0	NA	Intergenic	L2b|LINE|L2	-171723	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.002208	0.488987	
chunk0062_439_1	chr14	75404532	75404904	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-23088	NM_001135047	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.013441	0.426273	
chunk0033_241_1	chr11	18063115	18063623	+	0	NA	Intergenic	L2c|LINE|L2	-22581	NM_004179	7166	Hs.591999	NM_004179	ENSG00000129167	TPH1	TPRH|TRPH	tryptophan hydroxylase 1	protein-coding	0.021654	0.434185	
chunk0115_33_1	chr21	20941877	20942135	+	0	NA	Intergenic	Intergenic	-56309	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.007752	0.339768	
chunk0185_271_1	chr7	130823275	130823590	+	0	NA	Intergenic	Intergenic	53378	NR_029503	407021		NR_029503	ENSG00000284032	MIR29A	MIRN29|MIRN29A|hsa-mir-29|hsa-mir-29a|miRNA29A|mir-29a	microRNA 29a	ncRNA	0.003175	0.443038	
chunk0057_411_1	chr13	109809595	109809794	+	0	NA	Intergenic	Intergenic	-23127	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.015075	0.545000	14(AGGAACAGGCTGTGCA,-,0.00),15(GGAACAGGCTGTGCAG,+,0.00)
chunk0209_364_1	chrX	53658750	53659006	+	0	NA	intron (NM_031407, intron 3 of 83)	L1MC1|LINE|L1	27851	NM_031407	10075	Hs.136905	NM_031407	ENSG00000086758	HUWE1	ARF-BP1|HECTH9|HSPC272|Ib772|LASU1|MRXST|MULE|URE-B1|UREB1	HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1	protein-coding	0.003906	0.365759	
chunk0100_81_1	chr2	107064685	107064884	+	0	NA	Intergenic	Intergenic	-177677	NM_032528	84620	Hs.98265	NM_032528	ENSG00000144057	ST6GAL2	SIAT2|ST6GalII	ST6 beta-galactoside alpha-2,6-sialyltransferase 2	protein-coding	0.030151	0.540000	
chunk0036_111_1	chr11	61425196	61426085	+	0	NA	intron (NM_024811, intron 2 of 9)	intron (NM_024811, intron 2 of 9)	4271	NM_024811	79869	Hs.718984	NM_024811	ENSG00000149532	CPSF7	CFIm59	cleavage and polyadenylation specific factor 7	protein-coding	0.003375	0.389888	
chunk0205_179_1	chr9	108961026	108961545	+	0	NA	intron (NM_003798, intron 11 of 18)	intron (NM_003798, intron 11 of 18)	26892	NM_017832	54942	Hs.29276	NM_017832	ENSG00000119328	ABITRAM	C9orf6|CG-8|FAM206A|Simiate	actin binding transcription modulator	protein-coding	0.005780	0.426923	
chunk0007_155_1	chr1	79720642	79721063	+	0	NA	Intergenic	L1MD1|LINE|L1	-714042	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.000000	0.317536	
chunk0144_82_1	chr4	128163492	128163949	+	0	NA	intron (NM_018078, intron 12 of 19)	L1MC5|LINE|L1	102454	NM_001278604	55132	Hs.654971	NM_018078	ENSG00000138709	LARP1B	LARP2	La ribonucleoprotein domain family member 1B	protein-coding	0.006565	0.340611	
chunk0038_20_1	chr11	80941363	80941908	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-178832	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003670	0.274725	
chunk0126_116_1	chr3	75648808	75649439	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-15213	NM_001124759	100288801		NM_001124759	ENSG00000172969	FRG2C	-	FSHD region gene 2 family member C	protein-coding	0.003170	0.469937	
chunk0089_300_1	chr18	63681436	63682030	+	0	NA	Intergenic	Intergenic	-19770	NM_006919	6317	Hs.227948	NM_006919	ENSG00000057149	SERPINB3	HsT1196|SCC|SCCA-1|SCCA-PD|SCCA1|SSCA1|T4-A	serpin family B member 3	protein-coding	0.001684	0.371429	
chunk0008_182_1	chr1	93097867	93098443	+	0	NA	intron (NM_001164393, intron 1 of 12)	L2b|LINE|L2	18920	NM_007358	22823	Hs.31016	NM_007358	ENSG00000143033	MTF2	M96|PCL2|TDRD19A|dJ976O13.2	metal response element binding transcription factor 2	protein-coding	0.003472	0.367418	
chunk0036_274_1	chr11	65199777	65200337	+	0	NA	intron (NM_005186, intron 10 of 21)	AluJb|SINE|Alu	-13783	NM_001004326	440044	Hs.532372	NM_001004326	ENSG00000197847	SLC22A20P	Oat6|SLC22A20	solute carrier family 22 member 20, pseudogene	pseudo	0.016071	0.454545	
chunk0022_71_1	chr10	8790369	8790883	+	0	NA	Intergenic	Intergenic	-107363	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.003891	0.355340	
chunk0120_74_1	chr3	3486623	3487234	+	0	NA	Intergenic	Intergenic	-307211	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.004910	0.307190	
chunk0069_270_1	chr15	64740385	64740930	+	0	NA	3' UTR (NM_194272, exon 8 of 8)	3' UTR (NM_194272, exon 8 of 8)	21858	NR_031674	100302184		NR_031674	ENSG00000221033	MIR1272	MIRN1272|hsa-mir-1272|mir-1272	microRNA 1272	ncRNA	0.025688	0.582418	211(GAGAACAAACTGTACA,-,0.00),212(AGAACAAACTGTACAC,+,0.00)
chunk0200_51_1	chr9	15510931	15511338	+	0	NA	promoter-TSS (NM_033222)	promoter-TSS (NM_033222)	-129	NM_033222	11168	Hs.658434	NM_021144	ENSG00000164985	PSIP1	DFS70|LEDGF|PAIP|PSIP2|p52|p75	PC4 and SFRS1 interacting protein 1	protein-coding	0.095823	0.622549	
chunk0029_406_1	chr10	109899989	109900304	+	0	NA	intron (NM_001167604, intron 3 of 19)	intron (NM_001167604, intron 3 of 19)	23407	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.012698	0.458861	
chunk0175_164_1	chr7	4524629	4524957	+	0	NA	Intergenic	AluJo|SINE|Alu	-157506	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.012195	0.474164	
chunk0116_84_1	chr21	34730802	34731050	+	0	NA	intron (NR_024351, intron 4 of 5)	intron (NR_024351, intron 4 of 5)	6256	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.008065	0.469880	
chunk0076_351_1	chr16	71684399	71684893	+	0	NA	intron (NM_001289003, intron 4 of 17)	intron (NM_001289003, intron 4 of 17)	14055	NR_033337	100379141	Hs.725116	NR_033337	ENSG00000263666	SNORA70D	U70D	small nucleolar RNA, H/ACA box 70D	snoRNA	0.020243	0.466667	379(GAGTACACAATGATCC,-,0.00),380(AGTACACAATGATCCC,+,0.00)
chunk0212_19_1	chrY	8905760	8906010	+	0	NA	Intergenic	Intergenic	-88503	NR_001548	83866	Hs.122396	NR_001548	ENSG00000180910	TTTY11	NCRNA00134|TTY11	testis-specific transcript, Y-linked 11	ncRNA	0.004000	0.326693	
chunk0029_163_1	chr10	99812004	99812801	+	0	NA	intron (NM_000392, intron 15 of 31)	intron (NM_000392, intron 15 of 31)	29804	NM_000392	1244	Hs.368243	NM_000392	ENSG00000023839	ABCC2	ABC30|CMOAT|DJS|MRP2|cMRP	ATP binding cassette subfamily C member 2	protein-coding	0.002509	0.453634	
chunk0179_379_1	chr7	51263540	51264257	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	52920	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.006974	0.466574	
chunk0078_437_1	chr16	89506069	89506461	+	0	NA	Intergenic	MIRc|SINE|MIR	-2123	NM_003119	6687	Hs.185597	NM_003119	ENSG00000197912	SPG7	CAR|CMAR|PGN|SPG5C	SPG7 matrix AAA peptidase subunit, paraplegin	protein-coding	0.007653	0.458015	
chunk0144_47_1	chr4	126553421	126553620	+	0	NA	Intergenic	MER70B|LTR|ERVL	1046261	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.010050	0.465000	146(AGAAACAGGATGTCCT,-,0.00),147(GAAACAGGATGTCCTT,+,0.00)
chunk0155_348_1	chr5	97021469	97021814	+	0	NA	intron (NM_175920, intron 13 of 17)	intron (NM_175920, intron 13 of 17)	63189	NM_175920	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.002899	0.332370	
chunk0201_12_1	chr9	32947542	32948117	+	0	NA	Intergenic	L1M5|LINE|L1	53747	NR_036579									0.006957	0.309028	
chunk0139_401_1	chr4	63280121	63280464	+	0	NA	Intergenic	L1PA15|LINE|L1	-1118527	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.005831	0.316860	
chunk0138_125_1	chr4	36552968	36553509	+	0	NA	Intergenic	Intergenic	-126810	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.001848	0.370849	
chunk0201_73_1	chr9	34247803	34248002	+	0	NA	intron (NR_033243, intron 5 of 7)	L1ME3G|LINE|L1	68897	NM_001171203	51271	Hs.268963	NM_016525	ENSG00000165006	UBAP1	NAG20|SPG80|UAP|UBAP|UBAP-1	ubiquitin associated protein 1	protein-coding	0.000000	0.315000	
chunk0036_332_1	chr11	66616978	66617177	+	0	NA	intron (NM_001198846, intron 1 of 1)	CpG	495	NM_001198836	10432	Hs.533712	NM_006328	ENSG00000239306	RBM14	COAA|PSP2|SIP|SYTIP1|TMEM137	RNA binding motif protein 14	protein-coding	0.135678	0.715000	
chunk0054_325_1	chr13	49187628	49188128	+	0	NA	intron (NM_014923, intron 14 of 23)	intron (NM_014923, intron 14 of 23)	-32460	NM_001507	2862	Hs.248126	NM_001507	ENSG00000102539	MLNR	GPR38|MTLR1	motilin receptor	protein-coding	0.016000	0.363273	
chunk0077_389_1	chr16	84742479	84742730	+	0	NA	intron (NM_001272075, intron 4 of 14)	intron (NM_001272075, intron 4 of 14)	42655	NR_073577	9100	Hs.136778	NM_005153	ENSG00000103194	USP10	UBPO	ubiquitin specific peptidase 10	protein-coding	0.027888	0.531746	
chunk0140_360_1	chr4	74166941	74167140	+	0	NA	intron (NM_001144978, intron 1 of 7)	L1M3e|LINE|L1	8928	NM_001144978	441024	Hs.721011	NM_001004346	ENSG00000163738	MTHFD2L	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like	protein-coding	0.000000	0.580000	
chunk0123_307_1	chr3	47032944	47033455	+	0	NA	intron (NM_014159, intron 18 of 20)	L2c|LINE|L2	21657	NR_024046	100129354	Hs.201522	NR_024046		NRADDP	-	neurotrophin receptor associated death domain, pseudogene	pseudo	0.001957	0.398438	
chunk0058_81_1	chr14	21305144	21305626	+	0	NA	intron (NM_020366, intron 5 of 23)	L1MC1|LINE|L1	17408	NM_020366	57096	Hs.126035	NM_020366	ENSG00000092200	RPGRIP1	CORD13|LCA6|RGI1|RGRIP|RPGRIP|RPGRIP1d	RPGR interacting protein 1	protein-coding	0.010373	0.385093	
chunk0156_252_1	chr5	108981240	108981793	+	0	NA	intron (NM_001308028, intron 11 of 17)	intron (NM_001308028, intron 11 of 17)	56910	NM_001308031	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.003617	0.324910	
chunk0211_136_1	chrX	112827923	112828214	+	0	NA	intron (NM_133265, intron 2 of 11)	intron (NM_133265, intron 2 of 11)	-4942	NM_001113490	154796	Hs.528051	NM_133265	ENSG00000126016	AMOT	-	angiomotin	protein-coding	0.000000	0.404110	
chunk0046_321_1	chr12	62537166	62537600	+	0	NA	intron (NM_001278469, intron 15 of 35)	intron (NM_001278469, intron 15 of 35)	66051	NR_121682	283416	Hs.375881	NM_175895	ENSG00000221949	LINC01465	C12orf61	long intergenic non-protein coding RNA 1465	ncRNA	0.000000	0.285057	
chunk0138_283_1	chr4	40587792	40588336	+	0	NA	intron (NM_001098634, intron 1 of 6)	intron (NM_001098634, intron 1 of 6)	41802	NM_001098634	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.007353	0.451376	
chunk0167_280_1	chr6	70404229	70404785	+	0	NA	Intergenic	Intergenic	-8897	NM_001105531	57579	Hs.211700	NM_020819	ENSG00000082269	FAM135A	KIAA1411	family with sequence similarity 135 member A	protein-coding	0.000000	0.289048	
chunk0151_36_1	chr5	41969171	41969542	+	0	NA	Intergenic	L1ME3B|LINE|L1	44102	NM_033484	26272	Hs.165575	NM_012176	ENSG00000151876	FBXO4	FBX4	F-box protein 4	protein-coding	0.002695	0.341398	
chunk0011_214_1	chr1	150174386	150174711	+	0	NA	Intergenic	Intergenic	23962	NM_001304723	51177	Hs.438824	NM_016274	ENSG00000023902	PLEKHO1	CKIP-1|CKIP1|JBP|OC120	pleckstrin homology domain containing O1	protein-coding	0.012308	0.383436	3(TGGCCAGGCTGTTCTC,+,0.00)
chunk0149_9_1	chr5	15824303	15824597	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-110732	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.020408	0.389831	
chunk0021_164_1	chr10	5234049	5234534	+	0	NA	Intergenic	Intergenic	37456	NM_001818	1109	Hs.567245	NM_001818	ENSG00000198610	AKR1C4	3-alpha-HSD|C11|CDR|CHDR|DD-4|DD4|HAKRA	aldo-keto reductase family 1 member C4	protein-coding	0.006186	0.409465	
chunk0005_223_1	chr1	59354881	59355172	+	0	NA	intron (NM_001113411, intron 4 of 16)	L2a|LINE|L2	44948	NM_001244714	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.006873	0.496575	
chunk0050_370_1	chr12	108538149	108538657	+	0	NA	intron (NM_014706, intron 7 of 18)	L1MC5|LINE|L1	22986	NM_014706	9733	Hs.584842	NM_014706	ENSG00000075856	SART3	DSAP1|P100|RP11-13G14|TIP110|p110|p110(nrb)	spliceosome associated factor 3, U4/U6 recycling protein	protein-coding	0.011811	0.363458	
chunk0093_329_1	chr19	54172543	54172956	+	0	NA	TTS (NM_024298)	TTS (NM_024298)	501	NM_001145303	147798	Hs.355126	NM_144686	ENSG00000167608	TMC4	-	transmembrane channel like 4	protein-coding	0.004843	0.603865	
chunk0111_19_1	chr20	21989385	21989961	+	0	NA	Intergenic	Intergenic	-64417	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.012153	0.339688	
chunk0065_53_1	chr15	22801696	22801996	+	0	NA	intron (NM_144599, intron 1 of 4)	intron (NM_144599, intron 1 of 4)	15214	NM_144599	123606	Hs.511797	NM_144599	ENSG00000170113	NIPA1	FSP3|SLC57A1|SPG6	NIPA magnesium transporter 1	protein-coding	0.013333	0.445183	
chunk0001_54_1	chr1	1919191	1919390	+	0	NA	promoter-TSS (NM_178545)	promoter-TSS (NM_178545)	11	NM_178545	339456	Hs.123423	NM_178545	ENSG00000178821	TMEM52	-	transmembrane protein 52	protein-coding	0.100503	0.735000	
chunk0133_414_1	chr3	174538981	174539531	+	0	NA	Intergenic	Intergenic	-320065	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.000000	0.257713	
chunk0139_8_1	chr4	47870708	47870907	+	0	NA	intron (NR_103795, intron 19 of 23)	L1MC4|LINE|L1	-32701	NM_001278585	10699	Hs.518618	NM_006587	ENSG00000145244	CORIN	ATC2|CRN|Lrp4|PEE5|TMPRSS10	corin, serine peptidase	protein-coding	0.000000	0.375000	
chunk0005_185_1	chr1	58785426	58785886	+	0	NA	intron (NR_108106, intron 1 of 1)	intron (NR_108106, intron 1 of 1)	505	NR_034014	100131060	Hs.680604	NR_034014	ENSG00000234807	LINC01135	-	long intergenic non-protein coding RNA 1135	ncRNA	0.028261	0.548807	
chunk0117_96_1	chr22	17569434	17569739	+	0	NA	intron (NM_001303484, intron 1 of 9)	intron (NM_001303484, intron 1 of 9)	6147	NM_001303484	83733	Hs.282982	NM_031481	ENSG00000182902	SLC25A18	GC2	solute carrier family 25 member 18	protein-coding	0.016393	0.503268	
chunk0093_208_1	chr19	49614064	49614353	+	0	NA	intron (NM_020719, intron 6 of 13)	intron (NM_020719, intron 6 of 13)	22553	NM_020719	57479	Hs.590971	NM_020719	ENSG00000126464	PRR12	KIAA1205	proline rich 12	protein-coding	0.027682	0.500000	
chunk0157_244_1	chr5	119742233	119742504	+	0	NA	Intergenic	Intergenic	112809	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.007380	0.319853	
chunk0193_312_1	chr8	78288989	78289221	+	0	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	-226996	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.000000	0.218884	
chunk0151_425_1	chr5	55727993	55728392	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-9825	NM_024415	54514	Hs.223581	NM_019039	ENSG00000152670	DDX4	VASA	DEAD-box helicase 4	protein-coding	0.012531	0.442500	180(GAGGACACAGTGTTCT,-,0.00),181(AGGACACAGTGTTCTT,+,0.00)
chunk0182_193_1	chr7	95955627	95956298	+	0	NA	intron (NM_001278421, intron 5 of 15)	intron (NM_001278421, intron 5 of 15)	183456	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.008942	0.394345	
chunk0190_450_1	chr8	42036688	42036997	+	0	NA	intron (NM_001305878, intron 2 of 13)	intron (NM_001305878, intron 2 of 13)	15184	NM_001305878	7994	Hs.491577	NM_006766	ENSG00000083168	KAT6A	MOZ|MRD32|MYST-3|MYST3|RUNXBP2|ZC2HC6A|ZNF220	lysine acetyltransferase 6A	protein-coding	0.006472	0.419355	
chunk0179_79_1	chr7	44338335	44338911	+	0	NA	Intergenic	L1ME3A|LINE|L1	-12992	NM_172083	816	Hs.351887	NM_001220	ENSG00000058404	CAMK2B	CAM2|CAMK2|CAMKB|MRD54	calcium/calmodulin dependent protein kinase II beta	protein-coding	0.003472	0.348354	
chunk0002_277_1	chr1	22063008	22063214	+	0	NA	intron (NM_044472, intron 1 of 5)	(T)n|Simple_repeat|Simple_repeat	10484	NM_001039802	998	Hs.467637	NM_001791	ENSG00000070831	CDC42	CDC42Hs|G25K|TKS	cell division cycle 42	protein-coding	0.000000	0.338164	
chunk0116_205_1	chr21	37444016	37444331	+	0	NA	intron (NM_130436, intron 1 of 10)	intron (NM_130436, intron 1 of 10)	23873	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.009524	0.389241	
chunk0002_266_1	chr1	21623585	21623874	+	0	NA	intron (NM_001145657, intron 4 of 26)	intron (NM_001145657, intron 4 of 26)	28126	NM_001145658	5909	Hs.148178	NM_002885	ENSG00000076864	RAP1GAP	RAP1GA1|RAP1GAP1|RAP1GAPII|RAPGAP	RAP1 GTPase activating protein	protein-coding	0.017301	0.541379	
chunk0102_73_1	chr2	143001500	143001954	+	0	NA	intron (NM_003937, intron 10 of 13)	MIRb|SINE|MIR	124101	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.002203	0.400000	
chunk0186_279_1	chr7	142088018	142088439	+	0	NA	intron (NM_004668, intron 38 of 47)	intron (NM_004668, intron 38 of 47)	-23521	NM_001293626	93432	Hs.647098	NM_001008748	ENSG00000257743	MGAM2	-	maltase-glucoamylase 2 (putative)	protein-coding	0.004751	0.454976	
chunk0052_279_1	chr12	124231967	124232368	+	0	NA	intron (NM_001204299, intron 3 of 4)	intron (NM_001204299, intron 3 of 4)	-56997	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.024938	0.557214	
chunk0037_2_1	chr11	68839378	68839596	+	0	NA	intron (NM_001031847, intron 1 of 18)	CpG	2444	NM_001876	1374	Hs.503043	NM_001876	ENSG00000110090	CPT1A	CPT1|CPT1-L|L-CPT1	carnitine palmitoyltransferase 1A	protein-coding	0.091743	0.684932	
chunk0089_251_1	chr18	62226402	62226894	+	0	NA	intron (NM_020854, intron 5 of 28)	intron (NM_020854, intron 5 of 28)	39357	NM_020854	57614	Hs.465323	NM_020854	ENSG00000134444	RELCH	HsT3308|HsT885|KIAA1468	RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing	protein-coding	0.000000	0.247465	
chunk0206_171_1	chr9	122279196	122279527	+	0	NA	intron (NM_001173512, intron 2 of 5)	MIRc|SINE|MIR	8497	NM_199177	92399	Hs.368011	NM_138777	ENSG00000148187	MRRF	MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding	0.003021	0.331325	
chunk0135_122_1	chr3	187040980	187041881	+	0	NA	intron (NM_173217, intron 3 of 6)	intron (NM_173217, intron 3 of 6)	19553	NM_003032	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.006659	0.440133	293(GTGAACACCCAGTCCA,-,0.00)
chunk0023_343_1	chr10	29546660	29547232	+	0	NA	intron (NM_021738, intron 6 of 37)	intron (NM_021738, intron 6 of 37)	-1849	NR_030335	693189		NR_030335	ENSG00000207612	MIR604	MIRN604|hsa-mir-604	microRNA 604	ncRNA	0.006993	0.329843	
chunk0054_46_1	chr13	41610497	41610748	+	0	NA	intron (NM_015058, intron 39 of 44)	intron (NM_015058, intron 39 of 44)	-42227	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.015936	0.464286	
chunk0061_298_1	chr14	61735352	61735621	+	0	NA	intron (NM_001243084, intron 8 of 14)	L2c|LINE|L2	13603	NR_045406	100750247	Hs.597216	NR_045406		HIF1A-AS2	3'aHIF-1A|aHIF	HIF1A antisense RNA 2	ncRNA	0.000000	0.359259	
chunk0085_29_1	chr18	448194	448520	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	52372	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.012270	0.388379	
chunk0094_70_1	chr2	3469994	3470687	+	0	NA	intron (NM_016030, intron 9 of 11)	intron (NM_016030, intron 9 of 11)	47407	NM_001306077	55256	Hs.502773	NM_018269	ENSG00000182551	ADI1	APL1|ARD|Fe-ARD|HMFT1638|MTCBP1|Ni-ARD|SIPL|mtnD	acireductone dioxygenase 1	protein-coding	0.031746	0.551873	284(AAGAACACCCTGTTCC,-,0.00),285(AGAACACCCTGTTCCA,+,0.00)
chunk0133_164_1	chr3	169819414	169820170	+	0	NA	Intergenic	Intergenic	-2130	NM_001080460	344657	Hs.319484	NM_001080460	ENSG00000188306	LRRIQ4	LRRC64	leucine rich repeats and IQ motif containing 4	protein-coding	0.002646	0.376486	
chunk0082_384_1	chr17	60524530	60525057	+	0	NA	intron (NM_006380, intron 1 of 12)	intron (NM_006380, intron 1 of 12)	1447	NM_001282476	10513	Hs.84084	NM_006380	ENSG00000062725	APPBP2	APP-BP2|HS.84084|PAT1	amyloid beta precursor protein binding protein 2	protein-coding	0.009488	0.392045	
chunk0183_288_1	chr7	107642973	107643261	+	0	NA	Intergenic	LTR24B|LTR|ERV1	-17518	NM_000441	5172	Hs.571246	NM_000441	ENSG00000091137	SLC26A4	DFNB4|EVA|PDS|TDH2B	solute carrier family 26 member 4	protein-coding	0.006944	0.432526	
chunk0198_453_1	chr8	144233322	144233879	+	0	NA	intron (NM_032450, intron 14 of 43)	L1MB3|LINE|L1	29137	NR_107057	102465906		NR_107057	ENSG00000284054	MIR7112	MIR7112-1|MIR7112-2|hsa-mir-7112|hsa-mir-7112-1|hsa-mir-7112-2	microRNA 7112	ncRNA	0.025135	0.544803	
chunk0089_349_1	chr18	66004291	66004547	+	0	NA	Intergenic	L1M1|LINE|L1	253498	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.003906	0.498054	
chunk0021_414_1	chr1	246845739	246846097	+	0	NA	intron (NM_015446, intron 33 of 35)	MER63B|DNA|hAT-Blackjack	56301	NR_015422	149134	Hs.720494	NM_207326		LINC01341	-	long intergenic non-protein coding RNA 1341	ncRNA	0.002793	0.415042	
chunk0140_279_1	chr4	72242533	72242992	+	0	NA	Intergenic	Intergenic	203630	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.008715	0.382609	
chunk0196_54_1	chr8	102107800	102108392	+	0	NA	intron (NM_001040628, intron 1 of 7)	intron (NM_001040628, intron 1 of 7)	16238	NM_001040625	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.008446	0.505902	341(GGGGACTGCCTGTGCT,-,0.00),342(GGGACTGCCTGTGCTC,+,0.00)
chunk0150_188_1	chr5	34615752	34616143	+	0	NA	Intergenic	Intergenic	-40381	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.010230	0.479592	
chunk0004_272_1	chr1	48396074	48396631	+	0	NA	intron (NM_019073, intron 7 of 12)	L1MB3|LINE|L1	75856	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.005386	0.335125	
chunk0060_2_1	chr14	39025916	39026230	+	0	NA	Intergenic	Intergenic	77160	NM_006364	10484	Hs.272927	NM_006364	ENSG00000100934	SEC23A	CLSD|hSec23A	Sec23 homolog A, coat complex II component	protein-coding	0.006369	0.447619	
chunk0179_260_1	chr7	49162542	49163405	+	0	NA	Intergenic	Intergenic	238412	NR_003595									0.006952	0.365741	
chunk0038_94_1	chr11	83474542	83475051	+	0	NA	intron (NM_001142699, intron 22 of 27)	intron (NM_001142699, intron 22 of 27)	-188389	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.009823	0.376471	266(GAGCACATCAAGTTCC,-,0.00),267(AGCACATCAAGTTCCC,+,0.00)
chunk0001_120_1	chr1	4596829	4597565	+	0	NA	Intergenic	Intergenic	-57848	NM_001042478	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.017663	0.413840	
chunk0208_391_1	chrX	28889707	28890263	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	302421	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.010791	0.364452	
chunk0142_370_1	chr4	101974981	101975186	+	0	NA	intron (NM_017935, intron 7 of 16)	intron (NM_017935, intron 7 of 16)	161257	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.000000	0.378641	
chunk0138_31_1	chr4	31141282	31141614	+	0	NA	intron (NM_001173523, intron 2 of 2)	intron (NM_001173523, intron 2 of 2)	-29696	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.003012	0.312312	
chunk0054_11_1	chr13	40446354	40446907	+	0	NA	intron (NR_024506, intron 5 of 5)	MLT1C|LTR|ERVL-MaLR	34376	NR_024507	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.005425	0.431408	
chunk0189_210_1	chr8	24244290	24244517	+	0	NA	Intergenic	MIRb|SINE|MIR	-49637	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.004405	0.346491	
chunk0048_205_1	chr12	81381852	81382517	+	0	NA	intron (NM_001220474, intron 7 of 30)	L2a|LINE|L2	-12770	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.004511	0.394895	
chunk0058_373_1	chr14	29224997	29225196	+	0	NA	Intergenic	Intergenic	452392	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.015075	0.390000	
chunk0134_407_1	chr3	183182685	183183101	+	0	NA	intron (NM_015078, intron 27 of 29)	intron (NM_015078, intron 27 of 29)	-20014	NM_014398	27074	Hs.518448	NM_014398	ENSG00000078081	LAMP3	CD208|DC LAMP|DC-LAMP|DCLAMP|LAMP|LAMP-3|TSC403	lysosomal associated membrane protein 3	protein-coding	0.014423	0.561151	
chunk0202_434_1	chr9	81855355	81855959	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-57780	NR_026851	347127	Hs.215235	NM_198509	ENSG00000240632	SPATA31D5P	FAM75D5|FAM75D5P	SPATA31 subfamily D member 5, pseudogene	pseudo	0.003311	0.343802	
chunk0131_343_1	chr3	151475758	151476315	+	0	NA	Intergenic	Intergenic	-17327	NM_178822	285313	Hs.58561	NM_178822	ENSG00000152580	IGSF10	CMF608	immunoglobulin superfamily member 10	protein-coding	0.008977	0.356631	
chunk0172_2_1	chr6	132295271	132296006	+	0	NA	TTS (NM_015529)	TTS (NM_015529)	105896	NM_015529	26002	Hs.6909	NM_015529	ENSG00000079931	MOXD1	MOX|PRO5780|dJ248E1.1	monooxygenase DBH like 1	protein-coding	0.004082	0.304348	
chunk0192_441_1	chr8	69781041	69781247	+	0	NA	intron (NM_030958, intron 2 of 9)	intron (NM_030958, intron 2 of 9)	52025	NM_001146009	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.004854	0.473430	137(GTGACACACTGTACTT,+,0.00)
chunk0151_97_1	chr5	43122215	43122444	+	0	NA	intron (NR_123719, intron 2 of 7)	intron (NR_123719, intron 2 of 7)	821	NM_001297548	7690	Hs.535804	NM_003432	ENSG00000172262	ZNF131	ZBTB35|pHZ-10	zinc finger protein 131	protein-coding	0.017467	0.447826	
chunk0031_86_1	chr10	123254916	123255385	+	0	NA	Intergenic	(CAC)n|Simple_repeat|Simple_repeat	100906	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.002132	0.504255	
chunk0004_334_1	chr1	50473515	50473817	+	0	NA	intron (NM_007051, intron 18 of 18)	intron (NM_007051, intron 18 of 18)	-50219	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.000000	0.432343	
chunk0069_369_1	chr15	67232403	67233016	+	0	NA	intron (NM_024666, intron 4 of 9)	intron (NM_024666, intron 4 of 9)	22027	NM_024666	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.009788	0.390879	
chunk0012_190_1	chr1	159712033	159712936	+	0	NA	3' UTR (NM_000567, exon 2 of 2)	3' UTR (NM_000567, exon 2 of 2)	2105	NM_000567	1401	Hs.76452	NM_000567	ENSG00000132693	CRP	PTX1	C-reactive protein	protein-coding	0.006645	0.466814	
chunk0168_436_1	chr6	95681691	95682126	+	0	NA	Intergenic	PABL_A|LTR|ERV1	104411	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.004598	0.401376	178(TGGGACAGGGTGTTCC,-,0.00),179(GGGACAGGGTGTTCCT,+,0.00)
chunk0147_214_1	chr4	180574872	180575267	+	0	NA	Intergenic	Intergenic	584080	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.005063	0.353535	
chunk0126_405_1	chr3	85074991	85075257	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	-12860	NR_132777	106635529		NR_132777		SNORA95	-	small nucleolar RNA, H/ACA box 95	snoRNA	0.000000	0.348315	
chunk0171_61_1	chr6	121310612	121311362	+	0	NA	intron (NM_152730, intron 3 of 31)	intron (NM_152730, intron 3 of 31)	23513	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.000000	0.336884	407(GGGAACTGAATGTCCC,-,0.00),408(GGAACTGAATGTCCCA,+,0.00)
chunk0143_152_1	chr4	110058517	110059249	+	0	NA	intron (NM_001130721, intron 4 of 4)	intron (NM_001130721, intron 4 of 4)	139732	NM_001130721	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.004098	0.392906	313(CTGTACAATCTGTACC,-,0.00)
chunk0047_19_1	chr12	65567783	65568474	+	0	NA	intron (NR_120434, intron 4 of 4)	intron (NR_120434, intron 4 of 4)	74244	NR_120432	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.005789	0.419075	
chunk0084_257_1	chr17	79045948	79046334	+	0	NA	intron (NM_198593, intron 2 of 3)	intron (NM_198593, intron 2 of 3)	11842	NM_198593	114897	Hs.201398	NM_030968	ENSG00000173918	C1QTNF1	CTRP1|GIP|ZSIG37	C1q and TNF related 1	protein-coding	0.044041	0.550388	
chunk0063_149_1	chr14	79833827	79834368	+	0	NA	intron (NM_138970, intron 5 of 5)	intron (NM_138970, intron 5 of 5)	-377322	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.007394	0.365314	
chunk0207_139_1	chr9	129432523	129433214	+	0	NA	Intergenic	Intergenic	-55792	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.013025	0.598266	367(CAGAACACAGCGTGCT,-,0.00),368(AGAACACAGCGTGCTC,+,0.00),407(TGTAACACACTGTTCC,-,0.00),408(GTAACACACTGTTCCA,+,0.00)
chunk0052_360_1	chr12	127306610	127306963	+	0	NA	Intergenic	Intergenic	33286	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.002833	0.347458	313(GAAAACAGATTGTTCT,-,0.00),314(AAAACAGATTGTTCTG,+,0.00)
chunk0088_137_1	chr18	45877326	45877874	+	0	NA	intron (NM_020964, intron 34 of 43)	intron (NM_020964, intron 34 of 43)	52020	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.010949	0.389800	
chunk0124_314_1	chr3	58040132	58040559	+	0	NA	intron (NM_001164317, intron 1 of 46)	intron (NM_001164317, intron 1 of 46)	31945	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.009368	0.500000	
chunk0117_37_1	chr22	12099511	12099845	+	0	NA	Intergenic	Intergenic	202272	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.000000	0.304478	
chunk0041_96_1	chr11	124657024	124657439	+	0	NA	intron (NM_170601, intron 3 of 9)	intron (NM_170601, intron 3 of 9)	-16613	NM_017425	53340	Hs.286233	NM_017425	ENSG00000064199	SPA17	CT22|SP17|SP17-1	sperm autoantigenic protein 17	protein-coding	0.007229	0.466346	
chunk0059_3_1	chr14	29654556	29655054	+	0	NA	intron (NM_002742, intron 4 of 17)	intron (NM_002742, intron 4 of 17)	272888	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.010040	0.360721	
chunk0154_294_1	chr5	83106992	83107531	+	0	NA	intron (NM_022550, intron 2 of 7)	intron (NM_022550, intron 2 of 7)	29763	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.003711	0.294444	
chunk0130_280_1	chr3	136366304	136366865	+	0	NA	intron (NM_005862, intron 25 of 33)	intron (NM_005862, intron 25 of 33)	116259	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.000000	0.352313	
chunk0029_413_1	chr10	109935073	109935394	+	0	NA	Intergenic	Intergenic	-11680	NR_030724									0.009346	0.512422	227(GAAAACAACCTGTTCC,-,0.00),228(AAAACAACCTGTTCCC,+,0.00)
chunk0187_231_1	chr7	152460443	152460820	+	0	NA	Intergenic	L2a|LINE|L2	-3493	NR_027387	100128822	Hs.647112	NR_027387	ENSG00000261455	LINC01003	-	long intergenic non-protein coding RNA 1003	ncRNA	0.013263	0.436508	
chunk0175_414_1	chr6	168800276	168800475	+	0	NA	Intergenic	Intergenic	359224	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.005025	0.360000	
chunk0064_355_1	chr14	96839048	96839717	+	0	NA	intron (NM_003384, intron 3 of 12)	L1ME2|LINE|L1	42035	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.005979	0.338806	
chunk0161_64_1	chr5	166432352	166432674	+	0	NA	Intergenic	Intergenic	493857	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.018634	0.417957	
chunk0026_18_1	chr10	60590196	60590821	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	-17552	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.001600	0.324281	304(GGGAACTGAGTGTTTC,-,0.00)
chunk0105_63_1	chr2	183547445	183548140	+	0	NA	Intergenic	L1PA7|LINE|L1	423437	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.002878	0.370690	
chunk0073_119_1	chr16	4844561	4845104	+	0	NA	intron (NM_001308096, intron 3 of 15)	intron (NM_001308096, intron 3 of 15)	2470	NM_032569	84656	Hs.387255	NM_032569	ENSG00000140632	GLYR1	BM045|HIBDL|N-PAC|NP60	glyoxylate reductase 1 homolog	protein-coding	0.007366	0.437500	
chunk0083_169_1	chr17	66175247	66175624	+	0	NA	intron (NM_001302891, intron 3 of 24)	intron (NM_001302891, intron 3 of 24)	16434	NM_001302891	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.246032	
chunk0132_389_1	chr3	163707582	163708042	+	0	NA	Intergenic	Intergenic	-404511	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.000000	0.245119	375(AAGGTCAAAATGTTCT,-,0.00),376(AGGTCAAAATGTTCTT,+,0.00)
chunk0092_171_1	chr19	29944876	29945095	+	0	NA	intron (NR_045557, intron 1 of 9)	intron (NR_045557, intron 1 of 9)	2746	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.009132	0.386364	78(GAGTACAGTGAGTTCT,-,0.00),79(AGTACAGTGAGTTCTA,+,0.00)
chunk0031_307_1	chr10	128855003	128855477	+	0	NA	Intergenic	Intergenic	569290	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.012658	0.425263	
chunk0199_442_1	chr9	14026949	14027779	+	0	NA	Intergenic	Intergenic	99393	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.006024	0.462094	382(TGGAACACCGAGTGCT,-,0.00),383(GGAACACCGAGTGCTG,+,0.00)
chunk0145_318_1	chr4	150591414	150591678	+	0	NA	intron (NM_001199282, intron 38 of 56)	intron (NM_001199282, intron 38 of 56)	9621	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.018939	0.505660	
chunk0050_269_1	chr12	106096345	106096934	+	0	NA	intron (NM_014840, intron 2 of 6)	intron (NM_014840, intron 2 of 6)	43394	NM_014840	9891	Hs.524692	NM_014840	ENSG00000074590	NUAK1	ARK5	NUAK family kinase 1	protein-coding	0.023769	0.454237	
chunk0166_340_1	chr6	50938515	50938913	+	0	NA	Intergenic	Intergenic	119988	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.005025	0.403509	334(AAGAACATGATGTGTT,-,0.00),335(AGAACATGATGTGTTT,+,0.00)
chunk0118_321_1	chr22	35266238	35266761	+	0	NA	intron (NM_001003681, intron 5 of 10)	L2b|LINE|L2	9047	NM_001003681	10042	Hs.588815	NM_005487	ENSG00000100281	HMGXB4	HMG2L1|HMGBCG|THC211630	HMG-box containing 4	protein-coding	0.005736	0.383588	
chunk0045_202_1	chr12	47730212	47730708	+	0	NA	Intergenic	Intergenic	-4888	NM_001172440	8909	Hs.997	NM_006025	ENSG00000111405	ENDOU	P11|PP11|PRSS26	endonuclease, poly(U) specific	protein-coding	0.018145	0.484909	
chunk0139_344_1	chr4	59775815	59776364	+	0	NA	Intergenic	Intergenic	-1146530	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.001821	0.296364	
chunk0165_444_1	chr6	40543314	40543549	+	0	NA	intron (NM_020737, intron 1 of 2)	intron (NM_020737, intron 1 of 2)	44033	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.008511	0.466102	
chunk0125_158_1	chr3	66475281	66475729	+	0	NA	intron (NM_015541, intron 1 of 18)	intron (NM_015541, intron 1 of 18)	24916	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.008929	0.454343	
chunk0020_161_1	chr1	234365503	234365708	+	0	NA	Intergenic	Intergenic	7798	NR_125962	101927765	Hs.596703	NR_125961	ENSG00000231663	COA6-AS1	-	COA6 antisense RNA 1	ncRNA	0.004878	0.509709	
chunk0055_247_1	chr13	63065901	63066341	+	0	NA	Intergenic	L1MC5a|LINE|L1	-258762	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.000000	0.321995	
chunk0148_372_1	chr5	14633191	14633574	+	0	NA	Intergenic	L2c|LINE|L2	19000	NR_132980	106635683		NR_132980		SNORD141A	-	small nucleolar RNA, C/D box 141A	snoRNA	0.013055	0.375000	175(GATACAGTCTGTACTC,+,0.00)
chunk0120_450_1	chr3	14248859	14249525	+	0	NA	Intergenic	Intergenic	70464	NM_014463	27258	Hs.111632	NM_014463	ENSG00000170860	LSM3	SMX4|USS2|YLR438C	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.007508	0.469265	356(TGGAACATTGAGTTCC,-,0.00),357(GGAACATTGAGTTCCC,+,0.00)
chunk0177_446_1	chr7	28099776	28100299	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-80420	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.001912	0.358779	193(CTAAACATCGTGTTCT,-,0.00),194(TAAACATCGTGTTCTT,+,0.00),317(ATGGACAGTGTGTTCC,-,0.00),318(TGGACAGTGTGTTCCA,+,0.00)
chunk0073_391_1	chr16	16030465	16030913	+	0	NA	intron (NM_004996, intron 5 of 30)	L1MC5|LINE|L1	81112	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.015625	0.449889	
chunk0119_320_1	chr22	46775763	46776307	+	0	NA	intron (NM_001284305, intron 1 of 12)	intron (NM_001284305, intron 1 of 12)	2108	NM_001284305	25771	Hs.435044	NM_014346	ENSG00000054611	TBC1D22A	C22orf4|HSC79E021	TBC1 domain family member 22A	protein-coding	0.023897	0.530275	501(GAGTACAGGGTGTGTT,-,0.00),502(AGTACAGGGTGTGTTT,+,0.00)
chunk0130_166_1	chr3	133015705	133016021	+	0	NA	Intergenic	L1MA1|LINE|L1	-22425	NM_001136469	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.009494	0.350158	
chunk0130_177_1	chr3	133413529	133413840	+	0	NA	intron (NM_003571, intron 1 of 6)	intron (NM_003571, intron 1 of 6)	13689	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.016077	0.461538	
chunk0130_403_1	chr3	140373862	140374348	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	134684	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.000000	0.476386	
chunk0126_120_1	chr3	75684056	75684765	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	12019	NR_040004	401074	Hs.528540	NR_040004	ENSG00000242516	LINC00960	-	long intergenic non-protein coding RNA 960	ncRNA	0.002821	0.447887	
chunk0005_249_1	chr1	59666909	59667550	+	0	NA	intron (NM_001244714, intron 10 of 13)	intron (NM_001244714, intron 10 of 13)	66067	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.006240	0.409657	
chunk0174_124_1	chr6	157310291	157310575	+	0	NA	intron (NM_018452, intron 3 of 3)	intron (NM_018452, intron 3 of 3)	13826	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.003521	0.501754	
chunk0144_154_1	chr4	130601276	130601637	+	0	NA	Intergenic	Intergenic	-829978	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.008310	0.320442	
chunk0030_22_1	chr10	111107368	111107710	+	0	NA	Intergenic	MIR|SINE|MIR	30507	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.008772	0.454810	25(AGGTACATCCTGTTCC,-,0.00),26(GGTACATCCTGTTCCT,+,0.00)
chunk0106_414_1	chr2	208015393	208015979	+	0	NA	intron (NM_001080475, intron 1 of 7)	intron (NM_001080475, intron 1 of 7)	9874	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.010239	0.345826	
chunk0023_329_1	chr10	29279693	29280134	+	0	NA	Intergenic	Intergenic	-9148	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.011338	0.375566	
chunk0148_234_1	chr5	9523425	9524064	+	0	NA	intron (NM_003966, intron 1 of 22)	intron (NM_003966, intron 1 of 22)	12411	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.004695	0.417187	
chunk0091_164_1	chr19	7619197	7620022	+	0	NA	TTS (NM_020196)	TTS (NM_020196)	2170	NR_106850	102465475		NR_106850	ENSG00000273657	MIR6792	hsa-mir-6792	microRNA 6792	ncRNA	0.048485	0.686441	
chunk0180_192_1	chr7	66148466	66148841	+	0	NA	intron (NR_024548, intron 6 of 6)	intron (NR_024548, intron 6 of 6)	33835	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.016000	0.494681	182(AGGACTTGTTGTGCCC,+,0.00)
chunk0207_356_1	chr9	135289052	135289547	+	0	NA	Intergenic	Intergenic	-53950	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.038384	0.504032	
chunk0153_292_1	chr5	73344484	73345004	+	0	NA	Intergenic	L1ME1|LINE|L1	103783	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.003846	0.353167	
chunk0055_365_1	chr13	71807112	71807496	+	0	NA	intron (NM_004392, intron 1 of 6)	intron (NM_004392, intron 1 of 6)	59888	NM_080759	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.007812	0.316883	
chunk0119_242_1	chr22	45645604	45645833	+	0	NA	Intergenic	CpG	-26080	NM_001167621	25814	Hs.475125	NM_013236	ENSG00000130638	ATXN10	E46L|HUMEEP|SCA10	ataxin 10	protein-coding	0.104803	0.756522	
chunk0201_378_1	chr9	68822602	68823177	+	0	NA	intron (NM_003558, intron 4 of 15)	MLT1D|LTR|ERVL-MaLR	42841	NM_138333	116224	Hs.655572	NM_138333	ENSG00000187866	FAM122A	C9orf42	family with sequence similarity 122A	protein-coding	0.010435	0.434028	
chunk0123_312_1	chr3	47126755	47127010	+	0	NA	intron (NM_014159, intron 1 of 20)	L2c|LINE|L2	37095	NM_014159	29072	Hs.517941	NM_012271	ENSG00000181555	SETD2	HBP231|HIF-1|HIP-1|HSPC069|HYPB|KMT3A|LLS|SET2|p231HBP	SET domain containing 2, histone lysine methyltransferase	protein-coding	0.000000	0.332031	
chunk0104_305_1	chr2	178886103	178886456	+	0	NA	intron (NM_173648, intron 10 of 23)	intron (NM_173648, intron 10 of 23)	-78856	NM_001256850	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.005666	0.488701	
chunk0122_304_1	chr3	36708334	36708823	+	0	NA	Intergenic	Intergenic	31283	NM_033403	85443	Hs.631907	NM_033403	ENSG00000163673	DCLK3	CLR|DCAMKL3|DCDC3C|DCK3	doublecortin like kinase 3	protein-coding	0.002045	0.332653	
chunk0137_33_1	chr4	11231848	11232478	+	0	NA	Intergenic	Intergenic	-136664	NR_030298	693157		NR_030298	ENSG00000207716	MIR572	MIRN572|hsa-mir-572	microRNA 572	ncRNA	0.007937	0.407290	
chunk0023_208_1	chr10	25358793	25359149	+	0	NA	intron (NM_020752, intron 2 of 10)	L1M4|LINE|L1	-182695	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.002809	0.288515	
chunk0211_241_1	chrX	119702864	119703063	+	0	NA	Intergenic	Intergenic	-9593	NM_145800	23157	Hs.496666	NM_015129	ENSG00000125354	SEPTIN6	SEP2|SEPT2|SEPT6	septin 6	protein-coding	0.005025	0.355000	
chunk0052_10_1	chr13	19674119	19674387	+	0	NA	TTS (NR_044998)	TTS (NR_044998)	40605	NM_017520	54737	Hs.269654	NM_017520	ENSG00000196199	MPHOSPH8	HSMPP8|TWA3|mpp8	M-phase phosphoprotein 8	protein-coding	0.011194	0.356877	
chunk0132_417_1	chr3	164486887	164487305	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-315540	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.007177	0.343675	
chunk0074_430_1	chr16	46398834	46399592	+	0	NA	Intergenic	Intergenic	169884	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.035620	0.368906	
chunk0193_307_1	chr8	78081836	78082624	+	0	NA	Intergenic	Intergenic	-433871	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.003807	0.299113	372(ATGACATTATGTTCTG,+,0.00)
chunk0178_261_1	chr7	36303241	36303772	+	0	NA	Intergenic	MIRb|SINE|MIR	63667	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.009416	0.503759	
chunk0026_434_1	chr10	71210604	71211155	+	0	NA	Intergenic	Intergenic	-1656	NM_001244889	219699	Hs.522997	NM_170744	ENSG00000107731	UNC5B	UNC5H2|p53RDL1	unc-5 netrin receptor B	protein-coding	0.010889	0.501812	
chunk0114_133_1	chr21	9961764	9962257	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-140949	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.002028	0.301619	
chunk0015_195_1	chr1	187342923	187343147	+	0	NA	intron (NR_126347, intron 3 of 3)	intron (NR_126347, intron 3 of 3)	-100593	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008929	0.315556	
chunk0071_158_1	chr15	82942376	82942983	+	0	NA	intron (NM_199330, intron 1 of 8)	intron (NM_199330, intron 1 of 8)	10045	NM_004839	9455	Hs.578443	NM_004839	ENSG00000103942	HOMER2	ACPD|CPD|DFNA68|HOMER-2|VESL-2	homer scaffold protein 2	protein-coding	0.021417	0.519737	
chunk0188_211_1	chr8	12757003	12757821	+	0	NA	Intergenic	Intergenic	-1929	NM_152271	91694	Hs.180178	NM_152271	ENSG00000154359	LONRF1	RNF191	LON peptidase N-terminal domain and ring finger 1	protein-coding	0.009780	0.366300	
chunk0030_447_1	chr10	120945887	120946508	+	0	NA	Intergenic	Intergenic	-95018	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.014493	0.504823	
chunk0025_330_1	chr10	57912105	57912561	+	0	NA	Intergenic	Intergenic	355601	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.004386	0.308534	
chunk0206_335_1	chr9	125500864	125501465	+	0	NA	intron (NM_024117, intron 7 of 10)	L1ME4a|LINE|L1	202274	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.011647	0.337209	
chunk0208_119_1	chrX	14680788	14681540	+	0	NA	intron (NM_002063, intron 7 of 8)	intron (NM_002063, intron 7 of 8)	151866	NM_002063	2742	Hs.2700	NM_002063	ENSG00000101958	GLRA2	GLR	glycine receptor alpha 2	protein-coding	0.006649	0.371846	
chunk0077_176_1	chr16	79632310	79632667	+	0	NA	Intergenic	L2c|LINE|L2	-31763	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.019608	0.491620	209(AAGCACAGGATGCCCC,-,0.00),210(AGCACAGGATGCCCCA,+,0.00)
chunk0004_263_1	chr1	47970912	47971117	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	25876	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.009756	0.432039	
chunk0101_18_1	chr2	121530692	121531189	+	0	NA	promoter-TSS (NR_023343)	promoter-TSS (NR_023343)	60	NR_023343	100151683	Hs.689638	NR_023343	ENSG00000264229	RNU4ATAC	MOPD1|RFMN|RNU4ATAC1|TALS|U4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	snRNA	0.042254	0.457831	
chunk0155_203_1	chr5	94912540	94912822	+	0	NA	intron (NM_024717, intron 9 of 22)	intron (NM_024717, intron 9 of 22)	169185	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.000000	0.356890	
chunk0145_375_1	chr4	151540920	151541162	+	0	NA	intron (NM_001109977, intron 3 of 13)	intron (NM_001109977, intron 3 of 13)	131795	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.008264	0.370370	
chunk0184_196_1	chr7	116953048	116953256	+	0	NA	promoter-TSS (NM_018412)	promoter-TSS (NM_018412)	-175	NM_021908	7982	Hs.368131	NM_018412	ENSG00000004866	ST7	ETS7q|FAM4A|FAM4A1|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding	0.057692	0.502392	
chunk0144_58_1	chr4	126978191	126978686	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-654494	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.006061	0.322581	
chunk0190_74_1	chr8	29910206	29910551	+	0	NA	Intergenic	L1M2|LINE|L1	-11135	NR_024473	286135	Hs.376840	NR_024473	ENSG00000253279	LINC02209	FAM183CP	long intergenic non-protein coding RNA 2209	ncRNA	0.002899	0.523121	
chunk0058_362_1	chr14	28966935	28967163	+	0	NA	Intergenic	Intergenic	194345	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.000000	0.388646	185(GGGAACAAGATGTTCT,-,0.00),186(GGAACAAGATGTTCTT,+,0.00)
chunk0099_163_1	chr2	88471212	88471458	+	0	NA	Intergenic	Intergenic	-18800	NM_001135649	344167	Hs.131262	NM_001135649	ENSG00000214336	FOXI3	-	forkhead box I3	protein-coding	0.004065	0.352227	
chunk0145_246_1	chr4	148778181	148778532	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-335836	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.000000	0.352273	
chunk0161_397_1	chr5	177189485	177189904	+	0	NA	intron (NM_022455, intron 2 of 22)	intron (NM_022455, intron 2 of 22)	55862	NM_022455	64324	Hs.106861	NM_022455	ENSG00000165671	NSD1	ARA267|KMT3B|SOTOS|SOTOS1|STO	nuclear receptor binding SET domain protein 1	protein-coding	0.002387	0.302381	
chunk0179_186_1	chr7	47088354	47088655	+	0	NA	Intergenic	Intergenic	493640	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.013289	0.559603	
chunk0092_71_1	chr19	20589067	20589534	+	0	NA	Intergenic	AluJr|SINE|Alu	-23480	NM_001159293	100129842	Hs.515696	NM_001159293	ENSG00000237440	ZNF737	ZNF102	zinc finger protein 737	protein-coding	0.000000	0.373932	
chunk0055_42_1	chr13	52173222	52173997	+	0	NA	intron (NR_051963, intron 6 of 8)	intron (NR_051963, intron 6 of 8)	-13748	NM_002498	4752	Hs.409989	NM_002498	ENSG00000136098	NEK3	HSPK36	NIMA related kinase 3	protein-coding	0.009032	0.389175	
chunk0181_295_1	chr7	86982279	86982659	+	0	NA	intron (NM_001142749, intron 1 of 21)	L1PA6|LINE|L1	-16494	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.005263	0.506562	
chunk0041_128_1	chr11	125055111	125055656	+	0	NA	Intergenic	Intergenic	-7734	NM_001145290	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.003670	0.412088	
chunk0010_211_1	chr1	116172537	116173112	+	0	NA	Intergenic	Intergenic	61069	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.003478	0.453125	
chunk0102_378_1	chr2	154076970	154077399	+	0	NA	intron (NM_052917, intron 3 of 12)	intron (NM_052917, intron 3 of 12)	132790	NM_001301627	114805	Hs.470277	NM_052917	ENSG00000144278	GALNT13	GalNAc-T13	polypeptide N-acetylgalactosaminyltransferase 13	protein-coding	0.002331	0.297674	
chunk0003_274_1	chr1	36486989	36487312	+	0	NA	Intergenic	Intergenic	-3836	NM_000760	1441	Hs.524517	NM_000760	ENSG00000119535	CSF3R	CD114|GCSFR|SCN7	colony stimulating factor 3 receptor	protein-coding	0.024768	0.567901	274(TGCTCAGGCTGTTCTC,+,0.00)
chunk0080_253_1	chr17	30455536	30455772	+	0	NA	intron (NM_001304, intron 15 of 20)	intron (NM_001304, intron 15 of 20)	-21754	NM_001007024	9527	Hs.462680	NM_004871	ENSG00000108587	GOSR1	GOLIM2|GOS-28|GOS28|GOS28/P28|GS28|P28	golgi SNAP receptor complex member 1	protein-coding	0.000000	0.362869	
chunk0113_56_1	chr20	50380802	50381177	+	0	NA	Intergenic	Intergenic	-59647	NR_109950	101927586	Hs.637665	NR_109950	ENSG00000233077	LINC01271	-	long intergenic non-protein coding RNA 1271	ncRNA	0.016000	0.494681	
chunk0022_171_1	chr10	12720217	12720894	+	0	NA	intron (NM_020397, intron 3 of 9)	MamGypsy2-I|LTR|Gypsy	4798	NR_031752	100313841		NR_031752	ENSG00000221331	MIR548Q	-	microRNA 548q	ncRNA	0.008863	0.441003	
chunk0081_324_1	chr17	46157789	46157988	+	0	NA	intron (NM_001193465, intron 3 of 15)	intron (NM_001193465, intron 3 of 15)	34912	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.010050	0.385000	
chunk0077_417_1	chr16	85189180	85189484	+	0	NA	Intergenic	Intergenic	52182	NR_033984	400548	Hs.592054	NR_033984	ENSG00000278214	LINC02139	-	long intergenic non-protein coding RNA 2139	ncRNA	0.000000	0.390164	
chunk0176_40_1	chr7	10265599	10266396	+	0	NA	Intergenic	Intergenic	631727	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.003764	0.318296	
chunk0125_396_1	chr3	71978221	71978587	+	0	NA	Intergenic	MIR|SINE|MIR	122051	NR_104116	285286	Hs.559386	NR_104116	ENSG00000241163	LINC00877	-	long intergenic non-protein coding RNA 877	ncRNA	0.013661	0.414169	347(TGGACCAGGGTGTCCT,-,0.00),348(GGACCAGGGTGTCCTG,+,0.00)
chunk0096_18_1	chr2	26255875	26256239	+	0	NA	intron (NM_001281512, intron 3 of 14)	intron (NM_001281512, intron 3 of 14)	11309	NM_001281513	3032	Hs.515848	NM_000183	ENSG00000138029	HADHB	ECHB|MSTP029|MTPB|TP-BETA	hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta	protein-coding	0.008242	0.421918	243(ATAACATGGTGTTCCG,+,0.00)
chunk0112_359_1	chr20	45382916	45383628	+	0	NA	intron (NR_003189, intron 3 of 5)	L1ME1|LINE|L1	-4955	NM_014477	27296	Hs.710271	NM_014477	ENSG00000124251	TP53TG5	C20orf10|CLG01	TP53 target 5	protein-coding	0.002809	0.311360	
chunk0039_35_1	chr11	95859732	95859950	+	0	NA	intron (NM_201278, intron 7 of 16)	intron (NM_201278, intron 7 of 16)	64366	NM_001243571	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.004587	0.356164	
chunk0013_408_1	chr1	173077148	173077448	+	0	NA	Intergenic	L1P4e|LINE|L1	-26335	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.006667	0.488372	
chunk0083_387_1	chr17	71579034	71579426	+	0	NA	Intergenic	MIR|SINE|MIR	-377051	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.000000	0.335878	
chunk0065_45_1	chr15	21293808	21294150	+	0	NA	non-coding (NR_027053, exon 1 of 1)	non-coding (NR_027053, exon 1 of 1)	3850	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.014620	0.469388	
chunk0159_23_1	chr5	136480048	136480416	+	0	NA	Intergenic	L1MA10|LINE|L1	-114756	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.005435	0.365854	
chunk0084_130_1	chr17	76173911	76174610	+	0	NA	intron (NM_052916, intron 2 of 18)	intron (NM_052916, intron 2 of 18)	-32961	NM_001454	2302	Hs.651204	NM_001454	ENSG00000129654	FOXJ1	FKHL13|HFH-4|HFH4	forkhead box J1	protein-coding	0.017167	0.414286	
chunk0129_442_1	chr3	128072559	128072767	+	0	NA	TTS (NM_013336)	TTS (NM_013336)	-3147	NR_046645	100874089	Hs.581603	NR_046645	ENSG00000239608	RUVBL1-AS1	-	RUVBL1 antisense RNA 1	ncRNA	0.024038	0.622010	
chunk0063_123_1	chr14	79324885	79325709	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	45958	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.006068	0.393939	
chunk0205_94_1	chr9	107394934	107395294	+	0	NA	Intergenic	MIRc|SINE|MIR	71471	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.011111	0.368421	
chunk0035_391_1	chr11	56533006	56533832	+	0	NA	Intergenic	Intergenic	9838	NM_001005245	219487	Hs.553632	NM_001005245	ENSG00000255223	OR5M11	OR11-199	olfactory receptor family 5 subfamily M member 11	protein-coding	0.004843	0.391778	
chunk0110_250_1	chr20	16580355	16580559	+	0	NA	Intergenic	Intergenic	-7023	NM_001199865	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.009804	0.497561	
chunk0076_185_1	chr16	67678560	67678840	+	0	NA	intron (NR_027398, intron 1 of 1)	MIRb|SINE|MIR	11886	NM_001012984	388284	Hs.632208	NM_001012984	ENSG00000159761	C16orf86	-	chromosome 16 open reading frame 86	protein-coding	0.007143	0.434164	
chunk0203_437_1	chr9	91269760	91270138	+	0	NA	intron (NM_001306190, intron 5 of 8)	intron (NM_001306190, intron 5 of 8)	91975	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.005291	0.361478	
chunk0207_198_1	chr9	131125413	131125748	+	0	NA	promoter-TSS (NM_005085)	promoter-TSS (NM_005085)	19	NM_005085	8021	Hs.654530	NM_005085	ENSG00000126883	NUP214	CAIN|CAN	nucleoporin 214	protein-coding	0.110448	0.675595	
chunk0140_10_1	chr4	65378321	65378949	+	0	NA	intron (NM_001281765, intron 8 of 17)	MER58A|DNA|hAT-Charlie	-291326	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.003185	0.346582	
chunk0034_429_1	chr11	38624972	38625260	+	0	NA	intron (NR_120555, intron 3 of 4)	intron (NR_120555, intron 3 of 4)	21240	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.000000	0.342561	
chunk0099_413_1	chr2	102273793	102274122	+	0	NA	Intergenic	Intergenic	-37545	NM_001282408	9173	Hs.66	NM_003856	ENSG00000115602	IL1RL1	DER4|FIT-1|IL33R|ST2|ST2L|ST2V|T1	interleukin 1 receptor like 1	protein-coding	0.012158	0.403030	153(TAGCACAGGACGTTCC,-,0.00),154(AGCACAGGACGTTCCA,+,0.00)
chunk0134_412_1	chr3	183215732	183216089	+	0	NA	intron (NM_015078, intron 22 of 29)	intron (NM_015078, intron 22 of 29)	-37334	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.011204	0.460894	
chunk0151_100_1	chr5	43274723	43275072	+	0	NA	intron (NR_072980, intron 2 of 3)	MamRep434|DNA|TcMar-Tigger	38615	NM_001098272	3157	Hs.397729	NM_002130	ENSG00000112972	HMGCS1	HMGCS	3-hydroxy-3-methylglutaryl-CoA synthase 1	protein-coding	0.011461	0.368571	
chunk0100_431_1	chr2	120313469	120313669	+	0	NA	Intergenic	Intergenic	-32574	NM_002193	3625	Hs.1735	NM_002193	ENSG00000163083	INHBB	-	inhibin subunit beta B	protein-coding	0.035000	0.482587	
chunk0130_416_1	chr3	140704765	140705118	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	26917	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.000000	0.474576	
chunk0184_424_1	chr7	122844612	122844935	+	0	NA	intron (NM_017954, intron 1 of 29)	intron (NM_017954, intron 1 of 29)	41986	NM_001009571	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.000000	0.320988	
chunk0029_172_1	chr10	100370695	100371028	+	0	NA	Intergenic	Intergenic	-2715	NR_026762	90271	Hs.628088	NR_026762	ENSG00000235823	OLMALINC	C10orf75|HI-LNC80|LINC00263|NCRNA00263|OLMALINCAS	oligodendrocyte maturation-associated long intergenic non-coding RNA	ncRNA	0.012012	0.473054	
chunk0067_22_1	chr15	40340785	40341070	+	0	NA	promoter-TSS (NM_207380)	promoter-TSS (NM_207380)	40	NM_207380	388115	Hs.32433	NM_207380	ENSG00000188549	CCDC9B	C15orf52	coiled-coil domain containing 9B	protein-coding	0.049123	0.657343	
chunk0032_446_1	chr10	133068979	133069756	+	0	NA	Intergenic	Intergenic	17330	NR_111905	100128127	Hs.694139	NR_111905		ADGRA1-AS1	GPR123-AS1	adhesion G protein-coupled receptor A1 antisense RNA 1	ncRNA	0.038610	0.640103	
chunk0020_411_1	chr1	241457326	241457577	+	0	NA	Intergenic	MER67C|LTR|ERV1	62334	NM_000143	2271	Hs.592490	NM_000143	ENSG00000091483	FH	FMRD|HLRCC|HsFH|LRCC|MCL|MCUL1	fumarate hydratase	protein-coding	0.003984	0.420635	
chunk0160_33_1	chr5	149437346	149437789	+	0	NA	Intergenic	Intergenic	6921	NR_029686	406937		NR_029686	ENSG00000276365	MIR145	MIRN145|miR-145|miRNA145	microRNA 145	ncRNA	0.011287	0.418919	
chunk0092_335_1	chr19	35124528	35124744	+	0	NA	TTS (NM_001136007)	TTS (NM_001136007)	1936	NR_106947	102466205		NR_106947	ENSG00000284065	MIR6887	hsa-mir-6887	microRNA 6887	ncRNA	0.087963	0.654378	
chunk0184_358_1	chr7	120950632	120950896	+	0	NA	promoter-TSS (NM_198267)	promoter-TSS (NM_198267)	1	NM_198267	54556	Hs.489811	NM_019071	ENSG00000071243	ING3	Eaf4|ING2|MEAF4|p47ING3	inhibitor of growth family member 3	protein-coding	0.071970	0.562264	
chunk0045_217_1	chr12	48013510	48013847	+	0	NA	Intergenic	Intergenic	-9176	NM_001844	1280	Hs.408182	NM_001844	ENSG00000139219	COL2A1	ANFH|AOM|COL11A3|SEDC|STL1	collagen type II alpha 1 chain	protein-coding	0.011869	0.372781	
chunk0169_82_1	chr6	99491127	99491601	+	0	NA	intron (NM_001080481, intron 5 of 17)	intron (NM_001080481, intron 5 of 17)	24012	NM_001080481	85015	Hs.143410	NM_032929	ENSG00000123552	USP45	-	ubiquitin specific peptidase 45	protein-coding	0.000000	0.381053	
chunk0024_70_1	chr10	34185084	34185386	+	0	NA	intron (NM_019619, intron 22 of 24)	intron (NM_019619, intron 22 of 24)	-412555	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.003311	0.366337	
chunk0068_271_1	chr15	56676717	56676935	+	0	NA	intron (NM_001002843, intron 11 of 20)	intron (NM_001002843, intron 11 of 20)	57260	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.004587	0.310502	186(GAGAACATTATGTACT,-,0.00),187(AGAACATTATGTACTA,+,0.00)
chunk0126_54_1	chr3	74302778	74303366	+	0	NA	intron (NM_020872, intron 12 of 21)	intron (NM_020872, intron 12 of 21)	218068	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.001701	0.385399	
chunk0206_71_1	chr9	119868586	119869220	+	0	NA	Intergenic	Intergenic	-66157	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.011041	0.513386	
chunk0131_208_1	chr3	148948996	148949461	+	0	NA	Intergenic	Intergenic	-42180	NM_001184721	2992	Hs.477892	NM_004130	ENSG00000163754	GYG1	GSD15|GYG	glycogenin 1	protein-coding	0.015054	0.407725	
chunk0005_351_1	chr1	61301792	61302060	+	0	NA	intron (NM_001145511, intron 3 of 10)	intron (NM_001145511, intron 3 of 10)	-48408	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.003731	0.453532	
chunk0167_403_1	chr6	75211957	75212444	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-6293	NM_004370	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.006160	0.452869	
chunk0072_33_1	chr16	737560	738239	+	0	NA	intron (NM_022493, intron 2 of 10)	intron (NM_022493, intron 2 of 10)	3139	NM_022493	64428	Hs.513247	NM_022493	ENSG00000103245	CIAO3	HPRN|IOP1|LET1L|NAR1|NARFL|PRN	cytosolic iron-sulfur assembly component 3	protein-coding	0.030928	0.605882	277(AGGAACAAGGTGTTCC,-,0.00),278(GGAACAAGGTGTTCCA,+,0.00)
chunk0167_177_1	chr6	63573280	63573787	+	0	NA	intron (NM_003463, intron 1 of 5)	CpG	1521	NM_003463	7803	Hs.227777	NM_003463	ENSG00000112245	PTP4A1	HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1	protein tyrosine phosphatase 4A1	protein-coding	0.106509	0.677165	
chunk0068_114_1	chr15	52449354	52449605	+	0	NA	intron (NM_001142495, intron 1 of 39)	L2c|LINE|L2	79571	NM_000259	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.000000	0.488095	199(TGGAACACTCTGGCCT,-,0.00),200(GGAACACTCTGGCCTG,+,0.00)
chunk0003_338_1	chr1	38990776	38991033	+	0	NA	promoter-TSS (NM_024595)	promoter-TSS (NM_024595)	-340	NM_024595	79647	Hs.293563	NM_024595	ENSG00000174574	AKIRIN1	C1orf108|STRF2	akirin 1	protein-coding	0.042802	0.581395	
chunk0102_234_1	chr2	148861781	148862331	+	0	NA	Intergenic	Intergenic	-13167	NM_004522	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.003636	0.450091	
chunk0124_235_1	chr3	56684034	56684456	+	0	NA	Intergenic	Intergenic	-1138	NM_001112736	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.033175	0.387707	
chunk0135_37_1	chr3	185295579	185296396	+	0	NA	intron (NM_001242317, intron 2 of 12)	AluJr|SINE|Alu	13046	NM_001242314	9175	Hs.591306	NM_004721	ENSG00000073803	MAP3K13	LZK|MEKK13|MLK	mitogen-activated protein kinase kinase kinase 13	protein-coding	0.004896	0.440098	329(CAGTACTGTAAGTTCT,-,0.00),330(AGTACTGTAAGTTCTG,+,0.00)
chunk0146_356_1	chr4	167265084	167265631	+	0	NA	Intergenic	L1MC2|LINE|L1	-30767	NM_001204358	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.009141	0.348540	
chunk0169_47_1	chr6	97679484	97679715	+	0	NA	intron (NR_110757, intron 3 of 4)	intron (NR_110757, intron 3 of 4)	-344932	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.000000	0.323276	139(TACACACTCTGTCCTC,+,0.00)
chunk0183_91_1	chr7	105006337	105006911	+	0	NA	Intergenic	Intergenic	7517	NR_024586	100216545	Hs.631150	NR_024586		KMT2E-AS1	-	KMT2E antisense RNA 1	ncRNA	0.006969	0.372174	
chunk0055_313_1	chr13	67452935	67453211	+	0	NA	Intergenic	L1PA6|LINE|L1	80686	NR_130792	100874145	Hs.508194	NR_130792	ENSG00000230040	LINC00364	LncRNA00364	long intergenic non-protein coding RNA 364	ncRNA	0.003623	0.516245	
chunk0074_3_1	chr16	19577852	19578219	+	0	NA	intron (NM_001300743, intron 5 of 27)	L1M5|LINE|L1	22620	NM_001300743	57020	Hs.654964	NM_020314	ENSG00000103544	VPS35L	C16orf62	VPS35 endosomal protein sorting factor like	protein-coding	0.002725	0.437500	
chunk0093_217_1	chr19	49950208	49950551	+	0	NA	intron (NM_001135163, intron 9 of 9)	(TCAT)n|Simple_repeat|Simple_repeat	10793	NM_052884	114132	Hs.661852	NM_052884	ENSG00000161640	SIGLEC11	-	sialic acid binding Ig like lectin 11	protein-coding	0.005831	0.456395	
chunk0043_61_1	chr12	13963530	13963734	+	0	NA	intron (NM_000834, intron 1 of 12)	MIRb|SINE|MIR	16456	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.014706	0.482927	
chunk0122_19_1	chr3	27581852	27582261	+	0	NA	Intergenic	Intergenic	-97636	NM_001258379	9497	Hs.250072	NM_003615	ENSG00000033867	SLC4A7	NBC2|NBC3|NBCN1|SBC2|SLC4A6	solute carrier family 4 member 7	protein-coding	0.007335	0.487805	
chunk0088_301_1	chr18	50012130	50012468	+	0	NA	intron (NM_001080467, intron 4 of 39)	intron (NM_001080467, intron 4 of 39)	114264	NR_036204	100422865		NR_036204	ENSG00000283343	MIR4320	-	microRNA 4320	ncRNA	0.002959	0.371681	
chunk0164_9_1	chr6	17724990	17725374	+	0	NA	Intergenic	Intergenic	-18348	NM_001278210	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.015625	0.509091	53(CTGCACAGAATGTCCT,-,0.00),54(TGCACAGAATGTCCTT,+,0.00)
chunk0110_301_1	chr20	17985623	17985946	+	0	NA	intron (NM_001310338, intron 4 of 5)	Tigger3b|DNA|TcMar-Tigger	-16793	NM_001282454	27131	Hs.316890	NM_014426	ENSG00000089006	SNX5	-	sorting nexin 5	protein-coding	0.003096	0.395062	
chunk0133_190_1	chr3	170531586	170531831	+	0	NA	intron (NM_020949, intron 1 of 7)	intron (NM_020949, intron 1 of 7)	54366	NM_020949	57709	Hs.596660	NM_020949	ENSG00000013293	SLC7A14	PPP1R142	solute carrier family 7 member 14	protein-coding	0.000000	0.365854	27(GAGAACAAAATGTACA,-,0.00),28(AGAACAAAATGTACAA,+,0.00)
chunk0121_136_1	chr3	18627548	18628042	+	0	NA	Intergenic	Intergenic	182558	NR_125803	101927777	Hs.543235	NR_125803		SATB1-AS1	-	SATB1 antisense RNA 1	ncRNA	0.000000	0.317172	
chunk0141_119_1	chr4	79745904	79746400	+	0	NA	Intergenic	Intergenic	-81319	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.000000	0.346076	
chunk0067_48_1	chr15	40802972	40803709	+	0	NA	intron (NM_018163, intron 1 of 10)	intron (NM_018163, intron 1 of 10)	-3736	NM_001077268	84936	Hs.121676	NM_032850	ENSG00000166140	ZFYVE19	ANCHR|MPFYVE	zinc finger FYVE-type containing 19	protein-coding	0.004071	0.439024	
chunk0134_168_1	chr3	178054547	178054786	+	0	NA	Intergenic	L3|LINE|CR1	237801	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.008368	0.425000	
chunk0184_284_1	chr7	118709984	118710357	+	0	NA	Intergenic	L1ME3A|LINE|L1	485512	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.002681	0.377005	
chunk0171_293_1	chr6	128398158	128398660	+	0	NA	intron (NM_001291981, intron 1 of 32).2	MER51A|LTR|ERV1	122265	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.013944	0.411531	
chunk0018_198_1	chr1	219317174	219317759	+	0	NA	Intergenic	Intergenic	142497	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.003419	0.356655	312(CTGAACACAGTGTTCC,-,0.00),313(TGAACACAGTGTTCCC,+,0.00)
chunk0129_380_1	chr3	126076568	126076930	+	0	NA	intron (NM_001008485, intron 1 of 11)	L1ME3B|LINE|L1	7542	NM_001008485	54946	Hs.573007	NM_017836	ENSG00000114544	SLC41A3	SLC41A1-L2	solute carrier family 41 member 3	protein-coding	0.013812	0.402204	
chunk0001_116_1	chr1	3942849	3943117	+	0	NA	intron (NR_040065, intron 2 of 2)	intron (NR_040065, intron 2 of 2)	2371	NR_040065	728716	Hs.668359	NR_040065		LINC01346	-	long intergenic non-protein coding RNA 1346	ncRNA	0.029851	0.501859	
chunk0171_4_1	chr6	119491029	119491629	+	0	NA	promoter-TSS (NR_046100)	promoter-TSS (NR_046100)	-27	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.010000	0.376040	267(TAGTACTGGGTGTCCT,-,0.00),268(AGTACTGGGTGTCCTA,+,0.00)
chunk0191_241_1	chr8	53008763	53009103	+	0	NA	Intergenic	L1MB8|LINE|L1	69025	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.008824	0.390029	
chunk0188_53_1	chr8	6852149	6852758	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	-16809	NM_207411	389610	Hs.558840	NM_207411	ENSG00000275591	XKR5	HARL2754|UNQ2754|XRG5A|XRG5BM	XK related 5	protein-coding	0.009852	0.504918	
chunk0116_180_1	chr21	36846380	36847081	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	119926	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.008559	0.401709	
chunk0189_226_1	chr8	24436359	24437286	+	0	NA	intron (NR_125808, intron 1 of 5)	L2a|LINE|L2	-4174	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.010787	0.394397	
chunk0103_150_1	chr2	162213835	162214178	+	0	NA	exon (NM_004460, exon 11 of 26)	exon (NM_004460, exon 11 of 26)	29529	NM_001291807	2191	Hs.654370	NM_004460	ENSG00000078098	FAP	DPPIV|FAPA|FAPalpha|SIMP	fibroblast activation protein alpha	protein-coding	0.011662	0.363372	
chunk0148_378_1	chr5	14684775	14685123	+	0	NA	intron (NM_138348, intron 4 of 6)	intron (NM_138348, intron 4 of 6)	20275	NM_138348	90268	Hs.406335	NM_138348	ENSG00000154124	OTULIN	AIPDS|FAM105B|GUM	OTU deubiquitinase with linear linkage specificity	protein-coding	0.014368	0.544413	
chunk0011_71_1	chr1	144103469	144104086	+	0	NA	Intergenic	(TGGCTGGCT)n|Simple_repeat|Simple_repeat	131138	NR_120535	100996712	Hs.497575	NM_001271887		SRGAP2D	-	SLIT-ROBO Rho GTPase activating protein 2D (pseudogene)	pseudo	0.003241	0.665049	
chunk0034_289_1	chr11	34740401	34740788	+	0	NA	Intergenic	L1P3|LINE|L1	108130	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.000000	0.358247	335(AAAGACATAATGTACC,-,0.00)
chunk0125_152_1	chr3	66428692	66429386	+	0	NA	intron (NM_015541, intron 3 of 18)	intron (NM_015541, intron 3 of 18)	71382	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.012968	0.479137	
chunk0075_136_1	chr16	50188147	50189018	+	0	NA	intron (NM_001040284, intron 2 of 12)	Charlie29a|DNA|hAT-Charlie	35664	NM_001040284	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.009185	0.435780	
chunk0090_25_1	chr19	1065670	1066040	+	0	NA	promoter-TSS (NM_001258328)	promoter-TSS (NM_001258328)	-68	NM_001258328	23526	Hs.465521	NM_012292	ENSG00000180448	ARHGAP45	HA-1|HLA-HA1|HMHA1	Rho GTPase activating protein 45	protein-coding	0.043243	0.633423	
chunk0162_255_1	chr6	5158047	5158479	+	0	NA	intron (NM_001164841, intron 2 of 3)	intron (NM_001164841, intron 2 of 3)	-9941	NR_037462	100500900		NR_037462	ENSG00000265083	MIR3691	mir-3691	microRNA 3691	ncRNA	0.009259	0.360277	
chunk0109_371_1	chr2	239337623	239338542	+	0	NA	intron (NM_006037, intron 2 of 26)	intron (NM_006037, intron 2 of 26)	13722	NR_039948	100616360		NR_039948	ENSG00000264292	MIR2467	mir-2467	microRNA 2467	ncRNA	0.027203	0.542391	
chunk0056_357_1	chr13	92244194	92244761	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	107730	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.007055	0.311620	
chunk0023_202_1	chr10	25256639	25256962	+	0	NA	intron (NM_020752, intron 2 of 10)	L3b|LINE|CR1	-80524	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.006192	0.317901	
chunk0004_215_1	chr1	46750008	46750381	+	0	NA	Intergenic	Intergenic	-31130	NM_014774	9813	Hs.707688	NM_014774	ENSG00000159658	EFCAB14	KIAA0494	EF-hand calcium binding domain 14	protein-coding	0.013405	0.470588	
chunk0119_248_1	chr22	45761208	45761498	+	0	NA	TTS (NR_039919)	TTS (NR_039919)	829	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.006897	0.426117	
chunk0036_77_1	chr11	60370549	60371427	+	0	NA	Intergenic	Intergenic	-7497	NM_206939	58475	Hs.530735	NM_021201	ENSG00000166927	MS4A7	4SPAN2|CD20L4|CFFM4|MS4A8	membrane spanning 4-domains A7	protein-coding	0.007973	0.379977	641(CAGAACTGCCAGTTCA,-,0.00)
chunk0201_372_1	chr9	68711183	68711782	+	0	NA	intron (NM_001278253, intron 1 of 13)	L2c|LINE|L2	6068	NM_001278253	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.006678	0.308333	
chunk0153_298_1	chr5	73431372	73431613	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	17035	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.000000	0.351240	
chunk0147_335_1	chr4	185349938	185350668	+	0	NA	intron (NM_031953, intron 13 of 18)	intron (NM_031953, intron 13 of 18)	28695	NM_018409	55805	Hs.558513	NM_018409	ENSG00000109771	LRP2BP	-	LRP2 binding protein	protein-coding	0.016438	0.497948	
chunk0136_237_1	chr4	8792341	8792565	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	79364	NM_001306142	3166	Hs.104134	NM_018942	ENSG00000215612	HMX1	H6|NKX5-3	H6 family homeobox 1	protein-coding	0.013393	0.551111	
chunk0022_214_1	chr10	13877503	13877866	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-196600	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.013774	0.552198	
chunk0005_200_1	chr1	59061446	59061813	+	0	NA	intron (NR_110626, intron 2 of 2)	intron (NR_110626, intron 2 of 2)	41153	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.005450	0.475543	227(AGATACAGGGTGTCCT,-,0.00),228(GATACAGGGTGTCCTA,+,0.00)
chunk0063_425_1	chr14	88542892	88543761	+	0	NA	intron (NM_007039, intron 2 of 18)	intron (NM_007039, intron 2 of 18)	11453	NM_007039	11099	Hs.437040	NM_007039	ENSG00000070778	PTPN21	PTPD1|PTPRL10	protein tyrosine phosphatase non-receptor type 21	protein-coding	0.006904	0.357471	
chunk0204_142_1	chr9	95666024	95666545	+	0	NA	Intergenic	Intergenic	-149319	NM_001083603	5727	Hs.494538	NM_000264	ENSG00000185920	PTCH1	BCNS|NBCCS|PTC|PTC1|PTCH	patched 1	protein-coding	0.019194	0.478927	
chunk0040_225_1	chr11	114340706	114340930	+	0	NA	Intergenic	Intergenic	39221	NR_120567	101928940	Hs.409846	NR_120567	ENSG00000256195	LOC101928940	-	uncharacterized LOC101928940	ncRNA	0.031250	0.564444	
chunk0079_11_1	chr17	9444952	9445600	+	0	NA	intron (NR_033656, intron 4 of 5)	intron (NR_033656, intron 4 of 5)	130682	NM_004853	9482	Hs.431109	NM_004853	ENSG00000170310	STX8	CARB	syntaxin 8	protein-coding	0.015432	0.462250	
chunk0180_198_1	chr7	66247462	66247769	+	0	NA	intron (NM_003596, intron 2 of 5)	intron (NM_003596, intron 2 of 5)	42343	NM_003596	8460	Hs.421194	NM_003596	ENSG00000169902	TPST1	TANGO13A	tyrosylprotein sulfotransferase 1	protein-coding	0.006515	0.457792	
chunk0089_16_1	chr18	57698934	57699313	+	0	NA	intron (NM_005603, intron 6 of 27)	intron (NM_005603, intron 6 of 27)	68821	NM_001242804	100505549	Hs.660645	NM_001242804		LOC100505549	-	uncharacterized LOC100505549	protein-coding	0.007916	0.371053	
chunk0154_260_1	chr5	81755178	81755733	+	0	NA	Intergenic	Intergenic	-4202	NM_001256735	23635	Hs.102735	NM_012446	ENSG00000145687	SSBP2	HSPC116|SOSS-B2	single stranded DNA binding protein 2	protein-coding	0.005405	0.357914	249(AAGAACTCCATGTTCC,-,0.00),250(AGAACTCCATGTTCCT,+,0.00)
chunk0168_29_1	chr6	77653818	77654160	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-36667	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.000000	0.381924	
chunk0058_431_1	chr13	113158271	113158522	+	0	NA	promoter-TSS (NM_003891)	promoter-TSS (NM_003891)	-258	NM_001256134	8858	Hs.1011	NM_003891	ENSG00000126231	PROZ	PZ	protein Z, vitamin K dependent plasma glycoprotein	protein-coding	0.019920	0.539683	
chunk0013_389_1	chr1	172746152	172747018	+	0	NA	Intergenic	Intergenic	87577	NM_001302746	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.002309	0.410611	347(GTGGACATGGTGTACT,-,0.00),348(TGGACATGGTGTACTT,+,0.00)
chunk0006_359_1	chr1	72858846	72859406	+	0	NA	Intergenic	Intergenic	-447044	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.000000	0.317291	
chunk0140_394_1	chr4	75399781	75400102	+	0	NA	Intergenic	Intergenic	45865	NR_033964	441025	Hs.407667	NR_033964	ENSG00000251383	LINC02483	-	long intergenic non-protein coding RNA 2483	ncRNA	0.009346	0.394410	
chunk0086_225_1	chr18	22683419	22683761	+	0	NA	Intergenic	Intergenic	103247	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.023392	0.475219	
chunk0173_37_1	chr6	142207390	142207782	+	0	NA	intron (NM_016485, intron 7 of 7)	L1MA4|LINE|L1	60424	NM_001286372	51534	Hs.431367	NM_016485	ENSG00000009844	VTA1	C6orf55|DRG-1|DRG1|HSPC228|LIP5|My012|SBP1	vesicle trafficking 1	protein-coding	0.007653	0.458015	
chunk0055_87_1	chr13	54687010	54687731	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	-375322	NR_031628	100302187		NR_031628	ENSG00000283126	MIR1297	MIRN1297|hsa-mir-1297|mir-1297	microRNA 1297	ncRNA	0.001387	0.340720	
chunk0152_183_1	chr5	59768333	59768678	+	0	NA	exon (NM_001197218, exon 1 of 15)	exon (NM_001197218, exon 1 of 15)	107	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.037681	0.540462	
chunk0181_1_1	chr7	77593404	77594056	+	0	NA	intron (NM_001131008, intron 6 of 17)	MLT2B4|LTR|ERVL	55695	NM_001131008	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.001534	0.399694	377(GGGCACACTGTGGCCC,-,0.00)
chunk0086_183_1	chr18	22018261	22018677	+	0	NA	Intergenic	Intergenic	150499	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.004808	0.458034	
chunk0196_116_1	chr8	103419164	103419767	+	0	NA	intron (NM_015420, intron 1 of 10)	MIRb|SINE|MIR	-4130	NR_102338	81034	Hs.532265	NM_030780	ENSG00000164933	SLC25A32	MFT|MFTC|RREI	solute carrier family 25 member 32	protein-coding	0.019900	0.420530	
chunk0010_174_1	chr1	115753815	115754062	+	0	NA	intron (NM_001232, intron 1 of 10)	intron (NM_001232, intron 1 of 10)	14867	NM_001232	845	Hs.57975	NM_001232	ENSG00000118729	CASQ2	PDIB2	calsequestrin 2	protein-coding	0.008097	0.475806	
chunk0001_103_1	chr1	3430016	3430514	+	0	NA	intron (NM_022114, intron 14 of 16)	intron (NM_022114, intron 14 of 16)	-24318	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.024096	0.603206	
chunk0016_378_1	chr1	202624626	202625181	+	0	NA	intron (NM_177402, intron 1 of 8)	(GT)n|Simple_repeat|Simple_repeat	18550	NM_001136504	127833	Hs.25422	NM_177402	ENSG00000143858	SYT2	CMS7|MYSPC|SytII	synaptotagmin 2	protein-coding	0.009009	0.510791	
chunk0006_241_1	chr1	69060298	69060619	+	0	NA	Intergenic	Intergenic	-563237	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.006231	0.381988	
chunk0152_225_1	chr5	60438869	60439278	+	0	NA	intron (NM_001165899, intron 1 of 16)	L1ME4b|LINE|L1	-48640	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.012225	0.375610	220(AAGAACAATGCGTCCC,-,0.00),221(AGAACAATGCGTCCCC,+,0.00)
chunk0029_178_1	chr10	100728947	100729146	+	0	NA	Intergenic	Intergenic	-6663	NM_001304569	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.015075	0.525000	
chunk0066_327_1	chr15	36498023	36498542	+	0	NA	Intergenic	Intergenic	-81321	NM_001130010	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.019268	0.359615	
chunk0079_46_1	chr17	10551983	10552418	+	0	NA	intron (NR_125367, intron 2 of 10)	intron (NR_125367, intron 2 of 10)	-2500	NM_017534	4620	Hs.667534	NM_017534	ENSG00000125414	MYH2	IBM3|MYH2A|MYHSA2|MYHas8|MYPOP|MyHC-2A|MyHC-IIa	myosin heavy chain 2	protein-coding	0.006897	0.403670	
chunk0044_369_1	chr12	39442172	39443137	+	0	NA	intron (NM_017641, intron 1 of 36)	CpG	736	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.087047	0.654244	
chunk0131_202_1	chr3	148703159	148703690	+	0	NA	intron (NM_009585, intron 1 of 1)	intron (NM_009585, intron 1 of 1)	5553	NM_009585	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.009416	0.355263	240(AGAAACACAGTGTACC,-,0.00),241(GAAACACAGTGTACCG,+,0.00)
chunk0100_362_1	chr2	117771356	117771555	+	0	NA	Intergenic	Intergenic	-43224	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.000000	0.475000	
chunk0188_174_1	chr8	11174219	11174661	+	0	NA	intron (NM_173683, intron 1 of 2)	intron (NM_173683, intron 1 of 2)	26926	NM_173683	286046	Hs.657083	NM_173683	ENSG00000171044	XKR6	C8orf21|C8orf5|C8orf7|XRG6	XK related 6	protein-coding	0.020362	0.417607	376(TAGACATTCTGTTCTT,+,0.00)
chunk0191_359_1	chr8	56727683	56728265	+	0	NA	Intergenic	Intergenic	-168151	NR_038236	100507632	Hs.583755	NR_038236	ENSG00000246430	LINC00968	-	long intergenic non-protein coding RNA 968	ncRNA	0.001718	0.301887	
chunk0193_375_1	chr8	80121488	80121758	+	0	NA	intron (NR_105035, intron 1 of 6)	intron (NR_105035, intron 1 of 6)	-40792	NM_001287140	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.018519	0.424354	
chunk0031_318_1	chr10	129157724	129157968	+	0	NA	Intergenic	L2a|LINE|L2	-309338	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.000000	0.371429	
chunk0117_122_1	chr22	19014363	19014675	+	0	NA	intron (NR_110533, intron 5 of 5)	intron (NR_110533, intron 5 of 5)	-3315	NR_024159	25787	Hs.106311	NR_024159		DGCR9	DGS-A	DiGeorge syndrome critical region gene 9	ncRNA	0.012821	0.450479	
chunk0089_41_1	chr18	58046501	58046817	+	0	NA	promoter-TSS (NM_001144964)	promoter-TSS (NM_001144964)	-567	NM_001144964	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.006329	0.400631	
chunk0145_307_1	chr4	150372722	150372921	+	0	NA	intron (NM_001199282, intron 47 of 56)	MLT1F|LTR|ERVL-MaLR	-209104	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.010050	0.410000	
chunk0085_436_1	chr18	10953565	10953780	+	0	NA	intron (NM_022068, intron 3 of 51)	LTR53B|LTR|ERVL	-194023	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.013953	0.449074	
chunk0154_79_1	chr5	77642816	77643106	+	0	NA	Intergenic	Intergenic	-4264	NM_032109	23440	Hs.202247	NM_032109	ENSG00000171540	OTP	-	orthopedia homeobox	protein-coding	0.020690	0.446735	
chunk0129_448_1	chr3	128218950	128219236	+	0	NA	intron (NM_021937, intron 1 of 6)	intron (NM_021937, intron 1 of 6)	65636	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.027972	0.592334	
chunk0049_355_1	chr12	95428351	95428825	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	-45458	NM_006838	10988	Hs.444986	NM_006838	ENSG00000111142	METAP2	MAP2|MNPEP|p67eIF2	methionyl aminopeptidase 2	protein-coding	0.008439	0.458947	
chunk0205_20_1	chr9	105144009	105144385	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-100416	NM_080546	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.000000	0.371353	
chunk0012_414_1	chr1	164281330	164281529	+	0	NA	Intergenic	L1MCa|LINE|L1	-277931	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.005025	0.435000	67(CAGAACATTCTGTTCA,-,0.00),68(AGAACATTCTGTTCAT,+,0.00)
chunk0038_179_1	chr11	85748129	85748842	+	0	NA	intron (NM_001289608, intron 1 of 18)	intron (NM_001289608, intron 1 of 18)	9584	NM_001162951	54843	Hs.369520	NM_032379	ENSG00000137501	SYTL2	CHR11SYT|EXO4|PPP1R151|SGA72M|SLP2|SLP2A	synaptotagmin like 2	protein-coding	0.011220	0.397759	
chunk0198_381_1	chr8	141233967	141234246	+	0	NA	intron (NM_001286646, intron 1 of 7)	intron (NM_001286646, intron 1 of 7)	-5532	NM_001080431	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.028674	0.514286	
chunk0110_444_1	chr20	21089291	21089670	+	0	NA	Intergenic	Intergenic	-36503	NM_001276389	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.018470	0.415789	
chunk0101_147_1	chr2	127907678	127908070	+	0	NA	Intergenic	L1ME3A|LINE|L1	-21934	NM_001199140	83607	Hs.546449	NM_031445	ENSG00000144233	AMMECR1L	-	AMMECR1 like	protein-coding	0.007653	0.447837	
chunk0104_377_1	chr2	180249476	180249970	+	0	NA	Intergenic	Intergenic	-242670	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.004049	0.335354	
chunk0147_71_1	chr4	172942623	172943264	+	0	NA	intron (NM_001034845, intron 9 of 12)	intron (NM_001034845, intron 9 of 12)	-216065	NR_125894	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.009360	0.457944	
chunk0151_149_1	chr5	46097247	46097977	+	0	NA	Intergenic	Intergenic	-401494	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.002740	0.359781	
chunk0104_366_1	chr2	180092060	180092473	+	0	NA	Intergenic	Intergenic	-85213	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.000000	0.359903	
chunk0009_104_1	chr1	102248006	102248648	+	0	NA	Intergenic	L1M5|LINE|L1	-251093	NM_001288823	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.001558	0.284603	
chunk0145_86_1	chr4	145891546	145891911	+	0	NA	intron (NM_178835, intron 3 of 14)	intron (NM_178835, intron 3 of 14)	47232	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.005479	0.478142	
chunk0090_83_1	chr18	70500205	70500460	+	0	NA	Intergenic	Intergenic	-115741	NR_110764	101060542	Hs.586967	NR_110764	ENSG00000266278	LINC01910	-	long intergenic non-protein coding RNA 1910	ncRNA	0.019608	0.390625	
chunk0045_343_1	chr12	51232506	51233372	+	0	NA	Intergenic	L1ME1|LINE|L1	-5785	NM_001136264	9802	Hs.369761	NM_014764	ENSG00000183283	DAZAP2	PRTB	DAZ associated protein 2	protein-coding	0.003464	0.388697	
chunk0021_190_1	chr10	5659874	5660127	+	0	NA	intron (NR_037164, intron 1 of 6)	intron (NR_037164, intron 1 of 6)	6595	NM_024701	79754	Hs.445899	NM_024701	ENSG00000196372	ASB13	-	ankyrin repeat and SOCS box containing 13	protein-coding	0.015810	0.559055	
chunk0134_418_1	chr3	183291518	183292148	+	0	NA	intron (NM_015078, intron 13 of 29)	intron (NM_015078, intron 13 of 29)	38589	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.004762	0.386688	
chunk0033_136_1	chr11	15313808	15314256	+	0	NA	Intergenic	L2a|LINE|L2	164930	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.004464	0.380846	
chunk0019_69_1	chr1	224276986	224277991	+	0	NA	intron (NM_206840, intron 15 of 21)	intron (NM_206840, intron 15 of 21)	-20347	NR_031574	100313769		NR_031574	ENSG00000221406	MIR320B2	MIR320B-2|MIRN320B2|mir-320b-2	microRNA 320b-2	ncRNA	0.006965	0.340954	293(TAGCACACAGTGTGCA,-,0.00),294(AGCACACAGTGTGCAA,+,0.00)
chunk0053_64_1	chr13	28118040	28118252	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-17554	NR_130706	2322	Hs.507590	NM_004119	ENSG00000122025	FLT3	CD135|FLK-2|FLK2|STK1	fms related tyrosine kinase 3	protein-coding	0.009434	0.474178	
chunk0088_444_1	chr18	56661477	56662389	+	0	NA	intron (NM_015285, intron 1 of 27)	Charlie13a|DNA|hAT-Charlie	10548	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.006579	0.389923	
chunk0130_105_1	chr3	131155039	131155344	+	0	NA	intron (NM_145910, intron 10 of 14)	intron (NM_145910, intron 10 of 14)	-128337	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.006557	0.356209	224(AGGAACTTGGTGTTCC,-,0.00),225(GGAACTTGGTGTTCCA,+,0.00)
chunk0079_325_1	chr17	17416471	17417015	+	0	NA	Intergenic	Intergenic	-60243	NM_018019	55090	Hs.244595	NM_018019	ENSG00000141026	MED9	MED25	mediator complex subunit 9	protein-coding	0.014706	0.493578	
chunk0015_100_1	chr1	185078309	185078665	+	0	NA	intron (NM_007212, intron 1 of 6)	intron (NM_007212, intron 1 of 6)	33068	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.002809	0.406162	
chunk0175_166_1	chr7	4543006	4543485	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-139054	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.010438	0.527083	
chunk0175_177_1	chr7	5200161	5200893	+	0	NA	intron (NM_001033518, intron 3 of 12)	L1MD1|LINE|L1	10323	NM_001033518	26100	Hs.122363	NM_015610	ENSG00000157954	WIPI2	ATG18B|Atg21|CGI-50|IDDSSA|WIPI-2	WD repeat domain, phosphoinositide interacting 2	protein-coding	0.019126	0.488404	
chunk0175_403_1	chr6	168609794	168610342	+	0	NA	intron (NM_022138, intron 9 of 12)	intron (NM_022138, intron 9 of 12)	168917	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.020073	0.462659	522(AAGGTCAGCTTGTGCT,-,0.00),523(AGGTCAGCTTGTGCTG,+,0.00)
chunk0060_123_1	chr14	43901678	43902848	+	0	NA	Intergenic	Intergenic	605033	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.003419	0.338173	
chunk0117_439_1	chr21	46379789	46380161	+	0	NA	intron (NM_001315529, intron 15 of 46)	L1M4|LINE|L1	55087	NM_001315529	5116	Hs.474069	NM_006031	ENSG00000160299	PCNT	KEN|MOPD2|PCN|PCNT2|PCNTB|PCTN2|SCKL4	pericentrin	protein-coding	0.024194	0.546917	
chunk0209_305_1	chrX	49003612	49004162	+	0	NA	Intergenic	L1ME2|LINE|L1	-1623	NM_020137	56850	Hs.109929	NM_020137	ENSG00000068400	GRIPAP1	GRASP-1	GRIP1 associated protein 1	protein-coding	0.012727	0.410163	
chunk0036_276_1	chr11	65275227	65275842	+	0	NA	intron (NM_002689, intron 4 of 17)	intron (NM_002689, intron 4 of 17)	13682	NM_002689	23649	Hs.201897	NM_002689	ENSG00000014138	POLA2	-	DNA polymerase alpha 2, accessory subunit	protein-coding	0.006504	0.389610	
chunk0045_25_1	chr12	43810108	43810637	+	0	NA	Intergenic	Intergenic	-3997	NR_073473	5756	Hs.189075	NM_002822	ENSG00000151239	TWF1	A6|PTK9	twinfilin actin binding protein 1	protein-coding	0.005671	0.388679	
chunk0010_408_1	chr1	119618035	119618568	+	0	NA	Intergenic	Intergenic	-19010	NR_036540	644242	Hs.515383	NR_036540	ENSG00000260941	LINC00622	-	long intergenic non-protein coding RNA 622	ncRNA	0.007505	0.490637	
chunk0124_303_1	chr3	57917865	57918545	+	0	NA	3' UTR (NM_001311179, exon 7 of 7)	3' UTR (NM_001311179, exon 7 of 7)	28291	NM_001304422	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.005882	0.327460	358(AAGCACTTTGTGTCCT,-,0.00),359(AGCACTTTGTGTCCTT,+,0.00)
chunk0080_387_1	chr17	34725728	34726218	+	0	NA	Intergenic	MER121|DNA|hAT?	145224	NM_001304438	124842	Hs.310482	NM_207313	ENSG00000181291	TMEM132E	DFNB99	transmembrane protein 132E	protein-coding	0.008163	0.478615	
chunk0036_267_1	chr11	65117475	65117942	+	0	NA	promoter-TSS (NM_014205)	promoter-TSS (NM_014205)	30	NM_014205	741	Hs.121025	NM_014205	ENSG00000174276	ZNHIT2	C11orf5|FON	zinc finger HIT-type containing 2	protein-coding	0.113490	0.653846	
chunk0047_365_1	chr12	75078406	75078681	+	0	NA	intron (NM_139136, intron 2 of 5)	MIR|SINE|MIR	131205	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.000000	0.336957	
chunk0192_87_1	chr8	60983539	60983828	+	0	NA	Intergenic	Intergenic	-15935	NR_034003	100130298	Hs.636194	NR_034003		LOC100130298	-	hCG1816373-like	ncRNA	0.006920	0.506897	
chunk0095_183_1	chr2	17872927	17873306	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-4731	NM_001282428	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.005277	0.481579	185(AGGTACATGCTGTCCT,-,0.00),186(GGTACATGCTGTCCTC,+,0.00)
chunk0185_116_1	chr7	125929904	125930535	+	0	NA	Intergenic	Intergenic	-665928	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.001585	0.270570	
chunk0060_285_1	chr14	50534150	50534349	+	0	NA	intron (NM_001127713, intron 1 of 13)	intron (NM_001127713, intron 1 of 13)	1167	NM_001127713	51062	Hs.584905	NM_015915	ENSG00000198513	ATL1	AD-FSP|FSP1|GBP3|HSN1D|SPG3|SPG3A|atlastin1	atlastin GTPase 1	protein-coding	0.020101	0.355000	
chunk0192_28_1	chr8	58549705	58550190	+	0	NA	Intergenic	L1MC3|LINE|L1	-3222	NM_001007069	6386	Hs.200804	NM_005625	ENSG00000137575	SDCBP	MDA-9|MDA9|ST1|SYCL|TACIP18	syndecan binding protein	protein-coding	0.006186	0.343621	
chunk0142_153_1	chr4	95025644	95026202	+	0	NA	intron (NM_001256792, intron 1 of 10)	intron (NM_001256792, intron 1 of 10)	-25756	NM_001256793	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.003584	0.311270	
chunk0134_350_1	chr3	182540723	182540922	+	0	NA	Intergenic	Intergenic	-54460	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.000000	0.385000	
chunk0014_115_1	chr1	176969948	176970184	+	0	NA	intron (NM_004319, intron 8 of 22)	intron (NM_004319, intron 8 of 22)	59379	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.012712	0.459916	
chunk0109_148_1	chr20	3632482	3632760	+	0	NA	intron (NM_139321, intron 25 of 28)	L2a|LINE|L2	30778	NM_022139	64096	Hs.302025	NM_022139	ENSG00000125861	GFRA4	-	GDNF family receptor alpha 4	protein-coding	0.010791	0.483871	
chunk0054_230_1	chr13	45554731	45555149	+	0	NA	intron (NM_182542, intron 11 of 14)	intron (NM_182542, intron 11 of 14)	60799	NM_182542	220081	Hs.668747	NM_182542	ENSG00000165837	ERICH6B	FAM194B	glutamate rich 6B	protein-coding	0.007177	0.544153	
chunk0189_13_1	chr8	19501506	19502123	+	0	NA	intron (NM_001130518, intron 4 of 9)	intron (NM_001130518, intron 4 of 9)	100731	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.006483	0.404531	
chunk0126_271_1	chr3	79936058	79936307	+	0	NA	Intergenic	Intergenic	-168273	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004016	0.324000	
chunk0110_56_1	chr20	10800220	10800857	+	0	NA	Intergenic	Intergenic	47448	NR_110611	101929395	Hs.244862	NR_110611		LINC01752	-	long intergenic non-protein coding RNA 1752	ncRNA	0.014129	0.424765	
chunk0078_51_1	chr17	1356337	1356536	+	0	NA	intron (NR_024058, intron 5 of 6)	intron (NR_024058, intron 5 of 6)	43826	NR_024058	7531	Hs.513851	NM_006761	ENSG00000108953	YWHAE	14-3-3E|HEL2|KCIP-1|MDCR|MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	protein-coding	0.005025	0.395000	
chunk0103_431_1	chr2	169922439	169922692	+	0	NA	intron (NM_172070, intron 11 of 38)	L1MB2|LINE|L1	95057	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.007905	0.338583	
chunk0096_436_1	chr2	38613703	38614132	+	0	NA	Intergenic	L2c|LINE|L2	-10881	NM_138394	92906	Hs.445497	NM_138394	ENSG00000143889	HNRNPLL	HNRPLL|SRRF	heterogeneous nuclear ribonucleoprotein L like	protein-coding	0.011655	0.425581	
chunk0012_420_1	chr1	164485654	164486206	+	0	NA	Intergenic	Intergenic	-73430	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.005435	0.423146	301(AGGTACAAACAGTGCC,-,0.00),302(GGTACAAACAGTGCCT,+,0.00)
chunk0189_72_1	chr8	20829104	20829559	+	0	NA	Intergenic	Intergenic	-124302	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.019780	0.462719	
chunk0008_298_1	chr1	95007630	95008211	+	0	NA	intron (NR_131032, intron 2 of 2)	L2a|LINE|L2	-53676	NR_132786	101928098	Hs.730090	NR_132786	ENSG00000230427	LOC101928098	-	uncharacterized LOC101928098	ncRNA	0.003442	0.417526	
chunk0143_10_1	chr4	105831054	105831695	+	0	NA	intron (NM_001031720, intron 8 of 11)	MIR3|SINE|MIR	-4202	NR_125927	101929529	Hs.603751	NR_125927	ENSG00000251175	LOC101929529	-	uncharacterized LOC101929529	ncRNA	0.003120	0.348910	
chunk0181_200_1	chr7	83828565	83828857	+	0	NA	Intergenic	MSTA|LTR|ERVL-MaLR	-179548	NM_012431	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.006849	0.440273	
chunk0188_408_1	chr8	18852420	18852743	+	0	NA	intron (NM_015310, intron 4 of 15)	MamSINE1|SINE|tRNA-RTE	-43686	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.009288	0.503086	
chunk0036_345_1	chr11	66789515	66790567	+	0	NA	intron (NM_001302084, intron 3 of 14)	AluY|SINE|Alu	45305	NM_024650	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.013308	0.427350	
chunk0172_285_1	chr6	137776752	137777529	+	0	NA	Intergenic	Intergenic	-38103	NR_121618	100507406	Hs.556703	NR_121618	ENSG00000234956	LINC02539	-	long intergenic non-protein coding RNA 2539	ncRNA	0.016731	0.377892	636(AAGAACAAAGTGTTCA,-,0.00),637(AGAACAAAGTGTTCAA,+,0.00)
chunk0097_64_1	chr2	44104840	44105136	+	0	NA	Intergenic	Intergenic	-63815	NM_177968	5495	Hs.416769	NM_002706	ENSG00000138032	PPM1B	PP2C-beta|PP2C-beta-X|PP2CB|PP2CBETA|PPC2BETAX	protein phosphatase, Mg2+/Mn2+ dependent 1B	protein-coding	0.000000	0.356902	
chunk0200_437_1	chr9	30235509	30236098	+	0	NA	Intergenic	Intergenic	172651	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.005093	0.323729	
chunk0106_280_1	chr2	204069304	204069960	+	0	NA	Intergenic	Intergenic	132884	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.004573	0.331811	
chunk0207_91_1	chrX	9581791	9582185	+	0	NA	intron (NM_001139468, intron 3 of 17)	intron (NM_001139468, intron 3 of 17)	116827	NM_005647	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.010152	0.465823	196(TGGAACACAGTGTTCC,-,0.00),197(GGAACACAGTGTTCCC,+,0.00)
chunk0042_292_1	chr12	7601736	7602204	+	0	NA	Intergenic	HERVP71A-int|LTR|ERV1	63933	NM_005889	339	Hs.560	NM_001644	ENSG00000111701	APOBEC1	APOBEC-1|BEDP|CDAR1|HEPR	apolipoprotein B mRNA editing enzyme catalytic subunit 1	protein-coding	0.002137	0.394456	240(TAGAACACAGTGTACC,-,0.00),241(AGAACACAGTGTACCT,+,0.00)
chunk0061_182_1	chr14	60017135	60017502	+	0	NA	intron (NR_075071, intron 24 of 32)	L2b|LINE|L2	-74593	NM_022495	64430	Hs.509499	NM_022495	ENSG00000126773	PCNX4	C14orf135|FBP2|PCNXL4	pecanex 4	protein-coding	0.002725	0.353261	
chunk0023_411_1	chr10	31143619	31144278	+	0	NA	Intergenic	Intergenic	-112011	NR_026560	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.004552	0.493939	
chunk0021_403_1	chr1	246666904	246667437	+	0	NA	3' UTR (NM_152609, exon 11 of 11)	3' UTR (NM_152609, exon 11 of 11)	-56906	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.013133	0.348315	
chunk0024_347_1	chr10	43455446	43455874	+	0	NA	intron (NR_026693, intron 1 of 3)	CpG	18534	NR_026693									0.133178	0.720280	
chunk0031_450_1	chr10	132667432	132667683	+	0	NA	intron (NM_005539, intron 4 of 15)	intron (NM_005539, intron 4 of 15)	118476	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.023904	0.432540	
chunk0038_258_1	chr11	88660311	88660774	+	0	NA	intron (NM_001143831, intron 2 of 8)	intron (NM_001143831, intron 2 of 8)	155966	NR_049724	100873989	Hs.616625	NR_049724	ENSG00000255082	GRM5-AS1	-	GRM5 antisense RNA 1	ncRNA	0.004320	0.355603	205(AAGTACATTCTGTACC,-,0.00),206(AGTACATTCTGTACCC,+,0.00)
chunk0198_219_1	chr8	133929013	133929556	+	0	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	42788	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.007366	0.393382	352(GGAACTGCCCGTGCCT,+,0.00)
chunk0157_246_1	chr5	119784994	119785543	+	0	NA	Intergenic	MER68|LTR|ERVL	155709	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.001821	0.414545	
chunk0047_42_1	chr12	66744933	66745648	+	0	NA	Intergenic	Mam_R4|LINE|Dong-R4	-66145	NM_001178074	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.005594	0.368715	
chunk0179_60_1	chr7	43879240	43879525	+	0	NA	intron (NM_001290075, intron 5 of 5)	intron (NM_001290075, intron 5 of 5)	-9836	NM_032014	64951	Hs.284286	NM_032014	ENSG00000062582	MRPS24	HSPC335|MRP-S24|S24mt|bMRP-47|bMRP47	mitochondrial ribosomal protein S24	protein-coding	0.007018	0.503497	155(AGGCTCAGGGTGTGCT,-,0.00),156(GGCTCAGGGTGTGCTC,+,0.00)
chunk0034_138_1	chr11	28983675	28984306	+	0	NA	Intergenic	MER54A|LTR|ERVL	-506442	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.006339	0.447785	
chunk0133_416_1	chr3	174565305	174565875	+	0	NA	Intergenic	L1MC2|LINE|L1	-293731	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.007018	0.332750	
chunk0192_306_1	chr8	66818046	66818701	+	0	NA	intron (NM_001033578, intron 5 of 16)	intron (NM_001033578, intron 5 of 16)	43192	NM_170709	23678	Hs.613417	NM_013257	ENSG00000104205	SGK3	CISK|SGK2|SGKL	serum/glucocorticoid regulated kinase family member 3	protein-coding	0.001527	0.349085	
chunk0075_447_1	chr16	58124371	58124662	+	0	NA	intron (NM_013242, intron 1 of 5)	Tigger3b|DNA|TcMar-Tigger	4876	NM_013242	29105	Hs.532755	NM_013242	ENSG00000070761	CFAP20	BUG22|C16orf80|EVORF|GTL3|fSAP23	cilia and flagella associated protein 20	protein-coding	0.013746	0.404110	
chunk0158_338_1	chr5	133266203	133266719	+	0	NA	intron (NM_015082, intron 6 of 15)	intron (NM_015082, intron 6 of 15)	161245	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.019380	0.566731	
chunk0103_368_1	chr2	168484578	168485052	+	0	NA	intron (NM_001256126, intron 1 of 10)	intron (NM_001256126, intron 1 of 10)	28566	NM_203463	253782	Hs.506829	NM_203463	ENSG00000172292	CERS6	CERS5|LASS6	ceramide synthase 6	protein-coding	0.004219	0.389474	341(TGGAACAGAATGTACC,-,0.00),342(GGAACAGAATGTACCT,+,0.00)
chunk0002_264_1	chr1	21347275	21347474	+	0	NA	Intergenic	Intergenic	-1833	NM_001113348	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.010050	0.575000	
chunk0073_93_1	chr16	4260420	4260941	+	0	NA	intron (NM_003223, intron 4 of 6)	intron (NM_003223, intron 4 of 6)	-6891	NR_039999	100507501	Hs.632979	NR_039999		LINC01569	-	long intergenic non-protein coding RNA 1569	ncRNA	0.032630	0.624521	214(GAGCACACCCTGCCCT,-,0.00),215(AGCACACCCTGCCCTG,+,0.00)
chunk0024_265_1	chr10	41850921	41851260	+	0	NA	Intergenic	Intergenic	516955	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.041298	0.347059	
chunk0157_375_1	chr5	123712067	123712674	+	0	NA	Intergenic	L1M4|LINE|L1	166953	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.000000	0.296053	
chunk0077_45_1	chr16	75898199	75898398	+	0	NA	Intergenic	Intergenic	250561	NM_018975	54386	Hs.301419	NM_018975	ENSG00000166848	TERF2IP	DRIP5|RAP1	TERF2 interacting protein	protein-coding	0.000000	0.275000	
chunk0112_134_1	chr20	38571160	38571569	+	0	NA	intron (NM_020336, intron 28 of 29)	L1MA10|LINE|L1	-9831	NM_001018082	149685	Hs.368028	NM_174906	ENSG00000182035	ADIG	SMAF1	adipogenin	protein-coding	0.002445	0.346341	
chunk0104_390_1	chr2	180367923	180368661	+	0	NA	Intergenic	Intergenic	-323812	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.001355	0.349120	
chunk0210_246_1	chrX	82813539	82814236	+	0	NA	Intergenic	Intergenic	-694374	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.002869	0.385387	
chunk0121_22_1	chr3	14947955	14948318	+	0	NA	promoter-TSS (NR_046255)	promoter-TSS (NR_046255)	-243	NR_046255	100505641	Hs.517821	NR_046251	ENSG00000225733	FGD5-AS1	-	FGD5 antisense RNA 1	ncRNA	0.118457	0.730769	
chunk0065_417_1	chr14	105826271	105826495	+	0	NA	Intergenic	L1PB1|LINE|L1	31189	NR_130468	100616374		NR_130468	ENSG00000265612	MIR4539	-	microRNA 4539	ncRNA	0.004464	0.364444	
chunk0039_317_1	chr11	103450066	103450659	+	0	NA	intron (NM_001377, intron 85 of 88)	L1MEh|LINE|L1	340931	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.006745	0.303030	
chunk0045_83_1	chr12	45849367	45849737	+	0	NA	intron (NM_152641, intron 13 of 20)	intron (NM_152641, intron 13 of 20)	119715	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.010811	0.363881	
chunk0105_452_1	chr2	195099111	195099378	+	0	NA	Intergenic	L1PA16|LINE|L1	368649	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.003745	0.320896	
chunk0041_439_1	chr11	134527214	134527927	+	0	NA	Intergenic	MER53|DNA|hAT	91088	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.023843	0.462185	341(TAGTACAACATGTCCC,-,0.00),342(AGTACAACATGTCCCC,+,0.00)
chunk0085_147_1	chr18	3340878	3341302	+	0	NA	Intergenic	L1PA13|LINE|L1	-70837	NM_174886	7050	Hs.373550	NM_003244	ENSG00000177426	TGIF1	HPE4|TGIF	TGFB induced factor homeobox 1	protein-coding	0.002358	0.418824	
chunk0201_49_1	chr9	33819880	33820267	+	0	NA	intron (NM_017811, intron 1 of 4)	intron (NM_017811, intron 1 of 4)	2889	NM_017811	54926	Hs.643648	NM_017811	ENSG00000107341	UBE2R2	CDC34B|E2-CDC34B|UBC3B	ubiquitin conjugating enzyme E2 R2	protein-coding	0.012920	0.371134	
chunk0190_86_1	chr8	30091605	30091991	+	0	NA	Intergenic	(CACA)n|Simple_repeat|Simple_repeat	-3608	NM_001128208	23484	Hs.146585	NM_015344	ENSG00000104660	LEPROTL1	HSPC112|Vps55|my047	leptin receptor overlapping transcript like 1	protein-coding	0.051813	0.485788	
chunk0111_365_1	chr20	33718514	33718791	+	0	NA	intron (NM_183397, intron 1 of 2)	MIRb|SINE|MIR	1678	NM_183397	11264	Hs.654857	NM_007238	ENSG00000101417	PXMP4	PMP24	peroxisomal membrane protein 4	protein-coding	0.010830	0.478417	
chunk0133_177_1	chr3	170046331	170046759	+	0	NA	intron (NM_014373, intron 2 of 3)	intron (NM_014373, intron 2 of 3)	8598	NM_014373	26996	Hs.231320	NM_014373	ENSG00000173890	GPR160	GPCR1|GPCR150	G protein-coupled receptor 160	protein-coding	0.004673	0.433566	
chunk0082_386_1	chr17	60596733	60596968	+	0	NA	Intergenic	L2a|LINE|L2	-3333	NM_003620	8493	Hs.286073	NM_003620	ENSG00000170836	PPM1D	IDDGIP|PP2C-DELTA|WIP1	protein phosphatase, Mg2+/Mn2+ dependent 1D	protein-coding	0.008511	0.372881	
chunk0070_391_1	chr15	76887673	76888034	+	0	NA	Intergenic	L1PA6|LINE|L1	-3977	NM_020843	49855	Hs.458986	NM_020843	ENSG00000140386	SCAPER	IDDRP|MSTP063|ZNF291|Zfp291	S-phase cyclin A associated protein in the ER	protein-coding	0.008310	0.544199	
chunk0133_166_1	chr3	169835650	169835989	+	0	NA	intron (NM_001080460, intron 4 of 4)	L2a|LINE|L2	13897	NM_001080460	344657	Hs.319484	NM_001080460	ENSG00000188306	LRRIQ4	LRRC64	leucine rich repeats and IQ motif containing 4	protein-coding	0.002950	0.479412	
chunk0014_32_1	chr1	174872112	174872356	+	0	NA	intron (NM_001243765, intron 2 of 8)	intron (NM_001243765, intron 2 of 8)	-2152	NM_001243763	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.000000	0.314286	
chunk0156_386_1	chr5	113117562	113117930	+	0	NA	intron (NM_002387, intron 4 of 16)	intron (NM_002387, intron 4 of 16)	141036	NR_038352	167227	Hs.443875	NM_152624	ENSG00000172795	DCP2	NUDT20	decapping mRNA 2	protein-coding	0.005435	0.449864	
chunk0123_450_1	chr3	50860321	50860530	+	0	NA	intron (NM_004947, intron 3 of 52)	L1PA17|LINE|L1	185184	NM_004947	1795	Hs.476284	NM_004947	ENSG00000088538	DOCK3	MOCA|NEDIDHA|PBP	dedicator of cytokinesis 3	protein-coding	0.000000	0.504762	
chunk0023_161_1	chr10	24288498	24289017	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	13072	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.001927	0.453846	
chunk0021_416_1	chr1	246853375	246853595	+	0	NA	intron (NM_015446, intron 31 of 35)	intron (NM_015446, intron 31 of 35)	63868	NR_015422	149134	Hs.720494	NM_207326		LINC01341	-	long intergenic non-protein coding RNA 1341	ncRNA	0.009091	0.330317	
chunk0020_208_1	chr1	235079712	235079948	+	0	NA	Intergenic	Intergenic	-10012	NR_027454	731656	Hs.702477	NR_027454		LINC01348	-	long intergenic non-protein coding RNA 1348	ncRNA	0.016949	0.573840	
chunk0197_298_1	chr8	124479569	124479877	+	0	NA	intron (NM_007218, intron 1 of 1)	L1M5|LINE|L1	4956	NM_007218	11236	Hs.744151	NM_007218	ENSG00000170881	RNF139	HRCA1|RCA1|TRC8	ring finger protein 139	protein-coding	0.000000	0.398058	
chunk0022_342_1	chr10	16856595	16856914	+	0	NA	intron (NM_001081, intron 59 of 66)	intron (NM_001081, intron 59 of 66)	-39300	NM_012425	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.009404	0.450000	140(AGGTGCACAGTGTGCT,-,0.00),141(GGTGCACAGTGTGCTG,+,0.00)
chunk0120_312_1	chr3	10203936	10204433	+	0	NA	intron (NM_001570, intron 3 of 12)	MIRb|SINE|MIR	39305	NM_001570	3656	Hs.449207	NM_001570	ENSG00000134070	IRAK2	IRAK-2	interleukin 1 receptor associated kinase 2	protein-coding	0.010060	0.465863	
chunk0065_176_1	chr15	26120996	26121195	+	0	NA	intron (NR_038851, intron 2 of 3)	intron (NR_038851, intron 2 of 3)	5282	NR_038851	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.010050	0.460000	
chunk0132_45_1	chr3	154877442	154878212	+	0	NA	Intergenic	L1PA7|LINE|L1	-201820	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.009091	0.361868	
chunk0019_204_1	chr1	226951703	226952074	+	0	NA	intron (NM_020247, intron 1 of 14)	MER58A|DNA|hAT-Charlie	11651	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.010782	0.389785	
chunk0065_167_1	chr15	25825342	25825665	+	0	NA	intron (NM_024490, intron 1 of 20)	L1M4|LINE|L1	23322	NR_039865	100616474		NR_039865	ENSG00000266517	MIR4715	-	microRNA 4715	ncRNA	0.000000	0.462963	
chunk0108_64_1	chr2	227231014	227231269	+	0	NA	intron (NR_102371, intron 10 of 13)	intron (NR_102371, intron 10 of 13)	66576	NM_000091	1285	Hs.570065	NM_000091	ENSG00000169031	COL4A3	ATS2|ATS3	collagen type IV alpha 3 chain	protein-coding	0.003922	0.437500	
chunk0150_292_1	chr5	37370803	37371579	+	0	NA	promoter-TSS (NM_153485)	promoter-TSS (NM_153485)	-65	NM_153485	9631	Hs.547696	NM_004298	ENSG00000113569	NUP155	ATFB15|N155	nucleoporin 155	protein-coding	0.057990	0.563707	
chunk0127_239_1	chr3	96883562	96883761	+	0	NA	intron (NM_001080448, intron 2 of 17)	L1PB1|LINE|L1	69080	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.430000	
chunk0019_459_1	chr1	231421060	231421277	+	0	NA	exon (NM_022051, exon 1 of 5)	exon (NM_022051, exon 1 of 5)	3876	NM_022051	54583	Hs.444450	NM_022051	ENSG00000135766	EGLN1	C1orf12|ECYT3|HALAH|HIF-PH2|HIFPH2|HPH-2|HPH2|PHD2|SM20|ZMYND6	egl-9 family hypoxia inducible factor 1	protein-coding	0.087558	0.628440	
chunk0183_192_1	chr7	106284936	106285201	+	0	NA	5' UTR (NM_005746, exon 1 of 11)	5' UTR (NM_005746, exon 1 of 11)	124	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.120755	0.721805	
chunk0087_15_1	chr18	30959671	30960047	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	82956	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.002660	0.429708	
chunk0044_297_1	chr12	32865571	32865894	+	0	NA	intron (NM_001005242, intron 4 of 12)	L1ME1|LINE|L1	31114	NM_001005242	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.009288	0.379630	
chunk0168_434_1	chr6	95680166	95680704	+	0	NA	Intergenic	Intergenic	102938	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.003717	0.391466	
chunk0020_329_1	chr1	238162362	238162908	+	0	NA	Intergenic	L1MA2|LINE|L1	-271713	NM_021186	57829	Hs.136241	NM_021186	ENSG00000116996	ZP4	ZBP|ZP1|ZPB|Zp-4	zona pellucida glycoprotein 4	protein-coding	0.001832	0.314442	283(TATAACAGTCTGTGCT,-,0.00),284(ATAACAGTCTGTGCTT,+,0.00)
chunk0004_336_1	chr1	50633561	50634313	+	0	NA	intron (NM_007051, intron 8 of 18)	intron (NM_007051, intron 8 of 18)	-210490	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.007979	0.354582	430(GGGAACAATCAGTACC,-,0.00),431(GGAACAATCAGTACCA,+,0.00)
chunk0033_22_1	chr11	12691549	12691868	+	0	NA	intron (NM_021961, intron 2 of 12)	intron (NM_021961, intron 2 of 12)	17286	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.009404	0.418750	
chunk0111_247_1	chr20	29885654	29886095	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-5411	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.000000	0.355204	
chunk0212_365_1	chrX	149481170	149481369	+	0	NA	3' UTR (NM_000202, exon 9 of 9)	3' UTR (NM_000202, exon 9 of 9)	24085	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.030151	0.430000	
chunk0144_339_1	chr4	139296616	139297037	+	0	NA	intron (NM_001184988, intron 1 of 5)	intron (NM_001184988, intron 1 of 5)	4384	NM_001184986	4717	Hs.84549	NM_002494	ENSG00000109390	NDUFC1	KFYI	NADH:ubiquinone oxidoreductase subunit C1	protein-coding	0.002375	0.300948	
chunk0007_219_1	chr1	81699366	81699565	+	0	NA	promoter-TSS (NM_001297704)	promoter-TSS (NM_001297704)	-305	NM_001297704	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.020101	0.470000	
chunk0139_275_1	chr4	56906916	56907196	+	0	NA	promoter-TSS (NM_005612)	promoter-TSS (NM_005612)	-820	NM_005612	5978	Hs.307836	NM_005612	ENSG00000084093	REST	DFNA27|GINGF5|HGF5|NRSF|WT6|XBR	RE1 silencing transcription factor	protein-coding	0.032143	0.491103	
chunk0034_311_1	chr11	35083058	35083509	+	0	NA	Intergenic	Intergenic	54749	NR_120528	100507144	Hs.673491	NR_120528	ENSG00000255521	LOC100507144	-	uncharacterized LOC100507144	ncRNA	0.008869	0.469027	
chunk0211_57_1	chrX	109679729	109680396	+	0	NA	intron (NM_004458, intron 6 of 15)	LTR40b|LTR|ERVL	53330	NM_022977	2182	Hs.268785	NM_004458	ENSG00000068366	ACSL4	ACS4|FACL4|LACS4|MRX63|MRX68	acyl-CoA synthetase long chain family member 4	protein-coding	0.004498	0.416168	
chunk0033_447_1	chr11	25485346	25485545	+	0	NA	Intergenic	Intergenic	-703678	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.010050	0.380000	
chunk0005_1_1	chr1	53919072	53919312	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	25004	NM_001039716	1733	Hs.251415	NM_000792	ENSG00000211452	DIO1	5DI|TXDI1	iodothyronine deiodinase 1	protein-coding	0.008333	0.456432	
chunk0124_316_1	chr3	58059445	58059868	+	0	NA	intron (NM_001164317, intron 1 of 46)	intron (NM_001164317, intron 1 of 46)	51256	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.021277	0.500000	
chunk0154_296_1	chr5	83123346	83124067	+	0	NA	intron (NM_022550, intron 3 of 7)	L1ME1|LINE|L1	46208	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.004161	0.282548	
chunk0156_20_1	chr5	102216815	102217284	+	0	NA	Intergenic	MER67C|LTR|ERV1	79500	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.004264	0.361702	
chunk0107_222_1	chr2	216877861	216878527	+	0	NA	Intergenic	Intergenic	7422	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.009009	0.445277	
chunk0027_397_1	chr10	80265953	80266445	+	0	NA	Intergenic	Intergenic	23479	NM_000429	4143	Hs.282670	NM_000429	ENSG00000151224	MAT1A	MAT|MATA1|SAMS|SAMS1	methionine adenosyltransferase 1A	protein-coding	0.020325	0.612576	
chunk0083_253_1	chr17	68035877	68036191	+	0	NA	intron (NM_002266, intron 1 of 10)	CpG	302	NM_002266	3838	Hs.594238	NM_002266	ENSG00000182481	KPNA2	IPOA1|QIP2|RCH1|SRP1-alpha|SRP1alpha	karyopherin subunit alpha 2	protein-coding	0.114650	0.695238	
chunk0178_108_1	chr7	30919401	30920194	+	0	NA	intron (NM_198098, intron 1 of 3)	intron (NM_198098, intron 1 of 3)	-1503	NM_001185060	358	Hs.76152	NM_000385	ENSG00000240583	AQP1	AQP-CHIP|CHIP28|CO	aquaporin 1 (Colton blood group)	protein-coding	0.008827	0.445844	
chunk0029_341_1	chr10	106410605	106411717	+	0	NA	Intergenic	Intergenic	-590828	NR_120625	101927549	Hs.556885	NR_120625		LINC02627	-	long intergenic non-protein coding RNA 2627	ncRNA	0.007194	0.349506	
chunk0169_392_1	chr6	108030211	108030642	+	0	NA	Intergenic	Intergenic	44311	NM_014028	28962	Hs.226780	NM_014028	ENSG00000081087	OSTM1	GIPN|GL|HSPC019|OPTB5	osteoclastogenesis associated transmembrane protein 1	protein-coding	0.002320	0.372685	
chunk0011_203_1	chr1	150008699	150009327	+	0	NA	intron (NM_020205, intron 1 of 11)	intron (NM_020205, intron 1 of 11)	1724	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.012739	0.356121	
chunk0091_280_1	chr19	11696860	11697120	+	0	NA	Intergenic	Intergenic	22992	NR_028594	401898	Hs.672384	NM_001013691		ZNF833P	ZNF833	zinc finger protein 833, pseudogene	pseudo	0.000000	0.413793	
chunk0068_120_1	chr15	52529143	52529342	+	0	NA	promoter-TSS (NM_000259)	promoter-TSS (NM_000259)	-192	NM_001142495	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.120603	0.750000	
chunk0056_423_1	chr13	94595019	94595345	+	0	NA	intron (NM_014305, intron 1 of 11)	L2a|LINE|L2	1093	NM_014305	23483	Hs.12393	NM_014305	ENSG00000088451	TGDS	CATMANS|SDR2E1|TDPGD	TDP-glucose 4,6-dehydratase	protein-coding	0.003067	0.437309	
chunk0035_93_1	chr11	42136090	42136566	+	0	NA	Intergenic	L1MEf|LINE|L1	117362	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.255765	
chunk0199_435_1	chr9	13873146	13873350	+	0	NA	Intergenic	L1MA5|LINE|L1	-54723	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.004902	0.321951	
chunk0151_195_1	chr5	50592101	50592316	+	0	NA	Intergenic	Intergenic	-73691	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.004651	0.379630	
chunk0182_423_1	chr7	101169335	101169650	+	0	NA	Intergenic	Intergenic	-3921	NM_003378	7425	Hs.587325	NM_003378	ENSG00000128564	VGF	SCG7|SgVII	VGF nerve growth factor inducible	protein-coding	0.015873	0.506329	95(CATAACACACTGTCCT,-,0.00),96(ATAACACACTGTCCTA,+,0.00)
chunk0139_346_1	chr4	59823267	59823467	+	0	NA	Intergenic	Intergenic	-1099252	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.368159	
chunk0193_74_1	chr8	73164572	73165477	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	-71752	NM_153225	157869	Hs.439040	NM_153225	ENSG00000164764	SBSPON	C8orf84|RPESP	somatomedin B and thrombospondin type 1 domain containing	protein-coding	0.006630	0.356512	620(AAGATCACACAGTTCC,-,0.00),621(AGATCACACAGTTCCT,+,0.00)
chunk0050_153_1	chr12	102920134	102920805	+	0	NA	Intergenic	Intergenic	-2866	NM_000277	5053	Hs.560019	NM_000277	ENSG00000171759	PAH	PH|PKU|PKU1	phenylalanine hydroxylase	protein-coding	0.002981	0.355655	
chunk0037_285_1	chr11	75945931	75946675	+	0	NA	intron (NM_003369, intron 6 of 14)	intron (NM_003369, intron 6 of 14)	131136	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.006720	0.357047	
chunk0046_387_1	chr12	63805915	63806533	+	0	NA	intron (NM_014254, intron 5 of 5)	L2a|LINE|L2	15932	NR_126167	104169670	Hs.735874	NR_126167	ENSG00000255850	RXYLT1-AS1	TMEM5-AS1	RXYLT1 antisense RNA 1	ncRNA	0.003236	0.373183	
chunk0107_340_1	chr2	221346240	221346605	+	0	NA	Intergenic	Intergenic	225936	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.005479	0.387978	
chunk0098_309_1	chr2	76377980	76378661	+	0	NA	Intergenic	Intergenic	-607645	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.001468	0.304985	361(GAGAACACCATGACCC,-,0.00),362(AGAACACCATGACCCT,+,0.00)
chunk0034_132_1	chr11	28536885	28537189	+	0	NA	Intergenic	L1M5|LINE|L1	-59489	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.003289	0.357377	125(CTGTACACATTGTTCT,-,0.00),126(TGTACACATTGTTCTT,+,0.00)
chunk0037_425_1	chr11	80091042	80091379	+	0	NA	Intergenic	Intergenic	-650559	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.008902	0.399408	
chunk0158_332_1	chr5	133048943	133050011	+	0	NA	Intergenic	Intergenic	-2493	NM_002154	3308	Hs.90093	NM_002154	ENSG00000170606	HSPA4	APG-2|HEL-S-5a|HS24/P52|HSPH2|RY|hsp70|hsp70RY	heat shock protein family A (Hsp70) member 4	protein-coding	0.006554	0.375117	
chunk0038_252_1	chr11	88281345	88281544	+	0	NA	Intergenic	Intergenic	56329	NM_001814	1075	Hs.128065	NM_001814	ENSG00000109861	CTSC	CPPI|DPP-I|DPP1|DPPI|HMS|JP|JPD|PALS|PDON1|PLS	cathepsin C	protein-coding	0.000000	0.415000	
chunk0136_81_1	chr4	2256785	2257288	+	0	NA	intron (NM_006454, intron 3 of 5)	intron (NM_006454, intron 3 of 5)	4976	NM_006454	10608	Hs.655020	NM_006454	ENSG00000123933	MXD4	MAD4|MST149|MSTP149|bHLHc12	MAX dimerization protein 4	protein-coding	0.025845	0.628968	280(GAGAACACTGCGTTCT,-,0.00),281(AGAACACTGCGTTCTG,+,0.00)
chunk0013_174_1	chr1	168861502	168862187	+	0	NA	Intergenic	Intergenic	74903	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.000000	0.354227	
chunk0182_283_1	chr7	98218167	98218678	+	0	NA	intron (NM_015395, intron 23 of 25)	L1PB|LINE|L1	6168	NM_177455	168620	Hs.511979	NM_177455	ENSG00000180535	BHLHA15	BHLHB8|MIST1	basic helix-loop-helix family member a15	protein-coding	0.021526	0.498047	
chunk0092_216_1	chr19	31579351	31579680	+	0	NA	Intergenic	L1M5|LINE|L1	-8674	NM_001278575	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.003040	0.278788	
chunk0085_18_1	chr18	357430	357670	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	-89491	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.000000	0.286307	66(TGGTACATTGTGTTCC,-,0.00),67(GGTACATTGTGTTCCT,+,0.00)
chunk0151_2_1	chr5	40685014	40685609	+	0	NA	intron (NM_000958, intron 2 of 2)	intron (NM_000958, intron 2 of 2)	5381	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.001681	0.335570	
chunk0061_188_1	chr14	60164449	60164937	+	0	NA	intron (NM_016029, intron 1 of 6)	intron (NM_016029, intron 1 of 6)	800	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.026639	0.435583	
chunk0050_455_1	chr12	110983989	110984340	+	0	NA	Intergenic	AluJb|SINE|Alu	47562	NR_036513	100131138	Hs.152129	NR_036513	ENSG00000185847	LINC01405	-	long intergenic non-protein coding RNA 1405	ncRNA	0.022792	0.505682	127(AGGGACACTCTGTTAC,-,0.00),128(GGGACACTCTGTTACC,+,0.00)
chunk0172_97_1	chr6	134714088	134714524	+	0	NA	Intergenic	Intergenic	-174301	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.009174	0.430206	
chunk0182_125_1	chr7	94452308	94452754	+	0	NA	Intergenic	Intergenic	-57327	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.013453	0.469799	
chunk0143_394_1	chr4	123121398	123121918	+	0	NA	intron (NM_145207, intron 14 of 15)	Tigger3b|DNA|TcMar-Tigger	198588	NM_145207	166378	Hs.709648	NM_145207	ENSG00000145375	SPATA5	AFG2|EHLMRS|SPAF	spermatogenesis associated 5	protein-coding	0.001923	0.372361	298(AAGTACACTCTGTGAT,-,0.00)
chunk0042_298_1	chr12	7734046	7734555	+	0	NA	intron (NM_130441, intron 5 of 6)	intron (NM_130441, intron 5 of 6)	15173	NM_203503	170482	Hs.351812	NM_130441	ENSG00000198178	CLEC4C	BDCA2|CD303|CLECSF11|CLECSF7|DLEC|HECL|PRO34150	C-type lectin domain family 4 member C	protein-coding	0.009823	0.376471	
chunk0016_49_1	chr1	193241928	193242127	+	0	NA	intron (NM_024529, intron 15 of 16)	L1MA4A|LINE|L1	-55414	NM_003783	8707	Hs.518834	NM_003783	ENSG00000162630	B3GALT2	BETA3GALT2|GLCT2|beta3Gal-T2	beta-1,3-galactosyltransferase 2	protein-coding	0.015075	0.530000	
chunk0078_231_1	chr17	6591574	6591889	+	0	NA	intron (NM_014804, intron 16 of 18)	intron (NM_014804, intron 16 of 18)	-35174	NM_001165966	83394	Hs.183983	NM_031220	ENSG00000091622	PITPNM3	ACKR6|CORD5|NIR1|RDGBA3	PITPNM family member 3	protein-coding	0.015873	0.455696	105(GAGAACACTAAGTCCT,-,0.00),106(AGAACACTAAGTCCTC,+,0.00)
chunk0126_464_1	chr3	87673521	87673782	+	0	NA	Intergenic	Intergenic	-308925	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.011494	0.458015	27(CGGAACATCCTGCTCT,-,0.00),28(GGAACATCCTGCTCTT,+,0.00)
chunk0111_28_1	chr20	22058763	22059089	+	0	NA	intron (NR_038394, intron 1 of 3)	intron (NR_038394, intron 1 of 3)	4836	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.000000	0.388379	
chunk0125_360_1	chr3	71374673	71374969	+	0	NA	intron (NM_032682, intron 3 of 20)	intron (NM_032682, intron 3 of 20)	-70061	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.000000	0.397306	
chunk0212_306_1	chrX	142452399	142452658	+	0	NA	Intergenic	Intergenic	-247238	NM_016249	51438	Hs.123536	NM_016249	ENSG00000046774	MAGEC2	CT10|HCA587|MAGEE1	MAGE family member C2	protein-coding	0.003861	0.392308	
chunk0139_207_1	chr4	54871927	54872375	+	0	NA	Intergenic	Intergenic	214223	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.011161	0.416481	
chunk0062_37_1	chr14	67175518	67175878	+	0	NA	intron (NM_001024218, intron 20 of 21)	L1PA6|LINE|L1	-13695	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.002778	0.368421	
chunk0047_313_1	chr12	74057469	74057925	+	0	NA	Intergenic	Intergenic	234934	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.004386	0.264770	
chunk0185_405_1	chr7	134002705	134003161	+	0	NA	intron (NM_021807, intron 15 of 17)	L1ME1|LINE|L1	-124419	NM_144648	136332	Hs.149774	NM_144648	ENSG00000155530	LRGUK	CFAP246	leucine rich repeats and guanylate kinase domain containing	protein-coding	0.002193	0.350109	
chunk0060_97_1	chr14	43042170	43042451	+	0	NA	Intergenic	Intergenic	1434749	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.010676	0.358156	
chunk0190_375_1	chr8	39980295	39980846	+	0	NA	intron (NM_194294, intron 4 of 10)	intron (NM_194294, intron 4 of 10)	45615	NM_194294	169355	Hs.676257	NM_194294	ENSG00000188676	IDO2	INDOL1	indoleamine 2,3-dioxygenase 2	protein-coding	0.012704	0.414855	320(GAGAACAGCCTGTGCC,-,0.00),321(AGAACAGCCTGTGCCC,+,0.00)
chunk0104_233_1	chr2	176484653	176485269	+	0	NA	Intergenic	Intergenic	116091	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.004870	0.406807	
chunk0111_87_1	chr20	23344055	23344441	+	0	NA	Intergenic	Intergenic	-6488	NM_013248	29107	Hs.516933	NM_013248	ENSG00000132661	NXT1	MTR2|P15	nuclear transport factor 2 like export factor 1	protein-coding	0.010363	0.467700	
chunk0031_244_1	chr10	126910858	126911057	+	0	NA	intron (NM_001290223, intron 1 of 51)	L1MD1|LINE|L1	5548	NM_001380	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.010050	0.420000	
chunk0005_295_1	chr1	60245352	60245636	+	0	NA	Intergenic	Intergenic	-171724	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.007042	0.452632	
chunk0103_362_1	chr2	168256290	168256906	+	0	NA	Intergenic	Intergenic	-9003	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.003247	0.398703	
chunk0108_153_1	chr2	231040701	231041207	+	0	NA	intron (NM_001144994, intron 1 of 2)	intron (NM_001144994, intron 1 of 2)	3388	NM_001144994	257407	Hs.526596	NM_001144994	ENSG00000204128	C2orf72	-	chromosome 2 open reading frame 72	protein-coding	0.009881	0.333333	
chunk0206_203_1	chr9	123061182	123061739	+	0	NA	intron (NM_012197, intron 13 of 25)	MER58A|DNA|hAT-Charlie	27817	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.012567	0.422939	
chunk0109_142_1	chr20	3443556	3443760	+	0	NA	Intergenic	Intergenic	-27360	NM_001207047	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.000000	0.395122	92(TGGAACAGTCTGTGCT,-,0.00),93(GGAACAGTCTGTGCTA,+,0.00)
chunk0033_48_1	chr11	13319051	13319286	+	0	NA	intron (NM_001030272, intron 2 of 18)	L1ME3G|LINE|L1	41441	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.008511	0.334746	
chunk0048_264_1	chr12	82009052	82009289	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	55451	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.008439	0.441176	
chunk0191_134_1	chr8	48737635	48738467	+	0	NA	Intergenic	Intergenic	-2740	NR_024605	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.004808	0.349340	
chunk0113_444_1	chr20	62623757	62624545	+	0	NA	Intergenic	Intergenic	-18294	NM_016354	28231	Hs.235782	NM_016354	ENSG00000101187	SLCO4A1	OATP-E|OATP1|OATP4A1|OATPE|OATPRP1|POAT|SLC21A12	solute carrier organic anion transporter family member 4A1	protein-coding	0.025381	0.610900	383(AGGGACAGAACGTTCC,-,0.00),384(GGGACAGAACGTTCCA,+,0.00)
chunk0181_249_1	chr7	85502281	85502480	+	0	NA	Intergenic	L1MA2|LINE|L1	-380449	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.485000	
chunk0024_213_1	chr10	36917994	36918290	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-207715	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.000000	0.373737	
chunk0167_190_1	chr6	64268042	64268317	+	0	NA	intron (NM_001142800, intron 30 of 42)	L1ME4b|LINE|L1	621653	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.000000	0.286232	213(AAGAACACACTGTTCA,-,0.00),214(AGAACACACTGTTCAT,+,0.00)
chunk0138_193_1	chr4	38035810	38036294	+	0	NA	intron (NM_015173, intron 8 of 19)	intron (NM_015173, intron 8 of 19)	-74129	NM_001253913	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.004132	0.443299	
chunk0037_36_1	chr11	70247457	70248138	+	0	NA	Intergenic	Intergenic	-22903	NR_045286	8500	Hs.530749	NM_003626	ENSG00000131626	PPFIA1	LIP.1|LIP1|LIPRIN	PTPRF interacting protein alpha 1	protein-coding	0.013216	0.571848	2(GTGGACACCGTGTGCC,-,0.00),3(TGGACACCGTGTGCCT,+,0.00),157(CAGAACACCGTGCCCC,-,0.00),158(AGAACACCGTGCCCCC,+,0.00),537(TGGCTCAGAGTGTCCT,-,0.00),538(GGCTCAGAGTGTCCTG,+,0.00)
chunk0035_255_1	chr11	46339207	46339495	+	0	NA	intron (NM_201532, intron 1 of 30)	intron (NM_201532, intron 1 of 30)	-5916	NM_201533	8525	Hs.502461	NM_003646	ENSG00000149091	DGKZ	DAGK5|DAGK6|DGK-ZETA|hDGKzeta	diacylglycerol kinase zeta	protein-coding	0.017361	0.529412	106(ATCACATTCTGTCCTG,+,0.00)
chunk0212_28_1	chrY	10880686	10881048	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	970069	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.013812	0.446281	
chunk0152_61_1	chr5	57737284	57737957	+	0	NA	Intergenic	Intergenic	86960	NR_104668	101928505	Hs.119998	NR_104668		LOC101928505	-	uncharacterized LOC101928505	ncRNA	0.002972	0.360534	
chunk0188_402_1	chr8	18738277	18738477	+	0	NA	intron (NM_015310, intron 9 of 15)	MIR3|SINE|MIR	70518	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.005000	0.388060	
chunk0120_131_1	chr3	4935514	4935865	+	0	NA	intron (NR_125916, intron 1 of 2)	L2a|LINE|L2	-29188	NR_125914	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.000000	0.448864	
chunk0146_91_1	chr4	158130117	158130527	+	0	NA	intron (NM_001031700, intron 5 of 5)	intron (NM_001031700, intron 5 of 5)	42244	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.406326	
chunk0071_360_1	chr15	88905302	88905501	+	0	NA	intron (NM_001114614, intron 5 of 6)	L2a|LINE|L2	7361	NM_001310321	4240	Hs.3745	NM_005928	ENSG00000140545	MFGE8	BA46|EDIL1|HMFG|HsT19888|MFG-E8|MFGM|OAcGD3S|SED1|SPAG10|hP47	milk fat globule-EGF factor 8 protein	protein-coding	0.025126	0.460000	
chunk0050_64_1	chr12	101407723	101408202	+	0	NA	promoter-TSS (NM_001177)	promoter-TSS (NM_001177)	-142	NM_001301068	400	Hs.372616	NM_001177	ENSG00000120805	ARL1	ARFL1	ADP ribosylation factor like GTPase 1	protein-coding	0.081420	0.560417	
chunk0015_149_1	chr1	186355569	186355768	+	0	NA	exon (NM_003292, exon 16 of 51)	exon (NM_003292, exon 16 of 51)	19657	NM_003292	7175	Hs.279640	NM_003292	ENSG00000047410	TPR	-	translocated promoter region, nuclear basket protein	protein-coding	0.005025	0.425000	13(GGTAACACTGTGTTCT,-,0.00),14(GTAACACTGTGTTCTC,+,0.00)
chunk0128_327_1	chr3	111937836	111938421	+	0	NA	intron (NM_001134438, intron 6 of 17)	intron (NM_001134438, intron 6 of 17)	-40748	NM_018394	55347	Hs.477115	NM_018394	ENSG00000144827	ABHD10	-	abhydrolase domain containing 10	protein-coding	0.005128	0.348123	
chunk0008_292_1	chr1	94928879	94929543	+	0	NA	intron (NR_033998, intron 1 of 3)	intron (NR_033998, intron 1 of 3)	1183	NR_033998	729970	Hs.297988	NR_033998	ENSG00000235501	LOC729970	-	hCG2028352-like	ncRNA	0.007530	0.386466	
chunk0030_136_1	chr10	113485139	113485537	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-65493	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.005025	0.416040	
chunk0039_243_1	chr11	102096277	102096951	+	0	NA	Intergenic	Intergenic	-13847	NM_001282100	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.014837	0.429630	
chunk0161_269_1	chr5	172533149	172534233	+	0	NA	Intergenic	Intergenic	-79168	NM_001308175	285590	Hs.285666	NM_001017995	ENSG00000174705	SH3PXD2B	FAD49|FTHS|HOFI|KIAA1295|TKS4|TSK4	SH3 and PX domains 2B	protein-coding	0.018450	0.516129	734(AGACACAGTGTGTCCC,-,0.00),735(GACACAGTGTGTCCCA,+,0.00),943(CTGGACTGTTTGTTCT,-,0.00),944(TGGACTGTTTGTTCTT,+,0.00)
chunk0086_61_1	chr18	13026462	13027212	+	0	NA	intron (NM_032142, intron 9 of 44)	L1MB2|LINE|L1	35475	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.004000	0.395473	
chunk0212_87_1	chrY	12166607	12167028	+	0	NA	Intergenic	Intergenic	254773	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.007126	0.372038	
chunk0156_94_1	chr5	104807622	104807883	+	0	NA	Intergenic	Intergenic	-291722	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.003831	0.297710	
chunk0142_64_1	chr4	92437491	92437835	+	0	NA	intron (NM_001286838, intron 1 of 14)	intron (NM_001286838, intron 1 of 14)	133264	NM_001510	2895	Hs.162727	NM_001510	ENSG00000152208	GRID2	GluD2|SCAR18	glutamate ionotropic receptor delta type subunit 2	protein-coding	0.008721	0.385507	
chunk0136_373_1	chr3	196287653	196288159	+	0	NA	promoter-TSS (NM_005017)	promoter-TSS (NM_005017)	-154	NM_005017	5130	Hs.135997	NM_005017	ENSG00000161217	PCYT1A	CCTA|CT|CTA|CTPCT|PCYT1|SMDCRD	phosphate cytidylyltransferase 1, choline, alpha	protein-coding	0.094862	0.666667	
chunk0157_307_1	chr5	121541406	121541747	+	0	NA	Intergenic	L1PA10|LINE|L1	219026	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.002933	0.298246	
chunk0024_206_1	chr10	36740177	36740405	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-385566	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.008772	0.384279	34(CAGCACAGTCTGTTTA,-,0.00),35(AGCACAGTCTGTTTAC,+,0.00)
chunk0149_88_1	chr5	17526632	17526838	+	0	NA	Intergenic	Intergenic	-139425	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.029126	0.400966	
chunk0116_264_1	chr21	39137813	39138230	+	0	NA	Intergenic	Intergenic	45493	NR_049728	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.004796	0.392344	223(AAGAACAGCCTCTTCC,-,0.00),224(AGAACAGCCTCTTCCA,+,0.00)
chunk0004_62_1	chr1	43241330	43241972	+	0	NA	intron (NM_001195831, intron 22 of 23)	intron (NM_001195831, intron 22 of 23)	-28343	NM_144626	128218	Hs.104476	NM_144626	ENSG00000179178	TMEM125	-	transmembrane protein 125	protein-coding	0.009346	0.503888	188(AAGACCATCCTGTTCT,-,0.00),189(AGACCATCCTGTTCTC,+,0.00),253(AAGCACAGTTTGTTCC,-,0.00),254(AGCACAGTTTGTTCCT,+,0.00)
chunk0206_216_1	chr9	123268594	123269172	+	0	NA	promoter-TSS (NM_018387)	promoter-TSS (NM_018387)	-307	NM_001171137	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.124567	0.732297	
chunk0149_27_1	chr5	16211685	16211915	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-32012	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.000000	0.484848	
chunk0125_279_1	chr3	69458830	69459088	+	0	NA	Intergenic	Intergenic	-72655	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.003876	0.389961	
chunk0080_34_1	chr17	21163714	21164024	+	0	NA	intron (NM_015510, intron 1 of 6)	AluJb|SINE|Alu	36941	NM_015510	25979	Hs.386989	NM_015510	ENSG00000109016	DHRS7B	CGI-93|SDR32C1	dehydrogenase/reductase 7B	protein-coding	0.003226	0.495177	
chunk0172_36_1	chr6	133983991	133984577	+	0	NA	intron (NM_004865, intron 4 of 6)	intron (NM_004865, intron 4 of 6)	31121	NM_004865	9519	Hs.486507	NM_004865	ENSG00000028839	TBPL1	MGC:8389|MGC:9620|STUD|TLF|TLP|TRF2	TATA-box binding protein like 1	protein-coding	0.003413	0.287905	
chunk0170_96_1	chr6	110482944	110483401	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-6531	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.013129	0.347162	
chunk0067_136_1	chr15	43031952	43032410	+	0	NA	intron (NM_174916, intron 20 of 46)	intron (NM_174916, intron 20 of 46)	73907	NM_174916	197131	Hs.591121	NM_174916	ENSG00000159459	UBR1	JBS	ubiquitin protein ligase E3 component n-recognin 1	protein-coding	0.008734	0.335512	
chunk0203_146_1	chr9	85580491	85581044	+	0	NA	intron (NM_001286715, intron 22 of 24)	intron (NM_001286715, intron 22 of 24)	161262	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.005425	0.310469	
chunk0079_157_1	chr17	13387259	13387546	+	0	NA	Intergenic	MER21C|LTR|ERVL	156244	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.013937	0.427083	
chunk0134_201_1	chr3	178445988	178446319	+	0	NA	intron (NR_046786, intron 1 of 2)	intron (NR_046786, intron 1 of 2)	26952	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.006042	0.304217	
chunk0191_57_1	chr8	46583752	46584387	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-256817	NR_027013	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.015748	0.460692	
chunk0018_91_1	chr1	217568178	217568702	+	0	NA	intron (NM_018040, intron 5 of 9)	L2a|LINE|L2	62662	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.007634	0.390476	
chunk0049_127_1	chr12	91591519	91591729	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-408500	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.004762	0.345972	
chunk0021_105_1	chr10	3109257	3109460	+	0	NA	exon (NM_001242339, exon 12 of 24)	exon (NM_001242339, exon 12 of 24)	-24802	NR_132758	106633806		NR_132758		SNORD142	SNORA85|SNORD174|ZL68	small nucleolar RNA, C/D box 142	snoRNA	0.059113	0.642157	
chunk0210_307_1	chrX	89847264	89847496	+	0	NA	Intergenic	L1PA13|LINE|L1	-74561	NM_138960	90316	Hs.592220	NM_138960	ENSG00000153779	TGIF2LX	TGIFLX	TGFB induced factor homeobox 2 like X-linked	protein-coding	0.008621	0.377682	
chunk0047_28_1	chr12	65863124	65863686	+	0	NA	intron (NM_001292023, intron 2 of 2)	intron (NM_001292023, intron 2 of 2)	18173	NR_120478	100129940	Hs.685856	NR_120478	ENSG00000197301	HMGA2-AS1	-	HMGA2 antisense RNA 1	ncRNA	0.003559	0.412078	
chunk0118_34_1	chr22	27373804	27374008	+	0	NA	Intergenic	L1P2|LINE|L1	427592	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.004902	0.473171	
chunk0062_96_1	chr14	68164419	68165195	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	345028	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.006443	0.378378	
chunk0060_36_1	chr14	40414338	40414868	+	0	NA	Intergenic	Intergenic	-540108	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.005660	0.372881	
chunk0192_365_1	chr8	68221473	68221700	+	0	NA	intron (NM_024870, intron 38 of 39)	L2c|LINE|L2	-109136	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.000000	0.346491	
chunk0047_87_1	chr12	68406107	68406444	+	0	NA	Intergenic	Intergenic	45209	NR_120458	100507195	Hs.450772	NR_120458	ENSG00000251301	LINC02384	-	long intergenic non-protein coding RNA 2384	ncRNA	0.014837	0.585799	
chunk0111_313_1	chr20	32256517	32256907	+	0	NA	Intergenic	Intergenic	18917	NR_031726	100302183		NR_031726	ENSG00000284125	MIR1825	MIRN1825|hsa-mir-1825	microRNA 1825	ncRNA	0.007692	0.386189	
chunk0113_301_1	chr20	57762967	57763859	+	0	NA	Intergenic	LTR78|LTR|ERV1	-51877	NM_199171	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.010090	0.475924	655(GGGAACAGTTTGTGCA,-,0.00),656(GGAACAGTTTGTGCAA,+,0.00)
chunk0178_102_1	chr7	30750911	30751394	+	0	NA	promoter-TSS (NM_001199219)	promoter-TSS (NM_001199219)	-983	NM_006774	11185	Hs.632629	NM_006774	ENSG00000241644	INMT	TEMT	indolethylamine N-methyltransferase	protein-coding	0.020704	0.526860	
chunk0038_384_1	chr11	93504288	93504513	+	0	NA	intron (NM_020179, intron 1 of 2)	intron (NM_020179, intron 1 of 2)	38980	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.000000	0.446903	
chunk0154_55_1	chr5	77204898	77205391	+	0	NA	Intergenic	Intergenic	-5737	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.006085	0.437247	
chunk0024_38_1	chr10	33422729	33423537	+	0	NA	Intergenic	Intergenic	-88228	NM_001024628	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.014851	0.415328	248(AAGAACAAAGTGTCAC,-,0.00)
chunk0075_48_1	chr16	47462930	47463565	+	0	NA	intron (NM_000293, intron 1 of 30)	intron (NM_000293, intron 1 of 30)	1948	NM_001031835	5257	Hs.78060	NM_000293	ENSG00000102893	PHKB	-	phosphorylase kinase regulatory subunit beta	protein-coding	0.004724	0.312893	
chunk0159_126_1	chr5	138968038	138968309	+	0	NA	intron (NM_001037633, intron 8 of 10)	intron (NM_001037633, intron 8 of 10)	-92805	NM_015564	26045	Hs.656653	NM_015564	ENSG00000146006	LRRTM2	-	leucine rich repeat transmembrane neuronal 2	protein-coding	0.011070	0.591912	
chunk0161_370_1	chr5	176144443	176145242	+	0	NA	intron (NR_036494, intron 25 of 25)	intron (NR_036494, intron 25 of 25)	25293	NR_038402	100507387	Hs.368516	NR_038402	ENSG00000251623	LOC100507387	-	uncharacterized LOC100507387	ncRNA	0.003755	0.420000	232(ATGGACTGCATGTTCT,-,0.00),233(TGGACTGCATGTTCTC,+,0.00)
chunk0073_255_1	chr16	11793042	11793273	+	0	NA	intron (NM_014153, intron 1 of 22)	intron (NM_014153, intron 1 of 22)	4101	NM_014153	29066	Hs.371856	NM_014153	ENSG00000122299	ZC3H7A	HSPC055|ZC3H7|ZC3HDC7	zinc finger CCCH-type containing 7A	protein-coding	0.000000	0.418103	43(CAGAACATAATGTATT,-,0.00),44(AGAACATAATGTATTT,+,0.00)
chunk0012_280_1	chr1	161913973	161914240	+	0	NA	intron (NM_007348, intron 15 of 15)	intron (NM_007348, intron 15 of 15)	110359	NM_015441	25903	Hs.507515	NM_015441	ENSG00000162745	OLFML2B	-	olfactomedin like 2B	protein-coding	0.003745	0.324627	
chunk0057_343_1	chr13	107743450	107743933	+	0	NA	intron (NM_001080396, intron 1 of 2)	intron (NM_001080396, intron 1 of 2)	91767	NR_046848	100874375	Hs.653972	NR_046848		FAM155A-IT1	-	FAM155A intronic transcript 1	ncRNA	0.008282	0.382231	
chunk0166_67_1	chr6	42979296	42979852	+	0	NA	promoter-TSS (NM_000287)	promoter-TSS (NM_000287)	-331	NR_133009	5190	Hs.656425	NM_000287	ENSG00000124587	PEX6	HMLR2|PAF-2|PAF2|PBD4A|PDB4B|PXAAA1	peroxisomal biogenesis factor 6	protein-coding	0.030576	0.488330	
chunk0105_458_1	chr2	195161694	195162037	+	0	NA	Intergenic	Intergenic	431270	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.000000	0.345930	
chunk0013_53_1	chr1	167189040	167189626	+	0	NA	intron (NR_110811, intron 2 of 3)	intron (NR_110811, intron 2 of 3)	6472	NR_110811	101928484	Hs.568496	NR_110811		LINC01363	RBSG4	long intergenic non-protein coding RNA 1363	ncRNA	0.006826	0.417376	314(AAGGACAACCAGTGCT,-,0.00),315(AGGACAACCAGTGCTG,+,0.00)
chunk0010_389_1	chr1	119385537	119386176	+	0	NA	intron (NM_001005783, intron 5 of 8)	intron (NM_001005783, intron 5 of 8)	16910	NR_046780	100874270		NR_046780	ENSG00000230921	HAO2-IT1	-	HAO2 intronic transcript 1	ncRNA	0.003130	0.376563	
chunk0047_306_1	chr12	73888158	73888639	+	0	NA	Intergenic	Intergenic	404233	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.014553	0.373444	231(AAGAACATAATGTTAT,-,0.00),232(AGAACATAATGTTATT,+,0.00)
chunk0209_366_1	chrX	53914126	53914381	+	0	NA	Intergenic	L1MD2|LINE|L1	128941	NM_001184898	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.003922	0.378906	
chunk0139_98_1	chr4	49657479	49657961	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	671078	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.016598	0.426501	
chunk0192_42_1	chr8	58832934	58833564	+	0	NA	intron (NM_014729, intron 5 of 8)	intron (NM_014729, intron 5 of 8)	-173404	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.011111	0.399366	
chunk0155_71_1	chr5	91651696	91651895	+	0	NA	Intergenic	L1PB4|LINE|L1	-268463	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.510000	
chunk0043_225_1	chr12	19917013	19917369	+	0	NA	Intergenic	MER57C1|LTR|ERV1	-97494	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.008427	0.422969	
chunk0187_437_1	chr7	158894747	158895572	+	0	NA	intron (NM_018051, intron 8 of 24)	L1MC1|LINE|L1	38581	NM_018051	55112	Hs.389945	NM_018051	ENSG00000126870	WDR60	FAP163|SRPS6|SRTD8	WD repeat domain 60	protein-coding	0.008485	0.386199	769(CAGTACACACTGTCTT,-,0.00),770(AGTACACACTGTCTTG,+,0.00)
chunk0175_105_1	chr7	2879398	2879875	+	0	NA	Intergenic	Intergenic	-35311	NM_007353	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.016771	0.464435	
chunk0126_114_1	chr3	75380080	75380697	+	0	NA	Intergenic	Intergenic	54727	NR_024241	692099	Hs.591652	NR_024241	ENSG00000244026	FAM86DP	FAM86D	family with sequence similarity 86 member D, pseudogene	pseudo	0.021070	0.480583	
chunk0120_318_1	chr3	10312334	10312715	+	0	NA	intron (NM_183352, intron 4 of 8)	intron (NM_183352, intron 4 of 8)	8517	NM_001136232	6396	Hs.166924	NM_030673	ENSG00000157020	SEC13	D3S1231E|SEC13L1|SEC13R|npp-20	SEC13 homolog, nuclear pore and COPII coat complex component	protein-coding	0.026247	0.544503	
chunk0014_413_1	chr1	183075928	183076304	+	0	NA	intron (NM_002293, intron 1 of 27)	intron (NM_002293, intron 1 of 27)	52656	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.002660	0.376658	
chunk0150_298_1	chr5	37500967	37501748	+	0	NA	intron (NM_018034, intron 8 of 17)	L1PB3|LINE|L1	122047	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.006402	0.373402	
chunk0084_451_1	chr17	83046476	83047048	+	0	NA	intron (NM_001009905, intron 3 of 12)	L1MB5|LINE|L1	5048	NM_001009905	146712	Hs.607824	NM_001009905	ENSG00000175711	B3GNTL1	3-Gn-T8|B3GNT8|BGnT-8|beta-1|beta3Gn-T8|beta3GnTL1	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1	protein-coding	0.013986	0.404887	
chunk0174_110_1	chr6	156969222	156969701	+	0	NA	intron (NM_017519, intron 4 of 18)	MamSINE1|SINE|tRNA-RTE	-189730	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.010438	0.414583	
chunk0119_314_1	chr22	46704829	46705076	+	0	NA	intron (NM_022766, intron 6 of 12)	L1MC5|LINE|L1	33303	NM_022766	64781	Hs.200668	NM_022766	ENSG00000100422	CERK	LK4|dA59H18.2|dA59H18.3|hCERK	ceramide kinase	protein-coding	0.000000	0.391129	
chunk0184_160_1	chr7	116239358	116239583	+	0	NA	intron (NM_152829, intron 2 of 6)	MIR|SINE|MIR	16519	NM_152829	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.004444	0.367257	49(CAGCACTGTATGTACC,-,0.00),50(AGCACTGTATGTACCT,+,0.00)
chunk0043_183_1	chr12	18242752	18243203	+	0	NA	Intergenic	Intergenic	-18563	NM_001288772	5288	Hs.22500	NM_004570	ENSG00000139144	PIK3C2G	PI3K-C2-gamma|PI3K-C2GAMMA	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma	protein-coding	0.008869	0.316372	
chunk0020_202_1	chr1	234973900	234974193	+	0	NA	Intergenic	Intergenic	-10047	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.013652	0.493197	
chunk0210_86_1	chrX	70968476	70969052	+	0	NA	Intergenic	L1ME2|LINE|L1	-37639	NM_032803	84889	Hs.175220	NM_032803	ENSG00000165349	SLC7A3	ATRC3|CAT-3|CAT3	solute carrier family 7 member 3	protein-coding	0.006944	0.377816	468(AAGTACATACTGTTCA,-,0.00),469(AGTACATACTGTTCAA,+,0.00)
chunk0022_348_1	chr10	17029457	17029959	+	0	NA	intron (NM_001081, intron 27 of 66)	intron (NM_001081, intron 27 of 66)	100109	NM_001081	8029	Hs.166206	NM_001081	ENSG00000107611	CUBN	IFCR|MGA1|gp280	cubilin	protein-coding	0.013944	0.419483	
chunk0123_244_1	chr3	45692768	45693276	+	0	NA	intron (NM_014016, intron 1 of 19)	Tigger3a|DNA|TcMar-Tigger	3760	NM_014016	22908	Hs.156509	NM_014016	ENSG00000211456	SACM1L	SAC1	SAC1 like phosphatidylinositide phosphatase	protein-coding	0.005906	0.367387	
chunk0197_292_1	chr8	124350069	124350742	+	0	NA	intron (NM_194291, intron 1 of 6)	(TC)n|Simple_repeat|Simple_repeat	22294	NM_194291	157378	Hs.100691	NM_194291	ENSG00000164983	TMEM65	-	transmembrane protein 65	protein-coding	0.002972	0.356083	
chunk0093_25_1	chr2	553328	553693	+	0	NA	Intergenic	Intergenic	123929	NM_152834	129787	Hs.6729	NM_152834	ENSG00000151353	TMEM18	lncND	transmembrane protein 18	protein-coding	0.019178	0.598361	
chunk0142_455_1	chr4	105568914	105569512	+	0	NA	intron (NR_046840, intron 2 of 2)	intron (NR_046840, intron 2 of 2)	7622	NR_046840	100874374	Hs.668908	NR_046840	ENSG00000249885	ARHGEF38-IT1	-	ARHGEF38 intronic transcript 1	ncRNA	0.001672	0.352254	
chunk0140_158_1	chr4	69415459	69416094	+	0	NA	Intergenic	Intergenic	80132	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.003150	0.377358	
chunk0146_354_1	chr4	167227735	167228028	+	0	NA	intron (NM_001204352, intron 2 of 11)	intron (NM_001204352, intron 2 of 11)	6545	NM_001204353	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.003413	0.333333	144(TGGTACACGATGTTCC,-,0.00),145(GGTACACGATGTTCCT,+,0.00),229(AAGCACACTGTGTCCA,-,0.00),230(AGCACACTGTGTCCAC,+,0.00)
chunk0009_113_1	chr1	102743198	102743874	+	0	NA	Intergenic	L1ME1|LINE|L1	364960	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.008876	0.329394	359(AGGAACTGTATGTCCA,-,0.00),360(GGAACTGTATGTCCAC,+,0.00)
chunk0179_296_1	chr7	49841078	49841458	+	0	NA	intron (NM_198570, intron 3 of 3)	intron (NM_198570, intron 3 of 3)	67607	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.002632	0.385827	
chunk0185_54_1	chr7	124747428	124747642	+	0	NA	intron (NM_005302, intron 1 of 1)	intron (NM_005302, intron 1 of 1)	18490	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.004673	0.376744	
chunk0198_327_1	chr8	139919349	139919630	+	0	NA	intron (NM_001160372, intron 19 of 22)	L1MB8|LINE|L1	-216433	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.014235	0.326241	
chunk0045_161_1	chr12	46783977	46784233	+	0	NA	intron (NM_018018, intron 7 of 16)	intron (NM_018018, intron 7 of 16)	41892	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.015625	0.420233	
chunk0206_348_1	chr9	125593552	125594174	+	0	NA	intron (NM_001006618, intron 4 of 7)	intron (NM_001006618, intron 4 of 7)	113371	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.009646	0.444623	
chunk0145_450_1	chr4	153632353	153632552	+	0	NA	intron (NM_001131007, intron 31 of 34)	L2a|LINE|L2	-51837	NM_003264	7097	Hs.519033	NM_003264	ENSG00000137462	TLR2	CD282|TIL4	toll like receptor 2	protein-coding	0.015075	0.405000	
chunk0068_116_1	chr15	52456572	52457126	+	0	NA	intron (NM_001142495, intron 1 of 39)	L1MA4A|LINE|L1	72201	NM_000259	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.003610	0.336937	
chunk0033_57_1	chr11	13409154	13409637	+	0	NA	intron (NM_032320, intron 6 of 8)	L2a|LINE|L2	30884	NM_001297742	84280	Hs.332382	NM_032320	ENSG00000148925	BTBD10	GMRP-1|GMRP1	BTB domain containing 10	protein-coding	0.002070	0.367769	
chunk0190_131_1	chr8	30656778	30657188	+	0	NA	intron (NM_002095, intron 1 of 7)	MIRc|SINE|MIR	1238	NM_002095	2961	Hs.77100	NM_002095	ENSG00000197265	GTF2E2	FE|TF2E2|TFIIE-B|TTD6	general transcription factor IIE subunit 2	protein-coding	0.034146	0.445255	
chunk0062_128_1	chr14	68521254	68521511	+	0	NA	intron (NM_133509, intron 10 of 10)	intron (NM_133509, intron 10 of 10)	272532	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.003891	0.503876	
chunk0146_428_1	chr4	169359768	169360463	+	0	NA	Intergenic	L1M1|LINE|L1	-89017	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.007194	0.366379	365(ATGACATTCTGTGCTT,+,0.00)
chunk0106_105_1	chr2	197487411	197487862	+	0	NA	promoter-TSS (NR_132787)	promoter-TSS (NR_132787)	-733	NR_132787	106635539		NR_132787		SNORA105A	-	small nucleolar RNA, H/ACA box 105A	snoRNA	0.008869	0.444690	176(AGGAACAGGGTGTTCC,-,0.00),177(GGAACAGGGTGTTCCA,+,0.00)
chunk0012_177_1	chr1	159194283	159194493	+	0	NA	intron (NM_021189, intron 6 of 9)	intron (NM_021189, intron 6 of 9)	8034	NR_037870	100131825	Hs.701271	NR_037870		CADM3-AS1	-	CADM3 antisense RNA 1	ncRNA	0.019048	0.464455	
chunk0012_166_1	chr1	158262571	158262770	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	8533	NM_001763	909	Hs.1309	NM_001763	ENSG00000158477	CD1A	CD1|FCB6|HTA1|R4|T6	CD1a molecule	protein-coding	0.005025	0.305000	
chunk0124_242_1	chr3	56785499	56785994	+	0	NA	intron (NM_001128615, intron 4 of 12)	intron (NM_001128615, intron 4 of 12)	-10029	NM_001128616	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.012121	0.457661	218(AAGGACAGACTGTTCC,-,0.00),219(AGGACAGACTGTTCCA,+,0.00)
chunk0023_83_1	chr10	22288794	22289196	+	0	NA	Intergenic	L1MB5|LINE|L1	-27388	NM_012071	23412	Hs.534398	NM_012071	ENSG00000148444	COMMD3	BUP|C10orf8	COMM domain containing 3	protein-coding	0.004975	0.382134	
chunk0064_291_1	chr14	95302777	95303000	+	0	NA	intron (NM_024734, intron 1 of 12)	MIRb|SINE|MIR	17020	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.008969	0.459821	
chunk0012_403_1	chr1	163959432	163959670	+	0	NA	Intergenic	L1M3b|LINE|L1	-536360	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.000000	0.497908	
chunk0181_185_1	chr7	83266843	83267640	+	0	NA	Intergenic	Intergenic	-104360	NM_033026	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.005019	0.349624	
chunk0165_56_1	chr6	30626576	30627174	+	0	NA	promoter-TSS (NM_001254952)	promoter-TSS (NM_001254952)	-11	NM_001031722	79969	Hs.654798	NM_024909	ENSG00000137343	ATAT1	C6orf134|MEC17|Nbla00487|TAT|alpha-TAT|alpha-TAT1	alpha tubulin acetyltransferase 1	protein-coding	0.055184	0.622705	328(GTGGACGCGCTGTTCC,-,0.00),329(TGGACGCGCTGTTCCC,+,0.00)
chunk0078_146_1	chr17	3978571	3978814	+	0	NA	Intergenic	Intergenic	-14228	NM_174956	489	Hs.513870	NM_005173	ENSG00000074370	ATP2A3	SERCA3	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3	protein-coding	0.008230	0.463115	
chunk0039_229_1	chr11	101737432	101737932	+	0	NA	Intergenic	Intergenic	-153754	NM_004621	7225	Hs.159003	NM_004621	ENSG00000137672	TRPC6	FSGS2|TRP6	transient receptor potential cation channel subfamily C member 6	protein-coding	0.012000	0.355289	81(GGGCACTCGATGTTCT,-,0.00),82(GGCACTCGATGTTCTT,+,0.00)
chunk0112_22_1	chr20	36097957	36098194	+	0	NA	intron (NM_001258329, intron 1 of 22)	intron (NM_001258329, intron 1 of 22)	5365	NM_001258329	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.004219	0.542017	143(TAGAACAGGCTGTTCT,-,0.00),144(AGAACAGGCTGTTCTA,+,0.00)
chunk0205_252_1	chr9	110714162	110714915	+	0	NA	intron (NM_001166281, intron 5 of 11)	intron (NM_001166281, intron 5 of 11)	45767	NM_005592	4593	Hs.521653	NM_005592	ENSG00000030304	MUSK	CMS9|FADS|FADS1	muscle associated receptor tyrosine kinase	protein-coding	0.007968	0.383289	
chunk0184_286_1	chr7	118711857	118712354	+	0	NA	Intergenic	L1M4|LINE|L1	487447	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.006036	0.331325	
chunk0015_123_1	chr1	185457082	185457506	+	0	NA	Intergenic	Intergenic	-122255	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.007075	0.338824	
chunk0139_212_1	chr4	54989676	54990196	+	0	NA	Intergenic	L1MA4A|LINE|L1	135659	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.003846	0.284069	
chunk0017_93_1	chr1	205768099	205768475	+	0	NA	3' UTR (NM_001135662, exon 6 of 6)	3' UTR (NM_001135662, exon 6 of 6)	7195	NM_001135664	8934	Hs.115325	NM_003929	ENSG00000117280	RAB29	RAB7L|RAB7L1	RAB29, member RAS oncogene family	protein-coding	0.007979	0.379310	
chunk0101_29_1	chr2	121825263	121825861	+	0	NA	Intergenic	L2b|LINE|L2	70017	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.008361	0.527546	412(AGAGACATGGTGTGCT,-,0.00),413(GAGACATGGTGTGCTG,+,0.00)
chunk0175_420_1	chr6	168898484	168898993	+	0	NA	Intergenic	L2b|LINE|L2	263563	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.005894	0.362745	
chunk0124_320_1	chr3	58111887	58112355	+	0	NA	intron (NM_001164317, intron 17 of 46)	intron (NM_001164317, intron 17 of 46)	98882	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.025641	0.545842	
chunk0081_40_1	chr17	37623903	37624500	+	0	NA	intron (NM_001291476, intron 10 of 15)	intron (NM_001291476, intron 10 of 15)	-9162	NR_106744	102465136		NR_106744	ENSG00000274620	MIR378J	hsa-mir-378j	microRNA 378j	ncRNA	0.011725	0.391304	
chunk0170_128_1	chr6	110898369	110898761	+	0	NA	Intergenic	L1ME1|LINE|L1	23781	NM_001287216	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.012755	0.330789	
chunk0013_45_1	chr1	167082651	167083024	+	0	NA	intron (NM_005814, intron 1 of 6)	intron (NM_005814, intron 1 of 6)	7794	NM_005814	10223	Hs.651244	NM_005814	ENSG00000143167	GPA33	A33	glycoprotein A33	protein-coding	0.026810	0.553476	301(GGGGACAGGGTGATCT,-,0.00),302(GGGACAGGGTGATCTG,+,0.00)
chunk0176_324_1	chr7	17095085	17095351	+	0	NA	Intergenic	Intergenic	-203434	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.003759	0.483146	
chunk0201_236_1	chr9	37662935	37663518	+	0	NA	intron (NM_014907, intron 1 of 15)	intron (NM_014907, intron 1 of 15)	12171	NM_014907	22844	Hs.163990	NM_014907	ENSG00000070601	FRMPD1	FRMD2	FERM and PDZ domain containing 1	protein-coding	0.003431	0.450342	263(GTGAACAGAATGATCT,-,0.00),264(TGAACAGAATGATCTG,+,0.00)
chunk0189_224_1	chr8	24430337	24430748	+	0	NA	intron (NR_125808, intron 1 of 5)	intron (NR_125808, intron 1 of 5)	-10454	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.007299	0.422330	
chunk0112_447_1	chr20	48468657	48468898	+	0	NA	Intergenic	Intergenic	108866	NR_026958	284749	Hs.299080	NR_026958	ENSG00000235621	LINC00494	-	long intergenic non-protein coding RNA 494	ncRNA	0.016598	0.545455	
chunk0010_417_1	chr1	119660104	119660519	+	0	NA	Intergenic	Intergenic	-12544	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.002410	0.360577	
chunk0001_114_1	chr1	3828095	3828344	+	0	NA	intron (NM_014704, intron 15 of 21)	intron (NM_014704, intron 15 of 21)	29014	NM_014704	9731	Hs.133089	NM_014704	ENSG00000116198	CEP104	CFAP256|GlyBP|JBTS25|KIAA0562|ROC22	centrosomal protein 104	protein-coding	0.036145	0.592000	
chunk0040_330_1	chr11	118298053	118298833	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-6137	NM_000733	916	Hs.3003	NM_000733	ENSG00000198851	CD3E	IMD18|T3E|TCRE	CD3e molecule	protein-coding	0.006410	0.419974	
chunk0066_381_1	chr15	38873151	38873620	+	0	NA	Intergenic	Intergenic	176787	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.008529	0.451064	
chunk0131_25_1	chr3	142213201	142213755	+	0	NA	intron (NM_001039547, intron 3 of 15)	intron (NM_001039547, intron 3 of 15)	12129	NR_033289	256356	Hs.135904	NM_152776	ENSG00000175066	GK5	-	glycerol kinase 5	protein-coding	0.007220	0.326126	
chunk0051_33_1	chr12	112108492	112108833	+	0	NA	intron (NM_024953, intron 1 of 23)	CpG	169	NM_024953	80018	Hs.530941	NM_024953	ENSG00000111300	NAA25	C12orf30|MDM20|NAP1	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	protein-coding	0.117302	0.736842	
chunk0120_375_1	chr3	11949565	11950120	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-54518	NM_003178	6854	Hs.445503	NM_003178	ENSG00000157152	SYN2	SYNII	synapsin II	protein-coding	0.010811	0.451439	
chunk0153_182_1	chr5	71595483	71595768	+	0	NA	intron (NM_022132, intron 2 of 16)	intron (NM_022132, intron 2 of 16)	8337	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.003509	0.339161	
chunk0211_22_1	chrX	107896448	107896786	+	0	NA	intron (NR_110395, intron 3 of 3)	intron (NR_110395, intron 3 of 3)	39363	NR_110395	101928335	Hs.657090	NR_110395	ENSG00000236064	LOC101928335	-	uncharacterized LOC101928335	ncRNA	0.005917	0.339233	
chunk0208_255_1	chrX	20431631	20431958	+	0	NA	Intergenic	Intergenic	-165162	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.000000	0.362805	
chunk0022_216_1	chr10	13907553	13907752	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-166632	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.010050	0.500000	
chunk0028_309_1	chr10	91708451	91708695	+	0	NA	Intergenic	L1ME4a|LINE|L1	-75472	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.008197	0.440816	
chunk0120_246_1	chr3	8709894	8710434	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-23636	NM_001234	859	Hs.98303	NM_001234	ENSG00000182533	CAV3	LGMD1C|LQT9|MPDT|RMD2|VIP-21|VIP21	caveolin 3	protein-coding	0.011111	0.489834	
chunk0177_250_1	chr7	25125241	25126301	+	0	NA	promoter-TSS (NM_018947)	promoter-TSS (NM_018947)	-410	NM_018947	54205	Hs.437060	NM_018947	ENSG00000172115	CYCS	CYC|HCS|THC4	cytochrome c, somatic	protein-coding	0.057547	0.508954	
chunk0207_422_1	chr9	137223347	137223546	+	0	NA	Intergenic	CpG	-1189	NM_199001	375791	Hs.495540	NM_199001	ENSG00000197191	CYSRT1	C9orf169	cysteine rich tail 1	protein-coding	0.085427	0.720000	
chunk0204_135_1	chr9	95385338	95385688	+	0	NA	Intergenic	Intergenic	-67804	NM_000136	2176	Hs.494529	NM_000136	ENSG00000158169	FANCC	FA3|FAC|FACC	FA complementation group C	protein-coding	0.014286	0.455840	
chunk0018_282_1	chr1	220648187	220649012	+	0	NA	intron (NM_001286128, intron 12 of 15)	intron (NM_001286128, intron 12 of 15)	-41687	NM_024709	79762	Hs.519839	NM_024709	ENSG00000162817	C1orf115	-	chromosome 1 open reading frame 115	protein-coding	0.001212	0.349879	
chunk0132_211_1	chr3	157492074	157492474	+	0	NA	intron (NM_001167911, intron 2 of 12)	intron (NM_001167911, intron 2 of 12)	3232	NM_001167917	79674	Hs.658046	NM_024621	ENSG00000197415	VEPH1	MELT|VEPH	ventricular zone expressed PH domain containing 1	protein-coding	0.007500	0.374065	259(CAGTACATCGTGTTTT,-,0.00)
chunk0067_359_1	chr15	48585090	48585538	+	0	NA	intron (NM_000138, intron 6 of 65)	intron (NM_000138, intron 6 of 65)	60474	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.006696	0.338530	
chunk0028_228_1	chr10	89774657	89775119	+	0	NA	TTS (NM_016195)	TTS (NM_016195)	-54605	NR_038382	643529	Hs.618956	NR_038382	ENSG00000232229	LINC00865	-	long intergenic non-protein coding RNA 865	ncRNA	0.002165	0.343413	
chunk0184_30_1	chr7	112060646	112061066	+	0	NA	intron (NM_014705, intron 1 of 51)	L1MB3|LINE|L1	145551	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.004762	0.346793	
chunk0202_29_1	chr9	70601407	70602125	+	0	NA	intron (NM_024971, intron 20 of 25)	intron (NM_024971, intron 20 of 25)	-187109	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.027855	0.543811	372(GAGTACAGACTGCTCC,-,0.00),373(AGTACAGACTGCTCCC,+,0.00)
chunk0074_385_1	chr16	35177940	35178143	+	0	NA	Intergenic	Intergenic	-7650	NR_002837	606551	Hs.646441	NR_002837		UBE2MP1	-	ubiquitin conjugating enzyme E2 M pseudogene 1	pseudo	0.009852	0.416667	
chunk0122_42_1	chr3	28267502	28267987	+	0	NA	intron (NM_182523, intron 2 of 3)	MamRTE1|LINE|RTE-BovB	26111	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.002062	0.347737	
chunk0205_384_1	chr9	114328380	114328741	+	0	NA	Intergenic	MIRb|SINE|MIR	-1229	NM_000608	5005	Hs.719954	NM_000608	ENSG00000228278	ORM2	AGP-B|AGP-B'|AGP2	orosomucoid 2	protein-coding	0.013850	0.500000	
chunk0183_139_1	chr7	105777331	105777622	+	0	NA	intron (NM_152749, intron 3 of 3)	L2a|LINE|L2	-98314	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.010309	0.410959	
chunk0100_237_1	chr2	112626617	112626816	+	0	NA	Intergenic	Intergenic	17464	NR_033871	400999	Hs.585221	NR_033871		FLJ42351	-	uncharacterized LOC400999	ncRNA	0.010050	0.620000	
chunk0057_329_1	chr13	106958836	106959035	+	0	NA	Intergenic	Intergenic	305055	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.005025	0.350000	
chunk0154_60_1	chr5	77302446	77302777	+	0	NA	intron (NM_001029853, intron 1 of 20)	intron (NM_001029853, intron 1 of 20)	91730	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.018127	0.481928	
chunk0067_241_1	chr15	45510621	45511289	+	0	NA	promoter-TSS (NR_022014)	promoter-TSS (NR_022014)	-181	NR_022014	283651	Hs.574240	NM_173609		HMGN2P46	C15orf21|D-PCa-2	high mobility group nucleosomal binding domain 2 pseudogene 46	pseudo	0.007485	0.342302	
chunk0157_312_1	chr5	121777394	121778052	+	0	NA	Intergenic	Intergenic	-74232	NM_177478	94033	Hs.105324	NM_177478	ENSG00000181867	FTMT	MTF	ferritin mitochondrial	protein-coding	0.003040	0.338392	
chunk0203_231_1	chr9	87059792	87060019	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-17779	NR_027471	440173	Hs.127361	NR_027471	ENSG00000269994	LOC440173	-	uncharacterized LOC440173	ncRNA	0.004405	0.442982	
chunk0023_25_1	chr10	21087762	21088375	+	0	NA	intron (NM_213569, intron 2 of 6)	MLT1I|LTR|ERVL-MaLR	58491	NM_001010896	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.008157	0.431596	418(AGGGACACAGTGTACC,-,0.00),419(GGGACACAGTGTACCA,+,0.00)
chunk0127_292_1	chr3	97943265	97943598	+	0	NA	3' UTR (NM_153605, exon 22 of 22)	3' UTR (NM_153605, exon 22 of 22)	29020	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.006006	0.410180	
chunk0007_327_1	chr1	84611704	84612233	+	0	NA	intron (NR_125761, intron 2 of 2)	LTR19C|LTR|ERV1	9063	NR_125761	103695366	Hs.576097	NR_125761		LINC01461	TCONS_00001552	long intergenic non-protein coding RNA 1461	ncRNA	0.007561	0.443396	
chunk0193_244_1	chr8	76878830	76879161	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	87855	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.003021	0.376506	
chunk0190_318_1	chr8	38768107	38768332	+	0	NA	intron (NM_001146216, intron 1 of 12)	intron (NM_001146216, intron 1 of 12)	-18985	NM_006283	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.008889	0.482301	
chunk0196_114_1	chr8	103337926	103338125	+	0	NA	Intergenic	Intergenic	-33490	NM_138455	115908	Hs.405614	NM_138455	ENSG00000164932	CTHRC1	-	collagen triple helix repeat containing 1	protein-coding	0.010050	0.485000	
chunk0010_167_1	chr1	115644423	115644683	+	0	NA	intron (NM_001172412, intron 1 of 7)	(GTTTGAA)n|Simple_repeat|Simple_repeat	1924	NM_001172412	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.000000	0.409962	
chunk0119_95_1	chr22	41851066	41851344	+	0	NA	intron (NM_004599, intron 1 of 18)	intron (NM_004599, intron 1 of 18)	18126	NM_004599	6721	Hs.443258	NM_004599	ENSG00000198911	SREBF2	SREBP-2|SREBP2|bHLHd2	sterol regulatory element binding transcription factor 2	protein-coding	0.003597	0.318996	
chunk0178_117_1	chr7	31168118	31168616	+	0	NA	Intergenic	Intergenic	115906	NM_001118	117	Hs.377783	NM_001118	ENSG00000078549	ADCYAP1R1	PAC1|PAC1R|PACAPR|PACAPRI	ADCYAP receptor type I	protein-coding	0.008032	0.354709	
chunk0149_109_1	chr5	19184498	19184934	+	0	NA	Intergenic	L1PA15-16|LINE|L1	701556	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006881	0.526316	
chunk0152_330_1	chr5	62386657	62387251	+	0	NA	3' UTR (NM_004520, exon 20 of 20)	3' UTR (NM_004520, exon 20 of 20)	16947	NM_014473	27292	Hs.731665	NM_014473	ENSG00000086189	DIMT1	DIM1|DIMT1L|HSA9761|HUSSY5	DIMT1 rRNA methyltransferase and ribosome maturation factor	protein-coding	0.001684	0.368067	
chunk0209_7_1	chrX	34937579	34938163	+	0	NA	Intergenic	Intergenic	-4925	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.015411	0.393162	
chunk0125_10_1	chr3	61848103	61848506	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	286735	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.009926	0.497525	256(AAGCACTTTGTGTGCC,-,0.00),257(AGCACTTTGTGTGCCT,+,0.00)
chunk0032_250_1	chr11	8551772	8551971	+	0	NA	intron (NM_030906, intron 1 of 13)	intron (NM_030906, intron 1 of 13)	42137	NM_030906	65975	Hs.501833	NM_030906	ENSG00000130413	STK33	-	serine/threonine kinase 33	protein-coding	0.000000	0.480000	
chunk0188_176_1	chr8	11286629	11287397	+	0	NA	intron (NM_015458, intron 1 of 9)	L2b|LINE|L2	2522	NM_015458	66036	Hs.591395	NM_015458	ENSG00000104643	MTMR9	C8orf9|LIP-STYX|MTMR8	myotubularin related protein 9	protein-coding	0.016927	0.395319	
chunk0188_167_1	chr8	10776675	10777571	+	0	NA	intron (NM_001284356, intron 5 of 5)	intron (NM_001284356, intron 5 of 5)	-46549	NM_031439	83595	Hs.709543	NM_031439	ENSG00000171056	SOX7	-	SRY-box transcription factor 7	protein-coding	0.020089	0.499443	
chunk0094_38_1	chr2	1980696	1981012	+	0	NA	intron (NM_015025, intron 5 of 24)	intron (NM_015025, intron 5 of 24)	-236307	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.018987	0.470032	
chunk0069_297_1	chr15	65354426	65354876	+	0	NA	intron (NM_004884, intron 2 of 13)	L2c|LINE|L2	23389	NM_004884	9543	Hs.128292	NM_004884	ENSG00000174498	IGDCC3	HsT18880|PUNC	immunoglobulin superfamily DCC subclass member 3	protein-coding	0.017778	0.458980	
chunk0085_434_1	chr18	10916642	10917308	+	0	NA	intron (NM_022068, intron 3 of 51)	intron (NM_022068, intron 3 of 51)	-157326	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.018018	0.469265	
chunk0141_93_1	chr4	79083335	79083856	+	0	NA	intron (NR_038342, intron 2 of 5)	intron (NR_038342, intron 2 of 5)	111847	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.005758	0.415709	226(CTGAACAATGTGTTCT,-,0.00),227(TGAACAATGTGTTCTG,+,0.00)
chunk0146_282_1	chr4	163712534	163712817	+	0	NA	intron (NM_001166373, intron 3 of 7)	intron (NM_001166373, intron 3 of 7)	-99051	NM_017923	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.010601	0.369718	
chunk0089_395_1	chr18	68109229	68109453	+	0	NA	Intergenic	L1MC3|LINE|L1	-592611	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.000000	0.386667	
chunk0022_203_1	chr10	13686187	13686873	+	0	NA	intron (NM_018027, intron 15 of 24)	intron (NM_018027, intron 15 of 24)	99591	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.017493	0.449782	366(TAGCACAACCTGTTTT,-,0.00),367(AGCACAACCTGTTTTC,+,0.00)
chunk0133_420_1	chr3	174655958	174656408	+	0	NA	Intergenic	Kanga1|DNA|TcMar-Tc2	-203138	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.008889	0.343681	
chunk0086_330_1	chr18	24575954	24576435	+	0	NA	Intergenic	Intergenic	-51988	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.008316	0.348548	245(AGGTACTGTTTGTTCC,-,0.00),246(GGTACTGTTTGTTCCC,+,0.00)
chunk0087_261_1	chr18	37107998	37108379	+	0	NA	intron (NM_020776, intron 7 of 9)	L1PA16|LINE|L1	-278972	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.002625	0.382199	
chunk0110_446_1	chr20	21094010	21094618	+	0	NA	Intergenic	Intergenic	-31669	NM_001276389	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.004934	0.425287	319(CTGTACAGAGTGTTCT,-,0.00),320(TGTACAGAGTGTTCTT,+,0.00)
chunk0182_400_1	chr7	100673365	100673820	+	0	NA	promoter-TSS (NM_005273)	promoter-TSS (NM_005273)	-148	NM_005273	2783	Hs.185172	NM_005273	ENSG00000172354	GNB2	-	G protein subunit beta 2	protein-coding	0.079121	0.677632	
chunk0079_230_1	chr17	15470573	15470966	+	0	NA	intron (NM_001204478, intron 5 of 6)	L1MC5|LINE|L1	-3158	NM_001204477	284040	Hs.164595	NM_173622	ENSG00000239704	CDRT4	-	CMT1A duplicated region transcript 4	protein-coding	0.012723	0.428934	
chunk0018_354_1	chr1	221620363	221621165	+	0	NA	Intergenic	Intergenic	116136	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.003741	0.383562	
chunk0207_288_1	chr9	133022408	133022687	+	0	NA	Intergenic	Intergenic	2117	NR_132980	106635683		NR_132980		SNORD141A	-	small nucleolar RNA, C/D box 141A	snoRNA	0.021505	0.542857	
chunk0091_105_1	chr19	5888386	5888684	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	15478	NR_034166	126328	Hs.406062	NM_175614	ENSG00000174886	NDUFA11	B14.7|CI-B14.7|MC1DN14	NADH:ubiquinone oxidoreductase subunit A11	protein-coding	0.023490	0.454849	
chunk0012_416_1	chr1	164465889	164466188	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-93322	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.010033	0.443333	
chunk0076_295_1	chr16	69867258	69867461	+	0	NA	intron (NM_007014, intron 7 of 24)	Tigger12c|DNA|TcMar-Tigger	28622	NM_001270453	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.004926	0.470588	
chunk0045_411_1	chr12	53049521	53050110	+	0	NA	promoter-TSS (NM_170754)	promoter-TSS (NM_170754)	-236	NM_170754	23371	Hs.6147	NM_015319	ENSG00000111077	TNS2	C1-TEN|C1TEN|TENC1	tensin 2	protein-coding	0.023769	0.616949	212(TGGGACACACTGTTCC,-,0.00),213(GGGACACACTGTTCCC,+,0.00)
chunk0011_220_1	chr1	150205921	150206655	+	0	NA	Intergenic	LTR7B|LTR|ERV1	28390	NM_001136479	81611	Hs.656466	NM_030920	ENSG00000143401	ANP32E	LANP-L|LANPL	acidic nuclear phosphoprotein 32 family member E	protein-coding	0.014986	0.406803	
chunk0018_428_1	chr1	222814953	222815262	+	0	NA	promoter-TSS (NM_032890)	promoter-TSS (NM_032890)	18	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.132686	0.729032	
chunk0009_463_1	chr1	111656043	111656660	+	0	NA	intron (NM_001010935, intron 2 of 8)	intron (NM_001010935, intron 2 of 8)	36204	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.004862	0.357605	
chunk0135_439_1	chr3	193922141	193922830	+	0	NA	Intergenic	Intergenic	71753	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.011611	0.463768	
chunk0104_364_1	chr2	180007290	180007528	+	0	NA	promoter-TSS (NM_020943)	promoter-TSS (NM_020943)	-356	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.050420	0.439331	
chunk0169_339_1	chr6	106448041	106448315	+	0	NA	Intergenic	Intergenic	-63677	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.018248	0.552727	
chunk0056_400_1	chr13	93956853	93957396	+	0	NA	intron (NM_005708, intron 3 of 8)	intron (NM_005708, intron 3 of 8)	-98651	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.009208	0.352941	243(GAGAACAGTGTGTCCT,-,0.00),244(AGAACAGTGTGTCCTC,+,0.00)
chunk0063_195_1	chr14	80948646	80948909	+	0	NA	Intergenic	Intergenic	-6748	NM_001142626	7253	Hs.160411	NM_000369	ENSG00000165409	TSHR	CHNG1|LGR3|hTSHR-I	thyroid stimulating hormone receptor	protein-coding	0.003802	0.333333	
chunk0094_206_1	chr2	6460379	6460662	+	0	NA	Intergenic	Intergenic	-85098	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.000000	0.323944	
chunk0096_29_1	chr2	26663415	26663719	+	0	NA	Intergenic	L1MC2|LINE|L1	-22224	NM_001029881	130106	Hs.591579	NM_001029881	ENSG00000157884	CIB4	KIP4	calcium and integrin binding family member 4	protein-coding	0.003289	0.344262	
chunk0033_134_1	chr11	15287710	15288000	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	138753	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.003448	0.453608	
chunk0180_428_1	chr7	76307051	76307268	+	0	NA	Intergenic	Intergenic	4601	NM_001540	3315	Hs.520973	NM_001540	ENSG00000106211	HSPB1	CMT2F|HEL-S-102|HMN2B|HS.76067|HSP27|HSP28|Hsp25|SRP27	heat shock protein family B (small) member 1	protein-coding	0.023041	0.596330	
chunk0052_158_1	chr13	23941320	23941539	+	0	NA	non-coding (NR_073430, exon 3 of 5)	non-coding (NR_073430, exon 3 of 5)	7886	NR_073430	400110	Hs.744780	NM_207439		ANKRD20A19P	-	ankyrin repeat domain 20 family member A19, pseudogene	pseudo	0.009132	0.431818	135(ATGCACAGCCTGTGCC,-,0.00),136(TGCACAGCCTGTGCCT,+,0.00)
chunk0191_48_1	chr8	43365695	43365928	+	0	NA	Intergenic	L1PA12|LINE|L1	73369	NM_001005365	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.012876	0.576923	
chunk0185_120_1	chr7	126084489	126085090	+	0	NA	Intergenic	Intergenic	-820498	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.003328	0.347176	
chunk0122_247_1	chr3	34598967	34599166	+	0	NA	Intergenic	Intergenic	794957	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.010050	0.415000	
chunk0195_279_1	chr8	98367799	98368379	+	0	NA	Intergenic	Intergenic	-58933	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.008621	0.476764	296(AGCACACTCTCTCCCT,+,0.00)
chunk0088_446_1	chr18	56696969	56697321	+	0	NA	intron (NM_015285, intron 12 of 27)	intron (NM_015285, intron 12 of 27)	45760	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.005682	0.342776	
chunk0180_354_1	chr7	73715572	73716047	+	0	NA	intron (NM_004603, intron 1 of 9)	intron (NM_004603, intron 1 of 9)	3878	NM_004603	6804	Hs.647024	NM_004603	ENSG00000106089	STX1A	HPC-1|P35-1|STX1|SYN1A	syntaxin 1A	protein-coding	0.016842	0.596639	
chunk0144_392_1	chr4	140151113	140151414	+	0	NA	intron (NM_018717, intron 1 of 5)	CpG	2816	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.063123	0.662252	
chunk0177_444_1	chr7	28062355	28062826	+	0	NA	intron (NM_175061, intron 1 of 4)	LTR41B|LTR|ERVL	-117867	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.016985	0.502119	
chunk0153_188_1	chr5	71654006	71654740	+	0	NA	intron (NM_022132, intron 16 of 16)	intron (NM_022132, intron 16 of 16)	-64790	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.012262	0.365986	
chunk0028_340_1	chr10	92124033	92124390	+	0	NA	intron (NM_001178137, intron 6 of 9)	intron (NM_001178137, intron 6 of 9)	119068	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.002801	0.393855	149(TAGCACAGTGTGTACT,-,0.00),150(AGCACAGTGTGTACTT,+,0.00)
chunk0141_255_1	chr4	85604240	85604440	+	0	NA	intron (NM_001025616, intron 2 of 9)	intron (NM_001025616, intron 2 of 9)	-118128	NR_039656	100616349		NR_039656	ENSG00000266421	MIR4451	mir-4451	microRNA 4451	ncRNA	0.000000	0.308458	
chunk0040_293_1	chr11	117077235	117077844	+	0	NA	intron (NM_025164, intron 1 of 23)	intron (NM_025164, intron 1 of 23)	20876	NM_001281748	23387	Hs.167451	NM_025164	ENSG00000160584	SIK3	L19|QSK|SEMDK|SIK-3	SIK family kinase 3	protein-coding	0.003284	0.372131	
chunk0094_265_1	chr2	7791985	7792902	+	0	NA	Intergenic	Intergenic	107212	NR_110256	101929551	Hs.116006	NR_110256	ENSG00000226506	LOC101929551	-	uncharacterized LOC101929551	ncRNA	0.009815	0.468410	
chunk0168_18_1	chr6	76941537	76941736	+	0	NA	Intergenic	L1MA1|LINE|L1	521767	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.005025	0.505000	
chunk0191_22_1	chr8	42895437	42895665	+	0	NA	TTS (NR_039679)	TTS (NR_039679)	724	NR_039679	100616115		NR_039679	ENSG00000284062	MIR4469	mir-4469	microRNA 4469	ncRNA	0.013158	0.414847	
chunk0174_126_1	chr6	157312859	157313405	+	0	NA	intron (NM_018452, intron 3 of 3)	intron (NM_018452, intron 3 of 3)	11127	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.031136	0.575868	
chunk0180_288_1	chr7	70059523	70059835	+	0	NA	intron (NM_015570, intron 2 of 18)	L2c|LINE|L2	460760	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.019231	0.418530	194(AGGAACACGGTGTTAT,-,0.00),195(GGAACACGGTGTTATG,+,0.00)
chunk0130_164_1	chr3	132713888	132714535	+	0	NA	intron (NM_153240, intron 5 of 26)	MER58B|DNA|hAT-Charlie	-8131	NR_002811	348808	Hs.586111	NR_002811	ENSG00000248724	NPHP3-AS1	NCRNA00119	NPHP3 antisense RNA 1	ncRNA	0.004637	0.358025	
chunk0149_52_1	chr5	16776369	16777086	+	0	NA	intron (NM_012334, intron 9 of 40)	intron (NM_012334, intron 9 of 40)	159549	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.011158	0.357939	346(AAGAACAGACAGTTCT,-,0.00),347(AGAACAGACAGTTCTG,+,0.00),384(GAGAACACAGAGTACC,-,0.00),385(AGAACACAGAGTACCA,+,0.00)
chunk0074_26_1	chr16	20426479	20426836	+	0	NA	intron (NM_017888, intron 6 of 13)	L1MB3|LINE|L1	17123	NM_017888	54988	Hs.659606	NM_017888	ENSG00000183549	ACSM5	-	acyl-CoA synthetase medium chain family member 5	protein-coding	0.002801	0.363128	
chunk0032_301_1	chr11	9719609	9720001	+	0	NA	intron (NM_015055, intron 3 of 11)	intron (NM_015055, intron 3 of 11)	-38488	NR_036485	283104	Hs.632156	NR_036485	ENSG00000246273	SBF2-AS1	-	SBF2 antisense RNA 1	ncRNA	0.005102	0.310433	
chunk0167_414_1	chr6	75413333	75413817	+	0	NA	intron (NR_125859, intron 3 of 8)	intron (NR_125859, intron 3 of 8)	-14832	NR_039670	100616389		NR_039670	ENSG00000263533	MIR4463	-	microRNA 4463	ncRNA	0.000000	0.344330	232(AGGAACAGAGTGACCC,-,0.00),233(GGAACAGAGTGACCCA,+,0.00)
chunk0106_416_1	chr2	208025403	208025639	+	0	NA	promoter-TSS (NM_001080475)	promoter-TSS (NM_001080475)	39	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.097458	0.691983	
chunk0091_177_1	chr19	8180132	8180579	+	0	NA	Intergenic	L1ME4c|LINE|L1	-28978	NM_024552	79603	Hs.515111	NM_024552	ENSG00000090661	CERS4	LASS4|Trh1	ceramide synthase 4	protein-coding	0.011186	0.377232	
chunk0048_76_1	chr12	78985547	78986361	+	0	NA	intron (NM_001291901, intron 2 of 9)	intron (NM_001291901, intron 2 of 9)	-59699	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.007371	0.305521	
chunk0207_354_1	chr9	135275541	135276011	+	0	NA	Intergenic	Intergenic	-67473	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.029787	0.583864	
chunk0093_411_1	chr19	57280222	57280487	+	0	NA	promoter-TSS (NM_006635)	promoter-TSS (NM_006635)	-131	NM_006635	10794	Hs.99971	NM_006635	ENSG00000197714	ZNF460	HZF8|ZNF272	zinc finger protein 460	protein-coding	0.086792	0.624060	
chunk0028_222_1	chr10	89617457	89618024	+	0	NA	intron (NM_148977, intron 1 of 6)	MLT1I-int|LTR|ERVL-MaLR	-24913	NR_029524	406901		NR_029524	ENSG00000198997	MIR107	MIRN107|miR-107	microRNA 107	ncRNA	0.003527	0.380282	
chunk0108_397_1	chr2	237290390	237290589	+	0	NA	Intergenic	Intergenic	123718	NM_057166	1293	Hs.233240	NM_004369	ENSG00000163359	COL6A3	BTHLM1|DYT27|UCMD1	collagen type VI alpha 3 chain	protein-coding	0.050251	0.565000	113(CAGAACGTCATGTGCT,-,0.00),114(AGAACGTCATGTGCTT,+,0.00)
chunk0119_235_1	chr22	45402346	45402956	+	0	NA	intron (NM_148674, intron 4 of 24)	intron (NM_148674, intron 4 of 24)	10968	NM_001291501	27127	Hs.334176	NM_148674	ENSG00000077935	SMC1B	SMC1BETA|SMC1L2	structural maintenance of chromosomes 1B	protein-coding	0.004918	0.358429	333(TAGGACATAATGTTCT,-,0.00),334(AGGACATAATGTTCTT,+,0.00)
chunk0027_455_1	chr10	81367068	81367267	+	0	NA	Intergenic	Intergenic	-508147	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.000000	0.345000	
chunk0171_183_1	chr6	125197878	125198177	+	0	NA	intron (NM_001003395, intron 1 of 6)	intron (NM_001003395, intron 1 of 6)	43753	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.006689	0.526667	
chunk0159_110_1	chr5	138562648	138563060	+	0	NA	intron (NM_004134, intron 9 of 16)	intron (NM_004134, intron 9 of 16)	-1744	NR_002913	26785		NR_002913	ENSG00000206989	SNORD63	RNU63|SNORD63A|U63	small nucleolar RNA, C/D box 63	snoRNA	0.004854	0.384988	
chunk0147_348_1	chr4	185637312	185637880	+	0	NA	intron (NM_001145672, intron 10 of 20)	MIRb|SINE|MIR	19373	NM_001145674	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.015845	0.427065	
chunk0076_1_1	chr16	58444063	58444262	+	0	NA	Intergenic	Intergenic	-19483	NM_020465	65009	Hs.322430	NM_020465	ENSG00000103034	NDRG4	BDM1|SMAP-8|SMAP8	NDRG family member 4	protein-coding	0.000000	0.475000	
chunk0068_405_1	chr15	58962850	58963111	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-24686	NM_001270528	54778	Hs.404423	NM_017610	ENSG00000157450	RNF111	ARK|hRNF111	ring finger protein 111	protein-coding	0.003831	0.354962	
chunk0094_347_1	chr2	9338405	9338836	+	0	NA	intron (NM_003887, intron 9 of 27)	intron (NM_003887, intron 9 of 27)	84894	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.011601	0.543981	6(TAGAACAGTTTGTGCC,-,0.00),7(AGAACAGTTTGTGCCA,+,0.00)
chunk0034_199_1	chr11	32290639	32291128	+	0	NA	Intergenic	L2b|LINE|L2	139934	NM_001198552	7490	Hs.591980	NM_000378	ENSG00000184937	WT1	AWT1|GUD|NPHS4|WAGR|WIT-2|WT33	WT1 transcription factor	protein-coding	0.006135	0.440816	238(TAGAACATGCTGTACT,-,0.00),239(AGAACATGCTGTACTC,+,0.00)
chunk0128_219_1	chr3	108091046	108091419	+	0	NA	promoter-TSS (NM_001777)	promoter-TSS (NM_001777)	-144	NM_198793	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.134048	0.754011	
chunk0158_399_1	chr5	134680517	134680846	+	0	NA	intron (NM_001252231, intron 8 of 12)	AluSc|SINE|Alu	31896	NM_001252231	10802	Hs.595540	NM_021982	ENSG00000113615	SEC24A	-	SEC24 homolog A, COPII coat complex component	protein-coding	0.018237	0.527273	
chunk0124_248_1	chr3	56831640	56831968	+	0	NA	intron (NM_001128615, intron 4 of 12)	intron (NM_001128615, intron 4 of 12)	-29837	NM_019555	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.006098	0.419453	
chunk0118_169_1	chr22	30753709	30754344	+	0	NA	intron (NM_030758, intron 2 of 13)	intron (NM_030758, intron 2 of 13)	-10227	NM_001282740	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.006299	0.433962	
chunk0003_345_1	chr1	39065418	39065950	+	0	NA	Intergenic	Intergenic	-18483	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.011278	0.382739	
chunk0133_280_1	chr3	172051393	172051797	+	0	NA	intron (NM_001135095, intron 1 of 25)	L1PB1|LINE|L1	11041	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.004950	0.400000	202(GGGTTCAGTGTGTACT,-,0.00),203(GGTTCAGTGTGTACTG,+,0.00)
chunk0054_157_1	chr13	44125964	44126436	+	0	NA	intron (NR_104065, intron 1 of 4)	MIRb|SINE|MIR	15651	NR_104065	101929212	Hs.534877	NR_104064	ENSG00000227258	SMIM2-AS1	C13orf44-AS1|C3orf81-AS1	SMIM2 antisense RNA 1	ncRNA	0.006356	0.412262	204(AAGAACATGCAGTGCA,-,0.00),205(AGAACATGCAGTGCAA,+,0.00)
chunk0062_122_1	chr14	68470223	68470435	+	0	NA	intron (NM_133509, intron 10 of 10)	intron (NM_133509, intron 10 of 10)	323585	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.000000	0.478873	
chunk0026_436_1	chr10	71241306	71241899	+	0	NA	intron (NM_170744, intron 1 of 16)	intron (NM_170744, intron 1 of 16)	-23374	NR_038453	728978	Hs.646725	NR_038453	ENSG00000237512	UNC5B-AS1	-	UNC5B antisense RNA 1	ncRNA	0.016863	0.525253	
chunk0206_342_1	chr9	125544963	125545481	+	0	NA	intron (NM_001006618, intron 6 of 7)	intron (NM_001006618, intron 6 of 7)	162012	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.019305	0.425819	150(CTGAACACTCTGTTAC,-,0.00)
chunk0031_74_1	chr10	123140653	123141231	+	0	NA	Intergenic	Intergenic	4891	NM_001105574	340784	Hs.531194	NM_001105574	ENSG00000188620	HMX3	NKX-5.1|NKX5.1|Nkx5-1	H6 family homeobox 3	protein-coding	0.019031	0.455959	274(CAGAACACGATGTTAT,-,0.00),275(AGAACACGATGTTATC,+,0.00)
chunk0008_239_1	chr1	94236239	94236438	+	0	NA	intron (NM_004815, intron 1 of 22)	intron (NM_004815, intron 1 of 22)	1413	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.005025	0.460000	
chunk0136_431_1	chr3	197681112	197681478	+	0	NA	exon (NM_014687, exon 16 of 20)	exon (NM_014687, exon 16 of 20)	-6719	NR_030627	100126321		NR_030627	ENSG00000284146	MIR922	MIRN922|hsa-mir-922	microRNA 922	ncRNA	0.024590	0.517711	
chunk0060_149_1	chr14	45084150	45084715	+	0	NA	intron (NM_017922, intron 1 of 13)	intron (NM_017922, intron 1 of 13)	333	NM_017922	55015	Hs.274337	NM_017922	ENSG00000185246	PRPF39	-	pre-mRNA processing factor 39	protein-coding	0.042478	0.561837	
chunk0004_159_1	chr1	45500166	45500371	+	0	NA	promoter-TSS (NR_033298)	promoter-TSS (NR_033298)	84	NM_015506	25974	Hs.13024	NM_015506	ENSG00000132763	MMACHC	cblC	metabolism of cobalamin associated C	protein-coding	0.068293	0.529126	
chunk0077_174_1	chr16	79612151	79612661	+	0	NA	Intergenic	Intergenic	-11681	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.005882	0.344423	
chunk0157_131_1	chr5	117312988	117313498	+	0	NA	Intergenic	Intergenic	-102269	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.003922	0.379648	
chunk0179_184_1	chr7	47039722	47040371	+	0	NA	Intergenic	Intergenic	542098	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.003082	0.366154	
chunk0113_137_1	chr20	51953934	51954315	+	0	NA	Intergenic	L2b|LINE|L2	-91211	NR_110016	101927678	Hs.683840	NR_110016	ENSG00000227964	LINC01429	-	long intergenic non-protein coding RNA 1429	ncRNA	0.013123	0.442408	
chunk0065_402_1	chr14	105241999	105242198	+	0	NA	intron (NM_001242787, intron 5 of 17)	intron (NM_001242787, intron 5 of 17)	5787	NM_145685	2972	Hs.424484	NM_001519	ENSG00000185024	BRF1	BRF|BRF-1|CFDS|GTF3B|HEL-S-76p|TAF3B2|TAF3C|TAFIII90|TF3B90|TFIIIB90|hBRF	BRF1 RNA polymerase III transcription initiation factor subunit	protein-coding	0.035176	0.585000	
chunk0039_302_1	chr11	102991908	102992489	+	0	NA	Intergenic	Intergenic	-36464	NM_002427	4322	Hs.2936	NM_002427	ENSG00000137745	MMP13	CLG3|MANDP1|MDST|MMP-13	matrix metallopeptidase 13	protein-coding	0.008606	0.384880	
chunk0099_404_1	chr2	102048504	102048715	+	0	NA	Intergenic	Intergenic	-21767	NM_001288706	3554	Hs.701982	NM_000877	ENSG00000115594	IL1R1	CD121A|D2S1473|IL-1R-alpha|IL1R|IL1RA|P80	interleukin 1 receptor type 1	protein-coding	0.018957	0.533019	53(TGGATCATGCTGTCCT,-,0.00),54(GGATCATGCTGTCCTC,+,0.00)
chunk0139_218_1	chr4	55038178	55038800	+	0	NA	Intergenic	Intergenic	87106	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.003215	0.454254	250(TGGAACAGAGAGTACT,-,0.00),251(GGAACAGAGAGTACTA,+,0.00),518(CAGCTCAGTGTGTGCT,-,0.00),519(AGCTCAGTGTGTGCTG,+,0.00)
chunk0099_259_1	chr2	98036649	98036861	+	0	NA	Intergenic	Intergenic	-40864	NM_015348	23505	Hs.469376	NM_015348	ENSG00000075568	TMEM131	CC28|PRO1048|RW1|YR-23	transmembrane protein 131	protein-coding	0.000000	0.624413	
chunk0025_225_1	chr10	53997422	53997825	+	0	NA	intron (NM_001142769, intron 22 of 35)	intron (NM_001142769, intron 22 of 35)	610334	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.002481	0.334158	84(GAGCTCATTATGTTCT,-,0.00),85(AGCTCATTATGTTCTT,+,0.00)
chunk0003_276_1	chr1	36760963	36761407	+	0	NA	Intergenic	Intergenic	273058	NM_000831	2899	Hs.128848	NM_000831	ENSG00000163873	GRIK3	EAA5|GLR7|GLUR7|GluK3|GluR7a	glutamate ionotropic receptor kainate type subunit 3	protein-coding	0.000000	0.548315	
chunk0003_267_1	chr1	36296872	36297491	+	0	NA	intron (NM_005119, intron 9 of 11)	intron (NM_005119, intron 9 of 11)	-9212	NM_001162530	79729	Hs.524496	NM_024676	ENSG00000214193	SH3D21	C1orf113	SH3 domain containing 21	protein-coding	0.003231	0.362903	
chunk0132_53_1	chr3	155034796	155035183	+	0	NA	Intergenic	MER117|DNA|hAT-Charlie	-44658	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.010336	0.340206	
chunk0172_149_1	chr6	135619546	135619819	+	0	NA	intron (NR_026805, intron 1 of 3)	intron (NR_026805, intron 1 of 3)	121881	NR_026805	100131814	Hs.734007	NR_026805	ENSG00000231028	LINC00271	C6orf217|NCRNA00271	long intergenic non-protein coding RNA 271	ncRNA	0.007326	0.489051	
chunk0196_271_1	chr8	109001316	109001977	+	0	NA	Intergenic	Intergenic	-85778	NM_003301	7201	Hs.3022	NM_003301	ENSG00000174417	TRHR	TRH-R	thyrotropin releasing hormone receptor	protein-coding	0.003026	0.365559	
chunk0070_119_1	chr15	70717306	70718004	+	0	NA	intron (NM_018003, intron 1 of 18)	intron (NM_018003, intron 1 of 18)	-15374	NM_001008224	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.000000	0.389127	
chunk0122_28_1	chr3	27880593	27880886	+	0	NA	Intergenic	MER39|LTR|ERV1	-46603	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.006826	0.391156	
chunk0191_447_1	chr8	57991109	57991606	+	0	NA	Intergenic	Intergenic	-3197	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.008048	0.443775	
chunk0210_131_1	chrX	74251665	74252015	+	0	NA	intron (NR_028379, intron 5 of 6)	MER21C|LTR|ERVL	-33222	NR_030620	100126317		NR_030620	ENSG00000212027	MIR374B	MIRN374B|mir-374b	microRNA 374b	ncRNA	0.002857	0.393162	
chunk0125_394_1	chr3	71902917	71903116	+	0	NA	Intergenic	L2a|LINE|L2	-117810	NM_021935	60675	Hs.528665	NM_021935	ENSG00000163421	PROK2	BV8|HH4|KAL4|MIT1|PK2	prokineticin 2	protein-coding	0.000000	0.415000	
chunk0017_255_1	chr1	209299890	209300162	+	0	NA	Intergenic	L2a|LINE|L2	-128797	NM_001104548									0.000000	0.333333	
chunk0129_435_1	chr3	127780342	127780573	+	0	NA	intron (NM_001003794, intron 3 of 7)	intron (NM_001003794, intron 3 of 7)	42425	NM_007283	11343	Hs.277035	NM_007283	ENSG00000074416	MGLL	HU-K5|HUK5|MAGL|MGL	monoglyceride lipase	protein-coding	0.017316	0.340517	
chunk0204_433_1	chr9	103734584	103734885	+	0	NA	Intergenic	Intergenic	-264975	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.003322	0.380795	
chunk0155_214_1	chr5	95161866	95162778	+	0	NA	intron (NM_024717, intron 1 of 22)	intron (NM_024717, intron 1 of 22)	-80456	NM_001297777	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.003289	0.351588	
chunk0099_341_1	chr2	100106370	100106862	+	0	NA	intron (NM_002285, intron 1 of 23)	intron (NM_002285, intron 1 of 23)	-1033	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.018293	0.496957	232(AAGAACTGCAAGTTCT,-,0.00),233(AGAACTGCAAGTTCTG,+,0.00)
chunk0164_27_1	chr6	18262792	18263223	+	0	NA	intron (NM_003472, intron 2 of 10)	intron (NM_003472, intron 2 of 10)	1561	NM_003472	7913	Hs.484813	NM_003472	ENSG00000124795	DEK	D6S231E	DEK proto-oncogene	protein-coding	0.025522	0.416667	
chunk0002_333_1	chr1	24568006	24568231	+	0	NA	intron (NM_001010980, intron 1 of 3)	intron (NM_001010980, intron 1 of 3)	12042	NM_001010980	400746	Hs.200253	NM_001010980	ENSG00000184454	NCMAP	C1orf130|MP11	non-compact myelin associated protein	protein-coding	0.035556	0.584071	
chunk0081_326_1	chr17	46166621	46167227	+	0	NA	intron (NM_001193465, intron 3 of 15)	L4_A_Mam|LINE|RTE-X	25876	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.003300	0.326194	
chunk0118_419_1	chr22	38502908	38503143	+	0	NA	intron (NM_006386, intron 1 of 12)	intron (NM_006386, intron 1 of 12)	3315	NM_006386	10521	Hs.528305	NM_006386	ENSG00000100201	DDX17	P72|RH70	DEAD-box helicase 17	protein-coding	0.008511	0.411017	
chunk0207_282_1	chr9	132703288	132703715	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-33100	NM_138620	64794	Hs.660767	NM_022779	ENSG00000125485	DDX31	PPP1R25	DEAD-box helicase 31	protein-coding	0.004684	0.383178	271(GGGACACACTCTTCCT,+,0.00)
chunk0203_51_1	chr9	83132689	83133350	+	0	NA	Intergenic	Intergenic	-69891	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.001513	0.367069	
chunk0164_88_1	chr6	20186451	20186919	+	0	NA	intron (NM_001080480, intron 1 of 12)	intron (NM_001080480, intron 1 of 12)	25779	NM_001080480	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.010684	0.445629	
chunk0001_271_1	chr1	8612095	8612568	+	0	NA	intron (NM_001042681, intron 4 of 22)	intron (NM_001042681, intron 4 of 22)	-117418	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.000000	0.339662	
chunk0006_447_1	chr1	76855879	76856745	+	0	NA	Intergenic	Intergenic	-11189	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.009238	0.400231	413(CAGAACATAATGTACA,-,0.00),414(AGAACATAATGTACAG,+,0.00)
chunk0186_152_1	chr7	139110981	139111658	+	0	NA	Intergenic	Intergenic	-1600	NM_024625	56829	Hs.133512	NM_020119	ENSG00000105939	ZC3HAV1	ARTD13|FLB6421|PARP13|ZAP|ZC3H2|ZC3HDC2	zinc finger CCCH-type containing, antiviral 1	protein-coding	0.001477	0.356932	301(AGGGACATCTTGTTCC,-,0.00),302(GGGACATCTTGTTCCC,+,0.00)
chunk0011_348_1	chr1	152372627	152373066	+	0	NA	Intergenic	L1MD3|LINE|L1	-12840	NM_001014342	388698	Hs.156124	NM_001014342	ENSG00000143520	FLG2	IFPS|PSS6	filaggrin family member 2	protein-coding	0.002278	0.345455	
chunk0182_449_1	chr7	101882829	101883544	+	0	NA	intron (NM_181552, intron 1 of 23)	intron (NM_181552, intron 1 of 23)	65584	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.018182	0.462291	
chunk0194_316_1	chr8	88271619	88272229	+	0	NA	intron (NM_005941, intron 1 of 9)	MIRb|SINE|MIR	55564	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.011475	0.353519	
chunk0143_360_1	chr4	122086282	122087159	+	0	NA	Intergenic	Intergenic	-83883	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.004561	0.400911	
chunk0084_383_1	chr17	81964385	81965011	+	0	NA	Intergenic	L1MB5|LINE|L1	-3517	NM_178493	147111	Hs.106137	NM_178493	ENSG00000185269	NOTUM	hNOTUM	notum, palmitoleoyl-protein carboxylesterase	protein-coding	0.023962	0.484848	
chunk0120_307_1	chr3	10142938	10143137	+	0	NA	intron (NM_198156, intron 1 of 1)	intron (NM_198156, intron 1 of 1)	1402	NM_000551	7428	Hs.517792	NM_000551	ENSG00000134086	VHL	HRCA1|RCA1|VHL1|pVHL	von Hippel-Lindau tumor suppressor	protein-coding	0.020101	0.470000	
chunk0052_152_1	chr13	23804692	23805023	+	0	NA	intron (NM_005932, intron 16 of 18)	MIRc|SINE|MIR	-84032	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.012085	0.391566	
chunk0077_53_1	chr16	76328929	76329154	+	0	NA	intron (NM_138994, intron 2 of 22)	L1MC3|LINE|L1	19203	NM_138994	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.004444	0.331858	
chunk0014_178_1	chr1	178571903	178572148	+	0	NA	Intergenic	L1M4|LINE|L1	29229	NR_033186	400798	Hs.668085	NM_207467	ENSG00000213057	C1orf220	-	chromosome 1 open reading frame 220 (putative)	ncRNA	0.012245	0.463415	
chunk0037_149_1	chr11	73469381	73469832	+	0	NA	intron (NM_001286050, intron 1 of 8)	intron (NM_001286050, intron 1 of 8)	92938	NM_032871	84957	Hs.533720	NM_032871	ENSG00000054967	RELT	AI3C|TNFRSF19L|TRLT	RELT TNF receptor	protein-coding	0.006652	0.382743	239(GAGGACAGAATGTCCT,-,0.00),240(AGGACAGAATGTCCTA,+,0.00)
chunk0097_397_1	chr2	62042926	62043302	+	0	NA	intron (NM_152516, intron 2 of 2)	intron (NM_152516, intron 2 of 2)	137446	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.005319	0.381963	
chunk0180_422_1	chr7	76121422	76121875	+	0	NA	Intergenic	L1MEc|LINE|L1	73629	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.004415	0.339207	
chunk0064_127_1	chr14	91379834	91380585	+	0	NA	intron (NM_001080414, intron 3 of 29)	intron (NM_001080414, intron 3 of 29)	37635	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.021305	0.429521	
chunk0190_312_1	chr8	38509490	38510154	+	0	NA	Intergenic	Intergenic	18840	NM_001303531	389649	Hs.546586	NM_207412	ENSG00000196166	C8orf86	-	chromosome 8 open reading frame 86	protein-coding	0.010542	0.436090	
chunk0057_202_1	chr13	103556939	103557196	+	0	NA	Intergenic	Intergenic	131867	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.003891	0.399225	
chunk0149_140_1	chr5	19967374	19967573	+	0	NA	intron (NM_001167667, intron 2 of 12)	intron (NM_001167667, intron 2 of 12)	20771	NM_004934	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.325000	
chunk0090_208_1	chr18	73346728	73347384	+	0	NA	intron (NR_038340, intron 2 of 2)	intron (NR_038340, intron 2 of 2)	22115	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.003049	0.296804	325(CTGAACACTTTGTGCC,-,0.00),326(TGAACACTTTGTGCCT,+,0.00)
chunk0071_394_1	chr15	89334692	89335401	+	0	NA	promoter-TSS (NM_002693)	promoter-TSS (NM_002693)	-251	NM_002693	5428	Hs.706868	NM_002693	ENSG00000140521	POLG	MDP1|MIRAS|MTDPS4A|MTDPS4B|PEO|POLG1|POLGA|SANDO|SCAE	DNA polymerase gamma, catalytic subunit	protein-coding	0.088858	0.623944	
chunk0184_426_1	chr7	122846546	122846976	+	0	NA	intron (NM_017954, intron 1 of 29)	intron (NM_017954, intron 1 of 29)	39998	NM_001009571	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.004651	0.410673	
chunk0127_298_1	chr3	98225091	98225573	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-38953	NM_001005479	79295	Hs.554712	NM_001005479	ENSG00000230301	OR5H6	OR3-11	olfactory receptor family 5 subfamily H member 6 (gene/pseudogene)	protein-coding	0.004149	0.314700	
chunk0130_414_1	chr3	140603709	140604150	+	0	NA	Intergenic	L1ME1|LINE|L1	-74095	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.006803	0.325792	
chunk0112_48_1	chr20	36963789	36963988	+	0	NA	Intergenic	Intergenic	-12045	NM_015474	25939	Hs.580681	NM_015474	ENSG00000101347	SAMHD1	CHBL2|DCIP|HDDC1|MOP-5|SBBI88|hSAMHD1	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1	protein-coding	0.000000	0.395000	
chunk0208_93_1	chrX	13499113	13499750	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-70144	NM_001167890	25975	Hs.12844	NM_015507	ENSG00000198759	EGFL6	MAEG|W80	EGF like domain multiple 6	protein-coding	0.006279	0.390282	
chunk0065_389_1	chr14	104684836	104685251	+	0	NA	Intergenic	Intergenic	-4563	NM_001031714	64423	Hs.24956	NM_022489	ENSG00000203485	INF2	C14orf151|C14orf173|CMTDIE|FSGS5|pp9484	inverted formin, FH2 and WH2 domain containing	protein-coding	0.007229	0.420673	
chunk0090_329_1	chr18	76011863	76012536	+	0	NA	Intergenic	Intergenic	-110799	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.008915	0.367953	284(CAGAGCATTCTGTGCC,-,0.00),285(AGAGCATTCTGTGCCT,+,0.00)
chunk0152_293_1	chr5	61599823	61600164	+	0	NA	Intergenic	MER121|DNA|hAT?	-37788	NM_173667									0.005865	0.514620	
chunk0120_86_1	chr3	3861869	3862585	+	0	NA	Intergenic	L1MC4|LINE|L1	62790	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.004190	0.341702	
chunk0048_290_1	chr12	82738111	82738417	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	51109	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.000000	0.338762	
chunk0016_236_1	chr1	199794586	199795157	+	0	NA	Intergenic	Intergenic	-232731	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.008757	0.325175	202(AAGAACGTTCTGTTCT,-,0.00),203(AGAACGTTCTGTTCTT,+,0.00),284(TTAACATTCTGTTCTT,+,0.00)
chunk0122_313_1	chr3	36949404	36949649	+	0	NA	Intergenic	L1MC5a|LINE|L1	-4469	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.000000	0.361789	
chunk0020_343_1	chr1	239176311	239176730	+	0	NA	Intergenic	Intergenic	-452553	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.007160	0.338095	
chunk0152_4_1	chr5	56138379	56138609	+	0	NA	intron (NM_024669, intron 7 of 11)	L1MC1|LINE|L1	94865	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.004348	0.402597	
chunk0156_179_1	chr5	107677188	107677592	+	0	NA	Intergenic	Intergenic	-6495	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.002475	0.303704	
chunk0146_288_1	chr4	164402396	164403012	+	0	NA	Intergenic	Intergenic	-19449	NM_001166373	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.004870	0.372771	
chunk0092_220_1	chr19	31719481	31720055	+	0	NA	Intergenic	Intergenic	127487	NM_001205273	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.010453	0.340870	
chunk0106_403_1	chr2	207847735	207848203	+	0	NA	intron (NM_001080475, intron 7 of 7)	intron (NM_001080475, intron 7 of 7)	-78550	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.008547	0.469083	
chunk0082_179_1	chr17	56132746	56133523	+	0	NA	Intergenic	Intergenic	-20341	NM_153228	162282	Hs.673040	NM_153228	ENSG00000153930	ANKFN1	-	ankyrin repeat and fibronectin type III domain containing 1	protein-coding	0.006435	0.401028	
chunk0086_4_1	chr18	11963993	11964192	+	0	NA	Intergenic	Intergenic	-17336	NM_014214	3613	Hs.743311	NM_014214	ENSG00000141401	IMPA2	-	inositol monophosphatase 2	protein-coding	0.010050	0.535000	
chunk0106_177_1	chr2	201056897	201057365	+	0	NA	intron (NM_173822, intron 1 of 11)	ERVL-E-int|LTR|ERVL	14538	NM_173822	285172	Hs.24701	NM_173822	ENSG00000155744	FAM126B	HYCC2	family with sequence similarity 126 member B	protein-coding	0.002137	0.422175	
chunk0167_164_1	chr6	63025592	63026012	+	0	NA	Intergenic	Intergenic	294175	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.002381	0.318290	
chunk0106_166_1	chr2	200762822	200763358	+	0	NA	intron (NR_001557, intron 18 of 30)	L1ME3G|LINE|L1	-27913	NR_037886	100507140	Hs.382116	NR_037886	ENSG00000237166	LINC01792	-	long intergenic non-protein coding RNA 1792	ncRNA	0.001866	0.402235	344(GTGCACAGGATGTACA,-,0.00),345(TGCACAGGATGTACAG,+,0.00)
chunk0159_460_1	chr5	148909136	148909381	+	0	NA	Intergenic	L1ME1|LINE|L1	82665	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.004082	0.357724	
chunk0193_450_1	chr8	81161207	81161406	+	0	NA	Intergenic	L2a|LINE|L2	-49238	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.005025	0.440000	
chunk0086_293_1	chr18	23825861	23826471	+	0	NA	intron (NM_001127717, intron 21 of 73)	intron (NM_001127717, intron 21 of 73)	-46854	NM_001127718	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.009836	0.441899	
chunk0187_308_1	chr7	156401316	156401634	+	0	NA	Intergenic	Intergenic	44113	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.015723	0.410658	
chunk0058_145_1	chr14	23034989	23035188	+	0	NA	promoter-TSS (NM_002797)	promoter-TSS (NM_002797)	57	NM_001144932	5693	Hs.422990	NM_002797	ENSG00000100804	PSMB5	LMPX|MB1|X	proteasome subunit beta 5	protein-coding	0.025126	0.455000	
chunk0077_262_1	chr16	80951177	80951414	+	0	NA	Intergenic	Intergenic	-55203	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.008439	0.403361	70(GTCACAATCTGTTCTT,+,0.00)
chunk0004_280_1	chr1	48452719	48453424	+	0	NA	exon (NM_001286239, exon 2 of 12)	exon (NM_001286239, exon 2 of 12)	19137	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.001418	0.328612	
chunk0210_361_1	chrX	96519678	96519919	+	0	NA	Intergenic	L1PA16|LINE|L1	-164865	NM_006729	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.000000	0.396694	55(TTGAACAGGGAGTTCT,-,0.00),56(TGAACAGGGAGTTCTT,+,0.00)
chunk0197_170_1	chr8	120917297	120917559	+	0	NA	Intergenic	Intergenic	-105359	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.000000	0.403042	
chunk0083_58_1	chr17	63741764	63742058	+	0	NA	promoter-TSS (NM_153335)	promoter-TSS (NM_153335)	59	NM_001165969	92335	Hs.514402	NM_153335	ENSG00000266173	STRADA	LYK5|NY-BR-96|PMSE|STRAD|STRAD alpha|Stlk	STE20 related adaptor alpha	protein-coding	0.122449	0.722034	
chunk0080_339_1	chr17	32670976	32671175	+	0	NA	intron (NM_015194, intron 16 of 21)	LTR28|LTR|ERV1	183988	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.005025	0.560000	
chunk0207_121_1	chr9	128917098	128917562	+	0	NA	3' UTR (NM_019594, exon 4 of 4)	3' UTR (NM_019594, exon 4 of 4)	-3565	NM_174933	254295	Hs.709447	NM_174933	ENSG00000175287	PHYHD1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding	0.028017	0.522581	
chunk0096_248_1	chr2	31224778	31224977	+	0	NA	Intergenic	L1MC5|LINE|L1	-7332	NM_001145122	440854	Hs.468059	NM_001145122	ENSG00000214711	CAPN14	-	calpain 14	protein-coding	0.000000	0.245000	
chunk0187_229_1	chr7	152403765	152404036	+	0	NA	intron (NM_170606, intron 1 of 58)	L1PA16|LINE|L1	32105	NM_170606	58508	Hs.647120	NM_021230	ENSG00000055609	KMT2C	HALR|KLEFS2|MLL3	lysine methyltransferase 2C	protein-coding	0.011070	0.426471	
chunk0113_376_1	chr20	59773616	59773984	+	0	NA	intron (NM_080672, intron 6 of 12)	intron (NM_080672, intron 6 of 12)	52590	NM_183246	116154	Hs.473218	NM_080672	ENSG00000087495	PHACTR3	C20orf101|H17739|PPP1R123|SCAPIN1|SCAPININ	phosphatase and actin regulator 3	protein-coding	0.010870	0.493225	
chunk0131_175_1	chr3	147394269	147394765	+	0	NA	intron (NM_001243256, intron 2 of 3)	intron (NM_001243256, intron 2 of 3)	-2087	NR_033119	84107	Hs.415766	NM_032153	ENSG00000174963	ZIC4	-	Zic family member 4	protein-coding	0.040323	0.503018	
chunk0133_159_1	chr3	169772652	169772851	+	0	NA	promoter-TSS (NM_018657)	promoter-TSS (NM_018657)	-314	NR_033703	55892	Hs.507025	NM_018657	ENSG00000085274	MYNN	OSZF|SBBIZ1|ZBTB31|ZNF902	myoneurin	protein-coding	0.035176	0.460000	
chunk0156_230_1	chr5	108287095	108287540	+	0	NA	intron (NM_001163315, intron 4 of 8)	L1PA15|LINE|L1	94781	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.004494	0.302691	
chunk0035_209_1	chr11	44865929	44866556	+	0	NA	intron (NM_130783, intron 2 of 8)	intron (NM_130783, intron 2 of 8)	83966	NM_001258320	9537	Hs.554791	NM_006034	ENSG00000175274	TP53I11	PIG11	tumor protein p53 inducible protein 11	protein-coding	0.017544	0.550955	
chunk0116_115_1	chr21	35790124	35790418	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	69556	NR_030414	768219		NR_030414	ENSG00000211590	MIR802	MIRN802|hsa-mir-802	microRNA 802	ncRNA	0.010204	0.413559	
chunk0002_413_1	chr1	27560634	27560859	+	0	NA	intron (NM_001029882, intron 1 of 6)	intron (NM_001029882, intron 1 of 6)	42748	NM_001029882	27245	Hs.469280	NM_001029882	ENSG00000126705	AHDC1	MRD25	AT-hook DNA binding motif containing 1	protein-coding	0.022222	0.522124	
chunk0157_361_1	chr5	123397308	123398043	+	0	NA	intron (NM_001166226, intron 5 of 19)	intron (NM_001166226, intron 5 of 19)	25917	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.006803	0.385870	313(AAGAACACCAAGTTCT,-,0.00),314(AGAACACCAAGTTCTT,+,0.00),461(GTGGACATTTTGTTCC,-,0.00),462(TGGACATTTTGTTCCT,+,0.00)
chunk0069_354_1	chr15	66773177	66773447	+	0	NA	intron (NR_027654, intron 4 of 4)	intron (NR_027654, intron 4 of 4)	70976	NR_027654	4091	Hs.153863	NM_005585	ENSG00000137834	SMAD6	AOVD2|HsT17432|MADH6|MADH7	SMAD family member 6	protein-coding	0.018519	0.527675	
chunk0024_271_1	chr10	41859848	41860413	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	507915	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.017699	0.413428	
chunk0204_313_1	chr9	100306945	100307775	+	0	NA	intron (NM_017746, intron 13 of 14)	MER58A|DNA|hAT-Charlie	45211	NM_001161584	54881	Hs.494648	NM_017746	ENSG00000136891	TEX10	Ipi1|bA208F1.2	testis expressed 10	protein-coding	0.007229	0.339350	
chunk0095_352_1	chr2	21642789	21643645	+	0	NA	Intergenic	Intergenic	67435	NR_038837	645949	Hs.456782	NR_038837	ENSG00000229621	LINC01822	-	long intergenic non-protein coding RNA 1822	ncRNA	0.008178	0.417736	
chunk0100_443_1	chr2	120746710	120747301	+	0	NA	Intergenic	L1ME4a|LINE|L1	-50286	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.005076	0.329392	
chunk0208_17_1	chrX	10900593	10901010	+	0	NA	Intergenic	Intergenic	-67111	NM_033290	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.004796	0.363636	
chunk0036_350_1	chr11	66877502	66877701	+	0	NA	intron (NM_000920, intron 2 of 21)	L1ME4a|LINE|L1	20196	NM_024036	78999	Hs.209979	NM_024036	ENSG00000173621	LRFN4	FIGLER6|SALM3|SALM3.	leucine rich repeat and fibronectin type III domain containing 4	protein-coding	0.015075	0.395000	
chunk0113_245_1	chr20	54355332	54355867	+	0	NA	Intergenic	L2c|LINE|L2	-119873	NM_018431	55816	Hs.473133	NM_018431	ENSG00000101134	DOK5	C20orf180|IRS-6|IRS6	docking protein 5	protein-coding	0.005607	0.350746	302(TGGTACAAAATGTTCA,-,0.00),303(GGTACAAAATGTTCAG,+,0.00)
chunk0026_303_1	chr10	67956514	67957399	+	0	NA	exon (NM_001278186, exon 15 of 23)	exon (NM_001278186, exon 15 of 23)	53927	NR_131184	100009667		NR_131184		POU5F1P5	Oct4-pg5	POU class 5 homeobox 1 pseudogene 5	pseudo	0.004520	0.314898	254(AAGTACTTTGTGTACC,-,0.00),255(AGTACTTTGTGTACCT,+,0.00)
chunk0142_382_1	chr4	102312056	102312359	+	0	NA	intron (NM_022154, intron 2 of 7)	Tigger20a|DNA|TcMar-Tigger	12105	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.003300	0.361842	
chunk0069_428_1	chr15	68289088	68289337	+	0	NA	intron (NM_015322, intron 1 of 1)	intron (NM_015322, intron 1 of 1)	11409	NM_015322	10116	Hs.362733	NM_015322	ENSG00000169018	FEM1B	F1A-ALPHA|F1AA|FEM1-beta	fem-1 homolog B	protein-coding	0.004016	0.420000	148(AGGAACATGCTGTTCT,-,0.00),149(GGAACATGCTGTTCTC,+,0.00)
chunk0099_180_1	chr2	90309242	90309478	+	0	NA	Intergenic	AluSp|SINE|Alu	1350589	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.012712	0.451477	
chunk0035_328_1	chr11	47570288	47570627	+	0	NA	intron (NM_175732, intron 3 of 3)	intron (NM_175732, intron 3 of 3)	5027	NM_175732	114971	Hs.656205	NM_175732	ENSG00000110536	PTPMT1	DUSP23|MOSP|PLIP|PNAS-129	protein tyrosine phosphatase mitochondrial 1	protein-coding	0.005900	0.417647	
chunk0019_103_1	chr1	224929412	224929909	+	0	NA	promoter-TSS (NM_144989)	promoter-TSS (NM_144989)	-1	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.100604	0.688755	
chunk0031_65_1	chr10	122879492	122879743	+	0	NA	promoter-TSS (NM_001204364)	promoter-TSS (NM_001204364)	-16	NR_027282	399815	Hs.113871	NR_027282		LOC399815	-	chromosome 10 open reading frame 88 pseudogene	pseudo	0.091633	0.623016	
chunk0027_75_1	chr10	73291738	73292241	+	0	NA	exon (NM_145170, exon 18 of 28)	exon (NM_145170, exon 18 of 28)	-39296	NM_016065	51021	Hs.180312	NM_016065	ENSG00000182180	MRPS16	CGI-132|COXPD2|MRP-S16|RPMS16	mitochondrial ribosomal protein S16	protein-coding	0.007952	0.400794	
chunk0019_466_1	chr1	231545193	231545392	+	0	NA	intron (NR_028400, intron 4 of 7)	intron (NR_028400, intron 4 of 7)	16639	NR_028398	100303453	Hs.13318	NR_028393	ENSG00000270106	TSNAX-DISC1	-	TSNAX-DISC1 readthrough (NMD candidate)	ncRNA	0.005025	0.355000	
chunk0118_339_1	chr22	35622499	35623642	+	0	NA	intron (NM_203377, intron 1 of 3)	intron (NM_203377, intron 1 of 3)	284	NM_203377	4151	Hs.517586	NM_005368	ENSG00000198125	MB	PVALB|myoglobgin	myoglobin	protein-coding	0.012248	0.550699	
chunk0082_230_1	chr17	57286557	57286985	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	29758	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.030374	0.508159	
chunk0108_388_1	chr2	237048119	237048645	+	0	NA	Intergenic	Intergenic	-37059	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.003802	0.375712	
chunk0031_445_1	chr10	132596127	132596371	+	0	NA	intron (NM_005539, intron 1 of 15)	intron (NM_005539, intron 1 of 15)	58400	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.028689	0.510204	
chunk0009_335_1	chr1	109148599	109148836	+	0	NA	intron (NM_001284352, intron 1 of 20)	intron (NM_001284352, intron 1 of 20)	34754	NM_001284352	57535	Hs.708190	NM_020775	ENSG00000116299	KIAA1324	EIG121	KIAA1324	protein-coding	0.004219	0.403361	
chunk0047_371_1	chr12	75145239	75145514	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	64372	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.000000	0.300725	
chunk0072_395_1	chr15	100633580	100634165	+	0	NA	intron (NM_198243, intron 5 of 5)	intron (NM_198243, intron 5 of 5)	31322	NM_198243	140460	Hs.31845	NM_024708	ENSG00000183475	ASB7	-	ankyrin repeat and SOCS box containing 7	protein-coding	0.001709	0.443686	
chunk0122_433_1	chr3	39208538	39208828	+	0	NA	Intergenic	MER34A1|LTR|ERV1	-16087	NM_001198621	165904	Hs.447868	NM_194293	ENSG00000168334	XIRP1	CMYA1|Xin	xin actin binding repeat containing 1	protein-coding	0.017241	0.436426	
chunk0185_459_1	chr7	135425525	135425775	+	0	NA	intron (NM_001008225, intron 2 of 10)	intron (NM_001008225, intron 2 of 10)	84477	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.004000	0.294821	
chunk0113_80_1	chr20	50691675	50692036	+	0	NA	promoter-TSS (NR_110890)	promoter-TSS (NR_110890)	-325	NR_110890	140876	Hs.372578	NM_080829	ENSG00000042062	RIPOR3	C20orf175|C20orf176|FAM65C	RIPOR family member 3	protein-coding	0.022161	0.555249	
chunk0181_85_1	chr7	80334861	80335426	+	0	NA	Intergenic	Intergenic	39296	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.001770	0.358657	
chunk0185_204_1	chr7	128458885	128459178	+	0	NA	TTS (NM_013332)	TTS (NM_013332)	3201	NM_013332	29923	Hs.706124	NM_013332	ENSG00000135245	HILPDA	C7orf68|HIG-2|HIG2	hypoxia inducible lipid droplet associated	protein-coding	0.010239	0.397959	179(AAGTACAGTGTCTTCT,-,0.00)
chunk0078_35_1	chr17	924737	925347	+	0	NA	intron (NM_022463, intron 1 of 7)	intron (NM_022463, intron 1 of 7)	54716	NM_022463	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.013115	0.513912	
chunk0055_142_1	chr13	59749707	59750382	+	0	NA	intron (NM_001258366, intron 26 of 26)	intron (NM_001258366, intron 26 of 26)	-262674	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.001481	0.321006	
chunk0091_336_1	chr19	14138645	14139048	+	0	NA	intron (NR_045214, intron 1 of 2)	intron (NR_045214, intron 1 of 2)	1694	NR_045214	100507373	Hs.720437	NR_045214	ENSG00000267169	LOC100507373	-	uncharacterized LOC100507373	ncRNA	0.009926	0.492574	
chunk0117_191_1	chr22	21607655	21608304	+	0	NA	intron (NR_046082, intron 2 of 3)	intron (NR_046082, intron 2 of 3)	22072	NM_001017964	150223	Hs.355952	NM_001017964	ENSG00000161179	YDJC	-	YdjC chitooligosaccharide deacetylase homolog	protein-coding	0.007704	0.455385	
chunk0126_265_1	chr3	79872429	79872864	+	0	NA	Intergenic	Intergenic	-104737	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002299	0.323394	
chunk0130_334_1	chr3	138282636	138283484	+	0	NA	intron (NM_001267042, intron 17 of 20)	intron (NM_001267042, intron 17 of 20)	46826	NM_178130	347736	Hs.660992	NM_178130	ENSG00000181322	NME9	NM23-H9|TXL-2|TXL2|TXNDC6	NME/NM23 family member 9	protein-coding	0.004717	0.399293	
chunk0136_138_1	chr4	3955426	3955865	+	0	NA	promoter-TSS (NR_130742)	promoter-TSS (NR_130742)	-217	NR_130740	348926	Hs.591720	NR_024253	ENSG00000251669	FAM86EP	-	family with sequence similarity 86, member A pseudogene	pseudo	0.066059	0.690909	252(CGGGACAGGGTGATCC,-,0.00),253(GGGACAGGGTGATCCT,+,0.00)
chunk0160_395_1	chr5	163440779	163441408	+	0	NA	exon (NM_004060, exon 3 of 7)	exon (NM_004060, exon 3 of 7)	3522	NM_004060	900	Hs.79101	NM_004060	ENSG00000113328	CCNG1	CCNG	cyclin G1	protein-coding	0.004769	0.358730	
chunk0092_39_1	chr19	19361159	19361492	+	0	NA	Intergenic	Intergenic	-24508	NM_017660	54815	Hs.118964	NM_017660	ENSG00000167491	GATAD2A	p66alpha	GATA zinc finger domain containing 2A	protein-coding	0.030030	0.508982	
chunk0090_99_1	chr18	70801046	70801513	+	0	NA	Intergenic	Intergenic	-150422	NM_001278515									0.014989	0.433761	
chunk0126_347_1	chr3	82707641	82708107	+	0	NA	Intergenic	L1M2|LINE|L1	-946075	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.012876	0.402570	
chunk0050_409_1	chr12	109682044	109682929	+	0	NA	Intergenic	L1MC3|LINE|L1	-31896	NM_032829	84915	Hs.661785	NM_032829	ENSG00000139438	FAM222A	C12orf34	family with sequence similarity 222 member A	protein-coding	0.006780	0.409707	
chunk0050_254_1	chr12	105761075	105761564	+	0	NA	Intergenic	Intergenic	54545	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.002045	0.361224	121(AGGGACAGTATGCACC,-,0.00)
chunk0048_32_1	chr12	77752016	77752273	+	0	NA	Intergenic	Intergenic	-79145	NM_014903	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.007782	0.364341	
chunk0083_154_1	chr17	65907569	65907997	+	0	NA	intron (NM_001302891, intron 17 of 24)	intron (NM_001302891, intron 17 of 24)	-81240	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.009346	0.398601	
chunk0149_381_1	chr5	28522971	28523322	+	0	NA	Intergenic	MER6|DNA|TcMar-Tigger	-403724	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.005698	0.303977	
chunk0011_104_1	chr1	145986952	145987316	+	0	NA	Intergenic	MIR|SINE|MIR	8588	NM_001313972	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.002747	0.284932	
chunk0037_224_1	chr11	74940083	74940907	+	0	NA	intron (NM_001270381, intron 1 of 15)	intron (NM_001270381, intron 1 of 15)	8692	NM_001270381	143570	Hs.370145	NM_182969	ENSG00000166435	XRRA1	-	X-ray radiation resistance associated 1	protein-coding	0.008495	0.444848	
chunk0103_199_1	chr2	163670726	163671287	+	0	NA	intron (NM_018086, intron 2 of 2)	intron (NM_018086, intron 2 of 2)	64997	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.007130	0.352313	
chunk0139_261_1	chr4	56571782	56572501	+	0	NA	intron (NM_001256475, intron 4 of 8)	Tigger3b|DNA|TcMar-Tigger	41532	NM_001256475	100506564	Hs.573073	NM_001256475	ENSG00000249693	THEGL	-	theg spermatid protein like	protein-coding	0.005563	0.376389	
chunk0212_371_1	chrX	149999032	149999627	+	0	NA	intron (NR_027456, intron 9 of 11)	intron (NR_027456, intron 9 of 11)	60781	NR_027456	100272228	Hs.496916	NR_027456	ENSG00000235703	LINC00894	-	long intergenic non-protein coding RNA 894	ncRNA	0.005042	0.401007	
chunk0066_109_1	chr15	29887857	29888072	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1ME4c|LINE|L1	-65461	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.004651	0.342593	
chunk0158_92_1	chr5	126607679	126608021	+	0	NA	intron (NM_032177, intron 2 of 4)	MIRb|SINE|MIR	6935	NM_032177	51808	Hs.555731	NM_032177	ENSG00000164902	PHAX	RNUXA	phosphorylated adaptor for RNA export	protein-coding	0.005848	0.390671	
chunk0043_358_1	chr12	23197199	23197584	+	0	NA	Intergenic	Intergenic	21755	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.007792	0.388601	
chunk0142_254_1	chr4	98999627	99000183	+	0	NA	intron (NM_015143, intron 1 of 10)	intron (NM_015143, intron 1 of 10)	2518	NR_037455	100500867		NR_037455	ENSG00000265213	MIR3684	-	microRNA 3684	ncRNA	0.012590	0.387792	
chunk0146_297_1	chr4	164880950	164881346	+	0	NA	intron (NM_001297550, intron 2 of 2)	intron (NM_001297550, intron 2 of 2)	4160	NM_001297550	100506013	Hs.105196	NM_001297550	ENSG00000248329	APELA	ELA|Ende|tdl	apelin receptor early endogenous ligand	protein-coding	0.002525	0.337531	
chunk0196_69_1	chr8	102417193	102417437	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-4626	NM_001282873	51366	Hs.492445	NM_015902	ENSG00000104517	UBR5	DD5|EDD|EDD1|HYD	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.004098	0.453061	
chunk0093_331_1	chr19	54366285	54366574	+	0	NA	intron (NM_001289026, intron 1 of 9)	MST-int|LTR|ERVL-MaLR	-1315	NM_002287	3903	Hs.572535	NM_002287	ENSG00000167613	LAIR1	CD305|LAIR-1	leukocyte associated immunoglobulin like receptor 1	protein-coding	0.034602	0.479310	
chunk0200_302_1	chr9	22954855	22955521	+	0	NA	Intergenic	L1M4|LINE|L1	308988	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.010511	0.335832	324(TGTACTGGATGTTCTA,+,0.00)
chunk0106_336_1	chr2	206213010	206213705	+	0	NA	5' UTR (NM_005279, exon 2 of 3)	5' UTR (NM_005279, exon 2 of 3)	271	NM_001261454	2825	Hs.184907	NM_005279	ENSG00000183671	GPR1	-	G protein-coupled receptor 1	protein-coding	0.011511	0.425287	528(ATGAACATACTGTACA,-,0.00),529(TGAACATACTGTACAA,+,0.00)
chunk0175_159_1	chr7	4006531	4007214	+	0	NA	intron (NM_152744, intron 14 of 44)	intron (NM_152744, intron 14 of 44)	-122813	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.019034	0.473684	
chunk0069_282_1	chr15	65087455	65087697	+	0	NA	Intergenic	Intergenic	10760	NM_001101362	390594	Hs.586890	NM_001101362	ENSG00000234438	KBTBD13	HCG1645727|NEM6	kelch repeat and BTB domain containing 13	protein-coding	0.004132	0.543210	
chunk0051_323_1	chr12	120055230	120055638	+	0	NA	intron (NM_207311, intron 2 of 8)	intron (NM_207311, intron 2 of 8)	61405	NM_001167606	11021	Hs.524788	NM_006861	ENSG00000111737	RAB35	H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding	0.002451	0.330073	263(AGGAACACACTGTTAC,-,0.00),264(GGAACACACTGTTACT,+,0.00)
chunk0029_266_1	chr10	103153771	103153982	+	0	NA	intron (NM_001134373, intron 2 of 17)	intron (NM_001134373, intron 2 of 17)	39430	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.014218	0.301887	
chunk0129_73_1	chr3	117799187	117799788	+	0	NA	Intergenic	Intergenic	878056	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.006656	0.405316	304(CAGAACATTCAGTACT,-,0.00),305(AGAACATTCAGTACTT,+,0.00)
chunk0060_224_1	chr14	49429549	49429871	+	0	NA	Intergenic	L1PA15|LINE|L1	156706	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.003106	0.554180	
chunk0043_424_1	chr12	25928769	25929582	+	0	NA	Intergenic	Intergenic	28410	NR_038227	100506451	Hs.560092	NR_038227		RASSF8-AS1	-	RASSF8 antisense RNA 1	ncRNA	0.002460	0.383292	
chunk0029_277_1	chr10	103524099	103524328	+	0	NA	intron (NM_004210, intron 1 of 5)	L1MA5|LINE|L1	-6771	NR_120675	102724341	Hs.599425	NR_120675	ENSG00000235470	NEURL1-AS1	-	NEURL1 antisense RNA 1	ncRNA	0.000000	0.317391	
chunk0191_390_1	chr8	57209658	57210469	+	0	NA	Intergenic	MER50-int|LTR|ERV1	-8213	NR_038235	100507651	Hs.371831	NR_038235	ENSG00000253301	LINC01606	-	long intergenic non-protein coding RNA 1606	ncRNA	0.028360	0.571429	385(CGGTACAGACTGCCCC,-,0.00),386(GGTACAGACTGCCCCA,+,0.00)
chunk0095_284_1	chr2	20122138	20122416	+	0	NA	Intergenic	L2a|LINE|L2	-70249	NM_014713	9741	Hs.467807	NM_014713	ENSG00000068697	LAPTM4A	HUMORF13|LAPTM4|MBNT|Mtrp	lysosomal protein transmembrane 4 alpha	protein-coding	0.010791	0.473118	
chunk0129_12_1	chr3	116501753	116501952	+	0	NA	Intergenic	L1PA14|LINE|L1	-56314	NM_002338	4045	Hs.26409	NM_002338	ENSG00000185565	LSAMP	IGLON3|LAMP	limbic system associated membrane protein	protein-coding	0.010050	0.325000	
chunk0054_386_1	chr13	50313380	50313893	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	141618	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.003899	0.383268	
chunk0204_87_1	chr9	94087384	94087874	+	0	NA	intron (NM_177995, intron 3 of 9)	L1MC5a|LINE|L1	3200	NM_001253829	138639	Hs.437943	NM_152422	ENSG00000158079	PTPDC1	PTP9Q22	protein tyrosine phosphatase domain containing 1	protein-coding	0.004082	0.329939	
chunk0211_233_1	chrX	118928307	118928640	+	0	NA	Intergenic	LTR75|LTR|ERVL	-46141	NM_024778	79836	Hs.144266	NM_024778	ENSG00000175556	LONRF3	RNF127	LON peptidase N-terminal domain and ring finger 3	protein-coding	0.006006	0.446108	
chunk0127_287_1	chr3	97911034	97912077	+	0	NA	intron (NM_153605, intron 15 of 21)	intron (NM_153605, intron 15 of 21)	60896	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.005753	0.396552	
chunk0073_454_1	chr16	19484033	19484503	+	0	NA	intron (NM_001308161, intron 14 of 20)	intron (NM_001308161, intron 14 of 20)	27818	NM_024780	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.012766	0.392781	
chunk0073_209_1	chr16	10088224	10088583	+	0	NA	intron (NM_001134407, intron 2 of 12)	intron (NM_001134407, intron 2 of 12)	93664	NM_001134408	2903	Hs.411472	NM_000833	ENSG00000183454	GRIN2A	EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A	glutamate ionotropic receptor NMDA type subunit 2A	protein-coding	0.019499	0.519444	338(GGGAACATGCAGTTCT,-,0.00),339(GGAACATGCAGTTCTT,+,0.00)
chunk0138_186_1	chr4	37981923	37982288	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	21670	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.010959	0.428962	
chunk0045_112_1	chr12	46233420	46233976	+	0	NA	intron (NM_001077484, intron 3 of 16)	intron (NM_001077484, intron 3 of 16)	32797	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.003597	0.405745	
chunk0163_300_1	chr6	14390924	14391330	+	0	NA	Intergenic	Intergenic	-105673	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.009852	0.373464	
chunk0172_224_1	chr6	137037489	137037961	+	0	NA	intron (NM_014432, intron 1 of 6)	intron (NM_014432, intron 1 of 6)	6587	NM_001278722	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.002119	0.410148	342(CTGAACAGCTTGTCCA,-,0.00),343(TGAACAGCTTGTCCAG,+,0.00)
chunk0073_328_1	chr16	14442069	14442322	+	0	NA	intron (NM_002582, intron 23 of 23)	intron (NM_002582, intron 23 of 23)	-71929	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.003953	0.492126	
chunk0165_238_1	chr6	35601709	35602385	+	0	NA	intron (NM_001145777, intron 5 of 6)	intron (NM_001145777, intron 5 of 6)	62742	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.008876	0.398818	372(CAGAACACCCTGTTCT,-,0.00),373(AGAACACCCTGTTCTG,+,0.00),403(ATGAACTCGATGTGCT,-,0.00),404(TGAACTCGATGTGCTG,+,0.00)
chunk0181_23_1	chr7	77799565	77799817	+	0	NA	intron (NM_001127358, intron 1 of 17)	intron (NM_001127358, intron 1 of 17)	899	NM_001127358	57157	Hs.203965	NM_020432	ENSG00000006576	PHTF2	-	putative homeodomain transcription factor 2	protein-coding	0.019841	0.430830	
chunk0101_248_1	chr2	132286947	132287168	+	0	NA	Intergenic	ACRO1|Satellite|acro	-20087	NM_001304449	646915		NM_001304449		ZNF806	-	zinc finger protein 806	protein-coding	0.031674	0.585586	
chunk0015_72_1	chr1	184761624	184762079	+	0	NA	Intergenic	Intergenic	-6944	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.004396	0.350877	276(GTGCACAAAATGTACT,-,0.00)
chunk0111_371_1	chr20	33811341	33811632	+	0	NA	promoter-TSS (NR_110623)	promoter-TSS (NR_110623)	182	NM_176812	128866	Hs.472471	NM_176812	ENSG00000101421	CHMP4B	C20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4	charged multivesicular body protein 4B	protein-coding	0.116838	0.708904	
chunk0143_130_1	chr4	109631101	109631330	+	0	NA	intron (NM_017918, intron 1 of 7)	intron (NM_017918, intron 1 of 7)	71016	NM_017918	55013	Hs.234149	NM_017918	ENSG00000005059	MCUB	CCDC109B	mitochondrial calcium uniporter dominant negative beta subunit	protein-coding	0.008734	0.365217	
chunk0097_388_1	chr2	61955160	61955749	+	0	NA	intron (NM_152516, intron 1 of 2)	L1ME1|LINE|L1	49786	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.010187	0.401695	
chunk0154_423_1	chr5	89127512	89128034	+	0	NA	Intergenic	Intergenic	-223668	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.005747	0.338432	242(CTGGACAGGCTGTGTT,-,0.00),243(TGGACAGGCTGTGTTG,+,0.00)
chunk0023_175_1	chr10	24469872	24470268	+	0	NA	intron (NM_001282770, intron 1 of 11)	intron (NM_001282770, intron 1 of 11)	3565	NM_001282770	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.015152	0.415617	
chunk0050_382_1	chr12	108737831	108738480	+	0	NA	Intergenic	L1MD1|LINE|L1	-6605	NM_014325	23603	Hs.330384	NM_014325	ENSG00000110880	CORO1C	HCRNN4	coronin 1C	protein-coding	0.006163	0.400000	
chunk0193_50_1	chr8	71996771	71997373	+	0	NA	intron (NR_033652, intron 4 of 4)	intron (NR_033652, intron 4 of 4)	78512	NM_007332	8989	Hs.716816	NM_007332	ENSG00000104321	TRPA1	ANKTM1|FEPS|FEPS1	transient receptor potential cation channel subfamily A member 1	protein-coding	0.003322	0.368159	
chunk0041_191_1	chr11	126437176	126437407	+	0	NA	intron (NM_032531, intron 11 of 16)	(CA)n|Simple_repeat|Simple_repeat	31109	NM_001254759	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.021645	0.500000	
chunk0059_324_1	chr14	36683072	36683853	+	0	NA	intron (NM_030631, intron 9 of 9)	intron (NM_030631, intron 9 of 9)	25894	NM_006194	5083	Hs.132576	NM_006194	ENSG00000198807	PAX9	STHAG3	paired box 9	protein-coding	0.012804	0.425831	
chunk0112_233_1	chr20	41134684	41135330	+	0	NA	intron (NR_109889, intron 3 of 6)	intron (NR_109889, intron 3 of 6)	-2514	NM_002660	5335	Hs.268177	NM_002660	ENSG00000124181	PLCG1	NCKAP3|PLC-II|PLC1|PLC148|PLCgamma1	phospholipase C gamma 1	protein-coding	0.010836	0.477589	
chunk0189_100_1	chr8	21864368	21864848	+	0	NA	Intergenic	Intergenic	49086	NM_003974	9046	Hs.71215	NM_003974	ENSG00000147443	DOK2	p56DOK|p56dok-2	docking protein 2	protein-coding	0.002083	0.474012	169(AGGCACACAAAGTTCC,-,0.00),170(GGCACACAAAGTTCCA,+,0.00)
chunk0048_115_1	chr12	79659246	79659683	+	0	NA	intron (NM_002583, intron 2 of 6)	intron (NM_002583, intron 2 of 6)	31546	NM_002583	5074	Hs.643130	NM_002583	ENSG00000177425	PAWR	PAR4|Par-4	pro-apoptotic WT1 regulator	protein-coding	0.009153	0.356164	
chunk0054_20_1	chr13	40644971	40645462	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	21381	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.006110	0.406504	
chunk0056_296_1	chr13	90555379	90555867	+	0	NA	Intergenic	Intergenic	62335	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.006148	0.347648	
chunk0019_116_1	chr1	225307226	225307857	+	0	NA	exon (NM_001373, exon 57 of 84)	exon (NM_001373, exon 57 of 84)	120572	NM_002296	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.001585	0.316456	
chunk0105_26_1	chr2	182078876	182079396	+	0	NA	intron (NM_001080545, intron 4 of 4)	intron (NM_001080545, intron 4 of 4)	93312	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.005769	0.320537	
chunk0107_355_1	chr2	222452360	222452914	+	0	NA	intron (NM_152386, intron 1 of 4)	intron (NM_152386, intron 1 of 4)	28034	NM_152386	130367	Hs.210043	NM_152386	ENSG00000163082	SGPP2	SPP2|SPPase2	sphingosine-1-phosphate phosphatase 2	protein-coding	0.005415	0.470270	271(CAGGTCTGAGTGTTCC,-,0.00),301(CAGGACTGGATGTTCA,-,0.00),302(AGGACTGGATGTTCAG,+,0.00)
chunk0002_163_1	chr1	18417244	18417731	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-63443	NM_152375	127707	Hs.406913	NM_152375	ENSG00000179023	KLHDC7A	-	kelch domain containing 7A	protein-coding	0.004107	0.401639	
chunk0161_59_1	chr5	166353324	166353568	+	0	NA	Intergenic	(CTTCCT)n|Simple_repeat|Simple_repeat	572924	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.012295	0.330612	75(AAGTACAGTCTGAACC,-,0.00),76(AGTACAGTCTGAACCT,+,0.00)
chunk0136_311_1	chr3	195210140	195210348	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	37676	NM_001308069	152002	Hs.478741	NM_152531	ENSG00000173950	XXYLT1	C3orf21	xyloside xylosyltransferase 1	protein-coding	0.024038	0.588517	
chunk0002_406_1	chr1	27436571	27437048	+	0	NA	intron (NM_001201404, intron 1 of 7)	intron (NM_001201404, intron 1 of 7)	44165	NM_005281	2827	Hs.66542	NM_005281	ENSG00000181773	GPR3	ACCA	G protein-coupled receptor 3	protein-coding	0.002096	0.378661	
chunk0182_296_1	chr7	98384209	98384693	+	0	NA	intron (NM_018842, intron 1 of 13)	intron (NM_018842, intron 1 of 13)	16664	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.010331	0.364948	
chunk0206_39_1	chr9	116666686	116666998	+	0	NA	intron (NM_014010, intron 15 of 21)	L1MC5a|LINE|L1	20373	NM_198186	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.000000	0.300319	
chunk0170_281_1	chr6	114272633	114273112	+	0	NA	intron (NR_125845, intron 9 of 9)	L2a|LINE|L2	-209995	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.008351	0.456250	
chunk0046_339_1	chr12	62900770	62901166	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	33917	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.010101	0.445844	
chunk0015_13_1	chr1	184196987	184197544	+	0	NA	Intergenic	Intergenic	145614	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.000000	0.415771	
chunk0170_421_1	chr6	118362756	118363295	+	0	NA	Intergenic	L1M5|LINE|L1	-138348	NR_002730	23629	Hs.648050	NR_002730		BRD7P3	BP75	bromodomain containing 7 pseudogene 3	pseudo	0.001855	0.270370	
chunk0065_101_1	chr15	23998274	23998758	+	0	NA	intron (NR_126392, intron 3 of 5)	MER84-int|LTR|ERV1	23369	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.006198	0.412371	
chunk0050_440_1	chr12	110345190	110345543	+	0	NA	exon (NM_001681, exon 18 of 21)	exon (NM_001681, exon 18 of 21)	58364	NM_016238	51434	Hs.719935	NM_016238	ENSG00000196510	ANAPC7	APC7	anaphase promoting complex subunit 7	protein-coding	0.028329	0.480226	
chunk0152_410_1	chr5	65241876	65242075	+	0	NA	intron (NM_197941, intron 15 of 24)	intron (NM_197941, intron 15 of 24)	239902	NM_197941	11174	Hs.482291	NM_197941	ENSG00000049192	ADAMTS6	ADAM-TS 6|ADAM-TS6|ADAMTS-6	ADAM metallopeptidase with thrombospondin type 1 motif 6	protein-coding	0.000000	0.295000	
chunk0125_257_1	chr3	69166498	69167013	+	0	NA	Intergenic	Intergenic	-44160	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.001942	0.403101	
chunk0048_413_1	chr12	88247282	88247496	+	0	NA	Intergenic	Intergenic	105093	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.004673	0.400000	
chunk0006_233_1	chr1	68717814	68718650	+	0	NA	Intergenic	Intergenic	-221011	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.009569	0.338112	
chunk0055_148_1	chr13	59914671	59914908	+	0	NA	intron (NM_001258369, intron 19 of 26)	MLT1D|LTR|ERVL-MaLR	-97929	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004219	0.361345	
chunk0022_68_1	chr10	8602548	8602892	+	0	NA	Intergenic	Intergenic	-295269	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.005814	0.373913	
chunk0176_151_1	chr7	13098016	13098641	+	0	NA	Intergenic	Intergenic	411042	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.008000	0.329073	
chunk0041_44_1	chr11	122571445	122571924	+	0	NA	Intergenic	L2c|LINE|L2	-84006	NM_032873	84959	Hs.444075	NM_032873	ENSG00000154127	UBASH3B	STS-1|STS1|TULA-2|TULA2|p70	ubiquitin associated and SH3 domain containing B	protein-coding	0.006263	0.445833	270(GAGGACACTTTGTTCC,-,0.00),271(AGGACACTTTGTTCCA,+,0.00)
chunk0086_410_1	chr18	26772706	26773004	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	-69217	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.006711	0.397993	
chunk0204_365_1	chr9	101813798	101814579	+	0	NA	Intergenic	Intergenic	-75608	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.002561	0.349105	
chunk0116_406_1	chr21	42531597	42532137	+	0	NA	intron (NM_018964, intron 4 of 20)	intron (NM_018964, intron 4 of 20)	32235	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.020370	0.504621	223(CAGAACTCTTTGTGCT,-,0.00),224(AGAACTCTTTGTGCTG,+,0.00)
chunk0114_49_1	chr21	8452035	8452280	+	0	NA	Intergenic	AluSz|SINE|Alu	11011	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.102041	0.613821	
chunk0130_278_1	chr3	136353613	136354048	+	0	NA	intron (NM_005862, intron 28 of 33)	L1M4b|LINE|L1	103505	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.002299	0.350917	
chunk0108_382_1	chr2	236997709	236998899	+	0	NA	Intergenic	Intergenic	-87137	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.007563	0.369437	
chunk0116_163_1	chr21	36612978	36613574	+	0	NA	Intergenic	Intergenic	-36707	NM_001146077	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.023490	0.520938	227(AGGATCATGCTGTGCA,-,0.00)
chunk0210_432_1	chrX	103373753	103374157	+	0	NA	Intergenic	Intergenic	-2368	NM_001282674	27018	Hs.448588	NM_014380	ENSG00000166681	BEX3	Bex|DXS6984E|HGR74|NADE|NGFRAP1	brain expressed X-linked 3	protein-coding	0.002475	0.350617	
chunk0029_84_1	chr10	96902738	96903400	+	0	NA	intron (NM_032440, intron 2 of 7)	Tigger3c|DNA|TcMar-Tigger	70114	NM_032440	84458	Hs.427927	NM_015652	ENSG00000196233	LCOR	C10orf12|MLR2	ligand dependent nuclear receptor corepressor	protein-coding	0.009063	0.375566	
chunk0085_314_1	chr18	8298934	8299464	+	0	NA	intron (NM_001105244, intron 20 of 32)	intron (NM_001105244, intron 20 of 32)	67835	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.016981	0.467043	
chunk0204_247_1	chr9	98072662	98073201	+	0	NA	intron (NM_018946, intron 2 of 5)	intron (NM_018946, intron 2 of 5)	16254	NM_018946	54187	Hs.522310	NM_018946	ENSG00000095380	NANS	HEL-S-100|SAS|SEMDCG|SEMDG	N-acetylneuraminate synthase	protein-coding	0.014842	0.490741	
chunk0051_16_1	chr12	111653962	111654221	+	0	NA	intron (NM_006768, intron 10 of 11)	intron (NM_006768, intron 10 of 11)	31905	NM_006768	8315	Hs.530940	NM_006768	ENSG00000089234	BRAP	BRAP2|IMP|RNF52	BRCA1 associated protein	protein-coding	0.023166	0.519231	
chunk0146_121_1	chr4	159013521	159014242	+	0	NA	intron (NM_152543, intron 1 of 4)	L1MB3|LINE|L1	21300	NM_152543	152940	Hs.415576	NM_152543	ENSG00000164123	C4orf45	-	chromosome 4 open reading frame 45	protein-coding	0.006935	0.415512	
chunk0062_421_1	chr14	75200483	75201023	+	0	NA	Intergenic	L2a|LINE|L2	-24107	NM_006827	10972	Hs.74137	NM_006827	ENSG00000170348	TMED10	P24(DELTA)|S31I125|S31III125|TMP21|Tmp-21-I|p23|p24d1	transmembrane p24 trafficking protein 10	protein-coding	0.005556	0.469501	51(TGCACTTGCTGTGCCC,+,0.00)
chunk0177_189_1	chr7	23668257	23668725	+	0	NA	Intergenic	Intergenic	-11623	NM_001127365	340277	Hs.592178	NM_199136	ENSG00000188732	FAM221A	C7orf46	family with sequence similarity 221 member A	protein-coding	0.006410	0.341151	
chunk0034_81_1	chr11	27340975	27341548	+	0	NA	intron (NM_030771, intron 4 of 5)	intron (NM_030771, intron 4 of 5)	21987	NM_030771	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.001745	0.292683	
chunk0140_451_1	chr4	76412811	76413010	+	0	NA	Intergenic	Intergenic	-5605	NM_001042784	339965	Hs.529680	NM_178555	ENSG00000163749	CCDC158	-	coiled-coil domain containing 158	protein-coding	0.000000	0.365000	
chunk0136_132_1	chr4	3858050	3858419	+	0	NA	Intergenic	Intergenic	91665	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.002710	0.562162	
chunk0097_409_1	chr2	62527564	62528088	+	0	NA	Intergenic	Intergenic	-21357	NM_198276	200728	Hs.308028	NM_198276	ENSG00000186889	TMEM17	-	transmembrane protein 17	protein-coding	0.003817	0.354286	
chunk0038_325_1	chr11	92026100	92026430	+	0	NA	Intergenic	L1MC3|LINE|L1	-325831	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.009091	0.308157	
chunk0154_125_1	chr5	78923291	78923543	+	0	NA	intron (NM_198709, intron 5 of 7)	LTR16E2|LTR|ERVL	62526	NM_198709	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.011905	0.521739	
chunk0097_254_1	chr2	54143000	54143531	+	0	NA	intron (NM_138448, intron 3 of 3)	L1ME3G|LINE|L1	27992	NM_138448	98	Hs.516173	NM_138448	ENSG00000170634	ACYP2	ACYM|ACYP	acylphosphatase 2	protein-coding	0.007533	0.308271	
chunk0127_24_1	chr3	88364903	88365262	+	0	NA	Intergenic	MIR|SINE|MIR	-215216	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.005571	0.358333	
chunk0045_468_1	chr12	53900339	53901082	+	0	NA	Intergenic	Intergenic	-38082	NM_017410	3229	Hs.118608	NM_017410	ENSG00000123364	HOXC13	ECTD9|HOX3|HOX3G	homeobox C13	protein-coding	0.005384	0.385753	
chunk0071_257_1	chr15	85486032	85486238	+	0	NA	intron (NM_007200, intron 2 of 36)	intron (NM_007200, intron 2 of 36)	105519	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.000000	0.425121	
chunk0093_112_1	chr19	44340482	44340739	+	0	NA	intron (NM_013380, intron 1 of 3)	intron (NM_013380, intron 1 of 3)	16094	NM_001083335	7771	Hs.48589	NM_013380	ENSG00000062370	ZNF112	ZFP112|ZNF228	zinc finger protein 112	protein-coding	0.000000	0.445736	
chunk0184_61_1	chr7	112422811	112423475	+	0	NA	promoter-TSS (NM_001197080)	promoter-TSS (NM_001197080)	-1	NM_001197080	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.009036	0.464662	
chunk0174_66_1	chr6	155942203	155942929	+	0	NA	Intergenic	Intergenic	-4231	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.008264	0.325997	
chunk0204_42_1	chr9	92754186	92754591	+	0	NA	intron (NM_001003800, intron 1 of 6)	Tigger9b|DNA|TcMar-Tigger	10413	NM_001003800	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.014815	0.435961	
chunk0096_242_1	chr2	31091020	31091646	+	0	NA	intron (NR_045602, intron 1 of 15)	MER58B|DNA|hAT-Charlie	38307	NM_001253827	79623	Hs.468058	NM_024572	ENSG00000158089	GALNT14	GALNT15|GalNac-T10|GalNac-T14	polypeptide N-acetylgalactosaminyltransferase 14	protein-coding	0.001597	0.384370	
chunk0141_17_1	chr4	76703888	76704727	+	0	NA	intron (NM_020859, intron 2 of 10)	L2a|LINE|L2	128756	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.005959	0.439286	650(GAGAACAGCATGTGCA,-,0.00),651(AGAACAGCATGTGCAA,+,0.00)
chunk0104_57_1	chr2	171428574	171429167	+	0	NA	intron (NM_024770, intron 1 of 9)	L2c|LINE|L2	-5381	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.000000	0.382155	
chunk0092_104_1	chr19	23377525	23378015	+	0	NA	intron (NM_001300951, intron 1 of 2)	intron (NM_001300951, intron 1 of 2)	17790	NM_003430	7644	Hs.58834	NM_003430	ENSG00000167232	ZNF91	HPF7|HTF10	zinc finger protein 91	protein-coding	0.000000	0.342159	
chunk0105_385_1	chr2	192407216	192408461	+	0	NA	Intergenic	Intergenic	-212905	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.004819	0.340289	1028(AAGAACAGTTTGTCTT,-,0.00),1029(AGAACAGTTTGTCTTT,+,0.00)
chunk0179_449_1	chr7	52746792	52747148	+	0	NA	Intergenic	Intergenic	-288686	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008427	0.338936	
chunk0144_34_1	chr4	125095905	125096438	+	0	NA	Intergenic	Intergenic	-220241	NM_024582	79633	Hs.563205	NM_024582	ENSG00000196159	FAT4	CDHF14|CDHR11|FAT-J|FATJ|HKLLS2|NBLA00548|VMLDS2	FAT atypical cadherin 4	protein-coding	0.009381	0.355805	
chunk0087_218_1	chr18	36096936	36097599	+	0	NA	Intergenic	L1ME1|LINE|L1	-29673	NM_018170	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.001508	0.347892	
chunk0127_427_1	chr3	102691118	102691534	+	0	NA	Intergenic	Intergenic	256311	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.002404	0.311751	
chunk0193_129_1	chr8	74354760	74355087	+	0	NA	intron (NM_018972, intron 2 of 5)	intron (NM_018972, intron 2 of 5)	4540	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.015291	0.384146	
chunk0150_170_1	chr5	34125912	34126192	+	0	NA	Intergenic	Intergenic	-1524	NR_037951	100534612	Hs.171929	NR_037951	ENSG00000273294	C1QTNF3-AMACR	-	C1QTNF3-AMACR readthrough (NMD candidate)	ncRNA	0.003571	0.306050	
chunk0121_364_1	chr3	24846349	24846794	+	0	NA	Intergenic	Intergenic	-325136	NR_039955									0.002247	0.434978	
chunk0187_302_1	chr7	156237639	156237941	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	207798	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.006623	0.501650	149(GTGCACAGTGTGTGCA,-,0.00),150(TGCACAGTGTGTGCAC,+,0.00),197(GTGCACGGTCTGTGCT,-,0.00)
chunk0162_89_1	chr6	2118108	2118472	+	0	NA	intron (NM_001253846, intron 2 of 10)	UCON8|DNA|DNA	57701	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.005495	0.402740	
chunk0077_268_1	chr16	80991695	80992315	+	0	NA	intron (NM_020188, intron 2 of 3)	intron (NM_020188, intron 2 of 3)	-14493	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.009677	0.357488	424(GGGAACTCCCTGTACT,-,0.00),425(GGAACTCCCTGTACTG,+,0.00)
chunk0126_213_1	chr3	78784877	78785144	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	234449	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.406716	
chunk0038_46_1	chr11	82485113	82485633	+	0	NA	Intergenic	Intergenic	-81460	NR_120571	101928989	Hs.145117	NR_120571	ENSG00000245832	MIR4300HG	-	MIR4300 host gene	ncRNA	0.001923	0.397313	
chunk0156_393_1	chr5	113323051	113323250	+	0	NA	intron (NM_001085377, intron 3 of 18)	MLT1F|LTR|ERVL-MaLR	-28235	NM_002387	4163	Hs.593171	NM_002387	ENSG00000171444	MCC	MCC1	MCC regulator of WNT signaling pathway	protein-coding	0.000000	0.550000	
chunk0096_320_1	chr2	33309510	33309940	+	0	NA	intron (NM_000627, intron 19 of 29)	intron (NM_000627, intron 19 of 29)	-108791	NR_039628	100616136		NR_039628	ENSG00000283591	MIR4430	-	microRNA 4430	ncRNA	0.011628	0.373550	
chunk0142_388_1	chr4	102541814	102542013	+	0	NA	intron (NM_003998, intron 5 of 23)	intron (NM_003998, intron 5 of 23)	40584	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.020101	0.545000	
chunk0069_422_1	chr15	68084510	68084709	+	0	NA	intron (NM_016166, intron 1 of 13)	intron (NM_016166, intron 1 of 13)	30375	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.015075	0.360000	
chunk0035_322_1	chr11	47509428	47509636	+	0	NA	intron (NM_001172639, intron 1 of 15)	AluJo|SINE|Alu	14456	NM_001172639	10658	Hs.595333	NM_006560	ENSG00000149187	CELF1	BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50	CUGBP Elav-like family member 1	protein-coding	0.004808	0.507177	
chunk0095_358_1	chr2	22923024	22923229	+	0	NA	Intergenic	(GCACAT)n|Simple_repeat|Simple_repeat	386647	NR_110577	102723362	Hs.502887	NR_110577	ENSG00000233587	LINC01884	-	long intergenic non-protein coding RNA 1884	ncRNA	0.000000	0.422330	
chunk0135_319_1	chr3	190040027	190040797	+	0	NA	intron (NM_001134418, intron 1 of 14)	intron (NM_001134418, intron 1 of 14)	-80552	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.007792	0.368353	
chunk0169_419_1	chr6	108621104	108621457	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	60414	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.016997	0.466102	33(GGGCACATTCTGTACT,-,0.00),34(GGCACATTCTGTACTG,+,0.00)
chunk0070_89_1	chr15	70271312	70271629	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-173553	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.003155	0.474843	
chunk0209_359_1	chrX	53568813	53569132	+	0	NA	intron (NM_031407, intron 48 of 83)	intron (NM_031407, intron 48 of 83)	-11698	NR_029484	406889		NR_029484	ENSG00000208012	MIRLET7F2	LET7F2|MIRNLET7F2|let-7f-2	microRNA let-7f-2	ncRNA	0.006270	0.453125	
chunk0190_361_1	chr8	39763410	39764128	+	0	NA	intron (NM_001464, intron 14 of 20).2	LTR43B|LTR|ERV1	74520	NM_001278114	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.008357	0.404729	
chunk0082_393_1	chr17	60671312	60671898	+	0	NA	Intergenic	Intergenic	-6206	NM_017679	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.003413	0.383305	169(AAGTACACACTGATCT,-,0.00),170(AGTACACACTGATCTT,+,0.00)
chunk0091_62_1	chr19	4895512	4895753	+	0	NA	intron (NM_001080523, intron 2 of 2)	intron (NM_001080523, intron 2 of 2)	7235	NM_001080523	645432	Hs.660674	NM_001080523	ENSG00000205784	ARRDC5	-	arrestin domain containing 5	protein-coding	0.029046	0.595041	
chunk0041_227_1	chr11	127806679	127807110	+	0	NA	Intergenic	Intergenic	535824	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.006961	0.400463	
chunk0045_331_1	chr12	51024166	51024521	+	0	NA	intron (NM_001174125, intron 1 of 15)	intron (NM_001174125, intron 1 of 15)	1798	NM_001174129	4891	Hs.505545	NM_000617	ENSG00000110911	SLC11A2	AHMIO1|DCT1|DMT1|NRAMP2	solute carrier family 11 member 2	protein-coding	0.022535	0.469101	
chunk0050_388_1	chr12	109087227	109087640	+	0	NA	TTS (NM_001205179)	TTS (NM_001205179)	6055	NM_001205179	121642	Hs.374458	NM_001001655	ENSG00000189046	ALKBH2	ABH2	alkB homolog 2, alpha-ketoglutarate dependent dioxygenase	protein-coding	0.014528	0.512077	
chunk0056_184_1	chr13	85512545	85512901	+	0	NA	intron (NR_046989, intron 1 of 3)	intron (NR_046989, intron 1 of 3)	149120	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.011236	0.389356	
chunk0097_382_1	chr2	61533401	61533600	+	0	NA	intron (NM_003400, intron 2 of 24)	intron (NM_003400, intron 2 of 24)	4783	NM_003400	7514	Hs.370770	NM_003400	ENSG00000082898	XPO1	CRM-1|CRM1|emb|exp1	exportin 1	protein-coding	0.005025	0.280000	
chunk0209_241_1	chrX	45403177	45403409	+	0	NA	Intergenic	Intergenic	-102095	NR_104645	101927528	Hs.550772	NR_104644	ENSG00000229563	LINC01204	-	long intergenic non-protein coding RNA 1204	ncRNA	0.012931	0.347639	
chunk0110_299_1	chr20	17968684	17968883	+	0	NA	promoter-TSS (NM_014426)	promoter-TSS (NM_014426)	11	NM_014426	27131	Hs.316890	NM_014426	ENSG00000089006	SNX5	-	sorting nexin 5	protein-coding	0.105528	0.635000	
chunk0199_234_1	chr9	5391665	5391947	+	0	NA	intron (NM_018465, intron 3 of 5)	intron (NM_018465, intron 3 of 5)	46131	NM_018465	55848	Hs.584242	NM_018465	ENSG00000107020	PLGRKT	AD025|C9orf46|MDS030|PLG-RKT|Plg-R(KT)	plasminogen receptor with a C-terminal lysine	protein-coding	0.007092	0.459364	
chunk0165_232_1	chr6	35547559	35548107	+	0	NA	Intergenic	L1M7|LINE|L1	-34931	NM_001289395	7287	Hs.485208	NM_003322	ENSG00000112041	TULP1	LCA15|RP14|TUBL1	TUB like protein 1	protein-coding	0.014599	0.411658	
chunk0182_184_1	chr7	95630899	95631537	+	0	NA	Intergenic	MIR|SINE|MIR	-34605	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.006270	0.367762	
chunk0132_268_1	chr3	159532674	159533176	+	0	NA	intron (NM_001197108, intron 1 of 6)	intron (NM_001197108, intron 1 of 6)	235687	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.000000	0.381710	
chunk0033_364_1	chr11	23124904	23125578	+	0	NA	Intergenic	Intergenic	-264815	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.001484	0.357037	
chunk0036_201_1	chr11	63289615	63290149	+	0	NA	promoter-TSS (NM_001039752)	promoter-TSS (NM_001039752)	-76	NM_001039752	387775	Hs.188982	NM_001039752	ENSG00000184999	SLC22A10	OAT5|hOAT5	solute carrier family 22 member 10	protein-coding	0.011236	0.349533	
chunk0112_390_1	chr20	46715096	46715809	+	0	NA	intron (NM_030777, intron 1 of 4)	intron (NM_030777, intron 1 of 4)	5812	NM_030777	81031	Hs.305971	NM_030777	ENSG00000197496	SLC2A10	ATORS|ATS|GLUT10	solute carrier family 2 member 10	protein-coding	0.007013	0.481793	
chunk0088_299_1	chr18	49988745	49988951	+	0	NA	intron (NM_001080467, intron 7 of 39)	intron (NM_001080467, intron 7 of 39)	137715	NR_036204	100422865		NR_036204	ENSG00000283343	MIR4320	-	microRNA 4320	ncRNA	0.009709	0.526570	
chunk0104_134_1	chr2	173368851	173369457	+	0	NA	TTS (NM_031942)	TTS (NM_031942)	14321	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.004950	0.383855	
chunk0067_7_1	chr15	39935671	39936407	+	0	NA	intron (NM_001013703, intron 1 of 38)	Tigger15a|DNA|TcMar-Tigger	1915	NM_001013703	440275	Hs.656673	NM_001013703	ENSG00000128829	EIF2AK4	GCN2|PVOD2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding	0.001359	0.388060	
chunk0108_409_1	chr2	237501906	237502947	+	0	NA	intron (NM_001042467, intron 2 of 14)	intron (NM_001042467, intron 2 of 14)	-8505	NR_106869	102465486		NR_106869	ENSG00000277842	MIR6811	hsa-mir-6811	microRNA 6811	ncRNA	0.009606	0.450096	737(CGGAACACCCTGTTTT,-,0.00),738(GGAACACCCTGTTTTA,+,0.00)
chunk0038_11_1	chr11	80828409	80828971	+	0	NA	Intergenic	Intergenic	-65887	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.005338	0.355240	
chunk0042_170_1	chr12	4604003	4604343	+	0	NA	promoter-TSS (NM_001282286)	promoter-TSS (NM_001282286)	-690	NM_001282286	8798	Hs.439530	NM_003845	ENSG00000010219	DYRK4	-	dual specificity tyrosine phosphorylation regulated kinase 4	protein-coding	0.002941	0.325513	
chunk0124_29_1	chr3	52124968	52125568	+	0	NA	intron (NM_001161580, intron 7 of 9)	intron (NM_001161580, intron 7 of 9)	29422	NM_001161580	25886	Hs.476306	NM_015426	ENSG00000164087	POC1A	PIX2|SOFT|WDR51A	POC1 centriolar protein A	protein-coding	0.016667	0.522463	475(TGGGACAGTCTGCACT,-,0.00),476(GGGACAGTCTGCACTG,+,0.00)
chunk0126_206_1	chr3	78647865	78648174	+	0	NA	intron (NM_002941, intron 19 of 30)	intron (NM_002941, intron 19 of 30)	371440	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.006472	0.367742	
chunk0158_407_1	chr5	134816647	134817309	+	0	NA	intron (NM_001300860, intron 19 of 22)	intron (NM_001300860, intron 19 of 22)	-28702	NM_152409	134553	Hs.708536	NM_152409	ENSG00000181904	C5orf24	-	chromosome 5 open reading frame 24	protein-coding	0.006042	0.331825	
chunk0154_31_1	chr5	77017594	77018063	+	0	NA	Intergenic	Intergenic	-12557	NM_018046	55109	Hs.634849	NM_018046	ENSG00000164252	AGGF1	GPATC7|GPATCH7|HSU84971|HUS84971|VG5Q	angiogenic factor with G-patch and FHA domains 1	protein-coding	0.008529	0.321277	
chunk0054_94_1	chr13	42585782	42586233	+	0	NA	intron (NM_003701, intron 2 of 4)	Charlie7a|DNA|hAT-Charlie	11852	NM_003701	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.002217	0.365044	
chunk0073_240_1	chr16	11636403	11636653	+	0	NA	Intergenic	LTR9A1|LTR|ERV1	-31905	NM_003498	8303	Hs.618526	NM_003498	ENSG00000184602	SNN	-	stannin	protein-coding	0.016000	0.458167	98(AGGACTAGGTGTACCT,+,0.00)
chunk0153_221_1	chr5	72076087	72076302	+	0	NA	Intergenic	Intergenic	-31097	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.013953	0.356481	
chunk0086_160_1	chr18	21600676	21601134	+	0	NA	promoter-TSS (NM_052911)	promoter-TSS (NM_052911)	-173	NM_052911	114799	Hs.464733	NM_052911	ENSG00000141446	ESCO1	A930014I12Rik|CTF|ECO1|EFO1|ESO1	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.111354	0.660131	
chunk0164_155_1	chr6	21519612	21519985	+	0	NA	Intergenic	Intergenic	-7906	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.002681	0.320856	
chunk0069_288_1	chr15	65171397	65171798	+	0	NA	intron (NM_006660, intron 3 of 13)	intron (NM_006660, intron 3 of 13)	13628	NM_006660	10845	Hs.113823	NM_006660	ENSG00000166855	CLPX	EPP2	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding	0.012469	0.378109	
chunk0017_17_1	chr1	204417010	204417749	+	0	NA	Intergenic	Intergenic	-5562	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.010825	0.471622	
chunk0138_294_1	chr4	40989522	40989816	+	0	NA	intron (NM_004307, intron 6 of 17)	intron (NM_004307, intron 6 of 17)	-132477	NM_001166053	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.017007	0.423729	
chunk0076_110_1	chr16	66502942	66503515	+	0	NA	Intergenic	L2b|LINE|L2	-26826	NR_109960	101927726	Hs.739193	NR_109960	ENSG00000261656	BEAN1-AS1	CTD-2258A20.5	BEAN1 antisense RNA 1	ncRNA	0.006981	0.454704	294(TGGAACATGCTGAGCC,-,0.00),295(GGAACATGCTGAGCCT,+,0.00),328(CTGCACAGACTGTTCC,-,0.00),329(TGCACAGACTGTTCCC,+,0.00)
chunk0159_1_1	chr5	135857860	135858458	+	0	NA	intron (NM_145282, intron 4 of 4)	intron (NM_145282, intron 4 of 4)	23483	NM_145282	153328	Hs.412418	NM_145282	ENSG00000145832	SLC25A48	-	solute carrier family 25 member 48	protein-coding	0.006689	0.504174	
chunk0002_115_1	chr1	16091201	16091543	+	0	NA	Intergenic	Intergenic	-17740	NM_182623	348487	Hs.126825	NM_182623	ENSG00000185519	FAM131C	C1orf117	family with sequence similarity 131 member C	protein-coding	0.020468	0.597668	
chunk0168_235_1	chr6	87607991	87608268	+	0	NA	intron (NM_181837, intron 6 of 19)	intron (NM_181837, intron 6 of 19)	18062	NM_012381	23595	Hs.410228	NM_012381	ENSG00000135336	ORC3	LAT|LATHEO|ORC3L	origin recognition complex subunit 3	protein-coding	0.000000	0.330935	
chunk0186_451_1	chr7	148204809	148205009	+	0	NA	intron (NM_014141, intron 18 of 23)	MIRb|SINE|MIR	-385656	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.005000	0.417910	
chunk0052_451_1	chr12	132593724	132594124	+	0	NA	Intergenic	L1MEc|LINE|L1	11927	NR_106821	102465975		NR_106821	ENSG00000277052	MIR6763	hsa-mir-6763	microRNA 6763	ncRNA	0.045000	0.566085	
chunk0200_308_1	chr9	23103596	23104049	+	0	NA	Intergenic	Intergenic	457622	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.002208	0.284141	
chunk0206_104_1	chr9	120776474	120777143	+	0	NA	intron (NM_012164, intron 4 of 7)	intron (NM_012164, intron 4 of 7)	16654	NM_012164	26190	Hs.494985	NM_012164	ENSG00000119402	FBXW2	FBW2|Fwd2|Md6	F-box and WD repeat domain containing 2	protein-coding	0.004484	0.385075	
chunk0019_405_1	chr1	230656123	230656546	+	0	NA	intron (NM_001145036, intron 1 of 17)	L1P2|LINE|L1	13878	NM_007357	22796	Hs.211800	NM_007357	ENSG00000135775	COG2	CDG2Q|LDLC	component of oligomeric golgi complex 2	protein-coding	0.016548	0.377358	
chunk0202_242_1	chr9	76654579	76654891	+	0	NA	intron (NM_001308050, intron 2 of 10)	intron (NM_001308050, intron 2 of 10)	37680	NM_001308051	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.003205	0.341853	
chunk0188_337_1	chr8	17767804	17768447	+	0	NA	intron (NM_001001924, intron 1 of 14)	intron (NM_001001924, intron 1 of 14)	32792	NM_001001925	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.010886	0.392857	
chunk0191_233_1	chr8	52832016	52832485	+	0	NA	Intergenic	L1ME3B|LINE|L1	-107658	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.010661	0.353191	
chunk0048_406_1	chr12	88165990	88166538	+	0	NA	intron (NM_181783, intron 6 of 13)	intron (NM_181783, intron 6 of 13)	23968	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.001825	0.322404	
chunk0147_39_1	chr4	172045654	172046140	+	0	NA	intron (NM_001034845, intron 2 of 12)	L1MB1|LINE|L1	232473	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.002058	0.310062	
chunk0180_121_1	chr7	55552683	55552925	+	0	NA	promoter-TSS (NM_001284282)	promoter-TSS (NM_001284282)	-31	NM_001284282	81552	Hs.488307	NM_030796	ENSG00000154978	VOPP1	ECOP|GASP|WBP1L2	VOPP1 WW domain binding protein	protein-coding	0.033058	0.563786	57(CGGCACACGGAGTTCA,-,0.00),58(GGCACACGGAGTTCAC,+,0.00)
chunk0040_410_1	chr11	121067457	121067825	+	0	NA	intron (NM_152715, intron 7 of 7)	intron (NM_152715, intron 7 of 7)	-35025	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.005435	0.406504	247(AAGTTCAGTGTGTACT,-,0.00),248(AGTTCAGTGTGTACTG,+,0.00)
chunk0064_67_1	chr14	90121138	90121483	+	0	NA	intron (NM_022054, intron 1 of 1)	intron (NM_022054, intron 1 of 1)	59545	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.014493	0.421965	
chunk0010_337_1	chr1	118479407	118479818	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-294387	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.007299	0.342233	
chunk0039_144_1	chr11	98630930	98631390	+	0	NA	Intergenic	LTR22B|LTR|ERVK	-389816	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.015217	0.396963	
chunk0128_9_1	chr3	103685939	103686215	+	0	NA	Intergenic	L1MA9|LINE|L1	-161961	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.332130	
chunk0161_256_1	chr5	171940321	171940647	+	0	NA	intron (NM_033644, intron 1 of 12)	L1MC4a|LINE|L1	66389	NM_033644	23291	Hs.484138	NM_012300	ENSG00000072803	FBXW11	BTRC2|BTRCP2|FBW1B|FBXW1B|Fbw11|Hos	F-box and WD repeat domain containing 11	protein-coding	0.009202	0.418960	
chunk0058_443_1	chr13	113617254	113617479	+	0	NA	intron (NM_007111, intron 3 of 11)	intron (NM_007111, intron 3 of 11)	32625	NM_007111	7027	Hs.79353	NM_007111	ENSG00000198176	TFDP1	DILC|DP1|DRTF1|Dp-1	transcription factor Dp-1	protein-coding	0.026667	0.566372	
chunk0018_121_1	chr1	218470312	218470730	+	0	NA	intron (NR_031644, intron 2 of 6)	ERVL-E-int|LTR|ERVL	27895	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.014354	0.396181	
chunk0066_140_1	chr15	31352277	31352701	+	0	NA	intron (NM_001302461, intron 1 of 1).2	intron (NM_001302461, intron 1 of 1).2	25634	NM_001302461	51621	Hs.376443	NM_015995	ENSG00000169926	KLF13	BTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel like factor 13	protein-coding	0.021226	0.609412	
chunk0142_440_1	chr4	105236833	105237475	+	0	NA	exon (NM_001127208, exon 3 of 11)	exon (NM_001127208, exon 3 of 11)	90469	NM_001127208	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.004673	0.409020	
chunk0131_107_1	chr3	143877564	143877926	+	0	NA	Intergenic	MIR|SINE|MIR	-29214	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.002762	0.471074	
chunk0192_371_1	chr8	68416745	68417148	+	0	NA	intron (NM_052958, intron 1 of 13)	intron (NM_052958, intron 1 of 13)	-85455	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.004963	0.336634	
chunk0183_369_1	chr7	109309832	109310112	+	0	NA	Intergenic	L1PA15|LINE|L1	-425385	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.010714	0.562278	
chunk0167_278_1	chr6	70398967	70399672	+	0	NA	TTS (NR_125857)	TTS (NR_125857)	5117	NR_125857	101928353		NR_125857		EVADR	-	uncharacterized LOC101928353	ncRNA	0.007092	0.406516	
chunk0202_320_1	chr9	78272839	78273038	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-24137	NM_058179	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.000000	0.410000	
chunk0173_319_1	chr6	148649353	148649671	+	0	NA	Intergenic	MER57A1|LTR|ERV1	-97623	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.003145	0.467085	
chunk0117_227_1	chr22	22711013	22711286	+	0	NA	Intergenic	Intergenic	64837	NM_199127	91227	Hs.450000	NM_080839	ENSG00000100121	GGTLC2	GGTL4	gamma-glutamyltransferase light chain 2	protein-coding	0.010989	0.518248	
chunk0056_55_1	chr13	77700940	77701504	+	0	NA	intron (NM_001040153, intron 1 of 6)	intron (NM_001040153, intron 1 of 6)	2341	NM_001040153	122060	Hs.349955	NM_144595	ENSG00000139737	SLAIN1	C13orf32	SLAIN motif family member 1	protein-coding	0.000000	0.279646	
chunk0126_38_1	chr3	73748624	73749004	+	0	NA	Intergenic	Intergenic	-123893	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.010526	0.377953	
chunk0026_320_1	chr10	68106641	68107220	+	0	NA	intron (NR_045662, intron 2 of 19)	intron (NR_045662, intron 2 of 19)	813	NR_045662	84665	Hs.55205	NM_032578	ENSG00000138347	MYPN	CMD1DD|CMH22|MYOP|NEM11|RCM4	myopalladin	protein-coding	0.005181	0.341379	
chunk0205_325_1	chr9	112823561	112823800	+	0	NA	intron (NM_001012994, intron 3 of 8)	intron (NM_001012994, intron 3 of 8)	67233	NM_033051	57864	Hs.512668	NM_033051	ENSG00000119457	SLC46A2	Ly110|TSCOT	solute carrier family 46 member 2	protein-coding	0.000000	0.262500	
chunk0118_392_1	chr22	37686232	37686475	+	0	NA	promoter-TSS (NM_024313)	promoter-TSS (NM_024313)	16	NM_024313	79159	Hs.632778	NM_024313	ENSG00000273899	NOL12	Nop25|dJ37E16.7	nucleolar protein 12	protein-coding	0.082305	0.598361	
chunk0074_324_1	chr16	30875046	30875558	+	0	NA	promoter-TSS (NR_039744)	promoter-TSS (NR_039744)	21	NR_039744	100616231		NR_039744	ENSG00000265991	MIR4519	-	microRNA 4519	ncRNA	0.101562	0.684211	
chunk0193_143_1	chr8	74536675	74537156	+	0	NA	Intergenic	L1PA11|LINE|L1	-11628	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.000000	0.367220	
chunk0104_48_1	chr2	171309331	171310040	+	0	NA	Intergenic	Intergenic	-78371	NM_001136554	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.007052	0.404225	
chunk0030_377_1	chr10	119277634	119278382	+	0	NA	intron (NM_005308, intron 1 of 15)	L1ME1|LINE|L1	70323	NM_005308	2869	Hs.524625	NM_005308	ENSG00000198873	GRK5	FP2025|GPRK5	G protein-coupled receptor kinase 5	protein-coding	0.017380	0.455274	
chunk0086_286_1	chr18	23725743	23726373	+	0	NA	intron (NR_130106, intron 2 of 12)	intron (NR_130106, intron 2 of 12)	36615	NR_130106	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.004762	0.510301	277(TGGAACATTCAGTTCT,-,0.00),278(GGAACATTCAGTTCTT,+,0.00)
chunk0025_424_1	chr10	59873925	59874561	+	0	NA	intron (NM_005436, intron 1 of 8)	intron (NM_005436, intron 1 of 8)	32413	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.007862	0.381476	
chunk0019_120_1	chr1	225417889	225418337	+	0	NA	exon (NM_194442, exon 6 of 14)	exon (NM_194442, exon 6 of 14)	10000	NM_002296	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.008929	0.398664	
chunk0173_191_1	chr6	145168467	145168860	+	0	NA	Intergenic	L1MEd|LINE|L1	-566206	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.005089	0.340102	
chunk0001_206_1	chr1	7961316	7961875	+	0	NA	promoter-TSS (NM_001123377)	promoter-TSS (NM_001123377)	-59	NM_007262	11315	Hs.419640	NM_007262	ENSG00000116288	PARK7	DJ-1|DJ1|GATD2|HEL-S-67p	Parkinsonism associated deglycase	protein-coding	0.103757	0.694643	
chunk0179_423_1	chr7	51860433	51861008	+	0	NA	Intergenic	MIR|SINE|MIR	-543902	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.005217	0.390625	
chunk0099_205_1	chr2	94868090	94868317	+	0	NA	TTS (NR_037597)	TTS (NR_037597)	-3230	NM_001286559	150483	Hs.631517	NM_144705	ENSG00000163060	TEKT4	-	tektin 4	protein-coding	0.004405	0.315789	
chunk0037_72_1	chr11	71206124	71206450	+	0	NA	intron (NM_012309, intron 1 of 24)	intron (NM_012309, intron 1 of 24)	18509	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.030675	0.504587	
chunk0152_286_1	chr5	61510613	61511029	+	0	NA	intron (NM_020928, intron 4 of 13)	intron (NM_020928, intron 4 of 13)	-126960	NM_173667									0.004808	0.390887	
chunk0021_62_1	chr10	1278288	1278680	+	0	NA	intron (NM_018702, intron 3 of 9)	L1PA16|LINE|L1	118716	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.005102	0.414758	
chunk0025_358_1	chr10	58384996	58385195	+	0	NA	promoter-TSS (NM_003201)	promoter-TSS (NM_003201)	-48	NR_073073	7019	Hs.594250	NM_003201	ENSG00000108064	TFAM	MTDPS15|MTTF1|MTTFA|TCF6|TCF6L1|TCF6L2|TCF6L3	transcription factor A, mitochondrial	protein-coding	0.105528	0.700000	
chunk0111_433_1	chr20	35179487	35180003	+	0	NA	Intergenic	Intergenic	7808	NM_006404	10544	Hs.647450	NM_006404	ENSG00000101000	PROCR	CCCA|CCD41|EPCR	protein C receptor	protein-coding	0.007752	0.377176	
chunk0145_445_1	chr4	153519054	153519253	+	0	NA	intron (NM_001131007, intron 3 of 34)	intron (NM_001131007, intron 3 of 34)	52807	NM_001131007	23240	Hs.732450	NM_015196	ENSG00000121210	TMEM131L	KIAA0922	transmembrane 131 like	protein-coding	0.000000	0.445000	131(GGGTACTTTCTGTTCT,-,0.00),132(GGTACTTTCTGTTCTT,+,0.00)
chunk0071_130_1	chr15	81723579	81723951	+	0	NA	Intergenic	Intergenic	322378	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.008065	0.378016	
chunk0120_361_1	chr3	11653415	11654033	+	0	NA	intron (NM_014667, intron 2 of 5)	L1ME3A|LINE|L1	-9747	NM_001128219	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.014563	0.436187	
chunk0026_242_1	chr10	66287824	66288205	+	0	NA	intron (NM_001127384, intron 12 of 17)	L1MC4a|LINE|L1	-638020	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.002625	0.358639	
chunk0004_105_1	chr1	44213303	44213549	+	0	NA	promoter-TSS (NM_001034024)	promoter-TSS (NM_001034024)	-27	NM_001034024	55929	Hs.8008	NM_019100	ENSG00000178028	DMAP1	DNMAP1|DNMTAP1|EAF2|MEAF2|SWC4	DNA methyltransferase 1 associated protein 1	protein-coding	0.085366	0.635628	
chunk0056_43_1	chr13	77429733	77430312	+	0	NA	Intergenic	Intergenic	-102980	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.008636	0.401724	
chunk0185_70_1	chr7	125137145	125137375	+	0	NA	intron (NR_125718, intron 9 of 10)	intron (NR_125718, intron 9 of 10)	-47309	NR_110188	101928283	Hs.566650	NR_110188	ENSG00000224897	LOC101928283	-	uncharacterized LOC101928283	ncRNA	0.000000	0.350649	
chunk0155_165_1	chr5	94344449	94344977	+	0	NA	intron (NM_001145678, intron 20 of 20)	L1MB3|LINE|L1	-233014	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.003788	0.366730	
chunk0044_428_1	chr12	42088721	42089234	+	0	NA	intron (NM_001099650, intron 6 of 6)	intron (NM_001099650, intron 6 of 6)	55894	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.003899	0.375486	473(TAGCACACAGAGTGCT,-,0.00),474(AGCACACAGAGTGCTT,+,0.00)
chunk0023_112_1	chr10	23057633	23057991	+	0	NA	Intergenic	MER34A|LTR|ERV1	-37686	NM_012228	22921	Hs.461420	NM_012228	ENSG00000148450	MSRB2	CBS-1|CBS1|CGI-131|MSRB|PILB	methionine sulfoxide reductase B2	protein-coding	0.008380	0.445682	309(TGGAGCAGTGTGTTCT,-,0.00),310(GGAGCAGTGTGTTCTG,+,0.00)
chunk0191_364_1	chr8	56921518	56922195	+	0	NA	Intergenic	Intergenic	72015	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.002954	0.353982	
chunk0123_129_1	chr3	42582184	42582606	+	0	NA	promoter-TSS (NM_001201584)	promoter-TSS (NM_001201584)	-367	NM_001201584	9117	Hs.445892	NM_004206	ENSG00000093183	SEC22C	SEC22L3	SEC22 homolog C, vesicle trafficking protein	protein-coding	0.066351	0.593381	
chunk0149_453_1	chr5	29960484	29961177	+	0	NA	Intergenic	L1M1|LINE|L1	-564854	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.002886	0.465418	
chunk0080_392_1	chr17	35022616	35023101	+	0	NA	intron (NR_037713, intron 2 of 6)	intron (NR_037713, intron 2 of 6)	40882	NM_001017368	117584	Hs.13680	NM_057178	ENSG00000092871	RFFL	CARP-2|CARP2|FRING|RIFIFYLIN|RNF189|RNF34L	ring finger and FYVE like domain containing E3 ubiquitin protein ligase	protein-coding	0.014433	0.545267	242(AAGCACAGAGTGTCTC,-,0.00),243(AGCACAGAGTGTCTCA,+,0.00)
chunk0044_354_1	chr12	38917186	38917715	+	0	NA	Intergenic	L1ME4b|LINE|L1	-11832	NM_153634	144402	Hs.40910	NM_153634	ENSG00000139117	CPNE8	-	copine 8	protein-coding	0.000000	0.332075	
chunk0131_462_1	chr3	154144825	154145427	+	0	NA	intron (NM_015595, intron 4 of 14)	intron (NM_015595, intron 4 of 14)	23766	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.001661	0.393035	
chunk0079_20_1	chr17	9705718	9706224	+	0	NA	intron (NM_153210, intron 12 of 14)	L1ME4b|LINE|L1	60434	NM_153210	124739	Hs.709621	NM_153210	ENSG00000154914	USP43	-	ubiquitin specific peptidase 43	protein-coding	0.001976	0.366864	
chunk0171_424_1	chr6	131541248	131541622	+	0	NA	Intergenic	L1PA7|LINE|L1	-31769	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.008021	0.357333	
chunk0187_317_1	chr7	156596537	156596933	+	0	NA	intron (NR_103858, intron 1 of 1)	L1MD3|LINE|L1	6460	NR_103858	100506380	Hs.647014	NM_032625	ENSG00000182648	LINC01006	C7orf13|MY040	long intergenic non-protein coding RNA 1006	ncRNA	0.002525	0.335013	
chunk0068_204_1	chr15	54985960	54986450	+	0	NA	Intergenic	Intergenic	210828	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004082	0.307536	315(CAGGACTGTTTGTCCT,-,0.00),316(AGGACTGTTTGTCCTG,+,0.00)
chunk0148_442_1	chr4	189649119	189649320	+	0	NA	Intergenic	Intergenic	-10387	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.004975	0.425743	
chunk0177_376_1	chr7	26875681	26876362	+	0	NA	Intergenic	Intergenic	-11278	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.007342	0.321114	
chunk0027_409_1	chr10	80468707	80468952	+	0	NA	intron (NM_030927, intron 1 of 8)	AluJb|SINE|Alu	14547	NM_001128309	81619	Hs.308615	NM_030927	ENSG00000108219	TSPAN14	DC-TM4F2|TM4SF14|tspan-14	tetraspanin 14	protein-coding	0.016327	0.463415	
chunk0212_433_1	chrX	154029168	154029684	+	0	NA	TTS (NM_001110792)	TTS (NM_001110792)	-9437	NR_031757	100313781		NR_031757	ENSG00000284286	MIR718	hsa-mir-718	microRNA 718	ncRNA	0.015504	0.508704	
chunk0013_262_1	chr1	170097492	170098094	+	0	NA	Intergenic	Intergenic	-23055	NM_014970	22920	Hs.433442	NM_014970	ENSG00000075945	KIFAP3	FLA3|KAP-1|KAP-3|KAP3|SMAP|Smg-GDS|dJ190I16.1	kinesin associated protein 3	protein-coding	0.008306	0.417910	
chunk0171_358_1	chr6	130620375	130620817	+	0	NA	Intergenic	Intergenic	183479	NM_052913	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.004525	0.340858	
chunk0115_395_1	chr21	30535439	30536135	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	6077	NM_001303120	337973	Hs.553695	NM_181612	ENSG00000186925	KRTAP19-6	KAP19.6	keratin associated protein 19-6	protein-coding	0.010057	0.357245	320(AAGAACACCATGTAAT,-,0.00)
chunk0197_24_1	chr8	117934451	117935011	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	177088	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.014286	0.477718	
chunk0208_322_1	chrX	24184474	24184691	+	0	NA	intron (NM_001178095, intron 3 of 7)	intron (NM_001178095, intron 3 of 7)	34845	NM_003410	7543	Hs.336681	NM_003410	ENSG00000005889	ZFX	ZNF926	zinc finger protein X-linked	protein-coding	0.000000	0.284404	
chunk0119_434_1	chr22	50040366	50040882	+	0	NA	Intergenic	L1ME3|LINE|L1	-27998	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.021318	0.489362	61(GAGCACAGACTGTTCC,-,0.00),62(AGCACAGACTGTTCCC,+,0.00)
chunk0125_130_1	chr3	65870092	65870326	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-23607	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.012821	0.395745	
chunk0027_254_1	chr10	77207819	77208018	+	0	NA	intron (NM_001014797, intron 3 of 28)	intron (NM_001014797, intron 3 of 28)	67087	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.010050	0.435000	
chunk0167_215_1	chr6	66221904	66222195	+	0	NA	Intergenic	Intergenic	434170	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.000000	0.376712	
chunk0150_90_1	chr5	32331248	32331581	+	0	NA	Intergenic	Intergenic	-18406	NM_001294344	54545	Hs.481836	NM_019061	ENSG00000150712	MTMR12	3-PAP|PIP3AP	myotubularin related protein 12	protein-coding	0.009009	0.419162	
chunk0152_30_1	chr5	56833957	56834463	+	0	NA	intron (NM_005921, intron 1 of 19)	intron (NM_005921, intron 1 of 19)	19137	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.000000	0.378698	303(AGGAACTGAGTGAGCC,-,0.00)
chunk0205_46_1	chr9	105926411	105926610	+	0	NA	Intergenic	Intergenic	231985	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.000000	0.365000	
chunk0120_438_1	chr3	13524397	13524715	+	0	NA	Intergenic	Charlie1|DNA|hAT-Charlie	-24569	NM_001998	2199	Hs.198862	NM_001998	ENSG00000163520	FBLN2	-	fibulin 2	protein-coding	0.003145	0.401254	
chunk0014_333_1	chr1	182144091	182144468	+	0	NA	Intergenic	Intergenic	-82567	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.013263	0.576720	156(GGGAACAGTATGTTTC,-,0.00),157(GGAACAGTATGTTTCC,+,0.00)
chunk0093_107_1	chr19	44112611	44113108	+	0	NA	promoter-TSS (NM_013362)	promoter-TSS (NM_013362)	324	NR_033341	100379224	Hs.585869	NR_033341	ENSG00000186019	LOC100379224	-	uncharacterized LOC100379224	ncRNA	0.028169	0.401606	
chunk0145_65_1	chr4	145566655	145566995	+	0	NA	Intergenic	L1PREC2|LINE|L1	-49631	NR_126371	104326058	Hs.714527	NR_126371	ENSG00000250902	SMAD1-AS1	-	SMAD1 antisense RNA 1	ncRNA	0.008824	0.563050	
chunk0002_178_1	chr1	19010613	19010820	+	0	NA	Intergenic	LTR88a|LTR|Gypsy?	-54384	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.009662	0.576923	
chunk0164_381_1	chr6	26006167	26006603	+	0	NA	Intergenic	LTR33|LTR|ERVL	11427	NM_005325	3024	Hs.150206	NM_005325	ENSG00000124610	HIST1H1A	H1.1|H1A|H1F1|HIST1	histone cluster 1 H1 family member a	protein-coding	0.000000	0.464531	
chunk0141_328_1	chr4	87311732	87312506	+	0	NA	intron (NM_178135, intron 5 of 6)	intron (NM_178135, intron 5 of 6)	10787	NM_178135	345275	Hs.284414	NM_178135	ENSG00000170509	HSD17B13	HMFN0376|NIIL497|SCDR9|SDR16C3	hydroxysteroid 17-beta dehydrogenase 13	protein-coding	0.009044	0.423226	
chunk0079_386_1	chr17	18769815	18770014	+	0	NA	intron (NM_001267586, intron 10 of 12)	intron (NM_001267586, intron 10 of 12)	-11081	NM_001316924	51030	Hs.87295	NM_016078	ENSG00000171928	TVP23B	CGI-148|FAM18B|FAM18B1|NPD008|YDR084C	trans-golgi network vesicle protein 23 homolog B	protein-coding	0.035176	0.530000	
chunk0061_197_1	chr14	60256391	60256731	+	0	NA	intron (NM_177951, intron 2 of 3)	intron (NM_177951, intron 2 of 3)	7313	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.008824	0.337243	
chunk0033_233_1	chr11	17769914	17770327	+	0	NA	intron (NM_004976, intron 1 of 1)	intron (NM_004976, intron 1 of 1)	34172	NM_004976	3746	Hs.552896	NM_004976	ENSG00000129159	KCNC1	EPM7|KV3.1|KV4|NGK2	potassium voltage-gated channel subfamily C member 1	protein-coding	0.012107	0.550725	
chunk0208_240_1	chrX	19996280	19996732	+	0	NA	Intergenic	Intergenic	-6727	NR_024440	729609	Hs.554726	NR_024440		LOC729609	-	uncharacterized LOC729609	ncRNA	0.008850	0.403974	
chunk0085_95_1	chr18	2684174	2684554	+	0	NA	intron (NM_015295, intron 5 of 47)	intron (NM_015295, intron 5 of 47)	28477	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.005263	0.270341	
chunk0153_353_1	chr5	74408065	74408795	+	0	NA	intron (NR_126354, intron 2 of 2)	intron (NR_126354, intron 2 of 2)	85944	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.005479	0.359781	
chunk0092_68_1	chr19	20412838	20413226	+	0	NA	intron (NR_036455, intron 1 of 2)	intron (NR_036455, intron 1 of 2)	11933	NR_036455	664701	Hs.631635	NM_001039884		ZNF826P	ZNF826	zinc finger protein 826, pseudogene	pseudo	0.000000	0.311054	
chunk0042_287_1	chr12	7459339	7460087	+	0	NA	Intergenic	L1M1|LINE|L1	-15528	NM_174941	283316	Hs.631727	NM_174941	ENSG00000177675	CD163L1	CD163B|M160|SCARI2|WC1	CD163 molecule like 1	protein-coding	0.002674	0.433912	
chunk0141_454_1	chr4	89413383	89413729	+	0	NA	Intergenic	MIR|SINE|MIR	-105546	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.002890	0.331412	
chunk0163_323_1	chr6	14888720	14888927	+	0	NA	Intergenic	Intergenic	-357152	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.019324	0.567308	
chunk0198_9_1	chr9	298585	299546	+	0	NA	intron (NM_001190458, intron 3 of 45)	intron (NM_001190458, intron 3 of 45)	26017	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.007284	0.387734	
chunk0135_191_1	chr3	188210839	188211249	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	-1889	NM_005578	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.017073	0.394161	
chunk0205_11_1	chr9	104973904	104974360	+	0	NA	Intergenic	Intergenic	-45886	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.010965	0.417943	
chunk0100_289_1	chr2	114636373	114637299	+	0	NA	intron (NM_001178036, intron 2 of 26)	intron (NM_001178036, intron 2 of 26)	175233	NM_001178036	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.007559	0.368932	640(TAGTACAAATTGTACT,-,0.00),641(AGTACAAATTGTACTT,+,0.00)
chunk0032_367_1	chr11	10858170	10858497	+	0	NA	promoter-TSS (NM_021211)	promoter-TSS (NM_021211)	116	NR_034137	729013	Hs.726427	NR_034137	ENSG00000247271	ZBED5-AS1	-	ZBED5 antisense RNA 1	ncRNA	0.070336	0.603659	
chunk0183_187_1	chr7	106216999	106217710	+	0	NA	Intergenic	L2a|LINE|L2	67838	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.012658	0.470506	360(AGGGACAGTTTGTTCT,-,0.00),361(GGGACAGTTTGTTCTC,+,0.00)
chunk0044_282_1	chr12	32661789	32662062	+	0	NA	Intergenic	Intergenic	-17275	NM_012063	10059	Hs.556296	NM_005690	ENSG00000087470	DNM1L	DLP1|DRP1|DVLP|DYMPLE|EMPF|EMPF1|HDYNIV|OPA5	dynamin 1 like	protein-coding	0.021978	0.551095	
chunk0139_15_1	chr4	48119446	48119943	+	0	NA	intron (NM_003328, intron 1 of 14)	intron (NM_003328, intron 1 of 14)	14562	NM_003328	7294	Hs.479669	NM_003328	ENSG00000074966	TXK	BTKL|PSCTK5|PTK4|RLK|TKL	TXK tyrosine kinase	protein-coding	0.002012	0.421687	1(ATGGACATACAGTTCA,-,0.00)
chunk0032_376_1	chr11	11211750	11212501	+	0	NA	Intergenic	Intergenic	141232	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.001332	0.393617	
chunk0025_196_1	chr10	53364852	53365457	+	0	NA	Intergenic	Intergenic	-593454	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.003306	0.348185	22(AAGGACTGTTTGTTCT,-,0.00),23(AGGACTGTTTGTTCTG,+,0.00)
chunk0009_214_1	chr1	106276259	106276982	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-657685	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002766	0.360497	
chunk0150_287_1	chr5	37214508	37214836	+	0	NA	intron (NM_023073, intron 15 of 51)	Tigger2b_Pri|DNA|TcMar-Tigger	34756	NM_023073	65250	Hs.586199	NM_023073	ENSG00000197603	CPLANE1	C5orf42|Hug|JBTS17|OFD6	ciliogenesis and planar polarity effector 1	protein-coding	0.003049	0.355623	
chunk0196_38_1	chr8	101634067	101634337	+	0	NA	intron (NM_024915, intron 11 of 15)	intron (NM_024915, intron 11 of 15)	141762	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.000000	0.505535	
chunk0047_433_1	chr12	76352766	76353481	+	0	NA	3' UTR (NM_020841, exon 24 of 24)	3' UTR (NM_020841, exon 24 of 24)	-4681	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.002797	0.296089	
chunk0122_371_1	chr3	37668455	37669390	+	0	NA	intron (NM_002207, intron 17 of 27)	intron (NM_002207, intron 17 of 27)	192858	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.011765	0.510684	
chunk0209_136_1	chrX	41572848	41573361	+	0	NA	intron (NM_003688, intron 15 of 26)	AluSx3|SINE|Alu	-115869	NM_001097579	2857	Hs.495989	NM_005300	ENSG00000171659	GPR34	LYPSR1	G protein-coupled receptor 34	protein-coding	0.005848	0.375486	
chunk0094_114_1	chr2	4345989	4346410	+	0	NA	Intergenic	Intergenic	310023	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.002375	0.293839	
chunk0158_412_1	chr5	134920438	134920692	+	0	NA	intron (NM_032151, intron 2 of 3)	intron (NM_032151, intron 2 of 3)	-7474	NR_039666									0.011811	0.415686	
chunk0008_427_1	chr1	99327444	99327701	+	0	NA	Intergenic	Intergenic	63280	NM_001166252	9890	Hs.13245	NM_014839	ENSG00000117600	PLPPR4	LPPR4|LPR4|PHP1|PRG-1|PRG1	phospholipid phosphatase related 4	protein-coding	0.011673	0.391473	
chunk0040_30_1	chr11	110295244	110295570	+	0	NA	intron (NM_001260496, intron 1 of 7)	intron (NM_001260496, intron 1 of 7)	1305	NM_001260496	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.012270	0.302752	
chunk0032_245_1	chr11	8186598	8186952	+	0	NA	Intergenic	L1M5|LINE|L1	-17732	NM_024557	79608	Hs.231850	NM_024557	ENSG00000166405	RIC3	AYST720|PRO1385	RIC3 acetylcholine receptor chaperone	protein-coding	0.005650	0.329577	
chunk0036_5_1	chr11	58000808	58001344	+	0	NA	Intergenic	Intergenic	-22805	NM_001005212	219956	Hs.689841	NM_001005212	ENSG00000186509	OR9Q1	-	olfactory receptor family 9 subfamily Q member 1	protein-coding	0.009328	0.432030	
chunk0046_392_1	chr12	63869710	63870166	+	0	NA	intron (NM_020762, intron 1 of 21)	MIRb|SINE|MIR	25177	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.000000	0.371991	
chunk0189_285_1	chr8	25457271	25457593	+	0	NA	intron (NM_017634, intron 1 of 11)	intron (NM_017634, intron 1 of 11)	1036	NM_017634	54793	Hs.72071	NM_017634	ENSG00000104756	KCTD9	BTBD27	potassium channel tetramerization domain containing 9	protein-coding	0.031056	0.458204	
chunk0008_24_1	chr1	87844389	87844725	+	0	NA	Intergenic	L1ME1|LINE|L1	-472902	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.008929	0.332344	
chunk0081_430_1	chr17	48831008	48831380	+	0	NA	intron (NM_001261395, intron 1 of 11)	CpG	206	NM_001261391	10241	Hs.514920	NM_005831	ENSG00000136436	CALCOCO2	NDP52	calcium binding and coiled-coil domain 2	protein-coding	0.056452	0.662198	
chunk0060_13_1	chr14	39406178	39406784	+	0	NA	intron (NM_203301, intron 1 of 3)	L1MEc|LINE|L1	26019	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.006601	0.355848	
chunk0087_346_1	chr18	40612151	40612578	+	0	NA	Intergenic	Intergenic	546078	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.004684	0.411215	
chunk0172_72_1	chr6	134361489	134361839	+	0	NA	Intergenic	L2a|LINE|L2	-43606	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.005714	0.421652	
chunk0133_62_1	chr3	166838974	166839697	+	0	NA	Intergenic	L1MC|LINE|L1	540948	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.004149	0.263812	
chunk0171_196_1	chr6	125559129	125559375	+	0	NA	Intergenic	Intergenic	-115101	NR_038906	643623	Hs.520367	NR_038906	ENSG00000224506	LINC02523	-	long intergenic non-protein coding RNA 2523	ncRNA	0.004065	0.473684	
chunk0194_29_1	chr8	81749649	81749894	+	0	NA	intron (NM_152284, intron 1 of 4)	intron (NM_152284, intron 1 of 4)	17318	NM_152284	92421	Hs.183861	NM_152284	ENSG00000164695	CHMP4C	SNF7-3|Shax3|VPS32C	charged multivesicular body protein 4C	protein-coding	0.000000	0.406504	96(TAGAACATCATGCTCT,-,0.00),97(AGAACATCATGCTCTA,+,0.00)
chunk0169_387_1	chr6	107790496	107790899	+	0	NA	intron (NM_198081, intron 1 of 7)	intron (NM_198081, intron 1 of 7)	33620	NM_198081	256380	Hs.486109	NM_198081	ENSG00000146285	SCML4	dJ47M23.1	Scm polycomb group protein like 4	protein-coding	0.022333	0.485149	
chunk0003_201_1	chr1	34850322	34850841	+	0	NA	3' UTR (NM_138428, exon 2 of 2)	3' UTR (NM_138428, exon 2 of 2)	8464	NM_001164824	113444	Hs.27160	NM_138428	ENSG00000163866	SMIM12	C1orf212	small integral membrane protein 12	protein-coding	0.011561	0.407692	
chunk0129_372_1	chr3	125513607	125514084	+	0	NA	intron (NM_003794, intron 1 of 13)	MLT1A0|LTR|ERVL-MaLR	6369	NR_073435	8723	Hs.507243	NM_003794	ENSG00000114520	SNX4	ATG24B	sorting nexin 4	protein-coding	0.010482	0.416318	
chunk0032_80_1	chr11	2805517	2805716	+	0	NA	intron (NM_181798, intron 15 of 15)	MER58A|DNA|hAT-Charlie	55953	NR_130721	338653	Hs.639425	NR_130721	ENSG00000229414	KCNQ1-AS1	-	KCNQ1 antisense RNA 1	ncRNA	0.040201	0.475000	
chunk0027_382_1	chr10	79570958	79571329	+	0	NA	Intergenic	L1PA6|LINE|L1	-10736	NM_001098668	729238	Hs.523084	NM_001098668	ENSG00000185303	SFTPA2	COLEC5|PSAP|PSP-A|PSPA|SFTP1|SFTPA2B|SP-2A|SP-A|SPA2|SPAII	surfactant protein A2	protein-coding	0.002695	0.502688	
chunk0067_377_1	chr15	48994385	48994637	+	0	NA	intron (NM_001193489, intron 17 of 17)	L2c|LINE|L2	-31067	NM_203349	399694	Hs.642615	NM_203349	ENSG00000185634	SHC4	RaLP|SHCD	SHC adaptor protein 4	protein-coding	0.007937	0.458498	
chunk0206_68_1	chr9	119853022	119853606	+	0	NA	Intergenic	L2a|LINE|L2	-81746	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.003425	0.425641	340(AGGAACAGGGTGAGCA,-,0.00)
chunk0154_400_1	chr5	88562755	88563206	+	0	NA	intron (NR_015436, intron 3 of 4)	L2c|LINE|L2	103959	NR_030741	407047		NR_030741	ENSG00000284447	MIR9-2	MIRN9-2|hsa-mir-9-2|miRNA9-2|mir-9-2	microRNA 9-2	ncRNA	0.004435	0.384956	
chunk0006_364_1	chr1	73065941	73066140	+	0	NA	Intergenic	Intergenic	-240130	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.015075	0.395000	
chunk0172_13_1	chr6	132813283	132813846	+	0	NA	Intergenic	L2b|LINE|L2	-1005	NM_001016	6206	Hs.546289	NM_001016	ENSG00000112306	RPS12	S12	ribosomal protein S12	protein-coding	0.044405	0.501773	
chunk0131_112_1	chr3	143951293	143951614	+	0	NA	Intergenic	Intergenic	-20345	NM_173552	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.372671	
chunk0109_19_1	chr20	395603	395873	+	0	NA	intron (NM_001301188, intron 3 of 3)	MIRb|SINE|MIR	-12327	NM_031229	10616	Hs.29546	NM_006462	ENSG00000125826	RBCK1	C20orf18|HOIL-1|HOIL1|PBMEI|PGBM1|RBCK2|RNF54|UBCE7IP3|XAP3|XAP4|ZRANB4	RANBP2-type and C3HC4-type zinc finger containing 1	protein-coding	0.014815	0.523985	
chunk0017_328_1	chr1	211496614	211496924	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-3852	NM_183059	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.009677	0.472669	
chunk0142_75_1	chr4	93870655	93871284	+	0	NA	Intergenic	Intergenic	42042	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.009539	0.352381	34(GAAACAACTTGTTCTT,+,0.00),333(GGGTACTGTATGTTCC,-,0.00),334(GGTACTGTATGTTCCT,+,0.00)
chunk0201_380_1	chr9	68863752	68864020	+	0	NA	exon (NM_001278253, exon 4 of 14)	exon (NM_001278253, exon 4 of 14)	83838	NM_138333	116224	Hs.655572	NM_138333	ENSG00000187866	FAM122A	C9orf42	family with sequence similarity 122A	protein-coding	0.003731	0.408922	158(CAGAACGAGATGTTCT,-,0.00),159(AGAACGAGATGTTCTT,+,0.00)
chunk0095_78_1	chr2	14630344	14630836	+	0	NA	Intergenic	Intergenic	-2096	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.010163	0.397566	
chunk0174_295_1	chr6	162641251	162641864	+	0	NA	intron (NM_013988, intron 1 of 8)	LTR37-int|LTR|ERV1	-85575	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.004894	0.332248	
chunk0031_129_1	chr10	124878465	124878673	+	0	NA	Intergenic	Intergenic	-63554	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.004808	0.555024	
chunk0017_209_1	chr1	207830785	207831056	+	0	NA	Intergenic	Intergenic	12541	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.022140	0.580882	154(GGGGACAGCCTGTGCT,-,0.00),155(GGGACAGCCTGTGCTG,+,0.00)
chunk0075_233_1	chr16	52937675	52938236	+	0	NA	Intergenic	L1MC1|LINE|L1	-117078	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.005348	0.366548	
chunk0155_415_1	chr5	99471119	99471574	+	0	NA	Intergenic	Intergenic	-62644	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.002198	0.298246	
chunk0040_286_1	chr11	116946269	116946861	+	0	NA	intron (NM_025164, intron 3 of 23)	LTR40b|LTR|ERVL	-108943	NM_000039	335	Hs.93194	NM_000039	ENSG00000118137	APOA1	apo(a)	apolipoprotein A1	protein-coding	0.010135	0.455312	
chunk0087_275_1	chr18	37773324	37773626	+	0	NA	Intergenic	Intergenic	116340	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.003311	0.297030	
chunk0060_72_1	chr14	41974907	41975349	+	0	NA	Intergenic	Intergenic	367567	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.002262	0.325056	
chunk0017_454_1	chr1	214425307	214425578	+	0	NA	intron (NM_005401, intron 3 of 18)	intron (NM_005401, intron 3 of 18)	126239	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.007380	0.375000	
chunk0196_347_1	chr8	114425109	114425647	+	0	NA	Intergenic	Intergenic	-988365	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.000000	0.332096	
chunk0136_199_1	chr4	6957030	6957683	+	0	NA	intron (NM_001113361, intron 2 of 13)	intron (NM_001113361, intron 2 of 13)	-29806	NM_001113363	57533	Hs.518611	NM_020773	ENSG00000132405	TBC1D14	-	TBC1 domain family member 14	protein-coding	0.019908	0.500000	322(TGGAACAGTGTGTGAC,-,0.00),323(GGAACAGTGTGTGACT,+,0.00)
chunk0043_78_1	chr12	14432350	14432719	+	0	NA	intron (NM_001286514, intron 2 of 14)	Tigger20a|DNA|TcMar-Tigger	47470	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.002710	0.275676	
chunk0150_24_1	chr5	30665732	30665968	+	0	NA	Intergenic	L2a|LINE|L2	-527805	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.008475	0.396624	
chunk0120_432_1	chr3	13413421	13414008	+	0	NA	intron (NM_024923, intron 1 of 39)	L1MB3|LINE|L1	6605	NM_024923	23225	Hs.475525	NM_024923	ENSG00000132182	NUP210	GP210|POM210	nucleoporin 210	protein-coding	0.011925	0.416667	295(GGGTACAGAGTGTCCA,-,0.00),296(GGTACAGAGTGTCCAT,+,0.00)
chunk0067_305_1	chr15	47841399	47841754	+	0	NA	intron (NR_120336, intron 2 of 4)	intron (NR_120336, intron 2 of 4)	4660	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.005634	0.390449	
chunk0171_352_1	chr6	130305594	130306078	+	0	NA	intron (NM_001258275, intron 2 of 13)	MLT1A0|LTR|ERVL-MaLR	59589	NM_001258275	154075	Hs.440508	NM_152552	ENSG00000164483	SAMD3	-	sterile alpha motif domain containing 3	protein-coding	0.000000	0.344330	
chunk0013_268_1	chr1	170221845	170222065	+	0	NA	Intergenic	MamGypsy2-LTR|LTR|Gypsy	62253	NR_026957	284688	Hs.135668	NR_026957	ENSG00000224286	LINC01142	-	long intergenic non-protein coding RNA 1142	ncRNA	0.004545	0.312217	
chunk0022_39_1	chr10	8012493	8013221	+	0	NA	intron (NM_031923, intron 5 of 6)	intron (NM_031923, intron 5 of 6)	39634	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.006868	0.419753	
chunk0020_99_1	chr1	232919846	232920266	+	0	NA	Intergenic	L1M5|LINE|L1	-30568	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.002381	0.394299	219(TAGGACATCCAGTGCC,-,0.00),220(AGGACATCCAGTGCCC,+,0.00)
chunk0132_273_1	chr3	159627504	159628011	+	0	NA	intron (NM_001197108, intron 1 of 6)	L1MEg|LINE|L1	140855	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.007890	0.407480	
chunk0087_207_1	chr18	35942627	35943086	+	0	NA	Intergenic	Intergenic	-8714	NR_037497	100500864		NR_037497	ENSG00000265641	MIR3929	-	microRNA 3929	ncRNA	0.017429	0.489130	
chunk0028_355_1	chr10	92485432	92485770	+	0	NA	intron (NM_001165946, intron 3 of 14)	intron (NM_001165946, intron 3 of 14)	12160	NM_001165946	3416	Hs.500546	NM_004969	ENSG00000119912	IDE	INSULYSIN	insulin degrading enzyme	protein-coding	0.005917	0.415929	
chunk0202_316_1	chr9	78241126	78241782	+	0	NA	intron (NM_032171, intron 3 of 14)	intron (NM_032171, intron 3 of 14)	5379	NM_001098802	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.003049	0.340944	
chunk0174_1_1	chr6	152013397	152013679	+	0	NA	intron (NM_001291230, intron 6 of 8)	L1MA5A|LINE|L1	205859	NM_000125	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.000000	0.325088	
chunk0186_21_1	chr7	135798003	135798551	+	0	NA	Intergenic	Intergenic	-49431	NM_205855	389558	Hs.55200	NM_205855	ENSG00000189320	FAM180A	UNQ1940	family with sequence similarity 180 member A	protein-coding	0.010949	0.426230	
chunk0155_113_1	chr5	92945169	92945488	+	0	NA	Intergenic	Intergenic	626015	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.009404	0.365625	
chunk0141_240_1	chr4	84996863	84997062	+	0	NA	intron (NR_015359, intron 2 of 3)	intron (NR_015359, intron 2 of 3)	30144	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.005025	0.340000	
chunk0148_448_1	chr4	190179072	190179271	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	5397	NM_001306068	100288687	Hs.728749	NM_001205218	ENSG00000260596	DUX4	DUX4L	double homeobox 4	protein-coding	0.000000	0.485000	
chunk0183_14_1	chr7	102992912	102993274	+	0	NA	intron (NM_145032, intron 6 of 19)	intron (NM_145032, intron 6 of 19)	19656	NM_001085386	58160	Hs.621233	NM_001085386	ENSG00000230257	NFE4	NF-E4	nuclear factor, erythroid 4	protein-coding	0.002762	0.388430	
chunk0103_138_1	chr2	162089264	162089709	+	0	NA	Intergenic	Intergenic	-14944	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.006742	0.475336	
chunk0208_209_1	chrX	18076671	18076997	+	0	NA	intron (NR_133641, intron 1 of 4)	intron (NR_133641, intron 1 of 4)	27810	NR_133641	105373144		NR_133641	ENSG00000225882	LINC01456	-	long intergenic non-protein coding RNA 1456	ncRNA	0.012270	0.452599	
chunk0176_26_1	chr7	9322250	9322879	+	0	NA	Intergenic	MER54A|LTR|ERVL	-311706	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.014308	0.398413	
chunk0014_290_1	chr1	180633942	180634174	+	0	NA	intron (NM_001135669, intron 1 of 13)	intron (NM_001135669, intron 1 of 13)	2048	NM_001135669	9213	Hs.227656	NM_004736	ENSG00000143324	XPR1	IBGC6|SLC53A1|SYG1|X3	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.008621	0.381974	
chunk0208_454_1	chrX	33466762	33466990	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-127267	NM_000109	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.004386	0.414847	
chunk0109_441_1	chr2	241498657	241499138	+	0	NA	intron (NM_001282308, intron 6 of 10)	intron (NM_001282308, intron 6 of 10)	9463	NM_001271978	10494	Hs.516807	NM_006374	ENSG00000115694	STK25	SOK1|YSK1	serine/threonine kinase 25	protein-coding	0.047817	0.639004	
chunk0034_368_1	chr11	36141198	36141565	+	0	NA	intron (NM_174902, intron 4 of 5)	intron (NM_174902, intron 4 of 5)	131283	NR_039769	100616311		NR_039769	ENSG00000263389	MIR3973	-	microRNA 3973	ncRNA	0.016349	0.442935	
chunk0131_331_1	chr3	151154407	151155231	+	0	NA	intron (NM_053002, intron 4 of 42)	intron (NM_053002, intron 4 of 42)	48382	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.010922	0.328485	
chunk0051_251_1	chr12	117190214	117190413	+	0	NA	exon (NM_015002, exon 1 of 12)	exon (NM_015002, exon 1 of 12)	182	NM_015002	23014	Hs.740376	NM_015002	ENSG00000135108	FBXO21	FBX21	F-box protein 21	protein-coding	0.105528	0.705000	112(CAGCACAGGATGTACT,-,0.00),113(AGCACAGGATGTACTC,+,0.00)
chunk0041_319_1	chr11	130114094	130114324	+	0	NA	intron (NM_001142278, intron 3 of 12)	L1MC4|LINE|L1	43641	NM_001243299	334	Hs.370247	NM_001642	ENSG00000084234	APLP2	APLP-2|APPH|APPL2|CDEBP	amyloid beta precursor like protein 2	protein-coding	0.013043	0.363636	
chunk0021_336_1	chr1	245929691	245929969	+	0	NA	intron (NM_001167740, intron 6 of 11)	intron (NM_001167740, intron 6 of 11)	487582	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003597	0.405018	
chunk0033_390_1	chr11	24354807	24355049	+	0	NA	Intergenic	L1PBb|LINE|L1	-142042	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.008264	0.423868	
chunk0010_101_1	chr1	114033882	114034468	+	0	NA	Intergenic	MER41C|LTR|ERV1	54784	NM_001286352	56944	Hs.9315	NM_020190	ENSG00000116774	OLFML3	HNOEL-iso|OLF44	olfactomedin like 3	protein-coding	0.006826	0.403748	
chunk0163_16_1	chr6	7954697	7954896	+	0	NA	intron (NR_037616, intron 4 of 12)	LTR89|LTR|ERVL?	-31306	NR_027712	206426	Hs.676966	NR_027712		PIP5K1P1	-	phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1	pseudo	0.000000	0.320000	
chunk0141_322_1	chr4	87275245	87275798	+	0	NA	Intergenic	Intergenic	25062	NR_049891	100847027		NR_049891	ENSG00000263981	MIR5705	-	microRNA 5705	ncRNA	0.003617	0.382671	
chunk0196_265_1	chr8	108845730	108846258	+	0	NA	Intergenic	Intergenic	-58453	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.003788	0.334594	
chunk0027_440_1	chr10	81079458	81079657	+	0	NA	Intergenic	L1PA15|LINE|L1	538738	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.000000	0.340000	
chunk0189_425_1	chr8	27954756	27954955	+	0	NA	intron (NM_173833, intron 3 of 8)	intron (NM_173833, intron 3 of 8)	37997	NM_173833	286133	Hs.591833	NM_173833	ENSG00000168079	SCARA5	NET33|Tesr	scavenger receptor class A member 5	protein-coding	0.010050	0.455000	
chunk0107_181_1	chr2	215794505	215795063	+	0	NA	intron (NR_037195, intron 1 of 9)	intron (NR_037195, intron 1 of 9)	48752	NR_037195	646324	Hs.655713	NR_037195	ENSG00000235770	LINC00607	-	long intergenic non-protein coding RNA 607	ncRNA	0.007168	0.416816	
chunk0011_68_1	chr1	143735674	143736069	+	0	NA	Intergenic	Intergenic	-6301	NR_004408	26869		NR_004408	ENSG00000207513	RNU1-3	HSD4|RNU1G3	RNA, U1 small nuclear 3	snRNA	0.035443	0.487374	320(AAGCACTACCAGTTCT,-,0.00)
chunk0211_364_1	chrX	125866350	125867239	+	0	NA	Intergenic	L1PA16|LINE|L1	-242968	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.005624	0.355056	
chunk0025_352_1	chr10	58348282	58349050	+	0	NA	intron (NM_001204880, intron 1 of 5)	intron (NM_001204880, intron 1 of 5)	13687	NM_003338	7321	Hs.129683	NM_003338	ENSG00000072401	UBE2D1	E2(17)KB1|SFT|UBC4/5|UBCH5|UBCH5A	ubiquitin conjugating enzyme E2 D1	protein-coding	0.003906	0.369311	
chunk0058_289_1	chr14	26811469	26812073	+	0	NA	intron (NR_110557, intron 1 of 4)	intron (NR_110557, intron 1 of 4)	2423	NR_110556	102724890	Hs.569381	NR_110556	ENSG00000257185	LINC02293	-	long intergenic non-protein coding RNA 2293	ncRNA	0.000000	0.327273	
chunk0187_243_1	chr7	152900659	152901015	+	0	NA	Intergenic	Intergenic	141088	NR_073001									0.025281	0.523810	
chunk0169_34_1	chr6	97288142	97288710	+	0	NA	Intergenic	Intergenic	-5250	NM_198468	253714	Hs.444292	NM_198468	ENSG00000146263	MMS22L	C6orf167|dJ39B17.2	MMS22 like, DNA repair protein	protein-coding	0.000000	0.339192	
chunk0135_44_1	chr3	185499002	185499226	+	0	NA	promoter-TSS (NM_080652)	promoter-TSS (NM_080652)	-57	NM_080652	90407	Hs.677570	NM_080652	ENSG00000163900	TMEM41A	2900010K02Rik	transmembrane protein 41A	protein-coding	0.089286	0.680000	
chunk0008_287_1	chr1	94873201	94873429	+	0	NA	intron (NM_001258342, intron 11 of 13)	intron (NM_001258342, intron 11 of 13)	52493	NM_001286056	1266	Hs.483454	NM_001839	ENSG00000117519	CNN3	-	calponin 3	protein-coding	0.013158	0.471616	
chunk0003_350_1	chr1	39116768	39117594	+	0	NA	intron (NM_012090, intron 1 of 92)	intron (NM_012090, intron 1 of 92)	33014	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.003632	0.434099	
chunk0097_75_1	chr2	44455862	44456452	+	0	NA	intron (NM_024766, intron 3 of 10)	intron (NM_024766, intron 3 of 10)	94253	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.003390	0.306261	
chunk0096_303_1	chr2	32742288	32742559	+	0	NA	intron (NM_017735, intron 12 of 19)	intron (NM_017735, intron 12 of 19)	-83020	NR_027098	285045	Hs.434660	NR_027097	ENSG00000230876	LINC00486	-	long intergenic non-protein coding RNA 486	ncRNA	0.000000	0.341912	
chunk0101_316_1	chr2	135536255	135536532	+	0	NA	intron (NM_001282799, intron 1 of 22)	AluJo|SINE|Alu	4938	NM_015361	23518	Hs.412462	NM_015361	ENSG00000048991	R3HDM1	R3HDM	R3H domain containing 1	protein-coding	0.007220	0.424460	
chunk0034_431_1	chr11	38785734	38786014	+	0	NA	Intergenic	L1M1|LINE|L1	137016	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.014286	0.451957	113(CAGTACATACTGTTCT,-,0.00),114(AGTACATACTGTTCTC,+,0.00)
chunk0082_157_1	chr17	55631089	55631783	+	0	NA	Intergenic	L1MB7|LINE|L1	91428	NM_018286	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.004323	0.297842	
chunk0127_170_1	chr3	95012492	95012779	+	0	NA	Intergenic	Intergenic	74372	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.270833	
chunk0106_159_1	chr2	200665703	200666470	+	0	NA	intron (NM_001159, intron 31 of 34)	intron (NM_001159, intron 31 of 34)	-29637	NR_001557									0.001304	0.371094	
chunk0113_189_1	chr20	53332588	53333100	+	0	NA	intron (NM_001193421, intron 2 of 2)	L3|LINE|CR1	147561	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.009766	0.467836	256(TTGTACAGACTGTTCC,-,0.00),257(TGTACAGACTGTTCCT,+,0.00)
chunk0102_442_1	chr2	157931576	157931964	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-55908	NM_001111067	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.002577	0.347044	
chunk0138_260_1	chr4	40114911	40115238	+	0	NA	intron (NM_018177, intron 7 of 17)	L1MEd|LINE|L1	-57875	NR_027277	344967	Hs.534633	NR_027277	ENSG00000205794	LOC344967	-	acyl-CoA thioesterase 7 pseudogene	pseudo	0.003058	0.317073	
chunk0080_398_1	chr17	35159388	35159627	+	0	NA	exon (NM_001033576, exon 8 of 20)	exon (NM_001033576, exon 8 of 20)	11243	NM_001308281	146862	Hs.379636	NM_173167	ENSG00000141161	UNC45B	CMYA4|CTRCT43|SMUNC45|UNC-45B|UNC45	unc-45 myosin chaperone B	protein-coding	0.008368	0.520833	
chunk0086_194_1	chr18	22170455	22170654	+	0	NA	intron (NM_005257, intron 1 of 6)	CpG-12421	1117	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.085427	0.630000	
chunk0144_419_1	chr4	140557820	140558414	+	0	NA	Intergenic	MER49|LTR|ERV1	10688	NM_021833	7350	Hs.249211	NM_021833	ENSG00000109424	UCP1	SLC25A7|UCP	uncoupling protein 1	protein-coding	0.006734	0.423529	
chunk0179_31_1	chr7	43107405	43108054	+	0	NA	Intergenic	L2c|LINE|L2	-4870	NM_001287059	23072	Hs.164453	NM_015052	ENSG00000002746	HECW1	NEDL1	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.009245	0.360000	198(AAGTACATTCTGTTCT,-,0.00),199(AGTACATTCTGTTCTT,+,0.00)
chunk0044_422_1	chr12	42011930	42012595	+	0	NA	Intergenic	Intergenic	132609	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.007519	0.436937	
chunk0047_135_1	chr12	69553795	69554346	+	0	NA	intron (NM_006654, intron 4 of 9)	AmnSINE1|SINE|5S-Deu-L2	-30653	NR_037476	100500868		NR_037476	ENSG00000283677	MIR3913-2	mir-3913-2	microRNA 3913-2	ncRNA	0.001815	0.384058	294(TGGCCACTGTGTTCTT,+,0.00)
chunk0152_194_1	chr5	59908477	59908792	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-14840	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.003175	0.341772	
chunk0124_436_1	chr3	61254794	61255241	+	0	NA	Intergenic	Intergenic	-3558	NM_001166243	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.006711	0.370536	
chunk0100_429_1	chr2	120245465	120245748	+	0	NA	Intergenic	Intergenic	-7232	NM_002881	5899	Hs.469820	NM_002881	ENSG00000144118	RALB	-	RAS like proto-oncogene B	protein-coding	0.021201	0.644366	
chunk0137_457_1	chr4	29630318	29630810	+	0	NA	Intergenic	Intergenic	810982	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.002033	0.338742	
chunk0026_248_1	chr10	66414788	66415056	+	0	NA	intron (NM_001127384, intron 11 of 17)	L1MA4A|LINE|L1	-511112	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.000000	0.572491	
chunk0175_336_1	chr6	167226162	167226361	+	0	NA	Intergenic	Intergenic	55668	NM_001145121	401285		NM_001013683	ENSG00000166984	TCP10L2	-	t-complex 10 like 2	protein-coding	0.020101	0.415000	
chunk0042_427_1	chr12	12070700	12071326	+	0	NA	promoter-TSS (NM_138723)	promoter-TSS (NM_138723)	69	NM_138723	79370	Hs.210343	NM_030766	ENSG00000121380	BCL2L14	BCLG	BCL2 like 14	protein-coding	0.009585	0.438596	
chunk0129_378_1	chr3	126021492	126022090	+	0	NA	intron (NM_001008485, intron 6 of 11)	LTR23|LTR|ERV1	34984	NM_001008487	54946	Hs.573007	NM_017836	ENSG00000114544	SLC41A3	SLC41A1-L2	solute carrier family 41 member 3	protein-coding	0.005017	0.432387	358(AGGAAGAGGCTGTTCC,-,0.00),359(GGAAGAGGCTGTTCCT,+,0.00)
chunk0154_449_1	chr5	90528378	90528577	+	0	NA	intron (NM_198273, intron 1 of 2)	intron (NM_198273, intron 1 of 2)	1107	NM_198273	116068	Hs.136235	NM_198273	ENSG00000176018	LYSMD3	-	LysM domain containing 3	protein-coding	0.010050	0.375000	
chunk0186_383_1	chr7	144390266	144391081	+	0	NA	Intergenic	L2c|LINE|L2	19554	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.011043	0.439951	426(CAGTACTGTCTGTGCC,-,0.00),427(AGTACTGTCTGTGCCT,+,0.00),527(AAGAACAGTATGAACT,-,0.00),528(AGAACAGTATGAACTA,+,0.00)
chunk0096_316_1	chr2	33190400	33190817	+	0	NA	intron (NM_000627, intron 3 of 29)	MIRc|SINE|MIR	56011	NM_001166266	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.007194	0.411483	
chunk0130_263_1	chr3	136141739	136141949	+	0	NA	intron (NM_001190447, intron 12 of 12)	L2b|LINE|L2	52624	NM_001145417	55167	Hs.18631	NM_018133	ENSG00000174579	MSL2	MSL-2|MSL2L1|RNF184	MSL complex subunit 2	protein-coding	0.004762	0.469194	
chunk0081_3_1	chr17	37107458	37107933	+	0	NA	intron (NM_198836, intron 52 of 55).2	intron (NM_198836, intron 52 of 55).2	73950	NR_036056	100422969		NR_036056	ENSG00000276326	MIR2909	-	microRNA 2909	ncRNA	0.012632	0.573529	
chunk0103_311_1	chr2	167351499	167351795	+	0	NA	Intergenic	Intergenic	164364	NM_001199145	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.003378	0.329966	
chunk0101_303_1	chr2	135005274	135005827	+	0	NA	intron (NM_001018044, intron 2 of 7)	intron (NM_001018044, intron 2 of 7)	19128	NM_001018044	80122	Hs.659395	NM_025052	ENSG00000176601	MAP3K19	RCK|YSK4	mitogen-activated protein kinase kinase kinase 19	protein-coding	0.005425	0.395307	
chunk0159_66_1	chr5	137311327	137311852	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	187740	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.003810	0.325095	
chunk0160_457_1	chr5	165125951	165126475	+	0	NA	Intergenic	L2c|LINE|L2	655934	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.009542	0.371429	266(GGGTACAGAATGTTCC,-,0.00),267(GGTACAGAATGTTCCT,+,0.00)
chunk0052_383_1	chr12	129550353	129551048	+	0	NA	intron (NM_133448, intron 2 of 8)	intron (NM_133448, intron 2 of 8)	342099	NR_110058	101927735	Hs.569212	NR_110058	ENSG00000256699	TMEM132D-AS2	-	TMEM132D antisense RNA 2	ncRNA	0.004317	0.471264	349(AGGGACAGCTTGTACC,-,0.00),350(GGGACAGCTTGTACCT,+,0.00)
chunk0084_152_1	chr17	76660741	76661459	+	0	NA	Intergenic	L1MC4|LINE|L1	-10828	NR_130916	105274304	Hs.572495	NR_130916	ENSG00000261335	LOC105274304	-	uncharacterized LOC105274304	ncRNA	0.012535	0.374131	
chunk0193_65_1	chr8	73012909	73013187	+	0	NA	intron (NM_017489, intron 1 of 9)	intron (NM_017489, intron 1 of 9)	4186	NM_003218	7013	Hs.442707	NM_003218	ENSG00000147601	TERF1	PIN2|TRBF1|TRF|TRF1|hTRF1-AS|t-TRF1	telomeric repeat binding factor 1	protein-coding	0.003597	0.322581	
chunk0178_8_1	chr7	29045592	29046177	+	0	NA	intron (NM_019029, intron 11 of 12)	intron (NM_019029, intron 11 of 12)	65917	NR_038965	100506497	Hs.586328	NR_038965	ENSG00000272568	LOC100506497	-	uncharacterized LOC100506497	ncRNA	0.006838	0.361775	
chunk0143_257_1	chr4	115796153	115796362	+	0	NA	Intergenic	Intergenic	-503468	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.004785	0.266667	
chunk0040_194_1	chr11	114121712	114122617	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	61598	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.008840	0.423841	218(AGGTACTGGCTGTCCT,-,0.00),219(GGTACTGGCTGTCCTC,+,0.00)
chunk0046_398_1	chr12	63998687	63998978	+	0	NA	intron (NM_020762, intron 3 of 21)	intron (NM_020762, intron 3 of 21)	154071	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.000000	0.383562	
chunk0008_90_1	chr1	90883168	90883646	+	0	NA	Intergenic	MLT1G1-int|LTR|ERVL-MaLR	138101	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.002092	0.390397	
chunk0073_17_1	chr16	2212536	2212812	+	0	NA	3' UTR (NM_001042371, exon 2 of 2)	3' UTR (NM_001042371, exon 2 of 2)	-1606	NM_182563	283870	Hs.647399	NM_182563	ENSG00000182685	BRICD5	C16orf79	BRICHOS domain containing 5	protein-coding	0.021739	0.599278	113(AAGGACTTCCTGTTCT,-,0.00),114(AGGACTTCCTGTTCTT,+,0.00)
chunk0138_79_1	chr4	35253350	35253766	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-990558	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004808	0.407674	
chunk0165_299_1	chr6	36678384	36678600	+	0	NA	promoter-TSS (NM_001220778)	promoter-TSS (NM_001220778)	-187	NM_000389	1026	Hs.370771	NM_000389	ENSG00000124762	CDKN1A	CAP20|CDKN1|CIP1|MDA-6|P21|SDI1|WAF1|p21CIP1	cyclin dependent kinase inhibitor 1A	protein-coding	0.050926	0.635945	
chunk0117_319_1	chr22	24894356	24894932	+	0	NA	intron (NM_001039948, intron 18 of 25)	MLT1H|LTR|ERVL-MaLR	44703	NM_001001663	255349	Hs.329040	NM_001001663	ENSG00000206069	TMEM211	bA9F11.1	transmembrane protein 211	protein-coding	0.019097	0.457539	
chunk0173_227_1	chr6	146186319	146186781	+	0	NA	intron (NM_001278064, intron 2 of 7)	MLT1I-int|LTR|ERVL-MaLR	157352	NM_001278067	2911	Hs.32945	NM_000838	ENSG00000152822	GRM1	GPRC1A|MGLU1|MGLUR1|PPP1R85|SCA44|SCAR13	glutamate metabotropic receptor 1	protein-coding	0.002165	0.347732	
chunk0066_88_1	chr15	29734162	29734490	+	0	NA	exon (NM_001301025, exon 13 of 29).2	exon (NM_001301025, exon 13 of 29).2	87222	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.009146	0.343465	
chunk0110_232_1	chr20	16188544	16188743	+	0	NA	Intergenic	Intergenic	-202761	NR_130924	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.000000	0.485000	
chunk0131_118_1	chr3	144104513	144105159	+	0	NA	Intergenic	Intergenic	131511	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.003096	0.329212	
chunk0093_175_1	chr19	48531848	48532093	+	0	NA	Intergenic	LTR24|LTR|ERV1	-18781	NM_001080434	114783	Hs.207426	NM_001080434	ENSG00000142235	LMTK3	LMR3|PPP1R101|TYKLM3	lemur tyrosine kinase 3	protein-coding	0.012245	0.378049	191(CAGTACACAACGTTCT,-,0.00),192(AGTACACAACGTTCTG,+,0.00)
chunk0066_27_1	chr15	27545495	27546041	+	0	NA	Intergenic	Intergenic	-384449	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.010989	0.442413	
chunk0123_50_1	chr3	41126678	41126877	+	0	NA	Intergenic	Intergenic	-72674	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.015075	0.500000	
chunk0017_322_1	chr1	211433364	211433632	+	0	NA	TTS (NR_026761)	TTS (NR_026761)	50743	NR_026761	84791	Hs.523932	NM_032705		LINC00467	C1orf97	long intergenic non-protein coding RNA 467	ncRNA	0.011194	0.368030	
chunk0072_457_1	chr15	101857499	101857872	+	0	NA	Intergenic	MER101-int|LTR|ERV1	15566	NR_046417	390651	Hs.578689	NR_046417	ENSG00000214344	OR4F13P	GPCRLTM7	olfactory receptor family 4 subfamily F member 13 pseudogene	pseudo	0.002681	0.363636	
chunk0027_388_1	chr10	79890471	79890856	+	0	NA	Intergenic	Intergenic	-14235	NR_033857	100288974	Hs.733579	NR_033857		BMS1P21	-	BMS1 pseudogene 21	pseudo	0.000000	0.305699	241(AAGTACATAGTGTTTC,-,0.00),242(AGTACATAGTGTTTCC,+,0.00)
chunk0144_169_1	chr4	132653075	132653599	+	0	NA	intron (NR_126401, intron 2 of 3)	L1MA4A|LINE|L1	62248	NR_126401	104355285	Hs.123483	NR_126401	ENSG00000251398	LINC01256	TCONS_l2_00021715	long intergenic non-protein coding RNA 1256	ncRNA	0.003817	0.333333	
chunk0088_374_1	chr18	54194736	54195112	+	0	NA	intron (NM_003927, intron 2 of 6)	intron (NM_003927, intron 2 of 6)	27488	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.005319	0.334218	149(AAGAACTGACTGTGCC,-,0.00),150(AGAACTGACTGTGCCT,+,0.00)
chunk0075_390_1	chr16	56780084	56780636	+	0	NA	intron (NM_014669, intron 3 of 21)	intron (NM_014669, intron 3 of 21)	-1432	NM_001242795	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.003623	0.349005	
chunk0171_284_1	chr6	128104454	128104854	+	0	NA	intron (NM_001291981, intron 7 of 32).2	intron (NM_001291981, intron 7 of 32).2	76789	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.020000	0.359102	
chunk0197_287_1	chr8	124201416	124202097	+	0	NA	intron (NR_125420, intron 2 of 2)	intron (NR_125420, intron 2 of 2)	-30234	NR_103547	157376	Hs.662360	NM_182525	ENSG00000253868	FER1L6-AS2	C8orf78	FER1L6 antisense RNA 2	ncRNA	0.014684	0.492669	371(AAGCACACAGCGTTCC,-,0.00),372(AGCACACAGCGTTCCA,+,0.00)
chunk0147_68_1	chr4	172828997	172829196	+	0	NA	intron (NM_001034845, intron 7 of 12)	MLT1C|LTR|ERVL-MaLR	-102218	NR_125894	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.025126	0.495000	
chunk0184_293_1	chr7	119100911	119101147	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	806346	NR_131960	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.008475	0.421941	
chunk0202_303_1	chr9	77944976	77945301	+	0	NA	intron (NM_002072, intron 1 of 6)	Tigger19b|DNA|TcMar-Tigger	86311	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.009231	0.392638	
chunk0155_106_1	chr5	92740252	92740451	+	0	NA	Intergenic	Intergenic	830992	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.350000	
chunk0108_75_1	chr2	227535074	227535429	+	0	NA	intron (NM_001135189, intron 7 of 11)	intron (NM_001135189, intron 7 of 11)	63079	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.005634	0.266854	
chunk0004_166_1	chr1	45644023	45644260	+	0	NA	intron (NM_021639, intron 6 of 12)	intron (NM_021639, intron 6 of 12)	2544	NR_026768	728963	Hs.675157	NR_026768		RPS15AP10	RPS15A_4_42	ribosomal protein S15a pseudogene 10	pseudo	0.000000	0.445378	
chunk0051_349_1	chr12	120446256	120446543	+	0	NA	promoter-TSS (NM_016399)	promoter-TSS (NM_016399)	13	NM_016399	51499	Hs.69499	NM_016399	ENSG00000170855	TRIAP1	HSPC132|MDM35|P53CSV|WF-1	TP53 regulated inhibitor of apoptosis 1	protein-coding	0.111498	0.663194	
chunk0184_4_1	chr7	111613535	111614577	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-51539	NM_001244606	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.005758	0.348993	651(AAGAACAGTTTGTTAT,-,0.00)
chunk0004_177_1	chr1	45972688	45973088	+	0	NA	intron (NM_015112, intron 5 of 28)	L2|LINE|L2	159820	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.002500	0.384040	
chunk0065_337_1	chr14	103404235	103405341	+	0	NA	intron (NM_001128921, intron 1 of 15)	intron (NM_001128921, intron 1 of 15)	19424	NM_002376	4140	Hs.35828	NM_002376	ENSG00000075413	MARK3	CTAK1|KP78|PAR1A|Par-1a|VIPB	microtubule affinity regulating kinase 3	protein-coding	0.013562	0.406504	790(AAGTACTCTGTGTTCT,-,0.00),791(AGTACTCTGTGTTCTC,+,0.00)
chunk0061_221_1	chr14	60572976	60573294	+	0	NA	Intergenic	Intergenic	63915	NM_007374	4990	Hs.194756	NM_007374	ENSG00000184302	SIX6	MCOPCT2|ODRMD|OPTX2|Six9	SIX homeobox 6	protein-coding	0.006289	0.485893	
chunk0138_379_1	chr4	42573584	42574131	+	0	NA	intron (NM_006095, intron 14 of 36)	intron (NM_006095, intron 14 of 36)	83248	NM_001105529	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.005484	0.348540	
chunk0098_181_1	chr2	71340214	71340700	+	0	NA	intron (NM_014497, intron 1 of 27)	intron (NM_014497, intron 1 of 27)	8702	NM_001252612	27332	Hs.434401	NM_014497	ENSG00000075292	ZNF638	NP220|ZFML|Zfp638	zinc finger protein 638	protein-coding	0.006173	0.373717	
chunk0039_437_1	chr11	108034205	108034651	+	0	NA	intron (NM_003478, intron 2 of 18)	MER68|LTR|ERVL	25746	NM_003478	8065	Hs.440320	NM_003478	ENSG00000166266	CUL5	CUL-5|VACM-1|VACM1	cullin 5	protein-coding	0.002242	0.436242	
chunk0016_448_1	chr1	204132100	204132339	+	0	NA	exon (NM_001297762, exon 7 of 7)	exon (NM_001297762, exon 7 of 7)	-9189	NR_123739	101929441	Hs.736889	NR_123739	ENSG00000230550	ERLNC1	ElncRNA1|TC0101441	estrogen receptor responsive lncRNA 1	ncRNA	0.012552	0.562500	
chunk0118_156_1	chr22	30310489	30310770	+	0	NA	intron (NM_001204240, intron 1 of 8)	MIRb|SINE|MIR	16337	NM_031937	83874	Hs.655273	NM_031937	ENSG00000099992	TBC1D10A	EPI64|TBC1D10|dJ130H16.1|dJ130H16.2	TBC1 domain family member 10A	protein-coding	0.010676	0.471631	
chunk0087_98_1	chr18	32418127	32418655	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	52093	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.009470	0.402647	
chunk0178_401_1	chr7	40909289	40909488	+	0	NA	Intergenic	Intergenic	70551	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.030151	0.520000	
chunk0014_76_1	chr1	176379600	176380016	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-83363	NM_020318	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.009615	0.422062	
chunk0163_41_1	chr6	8510848	8511457	+	0	NA	intron (NR_038979, intron 2 of 3)	Tigger3a|DNA|TcMar-Tigger	75529	NR_038979	100506207	Hs.311049	NR_038979	ENSG00000285219	LOC100506207	-	uncharacterized LOC100506207	ncRNA	0.006568	0.386885	357(AGGAACATCTTGGTCC,-,0.00)
chunk0001_265_1	chr1	8510543	8510807	+	0	NA	intron (NM_001042681, intron 7 of 22)	intron (NM_001042681, intron 7 of 22)	-15762	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.007576	0.396226	
chunk0179_125_1	chr7	45691074	45691913	+	0	NA	intron (NM_021116, intron 14 of 19)	intron (NM_021116, intron 14 of 19)	77525	NR_024271	641977	Hs.723477	NR_024271	ENSG00000214765	SEPTIN7P2	SEPT13|SEPT7B|SEPT7P2	septin 7 pseudogene 2	pseudo	0.009535	0.423810	
chunk0030_305_1	chr10	117631823	117632063	+	0	NA	Intergenic	Intergenic	-86875	NR_002791	196047	Hs.312592	NR_002791	ENSG00000229847	EMX2OS	EMX2-AS1|NCRNA00045	EMX2 opposite strand/antisense RNA	ncRNA	0.012500	0.609959	
chunk0189_97_1	chr8	21768870	21769539	+	0	NA	intron (NM_001165039, intron 1 of 6)	intron (NM_001165039, intron 1 of 6)	19630	NM_001165038	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.017937	0.555224	
chunk0203_35_1	chr9	83003619	83004491	+	0	NA	intron (NM_152573, intron 9 of 16)	intron (NM_152573, intron 9 of 16)	59073	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.004587	0.316151	
chunk0193_445_1	chr8	81111490	81111689	+	0	NA	intron (NM_018440, intron 1 of 8)	intron (NM_018440, intron 1 of 8)	479	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.075377	0.620000	
chunk0179_283_1	chr7	49601656	49602059	+	0	NA	Intergenic	L1MC3|LINE|L1	-171804	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.002481	0.339109	
chunk0158_418_1	chr5	135080113	135080360	+	0	NA	intron (NM_001277348, intron 2 of 5)	intron (NM_001277348, intron 2 of 5)	-40189	NR_105050	101927953	Hs.436898	NR_105049	ENSG00000249082	C5orf66-AS1	Epist	C5orf66 antisense RNA 1	ncRNA	0.004049	0.322581	
chunk0145_143_1	chr4	146975905	146976586	+	0	NA	Intergenic	Intergenic	-30363	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.001468	0.372434	
chunk0151_210_1	chr5	50790217	50790847	+	0	NA	intron (NM_024615, intron 10 of 25)	intron (NM_024615, intron 10 of 25)	123594	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.003175	0.348653	
chunk0111_135_1	chr20	24694753	24695308	+	0	NA	Intergenic	Intergenic	225831	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.019820	0.525180	238(AGTCCATGCTGTCCCT,+,0.00)
chunk0025_284_1	chr10	56419012	56419475	+	0	NA	Intergenic	Intergenic	-57970	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.006479	0.338362	
chunk0121_390_1	chr3	25268967	25269166	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	-71736	NM_001290300	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.290000	
chunk0049_67_1	chr12	90170058	90170497	+	0	NA	Intergenic	Intergenic	461322	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.000000	0.379545	
chunk0099_266_1	chr2	98084761	98085274	+	0	NA	Intergenic	Intergenic	-2115	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.007797	0.468872	
chunk0199_257_1	chr9	6029195	6029763	+	0	NA	Intergenic	L1MC5a|LINE|L1	-13839	NM_001243202	26953	Hs.167496	NM_012416	ENSG00000137040	RANBP6	-	RAN binding protein 6	protein-coding	0.010563	0.360281	
chunk0153_276_1	chr5	72939882	72940635	+	0	NA	Intergenic	L1M7|LINE|L1	-15723	NM_001146032	115548	Hs.165762	NM_138782	ENSG00000157107	FCHO2	-	FCH domain only 2	protein-coding	0.009296	0.375332	
chunk0147_223_1	chr4	181590824	181591294	+	0	NA	Intergenic	Charlie24|DNA|hAT-Charlie	-431910	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.000000	0.316348	
chunk0075_386_1	chr16	56747587	56748564	+	0	NA	intron (NM_014669, intron 1 of 21)	intron (NM_014669, intron 1 of 21)	17970	NM_014669	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.012282	0.462168	
chunk0091_449_1	chr19	17475763	17476133	+	0	NA	intron (NM_198580, intron 1 of 11)	intron (NM_198580, intron 1 of 11)	5504	NM_198580	376497	Hs.363138	NM_198580	ENSG00000130304	SLC27A1	ACSVL5|FATP|FATP-1|FATP1	solute carrier family 27 member 1	protein-coding	0.018919	0.571429	
chunk0040_333_1	chr11	118315060	118315347	+	0	NA	intron (NM_000733, intron 8 of 8)	intron (NM_000733, intron 8 of 8)	10623	NM_000733	916	Hs.3003	NM_000733	ENSG00000198851	CD3E	IMD18|T3E|TCRE	CD3e molecule	protein-coding	0.013937	0.427083	
chunk0121_20_1	chr3	14826001	14826533	+	0	NA	intron (NM_152536, intron 1 of 19)	intron (NM_152536, intron 1 of 19)	7305	NM_152536	152273	Hs.412406	NM_152536	ENSG00000154783	FGD5	ZFYVE23	FYVE, RhoGEF and PH domain containing 5	protein-coding	0.007519	0.455910	396(GAGGACACCGTGGCCC,-,0.00),397(AGGACACCGTGGCCCG,+,0.00)
chunk0095_84_1	chr2	15023087	15023720	+	0	NA	Intergenic	L1ME3G|LINE|L1	388312	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.001580	0.299685	
chunk0170_117_1	chr6	110665429	110666040	+	0	NA	intron (NM_015076, intron 4 of 12)	intron (NM_015076, intron 4 of 12)	-148887	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.011457	0.423203	
chunk0180_167_1	chr7	65213370	65213599	+	0	NA	Intergenic	L2c|LINE|L2	-160315	NM_001287534	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.004367	0.452174	
chunk0180_176_1	chr7	65489475	65489986	+	0	NA	Intergenic	AluYj4|SINE|Alu	115931	NM_152626	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.013699	0.472656	
chunk0195_363_1	chr8	99876340	99876665	+	0	NA	3' UTR (NM_017890, exon 62 of 62)	3' UTR (NM_017890, exon 62 of 62)	17512	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.000000	0.343558	
chunk0103_269_1	chr2	165633103	165633392	+	0	NA	intron (NM_001172173, intron 4 of 6)	intron (NM_001172173, intron 4 of 6)	60911	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.013841	0.334483	
chunk0158_239_1	chr5	129110481	129110745	+	0	NA	intron (NM_016048, intron 4 of 4)	intron (NM_016048, intron 4 of 4)	12925	NR_039776	100616175		NR_039776	ENSG00000264563	MIR4633	-	microRNA 4633	ncRNA	0.003788	0.467925	
chunk0021_423_1	chr1	247078583	247078782	+	0	NA	non-coding (NR_037894, exon 1 of 7)	non-coding (NR_037894, exon 1 of 7)	131	NM_033213	93474	Hs.732305	NM_033213	ENSG00000277462	ZNF670	-	zinc finger protein 670	protein-coding	0.065327	0.645000	
chunk0049_175_1	chr12	92337418	92337648	+	0	NA	Intergenic	Intergenic	-83998	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.013043	0.428571	
chunk0111_63_1	chr20	22942769	22943050	+	0	NA	Intergenic	L1MC4|LINE|L1	-92511	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.003559	0.400709	
chunk0007_131_1	chr1	79190280	79190573	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-183616	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.010239	0.445578	
chunk0018_167_1	chr1	218931350	218931922	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	242152	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.006993	0.335079	
chunk0198_318_1	chr8	139763457	139763762	+	0	NA	intron (NM_001160372, intron 21 of 22)	L2a|LINE|L2	-60553	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.036066	0.529412	
chunk0177_253_1	chr7	25194214	25194514	+	0	NA	Intergenic	L2c|LINE|L2	-14166	NM_138811	136895	Hs.122055	NM_138811	ENSG00000153790	C7orf31	-	chromosome 7 open reading frame 31	protein-coding	0.010000	0.518272	
chunk0192_326_1	chr8	67200351	67200842	+	0	NA	intron (NM_006421, intron 37 of 38)	intron (NM_006421, intron 37 of 38)	116748	NM_001291339	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.012220	0.394309	
chunk0160_147_1	chr5	151469668	151470466	+	0	NA	intron (NM_001308151, intron 8 of 8)	intron (NM_001308151, intron 8 of 8)	22471	NM_078483	206358	Hs.269004	NM_078483	ENSG00000123643	SLC36A1	Dct1|LYAAT1|PAT1|TRAMD3	solute carrier family 36 member 1	protein-coding	0.003759	0.371715	269(CAGGACTTCTTGTGCT,-,0.00)
chunk0115_434_1	chr21	31891473	31891720	+	0	NA	intron (NM_014586, intron 1 of 10)	MER57B2|LTR|ERV1	18281	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.004049	0.338710	
chunk0129_130_1	chr3	119956936	119957493	+	0	NA	intron (NM_001146156, intron 2 of 10)	intron (NM_001146156, intron 2 of 10)	137203	NM_002093	2932	Hs.445733	NM_002093	ENSG00000082701	GSK3B	-	glycogen synthase kinase 3 beta	protein-coding	0.007181	0.331541	
chunk0084_442_1	chr17	82876116	82876595	+	0	NA	intron (NM_005993, intron 14 of 38)	intron (NM_005993, intron 14 of 38)	-36300	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.039666	0.504167	
chunk0117_261_1	chr22	23547856	23548136	+	0	NA	TTS (NR_109832)	TTS (NR_109832)	9894	NR_109832	101978785	Hs.575107	NR_109832		PCAT14	-	prostate cancer associated transcript 14	ncRNA	0.010714	0.491103	115(GGGAACAGAATGTTCC,-,0.00),116(GGAACAGAATGTTCCC,+,0.00)
chunk0008_77_1	chr1	89898753	89899066	+	0	NA	intron (NM_001134479, intron 2 of 2)	intron (NM_001134479, intron 2 of 2)	76988	NM_018103	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.009585	0.398089	
chunk0062_117_1	chr14	68448296	68448844	+	0	NA	intron (NM_133509, intron 9 of 10)	intron (NM_133509, intron 9 of 10)	345344	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.005474	0.397086	
chunk0108_237_1	chr2	233736459	233737285	+	0	NA	intron (NM_019093, intron 1 of 4)	L1PA6|LINE|L1	7143	NM_001001394	414061	Hs.725533	NM_001001394		DNAJB3	HCG3	DnaJ heat shock protein family (Hsp40) member B3	protein-coding	0.009685	0.483676	
chunk0116_330_1	chr21	41313043	41313469	+	0	NA	Intergenic	L1ME3|LINE|L1	-3478	NM_206964	54097	Hs.473877	NM_058186	ENSG00000183844	FAM3B	2-21|C21orf11|C21orf76|ORF9|PANDER|PRED44	family with sequence similarity 3 member B	protein-coding	0.007042	0.395785	
chunk0047_40_1	chr12	66682668	66683344	+	0	NA	Intergenic	Intergenic	-3861	NM_001178074	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.008876	0.348597	449(AAAACTCAGTGTTCTC,+,0.00)
chunk0179_62_1	chr7	43890988	43891674	+	0	NA	intron (NM_001077664, intron 1 of 5)	intron (NM_001077664, intron 1 of 5)	15301	NM_001204871	100534592		NM_001204871	ENSG00000270617	URGCP-MRPS24	-	URGCP-MRPS24 readthrough	protein-coding	0.008746	0.433770	
chunk0209_46_1	chrX	36719905	36720232	+	0	NA	Intergenic	Intergenic	-279776	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.021407	0.545732	
chunk0148_396_1	chr5	14832115	14832578	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	-6334	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.006479	0.316810	
chunk0080_446_1	chr17	36761349	36761621	+	0	NA	Intergenic	Intergenic	159889	NM_024864	79922	Hs.194864	NM_024864	ENSG00000278619	MRM1	-	mitochondrial rRNA methyltransferase 1	protein-coding	0.025735	0.523810	
chunk0189_70_1	chr8	20802256	20802637	+	0	NA	Intergenic	Intergenic	-151187	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.010499	0.363874	
chunk0008_399_1	chr1	97474000	97474466	+	0	NA	intron (NM_000110, intron 13 of 22)	intron (NM_000110, intron 13 of 22)	-322688	NR_046591	100873933	Hs.568669	NR_046591	ENSG00000235777	DPYD-AS2	-	DPYD antisense RNA 2	ncRNA	0.004292	0.248394	
chunk0182_416_1	chr7	101100203	101100551	+	0	NA	Intergenic	Intergenic	14938	NM_030961	81844	Hs.521092	NM_030961	ENSG00000169871	TRIM56	RNF109	tripartite motif containing 56	protein-coding	0.037356	0.601719	193(GAGAACGGCCTGTTCC,-,0.00),194(AGAACGGCCTGTTCCC,+,0.00)
chunk0159_165_1	chr5	139638360	139638934	+	0	NA	Intergenic	MIRb|SINE|MIR	-10069	NM_016463	51523	Hs.189119	NM_016463	ENSG00000171604	CXXC5	CF5|HSPC195|RINF|WID	CXXC finger protein 5	protein-coding	0.019164	0.598261	75(GAGGACAGGCTGGGCC,-,0.00),76(AGGACAGGCTGGGCCT,+,0.00)
chunk0031_381_1	chr10	130801484	130801894	+	0	NA	Intergenic	Intergenic	160979	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.019512	0.474453	
chunk0193_155_1	chr8	74687846	74688418	+	0	NA	intron (NR_033830, intron 2 of 5)	intron (NR_033830, intron 2 of 5)	-17561	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.001748	0.324607	
chunk0191_179_1	chr8	51128312	51128842	+	0	NA	Intergenic	LTR9|LTR|ERV1	680868	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.015094	0.419962	
chunk0037_116_1	chr11	72521297	72521892	+	0	NA	Intergenic	Intergenic	-49062	NR_126364	101928555	Hs.376950	NR_126364	ENSG00000227467	LINC01537	-	long intergenic non-protein coding RNA 1537	ncRNA	0.005042	0.416107	
chunk0181_220_1	chr7	85081892	85082091	+	0	NA	intron (NM_152754, intron 2 of 16)	intron (NM_152754, intron 2 of 16)	39940	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.375000	
chunk0058_397_1	chr13	111401865	111402527	+	0	NA	Intergenic	CpG	81552	NM_152324	121793	Hs.210677	NM_152324	ENSG00000153495	TEX29	C13orf16|bA474D23.1	testis expressed 29	protein-coding	0.040785	0.627451	
chunk0188_428_1	chr8	19027622	19028246	+	0	NA	Intergenic	L1ME1|LINE|L1	-14248	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.001603	0.337600	
chunk0028_217_1	chr10	89550637	89550836	+	0	NA	Intergenic	L2b|LINE|L2	-15180	NM_213606	387700	Hs.530338	NM_213606	ENSG00000152779	SLC16A12	CJMG|CRT2|CTRCT47|MCT12	solute carrier family 16 member 12	protein-coding	0.020101	0.505000	
chunk0134_197_1	chr3	178391753	178392071	+	0	NA	Intergenic	L1M5|LINE|L1	-27289	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.000000	0.241379	
chunk0009_110_1	chr1	102614066	102614421	+	0	NA	Intergenic	L1P4a|LINE|L1	494253	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.000000	0.469101	
chunk0209_325_1	chrX	50533865	50534462	+	0	NA	Intergenic	L2c|LINE|L2	-63425	NM_001013742	139189	Hs.38132	NM_001013742	ENSG00000274588	DGKK	-	diacylglycerol kinase kappa	protein-coding	0.010050	0.409699	
chunk0212_63_1	chrY	11327980	11328381	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1093410	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.012469	0.482587	
chunk0173_15_1	chr6	141329829	141330268	+	0	NA	Intergenic	L1MEd|LINE|L1	646234	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.009112	0.297727	
chunk0077_192_1	chr16	79768070	79768482	+	0	NA	intron (NR_104663, intron 2 of 5)	intron (NR_104663, intron 2 of 5)	-2195	NR_104660	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.016990	0.447942	
chunk0010_428_1	chr1	119776457	119776831	+	0	NA	Intergenic	L1MEh|LINE|L1	-7712	NM_005518	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.008021	0.365333	
chunk0124_323_1	chr3	58135990	58136606	+	0	NA	intron (NM_001164317, intron 29 of 46)	MIRb|SINE|MIR	74705	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.021104	0.452188	
chunk0093_67_1	chr19	40461746	40462304	+	0	NA	intron (NM_000713, intron 1 of 4)	intron (NM_000713, intron 1 of 4)	3793	NM_000713	645	Hs.515785	NM_000713	ENSG00000090013	BLVRB	BVRB|FLR|HEL-S-10|SDR43U1	biliverdin reductase B	protein-coding	0.008961	0.529517	
chunk0029_424_1	chr10	109996223	109996837	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-9438	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.004886	0.365854	327(AAGGACAGGATGTTCC,-,0.00),328(AGGACAGGATGTTCCT,+,0.00)
chunk0043_277_1	chr12	21000927	21001638	+	0	NA	Intergenic	L1PBb|LINE|L1	-14414	NM_001009562	338821	Hs.729117	NM_001009562	ENSG00000205754	SLCO1B7	LST-3|LST-3TM12|LST3|SLC21A21	solute carrier organic anion transporter family member 1B7 (putative)	protein-coding	0.005626	0.408708	
chunk0060_466_1	chr14	55301660	55302052	+	0	NA	intron (NM_152231, intron 1 of 1)	intron (NM_152231, intron 1 of 1)	29702	NM_152231	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.000000	0.450382	
chunk0143_73_1	chr4	108109395	108109744	+	0	NA	intron (NM_016269, intron 3 of 11)	MIR|SINE|MIR	57228	NM_001166119	51176	Hs.743478	NM_016269	ENSG00000138795	LEF1	LEF-1|TCF10|TCF1ALPHA|TCF7L3	lymphoid enhancer binding factor 1	protein-coding	0.000000	0.394286	118(AAGAACAGAGTGACCC,-,0.00),119(AGAACAGAGTGACCCT,+,0.00)
chunk0094_210_1	chr2	6497120	6497468	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-121872	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.002874	0.329513	173(CAGGACACTCTGTGAT,-,0.00)
chunk0175_423_1	chr6	168919555	168920311	+	0	NA	Intergenic	Intergenic	242368	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.018519	0.428005	403(AGGATCTCAGTGTTCT,-,0.00),404(GGATCTCAGTGTTCTG,+,0.00)
chunk0060_103_1	chr14	43384701	43385068	+	0	NA	Intergenic	L1MC1|LINE|L1	1122412	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.005450	0.315217	
chunk0010_354_1	chr1	118785131	118785558	+	0	NA	Intergenic	Intergenic	204212	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.004684	0.481308	
chunk0016_158_1	chr1	197648283	197648692	+	0	NA	intron (NM_144977, intron 7 of 15)	intron (NM_144977, intron 7 of 15)	127006	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.000000	0.304878	
chunk0095_205_1	chr2	18449558	18450283	+	0	NA	Intergenic	Intergenic	110773	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.002759	0.374656	403(CAGGACTCTTTGTTCT,-,0.00),404(AGGACTCTTTGTTCTA,+,0.00)
chunk0003_188_1	chr1	33758619	33759174	+	0	NA	intron (NM_052896, intron 13 of 69)	MLT1I|LTR|ERVL-MaLR	-101579	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.010811	0.431655	244(GAGAACAACATGCTCT,-,0.00)
chunk0118_446_1	chr22	39240876	39241075	+	0	NA	promoter-TSS (NM_033016)	promoter-TSS (NM_033016)	-66	NM_033016	5155	Hs.1976	NM_002608	ENSG00000100311	PDGFB	IBGC5|PDGF-2|PDGF2|SIS|SSV|c-sis	platelet derived growth factor subunit B	protein-coding	0.005025	0.545000	
chunk0029_358_1	chr10	107585699	107586678	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-421480	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.003064	0.395918	586(ATGTACTTTATGTTCT,-,0.00),587(TGTACTTTATGTTCTT,+,0.00)
chunk0056_166_1	chr13	84801926	84802255	+	0	NA	Intergenic	Intergenic	18436	NR_132852	106635542		NR_132852		SNORA107	-	small nucleolar RNA, H/ACA box 107	snoRNA	0.012158	0.409091	
chunk0109_151_1	chr20	3786106	3786309	+	0	NA	promoter-TSS (NM_001287518)	promoter-TSS (NM_001287518)	483	NM_001810	1059	Hs.516855	NM_001810	ENSG00000125817	CENPB	-	centromere protein B	protein-coding	0.083744	0.651961	
chunk0068_100_1	chr15	52259457	52259853	+	0	NA	intron (NM_018728, intron 10 of 40)	intron (NM_018728, intron 10 of 40)	17545	NR_031670	100302202		NR_031670	ENSG00000221052	MIR1266	MIRN1266|hsa-mir-1266|mir-1266	microRNA 1266	ncRNA	0.007576	0.380353	
chunk0015_54_1	chr1	184590317	184590627	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	164435	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.003226	0.363344	
chunk0056_177_1	chr13	85348062	85348725	+	0	NA	Intergenic	Intergenic	-15210	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.006033	0.334337	
chunk0056_403_1	chr13	94122404	94122640	+	0	NA	intron (NM_005708, intron 4 of 8)	intron (NM_005708, intron 4 of 8)	65469	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.004237	0.405063	
chunk0178_128_1	chr7	32108751	32109023	+	0	NA	intron (NM_001191058, intron 3 of 18)	intron (NM_001191058, intron 3 of 18)	-37451	NM_001191059	5137	Hs.143821	NM_005020	ENSG00000154678	PDE1C	DFNA74|Hcam3|cam-PDE 1C|hCam-3	phosphodiesterase 1C	protein-coding	0.003676	0.465201	
chunk0105_19_1	chr2	182004759	182005484	+	0	NA	intron (NM_001080545, intron 2 of 4)	intron (NM_001080545, intron 2 of 4)	19297	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.002759	0.342975	
chunk0201_152_1	chr9	35958839	35959142	+	0	NA	promoter-TSS (NM_019897)	promoter-TSS (NM_019897)	-836	NM_019897	56656	Hs.553540	NM_019897	ENSG00000278889	OR2S2	OR37A|OST715	olfactory receptor family 2 subfamily S member 2 (gene/pseudogene)	protein-coding	0.006601	0.361842	
chunk0011_223_1	chr1	150233742	150234388	+	0	NA	intron (NM_001136478, intron 1 of 5)	MIRc|SINE|MIR	613	NM_001136479	81611	Hs.656466	NM_030920	ENSG00000143401	ANP32E	LANP-L|LANPL	acidic nuclear phosphoprotein 32 family member E	protein-coding	0.020124	0.420402	
chunk0172_116_1	chr6	135109614	135110232	+	0	NA	Intergenic	Intergenic	-55025	NM_001145207	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.008091	0.347334	447(TGGTACAGGATGTGCA,-,0.00),448(GGTACAGGATGTGCAG,+,0.00)
chunk0099_78_1	chr2	85340129	85340840	+	0	NA	Intergenic	Intergenic	-12188	NM_001206841	10618	Hs.593382	NM_006464	ENSG00000152291	TGOLN2	TGN38|TGN46|TGN48|TGN51|TTGN2	trans-golgi network protein 2	protein-coding	0.015471	0.488764	
chunk0002_293_1	chr1	23019191	23019450	+	0	NA	promoter-TSS (NM_015013)	promoter-TSS (NM_015013)	-128	NM_001009999	23028	Hs.591518	NM_015013	ENSG00000004487	KDM1A	AOF2|BHC110|CPRF|KDM1|LSD1	lysine demethylase 1A	protein-coding	0.077220	0.603846	
chunk0079_233_1	chr17	15793535	15793955	+	0	NA	Intergenic	L1MA8|LINE|L1	6895	NR_002211	4213	Hs.356135	NR_002211		MEIS3P1	MEIS3|MEIS4|MRG2	Meis homeobox 3 pseudogene 1	pseudo	0.004762	0.308789	
chunk0006_179_1	chr1	67190308	67190868	+	0	NA	intron (NM_144701, intron 4 of 10)	L2a|LINE|L2	24102	NM_144701	149233	Hs.677426	NM_144701	ENSG00000162594	IL23R	-	interleukin 23 receptor	protein-coding	0.007143	0.361854	
chunk0182_403_1	chr7	100813622	100814582	+	0	NA	intron (NM_004444, intron 8 of 16)	intron (NM_004444, intron 8 of 16)	13419	NM_004444	2050	Hs.437008	NM_004444	ENSG00000196411	EPHB4	CMAVM2|HFASD|HTK|LMPHM7|MYK1|TYRO11	EPH receptor B4	protein-coding	0.021875	0.532778	
chunk0125_234_1	chr3	68313931	68314386	+	0	NA	intron (NM_213609, intron 2 of 4)	intron (NM_213609, intron 2 of 4)	309942	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.006593	0.335526	
chunk0033_386_1	chr11	24123364	24123741	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-373418	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.005305	0.335979	
chunk0002_4_1	chr1	11992457	11992661	+	0	NA	exon (NM_001127660, exon 3 of 18)	exon (NM_001127660, exon 3 of 18)	12378	NM_001127660	9927	Hs.376681	NM_014874	ENSG00000116688	MFN2	CMT2A|CMT2A2|CMT2A2A|CMT2A2B|CPRP1|HMSN6A|HSG|MARF	mitofusin 2	protein-coding	0.034314	0.556098	
chunk0027_150_1	chr10	74705205	74705409	+	0	NA	intron (NM_001123, intron 10 of 10)	intron (NM_001123, intron 10 of 10)	-121106	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.000000	0.439024	
chunk0070_146_1	chr15	71097972	71098230	+	0	NA	Intergenic	Intergenic	17399	NM_001102658	196993	Hs.646533	NM_001102658	ENSG00000225362	CT62	-	cancer/testis antigen 62	protein-coding	0.003876	0.370656	104(GAGCACACTGTGTCCC,-,0.00),105(AGCACACTGTGTCCCA,+,0.00)
chunk0185_285_1	chr7	130969139	130969394	+	0	NA	intron (NR_109851, intron 4 of 5)	intron (NR_109851, intron 4 of 5)	55802	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.011765	0.367188	
chunk0132_192_1	chr3	157134505	157135222	+	0	NA	Intergenic	Intergenic	-11861	NR_034007	339894	Hs.478050	NR_034007	ENSG00000243629	LINC00880	-	long intergenic non-protein coding RNA 880	ncRNA	0.002789	0.488858	
chunk0097_237_1	chr2	53547100	53547464	+	0	NA	Intergenic	L2a|LINE|L2	-220510	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.005495	0.435616	
chunk0103_370_1	chr2	168510282	168511037	+	0	NA	intron (NM_001256126, intron 1 of 10)	HAL1|LINE|L1	54410	NM_203463	253782	Hs.506829	NM_203463	ENSG00000172292	CERS6	CERS5|LASS6	ceramide synthase 6	protein-coding	0.009272	0.354497	245(GAGTACACTCTGTGTT,-,0.00),246(AGTACACTCTGTGTTG,+,0.00)
chunk0082_22_1	chr17	50542270	50542539	+	0	NA	3' UTR (NM_017957, exon 10 of 10)	3' UTR (NM_017957, exon 10 of 10)	-4685	NM_022827	64847	Hs.103147	NM_022827	ENSG00000006282	SPATA20	HEL-S-98|SSP411|Tisp78	spermatogenesis associated 20	protein-coding	0.070632	0.607407	
chunk0190_327_1	chr8	38929181	38929430	+	0	NA	intron (NM_021623, intron 2 of 11)	intron (NM_021623, intron 2 of 11)	28070	NM_021623	59339	Hs.369123	NM_021623	ENSG00000169499	PLEKHA2	TAPP2	pleckstrin homology domain containing A2	protein-coding	0.008032	0.552000	
chunk0194_251_1	chr8	86448329	86448556	+	0	NA	exon (NM_007013, exon 20 of 25)	exon (NM_007013, exon 20 of 25)	60338	NM_016033	51115	Hs.145386	NM_016033	ENSG00000176623	RMDN1	CGI-90|FAM82B|RMD-1|RMD1	regulator of microtubule dynamics 1	protein-coding	0.000000	0.328947	
chunk0187_93_1	chr8	3748629	3749144	+	0	NA	intron (NM_033225, intron 6 of 69)	intron (NM_033225, intron 6 of 69)	-1020435	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.007767	0.323643	
chunk0046_446_1	chr12	64878576	64878873	+	0	NA	3' UTR (NM_015279, exon 12 of 12)	3' UTR (NM_015279, exon 12 of 12)	-5050	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.006734	0.483221	
chunk0156_22_1	chr5	102230734	102231353	+	0	NA	Intergenic	L1MC4a|LINE|L1	65506	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.001616	0.319355	
chunk0014_286_1	chr1	180593330	180593786	+	0	NA	Intergenic	Intergenic	34584	NR_125716	148756		NR_125716	ENSG00000236719	OVAAL	LINC01131|OVAL	ovarian adenocarcinoma amplified long non-coding RNA	ncRNA	0.006579	0.437637	289(CAGGACAGTGTGTGCT,-,0.00),290(AGGACAGTGTGTGCTG,+,0.00)
chunk0107_202_1	chr2	216450355	216450554	+	0	NA	intron (NM_014140, intron 11 of 17)	intron (NM_014140, intron 11 of 17)	37704	NM_001127207	50485	Hs.516674	NM_014140	ENSG00000138375	SMARCAL1	HARP|HHARP	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1	protein-coding	0.000000	0.325000	
chunk0185_123_1	chr7	126208920	126209681	+	0	NA	Intergenic	Intergenic	848884	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.002628	0.324147	
chunk0148_158_1	chr5	6607515	6608022	+	0	NA	intron (NR_037947, intron 11 of 17)	intron (NR_037947, intron 11 of 17)	24492	NR_024424	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.009862	0.385827	109(ATATACAGCCTGTTCC,-,0.00),110(TATACAGCCTGTTCCT,+,0.00),202(AAGGACACAAAGTGCA,-,0.00),203(AGGACACAAAGTGCAC,+,0.00)
chunk0198_131_1	chr8	132222614	132222813	+	0	NA	intron (NM_004519, intron 1 of 14)	intron (NM_004519, intron 1 of 14)	-117448	NM_001145095	10086	Hs.285026	NM_005712	ENSG00000132297	HHLA1	PLA2L	HERV-H LTR-associating 1	protein-coding	0.010050	0.455000	128(AAGGACAGTCAGTTTC,-,0.00)
chunk0165_387_1	chr6	38702962	38703567	+	0	NA	promoter-TSS (NM_006708)	promoter-TSS (NM_006708)	-88	NM_006708	2739	Hs.268849	NM_006708	ENSG00000124767	GLO1	GLOD1|GLYI|HEL-S-74	glyoxalase I	protein-coding	0.052893	0.514851	
chunk0125_372_1	chr3	71520564	71521004	+	0	NA	intron (NM_032682, intron 2 of 20)	intron (NM_032682, intron 2 of 20)	21305	NR_031697	100302112		NR_031697	ENSG00000221264	MIR1284	MIRN1284|hsa-mir-1284|mir-1284	microRNA 1284	ncRNA	0.015909	0.419501	122(GAGAACAGTGTGTATC,-,0.00),123(AGAACAGTGTGTATCA,+,0.00)
chunk0060_116_1	chr14	43768811	43769010	+	0	NA	Intergenic	MER51B|LTR|ERV1	738386	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.005025	0.360000	
chunk0111_40_1	chr20	22295945	22296557	+	0	NA	Intergenic	Intergenic	-13450	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.004902	0.482871	
chunk0019_224_1	chr1	227306376	227306575	+	0	NA	intron (NM_014826, intron 1 of 34)	MamRTE1|LINE|RTE-BovB	11650	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.010050	0.390000	
chunk0082_447_1	chr17	62163861	62164195	+	0	NA	Intergenic	Intergenic	-98746	NM_005121	9969	Hs.282678	NM_005121	ENSG00000108510	MED13	ARC250|DRIP250|HSPC221|THRAP1|TRAP240	mediator complex subunit 13	protein-coding	0.008982	0.510448	
chunk0106_449_1	chr2	209348464	209349028	+	0	NA	Intergenic	Intergenic	-75301	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.012411	0.380531	
chunk0166_83_1	chr6	43683540	43684247	+	0	NA	intron (NM_018135, intron 1 of 5)	UCON55|DNA|TcMar-Tigger	3919	NM_001193343	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.001414	0.422316	
chunk0102_152_1	chr2	147133381	147134098	+	0	NA	Intergenic	Eulor2A|DNA?|DNA?	546682	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.002789	0.395543	
chunk0020_228_1	chr1	235517960	235518159	+	0	NA	intron (NR_039973, intron 1 of 1).3	intron (NR_039973, intron 1 of 1).3	5236	NR_039973									0.010050	0.360000	
chunk0164_129_1	chr6	20954223	20954688	+	0	NA	intron (NM_017774, intron 9 of 15)	intron (NM_017774, intron 9 of 15)	419998	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.006452	0.349785	
chunk0033_20_1	chr11	12534294	12534935	+	0	NA	3' UTR (NM_018222, exon 13 of 13)	3' UTR (NM_018222, exon 13 of 13)	-139808	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.006240	0.447040	304(TAGCACAGGCTGTCAT,-,0.00),305(AGCACAGGCTGTCATT,+,0.00)
chunk0143_315_1	chr4	119100667	119100987	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-34957	NM_016599	51778	Hs.732122	NM_016599	ENSG00000172399	MYOZ2	C4orf5|CMH16|CS-1|FATZ-2	myozenin 2	protein-coding	0.003125	0.395639	
chunk0151_271_1	chr5	52596222	52596478	+	0	NA	Intergenic	Intergenic	-191590	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.003906	0.342412	
chunk0071_234_1	chr15	85113890	85114269	+	0	NA	intron (NM_001243137, intron 14 of 21)	intron (NM_001243137, intron 14 of 21)	91208	NR_049748									0.002639	0.486842	
chunk0137_147_1	chr4	15662735	15662996	+	0	NA	Intergenic	Intergenic	-7453	NM_001193534	26234	Hs.643433	NM_012161	ENSG00000118564	FBXL5	FBL4|FBL5|FLR1	F-box and leucine rich repeat protein 5	protein-coding	0.000000	0.343511	
chunk0197_399_1	chr8	127101553	127102159	+	0	NA	Intergenic	Intergenic	-19635	NR_119373	103164619	Hs.571401	NR_119373	ENSG00000254166	PCAT2	CARLO4|CARLo-4|PCA2|TCONS_00015167	prostate cancer associated transcript 2	ncRNA	0.004950	0.400329	
chunk0156_447_1	chr5	114838855	114839648	+	0	NA	Intergenic	L1MA4A|LINE|L1	-65838	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.008827	0.483627	319(AGGCACTTGCTGTCCC,-,0.00),320(GGCACTTGCTGTCCCT,+,0.00),342(AGGACAGGGAGTTTCT,+,0.00)
chunk0194_6_1	chr8	81375270	81375697	+	0	NA	Intergenic	Intergenic	72001	NM_002677	5375	Hs.571512	NM_002677	ENSG00000147588	PMP2	CMT1G|FABP8|M-FABP|MP2|P2	peripheral myelin protein 2	protein-coding	0.009368	0.369159	
chunk0086_333_1	chr18	24636613	24637450	+	0	NA	intron (NR_040033, intron 1 of 2)	MLT1I|LTR|ERVL-MaLR	8849	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.003584	0.414081	
chunk0139_191_1	chr4	54517517	54517936	+	0	NA	Intergenic	Intergenic	-140202	NM_000222	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.000000	0.428571	
chunk0209_11_1	chrX	35202963	35203364	+	0	NA	Intergenic	Intergenic	260367	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.004988	0.363184	
chunk0146_176_1	chr4	160690365	160691173	+	0	NA	Intergenic	L1PA15|LINE|L1	-1331964	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.003713	0.348578	
chunk0074_142_1	chr16	23137862	23138166	+	0	NA	intron (NM_020718, intron 1 of 15)	intron (NM_020718, intron 1 of 15)	11256	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.009868	0.344262	
chunk0135_15_1	chr3	184275336	184275617	+	0	NA	promoter-TSS (NM_001100121)	promoter-TSS (NM_001100121)	-535	NM_001100121	9718	Hs.146161	NM_001037324	ENSG00000145194	ECE2	EEF1AKMT4	endothelin converting enzyme 2	protein-coding	0.039146	0.549645	
chunk0022_200_1	chr10	13569944	13570236	+	0	NA	Intergenic	L1PB3|LINE|L1	-16849	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.003425	0.337884	
chunk0005_214_1	chr1	59199119	59199548	+	0	NA	Intergenic	L2b|LINE|L2	-52526	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.004662	0.395349	
chunk0032_253_1	chr11	8670845	8671439	+	0	NA	Intergenic	Intergenic	-11306	NM_000990	6157	Hs.523463	NM_000990	ENSG00000166441	RPL27A	L27A	ribosomal protein L27a	protein-coding	0.011785	0.411765	
chunk0029_196_1	chr10	101512640	101513059	+	0	NA	intron (NM_033637, intron 4 of 14)	intron (NM_033637, intron 4 of 14)	75421	NM_001308382	27343	Hs.523230	NM_013274	ENSG00000166169	POLL	BETAN|POLKAPPA	DNA polymerase lambda	protein-coding	0.004773	0.395238	
chunk0188_282_1	chr8	15545808	15546311	+	0	NA	intron (NM_006765, intron 1 of 10)	intron (NM_006765, intron 1 of 10)	5972	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.005964	0.371032	
chunk0071_372_1	chr15	89115644	89115953	+	0	NA	intron (NM_007011, intron 6 of 14)	intron (NM_007011, intron 6 of 14)	27648	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.009709	0.516129	
chunk0048_330_1	chr12	83811781	83812280	+	0	NA	Intergenic	Intergenic	1100799	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.000000	0.316000	
chunk0014_30_1	chr1	174715263	174715770	+	0	NA	intron (NM_014857, intron 17 of 20)	MIRb|SINE|MIR	-84381	NM_001243765	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.001972	0.344488	
chunk0016_396_1	chr1	203151354	203151790	+	0	NA	intron (NM_001048230, intron 2 of 2)	intron (NM_001048230, intron 2 of 2)	23864	NM_001048230	134	Hs.77867	NM_000674	ENSG00000163485	ADORA1	RDC7	adenosine A1 receptor	protein-coding	0.011468	0.480549	
chunk0152_333_1	chr5	62412208	62412650	+	0	NA	promoter-TSS (NM_016338)	promoter-TSS (NM_016338)	-317	NM_016338	51194	Hs.482269	NM_016338	ENSG00000086200	IPO11	RanBP11	importin 11	protein-coding	0.036199	0.444695	
chunk0205_136_1	chr9	108142600	108143228	+	0	NA	Intergenic	Intergenic	-653194	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.012739	0.521463	233(GAGAACAGAAAGTCCC,-,0.00),234(AGAACAGAAAGTCCCA,+,0.00),368(GAGCACACCCTGGCCT,-,0.00),369(AGCACACCCTGGCCTT,+,0.00)
chunk0187_255_1	chr7	154574962	154575161	+	0	NA	intron (NM_001290252, intron 5 of 23)	(TG)n|Simple_repeat|Simple_repeat	269849	NM_001290252	1804	Hs.490684	NM_001936	ENSG00000130226	DPP6	DPL1|DPPX|MRD33|VF2	dipeptidyl peptidase like 6	protein-coding	0.005025	0.495000	
chunk0124_41_1	chr3	52339661	52339881	+	0	NA	intron (NM_015512, intron 8 of 77)	L1MC4|LINE|L1	23452	NM_015512	25981	Hs.655469	NM_015512	ENSG00000114841	DNAH1	CILD37|DNAHC1|HDHC7|HL-11|HL11|HSRF-1|SPGF18|XLHSRF-1	dynein axonemal heavy chain 1	protein-coding	0.013636	0.443439	
chunk0075_94_1	chr16	48383852	48384140	+	0	NA	intron (NM_003031, intron 1 of 1)	MIR|SINE|MIR	1322	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.017361	0.453287	
chunk0064_331_1	chr14	96431408	96431865	+	0	NA	intron (NM_152327, intron 5 of 17)	L1PA5|LINE|L1	39525	NM_152327	122481	Hs.667462	NM_152327	ENSG00000140057	AK7	AK 7|SPGF27	adenylate kinase 7	protein-coding	0.010941	0.390830	
chunk0161_368_1	chr5	176143062	176143350	+	0	NA	non-coding (NR_036494, exon 26 of 26)	non-coding (NR_036494, exon 26 of 26)	23657	NR_038402	100507387	Hs.368516	NR_038402	ENSG00000251623	LOC100507387	-	uncharacterized LOC100507387	ncRNA	0.006944	0.401384	
chunk0128_307_1	chr3	111584907	111585549	+	0	NA	intron (NM_005816, intron 4 of 13)	(ATTA)n|Simple_repeat|Simple_repeat	10107	NM_024508	79413	Hs.136912	NM_024508	ENSG00000177494	ZBED2	-	zinc finger BED-type containing 2	protein-coding	0.001558	0.365474	
chunk0133_125_1	chr3	168873888	168874597	+	0	NA	Intergenic	Intergenic	-27703	NR_109989	100507661	Hs.65918	NR_109989	ENSG00000242268	LINC02082	-	long intergenic non-protein coding RNA 2082	ncRNA	0.005642	0.404225	
chunk0188_422_1	chr8	19002293	19002492	+	0	NA	intron (NM_015310, intron 1 of 15)	intron (NM_015310, intron 1 of 15)	11294	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.010050	0.380000	
chunk0111_326_1	chr20	32432434	32432776	+	0	NA	intron (NM_015338, intron 9 of 11)	MER68|LTR|ERVL	50977	NM_080616	140688	Hs.516978	NM_080616	ENSG00000197183	NOL4L	C20orf112|C20orf113	nucleolar protein 4 like	protein-coding	0.005848	0.402332	
chunk0042_77_1	chr12	2166301	2166881	+	0	NA	intron (NM_001129846, intron 3 of 45)	MIRb|SINE|MIR	56890	NR_046578	100874234	Hs.372570	NR_046578	ENSG00000256025	CACNA1C-AS4	-	CACNA1C antisense RNA 4	ncRNA	0.006897	0.419966	133(ATAGACACACTGTCCC,-,0.00),134(TAGACACACTGTCCCC,+,0.00)
chunk0192_63_1	chr8	60343445	60343851	+	0	NA	Intergenic	L1PA14|LINE|L1	-62253	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.000000	0.334152	
chunk0142_237_1	chr4	98610991	98611243	+	0	NA	intron (NM_005723, intron 1 of 7)	intron (NM_005723, intron 1 of 7)	47544	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.007937	0.478261	155(GAGGACACACTGTACT,-,0.00),156(AGGACACACTGTACTA,+,0.00)
chunk0088_419_1	chr18	54948339	54948920	+	0	NA	intron (NM_025214, intron 1 of 11)	L2a|LINE|L2	9419	NM_001143829	80323	Hs.120790	NM_025214	ENSG00000166510	CCDC68	SE57-1	coiled-coil domain containing 68	protein-coding	0.006885	0.445017	
chunk0179_336_1	chr7	50677477	50677983	+	0	NA	intron (NM_001001549, intron 2 of 14)	intron (NM_001001549, intron 2 of 14)	27571	NM_001001550	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.019763	0.453649	
chunk0005_171_1	chr1	58584068	58584562	+	0	NA	Intergenic	Intergenic	-6821	NM_002353	4070	Hs.23582	NM_002353	ENSG00000184292	TACSTD2	EGP-1|EGP1|GA733-1|GA7331|GP50|M1S1|TROP2	tumor associated calcium signal transducer 2	protein-coding	0.008097	0.450505	
chunk0029_352_1	chr10	107130997	107131365	+	0	NA	intron (NM_052918, intron 1 of 25)	intron (NM_052918, intron 1 of 25)	33527	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.002717	0.395664	
chunk0195_315_1	chr8	98913201	98913938	+	0	NA	intron (NM_001256312, intron 1 of 12)	intron (NM_001256312, intron 1 of 12)	29002	NM_001256312	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004071	0.415989	361(TGGGACAAGGTGTCCA,-,0.00),362(GGGACAAGGTGTCCAC,+,0.00)
chunk0110_419_1	chr20	20650835	20651386	+	0	NA	intron (NM_020343, intron 4 of 39)	intron (NM_020343, intron 4 of 39)	61513	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.009074	0.347826	
chunk0016_152_1	chr1	197541954	197542846	+	0	NA	intron (NR_125340, intron 15 of 19)	intron (NR_125340, intron 15 of 19)	233093	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.003363	0.325868	
chunk0012_449_1	chr1	165092625	165093083	+	0	NA	Intergenic	LTR5B|LTR|ERVK	263387	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.008734	0.466231	235(AGGGACACAATGCACT,-,0.00),236(GGGACACAATGCACTG,+,0.00)
chunk0003_182_1	chr1	33687081	33687481	+	0	NA	intron (NM_052896, intron 25 of 69)	intron (NM_052896, intron 25 of 69)	-173194	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.002500	0.349127	
chunk0101_33_1	chr2	122294056	122294266	+	0	NA	Intergenic	L2c|LINE|L2	538616	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.000000	0.369668	
chunk0206_223_1	chr9	123319722	123320432	+	0	NA	Intergenic	Intergenic	-36090	NM_173689	286204	Hs.568340	NM_173689	ENSG00000148204	CRB2	FSGS9|VMCKD	crumbs cell polarity complex component 2	protein-coding	0.015493	0.506329	
chunk0165_34_1	chr6	29920100	29920783	+	0	NA	Intergenic	Charlie9|DNA|hAT-Charlie	6774	NR_001317	80868	Hs.661198	NR_001317		HCG4B	HCG4P6|HCGIV-06|HCGIV-6|HCGIV.5|bCX67J3.3|bPG309N1.1|bQB90C11.3	HLA complex group 4B	ncRNA	0.002928	0.336257	
chunk0139_44_1	chr4	48639077	48639481	+	0	NA	intron (NM_015030, intron 3 of 63)	L1MC2|LINE|L1	141020	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.004950	0.350617	
chunk0077_198_1	chr16	79838761	79839207	+	0	NA	Intergenic	Intergenic	43735	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.017937	0.418345	
chunk0010_422_1	chr1	119712099	119712321	+	0	NA	intron (NM_006623, intron 1 of 11)	intron (NM_006623, intron 1 of 11)	414	NM_006623	26227	Hs.487296	NM_006623	ENSG00000092621	PHGDH	3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA	phosphoglycerate dehydrogenase	protein-coding	0.045045	0.600897	
chunk0151_114_1	chr5	43539799	43540181	+	0	NA	intron (NM_006451, intron 4 of 10)	intron (NM_006451, intron 4 of 10)	17103	NM_006451	10605	Hs.482038	NM_006451	ENSG00000172239	PAIP1	-	poly(A) binding protein interacting protein 1	protein-coding	0.010471	0.352480	
chunk0211_179_1	chrX	116929459	116929722	+	0	NA	Intergenic	MER51-int|LTR|ERV1	-466557	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.000000	0.291667	
chunk0206_185_1	chr9	122847010	122847209	+	0	NA	Intergenic	Intergenic	-18453	NM_005388	5082	Hs.271749	NM_005388	ENSG00000136940	PDCL	PhLP	phosducin like	protein-coding	0.000000	0.350000	31(AAGAACAGGGAGTTAT,-,0.00)
chunk0025_180_1	chr10	53123291	53123490	+	0	NA	Intergenic	MER21-int|LTR|ERVL	-351690	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.005025	0.455000	
chunk0105_441_1	chr2	194639361	194639663	+	0	NA	Intergenic	L1PA6|LINE|L1	-91083	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.013245	0.524752	
chunk0139_227_1	chr4	55273316	55273579	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-72774	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.000000	0.405303	140(TGGATCAAGGTGTTCC,-,0.00),141(GGATCAAGGTGTTCCT,+,0.00)
chunk0161_431_1	chr5	178447732	178448041	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	142669	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.012945	0.480645	
chunk0021_31_1	chr10	792952	793629	+	0	NA	Intergenic	Intergenic	-103622	NM_014974	22982	Hs.432397	NM_014974	ENSG00000151240	DIP2C	KIAA0934	disco interacting protein 2 homolog C	protein-coding	0.008863	0.407080	
chunk0121_94_1	chr3	16760475	16760787	+	0	NA	Intergenic	L1MA2|LINE|L1	-124328	NM_001144382	23228	Hs.202010	NM_015184	ENSG00000154822	PLCL2	PLCE2	phospholipase C like 2	protein-coding	0.009615	0.527157	
chunk0156_48_1	chr5	103014196	103014722	+	0	NA	intron (NM_000919, intron 20 of 24)	intron (NM_000919, intron 20 of 24)	105679	NM_017676	54826	Hs.24088	NM_017676	ENSG00000145723	GIN1	GIN-1|TGIN1|ZH2C2	gypsy retrotransposon integrase 1	protein-coding	0.003802	0.326376	
chunk0014_426_1	chr1	183471828	183472199	+	0	NA	promoter-TSS (NM_201569)	promoter-TSS (NM_201569)	-31	NR_040063	284649	Hs.127384	NR_040063	ENSG00000232860	SMG7-AS1	DKFZP564C196	SMG7 antisense RNA 1	ncRNA	0.053908	0.604839	
chunk0137_18_1	chr4	10856006	10856214	+	0	NA	Intergenic	Intergenic	-171348	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.000000	0.258373	
chunk0066_74_1	chr15	29343048	29343324	+	0	NA	intron (NM_015307, intron 2 of 10)	MLT2C2|LTR|ERVL	-73370	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.007246	0.364621	
chunk0082_48_1	chr17	50977282	50977769	+	0	NA	intron (NM_001130528, intron 26 of 29)	intron (NM_001130528, intron 26 of 29)	69443	NM_001251971	9043	Hs.463439	NM_003971	ENSG00000008294	SPAG9	CT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6	sperm associated antigen 9	protein-coding	0.002053	0.405738	
chunk0185_425_1	chr7	134669932	134670194	+	0	NA	intron (NM_001724, intron 2 of 2)	intron (NM_001724, intron 2 of 2)	23284	NM_001293085	669	Hs.198365	NM_001724	ENSG00000172331	BPGM	DPGM|ECYT8	bisphosphoglycerate mutase	protein-coding	0.022901	0.463878	
chunk0028_343_1	chr10	92181613	92181905	+	0	NA	intron (NM_001178137, intron 3 of 9)	MER58C|DNA|hAT-Charlie	61520	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.006849	0.399317	
chunk0017_144_1	chr1	206692963	206693403	+	0	NA	intron (NM_032960, intron 1 of 9)	intron (NM_032960, intron 1 of 9)	8163	NM_032960	9261	Hs.643566	NM_004759	ENSG00000162889	MAPKAPK2	MAPKAP-K2|MK-2|MK2	MAPK activated protein kinase 2	protein-coding	0.020455	0.544218	
chunk0200_93_1	chr9	16528656	16528877	+	0	NA	intron (NM_017637, intron 5 of 6)	L1ME3G|LINE|L1	-252453	NR_073471									0.004525	0.346847	
chunk0186_236_1	chr7	140749047	140749363	+	0	NA	intron (NM_004333, intron 16 of 17)	intron (NM_004333, intron 16 of 17)	-52128	NR_024454	100134713	Hs.534141	NR_024454	ENSG00000240889	NDUFB2-AS1	-	NDUFB2 antisense RNA 1	ncRNA	0.015823	0.340694	
chunk0202_33_1	chr9	70675988	70676310	+	0	NA	intron (NM_024971, intron 9 of 25)	intron (NM_024971, intron 9 of 25)	133935	NR_029621	406987		NR_029621	ENSG00000207935	MIR204	MIRN204|RDICC|miRNA204|mir-204	microRNA 204	ncRNA	0.003106	0.380805	
chunk0022_351_1	chr10	17116426	17116683	+	0	NA	intron (NM_001081, intron 6 of 66)	intron (NM_001081, intron 6 of 66)	13263	NM_001081	8029	Hs.166206	NM_001081	ENSG00000107611	CUBN	IFCR|MGA1|gp280	cubilin	protein-coding	0.019455	0.507752	115(AGGAACAGGGCGTGCC,-,0.00),116(GGAACAGGGCGTGCCT,+,0.00)
chunk0098_329_1	chr2	76850799	76851422	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-134855	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.003210	0.395833	
chunk0037_405_1	chr11	79512348	79512547	+	0	NA	Intergenic	Intergenic	-71796	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.005025	0.510000	
chunk0084_448_1	chr17	82939830	82940059	+	0	NA	intron (NM_005993, intron 37 of 38)	intron (NM_005993, intron 37 of 38)	-99889	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.021834	0.530435	
chunk0076_71_1	chr16	63338958	63339578	+	0	NA	Intergenic	L1MC1|LINE|L1	-1302433	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.008065	0.330113	
chunk0056_105_1	chr13	82603039	82603238	+	0	NA	Intergenic	L1MA8|LINE|L1	1279255	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.365000	110(CTGAACATACTGTCCT,-,0.00),111(TGAACATACTGTCCTT,+,0.00)
chunk0004_43_1	chr1	42932232	42932530	+	0	NA	intron (NM_006516, intron 2 of 9)	intron (NM_006516, intron 2 of 9)	-26668	NR_033967	440584	Hs.260928	NR_033967	ENSG00000227533	SLC2A1-AS1	-	SLC2A1 antisense RNA 1	ncRNA	0.026846	0.575251	
chunk0116_4_1	chr21	32698313	32698693	+	0	NA	intron (NM_001160302, intron 4 of 31)	intron (NM_001160302, intron 4 of 31)	29436	NM_001160302	8867	Hs.473632	NM_003895	ENSG00000159082	SYNJ1	EIEE53|INPP5G|PARK20	synaptojanin 1	protein-coding	0.002632	0.383202	
chunk0039_17_1	chr11	95537556	95538207	+	0	NA	Intergenic	Intergenic	251909	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.004608	0.335890	
chunk0182_105_1	chr7	93305986	93306450	+	0	NA	intron (NM_001257998, intron 19 of 28)	intron (NM_001257998, intron 19 of 28)	73878	NM_024553	55610	Hs.202424	NM_017667	ENSG00000004766	VPS50	CCDC132|VPS54L	VPS50 subunit of EARP/GARPII complex	protein-coding	0.008621	0.333333	
chunk0171_180_1	chr6	125184965	125185164	+	0	NA	intron (NM_001003395, intron 1 of 6)	intron (NM_001003395, intron 1 of 6)	30790	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.000000	0.285000	
chunk0198_312_1	chr8	139634992	139635431	+	0	NA	intron (NM_001282534, intron 1 of 1)	intron (NM_001282534, intron 1 of 1)	67845	NM_001282534	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.022779	0.529545	79(AGGAGCAGGCAGTCCT,-,0.00),80(GGAGCAGGCAGTCCTG,+,0.00)
chunk0138_414_1	chr4	44692183	44692432	+	0	NA	intron (NM_021927, intron 13 of 16)	intron (NM_021927, intron 13 of 16)	13891	NM_021927	60558	Hs.546419	NM_021927	ENSG00000151806	GUF1	EF-4|EF4|EIEE40	GUF1 homolog, GTPase	protein-coding	0.008032	0.360000	85(AGGAACAGGTTGTCCT,-,0.00),86(GGAACAGGTTGTCCTC,+,0.00)
chunk0116_293_1	chr21	40324339	40325180	+	0	NA	intron (NR_073202, intron 8 of 32)	intron (NR_073202, intron 8 of 32)	-58324	NR_038896	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.004756	0.325416	
chunk0044_101_1	chr12	28519282	28519582	+	0	NA	intron (NM_018318, intron 11 of 11)	L1PB1|LINE|L1	262232	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.003333	0.352159	
chunk0152_76_1	chr5	58077149	58078048	+	0	NA	Intergenic	Intergenic	44743	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.007786	0.390000	
chunk0098_208_1	chr2	72914843	72915262	+	0	NA	Intergenic	MIR|SINE|MIR	-2423	NM_004097	2016	Hs.516090	NM_004097	ENSG00000135638	EMX1	-	empty spiracles homeobox 1	protein-coding	0.038186	0.564286	
chunk0091_400_1	chr19	16429159	16429530	+	0	NA	intron (NR_047665, intron 7 of 22)	intron (NR_047665, intron 7 of 22)	42668	NM_021235	58513	Hs.654639	NM_021235	ENSG00000127527	EPS15L1	EPS15R	epidermal growth factor receptor pathway substrate 15 like 1	protein-coding	0.026954	0.602151	
chunk0022_249_1	chr10	14571862	14572545	+	0	NA	promoter-TSS (NM_001282702)	promoter-TSS (NM_001282702)	-14	NM_001282701	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.014641	0.469298	
chunk0133_31_1	chr3	165946902	165947101	+	0	NA	Intergenic	MER89|LTR|ERV1	-109536	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.300000	
chunk0192_40_1	chr8	58759236	58759769	+	0	NA	Intergenic	Intergenic	-99657	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.005629	0.387640	
chunk0043_205_1	chr12	19458293	19458753	+	0	NA	intron (NM_001267043, intron 1 of 8)	intron (NM_001267043, intron 1 of 8)	17942	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.008696	0.407809	353(AAGTACATGAAGTACT,-,0.00)
chunk0053_373_1	chr13	35781805	35782103	+	0	NA	intron (NM_001195416, intron 12 of 12)	intron (NM_001195416, intron 12 of 12)	73907	NM_001195416	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.006711	0.404682	
chunk0150_399_1	chr5	39831648	39832258	+	0	NA	Intergenic	L1ME2z|LINE|L1	-220338	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.001639	0.325696	
chunk0127_332_1	chr3	100449473	100449890	+	0	NA	intron (NM_001085451, intron 2 of 3)	MER4-int|LTR|ERV1	-42938	NM_018004	55076	Hs.658956	NM_018004	ENSG00000181458	TMEM45A	DERP7|DNAPTP4	transmembrane protein 45A	protein-coding	0.002398	0.322967	
chunk0047_326_1	chr12	74329353	74329618	+	0	NA	Intergenic	Intergenic	-36854	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.000000	0.274436	
chunk0120_219_1	chr3	7735049	7735360	+	0	NA	intron (NM_181874, intron 10 of 10)	intron (NM_181874, intron 10 of 10)	-199920	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.000000	0.346154	141(AGGCACAGACAGTGCT,-,0.00),142(GGCACAGACAGTGCTT,+,0.00)
chunk0072_18_1	chr16	476306	476505	+	0	NA	intron (NM_001142272, intron 1 of 11)	intron (NM_001142272, intron 1 of 11)	1555	NM_001142272	9727	Hs.531642	NM_014700	ENSG00000090565	RAB11FIP3	CART1|FIP3-Rab11|Rab11-FIP3	RAB11 family interacting protein 3	protein-coding	0.015075	0.570000	
chunk0203_391_1	chr9	90524048	90524247	+	0	NA	intron (NR_034157, intron 1 of 5)	intron (NR_034157, intron 1 of 5)	58599	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.005025	0.480000	
chunk0020_222_1	chr1	235367689	235367945	+	0	NA	intron (NM_001079515, intron 1 of 16)	intron (NM_001079515, intron 1 of 16)	457	NM_001079515	6905	Hs.744998	NM_003193	ENSG00000284770	TBCE	HRD|KCS|KCS1|PEAMO|pac2	tubulin folding cofactor E	protein-coding	0.031250	0.443580	
chunk0100_397_1	chr2	119275923	119276223	+	0	NA	Intergenic	MER83|LTR|ERV1	-27002	NR_046721	100874111	Hs.704682	NR_046721	ENSG00000229867	STEAP3-AS1	-	STEAP3 antisense RNA 1	ncRNA	0.003333	0.451827	
chunk0175_283_1	chr7	7642207	7642475	+	0	NA	intron (NM_002947, intron 4 of 7)	AluJo|SINE|Alu	1705	NM_001302348	729852	Hs.652371	NM_001302348	ENSG00000219545	UMAD1	RPA3-AS1|RPA3OS	UBAP1-MVB12-associated (UMA) domain containing 1	protein-coding	0.022388	0.479554	
chunk0040_76_1	chr11	111334599	111335152	+	0	NA	Intergenic	Intergenic	-12882	NR_039712	100616330		NR_039712	ENSG00000264032	MIR4491	mir-4491	microRNA 4491	ncRNA	0.009042	0.483755	
chunk0064_118_1	chr14	91284205	91284428	+	0	NA	intron (NM_001080414, intron 25 of 29)	intron (NM_001080414, intron 25 of 29)	-30436	NM_003485	8111	Hs.8882	NM_003485	ENSG00000119714	GPR68	AI2A6|GPR12A|OGR1	G protein-coupled receptor 68	protein-coding	0.017937	0.491071	
chunk0140_236_1	chr4	71241700	71242051	+	0	NA	intron (NM_001098484, intron 2 of 25)	intron (NM_001098484, intron 2 of 25)	54589	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.005698	0.426136	150(CAGAACAGGTTGAGCC,-,0.00),151(AGAACAGGTTGAGCCC,+,0.00)
chunk0163_436_1	chr6	17388280	17388712	+	0	NA	Intergenic	Intergenic	-5009	NM_006366	10486	Hs.132902	NM_006366	ENSG00000112186	CAP2	-	cyclase associated actin cytoskeleton regulatory protein 2	protein-coding	0.011574	0.404157	
chunk0095_266_1	chr2	19774373	19774788	+	0	NA	Intergenic	Intergenic	-94274	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.002410	0.487981	
chunk0195_73_1	chr8	93969231	93969571	+	0	NA	Intergenic	L1PA6|LINE|L1	52350	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.017647	0.548387	
chunk0102_158_1	chr2	147243335	147243596	+	0	NA	Intergenic	Intergenic	-601052	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.011494	0.374046	
chunk0159_106_1	chr5	138548502	138549153	+	0	NA	Intergenic	L1MC5|LINE|L1	-5527	NM_001256302	2107	Hs.483494	NM_004730	ENSG00000120705	ETF1	D5S1995|ERF|ERF1|RF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding	0.003072	0.378834	
chunk0193_453_1	chr8	81295740	81296147	+	0	NA	Intergenic	Intergenic	15460	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.002457	0.367647	191(AAATACAGGATGTCCT,-,0.00),192(AATACAGGATGTCCTG,+,0.00)
chunk0195_12_1	chr8	92998816	92999476	+	0	NA	Intergenic	L2a|LINE|L2	-30605	NR_107051	102467005		NR_107051	ENSG00000277063	MIR8084	hsa-mir-8084	microRNA 8084	ncRNA	0.001515	0.328290	
chunk0127_274_1	chr3	97702704	97703828	+	0	NA	intron (NM_001080448, intron 14 of 17)	intron (NM_001080448, intron 14 of 17)	-61255	NR_103511	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.005338	0.357333	
chunk0106_400_1	chr2	207836932	207837172	+	0	NA	intron (NM_001080475, intron 7 of 7)	intron (NM_001080475, intron 7 of 7)	-67633	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.020833	0.402490	
chunk0054_364_1	chr13	49731713	49732323	+	0	NA	intron (NM_002267, intron 6 of 16)	intron (NM_002267, intron 6 of 16)	-40531	NR_103803	84650	Hs.433278	NM_032565	ENSG00000123179	EBPL	EBRP	EBP like	protein-coding	0.003279	0.333879	
chunk0172_405_1	chr6	140002274	140003142	+	0	NA	intron (NR_121623, intron 1 of 1)	intron (NR_121623, intron 1 of 1)	-11447	NR_121624	103352541	Hs.582647	NR_121624		LOC103352541	-	uncharacterized LOC103352541	ncRNA	0.006912	0.336018	
chunk0114_21_1	chr21	7290352	7290910	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	431460	NR_128718	103504736		NR_128718	ENSG00000278618	MIR8069-2	hsa-mir-8069-2	microRNA 8069-2	ncRNA	0.007168	0.372093	
chunk0077_356_1	chr16	83919228	83919588	+	0	NA	Intergenic	Intergenic	20283	NM_012213	23417	Hs.644610	NM_012213	ENSG00000103150	MLYCD	MCD	malonyl-CoA decarboxylase	protein-coding	0.002778	0.512465	244(GAGAACACACAGTGCA,-,0.00),245(AGAACACACAGTGCAC,+,0.00),265(GAGAACACACAGTGCA,-,0.00),266(AGAACACACAGTGCAC,+,0.00),300(GAGAACACACAGTGCA,-,0.00),301(AGAACACACAGTGCAC,+,0.00)
chunk0069_337_1	chr15	66400920	66401310	+	0	NA	intron (NM_002755, intron 1 of 10)	intron (NM_002755, intron 1 of 10)	14242	NM_002755	5604	Hs.145442	NM_002755	ENSG00000169032	MAP2K1	CFC3|MAPKK1|MEK1|MKK1|PRKMK1	mitogen-activated protein kinase kinase 1	protein-coding	0.005128	0.322251	
chunk0092_223_1	chr19	32033734	32034003	+	0	NA	intron (NR_110674, intron 1 of 2)	intron (NR_110674, intron 1 of 2)	8006	NR_110673	100996665	Hs.443685	NR_110673	ENSG00000267779	LINC01533	CTC-360P9.3	long intergenic non-protein coding RNA 1533	ncRNA	0.007435	0.448148	150(GAGGACAATTTGTGCA,-,0.00),151(AGGACAATTTGTGCAC,+,0.00)
chunk0048_4_1	chr12	76932372	76932571	+	0	NA	Intergenic	MER102c|DNA|hAT-Charlie	-53431	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.000000	0.405000	
chunk0074_148_1	chr16	23245234	23245728	+	0	NA	Intergenic	Intergenic	-56789	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.012146	0.563636	
chunk0152_290_1	chr5	61575595	61575945	+	0	NA	Intergenic	Intergenic	-62011	NM_173667									0.014286	0.467236	90(TGGTCACGCTGTTCTG,+,0.00)
chunk0145_155_1	chr4	147110998	147111465	+	0	NA	Intergenic	Intergenic	-165349	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.002141	0.339744	241(AAGCACTTTATGTTCT,-,0.00),242(AGCACTTTATGTTCTT,+,0.00)
chunk0122_310_1	chr3	36907893	36908691	+	0	NA	intron (NM_014831, intron 1 of 22)	intron (NM_014831, intron 1 of 22)	36765	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.018797	0.456821	
chunk0048_293_1	chr12	82745140	82746234	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	58532	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.006399	0.366210	786(AGAACGATTTGTTCTT,+,0.00)
chunk0210_327_1	chrX	94252337	94252536	+	0	NA	Intergenic	MIR|SINE|MIR	578423	NM_173698	286499	Hs.110069	NM_173698	ENSG00000179083	FAM133A	CT115	family with sequence similarity 133 member A	protein-coding	0.005025	0.385000	
chunk0144_374_1	chr4	140012756	140013115	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	141144	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.016713	0.391667	
chunk0207_167_1	chr9	130261118	130261430	+	0	NA	Intergenic	Intergenic	-4605	NM_001291815	256158	Hs.32194	NM_144655	ENSG00000148357	HMCN2	-	hemicentin 2	protein-coding	0.022436	0.485623	
chunk0207_176_1	chr9	130528889	130529491	+	0	NA	Intergenic	Intergenic	50304	NR_027440	100272217	Hs.601255	NR_027440		LOC100272217	-	uncharacterized LOC100272217	ncRNA	0.008306	0.417910	
chunk0178_122_1	chr7	31477401	31477659	+	0	NA	Intergenic	Intergenic	-36541	NM_001257967	223075	Hs.224269	NM_194300	ENSG00000180347	ITPRID1	CCDC129	ITPR interacting domain containing 1	protein-coding	0.019380	0.459459	
chunk0014_194_1	chr1	178953061	178953336	+	0	NA	Intergenic	Intergenic	-72741	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.014545	0.514493	
chunk0002_330_1	chr1	24389586	24390138	+	0	NA	intron (NM_178122, intron 2 of 7)	intron (NM_178122, intron 2 of 7)	23910	NM_178122	90529	Hs.403187	NM_178122	ENSG00000001460	STPG1	C1orf201|MAPO2	sperm tail PG-rich repeat containing 1	protein-coding	0.007246	0.401447	
chunk0076_335_1	chr16	71289383	71289963	+	0	NA	promoter-TSS (NM_018348)	promoter-TSS (NM_018348)	-67	NM_018348	55783	Hs.72782	NM_018348	ENSG00000180917	CMTR2	AFT|FTSJD1|HMTr2|MTr2	cap methyltransferase 2	protein-coding	0.055172	0.555938	
chunk0124_16_1	chr3	51652133	51652445	+	0	NA	intron (NM_015106, intron 18 of 21)	L1PA6|LINE|L1	-18886	NR_024012	51368	Hs.517864	NM_015926	ENSG00000164081	TEX264	ZSIG11	testis expressed 264, ER-phagy receptor	protein-coding	0.006410	0.383387	
chunk0126_2_1	chr3	73273049	73273669	+	0	NA	Intergenic	Intergenic	160637	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.004839	0.394525	
chunk0204_430_1	chr9	103398065	103398304	+	0	NA	Intergenic	L1PB4|LINE|L1	-73151	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.008368	0.491667	
chunk0113_321_1	chr20	58319103	58319302	+	0	NA	intron (NM_020673, intron 2 of 6)	L1M5|LINE|L1	9487	NM_020673	57403	Hs.529044	NM_020673	ENSG00000124209	RAB22A	-	RAB22A, member RAS oncogene family	protein-coding	0.005025	0.320000	
chunk0079_390_1	chr17	18987943	18988387	+	0	NA	intron (NM_001039999, intron 3 of 5)	L2b|LINE|L2	16582	NM_001039999	644815	Hs.710727	NM_001039999	ENSG00000188522	FAM83G	PAWS1	family with sequence similarity 83 member G	protein-coding	0.027027	0.550562	
chunk0157_327_1	chr5	122088817	122089353	+	0	NA	Intergenic	Intergenic	-10725	NM_002317	4015	Hs.102267	NM_002317	ENSG00000113083	LOX	AAT10	lysyl oxidase	protein-coding	0.003731	0.370577	324(AAAGACACTTTGTTCC,-,0.00),325(AAGACACTTTGTTCCA,+,0.00)
chunk0024_226_1	chr10	37976809	37977008	+	0	NA	promoter-TSS (NM_145011)	promoter-TSS (NM_145011)	-383	NM_145011	219749	Hs.499429	NM_145011	ENSG00000175395	ZNF25	KOX19|Zfp9	zinc finger protein 25	protein-coding	0.035176	0.500000	
chunk0007_312_1	chr1	84365891	84366182	+	0	NA	intron (NR_003927, intron 5 of 6)	intron (NR_003927, intron 5 of 6)	18765	NR_003927	391051	Hs.647646	NR_003927		UOX	UOXP|URICASE	urate oxidase (pseudogene)	pseudo	0.006873	0.500000	182(AAGGACAGCTTGTTCA,-,0.00),183(AGGACAGCTTGTTCAG,+,0.00)
chunk0125_378_1	chr3	71560865	71561131	+	0	NA	intron (NM_032682, intron 2 of 20)	L1MB7|LINE|L1	-17441	NM_001244816	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.011278	0.419476	
chunk0144_232_1	chr4	134846580	134847288	+	0	NA	Intergenic	Intergenic	-645186	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.004237	0.328632	167(AGGACAGACTGCCCAG,+,0.00)
chunk0083_137_1	chr17	65628358	65628608	+	0	NA	Intergenic	Intergenic	-66861	NM_004655	8313	Hs.156527	NM_004655	ENSG00000168646	AXIN2	AXIL|ODCRCS	axin 2	protein-coding	0.040000	0.509960	
chunk0084_380_1	chr17	81918073	81918364	+	0	NA	promoter-TSS (NM_016538)	promoter-TSS (NM_016538)	-36	NM_016538	51547	Hs.514636	NM_016538	ENSG00000187531	SIRT7	SIR2L7	sirtuin 7	protein-coding	0.082474	0.599315	
chunk0143_363_1	chr4	122159724	122160334	+	0	NA	Intergenic	Intergenic	-10574	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.006557	0.353519	
chunk0068_149_1	chr15	53694759	53695001	+	0	NA	intron (NR_102334, intron 13 of 19)	MER58A|DNA|hAT-Charlie	64782	NM_182758	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.004132	0.370370	
chunk0155_66_1	chr5	91608485	91608790	+	0	NA	Intergenic	Intergenic	-225305	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.274510	
chunk0134_221_1	chr3	178793833	178794186	+	0	NA	intron (NR_126560, intron 2 of 7)	intron (NR_126560, intron 2 of 7)	66396	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.008499	0.483051	
chunk0130_357_1	chr3	138915362	138915700	+	0	NA	Intergenic	CpG	28489	NR_121649	103344930	Hs.195033	NR_121649	ENSG00000244578	LINC01391	-	long intergenic non-protein coding RNA 1391	ncRNA	0.088757	0.693215	105(CAGATCACTTTGTCCC,-,0.00),106(AGATCACTTTGTCCCT,+,0.00)
chunk0004_60_1	chr1	43235450	43236004	+	0	NA	intron (NM_001195831, intron 22 of 23)	intron (NM_001195831, intron 22 of 23)	-34267	NM_144626	128218	Hs.104476	NM_144626	ENSG00000179178	TMEM125	-	transmembrane protein 125	protein-coding	0.012635	0.571171	
chunk0150_77_1	chr5	32174537	32175255	+	0	NA	promoter-TSS (NM_022130)	promoter-TSS (NM_022130)	-577	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.048747	0.514604	409(GAGTACAGTTAGTACC,-,0.00),410(AGTACAGTTAGTACCG,+,0.00)
chunk0132_198_1	chr3	157268506	157268856	+	0	NA	intron (NM_001167911, intron 11 of 12)	intron (NM_001167911, intron 11 of 12)	-107921	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.000000	0.398860	
chunk0050_237_1	chr12	105209452	105210040	+	0	NA	intron (NM_018171, intron 5 of 20)	intron (NM_018171, intron 5 of 20)	23659	NM_001251905	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.011905	0.409168	
chunk0107_329_1	chr2	220325736	220326186	+	0	NA	Intergenic	Intergenic	-419396	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.000000	0.368071	
chunk0096_33_1	chr2	26817852	26818240	+	0	NA	Intergenic	Intergenic	-30055	NM_020134	56896	Hs.299315	NM_020134	ENSG00000157851	DPYSL5	CRAM|CRMP-5|CRMP5|Ulip6	dihydropyrimidinase like 5	protein-coding	0.010309	0.383033	
chunk0028_329_1	chr10	92014578	92015139	+	0	NA	intron (NM_003972, intron 32 of 37)	Tigger3a|DNA|TcMar-Tigger	90879	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.001783	0.357651	
chunk0143_234_1	chr4	114465385	114465743	+	0	NA	Intergenic	Intergenic	-132891	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.002793	0.337047	
chunk0160_434_1	chr5	164580269	164580818	+	0	NA	Intergenic	Intergenic	110264	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.003643	0.350909	
chunk0071_315_1	chr15	86544039	86544365	+	0	NA	intron (NM_152336, intron 18 of 23)	MLT1H|LTR|ERVL-MaLR	-227234	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.006135	0.428135	
chunk0207_402_1	chr9	136804480	136804864	+	0	NA	non-coding (NR_024580, exon 5 of 5)	non-coding (NR_024580, exon 5 of 5)	-3250	NM_024718	55684	Hs.370555	NM_017995	ENSG00000196642	RABL6	C9orf86|PARF|RBEL1|pp8875	RAB, member RAS oncogene family like 6	protein-coding	0.039062	0.638961	
chunk0031_453_1	chr10	132685284	132686117	+	0	NA	intron (NM_005539, intron 4 of 15)	intron (NM_005539, intron 4 of 15)	100333	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.039616	0.557554	478(CGGGACGCGTTGTTCT,-,0.00),479(GGGACGCGTTGTTCTT,+,0.00)
chunk0081_365_1	chr17	47884269	47884569	+	0	NA	Intergenic	Intergenic	-11731	NM_003110	6668	Hs.514276	NM_003110	ENSG00000167182	SP2	-	Sp2 transcription factor	protein-coding	0.020000	0.604651	
chunk0211_20_1	chrX	107778808	107779042	+	0	NA	Intergenic	L2c|LINE|L2	-3138	NM_198057	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.000000	0.485106	
chunk0092_351_1	chr19	35395983	35396277	+	0	NA	Intergenic	MamRep4096|DNA|hAT-Tip100	-9477	NR_040046	100128682	Hs.570008	NR_040046	ENSG00000205786	LINC01531	-	long intergenic non-protein coding RNA 1531	ncRNA	0.027211	0.518644	
chunk0145_381_1	chr4	151629574	151629874	+	0	NA	exon (NM_001109977, exon 8 of 14)	exon (NM_001109977, exon 8 of 14)	131299	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.040000	0.521595	
chunk0002_61_1	chr1	13715332	13715702	+	0	NA	intron (NM_012231, intron 1 of 9)	intron (NM_012231, intron 1 of 9)	10662	NM_015866	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.000000	0.334232	
chunk0028_208_1	chr10	89251152	89251351	+	0	NA	intron (NM_000235, intron 1 of 9)	MIR|SINE|MIR	657	NM_001127605	3988	Hs.643030	NM_000235	ENSG00000107798	LIPA	CESD|LAL	lipase A, lysosomal acid type	protein-coding	0.025126	0.465000	
chunk0061_276_1	chr14	61534212	61534576	+	0	NA	intron (NM_006255, intron 12 of 13)	intron (NM_006255, intron 12 of 13)	35800	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.010989	0.408219	
chunk0021_400_1	chr1	246640619	246641153	+	0	NA	intron (NM_152609, intron 6 of 10)	L1ME3|LINE|L1	74549	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.003745	0.358879	
chunk0184_32_1	chr7	112067684	112068450	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	138340	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.006527	0.405476	
chunk0100_64_1	chr2	106554532	106554799	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-86320	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.014981	0.376866	98(CTGTACAGGCTGTACT,-,0.00),99(TGTACAGGCTGTACTC,+,0.00)
chunk0082_57_1	chr17	51260105	51260560	+	0	NA	promoter-TSS (NM_016001)	promoter-TSS (NM_016001)	-204	NM_016001	51096	Hs.709327	NM_016001	ENSG00000011260	UTP18	CGI-48|WDR50	UTP18 small subunit processome component	protein-coding	0.072527	0.614035	
chunk0164_65_1	chr6	19439041	19439240	+	0	NA	Intergenic	Intergenic	-258660	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.010050	0.415000	
chunk0143_372_1	chr4	122507839	122508556	+	0	NA	Intergenic	Intergenic	-51702	NM_000586	3558	Hs.89679	NM_000586	ENSG00000109471	IL2	IL-2|TCGF|lymphokine	interleukin 2	protein-coding	0.005579	0.356546	
chunk0191_94_1	chr8	47734830	47735579	+	0	NA	intron (NR_104581, intron 16 of 16)	intron (NR_104581, intron 16 of 16)	2960	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.022697	0.494667	421(GGGAACAGTACGTCCC,-,0.00),422(GGAACAGTACGTCCCA,+,0.00)
chunk0005_335_1	chr1	61132923	61133793	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	51050	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.004598	0.371986	
chunk0104_393_1	chr2	180413237	180413734	+	0	NA	Intergenic	Intergenic	-278619	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.004024	0.393574	
chunk0189_204_1	chr8	24101343	24101650	+	0	NA	Intergenic	MIR|SINE|MIR	-192544	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.006515	0.360390	
chunk0072_434_1	chr15	101245817	101246319	+	0	NA	intron (NM_014918, intron 1 of 2)	intron (NM_014918, intron 1 of 2)	5864	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.003984	0.379722	
chunk0059_142_1	chr14	32059592	32060295	+	0	NA	Intergenic	Intergenic	16756	NR_027263	84837	Hs.496755	NM_032751		ARHGAP5-AS1	C14orf128	ARHGAP5 antisense RNA 1 (head to head)	ncRNA	0.002845	0.390625	413(TGGAACAGTGAGTGCT,-,0.00),414(GGAACAGTGAGTGCTC,+,0.00)
chunk0013_192_1	chr1	169185459	169186121	+	0	NA	intron (NM_197972, intron 10 of 11)	L2b|LINE|L2	79081	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.001511	0.337858	
chunk0081_247_1	chr17	43030047	43030548	+	0	NA	3' UTR (NM_005440, exon 5 of 5)	3' UTR (NM_005440, exon 5 of 5)	5056	NM_005440	8153	Hs.603111	NM_005440	ENSG00000108830	RND2	ARHN|RHO7|RhoN	Rho family GTPase 2	protein-coding	0.009980	0.531873	
chunk0147_200_1	chr4	177824920	177825376	+	0	NA	intron (NR_108092, intron 1 of 1)	intron (NR_108092, intron 1 of 1)	82788	NR_108092	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.006579	0.310722	
chunk0211_386_1	chrX	127806330	127806631	+	0	NA	Intergenic	Intergenic	245923	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.000000	0.311258	
chunk0054_233_1	chr13	45678393	45678646	+	0	NA	Intergenic	Intergenic	22665	NR_125786	103752581		NR_125786		LINC01055	-	long intergenic non-protein coding RNA 1055	ncRNA	0.000000	0.417323	
chunk0039_209_1	chr11	101017379	101017755	+	0	NA	Intergenic	Intergenic	25487	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.000000	0.275862	
chunk0166_161_1	chr6	45556208	45556532	+	0	NA	Intergenic	Intergenic	133793	NM_001278478	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.012346	0.430769	165(CAGAGCAGGATGTTCT,-,0.00),166(AGAGCAGGATGTTCTT,+,0.00)
chunk0042_461_1	chr12	12576226	12576611	+	0	NA	Intergenic	MIRb|SINE|MIR	-13904	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.002597	0.417098	
chunk0174_415_1	chr6	165684018	165684320	+	0	NA	Intergenic	L2a|LINE|L2	-22069	NM_001130690	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.006623	0.445545	
chunk0112_20_1	chr20	36093856	36094625	+	0	NA	intron (NM_001258329, intron 1 of 22)	intron (NM_001258329, intron 1 of 22)	1530	NM_001258329	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.009103	0.459740	450(AGAAACATTCTGTACC,-,0.00),451(GAAACATTCTGTACCG,+,0.00)
chunk0125_315_1	chr3	70803253	70804351	+	0	NA	Intergenic	Intergenic	261121	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.008197	0.368517	
chunk0099_352_1	chr2	100302352	100303518	+	0	NA	exon (NM_198461, exon 3 of 12)	exon (NM_198461, exon 3 of 12)	19798	NM_198461	164832	Hs.21380	NM_198461	ENSG00000170500	LONRF2	RNF192	LON peptidase N-terminal domain and ring finger 2	protein-coding	0.010292	0.357326	
chunk0058_153_1	chr14	23193447	23193773	+	0	NA	Intergenic	HAL1|LINE|L1	-9950	NM_012244	23428	Hs.596643	NM_012244	ENSG00000092068	SLC7A8	LAT2|LPI-PC1	solute carrier family 7 member 8	protein-coding	0.009202	0.397554	
chunk0134_353_1	chr3	182606272	182606521	+	0	NA	Intergenic	L1MC3|LINE|L1	-120034	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.008032	0.416000	
chunk0142_150_1	chr4	94955356	94955661	+	0	NA	intron (NM_001203, intron 2 of 12)	intron (NM_001203, intron 2 of 12)	-40724	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.006557	0.372549	
chunk0124_300_1	chr3	57896173	57897138	+	0	NA	intron (NM_001311178, intron 2 of 10)	intron (NM_001311178, intron 2 of 10)	6741	NM_001304422	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.008290	0.343685	
chunk0036_182_1	chr11	62787277	62787493	+	0	NA	promoter-TSS (NM_199337)	promoter-TSS (NM_199337)	-17	NM_199337	374395	Hs.381134	NM_199337	ENSG00000185475	TMEM179B	-	transmembrane protein 179B	protein-coding	0.097222	0.649770	
chunk0008_274_1	chr1	94738450	94738812	+	0	NA	intron (NR_104131, intron 1 of 4)	L1PA16|LINE|L1	7269	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.005525	0.380165	
chunk0081_42_1	chr17	37646514	37646949	+	0	NA	Intergenic	Intergenic	-3267	NM_001291476	11056	Hs.590937	NM_007010	ENSG00000278053	DDX52	HUSSY19|ROK1	DExD-box helicase 52	protein-coding	0.006897	0.371560	
chunk0065_428_1	chr14	106191702	106191901	+	0	NA	Intergenic	L1PB4|LINE|L1	-95873	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.005025	0.315000	
chunk0176_304_1	chr7	16833161	16833801	+	0	NA	Intergenic	Intergenic	-28367	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.003125	0.357254	
chunk0077_139_1	chr16	78689073	78689597	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	589922	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.003817	0.462857	
chunk0100_455_1	chr2	121086650	121086881	+	0	NA	Intergenic	Intergenic	198437	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.030303	0.603448	119(GGGCACAGCCAGTGCC,-,0.00),120(GGCACAGCCAGTGCCC,+,0.00)
chunk0181_203_1	chr7	84450701	84451104	+	0	NA	Intergenic	L1M3|LINE|L1	-81574	NR_110080	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.002481	0.331683	
chunk0183_211_1	chr7	106449085	106449373	+	0	NA	Intergenic	Intergenic	-164037	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.006944	0.484429	
chunk0106_283_1	chr2	204086388	204086742	+	0	NA	Intergenic	Intergenic	149817	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.005650	0.385915	
chunk0164_445_1	chr6	28048928	28049544	+	0	NA	Intergenic	L1MEg2|LINE|L1	-31468	NM_003447	7718	Hs.55481	NM_003447	ENSG00000197279	ZNF165	CT53|LD65|ZSCAN7	zinc finger protein 165	protein-coding	0.008117	0.408428	278(AGGAACATTCTGAACT,-,0.00),279(GGAACATTCTGAACTG,+,0.00)
chunk0001_2_1	chr1	591068	591464	+	0	NA	Intergenic	L1MA4|LINE|L1	37743	NR_125957	101928626	Hs.637667	NR_125957	ENSG00000230021	LOC101928626	-	uncharacterized LOC101928626	ncRNA	0.035354	0.448363	
chunk0113_253_1	chr20	55004228	55004583	+	0	NA	Intergenic	Intergenic	-418638	NR_110629	102723578	Hs.446269	NR_110629	ENSG00000235166	LINC01440	-	long intergenic non-protein coding RNA 1440	ncRNA	0.002817	0.370787	
chunk0194_41_1	chr8	81920818	81921118	+	0	NA	Intergenic	Intergenic	-78682	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.375415	
chunk0046_56_1	chr12	55619264	55619485	+	0	NA	Intergenic	AluJb|SINE|Alu	-17518	NM_206899	121130	Hs.554551	NM_206899	ENSG00000175398	OR10P1	OR10P1P|OR10P2P|OR10P3P|OR12-7|OST701	olfactory receptor family 10 subfamily P member 1	protein-coding	0.000000	0.481982	
chunk0173_261_1	chr6	147154554	147154796	+	0	NA	intron (NR_034115, intron 3 of 10)	intron (NR_034115, intron 3 of 10)	-4250	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.004132	0.403292	
chunk0198_307_1	chr8	138521347	138521933	+	0	NA	Intergenic	L1ME4a|LINE|L1	-24818	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.005119	0.359455	
chunk0186_141_1	chr7	138733172	138733371	+	0	NA	intron (NM_130840, intron 15 of 20)	intron (NM_130840, intron 15 of 20)	40766	NM_130841	50617	Hs.98967	NM_020632	ENSG00000105929	ATP6V0A4	A4|ATP6N1B|ATP6N2|RDRTA2|RTA1C|RTADR|STV1|VPH1|VPP2	ATPase H+ transporting V0 subunit a4	protein-coding	0.015075	0.425000	1(AAGCACAAAATGTTCT,-,0.00),2(AGCACAAAATGTTCTA,+,0.00)
chunk0052_141_1	chr13	23743488	23744115	+	0	NA	intron (NM_005932, intron 18 of 18)	(AC)n|Simple_repeat|Simple_repeat	-145088	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.011164	0.390127	
chunk0106_125_1	chr2	198706678	198707094	+	0	NA	Intergenic	Intergenic	-331789	NR_110267	101927619	Hs.632942	NR_110267		LINC01923	-	long intergenic non-protein coding RNA 1923	ncRNA	0.002404	0.354916	
chunk0008_332_1	chr1	95540872	95541398	+	0	NA	Intergenic	L1MA9|LINE|L1	31019	NR_110621	100996635	Hs.639548	NR_110621	ENSG00000228971	LINC02607	-	long intergenic non-protein coding RNA 2607	ncRNA	0.003802	0.328273	
chunk0206_249_1	chr9	123753809	123754022	+	0	NA	intron (NM_024820, intron 5 of 20)	L2c|LINE|L2	176223	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.009390	0.509346	
chunk0012_423_1	chr1	164618590	164618805	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	59337	NM_001204963	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.004651	0.384259	
chunk0062_108_1	chr14	68274202	68274578	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	454611	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.005319	0.326260	
chunk0203_119_1	chr9	84898056	84898682	+	0	NA	intron (NM_001018064, intron 12 of 16)	intron (NM_001018064, intron 12 of 16)	227992	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.003195	0.393939	
chunk0122_63_1	chr3	28860310	28860685	+	0	NA	Intergenic	Intergenic	285219	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.008000	0.430851	249(CAGAACACCCTGTTAA,-,0.00)
chunk0150_111_1	chr5	32843592	32843791	+	0	NA	Intergenic	Intergenic	-103752	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.005025	0.395000	
chunk0087_439_1	chr18	42529371	42529704	+	0	NA	intron (NR_046454, intron 6 of 6)	intron (NR_046454, intron 6 of 6)	342869	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.003003	0.395210	
chunk0185_100_1	chr7	125573166	125573480	+	0	NA	Intergenic	Intergenic	-309032	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.012739	0.361905	
chunk0071_12_1	chr15	78914505	78914755	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	30448	NM_004390	1512	Hs.148641	NM_004390	ENSG00000103811	CTSH	ACC-4|ACC-5|ACC4|ACC5|CPSB	cathepsin H	protein-coding	0.008000	0.466135	163(AAGTACTCTCAGTCCC,-,0.00)
chunk0015_116_1	chr1	185317172	185317466	+	0	NA	promoter-TSS (NM_006469)	promoter-TSS (NM_006469)	10	NM_006469	10625	Hs.497183	NM_006469	ENSG00000116679	IVNS1ABP	ARA3|FLARA3|HSPC068|KLHL39|ND1|NS-1|NS1-BP|NS1BP	influenza virus NS1A binding protein	protein-coding	0.122449	0.694915	
chunk0195_378_1	chr8	100065981	100066220	+	0	NA	intron (NM_001286692, intron 7 of 27)	intron (NM_001286692, intron 7 of 27)	39526	NM_001286693	26166	Hs.120021	NM_015668	ENSG00000132554	RGS22	CT145|PRTD-NY2	regulator of G protein signaling 22	protein-coding	0.008368	0.358333	
chunk0110_387_1	chr20	20138619	20138898	+	0	NA	intron (NM_015585, intron 8 of 26)	L1M1|LINE|L1	82112	NM_001167816	26074	Hs.729168	NM_015585	ENSG00000089101	CFAP61	C20orf26|CaM-IP3|dJ1002M8.3|dJ1178H5.4	cilia and flagella associated protein 61	protein-coding	0.000000	0.378571	188(TTGTACAGTTTGTTCT,-,0.00),189(TGTACAGTTTGTTCTT,+,0.00)
chunk0174_165_1	chr6	158468101	158468376	+	0	NA	intron (NM_001007466, intron 6 of 12)	LTR22B|LTR|ERVK	-68198	NM_020823	57583	Hs.99145	NM_020823	ENSG00000146433	TMEM181	GPR178|KIAA1423	transmembrane protein 181	protein-coding	0.018182	0.365942	
chunk0070_51_1	chr15	69561997	69562904	+	0	NA	intron (NR_026979, intron 1 of 4)	MIRc|SINE|MIR	730	NR_026979	145837	Hs.410126	NR_026979		DRAIC	-	downregulated RNA in cancer, inhibitor of cell invasion and migration	ncRNA	0.014333	0.426211	
chunk0166_411_1	chr6	52332124	52332332	+	0	NA	Intergenic	L2c|LINE|L2	-29900	NM_133367	85315	Hs.239388	NM_133367	ENSG00000170915	PAQR8	C6orf33|LMPB1|MPRB	progestin and adipoQ receptor family member 8	protein-coding	0.004808	0.444976	
chunk0132_139_1	chr3	156316147	156316822	+	0	NA	intron (NM_001308222, intron 1 of 12)	MIR|SINE|MIR	25447	NM_001308222	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.001481	0.452663	346(GGGAACTGATTGTACT,-,0.00),347(GGAACTGATTGTACTG,+,0.00)
chunk0080_56_1	chr17	21861147	21861387	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	168744	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.033333	0.414938	180(AGAACAGAATGGACTG,+,0.00)
chunk0005_71_1	chr1	55833342	55833817	+	0	NA	Intergenic	Intergenic	607938	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.002105	0.371849	
chunk0019_13_1	chr1	223392686	223393084	+	0	NA	promoter-TSS (NM_152610)	promoter-TSS (NM_152610)	-488	NM_152610	164127	Hs.192090	NM_152610	ENSG00000178395	CCDC185	C1orf65	coiled-coil domain containing 185	protein-coding	0.025126	0.446115	
chunk0169_238_1	chr6	105107163	105107517	+	0	NA	intron (NM_007073, intron 7 of 7)	intron (NM_007073, intron 7 of 7)	29006	NM_147147	11149	Hs.221660	NM_007073	ENSG00000112276	BVES	CARICK|HBVES|LGMD2X|LGMDR25|POP1|POPDC1	blood vessel epicardial substance	protein-coding	0.000000	0.366197	
chunk0068_285_1	chr15	56967282	56967788	+	0	NA	intron (NM_003205, intron 3 of 19)	intron (NM_003205, intron 3 of 19)	48900	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.007905	0.384615	
chunk0091_125_1	chr19	6280044	6280475	+	0	NA	promoter-TSS (NM_005934)	promoter-TSS (NM_005934)	-311	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.104408	0.710648	
chunk0050_150_1	chr12	102874862	102875189	+	0	NA	intron (NM_000277, intron 4 of 12)	intron (NM_000277, intron 4 of 12)	42578	NM_000277	5053	Hs.560019	NM_000277	ENSG00000171759	PAH	PH|PKU|PKU1	phenylalanine hydroxylase	protein-coding	0.027523	0.542683	266(AGGAACAGAGAGAGCC,-,0.00)
chunk0182_420_1	chr7	101144428	101144628	+	0	NA	Intergenic	AluJb|SINE|Alu	-9877	NM_001283	1174	Hs.489365	NM_001283	ENSG00000106367	AP1S1	AP19|CLAPS1|EKV3|MEDNIK|SIGMA1A	adaptor related protein complex 1 subunit sigma 1	protein-coding	0.020000	0.532338	
chunk0118_56_1	chr22	27935777	27936528	+	0	NA	intron (NR_026963, intron 2 of 4)	Tigger2b_Pri|DNA|TcMar-Tigger	-15540	NR_036169	100423034		NR_036169	ENSG00000264073	MIR3199-1	mir-3199-1	microRNA 3199-1	ncRNA	0.002663	0.319149	260(TAGTACATACTGTGCT,-,0.00),261(AGTACATACTGTGCTA,+,0.00),363(GTGAGCAGTGTGTCCC,-,0.00),364(TGAGCAGTGTGTCCCG,+,0.00)
chunk0091_283_1	chr19	11794004	11794215	+	0	NA	Intergenic	L1M2|LINE|L1	-4467	NM_152356	126069	Hs.631634	NM_152356	ENSG00000177599	ZNF491	-	zinc finger protein 491	protein-coding	0.009479	0.358491	
chunk0181_216_1	chr7	84654221	84654805	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	122037	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.001712	0.377778	317(CAGAACACTCTGTCCC,-,0.00),318(AGAACACTCTGTCCCC,+,0.00)
chunk0068_123_1	chr15	52601094	52602229	+	0	NA	intron (NM_019600, intron 7 of 12)	intron (NM_019600, intron 7 of 12)	-32215	NM_001306191	10776	Hs.512908	NM_006628	ENSG00000128989	ARPP19	ARPP-16|ARPP-19|ARPP16|ENSAL	cAMP regulated phosphoprotein 19	protein-coding	0.005286	0.316021	
chunk0037_120_1	chr11	72813936	72814400	+	0	NA	promoter-TSS (NM_033388)	promoter-TSS (NM_033388)	-238	NM_033388	89849	Hs.653186	NM_033388	ENSG00000168010	ATG16L2	ATG16B|WDR80	autophagy related 16 like 2	protein-coding	0.112069	0.739785	
chunk0196_2_1	chr8	101396620	101397045	+	0	NA	Intergenic	Intergenic	27939	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.004706	0.478873	206(AGGAACACAAAGTTCT,-,0.00),207(GGAACACAAAGTTCTT,+,0.00)
chunk0207_389_1	chr9	136615324	136615928	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-43230	NR_046367	51162	Hs.91481	NM_016215	ENSG00000172889	EGFL7	NEU1|VE-STATIN|ZNEU1	EGF like domain multiple 7	protein-coding	0.023179	0.590083	
chunk0041_15_1	chr12	414780	415267	+	0	NA	intron (NM_032358, intron 4 of 12)	intron (NM_032358, intron 4 of 12)	13448	NM_001130146	84318	Hs.631656	NM_032358	ENSG00000120647	CCDC77	-	coiled-coil domain containing 77	protein-coding	0.008214	0.418033	
chunk0056_420_1	chr13	94455347	94455743	+	0	NA	intron (NM_001129889, intron 6 of 9)	MER58A|DNA|hAT-Charlie	24137	NM_001129889	1638	Hs.301865	NM_001922	ENSG00000080166	DCT	TRP-2|TYRP2	dopachrome tautomerase	protein-coding	0.005051	0.400504	
chunk0060_54_1	chr14	41465393	41465763	+	0	NA	Intergenic	Intergenic	-141983	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.005405	0.366577	
chunk0162_51_1	chr6	1295988	1296913	+	0	NA	Intergenic	Intergenic	-15990	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.011892	0.427646	
chunk0083_250_1	chr17	67991110	67991365	+	0	NA	3' UTR (NM_181656, exon 3 of 3)	3' UTR (NM_181656, exon 3 of 3)	2412	NM_181655	284018	Hs.90790	NM_181655	ENSG00000186665	C17orf58	-	chromosome 17 open reading frame 58	protein-coding	0.003922	0.339844	
chunk0009_126_1	chr1	103389938	103390380	+	0	NA	Intergenic	L2b|LINE|L2	135324	NM_001286997	101928436	Hs.558999	NM_001286997		LOC101928436	-	uncharacterized LOC101928436	protein-coding	0.006787	0.361174	
chunk0088_387_1	chr18	54307183	54307544	+	0	NA	Intergenic	L1PA6|LINE|L1	37884	NM_007195	11201	Hs.438533	NM_007195	ENSG00000101751	POLI	RAD30B|RAD3OB|eta2	DNA polymerase iota	protein-coding	0.011080	0.397790	100(GGTACATTGTGTCTTT,+,0.00)
chunk0018_408_1	chr1	222648910	222649330	+	0	NA	intron (NM_198551, intron 8 of 27)	intron (NM_198551, intron 8 of 27)	4817	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.004762	0.351544	
chunk0194_16_1	chr8	81551941	81552398	+	0	NA	Intergenic	L2b|LINE|L2	-20854	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.006565	0.438865	
chunk0071_73_1	chr15	80704605	80705333	+	0	NA	intron (NM_021214, intron 1 of 2)	intron (NM_021214, intron 1 of 2)	9658	NM_021214	58489	Hs.459072	NM_021214	ENSG00000136379	ABHD17C	FAM108C1	abhydrolase domain containing 17C	protein-coding	0.010989	0.513032	
chunk0171_277_1	chr6	127934549	127934878	+	0	NA	Intergenic	Intergenic	-16082	NM_001164687	387357	Hs.661756	NM_001010923	ENSG00000172673	THEMIS	C6orf190|C6orf207|GASP|SPOT|TSEPA	thymocyte selection associated	protein-coding	0.015198	0.430303	
chunk0055_324_1	chr13	68745485	68745846	+	0	NA	Intergenic	Intergenic	139660	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.002770	0.334254	
chunk0125_12_1	chr3	61862507	61863170	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	301269	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.015083	0.463855	
chunk0197_274_1	chr8	123911979	123912179	+	0	NA	intron (NM_001039112, intron 1 of 40)	intron (NM_001039112, intron 1 of 40)	60092	NM_001039112	654463	Hs.632058	NM_001039112	ENSG00000214814	FER1L6	C8ORFK23	fer-1 like family member 6	protein-coding	0.005000	0.452736	
chunk0063_271_1	chr14	84031449	84031954	+	0	NA	Intergenic	L1MC4a|LINE|L1	-1362178	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.001980	0.326087	
chunk0022_185_1	chr10	13327352	13327850	+	0	NA	intron (NM_001195602, intron 6 of 7)	intron (NM_001195602, intron 6 of 7)	20697	NM_001195604	22929	Hs.124027	NM_012247	ENSG00000086475	SEPHS1	SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding	0.008032	0.374749	
chunk0123_453_1	chr3	51108361	51108614	+	0	NA	intron (NM_004947, intron 9 of 52)	L1PREC2|LINE|L1	-276750	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.007905	0.397638	
chunk0149_129_1	chr5	19727204	19727669	+	0	NA	intron (NM_001167667, intron 4 of 12)	MLT1C|LTR|ERVL-MaLR	158836	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006452	0.407725	
chunk0004_184_1	chr1	46084634	46084909	+	0	NA	intron (NM_001303427, intron 1 of 9)	intron (NM_001303427, intron 1 of 9)	47937	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.000000	0.376812	49(AAAGACAAGGTGTTCC,-,0.00),50(AAGACAAGGTGTTCCC,+,0.00)
chunk0133_400_1	chr3	174335905	174336246	+	0	NA	Intergenic	Intergenic	-415279	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.000000	0.397661	
chunk0049_112_1	chr12	91309756	91310370	+	0	NA	Intergenic	Intergenic	-126939	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.003257	0.295935	
chunk0034_59_1	chr11	27118926	27119663	+	0	NA	intron (NM_003986, intron 6 of 8)	intron (NM_003986, intron 6 of 8)	78332	NM_003986	8424	Hs.591996	NM_003986	ENSG00000129151	BBOX1	BBH|BBOX|G-BBH|gamma-BBH	gamma-butyrobetaine hydroxylase 1	protein-coding	0.004071	0.338753	
chunk0192_310_1	chr8	66820211	66820949	+	0	NA	intron (NM_001033578, intron 5 of 16)	L1MB7|LINE|L1	45399	NM_170709	23678	Hs.613417	NM_013257	ENSG00000104205	SGK3	CISK|SGK2|SGKL	serum/glucocorticoid regulated kinase family member 3	protein-coding	0.004065	0.378890	
chunk0135_261_1	chr3	189078813	189079235	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	-92950	NM_198485	285386	Hs.729544	NM_198485	ENSG00000188001	TPRG1	FAM79B	tumor protein p63 regulated 1	protein-coding	0.004739	0.418440	
chunk0197_332_1	chr8	125160262	125160463	+	0	NA	intron (NM_173685, intron 4 of 7)	intron (NM_173685, intron 4 of 7)	68521	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.019900	0.450495	
chunk0190_219_1	chr8	35761699	35762082	+	0	NA	intron (NM_080872, intron 14 of 16)	intron (NM_080872, intron 14 of 16)	-51570	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.005222	0.427083	186(TAGAACATCATGTGCA,-,0.00),187(AGAACATCATGTGCAC,+,0.00)
chunk0030_258_1	chr10	115866208	115866590	+	0	NA	intron (NM_207303, intron 28 of 28)	MIRb|SINE|MIR	405908	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.002618	0.323760	
chunk0154_62_1	chr5	77320250	77320642	+	0	NA	intron (NM_001029854, intron 2 of 20)	intron (NM_001029854, intron 2 of 20)	109565	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.012755	0.437659	
chunk0092_249_1	chr19	32933595	32933974	+	0	NA	intron (NM_032816, intron 7 of 18)	intron (NM_032816, intron 7 of 18)	38245	NM_032816	84902	Hs.599703	NM_032816	ENSG00000121289	CEP89	CCDC123|CEP123	centrosomal protein 89	protein-coding	0.007916	0.460526	
chunk0156_134_1	chr5	106849094	106849723	+	0	NA	intron (NR_104671, intron 2 of 3)	intron (NR_104671, intron 2 of 3)	161606	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.004769	0.322222	
chunk0137_434_1	chr4	28444799	28445343	+	0	NA	Intergenic	Intergenic	-374511	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.003676	0.366972	
chunk0179_159_1	chr7	46557522	46557902	+	0	NA	Intergenic	Intergenic	-636440	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.018421	0.440945	
chunk0065_282_1	chr14	102472844	102473167	+	0	NA	intron (NM_014844, intron 17 of 19)	MIRb|SINE|MIR	36786	NM_152326	122416	Hs.432945	NM_152326	ENSG00000156381	ANKRD9	-	ankyrin repeat domain 9	protein-coding	0.030960	0.595679	
chunk0082_134_1	chr17	55313131	55313684	+	0	NA	intron (NM_002126, intron 2 of 3)	intron (NM_002126, intron 2 of 3)	48447	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.003617	0.413357	
chunk0006_94_1	chr1	65153548	65154118	+	0	NA	intron (NM_001005353, intron 2 of 5)	L2b|LINE|L2	5666	NM_013410	205	Hs.10862	NM_013410	ENSG00000162433	AK4	AK 4|AK3|AK3L1|AK3L2	adenylate kinase 4	protein-coding	0.007018	0.427320	257(AGGAACAGGTTGTTCC,-,0.00),258(GGAACAGGTTGTTCCA,+,0.00),280(AGGAACAGCAAGTGCA,-,0.00),281(GGAACAGCAAGTGCAA,+,0.00)
chunk0025_277_1	chr10	56245280	56245673	+	0	NA	Intergenic	MIRb|SINE|MIR	115797	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.327411	
chunk0025_266_1	chr10	55618915	55619202	+	0	NA	Intergenic	Intergenic	20068	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.010453	0.322917	
chunk0125_73_1	chr3	64501403	64502059	+	0	NA	Intergenic	Intergenic	-59615	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.010671	0.432268	
chunk0106_31_1	chr2	196079010	196079482	+	0	NA	Intergenic	Intergenic	-10434	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.004237	0.359408	
chunk0090_222_1	chr18	73563884	73564609	+	0	NA	Intergenic	Intergenic	239305	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.002759	0.384298	333(TAGAACATCTTGTTTC,-,0.00),334(AGAACATCTTGTTTCC,+,0.00)
chunk0024_210_1	chr10	36789877	36790482	+	0	NA	Intergenic	Intergenic	-335678	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.008264	0.354785	326(CAGGACACAATGTCCC,-,0.00),327(AGGACACAATGTCCCT,+,0.00)
chunk0068_36_1	chr15	51132654	51133069	+	0	NA	Intergenic	Intergenic	-27585	NM_207381	388121	Hs.306343	NM_207381	ENSG00000183578	TNFAIP8L3	TIPE3	TNF alpha induced protein 8 like 3	protein-coding	0.012048	0.420673	213(AAGTACAGGATGGTCC,-,0.00)
chunk0054_390_1	chr13	50334145	50334412	+	0	NA	intron (NR_109974, intron 2 of 6)	MIR3|SINE|MIR	162260	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.003745	0.395522	
chunk0036_188_1	chr11	62909405	62909835	+	0	NA	3' UTR (NM_000738, exon 2 of 2)	3' UTR (NM_000738, exon 2 of 2)	11920	NM_000738	1128	Hs.632119	NM_000738	ENSG00000168539	CHRM1	HM1|M1|M1R	cholinergic receptor muscarinic 1	protein-coding	0.037209	0.635731	
chunk0073_144_1	chr16	6602265	6602716	+	0	NA	intron (NM_018723, intron 2 of 15)	intron (NM_018723, intron 2 of 15)	-171319	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.008869	0.471239	216(AGGATCAGTCTGTGCT,-,0.00),217(GGATCAGTCTGTGCTG,+,0.00)
chunk0170_102_1	chr6	110534924	110535214	+	0	NA	Intergenic	LTR8|LTR|ERV1	-58428	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.003448	0.498282	116(GAGGACAGCCTGGACT,-,0.00),117(AGGACAGCCTGGACTC,+,0.00)
chunk0039_322_1	chr11	103673373	103673646	+	0	NA	Intergenic	Intergenic	-176397	NR_039842	100616457		NR_039842	ENSG00000264200	MIR4693	-	microRNA 4693	ncRNA	0.007326	0.379562	
chunk0139_319_1	chr4	58286500	58286722	+	0	NA	Intergenic	Intergenic	860739	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.009009	0.327354	
chunk0007_375_1	chr1	85264203	85264442	+	0	NA	Intergenic	HY1|scRNA|scRNA	-4650	NR_024113	148423	Hs.26226	NM_198077	ENSG00000162642	C1orf52	gm117	chromosome 1 open reading frame 52	protein-coding	0.008368	0.420833	
chunk0165_419_1	chr6	39450997	39451488	+	0	NA	intron (NM_001289021, intron 12 of 21)	L2a|LINE|L2	-19868	NM_001289024	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.004073	0.369919	
chunk0161_81_1	chr5	167061687	167061886	+	0	NA	Intergenic	Intergenic	-135416	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.020101	0.385000	
chunk0010_91_1	chr1	113650276	113650476	+	0	NA	intron (NM_152900, intron 13 of 20)	intron (NM_152900, intron 13 of 20)	108779	NM_006608	10745	Hs.655824	NM_006608	ENSG00000116793	PHTF1	PHTF	putative homeodomain transcription factor 1	protein-coding	0.000000	0.313433	
chunk0152_264_1	chr5	61099595	61099998	+	0	NA	intron (NM_174889, intron 3 of 3)	intron (NM_174889, intron 3 of 3)	-62520	NR_109908	101928630	Hs.575209	NR_109908		SMIM15-AS1	CTC-436P18.1	SMIM15 antisense RNA 1	ncRNA	0.002481	0.324257	
chunk0053_368_1	chr13	35619769	35620462	+	0	NA	intron (NM_001204197, intron 8 of 17)	L2a|LINE|L2	-77409	NR_132116	100507114	Hs.236298	NR_132115	ENSG00000236036	LINC00445	-	long intergenic non-protein coding RNA 445	ncRNA	0.008658	0.456772	
chunk0110_34_1	chr20	10549556	10549979	+	0	NA	intron (NM_001009608, intron 2 of 7)	MIRb|SINE|MIR	99928	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.007092	0.389151	
chunk0025_205_1	chr10	53579295	53579798	+	0	NA	Intergenic	L1MC3|LINE|L1	-807846	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.005964	0.287698	204(GGGAACAGTTTGTTCT,-,0.00),205(GGAACAGTTTGTTCTG,+,0.00)
chunk0112_94_1	chr20	38091548	38091747	+	0	NA	3' UTR (NM_021215, exon 7 of 7)	3' UTR (NM_021215, exon 7 of 7)	58101	NM_021215	58490	Hs.278839	NM_021215	ENSG00000101413	RPRD1B	C20orf77|CREPT|K-H|Kub5-Hera|NET60|dJ1057B20.2	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.015075	0.510000	
chunk0049_331_1	chr12	94874619	94875303	+	0	NA	Intergenic	Intergenic	40507	NR_036685	160313	Hs.527883	NR_036685	ENSG00000216306	KRT19P2	KRT19P5	keratin 19 pseudogene 2	pseudo	0.024854	0.468613	
chunk0062_102_1	chr14	68191735	68192258	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	372217	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.000000	0.379771	
chunk0146_402_1	chr4	168919698	168920393	+	0	NA	intron (NM_016081, intron 16 of 20)	intron (NM_016081, intron 16 of 20)	88040	NM_001166110	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.007194	0.451149	363(AGGAACAAGCAGTGCC,-,0.00),364(GGAACAAGCAGTGCCG,+,0.00)
chunk0188_91_1	chr8	8638157	8638867	+	0	NA	Intergenic	Intergenic	-63644	NM_194284	137075	Hs.183617	NM_194284	ENSG00000253958	CLDN23	CLDNL|hCG1646163	claudin 23	protein-coding	0.005634	0.386779	
chunk0007_246_1	chr1	82644172	82644608	+	0	NA	Intergenic	Intergenic	340532	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.006881	0.327231	
chunk0121_179_1	chr3	20073256	20073657	+	0	NA	intron (NM_003884, intron 2 of 17)	L5|LINE|RTE-X	33424	NM_003884	8850	Hs.533055	NM_003884	ENSG00000114166	KAT2B	CAF|P/CAF|PCAF	lysine acetyltransferase 2B	protein-coding	0.009975	0.393035	
chunk0123_155_1	chr3	43423081	43423623	+	0	NA	intron (NM_001204831, intron 11 of 12)	intron (NM_001204831, intron 11 of 12)	-71390	NR_046757	100873954	Hs.600984	NR_046757		SNRK-AS1	-	SNRK antisense RNA 1	ncRNA	0.005535	0.432781	
chunk0063_114_1	chr14	79124890	79125102	+	0	NA	intron (NR_073547, intron 14 of 20)	intron (NR_073547, intron 14 of 20)	-154343	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004717	0.300469	
chunk0178_96_1	chr7	30608542	30608924	+	0	NA	intron (NM_001316772, intron 6 of 16)	MIRb|SINE|MIR	13840	NM_002047	2617	Hs.404321	NM_002047	ENSG00000106105	GARS	CMT2D|DSMAV|GlyRS|HMN5|SMAD1	glycyl-tRNA synthetase	protein-coding	0.005236	0.360313	
chunk0083_301_1	chr17	69339880	69340401	+	0	NA	Intergenic	Intergenic	-12958	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.007678	0.365900	
chunk0175_449_1	chr6	170140228	170140718	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-20169	NR_125878	102724511	Hs.550045	NR_125878		LOC102724511	-	uncharacterized LOC102724511	ncRNA	0.024490	0.460285	
chunk0081_313_1	chr17	45867288	45867487	+	0	NA	intron (NR_024559, intron 1 of 1)	intron (NR_024559, intron 1 of 1)	22497	NM_175882	162540	Hs.144491	NM_175882	ENSG00000185294	SPPL2C	IMP5	signal peptide peptidase like 2C	protein-coding	0.020101	0.490000	124(GGGCACTCACTGTGCT,-,0.00),125(GGCACTCACTGTGCTC,+,0.00)
chunk0011_351_1	chr1	152470089	152470553	+	0	NA	Intergenic	Intergenic	-40523	NM_178438	254910	Hs.516410	NM_178438	ENSG00000186207	LCE5A	LEP18|SPRL5A	late cornified envelope 5A	protein-coding	0.002155	0.335484	
chunk0048_61_1	chr12	78398797	78399157	+	0	NA	Intergenic	L3|LINE|CR1	-465016	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.005556	0.354571	
chunk0071_363_1	chr15	89019363	89019970	+	0	NA	Intergenic	Intergenic	-68484	NM_152924	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.006590	0.453947	
chunk0124_349_1	chr3	58471132	58471686	+	0	NA	Intergenic	Intergenic	-20687	NM_001128214	200845	Hs.13982	NM_153331	ENSG00000168301	KCTD6	KCASH3	potassium channel tetramerization domain containing 6	protein-coding	0.007220	0.450450	
chunk0158_298_1	chr5	132290189	132290531	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-4092	NM_003059	6583	Hs.310591	NM_003059	ENSG00000197208	SLC22A4	DFNB60|OCTN1	solute carrier family 22 member 4	protein-coding	0.002924	0.434402	
chunk0149_50_1	chr5	16712156	16712640	+	0	NA	intron (NM_012334, intron 19 of 40)	intron (NM_012334, intron 19 of 40)	-95340	NM_001034850	54463	Hs.481704	NM_019000	ENSG00000154153	RETREG1	FAM134B|JK-1|JK1	reticulophagy regulator 1	protein-coding	0.006198	0.381443	
chunk0032_321_1	chr11	10052076	10052712	+	0	NA	intron (NM_030962, intron 2 of 39)	intron (NM_030962, intron 2 of 39)	213252	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.009434	0.354788	
chunk0028_202_1	chr10	89076233	89076876	+	0	NA	Intergenic	Intergenic	-13143	NR_039827	100616192		NR_039827	ENSG00000265375	MIR4679-2	-	microRNA 4679-2	ncRNA	0.006221	0.427019	
chunk0211_94_1	chrX	110675252	110675919	+	0	NA	3' UTR (NM_145234, exon 12 of 12)	3' UTR (NM_145234, exon 12 of 12)	120263	NM_145234	91851	Hs.496587	NM_145234	ENSG00000101938	CHRDL1	CHL|MGC1|MGCN|NRLN1|VOPT|dA141H5.1	chordin like 1	protein-coding	0.005997	0.380240	
chunk0140_49_1	chr4	66643364	66643645	+	0	NA	Intergenic	Intergenic	366680	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.000000	0.343972	
chunk0163_29_1	chr6	8108328	8108760	+	0	NA	Intergenic	L2b|LINE|L2	-5949	NM_001135650	9521	Hs.602353	NM_004280	ENSG00000124802	EEF1E1	AIMP3|P18	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.009259	0.434180	176(TGGAACAGAGTGATCA,-,0.00),177(GGAACAGAGTGATCAC,+,0.00)
chunk0067_252_1	chr15	45710696	45710999	+	0	NA	Intergenic	Intergenic	76107	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.016502	0.493421	
chunk0196_195_1	chr8	106198719	106199278	+	0	NA	Intergenic	Intergenic	-71180	NM_001198533	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.010733	0.326786	
chunk0147_249_1	chr4	183255535	183255836	+	0	NA	intron (NM_024949, intron 9 of 22)	intron (NM_024949, intron 9 of 22)	-15051	NR_126473	101928734	Hs.570713	NR_126473	ENSG00000251128	WWC2-AS1	-	WWC2 antisense RNA 1	ncRNA	0.009967	0.334437	
chunk0018_389_1	chr1	222529807	222530419	+	0	NA	intron (NM_024746, intron 6 of 8)	intron (NM_024746, intron 6 of 8)	17989	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.009804	0.484502	
chunk0068_425_1	chr15	59370385	59370705	+	0	NA	intron (NM_004998, intron 1 of 27)	MER130|DNA|DNA	2327	NM_004998	4643	Hs.654506	NM_004998	ENSG00000157483	MYO1E	FSGS6|HuncM-IC|MYO1C	myosin IE	protein-coding	0.009375	0.476636	197(AGTCACACACTGTCCT,-,0.00),198(GTCACACACTGTCCTC,+,0.00)
chunk0042_332_1	chr12	9746435	9746700	+	0	NA	Intergenic	L1MEg|LINE|L1	-13268	NM_001267701	160365	Hs.560087	NM_172004	ENSG00000184293	CLECL1	DCAL-1|DCAL1	C-type lectin like 1	protein-coding	0.003774	0.327068	
chunk0207_408_1	chr9	136961258	136961815	+	0	NA	Intergenic	Intergenic	9220	NM_178536	286256	Hs.440519	NM_178536	ENSG00000184925	LCN12	-	lipocalin 12	protein-coding	0.023339	0.672043	276(CAGCACTCCCTGTCCC,-,0.00),277(AGCACTCCCTGTCCCT,+,0.00)
chunk0199_130_1	chr9	3837081	3837675	+	0	NA	intron (NM_001042413, intron 9 of 10)	L1MC1|LINE|L1	-61268	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.010101	0.396639	
chunk0183_53_1	chr7	104029801	104030048	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-40408	NM_173054	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.008097	0.395161	
chunk0069_101_1	chr15	61411759	61412220	+	0	NA	Intergenic	Intergenic	-182686	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.004338	0.393939	
chunk0017_437_1	chr1	213871560	213872082	+	0	NA	intron (NR_037850, intron 4 of 5)	intron (NR_037850, intron 4 of 5)	-52928	NR_046189	100861504	Hs.742586	NR_046189		LINC00538	PROX1UT|Yiya	long intergenic non-protein coding RNA 538	ncRNA	0.017241	0.483748	
chunk0075_179_1	chr16	52070724	52070923	+	0	NA	intron (NM_001242473, intron 1 of 5)	intron (NM_001242473, intron 1 of 5)	3112	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.005025	0.365000	
chunk0013_198_1	chr1	169245776	169246107	+	0	NA	intron (NR_104229, intron 7 of 12)	intron (NR_104229, intron 7 of 12)	-122015	NM_003666	8548	Hs.130746	NM_003666	ENSG00000117475	BLZF1	GOLGIN-45|JEM-1|JEM-1s|JEM1	basic leucine zipper nuclear factor 1	protein-coding	0.000000	0.331325	
chunk0047_310_1	chr12	73964435	73965250	+	0	NA	Intergenic	Intergenic	327789	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.006135	0.365196	
chunk0079_364_1	chr17	17958944	17959143	+	0	NA	intron (NM_001033551, intron 1 of 13)	MER21B|LTR|ERVL	13427	NM_001033551	146691	Hs.462379	NM_144678	ENSG00000175662	TOM1L2	-	target of myb1 like 2 membrane trafficking protein	protein-coding	0.015075	0.450000	
chunk0125_363_1	chr3	71389844	71390556	+	0	NA	intron (NM_032682, intron 3 of 20)	intron (NM_032682, intron 3 of 20)	-85440	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.012640	0.453015	
chunk0184_413_1	chr7	122622406	122622755	+	0	NA	intron (NM_017954, intron 4 of 29)	intron (NM_017954, intron 4 of 29)	76574	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.005731	0.354286	174(GAGAGCACTTTGTTCC,-,0.00),175(AGAGCACTTTGTTCCC,+,0.00)
chunk0021_449_1	chr1	248731989	248732273	+	0	NA	Intergenic	Intergenic	23656	NM_001291283	646627	Hs.146268	NM_001085474	ENSG00000259823	LYPD8	-	LY6/PLAUR domain containing 8	protein-coding	0.010563	0.357895	
chunk0042_274_1	chr12	6988201	6988779	+	0	NA	intron (NM_005768, intron 1 of 12)	intron (NM_005768, intron 1 of 12)	17709	NM_006331	10436	Hs.558447	NM_006331	ENSG00000126749	EMG1	C2F|Grcc2f|NEP1	EMG1 N1-specific pseudouridine methyltransferase	protein-coding	0.022491	0.502591	
chunk0143_378_1	chr4	122626012	122626543	+	0	NA	non-coding (NR_104126, exon 6 of 11)	non-coding (NR_104126, exon 6 of 11)	-5220	NM_001207006	59067	Hs.567559	NM_021803	ENSG00000138684	IL21	CVID11|IL-21|Za11	interleukin 21	protein-coding	0.015066	0.426692	
chunk0089_314_1	chr18	64153480	64153686	+	0	NA	intron (NR_033881, intron 2 of 9)	L2a|LINE|L2	-4557	NR_027245	221241	Hs.567778	NM_152728	ENSG00000179676	LINC00305	C18orf20|HsT1235|NCRNA00305	long intergenic non-protein coding RNA 305	ncRNA	0.000000	0.328502	
chunk0191_20_1	chr8	42773256	42773606	+	0	NA	Intergenic	Intergenic	-4645	NM_001199279	8973	Hs.103128	NM_004198	ENSG00000147434	CHRNA6	CHNRA6	cholinergic receptor nicotinic alpha 6 subunit	protein-coding	0.005714	0.336182	
chunk0176_19_1	chr7	8294528	8294978	+	0	NA	intron (NR_125740, intron 3 of 5)	intron (NR_125740, intron 3 of 5)	-32141	NM_001276478	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.006667	0.330377	
chunk0174_106_1	chr6	156932563	156932922	+	0	NA	intron (NM_017519, intron 3 of 18)	intron (NM_017519, intron 3 of 18)	-153011	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.002786	0.288889	
chunk0051_436_1	chr12	123055397	123055800	+	0	NA	intron (NM_020845, intron 1 of 24)	intron (NM_020845, intron 1 of 24)	-25786	NR_038290	100507091	Hs.683912	NR_038290	ENSG00000251497	PITPNM2-AS1	-	PITPNM2 antisense RNA 1	ncRNA	0.017370	0.495050	
chunk0092_200_1	chr19	30969250	30969824	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	379747	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.005226	0.347826	
chunk0049_118_1	chr12	91400949	91401633	+	0	NA	Intergenic	Intergenic	-218167	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.000000	0.345985	
chunk0012_283_1	chr1	162010067	162010267	+	0	NA	intron (NM_001297713, intron 3 of 7)	intron (NM_001297713, intron 3 of 7)	14298	NM_015441	25903	Hs.507515	NM_015441	ENSG00000162745	OLFML2B	-	olfactomedin like 2B	protein-coding	0.005000	0.522388	
chunk0100_153_1	chr2	109031839	109032137	+	0	NA	Intergenic	Intergenic	-42616	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.040268	0.505017	
chunk0177_321_1	chr7	26258614	26259133	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-33022	NR_037670									0.001927	0.355769	
chunk0124_6_1	chr3	51499986	51500760	+	0	NA	promoter-TSS (NM_001171904)	promoter-TSS (NM_001171904)	-371	NM_001171904	9730	Hs.716623	NM_014703	ENSG00000145041	DCAF1	RIP|VPRBP	DDB1 and CUL4 associated factor 1	protein-coding	0.058140	0.495484	
chunk0164_143_1	chr6	21348539	21349183	+	0	NA	Intergenic	Intergenic	163031	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.010870	0.472868	
chunk0150_274_1	chr5	36908022	36908221	+	0	NA	intron (NM_015384, intron 1 of 45)	intron (NM_015384, intron 1 of 45)	31362	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.000000	0.310000	
chunk0070_231_1	chr15	72905317	72905903	+	0	NA	Intergenic	Intergenic	-121825	NR_023319									0.006826	0.436116	361(CAGGACGCTGTGTTCT,-,0.00),362(AGGACGCTGTGTTCTG,+,0.00)
chunk0161_373_1	chr5	176338187	176338543	+	0	NA	intron (NR_131772, intron 8 of 9)	L1MC4|LINE|L1	23442	NM_001079685	57179	Hs.743257	NM_020444	ENSG00000122203	KIAA1191	p33MONOX|p60MONOX	KIAA1191	protein-coding	0.005618	0.375350	185(AAGAACAGCATGTCCT,-,0.00),186(AGAACAGCATGTCCTA,+,0.00)
chunk0210_219_1	chrX	82217237	82217455	+	0	NA	Intergenic	L1PA13|LINE|L1	-1015404	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.013761	0.365297	
chunk0058_455_1	chr13	113970468	113971157	+	0	NA	Intergenic	Intergenic	-41821	NR_047495	100861555	Hs.353773	NR_047495	ENSG00000260910	LINC00565	-	long intergenic non-protein coding RNA 565	ncRNA	0.030479	0.576812	443(GAGCACACACTGCTCC,-,0.00),444(AGCACACACTGCTCCC,+,0.00)
chunk0090_228_1	chr18	73692104	73693030	+	0	NA	Intergenic	Intergenic	367626	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.004320	0.380798	358(GGGAACACCATGCTCT,-,0.00),359(GGAACACCATGCTCTG,+,0.00),407(GGGAACACCATGCTCT,-,0.00),408(GGAACACCATGCTCTG,+,0.00),456(GGGAACACCATGCTCT,-,0.00),457(GGAACACCATGCTCTG,+,0.00),505(GGGAACACCATGCTCT,-,0.00),506(GGAACACCATGCTCTG,+,0.00),554(GGGAACACCATGCTCT,-,0.00),555(GGAACACCATGCTCTG,+,0.00)
chunk0212_310_1	chrX	143042211	143042607	+	0	NA	Intergenic	Intergenic	16491	NM_001009613	441525	Hs.535082	NM_001009613	ENSG00000189326	SPANXN4	CT11.9	SPANX family member N4	protein-coding	0.005051	0.324937	
chunk0184_406_1	chr7	122304467	122304927	+	0	NA	promoter-TSS (NM_001160264)	promoter-TSS (NM_001160264)	-186	NM_001024613	389549	Hs.553970	NM_001024613	ENSG00000128610	FEZF1	FEZ|HH22|ZNF312B	FEZ family zinc finger 1	protein-coding	0.047826	0.544469	
chunk0014_410_1	chr1	183060332	183060875	+	0	NA	intron (NM_002293, intron 1 of 27)	L2c|LINE|L2	37143	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.007366	0.395221	
chunk0006_20_1	chr1	63980995	63981365	+	0	NA	intron (NM_001083592, intron 1 of 6)	MIRb|SINE|MIR	131025	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.005405	0.433962	
chunk0174_113_1	chr6	157076103	157076739	+	0	NA	intron (NM_017519, intron 4 of 18)	FRAM|SINE|Alu	247838	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.000000	0.334380	
chunk0081_28_1	chr17	37360148	37360410	+	0	NA	intron (NM_198839, intron 4 of 59)	intron (NM_198839, intron 4 of 59)	-1163	NM_198836	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.015267	0.452471	47(AAGAACAGGGTGAACT,-,0.00),48(AGAACAGGGTGAACTC,+,0.00)
chunk0015_405_1	chr1	191111660	191112226	+	0	NA	Intergenic	L1M7|LINE|L1	487053	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.003534	0.319224	378(TGGGACACAGTGTACC,-,0.00),379(GGGACACAGTGTACCA,+,0.00)
chunk0150_332_1	chr5	38515042	38515408	+	0	NA	intron (NM_002310, intron 5 of 19)	Charlie17a|DNA|hAT-Charlie	41421	NM_001127671	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.008197	0.411444	
chunk0052_49_1	chr13	20943476	20943741	+	0	NA	intron (NR_104058, intron 2 of 5)	intron (NR_104058, intron 2 of 5)	5820	NR_104058	101930748	Hs.637638	NR_104058	ENSG00000233780	LINC00367	-	long intergenic non-protein coding RNA 367	ncRNA	0.022642	0.421053	
chunk0197_338_1	chr8	125252957	125253592	+	0	NA	intron (NM_173685, intron 5 of 7)	intron (NM_173685, intron 5 of 7)	161433	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.004724	0.375786	
chunk0133_449_1	chr3	175127275	175127612	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	-12201	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.002967	0.384615	
chunk0162_231_1	chr6	4731000	4731250	+	0	NA	intron (NR_026590, intron 2 of 8)	L3b|LINE|CR1	24966	NR_026590									0.032000	0.430279	
chunk0030_252_1	chr10	115579948	115580396	+	0	NA	intron (NM_207303, intron 26 of 28)	L1MA9|LINE|L1	486807	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.000000	0.347439	
chunk0154_336_1	chr5	85541709	85542310	+	0	NA	Intergenic	L1ME3A|LINE|L1	-740435	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.000000	0.322259	292(AAGTACATCATGTGCC,-,0.00),293(AGTACATCATGTGCCT,+,0.00)
chunk0165_169_1	chr6	34224385	34225037	+	0	NA	Intergenic	L2a|LINE|L2	-12089	NM_145903	3159	Hs.518805	NM_002131	ENSG00000137309	HMGA1	HMG-R|HMGA1A|HMGIY	high mobility group AT-hook 1	protein-coding	0.024540	0.476263	
chunk0038_136_1	chr11	84127034	84127233	+	0	NA	intron (NM_001142699, intron 9 of 27)	L1M5|LINE|L1	146147	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.015075	0.355000	
chunk0034_256_1	chr11	34396221	34396429	+	0	NA	Intergenic	Intergenic	-38317	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.004808	0.406699	
chunk0011_249_1	chr1	150622075	150622274	+	0	NA	TTS (NM_207046)	TTS (NM_207046)	6959	NM_207045	2029	Hs.632456	NM_004436	ENSG00000143420	ENSA	ARPP-19e	endosulfine alpha	protein-coding	0.015075	0.455000	
chunk0128_131_1	chr3	106573364	106574068	+	0	NA	Intergenic	MER57C1|LTR|ERV1	666922	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.005682	0.409929	
chunk0136_370_1	chr3	196142328	196142593	+	0	NA	promoter-TSS (NR_034088)	promoter-TSS (NR_034088)	-176	NR_034088	401109	Hs.280133	NM_001001699	ENSG00000224652	LINC00885	-	long intergenic non-protein coding RNA 885	ncRNA	0.007547	0.552632	
chunk0180_402_1	chr7	75652790	75653286	+	0	NA	intron (NM_005338, intron 1 of 30)	MLT2B4|LTR|ERVL	85934	NM_001243198	3092	Hs.329266	NM_005338	ENSG00000127946	HIP1	HIP-I|ILWEQ|SHON|SHONbeta|SHONgamma	huntingtin interacting protein 1	protein-coding	0.006048	0.436620	
chunk0064_107_1	chr14	91149502	91149907	+	0	NA	intron (NM_001286470, intron 4 of 16)	intron (NM_001286470, intron 4 of 16)	23278	NR_003709	100124539	Hs.693444	NR_003709	ENSG00000221102	SNORA11B	-	small nucleolar RNA, H/ACA box 11B	snoRNA	0.012346	0.416256	
chunk0195_372_1	chr8	100017703	100018473	+	0	NA	intron (NM_001286692, intron 14 of 27)	intron (NM_001286692, intron 14 of 27)	5996	NR_031675									0.005195	0.374838	
chunk0124_251_1	chr3	56858272	56858891	+	0	NA	intron (NM_001128615, intron 4 of 12)	L2a|LINE|L2	-56614	NM_019555	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.001616	0.427419	
chunk0058_64_1	chr14	20715453	20715730	+	0	NA	Intergenic	LTR10A|LTR|ERV1	26814	NM_194431	6038	Hs.283749	NM_002937	ENSG00000258818	RNASE4	RAB1|RNS4	ribonuclease A family member 4	protein-coding	0.003610	0.399281	212(CAGAACTCATTGTACT,-,0.00),213(AGAACTCATTGTACTT,+,0.00)
chunk0031_155_1	chr10	125141541	125141956	+	0	NA	intron (NM_001290214, intron 1 of 10)	intron (NM_001290214, intron 1 of 10)	17067	NM_001290215	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.031325	0.555288	
chunk0081_306_1	chr17	45576856	45577268	+	0	NA	Intergenic	LTR10C|LTR|ERV1	24800	NR_026901	644172	Hs.448859	NR_026901		MAPK8IP1P2	-	mitogen-activated protein kinase 8 interacting protein 1 pseudogene 2	pseudo	0.019417	0.430993	
chunk0033_179_1	chr11	15947492	15947931	+	0	NA	Intergenic	Intergenic	21910	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.006834	0.375000	
chunk0013_356_1	chr1	172341711	172342215	+	0	NA	intron (NM_015569, intron 17 of 20)	L1PREC2|LINE|L1	-78725	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.011905	0.342574	
chunk0111_310_1	chr20	32227598	32227872	+	0	NA	intron (NM_015352, intron 4 of 6)	L2c|LINE|L2	-10060	NR_031726	100302183		NR_031726	ENSG00000284125	MIR1825	MIRN1825|hsa-mir-1825	microRNA 1825	ncRNA	0.007299	0.487273	
chunk0195_234_1	chr8	97475604	97475803	+	0	NA	Intergenic	L1PA16|LINE|L1	-29206	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.005025	0.570000	
chunk0097_150_1	chr2	48295308	48295861	+	0	NA	Intergenic	Intergenic	-19072	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.003617	0.339350	
chunk0055_452_1	chr13	75803009	75803665	+	0	NA	intron (NM_001306080, intron 7 of 30)	intron (NM_001306080, intron 7 of 30)	42676	NM_015842	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.006098	0.414003	
chunk0116_61_1	chr21	34033130	34033360	+	0	NA	Intergenic	L1ME2|LINE|L1	-40278	NM_006933	6526	Hs.302742	NM_006933	ENSG00000198743	SLC5A3	BCW2|SMIT|SMIT1|SMIT2	solute carrier family 5 member 3	protein-coding	0.004348	0.415584	
chunk0169_232_1	chr6	104935087	104935314	+	0	NA	Intergenic	L1ME4b|LINE|L1	5327	NR_046407	100113403	Hs.649249	NR_046407	ENSG00000203809	LIN28B-AS1	C6orf220|LINC00577|dJ439I14.1	LIN28B antisense RNA 1	ncRNA	0.013216	0.342105	
chunk0029_78_1	chr10	96758559	96758801	+	0	NA	Intergenic	Intergenic	8414	NR_026712	728658	Hs.645344	NR_026712	ENSG00000236552	RPL13AP5	RPL13A_8_1086|bA196N24.2	ribosomal protein L13a pseudogene 5	pseudo	0.004132	0.460905	
chunk0044_417_1	chr12	41651816	41652015	+	0	NA	Intergenic	Intergenic	214176	NM_013377	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.000000	0.340000	
chunk0138_215_1	chr4	38872607	38872985	+	0	NA	intron (NM_138389, intron 2 of 14)	MER58A|DNA|hAT-Charlie	4764	NR_030300	693159		NR_030300	ENSG00000207944	MIR574	MIR574-3p|MIRN574|hsa-mir-574|mir-574	microRNA 574	ncRNA	0.013228	0.448549	
chunk0048_30_1	chr12	77742481	77743229	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-88434	NM_014903	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.004011	0.304406	258(TAGTACATACTGTACT,-,0.00),259(AGTACATACTGTACTT,+,0.00)
chunk0159_171_1	chr5	139868966	139869428	+	0	NA	intron (NM_004883, intron 4 of 9)	intron (NM_004883, intron 4 of 9)	73376	NM_032289	84249	Hs.21963	NM_032289	ENSG00000146005	PSD2	EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding	0.017316	0.431965	221(AGGGACGGAGTGTGCC,-,0.00),222(GGGACGGAGTGTGCCT,+,0.00)
chunk0079_134_1	chr17	12790153	12790386	+	0	NA	promoter-TSS (NR_104607)	promoter-TSS (NR_104607)	15	NR_104607	100128006	Hs.567641	NR_104607	ENSG00000265489	LOC100128006	-	uncharacterized LOC100128006	ncRNA	0.060086	0.653846	
chunk0013_187_1	chr1	169078605	169079057	+	0	NA	intron (NR_104091, intron 1 of 4)	intron (NR_104091, intron 1 of 4)	8174	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.000000	0.423841	
chunk0212_430_1	chrX	153689068	153689437	+	0	NA	promoter-TSS (NM_001142806)	promoter-TSS (NM_001142806)	-259	NM_001142806	6535	Hs.540696	NM_005629	ENSG00000130821	SLC6A8	CCDS1|CRT|CRTR|CT1|CTR5	solute carrier family 6 member 8	protein-coding	0.075881	0.732432	182(TGGGCCACTCTGTCCC,-,0.00),183(GGGCCACTCTGTCCCT,+,0.00)
chunk0006_157_1	chr1	66349347	66349679	+	0	NA	intron (NM_001037339, intron 1 of 9)	intron (NM_001037339, intron 1 of 9)	-4865	NM_001297442	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.006024	0.381381	
chunk0186_442_1	chr7	147677049	147677796	+	0	NA	intron (NM_014141, intron 13 of 23)	L1MA8|LINE|L1	-299301	NR_031645	100313895		NR_031645	ENSG00000221442	MIR548F4	MIR548F-4|MIRN548F4|hsa-mir-548f-4	microRNA 548f-4	ncRNA	0.005355	0.328877	
chunk0182_159_1	chr7	95435283	95435482	+	0	NA	promoter-TSS (NM_000305)	promoter-TSS (NM_000305)	-310	NM_001018161	5445	Hs.514420	NM_000305	ENSG00000105854	PON2	-	paraoxonase 2	protein-coding	0.045226	0.400000	158(ATAAACATCCTGTGCC,-,0.00),159(TAAACATCCTGTGCCT,+,0.00)
chunk0125_133_1	chr3	65949178	65949508	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	55527	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.006061	0.377644	
chunk0022_23_1	chr10	7760290	7760836	+	0	NA	intron (NR_045609, intron 11 of 13)	MER44A|DNA|TcMar-Tigger	27464	NM_012311	22944	Hs.397918	NM_012311	ENSG00000151657	KIN	BTCD|KIN17|Rts2	Kin17 DNA and RNA binding protein	protein-coding	0.003663	0.316271	
chunk0037_204_1	chr11	74439983	74440408	+	0	NA	Intergenic	Intergenic	27360	NM_005472	10008	Hs.523899	NM_005472	ENSG00000175538	KCNE3	BRGDA6|HOKPP|HYPP|MiRP2	potassium voltage-gated channel subfamily E regulatory subunit 3	protein-coding	0.004706	0.377934	
chunk0056_159_1	chr13	84430430	84431183	+	0	NA	intron (NR_046871, intron 3 of 6)	intron (NR_046871, intron 3 of 6)	290204	NR_046871	100874128	Hs.578060	NR_046871		LINC00333	NCRNA00333	long intergenic non-protein coding RNA 333	ncRNA	0.006640	0.343501	
chunk0052_442_1	chr12	132351173	132351557	+	0	NA	Intergenic	Intergenic	21515	NR_120467	101928416		NR_120467	ENSG00000255916	LOC101928416	-	uncharacterized LOC101928416	ncRNA	0.010417	0.587013	244(GTGAGCACACTGTCCT,-,0.00),245(TGAGCACACTGTCCTC,+,0.00)
chunk0197_418_1	chr8	127339726	127340493	+	0	NA	intron (NR_117099, intron 3 of 3)	L2a|LINE|L2	-60290	NR_109834	101805488	Hs.745578	NR_109834	ENSG00000280997	CCAT2	LINC00873|NCCP1	colon cancer associated transcript 2	ncRNA	0.005215	0.398438	
chunk0032_58_1	chr11	2041246	2041544	+	0	NA	Intergenic	Intergenic	-39929	NR_131224	283120	Hs.533566	NR_002196	ENSG00000130600	H19	ASM|ASM1|BWS|D11S813E|LINC00008|MIR675HG|NCRNA00008|WT2	H19 imprinted maternally expressed transcript	ncRNA	0.016779	0.561873	
chunk0150_412_1	chr5	40172797	40173374	+	0	NA	Intergenic	Intergenic	120794	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.001733	0.394464	
chunk0011_124_1	chr1	147084724	147085112	+	0	NA	promoter-TSS (NR_121645)	promoter-TSS (NR_121645)	-162	NR_121645	101447996		NR_121645	ENSG00000286172	RNVU1-8	RNU1-145|vU1.8	RNA, variant U1 small nuclear 8	snRNA	0.067010	0.598972	
chunk0042_162_1	chr12	4082012	4082287	+	0	NA	Intergenic	AluJb|SINE|Alu	-191587	NM_001759	894	Hs.376071	NM_001759	ENSG00000118971	CCND2	KIAK0002|MPPH3	cyclin D2	protein-coding	0.010909	0.489130	
chunk0153_350_1	chr5	74392720	74393260	+	0	NA	intron (NR_126354, intron 2 of 2)	MLT1E1A|LTR|ERVL-MaLR	70504	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.003704	0.434381	
chunk0113_82_1	chr20	50721774	50722288	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-9513	NM_032521	84612	Hs.589848	NM_032521	ENSG00000124171	PARD6B	PAR6B	par-6 family cell polarity regulator beta	protein-coding	0.021401	0.499029	268(CGGAACAGCCTGTCCC,-,0.00),269(GGAACAGCCTGTCCCT,+,0.00)
chunk0158_287_1	chr5	131796234	131796648	+	0	NA	intron (NM_001008738, intron 1 of 16)	CpG	622	NM_133372	96459	Hs.591273	NM_133372	ENSG00000217128	FNIP1	-	folliculin interacting protein 1	protein-coding	0.089372	0.614458	
chunk0199_360_1	chr9	12705983	12706395	+	0	NA	intron (NM_000550, intron 6 of 7)	Tigger13a|DNA|TcMar-Tigger	12803	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.002427	0.312349	
chunk0051_316_1	chr12	119716423	119717107	+	0	NA	intron (NM_007174, intron 31 of 46)	L1ME3G|LINE|L1	-3041	NR_031589	100302274		NR_031589	ENSG00000283768	MIR1178	MIRN1178|hsa-mir-1178	microRNA 1178	ncRNA	0.004386	0.407299	359(AGGCACAGGATGTCCT,-,0.00),360(GGCACAGGATGTCCTC,+,0.00)
chunk0033_230_1	chr11	17614787	17615484	+	0	NA	intron (NM_001277269, intron 38 of 54)	L1ME1|LINE|L1	67762	NM_001292063	340990	Hs.688380	NM_198497	ENSG00000188162	OTOG	DFNB18B|MLEMP|OTGN	otogelin	protein-coding	0.005739	0.358166	415(AAGATCATGTTGTTCT,-,0.00),416(AGATCATGTTGTTCTA,+,0.00)
chunk0201_21_1	chr9	33136961	33137301	+	0	NA	intron (NM_001497, intron 1 of 5)	intron (NM_001497, intron 1 of 5)	-29817	NR_108109	101929639	Hs.545818	NR_108108	ENSG00000233554	B4GALT1-AS1	-	B4GALT1 antisense RNA 1	ncRNA	0.005882	0.533724	
chunk0057_181_1	chr13	102643198	102643559	+	0	NA	intron (NM_003291, intron 17 of 28)	intron (NM_003291, intron 17 of 28)	46442	NM_003291	7174	Hs.432424	NM_003291	ENSG00000134900	TPP2	TPP-2|TPP-II|TPPII	tripeptidyl peptidase 2	protein-coding	0.005540	0.323204	
chunk0111_430_1	chr20	35067907	35068586	+	0	NA	intron (NM_199368, intron 3 of 18)	L1ME4b|LINE|L1	24569	NM_015638	26133	Hs.168073	NM_015638	ENSG00000100991	TRPC4AP	C20orf188|PPP1R158|TRRP4AP|TRUSS	transient receptor potential cation channel subfamily C member 4 associated protein	protein-coding	0.002946	0.339706	
chunk0202_6_1	chr9	70298439	70298828	+	0	NA	intron (NM_015110, intron 9 of 24)	intron (NM_015110, intron 9 of 24)	39671	NM_015110	23137	Hs.534189	NM_015110	ENSG00000198887	SMC5	SMC5L1	structural maintenance of chromosomes 5	protein-coding	0.000000	0.307692	
chunk0019_285_1	chr1	228761068	228761610	+	0	NA	Intergenic	Intergenic	26262	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.009225	0.414365	526(GAAAACAGTGAGTTCC,-,0.00),527(AAAACAGTGAGTTCCC,+,0.00)
chunk0141_317_1	chr4	87240275	87240671	+	0	NA	Intergenic	Intergenic	-19865	NM_001292007	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.002525	0.387909	
chunk0114_158_1	chr21	10627516	10627796	+	0	NA	Intergenic	CpG	106142	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.085714	0.583630	
chunk0169_56_1	chr6	98129340	98129616	+	0	NA	Intergenic	Intergenic	104947	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.010870	0.386282	
chunk0035_229_1	chr11	45794190	45794403	+	0	NA	Intergenic	Intergenic	-9776	NM_001145265	55343	Hs.12211	NM_018389	ENSG00000181830	SLC35C1	CDG2C|FUCT1	solute carrier family 35 member C1	protein-coding	0.004695	0.546729	
chunk0048_286_1	chr12	82694349	82694625	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	7332	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.010870	0.361011	
chunk0152_172_1	chr5	59592055	59592314	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-5686	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.003861	0.411538	104(CAGAACAGTGTCTTCT,-,0.00),105(AGAACAGTGTCTTCTT,+,0.00)
chunk0117_346_1	chr21	44024937	44025144	+	0	NA	intron (NM_003274, intron 1 of 22)	L1MC5|LINE|L1	12715	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.028986	0.504808	2(CTGCACACACTGTCCC,-,0.00),3(TGCACACACTGTCCCA,+,0.00)
chunk0019_123_1	chr1	225489996	225490260	+	0	NA	3' UTR (NM_018212, exon 14 of 14)	3' UTR (NM_018212, exon 14 of 14)	-61273	NM_194442	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.003788	0.418868	
chunk0196_210_1	chr8	106630297	106631054	+	0	NA	intron (NM_001198532, intron 2 of 15)	intron (NM_001198532, intron 2 of 15)	-27133	NM_181354	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.009247	0.372032	
chunk0086_172_1	chr18	21833480	21834564	+	0	NA	intron (NM_020774, intron 12 of 20)	intron (NM_020774, intron 12 of 20)	-2616	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.006458	0.410138	
chunk0008_168_1	chr1	92831784	92832239	+	0	NA	promoter-TSS (NM_000969)	promoter-TSS (NM_000969)	-26	NM_000969	6125	Hs.532359	NM_000969	ENSG00000122406	RPL5	L5|MSTP030|PPP1R135|uL18	ribosomal protein L5	protein-coding	0.074725	0.598684	
chunk0059_441_1	chr14	38703571	38704069	+	0	NA	Intergenic	Intergenic	213062	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.012048	0.376754	
chunk0026_323_1	chr10	68155907	68156332	+	0	NA	intron (NM_001256268, intron 10 of 23)	intron (NM_001256268, intron 10 of 23)	46686	NM_001256268	84665	Hs.55205	NM_032578	ENSG00000138347	MYPN	CMD1DD|CMH22|MYOP|NEM11|RCM4	myopalladin	protein-coding	0.000000	0.403756	
chunk0193_140_1	chr8	74497513	74497941	+	0	NA	Intergenic	L1MA8|LINE|L1	-50816	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.007009	0.386946	207(CTGAACATAATGTCCT,-,0.00),208(TGAACATAATGTCCTC,+,0.00)
chunk0101_251_1	chr2	132611918	132612117	+	0	NA	intron (NM_001508, intron 1 of 1)	intron (NM_001508, intron 1 of 1)	58891	NM_144586	116372	Hs.432395	NM_144586	ENSG00000150551	LYPD1	LYPDC1|PHTS	LY6/PLAUR domain containing 1	protein-coding	0.010050	0.405000	
chunk0035_308_1	chr11	47204353	47204648	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-10442	NM_001300734	1643	Hs.700338	NM_000107	ENSG00000134574	DDB2	DDBB|UV-DDB2|XPE	damage specific DNA binding protein 2	protein-coding	0.006780	0.402027	
chunk0005_113_1	chr1	56634601	56634833	+	0	NA	Intergenic	L2c|LINE|L2	-10600	NM_006252	5563	Hs.437039	NM_006252	ENSG00000162409	PRKAA2	AMPK|AMPK2|AMPKa2|PRKAA	protein kinase AMP-activated catalytic subunit alpha 2	protein-coding	0.008621	0.377682	
chunk0032_154_1	chr11	4921871	4922177	+	0	NA	Intergenic	L1PB4|LINE|L1	2315	NM_001005237	79324	Hs.554541	NM_001005237	ENSG00000278870	OR51G1	OR11-29|OR51G3P	olfactory receptor family 51 subfamily G member 1 (gene/pseudogene)	protein-coding	0.003268	0.361564	
chunk0049_161_1	chr12	92063705	92064023	+	0	NA	intron (NR_132341, intron 1 of 4)	intron (NR_132341, intron 1 of 4)	77849	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.009434	0.391850	
chunk0189_54_1	chr8	20045041	20045240	+	0	NA	Intergenic	L1ME1|LINE|L1	106069	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.015075	0.390000	121(AAGGACACTACGTTCA,-,0.00)
chunk0207_101_1	chr9	128558640	128558964	+	0	NA	intron (NM_003127, intron 1 of 55)	intron (NM_003127, intron 1 of 55)	6244	NM_001195532	6709	Hs.372331	NM_003127	ENSG00000197694	SPTAN1	EIEE5|NEAS|SPTA2	spectrin alpha, non-erythrocytic 1	protein-coding	0.024691	0.483077	
chunk0187_328_1	chr7	156693666	156694044	+	0	NA	intron (NM_022458, intron 15 of 16)	L1M3|LINE|L1	50054	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.007937	0.387863	
chunk0053_138_1	chr13	29946035	29946446	+	0	NA	intron (NR_033889, intron 3 of 4)	MIR3|SINE|MIR	9709	NR_033889	440131	Hs.132371	NM_001010918		LINC00544	-	long intergenic non-protein coding RNA 544	ncRNA	0.012165	0.458738	232(CTGGACTGAATGTTCC,-,0.00),233(TGGACTGAATGTTCCC,+,0.00)
chunk0096_349_1	chr2	35799077	35799647	+	0	NA	Intergenic	Intergenic	327957	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.015789	0.443082	
chunk0154_416_1	chr5	89034650	89035145	+	0	NA	Intergenic	MIR|SINE|MIR	-130792	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.004040	0.437500	
chunk0080_238_1	chr17	30144922	30145284	+	0	NA	intron (NM_032141, intron 2 of 6)	L1ME5|LINE|L1	-27943	NR_036149	100423003		NR_036149	ENSG00000284399	MIR3184	-	microRNA 3184	ncRNA	0.002762	0.314050	
chunk0203_89_1	chr9	84055308	84055621	+	0	NA	Intergenic	Intergenic	-7979	NR_110995	101927575	Hs.459826	NR_110995	ENSG00000227463	LOC101927575	-	uncharacterized LOC101927575	ncRNA	0.000000	0.394904	
chunk0064_25_1	chr14	89422760	89423034	+	0	NA	intron (NM_001085471, intron 1 of 6)	intron (NM_001085471, intron 1 of 6)	5543	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.014599	0.480000	
chunk0117_275_1	chr22	24145999	24146671	+	0	NA	intron (NM_012295, intron 29 of 36)	intron (NM_012295, intron 29 of 36)	-35141	NM_019601	56241	Hs.131819	NM_019601	ENSG00000099994	SUSD2	BK65A6.2|W5C5	sushi domain containing 2	protein-coding	0.005952	0.496285	
chunk0187_454_1	chr7	159218778	159219244	+	0	NA	Intergenic	L1M4|LINE|L1	-74054	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.008584	0.402570	
chunk0102_21_1	chr2	141528641	141529268	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	602747	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.007974	0.350318	334(AAGAACAAAATGTCTT,-,0.00)
chunk0187_209_1	chr7	151831017	151831467	+	0	NA	intron (NM_016203, intron 1 of 15)	L1MB8|LINE|L1	-16371	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.008889	0.374723	
chunk0068_13_1	chr15	50590876	50591075	+	0	NA	intron (NM_001301212, intron 26 of 38)	intron (NM_001301212, intron 26 of 38)	-44270	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.000000	0.330000	
chunk0088_392_1	chr18	54351268	54351618	+	0	NA	intron (NM_139171, intron 2 of 5)	L1PB2|LINE|L1	3130	NM_139171	147323	Hs.438779	NM_139171	ENSG00000174448	STARD6	-	StAR related lipid transfer domain containing 6	protein-coding	0.002857	0.398860	
chunk0008_418_1	chr1	98488964	98489163	+	0	NA	Intergenic	Intergenic	-172617	NR_033716	51375	Hs.197015	NM_015976	ENSG00000162627	SNX7	-	sorting nexin 7	protein-coding	0.010050	0.455000	
chunk0046_238_1	chr12	60263032	60263437	+	0	NA	Intergenic	L1PB|LINE|L1	573897	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.000000	0.322660	
chunk0001_210_1	chr1	7976067	7976386	+	0	NA	intron (NM_007262, intron 5 of 6)	intron (NM_007262, intron 5 of 6)	14572	NM_001123377	11315	Hs.419640	NM_007262	ENSG00000116288	PARK7	DJ-1|DJ1|GATD2|HEL-S-67p	Parkinsonism associated deglycase	protein-coding	0.006270	0.384375	122(GTGTACAAACTGTGCC,-,0.00),123(TGTACAAACTGTGCCA,+,0.00)
chunk0096_251_1	chr2	31286415	31286614	+	0	NA	Intergenic	MIR3|SINE|MIR	52500	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.010050	0.495000	
chunk0144_446_1	chr4	141565417	141566052	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-70862	NR_037840	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.004724	0.375786	290(CTGTACAGCATGTACT,-,0.00),291(TGTACAGCATGTACTG,+,0.00)
chunk0027_145_1	chr10	74673387	74673611	+	0	NA	intron (NM_001123, intron 10 of 10)	LTR1D1|LTR|ERV1	-144175	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.035714	0.595556	
chunk0189_120_1	chr8	22156882	22157522	+	0	NA	promoter-TSS (NM_139278)	promoter-TSS (NM_139278)	-371	NM_139278	203190	Hs.33470	NM_139278	ENSG00000168481	LGI3	LGIL4	leucine rich repeat LGI family member 3	protein-coding	0.043750	0.535101	356(CTGAACAGAATGTACC,-,0.00),357(TGAACAGAATGTACCT,+,0.00)
chunk0103_256_1	chr2	165369139	165369338	+	0	NA	intron (NM_021007, intron 19 of 26)	intron (NM_021007, intron 19 of 26)	73465	NM_001040143	6326	Hs.93485	NM_021007	ENSG00000136531	SCN2A	BFIC3|BFIS3|BFNIS|EIEE11|HBA|HBSCI|HBSCII|NAC2|Na(v)1.2|Nav1.2|SCN2A1|SCN2A2	sodium voltage-gated channel alpha subunit 2	protein-coding	0.030151	0.515000	
chunk0204_326_1	chr9	100731699	100731929	+	0	NA	Intergenic	Intergenic	153735	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.030435	0.606061	
chunk0199_279_1	chr9	6477764	6478017	+	0	NA	intron (NM_152896, intron 6 of 15)	intron (NM_152896, intron 6 of 15)	64739	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.003953	0.346457	
chunk0022_85_1	chr10	9097732	9098014	+	0	NA	Intergenic	Intergenic	-177740	NR_108039	100507163	Hs.649223	NR_108039		LINC00709	-	long intergenic non-protein coding RNA 709	ncRNA	0.000000	0.332155	
chunk0081_433_1	chr17	48872185	48872384	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-20502	NM_001002027	516	Hs.80986	NM_005175	ENSG00000159199	ATP5MC1	ATP5A|ATP5G|ATP5G1	ATP synthase membrane subunit c locus 1	protein-coding	0.010050	0.520000	
chunk0002_426_1	chr1	27934797	27935412	+	0	NA	5' UTR (NM_001009568, exon 1 of 7)	5' UTR (NM_001009568, exon 1 of 7)	149	NM_001304579	27293	Hs.123659	NM_014474	ENSG00000130768	SMPDL3B	ASML3B	sphingomyelin phosphodiesterase acid like 3B	protein-coding	0.017886	0.574675	272(CAGGACAAGGAGTTCT,-,0.00),273(AGGACAAGGAGTTCTG,+,0.00)
chunk0147_124_1	chr4	174305637	174306362	+	0	NA	intron (NM_001040157, intron 6 of 11)	intron (NM_001040157, intron 6 of 11)	-21748	NM_012180	26269	Hs.76917	NM_012180	ENSG00000164117	FBXO8	DC10|FBS|FBX8	F-box protein 8	protein-coding	0.004138	0.301653	147(AGGAACACTGTGAGCA,-,0.00)
chunk0061_5_1	chr14	55523279	55523729	+	0	NA	Intergenic	L1MA3|LINE|L1	56588	NR_027123	100129075	Hs.633724	NR_027123	ENSG00000186615	KTN1-AS1	C14orf33|MYCLo-3	KTN1 antisense RNA 1	ncRNA	0.004444	0.394678	
chunk0015_70_1	chr1	184757731	184758332	+	0	NA	Intergenic	Intergenic	-3124	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.000000	0.350498	
chunk0151_347_1	chr5	54315699	54316146	+	0	NA	Intergenic	Intergenic	-5022	NR_126379	104355136	Hs.559024	NR_126379	ENSG00000249069	LINC01033	-	long intergenic non-protein coding RNA 1033	ncRNA	0.002237	0.428571	
chunk0201_383_1	chr9	68964136	68964446	+	0	NA	intron (NR_110647, intron 1 of 2)	intron (NR_110647, intron 1 of 2)	11550	NR_110647	101927069	Hs.663405	NR_110647		LOC101927069	-	uncharacterized LOC101927069	ncRNA	0.006452	0.356913	
chunk0097_289_1	chr2	55239486	55240225	+	0	NA	intron (NM_001005369, intron 15 of 16)	intron (NM_001005369, intron 15 of 16)	5691	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.006766	0.322973	
chunk0049_411_1	chr12	97272800	97273524	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-191859	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.008287	0.350345	
chunk0005_106_1	chr1	56610729	56611195	+	0	NA	Intergenic	L1PA6|LINE|L1	-31378	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.012876	0.391863	254(AAAGACACAATGTACC,-,0.00),255(AAGACACAATGTACCG,+,0.00)
chunk0193_52_1	chr8	72048869	72049407	+	0	NA	intron (NM_007332, intron 15 of 26)	intron (NM_007332, intron 15 of 26)	26446	NM_007332	8989	Hs.716816	NM_007332	ENSG00000104321	TRPA1	ANKTM1|FEPS|FEPS1	transient receptor potential cation channel subfamily A member 1	protein-coding	0.001859	0.320965	268(GTGCACAGGAAGTCCT,-,0.00),269(TGCACAGGAAGTCCTT,+,0.00),297(AAGAACAATAAGTGCT,-,0.00),298(AGAACAATAAGTGCTA,+,0.00)
chunk0154_177_1	chr5	80026802	80027245	+	0	NA	intron (NM_001306213, intron 2 of 22)	intron (NM_001306213, intron 2 of 22)	-8276	NM_003248	7060	Hs.211426	NM_003248	ENSG00000113296	THBS4	TSP-4|TSP4	thrombospondin 4	protein-coding	0.000000	0.409910	
chunk0154_166_1	chr5	79603064	79603322	+	0	NA	Intergenic	Intergenic	-9227	NM_001114393	167153	Hs.418198	NM_173797	ENSG00000164329	TENT2	APD4|GLD2|PAPD4|TUT2	terminal nucleotidyltransferase 2	protein-coding	0.015504	0.455598	
chunk0101_349_1	chr2	137807254	137807570	+	0	NA	Intergenic	L2a|LINE|L2	120520	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.003165	0.324921	
chunk0038_377_1	chr11	93465021	93465619	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	78060	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.005017	0.393990	
chunk0154_403_1	chr5	88652143	88652386	+	0	NA	intron (NR_015436, intron 3 of 4)	L2b|LINE|L2	14675	NR_030741	407047		NR_030741	ENSG00000284447	MIR9-2	MIRN9-2|hsa-mir-9-2|miRNA9-2|mir-9-2	microRNA 9-2	ncRNA	0.004115	0.352459	
chunk0165_339_1	chr6	37819131	37819549	+	0	NA	promoter-TSS (NM_021943)	promoter-TSS (NM_021943)	-191	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.100478	0.665871	
chunk0114_396_1	chr20	63462442	63462750	+	0	NA	intron (NM_172107, intron 1 of 16)	intron (NM_172107, intron 1 of 16)	10044	NM_172106	3785	Hs.161851	NM_004518	ENSG00000075043	KCNQ2	BFNC|EBN|EBN1|ENB1|HNSPC|KCNA11|KV7.2	potassium voltage-gated channel subfamily Q member 2	protein-coding	0.016234	0.527508	
chunk0197_168_1	chr8	120859459	120860065	+	0	NA	Intergenic	Intergenic	-47693	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.009901	0.415157	
chunk0073_229_1	chr16	11224121	11224780	+	0	NA	Intergenic	Intergenic	31732	NM_003745	8651	Hs.50640	NM_003745	ENSG00000185338	SOCS1	CIS1|CISH1|JAB|SOCS-1|SSI-1|SSI1|TIP-3|TIP3	suppressor of cytokine signaling 1	protein-coding	0.033384	0.610606	249(CTGAACAGCCTGTCCT,-,0.00),250(TGAACAGCCTGTCCTC,+,0.00),290(GGGAACAGCCTGTCCT,-,0.00),291(GGAACAGCCTGTCCTG,+,0.00)
chunk0145_109_1	chr4	146224457	146224936	+	0	NA	Intergenic	Intergenic	49013	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.014614	0.472917	
chunk0129_10_1	chr3	116483061	116483634	+	0	NA	Intergenic	L1MC1|LINE|L1	-37809	NM_002338	4045	Hs.26409	NM_002338	ENSG00000185565	LSAMP	IGLON3|LAMP	limbic system associated membrane protein	protein-coding	0.006981	0.344948	
chunk0041_346_1	chr11	130719174	130719655	+	0	NA	Intergenic	Intergenic	46458	NM_001271983	283171	Hs.376151	NM_001271983		C11orf44	-	chromosome 11 open reading frame 44	protein-coding	0.014553	0.464730	
chunk0172_204_1	chr6	136696831	136697464	+	0	NA	intron (NM_005923, intron 5 of 29)	intron (NM_005923, intron 5 of 29)	68033	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.011058	0.365931	
chunk0073_308_1	chr16	14151467	14152118	+	0	NA	intron (NM_001308142, intron 3 of 16)	intron (NM_001308142, intron 3 of 16)	80478	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.003072	0.369632	272(GGTACTGCCAGTTCCC,+,0.00)
chunk0089_434_1	chr18	70136696	70137030	+	0	NA	intron (NM_173630, intron 21 of 48)	intron (NM_173630, intron 21 of 48)	68863	NM_173630	25914	Hs.654809	NM_173630	ENSG00000176225	RTTN	MSSP	rotatin	protein-coding	0.000000	0.310448	
chunk0044_176_1	chr12	30133669	30134368	+	0	NA	Intergenic	Intergenic	-349259	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.011445	0.377143	
chunk0176_142_1	chr7	12803653	12803852	+	0	NA	Intergenic	Intergenic	116466	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.020101	0.395000	
chunk0085_395_1	chr18	10020004	10020705	+	0	NA	Intergenic	Intergenic	106396	NM_003574	9218	Hs.165195	NM_003574	ENSG00000101558	VAPA	VAP-33|VAP-A|VAP33|hVAP-33	VAMP associated protein A	protein-coding	0.011412	0.434473	
chunk0184_333_1	chr7	120569854	120570168	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	288112	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.009554	0.339683	
chunk0173_212_1	chr6	145520757	145521016	+	0	NA	Intergenic	L2a|LINE|L2	-213983	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.003861	0.380769	152(GGGAACAGCAAGTTCC,-,0.00),153(GGAACAGCAAGTTCCC,+,0.00)
chunk0096_6_1	chr2	25829983	25830355	+	0	NA	intron (NM_018263, intron 2 of 11)	L1MD2|LINE|L1	48274	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.008065	0.426273	
chunk0177_58_1	chr7	21108196	21108450	+	0	NA	Intergenic	Intergenic	272892	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.011811	0.490196	
chunk0191_157_1	chr8	49078345	49079190	+	0	NA	Intergenic	L2c|LINE|L2	6426	NM_001256597	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.007101	0.437352	445(CTGAACATTGTGTACC,-,0.00),446(TGAACATTGTGTACCC,+,0.00)
chunk0200_322_1	chr9	23608073	23608479	+	0	NA	intron (NR_121602, intron 9 of 27)	intron (NR_121602, intron 9 of 27)	64123	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.002463	0.380835	
chunk0209_384_1	chrX	54648693	54648990	+	0	NA	Intergenic	L1ME1|LINE|L1	118630	NM_019067	54552	Hs.654677	NM_019067	ENSG00000130119	GNL3L	GNL3B	G protein nucleolar 3 like	protein-coding	0.006734	0.312081	
chunk0054_447_1	chr13	51419190	51419760	+	0	NA	intron (NM_012141, intron 4 of 17)	L2c|LINE|L2	33664	NM_012141	26512	Hs.439440	NM_012141	ENSG00000102786	INTS6	DBI-1|DDX26|DDX26A|DICE1|HDB|INT6|Notchl2	integrator complex subunit 6	protein-coding	0.007018	0.381786	266(AGGTACATACAGTTCT,-,0.00),267(GGTACATACAGTTCTC,+,0.00)
chunk0009_66_1	chr1	100874040	100875600	+	0	NA	intron (NM_001261442, intron 3 of 3)	intron (NM_001261442, intron 3 of 3)	20359	NM_001261440	2135	Hs.357637	NM_001439	ENSG00000162694	EXTL2	EXTR2	exostosin like glycosyltransferase 2	protein-coding	0.005128	0.356182	
chunk0121_230_1	chr3	21914416	21914786	+	0	NA	Intergenic	Intergenic	-42538	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.005405	0.288410	
chunk0142_429_1	chr4	104815726	104815959	+	0	NA	Intergenic	Intergenic	-320941	NM_025212	80319	Hs.12248	NM_025212	ENSG00000168772	CXXC4	IDAX	CXXC finger protein 4	protein-coding	0.000000	0.401709	145(AAGGACAAGGAGTACT,-,0.00)
chunk0066_129_1	chr15	31098488	31098954	+	0	NA	intron (NM_001252024, intron 1 of 27)	intron (NM_001252024, intron 1 of 27)	3005	NM_001252024	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.012876	0.531049	
chunk0128_438_1	chr3	114994732	114995384	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	76356	NM_001164343	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.009202	0.349158	
chunk0158_90_1	chr5	126599967	126600438	+	0	NA	promoter-TSS (NM_032177)	promoter-TSS (NM_032177)	-713	NM_032177	51808	Hs.555731	NM_032177	ENSG00000164902	PHAX	RNUXA	phosphorylated adaptor for RNA export	protein-coding	0.014862	0.413136	
chunk0202_349_1	chr9	79736017	79736293	+	0	NA	Intergenic	L2|LINE|L2	-88375	NR_121213	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.007246	0.411552	
chunk0042_412_1	chr12	11694638	11694969	+	0	NA	intron (NM_001987, intron 1 of 7)	intron (NM_001987, intron 1 of 7)	44949	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.015106	0.394578	
chunk0163_242_1	chr6	12354430	12355075	+	0	NA	Intergenic	Intergenic	64456	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.007752	0.393189	243(GAGAACGCTATGTTCC,-,0.00),244(AGAACGCTATGTTCCC,+,0.00)
chunk0041_275_1	chr11	129317576	129317882	+	0	NA	Intergenic	Intergenic	-58257	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.003268	0.400651	74(TAGCACACAGTGAGCT,-,0.00),75(AGCACACAGTGAGCTC,+,0.00)
chunk0043_259_1	chr12	20700686	20701530	+	0	NA	intron (NM_017435, intron 2 of 14)	intron (NM_017435, intron 2 of 14)	5643	NM_017435	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.003555	0.356213	177(CTGTACATTATGTTCC,-,0.00),178(TGTACATTATGTTCCC,+,0.00)
chunk0140_442_1	chr4	76215055	76215428	+	0	NA	intron (NM_001242936, intron 1 of 7)	LTR16B2|LTR|ERVL	1201	NM_001242936	100129583	Hs.720509	NM_001136570	ENSG00000189157	FAM47E	-	family with sequence similarity 47 member E	protein-coding	0.010724	0.481283	
chunk0060_459_1	chr14	55130157	55130566	+	0	NA	intron (NM_002306, intron 1 of 5)	intron (NM_002306, intron 1 of 5)	1144	NM_002306	3958	Hs.531081	NM_002306	ENSG00000131981	LGALS3	CBP35|GAL3|GALBP|GALIG|L31|LGALS2|MAC2	galectin 3	protein-coding	0.026895	0.478049	
chunk0053_311_1	chr13	34048998	34049384	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	231122	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.002591	0.397933	188(GAGGACACAGTGTTCC,-,0.00),189(AGGACACAGTGTTCCT,+,0.00)
chunk0051_303_1	chr12	118630466	118630746	+	0	NA	Intergenic	Intergenic	254053	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.007143	0.430605	
chunk0060_204_1	chr14	48748860	48749308	+	0	NA	Intergenic	Intergenic	837332	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.369710	
chunk0115_95_1	chr21	22417545	22418259	+	0	NA	Intergenic	Intergenic	319285	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.000000	0.275524	
chunk0023_291_1	chr10	28580392	28580644	+	0	NA	intron (NM_016628, intron 3 of 13)	intron (NM_016628, intron 3 of 13)	47026	NM_100486	51322	Hs.743224	NM_016628	ENSG00000095787	WAC	BM-016|DESSH|PRO1741|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.003968	0.335968	101(TAGAACATACTGTTCA,-,0.00),102(AGAACATACTGTTCAA,+,0.00)
chunk0004_449_1	chr1	53390299	53390764	+	0	NA	Intergenic	Intergenic	49489	NR_002314	163742	Hs.99394	NR_002314	ENSG00000236253	SLC25A3P1	-	solute carrier family 25 member 3 pseudogene 1	pseudo	0.010753	0.527897	
chunk0064_83_1	chr14	90642403	90642814	+	0	NA	promoter-TSS (NR_110134)	promoter-TSS (NR_110134)	-21	NR_110134	101928909	Hs.662545	NR_110134	ENSG00000259163	LOC101928909	-	uncharacterized LOC101928909	ncRNA	0.004866	0.432039	
chunk0043_404_1	chr12	25671705	25672483	+	0	NA	Intergenic	Intergenic	-23532	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.005141	0.304236	
chunk0069_402_1	chr15	67914811	67915408	+	0	NA	Intergenic	Intergenic	-75064	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.006700	0.474916	
chunk0035_302_1	chr11	47046289	47046725	+	0	NA	intron (NR_103472, intron 2 of 7)	L1MB4|LINE|L1	109818	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.000000	0.320366	
chunk0209_258_1	chrX	46306110	46306325	+	0	NA	Intergenic	LOR1b|LTR|ERV1	21457	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.009302	0.435185	
chunk0086_178_1	chr18	21865114	21865351	+	0	NA	3' UTR (NM_020774, exon 21 of 21)	3' UTR (NM_020774, exon 21 of 21)	-33826	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.004219	0.327731	
chunk0095_404_1	chr2	24402483	24402702	+	0	NA	Intergenic	Intergenic	-42064	NM_147152	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.013699	0.422727	
chunk0008_162_1	chr1	92761097	92761919	+	0	NA	intron (NM_001308248, intron 1 of 18)	intron (NM_001308248, intron 1 of 18)	30896	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.006083	0.335358	
chunk0080_374_1	chr17	33572765	33572989	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-39117	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.008929	0.524444	
chunk0062_8_1	chr14	66119986	66120260	+	0	NA	Intergenic	Intergenic	-366248	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.003650	0.501818	
chunk0003_353_1	chr1	39133042	39133710	+	0	NA	intron (NM_012090, intron 1 of 92)	intron (NM_012090, intron 1 of 92)	49209	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.007485	0.461883	
chunk0187_240_1	chr7	152760094	152760578	+	0	NA	intron (NR_073000, intron 1 of 10)	CpG	587	NR_073001									0.068182	0.608247	455(AGGCCAAGCTGTCCCT,+,0.00)
chunk0114_152_1	chr21	10426870	10427072	+	0	NA	intron (NM_001187, intron 3 of 4)	(GTGGTG)n|Simple_repeat|Simple_repeat	13439	NM_182484	85316	Hs.545789	NM_182484		BAGE5	CT2.5	BAGE family member 5	protein-coding	0.009901	0.566502	
chunk0029_225_1	chr10	102335068	102335581	+	0	NA	intron (NM_001199378, intron 3 of 39)	intron (NM_001199378, intron 3 of 39)	-58786	NM_001288724	4791	Hs.73090	NM_002502	ENSG00000077150	NFKB2	CVID10|H2TF1|LYT-10|LYT10|NF-kB2|p100|p49/p100|p52	nuclear factor kappa B subunit 2	protein-coding	0.007797	0.459144	250(TGGACTGTTTGTGCCT,+,0.00)
chunk0041_207_1	chr11	126737967	126738378	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	82086	NR_120533	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.014599	0.470874	
chunk0142_289_1	chr4	100082763	100083500	+	0	NA	Intergenic	Intergenic	-106902	NR_125924	101929353	Hs.147584	NR_125924	ENSG00000249710	LOC101929353	-	uncharacterized LOC101929353	ncRNA	0.002714	0.341463	
chunk0130_79_1	chr3	130623741	130624063	+	0	NA	intron (NM_001102608, intron 23 of 35)	intron (NM_001102608, intron 23 of 35)	63568	NM_001102608	131873	Hs.591282	NM_001102608	ENSG00000206384	COL6A6	-	collagen type VI alpha 6 chain	protein-coding	0.003106	0.402477	
chunk0152_178_1	chr5	59699816	59700439	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	3576	NR_030308	693167		NR_030308	ENSG00000202601	MIR582	MIRN582|hsa-mir-582	microRNA 582	ncRNA	0.001605	0.341346	
chunk0204_40_1	chr9	92725245	92725506	+	0	NA	intron (NM_001003800, intron 2 of 6)	intron (NM_001003800, intron 2 of 6)	39426	NM_001003800	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.015326	0.572519	
chunk0170_8_1	chr6	109020067	109020556	+	0	NA	intron (NM_014454, intron 1 of 9)	intron (NM_014454, intron 1 of 9)	-10756	NM_001199933	27244	Hs.591336	NM_014454	ENSG00000080546	SESN1	PA26|SEST1	sestrin 1	protein-coding	0.002045	0.306122	
chunk0168_457_1	chr6	95974040	95974599	+	0	NA	Intergenic	Intergenic	-41650	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.007156	0.344643	
chunk0092_124_1	chr19	27825244	27825583	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-31473	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.005900	0.361765	
chunk0140_380_1	chr4	74902584	74903088	+	0	NA	Intergenic	MER89-int|LTR|ERV1	-30239	NM_015393	25849	Hs.105460	NM_015393	ENSG00000169116	PARM1	Cipar1|DKFZP564O0823|PARM-1|WSC4	prostate androgen-regulated mucin-like protein 1	protein-coding	0.005952	0.415842	
chunk0080_232_1	chr17	29922214	29922523	+	0	NA	intron (NM_001282129, intron 1 of 15)	intron (NM_001282129, intron 1 of 15)	-7488	NM_001145053	374786	Hs.662411	NM_198529	ENSG00000176927	EFCAB5	-	EF-hand calcium binding domain 5	protein-coding	0.006472	0.300000	
chunk0002_30_1	chr1	12464449	12465085	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-42479	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.009434	0.466248	
chunk0048_194_1	chr12	81146565	81147412	+	0	NA	intron (NM_024560, intron 5 of 15)	intron (NM_024560, intron 5 of 15)	-11400	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.004723	0.362028	
chunk0193_109_1	chr8	73965917	73966266	+	0	NA	intron (NM_001204858, intron 1 of 4)	intron (NM_001204858, intron 1 of 4)	5817	NM_001204862	6921	Hs.533437	NM_005648	ENSG00000154582	ELOC	SIII|TCEB1	elongin C	protein-coding	0.005731	0.405714	108(GTGAACAGTATGACCT,-,0.00),109(TGAACAGTATGACCTC,+,0.00)
chunk0151_38_1	chr5	42013401	42014160	+	0	NA	Intergenic	Intergenic	88526	NM_033484	26272	Hs.165575	NM_012176	ENSG00000151876	FBXO4	FBX4	F-box protein 4	protein-coding	0.011858	0.422368	
chunk0053_132_1	chr13	29815473	29816023	+	0	NA	intron (NM_007106, intron 1 of 4)	intron (NM_007106, intron 1 of 4)	34935	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.000000	0.353902	
chunk0127_173_1	chr3	95151305	95151911	+	0	NA	Intergenic	Intergenic	213345	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.003300	0.331137	
chunk0166_331_1	chr6	49999208	49999745	+	0	NA	Intergenic	L1MCa|LINE|L1	22505	NM_001037728	245913	Hs.571093	NM_001037497	ENSG00000203970	DEFB110	DEFB-10|DEFB-11|DEFB111	defensin beta 110	protein-coding	0.001862	0.284387	
chunk0118_374_1	chr22	36571940	36572398	+	0	NA	intron (NM_006078, intron 2 of 3)	MIR|SINE|MIR	-42939	NM_003753	8664	Hs.55682	NM_003753	ENSG00000100353	EIF3D	EIF3S7|eIF3-p66|eIF3-zeta	eukaryotic translation initiation factor 3 subunit D	protein-coding	0.004367	0.416122	
chunk0063_69_1	chr14	77470391	77470764	+	0	NA	Intergenic	Intergenic	12547	NM_012111	10598	Hs.204041	NM_012111	ENSG00000100591	AHSA1	AHA1|C14orf3|hAha1|p38	activator of HSP90 ATPase activity 1	protein-coding	0.010724	0.473262	
chunk0138_263_1	chr4	40190080	40190401	+	0	NA	promoter-TSS (NM_001278368)	promoter-TSS (NM_001278368)	-771	NM_001278368	399	Hs.654594	NM_004310	ENSG00000168421	RHOH	ARHH|TTF	ras homolog family member H	protein-coding	0.015576	0.381988	
chunk0127_407_1	chr3	102476032	102476695	+	0	NA	intron (NM_175056, intron 9 of 10)	intron (NM_175056, intron 9 of 10)	41348	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.009050	0.322289	
chunk0014_293_1	chr1	180791830	180792155	+	0	NA	intron (NM_001135669, intron 3 of 13)	intron (NM_001135669, intron 3 of 13)	-121185	NM_020950	57710	Hs.734816	NM_020950	ENSG00000135835	KIAA1614	-	KIAA1614	protein-coding	0.009231	0.398773	
chunk0146_101_1	chr4	158668735	158669051	+	0	NA	non-coding (NR_077235, exon 2 of 2)	non-coding (NR_077235, exon 2 of 2)	3157	NM_001008393	201725	Hs.380920	NM_001008393	ENSG00000205208	C4orf46	RCDG1	chromosome 4 open reading frame 46	protein-coding	0.000000	0.261830	
chunk0062_401_1	chr14	74922475	74922795	+	0	NA	promoter-TSS (NM_031464)	promoter-TSS (NM_031464)	-193	NM_031464	83694	Hs.414481	NM_031464	ENSG00000198208	RPS6KL1	RSKL2	ribosomal protein S6 kinase like 1	protein-coding	0.028125	0.610592	
chunk0212_3_1	chrY	4047291	4047665	+	0	NA	Intergenic	L1MC3|LINE|L1	468393	NM_139214	90655	Hs.112148	NM_139214	ENSG00000176679	TGIF2LY	TGIFLY	TGFB induced factor homeobox 2 like Y-linked	protein-coding	0.008021	0.336000	
chunk0150_418_1	chr5	40324114	40324469	+	0	NA	Intergenic	Intergenic	272000	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.008451	0.407303	
chunk0210_9_1	chrX	66868790	66869383	+	0	NA	Intergenic	L2c|LINE|L2	-229788	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.005059	0.377104	
chunk0021_184_1	chr10	5583703	5583962	+	0	NA	Intergenic	Intergenic	-57586	NR_120496	100132159	Hs.239600	NR_120496		CALML3-AS1	-	CALML3 antisense RNA 1	ncRNA	0.030888	0.565385	
chunk0014_4_1	chr1	174159307	174159516	+	0	NA	promoter-TSS (NR_121197)	promoter-TSS (NR_121197)	-3	NM_014857	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.157895	0.780952	
chunk0141_243_1	chr4	85000247	85000681	+	0	NA	intron (NR_015359, intron 2 of 3)	intron (NR_015359, intron 2 of 3)	33646	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.004608	0.278161	
chunk0197_412_1	chr8	127270967	127271404	+	0	NA	intron (NR_117099, intron 1 of 3)	MLT1K|LTR|ERVL-MaLR	26548	NR_117099	103021164	Hs.571531	NR_117099		CASC21	CARLO2|CARLo-2|LINC01244	cancer susceptibility 21	ncRNA	0.002288	0.388128	
chunk0155_110_1	chr5	92895536	92896000	+	0	NA	Intergenic	L2a|LINE|L2	675575	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.356989	
chunk0115_235_1	chr21	27340460	27340916	+	0	NA	Intergenic	Intergenic	-373568	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.002193	0.293217	
chunk0097_429_1	chr2	63434694	63435460	+	0	NA	intron (NR_122106, intron 2 of 11)	intron (NR_122106, intron 2 of 11)	2930	NR_122106	51057	Hs.414952	NM_015910	ENSG00000143951	WDPCP	BBS15|C2orf86|CHDTHP|CPLANE5|FRITZ|FRTZ	WD repeat containing planar cell polarity effector	protein-coding	0.006527	0.362451	
chunk0088_156_1	chr18	46659390	46659876	+	0	NA	Intergenic	L1ME1|LINE|L1	-2600	NM_144612	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.008230	0.422998	
chunk0038_305_1	chr11	90817669	90818059	+	0	NA	intron (NR_104190, intron 4 of 6)	intron (NR_104190, intron 4 of 6)	51338	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.002564	0.332481	
chunk0154_105_1	chr5	78430586	78430933	+	0	NA	intron (NM_004866, intron 6 of 8)	intron (NM_004866, intron 6 of 8)	-70218	NR_105014	728769	Hs.586193	NR_105014	ENSG00000245556	SCAMP1-AS1	-	SCAMP1 antisense RNA 1	ncRNA	0.002882	0.310345	
chunk0148_21_1	chr5	410430	410908	+	0	NA	intron (NM_020731, intron 4 of 11)	L1ME2|LINE|L1	32491	NR_126522	116349	Hs.446702	NM_138464	ENSG00000221990	EXOC3-AS1	C5orf55	EXOC3 antisense RNA 1	ncRNA	0.004184	0.336117	217(AGGAACACTGTGTATC,-,0.00),218(GGAACACTGTGTATCT,+,0.00)
chunk0186_448_1	chr7	148173227	148173728	+	0	NA	intron (NM_014141, intron 18 of 23)	intron (NM_014141, intron 18 of 23)	-417088	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.005988	0.404382	
chunk0174_71_1	chr6	156007056	156007276	+	0	NA	Intergenic	Intergenic	60369	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.000000	0.411765	
chunk0184_76_1	chr7	112771196	112771743	+	0	NA	intron (NM_022484, intron 4 of 4)	MIRb|SINE|MIR	18954	NM_001287497	64418	Hs.606345	NM_022484	ENSG00000146802	TMEM168	-	transmembrane protein 168	protein-coding	0.001828	0.337591	
chunk0084_236_1	chr17	78735559	78736194	+	0	NA	intron (NM_004762, intron 1 of 12)	intron (NM_004762, intron 1 of 12)	-12126	NM_001292018	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.012598	0.429245	
chunk0117_98_1	chr22	17601130	17601355	+	0	NA	intron (NM_001696, intron 4 of 8)	intron (NM_001696, intron 4 of 8)	-12050	NM_001288707	101929372	Hs.629929	NM_001288707		LOC101929372	-	uncharacterized LOC101929372	protein-coding	0.004444	0.446903	
chunk0110_156_1	chr20	13917090	13917381	+	0	NA	intron (NR_073206, intron 4 of 20)	intron (NR_073206, intron 4 of 20)	73384	NR_073206	80343	Hs.590879	NM_025229	ENSG00000101251	SEL1L2	C20orf50|sel-1L2	SEL1L2 adaptor subunit of ERAD E3 ligase	protein-coding	0.003436	0.503425	114(GAGAACTCTCTGTTCT,-,0.00),115(AGAACTCTCTGTTCTT,+,0.00)
chunk0002_286_1	chr1	22812952	22813326	+	0	NA	intron (NM_001309192, intron 3 of 13)	MIRc|SINE|MIR	50087	NR_036214	100422914		NR_036214	ENSG00000264014	MIR4253	-	microRNA 4253	ncRNA	0.005348	0.424000	
chunk0157_9_1	chr5	115197451	115197857	+	0	NA	Intergenic	Intergenic	-17108	NM_018700	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.004926	0.361179	
chunk0090_181_1	chr18	72843386	72844124	+	0	NA	intron (NM_138999, intron 4 of 4)	intron (NM_138999, intron 4 of 4)	9627	NR_049858	100847083		NR_049858	ENSG00000263750	MIR548AV	-	microRNA 548av	ncRNA	0.016260	0.364005	
chunk0130_379_1	chr3	139827513	139828095	+	0	NA	Intergenic	Intergenic	-107381	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.005155	0.433962	288(GAGTACAGGGTGTATC,-,0.00),289(AGTACAGGGTGTATCT,+,0.00)
chunk0123_27_1	chr3	40524859	40525067	+	0	NA	promoter-TSS (NM_001098414)	promoter-TSS (NM_001098414)	85	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.100962	0.708134	
chunk0170_401_1	chr6	117558907	117559315	+	0	NA	intron (NM_173674, intron 14 of 14)	intron (NM_173674, intron 14 of 14)	43431	NM_020399	57120	Hs.191539	NM_020399	ENSG00000047932	GOPC	CAL|FIG|GOPC1|PIST|dJ94G16.2	golgi associated PDZ and coiled-coil motif containing	protein-coding	0.009804	0.447433	
chunk0054_48_1	chr13	41668243	41668442	+	0	NA	intron (NM_015058, intron 37 of 44)	intron (NM_015058, intron 37 of 44)	-99947	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.000000	0.435000	
chunk0116_426_1	chr21	42914359	42914558	+	0	NA	Intergenic	HAL1b|LINE|L1	11140	NM_001308491	90625		NM_001308491		ERVH48-1	C21orf105|NDUFV3-AS1	endogenous retrovirus group 48 member 1	protein-coding	0.005025	0.435000	
chunk0123_88_1	chr3	42046627	42046859	+	0	NA	Intergenic	Intergenic	-44511	NM_001042646	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.004310	0.394850	
chunk0164_74_1	chr6	19686569	19687193	+	0	NA	Intergenic	Intergenic	-150489	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.004808	0.345600	
chunk0081_135_1	chr17	40558863	40559458	+	0	NA	intron (NM_001838, intron 1 of 2)	intron (NM_001838, intron 1 of 2)	1234	NM_001301718	1236	Hs.370036	NM_001838	ENSG00000126353	CCR7	BLR2|CC-CKR-7|CCR-7|CD197|CDw197|CMKBR7|EBI1	C-C motif chemokine receptor 7	protein-coding	0.015126	0.558725	
chunk0192_430_1	chr8	69640861	69641160	+	0	NA	intron (NM_015170, intron 22 of 22)	intron (NM_015170, intron 22 of 22)	48110	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.006689	0.426667	
chunk0151_206_1	chr5	50744775	50745187	+	0	NA	intron (NM_024615, intron 2 of 25)	intron (NM_024615, intron 2 of 25)	78043	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.009709	0.370460	
chunk0042_168_1	chr12	4586347	4586731	+	0	NA	Intergenic	Intergenic	-3533	NM_003845	8798	Hs.439530	NM_003845	ENSG00000010219	DYRK4	-	dual specificity tyrosine phosphorylation regulated kinase 4	protein-coding	0.015625	0.472727	183(TGGGGCACTGTGTGCC,-,0.00),184(GGGGCACTGTGTGCCT,+,0.00)
chunk0173_218_1	chr6	145809751	145809992	+	0	NA	intron (NM_032145, intron 1 of 2)	MIRc|SINE|MIR	4914	NM_032145	84085	Hs.421095	NM_032145	ENSG00000118496	FBXO30	Fbx30	F-box protein 30	protein-coding	0.004149	0.388430	91(TAGGACTGTATGTTCT,-,0.00),92(AGGACTGTATGTTCTA,+,0.00)
chunk0072_314_1	chr15	98803596	98804297	+	0	NA	intron (NM_001291858, intron 2 of 20)	Tigger3b|DNA|TcMar-Tigger	19520	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.017118	0.418803	
chunk0018_101_1	chr1	218131424	218131736	+	0	NA	Intergenic	L1MC3|LINE|L1	88075	NR_110794	101929631	Hs.407614	NR_110794	ENSG00000232100	LINC01653	-	long intergenic non-protein coding RNA 1653	ncRNA	0.000000	0.293930	
chunk0078_456_1	chr16	90077486	90077685	+	0	NA	Intergenic	CpG	-1655	NM_001098173	11105	Hs.406695	NM_052996	ENSG00000126856	PRDM7	PFM4|ZNF910	PR/SET domain 7	protein-coding	0.075377	0.660000	
chunk0005_415_1	chr1	62688235	62688444	+	0	NA	promoter-TSS (NM_033407)	promoter-TSS (NM_033407)	29	NM_033407	85440	Hs.744927	NM_033407	ENSG00000116641	DOCK7	EIEE23|ZIR2	dedicator of cytokinesis 7	protein-coding	0.153110	0.771429	
chunk0167_379_1	chr6	73781843	73782042	+	0	NA	intron (NM_133493, intron 17 of 32)	intron (NM_133493, intron 17 of 32)	-85811	NR_110889	101928489	Hs.660059	NR_110889	ENSG00000231652	LOC101928489	-	uncharacterized LOC101928489	ncRNA	0.005025	0.330000	
chunk0183_268_1	chr7	107472063	107472262	+	0	NA	5' UTR (NM_005295, exon 2 of 3)	5' UTR (NM_005295, exon 2 of 3)	2105	NM_005295	2845	Hs.657277	NM_005295	ENSG00000172209	GPR22	-	G protein-coupled receptor 22	protein-coding	0.010050	0.325000	
chunk0082_364_1	chr17	60269591	60269932	+	0	NA	intron (NM_032582, intron 6 of 33)	intron (NM_032582, intron 6 of 33)	-38116	NR_002999	677681		NR_002999	ENSG00000252577	SCARNA20	ACA66	small Cajal body-specific RNA 20	ncRNA	0.000000	0.280702	
chunk0170_344_1	chr6	116358614	116358888	+	0	NA	intron (NM_001080976, intron 1 of 5)	intron (NM_001080976, intron 1 of 5)	-12196	NM_013352	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.003650	0.367273	
chunk0156_364_1	chr5	112626647	112627075	+	0	NA	Intergenic	Intergenic	-1575	NR_104672	102467214	Hs.124613	NR_104672		LINC02200	-	long intergenic non-protein coding RNA 2200	ncRNA	0.009346	0.386946	
chunk0016_21_1	chr1	192861618	192862404	+	0	NA	Intergenic	Intergenic	52972	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.007634	0.318933	329(GAGTCCACTGTGTTCT,-,0.00),330(AGTCCACTGTGTTCTT,+,0.00),357(GAGAACACCGTGTACA,-,0.00),358(AGAACACCGTGTACAA,+,0.00)
chunk0150_168_1	chr5	34051066	34051875	+	0	NA	intron (NR_037951, intron 1 of 8)	L2c|LINE|L2	-8204	NM_030945	114899	Hs.171929	NM_030945	ENSG00000082196	C1QTNF3	C1ATNF3|CORCS|CORS|CORS-26|CORS26|CTRP3	C1q and TNF related 3	protein-coding	0.003708	0.393827	370(TATACAGCCTGTTCTG,+,0.00)
chunk0004_400_1	chr1	52191630	52192501	+	0	NA	intron (NM_007324, intron 1 of 17)	MamRTE1|LINE|RTE-BovB	49971	NM_007324	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.004592	0.395642	
chunk0077_270_1	chr16	80994547	80994922	+	0	NA	intron (NM_020188, intron 2 of 3)	L1ME1|LINE|L1	-11764	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.002667	0.388298	
chunk0103_59_1	chr2	159780286	159780646	+	0	NA	intron (NM_001198759, intron 36 of 38)	intron (NM_001198759, intron 36 of 38)	17789	NM_001198764	9936	Hs.130014	NM_014880	ENSG00000241399	CD302	BIMLEC|CLEC13A|DCL-1|DCL1	CD302 molecule	protein-coding	0.008333	0.263158	
chunk0131_127_1	chr3	144384116	144384908	+	0	NA	Intergenic	Intergenic	411187	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.002525	0.339218	658(TTGAACACTCTGTTCT,-,0.00),659(TGAACACTCTGTTCTA,+,0.00)
chunk0155_460_1	chr5	101771840	101772094	+	0	NA	Intergenic	Intergenic	524582	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.294118	
chunk0013_14_1	chr1	165823718	165824369	+	0	NA	Intergenic	Intergenic	-3452	NM_012474	7371	Hs.458360	NM_012474	ENSG00000143179	UCK2	TSA903|UK|UMPK	uridine-cytidine kinase 2	protein-coding	0.006144	0.371166	
chunk0184_290_1	chr7	118855212	118855710	+	0	NA	Intergenic	Intergenic	630803	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.008032	0.398798	37(GGAAACATTTTGTTCC,-,0.00),309(CAGACCAGGATGTCCC,-,0.00),310(AGACCAGGATGTCCCC,+,0.00)
chunk0140_448_1	chr4	76376581	76376863	+	0	NA	intron (NM_001042784, intron 8 of 23)	intron (NM_001042784, intron 8 of 23)	30583	NM_001042784	339965	Hs.529680	NM_178555	ENSG00000163749	CCDC158	-	coiled-coil domain containing 158	protein-coding	0.000000	0.353357	107(AGGCCAGAGTGTACTT,+,0.00)
chunk0062_344_1	chr14	73679372	73679665	+	0	NA	intron (NM_001201366, intron 6 of 8)	GA-rich|Low_complexity|Low_complexity	34643	NM_031427	83544	Hs.271270	NM_031427	ENSG00000119661	DNAL1	C14orf168|CILD16|LC1	dynein axonemal light chain 1	protein-coding	0.000000	0.357143	
chunk0163_248_1	chr6	12492360	12492845	+	0	NA	Intergenic	Intergenic	202306	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.008247	0.360082	
chunk0020_355_1	chr1	239538424	239539004	+	0	NA	Intergenic	Intergenic	-90359	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.001724	0.328744	
chunk0153_201_1	chr5	71752814	71753459	+	0	NA	Intergenic	Intergenic	33973	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.004651	0.331269	
chunk0151_213_1	chr5	50846230	50846576	+	0	NA	3' UTR (NM_001178056, exon 25 of 25)	3' UTR (NM_001178056, exon 25 of 25)	123784	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.005780	0.317003	
chunk0145_140_1	chr4	146872905	146873647	+	0	NA	intron (NM_001300761, intron 8 of 13)	intron (NM_001300761, intron 8 of 13)	72606	NM_001300761	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.005391	0.358008	
chunk0200_454_1	chr9	31510328	31511166	+	0	NA	Intergenic	Intergenic	-873856	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.002387	0.321812	
chunk0179_280_1	chr7	49563575	49563788	+	0	NA	Intergenic	L1PA16|LINE|L1	-209980	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.004695	0.574766	
chunk0160_314_1	chr5	159186132	159186861	+	0	NA	intron (NM_144726, intron 3 of 10)	intron (NM_144726, intron 3 of 10)	21152	NM_001199382	153830	Hs.349306	NM_144726	ENSG00000145860	RNF145	-	ring finger protein 145	protein-coding	0.005487	0.378082	292(AGGAACAACTTGTACA,-,0.00),293(GGAACAACTTGTACAT,+,0.00)
chunk0121_393_1	chr3	25286653	25287126	+	0	NA	intron (NM_001290216, intron 1 of 7)	MER113|DNA|hAT-Charlie	-53913	NM_001290300	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.008457	0.333333	
chunk0042_418_1	chr12	11763553	11764112	+	0	NA	intron (NM_001987, intron 2 of 7)	intron (NM_001987, intron 2 of 7)	113978	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.016100	0.412500	
chunk0031_27_1	chr10	121974393	121974901	+	0	NA	intron (NM_017615, intron 1 of 10)	CpG	581	NM_017615	54780	Hs.258798	NM_017615	ENSG00000107672	NSMCE4A	C10orf86|NS4EA|NSE4A	NSE4 homolog A, SMC5-SMC6 complex component	protein-coding	0.124016	0.715128	
chunk0128_432_1	chr3	114966595	114966809	+	0	NA	intron (NM_001164343, intron 2 of 11)	intron (NM_001164343, intron 2 of 11)	-66080	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.004673	0.330233	
chunk0158_24_1	chr5	125427444	125428038	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-65520	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.003367	0.322689	250(TAGTACATACTGTACT,-,0.00),251(AGTACATACTGTACTA,+,0.00)
chunk0069_389_1	chr15	67625092	67625741	+	0	NA	intron (NM_001206804, intron 8 of 21)	intron (NM_001206804, intron 8 of 21)	76412	NM_001206804	5607	Hs.114198	NM_002757	ENSG00000137764	MAP2K5	HsT17454|MAPKK5|MEK5|PRKMK5	mitogen-activated protein kinase kinase 5	protein-coding	0.004622	0.360000	
chunk0204_63_1	chr9	93505558	93506014	+	0	NA	intron (NM_001286722, intron 5 of 17)	intron (NM_001286722, intron 5 of 17)	-52194	NM_198841	158293	Hs.350364	NM_198841	ENSG00000188938	FAM120AOS	C9orf10OS	family with sequence similarity 120A opposite strand	protein-coding	0.006579	0.393873	
chunk0180_101_1	chr7	55261200	55261416	+	0	NA	Intergenic	L1M3e|LINE|L1	-5673	NR_110426	102725541	Hs.590524	NR_110426		ELDR	Fabl|LINC01156	EGFR long non-coding downstream RNA	ncRNA	0.000000	0.562212	
chunk0200_328_1	chr9	23750116	23750773	+	0	NA	intron (NM_001171195, intron 2 of 5)	intron (NM_001171195, intron 2 of 5)	71036	NM_001171197	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.003044	0.316109	
chunk0028_99_1	chr10	84287963	84288162	+	0	NA	intron (NR_038220, intron 1 of 5)	intron (NR_038220, intron 1 of 5)	8082	NR_038220	170425	Hs.434131	NR_038220	ENSG00000229404	LINC00858	CRCAL-2	long intergenic non-protein coding RNA 858	ncRNA	0.010050	0.470000	
chunk0206_124_1	chr9	120965921	120966570	+	0	NA	intron (NM_001735, intron 33 of 40)	intron (NM_001735, intron 33 of 40)	-37072	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.006163	0.392308	272(TGGAACATTTTGTCCC,-,0.00),273(GGAACATTTTGTCCCC,+,0.00)
chunk0108_429_1	chr2	237878817	237879439	+	0	NA	intron (NM_001308353, intron 3 of 3)	intron (NM_001308353, intron 3 of 3)	19584	NM_005855	10267	Hs.471783	NM_005855	ENSG00000132329	RAMP1	-	receptor activity modifying protein 1	protein-coding	0.014469	0.521669	267(CAGAACAGCCTGTTCT,-,0.00),268(AGAACAGCCTGTTCTT,+,0.00),475(ATGCACACAGTGTTCT,-,0.00),476(TGCACACAGTGTTCTA,+,0.00)
chunk0113_47_1	chr20	50019675	50020203	+	0	NA	Intergenic	Intergenic	21690	NR_051976	100887755	Hs.195705	NR_051976		TRERNA1	LINC00651|treRNA	translation regulatory long non-coding RNA 1	ncRNA	0.017045	0.553875	
chunk0181_68_1	chr7	80253052	80253804	+	0	NA	Intergenic	Intergenic	117673	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.006649	0.354582	
chunk0194_33_1	chr8	81776179	81776440	+	0	NA	Intergenic	L1PA14|LINE|L1	43856	NM_152284	92421	Hs.183861	NM_152284	ENSG00000164695	CHMP4C	SNF7-3|Shax3|VPS32C	charged multivesicular body protein 4C	protein-coding	0.011494	0.339695	
chunk0036_221_1	chr11	63858753	63859141	+	0	NA	intron (NM_001039469, intron 1 of 18)	intron (NM_001039469, intron 1 of 18)	20019	NM_001163296	2011	Hs.567261	NM_004954	ENSG00000072518	MARK2	EMK-1|EMK1|PAR-1|Par-1b|Par1b	microtubule affinity regulating kinase 2	protein-coding	0.005155	0.383033	
chunk0017_243_1	chr1	208298533	208299186	+	0	NA	Intergenic	Intergenic	-54539	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.007657	0.466361	
chunk0186_380_1	chr7	144256064	144256432	+	0	NA	intron (NR_126023, intron 3 of 4).2	intron (NR_126023, intron 3 of 4).2	3380	NM_001005328	401427	Hs.658609	NM_001005328	ENSG00000243896	OR2A7	HSDJ0798C17|OR2A21	olfactory receptor family 2 subfamily A member 7	protein-coding	0.005435	0.463415	
chunk0130_260_1	chr3	135980624	135981260	+	0	NA	intron (NM_001190447, intron 1 of 12)	intron (NM_001190447, intron 1 of 12)	15269	NM_002718	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.006289	0.425432	
chunk0126_226_1	chr3	78927052	78927454	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	92206	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004975	0.344913	
chunk0158_427_1	chr5	135295110	135295899	+	0	NA	intron (NM_001277348, intron 3 of 5)	L1MC4a|LINE|L1	-47327	NR_037895	340073	Hs.434422	NR_037895	ENSG00000249647	C5orf66-AS2	-	C5orf66 antisense RNA 2	ncRNA	0.007605	0.375949	
chunk0088_398_1	chr18	54443811	54444165	+	0	NA	Intergenic	Intergenic	83460	NM_001288982	162681	Hs.208701	NM_173529	ENSG00000166845	C18orf54	LAS2	chromosome 18 open reading frame 54	protein-coding	0.002825	0.473239	
chunk0046_232_1	chr12	60174855	60175693	+	0	NA	Intergenic	Intergenic	485937	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.002387	0.339690	521(AGGTACAGGCTGTACA,-,0.00),522(GGTACAGGCTGTACAA,+,0.00)
chunk0129_394_1	chr3	126389091	126389776	+	0	NA	Intergenic	CpG	5365	NR_103789	100506907	Hs.369473	NR_103787	ENSG00000249833	CCDC37-DT	CCDC37-AS1	CCDC37 divergent transcript	ncRNA	0.084672	0.647230	
chunk0132_369_1	chr3	161922492	161922937	+	0	NA	Intergenic	Intergenic	425906	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.002247	0.295964	
chunk0024_2_1	chr10	32552198	32552745	+	0	NA	intron (NM_001026383, intron 14 of 17)	L1PB1|LINE|L1	-15252	NM_024688	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.010969	0.370438	
chunk0112_157_1	chr20	39251921	39252256	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-27340	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.008955	0.455357	
chunk0125_435_1	chr3	72688808	72689079	+	0	NA	Intergenic	L1ME3G|LINE|L1	159504	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.003690	0.341912	
chunk0174_335_1	chr6	163793066	163793288	+	0	NA	Intergenic	MER110-int|LTR|ERV1	378534	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.000000	0.340807	
chunk0116_194_1	chr21	37105453	37106111	+	0	NA	intron (NM_001001894, intron 10 of 45)	L1ME3A|LINE|L1	22835	NM_003316	7267	Hs.368214	NM_003316	ENSG00000182670	TTC3	DCRR1|RNF105|TPRDIII	tetratricopeptide repeat domain 3	protein-coding	0.001520	0.367223	
chunk0095_341_1	chr2	20855325	20856049	+	0	NA	Intergenic	Intergenic	-32557	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.011050	0.502069	
chunk0026_16_1	chr10	60531167	60531488	+	0	NA	intron (NM_001204403, intron 2 of 43)	L1ME4b|LINE|L1	41629	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.003115	0.375776	
chunk0133_55_1	chr3	166588478	166588922	+	0	NA	Intergenic	L1MCb|LINE|L1	-751235	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.009009	0.408989	
chunk0046_374_1	chr12	63456019	63456562	+	0	NA	Intergenic	MIRc|SINE|MIR	212284	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.003683	0.303309	
chunk0193_27_1	chr8	71052582	71052838	+	0	NA	Intergenic	Intergenic	303801	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.007812	0.544747	
chunk0166_175_1	chr6	46035299	46035713	+	0	NA	intron (NM_001114086, intron 1 of 5)	intron (NM_001114086, intron 1 of 5)	-19617	NM_001256023	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.002415	0.390361	
chunk0141_308_1	chr4	87089313	87089840	+	0	NA	intron (NM_001313959, intron 4 of 19)	intron (NM_001313959, intron 4 of 19)	82575	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.007590	0.363636	
chunk0097_443_1	chr2	64322854	64323522	+	0	NA	Intergenic	Intergenic	-17571	NR_039632	100616265		NR_039632	ENSG00000283222	MIR4433A	MIR4433|hsa-mir-4433a	microRNA 4433a	ncRNA	0.008982	0.467862	
chunk0041_212_1	chr11	126949688	126950024	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	9110	NR_046986	100874251	Hs.319053	NR_046986	ENSG00000254960	KIRREL3-AS2	-	KIRREL3 antisense RNA 2	ncRNA	0.008929	0.433234	
chunk0006_393_1	chr1	75315448	75315686	+	0	NA	intron (NM_001130058, intron 4 of 23)	L2c|LINE|L2	180685	NM_001256114	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.004202	0.397490	
chunk0141_229_1	chr4	84808258	84808642	+	0	NA	intron (NM_014991, intron 14 of 67)	intron (NM_014991, intron 14 of 67)	157941	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.005208	0.412987	
chunk0130_186_1	chr3	133505609	133505976	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-67798	NM_017548	55573	Hs.518265	NM_017548	ENSG00000091527	CDV3	H41	CDV3 homolog	protein-coding	0.002725	0.334239	
chunk0035_317_1	chr11	47407176	47407488	+	0	NA	Intergenic	Intergenic	-1163	NM_001128225	91252	Hs.523664	NM_152264	ENSG00000165915	SLC39A13	EDSSPD3|LZT-Hs9|SCDEDS|ZIP13	solute carrier family 39 member 13	protein-coding	0.009615	0.552716	77(GGGAACAGAACGTCCT,-,0.00),78(GGAACAGAACGTCCTG,+,0.00)
chunk0091_184_1	chr19	8268766	8268965	+	0	NA	Intergenic	L1M1|LINE|L1	39491	NM_001165895	51293	Hs.558499	NM_016579	ENSG00000167775	CD320	8D6|8D6A|TCBLR|TCN2R	CD320 molecule	protein-coding	0.025126	0.600000	
chunk0068_224_1	chr15	55283539	55284226	+	0	NA	intron (NM_183235, intron 1 of 6)	intron (NM_183235, intron 1 of 6)	5933	NM_183235	5873	Hs.654978	NM_004580	ENSG00000069974	RAB27A	GS2|HsT18676|RAB27|RAM	RAB27A, member RAS oncogene family	protein-coding	0.004367	0.327035	
chunk0066_65_1	chr15	28972900	28973412	+	0	NA	intron (NM_001130414, intron 1 of 12)	MER97a|DNA|hAT-Tip100	51519	NM_001130414	321	Hs.618112	NM_005503	ENSG00000034053	APBA2	D15S1518E|HsT16821|LIN-10|MGC:14091|MINT2|X11-BETA|X11L	amyloid beta precursor protein binding family A member 2	protein-coding	0.003906	0.345029	
chunk0127_412_1	chr3	102550352	102550703	+	0	NA	Intergenic	Intergenic	115512	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.008547	0.389205	
chunk0137_95_1	chr4	13410430	13410911	+	0	NA	intron (NM_001017979, intron 4 of 6)	intron (NM_001017979, intron 4 of 6)	73695	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.002079	0.329876	
chunk0171_404_1	chr6	131258227	131258825	+	0	NA	intron (NM_138633, intron 2 of 2)	LTR106_Mam|LTR|LTR	8367	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.003344	0.325543	282(ATGAACAAACAGTTCC,-,0.00),283(TGAACAAACAGTTCCT,+,0.00)
chunk0086_32_1	chr18	12574864	12575120	+	0	NA	intron (NM_001128627, intron 2 of 15)	L2-3_Crp|LINE|L2	81740	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.007812	0.420233	
chunk0173_275_1	chr6	147769395	147770129	+	0	NA	Intergenic	Intergenic	261070	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.005450	0.376871	478(AAGAACAAATTGTACT,-,0.00),479(AGAACAAATTGTACTG,+,0.00)
chunk0061_350_1	chr14	63676574	63677189	+	0	NA	Intergenic	Intergenic	-34958	NM_001258272	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.006504	0.391234	
chunk0150_92_1	chr5	32414271	32414475	+	0	NA	intron (NM_016107, intron 5 of 19)	intron (NM_016107, intron 5 of 19)	-19898	NR_030305	693164		NR_030305	ENSG00000207956	MIR579	MIRN579|hsa-mir-579	microRNA 579	ncRNA	0.000000	0.365854	
chunk0175_60_1	chr7	1818837	1819046	+	0	NA	intron (NM_003550, intron 18 of 18)	intron (NM_003550, intron 18 of 18)	25312	NR_039799	100616160		NR_039799	ENSG00000265089	MIR4655	-	microRNA 4655	ncRNA	0.047847	0.623810	
chunk0093_127_1	chr19	45717535	45717776	+	0	NA	intron (NM_001080469, intron 1 of 1)	intron (NM_001080469, intron 1 of 1)	13238	NM_001080469	23403	Hs.128702	NM_001080469	ENSG00000177051	FBXO46	20D7-FC4|FBXO34L|Fbx46	F-box protein 46	protein-coding	0.045643	0.566116	
chunk0027_429_1	chr10	80946665	80947178	+	0	NA	Intergenic	MER34C|LTR|ERV1	406102	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.003899	0.383268	
chunk0163_316_1	chr6	14750163	14750596	+	0	NA	Intergenic	Intergenic	-464925	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.009238	0.451613	
chunk0054_57_1	chr13	41736367	41736642	+	0	NA	intron (NM_015058, intron 21 of 44)	intron (NM_015058, intron 21 of 44)	-168109	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.003636	0.253623	101(AAGCACAATCTGTTCT,-,0.00),102(AGCACAATCTGTTCTG,+,0.00)
chunk0208_302_1	chrX	23504842	23505476	+	0	NA	Intergenic	Intergenic	-162369	NM_006406	10549	Hs.83383	NM_006406	ENSG00000123131	PRDX4	AOE37-2|AOE372|HEL-S-97n|PRX-4	peroxiredoxin 4	protein-coding	0.006309	0.453543	325(GAGTACATTGTGTCCT,-,0.00),326(AGTACATTGTGTCCTC,+,0.00)
chunk0079_447_1	chr17	20206506	20206807	+	0	NA	intron (NM_001033553, intron 4 of 14)	L1ME4a|LINE|L1	50662	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.006645	0.264901	
chunk0011_23_1	chr1	143205340	143205558	+	0	NA	Intergenic	Intergenic	217143	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.059633	0.369863	
chunk0107_99_1	chr2	213660694	213660893	+	0	NA	intron (NR_047659, intron 12 of 17)	LTR14B|LTR|ERVK	-97274	NR_039640	100616375		NR_039640	ENSG00000265734	MIR4438	-	microRNA 4438	ncRNA	0.010050	0.405000	
chunk0044_408_1	chr12	41061067	41061717	+	0	NA	intron (NM_175038, intron 21 of 21)	intron (NM_175038, intron 21 of 21)	-127056	NM_001164595	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.003077	0.384025	
chunk0004_125_1	chr1	44668785	44669058	+	0	NA	intron (NM_001300748, intron 1 of 2)	MIR|SINE|MIR	5687	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.014652	0.383212	121(GAGTACATACTGTACA,-,0.00),122(AGTACATACTGTACAA,+,0.00)
chunk0185_72_1	chr7	125150826	125151405	+	0	NA	Intergenic	Intergenic	-33454	NR_110188	101928283	Hs.566650	NR_110188	ENSG00000224897	LOC101928283	-	uncharacterized LOC101928283	ncRNA	0.003454	0.341379	
chunk0178_281_1	chr7	37218633	37218931	+	0	NA	intron (NM_001206482, intron 10 of 21)	intron (NM_001206482, intron 10 of 21)	134886	NM_001206482	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.003356	0.314381	
chunk0022_124_1	chr10	11547101	11547486	+	0	NA	intron (NM_014688, intron 2 of 14)	MIR|SINE|MIR	-15013	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.015584	0.417098	
chunk0101_16_1	chr2	121489366	121489713	+	0	NA	intron (NM_015282, intron 8 of 38)	intron (NM_015282, intron 8 of 38)	-41341	NR_023343	100151683	Hs.689638	NR_023343	ENSG00000264229	RNU4ATAC	MOPD1|RFMN|RNU4ATAC1|TALS|U4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	snRNA	0.002882	0.387931	205(GATACAGGTTGTTCCC,+,0.00)
chunk0040_115_1	chr11	112016548	112016805	+	0	NA	intron (NM_001037954, intron 17 of 19)	intron (NM_001037954, intron 17 of 19)	-8138	NM_001931	1737	Hs.335551	NM_001931	ENSG00000150768	DLAT	DLTA|E2|PDC-E2|PDCE2	dihydrolipoamide S-acetyltransferase	protein-coding	0.011673	0.472868	
chunk0096_41_1	chr2	26900285	26900933	+	0	NA	intron (NM_020134, intron 2 of 12)	L1ME3A|LINE|L1	52185	NM_001253724	56896	Hs.299315	NM_020134	ENSG00000157851	DPYSL5	CRAM|CRMP-5|CRMP5|Ulip6	dihydropyrimidinase like 5	protein-coding	0.006173	0.417565	
chunk0197_173_1	chr8	121015412	121016154	+	0	NA	Intergenic	Intergenic	-203714	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.001348	0.335128	
chunk0084_141_1	chr17	76446779	76447406	+	0	NA	intron (NM_022066, intron 1 of 17)	intron (NM_022066, intron 1 of 17)	6114	NM_022066	63893	Hs.16130	NM_022066	ENSG00000175931	UBE2O	E2-230K	ubiquitin conjugating enzyme E2 O	protein-coding	0.009569	0.447452	
chunk0197_407_1	chr8	127231049	127231543	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-12028	NR_108049	100507056	Hs.343864	NR_108049		CCAT1	CARLO5|CARLo-5|onco-lncRNA-40	colon cancer associated transcript 1	ncRNA	0.004049	0.450505	
chunk0144_56_1	chr4	126953535	126954184	+	0	NA	Intergenic	Intergenic	-679073	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.004622	0.381538	
chunk0079_22_1	chr17	9730542	9730873	+	0	NA	Intergenic	Intergenic	60590	NM_001105571	201140	Hs.61684	NM_001105571	ENSG00000184544	DHRS7C	SDR32C2	dehydrogenase/reductase 7C	protein-coding	0.006042	0.430723	
chunk0123_109_1	chr3	42247644	42248282	+	0	NA	Intergenic	Intergenic	15984	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.012539	0.474178	
chunk0091_55_1	chr19	4723540	4724175	+	0	NA	promoter-TSS (NM_139159)	promoter-TSS (NM_139159)	-14	NM_139159	91039	Hs.515081	NM_139159	ENSG00000142002	DPP9	DP9|DPLP9|DPP IX|DPRP-2|DPRP2	dipeptidyl peptidase 9	protein-coding	0.105512	0.677673	
chunk0004_283_1	chr1	48552351	48552678	+	0	NA	intron (NM_032785, intron 11 of 13)	L2a|LINE|L2	-80306	NM_019073	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.003058	0.435976	
chunk0142_145_1	chr4	94930567	94930766	+	0	NA	intron (NM_001203, intron 2 of 12)	L2c|LINE|L2	-65566	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.000000	0.320000	
chunk0077_187_1	chr16	79745749	79746187	+	0	NA	intron (NR_104663, intron 4 of 5)	L2a|LINE|L2	-24503	NR_104660	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.004566	0.318907	264(AAGGACAACATGTACT,-,0.00),265(AGGACAACATGTACTG,+,0.00)
chunk0045_291_1	chr12	50251806	50252260	+	0	NA	intron (NM_001113546, intron 1 of 10)	intron (NM_001113546, intron 1 of 10)	-17821	NR_031625	100302220		NR_031625	ENSG00000221604	MIR1293	MIRN1293|hsa-mir-1293|mir-1293	microRNA 1293	ncRNA	0.006608	0.402198	
chunk0019_100_1	chr1	224809540	224809884	+	0	NA	Intergenic	Intergenic	-119942	NM_001145154	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.011628	0.513043	218(GGAACAAGAAGTACCT,+,0.00)
chunk0179_166_1	chr7	46661519	46661718	+	0	NA	Intergenic	Intergenic	-740346	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.000000	0.330000	141(TGGAACAGTGTGTCCA,-,0.00),142(GGAACAGTGTGTCCAC,+,0.00)
chunk0025_404_1	chr10	59578230	59578807	+	0	NA	Intergenic	Intergenic	131373	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.006932	0.378893	
chunk0082_233_1	chr17	57315275	57315899	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	58574	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.017628	0.497600	
chunk0025_259_1	chr10	55248857	55249245	+	0	NA	Intergenic	L1MC|LINE|L1	-349939	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.010309	0.321337	
chunk0179_403_1	chr7	51606099	51607284	+	0	NA	Intergenic	Intergenic	-289873	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.022785	0.482293	
chunk0205_305_1	chr9	112396701	112397354	+	0	NA	intron (NR_036651, intron 1 of 9)	HERVK11-int|LTR|ERVK	17118	NM_032303	84263	Hs.59486	NM_032303	ENSG00000119471	HSDL2	C9orf99|SDR13C1	hydroxysteroid dehydrogenase like 2	protein-coding	0.018377	0.478593	
chunk0026_300_1	chr10	67905107	67905432	+	0	NA	intron (NM_012238, intron 4 of 8)	intron (NM_012238, intron 4 of 8)	13867	NM_001314049	23411	Hs.369779	NM_012238	ENSG00000096717	SIRT1	SIR2|SIR2L1|SIR2alpha	sirtuin 1	protein-coding	0.000000	0.315951	
chunk0049_25_1	chr12	89632047	89632378	+	0	NA	intron (NM_001001323, intron 4 of 20)	intron (NM_001001323, intron 4 of 20)	23855	NM_001001323	490	Hs.506276	NM_001682	ENSG00000070961	ATP2B1	PMCA1|PMCA1kb	ATPase plasma membrane Ca2+ transporting 1	protein-coding	0.009063	0.307229	
chunk0074_304_1	chr16	30139860	30140230	+	0	NA	Intergenic	HAL1|LINE|L1	-16736	NM_002746	5595	Hs.861	NM_002746	ENSG00000102882	MAPK3	ERK-1|ERK1|ERT2|HS44KDAP|HUMKER1A|P44ERK1|P44MAPK|PRKM3|p44-ERK1|p44-MAPK	mitogen-activated protein kinase 3	protein-coding	0.010811	0.425876	242(CTGCACTGTTTGTTCC,-,0.00),243(TGCACTGTTTGTTCCT,+,0.00)
chunk0058_382_1	chr14	29458498	29458986	+	0	NA	Intergenic	Intergenic	468951	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.004098	0.316973	
chunk0100_440_1	chr2	120737730	120738218	+	0	NA	Intergenic	Intergenic	-59317	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.020492	0.525562	196(GAGACCAGTTTGTTCC,-,0.00),197(AGACCAGTTTGTTCCA,+,0.00)
chunk0164_450_1	chr6	28282983	28283182	+	0	NA	intron (NM_032507, intron 1 of 6)	MLT1H2|LTR|ERVL-MaLR	1545	NM_001184743	84547	Hs.144527	NM_032507	ENSG00000137338	PGBD1	HUCEP-4|SCAND4|dJ874C20.4	piggyBac transposable element derived 1	protein-coding	0.010050	0.480000	
chunk0036_353_1	chr11	66926216	66926483	+	0	NA	intron (NM_000920, intron 2 of 21)	L2a|LINE|L2	8157	NR_036121	100423029		NR_036121	ENSG00000266423	MIR3163	-	microRNA 3163	ncRNA	0.000000	0.294776	
chunk0177_82_1	chr7	21617902	21618107	+	0	NA	intron (NM_001277115, intron 23 of 81)	MER91A|DNA|hAT-Tip100	74789	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.019512	0.500000	
chunk0185_13_1	chr7	123900920	123901252	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-24146	NM_153189	6677	Hs.121494	NM_003117	ENSG00000106304	SPAM1	HEL-S-96n|HYA1|HYAL1|HYAL3|HYAL5|PH-20|PH20|SPAG15	sperm adhesion molecule 1	protein-coding	0.000000	0.264264	
chunk0064_161_1	chr14	92040112	92040320	+	0	NA	promoter-TSS (NM_004239)	promoter-TSS (NM_004239)	-157	NM_004239	9321	Hs.632339	NM_004239	ENSG00000100815	TRIP11	ACG1A|CEV14|GMAP-210|GMAP210|ODCD|TRIP-11|TRIP230	thyroid hormone receptor interactor 11	protein-coding	0.086538	0.665072	
chunk0099_225_1	chr2	96330334	96330769	+	0	NA	Intergenic	Intergenic	4344	NM_001163524	150771	Hs.65009	NM_178495	ENSG00000198885	ITPRIPL1	KIAA1754L	ITPRIP like 1	protein-coding	0.004598	0.396789	
chunk0156_233_1	chr5	108322163	108322945	+	0	NA	intron (NM_001163315, intron 4 of 8)	intron (NM_001163315, intron 4 of 8)	59544	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.005115	0.320562	
chunk0037_70_1	chr11	71165677	71165939	+	0	NA	intron (NM_012309, intron 1 of 24)	intron (NM_012309, intron 1 of 24)	58988	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.022901	0.558935	
chunk0105_148_1	chr2	186499380	186499650	+	0	NA	intron (NM_018471, intron 2 of 9)	intron (NM_018471, intron 2 of 9)	13357	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.003704	0.376384	124(CAGAGCACTATGTACT,-,0.00)
chunk0076_415_1	chr16	72923985	72924184	+	0	NA	intron (NM_006885, intron 3 of 9)	intron (NM_006885, intron 3 of 9)	124291	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.015075	0.415000	79(TAAAACACACTGTTCT,-,0.00),80(AAAACACACTGTTCTT,+,0.00)
chunk0012_296_1	chr1	162144394	162144801	+	0	NA	intron (NM_001164757, intron 1 of 9)	intron (NM_001164757, intron 1 of 9)	-12510	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.009828	0.448529	
chunk0021_60_1	chr10	1188251	1188633	+	0	NA	intron (NM_018702, intron 8 of 9)	intron (NM_018702, intron 8 of 9)	28674	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.013089	0.422977	191(AAACACATTCTGTTCC,-,0.00),192(AACACATTCTGTTCCC,+,0.00)
chunk0025_341_1	chr10	58076313	58076960	+	0	NA	Intergenic	Intergenic	191298	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.001546	0.375000	
chunk0165_392_1	chr6	38730516	38731134	+	0	NA	intron (NM_001206927, intron 4 of 92)	intron (NM_001206927, intron 4 of 92)	15484	NM_001206927	1769	Hs.520106	NM_001371	ENSG00000124721	DNAH8	ATPase|hdhc9	dynein axonemal heavy chain 8	protein-coding	0.009709	0.429725	226(CTGGACACGCAGTACT,-,0.00),227(TGGACACGCAGTACTT,+,0.00)
chunk0063_265_1	chr14	83795142	83795341	+	0	NA	Intergenic	Intergenic	-1598638	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.350000	
chunk0096_16_1	chr2	26115176	26115443	+	0	NA	intron (NM_016131, intron 3 of 5)	L1MB7|LINE|L1	-57782	NM_001168241	150946	Hs.187912	NM_001168241	ENSG00000157833	GAREM2	FAM59B|GAREML	GRB2 associated regulator of MAPK1 subtype 2	protein-coding	0.000000	0.339552	
chunk0106_55_1	chr2	196291300	196291732	+	0	NA	intron (NM_020760, intron 14 of 28)	MIRb|SINE|MIR	31492	NR_110226	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.006944	0.399538	
chunk0199_394_1	chr9	13264652	13264851	+	0	NA	intron (NM_003829, intron 1 of 45)	intron (NM_003829, intron 1 of 45)	14813	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.000000	0.350000	
chunk0110_339_1	chr20	19276356	19276775	+	0	NA	intron (NR_024564, intron 2 of 7)	Tigger3a|DNA|TcMar-Tigger	8031	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.011933	0.419048	
chunk0113_58_1	chr20	50395254	50395754	+	0	NA	Intergenic	Intergenic	-74162	NR_109950	101927586	Hs.637665	NR_109950	ENSG00000233077	LINC01271	-	long intergenic non-protein coding RNA 1271	ncRNA	0.022000	0.614770	223(GGGAACAGGACGTCCT,-,0.00),224(GGAACAGGACGTCCTG,+,0.00)
chunk0154_420_1	chr5	89047670	89048199	+	0	NA	Intergenic	Intergenic	-143829	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.000000	0.450943	
chunk0039_93_1	chr11	97261894	97262500	+	0	NA	Intergenic	Intergenic	-755320	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.008251	0.296540	
chunk0117_212_1	chr22	22073688	22073923	+	0	NA	Intergenic	Intergenic	-90962	NM_001282112	8940	Hs.436401	NM_003935	ENSG00000100038	TOP3B	TOP3B1	DNA topoisomerase III beta	protein-coding	0.008511	0.546610	83(AAAGACAGACTGTGCC,-,0.00),84(AAGACAGACTGTGCCT,+,0.00)
chunk0143_133_1	chr4	109707221	109707420	+	0	NA	Intergenic	Intergenic	-3847	NM_032992	839	Hs.654616	NM_001226	ENSG00000138794	CASP6	MCH2	caspase 6	protein-coding	0.005025	0.380000	
chunk0169_446_1	chr6	108765468	108765942	+	0	NA	intron (NR_033376, intron 3 of 4)	MIR3|SINE|MIR	14051	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.004219	0.431579	
chunk0135_346_1	chr3	190384106	190384822	+	0	NA	Intergenic	Intergenic	-3408	NM_006580	10686	Hs.251391	NM_006580	ENSG00000113946	CLDN16	HOMG3|PCLN1	claudin 16	protein-coding	0.005587	0.398884	246(AAGAGCTTGCTGTTCT,-,0.00)
chunk0060_70_1	chr14	41925536	41926124	+	0	NA	Intergenic	Intergenic	318269	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.005102	0.368421	
chunk0083_367_1	chr17	70999507	70999706	+	0	NA	Intergenic	Intergenic	202573	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.000000	0.280000	
chunk0200_17_1	chr9	14627504	14627961	+	0	NA	intron (NM_178566, intron 8 of 9)	intron (NM_178566, intron 8 of 9)	65750	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.002188	0.375546	
chunk0083_376_1	chr17	71176796	71177308	+	0	NA	intron (NR_104152, intron 2 of 3)	intron (NR_104152, intron 2 of 3)	25127	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.005859	0.313840	
chunk0135_275_1	chr3	189311486	189311998	+	0	NA	intron (NM_198485, intron 5 of 5)	LTR85a|LTR|Gypsy?	-71148	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.005859	0.403509	
chunk0102_451_1	chr2	158232378	158232861	+	0	NA	intron (NM_001301684, intron 8 of 11)	intron (NM_001301684, intron 8 of 11)	65969	NR_038850	554201	Hs.570262	NR_038850	ENSG00000227480	CCDC148-AS1	-	CCDC148 antisense RNA 1	ncRNA	0.002070	0.316116	
chunk0086_115_1	chr18	14921523	14921765	+	0	NA	Intergenic	Intergenic	-24623	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.000000	0.390947	
chunk0083_245_1	chr17	67742110	67742443	+	0	NA	intron (NM_015462, intron 16 of 17)	L1MC4a|LINE|L1	1606	NR_003706	100124536	Hs.693446	NR_003706	ENSG00000200394	SNORA38B	-	small nucleolar RNA, H/ACA box 38B	snoRNA	0.006006	0.335329	
chunk0124_33_1	chr3	52204288	52204711	+	0	NA	intron (NM_001304444, intron 5 of 11)	intron (NM_001304444, intron 5 of 11)	6416	NM_199166	211	Hs.476308	NM_000688	ENSG00000023330	ALAS1	ALAS|ALAS-H|ALAS3|ALASH|MIG4	5'-aminolevulinate synthase 1	protein-coding	0.009456	0.433962	
chunk0064_411_1	chr14	99561314	99561591	+	0	NA	intron (NM_001144995, intron 1 of 5)	intron (NM_001144995, intron 1 of 5)	42938	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.021661	0.618705	
chunk0063_347_1	chr14	85415310	85415628	+	0	NA	intron (NR_102737, intron 2 of 2)	L2a|LINE|L2	21554	NR_102738	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.025157	0.485893	
chunk0207_337_1	chr9	134374865	134375529	+	0	NA	intron (NM_002957, intron 1 of 9)	L2b|LINE|L2	-4098	NM_001291920	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.019578	0.618045	317(GGGAACAGCATGTTCA,-,0.00),318(GGAACAGCATGTTCAA,+,0.00)
chunk0153_5_1	chr5	66740031	66740547	+	0	NA	intron (NM_198828, intron 1 of 5)	intron (NM_198828, intron 1 of 5)	-88487	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.007752	0.456480	
chunk0050_145_1	chr12	102618389	102618821	+	0	NA	Intergenic	Intergenic	-137960	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.006944	0.508083	17(CGGCACATTCTGTGTC,-,0.00),18(GGCACATTCTGTGTCC,+,0.00)
chunk0179_416_1	chr7	51778536	51778806	+	0	NA	Intergenic	Intergenic	-461853	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.000000	0.380074	
chunk0152_115_1	chr5	58599440	58599639	+	0	NA	intron (NM_138453, intron 1 of 4)	intron (NM_138453, intron 1 of 4)	16427	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.005025	0.510000	
chunk0088_339_1	chr18	51255699	51256236	+	0	NA	Intergenic	Intergenic	-58286	NM_016626	51320	Hs.465144	NM_016626	ENSG00000176624	MEX3C	BM-013|MEX-3C|RKHD2|RNF194	mex-3 RNA binding family member C	protein-coding	0.005587	0.403346	
chunk0172_70_1	chr6	134350712	134350911	+	0	NA	Intergenic	Intergenic	-32753	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.000000	0.230000	
chunk0133_60_1	chr3	166829712	166830469	+	0	NA	Intergenic	Intergenic	550193	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.003963	0.333773	
chunk0189_103_1	chr8	21953271	21953813	+	0	NA	intron (NM_015024, intron 1 of 27)	L1MC2|LINE|L1	33873	NM_015024	23039	Hs.172685	NM_015024	ENSG00000130227	XPO7	EXP7|RANBP16	exportin 7	protein-coding	0.001845	0.372007	
chunk0004_31_1	chr1	42468348	42468848	+	0	NA	intron (NM_001287511, intron 2 of 2)	MLT1J|LTR|ERVL-MaLR	12104	NM_001077447	79717	Hs.706662	NM_024664	ENSG00000127125	PPCS	CMD2C	phosphopantothenoylcysteine synthetase	protein-coding	0.002000	0.389222	
chunk0147_23_1	chr4	171576758	171576957	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-236567	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.000000	0.340000	
chunk0008_407_1	chr1	98066758	98067355	+	0	NA	Intergenic	Intergenic	-17363	NR_046105	400765	Hs.451802	NM_001001688	ENSG00000225206	MIR137HG	-	MIR137 host gene	ncRNA	0.005025	0.403010	
chunk0188_297_1	chr8	15759132	15759695	+	0	NA	intron (NM_006765, intron 10 of 10)	intron (NM_006765, intron 10 of 10)	219326	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.010657	0.420213	286(CAGAACACTGTGTACA,-,0.00),287(AGAACACTGTGTACAT,+,0.00)
chunk0051_320_1	chr12	119884319	119884818	+	0	NA	Intergenic	L1MC1|LINE|L1	-7277	NM_001206999	11113	Hs.119594	NM_007174	ENSG00000122966	CIT	CITK|CRIK|MCPH17|STK21	citron rho-interacting serine/threonine kinase	protein-coding	0.016032	0.390000	
chunk0090_355_1	chr18	76662732	76663079	+	0	NA	Intergenic	Intergenic	-23894	NR_110784	101927651	Hs.569848	NR_110784		LINC01927	-	long intergenic non-protein coding RNA 1927	ncRNA	0.014409	0.359195	
chunk0069_176_1	chr15	62898852	62899525	+	0	NA	Intergenic	Intergenic	75231	NR_029709	406965		NR_029709	ENSG00000211137	MIR190A	MIR190|MIRN190|hsa-mir-190a|miR-190|mir-190a	microRNA 190a	ncRNA	0.010401	0.452522	336(GGGCACACCGTGTGCT,-,0.00),337(GGCACACCGTGTGCTG,+,0.00)
chunk0160_95_1	chr5	150269655	150270001	+	0	NA	intron (NM_171825, intron 2 of 17)	intron (NM_171825, intron 2 of 17)	20012	NM_015981	815	Hs.743976	NM_015981	ENSG00000070808	CAMK2A	CAMKA|CaMKIINalpha|MRD53|MRT63	calcium/calmodulin dependent protein kinase II alpha	protein-coding	0.017341	0.573487	91(GGGAACAGGAAGTACC,-,0.00),92(GGAACAGGAAGTACCT,+,0.00),118(TAGGACAGCCTGATCC,-,0.00),119(AGGACAGCCTGATCCT,+,0.00)
chunk0171_341_1	chr6	129992496	129993085	+	0	NA	Intergenic	MIR|SINE|MIR	-25793	NM_032438	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.008489	0.416949	
chunk0202_41_1	chr9	71190904	71191731	+	0	NA	Intergenic	Intergenic	-69719	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.006046	0.371981	
chunk0015_459_1	chr1	192617552	192618162	+	0	NA	Intergenic	Intergenic	-18281	NM_002927	6003	Hs.497220	NM_002927	ENSG00000127074	RGS13	-	regulator of G protein signaling 13	protein-coding	0.003279	0.286416	
chunk0104_94_1	chr2	172269686	172270571	+	0	NA	Intergenic	L1PA6|LINE|L1	-157226	NM_001316306	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.010169	0.514673	
chunk0174_171_1	chr6	158707076	158707474	+	0	NA	exon (NM_001009991, exon 8 of 17)	exon (NM_001009991, exon 8 of 17)	57261	NM_001242395	94120	Hs.436977	NM_001009991	ENSG00000164674	SYTL3	SLP3	synaptotagmin like 3	protein-coding	0.012563	0.378446	218(AAGGACAGACCGTCCC,-,0.00),219(AGGACAGACCGTCCCT,+,0.00)
chunk0054_134_1	chr13	43545359	43546168	+	0	NA	intron (NM_001242863, intron 2 of 16)	intron (NM_001242863, intron 2 of 16)	83714	NM_001127615	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.009889	0.444444	
chunk0138_334_1	chr4	41599222	41599899	+	0	NA	intron (NM_001112717, intron 4 of 25)	intron (NM_001112717, intron 4 of 25)	-13212	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.331858	
chunk0058_254_1	chr14	25696238	25696449	+	0	NA	Intergenic	Intergenic	-646046	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.009479	0.419811	
chunk0198_432_1	chr8	143330732	143331109	+	0	NA	intron (NM_001258446, intron 3 of 14)	intron (NM_001258446, intron 3 of 14)	3971	NM_052963	116447	Hs.528574	NM_052963	ENSG00000184428	TOP1MT	-	DNA topoisomerase I mitochondrial	protein-coding	0.031830	0.626984	254(AGGCACAGCCAGTGCA,-,0.00),255(GGCACAGCCAGTGCAG,+,0.00)
chunk0042_92_1	chr12	2692999	2693250	+	0	NA	3' UTR (NM_001129832, exon 48 of 48)	3' UTR (NM_001129832, exon 48 of 48)	-1967	NR_045725	100652846	Hs.683896	NR_045725	ENSG00000246627	CACNA1C-AS1	-	CACNA1C antisense RNA 1	ncRNA	0.007968	0.420635	
chunk0056_62_1	chr13	78374309	78374724	+	0	NA	intron (NR_047001, intron 3 of 5)	MLT1A|LTR|ERVL-MaLR	229044	NM_006237	5457	Hs.654522	NM_006237	ENSG00000152192	POU4F1	BRN3A|Oct-T1|RDC-1|brn-3A	POU class 4 homeobox 1	protein-coding	0.033735	0.444712	
chunk0109_452_1	chr2	241650189	241650393	+	0	NA	intron (NM_178326, intron 1 of 12)	intron (NM_178326, intron 1 of 12)	12679	NM_013325	23192	Hs.283610	NM_013325	ENSG00000168397	ATG4B	APG4B|AUTL1	autophagy related 4B cysteine peptidase	protein-coding	0.004902	0.512195	
chunk0072_95_1	chr15	91030155	91030359	+	0	NA	intron (NR_110104, intron 3 of 3)	MIRb|SINE|MIR	7635	NR_110104	101926911	Hs.459366	NR_110104	ENSG00000214432	VPS33B-DT	-	VPS33B divergent transcript	ncRNA	0.014706	0.390244	
chunk0163_303_1	chr6	14452161	14452450	+	0	NA	Intergenic	Intergenic	-166851	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.027682	0.406897	118(AAGCACAAGATGTCCT,-,0.00),119(AGCACAAGATGTCCTG,+,0.00)
chunk0136_59_1	chr4	1708589	1709051	+	0	NA	intron (NM_001306075, intron 1 of 6)	intron (NM_001306075, intron 1 of 6)	3921	NM_001306074	7884	Hs.298345	NM_006527	ENSG00000163950	SLBP	HBP	stem-loop binding protein	protein-coding	0.004329	0.386609	
chunk0211_230_1	chrX	118853477	118853956	+	0	NA	intron (NR_110393, intron 5 of 6)	intron (NR_110393, intron 5 of 6)	14160	NR_110393	101928287	Hs.496647	NR_110393	ENSG00000203650	LINC01285	-	long intergenic non-protein coding RNA 1285	ncRNA	0.006263	0.422917	
chunk0181_104_1	chr7	80515956	80516206	+	0	NA	Intergenic	Intergenic	-4155	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.008000	0.358566	
chunk0106_184_1	chr2	201232108	201232836	+	0	NA	promoter-TSS (NM_033355)	promoter-TSS (NM_033355)	-971	NM_001080124	841	Hs.599762	NM_001228	ENSG00000064012	CASP8	ALPS2B|CAP4|Casp-8|FLICE|MACH|MCH5	caspase 8	protein-coding	0.013736	0.438957	390(GAGAACAGAGTGGACT,-,0.00),391(AGAACAGAGTGGACTT,+,0.00)
chunk0113_154_1	chr20	52724393	52725150	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	103933	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.013210	0.405013	
chunk0100_388_1	chr2	118314593	118314990	+	0	NA	Intergenic	Intergenic	226317	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.007557	0.417085	
chunk0010_297_1	chr1	117632667	117632894	+	0	NA	Intergenic	Intergenic	26798	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.004405	0.482456	
chunk0150_173_1	chr5	34447488	34447716	+	0	NA	Intergenic	L1PA7|LINE|L1	-208726	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.008772	0.541485	
chunk0150_407_1	chr5	39970363	39970856	+	0	NA	Intergenic	Intergenic	-81682	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.004057	0.313765	249(AAGAACACCAAGTTCC,-,0.00),250(AGAACACCAAGTTCCT,+,0.00)
chunk0030_11_1	chr10	110853778	110854609	+	0	NA	Intergenic	Intergenic	16711	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.000000	0.346154	
chunk0132_14_1	chr3	154345370	154345922	+	0	NA	intron (NM_001038705, intron 3 of 3)	intron (NM_001038705, intron 3 of 3)	-21149	NM_020865	170506	Hs.446270	NM_020865	ENSG00000174953	DHX36	DDX36|G4R1|MLEL1|RHAU	DEAH-box helicase 36	protein-coding	0.005435	0.350814	
chunk0173_98_1	chr6	143124295	143124495	+	0	NA	intron (NM_001286587, intron 2 of 6)	LTR41B|LTR|ERVL	63553	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.025000	0.592040	
chunk0053_199_1	chr13	31925511	31926074	+	0	NA	intron (NR_027062, intron 1 of 3)	L1M5|LINE|L1	79009	NR_027062	196549	Hs.507667	NM_145293		EEF1DP3	-	eukaryotic translation elongation factor 1 delta pseudogene 3	pseudo	0.001776	0.289007	
chunk0019_149_1	chr1	225807407	225807695	+	0	NA	Intergenic	L5|LINE|RTE-X	-2523	NM_001136018	2052	Hs.89649	NM_000120	ENSG00000143819	EPHX1	EPHX|EPOX|HYL1|MEH	epoxide hydrolase 1	protein-coding	0.010417	0.387543	91(AAGAGCACACTGTACC,-,0.00),92(AGAGCACACTGTACCC,+,0.00)
chunk0044_402_1	chr12	41025586	41025966	+	0	NA	intron (NM_175038, intron 19 of 21)	intron (NM_175038, intron 19 of 21)	117419	NM_175038	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.005263	0.349081	
chunk0100_409_1	chr2	119707591	119707891	+	0	NA	Intergenic	Intergenic	28574	NM_001105199	80775	Hs.439991	NM_030577	ENSG00000144120	TMEM177	-	transmembrane protein 177	protein-coding	0.010000	0.561462	
chunk0164_244_1	chr6	23353792	23354472	+	0	NA	Intergenic	Intergenic	-772054	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.000000	0.289280	
chunk0183_273_1	chr7	107560160	107560704	+	0	NA	intron (NM_006348, intron 1 of 21)	L2|LINE|L2	-3525	NR_073003	11062	Hs.97627	NM_181581	ENSG00000105865	DUS4L	DUS4|PP35	dihydrouridine synthase 4 like	protein-coding	0.003676	0.357798	
chunk0161_132_1	chr5	168353054	168353924	+	0	NA	intron (NM_001161661, intron 1 of 22)	intron (NM_001161661, intron 1 of 22)	61429	NM_001161661	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.017241	0.538462	
chunk0063_38_1	chr14	76812273	76812859	+	0	NA	intron (NM_015305, intron 1 of 9)	CpG	374	NM_015305	23357	Hs.497448	NM_015305	ENSG00000013523	ANGEL1	Ccr4e|KIAA0759	angel homolog 1	protein-coding	0.098976	0.703578	
chunk0085_457_1	chr18	11597445	11598151	+	0	NA	Intergenic	HAL1|LINE|L1	-11760	NM_001282300	646000		NM_001282300	ENSG00000236396	SLC35G4	AMAC1L1|SLC35G4P	solute carrier family 35 member G4	protein-coding	0.008499	0.438472	
chunk0151_69_1	chr5	42582698	42583820	+	0	NA	intron (NM_001242460, intron 1 of 7)	intron (NM_001242460, intron 1 of 7)	17395	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.015152	0.484417	
chunk0159_335_1	chr5	143742925	143743480	+	0	NA	Intergenic	Intergenic	63342	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.014414	0.388489	267(GAGAACTGTGTGTTCT,-,0.00),268(AGAACTGTGTGTTCTT,+,0.00)
chunk0134_188_1	chr3	178252809	178253368	+	0	NA	Intergenic	Intergenic	-166113	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.000000	0.316071	
chunk0184_264_1	chr7	118267309	118267658	+	0	NA	Intergenic	Intergenic	42825	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.000000	0.360000	
chunk0096_323_1	chr2	33574024	33574656	+	0	NA	Intergenic	Intergenic	25022	NM_001304538	25940	Hs.468140	NM_015475	ENSG00000119812	FAM98A	-	family with sequence similarity 98 member A	protein-coding	0.009494	0.388626	
chunk0123_140_1	chr3	42805330	42805529	+	0	NA	promoter-TSS (NM_001099668)	promoter-TSS (NM_001099668)	-894	NM_014056	25994	Hs.593134	NM_014056	ENSG00000181061	HIGD1A	HIG1|RCF1a	HIG1 hypoxia inducible domain family member 1A	protein-coding	0.055276	0.630000	
chunk0058_388_1	chr13	110837259	110838279	+	0	NA	Intergenic	LTR5B|LTR|ERVK	32539	NR_027701	283487	Hs.245390	NM_178514	ENSG00000255874	LINC00346	C13orf29|NCRNA00346	long intergenic non-protein coding RNA 346	ncRNA	0.010784	0.458374	663(CAGTACACTGTGTCCC,-,0.00),664(AGTACACTGTGTCCCT,+,0.00)
chunk0039_255_1	chr11	102242187	102242439	+	0	NA	Intergenic	Intergenic	-75137	NM_182962	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.015873	0.446640	
chunk0091_296_1	chr19	12551521	12551815	+	0	NA	promoter-TSS (NM_144976)	promoter-TSS (NM_144976)	-126	NM_144976	163050	Hs.655615	NM_144976	ENSG00000249709	ZNF564	-	zinc finger protein 564	protein-coding	0.027211	0.552542	
chunk0074_19_1	chr16	20206965	20207421	+	0	NA	Intergenic	MIR|SINE|MIR	120427	NM_001007242	2813	Hs.53985	NM_001502	ENSG00000169347	GP2	ZAP75	glycoprotein 2	protein-coding	0.008772	0.387309	
chunk0129_360_1	chr3	125337369	125337817	+	0	NA	intron (NM_021964, intron 1 of 8)	intron (NM_021964, intron 1 of 8)	37761	NM_021964	7707	Hs.592591	NM_021964	ENSG00000163848	ZNF148	BERF-1|BFCOL1|GDACCF|HT-BETA|ZBP-89|ZFP148|pHZ-52	zinc finger protein 148	protein-coding	0.004464	0.345212	
chunk0018_337_1	chr1	221423569	221424217	+	0	NA	Intergenic	L1MEd|LINE|L1	-87597	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.004630	0.302003	171(AAGAACACCATGTGAC,-,0.00)
chunk0152_413_1	chr5	65430616	65430908	+	0	NA	intron (NM_197941, intron 7 of 24)	L2c|LINE|L2	51115	NM_197941	11174	Hs.482291	NM_197941	ENSG00000049192	ADAMTS6	ADAM-TS 6|ADAM-TS6|ADAMTS-6	ADAM metallopeptidase with thrombospondin type 1 motif 6	protein-coding	0.003425	0.365188	
chunk0165_156_1	chr6	33746143	33746393	+	0	NA	intron (NM_001142883, intron 1 of 6)	intron (NM_001142883, intron 1 of 6)	717	NM_001142883	117283	Hs.17253	NM_054111	ENSG00000161896	IP6K3	IHPK3|INSP6K3	inositol hexakisphosphate kinase 3	protein-coding	0.040000	0.645418	163(TAGGACATGCTGTTCC,-,0.00),164(AGGACATGCTGTTCCT,+,0.00)
chunk0006_230_1	chr1	68690616	68691128	+	0	NA	Intergenic	L2b|LINE|L2	-193651	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.000000	0.391813	
chunk0032_47_1	chr11	1559173	1559785	+	0	NA	intron (NM_004420, intron 3 of 6)	intron (NM_004420, intron 3 of 6)	12441	NM_004420	1850	Hs.41688	NM_004420	ENSG00000184545	DUSP8	C11orf81|HB5|HVH-5|HVH8	dual specificity phosphatase 8	protein-coding	0.039216	0.676998	
chunk0009_295_1	chr1	107782377	107783021	+	0	NA	intron (NM_006113, intron 2 of 26)	intron (NM_006113, intron 2 of 26)	-94195	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.007764	0.362791	
chunk0122_3_1	chr3	27319995	27320265	+	0	NA	intron (NM_199347, intron 7 of 24)	intron (NM_199347, intron 7 of 24)	49330	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.014815	0.450185	
chunk0120_9_1	chr3	921789	922160	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-170684	NM_001289080	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.002695	0.325269	
chunk0067_325_1	chr15	48044765	48045477	+	0	NA	Intergenic	Intergenic	-75851	NM_205850	283652	Hs.710240	NM_205850	ENSG00000188467	SLC24A5	JSX|NCKX5|OCA6|SHEP4	solute carrier family 24 member 5	protein-coding	0.002809	0.373072	
chunk0180_337_1	chr7	73358253	73358998	+	0	NA	TTS (NM_001281304)	TTS (NM_001281304)	30393	NM_001281304	8468	Hs.661266	NM_003602	ENSG00000077800	FKBP6	FKBP36	FKBP prolyl isomerase 6	protein-coding	0.032215	0.549598	
chunk0197_92_1	chr8	119345339	119345770	+	0	NA	Intergenic	L2c|LINE|L2	20383	NR_106755	102466162		NR_106755	ENSG00000276479	MIR548AZ	hsa-mir-548az	microRNA 548az	ncRNA	0.004640	0.305556	
chunk0012_55_1	chr1	155495219	155495803	+	0	NA	intron (NM_018489, intron 2 of 27)	Tigger3b|DNA|TcMar-Tigger	62331	NR_034180	645682	Hs.632482	NR_034180	ENSG00000237872	POU5F1P4	OCT3|OCT4|OTF-3|OTF3|Oct-3|Oct-4|Oct4-pg4|POU5F1|POU5FLC1	POU class 5 homeobox 1 pseudogene 4	pseudo	0.010274	0.376068	
chunk0208_308_1	chrX	23806698	23806897	+	0	NA	Intergenic	Intergenic	23639	NR_027783	6303	Hs.28491	NM_002970	ENSG00000130066	SAT1	DC21|KFSD|KFSDX|SAT|SSAT|SSAT-1	spermidine/spermine N1-acetyltransferase 1	protein-coding	0.025126	0.375000	
chunk0195_133_1	chr8	95037139	95037767	+	0	NA	intron (NM_152416, intron 3 of 8)	intron (NM_152416, intron 3 of 8)	12467	NM_152416	137682	Hs.435500	NM_152416	ENSG00000156170	NDUFAF6	C8orf38|MC1DN17	NADH:ubiquinone oxidoreductase complex assembly factor 6	protein-coding	0.009554	0.376789	
chunk0188_121_1	chr8	9104342	9104741	+	0	NA	Intergenic	Intergenic	46169	NM_024607	79660	Hs.458513	NM_024607	ENSG00000173281	PPP1R3B	GL|PPP1R4|PTG	protein phosphatase 1 regulatory subunit 3B	protein-coding	0.022556	0.517500	80(CTGCTCAGGCTGTTCT,-,0.00),81(TGCTCAGGCTGTTCTC,+,0.00)
chunk0149_74_1	chr5	17213043	17213420	+	0	NA	intron (NR_027253, intron 1 of 2)	intron (NR_027253, intron 1 of 2)	-3592	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.007958	0.415344	140(AAGGCCAGGCTGTCCC,-,0.00),141(AGGCCAGGCTGTCCCC,+,0.00)
chunk0094_195_1	chr2	6279741	6280256	+	0	NA	Intergenic	Intergenic	95424	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.001942	0.302326	
chunk0040_406_1	chr11	121040933	121041635	+	0	NA	intron (NM_152715, intron 1 of 7)	intron (NM_152715, intron 1 of 7)	17180	NM_152715	219899	Hs.504136	NM_152715	ENSG00000154114	TBCEL	El|LRRC35	tubulin folding cofactor E like	protein-coding	0.009972	0.361309	
chunk0206_85_1	chr9	120532452	120533085	+	0	NA	intron (NR_073556, intron 7 of 38)	intron (NR_073556, intron 7 of 38)	47402	NR_073557	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.015798	0.515773	155(GGGAACACGCTGATCC,-,0.00),156(GGAACACGCTGATCCT,+,0.00)
chunk0040_163_1	chr11	113856985	113857799	+	0	NA	intron (NM_020886, intron 1 of 24)	Kanga1c|DNA|TcMar-Tc2	18178	NM_001301029	57646	Hs.503891	NM_020886	ENSG00000048028	USP28	-	ubiquitin specific peptidase 28	protein-coding	0.006143	0.347239	659(AAGAACATCTTGATCT,-,0.00),660(AGAACATCTTGATCTC,+,0.00)
chunk0033_157_1	chr11	15602853	15603299	+	0	NA	Intergenic	Intergenic	-40809	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.008969	0.353468	214(GAGTACAGGATGTTCA,-,0.00),215(AGTACAGGATGTTCAT,+,0.00)
chunk0213_27_1	chrY	56728017	56728258	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	-226118	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.029046	0.384298	
chunk0208_229_1	chrX	19224626	19225140	+	0	NA	Intergenic	L1ME3E|LINE|L1	-102246	NM_001184837	10149	Hs.146978	NM_005756	ENSG00000173698	ADGRG2	CBAVDX|EDDM6|GPR64|HE6|TM7LN2	adhesion G protein-coupled receptor G2	protein-coding	0.001946	0.316505	282(CAGTACATTCTGTACA,-,0.00),283(AGTACATTCTGTACAA,+,0.00)
chunk0089_18_1	chr18	57741443	57741896	+	0	NA	intron (NM_005603, intron 1 of 27)	MLT1F2|LTR|ERVL-MaLR	61426	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.006623	0.411894	
chunk0013_369_1	chr1	172456232	172456441	+	0	NA	intron (NM_001300760, intron 1 of 4)	intron (NM_001300760, intron 1 of 4)	3443	NM_001300760	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.004785	0.542857	
chunk0108_145_1	chr2	230850433	230850734	+	0	NA	Intergenic	L1ME4a|LINE|L1	-14015	NM_001287241	81618	Hs.111577	NM_030926	ENSG00000135916	ITM2C	BRI3|BRICD2C|E25|E25C|ITM3	integral membrane protein 2C	protein-coding	0.016611	0.466887	
chunk0160_235_1	chr5	155651708	155652213	+	0	NA	Intergenic	L1MB8|LINE|L1	638260	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.005941	0.332016	
chunk0087_227_1	chr18	36332683	36333142	+	0	NA	intron (NM_001281739, intron 1 of 23)	MER5B|DNA|hAT-Charlie	35216	NM_001281739	80206	Hs.436636	NM_025135	ENSG00000134775	FHOD3	FHOS2|Formactin2	formin homology 2 domain containing 3	protein-coding	0.006536	0.521739	
chunk0092_23_1	chr19	18809515	18809758	+	0	NA	Intergenic	L1MB5|LINE|L1	-18331	NM_000095	1311	Hs.1584	NM_000095	ENSG00000105664	COMP	EDM1|EPD1|MED|PSACH|THBS5|TSP5	cartilage oligomeric matrix protein	protein-coding	0.028807	0.504098	
chunk0130_294_1	chr3	136893947	136894291	+	0	NA	intron (NM_001291999, intron 1 of 3)	ERVL-E-int|LTR|ERVL	31911	NM_001291999	4690	Hs.126889	NM_006153	ENSG00000158092	NCK1	NCK|NCKalpha|nck-1	NCK adaptor protein 1	protein-coding	0.005814	0.434783	
chunk0191_230_1	chr8	52789816	52790464	+	0	NA	Intergenic	Intergenic	-75674	NM_001083617	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.004630	0.395994	197(TAGAACATTGTGTACT,-,0.00),198(AGAACATTGTGTACTC,+,0.00)
chunk0198_438_1	chr8	143669499	143669700	+	0	NA	Intergenic	Intergenic	-14853	NM_173831	286075	Hs.521922	NM_173831	ENSG00000181135	ZNF707	-	zinc finger protein 707	protein-coding	0.000000	0.465347	
chunk0152_406_1	chr5	65006567	65006791	+	0	NA	intron (NM_005869, intron 13 of 13)	intron (NM_005869, intron 13 of 13)	237761	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.004464	0.293333	
chunk0205_366_1	chr9	113712043	113712417	+	0	NA	Intergenic	MIRb|SINE|MIR	118076	NM_001276262	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.005348	0.418667	
chunk0135_98_1	chr3	186554450	186554686	+	0	NA	exon (NM_001286749, exon 5 of 7)	exon (NM_001286749, exon 5 of 7)	-10190	NM_017541	1427	Hs.376209	NM_017541	ENSG00000213139	CRYGS	CRYG8|CTRCT20	crystallin gamma S	protein-coding	0.016949	0.455696	
chunk0152_163_1	chr5	59488299	59488785	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	97956	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004115	0.328542	
chunk0205_377_1	chr9	114049834	114050322	+	0	NA	exon (NM_133374, exon 14 of 14)	exon (NM_133374, exon 14 of 14)	28394	NM_001633	259	Hs.436911	NM_001633	ENSG00000106927	AMBP	A1M|EDC1|HCP|HI30|IATIL|ITI|ITIL|ITILC|UTI	alpha-1-microglobulin/bikunin precursor	protein-coding	0.045082	0.478528	
chunk0030_325_1	chr10	118243879	118244437	+	0	NA	Intergenic	Intergenic	98169	NM_022063	63877	Hs.105575	NM_022063	ENSG00000165669	FAM204A	C10orf84|bA319I23.1	family with sequence similarity 204 member A	protein-coding	0.016129	0.452594	139(TAGATCACTGTGTACT,-,0.00),140(AGATCACTGTGTACTC,+,0.00),422(TAGCACATACTGTCTT,-,0.00),423(AGCACATACTGTCTTC,+,0.00)
chunk0179_105_1	chr7	44891316	44891655	+	0	NA	Intergenic	Intergenic	-6100	NM_033224	5814	Hs.349150	NM_033224	ENSG00000146676	PURB	PURBETA	purine rich element binding protein B	protein-coding	0.005900	0.485294	
chunk0106_296_1	chr2	204497656	204497941	+	0	NA	Intergenic	Intergenic	-47995	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.003509	0.321678	
chunk0116_410_1	chr21	42591551	42591909	+	0	NA	Intergenic	Intergenic	23365	NR_131192	101928233	Hs.534827	NR_131192	ENSG00000225431	LINC01671	-	long intergenic non-protein coding RNA 1671	ncRNA	0.033520	0.512535	
chunk0137_235_1	chr4	20268616	20269463	+	0	NA	intron (NM_001289135, intron 4 of 35)	intron (NM_001289135, intron 4 of 35)	17134	NM_001289135	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.009445	0.334906	
chunk0093_291_1	chr19	52338711	52339347	+	0	NA	intron (NM_001161427, intron 1 of 4)	LTR5B|LTR|ERVK	2784	NM_001161426	162963	Hs.147025	NM_173530	ENSG00000167554	ZNF610	-	zinc finger protein 610	protein-coding	0.025157	0.502355	
chunk0086_163_1	chr18	21638219	21639386	+	0	NA	Intergenic	AluSx3|SINE|Alu	25412	NM_001308257	171586	Hs.397978	NM_138340	ENSG00000158201	ABHD3	LABH3	abhydrolase domain containing 3	protein-coding	0.004284	0.393836	
chunk0115_314_1	chr21	28642873	28643072	+	0	NA	Intergenic	LTR1C|LTR|ERV1	103654	NR_026553	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.020101	0.520000	
chunk0073_243_1	chr16	11689686	11690481	+	0	NA	intron (NM_015914, intron 8 of 11)	intron (NM_015914, intron 8 of 11)	21650	NM_003498	8303	Hs.618526	NM_003498	ENSG00000184602	SNN	-	stannin	protein-coding	0.006289	0.394472	
chunk0055_26_1	chr13	51919516	51919785	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	57669	NM_031290	83446	Hs.120573	NM_031290	ENSG00000123171	CCDC70	-	coiled-coil domain containing 70	protein-coding	0.029740	0.429630	
chunk0084_49_1	chr17	74208851	74209183	+	0	NA	TTS (NR_026914)	TTS (NR_026914)	4304	NR_026914	85001	Hs.706954	NM_032915	ENSG00000246731	MGC16275	-	uncharacterized protein MGC16275	ncRNA	0.015060	0.453453	
chunk0004_423_1	chr1	52604201	52604754	+	0	NA	intron (NM_015696, intron 1 of 2)	intron (NM_015696, intron 1 of 2)	2106	NM_015696	2882	Hs.43728	NM_015696	ENSG00000116157	GPX7	CL683|GPX6|GPx-7|GSHPx-7|NPGPx	glutathione peroxidase 7	protein-coding	0.001808	0.445848	73(GGGAACAGGGAGTCCA,-,0.00),74(GGAACAGGGAGTCCAG,+,0.00)
chunk0044_389_1	chr12	40035484	40035882	+	0	NA	intron (NM_052885, intron 2 of 9)	intron (NM_052885, intron 2 of 9)	70176	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.010050	0.365915	
chunk0127_168_1	chr3	95001830	95002356	+	0	NA	Intergenic	Intergenic	63830	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.296015	
chunk0100_382_1	chr2	118148702	118149236	+	0	NA	Intergenic	Intergenic	60495	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.007491	0.355140	253(CAGCACATTATGTTTT,-,0.00),254(AGCACATTATGTTTTT,+,0.00)
chunk0138_278_1	chr4	40524598	40525007	+	0	NA	intron (NM_001098634, intron 2 of 6)	intron (NM_001098634, intron 2 of 6)	-8829	NM_019027	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.019560	0.465854	
chunk0058_440_1	chr13	113437344	113437875	+	0	NA	intron (NM_138430, intron 2 of 6)	L1ME1|LINE|L1	11533	NM_199162	113622	Hs.98669	NM_138430	ENSG00000153531	ADPRHL1	ARH2	ADP-ribosylhydrolase like 1	protein-coding	0.033898	0.560150	
chunk0051_248_1	chr12	117166329	117166528	+	0	NA	intron (NM_033624, intron 8 of 11)	L1MC1|LINE|L1	24067	NM_015002	23014	Hs.740376	NM_015002	ENSG00000135108	FBXO21	FBX21	F-box protein 21	protein-coding	0.005025	0.440000	123(GGGAACTCTCTGTACT,-,0.00),124(GGAACTCTCTGTACTT,+,0.00)
chunk0178_421_1	chr7	41121114	41121574	+	0	NA	intron (NR_110832, intron 4 of 5)	intron (NR_110832, intron 4 of 5)	19740	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.004348	0.390456	
chunk0211_393_1	chrX	128439375	128439825	+	0	NA	Intergenic	Intergenic	-387197	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.008889	0.376940	
chunk0121_157_1	chr3	19365405	19365936	+	0	NA	intron (NM_144633, intron 5 of 15)	L2a|LINE|L2	-50739	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.011299	0.304511	
chunk0109_458_1	chr2	242004564	242005222	+	0	NA	intron (NR_110220, intron 3 of 3)	MLT2D|LTR|ERVL	34210	NR_110592	102723927	Hs.733585	NR_110592	ENSG00000237940	LINC01238	-	long intergenic non-protein coding RNA 1238	ncRNA	0.030395	0.543247	
chunk0045_127_1	chr12	46360995	46361260	+	0	NA	exon (NM_018976, exon 16 of 16)	exon (NM_018976, exon 16 of 16)	11735	NM_001307936	54407	Hs.221847	NM_018976	ENSG00000134294	SLC38A2	ATA2|PRO1068|SAT2|SNAT2	solute carrier family 38 member 2	protein-coding	0.003774	0.406015	
chunk0013_270_1	chr1	170224460	170224826	+	0	NA	Intergenic	MIRb|SINE|MIR	59565	NR_026957	284688	Hs.135668	NR_026957	ENSG00000224286	LINC01142	-	long intergenic non-protein coding RNA 1142	ncRNA	0.005464	0.340599	
chunk0014_61_1	chr1	175798913	175799281	+	0	NA	Intergenic	L1MA9|LINE|L1	-55481	NM_003285	7143	Hs.659864	NM_003285	ENSG00000116147	TNR	TN-R	tenascin R	protein-coding	0.008152	0.300813	
chunk0198_361_1	chr8	140832498	140832760	+	0	NA	intron (NM_001316342, intron 5 of 32)	L2|LINE|L2	-99976	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.011450	0.532319	
chunk0027_289_1	chr10	77586927	77587249	+	0	NA	intron (NM_001014797, intron 1 of 28)	5S|rRNA|rRNA	50731	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.012422	0.473684	
chunk0077_14_1	chr16	74922447	74922912	+	0	NA	intron (NM_030581, intron 9 of 25)	intron (NM_030581, intron 9 of 25)	62440	NM_030581	79726	Hs.280951	NM_030581	ENSG00000103091	WDR59	CDW12|FP977|p90-120	WD repeat domain 59	protein-coding	0.015054	0.442060	
chunk0030_46_1	chr10	111657515	111658130	+	0	NA	Intergenic	Intergenic	525957	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.004878	0.433442	219(GAGAACATCTTGTCCA,-,0.00),220(AGAACATCTTGTCCAT,+,0.00)
chunk0123_52_1	chr3	41141687	41141934	+	0	NA	Intergenic	Intergenic	-57641	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.012146	0.459677	
chunk0017_302_1	chr1	211148482	211148737	+	0	NA	Intergenic	Intergenic	-14494	NM_002238	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.007843	0.394531	
chunk0026_251_1	chr10	66509994	66510312	+	0	NA	intron (NM_001127384, intron 11 of 17)	L1MA5A|LINE|L1	-415881	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.000000	0.272727	
chunk0206_23_1	chr9	115978626	115979279	+	0	NA	Intergenic	MIR|SINE|MIR	-53854	NR_024032	58483	Hs.23367	NR_024032	ENSG00000204148	LINC00474	C9orf27|EST-YD1	long intergenic non-protein coding RNA 474	ncRNA	0.004594	0.406728	
chunk0097_145_1	chr2	47786516	47787013	+	0	NA	intron (NM_001281494, intron 1 of 9)	intron (NM_001281494, intron 1 of 9)	2809	NM_001281494	2956	Hs.445052	NM_000179	ENSG00000116062	MSH6	GTBP|GTMBP|HNPCC5|HSAP|p160	mutS homolog 6	protein-coding	0.018109	0.435743	
chunk0046_299_1	chr12	62259955	62260485	+	0	NA	promoter-TSS (NM_001252078)	promoter-TSS (NM_001252078)	-120	NM_001252078	9958	Hs.434951	NM_006313	ENSG00000135655	USP15	UNPH-2|UNPH4	ubiquitin specific peptidase 15	protein-coding	0.084906	0.659134	
chunk0145_88_1	chr4	145930678	145930877	+	0	NA	intron (NM_178835, intron 1 of 14)	intron (NM_178835, intron 1 of 14)	8183	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.035176	0.465000	
chunk0034_370_1	chr11	36263199	36263571	+	0	NA	Intergenic	Intergenic	26064	NM_001307937	29099	Hs.99443	NM_014186	ENSG00000110442	COMMD9	C11orf55|HSPC166|LINC00610	COMM domain containing 9	protein-coding	0.013441	0.445040	
chunk0067_11_1	chr15	39988234	39988663	+	0	NA	intron (NM_001013703, intron 15 of 38)	MER58B|DNA|hAT-Charlie	50754	NM_001309434	6727	Hs.533732	NM_003134	ENSG00000140319	SRP14	ALURBP	signal recognition particle 14	protein-coding	0.002331	0.351163	
chunk0042_173_1	chr12	4648982	4649209	+	0	NA	promoter-TSS (NM_005002)	promoter-TSS (NM_005002)	-3	NM_005002	4704	Hs.75227	NM_005002	ENSG00000139180	NDUFA9	CC6|CI-39k|CI39k|COQ11|MC1DN26|NDUFS2L|SDR22E1	NADH:ubiquinone oxidoreductase subunit A9	protein-coding	0.079295	0.574561	
chunk0166_107_1	chr6	43919179	43919668	+	0	NA	intron (NR_024478, intron 1 of 1)	L1MC3|LINE|L1	28395	NR_024478	100132354	Hs.376232	NR_024478		LINC01512	HI-LNC77	long intergenic non-protein coding RNA 1512	ncRNA	0.008180	0.387755	
chunk0042_407_1	chr12	11623171	11623913	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-26312	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.009434	0.403769	
chunk0158_170_1	chr5	127695332	127695567	+	0	NA	Intergenic	Intergenic	42434	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.000000	0.368644	
chunk0031_140_1	chr10	124994790	124995231	+	0	NA	intron (NM_001290215, intron 6 of 10)	intron (NM_001290215, intron 6 of 10)	32874	NM_022802	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.022676	0.540724	180(AAACACAGAGTGTTCT,-,0.00),181(AACACAGAGTGTTCTG,+,0.00)
chunk0092_85_1	chr19	21693892	21694295	+	0	NA	Intergenic	HERVS71-int|LTR|ERV1	-56652	NR_024523	641367	Hs.680128	NR_024523	ENSG00000269845	LOC641367	-	cyclin Y like 1 pseudogene	pseudo	0.014888	0.512376	174(CAGTACTGAGTGTTCT,-,0.00),175(AGTACTGAGTGTTCTG,+,0.00)
chunk0008_92_1	chr1	90896054	90896681	+	0	NA	Intergenic	Intergenic	125141	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.003190	0.372611	
chunk0038_7_1	chr11	80782499	80783119	+	0	NA	Intergenic	Intergenic	-20006	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.004839	0.413849	
chunk0136_256_1	chr4	10296524	10297010	+	0	NA	Intergenic	MER9B|LTR|ERVK	160641	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.008230	0.459959	243(AGGCACAGGCTGCTCA,-,0.00),244(GGCACAGGCTGCTCAT,+,0.00)
chunk0145_27_1	chr4	143532084	143532632	+	0	NA	intron (NM_003601, intron 9 of 23)	intron (NM_003601, intron 9 of 23)	-17521	NR_104027	100128055	Hs.707570	NR_104027	ENSG00000245112	SMARCA5-AS1	-	SMARCA5 antisense RNA 1	ncRNA	0.005474	0.349727	
chunk0056_336_1	chr13	91278444	91278643	+	0	NA	Intergenic	MER54A|LTR|ERVL	-66845	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.005025	0.425000	
chunk0075_157_1	chr16	51657692	51658312	+	0	NA	Intergenic	Intergenic	-104517	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.006452	0.355878	
chunk0080_376_1	chr17	33589131	33589399	+	0	NA	intron (NM_001094, intron 1 of 9)	L2c|LINE|L2	-55505	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.003731	0.431227	103(GAGTACAGTATGTTCC,-,0.00),104(AGTACAGTATGTTCCC,+,0.00)
chunk0047_385_1	chr12	75342212	75342767	+	0	NA	intron (NM_001304964, intron 1 of 5)	intron (NM_001304964, intron 1 of 5)	7850	NM_152779	256710	Hs.567788	NM_152779	ENSG00000173401	GLIPR1L1	ALKN2972|PRO7434	GLIPR1 like 1	protein-coding	0.000000	0.284173	
chunk0036_287_1	chr11	65467661	65468076	+	0	NA	Intergenic	L1MD1|LINE|L1	23410	NR_030343	693197		NR_030343	ENSG00000283791	MIR612	MIRN612|hsa-mir-612	microRNA 612	ncRNA	0.014458	0.444712	
chunk0095_406_1	chr2	24436043	24436252	+	0	NA	Intergenic	Intergenic	-75619	NM_147152	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.004785	0.480952	
chunk0149_246_1	chr5	23590414	23590990	+	0	NA	Intergenic	Intergenic	83047	NM_001310214	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.006944	0.258232	
chunk0063_70_1	chr14	77533382	77533773	+	0	NA	intron (NM_004863, intron 9 of 11)	intron (NM_004863, intron 9 of 11)	-34710	NM_182509	145501	Hs.29742	NM_182509	ENSG00000100593	ISM2	TAIL1|THSD3	isthmin 2	protein-coding	0.023018	0.392857	
chunk0070_317_1	chr15	75403866	75404457	+	0	NA	intron (NM_001145358, intron 9 of 20)	intron (NM_001145358, intron 9 of 20)	-35534	NM_006715	4123	Hs.26232	NM_006715	ENSG00000140400	MAN2C1	MAN6A8|MANA|MANA1	mannosidase alpha class 2C member 1	protein-coding	0.005076	0.341216	
chunk0059_42_1	chr14	29926634	29927108	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	822	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.044304	0.538947	
chunk0110_58_1	chr20	10840410	10840871	+	0	NA	Intergenic	MIR|SINE|MIR	68632	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.004338	0.411255	
chunk0060_265_1	chr14	50320969	50321414	+	0	NA	intron (NR_033761, intron 2 of 5)	intron (NR_033761, intron 2 of 5)	8862	NM_015684	27109	Hs.438489	NM_015684	ENSG00000125375	DMAC2L	ATP5S|ATPW|FB|HSU79253	distal membrane arm assembly complex 2 like	protein-coding	0.013483	0.432735	
chunk0192_26_1	chr8	58489061	58489471	+	0	NA	TTS (NM_000780)	TTS (NM_000780)	10895	NM_000780	1581	Hs.1644	NM_000780	ENSG00000167910	CYP7A1	CP7A|CYP7|CYPVII	cytochrome P450 family 7 subfamily A member 1	protein-coding	0.009756	0.379562	
chunk0026_395_1	chr10	69731337	69731693	+	0	NA	Intergenic	Intergenic	-70373	NM_001130103	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.000000	0.596639	
chunk0205_390_1	chr9	114424831	114425187	+	0	NA	exon (NM_001173425, exon 5 of 12)	exon (NM_001173425, exon 5 of 12)	-30604	NM_030767	80709	Hs.494895	NM_030767	ENSG00000106948	AKNA	-	AT-hook transcription factor	protein-coding	0.014045	0.546218	
chunk0176_433_1	chr7	19917234	19917537	+	0	NA	Intergenic	Intergenic	-144604	NM_152774	256130	Hs.487670	NM_152774	ENSG00000173452	TMEM196	-	transmembrane protein 196	protein-coding	0.000000	0.328947	
chunk0056_215_1	chr13	87666861	87667334	+	0	NA	intron (NR_033829, intron 1 of 5)	intron (NR_033829, intron 1 of 5)	3866	NR_033829	642345	Hs.508337	NR_033829	ENSG00000228824	MIR4500HG	-	MIR4500 host gene	ncRNA	0.002114	0.362869	
chunk0088_58_1	chr18	44184316	44184515	+	0	NA	Intergenic	Intergenic	347282	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.025126	0.365000	
chunk0048_196_1	chr12	81183561	81184070	+	0	NA	intron (NM_024560, intron 8 of 15)	L1MA9|LINE|L1	25427	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.000000	0.341176	
chunk0091_79_1	chr19	5250222	5250536	+	0	NA	intron (NM_130853, intron 6 of 28)	intron (NM_130853, intron 6 of 28)	90424	NM_002850	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.041401	0.625397	
chunk0053_145_1	chr13	30104193	30104480	+	0	NA	non-coding (NR_046998, exon 2 of 2)	non-coding (NR_046998, exon 2 of 2)	4539	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.006969	0.395833	
chunk0019_195_1	chr1	226724828	226725318	+	0	NA	intron (NM_002221, intron 2 of 7)	intron (NM_002221, intron 2 of 7)	14102	NM_002221	3707	Hs.528087	NM_002221	ENSG00000143772	ITPKB	IP3-3KB|IP3K|IP3K-B|IP3KB|PIG37	inositol-trisphosphate 3-kinase B	protein-coding	0.012245	0.466395	
chunk0092_126_1	chr19	27828573	27828992	+	0	NA	Intergenic	Intergenic	-34842	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.011933	0.426190	
chunk0029_330_1	chr10	104618417	104618674	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-22556	NM_014978	22986	Hs.671950	NM_014978	ENSG00000156395	SORCS3	SORCS	sortilin related VPS10 domain containing receptor 3	protein-coding	0.011673	0.562016	
chunk0060_347_1	chr14	52058162	52058912	+	0	NA	intron (NM_007361, intron 3 of 21)	intron (NM_007361, intron 3 of 21)	10691	NM_007361	22795	Hs.369840	NM_007361	ENSG00000087303	NID2	NID-2	nidogen 2	protein-coding	0.005333	0.386152	
chunk0118_376_1	chr22	36615544	36615958	+	0	NA	intron (NM_006078, intron 1 of 3)	L2a|LINE|L2	-86521	NM_003753	8664	Hs.55682	NM_003753	ENSG00000100353	EIF3D	EIF3S7|eIF3-p66|eIF3-zeta	eukaryotic translation initiation factor 3 subunit D	protein-coding	0.009662	0.359036	
chunk0107_331_1	chr2	220468944	220469637	+	0	NA	Intergenic	Intergenic	-562725	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.008658	0.416427	
chunk0054_359_1	chr13	49629190	49629698	+	0	NA	intron (NM_138450, intron 1 of 1)	Tigger3a|DNA|TcMar-Tigger	1145	NM_138450	115761	Hs.558599	NM_138450	ENSG00000152213	ARL11	ARLTS1	ADP ribosylation factor like GTPase 11	protein-coding	0.013780	0.434185	
chunk0098_118_1	chr2	68556406	68557168	+	0	NA	intron (NM_173545, intron 8 of 9)	intron (NM_173545, intron 8 of 9)	-89035	NM_138964	10887	Hs.683430	NM_138964	ENSG00000169618	PROKR1	GPR73|GPR73a|PK-R1|PKR1|ZAQ	prokineticin receptor 1	protein-coding	0.000000	0.365662	488(CAGAACACAATGTTTT,-,0.00),489(AGAACACAATGTTTTA,+,0.00),665(AAGTACAATCTGTCCC,-,0.00),666(AGTACAATCTGTCCCT,+,0.00)
chunk0172_265_1	chr6	137533773	137534388	+	0	NA	Intergenic	Intergenic	-39686	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.008130	0.339286	
chunk0106_260_1	chr2	203648212	203648774	+	0	NA	Intergenic	Intergenic	-57982	NM_001243077	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.005338	0.367673	
chunk0182_215_1	chr7	96331405	96331619	+	0	NA	Intergenic	Intergenic	-9365	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.004673	0.446512	
chunk0149_375_1	chr5	28249621	28250122	+	0	NA	Intergenic	Intergenic	-676999	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.007984	0.390438	
chunk0134_239_1	chr3	179081795	179082181	+	0	NA	Intergenic	LTR23|LTR|ERV1	-10120	NM_152240	64393	Hs.371609	NM_022470	ENSG00000172667	ZMAT3	PAG608|WIG-1|WIG1	zinc finger matrin-type 3	protein-coding	0.002591	0.387597	
chunk0159_203_1	chr5	140468169	140468569	+	0	NA	intron (NM_017747, intron 10 of 33)	intron (NM_017747, intron 10 of 33)	66555	NM_017978	54882	Hs.594084	NM_017747	ENSG00000131503	ANKHD1	MASK|MASK1|PP2500|VBARP	ankyrin repeat and KH domain containing 1	protein-coding	0.007500	0.356608	
chunk0021_186_1	chr10	5631976	5633050	+	0	NA	Intergenic	Intergenic	34082	NM_024701	79754	Hs.445899	NM_024701	ENSG00000196372	ASB13	-	ankyrin repeat and SOCS box containing 13	protein-coding	0.015829	0.504186	
chunk0137_316_1	chr4	24550054	24550363	+	0	NA	intron (NM_001358, intron 5 of 13)	Tigger3b|DNA|TcMar-Tigger	-29918	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.009709	0.325806	171(TAGGACATTCTGTACA,-,0.00),172(AGGACATTCTGTACAG,+,0.00)
chunk0034_397_1	chr11	37088028	37088784	+	0	NA	Intergenic	Intergenic	-490127	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.002646	0.354029	
chunk0094_149_1	chr2	5127159	5127375	+	0	NA	Intergenic	Intergenic	-471045	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009259	0.447005	
chunk0115_242_1	chr21	27475385	27475609	+	0	NA	Intergenic	L2b|LINE|L2	-246882	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.017857	0.440000	
chunk0207_273_1	chr9	132390909	132391427	+	0	NA	intron (NM_007344, intron 6 of 10)	intron (NM_007344, intron 6 of 10)	15683	NM_001205296	7270	Hs.54780	NM_007344	ENSG00000125482	TTF1	TTF-1|TTF-I	transcription termination factor 1	protein-coding	0.017375	0.379576	
chunk0080_80_1	chr17	22154150	22154619	+	0	NA	Intergenic	L1MB4|LINE|L1	-144380	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.004264	0.282979	
chunk0108_199_1	chr2	232319751	232320634	+	0	NA	intron (NR_046476, intron 14 of 20)	intron (NR_046476, intron 14 of 20)	-58342	NM_001632	250	Hs.284255	NM_001632	ENSG00000163283	ALPP	ALP|ALPI|IAP|PALP|PLAP|PLAP-1	alkaline phosphatase, placental	protein-coding	0.012458	0.507919	413(AAGCCCAGAATGTTCT,-,0.00),414(AGCCCAGAATGTTCTG,+,0.00)
chunk0163_95_1	chr6	9598301	9598770	+	0	NA	Intergenic	Intergenic	-813783	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.004264	0.361702	
chunk0093_355_1	chr19	55479713	55479912	+	0	NA	intron (NM_033113, intron 1 of 2)	L2a|LINE|L2	3480	NM_033113	89887	Hs.525209	NM_033113	ENSG00000197483	ZNF628	ZEC|Zfp628	zinc finger protein 628	protein-coding	0.020101	0.515000	36(AGGCACAGTTTGTCCC,-,0.00),37(GGCACAGTTTGTCCCA,+,0.00)
chunk0088_154_1	chr18	46468562	46468761	+	0	NA	Intergenic	HAL1|LINE|L1	50425	NM_001145473	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.020101	0.445000	
chunk0057_291_1	chr13	106232625	106232971	+	0	NA	Intergenic	Intergenic	-143765	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.008671	0.368876	
chunk0072_303_1	chr15	98758712	98758927	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-25607	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.000000	0.444444	
chunk0167_43_1	chr6	55351105	55351304	+	0	NA	intron (NM_207410, intron 4 of 8)	intron (NM_207410, intron 4 of 8)	23735	NM_207410	389400	Hs.526967	NM_207410	ENSG00000187871	GFRAL	C6orf144|GRAL|UNQ9356|bA360D14.1	GDNF family receptor alpha like	protein-coding	0.005025	0.395000	
chunk0027_311_1	chr10	77990913	77991266	+	0	NA	exon (NM_007055, exon 21 of 31)	exon (NM_007055, exon 21 of 31)	38451	NM_007055	11128	Hs.436896	NM_007055	ENSG00000148606	POLR3A	ADDH|HLD7|RPC1|RPC155|WDRTS|hRPC155	RNA polymerase III subunit A	protein-coding	0.011331	0.480226	
chunk0129_158_1	chr3	120661079	120661922	+	0	NA	intron (NM_000187, intron 4 of 13)	intron (NM_000187, intron 4 of 13)	21071	NM_000187	3081	Hs.368254	NM_000187	ENSG00000113924	HGD	AKU|HGO	homogentisate 1,2-dioxygenase	protein-coding	0.002372	0.394550	
chunk0007_50_1	chr1	77832386	77832686	+	0	NA	intron (NM_198549, intron 7 of 15)	L2c|LINE|L2	52912	NM_198549	374986	Hs.437755	NM_198549	ENSG00000180488	MIGA1	FAM73A	mitoguardin 1	protein-coding	0.006667	0.415282	
chunk0059_247_1	chr14	35045032	35045234	+	0	NA	5' UTR (NM_001079519, exon 1 of 7)	5' UTR (NM_001079519, exon 1 of 7)	226	NM_001079519	283635	Hs.446357	NM_173607	ENSG00000151327	FAM177A1	C14orf24	family with sequence similarity 177 member A1	protein-coding	0.004950	0.359606	
chunk0103_388_1	chr2	168803054	168803281	+	0	NA	intron (NM_052946, intron 1 of 14)	intron (NM_052946, intron 1 of 14)	570	NM_052946	115677	Hs.189780	NM_052946	ENSG00000163072	NOSTRIN	DaIP2	nitric oxide synthase trafficking	protein-coding	0.004405	0.451754	
chunk0002_284_1	chr1	22680811	22681106	+	0	NA	Intergenic	Intergenic	27769	NM_000491	713	Hs.8986	NM_000491	ENSG00000173369	C1QB	-	complement C1q B chain	protein-coding	0.027119	0.547297	
chunk0081_142_1	chr17	40680942	40681340	+	0	NA	Intergenic	Intergenic	-15977	NM_152349	125113	Hs.6920	NM_152349	ENSG00000213424	KRT222	KA21|KRT222P	keratin 222	protein-coding	0.000000	0.380952	
chunk0110_154_1	chr20	13842462	13842704	+	0	NA	Intergenic	MER34B|LTR|ERV1	57557	NM_024120	79133	Hs.472165	NM_024120	ENSG00000101247	NDUFAF5	C20orf7|MC1DN16|bA526K24.2|dJ842G6.1	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.020661	0.456790	
chunk0024_285_1	chr10	42070458	42070982	+	0	NA	Intergenic	Intergenic	297325	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.047710	0.371429	
chunk0101_457_1	chr2	140223803	140224117	+	0	NA	Intergenic	Intergenic	362725	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.015924	0.377778	184(TTGAACAAAGTGTTCT,-,0.00),185(TGAACAAAGTGTTCTG,+,0.00)
chunk0151_204_1	chr5	50727207	50727406	+	0	NA	intron (NM_024615, intron 2 of 25)	intron (NM_024615, intron 2 of 25)	60368	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.020101	0.470000	
chunk0155_85_1	chr5	92108049	92108386	+	0	NA	Intergenic	Intergenic	-724885	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.005935	0.301775	
chunk0084_372_1	chr17	81660431	81660630	+	0	NA	Intergenic	Intergenic	-3953	NR_026872	5148	Hs.654482	NM_002602	ENSG00000185527	PDE6G	PDEG|RP57	phosphodiesterase 6G	protein-coding	0.005025	0.435000	
chunk0115_320_1	chr21	28763885	28764572	+	0	NA	Intergenic	L2|LINE|L2	121145	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.004367	0.406977	
chunk0024_123_1	chr10	34864328	34865076	+	0	NA	Intergenic	Intergenic	48934	NR_108043	100505601	Hs.549790	NR_108043	ENSG00000226386	PARD3-AS1	-	PARD3 antisense RNA 1	ncRNA	0.014706	0.377837	
chunk0073_35_1	chr16	2693309	2693733	+	0	NA	intron (NM_018992, intron 1 of 5)	intron (NM_018992, intron 1 of 5)	11027	NM_018992	54442	Hs.61960	NM_018992	ENSG00000167977	KCTD5	-	potassium channel tetramerization domain containing 5	protein-coding	0.035377	0.640000	
chunk0009_249_1	chr1	107057836	107058092	+	0	NA	3' UTR (NM_018137, exon 1 of 1)	3' UTR (NM_018137, exon 1 of 1)	1319	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.031250	0.517510	
chunk0111_385_1	chr20	34068478	34068839	+	0	NA	intron (NM_016732, intron 2 of 9)	MER115|DNA|hAT-Tip100	19539	NR_039911	100616434		NR_039911	ENSG00000264616	MIR4755	mir-4755	microRNA 4755	ncRNA	0.002770	0.436464	
chunk0099_61_1	chr2	84904777	84905118	+	0	NA	promoter-TSS (NM_021103)	promoter-TSS (NM_021103)	-692	NM_021103	9168	Hs.446574	NM_021103	ENSG00000034510	TMSB10	MIG12|TB10	thymosin beta 10	protein-coding	0.058651	0.578947	111(CGGGACGCCCTGTTCC,-,0.00),112(GGGACGCCCTGTTCCC,+,0.00)
chunk0049_217_1	chr12	93360103	93360345	+	0	NA	intron (NR_040096, intron 1 of 4)	L1ME2|LINE|L1	17512	NR_040096	643339	Hs.741299	NR_040096		LOC643339	-	uncharacterized LOC643339	ncRNA	0.000000	0.333333	
chunk0078_454_1	chr16	90016434	90017096	+	0	NA	intron (NM_001288708, intron 1 of 4)	intron (NM_001288708, intron 1 of 4)	2790	NM_001042610	79007	Hs.301394	NM_024043	ENSG00000003249	DBNDD1	-	dysbindin domain containing 1	protein-coding	0.013595	0.600302	
chunk0082_366_1	chr17	60315408	60316050	+	0	NA	intron (NM_032582, intron 2 of 33)	L1MB4|LINE|L1	76496	NM_032582	84669	Hs.132868	NM_032582	ENSG00000170832	USP32	NY-REN-60|USP10	ubiquitin specific peptidase 32	protein-coding	0.003115	0.381026	
chunk0078_209_1	chr17	5467261	5467673	+	0	NA	intron (NM_020162, intron 1 of 11)	LTR19A|LTR|ERV1	1593	NM_020162	56919	Hs.250456	NM_020162	ENSG00000005100	DHX33	DDX33	DEAH-box helicase 33	protein-coding	0.029126	0.486683	112(AAGAACATGCCGTCCC,-,0.00),113(AGAACATGCCGTCCCT,+,0.00)
chunk0133_186_1	chr3	170368167	170368536	+	0	NA	intron (NM_001145097, intron 1 of 5)	intron (NM_001145097, intron 1 of 5)	8728	NM_001248008	6498	Hs.536655	NM_005414	ENSG00000136603	SKIL	SNO|SnoA|SnoI|SnoN	SKI like proto-oncogene	protein-coding	0.002710	0.291892	
chunk0072_316_1	chr15	98868628	98868922	+	0	NA	intron (NM_001291858, intron 2 of 20)	MIR|SINE|MIR	84349	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.017007	0.488136	
chunk0165_82_1	chr6	31307295	31307897	+	0	NA	Intergenic	Intergenic	-35460	NM_001243042	3107	Hs.656020	NM_002117	ENSG00000204525	HLA-C	D6S204|HLA-JY3|HLAC|HLC-C|MHC|PSORS1	major histocompatibility complex, class I, C	protein-coding	0.024917	0.527363	
chunk0061_412_1	chr14	65024880	65025444	+	0	NA	intron (NM_001202558, intron 5 of 12)	intron (NM_001202558, intron 5 of 12)	-19526	NR_039855	100616490		NR_039855	ENSG00000266531	MIR4706	mir-4706	microRNA 4706	ncRNA	0.008865	0.419469	184(GGGATCAGAATGTTCT,-,0.00),185(GGATCAGAATGTTCTG,+,0.00)
chunk0023_181_1	chr10	24526702	24527119	+	0	NA	intron (NM_019590, intron 13 of 20)	intron (NM_019590, intron 13 of 20)	60405	NM_001282770	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.007194	0.385167	
chunk0136_75_1	chr4	2196550	2197061	+	0	NA	intron (NM_181808, intron 6 of 25)	intron (NM_181808, intron 6 of 25)	45359	NM_001303143	79441	Hs.665869	NM_024511	ENSG00000214367	HAUS3	C4orf15|IT1|dgt3	HAUS augmin like complex subunit 3	protein-coding	0.013699	0.466797	
chunk0156_377_1	chr5	112821586	112822110	+	0	NA	intron (NM_001127511, intron 8 of 13)	intron (NM_001127511, intron 8 of 13)	-39340	NM_001204196	6728	Hs.637001	NM_003135	ENSG00000153037	SRP19	-	signal recognition particle 19	protein-coding	0.001908	0.300952	
chunk0156_366_1	chr5	112636195	112636664	+	0	NA	Intergenic	L2b|LINE|L2	7993	NR_104672	102467214	Hs.124613	NR_104672		LINC02200	-	long intergenic non-protein coding RNA 2200	ncRNA	0.000000	0.485106	
chunk0009_351_1	chr1	109553241	109553824	+	0	NA	intron (NM_006496, intron 1 of 8)	intron (NM_006496, intron 1 of 8)	4968	NM_006496	2773	Hs.73799	NM_006496	ENSG00000065135	GNAI3	87U6|ARCND1	G protein subunit alpha i3	protein-coding	0.003431	0.333904	
chunk0200_456_1	chr9	31608670	31609121	+	0	NA	Intergenic	MIRb|SINE|MIR	-775708	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.004435	0.351770	1(GAGAACATGGTGTGTT,-,0.00),2(AGAACATGGTGTGTTG,+,0.00)
chunk0098_331_1	chr2	76889880	76890169	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-95941	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.003460	0.372414	57(CAGGACACTCTGTTCT,-,0.00),58(AGGACACTCTGTTCTG,+,0.00)
chunk0107_118_1	chr2	214394918	214395546	+	0	NA	intron (NR_047659, intron 17 of 17)	L1MC1|LINE|L1	-16505	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.004777	0.346582	
chunk0160_316_1	chr5	159197471	159197892	+	0	NA	intron (NM_144726, intron 2 of 10)	Charlie20a|DNA|hAT-Charlie	9967	NM_001199382	153830	Hs.349306	NM_144726	ENSG00000145860	RNF145	-	ring finger protein 145	protein-coding	0.004751	0.357820	
chunk0025_172_1	chr10	52802569	52802979	+	0	NA	Intergenic	Intergenic	-31074	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.002439	0.262774	
chunk0046_80_1	chr12	56216038	56216784	+	0	NA	intron (NR_040053, intron 2 of 8)	intron (NR_040053, intron 2 of 8)	5290	NM_001242826	10193	Hs.524502	NM_005785	ENSG00000181852	RNF41	FLRF|NRDP1|SBBI03	ring finger protein 41	protein-coding	0.008043	0.441767	
chunk0062_346_1	chr14	73679848	73680217	+	0	NA	intron (NM_001201366, intron 6 of 8)	L1M5|LINE|L1	34393	NM_006029	9240	Hs.194709	NM_006029	ENSG00000176903	PNMA1	MA1	PNMA family member 1	protein-coding	0.002710	0.318919	
chunk0153_92_1	chr5	68229458	68229955	+	0	NA	intron (NM_181523, intron 2 of 15)	intron (NM_181523, intron 2 of 15)	13950	NM_181523	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.010060	0.417671	
chunk0048_358_1	chr12	85582190	85582569	+	0	NA	Intergenic	Intergenic	254161	NM_005447	9182	Hs.527881	NM_005447	ENSG00000198774	RASSF9	P-CIP1|PAMCI|PCIP1	Ras association domain family member 9	protein-coding	0.002639	0.389474	
chunk0085_323_1	chr18	8341402	8342668	+	0	NA	intron (NM_001105244, intron 22 of 32)	intron (NM_001105244, intron 22 of 32)	24999	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.008689	0.453828	166(AGGCACAAGCTGTCCA,-,0.00),167(GGCACAAGCTGTCCAT,+,0.00)
chunk0128_445_1	chr3	115086335	115086630	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	-13941	NR_046877	100874131		NR_046877	ENSG00000242767	ZBTB20-AS4	-	ZBTB20 antisense RNA 4	ncRNA	0.006780	0.361486	
chunk0003_170_1	chr1	33482210	33482958	+	0	NA	intron (NM_145238, intron 2 of 7)	L1MC1|LINE|L1	9953	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.006684	0.367156	
chunk0130_43_1	chr3	129205232	129205495	+	0	NA	Intergenic	Tigger12c|DNA|TcMar-Tigger	-21396	NM_001127193	7555	Hs.518249	NM_003418	ENSG00000169714	CNBP	CNBP1|DM2|PROMM|RNF163|ZCCHC22|ZNF9	CCHC-type zinc finger nucleic acid binding protein	protein-coding	0.015209	0.469697	
chunk0071_442_1	chr15	90046929	90047185	+	0	NA	intron (NM_198526, intron 1 of 4)	intron (NM_198526, intron 1 of 4)	40302	NR_036135	100422841		NR_036135	ENSG00000265871	MIR3174	-	microRNA 3174	ncRNA	0.027344	0.607004	
chunk0032_392_1	chr11	11606182	11606402	+	0	NA	intron (NM_198516, intron 1 of 10)	L2b|LINE|L2	15722	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.004545	0.398190	
chunk0048_424_1	chr12	88400988	88401527	+	0	NA	Intergenic	Intergenic	179216	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.007421	0.357407	
chunk0046_245_1	chr12	60469028	60469510	+	0	NA	Intergenic	L1PA8|LINE|L1	779932	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.000000	0.362319	
chunk0037_347_1	chr11	77450836	77451246	+	0	NA	intron (NM_001128620, intron 1 of 15)	intron (NM_001128620, intron 1 of 15)	23022	NM_001128620	5058	Hs.435714	NM_002576	ENSG00000149269	PAK1	IDDMSSD|PAKalpha	p21 (RAC1) activated kinase 1	protein-coding	0.002439	0.396594	186(CAGAACAAGAAGTTCT,-,0.00),187(AGAACAAGAAGTTCTG,+,0.00)
chunk0120_109_1	chr3	4533935	4534134	+	0	NA	intron (NM_002222, intron 4 of 57)	intron (NM_002222, intron 4 of 57)	40686	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.010050	0.490000	
chunk0027_138_1	chr10	74486658	74487057	+	0	NA	intron (NM_001202450, intron 6 of 9)	intron (NM_001202450, intron 6 of 9)	42467	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.002506	0.337500	159(TGGCACATGCTGTTCC,-,0.00),160(GGCACATGCTGTTCCC,+,0.00)
chunk0167_60_1	chr6	56024880	56025274	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-149500	NM_021073	653	Hs.296648	NM_021073	ENSG00000112175	BMP5	-	bone morphogenetic protein 5	protein-coding	0.010152	0.394937	175(ATGTACATAGAGTTCT,-,0.00),176(TGTACATAGAGTTCTC,+,0.00)
chunk0064_329_1	chr14	96391798	96392072	+	0	NA	promoter-TSS (NM_152327)	promoter-TSS (NM_152327)	-176	NM_152327	122481	Hs.667462	NM_152327	ENSG00000140057	AK7	AK 7|SPGF27	adenylate kinase 7	protein-coding	0.127737	0.785455	124(CGGCACAGCCTGCCCC,-,0.00),125(GGCACAGCCTGCCCCG,+,0.00)
chunk0126_224_1	chr3	78919154	78919850	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	99957	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004310	0.380201	
chunk0095_413_1	chr2	24560652	24560950	+	0	NA	Intergenic	Intergenic	-23676	NM_003743	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.003356	0.337793	
chunk0128_65_1	chr3	105140802	105141530	+	0	NA	Intergenic	Intergenic	-225547	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.005495	0.356653	339(AAGAACAATTTGTTCA,-,0.00),340(AGAACAATTTGTTCAA,+,0.00)
chunk0174_220_1	chr6	160418423	160418689	+	0	NA	intron (NM_021977, intron 5 of 10)	MLT2B3|LTR|ERVL	70183	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.007519	0.468165	
chunk0054_241_1	chr13	46135122	46135640	+	0	NA	intron (NM_002298, intron 13 of 15)	intron (NM_002298, intron 13 of 15)	-30305	NM_001872	1361	Hs.512937	NM_001872	ENSG00000080618	CPB2	CPU|PCPB|TAFI	carboxypeptidase B2	protein-coding	0.005792	0.433526	188(ATTACAGTGTGTGCTT,+,0.00)
chunk0064_208_1	chr14	93019236	93019674	+	0	NA	intron (NM_001142594, intron 3 of 10)	intron (NM_001142594, intron 3 of 10)	-47997	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.029680	0.599089	
chunk0091_260_1	chr19	11088913	11089332	+	0	NA	promoter-TSS (NM_001195799)	promoter-TSS (NM_001195799)	-240	NM_000527	3949	Hs.213289	NM_000527	ENSG00000130164	LDLR	FH|FHC|LDLCQ2	low density lipoprotein receptor	protein-coding	0.023866	0.404762	
chunk0116_196_1	chr21	37247019	37247509	+	0	NA	intron (NM_006052, intron 1 of 7)	intron (NM_006052, intron 1 of 7)	20268	NM_006052	10311	Hs.369488	NM_006052	ENSG00000157538	VPS26C	DCRA|DSCR3|DSCRA	VPS26 endosomal protein sorting factor C	protein-coding	0.008163	0.344196	
chunk0052_133_1	chr13	23626810	23627112	+	0	NA	intron (NM_148957, intron 5 of 9)	intron (NM_148957, intron 5 of 9)	47601	NM_018647	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.013245	0.508251	96(GTGTACAGTGTGTCCT,-,0.00),97(TGTACAGTGTGTCCTC,+,0.00),130(CAGGACAGAAAGTCCC,-,0.00),131(AGGACAGAAAGTCCCT,+,0.00)
chunk0144_250_1	chr4	136246799	136247045	+	0	NA	Intergenic	Intergenic	-333242	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.004065	0.364372	
chunk0129_396_1	chr3	126472495	126472867	+	0	NA	intron (NR_104249, intron 1 of 8)	MER106B|DNA|hAT-Charlie	3238	NR_104249	79364	Hs.440049	NM_025112	ENSG00000070476	ZXDC	ZXDL	ZXD family zinc finger C	protein-coding	0.016129	0.487936	
chunk0171_172_1	chr6	125020069	125020474	+	0	NA	intron (NM_152553, intron 3 of 8)	L2c|LINE|L2	36907	NR_104440	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.009877	0.421182	
chunk0103_440_1	chr2	170090223	170090877	+	0	NA	Intergenic	Intergenic	-87595	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.000000	0.348092	
chunk0028_175_1	chr10	87930943	87931293	+	0	NA	intron (NM_001304718, intron 3 of 8)	intron (NM_001304718, intron 3 of 8)	67680	NM_000314	5728	Hs.500466	NM_000314	ENSG00000171862	PTEN	10q23del|BZS|CWS1|DEC|GLM2|MHAM|MMAC1|PTEN1|PTENbeta|TEP1	phosphatase and tensin homolog	protein-coding	0.008571	0.279202	
chunk0106_79_1	chr2	197012006	197012545	+	0	NA	intron (NM_001195144, intron 18 of 27)	intron (NM_001195144, intron 18 of 27)	-85545	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.007421	0.368519	
chunk0046_367_1	chr12	63236712	63237032	+	0	NA	Intergenic	L2a|LINE|L2	-84062	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.009375	0.395639	
chunk0174_342_1	chr6	164152971	164153484	+	0	NA	Intergenic	Intergenic	668836	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.007797	0.352140	
chunk0035_35_1	chr11	40746200	40746497	+	0	NA	intron (NM_020929, intron 1 of 4)	L1MA4A|LINE|L1	-453218	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.020202	0.530201	140(AACACACCGTGTACTC,+,0.00)
chunk0125_442_1	chr3	72782997	72783206	+	0	NA	intron (NM_018130, intron 10 of 10)	intron (NM_018130, intron 10 of 10)	65346	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.000000	0.423810	
chunk0155_23_1	chr5	90956378	90957053	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	357687	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.007407	0.343195	264(TGCACTCGTTGTTCTT,+,0.00),291(AGGTACTTTATGTACT,-,0.00),292(GGTACTTTATGTACTT,+,0.00)
chunk0209_94_1	chrX	39598674	39599196	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-62281	NR_037501	100500822		NR_037501	ENSG00000263730	MIR3937	-	microRNA 3937	ncRNA	0.003831	0.489484	
chunk0031_9_1	chr10	121501636	121501937	+	0	NA	intron (NM_001144916, intron 7 of 14)	intron (NM_001144916, intron 7 of 14)	92181	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.013289	0.354305	139(AAGGGCAGCATGTGCT,-,0.00),140(AGGGCAGCATGTGCTA,+,0.00)
chunk0182_263_1	chr7	97738251	97738621	+	0	NA	intron (NM_003182, intron 6 of 6)	intron (NM_003182, intron 6 of 6)	6477	NM_013998	6863	Hs.2563	NM_003182	ENSG00000006128	TAC1	Hs.2563|NK2|NKNA|NPK|TAC2	tachykinin precursor 1	protein-coding	0.002703	0.401617	133(GAGGACATTATGTTCC,-,0.00),134(AGGACATTATGTTCCA,+,0.00),329(TGGCTCAGACTGTTCT,-,0.00),330(GGCTCAGACTGTTCTG,+,0.00)
chunk0002_196_1	chr1	19445972	19446260	+	0	NA	intron (NM_001313932, intron 1 of 4)	intron (NM_001313932, intron 1 of 4)	38591	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.031250	0.567474	
chunk0052_435_1	chr12	131952897	131953096	+	0	NA	intron (NM_015409, intron 1 of 52)	intron (NM_015409, intron 1 of 52)	3076	NM_015409	57634	Hs.723478	NM_015409	ENSG00000183495	EP400	CAGH32|P400|TNRC12	E1A binding protein p400	protein-coding	0.010050	0.405000	
chunk0127_201_1	chr3	96209052	96209373	+	0	NA	Intergenic	MLT1E1|LTR|ERVL-MaLR	-150752	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.006231	0.369565	
chunk0168_251_1	chr6	88849554	88849974	+	0	NA	exon (NM_001286428, exon 9 of 14)	exon (NM_001286428, exon 9 of 14)	113865	NM_003800	8732	Hs.567378	NM_003800	ENSG00000111880	RNGTT	CAP1A|HCE|HCE1|hCAP	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0.000000	0.280285	234(AGGAACAGCCTGTCCA,-,0.00),235(GGAACAGCCTGTCCAT,+,0.00)
chunk0186_435_1	chr7	146992179	146992735	+	0	NA	intron (NM_014141, intron 3 of 23)	MER61A|LTR|ERV1	105152	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.007194	0.402154	
chunk0011_126_1	chr1	147109692	147110398	+	0	NA	intron (NR_103466, intron 3 of 5)	intron (NR_103466, intron 3 of 5)	4301	NR_103466	644861	Hs.451804	NR_103466		NBPF13P	-	NBPF member 13, pseudogene	pseudo	0.008499	0.482320	300(TGGGACGTCCTGTTCC,-,0.00),301(GGGACGTCCTGTTCCT,+,0.00)
chunk0085_16_1	chr18	301761	302021	+	0	NA	Intergenic	Intergenic	-33832	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.007692	0.325670	
chunk0164_131_1	chr6	20996904	20997503	+	0	NA	intron (NM_017774, intron 10 of 15)	intron (NM_017774, intron 10 of 15)	462746	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.003339	0.360000	
chunk0037_206_1	chr11	74493355	74493606	+	0	NA	exon (NM_001144869, exon 1 of 2)	exon (NM_001144869, exon 1 of 2)	230	NM_001144869	387787	Hs.591971	NM_001144869	ENSG00000175536	LIPT2	-	lipoyl(octanoyl) transferase 2	protein-coding	0.139442	0.746032	
chunk0056_263_1	chr13	90027835	90028034	+	0	NA	Intergenic	THE1C-int|LTR|ERVL-MaLR	91783	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.000000	0.505000	
chunk0012_79_1	chr1	155884219	155884895	+	0	NA	3' UTR (NM_152280, exon 4 of 4)	3' UTR (NM_152280, exon 4 of 4)	25088	NM_152280	23208	Hs.32984	NM_152280	ENSG00000132718	SYT11	SYT12|sytXI	synaptotagmin 11	protein-coding	0.007396	0.472674	
chunk0061_168_1	chr14	59854624	59855304	+	0	NA	intron (NM_021136, intron 1 of 8)	intron (NM_021136, intron 1 of 8)	15875	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.002941	0.337739	
chunk0111_26_1	chr20	22055915	22056379	+	0	NA	intron (NR_038394, intron 1 of 3)	intron (NR_038394, intron 1 of 3)	2057	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.002155	0.309677	33(TAGAGCAATCTGTTCT,-,0.00),34(AGAGCAATCTGTTCTG,+,0.00)
chunk0051_314_1	chr12	119670067	119670553	+	0	NA	intron (NM_006253, intron 1 of 6)	intron (NM_006253, intron 1 of 6)	2354	NM_006253	5564	Hs.741184	NM_006253	ENSG00000111725	PRKAB1	AMPK|HAMPKb	protein kinase AMP-activated non-catalytic subunit beta 1	protein-coding	0.006173	0.422998	
chunk0125_380_1	chr3	71601624	71601823	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	-17734	NM_032682	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.010050	0.475000	
chunk0041_401_1	chr11	133530187	133530932	+	0	NA	intron (NM_001012393, intron 1 of 7)	intron (NM_001012393, intron 1 of 7)	1949	NM_001012393	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.014765	0.524129	391(AGGTACTGAGTGTTCC,-,0.00),392(GGTACTGAGTGTTCCG,+,0.00)
chunk0021_294_1	chr1	244694490	244695212	+	0	NA	intron (NR_123736, intron 3 of 3)	MER58B|DNA|hAT-Charlie	41803	NR_123736	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.020776	0.456432	
chunk0084_378_1	chr17	81821741	81822176	+	0	NA	TTS (NM_001288798)	TTS (NM_001288798)	11336	NM_001093767	348262	Hs.514632	NM_207368	ENSG00000225663	MCRIP1	FAM195B|GRAN2|MCRIP	MAPK regulated corepressor interacting protein 1	protein-coding	0.025287	0.637615	
chunk0107_462_1	chr2	225842993	225843565	+	0	NA	Intergenic	Intergenic	-299515	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.001748	0.324607	248(AAGAACACAGTGTCCT,-,0.00),249(AGAACACAGTGTCCTT,+,0.00)
chunk0185_226_1	chr7	129228651	129229037	+	0	NA	intron (NM_001130720, intron 1 of 16)	intron (NM_001130720, intron 1 of 16)	3830	NM_001130720	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.005181	0.405685	215(TAGCACTTCTTGTCCT,-,0.00),216(AGCACTTCTTGTCCTG,+,0.00)
chunk0014_183_1	chr1	178727251	178727810	+	0	NA	intron (NM_001286247, intron 1 of 18)	intron (NM_001286247, intron 1 of 18)	2383	NM_152663	55103	Hs.632485	NM_018037	ENSG00000116191	RALGPS2	dJ595C2.1	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.014311	0.383929	241(CAGAACACAACGTGCT,-,0.00),242(AGAACACAACGTGCTT,+,0.00)
chunk0001_13_1	chr1	1073888	1074115	+	0	NA	intron (NM_001205252, intron 1 of 1)	intron (NM_001205252, intron 1 of 1)	306	NM_001205252	401934	Hs.568137	NM_001205252	ENSG00000237330	RNF223	-	ring finger protein 223	protein-coding	0.052863	0.697368	
chunk0081_148_1	chr17	40795097	40795748	+	0	NA	intron (NM_181535, intron 5 of 7)	intron (NM_181535, intron 5 of 7)	4537	NM_181535	162605	Hs.59736	NM_181535	ENSG00000173908	KRT28	K25IRS4|KRT25D	keratin 28	protein-coding	0.015361	0.437117	344(GAGAACAGGATGAACT,-,0.00),345(AGAACAGGATGAACTT,+,0.00)
chunk0116_352_1	chr21	41560374	41560573	+	0	NA	Intergenic	Intergenic	-52315	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.015075	0.435000	
chunk0065_14_1	chr15	20293662	20294091	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	11132	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.006993	0.439535	
chunk0014_225_1	chr1	179718037	179718341	+	0	NA	Intergenic	L2c|LINE|L2	-24974	NM_173509	148753	Hs.400696	NM_173509	ENSG00000143340	FAM163A	C1orf76|NDSP	family with sequence similarity 163 member A	protein-coding	0.003289	0.383607	167(AGGAACACAATGTTCC,-,0.00),168(GGAACACAATGTTCCA,+,0.00)
chunk0120_52_1	chr3	3017884	3018216	+	0	NA	intron (NM_001206955, intron 13 of 23)	intron (NM_001206955, intron 13 of 23)	43095	NR_046554	100873975	Hs.581502	NR_046554		CNTN4-AS1	-	CNTN4 antisense RNA 1	ncRNA	0.003012	0.342342	
chunk0048_284_1	chr12	82686333	82686676	+	0	NA	promoter-TSS (NM_152588)	promoter-TSS (NM_152588)	-651	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.040816	0.581395	
chunk0117_344_1	chr21	43980673	43981292	+	0	NA	intron (NM_020132, intron 8 of 9)	intron (NM_020132, intron 8 of 9)	-31343	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.035541	0.525806	397(CTGAACTTCCTGTCCT,-,0.00),398(TGAACTTCCTGTCCTG,+,0.00)
chunk0128_143_1	chr3	106836751	106837192	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	403667	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.006803	0.371041	
chunk0024_97_1	chr10	34522354	34522738	+	0	NA	intron (NM_019619, intron 2 of 24)	intron (NM_019619, intron 2 of 24)	292779	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.010417	0.368831	
chunk0033_46_1	chr11	13277471	13277670	+	0	NA	promoter-TSS (NM_001030273)	promoter-TSS (NM_001030273)	-157	NM_001297719	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.115578	0.700000	
chunk0037_38_1	chr11	70270184	70270482	+	0	NA	promoter-TSS (NR_045286)	promoter-TSS (NR_045286)	-367	NR_045286	8500	Hs.530749	NM_003626	ENSG00000131626	PPFIA1	LIP.1|LIP1|LIPRIN	PTPRF interacting protein alpha 1	protein-coding	0.097315	0.688963	
chunk0170_207_1	chr6	112571450	112571865	+	0	NA	Intergenic	Intergenic	224327	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.007229	0.382212	
chunk0010_270_1	chr1	117128478	117129181	+	0	NA	Intergenic	Intergenic	-7040	NM_001145635	80263	Hs.301526	NM_025188	ENSG00000134253	TRIM45	RNF99	tripartite motif containing 45	protein-coding	0.004267	0.363636	
chunk0029_4_1	chr10	95289484	95289683	+	0	NA	intron (NM_020992, intron 1 of 6)	intron (NM_020992, intron 1 of 6)	1565	NM_020992	9124	Hs.368525	NM_020992	ENSG00000107438	PDLIM1	CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1	PDZ and LIM domain 1	protein-coding	0.010050	0.530000	
chunk0154_414_1	chr5	88964694	88965336	+	0	NA	intron (NR_104031, intron 3 of 3)	L2c|LINE|L2	-60910	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.001558	0.402799	
chunk0041_8_1	chr12	308489	308905	+	0	NA	intron (NM_001042603, intron 22 of 27)	intron (NM_001042603, intron 22 of 27)	-45824	NM_016615	6540	Hs.504398	NM_016615	ENSG00000010379	SLC6A13	GAT-2|GAT2|GAT3	solute carrier family 6 member 13	protein-coding	0.004808	0.335731	
chunk0212_26_1	chrY	10852463	10852779	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	941823	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.006329	0.463722	
chunk0032_156_1	chr11	4932648	4933470	+	0	NA	Intergenic	Intergenic	-8720	NM_001005237	79324	Hs.554541	NM_001005237	ENSG00000278870	OR51G1	OR11-29|OR51G3P	olfactory receptor family 51 subfamily G member 1 (gene/pseudogene)	protein-coding	0.012165	0.334143	
chunk0082_305_1	chr17	58939444	58939643	+	0	NA	intron (NR_048561, intron 1 of 5)	intron (NR_048561, intron 1 of 5)	167362	NM_001005207	4591	Hs.579079	NM_015294	ENSG00000108395	TRIM37	MUL|POB1|TEF3	tripartite motif containing 37	protein-coding	0.005025	0.315000	
chunk0165_47_1	chr6	30207772	30208380	+	0	NA	intron (NM_003449, intron 1 of 9).8	L2c|LINE|L2	5418	NM_001242783	7726	Hs.485041	NM_003449	ENSG00000234127	TRIM26	AFP|RNF95|ZNF173	tripartite motif containing 26	protein-coding	0.009868	0.440066	
chunk0012_379_1	chr1	163322331	163322795	+	0	NA	promoter-TSS (NM_001254748)	promoter-TSS (NM_001254748)	630	NM_145697	83540	Hs.651950	NM_031423	ENSG00000143228	NUF2	CDCA1|CT106|NUF2R	NUF2 component of NDC80 kinetochore complex	protein-coding	0.021552	0.359140	
chunk0098_112_1	chr2	68411514	68411859	+	0	NA	Intergenic	Intergenic	46496	NM_002664	5341	Hs.468840	NM_002664	ENSG00000115956	PLEK	P47	pleckstrin	protein-coding	0.002899	0.387283	
chunk0059_313_1	chr14	36409775	36410393	+	0	NA	Intergenic	L1P2|LINE|L1	-89408	NM_001308110	51562	Hs.368647	NM_016586	ENSG00000151332	MBIP	-	MAP3K12 binding inhibitory protein 1	protein-coding	0.003236	0.510501	
chunk0187_456_1	chr7	159304885	159305212	+	0	NA	Intergenic	L1ME3E|LINE|L1	-160091	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.000000	0.317073	
chunk0198_129_1	chr8	132181400	132181990	+	0	NA	intron (NM_004519, intron 3 of 14)	intron (NM_004519, intron 3 of 14)	-76430	NM_001145095	10086	Hs.285026	NM_005712	ENSG00000132297	HHLA1	PLA2L	HERV-H LTR-associating 1	protein-coding	0.013559	0.463621	
chunk0076_68_1	chr16	63191606	63192126	+	0	NA	Intergenic	Intergenic	-1155031	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.001923	0.339731	
chunk0197_5_1	chr8	116753497	116754108	+	0	NA	intron (NM_003756, intron 1 of 7)	L2a|LINE|L2	2021	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.003273	0.372549	
chunk0122_151_1	chr3	32104378	32104887	+	0	NA	Intergenic	Intergenic	-1879	NM_015141	23171	Hs.82432	NM_015141	ENSG00000152642	GPD1L	GPD1-L	glycerol-3-phosphate dehydrogenase 1 like	protein-coding	0.007859	0.386275	
chunk0103_409_1	chr2	169345263	169345633	+	0	NA	intron (NM_004525, intron 1 of 78)	intron (NM_004525, intron 1 of 78)	17164	NM_004525	4036	Hs.657729	NM_004525	ENSG00000081479	LRP2	DBS|GP330|LRP-2	LDL receptor related protein 2	protein-coding	0.010811	0.390836	
chunk0149_86_1	chr5	17330243	17330755	+	0	NA	Intergenic	Intergenic	56811	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.003906	0.354776	
chunk0144_444_1	chr4	141153846	141154682	+	0	NA	Intergenic	Intergenic	-20802	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.005981	0.424134	520(GAGGTCATTCTGTCCT,-,0.00),521(AGGTCATTCTGTCCTT,+,0.00)
chunk0201_130_1	chr9	35562933	35563286	+	0	NA	intron (NM_001099951, intron 2 of 5)	intron (NM_001099951, intron 2 of 5)	790	NM_001287238	730112	Hs.98959	NM_001099951	ENSG00000215187	FAM166B	-	family with sequence similarity 166 member B	protein-coding	0.019830	0.556497	
chunk0064_202_1	chr14	92963699	92964227	+	0	NA	intron (NM_001142594, intron 5 of 10)	intron (NM_001142594, intron 5 of 10)	40863	NM_001301690	1113	Hs.150793	NM_001275	ENSG00000100604	CHGA	CGA	chromogranin A	protein-coding	0.015152	0.489603	158(GGGACCACCCTGTACT,-,0.00),159(GGACCACCCTGTACTT,+,0.00)
chunk0103_254_1	chr2	165336853	165337255	+	0	NA	intron (NM_021007, intron 14 of 26)	L1MEf|LINE|L1	41281	NM_001040143	6326	Hs.93485	NM_021007	ENSG00000136531	SCN2A	BFIC3|BFIS3|BFNIS|EIEE11|HBA|HBSCI|HBSCII|NAC2|Na(v)1.2|Nav1.2|SCN2A1|SCN2A2	sodium voltage-gated channel alpha subunit 2	protein-coding	0.004975	0.292804	
chunk0002_358_1	chr1	25932348	25932903	+	0	NA	Intergenic	L2c|LINE|L2	-25748	NM_203399	3925	Hs.209983	NM_005563	ENSG00000117632	STMN1	C1orf215|LAP18|Lag|OP18|PP17|PP19|PR22|SMN	stathmin 1	protein-coding	0.012613	0.399281	
chunk0049_343_1	chr12	95096856	95097251	+	0	NA	intron (NM_018351, intron 14 of 20)	intron (NM_018351, intron 14 of 20)	-23425	NM_001032287	7181	Hs.108301	NM_003297	ENSG00000120798	NR2C1	TR2	nuclear receptor subfamily 2 group C member 1	protein-coding	0.007595	0.431818	
chunk0204_458_1	chr9	104572933	104573533	+	0	NA	Intergenic	Intergenic	4065	NM_001004483	138802	Hs.553599	NM_001004483	ENSG00000186943	OR13C8	OR37H|OR9-10	olfactory receptor family 13 subfamily C member 8	protein-coding	0.003333	0.364393	
chunk0121_46_1	chr3	15528810	15529254	+	0	NA	Intergenic	Intergenic	-7281	NM_005677	8292	Hs.146735	NM_005677	ENSG00000206561	COLQ	CMS5|EAD	collagen like tail subunit of asymmetric acetylcholinesterase	protein-coding	0.009009	0.435955	304(GTCACAGTATGTTCTG,+,0.00)
chunk0083_299_1	chr17	69326991	69327544	+	0	NA	promoter-TSS (NM_172232)	promoter-TSS (NM_172232)	-85	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.122966	0.732852	
chunk0015_69_1	chr1	184743532	184743959	+	0	NA	intron (NM_025191, intron 2 of 19)	L1ME1|LINE|L1	11162	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.000000	0.320093	
chunk0170_98_1	chr6	110516871	110517865	+	0	NA	Intergenic	Intergenic	-40727	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.006036	0.364824	
chunk0036_24_1	chr11	58449244	58449943	+	0	NA	Intergenic	L1PA16|LINE|L1	-9420	NM_001004733	390191	Hs.553754	NM_001004733	ENSG00000172362	OR5B12	OR11-241|OR5B12P|OR5B16|OST743	olfactory receptor family 5 subfamily B member 12	protein-coding	0.008584	0.361429	
chunk0147_126_1	chr4	174386195	174386622	+	0	NA	Intergenic	Intergenic	-37387	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.000000	0.252336	
chunk0033_11_1	chr11	12412459	12412749	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	35125	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.006897	0.522337	158(AAGGACAGGATGTACC,-,0.00),159(AGGACAGGATGTACCA,+,0.00)
chunk0204_324_1	chr9	100700974	100701280	+	0	NA	Intergenic	MIR|SINE|MIR	123048	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.006536	0.407166	
chunk0153_407_1	chr5	75403047	75403431	+	0	NA	intron (NM_031361, intron 8 of 16)	intron (NM_031361, intron 8 of 16)	66071	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.002604	0.337662	
chunk0153_173_1	chr5	71508566	71509187	+	0	NA	intron (NM_018429, intron 16 of 38)	intron (NM_018429, intron 16 of 38)	53261	NM_018429	55814	Hs.258272	NM_018429	ENSG00000145734	BDP1	DFNB112|HSA238520|TAF3B1|TFC5|TFIIIB''|TFIIIB150|TFIIIB90|TFNR	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.004831	0.356913	
chunk0075_325_1	chr16	54645282	54645877	+	0	NA	Intergenic	Intergenic	283199	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.006723	0.389262	
chunk0045_355_1	chr12	51759803	51760059	+	0	NA	intron (NM_014191, intron 14 of 26)	MSTD|LTR|ERVL-MaLR	71986	NM_001013690	401720	Hs.648218	NM_001013690	ENSG00000261308	FIGNL2	-	fidgetin like 2	protein-coding	0.000000	0.447471	
chunk0209_20_1	chrX	35530400	35530605	+	0	NA	Intergenic	L1M2|LINE|L1	-267840	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.009756	0.305825	
chunk0022_110_1	chr10	10164879	10165221	+	0	NA	Intergenic	MER31B|LTR|ERV1	106328	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.008772	0.419825	
chunk0117_401_1	chr21	45513202	45513646	+	0	NA	3' UTR (NM_030582, exon 42 of 42)	3' UTR (NM_030582, exon 42 of 42)	21204	NM_001205207	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.036036	0.620225	
chunk0120_140_1	chr3	5165698	5166084	+	0	NA	intron (NM_018184, intron 1 of 6)	intron (NM_018184, intron 1 of 6)	-21783	NM_014674	9695	Hs.224616	NM_014674	ENSG00000134109	EDEM1	EDEM	ER degradation enhancing alpha-mannosidase like protein 1	protein-coding	0.010363	0.359173	
chunk0169_137_1	chr6	101397092	101397489	+	0	NA	Intergenic	Intergenic	-1695	NM_001166247	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.010076	0.351759	327(TAGCACTAGGTGTTCC,-,0.00),328(AGCACTAGGTGTTCCT,+,0.00)
chunk0177_156_1	chr7	23015073	23015554	+	0	NA	Intergenic	L2c|LINE|L2	-1162	NM_032581	84668	Hs.85603	NM_032581	ENSG00000122591	FAM126A	DRCTNNB1A|HCC|HLD5|HYCC1	family with sequence similarity 126 member A	protein-coding	0.004158	0.417012	243(GAGAACACCATGTTCA,-,0.00),244(AGAACACCATGTTCAA,+,0.00)
chunk0174_348_1	chr6	164282900	164283497	+	0	NA	Intergenic	L2a|LINE|L2	538865	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.005025	0.387960	
chunk0154_164_1	chr5	79548870	79549147	+	0	NA	Intergenic	L2a|LINE|L2	-35172	NM_004272	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.003610	0.341727	
chunk0038_364_1	chr11	93355544	93356094	+	0	NA	intron (NM_181645, intron 3 of 13)	intron (NM_181645, intron 3 of 13)	25102	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.000000	0.339383	
chunk0171_178_1	chr6	125154654	125155536	+	0	NA	intron (NM_001003395, intron 1 of 6)	intron (NM_001003395, intron 1 of 6)	821	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.026077	0.466591	
chunk0060_38_1	chr14	40698079	40698429	+	0	NA	Intergenic	MER57C2|LTR|ERV1	-256457	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.002857	0.376068	
chunk0005_104_1	chr1	56573303	56573589	+	0	NA	intron (NM_003713, intron 1 of 5)	intron (NM_003713, intron 1 of 5)	6138	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.010490	0.390244	131(CAGAACATTCAGTGCA,-,0.00),132(AGAACATTCAGTGCAG,+,0.00)
chunk0192_385_1	chr8	68622159	68622425	+	0	NA	intron (NM_052958, intron 7 of 13)	MLT1F2|LTR|ERVL-MaLR	-290801	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.000000	0.415730	
chunk0059_306_1	chr14	36237664	36237960	+	0	NA	Intergenic	Intergenic	-61161	NR_049735	100886964	Hs.742592	NR_049735		PTCSC3	-	papillary thyroid carcinoma susceptibility candidate 3	ncRNA	0.000000	0.383838	
chunk0053_443_1	chr13	39735431	39735667	+	0	NA	intron (NM_001145079, intron 18 of 18)	L1M1|LINE|L1	-71414	NR_036190	100422940		NR_036190	ENSG00000264171	MIR4305	-	microRNA 4305	ncRNA	0.000000	0.312236	
chunk0176_135_1	chr7	12712333	12712532	+	0	NA	Intergenic	Intergenic	25146	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.010050	0.380000	113(AGGAACATCCTGTAAC,-,0.00)
chunk0061_418_1	chr14	65079501	65080032	+	0	NA	intron (NR_073137, intron 2 of 3)	intron (NR_073137, intron 2 of 3)	-10152	NR_045122	100506321	Hs.711267	NR_045122	ENSG00000259118	LOC100506321	-	uncharacterized LOC100506321	ncRNA	0.013183	0.422932	
chunk0078_322_1	chr17	8558027	8558536	+	0	NA	intron (NM_001256095, intron 7 of 41)	intron (NM_001256095, intron 7 of 41)	72480	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.003929	0.354902	273(AAGAACAATGTGGTCT,-,0.00),274(AGAACAATGTGGTCTG,+,0.00)
chunk0114_394_1	chr20	63355286	63355575	+	0	NA	intron (NM_000744, intron 4 of 5)	intron (NM_000744, intron 4 of 5)	-4558	NR_110634	100130587	Hs.640129	NR_110634	ENSG00000203900	LOC100130587	-	uncharacterized LOC100130587	ncRNA	0.020761	0.589655	
chunk0024_36_1	chr10	33388309	33388556	+	0	NA	Intergenic	Intergenic	-53527	NM_001024628	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.004049	0.362903	
chunk0157_88_1	chr5	116585162	116585591	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-10450	NM_001300780	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.009324	0.467442	
chunk0149_307_1	chr5	25892294	25892941	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-1052034	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.007728	0.379630	
chunk0121_325_1	chr3	24365113	24365646	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-128708	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.003752	0.410112	
chunk0089_436_1	chr18	70163320	70163752	+	0	NA	intron (NM_173630, intron 14 of 48)	L1MB3|LINE|L1	42190	NM_173630	25914	Hs.654809	NM_173630	ENSG00000176225	RTTN	MSSP	rotatin	protein-coding	0.004630	0.376443	
chunk0188_369_1	chr8	18179572	18180210	+	0	NA	intron (NM_001160179, intron 2 of 4)	intron (NM_001160179, intron 2 of 4)	9429	NM_001291962	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.004702	0.427230	
chunk0172_206_1	chr6	136707694	136707967	+	0	NA	intron (NM_005923, intron 2 of 29)	L1ME4b|LINE|L1	78716	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.007326	0.372263	
chunk0012_260_1	chr1	161440515	161440714	+	0	NA	Intergenic	CpG	-64801	NM_021642	2212	Hs.352642	NM_021642	ENSG00000143226	FCGR2A	CD32|CD32A|CDw32|FCG2|FCGR2|FCGR2A1|FcGR|IGFR2	Fc fragment of IgG receptor IIa	protein-coding	0.085427	0.685000	
chunk0044_174_1	chr12	30086932	30087355	+	0	NA	Intergenic	Intergenic	-302384	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.004728	0.344340	
chunk0133_294_1	chr3	172178138	172178337	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	137683	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.000000	0.540000	
chunk0032_398_1	chr11	11622703	11623318	+	0	NA	promoter-TSS (NM_198516)	promoter-TSS (NM_198516)	-996	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.009756	0.485390	322(CTGAACACCCCGTTCT,-,0.00),323(TGAACACCCCGTTCTC,+,0.00)
chunk0163_235_1	chr6	12324085	12324652	+	0	NA	Intergenic	Intergenic	34072	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.007055	0.434859	
chunk0071_448_1	chr15	90149293	90150031	+	0	NA	Intergenic	Intergenic	-35258	NM_020210	10509	Hs.474935	NM_020210	ENSG00000185033	SEMA4B	SEMAC|SemC	semaphorin 4B	protein-coding	0.010840	0.488498	
chunk0117_8_1	chr22	10727070	10727387	+	0	NA	Intergenic	(TCCATTCCAT)n|Simple_repeat|Simple_repeat	234301	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.031546	0.421384	
chunk0008_5_1	chr1	87106764	87107385	+	0	NA	3' UTR (NM_012262, exon 7 of 7)	3' UTR (NM_012262, exon 7 of 7)	-22691	NR_026988	339524	Hs.306423	NM_207357	ENSG00000267272	LINC01140	-	long intergenic non-protein coding RNA 1140	ncRNA	0.003221	0.381029	
chunk0139_96_1	chr4	49577907	49578113	+	0	NA	Intergenic	Intergenic	591368	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.009709	0.555556	
chunk0209_386_1	chrX	54779150	54779401	+	0	NA	intron (NM_198510, intron 5 of 12)	L1MA2|LINE|L1	18965	NM_198510	347365	Hs.454272	NM_198510	ENSG00000102313	ITIH6	ITIH5L|UNQ6369|dJ14O9.1	inter-alpha-trypsin inhibitor heavy chain family member 6	protein-coding	0.000000	0.301587	
chunk0184_180_1	chr7	116662775	116663136	+	0	NA	Intergenic	Intergenic	-9450	NM_001127500	4233	Hs.132966	NM_000245	ENSG00000105976	MET	AUTS9|DFNB97|HGFR|RCCP2|c-Met	MET proto-oncogene, receptor tyrosine kinase	protein-coding	0.011080	0.480663	
chunk0043_163_1	chr12	16934819	16935165	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-53755	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.002890	0.371758	
chunk0059_28_1	chr14	29846389	29846796	+	0	NA	intron (NM_002742, intron 1 of 17)	L2a|LINE|L2	81101	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.500000	259(AGGAACATGATGGGCT,-,0.00)
chunk0210_88_1	chrX	71081429	71081682	+	0	NA	Intergenic	Intergenic	-8129	NM_001256185	29934	Hs.260750	NM_013346	ENSG00000147164	SNX12	-	sorting nexin 12	protein-coding	0.000000	0.381890	
chunk0043_406_1	chr12	25681733	25682369	+	0	NA	Intergenic	Intergenic	-33489	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.006289	0.420722	
chunk0060_206_1	chr14	48786679	48787087	+	0	NA	Intergenic	Intergenic	799533	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.002451	0.322738	
chunk0168_349_1	chr6	93105095	93105708	+	0	NA	Intergenic	Intergenic	314181	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.003263	0.317590	
chunk0057_127_1	chr13	99481521	99481951	+	0	NA	Intergenic	Intergenic	17570	NR_110731	102725509	Hs.648968	NR_110731		LINC01232	TCONS_00021520	long intergenic non-protein coding RNA 1232	ncRNA	0.004651	0.368910	
chunk0036_427_1	chr11	68399557	68399756	+	0	NA	intron (NM_002335, intron 7 of 22)	intron (NM_002335, intron 7 of 22)	-61062	NM_001164164	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.025126	0.570000	
chunk0025_178_1	chr10	52945287	52945911	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-173899	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.008013	0.345600	343(ATGTACTTTATGTTCT,-,0.00),344(TGTACTTTATGTTCTT,+,0.00)
chunk0134_292_1	chr3	180045224	180045453	+	0	NA	Intergenic	L2c|LINE|L2	-8285	NM_001256750	51555	Hs.235331	NM_016559	ENSG00000114757	PEX5L	PEX5R|PEX5RP|PXR2|PXR2B|TRIP8b	peroxisomal biogenesis factor 5 like	protein-coding	0.004367	0.421739	
chunk0159_220_1	chr5	140813131	140813538	+	0	NA	intron (NM_018907, intron 1 of 3)	Tigger3b|DNA|TcMar-Tigger	6260	NM_031500	56144	Hs.199343	NM_018907	ENSG00000204967	PCDHA4	CNR1|CNRN1|CRNR1|PCDH-ALPHA4	protocadherin alpha 4	protein-coding	0.000000	0.335784	
chunk0079_241_1	chr17	16019998	16020451	+	0	NA	intron (NM_001271420, intron 7 of 9)	L1ME3Cz|LINE|L1	-20532	NM_001042697	125150	Hs.593985	NM_001042697	ENSG00000214941	ZSWIM7	SWS1	zinc finger SWIM-type containing 7	protein-coding	0.017660	0.359031	
chunk0164_246_1	chr6	23388208	23388453	+	0	NA	Intergenic	Intergenic	-737856	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.024490	0.402439	
chunk0192_151_1	chr8	62046505	62047133	+	0	NA	Intergenic	L1MC4a|LINE|L1	-202123	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.004777	0.308426	
chunk0181_165_1	chr7	82548291	82548700	+	0	NA	Intergenic	Intergenic	-104689	NM_001302890	781	Hs.282151	NM_000722	ENSG00000153956	CACNA2D1	CACNA2|CACNL2A|CCHL2A|LINC01112|lncRNA-N3	calcium voltage-gated channel auxiliary subunit alpha2delta 1	protein-coding	0.007335	0.302439	
chunk0127_5_1	chr3	87782766	87783155	+	0	NA	Intergenic	L1MA7|LINE|L1	-199616	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.002571	0.292308	
chunk0171_115_1	chr6	122460357	122460818	+	0	NA	intron (NM_020755, intron 1 of 9)	L1ME1|LINE|L1	11220	NM_020755	57515	Hs.146668	NM_020755	ENSG00000111897	SERINC1	TDE1L|TDE2|TMS-2|TMS2	serine incorporator 1	protein-coding	0.008677	0.378788	
chunk0092_460_1	chr19	39160364	39160891	+	0	NA	intron (NM_001014834, intron 1 of 7)	L2a|LINE|L2	34847	NM_001014834	10298	Hs.20447	NM_005884	ENSG00000130669	PAK4	-	p21 (RAC1) activated kinase 4	protein-coding	0.018975	0.537879	
chunk0151_70_1	chr5	42590826	42591261	+	0	NA	intron (NM_001242460, intron 1 of 7)	intron (NM_001242460, intron 1 of 7)	25179	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.011494	0.438073	
chunk0142_138_1	chr4	94759691	94760462	+	0	NA	intron (NM_001203, intron 1 of 12)	intron (NM_001203, intron 1 of 12)	2099	NM_001203	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.006485	0.331606	
chunk0128_129_1	chr3	106549733	106550192	+	0	NA	Intergenic	Intergenic	-680919	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.002179	0.341304	
chunk0164_375_1	chr6	25907377	25907728	+	0	NA	Intergenic	Intergenic	18327	NM_001286123	10246	Hs.591802	NM_005835	ENSG00000112337	SLC17A2	NPT3	solute carrier family 17 member 2	protein-coding	0.000000	0.389205	
chunk0165_58_1	chr6	30727867	30728358	+	0	NA	3' UTR (NM_005803, exon 13 of 13)	3' UTR (NM_005803, exon 13 of 13)	6563	NM_001293212	203068	Hs.636480	NM_178014	ENSG00000196230	TUBB	CDCBM6|CSCSC1|M40|OK/SW-cl.56|TUBB1|TUBB5	tubulin beta class I	protein-coding	0.010183	0.536585	245(AGGCTCAGGCTGTTCT,-,0.00),246(GGCTCAGGCTGTTCTC,+,0.00)
chunk0178_191_1	chr7	34350127	34350828	+	0	NA	non-coding (NR_033665, exon 4 of 4)	non-coding (NR_033665, exon 4 of 4)	-307762	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.009986	0.360399	615(TAGAACATCTTGTTTT,-,0.00),616(AGAACATCTTGTTTTT,+,0.00)
chunk0190_52_1	chr8	29503755	29504192	+	0	NA	Intergenic	Intergenic	-153223	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.004577	0.486301	319(TAGAACATGGTGTCCC,-,0.00),320(AGAACATGGTGTCCCC,+,0.00)
chunk0113_392_1	chr20	60053270	60053867	+	0	NA	Intergenic	Intergenic	-2357	NM_173644									0.023451	0.471572	
chunk0017_35_1	chr1	204897073	204897294	+	0	NA	intron (NM_001005389, intron 1 of 15)	L2b|LINE|L2	-47043	NM_001160331	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.000000	0.450450	
chunk0069_211_1	chr15	63502143	63502408	+	0	NA	Intergenic	L2b|LINE|L2	-2236	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.033962	0.454887	
chunk0159_342_1	chr5	144145268	144145723	+	0	NA	Intergenic	Intergenic	25219	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.004396	0.333333	
chunk0198_143_1	chr8	132891770	132892208	+	0	NA	intron (NM_003235, intron 10 of 47)	MIRb|SINE|MIR	25029	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.006849	0.407745	176(AAGGACAGCATGTGCC,-,0.00),177(AGGACAGCATGTGCCA,+,0.00)
chunk0077_297_1	chr16	81462459	81462937	+	0	NA	intron (NM_198390, intron 1 of 20)	intron (NM_198390, intron 1 of 20)	17528	NM_198390	80790	Hs.594095	NM_030629	ENSG00000153815	CMIP	TCMIP	c-Maf inducing protein	protein-coding	0.008368	0.444676	433(AGGGACAGAGTGACCA,-,0.00),434(GGGACAGAGTGACCAC,+,0.00)
chunk0084_73_1	chr17	74851552	74851902	+	0	NA	intron (NR_103735, intron 3 of 12)	intron (NR_103735, intron 3 of 12)	8157	NM_000835	2905	Hs.436980	NM_000835	ENSG00000161509	GRIN2C	GluN2C|NMDAR2C|NR2C	glutamate ionotropic receptor NMDA type subunit 2C	protein-coding	0.022857	0.612536	
chunk0184_266_1	chr7	118280225	118280832	+	0	NA	Intergenic	L1MEb|LINE|L1	55870	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.003295	0.370066	
chunk0043_172_1	chr12	17104554	17105050	+	0	NA	Intergenic	Intergenic	116055	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.006048	0.362173	
chunk0184_277_1	chr7	118625244	118625866	+	0	NA	Intergenic	Intergenic	400897	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.001608	0.298555	306(CTGCACAGTATGTACA,-,0.00),307(TGCACAGTATGTACAC,+,0.00),420(TAGAACAGAATGTTTA,-,0.00),421(AGAACAGAATGTTTAT,+,0.00)
chunk0161_145_1	chr5	168650999	168651476	+	0	NA	Intergenic	Intergenic	-55690	NR_130737	101927969	Hs.661903	NR_130737		LOC101927969	-	uncharacterized LOC101927969	ncRNA	0.006289	0.416318	238(AAAGACAAACTGTCCT,-,0.00),239(AAGACAAACTGTCCTG,+,0.00),267(AAAGACAAACTGTCCT,-,0.00),268(AAGACAAACTGTCCTG,+,0.00)
chunk0105_135_1	chr2	185978522	185978994	+	0	NA	Intergenic	Intergenic	107559	NR_110218	101927217	Hs.130011	NR_110218	ENSG00000237877	LINC01473	-	long intergenic non-protein coding RNA 1473	ncRNA	0.002119	0.304440	
chunk0177_339_1	chr7	26489307	26490063	+	0	NA	intron (NR_015364, intron 1 of 4)	intron (NR_015364, intron 1 of 4)	49140	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.003968	0.418758	459(CAGAACATTCTGTTCA,-,0.00),460(AGAACATTCTGTTCAA,+,0.00)
chunk0160_320_1	chr5	159396909	159397426	+	0	NA	Intergenic	Intergenic	65649	NR_037889	285626	Hs.449275	NR_037889	ENSG00000249738	LOC285626	-	uncharacterized LOC285626	ncRNA	0.013540	0.445946	
chunk0180_262_1	chr7	69596014	69596652	+	0	NA	non-coding (NR_108105, exon 2 of 2)	non-coding (NR_108105, exon 2 of 2)	1162	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.015674	0.417840	
chunk0136_382_1	chr3	196650797	196651302	+	0	NA	intron (NM_198565, intron 1 of 2)	intron (NM_198565, intron 1 of 2)	11353	NM_198565	375387	Hs.702186	NM_198565	ENSG00000174004	NRROS	ELLP3030|GARPL1|LRRC33|UNQ3030	negative regulator of reactive oxygen species	protein-coding	0.009901	0.500000	
chunk0072_242_1	chr15	95997237	95997485	+	0	NA	Intergenic	Intergenic	-328567	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.004032	0.369478	
chunk0076_104_1	chr16	66180366	66180829	+	0	NA	Intergenic	Intergenic	-186025	NM_001795	1003	Hs.76206	NM_001795	ENSG00000179776	CDH5	7B4|CD144	cadherin 5	protein-coding	0.012959	0.385776	
chunk0091_294_1	chr19	12401166	12401399	+	0	NA	promoter-TSS (NM_001080821)	promoter-TSS (NM_001080821)	-8	NM_001080821	90576	Hs.546637	NM_203381	ENSG00000196466	ZNF799	HIT-40|ZNF842	zinc finger protein 799	protein-coding	0.072961	0.606838	
chunk0195_380_1	chr8	100123740	100124211	+	0	NA	Intergenic	Intergenic	-17859	NM_001286692	26166	Hs.120021	NM_015668	ENSG00000132554	RGS22	CT145|PRTD-NY2	regulator of G protein signaling 22	protein-coding	0.002123	0.375000	
chunk0070_308_1	chr15	75054488	75054922	+	0	NA	Intergenic	L1ME4b|LINE|L1	11436	NM_001301104	60490	Hs.458922	NM_021823	ENSG00000138621	PPCDC	MDS018|PPC-DC|coaC	phosphopantothenoylcysteine decarboxylase	protein-coding	0.002304	0.381609	
chunk0158_353_1	chr5	133569217	133569662	+	0	NA	intron (NM_015082, intron 2 of 15)	L1M5|LINE|L1	43093	NM_015082	23105	Hs.483390	NM_015082	ENSG00000053108	FSTL4	-	follistatin like 4	protein-coding	0.006742	0.349776	254(AAAAACAGCTTGTTCC,-,0.00),255(AAAACAGCTTGTTCCT,+,0.00)
chunk0206_110_1	chr9	120837650	120838216	+	0	NA	intron (NM_005047, intron 1 of 9)	L1ME1|LINE|L1	5088	NM_005047	5711	Hs.193725	NM_005047	ENSG00000095261	PSMD5	S5B	proteasome 26S subunit, non-ATPase 5	protein-coding	0.003534	0.354497	
chunk0042_350_1	chr12	10113080	10113728	+	0	NA	Intergenic	L1PB3|LINE|L1	-14339	NM_001297748	51267	Hs.29549	NM_016511	ENSG00000150048	CLEC1A	CLEC-1|CLEC1	C-type lectin domain family 1 member A	protein-coding	0.001543	0.318952	
chunk0153_162_1	chr5	71011165	71011813	+	0	NA	intron (NM_004536, intron 4 of 16).3	intron (NM_004536, intron 4 of 16).3	13625	NM_004536	4671	Hs.646951	NM_004536	ENSG00000249437	NAIP	BIRC1|NLRB1|psiNAIP	NLR family apoptosis inhibitory protein	protein-coding	0.013889	0.466872	
chunk0034_153_1	chr11	30223855	30224081	+	0	NA	Intergenic	MER33|DNA|hAT-Charlie	-7048	NM_001018080	2488	Hs.36975	NM_000510	ENSG00000131808	FSHB	HH24	follicle stimulating hormone subunit beta	protein-coding	0.004425	0.290749	
chunk0067_230_1	chr15	45401106	45401503	+	0	NA	Intergenic	Intergenic	-1017	NM_024063	79029	Hs.369657	NM_024063	ENSG00000171763	SPATA5L1	-	spermatogenesis associated 5 like 1	protein-coding	0.005038	0.364322	
chunk0038_233_1	chr11	87020891	87021170	+	0	NA	Intergenic	Intergenic	-16814	NM_022918	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.003584	0.328571	227(AAGAACTTTCTGTTTT,-,0.00),228(AGAACTTTCTGTTTTC,+,0.00)
chunk0203_240_1	chr9	87285183	87285394	+	0	NA	Intergenic	Intergenic	136644	NM_001001709									0.004739	0.424528	
chunk0040_404_1	chr11	120648480	120649273	+	0	NA	intron (NM_001282470, intron 1 of 19)	intron (NM_001282470, intron 1 of 19)	84440	NM_001282470	2900	Hs.538738	NM_014619	ENSG00000149403	GRIK4	EAA1|GRIK|GluK4|KA1	glutamate ionotropic receptor kainate type subunit 4	protein-coding	0.010088	0.536524	
chunk0104_252_1	chr2	177598215	177598757	+	0	NA	Intergenic	Intergenic	20480	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.009225	0.390424	
chunk0162_308_1	chr6	6623806	6624123	+	0	NA	intron (NM_004271, intron 1 of 4)	intron (NM_004271, intron 1 of 4)	-1138	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.006309	0.396226	
chunk0020_291_1	chr1	237138382	237139122	+	0	NA	intron (NM_001035, intron 1 of 104)	intron (NM_001035, intron 1 of 104)	96350	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.002703	0.341430	
chunk0197_201_1	chr8	122467166	122467537	+	0	NA	intron (NR_131202, intron 2 of 3)	L1PREC2|LINE|L1	101293	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.008086	0.564516	
chunk0050_311_1	chr12	107043316	107043515	+	0	NA	intron (NM_004075, intron 1 of 12)	L1M2a|LINE|L1	50442	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.005025	0.520000	
chunk0160_242_1	chr5	156532909	156533241	+	0	NA	intron (NM_000337, intron 4 of 8)	intron (NM_000337, intron 4 of 8)	206318	NM_000337	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.009036	0.441441	
chunk0040_259_1	chr11	116028471	116029063	+	0	NA	Intergenic	L1PB1|LINE|L1	-268567	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.003378	0.367622	
chunk0072_320_1	chr15	98941498	98942380	+	0	NA	intron (NM_001291858, intron 18 of 20)	intron (NM_001291858, intron 18 of 20)	63717	NM_001102612	145814	Hs.592021	NM_001102612	ENSG00000183571	PGPEP1L	-	pyroglutamyl-peptidase I like	protein-coding	0.007937	0.382786	
chunk0108_132_1	chr2	230335449	230335648	+	0	NA	intron (NM_138402, intron 2 of 18)	L1ME3G|LINE|L1	8368	NM_001308163	93349	Hs.589661	NM_138402	ENSG00000185404	SP140L	-	SP140 nuclear body protein like	protein-coding	0.015075	0.400000	
chunk0006_325_1	chr1	71738822	71739177	+	0	NA	intron (NM_173808, intron 3 of 6)	intron (NM_173808, intron 3 of 6)	98013	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.002817	0.376404	
chunk0098_107_1	chr2	68279671	68280242	+	0	NA	Intergenic	Intergenic	-27437	NM_000945	5534	Hs.280604	NM_000945	ENSG00000221823	PPP3R1	CALNB1|CNB|CNB1	protein phosphatase 3 regulatory subunit B, alpha	protein-coding	0.007005	0.375874	253(AGAACTGGCTGTCTCG,+,0.00)
chunk0130_296_1	chr3	136925505	136926087	+	0	NA	intron (NM_001291999, intron 1 of 3)	L1MD1|LINE|L1	-4679	NM_001190796	4690	Hs.126889	NM_006153	ENSG00000158092	NCK1	NCK|NCKalpha|nck-1	NCK adaptor protein 1	protein-coding	0.012027	0.365352	
chunk0162_229_1	chr6	4660864	4661350	+	0	NA	Intergenic	Intergenic	-45052	NR_026590									0.022634	0.579055	
chunk0018_262_1	chr1	220429036	220429340	+	0	NA	Intergenic	Intergenic	-98995	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.006579	0.409836	
chunk0040_341_1	chr11	118435945	118436359	+	0	NA	promoter-TSS (NM_001197104)	promoter-TSS (NM_001197104)	-338	NM_005933	4297	Hs.258855	NM_005933	ENSG00000118058	KMT2A	ALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTS	lysine methyltransferase 2A	protein-coding	0.108696	0.720482	
chunk0032_339_1	chr11	10290823	10291197	+	0	NA	intron (NM_030962, intron 1 of 39)	L1MC4|LINE|L1	3197	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.002674	0.405333	
chunk0003_427_1	chr1	41003734	41004081	+	0	NA	intron (NM_001301237, intron 8 of 14)	MLT1H2|LTR|ERVL-MaLR	-10683	NR_037868	100507178	Hs.660056	NR_037868	ENSG00000281207	SLFNL1-AS1	-	SLFNL1 antisense RNA 1	ncRNA	0.020173	0.540230	
chunk0119_33_1	chr22	40387662	40388136	+	0	NA	intron (NM_015705, intron 1 of 21)	intron (NM_015705, intron 1 of 21)	17337	NM_015705	27352	Hs.474914	NM_015705	ENSG00000100359	SGSM3	CIP85|MAP|RABGAP5|RUSC3|RUTBC3|RabGAP-5|rabGAPLP	small G protein signaling modulator 3	protein-coding	0.012658	0.480000	
chunk0084_315_1	chr17	80437522	80437952	+	0	NA	3' UTR (NM_001164637, exon 9 of 9)	3' UTR (NM_001164637, exon 9 of 9)	18319	NR_039883	100616359		NR_039883	ENSG00000264961	MIR4730	-	microRNA 4730	ncRNA	0.027907	0.526682	
chunk0206_460_1	chr9	128473189	128473470	+	0	NA	intron (NM_002540, intron 9 of 22)	intron (NM_002540, intron 9 of 22)	16422	NM_153437	4957	Hs.129055	NM_002540	ENSG00000136811	ODF2	CT134|ODF2/1|ODF2/2|ODF84	outer dense fiber of sperm tails 2	protein-coding	0.007117	0.553191	
chunk0152_404_1	chr5	64947084	64947435	+	0	NA	intron (NM_001297644, intron 11 of 12)	intron (NM_001297644, intron 11 of 12)	178341	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.002849	0.434659	
chunk0189_271_1	chr8	25326478	25327262	+	0	NA	intron (NM_024940, intron 18 of 51)	L1ME4a|LINE|L1	-18532	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.015306	0.365605	444(AAGGACACGGTGAACT,-,0.00),445(AGGACACGGTGAACTT,+,0.00)
chunk0126_13_1	chr3	73511969	73512525	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-9075	NR_121660	101927296	Hs.662049	NR_121660		LOC101927296	-	uncharacterized LOC101927296	ncRNA	0.016187	0.394973	
chunk0205_364_1	chr9	113682407	113683024	+	0	NA	Intergenic	Intergenic	88561	NM_001276262	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.014587	0.514563	
chunk0171_32_1	chr6	120500488	120501022	+	0	NA	Intergenic	HSMAR2|DNA|TcMar-Mariner	485576	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.003745	0.334579	
chunk0010_187_1	chr1	115935536	115935855	+	0	NA	intron (NR_125970, intron 2 of 4)	intron (NR_125970, intron 2 of 4)	16319	NR_125969	101928995	Hs.559119	NR_125969	ENSG00000228127	LINC01649	-	long intergenic non-protein coding RNA 1649	ncRNA	0.000000	0.325000	
chunk0102_257_1	chr2	149366216	149366699	+	0	NA	intron (NM_194317, intron 1 of 4)	intron (NM_194317, intron 1 of 4)	35942	NM_194317	130574	Hs.21929	NM_194317	ENSG00000187123	LYPD6	-	LY6/PLAUR domain containing 6	protein-coding	0.006211	0.419421	
chunk0095_178_1	chr2	17741058	17741284	+	0	NA	intron (NM_024624, intron 3 of 26)	intron (NM_024624, intron 3 of 26)	12658	NM_024624	79677	Hs.526728	NM_024624	ENSG00000163029	SMC6	SMC-6|SMC6L1|hSMC6	structural maintenance of chromosomes 6	protein-coding	0.004425	0.392070	
chunk0167_296_1	chr6	71139597	71139873	+	0	NA	Intergenic	L1PA2|LINE|L1	-149039	NM_024576	79627	Hs.648434	NM_024576	ENSG00000119900	OGFRL1	dJ331H24.1	opioid growth factor receptor like 1	protein-coding	0.003623	0.548736	
chunk0064_217_1	chr14	93353720	93353970	+	0	NA	intron (NM_020818, intron 1 of 49)	L2a|LINE|L2	6654	NM_182971	341947	Hs.666459	NM_182971	ENSG00000187581	COX8C	COX8-3	cytochrome c oxidase subunit 8C	protein-coding	0.008000	0.378486	
chunk0053_429_1	chr13	38372864	38373113	+	0	NA	Intergenic	HSMAR2|DNA|TcMar-Mariner	23217	NR_104584	51569	Hs.643655	NM_016617	ENSG00000120686	UFM1	BM-002|C13orf20|HLD14	ubiquitin fold modifier 1	protein-coding	0.020080	0.388000	
chunk0109_326_1	chr20	9281676	9282211	+	0	NA	intron (NM_001172646, intron 2 of 37)	intron (NM_001172646, intron 2 of 37)	-25857	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.003738	0.341418	
chunk0155_124_1	chr5	93070952	93071327	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	500204	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.013333	0.412234	
chunk0188_187_1	chr8	11573338	11574084	+	0	NA	Intergenic	L1ME3G|LINE|L1	-2824	NR_040035	83655	Hs.742430	NR_040035	ENSG00000170983	LINC00208	C8orf14|NCRNA00208|VIR35	long intergenic non-protein coding RNA 208	ncRNA	0.012064	0.433735	
chunk0137_320_1	chr4	24630177	24630678	+	0	NA	Intergenic	L2a|LINE|L2	-45866	NM_001358	1665	Hs.696074	NM_001358	ENSG00000109606	DHX15	DBP1|DDX15|HRH2|PRP43|PRPF43|PrPp43p	DEAH-box helicase 15	protein-coding	0.009980	0.386454	
chunk0193_9_1	chr8	70484996	70485644	+	0	NA	non-coding (NR_110653, exon 4 of 4)	non-coding (NR_110653, exon 4 of 4)	14186	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.004630	0.345146	
chunk0141_35_1	chr4	76972268	76972617	+	0	NA	intron (NM_018243, intron 1 of 9)	intron (NM_018243, intron 1 of 9)	22728	NM_018243	55752	Hs.128199	NM_018243	ENSG00000138758	SEPTIN11	SEPT11	septin 11	protein-coding	0.000000	0.368571	
chunk0087_281_1	chr18	38677351	38677778	+	0	NA	Intergenic	L1PBa|LINE|L1	944611	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.004684	0.327103	243(TTGGACATAATGTTCC,-,0.00),244(TGGACATAATGTTCCG,+,0.00)
chunk0126_72_1	chr3	74610951	74611681	+	0	NA	Intergenic	MER131|DNA?|DNA?	-90176	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002740	0.339261	
chunk0150_350_1	chr5	38670638	38670972	+	0	NA	intron (NR_103554, intron 8 of 8)	intron (NR_103554, intron 8 of 8)	49468	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.008982	0.420896	
chunk0110_82_1	chr20	11205256	11205563	+	0	NA	Intergenic	Intergenic	67974	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.009772	0.425325	
chunk0191_325_1	chr8	55879667	55879866	+	0	NA	promoter-TSS (NM_002350)	promoter-TSS (NM_002350)	-61	NM_002350	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.080402	0.650000	158(AGAGACAGCCAGTTCC,-,0.00),159(GAGACAGCCAGTTCCT,+,0.00)
chunk0049_208_1	chr12	93164010	93164470	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-10126	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.008696	0.420824	
chunk0181_415_1	chr7	90227244	90227811	+	0	NA	intron (NM_152999, intron 3 of 4)	intron (NM_152999, intron 3 of 4)	13707	NM_001040666	261729	Hs.489051	NM_152999	ENSG00000157214	STEAP2	IPCA1|PCANAP1|PUMPCn|STAMP1|STMP	STEAP2 metalloreductase	protein-coding	0.008818	0.353873	253(AGGTACTGAATGTGCT,-,0.00),254(GGTACTGAATGTGCTT,+,0.00)
chunk0058_59_1	chr14	20627505	20627869	+	0	NA	Intergenic	LTR24B|LTR|ERV1	14004	NM_001001968	341799	Hs.513132	NM_001001968	ENSG00000181803	OR6S1	OR14-37|OR6S1Q	olfactory receptor family 6 subfamily S member 1	protein-coding	0.008242	0.361644	
chunk0149_312_1	chr5	26278135	26278577	+	0	NA	Intergenic	L2a|LINE|L2	760226	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.004525	0.363431	
chunk0195_448_1	chr8	101360810	101361345	+	0	NA	Intergenic	Intergenic	-7816	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.024299	0.500000	
chunk0092_110_1	chr19	23763024	23763509	+	0	NA	intron (NR_003662, intron 1 of 3)	CpG	252	NR_003662									0.055670	0.623457	
chunk0182_272_1	chr7	98112257	98112722	+	0	NA	intron (NM_014916, intron 1 of 13)	MER3|DNA|hAT-Charlie	5604	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.012903	0.478541	
chunk0122_385_1	chr3	37832890	37833173	+	0	NA	intron (NR_110532, intron 3 of 5)	LTR16E2|LTR|ERVL	28749	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.003534	0.492958	
chunk0056_272_1	chr13	90212942	90213214	+	0	NA	Intergenic	Intergenic	-18104	NR_030754	693207		NR_030754	ENSG00000283783	MIR622	MIRN622|hsa-mir-622	microRNA 622	ncRNA	0.003676	0.406593	
chunk0104_384_1	chr2	180356564	180357135	+	0	NA	Intergenic	L1PBb|LINE|L1	-335255	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.000000	0.316434	
chunk0074_42_1	chr16	20702489	20702887	+	0	NA	Intergenic	L1PA8|LINE|L1	-11432	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.005025	0.360902	126(GAGAACTATCTGTTCA,-,0.00),127(AGAACTATCTGTTCAT,+,0.00)
chunk0049_329_1	chr12	94762480	94762876	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-71720	NR_030171	574449		NR_030171	ENSG00000283998	MIR492	MIRN492|hsa-mir-492	microRNA 492	ncRNA	0.005051	0.375315	
chunk0201_257_1	chr9	38297623	38297869	+	0	NA	Intergenic	L2c|LINE|L2	-94918	NM_000692	219	Hs.436219	NM_000692	ENSG00000137124	ALDH1B1	ALDH5|ALDHX	aldehyde dehydrogenase 1 family member B1	protein-coding	0.004065	0.380567	
chunk0006_11_1	chr1	63901436	63902194	+	0	NA	intron (NM_001083592, intron 1 of 6)	L2c|LINE|L2	127796	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.003958	0.328063	
chunk0191_46_1	chr8	43296772	43297113	+	0	NA	intron (NM_001002920, intron 1 of 12)	intron (NM_001002920, intron 1 of 12)	4500	NM_001005365	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.002933	0.385965	
chunk0174_203_1	chr6	160172615	160173363	+	0	NA	Intergenic	Intergenic	51158	NM_003057	6580	Hs.117367	NM_003057	ENSG00000175003	SLC22A1	HOCT1|OCT1|oct1_cds	solute carrier family 22 member 1	protein-coding	0.013369	0.429907	
chunk0107_107_1	chr2	214154967	214155579	+	0	NA	intron (NR_047659, intron 17 of 17)	L1MEc|LINE|L1	-256464	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.004902	0.448613	
chunk0079_359_1	chr17	17906738	17907687	+	0	NA	intron (NM_001033551, intron 2 of 13)	intron (NM_001033551, intron 2 of 13)	65258	NM_001033551	146691	Hs.462379	NM_144678	ENSG00000175662	TOM1L2	-	target of myb1 like 2 membrane trafficking protein	protein-coding	0.011591	0.505263	225(AGGGGCAACGTGTTCT,-,0.00)
chunk0083_238_1	chr17	67585214	67585596	+	0	NA	intron (NM_181671, intron 5 of 9)	MLT1B|LTR|ERVL-MaLR	-113820	NR_030385	693131		NR_030385	ENSG00000263690	MIR548D2	MIRN548D2	microRNA 548d-2	ncRNA	0.010471	0.506527	
chunk0182_334_1	chr7	99144154	99144557	+	0	NA	promoter-TSS (NM_181349)	promoter-TSS (NM_181349)	-235	NM_181349	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.091811	0.665842	
chunk0056_334_1	chr13	91241024	91241776	+	0	NA	Intergenic	Intergenic	-29702	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.002660	0.391766	
chunk0176_371_1	chr7	18499455	18499807	+	0	NA	intron (NM_178425, intron 1 of 24)	intron (NM_178425, intron 1 of 24)	3369	NM_178425	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.002841	0.390935	
chunk0008_201_1	chr1	93483510	93484082	+	0	NA	intron (NM_017737, intron 1 of 14)	intron (NM_017737, intron 1 of 14)	35665	NM_017737	54874	Hs.134060	NM_017737	ENSG00000137942	FNBP1L	C1orf39|TOCA1	formin binding protein 1 like	protein-coding	0.003497	0.349040	
chunk0055_430_1	chr13	75446135	75446591	+	0	NA	intron (NM_001286659, intron 1 of 18)	intron (NM_001286659, intron 1 of 18)	35805	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.008772	0.328228	
chunk0097_132_1	chr2	47050812	47051103	+	0	NA	intron (NM_001288953, intron 18 of 20)	MER124|DNA?|DNA?	104421	NM_001163561	285051	Hs.531575	NM_173649	ENSG00000239605	STPG4	C2orf61|GSE	sperm-tail PG-rich repeat containing 4	protein-coding	0.013746	0.452055	
chunk0094_425_1	chr2	10623422	10623822	+	0	NA	intron (NR_048552, intron 12 of 19)	L2c|LINE|L2	66365	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.005000	0.379052	112(TGTACTATCTGTTCCT,+,0.00)
chunk0136_409_1	chr3	197340608	197340931	+	0	NA	Intergenic	LTR33|LTR|ERVL	-41497	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.009288	0.478395	166(CAGAACAGAGAGTCCT,-,0.00),167(AGAACAGAGAGTCCTG,+,0.00)
chunk0136_254_1	chr4	10293193	10293435	+	0	NA	Intergenic	Intergenic	164094	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.008264	0.407407	109(CTGTACAGGTTGTTCC,-,0.00),110(TGTACAGGTTGTTCCT,+,0.00)
chunk0157_109_1	chr5	116837243	116837596	+	0	NA	Intergenic	Intergenic	-75210	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.000000	0.395480	
chunk0149_131_1	chr5	19807660	19808139	+	0	NA	intron (NM_001167667, intron 3 of 12)	intron (NM_001167667, intron 3 of 12)	78373	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006263	0.320833	
chunk0094_285_1	chr2	8275105	8275647	+	0	NA	intron (NR_034135, intron 7 of 8)	L1MEg|LINE|L1	53043	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.005535	0.368324	
chunk0175_79_1	chr7	2315888	2316172	+	0	NA	Intergenic	(CACT)n|Simple_repeat|Simple_repeat	-1555	NM_013321	29886	Hs.584900	NM_013321	ENSG00000106266	SNX8	Mvp1	sorting nexin 8	protein-coding	0.003521	0.487719	
chunk0100_59_1	chr2	106327112	106327571	+	0	NA	Intergenic	L1ME4b|LINE|L1	-54773	NR_003506	285189	Hs.143436	NR_003506	ENSG00000240935	PLGLA	PLGLA1|PLGP2|PRGA	plasminogen like A (pseudogene)	pseudo	0.013072	0.343478	
chunk0107_175_1	chr2	215624299	215624740	+	0	NA	intron (NR_037195, intron 5 of 9)	intron (NR_037195, intron 5 of 9)	-93524	NR_132383	105373869	Hs.152812	NR_132383		LINC01614	LCAL4	long intergenic non-protein coding RNA 1614	ncRNA	0.015873	0.445701	
chunk0039_119_1	chr11	97982354	97982695	+	0	NA	Intergenic	LTR27D|LTR|ERV1	-1038452	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.011730	0.529240	
chunk0112_11_1	chr20	35871299	35871510	+	0	NA	intron (NM_016436, intron 8 of 17)	intron (NM_016436, intron 8 of 17)	83222	NM_033630	51282	Hs.584909	NM_016558	ENSG00000171222	SCAND1	RAZ1|SDP1	SCAN domain containing 1	protein-coding	0.014218	0.433962	
chunk0136_388_1	chr3	196793121	196793573	+	0	NA	intron (NM_002577, intron 2 of 14)	HAL1|LINE|L1	53490	NM_002577	5062	Hs.518530	NM_002577	ENSG00000180370	PAK2	PAK65|PAKgamma	p21 (RAC1) activated kinase 2	protein-coding	0.004425	0.421634	
chunk0180_268_1	chr7	69649216	69649589	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	50483	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.013405	0.454545	103(TGGTACACTGTGTTTC,-,0.00),104(GGTACACTGTGTTTCT,+,0.00)
chunk0173_344_1	chr6	149057735	149058062	+	0	NA	intron (NM_005715, intron 7 of 7)	intron (NM_005715, intron 7 of 7)	-93214	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.000000	0.250000	
chunk0072_248_1	chr15	96053175	96053665	+	0	NA	Intergenic	Intergenic	-272508	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.042857	0.519348	
chunk0015_213_1	chr1	187554633	187555242	+	0	NA	Intergenic	L2a|LINE|L2	111309	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006568	0.408197	
chunk0094_123_1	chr2	4578092	4578412	+	0	NA	Intergenic	Intergenic	77970	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.000000	0.267913	
chunk0070_302_1	chr15	74904784	74905029	+	0	NA	intron (NM_020447, intron 3 of 4)	intron (NM_020447, intron 3 of 4)	2215	NM_020447	57184	Hs.367690	NM_020447	ENSG00000178761	FAM219B	C15orf17	family with sequence similarity 219 member B	protein-coding	0.016327	0.483740	
chunk0085_251_1	chr18	7562454	7562659	+	0	NA	Intergenic	Intergenic	-4760	NM_001105244	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.004878	0.354369	
chunk0067_393_1	chr15	49146310	49146917	+	0	NA	intron (NM_001143887, intron 1 of 12)	L2c|LINE|L2	9044	NM_004236	9318	Hs.369614	NM_004236	ENSG00000166200	COPS2	ALIEN|CSN2|SGN2|TRIP15	COP9 signalosome subunit 2	protein-coding	0.004942	0.360197	
chunk0154_190_1	chr5	80194160	80194423	+	0	NA	intron (NM_178276, intron 2 of 12)	intron (NM_178276, intron 2 of 12)	61791	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.003802	0.405303	161(AGGTACAGTGTGCTCT,-,0.00),162(GGTACAGTGTGCTCTG,+,0.00)
chunk0170_218_1	chr6	113159742	113160440	+	0	NA	Intergenic	MIR3|SINE|MIR	489984	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.010029	0.367668	
chunk0009_223_1	chr1	106607539	106608347	+	0	NA	Intergenic	L2a|LINE|L2	-448702	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.000000	0.344870	
chunk0018_268_1	chr1	220474844	220475102	+	0	NA	Intergenic	LTR12C|LTR|ERV1	-53210	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.038760	0.501931	
chunk0024_149_1	chr10	35251159	35251762	+	0	NA	intron (NM_181698, intron 3 of 11)	intron (NM_181698, intron 3 of 11)	4479	NM_181698	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.006633	0.370861	
chunk0203_328_1	chr9	89667769	89668128	+	0	NA	intron (NR_024280, intron 2 of 5)	intron (NR_024280, intron 2 of 5)	28165	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.019499	0.569444	
chunk0074_28_1	chr16	20569298	20569533	+	0	NA	intron (NM_001105069, intron 1 of 13)	L1ME3Cz|LINE|L1	6958	NM_182617	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.008511	0.372881	
chunk0183_101_1	chr7	105216817	105217288	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	52025	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.006369	0.396186	
chunk0091_186_1	chr19	8308115	8308941	+	0	NA	promoter-TSS (NM_001165895)	promoter-TSS (NM_001165895)	-172	NM_016579	51293	Hs.558499	NM_016579	ENSG00000167775	CD320	8D6|8D6A|TCBLR|TCN2R	CD320 molecule	protein-coding	0.060533	0.550181	
chunk0181_113_1	chr7	80646707	80647006	+	0	NA	exon (NM_000072, exon 3 of 14)	exon (NM_000072, exon 3 of 14)	203	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.006689	0.393333	
chunk0069_53_1	chr15	60740888	60741545	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	59647	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.006088	0.455927	
chunk0188_14_1	chr8	6424652	6424865	+	0	NA	intron (NM_001172575, intron 3 of 6)	intron (NM_001172575, intron 3 of 6)	18166	NM_001172574	79648	Hs.593807	NM_024596	ENSG00000147316	MCPH1	BRIT1|MCT	microcephalin 1	protein-coding	0.014085	0.485981	
chunk0135_8_1	chr3	184120877	184121427	+	0	NA	Intergenic	AluSx|SINE|Alu	-13870	NM_003907	8893	Hs.283551	NM_003907	ENSG00000145191	EIF2B5	CACH|CLE|EIF-2B|EIF2Bepsilon|LVWM	eukaryotic translation initiation factor 2B subunit epsilon	protein-coding	0.021818	0.493648	
chunk0062_218_1	chr14	70954635	70955354	+	0	NA	intron (NM_001308160, intron 2 of 33)	intron (NM_001308160, intron 2 of 33)	47589	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.004172	0.313889	
chunk0203_209_1	chr9	86613328	86613542	+	0	NA	Intergenic	Intergenic	-258948	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.004673	0.362791	
chunk0108_138_1	chr2	230640625	230641064	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	59685	NR_040038	151475	Hs.528154	NR_040038	ENSG00000226125	LINC01907	-	long intergenic non-protein coding RNA 1907	ncRNA	0.013667	0.354545	
chunk0150_201_1	chr5	35026819	35027018	+	0	NA	intron (NM_001306173, intron 7 of 12)	intron (NM_001306173, intron 7 of 12)	21217	NM_001306173	64902	Hs.34494	NM_031900	ENSG00000113492	AGXT2	AGT2|BAIBA|DAIBAT	alanine--glyoxylate aminotransferase 2	protein-coding	0.015075	0.320000	
chunk0203_454_1	chr9	91502725	91503281	+	0	NA	Intergenic	Intergenic	-78377	NM_001290000	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.017986	0.482944	402(GGGGACAGCTTGTCTC,-,0.00),403(GGGACAGCTTGTCTCT,+,0.00)
chunk0097_311_1	chr2	56208376	56208846	+	0	NA	intron (NM_001080433, intron 2 of 5)	LTR89|LTR|ERVL?	-22841	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.002128	0.411890	
chunk0160_248_1	chr5	156630277	156630856	+	0	NA	intron (NM_000337, intron 6 of 8)	intron (NM_000337, intron 6 of 8)	-219972	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.003454	0.368966	
chunk0187_89_1	chr8	3559097	3559667	+	0	NA	intron (NM_033225, intron 10 of 69)	intron (NM_033225, intron 10 of 69)	-830931	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.010526	0.362522	
chunk0023_355_1	chr10	29797391	29798054	+	0	NA	Intergenic	Intergenic	-61921	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.007541	0.399096	
chunk0021_379_1	chr1	246470871	246471070	+	0	NA	intron (NM_001167740, intron 1 of 11)	L1MC4|LINE|L1	36372	NM_001167740	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.000000	0.310000	
chunk0066_432_1	chr15	39652591	39652834	+	0	NA	intron (NM_152597, intron 10 of 11)	Tigger3b|DNA|TcMar-Tigger	71633	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.004115	0.344262	
chunk0022_126_1	chr10	11566129	11566589	+	0	NA	intron (NR_125732, intron 2 of 2)	intron (NR_125732, intron 2 of 2)	-34079	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.013043	0.375271	
chunk0099_330_1	chr2	99960850	99961166	+	0	NA	intron (NM_001025108, intron 6 of 23)	intron (NM_001025108, intron 6 of 23)	144575	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.006329	0.520505	
chunk0096_395_1	chr2	37659138	37660131	+	0	NA	intron (NM_001270436, intron 1 of 1)	intron (NM_001270436, intron 1 of 1)	12565	NM_001270438	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.006042	0.389336	
chunk0087_421_1	chr18	42263262	42263532	+	0	NA	intron (NR_046454, intron 3 of 6)	intron (NR_046454, intron 3 of 6)	76729	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.007407	0.431734	188(AAGAACATGCAGTACT,-,0.00),189(AGAACATGCAGTACTC,+,0.00)
chunk0118_189_1	chr22	31302047	31302360	+	0	NA	Intergenic	Intergenic	-9669	NM_001135911	113791	Hs.26670	NM_052880	ENSG00000100100	PIK3IP1	HGFL|TrIP|hHGFL(S)	phosphoinositide-3-kinase interacting protein 1	protein-coding	0.000000	0.429936	
chunk0021_79_1	chr10	1650819	1651704	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	86215	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.028249	0.571106	
chunk0007_445_1	chr1	86926858	86927467	+	0	NA	intron (NM_012262, intron 1 of 6)	intron (NM_012262, intron 1 of 6)	12510	NM_012262	9653	Hs.743280	NM_012262	ENSG00000153936	HS2ST1	dJ604K5.2	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.003284	0.383607	
chunk0145_9_1	chr4	143321081	143321605	+	0	NA	Intergenic	L1ME1|LINE|L1	-15487	NM_002039	2549	Hs.80720	NM_002039	ENSG00000109458	GAB1	DFNB26	GRB2 associated binding protein 1	protein-coding	0.011450	0.382857	
chunk0110_47_1	chr20	10637925	10638166	+	0	NA	3' UTR (NM_000214, exon 26 of 26)	3' UTR (NM_000214, exon 26 of 26)	11650	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.016598	0.330579	34(GAGGCCACACTGTTCC,-,0.00),35(AGGCCACACTGTTCCA,+,0.00)
chunk0028_118_1	chr10	84590840	84591075	+	0	NA	Intergenic	Intergenic	165775	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.029787	0.504237	
chunk0043_178_1	chr12	17587227	17587583	+	0	NA	Intergenic	Intergenic	-85894	NR_039770	100616279		NR_039770	ENSG00000283665	MIR3974	-	microRNA 3974	ncRNA	0.005618	0.333333	
chunk0074_306_1	chr16	30408355	30408615	+	0	NA	intron (NM_016643, intron 2 of 2)	L2b|LINE|L2	1071	NM_016643	51333	Hs.148584	NM_016643	ENSG00000179965	ZNF771	DSC43	zinc finger protein 771	protein-coding	0.011538	0.482759	
chunk0114_360_1	chr21	19796466	19796758	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	1006496	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.003425	0.331058	
chunk0065_270_1	chr14	101931490	101931903	+	0	NA	Intergenic	Intergenic	-32832	NM_001376	1778	Hs.614080	NM_001376	ENSG00000197102	DYNC1H1	CMT2O|DHC1|DHC1a|DNCH1|DNCL|DNECL|DYHC|Dnchc1|HL-3|SMALED1|p22	dynein cytoplasmic 1 heavy chain 1	protein-coding	0.007264	0.429952	
chunk0179_164_1	chr7	46627390	46628000	+	0	NA	Intergenic	Intergenic	-706423	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.009836	0.418985	
chunk0001_224_1	chr1	8070660	8071416	+	0	NA	Intergenic	Intergenic	-44705	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.017196	0.396301	
chunk0130_55_1	chr3	129628032	129628231	+	0	NA	Intergenic	Intergenic	-21392	NM_015103	23129	Hs.301685	NM_015103	ENSG00000004399	PLXND1	PLEXD1	plexin D1	protein-coding	0.040201	0.480000	
chunk0122_26_1	chr3	27877395	27877926	+	0	NA	Intergenic	Intergenic	-43524	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.003766	0.422932	268(AGGACAAATAGTCCCT,+,0.00)
chunk0012_294_1	chr1	162131408	162131827	+	0	NA	intron (NM_001164757, intron 1 of 9)	intron (NM_001164757, intron 1 of 9)	-25490	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.004773	0.428571	
chunk0175_379_1	chr6	168162503	168162761	+	0	NA	Intergenic	Intergenic	-80306	NR_110870	101929420	Hs.571211	NR_110870	ENSG00000234647	LOC101929420	-	uncharacterized LOC101929420	ncRNA	0.015504	0.416988	
chunk0016_257_1	chr1	200121507	200121802	+	0	NA	intron (NM_205860, intron 7 of 7)	intron (NM_205860, intron 7 of 7)	78829	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.000000	0.351351	
chunk0157_52_1	chr5	116042016	116042550	+	0	NA	Intergenic	L2c|LINE|L2	-9183	NM_001195581	644100	Hs.98288	NM_001195581	ENSG00000268223	ARL14EPL	-	ADP ribosylation factor like GTPase 14 effector protein like	protein-coding	0.005618	0.465421	211(ATGCACATCTTGTGCT,-,0.00),212(TGCACATCTTGTGCTT,+,0.00)
chunk0003_287_1	chr1	37484500	37484968	+	0	NA	TTS (NM_025079)	TTS (NM_025079)	4504	NR_106790	102465438		NR_106790	ENSG00000283724	MIR6732	hsa-mir-6732	microRNA 6732	ncRNA	0.010684	0.539446	
chunk0169_301_1	chr6	106052237	106052463	+	0	NA	Intergenic	Intergenic	-33970	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.008850	0.317181	
chunk0080_189_1	chr17	28946313	28946633	+	0	NA	intron (NM_001033561, intron 2 of 14)	intron (NM_001033561, intron 2 of 14)	5017	NM_001290131	57649	Hs.444173	NM_020889	ENSG00000109118	PHF12	PF1	PHD finger protein 12	protein-coding	0.009375	0.411215	
chunk0167_55_1	chr6	55617070	55617435	+	0	NA	Intergenic	Intergenic	-38038	NM_001042406	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.002740	0.409836	
chunk0199_396_1	chr9	13278121	13279031	+	0	NA	intron (NM_003829, intron 1 of 45)	CpG	988	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.061538	0.602634	
chunk0112_325_1	chr20	44895165	44895650	+	0	NA	intron (NM_003404, intron 2 of 6)	intron (NM_003404, intron 2 of 6)	9808	NM_139323	7529	Hs.643544	NM_003404	ENSG00000166913	YWHAB	GW128|HEL-S-1|HS1|KCIP-1|YWHAA	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta	protein-coding	0.004124	0.456790	
chunk0109_63_1	chr20	1372187	1372501	+	0	NA	intron (NM_001199786, intron 2 of 3)	intron (NM_001199786, intron 2 of 3)	20617	NR_106929	102465524		NR_106929	ENSG00000284436	MIR6869	hsa-mir-6869	microRNA 6869	ncRNA	0.003185	0.501587	
chunk0061_407_1	chr14	64938595	64938876	+	0	NA	TTS (NM_002083)	TTS (NM_002083)	4170	NM_002083	2877	Hs.2704	NM_002083	ENSG00000176153	GPX2	GI-GPx|GPRP|GPRP-2|GPx-2|GPx-GI|GSHPX-GI|GSHPx-2	glutathione peroxidase 2	protein-coding	0.007117	0.460993	
chunk0046_189_1	chr12	58806113	58806401	+	0	NA	intron (NR_126341, intron 1 of 1)	intron (NR_126341, intron 1 of 1)	-24541	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.000000	0.352941	
chunk0172_69_1	chr6	134335631	134335922	+	0	NA	Intergenic	Intergenic	-17718	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.003436	0.373288	
chunk0021_260_1	chr1	243505811	243506181	+	0	NA	intron (NM_005465, intron 12 of 12)	intron (NM_005465, intron 12 of 12)	159820	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.013514	0.479784	
chunk0056_278_1	chr13	90362917	90363598	+	0	NA	Intergenic	Intergenic	-130031	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.001468	0.313783	
chunk0015_38_1	chr1	184459471	184459801	+	0	NA	intron (NM_030806, intron 1 of 5)	L2c|LINE|L2	72620	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.003030	0.416918	
chunk0077_121_1	chr16	78362609	78362934	+	0	NA	intron (NM_016373, intron 5 of 8)	MIRb|SINE|MIR	263358	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.009231	0.407975	
chunk0195_442_1	chr8	101231740	101231945	+	0	NA	Intergenic	Intergenic	-25778	NM_001267709	51123	Hs.374485	NM_016096	ENSG00000120963	ZNF706	HSPC038|PNAS-106|PNAS-113	zinc finger protein 706	protein-coding	0.009756	0.514563	
chunk0157_140_1	chr5	117486831	117487538	+	0	NA	intron (NR_046089, intron 3 of 5)	MER130|DNA|DNA	71672	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.001414	0.454802	
chunk0149_318_1	chr5	26368862	26369248	+	0	NA	Intergenic	Intergenic	669527	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.005181	0.279070	
chunk0064_343_1	chr14	96661512	96662000	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-135591	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.000000	0.480573	263(GTGCACATTCTGTACA,-,0.00)
chunk0182_278_1	chr7	98143475	98143980	+	0	NA	intron (NM_014916, intron 3 of 13)	L1ME4a|LINE|L1	36842	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.015842	0.377470	
chunk0098_175_1	chr2	71181282	71181789	+	0	NA	Intergenic	Intergenic	45568	NM_020459	400961	Hs.416735	NM_020459	ENSG00000124374	PAIP2B	-	poly(A) binding protein interacting protein 2B	protein-coding	0.003945	0.374016	
chunk0207_262_1	chr9	132282600	132283304	+	0	NA	intron (NM_015046, intron 19 of 25)	L3|LINE|CR1	72033	NM_015046	23064	Hs.460317	NM_015046	ENSG00000107290	SETX	ALS4|AOA2|SCAN2|SCAR1|Sen1|bA479K20.2	senataxin	protein-coding	0.005682	0.390071	
chunk0135_344_1	chr3	190378517	190379067	+	0	NA	Intergenic	Intergenic	-9080	NM_006580	10686	Hs.251391	NM_006580	ENSG00000113946	CLDN16	HOMG3|PCLN1	claudin 16	protein-coding	0.009091	0.379310	
chunk0164_86_1	chr6	20182925	20183473	+	0	NA	intron (NM_001080480, intron 1 of 12)	intron (NM_001080480, intron 1 of 12)	29265	NM_001080480	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.003650	0.459016	169(GAGAACTCCCTGTCCT,-,0.00),170(AGAACTCCCTGTCCTC,+,0.00)
chunk0101_395_1	chr2	138786635	138786929	+	0	NA	Intergenic	Intergenic	-6541	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.006803	0.383051	
chunk0169_444_1	chr6	108764630	108765010	+	0	NA	intron (NR_033376, intron 3 of 4)	UCON8|DNA|DNA	13166	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.005263	0.469816	163(CTGGACACTTTGTTCA,-,0.00),164(TGGACACTTTGTTCAG,+,0.00),247(CAGCACTGTGTGTGCC,-,0.00),248(AGCACTGTGTGTGCCA,+,0.00)
chunk0097_138_1	chr2	47287621	47287820	+	0	NA	intron (NR_110207, intron 1 of 2)	L1MB3|LINE|L1	-47595	NR_001568	618		NR_001568	ENSG00000236824	BCYRN1	BC200|BC200a|LINC00004|NCRNA00004	brain cytoplasmic RNA 1	ncRNA	0.010050	0.465000	
chunk0108_311_1	chr2	235335195	235335665	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-158659	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.012766	0.430998	
chunk0050_132_1	chr12	102342403	102343156	+	0	NA	Intergenic	Intergenic	135872	NM_001111284	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.005312	0.411141	
chunk0027_199_1	chr10	75739474	75740168	+	0	NA	intron (NR_132791, intron 1 of 2)	intron (NR_132791, intron 1 of 2)	27366	NR_132791	105378367	Hs.464836	NR_132791		LOC105378367	-	uncharacterized LOC105378367	ncRNA	0.011527	0.353957	
chunk0047_151_1	chr12	69705975	69706332	+	0	NA	Intergenic	L2a|LINE|L2	-6737	NM_032735	144453	Hs.280782	NM_032735	ENSG00000127325	BEST3	VMD2L3	bestrophin 3	protein-coding	0.005602	0.477654	
chunk0078_17_1	chr17	699355	699877	+	0	NA	intron (NM_001128159, intron 2 of 21)	MER58A|DNA|hAT-Charlie	15240	NM_001128159	55275	Hs.461819	NM_018289	ENSG00000141252	VPS53	HCCS1|PCH2E|hVps53L|pp13624	VPS53 subunit of GARP complex	protein-coding	0.021073	0.413002	
chunk0144_137_1	chr4	129722421	129723196	+	0	NA	Intergenic	L1PA14|LINE|L1	48670	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.006452	0.367268	
chunk0074_313_1	chr16	30533186	30533422	+	0	NA	intron (NM_023931, intron 1 of 1)	intron (NM_023931, intron 1 of 1)	1666	NM_001305019	65988	Hs.592032	NM_023931	ENSG00000169955	ZNF747	-	zinc finger protein 747	protein-coding	0.042373	0.616034	
chunk0196_224_1	chr8	107508825	107509349	+	0	NA	Intergenic	L1MB5|LINE|L1	-11032	NM_001146	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.005725	0.340952	284(GAGTACAAGGTGTCCT,-,0.00),285(AGTACAAGGTGTCCTT,+,0.00)
chunk0025_413_1	chr10	59688879	59689396	+	0	NA	intron (NM_194298, intron 1 of 5)	intron (NM_194298, intron 1 of 5)	20754	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.009671	0.418919	
chunk0084_363_1	chr17	81566493	81566785	+	0	NA	promoter-TSS (NR_130140)	promoter-TSS (NR_130140)	-4	NR_130140	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.013699	0.515358	
chunk0143_380_1	chr4	122646941	122647581	+	0	NA	intron (NR_104126, intron 7 of 10)	intron (NR_104126, intron 7 of 10)	-26204	NM_001207006	59067	Hs.567559	NM_021803	ENSG00000138684	IL21	CVID11|IL-21|Za11	interleukin 21	protein-coding	0.004687	0.349454	377(TAGAACAGTCTGAGCT,-,0.00),378(AGAACAGTCTGAGCTA,+,0.00)
chunk0179_414_1	chr7	51694231	51694504	+	0	NA	Intergenic	Intergenic	-377549	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.007326	0.489051	
chunk0198_65_1	chr8	129675623	129675866	+	0	NA	intron (NR_130917, intron 1 of 3)	intron (NR_130917, intron 1 of 3)	4495	NR_130917	137196	Hs.679457	NR_130917	ENSG00000229140	CCDC26	RAM	CCDC26 long non-coding RNA	ncRNA	0.008230	0.422131	
chunk0148_257_1	chr5	10310103	10310544	+	0	NA	Intergenic	Intergenic	-2267	NM_138809	134147	Hs.192586	NM_138809	ENSG00000164237	CMBL	JS-1	carboxymethylenebutenolidase homolog	protein-coding	0.006803	0.364253	
chunk0173_8_1	chr6	141203912	141204703	+	0	NA	Intergenic	Intergenic	520493	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.005057	0.363636	394(AAGAACACACAGTTCC,-,0.00),395(AGAACACACAGTTCCC,+,0.00)
chunk0015_206_1	chr1	187509101	187509446	+	0	NA	Intergenic	Intergenic	65645	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.343931	
chunk0020_127_1	chr1	233577149	233577875	+	0	NA	Intergenic	L1MEg2|LINE|L1	-36492	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.002755	0.302613	
chunk0198_445_1	chr8	144003406	144003783	+	0	NA	Intergenic	L1MEc|LINE|L1	-8820	NM_198572	375686	Hs.97726	NM_198572	ENSG00000186583	SPATC1	SPATA15	spermatogenesis and centriole associated 1	protein-coding	0.013263	0.431217	136(AGGAACACTATGATCA,-,0.00),137(GGAACACTATGATCAT,+,0.00)
chunk0028_331_1	chr10	92028739	92029559	+	0	NA	3' UTR (NM_003972, exon 38 of 38)	3' UTR (NM_003972, exon 38 of 38)	105170	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.001220	0.311815	
chunk0082_7_1	chr17	49813067	49813335	+	0	NA	intron (NM_007067, intron 7 of 14)	L1PA17|LINE|L1	24582	NM_001199158	11143	Hs.21907	NM_007067	ENSG00000136504	KAT7	HBO1|HBOA|MYST2|ZC2HC7	lysine acetyltransferase 7	protein-coding	0.003731	0.412639	195(GAGAACATGCTGTGTT,-,0.00),196(AGAACATGCTGTGTTT,+,0.00)
chunk0164_307_1	chr6	24960796	24961601	+	0	NA	intron (NM_001286446, intron 1 of 13)	L2b|LINE|L2	-25146	NM_001286445	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.007453	0.447891	453(GGAACAGTTTGAACTG,+,0.00)
chunk0208_35_1	chrX	11352208	11352565	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-33700	NR_049865	100847063		NR_049865	ENSG00000263652	MIR548AX	-	microRNA 548ax	ncRNA	0.000000	0.405028	
chunk0211_325_1	chrX	123986449	123986711	+	0	NA	intron (NM_001282418, intron 2 of 33)	MIRb|SINE|MIR	24874	NM_001042751	10735	Hs.496710	NM_006603	ENSG00000101972	STAG2	NEDXCF|SA-2|SA2|SCC3B|bA517O1.1	stromal antigen 2	protein-coding	0.003817	0.346008	
chunk0058_256_1	chr14	25833393	25833629	+	0	NA	Intergenic	Intergenic	764243	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.025424	0.510549	90(GAGAACATTGTGTCCT,-,0.00),91(AGAACATTGTGTCCTG,+,0.00)
chunk0137_248_1	chr4	20639217	20639838	+	0	NA	Intergenic	L2c|LINE|L2	-60886	NM_001258345	133015	Hs.479298	NM_145048	ENSG00000163138	PACRGL	C4orf28	parkin coregulated like	protein-coding	0.004831	0.376206	
chunk0114_279_1	chr21	16365869	16366202	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	171656	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.003003	0.347305	170(TTGAACAAACTGTGCT,-,0.00),171(TGAACAAACTGTGCTG,+,0.00)
chunk0161_443_1	chr5	178612325	178612627	+	0	NA	exon (NM_020666, exon 9 of 13)	exon (NM_020666, exon 9 of 13)	14577	NM_020666	57396	Hs.406557	NM_020666	ENSG00000113240	CLK4	-	CDC like kinase 4	protein-coding	0.019868	0.399340	
chunk0156_7_1	chr5	101932466	101933047	+	0	NA	Intergenic	L1MC3|LINE|L1	363793	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.008606	0.333333	
chunk0202_395_1	chr9	81236232	81236707	+	0	NA	Intergenic	Intergenic	453066	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.006316	0.327731	
chunk0184_205_1	chr7	117097841	117098487	+	0	NA	intron (NM_021908, intron 1 of 15)	intron (NM_021908, intron 1 of 15)	-7383	NR_109980	93654	Hs.628891	NR_002331	ENSG00000226367	ST7-AS2	ST7AS2|ST7OT2	ST7 antisense RNA 2	ncRNA	0.007740	0.423493	
chunk0112_46_1	chr20	36890582	36891179	+	0	NA	TTS (NM_015474)	TTS (NM_015474)	14759	NM_080628	140711	Hs.472630	NM_080628	ENSG00000101342	TLDC2	C20orf118	TBC/LysM-associated domain containing 2	protein-coding	0.016750	0.438127	250(AAGAACATAAAGTACA,-,0.00)
chunk0054_136_1	chr13	43553421	43553776	+	0	NA	intron (NM_001242863, intron 2 of 16)	intron (NM_001242863, intron 2 of 16)	75879	NM_001127615	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.005634	0.359551	
chunk0138_336_1	chr4	41601090	41601467	+	0	NA	intron (NM_001112717, intron 4 of 25)	L2a|LINE|L2	-11494	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.002653	0.439153	
chunk0065_369_1	chr14	104005659	104005865	+	0	NA	intron (NM_153046, intron 15 of 35)	intron (NM_153046, intron 15 of 35)	-63454	NM_001257268	647286	Hs.632325	NM_001257268	ENSG00000227729	RD3L	TDRD9-AS1|TDRD9AS1	retinal degeneration 3 like	protein-coding	0.014563	0.458937	72(GTGTACATACTGTGCT,-,0.00),73(TGTACATACTGTGCTG,+,0.00)
chunk0146_268_1	chr4	163100924	163101482	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	-7575	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.005376	0.440072	
chunk0178_44_1	chr7	29586234	29587027	+	0	NA	Intergenic	Intergenic	22819	NM_175887	222171	Hs.91109	NM_175887	ENSG00000176532	PRR15	-	proline rich 15	protein-coding	0.003783	0.450882	
chunk0103_75_1	chr2	160454055	160454594	+	0	NA	intron (NM_002897, intron 1 of 13)	L2c|LINE|L2	39483	NM_016836	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.000000	0.370370	
chunk0116_78_1	chr21	34722788	34723060	+	0	NA	TTS (NR_024351)	TTS (NR_024351)	14258	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.011029	0.586081	
chunk0171_413_1	chr6	131368616	131369204	+	0	NA	Intergenic	Intergenic	118751	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.013605	0.451613	
chunk0120_27_1	chr3	2026440	2026914	+	0	NA	Intergenic	MIRc|SINE|MIR	-72189	NM_175607	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.002110	0.294737	
chunk0011_110_1	chr1	146007132	146007454	+	0	NA	Intergenic	Intergenic	-10662	NM_006472	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.009317	0.408669	226(TGGGACATTGTGTGCT,-,0.00),227(GGGACATTGTGTGCTC,+,0.00)
chunk0030_393_1	chr10	119725987	119726189	+	0	NA	promoter-TSS (NM_001243195)	promoter-TSS (NM_001243195)	41	NM_001243195	22876	Hs.369755	NM_014937	ENSG00000198825	INPP5F	MSTP007|MSTPO47|SAC2|hSAC2	inositol polyphosphate-5-phosphatase F	protein-coding	0.123762	0.778325	
chunk0133_379_1	chr3	173920213	173920707	+	0	NA	intron (NR_046664, intron 1 of 3)	intron (NR_046664, intron 1 of 3)	336	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004049	0.381818	259(AGGTGCAGATTGTTCT,-,0.00),260(GGTGCAGATTGTTCTT,+,0.00)
chunk0181_106_1	chr7	80611676	80612253	+	0	NA	intron (NM_001289911, intron 1 of 11)	MER90a|LTR|ERV1	9757	NM_001289911	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.005199	0.397924	
chunk0131_355_1	chr3	151816253	151816452	+	0	NA	intron (NM_001086, intron 1 of 4)	L2c|LINE|L2	2279	NM_001086	13	Hs.506908	NM_001086	ENSG00000114771	AADAC	CES5A1|DAC	arylacetamide deacetylase	protein-coding	0.010050	0.405000	
chunk0093_181_1	chr19	48582173	48582638	+	0	NA	intron (NM_004605, intron 1 of 5)	L1ME4b|LINE|L1	6669	NM_004605	6820	Hs.369331	NM_004605	ENSG00000088002	SULT2B1	ARCI14|HSST2	sulfotransferase family 2B member 1	protein-coding	0.010753	0.388412	
chunk0113_156_1	chr20	52790949	52791656	+	0	NA	Intergenic	Intergenic	170464	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.002829	0.443503	202(GAGATCACACAGTCCT,-,0.00),203(AGATCACACAGTCCTT,+,0.00)
chunk0106_186_1	chr2	201382785	201383233	+	0	NA	intron (NM_015049, intron 15 of 15)	intron (NM_015049, intron 15 of 15)	-25611	NM_001289993	130540	Hs.107944	NM_139163	ENSG00000155749	FLACC1	ALS2CR12	flagellum associated containing coiled-coil domains 1	protein-coding	0.000000	0.345212	
chunk0167_184_1	chr6	63911260	63911536	+	0	NA	intron (NM_001142800, intron 35 of 42)	intron (NM_001142800, intron 35 of 42)	264872	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.000000	0.353791	
chunk0111_324_1	chr20	32370456	32370867	+	0	NA	intron (NM_015338, intron 3 of 11)	intron (NM_015338, intron 3 of 11)	12317	NM_015338	171023	Hs.374043	NM_015338	ENSG00000171456	ASXL1	BOPS|MDS	ASXL transcriptional regulator 1	protein-coding	0.009732	0.356796	
chunk0083_56_1	chr17	63722457	63722909	+	0	NA	intron (NM_001003786, intron 2 of 10)	intron (NM_001003786, intron 2 of 10)	19287	NM_001165969	92335	Hs.514402	NM_153335	ENSG00000266173	STRADA	LYK5|NY-BR-96|PMSE|STRAD|STRAD alpha|Stlk	STE20 related adaptor alpha	protein-coding	0.002212	0.375276	
chunk0036_239_1	chr11	64306215	64306665	+	0	NA	5' UTR (NM_001282450, exon 1 of 7)	5' UTR (NM_001282450, exon 1 of 7)	213	NM_001282450	2101	Hs.110849	NM_004451	ENSG00000173153	ESRRA	ERR1|ERRa|ERRalpha|ESRL1|NR3B1	estrogen related receptor alpha	protein-coding	0.064444	0.636364	
chunk0143_141_1	chr4	109878944	109879191	+	0	NA	Intergenic	Intergenic	30883	NM_198506	345193	Hs.308127	NM_198506	ENSG00000183423	LRIT3	CSNB1F|FIGLER4	leucine rich repeat, Ig-like and transmembrane domains 3	protein-coding	0.008097	0.544355	
chunk0155_200_1	chr5	94893495	94893771	+	0	NA	intron (NM_024717, intron 11 of 22)	intron (NM_024717, intron 11 of 22)	188233	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.003623	0.350181	
chunk0156_359_1	chr5	112420406	112420605	+	0	NA	non-coding (NR_027706, exon 1 of 1)	non-coding (NR_027706, exon 1 of 1)	922	NR_027706	54508	Hs.591264	NR_027706	ENSG00000278921	EPB41L4A-DT	EPB41L4A-AS2	EPB41L4A divergent transcript	ncRNA	0.060302	0.630000	
chunk0108_431_1	chr2	237895890	237896424	+	0	NA	intron (NM_001308353, intron 3 of 3)	intron (NM_001308353, intron 3 of 3)	36613	NM_005855	10267	Hs.471783	NM_005855	ENSG00000132329	RAMP1	-	receptor activity modifying protein 1	protein-coding	0.022472	0.629907	246(TAGGACAGTCTGTGAC,-,0.00),247(AGGACAGTCTGTGACT,+,0.00)
chunk0073_51_1	chr16	3038994	3039238	+	0	NA	TTS (NR_047572)	TTS (NR_047572)	-3575	NM_001103175	146439	Hs.513285	NM_001103175	ENSG00000162069	BICDL2	BICDR-2|BICDR2|CCDC64B	BICD family like cargo adaptor 2	protein-coding	0.016393	0.542857	
chunk0146_211_1	chr4	161539275	161539474	+	0	NA	intron (NM_001128427, intron 9 of 15)	intron (NM_001128427, intron 9 of 15)	-483359	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.010050	0.420000	
chunk0077_282_1	chr16	81213249	81213566	+	0	NA	intron (NR_126532, intron 3 of 42)	L1ME3Cz|LINE|L1	6963	NM_052892	114780	Hs.413525	NM_052892	ENSG00000166473	PKD1L2	PC1L2	polycystin 1 like 2 (gene/pseudogene)	protein-coding	0.015773	0.377358	
chunk0210_381_1	chrX	97524112	97524690	+	0	NA	intron (NM_006729, intron 26 of 26)	intron (NM_006729, intron 26 of 26)	40134	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.003460	0.357513	
chunk0183_408_1	chr7	110507586	110508038	+	0	NA	Intergenic	LTR67B|LTR|ERVL	-547599	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.331126	
chunk0106_357_1	chr2	206982596	206982937	+	0	NA	Intergenic	Intergenic	43212	NM_173077	130749	Hs.684103	NM_173077	ENSG00000144410	CPO	-	carboxypeptidase O	protein-coding	0.011730	0.453216	
chunk0059_371_1	chr14	37343325	37343903	+	0	NA	intron (NM_001195296, intron 11 of 14)	intron (NM_001195296, intron 11 of 14)	145701	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.005190	0.295337	
chunk0118_250_1	chr22	32885953	32886216	+	0	NA	intron (NM_003490, intron 3 of 12)	Helitron1Na_Mam|RC|Helitron	85268	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.007605	0.390152	
chunk0124_395_1	chr3	59679532	59680165	+	0	NA	Intergenic	Intergenic	-629859	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.001580	0.482650	544(CTGTACAGATTGTCCT,-,0.00),545(TGTACAGATTGTCCTG,+,0.00)
chunk0154_215_1	chr5	80558501	80558732	+	0	NA	exon (NM_001004441, exon 5 of 5)	exon (NM_001004441, exon 5 of 5)	11869	NM_001004441	340120	Hs.519404	NM_001004441	ENSG00000189127	ANKRD34B	DP58	ankyrin repeat domain 34B	protein-coding	0.008658	0.400862	
chunk0148_10_1	chr5	179094	179577	+	0	NA	intron (NM_052909, intron 16 of 17)	intron (NM_052909, intron 16 of 17)	-12176	NM_001080478	389257	Hs.103142	NM_001080478	ENSG00000185028	LRRC14B	-	leucine rich repeat containing 14B	protein-coding	0.006211	0.448347	
chunk0080_250_1	chr17	30370370	30370756	+	0	NA	Intergenic	AluJb|SINE|Alu	-8361	NM_001304	1362	Hs.446079	NM_001304	ENSG00000108582	CPD	GP180	carboxypeptidase D	protein-coding	0.005181	0.423773	
chunk0063_54_1	chr14	77034092	77034547	+	0	NA	Intergenic	Intergenic	-5620	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.026374	0.484649	
chunk0207_53_1	chrX	7154443	7155133	+	0	NA	Intergenic	Intergenic	-6598	NM_001178136	8226	Hs.185910	NM_012080	ENSG00000130021	PUDP	DXF68S1E|FAM16AX|GS1|HDHD1|HDHD1A	pseudouridine 5'-phosphatase	protein-coding	0.007246	0.377713	
chunk0151_116_1	chr5	43572460	43572873	+	0	NA	TTS (NR_073113)	TTS (NR_073113)	-15247	NM_183323	10605	Hs.482038	NM_006451	ENSG00000172239	PAIP1	-	poly(A) binding protein interacting protein 1	protein-coding	0.004843	0.369565	
chunk0179_272_1	chr7	49424006	49424682	+	0	NA	Intergenic	Intergenic	-349317	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.001479	0.288035	
chunk0142_362_1	chr4	101944469	101945063	+	0	NA	intron (NM_017935, intron 7 of 16)	intron (NM_017935, intron 7 of 16)	130940	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.001684	0.394958	353(GAGATCACAATGTACC,-,0.00),354(AGATCACAATGTACCT,+,0.00)
chunk0149_438_1	chr5	29750118	29750859	+	0	NA	Intergenic	Intergenic	-354512	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.002699	0.245283	
chunk0099_160_1	chr2	88261711	88262216	+	0	NA	Intergenic	Intergenic	88824	NM_018271	55258	Hs.739080	NM_018271	ENSG00000144115	THNSL2	SOFAT|THS2|TSH2	threonine synthase like 2	protein-coding	0.007921	0.476285	
chunk0014_424_1	chr1	183432324	183432858	+	0	NA	Intergenic	Intergenic	-14092	NM_015039	23057	Hs.497123	NM_015039	ENSG00000157064	NMNAT2	C1orf15|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.005618	0.435514	
chunk0126_123_1	chr3	75749341	75749636	+	0	NA	intron (NM_001290209, intron 2 of 4)	CER|Satellite|Satellite	11208	NR_036235	100422955		NR_036235	ENSG00000266396	MIR4273	-	microRNA 4273	ncRNA	0.013559	0.466216	
chunk0135_108_1	chr3	186843078	186843336	+	0	NA	intron (NM_004797, intron 1 of 2)	intron (NM_004797, intron 1 of 2)	533	NM_004797	9370	Hs.80485	NM_004797	ENSG00000181092	ADIPOQ	ACDC|ACRP30|ADIPQTL1|ADPN|APM-1|APM1|GBP28	adiponectin, C1Q and collagen domain containing	protein-coding	0.003876	0.420849	
chunk0007_74_1	chr1	78370903	78371225	+	0	NA	Intergenic	Intergenic	-119979	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.003106	0.349845	
chunk0186_372_1	chr7	144095326	144095587	+	0	NA	exon (NM_001004135, exon 1 of 1)	exon (NM_001004135, exon 1 of 1)	348	NM_001004135	346525	Hs.553708	NM_001004135	ENSG00000221858	OR2A12	OR2A12P|OR2A16P	olfactory receptor family 2 subfamily A member 12	protein-coding	0.011494	0.431298	
chunk0078_93_1	chr17	2084988	2085352	+	0	NA	intron (NM_001256827, intron 7 of 11)	(CA)n|Simple_repeat|Simple_repeat	3591	NM_001282326	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.021978	0.539726	
chunk0130_400_1	chr3	140308901	140309112	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	199783	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.000000	0.349057	
chunk0017_146_1	chr1	206712345	206712704	+	0	NA	intron (NM_032960, intron 1 of 9)	L3|LINE|CR1	27504	NM_032960	9261	Hs.643566	NM_004759	ENSG00000162889	MAPKAPK2	MAPKAP-K2|MK-2|MK2	MAPK activated protein kinase 2	protein-coding	0.002786	0.433333	
chunk0201_394_1	chr9	69125950	69126500	+	0	NA	intron (NM_001170414, intron 1 of 21)	intron (NM_001170414, intron 1 of 21)	4961	NM_001170414	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.005455	0.413793	
chunk0126_285_1	chr3	80158537	80159089	+	0	NA	Intergenic	Intergenic	-390904	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.365280	
chunk0052_372_1	chr12	128823452	128823761	+	0	NA	exon (NM_145648, exon 1 of 8)	exon (NM_145648, exon 1 of 8)	390	NM_145648	121260	Hs.507260	NM_145648	ENSG00000139370	SLC15A4	FP12591|PHT1|PTR4	solute carrier family 15 member 4	protein-coding	0.132686	0.758065	
chunk0060_271_1	chr14	50342584	50342971	+	0	NA	intron (NM_001282236, intron 4 of 8)	intron (NM_001282236, intron 4 of 8)	30448	NM_015684	27109	Hs.438489	NM_015684	ENSG00000125375	DMAC2L	ATP5S|ATPW|FB|HSU79253	distal membrane arm assembly complex 2 like	protein-coding	0.010336	0.479381	
chunk0171_333_1	chr6	129934165	129934548	+	0	NA	Intergenic	L1ME4b|LINE|L1	-73085	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.010444	0.354167	
chunk0041_117_1	chr11	124967955	124968450	+	0	NA	intron (NM_025004, intron 4 of 15)	L1PA6|LINE|L1	14081	NM_025004	80071	Hs.287555	NM_025004	ENSG00000149548	CCDC15	-	coiled-coil domain containing 15	protein-coding	0.022222	0.556452	
chunk0093_222_1	chr19	50024893	50025154	+	0	NA	promoter-TSS (NM_001006656)	promoter-TSS (NM_001006656)	363	NM_001308420	51231	Hs.443330	NM_016440	ENSG00000105053	VRK3	-	VRK serine/threonine kinase 3	protein-coding	0.072797	0.614504	
chunk0168_33_1	chr6	78066682	78066892	+	0	NA	Intergenic	L1MC3|LINE|L1	376131	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.009524	0.336493	
chunk0132_428_1	chr3	164935514	164935756	+	0	NA	Intergenic	Intergenic	-104155	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.004132	0.325103	
chunk0186_234_1	chr7	140673259	140673623	+	0	NA	exon (NM_052853, exon 1 of 8)	exon (NM_052853, exon 1 of 8)	288	NM_052853	90956	Hs.744886	NM_052853	ENSG00000133597	ADCK2	AARF	aarF domain containing kinase 2	protein-coding	0.098901	0.723288	
chunk0087_128_1	chr18	33708889	33709393	+	0	NA	intron (NM_030632, intron 8 of 11)	L1ME3A|LINE|L1	130564	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.001984	0.304950	
chunk0196_149_1	chr8	104589692	104590311	+	0	NA	promoter-TSS (NM_013437)	promoter-TSS (NM_013437)	-977	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.027464	0.461290	
chunk0136_397_1	chr3	197089895	197090168	+	0	NA	intron (NM_004087, intron 16 of 25)	intron (NM_004087, intron 16 of 25)	-60215	NM_005929	4241	Hs.184727	NM_005929	ENSG00000163975	MELTF	CD228|MAP97|MFI2|MTF1|MTf	melanotransferrin	protein-coding	0.010989	0.346715	
chunk0172_271_1	chr6	137570407	137570903	+	0	NA	Intergenic	Intergenic	-76261	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.020161	0.412475	
chunk0147_295_1	chr4	184440418	184440617	+	0	NA	intron (NM_002199, intron 1 of 8)	intron (NM_002199, intron 1 of 8)	34055	NM_002199	3660	Hs.654566	NM_002199	ENSG00000168310	IRF2	IRF-2	interferon regulatory factor 2	protein-coding	0.035176	0.585000	
chunk0192_452_1	chr8	70185400	70185660	+	0	NA	intron (NM_006540, intron 4 of 22)	intron (NM_006540, intron 4 of 22)	-114203	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.019231	0.555556	
chunk0153_338_1	chr5	74148377	74148725	+	0	NA	Intergenic	Intergenic	159774	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.000000	0.487106	
chunk0193_219_1	chr8	76443029	76443228	+	0	NA	intron (NR_105006, intron 2 of 5)	L1M5|LINE|L1	36474	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.000000	0.260000	
chunk0132_354_1	chr3	161420811	161421225	+	0	NA	Intergenic	L2a|LINE|L2	-5409	NR_102265	101243545	Hs.737526	NR_102265	ENSG00000240567	LINC02067	-	long intergenic non-protein coding RNA 2067	ncRNA	0.021739	0.414458	
chunk0033_258_1	chr11	18573827	18574204	+	0	NA	intron (NM_001261382, intron 2 of 10)	intron (NM_001261382, intron 2 of 10)	5503	NM_001261385	55293	Hs.407991	NM_018314	ENSG00000151116	UEVLD	ATTP|UEV3	UEV and lactate/malate dehyrogenase domains	protein-coding	0.005305	0.394180	
chunk0105_313_1	chr2	190467903	190468534	+	0	NA	intron (NM_017694, intron 3 of 7)	intron (NM_017694, intron 3 of 7)	59863	NM_017694	54842	Hs.418581	NM_017694	ENSG00000151690	MFSD6	MMR2|hMMR2	major facilitator superfamily domain containing 6	protein-coding	0.003170	0.395570	313(AAGAACATAATGTCCA,-,0.00),314(AGAACATAATGTCCAT,+,0.00)
chunk0149_361_1	chr5	27796397	27796730	+	0	NA	Intergenic	L1M1|LINE|L1	324271	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.000000	0.500000	
chunk0035_51_1	chr11	41283379	41283962	+	0	NA	intron (NM_001258419, intron 1 of 6)	MER58B|DNA|hAT-Charlie	175966	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005146	0.352740	
chunk0139_281_1	chr4	57100947	57101186	+	0	NA	intron (NM_001253835, intron 1 of 3)	MIRc|SINE|MIR	-8696	NR_034081	255130	Hs.691061	NR_034081	ENSG00000245067	IGFBP7-AS1	-	IGFBP7 antisense RNA 1	ncRNA	0.008368	0.362500	
chunk0038_22_1	chr11	81092412	81092741	+	0	NA	Intergenic	Intergenic	-329773	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.369697	
chunk0047_458_1	chr12	76850876	76851559	+	0	NA	3' UTR (NM_015336, exon 17 of 17)	3' UTR (NM_015336, exon 17 of 17)	27823	NM_001300965	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.010249	0.352339	
chunk0089_320_1	chr18	64850496	64851178	+	0	NA	Intergenic	Intergenic	-590782	NR_033983	400654	Hs.434235	NR_033983	ENSG00000266952	LINC01538	-	long intergenic non-protein coding RNA 1538	ncRNA	0.001466	0.322108	
chunk0127_345_1	chr3	100709392	100709591	+	0	NA	promoter-TSS (NM_001195478)	promoter-TSS (NM_001195478)	-51	NM_001195478	10342	Hs.518123	NM_006070	ENSG00000114354	TFG	HMSNP|SPG57|TF6|TRKT3	trafficking from ER to golgi regulator	protein-coding	0.105528	0.635000	
chunk0095_264_1	chr2	19651273	19651976	+	0	NA	Intergenic	Intergenic	-217230	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.005690	0.394886	
chunk0097_431_1	chr2	63615120	63615614	+	0	NA	Intergenic	LTR19C|LTR|ERV1	26216	NM_001199112	4190	Hs.526521	NM_005917	ENSG00000014641	MDH1	HEL-S-32|MDH-s|MDHA|MGC:1375|MOR2	malate dehydrogenase 1	protein-coding	0.014170	0.478788	
chunk0069_262_1	chr15	64599786	64600028	+	0	NA	intron (NM_015042, intron 1 of 8)	L2b|LINE|L2	100487	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.399177	
chunk0163_434_1	chr6	17366057	17366319	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-27317	NM_006366	10486	Hs.132902	NM_006366	ENSG00000112186	CAP2	-	cyclase associated actin cytoskeleton regulatory protein 2	protein-coding	0.000000	0.357414	
chunk0029_286_1	chr10	103785120	103785358	+	0	NA	intron (NM_014631, intron 2 of 13)	intron (NM_014631, intron 2 of 13)	38460	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.008403	0.606695	65(GGGGCCAGCCTGTCCC,-,0.00),66(GGGCCAGCCTGTCCCT,+,0.00)
chunk0144_80_1	chr4	128064432	128064665	+	0	NA	intron (NM_032239, intron 1 of 8)	intron (NM_032239, intron 1 of 8)	3282	NM_001278604	55132	Hs.654971	NM_018078	ENSG00000138709	LARP1B	LARP2	La ribonucleoprotein domain family member 1B	protein-coding	0.004292	0.337607	
chunk0140_234_1	chr4	71230902	71231101	+	0	NA	intron (NM_001098484, intron 1 of 25)	intron (NM_001098484, intron 1 of 25)	43715	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.010050	0.490000	
chunk0001_149_1	chr1	6058548	6059227	+	0	NA	intron (NM_001199862, intron 2 of 15)	intron (NM_001199862, intron 2 of 15)	12773	NM_001199863	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.026510	0.607353	
chunk0127_267_1	chr3	97565133	97565359	+	0	NA	intron (NM_001080448, intron 11 of 17)	intron (NM_001080448, intron 11 of 17)	125653	NM_173655	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.312775	
chunk0054_366_1	chr13	49792594	49792794	+	0	NA	5' UTR (NM_002267, exon 1 of 17)	5' UTR (NM_002267, exon 1 of 17)	227	NM_002267	3839	Hs.527919	NM_002267	ENSG00000102753	KPNA3	IPOA4|SRP1|SRP1gamma|SRP4|hSRP1	karyopherin subunit alpha 3	protein-coding	0.150000	0.761194	
chunk0167_400_1	chr6	75111442	75111932	+	0	NA	intron (NM_080645, intron 36 of 50)	intron (NM_080645, intron 36 of 50)	94220	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.002041	0.321792	
chunk0054_377_1	chr13	50001308	50001979	+	0	NA	intron (NM_001007278, intron 3 of 3)	intron (NM_001007278, intron 3 of 3)	4636	NM_005798	10206	Hs.436922	NM_005798	ENSG00000204977	TRIM13	CAR|DLEU5|LEU5|RFP2|RNF77	tripartite motif containing 13	protein-coding	0.002981	0.316964	181(GTGAACATTCTGTACT,-,0.00),182(TGAACATTCTGTACTA,+,0.00)
chunk0127_276_1	chr3	97705351	97705748	+	0	NA	intron (NM_001080448, intron 14 of 17)	L2a|LINE|L2	-58972	NR_103511	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.007557	0.376884	
chunk0065_139_1	chr15	25141831	25142334	+	0	NA	Intergenic	MER110-int|LTR|ERV1	6440	NR_022009	145624	Hs.612027	NR_022009	ENSG00000279050	PWAR1	D15S227E|PAR-1|PAR1	Prader Willi/Angelman region RNA 1	ncRNA	0.001988	0.386905	
chunk0105_306_1	chr2	190270254	190270642	+	0	NA	intron (NM_198047, intron 6 of 12)	intron (NM_198047, intron 6 of 12)	49597	NM_198047	26275	Hs.656685	NM_014362	ENSG00000198130	HIBCH	HIBYLCOAH	3-hydroxyisobutyryl-CoA hydrolase	protein-coding	0.005155	0.331620	
chunk0159_104_1	chr5	138543135	138543402	+	0	NA	promoter-TSS (NM_004730)	promoter-TSS (NM_004730)	32	NM_001291975	2107	Hs.483494	NM_004730	ENSG00000120705	ETF1	D5S1995|ERF|ERF1|RF1|SUP45L1|TB3-1	eukaryotic translation termination factor 1	protein-coding	0.101124	0.697761	
chunk0206_1_1	chr9	115525852	115526379	+	0	NA	Intergenic	MIRb|SINE|MIR	218124	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.000000	0.363636	
chunk0028_161_1	chr10	87007307	87007778	+	0	NA	intron (NM_133447, intron 10 of 11)	intron (NM_133447, intron 10 of 11)	-12747	NM_001146157	643161	Hs.729945	NM_001146157	ENSG00000188100	FAM25A	bA96C23.5	family with sequence similarity 25 member A	protein-coding	0.010616	0.362288	
chunk0089_242_1	chr18	62066395	62066631	+	0	NA	intron (NM_176787, intron 30 of 30)	intron (NM_176787, intron 30 of 30)	120543	NM_012327	23556	Hs.157031	NM_012327	ENSG00000197563	PIGN	MCAHS|MCAHS1|MCD4|MDC4|PIG-N	phosphatidylinositol glycan anchor biosynthesis class N	protein-coding	0.012712	0.388186	
chunk0037_271_1	chr11	75718532	75719394	+	0	NA	intron (NM_025098, intron 1 of 5)	MamRep38|DNA|hAT	1074	NM_025098	80168	Hs.288568	NM_025098	ENSG00000166391	MOGAT2	DGAT2L5|DGAT2L5.|MGAT2|hDC5	monoacylglycerol O-acyltransferase 2	protein-coding	0.006961	0.521437	
chunk0051_147_1	chr12	115777490	115778284	+	0	NA	Intergenic	Intergenic	370767	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.006297	0.410063	
chunk0004_379_1	chr1	51795654	51796107	+	0	NA	intron (NM_001101662, intron 22 of 30)	intron (NM_001101662, intron 22 of 30)	40522	NR_031580	100313892		NR_031580	ENSG00000283899	MIR761	hsa-mir-761	microRNA 761	ncRNA	0.002208	0.458150	
chunk0077_354_1	chr16	83802141	83802340	+	0	NA	intron (NR_120308, intron 2 of 2)	intron (NR_120308, intron 2 of 2)	1736	NR_120308	102724163		NR_120308	ENSG00000260228	LOC102724163	-	uncharacterized LOC102724163	ncRNA	0.000000	0.460000	70(AGGAACAAACTGTGTC,-,0.00)
chunk0204_26_1	chr9	92397778	92398511	+	0	NA	intron (NM_014057, intron 3 of 6)	L1MC4a|LINE|L1	6511	NM_033014	4969	Hs.109439	NM_014057	ENSG00000106809	OGN	OG|OIF|SLRR3A	osteoglycin	protein-coding	0.009550	0.314714	
chunk0140_372_1	chr4	74742133	74742578	+	0	NA	Intergenic	Intergenic	52331	NM_001316963	685	Hs.591704	NM_001729	ENSG00000174808	BTC	-	betacellulin	protein-coding	0.002247	0.316143	215(TTGCACATTATGTTCT,-,0.00),216(TGCACATTATGTTCTG,+,0.00)
chunk0121_258_1	chr3	23129763	23130453	+	0	NA	Intergenic	Intergenic	-73185	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005797	0.390738	
chunk0063_120_1	chr14	79315826	79316643	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	36895	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.011016	0.376528	
chunk0207_174_1	chr9	130460204	130460665	+	0	NA	intron (NM_054012, intron 4 of 14)	intron (NM_054012, intron 4 of 14)	15727	NM_000050	445	Hs.160786	NM_000050	ENSG00000130707	ASS1	ASS|CTLN1	argininosuccinate synthase 1	protein-coding	0.010846	0.549784	
chunk0091_357_1	chr19	15303968	15304878	+	0	NA	Intergenic	Intergenic	-23972	NM_058243	23476	Hs.187763	NM_014299	ENSG00000141867	BRD4	CAP|HUNK1|HUNKI|MCAP	bromodomain containing 4	protein-coding	0.017582	0.480790	
chunk0088_253_1	chr18	48930368	48930757	+	0	NA	intron (NM_001190822, intron 3 of 3)	intron (NM_001190822, intron 3 of 3)	12245	NM_001190823	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.028278	0.615385	243(AGGGACAGACTGTCCC,-,0.00),244(GGGACAGACTGTCCCC,+,0.00)
chunk0045_228_1	chr12	48177797	48178285	+	0	NA	Intergenic	Intergenic	-5542	NM_001013635	387856	Hs.251699	NM_001013635	ENSG00000177875	CCDC184	C12orf68	coiled-coil domain containing 184	protein-coding	0.006148	0.404908	
chunk0004_79_1	chr1	43642757	43643385	+	0	NA	Intergenic	L1MB7|LINE|L1	-7055	NM_014663	9682	Hs.155983	NM_014663	ENSG00000066135	KDM4A	JHDM3A|JMJD2|JMJD2A|TDRD14A	lysine demethylase 4A	protein-coding	0.000000	0.330684	
chunk0173_108_1	chr6	143407232	143407914	+	0	NA	Intergenic	L1MC4a|LINE|L1	35104	NM_001286259	134637	Hs.709561	NM_182503	ENSG00000189007	ADAT2	DEADC1|TAD2|dJ20N2|dJ20N2.1	adenosine deaminase tRNA specific 2	protein-coding	0.007331	0.405564	
chunk0076_342_1	chr16	71585264	71585677	+	0	NA	Intergenic	Intergenic	-8375	NM_000353	6898	Hs.161640	NM_000353	ENSG00000198650	TAT	-	tyrosine aminotransferase	protein-coding	0.009685	0.408213	189(TGGAACTTAGTGTTCC,-,0.00),190(GGAACTTAGTGTTCCT,+,0.00)
chunk0132_282_1	chr3	159866087	159866559	+	0	NA	intron (NM_001197107, intron 3 of 7)	intron (NM_001197107, intron 3 of 7)	26462	NM_001197109	29970	Hs.134665	NM_014575	ENSG00000151967	SCHIP1	SCHIP-1	schwannomin interacting protein 1	protein-coding	0.006356	0.380550	
chunk0144_376_1	chr4	140019691	140020260	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	134104	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.005272	0.403509	
chunk0018_211_1	chr1	219518086	219518692	+	0	NA	Intergenic	Intergenic	343420	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.001650	0.392092	
chunk0144_367_1	chr4	139886823	139887652	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	221469	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.015682	0.356627	538(AAGAACATTCTGTCCA,-,0.00),539(AGAACATTCTGTCCAC,+,0.00)
chunk0050_362_1	chr12	107903690	107904027	+	0	NA	promoter-TSS (NR_037629)	promoter-TSS (NR_037629)	-87	NR_037629	728739	Hs.741995	NR_037629		LOC728739	-	programmed cell death 2 pseudogene	pseudo	0.115727	0.710059	
chunk0029_30_1	chr10	95938038	95938326	+	0	NA	exon (NM_001130446, exon 8 of 8)	exon (NM_001130446, exon 8 of 8)	30217	NM_001130446	387707	Hs.652240	NM_001001732	ENSG00000188649	CC2D2B	C10orf130|C10orf131	coiled-coil and C2 domain containing 2B	protein-coding	0.003472	0.280277	
chunk0198_74_1	chr8	130015288	130015629	+	0	NA	intron (NR_046360, intron 1 of 14)	MIRc|SINE|MIR	1193	NR_046360									0.029326	0.561404	
chunk0141_146_1	chr4	81377177	81377714	+	0	NA	Intergenic	MamRep38|DNA|hAT	94483	NM_001300736	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.001862	0.395911	260(CTGGACAGACTGTACT,-,0.00),261(TGGACAGACTGTACTG,+,0.00)
chunk0016_10_1	chr1	192749419	192750025	+	0	NA	Intergenic	Intergenic	33394	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.000000	0.350906	
chunk0014_196_1	chr1	179012046	179012482	+	0	NA	Intergenic	L1ME3|LINE|L1	-13675	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.004587	0.416476	
chunk0045_309_1	chr12	50659880	50660513	+	0	NA	exon (NM_173602, exon 4 of 38)	exon (NM_173602, exon 4 of 38)	-103810	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.009479	0.394322	
chunk0062_261_1	chr14	71659211	71659551	+	0	NA	intron (NM_001284245, intron 6 of 20)	intron (NM_001284245, intron 6 of 20)	71810	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.000000	0.328446	
chunk0153_111_1	chr5	68549277	68549776	+	0	NA	Intergenic	Intergenic	256958	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.022044	0.480000	
chunk0151_103_1	chr5	43326118	43326437	+	0	NA	Intergenic	L1PA6|LINE|L1	-12765	NM_002130	3157	Hs.397729	NM_002130	ENSG00000112972	HMGCS1	HMGCS	3-hydroxy-3-methylglutaryl-CoA synthase 1	protein-coding	0.003135	0.409375	
chunk0166_208_1	chr6	46757722	46758122	+	0	NA	intron (NM_001162435, intron 4 of 4)	L2a|LINE|L2	11005	NM_001162435	100287718	Hs.736491	NM_001162435	ENSG00000230062	ANKRD66	-	ankyrin repeat domain 66	protein-coding	0.002500	0.374065	
chunk0105_28_1	chr2	182109098	182109308	+	0	NA	intron (NM_001080545, intron 4 of 4)	L1MC|LINE|L1	123379	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.004762	0.355450	
chunk0200_119_1	chr9	17117258	17117737	+	0	NA	Intergenic	L2c|LINE|L2	-17494	NM_001114395	54875	Hs.435381	NM_017738	ENSG00000044459	CNTLN	C9orf101|C9orf39|bA340N12.1	centlein	protein-coding	0.008351	0.385417	
chunk0099_410_1	chr2	102161376	102161755	+	0	NA	intron (NM_000877, intron 3 of 11)	L1MEc|LINE|L1	18789	NM_000877	3554	Hs.701982	NM_000877	ENSG00000115594	IL1R1	CD121A|D2S1473|IL-1R-alpha|IL1R|IL1RA|P80	interleukin 1 receptor type 1	protein-coding	0.005277	0.328947	
chunk0002_225_1	chr1	19987677	19988047	+	0	NA	Intergenic	L1MC4a|LINE|L1	-7423	NM_001161728	5320	Hs.466804	NM_000300	ENSG00000188257	PLA2G2A	MOM1|PLA2|PLA2B|PLA2L|PLA2S|PLAS1|sPLA2	phospholipase A2 group IIA	protein-coding	0.002703	0.366577	
chunk0166_329_1	chr6	49906598	49907319	+	0	NA	Intergenic	Intergenic	-29862	NM_001205220	167	Hs.109620	NM_001131	ENSG00000124812	CRISP1	AEGL1|ARP|CRISP-1|HEL-S-57|HSCRISP1D|HSCRISP1G|HUMARP	cysteine rich secretory protein 1	protein-coding	0.002774	0.383657	
chunk0134_90_1	chr3	176738921	176739558	+	0	NA	Intergenic	LTR40A1|LTR|ERVL	77762	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.003140	0.371473	
chunk0082_241_1	chr17	57363905	57364371	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	107125	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.010730	0.475375	276(AAGAACAGCAAGACCT,-,0.00)
chunk0170_261_1	chr6	113857352	113857642	+	0	NA	5' UTR (NM_002356, exon 1 of 2)	5' UTR (NM_002356, exon 1 of 2)	162	NM_002356	4082	Hs.519909	NM_002356	ENSG00000277443	MARCKS	80K-L|MACS|PKCSL|PRKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.037931	0.474227	
chunk0011_295_1	chr1	151539709	151539959	+	0	NA	promoter-TSS (NM_001126337)	promoter-TSS (NM_001126337)	-471	NM_020127	7286	Hs.489922	NM_020127	ENSG00000143367	TUFT1	-	tuftelin 1	protein-coding	0.016000	0.557769	
chunk0075_258_1	chr16	53464089	53464647	+	0	NA	intron (NM_005611, intron 12 of 21)	intron (NM_005611, intron 12 of 21)	29929	NM_005611	5934	Hs.513609	NM_005611	ENSG00000103479	RBL2	P130|Rb2	RB transcriptional corepressor like 2	protein-coding	0.003584	0.302326	
chunk0002_183_1	chr1	19079828	19080372	+	0	NA	intron (NM_020765, intron 103 of 105)	intron (NM_020765, intron 103 of 105)	-123768	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.007353	0.456881	
chunk0144_245_1	chr4	135368903	135369306	+	0	NA	Intergenic	MER41A|LTR|ERV1	518989	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.007444	0.400990	
chunk0105_87_1	chr2	184046267	184046508	+	0	NA	Intergenic	Intergenic	-332588	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.004149	0.297521	141(AGGGACATCTTGTCTT,-,0.00)
chunk0038_447_1	chr11	94788388	94788755	+	0	NA	intron (NM_001301007, intron 1 of 11)	intron (NM_001301007, intron 1 of 11)	20229	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.013624	0.434783	
chunk0180_211_1	chr7	66694179	66694417	+	0	NA	intron (NM_001287060, intron 1 of 9)	intron (NM_001287060, intron 1 of 9)	12207	NM_001287060	27342	Hs.530053	NM_014504	ENSG00000154710	RABGEF1	RABEX5|RAP1|rabex-5	RAB guanine nucleotide exchange factor 1	protein-coding	0.029412	0.552301	
chunk0116_225_1	chr21	38129744	38130063	+	0	NA	intron (NR_026839, intron 2 of 2)	L2b|LINE|L2	8452	NR_026841	84677	Hs.733345	NM_032589	ENSG00000198054	DSCR8	C21orf65|CT25.1a|CT25.1b|MMA-1|MMA-1a|MMA-1b|MMA1|MTAG2	Down syndrome critical region 8	ncRNA	0.000000	0.384375	
chunk0061_399_1	chr14	64632694	64632922	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-71600	NM_001308147	26030	Hs.509637	NM_015549	ENSG00000126822	PLEKHG3	ARHGEF43|KIAA0599	pleckstrin homology and RhoGEF domain containing G3	protein-coding	0.000000	0.436681	
chunk0014_352_1	chr1	182315289	182315558	+	0	NA	Intergenic	Intergenic	-1362	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.018587	0.507407	
chunk0151_405_1	chr5	55584907	55585783	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	-50267	NM_003711	8611	Hs.696231	NM_003711	ENSG00000067113	PLPP1	LLP1a|LPP1|PAP-2a|PAP2|PPAP2A	phospholipid phosphatase 1	protein-coding	0.002283	0.472064	
chunk0052_378_1	chr12	128954815	128955418	+	0	NA	intron (NR_133646, intron 9 of 10)	MIR|SINE|MIR	101682	NM_144669	144423	Hs.655668	NM_144669	ENSG00000151948	GLT1D1	-	glycosyltransferase 1 domain containing 1	protein-coding	0.006633	0.465232	
chunk0073_231_1	chr16	11296967	11297384	+	0	NA	Intergenic	L1ME2|LINE|L1	9352	NR_031678	100313773		NR_031678	ENSG00000221801	MIR548H2	MIR548H-2|MIRN548H2	microRNA 548h-2	ncRNA	0.016787	0.444976	
chunk0180_174_1	chr7	65429786	65430359	+	0	NA	Intergenic	(GTGACAC)n|Simple_repeat|Simple_repeat	56273	NM_152626	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.034904	0.468641	
chunk0108_362_1	chr2	236578099	236578498	+	0	NA	intron (NM_020311, intron 1 of 1)	intron (NM_020311, intron 1 of 1)	8561	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.027569	0.592500	128(CAGGACAGGGTGTCCT,-,0.00),129(AGGACAGGGTGTCCTC,+,0.00)
chunk0011_1_1	chr1	125149778	125150035	+	0	NA	Intergenic	Intergenic	3630794	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.054475	0.352713	
chunk0116_183_1	chr21	36861231	36861430	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	105326	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.010050	0.445000	
chunk0075_384_1	chr16	56715144	56715456	+	0	NA	Intergenic	Intergenic	-14805	NM_014669	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.009615	0.501597	
chunk0105_42_1	chr2	182913025	182913224	+	0	NA	Intergenic	Intergenic	-46354	NM_001463	2487	Hs.128453	NM_001463	ENSG00000162998	FRZB	FRE|FRITZ|FRP-3|FRZB-1|FRZB-PEN|FRZB1|FZRB|OS1|SFRP3|SRFP3|hFIZ	frizzled related protein	protein-coding	0.005025	0.385000	179(TAGGACACTATGTCCT,-,0.00),180(AGGACACTATGTCCTG,+,0.00)
chunk0171_290_1	chr6	128336017	128336473	+	0	NA	intron (NM_001291981, intron 2 of 32).2	intron (NM_001291981, intron 2 of 32).2	184429	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.004386	0.356674	
chunk0196_100_1	chr8	103046594	103047268	+	0	NA	intron (NM_001695, intron 3 of 12)	intron (NM_001695, intron 3 of 12)	25911	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.007418	0.351111	
chunk0205_57_1	chr9	106565262	106565461	+	0	NA	Intergenic	L1PA8A|LINE|L1	-35567	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.025126	0.570000	
chunk0033_252_1	chr11	18260269	18260580	+	0	NA	Intergenic	Intergenic	-5837	NM_000331	6288	Hs.632144	NM_000331	ENSG00000173432	SAA1	PIG4|SAA|SAA2|TP53I4	serum amyloid A1	protein-coding	0.016077	0.477564	
chunk0154_263_1	chr5	81851646	81852277	+	0	NA	Intergenic	Intergenic	-100708	NM_001256735	23635	Hs.102735	NM_012446	ENSG00000145687	SSBP2	HSPC116|SOSS-B2	single stranded DNA binding protein 2	protein-coding	0.049128	0.525316	
chunk0142_431_1	chr4	104878351	104878921	+	0	NA	Intergenic	Intergenic	-267239	NM_017628	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.001754	0.309982	
chunk0066_131_1	chr15	31100662	31101053	+	0	NA	intron (NM_001252024, intron 1 of 27)	L1ME3Cz|LINE|L1	869	NM_001252024	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.017903	0.469388	
chunk0130_449_1	chr3	141377241	141377967	+	0	NA	intron (NM_001080412, intron 3 of 7)	L1MD2|LINE|L1	53391	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.008264	0.419532	
chunk0087_122_1	chr18	33102820	33103143	+	0	NA	intron (NM_001308126, intron 19 of 22)	MER58A|DNA|hAT-Charlie	-329970	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.003096	0.370370	
chunk0005_203_1	chr1	59071144	59071819	+	0	NA	intron (NR_110626, intron 2 of 2)	LTR50|LTR|ERVL	51005	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.011852	0.446746	
chunk0093_309_1	chr19	53519361	53519890	+	0	NA	Intergenic	LTR46|LTR|ERV1	-1298	NM_018555	55422	Hs.185674	NM_018555	ENSG00000130844	ZNF331	RITA|ZNF361|ZNF463	zinc finger protein 331	protein-coding	0.017013	0.515094	
chunk0185_2_1	chr7	123734971	123735272	+	0	NA	intron (NM_003941, intron 1 of 10)	HAL1ME|LINE|L1	13950	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.000000	0.298013	
chunk0207_211_1	chr9	131383075	131383540	+	0	NA	Intergenic	Intergenic	-46783	NM_013318	84726	Hs.743955	NM_013318	ENSG00000130723	PRRC2B	BAT2L|BAT2L1|KIAA0515|LQFBS-1	proline rich coiled-coil 2B	protein-coding	0.015054	0.502146	
chunk0192_458_1	chr8	70270401	70271081	+	0	NA	intron (NM_006540, intron 2 of 22)	intron (NM_006540, intron 2 of 22)	133044	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.008824	0.327460	
chunk0032_419_1	chr11	12070158	12070960	+	0	NA	Intergenic	Intergenic	-40017	NM_001282663	9645	Hs.501928	NM_014632	ENSG00000133816	MICAL2	MICAL-2|MICAL2PV1|MICAL2PV2	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding	0.016209	0.514321	318(AGGTTCAGAGTGTTCT,-,0.00),319(GGTTCAGAGTGTTCTG,+,0.00),410(GGGAACACATTGTCCC,-,0.00),411(GGAACACATTGTCCCC,+,0.00)
chunk0051_18_1	chr12	111775680	111776125	+	0	NA	intron (NM_000690, intron 1 of 12)	intron (NM_000690, intron 1 of 12)	9015	NM_000690	217	Hs.604551	NM_000690	ENSG00000111275	ALDH2	ALDH-E2|ALDHI|ALDM	aldehyde dehydrogenase 2 family member	protein-coding	0.022472	0.526906	353(GAGAACATTCTGGGCT,-,0.00),354(AGAACATTCTGGGCTT,+,0.00)
chunk0132_422_1	chr3	164599380	164600132	+	0	NA	Intergenic	Intergenic	231724	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.002660	0.321381	
chunk0102_10_1	chr2	141336720	141337186	+	0	NA	intron (NM_018557, intron 3 of 90)	L1ME1|LINE|L1	-750268	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.002146	0.351178	
chunk0187_119_1	chr7	148950848	148951170	+	0	NA	Intergenic	L2c|LINE|L2	9521	NR_001571	6090		NR_001571		RNY5	Y5|hY5	RNA, Ro60-associated Y5	ncRNA	0.012422	0.390093	
chunk0040_180_1	chr11	114040722	114041300	+	0	NA	Intergenic	Intergenic	-18698	NM_006006	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.013841	0.481865	
chunk0115_436_1	chr21	31972597	31973045	+	0	NA	intron (NM_014586, intron 6 of 10)	intron (NM_014586, intron 6 of 10)	99506	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.015625	0.443207	
chunk0192_324_1	chr8	67100938	67101571	+	0	NA	intron (NM_001291339, intron 4 of 25)	MER68|LTR|ERVL	17406	NM_001291339	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.004739	0.399054	
chunk0093_228_1	chr19	50300912	50301494	+	0	NA	intron (NM_001077186, intron 38 of 41)	MER5A|DNA|hAT-Charlie	28174	NM_004977	3748	Hs.467146	NM_004977	ENSG00000131398	KCNC3	KSHIIID|KV3.3|SCA13	potassium voltage-gated channel subfamily C member 3	protein-coding	0.013746	0.411664	
chunk0182_414_1	chr7	101021740	101022126	+	0	NA	intron (NM_001040105, intron 1 of 12)	intron (NM_001040105, intron 1 of 12)	1850	NM_001040105	140453	Hs.271819	NM_001004430	ENSG00000169876	MUC17	MUC-17|MUC-3|MUC3	mucin 17, cell surface associated	protein-coding	0.005181	0.596899	212(CAAAACACAATGTCCT,-,0.00),213(AAAACACAATGTCCTG,+,0.00)
chunk0105_365_1	chr2	191932033	191932758	+	0	NA	Intergenic	Intergenic	-85115	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.001379	0.349862	
chunk0188_356_1	chr8	17977648	17977847	+	0	NA	intron (NM_001315508, intron 23 of 35)	L1MEj|LINE|L1	54890	NM_001315508	5108	Hs.491148	NM_006197	ENSG00000078674	PCM1	PTC4|RET/PCM-1	pericentriolar material 1	protein-coding	0.005025	0.460000	
chunk0183_402_1	chr7	110346217	110346443	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-386117	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.334802	
chunk0206_295_1	chr9	124632200	124632748	+	0	NA	intron (NM_033334, intron 2 of 9)	L1PA12|LINE|L1	-25962	NR_038975	100379345	Hs.660412	NR_038975	ENSG00000224020	MIR181A2HG	-	MIR181A2 host gene	ncRNA	0.007299	0.364299	
chunk0025_290_1	chr10	56797776	56798385	+	0	NA	Intergenic	Intergenic	-436807	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.001642	0.301639	
chunk0121_384_1	chr3	25229627	25230038	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	55500	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.004866	0.405340	
chunk0055_310_1	chr13	66394922	66395255	+	0	NA	intron (NM_203487, intron 4 of 4)	intron (NM_203487, intron 4 of 4)	176838	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.000000	0.329341	
chunk0077_288_1	chr16	81273998	81274249	+	0	NA	intron (NM_017429, intron 7 of 10)	intron (NM_017429, intron 7 of 10)	35432	NM_017429	53630	Hs.212172	NM_017429	ENSG00000135697	BCO1	BCDO|BCDO1|BCMO|BCMO1|BCO	beta-carotene oxygenase 1	protein-coding	0.011952	0.511905	
chunk0046_301_1	chr12	62267626	62268037	+	0	NA	intron (NM_006313, intron 1 of 20)	intron (NM_006313, intron 1 of 20)	7472	NR_106740	102465133		NR_106740	ENSG00000284360	MIR6125	hsa-mir-6125|mir-6125	microRNA 6125	ncRNA	0.002433	0.361650	
chunk0037_114_1	chr11	72431077	72431359	+	0	NA	intron (NM_030813, intron 1 of 16)	intron (NM_030813, intron 1 of 16)	3466	NM_001258394	81570	Hs.523877	NM_030813	ENSG00000162129	CLPB	ANKCLB|HSP78|MEGCANN|MGCA7|SKD3	ClpB homolog, mitochondrial AAA ATPase chaperonin	protein-coding	0.010638	0.526502	
chunk0209_230_1	chrX	45202158	45202668	+	0	NA	Intergenic	MER57E1|LTR|ERV1	-1512	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.001961	0.334638	
chunk0056_414_1	chr13	94305563	94305896	+	0	NA	intron (NM_005708, intron 5 of 8)	Tigger17a|DNA|TcMar-Tigger	-117738	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.000000	0.347305	
chunk0098_83_1	chr2	67516071	67516669	+	0	NA	Intergenic	Intergenic	119060	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.015050	0.407346	
chunk0009_85_1	chr1	101157221	101157420	+	0	NA	Intergenic	L1ME4a|LINE|L1	79208	NR_104626	101928370	Hs.534209	NR_104626		LOC101928370	-	uncharacterized LOC101928370	ncRNA	0.000000	0.280000	
chunk0179_278_1	chr7	49480438	49480737	+	0	NA	Intergenic	Intergenic	-293074	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.003344	0.320000	
chunk0038_48_1	chr11	82536590	82537142	+	0	NA	Intergenic	Intergenic	-132953	NR_120571	101928989	Hs.145117	NR_120571	ENSG00000245832	MIR4300HG	-	MIR4300 host gene	ncRNA	0.005435	0.390597	
chunk0126_97_1	chr3	74872441	74872860	+	0	NA	Intergenic	Intergenic	-341826	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.000000	0.290476	
chunk0105_247_1	chr2	188656339	188656761	+	0	NA	Intergenic	Intergenic	133554	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.009479	0.390071	171(AGGTACTCTCTGTTCC,-,0.00),172(GGTACTCTCTGTTCCT,+,0.00),262(CAGCACAGAAAGTCCT,-,0.00),263(AGCACAGAAAGTCCTG,+,0.00)
chunk0061_77_1	chr14	56682921	56683676	+	0	NA	Intergenic	L1MC2|LINE|L1	103505	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.010596	0.379630	
chunk0165_321_1	chr6	37148128	37148327	+	0	NA	Intergenic	Intergenic	-21919	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.000000	0.430000	
chunk0139_421_1	chr4	64122129	64122592	+	0	NA	Intergenic	L1PA13|LINE|L1	287100	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.008639	0.573276	
chunk0010_356_1	chr1	118797995	118798397	+	0	NA	Intergenic	L1MA7|LINE|L1	191360	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.004975	0.349876	
chunk0201_10_1	chr9	32401707	32401906	+	0	NA	intron (NM_001278352, intron 2 of 21)	intron (NM_001278352, intron 2 of 21)	17203	NM_001278352	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.005025	0.440000	
chunk0035_231_1	chr11	45843588	45843820	+	0	NA	Intergenic	Intergenic	-3414	NM_001127457	1408	Hs.532491	NM_021117	ENSG00000121671	CRY2	HCRY2|PHLL2	cryptochrome circadian regulator 2	protein-coding	0.004310	0.377682	
chunk0129_21_1	chr3	117122513	117123136	+	0	NA	Intergenic	Intergenic	201393	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.004815	0.310897	
chunk0031_327_1	chr10	129271819	129272395	+	0	NA	Intergenic	Intergenic	-195077	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.022569	0.478336	339(CAGCACACGGTGTCAC,-,0.00)
chunk0159_39_1	chr5	137059657	137059866	+	0	NA	intron (NM_004598, intron 6 of 10)	L1PA15|LINE|L1	439568	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.000000	0.328571	
chunk0113_34_1	chr20	49832587	49832834	+	0	NA	intron (NM_015266, intron 3 of 15)	intron (NM_015266, intron 3 of 15)	19997	NR_048538	23315	Hs.444202	NM_015266	ENSG00000197818	SLC9A8	NHE-8|NHE8	solute carrier family 9 member A8	protein-coding	0.012146	0.483871	
chunk0013_91_1	chr1	167697637	167698209	+	0	NA	intron (NM_052862, intron 6 of 6)	intron (NM_052862, intron 6 of 6)	-24027	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.024476	0.595113	245(AGGGCCAGTGTGTGCC,-,0.00),246(GGGCCAGTGTGTGCCT,+,0.00)
chunk0050_368_1	chr12	108232727	108232952	+	0	NA	exon (NM_001304447, exon 8 of 10)	exon (NM_001304447, exon 8 of 10)	87823	NM_001142345	1240	Hs.197143	NM_004072	ENSG00000174600	CMKLR1	CHEMERINR|ChemR23|DEZ|RVER1	chemerin chemokine-like receptor 1	protein-coding	0.017778	0.579646	
chunk0056_164_1	chr13	84697534	84697919	+	0	NA	Intergenic	L1PA10|LINE|L1	-85928	NR_132852	106635542		NR_132852		SNORA107	-	small nucleolar RNA, H/ACA box 107	snoRNA	0.002597	0.362694	
chunk0155_351_1	chr5	97097038	97097727	+	0	NA	intron (NM_153234, intron 4 of 5)	L1ME4b|LINE|L1	45434	NM_153234	167410	Hs.656702	NM_153234	ENSG00000145721	LIX1	C5orf11|Lft	limb and CNS expressed 1	protein-coding	0.005806	0.327536	
chunk0173_102_1	chr6	143220003	143220486	+	0	NA	intron (NM_001286587, intron 4 of 6)	L2a|LINE|L2	159402	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.010352	0.440083	
chunk0045_222_1	chr12	48109702	48110249	+	0	NA	intron (NM_001166686, intron 3 of 24)	L2b|LINE|L2	-3667	NM_001267594	29843	Hs.371957	NM_014554	ENSG00000079387	SENP1	SuPr-2	SUMO specific peptidase 1	protein-coding	0.001828	0.434307	
chunk0070_144_1	chr15	71078883	71079782	+	0	NA	Intergenic	Intergenic	36168	NM_001102658	196993	Hs.646533	NM_001102658	ENSG00000225362	CT62	-	cancer/testis antigen 62	protein-coding	0.007786	0.413333	
chunk0182_164_1	chr7	95547927	95548521	+	0	NA	Intergenic	L1ME2|LINE|L1	48389	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.003367	0.331092	
chunk0132_288_1	chr3	159992661	159992933	+	0	NA	intron (NM_000882, intron 2 of 6)	intron (NM_000882, intron 2 of 6)	3961	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.003676	0.424908	
chunk0125_236_1	chr3	68350495	68350785	+	0	NA	intron (NM_213609, intron 2 of 4)	intron (NM_213609, intron 2 of 4)	346424	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.003448	0.360825	
chunk0033_384_1	chr11	23866716	23866999	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-447667	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.003534	0.454225	
chunk0076_348_1	chr16	71663743	71664033	+	0	NA	intron (NM_001289003, intron 12 of 17)	intron (NM_001289003, intron 12 of 17)	34813	NR_033337	100379141	Hs.725116	NR_033337	ENSG00000263666	SNORA70D	U70D	small nucleolar RNA, H/ACA box 70D	snoRNA	0.010345	0.391753	
chunk0025_76_1	chr10	50325415	50325682	+	0	NA	intron (NM_147156, intron 8 of 10)	intron (NM_147156, intron 8 of 10)	-76938	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.011236	0.429104	
chunk0172_114_1	chr6	135073102	135073373	+	0	NA	Intergenic	Intergenic	-18339	NM_001145207	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.003690	0.411765	
chunk0118_301_1	chr22	34971008	34971766	+	0	NA	Intergenic	Intergenic	-94749	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.003958	0.458498	217(AAGAACTTGGAGTTCC,-,0.00),218(AGAACTTGGAGTTCCC,+,0.00)
chunk0027_81_1	chr10	73495902	73496368	+	0	NA	promoter-TSS (NM_001289969)	promoter-TSS (NM_001289969)	-111	NM_001289968	5532	Hs.500067	NM_021132	ENSG00000107758	PPP3CB	CALNA2|CALNB|CNA2|PP2Bbeta	protein phosphatase 3 catalytic subunit beta	protein-coding	0.053648	0.556745	
chunk0126_425_1	chr3	86694536	86694739	+	0	NA	Intergenic	HERV30-int|LTR|ERV1	296470	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.019704	0.519608	
chunk0080_301_1	chr17	31576357	31576722	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	1128	NR_029856	100126356		NR_029856	ENSG00000283978	MIR365B	MIR365-2|MIRN365-2|hsa-mir-365b|mir-365b	microRNA 365b	ncRNA	0.016438	0.483607	
chunk0075_252_1	chr16	53411269	53411748	+	0	NA	Intergenic	L1MC3|LINE|L1	-22931	NM_005611	5934	Hs.513609	NM_005611	ENSG00000103479	RBL2	P130|Rb2	RB transcriptional corepressor like 2	protein-coding	0.002088	0.339583	
chunk0134_24_1	chr3	175512593	175513212	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	143362	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.006462	0.383871	446(TTGAACATGCTGTTCT,-,0.00),447(TGAACATGCTGTTCTG,+,0.00)
chunk0045_340_1	chr12	51222326	51222957	+	0	NA	Intergenic	L2a|LINE|L2	-4948	NR_026893	5463	Hs.555886	NM_002702	ENSG00000184271	POU6F1	BRN5|MPOU|TCFB1	POU class 6 homeobox 1	protein-coding	0.026941	0.454114	
chunk0021_193_1	chr10	5762534	5762970	+	0	NA	intron (NM_017782, intron 20 of 20)	intron (NM_017782, intron 20 of 20)	50797	NM_001115156	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.006881	0.338673	
chunk0208_146_1	chrX	15991272	15991631	+	0	NA	Intergenic	L1ME2z|LINE|L1	-131850	NM_005314	2925	Hs.567282	NM_005314	ENSG00000126010	GRPR	BB2|BB2R	gastrin releasing peptide receptor	protein-coding	0.000000	0.319444	
chunk0060_114_1	chr14	43641033	43641289	+	0	NA	Intergenic	L1PB2|LINE|L1	866135	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.000000	0.361868	87(TAGGACACAGTGAACT,-,0.00),88(AGGACACAGTGAACTT,+,0.00)
chunk0162_144_1	chr6	3310531	3311268	+	0	NA	intron (NM_015482, intron 4 of 9)	intron (NM_015482, intron 4 of 9)	51971	NM_001135750	389362	Hs.207069	NM_001128591	ENSG00000180822	PSMG4	C6orf86|PAC4|bA506K6.2	proteasome assembly chaperone 4	protein-coding	0.017639	0.436314	
chunk0166_202_1	chr6	46645364	46645618	+	0	NA	intron (NM_016593, intron 1 of 11)	L1MD1|LINE|L1	7339	NM_001278739	51302	Hs.387367	NM_016593	ENSG00000146233	CYP39A1	-	cytochrome P450 family 39 subfamily A member 1	protein-coding	0.003937	0.345098	
chunk0188_198_1	chr8	11844160	11844359	+	0	NA	3' UTR (NM_147783, exon 11 of 11)	3' UTR (NM_147783, exon 11 of 11)	23878	NM_147783	1508	Hs.520898	NM_001908	ENSG00000164733	CTSB	APPS|CPSB|RECEUP	cathepsin B	protein-coding	0.015075	0.465000	53(AAGAACATGCAGTTCC,-,0.00),54(AGAACATGCAGTTCCA,+,0.00)
chunk0069_268_1	chr15	64669021	64669263	+	0	NA	intron (NM_015042, intron 2 of 8)	L1ME4b|LINE|L1	34139	NM_001301302	4947	Hs.744924	NM_002537	ENSG00000180304	OAZ2	AZ2	ornithine decarboxylase antizyme 2	protein-coding	0.004132	0.366255	
chunk0134_427_1	chr3	183409170	183409802	+	0	NA	intron (NM_015078, intron 1 of 29)	MIRb|SINE|MIR	18783	NM_015078	23101	Hs.208267	NM_015078	ENSG00000053524	MCF2L2	ARHGEF22	MCF.2 cell line derived transforming sequence-like 2	protein-coding	0.006329	0.382306	
chunk0086_180_1	chr18	21865710	21866108	+	0	NA	3' UTR (NM_020774, exon 21 of 21)	3' UTR (NM_020774, exon 21 of 21)	-34503	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.002513	0.298246	
chunk0050_431_1	chr12	110230635	110231011	+	0	NA	Intergenic	Intergenic	-50404	NM_170665	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.002660	0.347480	
chunk0001_100_1	chr1	3352376	3352974	+	0	NA	intron (NM_022114, intron 3 of 16)	intron (NM_022114, intron 3 of 16)	-101908	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.046823	0.585977	242(CAGCACAGCTTGTTCC,-,0.00),243(AGCACAGCTTGTTCCC,+,0.00)
chunk0143_49_1	chr4	107640173	107640522	+	0	NA	intron (NM_005443, intron 10 of 11)	intron (NM_005443, intron 10 of 11)	79916	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.005731	0.337143	
chunk0107_83_1	chr2	212915399	212915736	+	0	NA	Intergenic	Intergenic	-10690	NR_039935	100616267		NR_039935	ENSG00000266354	MIR4776-1	mir-4776-1	microRNA 4776-1	ncRNA	0.005935	0.393491	
chunk0092_295_1	chr19	34218270	34218684	+	0	NA	intron (NM_015578, intron 6 of 9).2	intron (NM_015578, intron 6 of 9).2	-36074	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.019324	0.409639	
chunk0048_183_1	chr12	80968269	80968710	+	0	NA	Intergenic	Intergenic	-30574	NM_004664	8825	Hs.144333	NM_004664	ENSG00000111052	LIN7A	LIN-7A|LIN7|MALS-1|MALS1|TIP-33|VELI1	lin-7 homolog A, crumbs cell polarity complex component	protein-coding	0.000000	0.361991	
chunk0152_180_1	chr5	59748696	59749154	+	0	NA	intron (NM_001165899, intron 3 of 16)	MLT1F|LTR|ERVL-MaLR	19687	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.008734	0.418301	123(AAGAACACCCAGCCCT,-,0.00),124(AGAACACCCAGCCCTT,+,0.00)
chunk0128_244_1	chr3	108548862	108549253	+	0	NA	TTS (NM_020890)	TTS (NM_020890)	-19735	NM_014981	22989	Hs.731060	NM_014981	ENSG00000144821	MYH15	-	myosin heavy chain 15	protein-coding	0.005115	0.303571	
chunk0098_25_1	chr2	65505448	65505747	+	0	NA	Intergenic	L1MC5a|LINE|L1	-73075	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.016722	0.503333	
chunk0071_236_1	chr15	85165191	85165580	+	0	NA	Intergenic	MER11A|LTR|ERVK	39902	NR_049748									0.005141	0.400000	
chunk0171_76_1	chr6	121612929	121613128	+	0	NA	Intergenic	Intergenic	177451	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.010050	0.340000	
chunk0072_29_1	chr16	690320	690597	+	0	NA	promoter-TSS (NM_032259)	promoter-TSS (NM_032259)	-34	NM_032259	84219	Hs.459632	NM_032259	ENSG00000127580	WDR24	C16orf21|JFP7	WD repeat domain 24	protein-coding	0.090253	0.647482	
chunk0121_252_1	chr3	22991015	22991325	+	0	NA	Intergenic	Intergenic	-212123	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.029032	0.543408	
chunk0140_378_1	chr4	74894848	74895218	+	0	NA	Intergenic	Intergenic	-38042	NM_015393	25849	Hs.105460	NM_015393	ENSG00000169116	PARM1	Cipar1|DKFZP564O0823|PARM-1|WSC4	prostate androgen-regulated mucin-like protein 1	protein-coding	0.005405	0.320755	177(GGGAACATGAAGTCCT,-,0.00),178(GGAACATGAAGTCCTC,+,0.00)
chunk0146_174_1	chr4	160495846	160496708	+	0	NA	Intergenic	L1MEd|LINE|L1	1228431	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.011601	0.363847	
chunk0089_248_1	chr18	62176560	62176964	+	0	NA	intron (NM_176787, intron 1 of 30)	intron (NM_176787, intron 1 of 30)	10294	NM_012327	23556	Hs.157031	NM_012327	ENSG00000197563	PIGN	MCAHS|MCAHS1|MCD4|MDC4|PIG-N	phosphatidylinositol glycan anchor biosynthesis class N	protein-coding	0.004950	0.316049	
chunk0177_419_1	chr7	27734149	27734370	+	0	NA	Intergenic	Intergenic	-5114	NM_001206901	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.009050	0.369369	
chunk0009_23_1	chr1	100132746	100133293	+	0	NA	promoter-TSS (NM_194292)	promoter-TSS (NM_194292)	76	NM_194292	163786	Hs.591447	NM_194292	ENSG00000156876	SASS6	MCPH14|SAS-6|SAS6	SAS-6 centriolar assembly protein	protein-coding	0.063985	0.571168	
chunk0016_394_1	chr1	203099651	203100202	+	0	NA	Intergenic	Intergenic	-13888	NM_002479	4656	Hs.2830	NM_002479	ENSG00000122180	MYOG	MYF4|bHLHc3|myf-4	myogenin	protein-coding	0.005445	0.516304	305(GGGAACACTGTGTTCC,-,0.00),306(GGAACACTGTGTTCCA,+,0.00)
chunk0074_135_1	chr16	22781118	22781589	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-33186	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.023355	0.425847	
chunk0010_198_1	chr1	116038638	116039222	+	0	NA	intron (NM_018420, intron 8 of 11)	intron (NM_018420, intron 8 of 11)	-61654	NR_125970	101928977	Hs.627914	NR_125970		LOC101928977	-	uncharacterized LOC101928977	ncRNA	0.006849	0.403419	
chunk0126_36_1	chr3	73743350	73744053	+	0	NA	Intergenic	Intergenic	-118780	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.005690	0.372159	350(TAGAACACTGTGTTTT,-,0.00),351(AGAACACTGTGTTTTT,+,0.00)
chunk0032_169_1	chr11	5463390	5464056	+	0	NA	intron (NR_038321, intron 1 of 4)	L2b|LINE|L2	10315	NM_001004754	390064	Hs.553733	NM_001004754	ENSG00000187918	OR51I2	OR11-38	olfactory receptor family 51 subfamily I member 2	protein-coding	0.004505	0.371814	
chunk0029_194_1	chr10	101450120	101450768	+	0	NA	intron (NM_001256856, intron 2 of 13)	intron (NM_001256856, intron 2 of 13)	96411	NM_033637	8945	Hs.643802	NM_003939	ENSG00000166167	BTRC	BETA-TRCP|FBW1A|FBXW1|FBXW1A|FWD1|bTrCP|bTrCP1|betaTrCP	beta-transducin repeat containing E3 ubiquitin protein ligase	protein-coding	0.007716	0.377504	
chunk0180_53_1	chr7	54774027	54774339	+	0	NA	intron (NR_110040, intron 1 of 2)	intron (NR_110040, intron 1 of 2)	14870	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.022436	0.412141	
chunk0183_389_1	chr7	110153476	110153682	+	0	NA	Intergenic	Intergenic	-193366	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.004854	0.371981	
chunk0005_216_1	chr1	59225571	59226021	+	0	NA	Intergenic	Intergenic	-71157	NM_018291	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.000000	0.407982	
chunk0175_193_1	chr7	5532020	5532556	+	0	NA	Intergenic	Intergenic	-1687	NM_001101	60	Hs.520640	NM_001101	ENSG00000075624	ACTB	BRWS1|PS1TP5BP1	actin beta	protein-coding	0.022388	0.612663	
chunk0119_16_1	chr22	40156034	40156838	+	0	NA	intron (NM_001024843, intron 4 of 23)	intron (NM_001024843, intron 4 of 23)	-21489	NM_001162501	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.008706	0.388820	399(AGGCTCAGTATGTTCC,-,0.00),400(GGCTCAGTATGTTCCA,+,0.00)
chunk0086_277_1	chr18	23664528	23665382	+	0	NA	Intergenic	Intergenic	-2070	NM_001308238	147463	Hs.355689	NM_173505	ENSG00000154065	ANKRD29	-	ankyrin repeat domain 29	protein-coding	0.017564	0.411696	
chunk0073_146_1	chr16	6605165	6605851	+	0	NA	intron (NM_018723, intron 2 of 15)	intron (NM_018723, intron 2 of 15)	-168301	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.014577	0.411936	
chunk0030_386_1	chr10	119542883	119543157	+	0	NA	promoter-TSS (NM_001005339)	promoter-TSS (NM_001005339)	-310	NM_001005339	6001	Hs.501200	NM_002925	ENSG00000148908	RGS10	-	regulator of G protein signaling 10	protein-coding	0.116788	0.763636	
chunk0086_266_1	chr18	23551671	23551915	+	0	NA	intron (NM_000271, intron 9 of 24)	L2c|LINE|L2	34824	NM_000271	4864	Hs.464779	NM_000271	ENSG00000141458	NPC1	NPC|POGZ|SLC65A1	NPC intracellular cholesterol transporter 1	protein-coding	0.004098	0.477551	
chunk0135_117_1	chr3	186976926	186977647	+	0	NA	intron (NM_173216, intron 2 of 7)	intron (NM_173216, intron 2 of 7)	-44591	NM_003032	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.018031	0.505540	
chunk0102_279_1	chr2	150188067	150188772	+	0	NA	Intergenic	Intergenic	299276	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.009929	0.348442	
chunk0099_426_1	chr2	102636714	102636918	+	0	NA	intron (NM_003048, intron 1 of 11)	intron (NM_003048, intron 1 of 11)	17127	NM_003048	6549	Hs.250083	NM_003048	ENSG00000115616	SLC9A2	NHE2	solute carrier family 9 member A2	protein-coding	0.004902	0.478049	
chunk0106_193_1	chr2	201649322	201649871	+	0	NA	exon (NM_033066, exon 20 of 22)	exon (NM_033066, exon 20 of 22)	-6067	NM_001044385	65062	Hs.12319	NM_152388	ENSG00000155755	TMEM237	ALS2CR4|JBTS14	transmembrane protein 237	protein-coding	0.005464	0.374545	
chunk0081_441_1	chr17	49039078	49039478	+	0	NA	intron (NM_006546, intron 6 of 14)	intron (NM_006546, intron 6 of 14)	41866	NM_001160423	10642	Hs.144936	NM_006546	ENSG00000159217	IGF2BP1	CRD-BP|CRDBP|IMP-1|IMP1|VICKZ1|ZBP1	insulin like growth factor 2 mRNA binding protein 1	protein-coding	0.022500	0.448878	
chunk0076_216_1	chr16	68299605	68299896	+	0	NA	TTS (NM_032178)	TTS (NM_032178)	11215	NM_032178	84138	Hs.729520	NM_032178	ENSG00000103061	SLC7A6OS	-	solute carrier family 7 member 6 opposite strand	protein-coding	0.013746	0.380137	
chunk0104_46_1	chr2	171167612	171168146	+	0	NA	intron (NM_001136554, intron 1 of 20)	intron (NM_001136554, intron 1 of 20)	-6979	NM_012290	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.001873	0.306542	
chunk0001_425_1	chr1	11255949	11256866	+	0	NA	intron (NM_004958, intron 4 of 57)	intron (NM_004958, intron 4 of 57)	6144	NM_004958	2475	Hs.338207	NM_004958	ENSG00000198793	MTOR	FRAP|FRAP1|FRAP2|RAFT1|RAPT1|SKS	mechanistic target of rapamycin kinase	protein-coding	0.014177	0.470588	
chunk0120_381_1	chr3	12265501	12266153	+	0	NA	Intergenic	Intergenic	-22023	NM_005037	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.004601	0.349158	349(AAATACACCATGTTCT,-,0.00),350(AATACACCATGTTCTT,+,0.00)
chunk0196_97_1	chr8	103021688	103022100	+	0	NA	intron (NM_001695, intron 1 of 12)	intron (NM_001695, intron 1 of 12)	874	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.016990	0.433414	
chunk0152_266_1	chr5	61122934	61123809	+	0	NA	intron (NM_174889, intron 3 of 3)	Tigger3a|DNA|TcMar-Tigger	-38945	NR_109908	101928630	Hs.575209	NR_109908		SMIM15-AS1	CTC-436P18.1	SMIM15 antisense RNA 1	ncRNA	0.009143	0.383562	
chunk0052_73_1	chr13	21402461	21402986	+	0	NA	intron (NM_001286638, intron 4 of 10)	intron (NM_001286638, intron 4 of 10)	56646	NM_153251	253832	Hs.564611	NM_153251	ENSG00000180776	ZDHHC20	4933421L13Rik|DHHC-20|DHHC20	zinc finger DHHC-type containing 20	protein-coding	0.007619	0.346008	
chunk0152_277_1	chr5	61386152	61386398	+	0	NA	intron (NM_020928, intron 1 of 13)	intron (NM_020928, intron 1 of 13)	54002	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.004065	0.417004	
chunk0155_185_1	chr5	94500393	94500853	+	0	NA	intron (NM_001145678, intron 5 of 20)	L2|LINE|L2	117981	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.013043	0.427332	
chunk0164_438_1	chr6	27651277	27651702	+	0	NA	Intergenic	L1ME3A|LINE|L1	-42546	NR_038294	100507173	Hs.635987	NR_038292	ENSG00000281706	LINC01012	-	long intergenic non-protein coding RNA 1012	ncRNA	0.016471	0.481221	
chunk0038_57_1	chr11	82901446	82901735	+	0	NA	promoter-TSS (NM_145018)	promoter-TSS (NM_145018)	-105	NM_145018	220042	Hs.165607	NM_145018	ENSG00000165490	DDIAS	C11orf82|noxin	DNA damage induced apoptosis suppressor	protein-coding	0.065744	0.558621	
chunk0052_12_1	chr13	19897667	19898268	+	0	NA	Intergenic	L1MB2|LINE|L1	-34331	NM_001142684	9205	Hs.530988	NM_014242	ENSG00000132950	ZMYM5	HSPC050|MYM|ZNF198L1|ZNF237	zinc finger MYM-type containing 5	protein-coding	0.003328	0.289037	343(CAGAACACTCTGCTCA,-,0.00),344(AGAACACTCTGCTCAA,+,0.00)
chunk0161_150_1	chr5	168826196	168826668	+	0	NA	intron (NM_003062, intron 6 of 35)	intron (NM_003062, intron 6 of 35)	-58177	NR_029632	407001		NR_029632	ENSG00000207739	MIR218-2	MIRN218-2|mir-218-2	microRNA 218-2	ncRNA	0.016949	0.435518	
chunk0007_244_1	chr1	82538916	82539166	+	0	NA	Intergenic	Intergenic	445881	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.000000	0.386454	
chunk0066_246_1	chr15	34501444	34501939	+	0	NA	Intergenic	Intergenic	26680	NR_036050	100302160		NR_036050	ENSG00000221649	MIR1233-1	MIR1233|MIRN1233|hsa-mir-1233|hsa-mir-1233-1	microRNA 1233-1	ncRNA	0.004040	0.377016	
chunk0100_370_1	chr2	117978363	117979152	+	0	NA	intron (NM_019044, intron 7 of 23)	AluSx|SINE|Alu	35406	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.010139	0.425316	
chunk0155_223_1	chr5	95360853	95361087	+	0	NA	Intergenic	L1PB1|LINE|L1	-30374	NM_152548	153643	Hs.276287	NM_152548	ENSG00000153347	FAM81B	-	family with sequence similarity 81 member B	protein-coding	0.004274	0.374468	
chunk0028_83_1	chr10	83871324	83871761	+	0	NA	Intergenic	Intergenic	-267887	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.022883	0.479452	
chunk0191_384_1	chr8	57084539	57084849	+	0	NA	Intergenic	L1PB1|LINE|L1	-90823	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.003226	0.337621	
chunk0036_292_1	chr11	65525300	65525499	+	0	NA	intron (NM_001048218, intron 1 of 17)	CpG	322	NM_001048218	57410	Hs.238839	NM_020680	ENSG00000142186	SCYL1	GKLP|HT019|NKTL|NTKL|P105|SCAR21|TAPK|TEIF|TRAP	SCY1 like pseudokinase 1	protein-coding	0.120603	0.745000	
chunk0023_309_1	chr10	29012449	29012648	+	0	NA	Intergenic	L1MD2|LINE|L1	166140	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.005025	0.365000	
chunk0122_458_1	chr3	39941854	39942349	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	132441	NR_104316	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.010101	0.399194	
chunk0097_373_1	chr2	61205854	61206508	+	0	NA	intron (NM_014709, intron 71 of 79)	intron (NM_014709, intron 71 of 79)	28761	NM_152392	130872	Hs.655602	NM_152392	ENSG00000173209	AHSA2P	AHA1|AHSA2|Hch1	activator of HSP90 ATPase homolog 2, pseudogene	pseudo	0.006116	0.345038	
chunk0140_315_1	chr4	73275100	73275849	+	0	NA	Intergenic	Intergenic	-16689	NM_198889	26057	Hs.601206	NM_015574	ENSG00000132466	ANKRD17	GTAR|MASK2|NY-BR-16	ankyrin repeat domain 17	protein-coding	0.002670	0.393333	
chunk0001_36_1	chr1	1433176	1433583	+	0	NA	intron (NR_125994, intron 1 of 1)	intron (NR_125994, intron 1 of 1)	1194	NR_125995	102724312		NR_125994		LINC01770	-	long intergenic non-protein coding RNA 1770	ncRNA	0.027027	0.671569	
chunk0030_20_1	chr10	110968879	110969460	+	0	NA	intron (NM_001269039, intron 1 of 6)	intron (NM_001269039, intron 1 of 6)	5044	NM_001269039	8036	Hs.104315	NM_007373	ENSG00000108061	SHOC2	SIAA0862|SOC2|SUR8	SHOC2 leucine rich repeat scaffold protein	protein-coding	0.001721	0.340206	169(TGGAACAGACTGTTCA,-,0.00),170(GGAACAGACTGTTCAG,+,0.00)
chunk0201_279_1	chr9	38702809	38703343	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	81988	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.011236	0.403738	
chunk0203_255_1	chr9	87569647	87570418	+	0	NA	intron (NM_001288730, intron 2 of 25)	intron (NM_001288730, intron 2 of 25)	71497	NM_001288729	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.005188	0.352332	173(GAGAACTATTTGTCCT,-,0.00),174(AGAACTATTTGTCCTC,+,0.00)
chunk0104_325_1	chr2	179432494	179432851	+	0	NA	Intergenic	Intergenic	129916	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.000000	0.385475	
chunk0122_324_1	chr3	37072915	37073377	+	0	NA	intron (NM_001282691, intron 12 of 18)	intron (NM_001282691, intron 12 of 18)	79369	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.004329	0.365011	
chunk0181_171_1	chr7	82822019	82822789	+	0	NA	3' UTR (NM_014510, exon 20 of 20)	3' UTR (NM_014510, exon 20 of 20)	340477	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.011688	0.396887	357(GAGAACAGGGTGAGCA,-,0.00),358(AGAACAGGGTGAGCAG,+,0.00)
chunk0013_282_1	chr1	170934317	170934903	+	0	NA	promoter-TSS (NM_001163629)	promoter-TSS (NM_001163629)	-861	NM_001163629	80133	Hs.591489	NM_025063	ENSG00000117501	MROH9	ARMC11|C1orf129	maestro heat like repeat family member 9	protein-coding	0.000000	0.298126	
chunk0006_252_1	chr1	69412891	69413337	+	0	NA	Intergenic	Intergenic	-347061	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.002242	0.366890	
chunk0108_81_1	chr2	227585446	227585938	+	0	NA	Intergenic	Intergenic	47628	NM_020161	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.006098	0.399594	
chunk0017_51_1	chr1	205325028	205325579	+	0	NA	Intergenic	L2c|LINE|L2	-3512	NM_030952	81788	Hs.497512	NM_030952	ENSG00000163545	NUAK2	SNARK	NUAK family kinase 2	protein-coding	0.005445	0.534420	
chunk0005_348_1	chr1	61278182	61278508	+	0	NA	intron (NM_001145511, intron 3 of 10)	intron (NM_001145511, intron 3 of 10)	-24827	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.006135	0.348624	
chunk0164_361_1	chr6	25564230	25564961	+	0	NA	intron (NM_017640, intron 29 of 36)	L4_A_Mam|LINE|RTE-X	-87606	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.002736	0.403005	433(CAGAACTGAATGTGCA,-,0.00),434(AGAACTGAATGTGCAT,+,0.00)
chunk0085_33_1	chr18	533696	534524	+	0	NA	Intergenic	Intergenic	-33381	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.010870	0.427021	
chunk0061_338_1	chr14	63444488	63444818	+	0	NA	intron (NR_104104, intron 2 of 12)	intron (NR_104104, intron 2 of 12)	63585	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.003030	0.299094	
chunk0157_453_1	chr5	124997612	124998438	+	0	NA	Intergenic	Intergenic	-38806	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.004843	0.371221	447(TAGCACTATGTGTCCC,-,0.00),448(AGCACTATGTGTCCCA,+,0.00)
chunk0015_271_1	chr1	188432555	188433090	+	0	NA	Intergenic	MIRb|SINE|MIR	989194	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007477	0.313433	
chunk0136_153_1	chr4	4773428	4773775	+	0	NA	intron (NR_125892, intron 2 of 2)	Charlie1a|DNA|hAT-Charlie	11841	NR_125892	101928279	Hs.586152	NR_125892		LOC101928279	-	uncharacterized LOC101928279	ncRNA	0.000000	0.356322	139(AAGAACAAAATGTTCA,-,0.00),140(AGAACAAAATGTTCAC,+,0.00)
chunk0042_276_1	chr12	6998737	6998938	+	0	NA	intron (NM_005768, intron 1 of 12)	MIR3|SINE|MIR	19701	NM_005768	10162	Hs.655248	NM_005768	ENSG00000111684	LPCAT3	C3F|LPCAT|LPLAT 5|LPSAT|MBOAT5|OACT5|nessy	lysophosphatidylcholine acyltransferase 3	protein-coding	0.000000	0.440594	
chunk0126_100_1	chr3	74911746	74912288	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-302459	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.003690	0.311234	
chunk0092_66_1	chr19	20318642	20318938	+	0	NA	Intergenic	HERVK14-int|LTR|ERVK	80564	NR_036053	100302179		NR_036053	ENSG00000238517	MIR1270	MIR1270-1|MIR1270-2|MIRN1270|hsa-mir-1270|hsa-mir-1270-1|mir-1270	microRNA 1270	ncRNA	0.010135	0.437710	
chunk0042_267_1	chr12	6873562	6873761	+	0	NA	promoter-TSS (NM_001146316)	promoter-TSS (NM_001146316)	-304	NM_032641	84727	Hs.479856	NM_032641	ENSG00000111671	SPSB2	GRCC9|SSB2	splA/ryanodine receptor domain and SOCS box containing 2	protein-coding	0.080402	0.655000	
chunk0174_104_1	chr6	156927491	156927913	+	0	NA	intron (NM_017519, intron 3 of 18)	intron (NM_017519, intron 3 of 18)	-147971	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.007109	0.408983	
chunk0089_316_1	chr18	64168468	64168905	+	0	NA	intron (NR_033881, intron 2 of 9)	intron (NR_033881, intron 2 of 9)	-19660	NR_027245	221241	Hs.567778	NM_152728	ENSG00000179676	LINC00305	C18orf20|HsT1235|NCRNA00305	long intergenic non-protein coding RNA 305	ncRNA	0.002288	0.351598	156(CAGCACAAGATGTTCT,-,0.00),157(AGCACAAGATGTTCTA,+,0.00)
chunk0119_300_1	chr22	46469772	46470017	+	0	NA	intron (NM_014246, intron 1 of 34)	L2a|LINE|L2	67276	NM_014246	9620	Hs.252387	NM_014246	ENSG00000075275	CELSR1	ADGRC1|CDHF9|FMI2|HFMI2|ME2	cadherin EGF LAG seven-pass G-type receptor 1	protein-coding	0.016327	0.524390	
chunk0079_366_1	chr17	17983303	17984045	+	0	NA	intron (NM_031294, intron 3 of 13)	intron (NM_031294, intron 3 of 13)	10861	NM_001130091	83450	Hs.579264	NM_031294	ENSG00000171962	DRC3	CFAP134|LRRC48	dynein regulatory complex subunit 3	protein-coding	0.014825	0.508748	353(AGGGACACAATGTTCC,-,0.00),354(GGGACACAATGTTCCT,+,0.00)
chunk0079_377_1	chr17	18166894	18167232	+	0	NA	intron (NM_016239, intron 60 of 64)	intron (NM_016239, intron 60 of 64)	-16490	NM_017758	54890	Hs.744130	NM_017758	ENSG00000091542	ALKBH5	ABH5|OFOXD|OFOXD1	alkB homolog 5, RNA demethylase	protein-coding	0.011834	0.489676	
chunk0178_439_1	chr7	41678339	41678688	+	0	NA	Intergenic	Intergenic	-15403	NR_027118	285954	Hs.656869	NR_027118	ENSG00000224116	INHBA-AS1	-	INHBA antisense RNA 1	ncRNA	0.002865	0.320000	
chunk0130_423_1	chr3	140829716	140830211	+	0	NA	Intergenic	L2a|LINE|L2	-111857	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.002020	0.393145	
chunk0024_72_1	chr10	34195525	34196024	+	0	NA	intron (NM_019619, intron 22 of 24)	intron (NM_019619, intron 22 of 24)	-423094	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.010020	0.412000	266(CAGGACAGAGTGTATC,-,0.00),267(AGGACAGAGTGTATCA,+,0.00)
chunk0100_269_1	chr2	113733063	113733474	+	0	NA	intron (NM_025181, intron 9 of 15)	MER58A|DNA|hAT-Charlie	-11900	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.002433	0.298544	
chunk0183_176_1	chr7	106179844	106180229	+	0	NA	Intergenic	Intergenic	-67389	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.023377	0.572539	
chunk0032_387_1	chr11	11562558	11562994	+	0	NA	intron (NM_198516, intron 1 of 10)	MIRb|SINE|MIR	59238	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.013761	0.498856	
chunk0044_262_1	chr12	32186903	32187446	+	0	NA	intron (NM_001003398, intron 1 of 8)	MER110A|LTR|ERV1	79923	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.014733	0.406250	
chunk0173_117_1	chr6	143626727	143627393	+	0	NA	intron (NM_001100166, intron 1 of 11)	intron (NM_001100166, intron 1 of 11)	18880	NM_014721	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.009009	0.382309	371(AGAACTGGAAGTGCTT,+,0.00)
chunk0035_146_1	chr11	42951140	42951755	+	0	NA	Intergenic	Intergenic	317922	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.004878	0.389610	
chunk0051_434_1	chr12	123034741	123035253	+	0	NA	intron (NM_020845, intron 1 of 24)	intron (NM_020845, intron 1 of 24)	-24269	NR_036187	100422931		NR_036187	ENSG00000265526	MIR4304	-	microRNA 4304	ncRNA	0.011719	0.446394	231(AAGAACACCGTGCTCT,-,0.00),232(AGAACACCGTGCTCTT,+,0.00)
chunk0099_194_1	chr2	90397207	90398770	+	0	NA	Intergenic	Intergenic	1261961	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.038388	0.363171	
chunk0150_276_1	chr5	36948006	36948385	+	0	NA	intron (NM_015384, intron 1 of 45)	L2a|LINE|L2	71436	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.000000	0.344737	
chunk0150_267_1	chr5	36745325	36745572	+	0	NA	Intergenic	CpG	131246	NR_046262	646719	Hs.355684	NR_046262	ENSG00000285967	NIPBL-DT	NIPBL-AS|NIPBL-AS1	NIPBL divergent transcript	ncRNA	0.052632	0.677419	
chunk0196_36_1	chr8	101607737	101608095	+	0	NA	intron (NM_024915, intron 8 of 15)	intron (NM_024915, intron 8 of 15)	115476	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.002793	0.339833	
chunk0117_108_1	chr22	17943669	17943886	+	0	NA	intron (NM_015241, intron 1 of 31)	intron (NM_015241, intron 1 of 31)	-36891	NM_001136004	57553	Hs.528024	NM_015241	ENSG00000243156	MICAL3	MICAL-3	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding	0.004608	0.431193	
chunk0065_192_1	chr14	100030474	100031001	+	0	NA	Intergenic	Intergenic	-34677	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.013283	0.445076	
chunk0109_3_1	chr20	121521	121845	+	0	NA	Intergenic	Intergenic	-20870	NM_030931	81623	Hs.124211	NM_030931	ENSG00000125788	DEFB126	C20orf8|DEFB-26|DEFB26|HBD26|bA530N10.1|hBD-26	defensin beta 126	protein-coding	0.009259	0.421538	197(GAGAACTGAGTGTGCC,-,0.00),198(AGAACTGAGTGTGCCA,+,0.00)
chunk0004_294_1	chr1	48917973	48918497	+	0	NA	intron (NM_032785, intron 5 of 13)	intron (NM_032785, intron 5 of 13)	-141266	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.015267	0.489524	
chunk0067_20_1	chr15	40245229	40245498	+	0	NA	intron (NM_001128628, intron 2 of 10)	intron (NM_001128628, intron 2 of 10)	5566	NM_020168	56924	Hs.732375	NM_020168	ENSG00000137843	PAK6	PAK5	p21 (RAC1) activated kinase 6	protein-coding	0.007435	0.529630	
chunk0052_315_1	chr12	125064787	125065245	+	0	NA	promoter-TSS (NM_023928)	promoter-TSS (NM_023928)	-363	NM_023928	65985	Hs.656073	NM_023928	ENSG00000081760	AACS	ACSF1|SUR-5	acetoacetyl-CoA synthetase	protein-coding	0.037118	0.477124	168(ATGTACACGATGTACT,-,0.00),169(TGTACACGATGTACTT,+,0.00)
chunk0166_217_1	chr6	46914165	46914364	+	0	NA	intron (NM_015234, intron 1 of 20)	intron (NM_015234, intron 1 of 20)	7713	NM_001098518	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.000000	0.375000	
chunk0163_147_1	chr6	10896259	10896496	+	0	NA	intron (NM_001040274, intron 4 of 29)	intron (NM_001040274, intron 4 of 29)	9546	NM_001040274	221711	Hs.729128	NM_194299	ENSG00000153157	SYCP2L	C6orf177|NO145|dJ62D2.1	synaptonemal complex protein 2 like	protein-coding	0.004219	0.478992	84(GAGAACTTCCTGTTCC,-,0.00),85(AGAACTTCCTGTTCCC,+,0.00)
chunk0184_259_1	chr7	118148597	118148796	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	-35336	NM_016200	51691	Hs.655046	NM_016200	ENSG00000128534	LSM8	NAA38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding	0.005025	0.445000	
chunk0150_345_1	chr5	38613993	38614446	+	0	NA	intron (NR_103554, intron 2 of 8)	intron (NR_103554, intron 2 of 8)	-18814	NM_002310	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.008830	0.405286	
chunk0184_404_1	chr7	122217155	122217457	+	0	NA	Intergenic	Intergenic	-73016	NM_005763	10157	Hs.156738	NM_005763	ENSG00000008311	AASS	LKR/SDH|LKRSDH|LORSDH	aminoadipate-semialdehyde synthase	protein-coding	0.003311	0.409241	
chunk0204_151_1	chr9	95740346	95740795	+	0	NA	Intergenic	Intergenic	-135048	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.013363	0.428889	
chunk0102_360_1	chr2	152642968	152643437	+	0	NA	intron (NM_052905, intron 25 of 25)	intron (NM_052905, intron 25 of 25)	74259	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.004264	0.395745	73(AAGAACGTGGAGTTCC,-,0.00)
chunk0024_13_1	chr10	32946266	32946645	+	0	NA	intron (NM_002211, intron 1 of 15)	intron (NM_002211, intron 1 of 15)	-10897	NM_033668	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.005277	0.402632	
chunk0208_231_1	chrX	19336505	19337164	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-7059	NM_001173455	5160	Hs.530331	NM_000284	ENSG00000131828	PDHA1	PDHA|PDHAD|PDHCE1A|PHE1A	pyruvate dehydrogenase E1 alpha 1 subunit	protein-coding	0.012140	0.453030	352(AGGCACAAAATGTGCC,-,0.00),353(GGCACAAAATGTGCCA,+,0.00)
chunk0186_315_1	chr7	143045487	143046169	+	0	NA	Intergenic	Intergenic	-6513	NM_001001667	346517	Hs.554721	NM_001001667	ENSG00000225781	OR6V1	GPR138	olfactory receptor family 6 subfamily V member 1	protein-coding	0.001466	0.430454	
chunk0028_25_1	chr10	82557454	82557999	+	0	NA	intron (NM_001010848, intron 2 of 8)	MIR|SINE|MIR	-324806	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.007339	0.391941	
chunk0198_244_1	chr8	134527924	134528465	+	0	NA	intron (NM_020863, intron 12 of 15)	MIRb|SINE|MIR	-69877	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.007394	0.402214	
chunk0140_12_1	chr4	65392620	65392952	+	0	NA	intron (NM_001281765, intron 8 of 17)	intron (NM_001281765, intron 8 of 17)	-277175	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.003012	0.294294	
chunk0187_391_1	chr7	157729928	157730661	+	0	NA	intron (NM_001308268, intron 12 of 22)	intron (NM_001308268, intron 12 of 22)	-124291	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.020464	0.505450	
chunk0034_409_1	chr11	38054692	38055023	+	0	NA	Intergenic	Intergenic	591499	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.000000	0.313253	
chunk0196_425_1	chr8	116312128	116312536	+	0	NA	intron (NR_046215, intron 1 of 13)	intron (NR_046215, intron 1 of 13)	12727	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.000000	0.369193	
chunk0034_254_1	chr11	34331453	34331652	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	26456	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.005025	0.475000	
chunk0074_371_1	chr16	34587985	34588228	+	0	NA	Intergenic	Intergenic	-428070	NR_038368									0.037037	0.368852	
chunk0038_134_1	chr11	84125484	84126031	+	0	NA	intron (NM_001142699, intron 9 of 27)	intron (NM_001142699, intron 9 of 27)	147523	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.359489	
chunk0001_97_1	chr1	3323196	3323516	+	0	NA	intron (NM_022114, intron 3 of 16)	CpG	-131227	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.056250	0.647975	
chunk0169_376_1	chr6	107271039	107271673	+	0	NA	intron (NM_020381, intron 3 of 7)	BLACKJACK|DNA|hAT-Blackjack	-156924	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.001577	0.374803	
chunk0146_45_1	chr4	155565488	155566178	+	0	NA	Intergenic	Intergenic	-100877	NM_000856	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.004348	0.357453	
chunk0062_15_1	chr14	66321018	66321576	+	0	NA	Intergenic	L1MA5|LINE|L1	-165074	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.003584	0.363148	
chunk0169_367_1	chr6	107100572	107100958	+	0	NA	intron (NM_001080450, intron 2 of 4)	intron (NM_001080450, intron 2 of 4)	13667	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.007772	0.431525	
chunk0108_373_1	chr2	236777020	236777251	+	0	NA	Intergenic	Intergenic	207398	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.021645	0.396552	
chunk0083_446_1	chr17	72872433	72872674	+	0	NA	intron (NM_139177, intron 5 of 9)	LTR8|LTR|ERV1	220161	NM_139177	201266	Hs.221127	NM_139177	ENSG00000133195	SLC39A11	C17orf26|ZIP-11|ZIP11	solute carrier family 39 member 11	protein-coding	0.020747	0.433884	
chunk0076_203_1	chr16	68099871	68100330	+	0	NA	intron (NM_173163, intron 1 of 10)	L1MD2|LINE|L1	14734	NM_004555	4775	Hs.436585	NM_004555	ENSG00000072736	NFATC3	NF-AT4c|NFAT4|NFATX	nuclear factor of activated T cells 3	protein-coding	0.008715	0.417391	
chunk0141_51_1	chr4	77472316	77472632	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-39279	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.006329	0.523659	
chunk0169_245_1	chr6	105224252	105224482	+	0	NA	Intergenic	Intergenic	-44384	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.017391	0.476190	
chunk0199_21_1	chr9	582564	583019	+	0	NA	intron (NM_001256877, intron 2 of 12)	intron (NM_001256877, intron 2 of 12)	78096	NM_001256877	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.006593	0.359649	212(CAGTACAAGCTGTACA,-,0.00),213(AGTACAAGCTGTACAT,+,0.00)
chunk0081_304_1	chr17	45412408	45412685	+	0	NA	intron (NM_001282290, intron 1 of 16).2	intron (NM_001282290, intron 1 of 16).2	13100	NM_199282	201176	Hs.205326	NM_174919	ENSG00000159314	ARHGAP27	CAMGAP1|PP905|SH3D20|SH3P20	Rho GTPase activating protein 27	protein-coding	0.010830	0.586331	143(GGGGACATGGTGTCCT,-,0.00),144(GGGACATGGTGTCCTT,+,0.00)
chunk0027_362_1	chr10	79015767	79016388	+	0	NA	intron (NR_015429, intron 3 of 7)	L2b|LINE|L2	51371	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.009662	0.524116	
chunk0206_66_1	chr9	119852176	119852569	+	0	NA	Intergenic	Intergenic	-82688	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.002545	0.467005	
chunk0176_42_1	chr7	10708614	10708813	+	0	NA	Intergenic	Intergenic	231473	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.020101	0.415000	
chunk0112_258_1	chr20	42487734	42488204	+	0	NA	intron (NM_133170, intron 7 of 31)	L1ME5|LINE|L1	-197514	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.010638	0.399151	
chunk0013_354_1	chr1	172261633	172261949	+	0	NA	intron (NM_001136127, intron 15 of 19)	L1MA4A|LINE|L1	-116956	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.003165	0.567823	
chunk0006_384_1	chr1	74652582	74652946	+	0	NA	intron (NM_001002912, intron 1 of 14)	intron (NM_001002912, intron 1 of 14)	20974	NM_001002912	127254	Hs.531182	NM_001002912	ENSG00000178965	ERICH3	C1orf173	glutamate rich 3	protein-coding	0.016484	0.506849	
chunk0067_386_1	chr15	49093517	49093796	+	0	NA	Intergenic	Intergenic	-47093	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.003584	0.335714	
chunk0061_111_1	chr14	58104726	58105357	+	0	NA	intron (NM_001001872, intron 4 of 7)	intron (NM_001001872, intron 4 of 7)	47088	NM_001001872	145407	Hs.26766	NM_001001872	ENSG00000139971	ARMH4	C14orf37|UT2|c14_5376	armadillo like helical domain containing 4	protein-coding	0.009509	0.327532	
chunk0140_73_1	chr4	67542052	67542298	+	0	NA	intron (NM_001812, intron 2 of 18)	MER58A|DNA|hAT-Charlie	3363	NM_001812	1060	Hs.479867	NM_001812	ENSG00000145241	CENPC	CENP-C|CENPC1|MIF2|hcp-4	centromere protein C	protein-coding	0.004065	0.392713	
chunk0040_266_1	chr11	116193668	116194238	+	0	NA	Intergenic	Intergenic	-433753	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.021053	0.507881	
chunk0090_67_1	chr19	2185902	2186356	+	0	NA	intron (NM_032482, intron 3 of 27)	intron (NM_032482, intron 3 of 27)	21980	NM_032482	84444	Hs.713641	NM_032482	ENSG00000104885	DOT1L	DOT1|KMT4	DOT1 like histone lysine methyltransferase	protein-coding	0.041850	0.531868	
chunk0195_236_1	chr8	97516894	97517565	+	0	NA	Intergenic	Intergenic	-70732	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.008942	0.419643	328(GAGAACATCATGTATT,-,0.00),329(AGAACATCATGTATTC,+,0.00)
chunk0013_428_1	chr1	173451836	173452552	+	0	NA	intron (NR_125960, intron 1 of 1)	intron (NR_125960, intron 1 of 1)	9168	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.004190	0.408647	638(TAAAACATAATGTGCT,-,0.00),639(AAAACATAATGTGCTA,+,0.00)
chunk0170_15_1	chr6	109112600	109112865	+	0	NA	intron (NM_001083535, intron 3 of 12)	L1PA7|LINE|L1	-16572	NM_173830	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.011321	0.379699	
chunk0095_76_1	chr2	14575981	14576247	+	0	NA	Intergenic	MER70B|LTR|ERVL	-56572	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.003759	0.483146	129(ATGACACACTGTGCTA,+,0.00),153(AAGGACATCCTGTTTC,-,0.00),154(AGGACATCCTGTTTCT,+,0.00)
chunk0189_347_1	chr8	26763975	26764241	+	0	NA	intron (NM_033302, intron 2 of 2)	intron (NM_033302, intron 2 of 2)	101297	NM_033302	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.011278	0.494382	100(GGGGACTCTCTGTGCC,-,0.00),101(GGGACTCTCTGTGCCT,+,0.00)
chunk0013_288_1	chr1	171017516	171017935	+	0	NA	intron (NM_001163629, intron 17 of 21)	L1PA8|LINE|L1	-73152	NM_001002294	2328	Hs.445350	NM_006894	ENSG00000007933	FMO3	FMOII|TMAU|dJ127D3.1	flavin containing dimethylaniline monoxygenase 3	protein-coding	0.007160	0.578571	
chunk0006_258_1	chr1	69530486	69530823	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-229521	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.002967	0.372781	
chunk0160_436_1	chr5	164610100	164610818	+	0	NA	Intergenic	Intergenic	140180	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.004178	0.342142	
chunk0043_76_1	chr12	14420773	14421329	+	0	NA	intron (NM_181352, intron 1 of 14)	L1M5|LINE|L1	35987	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.000000	0.355476	
chunk0143_236_1	chr4	114466220	114466754	+	0	NA	Intergenic	Intergenic	-131968	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.003745	0.368224	
chunk0176_87_1	chr7	11557535	11557960	+	0	NA	intron (NM_015204, intron 4 of 26)	L1MDa|LINE|L1	274451	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.004706	0.429577	
chunk0023_222_1	chr10	26691184	26691612	+	0	NA	Intergenic	AluJb|SINE|Alu	-6268	NM_014317	23590	Hs.558468	NM_014317	ENSG00000148459	PDSS1	COQ1|COQ10D2|COQ1A|DPS|SPS|TPRT|TPT|TPT 1|hDPS1	decaprenyl diphosphate synthase subunit 1	protein-coding	0.009346	0.480186	
chunk0123_219_1	chr3	45273200	45273450	+	0	NA	Intergenic	Intergenic	-47003	NM_015444	25907	Hs.740403	NM_015444	ENSG00000249992	TMEM158	BBP|RIS1|p40BBP	transmembrane protein 158 (gene/pseudogene)	protein-coding	0.012000	0.525896	
chunk0200_391_1	chr9	26956051	26956250	+	0	NA	promoter-TSS (NM_025103)	promoter-TSS (NM_025103)	157	NR_121605	101929602	Hs.127665	NR_121605	ENSG00000234676	IFT74-AS1	-	IFT74 antisense RNA 1	ncRNA	0.040201	0.435000	
chunk0032_34_1	chr11	1017699	1017950	+	0	NA	exon (NM_005961, exon 31 of 33)	exon (NM_005961, exon 31 of 33)	18882	NM_005961	4588	Hs.528432	NM_005961	ENSG00000184956	MUC6	MUC-6	mucin 6, oligomeric mucus/gel-forming	protein-coding	0.023904	0.551587	
chunk0030_94_1	chr10	112396245	112396958	+	0	NA	intron (NM_203379, intron 2 of 20)	intron (NM_203379, intron 2 of 20)	20403	NM_016234	51703	Hs.11638	NM_016234	ENSG00000197142	ACSL5	ACS2|ACS5|FACL5	acyl-CoA synthetase long chain family member 5	protein-coding	0.005610	0.401961	
chunk0119_349_1	chr22	47144856	47145387	+	0	NA	intron (NM_014346, intron 12 of 12)	MIRb|SINE|MIR	-229079	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.035782	0.601504	
chunk0153_399_1	chr5	75341900	75342155	+	0	NA	intron (NM_000859, intron 1 of 19)	L2c|LINE|L2	4859	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.000000	0.355469	
chunk0050_373_1	chr12	108567919	108568473	+	0	NA	intron (NM_001301141, intron 5 of 5)	intron (NM_001301141, intron 5 of 5)	6733	NM_213595	23479	Hs.615131	NM_014301	ENSG00000136003	ISCU	2310020H20Rik|HML|ISU2|NIFU|NIFUN|hnifU	iron-sulfur cluster assembly enzyme	protein-coding	0.005415	0.409009	
chunk0005_220_1	chr1	59261314	59261961	+	0	NA	Intergenic	Intergenic	-35316	NM_018291	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.001546	0.373457	
chunk0063_405_1	chr14	88189496	88189831	+	0	NA	intron (NM_021161, intron 5 of 6)	intron (NM_021161, intron 5 of 6)	81248	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.017910	0.428571	
chunk0071_49_1	chr15	80022383	80022649	+	0	NA	Intergenic	LTR33|LTR|ERVL	-37052	NM_001242912	54469	Hs.596679	NM_019006	ENSG00000086666	ZFAND6	AWP1|ZA20D3|ZFAND5B	zinc finger AN1-type containing 6	protein-coding	0.000000	0.426966	
chunk0040_205_1	chr11	114159928	114160447	+	0	NA	intron (NM_006006, intron 3 of 6)	intron (NM_006006, intron 3 of 6)	99621	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.028902	0.530769	275(GGGTACAGTATGTACA,-,0.00),276(GGTACAGTATGTACAG,+,0.00),284(ATGTACAGTGAGTGCT,-,0.00),285(TGTACAGTGAGTGCTG,+,0.00)
chunk0122_452_1	chr3	39839435	39840071	+	0	NA	intron (NM_015460, intron 1 of 16)	L1PA7|LINE|L1	30093	NR_104316	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.011006	0.403454	236(CGGTACATTGTGTCTT,-,0.00),237(GGTACATTGTGTCTTT,+,0.00)
chunk0061_274_1	chr14	61517441	61517847	+	0	NA	intron (NM_006255, intron 10 of 13)	intron (NM_006255, intron 10 of 13)	52550	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.007389	0.447174	
chunk0072_436_1	chr15	101277253	101277996	+	0	NA	promoter-TSS (NM_203472)	promoter-TSS (NM_203472)	-104	NM_203472	55829	Hs.32148	NM_018445	ENSG00000131871	SELENOS	AD-015|ADO15|SBBI8|SELS|SEPS1|VIMP	selenoprotein S	protein-coding	0.100942	0.646505	386(GGGAACGTTCTGTGCT,-,0.00),387(GGAACGTTCTGTGCTA,+,0.00)
chunk0189_206_1	chr8	24157417	24157770	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-136447	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.002833	0.341808	
chunk0196_123_1	chr8	103760586	103761021	+	0	NA	intron (NM_001100117, intron 2 of 23)	L2a|LINE|L2	-58385	NM_001282881	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.002299	0.307339	
chunk0068_2_1	chr15	50501545	50502174	+	0	NA	TTS (NM_001128610)	TTS (NM_001128610)	44846	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.006359	0.374603	
chunk0059_135_1	chr14	31894606	31894982	+	0	NA	Intergenic	Intergenic	180225	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.010638	0.514589	
chunk0034_388_1	chr11	36561210	36561601	+	0	NA	Intergenic	Intergenic	-6608	NM_000448	5896	Hs.73958	NM_000448	ENSG00000166349	RAG1	RAG-1|RNF74	recombination activating 1	protein-coding	0.007673	0.428571	
chunk0158_188_1	chr5	127910856	127911466	+	0	NA	Intergenic	Intergenic	171913	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.004918	0.373159	
chunk0148_279_1	chr5	10774148	10774516	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-13057	NM_004394	1611	Hs.75189	NM_004394	ENSG00000112977	DAP	-	death associated protein	protein-coding	0.008152	0.428184	
chunk0190_453_1	chr8	42052563	42052762	+	0	NA	promoter-TSS (NM_006766)	promoter-TSS (NM_006766)	-636	NM_006766	7994	Hs.491577	NM_006766	ENSG00000083168	KAT6A	MOZ|MRD32|MYST-3|MYST3|RUNXBP2|ZC2HC6A|ZNF220	lysine acetyltransferase 6A	protein-coding	0.035176	0.600000	
chunk0182_190_1	chr7	95805210	95805685	+	0	NA	intron (NM_001278421, intron 2 of 15)	intron (NM_001278421, intron 2 of 15)	32941	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.002105	0.331933	
chunk0005_342_1	chr1	61183435	61183880	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	69861	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.011236	0.493274	
chunk0163_18_1	chr6	7974990	7976362	+	0	NA	intron (NR_037616, intron 4 of 12)	intron (NR_037616, intron 4 of 12)	-10426	NR_027712	206426	Hs.676966	NR_027712		PIP5K1P1	-	phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1	pseudo	0.018950	0.495266	905(GAGAGCATGCTGTACC,-,0.00)
chunk0061_332_1	chr14	63293111	63293411	+	0	NA	3' UTR (NM_020663, exon 5 of 5)	3' UTR (NM_020663, exon 5 of 5)	25618	NM_145171	122876	Hs.375028	NM_145171	ENSG00000179600	GPHB5	B5|GPB5|ZLUT1	glycoprotein hormone subunit beta 5	protein-coding	0.010000	0.401993	
chunk0114_257_1	chr21	16124497	16124696	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	53482	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.000000	0.315000	
chunk0110_321_1	chr20	18922488	18922848	+	0	NA	Intergenic	Intergenic	-92465	NM_001302818									0.005556	0.457064	146(GGAGACAGAATGTCCT,-,0.00),147(GAGACAGAATGTCCTG,+,0.00)
chunk0058_269_1	chr14	26088342	26089057	+	0	NA	Intergenic	Intergenic	509055	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.001399	0.379888	293(AAGTTCATGGTGTGCT,-,0.00),294(AGTTCATGGTGTGCTT,+,0.00)
chunk0022_1_1	chr10	7082485	7082796	+	0	NA	Intergenic	MER134|DNA?|DNA?	104144	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.012862	0.391026	
chunk0107_161_1	chr2	215269654	215270166	+	0	NA	Intergenic	Intergenic	-42046	NM_004044	471	Hs.90280	NM_004044	ENSG00000138363	ATIC	AICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding	0.013672	0.333333	
chunk0118_137_1	chr22	29887558	29887887	+	0	NA	intron (NM_021090, intron 1 of 19)	intron (NM_021090, intron 1 of 19)	4553	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.003040	0.393939	
chunk0039_456_1	chr11	108538158	108538804	+	0	NA	promoter-TSS (NM_001144765)	promoter-TSS (NM_001144765)	-274	NM_001144765	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.015480	0.426584	
chunk0065_356_1	chr14	103772034	103772589	+	0	NA	intron (NM_015316, intron 4 of 16)	L1ME1|LINE|L1	56567	NM_024071	79038	Hs.592322	NM_024071	ENSG00000100711	ZFYVE21	HCVP7TP1|ZF21	zinc finger FYVE-type containing 21	protein-coding	0.001802	0.339928	
chunk0125_49_1	chr3	63936590	63936893	+	0	NA	intron (NM_001177387, intron 3 of 12)	intron (NM_001177387, intron 3 of 12)	-31003	NM_001128149	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.006601	0.398026	
chunk0029_160_1	chr10	99810146	99810513	+	0	NA	intron (NM_000392, intron 14 of 31)	MamRep1879|DNA|hAT-Tip100?	27731	NM_000392	1244	Hs.368243	NM_000392	ENSG00000023839	ABCC2	ABC30|CMOAT|DJS|MRP2|cMRP	ATP binding cassette subfamily C member 2	protein-coding	0.008174	0.429348	203(AGATACAAACTGTTCT,-,0.00),204(GATACAAACTGTTCTT,+,0.00)
chunk0087_37_1	chr18	31254859	31255390	+	0	NA	Intergenic	L1MA9|LINE|L1	-62965	NM_001942	1828	Hs.2633	NM_001942	ENSG00000134760	DSG1	CDHF4|DG1|DSG|EPKHE|EPKHIA|PPKS1|SPPK1	desmoglein 1	protein-coding	0.001883	0.353383	
chunk0017_231_1	chr1	208051680	208051930	+	0	NA	intron (NM_025179, intron 15 of 31)	L2c|LINE|L2	-140467	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.004000	0.430279	
chunk0129_451_1	chr3	128236620	128237243	+	0	NA	intron (NM_021937, intron 1 of 6)	L2a|LINE|L2	83474	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.016051	0.439103	
chunk0008_267_1	chr1	94639180	94639657	+	0	NA	Intergenic	L1ME3A|LINE|L1	-97561	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.010482	0.353556	
chunk0176_306_1	chr7	16847336	16847632	+	0	NA	Intergenic	Intergenic	34505	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.013514	0.424242	
chunk0174_39_1	chr6	154488817	154489070	+	0	NA	intron (NM_173515, intron 1 of 12)	intron (NM_173515, intron 1 of 12)	21676	NM_173515	154043	Hs.16064	NM_173515	ENSG00000153721	CNKSR3	CNK3|CNK3/IPCEF1|MAGI1	CNKSR family member 3	protein-coding	0.015810	0.397638	
chunk0036_298_1	chr11	65851091	65851328	+	0	NA	intron (NM_152760, intron 7 of 12)	intron (NM_152760, intron 7 of 12)	7124	NM_005507	1072	Hs.170622	NM_005507	ENSG00000172757	CFL1	CFL|HEL-S-15|cofilin	cofilin 1	protein-coding	0.046414	0.626050	
chunk0153_77_1	chr5	68074380	68074579	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-115397	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.000000	0.395000	
chunk0133_357_1	chr3	173434251	173434779	+	0	NA	intron (NM_014932, intron 1 of 6)	intron (NM_014932, intron 1 of 6)	36067	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.000000	0.323251	
chunk0008_345_1	chr1	96000714	96001168	+	0	NA	intron (NR_125991, intron 3 of 4)	L1MC|LINE|L1	8873	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.006608	0.296703	
chunk0138_280_1	chr4	40551399	40551684	+	0	NA	intron (NM_001098634, intron 1 of 6)	intron (NM_001098634, intron 1 of 6)	-35568	NM_019027	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.010526	0.328671	
chunk0167_283_1	chr6	70475037	70475384	+	0	NA	intron (NM_001105531, intron 5 of 21)	intron (NM_001105531, intron 5 of 21)	48771	NM_001162529	57579	Hs.211700	NM_020819	ENSG00000082269	FAM135A	KIAA1411	family with sequence similarity 135 member A	protein-coding	0.002882	0.287356	
chunk0064_99_1	chr14	91041575	91041959	+	0	NA	intron (NM_182398, intron 1 of 12)	intron (NM_182398, intron 1 of 12)	18882	NM_004755	9252	Hs.510225	NM_004755	ENSG00000100784	RPS6KA5	MSK1|MSPK1|RLPK	ribosomal protein S6 kinase A5	protein-coding	0.007812	0.381818	
chunk0194_395_1	chr8	90995748	90996422	+	0	NA	intron (NM_018710, intron 6 of 6)	intron (NM_018710, intron 6 of 6)	-10828	NM_001190972	100127983	Hs.733266	NM_001190972	ENSG00000253250	C8orf88	-	chromosome 8 open reading frame 88	protein-coding	0.004451	0.348148	
chunk0088_321_1	chr18	50902668	50903275	+	0	NA	intron (NM_001168335, intron 2 of 13)	intron (NM_001168335, intron 2 of 13)	23909	NM_001168335	4200	Hs.233119	NM_002396	ENSG00000082212	ME2	ODS1	malic enzyme 2	protein-coding	0.003295	0.378289	
chunk0140_363_1	chr4	74375022	74375246	+	0	NA	intron (NM_001432, intron 1 of 4)	intron (NM_001432, intron 1 of 4)	9991	NM_001432	2069	Hs.115263	NM_001432	ENSG00000124882	EREG	EPR|ER|Ep	epiregulin	protein-coding	0.004464	0.324444	
chunk0080_137_1	chr17	27452647	27452905	+	0	NA	Intergenic	Intergenic	-19234	NM_014238	8844	Hs.133534	NM_014238	ENSG00000141068	KSR1	KSR|RSU2	kinase suppressor of ras 1	protein-coding	0.011628	0.335907	
chunk0164_432_1	chr6	27516319	27516695	+	0	NA	Intergenic	Intergenic	-43389	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.005319	0.442971	
chunk0003_239_1	chr1	35954243	35954600	+	0	NA	intron (NM_177422, intron 2 of 16)	intron (NM_177422, intron 2 of 16)	23339	NM_177422	192669	Hs.657659	NM_024852	ENSG00000126070	AGO3	EIF2C3	argonaute RISC catalytic component 3	protein-coding	0.002801	0.270950	
chunk0157_155_1	chr5	117830513	117830848	+	0	NA	intron (NR_104997, intron 1 of 2)	L1PREC2|LINE|L1	100319	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.005970	0.354167	
chunk0094_224_1	chr2	6769554	6770055	+	0	NA	intron (NR_038369, intron 1 of 5)	(GT)n|Simple_repeat|Simple_repeat	507	NR_038369	400941	Hs.446195	NM_001001695	ENSG00000205837	LINC00487	-	long intergenic non-protein coding RNA 487	ncRNA	0.009980	0.432271	
chunk0130_283_1	chr3	136461654	136462269	+	0	NA	intron (NM_005862, intron 13 of 33)	L1MA4|LINE|L1	211636	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.004878	0.349026	
chunk0162_437_1	chr5	180536874	180537256	+	0	NA	intron (NM_001303241, intron 4 of 13)	L1MC1|LINE|L1	42666	NM_001303241	57472	Hs.608380	NM_015455	ENSG00000113300	CNOT6	CCR4|Ccr4a	CCR4-NOT transcription complex subunit 6	protein-coding	0.002618	0.375979	
chunk0046_137_1	chr12	57993002	57993693	+	0	NA	Intergenic	Intergenic	51685	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.001447	0.322254	
chunk0079_305_1	chr17	17090499	17090766	+	0	NA	intron (NM_015134, intron 3 of 22)	intron (NM_015134, intron 3 of 22)	47872	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.014981	0.503731	
chunk0130_125_1	chr3	131601415	131601879	+	0	NA	intron (NM_130808, intron 7 of 15)	intron (NM_130808, intron 7 of 15)	-98631	NM_007208	11222	Hs.205163	NM_007208	ENSG00000114686	MRPL3	COXPD9|MRL3|RPML3	mitochondrial ribosomal protein L3	protein-coding	0.006466	0.436559	
chunk0050_81_1	chr12	101652124	101653144	+	0	NA	intron (NM_206819, intron 16 of 30)	intron (NM_206819, intron 16 of 30)	-45005	NM_020244	56994	Hs.293077	NM_020244	ENSG00000111666	CHPT1	CPT|CPT1	choline phosphotransferase 1	protein-coding	0.000000	0.335945	
chunk0052_363_1	chr12	127505991	127506413	+	0	NA	Intergenic	Intergenic	130265	NR_120451	101927637	Hs.170413	NR_120451	ENSG00000256022	LINC02411	-	long intergenic non-protein coding RNA 2411	ncRNA	0.004739	0.408983	
chunk0107_411_1	chr2	224248591	224249671	+	0	NA	Intergenic	Intergenic	152863	NM_024785	79843	Hs.147585	NM_024785	ENSG00000124019	FAM124B	-	family with sequence similarity 124 member B	protein-coding	0.001852	0.337650	
chunk0210_155_1	chrX	77642584	77642994	+	0	NA	intron (NM_138270, intron 14 of 33)	L1M4c|LINE|L1	143480	NM_138270	546	Hs.533526	NM_000489	ENSG00000085224	ATRX	JMS|MRX52|RAD54|RAD54L|XH2|XNP|ZNF-HX	ATRX chromatin remodeler	protein-coding	0.007317	0.401460	
chunk0070_437_1	chr15	78207368	78207698	+	0	NA	intron (NM_001199377, intron 2 of 13)	intron (NM_001199377, intron 2 of 13)	27174	NM_015162	23205	Hs.655760	NM_015162	ENSG00000103740	ACSBG1	BG|BG1|BGM|GR-LACS|LPD	acyl-CoA synthetase bubblegum family member 1	protein-coding	0.003030	0.401813	
chunk0057_67_1	chr13	98157255	98157756	+	0	NA	intron (NM_001001715, intron 1 of 2)	intron (NM_001001715, intron 1 of 2)	14407	NM_001001715	10160	Hs.403917	NM_005766	ENSG00000152767	FARP1	CDEP|FARP1-IT1|PLEKHC2|PPP1R75	FERM, ARH/RhoGEF and pleckstrin domain protein 1	protein-coding	0.011976	0.496016	
chunk0205_22_1	chr9	105244188	105244559	+	0	NA	promoter-TSS (NM_080546)	promoter-TSS (NM_080546)	-240	NM_080546	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.097035	0.693548	
chunk0034_440_1	chr11	39437572	39438029	+	0	NA	Intergenic	LTR33C|LTR|ERVL	788942	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.004376	0.355895	
chunk0166_343_1	chr6	51044835	51045044	+	0	NA	Intergenic	Intergenic	226213	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.000000	0.290476	
chunk0009_124_1	chr1	103300269	103300606	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-191941	NM_080629	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.008902	0.369822	
chunk0154_278_1	chr5	82365971	82366194	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	86620	NM_001017971	92270	Hs.676227	NM_001017971	ENSG00000205464	ATP6AP1L	-	ATPase H+ transporting accessory protein 1 like	protein-coding	0.008969	0.473214	
chunk0027_368_1	chr10	79153755	79154172	+	0	NA	intron (NM_020338, intron 3 of 24)	intron (NM_020338, intron 3 of 24)	84928	NM_020338	57178	Hs.193118	NM_020338	ENSG00000108175	ZMIZ1	MIZ|RAI17|TRAFIP10|ZIMP10	zinc finger MIZ-type containing 1	protein-coding	0.021583	0.569378	224(GAGAACACTCAGTGCT,-,0.00),225(AGAACACTCAGTGCTC,+,0.00)
chunk0055_326_1	chr13	68780166	68780715	+	0	NA	Intergenic	LTR80A|LTR|ERVL	104885	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.005464	0.356364	
chunk0112_252_1	chr20	41775258	41775899	+	0	NA	Intergenic	MIR|SINE|MIR	-157084	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.004680	0.434579	
chunk0181_214_1	chr7	84615177	84615831	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	83028	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.001529	0.349618	
chunk0113_419_1	chr20	61859041	61859497	+	0	NA	intron (NM_001252339, intron 5 of 14)	L1MD2|LINE|L1	94393	NR_031658	100302168		NR_031658	ENSG00000284193	MIR1257	MIRN1257|hsa-mir-1257	microRNA 1257	ncRNA	0.032895	0.455142	
chunk0099_30_1	chr2	83578470	83578765	+	0	NA	Intergenic	Intergenic	-712065	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.003390	0.435811	103(TGGGACAATGTGTCCA,-,0.00),104(GGGACAATGTGTCCAT,+,0.00)
chunk0128_74_1	chr3	105253254	105253697	+	0	NA	Intergenic	Intergenic	-113238	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006772	0.355856	298(GGAACACTTAGTTCAG,+,0.00)
chunk0205_447_1	chr9	115444556	115445020	+	0	NA	Intergenic	Intergenic	299451	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.006466	0.363441	
chunk0081_19_1	chr17	37315457	37316105	+	0	NA	intron (NM_198836, intron 3 of 55).2	MER21C|LTR|ERVL	-16014	NM_198838	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.004630	0.453005	
chunk0117_102_1	chr22	17647361	17647953	+	0	NA	intron (NM_001270726, intron 1 of 5)	intron (NM_001270726, intron 1 of 5)	-8005	NR_073069	23786	Hs.631672	NM_015367	ENSG00000099968	BCL2L13	BCL-RAMBO|Bcl2-L-13|MIL1	BCL2 like 13	protein-coding	0.023649	0.408094	
chunk0004_186_1	chr1	46132548	46133127	+	0	NA	promoter-TSS (NM_001303429)	promoter-TSS (NM_001303429)	-42	NM_001303428	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.079447	0.656897	
chunk0197_276_1	chr8	123979809	123980226	+	0	NA	intron (NM_001039112, intron 10 of 40)	intron (NM_001039112, intron 10 of 40)	60765	NR_040044	439941	Hs.683919	NM_001038706	ENSG00000181171	FER1L6-AS1	C8orf54	FER1L6 antisense RNA 1	ncRNA	0.000000	0.404306	
chunk0197_267_1	chr8	123689485	123690507	+	0	NA	intron (NM_001003954, intron 9 of 11)	intron (NM_001003954, intron 9 of 11)	-37046	NM_001081675	340359	Hs.450252	NM_001081675	ENSG00000175946	KLHL38	C8ORFK36	kelch like family member 38	protein-coding	0.007828	0.429130	713(GAGAACATTTTGTTCA,-,0.00),714(AGAACATTTTGTTCAC,+,0.00)
chunk0131_222_1	chr3	149192038	149192411	+	0	NA	intron (NR_046371, intron 9 of 17)	L1M6|LINE|L1	29821	NR_046371	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.002681	0.294118	
chunk0147_66_1	chr4	172715590	172716256	+	0	NA	intron (NR_125894, intron 1 of 2)	intron (NR_125894, intron 1 of 2)	10955	NR_125894	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.009009	0.370315	290(AAGTACACTATGTTAC,-,0.00)
chunk0177_34_1	chr7	20804537	20805054	+	0	NA	Intergenic	Intergenic	-17906	NM_198956	221833	Hs.195922	NM_182700	ENSG00000164651	SP8	BTD	Sp8 transcription factor	protein-coding	0.011605	0.378378	
chunk0031_219_1	chr10	126058111	126058348	+	0	NA	intron (NM_001288973, intron 14 of 22)	intron (NM_001288973, intron 14 of 22)	-84956	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.016878	0.563025	195(AAGCACATCATGTCTC,-,0.00)
chunk0191_258_1	chr8	53383624	53384007	+	0	NA	Intergenic	L1MA7|LINE|L1	-132118	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.007833	0.367188	
chunk0077_91_1	chr16	77579497	77579822	+	0	NA	Intergenic	Intergenic	-142833	NM_001243660	283927	Hs.282665	NM_001105663	ENSG00000140876	NUDT7	-	nudix hydrolase 7	protein-coding	0.006154	0.420245	117(TGGAACATCCAGTCCA,-,0.00),118(GGAACATCCAGTCCAG,+,0.00)
chunk0137_436_1	chr4	28657641	28658055	+	0	NA	Intergenic	Intergenic	-161734	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.007246	0.322892	
chunk0131_340_1	chr3	151320201	151320755	+	0	NA	intron (NM_053002, intron 14 of 42)	intron (NM_053002, intron 14 of 42)	-3630	NM_023915	53836	Hs.591292	NM_023915	ENSG00000138271	GPR87	FKSG78|GPR95|KPG_002	G protein-coupled receptor 87	protein-coding	0.005415	0.387387	
chunk0001_285_1	chr1	8769969	8770485	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	47413	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.013566	0.379110	223(CTGAACACAGTGTTTT,-,0.00),224(TGAACACAGTGTTTTC,+,0.00)
chunk0109_430_1	chr2	241329593	241330221	+	0	NA	intron (NM_001008491, intron 4 of 13)	LTR10C|LTR|ERV1	14046	NM_004404	4735	Hs.721234	NM_004404	ENSG00000168385	SEPTIN2	DIFF6|NEDD-5|NEDD5|Pnutl3|SEPT2|hNedd5	septin 2	protein-coding	0.015924	0.397456	352(AAGAACATAAAGTACT,-,0.00),353(AGAACATAAAGTACTT,+,0.00)
chunk0086_205_1	chr18	22349735	22350405	+	0	NA	Intergenic	Intergenic	67845	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.022388	0.417288	107(CAGAACATTTTGTTCA,-,0.00),108(AGAACATTTTGTTCAT,+,0.00),335(AAGCACTTAGTGTGCC,-,0.00),336(AGCACTTAGTGTGCCT,+,0.00)
chunk0054_7_1	chr13	40236158	40236723	+	0	NA	Intergenic	Intergenic	-15938	NR_033877	400123	Hs.577960	NR_033877	ENSG00000215483	LINC00548	-	long intergenic non-protein coding RNA 548	ncRNA	0.024779	0.491166	
chunk0142_373_1	chr4	102049736	102049947	+	0	NA	intron (NM_017935, intron 11 of 16)	MER50|LTR|ERV1	236015	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.009479	0.452830	
chunk0167_31_1	chr6	53869945	53870370	+	0	NA	intron (NM_018214, intron 2 of 13)	intron (NM_018214, intron 2 of 13)	-59825	NR_125842	101927189	Hs.453592	NR_125842	ENSG00000236740	LOC101927189	-	uncharacterized LOC101927189	ncRNA	0.016471	0.422535	
chunk0027_431_1	chr10	80988874	80989073	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	448154	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.010050	0.390000	
chunk0152_205_1	chr5	60206367	60206731	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-281164	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.000000	0.312329	
chunk0134_170_1	chr3	178058996	178059451	+	0	NA	Intergenic	Intergenic	242358	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.002198	0.366228	
chunk0058_370_1	chr14	29198274	29198755	+	0	NA	Intergenic	Tigger19b|DNA|TcMar-Tigger	425810	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.004158	0.363071	
chunk0099_286_1	chr2	98699066	98699523	+	0	NA	intron (NM_012214, intron 2 of 15)	MER68|LTR|ERVL	31832	NM_012214	11320	Hs.177576	NM_012214	ENSG00000071073	MGAT4A	GNT-IV|GNT-IVA|GnT-4a	alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A	protein-coding	0.015317	0.454148	
chunk0189_213_1	chr8	24329099	24329520	+	0	NA	intron (NR_130709, intron 9 of 12)	intron (NR_130709, intron 9 of 12)	35269	NM_021777	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.002375	0.390995	
chunk0066_307_1	chr15	35693834	35694398	+	0	NA	intron (NR_038251, intron 1 of 2)	intron (NR_038251, intron 1 of 2)	-147913	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.007092	0.391150	
chunk0115_29_1	chr21	20900056	20900255	+	0	NA	Intergenic	Intergenic	-97047	NR_109788	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005025	0.320000	
chunk0203_93_1	chr9	84136148	84136875	+	0	NA	Intergenic	Intergenic	73068	NR_110995	101927575	Hs.459826	NR_110995	ENSG00000227463	LOC101927575	-	uncharacterized LOC101927575	ncRNA	0.017882	0.436813	
chunk0211_252_1	chrX	120554394	120554700	+	0	NA	intron (NM_003588, intron 4 of 21)	intron (NM_003588, intron 4 of 21)	6415	NM_001079872	8450	Hs.102914	NM_003588	ENSG00000158290	CUL4B	CUL-4B|MRXHF2|MRXS15|MRXSC|SFM2	cullin 4B	protein-coding	0.003268	0.332248	165(TAGAACAGCATGTTCT,-,0.00),166(AGAACAGCATGTTCTT,+,0.00)
chunk0197_345_1	chr8	125360658	125361007	+	0	NA	intron (NM_173685, intron 7 of 7)	intron (NM_173685, intron 7 of 7)	-69489	NM_025195	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.008596	0.422857	205(GGTCCATTGTGTTCTG,+,0.00)
chunk0136_64_1	chr4	1858021	1858363	+	0	NA	Intergenic	Intergenic	-1945	NM_012318	3954	Hs.120165	NM_012318	ENSG00000168924	LETM1	SLC55A1	leucine zipper and EF-hand containing transmembrane protein 1	protein-coding	0.014620	0.565598	68(TAGGACTGTATGTCCT,-,0.00),69(AGGACTGTATGTCCTA,+,0.00)
chunk0025_264_1	chr10	55415516	55415949	+	0	NA	Intergenic	Intergenic	-183258	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.000000	0.313364	
chunk0082_136_1	chr17	55344622	55344825	+	0	NA	Intergenic	Intergenic	77257	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.004926	0.431373	
chunk0067_94_1	chr15	42046585	42046938	+	0	NA	intron (NM_001206670, intron 1 of 19)	intron (NM_001206670, intron 1 of 19)	3942	NM_001206670	123745	Hs.668060	NM_001080490	ENSG00000188089	PLA2G4E	-	phospholipase A2 group IVE	protein-coding	0.005666	0.423729	
chunk0034_439_1	chr11	39409027	39409308	+	0	NA	Intergenic	L1MA4|LINE|L1	760309	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.000000	0.336879	
chunk0059_403_1	chr14	37653796	37654083	+	0	NA	intron (NM_001310135, intron 3 of 32)	intron (NM_001310135, intron 3 of 32)	58740	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.006969	0.284722	
chunk0005_364_1	chr1	61525826	61526364	+	0	NA	Intergenic	(TGTA)n|Simple_repeat|Simple_repeat	-128147	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.007435	0.382189	
chunk0093_156_1	chr19	47305448	47305679	+	0	NA	Intergenic	Intergenic	-4284	NM_001736	728	Hs.2161	NM_001736	ENSG00000197405	C5AR1	C5A|C5AR|C5R1|CD88	complement C5a receptor 1	protein-coding	0.043290	0.495690	132(CTGAACATCGTGTACC,-,0.00),133(TGAACATCGTGTACCC,+,0.00)
chunk0205_68_1	chr9	106780922	106781195	+	0	NA	Intergenic	Intergenic	-82039	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.003663	0.386861	78(AGAAACAGTATGTACT,-,0.00),79(GAAACAGTATGTACTC,+,0.00)
chunk0113_181_1	chr20	53236110	53236663	+	0	NA	intron (NM_001193421, intron 1 of 2)	Tigger9a|DNA|TcMar-Tigger	51103	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.003617	0.388087	
chunk0082_415_1	chr17	61289311	61289536	+	0	NA	intron (NM_017679, intron 22 of 23)	intron (NM_017679, intron 22 of 23)	110183	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.008889	0.433628	
chunk0030_85_1	chr10	112332432	112333041	+	0	NA	intron (NR_028134, intron 10 of 18)	intron (NR_028134, intron 10 of 18)	23859	NR_028134	390003	Hs.534691	NR_028134	ENSG00000243316	GUCY2GP	GUCY2G	guanylate cyclase 2G, pseudogene	pseudo	0.013136	0.470492	
chunk0106_151_1	chr2	200425320	200425573	+	0	NA	intron (NM_001100424, intron 6 of 11)	MIRb|SINE|MIR	84623	NM_152387	130535	Hs.605775	NM_152387	ENSG00000155729	KCTD18	6530404F10Rik	potassium channel tetramerization domain containing 18	protein-coding	0.015810	0.413386	
chunk0059_177_1	chr14	32587237	32587627	+	0	NA	intron (NM_004274, intron 5 of 13)	intron (NM_004274, intron 5 of 13)	258159	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.007692	0.396419	216(AAGACCAGTGTGTTCT,-,0.00),217(AGACCAGTGTGTTCTA,+,0.00)
chunk0081_272_1	chr17	43823358	43823818	+	0	NA	intron (NR_003562, intron 10 of 18)	intron (NR_003562, intron 10 of 18)	9591	NM_001932	4356	Hs.396566	NM_001932	ENSG00000161647	MPP3	DLG3	membrane palmitoylated protein 3	protein-coding	0.006522	0.451193	
chunk0180_445_1	chr7	77383087	77383695	+	0	NA	intron (NM_017439, intron 6 of 30)	intron (NM_017439, intron 6 of 30)	-31807	NR_110073	101927243	Hs.547753	NR_110073		LOC101927243	-	uncharacterized LOC101927243	ncRNA	0.009868	0.415435	
chunk0203_427_1	chr9	91120036	91120800	+	0	NA	Intergenic	Intergenic	-45286	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.006545	0.356863	
chunk0144_411_1	chr4	140409619	140410182	+	0	NA	intron (NM_001130675, intron 4 of 15)	intron (NM_001130675, intron 4 of 15)	17761	NM_001130675	1047	Hs.86368	NM_004362	ENSG00000153132	CLGN	-	calmegin	protein-coding	0.007105	0.329787	
chunk0017_350_1	chr1	211832597	211833257	+	0	NA	Intergenic	Intergenic	-2155	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.004545	0.413011	205(CAACACATTATGTTCC,-,0.00),206(AACACATTATGTTCCA,+,0.00),566(TGGAACAGCCAGTTCT,-,0.00),567(GGAACAGCCAGTTCTC,+,0.00)
chunk0057_82_1	chr13	98484837	98485038	+	0	NA	intron (NM_003576, intron 2 of 10)	intron (NM_003576, intron 2 of 10)	37188	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.024876	0.559406	
chunk0143_347_1	chr4	121741420	121742118	+	0	NA	Intergenic	L1ME3G|LINE|L1	-22816	NR_024365	100192379	Hs.607691	NR_024365	ENSG00000226757	PP12613	-	uncharacterized LOC100192379	ncRNA	0.012894	0.379113	164(AGGTACTCAATGTACC,-,0.00),165(GGTACTCAATGTACCT,+,0.00)
chunk0096_78_1	chr2	27915949	27916900	+	0	NA	intron (NM_199191, intron 2 of 11)	intron (NM_199191, intron 2 of 11)	-25310	NR_028308	100302650	Hs.729719	NR_028308		BABAM2-AS1	BRE-AS1	BABAM2 antisense RNA 1	ncRNA	0.001052	0.376050	
chunk0100_421_1	chr2	120067023	120067801	+	0	NA	intron (NM_020909, intron 3 of 24)	intron (NM_020909, intron 3 of 24)	54203	NM_001184938	57669	Hs.369232	NM_020909	ENSG00000115109	EPB41L5	BE37|YMO1|YRT	erythrocyte membrane protein band 4.1 like 5	protein-coding	0.008997	0.364570	
chunk0156_415_1	chr5	114332321	114333250	+	0	NA	Intergenic	Intergenic	-29534	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.005382	0.382796	
chunk0076_233_1	chr16	68885705	68886062	+	0	NA	intron (NM_024562, intron 7 of 17)	L1MB8|LINE|L1	42277	NM_024562	79613	Hs.13526	NM_024562	ENSG00000103047	TANGO6	TMCO7	transport and golgi organization 6 homolog	protein-coding	0.008403	0.365922	
chunk0092_46_1	chr19	19591155	19591711	+	0	NA	intron (NR_038198, intron 2 of 7)	intron (NR_038198, intron 2 of 7)	27483	NR_038198	80714	Hs.466257	NM_025245	ENSG00000105717	PBX4	-	PBX homeobox 4	protein-coding	0.017986	0.524237	
chunk0143_265_1	chr4	116346598	116347245	+	0	NA	Intergenic	Intergenic	47196	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.001546	0.310185	
chunk0045_392_1	chr12	52630787	52631358	+	0	NA	Intergenic	Intergenic	-12513	NM_175068	319101	Hs.55410	NM_175068	ENSG00000186049	KRT73	IRT6IRS3|K6IRS3|KRT6IRS3	keratin 73	protein-coding	0.007005	0.466783	
chunk0058_281_1	chr14	26437868	26438151	+	0	NA	Intergenic	Intergenic	159745	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.000000	0.232394	
chunk0207_143_1	chr9	129468788	129469153	+	0	NA	Intergenic	Intergenic	-19690	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.027397	0.543716	
chunk0159_22_1	chr5	136420589	136420849	+	0	NA	Intergenic	Intergenic	-55243	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.007692	0.467433	
chunk0140_70_1	chr4	67454141	67454370	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-32255	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.004367	0.360870	
chunk0157_187_1	chr5	118768667	118769110	+	0	NA	Intergenic	Intergenic	172700	NR_104998	102467225	Hs.582523	NR_104998	ENSG00000249128	LINC02215	-	long intergenic non-protein coding RNA 2215	ncRNA	0.002257	0.362613	
chunk0018_445_1	chr1	222971704	222972117	+	0	NA	intron (NM_032890, intron 4 of 9)	intron (NM_032890, intron 4 of 9)	156821	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.004843	0.265700	
chunk0195_206_1	chr8	96900330	96900945	+	0	NA	intron (NM_016134, intron 4 of 7)	intron (NM_016134, intron 4 of 7)	255410	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.004878	0.362013	
chunk0109_449_1	chr2	241617820	241618327	+	0	NA	promoter-TSS (NM_001164356)	promoter-TSS (NM_001164356)	-572	NM_001164356	51078	Hs.435759	NM_015963	ENSG00000176946	THAP4	CGI-36|Nb(III)|PP238	THAP domain containing 4	protein-coding	0.017751	0.517717	
chunk0018_65_1	chr1	216915634	216916014	+	0	NA	intron (NM_001243507, intron 2 of 7)	intron (NM_001243507, intron 2 of 7)	23849	NM_001243513	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.021053	0.461942	
chunk0016_224_1	chr1	199462574	199462908	+	0	NA	Intergenic	L1M1|LINE|L1	-443777	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.002994	0.498507	
chunk0007_268_1	chr1	83375217	83375416	+	0	NA	Intergenic	Intergenic	-389108	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.010050	0.320000	
chunk0001_257_1	chr1	8449031	8449407	+	0	NA	intron (NM_001042681, intron 11 of 22)	intron (NM_001042681, intron 11 of 22)	24574	NR_125999	102724552	Hs.568612	NR_125999		RERE-AS1	-	RERE antisense RNA 1	ncRNA	0.018617	0.472149	
chunk0010_109_1	chr1	114215327	114215772	+	0	NA	Intergenic	Intergenic	-61699	NM_001270805	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.004494	0.455157	193(CAGAACACCATGTACC,-,0.00),194(AGAACACCATGTACCA,+,0.00)
chunk0055_60_1	chr13	52646346	52646724	+	0	NA	Intergenic	L1ME1|LINE|L1	-6161	NM_001130912	10910	Hs.281902	NM_006704	ENSG00000165416	SUGT1	SGT1	SGT1 homolog, MIS12 kinetochore complex assembly cochaperone	protein-coding	0.007937	0.427441	
chunk0080_175_1	chr17	28746634	28747425	+	0	NA	intron (NM_004295, intron 1 of 6)	intron (NM_004295, intron 1 of 6)	3024	NM_004295	9618	Hs.8375	NM_004295	ENSG00000076604	TRAF4	CART1|MLN62|RNF83	TNF receptor associated factor 4	protein-coding	0.010114	0.606061	
chunk0072_32_1	chr16	707158	707478	+	0	NA	Intergenic	Intergenic	-1493	NM_153350	146330	Hs.513244	NM_153350	ENSG00000127585	FBXL16	C16orf22|Fbl16|c380A1.1	F-box and leucine rich repeat protein 16	protein-coding	0.025000	0.638629	144(GAGAACAAGCTGTGCT,-,0.00),145(AGAACAAGCTGTGCTT,+,0.00)
chunk0070_92_1	chr15	70309827	70310699	+	0	NA	Intergenic	MIRb|SINE|MIR	-212346	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.004587	0.383734	
chunk0047_186_1	chr12	70774048	70774292	+	0	NA	intron (NM_002849, intron 2 of 13)	intron (NM_002849, intron 2 of 13)	14760	NM_001207015	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.004098	0.493878	177(TGGCACACAGTGTGCC,-,0.00),178(GGCACACAGTGTGCCT,+,0.00)
chunk0087_59_1	chr18	31615149	31615538	+	0	NA	Intergenic	L1MC5a|LINE|L1	23576	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.012853	0.435897	
chunk0104_66_1	chr2	171714422	171714647	+	0	NA	intron (NM_001378, intron 6 of 17)	intron (NM_001378, intron 6 of 17)	26862	NM_001271787	1781	Hs.546250	NM_001378	ENSG00000077380	DYNC1I2	DIC74|DNCI2|IC2	dynein cytoplasmic 1 intermediate chain 2	protein-coding	0.004444	0.331858	
chunk0175_385_1	chr6	168288260	168288947	+	0	NA	Intergenic	Intergenic	31151	NM_001286350	168002	Hs.673059	NM_214462	ENSG00000164488	DACT2	C6orf116|DAPPER2|DPR2|bA503C24.7	dishevelled binding antagonist of beta catenin 2	protein-coding	0.014556	0.380814	
chunk0188_109_1	chr8	9023342	9023808	+	0	NA	intron (NM_153332, intron 6 of 6)	Charlie6|DNA|hAT-Charlie	20771	NM_153332	90459	Hs.20000	NM_153332	ENSG00000104626	ERI1	3'HEXO|HEXO|THEX1	exoribonuclease 1	protein-coding	0.006438	0.291221	
chunk0136_191_1	chr4	6791951	6792616	+	0	NA	intron (NM_001100590, intron 1 of 8)	L1ME4b|LINE|L1	9551	NM_001100590	9778	Hs.79276	NM_014743	ENSG00000170871	KIAA0232	-	KIAA0232	protein-coding	0.003008	0.355856	
chunk0089_333_1	chr18	65525586	65526392	+	0	NA	Intergenic	L1MA3|LINE|L1	-224263	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.002481	0.327138	
chunk0040_95_1	chr11	111693825	111694235	+	0	NA	intron (NM_015191, intron 4 of 14)	MIR|SINE|MIR	72415	NM_001177563	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.009756	0.379562	
chunk0184_434_1	chr7	123019975	123020310	+	0	NA	Intergenic	L1MB3|LINE|L1	-24442	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.005970	0.318452	
chunk0206_11_1	chr9	115670244	115670703	+	0	NA	Intergenic	Intergenic	73766	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.004357	0.413043	
chunk0015_442_1	chr1	191938579	191939202	+	0	NA	Intergenic	L1PA16|LINE|L1	-219572	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.004815	0.338141	
chunk0048_395_1	chr12	87728818	87729253	+	0	NA	Intergenic	Intergenic	55676	NR_033410	400058	Hs.572212	NR_033410		MKRN9P	MKRN5|MKRN9|MKRNP6|RNF65|ZNF127L3	makorin ring finger protein 9, pseudogene	pseudo	0.000000	0.339450	
chunk0195_38_1	chr8	93278784	93279043	+	0	NA	Intergenic	Intergenic	-112063	NM_001242668									0.007722	0.365385	
chunk0024_10_1	chr10	32851394	32851725	+	0	NA	intron (NM_024688, intron 19 of 22)	L1M3|LINE|L1	49913	NR_132768	106633814		NR_132768		SNORA86	-	small nucleolar RNA, H/ACA box 86	snoRNA	0.003021	0.313253	
chunk0162_92_1	chr6	2199878	2200333	+	0	NA	intron (NM_001500, intron 1 of 10)	L2a|LINE|L2	-24114	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.004396	0.368421	131(ATGAACACTGTGATCT,-,0.00),132(TGAACACTGTGATCTG,+,0.00)
chunk0092_325_1	chr19	34789339	34789538	+	0	NA	Intergenic	L1MA8|LINE|L1	-16209	NM_001007248	148103	Hs.590961	NM_001007247	ENSG00000153896	ZNF599	-	zinc finger protein 599	protein-coding	0.015075	0.375000	
chunk0053_346_1	chr13	34762411	34763139	+	0	NA	Intergenic	Tigger12|DNA|TcMar-Tigger	-122090	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.006868	0.397805	
chunk0150_35_1	chr5	31250570	31250848	+	0	NA	intron (NM_004932, intron 1 of 11)	intron (NM_004932, intron 1 of 11)	57054	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.010791	0.594982	
chunk0023_339_1	chr10	29521766	29522247	+	0	NA	intron (NM_021738, intron 16 of 37)	intron (NM_021738, intron 16 of 37)	23091	NR_030335	693189		NR_030335	ENSG00000207612	MIR604	MIRN604|hsa-mir-604	microRNA 604	ncRNA	0.002079	0.358921	
chunk0148_224_1	chr5	9055164	9055368	+	0	NA	intron (NM_003966, intron 18 of 22)	intron (NM_003966, intron 18 of 22)	-1371	NR_039779	100616326		NR_039779	ENSG00000266415	MIR4636	mir-4636	microRNA 4636	ncRNA	0.004902	0.409756	
chunk0146_65_1	chr4	156443724	156444106	+	0	NA	Intergenic	AluSp|SINE|Alu	-490019	NM_001334	1519	Hs.75262	NM_001334	ENSG00000256043	CTSO	CTSO1	cathepsin O	protein-coding	0.010471	0.389034	
chunk0093_398_1	chr19	56918640	56918992	+	0	NA	Intergenic	Intergenic	77914	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.008523	0.362606	
chunk0192_294_1	chr8	66559629	66560469	+	0	NA	Intergenic	Intergenic	53200	NM_001294282	4603	Hs.445898	NM_001080416	ENSG00000185697	MYBL1	A-MYB|AMYB	MYB proto-oncogene like 1	protein-coding	0.003571	0.380499	384(TAGGACATTATGTTCA,-,0.00),385(AGGACATTATGTTCAA,+,0.00),512(TAGCACATTCTGTACT,-,0.00),513(AGCACATTCTGTACTT,+,0.00)
chunk0171_242_1	chr6	127081333	127081532	+	0	NA	Intergenic	Intergenic	-37471	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.000000	0.325000	
chunk0030_23_1	chr10	111107985	111108343	+	0	NA	Intergenic	Intergenic	31132	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.011173	0.548747	
chunk0028_245_1	chr10	90293614	90294289	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	246854	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.007407	0.352071	
chunk0141_350_1	chr4	87739637	87740098	+	0	NA	Intergenic	L1MA3|LINE|L1	-59683	NM_004967	3381	Hs.518726	NM_004967	ENSG00000029559	IBSP	BNSP|BSP|BSP-II|SP-II	integrin binding sialoprotein	protein-coding	0.002169	0.374459	
chunk0043_316_1	chr12	22289286	22289792	+	0	NA	intron (NM_003034, intron 1 of 4)	intron (NM_003034, intron 1 of 4)	45175	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.011858	0.449704	
chunk0094_360_1	chr2	9608215	9608736	+	0	NA	intron (NM_006826, intron 2 of 5)	intron (NM_006826, intron 2 of 5)	22580	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.017274	0.415709	331(TGGAGCACAGTGTGCC,-,0.00),332(GGAGCACAGTGTGCCC,+,0.00)
chunk0212_186_1	chrX	133676451	133676896	+	0	NA	intron (NM_001164617, intron 6 of 8)	intron (NM_001164617, intron 6 of 8)	-261496	NM_001448	2239	Hs.58367	NM_001448	ENSG00000076716	GPC4	K-glypican	glypican 4	protein-coding	0.000000	0.446188	
chunk0086_95_1	chr18	13826115	13827191	+	0	NA	exon (NM_005913, exon 1 of 1)	exon (NM_005913, exon 1 of 1)	1109	NM_005913	4161	Hs.248145	NM_005913	ENSG00000176136	MC5R	MC2	melanocortin 5 receptor	protein-coding	0.039963	0.537604	627(AAGCACAAAGTGCTCC,-,0.00),628(AGCACAAAGTGCTCCT,+,0.00)
chunk0090_47_1	chr19	1829897	1830263	+	0	NA	intron (NM_020695, intron 1 of 15)	intron (NM_020695, intron 1 of 15)	7991	NR_034114	100288123	Hs.662426	NR_034114	ENSG00000267244	LOC100288123	-	uncharacterized LOC100288123	ncRNA	0.030055	0.506812	
chunk0046_175_1	chr12	58609762	58609961	+	0	NA	intron (NR_120452, intron 2 of 7)	intron (NR_120452, intron 2 of 7)	18159	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.000000	0.310000	
chunk0028_376_1	chr10	92849558	92850043	+	0	NA	intron (NM_019053, intron 1 of 21)	MIR3|SINE|MIR	1332	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.004124	0.362140	
chunk0028_367_1	chr10	92733174	92733749	+	0	NA	Intergenic	Intergenic	43537	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.006957	0.420139	
chunk0171_320_1	chr6	129677434	129677729	+	0	NA	intron (NM_033515, intron 1 of 14)	intron (NM_033515, intron 1 of 14)	32644	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.003390	0.334459	
chunk0161_212_1	chr5	170840435	170840810	+	0	NA	Intergenic	Intergenic	-21260	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.005333	0.375000	195(CAGTACTGGGTGTGCT,-,0.00),196(AGTACTGGGTGTGCTG,+,0.00)
chunk0098_189_1	chr2	71793464	71793717	+	0	NA	Intergenic	Intergenic	326888	NM_001130983	8291	Hs.252180	NM_003494	ENSG00000135636	DYSF	FER1L1|LGMD2B|LGMDR2|MMD1	dysferlin	protein-coding	0.007905	0.480315	40(GAGAACAGAGAGTCCC,-,0.00),41(AGAACAGAGAGTCCCC,+,0.00)
chunk0138_371_1	chr4	42331934	42332509	+	0	NA	Intergenic	Intergenic	-65618	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.008696	0.446181	
chunk0116_395_1	chr21	42383895	42384581	+	0	NA	intron (NR_046020, intron 6 of 12)	intron (NR_046020, intron 6 of 12)	4911	NM_032404	64699	Hs.208600	NM_024022	ENSG00000160183	TMPRSS3	DFNB10|DFNB8|ECHOS1|TADG12	transmembrane serine protease 3	protein-coding	0.008746	0.457060	
chunk0174_134_1	chr6	157443900	157444137	+	0	NA	intron (NM_024630, intron 1 of 8)	MIRb|SINE|MIR	62493	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.008439	0.357143	
chunk0119_330_1	chr22	46869703	46870391	+	0	NA	intron (NM_014346, intron 4 of 12)	intron (NM_014346, intron 4 of 12)	45995	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.002907	0.373004	
chunk0178_409_1	chr7	40977603	40977918	+	0	NA	intron (NR_110831, intron 1 of 2)	intron (NR_110831, intron 1 of 2)	2179	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.003175	0.433544	
chunk0206_46_1	chr9	117466374	117466573	+	0	NA	Intergenic	Intergenic	-51434	NM_014010	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.005025	0.300000	
chunk0176_62_1	chr7	11228424	11229293	+	0	NA	Intergenic	Intergenic	254986	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.002301	0.363218	291(GAGAACTGCTTGTCCA,-,0.00),292(AGAACTGCTTGTCCAG,+,0.00),364(GGAGACAATCTGTTCT,-,0.00),365(GAGACAATCTGTTCTA,+,0.00)
chunk0149_417_1	chr5	29485137	29485945	+	0	NA	Intergenic	Intergenic	-89565	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.009901	0.311496	
chunk0025_242_1	chr10	54372005	54372485	+	0	NA	intron (NM_001142769, intron 5 of 35)	intron (NM_001142769, intron 5 of 35)	235712	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.002083	0.365904	
chunk0169_25_1	chr6	96822966	96823364	+	0	NA	intron (NM_030784, intron 1 of 1)	Tigger3b|DNA|TcMar-Tigger	14312	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.007538	0.373434	
chunk0117_311_1	chr22	24595508	24596383	+	0	NA	intron (NM_013430, intron 1 of 15)	intron (NM_013430, intron 1 of 15)	-2877	NM_207644	388886	Hs.113314	NM_207644	ENSG00000178026	LRRC75B	C22orf36|FAM211B	leucine rich repeat containing 75B	protein-coding	0.008000	0.542237	514(GGAGACAGAATGTCCT,-,0.00),515(GAGACAGAATGTCCTC,+,0.00)
chunk0156_165_1	chr5	107556994	107557257	+	0	NA	intron (NM_001962, intron 1 of 4)	L2b|LINE|L2	113770	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.011407	0.443182	
chunk0003_240_1	chr1	36062687	36062979	+	0	NA	Intergenic	Intergenic	-21242	NM_014466	27285	Hs.127111	NM_014466	ENSG00000092850	TEKT2	TEKTB1|TEKTIN-T|h-tektin-t	tektin 2	protein-coding	0.000000	0.286689	
chunk0170_145_1	chr6	111299209	111299489	+	0	NA	3' UTR (NM_002912, exon 33 of 33)	3' UTR (NM_002912, exon 33 of 33)	40070	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.007143	0.302491	
chunk0091_151_1	chr19	7415553	7416243	+	0	NA	intron (NM_015318, intron 1 of 20)	Tigger17c|DNA|TcMar-Tigger	20785	NM_015318	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.021739	0.507959	
chunk0133_385_1	chr3	174046484	174046686	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	-125789	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.000000	0.364532	
chunk0073_5_1	chr16	1865631	1866112	+	0	NA	intron (NM_152764, intron 2 of 12)	intron (NM_152764, intron 2 of 12)	6230	NM_152764	254528	Hs.729604	NM_152764	ENSG00000162039	MEIOB	C16orf73|SPGF22|gs129	meiosis specific with OB-fold	protein-coding	0.002079	0.313278	
chunk0044_450_1	chr12	42593808	42594487	+	0	NA	Intergenic	L2b|LINE|L2	-4377	NM_153026	144165	Hs.524348	NM_153026	ENSG00000139174	PRICKLE1	EPM1B|RILP	prickle planar cell polarity protein 1	protein-coding	0.005891	0.439706	
chunk0144_161_1	chr4	131085087	131085373	+	0	NA	Intergenic	Intergenic	-679608	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.003497	0.334495	
chunk0072_115_1	chr15	91537796	91538361	+	0	NA	Intergenic	Intergenic	74739	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.014159	0.393993	268(ATAACAATCTGTCCCT,+,0.00)
chunk0025_320_1	chr10	57746905	57747173	+	0	NA	Intergenic	L1PA15|LINE|L1	-442480	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.000000	0.345725	
chunk0074_420_1	chr16	46381370	46381569	+	0	NA	Intergenic	Intergenic	187628	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.040201	0.365000	
chunk0026_424_1	chr10	70809387	70809709	+	0	NA	Intergenic	Intergenic	-6400	NM_003901	8879	Hs.499984	NM_003901	ENSG00000166224	SGPL1	NPHS14|S1PL|SPL	sphingosine-1-phosphate lyase 1	protein-coding	0.003106	0.544892	
chunk0195_213_1	chr8	97008151	97008715	+	0	NA	intron (NM_016134, intron 5 of 7)	intron (NM_016134, intron 5 of 7)	269515	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.001773	0.405310	
chunk0114_123_1	chr21	9702056	9702592	+	0	NA	Intergenic	Intergenic	118737	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.003731	0.430168	
chunk0092_11_1	chr19	18541955	18542274	+	0	NA	intron (NM_001308373, intron 1 of 8)	MIR|SINE|MIR	1482	NM_012181	23770	Hs.173464	NM_012181	ENSG00000105701	FKBP8	FKBP38|FKBPr38	FKBP prolyl isomerase 8	protein-coding	0.006270	0.484375	
chunk0160_115_1	chr5	150837269	150837968	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-8905	NM_001145805	345611	Hs.519680	NM_001145805	ENSG00000237693	IRGM	IFI1|IRGM1|LRG-47|LRG47	immunity related GTPase M	protein-coding	0.011445	0.362857	352(AAGAACAGGCTGTGAC,-,0.00),353(AGAACAGGCTGTGACC,+,0.00),432(AAGAACATAAAGTACA,-,0.00),433(AGAACATAAAGTACAT,+,0.00)
chunk0123_297_1	chr3	46665986	46667062	+	0	NA	Intergenic	Intergenic	10885	NM_182775	259173	Hs.517937	NM_147129	ENSG00000178038	ALS2CL	RN49018	ALS2 C-terminal like	protein-coding	0.013011	0.545032	
chunk0153_317_1	chr5	73728606	73728869	+	0	NA	intron (NM_001080479, intron 2 of 36)	intron (NM_001080479, intron 2 of 36)	-84781	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.011407	0.458333	45(CGGTACTGAATGTTCT,-,0.00),46(GGTACTGAATGTTCTG,+,0.00)
chunk0064_56_1	chr14	89910886	89911538	+	0	NA	intron (NM_145231, intron 5 of 5)	intron (NM_145231, intron 5 of 5)	43345	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.013804	0.405819	
chunk0019_158_1	chr1	225890953	225891503	+	0	NA	Intergenic	LTR32|LTR|ERVL	-2082	NM_020997	10637	Hs.656214	NM_020997	ENSG00000243709	LEFTY1	LEFTB|LEFTYB	left-right determination factor 1	protein-coding	0.007273	0.551724	134(GGGCACTTCCTGTTCT,-,0.00),135(GGCACTTCCTGTTCTC,+,0.00)
chunk0114_285_1	chr21	16511978	16512396	+	0	NA	intron (NR_111004, intron 5 of 5)	L1PA6|LINE|L1	-26902	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.002392	0.305489	
chunk0062_145_1	chr14	69094100	69094372	+	0	NA	intron (NM_001284206, intron 5 of 8)	intron (NM_001284206, intron 5 of 8)	58363	NM_001284207	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.000000	0.553114	
chunk0146_445_1	chr4	169869479	169869810	+	0	NA	Intergenic	Intergenic	106258	NR_037878	100506085	Hs.649173	NR_037878	ENSG00000248319	LINC02275	-	long intergenic non-protein coding RNA 2275	ncRNA	0.012085	0.418675	
chunk0026_358_1	chr10	68992943	68993418	+	0	NA	intron (NM_015634, intron 1 of 6)	intron (NM_015634, intron 1 of 6)	4459	NM_015634	26128	Hs.279580	NM_015634	ENSG00000198954	KIF1BP	KBP|KIAA1279|TTC20	KIF1 binding protein	protein-coding	0.004211	0.470588	223(CTGAACAGGCAGTACT,-,0.00),224(TGAACAGGCAGTACTC,+,0.00)
chunk0190_14_1	chr8	28844827	28845390	+	0	NA	intron (NR_026826, intron 2 of 14)	intron (NR_026826, intron 2 of 14)	44807	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.003552	0.336879	
chunk0164_389_1	chr6	26192201	26192779	+	0	NA	Intergenic	Intergenic	-3414	NM_003539	8360	Hs.248179	NM_003539	ENSG00000277157	HIST1H4D	H4/b|H4FB|dJ221C16.9	histone cluster 1 H4 family member d	protein-coding	0.012111	0.381693	
chunk0188_140_1	chr8	9516158	9516572	+	0	NA	Intergenic	Intergenic	-39570	NM_003747	8658	Hs.370267	NM_003747	ENSG00000173273	TNKS	ARTD5|PARP-5a|PARP5A|PARPL|TIN1|TINF1|TNKS1|pART5	tankyrase	protein-coding	0.004831	0.363855	189(TTGTACATTTTGTTCC,-,0.00),190(TGTACATTTTGTTCCT,+,0.00)
chunk0181_7_1	chr7	77667508	77668343	+	0	NA	Intergenic	LTR40b|LTR|ERVL	-28501	NM_198467	222194	Hs.72451	NM_198467	ENSG00000187257	RSBN1L	-	round spermatid basic protein 1 like	protein-coding	0.005988	0.433014	439(AAGGGCAGTCAGTGCT,-,0.00),440(AGGGCAGTCAGTGCTT,+,0.00)
chunk0026_284_1	chr10	67411886	67412299	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	-8682	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.000000	0.297101	
chunk0085_426_1	chr18	10661233	10661570	+	0	NA	promoter-TSS (NR_110777)	promoter-TSS (NR_110777)	-532	NR_110777	101927410	Hs.436902	NR_110777	ENSG00000260779	LOC101927410	-	uncharacterized LOC101927410	ncRNA	0.008902	0.464497	
chunk0074_280_1	chr16	28822432	28822689	+	0	NA	promoter-TSS (NM_017492)	promoter-TSS (NM_017492)	-488	NM_148415	11273	Hs.460499	NM_007245	ENSG00000168488	ATXN2L	A2D|A2LG|A2LP|A2RP	ataxin 2 like	protein-coding	0.089494	0.608527	
chunk0007_262_1	chr1	83022996	83023577	+	0	NA	Intergenic	Intergenic	-37078	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.003442	0.357388	296(AGGTACATGCTGTACT,-,0.00),297(GGTACATGCTGTACTT,+,0.00)
chunk0062_443_1	chr14	75440844	75441516	+	0	NA	intron (NM_001135047, intron 2 of 3)	intron (NM_001135047, intron 2 of 3)	9046	NM_001135049	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.019345	0.506686	
chunk0146_143_1	chr4	159544978	159545334	+	0	NA	Intergenic	Intergenic	277310	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.011236	0.378151	
chunk0160_413_1	chr5	164053225	164053424	+	0	NA	Intergenic	L2a|LINE|L2	414078	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.000000	0.375000	
chunk0141_201_1	chr4	84292084	84292391	+	0	NA	intron (NR_125909, intron 2 of 8)	intron (NR_125909, intron 2 of 8)	6932	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.003257	0.318182	
chunk0143_213_1	chr4	113618749	113619106	+	0	NA	intron (NM_172114, intron 3 of 17)	intron (NM_172114, intron 3 of 17)	143000	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.011204	0.371508	151(GAGAACAGTTAGTTCA,-,0.00),152(AGAACAGTTAGTTCAG,+,0.00)
chunk0011_46_1	chr1	143246868	143247190	+	0	NA	Intergenic	Intergenic	175563	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.037267	0.356037	
chunk0089_290_1	chr18	63199634	63200270	+	0	NA	intron (NM_000633, intron 2 of 2)	(AC)n|Simple_repeat|Simple_repeat	119428	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.025157	0.453689	
chunk0156_106_1	chr5	105392077	105392432	+	0	NA	Intergenic	LTR2752|LTR|ERV1	292780	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.030986	0.592697	
chunk0154_19_1	chr5	76754188	76754685	+	0	NA	Intergenic	L1ME3G|LINE|L1	38393	NM_001311313	2149	Hs.482562	NM_001992	ENSG00000181104	F2R	CF2R|HTR|PAR-1|PAR1|TR	coagulation factor II thrombin receptor	protein-coding	0.002012	0.319277	
chunk0168_160_1	chr6	83703877	83704487	+	0	NA	intron (NM_001256717, intron 2 of 29)	intron (NM_001256717, intron 2 of 29)	4619	NM_001256718	9892	Hs.368046	NM_014841	ENSG00000065609	SNAP91	AP180|CALM	synaptosome associated protein 91	protein-coding	0.004918	0.338789	
chunk0137_163_1	chr4	16110323	16110909	+	0	NA	Intergenic	L2b|LINE|L2	-26616	NM_001145848	8842	Hs.614734	NM_006017	ENSG00000007062	PROM1	AC133|CD133|CORD12|MCDR2|MSTP061|PROML1|RP41|STGD4	prominin 1	protein-coding	0.003413	0.441227	
chunk0128_273_1	chr3	110611926	110612557	+	0	NA	Intergenic	Intergenic	457718	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.007924	0.378165	
chunk0137_406_1	chr4	27414840	27415310	+	0	NA	Intergenic	MER110|LTR|ERV1	197596	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.004255	0.390658	
chunk0038_39_1	chr11	82006134	82006775	+	0	NA	intron (NR_120571, intron 6 of 7)	intron (NR_120571, intron 6 of 7)	-115618	NR_036186	100422823		NR_036186	ENSG00000264110	MIR4300	-	microRNA 4300	ncRNA	0.006240	0.323988	
chunk0109_400_1	chr2	240330640	240331119	+	0	NA	Intergenic	HAL1|LINE|L1	-104819	NM_002081	2817	Hs.328232	NM_002081	ENSG00000063660	GPC1	glypican	glypican 1	protein-coding	0.002088	0.302083	442(AAGAACACATTGTTAT,-,0.00)
chunk0086_235_1	chr18	22800318	22800545	+	0	NA	Intergenic	Intergenic	-13594	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.008811	0.429825	
chunk0068_451_1	chr15	59859696	59860027	+	0	NA	Intergenic	Intergenic	-144361	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.000000	0.367470	
chunk0112_110_1	chr20	38395202	38395649	+	0	NA	Intergenic	Intergenic	29905	NR_002910	26776	Hs.400876	NR_002910	ENSG00000235408	SNORA71B	RNU71B|U71b	small nucleolar RNA, H/ACA box 71B	snoRNA	0.004474	0.424107	
chunk0027_401_1	chr10	80406192	80406471	+	0	NA	Intergenic	Intergenic	-1498	NM_001243779	84293	Hs.500333	NM_032333	ENSG00000122378	PRXL2A	Adrx|C10orf58|FAM213A|PAMM	peroxiredoxin like 2A	protein-coding	0.014337	0.403571	65(GAGTTCAGCCTGTGCT,-,0.00),66(AGTTCAGCCTGTGCTT,+,0.00)
chunk0152_235_1	chr5	60496088	60496323	+	0	NA	intron (NR_024617, intron 1 of 3)	intron (NR_024617, intron 1 of 3)	-8107	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.017021	0.440678	
chunk0047_294_1	chr12	73571708	73571907	+	0	NA	Intergenic	Intergenic	412617	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.005025	0.315000	
chunk0072_413_1	chr15	100925570	100925803	+	0	NA	intron (NM_024652, intron 2 of 33)	L2c|LINE|L2	6471	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.030043	0.384615	
chunk0015_448_1	chr1	192023773	192024407	+	0	NA	Intergenic	Intergenic	-134372	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.006309	0.316535	
chunk0032_355_1	chr11	10527305	10527622	+	0	NA	intron (NM_016422, intron 3 of 5)	L2a|LINE|L2	13764	NM_016422	50862	Hs.44685	NM_016422	ENSG00000110315	RNF141	RFP141|ZFP26|ZNF230	ring finger protein 141	protein-coding	0.009464	0.449686	
chunk0090_82_1	chr18	70467395	70467716	+	0	NA	Intergenic	MIR3|SINE|MIR	-82964	NR_110764	101060542	Hs.586967	NR_110764	ENSG00000266278	LINC01910	-	long intergenic non-protein coding RNA 1910	ncRNA	0.006231	0.338509	
chunk0008_35_1	chr1	88785699	88785898	+	0	NA	intron (NM_006256, intron 7 of 21)	intron (NM_006256, intron 7 of 21)	-100594	NR_110682	101927891	Hs.637231	NR_110682	ENSG00000237505	PKN2-AS1	-	PKN2 antisense RNA 1	ncRNA	0.000000	0.305000	
chunk0166_299_1	chr6	49053790	49054468	+	0	NA	Intergenic	Intergenic	409199	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.007375	0.396171	
chunk0033_126_1	chr11	14637346	14637545	+	0	NA	intron (NM_148976, intron 1 of 10)	L2c|LINE|L2	6189	NM_148976	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.005025	0.350000	
chunk0162_173_1	chr6	3669709	3670361	+	0	NA	Intergenic	Intergenic	81977	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.010736	0.500766	
chunk0147_11_1	chr4	170668419	170668620	+	0	NA	Intergenic	L1MC1|LINE|L1	-372083	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.000000	0.371287	
chunk0065_88_1	chr15	23750173	23751247	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-63407	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.005587	0.395349	
chunk0122_260_1	chr3	35049122	35049519	+	0	NA	intron (NR_110817, intron 2 of 3)	intron (NR_110817, intron 2 of 3)	344703	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.007557	0.354271	
chunk0046_107_1	chr12	57218618	57218898	+	0	NA	intron (NM_007224, intron 1 of 1)	intron (NM_007224, intron 1 of 1)	1963	NM_007224	11247	Hs.745023	NM_007224	ENSG00000182379	NXPH4	NPH4	neurexophilin 4	protein-coding	0.017857	0.494662	
chunk0162_407_1	chr5	179830182	179830516	+	0	NA	intron (NM_003900, intron 5 of 7)	HAL1|LINE|L1	9507	NM_003900	8878	Hs.587290	NM_003900	ENSG00000161011	SQSTM1	A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B	sequestosome 1	protein-coding	0.011976	0.444776	
chunk0087_256_1	chr18	36965905	36966246	+	0	NA	intron (NM_020776, intron 6 of 9)	L1M4a2|LINE|L1	-136859	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.000000	0.353801	
chunk0178_388_1	chr7	40316446	40317041	+	0	NA	intron (NM_024728, intron 8 of 14)	intron (NM_024728, intron 8 of 14)	181767	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.013445	0.343960	
chunk0065_27_1	chr15	20643085	20644054	+	0	NA	Intergenic	Intergenic	81220	NR_027411	729786	Hs.592025	NR_027411	ENSG00000181984	GOLGA8CP	GOLGA8C	golgin A8 family member C, pseudogene	pseudo	0.008256	0.394845	424(GTGACATAGTGTTCTT,+,0.00)
chunk0079_335_1	chr17	17581451	17581722	+	0	NA	intron (NM_001267551, intron 1 of 6)	intron (NM_001267551, intron 1 of 6)	845	NM_007169	10400	Hs.714193	NM_007169	ENSG00000133027	PEMT	PEAMT|PEMPT|PEMT2|PLMT|PNMT	phosphatidylethanolamine N-methyltransferase	protein-coding	0.007380	0.503676	
chunk0013_9_1	chr1	165769244	165769443	+	0	NA	promoter-TSS (NM_001256165)	promoter-TSS (NM_001256165)	414	NR_125374	100147773	Hs.633824	NR_125374		TMCO1-AS1	-	TMCO1 antisense RNA 1	ncRNA	0.055276	0.515000	
chunk0002_395_1	chr1	27121213	27121784	+	0	NA	intron (NM_003047, intron 1 of 11)	intron (NM_003047, intron 1 of 11)	33632	NR_046474	6548	Hs.469116	NM_003047	ENSG00000090020	SLC9A1	APNH|LIKNS|NHE-1|NHE1|PPP1R143	solute carrier family 9 member A1	protein-coding	0.010508	0.513986	
chunk0114_36_1	chr21	8230611	8230854	+	0	NA	intron (NR_003287, intron 1 of 2)	(TCTC)n|Simple_repeat|Simple_repeat	16844	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.024691	0.512295	
chunk0076_390_1	chr16	72479324	72479828	+	0	NA	intron (NR_126330, intron 6 of 13)	L1MD1|LINE|L1	185433	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.000000	0.360396	
chunk0054_214_1	chr13	45252265	45252528	+	0	NA	intron (NM_004128, intron 5 of 7)	MER3|DNA|hAT-Charlie	-51356	NM_198404	386618	Hs.23406	NM_198404	ENSG00000180332	KCTD4	bA321C24.3	potassium channel tetramerization domain containing 4	protein-coding	0.000000	0.352273	
chunk0129_2_1	chr3	116129085	116129463	+	0	NA	intron (NM_002338, intron 1 of 6)	intron (NM_002338, intron 1 of 6)	-230750	NR_109998	101926903	Hs.26479	NR_109998	ENSG00000240922	LSAMP-AS1	-	LSAMP antisense RNA 1	ncRNA	0.010582	0.361478	
chunk0165_127_1	chr6	33139785	33140076	+	0	NA	Intergenic	MER57B1|LTR|ERV1	27414	NR_001435	3116	Hs.665450	NR_001435	ENSG00000224557	HLA-DPB2	DP2B|DPB2|DPbeta2|HLA-DP2B	major histocompatibility complex, class II, DP beta 2 (pseudogene)	pseudo	0.010309	0.414384	
chunk0095_316_1	chr2	20457635	20458234	+	0	NA	Intergenic	Intergenic	10863	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.006678	0.426667	
chunk0053_98_1	chr13	28597662	28598024	+	0	NA	Intergenic	Intergenic	-61161	NM_015932	51371	Hs.268742	NM_015932	ENSG00000132963	POMP	C13orf12|HSPC014|PNAS-110|PRAAS2|UMP1	proteasome maturation protein	protein-coding	0.008287	0.363636	195(GAGCACACCATGTACC,-,0.00),196(AGCACACCATGTACCA,+,0.00)
chunk0133_26_1	chr3	165752500	165752863	+	0	NA	Intergenic	Intergenic	84784	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.269231	
chunk0211_110_1	chrX	111668657	111669090	+	0	NA	Intergenic	Charlie1b|DNA|hAT-Charlie	-12245	NM_018466	79868	Hs.443061	NM_018466	ENSG00000101901	ALG13	CDG1S|CXorf45|EIEE36|GLT28D1|MDS031|TDRD13|YGL047W	ALG13 UDP-N-acetylglucosaminyltransferase subunit	protein-coding	0.011547	0.361751	
chunk0099_33_1	chr2	83650743	83651308	+	0	NA	Intergenic	Intergenic	-639657	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.003540	0.381625	
chunk0027_8_1	chr10	72011459	72012088	+	0	NA	3' UTR (NM_004273, exon 3 of 3)	3' UTR (NM_004273, exon 3 of 3)	47411	NM_004273	9469	Hs.158304	NM_004273	ENSG00000122863	CHST3	C6ST|C6ST1|HSD	carbohydrate sulfotransferase 3	protein-coding	0.015898	0.514286	
chunk0045_398_1	chr12	52800730	52801244	+	0	NA	Intergenic	Intergenic	-4879	NM_057088	3850	Hs.680652	NM_057088	ENSG00000186442	KRT3	CK3|K3	keratin 3	protein-coding	0.015564	0.456311	
chunk0120_369_1	chr3	11804312	11805063	+	0	NA	intron (NM_138807, intron 6 of 6)	intron (NM_138807, intron 6 of 6)	42232	NR_104314	132001	Hs.475472	NM_138807	ENSG00000144559	TAMM41	C3orf31|RAM41|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding	0.013316	0.390957	
chunk0198_262_1	chr8	134815597	134816374	+	0	NA	Intergenic	L2a|LINE|L2	-11040	NR_029599	407033		NR_029599	ENSG00000199153	MIR30D	MIRN30D|mir-30d	microRNA 30d	ncRNA	0.001287	0.366324	
chunk0041_132_1	chr11	125211068	125211701	+	0	NA	intron (NM_022062, intron 1 of 12)	L2a|LINE|L2	46721	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.007899	0.473186	
chunk0085_194_1	chr18	6509749	6510144	+	0	NA	Intergenic	Intergenic	-1470	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.005063	0.378788	
chunk0078_170_1	chr17	4342697	4343417	+	0	NA	intron (NM_003342, intron 1 of 5)	L2a|LINE|L2	23617	NM_003342	7326	Hs.741319	NM_003342	ENSG00000132388	UBE2G1	E217K|UBC7|UBE2G	ubiquitin conjugating enzyme E2 G1	protein-coding	0.009722	0.428571	
chunk0122_79_1	chr3	29897726	29897954	+	0	NA	intron (NM_001003792, intron 9 of 13)	intron (NM_001003792, intron 9 of 13)	36316	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.000000	0.353712	
chunk0118_107_1	chr22	29321344	29321707	+	0	NA	Intergenic	L1MC3|LINE|L1	-5769	NM_006477	10633	Hs.73088	NM_006477	ENSG00000100276	RASL10A	RRP22	RAS like family 10 member A	protein-coding	0.022039	0.491758	
chunk0031_121_1	chr10	124727377	124727858	+	0	NA	intron (NM_014661, intron 1 of 4)	intron (NM_014661, intron 1 of 4)	16744	NM_014661	9679	Hs.129195	NM_014661	ENSG00000189319	FAM53B	KIAA0140|bA12J10.2|smp	family with sequence similarity 53 member B	protein-coding	0.012474	0.481328	
chunk0155_157_1	chr5	94154079	94154329	+	0	NA	intron (NM_001145678, intron 20 of 20)	intron (NM_001145678, intron 20 of 20)	-42505	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.008000	0.414343	
chunk0176_336_1	chr7	17432723	17433253	+	0	NA	intron (NR_110015, intron 1 of 2)	L1M6|LINE|L1	58071	NR_110015	102659288	Hs.559488	NR_110014		KCCAT333	-	renal clear cell carcinoma-associated transcript 333	ncRNA	0.009434	0.316384	
chunk0147_46_1	chr4	172344496	172344975	+	0	NA	intron (NM_001034845, intron 4 of 12)	L2c|LINE|L2	344182	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.008351	0.385417	
chunk0026_352_1	chr10	68812616	68812875	+	0	NA	Intergenic	L1MDa|LINE|L1	-14792	NM_001130160	219736	Hs.37636	NM_152709	ENSG00000165730	STOX1	C10orf24	storkhead box 1	protein-coding	0.011583	0.553846	
chunk0003_328_1	chr1	38713505	38714077	+	0	NA	Intergenic	Intergenic	146032	NM_001271851	64121	Hs.532461	NM_022157	ENSG00000116954	RRAGC	GTR2|RAGC|TIB929	Ras related GTP binding C	protein-coding	0.005245	0.408377	
chunk0136_44_1	chr4	1192338	1192537	+	0	NA	intron (NM_001199021, intron 1 of 7)	intron (NM_001199021, intron 1 of 7)	16525	NM_001199021	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.010050	0.450000	
chunk0124_225_1	chr3	56494799	56495074	+	0	NA	Intergenic	Intergenic	-26573	NM_015576	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.007273	0.442029	
chunk0019_152_1	chr1	225821695	225822264	+	0	NA	intron (NM_001291163, intron 1 of 8)	intron (NM_001291163, intron 1 of 8)	-3322	NM_000120	2052	Hs.89649	NM_000120	ENSG00000143819	EPHX1	EPHX|EPOX|HYL1|MEH	epoxide hydrolase 1	protein-coding	0.003515	0.389474	
chunk0209_223_1	chrX	44937093	44937579	+	0	NA	intron (NR_111960, intron 2 of 27)	Tigger1|DNA|TcMar-Tigger	64161	NM_001291421	7403	Hs.522616	NM_021140	ENSG00000147050	KDM6A	KABUK2|UTX|bA386N14.2	lysine demethylase 6A	protein-coding	0.004115	0.336756	
chunk0111_294_1	chr20	31770526	31770876	+	0	NA	intron (NM_012112, intron 6 of 17)	intron (NM_012112, intron 6 of 17)	31600	NM_012112	22974	Hs.244580	NM_012112	ENSG00000088325	TPX2	C20orf1|C20orf2|DIL-2|DIL2|FLS353|GD:C20orf1|HCA519|HCTP4|REPP86|p100	TPX2 microtubule nucleation factor	protein-coding	0.005714	0.333333	
chunk0015_380_1	chr1	190548887	190549498	+	0	NA	Intergenic	Intergenic	70641	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.003273	0.310458	314(GAGCACAGAATGTTTT,-,0.00),315(AGCACAGAATGTTTTT,+,0.00)
chunk0021_26_1	chr10	613329	613528	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	28350	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.025126	0.515000	
chunk0124_183_1	chr3	55449289	55450122	+	0	NA	Intergenic	MIRb|SINE|MIR	31693	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.004802	0.359712	
chunk0209_185_1	chrX	43739523	43739901	+	0	NA	intron (NM_000240, intron 10 of 14)	intron (NM_000240, intron 10 of 14)	84805	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.002646	0.290237	
chunk0003_454_1	chr1	41485614	41485879	+	0	NA	Intergenic	Intergenic	-1063	NR_126098	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.015094	0.609023	
chunk0164_402_1	chr6	26529384	26529633	+	0	NA	Intergenic	L2b|LINE|L2	7802	NR_026790	493812	Hs.272939	NR_026790	ENSG00000228223	HCG11	CTA-14H9.3|bK14H9.3	HLA complex group 11	ncRNA	0.004016	0.468000	
chunk0044_244_1	chr12	31749273	31749631	+	0	NA	Intergenic	LTR8B|LTR|ERV1	-20278	NM_001278412	196394	Hs.585084	NM_001113402	ENSG00000151743	AMN1	-	antagonist of mitotic exit network 1 homolog	protein-coding	0.011173	0.454039	
chunk0003_209_1	chr1	35264942	35265256	+	0	NA	Intergenic	Intergenic	-3868	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.015924	0.492063	
chunk0136_227_1	chr4	8351805	8352477	+	0	NA	Intergenic	Intergenic	82376	NM_053044	94031	Hs.479119	NM_053044	ENSG00000170801	HTRA3	Prsp|Tasp	HtrA serine peptidase 3	protein-coding	0.019345	0.491828	
chunk0147_325_1	chr4	185150432	185150640	+	0	NA	TTS (NM_001151)	TTS (NM_001151)	7273	NM_001151	291	Hs.246506	NM_001151	ENSG00000151729	SLC25A4	AAC1|ANT|ANT 1|ANT1|MTDPS12|MTDPS12A|PEO2|PEO3|PEOA2|T1	solute carrier family 25 member 4	protein-coding	0.004808	0.411483	
chunk0075_126_1	chr16	49961164	49961450	+	0	NA	Intergenic	Intergenic	-63899	NR_104043	255919	Hs.59134	NM_153261	ENSG00000205423	CNEP1R1	C16orf69|NEP1-R1|NEP1R1|TMEM188|TMP125	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding	0.006993	0.372822	
chunk0120_270_1	chr3	9311185	9311578	+	0	NA	Intergenic	Intergenic	-51652	NM_015453	25917	Hs.443081	NM_015453	ENSG00000134077	THUMPD3	-	THUMP domain containing 3	protein-coding	0.017812	0.395939	
chunk0011_11_1	chr1	125178678	125178887	+	0	NA	Intergenic	Intergenic	3659670	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.038278	0.342857	
chunk0143_206_1	chr4	113497441	113497827	+	0	NA	intron (NM_172114, intron 15 of 17)	intron (NM_172114, intron 15 of 17)	264293	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.005181	0.439276	
chunk0160_163_1	chr5	151880342	151880829	+	0	NA	intron (NM_001292000, intron 2 of 7)	intron (NM_001292000, intron 2 of 7)	44251	NM_001146040	2741	Hs.121490	NM_000171	ENSG00000145888	GLRA1	HKPX1|STHE	glycine receptor alpha 1	protein-coding	0.002053	0.436475	
chunk0093_392_1	chr19	56651061	56651336	+	0	NA	intron (NM_001193628, intron 3 of 3)	MIR|SINE|MIR	8039	NM_001193628	147670	Hs.336588	NM_001193628	ENSG00000268182	SMIM17	-	small integral membrane protein 17	protein-coding	0.007273	0.456522	
chunk0195_265_1	chr8	98068655	98068947	+	0	NA	intron (NM_001170806, intron 1 of 1)	MER124|DNA?|DNA?	4279	NM_173549	203111	Hs.171455	NM_173549	ENSG00000177459	ERICH5	C8orf47	glutamate rich 5	protein-coding	0.006849	0.416382	
chunk0018_143_1	chr1	218656336	218656741	+	0	NA	intron (NR_031644, intron 3 of 6)	L2c|LINE|L2	213912	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.004938	0.408867	
chunk0171_248_1	chr6	127162297	127162719	+	0	NA	intron (NM_032784, intron 4 of 4)	intron (NM_032784, intron 4 of 4)	43605	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.004739	0.342790	
chunk0010_52_1	chr1	112906205	112906696	+	0	NA	Intergenic	MIRc|SINE|MIR	-16900	NR_002796	246182	Hs.647691	NR_002796		AKR7A2P1	AFARP1	aldo-keto reductase family 7 member A2 pseudogene 1	pseudo	0.004073	0.388211	
chunk0178_440_1	chr7	41696037	41696659	+	0	NA	intron (NR_027118, intron 1 of 3)	intron (NR_027118, intron 1 of 3)	2400	NR_027119	285954	Hs.656869	NR_027118	ENSG00000224116	INHBA-AS1	-	INHBA antisense RNA 1	ncRNA	0.032154	0.460674	
chunk0207_445_1	chr9	137664672	137665070	+	0	NA	intron (NM_001145527, intron 1 of 15)	intron (NM_001145527, intron 1 of 15)	45879	NM_001145527	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.017588	0.486216	
chunk0040_235_1	chr11	114477947	114478671	+	0	NA	Intergenic	MER67C|LTR|ERV1	38923	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.002762	0.384828	
chunk0072_163_1	chr15	93070173	93070428	+	0	NA	intron (NM_001166288, intron 2 of 3)	intron (NM_001166288, intron 2 of 3)	2860	NM_001166286	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.027451	0.507812	
chunk0180_143_1	chr7	56620543	56620837	+	0	NA	Intergenic	MER61B|LTR|ERV1	-82560	NR_108099	101928401	Hs.385614	NR_108099	ENSG00000233288	LOC101928401	-	uncharacterized LOC101928401	ncRNA	0.010204	0.464407	
chunk0135_199_1	chr3	188266149	188266512	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	40925	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.024793	0.469780	
chunk0195_347_1	chr8	99506997	99507750	+	0	NA	intron (NM_152564, intron 28 of 61)	intron (NM_152564, intron 28 of 61)	29357	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.001328	0.305040	
chunk0189_236_1	chr8	24546946	24547258	+	0	NA	intron (NR_125808, intron 1 of 5)	L2c|LINE|L2	1516	NR_125808	101929294	Hs.637673	NR_125808		LOC101929294	-	uncharacterized LOC101929294	ncRNA	0.012821	0.424920	
chunk0012_151_1	chr1	157795571	157795963	+	0	NA	3' UTR (NM_001159398, exon 11 of 11)	3' UTR (NM_001159398, exon 11 of 11)	-18635	NM_001159488	79368	Hs.437393	NM_030764	ENSG00000132704	FCRL2	CD307b|FCRH2|IFGP4|IRTA4|SPAP1|SPAP1A|SPAP1B|SPAP1C	Fc receptor like 2	protein-coding	0.010204	0.442748	
chunk0192_186_1	chr8	63216975	63217571	+	0	NA	Intergenic	Intergenic	48270	NM_001277814	253943	Hs.491861	NM_152758	ENSG00000185728	YTHDF3	-	YTH N6-methyladenosine RNA binding protein 3	protein-coding	0.008389	0.335008	
chunk0082_113_1	chr17	54881136	54881805	+	0	NA	Intergenic	Intergenic	-19221	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.013453	0.382090	126(TGAAACAGGCAGTTCT,-,0.00),127(GAAACAGGCAGTTCTC,+,0.00),391(GTGTACAAGATGTTCC,-,0.00),392(TGTACAAGATGTTCCA,+,0.00)
chunk0156_113_1	chr5	105688943	105689299	+	0	NA	Intergenic	Intergenic	589647	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.299720	
chunk0185_21_1	chr7	124085279	124085764	+	0	NA	Intergenic	Intergenic	-52052	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.006186	0.360082	
chunk0137_413_1	chr4	27941573	27942075	+	0	NA	Intergenic	Intergenic	724345	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.003984	0.278330	215(AAAACAAAGTGTACTC,+,0.00)
chunk0168_410_1	chr6	94973726	94973932	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	603622	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.004854	0.265700	
chunk0045_156_1	chr12	46556036	46556374	+	0	NA	intron (NR_125380, intron 3 of 3)	intron (NR_125380, intron 3 of 3)	172098	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.005917	0.356932	
chunk0212_294_1	chrX	140969707	140970051	+	0	NA	Intergenic	Intergenic	-32712	NM_032461	728695	Hs.434105	NM_032461	ENSG00000227234	SPANXB1	B1|CT11.2|SPANX-B|SPANXB|SPANXB2|SPANXF1|SPANXF2	SPANX family member B1	protein-coding	0.008721	0.408696	
chunk0175_26_1	chr7	705250	705795	+	0	NA	intron (NM_001164758, intron 2 of 10)	L1ME1|LINE|L1	7002	NM_002735	5575	Hs.520851	NM_002735	ENSG00000188191	PRKAR1B	PRKAR1	protein kinase cAMP-dependent type I regulatory subunit beta	protein-coding	0.020183	0.412088	
chunk0153_243_1	chr5	72308246	72308675	+	0	NA	intron (NM_015084, intron 2 of 10)	CpG	11797	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.095571	0.693023	
chunk0061_302_1	chr14	61777170	61777549	+	0	NA	intron (NM_003082, intron 5 of 9)	intron (NM_003082, intron 5 of 9)	15002	NM_003082	6617	Hs.179312	NM_003082	ENSG00000023608	SNAPC1	PTFgamma|SNAP43	small nuclear RNA activating complex polypeptide 1	protein-coding	0.005277	0.386842	
chunk0119_293_1	chr22	46225633	46225921	+	0	NA	intron (NM_001001928, intron 6 of 7)	(CA)n|Simple_repeat|Simple_repeat	24519	NM_207327	150383	Hs.103110	NM_207327	ENSG00000205643	CDPF1	C22orf40	cysteine rich DPF motif domain containing 1	protein-coding	0.024306	0.543253	
chunk0055_296_1	chr13	65471342	65471676	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	-394538	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.008982	0.352239	
chunk0141_5_1	chr4	76571138	76571816	+	0	NA	intron (NM_020859, intron 2 of 10)	intron (NM_020859, intron 2 of 10)	-2091	NR_039654	100616299		NR_039654	ENSG00000263445	MIR4450	mir-4450	microRNA 4450	ncRNA	0.005900	0.381443	284(AAGCACACACTGGGCC,-,0.00),285(AGCACACACTGGGCCC,+,0.00)
chunk0104_1_1	chr2	170307041	170307600	+	0	NA	intron (NR_045684, intron 7 of 34)	intron (NR_045684, intron 7 of 34)	43623	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.003578	0.373214	
chunk0160_172_1	chr5	153525047	153525246	+	0	NA	intron (NM_001258020, intron 3 of 16)	intron (NM_001258020, intron 3 of 16)	32974	NM_001258021	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.005025	0.415000	
chunk0025_316_1	chr10	57726034	57726639	+	0	NA	Intergenic	Intergenic	-421777	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.003306	0.346535	329(AAGGACAAACTGTTCT,-,0.00),330(AGGACAAACTGTTCTC,+,0.00)
chunk0074_416_1	chr16	35628791	35629695	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-117309	NR_033985	400533	Hs.499135	NR_033985	ENSG00000261122	LINC02167	-	long intergenic non-protein coding RNA 2167	ncRNA	0.007743	0.453039	
chunk0106_26_1	chr2	195937160	195937652	+	0	NA	intron (NM_018897, intron 19 of 64)	intron (NM_018897, intron 19 of 64)	131406	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.000000	0.290061	225(AGAGACAGACTGTTCC,-,0.00),226(GAGACAGACTGTTCCA,+,0.00)
chunk0173_138_1	chr6	143810958	143811580	+	0	NA	intron (NM_001100166, intron 11 of 11)	L1M5|LINE|L1	-32102	NM_032860	84946	Hs.185675	NM_032860	ENSG00000135521	LTV1	C6orf93|dJ468K18.4	LTV1 ribosome biogenesis factor	protein-coding	0.003215	0.276083	
chunk0169_411_1	chr6	108542326	108542525	+	0	NA	Intergenic	(TTCTCC)n|Simple_repeat|Simple_repeat	-17398	NM_201559	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.005025	0.465000	68(AGGGACAGTGTGTTTC,-,0.00),69(GGGACAGTGTGTTTCT,+,0.00)
chunk0029_33_1	chr10	96089789	96089988	+	0	NA	intron (NR_038444, intron 1 of 5)	CpG	347	NR_038444	728558	Hs.538374	NR_038444	ENSG00000226688	ENTPD1-AS1	-	ENTPD1 antisense RNA 1	ncRNA	0.070352	0.620000	
chunk0190_369_1	chr8	39893794	39894379	+	0	NA	Intergenic	L1ME3A|LINE|L1	-19723	NM_002164	3620	Hs.840	NM_002164	ENSG00000131203	IDO1	IDO|IDO-1|INDO	indoleamine 2,3-dioxygenase 1	protein-coding	0.006838	0.343003	
chunk0097_8_1	chr2	41158328	41158965	+	0	NA	Intergenic	Intergenic	-646211	NM_001112802	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.009419	0.343260	
chunk0016_13_1	chr1	192796340	192796609	+	0	NA	Intergenic	Intergenic	-12565	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.003717	0.437037	
chunk0045_339_1	chr12	51211507	51212005	+	0	NA	intron (NR_026893, intron 1 of 10)	AluJo|SINE|Alu	5937	NR_026893	5463	Hs.555886	NM_002702	ENSG00000184271	POU6F1	BRN5|MPOU|TCFB1	POU class 6 homeobox 1	protein-coding	0.008032	0.480962	302(AGGAACAGCAAGTGCT,-,0.00),303(GGAACAGCAAGTGCTA,+,0.00)
chunk0205_39_1	chr9	105737329	105737866	+	0	NA	intron (NM_018112, intron 4 of 5)	L1M2a|LINE|L1	43072	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.014898	0.555762	
chunk0151_133_1	chr5	44083595	44084273	+	0	NA	Intergenic	Intergenic	304748	NM_004465	2255	Hs.248049	NM_004465	ENSG00000070193	FGF10	-	fibroblast growth factor 10	protein-coding	0.002950	0.331370	
chunk0166_238_1	chr6	47161157	47161534	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-118982	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.000000	0.410053	
chunk0192_260_1	chr8	65928468	65928802	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-86901	NM_001242318	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.008982	0.373134	
chunk0108_344_1	chr2	236001921	236002471	+	0	NA	intron (NM_001037131, intron 13 of 17)	L2b|LINE|L2	165813	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.023636	0.522686	165(GAGAACAGAGAGTTTC,-,0.00),166(AGAACAGAGAGTTTCT,+,0.00)
chunk0072_172_1	chr15	93524231	93524829	+	0	NA	Intergenic	MIRc|SINE|MIR	-332030	NR_120321	101927153	Hs.371900	NR_120321		LINC02207	-	long intergenic non-protein coding RNA 2207	ncRNA	0.013378	0.452421	
chunk0020_82_1	chr1	232752333	232752729	+	0	NA	Intergenic	Intergenic	-9816	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.002525	0.340050	
chunk0179_441_1	chr7	52434292	52434835	+	0	NA	Intergenic	Intergenic	-601093	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.011050	0.389706	
chunk0134_93_1	chr3	176759813	176760502	+	0	NA	Intergenic	MER110|LTR|ERV1	56844	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.000000	0.395652	
chunk0059_420_1	chr14	38168438	38168961	+	0	NA	Intergenic	Intergenic	-39300	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.003824	0.381679	
chunk0094_394_1	chr2	10328219	10328419	+	0	NA	intron (NM_134421, intron 1 of 5)	L2b|LINE|L2	-1844	NM_001258357	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.010000	0.502488	
chunk0006_126_1	chr1	65912630	65913684	+	0	NA	promoter-TSS (NM_001297441)	promoter-TSS (NM_001297441)	-88	NM_001297441	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.002846	0.339336	
chunk0067_124_1	chr15	42786891	42787902	+	0	NA	intron (NM_173500, intron 10 of 14)	intron (NM_173500, intron 10 of 14)	-50177	NM_138477	146059	Hs.599232	NM_138477	ENSG00000140326	CDAN1	CDA1|CDAI|CDAN1A|DLT|PRO1295	codanin 1	protein-coding	0.008902	0.355731	
chunk0181_377_1	chr7	89123951	89124425	+	0	NA	intron (NM_181646, intron 1 of 3)	LTR108a_Mam|LTR|ERVL	-328471	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.004219	0.421053	
chunk0181_366_1	chr7	88695766	88696034	+	0	NA	Intergenic	LTR68|LTR|ERV1	-63468	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.000000	0.386617	
chunk0078_287_1	chr17	8041301	8041555	+	0	NA	intron (NM_001039130, intron 3 of 12)	intron (NM_001039130, intron 3 of 12)	2388	NM_001141	247	Hs.111256	NM_001141	ENSG00000179593	ALOX15B	15-LOX-2	arachidonate 15-lipoxygenase type B	protein-coding	0.003937	0.443137	90(CAGTTCACTCTGTTCC,-,0.00),91(AGTTCACTCTGTTCCA,+,0.00)
chunk0073_350_1	chr16	14658213	14658449	+	0	NA	intron (NM_016561, intron 5 of 7)	LTR9|LTR|ERV1	25520	NM_016561	51283	Hs.435556	NM_016561	ENSG00000103429	BFAR	BAR|RNF47	bifunctional apoptosis regulator	protein-coding	0.008475	0.472574	110(AGGAACTTTCTGTCCC,-,0.00),111(GGAACTTTCTGTCCCC,+,0.00)
chunk0118_462_1	chr22	39879504	39880061	+	0	NA	intron (NM_152512, intron 2 of 6)	L1MC1|LINE|L1	14008	NM_152512	150350	Hs.474869	NM_152512	ENSG00000176177	ENTHD1	CACNA1I|dJ370M22.3	ENTH domain containing 1	protein-coding	0.003591	0.392473	251(AGTACATCATGCTCCT,+,0.00)
chunk0012_385_1	chr1	163537944	163538144	+	0	NA	Intergenic	MIR|SINE|MIR	-114853	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.000000	0.427861	
chunk0146_129_1	chr4	159175382	159175602	+	0	NA	Intergenic	Intergenic	-46598	NR_037459	100500881		NR_037459	ENSG00000264105	MIR3688-1	MIR3688|mir-3688-1	microRNA 3688-1	ncRNA	0.013636	0.416290	
chunk0171_316_1	chr6	129656587	129656977	+	0	NA	intron (NM_033515, intron 1 of 14)	L3b|LINE|CR1	53443	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.012821	0.368286	
chunk0198_273_1	chr8	135418617	135418955	+	0	NA	Intergenic	L1MA1|LINE|L1	-38679	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.002959	0.333333	
chunk0202_352_1	chr9	79806891	79807313	+	0	NA	Intergenic	Intergenic	-17428	NR_121213	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.000000	0.309693	
chunk0177_181_1	chr7	23369249	23369780	+	0	NA	intron (NM_006547, intron 3 of 14)	LTR45B|LTR|ERV1	70193	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.003766	0.400376	
chunk0163_259_1	chr6	12979664	12980298	+	0	NA	intron (NM_030948, intron 4 of 14)	UCON84|Unknown|Unknown	263176	NM_030948	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.009464	0.365354	
chunk0097_401_1	chr2	62306813	62307235	+	0	NA	Intergenic	Intergenic	101198	NR_049824	100847087		NR_049824	ENSG00000266097	MIR5192	-	microRNA 5192	ncRNA	0.004739	0.515366	
chunk0184_147_1	chr7	116025573	116025876	+	0	NA	intron (NM_012252, intron 1 of 7)	intron (NM_012252, intron 1 of 7)	5089	NM_001018058	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.000000	0.381579	
chunk0004_452_1	chr1	53448279	53448499	+	0	NA	Intergenic	MER21C|LTR|ERVL	-8369	NR_002314	163742	Hs.99394	NR_002314	ENSG00000236253	SLC25A3P1	-	solute carrier family 25 member 3 pseudogene 1	pseudo	0.009091	0.447964	
chunk0140_204_1	chr4	70498175	70498614	+	0	NA	Intergenic	Intergenic	-20178	NM_001286731	401138	Hs.453069	NM_212557	ENSG00000187689	AMTN	AI3B|UNQ689	amelotin	protein-coding	0.006834	0.322727	177(AAGAACACTCTGTCTT,-,0.00),178(AGAACACTCTGTCTTT,+,0.00)
chunk0167_430_1	chr6	75735707	75736404	+	0	NA	Intergenic	Intergenic	-13121	NM_001300899	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.001435	0.310888	
chunk0138_433_1	chr4	45390676	45390909	+	0	NA	Intergenic	L1PA15|LINE|L1	-664158	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.004292	0.529915	
chunk0065_109_1	chr15	24368659	24368919	+	0	NA	Intergenic	L1MC3|LINE|L1	-72338	NR_130780	101928840	Hs.451285	NR_130780	ENSG00000259905	PWRN3	-	Prader-Willi region non-protein coding RNA 3	ncRNA	0.011538	0.310345	
chunk0170_429_1	chr6	118762888	118763159	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-19685	NR_037662	100287632	Hs.334026	NR_037662		SELENOKP3	-	selenoprotein K pseudogene 3	pseudo	0.000000	0.393382	
chunk0105_336_1	chr2	191214071	191214350	+	0	NA	Intergenic	L2c|LINE|L2	-31171	NM_001130158	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.010753	0.392857	
chunk0161_346_1	chr5	174358441	174358791	+	0	NA	intron (NR_125806, intron 1 of 5)	intron (NR_125806, intron 1 of 5)	22262	NR_125806	101928176	Hs.436014	NR_125806	ENSG00000249306	LINC01411	-	long intergenic non-protein coding RNA 1411	ncRNA	0.008571	0.370370	
chunk0195_69_1	chr8	93920091	93920502	+	0	NA	intron (NM_001161779, intron 2 of 2)	intron (NM_001161779, intron 2 of 2)	3245	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.004866	0.317961	
chunk0145_297_1	chr4	150024274	150024838	+	0	NA	Intergenic	MER21B|LTR|ERVL	-53718	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.008865	0.479646	
chunk0009_94_1	chr1	101288654	101288997	+	0	NA	Intergenic	Intergenic	-35012	NR_126402	104355286	Hs.568671	NR_126402	ENSG00000231671	LINC01307	-	long intergenic non-protein coding RNA 1307	ncRNA	0.011662	0.383721	
chunk0172_442_1	chr6	140857660	140858055	+	0	NA	Intergenic	Intergenic	174043	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.002532	0.340909	
chunk0176_159_1	chr7	13384644	13385215	+	0	NA	Intergenic	Intergenic	601585	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.008757	0.358392	
chunk0164_176_1	chr6	21980638	21980945	+	0	NA	intron (NR_015410, intron 6 of 11)	intron (NR_015410, intron 6 of 11)	166402	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.006515	0.568182	
chunk0164_167_1	chr6	21827087	21827314	+	0	NA	intron (NR_015410, intron 4 of 11)	intron (NR_015410, intron 4 of 11)	160756	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.030837	0.482456	
chunk0043_320_1	chr12	22331550	22332328	+	0	NA	intron (NM_003034, intron 1 of 4)	intron (NM_003034, intron 1 of 4)	2775	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.001285	0.356868	373(GGGTACACAATGTACC,-,0.00),374(GGTACACAATGTACCA,+,0.00)
chunk0096_284_1	chr2	32329049	32329548	+	0	NA	Intergenic	HAL1ME|LINE|L1	-27730	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.010020	0.386000	
chunk0070_412_1	chr15	77494395	77494866	+	0	NA	Intergenic	Intergenic	73979	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.004246	0.391949	
chunk0131_392_1	chr3	152649233	152649475	+	0	NA	Intergenic	Intergenic	-185339	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.004132	0.304527	
chunk0017_5_1	chr1	204378781	204379474	+	0	NA	Intergenic	Intergenic	-9408	NR_027022	127841	Hs.213144	NR_027022	ENSG00000280924	LINC00628	-	long intergenic non-protein coding RNA 628	ncRNA	0.012987	0.476945	297(AGGTACATACAGTTCC,-,0.00),298(GGTACATACAGTTCCA,+,0.00),372(GGGAGCAATGTGTTCC,-,0.00),373(GGAGCAATGTGTTCCA,+,0.00)
chunk0122_186_1	chr3	32714851	32715158	+	0	NA	intron (NM_001256741, intron 5 of 17)	intron (NM_001256741, intron 5 of 17)	19463	NM_001256742	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.013029	0.311688	
chunk0159_57_1	chr5	137254622	137255460	+	0	NA	intron (NM_004598, intron 3 of 10)	L4_A_Mam|LINE|RTE-X	244288	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.008353	0.441001	276(CTGAACTCCTTGTTCC,-,0.00),277(TGAACTCCTTGTTCCT,+,0.00),306(CAGAACTCTCTGTTCC,-,0.00),307(AGAACTCTCTGTTCCC,+,0.00),688(GGGAACATAGTGCTCT,-,0.00),689(GGAACATAGTGCTCTG,+,0.00)
chunk0108_8_1	chr2	225999635	226000246	+	0	NA	Intergenic	Intergenic	-142854	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.006547	0.339869	
chunk0003_17_1	chr1	28950083	28950526	+	0	NA	intron (NM_001166006, intron 1 of 14)	MIRb|SINE|MIR	35728	NM_001166006	2035	Hs.175437	NM_004437	ENSG00000159023	EPB41	4.1R|EL1|HE	erythrocyte membrane protein band 4.1	protein-coding	0.002257	0.342342	
chunk0018_129_1	chr1	218557823	218558069	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	115320	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.020325	0.554656	
chunk0125_347_1	chr3	71153744	71154091	+	0	NA	intron (NM_032682, intron 6 of 20)	intron (NM_032682, intron 6 of 20)	-22976	NM_001244815	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.005764	0.344828	
chunk0032_181_1	chr11	6227134	6227333	+	0	NA	intron (NM_001098794, intron 1 of 11)	MIR|SINE|MIR	7478	NM_001098794	84067	Hs.501793	NM_032127	ENSG00000051009	FAM160A2	C11orf56|FHIP	family with sequence similarity 160 member A2	protein-coding	0.005025	0.335000	
chunk0192_379_1	chr8	68586262	68586574	+	0	NA	intron (NM_052958, intron 7 of 13)	Charlie7|DNA|hAT-Charlie	-254927	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.006410	0.338658	
chunk0183_361_1	chr7	108740300	108740825	+	0	NA	Intergenic	L1PREC2|LINE|L1	144025	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.005714	0.334601	
chunk0118_112_1	chr22	29336793	29337274	+	0	NA	intron (NM_145730, intron 15 of 20)	intron (NM_145730, intron 15 of 20)	-3766	NR_037426									0.018711	0.510373	
chunk0171_303_1	chr6	128938187	128938666	+	0	NA	intron (NM_001079823, intron 1 of 63)	MIRb|SINE|MIR	55285	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.008351	0.352083	
chunk0080_112_1	chr17	27062241	27062636	+	0	NA	Intergenic	L1MA9|LINE|L1	231558	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.015190	0.383838	
chunk0190_270_1	chr8	37412697	37413381	+	0	NA	intron (NR_121620, intron 6 of 6)	intron (NR_121620, intron 6 of 6)	80874	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.005848	0.420438	
chunk0153_229_1	chr5	72139063	72139524	+	0	NA	intron (NM_005909, intron 2 of 6)	intron (NM_005909, intron 2 of 6)	-30174	NR_039967	100616377		NR_039967	ENSG00000264099	MIR4803	-	microRNA 4803	ncRNA	0.013015	0.435065	
chunk0164_417_1	chr6	27106265	27107001	+	0	NA	Intergenic	MIR|SINE|MIR	26163	NM_021058	8970	Hs.591807	NM_021058	ENSG00000124635	HIST1H2BJ	H2B/r|H2BFR|H2BJ	histone cluster 1 H2B family member j	protein-coding	0.005435	0.401628	
chunk0186_204_1	chr7	139827103	139827935	+	0	NA	intron (NM_001166254, intron 3 of 14)	L1PBa|LINE|L1	-1634	NM_001166253	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.003606	0.420168	
chunk0005_390_1	chr1	62151097	62151378	+	0	NA	intron (NM_176877, intron 42 of 42)	intron (NM_176877, intron 42 of 42)	-43565	NM_019079	54596	Hs.685462	NM_019079	ENSG00000240563	L1TD1	ECAT11	LINE1 type transposase domain containing 1	protein-coding	0.014235	0.436170	
chunk0101_284_1	chr2	134190971	134191390	+	0	NA	Intergenic	Intergenic	-63079	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.019093	0.452381	
chunk0070_162_1	chr15	71338754	71339313	+	0	NA	intron (NM_024817, intron 5 of 16)	intron (NM_024817, intron 5 of 16)	-149974	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.007156	0.446429	167(AAGACCTGTCTGTCCT,-,0.00),316(CAGGACATTTTGTCCT,-,0.00),317(AGGACATTTTGTCCTG,+,0.00)
chunk0056_142_1	chr13	83597231	83597483	+	0	NA	Intergenic	L1PREC2|LINE|L1	285036	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.343874	
chunk0037_442_1	chr11	80382210	80382463	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	380467	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003953	0.393701	
chunk0052_204_1	chr13	25116067	25116536	+	0	NA	Intergenic	MER41C|LTR|ERV1	20163	NM_030979	5042	Hs.458280	NM_030979	ENSG00000151846	PABPC3	PABP3|PABPL3|tPABP	poly(A) binding protein cytoplasmic 3	protein-coding	0.008529	0.406383	
chunk0125_265_1	chr3	69204547	69204902	+	0	NA	intron (NM_015123, intron 11 of 22)	L2c|LINE|L2	-82129	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.011268	0.404494	
chunk0127_35_1	chr3	88659074	88659628	+	0	NA	Intergenic	Intergenic	-448173	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.281081	
chunk0103_227_1	chr2	164551486	164552030	+	0	NA	intron (NM_004490, intron 2 of 13)	L2c|LINE|L2	16792	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.009191	0.438532	
chunk0057_58_1	chr13	97502239	97502645	+	0	NA	Intergenic	Intergenic	68221	NM_021033	5911	Hs.508480	NM_021033	ENSG00000125249	RAP2A	K-REV|KREV|RAP2|RbBP-30	RAP2A, member of RAS oncogene family	protein-coding	0.009852	0.464373	191(CTGCACTCGGTGTTCT,-,0.00),192(TGCACTCGGTGTTCTT,+,0.00)
chunk0053_212_1	chr13	32056182	32056673	+	0	NA	intron (NM_023037, intron 1 of 60)	intron (NM_023037, intron 1 of 60)	-24788	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.000000	0.412602	
chunk0180_129_1	chr7	55970752	55970958	+	0	NA	intron (NM_001483, intron 1 of 9)	L2c|LINE|L2	6278	NM_001483	2631	Hs.591069	NM_001483	ENSG00000146729	NIPSNAP2	GBAS	nipsnap homolog 2	protein-coding	0.000000	0.536232	17(CTGTACATGTTGTTCC,-,0.00),18(TGTACATGTTGTTCCC,+,0.00)
chunk0163_341_1	chr6	15425933	15426186	+	0	NA	intron (NM_001267040, intron 3 of 17)	intron (NM_001267040, intron 3 of 17)	177204	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.007905	0.488189	
chunk0036_454_1	chr11	68673814	68674063	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-10537	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.016064	0.528000	
chunk0115_115_1	chr21	22968374	22968751	+	0	NA	Intergenic	Intergenic	-110722	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.010610	0.335979	
chunk0036_209_1	chr11	63537381	63537693	+	0	NA	intron (NM_004585, intron 1 of 3)	intron (NM_004585, intron 1 of 3)	736	NM_004585	5920	Hs.17466	NM_004585	ENSG00000133321	PLAAT4	HRASLS4|HRSL4|PLA1/2-3|PLAAT-4|RARRES3|RIG1|TIG3	phospholipase A and acyltransferase 4	protein-coding	0.012821	0.527157	
chunk0071_347_1	chr15	88394636	88395327	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	72421	NM_022163	26589	Hs.534261	NM_022163	ENSG00000259494	MRPL46	C15orf4|LIECG2|P2ECSL	mitochondrial ribosomal protein L46	protein-coding	0.002894	0.416185	
chunk0169_161_1	chr6	101935614	101936177	+	0	NA	intron (NM_001166247, intron 13 of 16)	intron (NM_001166247, intron 13 of 16)	536910	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001776	0.315603	248(AAAACAAAATGTTCCT,+,0.00),268(CATGACATACTGTTCT,-,0.00),269(ATGACATACTGTTCTG,+,0.00)
chunk0194_225_1	chr8	86243893	86244384	+	0	NA	Intergenic	L1MC2|LINE|L1	-13763	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.006110	0.351626	
chunk0057_154_1	chr13	100377732	100378285	+	0	NA	intron (NM_001127692, intron 18 of 22)	L1M2|LINE|L1	103007	NR_047686	100885777	Hs.662554	NR_047686		PCCA-AS1	-	PCCA antisense RNA 1	ncRNA	0.010850	0.400722	
chunk0155_230_1	chr5	95536821	95537344	+	0	NA	exon (NM_014639, exon 9 of 43)	exon (NM_014639, exon 9 of 43)	17923	NM_014639	9652	Hs.482868	NM_014639	ENSG00000198677	TTC37	KIAA0372|Ski3|THES	tetratricopeptide repeat domain 37	protein-coding	0.003824	0.320611	
chunk0035_350_1	chr11	48088244	48088619	+	0	NA	intron (NM_002843, intron 1 of 24)	LTR83|LTR|ERVL	-8351	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.008000	0.484043	
chunk0108_401_1	chr2	237449446	237449951	+	0	NA	Intergenic	Intergenic	-35491	NM_004369	1293	Hs.233240	NM_004369	ENSG00000163359	COL6A3	BTHLM1|DYT27|UCMD1	collagen type VI alpha 3 chain	protein-coding	0.015842	0.509881	237(AGCACTGGCTGCTCTG,+,0.00),268(GGGAACACATCGTCCT,-,0.00),269(GGAACACATCGTCCTG,+,0.00)
chunk0069_450_1	chr15	68716240	68716791	+	0	NA	intron (NM_001190456, intron 8 of 11)	L2a|LINE|L2	84527	NM_001190457	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.005445	0.472826	
chunk0096_352_1	chr2	35943770	35944108	+	0	NA	Intergenic	Intergenic	411631	NR_037631	100288911	Hs.432924	NR_037631		CRIM1-DT	-	CRIM1 divergent transcript	ncRNA	0.008876	0.333333	
chunk0183_438_1	chr7	111174415	111174853	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	83628	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.011416	0.346241	
chunk0036_328_1	chr11	66421595	66421968	+	0	NA	intron (NM_178864, intron 1 of 7)	CpG	777	NM_178864	266743	Hs.256036	NM_178864	ENSG00000174576	NPAS4	Le-PAS|NXF|PASD10|bHLHe79	neuronal PAS domain protein 4	protein-coding	0.072386	0.625668	
chunk0030_124_1	chr10	113271558	113272000	+	0	NA	Intergenic	L1ME1|LINE|L1	226424	NR_132769	106635520		NR_132769		SNORA87	-	small nucleolar RNA, H/ACA box 87	snoRNA	0.015837	0.458239	
chunk0084_116_1	chr17	75984686	75984943	+	0	NA	intron (NR_037709, intron 1 of 9)	MER21-int|LTR|ERVL	-5380	NM_007292	51	Hs.464137	NM_004035	ENSG00000161533	ACOX1	ACOX|PALMCOX|SCOX	acyl-CoA oxidase 1	protein-coding	0.007782	0.496124	53(AGTCACAGTCTGTTCC,-,0.00),54(GTCACAGTCTGTTCCT,+,0.00)
chunk0103_44_1	chr2	159285720	159286178	+	0	NA	intron (NM_001307994, intron 1 of 6)	intron (NM_001307994, intron 1 of 6)	603	NM_152528	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.034934	0.511983	
chunk0144_25_1	chr4	124998514	124998987	+	0	NA	Intergenic	Intergenic	-286018	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.002114	0.341772	
chunk0187_197_1	chr7	151765865	151766394	+	0	NA	intron (NM_001040633, intron 3 of 15)	intron (NM_001040633, intron 3 of 15)	-29815	NM_001304527	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.009452	0.445283	
chunk0039_182_1	chr11	100632779	100633466	+	0	NA	Intergenic	Intergenic	-54554	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.008734	0.456395	
chunk0178_75_1	chr7	30349170	30349449	+	0	NA	intron (NM_147128, intron 2 of 4)	MIRc|SINE|MIR	-20741	NR_002186	222161	Hs.112423	NR_002186		DKFZP586I1420	-	uncharacterized protein DKFZp586I1420	pseudo	0.010753	0.378571	
chunk0091_26_1	chr19	3409615	3409875	+	0	NA	intron (NM_205843, intron 2 of 10)	intron (NM_205843, intron 2 of 10)	43178	NM_001245004	4782	Hs.170131	NM_005597	ENSG00000141905	NFIC	CTF|CTF5|NF-I|NFI	nuclear factor I C	protein-coding	0.034615	0.586207	
chunk0074_166_1	chr16	23452643	23452965	+	0	NA	intron (NM_153603, intron 1 of 16)	CpG	387	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.077640	0.662539	
chunk0148_13_1	chr5	208623	209063	+	0	NA	intron (NM_145265, intron 2 of 2)	L1MDa|LINE|L1	9339	NM_145265	133957	Hs.294145	NM_145265	ENSG00000164366	CCDC127	-	coiled-coil domain containing 127	protein-coding	0.022727	0.514739	
chunk0074_177_1	chr16	23643472	23644113	+	0	NA	intron (NM_001199743, intron 2 of 5)	intron (NM_001199743, intron 2 of 5)	2426	NR_037573	84516	Hs.435941	NM_032486	ENSG00000166847	DCTN5	-	dynactin subunit 5	protein-coding	0.003120	0.316199	
chunk0007_273_1	chr1	83671552	83672402	+	0	NA	intron (NR_119375, intron 2 of 2)	intron (NR_119375, intron 2 of 2)	188569	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.000000	0.396005	
chunk0192_79_1	chr8	60812642	60813221	+	0	NA	intron (NM_017780, intron 7 of 37)	L1MC4a|LINE|L1	71672	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.001727	0.277586	
chunk0061_317_1	chr14	62689708	62690169	+	0	NA	Intergenic	L2b|LINE|L2	355300	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.004338	0.376623	
chunk0202_284_1	chr9	77392360	77392743	+	0	NA	intron (NM_033305, intron 68 of 71)	MIRb|SINE|MIR	-55098	NR_121184	101927422	Hs.434324	NR_121184	ENSG00000231373	GNA14-AS1	-	GNA14 antisense RNA 1	ncRNA	0.015666	0.354167	
chunk0168_286_1	chr6	90842899	90843248	+	0	NA	Intergenic	L2a|LINE|L2	-255772	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.002865	0.385714	
chunk0191_126_1	chr8	48569257	48569641	+	0	NA	intron (NR_105002, intron 2 of 3)	intron (NR_105002, intron 2 of 3)	17882	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.005208	0.376623	
chunk0049_56_1	chr12	90063696	90064319	+	0	NA	Intergenic	Intergenic	355052	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.004815	0.301282	
chunk0174_22_1	chr6	153166050	153166426	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-34984	NM_012419	26575	Hs.166313	NM_012419	ENSG00000091844	RGS17	RGS-17|RGSZ2|hRGS17	regulator of G protein signaling 17	protein-coding	0.002660	0.320955	
chunk0207_50_1	chrX	7120355	7120903	+	0	NA	intron (NM_001135565, intron 1 of 4)	L1ME1|LINE|L1	-27231	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.003650	0.408015	
chunk0148_72_1	chr5	2369069	2369640	+	0	NA	Intergenic	(CATG)n|Simple_repeat|Simple_repeat	-57153	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.024518	0.503497	
chunk0137_172_1	chr4	17020953	17021152	+	0	NA	Intergenic	Intergenic	-122243	NR_130734	9079	Hs.714330	NM_001290	ENSG00000169744	LDB2	CLIM1|LDB-2|LDB1	LIM domain binding 2	protein-coding	0.005025	0.465000	
chunk0128_262_1	chr3	109853478	109853761	+	0	NA	Intergenic	Intergenic	250791	NR_039647	100616129		NR_039647	ENSG00000265956	MIR4445	-	microRNA 4445	ncRNA	0.000000	0.404930	
chunk0209_249_1	chrX	45761687	45761901	+	0	NA	Intergenic	HY3|scRNA|scRNA	-14670	NR_029636	407007		NR_029636	ENSG00000207725	MIR222	MIRN222|miRNA222|mir-222	microRNA 222	ncRNA	0.018692	0.362791	
chunk0110_291_1	chr20	17759415	17759749	+	0	NA	Intergenic	L1MD1|LINE|L1	59634	NM_178477	140836	Hs.115366	NM_178477	ENSG00000125888	BANF2	BAF-L|BAF2|BAFL|C20orf179	barrier to autointegration factor 2	protein-coding	0.008982	0.414925	
chunk0109_125_1	chr20	2868647	2869069	+	0	NA	intron (NM_002836, intron 5 of 27)	intron (NM_002836, intron 5 of 27)	-4638	NM_080840	5786	Hs.269577	NM_002836	ENSG00000132670	PTPRA	HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA	protein tyrosine phosphatase receptor type A	protein-coding	0.002370	0.364066	
chunk0081_215_1	chr17	42563534	42564024	+	0	NA	intron (NM_001042529, intron 2 of 9)	intron (NM_001042529, intron 2 of 9)	1705	NM_025233	80347	Hs.296422	NM_025233	ENSG00000068120	COASY	DPCK|NBIA6|NBP|PCH12|PPAT|UKR1|pOV-2	Coenzyme A synthase	protein-coding	0.004082	0.505092	393(AAGATCTCACTGTTCT,-,0.00),394(AGATCTCACTGTTCTT,+,0.00)
chunk0142_344_1	chr4	101400062	101400309	+	0	NA	Intergenic	Intergenic	52408	NR_033874	90024	Hs.534513	NR_033874	ENSG00000254531	FLJ20021	-	uncharacterized LOC90024	ncRNA	0.008097	0.411290	
chunk0043_248_1	chr12	20420576	20421059	+	0	NA	intron (NM_000921, intron 1 of 15)	intron (NM_000921, intron 1 of 15)	51572	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.012422	0.400826	
chunk0077_9_1	chr16	74627540	74628051	+	0	NA	intron (NM_018124, intron 11 of 12)	MER54A|LTR|ERVL	-20651	NM_001145666	2734	Hs.109731	NM_012201	ENSG00000090863	GLG1	CFR-1|ESL-1|MG-160|MG160	golgi glycoprotein 1	protein-coding	0.005871	0.480469	
chunk0060_448_1	chr14	54815028	54815518	+	0	NA	Intergenic	Intergenic	60485	NM_001161577	23034	Hs.98259	NM_015589	ENSG00000020577	SAMD4A	SAMD4|SMAUG|SMAUG1|SMG|SMGA	sterile alpha motif domain containing 4A	protein-coding	0.028571	0.525458	382(CAGCACTGACAGTCCT,-,0.00),383(AGCACTGACAGTCCTA,+,0.00)
chunk0200_197_1	chr9	20115599	20115804	+	0	NA	Intergenic	Intergenic	295537	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.004878	0.402913	83(AAGAACACCCTGTTAT,-,0.00),84(AGAACACCCTGTTATG,+,0.00)
chunk0004_458_1	chr1	53592587	53593140	+	0	NA	intron (NM_147193, intron 3 of 9)	intron (NM_147193, intron 3 of 9)	133464	NM_033067	63948	Hs.131654	NM_033067	ENSG00000143006	DMRTB1	-	DMRT like family B with proline rich C-terminal 1	protein-coding	0.007233	0.568592	431(GGGGACACTATGCCCC,-,0.00),432(GGGACACTATGCCCCT,+,0.00)
chunk0018_50_1	chr1	216399561	216399760	+	0	NA	intron (NM_206933, intron 3 of 71)	L1MDa|LINE|L1	23736	NM_206933	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.005025	0.525000	
chunk0202_358_1	chr9	80074275	80074921	+	0	NA	Intergenic	Intergenic	99575	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.009288	0.497682	451(AGGAACACCTTGGCCT,-,0.00)
chunk0050_401_1	chr12	109385574	109385773	+	0	NA	Intergenic	Intergenic	-3046	NM_001101421	283446	Hs.512008	NM_173597	ENSG00000174527	MYO1H	-	myosin IH	protein-coding	0.010050	0.360000	
chunk0046_118_1	chr12	57301168	57301729	+	0	NA	intron (NM_014925, intron 2 of 21)	MIRc|SINE|MIR	9015	NM_014925	22864	Hs.443673	NM_014925	ENSG00000179912	R3HDM2	CAG6|PR01365	R3H domain containing 2	protein-coding	0.005348	0.384342	
chunk0162_418_1	chr5	180047791	180048171	+	0	NA	intron (NM_018434, intron 1 of 8)	L4_A_Mam|LINE|RTE-X	24137	NM_001280801	55819	Hs.484363	NM_018434	ENSG00000113269	RNF130	G1RZFP|GOLIATH|GP	ring finger protein 130	protein-coding	0.018421	0.475066	
chunk0001_130_1	chr1	5099621	5100084	+	0	NA	Intergenic	Intergenic	444807	NM_018836	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.004320	0.428879	146(CAGCTCAACCTGTTCC,-,0.00),147(AGCTCAACCTGTTCCT,+,0.00)
chunk0040_314_1	chr11	117809491	117809731	+	0	NA	Intergenic	Intergenic	-12350	NM_020693	57453	Hs.659513	NM_020693	ENSG00000177103	DSCAML1	DSCAM2	DS cell adhesion molecule like 1	protein-coding	0.029167	0.593361	
chunk0022_325_1	chr10	16471621	16471883	+	0	NA	intron (NM_030664, intron 2 of 5)	L1ME4a|LINE|L1	34809	NM_030664	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.000000	0.273764	
chunk0004_324_1	chr1	50123062	50123955	+	0	NA	intron (NM_001294348, intron 1 of 6)	UCON105|Unknown|Unknown	13892	NM_001294348	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.003359	0.426174	
chunk0149_389_1	chr5	28678449	28678964	+	0	NA	Intergenic	Intergenic	-248164	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.003883	0.329457	
chunk0174_48_1	chr6	154794930	154795246	+	0	NA	exon (NM_001286189, exon 8 of 22)	exon (NM_001286189, exon 8 of 22)	-58272	NR_036100	100422821		NR_036100	ENSG00000264814	MIR1273C	-	microRNA 1273c	ncRNA	0.012658	0.365931	
chunk0055_55_1	chr13	52553392	52553684	+	0	NA	intron (NR_002793, intron 17 of 23)	L1MA8|LINE|L1	-63932	NM_001011724	144983	Hs.447506	NM_001011724	ENSG00000139675	HNRNPA1L2	-	heterogeneous nuclear ribonucleoprotein A1 like 2	protein-coding	0.010274	0.389078	
chunk0111_260_1	chr20	31054951	31055512	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	-202433	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.023173	0.418149	
chunk0109_423_1	chr2	241285221	241285696	+	0	NA	intron (NM_005336, intron 1 of 27)	intron (NM_005336, intron 1 of 27)	-12627	NM_203346	3069	Hs.471851	NM_005336	ENSG00000115677	HDLBP	HBP|PRO2900|VGL	high density lipoprotein binding protein	protein-coding	0.008421	0.403361	
chunk0070_418_1	chr15	77699558	77699790	+	0	NA	intron (NM_001301192, intron 2 of 4)	intron (NM_001301192, intron 2 of 4)	-3179	NM_001301199	84894	Hs.656765	NM_032808	ENSG00000169783	LINGO1	LERN1|LRRN6A|MRT64|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding	0.004310	0.429185	
chunk0189_49_1	chr8	20010452	20010885	+	0	NA	Intergenic	Intergenic	71597	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.004619	0.384793	
chunk0085_160_1	chr18	3671091	3671636	+	0	NA	intron (NM_001308390, intron 4 of 10)	intron (NM_001308390, intron 4 of 10)	67626	NR_119377	84777	Hs.659053	NM_032691		DLGAP1-AS2	-	DLGAP1 antisense RNA 2	ncRNA	0.003670	0.402930	
chunk0185_451_1	chr7	135074071	135074483	+	0	NA	intron (NM_178563, intron 12 of 16)	MLT1K|LTR|ERVL-MaLR	-73737	NM_018295	55281	Hs.521213	NM_018295	ENSG00000146859	TMEM140	-	transmembrane protein 140	protein-coding	0.004854	0.368039	
chunk0047_379_1	chr12	75248157	75248824	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-38742	NM_139137	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.001499	0.318862	
chunk0075_110_1	chr16	49061267	49061466	+	0	NA	Intergenic	Intergenic	220465	NM_004352	869	Hs.458423	NM_004352	ENSG00000102924	CBLN1	-	cerebellin 1 precursor	protein-coding	0.005025	0.520000	
chunk0172_448_1	chr6	140988757	140989241	+	0	NA	Intergenic	Intergenic	305185	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.002066	0.336082	
chunk0167_3_1	chr6	53433448	53434115	+	0	NA	Intergenic	Intergenic	-84602	NM_021814	60481	Hs.520189	NM_021814	ENSG00000012660	ELOVL5	HELO1|SCA38|dJ483K16.1	ELOVL fatty acid elongase 5	protein-coding	0.007496	0.369760	
chunk0115_413_1	chr21	31151634	31152062	+	0	NA	intron (NM_003253, intron 20 of 28)	intron (NM_003253, intron 20 of 28)	-113372	NM_001099219	728299	Hs.580875	NM_001099219	ENSG00000206102	KRTAP19-8	-	keratin associated protein 19-8	protein-coding	0.011682	0.391608	272(AAGGACACCGTGTGCT,-,0.00),273(AGGACACCGTGTGCTG,+,0.00)
chunk0009_20_1	chr1	100078386	100078740	+	0	NA	intron (NM_033055, intron 10 of 11)	intron (NM_033055, intron 10 of 11)	40330	NM_033055	64645	Hs.124156	NM_033055	ENSG00000156875	MFSD14A	HIAT1	major facilitator superfamily domain containing 14A	protein-coding	0.005650	0.391549	196(AAGTACAGAATGTTCT,-,0.00),197(AGTACAGAATGTTCTA,+,0.00)
chunk0054_71_1	chr13	42136762	42137328	+	0	NA	promoter-TSS (NM_001297429)	promoter-TSS (NM_001297429)	-997	NM_001297429	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.001767	0.324515	266(CAGAACAAAATGTTCT,-,0.00),267(AGAACAAAATGTTCTT,+,0.00)
chunk0205_104_1	chr9	107517798	107519092	+	0	NA	Intergenic	Intergenic	-28725	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.008501	0.430116	
chunk0038_68_1	chr11	83051869	83052214	+	0	NA	intron (NM_014488, intron 1 of 5)	intron (NM_014488, intron 1 of 5)	-10443	NR_033347	100379250	Hs.725115	NR_033347	ENSG00000207221	SNORA70E	U70E	small nucleolar RNA, H/ACA box 70E	snoRNA	0.002899	0.387283	
chunk0035_201_1	chr11	44648062	44648413	+	0	NA	Intergenic	L1ME1|LINE|L1	82646	NM_002231	3732	Hs.527778	NM_002231	ENSG00000085117	CD82	4F9|C33|GR15|IA4|KAI1|R2|SAR2|ST6|TSPAN27	CD82 molecule	protein-coding	0.002849	0.315341	
chunk0101_358_1	chr2	137943173	137943372	+	0	NA	Intergenic	Intergenic	-15340	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.005025	0.490000	
chunk0157_369_1	chr5	123546696	123547059	+	0	NA	intron (NM_001031812, intron 2 of 12)	intron (NM_001031812, intron 2 of 12)	1460	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.002755	0.280220	
chunk0050_8_1	chr12	99596656	99596861	+	0	NA	intron (NM_152788, intron 9 of 25)	intron (NM_152788, intron 9 of 25)	-50992	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.004878	0.315534	
chunk0188_27_1	chr8	6562110	6562635	+	0	NA	intron (NM_001147, intron 1 of 8)	intron (NM_001147, intron 1 of 8)	891	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.019048	0.425856	
chunk0101_424_1	chr2	139279321	139280022	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	382347	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005706	0.411681	356(AAGGACAGTCAGTACC,-,0.00),357(AGGACAGTCAGTACCA,+,0.00)
chunk0173_132_1	chr6	143745379	143745837	+	0	NA	intron (NM_001100166, intron 2 of 11)	intron (NM_001100166, intron 2 of 11)	67643	NM_001100165	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.024017	0.459695	
chunk0071_38_1	chr15	79823100	79823624	+	0	NA	Intergenic	Intergenic	73635	NR_037654	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.007634	0.428571	
chunk0212_260_1	chrX	139580906	139581452	+	0	NA	TTS (NM_005369)	TTS (NM_005369)	50443	NM_000133	2158	Hs.522798	NM_000133	ENSG00000101981	F9	F9 p22|FIX|HEMB|P19|PTC|THPH8	coagulation factor IX	protein-coding	0.009158	0.380256	
chunk0110_127_1	chr20	13090518	13091004	+	0	NA	intron (NM_018327, intron 4 of 11)	L1ME3A|LINE|L1	81782	NM_018327	55304	Hs.425023	NM_018327	ENSG00000172296	SPTLC3	C20orf38|LCB 3|LCB2B|LCB3|SPT 3|SPT3|SPTLC2L|dJ718P11|dJ718P11.1|hLCB2b	serine palmitoyltransferase long chain base subunit 3	protein-coding	0.002058	0.355236	240(GATACAGCCTGTACTT,+,0.00)
chunk0139_370_1	chr4	60662469	60662925	+	0	NA	Intergenic	LTR1E|LTR|ERV1	-259922	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.396061	
chunk0047_79_1	chr12	67801660	67802233	+	0	NA	Intergenic	Intergenic	-72471	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.003490	0.334495	
chunk0160_178_1	chr5	154008952	154009154	+	0	NA	intron (NM_018691, intron 9 of 13)	L1MC4|LINE|L1	29884	NM_018691	10827	Hs.166551	NM_018691	ENSG00000055147	FAM114A2	133K02|C5orf3	family with sequence similarity 114 member A2	protein-coding	0.004950	0.369458	
chunk0118_331_1	chr22	35467704	35468168	+	0	NA	Intergenic	Intergenic	67813	NM_006739	4174	Hs.517582	NM_006739	ENSG00000100297	MCM5	CDC46|MGORS8|P1-CDC46	minichromosome maintenance complex component 5	protein-coding	0.017241	0.630108	194(GAGGACAGGCTGTGCT,-,0.00),195(AGGACAGGCTGTGCTG,+,0.00)
chunk0107_376_1	chr2	223090048	223090439	+	0	NA	Intergenic	Intergenic	38313	NM_080671	23704	Hs.348522	NM_080671	ENSG00000152049	KCNE4	MIRP3	potassium voltage-gated channel subfamily E regulatory subunit 4	protein-coding	0.010230	0.405612	182(CTGAACTGCATGTTCT,-,0.00),183(TGAACTGCATGTTCTT,+,0.00),285(AGGAACAGCCAGAGCC,-,0.00)
chunk0009_386_1	chr1	109994682	109995128	+	0	NA	intron (NM_001242673, intron 1 of 16)	intron (NM_001242673, intron 1 of 16)	-6022	NM_001242674	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.002242	0.422819	256(GGGAACATGGTGTTCT,-,0.00),257(GGAACATGGTGTTCTC,+,0.00)
chunk0208_5_1	chrX	10083235	10083489	+	0	NA	intron (NM_015691, intron 5 of 22)	intron (NM_015691, intron 5 of 22)	67607	NM_015691	55841	Hs.527524	NM_015691	ENSG00000047644	WWC3	BM042	WWC family member 3	protein-coding	0.011811	0.584314	
chunk0055_184_1	chr13	61478874	61479720	+	0	NA	Intergenic	L1PREC2|LINE|L1	-63775	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.004728	0.342385	
chunk0088_127_1	chr18	45779305	45779721	+	0	NA	Intergenic	L1MEg|LINE|L1	-46067	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.012019	0.402878	
chunk0210_369_1	chrX	96969105	96969651	+	0	NA	intron (NM_006729, intron 17 of 26)	L1PA16|LINE|L1	85470	NM_013347	29935	Hs.659349	NM_013347	ENSG00000204086	RPA4	HSU24186	replication protein A4	protein-coding	0.003663	0.341865	
chunk0037_380_1	chr11	78534045	78534323	+	0	NA	intron (NR_120566, intron 1 of 3)	L1MC1|LINE|L1	1008	NR_120566	101928896	Hs.659055	NR_120566	ENSG00000255084	LOC101928896	-	uncharacterized LOC101928896	ncRNA	0.007194	0.401434	
chunk0107_245_1	chr2	217255338	217255910	+	0	NA	Intergenic	L1MA8|LINE|L1	-27109	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.003497	0.373473	
chunk0080_331_1	chr17	32570962	32571161	+	0	NA	intron (NM_015194, intron 21 of 21)	intron (NM_015194, intron 21 of 21)	83974	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.000000	0.515000	
chunk0207_129_1	chr9	129071687	129072020	+	0	NA	3' UTR (NM_032809, exon 16 of 16)	3' UTR (NM_032809, exon 16 of 16)	-9251	NM_020438	57171	Hs.21701	NM_020438	ENSG00000167130	DOLPP1	LSFR2	dolichyldiphosphatase 1	protein-coding	0.021021	0.586826	
chunk0072_178_1	chr15	93997170	93997570	+	0	NA	intron (NR_120320, intron 3 of 8)	intron (NR_120320, intron 3 of 8)	96669	NR_120323	101927129	Hs.652658	NR_120322	ENSG00000258785	LINC01580	-	long intergenic non-protein coding RNA 1580	ncRNA	0.010000	0.329177	
chunk0187_221_1	chr7	152162358	152162802	+	0	NA	exon (NM_170606, exon 43 of 59)	exon (NM_170606, exon 43 of 59)	136906	NM_022087	63917	Hs.647109	NM_022087	ENSG00000178234	GALNT11	GALNAC-T11|GALNACT11	polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0.011261	0.467416	
chunk0026_78_1	chr10	61323717	61324143	+	0	NA	Intergenic	Intergenic	-128709	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.000000	0.306792	
chunk0091_385_1	chr19	15981209	15981472	+	0	NA	Intergenic	Intergenic	32332	NM_001004465	126541	Hs.553579	NM_001004465	ENSG00000176231	OR10H4	OR19-28	olfactory receptor family 10 subfamily H member 4	protein-coding	0.007605	0.587121	148(GGGAGCACAATGTCCT,-,0.00),149(GGAGCACAATGTCCTG,+,0.00)
chunk0133_151_1	chr3	169428160	169428453	+	0	NA	intron (NM_004991, intron 1 of 16)	MER1B|DNA|hAT-Charlie	235469	NM_004991	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.010239	0.438776	
chunk0161_98_1	chr5	167371656	167372053	+	0	NA	intron (NM_001122679, intron 1 of 28)	intron (NM_001122679, intron 1 of 28)	87016	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.005038	0.369347	
chunk0166_232_1	chr6	47059257	47059456	+	0	NA	Intergenic	Intergenic	-16993	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.010050	0.490000	
chunk0048_457_1	chr12	88904834	88905070	+	0	NA	Intergenic	Intergenic	114740	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.008475	0.443038	
chunk0155_393_1	chr5	98779152	98779851	+	0	NA	intron (NM_001012761, intron 3 of 4)	intron (NM_001012761, intron 3 of 4)	-6417	NR_033932	503569	Hs.586188	NR_033932	ENSG00000246763	RGMB-AS1	-	RGMB antisense RNA 1	ncRNA	0.015737	0.417143	
chunk0083_99_1	chr17	64536712	64537384	+	0	NA	exon (NM_001316990, exon 18 of 19)	exon (NM_001316990, exon 18 of 19)	30312	NM_001316990	90799	Hs.569713	NM_138363	ENSG00000258890	CEP95	CCDC45	centrosomal protein 95	protein-coding	0.004464	0.377415	
chunk0202_196_1	chr9	75124329	75124715	+	0	NA	intron (NM_012383, intron 2 of 9)	L1MA2|LINE|L1	36040	NM_012383	26578	Hs.494192	NM_012383	ENSG00000134996	OSTF1	OSF|SH3P2|bA235O14.1	osteoclast stimulating factor 1	protein-coding	0.007772	0.369509	
chunk0079_214_1	chr17	14817381	14817964	+	0	NA	Intergenic	Intergenic	-213303	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.010292	0.364726	
chunk0060_380_1	chr14	52610508	52611008	+	0	NA	intron (NM_001099652, intron 3 of 6)	intron (NM_001099652, intron 3 of 6)	57610	NM_001099652	283554	Hs.416214	NM_001099652	ENSG00000180998	GPR137C	TM7SF1L2	G protein-coupled receptor 137C	protein-coding	0.006000	0.327345	
chunk0125_213_1	chr3	67561069	67561531	+	0	NA	intron (NM_001177599, intron 2 of 10)	intron (NM_001177599, intron 2 of 10)	93314	NM_001177599	8801	Hs.644919	NM_003848	ENSG00000172340	SUCLG2	G-SCS|GBETA|GTPSCS	succinate-CoA ligase GDP-forming beta subunit	protein-coding	0.002165	0.371490	
chunk0096_424_1	chr2	38284192	38284510	+	0	NA	Intergenic	Intergenic	92179	NM_001308076	64225	Hs.594950	NM_022374	ENSG00000119787	ATL2	ARL3IP2|ARL6IP2|aip-2|atlastin2	atlastin GTPase 2	protein-coding	0.000000	0.373041	
chunk0138_135_1	chr4	36740327	36740823	+	0	NA	Intergenic	Intergenic	-314147	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.006048	0.388330	
chunk0201_72_1	chr9	34185537	34186413	+	0	NA	intron (NM_001171201, intron 1 of 5)	MIRb|SINE|MIR	6970	NM_001171203	51271	Hs.268963	NM_016525	ENSG00000165006	UBAP1	NAG20|SPG80|UAP|UBAP|UBAP-1	ubiquitin associated protein 1	protein-coding	0.010274	0.415051	587(GTGAACTGCTTGTTCT,-,0.00),588(TGAACTGCTTGTTCTC,+,0.00)
chunk0183_432_1	chr7	111145352	111145845	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	54592	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.006085	0.364372	246(AGGAACAGCATGTACC,-,0.00),247(GGAACAGCATGTACCC,+,0.00)
chunk0168_194_1	chr6	85452072	85452673	+	0	NA	intron (NM_002526, intron 1 of 8)	intron (NM_002526, intron 1 of 8)	2788	NM_002526	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.006656	0.383721	
chunk0039_188_1	chr11	100757577	100758049	+	0	NA	intron (NM_152432, intron 1 of 23)	intron (NM_152432, intron 1 of 23)	-69858	NR_133571	100128386	Hs.635125	NR_133571	ENSG00000248027	LOC100128386	-	uncharacterized LOC100128386	ncRNA	0.002119	0.344609	
chunk0054_335_1	chr13	49384602	49384874	+	0	NA	intron (NM_001079670, intron 3 of 10)	Tigger1|DNA|TcMar-Tigger	16800	NM_030925	81617	Hs.87159	NM_030925	ENSG00000102547	CAB39L	MO25-BETA|MO2L|bA103J18.3	calcium binding protein 39 like	protein-coding	0.000000	0.344322	
chunk0212_79_1	chrY	11539074	11539621	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	882243	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.036563	0.383212	
chunk0096_358_1	chr2	36364154	36364509	+	0	NA	intron (NM_016441, intron 1 of 16)	intron (NM_016441, intron 1 of 16)	8104	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.002817	0.384831	
chunk0120_14_1	chr3	1238063	1238442	+	0	NA	intron (NM_001289080, intron 4 of 22)	L1PBa|LINE|L1	145594	NM_014461	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.010554	0.350000	
chunk0090_154_1	chr18	72393106	72393609	+	0	NA	Intergenic	L1MC3|LINE|L1	151131	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.005964	0.361111	
chunk0193_297_1	chr8	77814834	77815069	+	0	NA	Intergenic	L1PB4|LINE|L1	364254	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.347458	
chunk0046_331_1	chr12	62760760	62761232	+	0	NA	intron (NM_020700, intron 4 of 9)	Tigger15a|DNA|TcMar-Tigger	157310	NR_029661	406891		NR_029661	ENSG00000199179	MIRLET7I	LET7I|MIRNLET7I|hsa-let-7i|let-7i	microRNA let-7i	ncRNA	0.006356	0.382664	
chunk0211_126_1	chrX	112550840	112551234	+	0	NA	Intergenic	L1PA6|LINE|L1	129110	NM_178175	340596	Hs.297420	NM_178175	ENSG00000182508	LHFPL1	-	LHFPL tetraspan subfamily member 1	protein-coding	0.005076	0.468354	
chunk0170_289_1	chr6	115131824	115132146	+	0	NA	Intergenic	LTR28C|LTR|ERV1	-906746	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.003106	0.455108	
chunk0098_80_1	chr2	67446499	67447185	+	0	NA	Intergenic	Intergenic	49532	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.007289	0.384279	310(CAGGACAGTCTGTGAT,-,0.00),311(AGGACAGTCTGTGATT,+,0.00)
chunk0047_260_1	chr12	72757203	72757498	+	0	NA	Intergenic	L1MA4A|LINE|L1	-401840	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.003390	0.584459	
chunk0069_244_1	chr15	64249934	64250138	+	0	NA	intron (NM_022048, intron 4 of 11)	intron (NM_022048, intron 4 of 11)	-86881	NM_000942	5479	Hs.434937	NM_000942	ENSG00000166794	PPIB	B|CYP-S1|CYPB|HEL-S-39|OI9|SCYLP	peptidylprolyl isomerase B	protein-coding	0.000000	0.360976	
chunk0149_402_1	chr5	28998453	28998700	+	0	NA	Intergenic	Intergenic	-66668	NR_109948	101929645	Hs.531878	NR_109948		LOC101929645	-	uncharacterized LOC101929645	ncRNA	0.012146	0.379032	
chunk0172_380_1	chr6	139376721	139377103	+	0	NA	Intergenic	L2c|LINE|L2	-2262	NM_006079	10370	Hs.82071	NM_006079	ENSG00000164442	CITED2	ASD8|MRG-1|MRG1|P35SRJ|VSD2	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2	protein-coding	0.002618	0.493473	
chunk0036_240_1	chr11	64329540	64329739	+	0	NA	Intergenic	L1MB7|LINE|L1	-10579	NM_032251	283234	Hs.98564	NM_032251	ENSG00000168071	CCDC88B	BRLZ|CCDC88|HKRP3|gipie	coiled-coil domain containing 88B	protein-coding	0.020101	0.465000	
chunk0111_379_1	chr20	33998166	33998716	+	0	NA	intron (NM_016732, intron 1 of 9)	intron (NM_016732, intron 1 of 9)	-4074	NR_109885	101926888	Hs.405849	NR_109885	ENSG00000285230	RALY-AS1	-	RALY antisense RNA 1	ncRNA	0.009091	0.475499	239(AGGAACAGTAAGTTCA,-,0.00),240(GGAACAGTAAGTTCAG,+,0.00)
chunk0095_242_1	chr2	19178219	19179387	+	0	NA	Intergenic	L1MC2|LINE|L1	-169626	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.003425	0.395210	
chunk0181_305_1	chr7	87159449	87160073	+	0	NA	intron (NM_021145, intron 3 of 19)	Tigger3a|DNA|TcMar-Tigger	7207	NM_021145	9988	Hs.196129	NM_021145	ENSG00000135164	DMTF1	DMP1|DMTF|MRUL|hDMP1	cyclin D binding myb like transcription factor 1	protein-coding	0.009615	0.345600	
chunk0142_8_1	chr4	89847765	89848792	+	0	NA	Intergenic	AluJb|SINE|Alu	-9982	NM_001146055	6622	Hs.21374	NM_000345	ENSG00000145335	SNCA	NACP|PARK1|PARK4|PD1	synuclein alpha	protein-coding	0.004869	0.366732	
chunk0114_149_1	chr21	10403029	10403298	+	0	NA	Intergenic	Intergenic	-10357	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.029740	0.577778	
chunk0137_178_1	chr4	17490598	17491075	+	0	NA	intron (NM_001306140, intron 4 of 5)	intron (NM_001306140, intron 4 of 5)	21398	NM_001306140	5860	Hs.75438	NM_000320	ENSG00000151552	QDPR	DHPR|HDHPR|PKU2|SDR33C1	quinoid dihydropteridine reductase	protein-coding	0.012579	0.479079	
chunk0128_268_1	chr3	110538505	110538974	+	0	NA	Intergenic	MIRc|SINE|MIR	531220	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.002132	0.302128	
chunk0062_289_1	chr14	72433616	72434176	+	0	NA	intron (NM_001204418, intron 3 of 16)	MIR|SINE|MIR	-82924	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.014286	0.486631	
chunk0161_207_1	chr5	170596923	170597436	+	0	NA	intron (NM_001278339, intron 1 of 7)	intron (NM_001278339, intron 1 of 7)	93143	NM_001278340	30820	Hs.484111	NM_014592	ENSG00000182132	KCNIP1	KCHIP1|VABP	potassium voltage-gated channel interacting protein 1	protein-coding	0.011696	0.496109	5(GAGCACTGGCTGTGCA,-,0.00),6(AGCACTGGCTGTGCAC,+,0.00)
chunk0078_427_1	chr16	89410659	89411241	+	0	NA	intron (NM_001256182, intron 3 of 13)	intron (NM_001256182, intron 3 of 13)	-19968	NR_110931	101927817	Hs.667942	NR_110931		LOC101927817	-	uncharacterized LOC101927817	ncRNA	0.024055	0.571184	
chunk0201_13_1	chr9	32953838	32954098	+	0	NA	Intergenic	MER41D|LTR|ERV1	47608	NR_036579									0.003846	0.379310	
chunk0130_3_1	chr3	128335506	128335900	+	0	NA	intron (NM_021937, intron 4 of 6)	L2a|LINE|L2	-127891	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.010152	0.567089	
chunk0132_9_1	chr3	154324767	154325408	+	0	NA	promoter-TSS (NM_020865)	promoter-TSS (NM_020865)	-590	NM_020865	170506	Hs.446270	NM_020865	ENSG00000174953	DHX36	DDX36|G4R1|MLEL1|RHAU	DEAH-box helicase 36	protein-coding	0.010920	0.384735	319(TTGTACAAGCTGTTCT,-,0.00),320(TGTACAAGCTGTTCTT,+,0.00)
chunk0102_72_1	chr2	142997249	142997556	+	0	NA	intron (NM_003937, intron 10 of 13)	intron (NM_003937, intron 10 of 13)	119776	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.003257	0.327922	
chunk0081_263_1	chr17	43484002	43484273	+	0	NA	exon (NM_001302623, exon 1 of 23)	exon (NM_001302623, exon 1 of 23)	220	NM_004941	1659	Hs.463105	NM_004941	ENSG00000067596	DHX8	DDX8|Dhr2|HRH1|PRP22|PRPF22	DEAH-box helicase 8	protein-coding	0.033210	0.573529	
chunk0118_118_1	chr22	29417776	29418033	+	0	NA	Intergenic	Intergenic	-20679	NM_021026	5988	Hs.648249	NM_021026	ENSG00000128250	RFPL1	RNF78	ret finger protein like 1	protein-coding	0.007782	0.492248	
chunk0151_435_1	chr5	55995238	55995437	+	0	NA	promoter-TSS (NM_175767)	promoter-TSS (NM_175767)	170	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.090452	0.675000	
chunk0020_47_1	chr1	232306396	232306844	+	0	NA	Intergenic	Intergenic	208988	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.013393	0.561247	
chunk0101_196_1	chr2	129906986	129907246	+	0	NA	Intergenic	Intergenic	-16061	NR_110285	101927924	Hs.570248	NR_110285	ENSG00000237574	LINC01856	-	long intergenic non-protein coding RNA 1856	ncRNA	0.030769	0.559387	
chunk0184_18_1	chr7	111803223	111803948	+	0	NA	intron (NM_014705, intron 30 of 51)	intron (NM_014705, intron 30 of 51)	-4920	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.005517	0.349862	
chunk0146_50_1	chr4	155671123	155671322	+	0	NA	intron (NM_000856, intron 3 of 10)	intron (NM_000856, intron 3 of 10)	3559	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.005025	0.415000	
chunk0059_280_1	chr14	35526962	35527320	+	0	NA	Intergenic	Intergenic	-6901	NM_032594	84684	Hs.62813	NM_032594	ENSG00000168348	INSM2	IA-6|IA6|mlt1	INSM transcriptional repressor 2	protein-coding	0.005587	0.337047	
chunk0098_367_1	chr2	78302250	78302679	+	0	NA	Intergenic	L1MC|LINE|L1	-11733	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.002331	0.269767	
chunk0071_213_1	chr15	84716001	84716242	+	0	NA	non-coding (NR_073518, exon 1 of 7)	non-coding (NR_073518, exon 1 of 7)	339	NR_073518	23478	Hs.9534	NM_014300	ENSG00000140612	SEC11A	1810012E07Rik|SEC11L1|SPC18|SPCS4A|sid2895	SEC11 homolog A, signal peptidase complex subunit	protein-coding	0.103734	0.673554	
chunk0112_126_1	chr20	38491528	38492002	+	0	NA	intron (NM_020336, intron 2 of 29)	MIRc|SINE|MIR	18959	NM_001282917	57148	Hs.598850	NM_020336	ENSG00000170471	RALGAPB	KIAA1219|RalGAPbeta	Ral GTPase activating protein non-catalytic beta subunit	protein-coding	0.004219	0.383158	
chunk0199_195_1	chr9	4803584	4804168	+	0	NA	intron (NM_001286699, intron 1 of 6)	intron (NM_001286699, intron 1 of 6)	11042	NM_001286700	10171	Hs.194121	NM_005772	ENSG00000120158	RCL1	RNAC|RPCL1	RNA terminal phosphate cyclase like 1	protein-coding	0.018836	0.487179	271(TGGAACGGGCTGTTCC,-,0.00),272(GGAACGGGCTGTTCCC,+,0.00)
chunk0044_74_1	chr12	28021889	28022104	+	0	NA	Intergenic	Intergenic	-50013	NM_002820	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.009302	0.310185	
chunk0162_168_1	chr6	3640100	3640894	+	0	NA	Intergenic	Intergenic	111515	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.008816	0.387421	
chunk0028_189_1	chr10	88541261	88541722	+	0	NA	intron (NM_001031709, intron 4 of 6)	intron (NM_001031709, intron 4 of 6)	41834	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.013015	0.350649	322(GAGAACACATTGTACT,-,0.00),323(AGAACACATTGTACTA,+,0.00)
chunk0196_130_1	chr8	103979631	103980346	+	0	NA	intron (NM_001282881, intron 13 of 20)	L1MA2|LINE|L1	160800	NM_014677	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.005594	0.497207	335(GGGACAAAGTGCTCTG,+,0.00)
chunk0111_79_1	chr20	23199809	23200229	+	0	NA	Intergenic	L1M5|LINE|L1	-67383	NR_034149	200261	Hs.352228	NM_182535	ENSG00000233746	LINC00656	-	long intergenic non-protein coding RNA 656	ncRNA	0.004762	0.448931	
chunk0065_52_1	chr15	22786114	22786316	+	0	NA	promoter-TSS (NM_144599)	promoter-TSS (NM_144599)	-10	NM_001142275	123606	Hs.511797	NM_144599	ENSG00000170113	NIPA1	FSP3|SLC57A1|SPG6	NIPA magnesium transporter 1	protein-coding	0.108911	0.679803	
chunk0139_269_1	chr4	56699941	56700229	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-18379	NM_001145460	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.003472	0.397924	
chunk0066_101_1	chr15	29853189	29854097	+	0	NA	intron (NM_001301025, intron 2 of 28).2	intron (NM_001301025, intron 2 of 28).2	-31140	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.009912	0.365237	
chunk0142_401_1	chr4	102759677	102760393	+	0	NA	intron (NM_005908, intron 1 of 16)	intron (NM_005908, intron 1 of 16)	959	NM_005908	4126	Hs.480415	NM_005908	ENSG00000109323	MANBA	MANB1	mannosidase beta	protein-coding	0.020950	0.421199	
chunk0104_295_1	chr2	178735136	178735686	+	0	NA	intron (NM_133378, intron 47 of 311)	intron (NM_133378, intron 47 of 311)	-41515	NR_120594	101927055	Hs.570275	NR_120594	ENSG00000237298	LOC101927055	-	uncharacterized LOC101927055	ncRNA	0.001818	0.352087	
chunk0152_314_1	chr5	61934134	61935160	+	0	NA	Intergenic	Intergenic	-198949	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.006823	0.415774	
chunk0053_218_1	chr13	32130326	32130903	+	0	NA	intron (NM_023037, intron 7 of 60)	intron (NM_023037, intron 7 of 60)	-98975	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.005199	0.351211	
chunk0012_26_1	chr1	154975169	154975368	+	0	NA	promoter-TSS (NR_036212)	promoter-TSS (NR_036212)	-425	NR_036212	100423020		NR_036212	ENSG00000264349	MIR4258	-	microRNA 4258	ncRNA	0.030151	0.450000	
chunk0050_344_1	chr12	107525390	107525649	+	0	NA	intron (NM_001018072, intron 2 of 16)	Tigger3a|DNA|TcMar-Tigger	-55338	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.011583	0.426923	
chunk0084_405_1	chr17	82231802	82232194	+	0	NA	promoter-TSS (NM_001042423)	promoter-TSS (NM_001042423)	-234	NM_001042423	9123	Hs.500761	NM_004207	ENSG00000141526	SLC16A3	MCT 3|MCT 4|MCT-3|MCT-4|MCT3|MCT4	solute carrier family 16 member 3	protein-coding	0.066327	0.704835	
chunk0005_233_1	chr1	59451459	59452393	+	0	NA	intron (NM_001244714, intron 3 of 13)	L1MEj|LINE|L1	-63703	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.002141	0.321925	
chunk0056_148_1	chr13	84003760	84004207	+	0	NA	Intergenic	Intergenic	-121590	NM_001281503	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.241071	
chunk0093_339_1	chr19	54815145	54815548	+	0	NA	TTS (NM_001080770).30	TTS (NM_001080770).30	-1092	NM_013289	3811	Hs.645228	NM_013289	ENSG00000167633	KIR3DL1	CD158E1|KIR|KIR3DL1/S1|NKAT-3|NKAT3|NKB1|NKB1B	killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1	protein-coding	0.007444	0.334158	224(AGGGACTGTGTGTACA,-,0.00),225(GGGACTGTGTGTACAC,+,0.00)
chunk0090_58_1	chr19	2032186	2032856	+	0	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-16818	NM_017797	55643	Hs.465543	NM_017797	ENSG00000133243	BTBD2	-	BTB domain containing 2	protein-coding	0.035821	0.612519	303(GAAGACAAGCTGTTCC,-,0.00),304(AAGACAAGCTGTTCCT,+,0.00)
chunk0126_257_1	chr3	79535854	79536178	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	28129	NR_037488	100500877		NR_037488	ENSG00000265193	MIR3923	-	microRNA 3923	ncRNA	0.003086	0.301538	
chunk0061_243_1	chr14	60925336	60925628	+	0	NA	intron (NM_002431, intron 7 of 7)	intron (NM_002431, intron 7 of 7)	55597	NM_020810	57570	Hs.380159	NM_020810	ENSG00000126814	TRMT5	COXPD26|KIAA1393|TRM5	tRNA methyltransferase 5	protein-coding	0.000000	0.430034	
chunk0037_448_1	chr11	80587831	80588347	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	174714	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.007752	0.373308	
chunk0024_360_1	chr10	43981630	43982020	+	0	NA	Intergenic	L1MB3|LINE|L1	72521	NR_033846	283033	Hs.178244	NR_033846		LINC00841	-	long intergenic non-protein coding RNA 841	ncRNA	0.005128	0.378517	160(AAGTACTCTGTGTACC,-,0.00),161(AGTACTCTGTGTACCT,+,0.00),230(TGAGCACAGTGTTCTC,+,0.00)
chunk0085_410_1	chr18	10408884	10409257	+	0	NA	intron (NR_110775, intron 1 of 2)	intron (NR_110775, intron 1 of 2)	5300	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.005362	0.318182	
chunk0070_168_1	chr15	71414762	71415197	+	0	NA	intron (NM_024817, intron 6 of 16)	intron (NM_024817, intron 6 of 16)	-132223	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.004598	0.392202	
chunk0182_148_1	chr7	95287319	95287540	+	0	NA	intron (NM_017650, intron 14 of 15)	intron (NM_017650, intron 14 of 15)	37143	NM_000446	5444	Hs.370995	NM_000446	ENSG00000005421	PON1	ESA|MVCD5|PON	paraoxonase 1	protein-coding	0.009050	0.477477	
chunk0102_13_1	chr2	141455157	141455578	+	0	NA	intron (NM_018557, intron 3 of 90)	intron (NM_018557, intron 3 of 90)	676334	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.011876	0.369668	
chunk0076_364_1	chr16	71948496	71948695	+	0	NA	intron (NM_181536, intron 21 of 29)	intron (NM_181536, intron 21 of 29)	51383	NM_181536	342372	Hs.675286	NM_181536	ENSG00000277481	PKD1L3	-	polycystin 1 like 3, transient receptor potential channel interacting	protein-coding	0.010050	0.410000	126(GAGCACTGGCTGTTCA,-,0.00),127(AGCACTGGCTGTTCAT,+,0.00)
chunk0179_19_1	chr7	42628657	42629268	+	0	NA	Intergenic	Intergenic	77485	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.001637	0.390523	382(TACACAGTGTGTCCTT,+,0.00)
chunk0080_118_1	chr17	27226626	27226909	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	67229	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.003534	0.320423	
chunk0115_163_1	chr21	24737376	24737997	+	0	NA	Intergenic	Intergenic	-102864	NR_046198	339622	Hs.616316	NR_046198	ENSG00000226983	LINC01692	-	long intergenic non-protein coding RNA 1692	ncRNA	0.009662	0.355305	
chunk0017_345_1	chr1	211742479	211742765	+	0	NA	TTS (NM_014873)	TTS (NM_014873)	-66992	NM_001204182	4751	Hs.153704	NM_002497	ENSG00000117650	NEK2	HsPK21|NEK2A|NLK1|PPP1R111|RP67	NIMA related kinase 2	protein-coding	0.000000	0.442509	
chunk0148_285_1	chr5	11596518	11596923	+	0	NA	intron (NR_109988, intron 2 of 21)	intron (NR_109988, intron 2 of 21)	-7803	NM_001288715	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.007407	0.344828	160(TGGAACATTTTGTCCT,-,0.00),161(GGAACATTTTGTCCTT,+,0.00)
chunk0095_29_1	chr2	12882130	12882697	+	0	NA	Intergenic	Intergenic	124600	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.008818	0.385563	311(TGGCTCACTGTGTTCC,-,0.00),312(GGCTCACTGTGTTCCC,+,0.00)
chunk0102_97_1	chr2	144239007	144239582	+	0	NA	intron (NM_001164629, intron 1 of 11)	intron (NM_001164629, intron 1 of 11)	-1955	NM_024659	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.006957	0.380208	
chunk0053_261_1	chr13	33081625	33082219	+	0	NA	Intergenic	L2b|LINE|L2	65489	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.005051	0.363025	439(AAGAACATGCAGTTTT,-,0.00),440(AGAACATGCAGTTTTT,+,0.00)
chunk0186_120_1	chr7	138092488	138092698	+	0	NA	intron (NM_001190906, intron 3 of 7)	Tigger3b|DNA|TcMar-Tigger	16161	NM_001190907	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.019048	0.388626	
chunk0099_251_1	chr2	97858761	97858983	+	0	NA	intron (NM_015348, intron 5 of 40)	MLT1E3|LTR|ERVL-MaLR	124466	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.009009	0.448430	
chunk0148_123_1	chr5	5242579	5243127	+	0	NA	intron (NM_139056, intron 17 of 22)	intron (NM_139056, intron 17 of 22)	102523	NM_139056	170690	Hs.661915	NM_139056	ENSG00000145536	ADAMTS16	ADAMTS16s	ADAM metallopeptidase with thrombospondin type 1 motif 16	protein-coding	0.005474	0.304189	
chunk0052_120_1	chr13	23229503	23229923	+	0	NA	intron (NM_000231, intron 2 of 7)	L1PREC2|LINE|L1	48792	NM_000231	6445	Hs.37167	NM_000231	ENSG00000102683	SGCG	35DAG|A4|DAGA4|DMDA|DMDA1|LGMD2C|LGMDR5|MAM|SCARMD2|SCG3|gamma-SG	sarcoglycan gamma	protein-coding	0.000000	0.346793	
chunk0140_54_1	chr4	66663925	66664290	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	387283	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.005479	0.420765	196(AGGAACACTGTGTTCT,-,0.00),197(GGAACACTGTGTTCTC,+,0.00)
chunk0161_15_1	chr5	165650038	165650525	+	0	NA	Intergenic	(TGTA)n|Simple_repeat|Simple_repeat	1180002	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.002053	0.286885	
chunk0080_161_1	chr17	28144482	28145009	+	0	NA	intron (NM_016231, intron 3 of 10)	intron (NM_016231, intron 3 of 10)	-81818	NR_003064	23615	Hs.157195	NM_021093	ENSG00000237575	PYY2	-	peptide YY 2 (pseudogene)	pseudo	0.001898	0.393939	
chunk0196_279_1	chr8	109277624	109277981	+	0	NA	intron (NM_001128211, intron 6 of 9)	intron (NM_001128211, intron 6 of 9)	52131	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.000000	0.284916	
chunk0172_141_1	chr6	135403365	135403829	+	0	NA	intron (NM_017651, intron 21 of 27)	intron (NM_017651, intron 21 of 27)	94168	NM_001134831	54806	Hs.386684	NM_017651	ENSG00000135541	AHI1	AHI-1|JBTS3|ORF1|dJ71N10.1	Abelson helper integration site 1	protein-coding	0.004310	0.359140	138(AGTAGAGGCTGTTCTC,+,0.00)
chunk0070_111_1	chr15	70474655	70475220	+	0	NA	Intergenic	Intergenic	-140610	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.047788	0.551237	
chunk0180_450_1	chr7	77459182	77459746	+	0	NA	Intergenic	Intergenic	-43064	NM_017439	54103	Hs.186649	NM_017439	ENSG00000186088	GSAP	PION	gamma-secretase activating protein	protein-coding	0.003546	0.348673	
chunk0210_139_1	chrX	74646703	74646985	+	0	NA	Intergenic	L1MA1|LINE|L1	-32218	NM_016120	51132	Hs.653288	NM_016120	ENSG00000131263	RLIM	MRX61|NY-REN-43|RNF12|TOKAS	ring finger protein, LIM domain interacting	protein-coding	0.003546	0.363958	
chunk0118_161_1	chr22	30416779	30417555	+	0	NA	TTS (NM_033382)	TTS (NM_033382)	-8456	NM_001003704	51537	Hs.713636	NM_016498	ENSG00000242114	MTFP1	HSPC242|MTP18	mitochondrial fission process 1	protein-coding	0.005155	0.382239	
chunk0183_312_1	chr7	107971811	107972421	+	0	NA	intron (NM_002291, intron 13 of 33)	intron (NM_002291, intron 13 of 33)	31243	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.004918	0.415712	369(AAACACAACATGTTCT,-,0.00),370(AACACAACATGTTCTT,+,0.00)
chunk0174_233_1	chr6	160687176	160687501	+	0	NA	Intergenic	L1MA5A|LINE|L1	-14855	NM_001168338	5340	Hs.143436	NM_000301	ENSG00000122194	PLG	-	plasminogen	protein-coding	0.003077	0.377301	144(TAGCACTGCATGTTCT,-,0.00),145(AGCACTGCATGTTCTC,+,0.00)
chunk0075_295_1	chr16	54185502	54185730	+	0	NA	Intergenic	L1M4c|LINE|L1	85263	NR_126340	100996338	Hs.232014	NR_126340		LINC02169	-	long intergenic non-protein coding RNA 2169	ncRNA	0.000000	0.353712	
chunk0173_362_1	chr6	149385095	149385546	+	0	NA	intron (NM_001292034, intron 3 of 6)	intron (NM_001292034, intron 3 of 6)	-15039	NM_001002255	387082	Hs.657168	NM_001002255	ENSG00000177688	SUMO4	IDDM5|SMT3H4|SUMO-4|dJ281H8.4	small ubiquitin like modifier 4	protein-coding	0.006652	0.327434	
chunk0204_294_1	chr9	99824718	99825252	+	0	NA	intron (NM_173199, intron 1 of 4)	CpG-28596	3130	NM_173200	8013	Hs.279522	NM_006981	ENSG00000119508	NR4A3	CHN|CSMF|MINOR|NOR1|TEC	nuclear receptor subfamily 4 group A member 3	protein-coding	0.067416	0.600000	
chunk0182_304_1	chr7	98476607	98477085	+	0	NA	Intergenic	Intergenic	-75731	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.020921	0.503132	
chunk0083_208_1	chr17	66772402	66772896	+	0	NA	intron (NM_002737, intron 13 of 16)	intron (NM_002737, intron 13 of 16)	-14423	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.008097	0.385859	233(AGGTACACAGCGTACC,-,0.00),234(GGTACACAGCGTACCT,+,0.00)
chunk0050_108_1	chr12	101982109	101982612	+	0	NA	Intergenic	Intergenic	79764	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.013917	0.376984	244(AAGAACGGGCAGTTCC,-,0.00),245(AGAACGGGCAGTTCCT,+,0.00),367(ATGAACAAGCTGTTCC,-,0.00),368(TGAACAAGCTGTTCCC,+,0.00)
chunk0046_411_1	chr12	64428767	64429459	+	0	NA	intron (NM_007235, intron 16 of 24)	Ricksha_b|DNA|MULE-MuDR	-22947	NM_013254	29110	Hs.505874	NM_013254	ENSG00000183735	TBK1	FTDALS4|IIAE8|NAK|T2K	TANK binding kinase 1	protein-coding	0.005780	0.378066	
chunk0162_111_1	chr6	2715804	2716351	+	0	NA	intron (NM_001012418, intron 2 of 12)	intron (NM_001012418, intron 2 of 12)	34843	NM_001012418	340156	Hs.127830	NM_001012418	ENSG00000145949	MYLK4	SgK085	myosin light chain kinase family member 4	protein-coding	0.009141	0.403285	
chunk0017_276_1	chr1	209770944	209771206	+	0	NA	intron (NM_001287754, intron 1 of 6)	intron (NM_001287754, intron 1 of 6)	2587	NM_001287754	80342	Hs.147434	NM_025228	ENSG00000009790	TRAF3IP3	T3JAM	TRAF3 interacting protein 3	protein-coding	0.030534	0.566540	
chunk0008_231_1	chr1	94036697	94037152	+	0	NA	intron (NM_000350, intron 25 of 49)	intron (NM_000350, intron 25 of 49)	84225	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.013187	0.401316	
chunk0055_400_1	chr13	74145807	74146470	+	0	NA	Intergenic	Intergenic	-12209	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.003017	0.325301	547(AAGAACATGCTGGACC,-,0.00)
chunk0097_102_1	chr2	46024973	46025665	+	0	NA	intron (NM_005400, intron 10 of 14)	intron (NM_005400, intron 10 of 14)	-272083	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.015896	0.437229	344(AGGGACGAAGTGTTCT,-,0.00),345(GGGACGAAGTGTTCTG,+,0.00)
chunk0083_329_1	chr17	70059026	70059405	+	0	NA	intron (NR_104130, intron 1 of 1)	intron (NR_104130, intron 1 of 1)	7944	NR_104129	101928141	Hs.639899	NR_104129	ENSG00000267603	LINC01028	TCONS_00025127	long intergenic non-protein coding RNA 1028	ncRNA	0.013193	0.397368	
chunk0136_439_1	chr3	197874703	197875003	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	75072	NM_001134435	84223	Hs.591675	NM_032263	ENSG00000114473	IQCG	CFAP122|DRC9	IQ motif containing G	protein-coding	0.010000	0.415282	
chunk0157_139_1	chr5	117464251	117464670	+	0	NA	intron (NR_046089, intron 2 of 5)	intron (NR_046089, intron 2 of 5)	48948	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.002387	0.400000	101(AGACACACAGTGTACT,-,0.00),102(GACACACAGTGTACTT,+,0.00)
chunk0004_151_1	chr1	45314372	45315015	+	0	NA	Intergenic	MER4-int|LTR|ERV1	10783	NR_024270	400752	Hs.334348	NR_024270	ENSG00000281912	LINC01144	-	long intergenic non-protein coding RNA 1144	ncRNA	0.007776	0.361801	
chunk0120_192_1	chr3	6910344	6910816	+	0	NA	intron (NM_000844, intron 1 of 9)	intron (NM_000844, intron 1 of 9)	-16563	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.002119	0.439746	
chunk0131_387_1	chr3	152448059	152448484	+	0	NA	intron (NM_207292, intron 6 of 8)	intron (NM_207292, intron 6 of 8)	-107281	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.002353	0.295775	
chunk0133_458_1	chr3	175236624	175236914	+	0	NA	intron (NR_046713, intron 2 of 2)	intron (NR_046713, intron 2 of 2)	34327	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.006897	0.374570	
chunk0093_419_1	chr19	57505076	57505674	+	0	NA	exon (NM_001304336, exon 3 of 4)	exon (NM_001304336, exon 3 of 4)	5521	NM_001304334	374928	Hs.579576	NM_198542	ENSG00000152439	ZNF773	ZNF419B	zinc finger protein 773	protein-coding	0.010033	0.489149	
chunk0092_252_1	chr19	33025656	33026250	+	0	NA	intron (NM_033103, intron 3 of 14)	intron (NM_033103, intron 3 of 14)	38965	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.018519	0.394958	
chunk0038_216_1	chr11	86699257	86699886	+	0	NA	Intergenic	Intergenic	-26935	NM_001161586	10873	Hs.199743	NM_006680	ENSG00000151376	ME3	NADP-ME	malic enzyme 3	protein-coding	0.001590	0.422222	
chunk0124_196_1	chr3	55678468	55678981	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	-19255	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.003899	0.476654	283(CAGAACTCTGAGTTCC,-,0.00),284(AGAACTCTGAGTTCCC,+,0.00)
chunk0145_282_1	chr4	149736629	149737209	+	0	NA	Intergenic	L1ME2z|LINE|L1	-341355	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.003448	0.335628	
chunk0032_228_1	chr11	7590431	7590841	+	0	NA	intron (NM_003621, intron 3 of 23)	intron (NM_003621, intron 3 of 23)	-6550	NM_001256568	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.002439	0.428224	
chunk0133_324_1	chr3	172536604	172536968	+	0	NA	Intergenic	Intergenic	-13279	NM_003810	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.002747	0.452055	
chunk0128_211_1	chr3	108013374	108013598	+	0	NA	Intergenic	MamTip3|DNA|hAT-Tip100	77602	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.013393	0.431111	
chunk0034_191_1	chr11	31690492	31690936	+	0	NA	intron (NM_001288726, intron 10 of 11)	L5|LINE|RTE-X	113523	NM_001310161	5080	Hs.270303	NM_000280	ENSG00000007372	PAX6	AN|AN2|ASGD5|D11S812E|FVH1|MGDA|WAGR	paired box 6	protein-coding	0.004505	0.307865	
chunk0158_391_1	chr5	134591945	134592146	+	0	NA	Intergenic	MIRc|SINE|MIR	40798	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.000000	0.495050	
chunk0206_384_1	chr9	126753241	126753718	+	0	NA	Intergenic	Intergenic	-51527	NM_001135776	23099	Hs.355581	NM_014007	ENSG00000169155	ZBTB43	ZBTB22B|ZNF-X|ZNF297B	zinc finger and BTB domain containing 43	protein-coding	0.010482	0.533473	
chunk0006_66_1	chr1	64760647	64761313	+	0	NA	intron (NM_018211, intron 1 of 11)	MIRb|SINE|MIR	15885	NM_018211	55225	Hs.591443	NM_018211	ENSG00000162437	RAVER2	-	ribonucleoprotein, PTB binding 2	protein-coding	0.001502	0.337331	
chunk0151_315_1	chr5	53368514	53368756	+	0	NA	Intergenic	Intergenic	-111799	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.004132	0.353909	
chunk0076_57_1	chr16	61418384	61418818	+	0	NA	Intergenic	Intergenic	-362835	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.016129	0.370115	
chunk0169_112_1	chr6	100732276	100732793	+	0	NA	intron (NM_006828, intron 10 of 41)	intron (NM_006828, intron 10 of 41)	148838	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.001934	0.316602	
chunk0030_200_1	chr10	114349368	114350012	+	0	NA	intron (NM_001001936, intron 1 of 18)	intron (NM_001001936, intron 1 of 18)	55088	NM_001287824	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.009317	0.434109	
chunk0195_114_1	chr8	94744710	94745149	+	0	NA	intron (NM_181787, intron 6 of 18)	intron (NM_181787, intron 6 of 18)	25054	NM_181787	286148	Hs.567828	NM_181787	ENSG00000156162	DPY19L4	-	dpy-19 like 4	protein-coding	0.004556	0.279545	
chunk0115_333_1	chr21	28992669	28993031	+	0	NA	exon (NM_015565, exon 1 of 30)	exon (NM_015565, exon 1 of 30)	106	NM_015565	26046	Hs.288773	NM_015565	ENSG00000198862	LTN1	C21orf10|C21orf98|RNF160|ZNF294	listerin E3 ubiquitin protein ligase 1	protein-coding	0.085635	0.658402	219(GAGGACACCCTGTAAT,-,0.00)
chunk0074_62_1	chr16	21175409	21175874	+	0	NA	intron (NM_020422, intron 4 of 4)	MER58A|DNA|hAT-Charlie	-16200	NM_017539	55567	Hs.526500	NM_017539	ENSG00000158486	DNAH3	DNAHC3-B|DNAHC3B|HDHC8|HEL-36|HSADHC3	dynein axonemal heavy chain 3	protein-coding	0.002151	0.379828	
chunk0028_250_1	chr10	90550601	90551002	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-9996	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.002494	0.465174	229(CAGGACATTATGTTCT,-,0.00),230(AGGACATTATGTTCTG,+,0.00)
chunk0189_442_1	chr8	28215841	28216458	+	0	NA	Intergenic	Intergenic	-100983	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.008104	0.393204	
chunk0024_130_1	chr10	34966143	34966378	+	0	NA	Intergenic	Intergenic	108070	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.012766	0.546610	
chunk0076_134_1	chr16	66786772	66786971	+	0	NA	intron (NM_001136505, intron 6 of 18)	intron (NM_001136505, intron 6 of 18)	14749	NM_001136505	283847	Hs.376505	NM_173616	ENSG00000249961	TERB1	CCDC79	telomere repeat binding bouquet formation protein 1	protein-coding	0.005025	0.580000	
chunk0102_36_1	chr2	141835889	141836325	+	0	NA	intron (NM_018557, intron 1 of 90)	intron (NM_018557, intron 1 of 90)	295594	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.000000	0.283753	
chunk0156_171_1	chr5	107625906	107626384	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	44750	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.002092	0.367432	
chunk0014_395_1	chr1	182851842	182852043	+	0	NA	intron (NR_033302, intron 3 of 28)	intron (NR_033302, intron 3 of 28)	12638	NM_001357	1660	Hs.191518	NM_001357	ENSG00000135829	DHX9	DDX9|LKP|NDH2|NDHII|RHA	DExH-box helicase 9	protein-coding	0.000000	0.336634	
chunk0070_338_1	chr15	75659248	75659536	+	0	NA	TTS (NM_153271)	TTS (NM_153271)	10385	NM_153271	257364	Hs.8705	NM_153271	ENSG00000173548	SNX33	SH3PX3|SH3PXD3C|SNX30	sorting nexin 33	protein-coding	0.017361	0.595156	134(CAGGACTCCCTGTTCA,-,0.00),135(AGGACTCCCTGTTCAG,+,0.00)
chunk0009_157_1	chr1	105018643	105018983	+	0	NA	Intergenic	L1P3|LINE|L1	600122	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.014706	0.387097	
chunk0093_169_1	chr19	48422588	48422963	+	0	NA	intron (NM_000836, intron 10 of 12)	intron (NM_000836, intron 10 of 12)	-22998	NM_031485	83743	Hs.400625	NM_031485	ENSG00000105447	GRWD1	CDW4|GRWD|RRB1|WDR28	glutamate rich WD repeat containing 1	protein-coding	0.024000	0.420213	
chunk0021_324_1	chr1	245531589	245531789	+	0	NA	intron (NM_018012, intron 4 of 14)	intron (NM_018012, intron 4 of 14)	376704	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.010000	0.467662	
chunk0177_228_1	chr7	24480213	24480531	+	0	NA	Intergenic	Intergenic	-92974	NM_016447	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.009434	0.485893	
chunk0059_159_1	chr14	32282030	32282300	+	0	NA	Intergenic	L1MB7|LINE|L1	-47108	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.000000	0.354244	
chunk0144_175_1	chr4	133016418	133016903	+	0	NA	Intergenic	Intergenic	132456	NR_125885	101927359	Hs.649960	NR_125885	ENSG00000250241	LOC101927359	-	uncharacterized LOC101927359	ncRNA	0.002062	0.347737	5(AGGAACACCTTGCCCT,-,0.00),6(GGAACACCTTGCCCTG,+,0.00)
chunk0185_396_1	chr7	133724631	133725000	+	0	NA	intron (NM_021807, intron 10 of 17)	L2a|LINE|L2	100073	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.005420	0.421622	158(GGGAACAGCAAGTACA,-,0.00)
chunk0038_203_1	chr11	86244390	86244998	+	0	NA	5' UTR (NM_003797, exon 1 of 12)	5' UTR (NM_003797, exon 1 of 12)	310	NM_003797	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.055921	0.541872	
chunk0067_200_1	chr15	44899334	44900095	+	0	NA	Intergenic	Intergenic	-56988	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.006570	0.433071	
chunk0196_360_1	chr8	114794906	114795520	+	0	NA	Intergenic	Intergenic	872799	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.006515	0.273171	
chunk0040_434_1	chr11	121451547	121451885	+	0	NA	promoter-TSS (NM_003105)	promoter-TSS (NM_003105)	-487	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.023669	0.519174	
chunk0063_234_1	chr14	81903253	81903773	+	0	NA	Intergenic	L1MA8|LINE|L1	-280452	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.009615	0.566219	
chunk0197_231_1	chr8	123035436	123035650	+	0	NA	intron (NM_001134671, intron 1 of 7)	intron (NM_001134671, intron 1 of 7)	6880	NM_001134671	79139	Hs.241576	NM_024295	ENSG00000136986	DERL1	DER-1|DER1|derlin-1	derlin 1	protein-coding	0.014019	0.516279	
chunk0108_102_1	chr2	229410946	229411375	+	0	NA	intron (NM_139072, intron 9 of 12)	intron (NM_139072, intron 9 of 12)	-139819	NM_001100818	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.013986	0.418605	
chunk0147_258_1	chr4	183588037	183588498	+	0	NA	Intergenic	Intergenic	70952	NM_152682	201965	Hs.133337	NM_152682	ENSG00000182552	RWDD4	FAM28A|RWDD4A	RWD domain containing 4	protein-coding	0.017354	0.396104	203(AAGAACATTTTGTACT,-,0.00),204(AGAACATTTTGTACTG,+,0.00)
chunk0098_137_1	chr2	69509009	69509327	+	0	NA	intron (NM_014911, intron 14 of 21)	intron (NM_014911, intron 14 of 21)	11003	NR_003705	100124535	Hs.693447	NR_003705	ENSG00000207016	SNORA36C	-	small nucleolar RNA, H/ACA box 36C	snoRNA	0.006289	0.445141	
chunk0094_257_1	chr2	7397190	7397826	+	0	NA	Intergenic	L2c|LINE|L2	-23753	NR_038432	100506274	Hs.177930	NR_038432	ENSG00000229727	LOC100506274	-	uncharacterized LOC100506274	ncRNA	0.001572	0.357928	
chunk0090_321_1	chr18	75749831	75750086	+	0	NA	Intergenic	L1M4a1|LINE|L1	-322255	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.007843	0.375000	
chunk0044_65_1	chr12	27880025	27880269	+	0	NA	Intergenic	L1MA8|LINE|L1	89814	NM_198964	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.004098	0.334694	
chunk0170_150_1	chr6	111359983	111360328	+	0	NA	intron (NM_001286431, intron 19 of 34)	L1ME4b|LINE|L1	100876	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.002899	0.323699	
chunk0003_255_1	chr1	36232313	36232883	+	0	NA	intron (NM_005119, intron 1 of 11)	L2a|LINE|L2	8182	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.008772	0.367776	
chunk0080_411_1	chr17	35692703	35693121	+	0	NA	intron (NM_001030006, intron 18 of 21)	L3|LINE|CR1	-38748	NM_033315	91608	Hs.744994	NM_033315	ENSG00000270885	RASL10B	RRP17|VTS58635	RAS like family 10 member B	protein-coding	0.014354	0.427208	
chunk0127_146_1	chr3	94395455	94395861	+	0	NA	Intergenic	Intergenic	-332435	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.004926	0.368550	
chunk0010_453_1	chr1	125080174	125080679	+	0	NA	Intergenic	Intergenic	3561314	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.043564	0.371542	
chunk0201_36_1	chr9	33431298	33431897	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	16036	NM_004925	360	Hs.234642	NM_004925	ENSG00000165272	AQP3	AQP-3|GIL	aquaporin 3 (Gill blood group)	protein-coding	0.006678	0.451667	
chunk0124_358_1	chr3	58684135	58684481	+	0	NA	Intergenic	LTR89|LTR|ERVL?	-17474	NM_138805	131177	Hs.61265	NM_138805	ENSG00000198643	FAM3D	EF7|OIT1	family with sequence similarity 3 member D	protein-coding	0.002890	0.446686	
chunk0044_445_1	chr12	42484093	42484737	+	0	NA	promoter-TSS (NM_001144883)	promoter-TSS (NM_001144883)	-420	NM_001144883	144165	Hs.524348	NM_153026	ENSG00000139174	PRICKLE1	EPM1B|RILP	prickle planar cell polarity protein 1	protein-coding	0.055901	0.524031	
chunk0175_458_1	chr6	170346996	170347437	+	0	NA	intron (NM_032448, intron 4 of 10).2	intron (NM_032448, intron 4 of 10).2	16455	NR_039787	100616430		NR_039787	ENSG00000266245	MIR4644	-	microRNA 4644	ncRNA	0.011338	0.429864	
chunk0166_56_1	chr6	42890605	42891208	+	0	NA	promoter-TSS (NM_001008739)	promoter-TSS (NM_001008739)	-90	NM_001008739	441150	Hs.571098	NM_001008739	ENSG00000221821	C6orf226	-	chromosome 6 open reading frame 226	protein-coding	0.081260	0.619205	
chunk0176_420_1	chr7	19413370	19414037	+	0	NA	Intergenic	Intergenic	-268282	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.007496	0.360778	
chunk0102_425_1	chr2	157235618	157236149	+	0	NA	Intergenic	Intergenic	-21945	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.000000	0.347744	
chunk0056_441_1	chr13	95149023	95149334	+	0	NA	intron (NM_001105515, intron 19 of 20)	intron (NM_001105515, intron 19 of 20)	152268	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.012862	0.355769	
chunk0016_123_1	chr1	196910312	196910744	+	0	NA	intron (NM_001201550, intron 6 of 9)	intron (NM_001201550, intron 6 of 9)	22514	NM_001201551	10877	Hs.710100	NM_006684	ENSG00000134365	CFHR4	CFHL4|FHR-4|FHR4	complement factor H related 4	protein-coding	0.004630	0.346420	
chunk0199_210_1	chr9	5013421	5013643	+	0	NA	intron (NM_004972, intron 2 of 24)	intron (NM_004972, intron 2 of 24)	28287	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.000000	0.385650	151(AGGAACATGCTGTGTA,-,0.00)
chunk0124_424_1	chr3	61155649	61156222	+	0	NA	intron (NM_001166243, intron 2 of 9)	MER68|LTR|ERVL	95524	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.005236	0.418118	
chunk0206_252_1	chr9	123777619	123777818	+	0	NA	intron (NM_024820, intron 3 of 20)	intron (NM_024820, intron 3 of 20)	152420	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.005025	0.355000	
chunk0175_324_1	chr6	166929653	166929852	+	0	NA	exon (NM_003730, exon 9 of 9)	exon (NM_003730, exon 9 of 9)	26054	NR_046644	100861523	Hs.634640	NR_046644		RPS6KA2-AS1	-	RPS6KA2 antisense RNA 1	ncRNA	0.030151	0.505000	
chunk0151_73_1	chr5	42621704	42622104	+	0	NA	intron (NM_001242460, intron 1 of 7)	intron (NM_001242460, intron 1 of 7)	56040	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.002500	0.386534	
chunk0142_108_1	chr4	94457633	94458066	+	0	NA	TTS (NM_001256429)	TTS (NM_001256429)	5992	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.006928	0.423963	123(CAGAACACTGTGTACA,-,0.00),124(AGAACACTGTGTACAT,+,0.00)
chunk0051_266_1	chr12	117821453	117822109	+	0	NA	intron (NM_173598, intron 3 of 19)	L2b|LINE|L2	146442	NM_173598	283455	Hs.375836	NM_173598	ENSG00000171435	KSR2	-	kinase suppressor of ras 2	protein-coding	0.010671	0.403349	
chunk0005_48_1	chr1	54977932	54978246	+	0	NA	Intergenic	Intergenic	-2575	NM_182532	199964	Hs.663950	NM_182532	ENSG00000143001	TMEM61	-	transmembrane protein 61	protein-coding	0.000000	0.514286	187(GTGAACAGTGAGTTCA,-,0.00),188(TGAACAGTGAGTTCAG,+,0.00)
chunk0162_461_1	chr5	180936923	180937158	+	0	NA	intron (NM_001159708, intron 3 of 6)	intron (NM_001159708, intron 3 of 6)	27476	NM_001159710	79908	Hs.189109	NM_024850	ENSG00000113303	BTNL8	BTN9.2	butyrophilin like 8	protein-coding	0.012766	0.567797	
chunk0046_161_1	chr12	58342973	58343202	+	0	NA	Intergenic	L1MC2|LINE|L1	-248615	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.008734	0.356522	103(AAGAACAGGGAGTTCC,-,0.00),104(AGAACAGGGAGTTCCT,+,0.00)
chunk0186_54_1	chr7	136376080	136376784	+	0	NA	Intergenic	Intergenic	-398976	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.005682	0.340426	
chunk0145_354_1	chr4	151165588	151166405	+	0	NA	intron (NM_001009555, intron 7 of 20)	intron (NM_001009555, intron 7 of 20)	9556	NM_001128924	152503	Hs.744983	NM_001009555	ENSG00000109686	SH3D19	EBP|EVE1|Eve-1|Kryn|SH3P19	SH3 domain containing 19	protein-coding	0.009792	0.397311	
chunk0099_349_1	chr2	100203615	100203822	+	0	NA	Intergenic	Intergenic	-4536	NR_103730	150577	Hs.434127	NM_001102655	ENSG00000232084	LINC01104	-	long intergenic non-protein coding RNA 1104	ncRNA	0.009662	0.403846	
chunk0039_197_1	chr11	100890588	100891243	+	0	NA	intron (NM_152432, intron 4 of 23)	intron (NM_152432, intron 4 of 23)	-101165	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.006107	0.387195	
chunk0187_182_1	chr7	151058057	151058355	+	0	NA	promoter-TSS (NM_001199692)	promoter-TSS (NM_001199692)	-6	NM_001199692	6522	Hs.647069	NM_003040	ENSG00000164889	SLC4A2	AE2|BND3L|EPB3L1|HKB3|NBND3	solute carrier family 4 member 2	protein-coding	0.090604	0.638796	
chunk0146_450_1	chr4	170080374	170081016	+	0	NA	intron (NM_182662, intron 4 of 13)	L1MA4|LINE|L1	9337	NM_016228	51166	Hs.529735	NM_016228	ENSG00000109576	AADAT	KAT2|KATII|KYAT2	aminoadipate aminotransferase	protein-coding	0.004673	0.430793	321(TGGGACAGGCTGTTCT,-,0.00),322(GGGACAGGCTGTTCTC,+,0.00)
chunk0062_150_1	chr14	69145866	69146401	+	0	NA	intron (NM_001284206, intron 1 of 8)	intron (NM_001284206, intron 1 of 8)	6466	NM_001284207	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.001869	0.343284	
chunk0205_348_1	chr9	113399083	113399504	+	0	NA	intron (NM_000031, intron 1 of 11)	MIRb|SINE|MIR	2045	NM_000031	210	Hs.1227	NM_000031	ENSG00000148218	ALAD	ALADH|PBGS	aminolevulinate dehydratase	protein-coding	0.009501	0.462085	39(AGGGTCAGACAGTCCC,-,0.00),260(GGAACGAGATGTCCTG,+,0.00)
chunk0118_411_1	chr22	38167999	38168502	+	0	NA	intron (NM_001004426, intron 2 of 15)	L2b|LINE|L2	13504	NM_003560	8398	Hs.170479	NM_003560	ENSG00000184381	PLA2G6	CaI-PLA2|GVI|INAD1|IPLA2-VIA|NBIA2|NBIA2A|NBIA2B|PARK14|PLA2|PNPLA9|iPLA2|iPLA2beta	phospholipase A2 group VI	protein-coding	0.015905	0.573413	
chunk0138_365_1	chr4	42220569	42220917	+	0	NA	Intergenic	Intergenic	-67865	NM_207406	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.002874	0.300860	
chunk0145_428_1	chr4	153038855	153039136	+	0	NA	Intergenic	Intergenic	96012	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.014235	0.503546	
chunk0084_70_1	chr17	74770106	74770369	+	0	NA	TTS (NM_004252)	TTS (NM_004252)	6188	NM_001305081	26151	Hs.144058	NM_015654	ENSG00000109065	NAT9	EBSP, hNATL	N-acetyltransferase 9 (putative)	protein-coding	0.000000	0.579545	
chunk0140_120_1	chr4	68865122	68865570	+	0	NA	Intergenic	LTR10C|LTR|ERV1	49353	NM_001290091	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.004464	0.378619	
chunk0193_288_1	chr8	77550484	77550983	+	0	NA	Intergenic	L1PA16|LINE|L1	100036	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.006012	0.524000	
chunk0193_428_1	chr8	80908394	80908984	+	0	NA	Intergenic	L2c|LINE|L2	-33908	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.006780	0.439932	
chunk0015_236_1	chr1	187794896	187795313	+	0	NA	Intergenic	Intergenic	351476	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007194	0.320574	
chunk0163_180_1	chr6	11318782	11319548	+	0	NA	intron (NM_001142393, intron 1 of 7)	intron (NM_001142393, intron 1 of 7)	63183	NM_001142393	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.007833	0.431551	
chunk0115_76_1	chr21	21929859	21930447	+	0	NA	Intergenic	Intergenic	168306	NR_109959	101927843	Hs.652879	NR_109959	ENSG00000233215	LINC01687	-	long intergenic non-protein coding RNA 1687	ncRNA	0.008503	0.349745	
chunk0028_301_1	chr10	91591349	91591677	+	0	NA	intron (NR_024467, intron 1 of 4)	L2c|LINE|L2	19947	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.015244	0.513678	
chunk0110_67_1	chr20	10952049	10952649	+	0	NA	Intergenic	Intergenic	-43077	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.003333	0.397671	
chunk0164_337_1	chr6	25313307	25313667	+	0	NA	intron (NM_017640, intron 2 of 36)	intron (NM_017640, intron 2 of 36)	34059	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.005556	0.487535	
chunk0132_219_1	chr3	157764547	157764792	+	0	NA	Intergenic	L2|LINE|L2	221325	NR_024016	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.000000	0.353659	
chunk0193_354_1	chr8	79900530	79901008	+	0	NA	Intergenic	Intergenic	-29032	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.006276	0.379958	
chunk0092_258_1	chr19	33041659	33041867	+	0	NA	intron (NM_033103, intron 2 of 14)	L2a|LINE|L2	23155	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.004808	0.483254	
chunk0105_177_1	chr2	187218225	187218781	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	229791	NM_001271751	10203	Hs.470882	NM_005795	ENSG00000064989	CALCRL	CGRPR|CRLR	calcitonin receptor like receptor	protein-coding	0.003597	0.403950	
chunk0019_21_1	chr1	223650558	223650869	+	0	NA	intron (NM_001143962, intron 2 of 20)	MLT1K|LTR|ERVL-MaLR	15021	NM_001143962	388743	Hs.291487	NM_001143962	ENSG00000203697	CAPN8	nCL-2	calpain 8	protein-coding	0.003215	0.435897	
chunk0105_403_1	chr2	192582866	192583710	+	0	NA	Intergenic	Intergenic	-166557	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.003555	0.314793	
chunk0159_364_1	chr5	145829670	145831048	+	0	NA	intron (NM_138492, intron 1 of 7)	intron (NM_138492, intron 1 of 7)	5010	NM_182960	153768	Hs.314261	NM_138492	ENSG00000186314	PRELID2	-	PRELI domain containing 2	protein-coding	0.001451	0.361131	979(AAGTACATACAGTTCA,-,0.00),980(AGTACATACAGTTCAG,+,0.00)
chunk0067_351_1	chr15	48498832	48499288	+	0	NA	intron (NM_000138, intron 17 of 65)	intron (NM_000138, intron 17 of 65)	146728	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.008772	0.459519	
chunk0138_306_1	chr4	41261406	41261680	+	0	NA	intron (NM_004181, intron 4 of 8)	intron (NM_004181, intron 4 of 8)	4662	NM_004181	7345	Hs.518731	NM_004181	ENSG00000154277	UCHL1	HEL-117|HEL-S-53|NDGOA|PARK5|PGP 9.5|PGP9.5|PGP95|SPG79|Uch-L1	ubiquitin C-terminal hydrolase L1	protein-coding	0.003650	0.461818	
chunk0123_91_1	chr3	42071975	42072594	+	0	NA	Intergenic	Intergenic	-18970	NM_001042646	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.021002	0.522581	
chunk0111_193_1	chr20	25550371	25550799	+	0	NA	intron (NM_025176, intron 1 of 23)	LTR5B|LTR|ERVK	34932	NM_025176	22981	Hs.631508	NM_025176	ENSG00000101004	NINL	NLP	ninein like	protein-coding	0.016355	0.463869	
chunk0148_97_1	chr5	3774682	3774955	+	0	NA	Intergenic	Intergenic	178764	NM_024337	79192	Hs.424156	NM_024337	ENSG00000170549	IRX1	IRX-5|IRXA1	iroquois homeobox 1	protein-coding	0.021978	0.554745	
chunk0005_22_1	chr1	54328207	54328406	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	78089	NM_145716	23648	Hs.476706	NM_018070	ENSG00000157216	SSBP3	CSDP|SSDP|SSDP1	single stranded DNA binding protein 3	protein-coding	0.030151	0.565000	
chunk0124_284_1	chr3	57585879	57586436	+	0	NA	intron (NM_001660, intron 1 of 5)	intron (NM_001660, intron 1 of 5)	11331	NM_001660	378	Hs.652183	NM_001660	ENSG00000168374	ARF4	ARF2	ADP ribosylation factor 4	protein-coding	0.010772	0.369176	
chunk0169_118_1	chr6	100890999	100891491	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-9873	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.002033	0.294118	156(TAGAACATACAGTCCT,-,0.00),157(AGAACATACAGTCCTC,+,0.00)
chunk0102_285_1	chr2	150409130	150409651	+	0	NA	Intergenic	Intergenic	78305	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.003839	0.363985	268(AGTCACAGAATGTTCC,-,0.00),269(GTCACAGAATGTTCCT,+,0.00)
chunk0032_340_1	chr11	10291544	10291913	+	0	NA	intron (NM_030962, intron 1 of 39)	L1MC4|LINE|L1	2479	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.008130	0.386486	
chunk0066_389_1	chr15	38984507	38985110	+	0	NA	Intergenic	Intergenic	-265861	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.008292	0.379139	303(TTGTACAACCTGTCCT,-,0.00),304(TGTACAACCTGTCCTA,+,0.00)
chunk0117_81_1	chr22	17159181	17159482	+	0	NA	promoter-TSS (NR_024483)	promoter-TSS (NR_024483)	-52	NM_033070	27440	Hs.26890	NM_017829	ENSG00000069998	HDHD5	CECR5	haloacid dehalogenase like hydrolase domain containing 5	protein-coding	0.159468	0.741722	
chunk0051_205_1	chr12	116415130	116415531	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	12988	NR_039683	100616309		NR_039683	ENSG00000264037	MIR4472-2	-	microRNA 4472-2	ncRNA	0.019950	0.467662	
chunk0041_373_1	chr11	131643164	131643598	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	20175	NR_126159	101929637	Hs.730330	NM_207432	ENSG00000224795	NTM-AS1	C11orf39	NTM antisense RNA 1	ncRNA	0.023041	0.505747	199(CAGCACATGGTGTACC,-,0.00),200(AGCACATGGTGTACCC,+,0.00)
chunk0181_136_1	chr7	81244956	81245585	+	0	NA	Intergenic	Intergenic	-325919	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.007949	0.346032	426(GTGTACAAAATGTTCT,-,0.00),427(TGTACAAAATGTTCTT,+,0.00)
chunk0088_67_1	chr18	44516688	44517096	+	0	NA	intron (NR_110792, intron 2 of 4)	MLT1N2|LTR|ERVL-MaLR	14805	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.007353	0.369193	
chunk0102_123_1	chr2	145012145	145012743	+	0	NA	intron (NR_033870, intron 3 of 4)	intron (NR_033870, intron 3 of 4)	344477	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.008361	0.397329	280(GAGGACTCAATGTTCC,-,0.00),281(AGGACTCAATGTTCCC,+,0.00)
chunk0209_124_1	chrX	40840427	40840872	+	0	NA	Intergenic	L1MEc|LINE|L1	-7453	NR_027761	100132831	Hs.729923	NR_027761		LOC100132831	-	A20-binding inhibitor of NF-kappaB activation 2 pseudogene	pseudo	0.002247	0.401345	
chunk0016_425_1	chr1	203682819	203683178	+	0	NA	5' UTR (NM_001684, exon 2 of 21)	5' UTR (NM_001684, exon 2 of 21)	-46583	NR_003019	677843	Hs.676135	NR_003019	ENSG00000221643	SNORA77	ACA63|SNORA77A	small nucleolar RNA, H/ACA box 77	snoRNA	0.022284	0.508333	
chunk0018_244_1	chr1	220006905	220007500	+	0	NA	exon (NM_004446, exon 14 of 32)	exon (NM_004446, exon 14 of 32)	39456	NM_004446	2058	Hs.497788	NM_004446	ENSG00000136628	EPRS	EARS|GLUPRORS|HLD15|PARS|PIG32|QARS|QPRS	glutamyl-prolyl-tRNA synthetase	protein-coding	0.001681	0.323826	
chunk0147_384_1	chr4	186501958	186502612	+	0	NA	Intergenic	Intergenic	-1227	NR_033900	285441	Hs.481369	NR_033900	ENSG00000251165	F11-AS1	-	F11 antisense RNA 1	ncRNA	0.006116	0.384733	
chunk0033_1_1	chr11	12264789	12265158	+	0	NA	Intergenic	L2a|LINE|L2	-21927	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.010840	0.432432	
chunk0039_221_1	chr11	101492647	101492925	+	0	NA	intron (NM_004621, intron 2 of 12)	intron (NM_004621, intron 2 of 12)	27119	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.003597	0.365591	
chunk0061_437_1	chr14	65632502	65632897	+	0	NA	intron (NR_038170, intron 6 of 10)	L1PB1|LINE|L1	161597	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.002532	0.353535	
chunk0204_186_1	chr9	96320830	96321029	+	0	NA	3' UTR (NM_001286990, exon 9 of 9)	3' UTR (NM_001286990, exon 9 of 9)	-18777	NM_000197	3293	Hs.477	NM_000197	ENSG00000130948	HSD17B3	EDH17B3|SDR12C2	hydroxysteroid 17-beta dehydrogenase 3	protein-coding	0.015075	0.520000	
chunk0058_96_1	chr14	21603374	21604042	+	0	NA	Intergenic	Intergenic	31232	NM_001005466	26534	Hs.554580	NM_001005466	ENSG00000255582	OR10G2	OR14-41	olfactory receptor family 10 subfamily G member 2	protein-coding	0.008982	0.387145	
chunk0051_84_1	chr12	114274237	114274761	+	0	NA	Intergenic	Intergenic	131664	NM_181486	6910	Hs.381715	NM_000192	ENSG00000089225	TBX5	HOS	T-box transcription factor 5	protein-coding	0.003817	0.459048	
chunk0189_380_1	chr8	27384840	27385196	+	0	NA	intron (NM_004103, intron 2 of 31)	MIR|SINE|MIR	-48352	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.014045	0.501401	
chunk0049_232_1	chr12	93467565	93467781	+	0	NA	intron (NR_038160, intron 1 of 6)	CpG	183	NR_038160	28977	Hs.199579	NM_014050	ENSG00000198015	MRPL42	HSPC204|L31MT|L42MT|MRP-L31|MRP-L42|MRP-S32|MRPL31|MRPS32|PTD007|RPML31|S32MT	mitochondrial ribosomal protein L42	protein-coding	0.064815	0.626728	
chunk0151_363_1	chr5	54785939	54786356	+	0	NA	Intergenic	Intergenic	-41889	NR_104658	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.002398	0.531100	
chunk0129_226_1	chr3	121907454	121908116	+	0	NA	intron (NM_001145998, intron 3 of 20)	L1PA6|LINE|L1	13461	NM_021082	6565	Hs.518089	NM_021082	ENSG00000163406	SLC15A2	PEPT2	solute carrier family 15 member 2	protein-coding	0.012085	0.515837	
chunk0160_264_1	chr5	157024225	157024699	+	0	NA	Intergenic	Intergenic	33779	NM_012206	26762	Hs.129711	NM_012206	ENSG00000113249	HAVCR1	CD365|HAVCR|HAVCR-1|KIM-1|KIM1|TIM|TIM-1|TIM1|TIMD-1|TIMD1	hepatitis A virus cellular receptor 1	protein-coding	0.006329	0.328421	
chunk0174_390_1	chr6	165333515	165333723	+	0	NA	intron (NM_006661, intron 22 of 22)	intron (NM_006661, intron 22 of 22)	-23997	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.033654	0.444976	
chunk0156_214_1	chr5	108114856	108115410	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	266965	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.003610	0.315315	299(TAGAACAGTAAGTACT,-,0.00),300(AGAACAGTAAGTACTC,+,0.00)
chunk0201_285_1	chr9	39036941	39037235	+	0	NA	Intergenic	Intergenic	251215	NM_033655	79937	Hs.128474	NM_033655	ENSG00000106714	CNTNAP3	CASPR3|CNTNAP3A	contactin associated protein like 3	protein-coding	0.006803	0.376271	
chunk0120_198_1	chr3	7087035	7087234	+	0	NA	intron (NM_000844, intron 1 of 9)	intron (NM_000844, intron 1 of 9)	-193117	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.000000	0.300000	
chunk0126_394_1	chr3	84887559	84888116	+	0	NA	Intergenic	L1PA6|LINE|L1	-18262	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.003591	0.363799	
chunk0029_16_1	chr10	95513285	95513484	+	0	NA	intron (NM_001290294, intron 1 of 31)	intron (NM_001290294, intron 1 of 31)	48036	NM_001290294	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.020101	0.495000	
chunk0050_102_1	chr12	101940623	101940836	+	0	NA	Intergenic	Intergenic	63402	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.009390	0.415888	
chunk0087_370_1	chr18	41494338	41494887	+	0	NA	intron (NR_002838, intron 3 of 5)	MIRb|SINE|MIR	25985	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.001821	0.336364	114(AGGTACACAATGTACA,-,0.00),115(GGTACACAATGTACAT,+,0.00),305(CTGGTCACACTGTTCC,-,0.00),306(TGGTCACACTGTTCCT,+,0.00)
chunk0122_357_1	chr3	37517441	37518286	+	0	NA	intron (NM_002207, intron 10 of 27)	intron (NM_002207, intron 10 of 27)	65541	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.016568	0.518913	
chunk0153_144_1	chr5	69034983	69035514	+	0	NA	Intergenic	L1ME4b|LINE|L1	-5321	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.007533	0.360902	
chunk0119_194_1	chr22	44644854	44645687	+	0	NA	Intergenic	LTR40b|LTR|ERVL	-19851	NR_044991	414351	Hs.572878	NR_044991		LINC00229	C22orf10|NCRNA00229|dJ474I12.C22.2	long intergenic non-protein coding RNA 229	ncRNA	0.012005	0.456835	
chunk0072_264_1	chr15	96593739	96594031	+	0	NA	Intergenic	Intergenic	187769	NR_102754	100652749	Hs.303588	NR_102753	ENSG00000259282	SPATA8-AS1	-	SPATA8 antisense RNA 1 (head to head)	ncRNA	0.013699	0.406143	
chunk0173_368_1	chr6	149405960	149406509	+	0	NA	intron (NM_001292034, intron 6 of 6)	intron (NM_001292034, intron 6 of 6)	5875	NM_001002255	387082	Hs.657168	NM_001002255	ENSG00000177688	SUMO4	IDDM5|SMT3H4|SUMO-4|dJ281H8.4	small ubiquitin like modifier 4	protein-coding	0.003643	0.345455	
chunk0003_93_1	chr1	31897249	31898024	+	0	NA	Intergenic	Intergenic	22022	NM_001195100	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.009032	0.386598	
chunk0144_473_1	chr4	142605788	142606129	+	0	NA	intron (NM_003866, intron 2 of 26)	L1MA4A|LINE|L1	240493	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.000000	0.342105	139(AAGAACTGCCTGTACT,-,0.00),140(AGAACTGCCTGTACTT,+,0.00)
chunk0011_252_1	chr1	150745716	150746150	+	0	NA	intron (NM_004079, intron 7 of 7)	L1MA9|LINE|L1	20024	NM_004079	1520	Hs.181301	NM_004079	ENSG00000163131	CTSS	-	cathepsin S	protein-coding	0.004608	0.377011	
chunk0083_202_1	chr17	66675889	66676681	+	0	NA	intron (NM_002737, intron 5 of 16)	intron (NM_002737, intron 5 of 16)	-110787	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.036616	0.553594	309(GAGAACAGCGTGTTCT,-,0.00),310(AGAACAGCGTGTTCTT,+,0.00)
chunk0082_214_1	chr17	57054111	57054373	+	0	NA	Intergenic	Intergenic	8764	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.003817	0.471483	
chunk0183_318_1	chr7	108028030	108028509	+	0	NA	intron (NM_007356, intron 33 of 33)	intron (NM_007356, intron 33 of 33)	-24910	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.010438	0.410417	
chunk0064_299_1	chr14	95437514	95437853	+	0	NA	intron (NM_152592, intron 13 of 16)	(TTTTTTG)n|Simple_repeat|Simple_repeat	-27593	NR_026779									0.005900	0.420588	
chunk0121_1_1	chr3	14326991	14327721	+	0	NA	Intergenic	L1ME2|LINE|L1	25212	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.013699	0.455540	374(GAGAACATCCTGTACA,-,0.00),375(AGAACATCCTGTACAA,+,0.00)
chunk0099_300_1	chr2	99071610	99071809	+	0	NA	exon (NM_025244, exon 14 of 21)	exon (NM_025244, exon 14 of 21)	69865	NM_182911	80705	Hs.120267	NM_025244	ENSG00000135951	TSGA10	CEP4L|CT79|SPGF26	testis specific 10	protein-coding	0.005025	0.385000	
chunk0143_114_1	chr4	109207030	109207414	+	0	NA	intron (NR_045756, intron 3 of 35)	intron (NR_045756, intron 3 of 35)	95145	NM_001256074	84570	Hs.658842	NM_032518	ENSG00000188517	COL25A1	AMY|CFEOM5|CLAC|CLAC-P|CLACP	collagen type XXV alpha 1 chain	protein-coding	0.002604	0.425974	
chunk0019_383_1	chr1	230120328	230120650	+	0	NA	intron (NM_004481, intron 1 of 15)	intron (NM_004481, intron 1 of 15)	53294	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.027950	0.585139	175(GGGAACACTGTGTTCC,-,0.00),176(GGAACACTGTGTTCCA,+,0.00)
chunk0089_178_1	chr18	59690907	59691319	+	0	NA	intron (NM_133459, intron 2 of 10)	intron (NM_133459, intron 2 of 10)	6299	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.002427	0.409201	
chunk0206_258_1	chr9	123816850	123817155	+	0	NA	intron (NM_024820, intron 2 of 20)	intron (NM_024820, intron 2 of 20)	113136	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.006557	0.457516	200(AATAACACTCTGTTCC,-,0.00),201(ATAACACTCTGTTCCA,+,0.00)
chunk0112_66_1	chr20	37745265	37745812	+	0	NA	intron (NM_030877, intron 3 of 15)	MIR|SINE|MIR	51583	NM_030877	56259	Hs.472667	NM_030877	ENSG00000132792	CTNNBL1	C20orf33|NAP|P14L|PP8304|dJ633O20.1	catenin beta like 1	protein-coding	0.003656	0.408759	
chunk0175_452_1	chr6	170167694	170168429	+	0	NA	Intergenic	Intergenic	7419	NR_125878	102724511	Hs.550045	NR_125878		LOC102724511	-	uncharacterized LOC102724511	ncRNA	0.036735	0.578804	
chunk0034_44_1	chr11	26869868	26870289	+	0	NA	Intergenic	L1PB2|LINE|L1	-124003	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.000000	0.343602	
chunk0205_220_1	chr9	109723959	109724584	+	0	NA	intron (NM_001037293, intron 1 of 6)	L1M5|LINE|L1	-56026	NM_147150	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.008000	0.309904	298(GGAAACATCATGTTCT,-,0.00),299(GAAACATCATGTTCTT,+,0.00)
chunk0026_225_1	chr10	65083423	65083653	+	0	NA	Intergenic	LTR2752|LTR|ERV1	258010	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.013043	0.584416	
chunk0168_61_1	chr6	79167761	79168124	+	0	NA	Intergenic	Intergenic	-65732	NR_040671	100288198	Hs.586270	NR_040671	ENSG00000270362	HMGN3-AS1	-	HMGN3 antisense RNA 1	ncRNA	0.005510	0.304945	148(CAGGACTCTCTGTTCT,-,0.00),149(AGGACTCTCTGTTCTC,+,0.00)
chunk0047_193_1	chr12	71008529	71008898	+	0	NA	Intergenic	Intergenic	-87909	NM_002849	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.005420	0.478378	
chunk0193_282_1	chr8	77419149	77419532	+	0	NA	Intergenic	Intergenic	-31357	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.312500	
chunk0148_36_1	chr5	998656	999113	+	0	NA	Intergenic	Intergenic	-1544	NR_104615	100506688	Hs.532063	NM_001242737	ENSG00000215246	LOC100506688	-	uncharacterized LOC100506688	ncRNA	0.008753	0.510917	208(GGAAACAAACTGTGCC,-,0.00),209(GAAACAAACTGTGCCT,+,0.00)
chunk0074_336_1	chr16	31179785	31180269	+	0	NA	promoter-TSS (NR_028388)	promoter-TSS (NR_028388)	-83	NM_001170937	2521	Hs.46894	NM_004960	ENSG00000089280	FUS	ALS6|ETM4|FUS1|HNRNPP2|POMP75|TLS	FUS RNA binding protein	protein-coding	0.101240	0.641237	
chunk0145_422_1	chr4	152989205	152990035	+	0	NA	Intergenic	Intergenic	46637	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.004819	0.522262	421(GGGAACACACTGTGCC,-,0.00),422(GGAACACACTGTGCCC,+,0.00)
chunk0187_188_1	chr7	151471861	151472060	+	0	NA	intron (NM_005614, intron 4 of 7)	L2a|LINE|L2	-31147	NR_131779	155051	Hs.647104	NM_144727	ENSG00000127377	CRYGN	-	crystallin gamma N	protein-coding	0.005025	0.410000	
chunk0128_174_1	chr3	107289394	107289695	+	0	NA	intron (NR_028302, intron 1 of 3)	intron (NR_028302, intron 1 of 3)	48852	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.000000	0.407285	
chunk0117_373_1	chr21	45105746	45106515	+	0	NA	intron (NM_015834, intron 1 of 12)	intron (NM_015834, intron 1 of 12)	31552	NM_001160230	104	Hs.474018	NM_001112	ENSG00000197381	ADARB1	ADAR2|DRABA2|DRADA2|RED1	adenosine deaminase RNA specific B1	protein-coding	0.014304	0.412987	
chunk0041_81_1	chr11	124235121	124235346	+	0	NA	Intergenic	Intergenic	10594	NM_001291438	26492	Hs.381319	NM_001291438		OR8G2P	HSTPCR120|OR8G2|OR8G4|ORL206|ORL486|TPCR120	olfactory receptor family 8 subfamily G member 2 pseudogene	protein-coding	0.004444	0.411504	
chunk0178_64_1	chr7	30183677	30183928	+	0	NA	Intergenic	Intergenic	48866	NM_152793	222166	Hs.200100	NM_152793	ENSG00000180354	MTURN	C7orf41|Ells1	maturin, neural progenitor differentiation regulator homolog	protein-coding	0.003984	0.424603	
chunk0149_101_1	chr5	18984540	18984919	+	0	NA	Intergenic	MIR|SINE|MIR	901543	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.010554	0.410526	
chunk0105_416_1	chr2	192930208	192930826	+	0	NA	Intergenic	L1PA6|LINE|L1	180672	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.004854	0.478191	
chunk0211_66_1	chrX	109908824	109909096	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	38559	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003676	0.318681	
chunk0115_290_1	chr21	28245333	28246246	+	0	NA	Intergenic	L1MA3|LINE|L1	-17122	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.002191	0.344639	
chunk0178_455_1	chr7	42079323	42079930	+	0	NA	intron (NM_000168, intron 3 of 14)	intron (NM_000168, intron 3 of 14)	157393	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.013180	0.398026	
chunk0075_1_1	chr16	46526346	46526759	+	0	NA	intron (NR_026556, intron 8 of 16)	intron (NR_026556, intron 8 of 16)	42545	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.004843	0.330918	
chunk0207_450_1	chr9	137704142	137704471	+	0	NA	intron (NM_001145527, intron 1 of 15)	intron (NM_001145527, intron 1 of 15)	-58716	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.009119	0.472727	204(GGGCCACTTTGTTCTC,+,0.00)
chunk0138_313_1	chr4	41398468	41398970	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	37934	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.007968	0.425447	250(AAGCACACACTGTTCT,-,0.00),251(AGCACACACTGTTCTC,+,0.00)
chunk0177_222_1	chr7	24179822	24180133	+	0	NA	Intergenic	Intergenic	-104211	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.003215	0.362179	
chunk0109_43_1	chr20	740031	740579	+	0	NA	Intergenic	LTR8|LTR|ERV1	28279	NM_033409	113278	Hs.283865	NM_033409	ENSG00000101276	SLC52A3	BVVLS|BVVLS1|C20orf54|RFT2|RFVT3|bA371L19.1|hRFT2	solute carrier family 52 member 3	protein-coding	0.020073	0.446266	
chunk0077_219_1	chr16	80189632	80190493	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-350672	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.005807	0.410673	466(ATAACAGCTTGTTCTC,+,0.00),679(AAGCACAGTATGATCC,-,0.00),680(AGCACAGTATGATCCA,+,0.00)
chunk0189_448_1	chr8	28297090	28297468	+	0	NA	Intergenic	MIR3|SINE|MIR	-19853	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.010582	0.477573	96(GAGGACAGTGAGTTCC,-,0.00),97(AGGACAGTGAGTTCCA,+,0.00)
chunk0208_267_1	chrX	21454244	21454446	+	0	NA	intron (NM_014927, intron 4 of 21)	intron (NM_014927, intron 4 of 21)	79927	NM_001168648	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.004950	0.300493	
chunk0208_276_1	chrX	21784728	21785224	+	0	NA	Intergenic	Intergenic	-26816	NM_014332	23676	Hs.86492	NM_014332	ENSG00000091482	SMPX	DFN6|DFNX4	small muscle protein X-linked	protein-coding	0.002016	0.358149	215(AAGGTCTCTCTGTCCC,-,0.00)
chunk0162_274_1	chr6	5548368	5548845	+	0	NA	intron (NM_006567, intron 5 of 6)	intron (NM_006567, intron 5 of 6)	-90531	NR_125847	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.002096	0.292887	
chunk0063_378_1	chr14	86250084	86250484	+	0	NA	Intergenic	Intergenic	315606	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.002500	0.294264	
chunk0021_452_1	chr1	248873635	248873869	+	0	NA	Intergenic	CpG	-14636	NM_017865	55657	Hs.377705	NM_017865	ENSG00000171163	ZNF692	AREBP|Zfp692	zinc finger protein 692	protein-coding	0.098291	0.634043	
chunk0087_269_1	chr18	37382100	37382299	+	0	NA	intron (NM_001025088, intron 2 of 12)	MIR|SINE|MIR	84305	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.000000	0.475000	28(TGGCACTGACTGTTCT,-,0.00),29(GGCACTGACTGTTCTA,+,0.00)
chunk0172_49_1	chr6	134076858	134077534	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-24545	NM_145176	154091	Hs.486508	NM_145176	ENSG00000146411	SLC2A12	GLUT12|GLUT8	solute carrier family 2 member 12	protein-coding	0.005917	0.381093	
chunk0208_345_1	chrX	25198255	25198751	+	0	NA	Intergenic	Intergenic	-182555	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.006048	0.384306	241(CTGGACAAGATGTTCT,-,0.00),242(TGGACAAGATGTTCTT,+,0.00)
chunk0016_97_1	chr1	195218611	195218829	+	0	NA	Intergenic	LTR2752|LTR|ERV1	1363761	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.045872	0.602740	
chunk0183_131_1	chr7	105677016	105677758	+	0	NA	intron (NM_020725, intron 3 of 11)	L2b|LINE|L2	1775	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.010782	0.492598	82(GAGAACACACAGTGCA,-,0.00),83(AGAACACACAGTGCAG,+,0.00),385(GAGTACACTGAGTCCC,-,0.00),386(AGTACACTGAGTCCCT,+,0.00)
chunk0069_50_1	chr15	60735423	60736035	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	54160	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.006536	0.415987	
chunk0057_321_1	chr13	106753419	106753778	+	0	NA	Intergenic	Intergenic	99718	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.013928	0.386111	57(CTGGACAGGAAGTCCT,-,0.00),58(TGGACAGGAAGTCCTT,+,0.00)
chunk0120_356_1	chr3	11553592	11554456	+	0	NA	intron (NM_001136031, intron 17 of 17)	intron (NM_001136031, intron 17 of 17)	14900	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.017361	0.606936	290(GTAAACATGCTGTTCC,-,0.00),291(TAAACATGCTGTTCCT,+,0.00)
chunk0177_340_1	chr7	26507266	26507881	+	0	NA	Intergenic	CR1-16_AMi|LINE|CR1	31252	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.011382	0.448052	
chunk0067_249_1	chr15	45684433	45685604	+	0	NA	intron (NM_001271213, intron 8 of 10)	L1ME4b|LINE|L1	50278	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.008540	0.419795	794(TAGTACTAGCTGTTCC,-,0.00),795(AGTACTAGCTGTTCCC,+,0.00)
chunk0043_29_1	chr12	13129926	13130294	+	0	NA	Intergenic	Intergenic	-26414	NM_001080555	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.005435	0.295393	
chunk0203_239_1	chr9	87254974	87255640	+	0	NA	Intergenic	Intergenic	106663	NM_001001709									0.013514	0.472264	
chunk0060_49_1	chr14	41357807	41358282	+	0	NA	Intergenic	Intergenic	-249517	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.000000	0.268908	
chunk0108_108_1	chr2	229516129	229516328	+	0	NA	intron (NM_139072, intron 5 of 12)	LTR106_Mam|LTR|LTR	198342	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.005025	0.260000	
chunk0119_426_1	chr22	49973645	49973852	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	10882	NR_106879	102465493		NR_106879	ENSG00000276753	MIR6821	hsa-mir-6821	microRNA 6821	ncRNA	0.004831	0.432692	
chunk0034_227_1	chr11	33312852	33313051	+	0	NA	intron (NM_001278163, intron 2 of 15)	MIRb|SINE|MIR	54620	NM_001278162	10114	Hs.201918	NM_005734	ENSG00000110422	HIPK3	DYRK6|FIST3|PKY|YAK1	homeodomain interacting protein kinase 3	protein-coding	0.005025	0.310000	
chunk0030_351_1	chr10	118581105	118581851	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	14170	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.006702	0.473896	
chunk0148_425_1	chr5	15172388	15172587	+	0	NA	Intergenic	Intergenic	94073	NR_109944	101929454	Hs.453273	NR_109944		LINC02149	-	long intergenic non-protein coding RNA 2149	ncRNA	0.000000	0.420000	
chunk0081_190_1	chr17	41989842	41990224	+	0	NA	intron (NM_003315, intron 6 of 13)	A-rich|Low_complexity|Low_complexity	23292	NM_033133	1267	Hs.273621	NM_033133	ENSG00000173786	CNP	CNP1	2',3'-cyclic nucleotide 3' phosphodiesterase	protein-coding	0.005236	0.454308	194(AAACACAATCTGTTCT,-,0.00),195(AACACAATCTGTTCTT,+,0.00)
chunk0104_126_1	chr2	173049293	173049832	+	0	NA	intron (NM_001282899, intron 27 of 27)	intron (NM_001282899, intron 27 of 27)	-26275	NM_016653	51776	Hs.444451	NM_016653	ENSG00000091436	MAP3K20	AZK|CNM6|MLK7|MLT|MLTK|MLTKalpha|MLTKbeta|MRK|SFMMP|ZAK|mlklak|pk	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.005566	0.390741	
chunk0053_15_1	chr13	26397105	26397603	+	0	NA	intron (NM_001260, intron 9 of 12)	intron (NM_001260, intron 9 of 12)	142735	NM_001260	1024	Hs.382306	NM_001260	ENSG00000132964	CDK8	K35	cyclin dependent kinase 8	protein-coding	0.004016	0.318637	218(AGCACTCAGAGTGCTT,+,0.00)
chunk0157_192_1	chr5	118905928	118906450	+	0	NA	intron (NM_173666, intron 4 of 5)	L1ME1|LINE|L1	-68397	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.005747	0.332696	
chunk0027_108_1	chr10	74046089	74046335	+	0	NA	intron (NM_003373, intron 2 of 20)	intron (NM_003373, intron 2 of 20)	48098	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.012195	0.433198	34(TGTACAGCCTGTTTTG,+,0.00)
chunk0167_63_1	chr6	56148192	56148774	+	0	NA	intron (NM_030820, intron 10 of 29)	Plat_L3|LINE|CR1	99097	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.001718	0.370497	238(AGGTAGACACTGTTCT,-,0.00)
chunk0031_282_1	chr10	128215016	128215691	+	0	NA	Intergenic	Intergenic	-70597	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.019259	0.500000	
chunk0055_423_1	chr13	75213283	75213494	+	0	NA	Intergenic	Intergenic	26993	NR_027466	647288	Hs.567920	NR_027466	ENSG00000214249	CTAGE11P	-	CTAGE family member 11, pseudogene	pseudo	0.000000	0.311321	
chunk0196_394_1	chr8	115858628	115859071	+	0	NA	Intergenic	L1ME4c|LINE|L1	-189821	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.002257	0.272523	
chunk0109_55_1	chr20	1118277	1118619	+	0	NA	promoter-TSS (NM_006814)	promoter-TSS (NM_006814)	-149	NM_006814	9491	Hs.471917	NM_006814	ENSG00000125818	PSMF1	PI31	proteasome inhibitor subunit 1	protein-coding	0.090643	0.612245	
chunk0190_198_1	chr8	33805246	33805445	+	0	NA	Intergenic	Intergenic	-205239	NM_024025	78986	Hs.8719	NM_024025	ENSG00000133878	DUSP26	DSP-4|DUSP24|LDP-4|LDP4|MKP-8|MKP8|NATA1|NEAP|SKRP3	dual specificity phosphatase 26	protein-coding	0.010050	0.450000	
chunk0166_446_1	chr6	53086411	53086810	+	0	NA	intron (NM_012347, intron 6 of 11)	MER101-int|LTR|ERV1	15637	NM_012347	26268	Hs.216653	NM_012347	ENSG00000112146	FBXO9	FBX9|NY-REN-57|VCIA1|dJ341E18.2	F-box protein 9	protein-coding	0.005013	0.355000	
chunk0042_146_1	chr12	3851654	3852245	+	0	NA	intron (NR_104461, intron 1 of 8)	L1PA6|LINE|L1	21499	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.015228	0.498311	
chunk0107_444_1	chr2	225260230	225260429	+	0	NA	Intergenic	L1MA1|LINE|L1	-140557	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.000000	0.320000	
chunk0114_72_1	chr21	9129389	9129834	+	0	NA	intron (NR_038327, intron 1 of 3)	CpG	150	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.069663	0.665919	
chunk0068_158_1	chr15	53984392	53984813	+	0	NA	Intergenic	MIR|SINE|MIR	-28302	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.002375	0.317536	
chunk0161_261_1	chr5	172106988	172107344	+	0	NA	intron (NM_005990, intron 5 of 18)	intron (NM_005990, intron 5 of 18)	81176	NM_005990	6793	Hs.744005	NM_005990	ENSG00000072786	STK10	LOK|PRO2729	serine/threonine kinase 10	protein-coding	0.044944	0.540616	72(CGGAACACAGAGTCCT,-,0.00),73(GGAACACAGAGTCCTG,+,0.00)
chunk0045_387_1	chr12	52454775	52455041	+	0	NA	Intergenic	L1M7|LINE|L1	-2782	NM_005555	3854	Hs.708950	NM_005555	ENSG00000185479	KRT6B	CK-6B|CK6B|K6B|KRTL1|PC2|PC4	keratin 6B	protein-coding	0.003759	0.370787	
chunk0064_238_1	chr14	94339220	94339709	+	0	NA	Intergenic	L1MC3|LINE|L1	-16113	NM_001756	866	Hs.532635	NM_001756	ENSG00000170099	SERPINA6	CBG	serpin family A member 6	protein-coding	0.000000	0.373469	
chunk0140_116_1	chr4	68740580	68740849	+	0	NA	Intergenic	L1M4|LINE|L1	-69938	NM_001076	7366	Hs.150207	NM_001076	ENSG00000196620	UGT2B15	HLUG4|UDPGT 2B8|UDPGT2B15|UDPGTH3|UGT2B8	UDP glucuronosyltransferase family 2 member B15	protein-coding	0.000000	0.292593	
chunk0114_13_1	chr21	7257900	7258214	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	398886	NR_128718	103504736		NR_128718	ENSG00000278618	MIR8069-2	hsa-mir-8069-2	microRNA 8069-2	ncRNA	0.012739	0.466667	
chunk0089_115_1	chr18	58564392	58564871	+	0	NA	intron (NM_052947, intron 4 of 12)	intron (NM_052947, intron 4 of 12)	-35989	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.002088	0.347917	
chunk0210_192_1	chrX	80122542	80122774	+	0	NA	Intergenic	Intergenic	99598	NM_001303475	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.008621	0.433476	
chunk0118_25_1	chr22	26445486	26446086	+	0	NA	TTS (NM_020437)	TTS (NM_020437)	16472	NM_020437	57168	Hs.567547	NM_020437	ENSG00000128203	ASPHD2	-	aspartate beta-hydroxylase domain containing 2	protein-coding	0.020000	0.534110	
chunk0201_149_1	chr9	35871529	35871863	+	0	NA	Intergenic	Intergenic	-1295	NM_001004487	392309	Hs.527480	NM_001004487	ENSG00000168828	OR13J1	OR9-2	olfactory receptor family 13 subfamily J member 1	protein-coding	0.008982	0.489552	
chunk0004_26_1	chr1	42340040	42341341	+	0	NA	Intergenic	MIRb|SINE|MIR	-4813	NM_001198850	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.004612	0.421659	
chunk0204_379_1	chr9	102141731	102142007	+	0	NA	Intergenic	Intergenic	-377768	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.000000	0.339350	204(AGAAGATACTGTTCCT,+,0.00)
chunk0198_53_1	chr8	128523048	128523683	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	41314	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.006299	0.363208	
chunk0199_226_1	chr9	5360312	5360959	+	0	NA	intron (NM_018465, intron 5 of 5)	MER63C|DNA|hAT-Blackjack	-20762	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.001546	0.365741	
chunk0178_397_1	chr7	40795559	40796010	+	0	NA	intron (NM_024728, intron 14 of 14)	intron (NM_024728, intron 14 of 14)	184155	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.006652	0.349558	
chunk0155_20_1	chr5	90932211	90932410	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	373510	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.015075	0.400000	
chunk0006_1_1	chr1	63731609	63731958	+	0	NA	Intergenic	Intergenic	-42236	NM_005012	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.017192	0.465714	
chunk0030_223_1	chr10	114772607	114772873	+	0	NA	intron (NR_120628, intron 1 of 2)	L1MEd|LINE|L1	7952	NR_120628	101927692	Hs.576909	NR_120628	ENSG00000228484	LOC101927692	-	uncharacterized LOC101927692	ncRNA	0.000000	0.314607	
chunk0194_284_1	chr8	87413246	87413689	+	0	NA	Intergenic	Intergenic	460601	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.000000	0.310811	
chunk0078_239_1	chr17	6699974	6700753	+	0	NA	intron (NM_177550, intron 6 of 11)	L2b|LINE|L2	13058	NM_001284509	284111	Hs.399496	NM_177550	ENSG00000141485	SLC13A5	EIEE25|INDY|NACT|mIndy	solute carrier family 13 member 5	protein-coding	0.016688	0.500000	
chunk0066_167_1	chr15	32733534	32734145	+	0	NA	3' UTR (NM_013372, exon 2 of 2)	3' UTR (NM_013372, exon 2 of 2)	-14974	NR_109767	100131315	Hs.610545	NR_109767	ENSG00000259721	LOC100131315	-	uncharacterized LOC100131315	ncRNA	0.004910	0.330065	283(ATGTACACTTTGTGCT,-,0.00),284(TGTACACTTTGTGCTT,+,0.00)
chunk0007_174_1	chr1	80358097	80358477	+	0	NA	Intergenic	Intergenic	-177468	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.002632	0.398950	
chunk0066_176_1	chr15	33030135	33030914	+	0	NA	intron (NM_001103184, intron 2 of 16)	intron (NM_001103184, intron 2 of 16)	37508	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.011553	0.343590	725(ATGTACAGAATGTGCA,-,0.00),726(TGTACAGAATGTGCAG,+,0.00)
chunk0057_253_1	chr13	105227895	105228148	+	0	NA	Intergenic	Intergenic	-237846	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.003953	0.393701	
chunk0059_62_1	chr14	30251709	30252266	+	0	NA	Intergenic	Intergenic	-307136	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.007181	0.347670	
chunk0137_333_1	chr4	24846691	24847066	+	0	NA	intron (NM_001130726, intron 4 of 11)	intron (NM_001130726, intron 4 of 11)	51415	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.010667	0.422872	
chunk0073_276_1	chr16	12487511	12488055	+	0	NA	intron (NM_032167, intron 19 of 20)	intron (NM_032167, intron 19 of 20)	-232538	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.025735	0.482569	
chunk0202_225_1	chr9	76311397	76311910	+	0	NA	intron (NM_001190482, intron 29 of 36)	MLT1L|LTR|ERVL-MaLR	82875	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.009747	0.433852	
chunk0073_267_1	chr16	12137176	12137820	+	0	NA	intron (NM_032167, intron 13 of 20)	intron (NM_032167, intron 13 of 20)	160764	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.006211	0.488372	385(CAGATCATGCTGTCCT,-,0.00),386(AGATCATGCTGTCCTG,+,0.00)
chunk0046_83_1	chr12	56222024	56222257	+	0	NA	promoter-TSS (NM_005785)	promoter-TSS (NM_005785)	-171	NM_194359	10193	Hs.524502	NM_005785	ENSG00000181852	RNF41	FLRF|NRDP1|SBBI03	ring finger protein 41	protein-coding	0.042918	0.564103	105(GAGAACTCTATGTTCT,-,0.00),106(AGAACTCTATGTTCTT,+,0.00)
chunk0102_149_1	chr2	147001412	147001615	+	0	NA	Intergenic	Intergenic	414456	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.000000	0.294118	
chunk0123_428_1	chr3	50112604	50112861	+	0	NA	intron (NR_036627, intron 16 of 23)	intron (NR_036627, intron 16 of 23)	-11744	NR_045388	100775107	Hs.439480	NR_045388	ENSG00000281691	RBM5-AS1	LUST	RBM5 antisense RNA 1	ncRNA	0.003891	0.457364	
chunk0139_59_1	chr4	49000198	49000863	+	0	NA	intron (NM_025087, intron 6 of 15)	intron (NM_025087, intron 6 of 15)	13888	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.009023	0.382883	
chunk0083_217_1	chr17	67056413	67056878	+	0	NA	3' UTR (NM_000727, exon 4 of 4)	3' UTR (NM_000727, exon 4 of 4)	12109	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.019355	0.549356	202(AGGGACAACCTGTGTT,-,0.00),203(GGGACAACCTGTGTTT,+,0.00)
chunk0050_117_1	chr12	102031830	102032292	+	0	NA	intron (NM_016053, intron 5 of 6)	intron (NM_016053, intron 5 of 6)	30063	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.000000	0.369330	
chunk0109_184_1	chr20	4919488	4919927	+	0	NA	intron (NM_005116, intron 3 of 16)	intron (NM_005116, intron 3 of 16)	81792	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.013667	0.502273	
chunk0044_129_1	chr12	29317765	29318145	+	0	NA	promoter-TSS (NR_103860)	promoter-TSS (NR_103860)	-107	NR_103860	100506606	Hs.298851	NR_103860	ENSG00000257176	LOC100506606	-	uncharacterized LOC100506606	ncRNA	0.013158	0.425197	187(GGGAACACAGTGTGCT,-,0.00),188(GGAACACAGTGTGCTG,+,0.00)
chunk0155_386_1	chr5	98508569	98508963	+	0	NA	Intergenic	Intergenic	-260529	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.005076	0.362025	
chunk0202_183_1	chr9	74364762	74365031	+	0	NA	Intergenic	L1PA10|LINE|L1	-6635	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.007435	0.392593	
chunk0100_122_1	chr2	108608984	108609183	+	0	NA	intron (NM_001193482, intron 1 of 9)	intron (NM_001193482, intron 1 of 9)	1922	NM_001193482	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.020101	0.470000	
chunk0123_354_1	chr3	48183675	48184001	+	0	NA	intron (NM_201567, intron 3 of 13)	intron (NM_201567, intron 3 of 13)	4473	NM_001789	993	Hs.437705	NM_001789	ENSG00000164045	CDC25A	CDC25A2	cell division cycle 25A	protein-coding	0.000000	0.373089	
chunk0211_295_1	chrX	122880250	122880515	+	0	NA	Intergenic	Intergenic	-303861	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.003774	0.477444	
chunk0152_147_1	chr5	59231178	59232046	+	0	NA	intron (NM_001165899, intron 3 of 16)	MLT1J2|LTR|ERVL-MaLR	44507	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.009217	0.399310	
chunk0117_362_1	chr21	44785575	44785934	+	0	NA	intron (NM_001202489, intron 1 of 3)	intron (NM_001202489, intron 1 of 3)	16082	NM_001202489	7327	Hs.529420	NM_003343	ENSG00000184787	UBE2G2	UBC7	ubiquitin conjugating enzyme E2 G2	protein-coding	0.011142	0.413889	
chunk0098_444_1	chr2	82141134	82141730	+	0	NA	Intergenic	Intergenic	-674486	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.385260	
chunk0010_381_1	chr1	119253511	119253741	+	0	NA	intron (NR_125975, intron 4 of 6)	intron (NR_125975, intron 4 of 6)	-112954	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.004348	0.298701	
chunk0128_45_1	chr3	104658907	104659487	+	0	NA	Intergenic	L1MA4A|LINE|L1	-707516	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006897	0.430293	
chunk0169_175_1	chr6	102223687	102224309	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	825013	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.014469	0.354735	230(TAGTACATACTGTACT,-,0.00),231(AGTACATACTGTACTG,+,0.00)
chunk0190_356_1	chr8	39694874	39695488	+	0	NA	intron (NM_014237, intron 17 of 19)	L1MC2|LINE|L1	110613	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.003257	0.330081	
chunk0154_142_1	chr5	79344969	79345774	+	0	NA	Intergenic	L1ME1|LINE|L1	109269	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.013665	0.395782	
chunk0084_204_1	chr17	78128952	78129335	+	0	NA	promoter-TSS (NM_001127198)	promoter-TSS (NM_001127198)	-363	NM_001127198	11322	Hs.632227	NM_007267	ENSG00000141524	TMC6	EV1|EVER1|EVIN1|LAK-4P	transmembrane channel like 6	protein-coding	0.036554	0.585938	
chunk0009_393_1	chr1	110157872	110158491	+	0	NA	intron (NM_001010898, intron 1 of 11)	L2a|LINE|L2	7671	NM_001010898	388662	Hs.128382	NM_001010898	ENSG00000197106	SLC6A17	MRT48|NTT4	solute carrier family 6 member 17	protein-coding	0.011309	0.427419	300(TAGAACATAATGTTCA,-,0.00),301(AGAACATAATGTTCAG,+,0.00),503(CAGCCCACTGTGTCCT,-,0.00),504(AGCCCACTGTGTCCTT,+,0.00)
chunk0040_147_1	chr11	113376783	113377205	+	0	NA	Intergenic	L2b|LINE|L2	-10797	NM_178510	255239	Hs.448473	NM_178510	ENSG00000170209	ANKK1	PKK2|sgK288	ankyrin repeat and kinase domain containing 1	protein-coding	0.002370	0.470449	
chunk0142_117_1	chr4	94528020	94528266	+	0	NA	intron (NM_001011516, intron 3 of 9)	intron (NM_001011516, intron 3 of 9)	76286	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.012195	0.473684	
chunk0072_333_1	chr15	99227542	99228504	+	0	NA	intron (NR_109947, intron 4 of 12)	L2c|LINE|L2	21596	NM_001288615	64927	Hs.513195	NM_022905	ENSG00000103852	TTC23	HCC-8	tetratricopeptide repeat domain 23	protein-coding	0.008316	0.446521	
chunk0068_396_1	chr15	58637073	58637478	+	0	NA	intron (NM_001110, intron 8 of 15)	intron (NM_001110, intron 8 of 15)	56332	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.009877	0.352217	
chunk0167_40_1	chr6	54519194	54519467	+	0	NA	Intergenic	Intergenic	210925	NM_014464	27283	Hs.127011	NM_014464	ENSG00000137251	TINAG	TIN-AG	tubulointerstitial nephritis antigen	protein-coding	0.003663	0.324818	
chunk0069_65_1	chr15	60861633	60861893	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	180194	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.011538	0.417625	66(AGGAACGAGATGTCCC,-,0.00),67(GGAACGAGATGTCCCT,+,0.00)
chunk0118_83_1	chr22	29003907	29004404	+	0	NA	intron (NM_032173, intron 2 of 8)	intron (NM_032173, intron 2 of 8)	27321	NR_046851	100874123	Hs.674708	NR_046851	ENSG00000177993	ZNRF3-AS1	-	ZNRF3 antisense RNA 1	ncRNA	0.012072	0.441767	
chunk0007_53_1	chr1	77834692	77834996	+	0	NA	intron (NM_198549, intron 7 of 15)	intron (NM_198549, intron 7 of 15)	-53671	NM_001172309	91624	Hs.612385	NM_144573	ENSG00000162614	NEXN	CMH20|NELIN	nexilin F-actin binding protein	protein-coding	0.006579	0.377049	
chunk0038_220_1	chr11	86777080	86777279	+	0	NA	Intergenic	L1MB3|LINE|L1	-13880	NM_001293180	11098	Hs.25338	NM_007173	ENSG00000150687	PRSS23	SIG13|SPUVE|ZSIG13	serine protease 23	protein-coding	0.015075	0.435000	119(CAGTACACAGCGTTCT,-,0.00),120(AGTACACAGCGTTCTA,+,0.00)
chunk0031_428_1	chr10	132425432	132425690	+	0	NA	Intergenic	CpG	-19649	NM_173541									0.077519	0.617761	
chunk0151_234_1	chr5	51073002	51073311	+	0	NA	Intergenic	L1M2|LINE|L1	-102969	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.012945	0.587097	
chunk0091_452_1	chr19	17791289	17791804	+	0	NA	Intergenic	Intergenic	-3564	NM_014256	10331	Hs.69009	NM_014256	ENSG00000179913	B3GNT3	B3GAL-T8|B3GN-T3|B3GNT-3|HP10328|TMEM3|beta3Gn-T3	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	protein-coding	0.017476	0.490310	219(TGGTACAGAGTGATCC,-,0.00),220(GGTACAGAGTGATCCA,+,0.00)
chunk0071_271_1	chr15	85638167	85638562	+	0	NA	intron (NM_001270546, intron 1 of 28)	L1ME1|LINE|L1	18414	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.002532	0.290404	
chunk0188_381_1	chr8	18399015	18399314	+	0	NA	intron (NM_000015, intron 1 of 1)	L2a|LINE|L2	7919	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.003344	0.453333	159(TGGTACTTTCTGTTCC,-,0.00),160(GGTACTTTCTGTTCCA,+,0.00)
chunk0160_333_1	chr5	159868364	159868624	+	0	NA	non-coding (NR_109891, exon 1 of 3)	non-coding (NR_109891, exon 1 of 3)	2890	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.003846	0.371648	
chunk0144_462_1	chr4	142476267	142476742	+	0	NA	intron (NM_003866, intron 2 of 26)	L1PA14|LINE|L1	369947	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.004211	0.384454	219(ATGGACTGAATGTTCC,-,0.00),220(TGGACTGAATGTTCCA,+,0.00)
chunk0076_447_1	chr16	73990767	73991226	+	0	NA	Intergenic	LTR1E|LTR|ERV1	224525	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.010893	0.510870	
chunk0067_185_1	chr15	44555202	44555838	+	0	NA	intron (NM_001284335, intron 5 of 6)	intron (NM_001284335, intron 5 of 6)	18452	NM_001284335	8669	Hs.404056	NM_003758	ENSG00000104131	EIF3J	EIF3S1|eIF3-alpha|eIF3-p35	eukaryotic translation initiation factor 3 subunit J	protein-coding	0.003145	0.372057	
chunk0031_354_1	chr10	129715658	129716197	+	0	NA	intron (NM_002412, intron 3 of 4)	intron (NM_002412, intron 3 of 4)	127447	NR_036179	100422873		NR_036179	ENSG00000266676	MIR4297	-	microRNA 4297	ncRNA	0.031540	0.394444	
chunk0095_436_1	chr2	25166097	25166749	+	0	NA	intron (NM_001035256, intron 1 of 3)	intron (NM_001035256, intron 1 of 3)	2267	NM_000939	5443	Hs.1897	NM_000939	ENSG00000115138	POMC	ACTH|CLIP|LPH|MSH|NPP|OBAIRH|POC	proopiomelanocortin	protein-coding	0.012270	0.470138	228(AGGGACAGGCTGTTCC,-,0.00),229(GGGACAGGCTGTTCCC,+,0.00)
chunk0113_228_1	chr20	53940927	53941404	+	0	NA	Intergenic	Intergenic	-65456	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.004193	0.416318	
chunk0012_324_1	chr1	162421195	162421457	+	0	NA	Intergenic	Intergenic	-9188	NM_053282	117157	Hs.350581	NM_053282	ENSG00000198574	SH2D1B	EAT2	SH2 domain containing 1B	protein-coding	0.000000	0.467681	
chunk0163_266_1	chr6	13176316	13176573	+	0	NA	intron (NM_030948, intron 6 of 14)	intron (NM_030948, intron 6 of 14)	119142	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.007782	0.387597	180(GGAAGAGTATGTTCTT,+,0.00)
chunk0127_51_1	chr3	88996768	88997410	+	0	NA	Intergenic	Intergenic	-110435	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.009346	0.396579	
chunk0163_277_1	chr6	13561673	13562208	+	0	NA	Intergenic	Intergenic	-12589	NM_001193267	23408	Hs.567431	NM_012241	ENSG00000124523	SIRT5	SIR2L5	sirtuin 5	protein-coding	0.018692	0.412313	171(GGAACATCCTGCCCAT,+,0.00)
chunk0140_103_1	chr4	68460155	68460433	+	0	NA	intron (NM_014058, intron 1 of 9)	intron (NM_014058, intron 1 of 9)	12845	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.014388	0.405018	162(GAAACAGAGCGTTCTT,+,0.00)
chunk0123_282_1	chr3	46352351	46352931	+	0	NA	Intergenic	Intergenic	-1103	NM_001123396	729230	Hs.511794	NM_001123041	ENSG00000121807	CCR2	CC-CKR-2|CCR-2|CCR2A|CCR2B|CD192|CKR2|CKR2A|CKR2B|CMKBR2|MCP-1-R	C-C motif chemokine receptor 2	protein-coding	0.008621	0.452668	228(GGGCTCAGACTGTTCT,-,0.00),229(GGCTCAGACTGTTCTG,+,0.00),441(ATGACACCATGTTCTC,+,0.00)
chunk0076_22_1	chr16	58861451	58861990	+	0	NA	Intergenic	L2c|LINE|L2	-127363	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.001855	0.348148	
chunk0113_309_1	chr20	57986185	57986384	+	0	NA	Intergenic	L1ME4a|LINE|L1	90890	NR_039757									0.010050	0.290000	
chunk0105_280_1	chr2	189785087	189785502	+	0	NA	promoter-TSS (NM_016467)	promoter-TSS (NM_016467)	-923	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.009639	0.375000	
chunk0035_345_1	chr11	48049890	48050249	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	-46713	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.013928	0.369444	
chunk0001_394_1	chr1	10679673	10680015	+	0	NA	intron (NM_001079843, intron 4 of 20)	intron (NM_001079843, intron 4 of 20)	116832	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.011696	0.597668	
chunk0198_174_1	chr8	133311077	133311485	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-13977	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.004902	0.349633	
chunk0176_177_1	chr7	13724962	13725205	+	0	NA	Intergenic	Intergenic	261431	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.016461	0.426230	
chunk0130_63_1	chr3	129864406	129865154	+	0	NA	intron (NM_001128224, intron 1 of 5)	intron (NM_001128224, intron 1 of 5)	15779	NM_001017395	23023	Hs.477547	NM_015008	ENSG00000172765	TMCC1	-	transmembrane and coiled-coil domain family 1	protein-coding	0.004011	0.417891	
chunk0176_166_1	chr7	13432231	13432708	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	554045	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.004193	0.320084	
chunk0186_116_1	chr7	138074103	138074356	+	0	NA	Intergenic	LOR1b|LTR|ERV1	-2203	NM_005989	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.007905	0.437008	
chunk0046_25_1	chr12	54435376	54435898	+	0	NA	intron (NR_120487, intron 3 of 3)	L2b|LINE|L2	15852	NR_120488	102724050	Hs.670941	NR_120486	ENSG00000258137	LOC102724050	-	uncharacterized LOC102724050	ncRNA	0.013410	0.397706	
chunk0035_276_1	chr11	46589043	46589597	+	0	NA	intron (NM_001300731, intron 1 of 16)	intron (NM_001300731, intron 1 of 16)	2044	NM_017749	55626	Hs.654644	NM_017749	ENSG00000110497	AMBRA1	DCAF3|WDR94	autophagy and beclin 1 regulator 1	protein-coding	0.001805	0.362162	286(CAGGACAGGCTGTACC,-,0.00),287(AGGACAGGCTGTACCA,+,0.00)
chunk0065_453_1	chr14	106602107	106602761	+	0	NA	Intergenic	Intergenic	-34277	NR_106988									0.007645	0.381679	44(CAGAACAGAGTGTTTA,-,0.00),45(AGAACAGAGTGTTTAT,+,0.00)
chunk0039_353_1	chr11	105700909	105701625	+	0	NA	intron (NM_001112812, intron 2 of 9)	L2b|LINE|L2	90583	NM_001112812	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.005587	0.368201	
chunk0194_352_1	chr8	89472531	89472905	+	0	NA	Intergenic	Intergenic	284993	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.002674	0.328000	
chunk0052_116_1	chr13	23152686	23153006	+	0	NA	Intergenic	L1M4b|LINE|L1	-28075	NM_000231	6445	Hs.37167	NM_000231	ENSG00000102683	SGCG	35DAG|A4|DAGA4|DMDA|DMDA1|LGMD2C|LGMDR5|MAM|SCARMD2|SCG3|gamma-SG	sarcoglycan gamma	protein-coding	0.003125	0.305296	
chunk0150_146_1	chr5	33713187	33713729	+	0	NA	intron (NM_030955, intron 3 of 23)	intron (NM_030955, intron 3 of 23)	178561	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.003690	0.349908	35(CAGCACACATTGTTTT,-,0.00)
chunk0079_415_1	chr17	19670904	19671267	+	0	NA	intron (NM_001031806, intron 8 of 10)	intron (NM_001031806, intron 8 of 10)	22334	NM_000382	224	Hs.499886	NM_000382	ENSG00000072210	ALDH3A2	ALDH10|FALDH|SLS	aldehyde dehydrogenase 3 family member A2	protein-coding	0.002755	0.502747	
chunk0125_271_1	chr3	69282135	69282681	+	0	NA	intron (NM_015123, intron 5 of 22)	intron (NM_015123, intron 5 of 22)	103896	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.007326	0.411335	
chunk0063_12_1	chr14	76221397	76221872	+	0	NA	Intergenic	L1MC1|LINE|L1	67280	NR_110314	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.002105	0.369748	
chunk0041_362_1	chr11	131028289	131028813	+	0	NA	Intergenic	Intergenic	-112064	NM_001301089	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.005725	0.424762	
chunk0134_209_1	chr3	178516729	178517519	+	0	NA	Intergenic	Intergenic	-19174	NM_181361	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.001266	0.361568	
chunk0159_233_1	chr5	141603959	141604202	+	0	NA	intron (NM_001314007, intron 1 of 28)	intron (NM_001314007, intron 1 of 28)	14975	NM_005219	1729	Hs.529451	NM_005219	ENSG00000131504	DIAPH1	DFNA1|DIA1|DRF1|LFHL1|SCBMS|hDIA1	diaphanous related formin 1	protein-coding	0.008230	0.483607	
chunk0040_18_1	chr11	108975080	108975390	+	0	NA	Intergenic	Intergenic	310210	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.003226	0.472669	
chunk0090_253_1	chr18	74259297	74259580	+	0	NA	intron (NM_001914, intron 3 of 5)	intron (NM_001914, intron 3 of 5)	32578	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.003534	0.338028	
chunk0191_295_1	chr8	54309226	54309472	+	0	NA	Intergenic	Intergenic	-21337	NR_004385	26766		NR_004385	ENSG00000199212	RNU105C	E1-5|E1-6	RNA, U105C small nucleolar	snoRNA	0.008130	0.360324	
chunk0176_105_1	chr7	11714690	11715287	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	117210	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005025	0.341137	
chunk0102_100_1	chr2	144279929	144280498	+	0	NA	intron (NM_001164629, intron 1 of 11)	intron (NM_001164629, intron 1 of 11)	14280	NM_001006636	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.005272	0.352632	
chunk0156_71_1	chr5	103672908	103673146	+	0	NA	Intergenic	MIRc|SINE|MIR	-110226	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.004202	0.376569	
chunk0149_337_1	chr5	26901824	26902395	+	0	NA	intron (NM_016279, intron 7 of 11)	MIR|SINE|MIR	136473	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.001751	0.291958	
chunk0051_180_1	chr12	116130643	116131090	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	17788	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.000000	0.325893	
chunk0079_113_1	chr17	12383052	12383702	+	0	NA	Intergenic	MIR|SINE|MIR	-166591	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.001538	0.336406	
chunk0082_71_1	chr17	51439388	51439787	+	0	NA	Intergenic	Intergenic	102872	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.007519	0.477500	
chunk0109_296_1	chr20	8346024	8346565	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	214029	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.003697	0.330258	
chunk0168_4_1	chr6	76616739	76617054	+	0	NA	Intergenic	L2a|LINE|L2	-544218	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.009524	0.351266	
chunk0125_114_1	chr3	65673864	65674467	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-219651	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.009950	0.430464	
chunk0119_410_1	chr22	49664499	49665021	+	0	NA	Intergenic	Intergenic	-7218	NR_110522	348645	Hs.133159	NM_198851	ENSG00000188511	C22orf34	-	chromosome 22 open reading frame 34	protein-coding	0.044061	0.556405	
chunk0065_155_1	chr15	25513030	25513384	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-74179	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.008475	0.478873	
chunk0172_236_1	chr6	137115547	137116162	+	0	NA	Intergenic	Intergenic	57794	NM_181310	116379	Hs.126891	NM_052962	ENSG00000164485	IL22RA2	CRF2-10|CRF2-S1|CRF2X|IL-22BP|IL-22R-alpha-2|IL-22RA2|ZCYTOR16	interleukin 22 receptor subunit alpha 2	protein-coding	0.003252	0.297078	300(CAGATCTTCCTGTTCT,-,0.00),301(AGATCTTCCTGTTCTT,+,0.00)
chunk0033_66_1	chr11	13608557	13609015	+	0	NA	Intergenic	L1MB7|LINE|L1	-59873	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.004367	0.366013	294(ATGAACATCATGTACT,-,0.00),295(TGAACATCATGTACTA,+,0.00)
chunk0097_117_1	chr2	46378877	46379348	+	0	NA	intron (NM_001430, intron 11 of 15)	intron (NM_001430, intron 11 of 15)	-50078	NR_103805	101805491	Hs.304781	NR_103805	ENSG00000187600	LINC02583	-	long intergenic non-protein coding RNA 2583	ncRNA	0.006369	0.377119	
chunk0022_252_1	chr10	14617489	14617852	+	0	NA	intron (NM_001282695, intron 2 of 5)	intron (NM_001282695, intron 2 of 5)	-13252	NM_001282697	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.011019	0.428571	158(AAGAGCAAGCTGTCCT,-,0.00),159(AGAGCAAGCTGTCCTG,+,0.00)
chunk0105_420_1	chr2	193030147	193030751	+	0	NA	Intergenic	L1MA2|LINE|L1	280604	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.003311	0.345455	
chunk0163_205_1	chr6	11925895	11926229	+	0	NA	Intergenic	Intergenic	75182	NR_125853	101928253	Hs.128163	NR_125853		LOC101928253	-	uncharacterized LOC101928253	ncRNA	0.023952	0.546269	
chunk0194_196_1	chr8	85517282	85517733	+	0	NA	Intergenic	Intergenic	-52592	NR_121630	100996348	Hs.606624	NR_121630	ENSG00000253549	CA3-AS1	-	CA3 antisense RNA 1	ncRNA	0.008869	0.342920	
chunk0196_10_1	chr8	101438219	101438934	+	0	NA	Intergenic	Intergenic	-53864	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.040559	0.565642	
chunk0018_74_1	chr1	217152280	217152519	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-14644	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.008368	0.425000	
chunk0100_128_1	chr2	108632251	108633040	+	0	NA	intron (NM_001193484, intron 1 of 9)	intron (NM_001193484, intron 1 of 9)	11399	NM_001193484	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.005070	0.426582	292(CTGGACACCTTGTTCT,-,0.00),293(TGGACACCTTGTTCTT,+,0.00)
chunk0076_48_1	chr16	60583603	60584080	+	0	NA	Intergenic	Intergenic	-224078	NM_001282301	729159		NM_001282301		NPAP1L	-	nuclear pore associated protein 1 like	protein-coding	0.002096	0.361925	
chunk0167_326_1	chr6	72271461	72272048	+	0	NA	intron (NM_001168408, intron 15 of 20)	intron (NM_001168408, intron 15 of 20)	54994	NM_001168410	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.001704	0.329932	
chunk0023_419_1	chr10	31401396	31401738	+	0	NA	intron (NM_001128128, intron 1 of 8)	Tigger9b|DNA|TcMar-Tigger	80432	NM_001174094	6935	Hs.124503	NM_030751	ENSG00000148516	ZEB1	AREB6|BZP|DELTAEF1|FECD6|NIL2A|PPCD3|TCF8|ZFHEP|ZFHX1A	zinc finger E-box binding homeobox 1	protein-coding	0.008772	0.376093	
chunk0069_143_1	chr15	62436204	62436583	+	0	NA	Intergenic	L2b|LINE|L2	93364	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.013193	0.536842	
chunk0123_422_1	chr3	49747871	49748138	+	0	NA	exon (NM_001242829, exon 2 of 6)	exon (NM_001242829, exon 2 of 6)	-24030	NM_021971	29925	Hs.567488	NM_013334	ENSG00000173540	GMPPB	LGMDR19|MDDGA14|MDDGB14|MDDGC14	GDP-mannose pyrophosphorylase B	protein-coding	0.033708	0.570896	
chunk0198_211_1	chr8	133826910	133827330	+	0	NA	Intergenic	MIRb|SINE|MIR	-49768	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.002381	0.363420	265(TGGTACATTCTGCTCC,-,0.00),266(GGTACATTCTGCTCCT,+,0.00)
chunk0043_436_1	chr12	26174728	26175279	+	0	NA	Intergenic	L1ME1|LINE|L1	-20333	NM_001135823	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.019964	0.414855	
chunk0060_236_1	chr14	49644943	49645342	+	0	NA	intron (NM_002692, intron 18 of 18)	L1ME4b|LINE|L1	-9912	NM_001083908	55172	Hs.231761	NM_018139	ENSG00000165506	DNAAF2	C14orf104|CILD10|KTU|PF13	dynein axonemal assembly factor 2	protein-coding	0.010025	0.377500	
chunk0160_76_1	chr5	149911083	149911414	+	0	NA	intron (NM_000440, intron 6 of 21)	LTR54|LTR|ERV1	21729	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.003021	0.430723	
chunk0008_146_1	chr1	92289055	92289658	+	0	NA	intron (NM_053274, intron 5 of 18)	intron (NM_053274, intron 5 of 18)	-9609	NM_024813	79871	Hs.444421	NM_024813	ENSG00000122484	RPAP2	C1orf82|Rtr1	RNA polymerase II associated protein 2	protein-coding	0.004975	0.337748	
chunk0111_357_1	chr20	33569260	33569584	+	0	NA	intron (NM_001039709, intron 1 of 10)	intron (NM_001039709, intron 1 of 10)	7057	NM_001039709	9139	Hs.153934	NM_005093	ENSG00000078699	CBFA2T2	EHT|MTGR1|ZMYND3|p85	CBFA2/RUNX1 partner transcriptional co-repressor 2	protein-coding	0.003086	0.310769	
chunk0183_307_1	chr7	107933579	107933817	+	0	NA	intron (NM_002291, intron 27 of 33)	intron (NM_002291, intron 27 of 33)	42591	NM_001289751	1738	Hs.131711	NM_000108	ENSG00000091140	DLD	DLDD|DLDH|E3|GCSL|LAD|PHE3	dihydrolipoamide dehydrogenase	protein-coding	0.000000	0.380753	
chunk0165_67_1	chr6	31076703	31076905	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	23354	NR_003948	285834	Hs.207528	NM_001348249	ENSG00000228789	HCG22	PBMUCL2	HLA complex group 22 (gene/pseudogene)	protein-coding	0.000000	0.394089	
chunk0106_458_1	chr2	209415935	209416449	+	0	NA	Intergenic	L1MC2|LINE|L1	-7855	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.000000	0.306796	
chunk0131_169_1	chr3	146527977	146528176	+	0	NA	intron (NM_021105, intron 4 of 8)	intron (NM_021105, intron 4 of 8)	16765	NM_021105	5359	Hs.130759	NM_021105	ENSG00000188313	PLSCR1	MMTRA1B	phospholipid scramblase 1	protein-coding	0.005025	0.290000	
chunk0163_84_1	chr6	9463166	9463907	+	0	NA	Intergenic	Intergenic	811327	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.008097	0.376011	381(AAGAAGAGACTGTACT,-,0.00),382(AGAAGAGACTGTACTG,+,0.00)
chunk0201_100_1	chr9	34773300	34774253	+	0	NA	Intergenic	L1MC3|LINE|L1	-44238	NM_001141917	259308	Hs.522093	NM_001141917	ENSG00000205108	FAM205A	C9orf144B	family with sequence similarity 205 member A	protein-coding	0.004197	0.348008	
chunk0064_232_1	chr14	94157302	94157513	+	0	NA	Intergenic	Intergenic	-16905	NM_020958	57718	Hs.259599	NM_020958	ENSG00000119698	PPP4R4	CFAP14|KIAA1622|PP4R4	protein phosphatase 4 regulatory subunit 4	protein-coding	0.000000	0.405660	
chunk0063_363_1	chr14	85812360	85813136	+	0	NA	Intergenic	L2a|LINE|L2	-121930	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.006443	0.378378	
chunk0068_152_1	chr15	53837125	53837719	+	0	NA	Intergenic	Intergenic	-74544	NR_102334	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.006734	0.415126	
chunk0148_149_1	chr5	6495708	6496206	+	0	NA	3' UTR (NM_001145161, exon 2 of 2)	3' UTR (NM_001145161, exon 2 of 2)	47334	NM_001145161	134111	Hs.126856	NM_001145161	ENSG00000215218	UBE2QL1	-	ubiquitin conjugating enzyme E2 Q family like 1	protein-coding	0.014056	0.452906	291(GGGAGCAAAGTGTGCT,-,0.00),292(GGAGCAAAGTGTGCTG,+,0.00)
chunk0027_102_1	chr10	73836476	73836777	+	0	NA	intron (NM_172169, intron 14 of 20)	intron (NM_172169, intron 14 of 20)	-24795	NM_003635	8509	Hs.654758	NM_003635	ENSG00000166507	NDST2	HSST2|N-HSST 2|NST2	N-deacetylase and N-sulfotransferase 2	protein-coding	0.026578	0.569536	
chunk0081_164_1	chr17	41009269	41009812	+	0	NA	promoter-TSS (NM_031958)	promoter-TSS (NM_031958)	-426	NM_031958	83896	Hs.307027	NM_031958	ENSG00000212901	KRTAP3-1	KAP3.1|KRTAP3.1	keratin associated protein 3-1	protein-coding	0.007366	0.380515	
chunk0190_192_1	chr8	33553959	33554413	+	0	NA	intron (NM_024787, intron 2 of 5)	intron (NM_024787, intron 2 of 5)	12942	NM_024787	79845	Hs.151237	NM_024787	ENSG00000133874	RNF122	-	ring finger protein 122	protein-coding	0.006608	0.494505	
chunk0157_198_1	chr5	118988841	118989040	+	0	NA	promoter-TSS (NM_001308081)	promoter-TSS (NM_001308081)	-335	NM_173666	285605	Hs.655891	NM_173666	ENSG00000169570	DTWD2	-	DTW domain containing 2	protein-coding	0.030151	0.435000	
chunk0173_81_1	chr6	142753580	142753779	+	0	NA	exon (NM_006734, exon 10 of 10)	exon (NM_006734, exon 10 of 10)	-115790	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.030151	0.570000	
chunk0209_23_1	chrX	35664809	35665212	+	0	NA	Intergenic	MER92A|LTR|ERV1	-133332	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.004963	0.396040	
chunk0049_299_1	chr12	94278392	94278600	+	0	NA	intron (NR_037687, intron 2 of 11)	MamRep434|DNA|TcMar-Tigger	15975	NR_037687	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.004808	0.368421	
chunk0155_94_1	chr5	92368128	92368666	+	0	NA	Intergenic	Intergenic	-985065	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.007435	0.359926	224(CAGGACACTCTGAACC,-,0.00),225(AGGACACTCTGAACCA,+,0.00)
chunk0083_343_1	chr17	70218515	70219162	+	0	NA	Intergenic	Intergenic	49303	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.010819	0.345679	
chunk0064_374_1	chr14	98656399	98656935	+	0	NA	Intergenic	L1MEa|LINE|L1	-54946	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.001866	0.314711	
chunk0029_251_1	chr10	102813336	102813653	+	0	NA	3' UTR (NM_001083913, exon 4 of 4)	3' UTR (NM_001083913, exon 4 of 4)	24039	NM_000102	1586	Hs.438016	NM_000102	ENSG00000148795	CYP17A1	CPT7|CYP17|P450C17|S17AH	cytochrome P450 family 17 subfamily A member 1	protein-coding	0.006309	0.481132	
chunk0055_31_1	chr13	51977378	51978021	+	0	NA	intron (NM_001005918, intron 1 of 16)	Tigger3b|DNA|TcMar-Tigger	33795	NM_000053	540	Hs.492280	NM_000053	ENSG00000123191	ATP7B	PWD|WC1|WD|WND	ATPase copper transporting beta	protein-coding	0.010886	0.372671	
chunk0115_264_1	chr21	27831875	27832086	+	0	NA	Intergenic	Intergenic	109601	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.014218	0.377358	185(AAGCACAGGCTGTTTA,-,0.00),186(AGCACAGGCTGTTTAT,+,0.00)
chunk0025_29_1	chr10	48414026	48414225	+	0	NA	intron (NM_139049, intron 4 of 10)	L1MB8|LINE|L1	12513	NM_139046	5599	Hs.138211	NM_002750	ENSG00000107643	MAPK8	JNK|JNK-46|JNK1|JNK1A2|JNK21B1/2|PRKM8|SAPK1|SAPK1c	mitogen-activated protein kinase 8	protein-coding	0.000000	0.330000	
chunk0183_86_1	chr7	104971779	104972046	+	0	NA	Intergenic	Intergenic	19253	NR_039981	100216546	Hs.369356	NR_039981		LINC01004	-	long intergenic non-protein coding RNA 1004	ncRNA	0.003745	0.458955	
chunk0135_373_1	chr3	190862812	190863083	+	0	NA	promoter-TSS (NM_001146686)	promoter-TSS (NM_001146686)	-271	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.132841	0.772059	
chunk0205_216_1	chr9	109423729	109424162	+	0	NA	intron (NM_001145369, intron 7 of 20)	intron (NM_001145369, intron 7 of 20)	5098	NM_001145371	5774	Hs.436429	NM_002829	ENSG00000070159	PTPN3	PTP-H1|PTPH1	protein tyrosine phosphatase non-receptor type 3	protein-coding	0.002309	0.387097	209(TAGCACATCATGTACT,-,0.00),210(AGCACATCATGTACTA,+,0.00)
chunk0005_134_1	chr1	57186308	57186532	+	0	NA	intron (NM_021080, intron 4 of 16)	intron (NM_021080, intron 4 of 16)	-220280	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.004464	0.391111	
chunk0107_250_1	chr2	217311816	217312064	+	0	NA	intron (NR_133642, intron 4 of 5)	intron (NR_133642, intron 4 of 5)	29207	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.000000	0.437751	
chunk0210_198_1	chrX	80494967	80495383	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	74728	NM_152630	169966	Hs.367959	NM_152630	ENSG00000174016	TENT5D	CT1.26|CT112|FAM46D	terminal nucleotidyltransferase 5D	protein-coding	0.007212	0.369305	
chunk0061_144_1	chr14	59452521	59452993	+	0	NA	Intergenic	L1MC1|LINE|L1	12584	NM_022571	64582	Hs.647573	NM_022571	ENSG00000181619	GPR135	HUMNPIIY20	G protein-coupled receptor 135	protein-coding	0.004237	0.346723	
chunk0059_336_1	chr14	36935160	36935537	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	17043	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.002653	0.420635	195(GAGATCTCTCTGTCCC,-,0.00),196(AGATCTCTCTGTCCCT,+,0.00)
chunk0014_457_1	chr1	184025440	184025684	+	0	NA	intron (NM_001303421, intron 1 of 11)	intron (NM_001303421, intron 1 of 11)	12208	NM_001303420	23127	Hs.387995	NM_015101	ENSG00000198756	COLGALT2	C1orf17|ColGalT 2|GLT25D2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0.000000	0.506122	
chunk0029_349_1	chr10	106925354	106925553	+	0	NA	intron (NM_052918, intron 2 of 25)	intron (NM_052918, intron 2 of 25)	239255	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.000000	0.455000	
chunk0077_327_1	chr16	82318055	82318393	+	0	NA	Intergenic	MER77|LTR|ERVL	-148000	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.005917	0.445428	
chunk0081_414_1	chr17	48625428	48625984	+	0	NA	intron (NM_024017, intron 1 of 1)	CpG	767	NM_024017	3219	Hs.463350	NM_024017	ENSG00000170689	HOXB9	HOX-2.5|HOX2|HOX2E	homeobox B9	protein-coding	0.077338	0.649910	
chunk0013_219_1	chr1	169510658	169511146	+	0	NA	Intergenic	Intergenic	-24932	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.002049	0.355828	
chunk0016_149_1	chr1	197485558	197485757	+	0	NA	Intergenic	Intergenic	217453	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.010050	0.550000	
chunk0012_452_1	chr1	165173482	165173761	+	0	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	182620	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.007168	0.521429	117(GGACACAGGTTGTTCC,-,0.00),118(GACACAGGTTGTTCCT,+,0.00)
chunk0045_34_1	chr12	44307613	44307938	+	0	NA	intron (NM_001286211, intron 6 of 6)	intron (NM_001286211, intron 6 of 6)	471914	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.012308	0.475460	33(GGAGACAGAGTGTTCA,-,0.00),34(GAGACAGAGTGTTCAG,+,0.00)
chunk0004_385_1	chr1	51878333	51878946	+	0	NA	promoter-TSS (NM_001242361)	promoter-TSS (NM_001242361)	298	NM_001101662	4898	Hs.584782	NM_002525	ENSG00000078618	NRDC	NRD1|hNRD1|hNRD2	nardilysin convertase	protein-coding	0.070147	0.625407	
chunk0134_240_1	chr3	179136905	179137196	+	0	NA	intron (NR_125401, intron 1 of 2)	L1P4b|LINE|L1	10923	NR_125401	101928739	Hs.434553	NR_125401	ENSG00000229102	LOC101928739	-	uncharacterized LOC101928739	ncRNA	0.003436	0.527397	
chunk0123_288_1	chr3	46441704	46442366	+	0	NA	intron (NM_002343, intron 13 of 16)	HAL1|LINE|L1	21636	NM_001199149	4057	Hs.529517	NM_002343	ENSG00000012223	LTF	GIG12|HEL110|HLF2|LF	lactotransferrin	protein-coding	0.006042	0.417798	
chunk0075_66_1	chr16	47916339	47916538	+	0	NA	Intergenic	L1ME2z|LINE|L1	-29308	NR_110649	100507534	Hs.407601	NR_110649	ENSG00000261325	LINC02192	-	long intergenic non-protein coding RNA 2192	ncRNA	0.000000	0.355000	
chunk0085_61_1	chr18	1076864	1077122	+	0	NA	Intergenic	Intergenic	171797	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.003876	0.351351	
chunk0211_1_1	chrX	107626613	107627401	+	0	NA	Intergenic	L2a|LINE|L2	-1417	NM_001204402	5631	Hs.56	NM_002764	ENSG00000147224	PRPS1	ARTS|CMTX5|DFN2|DFNX1|PPRibP|PRS-I|PRSI	phosphoribosyl pyrophosphate synthetase 1	protein-coding	0.008883	0.396705	
chunk0070_77_1	chr15	70091565	70091982	+	0	NA	intron (NM_020908, intron 4 of 19)	intron (NM_020908, intron 4 of 19)	3012	NM_001282982	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.016787	0.480861	389(AAGTACAGACAGTCCC,-,0.00),390(AGTACAGACAGTCCCC,+,0.00)
chunk0205_203_1	chr9	109264939	109265351	+	0	NA	intron (NM_018424, intron 4 of 15)	intron (NM_018424, intron 4 of 15)	55819	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.019417	0.484262	
chunk0041_368_1	chr11	131415514	131416319	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	45440	NM_001048209	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.002484	0.382134	
chunk0197_146_1	chr8	120378246	120378845	+	0	NA	Intergenic	Intergenic	-66853	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.003339	0.366667	
chunk0158_119_1	chr5	126926345	126926952	+	0	NA	intron (NM_178450, intron 1 of 4)	intron (NM_178450, intron 1 of 4)	104160	NM_178450	115123	Hs.132441	NM_178450	ENSG00000173926	MARCH3	MARCH-III|RNF173	membrane associated ring-CH-type finger 3	protein-coding	0.004942	0.488487	
chunk0034_319_1	chr11	35255257	35256040	+	0	NA	3' UTR (NM_001252652, exon 12 of 12)	3' UTR (NM_001252652, exon 12 of 12)	116778	NM_001202557	960	Hs.502328	NM_000610	ENSG00000026508	CD44	CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1	CD44 molecule (Indian blood group)	protein-coding	0.005109	0.377551	
chunk0194_358_1	chr8	89611363	89611687	+	0	NA	Intergenic	MIR|SINE|MIR	146186	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.003086	0.412308	
chunk0134_322_1	chr3	181839369	181839568	+	0	NA	Intergenic	Intergenic	-112896	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.010050	0.360000	
chunk0162_77_1	chr6	1832476	1833243	+	0	NA	intron (NM_001253846, intron 7 of 10)	L3|LINE|CR1	222413	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.020860	0.459635	404(AAGCACACGATGAACT,-,0.00),405(AGCACACGATGAACTT,+,0.00)
chunk0156_335_1	chr5	111742568	111743077	+	0	NA	intron (NM_001142474, intron 2 of 3)	intron (NM_001142474, intron 2 of 3)	13429	NM_001142483	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.015717	0.443137	
chunk0058_122_1	chr14	22295958	22296482	+	0	NA	Intergenic	Charlie2a|DNA|hAT-Charlie	293017	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.032443	0.440000	
chunk0113_340_1	chr20	58682839	58683450	+	0	NA	intron (NR_037945, intron 8 of 22)	intron (NR_037945, intron 8 of 22)	-5987	NM_001204873	79716	Hs.654868	NM_024663	ENSG00000215440	NPEPL1	bA261P9.2	aminopeptidase like 1	protein-coding	0.016367	0.433007	
chunk0194_424_1	chr8	92358502	92359044	+	0	NA	Intergenic	Intergenic	-191262	NR_106988									0.009225	0.408840	
chunk0129_210_1	chr3	121749204	121749403	+	0	NA	intron (NM_001256488, intron 1 of 20)	CpG	464	NM_001256488	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.080402	0.635000	
chunk0130_326_1	chr3	138201681	138202413	+	0	NA	intron (NM_015396, intron 2 of 22)	intron (NM_015396, intron 2 of 22)	14799	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.010929	0.354707	
chunk0079_106_1	chr17	12255825	12256559	+	0	NA	Intergenic	Intergenic	174293	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.008174	0.371429	
chunk0184_314_1	chr7	120204122	120204755	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-69230	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.001580	0.268139	
chunk0015_49_1	chr1	184553589	184553841	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	166699	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.478261	
chunk0203_292_1	chr9	89001371	89001897	+	0	NA	exon (NM_005226, exon 2 of 2)	exon (NM_005226, exon 2 of 2)	10225	NM_005226	1903	Hs.585118	NM_005226	ENSG00000213694	S1PR3	EDG-3|EDG3|LPB3|S1P3	sphingosine-1-phosphate receptor 3	protein-coding	0.043726	0.550285	
chunk0089_413_1	chr18	68711949	68712274	+	0	NA	intron (NM_019022, intron 2 of 15)	MER76-int|LTR|ERVL	3005	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.009231	0.475460	307(AGGCCCACCATGTTCT,-,0.00)
chunk0126_360_1	chr3	83076103	83076302	+	0	NA	Intergenic	L1MA4|LINE|L1	-1314403	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.020101	0.410000	93(AGATACACTGTGTGCT,-,0.00),94(GATACACTGTGTGCTT,+,0.00)
chunk0174_364_1	chr6	164644491	164645260	+	0	NA	Intergenic	Intergenic	177188	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.003901	0.333766	
chunk0127_231_1	chr3	96786571	96786981	+	0	NA	Intergenic	Intergenic	-27805	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.007317	0.306569	
chunk0154_148_1	chr5	79420294	79421013	+	0	NA	intron (NM_004272, intron 5 of 8)	intron (NM_004272, intron 5 of 8)	93183	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.005563	0.418056	
chunk0009_230_1	chr1	106689934	106690200	+	0	NA	Intergenic	Intergenic	-366578	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.007519	0.325843	
chunk0112_1_1	chr20	35442995	35443429	+	0	NA	Intergenic	Intergenic	-5022	NM_000557	8200	Hs.1573	NM_000557	ENSG00000125965	GDF5	BDA1C|BMP-14|BMP14|CDMP1|LAP-4|LAP4|OS5|SYM1B|SYNS2	growth differentiation factor 5	protein-coding	0.013825	0.542529	283(TGGGACACAGCGTCCC,-,0.00),284(GGGACACAGCGTCCCT,+,0.00)
chunk0024_257_1	chr10	38918938	38919503	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	222624	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.007080	0.454064	
chunk0020_321_1	chr1	237725481	237725812	+	0	NA	intron (NM_001035, intron 74 of 104)	intron (NM_001035, intron 74 of 104)	-136529	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.003021	0.355422	
chunk0038_348_1	chr11	93061864	93062122	+	0	NA	Intergenic	Intergenic	92370	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.015504	0.444015	
chunk0157_356_1	chr5	123313546	123313842	+	0	NA	Intergenic	L1PA10|LINE|L1	109898	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.013514	0.558923	
chunk0164_101_1	chr6	20454214	20454469	+	0	NA	intron (NM_001243076, intron 1 of 6)	intron (NM_001243076, intron 1 of 6)	50662	NM_001243076	1871	Hs.269408	NM_001949	ENSG00000112242	E2F3	E2F-3	E2F transcription factor 3	protein-coding	0.003922	0.417969	
chunk0037_236_1	chr11	75328876	75329214	+	0	NA	intron (NM_004041, intron 1 of 15)	intron (NM_004041, intron 1 of 15)	6141	NR_029891	442900		NR_029891	ENSG00000199090	MIR326	MIRN326|hsa-mir-326|mir-326	microRNA 326	ncRNA	0.014793	0.489676	
chunk0137_76_1	chr4	12926021	12926560	+	0	NA	Intergenic	Intergenic	558075	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.005566	0.446296	
chunk0028_137_1	chr10	86361125	86361897	+	0	NA	intron (NM_017551, intron 2 of 15)	intron (NM_017551, intron 2 of 15)	4982	NM_017551	2894	Hs.530653	NM_017551	ENSG00000182771	GRID1	GluD1	glutamate ionotropic receptor delta type subunit 1	protein-coding	0.002591	0.482536	
chunk0072_290_1	chr15	98653604	98653861	+	0	NA	intron (NM_001291858, intron 1 of 20)	intron (NM_001291858, intron 1 of 20)	-2511	NR_126453	104472848	Hs.349049	NR_126453		IRAIN	IGF1R-AS	IGF1R antisense imprinted non-protein coding RNA	ncRNA	0.003891	0.352713	
chunk0121_66_1	chr3	15755824	15756133	+	0	NA	intron (NM_015199, intron 3 of 27)	intron (NM_015199, intron 3 of 27)	573	NM_001195099	23243	Hs.335239	NM_015199	ENSG00000206560	ANKRD28	PITK|PPP1R65	ankyrin repeat domain 28	protein-coding	0.006472	0.348387	
chunk0173_373_1	chr6	149503667	149504138	+	0	NA	TTS (NM_139126)	TTS (NM_139126)	-18890	NM_207360	340152	Hs.632618	NM_207360	ENSG00000178199	ZC3H12D	C6orf95|MCPIP4|TFL|dJ281H8.1|p34	zinc finger CCCH-type containing 12D	protein-coding	0.008493	0.396186	
chunk0144_468_1	chr4	142589166	142589545	+	0	NA	intron (NM_003866, intron 2 of 26)	L1MC3|LINE|L1	257096	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.002639	0.297368	
chunk0209_85_1	chrX	38998514	38998783	+	0	NA	Intergenic	L1ME4b|LINE|L1	-194765	NR_046706	100874211	Hs.662789	NR_046706		MID1IP1-AS1	-	MID1IP1 antisense RNA 1	ncRNA	0.000000	0.311111	
chunk0131_419_1	chr3	153138776	153139122	+	0	NA	Intergenic	Intergenic	-23263	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.011561	0.406340	
chunk0146_74_1	chr4	157192343	157193090	+	0	NA	Intergenic	Intergenic	-27868	NM_001083619	2891	Hs.32763	NM_000826	ENSG00000120251	GRIA2	GLUR2|GLURB|GluA2|GluR-K2|HBGR2	glutamate ionotropic receptor AMPA type subunit 2	protein-coding	0.005355	0.362299	358(AGGGTCATAGTGTACT,-,0.00),359(GGGTCATAGTGTACTG,+,0.00)
chunk0093_387_1	chr19	56404449	56404758	+	0	NA	intron (NM_152478, intron 1 of 4)	intron (NM_152478, intron 1 of 4)	254	NM_001159861	147949	Hs.146854	NM_152478	ENSG00000198440	ZNF583	-	zinc finger protein 583	protein-coding	0.042071	0.522581	
chunk0135_81_1	chr3	186117654	186118134	+	0	NA	Intergenic	L2c|LINE|L2	-8782	NM_004454	2119	Hs.43697	NM_004454	ENSG00000244405	ETV5	ERM	ETS variant 5	protein-coding	0.002083	0.451143	
chunk0160_290_1	chr5	158176176	158176559	+	0	NA	Intergenic	Intergenic	233406	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.013055	0.515625	
chunk0001_10_1	chr1	960505	960704	+	0	NA	promoter-TSS (NM_198317)	promoter-TSS (NM_198317)	17	NM_198317	339451	Hs.109212	NM_198317	ENSG00000187961	KLHL17	-	kelch like family member 17	protein-coding	0.155779	0.750000	
chunk0210_356_1	chrX	96407125	96407726	+	0	NA	Intergenic	Intergenic	-69523	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.009983	0.397010	
chunk0055_283_1	chr13	64459719	64460247	+	0	NA	Intergenic	Intergenic	-615858	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.007576	0.385633	
chunk0031_422_1	chr10	132332778	132333660	+	0	NA	intron (NM_001143757, intron 1 of 10)	intron (NM_001143757, intron 1 of 10)	982	NM_001143757	80313	Hs.119897	NM_030626	ENSG00000148814	LRRC27	-	leucine rich repeat containing 27	protein-coding	0.018141	0.426954	
chunk0091_324_1	chr19	13731407	13731829	+	0	NA	Intergenic	Intergenic	-16321	NM_030818	81576	Hs.24998	NM_030818	ENSG00000104957	CCDC130	-	coiled-coil domain containing 130	protein-coding	0.071090	0.574468	
chunk0147_20_1	chr4	171194175	171194658	+	0	NA	Intergenic	Intergenic	8232	NR_106730	102466953		NR_106730	ENSG00000278502	MIR6082	hsa-mir-6082	microRNA 6082	ncRNA	0.004141	0.316116	
chunk0109_379_1	chr2	239723709	239723908	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-39052	NR_037808	150935	Hs.555582	NR_037808		LOC150935	-	uncharacterized LOC150935	ncRNA	0.015075	0.545000	
chunk0008_437_1	chr1	99543903	99544607	+	0	NA	intron (NR_031666, intron 3 of 4)	intron (NR_031666, intron 3 of 4)	-56451	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.005682	0.394326	
chunk0096_61_1	chr2	27596645	27597156	+	0	NA	intron (NM_001271286, intron 2 of 12)	L1ME5|LINE|L1	13931	NM_001271288	84450	Hs.529178	NM_032434	ENSG00000243943	ZNF512	-	zinc finger protein 512	protein-coding	0.003914	0.388672	
chunk0046_217_1	chr12	59389920	59390119	+	0	NA	Intergenic	L1PA8A|LINE|L1	-206021	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.025126	0.525000	
chunk0017_461_1	chr1	214516150	214517205	+	0	NA	intron (NM_005401, intron 1 of 18)	intron (NM_005401, intron 1 of 18)	35004	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.005687	0.425189	
chunk0043_147_1	chr12	16329579	16329902	+	0	NA	Intergenic	Intergenic	-17402	NM_145792	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.009288	0.354938	
chunk0184_242_1	chr7	117705598	117705947	+	0	NA	Intergenic	L1MA8|LINE|L1	167735	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.008596	0.351429	
chunk0117_150_1	chr22	19728375	19729028	+	0	NA	Intergenic	Intergenic	5158	NM_000407	2812	Hs.283743	NM_000407	ENSG00000203618	GP1BB	BDPLT1|BS|CD42C|GPIBB|GPIbbeta	glycoprotein Ib platelet subunit beta	protein-coding	0.016845	0.633028	
chunk0200_298_1	chr9	22926978	22927578	+	0	NA	Intergenic	L1MEi|LINE|L1	281078	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.003333	0.319468	
chunk0083_83_1	chr17	64230789	64231056	+	0	NA	promoter-TSS (NM_001288733)	promoter-TSS (NM_001288733)	-166	NM_001288733	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.000000	0.388060	
chunk0091_310_1	chr19	12938300	12938640	+	0	NA	promoter-TSS (NM_004343)	promoter-TSS (NM_004343)	-130	NM_004343	811	Hs.515162	NM_004343	ENSG00000179218	CALR	CRT|HEL-S-99n|RO|SSA|cC1qR	calreticulin	protein-coding	0.076471	0.639296	
chunk0054_104_1	chr13	42852842	42853461	+	0	NA	intron (NR_126388, intron 2 of 2)	MamRTE1|LINE|RTE-BovB	19593	NR_126388	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.004847	0.396774	292(AAGAACAAAATGTACT,-,0.00),293(AGAACAAAATGTACTG,+,0.00)
chunk0078_182_1	chr17	4690705	4691083	+	0	NA	exon (NM_014389, exon 3 of 17)	exon (NM_014389, exon 3 of 17)	-13336	NR_103482	101559451	Hs.634966	NR_103482	ENSG00000244184	LOC101559451	-	uncharacterized LOC101559451	ncRNA	0.005291	0.472296	
chunk0205_71_1	chr9	106869431	106870122	+	0	NA	intron (NM_021224, intron 1 of 12)	intron (NM_021224, intron 1 of 12)	6679	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.005789	0.382948	
chunk0138_304_1	chr4	41142266	41142542	+	0	NA	intron (NM_004307, intron 2 of 17)	intron (NM_004307, intron 2 of 17)	72214	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.003623	0.393502	114(AGGACATTCTCTTCCC,+,0.00)
chunk0105_164_1	chr2	186877355	186877905	+	0	NA	Intergenic	L1MA8|LINE|L1	-28460	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.003636	0.306715	
chunk0198_402_1	chr8	141816117	141816360	+	0	NA	Intergenic	Intergenic	-29925	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.024691	0.487705	105(GAGAACAGCCTGTTCC,-,0.00),106(AGAACAGCCTGTTCCA,+,0.00)
chunk0058_439_1	chr13	113423157	113423384	+	0	NA	intron (NM_138430, intron 6 of 6)	AluSx|SINE|Alu	-8877	NM_001304433	101928841	Hs.646609	NM_001003399		LOC101928841	-	collagen alpha-1(II) chain-like	protein-coding	0.026432	0.548246	
chunk0159_377_1	chr5	146020054	146020675	+	0	NA	intron (NM_152550, intron 5 of 9)	intron (NM_152550, intron 5 of 9)	83801	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.004831	0.397106	285(ATGCACACCATGTACT,-,0.00),286(TGCACACCATGTACTA,+,0.00)
chunk0159_366_1	chr5	145902355	145902907	+	0	NA	Intergenic	Intergenic	-29663	NM_001080516	643226	Hs.570895	NM_001080516	ENSG00000204928	GRXCR2	DFNB101	glutaredoxin and cysteine rich domain containing 2	protein-coding	0.005435	0.394213	
chunk0207_86_1	chrX	9415356	9416055	+	0	NA	Intergenic	Intergenic	-47590	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.014306	0.338571	
chunk0049_80_1	chr12	90628019	90628490	+	0	NA	Intergenic	Intergenic	-289769	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.000000	0.360169	
chunk0124_286_1	chr3	57604968	57605349	+	0	NA	Intergenic	L1MEc|LINE|L1	7369	NR_132370	106144532	Hs.667207	NR_132369	ENSG00000272146	ARF4-AS1	-	ARF4 antisense RNA 1	ncRNA	0.005249	0.424084	
chunk0057_387_1	chr13	109494847	109495974	+	0	NA	Intergenic	Intergenic	94714	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.011535	0.382979	
chunk0164_262_1	chr6	23575288	23575497	+	0	NA	Intergenic	Intergenic	-550794	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.009569	0.380952	
chunk0163_333_1	chr6	15284759	15285098	+	0	NA	intron (NM_001267040, intron 1 of 17)	intron (NM_001267040, intron 1 of 17)	36073	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.002950	0.385294	
chunk0021_40_1	chr10	878220	878924	+	0	NA	intron (NM_015155, intron 3 of 17)	L1ME3A|LINE|L1	53133	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.014205	0.425532	
chunk0184_320_1	chr7	120358687	120359157	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	85254	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.004255	0.352442	
chunk0015_372_1	chr1	190478421	190479075	+	0	NA	intron (NR_110717, intron 1 of 1)	(TC)n|Simple_repeat|Simple_repeat	197	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.032110	0.506870	
chunk0191_249_1	chr8	53214463	53214935	+	0	NA	Intergenic	L1PREC2|LINE|L1	36935	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.004237	0.539112	
chunk0211_200_1	chrX	117985543	117985762	+	0	NA	promoter-TSS (NM_001168299)	promoter-TSS (NM_001168299)	-239	NM_001168299	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.000000	0.331818	60(AGGAACAAAGTGTTCA,-,0.00),61(GGAACAAAGTGTTCAT,+,0.00)
chunk0047_423_1	chr12	76117094	76117508	+	0	NA	Intergenic	AluJr|SINE|Alu	-32268	NM_139207	4673	Hs.524599	NM_004537	ENSG00000187109	NAP1L1	NAP1|NAP1L|NRP	nucleosome assembly protein 1 like 1	protein-coding	0.007246	0.392771	
chunk0181_134_1	chr7	81150849	81151203	+	0	NA	Intergenic	Intergenic	-231675	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.002825	0.484507	
chunk0209_126_1	chrX	40887355	40888050	+	0	NA	Intergenic	L1PA16|LINE|L1	-54506	NR_027761	100132831	Hs.729923	NR_027761		LOC100132831	-	A20-binding inhibitor of NF-kappaB activation 2 pseudogene	pseudo	0.004317	0.352011	
chunk0034_281_1	chr11	34654691	34655225	+	0	NA	intron (NM_001206616, intron 6 of 8)	intron (NM_001206616, intron 6 of 8)	22494	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.009363	0.448598	
chunk0145_192_1	chr4	147829449	147829987	+	0	NA	intron (NM_024605, intron 3 of 22)	intron (NM_024605, intron 3 of 22)	47123	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.014870	0.476809	240(CAGGACATGTTGTACT,-,0.00),241(AGGACATGTTGTACTT,+,0.00)
chunk0204_184_1	chr9	96261724	96261923	+	0	NA	intron (NM_000197, intron 2 of 10)	LTR78|LTR|ERV1	40329	NM_000197	3293	Hs.477	NM_000197	ENSG00000130948	HSD17B3	EDH17B3|SDR12C2	hydroxysteroid 17-beta dehydrogenase 3	protein-coding	0.005025	0.515000	
chunk0017_338_1	chr1	211603531	211604084	+	0	NA	Intergenic	Intergenic	-25050	NM_021194	7779	Hs.519469	NM_021194	ENSG00000170385	SLC30A1	ZNT1|ZRC1	solute carrier family 30 member 1	protein-coding	0.005425	0.391697	
chunk0049_245_1	chr12	93586140	93586570	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	13829	NM_001270471	8835	Hs.485572	NM_003877	ENSG00000120833	SOCS2	CIS2|Cish2|SOCS-2|SSI-2|SSI2|STATI2	suppressor of cytokine signaling 2	protein-coding	0.004651	0.324826	
chunk0075_185_1	chr16	52123971	52124184	+	0	NA	Intergenic	Intergenic	38796	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.004695	0.303738	
chunk0110_309_1	chr20	18396852	18397627	+	0	NA	intron (NM_001099407, intron 14 of 20)	intron (NM_001099407, intron 14 of 20)	18190	NR_034167	440757	Hs.120399	NM_001004344	ENSG00000237282	LINC00851	DZANK1-AS1	long intergenic non-protein coding RNA 851	ncRNA	0.009032	0.409794	
chunk0147_386_1	chr4	186554556	186554773	+	0	NA	intron (NM_005958, intron 1 of 1)	intron (NM_005958, intron 1 of 1)	719	NM_005958	4543	Hs.243467	NM_005958	ENSG00000168412	MTNR1A	MEL-1A-R|MT1	melatonin receptor 1A	protein-coding	0.050691	0.504587	
chunk0195_405_1	chr8	100468250	100468455	+	0	NA	Intergenic	Intergenic	85589	NR_039681	100616451		NR_039681	ENSG00000265599	MIR4471	-	microRNA 4471	ncRNA	0.000000	0.402913	
chunk0039_90_1	chr11	97238608	97239334	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-732094	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.002755	0.392022	
chunk0172_12_1	chr6	132798863	132799116	+	0	NA	promoter-TSS (NM_052831)	promoter-TSS (NM_052831)	-381	NM_052831	116843	Hs.347144	NM_052831	ENSG00000146409	SLC18B1	C6orf192|dJ55C23.6	solute carrier family 18 member B1	protein-coding	0.023715	0.370079	
chunk0180_375_1	chr7	74130020	74130350	+	0	NA	Intergenic	Intergenic	37029	NM_001204426	3984	Hs.647035	NM_002314	ENSG00000106683	LIMK1	LIMK|LIMK-1	LIM domain kinase 1	protein-coding	0.003030	0.308157	
chunk0143_103_1	chr4	108532655	108533016	+	0	NA	Intergenic	Intergenic	87622	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.005540	0.386740	194(GTGCACTGGCTGTACT,-,0.00),195(TGCACTGGCTGTACTG,+,0.00)
chunk0120_282_1	chr3	9648983	9649309	+	0	NA	promoter-TSS (NM_001077526)	promoter-TSS (NM_001077526)	-287	NM_022485	64419	Hs.475382	NM_022485	ENSG00000163719	MTMR14	C3orf29	myotubularin related protein 14	protein-coding	0.036810	0.559633	
chunk0194_410_1	chr8	91308460	91309070	+	0	NA	intron (NM_001282356, intron 5 of 19)	L1MC3|LINE|L1	59477	NM_134266	115111	Hs.354013	NM_052832	ENSG00000147606	SLC26A7	SUT2	solute carrier family 26 member 7	protein-coding	0.000000	0.355155	
chunk0160_277_1	chr5	157757544	157758226	+	0	NA	3' UTR (NM_173491, exon 4 of 4)	3' UTR (NM_173491, exon 4 of 4)	14190	NM_173491	134353	Hs.23648	NM_173491	ENSG00000155858	LSM11	-	LSM11, U7 small nuclear RNA associated	protein-coding	0.010264	0.368960	
chunk0110_228_1	chr20	15871223	15871473	+	0	NA	intron (NM_001033087, intron 5 of 13)	intron (NM_001033087, intron 5 of 13)	51966	NR_130925	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.000000	0.298805	
chunk0071_54_1	chr15	80162129	80162328	+	0	NA	intron (NM_000137, intron 4 of 13)	intron (NM_000137, intron 4 of 13)	9337	NM_000137	2184	Hs.73875	NM_000137	ENSG00000103876	FAH	-	fumarylacetoacetate hydrolase	protein-coding	0.025126	0.505000	
chunk0031_139_1	chr10	124955075	124955586	+	0	NA	intron (NM_017580, intron 1 of 8)	AluSx|SINE|Alu	13207	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.021526	0.427734	
chunk0060_12_1	chr14	39302215	39302525	+	0	NA	intron (NM_005930, intron 10 of 23)	intron (NM_005930, intron 10 of 23)	35246	NM_203355	4253	Hs.287694	NM_005930	ENSG00000150527	MIA2	CTAGE5|MEA6|MGEA|MGEA11|MGEA6|TALI	MIA SH3 domain ER export factor 2	protein-coding	0.006452	0.389068	155(GTGACACACTGTCCTT,+,0.00)
chunk0153_146_1	chr5	69094363	69094639	+	0	NA	intron (NM_001251969, intron 1 of 2)	CpG	552	NM_001251969	64924	Hs.631975	NM_022902	ENSG00000145740	SLC30A5	ZNT5|ZNTL1|ZTL1|ZnT-5	solute carrier family 30 member 5	protein-coding	0.076087	0.638989	
chunk0128_417_1	chr3	114799775	114800084	+	0	NA	intron (NM_001164343, intron 4 of 11)	intron (NM_001164343, intron 4 of 11)	-40652	NM_001164345	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.009709	0.422581	
chunk0095_18_1	chr2	12280332	12280797	+	0	NA	intron (NR_110196, intron 3 of 5)	L2c|LINE|L2	81434	NR_037452	100500884		NR_037452	ENSG00000264089	MIR3681	-	microRNA 3681	ncRNA	0.010753	0.360515	
chunk0156_216_1	chr5	108123966	108124175	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	258028	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.000000	0.309524	
chunk0124_30_1	chr3	52133246	52133542	+	0	NA	intron (NM_001161580, intron 7 of 9)	MLT1A1|LTR|ERVL-MaLR	21296	NM_001161580	25886	Hs.476306	NM_015426	ENSG00000164087	POC1A	PIX2|SOFT|WDR51A	POC1 centriolar protein A	protein-coding	0.023649	0.501684	
chunk0045_253_1	chr12	49225976	49226175	+	0	NA	Intergenic	Intergenic	-1851	NM_001303114	84790	Hs.652390	NM_032704	ENSG00000167553	TUBA1C	TUBA6|bcm948	tubulin alpha 1c	protein-coding	0.005025	0.495000	47(AGGTCCATCCTGTTCT,-,0.00),48(GGTCCATCCTGTTCTT,+,0.00)
chunk0088_228_1	chr18	48410482	48410745	+	0	NA	Intergenic	CpG	-128443	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.064639	0.636364	
chunk0081_420_1	chr17	48759356	48759591	+	0	NA	Intergenic	L2c|LINE|L2	-30724	NM_006361	10481	Hs.66731	NM_006361	ENSG00000159184	HOXB13	HPC9|PSGD	homeobox B13	protein-coding	0.000000	0.377119	
chunk0049_367_1	chr12	95674792	95675022	+	0	NA	TTS (NR_077225)	TTS (NR_077225)	25652	NR_077225	100132594	Hs.676211	NR_077225	ENSG00000257150	PGAM1P5	-	phosphoglycerate mutase 1 pseudogene 5	pseudo	0.004348	0.424242	98(CAGCACTTTATGTGCT,-,0.00),99(AGCACTTTATGTGCTT,+,0.00)
chunk0207_307_1	chr9	133593123	133593343	+	0	NA	Intergenic	MIRc|SINE|MIR	-12987	NM_001080515	642968	Hs.173134	NM_001080515	ENSG00000196990	FAM163B	C9orf166	family with sequence similarity 163 member B	protein-coding	0.004545	0.520362	
chunk0066_45_1	chr15	27908862	27909443	+	0	NA	intron (NM_001300984, intron 18 of 22)	L1MC4a|LINE|L1	190160	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.000000	0.305842	408(AGACACATCCTGTTCT,-,0.00),409(GACACATCCTGTTCTC,+,0.00)
chunk0142_15_1	chr4	90111387	90111930	+	0	NA	Intergenic	Intergenic	-15875	NM_001145065	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.007366	0.316176	
chunk0049_376_1	chr12	95829279	95829824	+	0	NA	Intergenic	Intergenic	-29380	NM_003095	6636	Hs.105465	NM_003095	ENSG00000139343	SNRPF	SMF|Sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding	0.000000	0.336996	
chunk0109_79_1	chr20	1943690	1944028	+	0	NA	Intergenic	L2b|LINE|L2	48679	NM_001040023	140885	Hs.581021	NM_080792	ENSG00000198053	SIRPA	BIT|CD172A|MFR|MYD-1|P84|PTPNS1|SHPS1|SIRP	signal regulatory protein alpha	protein-coding	0.008876	0.466077	
chunk0082_216_1	chr17	57075589	57076314	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-9241	NM_003488	8165	Hs.463506	NM_003488	ENSG00000121057	AKAP1	AKAP|AKAP121|AKAP149|AKAP84|D-AKAP1|PPP1R43|PRKA1|SAKAP84|TDRD17	A-kinase anchoring protein 1	protein-coding	0.005517	0.349862	386(GGTACACAGTGAACTT,+,0.00)
chunk0192_283_1	chr8	66404931	66405170	+	0	NA	Intergenic	Intergenic	23927	NR_040434	100505676	Hs.121613	NM_001242759	ENSG00000246145	RRS1-AS1	-	RRS1 antisense RNA 1 (head to head)	ncRNA	0.012552	0.570833	
chunk0036_391_1	chr11	67682119	67682452	+	0	NA	Intergenic	MER11D|LTR|ERVK	-1071	NM_001031615	222	Hs.87539	NM_000695	ENSG00000132746	ALDH3B2	ALDH8	aldehyde dehydrogenase 3 family member B2	protein-coding	0.012012	0.440120	
chunk0088_309_1	chr18	50586438	50586738	+	0	NA	intron (NM_001292039, intron 1 of 4)	MIR|SINE|MIR	26474	NM_001292040	5596	Hs.433728	NM_002747	ENSG00000141639	MAPK4	ERK-4|ERK4|PRKM4|p63-MAPK|p63MAPK	mitogen-activated protein kinase 4	protein-coding	0.006667	0.368771	
chunk0206_94_1	chr9	120650263	120650755	+	0	NA	intron (NM_001080497, intron 2 of 5)	intron (NM_001080497, intron 2 of 5)	63978	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.004065	0.361055	
chunk0172_73_1	chr6	134372898	134373542	+	0	NA	Intergenic	Intergenic	-55162	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.007764	0.364341	
chunk0112_200_1	chr20	40376747	40377179	+	0	NA	Intergenic	Intergenic	312277	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.004630	0.339492	
chunk0072_266_1	chr15	96720822	96721519	+	0	NA	Intergenic	Intergenic	60484	NR_102754	100652749	Hs.303588	NR_102753	ENSG00000259282	SPATA8-AS1	-	SPATA8 antisense RNA 1 (head to head)	ncRNA	0.005739	0.408309	
chunk0018_375_1	chr1	222140333	222140654	+	0	NA	Intergenic	L1MA3|LINE|L1	-299827	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.003115	0.319876	
chunk0189_133_1	chr8	22486983	22487213	+	0	NA	intron (NM_001243974, intron 3 of 14)	intron (NM_001243974, intron 3 of 14)	46128	NM_001243974	5533	Hs.731683	NM_005605	ENSG00000120910	PPP3CC	CALNA3|CNA3|PP2Bgamma	protein phosphatase 3 catalytic subunit gamma	protein-coding	0.008696	0.380952	
chunk0061_51_1	chr14	56286900	56287099	+	0	NA	intron (NM_021255, intron 3 of 5)	intron (NM_021255, intron 3 of 5)	168624	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.000000	0.335000	
chunk0143_116_1	chr4	109381344	109381543	+	0	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	-52329	NM_001042734	10427	Hs.292472	NM_006323	ENSG00000138802	SEC24B	SEC24	SEC24 homolog B, COPII coat complex component	protein-coding	0.010050	0.460000	
chunk0044_438_1	chr12	42290010	42290600	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	33554	NR_107005	102467003		NR_107005	ENSG00000278520	MIR7851	hsa-mir-7851	microRNA 7851	ncRNA	0.011864	0.319797	
chunk0141_461_1	chr4	89468618	89469060	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-160829	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.004525	0.399549	
chunk0187_292_1	chr7	155799202	155799498	+	0	NA	TTS (NM_001310462)	TTS (NM_001310462)	9722	NR_132318	6469	Hs.164537	NM_000193	ENSG00000164690	SHH	HHG1|HLP3|HPE3|MCOPCB5|SMMCI|ShhNC|TPT|TPTPS	sonic hedgehog signaling molecule	protein-coding	0.010135	0.441077	
chunk0083_25_1	chr17	63124101	63124312	+	0	NA	intron (NM_025185, intron 3 of 24)	intron (NM_025185, intron 3 of 24)	114669	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.009479	0.358491	
chunk0039_287_1	chr11	102667073	102667484	+	0	NA	Intergenic	MER102c|DNA|hAT-Charlie	38459	NM_022122	64066	Hs.534479	NM_022122	ENSG00000137675	MMP27	MMP-27	matrix metallopeptidase 27	protein-coding	0.002433	0.385922	
chunk0007_402_1	chr1	85534544	85535175	+	0	NA	intron (NM_001134445, intron 1 of 6)	intron (NM_001134445, intron 1 of 6)	43504	NM_001134445	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.009509	0.354430	124(ATAACAATATGTTCCT,+,0.00),206(CAGAACTGAATGTCCA,-,0.00),207(AGAACTGAATGTCCAA,+,0.00),405(AAAAACACAGTGTACC,-,0.00),406(AAAACACAGTGTACCA,+,0.00)
chunk0056_42_1	chr13	77387839	77388117	+	0	NA	Intergenic	Intergenic	-60936	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.010791	0.458781	135(CAGAACAGGCTGTCCT,-,0.00),136(AGAACAGGCTGTCCTA,+,0.00)
chunk0146_246_1	chr4	162422160	162422796	+	0	NA	Intergenic	L1ME2|LINE|L1	-258444	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.012579	0.350078	
chunk0037_12_1	chr11	68976329	68976858	+	0	NA	Intergenic	Intergenic	4393	NM_198923	116512	Hs.527802	NM_198923	ENSG00000172938	MRGPRD	MRGD|TGR7	MAS related GPR family member D	protein-coding	0.011342	0.530189	293(TGATCAAGCTGTTCTT,+,0.00)
chunk0193_198_1	chr8	75833776	75834241	+	0	NA	Intergenic	L1MC5|LINE|L1	294040	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.004301	0.270386	
chunk0182_42_1	chr7	91634845	91635215	+	0	NA	Intergenic	Intergenic	245690	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.002703	0.415094	
chunk0197_437_1	chr8	127539054	127539253	+	0	NA	Intergenic	L2b|LINE|L2	-57014	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.005025	0.430000	
chunk0123_139_1	chr3	42801040	42801379	+	0	NA	intron (NM_001099669, intron 1 of 3)	intron (NM_001099669, intron 1 of 3)	3233	NM_001099668	25994	Hs.593134	NM_014056	ENSG00000181061	HIGD1A	HIG1|RCF1a	HIG1 hypoxia inducible domain family member 1A	protein-coding	0.008850	0.438235	
chunk0202_61_1	chr9	71654737	71655080	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	113976	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.002915	0.290698	
chunk0050_15_1	chr12	99677919	99678508	+	0	NA	intron (NM_152788, intron 8 of 25)	intron (NM_152788, intron 8 of 25)	30463	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.005093	0.386441	219(GAGAACTTACTGTTCT,-,0.00),220(AGAACTTACTGTTCTA,+,0.00),251(GAGTACATACTGTTAC,-,0.00)
chunk0019_130_1	chr1	225606918	225607163	+	0	NA	intron (NM_001008493, intron 1 of 14)	intron (NM_001008493, intron 1 of 14)	46103	NM_001008493	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.008163	0.434959	
chunk0102_2_1	chr2	141003999	141004520	+	0	NA	intron (NM_018557, intron 15 of 90)	MLT2B4|LTR|ERVL	-417574	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.005758	0.375479	
chunk0025_434_1	chr10	60032620	60033042	+	0	NA	intron (NM_001204403, intron 43 of 43)	intron (NM_001204403, intron 43 of 43)	-71918	NR_024340	283025	Hs.522955	NM_001017982	ENSG00000235931	LINC01553	C10orf40	long intergenic non-protein coding RNA 1553	ncRNA	0.002370	0.378251	
chunk0082_203_1	chr17	56854074	56854355	+	0	NA	intron (NM_003647, intron 7 of 11)	L1MA7|LINE|L1	20115	NM_003647	8526	Hs.239514	NM_003647	ENSG00000153933	DGKE	AHUS7|DAGK5|DAGK6|DGK|NPHS7	diacylglycerol kinase epsilon	protein-coding	0.007117	0.319149	
chunk0179_433_1	chr7	52184565	52184764	+	0	NA	Intergenic	MER34B|LTR|ERV1	-850992	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.000000	0.420000	
chunk0029_395_1	chr10	109585363	109585898	+	0	NA	Intergenic	L1MB7|LINE|L1	337923	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.001869	0.363806	267(AGGGACAGAAAGTACA,-,0.00),268(GGGACAGAAAGTACAT,+,0.00)
chunk0026_330_1	chr10	68334999	68335200	+	0	NA	intron (NM_012207, intron 1 of 9)	intron (NM_012207, intron 1 of 9)	-2172	NM_022129	64081	Hs.198158	NM_022129	ENSG00000108187	PBLD	HEL-S-306|MAWBP|MAWDBP	phenazine biosynthesis like protein domain containing	protein-coding	0.014925	0.336634	140(TGGTACAGACTGATCC,-,0.00),141(GGTACAGACTGATCCA,+,0.00)
chunk0198_389_1	chr8	141312394	141312621	+	0	NA	Intergenic	Intergenic	-28042	NR_024441	731779	Hs.586414	NR_024441	ENSG00000253595	LINC01300	-	long intergenic non-protein coding RNA 1300	ncRNA	0.013216	0.539474	178(GAGAACACACTGGGCC,-,0.00),179(AGAACACACTGGGCCA,+,0.00)
chunk0154_371_1	chr5	87677392	87677822	+	0	NA	Intergenic	Intergenic	-264574	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.002326	0.357309	
chunk0074_334_1	chr16	31130733	31131326	+	0	NA	TTS (NM_002773)	TTS (NM_002773)	4801	NM_002773	5652	Hs.75799	NM_002773	ENSG00000052344	PRSS8	CAP1|PROSTASIN	serine protease 8	protein-coding	0.011804	0.590909	336(CAGCACAGCCTGCCCT,-,0.00),337(AGCACAGCCTGCCCTT,+,0.00)
chunk0027_261_1	chr10	77267876	77268089	+	0	NA	intron (NM_001271518, intron 1 of 27)	intron (NM_001271518, intron 1 of 27)	-82890	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.004695	0.411215	
chunk0016_195_1	chr1	198576240	198576585	+	0	NA	Intergenic	MIR|SINE|MIR	-35467	NM_133262	127124	Hs.127743	NM_133262	ENSG00000151418	ATP6V1G3	ATP6G3|Vma10	ATPase H+ transporting V1 subunit G3	protein-coding	0.002899	0.361272	
chunk0071_120_1	chr15	81404638	81405323	+	0	NA	intron (NR_120365, intron 6 of 6)	L1MC3|LINE|L1	-30903	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.002920	0.380466	303(CAGAACAAGCTGTGCA,-,0.00),304(AGAACAAGCTGTGCAA,+,0.00)
chunk0151_141_1	chr5	45312071	45312470	+	0	NA	intron (NM_021072, intron 5 of 7)	intron (NM_021072, intron 5 of 7)	383848	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.017544	0.380000	
chunk0137_277_1	chr4	22979628	22980146	+	0	NA	Intergenic	L1PBb|LINE|L1	265798	NR_102357	57733	Hs.653107	NM_020973	ENSG00000249948	GBA3	CBG|CBGL1|GLUC|KLRP	glucosylceramidase beta 3 (gene/pseudogene)	protein-coding	0.005792	0.423892	
chunk0137_266_1	chr4	22442986	22443418	+	0	NA	intron (NM_145290, intron 6 of 18)	intron (NM_145290, intron 6 of 18)	72852	NM_145290	166647	Hs.99195	NM_145290	ENSG00000152990	ADGRA3	GPR125|PGR21|TEM5L	adhesion G protein-coupled receptor A3	protein-coding	0.004630	0.302540	157(AAGAACAAGCTGTGCT,-,0.00),158(AGAACAAGCTGTGCTC,+,0.00)
chunk0161_108_1	chr5	167478068	167478707	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	193549	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.006260	0.389062	
chunk0118_217_1	chr22	31920957	31921263	+	0	NA	Intergenic	L2a|LINE|L2	17344	NM_001302820	25775	Hs.627602	NM_015372	ENSG00000128254	C22orf24	HSN44A4A	chromosome 22 open reading frame 24	protein-coding	0.006536	0.495114	
chunk0172_315_1	chr6	138241657	138241856	+	0	NA	intron (NM_020340, intron 6 of 33)	intron (NM_020340, intron 6 of 33)	-23266	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.010050	0.365000	
chunk0141_338_1	chr4	87432281	87433359	+	0	NA	intron (NM_001248011, intron 1 of 6)	L1M3|LINE|L1	10223	NM_198038	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.001855	0.333642	
chunk0033_185_1	chr11	16013020	16013607	+	0	NA	intron (NM_001145819, intron 13 of 15)	intron (NM_001145819, intron 13 of 15)	-43692	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.008518	0.384354	
chunk0191_351_1	chr8	56435641	56436196	+	0	NA	Intergenic	L1ME3A|LINE|L1	-9889	NR_125813	101929415	Hs.701520	NR_125813	ENSG00000254254	LOC101929415	-	uncharacterized LOC101929415	ncRNA	0.014414	0.397482	
chunk0182_365_1	chr7	99934713	99934926	+	0	NA	Intergenic	Intergenic	-5199	NM_181538	349149	Hs.647524	NM_181538	ENSG00000176402	GJC3	CX29|CX30.2|CX31.3|GJE1	gap junction protein gamma 3	protein-coding	0.028169	0.579439	
chunk0070_345_1	chr15	75904249	75904549	+	0	NA	intron (NR_037623, intron 1 of 5)	CpG	540	NM_147188	26263	Hs.591115	NM_012170	ENSG00000167196	FBXO22	FBX22|FISTC1	F-box protein 22	protein-coding	0.073333	0.598007	
chunk0105_414_1	chr2	192896233	192896889	+	0	NA	Intergenic	L1MC2|LINE|L1	146716	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.001524	0.295282	
chunk0122_400_1	chr3	38043441	38044153	+	0	NA	intron (NM_007335, intron 1 of 36)	AluSq2|SINE|Alu	4592	NM_007335	9940	Hs.714499	NM_007335	ENSG00000008226	DLEC1	CFAP81|DLC-1|DLC1|F56	DLEC1 cilia and flagella associated protein	protein-coding	0.007022	0.409537	489(AGGAACACTGTCTTCC,-,0.00),490(GGAACACTGTCTTCCT,+,0.00)
chunk0101_61_1	chr2	123463726	123464167	+	0	NA	Intergenic	Intergenic	-561341	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.334842	
chunk0162_276_1	chr6	5667558	5668078	+	0	NA	intron (NR_110842, intron 3 of 3)	intron (NR_110842, intron 3 of 3)	27454	NR_110842	101927950	Hs.571136	NR_110842	ENSG00000270174	LOC101927950	-	uncharacterized LOC101927950	ncRNA	0.007692	0.404990	154(TAGAACAATCTGTCCA,-,0.00),155(AGAACAATCTGTCCAA,+,0.00)
chunk0056_365_1	chr13	92644020	92644460	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	75715	NR_049776	100873969	Hs.577863	NR_046520	ENSG00000235984	GPC5-AS1	-	GPC5 antisense RNA 1	ncRNA	0.002273	0.342404	
chunk0181_57_1	chr7	80186243	80187121	+	0	NA	intron (NM_001256414, intron 1 of 7)	intron (NM_001256414, intron 1 of 7)	50927	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.007973	0.403868	
chunk0126_158_1	chr3	77635568	77635823	+	0	NA	intron (NM_001290065, intron 25 of 26)	Tigger3a|DNA|TcMar-Tigger	537683	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.019608	0.359375	
chunk0090_34_1	chr19	1269638	1269940	+	0	NA	intron (NM_001280, intron 1 of 6)	CpG-13015	471	NR_027271	148046	Hs.438829	NM_152480		CIRBP-AS1	C19orf23	CIRBP antisense RNA 1	ncRNA	0.109272	0.663366	
chunk0092_94_1	chr19	22935765	22935964	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	67344	NM_001267716	388523	Hs.616766	NM_001267716	ENSG00000269067	ZNF728	-	zinc finger protein 728	protein-coding	0.000000	0.480000	
chunk0060_315_1	chr14	51239559	51239777	+	0	NA	promoter-TSS (NM_030755)	promoter-TSS (NM_030755)	-500	NM_030755	81542	Hs.125221	NM_030755	ENSG00000139921	TMX1	PDIA11|TMX|TXNDC|TXNDC1	thioredoxin related transmembrane protein 1	protein-coding	0.009174	0.360731	
chunk0192_31_1	chr8	58635826	58636069	+	0	NA	intron (NM_001144772, intron 2 of 30)	intron (NM_001144772, intron 2 of 30)	23460	NM_001144772	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.000000	0.356557	80(AACACTGCCTGTTCTT,+,0.00)
chunk0190_91_1	chr8	30120075	30120543	+	0	NA	intron (NM_001128208, intron 3 of 3)	intron (NM_001128208, intron 3 of 3)	24375	NM_001100916	619373	Hs.627194	NM_001100916	ENSG00000177669	MBOAT4	FKSG89|GOAT|OACT4	membrane bound O-acyltransferase domain containing 4	protein-coding	0.002137	0.287846	
chunk0201_2_1	chr9	31998420	31998666	+	0	NA	Intergenic	Intergenic	-386060	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.008130	0.331984	183(GAGAACAGAATGTGAC,-,0.00)
chunk0053_117_1	chr13	29465883	29466175	+	0	NA	intron (NM_015233, intron 2 of 8)	intron (NM_015233, intron 2 of 8)	21721	NR_046378	100874107	Hs.577987	NR_046378		MTUS2-AS1	-	MTUS2 antisense RNA 1	ncRNA	0.010274	0.542662	
chunk0175_63_1	chr7	1926849	1927215	+	0	NA	intron (NM_003550, intron 17 of 18)	L1MDa|LINE|L1	13518	NM_001304525	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.008197	0.395095	
chunk0138_441_1	chr4	45757883	45758115	+	0	NA	Intergenic	MER34A1|LTR|ERV1	366066	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.008621	0.309013	
chunk0014_323_1	chr1	181649080	181649515	+	0	NA	intron (NM_000721, intron 6 of 46)	intron (NM_000721, intron 6 of 46)	165747	NM_001205293	777	Hs.437444	NM_000721	ENSG00000198216	CACNA1E	BII|CACH6|CACNL1A6|Cav2.3|EIEE69|gm139	calcium voltage-gated channel subunit alpha1 E	protein-coding	0.004598	0.410550	
chunk0212_423_1	chrX	153208175	153208502	+	0	NA	Intergenic	Intergenic	29054	NM_004988	4100	Hs.72879	NM_004988	ENSG00000198681	MAGEA1	CT1.1|MAGE1	MAGE family member A1	protein-coding	0.006116	0.301829	
chunk0006_249_1	chr1	69318760	69319277	+	0	NA	Intergenic	Intergenic	-441157	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.003868	0.320463	
chunk0208_332_1	chrX	24662284	24662815	+	0	NA	intron (NM_001163264, intron 1 of 7)	LTR75|LTR|ERVL	10313	NM_001163264	9468	Hs.660708	NM_004845	ENSG00000102230	PCYT1B	CCTB|CTB	phosphate cytidylyltransferase 1, choline, beta	protein-coding	0.011299	0.490602	
chunk0182_247_1	chr7	97117490	97117928	+	0	NA	5' UTR (NM_020186, exon 1 of 2)	5' UTR (NM_020186, exon 1 of 2)	1116	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.105023	0.619590	
chunk0119_424_1	chr22	49949016	49949818	+	0	NA	Intergenic	Intergenic	-11078	NM_001001852	415116	Hs.530381	NM_001001852	ENSG00000198355	PIM3	pim-3	Pim-3 proto-oncogene, serine/threonine kinase	protein-coding	0.043641	0.689913	462(CAGGACACGGTGTGCA,-,0.00),463(AGGACACGGTGTGCAG,+,0.00)
chunk0032_67_1	chr11	2320017	2320300	+	0	NA	Intergenic	Intergenic	18145	NM_139022	10077	Hs.271954	NM_005705	ENSG00000064201	TSPAN32	ART1|PHEMX|PHMX|TSSC6	tetraspanin 32	protein-coding	0.024735	0.528169	
chunk0119_284_1	chr22	46120227	46120694	+	0	NA	Intergenic	MER90a|LTR|ERV1	6774	NR_029479	406884		NR_029479	ENSG00000284520	MIRLET7B	LET7B|MIRNLET7B|hsa-let-7b|let-7b	microRNA let-7b	ncRNA	0.032120	0.606838	324(GGTACATTCTGTGTCT,+,0.00)
chunk0073_77_1	chr16	3837954	3838455	+	0	NA	intron (NM_001079846, intron 2 of 29)	Tigger3b|DNA|TcMar-Tigger	41916	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.005988	0.434263	84(TGCCCAGGCTGTTCTC,+,0.00)
chunk0173_237_1	chr6	146671115	146671619	+	0	NA	intron (NM_024694, intron 7 of 35)	L2c|LINE|L2	72367	NM_024694	79747	Hs.720870	NM_024694	ENSG00000118492	ADGB	C6orf103|CAPN16	androglobin	protein-coding	0.003968	0.417822	
chunk0110_222_1	chr20	15496442	15496920	+	0	NA	intron (NM_001033087, intron 3 of 13)	intron (NM_001033087, intron 3 of 13)	299823	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.002092	0.382046	
chunk0146_86_1	chr4	158110194	158110623	+	0	NA	Intergenic	Intergenic	62158	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.325581	
chunk0201_195_1	chr9	36530432	36530754	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-42269	NM_001256690	9833	Hs.184339	NM_014791	ENSG00000165304	MELK	HPK38	maternal embryonic leucine zipper kinase	protein-coding	0.006211	0.433437	
chunk0046_343_1	chr12	62925561	62926082	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	9064	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.003839	0.421456	
chunk0039_24_1	chr11	95652077	95652547	+	0	NA	Intergenic	Intergenic	137478	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.006383	0.401274	
chunk0212_125_1	chrX	130941261	130941885	+	0	NA	Intergenic	L1MA9|LINE|L1	-38256	NM_182314	10495	Hs.171458	NM_006375	ENSG00000165675	ENOX2	APK1|COVA1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.001603	0.345600	
chunk0017_332_1	chr1	211530038	211530470	+	0	NA	Intergenic	L2b|LINE|L2	-37337	NM_183059	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.004630	0.418014	
chunk0204_296_1	chr9	100004291	100004490	+	0	NA	intron (NM_015051, intron 10 of 11)	L1M3e|LINE|L1	94662	NM_015051	23071	Hs.154023	NM_015051	ENSG00000023318	ERP44	PDIA10|TXNDC4	endoplasmic reticulum protein 44	protein-coding	0.005025	0.600000	
chunk0206_20_1	chr9	115850941	115851280	+	0	NA	Intergenic	Intergenic	73988	NR_024032	58483	Hs.23367	NR_024032	ENSG00000204148	LINC00474	C9orf27|EST-YD1	long intergenic non-protein coding RNA 474	ncRNA	0.000000	0.405882	
chunk0182_306_1	chr7	98486753	98486987	+	0	NA	Intergenic	(GTGT)n|Simple_repeat|Simple_repeat	-85755	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.042735	0.493617	
chunk0110_340_1	chr20	19283500	19283991	+	0	NA	intron (NR_024564, intron 1 of 7)	MIRb|SINE|MIR	851	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.012220	0.481707	
chunk0132_155_1	chr3	156603248	156603802	+	0	NA	Intergenic	Intergenic	-48325	NM_001308197	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.003610	0.421622	302(AAGAACAGAGTGCTCC,-,0.00),303(AGAACAGAGTGCTCCC,+,0.00)
chunk0188_219_1	chr8	12780755	12781125	+	0	NA	intron (NR_015383, intron 2 of 3)	L1MA5|LINE|L1	-13303	NR_102423	101409254	Hs.571476	NR_102423	ENSG00000255494	LINC00681	-	long intergenic non-protein coding RNA 681	ncRNA	0.010811	0.366577	
chunk0042_437_1	chr12	12294222	12294541	+	0	NA	Intergenic	Intergenic	-27504	NM_002336	4040	Hs.584775	NM_002336	ENSG00000070018	LRP6	ADCAD2|STHAG7	LDL receptor related protein 6	protein-coding	0.009404	0.393750	
chunk0166_137_1	chr6	44826222	44826647	+	0	NA	TTS (NM_003599)	TTS (NM_003599)	371336	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.002353	0.380282	
chunk0137_84_1	chr4	13127205	13127704	+	0	NA	Intergenic	MIR|SINE|MIR	356911	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.006012	0.402000	15(AGACCTGGCTGTTCCG,+,0.00)
chunk0088_222_1	chr18	48250261	48250627	+	0	NA	Intergenic	MIR|SINE|MIR	-113135	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.005464	0.435967	
chunk0068_360_1	chr15	57987981	57988180	+	0	NA	intron (NM_170696, intron 6 of 11)	L1MEc|LINE|L1	26017	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.010050	0.335000	
chunk0056_306_1	chr13	90875810	90876049	+	0	NA	Intergenic	Intergenic	50668	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.000000	0.295833	
chunk0054_39_1	chr13	41061424	41061623	+	0	NA	promoter-TSS (NM_007187)	promoter-TSS (NM_007187)	-38	NM_007187	11193	Hs.411300	NM_007187	ENSG00000120688	WBP4	FBP21	WW domain binding protein 4	protein-coding	0.090452	0.645000	
chunk0138_19_1	chr4	30711062	30711490	+	0	NA	Intergenic	L1M2|LINE|L1	-9132	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.002336	0.515152	
chunk0024_21_1	chr10	33053498	33053854	+	0	NA	Intergenic	Intergenic	-95311	NM_002211	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.005618	0.436975	162(TGGAACATAATGGTCT,-,0.00),163(GGAACATAATGGTCTG,+,0.00)
chunk0087_455_1	chr18	42734787	42735046	+	0	NA	Intergenic	LTR81B|LTR|Gypsy	380776	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.403846	
chunk0191_200_1	chr8	51900608	51901249	+	0	NA	Intergenic	Intergenic	-1742	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.009360	0.369159	
chunk0176_190_1	chr7	13935973	13936238	+	0	NA	intron (NR_120445, intron 7 of 14)	intron (NR_120445, intron 7 of 14)	50409	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.003774	0.274436	
chunk0198_408_1	chr8	142332584	142332905	+	0	NA	intron (NM_001291931, intron 2 of 10)	intron (NM_001291931, intron 2 of 10)	70505	NM_001291931	203062	Hs.370931	NM_145003	ENSG00000171045	TSNARE1	-	t-SNARE domain containing 1	protein-coding	0.028037	0.583851	14(GAGGACAGCAAGTCCT,-,0.00),15(AGGACAGCAAGTCCTC,+,0.00)
chunk0102_195_1	chr2	147822060	147822424	+	0	NA	Intergenic	L1MB7|LINE|L1	-22275	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002747	0.372603	
chunk0152_436_1	chr5	66079784	66080244	+	0	NA	3' UTR (NM_001253699, exon 26 of 26)	3' UTR (NM_001253699, exon 26 of 26)	-64204	NM_001077199	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.000000	0.305857	
chunk0087_64_1	chr18	31666149	31666395	+	0	NA	exon (NM_004775, exon 2 of 9)	exon (NM_004775, exon 2 of 9)	18451	NM_004775	9331	Hs.591063	NM_004775	ENSG00000118276	B4GALT6	B4Gal-T6|beta4Gal-T6	beta-1,4-galactosyltransferase 6	protein-coding	0.012195	0.360324	
chunk0124_194_1	chr3	55632142	55632352	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	27222	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.000000	0.473934	
chunk0038_214_1	chr11	86582839	86583494	+	0	NA	intron (NM_001014811, intron 1 of 13)	intron (NM_001014811, intron 1 of 13)	89032	NM_001014811	10873	Hs.199743	NM_006680	ENSG00000151376	ME3	NADP-ME	malic enzyme 3	protein-coding	0.009160	0.384146	
chunk0078_188_1	chr17	4834207	4834527	+	0	NA	intron (NM_015716, intron 1 of 30)	intron (NM_015716, intron 1 of 30)	1027	NM_015716	50488	Hs.443417	NM_015716	ENSG00000141503	MINK1	B55|MAP4K6|MINK|YSK2|ZC3	misshapen like kinase 1	protein-coding	0.021875	0.526480	
chunk0179_135_1	chr7	45936080	45936279	+	0	NA	Intergenic	Charlie17a|DNA|hAT-Charlie	-14907	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.005025	0.450000	
chunk0016_2_1	chr1	192668246	192668636	+	0	NA	Intergenic	L1PA6|LINE|L1	32303	NM_144766	6003	Hs.497220	NM_002927	ENSG00000127074	RGS13	-	regulator of G protein signaling 13	protein-coding	0.012821	0.549872	
chunk0184_248_1	chr7	117907249	117907967	+	0	NA	Intergenic	L2c|LINE|L2	-34101	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.004178	0.393602	262(GGTGCATGCTGTTCCT,+,0.00)
chunk0047_31_1	chr12	66177376	66177717	+	0	NA	Intergenic	MER21C|LTR|ERVL	-7474	NM_001282606	51643	Hs.505934	NM_016056	ENSG00000155957	TMBIM4	CGI-119|GAAP|LFG4|S1R|ZPRO	transmembrane BAX inhibitor motif containing 4	protein-coding	0.005865	0.429825	
chunk0146_307_1	chr4	165210035	165210481	+	0	NA	intron (NM_001161521, intron 1 of 14)	intron (NM_001161521, intron 1 of 14)	239	NM_001161522	11275	Hs.388668	NM_007246	ENSG00000109466	KLHL2	ABP-KELCH|MAV|MAYVEN	kelch like family member 2	protein-coding	0.004484	0.407159	
chunk0137_205_1	chr4	18213165	18213430	+	0	NA	Intergenic	Intergenic	-191437	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.003774	0.526316	
chunk0200_292_1	chr9	22537668	22538198	+	0	NA	Intergenic	Intergenic	91092	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.009434	0.342750	
chunk0199_72_1	chr9	2401528	2402051	+	0	NA	Intergenic	L1PA7|LINE|L1	-220004	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.009560	0.385496	311(TGGTACTGGTTGTTCC,-,0.00),312(GGTACTGGTTGTTCCT,+,0.00)
chunk0111_125_1	chr20	24402191	24402589	+	0	NA	Intergenic	Intergenic	-66809	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.005025	0.511278	
chunk0147_94_1	chr4	173297625	173297871	+	0	NA	intron (NM_017423, intron 5 of 11)	intron (NM_017423, intron 5 of 11)	29588	NR_036093	100422849		NR_036093	ENSG00000221296	MIR548T	-	microRNA 548t	ncRNA	0.008130	0.364372	167(CAGAACTACATGTACT,-,0.00),168(AGAACTACATGTACTG,+,0.00)
chunk0133_326_1	chr3	172607750	172607988	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-84362	NM_003810	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.004202	0.447699	
chunk0086_436_1	chr18	28633981	28634181	+	0	NA	Intergenic	Intergenic	-456635	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.005000	0.437811	
chunk0211_249_1	chrX	120549846	120550264	+	0	NA	intron (NM_003588, intron 4 of 21)	intron (NM_003588, intron 4 of 21)	10907	NM_001079872	8450	Hs.102914	NM_003588	ENSG00000158290	CUL4B	CUL-4B|MRXHF2|MRXS15|MRXSC|SFM2	cullin 4B	protein-coding	0.011962	0.391408	
chunk0199_13_1	chr9	518238	518936	+	0	NA	intron (NM_015158, intron 1 of 11)	intron (NM_015158, intron 1 of 11)	13892	NM_001256877	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.018625	0.460658	
chunk0085_225_1	chr18	6893425	6893918	+	0	NA	intron (NM_001010000, intron 13 of 16)	MIRc|SINE|MIR	36198	NR_034100	400643	Hs.253920	NM_001103383	ENSG00000265933	LINC00668	-	long intergenic non-protein coding RNA 668	ncRNA	0.004057	0.356275	
chunk0020_169_1	chr1	234452435	234453171	+	0	NA	intron (NM_005646, intron 9 of 29)	L1MC2|LINE|L1	26300	NM_005646	6894	Hs.498115	NM_005646	ENSG00000059588	TARBP1	TRM3|TRMT3|TRP-185|TRP185	TAR (HIV-1) RNA binding protein 1	protein-coding	0.005435	0.394844	
chunk0145_198_1	chr4	147899701	147900027	+	0	NA	intron (NM_024605, intron 10 of 22)	intron (NM_024605, intron 10 of 22)	117269	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.003067	0.302752	
chunk0067_66_1	chr15	41231183	41231382	+	0	NA	promoter-TSS (NM_007236)	promoter-TSS (NM_007236)	43	NM_007236	11261	Hs.406234	NM_007236	ENSG00000187446	CHP1	CHP|SLC9A1BP|SPAX9|Sid470p|p22|p24	calcineurin like EF-hand protein 1	protein-coding	0.090452	0.725000	
chunk0206_386_1	chr9	126808661	126808945	+	0	NA	5' UTR (NM_014007, exon 2 of 3)	5' UTR (NM_014007, exon 2 of 3)	3797	NM_014007	23099	Hs.355581	NM_014007	ENSG00000169155	ZBTB43	ZBTB22B|ZNF-X|ZNF297B	zinc finger and BTB domain containing 43	protein-coding	0.010563	0.350877	
chunk0056_87_1	chr13	80486360	80486801	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-145629	NM_005842	10253	Hs.18676	NM_005842	ENSG00000136158	SPRY2	IGAN3|hSPRY2	sprouty RTK signaling antagonist 2	protein-coding	0.006803	0.411765	230(GAGTACAAGCAGTTCT,-,0.00),231(AGTACAAGCAGTTCTT,+,0.00)
chunk0136_96_1	chr4	2858682	2859035	+	0	NA	intron (NM_001286645, intron 1 of 17)	MIRb|SINE|MIR	14708	NM_001286645	118	Hs.183706	NM_001119	ENSG00000087274	ADD1	ADDA	adducin 1	protein-coding	0.014164	0.423729	
chunk0163_290_1	chr6	14049716	14050338	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-67229	NM_001251901	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.012862	0.415730	458(AAGGACATTATGAACT,-,0.00)
chunk0090_387_1	chr18	77391721	77391942	+	0	NA	Intergenic	L1M4|LINE|L1	141779	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.000000	0.328829	131(GGGCACTCTTTGTTCC,-,0.00),132(GGCACTCTTTGTTCCC,+,0.00)
chunk0182_87_1	chr7	92791513	92792268	+	0	NA	intron (NM_001145306, intron 2 of 7)	L2c|LINE|L2	42027	NM_001259	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.002649	0.411376	274(AGGAACAGCATGTCCA,-,0.00),275(GGAACAGCATGTCCAA,+,0.00)
chunk0056_28_1	chr13	77282988	77283424	+	0	NA	intron (NM_015057, intron 3 of 82)	L2c|LINE|L2	43836	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.004587	0.395881	
chunk0114_226_1	chr21	15837768	15837973	+	0	NA	intron (NM_013396, intron 17 of 23)	intron (NM_013396, intron 17 of 23)	107845	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.009756	0.402913	
chunk0085_183_1	chr18	6006265	6006658	+	0	NA	intron (NM_173464, intron 17 of 19)	intron (NM_173464, intron 17 of 19)	-114357	NM_001080209	645369		NM_001080209	ENSG00000206432	TMEM200C	TTMA	transmembrane protein 200C	protein-coding	0.007634	0.357868	
chunk0065_327_1	chr14	103225462	103226008	+	0	NA	Intergenic	Intergenic	-36707	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.031136	0.458867	
chunk0061_231_1	chr14	60647127	60647418	+	0	NA	intron (NM_005982, intron 1 of 1)	intron (NM_005982, intron 1 of 1)	2165	NM_005982	6495	Hs.633506	NM_005982	ENSG00000126778	SIX1	BOS3|DFNA23|TIP39	SIX homeobox 1	protein-coding	0.051546	0.589041	
chunk0005_241_1	chr1	59595702	59596296	+	0	NA	intron (NM_001244714, intron 6 of 13)	intron (NM_001244714, intron 6 of 13)	80370	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.005051	0.359664	45(CAGGACTGACTGTACC,-,0.00),46(AGGACTGACTGTACCC,+,0.00)
chunk0164_268_1	chr6	23692161	23692860	+	0	NA	Intergenic	Intergenic	-433676	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.002861	0.315714	
chunk0170_373_1	chr6	116924236	116924698	+	0	NA	intron (NM_173560, intron 14 of 18)	intron (NM_173560, intron 14 of 18)	47254	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.008658	0.399568	
chunk0151_49_1	chr5	42415477	42415968	+	0	NA	Intergenic	L1PA6|LINE|L1	-8053	NM_000163	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.008147	0.378049	26(GGTACATTGTGTCTTT,+,0.00),109(AGGGGCAGGTTGTTCC,-,0.00),110(GGGGCAGGTTGTTCCG,+,0.00)
chunk0055_357_1	chr13	70579797	70580469	+	0	NA	Intergenic	L1MD1|LINE|L1	-435008	NR_047699	100885781	Hs.372660	NR_047699	ENSG00000226846	LINC00348	-	long intergenic non-protein coding RNA 348	ncRNA	0.005952	0.334324	
chunk0183_74_1	chr7	104552179	104552418	+	0	NA	intron (NM_199000, intron 1 of 2)	intron (NM_199000, intron 1 of 2)	223642	NM_199000	375612	Hs.659164	NM_199000	ENSG00000187416	LHFPL3	LHFPL4	LHFPL tetraspan subfamily member 3	protein-coding	0.016736	0.466667	
chunk0030_66_1	chr10	112012448	112012647	+	0	NA	Intergenic	MER54B|LTR|ERVL	171232	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.010050	0.515000	
chunk0076_136_1	chr16	66937048	66937814	+	0	NA	intron (NR_036684, intron 1 of 11)	intron (NR_036684, intron 1 of 11)	2960	NR_036684									0.005222	0.481095	307(CAGTACACACAGTGCC,-,0.00),308(AGTACACACAGTGCCC,+,0.00)
chunk0174_7_1	chr6	152277735	152278227	+	0	NA	intron (NM_033071, intron 97 of 145)	intron (NM_033071, intron 97 of 145)	-102549	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.018293	0.496957	
chunk0148_2_1	chr5	56669	57263	+	0	NA	Intergenic	Intergenic	-83292	NM_052909	153478	Hs.535800	NM_052909	ENSG00000153404	PLEKHG4B	-	pleckstrin homology and RhoGEF domain containing G4B	protein-coding	0.013468	0.510924	
chunk0192_423_1	chr8	69581360	69581639	+	0	NA	intron (NM_015170, intron 6 of 22)	intron (NM_015170, intron 6 of 22)	-11401	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.007168	0.417857	38(TGGAACAGGTTGTCCT,-,0.00),39(GGAACAGGTTGTCCTA,+,0.00)
chunk0135_237_1	chr3	188647387	188647601	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-41287	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.004673	0.418605	
chunk0131_321_1	chr3	151003832	151004034	+	0	NA	intron (NR_024066, intron 1 of 5)	intron (NR_024066, intron 1 of 5)	-30934	NR_046380	7401	Hs.745448	NM_052995	ENSG00000163646	CLRN1	RP61|USH3|USH3A	clarin 1	protein-coding	0.009901	0.487685	
chunk0068_279_1	chr15	56772938	56773137	+	0	NA	Intergenic	L2|LINE|L2	-38951	NM_001002844	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.005025	0.450000	
chunk0035_77_1	chr11	41930871	41931199	+	0	NA	Intergenic	Intergenic	216467	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.003049	0.376900	
chunk0018_307_1	chr1	221118572	221119050	+	0	NA	Intergenic	Intergenic	217485	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.006276	0.388309	
chunk0185_394_1	chr7	133458955	133459345	+	0	NA	intron (NM_001037126, intron 7 of 9)	intron (NM_001037126, intron 7 of 9)	168269	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.005128	0.388747	
chunk0178_370_1	chr7	39707939	39708351	+	0	NA	TTS (NM_005402)	TTS (NM_005402)	-25423	NR_026999	349114	Hs.414183	NM_198284		LINC00265	NCRNA00265	long intergenic non-protein coding RNA 265	ncRNA	0.009709	0.377724	
chunk0014_41_1	chr1	175029673	175029972	+	0	NA	Intergenic	Intergenic	-6367	NM_022100	63931	Hs.654858	NM_022100	ENSG00000120333	MRPS14	COXPD38|DJ262D12.2|HSMRPS14|MRP-S14|S14mt	mitochondrial ribosomal protein S14	protein-coding	0.030100	0.510000	
chunk0072_205_1	chr15	95129456	95129984	+	0	NA	Intergenic	Intergenic	197380	NR_034095	400456	Hs.536404	NR_034095	ENSG00000248441	LINC01197	-	long intergenic non-protein coding RNA 1197	ncRNA	0.007576	0.385633	
chunk0006_200_1	chr1	67629599	67629930	+	0	NA	Intergenic	Intergenic	-55413	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.000000	0.421687	
chunk0212_31_1	chrY	10999813	11000028	+	0	NA	Intergenic	Intergenic	1089122	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.013953	0.416667	
chunk0005_359_1	chr1	61367819	61368123	+	0	NA	intron (NM_001145511, intron 6 of 10)	intron (NM_001145511, intron 6 of 10)	-114453	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.036184	0.403279	
chunk0210_91_1	chrX	71184446	71184761	+	0	NA	Intergenic	MIR|SINE|MIR	-30609	NM_001097642	2705	Hs.333303	NM_000166	ENSG00000169562	GJB1	CMTX|CMTX1|CX32	gap junction protein beta 1	protein-coding	0.006349	0.367089	
chunk0021_326_1	chr1	245581960	245582738	+	0	NA	intron (NM_018012, intron 5 of 14)	intron (NM_018012, intron 5 of 14)	427364	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.014139	0.410783	277(GGGGTCATTGTGTTCC,-,0.00),278(GGGTCATTGTGTTCCT,+,0.00)
chunk0093_253_1	chr19	50920460	50920760	+	0	NA	Intergenic	Intergenic	-9872	NM_001302961	9622	Hs.218366	NM_004917	ENSG00000167749	KLK4	AI2A1|ARM1|EMSP|EMSP1|KLK-L1|PRSS17|PSTS|kallikrein	kallikrein related peptidase 4	protein-coding	0.016667	0.385382	
chunk0043_18_1	chr12	13026161	13026812	+	0	NA	Intergenic	L1MEh|LINE|L1	-17895	NM_020853	57613	Hs.132660	NM_020853	ENSG00000084444	FAM234B	KIAA1467	family with sequence similarity 234 member B	protein-coding	0.004608	0.417178	312(AGGAACTCAAAGTTCT,-,0.00),313(GGAACTCAAAGTTCTA,+,0.00)
chunk0180_307_1	chr7	70614633	70614940	+	0	NA	intron (NM_015570, intron 5 of 18)	intron (NM_015570, intron 5 of 18)	-517751	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.022801	0.629870	
chunk0024_383_1	chr10	44729611	44729900	+	0	NA	Intergenic	L1MB8|LINE|L1	-181561	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.003460	0.282759	
chunk0195_103_1	chr8	94553460	94553793	+	0	NA	promoter-TSS (NM_015496)	promoter-TSS (NM_015496)	-108	NM_183009	25962	Hs.202238	NM_015496	ENSG00000164944	VIRMA	KIAA1429|MSTP054|fSAP121	vir like m6A methyltransferase associated	protein-coding	0.087087	0.655689	
chunk0163_76_1	chr6	9388756	9388955	+	0	NA	Intergenic	Intergenic	736646	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.010050	0.475000	
chunk0040_436_1	chr11	121466612	121466868	+	0	NA	intron (NM_003105, intron 1 of 47)	intron (NM_003105, intron 1 of 47)	14537	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.023438	0.552529	
chunk0207_246_1	chr9	132077655	132078433	+	0	NA	intron (NM_001253881, intron 1 of 6)	intron (NM_001253881, intron 1 of 6)	1843	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.005141	0.387677	323(CAGAACAGCAAGTACC,-,0.00),324(AGAACAGCAAGTACCT,+,0.00)
chunk0020_419_1	chr1	241590058	241590595	+	0	NA	intron (NM_003679, intron 14 of 14)	intron (NM_003679, intron 14 of 14)	45604	NM_001821	1122	Hs.654545	NM_001821	ENSG00000203668	CHML	REP2	CHM like Rab escort protein	protein-coding	0.005587	0.345725	
chunk0103_128_1	chr2	162016139	162016351	+	0	NA	intron (NM_001935, intron 18 of 25)	intron (NM_001935, intron 18 of 25)	58297	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.004717	0.366197	
chunk0057_34_1	chr13	95860725	95861452	+	0	NA	intron (NM_020121, intron 31 of 38)	intron (NM_020121, intron 31 of 38)	183949	NM_006260	5611	Hs.59214	NM_006260	ENSG00000102580	DNAJC3	ACPHD|ERdj6|HP58|P58|P58IPK|PRKRI	DnaJ heat shock protein family (Hsp40) member C3	protein-coding	0.004127	0.318681	
chunk0119_352_1	chr22	47292277	47293163	+	0	NA	Intergenic	Intergenic	194391	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.023702	0.537768	375(AAGAACATTCCGTACC,-,0.00),376(AGAACATTCCGTACCC,+,0.00),637(GAGGACTGTGTGTCCT,-,0.00),638(AGGACTGTGTGTCCTG,+,0.00)
chunk0160_205_1	chr5	154740851	154741423	+	0	NA	intron (NM_015315, intron 1 of 18)	intron (NM_015315, intron 1 of 18)	28235	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.012238	0.507853	
chunk0211_351_1	chrX	125310621	125310933	+	0	NA	Intergenic	L2c|LINE|L2	-9343	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.006410	0.364217	
chunk0143_405_1	chr4	123313139	123313795	+	0	NA	intron (NM_145207, intron 15 of 15)	intron (NM_145207, intron 15 of 15)	-83328	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.012195	0.430746	554(AAGAACAGAATGCTCT,-,0.00),555(AGAACAGAATGCTCTG,+,0.00)
chunk0092_20_1	chr19	18741097	18742252	+	0	NA	intron (NM_001098482, intron 1 of 14)	intron (NM_001098482, intron 1 of 14)	49631	NM_000095	1311	Hs.1584	NM_000095	ENSG00000105664	COMP	EDM1|EPD1|MED|PSACH|THBS5|TSP5	cartilage oligomeric matrix protein	protein-coding	0.025108	0.607266	859(GTGTACACAGTGTCCA,-,0.00),860(TGTACACAGTGTCCAC,+,0.00)
chunk0141_274_1	chr4	86572236	86572586	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-21904	NM_006264	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.002857	0.384615	
chunk0126_152_1	chr3	76781259	76781528	+	0	NA	Intergenic	L1MA10|LINE|L1	-258750	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.003717	0.300000	
chunk0122_449_1	chr3	39743790	39744023	+	0	NA	Intergenic	Intergenic	-65008	NM_001284423	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.000000	0.465812	
chunk0150_437_1	chr5	40495346	40495545	+	0	NA	Intergenic	Intergenic	-184485	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.010050	0.455000	
chunk0034_421_1	chr11	38496345	38496578	+	0	NA	Intergenic	MER67B|LTR|ERV1	149895	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.000000	0.435897	
chunk0118_343_1	chr22	35728987	35729201	+	0	NA	intron (NM_030642, intron 4 of 4)	intron (NM_030642, intron 4 of 4)	11222	NM_030642	80831	Hs.326561	NM_030642	ENSG00000128313	APOL5	APOL-V|APOLV	apolipoprotein L5	protein-coding	0.023364	0.539535	
chunk0127_144_1	chr3	94345260	94345566	+	0	NA	Intergenic	LTR17|LTR|ERV1	-282190	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.029412	0.521173	
chunk0084_69_1	chr17	74769844	74770080	+	0	NA	TTS (NM_004252)	TTS (NM_004252)	6463	NM_001305081	26151	Hs.144058	NM_015654	ENSG00000109065	NAT9	EBSP, hNATL	N-acetyltransferase 9 (putative)	protein-coding	0.008475	0.573840	
chunk0193_192_1	chr8	75594784	75594993	+	0	NA	Intergenic	Intergenic	54920	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.000000	0.490476	
chunk0097_15_1	chr2	41860508	41860887	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-16858	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.000000	0.281579	
chunk0047_283_1	chr12	73306890	73307149	+	0	NA	Intergenic	L1ME4a|LINE|L1	147829	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.273077	45(AAGAGCAAAATGTTCT,-,0.00),46(AGAGCAAAATGTTCTG,+,0.00),81(GTCACACACTGTTCTA,+,0.00)
chunk0007_408_1	chr1	85637480	85637718	+	0	NA	Intergenic	Intergenic	56838	NM_001554	3491	Hs.8867	NM_001554	ENSG00000142871	CCN1	CYR61|GIG1|IGFBP10	cellular communication network factor 1	protein-coding	0.004202	0.573222	172(GAGCACAGCCTGTAAT,-,0.00)
chunk0051_264_1	chr12	117802929	117803477	+	0	NA	intron (NM_173598, intron 3 of 19)	intron (NM_173598, intron 3 of 19)	165020	NM_173598	283455	Hs.375836	NM_173598	ENSG00000171435	KSR2	-	kinase suppressor of ras 2	protein-coding	0.020073	0.455373	309(AGGAACACAGCGTTCC,-,0.00),310(GGAACACAGCGTTCCA,+,0.00)
chunk0111_31_1	chr20	22126972	22127329	+	0	NA	Intergenic	Intergenic	73060	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.002801	0.522346	
chunk0062_81_1	chr14	67846215	67846426	+	0	NA	intron (NM_133509, intron 4 of 10)	L1PA16|LINE|L1	26541	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.037915	0.613208	
chunk0144_99_1	chr4	128509518	128510022	+	0	NA	intron (NR_125882, intron 6 of 8)	Charlie17b|DNA|hAT-Charlie	81754	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.003968	0.273267	
chunk0060_363_1	chr14	52351151	52351445	+	0	NA	Intergenic	Intergenic	37000	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.006803	0.444068	
chunk0044_432_1	chr12	42145536	42146054	+	0	NA	promoter-TSS (NM_173601)	promoter-TSS (NM_173601)	-924	NM_001099650	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.019305	0.447013	229(AGGAACAATCAGTTCT,-,0.00),230(GGAACAATCAGTTCTA,+,0.00)
chunk0104_85_1	chr2	172012652	172013425	+	0	NA	intron (NM_199227, intron 1 of 9)	intron (NM_199227, intron 1 of 9)	13141	NM_199227	254042	Hs.298250	NM_199227	ENSG00000172878	METAP1D	MAP 1D|MAP1D|MetAP 1D|Metap1l	methionyl aminopeptidase type 1D, mitochondrial	protein-coding	0.012937	0.447028	
chunk0187_298_1	chr7	156081445	156081939	+	0	NA	Intergenic	Intergenic	119060	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.022267	0.456566	
chunk0160_84_1	chr5	149996287	149997076	+	0	NA	intron (NM_030953, intron 1 of 1)	MIRc|SINE|MIR	-3925	NM_014983	22993	Hs.719189	NM_014983	ENSG00000113716	HMGXB3	HMGX3|SMF	HMG-box containing 3	protein-coding	0.007605	0.411392	
chunk0124_426_1	chr3	61183361	61183956	+	0	NA	intron (NM_001166243, intron 2 of 9)	MIRb|SINE|MIR	67801	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.003361	0.402685	
chunk0100_439_1	chr2	120702047	120702279	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-95128	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.025862	0.515021	
chunk0011_94_1	chr1	145823786	145824205	+	0	NA	promoter-TSS (NM_006468)	promoter-TSS (NM_006468)	-74	NM_006468	10623	Hs.515768	NM_006468	ENSG00000186141	POLR3C	RPC3|RPC62	RNA polymerase III subunit C	protein-coding	0.121718	0.702381	
chunk0208_461_1	chrX	34629384	34629603	+	0	NA	3' UTR (NM_031442, exon 3 of 3)	3' UTR (NM_031442, exon 3 of 3)	27795	NM_031442	83604	Hs.8769	NM_031442	ENSG00000147027	TMEM47	BCMP1|TM4SF10|VAB-9	transmembrane protein 47	protein-coding	0.009132	0.350000	
chunk0077_155_1	chr16	79089043	79089279	+	0	NA	intron (NM_016373, intron 8 of 8)	MIRb|SINE|MIR	511564	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.016949	0.413502	
chunk0026_4_1	chr10	60375422	60376085	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	14123	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.010558	0.456325	
chunk0056_313_1	chr13	91024841	91025848	+	0	NA	Intergenic	Intergenic	64273	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.002979	0.375992	380(AAGAACTTCCTGCTCT,-,0.00),381(AGAACTTCCTGCTCTC,+,0.00)
chunk0026_293_1	chr10	67803520	67804100	+	0	NA	intron (NM_021800, intron 4 of 4)	intron (NM_021800, intron 4 of 4)	34369	NM_021800	56521	Hs.260720	NM_021800	ENSG00000108176	DNAJC12	HPANBH4|JDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding	0.005172	0.401033	
chunk0145_356_1	chr4	151184153	151185109	+	0	NA	intron (NM_001009555, intron 3 of 20)	L2|LINE|L2	-9079	NM_001128924	152503	Hs.744983	NM_001009555	ENSG00000109686	SH3D19	EBP|EVE1|Eve-1|Kryn|SH3P19	SH3 domain containing 19	protein-coding	0.006276	0.385580	
chunk0136_37_1	chr4	1152244	1152566	+	0	NA	Intergenic	MIR|SINE|MIR	20464	NM_012445	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.012422	0.461300	
chunk0159_305_1	chr5	142982508	142982893	+	0	NA	intron (NM_015071, intron 11 of 22)	intron (NM_015071, intron 11 of 22)	-113790	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.005195	0.468912	
chunk0072_84_1	chr15	90717692	90717892	+	0	NA	promoter-TSS (NR_120372)	promoter-TSS (NR_120372)	465	NM_001287246	641	Hs.725208	NM_000057	ENSG00000197299	BLM	BS|MGRISCE1|RECQ2|RECQL2|RECQL3	BLM RecQ like helicase	protein-coding	0.020000	0.502488	123(AAAACACTTTGTACTT,+,0.00)
chunk0112_351_1	chr20	45236001	45236338	+	0	NA	Intergenic	L1M2c|LINE|L1	14800	NM_003008	6407	Hs.537218	NM_003008	ENSG00000124157	SEMG2	SGII	semenogelin 2	protein-coding	0.011869	0.568047	
chunk0182_313_1	chr7	98855831	98856079	+	0	NA	intron (NM_001134450, intron 4 of 7)	intron (NM_001134450, intron 4 of 7)	14095	NM_152913	222865	Hs.270753	NM_152913	ENSG00000166448	TMEM130	-	transmembrane protein 130	protein-coding	0.048387	0.618474	
chunk0080_343_1	chr17	32763909	32764352	+	0	NA	intron (NM_015194, intron 8 of 21)	L1ME3G|LINE|L1	113043	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.009029	0.398649	
chunk0172_363_1	chr6	139219341	139219596	+	0	NA	Intergenic	Intergenic	72603	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.019608	0.542969	
chunk0035_399_1	chr11	56693854	56694300	+	0	NA	Intergenic	L2a|LINE|L2	-6311	NM_001005213	390174	Hs.553752	NM_001005213	ENSG00000174914	OR9G1	OR9G5	olfactory receptor family 9 subfamily G member 1	protein-coding	0.004484	0.398210	
chunk0170_81_1	chr6	109822432	109822639	+	0	NA	intron (NM_014845, intron 22 of 22)	intron (NM_014845, intron 22 of 22)	-69319	NR_106988									0.000000	0.293269	142(AAGGACAAGATGTTCC,-,0.00),143(AGGACAAGATGTTCCA,+,0.00)
chunk0047_400_1	chr12	75782182	75782614	+	0	NA	Intergenic	L1MB2|LINE|L1	249378	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.006944	0.376443	173(ATAAACAGAATGTGCT,-,0.00)
chunk0211_223_1	chrX	118653844	118654068	+	0	NA	intron (NM_144658, intron 42 of 52)	intron (NM_144658, intron 42 of 52)	-73640	NM_001560	3597	Hs.496646	NM_001560	ENSG00000131724	IL13RA1	CD213A1|CT19|IL-13Ra|NR4	interleukin 13 receptor subunit alpha 1	protein-coding	0.004464	0.395556	
chunk0001_152_1	chr1	6199621	6200106	+	0	NA	promoter-TSS (NM_000983)	promoter-TSS (NM_000983)	-244	NM_000983	6146	Hs.515329	NM_000983	ENSG00000116251	RPL22	EAP|HBP15|HBP15/L22|L22	ribosomal protein L22	protein-coding	0.043299	0.524691	
chunk0145_139_1	chr4	146831300	146831786	+	0	NA	intron (NM_001300761, intron 10 of 13)	intron (NM_001300761, intron 10 of 13)	114339	NM_001300761	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.004115	0.416838	212(TGGAACAGAATGGTCC,-,0.00),213(GGAACAGAATGGTCCC,+,0.00)
chunk0129_13_1	chr3	116980723	116980990	+	0	NA	Intergenic	Intergenic	59425	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.302239	
chunk0186_271_1	chr7	141689547	141689824	+	0	NA	intron (NM_001080392, intron 1 of 8)	L1ME3A|LINE|L1	12468	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.000000	0.356115	
chunk0073_338_1	chr16	14520731	14521136	+	0	NA	intron (NM_002582, intron 21 of 23)	L1MC5|LINE|L1	109338	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.004938	0.394089	
chunk0103_96_1	chr2	161219218	161219451	+	0	NA	intron (NM_004180, intron 4 of 7)	intron (NM_004180, intron 4 of 7)	-25405	NR_110164	100996579	Hs.660929	NR_110163	ENSG00000227403	LINC01806	-	long intergenic non-protein coding RNA 1806	ncRNA	0.000000	0.384615	
chunk0202_4_1	chr9	70217019	70217371	+	0	NA	intron (NR_039990, intron 3 of 3)	intron (NR_039990, intron 3 of 3)	-41307	NR_040076	100507244	Hs.556816	NR_040076	ENSG00000204706	MAMDC2-AS1	-	MAMDC2 antisense RNA 1	ncRNA	0.042614	0.456091	
chunk0211_185_1	chrX	117298468	117299090	+	0	NA	Intergenic	L1PA13|LINE|L1	674959	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.003215	0.345104	
chunk0020_387_1	chr1	240253868	240254067	+	0	NA	intron (NM_020066, intron 6 of 17)	L1MA4A|LINE|L1	162082	NM_020066	56776	Hs.24889	NM_020066	ENSG00000155816	FMN2	-	formin 2	protein-coding	0.000000	0.520000	
chunk0184_303_1	chr7	120018483	120018796	+	0	NA	Intergenic	Intergenic	-111264	NR_131963	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.006390	0.299363	
chunk0060_372_1	chr14	52515655	52516133	+	0	NA	intron (NM_001160047, intron 7 of 20)	L1MEh|LINE|L1	36689	NM_001160047	57544	Hs.532609	NM_020784	ENSG00000087301	TXNDC16	ERp90|KIAA1344	thioredoxin domain containing 16	protein-coding	0.000000	0.315240	
chunk0125_116_1	chr3	65714159	65714465	+	0	NA	intron (NM_015520, intron 1 of 24)	LTR40c|LTR|ERVL	-179504	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.009804	0.504886	
chunk0109_294_1	chr20	8321024	8321408	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	188951	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.010417	0.340260	
chunk0004_3_1	chr1	41866648	41866885	+	0	NA	intron (NR_038260, intron 1 of 2)	intron (NR_038260, intron 1 of 2)	51941	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.008439	0.495798	
chunk0093_321_1	chr19	54008483	54009035	+	0	NA	intron (NM_145814, intron 3 of 3)	L2c|LINE|L2	16471	NM_031897	59285	Hs.631560	NM_031897	ENSG00000130433	CACNG6	-	calcium voltage-gated channel auxiliary subunit gamma 6	protein-coding	0.028986	0.508137	
chunk0121_200_1	chr3	21082575	21082790	+	0	NA	Intergenic	L1PA16|LINE|L1	-323044	NR_002311	391518	Hs.543226	NR_002311		VENTXP7	HPX42|VENTX1	VENT homeobox pseudogene 7	pseudo	0.004651	0.342593	
chunk0194_194_1	chr8	85346832	85347031	+	0	NA	intron (NM_001128830, intron 1 of 8)	intron (NM_001128830, intron 1 of 8)	-5217	NM_001164830	759	Hs.23118	NM_001738	ENSG00000133742	CA1	CA-I|CAB|Car1|HEL-S-11	carbonic anhydrase 1	protein-coding	0.000000	0.295000	
chunk0158_93_1	chr5	126609914	126610509	+	0	NA	intron (NM_032177, intron 3 of 4)	intron (NM_032177, intron 3 of 4)	9296	NM_032177	51808	Hs.555731	NM_032177	ENSG00000164902	PHAX	RNUXA	phosphorylated adaptor for RNA export	protein-coding	0.008403	0.419463	
chunk0207_318_1	chr9	134047055	134047339	+	0	NA	intron (NM_007371, intron 6 of 11)	intron (NM_007371, intron 6 of 11)	20822	NM_007371	8019	Hs.522472	NM_007371	ENSG00000169925	BRD3	ORFX|RING3L	bromodomain containing 3	protein-coding	0.038732	0.624561	
chunk0008_144_1	chr1	92186078	92186690	+	0	NA	Intergenic	Intergenic	19332	NM_015237	23285	Hs.21554	NM_015237	ENSG00000189195	KIAA1107	-	KIAA1107	protein-coding	0.003268	0.352365	
chunk0149_262_1	chr5	23990796	23991472	+	0	NA	intron (NR_131245, intron 4 of 4)	(TTGT)n|Simple_repeat|Simple_repeat	39786	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.004438	0.350074	
chunk0030_295_1	chr10	117327461	117327710	+	0	NA	intron (NM_173791, intron 2 of 4)	LTR54B|LTR|ERV1	47882	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.000000	0.360000	
chunk0051_333_1	chr12	120257035	120257471	+	0	NA	intron (NM_001243756, intron 1 of 10)	intron (NM_001243756, intron 1 of 10)	-7092	NM_025157	5829	Hs.446336	NM_002859	ENSG00000089159	PXN	-	paxillin	protein-coding	0.018349	0.496568	
chunk0064_80_1	chr14	90501109	90501536	+	0	NA	Intergenic	Intergenic	46092	NR_033986	400238	Hs.131037	NR_033986	ENSG00000233208	LINC00642	-	long intergenic non-protein coding RNA 642	ncRNA	0.018735	0.567757	292(AGGTACATGGTGTTCA,-,0.00),293(GGTACATGGTGTTCAG,+,0.00)
chunk0028_56_1	chr10	83233953	83234209	+	0	NA	Intergenic	Intergenic	-905348	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.003906	0.237354	
chunk0043_434_1	chr12	26172518	26172790	+	0	NA	Intergenic	Intergenic	-22682	NM_001135823	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.014706	0.318681	
chunk0084_347_1	chr17	81272544	81273160	+	0	NA	intron (NM_138570, intron 8 of 13)	intron (NM_138570, intron 8 of 13)	22487	NM_001037984	124565	Hs.352240	NM_138570	ENSG00000157637	SLC38A10	PP1744	solute carrier family 38 member 10	protein-coding	0.025974	0.520259	
chunk0046_208_1	chr12	59112013	59112269	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-191603	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.011719	0.470817	140(GGGAACATAGCGTTCA,-,0.00)
chunk0112_223_1	chr20	40892461	40893127	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-136028	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.004505	0.469265	
chunk0210_282_1	chrX	84889686	84890255	+	0	NA	Intergenic	HAL1ME|LINE|L1	-44181	NR_024062	100131816	Hs.460809	NM_178567	ENSG00000229547	UBE2DNL	-	ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)	pseudo	0.014060	0.382456	
chunk0077_381_1	chr16	84698017	84698571	+	0	NA	Intergenic	L1MC4|LINE|L1	-1655	NR_073578	9100	Hs.136778	NM_005153	ENSG00000103194	USP10	UBPO	ubiquitin specific peptidase 10	protein-coding	0.005415	0.340541	
chunk0046_329_1	chr12	62727228	62727479	+	0	NA	intron (NM_020700, intron 5 of 9)	intron (NM_020700, intron 5 of 9)	123667	NR_029661	406891		NR_029661	ENSG00000199179	MIRLET7I	LET7I|MIRNLET7I|hsa-let-7i|let-7i	microRNA let-7i	ncRNA	0.003984	0.349206	78(CAGGACATTCTGACCT,-,0.00),79(AGGACATTCTGACCTG,+,0.00)
chunk0059_272_1	chr14	35379094	35379790	+	0	NA	Intergenic	Intergenic	25312	NM_020529	4792	Hs.81328	NM_020529	ENSG00000100906	NFKBIA	EDAID2|IKBA|MAD-3|NFKBI	NFKB inhibitor alpha	protein-coding	0.005747	0.390244	
chunk0015_12_1	chr1	184180391	184180657	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	128873	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.003759	0.408240	
chunk0094_21_1	chr2	1231482	1232101	+	0	NA	intron (NM_018968, intron 9 of 16)	intron (NM_018968, intron 9 of 16)	-181670	NM_001206745	7173	Hs.467554	NM_000547	ENSG00000115705	TPO	MSA|TDH2A|TPX	thyroid peroxidase	protein-coding	0.019386	0.569355	
chunk0081_166_1	chr17	41212785	41213016	+	0	NA	Intergenic	Intergenic	-13748	NM_031961	83899	Hs.307013	NM_031961	ENSG00000239886	KRTAP9-2	KAP9.2|KRTAP9.2	keratin associated protein 9-2	protein-coding	0.008658	0.594828	
chunk0013_453_1	chr1	174018716	174018949	+	0	NA	Intergenic	Intergenic	-25760	NM_172071	149041	Hs.30258	NM_172071	ENSG00000135870	RC3H1	RNF198|ROQUIN	ring finger and CCCH-type domains 1	protein-coding	0.004292	0.435897	71(AGGAACATCCTGATCT,-,0.00),72(GGAACATCCTGATCTG,+,0.00)
chunk0064_245_1	chr14	94438603	94439156	+	0	NA	Intergenic	L1MEg|LINE|L1	13906	NM_001080451	256394	Hs.145890	NM_001080451	ENSG00000186910	SERPINA11	-	serpin family A member 11	protein-coding	0.001808	0.393502	
chunk0081_177_1	chr17	41600262	41600829	+	0	NA	Intergenic	MIRb|SINE|MIR	12282	NM_005557	3868	Hs.655160	NM_005557	ENSG00000186832	KRT16	CK16|FNEPPK|K16|K1CP|KRT16A|NEPPK|PC1	keratin 16	protein-coding	0.012346	0.461268	
chunk0112_185_1	chr20	40079956	40080566	+	0	NA	Intergenic	Intergenic	75800	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.009836	0.477905	
chunk0081_403_1	chr17	48310850	48311079	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	16617	NR_131240	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.034934	0.482609	
chunk0083_411_1	chr17	72149755	72150176	+	0	NA	Intergenic	Intergenic	28945	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.009501	0.497630	272(AAGGACACAATGTGAT,-,0.00)
chunk0190_288_1	chr8	37863802	37864525	+	0	NA	intron (NM_001002814, intron 5 of 5)	intron (NM_001002814, intron 5 of 5)	-14250	NM_018310	55290	Hs.709301	NM_018310	ENSG00000104221	BRF2	BRFU|TFIIIB50	BRF2 RNA polymerase III transcription initiation factor subunit	protein-coding	0.017981	0.531768	378(CAGAGCTGAGTGTTCC,-,0.00)
chunk0115_266_1	chr21	27872426	27872652	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-140824	NR_027246	246705	Hs.505079	NM_145180	ENSG00000178457	LINC00314	C21orf94|NCRNA00314	long intergenic non-protein coding RNA 314	ncRNA	0.008850	0.555066	
chunk0075_200_1	chr16	52500215	52500438	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	46568	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.008969	0.366071	
chunk0115_277_1	chr21	28150876	28151340	+	0	NA	intron (NR_126012, intron 5 of 5)	Tigger3b|DNA|TcMar-Tigger	60705	NR_126011	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.006466	0.376344	
chunk0031_192_1	chr10	125727110	125727891	+	0	NA	intron (NM_015608, intron 6 of 23)	intron (NM_015608, intron 6 of 23)	7985	NR_110858	26098	Hs.468688	NM_015608	ENSG00000107938	EDRF1	C10orf137	erythroid differentiation regulatory factor 1	protein-coding	0.007682	0.430946	
chunk0157_282_1	chr5	120656899	120657515	+	0	NA	intron (NM_001308088, intron 3 of 3)	LTR79|LTR|ERVL	125743	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.004870	0.353323	
chunk0181_22_1	chr7	77791907	77792520	+	0	NA	Intergenic	Intergenic	6217	NM_032936	85025	Hs.19025	NM_032936	ENSG00000135211	TMEM60	C7orf35|DC32	transmembrane protein 60	protein-coding	0.004894	0.358306	312(TGGAACATTCCGTTCC,-,0.00),313(GGAACATTCCGTTCCC,+,0.00),328(CAGTACTAACTGTTCT,-,0.00),329(AGTACTAACTGTTCTC,+,0.00)
chunk0153_51_1	chr5	67418081	67418543	+	0	NA	Intergenic	Intergenic	-221523	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.008658	0.354212	
chunk0064_367_1	chr14	98219689	98220138	+	0	NA	Intergenic	Intergenic	-241789	NR_015430	388011	Hs.651477	NR_015430	ENSG00000246223	LINC01550	C14orf64	long intergenic non-protein coding RNA 1550	ncRNA	0.017817	0.520000	124(GAGGACAAAATGTTCC,-,0.00),125(AGGACAAAATGTTCCA,+,0.00)
chunk0064_376_1	chr14	98773907	98774484	+	0	NA	Intergenic	Intergenic	62582	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.010399	0.410035	
chunk0166_250_1	chr6	47478576	47478775	+	0	NA	intron (NM_012120, intron 1 of 17)	intron (NM_012120, intron 1 of 17)	886	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.030151	0.450000	
chunk0179_371_1	chr7	51180427	51181022	+	0	NA	intron (NM_001287436, intron 5 of 13)	LTR49-int|LTR|ERV1	136094	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.003361	0.337248	
chunk0061_146_1	chr14	59453273	59453688	+	0	NA	Intergenic	Intergenic	11861	NM_022571	64582	Hs.647573	NM_022571	ENSG00000181619	GPR135	HUMNPIIY20	G protein-coupled receptor 135	protein-coding	0.002410	0.408654	
chunk0012_40_1	chr1	155177213	155177752	+	0	NA	intron (NR_104150, intron 5 of 9)	intron (NR_104150, intron 5 of 9)	2728	NM_001256601	80128	Hs.287735	NM_025058	ENSG00000163462	TRIM46	GENEY|TRIFIC	tripartite motif containing 46	protein-coding	0.018553	0.568519	236(CAGGCCAGGCTGTACC,-,0.00),237(AGGCCAGGCTGTACCT,+,0.00)
chunk0074_215_1	chr16	25677485	25677696	+	0	NA	Intergenic	Intergenic	-14436	NM_006040	9951	Hs.655275	NM_006040	ENSG00000182601	HS3ST4	3-OST-4|30ST4|3OST4|h3-OST-4	heparan sulfate-glucosamine 3-sulfotransferase 4	protein-coding	0.000000	0.372642	
chunk0142_261_1	chr4	99168547	99168810	+	0	NA	intron (NR_037884, intron 3 of 9)	L1PB3|LINE|L1	-7031	NR_028270	359806	Hs.537400	NR_028270		PCNAP1	p1PCNA	proliferating cell nuclear antigen pseudogene 1	pseudo	0.000000	0.321970	
chunk0139_409_1	chr4	63408469	63408972	+	0	NA	Intergenic	Intergenic	1000740	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.005964	0.345238	256(AAGAACAAGCTGTGCT,-,0.00),257(AGAACAAGCTGTGCTT,+,0.00)
chunk0205_214_1	chr9	109422680	109423003	+	0	NA	exon (NM_002829, exon 13 of 26)	exon (NM_002829, exon 13 of 26)	-5058	NR_026918	5774	Hs.436429	NM_002829	ENSG00000070159	PTPN3	PTP-H1|PTPH1	protein tyrosine phosphatase non-receptor type 3	protein-coding	0.018576	0.453704	
chunk0165_309_1	chr6	36973056	36973770	+	0	NA	intron (NR_130739, intron 7 of 11)	intron (NR_130739, intron 7 of 11)	13138	NR_130739	23787	Hs.485262	NM_014341	ENSG00000137409	MTCH1	CGI-64|PIG60|PSAP|SLC25A49	mitochondrial carrier 1	protein-coding	0.008403	0.405594	349(AGGTACAGAGTGCCCT,-,0.00),350(GGTACAGAGTGCCCTG,+,0.00)
chunk0183_450_1	chr7	111303205	111303550	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	212371	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.002899	0.294798	
chunk0096_293_1	chr2	32589547	32589985	+	0	NA	intron (NM_016252, intron 66 of 73)	intron (NM_016252, intron 66 of 73)	-14948	NR_125793	103752586	Hs.666092	NR_125793	ENSG00000279897	BIRC6-AS2	linc-birc6|megamind	BIRC6 antisense RNA 2	ncRNA	0.002283	0.312073	
chunk0071_103_1	chr15	81033097	81033296	+	0	NA	Intergenic	Intergenic	32242	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.000000	0.340000	
chunk0073_111_1	chr16	4669296	4669945	+	0	NA	intron (NM_015246, intron 8 of 16)	L2c|LINE|L2	-1698	NR_106827	102466731		NR_106827	ENSG00000276641	MIR6769A	hsa-mir-6769a	microRNA 6769a	ncRNA	0.013867	0.467692	
chunk0156_220_1	chr5	108220674	108220963	+	0	NA	intron (NM_001163315, intron 5 of 8)	intron (NM_001163315, intron 5 of 8)	161280	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.006920	0.372414	
chunk0083_161_1	chr17	65986676	65987168	+	0	NA	intron (NM_001302891, intron 15 of 24)	L1M6|LINE|L1	-160379	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.006098	0.318458	
chunk0018_312_1	chr1	221148594	221149127	+	0	NA	Intergenic	Intergenic	187436	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.009381	0.441948	
chunk0143_54_1	chr4	107683798	107684345	+	0	NA	intron (NM_005443, intron 4 of 11)	intron (NM_005443, intron 4 of 11)	36192	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.000000	0.375912	
chunk0076_241_1	chr16	69182609	69183444	+	0	NA	Intergenic	Intergenic	-4121	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.011976	0.450957	761(GAGGACACCTTGACCT,-,0.00),762(AGGACACCTTGACCTC,+,0.00)
chunk0096_4_1	chr2	25823349	25823903	+	0	NA	intron (NM_018263, intron 2 of 11)	intron (NM_018263, intron 2 of 11)	54817	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.003610	0.340541	
chunk0155_258_1	chr5	95763020	95763770	+	0	NA	intron (NM_014899, intron 6 of 11)	intron (NM_014899, intron 6 of 11)	32249	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.004000	0.351531	
chunk0050_261_1	chr12	105912669	105913259	+	0	NA	Intergenic	Intergenic	206190	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.001695	0.384095	
chunk0118_329_1	chr22	35452469	35453055	+	0	NA	Intergenic	Intergenic	52639	NM_006739	4174	Hs.517582	NM_006739	ENSG00000100297	MCM5	CDC46|MGORS8|P1-CDC46	minichromosome maintenance complex component 5	protein-coding	0.027304	0.550256	
chunk0082_220_1	chr17	57158129	57158635	+	0	NA	Intergenic	Intergenic	72608	NM_001242902	8165	Hs.463506	NM_003488	ENSG00000121057	AKAP1	AKAP|AKAP121|AKAP149|AKAP84|D-AKAP1|PPP1R43|PRKA1|SAKAP84|TDRD17	A-kinase anchoring protein 1	protein-coding	0.009881	0.481262	
chunk0062_362_1	chr14	73893987	73894587	+	0	NA	intron (NM_001242927, intron 3 of 10)	L2|LINE|L2	7672	NM_001242924	57862	Hs.270869	NM_021188	ENSG00000119725	ZNF410	APA-1|APA1	zinc finger protein 410	protein-coding	0.008333	0.439268	
chunk0069_438_1	chr15	68467636	68468334	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-35832	NM_001004439	22801	Hs.436416	NM_012211	ENSG00000137809	ITGA11	HsT18964	integrin subunit alpha 11	protein-coding	0.007163	0.409156	390(AGTAACAGAATGTTCC,-,0.00),391(GTAACAGAATGTTCCT,+,0.00)
chunk0035_338_1	chr11	47991052	47991839	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	10887	NM_002843	5795	Hs.318547	NM_002843	ENSG00000149177	PTPRJ	CD148|DEP1|HPTPeta|R-PTP-ETA|SCC1	protein tyrosine phosphatase receptor type J	protein-coding	0.015248	0.450508	
chunk0197_144_1	chr8	120373075	120373408	+	0	NA	Intergenic	Intergenic	-72157	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.003003	0.314371	
chunk0080_329_1	chr17	32558186	32558618	+	0	NA	intron (NM_015194, intron 21 of 21)	intron (NM_015194, intron 21 of 21)	71315	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.004630	0.448037	
chunk0207_131_1	chr9	129107232	129108064	+	0	NA	intron (NM_001257363, intron 3 of 14)	L2b|LINE|L2	3143	NM_001257363	1384	Hs.12068	NM_000755	ENSG00000095321	CRAT	CAT|CAT1|NBIA8	carnitine O-acetyltransferase	protein-coding	0.021635	0.555822	
chunk0066_211_1	chr15	33888056	33888481	+	0	NA	intron (NM_020371, intron 2 of 5)	L2c|LINE|L2	-80620	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.007059	0.403756	
chunk0156_342_1	chr5	111810116	111810620	+	0	NA	intron (NM_001142474, intron 2 of 3)	intron (NM_001142474, intron 2 of 3)	-52150	NM_001142476	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.007937	0.409901	
chunk0053_108_1	chr13	28885303	28885597	+	0	NA	Intergenic	MIRb|SINE|MIR	-139161	NM_001033602	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.006803	0.444068	
chunk0009_46_1	chr1	100474398	100474835	+	0	NA	intron (NM_003672, intron 10 of 15)	L1MDa|LINE|L1	-63556	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.002288	0.283105	
chunk0080_208_1	chr17	29390198	29390480	+	0	NA	promoter-TSS (NR_039749)	promoter-TSS (NR_039749)	-323	NR_039749	100616122		NR_039749	ENSG00000284162	MIR4523	-	microRNA 4523	ncRNA	0.102837	0.692580	
chunk0082_342_1	chr17	59837314	59837945	+	0	NA	intron (NM_030938, intron 10 of 11)	intron (NM_030938, intron 10 of 11)	-3637	NR_029493	406991	Hs.444569	NR_029493	ENSG00000284190	MIR21	MIRN21|hsa-mir-21|miR-21|miRNA21	microRNA 21	ncRNA	0.011094	0.401899	248(CAGAACAAGCTGTTAC,-,0.00),249(AGAACAAGCTGTTACT,+,0.00)
chunk0170_362_1	chr6	116794116	116794523	+	0	NA	intron (NM_001286354, intron 5 of 5)	intron (NM_001286354, intron 5 of 5)	-28596	NM_001085480	221303	Hs.126712	NM_001085480	ENSG00000183807	FAM162B	C6orf189|bA86F4.2	family with sequence similarity 162 member B	protein-coding	0.007371	0.424020	
chunk0194_426_1	chr8	92450790	92451197	+	0	NA	Intergenic	Intergenic	204501	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.004914	0.313725	
chunk0105_190_1	chr2	187570387	187570608	+	0	NA	Intergenic	L3|LINE|CR1	-16005	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.351351	133(AAGCACAGTGTGTTCA,-,0.00),134(AGCACAGTGTGTTCAG,+,0.00)
chunk0208_77_1	chrX	12934437	12934637	+	0	NA	intron (NR_030727, intron 2 of 4)	L2c|LINE|L2	8763	NR_030727	349408	Hs.685035	NR_030727	ENSG00000233338	TLR8-AS1	GS1-324M7.6	TLR8 antisense RNA 1	ncRNA	0.010000	0.393035	
chunk0180_312_1	chr7	70760597	70761292	+	0	NA	intron (NM_015570, intron 6 of 18)	intron (NM_015570, intron 6 of 18)	-371593	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.011511	0.448276	
chunk0068_10_1	chr15	50544263	50544831	+	0	NA	intron (NM_203494, intron 2 of 6)	intron (NM_203494, intron 2 of 6)	2158	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.014085	0.479789	
chunk0187_239_1	chr7	152698975	152699518	+	0	NA	Intergenic	Intergenic	-23081	NM_005431	7516	Hs.647093	NM_005431	ENSG00000196584	XRCC2	FANCU	X-ray repair cross complementing 2	protein-coding	0.000000	0.360294	
chunk0174_377_1	chr6	164928804	164929326	+	0	NA	Intergenic	Intergenic	-107002	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.011494	0.403442	
chunk0014_300_1	chr1	180987030	180987232	+	0	NA	intron (NM_005819, intron 6 of 7)	L2a|LINE|L2	35990	NM_005819	10228	Hs.518417	NM_005819	ENSG00000135823	STX6	-	syntaxin 6	protein-coding	0.009901	0.532020	
chunk0094_383_1	chr2	9954197	9954845	+	0	NA	intron (NM_198182, intron 1 of 15)	intron (NM_198182, intron 1 of 15)	2858	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.010802	0.416025	314(GGCACACGCTCTTCTC,+,0.00),496(GTGAACTGCCAGTTCT,-,0.00),497(TGAACTGCCAGTTCTC,+,0.00)
chunk0184_316_1	chr7	120225899	120226104	+	0	NA	Intergenic	Intergenic	-47667	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.310680	
chunk0079_104_1	chr17	12242488	12242773	+	0	NA	Intergenic	Intergenic	160731	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.017544	0.496503	
chunk0130_324_1	chr3	138174935	138175134	+	0	NA	promoter-TSS (NM_016216)	promoter-TSS (NM_016216)	-85	NM_016216	51163	Hs.477700	NM_016216	ENSG00000138231	DBR1	-	debranching RNA lariats 1	protein-coding	0.020101	0.350000	
chunk0212_400_1	chrX	150966444	150967243	+	0	NA	Intergenic	MIRc|SINE|MIR	-13665	NM_001301231	3149	Hs.19114	NM_005342	ENSG00000029993	HMGB3	HMG-2a|HMG-4|HMG2A|HMG4	high mobility group box 3	protein-coding	0.007509	0.441250	
chunk0136_128_1	chr4	3756946	3757408	+	0	NA	Intergenic	Intergenic	-9392	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.012987	0.464363	
chunk0125_103_1	chr3	65539140	65539736	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-354378	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.003356	0.425461	
chunk0139_382_1	chr4	61429034	61429524	+	0	NA	Intergenic	MIRb|SINE|MIR	-67842	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.334012	
chunk0037_234_1	chr11	75288975	75289441	+	0	NA	intron (NM_004041, intron 2 of 15)	intron (NM_004041, intron 2 of 15)	45978	NR_029891	442900		NR_029891	ENSG00000199090	MIR326	MIRN326|hsa-mir-326|mir-326	microRNA 326	ncRNA	0.017167	0.546039	
chunk0135_150_1	chr3	187695669	187696047	+	0	NA	Intergenic	Intergenic	-6508	NR_034062	100131635	Hs.434448	NR_034062	ENSG00000228804	LOC100131635	-	hCG1645011-like	ncRNA	0.002646	0.506596	
chunk0196_152_1	chr8	104609667	104609905	+	0	NA	Intergenic	L1PA15|LINE|L1	-20762	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.004202	0.368201	
chunk0067_295_1	chr15	47576651	47577200	+	0	NA	intron (NM_001198999, intron 3 of 19)	intron (NM_001198999, intron 3 of 19)	-141564	NM_153618	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.007286	0.367273	174(AGAACAAAATGAGCCT,+,0.00)
chunk0209_110_1	chrX	40450070	40450401	+	0	NA	Intergenic	Intergenic	-130729	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.009063	0.506024	
chunk0130_458_1	chr3	141462704	141463070	+	0	NA	Intergenic	Intergenic	-24160	NM_001303246	5922	Hs.98445	NM_006506	ENSG00000155903	RASA2	GAP1M	RAS p21 protein activator 2	protein-coding	0.010929	0.457766	
chunk0171_147_1	chr6	123740490	123741286	+	0	NA	Intergenic	L1MC3|LINE|L1	-62958	NM_001040214	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.005025	0.321205	
chunk0015_315_1	chr1	189245783	189246342	+	0	NA	Intergenic	L2a|LINE|L2	1231567	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003578	0.312500	
chunk0122_423_1	chr3	39101769	39102429	+	0	NA	intron (NM_001278789, intron 1 of 6)	Tigger3a|DNA|TcMar-Tigger	-5562	NM_145755	199223	Hs.443935	NM_145755	ENSG00000168026	TTC21A	IFT139A|SPGF37|STI2	tetratricopeptide repeat domain 21A	protein-coding	0.006061	0.396369	
chunk0009_325_1	chr1	108762814	108763233	+	0	NA	intron (NM_007269, intron 6 of 18)	intron (NM_007269, intron 6 of 18)	16360	NM_007269	6814	Hs.530436	NM_007269	ENSG00000116266	STXBP3	MUNC18-3|MUNC18C|PSP|UNC-18C	syntaxin binding protein 3	protein-coding	0.000000	0.347619	
chunk0033_200_1	chr11	16768794	16769223	+	0	NA	Intergenic	L1ME3B|LINE|L1	30407	NM_014267	10944	Hs.368226	NM_014267	ENSG00000110696	C11orf58	IMAGE145052|SMAP	chromosome 11 open reading frame 58	protein-coding	0.023310	0.448837	
chunk0012_63_1	chr1	155562851	155563424	+	0	NA	promoter-TSS (NM_018489)	promoter-TSS (NM_018489)	-604	NM_018489	55870	Hs.491060	NM_018489	ENSG00000116539	ASH1L	ASH1|ASH1L1|KMT2H|MRD52	ASH1 like histone lysine methyltransferase	protein-coding	0.102967	0.696864	
chunk0037_372_1	chr11	78259812	78260411	+	0	NA	intron (NM_012296, intron 2 of 9)	intron (NM_012296, intron 2 of 9)	71299	NM_020798	57558	Hs.531249	NM_020798	ENSG00000118369	USP35	-	ubiquitin specific peptidase 35	protein-coding	0.013356	0.416667	443(CAGAACATCCTGACCT,-,0.00),444(AGAACATCCTGACCTT,+,0.00)
chunk0089_341_1	chr18	65809042	65809580	+	0	NA	intron (NM_004361, intron 2 of 11)	intron (NM_004361, intron 2 of 11)	58390	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.005576	0.385900	
chunk0091_326_1	chr19	13747696	13747973	+	0	NA	promoter-TSS (NM_030818)	promoter-TSS (NM_030818)	-105	NM_030818	81576	Hs.24998	NM_030818	ENSG00000104957	CCDC130	-	coiled-coil domain containing 130	protein-coding	0.115523	0.697842	
chunk0023_253_1	chr10	27508415	27508873	+	0	NA	intron (NR_046172, intron 1 of 5)	intron (NR_046172, intron 1 of 5)	4470	NM_001256411	22931	Hs.406799	NM_021252	ENSG00000099246	RAB18	RAB18LI1|WARBM3	RAB18, member RAS oncogene family	protein-coding	0.004367	0.307190	
chunk0140_271_1	chr4	72083271	72083926	+	0	NA	intron (NM_001144756, intron 2 of 4)	L2|LINE|L2	44466	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.004580	0.365854	263(AGGAACACCATGTTCT,-,0.00),264(GGAACACCATGTTCTC,+,0.00)
chunk0161_117_1	chr5	167575870	167576487	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	-178758	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.008104	0.322006	337(AGTTCAGCATGTACTT,+,0.00)
chunk0210_354_1	chrX	96389553	96390087	+	0	NA	Intergenic	L2c|LINE|L2	-51918	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.009363	0.347664	
chunk0003_391_1	chr1	39876981	39877816	+	0	NA	intron (NR_132406, intron 1 of 8)	intron (NR_132406, intron 1 of 8)	6113	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.005988	0.410287	573(CAGAACACTTTGTTTC,-,0.00),574(AGAACACTTTGTTTCT,+,0.00)
chunk0106_63_1	chr2	196836314	196836975	+	0	NA	3' UTR (NM_024989, exon 27 of 27)	3' UTR (NM_024989, exon 27 of 27)	-26368	NM_213608	401027	Hs.245666	NM_213608	ENSG00000187944	C2orf66	IIDS6411|UNQ6411	chromosome 2 open reading frame 66	protein-coding	0.000000	0.299094	
chunk0198_417_1	chr8	142727195	142727729	+	0	NA	promoter-TSS (NR_038925)	promoter-TSS (NR_038925)	259	NM_016647	51337	Hs.368402	NM_016647	ENSG00000130193	THEM6	C8orf55|DSCD75	thioesterase superfamily member 6	protein-coding	0.146067	0.749533	
chunk0025_18_1	chr10	47966898	47967384	+	0	NA	Intergenic	HAL1ME|LINE|L1	32650	NM_001137549	100133093	Hs.723078	NM_001137549	ENSG00000189090	FAM25G	FAM25A|FAM25B|FAM25C|bA301J7.4	family with sequence similarity 25 member G	protein-coding	0.004115	0.375770	
chunk0196_396_1	chr8	115875297	115875727	+	0	NA	Intergenic	Intergenic	-206484	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.009302	0.350348	
chunk0122_125_1	chr3	31410736	31411020	+	0	NA	Intergenic	L1MC3|LINE|L1	-121623	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.003521	0.336842	
chunk0049_189_1	chr12	92858740	92859079	+	0	NA	intron (NM_003566, intron 3 of 28)	intron (NM_003566, intron 3 of 28)	70422	NM_003566	8411	Hs.567367	NM_003566	ENSG00000102189	EEA1	MST105|MSTP105|ZFYVE2	early endosome antigen 1	protein-coding	0.008850	0.450000	
chunk0075_249_1	chr16	53194994	53195193	+	0	NA	intron (NM_001308319, intron 1 of 37)	L1ME3A|LINE|L1	39167	NM_001308319	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.000000	0.250000	
chunk0059_278_1	chr14	35403588	35404427	+	0	NA	intron (NM_020529, intron 1 of 5)	CpG	747	NM_020529	4792	Hs.81328	NM_020529	ENSG00000100906	NFKBIA	EDAID2|IKBA|MAD-3|NFKBI	NFKB inhibitor alpha	protein-coding	0.095352	0.716667	446(CGGAACGCCCTGTACT,-,0.00),447(GGAACGCCCTGTACTT,+,0.00)
chunk0165_340_1	chr6	37826830	37827092	+	0	NA	intron (NM_021943, intron 1 of 5)	MER3|DNA|hAT-Charlie	7430	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.000000	0.361217	
chunk0210_288_1	chrX	85828604	85829587	+	0	NA	Intergenic	Intergenic	-6685	NR_031710	100302171		NR_031710	ENSG00000283435	MIR1321	MIRN1321|hsa-mir-1321	microRNA 1321	ncRNA	0.005086	0.350610	
chunk0139_440_1	chr4	65016557	65017151	+	0	NA	Intergenic	Intergenic	-12354	NR_033976	401134	Hs.165899	NR_033976	ENSG00000250125	LINC02232	-	long intergenic non-protein coding RNA 2232	ncRNA	0.005051	0.265546	
chunk0146_318_1	chr4	165433498	165433963	+	0	NA	intron (NM_001873, intron 1 of 8)	intron (NM_001873, intron 1 of 8)	47488	NR_030304	693163		NR_030304	ENSG00000207559	MIR578	MIRN578|hsa-mir-578	microRNA 578	ncRNA	0.015054	0.450644	
chunk0042_144_1	chr12	3843828	3844106	+	0	NA	intron (NR_104461, intron 1 of 8)	intron (NR_104461, intron 1 of 8)	29481	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.007194	0.362007	
chunk0107_446_1	chr2	225429715	225430031	+	0	NA	intron (NM_020864, intron 2 of 5)	intron (NM_020864, intron 2 of 5)	28987	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.012658	0.441640	133(TTGCACACTATGTACT,-,0.00),134(TGCACACTATGTACTT,+,0.00)
chunk0046_202_1	chr12	58977486	58977738	+	0	NA	Intergenic	Intergenic	-57074	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.007937	0.371542	
chunk0017_399_1	chr1	212565958	212566260	+	0	NA	intron (NM_001030287, intron 1 of 3)	MIRc|SINE|MIR	775	NM_001030287	467	Hs.460	NM_001674	ENSG00000162772	ATF3	-	activating transcription factor 3	protein-coding	0.000000	0.452145	
chunk0054_68_1	chr13	42084110	42084749	+	0	NA	intron (NM_152910, intron 1 of 28)	intron (NM_152910, intron 1 of 28)	35721	NM_152910	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.004695	0.260937	224(AGTACAATCTGTTTTC,+,0.00)
chunk0052_464_1	chr12	133130430	133130697	+	0	NA	promoter-TSS (NM_001277291)	promoter-TSS (NM_001277291)	-65	NM_015394	7556	Hs.573983	NM_015394	ENSG00000256223	ZNF10	KOX1	zinc finger protein 10	protein-coding	0.142322	0.716418	
chunk0065_219_1	chr14	100313855	100314167	+	0	NA	Intergenic	Intergenic	6152	NR_029906	442910		NR_029906	ENSG00000198984	MIR345	MIRN345|hsa-mir-345|mir-345	microRNA 345	ncRNA	0.032051	0.645367	162(AAGGACAACGTGTACT,-,0.00),163(AGGACAACGTGTACTG,+,0.00)
chunk0175_310_1	chr6	166655202	166655650	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	-28188	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.015625	0.474388	
chunk0067_1_1	chr15	39887914	39888419	+	0	NA	intron (NM_001271854, intron 1 of 3)	MER34A1|LTR|ERV1	32726	NM_001271854	11245	Hs.37196	NM_007223	ENSG00000166073	GPR176	HB-954	G protein-coupled receptor 176	protein-coding	0.003960	0.420949	
chunk0176_414_1	chr7	19364145	19364538	+	0	NA	Intergenic	L1ME2|LINE|L1	-218920	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.007634	0.289340	
chunk0190_282_1	chr8	37757851	37758250	+	0	NA	TTS (NM_007175)	TTS (NM_007175)	-4533	NM_007198	11212	Hs.304792	NM_007198	ENSG00000147471	PLPBP	EPVB6D|PROSC	pyridoxal phosphate binding protein	protein-coding	0.005013	0.365000	202(AAGTACTATGTGTCCT,-,0.00),203(AGTACTATGTGTCCTA,+,0.00)
chunk0199_224_1	chr9	5324352	5324893	+	0	NA	Intergenic	Intergenic	15251	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.003697	0.300738	
chunk0031_198_1	chr10	125824082	125824595	+	0	NA	intron (NM_078468, intron 1 of 6)	intron (NM_078468, intron 1 of 6)	803	NM_016567	56647	Hs.370292	NM_016567	ENSG00000107949	BCCIP	TOK-1|TOK1	BRCA2 and CDKN1A interacting protein	protein-coding	0.015595	0.437743	284(AGGACTGAATGATCCT,+,0.00)
chunk0124_410_1	chr3	60490990	60491333	+	0	NA	intron (NM_001166243, intron 5 of 9)	intron (NM_001166243, intron 5 of 9)	126709	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.002915	0.363372	
chunk0066_174_1	chr15	32970963	32971163	+	0	NA	intron (NM_001103184, intron 3 of 16)	MIRb|SINE|MIR	96969	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.035000	0.487562	122(GGGAACGCTGTGTCCC,-,0.00),123(GGAACGCTGTGTCCCT,+,0.00)
chunk0018_131_1	chr1	218570468	218570922	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	128069	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.006608	0.373626	
chunk0060_378_1	chr14	52609570	52609769	+	0	NA	intron (NM_001099652, intron 3 of 6)	L1MA4|LINE|L1	56521	NM_001099652	283554	Hs.416214	NM_001099652	ENSG00000180998	GPR137C	TM7SF1L2	G protein-coupled receptor 137C	protein-coding	0.015075	0.550000	
chunk0007_167_1	chr1	80130699	80131020	+	0	NA	Intergenic	L2|LINE|L2	-404896	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.003115	0.360248	
chunk0121_249_1	chr3	22947656	22948333	+	0	NA	Intergenic	Intergenic	-255299	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.002954	0.386431	318(TGGAACACATTGCTCT,-,0.00),319(GGAACACATTGCTCTC,+,0.00)
chunk0194_286_1	chr8	87493576	87494293	+	0	NA	Intergenic	Intergenic	380134	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.008368	0.292479	
chunk0084_213_1	chr17	78198791	78199214	+	0	NA	intron (NM_001145526, intron 2 of 10)	L1ME4b|LINE|L1	11685	NR_027083	125061	Hs.558614	NM_001010982	ENSG00000183077	AFMID	FKF|KF|KFA	arylformamidase	protein-coding	0.023641	0.500000	184(TAGTACACACAGTTCC,-,0.00),185(AGTACACACAGTTCCA,+,0.00)
chunk0171_18_1	chr6	119959191	119959755	+	0	NA	Intergenic	L1ME4c|LINE|L1	-55706	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.000000	0.265487	
chunk0073_332_1	chr16	14501631	14501944	+	0	NA	intron (NM_002582, intron 21 of 23)	intron (NM_002582, intron 21 of 23)	128484	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.009585	0.528662	
chunk0039_170_1	chr11	99645974	99646461	+	0	NA	intron (NM_175566, intron 1 of 21)	intron (NM_175566, intron 1 of 21)	90072	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004107	0.362705	
chunk0010_327_1	chr1	118296218	118296746	+	0	NA	Intergenic	Intergenic	-111257	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.001894	0.347826	
chunk0014_251_1	chr1	180098526	180099020	+	0	NA	intron (NM_014810, intron 36 of 37)	intron (NM_014810, intron 36 of 37)	-56060	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.012146	0.383838	
chunk0159_7_1	chr5	136089664	136090208	+	0	NA	Intergenic	Intergenic	-9339	NR_030583	100126299		NR_030583	ENSG00000278815	VTRNA2-1	CBL-3|CBL3|MIR886|MIRN886|VTRNA2|hsa-mir-886|hvg-5|nc886|pre-miR-886|svtRNA2-1a	vault RNA 2-1	ncRNA	0.016544	0.453211	
chunk0004_430_1	chr1	52867438	52867888	+	0	NA	intron (NM_001004339, intron 7 of 13)	intron (NM_001004339, intron 7 of 13)	25152	NM_001004339	440590	Hs.658458	NM_001004339	ENSG00000203995	ZYG11A	ZYG11	zyg-11 family member A, cell cycle regulator	protein-coding	0.002222	0.359202	
chunk0017_77_1	chr1	205698690	205699509	+	0	NA	Intergenic	L2b|LINE|L2	-18597	NM_033102	85414	Hs.278695	NM_033102	ENSG00000158715	SLC45A3	IPCA-2|IPCA-6|IPCA-8|IPCA6|PCANAP2|PCANAP6|PCANAP8|PRST	solute carrier family 45 member 3	protein-coding	0.010989	0.430488	337(TAGAGCAGATTGTCCT,-,0.00),338(AGAGCAGATTGTCCTG,+,0.00)
chunk0108_261_1	chr2	234082211	234083003	+	0	NA	Intergenic	Intergenic	31905	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.013889	0.438840	
chunk0117_237_1	chr22	23003882	23004751	+	0	NA	Intergenic	L1MA5|LINE|L1	-66167	NM_002073	2781	Hs.584760	NM_002073	ENSG00000128266	GNAZ	gz-alpha	G protein subunit alpha z	protein-coding	0.001151	0.333333	
chunk0001_158_1	chr1	6295043	6295701	+	0	NA	intron (NM_181864, intron 6 of 8)	L1MB8|LINE|L1	-34397	NM_207370	387509	Hs.531581	NM_207370	ENSG00000158292	GPR153	PGR1	G protein-coupled receptor 153	protein-coding	0.024316	0.497724	262(CAGAACAGCACGTGCT,-,0.00),263(AGAACAGCACGTGCTG,+,0.00)
chunk0057_169_1	chr13	101921685	101922267	+	0	NA	intron (NM_175929, intron 1 of 4)	L2a|LINE|L2	-5331	NM_004115	2259	Hs.508616	NM_004115	ENSG00000102466	FGF14	FGF-14|FHF-4|FHF4|SCA27	fibroblast growth factor 14	protein-coding	0.003436	0.375643	
chunk0202_330_1	chr9	78539880	78541007	+	0	NA	Intergenic	Intergenic	243368	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.004437	0.395390	
chunk0191_185_1	chr8	51501362	51501770	+	0	NA	intron (NM_144651, intron 4 of 22)	intron (NM_144651, intron 4 of 22)	307879	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.007353	0.447433	
chunk0033_351_1	chr11	22948637	22949061	+	0	NA	Intergenic	Intergenic	-88423	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.009434	0.352941	
chunk0168_225_1	chr6	86461966	86462251	+	0	NA	Intergenic	Intergenic	-475198	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.007018	0.409091	
chunk0207_312_1	chr9	133881834	133882379	+	0	NA	intron (NM_001134398, intron 2 of 29)	L2b|LINE|L2	110218	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.038532	0.611722	
chunk0153_231_1	chr5	72185715	72186302	+	0	NA	intron (NM_005909, intron 3 of 6)	intron (NM_005909, intron 3 of 6)	16541	NR_039967	100616377		NR_039967	ENSG00000264099	MIR4803	-	microRNA 4803	ncRNA	0.011925	0.489796	239(GTGCACAGAGAGTTCC,-,0.00),240(TGCACAGAGAGTTCCT,+,0.00)
chunk0073_274_1	chr16	12439797	12440089	+	0	NA	intron (NM_032167, intron 18 of 20)	intron (NM_032167, intron 18 of 20)	-280378	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.020548	0.580205	
chunk0172_378_1	chr6	139375065	139375799	+	0	NA	promoter-TSS (NM_006079)	promoter-TSS (NM_006079)	-782	NM_006079	10370	Hs.82071	NM_006079	ENSG00000164442	CITED2	ASD8|MRG-1|MRG1|P35SRJ|VSD2	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2	protein-coding	0.058583	0.565986	
chunk0047_449_1	chr12	76568789	76569356	+	0	NA	Intergenic	Intergenic	-9263	NM_020841	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.005291	0.325704	
chunk0040_29_1	chr11	110283854	110284074	+	0	NA	intron (NM_001260496, intron 1 of 7)	intron (NM_001260496, intron 1 of 7)	12748	NM_001260496	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.004545	0.262443	
chunk0168_183_1	chr6	84917718	84917972	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-153609	NM_001080508	9096	Hs.251830	NM_001080508	ENSG00000112837	TBX18	CAKUT2	T-box transcription factor 18	protein-coding	0.007874	0.392157	
chunk0191_223_1	chr8	52712487	52712753	+	0	NA	intron (NM_014781, intron 1 of 23)	intron (NM_014781, intron 1 of 23)	1846	NM_014781	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.011278	0.307116	
chunk0137_180_1	chr4	17512847	17513113	+	0	NA	promoter-TSS (NM_000320)	promoter-TSS (NM_000320)	-746	NM_000320	5860	Hs.75438	NM_000320	ENSG00000151552	QDPR	DHPR|HDHPR|PKU2|SDR33C1	quinoid dihydropteridine reductase	protein-coding	0.000000	0.400749	
chunk0204_60_1	chr9	93398872	93399071	+	0	NA	Intergenic	Intergenic	-52557	NM_001098808	445577	Hs.575636	NM_001098808	ENSG00000204352	C9orf129	bA165J3.3	chromosome 9 open reading frame 129	protein-coding	0.010050	0.580000	
chunk0180_131_1	chr7	56009762	56010223	+	0	NA	Intergenic	Intergenic	41583	NM_004577	5723	Hs.512656	NM_004577	ENSG00000146733	PSPH	PSP|PSPHD	phosphoserine phosphatase	protein-coding	0.015184	0.465368	
chunk0109_186_1	chr20	4936531	4937114	+	0	NA	intron (NM_005116, intron 2 of 16)	intron (NM_005116, intron 2 of 16)	64677	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.017153	0.506849	179(AGGAACACACAGTTCC,-,0.00),180(GGAACACACAGTTCCA,+,0.00)
chunk0195_54_1	chr8	93655384	93655863	+	0	NA	intron (NR_033858, intron 5 of 10)	L2a|LINE|L2	44810	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.010438	0.381250	
chunk0051_290_1	chr12	118342021	118342663	+	0	NA	intron (NM_016281, intron 1 of 20)	intron (NM_016281, intron 1 of 20)	30603	NM_016281	51347	Hs.644420	NM_016281	ENSG00000135090	TAOK3	DPK|JIK|MAP3K18|hKFC-A	TAO kinase 3	protein-coding	0.003115	0.318818	
chunk0155_384_1	chr5	98355780	98356064	+	0	NA	Intergenic	Charlie1b|DNA|hAT-Charlie	-413373	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.000000	0.315789	
chunk0122_31_1	chr3	27908917	27909446	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-75045	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.005671	0.422642	
chunk0146_131_1	chr4	159175705	159176437	+	0	NA	Intergenic	Intergenic	-47177	NR_037459	100500881		NR_037459	ENSG00000264105	MIR3688-1	MIR3688|mir-3688-1	microRNA 3688-1	ncRNA	0.012295	0.459754	554(TTGAACATGGTGTGCT,-,0.00),555(TGAACATGGTGTGCTT,+,0.00)
chunk0120_91_1	chr3	4252085	4252501	+	0	NA	Intergenic	Intergenic	-51011	NM_006515	6419	Hs.475300	NM_006515	ENSG00000170364	SETMAR	METNASE|Mar1	SET domain and mariner transposase fusion gene	protein-coding	0.007212	0.369305	
chunk0062_431_1	chr14	75297411	75297719	+	0	NA	Intergenic	Intergenic	3161	NR_038421	731223	Hs.534624	NR_038421		LINC01220	-	long intergenic non-protein coding RNA 1220	ncRNA	0.009740	0.446602	48(CAGAACTCTTAGTTCT,-,0.00),49(AGAACTCTTAGTTCTT,+,0.00)
chunk0033_249_1	chr11	18223822	18224384	+	0	NA	Intergenic	Intergenic	12734	NM_006512	6291	Hs.1955	NM_006512	ENSG00000148965	SAA4	C-SAA|CSAA	serum amyloid A4, constitutive	protein-coding	0.003559	0.374778	
chunk0185_279_1	chr7	130930348	130930873	+	0	NA	Intergenic	Intergenic	17146	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.013333	0.423954	
chunk0098_446_1	chr2	82224455	82224892	+	0	NA	Intergenic	Intergenic	-632130	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.006865	0.347032	
chunk0190_354_1	chr8	39673004	39673222	+	0	NA	intron (NM_014237, intron 14 of 19)	ERV3-16A3_I-int|LTR|ERVL	88545	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.004587	0.356164	
chunk0036_119_1	chr11	61626727	61627087	+	0	NA	intron (NR_002775, intron 2 of 4)	intron (NR_002775, intron 2 of 4)	11871	NR_002775	113157	Hs.502733	NR_002775	ENSG00000243742	RPLP0P2	RPLP0L2|RPLP0_3_1146	ribosomal protein lateral stalk subunit P0 pseudogene 2	pseudo	0.019444	0.590028	
chunk0115_205_1	chr21	26637343	26637858	+	0	NA	Intergenic	L1ME3A|LINE|L1	-64338	NM_052954	116159	Hs.37445	NM_052954	ENSG00000166265	CYYR1	C21orf95	cysteine and tyrosine rich 1	protein-coding	0.007767	0.364341	
chunk0020_34_1	chr1	232149536	232149772	+	0	NA	Intergenic	Intergenic	223820	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.008475	0.354430	
chunk0136_122_1	chr4	3662873	3663072	+	0	NA	Intergenic	Intergenic	14883	NR_034136	100133461	Hs.554274	NR_034136	ENSG00000250632	LINC02171	-	long intergenic non-protein coding RNA 2171	ncRNA	0.020101	0.535000	
chunk0181_48_1	chr7	79929061	79929368	+	0	NA	Intergenic	L1PA11|LINE|L1	-205610	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.009772	0.373377	
chunk0205_171_1	chr9	108789484	108790312	+	0	NA	Intergenic	L2a|LINE|L2	66097	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.004831	0.408926	484(TGGAACACTCTGAACC,-,0.00),485(GGAACACTCTGAACCC,+,0.00)
chunk0157_422_1	chr5	124676347	124676757	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	68560	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.009756	0.323601	
chunk0195_120_1	chr8	94912973	94913286	+	0	NA	Intergenic	Intergenic	-17875	NM_057749	9134	Hs.521693	NM_004702	ENSG00000175305	CCNE2	CYCE2	cyclin E2	protein-coding	0.003195	0.407643	
chunk0106_40_1	chr2	196192607	196192837	+	0	NA	Intergenic	Intergenic	-21110	NM_004226	9262	Hs.88297	NM_004226	ENSG00000081320	STK17B	DRAK2	serine/threonine kinase 17b	protein-coding	0.004348	0.376623	
chunk0068_394_1	chr15	58627802	58628056	+	0	NA	intron (NM_001110, intron 9 of 15)	intron (NM_001110, intron 9 of 15)	65678	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.003937	0.341176	
chunk0086_29_1	chr18	12497887	12498163	+	0	NA	intron (NM_001128627, intron 6 of 15)	intron (NM_001128627, intron 6 of 15)	77836	NM_001142406	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.007246	0.422383	
chunk0055_193_1	chr13	61783554	61783838	+	0	NA	Intergenic	HAL1b|LINE|L1	245852	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.000000	0.361404	
chunk0190_428_1	chr8	41561997	41562759	+	0	NA	intron (NR_125824, intron 1 of 2)	intron (NR_125824, intron 1 of 2)	-15810	NM_178819	137964	Hs.355753	NM_178819	ENSG00000158669	GPAT4	1-AGPAT 6|AGPAT6|LPAAT-zeta|LPAATZ|TSARG7	glycerol-3-phosphate acyltransferase 4	protein-coding	0.009186	0.401048	
chunk0158_255_1	chr5	130975175	130975510	+	0	NA	Intergenic	Intergenic	190006	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.008955	0.375000	
chunk0121_351_1	chr3	24687243	24687442	+	0	NA	Intergenic	Tigger10|DNA|TcMar-Tigger	-165907	NR_039955									0.010050	0.350000	
chunk0006_223_1	chr1	68450444	68450799	+	0	NA	promoter-TSS (NM_000329)	promoter-TSS (NM_000329)	-662	NM_000329	6121	Hs.2133	NM_000329	ENSG00000116745	RPE65	BCO3|LCA2|RP20|mRPE65|p63|rd12|sRPE65	retinoid isomerohydrolase RPE65	protein-coding	0.000000	0.401685	50(AAGCACATTGTGCACC,-,0.00),51(AGCACATTGTGCACCT,+,0.00)
chunk0141_399_1	chr4	88509737	88509952	+	0	NA	Intergenic	Intergenic	13957	NM_001042616	84992	Hs.26136	NM_001042616	ENSG00000255072	PIGY	HPMRS6|PIG-Y	phosphatidylinositol glycan anchor biosynthesis class Y	protein-coding	0.004651	0.490741	
chunk0203_182_1	chr9	86349422	86349621	+	0	NA	intron (NM_024617, intron 2 of 26)	intron (NM_024617, intron 2 of 26)	4966	NM_024617	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.005025	0.390000	
chunk0037_378_1	chr11	78497959	78498367	+	0	NA	intron (NM_024678, intron 6 of 13)	L2b|LINE|L2	-35013	NR_120566	101928896	Hs.659055	NR_120566	ENSG00000255084	LOC101928896	-	uncharacterized LOC101928896	ncRNA	0.004902	0.398533	
chunk0066_53_1	chr15	28208595	28209299	+	0	NA	intron (NM_004667, intron 44 of 92)	intron (NM_004667, intron 44 of 92)	-109635	NM_001300984	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.011364	0.424113	
chunk0011_179_1	chr1	148334677	148334876	+	0	NA	promoter-TSS (NR_049810)	promoter-TSS (NR_049810)	-222	NR_049810	100847044		NR_049810	ENSG00000283676	MIR5087	-	microRNA 5087	ncRNA	0.060302	0.560000	
chunk0006_185_1	chr1	67405111	67405351	+	0	NA	Intergenic	Intergenic	25209	NM_001018067	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.008333	0.344398	
chunk0072_180_1	chr15	94107739	94107995	+	0	NA	promoter-TSS (NR_120320)	promoter-TSS (NR_120320)	71	NR_120320	101927112	Hs.134687	NR_120320	ENSG00000259724	LINC01581	-	long intergenic non-protein coding RNA 1581	ncRNA	0.007812	0.470817	
chunk0031_356_1	chr10	129950625	129950974	+	0	NA	intron (NM_001005463, intron 6 of 15)	intron (NM_001005463, intron 6 of 15)	13028	NM_001005463	253738	Hs.591374	NM_001005463	ENSG00000108001	EBF3	COE3|EBF-3|HADDS|O/E-2|OE-2	EBF transcription factor 3	protein-coding	0.002865	0.377143	
chunk0081_105_1	chr17	39835519	39835878	+	0	NA	intron (NM_012481, intron 1 of 7)	intron (NM_012481, intron 1 of 7)	28490	NM_001284515	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.019499	0.527778	
chunk0192_400_1	chr8	68886765	68887615	+	0	NA	Intergenic	L1ME1|LINE|L1	217000	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.002353	0.319624	592(AGGAACATAATGTTTA,-,0.00),593(GGAACATAATGTTTAT,+,0.00)
chunk0051_76_1	chr12	113677122	113677321	+	0	NA	Intergenic	Intergenic	96462	NR_110025	100506465	Hs.211461	NR_110025	ENSG00000249550	LINC01234	LCAL84|onco-lncRNA-32	long intergenic non-protein coding RNA 1234	ncRNA	0.010050	0.490000	
chunk0151_236_1	chr5	51182590	51183008	+	0	NA	Intergenic	Intergenic	-200325	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.004785	0.326969	231(AAGAACAGTAAGTGCC,-,0.00),232(AGAACAGTAAGTGCCT,+,0.00)
chunk0133_310_1	chr3	172354678	172355066	+	0	NA	intron (NM_022763, intron 22 of 25)	(T)n|Simple_repeat|Simple_repeat	93584	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.002577	0.341902	96(CAGATCATGATGTTCT,-,0.00),97(AGATCATGATGTTCTA,+,0.00)
chunk0096_330_1	chr2	34985765	34986148	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	308399	NR_126404	104355288	Hs.624529	NR_126404	ENSG00000228262	LINC01320	-	long intergenic non-protein coding RNA 1320	ncRNA	0.002611	0.333333	
chunk0128_389_1	chr3	113906741	113907013	+	0	NA	intron (NM_001172105, intron 3 of 12)	Tigger3b|DNA|TcMar-Tigger	9406	NM_001172105	54762	Hs.24583	NM_017577	ENSG00000178075	GRAMD1C	-	GRAM domain containing 1C	protein-coding	0.007353	0.395604	
chunk0062_368_1	chr14	73994748	73994947	+	0	NA	intron (NM_001249, intron 3 of 15)	L2a|LINE|L2	24476	NM_001249	957	Hs.655070	NM_001249	ENSG00000187097	ENTPD5	CD39L4|NTPDase-5|PCPH	ectonucleoside triphosphate diphosphohydrolase 5 (inactive)	protein-coding	0.010050	0.360000	
chunk0163_264_1	chr6	13166540	13167514	+	0	NA	intron (NM_030948, intron 6 of 14)	intron (NM_030948, intron 6 of 14)	128559	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.011294	0.397949	
chunk0097_261_1	chr2	54466872	54467341	+	0	NA	intron (NM_003128, intron 1 of 35)	intron (NM_003128, intron 1 of 35)	10789	NM_003128	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.008529	0.395745	
chunk0035_332_1	chr11	47766766	47767023	+	0	NA	intron (NM_015308, intron 1 of 16)	CpG	547	NM_015308	23360	Hs.6834	NM_015308	ENSG00000109920	FNBP4	FBP30	formin binding protein 4	protein-coding	0.101167	0.720930	
chunk0155_252_1	chr5	95748126	95748426	+	0	NA	intron (NM_014899, intron 3 of 11)	intron (NM_014899, intron 3 of 11)	17130	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.003333	0.365449	
chunk0012_326_1	chr1	162475540	162475938	+	0	NA	Intergenic	L1MA3|LINE|L1	-21435	NM_001184763	127933	Hs.127310	NM_144624	ENSG00000152332	UHMK1	KIS|KIST|P-CIP2	U2AF homology motif kinase 1	protein-coding	0.005025	0.498747	59(AGGTACACCCTGGGCC,-,0.00)
chunk0169_99_1	chr6	100413383	100413956	+	0	NA	intron (NM_005068, intron 9 of 10)	intron (NM_005068, intron 9 of 10)	50006	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.003490	0.337979	
chunk0091_63_1	chr19	4915205	4915404	+	0	NA	intron (NM_001048201, intron 2 of 16)	intron (NM_001048201, intron 2 of 16)	4937	NM_001290052	29128	Hs.108106	NM_013282	ENSG00000276043	UHRF1	ICBP90|Np95|RNF106|TDRD22|hNP95|hUHRF1|huNp95	ubiquitin like with PHD and ring finger domains 1	protein-coding	0.040201	0.645000	
chunk0045_321_1	chr12	50786779	50787455	+	0	NA	intron (NM_005171, intron 2 of 6)	L1MCc|LINE|L1	23111	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.001479	0.418021	
chunk0141_77_1	chr4	78200936	78201323	+	0	NA	intron (NM_025074, intron 2 of 73)	intron (NM_025074, intron 2 of 73)	143559	NM_025074	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.002584	0.358247	
chunk0118_202_1	chr22	31636028	31636267	+	0	NA	Intergenic	Intergenic	-5323	NM_014338	23761	Hs.420559	NM_014338	ENSG00000241878	PISD	DJ858B16|PSD|PSDC|PSSC|dJ858B16.2	phosphatidylserine decarboxylase	protein-coding	0.033473	0.537500	
chunk0030_1_1	chr10	110754777	110755047	+	0	NA	intron (NM_001134363, intron 1 of 13)	L1MEd|LINE|L1	110515	NM_001134363	282996	Hs.116630	NM_001134363	ENSG00000203867	RBM20	-	RNA binding motif protein 20	protein-coding	0.011111	0.428044	
chunk0015_363_1	chr1	190404212	190404741	+	0	NA	intron (NM_199051, intron 2 of 7)	intron (NM_199051, intron 2 of 7)	73153	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.009452	0.298113	
chunk0180_318_1	chr7	71887763	71888015	+	0	NA	intron (NM_001017440, intron 4 of 5)	intron (NM_001017440, intron 4 of 5)	449334	NM_001017440	83698	Hs.592750	NM_031468	ENSG00000183166	CALN1	CABP8	calneuron 1	protein-coding	0.023810	0.501976	
chunk0204_43_1	chr9	92757314	92757635	+	0	NA	intron (NM_001003800, intron 1 of 6)	L1MC5|LINE|L1	7327	NM_001003800	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.009346	0.409938	
chunk0079_39_1	chr17	10293637	10294035	+	0	NA	Intergenic	MER63B|DNA|hAT-Blackjack	79169	NM_003802	8735	Hs.711142	NM_003802	ENSG00000006788	MYH13	MyHC-IIL|MyHC-eo	myosin heavy chain 13	protein-coding	0.007538	0.406015	
chunk0035_274_1	chr11	46554048	46554835	+	0	NA	intron (NM_001300731, intron 1 of 16)	intron (NM_001300731, intron 1 of 16)	36923	NM_017749	55626	Hs.654644	NM_017749	ENSG00000110497	AMBRA1	DCAF3|WDR94	autophagy and beclin 1 regulator 1	protein-coding	0.002541	0.365482	
chunk0075_351_1	chr16	55711966	55712504	+	0	NA	Intergenic	Intergenic	-12690	NR_033740	390732	Hs.554599	NR_033740		CES1P2	-	carboxylesterase 1 pseudogene 2	pseudo	0.011152	0.513915	
chunk0115_84_1	chr21	22202492	22202980	+	0	NA	Intergenic	Intergenic	104119	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.002049	0.339468	
chunk0080_202_1	chr17	29255278	29255493	+	0	NA	TTS (NM_020772)	TTS (NM_020772)	8528	NM_005208	1411	Hs.46275	NM_005208	ENSG00000108255	CRYBA1	CRYB1|CTRCT10	crystallin beta A1	protein-coding	0.009302	0.356481	
chunk0124_160_1	chr3	55010014	55010238	+	0	NA	intron (NM_018398, intron 34 of 37)	MIRb|SINE|MIR	-43038	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.004464	0.391111	
chunk0176_164_1	chr7	13422325	13422531	+	0	NA	Intergenic	L1M4|LINE|L1	564086	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.019417	0.410628	
chunk0002_33_1	chr1	12475795	12476527	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-31085	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.010929	0.403820	
chunk0164_273_1	chr6	23728848	23729047	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-397239	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.010050	0.460000	
chunk0183_244_1	chr7	107131304	107131523	+	0	NA	intron (NM_002736, intron 4 of 10)	intron (NM_002736, intron 4 of 10)	-37548	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.000000	0.281818	
chunk0170_368_1	chr6	116895651	116896054	+	0	NA	intron (NM_173560, intron 6 of 18)	intron (NM_173560, intron 6 of 18)	18639	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.002481	0.386139	
chunk0082_348_1	chr17	59893004	59893233	+	0	NA	promoter-TSS (NM_001193612)	promoter-TSS (NM_001193612)	72	NM_003161	6198	Hs.463642	NM_003161	ENSG00000108443	RPS6KB1	PS6K|S6K|S6K-beta-1|S6K1|STK14A|p70 S6KA|p70(S6K)-alpha|p70-S6K|p70-alpha	ribosomal protein S6 kinase B1	protein-coding	0.078603	0.639130	
chunk0193_139_1	chr8	74488371	74488864	+	0	NA	Intergenic	Intergenic	-59926	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.000000	0.364372	
chunk0156_348_1	chr5	111948687	111949075	+	0	NA	intron (NR_046678, intron 2 of 3)	intron (NR_046678, intron 2 of 3)	28050	NM_001142474	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.000000	0.352185	
chunk0150_144_1	chr5	33632534	33632733	+	0	NA	intron (NM_030955, intron 12 of 23)	intron (NM_030955, intron 12 of 23)	191857	NR_047676	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.015075	0.440000	
chunk0134_456_1	chr3	183998407	183998941	+	0	NA	intron (NM_001023587, intron 2 of 6)	A-rich|Low_complexity|Low_complexity	-7664	NR_046570	100873982	Hs.570696	NR_046570	ENSG00000223882	ABCC5-AS1	-	ABCC5 antisense RNA 1	ncRNA	0.009363	0.400000	
chunk0053_102_1	chr13	28750354	28750934	+	0	NA	Intergenic	Intergenic	-31631	NM_001135919	283537	Hs.117167	NM_181785	ENSG00000139508	SLC46A3	FKSG16	solute carrier family 46 member 3	protein-coding	0.006897	0.430293	
chunk0123_198_1	chr3	44501660	44502246	+	0	NA	intron (NM_001287349, intron 3 of 4)	MLT1M|LTR|ERVL-MaLR	8687	NM_001287349	285346	Hs.648974	NM_001287349	ENSG00000178917	ZNF852	-	zinc finger protein 852	protein-coding	0.010239	0.475298	316(GGGAACAGGAAGTACA,-,0.00)
chunk0052_114_1	chr13	23018088	23018407	+	0	NA	Intergenic	Intergenic	-120066	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.009404	0.409375	
chunk0019_257_1	chr1	227865158	227865814	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	49769	NM_183062	339501	Hs.97604	NM_183062	ENSG00000185888	PRSS38	MPN2	serine protease 38	protein-coding	0.001524	0.455099	333(GAGAACTTGGTGTTCC,-,0.00),334(AGAACTTGGTGTTCCT,+,0.00)
chunk0127_437_1	chr3	103182232	103182582	+	0	NA	Intergenic	L1M4c|LINE|L1	341709	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.002857	0.273504	
chunk0092_393_1	chr19	36686421	36686621	+	0	NA	intron (NR_110708, intron 2 of 3)	intron (NR_110708, intron 2 of 3)	928	NR_110708	101927621	Hs.125653	NR_110707	ENSG00000225975	LINC01534	-	long intergenic non-protein coding RNA 1534	ncRNA	0.010000	0.492537	
chunk0170_311_1	chr6	116059480	116060725	+	0	NA	exon (NM_002031, exon 1 of 8)	exon (NM_002031, exon 1 of 8)	656	NM_002031	2444	Hs.89426	NM_002031	ENSG00000111816	FRK	GTK|PTK5|RAK	fyn related Src family tyrosine kinase	protein-coding	0.010442	0.439807	
chunk0081_62_1	chr17	38798907	38799106	+	0	NA	intron (NM_003559, intron 1 of 9)	CpG	899	NM_003559	8396	Hs.260603	NM_003559	ENSG00000276293	PIP4K2B	PI5P4KB|PIP5K2B|PIP5KIIB|PIP5KIIbeta|PIP5P4KB	phosphatidylinositol-5-phosphate 4-kinase type 2 beta	protein-coding	0.055276	0.655000	
chunk0085_358_1	chr18	9285683	9286145	+	0	NA	TTS (NM_001083625)	TTS (NM_001083625)	-48853	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.012987	0.406048	
chunk0048_323_1	chr12	83558200	83558399	+	0	NA	Intergenic	Intergenic	871144	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.005025	0.275000	
chunk0180_361_1	chr7	73827584	73827963	+	0	NA	Intergenic	Intergenic	-3090	NM_001305	1364	Hs.647036	NM_001305	ENSG00000189143	CLDN4	CPE-R|CPER|CPETR|CPETR1|WBSCR8|hCPE-R	claudin 4	protein-coding	0.018470	0.573684	
chunk0136_281_1	chr3	194817066	194817610	+	0	NA	Intergenic	L3|LINE|CR1	108917	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.011029	0.460550	
chunk0072_341_1	chr15	99385933	99386292	+	0	NA	3' UTR (NM_144598, exon 10 of 10)	3' UTR (NM_144598, exon 10 of 10)	128587	NR_073383	7190	Hs.656611	NR_073383	ENSG00000259706	HSP90B2P	GRP94P1|GRP94b|HSP|HSPCP2|TRA1P1|TRAP1	heat shock protein 90 beta family member 2, pseudogene	pseudo	0.008357	0.469444	
chunk0061_35_1	chr14	55938587	55938909	+	0	NA	Intergenic	Intergenic	-142074	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.021739	0.498452	
chunk0112_85_1	chr20	37990380	37991055	+	0	NA	intron (NM_014657, intron 8 of 8)	intron (NM_014657, intron 8 of 8)	42751	NM_014657	9675	Hs.655481	NM_014657	ENSG00000101407	TTI1	KIAA0406|smg-10	TELO2 interacting protein 1	protein-coding	0.016296	0.445266	407(GAGAACATTCTGCTCC,-,0.00),408(AGAACATTCTGCTCCC,+,0.00)
chunk0152_320_1	chr5	62024233	62024754	+	0	NA	Intergenic	L1P2|LINE|L1	-281669	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.005758	0.367816	
chunk0133_430_1	chr3	174905937	174906382	+	0	NA	intron (NM_207015, intron 1 of 13)	L4_C_Mam|LINE|RTE-X	46838	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.004494	0.325112	
chunk0086_320_1	chr18	24263020	24263581	+	0	NA	intron (NM_001242508, intron 3 of 15)	MIRb|SINE|MIR	8932	NM_018030	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.005348	0.343416	285(AAGTACGTGCTGTACT,-,0.00)
chunk0085_424_1	chr18	10597693	10597892	+	0	NA	Intergenic	Intergenic	-64141	NR_110777	101927410	Hs.436902	NR_110777	ENSG00000260779	LOC101927410	-	uncharacterized LOC101927410	ncRNA	0.010050	0.320000	
chunk0026_286_1	chr10	67521285	67521484	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	-117974	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.000000	0.335000	
chunk0117_145_1	chr22	19605592	19605794	+	0	NA	Intergenic	Intergenic	-38854	NR_024381	150185	Hs.719752	NR_024381		LINC00895	-	long intergenic non-protein coding RNA 895	ncRNA	0.029703	0.556650	
chunk0141_92_1	chr4	79044110	79044387	+	0	NA	intron (NR_038342, intron 2 of 5)	intron (NR_038342, intron 2 of 5)	72500	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.003610	0.438849	
chunk0066_262_1	chr15	34850788	34851133	+	0	NA	Intergenic	MIR3|SINE|MIR	-55234	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.000000	0.355491	
chunk0171_95_1	chr6	121959780	121959979	+	0	NA	Intergenic	Intergenic	-439672	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.005025	0.360000	
chunk0202_160_1	chr9	73738718	73739299	+	0	NA	Intergenic	L1MC1|LINE|L1	587277	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.003442	0.340206	
chunk0104_351_1	chr2	179932694	179933213	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-71448	NM_152520	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.005780	0.405769	
chunk0097_218_1	chr2	51637592	51637978	+	0	NA	Intergenic	Intergenic	-605249	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.002591	0.307494	
chunk0150_308_1	chr5	37740026	37740329	+	0	NA	intron (NM_018034, intron 17 of 17)	intron (NM_018034, intron 17 of 17)	94645	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.006601	0.322368	
chunk0156_104_1	chr5	105261181	105261782	+	0	NA	Intergenic	MER90a|LTR|ERV1	162007	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.006656	0.342193	205(AGGAACAGCTAGTTCT,-,0.00),206(GGAACAGCTAGTTCTC,+,0.00),255(TAGGACTTTATGTTCC,-,0.00),256(AGGACTTTATGTTCCC,+,0.00)
chunk0152_242_1	chr5	60752840	60753474	+	0	NA	3' UTR (NM_001104558, exon 8 of 8)	3' UTR (NM_001104558, exon 8 of 8)	-52991	NM_018369	55789	Hs.482233	NM_018369	ENSG00000035499	DEPDC1B	BRCC3|XTP1	DEP domain containing 1B	protein-coding	0.003155	0.311811	
chunk0062_311_1	chr14	73137060	73137872	+	0	NA	intron (NM_007318, intron 1 of 11)	intron (NM_007318, intron 1 of 11)	1031	NM_007318	5663	Hs.3260	NM_000021	ENSG00000080815	PSEN1	ACNINV3|AD3|FAD|PS-1|PS1|S182	presenilin 1	protein-coding	0.020936	0.504305	
chunk0086_242_1	chr18	22983099	22983514	+	0	NA	intron (NM_002894, intron 7 of 18)	intron (NM_002894, intron 7 of 18)	49430	NM_203291	5932	Hs.546282	NM_002894	ENSG00000101773	RBBP8	COM1|CTIP|JWDS|RIM|SAE2|SCKL2	RB binding protein 8, endonuclease	protein-coding	0.007229	0.298077	
chunk0082_104_1	chr17	54721127	54721350	+	0	NA	Intergenic	Intergenic	-179453	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.000000	0.316964	
chunk0209_1_1	chrX	34906348	34906834	+	0	NA	Intergenic	Intergenic	-36205	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.002058	0.365503	
chunk0078_353_1	chr16	86869316	86869662	+	0	NA	Intergenic	Intergenic	-188295	NR_126008	440390	Hs.513789	NR_126008	ENSG00000232190	LINC02181	-	long intergenic non-protein coding RNA 2181	ncRNA	0.017341	0.628242	
chunk0047_296_1	chr12	73629337	73630023	+	0	NA	Intergenic	Intergenic	470490	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.004373	0.298399	
chunk0007_337_1	chr1	84779159	84779622	+	0	NA	Intergenic	Intergenic	-88833	NM_001166293	117178	Hs.22587	NM_014021	ENSG00000117155	SSX2IP	ADIP|hMsd1	SSX family member 2 interacting protein	protein-coding	0.015119	0.482759	
chunk0038_415_1	chr11	94183902	94184182	+	0	NA	Intergenic	Intergenic	55114	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.021429	0.498221	228(GGGAACTGCTTGTCCA,-,0.00),259(CAGGGCAGTTTGTGCC,-,0.00),260(AGGGCAGTTTGTGCCT,+,0.00)
chunk0083_112_1	chr17	64739890	64740089	+	0	NA	Intergenic	Intergenic	-40770	NR_106728	102464831		NR_106728	ENSG00000278581	MIR6080	hsa-mir-6080	microRNA 6080	ncRNA	0.010050	0.530000	
chunk0194_61_1	chr8	82390108	82390836	+	0	NA	Intergenic	Intergenic	-548186	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.002747	0.314129	
chunk0144_217_1	chr4	134426602	134427524	+	0	NA	Intergenic	Intergenic	-225315	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.002169	0.351029	70(ATGTACAAGGTGTACT,-,0.00),71(TGTACAAGGTGTACTT,+,0.00)
chunk0018_361_1	chr1	221727315	221727699	+	0	NA	intron (NR_111940, intron 1 of 2)	MIR3|SINE|MIR	9393	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.000000	0.353247	206(GTAACACCATGTTCTT,+,0.00)
chunk0087_409_1	chr18	42089699	42090577	+	0	NA	Intergenic	Intergenic	-96530	NR_046456	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.004556	0.294653	
chunk0134_391_1	chr3	182941955	182942395	+	0	NA	3' UTR (NM_020640, exon 7 of 7)	3' UTR (NM_020640, exon 7 of 7)	38426	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.002273	0.287982	
chunk0185_130_1	chr7	126839422	126839914	+	0	NA	intron (NR_028041, intron 5 of 10)	intron (NR_028041, intron 5 of 10)	218516	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.006098	0.397566	
chunk0087_254_1	chr18	36950928	36951554	+	0	NA	intron (NM_020776, intron 5 of 9)	intron (NM_020776, intron 5 of 9)	-122025	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.003195	0.368421	
chunk0058_191_1	chr14	24273595	24273954	+	0	NA	Intergenic	MIR|SINE|MIR	-2147	NM_182836	5875	Hs.377992	NM_004581	ENSG00000100949	RABGGTA	PTAR3	Rab geranylgeranyltransferase subunit alpha	protein-coding	0.002786	0.422222	
chunk0211_85_1	chrX	110146085	110146615	+	0	NA	intron (NM_032227, intron 5 of 6)	intron (NM_032227, intron 5 of 6)	64232	NR_039774	100616491		NR_039774	ENSG00000265584	MIR3978	-	microRNA 3978	ncRNA	0.005660	0.451977	
chunk0208_407_1	chrX	29392228	29392522	+	0	NA	intron (NM_014271, intron 3 of 10)	intron (NM_014271, intron 3 of 10)	-181903	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.013605	0.383051	
chunk0033_124_1	chr11	14619868	14620665	+	0	NA	intron (NM_148976, intron 1 of 10)	LFSINE_Vert|SINE|tRNA	23368	NM_148976	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.005019	0.377193	
chunk0100_44_1	chr2	105729606	105729805	+	0	NA	Intergenic	Intergenic	-15358	NM_001004722	8440	Hs.529244	NM_003581	ENSG00000071051	NCK2	GRB4|NCKbeta	NCK adaptor protein 2	protein-coding	0.000000	0.340000	
chunk0208_173_1	chrX	16859383	16859702	+	0	NA	intron (NM_002893, intron 3 of 11)	intron (NM_002893, intron 3 of 11)	10313	NM_001198719	5931	Hs.495755	NM_002893	ENSG00000102054	RBBP7	RbAp46	RB binding protein 7, chromatin remodeling factor	protein-coding	0.009404	0.356250	
chunk0107_299_1	chr2	219083675	219083888	+	0	NA	intron (NM_024782, intron 5 of 7)	intron (NM_024782, intron 5 of 7)	-23265	NM_002181	3549	Hs.654504	NM_002181	ENSG00000163501	IHH	BDA1|HHG2	Indian hedgehog signaling molecule	protein-coding	0.004695	0.406542	
chunk0180_438_1	chr7	76586464	76586834	+	0	NA	intron (NR_029411, intron 2 of 2)	MER57E1|LTR|ERV1	37308	NR_029411	100133091	Hs.712837	NR_029411	ENSG00000205485	LOC100133091	-	uncharacterized LOC100133091	ncRNA	0.008108	0.423181	
chunk0054_216_1	chr13	45340056	45340824	+	0	NA	promoter-TSS (NR_024458)	promoter-TSS (NR_024458)	844	NM_001286273	7178	Hs.374596	NM_003295	ENSG00000133112	TPT1	HRF|TCTP|p02|p23	tumor protein, translationally-controlled 1	protein-coding	0.062500	0.542263	
chunk0127_317_1	chr3	99901480	99901679	+	0	NA	intron (NM_001042459, intron 4 of 4)	intron (NM_001042459, intron 4 of 4)	-25376	NM_001282793	11259	Hs.104672	NM_014890	ENSG00000168386	FILIP1L	DOC-1|DOC1|GIP130|GIP90	filamin A interacting protein 1 like	protein-coding	0.015075	0.350000	
chunk0026_30_1	chr10	60719505	60720203	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	13672	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.001433	0.288984	
chunk0157_297_1	chr5	120985824	120986431	+	0	NA	Intergenic	AluSz6|SINE|Alu	-336423	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.009885	0.338816	337(GGGGACAGAGTGAGCC,-,0.00),338(GGGACAGAGTGAGCCT,+,0.00)
chunk0132_109_1	chr3	155854409	155854753	+	0	NA	promoter-TSS (NM_004733)	promoter-TSS (NM_004733)	-122	NM_001190992	9197	Hs.478031	NM_004733	ENSG00000169359	SLC33A1	ACATN|AT-1|AT1|CCHLND|SPG42	solute carrier family 33 member 1	protein-coding	0.072674	0.617391	
chunk0031_187_1	chr10	125685042	125685360	+	0	NA	intron (NR_033848, intron 1 of 4)	intron (NR_033848, intron 1 of 4)	1958	NR_033848	283038	Hs.144911	NR_033848	ENSG00000228021	LOC283038	-	uncharacterized LOC283038	ncRNA	0.015723	0.410658	
chunk0169_208_1	chr6	102918078	102918732	+	0	NA	Intergenic	Intergenic	1519420	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.010703	0.363359	
chunk0095_314_1	chr2	20438521	20439080	+	0	NA	Intergenic	Intergenic	-8271	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.005367	0.396429	262(AAAAACTGGATGTTCT,-,0.00),263(AAAACTGGATGTTCTG,+,0.00)
chunk0159_241_1	chr5	141849933	141850205	+	0	NA	Intergenic	CpG	16133	NM_001278615	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.069853	0.637363	
chunk0113_291_1	chr20	57452167	57452511	+	0	NA	Intergenic	L2a|LINE|L2	60941	NM_001291780	55544	Hs.236361	NM_017495	ENSG00000132819	RBM38	HSRNASEB|RNPC1|SEB4B|SEB4D|dJ800J21.2	RNA binding motif protein 38	protein-coding	0.017442	0.533333	297(GGGCGCAGGATGTGCC,-,0.00),320(GGGAACAACCAGTGCA,-,0.00)
chunk0025_95_1	chr10	50566136	50566513	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	57653	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.000000	0.349206	
chunk0101_160_1	chr2	128442392	128443075	+	0	NA	Intergenic	Intergenic	-124136	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.011713	0.448830	
chunk0135_429_1	chr3	193824209	193824976	+	0	NA	Intergenic	L1ME2|LINE|L1	169646	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.002608	0.380208	
chunk0169_329_1	chr6	106347123	106347750	+	0	NA	Intergenic	Intergenic	-21616	NM_001286111	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.004785	0.310510	
chunk0011_230_1	chr1	150389564	150390079	+	0	NA	intron (NM_001297673, intron 1 of 10)	intron (NM_001297673, intron 1 of 10)	25710	NM_015203	23248	Hs.213666	NM_015203	ENSG00000163125	RPRD2	HSPC099|KIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding	0.007767	0.416667	
chunk0071_70_1	chr15	80554671	80555097	+	0	NA	non-coding (NR_120363, exon 3 of 3)	non-coding (NR_120363, exon 3 of 3)	8060	NR_120363	101929586	Hs.569426	NR_120363	ENSG00000259175	LOC101929586	-	uncharacterized LOC101929586	ncRNA	0.002347	0.362998	
chunk0018_438_1	chr1	222928210	222928471	+	0	NA	intron (NM_032890, intron 2 of 9)	intron (NM_032890, intron 2 of 9)	113251	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.007663	0.480916	
chunk0051_115_1	chr12	115195051	115195267	+	0	NA	Intergenic	Intergenic	-510995	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.004630	0.447005	
chunk0039_239_1	chr11	102026213	102026811	+	0	NA	Intergenic	Intergenic	-20926	NM_032930	85016	Hs.98328	NM_032930	ENSG00000137691	CFAP300	C11orf70|CILD38	cilia and flagella associated protein 300	protein-coding	0.006689	0.415693	293(AAGGACACGATGTGCT,-,0.00),294(AGGACACGATGTGCTC,+,0.00),392(AAGCACTCCCAGTTCT,-,0.00),393(AGCACTCCCAGTTCTT,+,0.00)
chunk0054_203_1	chr13	45021733	45022171	+	0	NA	intron (NM_001316952, intron 7 of 8)	L1ME2z|LINE|L1	32422	NM_001316952	55425	Hs.731811	NM_018559	ENSG00000133114	GPALPP1	AD029|KIAA1704|LSR7|bA245H20.2	GPALPP motifs containing 1	protein-coding	0.002283	0.323462	
chunk0085_196_1	chr18	6540368	6540807	+	0	NA	intron (NR_120518, intron 2 of 5)	intron (NR_120518, intron 2 of 5)	29171	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.011390	0.354545	
chunk0045_58_1	chr12	45299020	45299470	+	0	NA	intron (NM_001142678, intron 1 of 19)	intron (NM_001142678, intron 1 of 19)	6562	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.002222	0.370288	
chunk0044_375_1	chr12	39831205	39831498	+	0	NA	intron (NM_052885, intron 6 of 9)	intron (NM_052885, intron 6 of 9)	205181	NM_001031748	283461	Hs.648205	NM_001031748	ENSG00000180116	C12orf40	HEL-206|HEL-S-94	chromosome 12 open reading frame 40	protein-coding	0.013652	0.380952	
chunk0112_23_1	chr20	36111219	36111429	+	0	NA	intron (NM_001258329, intron 1 of 22)	intron (NM_001258329, intron 1 of 22)	18614	NM_001258329	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.000000	0.492891	101(GGAGACTGACTGTTCT,-,0.00),102(GAGACTGACTGTTCTG,+,0.00)
chunk0105_263_1	chr2	189226058	189226414	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-46357	NM_000393	1290	Hs.445827	NM_000393	ENSG00000204262	COL5A2	EDSC|EDSCL2	collagen type V alpha 2 chain	protein-coding	0.002809	0.330532	
chunk0159_359_1	chr5	145025767	145026112	+	0	NA	Intergenic	Intergenic	809430	NM_182960	153768	Hs.314261	NM_138492	ENSG00000186314	PRELID2	-	PRELI domain containing 2	protein-coding	0.008696	0.401734	
chunk0149_211_1	chr5	21768780	21769204	+	0	NA	intron (NM_004061, intron 11 of 14)	L1M4|LINE|L1	-115462	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.011792	0.322353	225(AAGAACAAAATGTTAC,-,0.00)
chunk0124_330_1	chr3	58191519	58191718	+	0	NA	Intergenic	Intergenic	19385	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.015075	0.420000	
chunk0114_195_1	chr21	15203718	15204079	+	0	NA	Intergenic	Intergenic	-139093	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.005540	0.350829	
chunk0056_371_1	chr13	92968928	92969176	+	0	NA	Intergenic	Intergenic	-76289	NR_126360	104326053	Hs.578064	NR_126360		LINC00363	TCONS_00021586	long intergenic non-protein coding RNA 363	ncRNA	0.004032	0.357430	
chunk0002_16_1	chr1	12277687	12278018	+	0	NA	exon (NM_015378, exon 19 of 70)	exon (NM_015378, exon 19 of 70)	47813	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.024169	0.469880	
chunk0176_334_1	chr7	17389800	17390059	+	0	NA	intron (NR_110015, intron 1 of 2)	Charlie1|DNA|hAT-Charlie	15012	NR_110015	102659288	Hs.559488	NR_110014		KCCAT333	-	renal clear cell carcinoma-associated transcript 333	ncRNA	0.003861	0.384615	
chunk0041_145_1	chr11	125451548	125451903	+	0	NA	intron (NM_005103, intron 8 of 9)	intron (NM_005103, intron 8 of 9)	-43489	NM_001301851	403312	Hs.450611	NM_203452		LOC403312	-	putative uncharacterized protein MGC39545	protein-coding	0.011268	0.474719	
chunk0192_55_1	chr8	59670097	59670665	+	0	NA	Intergenic	Intergenic	-551173	NM_014729	9760	Hs.491805	NM_014729	ENSG00000198846	TOX	TOX1	thymocyte selection associated high mobility group box	protein-coding	0.003521	0.367311	
chunk0163_172_1	chr6	11207215	11207489	+	0	NA	intron (NM_182966, intron 2 of 2)	(TGTGTG)n|Simple_repeat|Simple_repeat	25330	NM_182966	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.007299	0.421818	
chunk0077_109_1	chr16	78228673	78229244	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	129545	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.008757	0.381119	
chunk0123_187_1	chr3	44315687	44315925	+	0	NA	intron (NM_001145030, intron 16 of 19)	intron (NM_001145030, intron 16 of 19)	-22313	NM_001282915	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.000000	0.351464	
chunk0017_92_1	chr1	205767304	205767796	+	0	NA	TTS (NM_001135662)	TTS (NM_001135662)	7932	NM_001135664	8934	Hs.115325	NM_003929	ENSG00000117280	RAB29	RAB7L|RAB7L1	RAB29, member RAS oncogene family	protein-coding	0.008130	0.417850	177(AAGCACATTCAGTTTT,-,0.00)
chunk0206_393_1	chr9	127024106	127024446	+	0	NA	intron (NM_001190729, intron 4 of 17)	HAL1ME|LINE|L1	62051	NM_001190728	9649	Hs.432842	NM_014636	ENSG00000136828	RALGPS1	RALGEF2|RALGPS1A	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.002941	0.334311	
chunk0175_430_1	chr6	169469485	169470047	+	0	NA	intron (NM_001202550, intron 21 of 21)	MLT1B-int|LTR|ERVL-MaLR	-215652	NM_003247	7058	Hs.371147	NM_003247	ENSG00000186340	THBS2	TSP2	thrombospondin 2	protein-coding	0.001779	0.440497	
chunk0200_170_1	chr9	19118943	19119426	+	0	NA	intron (NM_001122, intron 6 of 7)	intron (NM_001122, intron 6 of 7)	8422	NM_001122	123	Hs.3416	NM_001122	ENSG00000147872	PLIN2	ADFP|ADRP	perilipin 2	protein-coding	0.006211	0.396694	190(TGGTACATACTGTTCT,-,0.00),191(GGTACATACTGTTCTT,+,0.00)
chunk0102_226_1	chr2	148656446	148657035	+	0	NA	intron (NM_015630, intron 1 of 13)	L2c|LINE|L2	11749	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.003396	0.350847	
chunk0181_233_1	chr7	85242439	85242743	+	0	NA	Intergenic	L1MC1|LINE|L1	-120660	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.344262	
chunk0190_121_1	chr8	30542425	30542670	+	0	NA	intron (NM_006867, intron 5 of 9)	intron (NM_006867, intron 5 of 9)	-96053	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.004082	0.483740	
chunk0165_181_1	chr6	34359379	34360022	+	0	NA	intron (NM_001202470, intron 5 of 8)	L1MB5|LINE|L1	32980	NM_006703	11165	Hs.188882	NM_006703	ENSG00000272325	NUDT3	DIPP|DIPP-1|DIPP1	nudix hydrolase 3	protein-coding	0.003110	0.363354	
chunk0198_337_1	chr8	140096809	140097109	+	0	NA	intron (NM_001160372, intron 17 of 22)	intron (NM_001160372, intron 17 of 22)	360803	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.030000	0.578073	
chunk0003_456_1	chr1	41500453	41500810	+	0	NA	Intergenic	Intergenic	-15948	NR_126098	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.025210	0.603352	
chunk0154_42_1	chr5	77138729	77139483	+	0	NA	intron (NR_024398, intron 3 of 3)	intron (NR_024398, intron 3 of 3)	-51901	NM_032367	84327	Hs.584988	NM_032367	ENSG00000132846	ZBED3	-	zinc finger BED-type containing 3	protein-coding	0.010610	0.435762	
chunk0023_82_1	chr10	22285178	22285490	+	0	NA	Intergenic	MER130|DNA|DNA	-31049	NM_012071	23412	Hs.534398	NM_012071	ENSG00000148444	COMMD3	BUP|C10orf8	COMM domain containing 3	protein-coding	0.009615	0.463259	
chunk0176_272_1	chr7	16495201	16495555	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	-29529	NM_015464	25928	Hs.648106	NM_015464	ENSG00000171243	SOSTDC1	CDA019|DAND7|ECTODIN|USAG1	sclerostin domain containing 1	protein-coding	0.008475	0.394366	
chunk0146_438_1	chr4	169606115	169606809	+	0	NA	intron (NM_001199399, intron 2 of 32)	HAL1|LINE|L1	6165	NM_001199400	4750	Hs.481181	NM_012224	ENSG00000137601	NEK1	ALS24|NY-REN-55|SRPS2|SRPS2A|SRTD6	NIMA related kinase 1	protein-coding	0.002882	0.381295	
chunk0062_138_1	chr14	68869920	68870576	+	0	NA	Intergenic	Intergenic	-74005	NM_001244701	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.010671	0.378995	
chunk0108_218_1	chr2	233414978	233415288	+	0	NA	intron (NM_003648, intron 2 of 28)	intron (NM_003648, intron 2 of 28)	26979	NM_003648	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.009677	0.495177	
chunk0111_296_1	chr20	31797470	31797730	+	0	NA	intron (NM_012112, intron 16 of 17)	intron (NM_012112, intron 16 of 17)	-21775	NM_033118	85366	Hs.86092	NM_033118	ENSG00000101306	MYLK2	KMLC|MLCK|MLCK2|skMLCK	myosin light chain kinase 2	protein-coding	0.003846	0.440613	
chunk0096_160_1	chr2	29423228	29424122	+	0	NA	intron (NM_004304, intron 4 of 28)	intron (NM_004304, intron 4 of 28)	308249	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.007830	0.418994	
chunk0143_204_1	chr4	113197516	113197951	+	0	NA	intron (NM_020977, intron 3 of 44)	intron (NM_020977, intron 3 of 44)	45451	NR_107049	102465878		NR_107049	ENSG00000275810	MIR8082	hsa-mir-8082	microRNA 8082	ncRNA	0.004598	0.353211	
chunk0042_308_1	chr12	7937967	7938304	+	0	NA	Intergenic	Intergenic	-1839	NM_006931	6515	Hs.419240	NM_006931	ENSG00000059804	SLC2A3	GLUT3	solute carrier family 2 member 3	protein-coding	0.008902	0.428994	
chunk0207_432_1	chr9	137365745	137366139	+	0	NA	TTS (NM_001286823)	TTS (NM_001286823)	57320	NR_104598	54932	Hs.495553	NM_017820	ENSG00000187609	EXD3	mut-7	exonuclease 3'-5' domain containing 3	protein-coding	0.020305	0.501266	
chunk0040_242_1	chr11	114832563	114833074	+	0	NA	Intergenic	Intergenic	154340	NM_182495	120406	Hs.446760	NM_182495	ENSG00000204361	NXPE2	FAM55B	neurexophilin and PC-esterase domain family member 2	protein-coding	0.009785	0.443359	
chunk0063_442_1	chr14	88834510	88835087	+	0	NA	intron (NM_144596, intron 3 of 15)	intron (NM_144596, intron 3 of 15)	10645	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.000000	0.302768	
chunk0129_123_1	chr3	119858965	119859329	+	0	NA	intron (NM_001146156, intron 9 of 10)	Tigger1|DNA|TcMar-Tigger	76437	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.005495	0.315068	
chunk0189_372_1	chr8	27297941	27298431	+	0	NA	intron (NM_001304495, intron 1 of 3)	intron (NM_001304495, intron 1 of 3)	13133	NM_171982	23087	Hs.104223	NM_171982	ENSG00000104228	TRIM35	HLS5|MAIR	tripartite motif containing 35	protein-coding	0.012245	0.513238	
chunk0116_323_1	chr21	41165131	41165693	+	0	NA	Intergenic	PrimLTR79|LTR|ERV1	-2145	NR_036167	100423023		NR_036167	ENSG00000263681	MIR3197	-	microRNA 3197	ncRNA	0.019573	0.467140	
chunk0129_285_1	chr3	123269980	123270557	+	0	NA	intron (NM_012430, intron 6 of 6)	intron (NM_012430, intron 6 of 6)	68341	NM_012430	26984	Hs.477361	NM_012430	ENSG00000121542	SEC22A	SEC22L2	SEC22 homolog A, vesicle trafficking protein	protein-coding	0.003466	0.342561	
chunk0028_238_1	chr10	90020462	90020825	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-63270	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.002755	0.357143	
chunk0021_430_1	chr1	247605876	247606228	+	0	NA	exon (NM_001001914, exon 1 of 1)	exon (NM_001001914, exon 1 of 1)	466	NM_001001914	81469	Hs.653227	NM_001001914	ENSG00000177476	OR2G3	OR1-33	olfactory receptor family 2 subfamily G member 3	protein-coding	0.011364	0.475921	
chunk0027_346_1	chr10	78605064	78605538	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	337973	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.014768	0.381053	
chunk0073_412_1	chr16	18070162	18070361	+	0	NA	Intergenic	Intergenic	262401	NM_001282507	101059938	Hs.634612	NM_001282507	ENSG00000214967	NPIPA7	NPIPA8	nuclear pore complex interacting protein family member A7	protein-coding	0.005025	0.560000	
chunk0005_305_1	chr1	60504320	60504572	+	0	NA	Intergenic	MIRb|SINE|MIR	321138	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.007937	0.339921	
chunk0192_184_1	chr8	63175802	63176286	+	0	NA	intron (NR_102434, intron 3 of 3)	intron (NR_102434, intron 3 of 3)	7041	NM_001277814	253943	Hs.491861	NM_152758	ENSG00000185728	YTHDF3	-	YTH N6-methyladenosine RNA binding protein 3	protein-coding	0.004132	0.298969	
chunk0038_165_1	chr11	84958155	84958733	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	-35023	NM_001300983	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.006920	0.407599	
chunk0072_259_1	chr15	96259873	96260093	+	0	NA	intron (NR_125738, intron 2 of 4)	L1ME3G|LINE|L1	-65945	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.004545	0.361991	
chunk0027_275_1	chr10	77431087	77431506	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	80424	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.000000	0.440476	
chunk0154_365_1	chr5	87580238	87580693	+	0	NA	Intergenic	MADE2|DNA|TcMar-Mariner	-167432	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.000000	0.293860	
chunk0072_404_1	chr15	100771743	100772208	+	0	NA	Intergenic	Intergenic	-107717	NM_001293815	220	Hs.459538	NM_000693	ENSG00000184254	ALDH1A3	ALDH1A6|ALDH6|MCOP8|RALDH3	aldehyde dehydrogenase 1 family member A3	protein-coding	0.008602	0.484979	271(CAGGACAGTGTGTGCT,-,0.00),272(AGGACAGTGTGTGCTC,+,0.00)
chunk0202_410_1	chr9	81531368	81531917	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	157893	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.010929	0.490909	
chunk0087_382_1	chr18	41714916	41715406	+	0	NA	Intergenic	Intergenic	-194564	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.002041	0.372709	
chunk0139_397_1	chr4	62751150	62751852	+	0	NA	Intergenic	Intergenic	-589736	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.002849	0.268848	281(TGGTACAGAATGTTCT,-,0.00),282(GGTACAGAATGTTCTT,+,0.00)
chunk0212_296_1	chrX	141125515	141125891	+	0	NA	Intergenic	Intergenic	-7567	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.005319	0.326260	
chunk0051_32_1	chr12	112045879	112046460	+	0	NA	intron (NM_024953, intron 17 of 23)	MER68B|LTR|ERVL	-8454	NR_037430	100500889		NR_037430	ENSG00000266370	MIR3657	-	microRNA 3657	ncRNA	0.008606	0.414089	
chunk0162_350_1	chr6	7100800	7100999	+	0	NA	Intergenic	Intergenic	-6698	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.035176	0.550000	
chunk0173_429_1	chr6	151232799	151233480	+	0	NA	Intergenic	L1MD1|LINE|L1	-4682	NR_125868	102723831	Hs.684425	NR_125868		LOC102723831	-	uncharacterized LOC102723831	ncRNA	0.004405	0.353372	
chunk0004_310_1	chr1	49332833	49333553	+	0	NA	intron (NM_032785, intron 3 of 13)	intron (NM_032785, intron 3 of 13)	75782	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.018056	0.424411	
chunk0045_154_1	chr12	46519114	46519320	+	0	NA	intron (NR_125380, intron 3 of 3)	intron (NR_125380, intron 3 of 3)	135110	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.000000	0.314010	
chunk0027_207_1	chr10	75904441	75904880	+	0	NA	intron (NR_131178, intron 3 of 7)	intron (NR_131178, intron 3 of 7)	121899	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.029613	0.431818	
chunk0156_39_1	chr5	102691543	102691815	+	0	NA	Intergenic	L2b|LINE|L2	-20215	NR_103756	285708	Hs.533011	NR_103753		LINC00491	-	long intergenic non-protein coding RNA 491	ncRNA	0.000000	0.399267	
chunk0088_355_1	chr18	52499744	52499943	+	0	NA	intron (NM_005215, intron 1 of 28)	intron (NM_005215, intron 1 of 28)	159671	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.005025	0.395000	
chunk0038_106_1	chr11	83698090	83698289	+	0	NA	intron (NM_001142699, intron 18 of 27)	MIRb|SINE|MIR	-15764	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.355000	
chunk0126_21_1	chr3	73552497	73552996	+	0	NA	intron (NR_121660, intron 1 of 1)	intron (NR_121660, intron 1 of 1)	8932	NM_001303140	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.012024	0.386000	
chunk0005_377_1	chr1	61725065	61725383	+	0	NA	5' UTR (NM_032027, exon 1 of 7)	5' UTR (NM_032027, exon 1 of 7)	199	NM_032027	83941	Hs.656790	NM_032027	ENSG00000162604	TM2D1	BBP	TM2 domain containing 1	protein-coding	0.072327	0.589342	
chunk0005_366_1	chr1	61542657	61542885	+	0	NA	Intergenic	L1PB1|LINE|L1	-111471	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.017544	0.349345	
chunk0123_14_1	chr3	40264253	40264747	+	0	NA	intron (NR_033965, intron 2 of 2)	MER101-int|LTR|ERV1	-45182	NM_005875	10289	Hs.315230	NM_005875	ENSG00000114784	EIF1B	GC20	eukaryotic translation initiation factor 1B	protein-coding	0.004049	0.347475	
chunk0167_151_1	chr6	62523554	62524076	+	0	NA	Intergenic	L2a|LINE|L2	-237620	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.003831	0.386233	
chunk0059_164_1	chr14	32366237	32366707	+	0	NA	intron (NM_004274, intron 1 of 13)	intron (NM_004274, intron 1 of 13)	37199	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.000000	0.430998	312(AAGACAATCTGTCCTG,+,0.00)
chunk0128_101_1	chr3	105988008	105988311	+	0	NA	Intergenic	L2a|LINE|L2	-119116	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.342105	
chunk0079_348_1	chr17	17786127	17786681	+	0	NA	intron (NM_030665, intron 2 of 5)	L2a|LINE|L2	-6875	NR_024007	140771	Hs.352643	NM_144774	ENSG00000226746	SMCR5	NCRNA00034	Smith-Magenis syndrome chromosome region, candidate 5	ncRNA	0.009025	0.484685	
chunk0068_257_1	chr15	56236117	56236721	+	0	NA	intron (NM_022841, intron 1 of 8)	intron (NM_022841, intron 1 of 8)	6866	NM_022841	64864	Hs.745089	NM_022841	ENSG00000181827	RFX7	RFXDC2	regulatory factor X7	protein-coding	0.006623	0.337190	459(AAGAACATTCTGTCAC,-,0.00),460(AGAACATTCTGTCACG,+,0.00)
chunk0077_52_1	chr16	76309891	76310452	+	0	NA	intron (NM_138994, intron 1 of 22)	intron (NM_138994, intron 1 of 22)	333	NM_138994	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.012478	0.414591	
chunk0080_99_1	chr17	26885646	26885919	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	408214	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.007326	0.405109	
chunk0002_323_1	chr1	24283846	24284192	+	0	NA	Intergenic	L3|LINE|CR1	-35303	NM_198173	57822	Hs.657920	NM_021180	ENSG00000158055	GRHL3	SOM|TFCP2L4|VWS2	grainyhead like transcription factor 3	protein-coding	0.008671	0.420749	
chunk0018_432_1	chr1	222897617	222898236	+	0	NA	intron (NM_032890, intron 1 of 9)	intron (NM_032890, intron 1 of 9)	82837	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.004847	0.314516	
chunk0141_173_1	chr4	82552920	82553573	+	0	NA	intron (NM_001080506, intron 1 of 7)	intron (NM_001080506, intron 1 of 7)	8727	NM_001080506	441027	Hs.507676	NM_001080506	ENSG00000249242	TMEM150C	TTN3	transmembrane protein 150C	protein-coding	0.006126	0.389908	
chunk0118_99_1	chr22	29220075	29220383	+	0	NA	intron (NM_001267895, intron 3 of 14)	intron (NM_001267895, intron 3 of 14)	14317	NM_001267895	129080	Hs.289106	NM_133455	ENSG00000186998	EMID1	EMI5|EMU1	EMI domain containing 1	protein-coding	0.016234	0.598706	
chunk0204_423_1	chr9	103059605	103059862	+	0	NA	Intergenic	L1PB4|LINE|L1	64422	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.000000	0.341085	
chunk0087_440_1	chr18	42573942	42574445	+	0	NA	intron (NR_046174, intron 6 of 9)	intron (NR_046174, intron 6 of 9)	387525	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.007952	0.323413	
chunk0069_318_1	chr15	65869123	65869322	+	0	NA	promoter-TSS (NM_004663)	promoter-TSS (NM_004663)	-237	NM_004663	8766	Hs.321541	NM_004663	ENSG00000103769	RAB11A	YL8	RAB11A, member RAS oncogene family	protein-coding	0.060302	0.590000	
chunk0144_343_1	chr4	139501615	139502071	+	0	NA	intron (NM_001306199, intron 7 of 7)	intron (NM_001306199, intron 7 of 7)	48036	NM_031296	83452	Hs.591679	NM_031296	ENSG00000172007	RAB33B	SMC2	RAB33B, member RAS oncogene family	protein-coding	0.015351	0.479212	
chunk0011_393_1	chr1	153990610	153991015	+	0	NA	promoter-TSS (NM_001030)	promoter-TSS (NM_001030)	49	NM_001030	6232	Hs.546291	NM_001030	ENSG00000177954	RPS27	DBA17|MPS-1|MPS1|S27	ribosomal protein S27	protein-coding	0.069136	0.564039	220(GAGATCTCGCTGTTCT,-,0.00),221(AGATCTCGCTGTTCTG,+,0.00)
chunk0030_110_1	chr10	112779117	112779617	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-44129	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.004000	0.377246	
chunk0169_202_1	chr6	102870047	102871340	+	0	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	1471708	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.006187	0.328439	
chunk0044_86_1	chr12	28264766	28265318	+	0	NA	intron (NM_018318, intron 2 of 11)	intron (NM_018318, intron 2 of 11)	7842	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.005435	0.345389	189(AAGGACAGGATGTCTC,-,0.00),190(AGGACAGGATGTCTCA,+,0.00)
chunk0051_163_1	chr12	115973255	115973496	+	0	NA	intron (NM_015335, intron 25 of 30)	intron (NM_015335, intron 25 of 30)	175279	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.000000	0.417355	
chunk0051_406_1	chr12	122097877	122098611	+	0	NA	intron (NM_014938, intron 1 of 16)	intron (NM_014938, intron 1 of 16)	19516	NM_014938	22877	Hs.437153	NM_014938	ENSG00000175727	MLXIP	MIR|MONDOA|bHLHe36	MLX interacting protein	protein-coding	0.012262	0.540136	658(CAGAACAGCCAGCTCC,-,0.00),659(AGAACAGCCAGCTCCA,+,0.00)
chunk0089_180_1	chr18	59704279	59704737	+	0	NA	Intergenic	MIR|SINE|MIR	-7096	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.008734	0.407407	
chunk0085_352_1	chr18	9092610	9092973	+	0	NA	Intergenic	Intergenic	-9839	NM_021074	4729	Hs.464572	NM_021074	ENSG00000178127	NDUFV2	CI-24k|MC1DN7	NADH:ubiquinone oxidoreductase core subunit V2	protein-coding	0.005510	0.417582	
chunk0154_87_1	chr5	77946518	77947033	+	0	NA	intron (NR_105012, intron 1 of 1)	intron (NR_105012, intron 1 of 1)	-11472	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.003883	0.344961	
chunk0023_47_1	chr10	21496458	21496681	+	0	NA	promoter-TSS (NR_031736)	promoter-TSS (NR_031736)	72	NR_031736	100302129		NR_031736	ENSG00000222071	MIR1915	MIRN1915|hsa-mir-1915	microRNA 1915	ncRNA	0.094170	0.741071	
chunk0127_243_1	chr3	96986156	96986844	+	0	NA	intron (NM_001080448, intron 2 of 17)	L2a|LINE|L2	171919	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002907	0.346880	
chunk0133_3_1	chr3	165206828	165207027	+	0	NA	promoter-TSS (NR_125764)	promoter-TSS (NR_125764)	-33	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.065327	0.575000	
chunk0047_184_1	chr12	70717513	70717829	+	0	NA	intron (NM_130846, intron 2 of 9)	intron (NM_130846, intron 2 of 9)	36937	NM_130846	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.006329	0.372240	
chunk0055_79_1	chr13	53793680	53794091	+	0	NA	Intergenic	Intergenic	-21534	NR_047488	100861552	Hs.224691	NR_047488	ENSG00000261517	LINC00558	-	long intergenic non-protein coding RNA 558	ncRNA	0.002433	0.296117	
chunk0149_174_1	chr5	20711965	20712294	+	0	NA	Intergenic	Intergenic	-136256	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003040	0.342424	
chunk0184_436_1	chr7	123038808	123039039	+	0	NA	Intergenic	Intergenic	-43223	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.008658	0.327586	
chunk0073_168_1	chr16	8505542	8506292	+	0	NA	Intergenic	Intergenic	83921	NR_110736	283953	Hs.150849	NM_001146336	ENSG00000232258	TMEM114	-	transmembrane protein 114	protein-coding	0.010667	0.403462	
chunk0044_307_1	chr12	33323325	33323763	+	0	NA	Intergenic	Intergenic	116275	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.006849	0.307517	
chunk0022_157_1	chr10	12547727	12547984	+	0	NA	intron (NM_020397, intron 1 of 9)	intron (NM_020397, intron 1 of 9)	-30898	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.023346	0.410853	
chunk0187_170_1	chr7	150765301	150765995	+	0	NA	Intergenic	MER34|LTR|ERV1	28300	NM_018384	55340	Hs.647079	NM_018384	ENSG00000196329	GIMAP5	HIMAP3|IAN-5|IAN4|IAN4L1|IAN5|IMAP3|IROD	GTPase, IMAP family member 5	protein-coding	0.007205	0.379856	
chunk0015_435_1	chr1	191744724	191745068	+	0	NA	Intergenic	Intergenic	-413566	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.000000	0.269565	
chunk0041_443_1	chr11	134608358	134608628	+	0	NA	Intergenic	L2a|LINE|L2	172011	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.007407	0.498155	
chunk0097_212_1	chr2	51319640	51319955	+	0	NA	Intergenic	L1MEi|LINE|L1	-287261	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.003175	0.357595	155(CTGCACAGAGTGTACT,-,0.00),156(TGCACAGAGTGTACTT,+,0.00)
chunk0129_36_1	chr3	117279827	117280125	+	0	NA	Intergenic	Intergenic	358545	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.307692	
chunk0150_302_1	chr5	37661981	37662364	+	0	NA	intron (NM_018034, intron 10 of 17)	intron (NM_018034, intron 10 of 17)	172650	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.005222	0.364583	191(GGAACAAAGTGCACTT,+,0.00)
chunk0114_2_1	chr21	5222860	5223293	+	0	NA	Intergenic	Intergenic	-68346	NM_005049	5822	Hs.449076	NM_005049	ENSG00000241945	PWP2	EHOC-17|PWP2H|UTP1	PWP2 small subunit processome component	protein-coding	0.009238	0.398618	
chunk0093_58_1	chr19	40280159	40280390	+	0	NA	intron (NM_001243027, intron 1 of 13)	intron (NM_001243027, intron 1 of 13)	2367	NR_030371	693226		NR_030371	ENSG00000207631	MIR641	MIRN641|hsa-mir-641|mir-641	microRNA 641	ncRNA	0.034632	0.581897	
chunk0090_339_1	chr18	76363931	76364329	+	0	NA	intron (NM_014643, intron 6 of 6)	intron (NM_014643, intron 6 of 6)	131060	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.015075	0.443609	
chunk0152_248_1	chr5	60798582	60799100	+	0	NA	intron (NM_001104558, intron 1 of 7)	L1M3|LINE|L1	45433	NM_001297618	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.005792	0.315992	
chunk0074_190_1	chr16	24834430	24834717	+	0	NA	Intergenic	LTR16|LTR|ERVL	-11290	NM_001258413	115584	Hs.164118	NM_052944	ENSG00000158865	SLC5A11	KST1|RKST1|SGLT6|SMIT2	solute carrier family 5 member 11	protein-coding	0.006969	0.534722	
chunk0026_194_1	chr10	63672219	63672639	+	0	NA	Intergenic	LTR16C|LTR|ERVL	151066	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.004762	0.408551	
chunk0162_201_1	chr6	4008298	4008841	+	0	NA	Intergenic	Intergenic	-12766	NM_003913	8899	Hs.159014	NM_003913	ENSG00000112739	PRPF4B	PR4H|PRP4|PRP4H|PRP4K|dJ1013A10.1	pre-mRNA processing factor 4B	protein-coding	0.005525	0.365809	
chunk0192_296_1	chr8	66653600	66653812	+	0	NA	intron (NM_025054, intron 1 of 2)	intron (NM_025054, intron 1 of 2)	13511	NM_025054	80124	Hs.632066	NM_025054	ENSG00000175073	VCPIP1	DUBA3|VCIP135	valosin containing protein interacting protein 1	protein-coding	0.000000	0.380282	
chunk0024_152_1	chr10	35424545	35425287	+	0	NA	intron (NM_001282853, intron 2 of 10)	intron (NM_001282853, intron 2 of 10)	88042	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.010782	0.487214	255(GTGTACAGTGTGTTCT,-,0.00),256(TGTACAGTGTGTTCTT,+,0.00),564(AGACACACACTGTTCC,-,0.00),565(GACACACACTGTTCCT,+,0.00)
chunk0100_191_1	chr2	110991895	110992307	+	0	NA	intron (NM_001142807, intron 13 of 17)	intron (NM_001142807, intron 13 of 17)	123487	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.012136	0.397094	
chunk0149_53_1	chr5	16787456	16787661	+	0	NA	intron (NM_012334, intron 4 of 40)	intron (NM_012334, intron 4 of 40)	148718	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.000000	0.364078	
chunk0148_226_1	chr5	9208324	9208861	+	0	NA	intron (NM_003966, intron 8 of 22)	intron (NM_003966, intron 8 of 22)	-154697	NR_039779	100616326		NR_039779	ENSG00000266415	MIR4636	mir-4636	microRNA 4636	ncRNA	0.009311	0.533457	
chunk0135_289_1	chr3	189455222	189455426	+	0	NA	Intergenic	Intergenic	-176103	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.019608	0.590244	78(GGGCACACATTGTCCC,-,0.00),79(GGCACACATTGTCCCG,+,0.00)
chunk0058_44_1	chr14	20213594	20213801	+	0	NA	Intergenic	L1MA7|LINE|L1	-10013	NM_001004480	122748	Hs.553575	NM_001004480	ENSG00000176219	OR11H6	-	olfactory receptor family 11 subfamily H member 6	protein-coding	0.000000	0.408654	
chunk0131_47_1	chr3	142650061	142650263	+	0	NA	intron (NM_002670, intron 1 of 15)	intron (NM_002670, intron 1 of 15)	-6735	NM_001172312	5357	Hs.203637	NM_002670	ENSG00000120756	PLS1	-	plastin 1	protein-coding	0.004950	0.349754	
chunk0119_183_1	chr22	43993602	43993832	+	0	NA	intron (NM_015380, intron 14 of 14)	intron (NM_015380, intron 14 of 14)	-5494	NM_001003828	29780	Hs.475074	NM_013327	ENSG00000188677	PARVB	CGI-56	parvin beta	protein-coding	0.021739	0.454545	
chunk0142_218_1	chr4	97775350	97775835	+	0	NA	intron (NM_174952, intron 9 of 10)	intron (NM_174952, intron 9 of 10)	367648	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.002062	0.310700	
chunk0051_413_1	chr12	122266120	122266543	+	0	NA	exon (NM_022916, exon 1 of 13)	exon (NM_022916, exon 1 of 13)	190	NM_022916	65082	Hs.487883	NM_022916	ENSG00000139719	VPS33A	MPSPS	VPS33A core subunit of CORVET and HOPS complexes	protein-coding	0.096927	0.655660	
chunk0053_401_1	chr13	36374077	36374600	+	0	NA	Intergenic	Intergenic	-4158	NM_001142294	23111	Hs.440414	NM_015087	ENSG00000133104	SPART	SPG20|TAHCCP1	spartin	protein-coding	0.003824	0.412214	
chunk0189_378_1	chr8	27361869	27362181	+	0	NA	intron (NM_004103, intron 2 of 31)	intron (NM_004103, intron 2 of 31)	36461	NM_173175	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.016026	0.530351	
chunk0126_383_1	chr3	84178207	84178843	+	0	NA	Intergenic	L1MA6|LINE|L1	691050	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.004717	0.315542	
chunk0021_3_1	chr10	176139	176747	+	0	NA	intron (NM_001202464, intron 1 of 13)	intron (NM_001202464, intron 1 of 13)	-3551	NM_001202468	10771	Hs.292265	NM_006624	ENSG00000015171	ZMYND11	BRAM1|BS69|MRD30	zinc finger MYND-type containing 11	protein-coding	0.001645	0.311987	
chunk0203_197_1	chr9	86454442	86455087	+	0	NA	Intergenic	Intergenic	-100277	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.010853	0.376161	
chunk0063_448_1	chr14	89022654	89023067	+	0	NA	Intergenic	Intergenic	198707	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.009685	0.442029	354(TTGTACAAACTGTGCC,-,0.00),355(TGTACAAACTGTGCCC,+,0.00)
chunk0207_438_1	chr9	137481996	137482603	+	0	NA	intron (NM_001098537, intron 21 of 34)	L1MC1|LINE|L1	-22965	NM_015537	26012	Hs.455336	NM_015537	ENSG00000165802	NSMF	HH9|NELF	NMDA receptor synaptonuclear signaling and neuronal migration factor	protein-coding	0.023064	0.526316	
chunk0040_248_1	chr11	115345537	115345736	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	158887	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.000000	0.365000	
chunk0183_50_1	chr7	103971432	103971979	+	0	NA	intron (NM_005045, intron 1 of 64)	L1M5|LINE|L1	17811	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.005484	0.370438	273(TGGAACTTTCAGTTCT,-,0.00),274(GGAACTTTCAGTTCTA,+,0.00)
chunk0055_260_1	chr13	63461081	63461889	+	0	NA	Intergenic	Intergenic	-133391	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.003713	0.358467	
chunk0069_131_1	chr15	62060484	62060840	+	0	NA	promoter-TSS (NM_001018088)	promoter-TSS (NM_001018088)	-197	NM_018080	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.098315	0.652661	
chunk0017_407_1	chr1	212791620	212791964	+	0	NA	promoter-TSS (NM_015471)	promoter-TSS (NM_015471)	5	NM_001297739	25936	Hs.497692	NM_015471	ENSG00000117697	NSL1	C1orf48|DC8|MIS14	NSL1 component of MIS12 kinetochore complex	protein-coding	0.081395	0.643478	
chunk0116_41_1	chr21	33491236	33491963	+	0	NA	promoter-TSS (NM_017833)	promoter-TSS (NM_017833)	-116	NM_017833	54943	Hs.458308	NM_017833	ENSG00000177692	DNAJC28	C21orf55|C21orf78	DnaJ heat shock protein family (Hsp40) member C28	protein-coding	0.077029	0.623626	
chunk0076_7_1	chr16	58524559	58524993	+	0	NA	intron (NR_049763, intron 47 of 49)	intron (NR_049763, intron 47 of 49)	9297	NM_001160305	79918	Hs.731691	NM_024860	ENSG00000103037	SETD6	-	SET domain containing 6, protein lysine methyltransferase	protein-coding	0.004608	0.351724	
chunk0105_215_1	chr2	187986217	187986892	+	0	NA	Intergenic	Intergenic	301137	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.008889	0.420118	
chunk0178_256_1	chr7	36291191	36291460	+	0	NA	intron (NM_030636, intron 6 of 7)	intron (NM_030636, intron 6 of 7)	75848	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.014870	0.500000	
chunk0147_393_1	chr4	186687312	186687561	+	0	NA	intron (NM_005245, intron 2 of 26)	L1M5|LINE|L1	36397	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.004016	0.340000	
chunk0191_23_1	chr8	42909722	42909933	+	0	NA	intron (NM_032410, intron 2 of 21)	L1MA7|LINE|L1	12937	NM_032410	84376	Hs.162852	NM_032410	ENSG00000168172	HOOK3	HK3	hook microtubule tethering protein 3	protein-coding	0.014218	0.415094	
chunk0174_136_1	chr6	157450583	157450799	+	0	NA	intron (NM_024630, intron 1 of 8)	intron (NM_024630, intron 1 of 8)	69166	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.009259	0.373272	
chunk0073_418_1	chr16	18932306	18932971	+	0	NA	Intergenic	Intergenic	-6234	NM_015092	23049	Hs.460179	NM_015092	ENSG00000157106	SMG1	61E3.4|ATX|LIP	SMG1 nonsense mediated mRNA decay associated PI3K related kinase	protein-coding	0.007519	0.403904	555(GGGCACAAGAAGTGCT,-,0.00),556(GGCACAAGAAGTGCTG,+,0.00)
chunk0027_98_1	chr10	73743873	73744106	+	0	NA	promoter-TSS (NM_004922)	promoter-TSS (NM_004922)	-384	NM_004922	9632	Hs.81964	NM_004922	ENSG00000176986	SEC24C	-	SEC24 homolog C, COPII coat complex component	protein-coding	0.030043	0.508547	
chunk0113_127_1	chr20	51692996	51693596	+	0	NA	intron (NM_006045, intron 7 of 27)	intron (NM_006045, intron 7 of 27)	75115	NM_006045	10079	Hs.649234	NM_006045	ENSG00000054793	ATP9A	ATPIIA	ATPase phospholipid transporting 9A (putative)	protein-coding	0.020000	0.535774	
chunk0145_270_1	chr4	149405152	149405398	+	0	NA	Intergenic	Intergenic	250980	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.008130	0.372470	
chunk0031_14_1	chr10	121687264	121687467	+	0	NA	Intergenic	Intergenic	-88907	NM_000141	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.029557	0.583333	
chunk0158_17_1	chr5	125321492	125322038	+	0	NA	intron (NR_109882, intron 4 of 5)	L2a|LINE|L2	-171496	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.003663	0.345521	
chunk0175_3_1	chr7	107950	108297	+	0	NA	Intergenic	Intergenic	-41595	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.005764	0.494253	
chunk0034_37_1	chr11	26572602	26573225	+	0	NA	promoter-TSS (NM_145650)	promoter-TSS (NM_145650)	-645	NM_001135091	143662	Hs.407152	NM_145650	ENSG00000169550	MUC15	MUC-15|PAS3|PASIII	mucin 15, cell surface associated	protein-coding	0.016051	0.431090	
chunk0210_121_1	chrX	72634308	72634719	+	0	NA	intron (NM_001122670, intron 16 of 30)	intron (NM_001122670, intron 16 of 30)	-54436	NR_110391	101928259	Hs.666679	NR_110391	ENSG00000231944	PHKA1-AS1	-	PHKA1 antisense RNA 1	ncRNA	0.007299	0.371359	
chunk0124_293_1	chr3	57756693	57756967	+	0	NA	promoter-TSS (NM_007159)	promoter-TSS (NM_007159)	-426	NM_007159	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.135036	0.770909	
chunk0038_113_1	chr11	83784203	83785043	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	-102198	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.005952	0.321046	
chunk0053_8_1	chr13	26190739	26191186	+	0	NA	intron (NM_183045, intron 5 of 5)	intron (NM_183045, intron 5 of 5)	30795	NM_183044	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.004474	0.363839	
chunk0206_230_1	chr9	123537897	123538177	+	0	NA	intron (NM_024820, intron 13 of 20)	L1MC5|LINE|L1	-52415	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.007143	0.398577	
chunk0132_52_1	chr3	155019648	155019847	+	0	NA	Intergenic	L2a|LINE|L2	-59900	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.000000	0.445000	
chunk0207_361_1	chr9	135393541	135394052	+	0	NA	Intergenic	Intergenic	50547	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.021526	0.593750	
chunk0124_4_1	chr3	51484448	51484756	+	0	NA	intron (NM_001171904, intron 1 of 24)	intron (NM_001171904, intron 1 of 24)	15400	NM_014703	9730	Hs.716623	NM_014703	ENSG00000145041	DCAF1	RIP|VPRBP	DDB1 and CUL4 associated factor 1	protein-coding	0.012987	0.381877	
chunk0111_184_1	chr20	25353647	25354611	+	0	NA	intron (NM_001042472, intron 1 of 12)	intron (NM_001042472, intron 1 of 12)	36853	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.017635	0.494301	143(GGGACACACTGCTCAC,+,0.00),311(GGAACAGGCTGGTCAG,+,0.00),658(GGGTGCACACTGTCCT,-,0.00),659(GGTGCACACTGTCCTG,+,0.00)
chunk0146_432_1	chr4	169449135	169449724	+	0	NA	intron (NM_001199399, intron 24 of 32)	L1PA6|LINE|L1	163198	NM_001199400	4750	Hs.481181	NM_012224	ENSG00000137601	NEK1	ALS24|NY-REN-55|SRPS2|SRPS2A|SRTD6	NIMA related kinase 1	protein-coding	0.008489	0.500000	
chunk0013_88_1	chr1	167678655	167679237	+	0	NA	intron (NM_052862, intron 1 of 6)	L2a|LINE|L2	-43004	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.017182	0.456261	
chunk0130_151_1	chr3	132317269	132318010	+	0	NA	intron (NM_001099, intron 1 of 9)	intron (NM_001099, intron 1 of 9)	272	NM_001134194	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.008097	0.408356	
chunk0062_132_1	chr14	68607193	68607675	+	0	NA	Intergenic	Intergenic	186480	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.016598	0.515528	
chunk0006_85_1	chr1	64989379	64989834	+	0	NA	intron (NR_119383, intron 3 of 6)	L1MB4|LINE|L1	12870	NR_119383	101927084	Hs.734218	NR_119383	ENSG00000226891	LINC01359	-	long intergenic non-protein coding RNA 1359	ncRNA	0.006593	0.449561	
chunk0035_168_1	chr11	43846566	43847285	+	0	NA	intron (NM_016142, intron 9 of 10)	intron (NM_016142, intron 9 of 10)	-33882	NM_139178	221120	Hs.720708	NM_139178	ENSG00000166199	ALKBH3	ABH3|DEPC-1|DEPC1|PCA1|hABH3	alkB homolog 3, alpha-ketoglutaratedependent dioxygenase	protein-coding	0.008345	0.423611	
chunk0181_390_1	chr7	89684956	89685678	+	0	NA	Intergenic	Intergenic	-434083	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.001385	0.365145	
chunk0026_426_1	chr10	70851873	70852144	+	0	NA	intron (NM_003901, intron 4 of 14)	intron (NM_003901, intron 4 of 14)	36060	NM_003901	8879	Hs.499984	NM_003901	ENSG00000166224	SGPL1	NPHS14|S1PL|SPL	sphingosine-1-phosphate lyase 1	protein-coding	0.007380	0.503676	
chunk0008_308_1	chr1	95095888	95096590	+	0	NA	intron (NM_001199679, intron 1 of 6)	intron (NM_001199679, intron 1 of 6)	3722	NM_001199679	148534	Hs.483512	NM_152487	ENSG00000152078	TLCD4	TMEM56	TLC domain containing 4	protein-coding	0.007123	0.396871	
chunk0052_69_1	chr13	21373377	21373742	+	0	NA	non-coding (NR_104487, exon 13 of 13)	non-coding (NR_104487, exon 13 of 13)	-28700	NR_103841	100652865	Hs.659198	NR_103840		LINC00539	LINC00422	long intergenic non-protein coding RNA 539	ncRNA	0.005479	0.316940	
chunk0030_460_1	chr10	121324874	121325111	+	0	NA	Intergenic	L1MC3|LINE|L1	268975	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.008439	0.508403	
chunk0117_443_1	chr21	46486522	46487774	+	0	NA	intron (NM_206889, intron 2 of 21)	L1ME3B|LINE|L1	24677	NR_046400	100862692	Hs.737163	NR_046400	ENSG00000223692	DIP2A-IT1	-	DIP2A intronic transcript 1	ncRNA	0.006390	0.351157	601(AGGCACTGAGTGTTTT,-,0.00)
chunk0186_69_1	chr7	137171812	137172711	+	0	NA	Intergenic	Intergenic	-7920	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.005562	0.350000	
chunk0083_331_1	chr17	70095389	70095833	+	0	NA	intron (NM_001291622, intron 1 of 5)	MER89|LTR|ERV1	-9234	NM_001291623	3773	Hs.463985	NM_018658	ENSG00000153822	KCNJ16	BIR9|KIR5.1	potassium voltage-gated channel subfamily J member 16	protein-coding	0.009009	0.411236	
chunk0136_421_1	chr3	197472890	197473410	+	0	NA	Intergenic	Intergenic	82837	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.011538	0.449136	
chunk0020_156_1	chr1	234092979	234093520	+	0	NA	intron (NM_173508, intron 2 of 7)	intron (NM_173508, intron 2 of 7)	-120962	NM_001300845	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.005545	0.405904	
chunk0179_247_1	chr7	48295188	48295837	+	0	NA	intron (NM_152701, intron 20 of 61)	MIRc|SINE|MIR	124052	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.010786	0.409231	295(AAGAACAAGCTGTCTT,-,0.00),296(AGAACAAGCTGTCTTG,+,0.00)
chunk0145_187_1	chr4	147802464	147802668	+	0	NA	intron (NM_024605, intron 1 of 22)	intron (NM_024605, intron 1 of 22)	19971	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.009804	0.482927	
chunk0040_316_1	chr11	117929135	117929670	+	0	NA	promoter-TSS (NM_001077263)	promoter-TSS (NM_001077263)	51	NM_001206789	84000	Hs.266308	NM_032046	ENSG00000137747	TMPRSS13	MSP|MSPL|MSPS|TMPRSS11	transmembrane serine protease 13	protein-coding	0.020561	0.557836	31(AGGCACAGCCAGTTTC,-,0.00)
chunk0208_418_1	chrX	29627166	29628276	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	53443	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.009910	0.382538	
chunk0142_346_1	chr4	101522074	101522310	+	0	NA	Intergenic	Intergenic	174415	NR_033874	90024	Hs.534513	NR_033874	ENSG00000254531	FLJ20021	-	uncharacterized LOC90024	ncRNA	0.000000	0.379747	
chunk0071_459_1	chr15	90316153	90316511	+	0	NA	Intergenic	Intergenic	33115	NR_028287	23766	Hs.592014	NR_028287		GABARAPL3	ATG8D	GABA type A receptor associated protein like 3 pseudogene	pseudo	0.008380	0.392758	
chunk0202_426_1	chr9	81795301	81795599	+	0	NA	Intergenic	L2a|LINE|L2	105737	NR_109772	101927502	Hs.528628	NR_109772	ENSG00000233926	LOC101927502	-	uncharacterized LOC101927502	ncRNA	0.003356	0.448161	129(GAGAACTCAGTGTGCT,-,0.00),130(AGAACTCAGTGTGCTC,+,0.00)
chunk0127_308_1	chr3	98829955	98830355	+	0	NA	intron (NM_080927, intron 3 of 15)	L1PREC2|LINE|L1	71534	NM_080927	131566	Hs.203691	NM_080927	ENSG00000057019	DCBLD2	CLCP1|ESDN	discoidin, CUB and LCCL domain containing 2	protein-coding	0.002500	0.339152	
chunk0033_23_1	chr11	12693963	12694162	+	0	NA	intron (NM_021961, intron 2 of 12)	intron (NM_021961, intron 2 of 12)	19640	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.025126	0.510000	89(TGGCACACCCTGCTCT,-,0.00),90(GGCACACCCTGCTCTG,+,0.00)
chunk0090_398_1	chr18	78125825	78126110	+	0	NA	Intergenic	(TGTGCATG)n|Simple_repeat|Simple_repeat	-132240	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.017544	0.489510	
chunk0096_194_1	chr2	30146487	30146784	+	0	NA	promoter-TSS (NM_001127399)	promoter-TSS (NM_001127399)	-249	NM_001127400	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.067340	0.624161	
chunk0071_204_1	chr15	84001175	84001827	+	0	NA	intron (NM_207517, intron 23 of 29)	MIRb|SINE|MIR	-78686	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.007669	0.471669	
chunk0027_212_1	chr10	76072465	76072802	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	289872	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.000000	0.431953	
chunk0199_36_1	chr9	899607	900026	+	0	NA	intron (NM_021951, intron 3 of 4)	intron (NM_021951, intron 3 of 4)	58126	NM_021951	1761	Hs.98586	NM_021951	ENSG00000137090	DMRT1	CT154|DMT1	doublesex and mab-3 related transcription factor 1	protein-coding	0.023866	0.471429	
chunk0092_157_1	chr19	29671843	29672174	+	0	NA	intron (NM_024310, intron 1 of 1)	L2a|LINE|L2	6588	NM_024310	79156	Hs.466383	NM_024310	ENSG00000166289	PLEKHF1	APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology and FYVE domain containing 1	protein-coding	0.018127	0.500000	
chunk0168_424_1	chr6	95532556	95532960	+	0	NA	Intergenic	Intergenic	44693	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.007426	0.417284	
chunk0057_392_1	chr13	109509366	109510094	+	0	NA	Intergenic	Intergenic	109034	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.006868	0.406036	318(AGGTACATCGTGTCCC,-,0.00),319(GGTACATCGTGTCCCA,+,0.00),350(AGGTACATCGTGTCCC,-,0.00),351(GGTACATCGTGTCCCA,+,0.00)
chunk0020_339_1	chr1	239056878	239057386	+	0	NA	Intergenic	MER83C|LTR|ERV1	-571115	NR_015407	339535	Hs.532047	NR_015407	ENSG00000215808	LINC01139	LINK-A|LINKA	long intergenic non-protein coding RNA 1139	ncRNA	0.009843	0.461690	266(CAGGACATCCTGTTCC,-,0.00),267(AGGACATCCTGTTCCC,+,0.00)
chunk0023_58_1	chr10	21934327	21934841	+	0	NA	intron (NM_022365, intron 1 of 11)	Tigger3b|DNA|TcMar-Tigger	69137	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.001946	0.328155	230(AAGTACATTTTGTACC,-,0.00),231(AGTACATTTTGTACCT,+,0.00)
chunk0169_217_1	chr6	103722786	103723035	+	0	NA	Intergenic	Intergenic	1137009	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.004016	0.396000	
chunk0086_303_1	chr18	23986598	23986832	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-6058	NM_153211	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.000000	0.378723	
chunk0106_3_1	chr2	195322408	195322768	+	0	NA	Intergenic	Intergenic	-334220	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.011111	0.468144	
chunk0078_197_1	chr17	5237492	5237804	+	0	NA	Intergenic	Intergenic	-2788	NM_001271842	388325	Hs.462080	NM_207103	ENSG00000161929	SCIMP	C17orf87|UNQ5783	SLP adaptor and CSK interacting membrane protein	protein-coding	0.016026	0.549521	
chunk0022_230_1	chr10	14082618	14083175	+	0	NA	intron (NR_120638, intron 1 of 2)	L2a|LINE|L2	8612	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.010772	0.426523	
chunk0087_75_1	chr18	32018452	32018805	+	0	NA	5' UTR (NM_017831, exon 1 of 6)	5' UTR (NM_017831, exon 1 of 6)	146	NM_017831	54941	Hs.633703	NM_017831	ENSG00000101695	RNF125	TNORS|TRAC-1|TRAC1	ring finger protein 125	protein-coding	0.076487	0.629944	
chunk0141_412_1	chr4	88599948	88600950	+	0	NA	intron (NM_001271602, intron 2 of 24)	Tigger17|DNA|TcMar-Tigger	8026	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.002994	0.340977	
chunk0084_271_1	chr17	79658044	79658464	+	0	NA	Intergenic	Intergenic	48995	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.004762	0.543943	100(AAGGACTTGCAGTGCC,-,0.00),101(AGGACTTGCAGTGCCC,+,0.00)
chunk0212_43_1	chrY	11294869	11295845	+	0	NA	Intergenic	Intergenic	1126233	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.008197	0.442170	
chunk0179_365_1	chr7	51129361	51130060	+	0	NA	intron (NM_001287436, intron 6 of 13)	intron (NM_001287436, intron 6 of 13)	187108	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.008584	0.498571	
chunk0014_33_1	chr1	174874688	174875138	+	0	NA	promoter-TSS (NM_001035230)	promoter-TSS (NM_001035230)	527	NM_001243763	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.011111	0.356984	
chunk0177_291_1	chr7	25770117	25770486	+	0	NA	Intergenic	Intergenic	179685	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.002710	0.397297	
chunk0142_275_1	chr4	99455328	99455904	+	0	NA	Intergenic	Intergenic	-20106	NM_000673	131	Hs.389	NM_000673	ENSG00000196344	ADH7	ADH4	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding	0.001736	0.329289	
chunk0093_47_1	chr19	39969278	39969693	+	0	NA	Intergenic	AluJb|SINE|Alu	-1520	NM_153001	5704	Hs.211594	NM_006503	ENSG00000013275	PSMC4	MIP224|RPT3|S6|TBP-7|TBP7	proteasome 26S subunit, ATPase 4	protein-coding	0.014458	0.461538	75(CAGTACACAGAGTACT,-,0.00),76(AGTACACAGAGTACTG,+,0.00)
chunk0068_130_1	chr15	52678165	52678881	+	0	NA	non-coding (NR_104457, exon 1 of 13)	non-coding (NR_104457, exon 1 of 13)	111	NM_019600	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.060056	0.609484	159(AGGCCAATGTGTCCTT,+,0.00)
chunk0176_215_1	chr7	14777924	14778481	+	0	NA	intron (NM_145695, intron 1 of 23)	MIR3|SINE|MIR	63248	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.007181	0.329749	187(CTGAACACCCTGTTCT,-,0.00),188(TGAACACCCTGTTCTT,+,0.00)
chunk0056_433_1	chr13	95044998	95046014	+	0	NA	intron (NM_005845, intron 27 of 30)	intron (NM_005845, intron 27 of 30)	85465	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.005906	0.376598	
chunk0035_92_1	chr11	42127581	42127988	+	0	NA	Intergenic	L1MC1|LINE|L1	125906	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002457	0.350490	
chunk0199_425_1	chr9	13697388	13698008	+	0	NA	Intergenic	L1PA13|LINE|L1	-230273	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.008065	0.579710	
chunk0064_250_1	chr14	94559687	94559955	+	0	NA	Intergenic	Intergenic	-1599	NM_006215	5267	Hs.719893	NM_006215	ENSG00000100665	SERPINA4	KAL|KLST|KST|PI-4|PI4|kallistatin	serpin family A member 4	protein-coding	0.014925	0.527881	164(AGGGACAAGCTGTCCA,-,0.00),165(GGGACAAGCTGTCCAT,+,0.00)
chunk0186_265_1	chr7	141573438	141573940	+	0	NA	intron (NM_018238, intron 2 of 15)	intron (NM_018238, intron 2 of 15)	22411	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.015936	0.377734	
chunk0173_145_1	chr6	144028937	144029370	+	0	NA	intron (NM_001289040, intron 1 of 5)	L1M5|LINE|L1	-20423	NR_002768	57061	Hs.657760	NR_002768	ENSG00000283122	HYMAI	NCRNA00020	hydatidiform mole associated and imprinted	ncRNA	0.002309	0.290323	
chunk0052_265_1	chr12	123913319	123913679	+	0	NA	intron (NM_207437, intron 59 of 77)	intron (NM_207437, intron 59 of 77)	58591	NM_001304959	80212	Hs.114111	NM_025140	ENSG00000119242	CCDC92	-	coiled-coil domain containing 92	protein-coding	0.025000	0.459834	
chunk0166_376_1	chr6	51612380	51612805	+	0	NA	Intergenic	L1M6|LINE|L1	-9278	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.002353	0.267606	
chunk0174_359_1	chr6	164497738	164498339	+	0	NA	Intergenic	L1M5|LINE|L1	324025	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.000000	0.269103	
chunk0107_374_1	chr2	222932951	222933667	+	0	NA	intron (NM_004457, intron 15 of 16)	intron (NM_004457, intron 15 of 16)	72295	NM_203372	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.005587	0.386332	
chunk0149_45_1	chr5	16588458	16588892	+	0	NA	intron (NM_001034850, intron 1 of 8)	intron (NM_001034850, intron 1 of 8)	-27251	NR_109946	101929524	Hs.734029	NR_109946	ENSG00000246214	LOC101929524	-	uncharacterized LOC101929524	ncRNA	0.013825	0.457471	
chunk0079_203_1	chr17	14448561	14449366	+	0	NA	Intergenic	Intergenic	145223	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.007453	0.485112	
chunk0182_433_1	chr7	101441642	101441841	+	0	NA	intron (NM_133457, intron 2 of 12)	intron (NM_133457, intron 2 of 12)	78921	NM_133457	136227	Hs.654854	NM_133457	ENSG00000160963	COL26A1	EMI6|EMID2|EMU2|SH2B	collagen type XXVI alpha 1 chain	protein-coding	0.020101	0.595000	
chunk0121_85_1	chr3	16178215	16178503	+	0	NA	intron (NM_054110, intron 1 of 9)	MER81|DNA|hAT-Blackjack	3682	NM_054110	117248	Hs.411308	NM_054110	ENSG00000131386	GALNT15	GALNACT15|GALNT13|GALNT7|GALNTL2|PIH5|pp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.038194	0.536332	36(GGGTACATTTTGTGCT,-,0.00),37(GGTACATTTTGTGCTG,+,0.00)
chunk0166_245_1	chr6	47286068	47286295	+	0	NA	exon (NM_014452, exon 2 of 6)	exon (NM_014452, exon 2 of 6)	23766	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.026432	0.552632	
chunk0193_14_1	chr8	70608419	70608711	+	0	NA	promoter-TSS (NM_014294)	promoter-TSS (NM_014294)	-12	NR_038881	286190	Hs.662204	NR_038881	ENSG00000246366	LACTB2-AS1	-	LACTB2 antisense RNA 1	ncRNA	0.099315	0.703072	
chunk0023_154_1	chr10	24256077	24256444	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	-19425	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.008174	0.489130	
chunk0052_347_1	chr12	126561112	126561773	+	0	NA	Intergenic	L2b|LINE|L2	118961	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.004539	0.398792	
chunk0162_5_1	chr6	307580	307904	+	0	NA	intron (NR_104474, intron 2 of 5)	intron (NR_104474, intron 2 of 5)	15685	NR_104474	56940	Hs.29106	NM_020185	ENSG00000112679	DUSP22	JKAP|JSP-1|JSP1|LMW-DSP2|LMWDSP2|MKP-x|MKPX|VHX	dual specificity phosphatase 22	protein-coding	0.021605	0.544615	248(AAGACAGACAGTCCTG,+,0.00)
chunk0179_42_1	chr7	43318375	43318585	+	0	NA	intron (NM_015052, intron 4 of 29)	intron (NM_015052, intron 4 of 29)	167585	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.009524	0.417062	
chunk0209_66_1	chrX	37677418	37677618	+	0	NA	TTS (NM_001170331)	TTS (NM_001170331)	-8362	NM_021083	7504	Hs.78919	NM_021083	ENSG00000047597	XK	KX|NA|NAC|X1k|XKR1	X-linked Kx blood group	protein-coding	0.000000	0.348259	
chunk0097_207_1	chr2	51241787	51242057	+	0	NA	Intergenic	L2a|LINE|L2	-209386	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.361624	
chunk0150_317_1	chr5	38044289	38044915	+	0	NA	Intergenic	Intergenic	171177	NM_001278094	100861519	Hs.536820	NM_001278094		GDNF-AS1	GDNFOS	GDNF antisense RNA 1	ncRNA	0.004792	0.320574	
chunk0163_115_1	chr6	10193564	10193865	+	0	NA	Intergenic	Intergenic	-218604	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003322	0.427152	
chunk0120_297_1	chr3	9935073	9935379	+	0	NA	intron (NM_001031717, intron 3 of 11)	L2a|LINE|L2	1385	NM_001077415	78987	Hs.9383	NM_015513	ENSG00000163703	CRELD1	AVSD2|CIRRIN	cysteine rich with EGF like domains 1	protein-coding	0.013072	0.488599	
chunk0196_21_1	chr8	101512072	101512752	+	0	NA	intron (NM_024915, intron 1 of 15)	L1M5|LINE|L1	19972	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.016176	0.353891	
chunk0055_186_1	chr13	61515570	61516103	+	0	NA	Intergenic	Intergenic	-100314	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.009381	0.340824	
chunk0204_449_1	chr9	104297214	104297677	+	0	NA	Intergenic	LTR80A|LTR|ERVL	202895	NM_001042550	10592	Hs.119023	NM_006444	ENSG00000136824	SMC2	CAP-E|CAPE|SMC-2|SMC2L1	structural maintenance of chromosomes 2	protein-coding	0.010799	0.353448	
chunk0100_319_1	chr2	116439963	116440314	+	0	NA	Intergenic	Intergenic	1278031	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.000000	0.369318	
chunk0186_347_1	chr7	143419801	143420582	+	0	NA	intron (NR_033897, intron 2 of 4)	intron (NR_033897, intron 2 of 4)	-11299	NM_005232	2041	Hs.89839	NM_005232	ENSG00000146904	EPHA1	EPH|EPHT|EPHT1	EPH receptor A1	protein-coding	0.008963	0.390026	
chunk0144_208_1	chr4	134202596	134202907	+	0	NA	Intergenic	Intergenic	-1003	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.009646	0.426282	
chunk0111_43_1	chr20	22302232	22302520	+	0	NA	Intergenic	Intergenic	-19575	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.006944	0.494810	179(ATCACACAGTGTCCCT,+,0.00)
chunk0172_133_1	chr6	135295200	135295793	+	0	NA	intron (NM_017651, intron 26 of 27)	L1M4|LINE|L1	56336	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.003373	0.351852	
chunk0042_317_1	chr12	8655090	8655613	+	0	NA	intron (NR_123734, intron 5 of 9)	intron (NR_123734, intron 5 of 9)	7537	NM_001297710	8076	Hs.512842	NM_003480	ENSG00000197614	MFAP5	AAT9|MAGP-2|MAGP2|MFAP-5|MP25	microfibril associated protein 5	protein-coding	0.013384	0.421756	
chunk0012_430_1	chr1	164719674	164719993	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	54808	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.015674	0.462500	
chunk0089_277_1	chr18	62857681	62858027	+	0	NA	intron (NM_194449, intron 3 of 16)	L2b|LINE|L2	142415	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.005780	0.420749	
chunk0206_157_1	chr9	121592369	121592738	+	0	NA	intron (NM_032552, intron 1 of 16)	intron (NM_032552, intron 1 of 16)	25451	NM_032552	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.010840	0.408108	190(AAGTACATGTTGTTCT,-,0.00),191(AGTACATGTTGTTCTT,+,0.00)
chunk0089_266_1	chr18	62672656	62672893	+	0	NA	Intergenic	L1M4|LINE|L1	-42665	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.004219	0.403361	
chunk0168_196_1	chr6	85500339	85500602	+	0	NA	Intergenic	MSTA|LTR|ERVL-MaLR	50886	NM_002526	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.003802	0.450758	
chunk0189_73_1	chr8	20895368	20895619	+	0	NA	Intergenic	Intergenic	-58140	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.007968	0.321429	
chunk0079_216_1	chr17	14886249	14886476	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-144613	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.000000	0.429825	
chunk0202_194_1	chr9	74952357	74952633	+	0	NA	promoter-TSS (NR_121183)	promoter-TSS (NR_121183)	391	NM_017998	55071	Hs.532296	NM_017998	ENSG00000135045	C9orf40	-	chromosome 9 open reading frame 40	protein-coding	0.123188	0.714801	
chunk0051_172_1	chr12	116078405	116078870	+	0	NA	intron (NM_015335, intron 4 of 30)	MER58A|DNA|hAT-Charlie	70017	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.002151	0.354077	
chunk0140_347_1	chr4	73947107	73948370	+	0	NA	Intergenic	Intergenic	34386	NM_002619	5196	Hs.81564	NM_002619	ENSG00000163737	PF4	CXCL4|PF-4|SCYB4	platelet factor 4	protein-coding	0.005542	0.359968	
chunk0096_426_1	chr2	38322297	38322523	+	0	NA	intron (NR_024191, intron 1 of 11)	L2a|LINE|L2	54120	NM_001308076	64225	Hs.594950	NM_022374	ENSG00000119787	ATL2	ARL3IP2|ARL6IP2|aip-2|atlastin2	atlastin GTPase 2	protein-coding	0.000000	0.317181	
chunk0109_193_1	chr20	5070482	5071103	+	0	NA	Intergenic	AluJb|SINE|Alu	42295	NM_001009923	29058	Hs.472024	NM_014145	ENSG00000089063	TMEM230	C20orf30|HSPC274|dJ1116H23.2.1	transmembrane protein 230	protein-coding	0.009662	0.430868	
chunk0054_342_1	chr13	49453629	49453845	+	0	NA	intron (NM_001160308, intron 1 of 12)	L1MC3|LINE|L1	2185	NM_001160308	83852	Hs.631789	NM_031915	ENSG00000136169	SETDB2	C13orf4|CLLD8|CLLL8|KMT1F	SET domain bifurcated histone lysine methyltransferase 2	protein-coding	0.013889	0.350230	
chunk0164_211_1	chr6	22674278	22675150	+	0	NA	Intergenic	L1MA7|LINE|L1	105265	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.008028	0.347079	
chunk0200_427_1	chr9	29423064	29423451	+	0	NA	Intergenic	Intergenic	-210257	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.373711	
chunk0002_251_1	chr1	21110902	21111238	+	0	NA	intron (NM_001198801, intron 2 of 34)	intron (NM_001198801, intron 2 of 34)	313	NM_003760	8672	Hs.467084	NM_003760	ENSG00000075151	EIF4G3	eIF-4G 3|eIF4G 3|eIF4GII	eukaryotic translation initiation factor 4 gamma 3	protein-coding	0.000000	0.308605	
chunk0110_181_1	chr20	14422829	14423326	+	0	NA	intron (NM_080676, intron 3 of 16)	L1M4c|LINE|L1	-85410	NM_013281	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.008048	0.391566	
chunk0075_23_1	chr16	46882324	46882847	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-1795	NM_133443	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.013384	0.461832	
chunk0199_97_1	chr9	2817607	2818345	+	0	NA	intron (NM_014878, intron 13 of 17)	intron (NM_014878, intron 13 of 17)	26154	NM_014878	9933	Hs.493309	NM_014878	ENSG00000080608	PUM3	HA-8|HLA-HA8|KIAA0020|PEN|PUF-A|PUF6|XTP5	pumilio RNA binding family member 3	protein-coding	0.012195	0.378890	
chunk0167_385_1	chr6	74466091	74466342	+	0	NA	intron (NR_110856, intron 2 of 3)	L1PA13|LINE|L1	396765	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.003984	0.535714	65(GGGGTCAAGGTGTTCC,-,0.00),66(GGGTCAAGGTGTTCCC,+,0.00)
chunk0008_243_1	chr1	94321623	94322359	+	0	NA	Intergenic	Intergenic	-84240	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.008152	0.407056	
chunk0097_98_1	chr2	45943549	45943971	+	0	NA	intron (NM_005400, intron 2 of 14)	intron (NM_005400, intron 2 of 14)	291856	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.014218	0.453901	
chunk0131_154_1	chr3	146140816	146141243	+	0	NA	intron (NM_000935, intron 1 of 18)	intron (NM_000935, intron 1 of 18)	20466	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.000000	0.317757	
chunk0069_246_1	chr15	64344685	64345118	+	0	NA	intron (NM_022048, intron 1 of 11)	intron (NM_022048, intron 1 of 11)	11342	NM_022048	53944	Hs.646508	NM_022048	ENSG00000169118	CSNK1G1	CK1gamma1	casein kinase 1 gamma 1	protein-coding	0.000000	0.336406	
chunk0117_429_1	chr21	46162008	46162767	+	0	NA	intron (NM_032261, intron 2 of 3)	intron (NM_032261, intron 2 of 3)	-6820	NM_206965	10841	Hs.415846	NM_006657	ENSG00000160282	FTCD	LCHC1	formimidoyltransferase cyclodeaminase	protein-coding	0.052701	0.603947	
chunk0174_241_1	chr6	160963652	160964564	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-27619	NM_006724	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.014254	0.366922	145(TAGTACAGTATGTACT,-,0.00),146(AGTACAGTATGTACTC,+,0.00)
chunk0189_12_1	chr8	19495154	19495398	+	0	NA	intron (NM_001130518, intron 4 of 9)	intron (NM_001130518, intron 4 of 9)	107269	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.004098	0.400000	
chunk0039_292_1	chr11	102739519	102740126	+	0	NA	Intergenic	L1M1|LINE|L1	-14868	NM_001304442	4317	Hs.161839	NM_002424	ENSG00000118113	MMP8	CLG1|HNC|MMP-8|PMNL-CL	matrix metallopeptidase 8	protein-coding	0.003295	0.330592	195(AAGGACTTCCAGTACT,-,0.00)
chunk0187_287_1	chr7	155715507	155715846	+	0	NA	intron (NM_053043, intron 8 of 17)	intron (NM_053043, intron 8 of 17)	71167	NM_053043	155435	Hs.591815	NM_053043	ENSG00000184863	RBM33	PRR8	RNA binding motif protein 33	protein-coding	0.011799	0.414706	184(AAGGACAAAGTGTTCT,-,0.00),185(AGGACAAAGTGTTCTT,+,0.00)
chunk0001_21_1	chr1	1233501	1233822	+	0	NA	3' UTR (NM_080605, exon 1 of 1)	3' UTR (NM_080605, exon 1 of 1)	1412	NM_080605	126792	Hs.284284	NM_080605	ENSG00000176022	B3GALT6	EDSP2|EDSSPD2|SEMDJL1|beta3GalT6	beta-1,3-galactosyltransferase 6	protein-coding	0.062305	0.490683	
chunk0140_265_1	chr4	71826249	71826700	+	0	NA	Intergenic	L2b|LINE|L2	-20954	NM_001204306	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.002217	0.362832	
chunk0194_293_1	chr8	87663979	87664249	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	209954	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.003704	0.402214	
chunk0098_374_1	chr2	78925490	78925741	+	0	NA	Intergenic	MIRc|SINE|MIR	-100071	NM_001008387	130120	Hs.447084	NM_198448	ENSG00000143954	REG3G	LPPM429|PAP IB|PAP-1B|PAP1B|PAPIB|REG III|REG-III|UNQ429	regenerating family member 3 gamma	protein-coding	0.007968	0.301587	
chunk0081_159_1	chr17	40931381	40931640	+	0	NA	intron (NM_001282433, intron 1 of 7)	intron (NM_001282433, intron 1 of 7)	6133	NM_015515	25984	Hs.9029	NM_015515	ENSG00000108244	KRT23	CK23|HAIK1|K23	keratin 23	protein-coding	0.007722	0.419231	
chunk0013_109_1	chr1	167854181	167854495	+	0	NA	intron (NM_001167749, intron 15 of 29)	intron (NM_001167749, intron 15 of 29)	59888	NM_001167749	55811	Hs.320892	NM_018417	ENSG00000143199	ADCY10	HCA2|HEL-S-7a|SAC|SACI|Sacy|hsAC	adenylate cyclase 10	protein-coding	0.015924	0.438095	
chunk0151_442_1	chr5	56058133	56058767	+	0	NA	Intergenic	Intergenic	63283	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.012618	0.418898	276(AAGCACACACTGTAAT,-,0.00)
chunk0121_23_1	chr3	14990284	14990574	+	0	NA	intron (NM_001291694, intron 1 of 13)	intron (NM_001291694, intron 1 of 13)	-41988	NR_046251	100505641	Hs.517821	NR_046251	ENSG00000225733	FGD5-AS1	-	FGD5 antisense RNA 1	ncRNA	0.006897	0.463918	
chunk0112_124_1	chr20	38485512	38486101	+	0	NA	intron (NM_020336, intron 1 of 29)	intron (NM_020336, intron 1 of 29)	13000	NM_001282917	57148	Hs.598850	NM_020336	ENSG00000170471	RALGAPB	KIAA1219|RalGAPbeta	Ral GTPase activating protein non-catalytic beta subunit	protein-coding	0.018676	0.418644	
chunk0009_252_1	chr1	107087698	107088190	+	0	NA	Intergenic	L2c|LINE|L2	31299	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.004065	0.316430	
chunk0208_168_1	chrX	16662370	16662794	+	0	NA	intron (NM_019857, intron 13 of 18)	intron (NM_019857, intron 13 of 18)	12424	NM_004057	795	Hs.639	NM_004057	ENSG00000169906	S100G	CABP|CABP1|CABP9K|CALB3	S100 calcium binding protein G	protein-coding	0.004717	0.390588	
chunk0050_346_1	chr12	107654602	107655154	+	0	NA	intron (NM_001018072, intron 16 of 16)	intron (NM_001018072, intron 16 of 16)	-30935	NM_007062	11137	Hs.506652	NM_007062	ENSG00000136045	PWP1	IEF-SSP-9502	PWP1 homolog, endonuclein	protein-coding	0.001812	0.412297	
chunk0098_232_1	chr2	74044324	74044793	+	0	NA	intron (NM_001287491, intron 2 of 10)	Tigger5|DNA|TcMar-Tigger	58154	NM_001287491	200424	Hs.208546	NM_001287491	ENSG00000187605	TET3	hCG_40738	tet methylcytosine dioxygenase 3	protein-coding	0.017058	0.397872	106(GAGTACATGATGTTCC,-,0.00),107(AGTACATGATGTTCCT,+,0.00),439(GGGGACTGTCTGTACT,-,0.00),440(GGGACTGTCTGTACTG,+,0.00)
chunk0141_162_1	chr4	82308673	82308941	+	0	NA	Intergenic	L1M1|LINE|L1	65189	NM_002138	3184	Hs.480073	NM_002138	ENSG00000138668	HNRNPD	AUF1|AUF1A|HNRPD|P37|hnRNPD0	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.003731	0.338290	
chunk0163_32_1	chr6	8225146	8225530	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-122743	NM_001135650	9521	Hs.602353	NM_004280	ENSG00000124802	EEF1E1	AIMP3|P18	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.010417	0.420779	
chunk0122_296_1	chr3	36242290	36242489	+	0	NA	Intergenic	L2c|LINE|L2	-138098	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.015075	0.490000	
chunk0152_316_1	chr5	62000524	62001167	+	0	NA	Intergenic	Intergenic	-265147	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.000000	0.386646	
chunk0183_65_1	chr7	104176889	104177165	+	0	NA	intron (NM_002553, intron 8 of 13)	LOR1-int|LTR|ERV1	31020	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.003623	0.324910	
chunk0094_152_1	chr2	5176428	5176977	+	0	NA	Intergenic	Intergenic	514416	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.003643	0.309091	238(AGGAACAGATTGTTTC,-,0.00),239(GGAACAGATTGTTTCA,+,0.00)
chunk0115_259_1	chr21	27785443	27785642	+	0	NA	Intergenic	L2a|LINE|L2	63163	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.005025	0.410000	
chunk0196_383_1	chr8	115588379	115589180	+	0	NA	intron (NM_001282903, intron 4 of 6)	intron (NM_001282903, intron 4 of 6)	79233	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.003745	0.347880	
chunk0129_100_1	chr3	119575376	119575869	+	0	NA	Intergenic	L2a|LINE|L2	-3811	NM_001291950	141	Hs.99884	NM_001125	ENSG00000144843	ADPRH	ARH1|hARH1	ADP-ribosylarginine hydrolase	protein-coding	0.004057	0.386640	
chunk0200_24_1	chr9	14736511	14736746	+	0	NA	3' UTR (NM_001177704, exon 14 of 14)	3' UTR (NM_001177704, exon 14 of 14)	-13911	NM_005454	9350	Hs.248204	NM_005454	ENSG00000147869	CER1	DAND4	cerberus 1, DAN family BMP antagonist	protein-coding	0.000000	0.394068	
chunk0116_300_1	chr21	40445092	40445880	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	62402	NR_038899	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.003807	0.400507	
chunk0076_366_1	chr16	72001454	72001995	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-1746	NM_181536	342372	Hs.675286	NM_181536	ENSG00000277481	PKD1L3	-	polycystin 1 like 3, transient receptor potential channel interacting	protein-coding	0.011091	0.385609	
chunk0032_291_1	chr11	9527425	9528056	+	0	NA	3' UTR (NM_001282656, exon 16 of 16)	3' UTR (NM_001282656, exon 16 of 16)	-45941	NM_003390	7465	Hs.249441	NM_003390	ENSG00000166483	WEE1	WEE1A|WEE1hu	WEE1 G2 checkpoint kinase	protein-coding	0.011094	0.375000	
chunk0095_95_1	chr2	15213532	15214083	+	0	NA	intron (NR_052013, intron 47 of 50)	intron (NR_052013, intron 47 of 50)	347541	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.005445	0.382246	254(AGGAACACATTGTTCA,-,0.00),255(GGAACACATTGTTCAT,+,0.00)
chunk0165_355_1	chr6	38080866	38081193	+	0	NA	intron (NM_021943, intron 3 of 5)	intron (NM_021943, intron 3 of 5)	261498	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.006116	0.338415	
chunk0026_410_1	chr10	70254104	70254573	+	0	NA	TTS (NM_022146)	TTS (NM_022146)	-20904	NM_021129	5464	Hs.437403	NM_021129	ENSG00000180817	PPA1	HEL-S-66p|IOPPP|PP|PP1|SID6-8061	pyrophosphatase (inorganic) 1	protein-coding	0.023454	0.519149	265(GGGCACACCGTGTTCT,-,0.00),266(GGCACACCGTGTTCTT,+,0.00),411(CAGTTCACAGTGTTCT,-,0.00),412(AGTTCACAGTGTTCTA,+,0.00)
chunk0189_363_1	chr8	27083242	27083693	+	0	NA	Intergenic	L2a|LINE|L2	-34504	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.004435	0.358407	
chunk0151_380_1	chr5	55241755	55242263	+	0	NA	Intergenic	Intergenic	-8292	NR_125346	10309	Hs.3041	NM_021147	ENSG00000152669	CCNO	CCNU|CILD29|UDG2	cyclin O	protein-coding	0.009843	0.406680	249(CGGCACAGGCAGTACT,-,0.00),250(GGCACAGGCAGTACTG,+,0.00)
chunk0025_314_1	chr10	57703599	57704144	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-399312	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.001835	0.342491	261(AAATACAGTCTGTCCT,-,0.00),262(AATACAGTCTGTCCTA,+,0.00)
chunk0002_300_1	chr1	23377353	23377655	+	0	NA	Intergenic	Intergenic	-7640	NM_001077195	80818	Hs.293798	NM_030634	ENSG00000125945	ZNF436	ZNF|Zfp46	zinc finger protein 436	protein-coding	0.013245	0.422442	
chunk0076_305_1	chr16	70282788	70283207	+	0	NA	intron (NM_001605, intron 1 of 20)	intron (NM_001605, intron 1 of 20)	6512	NM_001605	16	Hs.315137	NM_001605	ENSG00000090861	AARS	CMT2N|EIEE29	alanyl-tRNA synthetase	protein-coding	0.011933	0.461905	
chunk0213_14_1	chrY	20929802	20930471	+	0	NA	Intergenic	L1PA6|LINE|L1	174068	NM_001039567	140032	Hs.367761	NM_001039567	ENSG00000280969	RPS4Y2	RPS4Y2P	ribosomal protein S4 Y-linked 2	protein-coding	0.008969	0.473134	
chunk0204_400_1	chr9	102569582	102570033	+	0	NA	intron (NR_103830, intron 1 of 4)	L1M1|LINE|L1	50170	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.004435	0.530973	
chunk0069_86_1	chr15	61132377	61133093	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	96568	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.011173	0.313808	
chunk0031_369_1	chr10	130447300	130447525	+	0	NA	Intergenic	L1ME4a|LINE|L1	311037	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.008889	0.367257	
chunk0135_443_1	chr3	194075362	194076024	+	0	NA	Intergenic	L1ME2|LINE|L1	-60449	NM_005524	3280	Hs.250666	NM_005524	ENSG00000114315	HES1	HES-1|HHL|HRY|bHLHb39	hes family bHLH transcription factor 1	protein-coding	0.009063	0.423831	
chunk0169_343_1	chr6	106514482	106515035	+	0	NA	intron (NM_001624, intron 1 of 19)	intron (NM_001624, intron 1 of 19)	2903	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.007233	0.350181	
chunk0044_318_1	chr12	33780454	33780918	+	0	NA	Intergenic	L1MC1|LINE|L1	-241595	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.008621	0.359140	
chunk0107_238_1	chr2	217147893	217148274	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-134650	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.007874	0.439791	
chunk0067_126_1	chr15	42821917	42822309	+	0	NA	intron (NM_173500, intron 6 of 14)	L1ME1|LINE|L1	-84894	NM_138477	146059	Hs.599232	NM_138477	ENSG00000140326	CDAN1	CDA1|CDAI|CDAN1A|DLT|PRO1295	codanin 1	protein-coding	0.005102	0.346056	
chunk0004_63_1	chr1	43265226	43265763	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	-4500	NM_144626	128218	Hs.104476	NM_144626	ENSG00000179178	TMEM125	-	transmembrane protein 125	protein-coding	0.007449	0.369888	
chunk0197_317_1	chr8	124854289	124854686	+	0	NA	Intergenic	(TAT)n|Simple_repeat|Simple_repeat	-32429	NR_039809	100616255		NR_039809	ENSG00000263735	MIR4662B	-	microRNA 4662b	ncRNA	0.005038	0.316583	
chunk0096_30_1	chr2	26772252	26772810	+	0	NA	intron (NM_017877, intron 1 of 5)	intron (NM_017877, intron 1 of 5)	8257	NM_017877	54978	Hs.1594	NM_017877	ENSG00000213699	SLC35F6	ANT2BP|C2orf18|TANGO9	solute carrier family 35 member F6	protein-coding	0.014337	0.518784	
chunk0105_272_1	chr2	189521827	189522481	+	0	NA	Intergenic	Intergenic	58657	NM_014585	30061	Hs.643005	NM_014585	ENSG00000138449	SLC40A1	FPN1|HFE4|IREG1|MST079|MSTP079|MTP1|SLC11A3	solute carrier family 40 member 1	protein-coding	0.001529	0.369466	
chunk0027_218_1	chr10	76196022	76196381	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	413440	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.002786	0.425000	
chunk0057_398_1	chr13	109576167	109576833	+	0	NA	Intergenic	Intergenic	-151774	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.012012	0.451274	211(GAGCACATAGTGACCT,-,0.00),212(AGCACATAGTGACCTC,+,0.00)
chunk0187_427_1	chr7	158658386	158658759	+	0	NA	intron (NR_104054, intron 19 of 30)	intron (NR_104054, intron 19 of 30)	46259	NR_104054	54892	Hs.18616	NM_017760	ENSG00000146918	NCAPG2	3KS|CAP-G2|CAPG2|LUZP5|MTB|hCAP-G2	non-SMC condensin II complex subunit G2	protein-coding	0.010724	0.352941	
chunk0060_435_1	chr14	54364967	54365169	+	0	NA	Intergenic	Intergenic	-31887	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.019802	0.482759	
chunk0181_364_1	chr7	88671768	88672341	+	0	NA	Intergenic	Intergenic	-87314	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.006981	0.311847	
chunk0127_302_1	chr3	98522842	98523079	+	0	NA	5' UTR (NM_001040182, exon 1 of 6)	5' UTR (NM_001040182, exon 1 of 6)	106	NM_019895	56650	Hs.531371	NM_019895	ENSG00000080822	CLDND1	C3orf4|GENX-3745|Z38	claudin domain containing 1	protein-coding	0.080169	0.697479	
chunk0090_392_1	chr18	77526694	77527471	+	0	NA	Intergenic	(TGTGCA)n|Simple_repeat|Simple_repeat	277030	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.020592	0.502571	
chunk0117_289_1	chr22	24360717	24361331	+	0	NA	intron (NM_001145468, intron 10 of 15)	intron (NM_001145468, intron 10 of 15)	18916	NM_001254733	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.001629	0.403252	
chunk0208_412_1	chrX	29532872	29533525	+	0	NA	intron (NM_014271, intron 5 of 10)	L1MB8|LINE|L1	-41080	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.003063	0.340979	
chunk0048_349_1	chr12	85030838	85031387	+	0	NA	intron (NM_001100917, intron 1 of 8)	intron (NM_001100917, intron 1 of 8)	5165	NM_001100917	144448	Hs.156962	NM_001100917	ENSG00000231738	TSPAN19	-	tetraspanin 19	protein-coding	0.009107	0.327273	
chunk0168_352_1	chr6	93193728	93194936	+	0	NA	Intergenic	L3|LINE|CR1	225250	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.002483	0.314309	
chunk0140_206_1	chr4	70517789	70518521	+	0	NA	promoter-TSS (NM_001286731)	promoter-TSS (NM_001286731)	-417	NM_001286731	401138	Hs.453069	NM_212557	ENSG00000187689	AMTN	AI3B|UNQ689	amelotin	protein-coding	0.002732	0.305593	
chunk0195_70_1	chr8	93927874	93928152	+	0	NA	Intergenic	Intergenic	10962	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.007194	0.326165	
chunk0032_127_1	chr11	4375258	4375949	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-7217	NM_001005161	143496	Hs.447463	NM_001005161	ENSG00000221996	OR52B4	OR11-3	olfactory receptor family 52 subfamily B member 4 (gene/pseudogene)	protein-coding	0.005789	0.417630	
chunk0105_334_1	chr2	191177342	191177768	+	0	NA	Intergenic	Intergenic	-25959	NM_001243835	6775	Hs.80642	NM_003151	ENSG00000138378	STAT4	SLEB11	signal transducer and activator of transcription 4	protein-coding	0.002347	0.362998	
chunk0150_243_1	chr5	36112452	36113091	+	0	NA	intron (NM_001007527, intron 13 of 17)	MIRc|SINE|MIR	35217	NR_030306	693165		NR_030306	ENSG00000207756	MIR580	MIRN580|hsa-mir-580	microRNA 580	ncRNA	0.003130	0.304688	
chunk0159_136_1	chr5	139137333	139137532	+	0	NA	intron (NM_022464, intron 1 of 9)	intron (NM_022464, intron 1 of 9)	60944	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.010050	0.420000	
chunk0161_344_1	chr5	174146814	174147156	+	0	NA	Intergenic	Intergenic	101381	NM_015980	51617	Hs.559412	NM_015980	ENSG00000170091	NSG2	CALY3|HMP19	neuronal vesicle trafficking associated 2	protein-coding	0.011696	0.475219	
chunk0089_205_1	chr18	60663198	60663397	+	0	NA	Intergenic	Intergenic	-290529	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.050251	0.575000	
chunk0148_210_1	chr5	8648971	8649368	+	0	NA	Intergenic	L2a|LINE|L2	188244	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.012594	0.391960	
chunk0132_27_1	chr3	154692941	154693605	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-263558	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.004518	0.305263	
chunk0106_430_1	chr2	208344150	208344642	+	0	NA	intron (NM_015040, intron 32 of 41)	intron (NM_015040, intron 32 of 41)	-15449	NM_001309516	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.000000	0.298174	
chunk0200_287_1	chr9	22386668	22387307	+	0	NA	Intergenic	Intergenic	-59854	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.003130	0.323437	328(GAAAACATTGTGTGCT,-,0.00),329(AAAACATTGTGTGCTA,+,0.00)
chunk0186_213_1	chr7	139950920	139951440	+	0	NA	intron (NM_001314028, intron 5 of 12)	intron (NM_001314028, intron 5 of 12)	112541	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.017308	0.451056	
chunk0096_286_1	chr2	32361825	32362290	+	0	NA	intron (NM_016252, intron 1 of 73)	L1MC1|LINE|L1	5029	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.006452	0.360515	
chunk0035_407_1	chr11	56801550	56802059	+	0	NA	Intergenic	Intergenic	-46674	NR_110137	101927120	Hs.472675	NR_110136	ENSG00000255433	LINC02735	-	long intergenic non-protein coding RNA 2735	ncRNA	0.000000	0.360784	
chunk0035_173_1	chr11	43894523	43894945	+	0	NA	intron (NM_139178, intron 7 of 9)	intron (NM_139178, intron 7 of 9)	-2569	NR_026952	729799	Hs.368920	NR_026952	ENSG00000213693	SEC14L1P1	-	SEC14 like 1 pseudogene 1	pseudo	0.004739	0.328605	
chunk0116_251_1	chr21	38802603	38802997	+	0	NA	Intergenic	L2c|LINE|L2	-2507	NM_001256295	2114	Hs.644231	NM_005239	ENSG00000157557	ETS2	ETS2IT1	ETS proto-oncogene 2, transcription factor	protein-coding	0.012690	0.412658	
chunk0132_88_1	chr3	155572077	155572807	+	0	NA	intron (NM_001130960, intron 5 of 22)	HAL1|LINE|L1	103874	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.005479	0.374829	
chunk0176_263_1	chr7	16342923	16343310	+	0	NA	intron (NM_001101417, intron 2 of 8)	intron (NM_001101417, intron 2 of 8)	78206	NM_001101417	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.005168	0.358247	
chunk0183_143_1	chr7	105816950	105817371	+	0	NA	intron (NM_020725, intron 2 of 11)	intron (NM_020725, intron 2 of 11)	59425	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.007126	0.376777	
chunk0140_213_1	chr4	70778924	70779351	+	0	NA	intron (NM_001130709, intron 8 of 11)	intron (NM_001130709, intron 8 of 11)	44791	NM_001291993	22902	Hs.740904	NM_014961	ENSG00000018189	RUFY3	RIPX|SINGAR1|ZFYVE30	RUN and FYVE domain containing 3	protein-coding	0.009368	0.413551	
chunk0163_413_1	chr6	17039222	17039849	+	0	NA	Intergenic	L1ME1|LINE|L1	-62723	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.009569	0.374204	
chunk0009_258_1	chr1	107301244	107301531	+	0	NA	intron (NM_001312688, intron 2 of 7)	intron (NM_001312688, intron 2 of 7)	153318	NM_001113226	22854	Hs.133046	NM_014917	ENSG00000162631	NTNG1	Lmnt1	netrin G1	protein-coding	0.000000	0.395833	
chunk0208_162_1	chrX	16385977	16386615	+	0	NA	Intergenic	L2c|LINE|L2	218815	NM_001277307	645864	Hs.632792	NM_001277307	ENSG00000182798	MAGEB17	-	MAGE family member B17	protein-coding	0.000000	0.328638	
chunk0179_87_1	chr7	44582074	44582368	+	0	NA	promoter-TSS (NM_001303058)	promoter-TSS (NM_001303058)	74	NM_001303059	222068	Hs.598832	NM_182547	ENSG00000158604	TMED4	ERS25|GMP25iso|HNLF|p24a3|p24alpha3	transmembrane p24 trafficking protein 4	protein-coding	0.108844	0.677966	
chunk0104_185_1	chr2	175002491	175003143	+	0	NA	intron (NR_038133, intron 1 of 11)	intron (NR_038133, intron 1 of 11)	2436	NM_001822	1123	Hs.380138	NM_001822	ENSG00000128656	CHN1	ARHGAP2|CHN|DURS2|NC|RHOGAP2	chimerin 1	protein-coding	0.003067	0.379786	
chunk0078_221_1	chr17	6437994	6438313	+	0	NA	Intergenic	L1ME3B|LINE|L1	-2954	NM_001285399	23746	Hs.279887	NM_014336	ENSG00000129221	AIPL1	AIPL2|LCA4	aryl hydrocarbon receptor interacting protein like 1	protein-coding	0.009404	0.393750	168(AAGTACAGTAAGTCCT,-,0.00),169(AGTACAGTAAGTCCTC,+,0.00)
chunk0122_184_1	chr3	32684750	32684960	+	0	NA	promoter-TSS (NR_046352)	promoter-TSS (NR_046352)	-290	NM_001256741	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.014286	0.402844	
chunk0116_349_1	chr21	41528554	41528785	+	0	NA	Intergenic	Intergenic	-20511	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.008658	0.512931	
chunk0031_270_1	chr10	127852582	127852781	+	0	NA	Intergenic	Intergenic	40266	NM_152311	119467	Hs.242014	NM_152311	ENSG00000180745	CLRN3	TMEM12|USH3AL1	clarin 3	protein-coding	0.020101	0.540000	
chunk0164_53_1	chr6	19142246	19142749	+	0	NA	intron (NR_110860, intron 5 of 10)	intron (NR_110860, intron 5 of 10)	37983	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.009940	0.404762	
chunk0179_28_1	chr7	42948335	42948608	+	0	NA	Intergenic	LTR24C|LTR|ERV1	16131	NM_031903	64983	Hs.50252	NM_031903	ENSG00000106591	MRPL32	HSPC283|L32mt|MRP-L32|bMRP-59b	mitochondrial ribosomal protein L32	protein-coding	0.000000	0.328467	
chunk0177_127_1	chr7	22359325	22359725	+	0	NA	Intergenic	Intergenic	-2611	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.007500	0.433915	
chunk0104_223_1	chr2	176423415	176423847	+	0	NA	Intergenic	Intergenic	154236	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.006944	0.383372	
chunk0013_140_1	chr1	168333601	168334126	+	0	NA	Intergenic	Intergenic	-41661	NR_030284	693142		NR_030284	ENSG00000207974	MIR557	MIRN557|hsa-mir-557	microRNA 557	ncRNA	0.009524	0.393536	
chunk0200_90_1	chr9	16486034	16486703	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-210055	NR_073471									0.002990	0.391045	326(TGGGACTTGATGTTCC,-,0.00),327(GGGACTTGATGTTCCT,+,0.00),391(AAGCACACCCTGTACT,-,0.00),392(AGCACACCCTGTACTT,+,0.00)
chunk0186_206_1	chr7	139865051	139865345	+	0	NA	intron (NM_001314028, intron 1 of 12)	intron (NM_001314028, intron 1 of 12)	36045	NM_001061	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.013605	0.481356	
chunk0059_190_1	chr14	32959848	32960333	+	0	NA	intron (NM_022123, intron 1 of 10)	intron (NM_022123, intron 1 of 10)	20837	NM_001164749	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.006186	0.327160	
chunk0184_29_1	chr7	112045319	112045751	+	0	NA	intron (NM_014705, intron 1 of 51)	L2a|LINE|L2	160872	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.000000	0.348730	
chunk0101_286_1	chr2	134274310	134274621	+	0	NA	intron (NM_002410, intron 2 of 15)	intron (NM_002410, intron 2 of 15)	20206	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.012862	0.403846	
chunk0155_46_1	chr5	91153337	91153921	+	0	NA	intron (NR_003149, intron 89 of 89)	intron (NR_003149, intron 89 of 89)	160773	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.005137	0.379487	
chunk0173_443_1	chr6	151563272	151563471	+	0	NA	intron (NM_025059, intron 5 of 10)	L1PA17|LINE|L1	69331	NM_025059	80129	Hs.660044	NM_025059	ENSG00000120262	CCDC170	C6orf97|bA282P11.1	coiled-coil domain containing 170	protein-coding	0.005025	0.510000	
chunk0008_317_1	chr1	95217479	95217740	+	0	NA	intron (NR_125949, intron 2 of 3)	intron (NR_125949, intron 2 of 3)	16373	NR_125949	101928118	Hs.656443	NR_125948	ENSG00000226026	LOC101928118	-	uncharacterized LOC101928118	ncRNA	0.003831	0.435115	
chunk0037_435_1	chr11	80248042	80248468	+	0	NA	Intergenic	Intergenic	514548	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.332553	
chunk0034_122_1	chr11	28258019	28258218	+	0	NA	intron (NM_001113528, intron 4 of 6)	L1MA2|LINE|L1	149867	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.000000	0.430000	
chunk0016_210_1	chr1	198890620	198891147	+	0	NA	intron (NR_040073, intron 2 of 2)	intron (NR_040073, intron 2 of 2)	-31730	NR_029626	406995		NR_029626	ENSG00000207759	MIR181A1	MIR213|MIRN181A1|MIRN213|hsa-mir-181a-1|mir-181a-1|mir-213	microRNA 181a-1	ncRNA	0.005693	0.304924	
chunk0199_123_1	chr9	3614597	3615090	+	0	NA	Intergenic	L1PA11|LINE|L1	-53243	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.006085	0.342105	
chunk0056_135_1	chr13	83224889	83225335	+	0	NA	Intergenic	Intergenic	657281	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.004484	0.290828	183(GTGCACACTGTGTTCC,-,0.00),184(TGCACACTGTGTTCCA,+,0.00)
chunk0004_40_1	chr1	42797937	42798204	+	0	NA	intron (NM_001242750, intron 6 of 6)	intron (NM_001242750, intron 6 of 6)	10080	NM_001242750	100129924	Hs.720780	NM_001242750	ENSG00000274386	TMEM269	-	transmembrane protein 269	protein-coding	0.011236	0.473881	
chunk0048_251_1	chr12	81626301	81627034	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-28296	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.001364	0.321526	319(CTGCACATTATGTTCT,-,0.00),320(TGCACATTATGTTCTT,+,0.00)
chunk0058_319_1	chr14	27583543	27583766	+	0	NA	Intergenic	Intergenic	-28934	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.004484	0.388393	
chunk0134_119_1	chr3	177253767	177254175	+	0	NA	Intergenic	L1ME3|LINE|L1	-40471	NR_047465	100820709	Hs.518409	NR_047465	ENSG00000203645	LINC00501	-	long intergenic non-protein coding RNA 501	ncRNA	0.014706	0.349633	204(ATGAACATGGTGTACC,-,0.00),205(TGAACATGGTGTACCT,+,0.00)
chunk0094_158_1	chr2	5275014	5275559	+	0	NA	Intergenic	L1PB3|LINE|L1	415832	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.005505	0.362637	
chunk0028_299_1	chr10	91559180	91559919	+	0	NA	intron (NR_024467, intron 1 of 4)	intron (NR_024467, intron 1 of 4)	51911	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.005413	0.395946	
chunk0077_88_1	chr16	77435436	77436031	+	0	NA	promoter-TSS (NM_199355)	promoter-TSS (NM_199355)	-619	NM_199355	170692	Hs.188746	NM_139054	ENSG00000140873	ADAMTS18	ADAMTS21|KNO2|MMCAT	ADAM metallopeptidase with thrombospondin type 1 motif 18	protein-coding	0.026891	0.464765	
chunk0044_131_1	chr12	29358247	29358576	+	0	NA	intron (NM_016570, intron 6 of 13)	L1MC1|LINE|L1	22799	NM_016570	51290	Hs.339453	NM_016570	ENSG00000087502	ERGIC2	CDA14|Erv41|PTX1|cd002	ERGIC and golgi 2	protein-coding	0.006079	0.327273	
chunk0052_206_1	chr13	25144109	25144659	+	0	NA	Intergenic	Intergenic	27783	NM_199138	219287	Hs.528335	NM_152704	ENSG00000165566	AMER2	FAM123A	APC membrane recruitment protein 2	protein-coding	0.003636	0.368421	
chunk0098_238_1	chr2	74597733	74598044	+	0	NA	intron (NM_138804, intron 4 of 10)	L1ME3F|LINE|L1	43503	NM_001381	1796	Hs.103854	NM_001381	ENSG00000115325	DOK1	P62DOK|pp62	docking protein 1	protein-coding	0.000000	0.342949	
chunk0091_430_1	chr19	16991910	16992208	+	0	NA	intron (NM_015692, intron 12 of 41)	intron (NM_015692, intron 12 of 41)	34756	NM_015692	27151	Hs.631644	NM_015692	ENSG00000160111	CPAMD8	ASGD8|K-CAP|VIP	C3 and PZP like alpha-2-macroglobulin domain containing 8	protein-coding	0.010067	0.535117	
chunk0064_301_1	chr14	95503224	95503522	+	0	NA	Intergenic	MIR|SINE|MIR	-27537	NM_152592	161176	Hs.41502	NM_024633	ENSG00000176438	SYNE3	C14orf139|C14orf49|KASH3|LINC00341|NCRNA00341|NET53|Nesp3	spectrin repeat containing nuclear envelope family member 3	protein-coding	0.003356	0.478261	
chunk0045_47_1	chr12	45131913	45132580	+	0	NA	Intergenic	L1MC5a|LINE|L1	-66835	NR_026583	83956	Hs.650500	NM_032032		RACGAP1P	FKSG42	Rac GTPase activating protein 1 pseudogene	pseudo	0.010495	0.431138	531(GGGAACTCCCTGTCCC,-,0.00),532(GGAACTCCCTGTCCCA,+,0.00)
chunk0012_3_1	chr1	154714137	154714430	+	0	NA	intron (NM_170782, intron 6 of 7)	(GT)n|Simple_repeat|Simple_repeat	-86303	NM_001025107	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.006826	0.513605	
chunk0010_9_1	chr1	111948542	111949334	+	0	NA	intron (NM_172198, intron 2 of 6)	intron (NM_172198, intron 2 of 6)	39281	NR_046619	100873995	Hs.535274	NR_046619	ENSG00000237556	KCND3-AS1	-	KCND3 antisense RNA 1	ncRNA	0.007576	0.524590	
chunk0161_8_1	chr5	165394927	165395714	+	0	NA	Intergenic	Intergenic	925041	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.006353	0.338832	
chunk0057_156_1	chr13	100518454	100518827	+	0	NA	intron (NM_001127692, intron 21 of 22)	intron (NM_001127692, intron 21 of 22)	15162	NM_033110	87769	Hs.350868	NM_033110	ENSG00000134864	GGACT	A2LD1	gamma-glutamylamine cyclotransferase	protein-coding	0.010724	0.323529	
chunk0138_148_1	chr4	37250437	37250801	+	0	NA	intron (NM_001144990, intron 1 of 6)	intron (NM_001144990, intron 1 of 6)	5551	NM_001144990	57495	Hs.4280	NM_001144990	ENSG00000174145	NWD2	KIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.000000	0.345205	
chunk0120_121_1	chr3	4742400	4742660	+	0	NA	intron (NM_002222, intron 40 of 57)	intron (NM_002222, intron 40 of 57)	9060	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.011538	0.459770	0(GGGTACAGCCTGGGCT,-,0.00)
chunk0051_178_1	chr12	116112637	116112848	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	35912	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.004739	0.339623	
chunk0041_289_1	chr11	129456380	129456600	+	0	NA	Intergenic	Intergenic	80504	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.036364	0.515837	
chunk0192_60_1	chr8	60281881	60282408	+	0	NA	promoter-TSS (NM_004056)	promoter-TSS (NM_004056)	-749	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.020873	0.401515	
chunk0142_207_1	chr4	97457125	97457744	+	0	NA	intron (NR_102713, intron 3 of 5)	MER57E1|LTR|ERV1	90508	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.004847	0.366129	
chunk0066_273_1	chr15	35080537	35080974	+	0	NA	Intergenic	Intergenic	-92459	NM_014106	54989	Hs.744990	NM_014106	ENSG00000198146	ZNF770	PRO1914	zinc finger protein 770	protein-coding	0.009153	0.410959	
chunk0084_114_1	chr17	75959064	75959496	+	0	NA	intron (NM_007292, intron 3 of 13)	intron (NM_007292, intron 3 of 13)	-18242	NM_001080542	85302	Hs.720068	NM_001080542	ENSG00000188878	FBF1	Alb|FBF-1	Fas binding factor 1	protein-coding	0.009259	0.360277	260(AAGGACAAAATGTTTT,-,0.00),261(AGGACAAAATGTTTTC,+,0.00)
chunk0062_199_1	chr14	69991399	69991782	+	0	NA	intron (NM_022137, intron 5 of 11)	intron (NM_022137, intron 5 of 11)	88627	NM_182936	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.000000	0.401042	139(AAGAACTCAGAGTCCT,-,0.00),140(AGAACTCAGAGTCCTG,+,0.00)
chunk0019_360_1	chr1	229691728	229691954	+	0	NA	Intergenic	L2c|LINE|L2	65625	NM_014777	9816	Hs.533628	NM_014777	ENSG00000135763	URB2	KIAA0133|NET10|NPA2	URB2 ribosome biogenesis homolog	protein-coding	0.004425	0.480176	
chunk0093_82_1	chr19	40854980	40855653	+	0	NA	Intergenic	Intergenic	-4869	NM_000762	1548	Hs.250615	NM_000762	ENSG00000255974	CYP2A6	CPA6|CYP2A|CYP2A3|CYPIIA6|P450C2A|P450PB	cytochrome P450 family 2 subfamily A member 6	protein-coding	0.005944	0.427300	
chunk0039_298_1	chr11	102876667	102877133	+	0	NA	Intergenic	Intergenic	-1866	NM_002426	4321	Hs.1695	NM_002426	ENSG00000262406	MMP12	HME|ME|MME|MMP-12	matrix metallopeptidase 12	protein-coding	0.004292	0.421842	
chunk0123_369_1	chr3	48422959	48423183	+	0	NA	intron (NM_001130082, intron 3 of 37)	intron (NM_001130082, intron 3 of 37)	6392	NM_002673	5364	Hs.476209	NM_002673	ENSG00000164050	PLXNB1	PLEXIN-B1|PLXN5|SEP	plexin B1	protein-coding	0.026786	0.573333	
chunk0048_6_1	chr12	76942978	76943670	+	0	NA	Intergenic	Intergenic	-64284	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.000000	0.412698	
chunk0168_284_1	chr6	90750099	90750638	+	0	NA	Intergenic	Intergenic	-163067	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.014842	0.424074	
chunk0101_30_1	chr2	121872829	121873225	+	0	NA	Intergenic	MamTip3|DNA|hAT-Tip100	117482	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.005051	0.410579	
chunk0202_286_1	chr9	77402078	77402281	+	0	NA	intron (NM_033305, intron 68 of 71)	L3b|LINE|CR1	-45470	NR_121184	101927422	Hs.434324	NR_121184	ENSG00000231373	GNA14-AS1	-	GNA14 antisense RNA 1	ncRNA	0.000000	0.284314	
chunk0186_38_1	chr7	136036267	136036814	+	0	NA	Intergenic	Tigger19b|DNA|TcMar-Tigger	-59084	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.009141	0.377737	
chunk0052_38_1	chr13	20789077	20789408	+	0	NA	intron (NM_022459, intron 19 of 22)	intron (NM_022459, intron 19 of 22)	-15324	NM_174928	221143	Hs.26674	NM_174928	ENSG00000150456	EEF1AKMT1	ESP13|N6AMT2	EEF1A lysine methyltransferase 1	protein-coding	0.009063	0.394578	
chunk0050_98_1	chr12	101894671	101894971	+	0	NA	intron (NM_018370, intron 1 of 6)	intron (NM_018370, intron 1 of 6)	17494	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.010000	0.491694	
chunk0122_55_1	chr3	28743779	28744125	+	0	NA	intron (NR_038840, intron 2 of 4)	intron (NR_038840, intron 2 of 4)	168674	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.005780	0.414986	
chunk0170_199_1	chr6	112433232	112433835	+	0	NA	Intergenic	MIRc|SINE|MIR	86203	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.003317	0.415563	
chunk0194_330_1	chr8	88926327	88926662	+	0	NA	Intergenic	Intergenic	-599006	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.002985	0.455357	
chunk0073_173_1	chr16	8740814	8741268	+	0	NA	intron (NM_020686, intron 2 of 15)	intron (NM_020686, intron 2 of 15)	20325	NM_001127448	18	Hs.336768	NM_000663	ENSG00000183044	ABAT	GABA-AT|GABAT|NPD009	4-aminobutyrate aminotransferase	protein-coding	0.011013	0.404396	
chunk0189_427_1	chr8	27957863	27958386	+	0	NA	intron (NM_173833, intron 3 of 8)	intron (NM_173833, intron 3 of 8)	34728	NM_173833	286133	Hs.591833	NM_173833	ENSG00000168079	SCARA5	NET33|Tesr	scavenger receptor class A member 5	protein-coding	0.013384	0.538168	281(GAGAACAGGGAGTACT,-,0.00),282(AGAACAGGGAGTACTT,+,0.00)
chunk0112_244_1	chr20	41493776	41494080	+	0	NA	exon (NM_032221, exon 9 of 37)	exon (NM_032221, exon 9 of 37)	124566	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.006579	0.442623	
chunk0013_348_1	chr1	172177673	172178285	+	0	NA	intron (NM_001136127, intron 14 of 19)	Tigger3a|DNA|TcMar-Tigger	-33144	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.003268	0.362153	
chunk0210_136_1	chrX	74440268	74440529	+	0	NA	intron (NM_006517, intron 1 of 5)	(GT)n|Simple_repeat|Simple_repeat	18905	NM_006517	6567	Hs.75317	NM_006517	ENSG00000147100	SLC16A2	AHDS|DXS128|DXS128E|MCT 7|MCT 8|MCT7|MCT8|MRX22|XPCT	solute carrier family 16 member 2	protein-coding	0.007663	0.408397	
chunk0064_184_1	chr14	92707557	92707942	+	0	NA	intron (NM_001008530, intron 12 of 14)	intron (NM_001008530, intron 12 of 14)	40953	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.005195	0.329016	
chunk0116_102_1	chr21	35324093	35324823	+	0	NA	Intergenic	Intergenic	256306	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.017808	0.471956	351(AGGAACAGTGTGTTCC,-,0.00),352(GGAACAGTGTGTTCCC,+,0.00)
chunk0029_218_1	chr10	102266679	102267147	+	0	NA	intron (NM_001199378, intron 3 of 39)	intron (NM_001199378, intron 3 of 39)	21415	NM_001199379	8729	Hs.290243	NM_004193	ENSG00000107862	GBF1	ARF1GEF	golgi brefeldin A resistant guanine nucleotide exchange factor 1	protein-coding	0.008547	0.434968	
chunk0196_276_1	chr8	109267609	109268139	+	0	NA	intron (NM_001128211, intron 8 of 9)	intron (NM_001128211, intron 8 of 9)	62059	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.003774	0.318267	
chunk0146_66_1	chr4	156713472	156714111	+	0	NA	Intergenic	Intergenic	257603	NR_036641	56034	Hs.570855	NM_016205	ENSG00000145431	PDGFC	FALLOTEIN|SCDGF	platelet derived growth factor C	protein-coding	0.012520	0.360938	
chunk0032_87_1	chr11	2998138	2998408	+	0	NA	Intergenic	L1MD2|LINE|L1	-5896	NM_005969	4676	Hs.731784	NM_005969	ENSG00000205531	NAP1L4	NAP1L4b|NAP2|NAP2L|hNAP2	nucleosome assembly protein 1 like 4	protein-coding	0.003704	0.453875	
chunk0152_96_1	chr5	58273517	58274242	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	-151538	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.005517	0.406336	
chunk0129_302_1	chr3	123633325	123633953	+	0	NA	intron (NM_053025, intron 29 of 33)	intron (NM_053025, intron 29 of 33)	-12956	NM_053031	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.006369	0.446741	
chunk0150_36_1	chr5	31416216	31416621	+	0	NA	intron (NM_013235, intron 29 of 34)	L2b|LINE|L2	115757	NM_001100412	29102	Hs.97997	NM_013235	ENSG00000113360	DROSHA	ETOHI2|HSA242976|RANSE3L|RN3|RNASE3L|RNASEN	drosha ribonuclease III	protein-coding	0.009877	0.431034	
chunk0003_271_1	chr1	36374627	36374925	+	0	NA	intron (NM_032017, intron 1 of 11)	intron (NM_032017, intron 1 of 11)	11151	NM_001282546	83931	Hs.471768	NM_032017	ENSG00000196182	STK40	SHIK|SgK495	serine/threonine kinase 40	protein-coding	0.013423	0.561873	
chunk0176_34_1	chr7	9532035	9532535	+	0	NA	Intergenic	L1M5|LINE|L1	-101985	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.004000	0.281437	
chunk0032_28_1	chr11	876741	876956	+	0	NA	intron (NM_001142674, intron 11 of 13)	intron (NM_001142674, intron 11 of 13)	32402	NM_001025237	7106	Hs.654836	NM_003271	ENSG00000214063	TSPAN4	NAG-2|NAG2|TETRASPAN|TM4SF7|TSPAN-4	tetraspanin 4	protein-coding	0.023256	0.634259	
chunk0200_73_1	chr9	16166689	16167133	+	0	NA	Intergenic	L1MC2|LINE|L1	86196	NM_001271829	100129385	Hs.586441	NM_001271829	ENSG00000205549	C9orf92	Em:AL513424.1	chromosome 9 open reading frame 92	protein-coding	0.002252	0.334831	
chunk0086_96_1	chr18	13834378	13834720	+	0	NA	Intergenic	L1ME4b|LINE|L1	9005	NM_005913	4161	Hs.248145	NM_005913	ENSG00000176136	MC5R	MC2	melanocortin 5 receptor	protein-coding	0.014620	0.408163	130(CAGCACAGACTGTAAC,-,0.00)
chunk0119_289_1	chr22	46178629	46179123	+	0	NA	intron (NM_005036, intron 3 of 8)	intron (NM_005036, intron 3 of 8)	28280	NM_005036	5465	Hs.103110	NM_005036	ENSG00000186951	PPARA	NR1C1|PPAR|PPARalpha|hPPAR	peroxisome proliferator activated receptor alpha	protein-coding	0.008097	0.474747	
chunk0094_350_1	chr2	9443332	9443540	+	0	NA	intron (NM_016207, intron 9 of 17)	intron (NM_016207, intron 9 of 17)	19899	NM_016207	51692	Hs.515972	NM_016207	ENSG00000119203	CPSF3	CPSF-73|CPSF73	cleavage and polyadenylation specific factor 3	protein-coding	0.009615	0.287081	
chunk0135_225_1	chr3	188583392	188583917	+	0	NA	intron (NM_001167671, intron 5 of 10)	L2a|LINE|L2	-14988	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.013333	0.412548	
chunk0076_91_1	chr16	64881015	64881289	+	0	NA	Intergenic	Intergenic	240985	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.007299	0.440000	130(GAGCACACTCTGTACA,-,0.00),131(AGCACACTCTGTACAG,+,0.00)
chunk0022_53_1	chr10	8229177	8229561	+	0	NA	Intergenic	Intergenic	38936	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.007812	0.470130	
chunk0141_360_1	chr4	87957435	87957752	+	0	NA	Intergenic	Intergenic	-18057	NM_001251829	6696	Hs.313	NM_000582	ENSG00000118785	SPP1	BNSP|BSPI|ETA-1|OPN	secreted phosphoprotein 1	protein-coding	0.003155	0.327044	
chunk0157_136_1	chr5	117426207	117427044	+	0	NA	intron (NR_046089, intron 1 of 5)	L1ME4b|LINE|L1	11113	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.001195	0.299523	
chunk0083_326_1	chr17	69761830	69762356	+	0	NA	intron (NR_109972, intron 3 of 4)	intron (NR_109972, intron 3 of 4)	168106	NR_109972	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.003802	0.398482	
chunk0028_357_1	chr10	92538105	92538949	+	0	NA	intron (NM_004969, intron 1 of 24)	intron (NM_004969, intron 1 of 24)	35568	NM_004969	3416	Hs.500546	NM_004969	ENSG00000119912	IDE	INSULYSIN	insulin degrading enzyme	protein-coding	0.008294	0.403550	824(CAGATCTGACTGTTCC,-,0.00),825(AGATCTGACTGTTCCT,+,0.00)
chunk0034_248_1	chr11	34263611	34263884	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	94261	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.010989	0.569343	
chunk0023_280_1	chr10	28327407	28327606	+	0	NA	Intergenic	Intergenic	-38156	NR_107053	102465880		NR_107053	ENSG00000275036	MIR8086	hsa-mir-8086	microRNA 8086	ncRNA	0.005025	0.280000	
chunk0026_431_1	chr10	71056944	71057447	+	0	NA	Intergenic	Intergenic	-155340	NM_001244889	219699	Hs.522997	NM_170744	ENSG00000107731	UNC5B	UNC5H2|p53RDL1	unc-5 netrin receptor B	protein-coding	0.015905	0.416667	
chunk0178_264_1	chr7	36406335	36406601	+	0	NA	exon (NM_001284302, exon 4 of 23)	exon (NM_001284302, exon 4 of 23)	-16343	NM_001100425	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.011278	0.426966	
chunk0206_45_1	chr9	117466162	117466361	+	0	NA	Intergenic	Intergenic	-51222	NM_014010	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.010050	0.365000	
chunk0005_282_1	chr1	60088651	60089196	+	0	NA	Intergenic	Intergenic	-15153	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.009174	0.366300	
chunk0201_51_1	chr9	33850424	33851056	+	0	NA	intron (NM_017811, intron 1 of 4)	intron (NM_017811, intron 1 of 4)	33556	NM_017811	54926	Hs.643648	NM_017811	ENSG00000107341	UBE2R2	CDC34B|E2-CDC34B|UBC3B	ubiquitin conjugating enzyme E2 R2	protein-coding	0.004747	0.372828	344(AGGAACAATCAGTTCC,-,0.00),345(GGAACAATCAGTTCCC,+,0.00)
chunk0196_345_1	chr8	114343195	114343681	+	0	NA	Intergenic	Intergenic	-906425	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.008230	0.347023	
chunk0137_64_1	chr4	11878290	11878704	+	0	NA	Intergenic	Intergenic	-344954	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.004831	0.339759	
chunk0187_363_1	chr7	157373589	157373900	+	0	NA	intron (NM_058246, intron 5 of 9)	intron (NM_058246, intron 5 of 9)	36727	NM_058246	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.016077	0.461538	
chunk0088_19_1	chr18	43422477	43423076	+	0	NA	Intergenic	Intergenic	-145126	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.010017	0.410000	
chunk0169_26_1	chr6	96885354	96885554	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	12437	NM_014165	29078	Hs.512144	NM_014165	ENSG00000123545	NDUFAF4	C6orf66|HRPAP20|HSPC125|MC1DN15|My013|bA22L21.1	NADH:ubiquinone oxidoreductase complex assembly factor 4	protein-coding	0.005000	0.442786	
chunk0137_455_1	chr4	29582144	29582393	+	0	NA	Intergenic	Intergenic	762686	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.000000	0.316000	
chunk0060_298_1	chr14	50763341	50764073	+	0	NA	intron (NM_016350, intron 15 of 28)	intron (NM_016350, intron 15 of 28)	67414	NM_182944	51199	Hs.310429	NM_016350	ENSG00000100503	NIN	SCKL7	ninein	protein-coding	0.016393	0.395634	
chunk0122_301_1	chr3	36564651	36565032	+	0	NA	Intergenic	L1MD1|LINE|L1	175020	NM_033403	85443	Hs.631907	NM_033403	ENSG00000163673	DCLK3	CLR|DCAMKL3|DCDC3C|DCK3	doublecortin like kinase 3	protein-coding	0.000000	0.306283	
chunk0087_84_1	chr18	32293006	32293627	+	0	NA	intron (NM_001242409, intron 3 of 5)	L1MC4|LINE|L1	103292	NM_001308171	4225	Hs.194777	NM_005925	ENSG00000141434	MEP1B	-	meprin A subunit beta	protein-coding	0.004831	0.376206	284(TGGTACAAGGTGTGCT,-,0.00),285(GGTACAAGGTGTGCTT,+,0.00)
chunk0211_244_1	chrX	120377040	120377715	+	0	NA	intron (NM_001142447, intron 6 of 7)	intron (NM_001142447, intron 6 of 7)	15292	NM_012069	23439	Hs.292599	NM_012069	ENSG00000101892	ATP1B4	-	ATPase Na+/K+ transporting family member beta 4	protein-coding	0.005926	0.368343	369(AAGCACATTCTGTTCT,-,0.00),370(AGCACATTCTGTTCTC,+,0.00)
chunk0138_222_1	chr4	39039971	39040216	+	0	NA	Intergenic	Intergenic	-4738	NM_001007075	51088	Hs.272251	NM_015990	ENSG00000109790	KLHL5	-	kelch like family member 5	protein-coding	0.024490	0.532520	
chunk0177_313_1	chr7	26087739	26088642	+	0	NA	Intergenic	Intergenic	-64037	NM_004289	9603	Hs.404741	NM_004289	ENSG00000050344	NFE2L3	NRF3	nuclear factor, erythroid 2 like 3	protein-coding	0.005537	0.405973	
chunk0047_137_1	chr12	69575362	69576128	+	0	NA	3' UTR (NM_001278357, exon 7 of 7)	3' UTR (NM_001278357, exon 7 of 7)	-8978	NR_037476	100500868		NR_037476	ENSG00000283677	MIR3913-2	mir-3913-2	microRNA 3913-2	ncRNA	0.003916	0.358540	
chunk0065_71_1	chr15	23463243	23463900	+	0	NA	Intergenic	Intergenic	-16328	NM_001304388	283685		NM_182561	ENSG00000174450	GOLGA6L2	CT105	golgin A6 family like 2	protein-coding	0.001522	0.367781	114(CTGAACATTCTGATCT,-,0.00),115(TGAACATTCTGATCTT,+,0.00)
chunk0038_219_1	chr11	86741922	86742313	+	0	NA	Intergenic	Intergenic	-48942	NM_001293180	11098	Hs.25338	NM_007173	ENSG00000150687	PRSS23	SIG13|SPUVE|ZSIG13	serine protease 23	protein-coding	0.000000	0.466837	
chunk0093_416_1	chr19	57410661	57410884	+	0	NA	promoter-TSS (NM_006959)	promoter-TSS (NM_006959)	-389	NM_006959	7565	Hs.729403	NM_006959	ENSG00000186272	ZNF17	HPF3|KOX10	zinc finger protein 17	protein-coding	0.022422	0.450893	151(GGGAACTTGCTGTGCT,-,0.00),152(GGAACTTGCTGTGCTT,+,0.00)
chunk0032_306_1	chr11	9840467	9841246	+	0	NA	intron (NM_030962, intron 25 of 39)	intron (NM_030962, intron 25 of 39)	1714	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.001284	0.303846	474(TGGTACTGCATGTTCT,-,0.00),475(GGTACTGCATGTTCTA,+,0.00)
chunk0106_411_1	chr2	207954852	207955092	+	0	NA	intron (NM_001080475, intron 3 of 7)	MER134|DNA?|DNA?	70588	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.008333	0.282158	
chunk0042_97_1	chr12	2775266	2776017	+	0	NA	Intergenic	Intergenic	-3972	NR_033958	283440	Hs.448720	NR_033958	ENSG00000256150	ITFG2-AS1	-	ITFG2 antisense RNA 1	ncRNA	0.013316	0.523936	414(CAGGACAGGTCGTCCC,-,0.00)
chunk0040_37_1	chr11	110509367	110509585	+	0	NA	Intergenic	Intergenic	79539	NM_004109	2230	Hs.744	NM_004109	ENSG00000137714	FDX1	ADX|FDX|LOH11CR1D	ferredoxin 1	protein-coding	0.004587	0.447489	
chunk0067_86_1	chr15	41839788	41840320	+	0	NA	intron (NM_001114633, intron 1 of 19)	intron (NM_001114633, intron 1 of 19)	1241	NM_001114633	100137049	Hs.198161	NM_001114633	ENSG00000243708	PLA2G4B	HsT16992|cPLA2-beta	phospholipase A2 group IVB	protein-coding	0.024436	0.587242	
chunk0172_298_1	chr6	138086526	138086986	+	0	NA	Intergenic	Intergenic	20767	NM_022121	64065	Hs.201446	NM_022121	ENSG00000112378	PERP	KCP1|KRTCAP1|PIGPC1|THW|dJ496H19.1	p53 apoptosis effector related to PMP22	protein-coding	0.006522	0.407809	
chunk0189_24_1	chr8	19678305	19678812	+	0	NA	intron (NR_024040, intron 1 of 9)	L3|LINE|CR1	4025	NM_018371	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.013807	0.403543	
chunk0109_238_1	chr20	5972950	5973458	+	0	NA	intron (NM_182802, intron 12 of 18)	intron (NM_182802, intron 12 of 18)	22552	NM_001281520	84515	Hs.597484	NM_032485	ENSG00000125885	MCM8	C20orf154|POF10|dJ967N21.5	minichromosome maintenance 8 homologous recombination repair factor	protein-coding	0.009843	0.371316	
chunk0174_121_1	chr6	157264608	157265205	+	0	NA	Intergenic	Intergenic	59353	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.026801	0.496656	
chunk0167_343_1	chr6	72760511	72760988	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	130254	NR_120503	100507381	Hs.662412	NR_120503	ENSG00000233844	KCNQ5-IT1	-	KCNQ5 intronic transcript 1	ncRNA	0.006289	0.361925	
chunk0138_340_1	chr4	41636677	41637050	+	0	NA	intron (NM_001289122, intron 8 of 25)	L1ME3A|LINE|L1	24091	NM_001112720	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.005362	0.299465	
chunk0020_164_1	chr1	234373016	234373740	+	0	NA	promoter-TSS (NM_001206641)	promoter-TSS (NM_001206641)	25	NR_125962	101927765	Hs.596703	NR_125961	ENSG00000231663	COA6-AS1	-	COA6 antisense RNA 1	ncRNA	0.074586	0.579310	
chunk0069_126_1	chr15	61936682	61937248	+	0	NA	intron (NM_017684, intron 45 of 82)	intron (NM_017684, intron 45 of 82)	123500	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.008834	0.380952	
chunk0026_368_1	chr10	69314977	69315518	+	0	NA	promoter-TSS (NM_033496)	promoter-TSS (NM_033496)	-607	NM_033496	3098	Hs.370365	NM_000188	ENSG00000156515	HK1	HK|HK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1|RP79|hexokinase	hexokinase 1	protein-coding	0.007394	0.464945	
chunk0102_51_1	chr2	142750936	142751386	+	0	NA	Intergenic	Intergenic	-126465	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.004444	0.303769	
chunk0051_370_1	chr12	121456052	121456251	+	0	NA	intron (NM_001005366, intron 12 of 22)	intron (NM_001005366, intron 12 of 22)	-11799	NR_106957	102465665		NR_106957	ENSG00000284402	MIR7107	hsa-mir-7107	microRNA 7107	ncRNA	0.020101	0.530000	
chunk0008_123_1	chr1	91747173	91747629	+	0	NA	intron (NR_036634, intron 5 of 17)	intron (NR_036634, intron 5 of 17)	138878	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.008772	0.472648	
chunk0182_67_1	chr7	92135543	92135854	+	0	NA	promoter-TSS (NM_001146152)	promoter-TSS (NM_001146152)	-953	NM_001146152	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.019293	0.435897	120(AGGCACAGCGAGTTCT,-,0.00),121(GGCACAGCGAGTTCTT,+,0.00)
chunk0019_168_1	chr1	226111595	226111847	+	0	NA	Intergenic	Intergenic	48994	NR_002315	440926	Hs.533624	NR_002315		H3F3AP4	p13	H3 histone, family 3A, pseudogene 4	pseudo	0.007937	0.545455	
chunk0173_183_1	chr6	144893640	144894235	+	0	NA	Intergenic	Intergenic	488282	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.003361	0.394295	
chunk0054_52_1	chr13	41696579	41696837	+	0	NA	intron (NM_015058, intron 29 of 44)	L2a|LINE|L2	-128313	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.000000	0.389961	
chunk0130_343_1	chr3	138715389	138715704	+	0	NA	intron (NM_006219, intron 6 of 21)	intron (NM_006219, intron 6 of 21)	-7925	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.003175	0.278481	
chunk0006_450_1	chr1	76951244	76951449	+	0	NA	intron (NM_030965, intron 2 of 4)	MER63C|DNA|hAT-Blackjack	83845	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.004878	0.417476	
chunk0212_137_1	chrX	131722173	131722396	+	0	NA	intron (NR_026975, intron 10 of 12)	MER4A1|LTR|ERV1	108359	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.008969	0.406250	
chunk0072_455_1	chr15	101849898	101850455	+	0	NA	non-coding (NR_046417, exon 5 of 5)	non-coding (NR_046417, exon 5 of 5)	8057	NR_046417	390651	Hs.578689	NR_046417	ENSG00000214344	OR4F13P	GPCRLTM7	olfactory receptor family 4 subfamily F member 13 pseudogene	pseudo	0.003591	0.322581	
chunk0150_97_1	chr5	32563484	32564074	+	0	NA	Intergenic	Intergenic	-21720	NM_006713	10923	Hs.229641	NM_006713	ENSG00000113387	SUB1	P15|PC4|p14	SUB1 regulator of transcription	protein-coding	0.006780	0.458545	260(TAGGTCACCCTGTTCC,-,0.00),261(AGGTCACCCTGTTCCC,+,0.00)
chunk0093_403_1	chr19	56958609	56959027	+	0	NA	Intergenic	L2a|LINE|L2	117916	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.014354	0.477327	234(ATGAACTGACTGTCCT,-,0.00),235(TGAACTGACTGTCCTG,+,0.00),291(AGGCACACTCTGATCT,-,0.00),292(GGCACACTCTGATCTG,+,0.00)
chunk0091_411_1	chr19	16659878	16660141	+	0	NA	intron (NM_024104, intron 1 of 4)	CpG-13958	148	NM_001300925	79086	Hs.356467	NM_024104	ENSG00000214046	SMIM7	C19orf42	small integral membrane protein 7	protein-coding	0.091255	0.617424	
chunk0093_177_1	chr19	48563090	48563557	+	0	NA	intron (NM_177973, intron 1 of 6)	L1ME2z|LINE|L1	11151	NM_177973	6820	Hs.369331	NM_004605	ENSG00000088002	SULT2B1	ARCI14|HSST2	sulfotransferase family 2B member 1	protein-coding	0.021413	0.457265	
chunk0005_354_1	chr1	61335214	61335413	+	0	NA	intron (NM_001145511, intron 4 of 10)	intron (NM_001145511, intron 4 of 10)	-81795	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.030151	0.495000	
chunk0032_313_1	chr11	9903771	9904442	+	0	NA	intron (NM_030962, intron 16 of 39)	L1MEd|LINE|L1	64964	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.005961	0.379464	
chunk0093_166_1	chr19	48261321	48261868	+	0	NA	Intergenic	Intergenic	-5648	NM_001184904	22900	Hs.68846	NM_014959	ENSG00000105483	CARD8	CARDINAL|DACAR|DAKAR|NDPP|NDPP1|TUCAN	caspase recruitment domain family member 8	protein-coding	0.007313	0.377737	
chunk0173_225_1	chr6	146154685	146154884	+	0	NA	intron (NM_001278064, intron 1 of 7)	L1ME3G|LINE|L1	125586	NM_001278067	2911	Hs.32945	NM_000838	ENSG00000152822	GRM1	GPRC1A|MGLU1|MGLUR1|PPP1R85|SCA44|SCAR13	glutamate metabotropic receptor 1	protein-coding	0.000000	0.300000	
chunk0068_274_1	chr15	56685371	56685643	+	0	NA	intron (NM_001002843, intron 8 of 20)	L1M7|LINE|L1	48579	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.000000	0.336996	
chunk0016_231_1	chr1	199704168	199704688	+	0	NA	Intergenic	Intergenic	-323174	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.000000	0.393474	
chunk0017_360_1	chr1	211928130	211928736	+	0	NA	Intergenic	Intergenic	-97661	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.001650	0.439868	
chunk0177_306_1	chr7	25989130	25989380	+	0	NA	Intergenic	Intergenic	-39269	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.012000	0.442231	
chunk0005_428_1	chr1	62875875	62876076	+	0	NA	Intergenic	Intergenic	91869	NM_178221	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.014925	0.391089	
chunk0078_49_1	chr17	1344007	1344409	+	0	NA	TTS (NM_006761)	TTS (NM_006761)	56054	NR_024058	7531	Hs.513851	NM_006761	ENSG00000108953	YWHAE	14-3-3E|HEL2|KCIP-1|MDCR|MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	protein-coding	0.000000	0.367246	
chunk0037_298_1	chr11	76289250	76289674	+	0	NA	Intergenic	L1ME3A|LINE|L1	-82932	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.018868	0.505882	277(TGGAACACTGTGTCAC,-,0.00)
chunk0020_414_1	chr1	241542464	241542677	+	0	NA	intron (NM_003679, intron 1 of 14)	intron (NM_003679, intron 1 of 14)	10436	NM_003679	8564	Hs.731056	NM_003679	ENSG00000117009	KMO	dJ317G22.1	kynurenine 3-monooxygenase	protein-coding	0.014085	0.345794	
chunk0141_279_1	chr4	86586999	86587973	+	0	NA	Intergenic	Intergenic	-6829	NM_006264	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.006160	0.386667	
chunk0092_45_1	chr19	19477748	19477949	+	0	NA	intron (NM_017660, intron 2 of 11)	intron (NM_017660, intron 2 of 11)	12508	NM_001300946	54815	Hs.118964	NM_017660	ENSG00000167491	GATAD2A	p66alpha	GATA zinc finger domain containing 2A	protein-coding	0.029851	0.554455	
chunk0160_455_1	chr5	165115777	165116285	+	0	NA	Intergenic	Intergenic	645752	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.000000	0.302554	
chunk0200_315_1	chr9	23342428	23342715	+	0	NA	Intergenic	Intergenic	329828	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.003484	0.430556	
chunk0061_2_1	chr14	55363656	55363855	+	0	NA	Intergenic	MER30|DNA|hAT-Charlie	48103	NM_014924	22863	Hs.414809	NM_014924	ENSG00000126775	ATG14	ATG14L|BARKOR|KIAA0831	autophagy related 14	protein-coding	0.010050	0.425000	
chunk0104_445_1	chr2	181499667	181499977	+	0	NA	intron (NM_000885, intron 15 of 27)	intron (NM_000885, intron 15 of 27)	42930	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.006452	0.295820	
chunk0019_418_1	chr1	230758163	230758413	+	0	NA	intron (NM_016452, intron 2 of 18)	L2b|LINE|L2	10873	NM_016452	10753	Hs.498021	NM_006615	ENSG00000135773	CAPN9	GC36|nCL-4	calpain 9	protein-coding	0.016000	0.517928	
chunk0002_108_1	chr1	15628643	15629184	+	0	NA	intron (NM_032341, intron 2 of 9)	L1MB7|LINE|L1	11455	NM_032341	84301	Hs.718857	NM_032341	ENSG00000197312	DDI2	-	DNA damage inducible 1 homolog 2	protein-coding	0.005545	0.359779	
chunk0134_69_1	chr3	176273942	176274189	+	0	NA	Intergenic	Intergenic	-241038	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.004049	0.342742	
chunk0042_425_1	chr12	12025832	12026035	+	0	NA	Intergenic	L1MEg|LINE|L1	-45011	NM_138723	79370	Hs.210343	NM_030766	ENSG00000121380	BCL2L14	BCLG	BCL2 like 14	protein-coding	0.004926	0.504902	87(AGAGACACTGTGTTCT,-,0.00),88(GAGACACTGTGTTCTC,+,0.00),128(ATGAACAGCCTGGGCT,-,0.00)
chunk0166_125_1	chr6	44639980	44640690	+	0	NA	Intergenic	Intergenic	204694	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.007042	0.450070	341(ATGGGCAGAGTGTCCC,-,0.00),342(TGGGCAGAGTGTCCCT,+,0.00)
chunk0193_22_1	chr8	70678647	70678934	+	0	NA	intron (NM_001287259, intron 3 of 5)	intron (NM_001287259, intron 3 of 5)	9343	NM_001287260	389668	Hs.458938	NM_001011720	ENSG00000221947	XKR9	XRG9	XK related 9	protein-coding	0.003484	0.298611	
chunk0007_258_1	chr1	82944885	82945141	+	0	NA	Intergenic	Intergenic	39909	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.003906	0.322957	
chunk0051_269_1	chr12	118013393	118013655	+	0	NA	Intergenic	Intergenic	-3177	NM_007370	5985	Hs.731908	NM_007370	ENSG00000111445	RFC5	RFC36	replication factor C subunit 5	protein-coding	0.003817	0.406844	
chunk0100_434_1	chr2	120470924	120471153	+	0	NA	Intergenic	Intergenic	-4689	NR_027181	84931	Hs.334519	NM_032845	ENSG00000280409	LINC01101	-	long intergenic non-protein coding RNA 1101	ncRNA	0.021834	0.569565	
chunk0111_137_1	chr20	24772653	24772926	+	0	NA	Intergenic	Intergenic	-176441	NM_003650	8530	Hs.143212	NM_003650	ENSG00000077984	CST7	CMAP	cystatin F	protein-coding	0.018315	0.521898	
chunk0177_87_1	chr7	21723735	21724358	+	0	NA	intron (NM_001277115, intron 44 of 81)	intron (NM_001277115, intron 44 of 81)	180831	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.006421	0.416667	46(GAGCACACCAAGTTCT,-,0.00),47(AGCACACCAAGTTCTT,+,0.00)
chunk0018_66_1	chr1	216922784	216923190	+	0	NA	intron (NM_001243507, intron 2 of 7)	intron (NM_001243507, intron 2 of 7)	16686	NM_001243513	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.012315	0.395577	
chunk0160_64_1	chr5	149785314	149785618	+	0	NA	intron (NM_001172699, intron 1 of 10)	MIRb|SINE|MIR	13526	NM_001172699	133522	Hs.483816	NM_133263	ENSG00000155846	PPARGC1B	ERRL1|PERC|PGC-1(beta)|PGC1B	PPARG coactivator 1 beta	protein-coding	0.009868	0.449180	
chunk0177_28_1	chr7	20684323	20684844	+	0	NA	intron (NM_001163941, intron 15 of 27)	FLAM_A|SINE|Alu	37240	NM_001163942	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.007678	0.392720	
chunk0104_65_1	chr2	171707771	171708013	+	0	NA	intron (NM_001271788, intron 4 of 15)	intron (NM_001271788, intron 4 of 15)	20220	NM_001271787	1781	Hs.546250	NM_001378	ENSG00000077380	DYNC1I2	DIC74|DNCI2|IC2	dynein cytoplasmic 1 intermediate chain 2	protein-coding	0.004132	0.320988	
chunk0179_127_1	chr7	45735434	45735778	+	0	NA	intron (NR_024271, intron 9 of 12)	Tigger3b|DNA|TcMar-Tigger	33412	NR_024271	641977	Hs.723477	NR_024271	ENSG00000214765	SEPTIN7P2	SEPT13|SEPT7B|SEPT7P2	septin 7 pseudogene 2	pseudo	0.002907	0.327536	
chunk0127_149_1	chr3	94418956	94419174	+	0	NA	Intergenic	L1PA15|LINE|L1	-355842	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.004587	0.538813	
chunk0001_267_1	chr1	8548236	8548484	+	0	NA	intron (NM_001042681, intron 6 of 22)	L1MC4a|LINE|L1	-53447	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.004032	0.405622	
chunk0001_276_1	chr1	8637815	8638015	+	0	NA	intron (NM_001042681, intron 2 of 22)	intron (NM_001042681, intron 2 of 22)	-143002	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.015000	0.378109	
chunk0062_61_1	chr14	67506221	67506546	+	0	NA	intron (NM_182526, intron 1 of 2)	LTR78|LTR|ERV1	8921	NM_182526	161145	Hs.509707	NM_182526	ENSG00000198133	TMEM229B	C14orf83	transmembrane protein 229B	protein-coding	0.006154	0.389571	
chunk0164_393_1	chr6	26269110	26269558	+	0	NA	Intergenic	LTR8|LTR|ERV1	2050	NM_003534	8355	Hs.247813	NM_003534	ENSG00000273983	HIST1H3G	H3/h|H3FH	histone cluster 1 H3 family member g	protein-coding	0.011161	0.387528	
chunk0042_36_1	chr12	1571612	1572252	+	0	NA	intron (NM_152441, intron 1 of 1)	L2a|LINE|L2	22233	NM_152441	144699	Hs.367956	NM_152441	ENSG00000171823	FBXL14	Fbl14	F-box and leucine rich repeat protein 14	protein-coding	0.006250	0.424337	
chunk0131_280_1	chr3	150278799	150279353	+	0	NA	intron (NR_110186, intron 2 of 3)	intron (NR_110186, intron 2 of 3)	40376	NR_110167	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.012635	0.423423	
chunk0035_394_1	chr11	56640915	56641314	+	0	NA	TTS (NM_001002925)	TTS (NM_001002925)	1325	NM_001002925	338675	Hs.449692	NM_001002925	ENSG00000172464	OR5AP2	OR9J1	olfactory receptor family 5 subfamily AP member 2	protein-coding	0.005013	0.382500	
chunk0001_345_1	chr1	9792234	9792504	+	0	NA	intron (NM_001009566, intron 1 of 18)	intron (NM_001009566, intron 1 of 18)	32157	NM_014944	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.007407	0.490775	
chunk0079_27_1	chr17	9924758	9925284	+	0	NA	intron (NM_001130831, intron 11 of 13)	intron (NM_001130831, intron 11 of 13)	-19654	NM_002903	5957	Hs.80539	NM_002903	ENSG00000109047	RCVRN	RCV1	recoverin	protein-coding	0.015209	0.516129	
chunk0065_335_1	chr14	103314006	103314452	+	0	NA	Intergenic	Intergenic	-19773	NM_001969	1983	Hs.433702	NM_001969	ENSG00000100664	EIF5	EIF-5|EIF-5A	eukaryotic translation initiation factor 5	protein-coding	0.020179	0.431767	255(AAGACAAGATGTTCCC,+,0.00)
chunk0079_88_1	chr17	11940038	11940564	+	0	NA	intron (NM_004662, intron 12 of 14)	intron (NM_004662, intron 12 of 14)	57071	NM_144680	7566	Hs.370473	NM_144680	ENSG00000154957	ZNF18	HDSG1|KOX11|ZKSCAN6|ZNF535|ZSCAN38|Zfp535	zinc finger protein 18	protein-coding	0.015209	0.440228	297(CAGAACTCTGTGTCCC,-,0.00),298(AGAACTCTGTGTCCCC,+,0.00)
chunk0085_237_1	chr18	7003453	7003997	+	0	NA	intron (NM_005559, intron 29 of 62)	intron (NM_005559, intron 29 of 62)	49048	NR_126040	101927188	Hs.680444	NR_126040	ENSG00000265069	LOC101927188	-	uncharacterized LOC101927188	ncRNA	0.011029	0.403670	131(AAGAACAAGCAGTTCT,-,0.00),132(AGAACAAGCAGTTCTT,+,0.00)
chunk0022_174_1	chr10	12785712	12785992	+	0	NA	intron (NM_020397, intron 5 of 9)	intron (NM_020397, intron 5 of 9)	-60499	NR_031752	100313841		NR_031752	ENSG00000221331	MIR548Q	-	microRNA 548q	ncRNA	0.032143	0.533808	
chunk0099_346_1	chr2	100121324	100121700	+	0	NA	intron (NM_002285, intron 1 of 23)	L2b|LINE|L2	-15929	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.005319	0.464191	189(TGGCACACGAAGTGCT,-,0.00),190(GGCACACGAAGTGCTC,+,0.00)
chunk0033_74_1	chr11	13763014	13763708	+	0	NA	Intergenic	Intergenic	94702	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.005764	0.349640	
chunk0072_64_1	chr16	1657170	1657637	+	0	NA	intron (NM_020825, intron 9 of 19)	intron (NM_020825, intron 9 of 19)	-20874	NM_144570	90861	Hs.513261	NM_144570	ENSG00000206053	JPT2	C16orf34|HN1L|L11	Jupiter microtubule associated homolog 2	protein-coding	0.025696	0.572650	
chunk0197_285_1	chr8	124186106	124186315	+	0	NA	Intergenic	L1MC4|LINE|L1	-14688	NR_103547	157376	Hs.662360	NM_182525	ENSG00000253868	FER1L6-AS2	C8orf78	FER1L6 antisense RNA 2	ncRNA	0.000000	0.300000	
chunk0186_391_1	chr7	144512911	144513268	+	0	NA	intron (NM_001042482, intron 7 of 7)	L2a|LINE|L2	-102862	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.002801	0.304469	
chunk0138_309_1	chr4	41318993	41320048	+	0	NA	Intergenic	L2a|LINE|L2	-40087	NM_001289124	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.008531	0.412879	
chunk0194_132_1	chr8	84315349	84315548	+	0	NA	intron (NM_001100391, intron 1 of 8)	L1ME4b|LINE|L1	130583	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.000000	0.285000	
chunk0083_63_1	chr17	63859077	63859322	+	0	NA	intron (NR_002947, intron 1 of 5)	intron (NR_002947, intron 1 of 5)	2183	NR_002947	146771	Hs.629177	NR_002947	ENSG00000240280	TCAM1P	TCAM1	testicular cell adhesion molecule 1, pseudogene	pseudo	0.004082	0.471545	
chunk0039_133_1	chr11	98375793	98375992	+	0	NA	Intergenic	Intergenic	-645084	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.335000	
chunk0054_109_1	chr13	42893756	42894228	+	0	NA	intron (NM_001002264, intron 11 of 12)	intron (NM_001002264, intron 11 of 12)	-21248	NR_126389	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.004237	0.342495	
chunk0178_471_1	chr7	42288454	42288807	+	0	NA	Intergenic	Intergenic	-51611	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.005666	0.395480	
chunk0096_81_1	chr2	27951904	27952259	+	0	NA	intron (NM_199191, intron 3 of 11)	L1MEf|LINE|L1	-44286	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.002817	0.289326	
chunk0198_252_1	chr8	134581170	134581557	+	0	NA	intron (NM_020863, intron 10 of 15)	intron (NM_020863, intron 10 of 15)	-16708	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.012920	0.435567	
chunk0058_434_1	chr13	113197203	113198013	+	0	NA	intron (NM_001127202, intron 3 of 13)	intron (NM_001127202, intron 3 of 13)	-10585	NM_001278513	8451	Hs.339735	NM_003589	ENSG00000139842	CUL4A	-	cullin 4A	protein-coding	0.007407	0.441430	569(AAGGACACAATCTTCT,-,0.00)
chunk0132_216_1	chr3	157691436	157692066	+	0	NA	Intergenic	L1ME3G|LINE|L1	148407	NR_024016	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.004762	0.337559	
chunk0147_45_1	chr4	172245399	172245977	+	0	NA	intron (NM_001034845, intron 3 of 12)	intron (NM_001034845, intron 3 of 12)	432264	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.001730	0.386874	
chunk0138_228_1	chr4	39207811	39208010	+	0	NA	intron (NM_025132, intron 9 of 36)	L1MEf|LINE|L1	25506	NM_025132	57728	Hs.438482	NM_025132	ENSG00000157796	WDR19	ATD5|CED4|DYF-2|IFT144|NPHP13|ORF26|Oseg6|PWDMP|SRTD5	WD repeat domain 19	protein-coding	0.015075	0.285000	
chunk0131_420_1	chr3	153140404	153140702	+	0	NA	Intergenic	Intergenic	-21659	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.003356	0.337793	
chunk0202_373_1	chr9	80637680	80638225	+	0	NA	Intergenic	Intergenic	662929	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.001835	0.384615	
chunk0155_167_1	chr5	94361635	94362507	+	0	NA	intron (NM_001145678, intron 20 of 20)	intron (NM_001145678, intron 20 of 20)	-250372	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.004587	0.400916	297(AAGAACAGTGTGTGCA,-,0.00),298(AGAACAGTGTGTGCAG,+,0.00)
chunk0022_211_1	chr10	13857471	13858017	+	0	NA	intron (NM_018027, intron 3 of 24)	intron (NM_018027, intron 3 of 24)	-216540	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.007326	0.383912	
chunk0143_93_1	chr4	108376853	108377231	+	0	NA	Intergenic	Intergenic	204922	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.010582	0.451187	60(GGGAGCAGCCTGTTCT,-,0.00),61(GGAGCAGCCTGTTCTG,+,0.00),211(CAGGACACAGTGCTCT,-,0.00),212(AGGACACAGTGCTCTT,+,0.00)
chunk0052_391_1	chr12	130398561	130398954	+	0	NA	3' UTR (NM_015347, exon 19 of 19)	3' UTR (NM_015347, exon 19 of 19)	60869	NM_001190971	9271	Hs.405659	NM_004764	ENSG00000125207	PIWIL1	CT80.1|HIWI|MIWI|PIWI	piwi like RNA-mediated gene silencing 1	protein-coding	0.010178	0.395939	
chunk0211_450_1	chrX	129842361	129843148	+	0	NA	intron (NM_001008222, intron 1 of 9)	intron (NM_001008222, intron 1 of 9)	831	NM_001008222	51114	Hs.193566	NM_016032	ENSG00000188706	ZDHHC9	CGI89|CXorf11|DHHC9|MMSA1|MRXSZ|ZDHHC10|ZNF379|ZNF380	zinc finger DHHC-type containing 9	protein-coding	0.019060	0.486041	
chunk0019_162_1	chr1	225975797	225976350	+	0	NA	Intergenic	Intergenic	23292	NM_152608	163859	Hs.520192	NM_152608	ENSG00000143751	SDE2	C1orf55|dJ671D7.1	SDE2 telomere maintenance homolog	protein-coding	0.023508	0.519856	
chunk0145_447_1	chr4	153556306	153556825	+	0	NA	intron (NM_001131007, intron 5 of 34)	intron (NM_001131007, intron 5 of 34)	90219	NM_001131007	23240	Hs.732450	NM_015196	ENSG00000121210	TMEM131L	KIAA0922	transmembrane 131 like	protein-coding	0.005780	0.371154	
chunk0181_139_1	chr7	81399464	81399809	+	0	NA	Intergenic	Intergenic	226580	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.005797	0.430636	170(AGGAACAGAGTGTGCA,-,0.00),171(GGAACAGAGTGTGCAA,+,0.00)
chunk0026_362_1	chr10	69204058	69204376	+	0	NA	intron (NM_001301683, intron 14 of 15)	L1ME4c|LINE|L1	-16086	NM_025130	80201	Hs.522988	NM_025130	ENSG00000156510	HKDC1	-	hexokinase domain containing 1	protein-coding	0.006289	0.416928	152(CAGAACTGTATGTACC,-,0.00),153(AGAACTGTATGTACCT,+,0.00)
chunk0207_66_1	chrX	8994770	8995222	+	0	NA	Intergenic	Intergenic	39131	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.006637	0.339956	
chunk0049_60_1	chr12	90119910	90120398	+	0	NA	Intergenic	L1MA4A|LINE|L1	411199	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.002049	0.329243	
chunk0007_384_1	chr1	85344990	85345531	+	0	NA	intron (NM_001134445, intron 5 of 6)	intron (NM_001134445, intron 5 of 6)	-68356	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.000000	0.335793	
chunk0189_90_1	chr8	21389070	21389701	+	0	NA	Intergenic	Intergenic	91146	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.000000	0.302215	
chunk0030_375_1	chr10	119271177	119271714	+	0	NA	intron (NM_005308, intron 1 of 15)	intron (NM_005308, intron 1 of 15)	63760	NM_005308	2869	Hs.524625	NM_005308	ENSG00000198873	GRK5	FP2025|GPRK5	G protein-coupled receptor kinase 5	protein-coding	0.026071	0.526022	
chunk0021_25_1	chr10	572557	572793	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	69103	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.012712	0.367089	
chunk0201_231_1	chr9	37576608	37576868	+	0	NA	promoter-TSS (NM_012166)	promoter-TSS (NM_012166)	-485	NM_012166	26267	Hs.709527	NM_012166	ENSG00000147912	FBXO10	FBX10|PRMT11	F-box protein 10	protein-coding	0.007692	0.444444	
chunk0160_153_1	chr5	151646396	151646595	+	0	NA	Intergenic	Intergenic	-30450	NR_109873	101927096	Hs.571023	NR_109873	ENSG00000249035	CLMAT3	CTB-113P19.1|SPARC-AS1	colorectal liver metastasis associated transcript 3	ncRNA	0.015075	0.540000	
chunk0129_229_1	chr3	121961231	121961850	+	0	NA	Intergenic	L1M1|LINE|L1	60740	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.000000	0.319355	270(TAGTACTGGATGTCCT,-,0.00),271(AGTACTGGATGTCCTA,+,0.00)
chunk0042_285_1	chr12	7374727	7374995	+	0	NA	exon (NM_001297650, exon 12 of 20)	exon (NM_001297650, exon 12 of 20)	69324	NM_001297650	283316	Hs.631727	NM_174941	ENSG00000177675	CD163L1	CD163B|M160|SCARI2|WC1	CD163 molecule like 1	protein-coding	0.011194	0.468401	
chunk0177_247_1	chr7	25061359	25061616	+	0	NA	Intergenic	Intergenic	63874	NM_018947	54205	Hs.437060	NM_018947	ENSG00000172115	CYCS	CYC|HCS|THC4	cytochrome c, somatic	protein-coding	0.019455	0.395349	
chunk0031_134_1	chr10	124940122	124940403	+	0	NA	Intergenic	Intergenic	-1861	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.000000	0.315603	
chunk0145_22_1	chr4	143423031	143423323	+	0	NA	intron (NM_002039, intron 2 of 9)	intron (NM_002039, intron 2 of 9)	79717	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.003425	0.351536	
chunk0184_281_1	chr7	118660642	118661093	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	436209	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.008869	0.387168	
chunk0061_195_1	chr14	60240212	60240748	+	0	NA	Intergenic	L1P3|LINE|L1	-5272	NM_177952	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.011194	0.433892	157(GGGAACATGCAGTGCT,-,0.00),158(GGAACATGCAGTGCTT,+,0.00)
chunk0073_10_1	chr16	2039297	2040018	+	0	NA	TTS (NM_002528)	TTS (NM_002528)	6393	NM_001252076	9351	Hs.440896	NM_004785	ENSG00000065054	SLC9A3R2	E3KARP|NHE3RF2|NHERF-2|NHERF2|OCTS2|SIP-1|SIP1|TKA-1	SLC9A3 regulator 2	protein-coding	0.040222	0.638504	
chunk0042_123_1	chr12	3370974	3371464	+	0	NA	Intergenic	Intergenic	-10130	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.008163	0.403259	
chunk0166_423_1	chr6	52615954	52616380	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	38869	NR_103447	401264	Hs.544586	NR_103446	ENSG00000225791	TRAM2-AS1	-	TRAM2 antisense RNA 1 (head to head)	ncRNA	0.004695	0.341920	
chunk0204_189_1	chr9	96408621	96408943	+	0	NA	intron (NM_153695, intron 1 of 4)	intron (NM_153695, intron 1 of 4)	9605	NM_153695	195828	Hs.494557	NM_153695	ENSG00000165244	ZNF367	AFF29|CDC14B|ZFF29	zinc finger protein 367	protein-coding	0.006211	0.377709	
chunk0158_120_1	chr5	126974283	126975012	+	0	NA	intron (NM_178450, intron 1 of 4)	intron (NM_178450, intron 1 of 4)	56161	NM_178450	115123	Hs.132441	NM_178450	ENSG00000173926	MARCH3	MARCH-III|RNF173	membrane associated ring-CH-type finger 3	protein-coding	0.004115	0.391781	
chunk0078_141_1	chr17	3890419	3890996	+	0	NA	promoter-TSS (NM_172206)	promoter-TSS (NM_172206)	36	NM_172206	84254	Hs.8417	NM_032294	ENSG00000004660	CAMKK1	CAMKKA	calcium/calmodulin dependent protein kinase kinase 1	protein-coding	0.015598	0.581315	334(CAGTACAAGCTGTGCC,-,0.00),335(AGTACAAGCTGTGCCT,+,0.00)
chunk0129_308_1	chr3	123765826	123766334	+	0	NA	intron (NM_053025, intron 4 of 33)	L1MB3|LINE|L1	76436	NR_046629	100873940	Hs.667316	NR_046629	ENSG00000250174	MYLK-AS2	-	MYLK antisense RNA 2	ncRNA	0.003937	0.375246	307(CAGAACTCTCTGTTCT,-,0.00),308(AGAACTCTCTGTTCTG,+,0.00)
chunk0013_342_1	chr1	172069480	172069966	+	0	NA	intron (NM_001136127, intron 11 of 19)	MIR3|SINE|MIR	-69085	NR_036066	100422882		NR_036066	ENSG00000283152	MIR3120	mir-3120	microRNA 3120	ncRNA	0.008230	0.357290	251(AATAACATCATGTTCT,-,0.00),252(ATAACATCATGTTCTT,+,0.00)
chunk0059_392_1	chr14	37522168	37522795	+	0	NA	intron (NM_001195296, intron 14 of 14)	intron (NM_001195296, intron 14 of 14)	72639	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.009569	0.291401	
chunk0029_212_1	chr10	102056183	102056456	+	0	NA	promoter-TSS (NM_024541)	promoter-TSS (NM_024541)	-144	NM_024541	79591	Hs.16004	NM_024541	ENSG00000120029	ARMH3	C10orf76	armadillo like helical domain containing 3	protein-coding	0.080586	0.562044	
chunk0197_36_1	chr8	118088497	118089075	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	23033	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.008651	0.376511	
chunk0101_373_1	chr2	138208450	138209122	+	0	NA	Intergenic	Intergenic	244548	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.002976	0.323923	
chunk0195_255_1	chr8	97926180	97926686	+	0	NA	intron (NM_030583, intron 2 of 18)	intron (NM_030583, intron 2 of 18)	57350	NM_030583	4147	Hs.189445	NM_002380	ENSG00000132561	MATN2	-	matrilin 2	protein-coding	0.003953	0.461538	105(GGAGACAGGATGTCCT,-,0.00),106(GAGACAGGATGTCCTT,+,0.00)
chunk0116_108_1	chr21	35425173	35425372	+	0	NA	intron (NR_073512, intron 2 of 2)	MLT1K|LTR|ERVL-MaLR	155492	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.005025	0.485000	
chunk0066_20_1	chr15	27398374	27399219	+	0	NA	intron (NM_033223, intron 5 of 9)	intron (NM_033223, intron 5 of 9)	-237477	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.013018	0.366430	
chunk0005_288_1	chr1	60102553	60103116	+	0	NA	Intergenic	Intergenic	-29064	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.005329	0.418440	
chunk0093_105_1	chr19	43694452	43695157	+	0	NA	Intergenic	Intergenic	-21258	NM_019612	56269	Hs.515444	NM_019612	ENSG00000124449	IRGC	CINEMA|IFGGE|IRGC1|Iigp5|R30953_1	immunity related GTPase cinema	protein-coding	0.009929	0.467422	
chunk0123_57_1	chr3	41188418	41188863	+	0	NA	Intergenic	L1MC4a|LINE|L1	-10811	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.006742	0.392377	397(CGGAACTCTGAGTACT,-,0.00),398(GGAACTCTGAGTACTG,+,0.00)
chunk0167_217_1	chr6	66333441	66333745	+	0	NA	Intergenic	L1ME1|LINE|L1	545714	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.013158	0.363934	
chunk0112_450_1	chr20	48790812	48791355	+	0	NA	intron (NM_020820, intron 1 of 39)	intron (NM_020820, intron 1 of 39)	36800	NM_020820	57580	Hs.153310	NM_020820	ENSG00000124126	PREX1	P-REX1	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	protein-coding	0.020258	0.512868	
chunk0115_397_1	chr21	30567507	30568117	+	0	NA	Intergenic	Intergenic	-6523	NM_181614	337974	Hs.553696	NM_181614	ENSG00000244362	KRTAP19-7	KAP19.7	keratin associated protein 19-7	protein-coding	0.001639	0.350245	238(CAGGACAAACAGTTCT,-,0.00),239(AGGACAAACAGTTCTT,+,0.00)
chunk0072_153_1	chr15	92811548	92811866	+	0	NA	Intergenic	AluJr|SINE|Alu	16223	NR_033769	728619	Hs.684129	NR_033769		ASB9P1	-	ankyrin repeat and SOCS box containing 9 pseudogene 1	pseudo	0.009434	0.404389	
chunk0088_304_1	chr18	50275642	50276023	+	0	NA	intron (NM_001204141, intron 6 of 14)	intron (NM_001204141, intron 6 of 14)	4185	NM_001204151	4152	Hs.405610	NM_002384	ENSG00000141644	MBD1	CXXC3|PCM1|RFT	methyl-CpG binding domain protein 1	protein-coding	0.034121	0.643979	
chunk0175_25_1	chr7	698602	698801	+	0	NA	intron (NM_001164758, intron 2 of 10)	intron (NM_001164758, intron 2 of 10)	13823	NM_002735	5575	Hs.520851	NM_002735	ENSG00000188191	PRKAR1B	PRKAR1	protein kinase cAMP-dependent type I regulatory subunit beta	protein-coding	0.035176	0.500000	
chunk0177_365_1	chr7	26714023	26714223	+	0	NA	intron (NM_001303468, intron 9 of 12)	intron (NM_001303468, intron 9 of 12)	75038	NM_001302625									0.005000	0.422886	
chunk0102_231_1	chr2	148770717	148771321	+	0	NA	intron (NM_015630, intron 9 of 13)	intron (NM_015630, intron 9 of 13)	-104204	NM_004522	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.008278	0.381818	
chunk0068_111_1	chr15	52436264	52437219	+	0	NA	intron (NM_001142495, intron 1 of 39)	Charlie18a|DNA|hAT-Charlie	92309	NM_000259	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.005236	0.374477	
chunk0133_83_1	chr3	167319021	167319405	+	0	NA	intron (NM_001199202, intron 12 of 20)	L1MC4a|LINE|L1	61070	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.005208	0.350649	
chunk0045_166_1	chr12	46803412	46803974	+	0	NA	5' UTR (NM_018018, exon 2 of 17)	5' UTR (NM_018018, exon 2 of 17)	22304	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.005338	0.326821	
chunk0179_291_1	chr7	49696499	49696740	+	0	NA	Intergenic	(TGCA)n|Simple_repeat|Simple_repeat	-77042	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.020747	0.446281	
chunk0045_177_1	chr12	46948633	46949010	+	0	NA	Intergenic	Intergenic	-122824	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.000000	0.367725	244(AAGAACACTGAGTCTC,-,0.00)
chunk0045_403_1	chr12	52880218	52880619	+	0	NA	Intergenic	Intergenic	24666	NM_002273	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.014963	0.487562	271(CAGGACAGGTTGTTTT,-,0.00),272(AGGACAGGTTGTTTTG,+,0.00)
chunk0187_315_1	chr7	156514590	156515013	+	0	NA	intron (NR_103858, intron 1 of 1)	intron (NR_103858, intron 1 of 1)	-25690	NR_024119	64433	Hs.404170	NR_024119	ENSG00000279418	LINC00244	C7orf4|NCRNA00244	long intergenic non-protein coding RNA 244	ncRNA	0.028369	0.488208	160(AAGAACAACCTGTACT,-,0.00),161(AGAACAACCTGTACTT,+,0.00)
chunk0176_387_1	chr7	18780549	18781060	+	0	NA	intron (NM_178425, intron 15 of 24)	L2b|LINE|L2	271527	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.001957	0.417969	
chunk0130_217_1	chr3	133993976	133994647	+	0	NA	intron (NM_005630, intron 1 of 13)	intron (NM_005630, intron 1 of 13)	35765	NM_005630	6578	Hs.518270	NM_005630	ENSG00000174640	SLCO2A1	MATR1|OATP2A1|PGT|PHOAR2|SLC21A2	solute carrier organic anion transporter family member 2A1	protein-coding	0.007452	0.491071	
chunk0088_441_1	chr18	56222249	56222728	+	0	NA	Intergenic	Intergenic	-84952	NR_040025	100505474	Hs.662191	NR_040025	ENSG00000267712	LINC01539	-	long intergenic non-protein coding RNA 1539	ncRNA	0.006263	0.400000	
chunk0123_134_1	chr3	42775774	42776151	+	0	NA	Intergenic	L1MD2|LINE|L1	-2709	NM_144719	152206	Hs.604182	NM_144719	ENSG00000244607	CCDC13	-	coiled-coil domain containing 13	protein-coding	0.000000	0.317460	
chunk0011_45_1	chr1	143245710	143245945	+	0	NA	Intergenic	Intergenic	176765	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.046809	0.377119	
chunk0200_363_1	chr9	25678405	25679112	+	0	NA	promoter-TSS (NM_001004125)	promoter-TSS (NM_001004125)	100	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.033946	0.508475	
chunk0008_425_1	chr1	99122288	99122531	+	0	NA	intron (NR_033940, intron 1 of 2)	LTR23|LTR|ERV1	-117516	NM_001010861	163404	Hs.483948	NM_001010861	ENSG00000117598	PLPPR5	LPPR5|PAP2|PAP2D|PRG5	phospholipid phosphatase related 5	protein-coding	0.008230	0.381148	
chunk0083_40_1	chr17	63493001	63493327	+	0	NA	intron (NM_001178057, intron 8 of 12)	intron (NM_001178057, intron 8 of 12)	8347	NM_001178057	1636	Hs.298469	NM_000789	ENSG00000159640	ACE	ACE1|CD143|DCP|DCP1	angiotensin I converting enzyme	protein-coding	0.012270	0.550459	116(AAGTACACAATGTCCC,-,0.00),117(AGTACACAATGTCCCA,+,0.00)
chunk0103_29_1	chr2	159065203	159065594	+	0	NA	intron (NM_001145909, intron 2 of 26)	intron (NM_001145909, intron 2 of 26)	96764	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.005115	0.377551	
chunk0048_108_1	chr12	79464767	79465097	+	0	NA	Intergenic	SATR2|Satellite|Satellite	45675	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.015152	0.386707	229(AGGTACACCCTGTGAT,-,0.00)
chunk0094_201_1	chr2	6392519	6392738	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-17206	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.031963	0.527273	
chunk0031_57_1	chr10	122811186	122811590	+	0	NA	Intergenic	L2a|LINE|L2	34787	NM_022034	50624	Hs.647182	NM_022034	ENSG00000138161	CUZD1	ERG-1|ERG1|ITMAP1|UO-44	CUB and zona pellucida like domains 1	protein-coding	0.007426	0.409877	
chunk0164_230_1	chr6	23073870	23074455	+	0	NA	Intergenic	Intergenic	504713	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.001709	0.385666	
chunk0137_153_1	chr4	15765758	15766214	+	0	NA	Intergenic	L2a|LINE|L2	-12279	NR_132660	952	Hs.479214	NM_001775	ENSG00000004468	CD38	ADPRC 1|ADPRC1	CD38 molecule	protein-coding	0.008772	0.420131	
chunk0032_365_1	chr11	10805817	10806103	+	0	NA	exon (NM_001172705, exon 4 of 22)	exon (NM_001172705, exon 4 of 22)	2036	NM_001172705	1982	Hs.183684	NM_001418	ENSG00000110321	EIF4G2	AAG1|DAP5|NAT1|P97	eukaryotic translation initiation factor 4 gamma 2	protein-coding	0.027972	0.421603	
chunk0021_83_1	chr10	1726794	1727267	+	0	NA	intron (NM_018702, intron 1 of 9)	L2b|LINE|L2	10446	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.025370	0.491561	
chunk0025_439_1	chr10	60140805	60141370	+	0	NA	promoter-TSS (NM_001149)	promoter-TSS (NM_001149)	-71	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.012389	0.478799	
chunk0074_339_1	chr16	31452447	31452767	+	0	NA	Intergenic	Intergenic	-5666	NM_001288767	79798	Hs.732945	NM_024742	ENSG00000140691	ARMC5	AIMAH2	armadillo repeat containing 5	protein-coding	0.006250	0.507788	
chunk0049_43_1	chr12	89863011	89863708	+	0	NA	Intergenic	Intergenic	154404	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.010043	0.405444	
chunk0110_441_1	chr20	21055949	21056464	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-69777	NM_001276389	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.013592	0.350775	
chunk0198_384_1	chr8	141264175	141264631	+	0	NA	Intergenic	Intergenic	-9774	NM_001286646	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.028509	0.512035	
chunk0122_250_1	chr3	34727679	34727995	+	0	NA	Intergenic	MIRc|SINE|MIR	666186	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.003165	0.350158	
chunk0087_277_1	chr18	38469033	38469256	+	0	NA	Intergenic	Intergenic	812009	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.008969	0.504464	
chunk0087_266_1	chr18	37270033	37270424	+	0	NA	intron (NM_001025088, intron 8 of 12)	intron (NM_001025088, intron 8 of 12)	196276	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.017903	0.507653	
chunk0155_417_1	chr5	99587013	99587212	+	0	NA	Intergenic	MLT1C-int|LTR|ERVL-MaLR	53122	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.000000	0.415000	
chunk0005_422_1	chr1	62742690	62743164	+	0	NA	Intergenic	L1PB1|LINE|L1	-41179	NM_032852	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.004219	0.360000	
chunk0213_22_1	chrY	22221316	22221734	+	0	NA	Intergenic	Intergenic	-38583	NM_152585	159163	Hs.567746	NM_152585	ENSG00000169800	RBMY1F	YRRM2	RNA binding motif protein, Y-linked, family 1, member F	protein-coding	0.004785	0.429594	
chunk0208_279_1	chrX	21816580	21817016	+	0	NA	Intergenic	Intergenic	-22740	NM_015884	51360	Hs.443490	NM_015884	ENSG00000012174	MBTPS2	BRESEK|IFAP|KFSD|KFSDX|OI19|OLMSX|S2P	membrane bound transcription factor peptidase, site 2	protein-coding	0.004587	0.409611	
chunk0107_193_1	chr2	216192828	216193260	+	0	NA	intron (NM_021141, intron 18 of 20)	intron (NM_021141, intron 18 of 20)	-23845	NR_037701	150967	Hs.56876	NM_001199924	ENSG00000260804	LINC01963	PKI55	long intergenic non-protein coding RNA 1963	ncRNA	0.009259	0.415704	
chunk0174_297_1	chr6	162646784	162646983	+	0	NA	intron (NM_013988, intron 1 of 8)	Tigger3a|DNA|TcMar-Tigger	-80249	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.005025	0.355000	
chunk0008_36_1	chr1	88800581	88801099	+	0	NA	intron (NM_006256, intron 8 of 21)	intron (NM_006256, intron 8 of 21)	90778	NM_001514	2959	Hs.481852	NM_001514	ENSG00000137947	GTF2B	TF2B|TFIIB	general transcription factor IIB	protein-coding	0.011583	0.381503	
chunk0077_216_1	chr16	80178073	80178753	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-362321	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.007353	0.397944	
chunk0023_420_1	chr10	31508265	31508464	+	0	NA	intron (NM_030751, intron 4 of 8)	L1MA4A|LINE|L1	187229	NM_001174094	6935	Hs.124503	NM_030751	ENSG00000148516	ZEB1	AREB6|BZP|DELTAEF1|FECD6|NIL2A|PPCD3|TCF8|ZFHEP|ZFHX1A	zinc finger E-box binding homeobox 1	protein-coding	0.010050	0.605000	
chunk0188_171_1	chr8	10838471	10838880	+	0	NA	intron (NM_017884, intron 1 of 6)	MIR3|SINE|MIR	1224	NM_017884	54984	Hs.490991	NM_017884	ENSG00000254093	PINX1	Gno1|LPTL|LPTS|Pxr1	PIN2 (TERF1) interacting telomerase inhibitor 1	protein-coding	0.017115	0.400000	
chunk0197_97_1	chr8	119614616	119615406	+	0	NA	intron (NM_001040092, intron 8 of 24)	intron (NM_001040092, intron 8 of 24)	-22003	NR_045555	5168	Hs.190977	NM_006209	ENSG00000136960	ENPP2	ATX|ATX-X|AUTOTAXIN|LysoPLD|NPP2|PD-IALPHA|PDNP2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.001266	0.374210	
chunk0067_375_1	chr15	48940267	48940694	+	0	NA	intron (NM_203349, intron 1 of 11)	intron (NM_203349, intron 1 of 11)	22964	NM_203349	399694	Hs.642615	NM_203349	ENSG00000185634	SHC4	RaLP|SHCD	SHC adaptor protein 4	protein-coding	0.009368	0.394860	
chunk0132_203_1	chr3	157311434	157311901	+	0	NA	intron (NM_001167911, intron 10 of 12)	intron (NM_001167911, intron 10 of 12)	-125124	NM_002852	5806	Hs.591286	NM_002852	ENSG00000163661	PTX3	TNFAIP5|TSG-14	pentraxin 3	protein-coding	0.002141	0.286325	
chunk0101_81_1	chr2	124039862	124040061	+	0	NA	intron (NM_130773, intron 1 of 23)	MER134|DNA?|DNA?	14674	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.005025	0.345000	
chunk0003_114_1	chr1	32321670	32322109	+	0	NA	intron (NM_004964, intron 3 of 13)	intron (NM_004964, intron 3 of 13)	14350	NM_023009	65108	Hs.75061	NM_023009	ENSG00000175130	MARCKSL1	F52|MACMARCKS|MLP|MLP1|MRP	MARCKS like 1	protein-coding	0.011390	0.475000	
chunk0169_385_1	chr6	107779484	107779806	+	0	NA	intron (NM_198081, intron 1 of 7)	intron (NM_198081, intron 1 of 7)	44672	NM_198081	256380	Hs.486109	NM_198081	ENSG00000146285	SCML4	dJ47M23.1	Scm polycomb group protein like 4	protein-coding	0.012422	0.473684	
chunk0002_102_1	chr1	15371556	15371755	+	0	NA	intron (NM_052929, intron 25 of 30)	intron (NM_052929, intron 25 of 30)	-38240	NM_024329	79180	Hs.465374	NM_024329	ENSG00000142634	EFHD2	SWS1	EF-hand domain family member D2	protein-coding	0.025126	0.570000	16(AAGCACAGGCTGTGAC,-,0.00)
chunk0032_42_1	chr11	1262525	1262724	+	0	NA	TTS (NM_002458)	TTS (NM_002458)	6019	NR_106802	102466725		NR_106802	ENSG00000275669	MIR6744	hsa-mir-6744	microRNA 6744	ncRNA	0.060302	0.685000	
chunk0203_236_1	chr9	87172332	87172631	+	0	NA	Intergenic	L1MEc|LINE|L1	23837	NM_001001709									0.000000	0.323333	
chunk0067_246_1	chr15	45552057	45552326	+	0	NA	intron (NR_022014, intron 5 of 5)	MIRc|SINE|MIR	-29387	NM_013309	7782	Hs.162989	NM_013309	ENSG00000104154	SLC30A4	ZNT4|znT-4	solute carrier family 30 member 4	protein-coding	0.000000	0.307407	
chunk0006_244_1	chr1	69110002	69110729	+	0	NA	Intergenic	Intergenic	-613144	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.004127	0.383242	
chunk0151_182_1	chr5	50364889	50365393	+	0	NA	Intergenic	Intergenic	76259	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.001984	0.334653	
chunk0120_359_1	chr3	11642803	11643002	+	0	NA	intron (NM_014667, intron 2 of 5)	CpG	1075	NM_001128219	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.095477	0.665000	
chunk0053_33_1	chr13	27091875	27092079	+	0	NA	intron (NM_182488, intron 4 of 8)	L2c|LINE|L2	-33556	NR_046547	100874070	Hs.524923	NR_046547		USP12-AS1	-	USP12 antisense RNA 1	ncRNA	0.004902	0.482927	116(ATAACACACTGTACTG,+,0.00)
chunk0019_412_1	chr1	230714131	230714438	+	0	NA	5' UTR (NM_000029, exon 1 of 5)	5' UTR (NM_000029, exon 1 of 5)	306	NM_000029	183	Hs.19383	NM_000029	ENSG00000135744	AGT	ANHU|SERPINA8|hFLT1	angiotensinogen	protein-coding	0.029316	0.571429	191(CTGAACAGAGTGAGCC,-,0.00),192(TGAACAGAGTGAGCCG,+,0.00)
chunk0187_12_1	chr8	572681	573315	+	0	NA	Intergenic	Intergenic	-27217	NM_175075	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.018927	0.519685	
chunk0140_391_1	chr4	75250933	75251376	+	0	NA	Intergenic	Intergenic	-102922	NR_033964	441025	Hs.407667	NR_033964	ENSG00000251383	LINC02483	-	long intergenic non-protein coding RNA 2483	ncRNA	0.009029	0.385135	
chunk0175_83_1	chr7	2411914	2412720	+	0	NA	intron (NM_018641, intron 1 of 1)	intron (NM_018641, intron 1 of 1)	8757	NM_018641	55501	Hs.288853	NM_018641	ENSG00000136213	CHST12	C4S-2|C4ST-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding	0.013648	0.423792	104(GAGAACAGGGTGAGCT,-,0.00),105(AGAACAGGGTGAGCTG,+,0.00)
chunk0171_439_1	chr6	131722339	131722890	+	0	NA	intron (NR_133007, intron 18 of 23)	intron (NR_133007, intron 18 of 23)	-11597	NM_001145659	643854	Hs.632613	NM_001145659	ENSG00000236761	CTAGE9	-	CTAGE family member 9	protein-coding	0.010889	0.422101	
chunk0189_287_1	chr8	25478453	25479155	+	0	NA	intron (NM_152562, intron 7 of 14)	L2a|LINE|L2	19807	NM_152562	157313	Hs.33366	NM_152562	ENSG00000184661	CDCA2	PPP1R81|Repo-Man	cell division cycle associated 2	protein-coding	0.007123	0.385491	
chunk0140_119_1	chr4	68855048	68855494	+	0	NA	Intergenic	MER57B1|LTR|ERV1	39278	NM_001290091	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.006726	0.369128	
chunk0154_127_1	chr5	78997188	78997431	+	0	NA	TTS (NM_013391)	TTS (NM_013391)	-10775	NM_000046	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.008230	0.364754	
chunk0004_112_1	chr1	44423895	44424177	+	0	NA	intron (NM_018150, intron 2 of 14)	intron (NM_018150, intron 2 of 14)	18748	NM_018150	55182	Hs.456557	NM_018150	ENSG00000187147	RNF220	C1orf164	ring finger protein 220	protein-coding	0.031915	0.473498	
chunk0038_327_1	chr11	92503231	92503640	+	0	NA	intron (NM_001008781, intron 1 of 24)	MIRb|SINE|MIR	151339	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.000000	0.304878	
chunk0023_105_1	chr10	22967951	22968502	+	0	NA	intron (NM_173081, intron 7 of 18)	intron (NM_173081, intron 7 of 18)	40202	NM_001282746	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.001815	0.367754	253(ATGACATTGTGTTCTG,+,0.00)
chunk0042_149_1	chr12	3863512	3864059	+	0	NA	intron (NR_104461, intron 1 of 8)	MER77|LTR|ERVL	9663	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.010969	0.443431	
chunk0106_83_1	chr2	197134189	197134666	+	0	NA	intron (NM_001195144, intron 4 of 27)	intron (NM_001195144, intron 4 of 27)	168092	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.004193	0.416318	
chunk0193_57_1	chr8	72476020	72476268	+	0	NA	Intergenic	L1PA17|LINE|L1	-61247	NM_004770	9312	Hs.661102	NM_004770	ENSG00000182674	KCNB2	KV2.2	potassium voltage-gated channel subfamily B member 2	protein-coding	0.004032	0.542169	
chunk0162_152_1	chr6	3380676	3380917	+	0	NA	intron (NM_015482, intron 3 of 9)	MLT1I|LTR|ERVL-MaLR	64217	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.012448	0.483471	
chunk0049_184_1	chr12	92674896	92675186	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-27802	NM_001037671	338809	Hs.326303	NM_001037671	ENSG00000187510	C12orf74	-	chromosome 12 open reading frame 74	protein-coding	0.013793	0.515464	
chunk0111_301_1	chr20	31943055	31943589	+	0	NA	TTS (NM_001008409)	TTS (NM_001008409)	8758	NM_030815	81572	Hs.435755	NM_030815	ENSG00000088356	PDRG1	C20orf126|PDRG	p53 and DNA damage regulated 1	protein-coding	0.005618	0.542056	
chunk0113_313_1	chr20	58031502	58032106	+	0	NA	Intergenic	Intergenic	-119123	NM_178456	128602	Hs.43977	NM_178456	ENSG00000124237	C20orf85	LLC1|bA196N14.1	chromosome 20 open reading frame 85	protein-coding	0.011589	0.442975	240(AAGTACAAGATGTGCA,-,0.00),241(AGTACAAGATGTGCAC,+,0.00)
chunk0120_136_1	chr3	4999910	5000119	+	0	NA	Intergenic	Intergenic	-20053	NR_037903	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.014354	0.528571	
chunk0104_129_1	chr2	173205334	173205674	+	0	NA	intron (NM_133646, intron 9 of 11)	intron (NM_133646, intron 9 of 11)	76532	NR_033882	339751	Hs.570083	NR_033882	ENSG00000238133	MAP3K20-AS1	MLK7-AS1	MAP3K20 antisense RNA 1	ncRNA	0.005882	0.419355	
chunk0204_245_1	chr9	98072263	98072466	+	0	NA	intron (NM_018946, intron 2 of 5)	intron (NM_018946, intron 2 of 5)	15687	NM_018946	54187	Hs.522310	NM_018946	ENSG00000095380	NANS	HEL-S-100|SAS|SEMDCG|SEMDG	N-acetylneuraminate synthase	protein-coding	0.019704	0.524510	
chunk0040_122_1	chr11	112293687	112294062	+	0	NA	non-coding (NR_126004, exon 2 of 4)	non-coding (NR_126004, exon 2 of 4)	23125	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.005333	0.404255	
chunk0211_74_1	chrX	110056473	110057056	+	0	NA	intron (NM_032227, intron 2 of 6)	L1MB8|LINE|L1	1435	NR_030381	724022		NR_030381	ENSG00000208013	MIR652	MIRN652|hsa-mir-652	microRNA 652	ncRNA	0.005146	0.349315	
chunk0204_367_1	chr9	101900734	101901180	+	0	NA	Intergenic	L2a|LINE|L2	-162377	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.008969	0.355705	
chunk0199_229_1	chr9	5365133	5365332	+	0	NA	intron (NM_018465, intron 3 of 5)	L1MC3|LINE|L1	-25359	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.000000	0.400000	
chunk0204_376_1	chr9	102083508	102083938	+	0	NA	Intergenic	Intergenic	-345143	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.002326	0.366589	
chunk0123_48_1	chr3	41014467	41014780	+	0	NA	Intergenic	Intergenic	-184828	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.006390	0.378981	
chunk0134_213_1	chr3	178612725	178613276	+	0	NA	intron (NM_001278911, intron 1 of 4)	L1MA1|LINE|L1	54300	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.005445	0.333333	
chunk0076_422_1	chr16	72967924	72968358	+	0	NA	intron (NM_006885, intron 1 of 9)	L1MC4|LINE|L1	80234	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.013825	0.409195	
chunk0189_170_1	chr8	23449318	23450000	+	0	NA	intron (NM_001128930, intron 2 of 12)	intron (NM_001128930, intron 2 of 12)	8072	NM_001128930	9583	Hs.444389	NM_004901	ENSG00000197217	ENTPD4	LALP70|LAP70|LYSAL1|NTPDase-4|UDPase	ectonucleoside triphosphate diphosphohydrolase 4	protein-coding	0.007331	0.387994	
chunk0054_27_1	chr13	40895734	40895933	+	0	NA	intron (NR_038258, intron 1 of 7)	intron (NR_038258, intron 1 of 7)	25917	NR_038259	100616668	Hs.660718	NR_038258		TPTE2P5	-	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 5	pseudo	0.000000	0.390000	
chunk0127_36_1	chr3	88661586	88661861	+	0	NA	Intergenic	Intergenic	-445801	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003636	0.297101	
chunk0065_214_1	chr14	100237963	100238197	+	0	NA	promoter-TSS (NM_003403)	promoter-TSS (NM_003403)	-685	NM_003403	7528	Hs.388927	NM_003403	ENSG00000100811	YY1	DELTA|GADEVS|INO80S|NF-E1|UCRBP|YIN-YANG-1	YY1 transcription factor	protein-coding	0.136752	0.663830	
chunk0199_308_1	chr9	7111457	7111770	+	0	NA	intron (NM_015061, intron 18 of 21)	L2b|LINE|L2	353972	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.006390	0.429936	129(GAGTCCAGGGTGTTCT,-,0.00),130(AGTCCAGGGTGTTCTA,+,0.00)
chunk0165_19_1	chr6	28985552	28985782	+	0	NA	Intergenic	Intergenic	19593	NM_001010877	282890	Hs.148218	NM_001010877	ENSG00000197935	ZNF311	zf31	zinc finger protein 311	protein-coding	0.052174	0.558442	
chunk0096_362_1	chr2	36456527	36456796	+	0	NA	intron (NM_016441, intron 4 of 16)	intron (NM_016441, intron 4 of 16)	100434	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.026022	0.555556	
chunk0041_225_1	chr11	127804967	127805484	+	0	NA	Intergenic	Intergenic	534155	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.003868	0.401544	
chunk0181_198_1	chr7	83649771	83650327	+	0	NA	promoter-TSS (NM_012431)	promoter-TSS (NM_012431)	-886	NM_012431	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.001799	0.307002	
chunk0169_151_1	chr6	101670278	101670667	+	0	NA	intron (NM_001166247, intron 3 of 16)	intron (NM_001166247, intron 3 of 16)	271487	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.005141	0.341026	
chunk0008_100_1	chr1	91120307	91120729	+	0	NA	Intergenic	Intergenic	-98263	NM_032186	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.009479	0.408983	175(AGGAACTGCATGTTCT,-,0.00),176(GGAACTGCATGTTCTT,+,0.00)
chunk0011_53_1	chr1	143265187	143265892	+	0	NA	Intergenic	(ATCGAATGGA)n|Simple_repeat|Simple_repeat	157053	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.051064	0.359773	
chunk0066_179_1	chr15	33068797	33069173	+	0	NA	promoter-TSS (NM_001103184)	promoter-TSS (NM_001103184)	-953	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.010638	0.503979	
chunk0212_301_1	chrX	141345730	141345929	+	0	NA	Intergenic	Intergenic	-103279	NM_022661	64663	Hs.375036	NM_022661	ENSG00000198573	SPANXC	CT11.3|CTp11|SPANX-C|SPANX-E|SPANXE	SPANX family member C	protein-coding	0.005025	0.370000	
chunk0091_25_1	chr19	3372462	3372765	+	0	NA	intron (NM_001245002, intron 1 of 10)	intron (NM_001245002, intron 1 of 10)	6046	NM_001245004	4782	Hs.170131	NM_005597	ENSG00000141905	NFIC	CTF|CTF5|NF-I|NFI	nuclear factor I C	protein-coding	0.042904	0.628289	
chunk0121_244_1	chr3	22727459	22727681	+	0	NA	Intergenic	L2c|LINE|L2	-475723	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.009009	0.443946	
chunk0188_71_1	chr8	8368198	8368714	+	0	NA	intron (NM_001080826, intron 2 of 4)	intron (NM_001080826, intron 2 of 4)	13378	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.013566	0.402321	
chunk0041_183_1	chr11	126335361	126335663	+	0	NA	intron (NM_014026, intron 3 of 5)	intron (NM_014026, intron 3 of 5)	20075	NR_033839	399972	Hs.585206	NR_033839		GSEC	DCPS-AS1|ST3GAL4-AS1	G-quadruplex forming sequence containing lncRNA	ncRNA	0.013245	0.524752	162(GGAGACAGGATGTACC,-,0.00),163(GAGACAGGATGTACCT,+,0.00)
chunk0062_4_1	chr14	66006014	66006483	+	0	NA	Intergenic	Intergenic	-480123	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.004264	0.419149	
chunk0146_1_1	chr4	154543812	154544026	+	0	NA	intron (NM_002669, intron 7 of 14)	L1MA1|LINE|L1	6514	NM_002669	5356	Hs.249996	NM_002669	ENSG00000171566	PLRG1	Cwc1|PRL1|PRP46|PRPF46|TANGO4	pleiotropic regulator 1	protein-coding	0.009346	0.339535	
chunk0077_348_1	chr16	83476527	83476958	+	0	NA	intron (NM_001220488, intron 7 of 14)	intron (NM_001220488, intron 7 of 14)	-31604	NR_036147	100422853		NR_036147	ENSG00000263785	MIR3182	mir-3182	microRNA 3182	ncRNA	0.011601	0.370370	
chunk0144_26_1	chr4	124999318	124999557	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-286705	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.016736	0.391667	
chunk0079_52_1	chr17	10727453	10727954	+	0	NA	intron (NM_001004313, intron 2 of 5)	intron (NM_001004313, intron 2 of 5)	-2074	NR_073455	101101775	Hs.569782	NR_073455	ENSG00000263400	TMEM220-AS1	-	TMEM220 antisense RNA 1	ncRNA	0.011976	0.418327	
chunk0014_401_1	chr1	182968981	182969820	+	0	NA	Intergenic	L2c|LINE|L2	-15982	NM_030933	81626	Hs.497034	NM_030933	ENSG00000157060	SHCBP1L	C1orf14|GE36	SHC binding and spindle associated 1 like	protein-coding	0.005959	0.397619	451(AGGTTCAGTATGTTCC,-,0.00),452(GGTTCAGTATGTTCCC,+,0.00)
chunk0062_293_1	chr14	72570418	72570791	+	0	NA	Intergenic	Charlie23a|DNA|hAT-Charlie	53784	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.008043	0.446524	
chunk0163_370_1	chr6	15985265	15985753	+	0	NA	Intergenic	L1MC5a|LINE|L1	-143577	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.008197	0.388548	306(GTAAACAGAGTGTTCT,-,0.00),307(TAAACAGAGTGTTCTC,+,0.00)
chunk0026_81_1	chr10	61326308	61326972	+	0	NA	Intergenic	Intergenic	-125999	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.001506	0.362406	314(GGGACTCTGAGTCCTC,+,0.00)
chunk0128_252_1	chr3	108888473	108888908	+	0	NA	Intergenic	Intergenic	65140	NM_005459	9626	Hs.233363	NM_005459	ENSG00000138472	GUCA1C	GCAP3	guanylate cyclase activator 1C	protein-coding	0.000000	0.410550	
chunk0049_55_1	chr12	90044036	90044319	+	0	NA	Intergenic	Intergenic	335222	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.003534	0.302817	
chunk0124_132_1	chr3	54354832	54355315	+	0	NA	intron (NM_018398, intron 3 of 37)	intron (NM_018398, intron 3 of 37)	232407	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.006211	0.409091	
chunk0127_425_1	chr3	102670857	102671537	+	0	NA	Intergenic	LTR40a|LTR|ERVL	236182	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.004412	0.384728	
chunk0155_389_1	chr5	98607911	98608255	+	0	NA	Intergenic	MIR|SINE|MIR	-161212	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.005814	0.371014	
chunk0044_126_1	chr12	29293267	29293621	+	0	NA	exon (NM_018099, exon 3 of 12)	exon (NM_018099, exon 3 of 12)	24404	NR_103860	100506606	Hs.298851	NR_103860	ENSG00000257176	LOC100506606	-	uncharacterized LOC100506606	ncRNA	0.005650	0.357746	
chunk0092_211_1	chr19	31518280	31518574	+	0	NA	Intergenic	Intergenic	-69762	NM_001278575	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.013605	0.508475	
chunk0105_387_1	chr2	192438215	192438433	+	0	NA	Intergenic	Intergenic	-243391	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.000000	0.433790	
chunk0102_146_1	chr2	146882078	146882470	+	0	NA	Intergenic	Intergenic	295217	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.007653	0.374046	
chunk0200_234_1	chr9	20816370	20817266	+	0	NA	intron (NM_017794, intron 13 of 45)	MER2|DNA|TcMar-Tigger	100713	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.004464	0.324415	
chunk0190_241_1	chr8	36797146	36797751	+	0	NA	intron (NM_001031836, intron 2 of 26)	intron (NM_001031836, intron 2 of 26)	13124	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.003306	0.293729	
chunk0015_298_1	chr1	188867933	188868560	+	0	NA	Intergenic	Intergenic	1424618	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001595	0.288217	530(AGGGACAAATTGTGCT,-,0.00),531(GGGACAAATTGTGCTA,+,0.00)
chunk0071_255_1	chr15	85477752	85478059	+	0	NA	intron (NM_007200, intron 1 of 36)	L2c|LINE|L2	97289	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.013029	0.490260	
chunk0167_202_1	chr6	64881607	64882348	+	0	NA	intron (NM_001142800, intron 19 of 42)	intron (NM_001142800, intron 19 of 42)	-419441	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.008097	0.327493	
chunk0073_279_1	chr16	12531876	12532451	+	0	NA	intron (NM_032167, intron 20 of 20)	MER99|DNA|hAT?	-188158	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.020870	0.454861	394(AAGCACAATAAGTCCT,-,0.00),395(AGCACAATAAGTCCTT,+,0.00)
chunk0094_5_1	chr2	668538	669101	+	0	NA	3' UTR (NM_152834, exon 5 of 5)	3' UTR (NM_152834, exon 5 of 5)	8620	NM_152834	129787	Hs.6729	NM_152834	ENSG00000151353	TMEM18	lncND	transmembrane protein 18	protein-coding	0.007105	0.455674	222(GGGAGCATTGTGTTCC,-,0.00),223(GGAGCATTGTGTTCCC,+,0.00)
chunk0113_28_1	chr20	49706737	49707601	+	0	NA	intron (NM_004776, intron 1 of 8)	intron (NM_004776, intron 1 of 8)	6715	NM_004776	9334	Hs.370487	NM_004776	ENSG00000158470	B4GALT5	B4Gal-T5|BETA4-GALT-IV|beta4Gal-T5|beta4GalT-V|gt-V	beta-1,4-galactosyltransferase 5	protein-coding	0.008102	0.408092	728(AGAAACTGAGTGTGCT,-,0.00)
chunk0084_456_1	chr17	83089173	83090004	+	0	NA	intron (NM_001004431, intron 2 of 3)	intron (NM_001004431, intron 2 of 3)	9897	NM_001004431	284207	Hs.378821	NM_001004431	ENSG00000176845	METRNL	-	meteorin like, glial cell differentiation regulator	protein-coding	0.054152	0.632212	
chunk0029_98_1	chr10	97344555	97344760	+	0	NA	Intergenic	L2a|LINE|L2	-9956	NM_012083	23401	Hs.140720	NM_012083	ENSG00000181274	FRAT2	FRAT-2	FRAT regulator of WNT signaling pathway 2	protein-coding	0.014634	0.553398	
chunk0207_295_1	chr9	133161090	133161306	+	0	NA	intron (NM_001288572, intron 3 of 6)	intron (NM_001288572, intron 3 of 6)	2747	NM_001288572	26301	Hs.495419	NM_021996	ENSG00000148288	GBGT1	A3GALNT|FS|UNQ2513	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group)	protein-coding	0.018519	0.525346	88(TTGCACTCTGTGTTCT,-,0.00),89(TGCACTCTGTGTTCTC,+,0.00)
chunk0018_1_1	chr1	214602783	214603318	+	0	NA	promoter-TSS (NM_016343)	promoter-TSS (NM_016343)	-139	NM_016343	1063	Hs.497741	NM_016343	ENSG00000117724	CENPF	CENF|CILD31|PRO1779|STROMS|hcp-1	centromere protein F	protein-coding	0.069159	0.533582	
chunk0130_202_1	chr3	133760033	133760237	+	0	NA	intron (NM_001063, intron 9 of 16)	MER21C|LTR|ERVL	14002	NM_001063	7018	Hs.518267	NM_001063	ENSG00000091513	TF	HEL-S-71p|PRO1557|PRO2086|TFQTL1	transferrin	protein-coding	0.004902	0.424390	64(GAGAACATGAAGTGCC,-,0.00),65(AGAACATGAAGTGCCA,+,0.00)
chunk0069_110_1	chr15	61670530	61671010	+	0	NA	Intergenic	L1MD|LINE|L1	389695	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.000000	0.282744	
chunk0076_288_1	chr16	69814679	69814964	+	0	NA	intron (NM_007014, intron 5 of 24)	intron (NM_007014, intron 5 of 24)	-23916	NM_001270453	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.010526	0.416084	
chunk0132_348_1	chr3	161395608	161396103	+	0	NA	Intergenic	MIRb|SINE|MIR	-23772	NM_001040100	165679	Hs.369104	NM_145035	ENSG00000196542	SPTSSB	ADMP|C3orf57|SSSPTB	serine palmitoyltransferase small subunit B	protein-coding	0.008081	0.377016	
chunk0033_244_1	chr11	18078181	18078604	+	0	NA	Intergenic	Intergenic	27699	NM_138421	113174	Hs.591998	NM_138421	ENSG00000166788	SAAL1	SPACIA1	serum amyloid A like 1	protein-coding	0.009456	0.389151	
chunk0209_361_1	chrX	53628684	53629080	+	0	NA	exon (NM_031407, exon 14 of 84)	exon (NM_031407, exon 14 of 84)	57847	NM_031407	10075	Hs.136905	NM_031407	ENSG00000086758	HUWE1	ARF-BP1|HECTH9|HSPC272|Ib772|LASU1|MRXST|MULE|URE-B1|UREB1	HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1	protein-coding	0.005051	0.365239	
chunk0190_359_1	chr8	39749802	39750139	+	0	NA	intron (NM_001278114, intron 15 of 19)	L2a|LINE|L2	88319	NM_001278114	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.005935	0.322485	
chunk0030_318_1	chr10	118030795	118031114	+	0	NA	intron (NM_014904, intron 3 of 4)	intron (NM_014904, intron 3 of 4)	15649	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.009404	0.337500	
chunk0113_87_1	chr20	50792834	50793374	+	0	NA	Intergenic	Intergenic	-1790	NM_198799	55653	Hs.381178	NM_017843	ENSG00000124243	BCAS4	CNOL	breast carcinoma amplified sequence 4	protein-coding	0.016667	0.484288	354(GGCTCAGTGAGTTCCT,+,0.00)
chunk0036_114_1	chr11	61538430	61538629	+	0	NA	intron (NM_004200, intron 3 of 8)	intron (NM_004200, intron 3 of 8)	29729	NM_001145077	390205	Hs.441122	NM_001145077	ENSG00000204950	LRRC10B	-	leucine rich repeat containing 10B	protein-coding	0.005025	0.560000	
chunk0047_301_1	chr12	73797628	73798044	+	0	NA	Intergenic	MER53|DNA|hAT	494795	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.000000	0.232614	142(AAGACATCCTGTACTG,+,0.00)
chunk0185_274_1	chr7	130900832	130901208	+	0	NA	intron (NR_110472, intron 2 of 3)	intron (NR_110472, intron 2 of 3)	12290	NR_110473	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.005319	0.424403	
chunk0115_455_1	chr21	32612939	32613138	+	0	NA	promoter-TSS (NR_036552)	promoter-TSS (NR_036552)	-430	NM_021254	56683	Hs.5811	NM_017835	ENSG00000159079	CFAP298	C21orf48|C21orf59|CILD26|FBB18|Kur	cilia and flagella associated protein 298	protein-coding	0.070352	0.600000	
chunk0122_137_1	chr3	31779400	31779994	+	0	NA	intron (NM_001174060, intron 3 of 10)	L1PB1|LINE|L1	75484	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.003367	0.317647	
chunk0057_414_1	chr13	109899298	109899868	+	0	NA	Intergenic	Intergenic	-113016	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.007018	0.360771	
chunk0180_1_1	chr7	52890496	52890695	+	0	NA	Intergenic	Intergenic	-145061	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.005025	0.325000	
chunk0011_174_1	chr1	148143146	148143579	+	0	NA	intron (NR_046188, intron 2 of 24)	L2a|LINE|L2	-7549	NM_001101663	200030	Hs.721588	NM_183372	ENSG00000263956	NBPF11	NBPF24	NBPF member 11	protein-coding	0.016166	0.495392	
chunk0058_18_1	chr14	19724846	19725452	+	0	NA	Intergenic	L1M2|LINE|L1	-10817	NM_001197287	79334	Hs.554706	NM_001197287	ENSG00000258453	OR11H2	C14orf15|OR11H13|OR11H2P|OR11H8P	olfactory receptor family 11 subfamily H member 2	protein-coding	0.009901	0.306425	
chunk0192_250_1	chr8	65758425	65759119	+	0	NA	intron (NM_002603, intron 3 of 12)	MER21-int|LTR|ERVL	30322	NM_002603	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.010086	0.473381	285(CTGTACAGTATGTTCC,-,0.00),286(TGTACAGTATGTTCCT,+,0.00)
chunk0134_38_1	chr3	175685693	175686105	+	0	NA	intron (NM_207015, intron 11 of 13)	MLT2B4|LTR|ERVL	90434	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.007282	0.394673	
chunk0079_140_1	chr17	12902795	12903040	+	0	NA	intron (NM_014859, intron 3 of 20)	intron (NM_014859, intron 3 of 20)	14425	NR_039747	100616494		NR_039747	ENSG00000265503	MIR1269B	-	microRNA 1269b	ncRNA	0.008163	0.471545	
chunk0045_280_1	chr12	49929482	49929761	+	0	NA	Intergenic	Intergenic	17668	NR_110048	101927292	Hs.129345	NR_110048	ENSG00000257771	LINC02395	-	long intergenic non-protein coding RNA 2395	ncRNA	0.014337	0.571429	
chunk0141_394_1	chr4	88372029	88372228	+	0	NA	Intergenic	L1MA4|LINE|L1	-6611	NM_001165136	55008	Hs.529317	NM_017912	ENSG00000138642	HERC6	-	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	protein-coding	0.005025	0.330000	
chunk0212_444_1	chrX	155614088	155614287	+	0	NA	intron (NM_001304990, intron 1 of 2)	L2a|LINE|L2	-1226	NM_018196	55217	Hs.133321	NM_018196	ENSG00000185973	TMLHE	AUTSX6|BBOX2|TMLD|TMLH|TMLHED|XAP130	trimethyllysine hydroxylase, epsilon	protein-coding	0.000000	0.385000	
chunk0127_97_1	chr3	89981524	89982189	+	0	NA	Intergenic	Intergenic	874332	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.007519	0.351351	339(GGGCACAAAGTGTACT,-,0.00),340(GGCACAAAGTGTACTA,+,0.00)
chunk0159_121_1	chr5	138793359	138793754	+	0	NA	intron (NM_001290307, intron 3 of 18)	intron (NM_001290307, intron 3 of 18)	40160	NM_001903	1495	Hs.445981	NM_001903	ENSG00000044115	CTNNA1	CAP102|MDPT2	catenin alpha 1	protein-coding	0.000000	0.325758	
chunk0119_443_1	chr22	50140130	50140329	+	0	NA	intron (NM_001164105, intron 15 of 25)	intron (NM_001164105, intron 15 of 25)	-6826	NM_001164106	54456	Hs.62880	NM_018995	ENSG00000073146	MOV10L1	CHAMP|DJ402G11.8	Mov10 like RISC complex RNA helicase 1	protein-coding	0.015075	0.500000	
chunk0093_420_1	chr19	57559892	57560099	+	0	NA	promoter-TSS (NM_001277092)	promoter-TSS (NM_001277092)	-132	NM_001277091	162972	Hs.180257	NM_153231	ENSG00000251369	ZNF550	-	zinc finger protein 550	protein-coding	0.028986	0.447115	
chunk0063_188_1	chr14	80696085	80696417	+	0	NA	intron (NM_152446, intron 18 of 23)	intron (NM_152446, intron 18 of 23)	243289	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.003012	0.360360	
chunk0153_2_1	chr5	66665156	66665450	+	0	NA	intron (NM_198828, intron 1 of 5)	L2a|LINE|L2	68955	NM_001290228	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.003401	0.393220	
chunk0073_360_1	chr16	14999924	15000208	+	0	NA	intron (NM_001285448, intron 4 of 21)	intron (NM_001285448, intron 4 of 21)	10331	NR_036054	100302243		NR_036054	ENSG00000238728	MIR1972-1	MIR1972|hsa-mir-1972|hsa-mir-1972-1	microRNA 1972-1	ncRNA	0.010563	0.424561	49(AGGATCACAGTGTGCC,-,0.00),50(GGATCACAGTGTGCCA,+,0.00)
chunk0113_306_1	chr20	57779266	57779792	+	0	NA	Intergenic	L2c|LINE|L2	-67993	NM_199171	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.003802	0.461101	
chunk0118_452_1	chr22	39618201	39618418	+	0	NA	intron (NM_021096, intron 3 of 36)	intron (NM_021096, intron 3 of 36)	47556	NM_001003406	8911	Hs.125116	NM_021096	ENSG00000100346	CACNA1I	Cav3.3|ca(v)3.3	calcium voltage-gated channel subunit alpha1 I	protein-coding	0.009217	0.522936	
chunk0147_53_1	chr4	172556647	172557014	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	132087	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.000000	0.342391	
chunk0004_462_1	chr1	53796199	53796609	+	0	NA	intron (NM_018087, intron 13 of 17)	L2a|LINE|L2	42148	NR_033142	55706	Hs.476525	NM_018087	ENSG00000058804	NDC1	NET3|TMEM48	NDC1 transmembrane nucleoporin	protein-coding	0.007317	0.316302	
chunk0117_183_1	chr22	21009735	21009973	+	0	NA	non-coding (NR_027051, exon 2 of 2)	non-coding (NR_027051, exon 2 of 2)	4433	NR_003608	113691	Hs.585006	NR_003608	ENSG00000161149	TUBA3FP	-	tubulin alpha 3f pseudogene	pseudo	0.008403	0.527197	
chunk0128_384_1	chr3	113667188	113667710	+	0	NA	intron (NM_001009899, intron 5 of 6)	intron (NM_001009899, intron 5 of 6)	29197	NM_001009899	205717	Hs.632570	NM_001009899	ENSG00000176542	USF3	KIAA2018	upstream transcription factor family member 3	protein-coding	0.005747	0.416826	
chunk0163_269_1	chr6	13315912	13316222	+	0	NA	intron (NM_001258457, intron 4 of 6)	MLT1J|LTR|ERVL-MaLR	12516	NM_016495	51256	Hs.484678	NM_016495	ENSG00000145979	TBC1D7	MGCPH|PIG51|TBC7	TBC1 domain family member 7	protein-coding	0.012903	0.495177	
chunk0074_398_1	chr16	35399042	35399548	+	0	NA	Intergenic	Intergenic	35764	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.003953	0.424063	
chunk0010_335_1	chr1	118388645	118388887	+	0	NA	Intergenic	Intergenic	-203541	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.008264	0.465021	184(GGGAGCTCTCTGTTCC,-,0.00)
chunk0209_438_1	chrX	63514335	63514679	+	0	NA	intron (NR_015353, intron 2 of 3)	intron (NR_015353, intron 2 of 3)	46486	NR_015353	92249	Hs.31532	NR_015353	ENSG00000235437	LINC01278	-	long intergenic non-protein coding RNA 1278	ncRNA	0.005814	0.411594	
chunk0095_439_1	chr2	25198685	25199028	+	0	NA	Intergenic	L1M5|LINE|L1	-5457	NR_132378	106144568	Hs.580474	NR_132378	ENSG00000230452	LINC01381	DADOT	long intergenic non-protein coding RNA 1381	ncRNA	0.011662	0.372093	
chunk0020_190_1	chr1	234875596	234876162	+	0	NA	Intergenic	Intergenic	88120	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.030035	0.603175	
chunk0202_362_1	chr9	80357340	80357567	+	0	NA	Intergenic	Intergenic	382430	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.004405	0.469298	
chunk0136_29_1	chr4	789060	789548	+	0	NA	intron (NM_006651, intron 3 of 3)	intron (NM_006651, intron 3 of 3)	-7456	NR_036511	100129917	Hs.731755	NR_036511	ENSG00000249592	LOC100129917	-	uncharacterized LOC100129917	ncRNA	0.028689	0.607362	
chunk0026_373_1	chr10	69375300	69375957	+	0	NA	intron (NM_033497, intron 10 of 20)	intron (NM_033497, intron 10 of 20)	41290	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.024353	0.603343	334(TGGAACAGATTGTTTT,-,0.00),335(GGAACAGATTGTTTTG,+,0.00)
chunk0067_131_1	chr15	42901551	42901989	+	0	NA	intron (NM_173500, intron 1 of 14)	L1M4|LINE|L1	19039	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.011416	0.373576	
chunk0193_134_1	chr8	74416304	74416506	+	0	NA	Intergenic	L1ME1|LINE|L1	66022	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.014851	0.522167	
chunk0086_122_1	chr18	14959551	14959750	+	0	NA	intron (NR_104164, intron 1 of 3)	intron (NR_104164, intron 1 of 3)	10818	NR_110783	101927642	Hs.711242	NR_110783	ENSG00000264301	LINC01444	-	long intergenic non-protein coding RNA 1444	ncRNA	0.020101	0.485000	
chunk0031_48_1	chr10	122620694	122620973	+	0	NA	intron (NM_017579, intron 39 of 51)	intron (NM_017579, intron 39 of 51)	60168	NM_007329	1755	Hs.279611	NM_004406	ENSG00000187908	DMBT1	GP340|SAG|SALSA|muclin	deleted in malignant brain tumors 1	protein-coding	0.010753	0.507143	
chunk0019_173_1	chr1	226386541	226386807	+	0	NA	intron (NM_001618, intron 5 of 22)	intron (NM_001618, intron 5 of 22)	21426	NM_001618	142	Hs.177766	NM_001618	ENSG00000143799	PARP1	ADPRT|ADPRT 1|ADPRT1|ARTD1|PARP|PARP-1|PPOL|pADPRT-1	poly(ADP-ribose) polymerase 1	protein-coding	0.011278	0.539326	
chunk0206_211_1	chr9	123149077	123149540	+	0	NA	intron (NR_033234, intron 11 of 18)	MER134|DNA?|DNA?	-33831	NR_026677	81571	Hs.708072	NM_030814	ENSG00000236901	MIR600HG	C9orf45|GL012|NCRNA00287	MIR600 host gene	ncRNA	0.002160	0.346983	
chunk0089_388_1	chr18	67754594	67755167	+	0	NA	intron (NR_033921, intron 1 of 4)	L1MA4|LINE|L1	-238150	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.001745	0.360627	158(CAGGACATACTGTGTT,-,0.00),159(AGGACATACTGTGTTC,+,0.00)
chunk0019_407_1	chr1	230663656	230663855	+	0	NA	intron (NM_001145036, intron 4 of 17)	intron (NM_001145036, intron 4 of 17)	21299	NM_007357	22796	Hs.211800	NM_007357	ENSG00000135775	COG2	CDG2Q|LDLC	component of oligomeric golgi complex 2	protein-coding	0.010050	0.260000	
chunk0002_117_1	chr1	16120922	16121335	+	0	NA	Intergenic	MIR|SINE|MIR	34959	NM_004431	1969	Hs.171596	NM_004431	ENSG00000142627	EPHA2	ARCC2|CTPA|CTPP1|CTRCT6|ECK	EPH receptor A2	protein-coding	0.007264	0.442029	
chunk0168_237_1	chr6	87723193	87723801	+	0	NA	Intergenic	Intergenic	-21230	NM_018064	55122	Hs.485915	NM_018064	ENSG00000135334	AKIRIN2	C6orf166|FBI1|dJ486L4.2	akirin 2	protein-coding	0.006579	0.471264	
chunk0068_77_1	chr15	51984580	51984994	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	-12986	NM_001286430	123169	Hs.567662	NM_138792	ENSG00000166477	LEO1	RDL	LEO1 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.012077	0.397590	
chunk0024_201_1	chr10	36408413	36408869	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	630339	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.008772	0.420131	
chunk0186_119_1	chr7	138090921	138091300	+	0	NA	intron (NM_001190906, intron 2 of 7)	intron (NM_001190906, intron 2 of 7)	14678	NM_001190907	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.007916	0.426316	
chunk0176_169_1	chr7	13602880	13603228	+	0	NA	Intergenic	Intergenic	383460	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.005747	0.306590	
chunk0208_10_1	chrX	10507180	10507548	+	0	NA	intron (NM_001193281, intron 2 of 2)	intron (NM_001193281, intron 2 of 2)	60239	NM_001193280	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.008152	0.395664	
chunk0080_452_1	chr17	37025302	37025662	+	0	NA	intron (NM_012138, intron 10 of 11)	intron (NM_012138, intron 10 of 11)	-8263	NR_036056	100422969		NR_036056	ENSG00000276326	MIR2909	-	microRNA 2909	ncRNA	0.022222	0.454294	
chunk0111_444_1	chr20	35319374	35319766	+	0	NA	intron (NM_018244, intron 7 of 9)	intron (NM_018244, intron 7 of 9)	-27148	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.010204	0.389313	
chunk0183_249_1	chr7	107150135	107150813	+	0	NA	intron (NM_002736, intron 6 of 10)	L1MA3|LINE|L1	-18487	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.007375	0.281296	
chunk0164_157_1	chr6	21556728	21557614	+	0	NA	Intergenic	Intergenic	-36570	NM_003107	6659	Hs.643910	NM_003107	ENSG00000124766	SOX4	EVI16	SRY-box transcription factor 4	protein-coding	0.010158	0.364149	348(GTGACAGGATGTGCCC,+,0.00)
chunk0149_393_1	chr5	28827095	28827924	+	0	NA	Intergenic	L1P4|LINE|L1	-99361	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.002413	0.322892	
chunk0100_147_1	chr2	108982271	108982743	+	0	NA	intron (NM_022336, intron 1 of 11)	intron (NM_022336, intron 1 of 11)	6865	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.008475	0.463002	
chunk0206_174_1	chr9	122305562	122306062	+	0	NA	intron (NM_199177, intron 4 of 4)	L2a|LINE|L2	34948	NM_199177	92399	Hs.368011	NM_138777	ENSG00000148187	MRRF	MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding	0.002000	0.393214	
chunk0089_254_1	chr18	62437280	62437479	+	0	NA	Intergenic	Intergenic	-86046	NM_017742	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.015075	0.395000	
chunk0172_239_1	chr6	137157596	137158024	+	0	NA	intron (NM_052962, intron 3 of 6)	intron (NM_052962, intron 3 of 6)	15838	NM_181310	116379	Hs.126891	NM_052962	ENSG00000164485	IL22RA2	CRF2-10|CRF2-S1|CRF2X|IL-22BP|IL-22R-alpha-2|IL-22RA2|ZCYTOR16	interleukin 22 receptor subunit alpha 2	protein-coding	0.011682	0.403263	
chunk0089_409_1	chr18	68484211	68484537	+	0	NA	Intergenic	Intergenic	230742	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.009202	0.385321	
chunk0134_265_1	chr3	179506698	179506980	+	0	NA	Intergenic	Intergenic	-55256	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.000000	0.360424	
chunk0210_241_1	chrX	82748090	82748317	+	0	NA	Intergenic	L1ME4b|LINE|L1	-760058	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.008811	0.298246	
chunk0113_247_1	chr20	54744279	54744694	+	0	NA	Intergenic	Intergenic	268768	NM_177959	55816	Hs.473133	NM_018431	ENSG00000101134	DOK5	C20orf180|IRS-6|IRS6	docking protein 5	protein-coding	0.004819	0.329327	
chunk0145_134_1	chr4	146441059	146441524	+	0	NA	TTS (NM_032128)	TTS (NM_032128)	32708	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.004301	0.345494	207(AAGAACAAGTTGTACT,-,0.00),208(AGAACAAGTTGTACTT,+,0.00)
chunk0159_297_1	chr5	142867068	142867309	+	0	NA	intron (NR_046680, intron 2 of 5)	intron (NR_046680, intron 2 of 5)	1722	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.012448	0.446281	
chunk0031_22_1	chr10	121886969	121887168	+	0	NA	intron (NM_001001976, intron 7 of 11)	intron (NM_001001976, intron 7 of 11)	40995	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.005025	0.320000	
chunk0129_317_1	chr3	124026948	124027197	+	0	NA	Intergenic	L1ME1|LINE|L1	-35720	NM_017578	54763	Hs.567516	NM_017578	ENSG00000065371	ROPN1	CT91|ODF6|RHPNAP1|ROPN1A|ropporin	rhophilin associated tail protein 1	protein-coding	0.004016	0.384000	
chunk0096_368_1	chr2	36536705	36537489	+	0	NA	intron (NM_016441, intron 13 of 16)	intron (NM_016441, intron 13 of 16)	61092	NM_005102	9637	Hs.258563	NM_005102	ENSG00000171055	FEZ2	HUM3CL	fasciculation and elongation protein zeta 2	protein-coding	0.015306	0.457325	
chunk0017_10_1	chr1	204398535	204398766	+	0	NA	Intergenic	Intergenic	13167	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.004329	0.517241	
chunk0090_164_1	chr18	72524668	72525046	+	0	NA	Intergenic	MER31-int|LTR|ERV1	19631	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.002646	0.248021	
chunk0181_192_1	chr7	83428162	83428629	+	0	NA	intron (NM_001178129, intron 4 of 16)	intron (NM_001178129, intron 4 of 16)	213036	NM_001178129	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.002141	0.299145	
chunk0116_117_1	chr21	35838561	35838760	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	117945	NR_030414	768219		NR_030414	ENSG00000211590	MIR802	MIRN802|hsa-mir-802	microRNA 802	ncRNA	0.005025	0.445000	
chunk0192_301_1	chr8	66713887	66714643	+	0	NA	intron (NM_001033578, intron 1 of 16)	intron (NM_001033578, intron 1 of 16)	1847	NM_001033578	23678	Hs.613417	NM_013257	ENSG00000104205	SGK3	CISK|SGK2|SGKL	serum/glucocorticoid regulated kinase family member 3	protein-coding	0.007937	0.396301	
chunk0015_292_1	chr1	188769881	188770514	+	0	NA	Intergenic	L1PA10|LINE|L1	1326569	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004739	0.380126	
chunk0133_411_1	chr3	174516094	174516524	+	0	NA	Intergenic	Intergenic	-343012	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.009302	0.366589	
chunk0167_208_1	chr6	65277599	65278182	+	0	NA	intron (NM_001142800, intron 12 of 42)	MLT2B4|LTR|ERVL	-23528	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.003431	0.388699	
chunk0008_149_1	chr1	92324763	92325127	+	0	NA	intron (NM_024813, intron 8 of 12)	MIRb|SINE|MIR	-25936	NM_053274	11146	Hs.49105	NM_007070	ENSG00000174842	GLMN	FAP|FAP48|FAP68|FKBPAP|GLML|GVM|VMGLOM	glomulin, FKBP associated protein	protein-coding	0.000000	0.315068	
chunk0113_365_1	chr20	59098770	59098979	+	0	NA	Intergenic	L1MC1|LINE|L1	-56028	NM_001256403	51012	Hs.656865	NM_016045	ENSG00000101166	PRELID3B	C20orf45|SLMO2|dJ543J19.5	PRELI domain containing 3B	protein-coding	0.004785	0.409524	
chunk0203_49_1	chr9	83130634	83130973	+	0	NA	Intergenic	L2c|LINE|L2	-67675	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.005900	0.429412	
chunk0060_239_1	chr14	49660004	49660455	+	0	NA	intron (NM_002692, intron 10 of 18)	Tigger3b|DNA|TcMar-Tigger	-24999	NM_001083908	55172	Hs.231761	NM_018139	ENSG00000165506	DNAAF2	C14orf104|CILD10|KTU|PF13	dynein axonemal assembly factor 2	protein-coding	0.004435	0.360619	
chunk0157_241_1	chr5	119590086	119590423	+	0	NA	Intergenic	Intergenic	-39305	NM_001163991	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.002967	0.343195	
chunk0167_329_1	chr6	72395168	72395500	+	0	NA	intron (NM_014989, intron 31 of 33)	L1MEi|LINE|L1	28604	NM_001168411	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.000000	0.312312	140(CTGAACAATCTGTACA,-,0.00)
chunk0124_138_1	chr3	54527487	54528079	+	0	NA	intron (NM_018398, intron 5 of 37)	L1MB8|LINE|L1	112074	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.008446	0.445194	
chunk0021_161_1	chr10	5045132	5045347	+	0	NA	Intergenic	HERVK13-int|LTR|ERVK	-3527	NM_001253908	8644	Hs.78183	NM_003739	ENSG00000196139	AKR1C3	DD3|DDX|HA1753|HAKRB|HAKRe|HSD17B5|PGFS|hluPGFS	aldo-keto reductase family 1 member C3	protein-coding	0.023256	0.490741	
chunk0134_347_1	chr3	182451271	182451727	+	0	NA	intron (NR_040105, intron 2 of 3)	intron (NR_040105, intron 2 of 3)	34863	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.010965	0.485777	
chunk0194_199_1	chr8	85552720	85553214	+	0	NA	Intergenic	Intergenic	-88052	NR_121630	100996348	Hs.606624	NR_121630	ENSG00000253549	CA3-AS1	-	CA3 antisense RNA 1	ncRNA	0.002024	0.359596	
chunk0128_258_1	chr3	109254669	109255099	+	0	NA	Intergenic	Intergenic	61633	NM_138815	151871	Hs.351113	NM_138815	ENSG00000163530	DPPA2	CT100|ECAT15-2|PESCRG1	developmental pluripotency associated 2	protein-coding	0.009302	0.406032	234(GAGAACATCCTGTATC,-,0.00),235(AGAACATCCTGTATCT,+,0.00)
chunk0058_147_1	chr14	23090304	23090566	+	0	NA	intron (NM_001164814, intron 3 of 18)	intron (NM_001164814, intron 3 of 18)	-5039	NM_017924	55017	Hs.525238	NM_017924	ENSG00000179933	C14orf119	-	chromosome 14 open reading frame 119	protein-coding	0.015267	0.433460	
chunk0098_357_1	chr2	77464665	77465143	+	0	NA	intron (NM_001282924, intron 3 of 3)	MER5A|DNA|hAT-Charlie	57464	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.002092	0.325678	
chunk0180_295_1	chr7	70178785	70178984	+	0	NA	intron (NM_015570, intron 4 of 18)	intron (NM_015570, intron 4 of 18)	579965	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.000000	0.410000	
chunk0093_280_1	chr19	51808676	51808942	+	0	NA	intron (NM_002030, intron 1 of 1)	HERVK3-int|LTR|ERVK	13651	NM_002030	2359	Hs.445466	NM_002030	ENSG00000187474	FPR3	FML2_HUMAN|FMLP-R-II|FMLPY|FPRH1|FPRH2|FPRL2|RMLP-R-I	formyl peptide receptor 3	protein-coding	0.018797	0.438202	
chunk0046_324_1	chr12	62602453	62603043	+	0	NA	promoter-TSS (NR_029661)	promoter-TSS (NR_029661)	686	NR_121682	283416	Hs.375881	NM_175895	ENSG00000221949	LINC01465	C12orf61	long intergenic non-protein coding RNA 1465	ncRNA	0.096610	0.636210	
chunk0013_203_1	chr1	169358164	169358672	+	0	NA	intron (NR_104229, intron 1 of 12)	intron (NR_104229, intron 1 of 12)	-9538	NM_003666	8548	Hs.130746	NM_003666	ENSG00000117475	BLZF1	GOLGIN-45|JEM-1|JEM-1s|JEM1	basic leucine zipper nuclear factor 1	protein-coding	0.000000	0.277014	
chunk0011_211_1	chr1	150089023	150089225	+	0	NA	intron (NM_007259, intron 10 of 14)	intron (NM_007259, intron 10 of 14)	21456	NM_001279355	11311	Hs.443750	NM_007259	ENSG00000136631	VPS45	H1|H1VPS45|SCN5|VPS45A|VPS45B|VPS54A|VSP45|VSP45A	vacuolar protein sorting 45 homolog	protein-coding	0.004950	0.359606	
chunk0081_253_1	chr17	43326394	43326816	+	0	NA	Intergenic	HERVK13-int|LTR|ERVK	-26374	NR_002716	6066		NR_002716	ENSG00000274585	RNU2-1	RNU2|U2	RNA, U2 small nuclear 1	snRNA	0.004739	0.382979	
chunk0045_420_1	chr12	53174752	53175412	+	0	NA	intron (NM_015989, intron 2 of 16)	intron (NM_015989, intron 2 of 16)	5564	NM_015989	51380	Hs.279815	NM_015989	ENSG00000139631	CSAD	CSD|PCAP	cysteine sulfinic acid decarboxylase	protein-coding	0.007576	0.493192	
chunk0148_146_1	chr5	6406072	6406480	+	0	NA	Intergenic	Intergenic	-27750	NM_032286	84246	Hs.13885	NM_032286	ENSG00000133398	MED10	L6|NUT2|TRG20	mediator complex subunit 10	protein-coding	0.000000	0.364303	
chunk0191_74_1	chr8	47353243	47354129	+	0	NA	intron (NR_104581, intron 5 of 16)	intron (NR_104581, intron 5 of 16)	92808	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.012415	0.386697	517(AAGAACACAGTGTTCT,-,0.00),518(AGAACACAGTGTTCTG,+,0.00)
chunk0046_458_1	chr12	64946167	64946645	+	0	NA	intron (NR_033988, intron 2 of 2)	intron (NR_033988, intron 2 of 2)	62632	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.006276	0.513570	
chunk0162_158_1	chr6	3457604	3458111	+	0	NA	Intergenic	Intergenic	-1298	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.047337	0.523622	
chunk0126_345_1	chr3	82672822	82673181	+	0	NA	Intergenic	Intergenic	-911202	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.005571	0.297222	
chunk0160_397_1	chr5	163483154	163483641	+	0	NA	intron (NM_012484, intron 15 of 17)	intron (NM_012484, intron 15 of 17)	10661	NR_109892	101927813	Hs.726818	NR_109892		HMMR-AS1	-	HMMR antisense RNA 1	ncRNA	0.006160	0.307377	
chunk0153_195_1	chr5	71713172	71713572	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-5791	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.005000	0.401496	
chunk0103_436_1	chr2	169964731	169965304	+	0	NA	intron (NM_172070, intron 24 of 38)	intron (NM_172070, intron 24 of 38)	137509	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.005236	0.404181	
chunk0004_118_1	chr1	44631537	44631832	+	0	NA	intron (NM_018150, intron 5 of 14)	CpG	42924	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.074576	0.658784	
chunk0126_267_1	chr3	79884203	79884804	+	0	NA	Intergenic	Intergenic	-116594	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004992	0.365449	
chunk0034_303_1	chr11	34957268	34957966	+	0	NA	intron (NM_001135024, intron 4 of 10)	intron (NM_001135024, intron 4 of 10)	15780	NR_039836	100616437		NR_039836	ENSG00000251862	MIR1343	-	microRNA 1343	ncRNA	0.011461	0.366237	
chunk0166_400_1	chr6	51976091	51976722	+	0	NA	intron (NM_138694, intron 35 of 66)	L1MB3|LINE|L1	111219	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.014263	0.370253	
chunk0158_103_1	chr5	126777500	126778078	+	0	NA	exon (NM_005573, exon 1 of 11)	exon (NM_005573, exon 1 of 11)	636	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.126298	0.699482	
chunk0139_404_1	chr4	63302716	63303198	+	0	NA	Intergenic	MER6|DNA|TcMar-Tigger	1106503	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.002075	0.370600	
chunk0012_25_1	chr1	154971166	154971633	+	0	NA	promoter-TSS (NM_001130040)	promoter-TSS (NM_001130040)	-652	NM_001130040	6464	Hs.433795	NM_003029	ENSG00000160691	SHC1	SHC|SHCA	SHC adaptor protein 1	protein-coding	0.014989	0.544872	
chunk0165_304_1	chr6	36893976	36894477	+	0	NA	intron (NM_152734, intron 1 of 7)	intron (NM_152734, intron 1 of 7)	8362	NM_152734	221477	Hs.433381	NM_152734	ENSG00000198663	C6orf89	BRAP|PS1TP5TP1	chromosome 6 open reading frame 89	protein-coding	0.005988	0.388446	187(CGGCACACCGTGTTCT,-,0.00),188(GGCACACCGTGTTCTC,+,0.00)
chunk0139_259_1	chr4	56526429	56526787	+	0	NA	Intergenic	Intergenic	-4001	NM_001256475	100506564	Hs.573073	NM_001256475	ENSG00000249693	THEGL	-	theg spermatid protein like	protein-coding	0.013966	0.462396	249(GGGAGCACCATGTGCC,-,0.00)
chunk0099_218_1	chr2	95665738	95666245	+	0	NA	Intergenic	Intergenic	73973	NM_138800	129868	Hs.232026	NM_138800	ENSG00000144015	TRIM43	TRIM43A	tripartite motif containing 43	protein-coding	0.005917	0.437008	
chunk0185_111_1	chr7	125750215	125750578	+	0	NA	Intergenic	Intergenic	-486105	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.005510	0.266484	
chunk0207_1_1	chrM	1	1042	+	0	NA	NA	Intergenic	NA	NA									0.028818	0.452015	
chunk0018_295_1	chr1	220786321	220786922	+	0	NA	promoter-TSS (NM_022746)	promoter-TSS (NM_022746)	-76	NM_022746	64757	Hs.497816	NM_022746	ENSG00000186205	MARC1	MOSC1	mitochondrial amidoxime reducing component 1	protein-coding	0.059900	0.629568	
chunk0075_450_1	chr16	58129365	58129564	+	0	NA	promoter-TSS (NM_013242)	promoter-TSS (NM_013242)	-72	NM_013242	29105	Hs.532755	NM_013242	ENSG00000070761	CFAP20	BUG22|C16orf80|EVORF|GTL3|fSAP23	cilia and flagella associated protein 20	protein-coding	0.080402	0.600000	
chunk0092_53_1	chr19	19788805	19789250	+	0	NA	Intergenic	Intergenic	-12614	NR_026956	284440	Hs.665307	NR_026956		LINC00663	-	long intergenic non-protein coding RNA 663	ncRNA	0.006742	0.470852	
chunk0115_153_1	chr21	23793914	23794458	+	0	NA	Intergenic	L1MC5|LINE|L1	-409351	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.005515	0.332110	
chunk0070_158_1	chr15	71279251	71279536	+	0	NA	intron (NM_024817, intron 5 of 16)	intron (NM_024817, intron 5 of 16)	-90334	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.021053	0.458042	
chunk0113_42_1	chr20	49909871	49910240	+	0	NA	intron (NM_006038, intron 1 of 2)	intron (NM_006038, intron 1 of 2)	3684	NM_001135773	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.037940	0.556757	
chunk0175_161_1	chr7	4152087	4152670	+	0	NA	intron (NM_001079653, intron 4 of 19)	intron (NM_001079653, intron 4 of 19)	22693	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.017153	0.510274	
chunk0155_408_1	chr5	99168201	99168571	+	0	NA	Intergenic	Intergenic	239252	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.008108	0.355795	
chunk0209_432_1	chrX	63123602	63124015	+	0	NA	Intergenic	L1M2|LINE|L1	227531	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.002421	0.345411	
chunk0074_392_1	chr16	35375142	35375402	+	0	NA	intron (NR_027079, intron 1 of 8)	L1M4|LINE|L1	11741	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.003846	0.421456	
chunk0118_324_1	chr22	35315886	35316200	+	0	NA	intron (NM_005488, intron 1 of 14)	intron (NM_005488, intron 1 of 14)	16239	NM_001135732	10043	Hs.474705	NM_005488	ENSG00000100284	TOM1	-	target of myb1 membrane trafficking protein	protein-coding	0.035032	0.590476	
chunk0127_123_1	chr3	93893468	93893706	+	0	NA	intron (NM_000313, intron 9 of 14)	intron (NM_000313, intron 9 of 14)	80494	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.008403	0.330544	
chunk0006_74_1	chr1	64932562	64932783	+	0	NA	intron (NM_002227, intron 1 of 24)	L1MD3|LINE|L1	33832	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.004525	0.364865	
chunk0125_93_1	chr3	65323443	65323798	+	0	NA	Intergenic	MIRc|SINE|MIR	-570196	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.002817	0.426966	
chunk0202_368_1	chr9	80517979	80518506	+	0	NA	Intergenic	L1PA11|LINE|L1	543219	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.007590	0.371212	
chunk0101_431_1	chr2	139327784	139328323	+	0	NA	Intergenic	Intergenic	430729	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.001855	0.312963	
chunk0111_250_1	chr20	30377028	30377439	+	0	NA	promoter-TSS (NR_003579)	promoter-TSS (NR_003579)	30	NR_003579	284802	Hs.653099	NM_207350		FRG1BP	C20orf80|FRG1B|bA348I14.2	FSHD region gene 1 family member B, pseudogene	pseudo	0.060827	0.633495	
chunk0055_56_1	chr13	52639136	52639879	+	0	NA	intron (NM_001011724, intron 6 of 6)	intron (NM_001011724, intron 6 of 6)	-13189	NM_001130912	10910	Hs.281902	NM_006704	ENSG00000165416	SUGT1	SGT1	SGT1 homolog, MIS12 kinetochore complex assembly cochaperone	protein-coding	0.008075	0.369624	
chunk0183_200_1	chr7	106375962	106376540	+	0	NA	Intergenic	MER90|LTR|ERV1	-91059	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.005190	0.426598	260(AAGGACACTCTGTGAC,-,0.00),261(AGGACACTCTGTGACT,+,0.00)
chunk0013_216_1	chr1	169492966	169493689	+	0	NA	Intergenic	L2a|LINE|L2	-7357	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.004149	0.390884	178(TAGAACAGTCTCTTCT,-,0.00),179(AGAACAGTCTCTTCTT,+,0.00)
chunk0029_346_1	chr10	106558468	106558767	+	0	NA	Intergenic	Intergenic	606091	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.010033	0.366667	
chunk0104_50_1	chr2	171346284	171346878	+	0	NA	intron (NM_024770, intron 3 of 9)	intron (NM_024770, intron 3 of 9)	-87670	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.005051	0.431933	270(GAGAACAACCAGTACT,-,0.00),271(AGAACAACCAGTACTT,+,0.00)
chunk0092_174_1	chr19	29951816	29952053	+	0	NA	intron (NR_045557, intron 1 of 9)	L1MC4|LINE|L1	9695	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.012658	0.436975	73(TGGCACAGGATGTTCC,-,0.00),74(GGCACAGGATGTTCCA,+,0.00)
chunk0124_311_1	chr3	58005695	58006164	+	0	NA	Intergenic	Intergenic	-2471	NM_001164317	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.006397	0.489362	414(CAGGGCACCCTGTGCC,-,0.00),415(AGGGCACCCTGTGCCT,+,0.00)
chunk0064_43_1	chr14	89672836	89673384	+	0	NA	Intergenic	Intergenic	-53960	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.025547	0.480874	
chunk0185_461_1	chr7	135457677	135458379	+	0	NA	intron (NM_001008225, intron 1 of 10)	L1M5|LINE|L1	52099	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.001425	0.332859	
chunk0085_150_1	chr18	3450257	3450635	+	0	NA	promoter-TSS (NM_170695)	promoter-TSS (NM_170695)	274	NM_003244	7050	Hs.373550	NM_003244	ENSG00000177426	TGIF1	HPE4|TGIF	TGFB induced factor homeobox 1	protein-coding	0.092593	0.656992	
chunk0187_234_1	chr7	152551400	152552078	+	0	NA	Intergenic	Intergenic	87615	NR_027387	100128822	Hs.647112	NR_027387	ENSG00000261455	LINC01003	-	long intergenic non-protein coding RNA 1003	ncRNA	0.011799	0.450663	
chunk0029_275_1	chr10	103487336	103487691	+	0	NA	intron (NR_120675, intron 3 of 3)	ORSL-2b|DNA|hAT-Tip100	-6465	NM_004210	9148	Hs.594708	NM_004210	ENSG00000107954	NEURL1	NEUR1|NEURL|RNF67|bA416N2.1|neu|neu-1	neuralized E3 ubiquitin protein ligase 1	protein-coding	0.002817	0.331461	
chunk0152_128_1	chr5	58851318	58851790	+	0	NA	TTS (NM_138453)	TTS (NM_138453)	148378	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.014831	0.422833	
chunk0080_324_1	chr17	32341884	32342405	+	0	NA	promoter-TSS (NM_022344)	promoter-TSS (NM_022344)	65	NM_022344	64149	Hs.655257	NM_022344	ENSG00000108666	C17orf75	NJMU-R1|SRI2	chromosome 17 open reading frame 75	protein-coding	0.078695	0.639847	
chunk0086_128_1	chr18	21020326	21020912	+	0	NA	intron (NM_005406, intron 11 of 32)	L2c|LINE|L2	91232	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.003413	0.316865	
chunk0089_382_1	chr18	67510553	67511096	+	0	NA	3' UTR (NM_032160, exon 2 of 2)	3' UTR (NM_032160, exon 2 of 2)	-5722	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.007366	0.387868	
chunk0197_149_1	chr8	120413136	120413531	+	0	NA	intron (NM_014078, intron 6 of 6)	L2c|LINE|L2	-32065	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.005063	0.356061	
chunk0022_45_1	chr10	8128413	8129033	+	0	NA	Intergenic	Intergenic	74019	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.006452	0.396135	57(GGGTCAGGTTGTCCTG,+,0.00),466(AAGTACACAGTGGGCT,-,0.00)
chunk0037_239_1	chr11	75342918	75343421	+	0	NA	intron (NM_004041, intron 1 of 15)	L2b|LINE|L2	-7983	NR_029891	442900		NR_029891	ENSG00000199090	MIR326	MIRN326|hsa-mir-326|mir-326	microRNA 326	ncRNA	0.009940	0.486111	
chunk0202_431_1	chr9	81847045	81847750	+	0	NA	Intergenic	Intergenic	-66040	NR_026851	347127	Hs.215235	NM_198509	ENSG00000240632	SPATA31D5P	FAM75D5|FAM75D5P	SPATA31 subfamily D member 5, pseudogene	pseudo	0.012766	0.405099	
chunk0157_359_1	chr5	123359930	123360314	+	0	NA	intron (NM_001166226, intron 18 of 19)	intron (NM_001166226, intron 18 of 19)	63470	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.007812	0.337662	
chunk0004_331_1	chr1	50369520	50369742	+	0	NA	Intergenic	MIRb|SINE|MIR	53816	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.009009	0.475336	
chunk0147_211_1	chr4	180478687	180479274	+	0	NA	Intergenic	Intergenic	680169	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.001704	0.272109	
chunk0132_342_1	chr3	161285090	161285358	+	0	NA	Intergenic	Intergenic	63913	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.007463	0.483271	
chunk0076_282_1	chr16	69619577	69619984	+	0	NA	intron (NM_138713, intron 2 of 14)	intron (NM_138713, intron 2 of 14)	53814	NM_006599	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.000000	0.387255	219(TGGACATAGAGTGCCC,+,0.00)
chunk0101_368_1	chr2	138121188	138121478	+	0	NA	Intergenic	Intergenic	157095	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.003448	0.309278	
chunk0090_414_1	chr18	78984994	78985319	+	0	NA	intron (NM_171999, intron 1 of 2)	intron (NM_171999, intron 1 of 2)	4881	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.024615	0.500000	
chunk0107_357_1	chr2	222656250	222656461	+	0	NA	promoter-TSS (NM_005687)	promoter-TSS (NM_005687)	0	NR_130154	10056	Hs.471452	NM_005687	ENSG00000116120	FARSB	FARSLB|FRSB|HSPC173|NEDBLLA|PheHB|PheRS|RILDBC	phenylalanyl-tRNA synthetase subunit beta	protein-coding	0.047393	0.551887	
chunk0208_394_1	chrX	29008804	29009383	+	0	NA	intron (NM_014271, intron 2 of 10)	L1PA16|LINE|L1	421529	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.005181	0.410345	104(GAGAACATGCTGTTTT,-,0.00),105(AGAACATGCTGTTTTT,+,0.00)
chunk0065_171_1	chr15	25862836	25863039	+	0	NA	exon (NM_024490, exon 1 of 21)	exon (NM_024490, exon 1 of 21)	265	NM_024490	57194	Hs.638517	NM_024490	ENSG00000206190	ATP10A	ATP10C|ATPVA|ATPVC	ATPase phospholipid transporting 10A (putative)	protein-coding	0.123153	0.725490	
chunk0048_117_1	chr12	79689653	79689852	+	0	NA	exon (NM_002583, exon 2 of 7)	exon (NM_002583, exon 2 of 7)	1258	NM_002583	5074	Hs.643130	NM_002583	ENSG00000177425	PAWR	PAR4|Par-4	pro-apoptotic WT1 regulator	protein-coding	0.090452	0.715000	
chunk0162_396_1	chr5	179696580	179697162	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-2058	NM_001746	821	Hs.567968	NM_001746	ENSG00000127022	CANX	CNX|IP90|P90	calnexin	protein-coding	0.008591	0.396226	
chunk0130_329_1	chr3	138240306	138240539	+	0	NA	intron (NM_001267042, intron 10 of 20)	intron (NM_001267042, intron 10 of 20)	53174	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.004292	0.329060	
chunk0079_109_1	chr17	12282035	12282552	+	0	NA	Intergenic	Intergenic	200394	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.001934	0.374517	
chunk0161_33_1	chr5	165808104	165808850	+	0	NA	Intergenic	Intergenic	1117893	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005362	0.299866	
chunk0012_83_1	chr1	156061097	156061296	+	0	NA	promoter-TSS (NM_020387)	promoter-TSS (NM_020387)	21	NM_020387	57111	Hs.632469	NM_020387	ENSG00000132698	RAB25	CATX-8|RAB11C	RAB25, member RAS oncogene family	protein-coding	0.015075	0.620000	
chunk0063_182_1	chr14	80601465	80601731	+	0	NA	intron (NM_152446, intron 18 of 23)	Tigger3c|DNA|TcMar-Tigger	337942	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.003759	0.340824	
chunk0105_34_1	chr2	182714850	182715355	+	0	NA	promoter-TSS (NM_001271581)	promoter-TSS (NM_001271581)	-939	NR_073366	54431	Hs.516632	NM_018981	ENSG00000077232	DNAJC10	ERdj5|JPDI|MTHr|PDIA19	DnaJ heat shock protein family (Hsp40) member C10	protein-coding	0.001980	0.377470	
chunk0023_166_1	chr10	24358740	24358984	+	0	NA	intron (NM_019590, intron 2 of 20)	MARNA|DNA|TcMar-Mariner	83177	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.000000	0.359184	
chunk0210_359_1	chrX	96430847	96431064	+	0	NA	Intergenic	Intergenic	-93053	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.000000	0.444954	94(AAGAACTCATTGTGCT,-,0.00),95(AGAACTCATTGTGCTA,+,0.00)
chunk0206_53_1	chr9	117929854	117930467	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	225985	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.001631	0.408795	
chunk0070_396_1	chr15	77069714	77069964	+	0	NA	intron (NM_198902, intron 1 of 5)	intron (NM_198902, intron 1 of 5)	1389	NM_001168412	10099	Hs.744863	NM_005724	ENSG00000140391	TSPAN3	TM4-A|TM4SF8|TSPAN-3	tetraspanin 3	protein-coding	0.016000	0.517928	
chunk0131_416_1	chr3	153060109	153060317	+	0	NA	Intergenic	Intergenic	-101999	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.000000	0.377990	
chunk0145_57_1	chr4	145228337	145228702	+	0	NA	Intergenic	L1PA6|LINE|L1	-48839	NM_001102653	54726	Hs.270851	NM_017493	ENSG00000164164	OTUD4	DUBA6|HIN1|HSHIN1	OTU deubiquitinase 4	protein-coding	0.010959	0.527322	
chunk0144_385_1	chr4	140096491	140097024	+	0	NA	intron (NM_018717, intron 1 of 5)	Tigger15a|DNA|TcMar-Tigger	57322	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.011257	0.400749	188(AAGAACACAAAGTACA,-,0.00),189(AGAACACAAAGTACAT,+,0.00),230(AGGGACAATGAGTTCC,-,0.00),231(GGGACAATGAGTTCCA,+,0.00)
chunk0009_176_1	chr1	105572862	105573075	+	0	NA	Intergenic	Intergenic	45967	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004695	0.364486	111(CTAAACAGCCTGTTCT,-,0.00),112(TAAACAGCCTGTTCTT,+,0.00)
chunk0100_95_1	chr2	107808607	107809032	+	0	NA	intron (NR_126370, intron 2 of 4)	intron (NR_126370, intron 2 of 4)	17950	NR_024439	729121	Hs.386155	NR_024439	ENSG00000230651	RGPD4-AS1	-	RGPD4 antisense RNA 1 (head to head)	ncRNA	0.016471	0.406103	
chunk0009_167_1	chr1	105394944	105395344	+	0	NA	Intergenic	L1MA2|LINE|L1	223791	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002500	0.306733	
chunk0164_94_1	chr6	20230733	20231277	+	0	NA	Intergenic	MIRb|SINE|MIR	-18541	NR_073465	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.005515	0.365138	228(AAGAACTGCATGTACA,-,0.00),229(AGAACTGCATGTACAG,+,0.00)
chunk0055_374_1	chr13	73167053	73167252	+	0	NA	Intergenic	Intergenic	108360	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.000000	0.330000	
chunk0175_331_1	chr6	167210669	167211499	+	0	NA	Intergenic	Intergenic	40491	NM_001145121	401285		NM_001013683	ENSG00000166984	TCP10L2	-	t-complex 10 like 2	protein-coding	0.016867	0.529483	
chunk0037_170_1	chr11	73910107	73910578	+	0	NA	intron (NM_001267803, intron 8 of 12)	intron (NM_001267803, intron 8 of 12)	33373	NM_025155	80227	Hs.525017	NM_025155	ENSG00000175575	PAAF1	PAAF|Rpn14|WDR71	proteasomal ATPase associated factor 1	protein-coding	0.008493	0.436441	154(AGGGACGGAGTGTTCC,-,0.00),155(GGGACGGAGTGTTCCC,+,0.00)
chunk0064_31_1	chr14	89474558	89474863	+	0	NA	intron (NM_001085471, intron 1 of 6)	Mam_R4|LINE|Dong-R4	57356	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.013115	0.359477	
chunk0028_260_1	chr10	90749681	90749941	+	0	NA	intron (NM_019859, intron 1 of 3)	MIRb|SINE|MIR	108103	NM_019859	3363	Hs.73739	NM_000872	ENSG00000148680	HTR7	5-HT7	5-hydroxytryptamine receptor 7	protein-coding	0.015385	0.452107	
chunk0068_407_1	chr15	59004927	59005529	+	0	NA	intron (NM_001270530, intron 1 of 13)	AluJo|SINE|Alu	17082	NM_001270530	54778	Hs.404423	NM_017610	ENSG00000157450	RNF111	ARK|hRNF111	ring finger protein 111	protein-coding	0.004983	0.383085	328(GGGCACAAGCAGTCCT,-,0.00),329(GGCACAAGCAGTCCTC,+,0.00)
chunk0019_77_1	chr1	224317300	224317828	+	0	NA	intron (NM_206840, intron 3 of 21)	L2c|LINE|L2	12625	NM_001243147	4931	Hs.497867	NM_002533	ENSG00000143748	NVL	NVL2	nuclear VCP like	protein-coding	0.005682	0.353497	
chunk0119_237_1	chr22	45572399	45572847	+	0	NA	intron (NM_006486, intron 14 of 16)	L1MC5|LINE|L1	33024	NR_131244	100506737	Hs.517692	NR_131244	ENSG00000238120	LINC01589	TCONS_00029353	long intergenic non-protein coding RNA 1589	ncRNA	0.006696	0.452116	
chunk0027_457_1	chr10	81749568	81749974	+	0	NA	Intergenic	Intergenic	-125543	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.000000	0.383292	
chunk0157_7_1	chr5	115176240	115177238	+	0	NA	TTS (NM_001017398)	TTS (NM_001017398)	3807	NM_001017398	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.005010	0.326326	
chunk0121_50_1	chr3	15601342	15601661	+	0	NA	promoter-TSS (NM_000060)	promoter-TSS (NM_000060)	149	NM_001281723	686	Hs.444197	NM_001281723	ENSG00000169814	BTD	-	biotinidase	protein-coding	0.065831	0.553125	
chunk0059_169_1	chr14	32397851	32398424	+	0	NA	intron (NM_004274, intron 1 of 13)	intron (NM_004274, intron 1 of 13)	68864	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.000000	0.423345	
chunk0133_118_1	chr3	168194063	168194354	+	0	NA	Intergenic	Intergenic	-55314	NR_021485	93556	Hs.478158	NR_021485		EGFEM1P	C3orf50|NCRNA00259	EGF like and EMI domain containing 1, pseudogene	pseudo	0.003436	0.315068	
chunk0093_159_1	chr19	47532220	47532610	+	0	NA	intron (NM_001277075, intron 8 of 14)	intron (NM_001277075, intron 8 of 14)	-17157	NR_038457	8775	Hs.126938	NM_003827	ENSG00000105402	NAPA	SNAPA	NSF attachment protein alpha	protein-coding	0.020513	0.529412	187(AGGTACGTGCTGTTCC,-,0.00),188(GGTACGTGCTGTTCCC,+,0.00)
chunk0091_175_1	chr19	8002475	8002718	+	0	NA	intron (NM_001419, intron 1 of 5)	intron (NM_001419, intron 1 of 5)	3049	NM_001419	1994	Hs.184492	NM_001419	ENSG00000066044	ELAVL1	ELAV1|HUR|Hua|MelG	ELAV like RNA binding protein 1	protein-coding	0.065844	0.610656	
chunk0103_303_1	chr2	166779452	166779651	+	0	NA	Intergenic	Intergenic	-108936	NM_001199143	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.010050	0.370000	
chunk0083_3_1	chr17	62511548	62512125	+	0	NA	intron (NM_001284363, intron 1 of 19)	L1MD2|LINE|L1	30723	NM_001284363	11011	Hs.445078	NM_006852	ENSG00000146872	TLK2	HsHPK|MRD57|PKU-ALPHA	tousled like kinase 2	protein-coding	0.005199	0.368512	
chunk0055_232_1	chr13	62729191	62730003	+	0	NA	intron (NR_047029, intron 5 of 7)	L1PA6|LINE|L1	67095	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.011084	0.507995	
chunk0147_268_1	chr4	183760153	183760705	+	0	NA	Intergenic	Intergenic	-37593	NR_132761	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.003623	0.341772	
chunk0025_44_1	chr10	49252806	49253230	+	0	NA	Intergenic	L1MD2|LINE|L1	45875	NR_108038	100506769	Hs.562293	NR_108038		C10orf71-AS1	-	C10orf71 antisense RNA 1	ncRNA	0.007075	0.385882	83(ATGGACAGTTTGTTCC,-,0.00),84(TGGACAGTTTGTTCCT,+,0.00)
chunk0049_449_1	chr12	98943201	98943440	+	0	NA	intron (NM_001204067, intron 4 of 11)	intron (NM_001204067, intron 4 of 11)	-48424	NM_001204081	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.000000	0.329167	
chunk0074_34_1	chr16	20625088	20625438	+	0	NA	intron (NM_052956, intron 11 of 12)	intron (NM_052956, intron 11 of 12)	-48890	NM_001105069	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.014286	0.475783	182(GAGTCCACACTGTCCC,-,0.00),183(AGTCCACACTGTCCCC,+,0.00)
chunk0169_452_1	chr6	108900465	108900664	+	0	NA	intron (NM_001286609, intron 6 of 16)	intron (NM_001286609, intron 6 of 16)	23539	NR_104137	101929716		NR_104137		ARMC2-AS1	-	ARMC2 antisense RNA 1	ncRNA	0.000000	0.510000	
chunk0196_350_1	chr8	114543154	114543386	+	0	NA	Intergenic	Intergenic	-1106257	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.000000	0.291845	
chunk0209_312_1	chrX	49901243	49901504	+	0	NA	Intergenic	MER67C|LTR|ERV1	-21242	NM_001272102	1184	Hs.166486	NM_000084	ENSG00000171365	CLCN5	CLC5|CLCK2|ClC-5|DENTS|NPHL1|NPHL2|XLRH|XRN|hCIC-K2	chloride voltage-gated channel 5	protein-coding	0.000000	0.400763	
chunk0044_66_1	chr12	27888766	27889085	+	0	NA	Intergenic	Intergenic	81036	NM_198964	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.003135	0.334375	
chunk0094_267_1	chr2	7932151	7932663	+	0	NA	intron (NR_015405, intron 2 of 2)	L1MB3|LINE|L1	-32752	NR_110256	101929551	Hs.116006	NR_110256	ENSG00000226506	LOC101929551	-	uncharacterized LOC101929551	ncRNA	0.003906	0.370370	
chunk0094_276_1	chr2	8205002	8205339	+	0	NA	intron (NR_034135, intron 7 of 8)	L1MA4|LINE|L1	123249	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.005935	0.334320	
chunk0071_17_1	chr15	78933930	78934324	+	0	NA	intron (NM_004390, intron 5 of 11)	intron (NM_004390, intron 5 of 11)	10951	NM_004390	1512	Hs.148641	NM_004390	ENSG00000103811	CTSH	ACC-4|ACC-5|ACC4|ACC5|CPSB	cathepsin H	protein-coding	0.012690	0.501266	
chunk0141_257_1	chr4	85748464	85748663	+	0	NA	intron (NM_001025616, intron 3 of 9)	intron (NM_001025616, intron 3 of 9)	26095	NR_039656	100616349		NR_039656	ENSG00000266421	MIR4451	mir-4451	microRNA 4451	ncRNA	0.005025	0.275000	
chunk0191_65_1	chr8	47129309	47129970	+	0	NA	Intergenic	Zaphod2|DNA|hAT-Tip100	-59668	NR_037168	100287846	Hs.21550	NR_037168		LOC100287846	-	uncharacterized LOC100287846	ncRNA	0.009077	0.391239	
chunk0166_184_1	chr6	46136937	46137627	+	0	NA	intron (NM_014936, intron 1 of 3)	intron (NM_014936, intron 1 of 3)	7318	NM_014936	22875	Hs.643497	NM_014936	ENSG00000001561	ENPP4	NPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding	0.007246	0.400868	
chunk0014_102_1	chr1	176740350	176740705	+	0	NA	intron (NM_020318, intron 14 of 22)	intron (NM_020318, intron 14 of 22)	277356	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.311798	171(AAAAACTCAATGTTCC,-,0.00),172(AAAACTCAATGTTCCT,+,0.00)
chunk0090_272_1	chr18	74620267	74620897	+	0	NA	Intergenic	Intergenic	-10381	NM_001146189	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.014286	0.464342	
chunk0180_110_1	chr7	55365823	55366335	+	0	NA	exon (NM_018697, exon 1 of 9)	exon (NM_018697, exon 1 of 9)	631	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.134766	0.730994	
chunk0047_189_1	chr12	70795523	70796072	+	0	NA	intron (NM_002849, intron 2 of 13)	intron (NM_002849, intron 2 of 13)	-6867	NM_001207015	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.007286	0.336364	
chunk0185_418_1	chr7	134450185	134450540	+	0	NA	intron (NM_001628, intron 3 of 9)	intron (NM_001628, intron 3 of 9)	8774	NM_001628	231	Hs.521212	NM_001628	ENSG00000085662	AKR1B1	ADR|ALDR1|ALR2|AR	aldo-keto reductase family 1 member B	protein-coding	0.014085	0.505618	
chunk0057_278_1	chr13	105972331	105972583	+	0	NA	Intergenic	Intergenic	265627	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.015873	0.446640	
chunk0003_265_1	chr1	36272958	36273234	+	0	NA	intron (NM_005119, intron 2 of 11)	intron (NM_005119, intron 2 of 11)	-33297	NM_001162530	79729	Hs.524496	NM_024676	ENSG00000214193	SH3D21	C1orf113	SH3 domain containing 21	protein-coding	0.010870	0.361011	82(AAGTACAAAGTGTCCA,-,0.00),83(AGTACAAAGTGTCCAC,+,0.00)
chunk0010_106_1	chr1	114122306	114122587	+	0	NA	intron (NM_205848, intron 3 of 7)	intron (NM_205848, intron 3 of 7)	29994	NM_205848	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.021352	0.528369	
chunk0170_160_1	chr6	111542275	111542865	+	0	NA	intron (NR_034109, intron 1 of 1)	L2a|LINE|L2	24790	NM_001164283	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.008475	0.429780	242(AAGAGCAAAGTGTACC,-,0.00)
chunk0082_140_1	chr17	55432881	55433562	+	0	NA	Intergenic	Intergenic	-11241	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.010279	0.438416	
chunk0161_41_1	chr5	165885883	165886431	+	0	NA	Intergenic	Intergenic	1040213	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.016423	0.387978	308(AGGAGCAGTGTGTGCC,-,0.00),309(GGAGCAGTGTGTGCCA,+,0.00)
chunk0025_227_1	chr10	54035045	54035441	+	0	NA	intron (NM_001142769, intron 20 of 35)	Tigger1|DNA|TcMar-Tigger	572714	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.010101	0.355164	182(AGGCACACTCTGTTTC,-,0.00),183(GGCACACTCTGTTTCA,+,0.00)
chunk0076_121_1	chr16	66642085	66642605	+	0	NA	intron (NM_181521, intron 1 of 3)	intron (NM_181521, intron 1 of 3)	37614	NR_037619	123920	Hs.298198	NM_144601	ENSG00000140931	CMTM3	BNAS2|CKLFSF3	CKLF like MARVEL transmembrane domain containing 3	protein-coding	0.003846	0.403071	
chunk0156_140_1	chr5	107112827	107113211	+	0	NA	Intergenic	Intergenic	-102005	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.005208	0.342857	
chunk0168_443_1	chr6	95780549	95781207	+	0	NA	Intergenic	L1MC4|LINE|L1	203381	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.004559	0.312595	
chunk0123_390_1	chr3	48811338	48812143	+	0	NA	intron (NM_004157, intron 1 of 10)	L1MB5|LINE|L1	36097	NM_004157	5576	Hs.631923	NM_004157	ENSG00000114302	PRKAR2A	PKR2|PRKAR2	protein kinase cAMP-dependent type II regulatory subunit alpha	protein-coding	0.006211	0.380893	338(GGGTACAGGTTGTTCT,-,0.00),339(GGTACAGGTTGTTCTT,+,0.00)
chunk0154_67_1	chr5	77389864	77390063	+	0	NA	intron (NM_001029854, intron 9 of 20)	L1ME2z|LINE|L1	102544	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.005025	0.405000	
chunk0113_135_1	chr20	51843869	51844068	+	0	NA	intron (NR_110016, intron 1 of 2)	intron (NR_110016, intron 1 of 2)	18945	NR_110016	101927678	Hs.683840	NR_110016	ENSG00000227964	LINC01429	-	long intergenic non-protein coding RNA 1429	ncRNA	0.005025	0.430000	152(CAGAACTTTGTGTTCC,-,0.00),153(AGAACTTTGTGTTCCT,+,0.00)
chunk0153_210_1	chr5	71925715	71925943	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-181462	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.008772	0.510917	
chunk0109_446_1	chr2	241568849	241569048	+	0	NA	intron (NM_032515, intron 3 of 4)	intron (NM_032515, intron 3 of 4)	-9805	NR_033346	100379249	Hs.621128	NR_033346		BOK-AS1	BOK-AS|BOKAS|NAToB|NCRNA00151	BOK antisense RNA 1	ncRNA	0.020101	0.540000	
chunk0090_334_1	chr18	76339052	76339645	+	0	NA	Intergenic	MIR|SINE|MIR	155842	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.010118	0.488215	
chunk0096_138_1	chr2	28747587	28747941	+	0	NA	Intergenic	Intergenic	-3984	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.005650	0.400000	
chunk0132_39_1	chr3	154791489	154792214	+	0	NA	Intergenic	Intergenic	-287796	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.002759	0.377410	
chunk0130_99_1	chr3	130905472	130905702	+	0	NA	intron (NM_001001485, intron 2 of 27)	L1MC4a|LINE|L1	10997	NM_001001486	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.000000	0.333333	
chunk0004_411_1	chr1	52334520	52334993	+	0	NA	exon (NM_004799, exon 15 of 19)	exon (NM_004799, exon 15 of 19)	31449	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.004228	0.373418	
chunk0145_364_1	chr4	151339590	151339983	+	0	NA	Intergenic	L2b|LINE|L2	62613	NM_183375	345062	Hs.651266	NM_183375	ENSG00000189099	PRSS48	ESSPL	serine protease 48	protein-coding	0.007634	0.390863	
chunk0162_451_1	chr5	180809899	180810426	+	0	NA	promoter-TSS (NM_001114618)	promoter-TSS (NM_001114618)	-25	NM_001114617	4245	Hs.519818	NM_002406	ENSG00000131446	MGAT1	GLCNAC-TI|GLCT1|GLYT1|GNT-1|GNT-I|GnTI|MGAT	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	protein-coding	0.083491	0.691288	
chunk0030_432_1	chr10	120653218	120653816	+	0	NA	Intergenic	Intergenic	55568	NR_103717	404216	Hs.196578	NM_001012711	ENSG00000177234	LINC01561	C10orf85	long intergenic non-protein coding RNA 1561	ncRNA	0.008361	0.439065	275(CTGCACACTCTGTTCC,-,0.00),276(TGCACACTCTGTTCCT,+,0.00)
chunk0171_44_1	chr6	120947614	120948049	+	0	NA	Intergenic	Intergenic	386669	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.000000	0.323394	
chunk0018_110_1	chr1	218285104	218285457	+	0	NA	promoter-TSS (NM_016052)	promoter-TSS (NM_016052)	-7	NM_016052	51018	Hs.660109	NM_016052	ENSG00000067533	RRP15	CGI-115|KIAA0507	ribosomal RNA processing 15 homolog	protein-coding	0.070822	0.559322	
chunk0069_1_1	chr15	59992365	59992564	+	0	NA	Intergenic	Intergenic	-11758	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.025126	0.455000	
chunk0058_235_1	chr14	25499426	25499750	+	0	NA	Intergenic	Intergenic	-449291	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.012346	0.440000	
chunk0159_288_1	chr5	142740491	142740846	+	0	NA	Intergenic	Intergenic	-4932	NR_110558	101926975	Hs.638583	NR_110558	ENSG00000236714	LINC01844	-	long intergenic non-protein coding RNA 1844	ncRNA	0.008451	0.443820	
chunk0178_413_1	chr7	41003339	41004023	+	0	NA	Intergenic	Intergenic	-23742	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.007310	0.400000	
chunk0149_179_1	chr5	21152741	21152940	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-306640	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.000000	0.375000	
chunk0054_155_1	chr13	44108096	44108861	+	0	NA	intron (NR_132368, intron 2 of 3)	intron (NR_132368, intron 2 of 3)	-2071	NR_104065	101929212	Hs.534877	NR_104064	ENSG00000227258	SMIM2-AS1	C13orf44-AS1|C3orf81-AS1	SMIM2 antisense RNA 1	ncRNA	0.005229	0.454308	
chunk0138_355_1	chr4	42081306	42081505	+	0	NA	intron (NM_006345, intron 17 of 17)	Charlie1a|DNA|hAT-Charlie	71473	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.000000	0.375000	
chunk0188_106_1	chr8	8907779	8908309	+	0	NA	Intergenic	Intergenic	-14423	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.001887	0.276836	414(ATCACACTCTGTGCTT,+,0.00)
chunk0064_125_1	chr14	91374394	91374845	+	0	NA	intron (NM_001080414, intron 3 of 29)	intron (NM_001080414, intron 3 of 29)	43225	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.015521	0.526549	230(CAGAACAGGCCGTGCA,-,0.00),231(AGAACAGGCCGTGCAG,+,0.00)
chunk0212_189_1	chrX	133799593	133800268	+	0	NA	intron (NM_001164619, intron 1 of 6)	intron (NM_001164619, intron 1 of 6)	185716	NM_004484	2719	Hs.644108	NM_004484	ENSG00000147257	GPC3	DGSX|GTR2-2|MXR7|OCI-5|SDYS|SGB|SGBS|SGBS1	glypican 3	protein-coding	0.005926	0.403846	
chunk0053_251_1	chr13	32934027	32934831	+	0	NA	Intergenic	Intergenic	-22777	NR_047020	100874167	Hs.406290	NR_047020		LINC00423	-	long intergenic non-protein coding RNA 423	ncRNA	0.002488	0.360248	
chunk0036_69_1	chr11	59776340	59776897	+	0	NA	intron (NM_004177, intron 2 of 10)	intron (NM_004177, intron 2 of 10)	21559	NM_004177	6809	Hs.180711	NM_004177	ENSG00000166900	STX3	STX3A	syntaxin 3	protein-coding	0.005386	0.405018	
chunk0086_421_1	chr18	27041283	27041482	+	0	NA	intron (NM_031422, intron 3 of 5)	intron (NM_031422, intron 3 of 5)	143956	NM_001256316	83539	Hs.44584	NM_031422	ENSG00000154080	CHST9	GALNAC4ST-2|GalNAc4ST2	carbohydrate sulfotransferase 9	protein-coding	0.000000	0.330000	
chunk0133_331_1	chr3	172622819	172623433	+	0	NA	Intergenic	Intergenic	88092	NM_001146278	57552	Hs.444099	NM_020792	ENSG00000144959	NCEH1	AADACL1|NCEH	neutral cholesterol ester hydrolase 1	protein-coding	0.011401	0.370732	
chunk0120_305_1	chr3	9976963	9977270	+	0	NA	intron (NM_018447, intron 2 of 7)	intron (NM_018447, intron 2 of 7)	9722	NM_018447	55831	Hs.475392	NM_018447	ENSG00000125037	EMC3	POB|TMEM111	ER membrane protein complex subunit 3	protein-coding	0.013029	0.409091	
chunk0112_143_1	chr20	38650402	38650965	+	0	NA	TTS (NM_001164431)	TTS (NM_001164431)	48749	NM_001164431	343578		NM_001164431	ENSG00000124143	ARHGAP40	C20orf95|dJ1100H13.4	Rho GTPase activating protein 40	protein-coding	0.015986	0.514184	
chunk0006_445_1	chr1	76771036	76771235	+	0	NA	Intergenic	Intergenic	-96366	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.010050	0.490000	
chunk0152_421_1	chr5	65749439	65749884	+	0	NA	intron (NM_020726, intron 1 of 12)	intron (NM_020726, intron 1 of 12)	27465	NM_020726	57486	Hs.247460	NM_020726	ENSG00000123213	NLN	AGTBP|EP24.16|MEP|MOP	neurolysin	protein-coding	0.002247	0.412556	
chunk0180_460_1	chr7	77563198	77563437	+	0	NA	intron (NM_001131008, intron 1 of 17)	intron (NM_001131008, intron 1 of 17)	25282	NM_001131008	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.008368	0.337500	
chunk0072_440_1	chr15	101447899	101448305	+	0	NA	intron (NM_002570, intron 1 of 21)	intron (NM_002570, intron 1 of 21)	41882	NM_138324	5046	Hs.498494	NM_002570	ENSG00000140479	PCSK6	PACE4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding	0.022167	0.447174	
chunk0143_322_1	chr4	119683616	119684011	+	0	NA	Intergenic	Intergenic	-54987	NM_001083	8654	Hs.647971	NM_001083	ENSG00000138735	PDE5A	CGB-PDE|CN5A|PDE5	phosphodiesterase 5A	protein-coding	0.007595	0.406566	
chunk0080_151_1	chr17	27962371	27962609	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-69107	NM_001076680	201229	Hs.687951	NM_001076680	ENSG00000232859	LYRM9	C17orf108|HSD24	LYR motif containing 9	protein-coding	0.012605	0.472803	
chunk0023_336_1	chr10	29384946	29385145	+	0	NA	Intergenic	MER83|LTR|ERV1	-24489	NR_110920	102724316	Hs.499209	NR_003930	ENSG00000224597	SVIL-AS1	-	SVIL antisense RNA 1	ncRNA	0.005025	0.505000	
chunk0135_284_1	chr3	189429162	189429917	+	0	NA	Intergenic	Intergenic	-188945	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.002649	0.371693	343(AAGAACAGTTAGTTCT,-,0.00),344(AGAACAGTTAGTTCTG,+,0.00)
chunk0178_163_1	chr7	33850957	33851286	+	0	NA	Intergenic	Intergenic	-53790	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.006079	0.375758	48(GAGAACAAGGTGTTCT,-,0.00),49(AGAACAAGGTGTTCTA,+,0.00),150(AAGAACAAACTGATCA,-,0.00),151(AGAACAAACTGATCAT,+,0.00)
chunk0114_231_1	chr21	15894665	15895524	+	0	NA	Intergenic	Intergenic	165069	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.003492	0.290698	
chunk0082_52_1	chr17	51153399	51153742	+	0	NA	promoter-TSS (NM_198175)	promoter-TSS (NM_198175)	11	NM_000269	4830	Hs.463456	NM_000269	ENSG00000239672	NME1	AWD|GAAD|NB|NBS|NDKA|NDPK-A|NDPKA|NM23|NM23-H1	NME/NM23 nucleoside diphosphate kinase 1	protein-coding	0.067055	0.563953	
chunk0077_39_1	chr16	75517200	75517462	+	0	NA	Intergenic	CpG	17839	NM_024533	23563	Hs.745424	NM_012126	ENSG00000135702	CHST5	I-GlcNAc-6-ST|I-GlcNAc6ST|glcNAc6ST-3|gn6st-3|hIGn6ST	carbohydrate sulfotransferase 5	protein-coding	0.076336	0.669202	
chunk0118_151_1	chr22	30021597	30022344	+	0	NA	intron (NM_153050, intron 17 of 19)	intron (NM_153050, intron 17 of 19)	14921	NR_106876	102466742		NR_106876	ENSG00000275818	MIR6818	hsa-mir-6818	microRNA 6818	ncRNA	0.008032	0.525401	
chunk0041_78_1	chr11	124167802	124168150	+	0	NA	Intergenic	LTR22B|LTR|ERVK	52572	NM_198315	4013	Hs.152944	NM_014622	ENSG00000110002	VWA5A	BCSC-1|BCSC1|LOH11CR2A	von Willebrand factor A domain containing 5A	protein-coding	0.014368	0.504298	
chunk0098_186_1	chr2	71700015	71700675	+	0	NA	Intergenic	Intergenic	233643	NM_001130983	8291	Hs.252180	NM_003494	ENSG00000135636	DYSF	FER1L1|LGMD2B|LGMDR2|MMD1	dysferlin	protein-coding	0.019697	0.602118	333(CAGCACACAGTGTTCC,-,0.00),334(AGCACACAGTGTTCCA,+,0.00)
chunk0188_113_1	chr8	9057333	9057928	+	0	NA	Intergenic	L2a|LINE|L2	9185	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.015126	0.464765	
chunk0165_148_1	chr6	33716979	33717634	+	0	NA	Intergenic	Intergenic	-5555	NM_032340	84300	Hs.732448	NM_032340	ENSG00000137288	UQCC2	C6orf125|C6orf126|Cbp6|M19|MC3DN7|MNF1|bA6B20.2	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding	0.009160	0.486280	
chunk0004_161_1	chr1	45521666	45521965	+	0	NA	5' UTR (NM_002574, exon 1 of 6)	5' UTR (NM_002574, exon 1 of 6)	123	NM_181697	5052	Hs.180909	NM_002574	ENSG00000117450	PRDX1	MSP23|NKEF-A|NKEFA|PAG|PAGA|PAGB|PRX1|PRXI|TDPX2	peroxiredoxin 1	protein-coding	0.093645	0.673333	
chunk0129_437_1	chr3	127817456	127817798	+	0	NA	intron (NM_001003794, intron 2 of 7)	L2c|LINE|L2	5255	NM_007283	11343	Hs.277035	NM_007283	ENSG00000074416	MGLL	HU-K5|HUK5|MAGL|MGL	monoglyceride lipase	protein-coding	0.011696	0.481050	
chunk0017_257_1	chr1	209371706	209372149	+	0	NA	Intergenic	Intergenic	-56896	NM_001104548									0.002257	0.414414	235(AGGGACACAGTGTAAT,-,0.00)
chunk0028_379_1	chr10	92889528	92889812	+	0	NA	intron (NM_019053, intron 1 of 21)	L1MC1|LINE|L1	41202	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.010563	0.375439	
chunk0104_450_1	chr2	181539652	181539971	+	0	NA	TTS (NM_000885)	TTS (NM_000885)	82919	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.006270	0.337500	
chunk0092_262_1	chr19	33085870	33086357	+	0	NA	intron (NM_018025, intron 1 of 19)	MER20|DNA|hAT-Charlie	5233	NM_018025	55094	Hs.466436	NM_018025	ENSG00000076650	GPATCH1	ECGP|GPATC1	G-patch domain containing 1	protein-coding	0.006160	0.475410	
chunk0172_170_1	chr6	136231438	136231637	+	0	NA	intron (NM_001099286, intron 7 of 7)	L2a|LINE|L2	18774	NM_138419	113115	Hs.121536	NM_138419	ENSG00000146410	MTFR2	DUFD1|FAM54A	mitochondrial fission regulator 2	protein-coding	0.020101	0.395000	153(CGGCACAGACTGAGCT,-,0.00),154(GGCACAGACTGAGCTC,+,0.00)
chunk0111_189_1	chr20	25395089	25395438	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-4281	NM_001042472	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.017192	0.417143	
chunk0012_107_1	chr1	156616314	156617031	+	0	NA	Intergenic	Intergenic	-2622	NM_021817	60484	Hs.410719	NM_021817	ENSG00000132702	HAPLN2	BRAL1	hyaluronan and proteoglycan link protein 2	protein-coding	0.009763	0.481894	342(TGGATCAGGGTGTCCT,-,0.00),343(GGATCAGGGTGTCCTG,+,0.00)
chunk0106_175_1	chr2	200811652	200811983	+	0	NA	promoter-TSS (NM_001207069)	promoter-TSS (NM_001207069)	271	NM_014670	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.081571	0.596386	
chunk0028_79_1	chr10	83816919	83817381	+	0	NA	Intergenic	Intergenic	-322279	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.004329	0.397408	
chunk0059_419_1	chr14	38108707	38108924	+	0	NA	Intergenic	Intergenic	-99184	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.004608	0.321101	
chunk0137_388_1	chr4	26872364	26872833	+	0	NA	intron (NM_020860, intron 1 of 11)	intron (NM_020860, intron 1 of 11)	11907	NM_001169117	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.000000	0.259574	
chunk0159_422_1	chr5	148090571	148091299	+	0	NA	intron (NM_006846, intron 7 of 32)	intron (NM_006846, intron 7 of 32)	26963	NM_001127699	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.012363	0.373114	
chunk0021_118_1	chr10	3531663	3531919	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	213096	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.007812	0.435798	
chunk0066_393_1	chr15	39045526	39045725	+	0	NA	Intergenic	L1PB1|LINE|L1	-205044	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.015075	0.335000	
chunk0211_143_1	chrX	113073101	113073318	+	0	NA	intron (NR_110399, intron 2 of 3)	L2c|LINE|L2	30482	NR_110399	101928437	Hs.640112	NR_110399		LOC101928437	-	uncharacterized LOC101928437	ncRNA	0.000000	0.353211	
chunk0033_50_1	chr11	13329886	13330404	+	0	NA	intron (NM_001178, intron 3 of 19)	intron (NM_001178, intron 3 of 19)	52418	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.011583	0.429672	
chunk0081_47_1	chr17	37769339	37770002	+	0	NA	Intergenic	Intergenic	-24592	NM_001165923	6928	Hs.191144	NM_000458	ENSG00000275410	HNF1B	FJHN|HNF-1-beta|HNF-1B|HNF1beta|HNF2|HPC11|LF-B3|LFB3|MODY5|TCF-2|TCF2|VHNF1	HNF1 homeobox B	protein-coding	0.012066	0.481928	
chunk0039_378_1	chr11	106450304	106450789	+	0	NA	Intergenic	Intergenic	199139	NR_120551	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.002062	0.333333	394(AAGAACAAGCAGTTCA,-,0.00),395(AGAACAAGCAGTTCAG,+,0.00)
chunk0085_289_1	chr18	7945913	7946159	+	0	NA	intron (NM_001105244, intron 5 of 32)	intron (NM_001105244, intron 5 of 32)	378720	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.012195	0.412955	
chunk0103_316_1	chr2	167435359	167435903	+	0	NA	Intergenic	Intergenic	248348	NM_001199145	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.007353	0.324771	501(AAGAACATTTAGTCCC,-,0.00),502(AGAACATTTAGTCCCT,+,0.00)
chunk0096_311_1	chr2	33064473	33064911	+	0	NA	intron (NM_206943, intron 3 of 33)	LTR40a|LTR|ERVL	-69905	NM_001166265	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.006849	0.400911	
chunk0202_138_1	chr9	73337093	73337819	+	0	NA	Intergenic	L1PA8|LINE|L1	185725	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.005510	0.393398	
chunk0186_89_1	chr7	137338173	137338716	+	0	NA	intron (NM_002825, intron 1 of 4)	intron (NM_002825, intron 1 of 4)	5356	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.007366	0.347426	
chunk0206_268_1	chr9	124038179	124038688	+	0	NA	Intergenic	Intergenic	26823	NM_004789	9355	Hs.696425	NM_004789	ENSG00000106689	LHX2	LH2|hLhx2	LIM homeobox 2	protein-coding	0.015717	0.501961	
chunk0112_65_1	chr20	37723651	37724152	+	0	NA	intron (NM_030877, intron 1 of 15)	intron (NM_030877, intron 1 of 15)	29946	NM_030877	56259	Hs.472667	NM_030877	ENSG00000132792	CTNNBL1	C20orf33|NAP|P14L|PP8304|dJ633O20.1	catenin beta like 1	protein-coding	0.001996	0.392430	
chunk0085_429_1	chr18	10726353	10726971	+	0	NA	intron (NM_022068, intron 33 of 51)	CpG	32987	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.087379	0.663974	
chunk0053_300_1	chr13	33761551	33762210	+	0	NA	Intergenic	Intergenic	-56189	NM_181558	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.015175	0.428788	160(GGAAACACGGTGTTCA,-,0.00),161(GAAACACGGTGTTCAT,+,0.00),229(AAGAACACACAGAGCT,-,0.00)
chunk0124_362_1	chr3	58918553	58919092	+	0	NA	intron (NM_198463, intron 5 of 15)	MIR|SINE|MIR	94351	NR_110820	101929238	Hs.683953	NR_110820	ENSG00000242428	C3orf67-AS1	-	C3orf67 antisense RNA 1	ncRNA	0.001855	0.362963	
chunk0164_386_1	chr6	26131466	26131947	+	0	NA	Intergenic	MLT1B-int|LTR|ERVL-MaLR	7561	NM_003512	8334	Hs.484950	NM_003512	ENSG00000180573	HIST1H2AC	H2A/l|H2AFL|dJ221C16.4	histone cluster 1 H2A family member c	protein-coding	0.006237	0.456432	
chunk0178_32_1	chr7	29449498	29450250	+	0	NA	intron (NM_001293069, intron 7 of 13)	intron (NM_001293069, intron 7 of 13)	-29838	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.005319	0.406375	
chunk0015_287_1	chr1	188713240	188713735	+	0	NA	Intergenic	Intergenic	1269859	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004040	0.322581	
chunk0090_278_1	chr18	74831025	74831584	+	0	NA	intron (NM_001146189, intron 3 of 6)	L1MB3|LINE|L1	200341	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.001789	0.360714	
chunk0175_462_1	chr6	170489236	170489788	+	0	NA	Intergenic	Intergenic	63817	NM_002793	5689	Hs.352768	NM_002793	ENSG00000008018	PSMB1	HC5|PMSB1|PSC5	proteasome subunit beta 1	protein-coding	0.019928	0.481013	
chunk0082_109_1	chr17	54819689	54820266	+	0	NA	Intergenic	Tigger3d|DNA|TcMar-Tigger	-80714	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.003466	0.349481	
chunk0007_11_1	chr1	77261545	77262276	+	0	NA	Intergenic	Intergenic	-20067	NM_174858	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.001368	0.398907	
chunk0181_187_1	chr7	83363252	83363728	+	0	NA	TTS (NM_012431)	TTS (NM_012431)	-200609	NM_033026	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.010504	0.360587	175(TGGCACACACTGTTAT,-,0.00),176(GGCACACACTGTTATG,+,0.00)
chunk0106_107_1	chr2	197499760	197500123	+	0	NA	promoter-TSS (NM_001202485)	promoter-TSS (NM_001202485)	-25	NM_002156	3329	Hs.595053	NM_002156	ENSG00000144381	HSPD1	CPN60|GROEL|HLD4|HSP-60|HSP60|HSP65|HuCHA60|SPG13	heat shock protein family D (Hsp60) member 1	protein-coding	0.118457	0.706044	
chunk0012_175_1	chr1	158846837	158847361	+	0	NA	intron (NM_002432, intron 5 of 6)	L1PB3|LINE|L1	15721	NM_002432	4332	Hs.153837	NM_002432	ENSG00000163563	MNDA	PYHIN3	myeloid cell nuclear differentiation antigen	protein-coding	0.003817	0.348571	
chunk0148_35_1	chr5	944988	945201	+	0	NA	Intergenic	Intergenic	52240	NM_001166260	9319	Hs.436187	NM_004237	ENSG00000071539	TRIP13	16E1BP|MVA3	thyroid hormone receptor interactor 13	protein-coding	0.018779	0.546729	
chunk0150_224_1	chr5	35488542	35489028	+	0	NA	Intergenic	L2a|LINE|L2	-129102	NM_144722	79925	Hs.298863	NM_024867	ENSG00000152582	SPEF2	CT122|KPL2	sperm flagellar 2	protein-coding	0.000000	0.355236	
chunk0142_395_1	chr4	102628114	102628372	+	0	NA	Intergenic	Intergenic	126914	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.003876	0.413127	
chunk0211_445_1	chrX	129661414	129661623	+	0	NA	Intergenic	Intergenic	-6562	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.004785	0.338095	
chunk0057_334_1	chr13	107043450	107044119	+	0	NA	Intergenic	Intergenic	389904	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.001495	0.337313	
chunk0194_81_1	chr8	82847003	82847357	+	0	NA	Intergenic	Intergenic	-556578	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.000000	0.335211	
chunk0183_124_1	chr7	105488051	105488257	+	0	NA	intron (NM_019042, intron 7 of 15)	intron (NM_019042, intron 7 of 15)	34084	NM_019042	54517	Hs.520619	NM_019042	ENSG00000091127	PUS7	IDDABS	pseudouridine synthase 7	protein-coding	0.004854	0.391304	
chunk0030_438_1	chr10	120838173	120838479	+	0	NA	intron (NR_033850, intron 1 of 2)	intron (NR_033850, intron 1 of 2)	-12849	NM_018117	55717	Hs.144447	NM_018117	ENSG00000120008	WDR11	BRWD2|DR11|HH14|SRI1|WDR15	WD repeat domain 11	protein-coding	0.000000	0.381107	
chunk0096_132_1	chr2	28729651	28730186	+	0	NA	Intergenic	Intergenic	-21830	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.000000	0.356343	
chunk0068_92_1	chr15	52147067	52147629	+	0	NA	intron (NM_016194, intron 6 of 12)	intron (NM_016194, intron 6 of 12)	32617	NM_006578	10681	Hs.155090	NM_006578	ENSG00000069966	GNB5	GB5|IDDCA|LADCI	G protein subunit beta 5	protein-coding	0.007117	0.419183	
chunk0137_409_1	chr4	27883251	27883649	+	0	NA	Intergenic	Intergenic	665971	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.005025	0.283208	
chunk0198_325_1	chr8	139864014	139864348	+	0	NA	intron (NM_001160372, intron 21 of 22)	intron (NM_001160372, intron 21 of 22)	-161125	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.017964	0.498507	187(TGGTACAGTAAGTCCC,-,0.00),188(GGTACAGTAAGTCCCA,+,0.00)
chunk0137_254_1	chr4	20856243	20856717	+	0	NA	intron (NM_147182, intron 2 of 8)	L2c|LINE|L2	-5812	NM_147181	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.002110	0.360000	
chunk0190_7_1	chr8	28799472	28799671	+	0	NA	intron (NR_026826, intron 6 of 14)	intron (NR_026826, intron 6 of 14)	90344	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.005025	0.425000	
chunk0207_460_1	chr9	137900638	137900837	+	0	NA	intron (NM_001243812, intron 3 of 45)	(TGTGTC)n|Simple_repeat|Simple_repeat	-8167	NR_121583	100133077	Hs.640081	NR_121583	ENSG00000203987	LOC100133077	-	uncharacterized LOC100133077	ncRNA	0.015075	0.530000	
chunk0136_242_1	chr4	9996837	9997090	+	0	NA	intron (NM_020041, intron 2 of 11)	intron (NM_020041, intron 2 of 11)	24527	NM_020041	56606	Hs.444612	NM_020041	ENSG00000109667	SLC2A9	GLUT9|GLUTX|UAQTL2|URATv1	solute carrier family 2 member 9	protein-coding	0.007905	0.421260	
chunk0211_65_1	chrX	109894203	109894820	+	0	NA	Intergenic	L1MD2|LINE|L1	24110	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.008104	0.347896	
chunk0178_465_1	chr7	42233158	42234128	+	0	NA	intron (NM_000168, intron 1 of 14)	intron (NM_000168, intron 1 of 14)	3376	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.006186	0.362513	
chunk0072_382_1	chr15	100350682	100351030	+	0	NA	promoter-TSS (NR_028139)	promoter-TSS (NR_028139)	-138	NR_028139	388182	Hs.136982	NM_207383	ENSG00000189419	SPATA41	HSD47	spermatogenesis associated 41	ncRNA	0.014368	0.415473	
chunk0132_104_1	chr3	155711855	155712144	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-7791	NM_014996	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.006920	0.393103	
chunk0127_13_1	chr3	88094055	88094500	+	0	NA	intron (NM_001195308, intron 2 of 3)	intron (NM_001195308, intron 2 of 3)	-35281	NM_003663	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.008989	0.336323	
chunk0195_240_1	chr8	97560089	97560288	+	0	NA	Intergenic	Intergenic	-83991	NM_178812	92140	Hs.377155	NM_178812	ENSG00000147649	MTDH	3D3|AEG-1|AEG1|LYRIC|LYRIC/3D3	metadherin	protein-coding	0.025126	0.460000	
chunk0087_259_1	chr18	37055776	37056147	+	0	NA	intron (NM_020776, intron 6 of 9)	intron (NM_020776, intron 6 of 9)	-226745	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.000000	0.314516	
chunk0204_137_1	chr9	95470462	95470661	+	0	NA	TTS (NR_038982)	TTS (NR_038982)	6952	NR_038982	100507346	Hs.661847	NR_038982		LOC100507346	-	uncharacterized LOC100507346	ncRNA	0.010050	0.370000	
chunk0033_129_1	chr11	14688232	14688799	+	0	NA	intron (NM_000922, intron 1 of 15)	intron (NM_000922, intron 1 of 15)	44792	NM_000922	5140	Hs.445711	NM_000922	ENSG00000152270	PDE3B	HcGIP1|cGIPDE1	phosphodiesterase 3B	protein-coding	0.001764	0.323944	
chunk0164_20_1	chr6	17972270	17972668	+	0	NA	intron (NM_001243423, intron 2 of 2)	intron (NM_001243423, intron 2 of 2)	15154	NM_022113	63971	Hs.94499	NM_022113	ENSG00000137177	KIF13A	RBKIN|bA500C11.2	kinesin family member 13A	protein-coding	0.015075	0.360902	
chunk0107_294_1	chr2	218732075	218732615	+	0	NA	intron (NM_014640, intron 2 of 19)	intron (NM_014640, intron 2 of 19)	21500	NM_014640	9654	Hs.471405	NM_014640	ENSG00000135912	TTLL4	-	tubulin tyrosine ligase like 4	protein-coding	0.007407	0.402957	
chunk0169_324_1	chr6	106300363	106300844	+	0	NA	intron (NR_104403, intron 1 of 4)	Tigger3a|DNA|TcMar-Tigger	15663	NR_104403	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.008316	0.336100	
chunk0120_377_1	chr3	12144141	12144347	+	0	NA	intron (NM_133625, intron 3 of 12)	intron (NM_133625, intron 3 of 12)	15107	NM_003256	7079	Hs.591665	NM_003256	ENSG00000157150	TIMP4	TIMP-4	TIMP metallopeptidase inhibitor 4	protein-coding	0.024272	0.507246	89(GGGAACATTCTGTACT,-,0.00),90(GGAACATTCTGTACTC,+,0.00)
chunk0014_108_1	chr1	176796128	176796654	+	0	NA	intron (NM_020318, intron 20 of 22)	intron (NM_020318, intron 20 of 22)	233054	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.003802	0.387097	
chunk0198_46_1	chr8	128429906	128430118	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	134667	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.023585	0.492958	
chunk0160_382_1	chr5	161312642	161313103	+	0	NA	intron (NM_000813, intron 9 of 9)	intron (NM_000813, intron 9 of 9)	235252	NM_000813	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.013015	0.415584	
chunk0136_320_1	chr3	195379754	195380403	+	0	NA	intron (NM_012287, intron 4 of 22)	L1M4|LINE|L1	63010	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.001541	0.324615	
chunk0064_423_1	chr14	99690835	99691247	+	0	NA	intron (NM_006668, intron 1 of 14)	intron (NM_006668, intron 1 of 14)	6623	NM_006668	10858	Hs.25121	NM_006668	ENSG00000036530	CYP46A1	CP46|CYP46	cytochrome P450 family 46 subfamily A member 1	protein-coding	0.007282	0.513317	
chunk0195_322_1	chr8	98983173	98983523	+	0	NA	Intergenic	Intergenic	-29918	NM_181661	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.005714	0.327635	
chunk0135_358_1	chr3	190626909	190627315	+	0	NA	intron (NM_134470, intron 7 of 8)	intron (NM_134470, intron 7 of 8)	113061	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.009852	0.351351	
chunk0001_201_1	chr1	7834978	7835326	+	0	NA	intron (NM_001289861, intron 20 of 22)	L2|LINE|L2	17892	NM_006786	10911	Hs.715862	NM_006786	ENSG00000049247	UTS2	PRO1068|U-II|UCN2|UII	urotensin 2	protein-coding	0.005747	0.392550	
chunk0030_361_1	chr10	118726103	118726302	+	0	NA	intron (NM_153810, intron 3 of 8)	intron (NM_153810, intron 3 of 8)	29044	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.005025	0.385000	
chunk0209_318_1	chrX	50318569	50319278	+	0	NA	intron (NM_033031, intron 7 of 11)	MER68|LTR|ERVL	34383	NM_033031	85417	Hs.130310	NM_033031	ENSG00000147082	CCNB3	-	cyclin B3	protein-coding	0.005642	0.401408	318(AGGCACAGAGTGTTTA,-,0.00),319(GGCACAGAGTGTTTAC,+,0.00)
chunk0086_281_1	chr18	23684445	23685201	+	0	NA	Intergenic	Intergenic	-4620	NM_001302996	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.006614	0.361955	
chunk0173_196_1	chr6	145249183	145249524	+	0	NA	Intergenic	Intergenic	-485516	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.017595	0.470760	
chunk0112_445_1	chr20	48002460	48002821	+	0	NA	Intergenic	LOR1a|LTR|ERV1	-12523	NR_110027	101927457	Hs.445823	NR_110027		LINC01522	-	long intergenic non-protein coding RNA 1522	ncRNA	0.008310	0.444751	
chunk0127_72_1	chr3	89474159	89474804	+	0	NA	intron (NM_005233, intron 16 of 16)	intron (NM_005233, intron 16 of 16)	366957	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.006202	0.321981	
chunk0131_62_1	chr3	142879409	142879648	+	0	NA	intron (NM_013363, intron 2 of 8)	intron (NM_013363, intron 2 of 8)	9675	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.004184	0.345833	
chunk0055_238_1	chr13	62854900	62855115	+	0	NA	Intergenic	Intergenic	-47648	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.004651	0.296296	
chunk0040_281_1	chr11	116852016	116852573	+	0	NA	intron (NM_025164, intron 20 of 23)	intron (NM_025164, intron 20 of 23)	-14672	NM_000039	335	Hs.93194	NM_000039	ENSG00000118137	APOA1	apo(a)	apolipoprotein A1	protein-coding	0.008977	0.496416	
chunk0021_112_1	chr10	3294991	3295547	+	0	NA	Intergenic	Intergenic	-23426	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.021583	0.457810	
chunk0159_428_1	chr5	148140869	148142157	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-27033	NM_001001325	408187	Hs.553815	NM_001001325	ENSG00000196800	SPINK14	SPINK5L2	serine peptidase inhibitor, Kazal type 14 (putative)	protein-coding	0.005435	0.366175	969(TAGGACATCCTGTTCT,-,0.00),970(AGGACATCCTGTTCTT,+,0.00)
chunk0137_382_1	chr4	26412758	26413089	+	0	NA	intron (NM_203283, intron 3 of 10)	intron (NM_203283, intron 3 of 10)	77497	NM_000730	886	Hs.129	NM_000730	ENSG00000163394	CCKAR	CCK-A|CCK1-R|CCK1R|CCKRA	cholecystokinin A receptor	protein-coding	0.003021	0.469880	
chunk0077_104_1	chr16	78133894	78134279	+	0	NA	intron (NM_016373, intron 4 of 8)	intron (NM_016373, intron 4 of 8)	34673	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.005195	0.357513	
chunk0188_165_1	chr8	10770851	10771375	+	0	NA	intron (NM_001284356, intron 5 of 5)	intron (NM_001284356, intron 5 of 5)	-40539	NM_031439	83595	Hs.709543	NM_031439	ENSG00000171056	SOX7	-	SRY-box transcription factor 7	protein-coding	0.007634	0.457143	263(CAGAACATTCTGTACC,-,0.00),264(AGAACATTCTGTACCT,+,0.00)
chunk0069_295_1	chr15	65342690	65342983	+	0	NA	intron (NM_004884, intron 2 of 13)	FLAM_A|SINE|Alu	35204	NM_004884	9543	Hs.128292	NM_004884	ENSG00000174498	IGDCC3	HsT18880|PUNC	immunoglobulin superfamily DCC subclass member 3	protein-coding	0.023891	0.496599	
chunk0159_354_1	chr5	144481915	144482421	+	0	NA	Intergenic	Intergenic	311295	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.003953	0.406312	197(TTGTACAATCTGTTCT,-,0.00),198(TGTACAATCTGTTCTC,+,0.00)
chunk0158_70_1	chr5	126280313	126280512	+	0	NA	intron (NR_105039, intron 1 of 2)	intron (NR_105039, intron 1 of 2)	4763	NR_105039	101927488	Hs.432319	NR_105039		LOC101927488	-	uncharacterized LOC101927488	ncRNA	0.000000	0.440000	
chunk0105_156_1	chr2	186688709	186689333	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-5041	NM_177454	165215	Hs.28872	NM_177454	ENSG00000144369	FAM171B	KIAA1946	family with sequence similarity 171 member B	protein-coding	0.004808	0.332800	
chunk0178_115_1	chr7	30977315	30977585	+	0	NA	intron (NM_000823, intron 12 of 12)	intron (NM_000823, intron 12 of 12)	13429	NM_000823	2692	Hs.767	NM_000823	ENSG00000106128	GHRHR	GHRFR|GRFR|IGHD1B|IGHD4	growth hormone releasing hormone receptor	protein-coding	0.003704	0.531365	
chunk0092_268_1	chr19	33274281	33274773	+	0	NA	Intergenic	Intergenic	28037	NM_001287424	1050	Hs.76171	NM_004364	ENSG00000245848	CEBPA	C/EBP-alpha|CEBP	CCAAT enhancer binding protein alpha	protein-coding	0.016260	0.547667	
chunk0193_364_1	chr8	79952338	79952622	+	0	NA	intron (NM_014018, intron 2 of 2)	intron (NM_014018, intron 2 of 2)	77791	NM_014018	28957	Hs.521124	NM_014018	ENSG00000147586	MRPS28	HSPC007|MRP-S28|MRP-S35|MRPS35	mitochondrial ribosomal protein S28	protein-coding	0.003521	0.368421	
chunk0003_206_1	chr1	35175024	35175394	+	0	NA	Intergenic	Intergenic	17933	NM_005066	6421	Hs.355934	NM_005066	ENSG00000116560	SFPQ	POMP100|PPP1R140|PSF	splicing factor proline and glutamine rich	protein-coding	0.016216	0.444744	
chunk0114_51_1	chr21	8455770	8456028	+	0	NA	Intergenic	(TCTC)n|Simple_repeat|Simple_repeat	14753	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.007752	0.482625	
chunk0171_191_1	chr6	125259316	125259774	+	0	NA	intron (NM_001003395, intron 6 of 6)	L3b|LINE|CR1	42591	NM_016063	51020	Hs.32826	NM_016063	ENSG00000111906	HDDC2	C6orf74|CGI-130|NS5ATP2|dJ167O5.2	HD domain containing 2	protein-coding	0.004367	0.385621	
chunk0196_201_1	chr8	106449125	106449657	+	0	NA	intron (NM_001198532, intron 1 of 15)	intron (NM_001198532, intron 1 of 15)	1467	NM_001198532	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.005639	0.365854	
chunk0191_143_1	chr8	48833143	48833838	+	0	NA	Intergenic	Intergenic	87950	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.002878	0.327586	
chunk0007_325_1	chr1	84544133	84544494	+	0	NA	intron (NM_001310156, intron 9 of 13)	intron (NM_001310156, intron 9 of 13)	30167	NM_004388	1486	Hs.513557	NM_004388	ENSG00000117151	CTBS	CTB	chitobiase	protein-coding	0.011080	0.370166	
chunk0198_11_1	chr9	300010	300480	+	0	NA	intron (NM_001190458, intron 3 of 45)	intron (NM_001190458, intron 3 of 45)	27197	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.004255	0.365180	
chunk0073_130_1	chr16	4922928	4923157	+	0	NA	intron (NM_002705, intron 1 of 21)	intron (NM_002705, intron 1 of 21)	14093	NM_002705	5493	Hs.192233	NM_002705	ENSG00000118898	PPL	-	periplakin	protein-coding	0.030568	0.578261	140(GGGTACAGGGTGTTCC,-,0.00),141(GGTACAGGGTGTTCCC,+,0.00)
chunk0122_80_1	chr3	29912571	29913374	+	0	NA	intron (NM_001003793, intron 10 of 14)	L4_C_Mam|LINE|RTE-X	21184	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.003736	0.359453	
chunk0087_341_1	chr18	40258312	40258961	+	0	NA	Intergenic	Intergenic	192350	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.003082	0.309231	
chunk0113_433_1	chr20	62337070	62337389	+	0	NA	intron (NM_005560, intron 16 of 79)	CpG	-4672	NR_039915	100616340		NR_039915	ENSG00000284074	MIR4758	-	microRNA 4758	ncRNA	0.081505	0.562500	
chunk0168_145_1	chr6	83083460	83084102	+	0	NA	intron (NM_001199942, intron 1 of 39)	intron (NM_001199942, intron 1 of 39)	16115	NM_015018	23033	Hs.520246	NM_015018	ENSG00000083097	DOP1A	DOP1|DOPEY1|KIAA1117|dJ202D23.2	DOP1 leucine zipper like protein A	protein-coding	0.006231	0.342146	
chunk0074_387_1	chr16	35244310	35244710	+	0	NA	Intergenic	Intergenic	-74119	NR_002837	606551	Hs.646441	NR_002837		UBE2MP1	-	ubiquitin conjugating enzyme E2 M pseudogene 1	pseudo	0.005000	0.339152	
chunk0185_162_1	chr7	127759127	127759407	+	0	NA	intron (NM_014390, intron 10 of 23)	L1MC4|LINE|L1	107119	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.007143	0.302491	106(GTAACAGAATGTTCTC,+,0.00)
chunk0175_112_1	chr7	3243357	3243556	+	0	NA	Intergenic	Intergenic	-57992	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005025	0.500000	
chunk0098_294_1	chr2	76007345	76007736	+	0	NA	Intergenic	L1M5|LINE|L1	-296555	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.002558	0.293367	
chunk0122_245_1	chr3	34386523	34386722	+	0	NA	Intergenic	Intergenic	588051	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.000000	0.370000	
chunk0104_244_1	chr2	177213079	177213286	+	0	NA	TTS (NR_049831)	TTS (NR_049831)	456	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.130435	0.759615	
chunk0160_409_1	chr5	163846648	163846943	+	0	NA	Intergenic	L1ME4b|LINE|L1	341267	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.003390	0.371622	
chunk0126_5_1	chr3	73441688	73441906	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-7801	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.013761	0.474886	111(GGAAACACAATGTACT,-,0.00),112(GAAACACAATGTACTC,+,0.00)
chunk0075_129_1	chr16	50120086	50120556	+	0	NA	Intergenic	Intergenic	-32597	NM_001040285	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.006383	0.435244	
chunk0203_448_1	chr9	91416887	91417223	+	0	NA	intron (NM_001290000, intron 1 of 1)	intron (NM_001290000, intron 1 of 1)	6807	NM_005384	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.000000	0.272997	
chunk0050_395_1	chr12	109169824	109170042	+	0	NA	intron (NM_001093, intron 3 of 51)	intron (NM_001093, intron 3 of 51)	30536	NM_001093	32	Hs.234898	NM_001093	ENSG00000076555	ACACB	ACC2|ACCB|HACC275	acetyl-CoA carboxylase beta	protein-coding	0.018349	0.465753	
chunk0031_233_1	chr10	126580764	126581415	+	0	NA	Intergenic	Intergenic	-59648	NM_001004298	118611	Hs.587663	NM_001004298	ENSG00000154493	C10orf90	FATS|bA422P15.2	chromosome 10 open reading frame 90	protein-coding	0.013825	0.470859	
chunk0063_197_1	chr14	80959637	80960054	+	0	NA	intron (NM_001018036, intron 1 of 8)	intron (NM_001018036, intron 1 of 8)	4320	NM_001018036	7253	Hs.160411	NM_000369	ENSG00000165409	TSHR	CHNG1|LGR3|hTSHR-I	thyroid stimulating hormone receptor	protein-coding	0.009592	0.377990	
chunk0020_215_1	chr1	235269364	235269741	+	0	NA	intron (NM_031371, intron 2 of 22)	intron (NM_031371, intron 2 of 22)	57935	NM_001206794	51742	Hs.575782	NM_016374	ENSG00000054267	ARID4B	BCAA|BRCAA1|RBBP1L1|RBP1L1|SAP180	AT-rich interaction domain 4B	protein-coding	0.007958	0.312169	179(CAGAACATTGTGTTTT,-,0.00),180(AGAACATTGTGTTTTA,+,0.00)
chunk0209_131_1	chrX	41049758	41050041	+	0	NA	Intergenic	Intergenic	-35736	NM_001039590	8239	Hs.77578	NM_004652	ENSG00000124486	USP9X	DFFRX|FAF|FAM|MRX99|MRXS99F	ubiquitin specific peptidase 9 X-linked	protein-coding	0.014134	0.457746	
chunk0029_15_1	chr10	95474264	95474789	+	0	NA	intron (NM_001290294, intron 2 of 31)	intron (NM_001290294, intron 2 of 31)	-33346	NM_001034956	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.011429	0.391635	286(GAGGACAGAATGTCCT,-,0.00),287(AGGACAGAATGTCCTG,+,0.00)
chunk0122_367_1	chr3	37621854	37622053	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	169631	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.000000	0.360000	
chunk0199_144_1	chr9	4119946	4120658	+	0	NA	intron (NM_001042413, intron 3 of 10)	intron (NM_001042413, intron 3 of 10)	31881	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.014045	0.405330	
chunk0045_159_1	chr12	46674203	46674402	+	0	NA	Intergenic	Intergenic	151695	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.000000	0.400000	
chunk0165_142_1	chr6	33599364	33599908	+	0	NA	Intergenic	Intergenic	-6298	NR_027908	401253	Hs.520075	NM_207497	ENSG00000197251	LINC00336	C6orf227|NCRNA00336	long intergenic non-protein coding RNA 336	ncRNA	0.018382	0.587156	
chunk0003_38_1	chr1	30502259	30502606	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-216340	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.008646	0.474138	
chunk0016_35_1	chr1	193097391	193097869	+	0	NA	exon (NM_197962, exon 3 of 4)	exon (NM_197962, exon 3 of 4)	7848	NM_197962	51022	Hs.458283	NM_016066	ENSG00000023572	GLRX2	CGI-133|GRX2	glutaredoxin 2	protein-coding	0.000000	0.356994	318(AAGAACAGGATGTTTT,-,0.00),319(AGAACAGGATGTTTTT,+,0.00)
chunk0025_191_1	chr10	53276849	53277448	+	0	NA	Intergenic	L1PB2|LINE|L1	-505448	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.003339	0.340000	
chunk0173_424_1	chr6	151052945	151053307	+	0	NA	intron (NM_001242767, intron 26 of 27)	intron (NM_001242767, intron 26 of 27)	175331	NR_125868	102723831	Hs.684425	NR_125868		LOC102723831	-	uncharacterized LOC102723831	ncRNA	0.008287	0.385675	
chunk0192_189_1	chr8	63290184	63290395	+	0	NA	Intergenic	Intergenic	121286	NM_001277814	253943	Hs.491861	NM_152758	ENSG00000185728	YTHDF3	-	YTH N6-methyladenosine RNA binding protein 3	protein-coding	0.004739	0.311321	
chunk0032_371_1	chr11	10976621	10977163	+	0	NA	Intergenic	Intergenic	118675	NR_034137	729013	Hs.726427	NR_034137	ENSG00000247271	ZBED5-AS1	-	ZBED5 antisense RNA 1	ncRNA	0.000000	0.430939	
chunk0007_46_1	chr1	77774057	77774566	+	0	NA	Intergenic	Intergenic	-5313	NM_001270384	374986	Hs.437755	NM_198549	ENSG00000180488	MIGA1	FAM73A	mitoguardin 1	protein-coding	0.031434	0.570588	
chunk0135_196_1	chr3	188257611	188257954	+	0	NA	intron (NM_005578, intron 2 of 10)	MIRb|SINE|MIR	32377	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.002915	0.386628	
chunk0072_254_1	chr15	96184221	96185230	+	0	NA	intron (NR_125738, intron 3 of 4)	intron (NR_125738, intron 3 of 4)	-141203	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.010902	0.386139	
chunk0011_262_1	chr1	150955278	150955763	+	0	NA	intron (NM_001145415, intron 14 of 21)	L2c|LINE|L2	19483	NM_181746	29956	Hs.744017	NM_013384	ENSG00000143418	CERS2	L3|LASS2|SP260|TMSG1	ceramide synthase 2	protein-coding	0.000000	0.390947	202(TTGCACATGCTGTGCC,-,0.00),203(TGCACATGCTGTGCCT,+,0.00)
chunk0089_64_1	chr18	58182984	58183593	+	0	NA	intron (NM_001144967, intron 2 of 30)	LTR32|LTR|ERVL	-12102	NM_001144970	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.006568	0.500000	
chunk0211_50_1	chrX	108719812	108720879	+	0	NA	Intergenic	Intergenic	16032	NM_003604	8471	Hs.407141	NM_003604	ENSG00000133124	IRS4	IRS-4|PY160	insulin receptor substrate 4	protein-coding	0.007498	0.351124	
chunk0045_336_1	chr12	51134455	51135016	+	0	NA	intron (NM_001173453, intron 1 of 13)	intron (NM_001173453, intron 1 of 13)	38408	NM_005653	7024	Hs.48849	NM_005653	ENSG00000135457	TFCP2	LBP1C|LSF|LSF1D|SEF|TFCP2C	transcription factor CP2	protein-coding	0.007130	0.409253	
chunk0033_143_1	chr11	15486841	15487427	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-156751	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.006826	0.345826	
chunk0174_422_1	chr6	165884891	165885150	+	0	NA	Intergenic	Intergenic	-102531	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.050193	0.557692	
chunk0177_135_1	chr7	22590441	22590909	+	0	NA	Intergenic	Intergenic	27338	NR_038393	100506178	Hs.668122	NR_038393	ENSG00000232759	LOC100506178	-	uncharacterized LOC100506178	ncRNA	0.004274	0.383795	
chunk0190_377_1	chr8	40014648	40015113	+	0	NA	intron (NM_194294, intron 10 of 10)	AluJo|SINE|Alu	79925	NM_194294	169355	Hs.676257	NM_194294	ENSG00000188676	IDO2	INDOL1	indoleamine 2,3-dioxygenase 2	protein-coding	0.010753	0.437768	
chunk0190_366_1	chr8	39854179	39854378	+	0	NA	Intergenic	L1M4|LINE|L1	-15989	NM_001278113	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.005025	0.270000	
chunk0036_213_1	chr11	63631344	63631806	+	0	NA	intron (NM_015459, intron 11 of 12)	intron (NM_015459, intron 11 of 12)	-17106	NM_001128203	11145	Hs.502775	NM_007069	ENSG00000176485	PLAAT3	AdPLA|H-REV107|H-REV107-1|HRASLS3|HREV107|HREV107-1|HREV107-3|HRSL3|PLA2G16|PLAAT-3	phospholipase A and acyltransferase 3	protein-coding	0.012987	0.393089	
chunk0185_407_1	chr7	134022504	134022927	+	0	NA	intron (NM_021807, intron 17 of 17)	intron (NM_021807, intron 17 of 17)	-104637	NM_144648	136332	Hs.149774	NM_144648	ENSG00000155530	LRGUK	CFAP246	leucine rich repeats and guanylate kinase domain containing	protein-coding	0.000000	0.391509	
chunk0185_173_1	chr7	127907218	127907754	+	0	NA	intron (NM_014390, intron 14 of 23)	intron (NM_014390, intron 14 of 23)	-90023	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.003731	0.405959	
chunk0082_88_1	chr17	52419057	52419795	+	0	NA	Intergenic	Intergenic	-259409	NM_001082534	56934	Hs.463466	NM_020178	ENSG00000154975	CA10	CA-RPX|CARPX|HUCEP-15	carbonic anhydrase 10	protein-coding	0.005420	0.423545	
chunk0204_250_1	chr9	98097825	98098093	+	0	NA	intron (NM_014788, intron 3 of 5)	intron (NM_014788, intron 3 of 5)	21394	NM_033219	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.011194	0.431227	
chunk0128_46_1	chr3	104677068	104677593	+	0	NA	Intergenic	L1PA15|LINE|L1	-689383	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.001905	0.366920	
chunk0082_27_1	chr17	50707325	50707524	+	0	NA	intron (NM_052855, intron 1 of 4)	CpG	485	NM_052855	91369	Hs.463426	NM_052855	ENSG00000154945	ANKRD40	-	ankyrin repeat domain 40	protein-coding	0.090452	0.720000	
chunk0103_320_1	chr2	167608129	167608379	+	0	NA	Intergenic	Intergenic	-210418	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.016000	0.314741	
chunk0156_88_1	chr5	104582321	104582676	+	0	NA	Intergenic	L1MC3|LINE|L1	-516976	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.005634	0.297753	
chunk0197_72_1	chr8	118897140	118897767	+	0	NA	Intergenic	Intergenic	54691	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.001595	0.350318	
chunk0049_31_1	chr12	89693564	89693998	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-15174	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.002304	0.356322	
chunk0074_419_1	chr16	46380636	46381154	+	0	NA	Intergenic	Intergenic	188202	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.029724	0.345339	
chunk0149_94_1	chr5	18547070	18547269	+	0	NA	Intergenic	LTR75_1|LTR|ERV1	-1159859	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.010050	0.385000	
chunk0025_319_1	chr10	57745909	57746143	+	0	NA	Intergenic	L1PA15|LINE|L1	-441467	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.008547	0.404255	
chunk0055_299_1	chr13	65942868	65943446	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	23272	NR_039692	100616302		NR_039692	ENSG00000263581	MIR548X2	-	microRNA 548x-2	ncRNA	0.001730	0.312608	271(AAGCACACATTGTGCT,-,0.00),272(AGCACACATTGTGCTT,+,0.00)
chunk0125_240_1	chr3	68538608	68539145	+	0	NA	exon (NM_001252216, exon 4 of 5)	exon (NM_001252216, exon 4 of 5)	393734	NM_001005527	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.011173	0.425651	39(GAGAACTTAGTGTGCT,-,0.00),40(AGAACTTAGTGTGCTT,+,0.00)
chunk0182_127_1	chr7	94477004	94477365	+	0	NA	Intergenic	Intergenic	-32674	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.011080	0.383978	
chunk0050_457_1	chr12	111031019	111032118	+	0	NA	Intergenic	L1MC4|LINE|L1	-2456	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.010009	0.353636	
chunk0162_383_1	chr6	7557738	7558573	+	0	NA	exon (NM_004415, exon 3 of 24)	exon (NM_004415, exon 3 of 24)	16518	NM_004415	1832	Hs.519873	NM_004415	ENSG00000096696	DSP	DCWHKTA|DP	desmoplakin	protein-coding	0.009581	0.413876	
chunk0116_8_1	chr21	32703153	32703741	+	0	NA	intron (NM_001160302, intron 2 of 31)	intron (NM_001160302, intron 2 of 31)	24492	NM_001160302	8867	Hs.473632	NM_003895	ENSG00000159082	SYNJ1	EIEE53|INPP5G|PARK20	synaptojanin 1	protein-coding	0.006803	0.325976	
chunk0031_364_1	chr10	130301420	130301639	+	0	NA	Intergenic	Intergenic	165154	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.054795	0.713636	192(AGGCTCAGCTTGTCCC,-,0.00)
chunk0178_178_1	chr7	34165988	34166248	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	261207	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.000000	0.409962	
chunk0004_83_1	chr1	43716094	43716474	+	0	NA	intron (NR_125986, intron 3 of 3)	Charlie7|DNA|hAT-Charlie	8751	NM_001270462	6487	Hs.597915	NM_006279	ENSG00000126091	ST3GAL3	EIEE15|MRT12|SIAT6|ST3GALII|ST3Gal III|ST3GalIII|ST3N	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding	0.010526	0.359580	
chunk0144_452_1	chr4	142035018	142035217	+	0	NA	intron (NM_001101669, intron 25 of 25)	intron (NM_001101669, intron 25 of 25)	398521	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.015075	0.550000	
chunk0056_127_1	chr13	83149340	83149840	+	0	NA	Intergenic	Intergenic	732803	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002000	0.345309	
chunk0091_462_1	chr19	18279605	18280312	+	0	NA	3' UTR (NM_005354, exon 1 of 1)	3' UTR (NM_005354, exon 1 of 1)	1698	NM_001286968	3727	Hs.2780	NM_005354	ENSG00000130522	JUND	AP-1	JunD proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.070721	0.588983	
chunk0037_427_1	chr11	80159556	80160397	+	0	NA	Intergenic	Intergenic	602827	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003567	0.345606	
chunk0106_112_1	chr2	197588215	197588823	+	0	NA	intron (NM_144629, intron 8 of 8)	L1ME4a|LINE|L1	72221	NM_001204094	25843	Hs.633165	NM_015387	ENSG00000115540	MOB4	2C4D|CGI-95|MOB1|MOB3|MOBKL3|PHOCN|PREI3	MOB family member 4, phocein	protein-coding	0.006579	0.395731	
chunk0117_284_1	chr22	24300369	24300568	+	0	NA	intron (NM_015330, intron 2 of 16)	L1PA8A|LINE|L1	29651	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.015075	0.405000	
chunk0163_256_1	chr6	12952267	12952778	+	0	NA	intron (NM_030948, intron 4 of 14)	L1MC1|LINE|L1	235717	NM_030948	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.007828	0.408203	
chunk0085_443_1	chr18	11114679	11115142	+	0	NA	intron (NM_022068, intron 1 of 51)	intron (NM_022068, intron 1 of 51)	33852	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.004320	0.385776	
chunk0026_132_1	chr10	62099374	62099746	+	0	NA	Intergenic	Intergenic	50349	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.008065	0.375335	173(AAGAACTAGGTGTTCT,-,0.00),174(AGAACTAGGTGTTCTG,+,0.00)
chunk0146_126_1	chr4	159119624	159119823	+	0	NA	Intergenic	Intergenic	-9082	NR_039963	100616303		NR_039963	ENSG00000283379	MIR3688-2	mir-3688-2	microRNA 3688-2	ncRNA	0.010050	0.295000	
chunk0124_81_1	chr3	53252217	53252804	+	0	NA	intron (NR_047580, intron 1 of 13)	intron (NR_047580, intron 1 of 13)	3604	NM_001135055	7086	Hs.89643	NM_001064	ENSG00000163931	TKT	HEL-S-48|HEL107|SDDHD|TK|TKT1	transketolase	protein-coding	0.013629	0.426871	
chunk0035_257_1	chr11	46449125	46449324	+	0	NA	intron (NM_001300731, intron 10 of 16)	L1MC1|LINE|L1	-2583	NR_036118	100422825		NR_036118	ENSG00000283497	MIR3160-2	mir-3160-2	microRNA 3160-2	ncRNA	0.005025	0.375000	
chunk0116_401_1	chr21	42516125	42516437	+	0	NA	intron (NM_018964, intron 2 of 20)	intron (NM_018964, intron 2 of 20)	16649	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.012821	0.514377	
chunk0001_5_1	chr1	633893	634165	+	0	NA	Intergenic	Intergenic	-1616	NR_106781									0.018382	0.446886	
chunk0176_156_1	chr7	13323813	13324095	+	0	NA	Intergenic	Intergenic	636668	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.003546	0.420495	
chunk0164_179_1	chr6	21987463	21987662	+	0	NA	intron (NR_015410, intron 6 of 11)	intron (NR_015410, intron 6 of 11)	159631	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.035176	0.450000	
chunk0044_1_1	chr12	26795824	26796408	+	0	NA	intron (NM_002223, intron 1 of 56)	MER91A|DNA|hAT-Tip100	37082	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.013699	0.410256	291(GAGAACAGCCTGTGCA,-,0.00),292(AGAACAGCCTGTGCAG,+,0.00)
chunk0071_240_1	chr15	85293293	85293844	+	0	NA	Intergenic	L2c|LINE|L2	53158	NM_001310153	100133220	Hs.454625	NM_001310153		GOLGA6L3	-	golgin A6 family like 3	protein-coding	0.014519	0.423913	263(AAGGGCACTCAGTCCC,-,0.00)
chunk0078_448_1	chr16	89803065	89803264	+	0	NA	intron (NM_001018112, intron 8 of 10)	L1MA5A|LINE|L1	13493	NM_001018112	2175	Hs.744083	NM_000135	ENSG00000187741	FANCA	FA|FA-H|FA1|FAA|FACA|FAH|FANCH	FA complementation group A	protein-coding	0.035176	0.430000	
chunk0020_278_1	chr1	236515021	236515801	+	0	NA	Intergenic	Intergenic	-2803	NM_201545	3964	Hs.4082	NM_006499	ENSG00000116977	LGALS8	Gal-8|PCTA-1|PCTA1|Po66-CBP	galectin 8	protein-coding	0.006410	0.391805	
chunk0161_349_1	chr5	174503546	174503820	+	0	NA	intron (NR_125806, intron 2 of 5)	intron (NR_125806, intron 2 of 5)	167329	NR_125806	101928176	Hs.436014	NR_125806	ENSG00000249306	LINC01411	-	long intergenic non-protein coding RNA 1411	ncRNA	0.018248	0.498182	
chunk0139_84_1	chr4	49490711	49491010	+	0	NA	Intergenic	L1MA5|LINE|L1	504218	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.000000	0.293333	
chunk0193_233_1	chr8	76649899	76650316	+	0	NA	intron (NR_024360, intron 2 of 3)	Tigger3a|DNA|TcMar-Tigger	-31173	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.007194	0.354067	
chunk0132_68_1	chr3	155187929	155188218	+	0	NA	Intergenic	Intergenic	-52872	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.003460	0.351724	
chunk0173_78_1	chr6	142695950	142696981	+	0	NA	Intergenic	Intergenic	-58576	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.011639	0.481589	
chunk0008_72_1	chr1	89852500	89852881	+	0	NA	intron (NM_001134479, intron 2 of 2)	L2b|LINE|L2	30769	NM_018103	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.007874	0.434555	
chunk0038_9_1	chr11	80814008	80814572	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-51487	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.007092	0.334513	
chunk0095_191_1	chr2	18009182	18009647	+	0	NA	Intergenic	L1ME3A|LINE|L1	130757	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.006452	0.390558	
chunk0179_67_1	chr7	43939122	43939450	+	0	NA	intron (NM_015983, intron 2 of 6)	intron (NM_015983, intron 2 of 6)	12850	NM_015983	51619	Hs.19196	NM_015983	ENSG00000078967	UBE2D4	HBUCE1	ubiquitin conjugating enzyme E2 D4 (putative)	protein-coding	0.006098	0.601824	222(CAGCACTGCCTGTTCC,-,0.00),223(AGCACTGCCTGTTCCA,+,0.00)
chunk0110_148_1	chr20	13701302	13702007	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-62718	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.001418	0.381020	
chunk0053_16_1	chr13	26459870	26460353	+	0	NA	Intergenic	Intergenic	-97592	NM_006646	10810	Hs.618732	NM_006646	ENSG00000132970	WASF3	Brush-1|SCAR3|WAVE3	WASP family member 3	protein-coding	0.012422	0.413223	
chunk0192_367_1	chr8	68254393	68254847	+	0	NA	Intergenic	L2b|LINE|L2	-76102	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.008811	0.450549	
chunk0115_440_1	chr21	32075492	32076528	+	0	NA	Intergenic	Intergenic	10285	NR_038033	100551499	Hs.224449	NR_038033		LINC00159	C21orf44|NCRNA00159	long intergenic non-protein coding RNA 159	ncRNA	0.013514	0.473481	
chunk0129_144_1	chr3	120473195	120473577	+	0	NA	Intergenic	Intergenic	-22315	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.005236	0.459530	
chunk0099_15_1	chr2	82873598	82873975	+	0	NA	Intergenic	L1PBa|LINE|L1	16983	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.000000	0.346561	207(TTGGACAGAATGTTCT,-,0.00),208(TGGACAGAATGTTCTG,+,0.00)
chunk0192_376_1	chr8	68468143	68468378	+	0	NA	intron (NM_052958, intron 3 of 13)	HAL1|LINE|L1	-136769	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.004255	0.309322	
chunk0018_126_1	chr1	218519755	218519954	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	77228	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.005025	0.330000	
chunk0009_408_1	chr1	110415100	110415402	+	0	NA	intron (NR_102697, intron 2 of 2)	intron (NR_102697, intron 2 of 2)	-7327	NM_006402	10542	Hs.439815	NM_006402	ENSG00000134248	LAMTOR5	HBXIP|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding	0.003311	0.455446	
chunk0172_24_1	chr6	132960018	132960468	+	0	NA	Intergenic	Intergenic	-45915	NR_039664									0.002222	0.368071	
chunk0036_38_1	chr11	58833444	58833936	+	0	NA	TTS (NM_145016)	TTS (NM_145016)	10834	NM_145016	219970	Hs.254271	NM_145016	ENSG00000156689	GLYATL2	BXMAS2-10|GATF-B	glycine-N-acyltransferase like 2	protein-coding	0.004065	0.363083	
chunk0189_298_1	chr8	25990526	25991204	+	0	NA	intron (NM_022659, intron 6 of 15)	intron (NM_022659, intron 6 of 15)	54259	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.008850	0.399116	
chunk0068_168_1	chr15	54107526	54107913	+	0	NA	intron (NM_001080534, intron 1 of 30)	L3b|LINE|CR1	94815	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.002584	0.342784	
chunk0021_107_1	chr10	3249129	3249817	+	0	NA	Intergenic	Intergenic	-69222	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.008721	0.339623	
chunk0122_189_1	chr3	32730674	32731055	+	0	NA	intron (NM_001256741, intron 10 of 17)	intron (NM_001256741, intron 10 of 17)	35323	NM_001256742	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.010499	0.342932	75(GAGGACATTTTGTCCT,-,0.00),76(AGGACATTTTGTCCTG,+,0.00)
chunk0070_21_1	chr15	69057117	69057368	+	0	NA	TTS (NR_033671)	TTS (NR_033671)	-23608	NR_026949	283673	Hs.177927	NM_173610	ENSG00000212766	EWSAT1	LINC00277|NCRNA00277|TMEM84	Ewing sarcoma associated transcript 1	ncRNA	0.000000	0.384921	
chunk0049_125_1	chr12	91554300	91554661	+	0	NA	Intergenic	AluJo|SINE|Alu	-371356	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.000000	0.403315	
chunk0134_114_1	chr3	177084531	177085247	+	0	NA	intron (NM_024665, intron 2 of 15)	L1MEb|LINE|L1	112371	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.006983	0.405858	
chunk0180_126_1	chr7	55668702	55668901	+	0	NA	Intergenic	L1MA5|LINE|L1	19231	NR_027340	360132	Hs.446691	NM_182827	ENSG00000176826	FKBP9P1	FKBP9L	FKBP prolyl isomerase 9 pseudogene 1	pseudo	0.005025	0.435000	75(AAGTACTGCATGTTCT,-,0.00),76(AGTACTGCATGTTCTC,+,0.00)
chunk0079_155_1	chr17	13297093	13297698	+	0	NA	Intergenic	Intergenic	246251	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.008264	0.399340	
chunk0118_26_1	chr22	26554211	26554539	+	0	NA	TTS (NR_031615)	TTS (NR_031615)	948	NR_031615	100313914		NR_031615	ENSG00000221760	MIR548J	MIRN548J|hsa-mir-548j	microRNA 548j	ncRNA	0.009146	0.598784	
chunk0058_314_1	chr14	27438678	27439386	+	0	NA	Intergenic	Intergenic	-173556	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.004237	0.318759	
chunk0088_148_1	chr18	46250351	46251270	+	0	NA	intron (NM_145055, intron 3 of 4)	intron (NM_145055, intron 3 of 4)	76788	NM_001008239	147339	Hs.116486	NM_145055	ENSG00000152242	C18orf25	ARKL1|Ark2N|RNF111L1	chromosome 18 open reading frame 25	protein-coding	0.004353	0.401087	
chunk0090_215_1	chr18	73484821	73485069	+	0	NA	Intergenic	Intergenic	160004	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.004032	0.333333	
chunk0162_21_1	chr6	837475	837770	+	0	NA	Intergenic	MIRc|SINE|MIR	-30876	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.013559	0.398649	
chunk0008_13_1	chr1	87385408	87385643	+	0	NA	Intergenic	Intergenic	-13870	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.012766	0.483051	129(TTGAGCAGTGTGTTCT,-,0.00),130(TGAGCAGTGTGTTCTC,+,0.00)
chunk0060_24_1	chr14	39781169	39781388	+	0	NA	Intergenic	L1PBa1|LINE|L1	-348778	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.018265	0.577273	
chunk0043_44_1	chr12	13443500	13444267	+	0	NA	Intergenic	L1ME2z|LINE|L1	-67138	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.001304	0.372396	
chunk0077_68_1	chr16	76944642	76944928	+	0	NA	Intergenic	Intergenic	75849	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.003497	0.386760	
chunk0153_226_1	chr5	72117237	72117696	+	0	NA	intron (NM_005909, intron 2 of 6)	intron (NM_005909, intron 2 of 6)	10175	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.004357	0.354348	
chunk0196_5_1	chr8	101407085	101407929	+	0	NA	Intergenic	Intergenic	38614	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.007109	0.369231	
chunk0004_25_1	chr1	42335222	42335509	+	0	NA	promoter-TSS (NM_001198852)	promoter-TSS (NM_001198852)	-133	NM_014947	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.135889	0.718750	
chunk0074_169_1	chr16	23485303	23485967	+	0	NA	intron (NM_015044, intron 8 of 16)	L1ME1|LINE|L1	24859	NM_015044	23062	Hs.460336	NM_015044	ENSG00000103365	GGA2	VEAR	golgi associated, gamma adaptin ear containing, ARF binding protein 2	protein-coding	0.013554	0.422556	
chunk0121_143_1	chr3	18818083	18818662	+	0	NA	Intergenic	L1MB8|LINE|L1	-330153	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.003454	0.384483	
chunk0041_284_1	chr11	129386700	129386899	+	0	NA	intron (NM_003658, intron 1 of 3)	intron (NM_003658, intron 1 of 3)	10813	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.005025	0.405000	
chunk0032_135_1	chr11	4588973	4589676	+	0	NA	Intergenic	Intergenic	2533	NM_001005170	143502	Hs.553607	NM_001005170	ENSG00000226288	OR52I2	OR11-12|OR52I1	olfactory receptor family 52 subfamily I member 2	protein-coding	0.004267	0.433239	
chunk0084_119_1	chr17	76003964	76004316	+	0	NA	intron (NR_037709, intron 9 of 9)	intron (NR_037709, intron 9 of 9)	3234	NM_001258	1018	Hs.706766	NM_001258	ENSG00000250506	CDK3	-	cyclin dependent kinase 3	protein-coding	0.017045	0.566572	138(CAGAACAGGCTGTTCC,-,0.00),139(AGAACAGGCTGTTCCC,+,0.00)
chunk0175_107_1	chr7	3028035	3028437	+	0	NA	intron (NM_032415, intron 1 of 24)	intron (NM_032415, intron 1 of 24)	15709	NM_032415	84433	Hs.648101	NM_032415	ENSG00000198286	CARD11	BENTA|BIMP3|CARMA1|IMD11|IMD11A|PPBL	caspase recruitment domain family member 11	protein-coding	0.022388	0.531017	130(TGGCACTGGCTGTTCC,-,0.00),131(GGCACTGGCTGTTCCG,+,0.00)
chunk0060_427_1	chr14	53942892	53943209	+	0	NA	Intergenic	Intergenic	5434	NR_049843	100847076		NR_049843	ENSG00000266431	MIR5580	-	microRNA 5580	ncRNA	0.006309	0.399371	
chunk0184_122_1	chr7	114372414	114373070	+	0	NA	intron (NR_033766, intron 2 of 19)	(GTTTT)n|Simple_repeat|Simple_repeat	-42255	NM_001172766	93986	Hs.282787	NM_014491	ENSG00000128573	FOXP2	CAGH44|SPCH1|TNRC10	forkhead box P2	protein-coding	0.012195	0.351598	
chunk0187_435_1	chr7	158795654	158795853	+	0	NA	intron (NM_020728, intron 3 of 21)	intron (NM_020728, intron 3 of 21)	33875	NM_020728	57488	Hs.490795	NM_020728	ENSG00000117868	ESYT2	CHR2SYT|E-Syt2|FAM62B	extended synaptotagmin 2	protein-coding	0.025126	0.465000	
chunk0043_227_1	chr12	19981821	19982340	+	0	NA	Intergenic	Intergenic	-32605	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.003854	0.361538	
chunk0093_62_1	chr19	40433313	40433749	+	0	NA	Intergenic	L2a|LINE|L2	-7506	NM_013376	29950	Hs.269898	NM_013376	ENSG00000197019	SERTAD1	SEI1|TRIP-Br1|TRIPBR1	SERTA domain containing 1	protein-coding	0.032110	0.501144	
chunk0124_373_1	chr3	59313423	59313938	+	0	NA	Intergenic	Intergenic	-263691	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.005825	0.501938	205(TGGAACATGGAGTTCC,-,0.00),206(GGAACATGGAGTTCCT,+,0.00)
chunk0057_263_1	chr13	105706732	105707397	+	0	NA	intron (NR_120418, intron 1 of 3)	intron (NR_120418, intron 1 of 3)	234	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.007519	0.457958	
chunk0209_375_1	chrX	54090771	54091580	+	0	NA	intron (NM_017848, intron 11 of 15)	intron (NM_017848, intron 11 of 15)	-46039	NM_001184896	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.007417	0.409877	
chunk0036_206_1	chr11	63504970	63505237	+	0	NA	promoter-TSS (NM_033101)	promoter-TSS (NM_033101)	-949	NM_001142536	85329	Hs.502774	NM_033101	ENSG00000133317	LGALS12	GAL12|GRIP1	galectin 12	protein-coding	0.003745	0.526119	
chunk0034_29_1	chr11	26420344	26420732	+	0	NA	intron (NM_031418, intron 1 of 26)	LTR33|LTR|ERVL	-53364	NM_001313727	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.002577	0.434447	
chunk0170_194_1	chr6	112202315	112202650	+	0	NA	intron (NM_001105207, intron 4 of 38)	intron (NM_001105207, intron 4 of 38)	-34114	NR_121193	101927640	Hs.510007	NR_121193		LOC101927640	-	uncharacterized LOC101927640	ncRNA	0.005970	0.357143	
chunk0176_398_1	chr7	18891209	18891461	+	0	NA	intron (NM_178425, intron 21 of 24)	intron (NM_178425, intron 21 of 24)	226337	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.003968	0.407115	104(AAGCACATGAAGTGCC,-,0.00),105(AGCACATGAAGTGCCT,+,0.00)
chunk0091_112_1	chr19	6020591	6021406	+	0	NA	TTS (NR_046376)	TTS (NR_046376)	42595	NR_046376	100128568	Hs.624525	NR_046376	ENSG00000266983	LOC100128568	-	uncharacterized LOC100128568	ncRNA	0.030675	0.522059	
chunk0106_462_1	chr2	209439627	209440261	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	15897	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.003155	0.300787	
chunk0181_270_1	chr7	86199582	86200311	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-443968	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.006859	0.360274	
chunk0059_34_1	chr14	29896300	29896879	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	31104	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.008636	0.368966	
chunk0013_39_1	chr1	166876003	166876570	+	0	NA	5' UTR (NM_053053, exon 1 of 8)	5' UTR (NM_053053, exon 1 of 8)	131	NM_053053	117143	Hs.435967	NM_053053	ENSG00000152382	TADA1	ADA1|HFI1|STAF42|TADA1L|hADA1	transcriptional adaptor 1	protein-coding	0.104056	0.669014	
chunk0117_352_1	chr21	44348033	44348637	+	0	NA	Intergenic	Intergenic	-5266	NR_038257	7226	Hs.369759	NM_003307	ENSG00000142185	TRPM2	EREG1|KNP3|LTRPC2|LTrpC-2|NUDT9H|NUDT9L1|TRPC7	transient receptor potential cation channel subfamily M member 2	protein-coding	0.044702	0.591736	202(AGGACCAGAGTGTGCC,-,0.00),203(GGACCAGAGTGTGCCA,+,0.00),316(AGAAACACTTTGTGCC,-,0.00)
chunk0135_78_1	chr3	186097634	186098265	+	0	NA	intron (NM_004454, intron 5 of 12)	intron (NM_004454, intron 5 of 12)	11163	NM_004454	2119	Hs.43697	NM_004454	ENSG00000244405	ETV5	ERM	ETS variant 5	protein-coding	0.023772	0.512658	
chunk0123_364_1	chr3	48297049	48297248	+	0	NA	intron (NM_001308434, intron 1 of 4)	intron (NM_001308434, intron 1 of 4)	4263	NM_005793	10201	Hs.465558	NM_005793	ENSG00000172113	NME6	IPIA-ALPHA|NDK 6|NM23-H6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding	0.005025	0.450000	
chunk0022_268_1	chr10	14954525	14955032	+	0	NA	promoter-TSS (NR_110297)	promoter-TSS (NR_110297)	-346	NR_110297	64421	Hs.655932	NM_022487	ENSG00000152457	DCLRE1C	A-SCID|DCLREC1C|RS-SCID|SCIDA|SNM1C	DNA cross-link repair 1C	protein-coding	0.017751	0.381890	
chunk0191_129_1	chr8	48576379	48577456	+	0	NA	intron (NR_105002, intron 2 of 3)	intron (NR_105002, intron 2 of 3)	25350	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.005571	0.434137	231(AGGAACTTGCTGTCCT,-,0.00),232(GGAACTTGCTGTCCTT,+,0.00),926(CAGGACAAAGAGTGCT,-,0.00),927(AGGACAAAGAGTGCTT,+,0.00)
chunk0172_427_1	chr6	140716998	140717364	+	0	NA	Intergenic	L1M4b|LINE|L1	33367	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.002732	0.346049	
chunk0159_91_1	chr5	137894502	137894988	+	0	NA	intron (NM_001258448, intron 4 of 14)	intron (NM_001258448, intron 4 of 14)	5309	NM_001300921	27039	Hs.716884	NM_014386	ENSG00000078795	PKD2L2	TRPP5	polycystin 2 like 2, transient receptor potential cation channel	protein-coding	0.000000	0.367556	
chunk0019_338_1	chr1	229280572	229280849	+	0	NA	intron (NM_001271998, intron 1 of 5)	L1MD1|LINE|L1	9648	NM_004578	5867	Hs.296169	NM_004578	ENSG00000168118	RAB4A	HRES-1|HRES-1/RAB4|HRES1|RAB4	RAB4A, member RAS oncogene family	protein-coding	0.007220	0.370504	
chunk0047_245_1	chr12	72278845	72279402	+	0	NA	intron (NM_013381, intron 1 of 18)	intron (NM_013381, intron 1 of 18)	-5614	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.007181	0.388889	
chunk0071_454_1	chr15	90231594	90232036	+	0	NA	intron (NM_001277764, intron 3 of 6)	intron (NM_001277764, intron 3 of 6)	2232	NM_001277764	10519	Hs.715556	NM_006384	ENSG00000185043	CIB1	CIB|CIBP|KIP1|PRKDCIP|SIP2-28	calcium and integrin binding 1	protein-coding	0.015837	0.487585	27(GTGAACAGTCAGTGCT,-,0.00),28(TGAACAGTCAGTGCTT,+,0.00)
chunk0012_462_1	chr1	165494782	165495235	+	0	NA	intron (NR_026744, intron 5 of 6)	L2b|LINE|L2	-49233	NM_001005214	440699	Hs.664975	NM_001005214	ENSG00000162763	LRRC52	-	leucine rich repeat containing 52	protein-coding	0.008830	0.436123	
chunk0118_385_1	chr22	37019457	37019771	+	0	NA	promoter-TSS (NM_001130517)	promoter-TSS (NM_001130517)	-28	NM_001013436	4357	Hs.248267	NM_021126	ENSG00000128309	MPST	MST|TST2|TUM1	mercaptopyruvate sulfurtransferase	protein-coding	0.156051	0.815873	
chunk0149_386_1	chr5	28670738	28671255	+	0	NA	Intergenic	LTR38|LTR|ERV1	-255874	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.003868	0.428571	
chunk0026_138_1	chr10	62175637	62176123	+	0	NA	Intergenic	L1MEc|LINE|L1	92983	NM_001282941	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.004115	0.299795	223(AAGAACTGGATGTTCC,-,0.00),224(AGAACTGGATGTTCCT,+,0.00)
chunk0168_429_1	chr6	95545127	95545669	+	0	NA	Intergenic	Intergenic	32053	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.005535	0.373849	273(CAGGACAATTTGTTCT,-,0.00),274(AGGACAATTTGTTCTT,+,0.00)
chunk0037_90_1	chr11	71928854	71929053	+	0	NA	promoter-TSS (NR_029192)	promoter-TSS (NR_029192)	231	NM_001300926	55298	Hs.368554	NM_018320	ENSG00000137522	RNF121	-	ring finger protein 121	protein-coding	0.065327	0.635000	
chunk0195_17_1	chr8	93068184	93068766	+	0	NA	Intergenic	Intergenic	38724	NR_107051	102467005		NR_107051	ENSG00000277063	MIR8084	hsa-mir-8084	microRNA 8084	ncRNA	0.005155	0.331046	
chunk0127_224_1	chr3	96685660	96685935	+	0	NA	Intergenic	L1MA1|LINE|L1	-128784	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.528986	
chunk0068_412_1	chr15	59120154	59120542	+	0	NA	intron (NM_004701, intron 7 of 8)	AluJr|SINE|Alu	15263	NM_004701	9133	Hs.194698	NM_004701	ENSG00000157456	CCNB2	HsT17299	cyclin B2	protein-coding	0.000000	0.447301	121(TAGAACAATTTGTGCC,-,0.00),122(AGAACAATTTGTGCCA,+,0.00)
chunk0071_328_1	chr15	87104563	87104851	+	0	NA	Intergenic	L1MA4A|LINE|L1	-472222	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.000000	0.529412	
chunk0075_65_1	chr16	47897257	47897917	+	0	NA	intron (NR_110650, intron 4 of 5)	L1PA6|LINE|L1	-10457	NR_110649	100507534	Hs.407601	NR_110649	ENSG00000261325	LINC02192	-	long intergenic non-protein coding RNA 2192	ncRNA	0.009091	0.497731	
chunk0161_300_1	chr5	173252066	173252328	+	0	NA	Intergenic	Intergenic	-16885	NM_001166175	1482	Hs.54473	NM_004387	ENSG00000183072	NKX2-5	CHNG5|CSX|CSX1|HLHS2|NKX2.5|NKX2E|NKX4-1|VSD3	NK2 homeobox 5	protein-coding	0.011450	0.532319	
chunk0194_368_1	chr8	89961357	89961853	+	0	NA	intron (NM_001024688, intron 9 of 16)	intron (NM_001024688, intron 9 of 16)	23066	NM_002485	4683	Hs.492208	NM_002485	ENSG00000104320	NBN	AT-V1|AT-V2|ATV|NBS|NBS1|P95	nibrin	protein-coding	0.010081	0.392354	236(TGGAACATGATGTTCA,-,0.00),237(GGAACATGATGTTCAA,+,0.00)
chunk0095_227_1	chr2	18889618	18889818	+	0	NA	Intergenic	Intergenic	-300138	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.005000	0.383085	
chunk0045_62_1	chr12	45464698	45464897	+	0	NA	Intergenic	Intergenic	172114	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.015075	0.485000	
chunk0091_331_1	chr19	13988974	13989242	+	0	NA	intron (NM_002918, intron 2 of 20)	L2a|LINE|L2	17214	NM_002918	5989	Hs.655215	NM_002918	ENSG00000132005	RFX1	EFC|RFX	regulatory factor X1	protein-coding	0.022388	0.576208	
chunk0014_117_1	chr1	177089836	177090083	+	0	NA	intron (NM_004319, intron 1 of 22)	intron (NM_004319, intron 1 of 22)	-60514	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.008097	0.391129	
chunk0020_272_1	chr1	236389199	236389830	+	0	NA	Intergenic	Intergenic	-4866	NM_145861	128178	Hs.352224	NM_080738	ENSG00000186197	EDARADD	ECTD11A|ECTD11B|ED3|EDA3	EDAR associated death domain	protein-coding	0.004754	0.431962	
chunk0041_358_1	chr11	130899039	130899424	+	0	NA	intron (NM_001301089, intron 8 of 10)	intron (NM_001301089, intron 8 of 10)	17256	NM_014758	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.015584	0.417098	105(TTGAACAGCATGTGCA,-,0.00),106(TGAACAGCATGTGCAT,+,0.00)
chunk0107_79_1	chr2	212856973	212857565	+	0	NA	Intergenic	L2a|LINE|L2	61938	NR_131942	102725079	Hs.176124	NR_131941	ENSG00000234308	LINC01878	-	long intergenic non-protein coding RNA 1878	ncRNA	0.003378	0.386172	
chunk0193_390_1	chr8	80381013	80381598	+	0	NA	Intergenic	Intergenic	-104314	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.006838	0.370307	
chunk0078_442_1	chr16	89581926	89582355	+	0	NA	intron (NM_014427, intron 3 of 16)	intron (NM_014427, intron 3 of 16)	6372	NM_014427	27132	Hs.461775	NM_014427	ENSG00000178773	CPNE7	-	copine 7	protein-coding	0.020979	0.534884	
chunk0080_385_1	chr17	34376347	34377013	+	0	NA	Intergenic	L1ME3F|LINE|L1	-13447	NM_002981	6346	Hs.72918	NM_002981	ENSG00000108702	CCL1	I-309|P500|SCYA1|SISe|TCA3	C-C motif chemokine ligand 1	protein-coding	0.007508	0.337331	
chunk0209_307_1	chrX	49610689	49611067	+	0	NA	Intergenic	MER77|LTR|ERVL	11865	NR_102272	2543	Hs.278606	NM_001468	ENSG00000205777	GAGE1	CT4.1|CT4.4|GAGE-1|GAGE-4|GAGE4	G antigen 1	protein-coding	0.013228	0.424802	
chunk0047_376_1	chr12	75175890	75176481	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	33563	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.001692	0.390203	253(TGAAACACTGTGTGCC,-,0.00),254(GAAACACTGTGTGCCT,+,0.00)
chunk0041_424_1	chr11	134330715	134331193	+	0	NA	promoter-TSS (NM_138342)	promoter-TSS (NM_138342)	-920	NM_138342	89944	Hs.436178	NM_138342	ENSG00000149328	GLB1L2	MST114|MSTP114	galactosidase beta 1 like 2	protein-coding	0.037657	0.473904	
chunk0187_133_1	chr7	149228765	149229250	+	0	NA	Intergenic	Intergenic	-10644	NM_012256	7988	Hs.490510	NM_012256	ENSG00000170260	ZNF212	C2H2-150|ZNF182|ZNFC150	zinc finger protein 212	protein-coding	0.004124	0.458848	233(AGGTACAAGGAGTGCT,-,0.00),234(GGTACAAGGAGTGCTC,+,0.00)
chunk0053_323_1	chr13	34317427	34317947	+	0	NA	Intergenic	L2a|LINE|L2	322998	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.015385	0.399232	121(GGGCACACCAAGTCCA,-,0.00),122(GGCACACCAAGTCCAT,+,0.00)
chunk0175_175_1	chr7	4909777	4910265	+	0	NA	exon (NM_001100600, exon 6 of 7)	exon (NM_001100600, exon 6 of 7)	-26317	NM_018059	55698	Hs.667336	NM_018059	ENSG00000157927	RADIL	RASIP2	Rap associating with DIL domain	protein-coding	0.020492	0.552147	
chunk0174_354_1	chr6	164415155	164415834	+	0	NA	Intergenic	Intergenic	406569	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.002946	0.330882	
chunk0065_415_1	chr14	105823725	105824069	+	0	NA	Intergenic	MER101-int|LTR|ERV1	33675	NR_130468	100616374		NR_130468	ENSG00000265612	MIR4539	-	microRNA 4539	ncRNA	0.008721	0.281159	
chunk0039_315_1	chr11	103413361	103413964	+	0	NA	intron (NM_001377, intron 84 of 88)	intron (NM_001377, intron 84 of 88)	304231	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.000000	0.309603	
chunk0019_461_1	chr1	231487817	231488195	+	0	NA	Intergenic	L1MC2|LINE|L1	-11481	NR_033826	645339	Hs.382049	NR_033826		SNRPD2P2	-	small nuclear ribonucleoprotein D2 pseudogene 2	pseudo	0.007937	0.369393	35(AAGAACAGAGAGTTCC,-,0.00),36(AGAACAGAGAGTTCCC,+,0.00)
chunk0149_20_1	chr5	16123809	16124147	+	0	NA	intron (NM_001102562, intron 2 of 3)	intron (NM_001102562, intron 2 of 3)	55810	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.008876	0.377581	
chunk0126_350_1	chr3	82815628	82815855	+	0	NA	Intergenic	MER52D|LTR|ERV1	-1053942	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.578947	
chunk0125_209_1	chr3	67412821	67413195	+	0	NA	intron (NM_001177599, intron 9 of 10)	intron (NM_001177599, intron 9 of 10)	187544	NR_036234	100422941		NR_036234	ENSG00000283298	MIR4272	-	microRNA 4272	ncRNA	0.002674	0.384000	
chunk0134_271_1	chr3	179556299	179556746	+	0	NA	Intergenic	L1ME4b|LINE|L1	-6358	NM_004301	86	Hs.435326	NM_004301	ENSG00000136518	ACTL6A	ACTL6|ARPN-BETA|Arp4|BAF53A|INO80K	actin like 6A	protein-coding	0.004474	0.332589	
chunk0095_44_1	chr2	13519371	13519961	+	0	NA	Intergenic	LTR23|LTR|ERV1	-512653	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.006780	0.384095	
chunk0125_454_1	chr3	73036510	73036772	+	0	NA	intron (NM_174907, intron 2 of 8)	intron (NM_174907, intron 2 of 8)	-25018	NM_018029	55096	Hs.658858	NM_018029	ENSG00000255423	EBLN2	EBLN-2	endogenous Bornavirus like nucleoprotein 2	protein-coding	0.011450	0.296578	131(AAGTACAAATTGTTCT,-,0.00),132(AGTACAAATTGTTCTT,+,0.00)
chunk0119_150_1	chr22	43018587	43018786	+	0	NA	Intergenic	Intergenic	-3508	NM_001184970	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.010050	0.495000	
chunk0174_428_1	chr6	165971761	165972163	+	0	NA	intron (NR_026860, intron 1 of 1)	intron (NR_026860, intron 1 of 1)	-15589	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.007463	0.384615	146(AAGAACTGTATGTACC,-,0.00),147(AGAACTGTATGTACCC,+,0.00)
chunk0121_65_1	chr3	15755359	15755591	+	0	NA	intron (NM_015199, intron 3 of 27)	intron (NM_015199, intron 3 of 27)	1076	NM_001195099	23243	Hs.335239	NM_015199	ENSG00000206560	ANKRD28	PITK|PPP1R65	ankyrin repeat domain 28	protein-coding	0.004310	0.339056	
chunk0024_276_1	chr10	41881767	41882738	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	485793	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.016478	0.417695	
chunk0157_377_1	chr5	123807358	123807699	+	0	NA	Intergenic	Intergenic	262111	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.002933	0.388889	
chunk0157_366_1	chr5	123513024	123513377	+	0	NA	intron (NM_001270574, intron 1 of 9)	intron (NM_001270574, intron 1 of 9)	1101	NM_001031812	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.019830	0.516949	
chunk0136_303_1	chr3	195143179	195143805	+	0	NA	intron (NM_001308069, intron 3 of 3)	MER102b|DNA|hAT-Charlie	-4379	NR_102711	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.009585	0.417863	
chunk0024_267_1	chr10	41858319	41858556	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	509608	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.016878	0.428571	
chunk0163_59_1	chr6	8939729	8940070	+	0	NA	Intergenic	Intergenic	287690	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.005865	0.406433	
chunk0125_328_1	chr3	71011649	71011888	+	0	NA	intron (NM_032682, intron 12 of 20)	intron (NM_032682, intron 12 of 20)	53155	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.008368	0.358333	
chunk0141_130_1	chr4	80615009	80615549	+	0	NA	intron (NM_001206997, intron 4 of 6)	intron (NM_001206997, intron 4 of 6)	279559	NM_152770	255119	Hs.527104	NM_152770	ENSG00000197826	CFAP299	C4orf22	cilia and flagella associated protein 299	protein-coding	0.005556	0.306839	
chunk0100_314_1	chr2	115924967	115925639	+	0	NA	Intergenic	L1PB1|LINE|L1	763196	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.001488	0.352155	
chunk0098_260_1	chr2	75268076	75268579	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-68808	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.007952	0.400794	
chunk0047_80_1	chr12	67931955	67932207	+	0	NA	intron (NR_120456, intron 1 of 2)	intron (NR_120456, intron 1 of 2)	2846	NR_120456	101927922	Hs.450769	NR_120456	ENSG00000255772	LINC01479	HRAT39	long intergenic non-protein coding RNA 1479	ncRNA	0.011905	0.537549	
chunk0059_387_1	chr14	37458993	37459192	+	0	NA	intron (NM_001195296, intron 13 of 14)	L1PB4|LINE|L1	136028	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.000000	0.365000	
chunk0091_468_1	chr19	18380080	18381084	+	0	NA	Intergenic	Intergenic	-5576	NM_004864	9518	Hs.616962	NM_004864	ENSG00000130513	GDF15	GDF-15|MIC-1|MIC1|NAG-1|PDF|PLAB|PTGFB	growth differentiation factor 15	protein-coding	0.021912	0.531343	
chunk0002_344_1	chr1	25141851	25142175	+	0	NA	Intergenic	MIR3|SINE|MIR	90509	NM_207170	25949	Hs.20013	NM_015484	ENSG00000117614	SYF2	CBPIN|NTC31|P29|fSAP29	SYF2 pre-mRNA splicing factor	protein-coding	0.015432	0.449231	
chunk0183_23_1	chr7	103392045	103392545	+	0	NA	intron (NR_120442, intron 8 of 16)	intron (NR_120442, intron 8 of 16)	44771	NM_001204453	5701	Hs.437366	NM_002803	ENSG00000161057	PSMC2	MSS1|Nbla10058|S7	proteasome 26S subunit, ATPase 2	protein-coding	0.004000	0.365269	
chunk0178_172_1	chr7	34121028	34121661	+	0	NA	intron (NM_133468, intron 14 of 15)	intron (NM_133468, intron 14 of 15)	216433	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.001580	0.282334	
chunk0024_345_1	chr10	43405955	43406410	+	0	NA	intron (NM_001098204, intron 1 of 3)	intron (NM_001098204, intron 1 of 3)	1669	NM_001098206	3185	Hs.808	NM_004966	ENSG00000169813	HNRNPF	HNRPF|OK/SW-cl.23|mcs94-1	heterogeneous nuclear ribonucleoprotein F	protein-coding	0.008791	0.464912	
chunk0144_458_1	chr4	142275233	142275584	+	0	NA	intron (NM_001101669, intron 9 of 25)	intron (NM_001101669, intron 9 of 25)	571043	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.002849	0.363636	
chunk0207_126_1	chr9	129038314	129038529	+	0	NA	intron (NM_032809, intron 1 of 15)	intron (NM_032809, intron 1 of 15)	1447	NM_032809	84895	Hs.632693	NM_032809	ENSG00000148343	MIGA2	C9orf54|FAM73B	mitoguardin 2	protein-coding	0.018605	0.625000	
chunk0043_191_1	chr12	19097005	19097324	+	0	NA	Intergenic	Intergenic	-32528	NM_001190860	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.006270	0.362500	
chunk0049_423_1	chr12	97767352	97767678	+	0	NA	Intergenic	Intergenic	-10998	NR_077240	643711	Hs.585557	NR_077240	ENSG00000257501	LOC643711	-	platelet activating factor acetylhydrolase 1b catalytic subunit 2 pseudogene	pseudo	0.003067	0.324159	101(TTGTACAGTATGTTCA,-,0.00),102(TGTACAGTATGTTCAT,+,0.00),213(AGAAACATTATGTACT,-,0.00),214(GAAACATTATGTACTG,+,0.00)
chunk0150_13_1	chr5	30498902	30499561	+	0	NA	Intergenic	L1PA6|LINE|L1	-694424	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.003035	0.478788	
chunk0021_175_1	chr10	5484347	5484964	+	0	NA	Intergenic	L1ME4a|LINE|L1	14915	NM_017422	51806	Hs.180142	NM_017422	ENSG00000178372	CALML5	CLSP	calmodulin like 5	protein-coding	0.006483	0.344660	
chunk0144_324_1	chr4	139015412	139015811	+	0	NA	promoter-TSS (NM_012118)	promoter-TSS (NM_012118)	-148	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.090226	0.635000	
chunk0111_245_1	chr20	29879012	29879359	+	0	NA	Intergenic	Intergenic	-1199	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.028818	0.643678	
chunk0145_233_1	chr4	148456048	148456450	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-13729	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.007463	0.421836	
chunk0170_286_1	chr6	114529720	114530326	+	0	NA	Intergenic	L1MA4|LINE|L1	-467146	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.004950	0.357496	
chunk0211_129_1	chrX	112612491	112612942	+	0	NA	Intergenic	Intergenic	67431	NM_178175	340596	Hs.297420	NM_178175	ENSG00000182508	LHFPL1	-	LHFPL tetraspan subfamily member 1	protein-coding	0.004435	0.442478	
chunk0204_301_1	chr9	100095930	100096140	+	0	NA	intron (NM_015051, intron 1 of 11)	intron (NM_015051, intron 1 of 11)	3017	NM_015051	23071	Hs.154023	NM_015051	ENSG00000023318	ERP44	PDIA10|TXNDC4	endoplasmic reticulum protein 44	protein-coding	0.014286	0.331754	
chunk0184_128_1	chr7	114923423	114923892	+	0	NA	TTS (NM_001166346)	TTS (NM_001166346)	1503	NM_001166345	29969	Hs.741413	NM_199072	ENSG00000135272	MDFIC	HIC|MDFIC1	MyoD family inhibitor domain containing	protein-coding	0.010661	0.391489	
chunk0090_263_1	chr18	74465692	74466175	+	0	NA	Intergenic	L1MC1|LINE|L1	-8665	NM_001044369	125704	Hs.371690	NM_001044369	ENSG00000187773	DIPK1C	C18orf51|FAM69C	divergent protein kinase domain 1C	protein-coding	0.010352	0.369835	
chunk0002_401_1	chr1	27342542	27342811	+	0	NA	intron (NM_032872, intron 1 of 14)	intron (NM_032872, intron 1 of 14)	684	NM_032872	84958	Hs.469175	NM_032872	ENSG00000142765	SYTL1	JFC1|SLP1	synaptotagmin like 1	protein-coding	0.018587	0.551852	
chunk0044_295_1	chr12	32843932	32844147	+	0	NA	intron (NM_004572, intron 5 of 13)	intron (NM_004572, intron 5 of 13)	52807	NM_001005242	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.000000	0.365741	
chunk0089_153_1	chr18	59068620	59069003	+	0	NA	Intergenic	Intergenic	33132	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.010444	0.416667	106(TAGCACTGATTGTCCT,-,0.00),107(AGCACTGATTGTCCTA,+,0.00),234(CTGGACACCGTGTGCT,-,0.00),235(TGGACACCGTGTGCTG,+,0.00)
chunk0206_273_1	chr9	124220751	124221439	+	0	NA	Intergenic	Intergenic	-36511	NM_001166167	10783	Hs.197071	NM_014397	ENSG00000119408	NEK6	SID6-1512	NIMA related kinase 6	protein-coding	0.011628	0.537010	569(CAGCACAGGCTGCTCT,-,0.00),570(AGCACAGGCTGCTCTC,+,0.00)
chunk0019_111_1	chr1	225116012	225116264	+	0	NA	intron (NM_001373, intron 23 of 83)	L2c|LINE|L2	186477	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.000000	0.399209	
chunk0072_75_1	chr15	90514688	90515113	+	0	NA	Intergenic	L1MC4|LINE|L1	-14986	NM_022769	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.007059	0.368545	
chunk0056_291_1	chr13	90526187	90526786	+	0	NA	intron (NR_120414, intron 3 of 5)	intron (NR_120414, intron 3 of 5)	33198	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.001669	0.296667	
chunk0202_199_1	chr9	75420329	75420837	+	0	NA	Intergenic	Intergenic	332101	NM_012383	26578	Hs.494192	NM_012383	ENSG00000134996	OSTF1	OSF|SH3P2|bA235O14.1	osteoclast stimulating factor 1	protein-coding	0.011811	0.432220	
chunk0026_311_1	chr10	68055126	68055659	+	0	NA	intron (NM_022079, intron 3 of 25)	intron (NM_022079, intron 3 of 25)	19954	NM_015601	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.001876	0.290262	
chunk0166_43_1	chr6	42303835	42304146	+	0	NA	intron (NM_001297573, intron 3 of 17)	intron (NM_001297573, intron 3 of 17)	-86095	NM_018141	55173	Hs.380887	NM_018141	ENSG00000048544	MRPS10	MRP-S10|PNAS-122	mitochondrial ribosomal protein S10	protein-coding	0.003215	0.423077	147(AGGAACATATTGTGCC,-,0.00),148(GGAACATATTGTGCCT,+,0.00)
chunk0041_196_1	chr11	126502287	126502588	+	0	NA	intron (NM_032531, intron 4 of 16)	intron (NM_032531, intron 4 of 16)	96255	NM_001254759	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.003322	0.529801	
chunk0081_58_1	chr17	38605557	38605810	+	0	NA	intron (NM_025248, intron 1 of 18)	intron (NM_025248, intron 1 of 18)	247	NM_025248	80725	Hs.448872	NM_025248	ENSG00000277363	SRCIN1	P140|SNIP	SRC kinase signaling inhibitor 1	protein-coding	0.110672	0.744094	
chunk0006_50_1	chr1	64514628	64514853	+	0	NA	intron (NM_001293274, intron 1 of 25)	L3|LINE|CR1	8826	NM_001293274	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.000000	0.331858	115(TGGAACATGCAGTACT,-,0.00),116(GGAACATGCAGTACTT,+,0.00)
chunk0005_121_1	chr1	56787979	56788726	+	0	NA	intron (NM_001004303, intron 3 of 19)	intron (NM_001004303, intron 3 of 19)	31344	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.001339	0.431818	329(CAGTACATTTTGTCCC,-,0.00),330(AGTACATTTTGTCCCA,+,0.00)
chunk0062_286_1	chr14	72300924	72301515	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	-215601	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.010152	0.361486	
chunk0114_146_1	chr21	10345233	10345669	+	0	NA	Intergenic	Intergenic	-68069	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.006881	0.528604	
chunk0133_175_1	chr3	170037722	170038017	+	0	NA	promoter-TSS (NM_014373)	promoter-TSS (NM_014373)	-78	NM_014373	26996	Hs.231320	NM_014373	ENSG00000173890	GPR160	GPCR1|GPCR150	G protein-coupled receptor 160	protein-coding	0.077966	0.682432	
chunk0131_159_1	chr3	146454997	146455355	+	0	NA	intron (NM_001199978, intron 6 of 9)	intron (NM_001199978, intron 6 of 9)	14125	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.011173	0.415042	
chunk0091_118_1	chr19	6239380	6239579	+	0	NA	intron (NM_005934, intron 3 of 11)	intron (NM_005934, intron 3 of 11)	40469	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.040201	0.585000	
chunk0111_376_1	chr20	33846514	33846722	+	0	NA	intron (NM_176812, intron 1 of 4)	intron (NM_176812, intron 1 of 4)	35314	NM_176812	128866	Hs.472471	NM_176812	ENSG00000101421	CHMP4B	C20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4	charged multivesicular body protein 4B	protein-coding	0.019231	0.497608	
chunk0111_367_1	chr20	33732361	33733007	+	0	NA	intron (NR_104259, intron 1 of 13)	CpG	924	NM_032819	84905	Hs.516989	NM_032819	ENSG00000131061	ZNF341	HIES3	zinc finger protein 341	protein-coding	0.069659	0.622875	329(CGGGACGCGGTGTTCC,-,0.00),330(GGGACGCGGTGTTCCC,+,0.00)
chunk0176_392_1	chr7	18835606	18835805	+	0	NA	intron (NM_178425, intron 19 of 24)	intron (NM_178425, intron 19 of 24)	281967	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.005025	0.405000	
chunk0117_424_1	chr21	46085033	46085279	+	0	NA	Intergenic	Intergenic	-12963	NM_058174	1292	Hs.420269	NM_001849	ENSG00000142173	COL6A2	BTHLM1|PP3610|UCMD1	collagen type VI alpha 2 chain	protein-coding	0.024390	0.639676	124(CAGGACACGGTGTGAC,-,0.00)
chunk0160_75_1	chr5	149896052	149896338	+	0	NA	intron (NM_000440, intron 12 of 21)	intron (NM_000440, intron 12 of 21)	36782	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.006993	0.369338	126(AGGAACAGCGTGTCTC,-,0.00),127(GGAACAGCGTGTCTCT,+,0.00)
chunk0104_74_1	chr2	171812142	171812765	+	0	NA	intron (NR_047549, intron 10 of 16)	intron (NR_047549, intron 10 of 16)	81853	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.012841	0.408654	
chunk0037_287_1	chr11	75985629	75986093	+	0	NA	intron (NM_003369, intron 8 of 14)	L1ME3A|LINE|L1	170694	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.006466	0.313978	
chunk0046_385_1	chr12	63764548	63765089	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-14985	NM_014254	10329	Hs.216386	NM_014254	ENSG00000118600	RXYLT1	HP10481|MDDGA10|TMEM5	ribitol xylosyltransferase 1	protein-coding	0.007394	0.485240	
chunk0068_162_1	chr15	54064530	54064760	+	0	NA	intron (NM_001080534, intron 1 of 30)	intron (NM_001080534, intron 1 of 30)	51741	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.008696	0.389610	
chunk0028_186_1	chr10	88488976	88489735	+	0	NA	intron (NM_001031709, intron 4 of 6)	intron (NM_001031709, intron 4 of 6)	93970	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.003953	0.394737	
chunk0002_8_1	chr1	12157764	12158024	+	0	NA	Intergenic	Intergenic	-9049	NR_107000	102465836		NR_107000	ENSG00000283789	MIR7846	hsa-mir-7846	microRNA 7846	ncRNA	0.011538	0.413793	
chunk0039_12_1	chr11	95339639	95339838	+	0	NA	Intergenic	Intergenic	-107197	NM_001271594	143686	Hs.120633	NM_144665	ENSG00000149212	SESN3	SEST3	sestrin 3	protein-coding	0.000000	0.400000	
chunk0170_30_1	chr6	109264200	109264916	+	0	NA	intron (NM_001277339, intron 7 of 9)	intron (NM_001277339, intron 7 of 9)	27944	NM_001277339	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.005587	0.465830	
chunk0172_90_1	chr6	134630295	134631001	+	0	NA	Intergenic	Intergenic	-90643	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.019830	0.431400	
chunk0012_112_1	chr1	156767207	156767592	+	0	NA	promoter-TSS (NM_005973)	promoter-TSS (NM_005973)	-83	NM_005973	5546	Hs.516948	NM_005973	ENSG00000143294	PRCC	RCCP1|TPRC	proline rich mitotic checkpoint control factor	protein-coding	0.054545	0.567358	
chunk0013_104_1	chr1	167796012	167796223	+	0	NA	Intergenic	Intergenic	74167	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.000000	0.443396	
chunk0081_154_1	chr17	40828407	40828970	+	0	NA	intron (NM_001195386, intron 1 of 2)	intron (NM_001195386, intron 1 of 2)	-6077	NM_000421	3858	Hs.99936	NM_000421	ENSG00000186395	KRT10	BCIE|BIE|CK10|EHK|K10|KPP	keratin 10	protein-coding	0.007105	0.367021	444(CAGTACTCATTGTTCT,-,0.00),445(AGTACTCATTGTTCTC,+,0.00)
chunk0115_409_1	chr21	30619450	30620040	+	0	NA	promoter-TSS (NR_023342)	promoter-TSS (NR_023342)	-882	NR_023342	100151643	Hs.580879	NM_001350977	ENSG00000206105	KRTAP20-4	KAP20.4	keratin associated protein 20-4	protein-coding	0.006780	0.324873	246(TGGAACAGGAAGTCCT,-,0.00),247(GGAACAGGAAGTCCTC,+,0.00)
chunk0183_85_1	chr7	104898469	104898710	+	0	NA	intron (NR_027374, intron 3 of 3)	MER67C|LTR|ERV1	28056	NR_027374	723809	Hs.124316	NR_027374	ENSG00000225329	LHFPL3-AS2	-	LHFPL3 antisense RNA 2	ncRNA	0.012448	0.462810	
chunk0027_395_1	chr10	80171287	80171566	+	0	NA	intron (NM_145868, intron 3 of 15)	intron (NM_145868, intron 3 of 15)	33065	NM_001278408	311	Hs.530291	NM_001157	ENSG00000122359	ANXA11	ALS23|ANX11|CAP-50|CAP50	annexin A11	protein-coding	0.014337	0.525000	
chunk0111_80_1	chr20	23235377	23235703	+	0	NA	Intergenic	Intergenic	-102904	NR_034149	200261	Hs.352228	NM_182535	ENSG00000233746	LINC00656	-	long intergenic non-protein coding RNA 656	ncRNA	0.018405	0.516820	
chunk0057_215_1	chr13	104015311	104015614	+	0	NA	Intergenic	Intergenic	590262	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.019802	0.421053	117(TGGAACATGGTGTATT,-,0.00),118(GGAACATGGTGTATTT,+,0.00)
chunk0115_254_1	chr21	27645248	27645759	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-76876	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.000000	0.375000	
chunk0017_130_1	chr1	206540205	206540811	+	0	NA	intron (NM_182663, intron 2 of 5)	intron (NM_182663, intron 2 of 5)	-16656	NM_182665	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.009901	0.535420	
chunk0108_457_1	chr2	238392126	238392550	+	0	NA	intron (NM_015650, intron 15 of 16)	L1MD1|LINE|L1	-34647	NM_001040445	51665	Hs.516788	NM_016114	ENSG00000065802	ASB1	ASB-1	ankyrin repeat and SOCS box containing 1	protein-coding	0.007075	0.435294	
chunk0029_261_1	chr10	103111258	103111729	+	0	NA	intron (NM_001134373, intron 3 of 17)	intron (NM_001134373, intron 3 of 17)	81813	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.004246	0.383475	92(CAGCACACAGTGTTCT,-,0.00),93(AGCACACAGTGTTCTC,+,0.00)
chunk0033_445_1	chr11	25433709	25433908	+	0	NA	Intergenic	Intergenic	-755315	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.015075	0.400000	
chunk0088_142_1	chr18	46088458	46088693	+	0	NA	intron (NM_001001935, intron 5 of 11)	LTR5B|LTR|ERVK	9778	NM_001257334	498	Hs.298280	NM_004046	ENSG00000152234	ATP5F1A	ATP5A|ATP5A1|ATP5AL2|ATPM|COXPD22|HEL-S-123m|MC5DN4|MOM2|OMR|ORM|hATP1	ATP synthase F1 subunit alpha	protein-coding	0.021277	0.500000	129(AGGGACACAATGCACT,-,0.00),130(GGGACACAATGCACTG,+,0.00)
chunk0003_69_1	chr1	31277041	31277725	+	0	NA	intron (NM_004814, intron 5 of 9)	L1ME4a|LINE|L1	19414	NM_004814	9410	Hs.33962	NM_004814	ENSG00000060688	SNRNP40	40K|HPRP8BP|PRP8BP|PRPF8BP|SPF38|WDR57	small nuclear ribonucleoprotein U5 subunit 40	protein-coding	0.007310	0.328467	
chunk0158_204_1	chr5	128106615	128107202	+	0	NA	intron (NR_046207, intron 1 of 26)	intron (NR_046207, intron 1 of 26)	23117	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.001704	0.314626	
chunk0107_260_1	chr2	217386515	217386724	+	0	NA	intron (NR_026597, intron 8 of 12)	intron (NR_026597, intron 8 of 12)	103886	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.009569	0.400000	
chunk0139_277_1	chr4	56976073	56976506	+	0	NA	intron (NM_032313, intron 1 of 6)	intron (NM_032313, intron 1 of 6)	1371	NM_032313	84273	Hs.8715	NM_032313	ENSG00000084092	NOA1	C4orf14|MTG3|hAtNOS1|hNOA1|mAtNOS1	nitric oxide associated 1	protein-coding	0.025404	0.495392	
chunk0212_367_1	chrX	149643663	149644200	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-12019	NM_001282302	84548	Hs.522172	NM_032508	ENSG00000269556	TMEM185A	CXorf13|FAM11A|FRAXF|ee3	transmembrane protein 185A	protein-coding	0.003724	0.310409	
chunk0139_266_1	chr4	56662854	56663509	+	0	NA	intron (NM_032495, intron 1 of 3)	intron (NM_032495, intron 1 of 3)	-6659	NM_001145459	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.004580	0.411585	388(TAGAACACGCTGCACT,-,0.00),389(AGAACACGCTGCACTT,+,0.00)
chunk0039_73_1	chr11	96420289	96420705	+	0	NA	Intergenic	L1MA3|LINE|L1	30503	NM_001261833	8690	Hs.105940	NM_003772	ENSG00000183340	JRKL	HHMJG	JRK like	protein-coding	0.002404	0.386091	
chunk0041_160_1	chr11	126006865	126007250	+	0	NA	intron (NM_016952, intron 8 of 19)	intron (NM_016952, intron 8 of 19)	56235	NM_001243597	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.005195	0.362694	
chunk0198_230_1	chr8	134033967	134034291	+	0	NA	Intergenic	Intergenic	147633	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006173	0.440000	
chunk0191_438_1	chr8	57902547	57903086	+	0	NA	Intergenic	L1M7|LINE|L1	-75542	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.001855	0.288889	217(AAGAACAGTAAGTTCT,-,0.00),218(AGAACAGTAAGTTCTT,+,0.00)
chunk0125_89_1	chr3	65022341	65022540	+	0	NA	Intergenic	MIRb|SINE|MIR	-334751	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.000000	0.365000	
chunk0141_451_1	chr4	89404426	89404661	+	0	NA	Intergenic	Intergenic	-96533	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.000000	0.283898	
chunk0076_14_1	chr16	58735862	58736264	+	0	NA	Intergenic	Intergenic	-1706	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.012438	0.384615	
chunk0083_26_1	chr17	63126131	63126424	+	0	NA	intron (NM_025185, intron 3 of 24)	intron (NM_025185, intron 3 of 24)	116740	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.006826	0.353741	
chunk0194_150_1	chr8	84604672	84605239	+	0	NA	intron (NM_001100393, intron 2 of 8)	intron (NM_001100393, intron 2 of 8)	-100972	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005291	0.338028	282(TGGGACATTCTGTTCT,-,0.00),283(GGGACATTCTGTTCTT,+,0.00)
chunk0035_383_1	chr11	55442634	55443194	+	0	NA	Intergenic	MIR|SINE|MIR	75030	NM_001005275	81328	Hs.554529	NM_001005275	ENSG00000181958	OR4A15	OR11-118	olfactory receptor family 4 subfamily A member 15	protein-coding	0.007143	0.376114	
chunk0050_16_1	chr12	99699294	99699868	+	0	NA	intron (NM_152788, intron 8 of 25)	intron (NM_152788, intron 8 of 25)	51831	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.005226	0.316522	279(AAGAACAGAGTCTTCT,-,0.00),280(AGAACAGAGTCTTCTT,+,0.00)
chunk0029_102_1	chr10	97508694	97509014	+	0	NA	intron (NM_024954, intron 1 of 2)	intron (NM_024954, intron 1 of 2)	9972	NM_024954	80019	Hs.500724	NM_024954	ENSG00000165886	UBTD1	-	ubiquitin domain containing 1	protein-coding	0.009375	0.448598	
chunk0159_198_1	chr5	140372688	140372917	+	0	NA	3' UTR (NM_001258426, exon 21 of 22)	3' UTR (NM_001258426, exon 21 of 22)	12600	NM_001258427	83697	Hs.550313	NM_031467	ENSG00000113073	SLC4A9	AE4	solute carrier family 4 member 9	protein-coding	0.004367	0.486957	
chunk0164_384_1	chr6	26063266	26063655	+	0	NA	Intergenic	Intergenic	-6989	NM_005319	3006	Hs.7644	NM_005319	ENSG00000187837	HIST1H1C	H1.2|H1C|H1F2|H1s-1	histone cluster 1 H1 family member c	protein-coding	0.000000	0.443590	
chunk0150_226_1	chr5	35684227	35684685	+	0	NA	intron (NM_024867, intron 10 of 36)	intron (NM_024867, intron 10 of 36)	66569	NM_024867	79925	Hs.298863	NM_024867	ENSG00000152582	SPEF2	CT122|KPL2	sperm flagellar 2	protein-coding	0.006550	0.420479	128(CTGCTCAGTGTGTTCC,-,0.00)
chunk0119_431_1	chr22	50022455	50023211	+	0	NA	Intergenic	L1MEd|LINE|L1	-10207	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.015873	0.421400	429(TGGGACACAGTGTCCA,-,0.00),430(GGGACACAGTGTCCAT,+,0.00),515(CAGGACAGAGTGTCCA,-,0.00),516(AGGACAGAGTGTCCAT,+,0.00),601(CAGGACACAGTGTCCA,-,0.00),602(AGGACACAGTGTCCAT,+,0.00)
chunk0040_44_1	chr11	110763527	110763812	+	0	NA	Intergenic	Intergenic	-50480	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.003509	0.430070	
chunk0063_24_1	chr14	76613511	76614072	+	0	NA	Intergenic	Intergenic	-148101	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.005348	0.411032	
chunk0096_145_1	chr2	29037495	29038267	+	0	NA	intron (NM_199280, intron 18 of 19)	intron (NM_199280, intron 18 of 19)	36380	NM_001029883	388939	Hs.354243	NM_001029883	ENSG00000179270	PCARE	C2orf71|RP54	photoreceptor cilium actin regulator	protein-coding	0.006477	0.489004	
chunk0047_299_1	chr12	73692290	73692896	+	0	NA	Intergenic	L1MA1|LINE|L1	533403	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.003300	0.375618	
chunk0142_41_1	chr4	90961865	90962511	+	0	NA	intron (NM_001145065, intron 9 of 10)	MIRb|SINE|MIR	727157	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.000000	0.276662	317(CAGAACATTCTGTACC,-,0.00),318(AGAACATTCTGTACCA,+,0.00)
chunk0066_11_1	chr15	26918251	26918872	+	0	NA	intron (NM_001165037, intron 7 of 10)	L1M3d|LINE|L1	51435	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.001610	0.332797	
chunk0093_215_1	chr19	49850676	49850986	+	0	NA	promoter-TSS (NM_001305108)	promoter-TSS (NM_001305108)	96	NR_130963	53635	Hs.587979	NM_017432	ENSG00000104960	PTOV1	ACID2|PTOV-1	PTOV1 extended AT-hook containing adaptor protein	protein-coding	0.067742	0.652733	
chunk0131_278_1	chr3	150268570	150269140	+	0	NA	intron (NR_110186, intron 2 of 3)	intron (NR_110186, intron 2 of 3)	30155	NR_110167	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.003509	0.397548	
chunk0167_107_1	chr6	57223573	57224031	+	0	NA	Intergenic	L1MB3|LINE|L1	-1488	NM_001278666	51715	Hs.555016	NM_016277	ENSG00000112210	RAB23	HSPC137	RAB23, member RAS oncogene family	protein-coding	0.008734	0.328976	
chunk0211_432_1	chrX	129433355	129434070	+	0	NA	Intergenic	L2c|LINE|L2	89793	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.004196	0.395251	
chunk0128_157_1	chr3	107171171	107171370	+	0	NA	intron (NR_028303, intron 1 of 3)	THE1D-int|LTR|ERVL-MaLR	69368	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.010050	0.525000	
chunk0051_440_1	chr12	123156232	123156463	+	0	NA	TTS (NR_103517)	TTS (NR_103517)	-45858	NM_001300801	57605	Hs.272759	NM_020845	ENSG00000090975	PITPNM2	NIR-3|NIR3|RDGB2|RDGBA2	phosphatidylinositol transfer protein membrane associated 2	protein-coding	0.008658	0.288793	
chunk0024_77_1	chr10	34319604	34319827	+	0	NA	intron (NM_019619, intron 19 of 24)	MamRTE1|LINE|RTE-BovB	495610	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.441964	
chunk0057_336_1	chr13	107069405	107069932	+	0	NA	Intergenic	Intergenic	415788	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.005693	0.363636	
chunk0124_237_1	chr3	56711519	56711818	+	0	NA	Intergenic	L1MDb|LINE|L1	-28561	NM_001112736	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.003344	0.583333	
chunk0109_250_1	chr20	6429504	6429825	+	0	NA	intron (NR_109953, intron 1 of 3)	L2c|LINE|L2	2932	NR_109953	101929244	Hs.542488	NR_109953	ENSG00000229876	CASC20	-	cancer susceptibility 20	ncRNA	0.006231	0.372671	
chunk0183_126_1	chr7	105512395	105512796	+	0	NA	intron (NM_019042, intron 1 of 15)	intron (NM_019042, intron 1 of 15)	9643	NM_019042	54517	Hs.520619	NM_019042	ENSG00000091127	PUS7	IDDABS	pseudouridine synthase 7	protein-coding	0.009975	0.502488	154(AGGTACAGCATGTGCA,-,0.00),155(GGTACAGCATGTGCAA,+,0.00)
chunk0068_201_1	chr15	54959719	54960402	+	0	NA	Intergenic	Intergenic	236973	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.001464	0.372807	
chunk0094_338_1	chr2	9247897	9248239	+	0	NA	intron (NM_003887, intron 1 of 27)	intron (NM_003887, intron 1 of 27)	41303	NM_003887	8853	Hs.555902	NM_003887	ENSG00000151693	ASAP2	AMAP2|CENTB3|DDEF2|PAG3|PAP|Pap-alpha|SHAG1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding	0.023392	0.565598	
chunk0071_89_1	chr15	80852689	80852989	+	0	NA	intron (NM_018689, intron 1 of 28)	intron (NM_018689, intron 1 of 28)	-10766	NR_030393	693132		NR_030393	ENSG00000208003	MIR549A	MIR549|MIRN549|hsa-mir-549|hsa-mir-549a|mir-549a	microRNA 549a	ncRNA	0.013333	0.491694	
chunk0191_361_1	chr8	56746125	56746403	+	0	NA	Intergenic	Intergenic	-186441	NR_038236	100507632	Hs.583755	NR_038236	ENSG00000246430	LINC00968	-	long intergenic non-protein coding RNA 968	ncRNA	0.000000	0.304659	
chunk0065_68_1	chr15	23397765	23398149	+	0	NA	Intergenic	Intergenic	43209	NR_038843	653061	Hs.528454	NM_001355465		GOLGA8S	-	golgin A8 family member S	protein-coding	0.018229	0.501299	
chunk0182_355_1	chr7	99697341	99697604	+	0	NA	intron (NM_001256497, intron 13 of 14)	intron (NM_001256497, intron 13 of 14)	-17446	NR_033807	1577	Hs.571258	NM_000777	ENSG00000106258	CYP3A5	CP35|CYPIIIA5|P450PCN3|PCN3	cytochrome P450 family 3 subfamily A member 5	protein-coding	0.007605	0.435606	
chunk0063_427_1	chr14	88548363	88548717	+	0	NA	intron (NM_007039, intron 2 of 18)	intron (NM_007039, intron 2 of 18)	6239	NM_007039	11099	Hs.437040	NM_007039	ENSG00000070778	PTPN21	PTPD1|PTPRL10	protein tyrosine phosphatase non-receptor type 21	protein-coding	0.005650	0.487324	
chunk0054_219_1	chr13	45416750	45417105	+	0	NA	intron (NM_001286807, intron 1 of 9)	intron (NM_001286807, intron 1 of 9)	-1235	NR_047031	100874259	Hs.658038	NR_047031	ENSG00000251015	SLC25A30-AS1	-	SLC25A30 antisense RNA 1	ncRNA	0.014085	0.370787	
chunk0154_222_1	chr5	80697213	80697442	+	0	NA	intron (NM_002439, intron 8 of 23)	intron (NM_002439, intron 8 of 23)	-42346	NM_001290357	1719	Hs.592364	NM_000791	ENSG00000228716	DHFR	DHFRP1|DYR	dihydrofolate reductase	protein-coding	0.008734	0.378261	
chunk0107_296_1	chr2	218780994	218781385	+	0	NA	promoter-TSS (NM_000784)	promoter-TSS (NM_000784)	-560	NM_000784	1593	Hs.516700	NM_000784	ENSG00000135929	CYP27A1	CP27|CTX|CYP27	cytochrome P450 family 27 subfamily A member 1	protein-coding	0.002558	0.403061	
chunk0166_294_1	chr6	48916510	48917205	+	0	NA	Intergenic	Intergenic	546471	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.000000	0.347701	
chunk0022_101_1	chr10	9987178	9987725	+	0	NA	Intergenic	L2a|LINE|L2	-71271	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.009141	0.403285	
chunk0117_410_1	chr21	45701087	45701435	+	0	NA	Intergenic	Intergenic	135158	NR_038876	100129027	Hs.689591	NR_038876	ENSG00000205424	LOC100129027	-	uncharacterized LOC100129027	ncRNA	0.000000	0.398281	
chunk0136_235_1	chr4	8453401	8453820	+	0	NA	intron (NM_152544, intron 5 of 10)	intron (NM_152544, intron 5 of 10)	12805	NM_152544	152992	Hs.566191	NM_024950	ENSG00000155275	TRMT44	C4orf23|METTL19|TRM44	tRNA methyltransferase 44 homolog	protein-coding	0.021480	0.530952	
chunk0147_337_1	chr4	185425887	185426393	+	0	NA	promoter-TSS (NM_018359)	promoter-TSS (NM_018359)	-155	NR_028085	55325	Hs.713548	NM_018359	ENSG00000109775	UFSP2	BHD|C4orf20|SEMDDR	UFM1 specific peptidase 2	protein-coding	0.092885	0.617357	
chunk0004_217_1	chr1	46798677	46799107	+	0	NA	promoter-TSS (NM_001099772)	promoter-TSS (NM_001099772)	-106	NM_001099772	1580	Hs.436317	NM_000779	ENSG00000142973	CYP4B1	CYPIVB1|P-450HP	cytochrome P450 family 4 subfamily B member 1	protein-coding	0.004651	0.487239	
chunk0056_355_1	chr13	92179276	92180013	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	172563	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.008141	0.341463	492(TAGAACTTTCTGTTCT,-,0.00),493(AGAACTTTCTGTTCTG,+,0.00)
chunk0188_39_1	chr8	6633029	6633579	+	0	NA	intron (NR_125386, intron 1 of 4)	L1M5|LINE|L1	-11084	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.003636	0.324864	
chunk0108_323_1	chr2	235588823	235589163	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	83242	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.026471	0.501466	
chunk0112_432_1	chr20	47527497	47527849	+	0	NA	intron (NM_001174087, intron 1 of 22)	L1ME1|LINE|L1	25816	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.005682	0.348442	
chunk0126_168_1	chr3	77801923	77802366	+	0	NA	Intergenic	Intergenic	704132	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.004515	0.315315	
chunk0169_326_1	chr6	106325464	106326075	+	0	NA	promoter-TSS (NM_001286107)	promoter-TSS (NM_001286107)	51	NM_004849	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.073650	0.607843	
chunk0135_426_1	chr3	193734969	193735168	+	0	NA	Intergenic	Intergenic	-107736	NR_046634	100873941	Hs.679364	NR_046634	ENSG00000224855	OPA1-AS1	-	OPA1 antisense RNA 1	ncRNA	0.015075	0.460000	
chunk0120_364_1	chr3	11719677	11720261	+	0	NA	intron (NM_014667, intron 1 of 5)	CpG	799	NM_014667	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.121575	0.741880	
chunk0010_39_1	chr1	112687983	112688510	+	0	NA	intron (NM_001286072, intron 3 of 21)	L2b|LINE|L2	13773	NM_001130079	4343	Hs.514941	NM_020963	ENSG00000155363	MOV10	fSAP113|gb110	Mov10 RISC complex RNA helicase	protein-coding	0.011385	0.537879	
chunk0012_99_1	chr1	156471447	156472055	+	0	NA	intron (NM_001271629, intron 8 of 10)	MER124|DNA?|DNA?	18848	NM_001271629	4209	Hs.314327	NM_005920	ENSG00000116604	MEF2D	-	myocyte enhancer factor 2D	protein-coding	0.006579	0.545156	
chunk0070_257_1	chr15	73654459	73654984	+	0	NA	Intergenic	MER34A1|LTR|ERV1	-21309	NM_017455	27020	Hs.744867	NM_012428	ENSG00000156642	NPTN	GP55|GP65|SDFR1|SDR1|np55|np65	neuroplastin	protein-coding	0.007619	0.403042	
chunk0074_321_1	chr16	30740087	30740955	+	0	NA	TTS (NM_006662)	TTS (NM_006662)	330	NM_001256829	100862671	Hs.667372	NM_001256829	ENSG00000281991	TMEM265	IFITMD8	transmembrane protein 265	protein-coding	0.012673	0.499425	158(CAGGACTATATGTTCC,-,0.00),159(AGGACTATATGTTCCA,+,0.00)
chunk0027_6_1	chr10	71959569	71959977	+	0	NA	Intergenic	HERVK14-int|LTR|ERVK	-4589	NM_004273	9469	Hs.158304	NM_004273	ENSG00000122863	CHST3	C6ST|C6ST1|HSD	carbohydrate sulfotransferase 3	protein-coding	0.007353	0.415648	
chunk0038_140_1	chr11	84304437	84305029	+	0	NA	intron (NM_001142699, intron 7 of 27)	MER58B|DNA|hAT-Charlie	12606	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.005068	0.338954	
chunk0001_92_1	chr1	2937883	2938333	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-83374	NM_080431	140625	Hs.236635	NM_080431	ENSG00000169717	ACTRT2	ARPM2|ARPT2|Arp-T2|HARPM2	actin related protein T2	protein-coding	0.006667	0.481153	
chunk0203_133_1	chr9	85333226	85333634	+	0	NA	Intergenic	Intergenic	408599	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.004902	0.383863	
chunk0140_17_1	chr4	65589377	65589767	+	0	NA	intron (NM_001281765, intron 3 of 17)	intron (NM_001281765, intron 3 of 17)	-80389	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.002564	0.388747	
chunk0173_194_1	chr6	145240904	145241475	+	0	NA	Intergenic	Intergenic	-493680	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.008757	0.403846	
chunk0025_421_1	chr10	59835571	59835784	+	0	NA	intron (NM_005436, intron 2 of 8)	intron (NM_005436, intron 2 of 8)	70979	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.004695	0.420561	
chunk0117_160_1	chr22	20084342	20084837	+	0	NA	intron (NM_022720, intron 1 of 13)	intron (NM_022720, intron 1 of 13)	-1157	NR_037412	100500860		NR_037412	ENSG00000284140	MIR3618	-	microRNA 3618	ncRNA	0.020202	0.560484	
chunk0129_231_1	chr3	121968935	121969135	+	0	NA	Intergenic	MER34B|LTR|ERV1	53245	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.005000	0.333333	
chunk0186_17_1	chr7	135756192	135756502	+	0	NA	Intergenic	Intergenic	-7501	NM_205855	389558	Hs.55200	NM_205855	ENSG00000189320	FAM180A	UNQ1940	family with sequence similarity 180 member A	protein-coding	0.016129	0.437299	
chunk0087_413_1	chr18	42203226	42203540	+	0	NA	intron (NR_046455, intron 1 of 4)	intron (NR_046455, intron 1 of 4)	16715	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.000000	0.460317	145(GTGCACAGCCTGTCCT,-,0.00),146(TGCACAGCCTGTCCTG,+,0.00)
chunk0145_305_1	chr4	150231948	150232487	+	0	NA	intron (NR_036614, intron 8 of 16)	intron (NR_036614, intron 8 of 16)	153943	NM_001040261	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.012987	0.437037	
chunk0155_273_1	chr5	95988104	95988381	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	-26171	NM_012081	22936	Hs.192221	NM_012081	ENSG00000118985	ELL2	MRCCAT1	elongation factor for RNA polymerase II 2	protein-coding	0.007220	0.395683	
chunk0100_320_1	chr2	116465150	116465349	+	0	NA	Intergenic	Intergenic	1303142	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.010050	0.405000	
chunk0193_366_1	chr8	80065966	80066954	+	0	NA	intron (NM_001025253, intron 1 of 7)	intron (NM_001025253, intron 1 of 7)	14371	NM_001025252	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.009109	0.418605	89(GAGAACTGCCAGTTCA,-,0.00),90(AGAACTGCCAGTTCAG,+,0.00)
chunk0132_113_1	chr3	155890851	155891203	+	0	NA	intron (NM_003875, intron 1 of 15)	Tigger6a|DNA|TcMar-Tigger	20491	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.002841	0.390935	
chunk0193_377_1	chr8	80122490	80123173	+	0	NA	intron (NR_105035, intron 1 of 6)	intron (NR_105035, intron 1 of 6)	-42000	NM_001287140	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.007321	0.479532	
chunk0007_230_1	chr1	81816526	81816834	+	0	NA	intron (NM_001297706, intron 1 of 18)	intron (NM_001297706, intron 1 of 18)	16283	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.000000	0.268608	
chunk0073_383_1	chr16	15964851	15965180	+	0	NA	intron (NM_004996, intron 1 of 30)	L1M5|LINE|L1	15438	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.003040	0.351515	
chunk0038_52_1	chr11	82682311	82682940	+	0	NA	Intergenic	HUERS-P3b-int|LTR|ERV1	51239	NM_175885	220382	Hs.448218	NM_175885	ENSG00000182103	FAM181B	-	family with sequence similarity 181 member B	protein-coding	0.009539	0.455556	
chunk0085_199_1	chr18	6566303	6566788	+	0	NA	intron (NR_120518, intron 2 of 5)	intron (NR_120518, intron 2 of 5)	55129	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.006186	0.384774	
chunk0139_76_1	chr4	49120864	49121175	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	134377	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.028939	0.423077	
chunk0066_325_1	chr15	36475479	36476119	+	0	NA	Intergenic	Intergenic	-103804	NM_001130010	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.010937	0.377535	
chunk0152_227_1	chr5	60447414	60448023	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-39995	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.008210	0.375410	
chunk0044_249_1	chr12	31960657	31960908	+	0	NA	5' UTR (NM_018169, exon 2 of 6)	5' UTR (NM_018169, exon 2 of 6)	1363	NM_018169	55196	Hs.445129	NM_018169	ENSG00000174718	RESF1	C12orf35|GET|KIAA1551|UTA2-1	retroelement silencing factor 1	protein-coding	0.015936	0.396825	
chunk0102_308_1	chr2	151030084	151030376	+	0	NA	Intergenic	Ricksha_c|DNA|MULE-MuDR	231645	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.006849	0.337884	
chunk0164_252_1	chr6	23450354	23450579	+	0	NA	Intergenic	Intergenic	-675720	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.013333	0.331858	
chunk0003_204_1	chr1	35010704	35011020	+	0	NA	exon (NM_007167, exon 9 of 16)	exon (NM_007167, exon 9 of 16)	21106	NM_007167	9204	Hs.533986	NM_007167	ENSG00000163867	ZMYM6	Buster2|MYM|ZBED7|ZNF198L4|ZNF258	zinc finger MYM-type containing 6	protein-coding	0.015823	0.482650	
chunk0100_242_1	chr2	112692720	112692919	+	0	NA	Intergenic	Intergenic	46962	NM_005415	6574	Hs.187946	NM_005415	ENSG00000144136	SLC20A1	GLVR1|Glvr-1|PIT1|PiT-1	solute carrier family 20 member 1	protein-coding	0.005025	0.570000	
chunk0207_85_1	chrX	9385865	9386383	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-77171	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.003861	0.435453	
chunk0158_69_1	chr5	126234221	126234460	+	0	NA	Intergenic	Intergenic	50835	NR_105039	101927488	Hs.432319	NR_105039		LOC101927488	-	uncharacterized LOC101927488	ncRNA	0.012552	0.404167	176(GAGCACAAACTGTTCT,-,0.00),177(AGCACAAACTGTTCTC,+,0.00)
chunk0003_459_1	chr1	41773194	41773400	+	0	NA	intron (NM_024503, intron 1 of 8)	MIRb|SINE|MIR	145410	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.009709	0.468599	
chunk0123_7_1	chr3	40137578	40138022	+	0	NA	intron (NM_001284426, intron 1 of 14)	intron (NM_001284426, intron 1 of 14)	37789	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.006757	0.424719	
chunk0051_388_1	chr12	121861352	121861910	+	0	NA	intron (NM_001171993, intron 2 of 15)	MER68-int|LTR|ERVL	-2768	NM_002150	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.016129	0.438283	
chunk0204_56_1	chr9	93248420	93248709	+	0	NA	intron (NM_001282394, intron 7 of 29)	intron (NM_001282394, intron 7 of 29)	63634	NM_001282394	65268	Hs.654856	NM_006648	ENSG00000165238	WNK2	NY-CO-43|P/OKcl.13|PRKWNK2|SDCCAG43	WNK lysine deficient protein kinase 2	protein-coding	0.006920	0.524138	126(AGGAACAGAGTGTGCT,-,0.00),127(GGAACAGAGTGTGCTG,+,0.00)
chunk0202_145_1	chr9	73510020	73510266	+	0	NA	Intergenic	L1ME2|LINE|L1	358412	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.008130	0.279352	
chunk0086_227_1	chr18	22731184	22731437	+	0	NA	intron (NR_110782, intron 1 of 1)	intron (NR_110782, intron 1 of 1)	55527	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.003953	0.425197	
chunk0126_418_1	chr3	86037898	86038322	+	0	NA	intron (NM_153184, intron 8 of 9)	L1PA8|LINE|L1	-210060	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.002358	0.388235	
chunk0102_229_1	chr2	148719998	148720200	+	0	NA	intron (NM_015630, intron 2 of 13)	L1PA11|LINE|L1	75108	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.000000	0.546798	83(CTGGACACTTTGTCCC,-,0.00),84(TGGACACTTTGTCCCA,+,0.00)
chunk0079_327_1	chr17	17458738	17459217	+	0	NA	Intergenic	Intergenic	-18009	NM_018019	55090	Hs.244595	NM_018019	ENSG00000141026	MED9	MED25	mediator complex subunit 9	protein-coding	0.016701	0.460417	
chunk0027_349_1	chr10	78649210	78649936	+	0	NA	Intergenic	Intergenic	382245	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.004132	0.370014	
chunk0062_78_1	chr14	67787629	67788073	+	0	NA	intron (NM_015346, intron 16 of 41)	MER68|LTR|ERVL	28738	NM_015346	23503	Hs.98041	NM_015346	ENSG00000072121	ZFYVE26	FYVE-CENT|SPG15	zinc finger FYVE-type containing 26	protein-coding	0.002252	0.397753	
chunk0042_226_1	chr12	6235306	6235760	+	0	NA	exon (NM_001769, exon 6 of 8)	exon (NM_001769, exon 6 of 8)	35217	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.026432	0.534066	
chunk0152_44_1	chr5	57232183	57232648	+	0	NA	intron (NM_022913, intron 5 of 11)	LTR10C|LTR|ERV1	18341	NM_001127236	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.006452	0.369099	
chunk0122_232_1	chr3	33798084	33798940	+	0	NA	promoter-TSS (NM_013374)	promoter-TSS (NM_013374)	-59	NM_001162429	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.067757	0.581097	
chunk0048_218_1	chr12	81416877	81417277	+	0	NA	intron (NM_001220478, intron 3 of 28)	intron (NM_001220478, intron 3 of 28)	-47663	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.005000	0.269327	
chunk0041_410_1	chr11	133965489	133965697	+	0	NA	Intergenic	L2b|LINE|L2	-8839	NM_001277285	22997	Hs.204121	NM_014987	ENSG00000080854	IGSF9B	-	immunoglobulin superfamily member 9B	protein-coding	0.019231	0.483254	
chunk0094_111_1	chr2	4258569	4258772	+	0	NA	Intergenic	Intergenic	-284638	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.000000	0.338235	
chunk0015_221_1	chr1	187655166	187655432	+	0	NA	Intergenic	Intergenic	211671	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.333333	
chunk0011_337_1	chr1	152191709	152192406	+	0	NA	Intergenic	L2a|LINE|L2	32139	NM_001009931	388697	Hs.490162	NM_001009931	ENSG00000197915	HRNR	FLG3|S100A16|S100a18	hornerin	protein-coding	0.000000	0.388252	
chunk0148_302_1	chr5	12510357	12510893	+	0	NA	Intergenic	L1PA11|LINE|L1	-64232	NR_033383	404663	Hs.552273	NR_033383		LINC01194	CT49|TAG	long intergenic non-protein coding RNA 1194	ncRNA	0.007463	0.331471	
chunk0104_246_1	chr2	177220638	177221010	+	0	NA	3' UTR (NM_194247, exon 11 of 11)	3' UTR (NM_194247, exon 11 of 11)	8098	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.005376	0.361930	81(AAGAACACACTGTTAT,-,0.00),82(AGAACACACTGTTATT,+,0.00)
chunk0210_390_1	chrX	97906552	97907075	+	0	NA	Intergenic	Intergenic	-342278	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.000000	0.332061	
chunk0201_308_1	chr9	42900252	42900510	+	0	NA	Intergenic	Intergenic	111981	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.007752	0.474903	
chunk0190_233_1	chr8	35872409	35872992	+	0	NA	Intergenic	MIRb|SINE|MIR	-162380	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.001715	0.388699	
chunk0105_58_1	chr2	183339258	183339491	+	0	NA	Intergenic	Intergenic	215019	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.000000	0.320513	
chunk0212_299_1	chrX	141142010	141142482	+	0	NA	Intergenic	Intergenic	-24110	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.002119	0.323467	
chunk0023_278_1	chr10	28276426	28276777	+	0	NA	intron (NM_173496, intron 2 of 18)	intron (NM_173496, intron 2 of 18)	5537	NM_173496	143098	Hs.499159	NM_173496	ENSG00000150054	MPP7	-	membrane palmitoylated protein 7	protein-coding	0.011396	0.366477	
chunk0122_374_1	chr3	37689636	37690062	+	0	NA	intron (NM_002207, intron 18 of 27)	L2c|LINE|L2	171931	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.007042	0.482436	
chunk0135_194_1	chr3	188239688	188239911	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	14394	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.004484	0.388393	
chunk0101_145_1	chr2	127897502	127898158	+	0	NA	Intergenic	L1MD1|LINE|L1	-11890	NM_001199140	83607	Hs.546449	NM_031445	ENSG00000144233	AMMECR1L	-	AMMECR1 like	protein-coding	0.001524	0.414003	
chunk0165_135_1	chr6	33374464	33374742	+	0	NA	Intergenic	LTR29|LTR|ERV1	-16933	NM_002263	3833	Hs.436912	NM_002263	ENSG00000237649	KIFC1	HSET|KNSL2	kinesin family member C1	protein-coding	0.007194	0.426523	
chunk0127_210_1	chr3	96447782	96448272	+	0	NA	Intergenic	Intergenic	88063	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.004082	0.346232	
chunk0066_46_1	chr15	27924392	27924714	+	0	NA	intron (NM_001300984, intron 18 of 22)	L1M4a2|LINE|L1	174759	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.009317	0.278638	
chunk0108_41_1	chr2	226676949	226677683	+	0	NA	Intergenic	Intergenic	-18523	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.006812	0.368707	313(TGGTACACAGTGTTCA,-,0.00),314(GGTACACAGTGTTCAT,+,0.00)
chunk0152_191_1	chr5	59833072	59833604	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	60456	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.009398	0.446529	68(AGGGCCAGAGTGTACT,-,0.00),69(GGGCCAGAGTGTACTG,+,0.00)
chunk0104_307_1	chr2	178909400	178910421	+	0	NA	intron (NM_173648, intron 7 of 23)	intron (NM_173648, intron 7 of 23)	-102487	NM_001256850	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.008815	0.372798	392(AAGAACACTGTGACCC,-,0.00),393(AGAACACTGTGACCCC,+,0.00)
chunk0030_65_1	chr10	111993521	111994034	+	0	NA	Intergenic	Intergenic	190002	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.003899	0.383268	
chunk0055_367_1	chr13	71845931	71846481	+	0	NA	intron (NM_004392, intron 1 of 6)	intron (NM_004392, intron 1 of 6)	20986	NM_080759	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.041818	0.490018	
chunk0205_88_1	chr9	107375610	107376250	+	0	NA	Intergenic	Intergenic	90655	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.014063	0.452418	
chunk0055_376_1	chr13	73189379	73189688	+	0	NA	Intergenic	Intergenic	130741	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.006472	0.383871	133(AAGGACATGTTGTTCT,-,0.00),134(AGGACATGTTGTTCTC,+,0.00)
chunk0205_27_1	chr9	105431734	105431933	+	0	NA	Intergenic	Intergenic	-16201	NM_001145313	83856	Hs.136901	NM_031919	ENSG00000106701	FSD1L	CCDC10|CSDUFD1|FSD1CL|FSD1NL|MIR1	fibronectin type III and SPRY domain containing 1 like	protein-coding	0.005025	0.380000	
chunk0059_253_1	chr14	35106989	35107407	+	0	NA	intron (NR_110415, intron 3 of 4)	L1ME4a|LINE|L1	-15123	NM_001256678	9692	Hs.458487	NM_014672	ENSG00000100890	PRORP	KIAA0391|MRPP3	protein only RNase P catalytic subunit	protein-coding	0.004785	0.324582	220(GAGAACAGCCTGTAAT,-,0.00),221(AGAACAGCCTGTAATC,+,0.00)
chunk0093_263_1	chr19	51197940	51198211	+	0	NA	Intergenic	Intergenic	8934	NR_107041	102465873		NR_107041	ENSG00000278617	MIR8074	hsa-mir-8074	microRNA 8074	ncRNA	0.022140	0.393382	129(AAGAACATCGTGTTCT,-,0.00),130(AGAACATCGTGTTCTC,+,0.00)
chunk0005_369_1	chr1	61601673	61601908	+	0	NA	Intergenic	L2c|LINE|L2	-52452	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.012766	0.406780	
chunk0034_434_1	chr11	39228039	39228536	+	0	NA	Intergenic	Intergenic	579429	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.006036	0.373494	
chunk0094_332_1	chr2	9102741	9103208	+	0	NA	Intergenic	MER65C|LTR|ERV1	-99227	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.025696	0.467949	241(AGGAACGTCTTGTGCC,-,0.00)
chunk0173_286_1	chr6	148134656	148135447	+	0	NA	Intergenic	Intergenic	-207542	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.016435	0.343434	
chunk0101_443_1	chr2	139561515	139562077	+	0	NA	Intergenic	Intergenic	664472	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005338	0.385435	273(GTGCACACTGTGTACT,-,0.00),274(TGCACACTGTGTACTC,+,0.00)
chunk0057_62_1	chr13	97798621	97798928	+	0	NA	Intergenic	L1MA9|LINE|L1	-154901	NM_002271	3843	Hs.712598	NM_002271	ENSG00000065150	IPO5	IMB3|KPNB3|Pse1|RANBP5|imp5	importin 5	protein-coding	0.019544	0.428571	8(GGGAACAACGCGTTCT,-,0.00),9(GGAACAACGCGTTCTG,+,0.00)
chunk0154_309_1	chr5	83645637	83646325	+	0	NA	intron (NM_001884, intron 3 of 4)	intron (NM_001884, intron 3 of 4)	75096	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.002907	0.332366	
chunk0165_433_1	chr6	39930067	39930612	+	0	NA	intron (NM_001075098, intron 1 of 10)	intron (NM_001075098, intron 1 of 10)	-2623	NM_005943	4337	Hs.357128	NM_005942	ENSG00000124615	MOCS1	MIG11|MOCOD|MOCS1A|MOCS1B	molybdenum cofactor synthesis 1	protein-coding	0.009174	0.476190	
chunk0185_5_1	chr7	123767293	123767670	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-18410	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.000000	0.388889	
chunk0130_175_1	chr3	133393752	133394450	+	0	NA	intron (NM_001136469, intron 5 of 5)	intron (NM_001136469, intron 5 of 5)	-5894	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.010029	0.482117	
chunk0107_184_1	chr2	215919008	215919212	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-75574	NR_037195	646324	Hs.655713	NR_037195	ENSG00000235770	LINC00607	-	long intergenic non-protein coding RNA 607	ncRNA	0.004902	0.419512	96(AGGCACATGATGACCC,-,0.00),97(GGCACATGATGACCCC,+,0.00)
chunk0166_186_1	chr6	46144299	46144619	+	0	NA	3' UTR (NM_014936, exon 4 of 4)	3' UTR (NM_014936, exon 4 of 4)	14495	NM_014936	22875	Hs.643497	NM_014936	ENSG00000001561	ENPP4	NPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding	0.003125	0.348910	
chunk0211_361_1	chrX	125756736	125757191	+	0	NA	Intergenic	Intergenic	-352799	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.008791	0.322368	
chunk0094_274_1	chr2	8120206	8120757	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	-143667	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.012704	0.414855	
chunk0055_245_1	chr13	63042741	63043323	+	0	NA	Intergenic	Intergenic	-235673	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.005155	0.332762	360(AAGCACAGTGTGCTCC,-,0.00),361(AGCACAGTGTGCTCCA,+,0.00)
chunk0081_339_1	chr17	46876314	46877097	+	0	NA	exon (NM_003396, exon 4 of 4).2	exon (NM_003396, exon 4 of 4).2	25103	NM_003396	7484	Hs.326420	NM_003396	ENSG00000158955	WNT9B	WNT14B|WNT15	Wnt family member 9B	protein-coding	0.021711	0.600765	
chunk0112_438_1	chr20	47643232	47643522	+	0	NA	intron (NM_001174087, intron 17 of 22)	intron (NM_001174087, intron 17 of 22)	141520	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.006897	0.439863	
chunk0001_407_1	chr1	10953586	10953964	+	0	NA	intron (NM_001170754, intron 10 of 12)	intron (NM_001170754, intron 10 of 12)	28262	NM_001170754	148345	Hs.127026	NM_173507	ENSG00000175262	C1orf127	-	chromosome 1 open reading frame 127	protein-coding	0.007937	0.501319	
chunk0113_142_1	chr20	52167674	52168133	+	0	NA	intron (NM_018197, intron 2 of 5)	MER113B|DNA|hAT-Charlie	24082	NM_022088	55734	Hs.473082	NM_018197	ENSG00000020256	ZFP64	ZNF338	ZFP64 zinc finger protein	protein-coding	0.004357	0.352174	
chunk0016_308_1	chr1	201435795	201436162	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-14232	NM_003281	7135	Hs.320890	NM_003281	ENSG00000159173	TNNI1	SSTNI|TNN1	troponin I1, slow skeletal type	protein-coding	0.016349	0.478261	
chunk0001_173_1	chr1	6885745	6886039	+	0	NA	intron (NR_038934, intron 3 of 3)	intron (NR_038934, intron 3 of 3)	100568	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.013605	0.552542	189(CAGTACAGCCTGTCCT,-,0.00),190(AGTACAGCCTGTCCTT,+,0.00)
chunk0097_16_1	chr2	42055673	42056253	+	0	NA	intron (NM_138370, intron 5 of 6)	intron (NM_138370, intron 5 of 6)	7942	NM_138370	91461	Hs.408542	NM_138370	ENSG00000162878	PKDCC	SGK493|Vlk	protein kinase domain containing, cytoplasmic	protein-coding	0.005172	0.521515	
chunk0142_323_1	chr4	100947105	100947466	+	0	NA	Intergenic	Intergenic	-272172	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.005540	0.364641	
chunk0178_341_1	chr7	38704223	38704615	+	0	NA	Intergenic	L2c|LINE|L2	-17330	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.005102	0.394402	
chunk0058_320_1	chr14	27638442	27638761	+	0	NA	non-coding (NR_039992, exon 5 of 5)	non-coding (NR_039992, exon 5 of 5)	-5323	NR_130461	100422830		NR_130461	ENSG00000264657	MIR3171	-	microRNA 3171	ncRNA	0.003135	0.403125	
chunk0116_212_1	chr21	37587248	37587447	+	0	NA	Intergenic	Intergenic	167047	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.010050	0.560000	
chunk0016_229_1	chr1	199679590	199679884	+	0	NA	Intergenic	Intergenic	-347865	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.003401	0.359322	200(ATCACATTCTGTGCTT,+,0.00)
chunk0131_334_1	chr3	151182641	151182878	+	0	NA	intron (NM_053002, intron 10 of 42)	intron (NM_053002, intron 10 of 42)	20442	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.004219	0.495798	
chunk0202_443_1	chr9	82169957	82170588	+	0	NA	Intergenic	Intergenic	181500	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.000000	0.346519	
chunk0104_86_1	chr2	172021676	172021875	+	0	NA	intron (NM_199227, intron 1 of 9)	intron (NM_199227, intron 1 of 9)	21878	NM_199227	254042	Hs.298250	NM_199227	ENSG00000172878	METAP1D	MAP 1D|MAP1D|MetAP 1D|Metap1l	methionyl aminopeptidase type 1D, mitochondrial	protein-coding	0.015075	0.545000	
chunk0161_395_1	chr5	177142357	177142556	+	0	NA	intron (NM_022455, intron 2 of 22)	L2c|LINE|L2	8624	NM_022455	64324	Hs.106861	NM_022455	ENSG00000165671	NSD1	ARA267|KMT3B|SOTOS|SOTOS1|STO	nuclear receptor binding SET domain protein 1	protein-coding	0.000000	0.415000	
chunk0060_353_1	chr14	52233645	52234089	+	0	NA	Intergenic	Intergenic	-33846	NM_000953	5729	Hs.306831	NM_000953	ENSG00000168229	PTGDR	AS1|ASRT1|DP|DP1|PTGDR1	prostaglandin D2 receptor	protein-coding	0.004505	0.422472	255(GAGGACATACTGCTCC,-,0.00),256(AGGACATACTGCTCCA,+,0.00)
chunk0191_432_1	chr8	57855166	57855845	+	0	NA	Intergenic	Intergenic	-122853	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.014728	0.458824	
chunk0051_254_1	chr12	117507499	117508053	+	0	NA	intron (NM_173598, intron 14 of 19)	MamRep434|DNA|TcMar-Tigger	-145974	NM_000620	4842	Hs.654410	NM_000620	ENSG00000089250	NOS1	IHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS	nitric oxide synthase 1	protein-coding	0.005415	0.484685	
chunk0004_343_1	chr1	50821615	50821814	+	0	NA	intron (NM_007051, intron 2 of 18)	MIR|SINE|MIR	138550	NM_007051	11124	Hs.530402	NM_007051	ENSG00000185104	FAF1	CGI-03|HFAF1s|UBXD12|UBXN3A|hFAF1	Fas associated factor 1	protein-coding	0.005025	0.305000	
chunk0055_80_1	chr13	53847445	53848008	+	0	NA	intron (NR_047488, intron 4 of 5)	intron (NR_047488, intron 4 of 5)	32307	NR_047488	100861552	Hs.224691	NR_047488	ENSG00000261517	LINC00558	-	long intergenic non-protein coding RNA 558	ncRNA	0.007105	0.368794	158(AAAAACTTCCTGTTCC,-,0.00)
chunk0145_377_1	chr4	151561487	151562056	+	0	NA	intron (NM_001109977, intron 3 of 13)	intron (NM_001109977, intron 3 of 13)	152525	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.001757	0.336842	
chunk0087_115_1	chr18	32694166	32694365	+	0	NA	intron (NM_020805, intron 4 of 8)	X6B_LINE|LINE|CR1	78746	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.005025	0.365000	
chunk0077_165_1	chr16	79372042	79372477	+	0	NA	Intergenic	Intergenic	228466	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.002299	0.364679	
chunk0208_451_1	chrX	32783868	32784310	+	0	NA	intron (NM_004010, intron 7 of 78)	intron (NM_004010, intron 7 of 78)	-142530	NR_031646	100302239		NR_031646	ENSG00000221348	MIR548F5	MIR548F-5|MIRN548F5|hsa-mir-548f-5	microRNA 548f-5	ncRNA	0.011312	0.349887	
chunk0058_242_1	chr14	25589964	25590398	+	0	NA	Intergenic	L1MC|LINE|L1	-539884	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004608	0.298851	
chunk0028_43_1	chr10	83142106	83142560	+	0	NA	Intergenic	Intergenic	-909413	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.006608	0.439560	
chunk0206_337_1	chr9	125511725	125512583	+	0	NA	intron (NM_001006620, intron 6 of 10)	intron (NM_001006620, intron 6 of 10)	195080	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.017483	0.438882	
chunk0211_438_1	chrX	129551034	129551297	+	0	NA	intron (NM_000276, intron 4 of 23)	L2a|LINE|L2	10890	NM_001587	4952	Hs.126357	NM_000276	ENSG00000122126	OCRL	INPP5F|LOCR|NPHL2|OCRL-1|OCRL1	OCRL inositol polyphosphate-5-phosphatase	protein-coding	0.003802	0.329545	
chunk0188_104_1	chr8	8885005	8885254	+	0	NA	intron (NM_004225, intron 1 of 2)	intron (NM_004225, intron 1 of 2)	8492	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.016064	0.424000	
chunk0172_353_1	chr6	139014898	139015457	+	0	NA	Intergenic	Intergenic	-13505	NM_021243	58527	Hs.600861	NM_021243	ENSG00000146386	ABRACL	C6orf115|Costars|HSPC280|PRO2013	ABRA C-terminal like	protein-coding	0.005367	0.426786	
chunk0015_197_1	chr1	187352100	187352702	+	0	NA	intron (NR_126347, intron 3 of 3)	L1PA11|LINE|L1	-91227	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008306	0.331675	
chunk0063_90_1	chr14	78270320	78270971	+	0	NA	intron (NR_073547, intron 2 of 20)	intron (NR_073547, intron 2 of 20)	100272	NR_073547	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004608	0.411043	448(AGGGACAATCAGTTCT,-,0.00),449(GGGACAATCAGTTCTG,+,0.00)
chunk0184_439_1	chr7	123116515	123117258	+	0	NA	intron (NM_022444, intron 14 of 14)	intron (NM_022444, intron 14 of 14)	83085	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.005384	0.372312	
chunk0193_305_1	chr8	78034185	78034707	+	0	NA	Intergenic	L2|LINE|L2	-481655	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.000000	0.363289	
chunk0132_415_1	chr3	164462536	164463028	+	0	NA	Intergenic	L1PA16|LINE|L1	-291226	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.004065	0.336714	
chunk0112_361_1	chr20	45449427	45449874	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-20104	NM_006103	10406	Hs.2719	NM_006103	ENSG00000101443	WFDC2	EDDM4|HE4|WAP5|dJ461P17.6	WAP four-disulfide core domain 2	protein-coding	0.011186	0.479911	134(GAGATCAGGGTGTCCA,-,0.00),135(AGATCAGGGTGTCCAC,+,0.00)
chunk0148_308_1	chr5	12935796	12936008	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	268043	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.004717	0.483568	
chunk0048_212_1	chr12	81401247	81401870	+	0	NA	intron (NM_001220474, intron 6 of 30)	intron (NM_001220474, intron 6 of 30)	-32144	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003210	0.299679	
chunk0006_432_1	chr1	76494852	76495434	+	0	NA	intron (NM_152996, intron 3 of 4)	MLT2B4|LTR|ERVL	-372358	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.005155	0.403087	98(AAAAACATGATGTCCC,-,0.00),99(AAAACATGATGTCCCA,+,0.00)
chunk0209_74_1	chrX	38045735	38045991	+	0	NA	intron (NM_138780, intron 2 of 16)	intron (NM_138780, intron 2 of 16)	12329	NM_001163334	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.007812	0.396887	
chunk0196_173_1	chr8	105888699	105888953	+	0	NA	intron (NR_125796, intron 2 of 7)	intron (NR_125796, intron 2 of 7)	171677	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.003937	0.321569	
chunk0135_286_1	chr3	189437761	189438456	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-193319	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.002878	0.428161	
chunk0148_229_1	chr5	9372324	9372956	+	0	NA	intron (NM_003966, intron 3 of 22)	intron (NM_003966, intron 3 of 22)	-138693	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.017405	0.527646	
chunk0122_238_1	chr3	33837137	33837561	+	0	NA	intron (NM_001162429, intron 8 of 17)	intron (NM_001162429, intron 8 of 17)	38778	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.007075	0.411765	
chunk0023_334_1	chr10	29364880	29365303	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-44443	NR_110920	102724316	Hs.499209	NR_003930	ENSG00000224597	SVIL-AS1	-	SVIL antisense RNA 1	ncRNA	0.014184	0.358491	260(CAGTACATGCTGTGCA,-,0.00),261(AGTACATGCTGTGCAG,+,0.00)
chunk0210_233_1	chrX	82541886	82542281	+	0	NA	Intergenic	L1PA17|LINE|L1	-966178	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.005063	0.330808	
chunk0067_445_1	chr15	50215634	50216207	+	0	NA	intron (NM_003645, intron 4 of 9)	L1PB1|LINE|L1	33724	NM_003645	11001	Hs.11729	NM_003645	ENSG00000140284	SLC27A2	ACSVL1|FACVL1|FATP2|HsT17226|VLACS|VLCS|hFACVL1	solute carrier family 27 member 2	protein-coding	0.008726	0.348432	
chunk0076_187_1	chr16	67701781	67702328	+	0	NA	intron (NM_030819, intron 1 of 2)	MER58A|DNA|hAT-Charlie	17316	NM_030819	81577	Hs.307084	NM_030819	ENSG00000141098	GFOD2	-	glucose-fructose oxidoreductase domain containing 2	protein-coding	0.009141	0.427007	
chunk0134_54_1	chr3	175978309	175978519	+	0	NA	Intergenic	Intergenic	-202081	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.042857	0.606635	
chunk0005_270_1	chr1	59892211	59892460	+	0	NA	TTS (NM_000775)	TTS (NM_000775)	34416	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.004016	0.400000	
chunk0174_139_1	chr6	157529494	157529839	+	0	NA	TTS (NR_037463)	TTS (NR_037463)	534	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.014493	0.442197	
chunk0098_184_1	chr2	71513256	71513599	+	0	NA	intron (NM_001130980, intron 6 of 54)	intron (NM_001130980, intron 6 of 54)	46725	NM_001130983	8291	Hs.252180	NM_003494	ENSG00000135636	DYSF	FER1L1|LGMD2B|LGMDR2|MMD1	dysferlin	protein-coding	0.020408	0.593023	
chunk0132_165_1	chr3	156680970	156681434	+	0	NA	intron (NM_015508, intron 2 of 5)	intron (NM_015508, intron 2 of 5)	4538	NM_001184718	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.008621	0.397849	
chunk0083_385_1	chr17	71572734	71573158	+	0	NA	Intergenic	Intergenic	-370767	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.011792	0.409412	
chunk0027_300_1	chr10	77835740	77836005	+	0	NA	exon (NM_004747, exon 8 of 32)	exon (NM_004747, exon 8 of 32)	90718	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.033962	0.605263	
chunk0190_390_1	chr8	40147240	40147462	+	0	NA	Intergenic	L2c|LINE|L2	-6117	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.027027	0.385650	
chunk0087_465_1	chr18	42972558	42973105	+	0	NA	intron (NM_001272077, intron 3 of 5)	intron (NM_001272077, intron 3 of 5)	142861	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.266423	
chunk0109_301_1	chr20	8757805	8758316	+	0	NA	intron (NM_015192, intron 24 of 31)	intron (NM_015192, intron 24 of 31)	-73125	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.003914	0.357422	
chunk0068_350_1	chr15	57826916	57827545	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	120709	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.015898	0.450794	
chunk0176_82_1	chr7	11496508	11497037	+	0	NA	intron (NM_015204, intron 6 of 26)	intron (NM_015204, intron 6 of 26)	335426	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.009452	0.349057	
chunk0037_353_1	chr11	77581501	77581705	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-8032	NM_173039	282679	Hs.503345	NM_173039	ENSG00000178301	AQP11	AQPX1	aquaporin 11	protein-coding	0.004902	0.297561	
chunk0077_415_1	chr16	85149696	85150131	+	0	NA	TTS (NR_033984)	TTS (NR_033984)	12763	NR_033984	400548	Hs.592054	NR_033984	ENSG00000278214	LINC02139	-	long intergenic non-protein coding RNA 2139	ncRNA	0.027586	0.589450	
chunk0167_175_1	chr6	63522525	63522773	+	0	NA	Intergenic	Intergenic	-49363	NM_003463	7803	Hs.227777	NM_003463	ENSG00000112245	PTP4A1	HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1	protein tyrosine phosphatase 4A1	protein-coding	0.000000	0.341365	
chunk0160_59_1	chr5	149719609	149720208	+	0	NA	Intergenic	Intergenic	-10344	NM_001172698	133522	Hs.483816	NM_133263	ENSG00000155846	PPARGC1B	ERRL1|PERC|PGC-1(beta)|PGC1B	PPARG coactivator 1 beta	protein-coding	0.006678	0.413333	
chunk0044_200_1	chr12	30791250	30791784	+	0	NA	Intergenic	LTR39|LTR|ERV1	-4164	NR_040245	100287314	Hs.355210	NR_040245		LINC00941	lncRNA-MUF	long intergenic non-protein coding RNA 941	ncRNA	0.005618	0.435514	
chunk0014_15_1	chr1	174438125	174438475	+	0	NA	intron (NM_014857, intron 13 of 20)	L1ME2|LINE|L1	-9774	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.017143	0.370370	
chunk0098_55_1	chr2	66655875	66656548	+	0	NA	intron (NR_110156, intron 1 of 5)	intron (NR_110156, intron 1 of 5)	47016	NR_110265	101927577	Hs.380543	NR_110264	ENSG00000237179	LINC01797	-	long intergenic non-protein coding RNA 1797	ncRNA	0.005944	0.385757	424(CAGTACATCCTGAGCT,-,0.00),425(AGTACATCCTGAGCTT,+,0.00)
chunk0008_226_1	chr1	94004119	94004644	+	0	NA	intron (NM_000350, intron 44 of 49)	L1MC4a|LINE|L1	-94783	NM_001308253	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.007619	0.361217	
chunk0067_65_1	chr15	41206380	41206650	+	0	NA	intron (NM_152596, intron 5 of 9)	HAL1|LINE|L1	24242	NM_152596	161829	Hs.307999	NM_152596	ENSG00000178997	EXD1	EXDL1	exonuclease 3'-5' domain containing 1	protein-coding	0.003704	0.354244	
chunk0136_95_1	chr4	2811912	2812376	+	0	NA	promoter-TSS (NM_001145855)	promoter-TSS (NM_001145855)	-75	NM_001145855	6452	Hs.167679	NM_003023	ENSG00000087266	SH3BP2	3BP-2|3BP2|CRBM|CRPM|RES4-23	SH3 domain binding protein 2	protein-coding	0.021552	0.630108	329(GGGAACAGGAAGTCCC,-,0.00),330(GGAACAGGAAGTCCCG,+,0.00)
chunk0126_412_1	chr3	85535218	85535808	+	0	NA	intron (NM_001256503, intron 2 of 9)	intron (NM_001256503, intron 2 of 9)	30454	NM_001256502	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.005085	0.392555	128(GGAACTCTCTGTTTCC,+,0.00)
chunk0153_13_1	chr5	66827798	66828071	+	0	NA	promoter-TSS (NM_015183)	promoter-TSS (NM_015183)	-842	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.010989	0.335766	
chunk0051_382_1	chr12	121839678	121840171	+	0	NA	intron (NM_001171993, intron 15 of 15)	intron (NM_001171993, intron 15 of 15)	18939	NM_002150	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.038540	0.603239	239(GGGGACAAGCAGTACC,-,0.00),240(GGGACAAGCAGTACCT,+,0.00)
chunk0164_258_1	chr6	23512072	23512648	+	0	NA	Intergenic	Intergenic	-613826	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.001736	0.313692	492(TGGAAGAGAGTGTTCT,-,0.00),493(GGAAGAGAGTGTTCTT,+,0.00)
chunk0102_302_1	chr2	150847537	150847736	+	0	NA	Intergenic	Intergenic	218739	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.005025	0.305000	
chunk0180_23_1	chr7	53700231	53700595	+	0	NA	intron (NR_038371, intron 4 of 5)	intron (NR_038371, intron 4 of 5)	111518	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.008242	0.361644	
chunk0100_248_1	chr2	112979251	112979450	+	0	NA	intron (NM_019618, intron 3 of 4)	intron (NM_019618, intron 3 of 4)	1331	NM_019618	56300	Hs.211238	NM_019618	ENSG00000136688	IL36G	IL-1F9|IL-1H1|IL-1RP2|IL1E|IL1F9|IL1H1|IL1RP2	interleukin 36 gamma	protein-coding	0.005025	0.530000	
chunk0168_138_1	chr6	82958725	82958968	+	0	NA	intron (NM_198920, intron 8 of 9)	MER34D|LTR|ERV1	106995	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.000000	0.401639	
chunk0110_371_1	chr20	19945697	19946127	+	0	NA	intron (NM_018993, intron 2 of 10)	intron (NM_018993, intron 2 of 10)	56346	NM_018993	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.011628	0.496520	
chunk0004_329_1	chr1	50181088	50181375	+	0	NA	intron (NM_021952, intron 3 of 6)	intron (NM_021952, intron 3 of 6)	71615	NM_001294348	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.006969	0.444444	
chunk0020_336_1	chr1	239026055	239026735	+	0	NA	Intergenic	Intergenic	-540378	NR_015407	339535	Hs.532047	NR_015407	ENSG00000215808	LINC01139	LINK-A|LINKA	long intergenic non-protein coding RNA 1139	ncRNA	0.010294	0.374449	
chunk0013_113_1	chr1	167926474	167927296	+	0	NA	intron (NR_026550, intron 1 of 4)	L2c|LINE|L2	9316	NR_026550	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.009732	0.427704	326(CAGTTCATGCTGTCCC,-,0.00),327(AGTTCATGCTGTCCCT,+,0.00)
chunk0011_101_1	chr1	145927515	145927714	+	0	NA	promoter-TSS (NM_005105)	promoter-TSS (NM_005105)	-78	NM_005105	9939	Hs.591455	NM_005105	ENSG00000265241	RBM8A	BOV-1A|BOV-1B|BOV-1C|C1DELq21.1|DEL1q21.1|MDS014|RBM8|RBM8B|TAR|Y14|ZNRP|ZRNP1	RNA binding motif protein 8A	protein-coding	0.045226	0.505000	
chunk0149_384_1	chr5	28542193	28542416	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-384566	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.004484	0.437500	
chunk0083_151_1	chr17	65840541	65841008	+	0	NA	intron (NM_001302891, intron 19 of 24)	L1MA4|LINE|L1	-14231	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.301282	
chunk0140_322_1	chr4	73500384	73500701	+	0	NA	intron (NM_001133, intron 12 of 14)	intron (NM_001133, intron 12 of 14)	-8261	NR_046377	728040	Hs.640574	NR_046377	ENSG00000250436	LINC02499	-	long intergenic non-protein coding RNA 2499	ncRNA	0.003155	0.364780	
chunk0173_410_1	chr6	150926655	150927198	+	0	NA	intron (NM_001242767, intron 11 of 27)	intron (NM_001242767, intron 11 of 27)	60593	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.003683	0.301471	
chunk0037_221_1	chr11	74856718	74856983	+	0	NA	intron (NM_001270381, intron 9 of 15)	L1MCc|LINE|L1	92337	NM_001270381	143570	Hs.370145	NM_182969	ENSG00000166435	XRRA1	-	X-ray radiation resistance associated 1	protein-coding	0.003774	0.522556	
chunk0016_243_1	chr1	199918304	199919257	+	0	NA	Intergenic	Intergenic	-108822	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.003148	0.364780	
chunk0123_305_1	chr3	47031016	47031712	+	0	NA	intron (NM_014159, intron 18 of 20)	L1MC1|LINE|L1	19822	NR_024046	100129354	Hs.201522	NR_024046		NRADDP	-	neurotrophin receptor associated death domain, pseudogene	pseudo	0.005747	0.348637	
chunk0187_380_1	chr7	157636689	157637128	+	0	NA	intron (NM_001308268, intron 14 of 22)	intron (NM_001308268, intron 14 of 22)	-62486	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.006834	0.293182	
chunk0130_331_1	chr3	138242412	138242852	+	0	NA	intron (NM_001282342, intron 9 of 19)	intron (NM_001282342, intron 9 of 19)	55384	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.002273	0.365079	
chunk0062_352_1	chr14	73758328	73758600	+	0	NA	promoter-TSS (NR_039727)	promoter-TSS (NR_039727)	-283	NR_039727	100616158		NR_039727	ENSG00000264741	MIR4505	mir-4505	microRNA 4505	ncRNA	0.022059	0.633700	
chunk0142_349_1	chr4	101693916	101694258	+	0	NA	Intergenic	Intergenic	-96520	NM_001127507	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.008772	0.416910	
chunk0054_327_1	chr13	49188489	49189274	+	0	NA	intron (NM_014923, intron 15 of 23)	intron (NM_014923, intron 15 of 23)	-31457	NM_001507	2862	Hs.248126	NM_001507	ENSG00000102539	MLNR	GPR38|MTLR1	motilin receptor	protein-coding	0.008917	0.360051	634(AAAGACATAATGTTCT,-,0.00),635(AAGACATAATGTTCTA,+,0.00)
chunk0050_251_1	chr12	105594788	105595108	+	0	NA	Intergenic	L2b|LINE|L2	-109255	NR_110109	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.012500	0.451713	191(TAGTACACAGTGTCCC,-,0.00),192(AGTACACAGTGTCCCT,+,0.00)
chunk0040_319_1	chr11	118041975	118042506	+	0	NA	intron (NR_038318, intron 2 of 3)	L1MB7|LINE|L1	-34772	NM_001173551	56649	Hs.161985	NM_019894	ENSG00000137648	TMPRSS4	CAPH2|MT-SP2|TMPRSS3	transmembrane serine protease 4	protein-coding	0.001883	0.340226	
chunk0200_442_1	chr9	30530738	30531075	+	0	NA	Intergenic	LTR1D|LTR|ERV1	-122452	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.011869	0.547337	
chunk0138_127_1	chr4	36578816	36579257	+	0	NA	Intergenic	L1PB1|LINE|L1	-152608	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.006803	0.352941	
chunk0155_268_1	chr5	95946492	95946793	+	0	NA	intron (NM_012081, intron 1 of 11)	intron (NM_012081, intron 1 of 11)	-15359	NR_130776	101929710		NR_130776	ENSG00000251314	LOC101929710	-	uncharacterized LOC101929710	ncRNA	0.003322	0.407285	
chunk0205_109_1	chr9	107614765	107615257	+	0	NA	Intergenic	Intergenic	-125291	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.016260	0.535497	
chunk0099_108_1	chr2	85725498	85725887	+	0	NA	Intergenic	HAL1|LINE|L1	-28094	NM_032827	84913	Hs.135569	NM_032827	ENSG00000168874	ATOH8	HATH6|bHLHa21	atonal bHLH transcription factor 8	protein-coding	0.005141	0.387179	
chunk0140_240_1	chr4	71284997	71285295	+	0	NA	intron (NM_001098484, intron 3 of 25)	intron (NM_001098484, intron 3 of 25)	-53907	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.003356	0.428094	
chunk0042_210_1	chr12	6037537	6037758	+	0	NA	intron (NM_000552, intron 18 of 51)	intron (NM_000552, intron 18 of 51)	87023	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.013575	0.603604	
chunk0038_27_1	chr11	81160818	81161398	+	0	NA	Intergenic	Intergenic	-398305	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.010345	0.292599	
chunk0128_393_1	chr3	113952987	113953918	+	0	NA	intron (NM_173570, intron 2 of 5)	intron (NM_173570, intron 2 of 5)	5551	NM_173570	254887	Hs.21902	NM_173570	ENSG00000184307	ZDHHC23	DHHC-23|NIDD	zinc finger DHHC-type containing 23	protein-coding	0.005371	0.412017	
chunk0078_435_1	chr16	89471870	89472581	+	0	NA	intron (NM_001256182, intron 1 of 13)	intron (NM_001256182, intron 1 of 13)	18336	NM_013275	29123	Hs.335003	NM_013275	ENSG00000167522	ANKRD11	ANCO-1|ANCO1|LZ16|T13	ankyrin repeat domain 11	protein-coding	0.014065	0.484551	
chunk0117_194_1	chr22	21629232	21629457	+	0	NA	exon (NM_001017964, exon 3 of 5)	exon (NM_001017964, exon 3 of 5)	707	NM_001017964	150223	Hs.355952	NM_001017964	ENSG00000161179	YDJC	-	YdjC chitooligosaccharide deacetylase homolog	protein-coding	0.080000	0.676991	
chunk0158_213_1	chr5	128324062	128324861	+	0	NA	intron (NM_001999, intron 34 of 64)	L1PA7|LINE|L1	213581	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.012516	0.401250	496(AGGAACAGGTTGTTCA,-,0.00),497(GGAACAGGTTGTTCAG,+,0.00)
chunk0027_16_1	chr10	72119351	72119967	+	0	NA	intron (NM_001198799, intron 10 of 12)	L1MCa|LINE|L1	-30627	NM_001134434	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.006494	0.447326	293(CAGTACATCATGTCCC,-,0.00),294(AGTACATCATGTCCCT,+,0.00)
chunk0089_370_1	chr18	67133459	67134120	+	0	NA	Intergenic	Intergenic	52205	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.009077	0.371601	
chunk0151_24_1	chr5	41670927	41671133	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-160402	NM_001005473	345557	Hs.145404	NM_001005473	ENSG00000182836	PLCXD3	-	phosphatidylinositol specific phospholipase C X domain containing 3	protein-coding	0.009709	0.507246	
chunk0038_88_1	chr11	83371516	83371721	+	0	NA	Intergenic	L1MC3|LINE|L1	-85211	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.000000	0.427184	
chunk0121_432_1	chr3	25950385	25951141	+	0	NA	Intergenic	LTR33|LTR|ERVL	-77068	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.002646	0.396301	473(AGGCACACAAAGTTCC,-,0.00),474(GGCACACAAAGTTCCA,+,0.00)
chunk0170_352_1	chr6	116417588	116418196	+	0	NA	intron (NM_001080976, intron 2 of 5)	MER67A|LTR|ERV1	-43478	NM_001010919	441168	Hs.381220	NM_001010919	ENSG00000188820	CALHM6	C6orf187|FAM26F|INAM|dJ93H18.5	calcium homeostasis modulator family member 6	protein-coding	0.006579	0.367816	
chunk0166_79_1	chr6	43601027	43601226	+	0	NA	intron (NM_001291969, intron 4 of 8)	intron (NM_001291969, intron 4 of 8)	24985	NM_006502	5429	Hs.655467	NM_006502	ENSG00000170734	POLH	RAD30|RAD30A|XP-V|XPV	DNA polymerase eta	protein-coding	0.010050	0.435000	
chunk0047_374_1	chr12	75167459	75167933	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	42052	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.002110	0.290526	
chunk0105_82_1	chr2	183927375	183927686	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-451445	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.419872	
chunk0101_429_1	chr2	139324080	139324448	+	0	NA	Intergenic	Intergenic	426940	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.002717	0.336043	
chunk0050_6_1	chr12	99553393	99553984	+	0	NA	intron (NM_152788, intron 9 of 25)	intron (NM_152788, intron 9 of 25)	-94062	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.008460	0.395270	
chunk0166_379_1	chr6	51633978	51634480	+	0	NA	intron (NM_138694, intron 64 of 66)	intron (NM_138694, intron 64 of 66)	12359	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.000000	0.345924	
chunk0174_356_1	chr6	164436374	164436660	+	0	NA	Intergenic	L2c|LINE|L2	385546	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.000000	0.414634	143(CTGATCAGAATGTTCT,-,0.00),144(TGATCAGAATGTTCTT,+,0.00)
chunk0177_148_1	chr7	22723395	22723688	+	0	NA	Intergenic	Intergenic	-3606	NM_000600	3569	Hs.654458	NM_000600	ENSG00000136244	IL6	BSF-2|BSF2|CDF|HGF|HSF|IFN-beta-2|IFNB2|IL-6	interleukin 6	protein-coding	0.010239	0.448980	
chunk0046_3_1	chr12	53978332	53978531	+	0	NA	Intergenic	Intergenic	-3475	NR_047517	100124700	Hs.197076	NR_003716	ENSG00000228630	HOTAIR	HOXAS|HOXC-AS4|HOXC11-AS1|NCRNA00072	HOX transcript antisense RNA	ncRNA	0.035176	0.605000	
chunk0141_383_1	chr4	88204546	88205293	+	0	NA	intron (NM_001257386, intron 1 of 15)	intron (NM_001257386, intron 1 of 15)	26403	NM_001257386	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.001339	0.366310	
chunk0017_21_1	chr1	204479654	204480089	+	0	NA	intron (NM_002646, intron 2 of 33)	intron (NM_002646, intron 2 of 33)	10475	NM_002646	5287	Hs.497487	NM_002646	ENSG00000133056	PIK3C2B	C2-PI3K	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta	protein-coding	0.018391	0.561927	
chunk0035_451_1	chr11	57741153	57741630	+	0	NA	TTS (NM_001144012)	TTS (NM_001144012)	141	NM_170746	280636	Hs.655373	NM_170746	ENSG00000211450	SELENOH	C11orf31|C17orf10|SELH	selenoprotein H	protein-coding	0.069182	0.635983	
chunk0157_364_1	chr5	123439633	123440102	+	0	NA	Intergenic	Intergenic	-16275	NM_153223	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.010661	0.400000	
chunk0076_270_1	chr16	69481970	69482343	+	0	NA	Intergenic	Intergenic	57561	NM_030579	80777	Hs.461131	NM_030579	ENSG00000103018	CYB5B	CYB5-M|CYPB5M|OMB5	cytochrome b5 type B	protein-coding	0.032172	0.574866	
chunk0002_275_1	chr1	21957300	21957665	+	0	NA	Intergenic	Intergenic	-19443	NM_007352	23436	Hs.728752	NM_007352	ENSG00000219073	CELA3B	CBPP|ELA3B	chymotrypsin like elastase 3B	protein-coding	0.032877	0.513661	
chunk0116_207_1	chr21	37450227	37450784	+	0	NA	intron (NM_130436, intron 1 of 10)	L2a|LINE|L2	30205	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.008977	0.435484	
chunk0001_412_1	chr1	11070952	11071198	+	0	NA	intron (NM_001001998, intron 20 of 24)	intron (NM_001001998, intron 20 of 24)	-11041	NM_003132	6723	Hs.76244	NM_003132	ENSG00000116649	SRM	PAPT|SPDSY|SPS1|SRML1	spermidine synthase	protein-coding	0.020325	0.619433	
chunk0065_39_1	chr15	21260965	21262058	+	0	NA	Intergenic	Intergenic	36318	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.031107	0.610603	
chunk0048_98_1	chr12	79327493	79328107	+	0	NA	intron (NM_001291901, intron 7 of 9)	intron (NM_001291901, intron 7 of 9)	-91457	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.003257	0.400000	382(AAGAACAAGATGTCCA,-,0.00),383(AGAACAAGATGTCCAG,+,0.00)
chunk0151_427_1	chr5	55797111	55797369	+	0	NA	intron (NM_024415, intron 17 of 21)	intron (NM_024415, intron 17 of 21)	30355	NM_001166534	54514	Hs.223581	NM_019039	ENSG00000152670	DDX4	VASA	DEAD-box helicase 4	protein-coding	0.003876	0.370656	129(TGGAACATAGTGTTCA,-,0.00),130(GGAACATAGTGTTCAG,+,0.00)
chunk0135_160_1	chr3	187801245	187801885	+	0	NA	Intergenic	Intergenic	-55840	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.009375	0.453978	
chunk0005_187_1	chr1	58886683	58886910	+	0	NA	intron (NR_108106, intron 1 of 1)	intron (NR_108106, intron 1 of 1)	101645	NR_034014	100131060	Hs.680604	NR_034014	ENSG00000234807	LINC01135	-	long intergenic non-protein coding RNA 1135	ncRNA	0.013216	0.513158	72(AGAAACACTGTGTTCC,-,0.00),73(GAAACACTGTGTTCCC,+,0.00)
chunk0100_316_1	chr2	116148568	116148767	+	0	NA	Intergenic	Intergenic	986560	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.000000	0.320000	
chunk0204_446_1	chr9	104105641	104105845	+	0	NA	intron (NM_001042550, intron 9 of 24)	MER70-int|LTR|ERVL	11193	NM_001042550	10592	Hs.119023	NM_006444	ENSG00000136824	SMC2	CAP-E|CAPE|SMC-2|SMC2L1	structural maintenance of chromosomes 2	protein-coding	0.000000	0.429268	142(AGGACCAGATTGTCCC,-,0.00),143(GGACCAGATTGTCCCT,+,0.00)
chunk0167_118_1	chr6	58116379	58117640	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-155563	NR_125729	106660612	Hs.561539	NR_125727	ENSG00000215190	LINC00680	-	long intergenic non-protein coding RNA 680	ncRNA	0.003172	0.426307	186(CAAAACATTATGTACC,-,0.00),187(AAAACATTATGTACCC,+,0.00),600(GTCACACTGTGTTCTT,+,0.00)
chunk0010_68_1	chr1	113072825	113073024	+	0	NA	promoter-TSS (NM_014813)	promoter-TSS (NM_014813)	178	NR_103777	100996251	Hs.382067	NR_103777	ENSG00000238198	LRIG2-DT	-	LRIG2 divergent transcript	ncRNA	0.040201	0.505000	
chunk0055_189_1	chr13	61628734	61628984	+	0	NA	Intergenic	L1PA6|LINE|L1	-213337	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.004000	0.565737	
chunk0024_332_1	chr10	43187126	43187699	+	0	NA	Intergenic	L1MC1|LINE|L1	42327	NM_001282862	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.006981	0.367596	
chunk0045_278_1	chr12	49873184	49873619	+	0	NA	intron (NM_012306, intron 11 of 11)	MamRep605|LTR?|LTR?	-30272	NM_181708	144233	Hs.142736	NM_181708	ENSG00000186666	BCDIN3D	-	BCDIN3 domain containing RNA methyltransferase	protein-coding	0.006897	0.479358	
chunk0210_364_1	chrX	96604625	96604859	+	0	NA	Intergenic	L2a|LINE|L2	-79921	NM_006729	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.004274	0.382979	
chunk0144_326_1	chr4	139071836	139072181	+	0	NA	exon (NM_001276457, exon 3 of 6)	exon (NM_001276457, exon 3 of 6)	12406	NM_006874	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.002899	0.369942	
chunk0175_99_1	chr7	2830586	2831420	+	0	NA	intron (NM_001293092, intron 1 of 2)	intron (NM_001293092, intron 1 of 2)	13322	NM_001293092	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.010791	0.443114	
chunk0207_124_1	chr9	128992575	128992903	+	0	NA	intron (NM_015354, intron 25 of 43)	L1ME4b|LINE|L1	35614	NM_001287045	56904	Hs.460238	NM_020145	ENSG00000148341	SH3GLB2	PP6569|PP9455|RRIG1	SH3 domain containing GRB2 like, endophilin B2	protein-coding	0.006098	0.313070	
chunk0063_170_1	chr14	80323331	80323703	+	0	NA	intron (NR_038355, intron 2 of 8)	intron (NR_038355, intron 2 of 8)	-92463	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.002688	0.327078	
chunk0130_118_1	chr3	131444140	131444427	+	0	NA	Intergenic	Intergenic	34950	NR_002985	677836	Hs.735762	NR_002985		SNORA58	ACA58|SNORA58B	small nucleolar RNA, H/ACA box 58	snoRNA	0.013937	0.430556	
chunk0022_337_1	chr10	16711663	16712187	+	0	NA	intron (NM_152724, intron 6 of 7)	L1MA6|LINE|L1	105529	NM_152724	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.001908	0.320000	
chunk0169_310_1	chr6	106103608	106104079	+	0	NA	intron (NM_182907, intron 2 of 4)	intron (NM_182907, intron 2 of 4)	4981	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.021231	0.470339	
chunk0135_410_1	chr3	192820710	192821400	+	0	NA	intron (NM_178496, intron 1 of 1)	intron (NM_178496, intron 1 of 1)	-93456	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.014493	0.447178	341(CAGAACATTACGTACC,-,0.00),342(AGAACATTACGTACCC,+,0.00)
chunk0118_3_1	chr22	25533708	25533907	+	0	NA	Intergenic	Intergenic	-31087	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.010050	0.455000	
chunk0196_412_1	chr8	116037487	116038099	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	287266	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.006536	0.342577	220(AAGGTCATGGTGTACC,-,0.00),221(AGGTCATGGTGTACCT,+,0.00)
chunk0032_148_1	chr11	4751094	4751651	+	0	NA	Intergenic	L2c|LINE|L2	18545	NM_001004752	256892		NM_001004752	ENSG00000280021	OR51F1	OR11-21|OR51F1P	olfactory receptor family 51 subfamily F member 1 (gene/pseudogene)	protein-coding	0.003591	0.327957	
chunk0170_284_1	chr6	114476155	114476424	+	0	NA	Intergenic	Intergenic	-413412	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.000000	0.277778	
chunk0209_450_1	chrX	65891721	65892248	+	0	NA	Intergenic	L1PA6|LINE|L1	-126886	NR_029637	407008		NR_029637	ENSG00000284567	MIR223	MIRN223|miRNA223|mir-223	microRNA 223	ncRNA	0.005693	0.375000	208(AGGAACAGGTTGTTCA,-,0.00),209(GGAACAGGTTGTTCAG,+,0.00)
chunk0001_162_1	chr1	6392212	6392545	+	0	NA	intron (NM_007274, intron 1 of 8)	intron (NM_007274, intron 1 of 8)	1388	NM_007274	11332	Hs.126137	NM_007274	ENSG00000097021	ACOT7	ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH	acyl-CoA thioesterase 7	protein-coding	0.012012	0.541916	
chunk0134_405_1	chr3	183155389	183156080	+	0	NA	intron (NM_014398, intron 1 of 5)	L2c|LINE|L2	7145	NM_014398	27074	Hs.518448	NM_014398	ENSG00000078081	LAMP3	CD208|DC LAMP|DC-LAMP|DCLAMP|LAMP|LAMP-3|TSC403	lysosomal associated membrane protein 3	protein-coding	0.008683	0.416185	
chunk0098_60_1	chr2	66840276	66840475	+	0	NA	Intergenic	Intergenic	-64061	NR_110169	101060019	Hs.116425	NR_110169	ENSG00000230525	LINC01799	-	long intergenic non-protein coding RNA 1799	ncRNA	0.010050	0.390000	124(AAGAACAGCCAGTGCT,-,0.00),125(AGAACAGCCAGTGCTT,+,0.00)
chunk0096_429_1	chr2	38426442	38426905	+	0	NA	Intergenic	MIR3|SINE|MIR	-49383	NR_024191									0.004320	0.372845	
chunk0079_219_1	chr17	14919069	14919660	+	0	NA	Intergenic	Intergenic	-111611	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.010152	0.440878	
chunk0187_448_1	chr7	159133603	159134264	+	0	NA	intron (NR_130758, intron 2 of 12)	intron (NR_130758, intron 2 of 12)	11024	NR_130758	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.006051	0.309668	
chunk0111_232_1	chr20	29262629	29263363	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	153965	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.005450	0.371429	
chunk0116_98_1	chr21	35254015	35254464	+	0	NA	Intergenic	Intergenic	-204941	NM_001754	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.017817	0.424444	246(AATGACACAATGTTCT,-,0.00),247(ATGACACAATGTTCTG,+,0.00)
chunk0062_284_1	chr14	72188856	72189515	+	0	NA	intron (NM_001204418, intron 2 of 16)	MER58A|DNA|hAT-Charlie	256116	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.009105	0.372727	
chunk0201_317_1	chr9	43346833	43347344	+	0	NA	Intergenic	(TCGAT)n|Simple_repeat|Simple_repeat	558688	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.041096	0.367188	
chunk0163_388_1	chr6	16422682	16422881	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	184201	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.005025	0.420000	
chunk0142_6_1	chr4	89839160	89839901	+	0	NA	intron (NR_045481, intron 2 of 3)	intron (NR_045481, intron 2 of 3)	-1234	NM_001146055	6622	Hs.21374	NM_000345	ENSG00000145335	SNCA	NACP|PARK1|PARK4|PD1	synuclein alpha	protein-coding	0.005398	0.319407	
chunk0114_144_1	chr21	10325704	10325972	+	0	NA	Intergenic	HSATI|Satellite|Satellite	-87682	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.007463	0.360595	
chunk0026_443_1	chr10	71414603	71414828	+	0	NA	intron (NM_001171931, intron 1 of 24)	L1MEg|LINE|L1	17781	NM_001171930	64072	Hs.656032	NM_022124	ENSG00000107736	CDH23	CDHR23|PITA5|USH1D	cadherin related 23	protein-coding	0.008889	0.323009	
chunk0179_340_1	chr7	50730631	50730830	+	0	NA	intron (NM_001001555, intron 2 of 16)	intron (NM_001001555, intron 2 of 16)	1623	NM_005311	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.005025	0.540000	
chunk0067_50_1	chr15	40831643	40832232	+	0	NA	Intergenic	L2b|LINE|L2	-3228	NM_001130143	54866	Hs.192927	NM_017726	ENSG00000166143	PPP1R14D	CPI17-like|GBPI-1|GBPI1	protein phosphatase 1 regulatory inhibitor subunit 14D	protein-coding	0.005093	0.440678	
chunk0117_426_1	chr21	46117131	46117400	+	0	NA	intron (NM_001849, intron 10 of 27)	intron (NM_001849, intron 10 of 27)	19146	NM_058175	1292	Hs.420269	NM_001849	ENSG00000142173	COL6A2	BTHLM1|PP3610|UCMD1	collagen type VI alpha 2 chain	protein-coding	0.037175	0.677778	
chunk0028_55_1	chr10	83225947	83226279	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-913316	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.006024	0.360360	
chunk0034_18_1	chr11	26061166	26061570	+	0	NA	Intergenic	Intergenic	-127755	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.007426	0.375309	
chunk0149_252_1	chr5	23823709	23824101	+	0	NA	Intergenic	MER77|LTR|ERVL	-127443	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.015306	0.437659	
chunk0080_3_1	chr17	20740767	20741326	+	0	NA	Intergenic	Intergenic	28600	NR_073509	100287072	Hs.676308	NR_073509		LOC100287072	-	ribosomal protein S6 kinase B1 pseudogene	pseudo	0.005367	0.314286	
chunk0082_9_1	chr17	49815675	49816094	+	0	NA	exon (NM_001199158, exon 5 of 12)	exon (NM_001199158, exon 5 of 12)	27265	NM_001199158	11143	Hs.21907	NM_007067	ENSG00000136504	KAT7	HBO1|HBOA|MYST2|ZC2HC7	lysine acetyltransferase 7	protein-coding	0.014320	0.416667	
chunk0131_263_1	chr3	150005719	150006049	+	0	NA	Intergenic	Intergenic	-22518	NM_001079809	653659	Hs.652908	NM_001079809		TMEM183B	C1ORF37DUP|C1orf37-DUP	transmembrane protein 183B	protein-coding	0.009091	0.368580	
chunk0100_303_1	chr2	115325280	115325605	+	0	NA	intron (NM_001178037, intron 2 of 25)	intron (NM_001178037, intron 2 of 25)	163335	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.003077	0.282209	
chunk0150_210_1	chr5	35188049	35188587	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	42271	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.018587	0.463822	
chunk0097_300_1	chr2	55839211	55839549	+	0	NA	Intergenic	Intergenic	84783	NM_001039349	2202	Hs.76224	NM_004105	ENSG00000115380	EFEMP1	DHRD|DRAD|FBLN3|FBNL|FIBL-3|MLVT|MTLV|S1-5	EGF containing fibulin extracellular matrix protein 1	protein-coding	0.011834	0.442478	
chunk0174_198_1	chr6	160099619	160099994	+	0	NA	intron (NM_000876, intron 45 of 47)	intron (NM_000876, intron 45 of 47)	6724	NR_003288	729603	Hs.674810	NR_003288	ENSG00000213073	LOC729603	-	calcineurin like EF-hand protein 1 pseudogene	pseudo	0.018667	0.433511	157(GAGGACACACTGTACT,-,0.00),158(AGGACACACTGTACTG,+,0.00)
chunk0120_390_1	chr3	12383271	12383629	+	0	NA	intron (NM_138711, intron 4 of 7)	intron (NM_138711, intron 4 of 7)	31948	NM_015869	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.005587	0.267409	
chunk0028_184_1	chr10	88449150	88449424	+	0	NA	intron (NM_001031709, intron 4 of 6)	L2c|LINE|L2	134038	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.003650	0.349091	51(AAGCACAAAATGTCCT,-,0.00),52(AGCACAAAATGTCCTC,+,0.00)
chunk0017_383_1	chr1	212202755	212202989	+	0	NA	Intergenic	Intergenic	31864	NR_125982	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.008547	0.523404	
chunk0186_240_1	chr7	140909622	140910324	+	0	NA	intron (NM_004333, intron 1 of 17)	MER20B|DNA|hAT-Charlie	14791	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.005698	0.365576	
chunk0173_160_1	chr6	144296822	144297121	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	5234	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.003344	0.423333	154(GAGGACAAACAGTCCT,-,0.00),155(AGGACAAACAGTCCTT,+,0.00)
chunk0081_156_1	chr17	40903190	40904006	+	0	NA	Intergenic	Intergenic	-18355	NM_019010	54474	Hs.84905	NM_019010	ENSG00000171431	KRT20	CD20|CK-20|CK20|K20|KRT21	keratin 20	protein-coding	0.014706	0.444308	209(AGGGACTGTGTGTCCT,-,0.00),210(GGGACTGTGTGTCCTT,+,0.00)
chunk0212_232_1	chrX	136453558	136454329	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-34023	NM_001727	680	Hs.121484	NM_001727	ENSG00000102239	BRS3	BB3|BB3R|BBR3	bombesin receptor subtype 3	protein-coding	0.003891	0.369171	
chunk0183_110_1	chr7	105328953	105329268	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	-30331	NM_001278273	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.003175	0.363924	103(AAGAACTGCAAGTTCC,-,0.00),104(AGAACTGCAAGTTCCA,+,0.00)
chunk0093_272_1	chr19	51573299	51573679	+	0	NA	intron (NM_007147, intron 2 of 4)	intron (NM_007147, intron 2 of 4)	2211	NM_007147	7728	Hs.119014	NM_007147	ENSG00000105497	ZNF175	OTK18	zinc finger protein 175	protein-coding	0.010526	0.524934	
chunk0060_221_1	chr14	49240954	49241192	+	0	NA	Intergenic	L1PA16|LINE|L1	345343	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.004202	0.497908	
chunk0043_421_1	chr12	25866851	25867185	+	0	NA	Intergenic	L1MB8|LINE|L1	7061	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.005988	0.528358	
chunk0076_369_1	chr16	72023749	72024425	+	0	NA	intron (NM_001361, intron 8 of 8)	intron (NM_001361, intron 8 of 8)	15343	NM_001361	1723	Hs.654427	NM_001361	ENSG00000102967	DHODH	DHOdehase|POADS|URA1	dihydroorotate dehydrogenase (quinone)	protein-coding	0.014793	0.502216	
chunk0102_317_1	chr2	151291736	151292016	+	0	NA	Intergenic	Intergenic	-1960	NM_004688	9111	Hs.54483	NM_004688	ENSG00000123609	NMI	-	N-myc and STAT interactor	protein-coding	0.007143	0.387900	
chunk0142_251_1	chr4	98946376	98946637	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-15871	NM_001968	1977	Hs.13211	NM_001968	ENSG00000151247	EIF4E	AUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding	0.000000	0.385496	
chunk0088_135_1	chr18	45859147	45859346	+	0	NA	intron (NM_020964, intron 40 of 43)	intron (NM_020964, intron 40 of 43)	33666	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.015075	0.380000	
chunk0152_319_1	chr5	62008606	62008853	+	0	NA	Intergenic	Intergenic	-273031	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.016194	0.528226	29(AAGGACGCTCAGTCCT,-,0.00)
chunk0186_322_1	chr7	143079971	143080386	+	0	NA	Intergenic	L1PB1|LINE|L1	-16393	NR_002140	89883	Hs.339818	NR_002140		OR6W1P	OR6W1|sdolf	olfactory receptor family 6 subfamily W member 1 pseudogene	pseudo	0.000000	0.355769	
chunk0033_432_1	chr11	25253011	25253285	+	0	NA	Intergenic	Intergenic	756178	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.010949	0.305455	
chunk0212_374_1	chrX	150077404	150077603	+	0	NA	Intergenic	Intergenic	138955	NR_027456	100272228	Hs.496916	NR_027456	ENSG00000235703	LINC00894	-	long intergenic non-protein coding RNA 894	ncRNA	0.005025	0.345000	
chunk0189_188_1	chr8	23620280	23621244	+	0	NA	Intergenic	Intergenic	62127	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.007261	0.375130	
chunk0167_331_1	chr6	72487998	72488637	+	0	NA	Intergenic	Intergenic	121587	NM_001168411	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.001565	0.264062	313(AAGAACATAGCGTCCC,-,0.00),314(AGAACATAGCGTCCCT,+,0.00)
chunk0126_173_1	chr3	78022216	78022802	+	0	NA	Intergenic	Intergenic	924497	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.010239	0.393526	
chunk0027_41_1	chr10	72535849	72536152	+	0	NA	intron (NM_006077, intron 4 of 11)	L1MA5A|LINE|L1	-12014	NM_001195519	10367	Hs.524367	NM_006077	ENSG00000107745	MICU1	CALC|CBARA1|EFHA3|MPXPS|ara CALC	mitochondrial calcium uptake 1	protein-coding	0.009901	0.384868	180(TAGAACAGGGTGTACC,-,0.00),181(AGAACAGGGTGTACCA,+,0.00)
chunk0084_255_1	chr17	79033000	79033548	+	0	NA	intron (NR_049769, intron 1 of 3)	MER3|DNA|hAT-Charlie	-1025	NM_198593	114897	Hs.201398	NM_030968	ENSG00000173918	C1QTNF1	CTRP1|GIP|ZSIG37	C1q and TNF related 1	protein-coding	0.016423	0.489982	256(GAGAACTGGATGTTTC,-,0.00)
chunk0050_349_1	chr12	107687045	107687403	+	0	NA	intron (NM_007062, intron 1 of 14)	intron (NM_007062, intron 1 of 14)	1411	NM_007062	11137	Hs.506652	NM_007062	ENSG00000136045	PWP1	IEF-SSP-9502	PWP1 homolog, endonuclein	protein-coding	0.005587	0.367688	160(GGGCACAGACTGTTTT,-,0.00),161(GGCACAGACTGTTTTA,+,0.00)
chunk0158_206_1	chr5	128156793	128156992	+	0	NA	intron (NR_046207, intron 15 of 26)	MLT1J2|LTR|ERVL-MaLR	73101	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.010050	0.445000	
chunk0093_334_1	chr19	54467922	54468132	+	0	NA	intron (NM_145057, intron 2 of 2).2	MIR|SINE|MIR	-4316	NM_001301782	94059	Hs.590976	NM_198988	ENSG00000275183	LENG9	-	leukocyte receptor cluster member 9	protein-coding	0.004762	0.317536	
chunk0192_238_1	chr8	65552473	65552768	+	0	NA	intron (NR_033893, intron 1 of 4)	L1MC1|LINE|L1	10046	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.010169	0.402027	
chunk0162_130_1	chr6	2968703	2968992	+	0	NA	5' UTR (NM_001195291, exon 2 of 8)	5' UTR (NM_001195291, exon 2 of 8)	2201	NM_001271823	5269	Hs.519523	NM_004568	ENSG00000124570	SERPINB6	CAP|DFNB91|MSTP057|PI-6|PI6|PTI|SPI3	serpin family B member 6	protein-coding	0.017301	0.503448	
chunk0046_430_1	chr12	64669307	64669730	+	0	NA	intron (NR_040718, intron 1 of 3)	intron (NR_040718, intron 1 of 3)	-46913	NR_037515	100500856		NR_037515	ENSG00000266016	MIR548Z	-	microRNA 548z	ncRNA	0.018913	0.476415	
chunk0008_210_1	chr1	93622572	93623058	+	0	NA	intron (NM_003567, intron 3 of 11)	intron (NM_003567, intron 3 of 11)	-8670	NM_001261410	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.010288	0.509240	
chunk0016_317_1	chr1	201565122	201565636	+	0	NA	Intergenic	Intergenic	45475	NR_026667	376693	Hs.605989	NR_026667		RPS10P7	RPS10_2_147	ribosomal protein S10 pseudogene 7	pseudo	0.013619	0.483495	
chunk0045_334_1	chr12	51059307	51059554	+	0	NA	exon (NM_015416, exon 9 of 9)	exon (NM_015416, exon 9 of 9)	11113	NR_045017									0.016194	0.508065	
chunk0158_265_1	chr5	131250724	131251197	+	0	NA	Intergenic	L1MC2|LINE|L1	-13049	NM_020240	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.004228	0.341772	270(GAGAACTCTCTGTACT,-,0.00),271(AGAACTCTCTGTACTT,+,0.00)
chunk0095_421_1	chr2	24792501	24793174	+	0	NA	promoter-TSS (NM_001199803)	promoter-TSS (NM_001199803)	-469	NM_001199803	79172	Hs.731569	NM_024322	ENSG00000138092	CENPO	CENP-O|ICEN-36|MCM21R	centromere protein O	protein-coding	0.038633	0.528190	
chunk0177_142_1	chr7	22688042	22688512	+	0	NA	Intergenic	Intergenic	-22744	NR_122075	401312	Hs.583393	NR_122075	ENSG00000105889	LOC401312	-	uncharacterized LOC401312	ncRNA	0.004255	0.418259	
chunk0088_433_1	chr18	55658595	55658951	+	0	NA	Intergenic	Intergenic	-22780	NM_001243226	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.005618	0.361345	
chunk0097_6_1	chr2	41142497	41142818	+	0	NA	Intergenic	Intergenic	-630222	NM_001112802	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.000000	0.465839	
chunk0043_281_1	chr12	21334726	21334986	+	0	NA	promoter-TSS (NM_021094)	promoter-TSS (NM_021094)	42	NM_021094	6579	Hs.46440	NM_005075	ENSG00000084453	SLCO1A2	OATP|OATP-A|OATP1A2|SLC21A3	solute carrier organic anion transporter family member 1A2	protein-coding	0.003846	0.272031	
chunk0176_58_1	chr7	11212933	11213156	+	0	NA	Intergenic	Intergenic	239172	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.000000	0.357143	
chunk0094_399_1	chr2	10381448	10382142	+	0	NA	intron (NM_001258359, intron 1 of 4)	L1MC1|LINE|L1	13031	NM_001258359	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.015850	0.460432	
chunk0158_347_1	chr5	133386478	133387184	+	0	NA	intron (NM_015082, intron 4 of 15)	intron (NM_015082, intron 4 of 15)	40875	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.014164	0.465347	
chunk0075_438_1	chr16	57938630	57939213	+	0	NA	intron (NM_001297, intron 16 of 32)	intron (NM_001297, intron 16 of 32)	32195	NM_001286130	1258	Hs.147062	NM_001297	ENSG00000070729	CNGB1	CNCG2|CNCG3L|CNCG4|CNG4|CNGB1B|GAR1|GARP|GARP2|RCNC2|RCNCb|RCNCbeta|RP45	cyclic nucleotide gated channel beta 1	protein-coding	0.018868	0.571918	
chunk0024_338_1	chr10	43222801	43223229	+	0	NA	intron (NM_145313, intron 1 of 12)	intron (NM_145313, intron 1 of 12)	6724	NM_001282862	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.004673	0.440559	
chunk0110_433_1	chr20	20821706	20821905	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-109182	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.015075	0.445000	
chunk0045_272_1	chr12	49748954	49749403	+	0	NA	intron (NM_001098576, intron 1 of 9)	intron (NM_001098576, intron 1 of 9)	7369	NM_001098576	7009	Hs.743965	NM_003217	ENSG00000139644	TMBIM6	BAXI1|BI-1|TEGT	transmembrane BAX inhibitor motif containing 6	protein-coding	0.008909	0.346667	219(CAGAACAGTTTGATCT,-,0.00),220(AGAACAGTTTGATCTC,+,0.00)
chunk0067_129_1	chr15	42865663	42866170	+	0	NA	intron (NM_173500, intron 3 of 14)	L1MD3|LINE|L1	54893	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.001972	0.346457	
chunk0103_235_1	chr2	164757909	164758417	+	0	NA	intron (NM_001278460, intron 2 of 13)	L2c|LINE|L2	-70386	NR_033309	100337591	Hs.664357	NR_033309	ENSG00000206869	SNORA70F	U70F	small nucleolar RNA, H/ACA box 70F	snoRNA	0.003937	0.318271	
chunk0208_383_1	chrX	28649488	28649690	+	0	NA	intron (NM_014271, intron 1 of 10)	intron (NM_014271, intron 1 of 10)	62025	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.004950	0.344828	
chunk0051_75_1	chr12	113303059	113303393	+	0	NA	intron (NM_024959, intron 15 of 15)	intron (NM_024959, intron 15 of 15)	11703	NR_106820	102465457		NR_106820	ENSG00000274822	MIR6762	hsa-mir-6762	microRNA 6762	ncRNA	0.023952	0.495522	
chunk0013_165_1	chr1	168752126	168752341	+	0	NA	Intergenic	Intergenic	-23029	NM_001937	1805	Hs.80552	NM_001937	ENSG00000143196	DPT	TRAMP	dermatopontin	protein-coding	0.009302	0.384259	
chunk0155_262_1	chr5	95843483	95844184	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-8399	NR_026936	202299	Hs.8373	NM_175616	ENSG00000236882	LINC01554	C5orf27|FIS	long intergenic non-protein coding RNA 1554	ncRNA	0.007133	0.444444	
chunk0019_345_1	chr1	229402247	229402465	+	0	NA	Intergenic	Intergenic	31740	NM_001100	58	Hs.1288	NM_001100	ENSG00000143632	ACTA1	ACTA|ASMA|CFTD|CFTD1|CFTDM|MPFD|NEM1|NEM2|NEM3|SHPM	actin alpha 1, skeletal muscle	protein-coding	0.009174	0.497717	
chunk0104_318_1	chr2	179272222	179272800	+	0	NA	Intergenic	Intergenic	-7888	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.000000	0.336788	
chunk0047_238_1	chr12	71962003	71962498	+	0	NA	intron (NM_173353, intron 5 of 10)	intron (NM_173353, intron 5 of 10)	23404	NM_173353	121278	Hs.736576	NM_173353	ENSG00000139287	TPH2	ADHD7|NTPH	tryptophan hydroxylase 2	protein-coding	0.014141	0.372984	
chunk0200_448_1	chr9	31313980	31314569	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	-905820	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.003396	0.305085	
chunk0053_395_1	chr13	36307752	36308407	+	0	NA	intron (NM_015087, intron 8 of 8)	intron (NM_015087, intron 8 of 8)	-10224	NM_001144985	728591	Hs.656745	NM_001144981	ENSG00000242715	CCDC169	C13orf38	coiled-coil domain containing 169	protein-coding	0.003053	0.292683	
chunk0163_409_1	chr6	16849567	16849820	+	0	NA	Intergenic	Intergenic	-88203	NM_001128164	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.011858	0.429134	
chunk0097_251_1	chr2	53906485	53906752	+	0	NA	exon (NM_014614, exon 26 of 47)	exon (NM_014614, exon 26 of 47)	-46585	NM_001164165	100302652	Hs.40763	NM_001164165	ENSG00000270898	GPR75-ASB3	ASB-3|ASB3	GPR75-ASB3 readthrough	protein-coding	0.014981	0.328358	
chunk0163_254_1	chr6	12924890	12925328	+	0	NA	intron (NM_030948, intron 4 of 14)	intron (NM_030948, intron 4 of 14)	208304	NM_030948	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.002283	0.341686	
chunk0144_63_1	chr4	127058769	127059019	+	0	NA	Intergenic	L1M1|LINE|L1	-574038	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.000000	0.290837	
chunk0094_77_1	chr2	3543101	3543556	+	0	NA	Intergenic	MER57C1|LTR|ERV1	15043	NM_002936	246243	Hs.568006	NM_002936	ENSG00000171865	RNASEH1	H1RNA|PEOB2|RNH1	ribonuclease H1	protein-coding	0.008791	0.464912	
chunk0198_157_1	chr8	133112126	133112447	+	0	NA	intron (NM_003235, intron 43 of 47)	intron (NM_003235, intron 43 of 47)	-9220	NM_001282965	6503	Hs.75367	NM_006748	ENSG00000155926	SLA	SLA1|SLAP	Src like adaptor	protein-coding	0.006231	0.515528	
chunk0146_124_1	chr4	159096426	159096912	+	0	NA	Intergenic	Intergenic	-32136	NR_039963	100616303		NR_039963	ENSG00000283379	MIR3688-2	mir-3688-2	microRNA 3688-2	ncRNA	0.008230	0.363450	
chunk0140_328_1	chr4	73672566	73673203	+	0	NA	Intergenic	Intergenic	-52253	NM_001270392	166824	Hs.529677	NM_177532	ENSG00000169435	RASSF6	-	Ras association domain family member 6	protein-coding	0.009419	0.371473	103(GAGAACAGTATGATCT,-,0.00),104(AGAACAGTATGATCTC,+,0.00)
chunk0176_154_1	chr7	13115290	13115635	+	0	NA	Intergenic	Intergenic	428176	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.011594	0.413295	192(TGGAACTTTGTGTTCC,-,0.00),193(GGAACTTTGTGTTCCC,+,0.00)
chunk0195_89_1	chr8	94226888	94227178	+	0	NA	Intergenic	Intergenic	-9730	NM_001144663	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.006897	0.439863	189(TAGTACACTTTGTTCC,-,0.00),190(AGTACACTTTGTTCCA,+,0.00)
chunk0170_358_1	chr6	116679991	116680250	+	0	NA	Intergenic	L2c|LINE|L2	-1084	NM_002269	3841	Hs.182971	NM_002269	ENSG00000196911	KPNA5	IPOA6|SRP6	karyopherin subunit alpha 5	protein-coding	0.011583	0.365385	
chunk0109_137_1	chr20	3341374	3341573	+	0	NA	intron (NM_001009984, intron 9 of 36)	intron (NM_001009984, intron 9 of 36)	66189	NM_001009984	25943	Hs.516853	NM_001009984	ENSG00000088854	C20orf194	-	chromosome 20 open reading frame 194	protein-coding	0.010050	0.555000	
chunk0124_150_1	chr3	54762290	54762602	+	0	NA	intron (NM_018398, intron 12 of 37)	L2b|LINE|L2	-122589	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.003205	0.444089	
chunk0085_311_1	chr18	8232771	8233229	+	0	NA	intron (NM_001105244, intron 14 of 32)	LTR3A|LTR|ERVK	134034	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.015284	0.494553	
chunk0128_230_1	chr3	108319357	108320006	+	0	NA	intron (NM_001282557, intron 1 of 9)	intron (NM_001282557, intron 1 of 9)	7896	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.010786	0.383077	
chunk0172_197_1	chr6	136652507	136653048	+	0	NA	intron (NM_005923, intron 10 of 29)	intron (NM_005923, intron 10 of 29)	23663	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.001848	0.335793	247(CTGAACTATGTGTCCC,-,0.00),248(TGAACTATGTGTCCCT,+,0.00)
chunk0015_353_1	chr1	190218810	190219097	+	0	NA	intron (NM_199051, intron 6 of 7)	intron (NM_199051, intron 6 of 7)	258676	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003484	0.371528	201(CAGGACTGCCAGTGCT,-,0.00),202(AGGACTGCCAGTGCTC,+,0.00)
chunk0121_438_1	chr3	26101517	26101985	+	0	NA	Intergenic	MER50|LTR|ERV1	-228056	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.008547	0.454158	
chunk0065_104_1	chr15	24054963	24055254	+	0	NA	intron (NR_126392, intron 4 of 5)	intron (NR_126392, intron 4 of 5)	79961	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.013746	0.523973	
chunk0170_424_1	chr6	118468924	118469373	+	0	NA	exon (NM_001178035, exon 13 of 14)	exon (NM_001178035, exon 13 of 14)	-32225	NR_002730	23629	Hs.648050	NR_002730		BRD7P3	BP75	bromodomain containing 7 pseudogene 3	pseudo	0.006682	0.386667	
chunk0019_276_1	chr1	228526929	228527128	+	0	NA	Intergenic	L1MB4|LINE|L1	-14740	NM_001287262	100129094	Hs.730208	NM_001287262		BTNL10	BTN4|BUTR1	butyrophilin like 10	protein-coding	0.010050	0.470000	
chunk0019_267_1	chr1	228174624	228174958	+	0	NA	exon (NM_001010867, exon 2 of 3)	exon (NM_001010867, exon 2 of 3)	241	NM_001310327	200205	Hs.237017	NM_001010867	ENSG00000181873	IBA57	C1orf69|MMDS3|SPG74	iron-sulfur cluster assembly factor IBA57	protein-coding	0.068862	0.671642	
chunk0002_98_1	chr1	14958072	14958511	+	0	NA	intron (NM_001017999, intron 1 of 7)	intron (NM_001017999, intron 1 of 7)	12372	NM_001017999	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.009112	0.525000	
chunk0099_102_1	chr2	85607819	85608398	+	0	NA	3' UTR (NM_001013649, exon 4 of 4)	3' UTR (NM_001013649, exon 4 of 4)	3948	NM_001013649	388969	Hs.516159	NM_001013649	ENSG00000168887	C2orf68	HCRCN81	chromosome 2 open reading frame 68	protein-coding	0.013817	0.451724	279(GAGGACAGTCTGTTCA,-,0.00),280(AGGACAGTCTGTTCAC,+,0.00)
chunk0058_303_1	chr14	26994953	26995351	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	86510	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.007538	0.471178	255(ATAACACCCTGTTCAT,+,0.00)
chunk0120_233_1	chr3	8431112	8431710	+	0	NA	intron (NR_033378, intron 3 of 3)	L1MC3|LINE|L1	70247	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.005017	0.393990	
chunk0192_374_1	chr8	68444038	68444237	+	0	NA	intron (NM_052958, intron 2 of 13)	L1M6|LINE|L1	-112646	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.000000	0.330000	
chunk0131_215_1	chr3	149129186	149129607	+	0	NA	promoter-TSS (NM_032383)	promoter-TSS (NM_032383)	-188	NM_032383	84343	Hs.558314	NM_032383	ENSG00000163755	HPS3	BLOC2S1|SUTAL	HPS3 biogenesis of lysosomal organelles complex 2 subunit 1	protein-coding	0.073634	0.573460	
chunk0129_146_1	chr3	120492147	120492435	+	0	NA	Intergenic	HERVIP10B3-int|LTR|ERV1	-41220	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.013889	0.446367	
chunk0212_238_1	chrX	136772990	136773443	+	0	NA	intron (NM_004840, intron 2 of 21)	intron (NM_004840, intron 2 of 21)	-5824	NM_001306177	9459	Hs.522795	NM_004840	ENSG00000129675	ARHGEF6	COOL2|Cool-2|MRX46|PIXA|alpha-PIX|alphaPIX	Rac/Cdc42 guanine nucleotide exchange factor 6	protein-coding	0.015453	0.449339	
chunk0197_210_1	chr8	122654658	122654926	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	39314	NR_126348	104266958	Hs.575540	NR_126348	ENSG00000253819	LINC01151	-	long intergenic non-protein coding RNA 1151	ncRNA	0.007463	0.446097	
chunk0050_300_1	chr12	106790330	106790773	+	0	NA	intron (NM_018157, intron 2 of 8)	intron (NM_018157, intron 2 of 8)	-15720	NR_040246	100287944	Hs.742087	NR_040246	ENSG00000257545	LOC100287944	-	uncharacterized LOC100287944	ncRNA	0.002257	0.319820	
chunk0039_141_1	chr11	98616025	98616550	+	0	NA	Intergenic	Intergenic	-404689	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.344106	
chunk0174_192_1	chr6	160003296	160003932	+	0	NA	non-coding (NR_047514, exon 1 of 1)	non-coding (NR_047514, exon 1 of 1)	4050	NR_047511	100271873	Hs.742166	NR_047511	ENSG00000268257	AIRN	AIR|IGF2R-AS|IGF2R-AS1|IGF2RAS|NCRNA00088	antisense of IGF2R non-protein coding RNA	ncRNA	0.007862	0.342229	
chunk0151_287_1	chr5	52861170	52861683	+	0	NA	intron (NM_181501, intron 2 of 28)	intron (NM_181501, intron 2 of 28)	73124	NM_181501	3672	Hs.644352	NM_181501	ENSG00000213949	ITGA1	CD49a|VLA1	integrin subunit alpha 1	protein-coding	0.007797	0.352140	
chunk0205_52_1	chr9	106157058	106157257	+	0	NA	Intergenic	L2c|LINE|L2	-443771	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.000000	0.375000	
chunk0052_454_1	chr12	132689874	132690268	+	0	NA	intron (NM_018663, intron 1 of 4)	intron (NM_018663, intron 1 of 4)	2465	NM_018663	5827	Hs.430299	NM_018663	ENSG00000176894	PXMP2	PMP22	peroxisomal membrane protein 2	protein-coding	0.015228	0.473418	
chunk0192_232_1	chr8	65484475	65484779	+	0	NA	Intergenic	Intergenic	78039	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.006579	0.327869	
chunk0206_101_1	chr9	120757493	120758049	+	0	NA	3' UTR (NM_012164, exon 8 of 8)	3' UTR (NM_012164, exon 8 of 8)	35691	NM_012164	26190	Hs.494985	NM_012164	ENSG00000119402	FBXW2	FBW2|Fwd2|Md6	F-box and WD repeat domain containing 2	protein-coding	0.003597	0.332136	
chunk0201_243_1	chr9	37800475	37800979	+	0	NA	promoter-TSS (NM_024345)	promoter-TSS (NM_024345)	-59	NM_024345	79269	Hs.118394	NM_024345	ENSG00000122741	DCAF10	WDR32	DDB1 and CUL4 associated factor 10	protein-coding	0.083333	0.679208	
chunk0028_296_1	chr10	91553090	91553289	+	0	NA	intron (NR_024467, intron 1 of 4)	intron (NR_024467, intron 1 of 4)	58271	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.000000	0.460000	
chunk0097_349_1	chr2	59029201	59029448	+	0	NA	intron (NR_033873, intron 11 of 13)	intron (NR_033873, intron 11 of 13)	-188384	NR_110219	101927285	Hs.570209	NR_110219	ENSG00000222030	LINC01793	-	long intergenic non-protein coding RNA 1793	ncRNA	0.020243	0.512097	
chunk0058_316_1	chr14	27544573	27545012	+	0	NA	Intergenic	L1MC1|LINE|L1	-67796	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.004556	0.320455	240(GAGAACTCTCTGTACT,-,0.00),241(AGAACTCTCTGTACTT,+,0.00)
chunk0037_197_1	chr11	74325517	74325716	+	0	NA	TTS (NR_120556)	TTS (NR_120556)	-13940	NM_182904	283208	Hs.660541	NM_182904	ENSG00000149380	P4HA3	-	prolyl 4-hydroxylase subunit alpha 3	protein-coding	0.005025	0.465000	
chunk0189_182_1	chr8	23581574	23581831	+	0	NA	Intergenic	Intergenic	52852	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.007782	0.414729	170(TGGAACATGAAGTTCT,-,0.00),171(GGAACATGAAGTTCTA,+,0.00)
chunk0185_350_1	chr7	132256024	132256255	+	0	NA	intron (NM_020911, intron 4 of 31)	intron (NM_020911, intron 4 of 31)	320425	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.017316	0.556034	
chunk0208_21_1	chrX	11035081	11035280	+	0	NA	Intergenic	(TTTTG)n|Simple_repeat|Simple_repeat	-76106	NM_001171991	3052	Hs.211571	NM_005333	ENSG00000004961	HCCS	CCHL|LSDMCA1|MCOPS7|MLS	holocytochrome c synthase	protein-coding	0.010050	0.285000	
chunk0153_224_1	chr5	72107025	72107383	+	0	NA	promoter-TSS (NM_005909)	promoter-TSS (NM_005909)	-87	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.089385	0.688022	
chunk0116_275_1	chr21	39364931	39365389	+	0	NA	Intergenic	Intergenic	-15127	NM_004627	7485	Hs.198308	NM_004627	ENSG00000182093	GET1	CHD5|WRB	guided entry of tail-anchored proteins factor 1	protein-coding	0.010917	0.331155	
chunk0101_289_1	chr2	134359461	134359670	+	0	NA	intron (NM_002410, intron 9 of 15)	intron (NM_002410, intron 9 of 15)	105306	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.009569	0.371429	
chunk0186_209_1	chr7	139897181	139897538	+	0	NA	intron (NM_001314028, intron 3 of 12)	intron (NM_001314028, intron 3 of 12)	68206	NM_001061	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.014006	0.533520	71(GGGAACAGCATGTGCA,-,0.00),72(GGAACAGCATGTGCAA,+,0.00),236(AAGGACATCATGTGCC,-,0.00),237(AGGACATCATGTGCCA,+,0.00)
chunk0138_291_1	chr4	40918461	40918660	+	0	NA	intron (NM_004307, intron 10 of 17)	intron (NM_004307, intron 10 of 17)	-61368	NM_001166053	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.010050	0.480000	
chunk0200_380_1	chr9	26709407	26709699	+	0	NA	Intergenic	Intergenic	183275	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.003425	0.324232	
chunk0148_317_1	chr5	13743472	13744111	+	0	NA	intron (NM_001369, intron 65 of 78)	L1MA5A|LINE|L1	200689	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.004695	0.367188	
chunk0014_261_1	chr1	180157586	180157884	+	0	NA	intron (NM_001004128, intron 1 of 12)	intron (NM_001004128, intron 1 of 12)	2902	NM_001004128	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.006711	0.424749	
chunk0111_238_1	chr20	29458329	29458588	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	-41497	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.019305	0.542308	
chunk0118_430_1	chr22	38613516	38613942	+	0	NA	intron (NM_001013647, intron 11 of 16)	MIRb|SINE|MIR	42900	NM_001291030	646851	Hs.542707	NM_001013647	ENSG00000184949	FAM227A	-	family with sequence similarity 227 member A	protein-coding	0.011737	0.426230	
chunk0179_309_1	chr7	50429952	50430473	+	0	NA	Intergenic	Intergenic	20178	NM_022116	63979	Hs.137516	NM_022116	ENSG00000132436	FIGNL1	-	fidgetin like 1	protein-coding	0.001919	0.333333	
chunk0062_196_1	chr14	69971728	69972156	+	0	NA	intron (NM_022137, intron 3 of 11)	intron (NM_022137, intron 3 of 11)	92545	NM_022137	64093	Hs.497349	NM_022137	ENSG00000198732	SMOC1	OAS	SPARC related modular calcium binding 1	protein-coding	0.009346	0.358974	
chunk0144_40_1	chr4	125672245	125672614	+	0	NA	Intergenic	L2a|LINE|L2	165170	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.005420	0.305405	
chunk0126_92_1	chr3	74832202	74832401	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-311161	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.015075	0.450000	
chunk0007_157_1	chr1	79847422	79847632	+	0	NA	Intergenic	Intergenic	-688228	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.004762	0.279621	
chunk0074_253_1	chr16	27822734	27823217	+	0	NA	intron (NM_144675, intron 4 of 5)	intron (NM_144675, intron 4 of 5)	65182	NM_144675	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.022774	0.502066	
chunk0187_442_1	chr7	158988100	158988373	+	0	NA	Intergenic	(TCCA)n|Simple_repeat|Simple_repeat	-20118	NR_024394	154822	Hs.544783	NM_198345	ENSG00000231419	LINC00689	-	long intergenic non-protein coding RNA 689	ncRNA	0.010989	0.470803	
chunk0165_371_1	chr6	38271968	38272568	+	0	NA	intron (NM_001099272, intron 8 of 10)	intron (NM_001099272, intron 8 of 10)	323799	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.003333	0.372712	
chunk0036_204_1	chr11	63494925	63495389	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-3949	NM_054108	117245	Hs.410316	NM_054108	ENSG00000168004	PLAAT5	HRASLS5|HRLP5|HRSL5|PLAAT-5|RLP1|iNAT	phospholipase A and acyltransferase 5	protein-coding	0.015086	0.415054	
chunk0179_228_1	chr7	47896498	47896898	+	0	NA	intron (NM_138295, intron 14 of 56)	intron (NM_138295, intron 14 of 56)	51776	NM_138295	168507	Hs.195979	NM_138295	ENSG00000158683	PKD1L1	HTX8|PRO19563	polycystin 1 like 1, transient receptor potential channel interacting	protein-coding	0.005000	0.483791	
chunk0104_131_1	chr2	173228032	173228274	+	0	NA	intron (NM_016653, intron 11 of 19)	intron (NM_016653, intron 11 of 19)	53883	NR_033882	339751	Hs.570083	NR_033882	ENSG00000238133	MAP3K20-AS1	MLK7-AS1	MAP3K20 antisense RNA 1	ncRNA	0.016529	0.469136	
chunk0057_159_1	chr13	100560569	100561071	+	0	NA	intron (NM_001195087, intron 2 of 2)	intron (NM_001195087, intron 2 of 2)	-27018	NM_033110	87769	Hs.350868	NM_033110	ENSG00000134864	GGACT	A2LD1	gamma-glutamylamine cyclotransferase	protein-coding	0.021912	0.538767	233(TAGGACATGGTGTCCT,-,0.00),234(AGGACATGGTGTCCTA,+,0.00)
chunk0001_168_1	chr1	6554944	6555208	+	0	NA	promoter-TSS (NM_024654)	promoter-TSS (NM_024654)	-202	NM_177540	80835	Hs.124574	NM_138697	ENSG00000173662	TAS1R1	GM148|GPR70|T1R1|TR1	taste 1 receptor member 1	protein-coding	0.030303	0.558491	
chunk0196_418_1	chr8	116097440	116097645	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	227517	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.004878	0.349515	
chunk0108_251_1	chr2	233953140	233953898	+	0	NA	intron (NM_024080, intron 9 of 25)	intron (NM_024080, intron 9 of 25)	36121	NM_024080	79054	Hs.366053	NM_024080	ENSG00000144481	TRPM8	LTRPC6|LTrpC-6|TRPP8|trp-p8	transient receptor potential cation channel subfamily M member 8	protein-coding	0.010554	0.417655	
chunk0130_112_1	chr3	131387686	131388086	+	0	NA	non-coding (NR_033268, exon 2 of 2)	non-coding (NR_033268, exon 2 of 2)	6105	NR_033268	131870	Hs.282050	NM_152395	ENSG00000198585	NUDT16	-	nudix hydrolase 16	protein-coding	0.002500	0.443890	
chunk0069_200_1	chr15	63449100	63449680	+	0	NA	Intergenic	Intergenic	-55121	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.005172	0.304647	
chunk0199_231_1	chr9	5378659	5379364	+	0	NA	intron (NM_018465, intron 3 of 5)	L1P4|LINE|L1	-39138	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.000000	0.254958	
chunk0102_243_1	chr2	149007151	149007442	+	0	NA	intron (NR_111932, intron 15 of 19)	intron (NR_111932, intron 15 of 19)	-31171	NM_001317003	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.006873	0.438356	
chunk0209_244_1	chrX	45634147	45634546	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-96742	NR_102268	392452	Hs.745266	NR_102268		LOC392452	-	mitochondrial fission factor pseudogene	pseudo	0.002506	0.325000	
chunk0013_415_1	chr1	173190452	173191063	+	0	NA	intron (NM_003326, intron 1 of 2)	intron (NM_003326, intron 1 of 2)	14801	NM_001297562	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.006547	0.449346	
chunk0033_361_1	chr11	23079257	23079456	+	0	NA	Intergenic	Intergenic	-218930	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.010050	0.335000	
chunk0149_258_1	chr5	23918693	23919221	+	0	NA	Intergenic	L1PA15|LINE|L1	-32391	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.001894	0.317580	
chunk0202_289_1	chr9	77488435	77489080	+	0	NA	intron (NR_121184, intron 2 of 4)	L1M3f|LINE|L1	41108	NR_121184	101927422	Hs.434324	NR_121184	ENSG00000231373	GNA14-AS1	-	GNA14 antisense RNA 1	ncRNA	0.001550	0.399381	
chunk0115_59_1	chr21	21412104	21412378	+	0	NA	intron (NM_004540, intron 10 of 17)	MLT1B|LTR|ERVL-MaLR	325078	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.014599	0.443636	
chunk0080_430_1	chr17	35898628	35899292	+	0	NA	Intergenic	Intergenic	12063	NR_126038	100533789	Hs.167595	NR_126038		LRRC37A8P	-	leucine rich repeat containing 37 member A8, pseudogene	pseudo	0.010542	0.520301	
chunk0044_223_1	chr12	31368810	31369009	+	0	NA	Intergenic	Intergenic	-42684	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.005025	0.545000	
chunk0056_181_1	chr13	85409518	85409717	+	0	NA	intron (NR_046989, intron 1 of 3)	LTR82A|LTR|ERVL	46014	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.000000	0.315000	
chunk0163_382_1	chr6	16300444	16301001	+	0	NA	3' UTR (NM_000332, exon 9 of 9)	3' UTR (NM_000332, exon 9 of 9)	62142	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.012567	0.370968	325(AGGAACAGGAAGTGCT,-,0.00),326(GGAACAGGAAGTGCTG,+,0.00)
chunk0061_13_1	chr14	55626204	55626431	+	0	NA	intron (NR_073128, intron 6 of 43)	L1M7|LINE|L1	46110	NR_073128	3895	Hs.509414	NM_004986	ENSG00000126777	KTN1	CG1|KNT|MU-RMS-40.19	kinectin 1	protein-coding	0.013216	0.350877	
chunk0085_138_1	chr18	3248711	3248916	+	0	NA	intron (NM_006471, intron 1 of 3)	intron (NM_006471, intron 1 of 3)	1283	NM_001303047	10627	Hs.190086	NM_006471	ENSG00000101608	MYL12A	HEL-S-24|MLC-2B|MLCB|MRCL3|MRLC3|MYL2B	myosin light chain 12A	protein-coding	0.019512	0.412621	
chunk0123_366_1	chr3	48301335	48301749	+	0	NA	promoter-TSS (NM_005793)	promoter-TSS (NM_005793)	-131	NM_001308427	10201	Hs.465558	NM_005793	ENSG00000172113	NME6	IPIA-ALPHA|NDK 6|NM23-H6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding	0.111111	0.732530	
chunk0005_14_1	chr1	54094089	54094640	+	0	NA	intron (NR_130900, intron 3 of 4)	L1ME3A|LINE|L1	40285	NR_039942	100616315		NR_039942	ENSG00000283749	MIR4781	mir-4781	microRNA 4781	ncRNA	0.003630	0.432971	
chunk0026_237_1	chr10	65890971	65891642	+	0	NA	Intergenic	Intergenic	319881	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.004471	0.357143	
chunk0159_369_1	chr5	145908130	145908571	+	0	NA	Intergenic	Intergenic	-28213	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.004535	0.389140	184(AGGAACAAAGAGTCCT,-,0.00),185(GGAACAAAGAGTCCTA,+,0.00)
chunk0058_436_1	chr13	113351394	113351874	+	0	NA	promoter-TSS (NR_120385)	promoter-TSS (NR_120385)	-39	NR_046541	100874068	Hs.661837	NR_046541		GRTP1-AS1	-	GRTP1 antisense RNA 1	ncRNA	0.029167	0.559252	197(CAGGACAGTGTGGCCT,-,0.00),198(AGGACAGTGTGGCCTT,+,0.00)
chunk0008_195_1	chr1	93332282	93332606	+	0	NA	intron (NR_034089, intron 5 of 8)	intron (NR_034089, intron 5 of 8)	13367	NR_034089	100131564	Hs.732666	NR_034089		CCDC18-AS1	-	CCDC18 antisense RNA 1	ncRNA	0.003086	0.363077	
chunk0193_359_1	chr8	79914359	79914655	+	0	NA	Intergenic	LTR16B1|LTR|ERVL	-42770	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.013514	0.481481	
chunk0033_318_1	chr11	20762023	20762373	+	0	NA	intron (NM_006157, intron 2 of 19)	intron (NM_006157, intron 2 of 19)	92647	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.020000	0.430199	
chunk0191_375_1	chr8	56993248	56993447	+	0	NA	exon (NM_017813, exon 1 of 5)	exon (NM_017813, exon 1 of 5)	524	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.155779	0.730000	
chunk0110_87_1	chr20	11259603	11259966	+	0	NA	Intergenic	Intergenic	13599	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.002755	0.376374	116(GGGAACAAACTGTTCT,-,0.00),117(GGAACAAACTGTTCTG,+,0.00)
chunk0105_253_1	chr2	188946242	188946514	+	0	NA	Intergenic	Intergenic	-27995	NM_000090	1281	Hs.443625	NM_000090	ENSG00000168542	COL3A1	EDS4A|EDSVASC|PMGEDSV	collagen type III alpha 1 chain	protein-coding	0.007353	0.355311	
chunk0030_244_1	chr10	115246906	115247377	+	0	NA	intron (NM_207303, intron 10 of 28)	L1MA5A|LINE|L1	153776	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.002123	0.326271	
chunk0172_188_1	chr6	136564401	136564848	+	0	NA	intron (NM_005923, intron 26 of 29)	intron (NM_005923, intron 26 of 29)	-13805	NM_001198616	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.008949	0.375000	
chunk0133_202_1	chr3	170815486	170815691	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	54668	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.039024	0.563107	
chunk0164_11_1	chr6	17795512	17795711	+	0	NA	intron (NM_022113, intron 23 of 38)	AluSx|SINE|Alu	-88777	NM_001278210	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.005025	0.420000	98(AAGAACATTGTGTACA,-,0.00),99(AGAACATTGTGTACAA,+,0.00)
chunk0168_373_1	chr6	93877742	93878184	+	0	NA	Intergenic	L1ME3C|LINE|L1	170880	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.004525	0.300226	
chunk0192_56_1	chr8	59718215	59718636	+	0	NA	Intergenic	Intergenic	562970	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.011876	0.431280	
chunk0109_367_1	chr2	239316640	239317598	+	0	NA	intron (NM_006037, intron 2 of 26)	L1MC4|LINE|L1	11657	NR_036229	100423043		NR_036229	ENSG00000265215	MIR4269	-	microRNA 4269	ncRNA	0.021921	0.499479	
chunk0110_28_1	chr20	10504810	10505380	+	0	NA	intron (NM_001009608, intron 2 of 7)	intron (NM_001009608, intron 2 of 7)	69792	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.010526	0.381786	343(GAGAACAAGCAGTCCT,-,0.00),344(AGAACAAGCAGTCCTC,+,0.00)
chunk0002_15_1	chr1	12232270	12232482	+	0	NA	intron (NM_018156, intron 1 of 68)	intron (NM_018156, intron 1 of 68)	2337	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.009434	0.502347	
chunk0049_79_1	chr12	90611082	90611380	+	0	NA	Intergenic	L1M4b|LINE|L1	-306792	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.006711	0.381271	
chunk0075_131_1	chr16	50173972	50174268	+	0	NA	intron (NM_001040284, intron 2 of 12)	AluSz6|SINE|Alu	21202	NM_001040284	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.013514	0.441077	
chunk0155_174_1	chr5	94385834	94386322	+	0	NA	intron (NM_001145678, intron 19 of 20)	intron (NM_001145678, intron 19 of 20)	232526	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.004098	0.355828	
chunk0150_2_1	chr5	30207201	30207797	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-811523	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.008389	0.366834	
chunk0114_302_1	chr21	16983462	16983796	+	0	NA	Intergenic	Intergenic	393392	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.000000	0.349254	
chunk0007_386_1	chr1	85355553	85356019	+	0	NA	intron (NM_001134445, intron 3 of 6)	L1ME3D|LINE|L1	-78882	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.000000	0.301927	
chunk0090_420_1	chr18	79110597	79110925	+	0	NA	intron (NM_001306085, intron 3 of 28)	intron (NM_001306085, intron 3 of 28)	41486	NM_001306085	374868	Hs.465475	NM_198531	ENSG00000166377	ATP9B	ATPASEP|ATPIIB|HUSSY-20|NEO1L|hMMR1	ATPase phospholipid transporting 9B (putative)	protein-coding	0.009146	0.291793	
chunk0060_188_1	chr14	47008852	47009287	+	0	NA	intron (NM_182830, intron 8 of 16)	intron (NM_182830, intron 8 of 16)	334177	NM_182830	161357	Hs.436380	NM_182830	ENSG00000139915	MDGA2	MAMDC1|c14_5286	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.004598	0.286697	
chunk0088_28_1	chr18	43803404	43804324	+	0	NA	Intergenic	L1M1|LINE|L1	-526214	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.002174	0.315961	
chunk0039_380_1	chr11	106937080	106937520	+	0	NA	intron (NM_001256424, intron 4 of 8)	intron (NM_001256424, intron 4 of 8)	81145	NM_000855	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.002273	0.310658	
chunk0095_128_1	chr2	16506151	16506658	+	0	NA	Intergenic	MIR|SINE|MIR	159462	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.005917	0.452756	
chunk0109_245_1	chr20	6055881	6056098	+	0	NA	Intergenic	Intergenic	-1909	NM_152611	164312	Hs.149133	NM_152611	ENSG00000125872	LRRN4	C20orf75|NLRR-4|NLRR4|dJ1056H1.1	leucine rich repeat neuronal 4	protein-coding	0.018433	0.513761	65(TAGAACATCATGTTTC,-,0.00),66(AGAACATCATGTTTCC,+,0.00)
chunk0014_218_1	chr1	179416629	179416828	+	0	NA	intron (NR_073544, intron 12 of 25)	LTR47B2|LTR|ERVL	50756	NR_073544	126859	Hs.658505	NM_144696	ENSG00000162779	AXDND1	C1orf125	axonemal dynein light chain domain containing 1	protein-coding	0.000000	0.395000	
chunk0191_246_1	chr8	53176824	53177337	+	0	NA	Intergenic	LTR55|LTR|ERVL?	74554	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.009747	0.443580	394(AGGTACAGTAAGTTCC,-,0.00),395(GGTACAGTAAGTTCCT,+,0.00)
chunk0174_14_1	chr6	152381422	152381621	+	0	NA	non-coding (NR_120501, exon 2 of 2)	non-coding (NR_120501, exon 2 of 2)	991	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.015075	0.445000	
chunk0035_152_1	chr11	43072511	43073117	+	0	NA	Intergenic	L2a|LINE|L2	196555	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.004950	0.387150	
chunk0088_87_1	chr18	44839652	44840470	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	130105	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.006112	0.435897	
chunk0096_150_1	chr2	29182839	29183252	+	0	NA	3' UTR (NM_024692, exon 16 of 16)	3' UTR (NM_024692, exon 16 of 16)	67619	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.002421	0.292271	
chunk0117_61_1	chr22	16465360	16465694	+	0	NA	Intergenic	L1PA15|LINE|L1	127283	NM_014406	150160	Hs.128342	NM_014406	ENSG00000198445	CCT8L2	CESK1	chaperonin containing TCP1 subunit 8 like 2	protein-coding	0.014970	0.414925	
chunk0003_103_1	chr1	31962601	31963243	+	0	NA	Intergenic	Charlie16a|DNA|hAT-Charlie	-24535	NM_080391	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.004673	0.365474	
chunk0124_289_1	chr3	57709374	57709875	+	0	NA	Intergenic	Intergenic	-16535	NM_152678	201627	Hs.91085	NM_152678	ENSG00000174839	DENND6A	AFI1A|FAM116A	DENN domain containing 6A	protein-coding	0.003992	0.372510	
chunk0183_1_1	chr7	102307230	102307799	+	0	NA	intron (NM_020979, intron 3 of 8)	intron (NM_020979, intron 3 of 8)	14411	NR_036245	100422858		NR_036245	ENSG00000264675	MIR4285	-	microRNA 4285	ncRNA	0.021090	0.580702	
chunk0031_136_1	chr10	124943603	124944081	+	0	NA	intron (NM_017580, intron 1 of 8)	intron (NM_017580, intron 1 of 8)	1719	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.004184	0.338205	
chunk0138_67_1	chr4	33408082	33408281	+	0	NA	Intergenic	Intergenic	631712	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.005025	0.365000	
chunk0023_190_1	chr10	25062486	25062754	+	0	NA	promoter-TSS (NM_001270383)	promoter-TSS (NM_001270383)	-341	NM_001270383	219670	Hs.534486	NM_145010	ENSG00000151023	ENKUR	C10orf63|CFAP106	enkurin, TRPC channel interacting protein	protein-coding	0.026119	0.579926	
chunk0079_9_1	chr17	9432246	9432914	+	0	NA	intron (NR_033656, intron 4 of 5)	intron (NR_033656, intron 4 of 5)	143378	NM_004853	9482	Hs.431109	NM_004853	ENSG00000170310	STX8	CARB	syntaxin 8	protein-coding	0.008982	0.372197	
chunk0013_335_1	chr1	171817005	171817496	+	0	NA	Intergenic	MIRb|SINE|MIR	-24228	NM_015569	26052	Hs.654775	NM_015569	ENSG00000197959	DNM3	Dyna III	dynamin 3	protein-coding	0.002037	0.373984	
chunk0176_321_1	chr7	17039383	17039906	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-157655	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.003824	0.414122	
chunk0109_80_1	chr20	1965880	1966079	+	0	NA	Intergenic	Intergenic	26827	NM_001190892	5173	Hs.22584	NM_024411	ENSG00000101327	PDYN	ADCA|PENKB|SCA23	prodynorphin	protein-coding	0.045226	0.615000	130(AGGAACAAGATGTCCT,-,0.00),131(GGAACAAGATGTCCTG,+,0.00)
chunk0147_389_1	chr4	186657007	186657405	+	0	NA	intron (NM_005245, intron 3 of 26)	L1ME1|LINE|L1	66627	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.015075	0.403509	
chunk0024_168_1	chr10	35690411	35691103	+	0	NA	Intergenic	Intergenic	-49323	NM_031866	8325	Hs.302634	NM_031866	ENSG00000177283	FZD8	FZ-8|hFZ8	frizzled class receptor 8	protein-coding	0.014451	0.430014	
chunk0121_131_1	chr3	18146371	18146934	+	0	NA	intron (NM_001257177, intron 4 of 4)	intron (NM_001257177, intron 4 of 4)	184080	NM_001257177									0.005329	0.418440	
chunk0005_192_1	chr1	58942756	58943376	+	0	NA	Intergenic	Intergenic	-77410	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.009677	0.458937	
chunk0110_306_1	chr20	18057752	18058178	+	0	NA	promoter-TSS (NM_021220)	promoter-TSS (NM_021220)	-83	NM_021220	58495	Hs.661013	NM_021220	ENSG00000125850	OVOL2	CHED|CHED1|CHED2|EUROIMAGE566589|PPCD1|ZNF339	ovo like zinc finger 2	protein-coding	0.065728	0.590164	236(CGGGGCTGCCTGTTCC,-,0.00)
chunk0182_340_1	chr7	99277364	99277563	+	0	NA	intron (NR_002147, intron 1 of 15)	intron (NR_002147, intron 1 of 15)	4162	NR_002147	84176	Hs.621401	NR_002147		MYH16	MHC20|MYH16P|MYH5	myosin heavy chain 16 pseudogene	pseudo	0.015075	0.600000	
chunk0070_360_1	chr15	76149484	76150203	+	0	NA	intron (NM_152335, intron 3 of 10)	MIR|SINE|MIR	31643	NR_120360	101929439	Hs.631721	NR_120360	ENSG00000259422	LOC101929439	-	uncharacterized LOC101929439	ncRNA	0.009736	0.423611	
chunk0080_310_1	chr17	31810889	31811516	+	0	NA	Intergenic	L1MB3|LINE|L1	48105	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.007974	0.390127	
chunk0051_64_1	chr12	112884404	112884676	+	0	NA	intron (NM_001143854, intron 16 of 21)	L1ME3G|LINE|L1	-22394	NM_016816	4938	Hs.524760	NM_002534	ENSG00000089127	OAS1	E18/E16|IFI-4|OIAS|OIASI	2'-5'-oligoadenylate synthetase 1	protein-coding	0.000000	0.304029	
chunk0103_147_1	chr2	162161610	162162008	+	0	NA	non-coding (NR_110255, exon 2 of 4)	non-coding (NR_110255, exon 2 of 4)	-9405	NM_002054	2641	Hs.516494	NM_002054	ENSG00000115263	GCG	GLP-1|GLP1|GLP2|GRPP	glucagon	protein-coding	0.007538	0.335840	
chunk0135_293_1	chr3	189562462	189562716	+	0	NA	Intergenic	Intergenic	-68838	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.003937	0.388235	
chunk0011_402_1	chr1	154193840	154194101	+	0	NA	promoter-TSS (NR_030600)	promoter-TSS (NR_030600)	-227	NR_030600	100126346		NR_030600	ENSG00000215938	MIR190B	MIRN190B|mir-190b	microRNA 190b	ncRNA	0.026820	0.580153	
chunk0154_355_1	chr5	87256095	87256384	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-12014	NM_002890	5921	Hs.664080	NM_002890	ENSG00000145715	RASA1	CM-AVM|CMAVM|CMAVM1|GAP|PKWS|RASA|RASGAP|p120|p120GAP|p120RASGAP	RAS p21 protein activator 1	protein-coding	0.006920	0.331034	227(AAGCACATCACGTTCT,-,0.00),228(AGCACATCACGTTCTC,+,0.00)
chunk0025_37_1	chr10	48907230	48907482	+	0	NA	intron (NM_020945, intron 47 of 61)	intron (NM_020945, intron 47 of 61)	6879	NM_001006939	474354	Hs.202438	NM_001006939	ENSG00000165383	LRRC18	UNQ933|UNQ9338|VKGE9338	leucine rich repeat containing 18	protein-coding	0.003968	0.395257	
chunk0072_269_1	chr15	96780090	96780427	+	0	NA	intron (NR_102754, intron 1 of 2)	intron (NR_102754, intron 1 of 2)	1396	NR_102754	100652749	Hs.303588	NR_102753	ENSG00000259282	SPATA8-AS1	-	SPATA8 antisense RNA 1 (head to head)	ncRNA	0.002967	0.529586	258(AGGGACACTGTGTTCT,-,0.00),259(GGGACACTGTGTTCTT,+,0.00)
chunk0180_249_1	chr7	69177663	69177868	+	0	NA	Intergenic	Intergenic	419730	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.014634	0.432039	
chunk0088_306_1	chr18	50301361	50301777	+	0	NA	Intergenic	Intergenic	-13247	NM_014593	30827	Hs.180933	NM_014593	ENSG00000154832	CXXC1	2410002I16Rik|5830420C16Rik|CFP1|CGBP|HsT2645|PCCX1|PHF18|SPP1|ZCGPC1|hCGBP	CXXC finger protein 1	protein-coding	0.012019	0.424460	
chunk0038_155_1	chr11	84777618	84778095	+	0	NA	intron (NM_001142699, intron 6 of 27)	L1PB4|LINE|L1	145565	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004193	0.322176	
chunk0083_452_1	chr17	73196552	73197004	+	0	NA	intron (NM_018714, intron 2 of 13)	intron (NM_018714, intron 2 of 13)	3744	NM_018714	9382	Hs.103555	NM_018714	ENSG00000166685	COG1	CDG2G|LDLB	component of oligomeric golgi complex 1	protein-coding	0.030973	0.516556	
chunk0187_49_1	chr8	1745408	1745607	+	0	NA	Intergenic	Intergenic	-18197	NM_018941	2055	Hs.127675	NM_018941	ENSG00000182372	CLN8	C8orf61|EPMR|TLCD6	CLN8 transmembrane ER and ERGIC protein	protein-coding	0.010050	0.385000	
chunk0169_3_1	chr6	96214871	96215248	+	0	NA	3' UTR (NM_006581, exon 3 of 3)	3' UTR (NM_006581, exon 3 of 3)	199090	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.007958	0.375661	
chunk0082_219_1	chr17	57126664	57127003	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	41059	NM_001242902	8165	Hs.463506	NM_003488	ENSG00000121057	AKAP1	AKAP|AKAP121|AKAP149|AKAP84|D-AKAP1|PPP1R43|PRKA1|SAKAP84|TDRD17	A-kinase anchoring protein 1	protein-coding	0.008850	0.441176	
chunk0056_222_1	chr13	88414499	88415143	+	0	NA	Intergenic	L1ME1|LINE|L1	-126008	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.004658	0.288372	
chunk0064_294_1	chr14	95339384	95340648	+	0	NA	Intergenic	Intergenic	10432	NR_110127	101929080	Hs.525567	NR_110127	ENSG00000258630	LINC02292	-	long intergenic non-protein coding RNA 2292	ncRNA	0.015032	0.473518	
chunk0135_4_1	chr3	184042668	184042968	+	0	NA	Intergenic	Intergenic	9987	NM_001163646	200909	Hs.448004	NM_182537	ENSG00000186090	HTR3D	5HT3D	5-hydroxytryptamine receptor 3D	protein-coding	0.000000	0.438538	80(AAGTACAGTTTGTGCT,-,0.00),81(AGTACAGTTTGTGCTA,+,0.00)
chunk0007_20_1	chr1	77433485	77433838	+	0	NA	intron (NM_012093, intron 8 of 13)	MER65-int|LTR|ERV1	151059	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.000000	0.290960	
chunk0074_47_1	chr16	20743399	20744137	+	0	NA	Intergenic	Intergenic	-1804	NM_017736	55623	Hs.700004	NM_017736	ENSG00000066654	THUMPD1	Tan1	THUMP domain containing 1	protein-coding	0.002710	0.378890	
chunk0148_437_1	chr4	189203780	189204376	+	0	NA	Intergenic	Intergenic	-455528	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.008389	0.346734	
chunk0049_379_1	chr12	95836740	95836939	+	0	NA	Intergenic	Intergenic	-22092	NM_003095	6636	Hs.105465	NM_003095	ENSG00000139343	SNRPF	SMF|Sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding	0.000000	0.420000	
chunk0034_235_1	chr11	33744557	33744954	+	0	NA	intron (NM_012175, intron 10 of 10)	intron (NM_012175, intron 10 of 10)	-8276	NM_203330	966	Hs.278573	NM_000611	ENSG00000085063	CD59	16.3A5|1F5|EJ16|EJ30|EL32|G344|HRF-20|HRF20|MAC-IP|MACIF|MEM43|MIC11|MIN1|MIN2|MIN3|MIRL|MSK21|p18-20	CD59 molecule (CD59 blood group)	protein-coding	0.007557	0.321608	
chunk0045_164_1	chr12	46792743	46793560	+	0	NA	5' UTR (NM_001143824, exon 2 of 16)	5' UTR (NM_001143824, exon 2 of 16)	32846	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.003672	0.354523	427(CAGAACACTCTGTTCT,-,0.00),428(AGAACACTCTGTTCTG,+,0.00)
chunk0126_399_1	chr3	84971360	84972069	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	12732	NM_001167675	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.004231	0.339437	
chunk0156_219_1	chr5	108199042	108199579	+	0	NA	intron (NM_001163315, intron 5 of 8)	intron (NM_001163315, intron 5 of 8)	182788	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.003724	0.299257	
chunk0182_222_1	chr7	96394979	96395240	+	0	NA	Intergenic	L1MA3|LINE|L1	-72962	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.003831	0.297710	
chunk0146_351_1	chr4	166997895	166998317	+	0	NA	intron (NM_001204355, intron 2 of 8)	intron (NM_001204355, intron 2 of 8)	236320	NM_001204353	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.004739	0.323877	
chunk0190_134_1	chr8	30676618	30676991	+	0	NA	Intergenic	Intergenic	-18583	NM_002095	2961	Hs.77100	NM_002095	ENSG00000197265	GTF2E2	FE|TF2E2|TFIIE-B|TTD6	general transcription factor IIE subunit 2	protein-coding	0.002681	0.481283	
chunk0162_360_1	chr6	7164599	7165180	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	57036	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.013769	0.455326	254(AAGGACATGGTGTTCT,-,0.00),255(AGGACATGGTGTTCTG,+,0.00),490(AGGCACAAGGAGTGCT,-,0.00),491(GGCACAAGGAGTGCTA,+,0.00)
chunk0032_19_1	chr11	742656	743286	+	0	NA	Intergenic	L1M5|LINE|L1	-4461	NM_006755	6888	Hs.438678	NM_006755	ENSG00000177156	TALDO1	TAL|TAL-H|TALDOR|TALH	transaldolase 1	protein-coding	0.006349	0.478605	350(TGGAACTGCCAGTTCC,-,0.00),351(GGAACTGCCAGTTCCC,+,0.00)
chunk0200_141_1	chr9	17989759	17990263	+	0	NA	Intergenic	Intergenic	411057	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.005952	0.328713	217(AAGAACAAGAAGTTCC,-,0.00),218(AGAACAAGAAGTTCCT,+,0.00)
chunk0061_36_1	chr14	55942177	55942429	+	0	NA	Intergenic	Intergenic	-145629	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.003968	0.411067	
chunk0184_227_1	chr7	117476358	117476643	+	0	NA	Intergenic	Intergenic	-3463	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.007018	0.405594	
chunk0112_86_1	chr20	38006541	38007063	+	0	NA	intron (NM_014657, intron 3 of 8)	L2c|LINE|L2	26666	NM_014657	9675	Hs.655481	NM_014657	ENSG00000101407	TTI1	KIAA0406|smg-10	TELO2 interacting protein 1	protein-coding	0.007663	0.403442	
chunk0024_418_1	chr10	45651861	45652331	+	0	NA	intron (NR_104256, intron 3 of 6)	intron (NR_104256, intron 3 of 6)	20636	NM_001282905	93550	Hs.89029	NM_174890	ENSG00000172671	ZFAND4	ANUBL1	zinc finger AN1-type containing 4	protein-coding	0.006383	0.322718	
chunk0085_368_1	chr18	9440251	9440741	+	0	NA	Intergenic	L1MB3|LINE|L1	-35036	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.010204	0.376782	
chunk0057_280_1	chr13	106003598	106004191	+	0	NA	Intergenic	Intergenic	297064	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.003373	0.340067	
chunk0012_343_1	chr1	162605412	162605813	+	0	NA	Intergenic	Intergenic	-26826	NM_001014796	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.004988	0.338308	
chunk0033_131_1	chr11	14882327	14882609	+	0	NA	intron (NM_024514, intron 2 of 4)	L1M5|LINE|L1	9737	NM_024514	120227	Hs.371427	NM_024514	ENSG00000186104	CYP2R1	-	cytochrome P450 family 2 subfamily R member 1	protein-coding	0.000000	0.459364	
chunk0190_57_1	chr8	29705799	29706016	+	0	NA	Intergenic	L1PB2|LINE|L1	42202	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.004608	0.385321	
chunk0197_195_1	chr8	121719851	121720094	+	0	NA	Intergenic	MER52A|LTR|ERV1	-78582	NM_005328	3037	Hs.159226	NM_005328	ENSG00000170961	HAS2	-	hyaluronan synthase 2	protein-coding	0.012346	0.627049	
chunk0066_252_1	chr15	34703567	34703979	+	0	NA	Intergenic	MIR|SINE|MIR	50808	NM_020660	57369	Hs.283816	NM_020660	ENSG00000159248	GJD2	CX36|GJA9	gap junction protein delta 2	protein-coding	0.004854	0.397094	
chunk0168_81_1	chr6	79819001	79819864	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-7186	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.005794	0.376157	588(AAGAACAGCATGTATT,-,0.00),589(AGAACAGCATGTATTG,+,0.00)
chunk0094_92_1	chr2	4068100	4068621	+	0	NA	Intergenic	Intergenic	-94328	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.007678	0.367816	
chunk0164_325_1	chr6	25154286	25154615	+	0	NA	Intergenic	Intergenic	-16058	NR_027626	8418	Hs.484918	NR_002174	ENSG00000168405	CMAHP	CMAH|CSAH	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	pseudo	0.009119	0.415152	
chunk0206_408_1	chr9	127407698	127408106	+	0	NA	TTS (NM_014580)	TTS (NM_014580)	10764	NM_001271712	29988	Hs.179522	NM_014580	ENSG00000136856	SLC2A8	GLUT8|GLUTX1	solute carrier family 2 member 8	protein-coding	0.000000	0.344743	
chunk0055_301_1	chr13	66172599	66172957	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-45472	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.005587	0.275766	
chunk0181_91_1	chr7	80385426	80385976	+	0	NA	Intergenic	Intergenic	-11262	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.000000	0.304900	
chunk0045_414_1	chr12	53079584	53080032	+	0	NA	promoter-TSS (NM_032840)	promoter-TSS (NM_032840)	-388	NM_032840	84926	Hs.343334	NM_032840	ENSG00000167778	SPRYD3	-	SPRY domain containing 3	protein-coding	0.073661	0.572383	
chunk0016_437_1	chr1	203976054	203976781	+	0	NA	Intergenic	Intergenic	64847	NR_027902	284573	Hs.406979	NR_027902	ENSG00000176754	LINC00303	C1orf157|NCRNA00303	long intergenic non-protein coding RNA 303	ncRNA	0.008253	0.381868	373(AGAGACATTGTGTGCC,-,0.00),374(GAGACATTGTGTGCCT,+,0.00)
chunk0202_150_1	chr9	73553039	73553794	+	0	NA	Intergenic	Intergenic	401685	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.007947	0.383598	
chunk0104_361_1	chr2	179965157	179965713	+	0	NA	intron (NM_020943, intron 12 of 19)	intron (NM_020943, intron 12 of 19)	41618	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.001799	0.298025	
chunk0039_448_1	chr11	108347361	108347560	+	0	NA	intron (NM_000051, intron 59 of 62)	intron (NM_000051, intron 59 of 62)	120071	NM_152587	160140	Hs.653180	NM_152587	ENSG00000166323	C11orf65	-	chromosome 11 open reading frame 65	protein-coding	0.000000	0.310000	
chunk0171_96_1	chr6	121971437	121971686	+	0	NA	Intergenic	Intergenic	-427990	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.000000	0.336000	
chunk0001_338_1	chr1	9606669	9607330	+	0	NA	intron (NM_001130924, intron 6 of 10)	intron (NM_001130924, intron 6 of 10)	18125	NM_001130924	199953	Hs.632365	NM_001010866	ENSG00000188807	TMEM201	Ima1|NET5|SAMP1	transmembrane protein 201	protein-coding	0.030257	0.558912	
chunk0046_310_1	chr12	62473167	62473907	+	0	NA	intron (NM_001278472, intron 2 of 35)	intron (NM_001278472, intron 2 of 35)	6720	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.005405	0.438596	
chunk0120_48_1	chr3	2942981	2943322	+	0	NA	intron (NM_001206955, intron 12 of 23)	L4_B_Mam|LINE|RTE-X	50936	NM_175613	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.011730	0.415205	
chunk0018_351_1	chr1	221602916	221603332	+	0	NA	Intergenic	L1ME3B|LINE|L1	133776	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.000000	0.362110	
chunk0088_313_1	chr18	50679647	50680010	+	0	NA	intron (NM_001292040, intron 2 of 3)	intron (NM_001292040, intron 2 of 3)	119714	NM_001292040	5596	Hs.433728	NM_002747	ENSG00000141639	MAPK4	ERK-4|ERK4|PRKM4|p63-MAPK|p63MAPK	mitogen-activated protein kinase 4	protein-coding	0.027548	0.587912	
chunk0084_17_1	chr17	73419958	73420306	+	0	NA	intron (NM_001144952, intron 15 of 44)	intron (NM_001144952, intron 15 of 44)	-108128	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.022989	0.518625	
chunk0159_270_1	chr5	142342024	142342640	+	0	NA	intron (NR_120664, intron 1 of 3)	MIR|SINE|MIR	17039	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.016234	0.505673	167(GTAACACCATGTCCTG,+,0.00)
chunk0041_61_1	chr11	123363592	123364039	+	0	NA	Intergenic	Intergenic	17697	NR_039714	100616319		NR_039714	ENSG00000265357	MIR4493	-	microRNA 4493	ncRNA	0.011186	0.448661	
chunk0091_217_1	chr19	9871702	9871982	+	0	NA	intron (NM_058164, intron 1 of 5)	L2c|LINE|L2	-13674	NM_001304348	93145	Hs.169743	NM_058164	ENSG00000105088	OLFM2	NOE2|NOELIN2|NOELIN2_V1|OlfC	olfactomedin 2	protein-coding	0.025000	0.533808	
chunk0073_152_1	chr16	6693279	6693663	+	0	NA	intron (NM_018723, intron 3 of 15)	(ATC)n|Simple_repeat|Simple_repeat	-80338	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.010417	0.457143	
chunk0177_19_1	chr7	20573669	20574508	+	0	NA	Intergenic	Intergenic	-41534	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.004768	0.291667	
chunk0166_193_1	chr6	46352631	46352927	+	0	NA	intron (NR_125838, intron 2 of 3)	intron (NR_125838, intron 2 of 3)	-26887	NM_005822	10231	Hs.440168	NM_005822	ENSG00000172348	RCAN2	CSP2|DSCR1L1|MCIP2|RCN2|ZAKI-4|ZAKI4	regulator of calcineurin 2	protein-coding	0.003378	0.488215	108(GAGGACACTGAGTACC,-,0.00),109(AGGACACTGAGTACCC,+,0.00)
chunk0121_318_1	chr3	24253638	24254024	+	0	NA	intron (NM_000461, intron 2 of 9)	intron (NM_000461, intron 2 of 9)	102507	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.007772	0.390181	
chunk0164_46_1	chr6	18465319	18466161	+	0	NA	3' UTR (NM_182757, exon 8 of 8)	3' UTR (NM_182757, exon 8 of 8)	78390	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.007126	0.417556	
chunk0203_372_1	chr9	90099137	90099447	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-57793	NR_038882	286370	Hs.407589	NR_038882	ENSG00000227555	MIR4290HG	-	MIR4290 host gene	ncRNA	0.009677	0.430868	
chunk0077_214_1	chr16	80084759	80085026	+	0	NA	Intergenic	Intergenic	289643	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.007491	0.526119	99(AGGCACAGCCTGTCCT,-,0.00),100(GGCACAGCCTGTCCTC,+,0.00)
chunk0021_202_1	chr10	5846535	5846752	+	0	NA	Intergenic	Intergenic	-33094	NM_001494	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.004608	0.444954	
chunk0087_264_1	chr18	37221573	37221877	+	0	NA	intron (NM_020776, intron 9 of 9)	MIR|SINE|MIR	244779	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.003289	0.386885	
chunk0098_423_1	chr2	80545313	80546145	+	0	NA	intron (NM_004389, intron 10 of 17)	intron (NM_004389, intron 10 of 17)	232350	NM_001282599	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.014423	0.454982	
chunk0211_86_1	chrX	110173160	110173921	+	0	NA	3' UTR (NM_017698, exon 6 of 6)	3' UTR (NM_017698, exon 6 of 6)	51520	NR_004379	692226		NR_004379	ENSG00000208883	SNORD96B	U96b	small nucleolar RNA, C/D box 96B	snoRNA	0.021025	0.507874	205(CTGGTCATCCTGTTCT,-,0.00),206(TGGTCATCCTGTTCTC,+,0.00),348(GAGAACACCCAGTTCT,-,0.00),349(AGAACACCCAGTTCTT,+,0.00)
chunk0037_188_1	chr11	74145847	74146358	+	0	NA	intron (NM_001286577, intron 3 of 32)	Charlie8|DNA|hAT-Charlie	24917	NM_015531	26005	Hs.557938	NM_015531	ENSG00000168014	C2CD3	OFD14	C2 domain containing 3 centriole elongation regulator	protein-coding	0.000000	0.302734	
chunk0006_375_1	chr1	74071226	74071548	+	0	NA	intron (NM_001105659, intron 6 of 7)	LTR80A|LTR|ERVL	126800	NM_001105659	127255	Hs.644625	NM_145258	ENSG00000162620	LRRIQ3	LRRC44	leucine rich repeats and IQ motif containing 3	protein-coding	0.003106	0.427245	
chunk0072_370_1	chr15	99954479	99954910	+	0	NA	Intergenic	Intergenic	-147767	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.004640	0.488426	
chunk0178_205_1	chr7	34747796	34748647	+	0	NA	intron (NR_015356, intron 2 of 4)	intron (NR_015356, intron 2 of 4)	10051	NR_033665	404744	Hs.487951	NM_207283	ENSG00000197085	NPSR1-AS1	AAA1	NPSR1 antisense RNA 1	ncRNA	0.009401	0.475352	732(CAGCCCATTCTGTTCC,-,0.00),733(AGCCCATTCTGTTCCT,+,0.00)
chunk0049_260_1	chr12	93727314	93727666	+	0	NA	intron (NR_110093, intron 2 of 2)	intron (NR_110093, intron 2 of 2)	10333	NR_110092	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.002841	0.433428	201(CAGAACATGATGTCCC,-,0.00),202(AGAACATGATGTCCCT,+,0.00)
chunk0061_425_1	chr14	65231338	65231931	+	0	NA	Intergenic	Intergenic	-9287	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.010118	0.425926	
chunk0101_150_1	chr2	127933263	127933760	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-47571	NM_001199140	83607	Hs.546449	NM_031445	ENSG00000144233	AMMECR1L	-	AMMECR1 like	protein-coding	0.004024	0.357430	
chunk0070_279_1	chr15	74444379	74444697	+	0	NA	Intergenic	Intergenic	-10580	NM_003612	8482	Hs.24640	NM_003612	ENSG00000138623	SEMA7A	CD108|CDw108|H-SEMA-K1|H-Sema-L|JMH|SEMAK1|SEMAL	semaphorin 7A (John Milton Hagen blood group)	protein-coding	0.003145	0.545455	
chunk0147_402_1	chr4	186802425	186803108	+	0	NA	Intergenic	Intergenic	-78933	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.010249	0.385965	
chunk0193_241_1	chr8	76789843	76790334	+	0	NA	intron (NM_024721, intron 4 of 10)	intron (NM_024721, intron 4 of 10)	-106813	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.008147	0.302846	240(CTGGACAATTTGTTCT,-,0.00),241(TGGACAATTTGTTCTG,+,0.00)
chunk0006_246_1	chr1	69160517	69160755	+	0	NA	Intergenic	MIRb|SINE|MIR	-599539	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.008403	0.397490	
chunk0173_4_1	chr6	141153308	141153708	+	0	NA	Intergenic	MER21C|LTR|ERVL	469694	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.005000	0.376559	
chunk0184_44_1	chr7	112257041	112257412	+	0	NA	intron (NM_021994, intron 1 of 11)	intron (NM_021994, intron 1 of 11)	50638	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.005391	0.354839	
chunk0003_116_1	chr1	32394596	32394795	+	0	NA	promoter-TSS (NM_001143889)	promoter-TSS (NM_001143889)	-234	NM_018045	55108	Hs.353454	NM_018045	ENSG00000160058	BSDC1	-	BSD domain containing 1	protein-coding	0.060302	0.570000	
chunk0104_438_1	chr2	181257801	181258542	+	0	NA	intron (NR_130784, intron 2 of 4)	intron (NR_130784, intron 2 of 4)	47481	NR_039637	100616213		NR_039637	ENSG00000266705	MIR4437	mir-4437	microRNA 4437	ncRNA	0.004049	0.370620	
chunk0198_20_1	chr8	128048819	128049118	+	0	NA	promoter-TSS (NR_031612)	promoter-TSS (NR_031612)	-184	NR_031612	100302175		NR_031612	ENSG00000221176	MIR1207	MIRN1207|hsa-mir-1207	microRNA 1207	ncRNA	0.003344	0.450000	173(CTGGACTCTGTGTTCT,-,0.00),174(TGGACTCTGTGTTCTG,+,0.00)
chunk0160_370_1	chr5	161190344	161190691	+	0	NA	Intergenic	L2c|LINE|L2	-251891	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.005764	0.367816	
chunk0028_449_1	chr10	94476356	94476580	+	0	NA	intron (NM_015188, intron 3 of 12)	intron (NM_015188, intron 3 of 12)	-69299	NM_001289068	3070	Hs.463677	NM_018063	ENSG00000119969	HELLS	ICF4|LSH|Nbla10143|PASG|SMARCA6	helicase, lymphoid specific	protein-coding	0.004464	0.302222	
chunk0196_274_1	chr8	109259814	109260253	+	0	NA	intron (NM_001128211, intron 8 of 9)	intron (NM_001128211, intron 8 of 9)	69900	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.002278	0.309091	
chunk0010_216_1	chr1	116203277	116203480	+	0	NA	Intergenic	Intergenic	91623	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.004926	0.573529	
chunk0210_134_1	chrX	74252836	74253315	+	0	NA	intron (NR_028379, intron 5 of 6)	MER68B|LTR|ERVL	34134	NR_030258	664614		NR_030258	ENSG00000207820	MIR545	MIRN545|hsa-mir-545|mir-545	microRNA 545	ncRNA	0.008351	0.431250	
chunk0112_246_1	chr20	41569008	41569230	+	0	NA	intron (NM_032221, intron 1 of 36)	intron (NM_032221, intron 1 of 36)	49375	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.000000	0.452915	
chunk0180_200_1	chr7	66303929	66304241	+	0	NA	intron (NM_003596, intron 3 of 5)	MLT2E|LTR|ERVL	96323	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.009615	0.450479	
chunk0024_162_1	chr10	35556364	35556673	+	0	NA	intron (NM_145012, intron 8 of 9)	intron (NM_145012, intron 8 of 9)	-48892	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.009709	0.416129	
chunk0201_437_1	chr9	70127031	70127293	+	0	NA	intron (NR_125850, intron 6 of 13)	Penelope1_Vert|LINE|Penelope	48726	NR_040076	100507244	Hs.556816	NR_040076	ENSG00000204706	MAMDC2-AS1	-	MAMDC2 antisense RNA 1	ncRNA	0.015267	0.387833	190(GAAAACAGAGTGTCCA,-,0.00),191(AAAACAGAGTGTCCAA,+,0.00)
chunk0078_12_1	chr17	394881	395138	+	0	NA	Intergenic	Intergenic	-15318	NM_001013672	400566	Hs.499607	NM_001013672	ENSG00000187624	C17orf97	CK20|LIAT1	chromosome 17 open reading frame 97	protein-coding	0.015564	0.565891	
chunk0005_198_1	chr1	58988681	58989151	+	0	NA	Intergenic	L2c|LINE|L2	-31560	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.002128	0.486200	249(TGGGACATGCTGTTCC,-,0.00),250(GGGACATGCTGTTCCC,+,0.00)
chunk0064_186_1	chr14	92719685	92720336	+	0	NA	intron (NM_001008530, intron 3 of 14)	intron (NM_001008530, intron 3 of 14)	28692	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.010753	0.415644	
chunk0153_100_1	chr5	68417333	68417864	+	0	NA	Intergenic	Intergenic	125030	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.005650	0.327068	
chunk0184_191_1	chr7	116862254	116862514	+	0	NA	promoter-TSS (NM_006136)	promoter-TSS (NM_006136)	-125	NM_006136	830	Hs.446123	NM_006136	ENSG00000198898	CAPZA2	CAPPA2|CAPZ	capping actin protein of muscle Z-line subunit alpha 2	protein-coding	0.107692	0.693487	29(GGGCTCAGAATGTACT,-,0.00),30(GGCTCAGAATGTACTC,+,0.00)
chunk0196_332_1	chr8	112458444	112458696	+	0	NA	intron (NM_198123, intron 32 of 70)	intron (NM_198123, intron 32 of 70)	-184923	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.003968	0.343874	
chunk0169_430_1	chr6	108677778	108678476	+	0	NA	intron (NM_201559, intron 3 of 3)	intron (NM_201559, intron 3 of 3)	-73527	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.007163	0.377682	
chunk0055_250_1	chr13	63108408	63108816	+	0	NA	Intergenic	Intergenic	219482	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.000000	0.259169	
chunk0157_134_1	chr5	117390517	117391061	+	0	NA	Intergenic	Intergenic	-24723	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.003676	0.315596	
chunk0077_171_1	chr16	79440619	79441050	+	0	NA	Intergenic	Chap1_Mam|DNA|hAT-Charlie	159891	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.011601	0.432870	
chunk0111_56_1	chr20	22673348	22673841	+	0	NA	Intergenic	Intergenic	-66077	NR_109883	101929685	Hs.563018	NR_109883	ENSG00000237396	LNCNEF	LINC01384|lncRNA-NEF	lncRNA neighboring enhancer of FOXA2	ncRNA	0.014199	0.485830	
chunk0182_228_1	chr7	96508366	96508864	+	0	NA	Intergenic	Intergenic	-5092	NM_001201450	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.002008	0.392786	
chunk0136_434_1	chr3	197787366	197787841	+	0	NA	Intergenic	Intergenic	-3623	NM_032773	84859	Hs.518414	NM_032773	ENSG00000186001	LRCH3	-	leucine rich repeats and calponin homology domain containing 3	protein-coding	0.008421	0.428571	
chunk0083_324_1	chr17	69579363	69579562	+	0	NA	Intergenic	MIR|SINE|MIR	-14525	NR_109971	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.010050	0.420000	
chunk0056_228_1	chr13	88600022	88600434	+	0	NA	Intergenic	Intergenic	59399	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.002427	0.355932	294(AAGTACACTTTGTTTC,-,0.00),295(AGTACACTTTGTTTCT,+,0.00)
chunk0048_15_1	chr12	77077428	77077955	+	0	NA	Intergenic	MLT1J2-int|LTR|ERVL-MaLR	-12111	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.001898	0.414773	
chunk0098_283_1	chr2	75714732	75714961	+	0	NA	Intergenic	Intergenic	-3861	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.013100	0.400000	
chunk0188_216_1	chr8	12766253	12766956	+	0	NA	intron (NR_015383, intron 3 of 3)	MER57C2|LTR|ERV1	-11121	NM_152271	91694	Hs.180178	NM_152271	ENSG00000154359	LONRF1	RNF191	LON peptidase N-terminal domain and ring finger 1	protein-coding	0.019915	0.475852	329(AAGTACACATCGTTCT,-,0.00),330(AGTACACATCGTTCTG,+,0.00)
chunk0061_123_1	chr14	58739958	58740555	+	0	NA	Intergenic	Intergenic	-88032	NR_110547	102723742	Hs.232734	NR_110547	ENSG00000258583	LINC01500	-	long intergenic non-protein coding RNA 1500	ncRNA	0.003350	0.391304	
chunk0007_94_1	chr1	78633312	78633524	+	0	NA	intron (NM_006820, intron 4 of 8)	L1M1|LINE|L1	13036	NM_006820	10964	Hs.744918	NM_006820	ENSG00000137959	IFI44L	C1orf29|GS3686	interferon induced protein 44 like	protein-coding	0.018868	0.572770	
chunk0044_23_1	chr12	27182028	27182467	+	0	NA	Intergenic	MER21C|LTR|ERVL	-61898	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.006834	0.488636	
chunk0081_387_1	chr17	48177126	48177468	+	0	NA	intron (NM_001075099, intron 9 of 12)	intron (NM_001075099, intron 9 of 12)	-20786	NR_031607	100302211		NR_031607	ENSG00000221739	MIR1203	MIRN1203|hsa-mir-1203	microRNA 1203	ncRNA	0.002924	0.457726	
chunk0018_200_1	chr1	219350966	219351475	+	0	NA	Intergenic	Intergenic	176251	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.000000	0.354902	
chunk0204_299_1	chr9	100052254	100052581	+	0	NA	exon (NM_015051, exon 4 of 12)	exon (NM_015051, exon 4 of 12)	46635	NM_015051	23071	Hs.154023	NM_015051	ENSG00000023318	ERP44	PDIA10|TXNDC4	endoplasmic reticulum protein 44	protein-coding	0.009174	0.356707	124(TGGGACAGTCTCTTCT,-,0.00),125(GGGACAGTCTCTTCTA,+,0.00)
chunk0182_309_1	chr7	98569951	98570448	+	0	NA	Intergenic	Intergenic	-47086	NM_002523	4885	Hs.3281	NM_002523	ENSG00000106236	NPTX2	NARP|NP-II|NP2	neuronal pentraxin 2	protein-coding	0.030181	0.520080	238(GGGAACGTTCTGTTCT,-,0.00),239(GGAACGTTCTGTTCTG,+,0.00)
chunk0078_73_1	chr17	1597825	1598214	+	0	NA	intron (NM_001284498, intron 5 of 14)	intron (NM_001284498, intron 5 of 14)	7015	NM_001284499	124935	Hs.160550	NM_152346	ENSG00000167703	SLC43A2	LAT4	solute carrier family 43 member 2	protein-coding	0.033419	0.530769	
chunk0006_307_1	chr1	71407604	71408320	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	326638	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.006983	0.365411	
chunk0211_246_1	chrX	120433680	120434148	+	0	NA	intron (NM_002294, intron 8 of 8)	intron (NM_002294, intron 8 of 8)	35435	NM_013995	3920	Hs.496684	NM_002294	ENSG00000005893	LAMP2	CD107b|LAMP-2|LAMPB|LGP-96|LGP110	lysosomal associated membrane protein 2	protein-coding	0.004274	0.424307	
chunk0133_329_1	chr3	172608365	172609072	+	0	NA	Intergenic	Intergenic	-85211	NM_003810	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.004243	0.375706	468(TAGAACTTCATGTGCT,-,0.00),469(AGAACTTCATGTGCTA,+,0.00)
chunk0086_439_1	chr18	28740173	28740458	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-562869	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.000000	0.293706	
chunk0102_437_1	chr2	157801006	157801905	+	0	NA	intron (NM_001111067, intron 2 of 10)	Charlie7|DNA|hAT-Charlie	73656	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.004449	0.333333	
chunk0120_22_1	chr3	1989505	1989850	+	0	NA	Intergenic	Intergenic	-109189	NM_175607	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.005797	0.361272	
chunk0172_182_1	chr6	136551855	136552390	+	0	NA	Intergenic	Intergenic	-1303	NM_001198616	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.007477	0.395522	280(ATAGACAGTGTGTTCC,-,0.00),281(TAGACAGTGTGTTCCA,+,0.00)
chunk0207_351_1	chr9	134980640	134981061	+	0	NA	Intergenic	Intergenic	-62890	NM_002003	2219	Hs.440898	NM_002003	ENSG00000085265	FCN1	FCNM	ficolin 1	protein-coding	0.021378	0.566351	
chunk0093_414_1	chr19	57362287	57362984	+	0	NA	promoter-TSS (NR_002166)	promoter-TSS (NR_002166)	-800	NM_173631	284306	Hs.446620	NM_173631	ENSG00000152433	ZNF547	MIP-2A|SEDLP1|TRAPPC2.19|TRAPPC2B|TRAPPC2P1	zinc finger protein 547	protein-coding	0.008608	0.391117	346(TGGCACAAAATGTCCT,-,0.00),347(GGCACAAAATGTCCTG,+,0.00)
chunk0099_8_1	chr2	82694548	82695408	+	0	NA	Intergenic	Intergenic	-161825	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.008140	0.368177	
chunk0167_411_1	chr6	75386243	75386442	+	0	NA	intron (NR_125859, intron 2 of 8)	MamGypsy2-I|LTR|Gypsy	3156	NR_125859	101928540	Hs.526972	NR_125859		LOC101928540	-	uncharacterized LOC101928540	ncRNA	0.005025	0.415000	
chunk0027_33_1	chr10	72330114	72330313	+	0	NA	Intergenic	MIR|SINE|MIR	24936	NM_001002762	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.005025	0.445000	
chunk0133_208_1	chr3	170901901	170902210	+	0	NA	intron (NM_020390, intron 3 of 4)	ERVL-E-int|LTR|ERVL	6582	NM_020390	56648	Hs.164144	NM_020390	ENSG00000163577	EIF5A2	EIF-5A2|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding	0.003236	0.412903	
chunk0032_304_1	chr11	9774819	9775486	+	0	NA	intron (NR_036485, intron 1 of 2)	MIR3|SINE|MIR	-15619	NR_033972	440028	Hs.677541	NR_033972	ENSG00000245522	LINC02709	-	long intergenic non-protein coding RNA 2709	ncRNA	0.008996	0.422156	
chunk0092_402_1	chr19	37377313	37377808	+	0	NA	intron (NM_032453, intron 2 of 4)	intron (NM_032453, intron 2 of 4)	6403	NM_032453	84503	Hs.590940	NM_032453	ENSG00000189164	ZNF527	-	zinc finger protein 527	protein-coding	0.004040	0.439516	311(AGGATCATGCTGTACT,-,0.00),312(GGATCATGCTGTACTC,+,0.00)
chunk0033_312_1	chr11	20522647	20523081	+	0	NA	Intergenic	Intergenic	-76536	NM_004211	9152	Hs.136557	NM_004211	ENSG00000165970	SLC6A5	GLYT-2|GLYT2|HKPX3|NET1	solute carrier family 6 member 5	protein-coding	0.006912	0.441379	292(CTGAACACACTGAGCC,-,0.00)
chunk0152_439_1	chr5	66143679	66144469	+	0	NA	promoter-TSS (NM_001270493)	promoter-TSS (NM_001270493)	-144	NM_001077199	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.081013	0.563843	
chunk0030_450_1	chr10	121051822	121052255	+	0	NA	Intergenic	Intergenic	-200859	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.002309	0.315668	
chunk0035_158_1	chr11	43408252	43408733	+	0	NA	intron (NM_018259, intron 15 of 23)	L2c|LINE|L2	49607	NM_018259	55761	Hs.191186	NM_018259	ENSG00000052841	TTC17	-	tetratricopeptide repeat domain 17	protein-coding	0.004158	0.348548	
chunk0195_119_1	chr8	94856548	94856965	+	0	NA	intron (NR_073444, intron 14 of 28)	intron (NR_073444, intron 14 of 28)	33466	NR_073444	55656	Hs.727669	NM_017864	ENSG00000164941	INTS8	C8orf52|INT8	integrator complex subunit 8	protein-coding	0.019185	0.385167	
chunk0114_229_1	chr21	15875240	15875593	+	0	NA	intron (NM_013396, intron 22 of 23)	intron (NM_013396, intron 22 of 23)	145391	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.005666	0.341808	252(ATGTACTTCCTGTCCT,-,0.00),253(TGTACTTCCTGTCCTC,+,0.00)
chunk0006_86_1	chr1	65031017	65031506	+	0	NA	Intergenic	L1MC4|LINE|L1	26581	NR_037443	100500854		NR_037443	ENSG00000265996	MIR3671	-	microRNA 3671	ncRNA	0.008180	0.400000	219(AAGTACGTGATGTTCT,-,0.00)
chunk0073_396_1	chr16	16041089	16041836	+	0	NA	intron (NM_004996, intron 7 of 30)	intron (NM_004996, intron 7 of 30)	91885	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.012048	0.505348	47(TGCCCAGGCTGTTCTC,+,0.00)
chunk0130_161_1	chr3	132659845	132660079	+	0	NA	promoter-TSS (NM_024818)	promoter-TSS (NM_024818)	169	NR_132427	84129	Hs.441378	NM_032169	ENSG00000240303	ACAD11	ACAD-11	acyl-CoA dehydrogenase family member 11	protein-coding	0.059829	0.561702	
chunk0197_2_1	chr8	116710701	116711032	+	0	NA	intron (NM_003756, intron 2 of 7)	intron (NM_003756, intron 2 of 7)	44957	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.000000	0.340361	
chunk0211_375_1	chrX	126620105	126620314	+	0	NA	Intergenic	Intergenic	-67350	NM_178470	139170	Hs.120403	NM_178470	ENSG00000198889	DCAF12L1	KIAA1892L|WDR40B	DDB1 and CUL4 associated factor 12 like 1	protein-coding	0.009569	0.466667	145(AAGAACATGCTGTTCC,-,0.00),146(AGAACATGCTGTTCCT,+,0.00)
chunk0177_441_1	chr7	28005363	28005989	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-174781	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.009585	0.449761	244(AGGAACACAGTGTTCA,-,0.00),245(GGAACACAGTGTTCAG,+,0.00)
chunk0057_420_1	chr13	109986383	109986783	+	0	NA	Intergenic	Intergenic	-66702	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.015000	0.408978	
chunk0020_177_1	chr1	234544667	234545272	+	0	NA	Intergenic	Intergenic	-13190	NR_038426	100506795	Hs.448989	NR_038426	ENSG00000231768	LINC01354	-	long intergenic non-protein coding RNA 1354	ncRNA	0.018182	0.501650	535(GGCACAGATAGTTCAG,+,0.00)
chunk0069_124_1	chr15	61856892	61857603	+	0	NA	intron (NM_017684, intron 80 of 82)	L2c|LINE|L2	203218	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.008439	0.369382	420(AGGAACAGATCGTACT,-,0.00),421(GGAACAGATCGTACTG,+,0.00)
chunk0020_166_1	chr1	234403077	234403767	+	0	NA	intron (NM_005646, intron 24 of 29)	L2a|LINE|L2	29721	NM_001301733	388753	Hs.23198	NM_001012985	ENSG00000168275	COA6	C1orf31|CEMCOX4	cytochrome c oxidase assembly factor 6	protein-coding	0.007246	0.434153	329(CTGAACAGTCTGTATT,-,0.00),330(TGAACAGTCTGTATTT,+,0.00)
chunk0060_182_1	chr14	46630690	46631373	+	0	NA	Intergenic	L2a|LINE|L2	20794	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.004392	0.380117	
chunk0114_308_1	chr21	17114992	17115259	+	0	NA	Intergenic	Intergenic	-323765	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.003745	0.395522	
chunk0020_403_1	chr1	240769256	240769975	+	0	NA	Intergenic	Intergenic	-157453	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.012517	0.394444	
chunk0134_70_1	chr3	176282026	176282287	+	0	NA	Intergenic	Intergenic	-232947	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.003831	0.297710	
chunk0012_217_1	chr1	160157034	160157834	+	0	NA	intron (NM_144699, intron 4 of 21)	L1PA15|LINE|L1	5872	NM_144699	480	Hs.662219	NM_144699	ENSG00000132681	ATP1A4	ATP1A1|ATP1AL2	ATPase Na+/K+ transporting subunit alpha 4	protein-coding	0.007500	0.379526	
chunk0059_154_1	chr14	32230465	32231095	+	0	NA	Intergenic	Intergenic	-27511	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.003175	0.469097	
chunk0093_164_1	chr19	48061293	48062117	+	0	NA	intron (NR_132364, intron 2 of 2)	L2c|LINE|L2	334	NR_132363	106144526	Hs.622570	NR_132363	ENSG00000269420	PLA2G4C-AS1	-	PLA2G4C antisense RNA 1	ncRNA	0.040049	0.551515	
chunk0078_315_1	chr17	8409984	8410193	+	0	NA	Intergenic	Intergenic	-12262	NM_001146684	643904	Hs.526550	NM_001146684	ENSG00000189051	RNF222	-	ring finger protein 222	protein-coding	0.023923	0.428571	
chunk0021_329_1	chr1	245690937	245691371	+	0	NA	intron (NM_018012, intron 12 of 14)	intron (NM_018012, intron 12 of 14)	536169	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.029954	0.471264	
chunk0074_82_1	chr16	21614081	21614280	+	0	NA	intron (NM_016025, intron 2 of 4)	intron (NM_016025, intron 2 of 4)	14704	NM_001077180	51108	Hs.279583	NM_016025	ENSG00000197006	METTL9	CGI-81|DREV|DREV1|PAP1	methyltransferase like 9	protein-coding	0.005025	0.325000	
chunk0067_450_1	chr15	50244869	50245584	+	0	NA	intron (NM_001306146, intron 9 of 10)	MER58A|DNA|hAT-Charlie	20739	NM_001306146	3067	Hs.1481	NM_002112	ENSG00000140287	HDC	-	histidine decarboxylase	protein-coding	0.004196	0.446927	
chunk0110_247_1	chr20	16516611	16516995	+	0	NA	intron (NM_001199865, intron 3 of 24)	MER5A|DNA|hAT-Charlie	56631	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.010417	0.496104	329(CAGCACAGGCAGTACA,-,0.00),330(AGCACAGGCAGTACAG,+,0.00)
chunk0189_197_1	chr8	23653687	23654273	+	0	NA	Intergenic	Intergenic	28909	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.008532	0.410562	
chunk0068_267_1	chr15	56627953	56628271	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	105974	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.006289	0.332288	
chunk0028_400_1	chr10	93244590	93244931	+	0	NA	Intergenic	Intergenic	170870	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.005865	0.418129	
chunk0177_304_1	chr7	25971433	25971958	+	0	NA	Intergenic	HAL1|LINE|L1	-21709	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.003810	0.395437	
chunk0076_139_1	chr16	66996333	66996842	+	0	NA	intron (NM_173815, intron 2 of 11)	intron (NM_173815, intron 2 of 11)	-3926	NM_001190202	283848	Hs.346947	NM_173815	ENSG00000172824	CES4A	CES6|CES8	carboxylesterase 4A	protein-coding	0.009823	0.484314	
chunk0121_312_1	chr3	24163018	24163217	+	0	NA	intron (NM_000461, intron 4 of 9)	intron (NM_000461, intron 4 of 9)	11793	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.010050	0.385000	
chunk0036_54_1	chr11	59071670	59071882	+	0	NA	Intergenic	Intergenic	-13324	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.009434	0.474178	
chunk0009_273_1	chr1	107495873	107496426	+	0	NA	Intergenic	Intergenic	192355	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.005425	0.411552	
chunk0151_292_1	chr5	52891040	52891745	+	0	NA	intron (NM_181501, intron 8 of 28)	L1ME2|LINE|L1	-97934	NR_073104	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.000000	0.269122	
chunk0122_446_1	chr3	39447916	39448638	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-19296	NR_103505	4336	Hs.121333	NM_182935	ENSG00000168314	MOBP	-	myelin associated oligodendrocyte basic protein	protein-coding	0.015235	0.438451	425(ATCACAGAGTGTACTT,+,0.00)
chunk0198_94_1	chr8	130304389	130304711	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	-8017	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.009317	0.377709	
chunk0107_283_1	chr2	218313332	218313869	+	0	NA	intron (NM_015488, intron 2 of 9)	L1M5|LINE|L1	-9579	NM_022572	25953	Hs.98475	NM_015488	ENSG00000127838	PNKD	BRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|TAHCCP2	PNKD metallo-beta-lactamase domain containing	protein-coding	0.001862	0.364312	212(AGGAACACTGAGTTCC,-,0.00),213(GGAACACTGAGTTCCA,+,0.00)
chunk0094_173_1	chr2	5549549	5550061	+	0	NA	Intergenic	Intergenic	141313	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.003906	0.384016	
chunk0098_31_1	chr2	65691691	65692061	+	0	NA	Intergenic	Intergenic	-259354	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.016216	0.396226	
chunk0047_56_1	chr12	67430995	67431420	+	0	NA	Intergenic	Intergenic	-88875	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.009412	0.441315	228(AAGAACTCACAGTCCC,-,0.00),229(AGAACTCACAGTCCCT,+,0.00)
chunk0044_85_1	chr12	28242142	28242551	+	0	NA	Intergenic	MER54A|LTR|ERVL	-14854	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.004890	0.470732	
chunk0104_432_1	chr2	181036531	181036792	+	0	NA	intron (NM_001278554, intron 3 of 5)	MER6A|DNA|TcMar-Tigger	55537	NM_001278554	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.000000	0.450382	93(AGGAGCATCCTGTCCA,-,0.00)
chunk0107_125_1	chr2	214567245	214567559	+	0	NA	intron (NM_001080500, intron 3 of 3)	intron (NM_001080500, intron 3 of 3)	57220	NR_047698	100885780	Hs.665982	NR_047698	ENSG00000224257	VWC2L-IT1	-	VWC2L intronic transcript 1	ncRNA	0.006369	0.466667	
chunk0091_343_1	chr19	14518125	14518437	+	0	NA	promoter-TSS (NM_001300914)	promoter-TSS (NM_001300914)	278	NM_006145	3337	Hs.515210	NM_006145	ENSG00000132002	DNAJB1	HSPF1|Hdj1|Hsp40|RSPH16B|Sis1	DnaJ heat shock protein family (Hsp40) member B1	protein-coding	0.137821	0.693291	
chunk0032_441_1	chr10	132965493	132965717	+	0	NA	promoter-TSS (NR_120627)	promoter-TSS (NR_120627)	71	NR_046231	399829	Hs.252872	NR_046231	ENSG00000240707	LINC01168	-	long intergenic non-protein coding RNA 1168	ncRNA	0.049107	0.546667	
chunk0110_365_1	chr20	19886324	19886589	+	0	NA	promoter-TSS (NM_001242581)	promoter-TSS (NM_001242581)	-65	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.030189	0.500000	
chunk0191_86_1	chr8	47627418	47628069	+	0	NA	intron (NM_001080394, intron 10 of 19)	intron (NM_001080394, intron 10 of 19)	110421	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.016897	0.421779	312(CTGCACACTCTGTTCA,-,0.00),313(TGCACACTCTGTTCAG,+,0.00)
chunk0147_408_1	chr4	186947403	186947804	+	0	NA	Intergenic	Intergenic	-223770	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.009975	0.420398	
chunk0004_99_1	chr1	43872475	43872764	+	0	NA	intron (NR_073021, intron 6 of 9)	MIRb|SINE|MIR	33997	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.006920	0.427586	
chunk0088_247_1	chr18	48709533	48709732	+	0	NA	intron (NM_014772, intron 6 of 11)	intron (NM_014772, intron 6 of 11)	39032	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.040201	0.650000	
chunk0124_429_1	chr3	61186009	61186402	+	0	NA	intron (NM_001166243, intron 2 of 9)	intron (NM_001166243, intron 2 of 9)	65254	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.007634	0.421320	
chunk0100_436_1	chr2	120630275	120630474	+	0	NA	Intergenic	Intergenic	-164025	NR_027181	84931	Hs.334519	NM_032845	ENSG00000280409	LINC01101	-	long intergenic non-protein coding RNA 1101	ncRNA	0.020101	0.500000	
chunk0206_402_1	chr9	127178457	127179240	+	0	NA	TTS (NM_001190730)	TTS (NM_001190730)	-56083	NM_012098	23452	Hs.653262	NM_012098	ENSG00000136859	ANGPTL2	ARP2|HARP	angiopoietin like 2	protein-coding	0.012771	0.526786	358(AGGCACATGCTGGCCC,-,0.00),359(GGCACATGCTGGCCCT,+,0.00)
chunk0019_5_1	chr1	223188232	223188811	+	0	NA	Intergenic	Intergenic	-45239	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.006908	0.387931	
chunk0163_397_1	chr6	16535253	16536022	+	0	NA	intron (NM_001128164, intron 4 of 7)	L1MC3|LINE|L1	225853	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.006502	0.418182	
chunk0066_258_1	chr15	34825103	34825716	+	0	NA	Intergenic	Intergenic	-29683	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.008157	0.457655	
chunk0175_329_1	chr6	167100925	167101138	+	0	NA	Intergenic	LTR47A|LTR|ERVL	-10776	NM_004367	1235	Hs.46468	NM_004367	ENSG00000112486	CCR6	BN-1|C-C CKR-6|CC-CKR-6|CCR-6|CD196|CKR-L3|CKRL3|CMKBR6|DCR2|DRY6|GPR29|GPRCY4|STRL22	C-C motif chemokine receptor 6	protein-coding	0.018779	0.462617	
chunk0003_405_1	chr1	40046418	40046870	+	0	NA	intron (NM_006367, intron 1 of 12)	Tigger3a|DNA|TcMar-Tigger	6061	NM_001105530	10487	Hs.370581	NM_006367	ENSG00000131236	CAP1	CAP|CAP1-PEN	cyclase associated actin cytoskeleton regulatory protein 1	protein-coding	0.013274	0.375276	
chunk0075_312_1	chr16	54446537	54446749	+	0	NA	Intergenic	Intergenic	-160177	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.000000	0.553991	185(TGGAGCAGGGTGTGCT,-,0.00),186(GGAGCAGGGTGTGCTT,+,0.00)
chunk0065_220_1	chr14	100326029	100326382	+	0	NA	exon (NM_207117, exon 3 of 6)	exon (NM_207117, exon 3 of 6)	2863	NM_207117	283600	Hs.108268	NM_207117	ENSG00000140107	SLC25A47	C14orf68|HDMCP|HMFN1655	solute carrier family 25 member 47	protein-coding	0.033994	0.632768	
chunk0088_42_1	chr18	43934801	43935778	+	0	NA	Intergenic	Intergenic	596408	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.004094	0.309816	
chunk0090_280_1	chr18	74874771	74875239	+	0	NA	intron (NM_001146189, intron 3 of 6)	intron (NM_001146189, intron 3 of 6)	244042	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.014957	0.437100	
chunk0043_128_1	chr12	15789147	15789762	+	0	NA	5' UTR (NM_004447, exon 1 of 21)	5' UTR (NM_004447, exon 1 of 21)	122	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.118699	0.696429	
chunk0024_412_1	chr10	45438713	45439077	+	0	NA	intron (NM_000698, intron 7 of 13)	(CTCC)n|Simple_repeat|Simple_repeat	14226	NR_120674	102724323	Hs.559151	NR_120674	ENSG00000231964	LOC102724323	-	uncharacterized LOC102724323	ncRNA	0.005495	0.476712	
chunk0085_362_1	chr18	9361053	9361500	+	0	NA	intron (NM_020648, intron 3 of 4)	HAL1|LINE|L1	26509	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.004474	0.332589	205(AGGAACATACTGTTCT,-,0.00),206(GGAACATACTGTTCTT,+,0.00)
chunk0183_295_1	chr7	107785819	107786494	+	0	NA	intron (NM_000111, intron 8 of 20)	intron (NM_000111, intron 8 of 20)	17077	NM_000111	1811	Hs.1650	NM_000111	ENSG00000091138	SLC26A3	CLD|DRA	solute carrier family 26 member 3	protein-coding	0.007407	0.374260	293(AAGGACAGAGTGTGCC,-,0.00),294(AGGACAGAGTGTGCCT,+,0.00)
chunk0035_396_1	chr11	56666498	56666990	+	0	NA	Intergenic	L1MA1|LINE|L1	3058	NM_001004730	219493	Hs.553633	NM_001004730	ENSG00000172459	OR5AR1	OR11-209	olfactory receptor family 5 subfamily AR member 1 (gene/pseudogene)	protein-coding	0.008130	0.288032	
chunk0008_2_1	chr1	87017927	87018482	+	0	NA	intron (NM_012262, intron 1 of 6)	LTR41|LTR|ERVL	103552	NM_012262	9653	Hs.743280	NM_012262	ENSG00000153936	HS2ST1	dJ604K5.2	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.003604	0.402878	
chunk0210_57_1	chrX	69273360	69273702	+	0	NA	Intergenic	Intergenic	93974	NR_103715	100996279		NR_103715	ENSG00000215162	LINC00269	CXorf62|NCRNA00269	long intergenic non-protein coding RNA 269	ncRNA	0.008772	0.381924	
chunk0188_203_1	chr8	12126355	12126817	+	0	NA	intron (NR_027425, intron 2 of 5)	L1PA10|LINE|L1	2711	NR_003275	392196	Hs.742129	NR_003275	ENSG00000254923	LOC392196	-	ubiquitin specific peptidase 17-like family member 2 pseudogene	pseudo	0.008658	0.399568	371(CAGAACTTCCAGTACT,-,0.00)
chunk0110_42_1	chr20	10578228	10579016	+	0	NA	intron (NM_001009608, intron 4 of 7)	L1MB8|LINE|L1	71073	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.006345	0.354880	385(GGGTCATTCTGTACCT,+,0.00)
chunk0073_158_1	chr16	7782413	7782757	+	0	NA	Intergenic	Intergenic	449835	NM_145892	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.008721	0.359420	
chunk0132_171_1	chr3	156817039	156817478	+	0	NA	promoter-TSS (NR_038387)	promoter-TSS (NR_038387)	-196	NR_038387	730091	Hs.659905	NR_038387	ENSG00000240875	LINC00886	-	long intergenic non-protein coding RNA 886	ncRNA	0.086560	0.600000	213(GAGGACACAGCGTCCC,-,0.00),214(AGGACACAGCGTCCCC,+,0.00)
chunk0092_389_1	chr19	36535023	36535251	+	0	NA	Intergenic	LTR78|LTR|ERV1	-6791	NM_001166038	339324	Hs.18103	NM_001012756	ENSG00000254004	ZNF260	OZRF1|PEX1|ZFP260	zinc finger protein 260	protein-coding	0.008772	0.436681	142(CAGAACATCCTGTTTA,-,0.00),143(AGAACATCCTGTTTAC,+,0.00)
chunk0065_342_1	chr14	103571385	103571784	+	0	NA	intron (NR_126431, intron 2 of 5)	intron (NR_126431, intron 2 of 5)	8627	NM_001302653	84334	Hs.598441	NM_001302652	ENSG00000256053	COA8	APOP|APOP1|APOPT1|C14orf153	cytochrome c oxidase assembly factor 8	protein-coding	0.012531	0.390000	
chunk0039_442_1	chr11	108234655	108235782	+	0	NA	intron (NM_000051, intron 4 of 62)	AluSz|SINE|Alu	12386	NM_000051	472	Hs.367437	NM_000051	ENSG00000149311	ATM	AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1	ATM serine/threonine kinase	protein-coding	0.004437	0.373227	
chunk0001_332_1	chr1	9556073	9556330	+	0	NA	intron (NM_032315, intron 2 of 6)	intron (NM_032315, intron 2 of 6)	16732	NM_032315	84275	Hs.568613	NM_032315	ENSG00000171612	SLC25A33	BMSC-MCP|PNC1	solute carrier family 25 member 33	protein-coding	0.011673	0.453488	12(AGGGACACTTTGCTCT,-,0.00),13(GGGACACTTTGCTCTC,+,0.00),144(AGGAACATGCAGTGCT,-,0.00),145(GGAACATGCAGTGCTT,+,0.00)
chunk0125_391_1	chr3	71853967	71854166	+	0	NA	Intergenic	L2a|LINE|L2	-68860	NM_021935	60675	Hs.528665	NM_021935	ENSG00000163421	PROK2	BV8|HH4|KAL4|MIT1|PK2	prokineticin 2	protein-coding	0.015075	0.380000	
chunk0116_15_1	chr21	32779885	32780154	+	0	NA	intron (NR_024622, intron 1 of 3)	MSTB|LTR|ERVL-MaLR	7919	NR_024622	54067	Hs.54725	NM_001006116		C21orf62-AS1	C21orf49	C21orf62 antisense RNA 1	ncRNA	0.007435	0.474074	
chunk0099_344_1	chr2	100116121	100116668	+	0	NA	intron (NM_002285, intron 1 of 23)	L1MEg|LINE|L1	-10811	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.003656	0.297445	
chunk0022_167_1	chr10	12687846	12688268	+	0	NA	intron (NM_020397, intron 3 of 9)	intron (NM_020397, intron 3 of 9)	-34860	NR_039701	100616320		NR_039701	ENSG00000283699	MIR4481	-	microRNA 4481	ncRNA	0.009479	0.406619	72(AAGAACAGCATGTTTC,-,0.00),73(AGAACAGCATGTTTCA,+,0.00)
chunk0022_176_1	chr10	12875001	12875200	+	0	NA	Intergenic	Intergenic	126604	NM_031455	83643	Hs.498720	NM_031455	ENSG00000151468	CCDC3	-	coiled-coil domain containing 3	protein-coding	0.015075	0.630000	
chunk0129_35_1	chr3	117271379	117272058	+	0	NA	Intergenic	Intergenic	350287	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.011782	0.377941	513(AGGTACAGTTTGTACT,-,0.00),514(GGTACAGTTTGTACTG,+,0.00)
chunk0059_58_1	chr14	30177794	30178264	+	0	NA	Intergenic	Intergenic	-250336	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.004255	0.411890	303(AGGAACACTCTGCACC,-,0.00),304(GGAACACTCTGCACCT,+,0.00)
chunk0146_200_1	chr4	161356265	161356845	+	0	NA	Intergenic	MIRc|SINE|MIR	-666178	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.005172	0.302926	
chunk0064_79_1	chr14	90404955	90405154	+	0	NA	3' UTR (NM_006888, exon 6 of 6)	3' UTR (NM_006888, exon 6 of 6)	8071	NM_006888	801	Hs.282410	NM_006888	ENSG00000198668	CALM1	CALML2|CAM2|CAM3|CAMB|CAMC|CAMI|CAMIII|CPVT4|DD132|LQT14|PHKD|caM	calmodulin 1	protein-coding	0.005025	0.335000	
chunk0206_167_1	chr9	122244480	122244708	+	0	NA	intron (NR_027125, intron 5 of 6)	MIRb|SINE|MIR	-15782	NM_199160	26468	Hs.103137	NM_014368	ENSG00000106852	LHX6	LHX6.1	LIM homeobox 6	protein-coding	0.004386	0.366812	
chunk0206_176_1	chr9	122390297	122390632	+	0	NA	intron (NM_001271164, intron 9 of 9)	L2c|LINE|L2	15142	NM_001271165	5742	Hs.201978	NM_000962	ENSG00000095303	PTGS1	COX1|COX3|PCOX1|PES-1|PGG/HS|PGHS-1|PGHS1|PHS1|PTGHS	prostaglandin-endoperoxide synthase 1	protein-coding	0.017910	0.514881	
chunk0089_256_1	chr18	62486386	62486745	+	0	NA	Intergenic	Intergenic	-36860	NM_017742	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.008357	0.483333	
chunk0015_188_1	chr1	187276346	187277366	+	0	NA	intron (NR_126347, intron 1 of 3)	intron (NR_126347, intron 1 of 3)	-166772	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004902	0.375122	
chunk0090_166_1	chr18	72633502	72633770	+	0	NA	Intergenic	Intergenic	-89148	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.000000	0.312268	
chunk0090_177_1	chr18	72743759	72744357	+	0	NA	3' UTR (NM_138966, exon 11 of 11)	3' UTR (NM_138966, exon 11 of 11)	109324	NR_049858	100847083		NR_049858	ENSG00000263750	MIR548AV	-	microRNA 548av	ncRNA	0.000000	0.312187	
chunk0085_373_1	chr18	9532102	9532333	+	0	NA	intron (NM_006788, intron 7 of 9)	intron (NM_006788, intron 7 of 9)	56685	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.017316	0.461207	
chunk0033_86_1	chr11	14029991	14030400	+	0	NA	intron (NM_006108, intron 2 of 15)	MamTip3|DNA|hAT-Tip100	67558	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.009780	0.504878	
chunk0145_136_1	chr4	146520974	146521201	+	0	NA	intron (NM_001029998, intron 1 of 11)	intron (NM_001029998, intron 1 of 11)	884	NM_001029998	84068	Hs.659209	NM_032128	ENSG00000120519	SLC10A7	C4orf13|P7|SSASKS	solute carrier family 10 member 7	protein-coding	0.022026	0.464912	
chunk0133_343_1	chr3	172903670	172904350	+	0	NA	intron (NM_031955, intron 10 of 10)	intron (NM_031955, intron 10 of 10)	153325	NM_001258316	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.004412	0.381791	
chunk0170_183_1	chr6	111865273	111865644	+	0	NA	intron (NM_002037, intron 1 of 13)	intron (NM_002037, intron 1 of 13)	7994	NM_002037	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.013477	0.392473	
chunk0190_22_1	chr8	29097340	29097784	+	0	NA	intron (NM_015254, intron 36 of 39)	L1MEf|LINE|L1	165531	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.000000	0.312360	167(TAGAACATCATGTCCC,-,0.00),168(AGAACATCATGTCCCC,+,0.00)
chunk0006_312_1	chr1	71439133	71439506	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	357995	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.010724	0.411765	
chunk0181_288_1	chr7	86916161	86916720	+	0	NA	intron (NM_001291990, intron 12 of 21)	L2c|LINE|L2	49535	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.001789	0.407143	259(AAGTACAGAGTGTTCC,-,0.00),260(AGTACAGAGTGTTCCA,+,0.00)
chunk0165_28_1	chr6	29775258	29775804	+	0	NA	Intergenic	Charlie9|DNA|hAT-Charlie	-16375	NR_132323	352962	Hs.60856	NM_001207043	ENSG00000181126	HLA-V	HLA-75|dJ377H14.4	major histocompatibility complex, class I, V (pseudogene)	pseudo	0.007326	0.336380	
chunk0165_87_1	chr6	31795803	31796076	+	0	NA	promoter-TSS (NM_006295).4	promoter-TSS (NM_006295).4	-4	NM_006295	7407	Hs.520026	NM_006295	ENSG00000204394	VARS	G7A|NDMSCA|VARS1|VARS2	valyl-tRNA synthetase	protein-coding	0.139194	0.781022	
chunk0062_183_1	chr14	69705977	69706244	+	0	NA	intron (NM_014734, intron 4 of 5)	intron (NM_014734, intron 4 of 5)	-61002	NM_001039465	6430	Hs.632326	NM_006925	ENSG00000100650	SRSF5	HRS|SFRS5|SRP40	serine and arginine rich splicing factor 5	protein-coding	0.000000	0.335821	
chunk0041_4_1	chr12	144125	144640	+	0	NA	non-coding (NR_033859, exon 2 of 10)	non-coding (NR_033859, exon 2 of 10)	4784	NR_033859	574538	Hs.589138	NR_033859	ENSG00000249695	LOC574538	-	uncharacterized LOC574538	ncRNA	0.031068	0.562016	
chunk0114_243_1	chr21	16007084	16007611	+	0	NA	Intergenic	Intergenic	-63175	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.001898	0.378788	
chunk0140_255_1	chr4	71480837	71481164	+	0	NA	intron (NM_001098484, intron 14 of 25)	MIRb|SINE|MIR	141947	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.000000	0.384146	
chunk0106_329_1	chr2	205852508	205852822	+	0	NA	Intergenic	Intergenic	170165	NM_201264	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.009554	0.501587	
chunk0082_327_1	chr17	59627317	59628447	+	0	NA	intron (NM_004859, intron 1 of 31)	intron (NM_004859, intron 1 of 31)	8193	NM_001288653	1213	Hs.491351	NM_004859	ENSG00000141367	CLTC	CHC|CHC17|CLH-17|CLTCL2|Hc|MRD56	clathrin heavy chain	protein-coding	0.005310	0.348364	
chunk0097_33_1	chr2	42474961	42475199	+	0	NA	intron (NM_172344, intron 1 of 1)	intron (NM_172344, intron 1 of 1)	19017	NM_133329	170850	Hs.352633	NM_133329	ENSG00000171126	KCNG3	KV10.1|KV6.3	potassium voltage-gated channel modifier subfamily G member 3	protein-coding	0.000000	0.355649	
chunk0119_132_1	chr22	42925776	42926560	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	20873	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.014031	0.508280	
chunk0033_307_1	chr11	20415442	20416010	+	0	NA	intron (NM_001145166, intron 7 of 13)	intron (NM_001145166, intron 7 of 13)	28196	NM_005788	10196	Hs.152337	NM_005788	ENSG00000185238	PRMT3	HRMT1L3	protein arginine methyltransferase 3	protein-coding	0.001761	0.405975	
chunk0081_169_1	chr17	41308609	41308808	+	0	NA	exon (NM_001146182, exon 1 of 1)	exon (NM_001146182, exon 1 of 1)	545	NM_001146182	100505753	Hs.721600	NM_001146182	ENSG00000212657	KRTAP16-1	KAP16.1	keratin associated protein 16-1	protein-coding	0.005025	0.590000	
chunk0046_326_1	chr12	62667514	62667870	+	0	NA	intron (NM_020700, intron 8 of 9)	intron (NM_020700, intron 8 of 9)	64006	NR_029661	406891		NR_029661	ENSG00000199179	MIRLET7I	LET7I|MIRNLET7I|hsa-let-7i|let-7i	microRNA let-7i	ncRNA	0.008427	0.386555	
chunk0211_131_1	chrX	112691205	112691824	+	0	NA	Intergenic	L1MB5|LINE|L1	-11367	NM_178175	340596	Hs.297420	NM_178175	ENSG00000182508	LHFPL1	-	LHFPL tetraspan subfamily member 1	protein-coding	0.003231	0.330645	
chunk0163_64_1	chr6	9070246	9070537	+	0	NA	Intergenic	Intergenic	418182	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.003436	0.380137	
chunk0208_158_1	chrX	16184605	16184994	+	0	NA	Intergenic	Intergenic	17318	NM_001277307	645864	Hs.632792	NM_001277307	ENSG00000182798	MAGEB17	-	MAGE family member B17	protein-coding	0.005141	0.466667	
chunk0171_122_1	chr6	122631132	122631443	+	0	NA	intron (NM_181795, intron 1 of 4)	intron (NM_181795, intron 1 of 4)	21055	NM_181795	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.003215	0.336538	
chunk0204_238_1	chr9	97950575	97950942	+	0	NA	Intergenic	L1PA6|LINE|L1	-5843	NM_018437	55363	Hs.176626	NM_018437	ENSG00000136929	HEMGN	CT155|EDAG|EDAG-1|NDR	hemogen	protein-coding	0.005450	0.519022	273(GGGGGCAGTCTGTCCA,-,0.00),274(GGGGCAGTCTGTCCAT,+,0.00)
chunk0148_144_1	chr5	6085604	6085847	+	0	NA	Intergenic	LTR34|LTR|ERV1	251567	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.012346	0.430328	
chunk0028_283_1	chr10	91254183	91254720	+	0	NA	intron (NM_001257101, intron 6 of 9)	intron (NM_001257101, intron 6 of 9)	33849	NM_032373	84333	Hs.500512	NM_032373	ENSG00000180628	PCGF5	RNF159	polycomb group ring finger 5	protein-coding	0.005587	0.375465	
chunk0165_306_1	chr6	36906717	36906938	+	0	NA	intron (NM_001286635, intron 4 of 8)	intron (NM_001286635, intron 4 of 8)	20963	NM_152734	221477	Hs.433381	NM_152734	ENSG00000198663	C6orf89	BRAP|PS1TP5TP1	chromosome 6 open reading frame 89	protein-coding	0.004525	0.414414	
chunk0139_406_1	chr4	63324936	63325631	+	0	NA	Intergenic	L1M2|LINE|L1	1084177	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.001439	0.298851	383(GGATCACCATGTACCG,+,0.00)
chunk0030_74_1	chr10	112183699	112184061	+	0	NA	promoter-TSS (NM_001244949)	promoter-TSS (NM_001244949)	-101	NM_001244949	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.074586	0.628099	
chunk0094_162_1	chr2	5365248	5365454	+	0	NA	Intergenic	Intergenic	325767	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.004854	0.314010	
chunk0139_163_1	chr4	53798816	53799933	+	0	NA	Intergenic	Intergenic	103473	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.005372	0.376565	268(AGGTACTGTGTGTTCA,-,0.00),269(GGTACTGTGTGTTCAC,+,0.00)
chunk0107_400_1	chr2	223957243	223957458	+	0	NA	promoter-TSS (NM_022915)	promoter-TSS (NM_022915)	-54	NM_022915	65080	Hs.203559	NM_022915	ENSG00000135900	MRPL44	COXPD16|L44MT|MRP-L44	mitochondrial ribosomal protein L44	protein-coding	0.106977	0.662037	
chunk0126_274_1	chr3	79999203	79999484	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-231434	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003559	0.407801	
chunk0014_207_1	chr1	179228787	179228986	+	0	NA	intron (NM_007314, intron 1 of 11)	intron (NM_007314, intron 1 of 11)	798	NM_001168238	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.020101	0.495000	
chunk0173_61_1	chr6	142385294	142385819	+	0	NA	intron (NM_020455, intron 6 of 25)	MER113|DNA|hAT-Charlie	83637	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.003810	0.269962	
chunk0005_139_1	chr1	57408042	57408241	+	0	NA	intron (NM_021080, intron 3 of 16)	intron (NM_021080, intron 3 of 16)	-442001	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.015075	0.460000	135(TAGCACATCGTGTTTC,-,0.00),136(AGCACATCGTGTTTCC,+,0.00)
chunk0064_379_1	chr14	98798091	98798606	+	0	NA	Intergenic	Intergenic	86735	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.007767	0.439922	
chunk0144_3_1	chr4	124437836	124438370	+	0	NA	Intergenic	L2a|LINE|L2	120331	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.000000	0.418692	252(AGGAACAATGTGTACC,-,0.00),253(GGAACAATGTGTACCA,+,0.00)
chunk0055_137_1	chr13	59518351	59518745	+	0	NA	Intergenic	HAL1|LINE|L1	-494170	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.007614	0.359494	
chunk0043_96_1	chr12	14803497	14803879	+	0	NA	promoter-TSS (NM_016312)	promoter-TSS (NM_016312)	116	NM_175874	144608	Hs.659951	NM_175874	ENSG00000182993	C12orf60	-	chromosome 12 open reading frame 60	protein-coding	0.044503	0.477807	
chunk0115_269_1	chr21	28035413	28035987	+	0	NA	Intergenic	L2a|LINE|L2	-12714	NR_126010	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.001742	0.340870	
chunk0022_389_1	chr10	17668429	17669281	+	0	NA	intron (NR_037774, intron 2 of 11)	L1MC2|LINE|L1	24730	NM_003473	8027	Hs.335391	NM_003473	ENSG00000136738	STAM	STAM-1|STAM1	signal transducing adaptor molecule	protein-coding	0.008216	0.344666	40(AGGTACACTTTGTTTT,-,0.00)
chunk0121_307_1	chr3	24133408	24134519	+	0	NA	intron (NM_000461, intron 7 of 9)	intron (NM_000461, intron 7 of 9)	-17361	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.005401	0.473921	
chunk0149_325_1	chr5	26577907	26578506	+	0	NA	Intergenic	Tigger4|DNA|TcMar-Tigger	460376	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.006678	0.350000	
chunk0118_326_1	chr22	35372005	35372323	+	0	NA	Intergenic	Intergenic	-8903	NM_002133	3162	Hs.517581	NM_002133	ENSG00000100292	HMOX1	HMOX1D|HO-1|HSP32|bK286B10	heme oxygenase 1	protein-coding	0.056604	0.583072	
chunk0157_48_1	chr5	116012095	116012569	+	0	NA	intron (NM_173800, intron 14 of 19)	intron (NM_173800, intron 14 of 19)	-39134	NM_001195581	644100	Hs.98288	NM_001195581	ENSG00000268223	ARL14EPL	-	ADP ribosylation factor like GTPase 14 effector protein like	protein-coding	0.004219	0.277895	
chunk0203_73_1	chr9	83700496	83700806	+	0	NA	intron (NM_053067, intron 1 of 9)	L2b|LINE|L2	7602	NM_013438	29979	Hs.9589	NM_013438	ENSG00000135018	UBQLN1	DA41|DSK2|PLIC-1|UBQN|XDRP1	ubiquilin 1	protein-coding	0.000000	0.385852	200(AAGAACAAACTGTACA,-,0.00),201(AGAACAAACTGTACAG,+,0.00)
chunk0181_422_1	chr7	90344684	90345187	+	0	NA	TTS (NR_110085)	TTS (NR_110085)	-1730	NM_033107	85865	Hs.593547	NM_033107	ENSG00000105793	GTPBP10	ObgH2|UG0751c10	GTP binding protein 10	protein-coding	0.000000	0.345238	311(CAGTACACAATGATCC,-,0.00),312(AGTACACAATGATCCT,+,0.00)
chunk0067_74_1	chr15	41402385	41402584	+	0	NA	promoter-TSS (NR_045620)	promoter-TSS (NR_045620)	-24	NR_045620	51103	Hs.106529	NM_016013	ENSG00000137806	NDUFAF1	CGI-65|CGI65|CIA30|MC1DN11	NADH:ubiquinone oxidoreductase complex assembly factor 1	protein-coding	0.065327	0.610000	
chunk0136_18_1	chr4	429344	429664	+	0	NA	intron (NR_002451, intron 2 of 2)	L1MB2|LINE|L1	44705	NR_002451	79963	Hs.677493	NM_024903	ENSG00000251595	ABCA11P	ABCA11|EST1133530	ATP binding cassette subfamily A member 11, pseudogene	pseudo	0.009375	0.345794	
chunk0112_318_1	chr20	44701398	44701597	+	0	NA	Intergenic	MIR|SINE|MIR	-13747	NM_003881	8839	Hs.592145	NM_003881	ENSG00000064205	CCN5	CT58|CTGF-L|WISP2	cellular communication network factor 5	protein-coding	0.015075	0.480000	
chunk0175_343_1	chr6	167457829	167458249	+	0	NA	Intergenic	Intergenic	-73529	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.004762	0.327791	
chunk0081_419_1	chr17	48756809	48757077	+	0	NA	Intergenic	Intergenic	-28194	NM_006361	10481	Hs.66731	NM_006361	ENSG00000159184	HOXB13	HPC9|PSGD	homeobox B13	protein-coding	0.011194	0.568773	
chunk0013_214_1	chr1	169485643	169486185	+	0	NA	promoter-TSS (NM_006996)	promoter-TSS (NM_006996)	56	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.101476	0.677716	
chunk0153_36_1	chr5	67154458	67155189	+	0	NA	intron (NM_001290226, intron 24 of 26)	intron (NM_001290226, intron 24 of 26)	41966	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.006840	0.411202	
chunk0199_35_1	chr9	840960	841162	+	0	NA	promoter-TSS (NM_021951)	promoter-TSS (NM_021951)	-629	NM_021951	1761	Hs.98586	NM_021951	ENSG00000137090	DMRT1	CT154|DMT1	doublesex and mab-3 related transcription factor 1	protein-coding	0.029703	0.453202	109(GAGAACAGAAAGTTCC,-,0.00),110(AGAACAGAAAGTTCCA,+,0.00)
chunk0092_176_1	chr19	29976532	29976733	+	0	NA	intron (NM_003796, intron 2 of 10)	intron (NM_003796, intron 2 of 10)	34393	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.009950	0.396040	
chunk0085_81_1	chr18	2255090	2255372	+	0	NA	Intergenic	L1PB1|LINE|L1	316272	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.010638	0.371025	
chunk0029_344_1	chr10	106508807	106509403	+	0	NA	Intergenic	LTR16C|LTR|ERVL	655603	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.003356	0.403685	
chunk0012_202_1	chr1	160042958	160043244	+	0	NA	intron (NM_002241, intron 1 of 1)	intron (NM_002241, intron 1 of 1)	-11108	NM_145167	93183	Hs.552810	NM_145167	ENSG00000143315	PIGM	GPI-MT-I	phosphatidylinositol glycan anchor biosynthesis class M	protein-coding	0.006993	0.393728	
chunk0010_348_1	chr1	118602226	118602965	+	0	NA	Intergenic	MER90a|LTR|ERV1	386961	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.005413	0.410811	
chunk0124_443_1	chr3	61418486	61418799	+	0	NA	Intergenic	Intergenic	-142927	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.003195	0.449045	196(GTAAACAGTCTGTCCC,-,0.00),197(TAAACAGTCTGTCCCT,+,0.00)
chunk0054_9_1	chr13	40389381	40389628	+	0	NA	intron (NR_024506, intron 5 of 5)	intron (NR_024506, intron 5 of 5)	91502	NR_024507	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.016194	0.536290	
chunk0209_445_1	chrX	65772621	65773285	+	0	NA	Intergenic	Intergenic	105309	NM_002444	4478	Hs.87752	NM_002444	ENSG00000147065	MSN	HEL70|IMD50	moesin	protein-coding	0.007530	0.473684	353(CAGGTCTGAGTGTTCC,-,0.00),368(CAGGACTGGATGTTCC,-,0.00),369(AGGACTGGATGTTCCG,+,0.00)
chunk0016_144_1	chr1	197380399	197380955	+	0	NA	intron (NM_201253, intron 5 of 11)	intron (NM_201253, intron 5 of 11)	112473	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.008993	0.421903	
chunk0187_236_1	chr7	152637723	152638413	+	0	NA	Intergenic	L1ME3G|LINE|L1	38097	NM_005431	7516	Hs.647093	NM_005431	ENSG00000196584	XRCC2	FANCU	X-ray repair cross complementing 2	protein-coding	0.013043	0.395080	409(AAGAACAGTATGTCCA,-,0.00),410(AGAACAGTATGTCCAG,+,0.00)
chunk0087_76_1	chr18	32024393	32024700	+	0	NA	intron (NM_017831, intron 1 of 5)	AluJo|SINE|Alu	6064	NM_017831	54941	Hs.633703	NM_017831	ENSG00000101695	RNF125	TNORS|TRAC-1|TRAC1	ring finger protein 125	protein-coding	0.000000	0.412338	
chunk0210_48_1	chrX	68488708	68489005	+	0	NA	Intergenic	Intergenic	-9926	NM_173834	286451	Hs.82719	NM_173834	ENSG00000181704	YIPF6	FinGER6	Yip1 domain family member 6	protein-coding	0.013468	0.436242	
chunk0108_33_1	chr2	226615351	226615914	+	0	NA	Intergenic	Intergenic	43161	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.003552	0.349291	
chunk0077_71_1	chr16	77063485	77063932	+	0	NA	Intergenic	Intergenic	-127211	NM_001286640	22879	Hs.513743	NM_014940	ENSG00000103111	MON1B	HSRG1|SAND2|SRG1	MON1 homolog B, secretory trafficking associated	protein-coding	0.006711	0.464286	
chunk0057_105_1	chr13	99061059	99061337	+	0	NA	intron (NM_001130049, intron 1 of 32)	intron (NM_001130049, intron 1 of 32)	25208	NM_001130049	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.000000	0.379928	
chunk0188_348_1	chr8	17850037	17850642	+	0	NA	Intergenic	Intergenic	45065	NM_201553	2267	Hs.491143	NM_004467	ENSG00000104760	FGL1	HFREP1|HP-041|HPS|LFIRE-1|LFIRE1	fibrinogen like 1	protein-coding	0.013223	0.336634	
chunk0139_413_1	chr4	63656462	63656889	+	0	NA	Intergenic	Intergenic	752785	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.002342	0.294393	
chunk0117_4_1	chr22	10695488	10695909	+	0	NA	Intergenic	Intergenic	265831	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.002375	0.267773	
chunk0165_313_1	chr6	37023341	37023649	+	0	NA	intron (NM_173558, intron 13 of 15)	Tigger19b|DNA|TcMar-Tigger	17848	NM_173558	221472	Hs.509664	NM_173558	ENSG00000146192	FGD2	ZFYVE4	FYVE, RhoGEF and PH domain containing 2	protein-coding	0.006494	0.517799	
chunk0020_280_1	chr1	236523085	236523284	+	0	NA	promoter-TSS (NM_201543)	promoter-TSS (NM_201543)	-255	NM_006499	3964	Hs.4082	NM_006499	ENSG00000116977	LGALS8	Gal-8|PCTA-1|PCTA1|Po66-CBP	galectin 8	protein-coding	0.015075	0.425000	
chunk0203_12_1	chr9	82651612	82651856	+	0	NA	Intergenic	L1M1|LINE|L1	411394	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.000000	0.502041	
chunk0080_326_1	chr17	32377783	32378324	+	0	NA	Intergenic	Intergenic	27915	NM_003457	7756	Hs.500775	NM_003457	ENSG00000010244	ZNF207	BuGZ|hBuGZ	zinc finger protein 207	protein-coding	0.001848	0.352399	
chunk0034_314_1	chr11	35157965	35158228	+	0	NA	intron (NM_001001389, intron 1 of 16)	intron (NM_001001389, intron 1 of 16)	19226	NM_001202557	960	Hs.502328	NM_000610	ENSG00000026508	CD44	CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1	CD44 molecule (Indian blood group)	protein-coding	0.011407	0.439394	
chunk0158_114_1	chr5	126887762	126888156	+	0	NA	intron (NM_178450, intron 3 of 4)	L2a|LINE|L2	110806	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.002538	0.407595	
chunk0186_255_1	chr7	141080678	141081135	+	0	NA	intron (NM_001195278, intron 1 of 3)	Tigger3b|DNA|TcMar-Tigger	6674	NM_001195278	100507421	Hs.283851	NM_001195278	ENSG00000261115	TMEM178B	-	transmembrane protein 178B	protein-coding	0.008753	0.406114	
chunk0028_31_1	chr10	82851401	82851854	+	0	NA	intron (NM_001165972, intron 3 of 8)	intron (NM_001165972, intron 3 of 8)	-618707	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.004415	0.354626	
chunk0024_407_1	chr10	45313682	45314043	+	0	NA	intron (NM_001004297, intron 1 of 3)	L1M4|LINE|L1	1746	NM_001004297	79290	Hs.532435	NM_001004297	ENSG00000256574	OR13A1	-	olfactory receptor family 13 subfamily A member 1	protein-coding	0.005540	0.301105	
chunk0064_260_1	chr14	94655026	94655764	+	0	NA	Intergenic	L1M5|LINE|L1	14670	NR_015340	388007	Hs.527795	NR_015340	ENSG00000187483	SERPINA13P	SERPINA13|UNQ6121	serpin family A member 13, pseudogene	pseudo	0.016260	0.339648	
chunk0058_29_1	chr14	19953792	19954358	+	0	NA	Intergenic	L2a|LINE|L2	18467	NM_001004063	79544	Hs.554584	NM_001004063	ENSG00000155249	OR4K1	OR14-19	olfactory receptor family 4 subfamily K member 1	protein-coding	0.000000	0.320988	
chunk0115_370_1	chr21	30215869	30216728	+	0	NA	promoter-TSS (NM_199328)	promoter-TSS (NM_199328)	-147	NM_199328	9073	Hs.162209	NM_012132	ENSG00000156284	CLDN8	HEL-S-79	claudin 8	protein-coding	0.009313	0.427907	
chunk0084_322_1	chr17	80696160	80696507	+	0	NA	intron (NM_020761, intron 3 of 33)	intron (NM_020761, intron 3 of 33)	109299	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.008646	0.370690	
chunk0192_446_1	chr8	69952907	69953254	+	0	NA	Intergenic	Intergenic	-118016	NM_030958	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.002882	0.431034	
chunk0153_425_1	chr5	75850735	75851115	+	0	NA	Intergenic	MER83|LTR|ERV1	-133437	NM_001099271	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.010526	0.454068	
chunk0128_94_1	chr3	105829081	105829509	+	0	NA	intron (NM_170662, intron 3 of 18)	intron (NM_170662, intron 3 of 18)	39748	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.009346	0.382284	
chunk0121_86_1	chr3	16329218	16329581	+	0	NA	intron (NM_015150, intron 7 of 9)	intron (NM_015150, intron 7 of 9)	64239	NM_138381	92106	Hs.655449	NM_138381	ENSG00000154814	OXNAD1	-	oxidoreductase NAD binding domain containing 1	protein-coding	0.019284	0.541209	40(AAGAACTGTCTGTCCT,-,0.00),41(AGAACTGTCTGTCCTT,+,0.00)
chunk0132_335_1	chr3	161225691	161226128	+	0	NA	intron (NM_015938, intron 3 of 15)	intron (NM_015938, intron 3 of 15)	4598	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.002288	0.335616	
chunk0063_298_1	chr14	84585091	84585290	+	0	NA	Intergenic	L1PA16|LINE|L1	-808689	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.010050	0.370000	
chunk0162_394_1	chr5	179683792	179684401	+	0	NA	Intergenic	L1ME1|LINE|L1	-3122	NM_001164444	646019	Hs.535767	NM_001164444	ENSG00000204659	CBY3	-	chibby family member 3	protein-coding	0.013136	0.418033	
chunk0184_319_1	chr7	120326554	120327071	+	0	NA	intron (NM_012281, intron 1 of 5)	L2a|LINE|L2	53144	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.301158	
chunk0208_396_1	chrX	29041536	29042021	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	454214	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.008247	0.358025	
chunk0149_46_1	chr5	16615745	16616174	+	0	NA	promoter-TSS (NR_109946)	promoter-TSS (NR_109946)	33	NR_109946	101929524	Hs.734029	NR_109946	ENSG00000246214	LOC101929524	-	uncharacterized LOC101929524	ncRNA	0.023310	0.462791	
chunk0174_369_1	chr6	164778051	164778345	+	0	NA	Intergenic	L1MEf|LINE|L1	43865	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.006803	0.247458	
chunk0166_357_1	chr6	51386519	51386759	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-235231	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.000000	0.365145	
chunk0211_318_1	chrX	123749609	123750072	+	0	NA	Intergenic	Intergenic	-16786	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.006479	0.340517	281(CAATACATGCTGTTCT,-,0.00),282(AATACATGCTGTTCTG,+,0.00)
chunk0019_201_1	chr1	226899143	226899440	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	28719	NM_000447	5664	Hs.25363	NM_000447	ENSG00000143801	PSEN2	AD3L|AD4|CMD1V|PS2|STM2	presenilin 2	protein-coding	0.003367	0.359060	
chunk0206_417_1	chr9	127504082	127504712	+	0	NA	TTS (NM_001190723)	TTS (NM_001190723)	52142	NM_001005374	90678	Hs.495188	NM_138361	ENSG00000148356	LRSAM1	CMT2P|RIFLE|TAL	leucine rich repeat and sterile alpha motif containing 1	protein-coding	0.023810	0.624406	
chunk0045_190_1	chr12	47338148	47338465	+	0	NA	Intergenic	(TTTA)n|Simple_repeat|Simple_repeat	25963	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.000000	0.283019	
chunk0052_255_1	chr12	123622055	123622258	+	0	NA	intron (NM_001414, intron 8 of 8)	intron (NM_001414, intron 8 of 8)	-11583	NM_001271866	2967	Hs.355348	NM_001516	ENSG00000111358	GTF2H3	BTF2|P34|TFB4|TFIIH	general transcription factor IIH subunit 3	protein-coding	0.019704	0.495098	
chunk0003_54_1	chr1	30834837	30835291	+	0	NA	Intergenic	Intergenic	73569	NM_014654	9672	Hs.158287	NM_014654	ENSG00000162512	SDC3	SDCN|SYND3	syndecan 3	protein-coding	0.008811	0.428571	
chunk0017_152_1	chr1	206842840	206843050	+	0	NA	TTS (NM_013371)	TTS (NM_013371)	14068	NM_013371	29949	Hs.661017	NM_013371	ENSG00000142224	IL19	IL-10C|MDA1|NG.1|ZMDA1	interleukin 19	protein-coding	0.000000	0.412322	86(TAGTACACATTGTACT,-,0.00),87(AGTACACATTGTACTG,+,0.00),181(GAGGACAGGGTGTTTC,-,0.00),182(AGGACAGGGTGTTTCT,+,0.00)
chunk0084_240_1	chr17	78763274	78763875	+	0	NA	intron (NM_004762, intron 1 of 12)	MER44A|DNA|TcMar-Tigger	18768	NM_004762	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.009983	0.362126	
chunk0159_14_1	chr5	136225779	136226425	+	0	NA	exon (NM_020389, exon 9 of 12)	exon (NM_020389, exon 9 of 12)	-32939	NR_024418	389332	Hs.127680	NM_001350994	ENSG00000271824	SMIM32	-	small integral membrane protein 32	protein-coding	0.010836	0.494590	
chunk0091_329_1	chr19	13833412	13833862	+	0	NA	TTS (NR_036515)	TTS (NR_036515)	2652	NR_036515	284454	Hs.436426	NR_036515		LOC284454	-	uncharacterized LOC284454	ncRNA	0.091111	0.671840	
chunk0023_164_1	chr10	24341965	24342164	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	66379	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.005025	0.440000	
chunk0191_312_1	chr8	55536359	55536981	+	0	NA	Intergenic	Intergenic	-81349	NR_027765	100133234	Hs.729852	NR_027765	ENSG00000248522	SBF1P1	-	SET binding factor 1 pseudogene 1	pseudo	0.014469	0.385233	
chunk0091_208_1	chr19	9621693	9621892	+	0	NA	promoter-TSS (NM_152289)	promoter-TSS (NM_152289)	310	NR_122038	284385	Hs.651747	NM_001242812	ENSG00000267106	ZNF561-AS1	C19orf82	ZNF561 antisense RNA 1 (head to head)	ncRNA	0.005025	0.475000	
chunk0098_400_1	chr2	79791985	79792580	+	0	NA	intron (NM_004389, intron 3 of 17)	LTR40b|LTR|ERVL	74301	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.001681	0.397651	
chunk0070_394_1	chr15	77058359	77058867	+	0	NA	intron (NM_198902, intron 1 of 5)	L2c|LINE|L2	12615	NM_001168412	10099	Hs.744863	NM_005724	ENSG00000140391	TSPAN3	TM4-A|TM4SF8|TSPAN-3	tetraspanin 3	protein-coding	0.011811	0.412574	
chunk0131_414_1	chr3	152955278	152955896	+	0	NA	Intergenic	L2c|LINE|L2	120894	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.004854	0.386107	325(CATAACATCCTGTTCT,-,0.00),326(ATAACATCCTGTTCTC,+,0.00)
chunk0043_37_1	chr12	13316422	13316844	+	0	NA	Intergenic	Intergenic	60112	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.009479	0.427896	
chunk0204_232_1	chr9	97735529	97735928	+	0	NA	Intergenic	Intergenic	-38319	NM_000380	7507	Hs.654364	NM_000380	ENSG00000136936	XPA	XP1|XPAC	XPA, DNA damage recognition and repair factor	protein-coding	0.012531	0.402500	
chunk0107_449_1	chr2	225471610	225471844	+	0	NA	intron (NM_020864, intron 2 of 5)	MIRb|SINE|MIR	70841	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.008547	0.382979	
chunk0100_29_1	chr2	105297224	105297607	+	0	NA	intron (NM_001142621, intron 3 of 11)	intron (NM_001142621, intron 3 of 11)	32299	NM_004257	9392	Hs.446350	NM_004257	ENSG00000135966	TGFBRAP1	TRAP-1|TRAP1|VPS3	transforming growth factor beta receptor associated protein 1	protein-coding	0.015666	0.489583	59(AATGACATTCTGTCCC,-,0.00),60(ATGACATTCTGTCCCT,+,0.00)
chunk0061_100_1	chr14	57592218	57592821	+	0	NA	intron (NM_001306087, intron 2 of 7)	Tigger14a|DNA|TcMar-Tigger	-98656	NM_018168	55195	Hs.659706	NM_018168	ENSG00000100557	CCDC198	C14orf105	coiled-coil domain containing 198	protein-coding	0.001658	0.331126	327(TGGAACATTTTGTTTT,-,0.00),328(GGAACATTTTGTTTTG,+,0.00)
chunk0095_37_1	chr2	13477598	13478009	+	0	NA	Intergenic	MER70C|LTR|ERVL	-470790	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.009732	0.483010	
chunk0018_223_1	chr1	219686866	219687318	+	0	NA	Intergenic	L3|LINE|CR1	241559	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.006637	0.366446	
chunk0080_40_1	chr17	21218684	21219349	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4421	NR_024547	8834	Hs.592945	NM_003876	ENSG00000178307	TMEM11	C17orf35|PM1|PMI	transmembrane protein 11	protein-coding	0.004511	0.397898	
chunk0203_363_1	chr9	89906593	89907106	+	0	NA	Intergenic	L1P2|LINE|L1	-62567	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.005848	0.500000	
chunk0171_128_1	chr6	122736537	122736998	+	0	NA	Intergenic	Intergenic	-42734	NM_001446	2173	Hs.26770	NM_001446	ENSG00000164434	FABP7	B-FABP|BLBP|FABPB|MRG	fatty acid binding protein 7	protein-coding	0.006508	0.322511	
chunk0120_134_1	chr3	4988918	4989577	+	0	NA	Intergenic	Intergenic	-9286	NR_037903	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.021244	0.550000	
chunk0126_338_1	chr3	82118113	82118312	+	0	NA	Intergenic	L1PA7|LINE|L1	-356413	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.015075	0.325000	
chunk0089_59_1	chr18	58152190	58152873	+	0	NA	intron (NM_001144971, intron 1 of 30)	intron (NM_001144971, intron 1 of 30)	3198	NM_001144971	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.011713	0.450292	
chunk0133_217_1	chr3	171127688	171127999	+	0	NA	intron (NM_001161565, intron 14 of 30)	intron (NM_001161565, intron 14 of 30)	-21084	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.003215	0.314103	
chunk0136_147_1	chr4	4618842	4619252	+	0	NA	intron (NR_037888, intron 2 of 5)	MLT1G1|LTR|ERVL-MaLR	76916	NR_037888	100507266	Hs.276795	NR_037888	ENSG00000247708	STX18-AS1	-	STX18 antisense RNA 1 (head to head)	ncRNA	0.002439	0.472019	
chunk0157_447_1	chr5	124932748	124933320	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-103797	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.006993	0.429319	
chunk0018_185_1	chr1	219249606	219249973	+	0	NA	Intergenic	L1ME3A|LINE|L1	74820	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.005450	0.323370	
chunk0113_441_1	chr20	62495043	62495674	+	0	NA	Intergenic	Intergenic	-19388	NM_080473	140628	Hs.352250	NM_080473	ENSG00000130700	GATA5	CHTD5|GATAS|bB379O24.1	GATA binding protein 5	protein-coding	0.036450	0.601266	
chunk0204_374_1	chr9	102041522	102042180	+	0	NA	Intergenic	L1PA17|LINE|L1	-303271	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.004559	0.344461	
chunk0069_23_1	chr15	60426863	60427478	+	0	NA	intron (NM_024611, intron 15 of 15)	intron (NM_024611, intron 15 of 15)	-29184	NM_001002858	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.003252	0.337662	
chunk0075_375_1	chr16	56551805	56552136	+	0	NA	Intergenic	Intergenic	-13079	NM_032935	84560	Hs.567624	NM_032935	ENSG00000102891	MT4	MT-4|MT-IV|MTIV	metallothionein 4	protein-coding	0.018127	0.533133	
chunk0074_58_1	chr16	21011962	21012818	+	0	NA	intron (NM_017539, intron 41 of 61)	intron (NM_017539, intron 41 of 61)	111286	NM_001302835	57149	Hs.745012	NM_020424	ENSG00000102897	LYRM1	A211C6.1	LYR motif containing 1	protein-coding	0.008178	0.353559	
chunk0093_190_1	chr19	49149623	49149930	+	0	NA	intron (NR_103842, intron 27 of 28)	CpG-14897	5648	NM_002152	3270	Hs.436885	NM_002152	ENSG00000130528	HRC	-	histidine rich calcium binding protein	protein-coding	0.052117	0.626623	
chunk0180_185_1	chr7	66008902	66009482	+	0	NA	Intergenic	Intergenic	-26878	NM_001284290	2990	Hs.255230	NM_000181	ENSG00000169919	GUSB	BG|MPS7	glucuronidase beta	protein-coding	0.017241	0.502582	
chunk0141_158_1	chr4	81746077	81746531	+	0	NA	Intergenic	Intergenic	-274376	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.006608	0.404396	
chunk0153_285_1	chr5	73262130	73262414	+	0	NA	Intergenic	LTR40b|LTR|ERVL	89076	NM_153217	134288	Hs.508588	NM_153217	ENSG00000164325	TMEM174	-	transmembrane protein 174	protein-coding	0.010563	0.438596	
chunk0094_168_1	chr2	5472571	5472862	+	0	NA	Intergenic	Intergenic	218402	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.006873	0.462329	
chunk0144_430_1	chr4	140756031	140756603	+	0	NA	promoter-TSS (NM_015130)	promoter-TSS (NM_015130)	0	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.127622	0.755672	
chunk0201_144_1	chr9	35815376	35815856	+	0	NA	promoter-TSS (NM_032593)	promoter-TSS (NM_032593)	-571	NM_032593	84681	Hs.70573	NM_032593	ENSG00000137133	HINT2	HIT-17	histidine triad nucleotide binding protein 2	protein-coding	0.037500	0.486486	
chunk0180_223_1	chr7	67162507	67163128	+	0	NA	intron (NM_018264, intron 13 of 15)	intron (NM_018264, intron 13 of 15)	-48420	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.008052	0.369775	
chunk0017_396_1	chr1	212495790	212496231	+	0	NA	Intergenic	Intergenic	-49684	NR_125985	101929565		NR_125985	ENSG00000228067	LINC01740	-	long intergenic non-protein coding RNA 1740	ncRNA	0.009070	0.418552	
chunk0114_317_1	chr21	17280181	17280381	+	0	NA	Intergenic	L1M1|LINE|L1	-158609	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.000000	0.502488	
chunk0210_447_1	chrX	106042174	106042540	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-3630	NM_000354	6906	Hs.76838	NM_000354	ENSG00000123561	SERPINA7	TBG|TBGQTL	serpin family A member 7	protein-coding	0.005464	0.411444	
chunk0191_131_1	chr8	48648998	48650051	+	0	NA	intron (NR_105002, intron 2 of 3)	intron (NR_105002, intron 2 of 3)	29121	NR_105004	101929217	Hs.547790	NR_105004	ENSG00000253455	LOC101929217	-	uncharacterized LOC101929217	ncRNA	0.012346	0.455408	
chunk0057_166_1	chr13	101616937	101617344	+	0	NA	intron (NM_001271754, intron 6 of 10)	intron (NM_001271754, intron 6 of 10)	127188	NM_001271756	9358	Hs.696554	NM_004791	ENSG00000198542	ITGBL1	OSCP|TIED	integrin subunit beta like 1	protein-coding	0.000000	0.294118	
chunk0057_177_1	chr13	102487673	102488350	+	0	NA	Intergenic	MER134|DNA?|DNA?	-86237	NM_175929	2259	Hs.508616	NM_004115	ENSG00000102466	FGF14	FGF-14|FHF-4|FHF4|SCA27	fibroblast growth factor 14	protein-coding	0.002954	0.336283	247(CAGCACTTCATGTTCA,-,0.00),248(AGCACTTCATGTTCAC,+,0.00),294(ATGAACATTATGTTCT,-,0.00),295(TGAACATTATGTTCTA,+,0.00)
chunk0057_403_1	chr13	109649688	109650152	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-78354	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.012931	0.423656	65(AAGCACACTCAGTCCA,-,0.00),66(AGCACACTCAGTCCAG,+,0.00)
chunk0025_128_1	chr10	51862050	51862283	+	0	NA	intron (NM_006258, intron 4 of 17)	LTR27E|LTR|ERV1	-162571	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.000000	0.491453	
chunk0015_182_1	chr1	187186491	187186884	+	0	NA	intron (NR_126347, intron 1 of 3)	L1PA14|LINE|L1	93845	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.002545	0.324873	
chunk0031_241_1	chr10	126813152	126813560	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-92053	NM_001290223	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.002451	0.327628	
chunk0158_271_1	chr5	131357572	131357771	+	0	NA	intron (NM_020240, intron 2 of 5)	intron (NM_020240, intron 2 of 5)	93662	NM_001038702	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.005025	0.300000	
chunk0019_350_1	chr1	229515893	229516449	+	0	NA	TTS (NM_012089)	TTS (NM_012089)	7741	NR_110630	101927478	Hs.229275	NR_110630		LOC101927478	-	uncharacterized LOC101927478	ncRNA	0.005396	0.369838	250(CAGAACACAGTGTTAC,-,0.00)
chunk0194_289_1	chr8	87572755	87573089	+	0	NA	Intergenic	L3|LINE|CR1	301146	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.005988	0.367164	182(CAGAACTGTGTGTCTT,-,0.00),183(AGAACTGTGTGTCTTG,+,0.00)
chunk0121_246_1	chr3	22875597	22875878	+	0	NA	Intergenic	Intergenic	-327556	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.003559	0.397163	
chunk0139_115_1	chr4	52604075	52604552	+	0	NA	intron (NM_022832, intron 6 of 8)	intron (NM_022832, intron 6 of 8)	52279	NM_001134223	64854	Hs.7966	NM_022832	ENSG00000109189	USP46	-	ubiquitin specific peptidase 46	protein-coding	0.006289	0.384937	
chunk0007_179_1	chr1	80640000	80640539	+	0	NA	intron (NR_125940, intron 2 of 3)	intron (NR_125940, intron 2 of 3)	-1018	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.001855	0.342593	
chunk0074_154_1	chr16	23343623	23344320	+	0	NA	intron (NM_000336, intron 1 of 12)	L4_B_Mam|LINE|RTE-X	41701	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.005739	0.388252	
chunk0205_155_1	chr9	108479163	108479489	+	0	NA	Intergenic	Intergenic	376669	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.000000	0.293578	
chunk0130_25_1	chr3	128775767	128776453	+	0	NA	intron (NM_004637, intron 1 of 5)	L1MA8|LINE|L1	49974	NM_004637	7879	Hs.684374	NM_004637	ENSG00000075785	RAB7A	PRO2706|RAB7	RAB7A, member RAS oncogene family	protein-coding	0.004373	0.394469	
chunk0044_124_1	chr12	29225875	29226332	+	0	NA	intron (NM_001271784, intron 1 of 10)	MIR|SINE|MIR	2480	NM_018099	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.004376	0.364629	
chunk0143_391_1	chr4	123108256	123108783	+	0	NA	intron (NM_145207, intron 14 of 15)	intron (NM_145207, intron 14 of 15)	185449	NM_145207	166378	Hs.709648	NM_145207	ENSG00000145375	SPATA5	AFG2|EHLMRS|SPAF	spermatogenesis associated 5	protein-coding	0.003795	0.289773	
chunk0196_77_1	chr8	102595330	102595629	+	0	NA	Intergenic	Intergenic	43859	NM_024410	4956	Hs.159274	NM_024410	ENSG00000155087	ODF1	CT133|HSPB10|ODF|ODF2|ODF27|ODFP|ODFPG|ODFPGA|ODFPGB|RT7|SODF	outer dense fiber of sperm tails 1	protein-coding	0.000000	0.303333	
chunk0022_408_1	chr10	18350330	18350547	+	0	NA	intron (NM_201590, intron 1 of 12)	MIRc|SINE|MIR	9753	NM_201590	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.023041	0.536697	119(CAGCACTGCCTGTGCC,-,0.00),120(AGCACTGCCTGTGCCT,+,0.00)
chunk0096_237_1	chr2	30885993	30886518	+	0	NA	Intergenic	Intergenic	-78810	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.011429	0.492395	
chunk0123_359_1	chr3	48232072	48232708	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-8716	NM_016089	51385	Hs.172602	NM_016089	ENSG00000164048	ZNF589	SZF1	zinc finger protein 589	protein-coding	0.009434	0.414443	318(AAGAACTCTGTGTTCC,-,0.00),319(AGAACTCTGTGTTCCC,+,0.00)
chunk0121_375_1	chr3	25055860	25056284	+	0	NA	Intergenic	Intergenic	-118260	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.004717	0.468235	
chunk0052_93_1	chr13	22261924	22262196	+	0	NA	intron (NR_103810, intron 1 of 1)	intron (NR_103810, intron 1 of 1)	51775	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.007353	0.395604	
chunk0186_93_1	chr7	137464488	137465114	+	0	NA	intron (NM_004717, intron 27 of 33)	intron (NM_004717, intron 27 of 33)	-121001	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.004792	0.430622	341(TGTACACGATGTGCAT,+,0.00)
chunk0181_282_1	chr7	86707617	86708017	+	0	NA	intron (NM_000840, intron 1 of 5)	intron (NM_000840, intron 1 of 5)	63903	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.005000	0.321696	
chunk0102_144_1	chr2	146642454	146642704	+	0	NA	Intergenic	L1PA6|LINE|L1	55522	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.012000	0.529880	
chunk0106_202_1	chr2	202091485	202091915	+	0	NA	intron (NM_001277372, intron 3 of 21)	MER53|DNA|hAT	18445	NM_001277372	100652824	Hs.686898	NM_001080445	ENSG00000182329	KIAA2012	-	KIAA2012	protein-coding	0.013953	0.422274	
chunk0209_143_1	chrX	41963102	41963577	+	0	NA	Intergenic	Intergenic	-40305	NM_001126055	8573	Hs.495984	NM_003688	ENSG00000147044	CASK	CAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK	calcium/calmodulin dependent serine protein kinase	protein-coding	0.008421	0.422269	
chunk0157_22_1	chr5	115504822	115505314	+	0	NA	Intergenic	Intergenic	39826	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.008130	0.363083	
chunk0124_145_1	chr3	54717517	54717842	+	0	NA	intron (NM_018398, intron 11 of 37)	(TG)n|Simple_repeat|Simple_repeat	-77822	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.043077	0.549080	
chunk0122_56_1	chr3	28781779	28782236	+	0	NA	Intergenic	L2c|LINE|L2	206729	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.004376	0.375546	
chunk0013_171_1	chr1	168835992	168836747	+	0	NA	Intergenic	MIRc|SINE|MIR	49428	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.005298	0.425926	
chunk0041_330_1	chr11	130315230	130315486	+	0	NA	promoter-TSS (NM_001301098)	promoter-TSS (NM_001301098)	-646	NM_001301098	29068	Hs.721470	NM_014155	ENSG00000196323	ZBTB44	BTBD15|HSPC063|ZNF851	zinc finger and BTB domain containing 44	protein-coding	0.050781	0.529183	
chunk0006_318_1	chr1	71473382	71473581	+	0	NA	intron (NM_173808, intron 6 of 6)	LTR80B|LTR|ERVL	363531	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005025	0.385000	
chunk0084_454_1	chr17	83064752	83065051	+	0	NA	Intergenic	Intergenic	-13091	NM_001009905	146712	Hs.607824	NM_001009905	ENSG00000175711	B3GNTL1	3-Gn-T8|B3GNT8|BGnT-8|beta-1|beta3Gn-T8|beta3GnTL1	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1	protein-coding	0.040134	0.606667	
chunk0211_312_1	chrX	123665079	123665716	+	0	NA	intron (NM_001081550, intron 12 of 38)	Tigger3a|DNA|TcMar-Tigger	67657	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.009419	0.352665	233(GGGAACATTCTGTACA,-,0.00),234(GGAACATTCTGTACAG,+,0.00)
chunk0142_33_1	chr4	90695241	90696006	+	0	NA	intron (NM_001145065, intron 6 of 10)	intron (NM_001145065, intron 6 of 10)	460592	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.001307	0.278068	
chunk0140_93_1	chr4	68324751	68325430	+	0	NA	intron (NM_133370, intron 8 of 15)	intron (NM_133370, intron 8 of 15)	25016	NM_133370	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.004418	0.305882	
chunk0126_111_1	chr3	75190266	75191072	+	0	NA	Intergenic	Intergenic	-23807	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.006203	0.400248	
chunk0084_209_1	chr17	78184319	78185186	+	0	NA	intron (NM_003258, intron 3 of 6)	MER20|DNA|hAT-Charlie	2452	NM_003258	7083	Hs.515122	NM_003258	ENSG00000167900	TK1	TK2	thymidine kinase 1	protein-coding	0.020761	0.524194	
chunk0123_241_1	chr3	45625988	45626199	+	0	NA	intron (NM_014240, intron 1 of 7)	intron (NM_014240, intron 1 of 7)	31262	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.004739	0.377358	
chunk0189_353_1	chr8	26944232	26945066	+	0	NA	Intergenic	L1PB1|LINE|L1	-79244	NM_033303	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.002398	0.368862	
chunk0095_96_1	chr2	15222760	15223080	+	0	NA	intron (NM_015909, intron 47 of 51)	intron (NM_015909, intron 47 of 51)	338428	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.006250	0.330218	145(TAGAACTTACTGTGCA,-,0.00),146(AGAACTTACTGTGCAG,+,0.00)
chunk0128_20_1	chr3	104160071	104160270	+	0	NA	Intergenic	Intergenic	-636054	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.005025	0.285000	
chunk0084_328_1	chr17	80896634	80896966	+	0	NA	intron (NM_020761, intron 20 of 33)	L1M5|LINE|L1	-91168	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.015060	0.423423	
chunk0098_449_1	chr2	82275474	82275923	+	0	NA	Intergenic	L1PREC2|LINE|L1	-581105	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.004454	0.382222	
chunk0185_267_1	chr7	130521454	130521731	+	0	NA	intron (NM_012133, intron 20 of 23)	intron (NM_012133, intron 20 of 23)	-21861	NR_024086	53844	Hs.6421	NR_024086		COPG2IT1	CIT1|COPG2AS|DKFZP761N09121|NCRNA00170	COPG2 imprinted transcript 1	ncRNA	0.007220	0.366906	
chunk0057_416_1	chr13	109955523	109956067	+	0	NA	Intergenic	MER67B|LTR|ERV1	-97490	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.007353	0.453211	
chunk0175_217_1	chr7	6194997	6195284	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	77471	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.003484	0.291667	232(AAGAACACAATGTTCA,-,0.00),233(AGAACACAATGTTCAG,+,0.00)
chunk0033_246_1	chr11	18105934	18106133	+	0	NA	promoter-TSS (NM_138421)	promoter-TSS (NM_138421)	58	NM_138421	113174	Hs.591998	NM_138421	ENSG00000166788	SAAL1	SPACIA1	serum amyloid A like 1	protein-coding	0.120603	0.695000	
chunk0028_423_1	chr10	93634438	93635111	+	0	NA	exon (NM_006204, exon 9 of 22)	exon (NM_006204, exon 9 of 22)	22186	NM_006204	5146	Hs.658121	NM_006204	ENSG00000095464	PDE6C	ACHM5|COD4|PDEA2	phosphodiesterase 6C	protein-coding	0.011887	0.345697	
chunk0091_202_1	chr19	9190629	9191143	+	0	NA	Intergenic	SATR2|Satellite|Satellite	5292	NM_175883	162998	Hs.531755	NM_175883	ENSG00000188000	OR7D2	HTPCRH03|OR19-10|OR19-4	olfactory receptor family 7 subfamily D member 2	protein-coding	0.011673	0.339806	
chunk0076_192_1	chr16	67779162	67779879	+	0	NA	intron (NM_020850, intron 2 of 13)	intron (NM_020850, intron 2 of 13)	27132	NM_020850	57610	Hs.368569	NM_020850	ENSG00000141084	RANBP10	-	RAN binding protein 10	protein-coding	0.005579	0.469359	
chunk0185_345_1	chr7	132176841	132177040	+	0	NA	intron (NM_020911, intron 20 of 31)	intron (NM_020911, intron 20 of 31)	266720	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.020101	0.475000	
chunk0031_359_1	chr10	130081748	130082457	+	0	NA	intron (NR_034125, intron 3 of 7)	L1MC4a|LINE|L1	-23907	NR_044994	119437	Hs.620802	NR_044994	ENSG00000233122	CTAGE7P	CTAGE7|CTAGEP|bA500G10.2|rcCTAGE5	CTAGE family member 7, pseudogene	pseudo	0.004231	0.369014	
chunk0011_167_1	chr1	147665122	147665900	+	0	NA	intron (NM_016361, intron 1 of 9)	intron (NM_016361, intron 1 of 9)	5001	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.005141	0.431322	
chunk0118_63_1	chr22	28395463	28395908	+	0	NA	intron (NM_001145418, intron 2 of 22)	intron (NM_001145418, intron 2 of 22)	-64184	NR_106713	102466081		NR_106713	ENSG00000276162	MIR5739	hsa-mir-5739	microRNA 5739	ncRNA	0.011236	0.392377	
chunk0011_176_1	chr1	148263480	148263941	+	0	NA	Intergenic	Intergenic	-16639	NR_120331	101927468	Hs.515867	NR_120331		LOC101927468	-	uncharacterized LOC101927468	ncRNA	0.041215	0.467532	
chunk0014_346_1	chr1	182270638	182271302	+	0	NA	intron (NR_104175, intron 2 of 2)	L1MC3|LINE|L1	43091	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.003012	0.389474	
chunk0141_396_1	chr4	88411302	88411981	+	0	NA	intron (NM_001165136, intron 11 of 21)	MLT1J2|LTR|ERVL-MaLR	32902	NM_017912	55008	Hs.529317	NM_017912	ENSG00000138642	HERC6	-	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	protein-coding	0.001473	0.405882	
chunk0165_247_1	chr6	35662979	35663573	+	0	NA	intron (NM_001145775, intron 2 of 11)	L2|LINE|L2	1513	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.013468	0.460504	
chunk0101_237_1	chr2	131361483	131361732	+	0	NA	3' UTR (NM_001077637, exon 1 of 1)	3' UTR (NM_001077637, exon 1 of 1)	2551	NM_001077637	150786	Hs.645670	NM_001077637	ENSG00000233087	RAB6D	RAB6CL|WTH3DI	RAB6D, member RAS oncogene family	protein-coding	0.008032	0.320000	
chunk0001_77_1	chr1	2541623	2541825	+	0	NA	Intergenic	Intergenic	-11479	NM_001010926	388585	Hs.57971	NM_001010926	ENSG00000197921	HES5	bHLHb38	hes family bHLH transcription factor 5	protein-coding	0.039604	0.522167	
chunk0012_208_1	chr1	160080790	160081114	+	0	NA	promoter-TSS (NM_004983)	promoter-TSS (NM_004983)	-618	NM_004983	3765	Hs.66726	NM_004983	ENSG00000162728	KCNJ9	GIRK3|KIR3.3	potassium voltage-gated channel subfamily J member 9	protein-coding	0.006173	0.436923	
chunk0154_181_1	chr5	80060534	80060741	+	0	NA	intron (NM_001306213, intron 8 of 22)	AluJb|SINE|Alu	23028	NR_109930	101929215		NR_109930	ENSG00000249825	CTD-2201I18.1	-	uncharacterized LOC101929215	ncRNA	0.004831	0.528846	
chunk0001_399_1	chr1	10765783	10766230	+	0	NA	intron (NM_001079843, intron 1 of 20)	intron (NM_001079843, intron 1 of 20)	30670	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.022371	0.537946	
chunk0165_42_1	chr6	30059449	30059818	+	0	NA	intron (NR_026751, intron 2 of 5).8	intron (NR_026751, intron 2 of 5).8	1551	NR_026751	80862	Hs.653168	NR_026751	ENSG00000204623	ZNRD1ASP	C6orf12|HCG8|HCGVIII|HCGVIII-1|HTEX4|NCRNA00171|TCTEX4|ZNRD1-AS|ZNRD1-AS1|ZNRD1AS|ZNRD1AS1	zinc ribbon domain containing 1 antisense, pseudogene	pseudo	0.002710	0.345946	
chunk0021_217_1	chr10	6174003	6174491	+	0	NA	intron (NM_001282630, intron 1 of 14)	intron (NM_001282630, intron 1 of 14)	-21985	NR_039698	100628560		NR_039698	ENSG00000283634	MIR3155B	hsa-mir-3155b	microRNA 3155b	ncRNA	0.030738	0.519427	
chunk0139_32_1	chr4	48419874	48420087	+	0	NA	intron (NM_020846, intron 6 of 7)	intron (NM_020846, intron 6 of 7)	-63363	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.000000	0.341121	
chunk0070_10_1	chr15	68833997	68834243	+	0	NA	Intergenic	Intergenic	-13198	NM_006305	8125	Hs.458747	NM_006305	ENSG00000140350	ANP32A	C15orf1|HPPCn|I1PP2A|LANP|MAPM|PHAP1|PHAPI|PP32	acidic nuclear phosphoprotein 32 family member A	protein-coding	0.016260	0.510121	217(AGGTACAGTCTGTTCA,-,0.00),218(GGTACAGTCTGTTCAA,+,0.00)
chunk0146_185_1	chr4	160878152	160878395	+	0	NA	Intergenic	L1MC1|LINE|L1	-1144460	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.364754	
chunk0190_48_1	chr8	29386104	29386783	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-35693	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.008837	0.427941	
chunk0163_153_1	chr6	11015599	11015881	+	0	NA	intron (NM_017770, intron 1 of 7)	intron (NM_017770, intron 1 of 7)	-28018	NR_038963	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.000000	0.515901	
chunk0010_220_1	chr1	116242594	116243281	+	0	NA	Intergenic	Intergenic	-130236	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.013100	0.498547	271(CAAGACAGAATGTTCC,-,0.00),272(AAGACAGAATGTTCCA,+,0.00)
chunk0006_131_1	chr1	65946807	65947102	+	0	NA	intron (NM_002600, intron 3 of 16)	ERV3-16A3_I-int|LTR|ERVL	33709	NM_001297441	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.013559	0.412162	
chunk0134_204_1	chr3	178474699	178475184	+	0	NA	Intergenic	Intergenic	55740	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.014433	0.421811	
chunk0094_418_1	chr2	10555215	10555689	+	0	NA	Intergenic	Intergenic	105724	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.025316	0.498947	
chunk0176_253_1	chr7	16271343	16271920	+	0	NA	intron (NM_001101417, intron 5 of 8)	L2c|LINE|L2	61145	NR_038947	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.001733	0.359862	
chunk0111_446_1	chr20	35333872	35334525	+	0	NA	intron (NM_018244, intron 7 of 9)	intron (NM_018244, intron 7 of 9)	-41776	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.006126	0.422018	
chunk0188_342_1	chr8	17800208	17800758	+	0	NA	intron (NM_001001924, intron 1 of 14)	intron (NM_001001924, intron 1 of 14)	434	NM_001001925	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.027273	0.448276	
chunk0147_417_1	chr4	187179574	187179835	+	0	NA	Intergenic	Intergenic	325909	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.011494	0.404580	
chunk0162_10_1	chr6	374920	375129	+	0	NA	Intergenic	L1MC4a|LINE|L1	-16715	NM_002460	3662	Hs.401013	NM_002460	ENSG00000137265	IRF4	LSIRF|MUM1|NF-EM5|SHEP8	interferon regulatory factor 4	protein-coding	0.014354	0.495238	
chunk0117_330_1	chr22	25110103	25110718	+	0	NA	intron (NR_038941, intron 3 of 4)	L2b|LINE|L2	2282	NR_038941	100128531	Hs.662126	NR_038941	ENSG00000203280	LOC100128531	-	uncharacterized LOC100128531	ncRNA	0.006504	0.487013	
chunk0090_105_1	chr18	71045746	71045967	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-394999	NM_001278515									0.000000	0.337838	
chunk0168_401_1	chr6	94657880	94658196	+	0	NA	Intergenic	L1M1|LINE|L1	919413	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.511041	
chunk0201_162_1	chr9	36046889	36047215	+	0	NA	intron (NM_001316345, intron 1 of 22)	intron (NM_001316345, intron 1 of 22)	10139	NM_001316346	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.003067	0.376147	
chunk0009_450_1	chr1	111590744	111591178	+	0	NA	Intergenic	L1M5|LINE|L1	17357	NR_034126	100129269	Hs.689728	NR_034126		LINC01160	-	long intergenic non-protein coding RNA 1160	ncRNA	0.002304	0.301149	
chunk0024_437_1	chr10	46216267	46216470	+	0	NA	Intergenic	Intergenic	53240	NR_103828	100996567	Hs.546758	NR_103827		ANTXRLP1	-	ANTXR like pseudogene 1	pseudo	0.009852	0.573529	
chunk0151_240_1	chr5	51236715	51236914	+	0	NA	Intergenic	Intergenic	-146310	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.000000	0.365000	
chunk0095_59_1	chr2	14231676	14232048	+	0	NA	non-coding (NR_103814, exon 4 of 4)	non-coding (NR_103814, exon 4 of 4)	169096	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.000000	0.329759	
chunk0145_113_1	chr4	146252006	146252205	+	0	NA	Intergenic	Intergenic	76422	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.015075	0.565000	112(AGGAACAGGATGTACA,-,0.00),113(GGAACAGGATGTACAG,+,0.00)
chunk0071_221_1	chr15	84818782	84819123	+	0	NA	intron (NM_020778, intron 1 of 13)	intron (NM_020778, intron 1 of 13)	2272	NM_020778	57538	Hs.459183	NM_020778	ENSG00000136383	ALPK3	CMH27|MAK|MIDORI	alpha kinase 3	protein-coding	0.002933	0.497076	
chunk0075_337_1	chr16	54912982	54913374	+	0	NA	Intergenic	Intergenic	15600	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.007653	0.374046	
chunk0027_160_1	chr10	74841565	74841989	+	0	NA	intron (NM_001256468, intron 2 of 17)	intron (NM_001256468, intron 2 of 17)	15364	NM_001256468	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.004717	0.371765	140(GAGCACACTCTGTACA,-,0.00),141(AGCACACTCTGTACAG,+,0.00)
chunk0182_156_1	chr7	95385450	95386144	+	0	NA	intron (NM_000940, intron 3 of 8)	L1PA6|LINE|L1	10578	NM_000940	5446	Hs.440967	NM_000940	ENSG00000105852	PON3	-	paraoxonase 3	protein-coding	0.005764	0.378417	341(CTGAACAACCTGTTCC,-,0.00),342(TGAACAACCTGTTCCT,+,0.00),424(AAAGACACAATGTACC,-,0.00)
chunk0089_37_1	chr18	57924456	57925358	+	0	NA	Intergenic	Intergenic	-119471	NM_001243960	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.004435	0.403101	
chunk0193_415_1	chr8	80708259	80708967	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	166168	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.008475	0.382228	
chunk0067_273_1	chr15	46728853	46729073	+	0	NA	Intergenic	L1M3b|LINE|L1	-455243	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.000000	0.493213	
chunk0038_270_1	chr11	89627728	89628111	+	0	NA	Intergenic	Intergenic	-31378	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.005222	0.338542	
chunk0042_21_1	chr12	1332377	1332576	+	0	NA	intron (NM_178040, intron 15 of 18)	HAL1ME|LINE|L1	-168015	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.005025	0.415000	
chunk0019_231_1	chr1	227369074	227369408	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-51116	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.008982	0.522388	
chunk0050_426_1	chr12	109998840	109999506	+	0	NA	promoter-TSS (NM_033121)	promoter-TSS (NM_033121)	-257	NM_033121	88455	Hs.528703	NM_033121	ENSG00000076513	ANKRD13A	ANKRD13|NY-REN-25	ankyrin repeat domain 13A	protein-coding	0.058559	0.584708	
chunk0108_286_1	chr2	234845702	234846243	+	0	NA	Intergenic	Intergenic	-106012	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.007394	0.365314	
chunk0013_7_1	chr1	165698026	165698387	+	0	NA	promoter-TSS (NR_036683)	promoter-TSS (NR_036683)	457	NM_000696	223	Hs.2533	NM_000696	ENSG00000143149	ALDH9A1	ALDH4|ALDH7|ALDH9|E3|TMABADH	aldehyde dehydrogenase 9 family member A1	protein-coding	0.052632	0.541436	
chunk0151_322_1	chr5	53604514	53604800	+	0	NA	intron (NM_002495, intron 2 of 4)	L2b|LINE|L2	44022	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.006993	0.414634	
chunk0001_317_1	chr1	9411114	9411363	+	0	NA	Intergenic	Intergenic	17678	NR_104623	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.004016	0.488000	
chunk0187_38_1	chr8	1260938	1261341	+	0	NA	Intergenic	Intergenic	41468	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.019851	0.509901	
chunk0051_319_1	chr12	119807479	119807694	+	0	NA	intron (NM_007174, intron 9 of 46)	L2b|LINE|L2	69705	NM_007174	11113	Hs.119594	NM_007174	ENSG00000122966	CIT	CITK|CRIK|MCPH17|STK21	citron rho-interacting serine/threonine kinase	protein-coding	0.000000	0.375000	
chunk0041_251_1	chr11	128881175	128881849	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-9906	NM_000890	3762	Hs.444595	NM_000890	ENSG00000120457	KCNJ5	CIR|GIRK4|KATP1|KIR3.4|LQT13	potassium voltage-gated channel subfamily J member 5	protein-coding	0.014837	0.481481	
chunk0091_238_1	chr19	10660303	10660634	+	0	NA	intron (NM_001137673, intron 1 of 17)	MIRc|SINE|MIR	6207	NM_017620	3609	Hs.465885	NM_004516	ENSG00000129351	ILF3	CBTF|DRBF|DRBP76|MMP4|MPHOSPH4|MPP4|MPP4110|NF-AT-90|NF110|NF110b|NF90|NF90a|NF90b|NF90c|NF90ctv|NFAR|NFAR-1|NFAR-2|NFAR110|NFAR2|NFAR90|TCP110|TCP80	interleukin enhancer binding factor 3	protein-coding	0.006042	0.475904	
chunk0098_430_1	chr2	81814154	81814800	+	0	NA	Intergenic	Intergenic	-347531	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.319938	
chunk0148_168_1	chr5	7131365	7131785	+	0	NA	Intergenic	Intergenic	137779	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.014286	0.479810	
chunk0169_125_1	chr6	101039808	101040007	+	0	NA	Intergenic	L1ME1|LINE|L1	-158535	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.005025	0.300000	
chunk0121_337_1	chr3	24507396	24507809	+	0	NA	Intergenic	Intergenic	-12780	NM_001128176	7068	Hs.187861	NM_000461	ENSG00000151090	THRB	C-ERBA-2|C-ERBA-BETA|ERBA2|GRTH|NR1A2|PRTH|THR1|THRB1|THRB2	thyroid hormone receptor beta	protein-coding	0.004843	0.376812	
chunk0063_17_1	chr14	76396273	76396952	+	0	NA	intron (NM_004452, intron 1 of 10)	intron (NM_004452, intron 1 of 10)	25265	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.016200	0.477941	347(CTGGACACACAGTCCT,-,0.00),348(TGGACACACAGTCCTC,+,0.00)
chunk0102_162_1	chr2	147294459	147294830	+	0	NA	Intergenic	Intergenic	-549873	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.389785	
chunk0131_148_1	chr3	146089333	146089928	+	0	NA	intron (NM_000935, intron 8 of 18)	intron (NM_000935, intron 8 of 18)	71865	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.003361	0.310403	338(AAGTACACCTTGTACA,-,0.00),339(AGTACACCTTGTACAC,+,0.00)
chunk0168_8_1	chr6	76847644	76848048	+	0	NA	Intergenic	L1PA7|LINE|L1	615557	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.000000	0.362963	19(GGTACATTGTGTCTTT,+,0.00)
chunk0203_70_1	chr9	83636389	83636802	+	0	NA	intron (NM_001001551, intron 3 of 4)	intron (NM_001001551, intron 3 of 4)	13546	NR_046422	414328	Hs.530261	NM_001001551	ENSG00000148057	IDNK	C9orf103|bA522I20.2|hGntK	IDNK gluconokinase	protein-coding	0.000000	0.352657	
chunk0117_349_1	chr21	44067279	44067627	+	0	NA	intron (NM_003274, intron 7 of 22)	intron (NM_003274, intron 7 of 22)	-39874	NM_005049	5822	Hs.449076	NM_005049	ENSG00000241945	PWP2	EHOC-17|PWP2H|UTP1	PWP2 small subunit processome component	protein-coding	0.008621	0.535817	
chunk0048_289_1	chr12	82728841	82729040	+	0	NA	intron (NM_152588, intron 1 of 11)	LTR12C|LTR|ERV1	41785	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.060302	0.720000	
chunk0058_178_1	chr14	23953971	23954310	+	0	NA	promoter-TSS (NR_023923)	promoter-TSS (NR_023923)	57	NR_023923	55449	Hs.569361	NM_018583	ENSG00000215256	DHRS4-AS1	AS1DHRS4|C14orf167|C14orf67|DHRS4AS1|PRO1488	DHRS4 antisense RNA 1	ncRNA	0.029499	0.570588	
chunk0012_232_1	chr1	160526992	160527269	+	0	NA	Intergenic	L1PA7|LINE|L1	-3868	NM_001184714	114836	Hs.492348	NM_052931	ENSG00000162739	SLAMF6	CD352|KALI|KALIb|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding	0.000000	0.363309	146(GGTACATTGTGTCTTT,+,0.00)
chunk0200_265_1	chr9	21994162	21994458	+	0	NA	promoter-TSS (NR_047543)	promoter-TSS (NR_047543)	181	NM_058195	1029	Hs.512599	NM_000077	ENSG00000147889	CDKN2A	ARF|CDK4I|CDKN2|CMM2|INK4|INK4A|MLM|MTS-1|MTS1|P14|P14ARF|P16|P16-INK4A|P16INK4|P16INK4A|P19|P19ARF|TP16	cyclin dependent kinase inhibitor 2A	protein-coding	0.101351	0.707071	
chunk0135_16_1	chr3	184314901	184315394	+	0	NA	promoter-TSS (NM_182917)	promoter-TSS (NM_182917)	-17	NM_182917	1981	Hs.433750	NM_004953	ENSG00000114867	EIF4G1	EIF-4G1|EIF4F|EIF4G|EIF4GI|P220|PARK18	eukaryotic translation initiation factor 4 gamma 1	protein-coding	0.113590	0.761134	148(GTGACACGTTGTTCTT,+,0.00)
chunk0062_457_1	chr14	75815525	75815778	+	0	NA	intron (NM_015072, intron 27 of 31)	intron (NM_015072, intron 27 of 31)	154443	NM_015072	23093	Hs.709609	NM_015072	ENSG00000119685	TTLL5	CORD19|KIAA0998|STAMP	tubulin tyrosine ligase like 5	protein-coding	0.003953	0.303150	
chunk0187_206_1	chr7	151819073	151819656	+	0	NA	intron (NM_016203, intron 1 of 15)	LTR82B|LTR|ERVL	-4493	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.022298	0.534247	
chunk0146_157_1	chr4	159864269	159864625	+	0	NA	Intergenic	Intergenic	596601	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.008427	0.369748	
chunk0150_383_1	chr5	39407939	39408425	+	0	NA	intron (NM_001343, intron 1 of 14)	intron (NM_001343, intron 1 of 14)	17051	NM_001343	1601	Hs.696631	NM_001343	ENSG00000153071	DAB2	DOC-2|DOC2	DAB adaptor protein 2	protein-coding	0.008230	0.388090	179(AAGGACACACTGTTTA,-,0.00)
chunk0041_6_1	chr12	201938	202320	+	0	NA	intron (NM_001122847, intron 5 of 15)	intron (NM_001122847, intron 5 of 15)	-1516	NR_120475	101929384	Hs.569138	NR_120475	ENSG00000256577	LOC101929384	-	uncharacterized LOC101929384	ncRNA	0.015707	0.587467	
chunk0198_124_1	chr8	131953663	131953910	+	0	NA	intron (NM_015137, intron 5 of 22)	intron (NM_015137, intron 5 of 22)	49677	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.020243	0.318548	
chunk0065_390_1	chr14	104723418	104723837	+	0	NA	promoter-TSS (NM_152328)	promoter-TSS (NM_152328)	-570	NM_152328	122622	Hs.592327	NM_152328	ENSG00000185100	ADSSL1	Adss1|MPD5	adenylosuccinate synthase like 1	protein-coding	0.083532	0.719048	261(GGGGACACAAAGTCCT,-,0.00),262(GGGACACAAAGTCCTC,+,0.00)
chunk0076_27_1	chr16	59224007	59224719	+	0	NA	Intergenic	Intergenic	-490006	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.002809	0.305750	
chunk0104_417_1	chr2	180794453	180794925	+	0	NA	intron (NR_104324, intron 3 of 4)	L1M1|LINE|L1	102585	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.000000	0.236786	
chunk0183_325_1	chr7	108108100	108108498	+	0	NA	intron (NM_007356, intron 5 of 33)	intron (NM_007356, intron 5 of 33)	22057	NM_007356	22798	Hs.62022	NM_007356	ENSG00000091128	LAMB4	-	laminin subunit beta 4	protein-coding	0.000000	0.368421	38(TGCCCAGACTGTTCTC,+,0.00)
chunk0200_347_1	chr9	24547928	24548400	+	0	NA	Intergenic	L2c|LINE|L2	-2488	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.002119	0.344609	
chunk0017_210_1	chr1	207838613	207838841	+	0	NA	Intergenic	Intergenic	20348	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.026316	0.589520	
chunk0142_194_1	chr4	96777007	96777598	+	0	NA	Intergenic	Intergenic	-589624	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.003384	0.327703	202(AAGCACATGCTGTTTA,-,0.00),289(AGGAACACAGCGTTCT,-,0.00),290(GGAACACAGCGTTCTG,+,0.00)
chunk0054_422_1	chr13	50979249	50979702	+	0	NA	Intergenic	L1M7|LINE|L1	-68763	NR_046552	100874255	Hs.741501	NR_046552		RNASEH2B-AS1	-	RNASEH2B antisense RNA 1	ncRNA	0.002208	0.392070	
chunk0057_135_1	chr13	99822888	99823285	+	0	NA	intron (NR_120421, intron 1 of 4)	HAL1|LINE|L1	-94085	NR_120383	101927465	Hs.130690	NR_046525		CLYBL-AS1	-	CLYBL antisense RNA 1	ncRNA	0.002519	0.301508	
chunk0140_427_1	chr4	76115329	76116122	+	0	NA	intron (NR_103782, intron 11 of 11)	L4_C_Mam|LINE|RTE-X	32790	NM_001278603	53371	Hs.430435	NM_017426	ENSG00000138750	NUP54	-	nucleoporin 54	protein-coding	0.003783	0.335013	
chunk0096_346_1	chr2	35651659	35651995	+	0	NA	Intergenic	L1MEf|LINE|L1	180422	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.011905	0.442136	
chunk0103_341_1	chr2	168058100	168058384	+	0	NA	intron (NM_013233, intron 14 of 17)	L2a|LINE|L2	-117098	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.000000	0.410526	
chunk0076_88_1	chr16	64773377	64773657	+	0	NA	Intergenic	Intergenic	348620	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.010714	0.320285	
chunk0113_278_1	chr20	56745234	56745483	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	116056	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.020080	0.572000	
chunk0032_263_1	chr11	8919475	8919674	+	0	NA	TTS (NM_020643)	TTS (NM_020643)	8382	NR_045417	56672	Hs.131180	NM_020642	ENSG00000166452	AKIP1	BCA3|C11orf17	A-kinase interacting protein 1	protein-coding	0.005025	0.390000	
chunk0119_102_1	chr22	42090902	42091246	+	0	NA	promoter-TSS (NM_002490)	promoter-TSS (NM_002490)	141	NR_034118	100132273	Hs.709677	NR_034118	ENSG00000237037	NDUFA6-DT	NDUFA6-AS1	NDUFA6 divergent transcript	ncRNA	0.107558	0.678261	
chunk0026_218_1	chr10	64574252	64574687	+	0	NA	Intergenic	L2a|LINE|L2	-251059	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.004598	0.479358	
chunk0033_337_1	chr11	22685628	22686167	+	0	NA	intron (NM_177553, intron 3 of 7)	intron (NM_177553, intron 3 of 7)	11124	NM_005256	2620	Hs.711297	NM_005256	ENSG00000148935	GAS2	GAS-2	growth arrest specific 2	protein-coding	0.001855	0.309259	283(AAGTACAGAGAGTTCT,-,0.00),284(AGTACAGAGAGTTCTT,+,0.00)
chunk0186_427_1	chr7	146653848	146654497	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	443437	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.007704	0.413846	309(ATGGACACGATGTCCT,-,0.00),310(TGGACACGATGTCCTT,+,0.00)
chunk0050_194_1	chr12	104056619	104056975	+	0	NA	intron (NM_031302, intron 1 of 11)	Tigger6a|DNA|TcMar-Tigger	7380	NM_001316967	83468	Hs.631650	NM_031302	ENSG00000120820	GLT8D2	-	glycosyltransferase 8 domain containing 2	protein-coding	0.008427	0.366947	
chunk0126_302_1	chr3	80770582	80771235	+	0	NA	Intergenic	LTR1A2|LTR|ERV1	-222960	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.030628	0.489297	
chunk0034_180_1	chr11	31507294	31507935	+	0	NA	intron (NM_144981, intron 1 of 6)	L1MA8|LINE|L1	2014	NM_001304274	196294	Hs.502223	NM_144981	ENSG00000148950	IMMP1L	IMMP1|IMP1|IMP1-LIKE	inner mitochondrial membrane peptidase subunit 1	protein-coding	0.007800	0.327103	
chunk0153_257_1	chr5	72744189	72744695	+	0	NA	Intergenic	Intergenic	-72149	NM_002270	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.005929	0.386588	
chunk0042_383_1	chr12	10663809	10664556	+	0	NA	intron (NM_018423, intron 1 of 10)	intron (NM_018423, intron 1 of 10)	10110	NM_018423	55359	Hs.24979	NM_018423	ENSG00000060140	STYK1	NOK|SuRTK106	serine/threonine/tyrosine kinase 1	protein-coding	0.005355	0.398396	673(CAGAACAGAGAGTTCT,-,0.00),674(AGAACAGAGAGTTCTA,+,0.00)
chunk0199_276_1	chr9	6439322	6439864	+	0	NA	intron (NM_152896, intron 3 of 15)	intron (NM_152896, intron 3 of 15)	26442	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.011070	0.395948	
chunk0204_329_1	chr9	101178281	101178593	+	0	NA	intron (NM_207299, intron 1 of 7)	HERVL-int|LTR|ERVL	-6598	NM_017753	54886	Hs.382683	NM_017753	ENSG00000148123	PLPPR1	LPPR1|PRG-3	phospholipid phosphatase related 1	protein-coding	0.006410	0.485623	
chunk0199_267_1	chr9	6320475	6320993	+	0	NA	Intergenic	L1PB1|LINE|L1	-7615	NM_001001874	89882	Hs.351815	NM_033516	ENSG00000170777	TPD52L3	D55|NYDSP25|hD55	TPD52 like 3	protein-coding	0.001931	0.341040	
chunk0149_66_1	chr5	17077626	17078327	+	0	NA	Intergenic	Intergenic	-138847	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.012839	0.415954	396(AGGATCAGTTTGTTCC,-,0.00),397(GGATCAGTTTGTTCCA,+,0.00)
chunk0158_380_1	chr5	134299466	134300121	+	0	NA	intron (NM_001300853, intron 11 of 12)	intron (NM_001300853, intron 11 of 12)	67281	NM_001113575	51265	Hs.719926	NM_016508	ENSG00000006837	CDKL3	NKIAMRE	cyclin dependent kinase like 3	protein-coding	0.004580	0.352134	
chunk0023_148_1	chr10	24207780	24207988	+	0	NA	promoter-TSS (NM_001282767)	promoter-TSS (NM_001282767)	-907	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.009615	0.459330	
chunk0101_275_1	chr2	133717595	133717794	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-149234	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.005025	0.410000	
chunk0103_259_1	chr2	165448441	165448994	+	0	NA	Intergenic	Intergenic	-20930	NM_001172173	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.005425	0.346570	
chunk0195_353_1	chr8	99705515	99706233	+	0	NA	intron (NM_152564, intron 36 of 61)	intron (NM_152564, intron 36 of 61)	-169013	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.006964	0.349096	425(GTGAACATGATGTACC,-,0.00),426(TGAACATGATGTACCT,+,0.00)
chunk0116_289_1	chr21	40286879	40287128	+	0	NA	intron (NR_073202, intron 10 of 32)	intron (NR_073202, intron 10 of 32)	-74572	NR_039917	100616148		NR_039917	ENSG00000263973	MIR4760	-	microRNA 4760	ncRNA	0.012048	0.492000	
chunk0180_157_1	chr7	64562694	64562941	+	0	NA	intron (NM_001130022, intron 1 of 3)	intron (NM_001130022, intron 1 of 3)	310	NM_001130022	340252	Hs.520886	NM_178558	ENSG00000173041	ZNF680	-	zinc finger protein 680	protein-coding	0.060729	0.649194	
chunk0103_404_1	chr2	169085509	169086023	+	0	NA	intron (NM_199204, intron 4 of 5)	L1MA3|LINE|L1	4659	NM_001142271	10170	Hs.179608	NM_005771	ENSG00000073737	DHRS9	3-alpha-HSD|3ALPHA-HSD|RDH-E2|RDH-TBE|RDH15|RDHL|RDHTBE|RETSDR8|SDR9C4	dehydrogenase/reductase 9	protein-coding	0.000000	0.310680	
chunk0089_96_1	chr18	58362577	58363114	+	0	NA	intron (NM_001144970, intron 17 of 28)	intron (NM_001144970, intron 17 of 28)	-88229	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.007449	0.381041	
chunk0144_449_1	chr4	141870146	141870514	+	0	NA	Intergenic	L1MEh|LINE|L1	233734	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.002717	0.379404	208(CAGGACAAACAGTTCC,-,0.00),209(AGGACAAACAGTTCCT,+,0.00)
chunk0179_34_1	chr7	43148178	43148704	+	0	NA	intron (NM_015052, intron 2 of 29)	MIRb|SINE|MIR	-2454	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.000000	0.481973	
chunk0079_91_1	chr17	11986376	11987246	+	0	NA	intron (NM_001303281, intron 4 of 6)	intron (NM_001303281, intron 4 of 6)	10561	NM_144680	7566	Hs.370473	NM_144680	ENSG00000154957	ZNF18	HDSG1|KOX11|ZKSCAN6|ZNF535|ZSCAN38|Zfp535	zinc finger protein 18	protein-coding	0.006897	0.402985	821(GTTACACGCTGTTCCT,+,0.00)
chunk0182_398_1	chr7	100626419	100626754	+	0	NA	intron (NM_003227, intron 17 of 17)	intron (NM_003227, intron 17 of 17)	7064	NM_001206855	7036	Hs.544932	NM_003227	ENSG00000106327	TFR2	HFE3|TFRC2	transferrin receptor 2	protein-coding	0.050746	0.651786	186(GAGCACTGCGTGTCCA,-,0.00),187(AGCACTGCGTGTCCAG,+,0.00)
chunk0204_208_1	chr9	96868843	96869089	+	0	NA	promoter-TSS (NR_038890)	promoter-TSS (NR_038890)	66	NR_038890	100132781	Hs.710921	NR_038890		LOC100132781	-	cyclin Y like 1 pseudogene	pseudo	0.012195	0.441296	
chunk0083_294_1	chr17	69266253	69266505	+	0	NA	intron (NM_172232, intron 23 of 38)	L1MD1|LINE|L1	-21564	NM_080282	10349	Hs.25377	NM_080282	ENSG00000154263	ABCA10	EST698739	ATP binding cassette subfamily A member 10	protein-coding	0.003968	0.347826	
chunk0052_427_1	chr12	131721520	131722068	+	0	NA	intron (NM_004592, intron 4 of 17)	intron (NM_004592, intron 4 of 17)	10707	NM_001261411	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.003650	0.316940	
chunk0102_412_1	chr2	156552331	156552703	+	0	NA	intron (NM_001083112, intron 8 of 16)	intron (NM_001083112, intron 8 of 16)	116129	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.008065	0.302949	
chunk0165_336_1	chr6	37502217	37502477	+	0	NA	Intergenic	Intergenic	-2423	NM_138493	154467	Hs.284207	NM_138493	ENSG00000198937	CCDC167	C6orf129|HSPC265	coiled-coil domain containing 167	protein-coding	0.015385	0.467433	161(AAAAACACTGTGTTCT,-,0.00),162(AAAACACTGTGTTCTT,+,0.00)
chunk0154_169_1	chr5	79673359	79673795	+	0	NA	intron (NM_001297744, intron 13 of 15)	L1MA3|LINE|L1	-16259	NM_153610	202333	Hs.482625	NM_153610	ENSG00000164309	CMYA5	C5orf10|SPRYD2|TRIM76	cardiomyopathy associated 5	protein-coding	0.002294	0.359268	
chunk0005_109_1	chr1	56627495	56627971	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-17584	NM_006252	5563	Hs.437039	NM_006252	ENSG00000162409	PRKAA2	AMPK|AMPK2|AMPKa2|PRKAA	protein kinase AMP-activated catalytic subunit alpha 2	protein-coding	0.008403	0.375262	
chunk0187_213_1	chr7	151923344	151924091	+	0	NA	Intergenic	L2c|LINE|L2	-32662	NR_033169	168391	Hs.647077	NM_145292	ENSG00000106648	GALNTL5	GALNACT19|GALNT15|GalNAc-T5L	polypeptide N-acetylgalactosaminyltransferase like 5	protein-coding	0.018742	0.470588	416(GAGGACGTGGTGTTCT,-,0.00),417(AGGACGTGGTGTTCTA,+,0.00)
chunk0169_31_1	chr6	97258102	97258615	+	0	NA	intron (NM_198468, intron 9 of 24)	L1MC4a|LINE|L1	24818	NM_198468	253714	Hs.444292	NM_198468	ENSG00000146263	MMS22L	C6orf167|dJ39B17.2	MMS22 like, DNA repair protein	protein-coding	0.001949	0.346304	
chunk0117_251_1	chr22	23365567	23365912	+	0	NA	intron (NR_037839, intron 5 of 6)	L2a|LINE|L2	16387	NR_037839	649264	Hs.600549	NR_037839		CES5AP1	-	carboxylesterase 5A pseudogene 1	pseudo	0.014493	0.436416	
chunk0055_107_1	chr13	56687069	56687409	+	0	NA	Intergenic	Intergenic	-453679	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.002941	0.316716	
chunk0199_345_1	chr9	11323269	11323635	+	0	NA	Intergenic	Intergenic	710246	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.002732	0.305177	
chunk0104_167_1	chr2	174458061	174458581	+	0	NA	intron (NM_001033045, intron 11 of 16)	L3|LINE|CR1	28767	NM_152529	151556	Hs.516604	NM_152529	ENSG00000163328	GPR155	DEP.7|DEPDC3|PGR22	G protein-coupled receptor 155	protein-coding	0.001923	0.370441	
chunk0177_263_1	chr7	25356588	25357321	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-128468	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.005457	0.322888	296(GTGAACATTTTGTACT,-,0.00),297(TGAACATTTTGTACTC,+,0.00)
chunk0104_176_1	chr2	174606254	174606689	+	0	NA	intron (NM_001077269, intron 1 of 7)	MER33|DNA|hAT-Charlie	28108	NM_003387	7456	Hs.128067	NM_003387	ENSG00000115935	WIPF1	PRPL-2|WAS2|WASPIP|WIP	WAS/WASL interacting protein family member 1	protein-coding	0.006897	0.380734	
chunk0178_314_1	chr7	38178583	38179092	+	0	NA	intron (NM_032016, intron 1 of 8)	intron (NM_032016, intron 1 of 8)	631	NM_032016	83930	Hs.309753	NM_032016	ENSG00000010270	STARD3NL	MENTHO	STARD3 N-terminal like	protein-coding	0.033399	0.490196	
chunk0166_26_1	chr6	41902309	41902619	+	0	NA	Intergenic	Intergenic	-7103	NM_018561	25862	Hs.593575	NM_018561	ENSG00000164663	USP49	-	ubiquitin specific peptidase 49	protein-coding	0.000000	0.430868	
chunk0193_165_1	chr8	74757725	74758211	+	0	NA	non-coding (NR_033830, exon 6 of 6)	non-coding (NR_033830, exon 6 of 6)	52275	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.006173	0.340862	
chunk0112_101_1	chr20	38204788	38205424	+	0	NA	Intergenic	L1MA9|LINE|L1	-39808	NM_198951	7052	Hs.517033	NM_004613	ENSG00000198959	TGM2	TG(C)|TGC	transglutaminase 2	protein-coding	0.006289	0.343799	
chunk0027_410_1	chr10	80530364	80530781	+	0	NA	promoter-TSS (NR_120662)	promoter-TSS (NR_120662)	-678	NR_120662	81619	Hs.308615	NM_030927	ENSG00000108219	TSPAN14	DC-TM4F2|TM4SF14|tspan-14	tetraspanin 14	protein-coding	0.004796	0.540670	
chunk0159_155_1	chr5	139373569	139374282	+	0	NA	intron (NM_005847, intron 13 of 14)	intron (NM_005847, intron 13 of 14)	9425	NM_152685	9963	Hs.643467	NM_005847	ENSG00000170482	SLC23A1	SLC23A2|SVCT1|YSPL3	solute carrier family 23 member 1	protein-coding	0.007013	0.504202	
chunk0044_179_1	chr12	30197847	30198157	+	0	NA	Intergenic	Intergenic	-413243	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.006452	0.427653	
chunk0054_288_1	chr13	47479009	47479418	+	0	NA	Intergenic	Ricksha_b|DNA|MULE-MuDR	453409	NR_047492	100861549	Hs.660978	NR_047492	ENSG00000260388	LINC00562	-	long intergenic non-protein coding RNA 562	ncRNA	0.000000	0.412195	
chunk0100_172_1	chr2	109620197	109620473	+	0	NA	Intergenic	MamRep137|DNA|TcMar-Tigger	6001	NM_023016	65124	Hs.355455	NM_023016	ENSG00000198142	SOWAHC	ANKRD57|C2orf26	sosondowah ankyrin repeat domain family member C	protein-coding	0.018116	0.364621	
chunk0164_1_1	chr6	17628847	17629073	+	0	NA	exon (NM_001278209, exon 19 of 23)	exon (NM_001278209, exon 19 of 23)	28673	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.004425	0.462555	
chunk0201_412_1	chr9	69564509	69565101	+	0	NA	intron (NM_001163, intron 1 of 12)	L1M3|LINE|L1	107554	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.003378	0.382799	
chunk0090_433_1	chr18	79491080	79491788	+	0	NA	intron (NM_172387, intron 9 of 9)	intron (NM_172387, intron 9 of 9)	91160	NM_001278672	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.043785	0.588152	
chunk0109_411_1	chr2	240973303	240973558	+	0	NA	Intergenic	Intergenic	-5979	NR_033841	200772	Hs.647893	NR_033841	ENSG00000233392	LOC200772	-	uncharacterized LOC200772	ncRNA	0.043137	0.667969	
chunk0145_106_1	chr4	146158393	146158733	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-17120	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.005882	0.392962	
chunk0202_275_1	chr9	77156818	77157342	+	0	NA	Intergenic	Intergenic	-20365	NM_033305	23230	Hs.459790	NM_015186	ENSG00000197969	VPS13A	CHAC|CHOREIN	vacuolar protein sorting 13 homolog A	protein-coding	0.000000	0.407619	238(AAGTTCAATGTGTTCT,-,0.00)
chunk0114_399_1	chr20	63588317	63588909	+	0	NA	3' UTR (NM_012384, exon 10 of 10)	3' UTR (NM_012384, exon 10 of 10)	-14374	NM_001037335	85441	Hs.517180	NM_033405	ENSG00000130589	HELZ2	PDIP-1|PRIC285	helicase with zinc finger 2	protein-coding	0.030405	0.593592	
chunk0183_11_1	chr7	102906405	102906695	+	0	NA	intron (NM_145032, intron 11 of 19)	L1MA1|LINE|L1	-6347	NM_005824	10234	Hs.567412	NM_005824	ENSG00000128606	LRRC17	P37NB	leucine rich repeat containing 17	protein-coding	0.003448	0.343643	
chunk0059_67_1	chr14	30327285	30327487	+	0	NA	Intergenic	Intergenic	-231737	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.000000	0.315271	153(CAGAACAATCTGGTCC,-,0.00),154(AGAACAATCTGGTCCC,+,0.00)
chunk0060_456_1	chr14	55118097	55118407	+	0	NA	Intergenic	Intergenic	-10965	NM_001177388	3958	Hs.531081	NM_002306	ENSG00000131981	LGALS3	CBP35|GAL3|GALBP|GALIG|L31|LGALS2|MAC2	galectin 3	protein-coding	0.009677	0.421222	
chunk0043_256_1	chr12	20643350	20643950	+	0	NA	intron (NM_000921, intron 10 of 15)	intron (NM_000921, intron 10 of 15)	-51705	NM_001145946	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.005000	0.352745	
chunk0205_187_1	chr9	109060218	109060844	+	0	NA	intron (NM_032012, intron 10 of 17)	intron (NM_032012, intron 10 of 17)	-14233	NR_029506	407036		NR_029506	ENSG00000207698	MIR32	MIRN32|hsa-mir-32|miR-32|miRNA32	microRNA 32	ncRNA	0.006390	0.344498	152(TGATACAGTCTGTCCC,-,0.00),153(GATACAGTCTGTCCCA,+,0.00)
chunk0117_6_1	chr22	10711755	10712108	+	0	NA	Intergenic	Intergenic	249598	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.002833	0.305085	93(CTGTACACAGTGTTCA,-,0.00),94(TGTACACAGTGTTCAT,+,0.00)
chunk0115_421_1	chr21	31410537	31410736	+	0	NA	intron (NM_003253, intron 2 of 28)	intron (NM_003253, intron 2 of 28)	148341	NM_003253	7074	Hs.517228	NM_003253	ENSG00000156299	TIAM1	TIAM-1	T cell lymphoma invasion and metastasis 1	protein-coding	0.010050	0.430000	
chunk0202_346_1	chr9	79571460	79571755	+	0	NA	promoter-TSS (NR_104239)	promoter-TSS (NR_104239)	-166	NM_001282749	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.081356	0.587838	
chunk0141_210_1	chr4	84582274	84582644	+	0	NA	promoter-TSS (NM_001263)	promoter-TSS (NM_001263)	-445	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.059459	0.579515	
chunk0106_238_1	chr2	202925544	202925845	+	0	NA	intron (NM_024744, intron 3 of 16)	intron (NM_024744, intron 3 of 16)	-13468	NM_018256	55759	Hs.73291	NM_018256	ENSG00000138442	WDR12	YTM1	WD repeat domain 12	protein-coding	0.003322	0.529801	
chunk0173_16_1	chr6	141403742	141404367	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	684745	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.004800	0.391374	312(TAGTACATGATGTTCT,-,0.00),313(AGTACATGATGTTCTT,+,0.00)
chunk0022_432_1	chr10	19352029	19352782	+	0	NA	intron (NM_001142308, intron 26 of 39)	intron (NM_001142308, intron 26 of 39)	303634	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.005312	0.364721	242(AAGAACTGGCAGTGCC,-,0.00),243(AGAACTGGCAGTGCCT,+,0.00)
chunk0142_426_1	chr4	104490781	104491003	+	0	NA	promoter-TSS (NR_125926)	promoter-TSS (NR_125926)	-73	NR_125926	101929468	Hs.480435	NR_125926	ENSG00000245384	CXXC4-AS1	-	CXXC4 antisense RNA 1	ncRNA	0.036036	0.551570	
chunk0007_124_1	chr1	79115535	79116058	+	0	NA	Intergenic	Intergenic	-108986	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.009560	0.406489	
chunk0133_299_1	chr3	172204880	172205370	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	164571	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.008163	0.431772	344(CAGGACTAACTGTACT,-,0.00),345(AGGACTAACTGTACTC,+,0.00)
chunk0029_368_1	chr10	107749177	107749782	+	0	NA	Intergenic	L1ME1|LINE|L1	319814	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.008264	0.344884	
chunk0196_317_1	chr8	110733599	110734041	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	293613	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.011312	0.426637	
chunk0120_39_1	chr3	2650737	2651035	+	0	NA	intron (NM_001206955, intron 3 of 23)	Tigger1|DNA|TcMar-Tigger	-241329	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.003356	0.297659	
chunk0122_99_1	chr3	30440334	30441252	+	0	NA	Intergenic	Intergenic	-165709	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.005447	0.369967	683(AAGCACACAAAGTTCT,-,0.00),684(AGCACACAAAGTTCTT,+,0.00)
chunk0150_21_1	chr5	30605589	30606202	+	0	NA	Intergenic	L2|LINE|L2	-587760	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.003263	0.353420	
chunk0097_30_1	chr2	42446472	42446915	+	0	NA	intron (NM_172344, intron 1 of 1)	intron (NM_172344, intron 1 of 1)	47404	NM_133329	170850	Hs.352633	NM_133329	ENSG00000171126	KCNG3	KV10.1|KV6.3	potassium voltage-gated channel modifier subfamily G member 3	protein-coding	0.002257	0.351351	
chunk0010_364_1	chr1	118900584	118901435	+	0	NA	intron (NM_152380, intron 6 of 7)	intron (NM_152380, intron 6 of 7)	88547	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.000000	0.399061	
chunk0210_68_1	chrX	69948272	69948966	+	0	NA	intron (NM_001005612, intron 1 of 7)	intron (NM_001005612, intron 1 of 7)	-74238	NR_037494	100500887		NR_037494	ENSG00000211991	MIR676	hsa-mir-676|mir-676	microRNA 676	ncRNA	0.005764	0.401439	318(TGGCACACTCTGTTCA,-,0.00),319(GGCACACTCTGTTCAG,+,0.00),339(TAGCACATACTGTGCT,-,0.00),340(AGCACATACTGTGCTT,+,0.00)
chunk0016_168_1	chr1	197865720	197866271	+	0	NA	Intergenic	Intergenic	-36557	NM_001024594	388722	Hs.61329	NM_001024594	ENSG00000203724	C1orf53	-	chromosome 1 open reading frame 53	protein-coding	0.003630	0.295290	
chunk0179_387_1	chr7	51340214	51340727	+	0	NA	Intergenic	Intergenic	-23652	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.011696	0.424125	
chunk0161_196_1	chr5	170355666	170356409	+	0	NA	intron (NM_001034838, intron 1 of 7)	intron (NM_001034838, intron 1 of 7)	2550	NM_001034838	30820	Hs.484111	NM_014592	ENSG00000182132	KCNIP1	KCHIP1|VABP	potassium voltage-gated channel interacting protein 1	protein-coding	0.012113	0.495968	
chunk0012_238_1	chr1	160781320	160781700	+	0	NA	Intergenic	Intergenic	-14564	NM_002348	4063	Hs.403857	NM_002348	ENSG00000122224	LY9	CD229|SLAMF3|hly9|mLY9	lymphocyte antigen 9	protein-coding	0.010526	0.490814	
chunk0155_445_1	chr5	101632212	101632435	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	664226	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.455357	
chunk0162_72_1	chr6	1802740	1803052	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	192450	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.012821	0.402556	
chunk0142_286_1	chr4	100037540	100037812	+	0	NA	TTS (NR_125923)	TTS (NR_125923)	87182	NR_125923	256880	Hs.448554	NR_002799	ENSG00000245322	LOC256880	-	uncharacterized LOC256880	ncRNA	0.000000	0.428571	
chunk0134_372_1	chr3	182777134	182777445	+	0	NA	Intergenic	L1M2|LINE|L1	-16214	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.000000	0.580128	
chunk0058_172_1	chr14	23689546	23690509	+	0	NA	Intergenic	L1P2|LINE|L1	53663	NM_005794	10202	Hs.272499	NM_005794	ENSG00000100867	DHRS2	HEP27|SDR25C1	dehydrogenase/reductase 2	protein-coding	0.004154	0.502075	
chunk0131_142_1	chr3	145976722	145977490	+	0	NA	Intergenic	Intergenic	184389	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.001302	0.297789	
chunk0095_256_1	chr2	19461223	19461633	+	0	NA	Intergenic	Intergenic	-102817	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.002439	0.374696	206(ATGTTCAGAGTGTTCT,-,0.00)
chunk0070_13_1	chr15	68938882	68939314	+	0	NA	intron (NM_001184780, intron 1 of 15)	intron (NM_001184780, intron 1 of 15)	8598	NM_145658	246777	Hs.657932	NM_145658	ENSG00000258484	SPESP1	ESP|SP-ESP	sperm equatorial segment protein 1	protein-coding	0.000000	0.408776	
chunk0102_168_1	chr2	147484981	147485760	+	0	NA	Intergenic	Intergenic	-359147	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.366667	
chunk0115_281_1	chr21	28167176	28167383	+	0	NA	intron (NR_126012, intron 4 of 5)	intron (NR_126012, intron 4 of 5)	61388	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.000000	0.403846	
chunk0138_154_1	chr4	37478340	37478540	+	0	NA	intron (NM_001104629, intron 1 of 3)	intron (NM_001104629, intron 1 of 3)	24510	NM_001104629	55286	Hs.107527	NM_018302	ENSG00000154274	C4orf19	-	chromosome 4 open reading frame 19	protein-coding	0.020000	0.412935	
chunk0070_72_1	chr15	69930235	69930741	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	95254	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.005929	0.420118	
chunk0006_101_1	chr1	65276870	65277202	+	0	NA	intron (NM_014787, intron 1 of 18)	L1MEg|LINE|L1	12342	NM_001256865	9829	Hs.647643	NM_014787	ENSG00000116675	DNAJC6	DJC6|PARK19	DnaJ heat shock protein family (Hsp40) member C6	protein-coding	0.006024	0.396396	
chunk0134_234_1	chr3	178954992	178955193	+	0	NA	Intergenic	Intergenic	-94687	NR_126561	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.009950	0.321782	
chunk0005_52_1	chr1	55049784	55050302	+	0	NA	intron (NM_174936, intron 3 of 11)	intron (NM_174936, intron 3 of 11)	9821	NR_110451	255738	Hs.18844	NM_174936	ENSG00000169174	PCSK9	FH3|HCHOLA3|LDLCQ1|NARC-1|NARC1|PC9	proprotein convertase subtilisin/kexin type 9	protein-coding	0.021236	0.606936	
chunk0164_295_1	chr6	24779377	24780050	+	0	NA	intron (NM_015895, intron 2 of 6)	intron (NM_015895, intron 2 of 6)	4300	NM_001251991	51053	Hs.234896	NM_015895	ENSG00000112312	GMNN	Gem|MGORS6	geminin DNA replication inhibitor	protein-coding	0.004458	0.353116	
chunk0081_181_1	chr17	41689321	41689536	+	0	NA	intron (NM_005801, intron 1 of 3)	CpG	553	NM_005801	10209	Hs.150580	NM_005801	ENSG00000173812	EIF1	A121|EIF-1|EIF1A|ISO1|SUI1	eukaryotic translation initiation factor 1	protein-coding	0.088372	0.699074	
chunk0193_106_1	chr8	73960389	73961057	+	0	NA	intron (NM_001204857, intron 1 of 3)	intron (NM_001204857, intron 1 of 3)	11185	NM_001204862	6921	Hs.533437	NM_005648	ENSG00000154582	ELOC	SIII|TCEB1	elongin C	protein-coding	0.000000	0.408072	
chunk0197_383_1	chr8	127011475	127011796	+	0	NA	Intergenic	Intergenic	-1519	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.009346	0.403727	
chunk0087_316_1	chr18	39682367	39682849	+	0	NA	intron (NR_024391, intron 2 of 3)	L2c|LINE|L2	-5831	NR_049848	100846997		NR_049848	ENSG00000283645	MIR5583-2	-	microRNA 5583-2	ncRNA	0.000000	0.395445	12(AGGAACAAAATGACCT,-,0.00),13(GGAACAAAATGACCTT,+,0.00)
chunk0184_397_1	chr7	121761698	121761937	+	0	NA	Intergenic	L1MB5|LINE|L1	-111288	NM_001206838	5803	Hs.489824	NM_002851	ENSG00000106278	PTPRZ1	HPTPZ|HPTPzeta|PTP-ZETA|PTP18|PTPRZ|PTPZ|R-PTP-zeta-2|RPTPB|RPTPbeta|phosphacan	protein tyrosine phosphatase receptor type Z1	protein-coding	0.012552	0.366667	
chunk0054_428_1	chr13	51118875	51119411	+	0	NA	intron (NR_102431, intron 1 of 4)	intron (NR_102431, intron 1 of 4)	-52986	NR_003923	2974	Hs.411573	NM_004129	ENSG00000123201	GUCY1B2	GC-SB2	guanylate cyclase 1 soluble subunit beta 2 (pseudogene)	pseudo	0.007463	0.525140	
chunk0145_165_1	chr4	147238146	147238663	+	0	NA	Intergenic	Intergenic	106313	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.007737	0.382239	
chunk0117_300_1	chr22	24529770	24530334	+	0	NA	Intergenic	L1M4|LINE|L1	25255	NM_001284254	83606	Hs.9850	NM_031444	ENSG00000138867	GUCD1	C22orf13|LLN4	guanylyl cyclase domain containing 1	protein-coding	0.003546	0.389381	
chunk0008_21_1	chr1	87715007	87715614	+	0	NA	Intergenic	Intergenic	-343655	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.008237	0.330592	
chunk0090_135_1	chr18	71979653	71979987	+	0	NA	Intergenic	MER57E1|LTR|ERV1	-197594	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.002994	0.388060	
chunk0142_30_1	chr4	90603487	90603840	+	0	NA	intron (NM_001145065, intron 5 of 10)	L1ME3G|LINE|L1	368632	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.005666	0.384181	
chunk0207_157_1	chr9	130047775	130048102	+	0	NA	Intergenic	MIR|SINE|MIR	-4744	NM_015033	23048	Hs.189409	NM_015033	ENSG00000187239	FNBP1	FBP17	formin binding protein 1	protein-coding	0.018349	0.423780	
chunk0108_194_1	chr2	232300959	232301241	+	0	NA	intron (NR_046476, intron 14 of 20)	MIRb|SINE|MIR	-77434	NM_001632	250	Hs.284255	NM_001632	ENSG00000163283	ALPP	ALP|ALPI|IAP|PALP|PLAP|PLAP-1	alkaline phosphatase, placental	protein-coding	0.017730	0.441696	
chunk0088_159_1	chr18	46702419	46702727	+	0	NA	intron (NM_001307987, intron 1 of 5)	L2b|LINE|L2	-45540	NM_144612	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.019481	0.579288	169(TTGTACAGACTGTTCC,-,0.00),170(TGTACAGACTGTTCCC,+,0.00)
chunk0097_426_1	chr2	63283222	63284200	+	0	NA	intron (NR_122106, intron 7 of 11)	Tigger4b|DNA|TcMar-Tigger	154296	NR_122106	51057	Hs.414952	NM_015910	ENSG00000143951	WDPCP	BBS15|C2orf86|CHDTHP|CPLANE5|FRITZ|FRTZ	WD repeat containing planar cell polarity effector	protein-coding	0.010225	0.363636	
chunk0130_245_1	chr3	135538084	135538588	+	0	NA	Intergenic	Intergenic	-427337	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.005952	0.429703	
chunk0128_23_1	chr3	104206892	104207341	+	0	NA	Intergenic	MER1A|DNA|hAT-Charlie	-683000	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.004454	0.460000	
chunk0158_442_1	chr5	135704391	135704942	+	0	NA	Intergenic	MIR|SINE|MIR	-50731	NR_027127	340074	Hs.434633	NR_027127	ENSG00000251045	SLC25A48-AS1	LINC01959	SLC25A48 antisense RNA 1	ncRNA	0.003630	0.403986	
chunk0055_175_1	chr13	61044704	61045272	+	0	NA	Intergenic	Intergenic	154892	NR_036128	100422973		NR_036128	ENSG00000266663	MIR3169	-	microRNA 3169	ncRNA	0.001761	0.333919	
chunk0124_15_1	chr3	51637923	51638276	+	0	NA	intron (NM_015106, intron 10 of 21)	intron (NM_015106, intron 10 of 21)	-33076	NR_024012	51368	Hs.517864	NM_015926	ENSG00000164081	TEX264	ZSIG11	testis expressed 264, ER-phagy receptor	protein-coding	0.016997	0.497175	223(GAGGCCACACTGTGCT,-,0.00),224(AGGCCACACTGTGCTG,+,0.00)
chunk0201_168_1	chr9	36090861	36091362	+	0	NA	intron (NM_001316345, intron 11 of 22)	intron (NM_001316345, intron 11 of 22)	-45425	NR_104638	152007	Hs.493819	NM_022343	ENSG00000122694	GLIPR2	C9orf19|GAPR-1|GAPR1	GLI pathogenesis related 2	protein-coding	0.009980	0.372510	
chunk0173_323_1	chr6	148682241	148682440	+	0	NA	Intergenic	Intergenic	-64795	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.040201	0.500000	
chunk0138_58_1	chr4	31937778	31938307	+	0	NA	Intergenic	L1ME2|LINE|L1	-59337	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.003781	0.330189	
chunk0166_385_1	chr6	51737516	51738159	+	0	NA	intron (NM_170724, intron 60 of 60)	intron (NM_170724, intron 60 of 60)	115967	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.006221	0.349379	
chunk0096_98_1	chr2	28164180	28165048	+	0	NA	intron (NR_120504, intron 1 of 2)	intron (NR_120504, intron 1 of 2)	42347	NR_120504	100505736	Hs.659540	NR_120504		LOC100505736	-	uncharacterized LOC100505736	ncRNA	0.010369	0.402762	
chunk0091_232_1	chr19	10502569	10502863	+	0	NA	promoter-TSS (NM_012289)	promoter-TSS (NM_012289)	89	NM_012289	9817	Hs.465870	NM_012289	ENSG00000079999	KEAP1	INrf2|KLHL19	kelch like ECH associated protein 1	protein-coding	0.139456	0.762712	
chunk0052_287_1	chr12	124369615	124370019	+	0	NA	intron (NM_006312, intron 22 of 48)	intron (NM_006312, intron 22 of 48)	-32575	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.044554	0.681481	
chunk0009_244_1	chr1	106998383	106999029	+	0	NA	Intergenic	MER70A|LTR|ERVL	-57939	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.004644	0.421947	285(AAAAACTTCCTGTTCT,-,0.00),286(AAAACTTCCTGTTCTC,+,0.00)
chunk0118_60_1	chr22	28034720	28035119	+	0	NA	intron (NM_001145418, intron 12 of 22)	intron (NM_001145418, intron 12 of 22)	-114307	NR_036169	100423034		NR_036169	ENSG00000264073	MIR3199-1	mir-3199-1	microRNA 3199-1	ncRNA	0.007519	0.552500	268(GAGCTCATCCTGTTCT,-,0.00),269(AGCTCATCCTGTTCTT,+,0.00)
chunk0151_328_1	chr5	53753966	53754464	+	0	NA	Intergenic	L1PA6|LINE|L1	193580	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.002008	0.376754	435(AAAGACACAATGTACC,-,0.00)
chunk0016_412_1	chr1	203322166	203322523	+	0	NA	Intergenic	Intergenic	16808	NM_006763	7832	Hs.519162	NM_006763	ENSG00000159388	BTG2	APRO1|PC3|TIS21	BTG anti-proliferation factor 2	protein-coding	0.002801	0.407821	
chunk0205_14_1	chr9	104999844	105000225	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-71788	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.007874	0.410995	
chunk0098_3_1	chr2	64954400	64954599	+	0	NA	Intergenic	Intergenic	-22052	NR_036586	400958	Hs.591565	NR_036586		LINC02245	-	long intergenic non-protein coding RNA 2245	ncRNA	0.010050	0.350000	
chunk0130_376_1	chr3	139558277	139558637	+	0	NA	intron (NR_121609, intron 3 of 4)	intron (NR_121609, intron 3 of 4)	-18628	NM_002899	5947	Hs.529571	NM_002899	ENSG00000114115	RBP1	CRABP-I|CRBP|CRBP1|CRBPI|RBPC	retinol binding protein 1	protein-coding	0.011111	0.418283	
chunk0186_287_1	chr7	142586325	142586901	+	0	NA	Intergenic	L2a|LINE|L2	-79686	NM_001190487	100463482		NM_001190487	ENSG00000270672	MTRNR2L6	HN6	MT-RNR2 like 6	protein-coding	0.003472	0.398614	
chunk0002_289_1	chr1	22853395	22853976	+	0	NA	intron (NM_001309192, intron 3 of 13)	L2c|LINE|L2	9541	NR_036214	100422914		NR_036214	ENSG00000264014	MIR4253	-	microRNA 4253	ncRNA	0.013769	0.611684	287(AAGCACAGCTTGTTCC,-,0.00),288(AGCACAGCTTGTTCCA,+,0.00),303(AGGAACTGGCAGTGCC,-,0.00),304(GGAACTGGCAGTGCCT,+,0.00)
chunk0101_207_1	chr2	130240505	130240926	+	0	NA	Intergenic	Intergenic	-42254	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.016627	0.424171	
chunk0110_159_1	chr20	13960043	13960397	+	0	NA	intron (NR_073207, intron 1 of 18)	intron (NR_073207, intron 1 of 18)	30399	NR_073206	80343	Hs.590879	NM_025229	ENSG00000101251	SEL1L2	C20orf50|sel-1L2	SEL1L2 adaptor subunit of ERAD E3 ligase	protein-coding	0.005650	0.315493	
chunk0177_215_1	chr7	24130530	24131040	+	0	NA	Intergenic	Intergenic	-153403	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.000000	0.397260	
chunk0057_433_1	chr13	110474838	110475196	+	0	NA	intron (NM_001846, intron 29 of 47)	(CA)n|Simple_repeat|Simple_repeat	33162	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.041899	0.520891	
chunk0189_391_1	chr8	27478181	27478702	+	0	NA	intron (NM_000742, intron 1 of 6)	intron (NM_000742, intron 1 of 6)	855	NM_001282455	1135	Hs.57718	NM_000742	ENSG00000120903	CHRNA2	-	cholinergic receptor nicotinic alpha 2 subunit	protein-coding	0.001919	0.429119	
chunk0165_62_1	chr6	30885454	30886224	+	0	NA	intron (NM_013993, intron 2 of 18)	intron (NM_013993, intron 2 of 18)	859	NM_001202523	780	Hs.631988	NM_001954	ENSG00000204580	DDR1	CAK|CD167|DDR|EDDR1|HGK2|MCK10|NEP|NTRK4|PTK3|PTK3A|RTK6|TRKE	discoidin domain receptor tyrosine kinase 1	protein-coding	0.020779	0.561608	
chunk0161_358_1	chr5	175204409	175204695	+	0	NA	Intergenic	Intergenic	-208821	NR_046113	441116	Hs.533036	NM_001004348	ENSG00000204754	LINC01951	-	long intergenic non-protein coding RNA 1951	ncRNA	0.010490	0.348432	
chunk0140_287_1	chr4	72337689	72338248	+	0	NA	intron (NM_014243, intron 5 of 21)	intron (NM_014243, intron 5 of 21)	230831	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.007156	0.323214	500(CAGGACAGAGAGTCCA,-,0.00),501(AGGACAGAGAGTCCAA,+,0.00)
chunk0099_81_1	chr2	85382173	85382652	+	0	NA	intron (NM_032213, intron 9 of 10)	AluY|SINE|Alu	27692	NM_001135021	84173	Hs.269990	NM_032213	ENSG00000115459	ELMOD3	DFNB88|LST3|RBED1|RBM29	ELMO domain containing 3	protein-coding	0.025052	0.506250	287(CAGGACACGGTGTTCC,-,0.00),288(AGGACACGGTGTTCCT,+,0.00)
chunk0185_35_1	chr7	124403377	124404126	+	0	NA	Intergenic	Intergenic	-51655	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.002670	0.349333	281(TAAAACAGGATGTTCC,-,0.00),282(AAAACAGGATGTTCCT,+,0.00)
chunk0208_210_1	chrX	18173418	18173874	+	0	NA	intron (NM_001184767, intron 10 of 10)	intron (NM_001184767, intron 10 of 10)	47258	NM_001184767	139105	Hs.403802	NM_153346	ENSG00000177324	BEND2	CXorf20	BEN domain containing 2	protein-coding	0.015351	0.477024	210(GGGAGCACAATGTTCT,-,0.00),211(GGAGCACAATGTTCTG,+,0.00)
chunk0078_204_1	chr17	5352802	5353360	+	0	NA	intron (NM_001083585, intron 7 of 16)	intron (NM_001083585, intron 7 of 16)	-66560	NR_027679	84268	Hs.462086	NM_032308	ENSG00000129197	RPAIN	HRIP|RIP	RPA interacting protein	protein-coding	0.003584	0.398927	
chunk0167_367_1	chr6	73521432	73521974	+	0	NA	promoter-TSS (NM_001402)	promoter-TSS (NM_001402)	-671	NM_001402	1915	Hs.535192	NM_001402	ENSG00000156508	EEF1A1	CCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|HNGC:16303|LENG7|PTI1|eEF1A-1	eukaryotic translation elongation factor 1 alpha 1	protein-coding	0.055351	0.574586	
chunk0167_245_1	chr6	67717234	67717620	+	0	NA	Intergenic	Intergenic	-337924	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.007772	0.348837	
chunk0008_383_1	chr1	97048770	97049121	+	0	NA	Intergenic	L2b|LINE|L2	-46978	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.000000	0.355114	
chunk0016_162_1	chr1	197768365	197768707	+	0	NA	intron (NM_001300858, intron 2 of 15)	intron (NM_001300858, intron 2 of 15)	6957	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.002924	0.405248	
chunk0046_60_1	chr12	55847989	55848211	+	0	NA	Intergenic	Intergenic	-5117	NR_073606	4327	Hs.591033	NM_002429	ENSG00000123342	MMP19	CODA|MMP18|RASI-1	matrix metallopeptidase 19	protein-coding	0.009009	0.533632	120(CAGCACATTCTGTTCC,-,0.00),121(AGCACATTCTGTTCCC,+,0.00)
chunk0096_207_1	chr2	30363112	30363365	+	0	NA	Intergenic	Intergenic	16592	NR_122048	285043	Hs.429119	NR_122048		LINC01936	-	long intergenic non-protein coding RNA 1936	ncRNA	0.019763	0.448819	119(AGGTACAGCGCGTGCC,-,0.00),120(GGTACAGCGCGTGCCT,+,0.00)
chunk0069_386_1	chr15	67598124	67598473	+	0	NA	intron (NM_001206804, intron 7 of 21)	intron (NM_001206804, intron 7 of 21)	49294	NM_001206804	5607	Hs.114198	NM_002757	ENSG00000137764	MAP2K5	HsT17454|MAPKK5|MEK5|PRKMK5	mitogen-activated protein kinase kinase 5	protein-coding	0.002865	0.351429	
chunk0052_90_1	chr13	22135711	22136225	+	0	NA	Intergenic	Intergenic	-74317	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.005837	0.372816	
chunk0197_21_1	chr8	117520716	117521285	+	0	NA	exon (NM_001282986, exon 1 of 3)	exon (NM_001282986, exon 1 of 3)	287	NM_001282986	90390	Hs.492612	NM_080651	ENSG00000164758	MED30	MED30S|THRAP6|TRAP25	mediator complex subunit 30	protein-coding	0.068541	0.621053	284(CAGGACATCGTGTACC,-,0.00),285(AGGACATCGTGTACCG,+,0.00)
chunk0029_362_1	chr10	107626764	107627358	+	0	NA	Intergenic	L1MB8|LINE|L1	442232	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.006734	0.326050	
chunk0050_30_1	chr12	99985399	99985923	+	0	NA	Intergenic	Intergenic	-1007	NM_152788	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.013359	0.390476	
chunk0174_381_1	chr6	164982541	164982820	+	0	NA	Intergenic	Intergenic	-160617	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.010753	0.328571	
chunk0200_206_1	chr9	20476276	20476551	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	25929	NR_039685	100616441		NR_039685	ENSG00000264941	MIR4474	-	microRNA 4474	ncRNA	0.003636	0.329710	
chunk0186_90_1	chr7	137344081	137344287	+	0	NA	promoter-TSS (NM_002825)	promoter-TSS (NM_002825)	-384	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.009709	0.420290	93(AAGCACAAAATGTACA,-,0.00)
chunk0101_98_1	chr2	124801481	124801791	+	0	NA	intron (NM_130773, intron 19 of 23)	intron (NM_130773, intron 19 of 23)	776349	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.003226	0.344051	
chunk0106_232_1	chr2	202749213	202749412	+	0	NA	intron (NM_173511, intron 4 of 7)	L1ME4a|LINE|L1	79922	NM_001288624	130026	Hs.516629	NM_138468	ENSG00000163596	ICA1L	ALS2CR14|ALS2CR15	islet cell autoantigen 1 like	protein-coding	0.005025	0.295000	
chunk0148_412_1	chr5	14955910	14956181	+	0	NA	Intergenic	Intergenic	-84267	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.000000	0.238971	
chunk0187_347_1	chr7	157057459	157058342	+	0	NA	Intergenic	Intergenic	47043	NR_038835	645249	Hs.224879	NR_038835	ENSG00000243479	MNX1-AS1	CCAT5	MNX1 antisense RNA 1 (head to head)	ncRNA	0.019253	0.480769	
chunk0204_202_1	chr9	96654204	96654639	+	0	NA	intron (NM_153698, intron 2 of 5)	intron (NM_153698, intron 2 of 5)	896	NM_153698	195827	Hs.44640	NM_153698	ENSG00000158122	PRXL2C	AAED1|C9orf21	peroxiredoxin like 2C	protein-coding	0.020690	0.449541	
chunk0005_140_1	chr1	57512458	57512903	+	0	NA	intron (NM_021080, intron 3 of 16)	intron (NM_021080, intron 3 of 16)	-347863	NR_104362	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.006742	0.450673	
chunk0167_80_1	chr6	56545719	56546004	+	0	NA	intron (NM_183380, intron 52 of 93)	intron (NM_183380, intron 52 of 93)	97035	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.010526	0.328671	
chunk0126_229_1	chr3	79010841	79011308	+	0	NA	intron (NM_002941, intron 3 of 30)	intron (NM_002941, intron 3 of 30)	8385	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.008565	0.350427	
chunk0061_130_1	chr14	59076770	59077341	+	0	NA	Intergenic	Intergenic	-111608	NM_001270520	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.003503	0.360140	
chunk0080_43_1	chr17	21262539	21262809	+	0	NA	Intergenic	Intergenic	-9408	NM_152914	256302	Hs.654713	NM_152914	ENSG00000274180	NATD1	C17orf103|Gtlf3b	N-acetyltransferase domain containing 1	protein-coding	0.011111	0.535055	
chunk0163_191_1	chr6	11650775	11651052	+	0	NA	Intergenic	Intergenic	112686	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.003610	0.453237	127(GAAGACAGGGTGTTCA,-,0.00),128(AAGACAGGGTGTTCAA,+,0.00)
chunk0120_104_1	chr3	4504511	4504722	+	0	NA	intron (NM_002222, intron 2 of 57)	intron (NM_002222, intron 2 of 57)	11268	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.014218	0.443396	
chunk0135_323_1	chr3	190060587	190061273	+	0	NA	intron (NM_001134418, intron 1 of 14)	L1PB4|LINE|L1	-60034	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.002915	0.352256	
chunk0169_423_1	chr6	108650306	108650746	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	89660	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.002273	0.385488	
chunk0097_194_1	chr2	50622318	50622653	+	0	NA	intron (NM_001135659, intron 7 of 23)	intron (NM_001135659, intron 7 of 23)	73777	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.011940	0.306548	
chunk0026_212_1	chr10	64116846	64117091	+	0	NA	Intergenic	MER41C|LTR|ERV1	595605	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.004082	0.398374	
chunk0128_85_1	chr3	105616277	105617063	+	0	NA	Intergenic	Intergenic	249957	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006361	0.353240	
chunk0119_108_1	chr22	42233203	42233718	+	0	NA	intron (NM_005650, intron 1 of 5)	intron (NM_005650, intron 1 of 5)	-18119	NM_181492	6942	Hs.475018	NM_005650	ENSG00000100207	TCF20	AR1|DDVIBA|SPBP|TCF-20	transcription factor 20	protein-coding	0.011650	0.430233	
chunk0064_324_1	chr14	96051153	96051398	+	0	NA	intron (NM_001282463, intron 2 of 2)	intron (NM_001282463, intron 2 of 2)	11951	NM_001252507	56967	Hs.6434	NM_020215	ENSG00000227051	C14orf132	C14orf88	chromosome 14 open reading frame 132	protein-coding	0.004082	0.528455	77(GTGACAGGATGTTCCA,+,0.00)
chunk0056_392_1	chr13	93746055	93746460	+	0	NA	intron (NM_005708, intron 2 of 8)	Tigger5|DNA|TcMar-Tigger	112216	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.012346	0.396552	
chunk0125_197_1	chr3	66845267	66845713	+	0	NA	Intergenic	L1PA3|LINE|L1	-152813	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.011211	0.409396	
chunk0145_415_1	chr4	152938048	152938716	+	0	NA	Intergenic	Intergenic	-4601	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.035928	0.490284	288(GGGAACGCGTTGTCCT,-,0.00),289(GGAACGCGTTGTCCTG,+,0.00)
chunk0022_361_1	chr10	17245077	17245465	+	0	NA	Intergenic	Tigger5b|DNA|TcMar-Tigger	-15286	NR_108061	100507347	Hs.740502	NR_108060	ENSG00000229124	VIM-AS1	-	VIM antisense RNA 1	ncRNA	0.007732	0.403599	
chunk0086_75_1	chr18	13245650	13246069	+	0	NA	intron (NM_181482, intron 1 of 5)	intron (NM_181482, intron 1 of 5)	27129	NM_181482	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.007160	0.502381	
chunk0196_243_1	chr8	108468549	108469031	+	0	NA	intron (NM_014673, intron 5 of 10)	intron (NM_014673, intron 5 of 10)	25166	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.010373	0.356108	
chunk0118_43_1	chr22	27805678	27805892	+	0	NA	Intergenic	Intergenic	-4287	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.004673	0.520930	
chunk0132_366_1	chr3	161644839	161645247	+	0	NA	Intergenic	Intergenic	148235	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.009804	0.413203	158(GAGAACAGAATGATCT,-,0.00),159(AGAACAGAATGATCTG,+,0.00)
chunk0202_98_1	chr9	72365484	72366126	+	0	NA	promoter-TSS (NM_001102421)	promoter-TSS (NM_001102421)	-558	NM_001102421	7763	Hs.406096	NM_006007	ENSG00000107372	ZFAND5	ZA20D2|ZFAND5A|ZNF216	zinc finger AN1-type containing 5	protein-coding	0.056075	0.553655	
chunk0043_59_1	chr12	13953807	13954386	+	0	NA	intron (NM_000834, intron 1 of 12)	MIR3|SINE|MIR	25992	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.006908	0.439655	
chunk0191_101_1	chr8	48008338	48008545	+	0	NA	promoter-TSS (NM_003350)	promoter-TSS (NM_003350)	6	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.164251	0.754808	
chunk0083_186_1	chr17	66467168	66467675	+	0	NA	intron (NM_002737, intron 2 of 16)	MIR3|SINE|MIR	-50567	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.007890	0.405512	
chunk0176_291_1	chr7	16740024	16740508	+	0	NA	Intergenic	Intergenic	-13460	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.006198	0.377320	
chunk0109_25_1	chr20	461262	462000	+	0	NA	intron (NR_111901, intron 1 of 9)	AluJr4|SINE|Alu	922	NR_111901	128637	Hs.590876	NM_144628	ENSG00000125875	TBC1D20	C20orf140|WARBM4	TBC1 domain family member 20	protein-coding	0.056911	0.497970	14(GAGAACATCATGTGCA,-,0.00),15(AGAACATCATGTGCAA,+,0.00)
chunk0173_349_1	chr6	149076426	149076842	+	0	NA	3' UTR (NM_005715, exon 8 of 8)	3' UTR (NM_005715, exon 8 of 8)	-111950	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.002404	0.328537	
chunk0085_401_1	chr18	10188931	10189547	+	0	NA	Intergenic	Intergenic	225131	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.009740	0.465154	
chunk0130_189_1	chr3	133587943	133588575	+	0	NA	3' UTR (NM_017548, exon 5 of 5)	3' UTR (NM_017548, exon 5 of 5)	13825	NM_001282765	55573	Hs.518265	NM_017548	ENSG00000091527	CDV3	H41	CDV3 homolog	protein-coding	0.007911	0.404423	
chunk0021_232_1	chr10	6365403	6365775	+	0	NA	Intergenic	Intergenic	39045	NR_040079	399715		NR_040079	ENSG00000215244	LINC02649	-	long intergenic non-protein coding RNA 2649	ncRNA	0.008065	0.426273	
chunk0051_44_1	chr12	112296372	112296835	+	0	NA	intron (NM_001109662, intron 7 of 75)	intron (NM_001109662, intron 7 of 75)	85489	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.002160	0.523707	
chunk0141_226_1	chr4	84725863	84726243	+	0	NA	intron (NM_014991, intron 45 of 67)	intron (NM_014991, intron 45 of 67)	143149	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.002632	0.320210	
chunk0161_78_1	chr5	166957924	166958298	+	0	NA	Intergenic	Intergenic	-31741	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005348	0.397333	
chunk0112_337_1	chr20	45044734	45045932	+	0	NA	intron (NM_006282, intron 10 of 10)	MIRc|SINE|MIR	55779	NM_002251	3787	Hs.117780	NM_002251	ENSG00000124134	KCNS1	Kv9.1	potassium voltage-gated channel modifier subfamily S member 1	protein-coding	0.008347	0.357798	
chunk0079_288_1	chr17	16642392	16643131	+	0	NA	intron (NM_020787, intron 3 of 5)	L1MB7|LINE|L1	11092	NM_020787	57547	Hs.128078	NM_020787	ENSG00000197566	ZNF624	-	zinc finger protein 624	protein-coding	0.005413	0.344595	
chunk0178_235_1	chr7	35987858	35988316	+	0	NA	Intergenic	Intergenic	-107223	NR_108089	101928618	Hs.561704	NR_108089	ENSG00000261184	LOC101928618	-	uncharacterized LOC101928618	ncRNA	0.008734	0.496732	
chunk0142_410_1	chr4	103072320	103072740	+	0	NA	intron (NM_001300754, intron 1 of 10)	intron (NM_001300754, intron 1 of 10)	4243	NM_178833	133308	Hs.546482	NM_178833	ENSG00000164038	SLC9B2	NHA2|NHE10|NHEDC2	solute carrier family 9 member B2	protein-coding	0.014286	0.375297	
chunk0066_110_1	chr15	29923189	29923456	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1M5|LINE|L1	45477	NM_001301025	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.003745	0.376866	
chunk0138_47_1	chr4	31415552	31416177	+	0	NA	Intergenic	Intergenic	244720	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.006400	0.348243	
chunk0080_55_1	chr17	21846095	21846299	+	0	NA	Intergenic	L1MEd|LINE|L1	153674	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.000000	0.273171	
chunk0207_230_1	chr9	131897382	131897878	+	0	NA	intron (NM_004269, intron 4 of 7)	L1MC5|LINE|L1	-157686	NM_001304275	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.010081	0.386318	
chunk0063_240_1	chr14	82313806	82314381	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-691032	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.001739	0.357639	
chunk0206_361_1	chr9	125797298	125797845	+	0	NA	intron (NR_024122, intron 2 of 7)	L1MA9|LINE|L1	49372	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.306569	
chunk0174_155_1	chr6	157870125	157870487	+	0	NA	intron (NM_016224, intron 2 of 17)	intron (NM_016224, intron 2 of 17)	47135	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.019337	0.542700	
chunk0028_3_1	chr10	81968306	81968512	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	90722	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.009709	0.502415	
chunk0007_85_1	chr1	78500636	78501618	+	0	NA	intron (NM_001039585, intron 3 of 3)	MER121|DNA|hAT?	10084	NM_000959	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.004073	0.350966	
chunk0144_125_1	chr4	128904383	128904762	+	0	NA	intron (NM_144643, intron 18 of 20)	L1PA16|LINE|L1	92728	NM_001287443	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.005277	0.294737	
chunk0163_319_1	chr6	14777458	14777657	+	0	NA	Intergenic	Intergenic	-468418	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.005025	0.450000	
chunk0150_451_1	chr5	40669574	40670131	+	0	NA	Intergenic	MIRb|SINE|MIR	-10078	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.005386	0.405018	
chunk0203_204_1	chr9	86550774	86551359	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-196579	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.003419	0.354949	
chunk0084_298_1	chr17	80008467	80008890	+	0	NA	intron (NM_019020, intron 3 of 11)	intron (NM_019020, intron 3 of 11)	27180	NM_019020	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.035461	0.615566	
chunk0027_426_1	chr10	80862206	80862768	+	0	NA	Intergenic	Intergenic	321668	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.001779	0.360568	
chunk0021_374_1	chr1	246404471	246405117	+	0	NA	intron (NM_001167740, intron 1 of 11)	MER3|DNA|hAT-Charlie	12618	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.009288	0.412674	
chunk0082_121_1	chr17	55148255	55148524	+	0	NA	intron (NM_178509, intron 17 of 17)	intron (NM_178509, intron 17 of 17)	-116571	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.003717	0.300000	
chunk0050_160_1	chr12	103372888	103373783	+	0	NA	intron (NM_198521, intron 3 of 5)	intron (NM_198521, intron 3 of 5)	122675	NM_001099336	374470	Hs.534649	NM_198521	ENSG00000179088	C12orf42	-	chromosome 12 open reading frame 42	protein-coding	0.005587	0.397321	
chunk0202_212_1	chr9	76097457	76097910	+	0	NA	intron (NM_001190482, intron 8 of 36)	MIR|SINE|MIR	207039	NM_006200	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.008830	0.416300	
chunk0177_278_1	chr7	25581323	25581692	+	0	NA	Intergenic	Intergenic	-353021	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.002710	0.435135	
chunk0116_443_1	chr21	43344262	43344726	+	0	NA	Intergenic	Intergenic	-12455	NR_103713	100126693	Hs.473952	NR_103713		LINC00322	C21orf136|NCRNA00322	long intergenic non-protein coding RNA 322	ncRNA	0.043103	0.582796	
chunk0171_256_1	chr6	127266327	127266769	+	0	NA	promoter-TSS (NM_001242845)	promoter-TSS (NM_001242845)	-134	NM_001242851	81847	Hs.267120	NM_030963	ENSG00000118518	RNF146	-	ring finger protein 146	protein-coding	0.033937	0.494357	130(GGGAACAAGCAGTACT,-,0.00),131(GGAACAAGCAGTACTT,+,0.00)
chunk0024_144_1	chr10	35189007	35189487	+	0	NA	intron (NM_181571, intron 6 of 7)	intron (NM_181571, intron 6 of 7)	-5880	NM_182720	1390	Hs.200250	NM_001881	ENSG00000095794	CREM	CREM-2|ICER|hCREM-2	cAMP responsive element modulator	protein-coding	0.004167	0.316008	
chunk0002_145_1	chr1	17531988	17532315	+	0	NA	Intergenic	Intergenic	-7684	NM_018125	55160	Hs.443460	NM_018125	ENSG00000074964	ARHGEF10L	GrinchGEF	Rho guanine nucleotide exchange factor 10 like	protein-coding	0.012232	0.615854	
chunk0156_121_1	chr5	106465366	106466106	+	0	NA	Intergenic	Intergenic	545278	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.006757	0.360324	
chunk0144_283_1	chr4	138070769	138071347	+	0	NA	intron (NR_037866, intron 7 of 10)	L1MA4A|LINE|L1	-17956	NR_038380	641364	Hs.570846	NR_038380	ENSG00000250033	SLC7A11-AS1	-	SLC7A11 antisense RNA 1	ncRNA	0.003460	0.355786	
chunk0100_115_1	chr2	108449036	108449256	+	0	NA	promoter-TSS (NM_181453)	promoter-TSS (NM_181453)	25	NR_028063	9648	Hs.436505	NM_181453	ENSG00000135968	GCC2	GCC185|RANBP2L4|REN53	GRIP and coiled-coil domain containing 2	protein-coding	0.109091	0.669683	
chunk0041_16_1	chr12	419122	419501	+	0	NA	intron (NM_032358, intron 5 of 12)	LTR16|LTR|ERVL	17736	NM_001130146	84318	Hs.631656	NM_032358	ENSG00000120647	CCDC77	-	coiled-coil domain containing 77	protein-coding	0.005277	0.471053	
chunk0073_210_1	chr16	10181619	10181853	+	0	NA	intron (NM_001134407, intron 1 of 12)	CpG	331	NM_001134408	2903	Hs.411472	NM_000833	ENSG00000183454	GRIN2A	EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A	glutamate ionotropic receptor NMDA type subunit 2A	protein-coding	0.102564	0.714894	
chunk0063_322_1	chr14	85168465	85168665	+	0	NA	Intergenic	Intergenic	-225314	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.015000	0.308458	
chunk0135_6_1	chr3	184050087	184050626	+	0	NA	Intergenic	Intergenic	-2691	NM_130770	170572	Hs.632579	NM_130770	ENSG00000178084	HTR3C	-	5-hydroxytryptamine receptor 3C	protein-coding	0.007421	0.472222	
chunk0004_56_1	chr1	43065088	43065667	+	0	NA	Intergenic	Intergenic	-82546	NM_001101376	440585	Hs.657614	NM_001101376	ENSG00000186973	FAM183A	-	family with sequence similarity 183 member A	protein-coding	0.017271	0.570690	373(AGGCTCAGTGTGTACT,-,0.00),374(GGCTCAGTGTGTACTC,+,0.00)
chunk0175_232_1	chr7	6392793	6393075	+	0	NA	intron (NM_006908, intron 3 of 5)	MIR|SINE|MIR	18439	NM_006908	5879	Hs.413812	NM_006908	ENSG00000136238	RAC1	MIG5|MRD48|Rac-1|TC-25|p21-Rac1	Rac family small GTPase 1	protein-coding	0.024823	0.544170	
chunk0037_89_1	chr11	71796665	71797089	+	0	NA	intron (NM_018172, intron 4 of 4)	intron (NM_018172, intron 4 of 4)	9366	NM_018172	55199	Hs.567527	NM_018172	ENSG00000158483	FAM86C1	FAM86C	family with sequence similarity 86 member C1	protein-coding	0.030660	0.607059	
chunk0038_14_1	chr11	80900667	80900959	+	0	NA	Intergenic	Intergenic	-138010	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003425	0.395904	
chunk0085_8_1	chr18	199263	200404	+	0	NA	intron (NM_001037334, intron 9 of 14)	Tigger17a|DNA|TcMar-Tigger	41350	NM_001037334	9097	Hs.464416	NM_005151	ENSG00000101557	USP14	TGT	ubiquitin specific peptidase 14	protein-coding	0.006135	0.370403	
chunk0154_34_1	chr5	77019800	77020316	+	0	NA	Intergenic	Intergenic	-10327	NM_018046	55109	Hs.634849	NM_018046	ENSG00000164252	AGGF1	GPATC7|GPATCH7|HSU84971|HUS84971|VG5Q	angiogenic factor with G-patch and FHA domains 1	protein-coding	0.001938	0.411992	
chunk0010_390_1	chr1	119403326	119403628	+	0	NA	Intergenic	L1MC1|LINE|L1	-11454	NM_001166120	3284	Hs.654399	NM_000198	ENSG00000203859	HSD3B2	HSD3B|HSDB|SDR11E2	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	protein-coding	0.006623	0.333333	
chunk0033_101_1	chr11	14288065	14288836	+	0	NA	intron (NM_001102669, intron 4 of 5)	intron (NM_001102669, intron 4 of 5)	70035	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.003891	0.404145	
chunk0031_113_1	chr10	124588762	124589386	+	0	NA	intron (NM_022126, intron 6 of 6)	intron (NM_022126, intron 6 of 6)	-114954	NR_120630	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.022436	0.571200	405(GGGGACAGTCCGTGCA,-,0.00),406(GGGACAGTCCGTGCAG,+,0.00)
chunk0020_135_1	chr1	233654542	233655124	+	0	NA	intron (NM_002245, intron 1 of 2)	MLT1A0-int|LTR|ERVL-MaLR	30681	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.010309	0.478559	
chunk0118_184_1	chr22	31193169	31193458	+	0	NA	intron (NM_001135825, intron 3 of 4)	intron (NM_001135825, intron 3 of 4)	-18951	NM_005569	3985	Hs.474596	NM_005569	ENSG00000182541	LIMK2	-	LIM domain kinase 2	protein-coding	0.010381	0.465517	156(CTGCACATTCTGTCCC,-,0.00),157(TGCACATTCTGTCCCC,+,0.00)
chunk0127_383_1	chr3	102113282	102113722	+	0	NA	Intergenic	MIR|SINE|MIR	172643	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.006818	0.369615	
chunk0211_337_1	chrX	124238892	124239504	+	0	NA	Intergenic	Intergenic	-107084	NM_001114937	4068	Hs.349094	NM_002351	ENSG00000183918	SH2D1A	DSHP|EBVS|IMD5|LYP|MTCP1|SAP|SAP/SH2D1A|XLP|XLPD|XLPD1	SH2 domain containing 1A	protein-coding	0.001634	0.368679	
chunk0206_438_1	chr9	127955469	127956046	+	0	NA	intron (NM_001035254, intron 1 of 10)	intron (NM_001035254, intron 1 of 10)	-5043	NM_203305	399665	Hs.535972	NM_203305	ENSG00000167106	FAM102A	C9orf132|EEIG1|SYM-3A|bA203J24.7	family with sequence similarity 102 member A	protein-coding	0.012132	0.567474	
chunk0188_390_1	chr8	18563015	18563518	+	0	NA	intron (NM_015310, intron 14 of 15)	L2b|LINE|L2	172021	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.009940	0.384921	
chunk0175_374_1	chr6	167975151	167975350	+	0	NA	TTS (NM_001129895)	TTS (NM_001129895)	1689	NM_001129895	100128124	Hs.448059	NM_001129895		HGC6.3	-	uncharacterized LOC100128124	protein-coding	0.005025	0.495000	
chunk0139_29_1	chr4	48403679	48403938	+	0	NA	intron (NM_020846, intron 6 of 7)	L1PA10|LINE|L1	62212	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.023166	0.553846	
chunk0101_212_1	chr2	130294357	130294878	+	0	NA	Intergenic	L1PB|LINE|L1	47766	NM_032357	84317	Hs.104203	NM_032357	ENSG00000136710	CCDC115	CDG2O|ccp1	coiled-coil domain containing 115	protein-coding	0.000000	0.386973	198(TTGAACAGGGTGTCCT,-,0.00),199(TGAACAGGGTGTCCTT,+,0.00)
chunk0029_373_1	chr10	108040423	108040883	+	0	NA	intron (NR_125760, intron 3 of 4)	MIRb|SINE|MIR	28640	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.008696	0.381779	
chunk0086_388_1	chr18	26545241	26545783	+	0	NA	intron (NM_001258222, intron 1 of 4)	intron (NM_001258222, intron 1 of 4)	3024	NM_001142730	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.005535	0.412523	261(AGGGTCAGTGTGTCCA,-,0.00),262(GGGTCAGTGTGTCCAG,+,0.00),434(TAGAACACAGTGTCCA,-,0.00),435(AGAACACAGTGTCCAA,+,0.00)
chunk0209_211_1	chrX	44649113	44649750	+	0	NA	Intergenic	Intergenic	-106456	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.018838	0.503135	
chunk0030_268_1	chr10	116392089	116392601	+	0	NA	Intergenic	HAL1|LINE|L1	-35567	NM_001011709	119548	Hs.276724	NM_001011709	ENSG00000203837	PNLIPRP3	-	pancreatic lipase related protein 3	protein-coding	0.011719	0.436647	187(GGGAACAGCCTCTTCC,-,0.00),188(GGAACAGCCTCTTCCT,+,0.00)
chunk0089_122_1	chr18	58670006	58670218	+	0	NA	3' UTR (NM_001289967, exon 2 of 2)	3' UTR (NM_001289967, exon 2 of 2)	-1274	NM_173844	10892	Hs.601217	NM_006785	ENSG00000172175	MALT1	IMD12|MLT|MLT1|PCASP1	MALT1 paracaspase	protein-coding	0.018868	0.413146	
chunk0001_308_1	chr1	9238528	9238895	+	0	NA	intron (NM_004285, intron 1 of 4)	L2a|LINE|L2	-1133	NM_001282587	9563	Hs.463511	NM_004285	ENSG00000049239	H6PD	CORTRD1|G6PDH|GDH	hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase	protein-coding	0.008174	0.426630	
chunk0016_173_1	chr1	198056205	198056613	+	0	NA	Intergenic	L1M2|LINE|L1	-100569	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.004902	0.569682	
chunk0053_284_1	chr13	33379425	33379837	+	0	NA	intron (NM_001243476, intron 5 of 17)	intron (NM_001243476, intron 5 of 17)	-93867	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.000000	0.384988	
chunk0146_393_1	chr4	168689806	168690227	+	0	NA	intron (NM_016081, intron 6 of 20)	intron (NM_016081, intron 6 of 20)	58399	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.002375	0.353081	227(AAGTACAGCATGTTTC,-,0.00),228(AGTACAGCATGTTTCA,+,0.00)
chunk0025_256_1	chr10	54936114	54936570	+	0	NA	Intergenic	L1MB8|LINE|L1	-135051	NM_001142773	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.004386	0.312910	220(TTGAACATTGTGTACA,-,0.00),221(TGAACATTGTGTACAG,+,0.00)
chunk0081_355_1	chr17	47649820	47650019	+	0	NA	promoter-TSS (NM_002265)	promoter-TSS (NM_002265)	81	NM_002265	3837	Hs.532793	NM_002265	ENSG00000108424	KPNB1	IMB1|IPO1|IPOB|Impnb|NTF97	karyopherin subunit beta 1	protein-coding	0.105528	0.700000	
chunk0083_379_1	chr17	71460339	71460652	+	0	NA	Intergenic	L1PA13|LINE|L1	-258316	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.025559	0.484076	
chunk0031_106_1	chr10	124349130	124349478	+	0	NA	Intergenic	Intergenic	69672	NM_001171814	4942	Hs.523332	NM_000274	ENSG00000065154	OAT	GACR|HOGA|OATASE|OKT	ornithine aminotransferase	protein-coding	0.020115	0.553009	
chunk0092_361_1	chr19	35643256	35643849	+	0	NA	exon (NM_001300974, exon 4 of 6)	exon (NM_001300974, exon 4 of 6)	1815	NM_001300974	2116	Hs.194061	NM_014209	ENSG00000105672	ETV2	ER71|ETSRP71	ETS variant 2	protein-coding	0.094435	0.700337	
chunk0067_268_1	chr15	45982742	45983162	+	0	NA	Intergenic	MIR|SINE|MIR	348212	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.002381	0.318290	
chunk0013_305_1	chr1	171267344	171267640	+	0	NA	intron (NM_001282694, intron 2 of 7)	intron (NM_001282694, intron 2 of 7)	9569	NM_001282692	2326	Hs.1424	NM_002021	ENSG00000010932	FMO1	-	flavin containing dimethylaniline monoxygenase 1	protein-coding	0.003378	0.410774	
chunk0135_349_1	chr3	190424800	190425093	+	0	NA	Intergenic	Intergenic	24930	NM_207316	131920	Hs.335321	NM_207316	ENSG00000198398	TMEM207	UNQ846	transmembrane protein 207	protein-coding	0.017065	0.391156	
chunk0169_449_1	chr6	108769169	108769499	+	0	NA	non-coding (NR_033376, exon 4 of 5)	non-coding (NR_033376, exon 4 of 5)	17680	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.015152	0.486405	
chunk0109_83_1	chr20	2026453	2026803	+	0	NA	Intergenic	MER52A|LTR|ERV1	-32343	NM_024411	5173	Hs.22584	NM_024411	ENSG00000101327	PDYN	ADCA|PENKB|SCA23	prodynorphin	protein-coding	0.011429	0.532764	
chunk0017_226_1	chr1	208043611	208044141	+	0	NA	intron (NM_025179, intron 20 of 31)	intron (NM_025179, intron 20 of 31)	-132538	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.022642	0.564972	
chunk0164_66_1	chr6	19454861	19455514	+	0	NA	Intergenic	Intergenic	-274707	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.009188	0.359327	442(GGTACTTGTTGTGCTT,+,0.00)
chunk0121_101_1	chr3	16998446	16998848	+	0	NA	intron (NM_015184, intron 1 of 5)	intron (NM_015184, intron 1 of 5)	65451	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.004975	0.327543	
chunk0123_113_1	chr3	42328447	42328870	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-62488	NM_000729	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.009456	0.410377	
chunk0061_257_1	chr14	61323044	61323325	+	0	NA	intron (NM_006255, intron 1 of 13)	intron (NM_006255, intron 1 of 13)	1741	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.017794	0.496454	
chunk0046_184_1	chr12	58775471	58775711	+	0	NA	intron (NR_120452, intron 1 of 7)	intron (NR_120452, intron 1 of 7)	6125	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.004167	0.315353	
chunk0040_388_1	chr11	119729385	119729621	+	0	NA	promoter-TSS (NM_002855)	promoter-TSS (NM_002855)	-80	NR_120587	102724301	Hs.637640	NR_120587	ENSG00000254854	LOC102724301	-	uncharacterized LOC102724301	ncRNA	0.097458	0.746835	
chunk0088_336_1	chr18	51195010	51195407	+	0	NA	intron (NM_016626, intron 1 of 1)	intron (NM_016626, intron 1 of 1)	2473	NM_016626	51320	Hs.465144	NM_016626	ENSG00000176624	MEX3C	BM-013|MEX-3C|RKHD2|RNF194	mex-3 RNA binding family member C	protein-coding	0.007557	0.361809	
chunk0044_94_1	chr12	28339670	28339936	+	0	NA	intron (NM_018318, intron 5 of 11)	MIR|SINE|MIR	82603	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.003759	0.430712	
chunk0179_419_1	chr7	51792783	51793298	+	0	NA	Intergenic	L1MC2|LINE|L1	-476222	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.001942	0.323643	
chunk0060_89_1	chr14	42497256	42498033	+	0	NA	Intergenic	Intergenic	890083	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.000000	0.300771	
chunk0144_31_1	chr4	125052041	125052385	+	0	NA	Intergenic	Intergenic	-264199	NM_024582	79633	Hs.563205	NM_024582	ENSG00000196159	FAT4	CDHF14|CDHR11|FAT-J|FATJ|HKLLS2|NBLA00548|VMLDS2	FAT atypical cadherin 4	protein-coding	0.014535	0.388406	
chunk0111_99_1	chr20	23601425	23601973	+	0	NA	TTS (NM_001008693)	TTS (NM_001008693)	4274	NM_001008693	128822	Hs.698020	NM_001008693	ENSG00000173335	CST9	CLM|CTES7A	cystatin 9	protein-coding	0.007299	0.506375	
chunk0007_23_1	chr1	77509016	77509866	+	0	NA	intron (NM_012093, intron 10 of 13)	intron (NM_012093, intron 10 of 13)	173217	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.005882	0.403055	
chunk0148_407_1	chr5	14917749	14918201	+	0	NA	Intergenic	Intergenic	-46197	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.002212	0.417219	
chunk0052_170_1	chr13	24148567	24149049	+	0	NA	intron (NM_001286792, intron 3 of 14)	intron (NM_001286792, intron 3 of 14)	-11908	NM_001166271	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.006224	0.455487	197(AGGAGCATTCTGTCCT,-,0.00),198(GGAGCATTCTGTCCTA,+,0.00)
chunk0186_170_1	chr7	139340195	139340498	+	0	NA	promoter-TSS (NM_001244585)	promoter-TSS (NM_001244585)	-13	NM_001244585	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.132013	0.638158	
chunk0102_92_1	chr2	143954118	143954487	+	0	NA	intron (NM_024659, intron 7 of 9)	intron (NM_024659, intron 7 of 9)	17235	NR_110237	101928386	Hs.668251	NR_110237	ENSG00000232377	LOC101928386	-	uncharacterized LOC101928386	ncRNA	0.010840	0.318919	
chunk0198_85_1	chr8	130203229	130203428	+	0	NA	intron (NM_001247996, intron 6 of 30)	MER91A|DNA|hAT-Tip100	93205	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.015075	0.535000	
chunk0196_308_1	chr8	109967378	109967638	+	0	NA	3' UTR (NM_014379, exon 3 of 3)	3' UTR (NM_014379, exon 3 of 3)	7222	NM_014379	27012	Hs.13285	NM_014379	ENSG00000164794	KCNV1	HNKA|KCNB3|KV2.3|KV8.1	potassium voltage-gated channel modifier subfamily V member 1	protein-coding	0.003846	0.356322	
chunk0117_16_1	chr22	11212924	11213180	+	0	NA	Intergenic	SAR|Satellite|Satellite	-251523	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.007812	0.202335	
chunk0190_104_1	chr8	30364360	30364559	+	0	NA	Intergenic	Intergenic	-20042	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.000000	0.335000	20(AGGAACTCTGTGTCTC,-,0.00)
chunk0027_194_1	chr10	75664194	75664393	+	0	NA	intron (NR_131178, intron 1 of 7)	intron (NR_131178, intron 1 of 7)	16784	NR_131178	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.000000	0.415000	
chunk0093_142_1	chr19	46443125	46443436	+	0	NA	Intergenic	Intergenic	28283	NM_018215	55228	Hs.8395	NM_018215	ENSG00000182013	PNMA8A	PNMAL1	PNMA family member 8A	protein-coding	0.012862	0.464744	
chunk0184_64_1	chr7	112436410	112436761	+	0	NA	intron (NM_001197080, intron 1 of 11)	L2a|LINE|L2	13441	NM_001007245	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.005698	0.375000	
chunk0092_438_1	chr19	38336124	38336332	+	0	NA	intron (NM_021185, intron 1 of 28)	CpG	425	NM_021185	57828	Hs.324335	NM_021185	ENSG00000099338	CATSPERG	C19orf15	cation channel sperm associated auxiliary subunit gamma	protein-coding	0.062500	0.583732	
chunk0157_39_1	chr5	115799568	115799890	+	0	NA	Intergenic	Intergenic	16979	NM_001801	1036	Hs.442378	NM_001801	ENSG00000129596	CDO1	CDO-I	cysteine dioxygenase type 1	protein-coding	0.003106	0.362229	
chunk0053_352_1	chr13	34941815	34942169	+	0	NA	promoter-TSS (NM_015678)	promoter-TSS (NM_015678)	-295	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.031073	0.597183	197(ATGCACACTGTGTCCT,-,0.00),198(TGCACACTGTGTCCTT,+,0.00)
chunk0026_207_1	chr10	63798950	63799610	+	0	NA	Intergenic	Intergenic	277917	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.013636	0.429652	452(CAGTACTGTGTGTTCC,-,0.00),453(AGTACTGTGTGTTCCT,+,0.00),644(ATGTACAGGATGTGCA,-,0.00),645(TGTACAGGATGTGCAG,+,0.00)
chunk0058_406_1	chr13	112011888	112012402	+	0	NA	intron (NR_120392, intron 1 of 3)	intron (NR_120392, intron 1 of 3)	39835	NR_120392	100505996	Hs.654853	NR_120392	ENSG00000224243	SOX1-OT	LINC00403	SOX1 overlapping transcript	ncRNA	0.036965	0.563107	235(CAGAACTGGCCGTGCC,-,0.00),236(AGAACTGGCCGTGCCT,+,0.00)
chunk0058_163_1	chr14	23321232	23321431	+	0	NA	5' UTR (NM_004643, exon 1 of 7)	5' UTR (NM_004643, exon 1 of 7)	1143	NM_004643	8106	Hs.707712	NM_004643	ENSG00000100836	PABPN1	OPMD|PAB2|PABII|PABP-2|PABP2	poly(A) binding protein nuclear 1	protein-coding	0.055276	0.555000	
chunk0127_21_1	chr3	88321845	88322060	+	0	NA	Intergenic	Intergenic	-172086	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.009302	0.458333	
chunk0099_362_1	chr2	100814534	100814911	+	0	NA	Intergenic	Intergenic	-5429	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.002653	0.444444	
chunk0065_364_1	chr14	103911137	103911336	+	0	NA	Intergenic	MIRc|SINE|MIR	10330	NM_004894	9556	Hs.109052	NM_004894	ENSG00000156411	ATP5MPL	6.8PL|C14orf2|MLQ|MP68|PLPM	ATP synthase membrane subunit 6.8PL	protein-coding	0.005025	0.515000	
chunk0034_84_1	chr11	27394678	27395039	+	0	NA	intron (NM_018490, intron 2 of 17)	intron (NM_018490, intron 2 of 17)	-31610	NM_080654	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.008310	0.439227	194(AAGAACAGGATGTGCA,-,0.00),195(AGAACAGGATGTGCAT,+,0.00)
chunk0133_232_1	chr3	171286440	171287108	+	0	NA	intron (NM_001161560, intron 2 of 31)	intron (NM_001161560, intron 2 of 31)	173634	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.002994	0.387145	
chunk0166_151_1	chr6	45253852	45254246	+	0	NA	intron (NM_001261823, intron 2 of 9)	intron (NM_001261823, intron 2 of 9)	-56279	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.007614	0.318987	
chunk0042_451_1	chr12	12450075	12450991	+	0	NA	intron (NM_058169, intron 3 of 3)	intron (NM_058169, intron 3 of 3)	93454	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.005459	0.382770	
chunk0149_1_1	chr5	15392814	15393197	+	0	NA	Intergenic	L2a|LINE|L2	-107191	NM_012304	23194	Hs.433057	NM_012304	ENSG00000183580	FBXL7	FBL6|FBL7	F-box and leucine rich repeat protein 7	protein-coding	0.005222	0.268229	
chunk0015_456_1	chr1	192511118	192511366	+	0	NA	Intergenic	Intergenic	-64485	NM_002922	5996	Hs.75256	NM_002922	ENSG00000090104	RGS1	1R20|BL34|HEL-S-87|IER1|IR20	regulator of G protein signaling 1	protein-coding	0.000000	0.345382	
chunk0204_217_1	chr9	97316495	97317061	+	0	NA	intron (NR_036527, intron 22 of 48)	intron (NR_036527, intron 22 of 48)	9150	NM_020893	100499483	Hs.435629	NM_020893	ENSG00000197816	CCDC180	C9orf174	coiled-coil domain containing 180	protein-coding	0.010601	0.541446	
chunk0076_52_1	chr16	61107987	61108402	+	0	NA	Intergenic	Intergenic	-52428	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.007229	0.331731	
chunk0143_221_1	chr4	113844116	113844713	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-82487	NM_172114	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.008375	0.458194	
chunk0160_421_1	chr5	164238815	164239084	+	0	NA	Intergenic	L1MB7|LINE|L1	228453	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.011152	0.425926	
chunk0173_251_1	chr6	147026508	147027430	+	0	NA	intron (NR_034115, intron 5 of 10)	intron (NR_034115, intron 5 of 10)	-131956	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.002169	0.306609	225(AAGAACGGAGAGTCCC,-,0.00),226(AGAACGGAGAGTCCCT,+,0.00)
chunk0046_55_1	chr12	55430221	55430618	+	0	NA	Intergenic	Intergenic	4165	NM_001005183	390326	Hs.553764	NM_001005183	ENSG00000185821	OR6C76	-	olfactory receptor family 6 subfamily C member 76	protein-coding	0.005038	0.319095	
chunk0210_39_1	chrX	68246936	68247663	+	0	NA	intron (NM_002547, intron 5 of 24)	L2c|LINE|L2	186158	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.011004	0.401099	
chunk0212_99_1	chrY	13486020	13486616	+	0	NA	Intergenic	L1PA8|LINE|L1	-5648	NR_047617	7404	Hs.115277	NM_007125	ENSG00000183878	UTY	KDM6AL|KDM6C|UTY1	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	protein-coding	0.005034	0.350084	
chunk0114_332_1	chr21	17549385	17549597	+	0	NA	intron (NM_001207065, intron 2 of 2)	intron (NM_001207065, intron 2 of 2)	36585	NM_001207064	1525	Hs.627078	NM_001338	ENSG00000154639	CXADR	CAR|CAR4/6|HCAR	CXADR Ig-like cell adhesion molecule	protein-coding	0.009434	0.394366	
chunk0029_81_1	chr10	96858548	96859269	+	0	NA	intron (NM_032440, intron 2 of 7)	intron (NM_032440, intron 2 of 7)	25953	NM_032440	84458	Hs.427927	NM_015652	ENSG00000196233	LCOR	C10orf12|MLR2	ligand dependent nuclear receptor corepressor	protein-coding	0.006935	0.389197	
chunk0085_344_1	chr18	8741619	8741903	+	0	NA	intron (NM_015210, intron 4 of 16)	intron (NM_015210, intron 4 of 16)	24390	NM_015210	23255	Hs.707920	NM_015210	ENSG00000168502	MTCL1	CCDC165|KIAA0802|SOGA2	microtubule crosslinking factor 1	protein-coding	0.021127	0.477193	
chunk0167_189_1	chr6	64254646	64254874	+	0	NA	intron (NM_001142800, intron 30 of 42)	LTR33|LTR|ERVL	608234	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.008772	0.406114	
chunk0133_374_1	chr3	173807895	173808277	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	112710	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.010471	0.352480	
chunk0041_41_1	chr12	953311	953888	+	0	NA	intron (NM_001297419, intron 1 of 11)	intron (NM_001297419, intron 1 of 11)	-3877	NM_001297421	5893	Hs.410355	NM_134422	ENSG00000002016	RAD52	-	RAD52 homolog, DNA repair protein	protein-coding	0.013865	0.415225	
chunk0086_440_1	chr18	29003189	29003531	+	0	NA	Intergenic	MER110|LTR|ERV1	-825914	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.005848	0.411079	
chunk0083_79_1	chr17	64216497	64216876	+	0	NA	intron (NM_018469, intron 1 of 11)	intron (NM_018469, intron 1 of 11)	14070	NM_001288733	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.021108	0.560526	
chunk0048_443_1	chr12	88630420	88631121	+	0	NA	Intergenic	Intergenic	-50297	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.004280	0.310541	
chunk0003_133_1	chr1	32743801	32744000	+	0	NA	intron (NM_020888, intron 1 of 6)	intron (NM_020888, intron 1 of 6)	1989	NM_020888	57648	Hs.591502	NM_020888	ENSG00000162522	KIAA1522	-	KIAA1522	protein-coding	0.010050	0.555000	
chunk0050_410_1	chr12	109695706	109696477	+	0	NA	Intergenic	Intergenic	-18291	NM_032829	84915	Hs.661785	NM_032829	ENSG00000139438	FAM222A	C12orf34	family with sequence similarity 222 member A	protein-coding	0.016861	0.554404	
chunk0009_74_1	chr1	100946975	100947697	+	0	NA	intron (NM_001144884, intron 8 of 11)	L1PA6|LINE|L1	51258	NM_133496	148867	Hs.533903	NM_133496	ENSG00000162695	SLC30A7	ZNT7|ZnT-7|ZnTL2	solute carrier family 30 member 7	protein-coding	0.004155	0.367911	354(AGGAACAGGTTGTTCA,-,0.00),355(GGAACAGGTTGTTCAG,+,0.00)
chunk0100_406_1	chr2	119365929	119367173	+	0	NA	promoter-TSS (NM_001178017)	promoter-TSS (NM_001178017)	131	NM_001017927	130355	Hs.99488	NM_001017927	ENSG00000186132	C2orf76	AIM29	chromosome 2 open reading frame 76	protein-coding	0.053055	0.562249	
chunk0206_432_1	chr9	127793499	127793892	+	0	NA	Intergenic	Intergenic	7669	NM_001261	1025	Hs.150423	NM_001261	ENSG00000136807	CDK9	C-2k|CDC2L4|CTK1|PITALRE|TAK	cyclin dependent kinase 9	protein-coding	0.010178	0.426396	
chunk0117_323_1	chr22	24934868	24935410	+	0	NA	TTS (NM_001001663)	TTS (NM_001001663)	4208	NM_001001663	255349	Hs.329040	NM_001001663	ENSG00000206069	TMEM211	bA9F11.1	transmembrane protein 211	protein-coding	0.005535	0.386740	
chunk0080_296_1	chr17	31537824	31538302	+	0	NA	3' UTR (NM_001303542, exon 13 of 13)	3' UTR (NM_001303542, exon 13 of 13)	3180	NR_039877	100616248		NR_039877	ENSG00000284424	MIR4724	mir-4724	microRNA 4724	ncRNA	0.006276	0.569937	
chunk0053_196_1	chr13	31706066	31706518	+	0	NA	Intergenic	L2|LINE|L2	-33250	NM_130806	122042	Hs.680763	NM_130806	ENSG00000133105	RXFP2	GPR106|GREAT|INSL3R|LGR8|LGR8.1|RXFPR2	relaxin family peptide receptor 2	protein-coding	0.002212	0.399558	
chunk0010_233_1	chr1	116389093	116389318	+	0	NA	intron (NM_000701, intron 7 of 22)	intron (NM_000701, intron 7 of 22)	5835	NM_001160234	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.000000	0.513274	
chunk0114_111_1	chr21	9560993	9561521	+	0	NA	Intergenic	L1MEd|LINE|L1	259804	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.009470	0.317580	
chunk0195_221_1	chr8	97104403	97104730	+	0	NA	intron (NM_016134, intron 7 of 7)	LTR82A|LTR|ERVL	173382	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.000000	0.375000	
chunk0026_275_1	chr10	67116437	67116934	+	0	NA	intron (NM_001127384, intron 7 of 17)	intron (NM_001127384, intron 7 of 17)	104419	NR_111909	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.002012	0.307229	
chunk0030_262_1	chr10	116143040	116143715	+	0	NA	intron (NM_145793, intron 3 of 8)	intron (NM_145793, intron 3 of 8)	128930	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.008889	0.406805	
chunk0001_302_1	chr1	9076352	9076618	+	0	NA	Intergenic	Tigger9a|DNA|TcMar-Tigger	-6657	NM_001135585	6518	Hs.530003	NM_003039	ENSG00000142583	SLC2A5	GLUT-5|GLUT5	solute carrier family 2 member 5	protein-coding	0.007519	0.426966	
chunk0146_230_1	chr4	162115309	162115936	+	0	NA	intron (NM_001128427, intron 1 of 15)	UCON24|Unknown|Unknown	48412	NM_001128428	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.007974	0.353503	
chunk0101_218_1	chr2	130736489	130736745	+	0	NA	Intergenic	Intergenic	7547	NM_207364	344561	Hs.452574	NM_207364	ENSG00000173302	GPR148	BTR|PGR6	G protein-coupled receptor 148	protein-coding	0.019531	0.513619	142(AGGGACAGAACGTGCC,-,0.00),143(GGGACAGAACGTGCCC,+,0.00)
chunk0034_266_1	chr11	34560549	34560900	+	0	NA	Intergenic	Intergenic	-46924	NM_001243080	2001	Hs.11713	NM_001422	ENSG00000135374	ELF5	ESE2	E74 like ETS transcription factor 5	protein-coding	0.011396	0.426136	238(CAGAACATAATGTTTC,-,0.00),239(AGAACATAATGTTTCT,+,0.00)
chunk0045_142_1	chr12	46461535	46461862	+	0	NA	intron (NR_125378, intron 3 of 3)	intron (NR_125378, intron 3 of 3)	77591	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.015291	0.399390	
chunk0079_282_1	chr17	16480992	16481482	+	0	NA	intron (NM_207387, intron 1 of 2)	OldhAT1|DNA|hAT-Ac	10954	NM_001113567	388341	Hs.25425	NM_207387	ENSG00000181350	LRRC75A	C17orf76|FAM211A	leucine rich repeat containing 75A	protein-coding	0.014286	0.543788	216(AAGAACACAATGTGCA,-,0.00),217(AGAACACAATGTGCAA,+,0.00)
chunk0165_159_1	chr6	33812788	33813063	+	0	NA	Intergenic	Intergenic	-8909	NM_002418	4295	Hs.2813	NM_002418	ENSG00000096395	MLN	-	motilin	protein-coding	0.025455	0.536232	
chunk0070_224_1	chr15	72754475	72754779	+	0	NA	intron (NR_023319, intron 4 of 4)	L1ME4b|LINE|L1	-28208	NR_040107	100287559	Hs.562587	NR_040107	ENSG00000260898	ADPGK-AS1	-	ADPGK antisense RNA 1	ncRNA	0.003289	0.380328	
chunk0021_238_1	chr1	242461662	242462239	+	0	NA	intron (NM_152666, intron 2 of 10)	L1PA16|LINE|L1	-12468	NM_001195811	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.005199	0.375433	
chunk0124_261_1	chr3	57073709	57074037	+	0	NA	exon (NM_181727, exon 2 of 2)	exon (NM_181727, exon 2 of 2)	5435	NM_001128615	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.006098	0.534954	
chunk0057_371_1	chr13	109074457	109074656	+	0	NA	intron (NM_001198950, intron 27 of 34)	THE1D|LTR|ERVL-MaLR	92747	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.010050	0.505000	
chunk0091_299_1	chr19	12737203	12737806	+	0	NA	promoter-TSS (NM_004317)	promoter-TSS (NM_004317)	12	NM_004317	439	Hs.465985	NM_004317	ENSG00000198356	GET3	ARSA-I|ARSA1|ASNA-I|ASNA1|TRC40	guided entry of tail-anchored proteins factor 3, ATPase	protein-coding	0.038143	0.536424	
chunk0016_92_1	chr1	194889390	194889667	+	0	NA	Intergenic	MER52D|LTR|ERV1	1584783	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.010830	0.611511	
chunk0025_59_1	chr10	49532424	49532808	+	0	NA	exon (NM_000124, exon 2 of 21)	exon (NM_000124, exon 2 of 21)	6507	NM_001277058	2074	Hs.49063	NM_000124	ENSG00000225830	ERCC6	ARMD5|CKN2|COFS|COFS1|CSB|CSB-PGBD3|POF11|RAD26|UVSS1	ERCC excision repair 6, chromatin remodeling factor	protein-coding	0.033854	0.555844	211(AAGCACTCCCTGTTCC,-,0.00),212(AGCACTCCCTGTTCCA,+,0.00)
chunk0162_224_1	chr6	4466220	4466650	+	0	NA	Intergenic	Intergenic	38433	NR_106988									0.016279	0.468677	
chunk0173_300_1	chr6	148367332	148367556	+	0	NA	intron (NM_015278, intron 1 of 19)	intron (NM_015278, intron 1 of 19)	24851	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.017857	0.471111	
chunk0159_381_1	chr5	146284702	146285186	+	0	NA	intron (NM_018989, intron 20 of 20)	intron (NM_018989, intron 20 of 20)	-54080	NM_002700	5459	Hs.553499	NM_002700	ENSG00000091010	POU4F3	BRN3C|DFNA15|DFNA42|DFNA52	POU class 4 homeobox 3	protein-coding	0.002066	0.286598	
chunk0208_226_1	chrX	19118878	19119077	+	0	NA	intron (NM_001184837, intron 1 of 26)	L1ME1|LINE|L1	3660	NM_001079859	10149	Hs.146978	NM_005756	ENSG00000173698	ADGRG2	CBAVDX|EDDM6|GPR64|HE6|TM7LN2	adhesion G protein-coupled receptor G2	protein-coding	0.005025	0.425000	
chunk0031_165_1	chr10	125355222	125355592	+	0	NA	Intergenic	Intergenic	-194352	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.013514	0.458221	
chunk0063_454_1	chr14	89089797	89090378	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	265934	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.001721	0.383162	
chunk0104_402_1	chr2	180672251	180672892	+	0	NA	Intergenic	Intergenic	-19533	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.001560	0.362928	
chunk0040_254_1	chr11	115830679	115830918	+	0	NA	Intergenic	(CTGTACA)n|Simple_repeat|Simple_repeat	-70598	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.000000	0.500000	
chunk0197_451_1	chr8	127849082	127849680	+	0	NA	intron (NR_003367, intron 1 of 8)	intron (NR_003367, intron 1 of 8)	53419	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.011706	0.490818	334(CGAAACAAGGTGTTCC,-,0.00),335(GAAACAAGGTGTTCCC,+,0.00),543(GTGCACAGCCTGTACA,-,0.00),544(TGCACAGCCTGTACAT,+,0.00)
chunk0202_218_1	chr9	76291842	76292318	+	0	NA	intron (NM_001190482, intron 24 of 36)	intron (NM_001190482, intron 24 of 36)	102448	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.008403	0.381551	240(CAGTACAATCTGTTCA,-,0.00),241(AGTACAATCTGTTCAA,+,0.00)
chunk0147_438_1	chr4	187499859	187500455	+	0	NA	intron (NR_038931, intron 1 of 4)	Tigger3c|DNA|TcMar-Tigger	5456	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.006711	0.380235	339(AAGTACACTCTGTGAT,-,0.00)
chunk0055_462_1	chr13	76832276	76832519	+	0	NA	Intergenic	Intergenic	54008	NM_138444	115207	Hs.644125	NM_138444	ENSG00000178695	KCTD12	C13orf2|PFET1|PFETIN	potassium channel tetramerization domain containing 12	protein-coding	0.012346	0.352459	
chunk0143_197_1	chr4	112884112	112884829	+	0	NA	intron (NM_001127493, intron 1 of 46)	MER58B|DNA|hAT-Charlie	66387	NM_001127493	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.002789	0.341226	577(AAACACAGTGTGTTCA,-,0.00),578(AACACAGTGTGTTCAC,+,0.00)
chunk0084_292_1	chr17	79935465	79935666	+	0	NA	3' UTR (NM_001271845, exon 8 of 8)	3' UTR (NM_001271845, exon 8 of 8)	-8840	NR_110850	101928766	Hs.630666	NR_110850	ENSG00000262585	LINC01979	-	long intergenic non-protein coding RNA 1979	ncRNA	0.029851	0.599010	
chunk0123_415_1	chr3	49471821	49472169	+	0	NA	intron (NM_001177634, intron 2 of 5)	intron (NM_001177634, intron 2 of 5)	1863	NM_001177640	1605	Hs.76111	NM_004393	ENSG00000173402	DAG1	156DAG|A3a|AGRNR|DAG|LGMDR16|MDDGA9|MDDGC7|MDDGC9	dystroglycan 1	protein-coding	0.011494	0.530086	
chunk0005_88_1	chr1	56239942	56240310	+	0	NA	Intergenic	L1MC5|LINE|L1	339458	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.002717	0.333333	
chunk0088_62_1	chr18	44332004	44332248	+	0	NA	intron (NR_110792, intron 2 of 4)	L1PA15|LINE|L1	199571	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.008197	0.342857	
chunk0086_254_1	chr18	23386547	23386905	+	0	NA	intron (NM_032933, intron 4 of 14)	A-rich|Low_complexity|Low_complexity	51235	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.002793	0.398329	
chunk0102_407_1	chr2	156182023	156182506	+	0	NA	intron (NR_110250, intron 1 of 3)	intron (NR_110250, intron 1 of 3)	72667	NR_110250	101929378	Hs.171192	NR_110249	ENSG00000226383	LINC01876	-	long intergenic non-protein coding RNA 1876	ncRNA	0.006211	0.417355	197(AGGCACACCATGCCCT,-,0.00),198(GGCACACCATGCCCTT,+,0.00)
chunk0082_297_1	chr17	58659193	58659595	+	0	NA	intron (NM_001201457, intron 1 of 32)	CpG	32661	NM_001201457	56155	Hs.390221	NM_031272	ENSG00000121101	TEX14	CT113|SPGF23	testis expressed 14, intercellular bridge forming factor	protein-coding	0.057214	0.456576	
chunk0068_35_1	chr15	51096973	51097173	+	0	NA	intron (NM_207381, intron 1 of 2)	intron (NM_207381, intron 1 of 2)	-2368	NM_001311175	388121	Hs.306343	NM_207381	ENSG00000183578	TNFAIP8L3	TIPE3	TNF alpha induced protein 8 like 3	protein-coding	0.000000	0.378109	
chunk0106_299_1	chr2	204593551	204593765	+	0	NA	intron (NM_205863, intron 1 of 21)	intron (NM_205863, intron 1 of 21)	47865	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.000000	0.344186	
chunk0190_39_1	chr8	29327223	29327992	+	0	NA	Intergenic	Intergenic	21198	NM_057158	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.002601	0.281818	
chunk0192_99_1	chr8	61615210	61615835	+	0	NA	intron (NM_001164750, intron 14 of 24)	L2a|LINE|L2	74327	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.008000	0.391374	
chunk0156_297_1	chr5	110086870	110087275	+	0	NA	Intergenic	Intergenic	203890	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.007407	0.428571	238(AGGCACATTCAGTCCT,-,0.00),239(GGCACATTCAGTCCTC,+,0.00)
chunk0027_30_1	chr10	72298414	72298629	+	0	NA	Intergenic	Intergenic	24602	NM_019058	54541	Hs.744875	NM_019058	ENSG00000168209	DDIT4	Dig2|REDD-1|REDD1	DNA damage inducible transcript 4	protein-coding	0.037209	0.587963	
chunk0119_117_1	chr22	42620609	42621473	+	0	NA	intron (NM_007326, intron 8 of 8)	L4_A_Mam|LINE|RTE-X	5796	NR_029422	267010	Hs.574857	NR_029422	ENSG00000276027	RNU12	RNU12-1|RNU12L|RNU12P|dJ222E13.7	RNA, U12 small nuclear	snRNA	0.010417	0.495954	
chunk0152_254_1	chr5	60841688	60842358	+	0	NA	intron (NM_024930, intron 1 of 8)	intron (NM_024930, intron 1 of 8)	2251	NM_001297618	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.010448	0.390462	
chunk0053_358_1	chr13	35179792	35180130	+	0	NA	intron (NM_015678, intron 28 of 57)	intron (NM_015678, intron 28 of 57)	237674	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.000000	0.303835	
chunk0092_432_1	chr19	38290681	38291396	+	0	NA	intron (NM_001166103, intron 5 of 5)	intron (NM_001166103, intron 5 of 5)	-13126	NM_033520	64073	Hs.631544	NM_022125	ENSG00000167644	C19orf33	H2RSP|IMUP|IMUP-1|IMUP-2	chromosome 19 open reading frame 33	protein-coding	0.025175	0.590782	
chunk0205_369_1	chr9	113910337	113910536	+	0	NA	intron (NM_133374, intron 1 of 13)	intron (NM_133374, intron 1 of 13)	34154	NM_133374	114991	Hs.349208	NM_133374	ENSG00000157657	ZNF618	FP13169|NEDD10	zinc finger protein 618	protein-coding	0.035176	0.545000	
chunk0152_409_1	chr5	65143285	65143507	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	338481	NM_197941	11174	Hs.482291	NM_197941	ENSG00000049192	ADAMTS6	ADAM-TS 6|ADAM-TS6|ADAMTS-6	ADAM metallopeptidase with thrombospondin type 1 motif 6	protein-coding	0.004505	0.340807	
chunk0099_368_1	chr2	100997917	100998518	+	0	NA	Intergenic	Intergenic	-4012	NM_001098577	6160	Hs.469473	NM_000993	ENSG00000071082	RPL31	L31	ribosomal protein L31	protein-coding	0.009983	0.318937	259(AAGGGCAGAGTGTGCC,-,0.00),260(AGGGCAGAGTGTGCCT,+,0.00)
chunk0005_27_1	chr1	54488212	54488468	+	0	NA	Intergenic	CpG	-59794	NM_147161	26027	Hs.745173	NM_015547	ENSG00000162390	ACOT11	BFIT|STARD14|THEA|THEM1	acyl-CoA thioesterase 11	protein-coding	0.152344	0.774319	
chunk0178_95_1	chr7	30594683	30595316	+	0	NA	exon (NM_002047, exon 1 of 17)	exon (NM_002047, exon 1 of 17)	106	NM_002047	2617	Hs.404321	NM_002047	ENSG00000106105	GARS	CMT2D|DSMAV|GlyRS|HMN5|SMAD1	glycyl-tRNA synthetase	protein-coding	0.107425	0.678233	
chunk0105_127_1	chr2	185582411	185583167	+	0	NA	Intergenic	L1M1|LINE|L1	-155839	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.006614	0.379128	
chunk0123_165_1	chr3	43621254	43621634	+	0	NA	intron (NM_018075, intron 1 of 12)	intron (NM_018075, intron 1 of 12)	624	NM_001204833	55129	Hs.656657	NM_018075	ENSG00000160746	ANO10	SCAR10|TMEM16K	anoctamin 10	protein-coding	0.044737	0.577428	71(CTGTACAGTATGTCCC,-,0.00),72(TGTACAGTATGTCCCA,+,0.00)
chunk0097_410_1	chr2	62590417	62590618	+	0	NA	Intergenic	Tigger20a|DNA|TcMar-Tigger	-83334	NM_001142615	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.004975	0.371287	
chunk0155_129_1	chr5	93240174	93240373	+	0	NA	Intergenic	Intergenic	331070	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.005025	0.410000	
chunk0071_353_1	chr15	88631329	88632000	+	0	NA	3' UTR (NM_022767, exon 4 of 4)	3' UTR (NM_022767, exon 4 of 4)	-3973	NM_001303234	3669	Hs.459265	NM_002201	ENSG00000172183	ISG20	CD25|HEM45	interferon stimulated exonuclease gene 20	protein-coding	0.017884	0.502976	
chunk0044_386_1	chr12	39919082	39919365	+	0	NA	intron (NM_052885, intron 4 of 9)	AluJr|SINE|Alu	186636	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.014134	0.415493	
chunk0011_361_1	chr1	153049765	153049964	+	0	NA	Intergenic	L1PA11|LINE|L1	7648	NM_005988	6700	Hs.355542	NM_005988	ENSG00000241794	SPRR2A	-	small proline rich protein 2A	protein-coding	0.005025	0.550000	
chunk0031_415_1	chr10	132176196	132176509	+	0	NA	intron (NM_001105521, intron 23 of 23)	intron (NM_001105521, intron 23 of 23)	-10558	NM_006426	10570	Hs.100058	NM_006426	ENSG00000151640	DPYSL4	CRMP3|DRP-4|ULIP4	dihydropyrimidinase like 4	protein-coding	0.025559	0.592357	
chunk0114_338_1	chr21	17632249	17632562	+	0	NA	Intergenic	Intergenic	-19455	NM_001130914	10950	Hs.473420	NM_006806	ENSG00000154640	BTG3	ANA|ANA/BTG3|APRO4|TOB5|TOB55|TOFA	BTG anti-proliferation factor 3	protein-coding	0.006390	0.394904	237(TAGAACAGGCTGGTCA,-,0.00)
chunk0020_433_1	chr1	241797668	241798188	+	0	NA	intron (NM_144625, intron 26 of 26)	Tigger19a|DNA|TcMar-Tigger	-50263	NM_130398	9156	Hs.498248	NM_003686	ENSG00000174371	EXO1	HEX1|hExoI	exonuclease 1	protein-coding	0.001923	0.266795	
chunk0051_191_1	chr12	116257253	116257583	+	0	NA	intron (NM_015335, intron 1 of 30)	MLT1J|LTR|ERVL-MaLR	19768	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.006061	0.462236	184(AAGGACGGTGTGTCCT,-,0.00),185(AGGACGGTGTGTCCTT,+,0.00)
chunk0040_382_1	chr11	119362511	119362918	+	0	NA	intron (NM_001243759, intron 1 of 11)	intron (NM_001243759, intron 1 of 11)	1468	NM_171997	9099	Hs.524085	NM_004205	ENSG00000036672	USP2	UBP41|USP9	ubiquitin specific peptidase 2	protein-coding	0.007371	0.517157	119(GGGAACAAAATGTCCC,-,0.00),120(GGAACAAAATGTCCCC,+,0.00)
chunk0180_230_1	chr7	67381047	67381246	+	0	NA	Intergenic	(GTGT)n|Simple_repeat|Simple_repeat	45170	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.010050	0.485000	
chunk0201_173_1	chr9	36190828	36191027	+	0	NA	promoter-TSS (NM_007096)	promoter-TSS (NM_007096)	71	NM_001311205	1211	Hs.522114	NM_001833	ENSG00000122705	CLTA	LCA	clathrin light chain A	protein-coding	0.075377	0.610000	
chunk0201_407_1	chr9	69347317	69348183	+	0	NA	intron (NM_004816, intron 2 of 10)	LTR78|LTR|ERV1	18425	NM_004816	9413	Hs.118003	NM_004816	ENSG00000135063	FAM189A2	C9orf61|X123	family with sequence similarity 189 member A2	protein-coding	0.006928	0.427912	337(GAGGACTTTTTGTACC,-,0.00),338(AGGACTTTTTGTACCT,+,0.00)
chunk0137_281_1	chr4	23632682	23633064	+	0	NA	Intergenic	Intergenic	257204	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.000000	0.347258	
chunk0087_320_1	chr18	39801299	39801725	+	0	NA	Intergenic	Intergenic	-49517	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.046948	0.421546	
chunk0129_345_1	chr3	124841470	124842082	+	0	NA	intron (NM_002213, intron 4 of 14)	intron (NM_002213, intron 4 of 14)	45529	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.006536	0.469821	
chunk0002_443_1	chr1	28259759	28260095	+	0	NA	exon (NM_031459, exon 1 of 10)	exon (NM_031459, exon 1 of 10)	475	NM_031459	83667	Hs.469543	NM_031459	ENSG00000130766	SESN2	HI95|SES2|SEST2	sestrin 2	protein-coding	0.139881	0.721068	
chunk0038_187_1	chr11	86061435	86062091	+	0	NA	intron (NM_001206947, intron 1 of 18)	L1MC1|LINE|L1	7334	NM_001206946	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.015244	0.359209	
chunk0200_69_1	chr9	15870443	15870918	+	0	NA	intron (NM_173550, intron 23 of 25)	intron (NM_173550, intron 23 of 25)	317581	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.000000	0.329832	234(TGGAACATAGAGTCCA,-,0.00),235(GGAACATAGAGTCCAG,+,0.00)
chunk0196_302_1	chr8	109636088	109636576	+	0	NA	intron (NM_001099746, intron 1 of 5)	intron (NM_001099746, intron 1 of 5)	6858	NM_001099756	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.004098	0.396728	
chunk0129_267_1	chr3	122564140	122564747	+	0	NA	promoter-TSS (NM_001146106)	promoter-TSS (NM_001146106)	-96	NM_001146106	83666	Hs.518200	NM_031458	ENSG00000138496	PARP9	ARTD9|BAL|BAL1|MGC:7868	poly(ADP-ribose) polymerase family member 9	protein-coding	0.085667	0.707237	
chunk0056_339_1	chr13	91341608	91342017	+	0	NA	Intergenic	Intergenic	-6008	NR_027349	407975	Hs.24115	NR_027349	ENSG00000215417	MIR17HG	C13orf25|FGLDS2|LINC00048|MIHG1|MIRH1|MIRHG1|NCRNA00048|miR-17-92	miR-17-92a-1 cluster host gene	ncRNA	0.004890	0.370732	
chunk0093_148_1	chr19	46925270	46925581	+	0	NA	intron (NM_004491, intron 1 of 5)	intron (NM_004491, intron 1 of 5)	6749	NM_004491	2909	Hs.509447	NM_004491	ENSG00000160007	ARHGAP35	GRF-1|GRLF1|P190-A|P190A|p190ARhoGAP|p190RhoGAP	Rho GTPase activating protein 35	protein-coding	0.009646	0.477564	
chunk0169_400_1	chr6	108231513	108232215	+	0	NA	intron (NM_001300929, intron 1 of 3)	intron (NM_001300929, intron 1 of 3)	29396	NM_001300928	8724	Hs.12102	NM_003795	ENSG00000112335	SNX3	Grd19|MCOPS8|SDP3	sorting nexin 3	protein-coding	0.005698	0.347084	383(AAGTACAGAATGTTTT,-,0.00),384(AGTACAGAATGTTTTC,+,0.00)
chunk0135_300_1	chr3	189717927	189718622	+	0	NA	intron (NM_001114978, intron 1 of 12)	THE1D|LTR|ERVL-MaLR	-71386	NM_001114981	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.007194	0.415230	
chunk0129_276_1	chr3	123068053	123068363	+	0	NA	intron (NM_006810, intron 1 of 16)	intron (NM_006810, intron 1 of 16)	1199	NR_028444	10954	Hs.477352	NM_006810	ENSG00000065485	PDIA5	PDIR	protein disulfide isomerase family A member 5	protein-coding	0.012903	0.517685	132(GGGAACTTCCTGTTCC,-,0.00),133(GGAACTTCCTGTTCCT,+,0.00)
chunk0008_451_1	chr1	99740291	99740684	+	0	NA	intron (NM_001013660, intron 6 of 16)	intron (NM_001013660, intron 6 of 16)	25306	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.002545	0.375635	
chunk0136_259_1	chr4	10421764	10422156	+	0	NA	Intergenic	MER68|LTR|ERVL	35448	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.005102	0.458015	
chunk0108_160_1	chr2	231159409	231159665	+	0	NA	intron (NR_034059, intron 18 of 23)	MER102b|DNA|hAT-Charlie	-34427	NM_000867	3357	Hs.421649	NM_000867	ENSG00000135914	HTR2B	5-HT(2B)|5-HT-2B|5-HT2B	5-hydroxytryptamine receptor 2B	protein-coding	0.000000	0.408560	
chunk0136_404_1	chr3	197222415	197223081	+	0	NA	intron (NM_004087, intron 4 of 25)	intron (NM_004087, intron 4 of 25)	-38617	NM_001204388	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.009009	0.385307	
chunk0039_271_1	chr11	102411194	102411443	+	0	NA	intron (NM_052932, intron 2 of 4)	MER21C|LTR|ERVL	41726	NM_052932	114908	Hs.503709	NM_052932	ENSG00000152558	TMEM123	KCT3|PORIMIN|PORMIN	transmembrane protein 123	protein-coding	0.020080	0.452000	
chunk0138_82_1	chr4	35458540	35458979	+	0	NA	Intergenic	L1M1|LINE|L1	-785357	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004556	0.302273	
chunk0044_20_1	chr12	27179737	27180224	+	0	NA	Intergenic	Intergenic	-64165	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.002053	0.389344	
chunk0046_296_1	chr12	62192870	62193247	+	0	NA	promoter-TSS (NM_178539)	promoter-TSS (NM_178539)	-219	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.023873	0.370370	
chunk0058_115_1	chr14	22229828	22230254	+	0	NA	Intergenic	Intergenic	359196	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.007042	0.449649	
chunk0018_230_1	chr1	219774334	219774579	+	0	NA	Intergenic	L2a|LINE|L2	154195	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.000000	0.406504	
chunk0182_339_1	chr7	99267886	99268297	+	0	NA	Intergenic	L2a|LINE|L2	-5210	NR_002147	84176	Hs.621401	NR_002147		MYH16	MHC20|MYH16P|MYH5	myosin heavy chain 16 pseudogene	pseudo	0.012165	0.487864	
chunk0006_337_1	chr1	72058176	72058874	+	0	NA	intron (NM_173808, intron 1 of 6)	intron (NM_173808, intron 1 of 6)	-221513	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.002865	0.311874	
chunk0134_315_1	chr3	181590681	181591114	+	0	NA	intron (NR_075092, intron 4 of 6)	L1PA5|LINE|L1	-19437	NR_004053	347689	Hs.654932	NR_004053		SOX2-OT	NCRNA00043|SOX2OT	SOX2 overlapping transcript	ncRNA	0.025404	0.550691	
chunk0103_277_1	chr2	165892044	165892317	+	0	NA	intron (NM_024753, intron 22 of 28)	intron (NM_024753, intron 22 of 28)	-20239	NR_045375	100506124	Hs.709870	NR_045375		LOC100506124	-	uncharacterized LOC100506124	ncRNA	0.003663	0.313869	
chunk0097_330_1	chr2	57499361	57499583	+	0	NA	Intergenic	Intergenic	-408179	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.000000	0.345291	
chunk0103_266_1	chr2	165584065	165584391	+	0	NA	intron (NM_024969, intron 1 of 4)	MER41C|LTR|ERV1	11892	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.009202	0.394495	
chunk0110_105_1	chr20	11907556	11907766	+	0	NA	intron (NM_001282550, intron 1 of 4)	intron (NM_001282550, intron 1 of 4)	-10204	NM_001282551	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.009524	0.464455	
chunk0180_179_1	chr7	65760311	65760902	+	0	NA	intron (NR_003110, intron 9 of 11)	intron (NR_003110, intron 9 of 11)	5080	NR_002961	677807	Hs.675336	NR_002961	ENSG00000206634	SNORA22	ACA22|SNORA22A	small nucleolar RNA, H/ACA box 22	snoRNA	0.011844	0.373311	
chunk0083_193_1	chr17	66525574	66526152	+	0	NA	intron (NM_002737, intron 3 of 16)	intron (NM_002737, intron 3 of 16)	-109009	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.003460	0.364421	303(GGGAACATTCTGTGCA,-,0.00),304(GGAACATTCTGTGCAC,+,0.00)
chunk0091_446_1	chr19	17305327	17305604	+	0	NA	promoter-TSS (NM_023937)	promoter-TSS (NM_023937)	-203	NM_023937	64981	Hs.515242	NM_023937	ENSG00000130312	MRPL34	L34mt	mitochondrial ribosomal protein L34	protein-coding	0.046931	0.640288	
chunk0089_421_1	chr18	69698072	69698479	+	0	NA	intron (NM_152721, intron 4 of 7)	intron (NM_152721, intron 4 of 7)	249578	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.009828	0.365196	
chunk0009_445_1	chr1	111420405	111420628	+	0	NA	intron (NM_002557, intron 8 of 10)	L2a|LINE|L2	7261	NM_002557	5016	Hs.1154	NM_002557	ENSG00000085465	OVGP1	CHIT5|EGP|MUC9|OGP	oviductal glycoprotein 1	protein-coding	0.008969	0.495536	
chunk0114_418_1	chr20	64088725	64088924	+	0	NA	intron (NM_001200019, intron 2 of 5)	intron (NM_001200019, intron 2 of 5)	3808	NM_001200019	4987	Hs.2859	NM_000913	ENSG00000125510	OPRL1	KOR-3|NOCIR|NOP|NOPr|OOR|ORL1	opioid related nociceptin receptor 1	protein-coding	0.000000	0.620000	
chunk0061_394_1	chr14	64602857	64603351	+	0	NA	Intergenic	Intergenic	53202	NM_172365	145376	Hs.144696	NM_172365	ENSG00000165807	PPP1R36	C14orf50	protein phosphatase 1 regulatory subunit 36	protein-coding	0.004049	0.410101	
chunk0020_313_1	chr1	237648367	237648994	+	0	NA	intron (NM_001035, intron 49 of 104)	intron (NM_001035, intron 49 of 104)	177561	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.007974	0.399682	
chunk0165_280_1	chr6	36114890	36115166	+	0	NA	Intergenic	Intergenic	-15456	NR_072996	5603	Hs.178695	NM_002754	ENSG00000156711	MAPK13	MAPK 13|MAPK-13|PRKM13|SAPK4|p38delta	mitogen-activated protein kinase 13	protein-coding	0.014493	0.472924	110(GGGAACAGTGTGTGTC,-,0.00),111(GGAACAGTGTGTGTCT,+,0.00)
chunk0210_348_1	chrX	96179571	96179900	+	0	NA	Intergenic	L1PB4|LINE|L1	158167	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.006079	0.348485	
chunk0013_136_1	chr1	168279202	168279518	+	0	NA	Intergenic	L2b|LINE|L2	-1680	NM_005149	9095	Hs.716656	NM_005149	ENSG00000143178	TBX19	TBS19|TPIT|dJ747L4.1	T-box transcription factor 19	protein-coding	0.003165	0.438486	
chunk0031_335_1	chr10	129502114	129502594	+	0	NA	intron (NM_002412, intron 1 of 4)	MIRb|SINE|MIR	35170	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.018750	0.442827	
chunk0022_86_1	chr10	9150477	9150713	+	0	NA	Intergenic	Intergenic	-125018	NR_108039	100507163	Hs.649223	NR_108039		LINC00709	-	long intergenic non-protein coding RNA 709	ncRNA	0.016949	0.472574	
chunk0050_293_1	chr12	106739274	106739925	+	0	NA	intron (NM_032491, intron 11 of 13)	intron (NM_032491, intron 11 of 13)	-35022	NM_018157	55188	Hs.131306	NM_018157	ENSG00000111785	RIC8B	RIC8|hSyn	RIC8 guanine nucleotide exchange factor B	protein-coding	0.007680	0.386503	
chunk0153_279_1	chr5	73030563	73030872	+	0	NA	intron (NM_001146032, intron 7 of 24)	MER5A|DNA|hAT-Charlie	74736	NM_138782	115548	Hs.165762	NM_138782	ENSG00000157107	FCHO2	-	FCH domain only 2	protein-coding	0.003236	0.409677	
chunk0151_255_1	chr5	52124779	52125214	+	0	NA	Intergenic	L1MC1|LINE|L1	-662944	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.004598	0.291284	
chunk0143_188_1	chr4	112257295	112257626	+	0	NA	intron (NM_001128426, intron 3 of 8)	intron (NM_001128426, intron 3 of 8)	25721	NM_001128426	55435	Hs.435991	NM_018569	ENSG00000138660	AP1AR	2C18|C4orf16|GBAR|PRO0971|gamma-BAR	adaptor related protein complex 1 associated regulatory protein	protein-coding	0.000000	0.286145	
chunk0200_271_1	chr9	22088412	22089136	+	0	NA	intron (NR_003529, intron 12 of 18)	intron (NR_003529, intron 12 of 18)	-79461	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.004144	0.393103	
chunk0122_343_1	chr3	37263000	37263346	+	0	NA	intron (NM_002078, intron 2 of 23)	Tigger3c|DNA|TcMar-Tigger	19982	NM_001172713	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.005780	0.374640	
chunk0148_399_1	chr5	14862336	14863088	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	9066	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.009309	0.413015	
chunk0128_351_1	chr3	112774438	112774847	+	0	NA	Intergenic	L1ME5|LINE|L1	-25323	NR_110017	101929694	Hs.385630	NR_110017	ENSG00000240893	LINC02042	-	long intergenic non-protein coding RNA 2042	ncRNA	0.014670	0.436585	
chunk0010_48_1	chr1	112891065	112891608	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-32014	NR_002796	246182	Hs.647691	NR_002796		AKR7A2P1	AFARP1	aldo-keto reductase family 7 member A2 pseudogene 1	pseudo	0.014733	0.409926	
chunk0177_164_1	chr7	23211574	23212312	+	0	NA	Intergenic	LTR39|LTR|ERV1	30116	NM_007342	11097	Hs.408241	NM_007342	ENSG00000136243	NUP42	CG1|NLP-1|NLP_1|NUPL2|hCG1	nucleoporin 42	protein-coding	0.017615	0.480379	
chunk0088_105_1	chr18	45085465	45085951	+	0	NA	Intergenic	Intergenic	-115542	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.010288	0.400411	
chunk0149_110_1	chr5	19209477	19209827	+	0	NA	Intergenic	MER52A|LTR|ERV1	676620	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.011429	0.589744	
chunk0033_402_1	chr11	24612909	24613289	+	0	NA	intron (NM_001252008, intron 1 of 11)	intron (NM_001252008, intron 1 of 11)	116129	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.364829	
chunk0003_12_1	chr1	28748117	28748654	+	0	NA	intron (NM_016258, intron 4 of 4)	intron (NM_016258, intron 4 of 4)	11445	NM_001172828	51441	Hs.532286	NM_016258	ENSG00000198492	YTHDF2	CAHL|HGRG8|NY-REN-2	YTH N6-methyladenosine RNA binding protein 2	protein-coding	0.001862	0.382900	
chunk0130_444_1	chr3	141276145	141276737	+	0	NA	intron (NM_001282728, intron 3 of 6)	L1ME3G|LINE|L1	44616	NM_001037172	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.016892	0.374368	383(AGGGACATAACGTTCT,-,0.00),384(GGGACATAACGTTCTG,+,0.00)
chunk0005_453_1	chr1	63523165	63523639	+	0	NA	promoter-TSS (NM_001206739)	promoter-TSS (NM_001206739)	101	NM_032437	84455	Hs.652324	NM_032437	ENSG00000203965	EFCAB7	-	EF-hand calcium binding domain 7	protein-coding	0.075949	0.564211	
chunk0167_301_1	chr6	71323266	71323607	+	0	NA	Intergenic	Intergenic	34662	NM_024576	79627	Hs.648434	NM_024576	ENSG00000119900	OGFRL1	dJ331H24.1	opioid growth factor receptor like 1	protein-coding	0.005865	0.289474	
chunk0032_414_1	chr11	12025650	12025859	+	0	NA	Intergenic	MER21C|LTR|ERVL	-16384	NM_013253	27122	Hs.292156	NM_013253	ENSG00000050165	DKK3	REIC|RIG	dickkopf WNT signaling pathway inhibitor 3	protein-coding	0.009569	0.452381	
chunk0058_76_1	chr14	21220445	21221048	+	0	NA	intron (NM_001077442, intron 4 of 7)	intron (NM_001077442, intron 4 of 7)	-13846	NR_038971	283624	Hs.525210	NR_038970	ENSG00000258441	LINC00641	-	long intergenic non-protein coding RNA 641	ncRNA	0.023217	0.425497	
chunk0158_236_1	chr5	129074934	129075328	+	0	NA	Intergenic	Intergenic	-19618	NM_016048	51015	Hs.483296	NM_016048	ENSG00000066583	ISOC1	CGI-111	isochorismatase domain containing 1	protein-coding	0.007614	0.372152	
chunk0126_437_1	chr3	87047995	87048262	+	0	NA	Intergenic	Intergenic	-41152	NR_104153	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.003745	0.335821	
chunk0192_208_1	chr8	64989656	64990200	+	0	NA	Intergenic	Intergenic	190412	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.003676	0.304587	
chunk0147_131_1	chr4	174437154	174437812	+	0	NA	Intergenic	Intergenic	13688	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.003040	0.359636	
chunk0150_152_1	chr5	33748445	33748953	+	0	NA	intron (NM_030955, intron 3 of 23)	intron (NM_030955, intron 3 of 23)	143320	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.003937	0.337917	
chunk0121_389_1	chr3	25262173	25263035	+	0	NA	intron (NM_001290216, intron 1 of 7)	MLT1D|LTR|ERVL-MaLR	-78198	NM_001290300	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.011601	0.412514	688(ATAACATTCTGTGCTT,+,0.00)
chunk0082_422_1	chr17	61360504	61360703	+	0	NA	intron (NM_017679, intron 22 of 23)	MLT1B|LTR|ERVL-MaLR	39003	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.000000	0.485000	6(AGGGCCATGCTGTCCT,-,0.00),7(GGGCCATGCTGTCCTT,+,0.00)
chunk0174_88_1	chr6	156557023	156557752	+	0	NA	Intergenic	Intergenic	-220543	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.015089	0.494521	
chunk0197_158_1	chr8	120480941	120481698	+	0	NA	intron (NM_022045, intron 11 of 21)	L1ME1|LINE|L1	-35912	NM_014078	28998	Hs.333823	NM_014078	ENSG00000172172	MRPL13	L13|L13A|L13mt|RPL13|RPML13	mitochondrial ribosomal protein L13	protein-coding	0.003963	0.353562	
chunk0037_119_1	chr11	72778032	72778237	+	0	NA	intron (NM_006645, intron 2 of 6)	MIR1_Amn|SINE|MIR	-5396	NR_039841	100616410		NR_039841	ENSG00000265064	MIR4692	-	microRNA 4692	ncRNA	0.019512	0.563107	86(GAGAACAACGCGTCCT,-,0.00),87(AGAACAACGCGTCCTC,+,0.00)
chunk0134_435_1	chr3	183635453	183635796	+	0	NA	promoter-TSS (NM_017644)	promoter-TSS (NM_017644)	1	NM_017644	54800	Hs.407709	NM_017644	ENSG00000114796	KLHL24	DRE1|EBSSH|KRIP6	kelch like family member 24	protein-coding	0.096210	0.694767	
chunk0191_167_1	chr8	50115508	50116093	+	0	NA	intron (NM_001287814, intron 1 of 16)	L1MD|LINE|L1	204021	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.010256	0.395904	
chunk0148_77_1	chr5	2550446	2550939	+	0	NA	Intergenic	Intergenic	200963	NM_033267	153572	Hs.282089	NM_033267	ENSG00000170561	IRX2	IRXA2	iroquois homeobox 2	protein-coding	0.012170	0.303644	
chunk0174_27_1	chr6	153602599	153603005	+	0	NA	Intergenic	L1MC4a|LINE|L1	182325	NR_106988									0.007389	0.324324	181(GGGAACACTCTGTACT,-,0.00),182(GGAACACTCTGTACTA,+,0.00)
chunk0098_63_1	chr2	66853096	66853762	+	0	NA	Intergenic	Intergenic	-51007	NR_110169	101060019	Hs.116425	NR_110169	ENSG00000230525	LINC01799	-	long intergenic non-protein coding RNA 1799	ncRNA	0.012012	0.440780	
chunk0156_422_1	chr5	114377854	114378350	+	0	NA	intron (NM_001278204, intron 2 of 6)	intron (NM_001278204, intron 2 of 6)	15783	NM_021614	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.012097	0.418511	
chunk0182_419_1	chr7	101143862	101144130	+	0	NA	Intergenic	AluJb|SINE|Alu	-10409	NM_001283	1174	Hs.489365	NM_001283	ENSG00000106367	AP1S1	AP19|CLAPS1|EKV3|MEDNIK|SIGMA1A	adaptor related protein complex 1 subunit sigma 1	protein-coding	0.033582	0.546468	
chunk0011_318_1	chr1	151960895	151961194	+	0	NA	Intergenic	Intergenic	33194	NM_002966	6281	Hs.143873	NM_002966	ENSG00000197747	S100A10	42C|ANX2L|ANX2LG|CAL1L|CLP11|Ca[1]|GP11|P11|p10	S100 calcium binding protein A10	protein-coding	0.006689	0.366667	
chunk0008_396_1	chr1	97356257	97356706	+	0	NA	intron (NM_000110, intron 16 of 22)	L1MA7|LINE|L1	260558	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.002227	0.340000	
chunk0087_29_1	chr18	31144106	31144848	+	0	NA	intron (NM_024421, intron 7 of 15)	L1MC1|LINE|L1	18379	NM_024421	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.005391	0.345895	
chunk0044_157_1	chr12	29840570	29840904	+	0	NA	Intergenic	L1MA3|LINE|L1	-55978	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.000000	0.510448	
chunk0080_449_1	chr17	36948657	36948943	+	0	NA	promoter-TSS (NM_012138)	promoter-TSS (NM_012138)	-75	NM_012138	26574	Hs.195740	NM_012138	ENSG00000275700	AATF	BFR2|CHE-1|CHE1|DED	apoptosis antagonizing transcription factor	protein-coding	0.125874	0.630662	
chunk0111_202_1	chr20	26142944	26144310	+	0	NA	Intergenic	L1M4b|LINE|L1	-29586	NR_003678	149934	Hs.711274	NM_001039379	ENSG00000240108	NCOR1P1	C20orf191|bB329D4.2	nuclear receptor corepressor 1 pseudogene 1	pseudo	0.002196	0.316752	
chunk0069_393_1	chr15	67750532	67750731	+	0	NA	intron (NM_001206804, intron 19 of 21)	MER5A|DNA|hAT-Charlie	-69073	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.015075	0.435000	
chunk0074_127_1	chr16	22699051	22699429	+	0	NA	Intergenic	L2a|LINE|L2	-115299	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.010582	0.474934	
chunk0085_102_1	chr18	2743497	2744005	+	0	NA	intron (NM_015295, intron 28 of 47)	intron (NM_015295, intron 28 of 47)	87864	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.005906	0.363458	
chunk0118_449_1	chr22	39411447	39412094	+	0	NA	intron (NM_006116, intron 1 of 10)	L1ME1|LINE|L1	12016	NM_153497	10454	Hs.507681	NM_006116	ENSG00000100324	TAB1	3'-Tab1|MAP3K7IP1	TGF-beta activated kinase 1 (MAP3K7) binding protein 1	protein-coding	0.015456	0.399691	
chunk0030_174_1	chr10	114163859	114164072	+	0	NA	intron (NM_018017, intron 1 of 15)	intron (NM_018017, intron 1 of 15)	10214	NR_031747	100302224		NR_031747	ENSG00000284442	MIR2110	hsa-mir-2110|mir-2110	microRNA 2110	ncRNA	0.000000	0.373832	
chunk0203_54_1	chr9	83141720	83142403	+	0	NA	Intergenic	L1M6|LINE|L1	-78933	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002928	0.358187	336(GAGCTCACCATGTCCC,-,0.00),337(AGCTCACCATGTCCCT,+,0.00)
chunk0067_53_1	chr15	40857523	40857834	+	0	NA	TTS (NM_001032367)	TTS (NM_001032367)	13233	NM_001032367	6692	Hs.233950	NM_003710	ENSG00000166145	SPINT1	HAI|HAI1|MANSC2	serine peptidase inhibitor, Kunitz type 1	protein-coding	0.016077	0.592949	
chunk0123_71_1	chr3	41462889	41463282	+	0	NA	intron (NM_017886, intron 33 of 36)	intron (NM_017886, intron 33 of 36)	263634	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005089	0.408629	
chunk0115_96_1	chr21	22516231	22516700	+	0	NA	Intergenic	LTR77|LTR|ERV1	417848	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.006397	0.440426	
chunk0099_311_1	chr2	99420724	99421193	+	0	NA	intron (NM_001037872, intron 11 of 22)	L2|LINE|L2	69060	NM_001037872	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.006397	0.457447	
chunk0043_269_1	chr12	20848055	20848511	+	0	NA	intron (NM_019844, intron 3 of 15)	L1MC2|LINE|L1	37579	NM_019844	28234	Hs.504966	NM_019844	ENSG00000111700	SLCO1B3	HBLRR|LST-2|LST-3TM13|LST3|OATP-8|OATP1B3|OATP8|SLC21A8	solute carrier organic anion transporter family member 1B3	protein-coding	0.000000	0.326039	
chunk0060_469_1	chr14	55332663	55332992	+	0	NA	intron (NM_152231, intron 1 of 1)	intron (NM_152231, intron 1 of 1)	60673	NM_152231	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.012158	0.406061	
chunk0189_89_1	chr8	21359090	21359508	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	61060	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.007177	0.470167	
chunk0194_275_1	chr8	87204326	87204833	+	0	NA	intron (NM_173538, intron 4 of 10)	MLT1J1-int|LTR|ERVL-MaLR	338131	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.000000	0.368110	
chunk0155_244_1	chr5	95719735	95720082	+	0	NA	Intergenic	Intergenic	-11238	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.005764	0.367816	
chunk0070_149_1	chr15	71114293	71114533	+	0	NA	intron (NM_001102658, intron 1 of 3)	intron (NM_001102658, intron 1 of 3)	1087	NM_001102658	196993	Hs.646533	NM_001102658	ENSG00000225362	CT62	-	cancer/testis antigen 62	protein-coding	0.012500	0.514523	
chunk0193_171_1	chr8	74785367	74785956	+	0	NA	Intergenic	MIRb|SINE|MIR	-38876	NM_015886	51050	Hs.98558	NM_015886	ENSG00000137558	PI15	CRISP8|P24TI|P25TI	peptidase inhibitor 15	protein-coding	0.005093	0.330508	
chunk0030_53_1	chr10	111810215	111810962	+	0	NA	Intergenic	Intergenic	373191	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.004016	0.419786	575(GGGCACAGCAAGTGCA,-,0.00)
chunk0033_389_1	chr11	24304462	24304919	+	0	NA	Intergenic	Intergenic	-192280	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.006565	0.371179	
chunk0067_174_1	chr15	44208976	44209501	+	0	NA	Intergenic	(AAGAAA)n|Simple_repeat|Simple_repeat	-13944	NM_032892	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.007619	0.391635	
chunk0191_417_1	chr8	57739241	57739477	+	0	NA	Intergenic	Intergenic	-238999	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.004237	0.354430	
chunk0006_176_1	chr1	66932915	66933530	+	0	NA	intron (NM_001077701, intron 1 of 12)	intron (NM_001077701, intron 1 of 12)	2979	NM_001077704	57708	Hs.605432	NM_020948	ENSG00000198160	MIER1	ER1|MI-ER1	MIER1 transcriptional regulator	protein-coding	0.008130	0.314935	
chunk0172_119_1	chr6	135124303	135124909	+	0	NA	Intergenic	Intergenic	-56709	NM_001161660	4602	Hs.606320	NM_005375	ENSG00000118513	MYB	Cmyb|c-myb|c-myb_CDS|efg	MYB proto-oncogene, transcription factor	protein-coding	0.011551	0.372323	
chunk0020_28_1	chr1	231966670	231966939	+	0	NA	intron (NM_001012957, intron 10 of 12)	intron (NM_001012957, intron 10 of 12)	40970	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.011152	0.374074	
chunk0020_87_1	chr1	232780224	232780823	+	0	NA	Intergenic	LTR105_Mam|LTR|ERVL	-24369	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.018364	0.506667	
chunk0072_122_1	chr15	92527074	92527644	+	0	NA	Intergenic	Intergenic	44904	NR_021493	100144604	Hs.245476	NR_021493	ENSG00000258647	LINC00930	-	long intergenic non-protein coding RNA 930	ncRNA	0.003509	0.471103	234(AGGTACATGGTGTTTT,-,0.00),235(GGTACATGGTGTTTTT,+,0.00)
chunk0139_248_1	chr4	56106753	56106952	+	0	NA	Intergenic	Intergenic	9423	NR_106988									0.010050	0.410000	70(AAGCACACGGCGTACT,-,0.00),71(AGCACACGGCGTACTG,+,0.00)
chunk0016_77_1	chr1	193854907	193855323	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	550370	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.004808	0.342926	
chunk0145_214_1	chr4	148013819	148014291	+	0	NA	intron (NM_024605, intron 18 of 22)	intron (NM_024605, intron 18 of 22)	231460	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.004237	0.376321	
chunk0202_261_1	chr9	76905129	76905378	+	0	NA	intron (NM_015225, intron 1 of 18)	intron (NM_015225, intron 1 of 18)	834	NR_131751	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.012048	0.448000	
chunk0056_169_1	chr13	85184429	85184756	+	0	NA	Intergenic	LTR78B|LTR|ERV1	-36535	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.012232	0.368902	
chunk0060_119_1	chr14	43796408	43797142	+	0	NA	Intergenic	Intergenic	710521	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.008174	0.370068	
chunk0199_350_1	chr9	12216553	12217444	+	0	NA	Intergenic	L1ME2|LINE|L1	-476388	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.005612	0.306054	
chunk0014_289_1	chr1	180630976	180631374	+	0	NA	promoter-TSS (NM_004736)	promoter-TSS (NM_004736)	-835	NM_004736	9213	Hs.227656	NM_004736	ENSG00000143324	XPR1	IBGC6|SLC53A1|SYG1|X3	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.005025	0.498747	188(AGGAACAGTGAGTGCT,-,0.00),189(GGAACAGTGAGTGCTC,+,0.00)
chunk0206_312_1	chr9	125099852	125100427	+	0	NA	intron (NM_173690, intron 2 of 18)	intron (NM_173690, intron 2 of 18)	43420	NM_001144877	286205	Hs.59504	NM_173690	ENSG00000173611	SCAI	C9orf126|NET40	suppressor of cancer cell invasion	protein-coding	0.003478	0.369792	
chunk0162_149_1	chr6	3357240	3357439	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	87674	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.005025	0.390000	
chunk0046_449_1	chr12	64888230	64888641	+	0	NA	intron (NR_033988, intron 1 of 2)	MIR|SINE|MIR	4661	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.004866	0.356796	
chunk0027_61_1	chr10	73082467	73082940	+	0	NA	intron (NM_001142595, intron 1 of 15)	intron (NM_001142595, intron 1 of 15)	14271	NM_001142595	5033	Hs.500047	NM_000917	ENSG00000122884	P4HA1	P4HA	prolyl 4-hydroxylase subunit alpha 1	protein-coding	0.002114	0.358650	
chunk0024_302_1	chr10	42475298	42475497	+	0	NA	promoter-TSS (NR_026827)	promoter-TSS (NR_026827)	-94	NR_026827	84856	Hs.55977	NM_032770	ENSG00000185904	LINC00839	-	long intergenic non-protein coding RNA 839	ncRNA	0.025126	0.530000	
chunk0195_182_1	chr8	96365259	96365843	+	0	NA	Intergenic	MIRb|SINE|MIR	21097	NR_125829	102724804	Hs.571415	NR_125828	ENSG00000253105	LOC102724804	-	uncharacterized LOC102724804	ncRNA	0.006849	0.396581	319(TGGAACACAGTGAGCT,-,0.00),320(GGAACACAGTGAGCTT,+,0.00)
chunk0124_218_1	chr3	56173352	56173551	+	0	NA	exon (NM_015576, exon 4 of 17)	exon (NM_015576, exon 4 of 17)	294912	NR_132749	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.025126	0.460000	
chunk0169_184_1	chr6	102422427	102423071	+	0	NA	Intergenic	L1PA15|LINE|L1	1023764	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.007764	0.356589	
chunk0160_122_1	chr5	150946205	150946888	+	0	NA	promoter-TSS (NR_026867)	promoter-TSS (NR_026867)	38	NR_026867	134466	Hs.661876	NR_026867		ZNF300P1	-	zinc finger protein 300 pseudogene 1	pseudo	0.052709	0.530702	
chunk0075_402_1	chr16	56937960	56938283	+	0	NA	intron (NM_001272103, intron 4 of 7)	intron (NM_001272103, intron 4 of 7)	6031	NM_001272103	9709	Hs.146393	NM_014685	ENSG00000051108	HERPUD1	HERP|Mif1|SUP	homocysteine inducible ER protein with ubiquitin like domain 1	protein-coding	0.003096	0.370370	
chunk0084_427_1	chr17	82568348	82568742	+	0	NA	intron (NM_004514, intron 3 of 8)	intron (NM_004514, intron 3 of 8)	48827	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.017766	0.470886	
chunk0154_398_1	chr5	88386462	88386896	+	0	NA	intron (NR_105019, intron 6 of 7)	intron (NR_105019, intron 6 of 7)	-5516	NR_105020	100505894	Hs.559426	NR_039993	ENSG00000247828	TMEM161B-AS1	linc-POLR3G-8	TMEM161B antisense RNA 1	ncRNA	0.004608	0.363218	
chunk0094_317_1	chr2	8938719	8938918	+	0	NA	intron (NM_138799, intron 3 of 12)	intron (NM_138799, intron 3 of 12)	64929	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.030151	0.525000	
chunk0128_249_1	chr3	108700217	108700592	+	0	NA	Intergenic	L1MA2|LINE|L1	56879	NM_032579	84666	Hs.307047	NM_032579	ENSG00000163515	RETNLB	FIZZ1|FIZZ2|HXCP2|RELM-beta|RELMb|RELMbeta|XCP2	resistin like beta	protein-coding	0.005333	0.329787	
chunk0011_131_1	chr1	147172352	147172786	+	0	NA	promoter-TSS (NM_005399)	promoter-TSS (NM_005399)	20	NR_103870	5565	Hs.50732	NM_005399	ENSG00000131791	PRKAB2	-	protein kinase AMP-activated non-catalytic subunit beta 2	protein-coding	0.096774	0.687356	
chunk0107_63_1	chr2	211604088	211604372	+	0	NA	intron (NM_001042599, intron 19 of 26)	intron (NM_001042599, intron 19 of 26)	822130	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.010563	0.336842	
chunk0043_370_1	chr12	24122937	24123136	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	-89385	NR_030625	100126320		NR_030625	ENSG00000216192	MIR920	MIRN920|hsa-mir-920	microRNA 920	ncRNA	0.005025	0.450000	
chunk0169_55_1	chr6	98014833	98015382	+	0	NA	Intergenic	Intergenic	-9424	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.007286	0.420000	
chunk0178_18_1	chr7	29230610	29231216	+	0	NA	intron (NM_001293072, intron 1 of 12)	intron (NM_001293072, intron 1 of 12)	-21943	NR_120522	102724484	Hs.638665	NR_120522		LOC102724484	-	uncharacterized LOC102724484	ncRNA	0.008251	0.375618	
chunk0101_261_1	chr2	133393021	133393370	+	0	NA	intron (NM_207481, intron 3 of 17)	intron (NM_207481, intron 3 of 17)	127000	NR_110294	101928161	Hs.661917	NR_110294	ENSG00000226953	NCKAP5-AS2	-	NCKAP5 antisense RNA 2	ncRNA	0.005731	0.382857	
chunk0130_301_1	chr3	136958386	136959395	+	0	NA	intron (NM_144717, intron 1 of 6)	intron (NM_144717, intron 1 of 6)	1025	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.004955	0.375248	732(CAGCACATGGTGTCCA,-,0.00),733(AGCACATGGTGTCCAA,+,0.00)
chunk0079_121_1	chr17	12516577	12516783	+	0	NA	Intergenic	Intergenic	-33288	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.000000	0.328502	
chunk0113_190_1	chr20	53378923	53379146	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	-173736	NR_110051	101927770		NR_110051		LOC101927770	-	uncharacterized LOC101927770	ncRNA	0.008969	0.446429	
chunk0084_24_1	chr17	73533110	73533726	+	0	NA	intron (NM_001144952, intron 1 of 44)	intron (NM_001144952, intron 1 of 44)	110670	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.025974	0.635332	
chunk0167_444_1	chr6	75880253	75880606	+	0	NA	intron (NM_001300899, intron 22 of 32)	MER30|DNA|hAT-Charlie	131237	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.002833	0.361582	
chunk0106_446_1	chr2	209278205	209278787	+	0	NA	Intergenic	Intergenic	-145551	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.005155	0.394511	
chunk0073_2_1	chr16	1685822	1686071	+	0	NA	intron (NM_144570, intron 2 of 4)	Charlie4z|DNA|hAT-Charlie	7669	NM_144570	90861	Hs.513261	NM_144570	ENSG00000206053	JPT2	C16orf34|HN1L|L11	Jupiter microtubule associated homolog 2	protein-coding	0.016064	0.448000	
chunk0047_202_1	chr12	71195672	71195909	+	0	NA	Intergenic	Intergenic	-37791	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.012658	0.428571	97(ATGAACACTCTGTCTT,-,0.00),98(TGAACACTCTGTCTTG,+,0.00)
chunk0093_441_1	chr19	58372871	58373356	+	0	NA	intron (NM_138466, intron 1 of 2)	intron (NM_138466, intron 1 of 2)	7909	NR_049780	116412	Hs.222236	NM_138466	ENSG00000152475	ZNF837	-	zinc finger protein 837	protein-coding	0.014433	0.572016	
chunk0008_158_1	chr1	92608629	92609011	+	0	NA	intron (NM_001308248, intron 15 of 18)	MIRb|SINE|MIR	-121944	NM_005263	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.005236	0.360313	
chunk0209_262_1	chrX	46627562	46628347	+	0	NA	intron (NM_001257291, intron 14 of 16)	intron (NM_001257291, intron 14 of 16)	54267	NM_019886	56548	Hs.129955	NM_019886	ENSG00000147119	CHST7	C6ST-2|GST-5	carbohydrate sulfotransferase 7	protein-coding	0.012739	0.449109	
chunk0205_139_1	chr9	108180375	108180954	+	0	NA	Intergenic	Intergenic	675331	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.001727	0.460345	
chunk0161_225_1	chr5	171039524	171040196	+	0	NA	intron (NM_022897, intron 14 of 27)	L1P4|LINE|L1	177978	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.013393	0.377415	
chunk0045_19_1	chr12	43728038	43728392	+	0	NA	TTS (NM_001098615)	TTS (NM_001098615)	30543	NM_001098615	83448	Hs.23554	NM_031292	ENSG00000129317	PUS7L	-	pseudouridine synthase 7 like	protein-coding	0.002825	0.290141	
chunk0149_460_1	chr5	30103049	30103262	+	0	NA	Intergenic	Intergenic	-707179	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004695	0.275701	
chunk0099_138_1	chr2	86512805	86513209	+	0	NA	intron (NR_036454, intron 1 of 3)	L1MC1|LINE|L1	50490	NR_036454	51652	Hs.591582	NM_016079	ENSG00000115561	CHMP3	CGI-149|NEDF|VPS24	charged multivesicular body protein 3	protein-coding	0.007426	0.392593	
chunk0049_151_1	chr12	91931045	91931363	+	0	NA	Intergenic	Intergenic	210509	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.003145	0.404389	
chunk0078_405_1	chr16	88770320	88770550	+	0	NA	intron (NM_001142864, intron 1 of 50)	intron (NM_001142864, intron 1 of 50)	14785	NM_001142864	9780	Hs.377001	NM_001142864	ENSG00000103335	PIEZO1	DHS|FAM38A|LMPH3|LMPHM6|Mib	piezo type mechanosensitive ion channel component 1	protein-coding	0.047826	0.658009	
chunk0029_199_1	chr10	101588247	101588563	+	0	NA	promoter-TSS (NM_001174085)	promoter-TSS (NM_001174085)	73	NM_015448	25911	Hs.658128	NM_015448	ENSG00000166171	DPCD	-	deleted in primary ciliary dyskinesia homolog (mouse)	protein-coding	0.060127	0.634069	
chunk0082_288_1	chr17	58219702	58220243	+	0	NA	promoter-TSS (NM_001165927)	promoter-TSS (NM_001165927)	-367	NM_001165927	54903	Hs.408843	NM_017777	ENSG00000011143	MKS1	BBS13|JBTS28|MES|MKS|POC12	MKS transition zone complex subunit 1	protein-coding	0.012939	0.409594	265(AAGGACATGCTGTAAC,-,0.00)
chunk0183_384_1	chr7	109964169	109964796	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-4269	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.007974	0.337580	
chunk0146_179_1	chr4	160755754	160756225	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-1266744	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.002123	0.415254	253(AAGAACATGATGTTCT,-,0.00),254(AGAACATGATGTTCTG,+,0.00)
chunk0115_37_1	chr21	21077484	21077722	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	79288	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.004202	0.284519	
chunk0198_223_1	chr8	134000118	134000317	+	0	NA	Intergenic	L2c|LINE|L2	113721	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.005025	0.445000	
chunk0121_402_1	chr3	25492198	25492584	+	0	NA	intron (NM_001290216, intron 2 of 7)	intron (NM_001290216, intron 2 of 7)	34081	NM_001290217	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.005181	0.369509	201(AAGAACATTGTGAACT,-,0.00),202(AGAACATTGTGAACTG,+,0.00)
chunk0177_414_1	chr7	27657226	27657579	+	0	NA	intron (NM_152740, intron 1 of 7)	intron (NM_152740, intron 1 of 7)	5599	NM_152740	11112	Hs.406758	NM_152740	ENSG00000106049	HIBADH	NS5ATP1	3-hydroxyisobutyrate dehydrogenase	protein-coding	0.000000	0.384181	
chunk0064_26_1	chr14	89424121	89424382	+	0	NA	intron (NM_001085471, intron 1 of 6)	intron (NM_001085471, intron 1 of 6)	6897	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.007663	0.385496	
chunk0185_231_1	chr7	129348026	129348415	+	0	NA	intron (NM_001130720, intron 1 of 16)	L1ME4b|LINE|L1	-19903	NM_001130723	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.002571	0.356410	
chunk0181_327_1	chr7	87937557	87938171	+	0	NA	intron (NM_021721, intron 2 of 27)	intron (NM_021721, intron 2 of 27)	3613	NM_021721	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.001629	0.367480	
chunk0028_310_1	chr10	91709356	91709589	+	0	NA	Intergenic	Intergenic	-76371	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.000000	0.324786	
chunk0142_293_1	chr4	100206028	100206227	+	0	NA	intron (NR_125924, intron 4 of 4)	MER57B2|LTR|ERV1	-15629	NM_145244	115265	Hs.480378	NM_145244	ENSG00000145358	DDIT4L	REDD2|Rtp801L	DNA damage inducible transcript 4 like	protein-coding	0.015075	0.395000	
chunk0078_103_1	chr17	2336466	2336667	+	0	NA	promoter-TSS (NM_014853)	promoter-TSS (NM_014853)	818	NM_018128	55720	Hs.388170	NM_018128	ENSG00000167721	TSR1	-	TSR1 ribosome maturation factor	protein-coding	0.089552	0.663366	
chunk0183_258_1	chr7	107234904	107235338	+	0	NA	intron (NM_006348, intron 18 of 21)	intron (NM_006348, intron 18 of 21)	66106	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.004608	0.372414	
chunk0082_354_1	chr17	60062343	60062647	+	0	NA	intron (NM_022070, intron 9 of 19)	intron (NM_022070, intron 9 of 19)	16436	NM_022070	63897	Hs.221899	NM_022070	ENSG00000068097	HEATR6	ABC1	HEAT repeat containing 6	protein-coding	0.003289	0.380328	
chunk0179_339_1	chr7	50718895	50719281	+	0	NA	intron (NM_001001555, intron 2 of 16)	L2a|LINE|L2	13265	NM_005311	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.005181	0.421189	
chunk0144_43_1	chr4	125992565	125993211	+	0	NA	Intergenic	Intergenic	485629	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.006192	0.307573	
chunk0102_399_1	chr2	154900917	154901583	+	0	NA	Intergenic	Intergenic	202669	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.004505	0.322339	
chunk0137_128_1	chr4	15032810	15033009	+	0	NA	intron (NR_125911, intron 2 of 5)	intron (NR_125911, intron 2 of 5)	30235	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.000000	0.240000	
chunk0088_416_1	chr18	54825962	54826499	+	0	NA	Intergenic	Intergenic	-2247	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.001862	0.366171	
chunk0156_428_1	chr5	114486466	114486745	+	0	NA	intron (NR_130785, intron 5 of 12)	intron (NR_130785, intron 5 of 12)	53075	NM_170775	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.010753	0.407143	
chunk0011_312_1	chr1	151909398	151909777	+	0	NA	5' UTR (NM_053055, exon 1 of 6)	5' UTR (NM_053055, exon 1 of 6)	298	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.108179	0.705263	
chunk0082_428_1	chr17	61431725	61432441	+	0	NA	Intergenic	Tigger4|DNA|TcMar-Tigger	20332	NM_203425	388407	Hs.434459	NM_203425		C17orf82	-	chromosome 17 open reading frame 82	ncRNA	0.012570	0.426778	
chunk0036_234_1	chr11	64219037	64219241	+	0	NA	intron (NM_178443, intron 6 of 14)	intron (NM_178443, intron 6 of 14)	6730	NM_001160393	83707	Hs.326586	NM_031472	ENSG00000149743	TRPT1	-	tRNA phosphotransferase 1	protein-coding	0.009804	0.643902	
chunk0152_397_1	chr5	64818189	64819170	+	0	NA	intron (NM_001297644, intron 10 of 12)	intron (NM_001297644, intron 10 of 12)	49761	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.005097	0.316701	739(TAGAACAAAATGTGCT,-,0.00),740(AGAACAAAATGTGCTT,+,0.00)
chunk0104_101_1	chr2	172459631	172459982	+	0	NA	intron (NM_000210, intron 1 of 25)	HAL1|LINE|L1	32251	NM_001079818	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.008547	0.448864	
chunk0066_295_1	chr15	35510942	35511660	+	0	NA	intron (NM_080650, intron 3 of 8)	intron (NM_080650, intron 3 of 8)	-34894	NR_038251	100507466	Hs.536420	NR_038251	ENSG00000248079	DPH6-DT	ATPBD4-AS1|DPH6-AS1	DPH6 divergent transcript	ncRNA	0.006964	0.365786	305(CAGAACAACCAGTGCT,-,0.00),306(AGAACAACCAGTGCTC,+,0.00)
chunk0093_19_1	chr2	255989	256486	+	0	NA	5' UTR (NM_001282687, exon 1 of 12)	5' UTR (NM_001282687, exon 1 of 12)	103	NM_001282687	26751	Hs.515951	NM_015677	ENSG00000035115	SH3YL1	RAY	SH3 and SYLF domain containing 1	protein-coding	0.008048	0.437751	299(TAGCACAATTTGTCCT,-,0.00),300(AGCACAATTTGTCCTT,+,0.00)
chunk0197_152_1	chr8	120431503	120431702	+	0	NA	intron (NM_014078, intron 3 of 6)	L3|LINE|CR1	-13796	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.005025	0.365000	
chunk0020_247_1	chr1	236038096	236038357	+	0	NA	exon (NM_002508, exon 5 of 20)	exon (NM_002508, exon 5 of 20)	26955	NM_002508	4811	Hs.356624	NM_002508	ENSG00000116962	NID1	NID	nidogen 1	protein-coding	0.038314	0.545802	
chunk0156_354_1	chr5	112329916	112330225	+	0	NA	intron (NM_022140, intron 1 of 22)	MIRc|SINE|MIR	89243	NM_022140	64097	Hs.584954	NM_022140	ENSG00000129595	EPB41L4A	EPB41L4|NBL4	erythrocyte membrane protein band 4.1 like 4A	protein-coding	0.009709	0.416129	
chunk0150_158_1	chr5	33990642	33991242	+	0	NA	intron (NM_014324, intron 4 of 4)	intron (NM_014324, intron 4 of 4)	-6267	NM_001012509	51151	Hs.278962	NM_016180	ENSG00000164175	SLC45A2	1A1|AIM1|MATP|OCA4|SHEP5	solute carrier family 45 member 2	protein-coding	0.001667	0.369384	
chunk0199_201_1	chr9	4866120	4866807	+	0	NA	Intergenic	Intergenic	16166	NR_029836	406894		NR_029836	ENSG00000199065	MIR101-2	MIRN101-2|mir-101-2	microRNA 101-2	ncRNA	0.007278	0.434593	349(GAGGTCAAACTGTCCC,-,0.00),413(GAGTTCACCGTGTTCC,-,0.00),414(AGTTCACCGTGTTCCA,+,0.00)
chunk0211_176_1	chrX	116472628	116472896	+	0	NA	Intergenic	L1MA2|LINE|L1	-9729	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.000000	0.334572	
chunk0211_167_1	chrX	115236597	115237136	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	-2794	NM_001243963	57631	Hs.65366	NM_020871	ENSG00000130224	LRCH2	dA204F4.4	leucine rich repeats and calponin homology domain containing 2	protein-coding	0.003711	0.344444	273(AAGTACAGGATGTTCT,-,0.00),274(AGTACAGGATGTTCTT,+,0.00)
chunk0200_464_1	chr9	31908142	31908760	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-476152	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.004854	0.436187	
chunk0045_441_1	chr12	53575921	53576120	+	0	NA	intron (NM_006856, intron 2 of 11)	intron (NM_006856, intron 2 of 11)	49976	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.000000	0.465000	
chunk0020_365_1	chr1	239719194	239719922	+	0	NA	promoter-TSS (NR_103776)	promoter-TSS (NR_103776)	-439	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.013736	0.414266	
chunk0201_77_1	chr9	34425527	34426172	+	0	NA	intron (NM_001184942, intron 1 of 5)	intron (NM_001184942, intron 1 of 5)	-27998	NM_032596	84688	Hs.50334	NM_032596	ENSG00000164972	C9orf24	CBE1|NYD-SP22|SMRP1|bA573M23.4	chromosome 9 open reading frame 24	protein-coding	0.003101	0.417957	296(AAGAACAGCCTGTGCT,-,0.00),297(AGAACAGCCTGTGCTT,+,0.00)
chunk0080_400_1	chr17	35257296	35257720	+	0	NA	intron (NM_144975, intron 1 of 4)	intron (NM_144975, intron 1 of 4)	14441	NM_144975	162394	Hs.585792	NM_144975	ENSG00000166750	SLFN5	-	schlafen family member 5	protein-coding	0.007075	0.423529	
chunk0110_416_1	chr20	20593677	20593876	+	0	NA	intron (NM_020343, intron 16 of 39)	intron (NM_020343, intron 16 of 39)	118847	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.015075	0.480000	
chunk0100_290_1	chr2	114754665	114755489	+	0	NA	intron (NM_001178036, intron 2 of 26)	intron (NM_001178036, intron 2 of 26)	78471	NR_132105	101927591	Hs.553019	NR_132105	ENSG00000231538	DPP10-AS3	-	DPP10 antisense RNA 3	ncRNA	0.006068	0.367273	
chunk0073_195_1	chr16	9061513	9061866	+	0	NA	Intergenic	Intergenic	-29991	NM_014117	29035	Hs.221497	NM_014117	ENSG00000182831	C16orf72	PRO0149	chromosome 16 open reading frame 72	protein-coding	0.008499	0.426554	
chunk0085_108_1	chr18	2766580	2766878	+	0	NA	intron (NM_015295, intron 37 of 47)	intron (NM_015295, intron 37 of 47)	-80301	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.003356	0.337793	
chunk0143_182_1	chr4	112175928	112176191	+	0	NA	intron (NM_152400, intron 1 of 1)	intron (NM_152400, intron 1 of 1)	30662	NM_152400	132720	Hs.23439	NM_152400	ENSG00000174749	FAM241A	C4orf32	family with sequence similarity 241 member A	protein-coding	0.011407	0.348485	179(GTGCACAAATTGTTCT,-,0.00),180(TGCACAAATTGTTCTG,+,0.00)
chunk0084_287_1	chr17	79908215	79908515	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-10992	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.026667	0.508306	120(GGGACACTGTGCTCAT,+,0.00)
chunk0120_203_1	chr3	7280521	7280759	+	0	NA	intron (NM_000844, intron 2 of 9)	MIR|SINE|MIR	254644	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.021008	0.372385	
chunk0201_399_1	chr9	69169065	69169309	+	0	NA	intron (NM_001170414, intron 2 of 21)	L2c|LINE|L2	-4868	NM_004817	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.016393	0.412245	
chunk0097_293_1	chr2	55516632	55517069	+	0	NA	Intergenic	Intergenic	-2745	NM_080667	112942	Hs.264208	NM_080667	ENSG00000163001	CFAP36	BARTL1|CCDC104	cilia and flagella associated protein 36	protein-coding	0.009153	0.353881	
chunk0210_342_1	chrX	95841996	95842441	+	0	NA	Intergenic	Intergenic	495684	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.000000	0.381166	
chunk0157_220_1	chr5	119365483	119365846	+	0	NA	intron (NM_001286813, intron 2 of 2)	intron (NM_001286813, intron 2 of 2)	9844	NM_014350	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.002755	0.359890	189(GTGCACTGAGTGTTCT,-,0.00),190(TGCACTGAGTGTTCTT,+,0.00)
chunk0114_412_1	chr20	63912175	63912654	+	0	NA	intron (NM_025219, intron 1 of 4)	intron (NM_025219, intron 1 of 4)	-7035	NR_030637	100126329		NR_030637	ENSG00000283206	MIR941-1	MIRN941-1|mir-941-1	microRNA 941-1	ncRNA	0.022965	0.454167	
chunk0077_241_1	chr16	80708620	80709475	+	0	NA	intron (NM_152342, intron 1 of 6)	intron (NM_152342, intron 1 of 6)	95231	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.017544	0.407710	178(AGTTCAGGTTGTTCTC,+,0.00)
chunk0212_208_1	chrX	135079306	135080186	+	0	NA	Intergenic	MIRb|SINE|MIR	18888	NR_024493									0.002273	0.377980	313(CAATACACTGTGTTCT,-,0.00),314(AATACACTGTGTTCTT,+,0.00)
chunk0050_330_1	chr12	107288523	107289227	+	0	NA	Intergenic	MIRc|SINE|MIR	-29545	NM_001018072	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.021307	0.458156	
chunk0014_429_1	chr1	183480496	183480931	+	0	NA	intron (NM_001174061, intron 1 of 21)	L2c|LINE|L2	8342	NM_201569	9887	Hs.591463	NM_014837	ENSG00000116698	SMG7	C1orf16|EST1C|SGA56M	SMG7 nonsense mediated mRNA decay factor	protein-coding	0.002299	0.410550	
chunk0194_98_1	chr8	83314180	83314479	+	0	NA	Intergenic	MER83|LTR|ERV1	-89429	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.000000	0.386667	
chunk0178_147_1	chr7	33255154	33255639	+	0	NA	intron (NM_014451, intron 5 of 20)	L1MA9|LINE|L1	125856	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.004124	0.339506	245(TGAAGAGACTGTTCTT,+,0.00)
chunk0212_329_1	chrX	144275762	144276319	+	0	NA	Intergenic	Intergenic	391969	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.005386	0.360215	278(TTGGACACACTGTTCC,-,0.00),279(TGGACACACTGTTCCT,+,0.00)
chunk0130_250_1	chr3	135686307	135686521	+	0	NA	Intergenic	L2b|LINE|L2	-279259	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.004673	0.539535	
chunk0190_348_1	chr8	39282601	39282897	+	0	NA	intron (NM_001313994, intron 20 of 21)	intron (NM_001313994, intron 20 of 21)	-31914	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.003378	0.319865	
chunk0052_239_1	chr13	25963556	25963963	+	0	NA	intron (NM_001313741, intron 33 of 35)	intron (NM_001313741, intron 33 of 35)	87301	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.002457	0.338235	
chunk0015_391_1	chr1	190735642	190735943	+	0	NA	intron (NR_033922, intron 1 of 4)	intron (NR_033922, intron 1 of 4)	110902	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.000000	0.201987	
chunk0206_131_1	chr9	121009126	121009325	+	0	NA	intron (NM_001735, intron 17 of 40)	intron (NM_001735, intron 17 of 40)	41051	NM_001735	727	Hs.494997	NM_001735	ENSG00000106804	C5	C5D|C5a|C5b|CPAMD4|ECLZB	complement C5	protein-coding	0.000000	0.290000	
chunk0112_176_1	chr20	39948571	39949017	+	0	NA	Intergenic	Intergenic	-55667	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.004484	0.398210	240(ATGGTCAGCATGTTCC,-,0.00),241(TGGTCAGCATGTTCCT,+,0.00)
chunk0033_408_1	chr11	24742703	24742902	+	0	NA	intron (NM_001009909, intron 4 of 11)	L1PB1|LINE|L1	245832	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.010050	0.330000	
chunk0019_35_1	chr1	223886414	223887071	+	0	NA	Intergenic	Intergenic	-40770	NM_005426	7159	Hs.523968	NM_005426	ENSG00000143514	TP53BP2	53BP2|ASPP2|BBP|P53BP2|PPP1R13A	tumor protein p53 binding protein 2	protein-coding	0.009132	0.455927	
chunk0067_211_1	chr15	45037108	45037634	+	0	NA	intron (NR_034039, intron 1 of 8)	intron (NR_034039, intron 1 of 8)	14267	NR_034039	6652	Hs.878	NM_003104	ENSG00000140263	SORD	HEL-S-95n|RDH|SDH|SORD1|XDH	sorbitol dehydrogenase	protein-coding	0.011407	0.457306	
chunk0157_342_1	chr5	122607065	122607276	+	0	NA	Intergenic	L1M5|LINE|L1	123390	NR_109881	101927379	Hs.536399	NR_109881	ENSG00000251538	LINC02201	-	long intergenic non-protein coding RNA 2201	ncRNA	0.009479	0.367925	
chunk0210_220_1	chrX	82315811	82316418	+	0	NA	Intergenic	L1MD|LINE|L1	-1114172	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.001647	0.274671	
chunk0112_167_1	chr20	39855284	39855948	+	0	NA	Intergenic	L1MB1|LINE|L1	-148845	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.006024	0.387970	
chunk0132_359_1	chr3	161576772	161577141	+	0	NA	Intergenic	Intergenic	80148	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.018970	0.424324	
chunk0079_297_1	chr17	17008782	17008981	+	0	NA	Intergenic	Intergenic	-33879	NM_201274	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.015075	0.555000	
chunk0145_171_1	chr4	147326418	147326865	+	0	NA	Intergenic	Intergenic	18076	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.004474	0.334821	
chunk0098_326_1	chr2	76821746	76822465	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-163860	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.005563	0.316667	415(TGAACAGCACGTGCCT,+,0.00)
chunk0102_77_1	chr2	143165408	143165628	+	0	NA	intron (NM_018460, intron 2 of 13)	intron (NM_018460, intron 2 of 13)	36188	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.004545	0.380090	
chunk0168_117_1	chr6	81946172	81946463	+	0	NA	Intergenic	Intergenic	-132125	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.000000	0.315068	
chunk0186_239_1	chr7	140858866	140859099	+	0	NA	intron (NM_004333, intron 1 of 17)	L1ME3Cz|LINE|L1	65782	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.000000	0.303419	
chunk0133_56_1	chr3	166755326	166755699	+	0	NA	Intergenic	L1MCa|LINE|L1	624771	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.002681	0.286096	
chunk0042_396_1	chr12	11130708	11130907	+	0	NA	intron (NM_001316893, intron 1 of 4)	intron (NM_001316893, intron 1 of 4)	3437	NM_001097643	259293	Hs.679464	NM_001097643	ENSG00000256188	TAS2R30	T2R30|T2R47|TAS2R47	taste 2 receptor member 30	protein-coding	0.005025	0.460000	
chunk0188_447_1	chr8	19323804	19324031	+	0	NA	intron (NM_001174159, intron 2 of 9)	MIRb|SINE|MIR	9941	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.008811	0.416667	
chunk0209_268_1	chrX	46739622	46740469	+	0	NA	intron (NM_001257291, intron 1 of 16)	intron (NM_001257291, intron 1 of 16)	19127	NM_032591	84679	Hs.91389	NM_032591	ENSG00000065923	SLC9A7	MRX108|NHE-7|NHE7|SLC9A6	solute carrier family 9 member A7	protein-coding	0.003542	0.373821	
chunk0163_439_1	chr6	17412058	17412360	+	0	NA	intron (NM_006366, intron 1 of 12)	intron (NM_006366, intron 1 of 12)	18704	NM_006366	10486	Hs.132902	NM_006366	ENSG00000112186	CAP2	-	cyclase associated actin cytoskeleton regulatory protein 2	protein-coding	0.009934	0.544554	
chunk0103_84_1	chr2	160611173	160611577	+	0	NA	Intergenic	Intergenic	-117568	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.002475	0.397531	
chunk0084_90_1	chr17	75228343	75228598	+	0	NA	intron (NM_024844, intron 11 of 18)	intron (NM_024844, intron 11 of 18)	23020	NM_001303276	79902	Hs.362817	NM_024844	ENSG00000125450	NUP85	FROUNT|NPHS17|Nup75	nucleoporin 85	protein-coding	0.003922	0.488281	
chunk0132_241_1	chr3	158680658	158681865	+	0	NA	intron (NM_001308164, intron 14 of 18)	intron (NM_001308164, intron 14 of 18)	-8568	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.006628	0.343543	993(AAGAACACTGTGTTCC,-,0.00),994(AGAACACTGTGTTCCA,+,0.00)
chunk0147_312_1	chr4	184907855	184908228	+	0	NA	Intergenic	Intergenic	-8580	NR_039976	100506229	Hs.378150	NR_039975		LINC01093	-	long intergenic non-protein coding RNA 1093	ncRNA	0.000000	0.443850	207(GAGGACATTATGTCCT,-,0.00),208(AGGACATTATGTCCTC,+,0.00)
chunk0144_60_1	chr4	127004336	127004535	+	0	NA	Intergenic	Intergenic	-628497	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.000000	0.300000	
chunk0194_207_1	chr8	85865469	85866652	+	0	NA	Intergenic	Intergenic	-38118	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.005917	0.357264	879(AGGAGCAGGATGTTCT,-,0.00),880(GGAGCAGGATGTTCTG,+,0.00)
chunk0120_216_1	chr3	7433097	7433547	+	0	NA	intron (NM_000844, intron 5 of 9)	ERVL-E-int|LTR|ERVL	101962	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.006667	0.416851	235(CAGAGCTCCGTGTTCT,-,0.00),236(AGAGCTCCGTGTTCTT,+,0.00)
chunk0047_329_1	chr12	74366734	74367327	+	0	NA	Intergenic	L1MC3|LINE|L1	-74399	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.003373	0.301347	
chunk0150_396_1	chr5	39808336	39808554	+	0	NA	Intergenic	MLT1B-int|LTR|ERVL-MaLR	-243846	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.000000	0.397260	
chunk0114_162_1	chr21	10745798	10746037	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	224403	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.004184	0.366667	
chunk0109_107_1	chr20	2452362	2453113	+	0	NA	Intergenic	L2a|LINE|L2	10310	NR_003684	100113378		NR_003684		SNORD119	-	small nucleolar RNA, C/D box 119	snoRNA	0.009321	0.394947	
chunk0156_282_1	chr5	109912151	109912531	+	0	NA	Intergenic	Intergenic	29159	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.002632	0.433071	
chunk0151_93_1	chr5	42891680	42892098	+	0	NA	Intergenic	Intergenic	-79967	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.004785	0.424821	155(AAGTACAGTTAGTGCT,-,0.00),156(AGTACAGTTAGTGCTG,+,0.00)
chunk0022_375_1	chr10	17545792	17545991	+	0	NA	Intergenic	L1MB1|LINE|L1	71483	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.010050	0.400000	
chunk0128_200_1	chr3	107713413	107713748	+	0	NA	intron (NM_001276286, intron 4 of 16)	intron (NM_001276286, intron 4 of 16)	164488	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.008955	0.309524	
chunk0138_253_1	chr4	39854403	39855003	+	0	NA	intron (NM_001100399, intron 26 of 32)	L2c|LINE|L2	123253	NM_001100399	23244	Hs.331431	NM_015200	ENSG00000121892	PDS5A	PIG54|SCC-112|SCC112	PDS5 cohesin associated factor A	protein-coding	0.005000	0.329451	
chunk0065_134_1	chr15	24961928	24962414	+	0	NA	exon (NM_022804, exon 2 of 4)	exon (NM_022804, exon 2 of 4)	7183	NM_003097	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.008230	0.332649	212(CAGAACAGCACGTACC,-,0.00),213(AGAACAGCACGTACCA,+,0.00),284(GAGTACAGACTGTGTT,-,0.00),285(AGTACAGACTGTGTTG,+,0.00)
chunk0082_282_1	chr17	58079107	58079888	+	0	NA	non-coding (NR_110809, exon 2 of 3)	non-coding (NR_110809, exon 2 of 3)	3707	NR_110809	101927666	Hs.552237	NR_110809	ENSG00000266290	LOC101927666	-	uncharacterized LOC101927666	ncRNA	0.006402	0.456522	
chunk0001_144_1	chr1	5975162	5975461	+	0	NA	intron (NM_001291594, intron 1 of 25)	intron (NM_001291594, intron 1 of 25)	-16987	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.010033	0.523333	137(CAGAACACGCTGCTCA,-,0.00),138(AGAACACGCTGCTCAA,+,0.00)
chunk0142_330_1	chr4	101199013	101199230	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	41751	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.004608	0.389908	
chunk0099_132_1	chr2	86254878	86255182	+	0	NA	intron (NM_001164731, intron 2 of 5)	intron (NM_001164731, intron 2 of 5)	55597	NM_016622	51318	Hs.433439	NM_016622	ENSG00000132313	MRPL35	L35mt|MRP-L35	mitochondrial ribosomal protein L35	protein-coding	0.016447	0.554098	
chunk0112_417_1	chr20	47318511	47319207	+	0	NA	non-coding (NR_024594, exon 1 of 1)	non-coding (NR_024594, exon 1 of 1)	357	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.030172	0.545194	374(AGGAACATCAAGTACC,-,0.00),375(GGAACATCAAGTACCT,+,0.00)
chunk0162_100_1	chr6	2478141	2478400	+	0	NA	Intergenic	Intergenic	156333	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.030888	0.550000	
chunk0046_400_1	chr12	64069035	64069449	+	0	NA	intron (NM_020762, intron 8 of 21)	MER102c|DNA|hAT-Charlie	153054	NM_001300941	144577	Hs.444671	NM_152440	ENSG00000174206	C12orf66	-	chromosome 12 open reading frame 66	protein-coding	0.004831	0.354217	
chunk0074_291_1	chr16	29789893	29790773	+	0	NA	promoter-TSS (NM_001256269)	promoter-TSS (NM_001256269)	-380	NM_007317	3835	Hs.612151	NM_007317	ENSG00000079616	KIF22	A-328A3.2|KID|KNSL4|OBP|OBP-1|OBP-2|SEMDJL2	kinesin family member 22	protein-coding	0.070455	0.620885	
chunk0094_243_1	chr2	7057684	7058105	+	0	NA	Intergenic	Intergenic	19986	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.002375	0.357820	
chunk0045_304_1	chr12	50612914	50613200	+	0	NA	intron (NM_173602, intron 1 of 37)	intron (NM_173602, intron 1 of 37)	108072	NM_173602	57609	Hs.505516	NM_020849	ENSG00000066084	DIP2B	-	disco interacting protein 2 homolog B	protein-coding	0.010490	0.487805	49(AAAAACATTCTGTTCT,-,0.00),50(AAAACATTCTGTTCTC,+,0.00),93(TAGCACAGCATGTGCC,-,0.00),94(AGCACAGCATGTGCCT,+,0.00)
chunk0072_128_1	chr15	92617633	92617935	+	0	NA	3' UTR (NM_207446, exon 3 of 3)	3' UTR (NM_207446, exon 3 of 3)	38017	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.039735	0.600660	
chunk0187_271_1	chr7	155252781	155253178	+	0	NA	Intergenic	Intergenic	-44797	NM_198337	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.025189	0.505025	
chunk0005_155_1	chr1	58184440	58184651	+	0	NA	intron (NM_021080, intron 1 of 16)	intron (NM_021080, intron 1 of 16)	65994	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.004739	0.363208	
chunk0184_75_1	chr7	112692161	112692433	+	0	NA	intron (NR_110158, intron 5 of 7)	L1MC5|LINE|L1	69916	NR_110158	101928012	Hs.521131	NR_110158	ENSG00000223646	LOC101928012	-	uncharacterized LOC101928012	ncRNA	0.000000	0.336996	
chunk0010_22_1	chr1	112435508	112435942	+	0	NA	intron (NM_018704, intron 3 of 5)	intron (NM_018704, intron 3 of 5)	26108	NR_036210	100422976		NR_036210	ENSG00000283296	MIR4256	-	microRNA 4256	ncRNA	0.006912	0.301149	114(AGGAACAATTTGTTCT,-,0.00),115(GGAACAATTTGTTCTT,+,0.00)
chunk0088_403_1	chr18	54612197	54612770	+	0	NA	Intergenic	Intergenic	21324	NM_173629	284254	Hs.376146	NM_173629	ENSG00000178690	DYNAP	C18orf26	dynactin associated protein	protein-coding	0.006981	0.425087	
chunk0108_4_1	chr2	225930567	225931190	+	0	NA	Intergenic	Intergenic	-211916	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003210	0.328526	91(CAGCACTTTTTGTGCC,-,0.00)
chunk0088_166_1	chr18	46831141	46831600	+	0	NA	intron (NM_004671, intron 9 of 13)	L1ME1|LINE|L1	-74201	NM_013305	29906	Hs.465025	NM_013305	ENSG00000101638	ST8SIA5	SIAT8-E|SIAT8E|ST8SiaV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding	0.000000	0.310870	
chunk0169_296_1	chr6	105983845	105984119	+	0	NA	Intergenic	MIRb|SINE|MIR	-102338	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.000000	0.327273	
chunk0038_192_1	chr11	86080330	86081095	+	0	NA	Intergenic	L1MC1|LINE|L1	-10831	NM_001206947	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.011765	0.404700	
chunk0124_212_1	chr3	56059719	56060206	+	0	NA	intron (NR_132749, intron 7 of 17)	LTR37A|LTR|ERV1	-207368	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.004107	0.334016	
chunk0107_326_1	chr2	220310021	220310468	+	0	NA	Intergenic	Intergenic	-403679	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.000000	0.308036	
chunk0166_324_1	chr6	49834869	49835162	+	0	NA	3' UTR (NM_001131, exon 8 of 8)	3' UTR (NM_001131, exon 8 of 8)	-10249	NR_110843	101927048	Hs.742154	NR_110843		LOC101927048	-	uncharacterized LOC101927048	ncRNA	0.003413	0.353741	
chunk0154_392_1	chr5	88175220	88175562	+	0	NA	Intergenic	L1MC3|LINE|L1	93488	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.011696	0.422741	142(TGGCACAAGATGTTCC,-,0.00),143(GGCACAAGATGTTCCA,+,0.00)
chunk0075_408_1	chr16	57179175	57179523	+	0	NA	intron (NM_024946, intron 1 of 6)	intron (NM_024946, intron 1 of 6)	6715	NM_024946	80011	Hs.396740	NM_024946	ENSG00000172775	FAM192A	C16orf94|CDA018|CDA10|NIP30|PIP30	family with sequence similarity 192 member A	protein-coding	0.008621	0.332378	
chunk0103_205_1	chr2	163754882	163755339	+	0	NA	Intergenic	Intergenic	-19107	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.004376	0.353712	
chunk0110_166_1	chr20	14093599	14094085	+	0	NA	intron (NM_080676, intron 3 of 16)	L2c|LINE|L2	98342	NM_080676	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.004115	0.373717	
chunk0195_188_1	chr8	96583931	96584258	+	0	NA	intron (NM_002998, intron 1 of 4)	intron (NM_002998, intron 1 of 4)	-61133	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.000000	0.381098	
chunk0070_100_1	chr15	70353832	70354297	+	0	NA	Intergenic	Intergenic	-256147	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.010753	0.495708	
chunk0110_177_1	chr20	14352582	14352941	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	-15094	NM_013281	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.002786	0.291667	
chunk0206_318_1	chr9	125177894	125178441	+	0	NA	intron (NM_001123369, intron 1 of 5)	L1MC1|LINE|L1	11772	NM_001123369	5537	Hs.744091	NM_002721	ENSG00000119414	PPP6C	PP6|PP6C	protein phosphatase 6 catalytic subunit	protein-coding	0.005484	0.363139	
chunk0089_281_1	chr18	62933165	62933804	+	0	NA	intron (NM_194449, intron 10 of 16)	L1PA17|LINE|L1	218045	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.003130	0.339062	
chunk0068_146_1	chr15	53625410	53625894	+	0	NA	intron (NR_102334, intron 14 of 19)	intron (NR_102334, intron 14 of 19)	-84549	NR_102335	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.004132	0.379381	
chunk0200_114_1	chr9	16985920	16986196	+	0	NA	Intergenic	Intergenic	-115270	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.010870	0.516245	
chunk0175_56_1	chr7	1659664	1660139	+	0	NA	Intergenic	L1MB7|LINE|L1	45431	NR_001288	260341	Hs.534596	NR_001288		TFAMP1	MTTF1|TCF6L1	transcription factor A, mitochondrial pseudogene 1	pseudo	0.016842	0.386555	
chunk0042_158_1	chr12	3939337	3939550	+	0	NA	Intergenic	Intergenic	-65995	NM_001286521	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.004695	0.355140	
chunk0211_417_1	chrX	128961259	128961891	+	0	NA	Intergenic	L2c|LINE|L2	561930	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.001582	0.323855	
chunk0040_397_1	chr11	120382021	120382401	+	0	NA	intron (NM_001198665, intron 1 of 39)	L1MC3|LINE|L1	-3083	NM_001301084	23365	Hs.24598	NM_015313	ENSG00000196914	ARHGEF12	LARG|PRO2792	Rho guanine nucleotide exchange factor 12	protein-coding	0.005263	0.317585	
chunk0009_143_1	chr1	104807380	104807970	+	0	NA	Intergenic	L1M4a2|LINE|L1	734652	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.005085	0.382403	
chunk0024_229_1	chr10	38094179	38094467	+	0	NA	promoter-TSS (NM_003421)	promoter-TSS (NM_003421)	-13	NM_001007094	7587	Hs.292575	NM_003421	ENSG00000075407	ZNF37A	KOX21|ZNF37	zinc finger protein 37A	protein-coding	0.065972	0.595156	
chunk0100_76_1	chr2	106842191	106842619	+	0	NA	intron (NM_032528, intron 2 of 5)	intron (NM_032528, intron 2 of 5)	43749	NM_001142351	84620	Hs.98265	NM_032528	ENSG00000144057	ST6GAL2	SIAT2|ST6GalII	ST6 beta-galactoside alpha-2,6-sialyltransferase 2	protein-coding	0.007009	0.515152	
chunk0185_51_1	chr7	124734924	124735171	+	0	NA	Intergenic	Intergenic	30978	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.000000	0.354839	
chunk0176_67_1	chr7	11238360	11238749	+	0	NA	Intergenic	Intergenic	264682	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.000000	0.287179	
chunk0130_137_1	chr3	132227059	132227474	+	0	NA	Intergenic	L1PA10|LINE|L1	-90101	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.009639	0.444712	204(GAGAACATGCAGTGCT,-,0.00),205(AGAACATGCAGTGCTT,+,0.00)
chunk0153_394_1	chr5	75319859	75320129	+	0	NA	Intergenic	Intergenic	-17174	NM_000859	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.003704	0.446494	
chunk0022_318_1	chr10	16250537	16250966	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-186192	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.004662	0.446512	
chunk0212_343_1	chrX	146708161	146708600	+	0	NA	Intergenic	LTR22B|LTR|ERVK	-101404	NM_001144064	100129239	Hs.592233	NM_001144064	ENSG00000224440	CXorf51A	CXorf51|CXorf51B	chromosome X open reading frame 51A	protein-coding	0.011390	0.422727	
chunk0126_144_1	chr3	76429358	76430271	+	0	NA	Intergenic	Intergenic	-610329	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.004381	0.397155	646(GGGAACAAAGTGAGCC,-,0.00),647(GGAACAAAGTGAGCCT,+,0.00)
chunk0040_455_1	chr11	122461871	122462070	+	0	NA	Intergenic	L1MA4A|LINE|L1	-193720	NM_032873	84959	Hs.444075	NM_032873	ENSG00000154127	UBASH3B	STS-1|STS1|TULA-2|TULA2|p70	ubiquitin associated and SH3 domain containing B	protein-coding	0.005025	0.605000	
chunk0096_15_1	chr2	26075124	26075323	+	0	NA	intron (NM_016131, intron 1 of 5)	intron (NM_016131, intron 1 of 5)	41363	NM_016131	10890	Hs.467960	NM_016131	ENSG00000084733	RAB10	-	RAB10, member RAS oncogene family	protein-coding	0.000000	0.340000	72(AAGAACATTGTGTTCA,-,0.00),73(AGAACATTGTGTTCAA,+,0.00)
chunk0014_443_1	chr1	183789651	183789936	+	0	NA	intron (NM_001297669, intron 3 of 18)	MLT1J|LTR|ERVL-MaLR	-15288	NM_001297672	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.003509	0.363636	
chunk0054_121_1	chr13	43168677	43168876	+	0	NA	Intergenic	MER72|LTR|ERV1	55611	NR_047013	100874159	Hs.633241	NR_047013		LINC00400	-	long intergenic non-protein coding RNA 400	ncRNA	0.010050	0.420000	59(AAGCACACAGTGTGCA,-,0.00),60(AGCACACAGTGTGCAG,+,0.00)
chunk0046_283_1	chr12	61896335	61896901	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	296221	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.001767	0.343915	
chunk0174_140_1	chr6	157550762	157551037	+	0	NA	intron (NM_024630, intron 2 of 8)	intron (NM_024630, intron 2 of 8)	21767	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.007273	0.456522	
chunk0083_357_1	chr17	70492176	70492699	+	0	NA	Intergenic	L1MB8|LINE|L1	322902	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.003824	0.333969	
chunk0065_48_1	chr15	22292398	22292775	+	0	NA	Intergenic	Intergenic	33972	NR_033735	646396	Hs.451294	NR_033735		REREP3	-	arginine-glutamic acid dipeptide repeats pseudogene 3	pseudo	0.002653	0.367725	
chunk0006_408_1	chr1	75745564	75746042	+	0	NA	promoter-TSS (NR_130749)	promoter-TSS (NR_130749)	-790	NR_130749	1744	Hs.525459	NR_130749		DLSTP1	DLSTP	dihydrolipoamide S-succinyltransferase pseudogene 1	pseudo	0.008368	0.334029	
chunk0155_74_1	chr5	91775438	91775879	+	0	NA	Intergenic	L2b|LINE|L2	-392326	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.391403	189(CAGCACTCATTGTGCC,-,0.00),190(AGCACTCATTGTGCCT,+,0.00)
chunk0011_307_1	chr1	151775947	151776146	+	0	NA	intron (NM_006862, intron 8 of 13)	intron (NM_006862, intron 8 of 13)	9391	NM_016178	51686	Hs.713789	NM_016178	ENSG00000143450	OAZ3	AZ3|OAZ-t|TISP15	ornithine decarboxylase antizyme 3	protein-coding	0.005025	0.500000	
chunk0162_425_1	chr5	180213814	180214111	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-4832	NM_175062	255426	Hs.190559	NM_175062	ENSG00000146090	RASGEF1C	-	RasGEF domain family member 1C	protein-coding	0.003367	0.479866	
chunk0090_42_1	chr19	1507710	1507932	+	0	NA	intron (NM_213604, intron 7 of 11)	intron (NM_213604, intron 7 of 11)	5368	NM_213604	339366	Hs.371674	NM_213604	ENSG00000185761	ADAMTSL5	THSD6	ADAMTS like 5	protein-coding	0.031532	0.529148	
chunk0148_332_1	chr5	14228144	14228343	+	0	NA	intron (NM_007118, intron 1 of 56)	intron (NM_007118, intron 1 of 56)	84523	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.005025	0.420000	
chunk0186_298_1	chr7	142787410	142787609	+	0	NA	Intergenic	Intergenic	16566	NR_130149	5645	Hs.449281	NM_002770	ENSG00000275896	PRSS2	TRY2|TRY8|TRYP2	serine protease 2	protein-coding	0.005025	0.525000	86(GGGAACACAGAGTACT,-,0.00),87(GGAACACAGAGTACTG,+,0.00)
chunk0028_326_1	chr10	91969387	91970323	+	0	NA	intron (NM_003972, intron 14 of 37)	AluSz6|SINE|Alu	45876	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.011752	0.395945	
chunk0201_338_1	chr9	64087509	64087714	+	0	NA	Intergenic	AluSq2|SINE|Alu	70661	NR_033856	644316	Hs.632789	NR_033856		FLJ43315	-	asparagine synthetase pseudogene	pseudo	0.009756	0.383495	
chunk0076_155_1	chr16	67301705	67302308	+	0	NA	intron (NM_001100915, intron 4 of 15)	intron (NM_001100915, intron 4 of 15)	22482	NM_001129729	25894	Hs.188781	NM_015432	ENSG00000196155	PLEKHG4	ARHGEF44|PRTPHN1|SCA4	pleckstrin homology and RhoGEF domain containing G4	protein-coding	0.019900	0.500000	
chunk0110_280_1	chr20	17558274	17558848	+	0	NA	intron (NM_001278606, intron 1 of 8)	intron (NM_001278606, intron 1 of 8)	399	NM_001161705	631	Hs.129702	NM_001195	ENSG00000125864	BFSP1	CP115|CP94|CTRCT33|LIFL-H	beaded filament structural protein 1	protein-coding	0.010453	0.436522	
chunk0027_4_1	chr10	71832192	71832447	+	0	NA	intron (NM_001042465, intron 2 of 14)	intron (NM_001042465, intron 2 of 14)	19006	NM_001042465	5660	Hs.523004	NM_002778	ENSG00000197746	PSAP	GLBA|SAP1	prosaposin	protein-coding	0.011765	0.539062	
chunk0002_150_1	chr1	17892114	17892855	+	0	NA	Intergenic	Intergenic	137171	NM_030812	81569	Hs.2149	NM_030812	ENSG00000117148	ACTL8	CT57	actin like 8	protein-coding	0.012146	0.520216	443(AAGGACAGTATGTCCT,-,0.00),444(AGGACAGTATGTCCTA,+,0.00)
chunk0190_203_1	chr8	34696740	34697415	+	0	NA	Intergenic	L1MD|LINE|L1	-86844	NR_125746	103689844	Hs.590682	NR_125746	ENSG00000254344	LINC01288	TCONS_00014671	long intergenic non-protein coding RNA 1288	ncRNA	0.004444	0.304734	
chunk0057_313_1	chr13	106700710	106700945	+	0	NA	Intergenic	Intergenic	46947	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.012766	0.398305	
chunk0164_110_1	chr6	20637704	20638351	+	0	NA	intron (NM_017774, intron 4 of 15)	intron (NM_017774, intron 4 of 15)	103570	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.003091	0.331790	
chunk0027_293_1	chr10	77614823	77615188	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	22814	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.005479	0.472678	167(AGGAACTTGGTGTACA,-,0.00)
chunk0124_98_1	chr3	53580736	53580983	+	0	NA	intron (NM_000720, intron 3 of 48)	intron (NM_000720, intron 3 of 48)	85810	NM_001128840	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.000000	0.383065	
chunk0070_425_1	chr15	77966007	77966256	+	0	NA	Intergenic	Intergenic	28094	NR_026998	91450	Hs.406766	NR_026998		LOC91450	-	uncharacterized LOC91450	ncRNA	0.008032	0.496000	
chunk0189_456_1	chr8	28505984	28506516	+	0	NA	intron (NM_017412, intron 3 of 7)	intron (NM_017412, intron 3 of 7)	-1068	NR_036250	100422903		NR_036250	ENSG00000265251	MIR4288	-	microRNA 4288	ncRNA	0.007519	0.371482	
chunk0165_105_1	chr6	32405614	32406272	+	0	NA	intron (NM_001304561, intron 1 of 7).3	intron (NM_001304561, intron 1 of 7).3	1187	NM_001304561	56244	Hs.534471	NM_019602	ENSG00000204290	BTNL2	BTL-II|BTN7|HSBLMHC1|SS2	butyrophilin like 2	protein-coding	0.003040	0.342944	284(AAGGACATTTTGTGCT,-,0.00),285(AGGACATTTTGTGCTG,+,0.00)
chunk0032_190_1	chr11	6455099	6455689	+	0	NA	intron (NM_001248006, intron 7 of 11)	intron (NM_001248006, intron 7 of 11)	-14370	NM_000613	3263	Hs.426485	NM_000613	ENSG00000110169	HPX	HX	hemopexin	protein-coding	0.005085	0.455161	
chunk0044_393_1	chr12	40402454	40402772	+	0	NA	intron (NM_173600, intron 3 of 172)	intron (NM_173600, intron 3 of 172)	9219	NM_173600	283463	Hs.632712	NM_173600		MUC19	MUC-19	mucin 19, oligomeric	protein-coding	0.003145	0.335423	
chunk0090_365_1	chr18	77073402	77073985	+	0	NA	intron (NM_001025101, intron 2 of 8)	LTR40a|LTR|ERVL	-56594	NM_001025090	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.013722	0.458904	
chunk0011_86_1	chr1	145527823	145528560	+	0	NA	Intergenic	Intergenic	79667	NR_104217	101929780	Hs.534675	NR_104217	ENSG00000272150	NBPF25P	WI2-925H4.1	NBPF member 25, pseudogene	pseudo	0.004071	0.337398	215(TGGTACACTGTGTTTT,-,0.00),216(GGTACACTGTGTTTTT,+,0.00),414(TTGGACATTCAGTTCT,-,0.00),415(TGGACATTCAGTTCTG,+,0.00)
chunk0069_157_1	chr15	62539548	62539903	+	0	NA	Intergenic	Intergenic	105456	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.008451	0.466292	
chunk0160_96_1	chr5	150310806	150311361	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-8121	NM_001012301	340075	Hs.591252	NM_001012301	ENSG00000183876	ARSI	ASI|SPG66	arylsulfatase family member I	protein-coding	0.003604	0.424460	274(GGGAACAATACGTTCC,-,0.00),275(GGAACAATACGTTCCT,+,0.00)
chunk0077_136_1	chr16	78607455	78608113	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	508371	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.013678	0.393020	282(AAGGGCAGAGTGTGCT,-,0.00),283(AGGGCAGAGTGTGCTG,+,0.00)
chunk0162_36_1	chr6	1044244	1044980	+	0	NA	intron (NR_027115, intron 1 of 4)	intron (NR_027115, intron 1 of 4)	56720	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.005435	0.485753	
chunk0129_201_1	chr3	121640208	121640440	+	0	NA	intron (NM_005335, intron 6 of 13)	L1MEi|LINE|L1	20624	NM_001292041	3059	Hs.14601	NM_005335	ENSG00000180353	HCLS1	CTTNL|HS1|lckBP1|p75	hematopoietic cell-specific Lyn substrate 1	protein-coding	0.004310	0.330472	
chunk0114_407_1	chr20	63829305	63829537	+	0	NA	Intergenic	Intergenic	21345	NR_110081	101928604	Hs.676054	NR_110081		ZBTB46-AS1	-	ZBTB46 antisense RNA 1	ncRNA	0.025862	0.463519	
chunk0114_173_1	chr21	14741457	14741792	+	0	NA	Intergenic	MIRc|SINE|MIR	-98517	NM_001256579	388813	Hs.334177	NM_001256579		LOC388813	-	uncharacterized protein ENSP00000383407-like	protein-coding	0.005970	0.360119	
chunk0058_264_1	chr14	25967024	25967286	+	0	NA	Intergenic	Intergenic	630599	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.000000	0.403042	99(GAGAACACAATGTTCC,-,0.00),100(AGAACACAATGTTCCT,+,0.00)
chunk0118_31_1	chr22	26763871	26764236	+	0	NA	intron (NR_110543, intron 2 of 5)	intron (NR_110543, intron 2 of 5)	91210	NR_110543	102724827	Hs.642767	NR_110543		MIATNB	-	MIAT neighbor	ncRNA	0.024658	0.546448	
chunk0018_94_1	chr1	217638276	217638511	+	0	NA	intron (NM_138796, intron 1 of 10)	intron (NM_138796, intron 1 of 10)	7069	NM_138796	128153	Hs.171130	NM_138796	ENSG00000162814	SPATA17	IQCH|MSRG-11|MSRG11	spermatogenesis associated 17	protein-coding	0.000000	0.330508	
chunk0025_370_1	chr10	58678850	58679143	+	0	NA	intron (NM_001080512, intron 2 of 20)	L1PA7|LINE|L1	-36019	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.003413	0.357143	61(CTGAACAACCTGTTCC,-,0.00),62(TGAACAACCTGTTCCT,+,0.00),144(GAAGACACAATGTACC,-,0.00)
chunk0206_375_1	chr9	126356969	126357500	+	0	NA	intron (NM_033446, intron 2 of 9)	L1ME1|LINE|L1	30390	NM_033446	89853	Hs.162659	NM_033446	ENSG00000196814	MVB12B	C9orf28|FAM125B	multivesicular body subunit 12B	protein-coding	0.003766	0.387218	
chunk0039_206_1	chr11	100954263	100954462	+	0	NA	intron (NM_152432, intron 12 of 23)	intron (NM_152432, intron 12 of 23)	-37718	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.010050	0.350000	
chunk0211_389_1	chrX	128103996	128105005	+	0	NA	Intergenic	L1PA16|LINE|L1	-52097	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.005946	0.335644	
chunk0080_31_1	chr17	21127288	21127527	+	0	NA	intron (NM_015510, intron 1 of 6)	CpG	479	NM_015510	25979	Hs.386989	NM_015510	ENSG00000109016	DHRS7B	CGI-93|SDR32C1	dehydrogenase/reductase 7B	protein-coding	0.066946	0.604167	
chunk0203_116_1	chr9	84750136	84750924	+	0	NA	intron (NM_001007097, intron 11 of 12)	intron (NM_001007097, intron 11 of 12)	80153	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.007614	0.437262	
chunk0179_398_1	chr7	51543570	51544095	+	0	NA	Intergenic	L1PB1|LINE|L1	-227014	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.011429	0.509506	
chunk0003_234_1	chr1	35855194	35855669	+	0	NA	3' UTR (NM_017629, exon 18 of 18)	3' UTR (NM_017629, exon 18 of 18)	-27778	NM_012199	26523	Hs.22867	NM_012199	ENSG00000092847	AGO1	EIF2C|EIF2C1|GERP95|Q99|hAgo1	argonaute RISC component 1	protein-coding	0.016842	0.420168	
chunk0206_246_1	chr9	123686859	123687113	+	0	NA	intron (NM_024820, intron 5 of 20)	X2_LINE|LINE|CR1	-201364	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.007874	0.411765	
chunk0180_94_1	chr7	55081733	55082334	+	0	NA	intron (NM_201283, intron 1 of 9)	MER112|DNA|hAT-Charlie	63001	NM_005228	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.003328	0.395349	
chunk0090_247_1	chr18	73908342	73908550	+	0	NA	Intergenic	Intergenic	239318	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.019231	0.540670	
chunk0040_64_1	chr11	111236925	111237913	+	0	NA	Intergenic	L1ME4b|LINE|L1	-18563	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.008097	0.369060	
chunk0113_164_1	chr20	52897300	52897537	+	0	NA	Intergenic	Intergenic	-74989	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.004219	0.289916	
chunk0156_91_1	chr5	104770849	104771381	+	0	NA	Intergenic	Intergenic	-328359	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.001880	0.300188	
chunk0192_217_1	chr8	65233688	65234068	+	0	NA	Intergenic	Intergenic	-53538	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.005263	0.354331	
chunk0142_61_1	chr4	92254800	92255028	+	0	NA	Intergenic	L1P3b|LINE|L1	22388	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.013158	0.567686	
chunk0023_19_1	chr10	20979356	20979862	+	0	NA	intron (NM_213569, intron 3 of 6)	intron (NM_213569, intron 3 of 6)	-82007	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.005929	0.368836	
chunk0177_190_1	chr7	23685571	23686085	+	0	NA	intron (NM_001127364, intron 2 of 5)	intron (NM_001127364, intron 2 of 5)	5714	NM_001127364	340277	Hs.592178	NM_199136	ENSG00000188732	FAM221A	C7orf46	family with sequence similarity 221 member A	protein-coding	0.007782	0.370874	
chunk0094_308_1	chr2	8802066	8802575	+	0	NA	intron (NM_020738, intron 8 of 29)	L2b|LINE|L2	35305	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.001965	0.433333	
chunk0086_64_1	chr18	13052046	13052354	+	0	NA	intron (NM_032142, intron 17 of 44)	intron (NM_032142, intron 17 of 44)	60838	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.012987	0.449838	
chunk0132_136_1	chr3	156274996	156275520	+	0	NA	intron (NM_003471, intron 1 of 13)	Tigger1|DNA|TcMar-Tigger	-15729	NM_172159	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.000000	0.339048	
chunk0125_188_1	chr3	66729702	66730248	+	0	NA	Intergenic	Intergenic	-229554	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.003663	0.418647	
chunk0194_212_1	chr8	86101984	86102798	+	0	NA	intron (NM_152565, intron 1 of 7)	intron (NM_152565, intron 1 of 7)	3481	NM_152565	245972	Hs.436360	NM_152565	ENSG00000147614	ATP6V0D2	ATP6D2|VMA6	ATPase H+ transporting V0 subunit d2	protein-coding	0.001229	0.369325	
chunk0084_170_1	chr17	77451962	77452486	+	0	NA	intron (NM_001293697, intron 1 of 9)	intron (NM_001293697, intron 1 of 9)	980	NM_001293697	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.041985	0.598095	
chunk0159_27_1	chr5	136812439	136812662	+	0	NA	Intergenic	L1PB1|LINE|L1	-447074	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.008969	0.348214	
chunk0039_213_1	chr11	101113550	101113793	+	0	NA	intron (NM_000926, intron 2 of 7)	intron (NM_000926, intron 2 of 7)	15392	NR_073143	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.004115	0.389344	
chunk0046_31_1	chr12	54455965	54456645	+	0	NA	intron (NM_144594, intron 8 of 8)	intron (NM_144594, intron 8 of 8)	17297	NM_144594	121355	Hs.524476	NM_144594	ENSG00000170627	GTSF1	Cue110|FAM112B	gametocyte specific factor 1	protein-coding	0.000000	0.345081	326(CAGAACACCAAGTACC,-,0.00),327(AGAACACCAAGTACCT,+,0.00)
chunk0022_131_1	chr10	11706918	11707322	+	0	NA	Intergenic	Intergenic	-35237	NM_024693	79746	Hs.22242	NM_024693	ENSG00000134463	ECHDC3	-	enoyl-CoA hydratase domain containing 3	protein-coding	0.017327	0.459259	
chunk0159_88_1	chr5	137833636	137833839	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	32544	NR_002713	4888	Hs.643466	NR_002713	ENSG00000226306	NPY6R	NPY1RL|NPY6RP|PP2|Y2B	neuropeptide Y receptor Y6 (pseudogene)	pseudo	0.004926	0.362745	
chunk0050_61_1	chr12	101237079	101237460	+	0	NA	Intergenic	Intergenic	-27031	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.002625	0.356021	
chunk0136_205_1	chr4	7034737	7035037	+	0	NA	intron (NR_033828, intron 3 of 3)	intron (NR_033828, intron 3 of 3)	8114	NM_153376	257236	Hs.656757	NM_153376	ENSG00000173013	CCDC96	-	coiled-coil domain containing 96	protein-coding	0.026667	0.607973	
chunk0202_15_1	chr9	70419530	70420518	+	0	NA	Intergenic	CpG	-5367	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.068826	0.637007	594(TGGAACAGTTTGTCCT,-,0.00),595(GGAACAGTTTGTCCTT,+,0.00)
chunk0147_307_1	chr4	184873871	184874255	+	0	NA	Intergenic	Intergenic	-18411	NR_132989	731424	Hs.427740	NR_037867		MIR3945HG	-	MIR3945 host gene	ncRNA	0.007812	0.501299	
chunk0015_119_1	chr1	185342727	185343422	+	0	NA	Intergenic	Intergenic	-8035	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.004317	0.362069	
chunk0094_229_1	chr2	6946597	6947189	+	0	NA	intron (NM_014746, intron 2 of 8)	Charlie2a|DNA|hAT-Charlie	-28211	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.005068	0.300169	
chunk0152_64_1	chr5	57797948	57798147	+	0	NA	Intergenic	MIR|SINE|MIR	101115	NR_109900	101928539	Hs.639385	NR_109900	ENSG00000249584	LINC02225	-	long intergenic non-protein coding RNA 2225	ncRNA	0.005025	0.320000	
chunk0146_94_1	chr4	158171017	158171632	+	0	NA	exon (NM_016613, exon 2 of 5)	exon (NM_016613, exon 2 of 5)	1242	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.040650	0.568182	223(TGGCACACGCAGTGCC,-,0.00),224(GGCACACGCAGTGCCC,+,0.00)
chunk0171_269_1	chr6	127589000	127589592	+	0	NA	intron (NM_001010905, intron 4 of 5)	intron (NM_001010905, intron 4 of 5)	12122	NM_001010905	352999	Hs.226268	NM_001010905	ENSG00000184530	C6orf58	LEG1	chromosome 6 open reading frame 58	protein-coding	0.001689	0.333895	295(TGAAACAGAATGTACC,-,0.00),296(GAAACAGAATGTACCT,+,0.00),327(GAGTACACAATGTCTC,-,0.00)
chunk0009_129_1	chr1	103953739	103954093	+	0	NA	Intergenic	L1MC1|LINE|L1	-119107	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.008475	0.323944	
chunk0112_402_1	chr20	47008706	47009599	+	0	NA	intron (NM_172110, intron 4 of 13)	intron (NM_172110, intron 4 of 13)	114528	NM_172110	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.007839	0.430649	
chunk0066_66_1	chr15	29012421	29012664	+	0	NA	intron (NM_001130414, intron 2 of 12)	L1MC3|LINE|L1	90905	NM_001130414	321	Hs.618112	NM_005503	ENSG00000034053	APBA2	D15S1518E|HsT16821|LIN-10|MGC:14091|MINT2|X11-BETA|X11L	amyloid beta precursor protein binding family A member 2	protein-coding	0.004115	0.352459	
chunk0057_87_1	chr13	98647931	98648475	+	0	NA	Intergenic	Intergenic	-71052	NM_001032296	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.001838	0.418349	
chunk0137_96_1	chr4	13432008	13432500	+	0	NA	intron (NM_001017979, intron 4 of 6)	L1PA17|LINE|L1	52111	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.002033	0.336714	
chunk0207_386_1	chr9	136439570	136439872	+	0	NA	promoter-TSS (NM_019892)	promoter-TSS (NM_019892)	83	NM_019892	56623	Hs.120998	NM_019892	ENSG00000148384	INPP5E	CORS1|CPD4|JBTS1|MORMS|PPI5PIV|pharbin	inositol polyphosphate-5-phosphatase E	protein-coding	0.139073	0.795380	
chunk0181_219_1	chr7	84906869	84907244	+	0	NA	Intergenic	Intergenic	214875	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.010667	0.430851	
chunk0081_222_1	chr17	42668001	42668377	+	0	NA	exon (NM_024927, exon 13 of 13)	exon (NM_024927, exon 13 of 13)	7901	NR_073574	79990	Hs.632251	NM_024927	ENSG00000068137	PLEKHH3	-	pleckstrin homology, MyTH4 and FERM domain containing H3	protein-coding	0.013298	0.615385	
chunk0057_28_1	chr13	95652423	95652803	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-7907	NM_198968	22873	Hs.656580	NM_014934	ENSG00000134874	DZIP1	DZIP|DZIPt1	DAZ interacting zinc finger protein 1	protein-coding	0.002632	0.435696	
chunk0201_111_1	chr9	35127318	35127953	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-11739	NM_025182	80256	Hs.301696	NM_025182	ENSG00000005238	FAM214B	KIAA1539	family with sequence similarity 214 member B	protein-coding	0.011024	0.361635	
chunk0131_19_1	chr3	142105523	142105838	+	0	NA	intron (NM_001178138, intron 1 of 13)	intron (NM_001178138, intron 1 of 13)	43864	NM_001178138	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.006349	0.341772	
chunk0061_360_1	chr14	63888033	63888249	+	0	NA	intron (NM_182914, intron 1 of 115)	MIR3|SINE|MIR	35176	NM_015180	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.023148	0.465438	
chunk0031_214_1	chr10	125911972	125912548	+	0	NA	intron (NM_145235, intron 1 of 10)	intron (NM_145235, intron 1 of 10)	15721	NM_145235	92565	Hs.352591	NM_145235	ENSG00000203780	FANK1	HSD13	fibronectin type III and ankyrin repeat domains 1	protein-coding	0.006944	0.400347	
chunk0092_375_1	chr19	36214010	36214209	+	0	NA	promoter-TSS (NM_007145)	promoter-TSS (NM_007145)	-493	NM_001099638	7705	Hs.643436	NM_007145	ENSG00000167635	ZNF146	OZF	zinc finger protein 146	protein-coding	0.025126	0.525000	
chunk0160_37_1	chr5	149482788	149483200	+	0	NA	Intergenic	Intergenic	52348	NR_029686	406937		NR_029686	ENSG00000276365	MIR145	MIRN145|miR-145|miRNA145	microRNA 145	ncRNA	0.002427	0.423729	
chunk0162_97_1	chr6	2236934	2237407	+	0	NA	intron (NM_001500, intron 1 of 10)	intron (NM_001500, intron 1 of 10)	8464	NM_001500	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.002114	0.335443	
chunk0147_86_1	chr4	173180725	173181105	+	0	NA	intron (NM_017423, intron 1 of 11)	intron (NM_017423, intron 1 of 11)	12162	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.002632	0.330709	
chunk0198_200_1	chr8	133625844	133626222	+	0	NA	Intergenic	L2c|LINE|L2	-54093	NM_173344	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.015873	0.445910	
chunk0191_408_1	chr8	57637230	57637764	+	0	NA	Intergenic	Intergenic	293710	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.009363	0.314019	311(AAGAACAGTTTCTTCC,-,0.00),312(AGAACAGTTTCTTCCT,+,0.00)
chunk0118_283_1	chr22	33812469	33813097	+	0	NA	intron (NM_133642, intron 1 of 14)	L2b|LINE|L2	87797	NR_038950	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.009554	0.457870	384(GAAAACTGTCTGTCCT,-,0.00),385(AAAACTGTCTGTCCTT,+,0.00)
chunk0047_343_1	chr12	74759528	74760106	+	0	NA	Intergenic	L1PB1|LINE|L1	222046	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.005190	0.340242	
chunk0149_126_1	chr5	19546669	19546974	+	0	NA	intron (NM_001167667, intron 8 of 12)	intron (NM_001167667, intron 8 of 12)	339451	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003279	0.333333	
chunk0091_56_1	chr19	4791386	4791762	+	0	NA	promoter-TSS (NM_018708)	promoter-TSS (NM_018708)	-142	NM_018708	55527	Hs.515082	NM_018708	ENSG00000141965	FEM1A	EPRAP	fem-1 homolog A	protein-coding	0.079787	0.583554	
chunk0029_132_1	chr10	98900013	98900537	+	0	NA	intron (NM_001166246, intron 3 of 12)	L1ME1|LINE|L1	24293	NR_106762	102465253		NR_106762	ENSG00000274056	MIR6507	hsa-mir-6507	microRNA 6507	ncRNA	0.003817	0.331429	
chunk0118_125_1	chr22	29630182	29630458	+	0	NA	intron (NM_181830, intron 1 of 14)	intron (NM_181830, intron 1 of 14)	26764	NM_181830	4771	Hs.187898	NM_000268	ENSG00000186575	NF2	ACN|BANF|SCH	neurofibromin 2	protein-coding	0.003623	0.382671	
chunk0152_455_1	chr5	66507118	66507630	+	0	NA	TTS (NR_105001)	TTS (NR_105001)	4230	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.007812	0.385965	295(TAGCACATAATGTTCT,-,0.00),296(AGCACATAATGTTCTG,+,0.00)
chunk0207_20_1	chrM	14294	14535	+	0	NA	NA	Intergenic	NA	NA									0.008299	0.433884	
chunk0174_52_1	chr6	154852523	154853125	+	0	NA	promoter-TSS (NR_036100)	promoter-TSS (NR_036100)	-536	NR_036100	100422821		NR_036100	ENSG00000264814	MIR1273C	-	microRNA 1273c	ncRNA	0.006645	0.354892	
chunk0053_183_1	chr13	30983963	30984498	+	0	NA	Intergenic	L1ME1|LINE|L1	51533	NM_152325	122046	Hs.124463	NM_152325	ENSG00000175664	TEX26	C13orf26	testis expressed 26	protein-coding	0.005607	0.378731	
chunk0025_269_1	chr10	55910612	55911049	+	0	NA	Intergenic	Intergenic	311840	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.006865	0.394977	
chunk0140_298_1	chr4	72893235	72893880	+	0	NA	Intergenic	Intergenic	176202	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.001550	0.382353	392(CAGAACACTCTGAGCA,-,0.00),393(AGAACACTCTGAGCAG,+,0.00)
chunk0167_137_1	chr6	62248707	62249211	+	0	NA	intron (NM_152688, intron 1 of 8)	intron (NM_152688, intron 1 of 8)	37236	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.003968	0.324752	
chunk0070_97_1	chr15	70324079	70324534	+	0	NA	Intergenic	Intergenic	-226389	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.015385	0.436404	
chunk0179_156_1	chr7	46341321	46342060	+	0	NA	Intergenic	L1P2|LINE|L1	-420418	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.016238	0.478378	
chunk0211_402_1	chrX	128700649	128701233	+	0	NA	Intergenic	L1MC1|LINE|L1	-648538	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.001712	0.336752	
chunk0072_37_1	chr16	881242	881519	+	0	NA	intron (NR_033645, intron 6 of 11)	intron (NR_033645, intron 6 of 11)	-39653	NR_110946	101929387	Hs.737087	NR_110945	ENSG00000260439	LMF1-AS1	LA16c-366D3.1	LMF1 antisense RNA 1	ncRNA	0.025271	0.568345	
chunk0064_151_1	chr14	91770128	91770660	+	0	NA	Intergenic	Intergenic	33540	NR_106988									0.003759	0.363977	
chunk0057_306_1	chr13	106550595	106550978	+	0	NA	intron (NM_018011, intron 3 of 3)	MLT1D|LTR|ERVL-MaLR	-15746	NM_004093	1948	Hs.149239	NM_004093	ENSG00000125266	EFNB2	EPLG5|HTKL|Htk-L|LERK5	ephrin B2	protein-coding	0.002611	0.445312	
chunk0080_283_1	chr17	31202650	31202987	+	0	NA	intron (NM_001042492, intron 11 of 57)	intron (NM_001042492, intron 11 of 57)	94544	NM_002544	4974	Hs.113874	NM_002544	ENSG00000126861	OMG	OMGP	oligodendrocyte myelin glycoprotein	protein-coding	0.005935	0.334320	
chunk0190_216_1	chr8	35716820	35717293	+	0	NA	intron (NM_080872, intron 8 of 16)	intron (NM_080872, intron 8 of 16)	-6736	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.008457	0.377637	
chunk0036_363_1	chr11	67091552	67091955	+	0	NA	Intergenic	L1PA8|LINE|L1	-27516	NR_027473	22992	Hs.124147	NM_012308	ENSG00000173120	KDM2A	CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA	lysine demethylase 2A	protein-coding	0.022333	0.465347	
chunk0102_111_1	chr2	144470432	144470703	+	0	NA	intron (NM_014795, intron 2 of 9)	intron (NM_014795, intron 2 of 9)	-49047	NR_040248	100303491	Hs.560789	NR_040248	ENSG00000238057	ZEB2-AS1	ZEB2-AS|ZEB2AS|ZEB2NAT	ZEB2 antisense RNA 1	ncRNA	0.003690	0.338235	
chunk0016_274_1	chr1	200586305	200586550	+	0	NA	intron (NM_001305792, intron 16 of 27)	intron (NM_001305792, intron 16 of 27)	32411	NM_001305792	9928	Hs.3104	NM_014875	ENSG00000118193	KIF14	MCPH20|MKS12	kinesin family member 14	protein-coding	0.004082	0.231707	
chunk0068_231_1	chr15	55586793	55587346	+	0	NA	intron (NM_015617, intron 1 of 2)	intron (NM_015617, intron 1 of 2)	1783	NM_015617	26108	Hs.87194	NM_015617	ENSG00000171016	PYGO1	-	pygopus family PHD finger 1	protein-coding	0.009042	0.373646	244(ATGAACAGTGAGTACT,-,0.00),245(TGAACAGTGAGTACTA,+,0.00)
chunk0044_230_1	chr12	31459868	31460574	+	0	NA	exon (NM_144973, exon 4 of 21)	exon (NM_144973, exon 4 of 21)	-129702	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.008499	0.355021	346(TAGAACGGTCAGTTCC,-,0.00),347(AGAACGGTCAGTTCCT,+,0.00)
chunk0018_20_1	chr1	215500579	215500778	+	0	NA	Intergenic	Intergenic	-66714	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.000000	0.320000	
chunk0205_356_1	chr9	113481206	113481878	+	0	NA	intron (NM_017790, intron 2 of 17)	intron (NM_017790, intron 2 of 17)	17842	NM_001282923	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.014881	0.563150	
chunk0184_382_1	chr7	121454631	121454994	+	0	NA	Intergenic	L1MA3|LINE|L1	-58444	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.002755	0.307692	
chunk0165_416_1	chr6	39101801	39102057	+	0	NA	Intergenic	Intergenic	13257	NM_001304793	55776	Hs.58382	NM_018322	ENSG00000112167	SAYSD1	C6orf64	SAYSVFN motif domain containing 1	protein-coding	0.003906	0.357977	
chunk0212_217_1	chrX	136010715	136011074	+	0	NA	intron (NM_006359, intron 7 of 15)	intron (NM_006359, intron 7 of 15)	25467	NM_001042537	10479	Hs.62185	NM_006359	ENSG00000198689	SLC9A6	MRSA|NHE6	solute carrier family 9 member A6	protein-coding	0.013928	0.388889	
chunk0139_316_1	chr4	58147039	58147653	+	0	NA	Intergenic	L1M4|LINE|L1	721474	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.000000	0.333333	
chunk0016_111_1	chr1	196016312	196016534	+	0	NA	Intergenic	Intergenic	566058	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.018018	0.354260	
chunk0086_153_1	chr18	21391136	21391524	+	0	NA	intron (NM_001142966, intron 4 of 32)	Tigger3b|DNA|TcMar-Tigger	149088	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.005155	0.388175	
chunk0209_273_1	chrX	46918364	46918807	+	0	NA	intron (NM_014735, intron 1 of 10)	intron (NM_014735, intron 1 of 10)	6152	NM_014735	9767	Hs.371977	NM_014735	ENSG00000102221	JADE3	JADE-3|PHF16	jade family PHD finger 3	protein-coding	0.002257	0.425676	
chunk0169_43_1	chr6	97413900	97414350	+	0	NA	intron (NR_110757, intron 1 of 4)	MER2|DNA|TcMar-Tigger	108539	NR_110757	101927314	Hs.520283	NR_110757	ENSG00000271860	LOC101927314	-	uncharacterized LOC101927314	ncRNA	0.008889	0.283814	215(AAGGACTGGCTGTGCT,-,0.00),216(AGGACTGGCTGTGCTT,+,0.00)
chunk0135_33_1	chr3	185162853	185163228	+	0	NA	intron (NR_038990, intron 1 of 6)	intron (NR_038990, intron 1 of 6)	139	NR_038990	339926	Hs.567848	NR_038990	ENSG00000223358	EHHADH-AS1	-	EHHADH antisense RNA 1	ncRNA	0.021333	0.494681	110(CAGAACTCAGTGTGCT,-,0.00),111(AGAACTCAGTGTGCTT,+,0.00)
chunk0013_241_1	chr1	169633051	169633795	+	0	NA	Intergenic	Intergenic	-3284	NM_003005	6403	Hs.73800	NM_003005	ENSG00000174175	SELP	CD62|CD62P|GMP140|GRMP|LECAM3|PADGEM|PSEL	selectin P	protein-coding	0.002688	0.515436	
chunk0009_50_1	chr1	100493228	100493574	+	0	NA	intron (NM_003672, intron 11 of 15)	LTR86B2|LTR|ERVL	-44771	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.002890	0.455331	
chunk0124_346_1	chr3	58433528	58433882	+	0	NA	non-coding (NR_033384, exon 1 of 9)	non-coding (NR_033384, exon 1 of 9)	134	NR_033384	5162	Hs.161357	NM_000925	ENSG00000168291	PDHB	PDHBD|PDHE1-B|PDHE1B|PHE1B	pyruvate dehydrogenase E1 beta subunit	protein-coding	0.107345	0.704225	
chunk0057_247_1	chr13	104683515	104684198	+	0	NA	Intergenic	L2a|LINE|L2	-782011	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.002928	0.368421	
chunk0153_10_1	chr5	66776076	66776306	+	0	NA	intron (NM_198828, intron 2 of 5)	intron (NM_198828, intron 2 of 5)	-52585	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.004348	0.380952	
chunk0033_417_1	chr11	24808219	24808435	+	0	NA	intron (NM_001252010, intron 5 of 9)	intron (NM_001252010, intron 5 of 9)	311357	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004630	0.341014	
chunk0092_307_1	chr19	34365705	34365904	+	0	NA	intron (NM_001184722, intron 2 of 17)	CpG	677	NM_001289790	2821	Hs.466471	NM_000175	ENSG00000105220	GPI	AMF|GNPI|NLK|PGI|PHI|SA-36|SA36	glucose-6-phosphate isomerase	protein-coding	0.060302	0.640000	
chunk0175_446_1	chr6	170068514	170068868	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-91951	NR_125878	102724511	Hs.550045	NR_125878		LOC102724511	-	uncharacterized LOC102724511	ncRNA	0.016949	0.580282	
chunk0158_141_1	chr5	127381277	127381687	+	0	NA	intron (NM_001308121, intron 5 of 13)	intron (NM_001308121, intron 5 of 13)	90718	NM_001308121	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.012195	0.360097	
chunk0078_120_1	chr17	2952214	2952709	+	0	NA	intron (NM_015085, intron 3 of 24)	L1M5|LINE|L1	13434	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.014141	0.447581	
chunk0204_99_1	chr9	94607934	94608618	+	0	NA	intron (NM_001127628, intron 5 of 7)	intron (NM_001127628, intron 5 of 7)	-14444	NM_003837	8789	Hs.61255	NM_003837	ENSG00000130957	FBP2	-	fructose-bisphosphatase 2	protein-coding	0.019006	0.480292	
chunk0180_20_1	chr7	53644241	53644779	+	0	NA	Intergenic	L1MC3|LINE|L1	167421	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.001859	0.376623	
chunk0118_423_1	chr22	38530934	38531488	+	0	NA	intron (NM_007068, intron 12 of 13)	intron (NM_007068, intron 12 of 13)	-24871	NM_001098504	10521	Hs.528305	NM_006386	ENSG00000100201	DDX17	P72|RH70	DEAD-box helicase 17	protein-coding	0.010830	0.423423	
chunk0028_63_1	chr10	83352534	83352883	+	0	NA	Intergenic	Intergenic	-786721	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.005731	0.197143	
chunk0121_167_1	chr3	19889095	19889572	+	0	NA	intron (NM_144715, intron 9 of 12)	HERVL40-int|LTR|ERVL	44881	NM_144715	151651	Hs.733920	NM_144715	ENSG00000163576	EFHB	CFAP21	EF-hand domain family member B	protein-coding	0.004193	0.462343	
chunk0179_392_1	chr7	51357180	51357540	+	0	NA	Intergenic	Intergenic	-40542	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.019444	0.468144	
chunk0122_329_1	chr3	37128689	37129117	+	0	NA	intron (NM_006309, intron 3 of 27)	intron (NM_006309, intron 3 of 27)	45702	NM_006309	9209	Hs.740522	NM_006309	ENSG00000093167	LRRFIP2	HUFI-2	LRR binding FLII interacting protein 2	protein-coding	0.009346	0.317016	
chunk0049_385_1	chr12	96064654	96064956	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-21285	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.009934	0.379538	
chunk0111_217_1	chr20	28887876	28888277	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-192314	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.002494	0.370647	
chunk0057_42_1	chr13	96248024	96248512	+	0	NA	intron (NM_153456, intron 1 of 1)	MERX|DNA|TcMar-Tigger	157429	NM_153456	266722	Hs.171001	NM_153456	ENSG00000185352	HS6ST3	HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.004098	0.355828	
chunk0006_402_1	chr1	75588668	75589132	+	0	NA	intron (NM_001130058, intron 1 of 23)	L2c|LINE|L2	22214	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.006466	0.348387	
chunk0198_351_1	chr8	140457369	140457568	+	0	NA	intron (NM_031466, intron 1 of 22)	CpG	294	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.115578	0.725000	
chunk0120_342_1	chr3	11314282	11314857	+	0	NA	intron (NM_001136031, intron 6 of 17)	L1MB8|LINE|L1	42245	NM_001144912	10533	Hs.38032	NM_006395	ENSG00000197548	ATG7	APG7-LIKE|APG7L|GSA7	autophagy related 7	protein-coding	0.010435	0.420139	
chunk0052_292_1	chr12	124504339	124504872	+	0	NA	intron (NM_006312, intron 2 of 48)	L1MB5|LINE|L1	62859	NM_006312	9612	Hs.137510	NM_006312	ENSG00000196498	NCOR2	CTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1	nuclear receptor corepressor 2	protein-coding	0.020638	0.503745	
chunk0210_203_1	chrX	80645643	80646096	+	0	NA	Intergenic	L1MEd|LINE|L1	163865	NM_153252	254065	Hs.147027	NM_153252	ENSG00000165288	BRWD3	BRODL|MRX93	bromodomain and WD repeat domain containing 3	protein-coding	0.004415	0.387665	
chunk0203_405_1	chr9	90733372	90733644	+	0	NA	Intergenic	L1MD1|LINE|L1	-68172	NM_001135052	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.011029	0.432234	
chunk0022_312_1	chr10	15866683	15866986	+	0	NA	Intergenic	Intergenic	-6314	NM_024948	80013	Hs.158870	NM_024948	ENSG00000148481	MINDY3	C10orf97|CARP|DERP5|FAM188A|MST126|MSTP126|my042	MINDY lysine 48 deubiquitinase 3	protein-coding	0.003300	0.355263	
chunk0174_109_1	chr6	156961429	156961899	+	0	NA	intron (NM_017519, intron 4 of 18)	intron (NM_017519, intron 4 of 18)	-181933	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.029787	0.511677	
chunk0114_92_1	chr21	9324921	9325378	+	0	NA	Intergenic	CpG	-195388	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.070022	0.672489	
chunk0027_330_1	chr10	78458913	78459313	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	191785	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.000000	0.374065	
chunk0010_57_1	chr1	112976822	112977285	+	0	NA	Intergenic	Intergenic	20638	NR_103744	100506392	Hs.418285	NR_103743	ENSG00000226419	SLC16A1-AS1	-	SLC16A1 antisense RNA 1	ncRNA	0.004320	0.344828	
chunk0208_2_1	chrX	10048685	10049380	+	0	NA	intron (NM_015691, intron 1 of 22)	intron (NM_015691, intron 1 of 22)	33277	NM_015691	55841	Hs.527524	NM_015691	ENSG00000047644	WWC3	BM042	WWC family member 3	protein-coding	0.012950	0.452586	329(CTGCACATTCAGTGCT,-,0.00),330(TGCACATTCAGTGCTC,+,0.00),474(ATGTACATACTGTACT,-,0.00),475(TGTACATACTGTACTG,+,0.00)
chunk0178_434_1	chr7	41225267	41225466	+	0	NA	Intergenic	Intergenic	123762	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.005025	0.475000	
chunk0017_195_1	chr1	207476410	207476897	+	0	NA	intron (NM_001006658, intron 15 of 19)	intron (NM_001006658, intron 15 of 19)	-19475	NM_000573	1378	Hs.334019	NM_000573	ENSG00000203710	CR1	C3BR|C4BR|CD35|KN	complement C3b/C4b receptor 1 (Knops blood group)	protein-coding	0.000000	0.282787	272(AAGCACAGATTGTATT,-,0.00)
chunk0075_167_1	chr16	51761467	51762326	+	0	NA	promoter-TSS (NR_110916)	promoter-TSS (NR_110916)	-623	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.018626	0.440698	
chunk0120_220_1	chr3	7837280	7837632	+	0	NA	Intergenic	Intergenic	178851	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.002841	0.320113	153(AAGGACATTCTGCACT,-,0.00),154(AGGACATTCTGCACTT,+,0.00)
chunk0131_441_1	chr3	153871700	153871942	+	0	NA	Intergenic	L1MA2|LINE|L1	-249182	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.000000	0.312757	
chunk0075_176_1	chr16	52023418	52023923	+	0	NA	Intergenic	Intergenic	50265	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.003960	0.304348	
chunk0192_343_1	chr8	67677372	67677815	+	0	NA	intron (NM_020361, intron 1 of 10)	intron (NM_020361, intron 1 of 10)	68792	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.002257	0.351351	
chunk0109_331_1	chr20	9334663	9335461	+	0	NA	intron (NM_001172646, intron 3 of 37)	intron (NM_001172646, intron 3 of 37)	27262	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.006266	0.395494	450(TTGTACACTGTGTACC,-,0.00),451(TGTACACTGTGTACCA,+,0.00)
chunk0172_391_1	chr6	139597225	139597715	+	0	NA	Intergenic	Intergenic	-122874	NR_033919	645434	Hs.666240	NR_033919	ENSG00000238099	LINC01625	-	long intergenic non-protein coding RNA 1625	ncRNA	0.002041	0.384929	
chunk0136_277_1	chr3	194686908	194687107	+	0	NA	exon (NM_153690, exon 1 of 1)	exon (NM_153690, exon 1 of 1)	1114	NM_153690	131583	Hs.435080	NM_153690	ENSG00000185112	FAM43A	-	family with sequence similarity 43 member A	protein-coding	0.100503	0.670000	
chunk0147_375_1	chr4	186012177	186012415	+	0	NA	Intergenic	Intergenic	-55580	NM_001270771	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.042017	0.518828	
chunk0036_73_1	chr11	59787020	59787283	+	0	NA	intron (NM_004177, intron 3 of 10)	intron (NM_004177, intron 3 of 10)	23721	NM_017840	54948	Hs.530734	NM_017840	ENSG00000166902	MRPL16	L16mt|MRP-L16|PNAS-111	mitochondrial ribosomal protein L16	protein-coding	0.011407	0.435606	
chunk0136_266_1	chr3	194440058	194440313	+	0	NA	intron (NM_024524, intron 15 of 31)	intron (NM_024524, intron 15 of 31)	28054	NM_024524	79572	Hs.529609	NM_024524	ENSG00000133657	ATP13A3	AFURS1	ATPase 13A3	protein-coding	0.007843	0.480469	
chunk0180_386_1	chr7	74496046	74496379	+	0	NA	intron (NM_001199207, intron 1 of 26)	(TGTA)n|Simple_repeat|Simple_repeat	42422	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.015015	0.500000	
chunk0085_117_1	chr18	2948099	2948669	+	0	NA	intron (NM_014646, intron 4 of 19)	intron (NM_014646, intron 4 of 19)	-1761	NR_026659	727896	Hs.673126	NR_026659		LOC727896	-	cysteine and histidine rich domain containing 1 pseudogene	pseudo	0.007018	0.373030	
chunk0092_86_1	chr19	21699894	21700493	+	0	NA	Intergenic	Intergenic	-50552	NR_024523	641367	Hs.680128	NR_024523	ENSG00000269845	LOC641367	-	cyclin Y like 1 pseudogene	pseudo	0.006678	0.345000	
chunk0001_437_1	chr1	11478944	11479162	+	0	NA	promoter-TSS (NM_020780)	promoter-TSS (NM_020780)	-185	NM_020780	57540	Hs.202355	NM_020780	ENSG00000204624	DISP3	PTCHD2	dispatched RND transporter family member 3	protein-coding	0.155963	0.748858	
chunk0016_338_1	chr1	201850342	201850574	+	0	NA	intron (NM_018085, intron 4 of 23)	intron (NM_018085, intron 4 of 23)	-12915	NR_106797	102466724		NR_106797	ENSG00000277681	MIR6739	hsa-mir-6739	microRNA 6739	ncRNA	0.004310	0.369099	
chunk0010_134_1	chr1	114734586	114735158	+	0	NA	intron (NM_001242893, intron 4 of 17)	intron (NM_001242893, intron 4 of 17)	-17978	NM_002524	4893	Hs.486502	NM_002524	ENSG00000213281	NRAS	ALPS4|CMNS|N-ras|NCMS|NRAS1|NS6	NRAS proto-oncogene, GTPase	protein-coding	0.006993	0.335079	
chunk0099_199_1	chr2	94209028	94209258	+	0	NA	Intergenic	REP522|Satellite|telo	378040	NR_024443	100133920	Hs.645503	NR_024443	ENSG00000261522	LOC100133920	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like pseudogene	pseudo	0.039130	0.619048	
chunk0039_347_1	chr11	105468186	105468623	+	0	NA	Intergenic	Intergenic	-141669	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.009153	0.404110	158(TGGGACTCTGTGTTCT,-,0.00),159(GGGACTCTGTGTTCTG,+,0.00)
chunk0210_216_1	chrX	81957566	81957765	+	0	NA	Intergenic	Intergenic	-755723	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.020101	0.380000	
chunk0029_138_1	chr10	99266437	99266861	+	0	NA	Intergenic	L1PB1|LINE|L1	-30774	NM_001166245	60495	Hs.500750	NM_021828	ENSG00000172987	HPSE2	HPA2|HPR2|UFS|UFS1	heparanase 2 (inactive)	protein-coding	0.009434	0.508235	
chunk0146_386_1	chr4	168662603	168662837	+	0	NA	intron (NM_001166109, intron 1 of 18)	intron (NM_001166109, intron 1 of 18)	31103	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.004274	0.382979	
chunk0173_33_1	chr6	142147069	142147268	+	0	NA	promoter-TSS (NM_001286372)	promoter-TSS (NM_001286372)	6	NM_001286372	51534	Hs.431367	NM_016485	ENSG00000009844	VTA1	C6orf55|DRG-1|DRG1|HSPC228|LIP5|My012|SBP1	vesicle trafficking 1	protein-coding	0.095477	0.610000	
chunk0100_264_1	chr2	113702045	113702378	+	0	NA	Intergenic	Intergenic	19157	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.012012	0.398204	
chunk0098_310_1	chr2	76428800	76429411	+	0	NA	Intergenic	Intergenic	-556860	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.004910	0.338235	
chunk0051_439_1	chr12	123149143	123149751	+	0	NA	Intergenic	Intergenic	-38958	NM_001300801	57605	Hs.272759	NM_020845	ENSG00000090975	PITPNM2	NIR-3|NIR3|RDGB2|RDGBA2	phosphatidylinositol transfer protein membrane associated 2	protein-coding	0.014803	0.532020	
chunk0191_402_1	chr8	57545077	57545385	+	0	NA	Intergenic	L2|LINE|L2	201444	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.003247	0.375405	
chunk0128_223_1	chr3	108214276	108214600	+	0	NA	intron (NM_018010, intron 3 of 10)	L1ME4b|LINE|L1	8132	NM_018010	55081	Hs.412196	NM_018010	ENSG00000114446	IFT57	ESRRBL1|HIPPI|MHS4R2|OFD18	intraflagellar transport 57	protein-coding	0.000000	0.301538	
chunk0055_83_1	chr13	54029630	54030140	+	0	NA	Intergenic	Intergenic	102986	NR_108063	100507428	Hs.351262	NR_108062	ENSG00000234787	LINC00458	LncRNA-ES3	long intergenic non-protein coding RNA 458	ncRNA	0.011765	0.395303	
chunk0133_446_1	chr3	175120318	175120689	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	-5261	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.002695	0.325269	
chunk0075_417_1	chr16	57339670	57340094	+	0	NA	Intergenic	AluJb|SINE|Alu	-18901	NM_002990	6367	Hs.534347	NM_002990	ENSG00000102962	CCL22	A-152E5.1|ABCD-1|DC/B-CK|MDC|SCYA22|STCP-1	C-C motif chemokine ligand 22	protein-coding	0.016509	0.508235	
chunk0024_317_1	chr10	42782434	42782812	+	0	NA	5' UTR (NM_014753, exon 1 of 23)	5' UTR (NM_014753, exon 1 of 23)	117	NM_014753	9790	Hs.10848	NM_014753	ENSG00000165733	BMS1	ACC|BMS1L	BMS1 ribosome biogenesis factor	protein-coding	0.097884	0.646438	
chunk0198_249_1	chr8	134558801	134559009	+	0	NA	intron (NM_020863, intron 11 of 15)	MIRb|SINE|MIR	-39166	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.000000	0.373206	
chunk0157_216_1	chr5	119328651	119329243	+	0	NA	intron (NM_001286815, intron 2 of 2)	intron (NM_001286815, intron 2 of 2)	-4228	NM_001286814	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.013514	0.408094	
chunk0085_467_1	chr18	11856241	11857413	+	0	NA	promoter-TSS (NM_001261444)	promoter-TSS (NM_001261444)	-611	NM_001261444	2774	Hs.136295	NM_002071	ENSG00000141404	GNAL	DYT25	G protein subunit alpha L	protein-coding	0.010239	0.456948	
chunk0054_297_1	chr13	48221473	48222226	+	0	NA	Intergenic	Intergenic	-11289	NM_021999	9445	Hs.643683	NM_021999	ENSG00000136156	ITM2B	ABRI|BRI|BRI2|BRICD2B|E25B|E3-16|FBD|RDGCA|imBRI2	integral membrane protein 2B	protein-coding	0.010624	0.396552	463(AGAACGACTTGTTCTT,+,0.00)
chunk0127_396_1	chr3	102345160	102345404	+	0	NA	Intergenic	L2a|LINE|L2	-89733	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.326531	115(TAGCACATTGTGTGCT,-,0.00),116(AGCACATTGTGTGCTC,+,0.00)
chunk0028_40_1	chr10	83052627	83052870	+	0	NA	Intergenic	Intergenic	-819828	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.000000	0.340164	
chunk0140_292_1	chr4	72508558	72508759	+	0	NA	intron (NM_014243, intron 3 of 21)	intron (NM_014243, intron 3 of 21)	60141	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.009950	0.262376	
chunk0206_307_1	chr9	124908642	124909007	+	0	NA	intron (NM_002077, intron 11 of 22)	intron (NM_002077, intron 11 of 22)	32283	NM_002077	2800	Hs.59504	NM_002077	ENSG00000136935	GOLGA1	golgin-97	golgin A1	protein-coding	0.008219	0.445355	
chunk0067_45_1	chr15	40787296	40787764	+	0	NA	intron (NM_018163, intron 1 of 10)	intron (NM_018163, intron 1 of 10)	17569	NM_001130448	643338	Hs.631715	NM_001130448	ENSG00000188277	C15orf62	-	chromosome 15 open reading frame 62	protein-coding	0.008547	0.486141	
chunk0188_134_1	chr8	9382695	9383339	+	0	NA	Intergenic	Intergenic	57966	NR_040039	157273	Hs.650222	NR_040039	ENSG00000248538	LOC157273	-	uncharacterized LOC157273	ncRNA	0.017081	0.491473	
chunk0004_299_1	chr1	48973650	48974175	+	0	NA	intron (NM_032785, intron 5 of 13)	L1M6|LINE|L1	-196943	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.007619	0.395437	
chunk0063_93_1	chr14	78313064	78313443	+	0	NA	intron (NR_073547, intron 4 of 20)	intron (NR_073547, intron 4 of 20)	-90478	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.010554	0.421053	
chunk0184_409_1	chr7	122556634	122557396	+	0	NA	intron (NM_017954, intron 7 of 29)	LTR33A|LTR|ERVL	142139	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.006562	0.389253	
chunk0037_391_1	chr11	78907627	78907961	+	0	NA	intron (NM_001098816, intron 6 of 33)	intron (NM_001098816, intron 6 of 33)	-332930	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.011976	0.450746	
chunk0207_94_1	chrX	9633468	9633978	+	0	NA	intron (NM_001139468, intron 3 of 17)	intron (NM_001139468, intron 3 of 17)	132242	NM_000273	4935	Hs.74124	NM_000273	ENSG00000101850	GPR143	NYS6|OA1	G protein-coupled receptor 143	protein-coding	0.013725	0.416830	
chunk0184_254_1	chr7	117982624	117982823	+	0	NA	Intergenic	Intergenic	-109216	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.020101	0.490000	18(CAGGTCAAGCTGTTCT,-,0.00),19(AGGTCAAGCTGTTCTC,+,0.00)
chunk0097_61_1	chr2	43995989	43996255	+	0	NA	promoter-TSS (NM_133259)	promoter-TSS (NM_133259)	-117	NM_133259	10128	Hs.368084	NM_133259	ENSG00000138095	LRPPRC	CLONE-23970|GP130|LRP130|LSFC	leucine rich pentatricopeptide repeat containing	protein-coding	0.063910	0.531835	
chunk0036_315_1	chr11	66179469	66179976	+	0	NA	intron (NM_018026, intron 1 of 23)	intron (NM_018026, intron 1 of 23)	-77572	NM_001134775	64837	Hs.280792	NM_022822	ENSG00000174996	KLC2	-	kinesin light chain 2	protein-coding	0.001972	0.399606	342(TGTTCAGCCTGTTCCT,+,0.00)
chunk0104_337_1	chr2	179612242	179612452	+	0	NA	intron (NM_152520, intron 3 of 9)	L1MA3|LINE|L1	-26441	NM_001282725	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.004762	0.426540	
chunk0070_285_1	chr15	74575277	74575641	+	0	NA	intron (NM_001307939, intron 4 of 8)	intron (NM_001307939, intron 4 of 8)	-32913	NM_003992	1198	Hs.511790	NM_001292	ENSG00000179335	CLK3	PHCLK3|PHCLK3/152	CDC like kinase 3	protein-coding	0.005495	0.487671	
chunk0076_453_1	chr16	74101856	74102407	+	0	NA	Intergenic	Intergenic	113390	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.000000	0.375000	
chunk0115_128_1	chr21	23231139	23231479	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	152025	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.005882	0.360704	
chunk0034_259_1	chr11	34418343	34418864	+	0	NA	Intergenic	L1ME3G|LINE|L1	-20322	NM_001752	847	Hs.502302	NM_001752	ENSG00000121691	CAT	-	catalase	protein-coding	0.005758	0.454023	
chunk0034_404_1	chr11	37994205	37994404	+	0	NA	Intergenic	Intergenic	652052	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.005025	0.360000	
chunk0148_111_1	chr5	4819378	4819642	+	0	NA	Intergenic	Intergenic	46029	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.011364	0.433962	
chunk0165_177_1	chr6	34341136	34341835	+	0	NA	intron (NM_006703, intron 2 of 4)	intron (NM_006703, intron 2 of 4)	51195	NM_006703	11165	Hs.188882	NM_006703	ENSG00000272325	NUDT3	DIPP|DIPP-1|DIPP1	nudix hydrolase 3	protein-coding	0.007153	0.402857	
chunk0038_139_1	chr11	84268851	84269523	+	0	NA	intron (NM_001142699, intron 7 of 27)	L2a|LINE|L2	4093	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004464	0.356612	
chunk0165_166_1	chr6	34045038	34045332	+	0	NA	intron (NM_001256809, intron 4 of 8)	intron (NM_001256809, intron 4 of 8)	-45134	NR_031681	100302123		NR_031681	ENSG00000221697	MIR1275	MIRN1275|hsa-mir-1275|mir-1275	microRNA 1275	ncRNA	0.027211	0.593220	
chunk0125_182_1	chr3	66642085	66642475	+	0	NA	Intergenic	Intergenic	-141859	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.010256	0.358056	
chunk0154_339_1	chr5	86093425	86093882	+	0	NA	Intergenic	Intergenic	-188791	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.004376	0.340611	
chunk0139_303_1	chr4	57633470	57633791	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	207758	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.006231	0.369565	
chunk0165_403_1	chr6	38861209	38861653	+	0	NA	intron (NM_001206927, intron 43 of 92)	L1MC5|LINE|L1	91676	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.011261	0.391011	
chunk0014_145_1	chr1	177975711	177976002	+	0	NA	Intergenic	Intergenic	-5941	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.006873	0.520548	
chunk0109_118_1	chr20	2768050	2768729	+	0	NA	Intergenic	Intergenic	32257	NM_019609	56265	Hs.659346	NM_019609	ENSG00000088882	CPXM1	CPX1|CPXM	carboxypeptidase X, M14 family member 1	protein-coding	0.019146	0.616176	
chunk0056_387_1	chr13	93692175	93692668	+	0	NA	intron (NM_005708, intron 2 of 8)	intron (NM_005708, intron 2 of 8)	166052	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.006085	0.283401	
chunk0090_28_1	chr19	1181541	1182130	+	0	NA	Intergenic	Intergenic	-7552	NM_014963	22904	Hs.408708	NM_014963	ENSG00000064932	SBNO2	KIAA0963|SNO|STNO	strawberry notch homolog 2	protein-coding	0.023769	0.598305	
chunk0162_285_1	chr6	6195335	6196036	+	0	NA	intron (NM_000129, intron 10 of 14)	intron (NM_000129, intron 10 of 14)	-26250	NR_107007	102466866		NR_107007	ENSG00000263572	MIR7853	hsa-mir-7853	microRNA 7853	ncRNA	0.009986	0.437322	
chunk0012_56_1	chr1	155500508	155500707	+	0	NA	intron (NM_018489, intron 2 of 27)	intron (NM_018489, intron 2 of 27)	-61374	NR_027023	645676	Hs.568693	NR_027023	ENSG00000235919	ASH1L-AS1	-	ASH1L antisense RNA 1	ncRNA	0.015075	0.445000	111(ATGACAGAATGTGCCT,+,0.00)
chunk0088_420_1	chr18	54957235	54957844	+	0	NA	intron (NM_025214, intron 1 of 11)	L2b|LINE|L2	509	NM_001143829	80323	Hs.120790	NM_025214	ENSG00000166510	CCDC68	SE57-1	coiled-coil domain containing 68	protein-coding	0.003284	0.352459	283(CAGAACACAGTGTCCT,-,0.00),284(AGAACACAGTGTCCTC,+,0.00)
chunk0141_195_1	chr4	83638879	83639398	+	0	NA	Intergenic	Intergenic	102821	NM_032717	84803	Hs.99196	NM_032717	ENSG00000138678	GPAT3	AGPAT 10|AGPAT10|AGPAT8|AGPAT9|HMFN0839|LPAAT-theta|MAG1	glycerol-3-phosphate acyltransferase 3	protein-coding	0.000000	0.351923	
chunk0065_22_1	chr15	20386237	20386639	+	0	NA	Intergenic	Intergenic	103694	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.000000	0.454094	
chunk0121_417_1	chr3	25789867	25790082	+	0	NA	promoter-TSS (NM_001145294)	promoter-TSS (NM_001145294)	65	NM_001145294	55768	Hs.368960	NM_018297	ENSG00000151092	NGLY1	CDDG|CDG1V|PNG1|PNGase	N-glycanase 1	protein-coding	0.125581	0.620370	
chunk0068_51_1	chr15	51499960	51500458	+	0	NA	exon (NM_001174116, exon 18 of 43)	exon (NM_001174116, exon 18 of 43)	122561	NM_015263	23312	Hs.511386	NM_015263	ENSG00000104093	DMXL2	DFNA71|PEPNS|RC3	Dmx like 2	protein-coding	0.004016	0.366733	
chunk0011_375_1	chr1	153670961	153671160	+	0	NA	promoter-TSS (NM_001267809)	promoter-TSS (NM_001267809)	-32	NM_001267809	3608	Hs.75117	NM_004515	ENSG00000143621	ILF2	NF45|PRO3063	interleukin enhancer binding factor 2	protein-coding	0.050251	0.490000	
chunk0013_359_1	chr1	172356631	172357141	+	0	NA	intron (NM_015569, intron 17 of 20)	L1MC4a|LINE|L1	-63802	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.000000	0.360078	
chunk0006_389_1	chr1	75003069	75003738	+	0	NA	Intergenic	MIRb|SINE|MIR	-125031	NM_001001933	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.007474	0.394030	
chunk0112_408_1	chr20	47117895	47118215	+	0	NA	intron (NM_172110, intron 9 of 13)	intron (NM_172110, intron 9 of 13)	-48912	NR_037410	100500814		NR_037410	ENSG00000264901	MIR3616	mir-3616	microRNA 3616	ncRNA	0.012500	0.417445	
chunk0081_309_1	chr17	45584409	45584858	+	0	NA	Intergenic	Intergenic	17229	NR_026901	644172	Hs.448859	NR_026901		MAPK8IP1P2	-	mitogen-activated protein kinase 8 interacting protein 1 pseudogene 2	pseudo	0.071269	0.666667	
chunk0033_176_1	chr11	15756441	15756746	+	0	NA	Intergenic	Intergenic	112708	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.000000	0.359477	178(TAGCACATCATGATCT,-,0.00),179(AGCACATCATGATCTG,+,0.00)
chunk0182_387_1	chr7	100158547	100158768	+	0	NA	promoter-TSS (NM_001303470)	promoter-TSS (NM_001303470)	64	NM_018275	55262	Hs.533139	NM_018275	ENSG00000146826	MAP11	C7orf43|MCPH25	microtubule associated protein 11	protein-coding	0.122172	0.747748	
chunk0088_414_1	chr18	54801434	54801695	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-26913	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.003831	0.454198	
chunk0189_17_1	chr8	19608237	19608962	+	0	NA	intron (NR_024040, intron 1 of 9)	intron (NR_024040, intron 1 of 9)	-6054	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.005517	0.415978	
chunk0082_356_1	chr17	60154481	60155032	+	0	NA	intron (NM_000717, intron 1 of 7)	intron (NM_000717, intron 1 of 7)	4815	NM_000717	762	Hs.89485	NM_000717	ENSG00000167434	CA4	CAIV|Car4|RP17	carbonic anhydrase 4	protein-coding	0.014519	0.534420	
chunk0032_105_1	chr11	3737488	3738122	+	0	NA	intron (NM_016320, intron 12 of 32)	intron (NM_016320, intron 12 of 32)	-59919	NM_001256235	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.015773	0.382677	
chunk0054_270_1	chr13	46595468	46595968	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	42557	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.006000	0.387226	
chunk0127_360_1	chr3	101512562	101512847	+	0	NA	intron (NM_001077203, intron 1 of 22)	intron (NM_001077203, intron 1 of 22)	537	NM_001077203	57337	Hs.529551	NM_020654	ENSG00000138468	SENP7	-	SUMO specific peptidase 7	protein-coding	0.052632	0.562937	
chunk0126_231_1	chr3	79019387	79019850	+	0	NA	promoter-TSS (NM_001145845)	promoter-TSS (NM_001145845)	-159	NM_001145845	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.036717	0.553879	
chunk0175_137_1	chr7	3501287	3502194	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	200292	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.004410	0.312775	
chunk0187_405_1	chr7	157973868	157974163	+	0	NA	intron (NM_001308268, intron 11 of 22)	intron (NM_001308268, intron 11 of 22)	119430	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.033898	0.540541	207(GAGCACAGGCTGAGCT,-,0.00),208(AGCACAGGCTGAGCTG,+,0.00)
chunk0134_448_1	chr3	183809151	183809674	+	0	NA	intron (NM_018023, intron 30 of 30)	intron (NM_018023, intron 30 of 30)	16193	NM_024871	79929	Hs.478465	NM_024871	ENSG00000180834	MAP6D1	MAPO6D1|SL21	MAP6 domain containing 1	protein-coding	0.009560	0.425573	
chunk0009_361_1	chr1	109725442	109725942	+	0	NA	Intergenic	LTR3|LTR|ERVK	13450	NM_000851	2949	Hs.75652	NM_000851	ENSG00000134201	GSTM5	GSTM5-5|GTM5	glutathione S-transferase mu 5	protein-coding	0.008000	0.451098	
chunk0036_236_1	chr11	64237628	64237965	+	0	NA	intron (NM_003377, intron 6 of 6)	intron (NM_003377, intron 6 of 6)	-3145	NM_004470	2286	Hs.227729	NM_004470	ENSG00000173486	FKBP2	FKBP-13|FKBP13|PPIase	FKBP prolyl isomerase 2	protein-coding	0.008902	0.547337	
chunk0007_295_1	chr1	84142616	84142970	+	0	NA	intron (NM_207578, intron 1 of 8)	intron (NM_207578, intron 1 of 8)	-1455	NM_001300916	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.000000	0.256338	
chunk0048_368_1	chr12	85986303	85986551	+	0	NA	intron (NM_013244, intron 5 of 6)	intron (NM_013244, intron 5 of 6)	112132	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.004032	0.397590	
chunk0199_92_1	chr9	2663899	2664449	+	0	NA	Intergenic	LTR85a|LTR|Gypsy?	-41801	NR_015375	401491	Hs.416043	NR_015375	ENSG00000236404	VLDLR-AS1	linc-VLDLR|lincRNA-VLDLR	VLDLR antisense RNA 1	ncRNA	0.007273	0.459165	229(AGGCACACGGTGTGCC,-,0.00),230(GGCACACGGTGTGCCG,+,0.00)
chunk0211_174_1	chrX	116096191	116096390	+	0	NA	Intergenic	L1M3|LINE|L1	-74415	NM_000686	186	Hs.405348	NM_000686	ENSG00000180772	AGTR2	AT2|ATGR2|MRX88	angiotensin II receptor type 2	protein-coding	0.000000	0.345000	
chunk0132_48_1	chr3	154945430	154946256	+	0	NA	Intergenic	L1PA6|LINE|L1	-133804	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.006053	0.504232	
chunk0151_119_1	chr5	43699682	43700335	+	0	NA	intron (NM_182977, intron 19 of 21)	intron (NM_182977, intron 19 of 21)	-96778	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.003063	0.368502	343(AAGAACAAAGTGTGCA,-,0.00),344(AGAACAAAGTGTGCAG,+,0.00),383(CTGTACATTATGTCCT,-,0.00),384(TGTACATTATGTCCTG,+,0.00)
chunk0051_122_1	chr12	115314265	115314464	+	0	NA	Intergenic	Intergenic	-630200	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.005025	0.370000	
chunk0110_414_1	chr20	20577120	20577722	+	0	NA	intron (NM_020343, intron 20 of 39)	intron (NM_020343, intron 20 of 39)	135202	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.003322	0.394693	257(TGGCACATGGTGTCTT,-,0.00),258(GGCACATGGTGTCTTG,+,0.00)
chunk0101_117_1	chr2	126482305	126482582	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-173492	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.021661	0.341727	
chunk0087_18_1	chr18	30985851	30986145	+	0	NA	Intergenic	Intergenic	56817	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.030612	0.505085	
chunk0129_418_1	chr3	127112902	127114037	+	0	NA	Intergenic	L1M4|LINE|L1	-79662	NM_001007534	285311	Hs.591284	NM_001007534	ENSG00000214324	C3orf56	-	chromosome 3 open reading frame 56	protein-coding	0.007048	0.450704	
chunk0089_227_1	chr18	61636230	61636820	+	0	NA	Intergenic	Intergenic	-111651	NR_103449	100996669	Hs.586981	NR_103449		LINC01544	-	long intergenic non-protein coding RNA 1544	ncRNA	0.005085	0.514382	
chunk0076_327_1	chr16	70747835	70748092	+	0	NA	intron (NM_018052, intron 12 of 18)	intron (NM_018052, intron 12 of 18)	-7097	NR_034083	100130894	Hs.678899	NR_034083	ENSG00000214353	VAC14-AS1	-	VAC14 antisense RNA 1	ncRNA	0.019455	0.577519	150(AGGAGCAGGCTGTCCT,-,0.00),151(GGAGCAGGCTGTCCTC,+,0.00)
chunk0031_348_1	chr10	129622400	129622757	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	155394	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.005602	0.340782	
chunk0002_362_1	chr1	26072939	26073262	+	0	NA	Intergenic	Intergenic	-5466	NM_032588	84676	Hs.279709	NM_032588	ENSG00000158022	TRIM63	IRF|MURF1|MURF2|RNF28|SMRZ	tripartite motif containing 63	protein-coding	0.009288	0.425926	
chunk0009_438_1	chr1	111387492	111387691	+	0	NA	intron (NR_029429, intron 3 of 4)	intron (NR_029429, intron 3 of 4)	2260	NR_029429	441897	Hs.568387	NR_029429	ENSG00000227179	PGCP1	-	progastricsin pseudogene 1	pseudo	0.000000	0.370000	
chunk0021_137_1	chr10	3899025	3899313	+	0	NA	Intergenic	Intergenic	-91991	NR_106726	102464829		NR_106726	ENSG00000274809	MIR6078	hsa-mir-6078	microRNA 6078	ncRNA	0.006944	0.394464	
chunk0163_37_1	chr6	8410666	8411126	+	0	NA	Intergenic	Intergenic	24671	NR_109914	51000	Hs.285847	NM_015948	ENSG00000124786	SLC35B3	C6orf196|CGI-19|PAPST2	solute carrier family 35 member B3	protein-coding	0.002174	0.396963	
chunk0048_431_1	chr12	88425008	88425717	+	0	NA	Intergenic	MIR3|SINE|MIR	155111	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.007052	0.402817	
chunk0083_283_1	chr17	68648115	68648314	+	0	NA	intron (NR_110825, intron 2 of 4)	L1ME1|LINE|L1	20060	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.005025	0.335000	
chunk0144_260_1	chr4	136730962	136731413	+	0	NA	Intergenic	L1M4|LINE|L1	801311	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.002217	0.323009	
chunk0196_146_1	chr8	104562825	104563565	+	0	NA	intron (NM_013437, intron 1 of 6)	MIR|SINE|MIR	25829	NM_001135703	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.005405	0.295547	
chunk0138_419_1	chr4	45085151	45085582	+	0	NA	Intergenic	Intergenic	-358732	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.000000	0.340278	
chunk0050_225_1	chr12	104779236	104779636	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	149258	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.005000	0.359102	81(AGGGACTCTGTGTGCT,-,0.00),82(GGGACTCTGTGTGCTC,+,0.00)
chunk0083_125_1	chr17	65055703	65055960	+	0	NA	promoter-TSS (NM_001282425)	promoter-TSS (NM_001282425)	-57	NM_001282425	10672	Hs.515018	NM_006572	ENSG00000120063	GNA13	G13	G protein subunit alpha 13	protein-coding	0.066148	0.604651	
chunk0038_422_1	chr11	94301016	94301459	+	0	NA	Intergenic	Intergenic	-4400	NM_001199206	390243	Hs.553758	NM_001080486	ENSG00000183560	IZUMO1R	FOLR4|Folbp3|JUNO	IZUMO1 receptor, JUNO	protein-coding	0.006772	0.457207	
chunk0143_298_1	chr4	118746349	118747005	+	0	NA	intron (NM_014822, intron 13 of 22)	L2b|LINE|L2	61307	NM_020961	57721	Hs.596872	NM_020961	ENSG00000145388	METTL14	hMETTL14	methyltransferase like 14	protein-coding	0.000000	0.441400	308(GTGCACATTCTGTTCC,-,0.00),309(TGCACATTCTGTTCCC,+,0.00)
chunk0042_394_1	chr12	11006700	11006966	+	0	NA	intron (NM_001291314, intron 2 of 6).3	intron (NM_001291314, intron 2 of 6).3	-8958	NM_176889	259295	Hs.686384	NM_176889	ENSG00000255837	TAS2R20	T2R20|T2R49|T2R56|TAS2R49	taste 2 receptor member 20	protein-coding	0.007519	0.318352	
chunk0008_10_1	chr1	87328928	87329127	+	0	NA	5' UTR (NM_006769, exon 1 of 5)	5' UTR (NM_006769, exon 1 of 5)	559	NM_006769	8543	Hs.436792	NM_006769	ENSG00000143013	LMO4	-	LIM domain only 4	protein-coding	0.105528	0.650000	
chunk0037_255_1	chr11	75516682	75516881	+	0	NA	intron (NM_030792, intron 1 of 16)	MIR|SINE|MIR	8773	NM_030792	81544	Hs.503297	NM_030792	ENSG00000158555	GDPD5	GDE2|PP1665	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding	0.010050	0.410000	
chunk0069_46_1	chr15	60682528	60683164	+	0	NA	intron (NR_120318, intron 2 of 2)	intron (NR_120318, intron 2 of 2)	1277	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.014151	0.488226	253(AAGAACACCAAGATCC,-,0.00)
chunk0098_324_1	chr2	76768841	76769468	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-216811	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.003190	0.350318	
chunk0202_117_1	chr9	72898720	72898930	+	0	NA	Intergenic	Intergenic	-24716	NR_121181	101927258	Hs.586433	NR_121120	ENSG00000236849	LINC01474	-	long intergenic non-protein coding RNA 1474	ncRNA	0.004762	0.279621	
chunk0082_198_1	chr17	56808343	56809034	+	0	NA	intron (NM_001085430, intron 6 of 7)	intron (NM_001085430, intron 6 of 7)	25207	NM_001085430	339210	Hs.658949	NM_001085430	ENSG00000214226	C17orf67	-	chromosome 17 open reading frame 67	protein-coding	0.008683	0.465318	377(GGGCACAGCTTGTCTC,-,0.00)
chunk0029_289_1	chr10	103812008	103812427	+	0	NA	intron (NM_014631, intron 1 of 13)	intron (NM_014631, intron 1 of 13)	43189	NM_014631	9644	Hs.678727	NM_014631	ENSG00000107957	SH3PXD2A	FISH|SH3MD1|TKS5	SH3 and PX domains 2A	protein-coding	0.007160	0.530952	
chunk0093_42_1	chr19	39677388	39677589	+	0	NA	Intergenic	L1PA12|LINE|L1	-1886	NR_034156	400696	Hs.456377	NM_207646	ENSG00000226025	LGALS17A	-	galectin 14 pseudogene	pseudo	0.004975	0.336634	
chunk0142_225_1	chr4	98226546	98226745	+	0	NA	Intergenic	L1MEi|LINE|L1	-34731	NM_001100428	5910	Hs.132858	NM_021159	ENSG00000138698	RAP1GDS1	GDS1|SmgGDS	Rap1 GTPase-GDP dissociation stimulator 1	protein-coding	0.020101	0.450000	
chunk0112_53_1	chr20	37178937	37179433	+	0	NA	5' UTR (NM_002951, exon 1 of 17)	5' UTR (NM_002951, exon 1 of 17)	132	NM_001135771	6185	Hs.370895	NM_002951	ENSG00000118705	RPN2	RIBIIR|RPN-II|RPNII|SWP1	ribophorin II	protein-coding	0.100806	0.684105	
chunk0204_112_1	chr9	94910777	94911076	+	0	NA	intron (NM_032823, intron 5 of 14)	intron (NM_032823, intron 5 of 14)	100964	NR_031755	100313780		NR_031755	ENSG00000252153	MIR2278	mir-2278	microRNA 2278	ncRNA	0.003344	0.386667	
chunk0095_153_1	chr2	16975081	16975326	+	0	NA	Intergenic	Intergenic	-309337	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.004082	0.378049	
chunk0079_14_1	chr17	9557608	9557858	+	0	NA	intron (NM_004853, intron 2 of 7)	intron (NM_004853, intron 2 of 7)	18225	NM_004853	9482	Hs.431109	NM_004853	ENSG00000170310	STX8	CARB	syntaxin 8	protein-coding	0.016000	0.557769	
chunk0198_295_1	chr8	136752051	136752250	+	0	NA	Intergenic	L1M3b|LINE|L1	661438	NR_125428	101927915	Hs.695851	NR_125428		LOC101927915	-	uncharacterized LOC101927915	ncRNA	0.000000	0.440000	
chunk0080_357_1	chr17	32912248	32912450	+	0	NA	Intergenic	Intergenic	-15561	NM_001301746	26022	Hs.3447	NM_015544	ENSG00000006042	TMEM98	TADA1	transmembrane protein 98	protein-coding	0.014851	0.546798	
chunk0004_245_1	chr1	47354407	47354966	+	0	NA	intron (NM_001136140, intron 1 of 4)	L1ME3G|LINE|L1	20889	NM_016308	51727	Hs.731647	NM_016308	ENSG00000162368	CMPK1	CK|CMK|CMPK|UMK|UMP-CMPK|UMPK	cytidine/uridine monophosphate kinase 1	protein-coding	0.007156	0.332143	
chunk0161_4_1	chr5	165327454	165328097	+	0	NA	Intergenic	L3|LINE|CR1	857496	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.007776	0.363354	324(GGATACACAATGTTCT,-,0.00),325(GATACACAATGTTCTG,+,0.00)
chunk0142_183_1	chr4	95964339	95964891	+	0	NA	Intergenic	Intergenic	124527	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.007246	0.406872	288(GAGAACAAACTGTTCT,-,0.00),289(AGAACAAACTGTTCTA,+,0.00)
chunk0026_102_1	chr10	61801710	61802309	+	0	NA	Intergenic	Intergenic	-99245	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.011686	0.386667	
chunk0022_244_1	chr10	14449663	14449957	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	13234	NR_031668	100302116		NR_031668	ENSG00000221371	MIR1265	MIRN1265|hsa-mir-1265	microRNA 1265	ncRNA	0.006803	0.366102	
chunk0060_255_1	chr14	50055549	50056220	+	0	NA	intron (NR_131171, intron 2 of 8)	intron (NR_131171, intron 2 of 8)	-48364	NR_126498	283551	Hs.292580	NM_001012706	ENSG00000214900	LINC01588	C14orf182	long intergenic non-protein coding RNA 1588	ncRNA	0.017884	0.495536	
chunk0043_455_1	chr12	26723404	26724078	+	0	NA	intron (NM_002223, intron 4 of 56)	L4_A_Mam|LINE|RTE-X	109457	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.011869	0.420741	
chunk0120_214_1	chr3	7432011	7432374	+	0	NA	intron (NM_000844, intron 5 of 9)	intron (NM_000844, intron 5 of 9)	103092	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.011019	0.387363	
chunk0019_302_1	chr1	228902971	228903632	+	0	NA	Intergenic	Intergenic	168224	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.015129	0.480363	
chunk0133_137_1	chr3	169204317	169205189	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-57019	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.004587	0.365407	
chunk0178_29_1	chr7	29399006	29399332	+	0	NA	intron (NM_001293069, intron 6 of 13)	intron (NM_001293069, intron 6 of 13)	-80543	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.015337	0.504587	
chunk0144_79_1	chr4	128062204	128062403	+	0	NA	intron (NM_032239, intron 1 of 8)	CpG	1037	NM_001278604	55132	Hs.654971	NM_018078	ENSG00000138709	LARP1B	LARP2	La ribonucleoprotein domain family member 1B	protein-coding	0.065327	0.640000	
chunk0099_145_1	chr2	86673914	86674393	+	0	NA	intron (NM_001198954, intron 2 of 7)	intron (NM_001198954, intron 2 of 7)	-46138	NM_022780	64795	Hs.75277	NM_022780	ENSG00000153561	RMND5A	CTLH|GID2|GID2A|RMD5|p44CTLH	required for meiotic nuclear division 5 homolog A	protein-coding	0.002088	0.491667	
chunk0004_376_1	chr1	51686665	51686864	+	0	NA	intron (NM_148908, intron 3 of 22)	intron (NM_148908, intron 3 of 22)	-43050	NM_148907	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.005025	0.445000	
chunk0116_431_1	chr21	43001322	43001723	+	0	NA	intron (NM_004571, intron 1 of 10)	L2b|LINE|L2	27012	NM_001286258	5316	Hs.431043	NM_004571	ENSG00000160199	PKNOX1	PREP1|pkonx1c	PBX/knotted 1 homeobox 1	protein-coding	0.009975	0.537313	274(TAGCACAGGCTGTTCT,-,0.00),275(AGCACAGGCTGTTCTC,+,0.00)
chunk0004_367_1	chr1	51567388	51568284	+	0	NA	Intergenic	Intergenic	-48513	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.000000	0.433668	
chunk0155_307_1	chr5	96402513	96403129	+	0	NA	intron (NM_001177875, intron 9 of 13)	intron (NM_001177875, intron 9 of 13)	29338	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.011364	0.471637	
chunk0011_74_1	chr1	144104324	144104670	+	0	NA	Intergenic	(TGGCTGGCT)n|Simple_repeat|Simple_repeat	131858	NR_120535	100996712	Hs.497575	NM_001271887		SRGAP2D	-	SLIT-ROBO Rho GTPase activating protein 2D (pseudogene)	pseudo	0.028902	0.688761	
chunk0193_203_1	chr8	75951754	75952643	+	0	NA	Intergenic	Intergenic	412230	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.007874	0.350562	
chunk0191_211_1	chr8	52276176	52276448	+	0	NA	intron (NM_014682, intron 2 of 25)	(AC)n|Simple_repeat|Simple_repeat	133567	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.014706	0.461538	
chunk0105_309_1	chr2	190372250	190372661	+	0	NA	TTS (NM_002194)	TTS (NM_002194)	28985	NM_002194	3628	Hs.32309	NM_002194	ENSG00000151689	INPP1	-	inositol polyphosphate-1-phosphatase	protein-coding	0.004866	0.407767	
chunk0172_255_1	chr6	137350092	137350811	+	0	NA	Intergenic	Intergenic	-131021	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.013908	0.436111	355(CAGAACAGGCTGTTTT,-,0.00),356(AGAACAGGCTGTTTTT,+,0.00)
chunk0138_169_1	chr4	37875393	37875852	+	0	NA	Intergenic	L1MEd|LINE|L1	-15462	NM_001253912	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.008715	0.300000	
chunk0113_280_1	chr20	56921895	56922100	+	0	NA	Intergenic	L2c|LINE|L2	-291699	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.000000	0.451456	
chunk0106_250_1	chr2	203522151	203522459	+	0	NA	intron (NM_213589, intron 1 of 13)	intron (NM_213589, intron 1 of 13)	13030	NM_213589	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.006494	0.310680	
chunk0065_136_1	chr15	24976520	24976719	+	0	NA	intron (NM_022808, intron 8 of 11)	intron (NM_022808, intron 8 of 11)	-5375	NR_022011	347746	Hs.733072	NR_022011		PWARSN	PAR-SN|PARSN	Prader Willi/Angelman region RNA, SNRPN neighbor	ncRNA	0.005025	0.355000	
chunk0118_357_1	chr22	36330585	36330829	+	0	NA	intron (NM_002473, intron 3 of 40)	intron (NM_002473, intron 3 of 40)	-43800	NR_106877	102465491		NR_106877	ENSG00000278420	MIR6819	hsa-mir-6819	microRNA 6819	ncRNA	0.028689	0.555102	
chunk0001_146_1	chr1	5986013	5986605	+	0	NA	non-coding (NR_111987, exon 2 of 33)	non-coding (NR_111987, exon 2 of 33)	-5989	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.023649	0.480607	
chunk0014_199_1	chr1	179053153	179053352	+	0	NA	intron (NM_014864, intron 3 of 7)	intron (NM_014864, intron 3 of 7)	27313	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.015075	0.495000	
chunk0208_100_1	chrX	13749766	13750077	+	0	NA	intron (NM_003611, intron 9 of 22)	L3|LINE|CR1	15208	NM_003611	8481	Hs.6483	NM_003611	ENSG00000046651	OFD1	71-7A|CXorf5|JBTS10|RP23|SGBS2	OFD1 centriole and centriolar satellite protein	protein-coding	0.006431	0.403846	
chunk0177_105_1	chr7	22066498	22067016	+	0	NA	Intergenic	Intergenic	-120833	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.017375	0.431599	
chunk0141_149_1	chr4	81472219	81472513	+	0	NA	promoter-TSS (NM_001300735)	promoter-TSS (NM_001300735)	-438	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.020408	0.423729	
chunk0157_71_1	chr5	116369705	116370009	+	0	NA	non-coding (NR_104675, exon 3 of 3)	non-coding (NR_104675, exon 3 of 3)	4713	NR_104675	101927190	Hs.639849	NR_104675		LOC101927190	-	uncharacterized LOC101927190	ncRNA	0.009868	0.442623	
chunk0185_437_1	chr7	134919095	134919812	+	0	NA	intron (NM_033139, intron 1 of 12)	intron (NM_033139, intron 1 of 12)	28053	NM_033140	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.002789	0.405292	157(CAGAACTCTCAGTACT,-,0.00),158(AGAACTCTCAGTACTC,+,0.00),222(TTGGACAGGATGTTCC,-,0.00),223(TGGACAGGATGTTCCA,+,0.00),454(AAGTACACAGTGTTTT,-,0.00),455(AGTACACAGTGTTTTA,+,0.00)
chunk0179_47_1	chr7	43454142	43454341	+	0	NA	intron (NM_015052, intron 12 of 29)	L2c|LINE|L2	68301	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.005025	0.450000	
chunk0144_379_1	chr4	140038249	140038685	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	115612	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.004587	0.443936	
chunk0169_294_1	chr6	105968520	105968990	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-117565	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.004255	0.343949	394(AAGTACAGATTGTACT,-,0.00),395(AGTACAGATTGTACTT,+,0.00)
chunk0038_288_1	chr11	90119813	90120052	+	0	NA	Intergenic	L1ME1|LINE|L1	-14718	NM_005467	10003	Hs.112482	NM_005467	ENSG00000077616	NAALAD2	GCPIII|GPCIII|NAADALASE2|NAALADASE2	N-acetylated alpha-linked acidic dipeptidase 2	protein-coding	0.004184	0.345833	
chunk0195_292_1	chr8	98591348	98591734	+	0	NA	intron (NM_006281, intron 7 of 10)	L3|LINE|CR1	164519	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.005181	0.354005	
chunk0078_114_1	chr17	2626798	2627213	+	0	NA	intron (NM_000430, intron 1 of 10)	L1PBa|LINE|L1	33376	NM_000430	5048	Hs.77318	NM_000430	ENSG00000007168	PAFAH1B1	LIS1|LIS2|MDCR|MDS|NudF|PAFAH	platelet activating factor acetylhydrolase 1b regulatory subunit 1	protein-coding	0.009639	0.401442	
chunk0059_355_1	chr14	37254378	37254611	+	0	NA	intron (NM_001195296, intron 5 of 14)	L1MC1|LINE|L1	56581	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.000000	0.329060	139(AAGTACAGAGTGTTCC,-,0.00),140(AGTACAGAGTGTTCCC,+,0.00)
chunk0136_290_1	chr3	194943403	194943604	+	0	NA	Intergenic	Intergenic	-151085	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.000000	0.574257	
chunk0012_301_1	chr1	162189252	162189931	+	0	NA	intron (NM_001164757, intron 2 of 9)	L2a|LINE|L2	32484	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.004418	0.373529	
chunk0096_117_1	chr2	28602902	28603797	+	0	NA	intron (NM_001170585, intron 38 of 56)	L1ME3E|LINE|L1	107278	NM_153021	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.003352	0.482143	
chunk0101_467_1	chr2	140780666	140781104	+	0	NA	intron (NM_018557, intron 32 of 90)	intron (NM_018557, intron 32 of 90)	-194200	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.002283	0.382688	
chunk0116_368_1	chr21	41849007	41849269	+	0	NA	intron (NR_104257, intron 5 of 24)	L1ME1|LINE|L1	14164	NR_104260	63977	Hs.473893	NM_022115	ENSG00000141956	PRDM15	C21orf83|PFM15|ZNF298	PR/SET domain 15	protein-coding	0.022901	0.490494	
chunk0197_10_1	chr8	116866409	116866985	+	0	NA	exon (NM_006265, exon 2 of 14)	exon (NM_006265, exon 2 of 14)	-7727	NR_033886	644660	Hs.706174	NR_033886	ENSG00000253327	RAD21-AS1	C8orf81|NCRNA00255	RAD21 antisense RNA 1	ncRNA	0.006944	0.320624	
chunk0129_168_1	chr3	120693348	120693766	+	0	NA	intron (NM_173825, intron 6 of 7)	intron (NM_173825, intron 6 of 7)	-10986	NM_000187	3081	Hs.368254	NM_000187	ENSG00000113924	HGD	AKU|HGO	homogentisate 1,2-dioxygenase	protein-coding	0.000000	0.324582	
chunk0077_48_1	chr16	76220530	76221086	+	0	NA	Intergenic	Intergenic	-56470	NM_033401	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.005396	0.312388	
chunk0093_247_1	chr19	50869290	50869938	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-3819	NM_001256080	3817	Hs.515560	NM_005551	ENSG00000167751	KLK2	KLK2A2|hGK-1|hK2	kallikrein related peptidase 2	protein-coding	0.007716	0.420647	110(ATGAACTTTGTGTTCA,-,0.00)
chunk0166_326_1	chr6	49897071	49897339	+	0	NA	Intergenic	L1PB1|LINE|L1	-20109	NM_001205220	167	Hs.109620	NM_001131	ENSG00000124812	CRISP1	AEGL1|ARP|CRISP-1|HEL-S-57|HSCRISP1D|HSCRISP1G|HUMARP	cysteine rich secretory protein 1	protein-coding	0.011194	0.356877	
chunk0107_324_1	chr2	220277463	220278106	+	0	NA	Intergenic	Intergenic	-371219	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.004666	0.357143	
chunk0073_36_1	chr16	2703320	2703806	+	0	NA	intron (NM_018992, intron 5 of 5)	intron (NM_018992, intron 5 of 5)	16988	NM_031948	83886	Hs.332878	NM_031948	ENSG00000172382	PRSS27	CAPH2|MPN	serine protease 27	protein-coding	0.039095	0.665298	
chunk0004_80_1	chr1	43671107	43671659	+	0	NA	intron (NM_014663, intron 10 of 21)	MIRb|SINE|MIR	21257	NM_014663	9682	Hs.155983	NM_014663	ENSG00000066135	KDM4A	JHDM3A|JMJD2|JMJD2A|TDRD14A	lysine demethylase 4A	protein-coding	0.007246	0.491863	
chunk0055_343_1	chr13	70049231	70049430	+	0	NA	intron (NM_020866, intron 1 of 10)	intron (NM_020866, intron 1 of 10)	-57883	NR_002717	6315	Hs.676453	NR_002717		ATXN8OS	KLHL1AS|NCRNA00003|SCA8	ATXN8 opposite strand lncRNA	ncRNA	0.000000	0.250000	
chunk0200_116_1	chr9	17065184	17065448	+	0	NA	Intergenic	Intergenic	-69675	NM_001114395	54875	Hs.435381	NM_017738	ENSG00000044459	CNTLN	C9orf101|C9orf39|bA340N12.1	centlein	protein-coding	0.003788	0.426415	
chunk0174_9_1	chr6	152305689	152306116	+	0	NA	intron (NM_033071, intron 90 of 145)	MIRc|SINE|MIR	-74628	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.002342	0.383178	
chunk0083_31_1	chr17	63249695	63249958	+	0	NA	intron (NM_025185, intron 6 of 24)	intron (NM_025185, intron 6 of 24)	191020	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.003802	0.375000	
chunk0107_458_1	chr2	225799353	225799864	+	0	NA	Intergenic	Intergenic	-343186	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003914	0.351562	
chunk0035_97_1	chr11	42267043	42267341	+	0	NA	Intergenic	Intergenic	-13502	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.003356	0.324415	
chunk0155_86_1	chr5	92126186	92126495	+	0	NA	Intergenic	Intergenic	-743008	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003236	0.303226	
chunk0121_45_1	chr3	15479516	15479993	+	0	NA	intron (NM_080539, intron 2 of 15)	intron (NM_080539, intron 2 of 15)	16554	NR_036232	100422868		NR_036232	ENSG00000263573	MIR4270	-	microRNA 4270	ncRNA	0.000000	0.435146	
chunk0091_444_1	chr19	17240041	17240558	+	0	NA	intron (NM_005234, intron 2 of 3)	intron (NM_005234, intron 2 of 3)	5043	NM_005234	2063	Hs.466148	NM_005234	ENSG00000160113	NR2F6	EAR-2|EAR2|ERBAL2	nuclear receptor subfamily 2 group F member 6	protein-coding	0.030948	0.592664	
chunk0126_51_1	chr3	74129117	74129371	+	0	NA	Intergenic	Intergenic	391896	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.419608	
chunk0103_264_1	chr2	165565527	165566191	+	0	NA	intron (NM_001172173, intron 3 of 6)	intron (NM_001172173, intron 3 of 6)	-6477	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.006024	0.327820	396(AAGCACTCTTTGTTCT,-,0.00),397(AGCACTCTTTGTTCTT,+,0.00)
chunk0172_93_1	chr6	134663732	134664058	+	0	NA	Intergenic	Intergenic	-123890	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.009202	0.418960	165(CAGTACTCAGTGTTCT,-,0.00),166(AGTACTCAGTGTTCTT,+,0.00)
chunk0206_74_1	chr9	119967855	119968207	+	0	NA	Intergenic	L2c|LINE|L2	32971	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.017045	0.399433	
chunk0031_342_1	chr10	129573589	129573808	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	106514	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.004566	0.300000	
chunk0077_22_1	chr16	75053581	75054590	+	0	NA	intron (NM_032268, intron 1 of 4)	intron (NM_032268, intron 1 of 4)	55068	NM_032268	84937	Hs.427284	NM_032268	ENSG00000186187	ZNRF1	NIN283	zinc and ring finger 1	protein-coding	0.003964	0.463366	
chunk0013_134_1	chr1	168235883	168236416	+	0	NA	intron (NM_199344, intron 4 of 7)	intron (NM_199344, intron 4 of 7)	10132	NM_199344	375035	Hs.645435	NM_199344	ENSG00000213064	SFT2D2	UNQ512|dJ747L4.C1.2	SFT2 domain containing 2	protein-coding	0.005629	0.411985	
chunk0061_396_1	chr14	64611173	64611931	+	0	NA	Intergenic	Intergenic	61650	NM_172365	145376	Hs.144696	NM_172365	ENSG00000165807	PPP1R36	C14orf50	protein phosphatase 1 regulatory subunit 36	protein-coding	0.001319	0.380764	
chunk0095_64_1	chr2	14406132	14406780	+	0	NA	Intergenic	L2a|LINE|L2	-5498	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.001543	0.400616	
chunk0079_187_1	chr17	14200746	14201300	+	0	NA	intron (NM_001303, intron 6 of 6)	intron (NM_001303, intron 6 of 6)	35810	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.007220	0.418018	283(GAAAACAGACTGTGCC,-,0.00),284(AAAACAGACTGTGCCT,+,0.00)
chunk0115_439_1	chr21	32021681	32022138	+	0	NA	Intergenic	Intergenic	64386	NR_038033	100551499	Hs.224449	NR_038033		LINC00159	C21orf44|NCRNA00159	long intergenic non-protein coding RNA 159	ncRNA	0.017505	0.478166	
chunk0177_403_1	chr7	27438912	27439406	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-176815	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.008097	0.391919	
chunk0190_335_1	chr8	39089404	39090105	+	0	NA	intron (NR_027638, intron 18 of 20)	L1ME4b|LINE|L1	-17775	NM_145004	203102	Hs.521545	NM_145004	ENSG00000197140	ADAM32	-	ADAM metallopeptidase domain 32	protein-coding	0.007133	0.314815	
chunk0104_273_1	chr2	178112111	178112327	+	0	NA	promoter-TSS (NM_152945)	promoter-TSS (NM_152945)	-205	NM_152945	129831	Hs.377257	NM_152945	ENSG00000155636	RBM45	DRB1|RB-1	RNA binding motif protein 45	protein-coding	0.023148	0.488479	
chunk0111_83_1	chr20	23296776	23297349	+	0	NA	Intergenic	Intergenic	-53674	NM_013248	29107	Hs.516933	NM_013248	ENSG00000132661	NXT1	MTR2|P15	nuclear transport factor 2 like export factor 1	protein-coding	0.012216	0.505226	269(AAGAACAAAGTGTCCA,-,0.00),270(AGAACAAAGTGTCCAC,+,0.00)
chunk0177_177_1	chr7	23338479	23338756	+	0	NA	intron (NM_006547, intron 10 of 14)	intron (NM_006547, intron 10 of 14)	39296	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.007220	0.388489	
chunk0177_166_1	chr7	23273085	23273567	+	0	NA	intron (NM_002510, intron 9 of 10)	intron (NM_002510, intron 9 of 10)	-25995	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.029046	0.507246	
chunk0017_100_1	chr1	205843124	205843323	+	0	NA	intron (NM_152491, intron 6 of 12)	intron (NM_152491, intron 6 of 12)	6925	NM_152491	148811	Hs.177744	NM_152491	ENSG00000162877	PM20D1	Cps1	peptidase M20 domain containing 1	protein-coding	0.005025	0.450000	
chunk0031_220_1	chr10	126059460	126059846	+	0	NA	intron (NM_001288973, intron 14 of 22)	intron (NM_001288973, intron 14 of 22)	-86380	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.005181	0.392765	
chunk0187_116_1	chr7	148698780	148699276	+	0	NA	5' UTR (NM_003592, exon 1 of 22)	5' UTR (NM_003592, exon 1 of 22)	187	NM_003592	8454	Hs.146806	NM_003592	ENSG00000055130	CUL1	-	cullin 1	protein-coding	0.137097	0.782696	
chunk0097_183_1	chr2	50336713	50336912	+	0	NA	intron (NM_001135659, intron 18 of 23)	intron (NM_001135659, intron 18 of 23)	10944	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.015075	0.360000	
chunk0020_441_1	chr1	242063318	242063843	+	0	NA	Intergenic	Intergenic	-64497	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.007619	0.458175	
chunk0045_365_1	chr12	52032227	52032741	+	0	NA	intron (NM_001202233, intron 1 of 7)	MLT2B1|LTR|ERVL	-5231	NM_001202234	3164	Hs.524430	NM_002135	ENSG00000123358	NR4A1	GFRP1|HMR|N10|NAK-1|NGFIB|NP10|NUR77|TR3	nuclear receptor subfamily 4 group A member 1	protein-coding	0.017510	0.467961	
chunk0143_292_1	chr4	118295298	118295896	+	0	NA	intron (NM_003619, intron 10 of 12)	intron (NM_003619, intron 10 of 12)	16407	NR_002963	677809	Hs.744742	NR_002963	ENSG00000275994	SNORA24	ACA24|SNORA24A	small nucleolar RNA, H/ACA box 24	snoRNA	0.006689	0.327212	
chunk0047_25_1	chr12	65718075	65718490	+	0	NA	Intergenic	Intergenic	-75910	NR_120433	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.000000	0.427885	
chunk0179_82_1	chr7	44411833	44412507	+	0	NA	intron (NM_015332, intron 3 of 5)	intron (NM_015332, intron 3 of 5)	78616	NM_015332	23386	Hs.488171	NM_015332	ENSG00000015676	NUDCD3	NudCL	NudC domain containing 3	protein-coding	0.005935	0.391111	
chunk0032_416_1	chr11	12050352	12050918	+	0	NA	Intergenic	Intergenic	-41265	NM_013253	27122	Hs.292156	NM_013253	ENSG00000050165	DKK3	REIC|RIG	dickkopf WNT signaling pathway inhibitor 3	protein-coding	0.014134	0.493827	
chunk0106_301_1	chr2	204669470	204669737	+	0	NA	intron (NM_205863, intron 1 of 21)	HAL1ME|LINE|L1	123810	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.007491	0.324627	
chunk0093_306_1	chr19	53497402	53497601	+	0	NA	Intergenic	Intergenic	-23422	NM_018555	55422	Hs.185674	NM_018555	ENSG00000130844	ZNF331	RITA|ZNF361|ZNF463	zinc finger protein 331	protein-coding	0.025126	0.490000	
chunk0078_271_1	chr17	7857490	7857844	+	0	NA	promoter-TSS (NM_144607)	promoter-TSS (NM_144607)	-79	NM_144607	124637	Hs.27475	NM_144607	ENSG00000182224	CYB5D1	-	cytochrome b5 domain containing 1	protein-coding	0.056497	0.501408	
chunk0130_446_1	chr3	141366446	141366756	+	0	NA	intron (NM_001080412, intron 1 of 7)	intron (NM_001080412, intron 1 of 7)	42388	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.000000	0.495177	
chunk0154_154_1	chr5	79485608	79486195	+	0	NA	intron (NM_001277077, intron 1 of 5)	MLT1G1|LTR|ERVL-MaLR	27935	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.001704	0.442177	353(GTAACACTGTGTACTT,+,0.00)
chunk0039_70_1	chr11	96403404	96403859	+	0	NA	Intergenic	L1MB7|LINE|L1	13637	NM_001261833	8690	Hs.105940	NM_003772	ENSG00000183340	JRKL	HHMJG	JRK like	protein-coding	0.010989	0.348684	
chunk0073_123_1	chr16	4869102	4869301	+	0	NA	intron (NM_001288656, intron 8 of 16)	intron (NM_001288656, intron 8 of 16)	20821	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.010050	0.495000	
chunk0154_58_1	chr5	77265892	77266352	+	0	NA	intron (NM_001029853, intron 1 of 20)	Tigger17a|DNA|TcMar-Tigger	55241	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.008696	0.425163	
chunk0024_35_1	chr10	33336056	33336273	+	0	NA	Intergenic	CpG-2786	-1259	NM_001024628	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.032258	0.568807	
chunk0194_344_1	chr8	89173616	89174281	+	0	NA	Intergenic	Intergenic	583763	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.003008	0.306306	
chunk0113_420_1	chr20	61909991	61910446	+	0	NA	intron (NM_001252339, intron 7 of 14)	intron (NM_001252339, intron 7 of 14)	43444	NR_031658	100302168		NR_031658	ENSG00000284193	MIR1257	MIRN1257|hsa-mir-1257	microRNA 1257	ncRNA	0.041758	0.539474	
chunk0204_331_1	chr9	101335154	101335562	+	0	NA	Intergenic	Intergenic	48161	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.004902	0.410758	
chunk0099_443_1	chr2	103265651	103265921	+	0	NA	Intergenic	Intergenic	503755	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.022222	0.461255	
chunk0002_431_1	chr1	28072441	28072947	+	0	NA	intron (NM_001282560, intron 1 of 16)	L1ME1|LINE|L1	15943	NR_104214	2140	Hs.185774	NM_001990	ENSG00000158161	EYA3	-	EYA transcriptional coactivator and phosphatase 3	protein-coding	0.001976	0.368836	
chunk0075_45_1	chr16	47433390	47433752	+	0	NA	intron (NM_030790, intron 5 of 17)	intron (NM_030790, intron 5 of 17)	27703	NM_030790	81533	Hs.42217	NM_030790	ENSG00000129636	ITFG1	2310047C21Rik|CDA08|LNKN-1|TIP	integrin alpha FG-GAP repeat containing 1	protein-coding	0.008287	0.344353	
chunk0073_285_1	chr16	13480302	13480588	+	0	NA	Intergenic	Intergenic	-439712	NM_005236	2072	Hs.567265	NM_005236	ENSG00000175595	ERCC4	ERCC11|FANCQ|RAD1|XFEPS|XPF	ERCC excision repair 4, endonuclease catalytic subunit	protein-coding	0.013986	0.512195	
chunk0100_180_1	chr2	110768605	110769027	+	0	NA	intron (NM_001142807, intron 2 of 17)	L1PA15|LINE|L1	36243	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.026066	0.479905	
chunk0012_250_1	chr1	161154203	161154415	+	0	NA	intron (NM_016406, intron 1 of 5)	intron (NM_016406, intron 1 of 5)	565	NM_016406	51506	Hs.301412	NM_016406	ENSG00000143222	UFC1	HSPC155|NEDSG	ubiquitin-fold modifier conjugating enzyme 1	protein-coding	0.037736	0.530516	
chunk0191_174_1	chr8	51014829	51015297	+	0	NA	Intergenic	Intergenic	794382	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.004274	0.388060	
chunk0166_40_1	chr6	42153592	42154035	+	0	NA	Intergenic	Intergenic	-1593	NM_000409	2978	Hs.92858	NM_000409	ENSG00000048545	GUCA1A	C6orf131|COD3|CORD14|GCAP|GCAP1|GUCA|GUCA1	guanylate cyclase activator 1A	protein-coding	0.009029	0.556306	47(CAGGTCACCCAGTTCT,-,0.00),48(AGGTCACCCAGTTCTC,+,0.00),106(AAGTACAATGTGTGCT,-,0.00),107(AGTACAATGTGTGCTA,+,0.00)
chunk0095_455_1	chr2	25754324	25754816	+	0	NA	intron (NM_018263, intron 9 of 11)	intron (NM_018263, intron 9 of 11)	-80923	NM_001256303	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.008130	0.389452	
chunk0129_412_1	chr3	126960154	126960677	+	0	NA	TTS (NM_032343)	TTS (NM_032343)	-28179	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.022945	0.587786	
chunk0093_87_1	chr19	41376210	41376547	+	0	NA	promoter-TSS (NM_001042595)	promoter-TSS (NM_001042595)	-155	NM_001098824	641649	Hs.709417	NM_001042595	ENSG00000142046	TMEM91	DSPC3|IFITMD6	transmembrane protein 91	protein-coding	0.035608	0.505917	41(GGGTACAGTCTGCCCT,-,0.00),42(GGTACAGTCTGCCCTC,+,0.00)
chunk0006_53_1	chr1	64537162	64537495	+	0	NA	intron (NM_001293274, intron 1 of 25)	intron (NM_001293274, intron 1 of 25)	31414	NM_001293274	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.015015	0.461078	
chunk0051_128_1	chr12	115473130	115473672	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	675253	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.011070	0.480663	
chunk0212_83_1	chrY	11680310	11680514	+	0	NA	Intergenic	Intergenic	741178	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.024510	0.370732	
chunk0198_1_1	chr9	111511	111729	+	0	NA	Intergenic	L1MC5|LINE|L1	6797	NM_207305	2298	Hs.584759	NM_207305	ENSG00000170122	FOXD4	FKHL9|FOXD4A|FREAC-5|FREAC5	forkhead box D4	protein-coding	0.018349	0.360731	
chunk0066_223_1	chr15	34003033	34003606	+	0	NA	intron (NM_020371, intron 1 of 5)	intron (NM_020371, intron 1 of 5)	34431	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.003490	0.357143	
chunk0045_42_1	chr12	44920674	44921025	+	0	NA	Intergenic	Intergenic	-6921	NM_001145110	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.000000	0.315341	
chunk0155_246_1	chr5	95720254	95720859	+	0	NA	Intergenic	Intergenic	-10590	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.006612	0.356436	290(AGTAACAGACTGTTCC,-,0.00),291(GTAACAGACTGTTCCA,+,0.00)
chunk0120_171_1	chr3	5885165	5885751	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-635203	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.005119	0.282794	
chunk0093_28_1	chr2	558709	559318	+	0	NA	Intergenic	Intergenic	118426	NM_152834	129787	Hs.6729	NM_152834	ENSG00000151353	TMEM18	lncND	transmembrane protein 18	protein-coding	0.032841	0.457377	
chunk0066_185_1	chr15	33120114	33120607	+	0	NA	intron (NM_001277313, intron 4 of 20)	intron (NM_001277313, intron 4 of 20)	-52328	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.010142	0.398785	
chunk0048_362_1	chr12	85768653	85769177	+	0	NA	Intergenic	Intergenic	67625	NM_005447	9182	Hs.527881	NM_005447	ENSG00000198774	RASSF9	P-CIP1|PAMCI|PCIP1	Ras association domain family member 9	protein-coding	0.001908	0.293333	278(ATGTACACAGTGTTCA,-,0.00),279(TGTACACAGTGTTCAT,+,0.00)
chunk0029_429_1	chr10	110003443	110003642	+	0	NA	intron (NR_038943, intron 2 of 4)	MIRc|SINE|MIR	-2426	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.015075	0.340000	
chunk0043_153_1	chr12	16435895	16436625	+	0	NA	Intergenic	L2a|LINE|L2	82843	NM_145764	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.004110	0.354309	495(TGAAACAAGGTGTTCT,-,0.00),496(GAAACAAGGTGTTCTT,+,0.00)
chunk0010_241_1	chr1	116453644	116453843	+	0	NA	intron (NR_125973, intron 3 of 3)	MIRb|SINE|MIR	25083	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.005025	0.415000	
chunk0195_298_1	chr8	98725784	98726197	+	0	NA	intron (NM_006281, intron 4 of 10)	MIRc|SINE|MIR	99681	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004843	0.434783	
chunk0149_23_1	chr5	16141391	16141885	+	0	NA	intron (NM_001102562, intron 2 of 3)	intron (NM_001102562, intron 2 of 3)	38150	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.008097	0.381818	
chunk0038_282_1	chr11	89765687	89765934	+	0	NA	Intergenic	Intergenic	42765	NM_020358	57093	Hs.534218	NM_020358	ENSG00000168930	TRIM49	RNF18|TRIM49A|TRIM49L2	tripartite motif containing 49	protein-coding	0.008097	0.455645	
chunk0067_176_1	chr15	44288523	44288925	+	0	NA	promoter-TSS (NM_138423)	promoter-TSS (NM_138423)	13	NM_138423	113201	Hs.512867	NM_138423	ENSG00000166734	CASC4	H63	cancer susceptibility 4	protein-coding	0.077114	0.640199	
chunk0112_211_1	chr20	40473888	40474133	+	0	NA	Intergenic	Intergenic	215230	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.000000	0.390244	
chunk0061_158_1	chr14	59761022	59761275	+	0	NA	intron (NM_021136, intron 1 of 8)	intron (NM_021136, intron 1 of 8)	109691	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.007905	0.385827	
chunk0145_216_1	chr4	148041607	148042029	+	0	NA	intron (NM_024605, intron 19 of 22)	intron (NM_024605, intron 19 of 22)	259223	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.009479	0.385343	
chunk0092_74_1	chr19	20608618	20609059	+	0	NA	Intergenic	Intergenic	-43018	NM_001159293	100129842	Hs.515696	NM_001159293	ENSG00000237440	ZNF737	ZNF102	zinc finger protein 737	protein-coding	0.004535	0.361991	
chunk0056_253_1	chr13	89670048	89670556	+	0	NA	Intergenic	Intergenic	-105889	NR_046991	100874139	Hs.742173	NR_046991		LINC00353	-	long intergenic non-protein coding RNA 353	ncRNA	0.003937	0.310413	50(GAGGACACAGAGTTCT,-,0.00),51(AGGACACAGAGTTCTA,+,0.00)
chunk0064_430_1	chr14	99878474	99878812	+	0	NA	intron (NM_004434, intron 4 of 21)	intron (NM_004434, intron 4 of 21)	85235	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.017751	0.495575	
chunk0136_333_1	chr3	195621541	195621914	+	0	NA	Intergenic	Intergenic	-36312	NR_003265	727956	Hs.596261	NR_003265	ENSG00000242086	SDHAP2	SDHAL2|SDHALP2	succinate dehydrogenase complex flavoprotein subunit A pseudogene 2	pseudo	0.010724	0.328877	
chunk0089_191_1	chr18	59908510	59909379	+	0	NA	Intergenic	Intergenic	8984	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.012658	0.410345	
chunk0168_261_1	chr6	89335166	89335522	+	0	NA	exon (NM_016021, exon 6 of 8)	exon (NM_016021, exon 6 of 8)	17556	NM_016021	51465	Hs.163776	NM_016021	ENSG00000198833	UBE2J1	CGI-76|HSPC153|HSPC205|HSU93243|NCUBE-1|NCUBE1|UBC6|UBC6E|Ubc6p	ubiquitin conjugating enzyme E2 J1	protein-coding	0.008427	0.336134	
chunk0087_147_1	chr18	33956836	33957238	+	0	NA	intron (NM_001282527, intron 8 of 10)	intron (NM_001282527, intron 8 of 10)	91575	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.009950	0.364764	
chunk0194_401_1	chr8	91099725	91100265	+	0	NA	Intergenic	Intergenic	-2624	NM_001129890	100130742	Hs.733070	NM_001129890	ENSG00000214954	LRRC69	-	leucine rich repeat containing 69	protein-coding	0.003704	0.330869	
chunk0141_100_1	chr4	79224246	79224810	+	0	NA	intron (NR_038342, intron 4 of 5)	L2b|LINE|L2	101489	NM_032693	84779	Hs.676048	NM_032693	ENSG00000156269	NAA11	ARD1B|ARD2|hARD2	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding	0.007092	0.394690	
chunk0047_83_1	chr12	67999231	67999738	+	0	NA	intron (NR_104125, intron 2 of 3)	L1MC4a|LINE|L1	10039	NR_104125	100885789	Hs.439832	NR_104124	ENSG00000255733	IFNG-AS1	GS1-410F4.2|NEST|Tmevpg1	IFNG antisense RNA 1	ncRNA	0.001972	0.348425	205(TGGAACATCTTGTGCC,-,0.00),206(GGAACATCTTGTGCCA,+,0.00)
chunk0003_49_1	chr1	30788511	30789041	+	0	NA	Intergenic	L2c|LINE|L2	-30940	NM_006762	7805	Hs.371021	NM_006762	ENSG00000162511	LAPTM5	CLAST6	lysosomal protein transmembrane 5	protein-coding	0.009434	0.523540	264(GGGAACAGCATGTACA,-,0.00),265(GGAACAGCATGTACAA,+,0.00)
chunk0074_181_1	chr16	24068747	24069584	+	0	NA	intron (NM_212535, intron 5 of 16)	MIR|SINE|MIR	-133951	NR_106996	102466247		NR_106996	ENSG00000274466	MIR1273H	hsa-mir-1273h	microRNA 1273h	ncRNA	0.008363	0.439141	505(GAGGACAGTTTGGTCC,-,0.00),558(CAGAACAGCCTGTTTT,-,0.00),559(AGAACAGCCTGTTTTT,+,0.00)
chunk0183_20_1	chr7	103373169	103373517	+	0	NA	TTS (NM_198999)	TTS (NM_198999)	25819	NM_001204453	5701	Hs.437366	NM_002803	ENSG00000161057	PSMC2	MSS1|Nbla10058|S7	proteasome 26S subunit, ATPase 2	protein-coding	0.008621	0.349570	
chunk0108_225_1	chr2	233535050	233535294	+	0	NA	intron (NM_018218, intron 9 of 30)	intron (NM_018218, intron 9 of 30)	30418	NM_018218	55230	Hs.96513	NM_018218	ENSG00000085982	USP40	-	ubiquitin specific peptidase 40	protein-coding	0.008197	0.469388	
chunk0030_417_1	chr10	120253077	120254101	+	0	NA	Intergenic	L2c|LINE|L2	101634	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.005859	0.391220	
chunk0150_10_1	chr5	30409776	30410365	+	0	NA	Intergenic	Intergenic	-783585	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.001698	0.283051	
chunk0019_308_1	chr1	228983555	228984097	+	0	NA	Intergenic	Intergenic	190975	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.009225	0.441989	
chunk0033_45_1	chr11	13270856	13271448	+	0	NA	Intergenic	L2b|LINE|L2	-6575	NM_001297719	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.003378	0.392917	
chunk0200_405_1	chr9	27332426	27332897	+	0	NA	intron (NM_024761, intron 3 of 3)	MIRb|SINE|MIR	-35522	NM_001161585	54586	Hs.163070	NM_020641	ENSG00000120160	EQTN	AFAF|C9orf11|SPACA8	equatorin	protein-coding	0.006369	0.406780	
chunk0156_192_1	chr5	107918135	107918334	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-247339	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.010050	0.575000	
chunk0164_124_1	chr6	20825511	20825745	+	0	NA	intron (NM_017774, intron 8 of 15)	intron (NM_017774, intron 8 of 15)	291171	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.004274	0.319149	74(GTCACACACTGTGCTT,+,0.00)
chunk0166_63_1	chr6	42954018	42954811	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-6348	NM_018960	27232	Hs.144914	NM_018960	ENSG00000124713	GNMT	HEL-S-182mP	glycine N-methyltransferase	protein-coding	0.016393	0.416877	
chunk0026_108_1	chr10	61848079	61848278	+	0	NA	Intergenic	L1ME3G|LINE|L1	-53076	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.000000	0.240000	
chunk0037_93_1	chr11	71958030	71958607	+	0	NA	intron (NM_018320, intron 2 of 8)	L3|LINE|CR1	29596	NM_001300926	55298	Hs.368554	NM_018320	ENSG00000137522	RNF121	-	ring finger protein 121	protein-coding	0.003466	0.365052	
chunk0119_212_1	chr22	44968666	44969287	+	0	NA	intron (NM_001284296, intron 2 of 13)	L1MC3|LINE|L1	40017	NM_001284296	112885	Hs.254097	NM_138415	ENSG00000056487	PHF21B	BHC80L|PHF4	PHD finger protein 21B	protein-coding	0.017713	0.487138	
chunk0020_304_1	chr1	237448878	237449691	+	0	NA	intron (NM_001035, intron 14 of 104)	L1MEc|LINE|L1	-21835	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.008610	0.313268	255(AAGAACACTTTGTCAT,-,0.00)
chunk0063_391_1	chr14	87032131	87032774	+	0	NA	Intergenic	Intergenic	126674	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.009331	0.375776	
chunk0197_394_1	chr8	127090893	127091507	+	0	NA	non-coding (NR_109833, exon 1 of 1)	non-coding (NR_109833, exon 1 of 1)	-8979	NR_119373	103164619	Hs.571401	NR_119373	ENSG00000254166	PCAT2	CARLO4|CARLo-4|PCA2|TCONS_00015167	prostate cancer associated transcript 2	ncRNA	0.006515	0.386992	287(ATGTACTTTATGTTCT,-,0.00),288(TGTACTTTATGTTCTT,+,0.00)
chunk0204_118_1	chr9	95094933	95095272	+	0	NA	Intergenic	L1MB3|LINE|L1	-9008	NR_036109	100422842		NR_036109	ENSG00000207617	MIR3074	mir-3074	microRNA 3074	ncRNA	0.014749	0.476471	124(AGGAACATGGCGTCCA,-,0.00)
chunk0167_446_1	chr6	75934865	75935080	+	0	NA	intron (NM_001282368, intron 13 of 15)	intron (NM_001282368, intron 13 of 15)	137706	NM_001282368	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.027907	0.467593	
chunk0132_22_1	chr3	154521739	154522739	+	0	NA	Intergenic	Intergenic	-92524	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.001000	0.335664	181(AGGCACTGAATGTTCT,-,0.00),182(GGCACTGAATGTTCTG,+,0.00)
chunk0105_340_1	chr2	191262838	191263496	+	0	NA	intron (NM_001130158, intron 1 of 30)	intron (NM_001130158, intron 1 of 30)	17639	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.007599	0.394537	
chunk0082_192_1	chr17	56611793	56612203	+	0	NA	Intergenic	Intergenic	18299	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.012195	0.389294	
chunk0035_285_1	chr11	46760658	46760898	+	0	NA	exon (NM_014756, exon 33 of 43)	exon (NM_014756, exon 33 of 43)	1721	NR_003056	692108	Hs.693252	NR_003056	ENSG00000212135	SNORD67	HBII-166	small nucleolar RNA, C/D box 67	snoRNA	0.012500	0.398340	
chunk0161_330_1	chr5	173810728	173810927	+	0	NA	Intergenic	(TGGTGA)n|Simple_repeat|Simple_repeat	-19885	NR_108028	101928154	Hs.366725	NR_108028		LINC01485	-	long intergenic non-protein coding RNA 1485	ncRNA	0.015075	0.570000	
chunk0212_25_1	chrY	10792957	10793186	+	0	NA	Intergenic	(ATTCC)n|Simple_repeat|Simple_repeat	882273	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.013100	0.413043	
chunk0005_219_1	chr1	59242348	59243024	+	0	NA	Intergenic	Intergenic	-54267	NM_018291	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.002959	0.426883	
chunk0032_177_1	chr11	5898204	5898814	+	0	NA	Intergenic	L1PA17|LINE|L1	14216	NM_001005165	390081	Hs.553739	NM_001005165	ENSG00000180974	OR52E4	OR11-55	olfactory receptor family 52 subfamily E member 4	protein-coding	0.003279	0.330606	
chunk0183_386_1	chr7	109998668	109999305	+	0	NA	Intergenic	Intergenic	-38773	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.007849	0.485893	
chunk0093_313_1	chr19	53621913	53622580	+	0	NA	Intergenic	LTR80B|LTR|ERVL	-9810	NM_001012728	503834	Hs.579941	NM_001012728	ENSG00000204595	DPRX	-	divergent-paired related homeobox	protein-coding	0.008996	0.446108	
chunk0091_301_1	chr19	12784555	12784754	+	0	NA	Intergenic	Intergenic	-2474	NR_049864	100847071		NR_049864	ENSG00000263800	MIR5684	-	microRNA 5684	ncRNA	0.015075	0.500000	
chunk0032_166_1	chr11	5252748	5253265	+	0	NA	TTS (NM_000184)	TTS (NM_000184)	1775	NM_000184	3048	Hs.302145	NM_000184	ENSG00000196565	HBG2	HBG-T1|TNCY	hemoglobin subunit gamma 2	protein-coding	0.005803	0.403475	
chunk0123_220_1	chr3	45274218	45274417	+	0	NA	Intergenic	Intergenic	-47995	NM_015444	25907	Hs.740403	NM_015444	ENSG00000249992	TMEM158	BBP|RIS1|p40BBP	transmembrane protein 158 (gene/pseudogene)	protein-coding	0.005025	0.510000	
chunk0122_161_1	chr3	32234077	32234479	+	0	NA	Intergenic	L1MC4a|LINE|L1	-4401	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.002488	0.332506	
chunk0177_416_1	chr7	27689750	27690342	+	0	NA	Intergenic	Intergenic	-27045	NM_152740	11112	Hs.406758	NM_152740	ENSG00000106049	HIBADH	NS5ATP1	3-hydroxyisobutyrate dehydrogenase	protein-coding	0.003378	0.435076	
chunk0013_57_1	chr1	167198313	167198761	+	0	NA	Intergenic	Intergenic	-2732	NR_110811	101928484	Hs.568496	NR_110811		LINC01363	RBSG4	long intergenic non-protein coding RNA 1363	ncRNA	0.008929	0.438753	
chunk0187_103_1	chr8	4894558	4895097	+	0	NA	intron (NM_033225, intron 1 of 69)	intron (NM_033225, intron 1 of 69)	99979	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.005566	0.353704	
chunk0025_397_1	chr10	59395945	59396223	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-33181	NM_001143773	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.000000	0.376344	
chunk0055_217_1	chr13	62343250	62343484	+	0	NA	Intergenic	MER52A|LTR|ERV1	131085	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.017094	0.557447	
chunk0007_1_1	chr1	77126935	77127813	+	0	NA	intron (NM_005482, intron 9 of 10)	intron (NM_005482, intron 9 of 10)	67231	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.003417	0.336746	
chunk0152_269_1	chr5	61174551	61174795	+	0	NA	intron (NR_109908, intron 1 of 3)	L1MC4|LINE|L1	-12198	NM_001048249	643155	Hs.508479	NM_001048249	ENSG00000188725	SMIM15	C5orf43	small integral membrane protein 15	protein-coding	0.004098	0.416327	127(TGGTACAAGATGTTCC,-,0.00),128(GGTACAAGATGTTCCA,+,0.00)
chunk0139_314_1	chr4	58132010	58132403	+	0	NA	Intergenic	Intergenic	706334	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.015267	0.461929	
chunk0128_1_1	chr3	103325710	103326288	+	0	NA	Intergenic	L1MC4|LINE|L1	198117	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.006920	0.348877	
chunk0165_414_1	chr6	39097307	39097586	+	0	NA	Intergenic	L1MC4|LINE|L1	17740	NM_001304793	55776	Hs.58382	NM_018322	ENSG00000112167	SAYSD1	C6orf64	SAYSVFN motif domain containing 1	protein-coding	0.003584	0.317857	
chunk0074_355_1	chr16	34035279	34035862	+	0	NA	Intergenic	Intergenic	124466	NR_038368									0.005146	0.335616	
chunk0145_348_1	chr4	151035253	151035686	+	0	NA	Intergenic	Intergenic	-19972	NM_006726	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.004619	0.405530	
chunk0154_47_1	chr5	77173000	77173417	+	0	NA	Intergenic	Intergenic	-37673	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.000000	0.423445	
chunk0012_137_1	chr1	157253298	157253522	+	0	NA	Intergenic	Intergenic	-114819	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.000000	0.484444	
chunk0176_222_1	chr7	15109180	15109425	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-267852	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.012245	0.487805	
chunk0166_310_1	chr6	49664681	49665321	+	0	NA	Intergenic	Intergenic	-28127	NM_000324	6005	Hs.120950	NM_000324	ENSG00000112077	RHAG	CD241|OHS|OHST|RH2|RH50A|RHNR|Rh50|Rh50GP|SLC42A1	Rh associated glycoprotein	protein-coding	0.004687	0.354134	286(AAGAACTTTCTGTTCT,-,0.00),287(AGAACTTTCTGTTCTC,+,0.00)
chunk0034_413_1	chr11	38254682	38255099	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	391466	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.007194	0.342105	
chunk0023_28_1	chr10	21118188	21118430	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	28250	NM_001010896	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.008264	0.415638	
chunk0076_219_1	chr16	68406461	68407309	+	0	NA	intron (NM_018667, intron 1 of 8)	intron (NM_018667, intron 1 of 8)	41621	NM_018667	55512	Hs.368421	NM_018667	ENSG00000103056	SMPD3	NSMASE2	sphingomyelin phosphodiesterase 3	protein-coding	0.022406	0.486455	
chunk0099_429_1	chr2	102796289	102796727	+	0	NA	intron (NM_144632, intron 3 of 4)	intron (NM_144632, intron 3 of 4)	34477	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.004566	0.396355	
chunk0102_276_1	chr2	150166130	150166767	+	0	NA	Intergenic	Intergenic	321247	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.006279	0.468652	
chunk0161_61_1	chr5	166378869	166379127	+	0	NA	Intergenic	MER52A|LTR|ERV1	547372	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.015504	0.517375	
chunk0102_267_1	chr2	150043110	150043469	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	444406	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.002786	0.416667	
chunk0119_98_1	chr22	41947925	41948124	+	0	NA	promoter-TSS (NM_024053)	promoter-TSS (NM_024053)	-860	NM_024053	79019	Hs.208912	NM_024053	ENSG00000100162	CENPM	C22orf18|CENP-M|PANE1	centromere protein M	protein-coding	0.005025	0.495000	
chunk0030_389_1	chr10	119653253	119653665	+	0	NA	intron (NM_004281, intron 1 of 3)	intron (NM_004281, intron 1 of 3)	2089	NM_004281	9531	Hs.523309	NM_004281	ENSG00000151929	BAG3	BAG-3|BIS|CAIR-1|MFM6	BCL2 associated athanogene 3	protein-coding	0.002427	0.380145	
chunk0159_9_1	chr5	136094875	136095125	+	0	NA	Intergenic	Intergenic	-14403	NR_030583	100126299		NR_030583	ENSG00000278815	VTRNA2-1	CBL-3|CBL3|MIR886|MIRN886|VTRNA2|hsa-mir-886|hvg-5|nc886|pre-miR-886|svtRNA2-1a	vault RNA 2-1	ncRNA	0.016000	0.466135	
chunk0029_443_1	chr10	110269584	110269970	+	0	NA	intron (NM_005962, intron 3 of 5)	intron (NM_005962, intron 3 of 5)	35172	NM_005871	10285	Hs.632093	NM_005871	ENSG00000119953	SMNDC1	SMNR|SPF30|TDRD16C	survival motor neuron domain containing 1	protein-coding	0.005181	0.397933	
chunk0163_122_1	chr6	10310775	10311345	+	0	NA	Intergenic	Intergenic	-101258	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.017544	0.411559	
chunk0124_344_1	chr3	58372079	58372368	+	0	NA	intron (NM_017771, intron 3 of 17)	L1ME4a|LINE|L1	39333	NM_001289101	54899	Hs.190544	NM_017771	ENSG00000168297	PXK	MONAKA|SLOB	PX domain containing serine/threonine kinase like	protein-coding	0.003460	0.337931	
chunk0094_35_1	chr2	1792228	1792452	+	0	NA	exon (NM_001303052, exon 24 of 25)	exon (NM_001303052, exon 24 of 25)	-47793	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.040179	0.520000	
chunk0056_321_1	chr13	91090813	91091240	+	0	NA	Intergenic	Intergenic	-1409	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.007026	0.359813	
chunk0176_340_1	chr7	17680220	17680603	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-121502	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.007833	0.401042	
chunk0032_280_1	chr11	9137817	9138017	+	0	NA	TTS (NM_001243254)	TTS (NM_001243254)	43554	NR_027713	283102	Hs.689472	NR_027713	ENSG00000213538	KRT8P41	-	keratin 8 pseudogene 41	pseudo	0.030000	0.621891	
chunk0066_249_1	chr15	34664199	34664712	+	0	NA	Intergenic	L1ME1|LINE|L1	-80885	NR_027410	440270	Hs.720151	NM_001023567	ENSG00000215252	GOLGA8B	GOLGA5	golgin A8 family member B	protein-coding	0.001949	0.340467	
chunk0150_360_1	chr5	38979408	38980106	+	0	NA	intron (NM_001285439, intron 8 of 38)	MLT1F|LTR|ERVL-MaLR	94651	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.004298	0.340486	
chunk0182_321_1	chr7	99002298	99002581	+	0	NA	intron (NM_003496, intron 65 of 70)	L1MD2|LINE|L1	-10726	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.014134	0.482394	
chunk0121_174_1	chr3	19947802	19948005	+	0	NA	intron (NM_004162, intron 1 of 5)	intron (NM_004162, intron 1 of 5)	823	NM_004162	5868	Hs.475663	NM_004162	ENSG00000144566	RAB5A	RAB5	RAB5A, member RAS oncogene family	protein-coding	0.039409	0.612745	
chunk0171_64_1	chr6	121388482	121388904	+	0	NA	Intergenic	L2b|LINE|L2	-46884	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.002370	0.498818	
chunk0202_108_1	chr9	72539957	72540627	+	0	NA	intron (NM_138691, intron 1 of 23)	intron (NM_138691, intron 1 of 23)	18491	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.010448	0.451565	
chunk0171_455_1	chr6	132257383	132257969	+	0	NA	Intergenic	Intergenic	123698	NR_038981	100507254	Hs.103070	NR_038981	ENSG00000228495	LINC01013	-	long intergenic non-protein coding RNA 1013	ncRNA	0.001706	0.385009	
chunk0027_183_1	chr10	75220296	75220636	+	0	NA	intron (NM_003375, intron 6 of 9)	intron (NM_003375, intron 6 of 9)	9924	NR_033675									0.011765	0.457478	
chunk0018_384_1	chr1	222388493	222388927	+	0	NA	Intergenic	Intergenic	159392	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.013825	0.406897	
chunk0147_244_1	chr4	183057230	183057912	+	0	NA	Intergenic	L1ME3B|LINE|L1	19906	NR_003612	403315	Hs.652187	NR_003612	ENSG00000230219	FAM92A1P2	FAM92A3	family with sequence similarity 92, member A3	pseudo	0.011730	0.417277	
chunk0110_190_1	chr20	14729468	14730123	+	0	NA	intron (NM_080676, intron 5 of 16)	L1MEd|LINE|L1	175411	NR_104193	140848	Hs.570367	NR_104193	ENSG00000227927	MACROD2-IT1	C20orf68|NCRNA00227|bA467D7.4	MACROD2 intronic transcript 1	ncRNA	0.007634	0.352134	453(GGGAACTAAATGTTCT,-,0.00),454(GGAACTAAATGTTCTT,+,0.00)
chunk0207_258_1	chr9	132224406	132225035	+	0	NA	intron (NM_032536, intron 3 of 7)	L1ME4b|LINE|L1	62773	NM_032536	84628	Hs.163642	NM_032536	ENSG00000196358	NTNG2	LHLL9381|Lmnt2|NTNG1|bA479K20.1	netrin G2	protein-coding	0.007949	0.426984	323(GAGCACACTCTGTCTC,-,0.00),324(AGCACACTCTGTCTCT,+,0.00)
chunk0192_411_1	chr8	69137575	69138058	+	0	NA	Intergenic	Intergenic	-33626	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.010352	0.326446	
chunk0120_335_1	chr3	10855398	10855893	+	0	NA	intron (NM_014229, intron 5 of 13)	L2c|LINE|L2	39413	NM_014229	6538	Hs.655078	NM_014229	ENSG00000132164	SLC6A11	GAT-3|GAT3|GAT4	solute carrier family 6 member 11	protein-coding	0.006061	0.485887	
chunk0051_37_1	chr12	112232316	112232595	+	0	NA	intron (NM_001109662, intron 38 of 75)	L1MC4a|LINE|L1	-69134	NR_106921	102465519		NR_106921	ENSG00000283793	MIR6861	hsa-mir-6861	microRNA 6861	ncRNA	0.003584	0.421429	
chunk0201_267_1	chr9	38569454	38569653	+	0	NA	Intergenic	Intergenic	-24181	NR_047651	100289137	Hs.644630	NR_047651	ENSG00000283486	FAM95C	-	family with sequence similarity 95 member C	ncRNA	0.015075	0.545000	
chunk0054_14_1	chr13	40484892	40485222	+	0	NA	Intergenic	Intergenic	-4051	NR_024506	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.018182	0.525680	
chunk0027_225_1	chr10	76269793	76270469	+	0	NA	intron (NR_131178, intron 6 of 7)	L2a|LINE|L2	487370	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.007396	0.434269	271(GTGCACACCCTGTTCT,-,0.00),272(TGCACACCCTGTTCTG,+,0.00)
chunk0028_452_1	chr10	94489224	94489554	+	0	NA	intron (NM_015188, intron 3 of 12)	L1MA2|LINE|L1	-56378	NM_001289068	3070	Hs.463677	NM_018063	ENSG00000119969	HELLS	ICF4|LSH|Nbla10143|PASG|SMARCA6	helicase, lymphoid specific	protein-coding	0.003030	0.480363	
chunk0040_370_1	chr11	118930123	118930357	+	0	NA	Intergenic	Intergenic	-19336	NM_182557	283149	Hs.414740	NM_182557	ENSG00000186174	BCL9L	B9L|BCL9-2|DLNB11	BCL9 like	protein-coding	0.047009	0.608511	
chunk0196_51_1	chr8	101977768	101977967	+	0	NA	intron (NM_001040629, intron 2 of 6)	intron (NM_001040629, intron 2 of 6)	-6565	NR_126152	104054148	Hs.683917	NR_126152		LOC104054148	-	uncharacterized LOC104054148	ncRNA	0.010050	0.425000	
chunk0046_193_1	chr12	58877101	58877568	+	0	NA	intron (NM_001136051, intron 15 of 18)	intron (NM_001136051, intron 15 of 18)	42212	NM_001136051	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.025696	0.448718	
chunk0114_201_1	chr21	15374082	15374316	+	0	NA	Intergenic	Intergenic	-309394	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.004274	0.400000	
chunk0201_345_1	chr9	65662923	65663296	+	0	NA	Intergenic	Intergenic	-12725	NM_001024916	220869	Hs.355950	NM_001024916	ENSG00000147996	CBWD5	CBWD3|DC36	COBW domain containing 5	protein-coding	0.002681	0.363636	
chunk0079_369_1	chr17	18021577	18021776	+	0	NA	intron (NM_145691, intron 6 of 7)	intron (NM_145691, intron 6 of 7)	17490	NM_145691	91647	Hs.528889	NM_145691	ENSG00000171953	ATPAF2	ATP12|ATP12p|LP3663|MC5DN1	ATP synthase mitochondrial F1 complex assembly factor 2	protein-coding	0.005025	0.555000	55(CAGAACACTCTGTGCC,-,0.00),56(AGAACACTCTGTGCCT,+,0.00)
chunk0162_2_1	chr6	189525	189827	+	0	NA	intron (NR_126020, intron 2 of 7)	intron (NR_126020, intron 2 of 7)	15808	NR_126020	285766	Hs.657946	NR_126020	ENSG00000263667	LOC285766	-	uncharacterized LOC285766	ncRNA	0.003311	0.425743	151(AAGTACATCTTGTTCT,-,0.00),152(AGTACATCTTGTTCTC,+,0.00)
chunk0191_45_1	chr8	43240687	43241059	+	0	NA	Intergenic	SAR|Satellite|Satellite	-51569	NM_001002920	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.000000	0.206434	
chunk0042_279_1	chr12	7079290	7079719	+	0	NA	TTS (NM_001733)	TTS (NM_001733)	12943	NM_001733	715	Hs.524224	NM_001733	ENSG00000159403	C1R	EDSPD1	complement C1r	protein-coding	0.000000	0.353488	
chunk0136_264_1	chr3	194375576	194375969	+	0	NA	Intergenic	Intergenic	-6029	NM_130830	131578	Hs.288467	NM_130830	ENSG00000172061	LRRC15	LIB	leucine rich repeat containing 15	protein-coding	0.010178	0.469543	
chunk0180_384_1	chr7	74470550	74470783	+	0	NA	intron (NM_001199207, intron 1 of 26)	L1MB7|LINE|L1	16876	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.012876	0.418803	
chunk0101_108_1	chr2	125463390	125463756	+	0	NA	Intergenic	L1ME2|LINE|L1	-1192362	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.002732	0.321526	
chunk0189_322_1	chr8	26293128	26293561	+	0	NA	intron (NM_001177591, intron 1 of 9)	intron (NM_001177591, intron 1 of 9)	128	NM_001177591	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.006928	0.384793	
chunk0075_174_1	chr16	52001241	52001634	+	0	NA	Intergenic	MER53|DNA|hAT	72498	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.010178	0.352792	
chunk0155_131_1	chr5	93358342	93358712	+	0	NA	Intergenic	Intergenic	212816	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.002703	0.301887	214(AGTCACATACTGTTCC,-,0.00),215(GTCACATACTGTTCCT,+,0.00)
chunk0129_173_1	chr3	120858176	120858950	+	0	NA	Intergenic	L2a|LINE|L2	-49640	NM_014980	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.007752	0.398710	
chunk0141_425_1	chr4	88770868	88771330	+	0	NA	intron (NM_014883, intron 11 of 23)	intron (NM_014883, intron 11 of 23)	52262	NM_001265580	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.004329	0.334773	193(AGGTACACAGTGTTCC,-,0.00),194(GGTACACAGTGTTCCT,+,0.00)
chunk0203_271_1	chr9	88414373	88414612	+	0	NA	intron (NM_006717, intron 1 of 5)	intron (NM_006717, intron 1 of 5)	26110	NM_006717	10927	Hs.146804	NM_006717	ENSG00000106723	SPIN1	SPIN|TDRD24	spindlin 1	protein-coding	0.008368	0.504167	
chunk0210_214_1	chrX	81286558	81287023	+	0	NA	intron (NM_003022, intron 3 of 3)	intron (NM_003022, intron 3 of 3)	-84848	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.002151	0.319742	
chunk0140_188_1	chr4	69930301	69930713	+	0	NA	promoter-TSS (NM_001890)	promoter-TSS (NM_001890)	-574	NM_001890	1446	Hs.3155	NM_001890	ENSG00000126545	CSN1S1	CASA|CSN1	casein alpha s1	protein-coding	0.002427	0.278450	
chunk0150_279_1	chr5	36949315	36949823	+	0	NA	intron (NM_015384, intron 1 of 45)	intron (NM_015384, intron 1 of 45)	72810	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.001969	0.306483	
chunk0193_220_1	chr8	76450645	76450907	+	0	NA	intron (NR_105006, intron 2 of 5)	intron (NR_105006, intron 2 of 5)	44122	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.003817	0.342205	
chunk0053_293_1	chr13	33630965	33631286	+	0	NA	intron (NM_001243476, intron 3 of 17)	intron (NM_001243476, intron 3 of 17)	45710	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.003115	0.366460	
chunk0019_243_1	chr1	227440270	227440578	+	0	NA	Intergenic	Intergenic	-122299	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.016234	0.411003	105(GGAACACTGAGATCTC,+,0.00)
chunk0010_136_1	chr1	114755434	114756068	+	0	NA	intron (NM_001130523, intron 1 of 19)	intron (NM_001130523, intron 1 of 19)	2299	NM_001242891	7812	Hs.69855	NM_007158	ENSG00000009307	CSDE1	D1S155E|UNR	cold shock domain containing E1	protein-coding	0.006309	0.352756	
chunk0023_313_1	chr10	29050801	29051064	+	0	NA	Intergenic	Intergenic	204524	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.011407	0.378788	
chunk0095_397_1	chr2	24203276	24203497	+	0	NA	3' UTR (NM_006277, exon 40 of 40)	3' UTR (NM_006277, exon 40 of 40)	28343	NM_001040710	653140	Hs.741736	NM_001040710	ENSG00000186453	FAM228A	C2orf84	family with sequence similarity 228 member A	protein-coding	0.013575	0.432432	
chunk0035_149_1	chr11	43036509	43036856	+	0	NA	Intergenic	L2a|LINE|L2	232687	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.011527	0.433908	
chunk0080_193_1	chr17	29039097	29039374	+	0	NA	Intergenic	L1ME4c|LINE|L1	-3665	NM_016518	51268	Hs.462585	NM_016518	ENSG00000179761	PIPOX	LPIPOX	pipecolic acid and sarcosine oxidase	protein-coding	0.003610	0.413669	
chunk0092_450_1	chr19	38862431	38862990	+	0	NA	Intergenic	LTR35A|LTR|ERV1	-10371	NM_001005335	3191	Hs.644906	NM_001533	ENSG00000104824	HNRNPL	HNRPL|P/OKcl.14|hnRNP-L	heterogeneous nuclear ribonucleoprotein L	protein-coding	0.010733	0.478571	
chunk0192_161_1	chr8	62425373	62425761	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	176625	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.000000	0.285347	
chunk0183_179_1	chr7	106196514	106197162	+	0	NA	Intergenic	Intergenic	-84191	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.003086	0.436055	
chunk0113_105_1	chr20	51121391	51122369	+	0	NA	Intergenic	MamRep38|DNA|hAT	-98742	NM_002237	3755	Hs.118695	NM_002237	ENSG00000026559	KCNG1	K13|KCNG|KV6.1|kH2	potassium voltage-gated channel modifier subfamily G member 1	protein-coding	0.009202	0.518897	
chunk0157_214_1	chr5	119303330	119303818	+	0	NA	intron (NM_001077654, intron 1 of 1)	intron (NM_001077654, intron 1 of 1)	-29601	NM_001286814	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.002049	0.435583	
chunk0017_36_1	chr1	204976793	204977010	+	0	NA	3' UTR (NM_001160333, exon 15 of 15)	3' UTR (NM_001160333, exon 15 of 15)	32675	NM_001160331	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.023041	0.605505	172(CAGAACAAGCTGTGCT,-,0.00),173(AGAACAAGCTGTGCTG,+,0.00)
chunk0071_298_1	chr15	85926046	85926625	+	0	NA	Intergenic	L2|LINE|L2	100700	NR_049805	100847084		NR_049805	ENSG00000264406	MIR548AP	-	microRNA 548ap	ncRNA	0.010363	0.458621	
chunk0096_108_1	chr2	28342242	28342989	+	0	NA	Intergenic	Intergenic	-32156	NR_038319	100505716	Hs.679092	NR_038319	ENSG00000223522	LOC100505716	-	uncharacterized LOC100505716	ncRNA	0.020080	0.486631	716(GGGACCAGCCTGTCCC,-,0.00),717(GGACCAGCCTGTCCCA,+,0.00)
chunk0015_255_1	chr1	188061483	188062318	+	0	NA	Intergenic	L1PA15|LINE|L1	618272	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003593	0.340909	
chunk0193_342_1	chr8	79443022	79443826	+	0	NA	Intergenic	L1M4|LINE|L1	-167390	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.006219	0.346584	
chunk0127_394_1	chr3	102302085	102302419	+	0	NA	Intergenic	HAL1ME|LINE|L1	-132763	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.005988	0.337313	
chunk0141_97_1	chr4	79172291	79172722	+	0	NA	intron (NR_038342, intron 3 of 5)	intron (NR_038342, intron 3 of 5)	153511	NM_032693	84779	Hs.676048	NM_032693	ENSG00000156269	NAA11	ARD1B|ARD2|hARD2	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding	0.002320	0.349537	
chunk0118_193_1	chr22	31503343	31503542	+	0	NA	intron (NM_001258326, intron 1 of 30)	intron (NM_001258326, intron 1 of 30)	7303	NM_001258326	9814	Hs.62209	NM_014775	ENSG00000198089	SFI1	PISD|PPP1R139|hSfi1p	SFI1 centrin binding protein	protein-coding	0.010050	0.395000	
chunk0133_444_1	chr3	175108589	175108878	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	6509	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.000000	0.300000	21(AAGATCAGCTTGTACC,-,0.00)
chunk0086_370_1	chr18	26106337	26106543	+	0	NA	Intergenic	Intergenic	-15223	NM_001308201	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.009709	0.386473	
chunk0030_402_1	chr10	120052503	120053377	+	0	NA	Intergenic	Intergenic	94427	NR_039830	100616322		NR_039830	ENSG00000265370	MIR4682	-	microRNA 4682	ncRNA	0.003432	0.453714	
chunk0058_205_1	chr14	24846191	24846400	+	0	NA	intron (NM_014178, intron 4 of 5)	intron (NM_014178, intron 4 of 5)	202705	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004785	0.300000	
chunk0001_51_1	chr1	1892492	1892896	+	0	NA	Intergenic	L1MC4a|LINE|L1	-1577	NM_001282538	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.019802	0.538272	
chunk0205_282_1	chr9	111652861	111653756	+	0	NA	non-coding (NR_037148, exon 5 of 5)	non-coding (NR_037148, exon 5 of 5)	-8263	NM_001198664	2790	Hs.534196	NM_001017998	ENSG00000242616	GNG10	-	G protein subunit gamma 10	protein-coding	0.003352	0.287946	
chunk0184_256_1	chr7	118009968	118010580	+	0	NA	Intergenic	Intergenic	-136767	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.006536	0.384992	
chunk0152_370_1	chr5	64331868	64332544	+	0	NA	intron (NM_001113561, intron 7 of 7)	MER52A|LTR|ERV1	166362	NM_178532	285671	Hs.657843	NM_178532	ENSG00000164197	RNF180	RINES	ring finger protein 180	protein-coding	0.011834	0.481536	307(AGGCACAAGCAGTACT,-,0.00),308(GGCACAAGCAGTACTC,+,0.00)
chunk0006_45_1	chr1	64484529	64485138	+	0	NA	intron (NM_020925, intron 1 of 26)	L1MB3|LINE|L1	14040	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.008210	0.393443	
chunk0013_48_1	chr1	167136156	167136673	+	0	NA	Intergenic	Intergenic	41564	NM_001080426	92235	Hs.632462	NM_001080426	ENSG00000198842	DUSP27	-	dual specificity phosphatase 27, atypical	protein-coding	0.009671	0.498069	
chunk0169_79_1	chr6	99425615	99425875	+	0	NA	promoter-TSS (NM_015491)	promoter-TSS (NM_015491)	-414	NM_032870	25957	Hs.520287	NM_015491	ENSG00000132424	PNISR	C6orf111|HSPC306|SFRS18|SRrp130|bA98I9.2	PNN interacting serine and arginine rich protein	protein-coding	0.042308	0.517241	
chunk0081_67_1	chr17	38888932	38889167	+	0	NA	intron (NM_001271608, intron 2 of 5)	MIRb|SINE|MIR	19190	NR_073384	3927	Hs.741156	NM_006148	ENSG00000002834	LASP1	Lasp-1|MLN50	LIM and SH3 protein 1	protein-coding	0.021277	0.457627	
chunk0175_301_1	chr7	7894036	7894614	+	0	NA	Intergenic	Intergenic	-74418	NM_138426	113263	Hs.131673	NM_138426	ENSG00000106415	GLCCI1	FAM117C|GCTR|GIG18|TSSN1	glucocorticoid induced 1	protein-coding	0.005190	0.373057	276(AGGAACATTCTGTGTA,-,0.00)
chunk0083_449_1	chr17	72972529	72973055	+	0	NA	intron (NM_001159770, intron 4 of 9)	intron (NM_001159770, intron 4 of 9)	119922	NM_139177	201266	Hs.221127	NM_139177	ENSG00000133195	SLC39A11	C17orf26|ZIP-11|ZIP11	solute carrier family 39 member 11	protein-coding	0.011407	0.480076	
chunk0144_294_1	chr4	138330538	138331033	+	0	NA	intron (NR_051987, intron 1 of 2)	intron (NR_051987, intron 1 of 2)	21074	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.004040	0.356855	
chunk0049_3_1	chr12	89163925	89164498	+	0	NA	Intergenic	L2a|LINE|L2	-144519	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.003490	0.398955	
chunk0124_401_1	chr3	59816164	59816569	+	0	NA	intron (NM_001166243, intron 8 of 9)	intron (NM_001166243, intron 8 of 9)	-766377	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.002469	0.408867	107(TGGCACACAGTGTACA,-,0.00),108(GGCACACAGTGTACAC,+,0.00)
chunk0131_87_1	chr3	143332949	143333271	+	0	NA	intron (NM_173653, intron 14 of 15)	intron (NM_173653, intron 14 of 15)	-9136	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.003106	0.421053	
chunk0051_96_1	chr12	114670779	114671057	+	0	NA	3' UTR (NM_016569, exon 8 of 8)	3' UTR (NM_016569, exon 8 of 8)	13246	NM_005996	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.003597	0.283154	
chunk0068_437_1	chr15	59604900	59605258	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-6704	NM_004751	9245	Hs.194710	NM_004751	ENSG00000140297	GCNT3	C2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding	0.005587	0.359331	
chunk0169_379_1	chr6	107400636	107401058	+	0	NA	intron (NM_020381, intron 1 of 7)	intron (NM_020381, intron 1 of 7)	58728	NM_020381	57107	Hs.745008	NM_020381	ENSG00000164494	PDSS2	C6orf210|COQ10D3|COQ1B|DLP1|bA59I9.3|hDLP1	decaprenyl diphosphate synthase subunit 2	protein-coding	0.009479	0.513002	
chunk0165_164_1	chr6	33840596	33840945	+	0	NA	Intergenic	Intergenic	-36754	NM_002418	4295	Hs.2813	NM_002418	ENSG00000096395	MLN	-	motilin	protein-coding	0.020057	0.514286	
chunk0079_270_1	chr17	16216966	16217594	+	0	NA	promoter-TSS (NM_004278)	promoter-TSS (NM_004278)	85	NM_004278	9487	Hs.499793	NM_004278	ENSG00000108474	PIGL	CHIME	phosphatidylinositol glycan anchor biosynthesis class L	protein-coding	0.044586	0.540541	462(AGGCACTGGGTGTACC,-,0.00),463(GGCACTGGGTGTACCT,+,0.00)
chunk0119_207_1	chr22	44866359	44867047	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	114145	NM_001017526	23779	Hs.102336	NM_181335	ENSG00000241484	ARHGAP8	BPGAP1|PP610	Rho GTPase activating protein 8	protein-coding	0.014535	0.523948	
chunk0131_28_1	chr3	142325585	142325943	+	0	NA	intron (NM_001282857, intron 37 of 40)	L1M1|LINE|L1	-100157	NM_001039547	256356	Hs.135904	NM_152776	ENSG00000175066	GK5	-	glycerol kinase 5	protein-coding	0.002793	0.348189	
chunk0058_84_1	chr14	21408816	21409537	+	0	NA	intron (NM_020920, intron 11 of 37)	MER3|DNA|hAT-Charlie	-11775	NR_002916	319103	Hs.680078	NR_002916	ENSG00000200785	SNORD8	RNU6C|mgU6-53	small nucleolar RNA, C/D box 8	snoRNA	0.008322	0.339335	
chunk0042_360_1	chr12	10330681	10330940	+	0	NA	Intergenic	Intergenic	22992	NM_007334	3824	Hs.562457	NM_002262	ENSG00000134539	KLRD1	CD94	killer cell lectin like receptor D1	protein-coding	0.011583	0.350000	
chunk0121_53_1	chr3	15614947	15615538	+	0	NA	intron (NM_001281725, intron 1 of 3)	intron (NM_001281725, intron 1 of 3)	13273	NM_001281725	686	Hs.444197	NM_001281723	ENSG00000169814	BTD	-	biotinidase	protein-coding	0.001692	0.380068	
chunk0034_163_1	chr11	30553699	30554271	+	0	NA	intron (NM_001145399, intron 2 of 6)	intron (NM_001145399, intron 2 of 6)	26508	NM_001584	744	Hs.289795	NM_001584	ENSG00000066382	MPPED2	239FB|C11orf8	metallophosphoesterase domain containing 2	protein-coding	0.006993	0.450262	
chunk0153_152_1	chr5	69332815	69333097	+	0	NA	promoter-TSS (NM_176816)	promoter-TSS (NM_176816)	-163	NM_001297697	202243	Hs.654850	NM_176816	ENSG00000183323	CCDC125	KENAE	coiled-coil domain containing 125	protein-coding	0.060284	0.547703	
chunk0036_49_1	chr11	59024874	59025790	+	0	NA	intron (NR_033853, intron 3 of 5)	intron (NR_033853, intron 3 of 5)	33120	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.005459	0.360960	
chunk0034_406_1	chr11	38019621	38019820	+	0	NA	Intergenic	L1PA13|LINE|L1	626636	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.010050	0.570000	
chunk0103_333_1	chr2	167793995	167794639	+	0	NA	Intergenic	Intergenic	-24355	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.009317	0.350388	
chunk0195_239_1	chr8	97559336	97559635	+	0	NA	Intergenic	Intergenic	-84694	NM_178812	92140	Hs.377155	NM_178812	ENSG00000147649	MTDH	3D3|AEG-1|AEG1|LYRIC|LYRIC/3D3	metadherin	protein-coding	0.003344	0.350000	
chunk0055_202_1	chr13	61936970	61937620	+	0	NA	Intergenic	L1ME1|LINE|L1	92253	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004615	0.307220	
chunk0125_298_1	chr3	70000335	70000931	+	0	NA	intron (NR_110000, intron 1 of 3)	intron (NR_110000, intron 1 of 3)	889	NR_110000	101927152	Hs.382046	NR_110000	ENSG00000240405	SAMMSON	LINC01212	survival associated mitochondrial melanoma specific oncogenic non-coding RNA	ncRNA	0.006711	0.331658	265(CATAACAGAATGTTCT,-,0.00),266(ATAACAGAATGTTCTA,+,0.00)
chunk0040_269_1	chr11	116642689	116642993	+	0	NA	Intergenic	Intergenic	130157	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.003289	0.465574	159(TAGTACAGATTGTCCT,-,0.00),160(AGTACAGATTGTCCTC,+,0.00)
chunk0155_318_1	chr5	96647546	96647899	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-14315	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.019830	0.409605	
chunk0104_262_1	chr2	177756657	177756983	+	0	NA	intron (NM_001077197, intron 11 of 20)	intron (NM_001077197, intron 11 of 20)	131919	NM_001077196	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.015337	0.403670	
chunk0177_280_1	chr7	25620060	25620774	+	0	NA	Intergenic	Intergenic	329569	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.011204	0.439161	323(CAGTACATGATGTTCA,-,0.00),324(AGTACATGATGTTCAA,+,0.00)
chunk0120_71_1	chr3	3454730	3455022	+	0	NA	Intergenic	Intergenic	-275159	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.003425	0.361775	
chunk0200_54_1	chr9	15573769	15574112	+	0	NA	intron (NM_173550, intron 3 of 25)	intron (NM_173550, intron 3 of 25)	20841	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.005831	0.363372	195(CAGAACACACTGTTCT,-,0.00),196(AGAACACACTGTTCTC,+,0.00)
chunk0018_252_1	chr1	220226855	220227108	+	0	NA	intron (NM_012414, intron 2 of 34)	MLT1B|LTR|ERVL-MaLR	-26305	NR_002994	677818	Hs.730572	NR_002994	ENSG00000222370	SNORA36B	ACA36b	small nucleolar RNA, H/ACA box 36B	snoRNA	0.011858	0.448819	
chunk0208_123_1	chrX	15311274	15311505	+	0	NA	intron (NM_001201583, intron 1 of 6)	intron (NM_001201583, intron 1 of 6)	3170	NM_001012428	140456	Hs.352183	NM_080873	ENSG00000165192	ASB11	-	ankyrin repeat and SOCS box containing 11	protein-coding	0.008658	0.482759	84(AAGGACTGGTTGTCCC,-,0.00),85(AGGACTGGTTGTCCCA,+,0.00)
chunk0033_174_1	chr11	15707873	15708449	+	0	NA	Intergenic	Intergenic	64276	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.008681	0.480069	
chunk0185_144_1	chr7	127566130	127566969	+	0	NA	Intergenic	Intergenic	19051	NM_024523	79571	Hs.521168	NM_024523	ENSG00000179562	GCC1	GCC1P|GCC88	GRIP and coiled-coil domain containing 1	protein-coding	0.009535	0.394048	
chunk0022_74_1	chr10	8811974	8812426	+	0	NA	Intergenic	L1ME1|LINE|L1	-85789	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.004425	0.306843	
chunk0017_425_1	chr1	213177006	213177338	+	0	NA	intron (NM_001287220, intron 8 of 12)	intron (NM_001287220, intron 8 of 12)	125939	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.006024	0.348348	
chunk0126_146_1	chr3	76550777	76550980	+	0	NA	Intergenic	MER52A|LTR|ERV1	-489265	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.014778	0.602941	
chunk0148_345_1	chr5	14428156	14428777	+	0	NA	intron (NM_007118, intron 34 of 56)	intron (NM_007118, intron 34 of 56)	-153316	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.012882	0.355305	
chunk0028_458_1	chr10	95171985	95172298	+	0	NA	Intergenic	MIRb|SINE|MIR	-22059	NM_207321	142827	Hs.134229	NM_207321	ENSG00000173124	ACSM6	C10orf129|bA310E22.3	acyl-CoA synthetase medium chain family member 6	protein-coding	0.003195	0.439490	
chunk0021_250_1	chr1	243316747	243317254	+	0	NA	intron (NM_006642, intron 9 of 17)	intron (NM_006642, intron 9 of 17)	-29176	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.005917	0.326772	
chunk0123_216_1	chr3	45139439	45139998	+	0	NA	intron (NM_022842, intron 1 of 8)	intron (NM_022842, intron 1 of 8)	6704	NM_178181	64866	Hs.476093	NM_022842	ENSG00000163814	CDCP1	CD318|SIMA135|TRASK	CUB domain containing protein 1	protein-coding	0.008945	0.517857	304(CAGAGCACAGAGTTCC,-,0.00)
chunk0015_93_1	chr1	185035177	185035390	+	0	NA	Intergenic	Intergenic	-10136	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.004695	0.331776	
chunk0177_420_1	chr7	27743023	27743260	+	0	NA	intron (NM_006024, intron 1 of 16)	intron (NM_006024, intron 1 of 16)	3046	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.008439	0.386555	
chunk0017_123_1	chr1	206280597	206280799	+	0	NA	intron (NM_001170637, intron 1 of 21)	intron (NM_001170637, intron 1 of 21)	75269	NM_001170637	23380	Hs.497575	NM_015326	ENSG00000266028	SRGAP2	ARHGAP34|FNBP2|SRGAP2A|SRGAP3	SLIT-ROBO Rho GTPase activating protein 2	protein-coding	0.000000	0.374384	178(CAGAACATTATGCTCT,-,0.00),179(AGAACATTATGCTCTT,+,0.00)
chunk0207_252_1	chr9	132164231	132164882	+	0	NA	intron (NM_032536, intron 1 of 7)	CpG	2609	NM_032536	84628	Hs.163642	NM_032536	ENSG00000196358	NTNG2	LHLL9381|Lmnt2|NTNG1|bA479K20.1	netrin G2	protein-coding	0.061444	0.596626	296(AGGAACGTGCTGTGCT,-,0.00),297(GGAACGTGCTGTGCTC,+,0.00)
chunk0100_84_1	chr2	107711131	107712569	+	0	NA	Intergenic	Intergenic	-42262	NR_126370	104326057	Hs.585967	NR_126369	ENSG00000232991	GACAT1	LINC00876	gastric cancer associated transcript 1	ncRNA	0.006954	0.357192	17(AATGACACTATGTTCT,-,0.00),18(ATGACACTATGTTCTG,+,0.00),248(AAGTACATGATGTACA,-,0.00),249(AGTACATGATGTACAG,+,0.00),1015(AGCACACAGTCTTCTC,+,0.00),1052(TAGGACACTGTGTTCT,-,0.00),1053(AGGACACTGTGTTCTT,+,0.00)
chunk0160_439_1	chr5	164686785	164687234	+	0	NA	Intergenic	Intergenic	216730	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.011136	0.362222	
chunk0036_141_1	chr11	62050517	62051261	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-73084	NM_001040694	3619	Hs.142179	NM_020238	ENSG00000149503	INCENP	-	inner centromere protein	protein-coding	0.014785	0.389262	
chunk0033_211_1	chr11	17012521	17013494	+	0	NA	intron (NM_175058, intron 3 of 22)	intron (NM_175058, intron 3 of 22)	1409	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.038027	0.525667	
chunk0031_203_1	chr10	125859194	125859495	+	0	NA	intron (NM_018180, intron 3 of 10)	intron (NM_018180, intron 3 of 10)	21971	NM_018180	55760	Hs.370292	NM_018180	ENSG00000089876	DHX32	DDX32|DHLP1	DEAH-box helicase 32 (putative)	protein-coding	0.003322	0.476821	
chunk0208_425_1	chrX	29926177	29926717	+	0	NA	intron (NM_014271, intron 8 of 10)	intron (NM_014271, intron 8 of 10)	-289111	NM_002364	4113	Hs.113824	NM_002364	ENSG00000099399	MAGEB2	CT3.2|DAM6|MAGE-XP-2	MAGE family member B2	protein-coding	0.005556	0.351201	
chunk0211_45_1	chrX	108601889	108602424	+	0	NA	intron (NM_033380, intron 27 of 50)	intron (NM_033380, intron 27 of 50)	134221	NM_003604	8471	Hs.407141	NM_003604	ENSG00000133124	IRS4	IRS-4|PY160	insulin receptor substrate 4	protein-coding	0.000000	0.341418	
chunk0209_101_1	chrX	39876862	39877264	+	0	NA	Intergenic	Intergenic	39502	NR_039763	100616251		NR_039763	ENSG00000263972	MIR1587	-	microRNA 1587	ncRNA	0.007463	0.553350	
chunk0187_54_1	chr8	1858640	1859606	+	0	NA	intron (NM_001308152, intron 3 of 27).2	intron (NM_001308152, intron 3 of 27).2	35147	NM_001308153	9639	Hs.98594	NM_014629	ENSG00000104728	ARHGEF10	GEF10|SNCV	Rho guanine nucleotide exchange factor 10	protein-coding	0.042443	0.536711	
chunk0186_182_1	chr7	139647170	139647506	+	0	NA	intron (NM_001113239, intron 2 of 14)	intron (NM_001113239, intron 2 of 14)	123410	NM_001080511	154790	Hs.57806	NM_001080511	ENSG00000236279	CLEC2L	-	C-type lectin domain family 2 member L	protein-coding	0.011905	0.442136	
chunk0131_42_1	chr3	142578518	142579030	+	0	NA	promoter-TSS (NM_001184)	promoter-TSS (NM_001184)	52	NM_001184	545	Hs.271791	NM_001184	ENSG00000175054	ATR	FCTCS|FRP1|MEC1|SCKL|SCKL1	ATR serine/threonine kinase	protein-coding	0.087891	0.666667	
chunk0147_450_1	chr4	188017569	188018053	+	0	NA	Intergenic	L2a|LINE|L2	22040	NM_001304358	132625	Hs.335787	NM_174900	ENSG00000179059	ZFP42	REX-1|REX1|ZNF754|zfp-42	ZFP42 zinc finger protein	protein-coding	0.012397	0.317526	
chunk0101_102_1	chr2	125144163	125144444	+	0	NA	Intergenic	L1MEg|LINE|L1	1119016	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.007117	0.382979	
chunk0091_137_1	chr19	6843523	6844202	+	0	NA	intron (NM_001258206, intron 21 of 25)	MER104|DNA|TcMar-Tc2	-43687	NM_001256254	2015	Hs.2375	NM_001974	ENSG00000174837	ADGRE1	EMR1|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding	0.008837	0.388235	
chunk0148_276_1	chr5	10703445	10704170	+	0	NA	intron (NM_004394, intron 2 of 3)	intron (NM_004394, intron 2 of 3)	57468	NM_001291963	1611	Hs.75189	NM_004394	ENSG00000112977	DAP	-	death associated protein	protein-coding	0.011034	0.480716	570(GGGAACAGGGCGTCCT,-,0.00),571(GGAACAGGGCGTCCTG,+,0.00)
chunk0198_66_1	chr8	129816248	129816520	+	0	NA	Intergenic	L1PA16|LINE|L1	-29496	NM_031415	56169	Hs.133244	NM_031415	ENSG00000147697	GSDMC	MLZE	gasdermin C	protein-coding	0.000000	0.545788	
chunk0084_353_1	chr17	81329486	81329908	+	0	NA	intron (NM_178520, intron 1 of 2)	intron (NM_178520, intron 1 of 2)	977	NM_178520	284186	Hs.364191	NM_178520		TMEM105	-	TMEM105 long non-coding RNA	ncRNA	0.033175	0.692671	
chunk0052_182_1	chr13	24236643	24237026	+	0	NA	intron (NM_001286792, intron 4 of 14)	L1MB3|LINE|L1	17605	NR_046531	100874231	Hs.577998	NR_046531	ENSG00000227213	SPATA13-AS1	-	SPATA13 antisense RNA 1	ncRNA	0.005222	0.375000	
chunk0072_439_1	chr15	101398260	101398604	+	0	NA	exon (NM_001291309, exon 7 of 20)	exon (NM_001291309, exon 7 of 20)	63995	NR_132373	105371027		NR_132373	ENSG00000259764	PCSK6-AS1	-	PCSK6 antisense RNA 1	ncRNA	0.052326	0.573913	
chunk0212_411_1	chrX	152030277	152030682	+	0	NA	Intergenic	Intergenic	-55800	NM_004961	2564	Hs.22785	NM_004961	ENSG00000102287	GABRE	-	gamma-aminobutyric acid type A receptor epsilon subunit	protein-coding	0.007407	0.435961	
chunk0189_454_1	chr8	28472985	28473262	+	0	NA	intron (NM_001258211, intron 2 of 7)	LTR50|LTR|ERVL	17195	NM_172366	157574	Hs.741522	NM_172366	ENSG00000214050	FBXO16	FBX16	F-box protein 16	protein-coding	0.003610	0.424460	
chunk0176_309_1	chr7	16880651	16880905	+	0	NA	intron (NM_176813, intron 1 of 7)	intron (NM_176813, intron 1 of 7)	1211	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.000000	0.411765	
chunk0013_22_1	chr1	166160330	166160553	+	0	NA	intron (NM_001017961, intron 1 of 1)	intron (NM_001017961, intron 1 of 1)	-5643	NR_030626	100126349		NR_030626	ENSG00000215952	MIR921	MIRN921|hsa-mir-921	microRNA 921	ncRNA	0.013453	0.491071	
chunk0205_422_1	chr9	115034517	115035065	+	0	NA	intron (NM_002160, intron 22 of 27)	intron (NM_002160, intron 22 of 27)	83466	NM_002160	3371	Hs.143250	NM_002160	ENSG00000041982	TNC	150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C	tenascin C	protein-coding	0.005474	0.327869	
chunk0157_171_1	chr5	118093437	118093636	+	0	NA	intron (NR_104997, intron 2 of 2)	L1MCa|LINE|L1	-189038	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.010050	0.360000	
chunk0129_92_1	chr3	119357190	119357559	+	0	NA	intron (NM_020754, intron 1 of 11)	L2b|LINE|L2	-34614	NR_046748	100874246	Hs.607097	NR_046748	ENSG00000241155	ARHGAP31-AS1	-	ARHGAP31 antisense RNA 1	ncRNA	0.016260	0.508108	
chunk0175_250_1	chr7	7098345	7098894	+	0	NA	Intergenic	Intergenic	-1833	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.000000	0.380000	
chunk0077_134_1	chr16	78593534	78594180	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	494444	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.015480	0.446677	
chunk0039_204_1	chr11	100942078	100942674	+	0	NA	intron (NM_152432, intron 9 of 23)	intron (NM_152432, intron 9 of 23)	-49704	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.008389	0.423786	
chunk0112_45_1	chr20	36861889	36862328	+	0	NA	intron (NM_080627, intron 1 of 14)	intron (NM_080627, intron 1 of 14)	1576	NM_080627	140710	Hs.460807	NM_080627	ENSG00000149639	SOGA1	C20orf117|KIAA0889|SOGA	suppressor of glucose, autophagy associated 1	protein-coding	0.031891	0.609091	
chunk0176_228_1	chr7	15555630	15555876	+	0	NA	intron (NM_001004320, intron 2 of 12)	intron (NM_001004320, intron 2 of 12)	6262	NM_001004320	392636	Hs.670634	NM_001004320	ENSG00000187546	AGMO	TMEM195	alkylglycerol monooxygenase	protein-coding	0.004065	0.295547	
chunk0158_73_1	chr5	126327891	126328090	+	0	NA	Intergenic	Intergenic	-32106	NM_001146319	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.010050	0.505000	
chunk0058_266_1	chr14	26034215	26034593	+	0	NA	Intergenic	Intergenic	563350	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.002646	0.332454	
chunk0058_277_1	chr14	26317611	26318088	+	0	NA	Intergenic	L1M7|LINE|L1	279905	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.004193	0.338912	
chunk0206_244_1	chr9	123679492	123680163	+	0	NA	intron (NM_024820, intron 5 of 20)	intron (NM_024820, intron 5 of 20)	-194205	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.023845	0.523810	
chunk0003_236_1	chr1	35901246	35901583	+	0	NA	intron (NM_012199, intron 8 of 18)	intron (NM_012199, intron 8 of 18)	18205	NM_012199	26523	Hs.22867	NM_012199	ENSG00000092847	AGO1	EIF2C|EIF2C1|GERP95|Q99|hAgo1	argonaute RISC component 1	protein-coding	0.023739	0.491124	
chunk0103_76_1	chr2	160454876	160455454	+	0	NA	intron (NM_002897, intron 1 of 13)	intron (NM_002897, intron 1 of 13)	38642	NM_016836	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.005190	0.321244	385(TGGTACAGGCTGTTAT,-,0.00),386(GGTACAGGCTGTTATT,+,0.00)
chunk0196_231_1	chr8	107667718	107667996	+	0	NA	Intergenic	Intergenic	-169802	NM_001146	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.007194	0.383513	
chunk0202_102_1	chr9	72406918	72407362	+	0	NA	Intergenic	Intergenic	-41893	NM_001102421	7763	Hs.406096	NM_006007	ENSG00000107372	ZFAND5	ZA20D2|ZFAND5A|ZNF216	zinc finger AN1-type containing 5	protein-coding	0.006757	0.375281	
chunk0043_397_1	chr12	25412854	25413360	+	0	NA	Intergenic	Intergenic	140176	NM_001256266	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.007905	0.424063	
chunk0158_12_1	chr5	125229779	125229982	+	0	NA	intron (NR_109882, intron 4 of 5)	L1MC3|LINE|L1	193049	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.019704	0.421569	
chunk0146_258_1	chr4	162723126	162723827	+	0	NA	Intergenic	L3|LINE|CR1	370152	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.001427	0.290598	
chunk0203_114_1	chr9	84743893	84744287	+	0	NA	intron (NM_001007097, intron 10 of 12)	intron (NM_001007097, intron 10 of 12)	73713	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.002538	0.341772	
chunk0034_32_1	chr11	26471235	26471902	+	0	NA	intron (NM_031418, intron 4 of 26)	intron (NM_031418, intron 4 of 26)	-2334	NM_001313727	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.004498	0.347305	
chunk0210_171_1	chrX	78321628	78322241	+	0	NA	intron (NM_001282188, intron 1 of 3)	intron (NM_001282188, intron 1 of 3)	5757	NM_001282187	10800	Hs.733809	NM_006639	ENSG00000173198	CYSLTR1	CYSLT1|CYSLT1R|CYSLTR|HMTMF81	cysteinyl leukotriene receptor 1	protein-coding	0.006525	0.446254	
chunk0113_177_1	chr20	53162321	53162760	+	0	NA	intron (NM_173485, intron 1 of 2)	intron (NM_173485, intron 1 of 2)	-22743	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.020501	0.465909	
chunk0145_220_1	chr4	148055659	148056413	+	0	NA	intron (NM_024605, intron 20 of 22)	MER58A|DNA|hAT-Charlie	273441	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.010610	0.454305	
chunk0100_205_1	chr2	111418234	111418818	+	0	NA	intron (NR_015395, intron 1 of 1)	intron (NR_015395, intron 1 of 1)	76589	NR_024373	541471	Hs.560805	NR_015395	ENSG00000172965	MIR4435-2HG	AGD2|LINC00978|MIR4435-1HG|MORRBID|lncRNA-AWPPH	MIR4435-2 host gene	ncRNA	0.005137	0.406838	
chunk0113_166_1	chr20	53022091	53022632	+	0	NA	intron (NM_173485, intron 1 of 2)	intron (NM_173485, intron 1 of 2)	49954	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.014787	0.394834	
chunk0073_100_1	chr16	4481416	4481940	+	0	NA	intron (NM_001286268, intron 1 of 5).2	L2c|LINE|L2	5338	NM_001286268	3163	Hs.284279	NM_002134	ENSG00000103415	HMOX2	HO-2	heme oxygenase 2	protein-coding	0.005725	0.407619	
chunk0122_83_1	chr3	29937084	29937847	+	0	NA	intron (NM_001177711, intron 11 of 13)	intron (NM_001177711, intron 11 of 13)	-3309	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.005242	0.335079	
chunk0131_365_1	chr3	151978056	151978340	+	0	NA	Intergenic	L1ME3F|LINE|L1	-50023	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.000000	0.382456	93(GAGTACAGAGAGTACT,-,0.00),94(AGTACAGAGAGTACTG,+,0.00)
chunk0113_403_1	chr20	60533501	60533983	+	0	NA	Intergenic	Intergenic	-30820	NR_039653	100616440		NR_039653	ENSG00000265617	MIR548AG2	-	microRNA 548ag-2	ncRNA	0.010373	0.374741	
chunk0111_411_1	chr20	34580201	34580501	+	0	NA	intron (NM_080476, intron 10 of 11)	intron (NM_080476, intron 10 of 11)	21654	NM_032514	84557	Hs.632273	NM_032514	ENSG00000101460	MAP1LC3A	ATG8E|LC3|LC3A|MAP1ALC3|MAP1BLC3	microtubule associated protein 1 light chain 3 alpha	protein-coding	0.006667	0.564784	
chunk0049_430_1	chr12	97939158	97939548	+	0	NA	promoter-TSS (NR_039716)	promoter-TSS (NR_039716)	-232	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.002564	0.396419	
chunk0199_168_1	chr9	4463006	4463205	+	0	NA	Intergenic	Intergenic	-27322	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.005025	0.365000	
chunk0023_247_1	chr10	27229886	27230228	+	0	NA	intron (NM_001042473, intron 4 of 12)	intron (NM_001042473, intron 4 of 12)	10822	NM_001301252	91452	Hs.530597	NM_145698	ENSG00000107897	ACBD5	-	acyl-CoA binding domain containing 5	protein-coding	0.005848	0.297376	
chunk0026_117_1	chr10	61980397	61980884	+	0	NA	intron (NM_032199, intron 3 of 9)	intron (NM_032199, intron 3 of 9)	-68571	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.006160	0.418033	
chunk0132_134_1	chr3	156254535	156254836	+	0	NA	intron (NM_003471, intron 1 of 13)	intron (NM_003471, intron 1 of 13)	-26802	NR_046617	100874083	Hs.603823	NR_046617	ENSG00000240596	KCNAB1-AS2	-	KCNAB1 antisense RNA 2	ncRNA	0.006645	0.387417	
chunk0204_107_1	chr9	94772928	94773500	+	0	NA	intron (NM_032823, intron 3 of 14)	intron (NM_032823, intron 3 of 14)	13565	NM_001193329	84909	Hs.434253	NM_032823	ENSG00000148120	AOPEP	AP-O|APO|C90RF3|C9orf3|ONPEP	aminopeptidase O (putative)	protein-coding	0.008741	0.445026	
chunk0075_211_1	chr16	52597973	52598663	+	0	NA	intron (NR_033920, intron 1 of 3)	intron (NR_033920, intron 1 of 3)	8657	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.007246	0.419682	
chunk0141_123_1	chr4	80103522	80104079	+	0	NA	Intergenic	Intergenic	-30328	NM_001286780	118429	Hs.162963	NM_058172	ENSG00000163297	ANTXR2	CMG-2|CMG2|HFS|ISH|JHF	ANTXR cell adhesion molecule 2	protein-coding	0.010772	0.394265	242(TAGAACTGCTTGTGCC,-,0.00),243(AGAACTGCTTGTGCCA,+,0.00)
chunk0179_58_1	chr7	43702000	43702253	+	0	NA	intron (NR_047701, intron 1 of 7)	L1PA15|LINE|L1	27415	NR_047701	55744	Hs.268887	NM_018224	ENSG00000106603	COA1	C7orf44|MITRAC15	cytochrome c oxidase assembly factor 1 homolog	protein-coding	0.007905	0.346457	
chunk0002_373_1	chr1	26406384	26406733	+	0	NA	Intergenic	Intergenic	-4210	NM_024674	79727	Hs.86154	NM_024674	ENSG00000131914	LIN28A	CSDD1|LIN-28|LIN28|ZCCHC1|lin-28A	lin-28 homolog A	protein-coding	0.011461	0.368571	
chunk0085_261_1	chr18	7637368	7637670	+	0	NA	intron (NM_001105244, intron 1 of 32)	L2a|LINE|L2	70203	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.006623	0.356436	
chunk0180_258_1	chr7	69422570	69422913	+	0	NA	Intergenic	Intergenic	174754	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.008746	0.427326	
chunk0207_384_1	chr9	136297117	136297316	+	0	NA	intron (NR_111982, intron 4 of 9)	intron (NR_111982, intron 4 of 9)	6878	NR_111982	399693	Hs.530383	NM_001291516	ENSG00000260220	CCDC187	-	coiled-coil domain containing 187	protein-coding	0.055276	0.665000	
chunk0007_66_1	chr1	78231891	78232315	+	0	NA	intron (NR_027310, intron 1 of 5)	intron (NR_027310, intron 1 of 5)	2504	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.002358	0.343529	
chunk0103_290_1	chr2	166129905	166130444	+	0	NA	intron (NR_110260, intron 2 of 11)	intron (NR_110260, intron 2 of 11)	18958	NM_001202435	6323	Hs.22654	NM_006920	ENSG00000144285	SCN1A	EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI	sodium voltage-gated channel alpha subunit 1	protein-coding	0.007421	0.442593	
chunk0014_138_1	chr1	177872223	177873014	+	0	NA	Intergenic	Intergenic	97297	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.012642	0.438131	
chunk0070_195_1	chr15	72112136	72112541	+	0	NA	intron (NM_006901, intron 1 of 41)	intron (NM_006901, intron 1 of 41)	-1920	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.004938	0.327586	135(CAGGACAGCTAGTCCA,-,0.00),136(AGGACAGCTAGTCCAT,+,0.00)
chunk0077_57_1	chr16	76574235	76574455	+	0	NA	Intergenic	Intergenic	-60653	NR_110934	101928203	Hs.737035	NR_110934	ENSG00000250514	LINC02125	-	long intergenic non-protein coding RNA 2125	ncRNA	0.000000	0.389140	
chunk0083_400_1	chr17	71966578	71966777	+	0	NA	Intergenic	Intergenic	59302	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.025126	0.505000	
chunk0055_329_1	chr13	68860938	68861172	+	0	NA	TTS (NR_038878)	TTS (NR_038878)	24270	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.004274	0.272340	
chunk0144_186_1	chr4	133484363	133484825	+	0	NA	Intergenic	Intergenic	335304	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.004329	0.334773	
chunk0018_258_1	chr1	220265947	220266146	+	0	NA	TTS (NR_001587)	TTS (NR_001587)	1669	NR_001587	6791	Hs.654849	NR_001587		AURKAP1	AURKAPS1|AurAps1|STK6P	aurora kinase A pseudogene 1	pseudo	0.000000	0.295000	
chunk0023_365_1	chr10	30027768	30028162	+	0	NA	exon (NM_020848, exon 3 of 4)	exon (NM_020848, exon 3 of 4)	31594	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.040609	0.572152	
chunk0005_327_1	chr1	61062730	61063238	+	0	NA	Intergenic	Intergenic	-14290	NM_001145511	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.001969	0.314342	
chunk0125_292_1	chr3	69932424	69932932	+	0	NA	intron (NM_198159, intron 2 of 9)	intron (NM_198159, intron 2 of 9)	-3922	NM_198178	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.007874	0.369352	
chunk0104_268_1	chr2	177929739	177930689	+	0	NA	intron (NM_001077197, intron 3 of 20)	intron (NM_001077197, intron 3 of 20)	-7377	NM_001077358	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.002105	0.366982	532(GGAGACAGACTGTGCA,-,0.00),533(GAGACAGACTGTGCAT,+,0.00)
chunk0065_241_1	chr14	101286471	101287010	+	0	NA	Intergenic	Intergenic	121182	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.027829	0.529630	
chunk0055_208_1	chr13	62040772	62041201	+	0	NA	Intergenic	Intergenic	-11438	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004662	0.372093	
chunk0133_250_1	chr3	171671510	171671802	+	0	NA	intron (NM_001130081, intron 18 of 25)	MER103C|DNA|hAT-Charlie	138838	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.003425	0.348123	
chunk0138_387_1	chr4	42703701	42704276	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-46883	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.012174	0.447917	227(CTGGACAGGATGTACC,-,0.00),228(TGGACAGGATGTACCC,+,0.00)
chunk0031_216_1	chr10	125936290	125936866	+	0	NA	intron (NM_145235, intron 1 of 10)	L1ME3A|LINE|L1	36695	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.010417	0.370884	
chunk0187_120_1	chr7	149028567	149028933	+	0	NA	promoter-TSS (NM_004911)	promoter-TSS (NM_004911)	-60	NM_004911	9601	Hs.93659	NM_004911	ENSG00000155660	PDIA4	ERP70|ERP72|ERp-72	protein disulfide isomerase family A member 4	protein-coding	0.122951	0.722071	
chunk0032_420_1	chr11	12137159	12137749	+	0	NA	promoter-TSS (NM_001282665)	promoter-TSS (NM_001282665)	-936	NM_001282665	9645	Hs.501928	NM_014632	ENSG00000133816	MICAL2	MICAL-2|MICAL2PV1|MICAL2PV2	microtubule associated monooxygenase, calponin and LIM domain containing 2	protein-coding	0.016949	0.532995	193(AGGGGCAGCCAGTCCT,-,0.00),372(CTGAACAGTGAGTCCC,-,0.00),373(TGAACAGTGAGTCCCA,+,0.00)
chunk0197_279_1	chr8	124068004	124068297	+	0	NA	intron (NM_001039112, intron 28 of 40)	L3|LINE|CR1	-27368	NR_040044	439941	Hs.683919	NM_001038706	ENSG00000181171	FER1L6-AS1	C8orf54	FER1L6 antisense RNA 1	ncRNA	0.010239	0.387755	
chunk0149_124_1	chr5	19533195	19533948	+	0	NA	intron (NM_001167667, intron 9 of 12)	L2|LINE|L2	352701	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003984	0.343501	
chunk0004_189_1	chr1	46303362	46303680	+	0	NA	promoter-TSS (NM_006369)	promoter-TSS (NM_006369)	-92	NM_006004	7388	Hs.481571	NM_006004	ENSG00000173660	UQCRH	QCR6|UQCR8	ubiquinol-cytochrome c reductase hinge protein	protein-coding	0.044025	0.473354	
chunk0121_211_1	chr3	21682820	21683066	+	0	NA	intron (NM_024697, intron 1 of 7)	MER58A|DNA|hAT-Charlie	68381	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.000000	0.437247	
chunk0123_203_1	chr3	44867377	44867914	+	0	NA	Intergenic	Intergenic	5736	NM_144638	131616	Hs.646856	NM_144638	ENSG00000169964	TMEM42	-	transmembrane protein 42	protein-coding	0.007449	0.408922	
chunk0082_139_1	chr17	55384259	55384458	+	0	NA	Intergenic	LTR34|LTR|ERV1	37622	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.005025	0.450000	
chunk0025_153_1	chr10	52353912	52354241	+	0	NA	Intergenic	Intergenic	39795	NM_012242	22943	Hs.40499	NM_012242	ENSG00000107984	DKK1	DKK-1|SK	dickkopf WNT signaling pathway inhibitor 1	protein-coding	0.003040	0.363636	
chunk0130_56_1	chr3	129673778	129674328	+	0	NA	intron (NM_001128224, intron 3 of 5)	Tigger3a|DNA|TcMar-Tigger	14679	NR_033361									0.007273	0.377495	
chunk0158_315_1	chr5	132651833	132652346	+	0	NA	intron (NR_132125, intron 1 of 2)	L2a|LINE|L2	3803	NR_132126	101927761	Hs.598812	NR_132124	ENSG00000223442	TH2LCRR	TH2-LCR	T helper type 2 locus control region associated RNA	ncRNA	0.007797	0.420233	
chunk0179_154_1	chr7	46332071	46332592	+	0	NA	Intergenic	L1PB|LINE|L1	-411059	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.003839	0.339080	
chunk0128_295_1	chr3	111079938	111080137	+	0	NA	intron (NM_001243288, intron 1 of 8)	intron (NM_001243288, intron 1 of 8)	7869	NM_001243288	25945	Hs.293917	NM_015480	ENSG00000177707	NECTIN3	CD113|CDW113|NECTIN-3|PPR3|PRR3|PVRL3|PVRR3	nectin cell adhesion molecule 3	protein-coding	0.000000	0.280000	
chunk0034_115_1	chr11	28027969	28028453	+	0	NA	intron (NM_031217, intron 15 of 16)	L1PA5|LINE|L1	-28604	NR_030341	693195		NR_030341	ENSG00000207874	MIR610	MIRN610|hsa-mir-610	microRNA 610	ncRNA	0.006198	0.364948	346(TAGAACAATCTGTCTC,-,0.00),347(AGAACAATCTGTCTCT,+,0.00)
chunk0106_137_1	chr2	199991963	199992246	+	0	NA	Intergenic	Intergenic	-36368	NR_109906	129450	Hs.204619	NM_152382	ENSG00000162971	TYW5	C2orf60|hTYW5	tRNA-yW synthesizing protein 5	protein-coding	0.003534	0.411972	
chunk0099_289_1	chr2	98762273	98762472	+	0	NA	non-coding (NR_126337, exon 4 of 4)	non-coding (NR_126337, exon 4 of 4)	9526	NR_126337	101927070	Hs.469395	NR_126337		LINC02611	-	long intergenic non-protein coding RNA 2611	ncRNA	0.000000	0.400000	
chunk0212_161_1	chrX	132397106	132397772	+	0	NA	intron (NM_133486, intron 2 of 8)	intron (NM_133486, intron 2 of 8)	16136	NM_001170702	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.006006	0.316342	
chunk0205_288_1	chr9	111890364	111890820	+	0	NA	Intergenic	Intergenic	-6174	NM_003358	7357	Hs.304249	NM_003358	ENSG00000148154	UGCG	GCS|GLCT1	UDP-glucose ceramide glucosyltransferase	protein-coding	0.004386	0.339168	
chunk0008_360_1	chr1	96628391	96628680	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-93070	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.006920	0.420690	
chunk0190_214_1	chr8	35715124	35715680	+	0	NA	intron (NM_080872, intron 8 of 16)	intron (NM_080872, intron 8 of 16)	-5082	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.003597	0.324955	
chunk0057_304_1	chr13	106476046	106476245	+	0	NA	Intergenic	Intergenic	58895	NM_004093	1948	Hs.149239	NM_004093	ENSG00000125266	EFNB2	EPLG5|HTKL|Htk-L|LERK5	ephrin B2	protein-coding	0.005025	0.390000	
chunk0016_276_1	chr1	200669449	200669769	+	0	NA	non-coding (NR_110787, exon 1 of 3)	non-coding (NR_110787, exon 1 of 3)	102	NR_110787	101929224	Hs.639369	NR_110787	ENSG00000260088	DDX59-AS1	-	DDX59 antisense RNA 1	ncRNA	0.121875	0.757009	
chunk0047_411_1	chr12	75908753	75909398	+	0	NA	Intergenic	Intergenic	122701	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.006202	0.431889	
chunk0030_408_1	chr10	120111414	120112040	+	0	NA	Intergenic	Intergenic	153214	NR_039830	100616322		NR_039830	ENSG00000265370	MIR4682	-	microRNA 4682	ncRNA	0.007987	0.432217	
chunk0096_102_1	chr2	28269224	28269748	+	0	NA	intron (NM_199191, intron 10 of 11)	intron (NM_199191, intron 10 of 11)	40973	NR_038319	100505716	Hs.679092	NR_038319	ENSG00000223522	LOC100505716	-	uncharacterized LOC100505716	ncRNA	0.005725	0.434286	
chunk0137_439_1	chr4	28772809	28773194	+	0	NA	Intergenic	Arthur1B|DNA|hAT-Tip100	-46581	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.005195	0.334197	190(TGGGACACAAAGTTCT,-,0.00),191(GGGACACAAAGTTCTT,+,0.00)
chunk0122_25_1	chr3	27792817	27793170	+	0	NA	Intergenic	Intergenic	41143	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.008499	0.463277	155(GAGCACTGTGTGTGCT,-,0.00),156(AGCACTGTGTGTGCTC,+,0.00)
chunk0035_100_1	chr11	42320175	42320376	+	0	NA	Intergenic	Intergenic	-66585	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.301980	
chunk0092_244_1	chr19	32907928	32908195	+	0	NA	intron (NM_032816, intron 14 of 18)	Tigger3c|DNA|TcMar-Tigger	-38284	NM_014270	11136	Hs.743345	NM_014270	ENSG00000021488	SLC7A9	BAT1|CSNU3	solute carrier family 7 member 9	protein-coding	0.007491	0.429104	157(GAGCACACTCTGTGAT,-,0.00)
chunk0193_348_1	chr8	79793711	79793910	+	0	NA	intron (NR_125410, intron 3 of 3)	Tigger7|DNA|TcMar-Tigger	25668	NR_125410	101927067	Hs.144030	NR_125410	ENSG00000272138	LINC01607	-	long intergenic non-protein coding RNA 1607	ncRNA	0.010050	0.420000	
chunk0156_139_1	chr5	107047074	107047381	+	0	NA	Intergenic	Intergenic	-36213	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.000000	0.318182	
chunk0062_6_1	chr14	66077853	66078277	+	0	NA	Intergenic	Intergenic	-408306	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.007075	0.503529	
chunk0142_284_1	chr4	100017798	100018580	+	0	NA	intron (NR_125923, intron 1 of 3)	Charlie7|DNA|hAT-Charlie	67695	NR_125923	256880	Hs.448554	NR_002799	ENSG00000245322	LOC256880	-	uncharacterized LOC256880	ncRNA	0.006394	0.362708	429(TTGAACACTTTGTCCT,-,0.00),430(TGAACACTTTGTCCTT,+,0.00)
chunk0212_118_1	chrX	130676822	130677322	+	0	NA	intron (NM_006375, intron 6 of 14)	intron (NM_006375, intron 6 of 14)	182131	NR_027141	55855	Hs.567120	NM_018472		DENND10P1	FAM45B|FAM45BP|HT011	DENND10 pseudogene 1	pseudo	0.004000	0.383234	
chunk0131_135_1	chr3	144727533	144727969	+	0	NA	Intergenic	L1PA16|LINE|L1	754426	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.009174	0.368421	
chunk0183_393_1	chr7	110201999	110202251	+	0	NA	Intergenic	L1MA2|LINE|L1	-241912	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.300395	
chunk0055_99_1	chr13	56110510	56111140	+	0	NA	Intergenic	L1M4|LINE|L1	936371	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.006349	0.318542	
chunk0069_252_1	chr15	64453509	64453913	+	0	NA	intron (NM_016213, intron 12 of 12)	intron (NM_016213, intron 12 of 12)	-45709	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.390123	179(AAGGACATAATGTTCT,-,0.00),180(AGGACATAATGTTCTT,+,0.00)
chunk0091_80_1	chr19	5261252	5261648	+	0	NA	intron (NM_002850, intron 6 of 37)	intron (NM_002850, intron 6 of 37)	79353	NM_002850	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.022727	0.556675	
chunk0010_305_1	chr1	117924350	117924869	+	0	NA	intron (NM_017686, intron 1 of 13)	intron (NM_017686, intron 1 of 13)	5070	NM_017686	54834	Hs.310809	NM_017686	ENSG00000196505	GDAP2	MACROD3|SCAR27	ganglioside induced differentiation associated protein 2	protein-coding	0.005780	0.351923	
chunk0197_130_1	chr8	120036348	120036580	+	0	NA	intron (NM_022783, intron 8 of 8)	intron (NM_022783, intron 8 of 8)	-88644	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.004310	0.450644	
chunk0209_408_1	chrX	56020727	56021192	+	0	NA	Intergenic	L2c|LINE|L2	-211430	NM_007250	11279	Hs.646614	NM_007250	ENSG00000102349	KLF8	BKLF3|ZNF741	Kruppel like factor 8	protein-coding	0.000000	0.334764	197(TTGTACATATTGTTCC,-,0.00),198(TGTACATATTGTTCCC,+,0.00)
chunk0095_409_1	chr2	24539876	24540501	+	0	NA	Intergenic	Intergenic	-44289	NM_003743	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.006400	0.375399	
chunk0080_379_1	chr17	33634828	33635538	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-101423	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.015493	0.390999	
chunk0034_76_1	chr11	27201480	27201964	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	17046	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.008264	0.474227	
chunk0090_142_1	chr18	72218211	72218768	+	0	NA	Intergenic	Intergenic	325999	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.010772	0.370968	
chunk0193_104_1	chr8	73784107	73784717	+	0	NA	intron (NM_001271015, intron 5 of 5)	intron (NM_001271015, intron 5 of 5)	-36704	NM_001164384	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.001639	0.433715	
chunk0188_305_1	chr8	16489926	16490313	+	0	NA	Intergenic	L2a|LINE|L2	-297328	NM_138716	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.000000	0.394330	
chunk0082_270_1	chr17	57918343	57918632	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	-15098	NM_001292025	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.006920	0.451724	
chunk0054_356_1	chr13	49601977	49602480	+	0	NA	Intergenic	Intergenic	-16645	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.003976	0.371032	
chunk0118_379_1	chr22	36621741	36622172	+	0	NA	intron (NM_006078, intron 1 of 3)	intron (NM_006078, intron 1 of 3)	80689	NM_006078	10369	Hs.146766	NM_006078	ENSG00000166862	CACNG2	MRD10	calcium voltage-gated channel auxiliary subunit gamma 2	protein-coding	0.016241	0.444444	
chunk0170_6_1	chr6	109010631	109011205	+	0	NA	intron (NM_014454, intron 1 of 9)	L4_A_Mam|LINE|RTE-X	-1363	NM_001199933	27244	Hs.591336	NM_014454	ENSG00000080546	SESN1	PA26|SEST1	sestrin 1	protein-coding	0.003484	0.339130	
chunk0127_257_1	chr3	97228991	97229284	+	0	NA	intron (NM_001080448, intron 4 of 17)	L1PB1|LINE|L1	-210456	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.350340	
chunk0103_32_1	chr2	159093370	159093969	+	0	NA	intron (NM_001145909, intron 3 of 26)	intron (NM_001145909, intron 3 of 26)	-93166	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.008347	0.413333	
chunk0019_437_1	chr1	231049545	231049898	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-9472	NM_198552	375061	Hs.38516	NM_198552	ENSG00000182118	FAM89A	C1orf153	family with sequence similarity 89 member A	protein-coding	0.008499	0.435028	115(CTGTACAGCAAGTTCC,-,0.00),116(TGTACAGCAAGTTCCT,+,0.00)
chunk0036_448_1	chr11	68579278	68579883	+	0	NA	intron (NM_018312, intron 14 of 22)	L2a|LINE|L2	-104895	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.014876	0.366337	
chunk0092_129_1	chr19	27908896	27909177	+	0	NA	Intergenic	AluJr|SINE|Alu	-115096	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.007117	0.425532	
chunk0121_268_1	chr3	23288084	23288768	+	0	NA	intron (NM_152653, intron 3 of 5)	L1MA3|LINE|L1	85133	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.004386	0.332847	311(TGGGACAAAATGTTCT,-,0.00),312(GGGACAAAATGTTCTG,+,0.00)
chunk0024_231_1	chr10	38197037	38197651	+	0	NA	intron (NR_024524, intron 3 of 6)	intron (NR_024524, intron 3 of 6)	21673	NR_024524	100129055	Hs.148265	NR_024524		LOC100129055	-	cyclin Y like 1 pseudogene	pseudo	0.003257	0.357724	
chunk0077_364_1	chr16	84199856	84200398	+	0	NA	Intergenic	Intergenic	9010	NM_001145400	161931	Hs.8977	NM_139174	ENSG00000140955	ADAD2	TENRL	adenosine deaminase domain containing 2	protein-coding	0.022140	0.546961	299(TGGGACAGAGTGTGCC,-,0.00),300(GGGACAGAGTGTGCCG,+,0.00)
chunk0087_314_1	chr18	39636287	39636827	+	0	NA	intron (NR_024391, intron 2 of 3)	intron (NR_024391, intron 2 of 3)	-14382	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.001852	0.332717	
chunk0208_13_1	chrX	10761812	10762315	+	0	NA	intron (NM_033290, intron 1 of 9)	MIRb|SINE|MIR	71627	NM_033290	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.009940	0.313492	
chunk0048_199_1	chr12	81209887	81210102	+	0	NA	intron (NM_024560, intron 9 of 15)	MER41B|LTR|ERV1	51606	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.000000	0.416667	
chunk0028_151_1	chr10	86831163	86831409	+	0	NA	intron (NM_004329, intron 1 of 12)	intron (NM_004329, intron 1 of 12)	74647	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.024390	0.340081	
chunk0163_421_1	chr6	17120106	17120309	+	0	NA	intron (NM_001190766, intron 2 of 4)	intron (NM_001190766, intron 2 of 4)	17949	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.024631	0.397059	
chunk0140_221_1	chr4	70961531	70962143	+	0	NA	intron (NM_001244766, intron 3 of 6)	intron (NM_001244766, intron 3 of 6)	-31711	NM_000788	1633	Hs.709	NM_000788	ENSG00000156136	DCK	-	deoxycytidine kinase	protein-coding	0.004902	0.383361	
chunk0169_193_1	chr6	102628347	102628600	+	0	NA	Intergenic	L1MA3|LINE|L1	1229488	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003953	0.468504	
chunk0088_263_1	chr18	49160195	49160843	+	0	NA	intron (NM_017653, intron 14 of 16)	intron (NM_017653, intron 14 of 16)	-110751	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.004630	0.342065	259(AAGTACTCTATGTACT,-,0.00),260(AGTACTCTATGTACTA,+,0.00)
chunk0097_424_1	chr2	63224155	63224713	+	0	NA	intron (NR_122106, intron 8 of 11)	L1MC1|LINE|L1	-104892	NR_036635	100169989	Hs.606147	NR_036635	ENSG00000242412	DBIL5P2	ELP1P	diazepam binding inhibitor-like 5 pseudogene 2	pseudo	0.005376	0.348837	
chunk0091_376_1	chr19	15815281	15815788	+	0	NA	Intergenic	Intergenic	-7408	NM_013940	26539	Hs.533925	NM_013940	ENSG00000186723	OR10H1	-	olfactory receptor family 10 subfamily H member 1	protein-coding	0.019724	0.553150	
chunk0078_213_1	chr17	5974484	5975081	+	0	NA	Intergenic	Intergenic	-95832	NM_015253	23302	Hs.370166	NM_015253	ENSG00000179314	WSCD1	-	WSC domain containing 1	protein-coding	0.001675	0.426421	
chunk0091_367_1	chr19	15563498	15564003	+	0	NA	Intergenic	Intergenic	-51468	NM_007253	11283	Hs.268554	NM_007253	ENSG00000186526	CYP4F8	CPF8|CYPIVF8	cytochrome P450 family 4 subfamily F member 8	protein-coding	0.005941	0.606719	137(GGGACAAGCTGCTCCT,+,0.00)
chunk0037_322_1	chr11	76939197	76939860	+	0	NA	intron (NM_001300955, intron 2 of 9)	AluJb|SINE|Alu	78655	NM_001300955	55331	Hs.23862	NM_018367	ENSG00000078124	ACER3	APHC|PHCA|PLDECO	alkaline ceramidase 3	protein-coding	0.004525	0.376506	
chunk0158_435_1	chr5	135438139	135438655	+	0	NA	Intergenic	Intergenic	8951	NM_130848	140947	Hs.152477	NM_130848	ENSG00000251380	DCANP1	C5orf20|DCNP1	dendritic cell associated nuclear protein	protein-coding	0.021318	0.547389	394(GTGCACTGAGTGTCCT,-,0.00),395(TGCACTGAGTGTCCTG,+,0.00)
chunk0111_118_1	chr20	24014778	24015117	+	0	NA	Intergenic	Intergenic	-26168	NM_178311	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.014749	0.467647	
chunk0071_24_1	chr15	79067431	79067842	+	0	NA	intron (NM_001145648, intron 1 of 26)	intron (NM_001145648, intron 1 of 26)	23237	NM_001145648	5923	Hs.459035	NM_002891	ENSG00000058335	RASGRF1	CDC25|CDC25L|GNRP|GRF1|GRF55|H-GRF55|PP13187|ras-GRF1	Ras protein specific guanine nucleotide releasing factor 1	protein-coding	0.007299	0.490291	138(GAGAGCAGTTTGTTCC,-,0.00),139(AGAGCAGTTTGTTCCC,+,0.00)
chunk0130_232_1	chr3	134485974	134486270	+	0	NA	promoter-TSS (NM_001242375)	promoter-TSS (NM_001242375)	67	NM_001042400	80254	Hs.443301	NM_025180	ENSG00000182923	CEP63	SCKL6	centrosomal protein 63	protein-coding	0.097973	0.636364	
chunk0137_319_1	chr4	24615815	24616157	+	0	NA	Intergenic	Intergenic	-31425	NM_001358	1665	Hs.696074	NM_001358	ENSG00000109606	DHX15	DBP1|DDX15|HRH2|PRP43|PRPF43|PrPp43p	DEAH-box helicase 15	protein-coding	0.002924	0.443149	
chunk0097_358_1	chr2	60346965	60347565	+	0	NA	Intergenic	L1ME2|LINE|L1	35771	NR_132991	106660609	Hs.565545	NR_132991	ENSG00000228590	MIR4432HG	-	MIR4432 host gene	ncRNA	0.006667	0.327787	
chunk0047_331_1	chr12	74391916	74392719	+	0	NA	Intergenic	HAL1ME|LINE|L1	-99686	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.002491	0.342040	
chunk0021_189_1	chr10	5651972	5652726	+	0	NA	intron (NR_037164, intron 2 of 6)	MER63A|DNA|hAT-Blackjack	14246	NM_024701	79754	Hs.445899	NM_024701	ENSG00000196372	ASB13	-	ankyrin repeat and SOCS box containing 13	protein-coding	0.011936	0.508609	
chunk0122_107_1	chr3	30597391	30597748	+	0	NA	Intergenic	Intergenic	-8933	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.002801	0.335196	
chunk0118_79_1	chr22	28904275	28904927	+	0	NA	intron (NM_001206998, intron 1 of 8)	(CT)n|Simple_repeat|Simple_repeat	-12788	NM_032173	84133	Hs.604200	NM_032173	ENSG00000183579	ZNRF3	BK747E2.3|RNF203	zinc and ring finger 3	protein-coding	0.007669	0.418070	
chunk0050_352_1	chr12	107764249	107764475	+	0	NA	Intergenic	Intergenic	-3225	NM_012406	11108	Hs.506655	NM_012406	ENSG00000110851	PRDM4	PFM1	PR/SET domain 4	protein-coding	0.004425	0.414097	
chunk0068_243_1	chr15	55917839	55918447	+	0	NA	intron (NM_006154, intron 5 of 28)	intron (NM_006154, intron 5 of 28)	-1012	NM_001284338	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.001645	0.325123	359(GTGGACTGTTTGTCCT,-,0.00),360(TGGACTGTTTGTCCTT,+,0.00)
chunk0107_385_1	chr2	223447037	223447507	+	0	NA	Intergenic	Intergenic	155227	NM_003469	7857	Hs.516726	NM_003469	ENSG00000171951	SCG2	CHGC|EM66|SN|SgII	secretogranin II	protein-coding	0.000000	0.280255	
chunk0136_178_1	chr4	6632971	6633784	+	0	NA	Intergenic	Intergenic	-6714	NM_001272053	93621	Hs.406590	NM_033296	ENSG00000179010	MRFAP1	PAM14|PGR1	Morf4 family associated protein 1	protein-coding	0.011070	0.486486	389(TAGGACTGGGAGTTCC,-,0.00),390(AGGACTGGGAGTTCCA,+,0.00),445(CAGGACAAACTGTTCT,-,0.00),446(AGGACAAACTGTTCTC,+,0.00)
chunk0061_21_1	chr14	55753011	55753563	+	0	NA	Intergenic	Intergenic	-12958	NR_004844	645683	Hs.663461	NR_004844	ENSG00000177350	RPL13AP3	RPL13A_11_1370	ribosomal protein L13a pseudogene 3	pseudo	0.003623	0.461121	
chunk0125_427_1	chr3	72433069	72433324	+	0	NA	intron (NM_012234, intron 1 of 3)	intron (NM_012234, intron 1 of 3)	13427	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.000000	0.285156	
chunk0075_268_1	chr16	53732507	53732722	+	0	NA	intron (NM_001080432, intron 1 of 8)	intron (NM_001080432, intron 1 of 8)	28651	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.009302	0.425926	
chunk0185_302_1	chr7	131211541	131211854	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	101601	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.003195	0.369427	112(AGGAACACTATGTTCC,-,0.00),113(GGAACACTATGTTCCC,+,0.00)
chunk0170_251_1	chr6	113685820	113686591	+	0	NA	Intergenic	Intergenic	-36130	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.001297	0.319948	360(AAGTACAGAGAGTTCT,-,0.00),361(AGTACAGAGAGTTCTT,+,0.00)
chunk0174_327_1	chr6	163547386	163547585	+	0	NA	intron (NM_206853, intron 4 of 6)	intron (NM_206853, intron 4 of 6)	132842	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.010050	0.420000	51(CTGGACAGTCTGTTCT,-,0.00),52(TGGACAGTCTGTTCTG,+,0.00)
chunk0004_250_1	chr1	47591994	47592262	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-154811	NR_126355	102724077	Hs.159718	NR_126355		LINC01389	-	long intergenic non-protein coding RNA 1389	ncRNA	0.018657	0.516729	
chunk0156_369_1	chr5	112707559	112707826	+	0	NA	5' UTR (NM_001127511, exon 1 of 14)	5' UTR (NM_001127511, exon 1 of 14)	187	NM_001127511	324	Hs.158932	NM_000038	ENSG00000134982	APC	BTPS2|DP2|DP2.5|DP3|GS|PPP1R46	APC regulator of WNT signaling pathway	protein-coding	0.082397	0.686567	
chunk0060_240_1	chr14	49767040	49767376	+	0	NA	promoter-TSS (NM_014315)	promoter-TSS (NM_014315)	-861	NM_014315	23588	Hs.509264	NM_014315	ENSG00000165516	KLHDC2	HCLP-1|HCLP1|LCP	kelch domain containing 2	protein-coding	0.005952	0.403561	
chunk0043_440_1	chr12	26253800	26254678	+	0	NA	Intergenic	Intergenic	58666	NM_005086	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.002278	0.326507	154(AGGGACATAGTGTGCA,-,0.00),155(GGGACATAGTGTGCAA,+,0.00)
chunk0129_77_1	chr3	117809568	117809909	+	0	NA	Intergenic	Intergenic	888307	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.339181	
chunk0205_297_1	chr9	112033657	112033943	+	0	NA	Intergenic	Intergenic	101700	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.010490	0.463415	
chunk0083_55_1	chr17	63702953	63703152	+	0	NA	TTS (NR_046273)	TTS (NR_046273)	2714	NR_046273	729683	Hs.534931	NR_046273		LOC729683	-	uncharacterized LOC729683	ncRNA	0.010050	0.515000	
chunk0172_322_1	chr6	138344103	138344847	+	0	NA	3' UTR (NM_020340, exon 34 of 34)	3' UTR (NM_020340, exon 34 of 34)	-59724	NM_014320	23593	Hs.486589	NM_014320	ENSG00000051620	HEBP2	C6ORF34B|C6orf34|PP23|SOUL	heme binding protein 2	protein-coding	0.000000	0.300671	
chunk0008_130_1	chr1	91815331	91815709	+	0	NA	intron (NR_036634, intron 2 of 17)	intron (NR_036634, intron 2 of 17)	70759	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.002646	0.387863	
chunk0065_7_1	chr15	20231507	20231796	+	0	NA	Intergenic	Intergenic	-51093	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.010381	0.534483	
chunk0011_50_1	chr1	143256028	143256424	+	0	NA	Intergenic	Intergenic	166366	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.055556	0.377834	
chunk0161_426_1	chr5	178379240	178379499	+	0	NA	intron (NM_173465, intron 2 of 28)	L1ME3G|LINE|L1	-146547	NM_001278346	85007	Hs.248746	NM_153373	ENSG00000175309	PHYKPL	AGXT2L2|PHLU	5-phosphohydroxy-L-lysine phospho-lyase	protein-coding	0.007722	0.430769	
chunk0212_331_1	chrX	144658214	144658500	+	0	NA	Intergenic	Intergenic	-589230	NM_001009614	494118		NM_001009614	ENSG00000203923	SPANXN1	CT11.6	SPANX family member N1	protein-coding	0.003497	0.376307	
chunk0046_79_1	chr12	56198176	56198375	+	0	NA	Intergenic	Intergenic	-8708	NM_001130420	6601	Hs.236030	NM_003075	ENSG00000139613	SMARCC2	BAF170|CRACC2|CSS8|Rsc8	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2	protein-coding	0.000000	0.380000	
chunk0093_371_1	chr19	55753464	55753778	+	0	NA	Intergenic	Intergenic	-5520	NM_001145014	342931	Hs.631553	NM_001145014	ENSG00000223638	RFPL4A	RFPL4|RNF210	ret finger protein like 4A	protein-coding	0.006369	0.428571	157(AGGTACAGTGTGTGCA,-,0.00),158(GGTACAGTGTGTGCAC,+,0.00)
chunk0133_189_1	chr3	170492905	170493271	+	0	NA	intron (NM_020949, intron 4 of 7)	intron (NM_020949, intron 4 of 7)	69985	NR_106886	102465497		NR_106886	ENSG00000283474	MIR6828	hsa-mir-6828	microRNA 6828	ncRNA	0.005464	0.419619	
chunk0078_206_1	chr17	5362512	5362711	+	0	NA	intron (NM_001083585, intron 9 of 16)	intron (NM_001083585, intron 9 of 16)	-57030	NR_027679	84268	Hs.462086	NM_032308	ENSG00000129197	RPAIN	HRIP|RIP	RPA interacting protein	protein-coding	0.010050	0.395000	
chunk0118_260_1	chr22	33210348	33210827	+	0	NA	Intergenic	Intergenic	-152196	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.029228	0.595833	
chunk0082_369_1	chr17	60353660	60354660	+	0	NA	intron (NM_032582, intron 1 of 33)	intron (NM_032582, intron 1 of 33)	38065	NM_032582	84669	Hs.132868	NM_032582	ENSG00000170832	USP32	NY-REN-60|USP10	ubiquitin specific peptidase 32	protein-coding	0.005000	0.355644	146(CAGAACTCACTGTCCA,-,0.00),147(AGAACTCACTGTCCAT,+,0.00)
chunk0170_349_1	chr6	116404053	116404355	+	0	NA	intron (NM_001080976, intron 2 of 5)	intron (NM_001080976, intron 2 of 5)	33257	NM_013352	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.003311	0.353135	
chunk0014_431_1	chr1	183524852	183525051	+	0	NA	intron (NM_001174061, intron 3 of 21)	intron (NM_001174061, intron 3 of 21)	52580	NM_201569	9887	Hs.591463	NM_014837	ENSG00000116698	SMG7	C1orf16|EST1C|SGA56M	SMG7 nonsense mediated mRNA decay factor	protein-coding	0.000000	0.405000	
chunk0106_376_1	chr2	207268081	207269489	+	0	NA	TTS (NR_031633)	TTS (NR_031633)	639	NR_031633	100302130		NR_031633	ENSG00000221628	MIR1302-4	MIRN1302-4|hsa-mir-1302-4	microRNA 1302-4	ncRNA	0.006392	0.371185	424(CAGAACACCGTGTGCC,-,0.00),425(AGAACACCGTGTGCCT,+,0.00)
chunk0069_384_1	chr15	67521826	67522502	+	0	NA	promoter-TSS (NR_040054)	promoter-TSS (NR_040054)	-320	NR_040051	100506686	Hs.656245	NR_040051	ENSG00000259673	IQCH-AS1	-	IQCH antisense RNA 1	ncRNA	0.020710	0.426883	
chunk0138_398_1	chr4	42871696	42871985	+	0	NA	Intergenic	Intergenic	-21426	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.003460	0.465517	
chunk0054_198_1	chr13	44961119	44961716	+	0	NA	intron (NM_012345, intron 6 of 9)	MIRb|SINE|MIR	28061	NM_012345	26747	Hs.525006	NM_012345	ENSG00000083635	NUFIP1	NUFIP|bA540M5.1	nuclear FMR1 interacting protein 1	protein-coding	0.003350	0.347826	
chunk0103_115_1	chr2	161573349	161573868	+	0	NA	Intergenic	L1PA15|LINE|L1	-50727	NM_001178015	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.001927	0.365385	
chunk0060_322_1	chr14	51367500	51367806	+	0	NA	Intergenic	Intergenic	34260	NR_038358	283553	Hs.325752	NR_038358	ENSG00000258479	LINC00640	-	long intergenic non-protein coding RNA 640	ncRNA	0.000000	0.374593	
chunk0070_210_1	chr15	72358734	72359322	+	0	NA	intron (NM_000520, intron 1 of 13)	intron (NM_000520, intron 1 of 13)	-17085	NR_027262	80072	Hs.591113	NM_025005	ENSG00000260339	HEXA-AS1	C15orf34	HEXA antisense RNA 1	ncRNA	0.008503	0.517827	
chunk0124_102_1	chr3	53711434	53711841	+	0	NA	intron (NM_000720, intron 9 of 48)	intron (NM_000720, intron 9 of 48)	134756	NM_018397	55349	Hs.126688	NM_018397	ENSG00000016391	CHDH	-	choline dehydrogenase	protein-coding	0.017199	0.514706	199(GGGGACACACTGTACT,-,0.00),200(GGGACACACTGTACTC,+,0.00)
chunk0036_380_1	chr11	67548440	67549068	+	0	NA	Intergenic	Intergenic	-25326	NM_016366	51475	Hs.278984	NM_016366	ENSG00000167791	CABP2	DFNB93	calcium binding protein 2	protein-coding	0.012739	0.430843	450(CTGGACTGAGTGTCCC,-,0.00),451(TGGACTGAGTGTCCCT,+,0.00)
chunk0080_260_1	chr17	30600009	30600228	+	0	NA	intron (NR_015341, intron 2 of 8)	CpG	23653	NR_015341	107133515	Hs.568209	NR_015341		SMURF2P1-LRRC37BP1	-	SMURF2P1-LRRC37BP1 readthrough transcribed pseudogene	pseudo	0.059361	0.600000	
chunk0106_245_1	chr2	203258558	203258973	+	0	NA	intron (NM_177538, intron 4 of 12)	intron (NM_177538, intron 4 of 12)	20324	NM_177538	57404	Hs.446065	NM_020674	ENSG00000119004	CYP20A1	CYP-M	cytochrome P450 family 20 subfamily A member 1	protein-coding	0.004819	0.408654	
chunk0095_382_1	chr2	23728283	23728482	+	0	NA	Intergenic	L1MC4a|LINE|L1	198732	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.005025	0.350000	
chunk0102_5_1	chr2	141041086	141041354	+	0	NA	intron (NM_018557, intron 11 of 90)	intron (NM_018557, intron 11 of 90)	-454535	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.007463	0.375465	
chunk0206_129_1	chr9	120985639	120986127	+	0	NA	intron (NM_001735, intron 25 of 40)	LTR38A1|LTR|ERV1	-56710	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.004098	0.374233	
chunk0186_221_1	chr7	140128389	140128670	+	0	NA	intron (NM_030647, intron 4 of 19)	intron (NM_030647, intron 4 of 19)	48412	NM_030647	80853	Hs.308710	NM_030647	ENSG00000006459	KDM7A	JHDM1D	lysine demethylase 7A	protein-coding	0.007117	0.361702	
chunk0062_349_1	chr14	73731155	73731452	+	0	NA	intron (NM_001043318, intron 3 of 11)	intron (NM_001043318, intron 3 of 11)	-16878	NM_006029	9240	Hs.194709	NM_006029	ENSG00000176903	PNMA1	MA1	PNMA family member 1	protein-coding	0.010101	0.503356	
chunk0027_78_1	chr10	73359727	73359926	+	0	NA	promoter-TSS (NM_145170)	promoter-TSS (NM_145170)	-967	NM_145170	118491	Hs.591367	NM_145170	ENSG00000156042	CFAP70	TTC18	cilia and flagella associated protein 70	protein-coding	0.010050	0.430000	
chunk0160_319_1	chr5	159377626	159378085	+	0	NA	Intergenic	L1PB2|LINE|L1	46337	NR_037889	285626	Hs.449275	NR_037889	ENSG00000249738	LOC285626	-	uncharacterized LOC285626	ncRNA	0.000000	0.415217	316(TAGGACACAGTGAACT,-,0.00),317(AGGACACAGTGAACTG,+,0.00)
chunk0153_451_1	chr5	76410946	76411585	+	0	NA	intron (NM_006633, intron 1 of 35)	intron (NM_006633, intron 1 of 35)	8010	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.009390	0.435937	
chunk0200_204_1	chr9	20398940	20399345	+	0	NA	intron (NM_001286691, intron 5 of 10)	intron (NM_001286691, intron 5 of 10)	12096	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.007407	0.406404	215(TTGTACAGGGAGTTCT,-,0.00),216(TGTACAGGGAGTTCTC,+,0.00)
chunk0031_68_1	chr10	122997643	122997985	+	0	NA	intron (NR_073476, intron 3 of 4)	MER58B|DNA|hAT-Charlie	10873	NM_001271840	64376	Hs.501289	NM_001271840	ENSG00000095574	IKZF5	PEGASUS|ZNFN1A5	IKAROS family zinc finger 5	protein-coding	0.005848	0.364431	
chunk0200_459_1	chr9	31869551	31869758	+	0	NA	Intergenic	L1MA5A|LINE|L1	-514949	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.000000	0.524038	
chunk0108_358_1	chr2	236444179	236444619	+	0	NA	intron (NR_073043, intron 6 of 19)	Charlie1a|DNA|hAT-Charlie	59298	NM_001270585	79781	Hs.591594	NM_024726	ENSG00000132321	IQCA1	4930465P12Rik|DRC11|IQCA	IQ motif containing with AAA domain 1	protein-coding	0.006818	0.444444	
chunk0181_88_1	chr7	80353109	80353835	+	0	NA	Intergenic	Intergenic	20967	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.004132	0.341128	361(CTGAACACAGTGTGCC,-,0.00),362(TGAACACAGTGTGCCA,+,0.00)
chunk0047_118_1	chr12	68953475	68953959	+	0	NA	intron (NM_001874, intron 1 of 8)	intron (NM_001874, intron 1 of 8)	9523	NM_001874	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.004132	0.402062	260(AGGCACAGCCTCTTCT,-,0.00),261(GGCACAGCCTCTTCTG,+,0.00)
chunk0059_340_1	chr14	36975735	36976449	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	-23701	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.008403	0.453147	
chunk0030_101_1	chr10	112619616	112619900	+	0	NA	intron (NM_145206, intron 5 of 7)	intron (NM_145206, intron 5 of 7)	-14412	NR_036177	100422909		NR_036177	ENSG00000264763	MIR4295	-	microRNA 4295	ncRNA	0.007042	0.449123	
chunk0078_38_1	chr17	1005827	1006311	+	0	NA	3' UTR (NM_001159746, exon 23 of 23)	3' UTR (NM_001159746, exon 23 of 23)	8952	NM_013337	29928	Hs.745034	NM_013337	ENSG00000177370	TIMM22	TEX4|TIM22	translocase of inner mitochondrial membrane 22	protein-coding	0.035124	0.612371	269(AAGTACAGTGTGTTCC,-,0.00),270(AGTACAGTGTGTTCCG,+,0.00)
chunk0064_326_1	chr14	96204799	96205162	+	0	NA	intron (NM_000623, intron 1 of 2)	intron (NM_000623, intron 1 of 2)	182	NM_000623	624	Hs.654542	NM_000623	ENSG00000168398	BDKRB2	B2R|BK-2|BK2|BKR2|BRB2	bradykinin receptor B2	protein-coding	0.044077	0.656593	206(GAGGACAAACTGTCCC,-,0.00),207(AGGACAAACTGTCCCA,+,0.00)
chunk0181_27_1	chr7	77969111	77969654	+	0	NA	Intergenic	L1ME1|LINE|L1	129252	NM_001127357	57157	Hs.203965	NM_020432	ENSG00000006576	PHTF2	-	putative homeodomain transcription factor 2	protein-coding	0.005525	0.325368	
chunk0108_424_1	chr2	237774775	237775302	+	0	NA	intron (NM_001137551, intron 11 of 11)	L2a|LINE|L2	-23707	NM_001080504	375316	Hs.607265	NM_198852	ENSG00000177483	RBM44	-	RNA binding motif protein 44	protein-coding	0.015180	0.558712	
chunk0143_170_1	chr4	110850466	110850866	+	0	NA	Intergenic	Intergenic	9981	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.005000	0.314214	
chunk0111_331_1	chr20	32833493	32834048	+	0	NA	exon (NM_012325, exon 3 of 7)	exon (NM_012325, exon 3 of 7)	13877	NM_012325	22919	Hs.472437	NM_012325	ENSG00000101367	MAPRE1	EB1	microtubule associated protein RP/EB family member 1	protein-coding	0.009009	0.374101	244(ATGGACATGCTGTTCC,-,0.00),245(TGGACATGCTGTTCCC,+,0.00)
chunk0120_106_1	chr3	4505569	4506046	+	0	NA	intron (NM_002222, intron 2 of 57)	intron (NM_002222, intron 2 of 57)	12459	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.006289	0.435146	
chunk0120_463_1	chr22	50613586	50613883	+	0	NA	Intergenic	Intergenic	13049	NM_012324	23542	Hs.558180	NM_012324	ENSG00000008735	MAPK8IP2	IB-2|IB2|JIP2|PRKM8IPL	mitogen-activated protein kinase 8 interacting protein 2	protein-coding	0.033670	0.640940	
chunk0081_127_1	chr17	40448677	40449301	+	0	NA	intron (NM_001552, intron 1 of 3)	intron (NM_001552, intron 1 of 3)	5565	NM_001552	3487	Hs.462998	NM_001552	ENSG00000141753	IGFBP4	BP-4|HT29-IGFBP|IBP4|IGFBP-4	insulin like growth factor binding protein 4	protein-coding	0.009615	0.512000	
chunk0201_5_1	chr9	32016031	32016230	+	0	NA	Intergenic	MER52A|LTR|ERV1	-368473	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.000000	0.555000	
chunk0128_110_1	chr3	106212719	106213357	+	0	NA	Intergenic	Intergenic	-343995	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.001567	0.338028	
chunk0046_379_1	chr12	63485931	63486169	+	0	NA	Intergenic	L2|LINE|L2	182524	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.004202	0.368201	
chunk0109_217_1	chr20	5724634	5724960	+	0	NA	Intergenic	Intergenic	-25590	NM_001303479	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.006135	0.345566	
chunk0061_383_1	chr14	64296529	64296924	+	0	NA	intron (NM_001291723, intron 1 of 8)	intron (NM_001291723, intron 1 of 8)	-2316	NM_001040275	2100	Hs.660607	NM_001437	ENSG00000140009	ESR2	ER-BETA|ESR-BETA|ESRB|ESTRB|Erb|NR3A2|ODG8	estrogen receptor 2	protein-coding	0.000000	0.452020	206(AGGAACAGCATGTTCT,-,0.00),207(GGAACAGCATGTTCTC,+,0.00)
chunk0166_3_1	chr6	41338742	41339022	+	0	NA	intron (NM_001199509, intron 2 of 5)	Charlie10|DNA|hAT-Charlie	3092	NM_004828	9436	Hs.194721	NM_004828	ENSG00000096264	NCR2	CD336|LY95|NK-p44|NKP44|dJ149M18.1	natural cytotoxicity triggering receptor 2	protein-coding	0.010714	0.359431	
chunk0059_222_1	chr14	34138089	34138833	+	0	NA	Intergenic	Intergenic	-187383	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.005376	0.420134	
chunk0015_17_1	chr1	184284044	184284749	+	0	NA	Intergenic	Intergenic	-102620	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.004255	0.473088	
chunk0159_219_1	chr5	140808299	140808498	+	0	NA	exon (NM_031500, exon 1 of 1)	exon (NM_031500, exon 1 of 1)	1324	NM_031500	56144	Hs.199343	NM_018907	ENSG00000204967	PCDHA4	CNR1|CNRN1|CRNR1|PCDH-ALPHA4	protocadherin alpha 4	protein-coding	0.070352	0.610000	
chunk0129_399_1	chr3	126602049	126602751	+	0	NA	intron (NM_001039783, intron 2 of 3)	intron (NM_001039783, intron 2 of 3)	6155	NM_001039783	114112	Hs.477475	NM_052883	ENSG00000197763	TXNRD3	TGR|TR2|TR2IT1|TRXR3|TXNRD3IT1|TXNRD3NB|TXNRD3NT1	thioredoxin reductase 3	protein-coding	0.002849	0.413940	
chunk0168_98_1	chr6	80084580	80085183	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-21746	NM_183050	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.006633	0.382450	418(CTGAACTGTGTGTTCT,-,0.00),419(TGAACTGTGTGTTCTA,+,0.00)
chunk0145_39_1	chr4	144414197	144414570	+	0	NA	Intergenic	Intergenic	-231613	NM_022475	64399	Hs.507991	NM_022475	ENSG00000164161	HHIP	HIP	hedgehog interacting protein	protein-coding	0.005362	0.270053	
chunk0098_385_1	chr2	79422841	79423040	+	0	NA	Intergenic	Intergenic	77904	NR_110289	101927987	Hs.574704	NR_110289	ENSG00000229385	LOC101927987	-	uncharacterized LOC101927987	ncRNA	0.000000	0.355000	
chunk0050_358_1	chr12	107776304	107776503	+	0	NA	3' UTR (NM_203436, exon 1 of 1)	3' UTR (NM_203436, exon 1 of 1)	2018	NM_203436	121549	Hs.149910	NM_203436	ENSG00000187855	ASCL4	HASH4|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding	0.015075	0.425000	74(TGGTACACACTGTTTC,-,0.00),75(GGTACACACTGTTTCA,+,0.00)
chunk0202_401_1	chr9	81395249	81395591	+	0	NA	Intergenic	Intergenic	294115	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002924	0.405248	218(ATGGACATAATGTTCA,-,0.00),219(TGGACATAATGTTCAC,+,0.00)
chunk0056_154_1	chr13	84207022	84207640	+	0	NA	intron (NR_046871, intron 1 of 6)	L2a|LINE|L2	66729	NR_046871	100874128	Hs.578060	NR_046871		LINC00333	NCRNA00333	long intergenic non-protein coding RNA 333	ncRNA	0.006472	0.384491	
chunk0130_238_1	chr3	134983625	134983923	+	0	NA	intron (NM_004441, intron 3 of 15)	intron (NM_004441, intron 3 of 15)	188517	NM_004441	2047	Hs.116092	NM_004441	ENSG00000154928	EPHB1	ELK|EPHT2|Hek6|NET	EPH receptor B1	protein-coding	0.003356	0.508361	
chunk0004_301_1	chr1	48991324	48991567	+	0	NA	intron (NM_032785, intron 5 of 13)	L1MA3|LINE|L1	-214476	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.004115	0.336066	
chunk0011_129_1	chr1	147122782	147123082	+	0	NA	Intergenic	MIR|SINE|MIR	-8586	NR_103466	644861	Hs.451804	NR_103466		NBPF13P	-	NBPF member 13, pseudogene	pseudo	0.003333	0.355482	
chunk0193_39_1	chr8	71486011	71486334	+	0	NA	Intergenic	Intergenic	-123940	NM_001288575	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.012384	0.475309	
chunk0002_199_1	chr1	19458865	19459477	+	0	NA	intron (NM_001206541, intron 1 of 8)	intron (NM_001206541, intron 1 of 8)	25536	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.009804	0.442088	362(AAGAACAGGCTGAACA,-,0.00)
chunk0111_112_1	chr20	23866809	23867071	+	0	NA	Intergenic	L1MA8|LINE|L1	12803	NM_001900	1473	Hs.121489	NM_001900	ENSG00000170367	CST5	-	cystatin D	protein-coding	0.007634	0.422053	
chunk0050_424_1	chr12	109982864	109983223	+	0	NA	intron (NM_001135214, intron 6 of 18)	intron (NM_001135214, intron 6 of 18)	13346	NM_057169	9815	Hs.434996	NM_014776	ENSG00000139436	GIT2	CAT-2|CAT2|PKL	GIT ArfGAP 2	protein-coding	0.005571	0.388889	
chunk0182_154_1	chr7	95375614	95375813	+	0	NA	intron (NM_000940, intron 3 of 8)	intron (NM_000940, intron 3 of 8)	20662	NM_000940	5446	Hs.440967	NM_000940	ENSG00000105852	PON3	-	paraoxonase 3	protein-coding	0.000000	0.385000	
chunk0178_303_1	chr7	37873581	37873809	+	0	NA	intron (NM_016616, intron 11 of 17)	Zaphod3|DNA|hAT-Tip100	25098	NM_016616	51314	Hs.723454	NM_016616	ENSG00000086288	NME8	CILD6|HEL-S-99|NM23-H8|SPTRX2|TXNDC3|sptrx-2	NME/NM23 family member 8	protein-coding	0.004386	0.336245	
chunk0025_75_1	chr10	50315929	50316674	+	0	NA	intron (NM_147156, intron 8 of 10)	intron (NM_147156, intron 8 of 10)	-67691	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.004027	0.423592	214(GGGCACTGACTGTACT,-,0.00),215(GGCACTGACTGTACTT,+,0.00)
chunk0079_139_1	chr17	12900539	12900999	+	0	NA	intron (NM_014859, intron 3 of 20)	intron (NM_014859, intron 3 of 20)	16573	NR_039747	100616494		NR_039747	ENSG00000265503	MIR1269B	-	microRNA 1269b	ncRNA	0.019565	0.466377	330(GAGGACAAGATGTGCC,-,0.00),331(AGGACAAGATGTGCCA,+,0.00)
chunk0006_273_1	chr1	70347092	70347520	+	0	NA	intron (NM_030816, intron 1 of 12)	intron (NM_030816, intron 1 of 12)	7428	NM_030816	81573	Hs.744989	NM_030816	ENSG00000118454	ANKRD13C	dJ677H15.3	ankyrin repeat domain 13C	protein-coding	0.004673	0.384615	
chunk0161_30_1	chr5	165801361	165801573	+	0	NA	Intergenic	L1MB3|LINE|L1	1124903	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.000000	0.262911	
chunk0023_433_1	chr10	31854432	31854651	+	0	NA	intron (NM_001270696, intron 4 of 17)	intron (NM_001270696, intron 4 of 17)	54385	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.013699	0.413636	
chunk0012_80_1	chr1	155909919	155910150	+	0	NA	intron (NM_001256820, intron 2 of 4)	intron (NM_001256820, intron 2 of 4)	881	NM_001256821	6016	Hs.491234	NM_006912	ENSG00000143622	RIT1	NS8|RIBB|RIT|ROC1	Ras like without CAAX 1	protein-coding	0.008658	0.422414	
chunk0185_308_1	chr7	131324970	131325339	+	0	NA	intron (NR_125364, intron 2 of 5)	L2a|LINE|L2	2625	NR_125364	100506881	Hs.660830	NR_125364	ENSG00000236753	MKLN1-AS	MKLN1-AS2	MKLN1 antisense RNA	ncRNA	0.002710	0.340541	
chunk0205_121_1	chr9	107836348	107836596	+	0	NA	Intergenic	L2c|LINE|L2	-346752	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.000000	0.437751	
chunk0136_172_1	chr4	6462581	6463119	+	0	NA	intron (NM_001206995, intron 2 of 9)	L1MC5a|LINE|L1	9749	NM_020416	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.007435	0.448980	
chunk0206_50_1	chr9	117599004	117599203	+	0	NA	Intergenic	L1MA5|LINE|L1	-49503	NR_109806	101928797	Hs.382317	NR_109806	ENSG00000233569	LOC101928797	-	uncharacterized LOC101928797	ncRNA	0.010050	0.515000	
chunk0085_212_1	chr18	6731344	6731607	+	0	NA	Intergenic	Intergenic	-102958	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.019011	0.416667	
chunk0195_170_1	chr8	95874091	95874317	+	0	NA	Intergenic	L1PA13|LINE|L1	74144	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.004425	0.365639	
chunk0113_62_1	chr20	50415390	50416144	+	0	NA	Intergenic	Intergenic	-94425	NR_109950	101927586	Hs.637665	NR_109950	ENSG00000233077	LINC01271	-	long intergenic non-protein coding RNA 1271	ncRNA	0.031830	0.593377	399(AGGGACATAATGTGCT,-,0.00),400(GGGACATAATGTGCTG,+,0.00)
chunk0185_229_1	chr7	129295089	129295318	+	0	NA	intron (NM_001130720, intron 1 of 16)	intron (NM_001130720, intron 1 of 16)	70189	NM_001130720	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.004367	0.404348	
chunk0081_291_1	chr17	44804356	44804686	+	0	NA	3' UTR (NM_001080383, exon 3 of 3)	3' UTR (NM_001080383, exon 3 of 3)	25718	NM_005497	10052	Hs.712052	NM_005497	ENSG00000182963	GJC1	CX45|GJA7	gap junction protein gamma 1	protein-coding	0.009091	0.459215	83(GGGAACACTGTGTTTC,-,0.00),84(GGAACACTGTGTTTCC,+,0.00)
chunk0209_402_1	chrX	55774818	55775175	+	0	NA	Intergenic	L1PA6|LINE|L1	57319	NM_006064	10325	Hs.50282	NM_006064	ENSG00000083750	RRAGB	RAGB|bA465E19.1	Ras related GTP binding B	protein-coding	0.022409	0.500000	244(TGGAACACTCTGTTCC,-,0.00),245(GGAACACTCTGTTCCC,+,0.00)
chunk0155_438_1	chr5	101009421	101010000	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-106425	NM_175052	7903	Hs.308628	NM_005668	ENSG00000113532	ST8SIA4	PST|PST1|SIAT8D|ST8SIA-IV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding	0.010363	0.425862	
chunk0012_245_1	chr1	160951681	160951897	+	0	NA	intron (NM_080878, intron 3 of 7)	LTR75|LTR|ERVL	3010	NM_080878	142683	Hs.385631	NM_080878	ENSG00000158764	ITLN2	HL-2|HL2	intelectin 2	protein-coding	0.013889	0.548387	
chunk0202_8_1	chr9	70321806	70322486	+	0	NA	intron (NM_015110, intron 15 of 24)	intron (NM_015110, intron 15 of 24)	63184	NM_015110	23137	Hs.534189	NM_015110	ENSG00000198887	SMC5	SMC5L1	structural maintenance of chromosomes 5	protein-coding	0.010294	0.328928	
chunk0110_215_1	chr20	15406161	15406605	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	209525	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.009009	0.359551	
chunk0069_258_1	chr15	64536267	64536474	+	0	NA	intron (NM_015042, intron 1 of 8)	MLT1N2|LTR|ERVL-MaLR	36950	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.009662	0.461538	
chunk0171_75_1	chr6	121608147	121608600	+	0	NA	Intergenic	Intergenic	172796	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.006623	0.325991	
chunk0164_223_1	chr6	22939689	22940756	+	0	NA	Intergenic	Intergenic	370773	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.002812	0.348315	271(AGTACTGCTTGTACTT,+,0.00),398(CAGTACTCCATGTACC,-,0.00),399(AGTACTCCATGTACCT,+,0.00),751(GGGGACTGTATGTTCC,-,0.00),752(GGGACTGTATGTTCCA,+,0.00)
chunk0183_230_1	chr7	106892662	106892991	+	0	NA	intron (NM_002649, intron 10 of 10)	L2c|LINE|L2	27347	NM_002649	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.003040	0.406061	
chunk0141_13_1	chr4	76611311	76612156	+	0	NA	intron (NM_020859, intron 2 of 10)	intron (NM_020859, intron 2 of 10)	36182	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.013018	0.437352	341(AAGGTCACAGTGTCCT,-,0.00),342(AGGTCACAGTGTCCTT,+,0.00),490(AGGCACACCCTGTGCT,-,0.00),491(GGCACACCCTGTGCTG,+,0.00)
chunk0098_26_1	chr2	65534569	65534779	+	0	NA	Intergenic	Intergenic	-102152	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.009524	0.374408	
chunk0043_382_1	chr12	24969172	24969536	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-19895	NM_005504	586	Hs.438993	NM_005504	ENSG00000060982	BCAT1	BCATC|BCT1|ECA39|MECA39|PNAS121|PP18	branched chain amino acid transaminase 1	protein-coding	0.002747	0.367123	
chunk0212_112_1	chrY	19398216	19398981	+	0	NA	Intergenic	L1P3|LINE|L1	104555	NR_002923	286554	Hs.211713	NM_173700	ENSG00000215580	BCORP1	BCORL2	BCL6 corepressor pseudogene 1	pseudo	0.001307	0.308094	
chunk0035_224_1	chr11	45356256	45356666	+	0	NA	non-coding (NR_120557, exon 2 of 2)	non-coding (NR_120557, exon 2 of 2)	1090	NR_120557	101928812	Hs.444059	NR_120557	ENSG00000254427	LINC02696	-	long intergenic non-protein coding RNA 2696	ncRNA	0.002439	0.420925	251(AAGTGCACTGTGTACC,-,0.00)
chunk0068_317_1	chr15	57412181	57412836	+	0	NA	intron (NM_032866, intron 1 of 18)	intron (NM_032866, intron 1 of 18)	36003	NM_001252335	84952	Hs.148989	NM_032866	ENSG00000128849	CGNL1	JACOP|PCING	cingulin like 1	protein-coding	0.007634	0.458841	
chunk0182_58_1	chr7	92021165	92021499	+	0	NA	intron (NM_147185, intron 12 of 49)	intron (NM_147185, intron 12 of 49)	80457	NM_147185	10142	Hs.651221	NM_005751	ENSG00000127914	AKAP9	AKAP-9|AKAP350|AKAP450|CG-NAP|HYPERION|LQT11|MU-RMS-40.16A|PPP1R45|PRKA9|YOTIAO	A-kinase anchoring protein 9	protein-coding	0.005988	0.316418	
chunk0142_196_1	chr4	96848661	96849102	+	0	NA	Intergenic	Intergenic	-518045	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.002268	0.237557	
chunk0121_262_1	chr3	23159952	23160445	+	0	NA	Intergenic	Intergenic	-43095	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.006085	0.417004	
chunk0187_204_1	chr7	151804874	151805091	+	0	NA	intron (NM_016203, intron 1 of 15)	intron (NM_016203, intron 1 of 15)	9889	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.027650	0.545872	
chunk0141_72_1	chr4	78018398	78018651	+	0	NA	Intergenic	Intergenic	-39046	NM_001166133	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.000000	0.401575	
chunk0161_286_1	chr5	172904640	172905022	+	0	NA	intron (NM_001031711, intron 3 of 9)	intron (NM_001031711, intron 3 of 9)	53944	NR_026683	100268168	Hs.519766	NR_026682	ENSG00000204758	LOC100268168	-	uncharacterized LOC100268168	ncRNA	0.023560	0.595300	235(GGGAGCAGCCAGTTCT,-,0.00),236(GGAGCAGCCAGTTCTG,+,0.00)
chunk0198_126_1	chr8	132046511	132047360	+	0	NA	intron (NM_001080399, intron 2 of 13)	MER20|DNA|hAT-Charlie	12445	NM_001080399	729330	Hs.653174	NM_001080399	ENSG00000253117	OC90	PLA2L	otoconin 90	protein-coding	0.004711	0.427059	
chunk0012_367_1	chr1	162930479	162931104	+	0	NA	Intergenic	MIR3|SINE|MIR	-61976	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.001600	0.370607	
chunk0057_142_1	chr13	99941300	99941639	+	0	NA	intron (NR_120421, intron 1 of 4)	L1MC5a|LINE|L1	15696	NR_120421	101927437	Hs.619936	NR_120421		LOC101927437	-	uncharacterized LOC101927437	ncRNA	0.014749	0.417647	
chunk0095_440_1	chr2	25257371	25257570	+	0	NA	intron (NM_175629, intron 6 of 22)	intron (NM_175629, intron 6 of 22)	-5155	NM_153759	1788	Hs.515840	NM_022552	ENSG00000119772	DNMT3A	DNMT3A2|M.HsaIIIA|TBRS	DNA methyltransferase 3 alpha	protein-coding	0.010050	0.570000	
chunk0119_15_1	chr22	40137202	40137511	+	0	NA	intron (NM_001024843, intron 3 of 23)	MIRb|SINE|MIR	-40569	NM_001162501	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.009709	0.412903	
chunk0012_376_1	chr1	163321662	163322111	+	0	NA	promoter-TSS (NM_001254748)	promoter-TSS (NM_001254748)	-47	NM_031423	83540	Hs.651950	NM_031423	ENSG00000143228	NUF2	CDCA1|CT106|NUF2R	NUF2 component of NDC80 kinetochore complex	protein-coding	0.089087	0.608889	
chunk0078_265_1	chr17	7686204	7686719	+	0	NA	promoter-TSS (NM_001143991)	promoter-TSS (NM_001143991)	390	NM_001143990	55135	Hs.408312	NM_018081	ENSG00000141499	WRAP53	DKCB3|TCAB1|WDR79	WD repeat containing antisense to TP53	protein-coding	0.033010	0.478682	
chunk0192_118_1	chr8	61738118	61738666	+	0	NA	Intergenic	LTR107_Mam|LTR|LTR	23604	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.005474	0.420765	
chunk0032_159_1	chr11	4947771	4948247	+	0	NA	promoter-TSS (NM_001005329)	promoter-TSS (NM_001005329)	-909	NM_001005329	401666	Hs.555481	NM_001005329	ENSG00000205497	OR51A4	-	olfactory receptor family 51 subfamily A member 4	protein-coding	0.004202	0.368973	
chunk0096_344_1	chr2	35614484	35615176	+	0	NA	Intergenic	L1MEg|LINE|L1	143425	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.002890	0.341991	
chunk0056_58_1	chr13	77820214	77820464	+	0	NA	intron (NR_103853, intron 1 of 6)	intron (NR_103853, intron 1 of 6)	1402	NR_103853	100505518	Hs.742215	NR_103853		EDNRB-AS1	-	EDNRB antisense RNA 1	ncRNA	0.004000	0.406375	
chunk0090_148_1	chr18	72305166	72305588	+	0	NA	Intergenic	Intergenic	239111	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.007109	0.366430	
chunk0203_69_1	chr9	83634052	83634698	+	0	NA	intron (NM_001001551, intron 3 of 4)	intron (NM_001001551, intron 3 of 4)	11326	NR_046422	414328	Hs.530261	NM_001001551	ENSG00000148057	IDNK	C9orf103|bA522I20.2|hGntK	IDNK gluconokinase	protein-coding	0.003096	0.312210	
chunk0014_362_1	chr1	182441654	182441978	+	0	NA	Intergenic	Intergenic	-8305	NM_001137669	353299	Hs.121200	NM_032267	ENSG00000121446	RGSL1	RGSL|RGSL2	regulator of G protein signaling like 1	protein-coding	0.009259	0.486154	
chunk0199_274_1	chr9	6423287	6423635	+	0	NA	intron (NM_152896, intron 2 of 15)	intron (NM_152896, intron 2 of 15)	10310	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.000000	0.269341	
chunk0013_233_1	chr1	169572093	169572637	+	0	NA	intron (NM_000130, intron 2 of 24)	intron (NM_000130, intron 2 of 24)	14166	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.003676	0.370642	
chunk0147_129_1	chr4	174398704	174399051	+	0	NA	Intergenic	Intergenic	-24918	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.005764	0.376437	
chunk0125_287_1	chr3	69807641	69807999	+	0	NA	intron (NM_006722, intron 1 of 9)	intron (NM_006722, intron 1 of 9)	44009	NM_006722	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.002793	0.345404	56(GGGTCAAAATGTTCTT,+,0.00)
chunk0083_296_1	chr17	69269236	69269777	+	0	NA	intron (NM_172232, intron 22 of 38)	L1MB8|LINE|L1	-24691	NM_080282	10349	Hs.25377	NM_080282	ENSG00000154263	ABCA10	EST698739	ATP binding cassette subfamily A member 10	protein-coding	0.009242	0.330258	
chunk0022_65_1	chr10	8535001	8535670	+	0	NA	Intergenic	Intergenic	-267030	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.008969	0.422388	
chunk0096_401_1	chr2	37802877	37803571	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	26487	NR_110011	101929559	Hs.468200	NR_110011	ENSG00000237803	LINC00211	NCRNA00211	long intergenic non-protein coding RNA 211	ncRNA	0.000000	0.388489	
chunk0103_406_1	chr2	169241564	169241763	+	0	NA	intron (NM_004525, intron 24 of 78)	intron (NM_004525, intron 24 of 78)	120949	NM_004525	4036	Hs.657729	NM_004525	ENSG00000081479	LRP2	DBS|GP330|LRP-2	LDL receptor related protein 2	protein-coding	0.010050	0.350000	66(AAGAACATCCTGTTTC,-,0.00),67(AGAACATCCTGTTTCC,+,0.00)
chunk0108_352_1	chr2	236088390	236088840	+	0	NA	intron (NM_001037131, intron 16 of 17)	intron (NM_001037131, intron 16 of 17)	79394	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.006667	0.403548	
chunk0034_333_1	chr11	35426691	35427371	+	0	NA	Intergenic	Intergenic	-6968	NM_001252652	6506	Hs.502338	NM_004171	ENSG00000110436	SLC1A2	EAAT2|EIEE41|GLT-1|HBGT	solute carrier family 1 member 2	protein-coding	0.007353	0.367107	277(TGTAACACCCTGTTCC,-,0.00),278(GTAACACCCTGTTCCC,+,0.00)
chunk0059_309_1	chr14	36255956	36256534	+	0	NA	Intergenic	Intergenic	64431	NM_001144891	51562	Hs.368647	NM_016586	ENSG00000151332	MBIP	-	MAP3K12 binding inhibitory protein 1	protein-coding	0.010381	0.412781	
chunk0166_430_1	chr6	52725780	52726277	+	0	NA	Intergenic	Intergenic	19131	NR_033760	730152	Hs.739662	NR_033760		GSTA7P	GSTAP2|GSTAP6	glutathione S-transferase alpha 7, pseudogene	pseudo	0.002012	0.359438	
chunk0042_130_1	chr12	3721749	3722072	+	0	NA	intron (NM_032680, intron 2 of 10)	intron (NM_032680, intron 2 of 10)	31290	NM_032680	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.006192	0.441358	160(GGGAACAGGGTGCACT,-,0.00),161(GGAACAGGGTGCACTG,+,0.00)
chunk0199_332_1	chr9	10204915	10205155	+	0	NA	intron (NM_002839, intron 3 of 45)	intron (NM_002839, intron 3 of 45)	407688	NM_002839	5789	Hs.446083	NM_002839	ENSG00000153707	PTPRD	HPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA	protein tyrosine phosphatase receptor type D	protein-coding	0.000000	0.273859	
chunk0165_334_1	chr6	37367704	37367960	+	0	NA	intron (NM_003958, intron 2 of 7)	MIR|SINE|MIR	13860	NR_046399	9025	Hs.485278	NM_003958	ENSG00000112130	RNF8	hRNF8	ring finger protein 8	protein-coding	0.003906	0.400778	
chunk0033_262_1	chr11	18733904	18734105	+	0	NA	intron (NM_001039970, intron 9 of 14)	MIRc|SINE|MIR	-7774	NM_173588	283284	Hs.434152	NM_173588	ENSG00000179057	IGSF22	IGFN2	immunoglobulin superfamily member 22	protein-coding	0.000000	0.435644	98(GAGTACACACTGTCAT,-,0.00)
chunk0101_344_1	chr2	137528955	137529461	+	0	NA	intron (NM_001316349, intron 15 of 27)	intron (NM_001316349, intron 15 of 27)	398724	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.001976	0.345168	
chunk0135_395_1	chr3	192170713	192171231	+	0	NA	intron (NM_021032, intron 3 of 4)	intron (NM_021032, intron 3 of 4)	-67658	NR_046596	100873986	Hs.581652	NR_046596	ENSG00000231383	FGF12-AS1	-	FGF12 antisense RNA 1	ncRNA	0.005792	0.358382	
chunk0122_175_1	chr3	32422048	32422726	+	0	NA	intron (NM_181472, intron 1 of 3)	intron (NM_181472, intron 1 of 3)	30716	NM_181472	112616	Hs.440494	NM_138410	ENSG00000153551	CMTM7	CKLFSF7	CKLF like MARVEL transmembrane domain containing 7	protein-coding	0.013274	0.459499	
chunk0092_50_1	chr19	19763170	19763615	+	0	NA	intron (NR_026956, intron 1 of 2)	ERVL-B4-int|LTR|ERVL	13021	NR_026956	284440	Hs.665307	NR_026956		LINC00663	-	long intergenic non-protein coding RNA 663	ncRNA	0.011236	0.399103	
chunk0177_159_1	chr7	23100686	23101468	+	0	NA	TTS (NR_046220)	TTS (NR_046220)	4626	NR_046220	100775104		NR_046220	ENSG00000230658	KLHL7-DT	KLHL7-AS1|PLATAK	KLHL7 divergent transcript	ncRNA	0.003836	0.416347	260(CAGTACACCCTGTTCT,-,0.00),261(AGTACACCCTGTTCTG,+,0.00)
chunk0097_284_1	chr2	55122548	55123138	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	-72245	NM_020532	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.003390	0.451777	321(AGGAACTGCCAGTGCT,-,0.00),322(GGAACTGCCAGTGCTC,+,0.00)
chunk0009_307_1	chr1	108158245	108158741	+	0	NA	intron (NM_213651, intron 4 of 9)	intron (NM_213651, intron 4 of 9)	34316	NM_213651	29957	Hs.656870	NM_013386	ENSG00000085491	SLC25A24	APC1|SCAMC-1|SCAMC1	solute carrier family 25 member 24	protein-coding	0.008065	0.325956	
chunk0163_281_1	chr6	13679477	13679972	+	0	NA	intron (NM_005493, intron 2 of 13)	intron (NM_005493, intron 2 of 13)	31840	NM_005493	10048	Hs.708182	NM_005493	ENSG00000010017	RANBP9	BPM-L|BPM90|RANBPM|RanBP7	RAN binding protein 9	protein-coding	0.004040	0.256048	
chunk0172_209_1	chr6	136711633	136711943	+	0	NA	intron (NM_005923, intron 2 of 29)	intron (NM_005923, intron 2 of 29)	80730	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.006452	0.372990	
chunk0071_287_1	chr15	85819513	85820266	+	0	NA	Intergenic	L1MC5a|LINE|L1	-5746	NR_049805	100847084		NR_049805	ENSG00000264406	MIR548AP	-	microRNA 548ap	ncRNA	0.006640	0.371353	730(GGAACATTCAGTTTCT,+,0.00)
chunk0188_366_1	chr8	18149543	18149742	+	0	NA	Intergenic	Intergenic	-20820	NM_001160179	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.000000	0.525000	
chunk0089_439_1	chr18	70205337	70206016	+	0	NA	promoter-TSS (NM_173630)	promoter-TSS (NM_173630)	50	NM_173630	25914	Hs.654809	NM_173630	ENSG00000176225	RTTN	MSSP	rotatin	protein-coding	0.089838	0.600000	
chunk0188_377_1	chr8	18260649	18260924	+	0	NA	Intergenic	LTR48B|LTR|ERV1	39118	NM_001160174	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.010909	0.489130	15(AAGGTCAGTTTGTTCC,-,0.00),16(AGGTCAGTTTGTTCCT,+,0.00)
chunk0191_273_1	chr8	53692742	53693148	+	0	NA	Intergenic	L2a|LINE|L2	150097	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.036946	0.493857	
chunk0107_26_1	chr2	210389804	210390433	+	0	NA	intron (NR_110605, intron 1 of 5)	intron (NR_110605, intron 1 of 5)	65406	NR_110604	102724820	Hs.659232	NR_110604		LANCL1-AS1	LANCLOT	LANCL1 antisense RNA 1	ncRNA	0.007949	0.425397	
chunk0172_328_1	chr6	138440439	138440930	+	0	NA	intron (NM_020464, intron 4 of 6)	intron (NM_020464, intron 4 of 6)	-5390	NR_036099	100423001		NR_036099	ENSG00000266555	MIR3145	mir-3145	microRNA 3145	ncRNA	0.004073	0.410569	
chunk0096_8_1	chr2	25937090	25937410	+	0	NA	intron (NM_002254, intron 5 of 7)	intron (NM_002254, intron 5 of 7)	45324	NM_002254	3797	Hs.21611	NM_002254	ENSG00000084731	KIF3C	-	kinesin family member 3C	protein-coding	0.009375	0.433022	135(TAGGACATTCTGTCCT,-,0.00),136(AGGACATTCTGTCCTT,+,0.00),158(CAGAACAAGCTGTGCA,-,0.00),159(AGAACAAGCTGTGCAG,+,0.00)
chunk0017_13_1	chr1	204405813	204406408	+	0	NA	exon (NM_032833, exon 2 of 2)	exon (NM_032833, exon 2 of 2)	5707	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.003361	0.369128	291(GAGAACATTAAGTCCT,-,0.00),292(AGAACATTAAGTCCTT,+,0.00)
chunk0168_275_1	chr6	90469908	90470388	+	0	NA	Intergenic	Intergenic	117153	NM_003188	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.008333	0.376299	119(AGGAACAAGCAGTTCC,-,0.00),120(GGAACAAGCAGTTCCT,+,0.00),321(ATGGACATACTGTTCC,-,0.00),322(TGGACATACTGTTCCC,+,0.00)
chunk0120_415_1	chr3	12957157	12957577	+	0	NA	intron (NM_001134382, intron 1 of 13)	intron (NM_001134382, intron 1 of 13)	10331	NM_014869	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.014286	0.501188	
chunk0109_343_1	chr2	238695602	238695830	+	0	NA	Intergenic	Intergenic	-140217	NR_037809	151171	Hs.652076	NR_037809	ENSG00000225493	LINC01107	-	long intergenic non-protein coding RNA 1107	ncRNA	0.008772	0.445415	
chunk0140_197_1	chr4	70294803	70295002	+	0	NA	Intergenic	L1M3b|LINE|L1	-40052	NM_033122	85438	Hs.120316	NM_033122	ENSG00000145309	CABS1	C4orf35|CLPH|NYD-SP26	calcium binding protein, spermatid associated 1	protein-coding	0.000000	0.455000	
chunk0202_344_1	chr9	79535432	79535703	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-36206	NM_001282749	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.000000	0.430147	
chunk0168_346_1	chr6	93050823	93051072	+	0	NA	Intergenic	Intergenic	368635	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.000000	0.304000	
chunk0004_444_1	chr1	53176501	53177095	+	0	NA	Intergenic	Intergenic	-19631	NM_000098	1376	Hs.713535	NM_000098	ENSG00000157184	CPT2	CPT1|CPTASE|IIAE4	carnitine palmitoyltransferase 2	protein-coding	0.016835	0.499160	483(CAGGACTGCCTGTGCA,-,0.00),484(AGGACTGCCTGTGCAG,+,0.00)
chunk0009_86_1	chr1	101162127	101162384	+	0	NA	Intergenic	Intergenic	74273	NR_104626	101928370	Hs.534209	NR_104626		LOC101928370	-	uncharacterized LOC101928370	ncRNA	0.000000	0.329457	
chunk0043_409_1	chr12	25731378	25731740	+	0	NA	Intergenic	L1M4b|LINE|L1	-82997	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.002762	0.369146	220(TAGTTCATAGTGTTCC,-,0.00),221(AGTTCATAGTGTTCCT,+,0.00)
chunk0043_254_1	chr12	20632006	20632205	+	0	NA	intron (NM_000921, intron 6 of 15)	intron (NM_000921, intron 6 of 15)	60241	NM_001244683	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.010050	0.345000	
chunk0022_445_1	chr10	19780915	19781134	+	0	NA	Intergenic	Intergenic	-35419	NM_032812	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.000000	0.263636	
chunk0017_72_1	chr1	205633075	205633593	+	0	NA	promoter-TSS (NM_021795)	promoter-TSS (NM_021795)	-462	NM_001973	2005	Hs.497520	NM_001973	ENSG00000158711	ELK4	SAP1	ETS transcription factor ELK4	protein-coding	0.005792	0.364162	
chunk0064_63_1	chr14	90054768	90055290	+	0	NA	Intergenic	L1MC1|LINE|L1	-6736	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.003831	0.367113	
chunk0010_377_1	chr1	119187350	119187821	+	0	NA	intron (NR_125975, intron 4 of 6)	L1M2|LINE|L1	-46913	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.004246	0.362288	
chunk0010_366_1	chr1	118995786	118996119	+	0	NA	Intergenic	Intergenic	-6396	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.006006	0.428144	
chunk0170_300_1	chr6	115657055	115657453	+	0	NA	Intergenic	L1PB1|LINE|L1	-381477	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.002513	0.353383	
chunk0039_120_1	chr11	97994752	97994951	+	0	NA	Intergenic	Intergenic	-1026125	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.230000	
chunk0138_392_1	chr4	42734339	42734905	+	0	NA	Intergenic	Intergenic	-77517	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.007067	0.393298	
chunk0007_126_1	chr1	79132988	79133514	+	0	NA	Intergenic	HAL1|LINE|L1	-126441	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.000000	0.311195	
chunk0066_124_1	chr15	31069505	31070669	+	0	NA	exon (NM_002420, exon 3 of 27).2	exon (NM_002420, exon 3 of 27).2	-4946	NR_029624	406993		NR_029624	ENSG00000207702	MIR211	MIRN211|mir-211	microRNA 211	ncRNA	0.009450	0.474678	
chunk0191_262_1	chr8	53415738	53416245	+	0	NA	Intergenic	Intergenic	-164294	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.001972	0.389764	
chunk0146_325_1	chr4	165686606	165686850	+	0	NA	intron (NR_121676, intron 2 of 5)	MIRb|SINE|MIR	2089	NR_121676	101928151	Hs.639858	NR_121676	ENSG00000249500	LINC01179	-	long intergenic non-protein coding RNA 1179	ncRNA	0.008197	0.444898	
chunk0128_126_1	chr3	106474641	106475182	+	0	NA	Intergenic	L1MA9|LINE|L1	-605868	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.003697	0.330258	
chunk0111_107_1	chr20	23694247	23695349	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-5773	NM_001899	1472	Hs.654549	NM_001899	ENSG00000101441	CST4	-	cystatin S	protein-coding	0.009982	0.466002	
chunk0012_189_1	chr1	159681523	159681762	+	0	NA	Intergenic	Intergenic	32947	NM_000567	1401	Hs.76452	NM_000567	ENSG00000132693	CRP	PTX1	C-reactive protein	protein-coding	0.004184	0.491667	
chunk0071_170_1	chr15	83192362	83192629	+	0	NA	intron (NM_016073, intron 1 of 5)	intron (NM_016073, intron 1 of 5)	15523	NM_016073	50810	Hs.513954	NM_016073	ENSG00000166503	HDGFL3	CGI-142|HDGF-2|HDGF2|HDGFRP3|HRP-3	HDGF like 3	protein-coding	0.003745	0.324627	
chunk0038_121_1	chr11	83956503	83957559	+	0	NA	intron (NM_001142699, intron 14 of 27)	intron (NM_001142699, intron 14 of 27)	-274606	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.008523	0.394513	
chunk0020_148_1	chr1	233754714	233755281	+	0	NA	Intergenic	L1ME2z|LINE|L1	130845	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.000000	0.278169	
chunk0196_35_1	chr8	101601875	101602288	+	0	NA	intron (NM_024915, intron 8 of 15)	L1PA8|LINE|L1	109641	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.007264	0.410628	
chunk0210_113_1	chrX	72300443	72301127	+	0	NA	TTS (NM_001144886)	TTS (NM_001144886)	5129	NM_001144887	4435	Hs.40403	NM_004143	ENSG00000125931	CITED1	MSG1	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1	protein-coding	0.005848	0.493431	319(ATGGACAGAGTGTCCA,-,0.00),320(TGGACAGAGTGTCCAG,+,0.00),588(CAGCTCAGAGTGTCCC,-,0.00),589(AGCTCAGAGTGTCCCA,+,0.00)
chunk0026_344_1	chr10	68620428	68620815	+	0	NA	intron (NM_030625, intron 3 of 11)	L1MB8|LINE|L1	60261	NM_030625	80312	Hs.258855	NM_030625	ENSG00000138336	TET1	CXXC6|LCX|bA119F7.1	tet methylcytosine dioxygenase 1	protein-coding	0.000000	0.381443	
chunk0074_340_1	chr16	31508326	31508634	+	0	NA	promoter-TSS (NM_022744)	promoter-TSS (NM_022744)	-61	NM_022744	64755	Hs.9003	NM_022744	ENSG00000140688	C16orf58	RUS	chromosome 16 open reading frame 58	protein-coding	0.110390	0.682848	
chunk0053_194_1	chr13	31657432	31657757	+	0	NA	Intergenic	MER110|LTR|ERV1	-81948	NM_130806	122042	Hs.680763	NM_130806	ENSG00000133105	RXFP2	GPR106|GREAT|INSL3R|LGR8|LGR8.1|RXFPR2	relaxin family peptide receptor 2	protein-coding	0.000000	0.401840	
chunk0030_337_1	chr10	118394432	118395024	+	0	NA	Intergenic	Intergenic	37620	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.006757	0.391231	
chunk0206_445_1	chr9	128055509	128056171	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	11480	NM_197956	203245	Hs.373606	NM_197956	ENSG00000171169	NAIF1	C9orf90|bA379C10.2	nuclear apoptosis inducing factor 1	protein-coding	0.009063	0.497738	386(AAGGACAAGCTGTTCC,-,0.00),387(AGGACAAGCTGTTCCC,+,0.00)
chunk0184_269_1	chr7	118490769	118491080	+	0	NA	Intergenic	Intergenic	266266	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.009646	0.397436	
chunk0174_219_1	chr6	160408462	160408896	+	0	NA	intron (NM_021977, intron 3 of 10)	intron (NM_021977, intron 3 of 10)	60306	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.013825	0.441379	
chunk0195_90_1	chr8	94236153	94236441	+	0	NA	Intergenic	Intergenic	-18994	NM_001144663	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.024306	0.501730	173(AAGCACACGGTGTCCA,-,0.00),174(AGCACACGGTGTCCAA,+,0.00)
chunk0065_305_1	chr14	102940325	102940569	+	0	NA	intron (NM_006035, intron 30 of 36)	intron (NM_006035, intron 30 of 36)	17791	NM_030943	81693	Hs.534494	NM_030943	ENSG00000166126	AMN	PRO1028|amnionless	amnion associated transmembrane protein	protein-coding	0.032787	0.502041	
chunk0182_47_1	chr7	91829301	91829651	+	0	NA	Intergenic	L2c|LINE|L2	51244	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.000000	0.356125	
chunk0157_113_1	chr5	116864580	116864877	+	0	NA	Intergenic	Intergenic	-102519	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.010101	0.422819	
chunk0085_207_1	chr18	6626599	6627018	+	0	NA	Intergenic	Intergenic	115392	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.011933	0.400000	
chunk0136_413_1	chr3	197394867	197395467	+	0	NA	Intergenic	Intergenic	-95895	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.015000	0.505824	
chunk0064_310_1	chr14	95741185	95741389	+	0	NA	Intergenic	MIR|SINE|MIR	-27091	NM_021966	8115	Hs.2484	NM_021966	ENSG00000100721	TCL1A	TCL1	T cell leukemia/lymphoma 1A	protein-coding	0.014706	0.507317	
chunk0118_294_1	chr22	34282207	34282582	+	0	NA	Intergenic	L2b|LINE|L2	-361966	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.008000	0.444149	
chunk0102_350_1	chr2	152467383	152467953	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	132431	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.017544	0.443082	224(AGGAACTGTCTGTGCT,-,0.00),225(GGAACTGTCTGTGCTT,+,0.00)
chunk0165_263_1	chr6	35778359	35778828	+	0	NA	intron (NM_001286550, intron 3 of 3)	intron (NM_001286550, intron 3 of 3)	1999	NR_104467	389383	Hs.259563	NM_207409	ENSG00000196748	CLPSL2	AAAL3045|C6orf126|UNQ3045|dJ510O8.5	colipase like 2	protein-coding	0.004264	0.508511	274(CAGTACGCCCTGTTCC,-,0.00),275(AGTACGCCCTGTTCCT,+,0.00)
chunk0212_107_1	chrY	16500944	16501564	+	0	NA	Intergenic	Intergenic	-999704	NR_028084	100302526	Hs.434364	NR_028084		FAM41AY2	-	family with sequence similarity 41 member A, Y-linked 2	ncRNA	0.000000	0.326892	
chunk0125_170_1	chr3	66593990	66594527	+	0	NA	Intergenic	L1ME2z|LINE|L1	-93837	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.003724	0.381041	
chunk0084_188_1	chr17	77852029	77852228	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	31959	NR_028337	400624	Hs.514521	NM_001001685	ENSG00000204283	LINC01973	-	long intergenic non-protein coding RNA 1973	ncRNA	0.010050	0.440000	
chunk0018_11_1	chr1	215115318	215115830	+	0	NA	intron (NM_001017424, intron 2 of 6)	intron (NM_001017424, intron 2 of 6)	32357	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.003906	0.352827	
chunk0014_373_1	chr1	182641564	182642083	+	0	NA	Intergenic	Intergenic	26683	NR_036490	284648	Hs.253475	NR_036490	ENSG00000261504	LINC01686	-	long intergenic non-protein coding RNA 1686	ncRNA	0.021195	0.519231	
chunk0051_421_1	chr12	122609030	122609239	+	0	NA	intron (NM_014708, intron 51 of 63)	L2a|LINE|L2	81872	NM_014708	9735	Hs.300559	NM_014708	ENSG00000184445	KNTC1	ROD	kinetochore associated 1	protein-coding	0.000000	0.338095	
chunk0103_172_1	chr2	163037798	163038019	+	0	NA	Intergenic	Intergenic	-199161	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.004525	0.342342	
chunk0011_143_1	chr1	147350660	147352063	+	0	NA	Intergenic	Intergenic	108720	NM_004284	9557	Hs.191164	NM_004284	ENSG00000131778	CHD1L	ALC1|CHDL	chromodomain helicase DNA binding protein 1 like	protein-coding	0.004989	0.386040	
chunk0045_135_1	chr12	46435242	46435985	+	0	NA	intron (NR_125381, intron 2 of 2)	L1MC2|LINE|L1	51506	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.000000	0.345430	
chunk0144_193_1	chr4	133632575	133632789	+	0	NA	Intergenic	Intergenic	483392	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.000000	0.395349	
chunk0209_417_1	chrX	56946206	56946544	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	49180	NR_027139	169981	Hs.522672	NM_001010862	ENSG00000204271	SPIN3	SPIN-3|TDRD27|bA445O16.1	spindlin family member 3	protein-coding	0.005917	0.427729	
chunk0094_51_1	chr2	3105477	3105678	+	0	NA	intron (NR_110228, intron 3 of 6)	HAL1M8|LINE|L1	20449	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.024876	0.425743	
chunk0062_16_1	chr14	66396228	66396477	+	0	NA	Intergenic	Intergenic	-90019	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.004016	0.356000	
chunk0177_336_1	chr7	26441762	26442053	+	0	NA	intron (NR_015364, intron 1 of 4)	intron (NR_015364, intron 1 of 4)	38419	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.003436	0.513699	
chunk0169_357_1	chr6	106739500	106739741	+	0	NA	intron (NR_033557, intron 2 of 6)	MamGypLTR2c|LTR|Gypsy	-44505	NR_030314	693172		NR_030314	ENSG00000207577	MIR587	MIRN587|hsa-mir-587	microRNA 587	ncRNA	0.016598	0.557851	120(GAGGACAAGATGTGCC,-,0.00),121(AGGACAAGATGTGCCA,+,0.00)
chunk0206_65_1	chr9	119833903	119834376	+	0	NA	Intergenic	L2a|LINE|L2	-100921	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.006342	0.400844	175(AAGAACTCTATGTTCA,-,0.00),176(AGAACTCTATGTTCAC,+,0.00)
chunk0181_52_1	chr7	80094346	80095040	+	0	NA	Intergenic	Intergenic	-40131	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.001441	0.300719	324(GGGAACAAAATGTTCT,-,0.00),325(GGAACAAAATGTTCTC,+,0.00)
chunk0112_268_1	chr20	43162899	43163428	+	0	NA	intron (NM_133170, intron 1 of 31)	intron (NM_133170, intron 1 of 31)	26754	NM_133170	11122	Hs.526879	NM_007050	ENSG00000196090	PTPRT	RPTPrho	protein tyrosine phosphatase receptor type T	protein-coding	0.020794	0.492453	446(AAGAACAGGCTGGGCC,-,0.00),447(AGAACAGGCTGGGCCA,+,0.00)
chunk0027_352_1	chr10	78729604	78730559	+	0	NA	Intergenic	Intergenic	337367	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.008377	0.410042	434(GAGCACAAAGTGTCCC,-,0.00),435(AGCACAAAGTGTCCCT,+,0.00)
chunk0123_39_1	chr3	40877382	40878414	+	0	NA	Intergenic	Intergenic	-321553	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.010659	0.485963	
chunk0208_224_1	chrX	19110550	19111156	+	0	NA	intron (NM_001184837, intron 1 of 26)	intron (NM_001184837, intron 1 of 26)	11784	NM_001079859	10149	Hs.146978	NM_005756	ENSG00000173698	ADGRG2	CBAVDX|EDDM6|GPR64|HE6|TM7LN2	adhesion G protein-coupled receptor G2	protein-coding	0.009901	0.433278	
chunk0105_181_1	chr2	187478410	187479163	+	0	NA	exon (NM_001032281, exon 7 of 7)	exon (NM_001032281, exon 7 of 7)	-30492	NM_005795	10203	Hs.470882	NM_005795	ENSG00000064989	CALCRL	CGRPR|CRLR	calcitonin receptor like receptor	protein-coding	0.006640	0.346154	492(AGTACATTATGTTTTT,+,0.00)
chunk0033_273_1	chr11	19145432	19146181	+	0	NA	intron (NM_019028, intron 2 of 16)	intron (NM_019028, intron 2 of 16)	28661	NM_019028	54503	Hs.188569	NM_019028	ENSG00000177054	ZDHHC13	HIP14L|HIP3RP	zinc finger DHHC-type containing 13	protein-coding	0.002670	0.348000	
chunk0130_299_1	chr3	136944768	136945165	+	0	NA	intron (NM_001190796, intron 1 of 2)	L2a|LINE|L2	-12899	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.005038	0.336683	194(CAAAACTCCCTGTCCT,-,0.00),195(AAAACTCCCTGTCCTT,+,0.00)
chunk0162_226_1	chr6	4545981	4546426	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-64362	NR_122107	497048	Hs.591355	NM_001011540	ENSG00000205444	KU-MEL-3	-	uncharacterized LOC497048	ncRNA	0.013483	0.493274	
chunk0142_78_1	chr4	93883548	93883965	+	0	NA	Intergenic	L1M3|LINE|L1	54829	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.007194	0.368421	277(CGGAACAGAGTGCCCC,-,0.00),278(GGAACAGAGTGCCCCT,+,0.00)
chunk0137_44_1	chr4	11489464	11490258	+	0	NA	Intergenic	Intergenic	-60948	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.005038	0.353459	
chunk0185_243_1	chr7	129998564	129998763	+	0	NA	Intergenic	L2c|LINE|L2	-45703	NM_182697	7328	Hs.643548	NM_003344	ENSG00000186591	UBE2H	E2-20K|GID3|UBC8|UBCH|UBCH2	ubiquitin conjugating enzyme E2 H	protein-coding	0.005025	0.470000	
chunk0095_75_1	chr2	14574089	14574350	+	0	NA	Intergenic	Intergenic	-58467	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.003831	0.335878	
chunk0082_14_1	chr17	50305096	50305411	+	0	NA	Intergenic	Intergenic	-17398	NR_125805	103752589	Hs.612913	NR_125805	ENSG00000251179	TMEM92-AS1	TCONS_00025237|lncRNA-508851	TMEM92 antisense RNA 1	ncRNA	0.019048	0.544304	
chunk0170_16_1	chr6	109115323	109115522	+	0	NA	intron (NM_001083535, intron 3 of 12)	intron (NM_001083535, intron 3 of 12)	-13882	NM_173830	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.005025	0.345000	
chunk0161_410_1	chr5	177525006	177525473	+	0	NA	intron (NM_001190946, intron 5 of 8)	intron (NM_001190946, intron 5 of 8)	-8273	NM_016222	51428	Hs.484288	NM_016222	ENSG00000183258	DDX41	ABS|MPLPF	DEAD-box helicase 41	protein-coding	0.014989	0.557692	
chunk0002_138_1	chr1	16948440	16948711	+	0	NA	intron (NM_014675, intron 18 of 36)	intron (NM_014675, intron 18 of 36)	26625	NM_014675	9696	Hs.309403	NM_014675	ENSG00000058453	CROCC	ROLT|TAX1BP2	ciliary rootlet coiled-coil, rootletin	protein-coding	0.036900	0.676471	
chunk0168_218_1	chr6	85993309	85993898	+	0	NA	Intergenic	Intergenic	-314870	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.005093	0.374576	
chunk0068_302_1	chr15	57156479	57156883	+	0	NA	intron (NM_003205, intron 5 of 19)	intron (NM_003205, intron 5 of 19)	-62749	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.002475	0.404938	
chunk0079_198_1	chr17	14386762	14387622	+	0	NA	Intergenic	Intergenic	83452	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.019767	0.416957	
chunk0180_11_1	chr7	53196933	53197132	+	0	NA	Intergenic	Intergenic	161376	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.005025	0.315000	
chunk0104_45_1	chr2	171159685	171160043	+	0	NA	intron (NM_001136554, intron 1 of 20)	intron (NM_001136554, intron 1 of 20)	1036	NM_012290	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.047486	0.612813	250(GAGTACTGAGTGTACT,-,0.00),251(AGTACTGAGTGTACTG,+,0.00)
chunk0053_426_1	chr13	38111301	38111975	+	0	NA	intron (NR_047500, intron 1 of 5)	intron (NR_047500, intron 1 of 5)	31594	NR_047500	100874188	Hs.569249	NR_047500	ENSG00000223685	LINC00571	-	long intergenic non-protein coding RNA 571	ncRNA	0.005935	0.312593	
chunk0092_445_1	chr19	38831036	38831646	+	0	NA	exon (NM_001398, exon 2 of 10)	exon (NM_001398, exon 2 of 10)	516	NM_001398	1891	Hs.196176	NM_001398	ENSG00000104823	ECH1	HPXEL	enoyl-CoA hydratase 1	protein-coding	0.039344	0.569558	
chunk0167_299_1	chr6	71284759	71285313	+	0	NA	Intergenic	Intergenic	-3738	NM_024576	79627	Hs.648434	NM_024576	ENSG00000119900	OGFRL1	dJ331H24.1	opioid growth factor receptor like 1	protein-coding	0.000000	0.374775	270(AAGAACACAAAGTTCT,-,0.00),271(AGAACACAAAGTTCTC,+,0.00)
chunk0143_24_1	chr4	105994132	105994412	+	0	NA	Intergenic	Intergenic	28206	NR_125928	101929577	Hs.631131	NR_125928	ENSG00000249635	LOC101929577	-	uncharacterized LOC101929577	ncRNA	0.021429	0.448399	
chunk0160_44_1	chr5	149562922	149563127	+	0	NA	Intergenic	Intergenic	-11472	NM_001892	1452	Hs.529862	NM_001892	ENSG00000113712	CSNK1A1	CK1|CK1a|CKIa|HEL-S-77p|HLCDGP1|PRO2975	casein kinase 1 alpha 1	protein-coding	0.009756	0.495146	
chunk0062_41_1	chr14	67250124	67250650	+	0	NA	intron (NM_022474, intron 1 of 14)	intron (NM_022474, intron 1 of 14)	9092	NM_001256550	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.005703	0.345351	
chunk0146_11_1	chr4	154983643	154984227	+	0	NA	Intergenic	Intergenic	202430	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.010274	0.420513	271(GGGCACACAGTGTCTC,-,0.00),272(GGCACACAGTGTCTCC,+,0.00)
chunk0190_415_1	chr8	41055380	41055971	+	0	NA	Intergenic	hAT-N1_Mam|DNA|hAT-Tip100?	-157851	NM_024645	79698	Hs.591850	NM_024645	ENSG00000165061	ZMAT4	-	zinc finger matrin-type 4	protein-coding	0.000000	0.396959	
chunk0181_140_1	chr7	81410086	81410984	+	0	NA	Intergenic	Intergenic	215681	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.005568	0.309232	
chunk0188_7_1	chr8	6303804	6304352	+	0	NA	Intergenic	Intergenic	102470	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.005474	0.362477	
chunk0209_167_1	chrX	43589611	43590226	+	0	NA	Intergenic	Intergenic	-64989	NM_001270458	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.004878	0.360390	363(CAGAACTAGATGTTCT,-,0.00),364(AGAACTAGATGTTCTA,+,0.00)
chunk0209_176_1	chrX	43669543	43670116	+	0	NA	intron (NM_001270458, intron 2 of 15)	intron (NM_001270458, intron 2 of 15)	14922	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.003490	0.362369	268(GGAACACAATGAACTT,+,0.00)
chunk0184_370_1	chr7	121300646	121300866	+	0	NA	Intergenic	Intergenic	-24611	NM_016087	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.004545	0.316742	
chunk0152_256_1	chr5	60886065	60886459	+	0	NA	intron (NM_001007233, intron 12 of 12)	L2b|LINE|L2	-41988	NM_024930	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.010152	0.351899	
chunk0018_46_1	chr1	215938569	215938829	+	0	NA	intron (NM_206933, intron 37 of 71)	intron (NM_206933, intron 37 of 71)	-133766	NR_125992	102723833	Hs.232072	NR_125992	ENSG00000233620	LOC102723833	-	uncharacterized LOC102723833	ncRNA	0.015385	0.517241	
chunk0194_108_1	chr8	83595043	83595335	+	0	NA	Intergenic	MIRc|SINE|MIR	191431	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003425	0.368601	
chunk0077_390_1	chr16	84762100	84762477	+	0	NA	intron (NR_073577, intron 6 of 11)	intron (NR_073577, intron 6 of 11)	-57693	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.013263	0.436508	
chunk0025_388_1	chr10	59315523	59315845	+	0	NA	intron (NM_001001971, intron 4 of 11)	intron (NM_001001971, intron 4 of 11)	46910	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.000000	0.448916	
chunk0032_336_1	chr11	10244102	10244590	+	0	NA	intron (NM_030962, intron 1 of 39)	L1MA10|LINE|L1	49861	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.004098	0.366053	261(GTGAACAGACTGTTCT,-,0.00),262(TGAACAGACTGTTCTT,+,0.00)
chunk0009_312_1	chr1	108526655	108526854	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-33595	NM_001010883	284611	Hs.200230	NM_001010883	ENSG00000162636	FAM102B	SYM-3B	family with sequence similarity 102 member B	protein-coding	0.005025	0.510000	
chunk0031_39_1	chr10	122155009	122155473	+	0	NA	intron (NM_206862, intron 7 of 22)	intron (NM_206862, intron 7 of 22)	-8185	NM_006997	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.028017	0.498925	
chunk0121_273_1	chr3	23320811	23321509	+	0	NA	intron (NM_152653, intron 3 of 5)	MLT1C|LTR|ERVL-MaLR	117867	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.008596	0.449213	
chunk0170_41_1	chr6	109370700	109371266	+	0	NA	intron (NM_001142401, intron 3 of 4)	MER58A|DNA|hAT-Charlie	11576	NM_001142404	8763	Hs.520313	NM_006016	ENSG00000135535	CD164	DFNA66|MGC-24|MGC-24v|MUC-24|endolyn	CD164 molecule	protein-coding	0.007067	0.377425	
chunk0159_327_1	chr5	143602002	143602304	+	0	NA	Intergenic	MIR|SINE|MIR	-77707	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.009934	0.438944	
chunk0161_160_1	chr5	169119088	169119331	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	105982	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.004115	0.442623	
chunk0180_46_1	chr7	54658527	54659306	+	0	NA	Intergenic	Intergenic	100330	NM_001012456	23480	Hs.488282	NM_014302	ENSG00000132432	SEC61G	SSS1	SEC61 translocon gamma subunit	protein-coding	0.010270	0.461538	
chunk0109_208_1	chr20	5301917	5302159	+	0	NA	TTS (NM_144773)	TTS (NM_144773)	12331	NM_144773	128674	Hs.375029	NM_144773	ENSG00000101292	PROKR2	GPR73L1|GPR73b|GPRg2|HH3|KAL3|PKR2|dJ680N4.3	prokineticin receptor 2	protein-coding	0.016529	0.555556	
chunk0061_451_1	chr14	65865279	65865572	+	0	NA	Intergenic	Intergenic	394323	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.003413	0.411565	200(TAGCACAGCCTGTTCC,-,0.00),201(AGCACAGCCTGTTCCA,+,0.00)
chunk0015_240_1	chr1	187837714	187838338	+	0	NA	Intergenic	MamGyp-int|LTR|Gypsy	394398	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004808	0.384000	311(CAAAACAAACTGTGCC,-,0.00),312(AAAACAAACTGTGCCC,+,0.00)
chunk0010_7_1	chr1	111878478	111879125	+	0	NA	intron (NM_172198, intron 2 of 6)	MLT2B4|LTR|ERVL	-21896	NR_046783	100874295	Hs.738190	NR_046783	ENSG00000232558	KCND3-IT1	-	KCND3 intronic transcript 1	ncRNA	0.007728	0.518519	
chunk0044_384_1	chr12	39912469	39913538	+	0	NA	intron (NM_052885, intron 4 of 9)	L1MEh|LINE|L1	192856	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.007484	0.358879	
chunk0109_329_1	chr20	9306377	9307124	+	0	NA	intron (NM_001172646, intron 2 of 37)	intron (NM_001172646, intron 2 of 37)	-1050	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.006693	0.426471	416(AGGAACGCTGAGTTCT,-,0.00),417(GGAACGCTGAGTTCTT,+,0.00)
chunk0018_325_1	chr1	221307209	221307760	+	0	NA	Intergenic	Intergenic	28812	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.001815	0.378623	
chunk0049_326_1	chr12	94704630	94704918	+	0	NA	Intergenic	Intergenic	-54212	NM_020698	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.003472	0.397924	
chunk0200_70_1	chr9	15942669	15943021	+	0	NA	intron (NM_173550, intron 25 of 25)	intron (NM_173550, intron 25 of 25)	310262	NM_001271829	100129385	Hs.586441	NM_001271829	ENSG00000205549	C9orf92	Em:AL513424.1	chromosome 9 open reading frame 92	protein-coding	0.002841	0.348442	
chunk0006_262_1	chr1	69970474	69970696	+	0	NA	intron (NM_020794, intron 6 of 24)	L1PB1|LINE|L1	51263	NR_023916	5301	Hs.654711	NR_023916	ENSG00000229359	PIN1P1	PIN1L	peptidylprolyl cis/trans isomerase, NIMA-interacting 1 pseudogene 1	pseudo	0.004505	0.363229	
chunk0081_470_1	chr17	49597037	49597321	+	0	NA	Intergenic	Intergenic	21243	NM_007225	11248	Hs.55069	NM_007225	ENSG00000182575	NXPH3	NPH3	neurexophilin 3	protein-coding	0.003521	0.410526	
chunk0147_143_1	chr4	174875373	174875741	+	0	NA	intron (NR_125900, intron 4 of 4)	MER58A|DNA|hAT-Charlie	-42801	NM_001130705	11086	Hs.126838	NM_014269	ENSG00000168594	ADAM29	CT73|svph1	ADAM metallopeptidase domain 29	protein-coding	0.005435	0.409214	
chunk0192_175_1	chr8	62774619	62774840	+	0	NA	intron (NR_130764, intron 4 of 6)	L1MA3|LINE|L1	-203132	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.000000	0.297297	
chunk0157_106_1	chr5	116799318	116799801	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-37350	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.006211	0.402893	
chunk0134_49_1	chr3	175940761	175941136	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-164615	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.010667	0.539894	
chunk0136_406_1	chr3	197240852	197241186	+	0	NA	intron (NM_004087, intron 4 of 25)	L1M3f|LINE|L1	52929	NR_039960	100616216		NR_039960	ENSG00000265850	MIR4797	-	microRNA 4797	ncRNA	0.000000	0.295522	
chunk0002_311_1	chr1	23984239	23985037	+	0	NA	Intergenic	Intergenic	-4175	NM_001191005	10772	Hs.3530	NM_006625	ENSG00000188529	SRSF10	FUSIP1|FUSIP2|NSSR|PPP1R149|SFRS13|SFRS13A|SRp38|SRrp40|TASR|TASR1|TASR2	serine and arginine rich splicing factor 10	protein-coding	0.002506	0.395494	502(GAGAACTCAGTGTTCT,-,0.00),503(AGAACTCAGTGTTCTC,+,0.00)
chunk0195_287_1	chr8	98555000	98555199	+	0	NA	intron (NM_006281, intron 8 of 10)	intron (NM_006281, intron 8 of 10)	128077	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.000000	0.365000	
chunk0157_463_1	chr5	125056263	125056994	+	0	NA	intron (NR_109882, intron 2 of 5)	intron (NR_109882, intron 2 of 5)	19797	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.004104	0.385246	
chunk0110_278_1	chr20	17557672	17557964	+	0	NA	intron (NM_001278606, intron 1 of 8)	intron (NM_001278606, intron 1 of 8)	1142	NM_001161705	631	Hs.129702	NM_001195	ENSG00000125864	BFSP1	CP115|CP94|CTRCT33|LIFL-H	beaded filament structural protein 1	protein-coding	0.006849	0.402730	
chunk0075_273_1	chr16	53793806	53794212	+	0	NA	intron (NM_001080432, intron 1 of 8)	L1M5|LINE|L1	90046	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.007389	0.314496	
chunk0204_411_1	chr9	102840246	102840725	+	0	NA	Intergenic	Intergenic	-154826	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.006263	0.377083	
chunk0100_341_1	chr2	117008022	117008881	+	0	NA	Intergenic	L1MC1|LINE|L1	-806228	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.002328	0.345349	571(GAGAACAATGTGTACA,-,0.00),572(AGAACAATGTGTACAT,+,0.00)
chunk0087_235_1	chr18	36482546	36483171	+	0	NA	intron (NM_001281739, intron 3 of 23)	(AC)n|Simple_repeat|Simple_repeat	180560	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.008000	0.471246	
chunk0129_274_1	chr3	122846367	122846566	+	0	NA	intron (NM_032839, intron 5 of 8)	L1MEg|LINE|L1	-40047	NR_024618	100129550	Hs.61558	NR_024618	ENSG00000273033	LINC02035	-	long intergenic non-protein coding RNA 2035	ncRNA	0.000000	0.330000	
chunk0160_227_1	chr5	155239655	155239861	+	0	NA	Intergenic	Intergenic	226058	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.000000	0.478261	
chunk0026_401_1	chr10	69911337	69912116	+	0	NA	intron (NM_080798, intron 13 of 34)	intron (NM_080798, intron 13 of 34)	109838	NM_080798	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.010270	0.514103	387(GAGAACAGGGAGTACT,-,0.00),388(AGAACAGGGAGTACTT,+,0.00)
chunk0046_294_1	chr12	62158837	62159688	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	33577	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.003525	0.347418	636(AGGAACAGACTGTTCC,-,0.00),637(GGAACAGACTGTTCCT,+,0.00)
chunk0172_17_1	chr6	132873601	132874248	+	0	NA	Intergenic	Intergenic	40404	NR_039664									0.007728	0.311728	
chunk0180_325_1	chr7	72613043	72613606	+	0	NA	intron (NM_001145440, intron 13 of 13)	MER58C|DNA|hAT-Charlie	-84579	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.007105	0.393617	
chunk0079_356_1	chr17	17841741	17842032	+	0	NA	Intergenic	Intergenic	-4875	NM_001005291	6720	Hs.592123	NM_004176	ENSG00000072310	SREBF1	SREBP1|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.000000	0.585616	
chunk0067_337_1	chr15	48397794	48398212	+	0	NA	Intergenic	Intergenic	65835	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.011962	0.522673	
chunk0153_383_1	chr5	75010897	75011423	+	0	NA	Intergenic	L2b|LINE|L2	19739	NM_016591	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.001901	0.341556	
chunk0092_65_1	chr19	20314973	20315263	+	0	NA	Intergenic	Intergenic	84236	NR_036053	100302179		NR_036053	ENSG00000238517	MIR1270	MIR1270-1|MIR1270-2|MIRN1270|hsa-mir-1270|hsa-mir-1270-1|mir-1270	microRNA 1270	ncRNA	0.010345	0.384880	
chunk0035_13_1	chr11	40189012	40189381	+	0	NA	intron (NM_020929, intron 3 of 4)	intron (NM_020929, intron 3 of 4)	103934	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.010840	0.343243	
chunk0129_111_1	chr3	119786278	119786896	+	0	NA	intron (NM_022002, intron 1 of 8)	intron (NM_022002, intron 1 of 8)	3877	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.003236	0.441034	311(GAGGCCACTGTGTCCT,-,0.00),312(AGGCCACTGTGTCCTG,+,0.00),343(GGGTACTGTGTGTACT,-,0.00),344(GGTACTGTGTGTACTT,+,0.00)
chunk0187_70_1	chr8	2086328	2086541	+	0	NA	intron (NM_003970, intron 14 of 36)	intron (NM_003970, intron 14 of 36)	9845	NR_106983	102465695		NR_106983	ENSG00000273593	MIR7160	hsa-mir-7160	microRNA 7160	ncRNA	0.042254	0.602804	
chunk0141_224_1	chr4	84722748	84723025	+	0	NA	intron (NM_014991, intron 46 of 67)	intron (NM_014991, intron 46 of 67)	139982	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.003610	0.384892	
chunk0103_178_1	chr2	163250128	163250491	+	0	NA	Intergenic	Intergenic	-411562	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.002755	0.260989	
chunk0178_242_1	chr7	36137115	36137380	+	0	NA	Intergenic	Intergenic	-15980	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.000000	0.417293	
chunk0186_353_1	chr7	143487498	143487952	+	0	NA	intron (NR_033897, intron 2 of 4)	intron (NR_033897, intron 2 of 4)	9852	NM_176883	259287	Hs.650648	NM_176883	ENSG00000221855	TAS2R41	T2R41|T2R59	taste 2 receptor member 41	protein-coding	0.008811	0.474725	
chunk0157_165_1	chr5	118022260	118022530	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	-260179	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.007407	0.324723	
chunk0052_353_1	chr12	126926777	126927285	+	0	NA	intron (NR_104646, intron 4 of 6)	intron (NR_104646, intron 4 of 6)	-52341	NR_033970	440117	Hs.127100	NR_033970	ENSG00000249873	LINC02372	-	long intergenic non-protein coding RNA 2372	ncRNA	0.009843	0.326130	335(ATGAACATTATGTTCT,-,0.00),336(TGAACATTATGTTCTC,+,0.00)
chunk0193_68_1	chr8	73095305	73095885	+	0	NA	Intergenic	Intergenic	-2323	NM_153225	157869	Hs.439040	NM_153225	ENSG00000164764	SBSPON	C8orf84|RPESP	somatomedin B and thrombospondin type 1 domain containing	protein-coding	0.005172	0.440620	
chunk0143_287_1	chr4	118175616	118176096	+	0	NA	intron (NM_004784, intron 6 of 13)	intron (NM_004784, intron 6 of 13)	-102906	NR_003584	100093630	Hs.535762	NR_003584	ENSG00000269893	SNHG8	LINC00060|NCRNA00060	small nucleolar RNA host gene 8	ncRNA	0.008333	0.415800	
chunk0084_182_1	chr17	77622475	77623107	+	0	NA	Intergenic	L1MD1|LINE|L1	75850	NR_040050	100507351	Hs.514518	NR_040050		LOC100507351	-	uncharacterized LOC100507351	ncRNA	0.009494	0.357030	
chunk0039_116_1	chr11	97797007	97797442	+	0	NA	Intergenic	Intergenic	-1223752	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.376147	
chunk0021_245_1	chr1	243235735	243236186	+	0	NA	intron (NM_001042405, intron 1 of 18)	intron (NM_001042405, intron 1 of 18)	19446	NM_001042404	9859	Hs.533635	NM_014812	ENSG00000143702	CEP170	FAM68A|KAB|KIAA0470	centrosomal protein 170	protein-coding	0.002217	0.298673	
chunk0195_427_1	chr8	100878013	100878633	+	0	NA	Intergenic	Intergenic	72248	NM_001135702	7534	Hs.492407	NM_003406	ENSG00000164924	YWHAZ	14-3-3-zeta|HEL-S-3|HEL-S-93|HEL4|KCIP-1|POPCHAS|YWHAD	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	protein-coding	0.014516	0.434783	501(CAGGACAGGAAGTGCT,-,0.00),502(AGGACAGGAAGTGCTG,+,0.00)
chunk0132_233_1	chr3	158467259	158467696	+	0	NA	intron (NM_001271834, intron 6 of 8)	MIRc|SINE|MIR	103589	NR_104147	100996447	Hs.369810	NR_104147	ENSG00000243150	LOC100996447	-	uncharacterized LOC100996447	ncRNA	0.004577	0.333333	
chunk0007_110_1	chr1	78919945	78920334	+	0	NA	intron (NM_022159, intron 10 of 14)	intron (NM_022159, intron 10 of 14)	86671	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.002571	0.333333	
chunk0068_308_1	chr15	57196468	57197194	+	0	NA	intron (NM_003205, intron 7 of 19)	intron (NM_003205, intron 7 of 19)	-22599	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.000000	0.299862	312(AAGGACAAATTGTACA,-,0.00)
chunk0207_325_1	chr9	134231078	134231608	+	0	NA	Intergenic	Intergenic	-66779	NR_023344	100151684	Hs.545589	NR_023344	ENSG00000221676	RNU6ATAC	RNU6ATAC1|U6ATAC	RNA, U6atac small nuclear (U12-dependent splicing)	snRNA	0.035849	0.610169	314(AAGAACATTTTGTCTC,-,0.00),315(AGAACATTTTGTCTCC,+,0.00)
chunk0002_132_1	chr1	16623838	16624244	+	0	NA	intron (NR_026752, intron 5 of 6)	intron (NR_026752, intron 5 of 6)	6865	NR_026752	84809	Hs.631865	NR_026752	ENSG00000215908	CROCCP2	CROCCL1	CROCC pseudogene 2	pseudo	0.022167	0.660934	
chunk0178_320_1	chr7	38240979	38241661	+	0	NA	Intergenic	MIR|SINE|MIR	32327	NM_001003799	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.011730	0.383602	
chunk0168_212_1	chr6	85908144	85908672	+	0	NA	Intergenic	L1PA7|LINE|L1	-229675	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.011364	0.491493	
chunk0066_85_1	chr15	29711864	29712413	+	0	NA	intron (NM_175610, intron 22 of 26)	intron (NM_175610, intron 22 of 26)	109410	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.003643	0.350909	
chunk0058_341_1	chr14	28820646	28821278	+	0	NA	Intergenic	Intergenic	48258	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.003165	0.369668	
chunk0134_141_1	chr3	177597928	177598178	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	156132	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.012000	0.398406	
chunk0210_165_1	chrX	77963901	77964385	+	0	NA	intron (NR_104109, intron 1 of 9)	intron (NR_104109, intron 1 of 9)	5495	NM_001029891	441531	Hs.632822	NM_001029891	ENSG00000226784	PGAM4	PGAM-B|PGAM1|PGAM3|dJ1000K24.1	phosphoglycerate mutase family member 4	protein-coding	0.006198	0.296907	
chunk0053_30_1	chr13	26924025	26924607	+	0	NA	Intergenic	Intergenic	-163531	NM_005288	2835	Hs.123034	NM_005288	ENSG00000132975	GPR12	GPCR12|GPCR21|PPP1R84	G protein-coupled receptor 12	protein-coding	0.010309	0.440823	270(AAGAACACTATGTGAT,-,0.00)
chunk0035_72_1	chr11	41781370	41782070	+	0	NA	intron (NR_120584, intron 2 of 5)	intron (NR_120584, intron 2 of 5)	67152	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.002857	0.326676	
chunk0131_371_1	chr3	152055859	152056580	+	0	NA	Intergenic	L2c|LINE|L2	-128044	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.008322	0.360111	
chunk0091_189_1	chr19	8373985	8374782	+	0	NA	TTS (NM_001039667)	TTS (NM_001039667)	10256	NM_139314	51129	Hs.9613	NM_016109	ENSG00000167772	ANGPTL4	ARP4|FIAF|HARP|HFARP|NL2|PGAR|TGQTL|UNQ171|pp1158	angiopoietin like 4	protein-coding	0.025094	0.532581	379(CAGAACACTTTGTTCT,-,0.00),380(AGAACACTTTGTTCTT,+,0.00)
chunk0068_229_1	chr15	55348273	55348603	+	0	NA	intron (NM_004855, intron 9 of 11)	MSTB1|LTR|ERVL-MaLR	24596	NR_030358	693213		NR_030358	ENSG00000283891	MIR628	MIRN628|hsa-mir-628|mir-628	microRNA 628	ncRNA	0.015152	0.465257	82(GAGAACAAACTGTATC,-,0.00),83(AGAACAAACTGTATCT,+,0.00)
chunk0112_262_1	chr20	42561434	42561855	+	0	NA	intron (NM_133170, intron 7 of 31)	intron (NM_133170, intron 7 of 31)	-123839	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.004751	0.473934	145(TGGAACTGTGTGTACT,-,0.00),146(GGAACTGTGTGTACTG,+,0.00)
chunk0024_146_1	chr10	35216580	35217042	+	0	NA	Intergenic	Intergenic	20909	NR_051972									0.008658	0.447084	211(GGGAACACCCAGACCT,-,0.00),212(GGAACACCCAGACCTT,+,0.00)
chunk0171_409_1	chr6	131286496	131286971	+	0	NA	Intergenic	AluJr|SINE|Alu	36574	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.004211	0.422269	
chunk0147_445_1	chr4	187767586	187767785	+	0	NA	Intergenic	MER34B|LTR|ERV1	-95044	NR_110436	100506272	Hs.508163	NR_110436	ENSG00000250590	LINC02492	-	long intergenic non-protein coding RNA 2492	ncRNA	0.000000	0.420000	
chunk0027_358_1	chr10	78973460	78973696	+	0	NA	intron (NR_015429, intron 3 of 7)	CpG	93870	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.076271	0.738397	
chunk0197_257_1	chr8	123460962	123461176	+	0	NA	Intergenic	Intergenic	44344	NM_001283024	55093	Hs.18029	NM_018024	ENSG00000156795	WDYHV1	C8orf32	WDYHV motif containing 1	protein-coding	0.009346	0.497674	
chunk0044_258_1	chr12	32176357	32177077	+	0	NA	intron (NM_001003398, intron 1 of 8)	L1ME2|LINE|L1	69466	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.008333	0.335645	
chunk0083_43_1	chr17	63503156	63503848	+	0	NA	Intergenic	LTR24C|LTR|ERV1	18685	NM_001178057	1636	Hs.298469	NM_000789	ENSG00000159640	ACE	ACE1|CD143|DCP|DCP1	angiotensin I converting enzyme	protein-coding	0.014451	0.388167	350(CAGAACACTGTGTGCA,-,0.00),351(AGAACACTGTGTGCAA,+,0.00)
chunk0136_32_1	chr4	887389	887803	+	0	NA	intron (NM_001286833, intron 8 of 24)	(GCACAC)n|Simple_repeat|Simple_repeat	44790	NM_005255	2580	Hs.369607	NM_005255	ENSG00000178950	GAK	DNAJ26|DNAJC26	cyclin G associated kinase	protein-coding	0.062802	0.556627	
chunk0003_448_1	chr1	41432317	41432825	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	52112	NM_001956	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.031496	0.565815	376(AAGCTCAGTCTGTTCT,-,0.00),377(AGCTCAGTCTGTTCTT,+,0.00)
chunk0191_268_1	chr8	53589600	53590096	+	0	NA	Intergenic	Intergenic	253194	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.014113	0.434608	
chunk0198_460_1	chr8	144444882	144445164	+	0	NA	promoter-TSS (NM_013432)	promoter-TSS (NM_013432)	-594	NM_013432	4796	Hs.675285	NM_013432	ENSG00000160949	TONSL	IKBR|NFKBIL2	tonsoku like, DNA repair protein	protein-coding	0.067376	0.547703	
chunk0022_129_1	chr10	11687716	11688105	+	0	NA	Intergenic	Intergenic	-54447	NM_024693	79746	Hs.22242	NM_024693	ENSG00000134463	ECHDC3	-	enoyl-CoA hydratase domain containing 3	protein-coding	0.015424	0.546154	
chunk0175_245_1	chr7	7023094	7023415	+	0	NA	Intergenic	L1PA11|LINE|L1	43791	NR_037454	100500886		NR_037454	ENSG00000266287	MIR3683	-	microRNA 3683	ncRNA	0.015576	0.397516	
chunk0149_185_1	chr5	21205716	21206059	+	0	NA	Intergenic	(AAAC)n|Simple_repeat|Simple_repeat	-253593	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.017493	0.334302	
chunk0087_95_1	chr18	32406253	32406684	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	64016	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.013921	0.381944	
chunk0094_231_1	chr2	6959204	6959619	+	0	NA	intron (NM_014746, intron 2 of 8)	intron (NM_014746, intron 2 of 8)	-40729	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.014458	0.468750	
chunk0190_113_1	chr8	30476222	30476510	+	0	NA	intron (NM_006867, intron 2 of 9)	intron (NM_006867, intron 2 of 9)	-90965	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.000000	0.411765	
chunk0080_186_1	chr17	28937123	28937659	+	0	NA	intron (NM_001033561, intron 2 of 14)	intron (NM_001033561, intron 2 of 14)	11116	NR_110803	101927018	Hs.665702	NR_110803	ENSG00000265845	LOC101927018	-	uncharacterized LOC101927018	ncRNA	0.007463	0.404097	
chunk0203_38_1	chr9	83056215	83056633	+	0	NA	intron (NM_152573, intron 1 of 16)	intron (NM_152573, intron 1 of 16)	6704	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002392	0.372315	
chunk0047_175_1	chr12	70553364	70554050	+	0	NA	intron (NM_001109754, intron 20 of 33)	intron (NM_001109754, intron 20 of 33)	56137	NM_001206971	5787	Hs.201030	NM_002837	ENSG00000127329	PTPRB	HPTP-BETA|HPTPB|PTPB|R-PTP-BETA|VEPTP	protein tyrosine phosphatase receptor type B	protein-coding	0.004373	0.406114	
chunk0185_317_1	chr7	131443581	131443797	+	0	NA	exon (NM_013255, exon 11 of 18)	exon (NM_013255, exon 11 of 18)	112928	NM_001018111	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.018519	0.396313	
chunk0025_254_1	chr10	54866691	54867532	+	0	NA	Intergenic	Intergenic	-65820	NM_001142773	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.002378	0.330166	
chunk0127_130_1	chr3	94026538	94027213	+	0	NA	intron (NM_001001850, intron 1 of 1)	intron (NM_001001850, intron 1 of 1)	1735	NM_001001850	415117	Hs.679768	NM_001001850	ENSG00000178750	STX19	-	syntaxin 19	protein-coding	0.002963	0.289941	364(TTGGACAACTTGTTCT,-,0.00),365(TGGACAACTTGTTCTG,+,0.00)
chunk0179_253_1	chr7	48505609	48506070	+	0	NA	intron (NM_152701, intron 48 of 61)	intron (NM_152701, intron 48 of 61)	334379	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.008677	0.363636	
chunk0025_409_1	chr10	59649911	59650377	+	0	NA	TTS (NM_194298)	TTS (NM_194298)	59747	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.006438	0.400428	
chunk0049_40_1	chr12	89828912	89829379	+	0	NA	Intergenic	L2|LINE|L2	120190	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.017131	0.356838	
chunk0207_46_1	chrX	7065419	7065953	+	0	NA	intron (NM_001178135, intron 3 of 3)	intron (NM_001178135, intron 3 of 3)	-82174	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.016854	0.452336	268(AGGTACAACATGTCCA,-,0.00),269(GGTACAACATGTCCAG,+,0.00)
chunk0119_261_1	chr22	45833876	45834774	+	0	NA	intron (NM_001167621, intron 9 of 10)	intron (NM_001167621, intron 9 of 10)	73801	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.013363	0.474972	185(TGGCACATCCTGTGTC,-,0.00),186(GGCACATCCTGTGTCC,+,0.00)
chunk0053_286_1	chr13	33451990	33452455	+	0	NA	intron (NM_001243476, intron 4 of 17)	intron (NM_001243476, intron 4 of 17)	-166458	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.006452	0.502146	283(AGGAACTCTCAGTTCT,-,0.00),284(GGAACTCTCAGTTCTC,+,0.00)
chunk0165_215_1	chr6	35063575	35063998	+	0	NA	intron (NM_015245, intron 13 of 23)	intron (NM_015245, intron 13 of 23)	77624	NM_001093728									0.016548	0.495283	
chunk0017_224_1	chr1	208036600	208036914	+	0	NA	intron (NM_025179, intron 26 of 31)	intron (NM_025179, intron 26 of 31)	-125419	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.006369	0.438095	
chunk0043_75_1	chr12	14418432	14418777	+	0	NA	intron (NM_181352, intron 1 of 14)	intron (NM_181352, intron 1 of 14)	33540	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.008696	0.343931	
chunk0198_110_1	chr8	131618149	131618893	+	0	NA	Intergenic	L1MC3|LINE|L1	-285588	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.002688	0.300671	
chunk0171_382_1	chr6	131082333	131082718	+	0	NA	Intergenic	Intergenic	-19203	NM_001199388	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.002597	0.316062	
chunk0088_272_1	chr18	49273370	49273822	+	0	NA	intron (NM_017653, intron 10 of 16)	Tigger3a|DNA|TcMar-Tigger	187113	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.008850	0.348786	
chunk0122_462_1	chr3	39978292	39978655	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	-121538	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.005510	0.445055	247(GTGGACTTTATGTTCC,-,0.00)
chunk0028_385_1	chr10	92903372	92904490	+	0	NA	intron (NM_019053, intron 5 of 21)	L1MC2|LINE|L1	55463	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.002683	0.340483	
chunk0086_59_1	chr18	13013817	13014601	+	0	NA	intron (NM_032142, intron 5 of 44)	intron (NM_032142, intron 5 of 44)	22847	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.006378	0.374522	636(GAGTACACAGTGTTCT,-,0.00),637(AGTACACAGTGTTCTC,+,0.00)
chunk0046_186_1	chr12	58781575	58782046	+	0	NA	promoter-TSS (NR_120452)	promoter-TSS (NR_120452)	-94	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.012739	0.449153	208(TAGGACATCCTGTTCT,-,0.00),209(AGGACATCCTGTTCTA,+,0.00)
chunk0199_399_1	chr9	13397424	13397623	+	0	NA	Intergenic	Intergenic	33806	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.005025	0.305000	
chunk0110_334_1	chr20	19130050	19130676	+	0	NA	Intergenic	Intergenic	-82283	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.007987	0.505582	
chunk0116_138_1	chr21	36245934	36246606	+	0	NA	exon (NM_005128, exon 19 of 37)	exon (NM_005128, exon 19 of 37)	-73919	NM_015358	23515	Hs.421150	NM_015358	ENSG00000159256	MORC3	NXP2|ZCW5|ZCWCC3	MORC family CW-type zinc finger 3	protein-coding	0.046131	0.598811	
chunk0066_23_1	chr15	27510109	27510439	+	0	NA	intron (NM_033223, intron 6 of 9)	L1MCa|LINE|L1	-348955	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.006061	0.474320	
chunk0093_135_1	chr19	46213008	46213426	+	0	NA	intron (NR_027003, intron 4 of 5)	intron (NR_027003, intron 4 of 5)	2975	NR_027003	93429	Hs.569940	NR_027003	ENSG00000268460	LOC93429	-	uncharacterized LOC93429	ncRNA	0.011962	0.534606	
chunk0212_175_1	chrX	132654419	132655256	+	0	NA	intron (NM_147175, intron 3 of 3)	intron (NM_147175, intron 3 of 3)	-12805	NR_046691	100874102	Hs.619341	NR_046691	ENSG00000235849	HS6ST2-AS1	-	HS6ST2 antisense RNA 1	ncRNA	0.003584	0.393795	
chunk0051_281_1	chr12	118227637	118228311	+	0	NA	intron (NM_016281, intron 9 of 20)	L1ME3Cz|LINE|L1	92090	NM_002567	5037	Hs.433863	NM_002567	ENSG00000089220	PEBP1	HCNP|HCNPpp|HEL-210|HEL-S-34|HEL-S-96|PBP|PEBP|PEBP-1|RKIP	phosphatidylethanolamine binding protein 1	protein-coding	0.004451	0.370370	
chunk0088_334_1	chr18	51095972	51096326	+	0	NA	Intergenic	L1PA7|LINE|L1	65936	NM_005359	4089	Hs.75862	NM_005359	ENSG00000141646	SMAD4	DPC4|JIP|MADH4|MYHRS	SMAD family member 4	protein-coding	0.019774	0.397183	
chunk0038_297_1	chr11	90414262	90414914	+	0	NA	intron (NR_104190, intron 1 of 6)	intron (NR_104190, intron 1 of 6)	141269	NR_039711	100616186		NR_039711	ENSG00000266703	MIR4490	-	microRNA 4490	ncRNA	0.003067	0.367534	17(AAGTACAGATTGTTCA,-,0.00),18(AGTACAGATTGTTCAG,+,0.00),385(AGGTACATTTAGTTCT,-,0.00),386(GGTACATTTAGTTCTG,+,0.00)
chunk0124_117_1	chr3	54132206	54132510	+	0	NA	intron (NM_018398, intron 2 of 37)	intron (NM_018398, intron 2 of 37)	9692	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.019737	0.403279	
chunk0102_201_1	chr2	147996671	147996921	+	0	NA	intron (NM_001190879, intron 1 of 14)	L1MC2|LINE|L1	23941	NM_001190882	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.000000	0.354582	
chunk0027_196_1	chr10	75733148	75733775	+	0	NA	intron (NR_132791, intron 1 of 2)	intron (NR_132791, intron 1 of 2)	21006	NR_132791	105378367	Hs.464836	NR_132791		LOC105378367	-	uncharacterized LOC105378367	ncRNA	0.003190	0.437898	
chunk0133_80_1	chr3	167252944	167253497	+	0	NA	intron (NM_001199202, intron 19 of 20)	intron (NM_001199202, intron 19 of 20)	127063	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.001808	0.339350	
chunk0032_62_1	chr11	2156710	2157158	+	0	NA	intron (NM_001042376, intron 2 of 4)	intron (NM_001042376, intron 2 of 4)	4275	NM_000207	3630	Hs.272259	NM_000207	ENSG00000254647	INS	IDDM|IDDM1|IDDM2|ILPR|IRDN|MODY10	insulin	protein-coding	0.026786	0.612472	89(AAACACTGCCTGTCCT,-,0.00)
chunk0045_433_1	chr12	53501307	53501622	+	0	NA	promoter-TSS (NM_134324)	promoter-TSS (NM_134324)	-129	NM_134324	6895	Hs.326	NM_004178	ENSG00000139546	TARBP2	LOQS|TRBP|TRBP1|TRBP2	TARBP2 subunit of RISC loading complex	protein-coding	0.098413	0.705696	
chunk0065_366_1	chr14	103962938	103963285	+	0	NA	exon (NM_153046, exon 3 of 36)	exon (NM_153046, exon 3 of 36)	-20803	NM_001257268	647286	Hs.632325	NM_001257268	ENSG00000227729	RD3L	TDRD9-AS1|TDRD9AS1	retinal degeneration 3 like	protein-coding	0.002882	0.359195	
chunk0138_339_1	chr4	41611225	41611502	+	0	NA	intron (NM_001112717, intron 6 of 25)	Tigger3a|DNA|TcMar-Tigger	-1409	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.384892	
chunk0065_377_1	chr14	104082759	104083192	+	0	NA	Intergenic	L2a|LINE|L2	-2711	NM_001080464	374569	Hs.146239	NM_001080464	ENSG00000166183	ASPG	C14orf76|GPA/WT|LYSOLP	asparaginase	protein-coding	0.027714	0.589862	
chunk0083_60_1	chr17	63784051	63784284	+	0	NA	intron (NM_007372, intron 2 of 18)	intron (NM_007372, intron 2 of 18)	9978	NM_007372	11325	Hs.702010	NM_007372	ENSG00000198231	DDX42	DDX42P|RHELP|RNAHP|SF3B8|SF3b125	DEAD-box helicase 42	protein-coding	0.004292	0.320513	
chunk0107_151_1	chr2	215166705	215166940	+	0	NA	Intergenic	L1PB1|LINE|L1	-28394	NM_173076	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.008511	0.351695	
chunk0054_139_1	chr13	43682019	43682618	+	0	NA	intron (NM_017993, intron 1 of 16)	UCON27|Unknown|Unknown	-52841	NM_001127615	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.003339	0.358333	
chunk0039_103_1	chr11	97498119	97498380	+	0	NA	Intergenic	L1M4b|LINE|L1	-991372	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.003831	0.366412	
chunk0011_65_1	chr1	143275387	143275983	+	0	NA	Intergenic	Intergenic	146907	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.053691	0.366834	
chunk0025_382_1	chr10	59245703	59246317	+	0	NA	TTS (NM_001143773)	TTS (NM_001143773)	68543	NM_001143774	84457	Hs.499704	NM_032439	ENSG00000165443	PHYHIPL	-	phytanoyl-CoA 2-hydroxylase interacting protein like	protein-coding	0.003257	0.305691	
chunk0058_404_1	chr13	111658464	111659178	+	0	NA	Intergenic	Intergenic	-234557	NR_046992	101928616	Hs.528450	NR_046992		LINC00354	-	long intergenic non-protein coding RNA 354	ncRNA	0.011204	0.450350	
chunk0015_328_1	chr1	189615892	189616358	+	0	NA	Intergenic	L1MEd|LINE|L1	861504	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.336188	
chunk0114_267_1	chr21	16211920	16212206	+	0	NA	intron (NR_027791, intron 1 of 5)	intron (NR_027791, intron 1 of 5)	17684	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.006993	0.390244	
chunk0048_311_1	chr12	82975968	82976286	+	0	NA	intron (NM_152588, intron 7 of 11)	intron (NM_152588, intron 7 of 11)	288972	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.009434	0.351097	
chunk0114_276_1	chr21	16318765	16319356	+	0	NA	intron (NR_027790, intron 4 of 7)	L2a|LINE|L2	124681	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.003384	0.427365	
chunk0182_82_1	chr7	92636010	92636236	+	0	NA	intron (NM_001145306, intron 5 of 7)	AluJo|SINE|Alu	-45729	NR_109929	257415	Hs.18564	NM_152789	ENSG00000234545	FAM133B	-	family with sequence similarity 133 member B	protein-coding	0.004425	0.405286	
chunk0058_259_1	chr14	25884116	25884367	+	0	NA	Intergenic	L2b|LINE|L2	713513	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.003984	0.357143	
chunk0003_380_1	chr1	39750908	39751517	+	0	NA	intron (NM_006112, intron 8 of 9)	MER20B|DNA|hAT-Charlie	12367	NM_001195007	10450	Hs.524690	NM_006112	ENSG00000084072	PPIE	CYP-33|CYP33	peptidylprolyl isomerase E	protein-coding	0.013136	0.391803	
chunk0056_82_1	chr13	79791432	79791631	+	0	NA	Intergenic	L1MA8|LINE|L1	-12855	NR_125785	102724076	Hs.208617	NR_125785	ENSG00000229011	LINC01038	-	long intergenic non-protein coding RNA 1038	ncRNA	0.000000	0.555000	
chunk0133_245_1	chr3	171569421	171569818	+	0	NA	Intergenic	Intergenic	-109211	NM_001161563	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.002519	0.391960	
chunk0008_257_1	chr1	94534541	94535228	+	0	NA	intron (NM_001178096, intron 3 of 4)	intron (NM_001178096, intron 3 of 4)	6973	NM_001993	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.010189	0.454942	
chunk0029_150_1	chr10	99395617	99396280	+	0	NA	TTS (NM_002079)	TTS (NM_002079)	34825	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.007541	0.459337	
chunk0085_275_1	chr18	7797543	7797879	+	0	NA	intron (NM_001105244, intron 2 of 32)	intron (NM_001105244, intron 2 of 32)	230395	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.002976	0.459941	179(TGGAACATCGAGTTCC,-,0.00),180(GGAACATCGAGTTCCT,+,0.00)
chunk0015_454_1	chr1	192496104	192496947	+	0	NA	Intergenic	L1M5|LINE|L1	-79202	NM_002922	5996	Hs.75256	NM_002922	ENSG00000090104	RGS1	1R20|BL34|HEL-S-87|IER1|IR20	regulator of G protein signaling 1	protein-coding	0.002372	0.287915	385(AAGAACAAATAGTTCT,-,0.00),386(AGAACAAATAGTTCTT,+,0.00),443(AAGAACAAATAGTCCT,-,0.00),444(AGAACAAATAGTCCTC,+,0.00)
chunk0143_90_1	chr4	108328019	108328705	+	0	NA	Intergenic	Intergenic	156242	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.005831	0.395924	
chunk0004_137_1	chr1	44800113	44800379	+	0	NA	promoter-TSS (NM_004073)	promoter-TSS (NM_004073)	21	NM_004073	1263	Hs.632415	NM_004073	ENSG00000173846	PLK3	CNK|FNK|PLK-3|PRK	polo like kinase 3	protein-coding	0.078947	0.696629	
chunk0136_115_1	chr4	3387740	3388127	+	0	NA	intron (NM_198227, intron 2 of 15)	intron (NM_198227, intron 2 of 15)	17936	NM_198227	6002	Hs.527061	NM_002926	ENSG00000159788	RGS12	-	regulator of G protein signaling 12	protein-coding	0.015504	0.479381	
chunk0106_189_1	chr2	201440186	201440600	+	0	NA	intron (NM_015049, intron 1 of 15)	intron (NM_015049, intron 1 of 15)	11203	NM_015049	66008	Hs.152774	NM_015049	ENSG00000115993	TRAK2	ALS2CR3|CALS-C|GRIF-1|GRIF1|MILT2|OIP98	trafficking kinesin protein 2	protein-coding	0.002415	0.431325	365(GAACACACTCTGTCCT,-,0.00),366(AACACACTCTGTCCTT,+,0.00)
chunk0113_159_1	chr20	52801270	52801990	+	0	NA	Intergenic	Intergenic	-170777	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.012500	0.446602	
chunk0133_367_1	chr3	173680643	173681116	+	0	NA	intron (NM_014932, intron 3 of 6)	intron (NM_014932, intron 3 of 6)	239917	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004228	0.335443	174(CAGAACAGAACGTTCT,-,0.00),175(AGAACAGAACGTTCTG,+,0.00)
chunk0082_187_1	chr17	56471272	56471471	+	0	NA	intron (NM_153228, intron 14 of 16)	intron (NM_153228, intron 14 of 16)	-122328	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.005025	0.450000	
chunk0181_109_1	chr7	80630806	80631229	+	0	NA	intron (NM_001289911, intron 1 of 11)	intron (NM_001289911, intron 1 of 11)	-7499	NM_001001548	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.011820	0.393868	
chunk0133_376_1	chr3	173838307	173838603	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	82341	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.006757	0.319865	
chunk0062_323_1	chr14	73358787	73359288	+	0	NA	intron (NM_001005743, intron 3 of 12)	L3|LINE|CR1	99543	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.007984	0.386454	
chunk0199_77_1	chr9	2463533	2464273	+	0	NA	Intergenic	Intergenic	-157890	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.004054	0.345479	376(CAGGACAAGGTGTTCT,-,0.00),377(AGGACAAGGTGTTCTT,+,0.00),511(CAGAACAACATGTCTT,-,0.00),512(AGAACAACATGTCTTT,+,0.00)
chunk0085_346_1	chr18	8827157	8827682	+	0	NA	intron (NM_015210, intron 15 of 16)	MADE2|DNA|TcMar-Mariner	110048	NM_015210	23255	Hs.707920	NM_015210	ENSG00000168502	MTCL1	CCDC165|KIAA0802|SOGA2	microtubule crosslinking factor 1	protein-coding	0.015238	0.513308	
chunk0099_237_1	chr2	96786887	96787086	+	0	NA	intron (NM_020184, intron 1 of 6)	intron (NM_020184, intron 1 of 6)	-11292	NR_036074	100422928		NR_036074	ENSG00000264157	MIR3127	mir-3127	microRNA 3127	ncRNA	0.005025	0.345000	
chunk0049_63_1	chr12	90133257	90133681	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	424514	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.000000	0.376471	
chunk0206_143_1	chr9	121201280	121201530	+	0	NA	intron (NM_016322, intron 1 of 7)	CpG	682	NM_016322	51552	Hs.371563	NM_016322	ENSG00000119396	RAB14	FBP|RAB-14	RAB14, member RAS oncogene family	protein-coding	0.128000	0.788845	
chunk0109_202_1	chr20	5143280	5143522	+	0	NA	intron (NM_003818, intron 1 of 12)	L1M5|LINE|L1	16640	NM_003818	8760	Hs.126857	NM_003818	ENSG00000101290	CDS2	-	CDP-diacylglycerol synthase 2	protein-coding	0.004132	0.395062	
chunk0189_93_1	chr8	21583813	21584123	+	0	NA	Intergenic	Intergenic	204866	NM_001165038	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.019355	0.472669	129(CAGTGCACAATGTTCT,-,0.00),130(AGTGCACAATGTTCTT,+,0.00)
chunk0140_353_1	chr4	74101928	74102402	+	0	NA	Intergenic	Intergenic	-2885	NM_002089	2920	Hs.75765	NM_002089	ENSG00000081041	CXCL2	CINC-2a|GRO2|GROb|MGSA-b|MIP-2a|MIP2|MIP2A|SCYB2	C-X-C motif chemokine ligand 2	protein-coding	0.006329	0.393684	
chunk0156_187_1	chr5	107873613	107874227	+	0	NA	intron (NM_001163315, intron 8 of 8)	intron (NM_001163315, intron 8 of 8)	-203025	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004886	0.398374	
chunk0201_201_1	chr9	36802016	36802646	+	0	NA	Intergenic	Intergenic	21268	NR_039686	100616289		NR_039686	ENSG00000266255	MIR4475	-	microRNA 4475	ncRNA	0.022222	0.515055	
chunk0109_181_1	chr20	4691688	4692229	+	0	NA	intron (NM_001080123, intron 1 of 1)	L1M2|LINE|L1	5447	NM_001080123	5621	Hs.472010	NM_000311	ENSG00000171867	PRNP	ASCR|AltPrP|CD230|CJD|GSS|KURU|PRIP|PrP|PrP27-30|PrP33-35C|PrPc|p27-30	prion protein	protein-coding	0.003697	0.348708	
chunk0050_205_1	chr12	104213858	104214388	+	0	NA	Intergenic	Intergenic	-1656	NM_001093771	7296	Hs.654922	NM_003330	ENSG00000198431	TXNRD1	GRIM-12|TR|TR1|TRXR1|TXNR	thioredoxin reductase 1	protein-coding	0.011321	0.433145	
chunk0197_315_1	chr8	124848412	124848786	+	0	NA	Intergenic	Intergenic	-26541	NR_039809	100616255		NR_039809	ENSG00000263735	MIR4662B	-	microRNA 4662b	ncRNA	0.016043	0.501333	143(CAGTACACTTTGTACT,-,0.00),144(AGTACACTTTGTACTT,+,0.00)
chunk0136_61_1	chr4	1712472	1712721	+	0	NA	5' UTR (NM_006527, exon 1 of 8)	5' UTR (NM_006527, exon 1 of 8)	145	NM_001306074	7884	Hs.298345	NM_006527	ENSG00000163950	SLBP	HBP	stem-loop binding protein	protein-coding	0.148594	0.744000	
chunk0040_373_1	chr11	119102170	119102560	+	0	NA	promoter-TSS (NM_001382)	promoter-TSS (NM_001382)	-290	NM_001382	1798	Hs.524081	NM_001382	ENSG00000172269	DPAGT1	ALG7|CDG-Ij|CDG1J|CMS13|CMSTA2|D11S366|DGPT|DPAGT|DPAGT2|G1PT|GPT|UAGT|UGAT	dolichyl-phosphate N-acetylglucosaminephosphotransferase 1	protein-coding	0.041026	0.529412	
chunk0201_182_1	chr9	36282250	36282693	+	0	NA	Intergenic	LTR75|LTR|ERVL	-5415	NM_001128227	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.015801	0.461712	
chunk0143_399_1	chr4	123265288	123265910	+	0	NA	intron (NM_145207, intron 15 of 15)	intron (NM_145207, intron 15 of 15)	-131196	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.003215	0.349920	259(CAGAACACCTTGTGCT,-,0.00),260(AGAACACCTTGTGCTG,+,0.00)
chunk0180_136_1	chr7	56074550	56074749	+	0	NA	exon (NM_001130069, exon 5 of 8)	exon (NM_001130069, exon 5 of 8)	10425	NM_001130069	25870	Hs.279696	NM_015411	ENSG00000129103	SUMF2	pFGE	sulfatase modifying factor 2	protein-coding	0.050251	0.600000	
chunk0189_243_1	chr8	24909648	24909917	+	0	NA	Intergenic	Intergenic	-3979	NM_005382	4741	Hs.458657	NM_005382	ENSG00000104722	NEFM	NEF3|NF-M|NFM	neurofilament medium	protein-coding	0.000000	0.322222	137(AGGAACACTGTGGTCT,-,0.00),138(GGAACACTGTGGTCTA,+,0.00)
chunk0110_193_1	chr20	14775662	14776263	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	153556	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.004992	0.418605	
chunk0099_75_1	chr2	85285465	85285714	+	0	NA	intron (NM_031283, intron 4 of 11)	intron (NM_031283, intron 4 of 11)	42707	NM_001206844	10618	Hs.593382	NM_006464	ENSG00000152291	TGOLN2	TGN38|TGN46|TGN48|TGN51|TTGN2	trans-golgi network protein 2	protein-coding	0.032129	0.616000	
chunk0153_236_1	chr5	72267281	72267820	+	0	NA	intron (NM_001286748, intron 4 of 11)	intron (NM_001286748, intron 4 of 11)	52707	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.000000	0.296296	
chunk0098_304_1	chr2	76287349	76288035	+	0	NA	Intergenic	LTR78B|LTR|ERV1	-576707	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.004373	0.379913	
chunk0083_105_1	chr17	64620721	64621303	+	0	NA	intron (NM_022739, intron 1 of 18)	intron (NM_022739, intron 1 of 18)	41256	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.005155	0.351630	
chunk0027_180_1	chr10	75155951	75156614	+	0	NA	intron (NM_001174156, intron 2 of 5)	intron (NM_001174156, intron 2 of 5)	44647	NM_001174156	142891	Hs.744986	NM_144660	ENSG00000156671	SAMD8	HEL-177|SMSr	sterile alpha motif domain containing 8	protein-coding	0.009050	0.447289	
chunk0033_356_1	chr11	23013609	23014189	+	0	NA	Intergenic	Intergenic	-153473	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.012069	0.382100	
chunk0038_402_1	chr11	93744793	93745558	+	0	NA	intron (NM_001286067, intron 2 of 9)	LTR5B|LTR|ERVK	3581	NM_014039	28970	Hs.8360	NM_014039	ENSG00000182919	C11orf54	PTD012|PTOD012	chromosome 11 open reading frame 54	protein-coding	0.018301	0.480418	365(GGAGACATTCTGTTCC,-,0.00),366(GAGACATTCTGTTCCC,+,0.00)
chunk0008_12_1	chr1	87372514	87372921	+	0	NA	Intergenic	Intergenic	-1062	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.002457	0.416667	
chunk0013_179_1	chr1	168926354	168926614	+	0	NA	intron (NR_104091, intron 3 of 4)	MER119|DNA|hAT-Charlie	139543	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.003846	0.371648	
chunk0169_263_1	chr6	105461539	105462151	+	0	NA	Intergenic	L1MD1|LINE|L1	-58721	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.006536	0.360522	
chunk0088_193_1	chr18	47584254	47585080	+	0	NA	Intergenic	Intergenic	204171	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.009685	0.470375	350(GGGAACTCTGTGTTCC,-,0.00),351(GGAACTCTGTGTTCCT,+,0.00)
chunk0129_170_1	chr3	120796090	120796333	+	0	NA	Intergenic	Intergenic	53500	NM_005513	2960	Hs.445272	NM_005513	ENSG00000153767	GTF2E1	FE|TF2E1|TFIIE-A	general transcription factor IIE subunit 1	protein-coding	0.000000	0.352459	
chunk0185_255_1	chr7	130204942	130205262	+	0	NA	intron (NM_032842, intron 1 of 14)	intron (NM_032842, intron 1 of 14)	396	NM_032842	84928	Hs.267245	NM_032842	ENSG00000146842	TMEM209	NET31	transmembrane protein 209	protein-coding	0.043750	0.523364	
chunk0108_277_1	chr2	234579332	234579920	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-82573	NM_001282431	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.013605	0.550085	212(CAGGACTGTTTGTCCT,-,0.00),213(AGGACTGTTTGTCCTG,+,0.00)
chunk0008_73_1	chr1	89872056	89872450	+	0	NA	intron (NM_001134479, intron 2 of 2)	intron (NM_001134479, intron 2 of 2)	50332	NM_018103	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.020305	0.432911	217(TGGAACATAGCGTTCT,-,0.00),218(GGAACATAGCGTTCTG,+,0.00)
chunk0108_266_1	chr2	234243849	234244435	+	0	NA	Intergenic	MER51B|LTR|ERV1	193440	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.003413	0.391823	
chunk0177_31_1	chr7	20729232	20729531	+	0	NA	intron (NM_001163941, intron 23 of 27)	MARNA|DNA|TcMar-Mariner	57508	NM_182700	221833	Hs.195922	NM_182700	ENSG00000164651	SP8	BTD	Sp8 transcription factor	protein-coding	0.000000	0.393333	
chunk0076_307_1	chr16	70325089	70325288	+	0	NA	intron (NM_001014449, intron 4 of 9)	intron (NM_001014449, intron 4 of 9)	21559	NR_039997	100506083	Hs.635008	NR_039997	ENSG00000261777	LOC100506083	-	uncharacterized LOC100506083	ncRNA	0.010050	0.405000	
chunk0031_249_1	chr10	127115654	127116251	+	0	NA	intron (NM_001290223, intron 25 of 51)	intron (NM_001290223, intron 25 of 51)	80206	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.000000	0.411371	
chunk0116_370_1	chr21	41964958	41965186	+	0	NA	Intergenic	Intergenic	-11182	NM_015500	25966	Hs.473894	NM_015500	ENSG00000157617	C2CD2	C21orf25|C21orf258|TMEM24L	C2 calcium dependent domain containing 2	protein-coding	0.021930	0.423581	
chunk0014_256_1	chr1	180126710	180127157	+	0	NA	Intergenic	MIR|SINE|MIR	-27900	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.024609	0.477679	
chunk0158_279_1	chr5	131630569	131631128	+	0	NA	intron (NM_016340, intron 1 of 27)	intron (NM_016340, intron 1 of 27)	4388	NM_001164386	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.010733	0.389286	515(TGGTACTCACTGTCCT,-,0.00),516(GGTACTCACTGTCCTT,+,0.00)
chunk0148_188_1	chr5	8060945	8061440	+	0	NA	Intergenic	Intergenic	192088	NM_002454	4552	Hs.481551	NM_002454	ENSG00000124275	MTRR	MSR|cblE	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding	0.016162	0.483871	
chunk0046_190_1	chr12	58827241	58827532	+	0	NA	Intergenic	L1MA4A|LINE|L1	-45670	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.003436	0.352740	
chunk0018_136_1	chr1	218620906	218621489	+	0	NA	intron (NR_031644, intron 3 of 6)	intron (NR_031644, intron 3 of 6)	178571	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.003431	0.409247	
chunk0205_417_1	chr9	114986202	114986516	+	0	NA	Intergenic	MIRb|SINE|MIR	-55764	NM_001252290	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.006369	0.374603	
chunk0111_67_1	chr20	23000498	23000758	+	0	NA	Intergenic	Intergenic	-34792	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.007692	0.452107	
chunk0183_48_1	chr7	103944156	103944637	+	0	NA	intron (NM_005045, intron 1 of 64)	intron (NM_005045, intron 1 of 64)	45120	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.008316	0.414938	
chunk0102_182_1	chr2	147560652	147561353	+	0	NA	Intergenic	Intergenic	-283515	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.005706	0.341880	
chunk0181_244_1	chr7	85341285	85341484	+	0	NA	Intergenic	Tigger14a|DNA|TcMar-Tigger	-219453	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.330000	
chunk0208_54_1	chrX	11470179	11470536	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-42572	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.002801	0.388268	
chunk0128_71_1	chr3	105154676	105155071	+	0	NA	Intergenic	Intergenic	-211840	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.323232	
chunk0069_305_1	chr15	65555934	65556154	+	0	NA	intron (NM_016395, intron 3 of 10)	intron (NM_016395, intron 3 of 10)	25555	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.004545	0.479638	96(AAGGACATTATGTCCT,-,0.00),97(AGGACATTATGTCCTT,+,0.00)
chunk0035_405_1	chr11	56737085	56737388	+	0	NA	Intergenic	Intergenic	6575	NM_001005284	283189	Hs.554521	NM_001005284	ENSG00000172457	OR9G4	OR11-216	olfactory receptor family 9 subfamily G member 4	protein-coding	0.003300	0.361842	
chunk0206_453_1	chr9	128322126	128322325	+	0	NA	promoter-TSS (NM_016035)	promoter-TSS (NM_016035)	193	NM_015679	26995	Hs.632685	NM_015679	ENSG00000167112	TRUB2	CLONE24922	TruB pseudouridine synthase family member 2	protein-coding	0.045226	0.520000	
chunk0089_207_1	chr18	60674694	60674916	+	0	NA	Intergenic	L1MC4|LINE|L1	-302037	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.009009	0.408072	
chunk0166_313_1	chr6	49695252	49695972	+	0	NA	intron (NM_001142417, intron 9 of 9)	intron (NM_001142417, intron 9 of 9)	17978	NM_001142417	7180	Hs.2042	NM_003296	ENSG00000124490	CRISP2	CRISP-2|CT36|GAPDL5|TPX1|TSP1	cysteine rich secretory protein 2	protein-coding	0.006944	0.296810	617(CGGCACAAGGTGTTCC,-,0.00),618(GGCACAAGGTGTTCCT,+,0.00)
chunk0051_102_1	chr12	114853611	114854020	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-169651	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.012225	0.407317	203(CAGAACTTACTGTACT,-,0.00),204(AGAACTTACTGTACTC,+,0.00)
chunk0048_269_1	chr12	82174927	82175565	+	0	NA	Intergenic	Intergenic	183174	NM_014167	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.006270	0.350548	
chunk0191_139_1	chr8	48786491	48786951	+	0	NA	Intergenic	Intergenic	-51410	NR_024605	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.006522	0.418655	
chunk0050_84_1	chr12	101713249	101713658	+	0	NA	intron (NM_020244, intron 1 of 8)	L1MEc|LINE|L1	15814	NM_020244	56994	Hs.293077	NM_020244	ENSG00000111666	CHPT1	CPT|CPT1	choline phosphotransferase 1	protein-coding	0.012225	0.453659	
chunk0032_125_1	chr11	4196684	4197248	+	0	NA	intron (NR_047550, intron 1 of 1)	MER65D|LTR|ERV1	9814	NR_047550	100506082	Hs.445705	NR_047550	ENSG00000254480	LINC02749	-	long intergenic non-protein coding RNA 2749	ncRNA	0.007092	0.382301	
chunk0135_18_1	chr3	184336857	184337206	+	0	NA	promoter-TSS (NM_144635)	promoter-TSS (NM_144635)	-457	NM_144635	131408	Hs.591307	NM_144635	ENSG00000175182	FAM131A	C3orf40|FLAT715|PRO1378	family with sequence similarity 131 member A	protein-coding	0.017192	0.537143	169(TGGTACTTGATGTTCT,-,0.00),170(GGTACTTGATGTTCTT,+,0.00)
chunk0161_264_1	chr5	172383109	172383814	+	0	NA	intron (NM_001017995, intron 4 of 12)	intron (NM_001017995, intron 4 of 12)	71062	NM_001017995	285590	Hs.285666	NM_001017995	ENSG00000174705	SH3PXD2B	FAD49|FTHS|HOFI|KIAA1295|TKS4|TSK4	SH3 and PX domains 2B	protein-coding	0.011348	0.464589	
chunk0152_81_1	chr5	58116383	58116899	+	0	NA	non-coding (NR_104669, exon 3 of 5)	non-coding (NR_104669, exon 3 of 5)	5700	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.007752	0.400387	209(GGGAACACAGTGTTAT,-,0.00),210(GGAACACAGTGTTATT,+,0.00)
chunk0086_81_1	chr18	13427438	13427822	+	0	NA	promoter-TSS (NR_040031)	promoter-TSS (NR_040031)	-96	NR_040031	100288122	Hs.646264	NR_040031	ENSG00000267690	LDLRAD4-AS1	-	LDLRAD4 antisense RNA 1	ncRNA	0.005208	0.431169	
chunk0188_252_1	chr8	14448925	14449313	+	0	NA	intron (NM_139167, intron 2 of 7)	intron (NM_139167, intron 2 of 7)	404391	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.002577	0.390746	
chunk0212_67_1	chrY	11333097	11333315	+	0	NA	Intergenic	CpG	1088384	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.077982	0.744292	81(TGGGACAGCCTGGGCC,-,0.00),82(GGGACAGCCTGGGCCC,+,0.00)
chunk0032_283_1	chr11	9286238	9286592	+	0	NA	intron (NR_028491, intron 6 of 7)	intron (NR_028491, intron 6 of 7)	-21089	NM_015213	23258	Hs.501857	NM_015213	ENSG00000184014	DENND5A	EIEE49|RAB6IP1	DENN domain containing 5A	protein-coding	0.008475	0.371831	
chunk0143_77_1	chr4	108152926	108153421	+	0	NA	intron (NM_016269, intron 3 of 11)	LTR79|LTR|ERVL	13624	NM_001166119	51176	Hs.743478	NM_016269	ENSG00000138795	LEF1	LEF-1|TCF10|TCF1ALPHA|TCF7L3	lymphoid enhancer binding factor 1	protein-coding	0.002020	0.463710	260(AAGGACAGACTGACCC,-,0.00),261(AGGACAGACTGACCCT,+,0.00)
chunk0029_440_1	chr10	110225955	110226154	+	0	NA	promoter-TSS (NM_005962)	promoter-TSS (NM_005962)	50	NM_005962	4601	Hs.602078	NM_005962	ENSG00000119950	MXI1	MAD2|MXD2|MXI|bHLHc11	MAX interactor 1, dimerization protein	protein-coding	0.185930	0.820000	
chunk0060_437_1	chr14	54474311	54474510	+	0	NA	TTS (NM_004124)	TTS (NM_004124)	14616	NM_004124	2764	Hs.151413	NM_004124	ENSG00000197045	GMFB	GMF	glia maturation factor beta	protein-coding	0.000000	0.340000	
chunk0015_144_1	chr1	186137459	186137750	+	0	NA	exon (NM_031935, exon 88 of 107)	exon (NM_031935, exon 88 of 107)	-158669	NM_005807	10216	Hs.647723	NM_005807	ENSG00000116690	PRG4	CACP|HAPO|JCAP|MSF|SZP	proteoglycan 4	protein-coding	0.006873	0.452055	
chunk0187_425_1	chr7	158631870	158632337	+	0	NA	intron (NR_104054, intron 30 of 30)	L1MEj|LINE|L1	40487	NR_049893	100847032		NR_049893	ENSG00000265598	MIR5707	-	microRNA 5707	ncRNA	0.017131	0.497863	
chunk0093_63_1	chr19	40434066	40434372	+	0	NA	Intergenic	Intergenic	-8194	NM_013376	29950	Hs.269898	NM_013376	ENSG00000197019	SERTAD1	SEI1|TRIP-Br1|TRIPBR1	SERTA domain containing 1	protein-coding	0.062092	0.638436	
chunk0076_86_1	chr16	64640142	64640958	+	0	NA	Intergenic	L1PA8A|LINE|L1	481587	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.000000	0.357405	
chunk0003_396_1	chr1	39902277	39902503	+	0	NA	promoter-TSS (NM_001033081)	promoter-TSS (NM_001033081)	-375	NM_005376	4610	Hs.437922	NM_005376	ENSG00000116990	MYCL	L-Myc|LMYC|MYCL1|bHLHe38	MYCL proto-oncogene, bHLH transcription factor	protein-coding	0.092920	0.709251	
chunk0042_363_1	chr12	10372579	10373117	+	0	NA	3' UTR (NM_001199805, exon 13 of 13)	3' UTR (NM_001199805, exon 13 of 13)	9079	NR_120430	101928100	Hs.638425	NR_120430	ENSG00000245648	LOC101928100	-	uncharacterized LOC101928100	ncRNA	0.003717	0.497217	
chunk0158_360_1	chr5	133828382	133828776	+	0	NA	Intergenic	Intergenic	-85098	NR_131252	105664404	Hs.582536	NR_131252	ENSG00000249073	WSPAR	LncTCF7|TCONS_00009511	WNT signaling pathway activating non-coding RNA	ncRNA	0.015228	0.394937	175(GTAACAGACTGTGCCT,+,0.00)
chunk0149_68_1	chr5	17087088	17087461	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-129549	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.021448	0.500000	234(AGACACAGTATGTCCC,-,0.00),235(GACACAGTATGTCCCT,+,0.00)
chunk0199_287_1	chr9	6604047	6604313	+	0	NA	intron (NM_000170, intron 7 of 24)	intron (NM_000170, intron 7 of 24)	41512	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.030075	0.397004	
chunk0164_39_1	chr6	18434298	18434709	+	0	NA	intron (NM_182757, intron 3 of 7)	intron (NM_182757, intron 3 of 7)	47153	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.017032	0.436893	305(AGGAACTGAGTGTTTT,-,0.00),306(GGAACTGAGTGTTTTT,+,0.00)
chunk0040_81_1	chr11	111402446	111402756	+	0	NA	Intergenic	L2a|LINE|L2	15585	NR_046085	100132078	Hs.672662	NR_046085	ENSG00000255428	LOC100132078	-	uncharacterized LOC100132078	ncRNA	0.006452	0.469453	
chunk0107_304_1	chr2	219126355	219127063	+	0	NA	intron (NM_024782, intron 5 of 7)	L2c|LINE|L2	34156	NM_024782	79840	Hs.225988	NM_024782	ENSG00000187736	NHEJ1	XLF	non-homologous end joining factor 1	protein-coding	0.008475	0.428773	507(GGGAACGGCATGTGCC,-,0.00),508(GGAACGGCATGTGCCA,+,0.00)
chunk0142_84_1	chr4	93906815	93907356	+	0	NA	Intergenic	Intergenic	78158	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.003697	0.321033	
chunk0079_273_1	chr17	16331303	16331683	+	0	NA	Intergenic	Intergenic	22005	NM_181716	201161	Hs.433422	NM_181716	ENSG00000166582	CENPV	3110013H01Rik|CENP-V|PRR6|p30	centromere protein V	protein-coding	0.005263	0.364829	
chunk0134_451_1	chr3	183958096	183958712	+	0	NA	intron (NM_005688, intron 17 of 29)	intron (NM_005688, intron 17 of 29)	-47934	NR_046570	100873982	Hs.570696	NR_046570	ENSG00000223882	ABCC5-AS1	-	ABCC5 antisense RNA 1	ncRNA	0.016234	0.400324	
chunk0056_137_1	chr13	83258779	83259257	+	0	NA	Intergenic	L1MB1|LINE|L1	623375	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.004184	0.325678	362(GAGGACAGTATGCTCA,-,0.00),363(AGGACAGTATGCTCAG,+,0.00)
chunk0033_198_1	chr11	16632651	16632850	+	0	NA	Intergenic	L1PA16|LINE|L1	-105851	NM_014267	10944	Hs.368226	NM_014267	ENSG00000110696	C11orf58	IMAGE145052|SMAP	chromosome 11 open reading frame 58	protein-coding	0.030151	0.560000	
chunk0008_315_1	chr1	95189553	95189752	+	0	NA	intron (NR_125948, intron 3 of 4)	L1MC3|LINE|L1	44330	NR_125949	101928118	Hs.656443	NR_125948	ENSG00000226026	LOC101928118	-	uncharacterized LOC101928118	ncRNA	0.005025	0.325000	
chunk0037_437_1	chr11	80280812	80281513	+	0	NA	Intergenic	Intergenic	481641	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.005706	0.457265	
chunk0116_269_1	chr21	39197394	39197927	+	0	NA	intron (NM_018963, intron 40 of 41)	Tigger3c|DNA|TcMar-Tigger	-14146	NM_003720	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.007505	0.370787	234(ATCACAGAGTGTGCTT,+,0.00)
chunk0004_82_1	chr1	43710503	43710713	+	0	NA	intron (NR_125986, intron 3 of 3)	intron (NR_125986, intron 3 of 3)	3075	NM_001270462	6487	Hs.597915	NM_006279	ENSG00000126091	ST3GAL3	EIEE15|MRT12|SIAT6|ST3GALII|ST3Gal III|ST3GalIII|ST3N	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	protein-coding	0.004762	0.436019	
chunk0147_155_1	chr4	175703590	175703941	+	0	NA	intron (NM_201592, intron 1 of 6)	intron (NM_201592, intron 1 of 6)	83911	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.000000	0.389205	
chunk0089_98_1	chr18	58391337	58391536	+	0	NA	intron (NM_001144970, intron 27 of 28)	intron (NM_001144970, intron 27 of 28)	-59638	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.000000	0.480000	
chunk0177_125_1	chr7	22350601	22351486	+	0	NA	intron (NM_012294, intron 1 of 25)	intron (NM_012294, intron 1 of 25)	5871	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.002260	0.382619	
chunk0174_432_1	chr6	166059606	166060195	+	0	NA	Intergenic	L1P3|LINE|L1	-71861	NR_026860	90632	Hs.31917	NR_026860	ENSG00000112541	LINC00473	C6orf176|LNC473|bA142J11.1	long intergenic non-protein coding RNA 473	ncRNA	0.006791	0.345763	
chunk0198_171_1	chr8	133273631	133274209	+	0	NA	intron (NM_001258432, intron 1 of 13)	intron (NM_001258432, intron 1 of 13)	23384	NM_001258432	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.017301	0.519862	
chunk0074_99_1	chr16	22205973	22206291	+	0	NA	promoter-TSS (NM_013302)	promoter-TSS (NM_013302)	-139	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.084906	0.689655	
chunk0154_189_1	chr5	80193376	80193844	+	0	NA	intron (NM_178276, intron 2 of 12)	intron (NM_178276, intron 2 of 12)	62472	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.017094	0.458422	205(AAGGACAGTATGTATT,-,0.00),206(AGGACAGTATGTATTG,+,0.00)
chunk0001_391_1	chr1	10652682	10653043	+	0	NA	intron (NM_001079843, intron 11 of 20)	intron (NM_001079843, intron 11 of 20)	143814	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.027701	0.604972	
chunk0144_278_1	chr4	137881029	137881408	+	0	NA	Intergenic	L1M7|LINE|L1	-207796	NR_038380	641364	Hs.570846	NR_038380	ENSG00000250033	SLC7A11-AS1	-	SLC7A11 antisense RNA 1	ncRNA	0.000000	0.342105	
chunk0125_332_1	chr3	71031283	71031544	+	0	NA	intron (NM_032682, intron 11 of 20)	intron (NM_032682, intron 11 of 20)	33510	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.000000	0.362595	
chunk0120_1_1	chr3	203672	203871	+	0	NA	intron (NR_045572, intron 1 of 2)	intron (NR_045572, intron 1 of 2)	6128	NR_045572	10752	Hs.148909	NM_006614	ENSG00000134121	CHL1	CALL|L1CAM2	cell adhesion molecule L1 like	protein-coding	0.010050	0.500000	
chunk0104_187_1	chr2	175028129	175028861	+	0	NA	Intergenic	Intergenic	-23116	NM_001025201	1123	Hs.380138	NM_001822	ENSG00000128656	CHN1	ARHGAP2|CHN|DURS2|NC|RHOGAP2	chimerin 1	protein-coding	0.015027	0.406548	127(CAGGACAGATTGTTCC,-,0.00),128(AGGACAGATTGTTCCC,+,0.00)
chunk0012_321_1	chr1	162382214	162382538	+	0	NA	intron (NM_001135240, intron 2 of 2)	intron (NM_001135240, intron 2 of 2)	646	NM_001085375	400793	Hs.447011	NM_001085375	ENSG00000239887	C1orf226	-	chromosome 1 open reading frame 226	protein-coding	0.012346	0.572308	246(GTGCACACCATGTCCT,-,0.00),247(TGCACACCATGTCCTC,+,0.00)
chunk0103_330_1	chr2	167783288	167783917	+	0	NA	Intergenic	Intergenic	-35070	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.006359	0.447619	
chunk0097_266_1	chr2	54559825	54560076	+	0	NA	intron (NM_178313, intron 1 of 30)	intron (NM_178313, intron 1 of 30)	1556	NM_178313	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.015936	0.480159	
chunk0127_378_1	chr3	102007187	102007495	+	0	NA	Intergenic	LTR16A|LTR|ERVL	66482	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003247	0.401294	
chunk0061_49_1	chr14	56273917	56274116	+	0	NA	intron (NM_021255, intron 2 of 5)	intron (NM_021255, intron 2 of 5)	155641	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.010050	0.490000	
chunk0073_405_1	chr16	17304505	17304710	+	0	NA	intron (NM_022166, intron 2 of 11)	intron (NM_022166, intron 2 of 11)	166274	NM_022166	64131	Hs.22907	NM_022166	ENSG00000103489	XYLT1	DBQD2|PXYLT1|XT-I|XT1|XTI|XYLTI|xylT-I	xylosyltransferase 1	protein-coding	0.009756	0.398058	
chunk0005_312_1	chr1	60598020	60598355	+	0	NA	Intergenic	L2c|LINE|L2	227397	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.002985	0.392857	118(GGAAACAGTTTGTGCT,-,0.00),119(GAAACAGTTTGTGCTT,+,0.00)
chunk0054_268_1	chr13	46571127	46571469	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	18137	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.017544	0.472303	
chunk0071_274_1	chr15	85672789	85673132	+	0	NA	intron (NM_007200, intron 14 of 36)	intron (NM_007200, intron 14 of 36)	53010	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.000000	0.398256	5(GAGCACATGCTGTCAT,-,0.00),173(AGGAACAGAATGTTTT,-,0.00),174(GGAACAGAATGTTTTC,+,0.00)
chunk0155_327_1	chr5	96796489	96796940	+	0	NA	intron (NM_016442, intron 4 of 19)	intron (NM_016442, intron 4 of 19)	11475	NM_016442	51752	Hs.666524	NM_016442	ENSG00000164307	ERAP1	A-LAP|ALAP|APPILS|ARTS-1|ARTS1|ERAAP|ERAAP1|PILS-AP|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding	0.004435	0.469027	
chunk0188_384_1	chr8	18411986	18412511	+	0	NA	Intergenic	L1PA17|LINE|L1	21003	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.000000	0.351711	
chunk0193_185_1	chr8	75235729	75236032	+	0	NA	intron (NR_103849, intron 1 of 1)	intron (NR_103849, intron 1 of 1)	42601	NR_103848	101805492	Hs.571424	NR_103848		CASC9	ESCCAL-1|ESSCAL1|LINC00981|linc-JPH1	cancer susceptibility 9	ncRNA	0.000000	0.302632	
chunk0031_351_1	chr10	129647687	129648185	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	180752	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.008032	0.334669	
chunk0092_453_1	chr19	39057893	39058110	+	0	NA	Intergenic	Intergenic	-25405	NM_178820	126433	Hs.187461	NM_178820	ENSG00000161243	FBXO27	FBG5|Fbx27	F-box protein 27	protein-coding	0.023041	0.458716	
chunk0080_190_1	chr17	28974717	28974920	+	0	NA	intron (NM_001290202, intron 3 of 16)	intron (NM_001290202, intron 3 of 16)	-23328	NM_001033561	57649	Hs.444173	NM_020889	ENSG00000109118	PHF12	PF1	PHD finger protein 12	protein-coding	0.014778	0.573529	
chunk0019_240_1	chr1	227406369	227406820	+	0	NA	Intergenic	L1PB1|LINE|L1	-88469	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.000000	0.338496	
chunk0053_290_1	chr13	33498089	33498387	+	0	NA	intron (NM_001243476, intron 4 of 17)	intron (NM_001243476, intron 4 of 17)	178597	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.000000	0.321070	
chunk0157_66_1	chr5	116275281	116275845	+	0	NA	intron (NM_001308080, intron 5 of 6)	L2c|LINE|L2	99007	NR_104675	101927190	Hs.639849	NR_104675		LOC101927190	-	uncharacterized LOC101927190	ncRNA	0.005319	0.352212	366(AAATACACCATGTTCT,-,0.00),367(AATACACCATGTTCTG,+,0.00)
chunk0166_87_1	chr6	43704795	43705204	+	0	NA	Intergenic	L1ME4b|LINE|L1	-17187	NM_018135	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.012225	0.402439	
chunk0121_356_1	chr3	24790529	24790969	+	0	NA	Intergenic	L1ME4b|LINE|L1	-269314	NR_039955									0.006818	0.326531	
chunk0193_223_1	chr8	76578080	76578552	+	0	NA	Intergenic	Intergenic	-102964	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.006356	0.382664	
chunk0105_329_1	chr2	191049932	191050584	+	0	NA	intron (NM_003151, intron 14 of 23)	intron (NM_003151, intron 14 of 23)	-36008	NM_007315	6772	Hs.642990	NM_007315	ENSG00000115415	STAT1	CANDF7|IMD31A|IMD31B|IMD31C|ISGF-3|STAT91	signal transducer and activator of transcription 1	protein-coding	0.004601	0.395100	
chunk0130_34_1	chr3	129005821	129006043	+	0	NA	intron (NM_024768, intron 2 of 7)	intron (NM_024768, intron 2 of 7)	4303	NM_024768	79825	Hs.134807	NM_024768	ENSG00000114654	EFCC1	C3orf73|CCDC48	EF-hand and coiled-coil domain containing 1	protein-coding	0.000000	0.426009	
chunk0132_94_1	chr3	155622809	155623008	+	0	NA	intron (NM_014996, intron 1 of 21)	L1PA7|LINE|L1	53408	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.015075	0.395000	
chunk0071_332_1	chr15	87617808	87618125	+	0	NA	Intergenic	Intergenic	41037	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.003155	0.399371	
chunk0032_31_1	chr11	986675	987135	+	0	NA	exon (NM_012305, exon 9 of 22)	exon (NM_012305, exon 9 of 22)	49801	NM_005961	4588	Hs.528432	NM_005961	ENSG00000184956	MUC6	MUC-6	mucin 6, oligomeric mucus/gel-forming	protein-coding	0.043478	0.620390	
chunk0048_370_1	chr12	86185288	86185691	+	0	NA	intron (NM_013244, intron 3 of 6)	intron (NM_013244, intron 3 of 6)	311194	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.000000	0.294554	
chunk0020_452_1	chr1	242243008	242243866	+	0	NA	intron (NM_001195812, intron 3 of 8)	intron (NM_001195812, intron 3 of 8)	206045	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.008159	0.441211	
chunk0205_167_1	chr9	108708444	108708749	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	147399	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.022951	0.571895	63(TGGTACAGACTGTGCC,-,0.00),64(GGTACAGACTGTGCCC,+,0.00)
chunk0044_7_1	chr12	26912980	26913269	+	0	NA	intron (NM_018164, intron 14 of 16)	L2c|LINE|L2	25197	NM_018164	55726	Hs.505077	NM_018164	ENSG00000064102	INTS13	ASUN|C12orf11|GCT1|Mat89Bb|NET48|SPATA30	integrator complex subunit 13	protein-coding	0.003460	0.396552	
chunk0086_373_1	chr18	26307363	26307614	+	0	NA	intron (NR_121653, intron 10 of 15)	L1MC5|LINE|L1	80605	NM_001293725	6875	Hs.369519	NM_005640	ENSG00000141384	TAF4B	SPGF13|TAF2C2|TAFII105	TATA-box binding protein associated factor 4b	protein-coding	0.003984	0.305556	
chunk0078_2_1	chr17	143938	144236	+	0	NA	Intergenic	(GGCGCGGC)n|Simple_repeat|Simple_repeat	6516	NM_001097610	653486	Hs.127059	NM_001097610	ENSG00000268320	SCGB1C2	SCGB1C1	secretoglobin family 1C member 2	protein-coding	0.114094	0.688963	
chunk0010_384_1	chr1	119346528	119346940	+	0	NA	Intergenic	LTR8|LTR|ERV1	-22042	NM_001005783	51179	Hs.659767	NM_016527	ENSG00000116882	HAO2	GIG16|HAOX2	hydroxyacid oxidase 2	protein-coding	0.000000	0.305085	
chunk0098_441_1	chr2	82120341	82120540	+	0	NA	Intergenic	L2a|LINE|L2	-653494	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.420000	
chunk0016_188_1	chr1	198287603	198288172	+	0	NA	intron (NM_133494, intron 7 of 9)	intron (NM_133494, intron 7 of 9)	130909	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.005272	0.354386	
chunk0210_66_1	chrX	69936344	69936668	+	0	NA	intron (NM_001005612, intron 1 of 7)	intron (NM_001005612, intron 1 of 7)	-86351	NR_037494	100500887		NR_037494	ENSG00000211991	MIR676	hsa-mir-676|mir-676	microRNA 676	ncRNA	0.003086	0.363077	
chunk0003_158_1	chr1	33300788	33301003	+	0	NA	TTS (NM_152493)	TTS (NM_152493)	20203	NM_001080438	127550		NM_001080438	ENSG00000184389	A3GALT2	A3GALT2P|IGB3S|IGBS3S	alpha 1,3-galactosyltransferase 2	protein-coding	0.004651	0.541667	
chunk0128_335_1	chr3	112109382	112109616	+	0	NA	intron (NM_001171747, intron 3 of 3)	intron (NM_001171747, intron 3 of 3)	-3302	NR_030292	693152		NR_030292	ENSG00000207940	MIR567	MIRN567|hsa-mir-567	microRNA 567	ncRNA	0.017094	0.421277	
chunk0118_190_1	chr22	31399360	31399655	+	0	NA	promoter-TSS (NM_004147)	promoter-TSS (NM_004147)	-46	NM_004147	4733	Hs.115242	NM_004147	ENSG00000185721	DRG1	NEDD3	developmentally regulated GTP binding protein 1	protein-coding	0.122034	0.722973	
chunk0146_136_1	chr4	159248718	159248936	+	0	NA	Intergenic	Intergenic	-19019	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.004587	0.337900	
chunk0062_436_1	chr14	75389608	75390021	+	0	NA	Intergenic	L1MC3|LINE|L1	-37992	NM_001135047	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.007264	0.386473	
chunk0192_67_1	chr8	60418119	60418430	+	0	NA	Intergenic	Intergenic	-4456	NR_103854	100505532	Hs.720321	NR_103854		LINC01301	-	long intergenic non-protein coding RNA 1301	ncRNA	0.006431	0.403846	
chunk0042_73_1	chr12	2142165	2142624	+	0	NA	intron (NM_001129846, intron 3 of 45)	Tigger3b|DNA|TcMar-Tigger	81087	NR_046578	100874234	Hs.372570	NR_046578	ENSG00000256025	CACNA1C-AS4	-	CACNA1C antisense RNA 4	ncRNA	0.021786	0.430435	238(TAGCACAGACAGTTCT,-,0.00),239(AGCACAGACAGTTCTG,+,0.00)
chunk0051_108_1	chr12	114993371	114993730	+	0	NA	Intergenic	Intergenic	-309386	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.008357	0.372222	
chunk0179_376_1	chr7	51245621	51246089	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	70963	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.002137	0.339019	
chunk0061_141_1	chr14	59361265	59361580	+	0	NA	intron (NM_014992, intron 22 of 24)	intron (NM_014992, intron 22 of 24)	97981	NM_014992	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.015873	0.500000	
chunk0121_192_1	chr3	20650455	20650865	+	0	NA	Intergenic	Intergenic	308192	NR_110814	101927829	Hs.639381	NR_110814	ENSG00000231304	LOC101927829	-	uncharacterized LOC101927829	ncRNA	0.004878	0.428224	
chunk0005_131_1	chr1	57065305	57066078	+	0	NA	intron (NM_021080, intron 10 of 16)	intron (NM_021080, intron 10 of 16)	-99551	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.011643	0.419897	689(CAGCACATTCCGTACT,-,0.00)
chunk0199_24_1	chr9	653725	654050	+	0	NA	intron (NM_001256877, intron 2 of 12)	intron (NM_001256877, intron 2 of 12)	-52919	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.000000	0.377301	
chunk0117_434_1	chr21	46242595	46242912	+	0	NA	non-coding (NR_110566, exon 3 of 3)	non-coding (NR_110566, exon 3 of 3)	13522	NR_110565	114044	Hs.655095	NR_002776	ENSG00000215424	MCM3AP-AS1	C21orf85|MCM3AP-AS|MCM3APAS|MCM3APASB|NCRNA00031	MCM3AP antisense RNA 1	ncRNA	0.012618	0.396226	
chunk0078_195_1	chr17	5232073	5232661	+	0	NA	intron (NR_034082, intron 5 of 7)	LTR85a|LTR|Gypsy?	2493	NM_207103	388325	Hs.462080	NM_207103	ENSG00000161929	SCIMP	C17orf87|UNQ5783	SLP adaptor and CSK interacting membrane protein	protein-coding	0.020408	0.499151	
chunk0029_254_1	chr10	102920732	102921074	+	0	NA	intron (NM_199076, intron 1 of 6)	intron (NM_199076, intron 1 of 6)	2585	NM_017649	54805	Hs.643509	NM_017649	ENSG00000148842	CNNM2	ACDP2|HOMG6|HOMGSMR	cyclin and CBS domain divalent metal cation transport mediator 2	protein-coding	0.014620	0.370262	
chunk0029_409_1	chr10	109915421	109916008	+	0	NA	intron (NM_001167604, intron 1 of 19)	intron (NM_001167604, intron 1 of 19)	7839	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.003407	0.391156	
chunk0045_40_1	chr12	44574525	44574988	+	0	NA	intron (NM_001145108, intron 15 of 19)	L2a|LINE|L2	300905	NM_001145109	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.000000	0.301724	
chunk0102_188_1	chr2	147643335	147643777	+	0	NA	Intergenic	Intergenic	-200961	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.395034	
chunk0169_215_1	chr6	103236942	103237301	+	0	NA	Intergenic	Intergenic	1622798	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.363889	123(CAGCACAGCCTGTCTC,-,0.00),124(AGCACAGCCTGTCTCA,+,0.00)
chunk0083_416_1	chr17	72182934	72183549	+	0	NA	Intergenic	L3|LINE|CR1	62221	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.013008	0.500000	
chunk0104_14_1	chr2	170498202	170498632	+	0	NA	intron (NR_045684, intron 25 of 34)	intron (NR_045684, intron 25 of 34)	-147474	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.004651	0.308585	
chunk0092_155_1	chr19	29606216	29606415	+	0	NA	promoter-TSS (NM_006627)	promoter-TSS (NM_006627)	52	NR_027368	10775	Hs.412870	NM_006627	ENSG00000105171	POP4	RPP29	POP4 homolog, ribonuclease P/MRP subunit	protein-coding	0.095477	0.625000	
chunk0141_54_1	chr4	77604398	77604777	+	0	NA	intron (NM_006419, intron 1 of 4)	L3|LINE|CR1	92834	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.005277	0.434211	
chunk0081_161_1	chr17	40957966	40958453	+	0	NA	TTS (NM_213656)	TTS (NM_213656)	8683	NM_213656	390792	Hs.28467	NM_213656	ENSG00000196859	KRT39	CK-39|K39|KA35	keratin 39	protein-coding	0.006160	0.383197	
chunk0073_103_1	chr16	4488066	4488503	+	0	NA	intron (NM_001127204, intron 2 of 6).2	intron (NM_001127204, intron 2 of 6).2	-7535	NM_001286270	3163	Hs.284279	NM_002134	ENSG00000103415	HMOX2	HO-2	heme oxygenase 2	protein-coding	0.006865	0.383562	
chunk0071_111_1	chr15	81301818	81302018	+	0	NA	intron (NM_001172128, intron 15 of 18)	intron (NM_001172128, intron 15 of 18)	5005	NM_004513	3603	Hs.459095	NM_004513	ENSG00000172349	IL16	LCF|NIL16|PRIL16|prIL-16	interleukin 16	protein-coding	0.005000	0.497512	
chunk0181_450_1	chr7	90738305	90738829	+	0	NA	intron (NM_001287137, intron 2 of 12)	intron (NM_001287137, intron 2 of 12)	28751	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.007634	0.352381	155(TGGAACATTATGTGCA,-,0.00),156(GGAACATTATGTGCAC,+,0.00)
chunk0188_258_1	chr8	14611465	14612142	+	0	NA	intron (NM_139167, intron 1 of 7)	L1MC5a|LINE|L1	241707	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.004431	0.293510	
chunk0145_223_1	chr4	148248530	148248963	+	0	NA	intron (NM_000901, intron 3 of 8)	intron (NM_000901, intron 3 of 8)	193774	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.009238	0.334101	
chunk0113_400_1	chr20	60341152	60341647	+	0	NA	Intergenic	Intergenic	32925	NR_030376	693231		NR_030376	ENSG00000207802	MIR646	MIRN646|hsa-mir-646	microRNA 646	ncRNA	0.016162	0.437500	
chunk0097_84_1	chr2	45259206	45259493	+	0	NA	Intergenic	Intergenic	-4408	NR_033831	400952	Hs.468368	NR_033831	ENSG00000205054	LINC01121	UNQ6975	long intergenic non-protein coding RNA 1121	ncRNA	0.024390	0.506944	
chunk0042_12_1	chr12	1217142	1217629	+	0	NA	intron (NR_027946, intron 12 of 18)	intron (NR_027946, intron 12 of 18)	189637	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.004107	0.393443	
chunk0166_42_1	chr6	42260966	42261499	+	0	NA	intron (NM_033502, intron 8 of 17)	intron (NM_033502, intron 8 of 17)	-43337	NM_018141	55173	Hs.380887	NM_018141	ENSG00000048544	MRPS10	MRP-S10|PNAS-122	mitochondrial ribosomal protein S10	protein-coding	0.022514	0.589888	234(AGATACACTCTGTTCC,-,0.00),235(GATACACTCTGTTCCC,+,0.00),272(AAGAACATGCAGACCT,-,0.00),273(AGAACATGCAGACCTT,+,0.00)
chunk0197_363_1	chr8	125925971	125926413	+	0	NA	intron (NR_038447, intron 3 of 3)	L1MEc|LINE|L1	25005	NR_038446	100130231	Hs.729642	NR_038446	ENSG00000245164	LINC00861	-	long intergenic non-protein coding RNA 861	ncRNA	0.004525	0.408578	
chunk0098_19_1	chr2	65396373	65396572	+	0	NA	intron (NM_181784, intron 1 of 5)	L2c|LINE|L2	-29675	NM_001128210	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.015075	0.450000	
chunk0179_245_1	chr7	48204669	48204951	+	0	NA	intron (NM_152701, intron 3 of 61)	intron (NM_152701, intron 3 of 61)	33350	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.021277	0.540636	
chunk0145_185_1	chr4	147782464	147782861	+	0	NA	promoter-TSS (NR_039962)	promoter-TSS (NR_039962)	67	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.007557	0.424623	227(TGGTACAACTTGTTCT,-,0.00),228(GGTACAACTTGTTCTG,+,0.00)
chunk0031_200_1	chr10	125836520	125837064	+	0	NA	TTS (NM_078468)	TTS (NM_078468)	13257	NM_016567	56647	Hs.370292	NM_016567	ENSG00000107949	BCCIP	TOK-1|TOK1	BRCA2 and CDKN1A interacting protein	protein-coding	0.012868	0.403670	
chunk0038_408_1	chr11	93932758	93933295	+	0	NA	Intergenic	Intergenic	-82524	NM_001144871	387804	Hs.512252	NM_001144871	ENSG00000214376	VSTM5	C11orf90	V-set and transmembrane domain containing 5	protein-coding	0.003724	0.403346	168(AGGCACTGCTTGTTCT,-,0.00),169(GGCACTGCTTGTTCTA,+,0.00)
chunk0186_345_1	chr7	143408690	143408889	+	0	NA	exon (NM_005232, exon 1 of 18)	exon (NM_005232, exon 1 of 18)	103	NM_005232	2041	Hs.89839	NM_005232	ENSG00000146904	EPHA1	EPH|EPHT|EPHT1	EPH receptor A1	protein-coding	0.105528	0.785000	
chunk0075_192_1	chr16	52425508	52425744	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	121268	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.004237	0.396624	
chunk0198_214_1	chr8	133869717	133869937	+	0	NA	Intergenic	Intergenic	-16669	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.013636	0.524887	
chunk0177_423_1	chr7	27777590	27778268	+	0	NA	intron (NM_001206901, intron 5 of 16)	L1MEc|LINE|L1	37834	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.005900	0.394698	
chunk0017_120_1	chr1	206122106	206122459	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-5234	NM_000707	553	Hs.1372	NM_000707	ENSG00000198049	AVPR1B	AVPR3|V1bR	arginine vasopressin receptor 1B	protein-coding	0.000000	0.440678	253(AGGCACAAAGAGTTCC,-,0.00),254(GGCACAAAGAGTTCCC,+,0.00)
chunk0163_117_1	chr6	10235976	10236302	+	0	NA	Intergenic	Intergenic	-176179	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003067	0.379205	229(TGGAGCACAGTGTCCC,-,0.00),230(GGAGCACAGTGTCCCA,+,0.00)
chunk0201_188_1	chr9	36400731	36400961	+	0	NA	promoter-TSS (NM_194332)	promoter-TSS (NM_194332)	77	NM_194328	152006	Hs.333503	NM_022781	ENSG00000137075	RNF38	-	ring finger protein 38	protein-coding	0.139130	0.770563	
chunk0120_295_1	chr3	9916958	9917454	+	0	NA	TTS (NM_001193380)	TTS (NM_001193380)	108	NM_153461	84818	Hs.129959	NM_032732	ENSG00000163702	IL17RC	CANDF9|IL17-RL|IL17RL	interleukin 17 receptor C	protein-coding	0.022177	0.645875	187(CAGGACAGAGAGTGCA,-,0.00),188(AGGACAGAGAGTGCAC,+,0.00)
chunk0150_315_1	chr5	38028744	38029198	+	0	NA	Intergenic	Intergenic	155546	NM_001278094	100861519	Hs.536820	NM_001278094		GDNF-AS1	GDNFOS	GDNF antisense RNA 1	ncRNA	0.000000	0.345055	
chunk0138_56_1	chr4	31837290	31837725	+	0	NA	Intergenic	Intergenic	-159872	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.013793	0.360092	
chunk0039_72_1	chr11	96404895	96405476	+	0	NA	Intergenic	Intergenic	15191	NM_001261833	8690	Hs.105940	NM_003772	ENSG00000183340	JRKL	HHMJG	JRK like	protein-coding	0.005164	0.335052	
chunk0009_9_1	chr1	99858960	99859274	+	0	NA	intron (NM_000646, intron 2 of 33)	intron (NM_000646, intron 2 of 33)	-2093	NM_000645	178	Hs.904	NM_000028	ENSG00000162688	AGL	GDE	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	protein-coding	0.000000	0.320635	129(GGGGACAGGTTGTACA,-,0.00),130(GGGACAGGTTGTACAC,+,0.00)
chunk0179_80_1	chr7	44391976	44392431	+	0	NA	intron (NM_015332, intron 5 of 5)	intron (NM_015332, intron 5 of 5)	-66572	NM_172083	816	Hs.351887	NM_001220	ENSG00000058404	CAMK2B	CAM2|CAMK2|CAMKB|MRD54	calcium/calmodulin dependent protein kinase II beta	protein-coding	0.017582	0.552632	
chunk0052_345_1	chr12	126545447	126545682	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	103083	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.012766	0.436441	
chunk0106_321_1	chr2	205564748	205564947	+	0	NA	intron (NM_205863, intron 21 of 21)	MamGypsy2-I|LTR|Gypsy	-117653	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.005025	0.475000	
chunk0021_253_1	chr1	243397628	243398182	+	0	NA	intron (NM_006642, intron 13 of 17)	intron (NM_006642, intron 13 of 17)	51729	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.009025	0.383784	
chunk0093_326_1	chr19	54115325	54115894	+	0	NA	promoter-TSS (NM_013342)	promoter-TSS (NM_013342)	66	NM_013342	29844	Hs.590939	NM_013342	ENSG00000105619	TFPT	FB1|INO80F|amida	TCF3 fusion partner	protein-coding	0.075571	0.582456	
chunk0166_247_1	chr6	47440528	47440727	+	0	NA	Intergenic	Intergenic	-37162	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.010050	0.405000	
chunk0125_111_1	chr3	65632166	65633051	+	0	NA	intron (NM_015520, intron 1 of 24)	MER58A|DNA|hAT-Charlie	-261208	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.000000	0.370203	
chunk0039_13_1	chr11	95348681	95349445	+	0	NA	Intergenic	L1M1|LINE|L1	-116522	NM_001271594	143686	Hs.120633	NM_144665	ENSG00000149212	SESN3	SEST3	sestrin 3	protein-coding	0.000000	0.328105	478(AGGCACAGTCAGTACA,-,0.00),479(GGCACAGTCAGTACAG,+,0.00)
chunk0148_182_1	chr5	7813826	7814179	+	0	NA	intron (NM_020546, intron 22 of 24)	intron (NM_020546, intron 22 of 24)	37488	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.005666	0.364407	
chunk0096_96_1	chr2	28154678	28155505	+	0	NA	intron (NR_120504, intron 1 of 2)	Tigger16a|DNA|TcMar-Tigger	51870	NR_120504	100505736	Hs.659540	NR_120504		LOC100505736	-	uncharacterized LOC100505736	ncRNA	0.007255	0.327295	661(AAGAACAGTTAGTTCT,-,0.00),662(AGAACAGTTAGTTCTT,+,0.00)
chunk0052_276_1	chr12	124222618	124223331	+	0	NA	intron (NM_001204299, intron 3 of 4)	intron (NM_001204299, intron 3 of 4)	-66190	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.014025	0.500000	
chunk0202_37_1	chr9	71096557	71096986	+	0	NA	intron (NM_001007471, intron 1 of 24)	intron (NM_001007471, intron 1 of 24)	24827	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.000000	0.404651	
chunk0186_276_1	chr7	141738217	141738511	+	0	NA	promoter-TSS (NM_001256511)	promoter-TSS (NM_001256511)	43	NM_003143	6742	Hs.490394	NM_003143	ENSG00000106028	SSBP1	Mt-SSB|SOSS-B1|SSBP|mtSSB	single stranded DNA binding protein 1	protein-coding	0.085034	0.589831	
chunk0200_97_1	chr9	16607463	16607806	+	0	NA	intron (NM_017637, intron 3 of 6)	intron (NM_017637, intron 3 of 6)	263154	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.008746	0.325581	
chunk0186_267_1	chr7	141648835	141649094	+	0	NA	intron (NM_018238, intron 13 of 15)	intron (NM_018238, intron 13 of 15)	53189	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.011583	0.430769	
chunk0035_116_1	chr11	42561934	42562669	+	0	NA	Intergenic	Intergenic	-308611	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.389946	
chunk0147_453_1	chr4	188354321	188354520	+	0	NA	Intergenic	L1M3b|LINE|L1	-101158	NR_033869	401164	Hs.435756	NR_033869	ENSG00000249378	LINC01060	-	long intergenic non-protein coding RNA 1060	ncRNA	0.000000	0.510000	
chunk0077_20_1	chr16	75044946	75045742	+	0	NA	intron (NM_032268, intron 1 of 4)	intron (NM_032268, intron 1 of 4)	46327	NM_032268	84937	Hs.427284	NM_032268	ENSG00000186187	ZNRF1	NIN283	zinc and ring finger 1	protein-coding	0.006281	0.421581	
chunk0004_47_1	chr1	42942262	42942747	+	0	NA	intron (NM_006516, intron 2 of 9)	intron (NM_006516, intron 2 of 9)	-16545	NR_033967	440584	Hs.260928	NR_033967	ENSG00000227533	SLC2A1-AS1	-	SLC2A1 antisense RNA 1	ncRNA	0.012371	0.543210	
chunk0176_217_1	chr7	14938228	14938568	+	0	NA	Intergenic	Intergenic	-96948	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.002941	0.325513	
chunk0140_267_1	chr4	71884671	71884980	+	0	NA	Intergenic	L2b|LINE|L2	-79305	NM_001204306	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.003236	0.387097	
chunk0187_285_1	chr7	155670191	155670694	+	0	NA	intron (NM_053043, intron 2 of 17)	intron (NM_053043, intron 2 of 17)	25933	NM_053043	155435	Hs.591815	NM_053043	ENSG00000184863	RBM33	PRR8	RNA binding motif protein 33	protein-coding	0.007952	0.426587	
chunk0140_276_1	chr4	72238291	72238760	+	0	NA	Intergenic	Intergenic	199393	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.000000	0.348936	
chunk0095_237_1	chr2	19102737	19102936	+	0	NA	Intergenic	Intergenic	-245593	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.005025	0.395000	
chunk0045_63_1	chr12	45476287	45476594	+	0	NA	Intergenic	Intergenic	183757	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.003257	0.334416	
chunk0091_321_1	chr19	13162631	13163305	+	0	NA	Intergenic	CpG	12500	NM_004907	9592	Hs.501629	NM_004907	ENSG00000160888	IER2	ETR101	immediate early response 2	protein-coding	0.077151	0.660741	
chunk0195_77_1	chr8	94037495	94037700	+	0	NA	Intergenic	Intergenic	120546	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.000000	0.398058	
chunk0187_123_1	chr7	149090637	149090870	+	0	NA	promoter-TSS (NM_152411)	promoter-TSS (NM_152411)	24	NM_152411	136051	Hs.729572	NM_152411	ENSG00000197362	ZNF786	-	zinc finger protein 786	protein-coding	0.128755	0.764957	
chunk0105_202_1	chr2	187780526	187780728	+	0	NA	Intergenic	Intergenic	-226135	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.177340	
chunk0053_333_1	chr13	34386046	34386335	+	0	NA	Intergenic	LTR33|LTR|ERVL	254495	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.000000	0.531034	
chunk0185_93_1	chr7	125486759	125487091	+	0	NA	Intergenic	L1MC3|LINE|L1	-222634	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.009036	0.378378	
chunk0167_387_1	chr6	74616170	74616436	+	0	NA	intron (NR_110856, intron 2 of 3)	L1PREC2|LINE|L1	546852	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.000000	0.318352	
chunk0168_439_1	chr6	95729494	95729951	+	0	NA	Intergenic	L2a|LINE|L2	152225	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.008753	0.340611	
chunk0026_128_1	chr10	62036368	62036624	+	0	NA	intron (NM_032199, intron 4 of 9)	intron (NM_032199, intron 4 of 9)	-12715	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.011719	0.509728	
chunk0069_366_1	chr15	67186386	67186777	+	0	NA	intron (NM_001145102, intron 7 of 8)	intron (NM_001145102, intron 7 of 8)	20426	NM_001145104	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.010230	0.471939	
chunk0020_324_1	chr1	237779585	237779879	+	0	NA	intron (NM_001035, intron 88 of 104)	MER67A|LTR|ERV1	-82443	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.006803	0.396610	
chunk0029_382_1	chr10	109245592	109245874	+	0	NA	Intergenic	Intergenic	677820	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.007092	0.477032	
chunk0035_103_1	chr11	42329986	42330392	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-76499	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.012315	0.380835	279(TGGAACAGATTGTCTC,-,0.00),280(GGAACAGATTGTCTCC,+,0.00)
chunk0183_447_1	chr7	111262317	111263207	+	0	NA	intron (NM_032549, intron 3 of 5)	LTR80A|LTR|ERVL	171756	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.005618	0.409652	
chunk0008_363_1	chr1	96684060	96684295	+	0	NA	Intergenic	L1MD3|LINE|L1	-37428	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.343220	82(TAGTACAGAGAGTTCC,-,0.00),83(AGTACAGAGAGTTCCC,+,0.00)
chunk0200_425_1	chr9	29284011	29284766	+	0	NA	Intergenic	Intergenic	-71388	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.002649	0.373016	
chunk0107_19_1	chr2	210208960	210209460	+	0	NA	intron (NM_001608, intron 5 of 10)	intron (NM_001608, intron 5 of 10)	16281	NM_001608	33	Hs.471277	NM_001608	ENSG00000115361	ACADL	ACAD4|LCAD	acyl-CoA dehydrogenase long chain	protein-coding	0.006000	0.343313	
chunk0003_152_1	chr1	33055280	33056080	+	0	NA	Intergenic	Intergenic	-18769	NM_001199199	204	Hs.470907	NM_001625	ENSG00000004455	AK2	ADK2	adenylate kinase 2	protein-coding	0.013750	0.539326	
chunk0114_353_1	chr21	18133447	18133795	+	0	NA	intron (NM_001204176, intron 2 of 6)	LTR40a|LTR|ERVL	-111212	NM_024944	140578	Hs.283725	NM_024944	ENSG00000154645	CHODL	C21orf68|MT75|PRED12	chondrolectin	protein-coding	0.005747	0.383954	
chunk0174_361_1	chr6	164546990	164547665	+	0	NA	Intergenic	(AT)n|Simple_repeat|Simple_repeat	274736	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.008889	0.334320	
chunk0089_275_1	chr18	62822620	62822862	+	0	NA	intron (NM_194449, intron 1 of 16)	intron (NM_194449, intron 1 of 16)	107302	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.000000	0.337449	
chunk0127_234_1	chr3	96819449	96820115	+	0	NA	intron (NM_001080448, intron 1 of 17)	intron (NM_001080448, intron 1 of 17)	5201	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.004505	0.343328	315(AGATACATTCTGTTCT,-,0.00),316(GATACATTCTGTTCTT,+,0.00)
chunk0042_315_1	chr12	8577590	8577882	+	0	NA	Intergenic	MIR|SINE|MIR	35110	NM_020661	57379	Hs.149342	NM_020661	ENSG00000111732	AICDA	AID|ARP2|CDA2|HEL-S-284|HIGM2	activation induced cytidine deaminase	protein-coding	0.010274	0.361775	
chunk0019_209_1	chr1	227016694	227017539	+	0	NA	intron (NM_014826, intron 30 of 34)	intron (NM_014826, intron 30 of 34)	76879	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.007101	0.334515	
chunk0101_96_1	chr2	124639447	124639888	+	0	NA	intron (NM_130773, intron 12 of 23)	intron (NM_130773, intron 12 of 23)	614380	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.006803	0.402715	166(AGGGACAACAAGTACT,-,0.00),243(CAGTACATTATGTACT,-,0.00),244(AGTACATTATGTACTT,+,0.00)
chunk0094_89_1	chr2	3971499	3971717	+	0	NA	intron (NR_037881, intron 1 of 2)	(GT)n|Simple_repeat|Simple_repeat	2424	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.004587	0.433790	
chunk0002_370_1	chr1	26238770	26238969	+	0	NA	intron (NM_022778, intron 1 of 13)	intron (NM_022778, intron 1 of 13)	4716	NM_001281517	64793	Hs.63795	NM_022778	ENSG00000130695	CEP85	CCDC21	centrosomal protein 85	protein-coding	0.015075	0.380000	
chunk0108_205_1	chr2	232833438	232833780	+	0	NA	intron (NM_001103146, intron 22 of 28)	intron (NM_001103146, intron 22 of 28)	-36675	NM_206895	389084	Hs.657509	NM_206895	ENSG00000182600	SNORC	ASCL830|C2orf82|UNQ830	secondary ossification center associated regulator of chondrocyte maturation	protein-coding	0.008772	0.387755	
chunk0194_421_1	chr8	92174168	92174496	+	0	NA	Intergenic	L1MEi|LINE|L1	-6821	NR_106988									0.006098	0.382979	
chunk0137_15_1	chr4	10797584	10798082	+	0	NA	Intergenic	L1PB1|LINE|L1	-113071	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.004016	0.348697	
chunk0033_192_1	chr11	16321413	16321796	+	0	NA	intron (NM_001145819, intron 2 of 15)	intron (NM_001145819, intron 2 of 15)	81263	NM_017508	55553	Hs.368226	NM_017508	ENSG00000110693	SOX6	HSSOX6|SOXD	SRY-box transcription factor 6	protein-coding	0.005222	0.411458	
chunk0141_120_1	chr4	79831077	79831767	+	0	NA	intron (NR_026555, intron 1 of 1)	LTR33A|LTR|ERVL	3951	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.004348	0.380608	
chunk0156_45_1	chr5	102795980	102796527	+	0	NA	Intergenic	Intergenic	-69570	NR_033440	5066	Hs.369430	NM_000919	ENSG00000145730	PAM	PAL|PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding	0.003656	0.417883	
chunk0082_45_1	chr17	50961663	50962035	+	0	NA	TTS (NM_003971)	TTS (NM_003971)	85119	NM_001251971	9043	Hs.463439	NM_003971	ENSG00000008294	SPAG9	CT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6	sperm associated antigen 9	protein-coding	0.018817	0.439678	
chunk0144_334_1	chr4	139118321	139118626	+	0	NA	intron (NM_201999, intron 3 of 8)	intron (NM_201999, intron 3 of 8)	21003	NM_201999	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.003279	0.392157	
chunk0066_216_1	chr15	33929711	33930027	+	0	NA	intron (NM_020371, intron 2 of 5)	intron (NM_020371, intron 2 of 5)	-39019	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.009494	0.331230	75(GGAAACACAGTGTCCC,-,0.00),76(GAAACACAGTGTCCCT,+,0.00)
chunk0207_136_1	chr9	129383002	129383485	+	0	NA	Intergenic	Intergenic	46320	NR_120685	100506119	Hs.624047	NR_120685	ENSG00000233901	LINC01503	-	long intergenic non-protein coding RNA 1503	ncRNA	0.041408	0.648760	317(AGGGACAGTCCGTGCA,-,0.00),318(GGGACAGTCCGTGCAG,+,0.00)
chunk0063_146_1	chr14	79801042	79801584	+	0	NA	intron (NR_073547, intron 18 of 20)	intron (NR_073547, intron 18 of 20)	-410106	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.007380	0.388582	
chunk0150_12_1	chr5	30451808	30452041	+	0	NA	Intergenic	Intergenic	-741731	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.000000	0.316239	
chunk0049_433_1	chr12	97970776	97970989	+	0	NA	Intergenic	Intergenic	24566	NR_036189	100422924		NR_036189	ENSG00000263890	MIR4303	-	microRNA 4303	ncRNA	0.014085	0.369159	
chunk0050_277_1	chr12	106301875	106302256	+	0	NA	promoter-TSS (NM_152772)	promoter-TSS (NM_152772)	-726	NM_152772	255394	Hs.696047	NM_152772	ENSG00000166046	TCP11L2	-	t-complex 11 like 2	protein-coding	0.060367	0.589005	298(GGGCACTCAATGTTCC,-,0.00),299(GGCACTCAATGTTCCA,+,0.00)
chunk0050_266_1	chr12	106035205	106035975	+	0	NA	Intergenic	Intergenic	104443	NM_014840	9891	Hs.524692	NM_014840	ENSG00000074590	NUAK1	ARK5	NUAK family kinase 1	protein-coding	0.007792	0.413748	
chunk0150_73_1	chr5	32153725	32154109	+	0	NA	intron (NM_022130, intron 1 of 3)	L1MC5a|LINE|L1	20402	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.007812	0.379221	
chunk0096_37_1	chr2	26892040	26892528	+	0	NA	intron (NM_001253724, intron 1 of 12)	MIRb|SINE|MIR	43860	NM_001253724	56896	Hs.299315	NM_020134	ENSG00000157851	DPYSL5	CRAM|CRMP-5|CRMP5|Ulip6	dihydropyrimidinase like 5	protein-coding	0.006148	0.400818	239(AGGCACAGGGTGTTTA,-,0.00),240(GGCACAGGGTGTTTAT,+,0.00)
chunk0171_150_1	chr6	123887301	123887620	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	83614	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.006270	0.384375	
chunk0081_411_1	chr17	48522205	48522629	+	0	NA	Intergenic	Intergenic	8493	NM_002144	3211	Hs.99992	NM_002144	ENSG00000120094	HOXB1	HCFP3|HOX2|HOX2I|Hox-2.9	homeobox B1	protein-coding	0.011792	0.567059	
chunk0144_272_1	chr4	137519511	137519866	+	0	NA	3' UTR (NM_019035, exon 4 of 4)	3' UTR (NM_019035, exon 4 of 4)	12810	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.005634	0.367978	
chunk0076_246_1	chr16	69234564	69234763	+	0	NA	intron (NM_006750, intron 1 of 6)	intron (NM_006750, intron 1 of 6)	47516	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.010050	0.375000	
chunk0103_4_1	chr2	158802722	158803357	+	0	NA	intron (NM_001017920, intron 1 of 3)	L1ME4b|LINE|L1	7722	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.001575	0.336478	216(AAACACAGGATGTTCA,-,0.00),217(AACACAGGATGTTCAT,+,0.00)
chunk0071_461_1	chr15	90397248	90397551	+	0	NA	intron (NM_003870, intron 2 of 37)	MIRb|SINE|MIR	9158	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.009901	0.355263	
chunk0195_399_1	chr8	100392580	100392983	+	0	NA	Intergenic	Intergenic	10018	NR_039681	100616451		NR_039681	ENSG00000265599	MIR4471	-	microRNA 4471	ncRNA	0.009926	0.425743	
chunk0026_96_1	chr10	61626452	61626755	+	0	NA	Intergenic	L1ME1|LINE|L1	-36358	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.000000	0.361842	
chunk0161_76_1	chr5	166853807	166854119	+	0	NA	Intergenic	L3|LINE|CR1	72407	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.006410	0.383387	
chunk0061_236_1	chr14	60710549	60710802	+	0	NA	3' UTR (NM_017420, exon 3 of 3)	3' UTR (NM_017420, exon 3 of 3)	13459	NM_017420	51804	Hs.97849	NM_017420	ENSG00000100625	SIX4	AREC3	SIX homeobox 4	protein-coding	0.000000	0.409449	232(AAGAACAATAAGTTCT,-,0.00),233(AGAACAATAAGTTCTT,+,0.00)
chunk0195_111_1	chr8	94722626	94722891	+	0	NA	intron (NM_181787, intron 1 of 18)	intron (NM_181787, intron 1 of 18)	2883	NM_181787	286148	Hs.567828	NM_181787	ENSG00000156162	DPY19L4	-	dpy-19 like 4	protein-coding	0.015094	0.357143	
chunk0110_357_1	chr20	19759016	19759575	+	0	NA	Intergenic	Intergenic	-127226	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.035778	0.494643	303(AGGAACACGCTGTCAT,-,0.00),304(GGAACACGCTGTCATC,+,0.00)
chunk0114_221_1	chr21	15749114	15749394	+	0	NA	intron (NM_013396, intron 1 of 23)	intron (NM_013396, intron 1 of 23)	19229	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.007143	0.334520	
chunk0082_53_1	chr17	51153772	51154018	+	0	NA	intron (NM_000269, intron 1 of 4)	L2c|LINE|L2	336	NM_000269	4830	Hs.463456	NM_000269	ENSG00000239672	NME1	AWD|GAAD|NB|NBS|NDKA|NDPK-A|NDPKA|NM23|NM23-H1	NME/NM23 nucleoside diphosphate kinase 1	protein-coding	0.081301	0.603239	
chunk0130_169_1	chr3	133110288	133110501	+	0	NA	intron (NM_001136469, intron 2 of 5)	intron (NM_001136469, intron 2 of 5)	-14427	NM_001282865	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.004695	0.439252	
chunk0156_53_1	chr5	103117721	103118158	+	0	NA	intron (NM_017676, intron 1 of 7)	intron (NM_017676, intron 1 of 7)	2199	NM_017676	54826	Hs.24088	NM_017676	ENSG00000145723	GIN1	GIN-1|TGIN1|ZH2C2	gypsy retrotransposon integrase 1	protein-coding	0.004577	0.310502	
chunk0129_427_1	chr3	127542323	127542802	+	0	NA	Intergenic	Intergenic	-4782	NR_125397	101927149	Hs.407798	NR_125397	ENSG00000239921	LINC01471	-	long intergenic non-protein coding RNA 1471	ncRNA	0.022965	0.606250	
chunk0143_274_1	chr4	116650109	116650582	+	0	NA	Intergenic	Intergenic	350620	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.004228	0.324895	
chunk0206_381_1	chr9	126704825	126705035	+	0	NA	Intergenic	Intergenic	90487	NM_001174147	4010	Hs.129133	NM_002316	ENSG00000136944	LMX1B	LMX1.2|NPS1	LIM homeobox transcription factor 1 beta	protein-coding	0.009524	0.511848	132(GTCACATCCTGTTCTT,+,0.00)
chunk0089_218_1	chr18	61285800	61286295	+	0	NA	Intergenic	L2c|LINE|L2	-204495	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.006061	0.368952	
chunk0177_449_1	chr7	28103957	28104634	+	0	NA	intron (NM_175061, intron 1 of 4)	L2a|LINE|L2	-76162	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.007386	0.460177	
chunk0141_405_1	chr4	88584358	88584884	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-7802	NM_014606	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.007605	0.423150	297(GAGGACACAGAGTTCC,-,0.00),298(AGGACACAGAGTTCCT,+,0.00)
chunk0079_268_1	chr17	16206581	16207003	+	0	NA	intron (NM_006311, intron 1 of 45)	intron (NM_006311, intron 1 of 45)	8768	NM_006311	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.007109	0.342790	214(AGTACATTATGATCCC,+,0.00)
chunk0189_302_1	chr8	26019698	26019897	+	0	NA	intron (NM_022659, intron 6 of 15)	intron (NM_022659, intron 6 of 15)	25327	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.000000	0.470000	
chunk0068_255_1	chr15	56225694	56226058	+	0	NA	intron (NM_022841, intron 1 of 8)	intron (NM_022841, intron 1 of 8)	17409	NM_022841	64864	Hs.745089	NM_022841	ENSG00000181827	RFX7	RFXDC2	regulatory factor X7	protein-coding	0.005495	0.301370	
chunk0050_180_1	chr12	103858967	103859372	+	0	NA	intron (NR_027249, intron 13 of 15)	intron (NR_027249, intron 13 of 15)	-17972	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.022222	0.507389	
chunk0067_422_1	chr15	49824748	49825167	+	0	NA	Intergenic	Intergenic	203928	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.002387	0.419048	
chunk0158_394_1	chr5	134626383	134626758	+	0	NA	intron (NM_016103, intron 1 of 6)	intron (NM_016103, intron 1 of 6)	6273	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.002667	0.345745	
chunk0034_194_1	chr11	32050163	32050669	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-9098	NR_120527	100506675	Hs.446169	NR_120526	ENSG00000254584	LOC100506675	-	uncharacterized LOC100506675	ncRNA	0.009881	0.398422	
chunk0207_359_1	chr9	135320678	135320877	+	0	NA	Intergenic	Intergenic	-22472	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.015075	0.465000	
chunk0143_332_1	chr4	120242154	120242677	+	0	NA	Intergenic	Intergenic	-175557	NM_002358	4085	Hs.591697	NM_002358	ENSG00000164109	MAD2L1	HSMAD2|MAD2	mitotic arrest deficient 2 like 1	protein-coding	0.001912	0.339695	
chunk0023_326_1	chr10	29241087	29241639	+	0	NA	Intergenic	Intergenic	-47698	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.023551	0.553345	135(GAGGACAGGCTGTTTA,-,0.00),136(AGGACAGGCTGTTTAC,+,0.00),319(CAGATCAGGGTGTTCT,-,0.00),320(AGATCAGGGTGTTCTC,+,0.00)
chunk0091_253_1	chr19	10870810	10871154	+	0	NA	promoter-TSS (NM_199141)	promoter-TSS (NM_199141)	-595	NM_199141	10498	Hs.323213	NM_199141	ENSG00000142453	CARM1	PRMT4	coactivator associated arginine methyltransferase 1	protein-coding	0.104651	0.750725	
chunk0004_58_1	chr1	43152982	43153333	+	0	NA	intron (NM_001101376, intron 3 of 3)	MIR|SINE|MIR	5234	NM_001101376	440585	Hs.657614	NM_001101376	ENSG00000186973	FAM183A	-	family with sequence similarity 183 member A	protein-coding	0.008547	0.440341	
chunk0167_419_1	chr6	75482636	75482988	+	0	NA	intron (NR_110608, intron 1 of 1)	intron (NR_110608, intron 1 of 1)	11017	NM_001289987	27145	Hs.201488	NM_015687	ENSG00000118407	FILIP1	FILIP	filamin A interacting protein 1	protein-coding	0.002841	0.286119	
chunk0062_29_1	chr14	66993490	66993904	+	0	NA	intron (NM_001024218, intron 8 of 21)	intron (NM_001024218, intron 8 of 21)	-195696	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.002415	0.306024	
chunk0152_431_1	chr5	66009067	66009693	+	0	NA	intron (NM_018695, intron 4 of 24)	intron (NM_018695, intron 4 of 24)	-63807	NR_028474	100303749	Hs.608060	NR_028474		LOC100303749	-	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene	pseudo	0.004792	0.360447	
chunk0144_263_1	chr4	137029624	137029950	+	0	NA	Intergenic	L1PA15|LINE|L1	502711	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.006135	0.363914	208(TTGAACAGGAAGTCCT,-,0.00),209(TGAACAGGAAGTCCTT,+,0.00)
chunk0008_234_1	chr1	94171118	94171614	+	0	NA	3' UTR (NM_004815, exon 23 of 23)	3' UTR (NM_004815, exon 23 of 23)	-50217	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.010081	0.400402	
chunk0162_114_1	chr6	2767255	2767770	+	0	NA	intron (NM_020135, intron 1 of 6)	intron (NM_020135, intron 1 of 6)	2080	NM_130395	56897	Hs.236828	NM_020135	ENSG00000124535	WRNIP1	WHIP|bA420G6.2	WRN helicase interacting protein 1	protein-coding	0.007767	0.422481	
chunk0046_414_1	chr12	64446249	64446849	+	0	NA	intron (NM_007235, intron 24 of 24)	intron (NM_007235, intron 24 of 24)	-5511	NM_013254	29110	Hs.505874	NM_013254	ENSG00000183735	TBK1	FTDALS4|IIAE8|NAK|T2K	TANK binding kinase 1	protein-coding	0.001667	0.376040	
chunk0045_310_1	chr12	50672639	50673288	+	0	NA	intron (NM_173602, intron 5 of 37)	L1ME4a|LINE|L1	-91043	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.003082	0.289231	
chunk0004_154_1	chr1	45373652	45373922	+	0	NA	intron (NM_007170, intron 4 of 10)	intron (NM_007170, intron 4 of 10)	-33317	NM_001293192	4595	Hs.271353	NM_012222	ENSG00000132781	MUTYH	MYH	mutY DNA glycosylase	protein-coding	0.000000	0.416974	
chunk0163_102_1	chr6	9675013	9675499	+	0	NA	Intergenic	Intergenic	-737062	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.008230	0.379877	
chunk0066_348_1	chr15	37943807	37944323	+	0	NA	intron (NM_152453, intron 10 of 11)	intron (NM_152453, intron 10 of 11)	9458	NM_152453	145942	Hs.179646	NM_152453	ENSG00000166069	TMCO5A	TMCO5	transmembrane and coiled-coil domains 5A	protein-coding	0.005814	0.371373	
chunk0022_155_1	chr10	12531184	12531855	+	0	NA	intron (NM_020397, intron 1 of 9)	intron (NM_020397, intron 1 of 9)	-47234	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.019374	0.446429	
chunk0015_437_1	chr1	191765195	191765778	+	0	NA	Intergenic	Intergenic	-392976	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.005146	0.383562	
chunk0208_116_1	chrX	14295980	14296451	+	0	NA	Intergenic	Intergenic	51950	NR_110506	286480	Hs.567831	NR_110506		UBE2E4P	UbcM2	ubiquitin conjugating enzyme E2 E4 pseudogene	pseudo	0.008493	0.368644	207(CAGTACATCCTGTTCC,-,0.00),208(AGTACATCCTGTTCCT,+,0.00)
chunk0060_144_1	chr14	45003746	45004460	+	0	NA	exon (NM_015091, exon 4 of 19)	exon (NM_015091, exon 4 of 19)	41913	NM_001308120	23116	Hs.371078	NM_015091	ENSG00000198718	TOGARAM1	FAM179B|KIAA0423	TOG array regulator of axonemal microtubules 1	protein-coding	0.005602	0.323077	
chunk0044_305_1	chr12	33256561	33256974	+	0	NA	Intergenic	Intergenic	183052	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.012107	0.371981	186(TGGGACTGCATGTACT,-,0.00),187(GGGACTGCATGTACTG,+,0.00)
chunk0127_363_1	chr3	101651110	101651360	+	0	NA	exon (NM_014415, exon 11 of 11)	exon (NM_014415, exon 11 of 11)	-25195	NR_024407	100009676	Hs.743292	NR_024407	ENSG00000256628	ZBTB11-AS1	-	ZBTB11 antisense RNA 1	ncRNA	0.004000	0.386454	
chunk0118_164_1	chr22	30592110	30592309	+	0	NA	promoter-TSS (NM_001243225)	promoter-TSS (NM_001243225)	-269	NM_014303	23481	Hs.517543	NM_014303	ENSG00000100029	PES1	NOP7|PES	pescadillo ribosomal biogenesis factor 1	protein-coding	0.080402	0.575000	
chunk0054_273_1	chr13	46615824	46616294	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	62898	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.010638	0.394904	
chunk0202_128_1	chr9	73199958	73200424	+	0	NA	Intergenic	Intergenic	48460	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.019313	0.402570	
chunk0204_291_1	chr9	99381309	99381701	+	0	NA	Intergenic	L2c|LINE|L2	-6248	NR_102271	100996569	Hs.745280	NR_102270	ENSG00000271086	NAMA	-	non-protein coding RNA, associated with MAP kinase pathway and growth arrest	ncRNA	0.007653	0.437659	
chunk0030_288_1	chr10	116973377	116973948	+	0	NA	intron (NM_001258298, intron 1 of 15)	intron (NM_001258298, intron 1 of 15)	31915	NM_001127211	57698	Hs.501140	NM_018330	ENSG00000187164	SHTN1	KIAA1598|shootin-1	shootin 1	protein-coding	0.008757	0.372378	
chunk0086_368_1	chr18	26073767	26074139	+	0	NA	intron (NM_001308201, intron 3 of 10)	Charlie1a|DNA|hAT-Charlie	16694	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.005376	0.343164	
chunk0080_164_1	chr17	28335529	28335768	+	0	NA	promoter-TSS (NM_001267775)	promoter-TSS (NM_001267775)	126	NM_021137	7126	Hs.76090	NM_021137	ENSG00000109079	TNFAIP1	B12|B61|BTBD34|EDP1|hBACURD2	TNF alpha induced protein 1	protein-coding	0.071130	0.658333	
chunk0172_144_1	chr6	135494405	135494742	+	0	NA	intron (NM_001134830, intron 1 of 26)	MIRb|SINE|MIR	3192	NM_001134831	54806	Hs.386684	NM_017651	ENSG00000135541	AHI1	AHI-1|JBTS3|ORF1|dJ71N10.1	Abelson helper integration site 1	protein-coding	0.005935	0.355030	
chunk0176_202_1	chr7	14682462	14682720	+	0	NA	exon (NM_004080, exon 11 of 25)	exon (NM_004080, exon 11 of 25)	158859	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.003876	0.432432	
chunk0122_67_1	chr3	29192083	29192643	+	0	NA	Intergenic	L1MA8|LINE|L1	88576	NR_109804	100873979	Hs.99391	NR_109804		RBMS3-AS3	-	RBMS3 antisense RNA 3	ncRNA	0.007143	0.286988	
chunk0070_114_1	chr15	70611190	70611469	+	0	NA	Intergenic	L1M5|LINE|L1	-4218	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.007168	0.489286	
chunk0200_100_1	chr9	16701271	16701696	+	0	NA	intron (NM_017637, intron 3 of 6)	MIRb|SINE|MIR	169305	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.002353	0.340376	
chunk0145_249_1	chr4	148821511	148822005	+	0	NA	Intergenic	Intergenic	-332537	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.002024	0.323232	
chunk0159_432_1	chr5	148193568	148194050	+	0	NA	Intergenic	L2c|LINE|L2	-8985	NM_001195290	404203	Hs.334274	NM_205841	ENSG00000178172	SPINK6	BUSI2|UNQ844	serine peptidase inhibitor, Kazal type 6	protein-coding	0.008299	0.354037	296(GGGCACATTCTGTTTT,-,0.00),297(GGCACATTCTGTTTTC,+,0.00)
chunk0099_254_1	chr2	97934703	97935468	+	0	NA	intron (NM_015348, intron 1 of 40)	L1MDb|LINE|L1	60806	NM_015348	23505	Hs.469376	NM_015348	ENSG00000075568	TMEM131	CC28|PRO1048|RW1|YR-23	transmembrane protein 131	protein-coding	0.001307	0.319843	
chunk0053_264_1	chr13	33100966	33101490	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	84795	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.001908	0.354286	
chunk0118_414_1	chr22	38187484	38187775	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-5800	NM_001199562	8398	Hs.170479	NM_003560	ENSG00000184381	PLA2G6	CaI-PLA2|GVI|INAD1|IPLA2-VIA|NBIA2|NBIA2A|NBIA2B|PARK14|PLA2|PNPLA9|iPLA2|iPLA2beta	phospholipase A2 group VI	protein-coding	0.010309	0.428082	
chunk0157_1_1	chr5	115124891	115125123	+	0	NA	3' UTR (NM_018700, exon 10 of 10)	3' UTR (NM_018700, exon 10 of 10)	44956	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.004310	0.360515	
chunk0092_381_1	chr19	36332111	36332566	+	0	NA	promoter-TSS (NR_038279)	promoter-TSS (NR_038279)	-620	NR_038279	100506930	Hs.595153	NR_038278	ENSG00000232677	LINC00665	-	long intergenic non-protein coding RNA 665	ncRNA	0.024176	0.491228	
chunk0132_179_1	chr3	157013823	157014059	+	0	NA	intron (NM_001004316, intron 10 of 12)	intron (NM_001004316, intron 10 of 12)	-75940	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.004237	0.244726	
chunk0136_4_1	chr4	28585	29780	+	0	NA	Intergenic	Intergenic	-24103	NM_001286054	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.003347	0.396321	
chunk0067_288_1	chr15	47428698	47428928	+	0	NA	intron (NM_001198999, intron 2 of 19)	intron (NM_001198999, intron 2 of 19)	244607	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.004348	0.406926	
chunk0019_17_1	chr1	223430112	223430714	+	0	NA	Intergenic	Intergenic	37040	NM_152610	164127	Hs.192090	NM_152610	ENSG00000178395	CCDC185	C1orf65	coiled-coil domain containing 185	protein-coding	0.003322	0.451078	
chunk0055_222_1	chr13	62510794	62511214	+	0	NA	Intergenic	L1PA16|LINE|L1	285688	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.002381	0.358670	
chunk0155_219_1	chr5	95323218	95323894	+	0	NA	Intergenic	HAL1|LINE|L1	-38981	NM_024717	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.005917	0.373708	
chunk0162_464_1	chr5	181044836	181045151	+	0	NA	intron (NM_001308245, intron 1 of 10)	intron (NM_001308245, intron 1 of 10)	-1509	NR_107056	102465882		NR_107056	ENSG00000277912	MIR8089	hsa-mir-8089	microRNA 8089	ncRNA	0.022222	0.547468	
chunk0017_405_1	chr1	212721561	212721884	+	0	NA	Intergenic	Intergenic	-21737	NM_018664	55509	Hs.62919	NM_018664	ENSG00000123685	BATF3	JDP1|JUNDM1|SNFT	basic leucine zipper ATF-like transcription factor 3	protein-coding	0.009288	0.447531	
chunk0164_68_1	chr6	19536763	19536962	+	0	NA	Intergenic	L2b|LINE|L2	-300508	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.005025	0.365000	
chunk0195_338_1	chr8	99322922	99323407	+	0	NA	intron (NM_152564, intron 19 of 61)	intron (NM_152564, intron 19 of 61)	213566	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.012371	0.370370	
chunk0037_144_1	chr11	73255225	73255545	+	0	NA	Intergenic	L1ME4b|LINE|L1	-9120	NM_176796	5031	Hs.16362	NM_004154	ENSG00000171631	P2RY6	P2Y6	pyrimidinergic receptor P2Y6	protein-coding	0.003125	0.317757	
chunk0203_195_1	chr9	86439589	86440281	+	0	NA	Intergenic	Intergenic	-85448	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.002890	0.367965	
chunk0056_444_1	chr13	95197608	95197951	+	0	NA	intron (NM_001105515, intron 8 of 20)	intron (NM_001105515, intron 8 of 20)	103667	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.011662	0.380814	
chunk0171_237_1	chr6	126931754	126932314	+	0	NA	Intergenic	Intergenic	-186869	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.000000	0.344029	
chunk0175_321_1	chr6	166875020	166875543	+	0	NA	Intergenic	L1M5|LINE|L1	-12998	NM_001006932	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.003824	0.301527	
chunk0071_77_1	chr15	80749566	80750053	+	0	NA	intron (NM_021214, intron 2 of 2)	L2b|LINE|L2	-29534	NM_001293298	57214	Hs.459088	NM_018689	ENSG00000103888	CEMIP	CCSP1|HYBID|KIAA1199|TMEM2L	cell migration inducing hyaluronidase 1	protein-coding	0.018480	0.444672	
chunk0117_18_1	chr22	11298337	11298647	+	0	NA	Intergenic	Intergenic	-336963	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.006452	0.556270	
chunk0080_414_1	chr17	35705884	35706537	+	0	NA	intron (NM_001030006, intron 18 of 21)	Charlie4z|DNA|hAT-Charlie	-25450	NM_033315	91608	Hs.744994	NM_033315	ENSG00000270885	RASL10B	RRP17|VTS58635	RAS like family 10 member B	protein-coding	0.003063	0.406728	
chunk0182_444_1	chr7	101819429	101819628	+	0	NA	intron (NM_181552, intron 1 of 23)	intron (NM_181552, intron 1 of 23)	1926	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.000000	0.340000	
chunk0161_290_1	chr5	172999455	173000554	+	0	NA	intron (NM_003945, intron 2 of 3)	intron (NM_003945, intron 2 of 3)	16244	NM_003945	8992	Hs.484188	NM_003945	ENSG00000113732	ATP6V0E1	ATP6H|ATP6V0E|M9.2|Vma21|Vma21p	ATPase H+ transporting V0 subunit e1	protein-coding	0.003640	0.365455	324(TGGTACACAGTGTTCC,-,0.00),325(GGTACACAGTGTTCCA,+,0.00)
chunk0211_356_1	chrX	125583445	125584131	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	263668	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.010204	0.430859	269(AAGAACAGATTGTCTC,-,0.00),270(AGAACAGATTGTCTCT,+,0.00),564(AAGAACTGGTTGTTCA,-,0.00),565(AGAACTGGTTGTTCAA,+,0.00)
chunk0030_422_1	chr10	120279102	120279610	+	0	NA	Intergenic	Intergenic	75867	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.003937	0.361493	
chunk0099_382_1	chr2	101215084	101215600	+	0	NA	Intergenic	Intergenic	-37541	NM_017546	55571	Hs.744080	NM_017546	ENSG00000158435	CNOT11	C2orf29|C40	CCR4-NOT transcription complex subunit 11	protein-coding	0.001938	0.384913	275(CAGTACACTGTGTGCT,-,0.00),276(AGTACACTGTGTGCTG,+,0.00)
chunk0058_183_1	chr14	24019843	24020412	+	0	NA	intron (NR_102687, intron 1 of 3)	MER102a|DNA|hAT-Charlie	13118	NR_102687	728635	Hs.647569	NM_001082488		DHRS4L1	SDR25C4	dehydrogenase/reductase 4 like 1	protein-coding	0.007030	0.375439	290(TGGAACTGGGTGTGCC,-,0.00),291(GGAACTGGGTGTGCCT,+,0.00)
chunk0187_149_1	chr7	149962585	149962788	+	0	NA	Intergenic	Intergenic	-88824	NR_027040	401431	Hs.556998	NM_001008745	ENSG00000204934	ATP6V0E2-AS1	-	ATP6V0E2 antisense RNA 1	ncRNA	0.004926	0.460784	
chunk0153_49_1	chr5	67412960	67413184	+	0	NA	Intergenic	Intergenic	-216283	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.004464	0.404444	
chunk0197_234_1	chr8	123096586	123096893	+	0	NA	intron (NM_001145088, intron 5 of 19)	intron (NM_001145088, intron 5 of 19)	24059	NM_001145088	93594	Hs.492716	NM_145647	ENSG00000156787	TBC1D31	Gm85|WDR67	TBC1 domain family member 31	protein-coding	0.003257	0.386364	
chunk0119_44_1	chr22	40678294	40678701	+	0	NA	promoter-TSS (NM_005297)	promoter-TSS (NM_005297)	-681	NM_005297	2847	Hs.248122	NM_005297	ENSG00000128285	MCHR1	GPR24|MCH-1R|MCH1R|SLC-1|SLC1	melanin concentrating hormone receptor 1	protein-coding	0.012285	0.490196	
chunk0036_152_1	chr11	62323705	62324112	+	0	NA	Intergenic	Intergenic	-13394	NM_001083926	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.002457	0.428922	
chunk0040_431_1	chr11	121421153	121421689	+	0	NA	Intergenic	Intergenic	-30782	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.003731	0.387337	
chunk0032_449_1	chr10	133132088	133132312	+	0	NA	TTS (NM_001083909)	TTS (NM_001083909)	-28267	NM_152643	85442	Hs.530685	NM_152643	ENSG00000171798	KNDC1	C10orf23|RASGEF2|Very-KIND|bB439H18.3|v-KIND	kinase non-catalytic C-lobe domain containing 1	protein-coding	0.084821	0.635556	
chunk0207_241_1	chr9	132009104	132009323	+	0	NA	intron (NM_001253881, intron 3 of 6)	L2c|LINE|L2	70674	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.013699	0.386364	
chunk0024_89_1	chr10	34438381	34438774	+	0	NA	intron (NM_001184790, intron 4 of 22)	intron (NM_001184790, intron 4 of 22)	376748	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.296954	198(AGGGACATTATGAACT,-,0.00),199(GGGACATTATGAACTT,+,0.00)
chunk0063_231_1	chr14	81694315	81694881	+	0	NA	Intergenic	Intergenic	-71537	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.001767	0.384480	
chunk0130_419_1	chr3	140720022	140720723	+	0	NA	Intergenic	Intergenic	42348	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.004280	0.415954	362(GAGAACAAAATGTTCC,-,0.00),363(AGAACAAAATGTTCCC,+,0.00)
chunk0058_225_1	chr14	25112781	25113087	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-62637	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.003268	0.368078	134(GAGTACAGTGTGTACC,-,0.00),135(AGTACAGTGTGTACCT,+,0.00)
chunk0071_399_1	chr15	89379788	89380198	+	0	NA	intron (NR_133001, intron 3 of 6)	MIRb|SINE|MIR	1951	NR_015411	254559	Hs.136313	NR_015411	ENSG00000255571	MIR9-3HG	LINC00925	MIR9-3 host gene	ncRNA	0.014634	0.515815	
chunk0106_253_1	chr2	203578826	203579498	+	0	NA	Intergenic	Intergenic	-43827	NM_203365	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.002976	0.420505	195(CAGGACATGATGTCTT,-,0.00),196(AGGACATGATGTCTTT,+,0.00)
chunk0113_283_1	chr20	57006847	57007137	+	0	NA	Intergenic	Intergenic	-206704	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.020690	0.439863	
chunk0025_237_1	chr10	54257963	54258503	+	0	NA	intron (NM_001142769, intron 9 of 35)	intron (NM_001142769, intron 9 of 35)	349724	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.005556	0.330869	
chunk0082_174_1	chr17	56098783	56099210	+	0	NA	Intergenic	Intergenic	-54479	NM_153228	162282	Hs.673040	NM_153228	ENSG00000153930	ANKFN1	-	ankyrin repeat and fibronectin type III domain containing 1	protein-coding	0.009368	0.429907	125(AAGGACACAATGTCTT,-,0.00),126(AGGACACAATGTCTTT,+,0.00)
chunk0021_321_1	chr1	245326028	245326380	+	0	NA	intron (NM_018012, intron 2 of 14)	intron (NM_018012, intron 2 of 14)	171219	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.017045	0.430595	
chunk0209_297_1	chrX	48621007	48621375	+	0	NA	Intergenic	Intergenic	23355	NM_001166426	64743	Hs.521973	NM_017883	ENSG00000101940	WDR13	MG21	WD repeat domain 13	protein-coding	0.008152	0.417344	
chunk0120_66_1	chr3	3230180	3230702	+	0	NA	Intergenic	Intergenic	-50724	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.011494	0.390057	
chunk0193_200_1	chr8	75921959	75922347	+	0	NA	Intergenic	Intergenic	382185	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.000000	0.318766	
chunk0197_372_1	chr8	126563791	126564085	+	0	NA	Intergenic	Intergenic	-5472	NM_174911	157638	Hs.124951	NM_174911	ENSG00000168672	LRATD2	BCMP101|FAM84B|NSE2	LRAT domain containing 2	protein-coding	0.010204	0.505085	
chunk0156_174_1	chr5	107646127	107646866	+	0	NA	intron (NM_001962, intron 1 of 4)	L2b|LINE|L2	24399	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.002706	0.320270	
chunk0144_215_1	chr4	134415186	134415647	+	0	NA	Intergenic	Intergenic	-213668	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.008677	0.374459	242(AGGAACACCGTGTTCT,-,0.00),243(GGAACACCGTGTTCTC,+,0.00)
chunk0007_335_1	chr1	84772694	84773626	+	0	NA	Intergenic	Intergenic	-82603	NM_001166293	117178	Hs.22587	NM_014021	ENSG00000117155	SSX2IP	ADIP|hMsd1	SSX family member 2 interacting protein	protein-coding	0.011803	0.474812	
chunk0180_241_1	chr7	67692407	67692707	+	0	NA	Intergenic	L1MEd|LINE|L1	-327696	NR_120514	102723427	Hs.583491	NR_120514	ENSG00000225209	LOC102723427	-	uncharacterized LOC102723427	ncRNA	0.010000	0.421927	
chunk0036_396_1	chr11	67745188	67745451	+	0	NA	Intergenic	Intergenic	60017	NR_024249	645332	Hs.535094	NR_024249	ENSG00000160172	FAM86C2P	-	family with sequence similarity 86, member A pseudogene	pseudo	0.019011	0.469697	
chunk0034_30_1	chr11	26446133	26446601	+	0	NA	intron (NM_031418, intron 3 of 26)	intron (NM_031418, intron 3 of 26)	-27535	NM_001313727	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.006410	0.358209	
chunk0049_371_1	chr12	95735484	95735988	+	0	NA	intron (NM_021229, intron 3 of 9)	intron (NM_021229, intron 3 of 9)	55022	NM_021229	59277	Hs.201034	NM_021229	ENSG00000074527	NTN4	PRO3091	netrin 4	protein-coding	0.001984	0.291089	
chunk0012_253_1	chr1	161314239	161314438	+	0	NA	promoter-TSS (NM_003001)	promoter-TSS (NM_003001)	-38	NR_103459	6391	Hs.444472	NM_003001	ENSG00000143252	SDHC	CYB560|CYBL|PGL3|QPS1|SDH3	succinate dehydrogenase complex subunit C	protein-coding	0.070352	0.635000	
chunk0202_122_1	chr9	73039272	73039471	+	0	NA	Intergenic	Intergenic	-86054	NM_000689	216	Hs.76392	NM_000689	ENSG00000165092	ALDH1A1	ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1	aldehyde dehydrogenase 1 family member A1	protein-coding	0.005025	0.450000	123(AGGAACAGAATGTGCT,-,0.00),124(GGAACAGAATGTGCTT,+,0.00)
chunk0100_183_1	chr2	110773510	110774033	+	0	NA	intron (NM_001142807, intron 2 of 17)	intron (NM_001142807, intron 2 of 17)	41198	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.013384	0.568702	
chunk0163_108_1	chr6	10079315	10079514	+	0	NA	Intergenic	Intergenic	-332904	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.000000	0.385000	
chunk0023_63_1	chr10	22053987	22054374	+	0	NA	Intergenic	Intergenic	-50459	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.005168	0.414948	
chunk0126_391_1	chr3	84885199	84886023	+	0	NA	Intergenic	L1PA6|LINE|L1	-16036	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.016990	0.516364	
chunk0156_211_1	chr5	108113996	108114448	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	267876	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.004425	0.293598	
chunk0146_359_1	chr4	168164935	168165351	+	0	NA	intron (NM_007193, intron 5 of 11)	intron (NM_007193, intron 5 of 11)	72606	NM_007193	11199	Hs.188401	NM_007193	ENSG00000109511	ANXA10	ANX14	annexin A10	protein-coding	0.002404	0.350120	
chunk0066_342_1	chr15	37292053	37292252	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-190853	NM_002399	4212	Hs.510989	NM_002399	ENSG00000134138	MEIS2	CPCMR|HsT18361|MRG1	Meis homeobox 2	protein-coding	0.005025	0.360000	
chunk0145_200_1	chr4	147916273	147916949	+	0	NA	intron (NM_024605, intron 13 of 22)	intron (NM_024605, intron 13 of 22)	134016	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.008876	0.400295	283(GAGAACTGGCAGTGCC,-,0.00),284(AGAACTGGCAGTGCCC,+,0.00)
chunk0153_141_1	chr5	69030663	69031102	+	0	NA	promoter-TSS (NR_130778)	promoter-TSS (NR_130778)	-955	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.006834	0.363636	196(CAGAACTGCATGTACT,-,0.00),197(AGAACTGCATGTACTC,+,0.00)
chunk0100_225_1	chr2	112027809	112028224	+	0	NA	intron (NM_006343, intron 18 of 18)	MER58A|DNA|hAT-Charlie	-27207	NM_032824	84910	Hs.656298	NM_032824	ENSG00000153214	TMEM87B	-	transmembrane protein 87B	protein-coding	0.007229	0.384615	
chunk0119_191_1	chr22	44569197	44569482	+	0	NA	promoter-TSS (NR_028411)	promoter-TSS (NR_028411)	-1	NR_028411	388910	Hs.332685	NM_001012986	ENSG00000187012	LINC00207	NCRNA00207	long intergenic non-protein coding RNA 207	ncRNA	0.017544	0.482517	
chunk0113_423_1	chr20	62105157	62105379	+	0	NA	Intergenic	L2c|LINE|L2	-17193	NM_144703	149986	Hs.105379	NM_144703	ENSG00000149657	LSM14B	C20orf40|FAM61B|FT005|LSM13|RAP55B|bA11M20.3	LSM family member 14B	protein-coding	0.009009	0.484305	
chunk0205_402_1	chr9	114621965	114622176	+	0	NA	intron (NM_153045, intron 2 of 8)	intron (NM_153045, intron 2 of 8)	10644	NM_153045	203197	Hs.522357	NM_153045	ENSG00000157693	TMEM268	C9orf91	transmembrane protein 268	protein-coding	0.000000	0.528302	
chunk0129_90_1	chr3	119279052	119279251	+	0	NA	intron (NR_046574, intron 3 of 3)	MIRb|SINE|MIR	-15222	NM_020754	57514	Hs.668218	NM_020754	ENSG00000031081	ARHGAP31	AOS1|CDGAP	Rho GTPase activating protein 31	protein-coding	0.005025	0.525000	
chunk0152_362_1	chr5	63773818	63774138	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	188314	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.003125	0.339564	
chunk0043_150_1	chr12	16357610	16358091	+	0	NA	intron (NM_001267598, intron 3 of 3)	intron (NM_001267598, intron 3 of 3)	4433	NM_145764	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.010395	0.383817	
chunk0160_261_1	chr5	156972105	156972770	+	0	NA	Intergenic	Intergenic	-9182	NM_138379	91937	Hs.334907	NM_138379	ENSG00000145850	TIMD4	SMUCKLER|TIM4	T cell immunoglobulin and mucin domain containing 4	protein-coding	0.003008	0.442943	339(AGGAACAGAAAGTCCA,-,0.00),340(GGAACAGAAAGTCCAA,+,0.00)
chunk0176_329_1	chr7	17260515	17261072	+	0	NA	Intergenic	Intergenic	-37859	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.000000	0.284946	
chunk0198_71_1	chr8	129985278	129985939	+	0	NA	intron (NR_046360, intron 1 of 14)	intron (NR_046360, intron 1 of 14)	22845	NR_049826	100847051		NR_049826	ENSG00000264653	MIR5194	mir-5194	microRNA 5194	ncRNA	0.012103	0.527190	
chunk0141_116_1	chr4	79690387	79690841	+	0	NA	Intergenic	L1PB3|LINE|L1	-136857	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.004405	0.353846	
chunk0013_20_1	chr1	165894548	165894747	+	0	NA	intron (NM_012474, intron 3 of 6)	intron (NM_012474, intron 3 of 6)	-13274	NR_037431	100500832		NR_037431	ENSG00000283936	MIR3658	-	microRNA 3658	ncRNA	0.010050	0.470000	
chunk0147_381_1	chr4	186445021	186445375	+	0	NA	intron (NR_033900, intron 1 of 3)	intron (NR_033900, intron 1 of 3)	55860	NR_033900	285441	Hs.481369	NR_033900	ENSG00000251165	F11-AS1	-	F11 antisense RNA 1	ncRNA	0.016949	0.363380	
chunk0066_220_1	chr15	33965924	33966620	+	0	NA	intron (NM_020371, intron 2 of 5)	intron (NM_020371, intron 2 of 5)	-2616	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.002874	0.354376	437(GGCACATATAGTCCTT,+,0.00)
chunk0076_312_1	chr16	70364739	70364963	+	0	NA	intron (NM_018332, intron 6 of 11)	intron (NM_018332, intron 6 of 11)	17930	NM_018332	55308	Hs.656037	NM_018332	ENSG00000168872	DDX19A	DDX19-DDX19L|DDX19L	DEAD-box helicase 19A	protein-coding	0.000000	0.551111	
chunk0121_139_1	chr3	18767848	18768394	+	0	NA	Intergenic	L2b|LINE|L2	322884	NR_125803	101927777	Hs.543235	NR_125803		SATB1-AS1	-	SATB1 antisense RNA 1	ncRNA	0.007326	0.455210	248(AAGCACAGACTCTGCT,-,0.00)
chunk0086_362_1	chr18	25974100	25974751	+	0	NA	Intergenic	Intergenic	116222	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.009217	0.394172	
chunk0030_282_1	chr10	116848362	116848870	+	0	NA	promoter-TSS (NM_001242699)	promoter-TSS (NM_001242699)	-896	NM_001242699	387712	Hs.693248	NM_001242699	ENSG00000188316	ENO4	C10orf134	enolase 4	protein-coding	0.021654	0.483301	
chunk0008_378_1	chr1	96931069	96931571	+	0	NA	Intergenic	Intergenic	-164603	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.001992	0.353877	
chunk0039_224_1	chr11	101511295	101511514	+	0	NA	intron (NM_004621, intron 1 of 12)	L2b|LINE|L2	8501	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.009132	0.381818	
chunk0191_198_1	chr8	51859624	51859892	+	0	NA	intron (NM_001286783, intron 1 of 5)	MER94|DNA|hAT-Blackjack	39428	NM_052937	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.000000	0.345725	
chunk0051_117_1	chr12	115204165	115204610	+	0	NA	Intergenic	L1ME4a|LINE|L1	-520223	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.002247	0.369955	
chunk0131_40_1	chr3	142553239	142553902	+	0	NA	intron (NM_001184, intron 12 of 46)	intron (NM_001184, intron 12 of 46)	25256	NM_001184	545	Hs.271791	NM_001184	ENSG00000175054	ATR	FCTCS|FRP1|MEC1|SCKL|SCKL1	ATR serine/threonine kinase	protein-coding	0.004525	0.338855	
chunk0189_308_1	chr8	26053899	26054432	+	0	NA	Intergenic	Intergenic	-9041	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.005629	0.327715	
chunk0101_122_1	chr2	126998247	126998482	+	0	NA	Intergenic	L1ME3|LINE|L1	108963	NM_139349	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.004255	0.296610	
chunk0034_286_1	chr11	34670919	34671666	+	0	NA	Intergenic	HAL1b|LINE|L1	38828	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.004016	0.356952	
chunk0042_372_1	chr12	10548773	10549009	+	0	NA	Intergenic	Intergenic	50944	NR_028045	10748	Hs.159297	NM_006611		KLRA1P	KLRA1|KLRAP1|LY49L|Ly-49L|Ly49	killer cell lectin like receptor A1, pseudogene	pseudo	0.008475	0.367089	
chunk0210_295_1	chrX	87040012	87040295	+	0	NA	Intergenic	Intergenic	-477559	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.000000	0.316901	
chunk0199_170_1	chr9	4504342	4504645	+	0	NA	intron (NM_004170, intron 1 of 11)	intron (NM_004170, intron 1 of 11)	14066	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.009901	0.407895	
chunk0089_212_1	chr18	61045677	61046038	+	0	NA	Intergenic	L1PB2|LINE|L1	-444685	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.008310	0.359116	
chunk0189_229_1	chr8	24443046	24443439	+	0	NA	intron (NM_003817, intron 2 of 21)	LTR78|LTR|ERV1	2246	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.010178	0.350254	
chunk0001_119_1	chr1	4411322	4411667	+	0	NA	promoter-TSS (NR_027088)	promoter-TSS (NR_027088)	-557	NR_027088	284661	Hs.278112	NR_027088	ENSG00000235054	LINC01777	-	long intergenic non-protein coding RNA 1777	ncRNA	0.020290	0.416185	
chunk0124_281_1	chr3	57568799	57569397	+	0	NA	Intergenic	Intergenic	12844	NM_177966	201626	Hs.572993	NM_177966	ENSG00000174840	PDE12	2'-PDE|2-PDE	phosphodiesterase 12	protein-coding	0.005017	0.332220	
chunk0112_192_1	chr20	40239610	40240013	+	0	NA	Intergenic	Intergenic	235350	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.002481	0.371287	
chunk0159_361_1	chr5	145192399	145193036	+	0	NA	Intergenic	Intergenic	642652	NM_182960	153768	Hs.314261	NM_138492	ENSG00000186314	PRELID2	-	PRELI domain containing 2	protein-coding	0.003140	0.373041	292(TGAAACACACTGTGCC,-,0.00),293(GAAACACACTGTGCCA,+,0.00)
chunk0013_386_1	chr1	172680788	172680987	+	0	NA	Intergenic	LTR33A_|LTR|ERVL	21879	NM_001302746	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.005025	0.595000	
chunk0193_351_1	chr8	79890586	79890979	+	0	NA	Intergenic	Intergenic	-19045	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.030534	0.492386	
chunk0143_338_1	chr4	121220670	121220924	+	0	NA	intron (NM_001244764, intron 1 of 12)	Tigger13a|DNA|TcMar-Tigger	-4170	NM_001128843	79931	Hs.208206	NM_024873	ENSG00000050730	TNIP3	ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding	0.023622	0.443137	
chunk0157_295_1	chr5	120941898	120942172	+	0	NA	Intergenic	Intergenic	-380515	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.003650	0.421818	232(AAGAAGAGGCTGTTCA,-,0.00)
chunk0097_180_1	chr2	50209558	50209930	+	0	NA	intron (NM_001135659, intron 19 of 23)	intron (NM_001135659, intron 19 of 23)	138012	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.249330	
chunk0208_405_1	chrX	29257503	29258019	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	-316517	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.007752	0.353965	
chunk0029_75_1	chr10	96710580	96710824	+	0	NA	intron (NM_152309, intron 1 of 16)	MIR|SINE|MIR	9820	NM_152309	118788	Hs.310456	NM_152309	ENSG00000155629	PIK3AP1	BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.004098	0.346939	
chunk0017_466_1	chr1	214583882	214584514	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-18991	NM_016343	1063	Hs.497741	NM_016343	ENSG00000117724	CENPF	CENF|CILD31|PRO1779|STROMS|hcp-1	centromere protein F	protein-coding	0.009494	0.352291	30(AACACAGACTGTGCAT,+,0.00),121(TAGTACATACTGTACT,-,0.00),122(AGTACATACTGTACTA,+,0.00)
chunk0177_400_1	chr7	27424123	27424627	+	0	NA	Intergenic	Intergenic	-177146	NR_120507	101410536	Hs.687800	NR_120507	ENSG00000253405	EVX1-AS	EVX1-AS1	EVX1 antisense RNA	ncRNA	0.007937	0.447525	
chunk0103_61_1	chr2	159863705	159864331	+	0	NA	intron (NM_001198759, intron 14 of 38)	Tigger3a|DNA|TcMar-Tigger	40738	NM_001198759	100526664	Hs.153563	NM_001198759	ENSG00000248672	LY75-CD302	CD205|CLEC13B|DEC-205|LY75|Ly-75|gp200-MR6	LY75-CD302 readthrough	protein-coding	0.004792	0.374801	
chunk0017_103_1	chr1	205913642	205913841	+	0	NA	3' UTR (NM_134325, exon 22 of 22)	3' UTR (NM_134325, exon 22 of 22)	-21172	NR_110984	103021296	Hs.613648	NR_110983		SLC26A9-AS1	-	SLC26A9 and RAB7B antisense RNA 1	ncRNA	0.015075	0.500000	
chunk0104_270_1	chr2	178106034	178106273	+	0	NA	intron (NM_001077197, intron 1 of 20)	intron (NM_001077197, intron 1 of 20)	2186	NM_001077197	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.004184	0.320833	3(AAGCACATATTGATCT,-,0.00)
chunk0193_249_1	chr8	76909003	76909465	+	0	NA	Intergenic	Intergenic	57616	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004329	0.423326	
chunk0154_80_1	chr5	77673217	77673658	+	0	NA	Intergenic	Intergenic	-34740	NM_032109	23440	Hs.202247	NM_032109	ENSG00000171540	OTP	-	orthopedia homeobox	protein-coding	0.018141	0.511312	
chunk0105_343_1	chr2	191278534	191278955	+	0	NA	intron (NM_001130158, intron 2 of 30)	intron (NM_001130158, intron 2 of 30)	33216	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.009501	0.398104	
chunk0023_40_1	chr10	21237893	21238121	+	0	NA	Intergenic	Intergenic	63705	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.004386	0.414847	
chunk0161_333_1	chr5	173902866	173903065	+	0	NA	intron (NM_001308192, intron 1 of 8)	L4_C_Mam|LINE|RTE-X	9914	NM_001308193	80315	Hs.127126	NM_030627	ENSG00000113742	CPEB4	CPE-BP4|hCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding	0.000000	0.355000	
chunk0138_446_1	chr4	46583146	46583534	+	0	NA	Intergenic	Intergenic	-193301	NM_001286827	2555	Hs.48372	NM_000807	ENSG00000151834	GABRA2	-	gamma-aminobutyric acid type A receptor alpha2 subunit	protein-coding	0.002577	0.313625	
chunk0036_158_1	chr11	62370797	62371043	+	0	NA	intron (NM_001083926, intron 4 of 6)	HERVK-int|LTR|ERVK	33618	NM_025080	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.012195	0.429150	
chunk0196_119_1	chr8	103597189	103597644	+	0	NA	intron (NM_001100117, intron 1 of 23)	intron (NM_001100117, intron 1 of 23)	96668	NM_001100117	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.000000	0.403509	
chunk0068_93_1	chr15	52172937	52173136	+	0	NA	intron (NM_016194, intron 3 of 12)	L2a|LINE|L2	6929	NM_006578	10681	Hs.155090	NM_006578	ENSG00000069966	GNB5	GB5|IDDCA|LADCI	G protein subunit beta 5	protein-coding	0.010050	0.325000	
chunk0205_389_1	chr9	114392194	114393062	+	0	NA	intron (NM_030767, intron 1 of 21)	MIRb|SINE|MIR	1777	NM_030767	80709	Hs.494895	NM_030767	ENSG00000106948	AKNA	-	AT-hook transcription factor	protein-coding	0.009217	0.479862	240(GAGAACTCCATGTTCT,-,0.00),241(AGAACTCCATGTTCTC,+,0.00)
chunk0198_335_1	chr8	140042749	140043534	+	0	NA	intron (NM_001160372, intron 17 of 22)	intron (NM_001160372, intron 17 of 22)	-340085	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.012739	0.469466	
chunk0035_120_1	chr11	42572344	42572854	+	0	NA	Intergenic	Intergenic	-318909	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.003922	0.342466	
chunk0057_324_1	chr13	106859319	106859822	+	0	NA	Intergenic	Intergenic	205690	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.011928	0.448413	
chunk0030_428_1	chr10	120428449	120428714	+	0	NA	Intergenic	Intergenic	-28373	NM_001030059	196051	Hs.40479	NM_001030059	ENSG00000203805	PLPP4	DPPL2|PPAPDC1|PPAPDC1A	phospholipid phosphatase 4	protein-coding	0.007547	0.526316	
chunk0081_83_1	chr17	39380444	39380962	+	0	NA	intron (NM_001184906, intron 1 of 13)	L2a|LINE|L2	20953	NM_032875	84961	Hs.462946	NM_032875	ENSG00000108306	FBXL20	Fbl2|Fbl20	F-box and leucine rich repeat protein 20	protein-coding	0.009653	0.396917	
chunk0123_185_1	chr3	44292799	44293514	+	0	NA	intron (NM_001145030, intron 12 of 19)	Tigger3b|DNA|TcMar-Tigger	-44963	NM_001282915	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.001399	0.354749	
chunk0022_453_1	chr10	19937736	19938009	+	0	NA	intron (NM_032812, intron 1 of 13)	intron (NM_032812, intron 1 of 13)	121429	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.007326	0.478102	
chunk0085_439_1	chr18	11041267	11041962	+	0	NA	intron (NM_022068, intron 2 of 51)	intron (NM_022068, intron 2 of 51)	107148	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.005755	0.372126	
chunk0041_147_1	chr11	125570434	125570653	+	0	NA	intron (NR_132372, intron 2 of 2)	intron (NR_132372, intron 2 of 2)	1156	NR_110769	9538	Hs.643514	NM_004879	ENSG00000149547	EI24	EPG4|PIG8|TP53I8	EI24 autophagy associated transmembrane protein	protein-coding	0.000000	0.454545	
chunk0197_378_1	chr8	126866732	126866982	+	0	NA	Intergenic	Intergenic	-146297	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.008000	0.354582	97(GAAAACTTACTGTTCC,-,0.00),98(AAAACTTACTGTTCCT,+,0.00)
chunk0109_355_1	chr2	239052622	239052984	+	0	NA	3' UTR (NM_006037, exon 27 of 27)	3' UTR (NM_006037, exon 27 of 27)	16111	NR_039642	100616397		NR_039642	ENSG00000266109	MIR4440	mir-4440	microRNA 4440	ncRNA	0.069061	0.559229	
chunk0114_197_1	chr21	15282955	15283763	+	0	NA	Intergenic	Intergenic	-218554	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.004950	0.338690	
chunk0162_271_1	chr6	5458000	5458398	+	0	NA	promoter-TSS (NR_125848)	promoter-TSS (NR_125848)	-124	NR_125847	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.017588	0.581454	
chunk0191_356_1	chr8	56474219	56474747	+	0	NA	intron (NR_125813, intron 1 of 3)	intron (NR_125813, intron 1 of 3)	-27749	NM_001135690	5179	Hs.339831	NM_006211	ENSG00000181195	PENK	PE|PENK-A	proenkephalin	protein-coding	0.005682	0.310019	252(GGGAACAAATTGTTCA,-,0.00),253(GGAACAAATTGTTCAG,+,0.00)
chunk0123_223_1	chr3	45327032	45327657	+	0	NA	Intergenic	L1ME1|LINE|L1	-61239	NM_015340	23395	Hs.526975	NM_015340	ENSG00000011376	LARS2	HLASA|LEURS|PRLTS4|mtLeuRS	leucyl-tRNA synthetase 2, mitochondrial	protein-coding	0.011200	0.410543	
chunk0032_400_1	chr11	11691998	11692197	+	0	NA	Intergenic	L1P2|LINE|L1	-35375	NR_036184	100423026		NR_036184	ENSG00000266645	MIR4299	-	microRNA 4299	ncRNA	0.010050	0.520000	
chunk0044_377_1	chr12	39863969	39864591	+	0	NA	intron (NM_052885, intron 6 of 9)	intron (NM_052885, intron 6 of 9)	238110	NM_001031748	283461	Hs.648205	NM_001031748	ENSG00000180116	C12orf40	HEL-206|HEL-S-94	chromosome 12 open reading frame 40	protein-coding	0.003215	0.351525	257(TAGAACATTTTGTTTT,-,0.00),258(AGAACATTTTGTTTTC,+,0.00)
chunk0093_310_1	chr19	53530599	53530931	+	0	NA	intron (NM_018555, intron 2 of 6)	intron (NM_018555, intron 2 of 6)	-7314	NM_001079906	55422	Hs.185674	NM_018555	ENSG00000130844	ZNF331	RITA|ZNF361|ZNF463	zinc finger protein 331	protein-coding	0.024096	0.516517	
chunk0083_420_1	chr17	72394347	72395098	+	0	NA	Intergenic	Intergenic	198082	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.015979	0.514628	
chunk0064_433_1	chr14	99920309	99920528	+	0	NA	intron (NM_004434, intron 16 of 21)	intron (NM_004434, intron 16 of 21)	127010	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.009132	0.568182	
chunk0137_261_1	chr4	21897952	21898233	+	0	NA	intron (NM_147182, intron 1 of 8)	L1M1|LINE|L1	-44904	NR_002813	359822	Hs.354058	NR_002813	ENSG00000280650	KCNIP4-IT1	NCRNA00099|UM9(5)|UM9-5	KCNIP4 intronic transcript 1	ncRNA	0.003559	0.521277	
chunk0195_332_1	chr8	99175860	99176251	+	0	NA	intron (NM_015243, intron 16 of 17)	Tigger2|DNA|TcMar-Tigger	162789	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.010230	0.400510	
chunk0151_146_1	chr5	46096042	46096667	+	0	NA	Intergenic	Intergenic	-400236	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.006400	0.362620	
chunk0056_250_1	chr13	89355239	89355976	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	-118717	NR_131229	105616982	Hs.564527	NR_131229	ENSG00000232225	LINC01047	-	long intergenic non-protein coding RNA 1047	ncRNA	0.009498	0.391599	
chunk0139_395_1	chr4	62519650	62519889	+	0	NA	Intergenic	Intergenic	-358004	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.004184	0.300000	
chunk0027_266_1	chr10	77325082	77325536	+	0	NA	intron (NM_001271518, intron 1 of 27)	intron (NM_001271518, intron 1 of 27)	-25563	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.011013	0.518681	
chunk0063_51_1	chr14	77009078	77009297	+	0	NA	Intergenic	Intergenic	19512	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.009132	0.527273	184(AGGCACTTTTTGTACC,-,0.00)
chunk0182_250_1	chr7	97153348	97153892	+	0	NA	intron (NM_020186, intron 1 of 1)	L1MC1|LINE|L1	37027	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.011029	0.381651	
chunk0018_359_1	chr1	221715313	221716111	+	0	NA	intron (NR_111940, intron 1 of 2)	intron (NR_111940, intron 1 of 2)	21188	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.002506	0.473091	
chunk0131_63_1	chr3	142881402	142881880	+	0	NA	intron (NM_013363, intron 2 of 8)	Tigger3a|DNA|TcMar-Tigger	7562	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.004184	0.327766	206(CTGTACAGCATGTTCC,-,0.00),207(TGTACAGCATGTTCCT,+,0.00)
chunk0038_176_1	chr11	85638475	85638674	+	0	NA	Intergenic	MIR|SINE|MIR	-9345	NM_032273	84233	Hs.533725	NM_032273	ENSG00000171202	TMEM126A	OPA7	transmembrane protein 126A	protein-coding	0.005025	0.325000	
chunk0067_282_1	chr15	47397821	47398512	+	0	NA	intron (NM_001198999, intron 1 of 19)	intron (NM_001198999, intron 1 of 19)	213960	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.007236	0.382948	
chunk0190_1_1	chr8	28556680	28556897	+	0	NA	intron (NM_017412, intron 7 of 7)	MER58A|DNA|hAT-Charlie	26338	NR_106988									0.000000	0.422018	
chunk0005_307_1	chr1	60572910	60573554	+	0	NA	Intergenic	L3|LINE|CR1	252352	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.003106	0.356589	350(AAGAACAAGTTGTACC,-,0.00),351(AGAACAAGTTGTACCA,+,0.00)
chunk0127_12_1	chr3	88075144	88075942	+	0	NA	intron (NM_001195308, intron 2 of 3)	intron (NM_001195308, intron 2 of 3)	-16547	NM_003663	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.003759	0.381727	23(GGCACTCCTTGTGCTG,+,0.00)
chunk0154_245_1	chr5	81303957	81304369	+	0	NA	intron (NM_032280, intron 1 of 5)	intron (NM_032280, intron 1 of 5)	2580	NM_032280	84240	Hs.15536	NM_032280	ENSG00000131732	ZCCHC9	PPP1R41	zinc finger CCHC-type containing 9	protein-coding	0.004854	0.324455	
chunk0169_272_1	chr6	105567718	105567917	+	0	NA	Intergenic	Intergenic	-164693	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.010050	0.400000	
chunk0129_287_1	chr3	123270768	123271265	+	0	NA	intron (NM_012430, intron 6 of 6)	intron (NM_012430, intron 6 of 6)	69089	NM_012430	26984	Hs.477361	NM_012430	ENSG00000121542	SEC22A	SEC22L2	SEC22 homolog A, vesicle trafficking protein	protein-coding	0.006036	0.367470	
chunk0033_139_1	chr11	15360289	15360967	+	0	NA	Intergenic	L2a|LINE|L2	211526	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.002950	0.354934	
chunk0073_54_1	chr16	3220932	3221385	+	0	NA	Intergenic	Intergenic	5596	NR_002169	26184	Hs.651203	NR_002169	ENSG00000203581	OR1F2P	OLFMF2|OR16-3|OR1F11|OR1F2|OR1F3P|hg91	olfactory receptor family 1 subfamily F member 2 pseudogene	pseudo	0.026490	0.544053	
chunk0094_456_1	chr2	11571061	11571657	+	0	NA	intron (NM_014668, intron 4 of 32)	intron (NM_014668, intron 4 of 32)	28634	NM_033090	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.015101	0.428811	353(TGGAACAGCCAGTCCC,-,0.00),354(GGAACAGCCAGTCCCA,+,0.00)
chunk0084_5_1	chr18	110867	111068	+	0	NA	intron (NR_033770, intron 1 of 4)	BSR/Beta|Satellite|Satellite	1372	NR_107045	102466878		NR_107045	ENSG00000277521	MIR8078	hsa-mir-8078	microRNA 8078	ncRNA	0.009950	0.455446	
chunk0141_103_1	chr4	79379943	79380207	+	0	NA	Intergenic	L1MA4A|LINE|L1	28143	NM_033214	2712	Hs.98008	NM_033214	ENSG00000196475	GK2	GKP2|GKTA	glycerol kinase 2	protein-coding	0.003788	0.566038	
chunk0132_393_1	chr3	163824364	163824899	+	0	NA	Intergenic	L1MA4A|LINE|L1	346925	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.001869	0.311567	
chunk0022_27_1	chr10	7894524	7894816	+	0	NA	intron (NM_031923, intron 2 of 6)	intron (NM_031923, intron 2 of 6)	76166	NM_031923	83860	Hs.527688	NM_031923	ENSG00000165632	TAF3	TAF140|TAFII-140|TAFII140	TATA-box binding protein associated factor 3	protein-coding	0.000000	0.286689	
chunk0144_190_1	chr4	133507728	133508278	+	0	NA	Intergenic	L1PA8A|LINE|L1	358713	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.001818	0.352087	491(AATACACATTGTTCTC,+,0.00)
chunk0116_256_1	chr21	38834689	38835166	+	0	NA	Intergenic	Intergenic	-22612	NR_109926	101928398	Hs.122403	NR_109926		LOC101928398	-	uncharacterized LOC101928398	ncRNA	0.008386	0.497908	
chunk0103_286_1	chr2	165969135	165969745	+	0	NA	intron (NR_110598, intron 1 of 3)	intron (NR_110598, intron 1 of 3)	12022	NR_110598	102724058	Hs.570269	NR_110598	ENSG00000236107	LOC102724058	-	uncharacterized LOC102724058	ncRNA	0.004918	0.307692	438(TAGAACAAATTGTTCT,-,0.00),439(AGAACAAATTGTTCTC,+,0.00)
chunk0096_281_1	chr2	32128471	32128862	+	0	NA	intron (NM_014946, intron 9 of 16)	MLT1C|LTR|ERVL-MaLR	-37175	NM_001193513	55676	Hs.23248	NM_017964	ENSG00000152683	SLC30A6	MST103|MSTP103|ZNT6	solute carrier family 30 member 6	protein-coding	0.007673	0.362245	
chunk0018_7_1	chr1	215092650	215092898	+	0	NA	intron (NM_001017424, intron 2 of 6)	MER68C|LTR|ERVL	9557	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.012097	0.473896	
chunk0093_430_1	chr19	58181844	58182606	+	0	NA	promoter-TSS (NM_016325)	promoter-TSS (NM_016325)	-764	NM_001278734	10782	Hs.83761	NM_016324	ENSG00000171606	ZNF274	HFB101|ZF2|ZKSCAN19|ZSCAN51	zinc finger protein 274	protein-coding	0.006562	0.490170	
chunk0143_168_1	chr4	110845592	110846011	+	0	NA	Intergenic	MIRb|SINE|MIR	14846	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.007160	0.380952	
chunk0185_322_1	chr7	131486190	131486736	+	0	NA	intron (NM_001145354, intron 18 of 18)	intron (NM_001145354, intron 18 of 18)	70154	NM_001018111	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.005495	0.323583	
chunk0014_370_1	chr1	182616221	182616552	+	0	NA	non-coding (NR_036490, exon 1 of 1)	non-coding (NR_036490, exon 1 of 1)	1246	NR_036490	284648	Hs.253475	NR_036490	ENSG00000261504	LINC01686	-	long intergenic non-protein coding RNA 1686	ncRNA	0.042296	0.593373	
chunk0125_407_1	chr3	72265982	72266622	+	0	NA	Intergenic	HAL1|LINE|L1	115045	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.007812	0.447738	
chunk0079_174_1	chr17	13962743	13963018	+	0	NA	Intergenic	Intergenic	-61618	NR_003261	94158	Hs.633073	NR_003261		CDRT15P1	CDRT15P	CMT1A duplicated region transcript 15 pseudogene 1	pseudo	0.003636	0.333333	
chunk0188_46_1	chr8	6718221	6718486	+	0	NA	intron (NM_018361, intron 1 of 7)	intron (NM_018361, intron 1 of 7)	9996	NM_018361	55326	Hs.624002	NM_018361	ENSG00000155189	AGPAT5	1AGPAT5|LPAATE	1-acylglycerol-3-phosphate O-acyltransferase 5	protein-coding	0.030189	0.533835	
chunk0125_173_1	chr3	66602583	66603237	+	0	NA	Intergenic	Intergenic	-102489	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.007645	0.429008	306(AGGAACAACCTGTGTC,-,0.00)
chunk0037_302_1	chr11	76369569	76369878	+	0	NA	intron (NR_130898, intron 1 of 5)	MER68B|LTR|ERVL	11242	NR_130898	5612	Hs.503315	NM_004705	ENSG00000137492	THAP12	DAP4|P52rIPK|PRKRIR|THAP0	THAP domain containing 12	protein-coding	0.022654	0.483871	
chunk0097_259_1	chr2	54350246	54350445	+	0	NA	intron (NM_001100396, intron 3 of 4)	MLT1H2|LTR|ERVL-MaLR	19411	NM_001100396	129852	Hs.732626	NM_173486	ENSG00000177994	C2orf73	-	chromosome 2 open reading frame 73	protein-coding	0.005025	0.415000	
chunk0137_218_1	chr4	19826052	19826506	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-425626	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.008811	0.351648	
chunk0163_401_1	chr6	16754749	16755283	+	0	NA	intron (NM_000332, intron 1 of 8)	intron (NM_000332, intron 1 of 8)	6474	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.001873	0.377570	
chunk0161_413_1	chr5	177599792	177600021	+	0	NA	promoter-TSS (NM_007255)	promoter-TSS (NM_007255)	-212	NM_007255	11285	Hs.455109	NM_007255	ENSG00000027847	B4GALT7	EDSP1|EDSSLA|EDSSPD1|XGALT1|XGPT|XGPT1	beta-1,4-galactosyltransferase 7	protein-coding	0.078603	0.686957	
chunk0097_404_1	chr2	62424830	62425480	+	0	NA	Intergenic	Intergenic	81314	NM_198276	200728	Hs.308028	NM_198276	ENSG00000186889	TMEM17	-	transmembrane protein 17	protein-coding	0.013846	0.486943	
chunk0010_46_1	chr1	112880361	112881085	+	0	NA	Intergenic	Intergenic	-30080	NR_103746	100996702	Hs.632431	NR_103746	ENSG00000215866	LINC01356	-	long intergenic non-protein coding RNA 1356	ncRNA	0.002762	0.445517	
chunk0168_44_1	chr6	78484275	78485049	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-382882	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.001292	0.358710	610(GGGAACTTCATGTGCC,-,0.00),611(GGAACTTCATGTGCCA,+,0.00)
chunk0122_127_1	chr3	31471448	31471847	+	0	NA	Intergenic	L2a|LINE|L2	-60854	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.005013	0.417500	172(AAGAACACGGTGAGCC,-,0.00),173(AGAACACGGTGAGCCA,+,0.00)
chunk0033_270_1	chr11	19119572	19119884	+	0	NA	intron (NM_001001483, intron 1 of 15)	L2a|LINE|L2	2583	NM_019028	54503	Hs.188569	NM_019028	ENSG00000177054	ZDHHC13	HIP14L|HIP3RP	zinc finger DHHC-type containing 13	protein-coding	0.006410	0.399361	
chunk0180_7_1	chr7	53066401	53066832	+	0	NA	Intergenic	Intergenic	30960	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.004640	0.314815	
chunk0025_443_1	chr10	60182687	60183128	+	0	NA	intron (NM_001204403, intron 18 of 43)	intron (NM_001204403, intron 18 of 43)	-41891	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.002268	0.427602	368(GGGCACATGTTGTCCC,-,0.00),369(GGCACATGTTGTCCCC,+,0.00)
chunk0086_132_1	chr18	21100264	21100471	+	0	NA	intron (NM_005406, intron 1 of 32)	L1MC5|LINE|L1	11484	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.000000	0.375000	
chunk0094_391_1	chr2	10270657	10271147	+	0	NA	Intergenic	Intergenic	-32002	NM_002149	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.024490	0.562118	
chunk0188_325_1	chr8	17527750	17528207	+	0	NA	intron (NM_001008539, intron 1 of 11)	L2c|LINE|L2	-10799	NM_001164771	6542	Hs.448520	NM_003046	ENSG00000003989	SLC7A2	ATRC2|CAT2|HCAT2	solute carrier family 7 member 2	protein-coding	0.008753	0.462882	214(GAGAACAGGGTGACCT,-,0.00),215(AGAACAGGGTGACCTA,+,0.00)
chunk0179_444_1	chr7	52637250	52637733	+	0	NA	Intergenic	L1MA9|LINE|L1	-398165	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.006211	0.361570	
chunk0174_86_1	chr6	156523680	156523879	+	0	NA	Intergenic	Intergenic	-254151	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.015075	0.520000	
chunk0210_110_1	chrX	72217713	72217943	+	0	NA	intron (NM_017669, intron 1 of 1)	intron (NM_017669, intron 1 of 1)	21180	NM_017669	54821	Hs.47558	NM_017669	ENSG00000186871	ERCC6L	PICH|RAD26L	ERCC excision repair 6 like, spindle assembly checkpoint helicase	protein-coding	0.004348	0.359307	
chunk0121_369_1	chr3	24889591	24890047	+	0	NA	Intergenic	Intergenic	-284513	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.002193	0.332604	
chunk0162_69_1	chr6	1679536	1680134	+	0	NA	intron (NM_001253846, intron 9 of 10)	intron (NM_001253846, intron 9 of 10)	69389	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.013378	0.387312	
chunk0071_173_1	chr15	83292509	83292733	+	0	NA	Intergenic	Intergenic	-7905	NM_001717	646	Hs.459153	NM_001717	ENSG00000169594	BNC1	BNC|BSN1|HsT19447	basonuclin 1	protein-coding	0.008929	0.431111	
chunk0092_109_1	chr19	23680119	23680591	+	0	NA	intron (NM_138330, intron 1 of 3)	L1PREC2|LINE|L1	6860	NM_138330	171392	Hs.264345	NM_138330	ENSG00000197372	ZNF675	TBZF|TIZ	zinc finger protein 675	protein-coding	0.008475	0.458774	
chunk0168_227_1	chr6	86992267	86992722	+	0	NA	intron (NM_000865, intron 1 of 1)	intron (NM_000865, intron 1 of 1)	55188	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.008791	0.348684	
chunk0108_341_1	chr2	235831738	235832011	+	0	NA	intron (NM_001037131, intron 9 of 17)	L1MC1|LINE|L1	326123	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.000000	0.386861	
chunk0152_132_1	chr5	58980016	58980557	+	0	NA	intron (NM_006203, intron 11 of 14)	MIR|SINE|MIR	19646	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.001848	0.380074	
chunk0209_354_1	chrX	53225826	53226328	+	0	NA	promoter-TSS (NM_001146702)	promoter-TSS (NM_001146702)	-655	NM_001146702	8242	Hs.631768	NM_004187	ENSG00000126012	KDM5C	DXS1272E|JARID1C|MRX13|MRXJ|MRXSCJ|MRXSJ|SMCX|XE169	lysine demethylase 5C	protein-coding	0.011952	0.391650	
chunk0080_278_1	chr17	31147094	31147338	+	0	NA	intron (NM_001042492, intron 1 of 57)	L1ME3A|LINE|L1	52289	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.004098	0.346939	
chunk0208_70_1	chrX	12787665	12788092	+	0	NA	Intergenic	MER33|DNA|hAT-Charlie	-3477	NM_001039091	5634	Hs.654581	NM_002765	ENSG00000101911	PRPS2	PRSII	phosphoribosyl pyrophosphate synthetase 2	protein-coding	0.002342	0.287383	174(TAGAACTTCTTGTTCT,-,0.00),175(AGAACTTCTTGTTCTA,+,0.00)
chunk0147_52_1	chr4	172552322	172552846	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	136333	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.013359	0.281905	
chunk0102_353_1	chr2	152476078	152476492	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	141048	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.002415	0.400000	
chunk0117_235_1	chr22	22990756	22990976	+	0	NA	Intergenic	Intergenic	-79617	NM_002073	2781	Hs.584760	NM_002073	ENSG00000128266	GNAZ	gz-alpha	G protein subunit alpha z	protein-coding	0.004545	0.321267	
chunk0029_455_1	chr10	110501245	110501467	+	0	NA	intron (NM_004419, intron 1 of 3)	intron (NM_004419, intron 1 of 3)	3489	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.027027	0.578475	
chunk0195_412_1	chr8	100659359	100659742	+	0	NA	Intergenic	Intergenic	-9885	NM_152628	169166	Hs.567758	NM_152628	ENSG00000174226	SNX31	-	sorting nexin 31	protein-coding	0.007833	0.346354	
chunk0149_348_1	chr5	27387503	27387951	+	0	NA	Intergenic	MER67C|LTR|ERV1	-84565	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.006696	0.380846	
chunk0157_110_1	chr5	116849228	116849896	+	0	NA	Intergenic	Intergenic	-87353	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.002994	0.426009	305(GAGTACATTATGTCCT,-,0.00),306(AGTACATTATGTCCTC,+,0.00)
chunk0064_313_1	chr14	95862321	95862548	+	0	NA	Intergenic	Intergenic	-13958	NR_132399	100507043	Hs.455955	NR_038861	ENSG00000250366	TUNAR	HI-LNC78|LINC00617|TUNA	TCL1 upstream neural differentiation-associated RNA	ncRNA	0.013216	0.464912	
chunk0136_410_1	chr3	197352278	197352703	+	0	NA	Intergenic	Intergenic	-53218	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.021176	0.488263	
chunk0091_82_1	chr19	5268924	5269706	+	0	NA	intron (NM_130853, intron 4 of 28)	intron (NM_130853, intron 4 of 28)	71488	NM_002850	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.039642	0.596424	
chunk0010_325_1	chr1	118155786	118156069	+	0	NA	intron (NM_206996, intron 1 of 48)	intron (NM_206996, intron 1 of 48)	29298	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.007067	0.338028	
chunk0209_428_1	chrX	57902346	57902929	+	0	NA	Intergenic	Intergenic	7996	NM_007156	7789	Hs.550094	NM_007156	ENSG00000198205	ZXDA	ZNF896	zinc finger X-linked duplicated A	protein-coding	0.003431	0.352740	
chunk0115_98_1	chr21	22523706	22524280	+	0	NA	Intergenic	L1M5|LINE|L1	425376	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.005226	0.269565	
chunk0007_165_1	chr1	80054172	80054389	+	0	NA	Intergenic	LTR18A|LTR|ERVL	-481475	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.018433	0.522936	
chunk0043_289_1	chr12	21444069	21444663	+	0	NA	intron (NM_024854, intron 2 of 11)	L2a|LINE|L2	6762	NM_024854	79912	Hs.709545	NM_024854	ENSG00000121350	PYROXD1	MFM8	pyridine nucleotide-disulphide oxidoreductase domain 1	protein-coding	0.003367	0.329412	
chunk0053_178_1	chr13	30939711	30940050	+	0	NA	intron (NM_152325, intron 2 of 6)	intron (NM_152325, intron 2 of 6)	7183	NM_152325	122046	Hs.124463	NM_152325	ENSG00000175664	TEX26	C13orf26	testis expressed 26	protein-coding	0.017699	0.408824	
chunk0070_69_1	chr15	69818550	69818971	+	0	NA	Intergenic	Intergenic	-16474	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.019002	0.445498	
chunk0110_294_1	chr20	17917799	17918519	+	0	NA	Intergenic	L1MC1|LINE|L1	44787	NR_003045	692086	Hs.680747	NR_003045	ENSG00000212232	SNORD17	HBI-43	small nucleolar RNA, C/D box 17	snoRNA	0.008333	0.399445	
chunk0199_239_1	chr9	5457916	5458299	+	0	NA	intron (NM_001314029, intron 3 of 3)	intron (NM_001314029, intron 3 of 3)	7604	NM_001267706	29126	Hs.521989	NM_014143	ENSG00000120217	CD274	B7-H|B7H1|PD-L1|PDCD1L1|PDCD1LG1|PDL1|hPD-L1	CD274 molecule	protein-coding	0.002611	0.375000	
chunk0020_26_1	chr1	231861808	231862164	+	0	NA	intron (NM_001164541, intron 9 of 9)	MER63B|DNA|hAT-Blackjack	-43469	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.011236	0.394958	
chunk0129_298_1	chr3	123618871	123619106	+	0	NA	intron (NM_053025, intron 32 of 33)	intron (NM_053025, intron 32 of 33)	1695	NM_053032	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.004255	0.487288	
chunk0033_369_1	chr11	23274916	23275258	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	144103	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.002924	0.352770	
chunk0013_157_1	chr1	168639944	168640987	+	0	NA	Intergenic	Intergenic	63992	NM_002995	6375	Hs.546295	NM_002995	ENSG00000143184	XCL1	ATAC|LPTN|LTN|SCM-1|SCM-1a|SCM1|SCM1A|SCYC1	X-C motif chemokine ligand 1	protein-coding	0.003835	0.345785	
chunk0176_99_1	chr7	11642846	11643538	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	189006	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005780	0.305916	356(TGGAACAGCATGTCCT,-,0.00),357(GGAACAGCATGTCCTA,+,0.00)
chunk0202_281_1	chr9	77277463	77278171	+	0	NA	intron (NM_001018038, intron 26 of 68)	L1MC1|LINE|L1	-99900	NR_026668	100286938	Hs.662256	NR_026668	ENSG00000232998	VPS13A-AS1	-	VPS13A antisense RNA 1	ncRNA	0.005650	0.386460	
chunk0032_55_1	chr11	1827284	1827581	+	0	NA	Intergenic	Intergenic	-6878	NM_001290334	90019	Hs.161031	NM_138567	ENSG00000149043	SYT8	-	synaptotagmin 8	protein-coding	0.040404	0.614094	156(ATGCACAGACTGTCTC,-,0.00),157(TGCACAGACTGTCTCT,+,0.00)
chunk0210_460_1	chrX	106998242	106998752	+	0	NA	intron (NM_024657, intron 2 of 16)	intron (NM_024657, intron 2 of 16)	1747	NM_024657	79710	Hs.496544	NM_024657	ENSG00000133131	MORC4	ZCW4|ZCWCC2|dJ75H8.2	MORC family CW-type zinc finger 4	protein-coding	0.017647	0.387476	
chunk0189_144_1	chr8	22915327	22915826	+	0	NA	intron (NM_144962, intron 3 of 6)	L2b|LINE|L2	12332	NM_144962	157310	Hs.491242	NM_144962	ENSG00000134020	PEBP4	CORK-1|CORK1|GWTM1933|HEL-S-300|PEBP-4|PRO4408|hPEBP4	phosphatidylethanolamine binding protein 4	protein-coding	0.028056	0.558000	
chunk0153_380_1	chr5	74963917	74964223	+	0	NA	Intergenic	L2b|LINE|L2	66829	NM_016591	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.006536	0.342020	
chunk0106_82_1	chr2	197086305	197086701	+	0	NA	intron (NM_001195144, intron 13 of 27)	intron (NM_001195144, intron 13 of 27)	-159773	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.005051	0.380353	
chunk0028_148_1	chr10	86748234	86748611	+	0	NA	Intergenic	Intergenic	-8217	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.005305	0.341270	
chunk0030_121_1	chr10	113031188	113031498	+	0	NA	intron (NM_001198531, intron 4 of 12)	MER5B|DNA|hAT-Charlie	-14012	NR_132769	106635520		NR_132769		SNORA87	-	small nucleolar RNA, H/ACA box 87	snoRNA	0.003226	0.382637	
chunk0154_137_1	chr5	79237564	79237792	+	0	NA	exon (NM_152405, exon 1 of 11)	exon (NM_152405, exon 1 of 11)	1576	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.061404	0.576419	
chunk0012_47_1	chr1	155342022	155342501	+	0	NA	intron (NM_018489, intron 24 of 27)	intron (NM_018489, intron 24 of 27)	4184	NR_030282	693140		NR_030282	ENSG00000283701	MIR555	MIRN555|hsa-mir-555	microRNA 555	ncRNA	0.004175	0.431250	237(CTGGACAAAGAGTTCT,-,0.00),238(TGGACAAAGAGTTCTC,+,0.00)
chunk0165_379_1	chr6	38371514	38371734	+	0	NA	intron (NM_001099272, intron 6 of 10)	intron (NM_001099272, intron 6 of 10)	224443	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.013636	0.452489	
chunk0115_207_1	chr21	26799189	26799457	+	0	NA	Intergenic	Intergenic	46086	NM_006988	9510	Hs.643357	NM_006988	ENSG00000154734	ADAMTS1	C3-C5|METH1	ADAM metallopeptidase with thrombospondin type 1 motif 1	protein-coding	0.000000	0.386617	
chunk0169_164_1	chr6	102023958	102024485	+	0	NA	intron (NM_001166247, intron 13 of 16)	intron (NM_001166247, intron 13 of 16)	625236	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001898	0.359848	
chunk0057_151_1	chr13	100302426	100303007	+	0	NA	intron (NM_001127692, intron 12 of 22)	intron (NM_001127692, intron 12 of 22)	178299	NR_047686	100885777	Hs.662554	NR_047686		PCCA-AS1	-	PCCA antisense RNA 1	ncRNA	0.005164	0.314433	
chunk0120_126_1	chr3	4895867	4896313	+	0	NA	TTS (NR_037903)	TTS (NR_037903)	10411	NR_125914	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.008969	0.425056	
chunk0088_294_1	chr18	49745162	49745361	+	0	NA	Intergenic	Intergenic	68620	NM_006111	10449	Hs.200136	NM_006111	ENSG00000167315	ACAA2	DSAEC	acetyl-CoA acyltransferase 2	protein-coding	0.005025	0.540000	
chunk0104_139_1	chr2	173432132	173432672	+	0	NA	Intergenic	Intergenic	77569	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.011111	0.399261	
chunk0036_451_1	chr11	68618846	68619093	+	0	NA	Intergenic	Intergenic	-65506	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.008097	0.395161	
chunk0040_132_1	chr11	112479519	112479790	+	0	NA	Intergenic	L1M4|LINE|L1	-2578	NR_120559	101928823	Hs.126118	NR_120559	ENSG00000254968	LINC02763	-	long intergenic non-protein coding RNA 2763	ncRNA	0.007380	0.408088	
chunk0136_160_1	chr4	5837069	5837438	+	0	NA	intron (NM_001014809, intron 9 of 13)	intron (NM_001014809, intron 9 of 13)	50560	NM_001288662	1400	Hs.135270	NM_001313	ENSG00000072832	CRMP1	CRMP-1|DPYSL1|DRP-1|DRP1|ULIP-3	collapsin response mediator protein 1	protein-coding	0.005420	0.470270	
chunk0066_39_1	chr15	27737172	27737722	+	0	NA	Intergenic	L1ME3A|LINE|L1	361865	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.003636	0.323049	
chunk0064_306_1	chr14	95571307	95571639	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	36487	NM_016417	51218	Hs.744943	NM_016417	ENSG00000182512	GLRX5	C14orf87|FLB4739|GRX5|PR01238|PRO1238|PRSA|SIDBA3|SPAHGC	glutaredoxin 5	protein-coding	0.009036	0.459459	
chunk0195_162_1	chr8	95729724	95730124	+	0	NA	intron (NR_038205, intron 2 of 2)	Tigger19b|DNA|TcMar-Tigger	218424	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.005000	0.396509	
chunk0108_404_1	chr2	237479788	237480127	+	0	NA	Intergenic	Intergenic	-6453	NM_001281474	79083	Hs.102406	NM_024101	ENSG00000115648	MLPH	SLAC2-A	melanophilin	protein-coding	0.011799	0.391176	142(CAGCACAGTCTGCACT,-,0.00),143(AGCACAGTCTGCACTA,+,0.00)
chunk0019_255_1	chr1	227846258	227846690	+	0	NA	TTS (NM_183062)	TTS (NM_183062)	30757	NM_183062	339501	Hs.97604	NM_183062	ENSG00000185888	PRSS38	MPN2	serine protease 38	protein-coding	0.013889	0.545035	
chunk0124_122_1	chr3	54222222	54222905	+	0	NA	intron (NM_018398, intron 2 of 37)	MLT2B4|LTR|ERVL	99897	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.001464	0.358187	
chunk0052_201_1	chr13	24986207	24986708	+	0	NA	Intergenic	L1MB5|LINE|L1	-17988	NR_026730	646405	Hs.620592	NM_001126062		TPTE2P1	-	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 1	pseudo	0.007984	0.388446	
chunk0160_218_1	chr5	154923317	154923848	+	0	NA	intron (NM_001252156, intron 9 of 27)	MER58B|DNA|hAT-Charlie	14634	NM_001252156	25929	Hs.483921	NM_015465	ENSG00000082516	GEMIN5	GEMIN-5	gem nuclear organelle associated protein 5	protein-coding	0.007533	0.392857	
chunk0178_16_1	chr7	29212661	29213363	+	0	NA	intron (NM_001293072, intron 1 of 12)	intron (NM_001293072, intron 1 of 12)	-4042	NR_120522	102724484	Hs.638665	NR_120522		LOC102724484	-	uncharacterized LOC102724484	ncRNA	0.005698	0.486486	268(CAGAACATCTAGTGCT,-,0.00),269(AGAACATCTAGTGCTG,+,0.00),299(GGAACACTCAGACCTG,+,0.00)
chunk0206_109_1	chr9	120819845	120820727	+	0	NA	intron (NM_005047, intron 9 of 9)	L2a|LINE|L2	22735	NM_005047	5711	Hs.193725	NM_005047	ENSG00000095261	PSMD5	S5B	proteasome 26S subunit, non-ATPase 5	protein-coding	0.007937	0.388448	
chunk0184_373_1	chr7	121327042	121327436	+	0	NA	intron (NM_016087, intron 1 of 3)	L2c|LINE|L2	-1797	NM_057168	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.012690	0.417722	180(TGGTACATAGTGTACA,-,0.00),181(GGTACATAGTGTACAC,+,0.00)
chunk0146_7_1	chr4	154908209	154908486	+	0	NA	Intergenic	Intergenic	126842	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.003610	0.438849	
chunk0114_188_1	chr21	15053487	15054086	+	0	NA	intron (NM_003489, intron 1 of 3)	intron (NM_003489, intron 1 of 3)	11019	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.003339	0.306667	
chunk0097_341_1	chr2	58104770	58105163	+	0	NA	intron (NM_006296, intron 7 of 12)	L1P4|LINE|L1	58254	NM_001130481	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.000000	0.365482	190(AAGGACACCCTGTTCA,-,0.00),191(AGGACACCCTGTTCAA,+,0.00)
chunk0048_256_1	chr12	81822215	81822929	+	0	NA	Intergenic	Intergenic	-63242	NM_003625	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.004202	0.283916	
chunk0060_302_1	chr14	50844153	50844507	+	0	NA	Intergenic	Intergenic	-13209	NM_016350	51199	Hs.310429	NM_016350	ENSG00000100503	NIN	SCKL7	ninein	protein-coding	0.005650	0.371831	
chunk0200_224_1	chr9	20639794	20639993	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-17350	NM_004529	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.005025	0.380000	
chunk0209_282_1	chrX	47218324	47218736	+	0	NA	promoter-TSS (NM_006201)	promoter-TSS (NM_006201)	-147	NM_006201	5127	Hs.496068	NM_006201	ENSG00000102225	CDK16	PCTAIRE|PCTAIRE1|PCTGAIRE|PCTK1	cyclin dependent kinase 16	protein-coding	0.080097	0.602906	
chunk0165_79_1	chr6	31275142	31275649	+	0	NA	Intergenic	Intergenic	-3259	NM_001243042	3107	Hs.656020	NM_002117	ENSG00000204525	HLA-C	D6S204|HLA-JY3|HLAC|HLC-C|MHC|PSORS1	major histocompatibility complex, class I, C	protein-coding	0.007890	0.383858	
chunk0024_119_1	chr10	34838310	34839084	+	0	NA	Intergenic	Intergenic	22929	NR_108043	100505601	Hs.549790	NR_108043	ENSG00000226386	PARD3-AS1	-	PARD3 antisense RNA 1	ncRNA	0.012920	0.473548	
chunk0138_299_1	chr4	41120886	41121090	+	0	NA	intron (NM_004307, intron 2 of 17)	intron (NM_004307, intron 2 of 17)	93630	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.009804	0.400000	
chunk0172_302_1	chr6	138112467	138113073	+	0	NA	Intergenic	Intergenic	-5247	NM_022121	64065	Hs.201446	NM_022121	ENSG00000112378	PERP	KCP1|KRTCAP1|PIGPC1|THW|dJ496H19.1	p53 apoptosis effector related to PMP22	protein-coding	0.006601	0.429984	279(CTGTACAAACTGTCCT,-,0.00),280(TGTACAAACTGTCCTA,+,0.00)
chunk0183_364_1	chr7	108999036	108999272	+	0	NA	Intergenic	MER67C|LTR|ERV1	-114567	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.000000	0.320675	
chunk0011_52_1	chr1	143264147	143264400	+	0	NA	Intergenic	Intergenic	158319	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.039526	0.358268	
chunk0072_218_1	chr15	95653158	95653391	+	0	NA	Intergenic	L2b|LINE|L2	220181	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.012876	0.405983	
chunk0173_314_1	chr6	148611250	148611533	+	0	NA	Intergenic	Intergenic	-135744	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.017668	0.468310	
chunk0015_243_1	chr1	187887277	187887558	+	0	NA	Intergenic	Intergenic	443789	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.297872	
chunk0064_87_1	chr14	90719339	90719659	+	0	NA	intron (NM_001010854, intron 5 of 19)	LTR87|LTR|ERVL?	76870	NR_110134	101928909	Hs.662545	NR_110134	ENSG00000259163	LOC101928909	-	uncharacterized LOC101928909	ncRNA	0.003125	0.473520	110(AGGAACACTGTGTCTT,-,0.00),111(GGAACACTGTGTCTTT,+,0.00)
chunk0039_149_1	chr11	98710756	98711012	+	0	NA	Intergenic	Intergenic	-310092	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.381323	
chunk0099_397_1	chr2	101829053	101829772	+	0	NA	intron (NM_145686, intron 5 of 30)	intron (NM_145686, intron 5 of 30)	131336	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.011127	0.456944	
chunk0112_14_1	chr20	35907241	35907923	+	0	NA	intron (NM_016436, intron 10 of 17)	MIR|SINE|MIR	47044	NM_033630	51282	Hs.584909	NM_016558	ENSG00000171222	SCAND1	RAZ1|SDP1	SCAN domain containing 1	protein-coding	0.007331	0.456808	331(GAGTACTTCATGTGCT,-,0.00),332(AGTACTTCATGTGCTG,+,0.00)
chunk0161_406_1	chr5	177426524	177426760	+	0	NA	promoter-TSS (NM_001004106)	promoter-TSS (NM_001004106)	-44	NM_001004105	2870	Hs.235116	NM_002082	ENSG00000198055	GRK6	GPRK6	G protein-coupled receptor kinase 6	protein-coding	0.118644	0.738397	
chunk0121_270_1	chr3	23316917	23317116	+	0	NA	intron (NM_152653, intron 3 of 5)	L1M1|LINE|L1	113723	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005025	0.515000	
chunk0010_11_1	chr1	111976289	111977293	+	0	NA	intron (NM_172198, intron 2 of 6)	intron (NM_172198, intron 2 of 6)	12364	NM_004980	3752	Hs.666367	NM_004980	ENSG00000171385	KCND3	BRGDA9|KCND3L|KCND3S|KSHIVB|KV4.3|SCA19|SCA22	potassium voltage-gated channel subfamily D member 3	protein-coding	0.007968	0.457711	
chunk0002_59_1	chr1	13714153	13714512	+	0	NA	intron (NM_012231, intron 1 of 9)	intron (NM_012231, intron 1 of 9)	9477	NM_015866	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.005571	0.363889	
chunk0187_224_1	chr7	152330354	152331091	+	0	NA	exon (NM_170606, exon 3 of 59)	exon (NM_170606, exon 3 of 59)	105283	NM_170606	58508	Hs.647120	NM_021230	ENSG00000055609	KMT2C	HALR|KLEFS2|MLL3	lysine methyltransferase 2C	protein-coding	0.006784	0.384824	
chunk0198_463_1	chr8	144600435	144600740	+	0	NA	intron (NM_001308208, intron 2 of 10)	CpG	5108	NM_025251	80728	Hs.148988	NM_025251	ENSG00000147799	ARHGAP39	CrGAP|Vilse	Rho GTPase activating protein 39	protein-coding	0.078689	0.598039	
chunk0152_138_1	chr5	59117110	59117786	+	0	NA	intron (NM_006203, intron 5 of 14)	intron (NM_006203, intron 5 of 14)	-77936	NM_001197222	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004438	0.384047	
chunk0198_106_1	chr8	130743456	130744008	+	0	NA	Intergenic	LTR89|LTR|ERVL?	296857	NM_001115	114	Hs.591859	NM_001115	ENSG00000155897	ADCY8	AC8|ADCY3|HBAC1	adenylate cyclase 8	protein-coding	0.010870	0.406872	
chunk0133_154_1	chr3	169542962	169543161	+	0	NA	intron (NM_004991, intron 1 of 16)	intron (NM_004991, intron 1 of 16)	120714	NM_004991	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.010050	0.320000	
chunk0118_272_1	chr22	33605610	33606057	+	0	NA	intron (NM_133642, intron 4 of 14)	intron (NM_133642, intron 4 of 14)	-119153	NR_038949	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.026846	0.482143	238(AAGAACACAAAGTTCC,-,0.00),239(AGAACACAAAGTTCCA,+,0.00)
chunk0055_181_1	chr13	61362844	61363265	+	0	NA	Intergenic	Intergenic	52468	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.002375	0.317536	
chunk0003_21_1	chr1	29136401	29136781	+	0	NA	Intergenic	L1ME4c|LINE|L1	-12682	NM_001003682	399474	Hs.712722	NM_001003682	ENSG00000253304	TMEM200B	TTMB	transmembrane protein 200B	protein-coding	0.026316	0.514436	
chunk0080_334_1	chr17	32608998	32609507	+	0	NA	intron (NM_015194, intron 20 of 21)	intron (NM_015194, intron 20 of 21)	122165	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.015717	0.450980	
chunk0086_138_1	chr18	21218414	21218685	+	0	NA	Intergenic	Intergenic	-23693	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.000000	0.283088	
chunk0101_421_1	chr2	139252511	139252710	+	0	NA	Intergenic	HAL1b|LINE|L1	355286	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.000000	0.285000	
chunk0020_385_1	chr1	240112516	240112979	+	0	NA	intron (NM_020066, intron 1 of 17)	intron (NM_020066, intron 1 of 17)	20862	NM_020066	56776	Hs.24889	NM_020066	ENSG00000155816	FMN2	-	formin 2	protein-coding	0.006479	0.469828	274(TGGGACAGTGTGTGCT,-,0.00),275(GGGACAGTGTGTGCTT,+,0.00)
chunk0209_422_1	chrX	57335780	57336090	+	0	NA	intron (NM_174912, intron 4 of 10)	LTR5_Hs|LTR|ERVK	49258	NM_174912	158584	Hs.496205	NM_174912	ENSG00000165591	FAAH2	AMDD	fatty acid amide hydrolase 2	protein-coding	0.006452	0.479100	
chunk0118_334_1	chr22	35506651	35506883	+	0	NA	Intergenic	Intergenic	-34538	NM_014310	23551	Hs.474711	NM_014310	ENSG00000100302	RASD2	Rhes|TEM2	RASD family member 2	protein-coding	0.025862	0.502146	
chunk0166_371_1	chr6	51567462	51567975	+	0	NA	Intergenic	Intergenic	-54152	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.009747	0.354086	239(GTGTACTTGCTGTTCT,-,0.00),240(TGTACTTGCTGTTCTG,+,0.00)
chunk0211_187_1	chrX	117328256	117328575	+	0	NA	Intergenic	Intergenic	645323	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.006270	0.390625	
chunk0069_359_1	chr15	67079432	67079829	+	0	NA	intron (NM_005902, intron 1 of 8)	MIRb|SINE|MIR	13773	NM_005902	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.007557	0.487437	
chunk0195_418_1	chr8	100750207	100750772	+	0	NA	Intergenic	Intergenic	-28402	NM_002568	26986	Hs.387804	NM_002568	ENSG00000070756	PABPC1	PAB1|PABP|PABP1|PABPC2|PABPL1	poly(A) binding protein cytoplasmic 1	protein-coding	0.010619	0.496466	
chunk0149_342_1	chr5	26940434	26941094	+	0	NA	intron (NM_016279, intron 2 of 11)	intron (NM_016279, intron 2 of 11)	97818	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.006061	0.340393	
chunk0092_140_1	chr19	28199390	28199824	+	0	NA	Intergenic	Intergenic	-405667	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.018433	0.519540	127(AAGAACACAAAGTACA,-,0.00),128(AGAACACAAAGTACAG,+,0.00)
chunk0031_85_1	chr10	123227354	123228372	+	0	NA	Intergenic	Intergenic	73619	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.003929	0.400393	653(CAGGTCACTGTGTTCA,-,0.00),654(AGGTCACTGTGTTCAT,+,0.00)
chunk0080_272_1	chr17	31088345	31089003	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	5751	NR_039886	100616266		NR_039886	ENSG00000265444	MIR4733	-	microRNA 4733	ncRNA	0.004559	0.464340	
chunk0177_296_1	chr7	25830981	25831520	+	0	NA	Intergenic	Intergenic	118736	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.011132	0.412963	313(TGACCAGTATGTTCTG,+,0.00)
chunk0007_113_1	chr1	78965195	78965531	+	0	NA	intron (NM_022159, intron 2 of 14)	intron (NM_022159, intron 2 of 14)	41447	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.005952	0.278932	
chunk0106_47_1	chr2	196259693	196260403	+	0	NA	promoter-TSS (NR_110226)	promoter-TSS (NR_110226)	24	NR_110226	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.005634	0.402250	
chunk0132_230_1	chr3	158381398	158382051	+	0	NA	intron (NM_001271834, intron 5 of 8)	Tigger3b|DNA|TcMar-Tigger	189342	NR_104147	100996447	Hs.369810	NR_104147	ENSG00000243150	LOC100996447	-	uncharacterized LOC100996447	ncRNA	0.003063	0.319572	
chunk0074_217_1	chr16	25689053	25689712	+	0	NA	Intergenic	Intergenic	-2644	NM_006040	9951	Hs.655275	NM_006040	ENSG00000182601	HS3ST4	3-OST-4|30ST4|3OST4|h3-OST-4	heparan sulfate-glucosamine 3-sulfotransferase 4	protein-coding	0.013657	0.434848	
chunk0113_60_1	chr20	50400048	50400640	+	0	NA	Intergenic	L2a|LINE|L2	-79002	NR_109950	101927586	Hs.637665	NR_109950	ENSG00000233077	LINC01271	-	long intergenic non-protein coding RNA 1271	ncRNA	0.023649	0.519393	
chunk0084_267_1	chr17	79413683	79413882	+	0	NA	intron (NM_001082575, intron 2 of 14)	intron (NM_001082575, intron 2 of 14)	102366	NM_001082575	146713	Hs.135229	NM_001025448	ENSG00000167281	RBFOX3	FOX-3|FOX3|HRNBP3|NEUN	RNA binding fox-1 homolog 3	protein-coding	0.035176	0.705000	
chunk0143_162_1	chr4	110567381	110567637	+	0	NA	Intergenic	Intergenic	55589	NM_000325	5308	Hs.643588	NM_000325	ENSG00000164093	PITX2	ARP1|ASGD4|Brx1|IDG2|IGDS|IGDS2|IHG2|IRID2|Otlx2|PTX2|RGS|RIEG|RIEG1|RS	paired like homeodomain 2	protein-coding	0.019531	0.482490	170(CTGAACTCTATGTCCC,-,0.00),171(TGAACTCTATGTCCCT,+,0.00)
chunk0052_350_1	chr12	126600102	126600400	+	0	NA	Intergenic	Intergenic	90067	NR_110036	100996671	Hs.121392	NR_110034	ENSG00000256732	LOC100996671	-	uncharacterized LOC100996671	ncRNA	0.016779	0.414716	
chunk0084_276_1	chr17	79739101	79739300	+	0	NA	intron (NM_178543, intron 5 of 5)	L2a|LINE|L2	8097	NM_178543	339221	Hs.114084	NM_178543	ENSG00000182156	ENPP7	ALK-SMase|E-NPP 7|NPP-7|NPP7	ectonucleotide pyrophosphatase/phosphodiesterase 7	protein-coding	0.025126	0.585000	
chunk0012_82_1	chr1	155934968	155935241	+	0	NA	promoter-TSS (NM_014949)	promoter-TSS (NM_014949)	-662	NM_014949	22889	Hs.24656	NM_014949	ENSG00000132680	KHDC4	BLOM7|KIAA0907|SNORA80EHG	KH domain containing 4, pre-mRNA splicing factor	protein-coding	0.021978	0.423358	124(TGGAGCACCCTGTTCT,-,0.00),125(GGAGCACCCTGTTCTG,+,0.00)
chunk0185_328_1	chr7	131672141	131672351	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-115629	NM_005397	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.019048	0.488152	
chunk0194_96_1	chr8	83209969	83210645	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	-193451	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.005917	0.347120	
chunk0064_365_1	chr14	97850964	97851163	+	0	NA	Intergenic	MIRc|SINE|MIR	127061	NR_015430	388011	Hs.651477	NR_015430	ENSG00000246223	LINC01550	C14orf64	long intergenic non-protein coding RNA 1550	ncRNA	0.015075	0.515000	
chunk0185_209_1	chr7	128745652	128746116	+	0	NA	intron (NR_074086, intron 1 of 4)	L1ME3G|LINE|L1	6592	NR_074086	813	Hs.7753	NM_001219	ENSG00000128595	CALU	-	calumenin	protein-coding	0.006466	0.361290	
chunk0185_454_1	chr7	135157645	135157904	+	0	NA	intron (NM_018295, intron 1 of 1)	L1M2a1|LINE|L1	9760	NM_018295	55281	Hs.521213	NM_018295	ENSG00000146859	TMEM140	-	transmembrane protein 140	protein-coding	0.000000	0.519231	
chunk0115_275_1	chr21	28137720	28138619	+	0	NA	TTS (NR_126010)	TTS (NR_126010)	47766	NR_126011	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.006674	0.320000	
chunk0011_109_1	chr1	146005610	146005971	+	0	NA	Intergenic	Intergenic	-9159	NM_006472	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.013850	0.414365	148(GAGCACTCAGTGTTCC,-,0.00),149(AGCACTCAGTGTTCCC,+,0.00)
chunk0083_159_1	chr17	65978208	65978674	+	0	NA	intron (NM_001302891, intron 15 of 24)	MIRc|SINE|MIR	-151898	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.010730	0.368308	192(TAGGACTCGGTGTGCC,-,0.00),193(AGGACTCGGTGTGCCC,+,0.00)
chunk0202_421_1	chr9	81717046	81718172	+	0	NA	intron (NR_109772, intron 1 of 3)	intron (NR_109772, intron 1 of 3)	27896	NR_109772	101927502	Hs.528628	NR_109772	ENSG00000233926	LOC101927502	-	uncharacterized LOC101927502	ncRNA	0.004440	0.391304	
chunk0137_212_1	chr4	19405628	19406181	+	0	NA	Intergenic	Intergenic	-846001	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.001808	0.337545	
chunk0178_323_1	chr7	38245266	38245784	+	0	NA	Intergenic	Intergenic	28122	NM_001003799	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.003861	0.369942	
chunk0019_93_1	chr1	224639819	224640577	+	0	NA	intron (NM_152495, intron 1 of 5)	intron (NM_152495, intron 1 of 5)	23721	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.014512	0.469038	
chunk0142_341_1	chr4	101271257	101271786	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	-30649	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.003781	0.367925	
chunk0130_339_1	chr3	138669541	138670089	+	0	NA	intron (NM_001256045, intron 8 of 12)	intron (NM_001256045, intron 8 of 12)	37806	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.007299	0.360656	
chunk0133_58_1	chr3	166777818	166778725	+	0	NA	Intergenic	L1PA16|LINE|L1	602012	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.002205	0.340308	649(TAGCACAATGTGTACT,-,0.00),650(AGCACAATGTGTACTC,+,0.00)
chunk0050_259_1	chr12	105855775	105856457	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	149342	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.002933	0.390922	295(CAGGACACCATGTATT,-,0.00),296(AGGACACCATGTATTT,+,0.00)
chunk0123_23_1	chr3	40414177	40414721	+	0	NA	intron (NM_001248, intron 5 of 10)	intron (NM_001248, intron 5 of 10)	27204	NM_001291960	956	Hs.441145	NM_001248	ENSG00000168032	ENTPD3	CD39L3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding	0.003676	0.442202	40(AAAAACTCAATGTTCT,-,0.00),41(AAAACTCAATGTTCTT,+,0.00),246(GAGAACAAATTGTACT,-,0.00),247(AGAACAAATTGTACTT,+,0.00)
chunk0037_308_1	chr11	76771066	76771285	+	0	NA	Intergenic	Intergenic	-11138	NM_001258210	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.000000	0.563636	
chunk0040_311_1	chr11	117703155	117703725	+	0	NA	intron (NM_020693, intron 3 of 32)	intron (NM_020693, intron 3 of 32)	93821	NM_020693	57453	Hs.659513	NM_020693	ENSG00000177103	DSCAML1	DSCAM2	DS cell adhesion molecule like 1	protein-coding	0.012281	0.490368	
chunk0153_442_1	chr5	76347973	76348737	+	0	NA	intron (NM_001297716, intron 12 of 12)	L1MC1|LINE|L1	-54900	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.005236	0.385621	
chunk0084_345_1	chr17	81249308	81249537	+	0	NA	intron (NM_001037984, intron 14 of 15)	intron (NM_001037984, intron 14 of 15)	10111	NM_001086521	284184	Hs.356545	NM_001086521	ENSG00000224877	NDUFAF8	C17orf89	NADH:ubiquinone oxidoreductase complex assembly factor 8	protein-coding	0.000000	0.617391	
chunk0050_404_1	chr12	109477541	109477742	+	0	NA	promoter-TSS (NM_001270449)	promoter-TSS (NM_001270449)	18	NM_130466	89910	Hs.374067	NM_130466	ENSG00000151148	UBE3B	BPIDS|KOS	ubiquitin protein ligase E3B	protein-coding	0.074627	0.623762	
chunk0032_296_1	chr11	9568771	9569424	+	0	NA	Intergenic	Intergenic	-4584	NM_003390	7465	Hs.249441	NM_003390	ENSG00000166483	WEE1	WEE1A|WEE1hu	WEE1 G2 checkpoint kinase	protein-coding	0.007657	0.397554	331(CAGTACAGTGTGTGCT,-,0.00),332(AGTACAGTGTGTGCTT,+,0.00)
chunk0029_153_1	chr10	99430842	99431397	+	0	NA	promoter-TSS (NM_002079)	promoter-TSS (NM_002079)	-346	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.072072	0.631295	
chunk0076_361_1	chr16	71808901	71809100	+	0	NA	promoter-TSS (NM_001030007)	promoter-TSS (NM_001030007)	73	NM_001128	164	Hs.461253	NM_001128	ENSG00000166747	AP1G1	ADTG|CLAPG1	adaptor related protein complex 1 subunit gamma 1	protein-coding	0.065327	0.520000	
chunk0043_429_1	chr12	26029032	26029486	+	0	NA	intron (NM_001164747, intron 2 of 5)	intron (NM_001164747, intron 2 of 5)	-23299	NM_001164746	11228	Hs.696433	NM_007211	ENSG00000123094	RASSF8	C12orf2|HOJ1	Ras association domain family member 8	protein-coding	0.002203	0.415385	
chunk0175_154_1	chr7	3777155	3777511	+	0	NA	intron (NM_152744, intron 4 of 44)	intron (NM_152744, intron 4 of 44)	-352352	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.016854	0.420168	
chunk0017_70_1	chr1	205610537	205611173	+	0	NA	3' UTR (NM_001973, exon 5 of 5)	3' UTR (NM_001973, exon 5 of 5)	22017	NM_021795	2005	Hs.497520	NM_001973	ENSG00000158711	ELK4	SAP1	ETS transcription factor ELK4	protein-coding	0.003145	0.334380	
chunk0016_353_1	chr1	202064512	202064917	+	0	NA	Intergenic	L1MB7|LINE|L1	54152	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.019753	0.423645	
chunk0095_289_1	chr2	20168264	20168608	+	0	NA	Intergenic	Intergenic	56730	NM_002997	6382	Hs.224607	NM_002997	ENSG00000115884	SDC1	CD138|SDC|SYND1|syndecan	syndecan 1	protein-coding	0.020349	0.568116	
chunk0003_383_1	chr1	39842399	39842714	+	0	NA	intron (NR_132414, intron 1 of 1)	intron (NR_132414, intron 1 of 1)	40955	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.009524	0.481013	103(AGGCACACACTGCTCC,-,0.00),104(GGCACACACTGCTCCA,+,0.00)
chunk0209_288_1	chrX	48083412	48083925	+	0	NA	Intergenic	ERVL47-int|LTR|ERVL	-12010	NM_001282202	57232	Hs.650883	NM_001037735	ENSG00000221994	ZNF630	dJ54B20.2	zinc finger protein 630	protein-coding	0.011696	0.414397	82(AGGGACAGAATGTACT,-,0.00),83(GGGACAGAATGTACTT,+,0.00)
chunk0062_242_1	chr14	71437669	71438213	+	0	NA	Intergenic	L1ME3G|LINE|L1	39604	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.005515	0.337615	
chunk0091_47_1	chr19	4472040	4472239	+	0	NA	promoter-TSS (NM_001001520)	promoter-TSS (NM_001001520)	-57	NM_032631	84717	Hs.43071	NM_032631	ENSG00000167674	HDGFL2	HDGF-2|HDGF2|HDGFRP2|HRP-2|HRP2	HDGF like 2	protein-coding	0.090452	0.640000	
chunk0142_259_1	chr4	99155048	99155365	+	0	NA	non-coding (NR_037884, exon 3 of 10)	non-coding (NR_037884, exon 3 of 10)	6441	NR_028270	359806	Hs.537400	NR_028270		PCNAP1	p1PCNA	proliferating cell nuclear antigen pseudogene 1	pseudo	0.006309	0.380503	
chunk0152_311_1	chr5	61919892	61920472	+	0	NA	Intergenic	Intergenic	-184484	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.010345	0.406196	
chunk0122_291_1	chr3	36172624	36173264	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-207543	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.004687	0.411856	
chunk0114_182_1	chr21	14945202	14945562	+	0	NA	Intergenic	MER97a|DNA|hAT-Tip100	119423	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.008333	0.335180	
chunk0007_106_1	chr1	78878382	78878855	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	128192	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.008457	0.464135	
chunk0142_404_1	chr4	102813381	102813824	+	0	NA	intron (NM_181893, intron 1 of 6)	L2|LINE|L2	12258	NM_001300795	7323	Hs.518773	NM_003340	ENSG00000109332	UBE2D3	E2(17)KB3|UBC4/5|UBCH5C	ubiquitin conjugating enzyme E2 D3	protein-coding	0.004515	0.346847	
chunk0066_104_1	chr15	29854403	29854602	+	0	NA	intron (NM_001301025, intron 2 of 28).2	MLT1C|LTR|ERVL-MaLR	-31999	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.020101	0.515000	
chunk0167_339_1	chr6	72636685	72637205	+	0	NA	intron (NR_120503, intron 1 of 3)	intron (NR_120503, intron 1 of 3)	6450	NR_120503	100507381	Hs.662412	NR_120503	ENSG00000233844	KCNQ5-IT1	-	KCNQ5 intronic transcript 1	ncRNA	0.005769	0.376200	
chunk0124_128_1	chr3	54341554	54342349	+	0	NA	intron (NM_018398, intron 3 of 37)	MIR|SINE|MIR	219285	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.003774	0.363065	
chunk0050_341_1	chr12	107493570	107494092	+	0	NA	intron (NM_001018072, intron 1 of 16)	MLT1C|LTR|ERVL-MaLR	-87026	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.003831	0.443595	
chunk0160_212_1	chr5	154844718	154845308	+	0	NA	intron (NM_032385, intron 1 of 8)	intron (NM_032385, intron 1 of 8)	5640	NM_032385	10826	Hs.519694	NM_016348	ENSG00000170271	FAXDC2	C5orf4	fatty acid hydroxylase domain containing 2	protein-coding	0.008475	0.433164	
chunk0156_262_1	chr5	109349254	109349453	+	0	NA	intron (NM_014819, intron 7 of 9)	LTR41|LTR|ERVL	60621	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.010050	0.490000	
chunk0140_350_1	chr4	74100446	74100798	+	0	NA	Intergenic	MIR|SINE|MIR	-1342	NM_002089	2920	Hs.75765	NM_002089	ENSG00000081041	CXCL2	CINC-2a|GRO2|GROb|MGSA-b|MIP-2a|MIP2|MIP2A|SCYB2	C-X-C motif chemokine ligand 2	protein-coding	0.005682	0.413598	
chunk0203_210_1	chr9	86639791	86640420	+	0	NA	Intergenic	Intergenic	-285618	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.011129	0.476190	
chunk0206_140_1	chr9	121169024	121169253	+	0	NA	intron (NM_007018, intron 36 of 41)	intron (NM_007018, intron 36 of 41)	32949	NM_016322	51552	Hs.371563	NM_016322	ENSG00000119396	RAB14	FBP|RAB-14	RAB14, member RAS oncogene family	protein-coding	0.013100	0.421739	
chunk0172_229_1	chr6	137072778	137073193	+	0	NA	Intergenic	L1PA7|LINE|L1	-27805	NM_001278723	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.002410	0.382212	
chunk0151_35_1	chr5	41908353	41908764	+	0	NA	intron (NM_175921, intron 2 of 5)	intron (NM_175921, intron 2 of 5)	4190	NM_175921	285636	Hs.29899	NM_175921	ENSG00000205765	C5orf51	-	chromosome 5 open reading frame 51	protein-coding	0.002433	0.366505	336(CAGAAGACTCTGTGCT,-,0.00),337(AGAAGACTCTGTGCTT,+,0.00)
chunk0062_320_1	chr14	73286547	73287440	+	0	NA	intron (NM_001005743, intron 9 of 12)	Tigger9a|DNA|TcMar-Tigger	49496	NM_173462	89932	Hs.509909	NM_173462	ENSG00000100767	PAPLN	PPN	papilin, proteoglycan like sulfated glycoprotein	protein-coding	0.007839	0.383669	548(TAGAACAGATTGTACC,-,0.00),549(AGAACAGATTGTACCT,+,0.00)
chunk0073_204_1	chr16	9579929	9580128	+	0	NA	Intergenic	Intergenic	-124523	NR_126349	104266959	Hs.578888	NR_126349	ENSG00000261075	LINC01195	-	long intergenic non-protein coding RNA 1195	ncRNA	0.005025	0.490000	
chunk0145_124_1	chr4	146367665	146367944	+	0	NA	intron (NM_001029998, intron 5 of 11)	intron (NM_001029998, intron 5 of 11)	-40779	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.003584	0.307143	
chunk0082_262_1	chr17	57834262	57834758	+	0	NA	Intergenic	Intergenic	15562	NM_016070	51649	Hs.5836	NM_016070	ENSG00000181610	MRPS23	CGI-138|HSPC329|MRP-S23	mitochondrial ribosomal protein S23	protein-coding	0.020161	0.551308	
chunk0170_242_1	chr6	113642795	113643282	+	0	NA	intron (NR_125844, intron 1 of 2)	intron (NR_125844, intron 1 of 2)	7037	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.002053	0.426230	1(AGGAACAACCTGTGTT,-,0.00),2(GGAACAACCTGTGTTG,+,0.00)
chunk0059_329_1	chr14	36856013	36856509	+	0	NA	intron (NM_030631, intron 2 of 9)	intron (NM_030631, intron 2 of 9)	96130	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.020161	0.482897	
chunk0021_154_1	chr10	4678051	4678250	+	0	NA	promoter-TSS (NR_024475)	promoter-TSS (NR_024475)	-80	NR_024475	100216001	Hs.634869	NR_024475	ENSG00000231298	MANCR	LINC00704	mitotically associated long non coding RNA	ncRNA	0.010050	0.385000	
chunk0191_14_1	chr8	42580747	42581016	+	0	NA	Intergenic	Intergenic	-38668	NM_006749	6575	Hs.653173	NM_006749	ENSG00000168575	SLC20A2	GLVR-2|GLVR2|IBGC1|IBGC3|MLVAR|PIT-2|PIT2|RAM1|Ram-1	solute carrier family 20 member 2	protein-coding	0.003717	0.385185	
chunk0046_272_1	chr12	61300746	61300987	+	0	NA	Intergenic	MER67C|LTR|ERV1	891973	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.008299	0.376033	
chunk0174_246_1	chr6	161001318	161001781	+	0	NA	intron (NM_006724, intron 1 of 25)	L2a|LINE|L2	9822	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.008639	0.400862	
chunk0113_43_1	chr20	49916406	49916605	+	0	NA	promoter-TSS (NM_006038)	promoter-TSS (NM_006038)	-962	NM_006038	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.015075	0.495000	
chunk0129_292_1	chr3	123503947	123504662	+	0	NA	intron (NM_198402, intron 4 of 6)	intron (NM_198402, intron 4 of 6)	-55759	NM_183357	111	Hs.593292	NM_183357	ENSG00000173175	ADCY5	AC5|FDFM	adenylate cyclase 5	protein-coding	0.008392	0.350559	435(AAAAACACTTTGTGCT,-,0.00),436(AAAACACTTTGTGCTT,+,0.00)
chunk0009_327_1	chr1	108953307	108953753	+	0	NA	intron (NM_015127, intron 1 of 11)	L2c|LINE|L2	-3082	NM_001278203	23155	Hs.658489	NM_015127	ENSG00000121940	CLCC1	MCLC	chloride channel CLIC like 1	protein-coding	0.008969	0.447427	
chunk0194_37_1	chr8	81827124	81827323	+	0	NA	intron (NM_152837, intron 2 of 6)	intron (NM_152837, intron 2 of 6)	15063	NM_022133	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.255000	
chunk0069_241_1	chr15	64116664	64117140	+	0	NA	intron (NM_148955, intron 2 of 12)	Tigger15a|DNA|TcMar-Tigger	21018	NM_001242933	6642	Hs.188634	NM_003099	ENSG00000028528	SNX1	HsT17379|VPS5	sorting nexin 1	protein-coding	0.002101	0.345912	
chunk0159_312_1	chr5	143140864	143141228	+	0	NA	intron (NM_015071, intron 19 of 22)	intron (NM_015071, intron 19 of 22)	-51454	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.013736	0.446575	
chunk0088_186_1	chr18	47466026	47466406	+	0	NA	Intergenic	Intergenic	85720	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.013158	0.488189	
chunk0048_59_1	chr12	78331894	78332679	+	0	NA	Intergenic	Intergenic	500997	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.005096	0.354962	
chunk0117_95_1	chr22	17387287	17387940	+	0	NA	intron (NM_001290047, intron 1 of 18)	intron (NM_001290047, intron 1 of 18)	18247	NM_001290047	27443	Hs.231895	NM_031413	ENSG00000099954	CECR2	-	CECR2 histone acetyl-lysine reader	protein-coding	0.018377	0.426606	
chunk0059_208_1	chr14	33536496	33537031	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-172174	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.003738	0.328358	
chunk0015_317_1	chr1	189336174	189336632	+	0	NA	Intergenic	L1PA15|LINE|L1	1141226	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.021834	0.557734	
chunk0147_109_1	chr4	174163697	174164247	+	0	NA	intron (NR_125896, intron 1 of 4)	intron (NR_125896, intron 1 of 4)	56426	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.003636	0.341198	
chunk0090_151_1	chr18	72345289	72346067	+	0	NA	Intergenic	Intergenic	198810	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.000000	0.300385	428(AAGAACAACTTGTGCC,-,0.00),429(AGAACAACTTGTGCCT,+,0.00)
chunk0067_297_1	chr15	47719674	47720336	+	0	NA	intron (NM_020858, intron 1 of 16)	intron (NM_020858, intron 1 of 16)	1516	NM_024966	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.003021	0.351433	
chunk0164_216_1	chr6	22764323	22764972	+	0	NA	Intergenic	Intergenic	195198	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.001541	0.386154	
chunk0190_460_1	chr8	42290034	42290662	+	0	NA	intron (NR_040009, intron 4 of 21)	intron (NR_040009, intron 4 of 21)	19046	NM_001190720	3551	Hs.597664	NM_001556	ENSG00000104365	IKBKB	IKK-beta|IKK2|IKKB|IMD15|IMD15A|IMD15B|NFKBIKB	inhibitor of nuclear factor kappa B kinase subunit beta	protein-coding	0.015924	0.593005	
chunk0123_85_1	chr3	41961859	41962471	+	0	NA	promoter-TSS (NM_017886)	promoter-TSS (NM_017886)	3	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.068627	0.624796	
chunk0096_421_1	chr2	38223203	38223677	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	92335	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.008439	0.385263	
chunk0100_78_1	chr2	106896254	106896683	+	0	NA	Intergenic	Intergenic	-9361	NM_032528	84620	Hs.98265	NM_032528	ENSG00000144057	ST6GAL2	SIAT2|ST6GalII	ST6 beta-galactoside alpha-2,6-sialyltransferase 2	protein-coding	0.009324	0.432558	
chunk0103_426_1	chr2	169798737	169798978	+	0	NA	promoter-TSS (NM_001294145)	promoter-TSS (NM_001294145)	45	NM_003142	6741	Hs.632535	NM_003142	ENSG00000138385	SSB	LARP3|La|La/SSB	small RNA binding exonuclease protection factor La	protein-coding	0.074689	0.673554	
chunk0079_211_1	chr17	14715563	14716057	+	0	NA	Intergenic	Intergenic	-315165	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.000000	0.367677	169(AAGAACAGCATGTCTT,-,0.00),170(AGAACAGCATGTCTTC,+,0.00)
chunk0089_261_1	chr18	62537526	62537973	+	0	NA	intron (NR_126534, intron 1 of 14)	L1MB4|LINE|L1	14324	NR_126534	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.000000	0.348214	
chunk0168_191_1	chr6	85416041	85416627	+	0	NA	Intergenic	Intergenic	-33250	NM_001204813	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.005119	0.366269	281(TGGAACACTCTGTTCT,-,0.00),282(GGAACACTCTGTTCTG,+,0.00)
chunk0175_58_1	chr7	1773596	1773890	+	0	NA	Intergenic	L1MA7|LINE|L1	-31433	NR_120509	101927125	Hs.633957	NR_120508	ENSG00000236081	ELFN1-AS1	MYCLo-2	ELFN1 antisense RNA 1	ncRNA	0.017007	0.444068	
chunk0174_375_1	chr6	164912325	164912799	+	0	NA	Intergenic	Intergenic	-90499	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.004219	0.429474	
chunk0046_263_1	chr12	60714374	60714964	+	0	NA	Intergenic	Intergenic	1025332	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.005085	0.270728	
chunk0107_142_1	chr2	214971058	214971295	+	0	NA	intron (NR_103740, intron 38 of 54)	intron (NR_103740, intron 38 of 54)	60910	NM_015657	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.008439	0.344538	149(AAGAACATAAAGTTCC,-,0.00),150(AGAACATAAAGTTCCA,+,0.00)
chunk0181_50_1	chr7	80078224	80078455	+	0	NA	Intergenic	L2c|LINE|L2	-56485	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.008658	0.383621	
chunk0113_55_1	chr20	50278752	50279240	+	0	NA	3' UTR (NM_001278655, exon 4 of 4)	3' UTR (NM_001278655, exon 4 of 4)	11510	NM_001278655	100506115	Hs.235484	NM_001278655		SMIM25	GCRL1|LINC01272	small integral membrane protein 25	protein-coding	0.024590	0.586912	373(GAGGACTGTGTGTTCC,-,0.00),374(AGGACTGTGTGTTCCC,+,0.00)
chunk0208_204_1	chrX	17792705	17793365	+	0	NA	Intergenic	Intergenic	55586	NM_001037540	6322	Hs.109655	NM_006746	ENSG00000047634	SCML1	-	Scm polycomb group protein like 1	protein-coding	0.006061	0.488654	
chunk0168_319_1	chr6	92337558	92338035	+	0	NA	Intergenic	Intergenic	-647368	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.004193	0.336820	
chunk0068_322_1	chr15	57497146	57497440	+	0	NA	intron (NM_001252335, intron 9 of 19)	intron (NM_001252335, intron 9 of 19)	-94611	NM_001018091	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.017007	0.562712	
chunk0078_210_1	chr17	5928886	5929223	+	0	NA	intron (NR_040000, intron 3 of 3)	L2c|LINE|L2	-141560	NM_015253	23302	Hs.370166	NM_015253	ENSG00000179314	WSCD1	-	WSC domain containing 1	protein-coding	0.011869	0.461538	
chunk0071_418_1	chr15	89755463	89755762	+	0	NA	Intergenic	Intergenic	-4303	NM_018670	55897	Hs.447531	NM_018670	ENSG00000166823	MESP1	bHLHc5	mesoderm posterior bHLH transcription factor 1	protein-coding	0.000000	0.370000	
chunk0042_435_1	chr12	12221490	12221795	+	0	NA	intron (NM_002336, intron 2 of 22)	MER5B|DNA|hAT-Charlie	45235	NM_002336	4040	Hs.584775	NM_002336	ENSG00000070018	LRP6	ADCAD2|STHAG7	LDL receptor related protein 6	protein-coding	0.003279	0.362745	197(AGGAACATAATGTTCT,-,0.00),198(GGAACATAATGTTCTC,+,0.00)
chunk0193_23_1	chr8	70803945	70804144	+	0	NA	Intergenic	L1PA15|LINE|L1	134597	NM_001287260	389668	Hs.458938	NM_001011720	ENSG00000221947	XKR9	XRG9	XK related 9	protein-coding	0.000000	0.570000	
chunk0130_398_1	chr3	140269058	140269619	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	239451	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.005348	0.398577	
chunk0136_194_1	chr4	6811775	6812383	+	0	NA	intron (NM_014743, intron 2 of 9)	intron (NM_014743, intron 2 of 9)	29347	NM_001100590	9778	Hs.79276	NM_014743	ENSG00000170871	KIAA0232	-	KIAA0232	protein-coding	0.004934	0.385878	291(GGGCACATTGTGTTAT,-,0.00)
chunk0184_431_1	chr7	122971299	122971827	+	0	NA	Intergenic	Intergenic	24137	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.005682	0.361059	
chunk0065_46_1	chr15	21301518	21301973	+	0	NA	Intergenic	L1MD2|LINE|L1	-3916	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.008791	0.331140	
chunk0039_36_1	chr11	95879189	95879389	+	0	NA	intron (NM_201281, intron 3 of 15)	intron (NM_201281, intron 3 of 15)	44918	NM_001243571	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.005000	0.412935	
chunk0132_157_1	chr3	156653910	156654537	+	0	NA	Intergenic	Intergenic	-20193	NM_015508	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.006380	0.394904	127(AAGAACATTCTGTTTT,-,0.00),128(AGAACATTCTGTTTTT,+,0.00)
chunk0088_260_1	chr18	49094426	49094915	+	0	NA	intron (NM_017653, intron 16 of 16)	intron (NM_017653, intron 16 of 16)	-44902	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.006135	0.361224	
chunk0169_190_1	chr6	102524138	102524480	+	0	NA	Intergenic	Intergenic	1125324	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.311953	
chunk0081_468_1	chr17	49585570	49586037	+	0	NA	Intergenic	Intergenic	9867	NM_007225	11248	Hs.55069	NM_007225	ENSG00000182575	NXPH3	NPH3	neurexophilin 3	protein-coding	0.006424	0.557692	224(CAGTACAGCCTGTTCT,-,0.00),225(AGTACAGCCTGTTCTG,+,0.00)
chunk0054_53_1	chr13	41703084	41703682	+	0	NA	exon (NM_015058, exon 27 of 45)	exon (NM_015058, exon 27 of 45)	-134988	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.008361	0.328881	
chunk0178_349_1	chr7	38774997	38775284	+	0	NA	intron (NM_080631, intron 10 of 27)	intron (NM_080631, intron 10 of 27)	-88051	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.010453	0.361111	
chunk0212_127_1	chrX	130995386	130995962	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	62472	NR_126350	104266960	Hs.573575	NR_126350	ENSG00000228659	LINC01201	TCONS_00017091	long intergenic non-protein coding RNA 1201	ncRNA	0.008681	0.516464	
chunk0070_206_1	chr15	72173702	72174386	+	0	NA	intron (NM_001012642, intron 1 of 11)	intron (NM_001012642, intron 1 of 11)	23751	NM_001012642	196996	Hs.596332	NM_001012642	ENSG00000175318	GRAMD2A	GRAMD2	GRAM domain containing 2A	protein-coding	0.017544	0.508029	
chunk0016_221_1	chr1	199242412	199242650	+	0	NA	Intergenic	Intergenic	-223567	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.021008	0.510460	
chunk0061_448_1	chr14	65852460	65853072	+	0	NA	Intergenic	Intergenic	381664	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.006536	0.491028	
chunk0201_197_1	chr9	36567123	36567524	+	0	NA	Intergenic	L2c|LINE|L2	-5539	NM_001256690	9833	Hs.184339	NM_014791	ENSG00000165304	MELK	HPK38	maternal embryonic leucine zipper kinase	protein-coding	0.007481	0.490050	
chunk0085_44_1	chr18	769652	770036	+	0	NA	intron (NM_005433, intron 1 of 11)	L1MEc|LINE|L1	42482	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.010417	0.350649	
chunk0005_438_1	chr1	63298847	63299128	+	0	NA	intron (NR_038252, intron 3 of 11)	L2c|LINE|L2	18270	NR_038252	199899	Hs.116210	NR_038252	ENSG00000224209	LINC00466	-	long intergenic non-protein coding RNA 466	ncRNA	0.007117	0.411348	
chunk0053_413_1	chr13	36913403	36914080	+	0	NA	intron (NM_001127217, intron 1 of 6)	intron (NM_001127217, intron 1 of 6)	6531	NM_005905	4093	Hs.123119	NM_005905	ENSG00000120693	SMAD9	MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B	SMAD family member 9	protein-coding	0.000000	0.331858	
chunk0051_401_1	chr12	122062699	122063468	+	0	NA	Intergenic	Intergenic	-15645	NM_014938	22877	Hs.437153	NM_014938	ENSG00000175727	MLXIP	MIR|MONDOA|bHLHe36	MLX interacting protein	protein-coding	0.020806	0.549351	
chunk0124_96_1	chr3	53537653	53538238	+	0	NA	intron (NM_000720, intron 3 of 48)	L1MC5|LINE|L1	42896	NM_001128840	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.001709	0.356655	
chunk0173_235_1	chr6	146637478	146637910	+	0	NA	intron (NM_024694, intron 2 of 35)	L1MEg|LINE|L1	38694	NM_024694	79747	Hs.720870	NM_024694	ENSG00000118492	ADGB	C6orf103|CAPN16	androglobin	protein-coding	0.002315	0.374134	187(AGGTACATCTTGTACT,-,0.00),188(GGTACATCTTGTACTC,+,0.00)
chunk0197_133_1	chr8	120102699	120102942	+	0	NA	Intergenic	Intergenic	-22288	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.012346	0.319672	
chunk0195_92_1	chr8	94331216	94331792	+	0	NA	Intergenic	Intergenic	-69185	NM_181702	2669	Hs.654463	NM_005261	ENSG00000164949	GEM	KIR	GTP binding protein overexpressed in skeletal muscle	protein-coding	0.010417	0.415945	264(AAGCTCAGTGTGTCCC,-,0.00),265(AGCTCAGTGTGTCCCT,+,0.00)
chunk0065_325_1	chr14	103213497	103214032	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-24736	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.007477	0.472015	
chunk0039_425_1	chr11	107830570	107831469	+	0	NA	intron (NM_017515, intron 1 of 7)	L2c|LINE|L2	28169	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.004449	0.371111	45(GAGAACAGCCTCTACT,-,0.00),46(AGAACAGCCTCTACTT,+,0.00)
chunk0183_390_1	chr7	110155242	110155778	+	0	NA	Intergenic	Intergenic	-195297	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.013060	0.387337	
chunk0090_385_1	chr18	77376149	77376647	+	0	NA	Intergenic	Intergenic	126346	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.046185	0.505010	
chunk0011_88_1	chr1	145532581	145533097	+	0	NA	Intergenic	Intergenic	75019	NR_104217	101929780	Hs.534675	NR_104217	ENSG00000272150	NBPF25P	WI2-925H4.1	NBPF member 25, pseudogene	pseudo	0.009690	0.427466	
chunk0160_98_1	chr5	150344182	150344670	+	0	NA	Intergenic	Intergenic	-13213	NM_001135243	6949	Hs.519672	NM_000356	ENSG00000070814	TCOF1	MFD1|TCS|TCS1|treacle	treacle ribosome biogenesis factor 1	protein-coding	0.008197	0.460123	
chunk0120_110_1	chr3	4575043	4575507	+	0	NA	intron (NM_002222, intron 4 of 57)	intron (NM_002222, intron 4 of 57)	81927	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.002155	0.359140	
chunk0011_27_1	chr1	143215904	143216570	+	0	NA	Intergenic	Intergenic	206355	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.057057	0.379310	
chunk0174_318_1	chr6	163129452	163129660	+	0	NA	intron (NM_001080378, intron 5 of 5)	intron (NM_001080378, intron 5 of 5)	62446	NR_122120	729658	Hs.728991	NR_122120		PACRG-AS3	-	PACRG antisense RNA 3	ncRNA	0.019231	0.468900	128(CAGTACTCTGTGTCCA,-,0.00),129(AGTACTCTGTGTCCAG,+,0.00)
chunk0184_368_1	chr7	121209202	121209643	+	0	NA	intron (NM_001105533, intron 15 of 17)	intron (NM_001105533, intron 15 of 17)	-115945	NM_016087	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.004535	0.303167	
chunk0085_227_1	chr18	6901336	6901570	+	0	NA	intron (NM_001010000, intron 15 of 16)	L1MC3|LINE|L1	28416	NR_034100	400643	Hs.253920	NM_001103383	ENSG00000265933	LINC00668	-	long intergenic non-protein coding RNA 668	ncRNA	0.004274	0.361702	
chunk0081_331_1	chr17	46270073	46270346	+	0	NA	Intergenic	Intergenic	-24922	NM_014834	9884	Hs.579108	NM_014834	ENSG00000176681	LRRC37A	LRRC37	leucine rich repeat containing 37A	protein-coding	0.018315	0.474453	
chunk0074_202_1	chr16	25000757	25001337	+	0	NA	intron (NM_018054, intron 1 of 18)	intron (NM_018054, intron 1 of 18)	14331	NM_018054	55114	Hs.373793	NM_018054	ENSG00000140750	ARHGAP17	MST066|MST110|MSTP038|MSTP066|MSTP110|NADRIN|PP367|PP4534|RICH-1|RICH1|WBP15	Rho GTPase activating protein 17	protein-coding	0.003448	0.323580	
chunk0022_140_1	chr10	12167625	12168017	+	0	NA	non-coding (NR_024577, exon 13 of 14)	non-coding (NR_024577, exon 13 of 14)	-28141	NM_006023	8872	Hs.412842	NM_006023	ENSG00000151465	CDC123	C10orf7|D123	cell division cycle 123	protein-coding	0.015306	0.396947	
chunk0058_284_1	chr14	26525117	26525600	+	0	NA	intron (NM_002515, intron 2 of 4)	intron (NM_002515, intron 2 of 4)	72396	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.002070	0.303719	
chunk0100_424_1	chr2	120107818	120108462	+	0	NA	intron (NM_020909, intron 16 of 24)	intron (NM_020909, intron 16 of 24)	94931	NM_001184938	57669	Hs.369232	NM_020909	ENSG00000115109	EPB41L5	BE37|YMO1|YRT	erythrocyte membrane protein band 4.1 like 5	protein-coding	0.000000	0.331783	
chunk0033_14_1	chr11	12439405	12439833	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	62140	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.004673	0.491841	
chunk0111_127_1	chr20	24406874	24407625	+	0	NA	Intergenic	Intergenic	-61950	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.006658	0.444149	
chunk0152_199_1	chr5	59996838	59997387	+	0	NA	intron (NM_001165899, intron 2 of 16)	intron (NM_001165899, intron 2 of 16)	-103318	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.001821	0.321818	
chunk0156_273_1	chr5	109653926	109654603	+	0	NA	Intergenic	MIR|SINE|MIR	-35102	NM_002372	4124	Hs.432822	NM_002372	ENSG00000112893	MAN2A1	AMan II|GOLIM7|MANA2|MANII	mannosidase alpha class 2A member 1	protein-coding	0.001477	0.417404	414(CAGGACTTTCAGTGCT,-,0.00),415(AGGACTTTCAGTGCTG,+,0.00)
chunk0146_305_1	chr4	165191955	165192415	+	0	NA	Intergenic	Intergenic	-15433	NM_007246	11275	Hs.388668	NM_007246	ENSG00000109466	KLHL2	ABP-KELCH|MAV|MAYVEN	kelch like family member 2	protein-coding	0.010870	0.401302	
chunk0137_207_1	chr4	18593111	18593310	+	0	NA	Intergenic	Intergenic	-571350	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.000000	0.305000	
chunk0128_106_1	chr3	106086065	106086427	+	0	NA	Intergenic	MER72B|LTR|ERV1	-217203	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.002762	0.446281	
chunk0161_178_1	chr5	169641284	169641695	+	0	NA	intron (NM_004946, intron 1 of 51)	intron (NM_004946, intron 1 of 51)	4242	NM_004946	1794	Hs.586174	NM_004946	ENSG00000134516	DOCK2	IMD40	dedicator of cytokinesis 2	protein-coding	0.012165	0.497573	
chunk0036_21_1	chr11	58430461	58431251	+	0	NA	Intergenic	L1PB4|LINE|L1	-7543	NM_001005566	390190	Hs.553753	NM_001005566	ENSG00000172365	OR5B2	OR11-240|OST073	olfactory receptor family 5 subfamily B member 2	protein-coding	0.001266	0.307206	
chunk0049_313_1	chr12	94591811	94592474	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	-20790	NR_106998	102465834		NR_106998	ENSG00000283818	MIR7844	hsa-mir-7844	microRNA 7844	ncRNA	0.010558	0.445783	393(TAGCACACTCTGAACT,-,0.00),394(AGCACACTCTGAACTT,+,0.00)
chunk0106_154_1	chr2	200458186	200458821	+	0	NA	intron (NM_001282735, intron 8 of 12)	L1MC5|LINE|L1	51566	NM_152387	130535	Hs.605775	NM_152387	ENSG00000155729	KCTD18	6530404F10Rik	potassium channel tetramerization domain containing 18	protein-coding	0.001575	0.312893	
chunk0179_137_1	chr7	45959172	45959627	+	0	NA	Intergenic	L1MEf|LINE|L1	-38127	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.006593	0.300439	
chunk0100_358_1	chr2	117678899	117679380	+	0	NA	Intergenic	MIR3|SINE|MIR	-135540	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.002079	0.350622	
chunk0082_273_1	chr17	57938123	57938508	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	17008	NM_001271875	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.018182	0.497409	
chunk0051_8_1	chr12	111495620	111495876	+	0	NA	intron (NM_001310121, intron 14 of 25)	L1M1|LINE|L1	60886	NM_001291424	10019	Hs.506784	NM_005475	ENSG00000111252	SH2B3	IDDM20|LNK	SH2B adaptor protein 3	protein-coding	0.007812	0.392996	135(CAGAACATTGTGTCCA,-,0.00),136(AGAACATTGTGTCCAA,+,0.00)
chunk0038_101_1	chr11	83674233	83674766	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	7926	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.001876	0.406367	
chunk0102_197_1	chr2	147858491	147859141	+	0	NA	intron (NM_001616, intron 1 of 10)	MER58B|DNA|hAT-Charlie	13821	NM_001616	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.004615	0.359447	
chunk0154_301_1	chr5	83265180	83265704	+	0	NA	intron (NM_022550, intron 7 of 7)	intron (NM_022550, intron 7 of 7)	187944	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.003817	0.297143	
chunk0143_407_1	chr4	123326533	123327067	+	0	NA	Intergenic	L2a|LINE|L2	-69995	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.007491	0.349533	
chunk0120_460_1	chr22	50427123	50427531	+	0	NA	intron (NM_001242900, intron 10 of 22)	L1MB4|LINE|L1	47744	NM_002972	6305	Hs.589924	NM_002972	ENSG00000100241	SBF1	CMT4B3|DENND7A|MTMR5	SET binding factor 1	protein-coding	0.012255	0.393643	111(CTGGACTCTCTGTTCT,-,0.00),112(TGGACTCTCTGTTCTG,+,0.00)
chunk0160_207_1	chr5	154780417	154780661	+	0	NA	intron (NM_015315, intron 1 of 18)	MIR3|SINE|MIR	-48919	NR_039667	100616306		NR_039667	ENSG00000263361	MIR378H	-	microRNA 378h	ncRNA	0.000000	0.481633	50(GGGCACAGAGTGTATT,-,0.00),51(GGCACAGAGTGTATTT,+,0.00),123(AAGAACTTGATGTTCC,-,0.00),124(AGAACTTGATGTTCCA,+,0.00)
chunk0104_192_1	chr2	175175445	175175652	+	0	NA	TTS (NM_001689)	TTS (NM_001689)	6115	NM_001002258	518	Hs.429	NM_001689	ENSG00000154518	ATP5MC3	ATP5G3|P3	ATP synthase membrane subunit c locus 3	protein-coding	0.009662	0.427885	
chunk0157_126_1	chr5	117160173	117160745	+	0	NA	Intergenic	Intergenic	-255053	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.003497	0.349040	
chunk0040_199_1	chr11	114147618	114148144	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	87315	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.011407	0.383302	
chunk0125_168_1	chr3	66577873	66578368	+	0	NA	Intergenic	Intergenic	-77699	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.010101	0.375000	
chunk0200_13_1	chr9	14616214	14616705	+	0	NA	3' UTR (NM_178566, exon 10 of 10)	3' UTR (NM_178566, exon 10 of 10)	77023	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.006110	0.317073	
chunk0026_421_1	chr10	70725908	70726142	+	0	NA	intron (NM_139155, intron 4 of 21)	intron (NM_139155, intron 4 of 21)	53222	NM_080722	140766	Hs.352156	NM_080722	ENSG00000138316	ADAMTS14	-	ADAM metallopeptidase with thrombospondin type 1 motif 14	protein-coding	0.008547	0.582979	
chunk0178_6_1	chr7	29022284	29022549	+	0	NA	intron (NM_019029, intron 12 of 12)	L1MA4|LINE|L1	42449	NR_038965	100506497	Hs.586328	NR_038965	ENSG00000272568	LOC100506497	-	uncharacterized LOC100506497	ncRNA	0.011321	0.560150	
chunk0193_85_1	chr8	73575072	73575589	+	0	NA	intron (NM_001164384, intron 10 of 10)	L1ME4b|LINE|L1	155256	NR_038406	100128126	Hs.679921	NR_038406	ENSG00000253302	STAU2-AS1	-	STAU2 antisense RNA 1	ncRNA	0.003868	0.328185	264(TAGCACACTGTGTTCC,-,0.00),265(AGCACACTGTGTTCCT,+,0.00)
chunk0154_444_1	chr5	90309284	90309546	+	0	NA	Intergenic	Intergenic	-19344	NR_120601	101929495	Hs.346679	NR_120601		LINC01339	-	long intergenic non-protein coding RNA 1339	ncRNA	0.007634	0.334601	
chunk0039_97_1	chr11	97296604	97297277	+	0	NA	Intergenic	Intergenic	-790063	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.002972	0.330861	
chunk0159_86_1	chr5	137815146	137815993	+	0	NA	Intergenic	Intergenic	14376	NR_002713	4888	Hs.643466	NR_002713	ENSG00000226306	NPY6R	NPY1RL|NPY6RP|PP2|Y2B	neuropeptide Y receptor Y6 (pseudogene)	pseudo	0.003542	0.411557	
chunk0207_377_1	chr9	136032036	136032521	+	0	NA	intron (NM_144653, intron 2 of 5)	L1ME1|LINE|L1	63007	NM_144653	138151	Hs.112895	NM_144653	ENSG00000148411	NACC2	BEND9|BTBD14|BTBD14A|BTBD31|NAC-2|RBB	NACC family member 2	protein-coding	0.012371	0.438272	
chunk0066_68_1	chr15	29166918	29167470	+	0	NA	intron (NM_015307, intron 4 of 10)	L1PB1|LINE|L1	102622	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.007246	0.359855	
chunk0207_366_1	chr9	135827484	135827914	+	0	NA	intron (NM_015447, intron 7 of 16)	intron (NM_015447, intron 7 of 16)	79460	NM_015447	157922	Hs.522493	NM_015447	ENSG00000130559	CAMSAP1	-	calmodulin regulated spectrin associated protein 1	protein-coding	0.027907	0.447796	
chunk0137_98_1	chr4	13441486	13442318	+	0	NA	intron (NM_001017979, intron 4 of 6)	intron (NM_001017979, intron 4 of 6)	42463	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.004808	0.351741	
chunk0091_154_1	chr19	7424956	7425395	+	0	NA	intron (NM_015318, intron 1 of 20)	intron (NM_015318, intron 1 of 20)	-14513	NM_001130955	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.011390	0.404545	
chunk0112_270_1	chr20	43208984	43209576	+	0	NA	Intergenic	Intergenic	-19363	NM_007050	11122	Hs.526879	NM_007050	ENSG00000196090	PTPRT	RPTPrho	protein tyrosine phosphatase receptor type T	protein-coding	0.008446	0.404722	
chunk0189_437_1	chr8	28147169	28148589	+	0	NA	intron (NM_018091, intron 10 of 14)	L1MC4|LINE|L1	54812	NM_001284224	55140	Hs.491336	NM_018091	ENSG00000134014	ELP3	KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.006338	0.377199	553(AAACACAGTGAGTTCC,-,0.00),666(CAGAACATCTTGTCTT,-,0.00),667(AGAACATCTTGTCTTT,+,0.00)
chunk0088_379_1	chr18	54235778	54236465	+	0	NA	Intergenic	Intergenic	-11333	NM_003927	8932	Hs.25674	NM_003927	ENSG00000134046	MBD2	DMTase|NY-CO-41	methyl-CpG binding domain protein 2	protein-coding	0.013100	0.385174	
chunk0171_289_1	chr6	128319748	128320291	+	0	NA	intron (NM_001291983, intron 2 of 18)	intron (NM_001291983, intron 2 of 18)	200655	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.001842	0.318015	384(AGGCACTTTTTGTACT,-,0.00),385(GGCACTTTTTGTACTT,+,0.00)
chunk0210_126_1	chrX	73981162	73981579	+	0	NA	intron (NR_024582, intron 2 of 4)	L1MB8|LINE|L1	37046	NR_024582	554203	Hs.648316	NR_024582	ENSG00000225470	JPX	DCBALD06|ENOX|LINC00183|NCRNA00183	JPX transcript, XIST activator	ncRNA	0.002398	0.320574	
chunk0072_207_1	chr15	95349765	95350020	+	0	NA	Intergenic	Intergenic	-22792	NR_034095	400456	Hs.536404	NR_034095	ENSG00000248441	LINC01197	-	long intergenic non-protein coding RNA 1197	ncRNA	0.007843	0.460938	
chunk0144_164_1	chr4	131712235	131712440	+	0	NA	Intergenic	LTR33A|LTR|ERVL	-52501	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.000000	0.354369	
chunk0018_305_1	chr1	221007510	221007876	+	0	NA	Intergenic	L1MD3|LINE|L1	-127553	NR_046901	100873924	Hs.645593	NR_046901	ENSG00000257551	HLX-AS1	-	HLX antisense RNA 1	ncRNA	0.000000	0.277929	
chunk0175_47_1	chr7	1175997	1176312	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	15369	NR_110070	101927021	Hs.529566	NR_110065		LOC101927021	-	uncharacterized LOC101927021	ncRNA	0.044444	0.560127	
chunk0061_380_1	chr14	64162432	64162757	+	0	NA	intron (NM_182914, intron 88 of 115)	intron (NM_182914, intron 88 of 115)	-51547	NM_182913	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.012308	0.411043	
chunk0034_4_1	chr11	25848772	25849040	+	0	NA	Intergenic	L1M3c|LINE|L1	-340217	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.000000	0.505576	
chunk0165_294_1	chr6	36455351	36455874	+	0	NA	intron (NR_104481, intron 1 of 3)	(GT)n|Simple_repeat|Simple_repeat	-12723	NM_152990	222659	Hs.520097	NM_152990	ENSG00000179165	PXT1	STEPP	peroxisomal testis enriched protein 1	protein-coding	0.007648	0.431298	
chunk0022_52_1	chr10	8163689	8164001	+	0	NA	Intergenic	Intergenic	104460	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.003205	0.421725	
chunk0034_293_1	chr11	34825534	34826127	+	0	NA	Intergenic	Intergenic	-90300	NM_001166158	8050	Hs.502315	NM_003477	ENSG00000110435	PDHX	DLDBP|E3BP|OPDX|PDHXD|PDX1|proX	pyruvate dehydrogenase complex component X	protein-coding	0.011804	0.488215	208(TAGAACACTGTGTCTT,-,0.00),209(AGAACACTGTGTCTTT,+,0.00)
chunk0117_314_1	chr22	24802265	24802482	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-3848	NM_001098497	129049	Hs.474397	NM_133454	ENSG00000167037	SGSM1	RUTBC2	small G protein signaling modulator 1	protein-coding	0.018433	0.440367	
chunk0057_26_1	chr13	95620438	95621522	+	0	NA	intron (NM_198968, intron 9 of 22)	intron (NM_198968, intron 9 of 22)	23726	NM_014934	22873	Hs.656580	NM_014934	ENSG00000134874	DZIP1	DZIP|DZIPt1	DAZ interacting zinc finger protein 1	protein-coding	0.009225	0.471889	
chunk0095_145_1	chr2	16917580	16918094	+	0	NA	Intergenic	Intergenic	-251971	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.000000	0.275728	
chunk0118_263_1	chr22	33292918	33293309	+	0	NA	intron (NM_133642, intron 12 of 14)	L2b|LINE|L2	143556	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.002558	0.395408	
chunk0174_131_1	chr6	157401989	157402288	+	0	NA	intron (NM_024630, intron 1 of 8)	intron (NM_024630, intron 1 of 8)	20613	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.013378	0.536667	
chunk0198_472_1	chr8	144895322	144895686	+	0	NA	intron (NM_021061, intron 1 of 5)	intron (NM_021061, intron 1 of 5)	5957	NM_021061	58500	Hs.532277	NM_021061	ENSG00000196150	ZNF250	ZFP647|ZNF647	zinc finger protein 250	protein-coding	0.005495	0.484932	
chunk0081_118_1	chr17	40074839	40075769	+	0	NA	intron (NM_199334, intron 2 of 8)	intron (NM_199334, intron 2 of 8)	12489	NM_199334	7067	Hs.724	NM_003250	ENSG00000126351	THRA	AR7|CHNG6|EAR7|ERB-T-1|ERBA|ERBA1|NR1A1|THRA1|THRA2|c-ERBA-1	thyroid hormone receptor alpha	protein-coding	0.013978	0.564984	432(GGGTACAGCCTGTGCC,-,0.00),433(GGTACAGCCTGTGCCT,+,0.00),747(GGAAGAGTCTGTGCTT,+,0.00)
chunk0147_88_1	chr4	173214769	173215028	+	0	NA	intron (NM_017423, intron 1 of 11)	intron (NM_017423, intron 1 of 11)	46145	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.007722	0.415385	
chunk0147_27_1	chr4	171618888	171619404	+	0	NA	Intergenic	L1PB4|LINE|L1	-194278	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.005814	0.363636	
chunk0162_213_1	chr6	4235144	4235945	+	0	NA	Intergenic	Intergenic	-45515	NR_125874	102724096	Hs.571140	NR_125874		LOC102724096	-	uncharacterized LOC102724096	ncRNA	0.003745	0.366584	
chunk0109_309_1	chr20	8903976	8904416	+	0	NA	Intergenic	Intergenic	73011	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.000000	0.426304	
chunk0051_344_1	chr12	120321580	120321779	+	0	NA	TTS (NM_000928)	TTS (NM_000928)	6110	NM_000928	5319	Hs.992	NM_000928	ENSG00000170890	PLA2G1B	PLA2|PLA2A|PPLA2	phospholipase A2 group IB	protein-coding	0.020101	0.440000	11(ATGGACACACAGTCCT,-,0.00),12(TGGACACACAGTCCTG,+,0.00)
chunk0088_79_1	chr18	44737368	44737618	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	56595	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.000000	0.434263	
chunk0091_58_1	chr19	4811589	4811788	+	0	NA	Intergenic	Intergenic	19972	NM_018708	55527	Hs.515082	NM_018708	ENSG00000141965	FEM1A	EPRAP	fem-1 homolog A	protein-coding	0.015075	0.570000	
chunk0004_253_1	chr1	47733567	47734128	+	0	NA	Intergenic	L1ME4b|LINE|L1	263043	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.003565	0.334520	
chunk0077_157_1	chr16	79162863	79163330	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	437629	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.006424	0.433761	
chunk0043_443_1	chr12	26428931	26429584	+	0	NA	intron (NM_002223, intron 48 of 56)	intron (NM_002223, intron 48 of 56)	233684	NM_005086	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.003063	0.371560	
chunk0060_243_1	chr14	49888299	49888770	+	0	NA	Intergenic	Intergenic	-4484	NM_001663	382	Hs.525330	NM_001663	ENSG00000165527	ARF6	-	ADP ribosylation factor 6	protein-coding	0.006369	0.322034	
chunk0047_127_1	chr12	69332919	69333295	+	0	NA	Intergenic	LTR22|LTR|ERVK	-15247	NM_000239	4069	Hs.524579	NM_000239	ENSG00000090382	LYZ	LYZF1|LZM	lysozyme	protein-coding	0.007979	0.419098	
chunk0099_153_1	chr2	87136205	87136406	+	0	NA	Intergenic	L1ME1|LINE|L1	-58481	NR_039928	100616370		NR_039928	ENSG00000264793	MIR4771-1	-	microRNA 4771-1	ncRNA	0.009950	0.386139	
chunk0058_352_1	chr14	28936290	28937014	+	0	NA	Intergenic	Intergenic	163948	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.001381	0.289655	
chunk0053_406_1	chr13	36735329	36735746	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	61625	NM_203451	400120	Hs.422375	NM_203451	ENSG00000180440	SERTM1	C13orf36	serine rich and transmembrane domain containing 1	protein-coding	0.007194	0.425837	
chunk0134_152_1	chr3	177722067	177722413	+	0	NA	intron (NR_047568, intron 3 of 3)	L1MEc|LINE|L1	-94625	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.000000	0.391931	
chunk0049_28_1	chr12	89645059	89645928	+	0	NA	intron (NM_001001323, intron 1 of 20)	L2a|LINE|L2	10574	NM_001001323	490	Hs.506276	NM_001682	ENSG00000070961	ATP2B1	PMCA1|PMCA1kb	ATPase plasma membrane Ca2+ transporting 1	protein-coding	0.002301	0.371264	
chunk0126_89_1	chr3	74756131	74756422	+	0	NA	Intergenic	Intergenic	-235136	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.003436	0.301370	
chunk0053_163_1	chr13	30562935	30563271	+	0	NA	intron (NM_001313893, intron 1 of 4)	intron (NM_001313893, intron 1 of 4)	54494	NM_001313893	3146	Hs.434102	NM_002128	ENSG00000189403	HMGB1	HMG-1|HMG1|HMG3|SBP-1	high mobility group box 1	protein-coding	0.011905	0.415430	
chunk0049_87_1	chr12	90791050	90791451	+	0	NA	Intergenic	Intergenic	-126773	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.007481	0.308458	
chunk0194_128_1	chr8	84108676	84109247	+	0	NA	Intergenic	Tigger12|DNA|TcMar-Tigger	-74257	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.000000	0.321678	
chunk0115_218_1	chr21	27000417	27000635	+	0	NA	Intergenic	L1PA15|LINE|L1	-33406	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.009174	0.360731	
chunk0172_243_1	chr6	137174878	137175097	+	0	NA	Intergenic	L2a|LINE|L2	-1339	NM_052962	116379	Hs.126891	NM_052962	ENSG00000164485	IL22RA2	CRF2-10|CRF2-S1|CRF2X|IL-22BP|IL-22R-alpha-2|IL-22RA2|ZCYTOR16	interleukin 22 receptor subunit alpha 2	protein-coding	0.000000	0.436364	
chunk0131_3_1	chr3	141644802	141645199	+	0	NA	Intergenic	Intergenic	-93209	NM_014245	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.012594	0.484925	
chunk0167_398_1	chr6	74976832	74977436	+	0	NA	Intergenic	Intergenic	228773	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.004967	0.370248	
chunk0015_302_1	chr1	188940016	188940215	+	0	NA	Intergenic	Intergenic	1496487	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.300000	
chunk0100_196_1	chr2	111139657	111139998	+	0	NA	intron (NM_138625, intron 3 of 4)	intron (NM_138625, intron 3 of 4)	18913	NM_001204106	10018	Hs.469658	NM_006538	ENSG00000153094	BCL2L11	BAM|BIM|BOD	BCL2 like 11	protein-coding	0.023460	0.494152	
chunk0150_435_1	chr5	40431698	40432122	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-248020	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.002358	0.388235	
chunk0070_213_1	chr15	72474972	72475323	+	0	NA	intron (NM_005744, intron 1 of 13)	CpG	821	NM_005744	25820	Hs.268787	NM_005744	ENSG00000166233	ARIH1	ARI|HARI|HHARI|UBCH7BP	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding	0.082621	0.673295	
chunk0184_362_1	chr7	121023856	121024150	+	0	NA	intron (NM_001105533, intron 2 of 17)	intron (NM_001105533, intron 2 of 17)	34612	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.017007	0.355932	26(AGGCACTGTGTGTTTT,-,0.00)
chunk0135_95_1	chr3	186453568	186454042	+	0	NA	Intergenic	MSTC|LTR|ERVL-MaLR	39856	NR_033844	253573	Hs.97386	NR_033844	ENSG00000224406	LINC02052	-	long intergenic non-protein coding RNA 2052	ncRNA	0.008439	0.452632	
chunk0074_208_1	chr16	25206852	25207132	+	0	NA	Intergenic	AluJb|SINE|Alu	-9972	NM_001169	343	Hs.176658	NM_001169	ENSG00000103375	AQP8	AQP-8	aquaporin 8	protein-coding	0.010714	0.544484	
chunk0209_91_1	chrX	39266096	39266521	+	0	NA	Intergenic	MIR|SINE|MIR	61054	NR_038968	286442	Hs.638478	NR_038968	ENSG00000235304	LINC01281	-	long intergenic non-protein coding RNA 1281	ncRNA	0.002353	0.417840	
chunk0183_233_1	chr7	106950541	106950830	+	0	NA	Intergenic	L2a|LINE|L2	85206	NM_002649	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.017301	0.393103	
chunk0174_312_1	chr6	162854087	162854585	+	0	NA	intron (NM_152410, intron 3 of 6)	intron (NM_152410, intron 3 of 6)	126366	NM_001080379	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.002008	0.310621	
chunk0150_133_1	chr5	33337621	33338018	+	0	NA	Intergenic	Intergenic	-102877	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.007557	0.417085	
chunk0074_329_1	chr16	31094106	31094312	+	0	NA	intron (NM_024006, intron 1 of 2)	CpG	790	NM_001311311	79001	Hs.324844	NM_024006	ENSG00000167397	VKORC1	EDTP308|MST134|MST576|VKCFD2|VKOR	vitamin K epoxide reductase complex subunit 1	protein-coding	0.067961	0.613527	82(GGGCCACCTTGTTCCT,+,0.00)
chunk0103_410_1	chr2	169415256	169415481	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-52756	NM_004525	4036	Hs.657729	NM_004525	ENSG00000081479	LRP2	DBS|GP330|LRP-2	LDL receptor related protein 2	protein-coding	0.013333	0.522124	
chunk0021_82_1	chr10	1715900	1716099	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	21477	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.045226	0.605000	
chunk0057_385_1	chr13	109411327	109411884	+	0	NA	Intergenic	Intergenic	10909	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.008977	0.394265	321(TGGTACAAGTTGTTCT,-,0.00),322(GGTACAAGTTGTTCTT,+,0.00)
chunk0025_429_1	chr10	59957896	59958283	+	0	NA	TTS (NR_024340)	TTS (NR_024340)	2824	NR_024340	283025	Hs.522955	NM_001017982	ENSG00000235931	LINC01553	C10orf40	long intergenic non-protein coding RNA 1553	ncRNA	0.000000	0.332474	
chunk0149_203_1	chr5	21655028	21655892	+	0	NA	Intergenic	Intergenic	195980	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.008102	0.286705	
chunk0191_369_1	chr8	56958499	56958826	+	0	NA	3' UTR (NM_017813, exon 5 of 5)	3' UTR (NM_017813, exon 5 of 5)	35209	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.003058	0.399390	
chunk0024_391_1	chr10	44883998	44884359	+	0	NA	intron (NR_033842, intron 2 of 7)	L1MD2|LINE|L1	-27138	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.011080	0.475138	
chunk0095_443_1	chr2	25373467	25373717	+	0	NA	Intergenic	Intergenic	-31002	NM_175629	1788	Hs.515840	NM_022552	ENSG00000119772	DNMT3A	DNMT3A2|M.HsaIIIA|TBRS	DNA methyltransferase 3 alpha	protein-coding	0.036000	0.633466	57(CAGCACAGGCTGCTCT,-,0.00),58(AGCACAGGCTGCTCTC,+,0.00),158(GAGGACTCTCTGTGCA,-,0.00),159(AGGACTCTCTGTGCAC,+,0.00)
chunk0079_45_1	chr17	10545838	10546162	+	0	NA	intron (NM_001100112, intron 4 of 39)	intron (NM_001100112, intron 4 of 39)	3623	NM_001100112	4620	Hs.667534	NM_017534	ENSG00000125414	MYH2	IBM3|MYH2A|MYHSA2|MYHas8|MYPOP|MyHC-2A|MyHC-IIa	myosin heavy chain 2	protein-coding	0.000000	0.341538	
chunk0054_211_1	chr13	45168341	45168540	+	0	NA	intron (NM_004128, intron 4 of 7)	LTR16C|LTR|ERVL	32600	NM_198404	386618	Hs.23406	NM_198404	ENSG00000180332	KCTD4	bA321C24.3	potassium channel tetramerization domain containing 4	protein-coding	0.005025	0.465000	
chunk0022_109_1	chr10	10114844	10115130	+	0	NA	Intergenic	L1PA16|LINE|L1	56265	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.003497	0.317073	
chunk0121_187_1	chr3	20097071	20097344	+	0	NA	intron (NM_003884, intron 3 of 17)	intron (NM_003884, intron 3 of 17)	-40358	NR_036086	100422901		NR_036086	ENSG00000266745	MIR3135A	MIR3135|hsa-mir-3135a	microRNA 3135a	ncRNA	0.003663	0.441606	
chunk0161_172_1	chr5	169442383	169442906	+	0	NA	Intergenic	Intergenic	-140990	NM_017785	54908	Hs.368710	NM_017785	ENSG00000040275	SPDL1	CCDC99	spindle apparatus coiled-coil protein 1	protein-coding	0.003824	0.421756	
chunk0043_145_1	chr12	16266077	16266427	+	0	NA	intron (NM_001170798, intron 2 of 8)	intron (NM_001170798, intron 2 of 8)	11433	NM_001170798	729025	Hs.692712	NM_001170798	ENSG00000188991	SLC15A5	-	solute carrier family 15 member 5	protein-coding	0.002857	0.396011	253(GGGAACACCGTGTGAC,-,0.00)
chunk0008_435_1	chr1	99457642	99457908	+	0	NA	Intergenic	Intergenic	30029	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.003759	0.329588	
chunk0058_196_1	chr14	24403341	24403789	+	0	NA	intron (NM_025081, intron 2 of 8)	intron (NM_025081, intron 2 of 8)	4779	NM_025081	57523	Hs.288348	NM_025081	ENSG00000205978	NYNRIN	CGIN1|KIAA1305	NYN domain and retroviral integrase containing	protein-coding	0.013393	0.440980	262(CTGAACTAGCTGTCCT,-,0.00),263(TGAACTAGCTGTCCTG,+,0.00)
chunk0037_317_1	chr11	76836347	76837111	+	0	NA	Intergenic	L2|LINE|L2	-24144	NM_001300954	55331	Hs.23862	NM_018367	ENSG00000078124	ACER3	APHC|PHCA|PLDECO	alkaline ceramidase 3	protein-coding	0.007853	0.505882	
chunk0134_396_1	chr3	182968909	182969152	+	0	NA	intron (NM_001308101, intron 1 of 6)	intron (NM_001308101, intron 1 of 6)	11571	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.004115	0.409836	58(AGAAACAGGGTGTACC,-,0.00),59(GAAACAGGGTGTACCT,+,0.00)
chunk0178_300_1	chr7	37724765	37724974	+	0	NA	Intergenic	Intergenic	-15525	NM_181791	353345	Hs.563492	NM_181791	ENSG00000187037	GPR141	PGR13	G protein-coupled receptor 141	protein-coding	0.004785	0.533333	
chunk0018_366_1	chr1	221845803	221846516	+	0	NA	Intergenic	Intergenic	-5493	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.016830	0.523810	441(CAGGACATCCAGTTCC,-,0.00),442(AGGACATCCAGTTCCC,+,0.00)
chunk0027_259_1	chr10	77242997	77243468	+	0	NA	intron (NM_001014797, intron 3 of 28)	intron (NM_001014797, intron 3 of 28)	102401	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.004246	0.485169	
chunk0119_439_1	chr22	50131258	50132025	+	0	NA	intron (NM_001164105, intron 13 of 25)	L1M5|LINE|L1	-15414	NM_001164106	54456	Hs.62880	NM_018995	ENSG00000073146	MOV10L1	CHAMP|DJ402G11.8	Mov10 like RISC complex RNA helicase 1	protein-coding	0.006519	0.380208	
chunk0032_43_1	chr11	1429159	1429435	+	0	NA	intron (NM_001256630, intron 1 of 19)	(GT)n|Simple_repeat|Simple_repeat	18145	NM_001256630	9024	Hs.170819	NM_003957	ENSG00000174672	BRSK2	C11orf7|PEN11B|SAD1|SADA|STK29	BR serine/threonine kinase 2	protein-coding	0.043478	0.617329	
chunk0006_270_1	chr1	70330959	70331351	+	0	NA	intron (NM_030816, intron 2 of 12)	intron (NM_030816, intron 2 of 12)	23579	NM_030816	81573	Hs.744989	NM_030816	ENSG00000118454	ANKRD13C	dJ677H15.3	ankyrin repeat domain 13C	protein-coding	0.015306	0.371501	
chunk0072_275_1	chr15	97652041	97652498	+	0	NA	Intergenic	Intergenic	-91571	NR_110756	101927310	Hs.560324	NR_110756	ENSG00000259582	LOC101927310	-	uncharacterized LOC101927310	ncRNA	0.008753	0.443231	
chunk0068_328_1	chr15	57562438	57562637	+	0	NA	Intergenic	Intergenic	-29367	NM_001018091	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.030151	0.550000	
chunk0130_392_1	chr3	140165209	140165651	+	0	NA	intron (NM_022131, intron 1 of 16)	intron (NM_022131, intron 1 of 16)	230245	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.015837	0.492099	
chunk0175_82_1	chr7	2402896	2403200	+	0	NA	promoter-TSS (NM_001243795)	promoter-TSS (NM_001243795)	-512	NM_001243795	55501	Hs.288853	NM_018641	ENSG00000136213	CHST12	C4S-2|C4ST-2|C4ST2	carbohydrate sulfotransferase 12	protein-coding	0.036184	0.462295	
chunk0062_316_1	chr14	73224176	73224487	+	0	NA	TTS (NM_000021)	TTS (NM_000021)	-13166	NM_173462	89932	Hs.509909	NM_173462	ENSG00000100767	PAPLN	PPN	papilin, proteoglycan like sulfated glycoprotein	protein-coding	0.006431	0.400641	
chunk0171_429_1	chr6	131629736	131630132	+	0	NA	Intergenic	HAL1|LINE|L1	-1695	NM_001270522	9439	Hs.29679	NM_004830	ENSG00000112282	MED23	ARC130|CRSP130|CRSP133|CRSP3|DRIP130|MRT18|SUR-2|SUR2	mediator complex subunit 23	protein-coding	0.007576	0.430730	
chunk0148_197_1	chr5	8335734	8336036	+	0	NA	intron (NR_039984, intron 4 of 5)	intron (NR_039984, intron 4 of 5)	121679	NR_039984	729506	Hs.566412	NR_039984	ENSG00000245729	LINC02226	-	long intergenic non-protein coding RNA 2226	ncRNA	0.000000	0.349835	
chunk0068_454_1	chr15	59879507	59879894	+	0	NA	Intergenic	Intergenic	-124522	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.005168	0.409794	
chunk0053_32_1	chr13	27088373	27088876	+	0	NA	intron (NM_182488, intron 6 of 8)	MER68|LTR|ERVL	-36909	NR_046547	100874070	Hs.524923	NR_046547		USP12-AS1	-	USP12 antisense RNA 1	ncRNA	0.013917	0.448413	463(GAGCACTGTGAGTCCT,-,0.00),464(AGCACTGTGAGTCCTT,+,0.00)
chunk0107_148_1	chr2	215098255	215098470	+	0	NA	intron (NR_103740, intron 2 of 54)	intron (NR_103740, intron 2 of 54)	40066	NR_103740	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.000000	0.393519	156(TGAACATGGTGCCCTT,+,0.00)
chunk0213_23_1	chrY	26364808	26365217	+	0	NA	Intergenic	Intergenic	636522	NR_001524	114760	Hs.511777	NR_001524	ENSG00000231141	TTTY3	LINC00121|NCRNA00121|TTTY3A|TTY3	testis-specific transcript, Y-linked 3	ncRNA	0.002445	0.436585	207(CAGATCACTCTGTGCC,-,0.00),208(AGATCACTCTGTGCCC,+,0.00)
chunk0061_442_1	chr14	65676578	65677156	+	0	NA	intron (NR_038167, intron 7 of 8)	intron (NR_038167, intron 7 of 8)	205765	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.008651	0.379965	
chunk0187_72_1	chr8	2148309	2148915	+	0	NA	Intergenic	L1MC4|LINE|L1	72023	NR_106983	102465695		NR_106983	ENSG00000273593	MIR7160	hsa-mir-7160	microRNA 7160	ncRNA	0.036304	0.515651	333(AGGAGCAGAGTGTTCC,-,0.00),334(GGAGCAGAGTGTTCCC,+,0.00)
chunk0005_432_1	chr1	63044409	63044650	+	0	NA	Intergenic	Intergenic	260423	NM_178221	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.008299	0.500000	
chunk0180_377_1	chr7	74187915	74188379	+	0	NA	intron (NM_031992, intron 2 of 5)	intron (NM_031992, intron 2 of 5)	-3051	NR_030321	693175		NR_030321	ENSG00000207741	MIR590	MIRN590|hsa-mir-590|mir-590	microRNA 590	ncRNA	0.012931	0.470968	
chunk0072_346_1	chr15	99572327	99572871	+	0	NA	intron (NM_001130927, intron 1 of 9)	L2a|LINE|L2	6671	NM_005587	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.001838	0.354128	
chunk0136_286_1	chr3	194854207	194854694	+	0	NA	Intergenic	Intergenic	146029	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.014374	0.432377	
chunk0195_173_1	chr8	96136140	96136620	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	24412	NM_001001557	392255	Hs.492277	NM_001001557	ENSG00000156466	GDF6	BMP-13|BMP13|CDMP2|KFM|KFS|KFS1|KFSL|SGM1|SYNS4	growth differentiation factor 6	protein-coding	0.000000	0.388773	249(CAGGACAAACTGTACC,-,0.00),250(AGGACAAACTGTACCA,+,0.00)
chunk0092_88_1	chr19	21986266	21986564	+	0	NA	intron (NM_007153, intron 3 of 3)	L1M3a|LINE|L1	24528	NM_007153	7757	Hs.732975	NM_007153	ENSG00000160321	ZNF208	PMIDP|ZNF95	zinc finger protein 208	protein-coding	0.000000	0.234114	
chunk0049_247_1	chr12	93653666	93654043	+	0	NA	Intergenic	L2|LINE|L2	-23521	NM_003805	8738	Hs.38533	NM_003805	ENSG00000169372	CRADD	MRT34|RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.010610	0.436508	
chunk0099_64_1	chr2	84912886	84913395	+	0	NA	Intergenic	Intergenic	7501	NM_021103	9168	Hs.446574	NM_021103	ENSG00000034510	TMSB10	MIG12|TB10	thymosin beta 10	protein-coding	0.009823	0.384314	
chunk0075_187_1	chr16	52243257	52243576	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	158135	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.006270	0.456250	
chunk0023_430_1	chr10	31782720	31782939	+	0	NA	Intergenic	Intergenic	126097	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.009132	0.427273	
chunk0062_303_1	chr14	73058350	73058625	+	0	NA	promoter-TSS (NM_021239)	promoter-TSS (NM_021239)	-26	NM_021239	58517	Hs.531106	NM_021239	ENSG00000119707	RBM25	NET52|RED120|RNPC7|S164|Snu71|fSAP94	RNA binding motif protein 25	protein-coding	0.094545	0.590580	
chunk0128_165_1	chr3	107260077	107260647	+	0	NA	intron (NR_028302, intron 1 of 3)	L1MEg|LINE|L1	19670	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.001754	0.353765	
chunk0009_219_1	chr1	106498211	106498684	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-558198	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.002114	0.286920	
chunk0137_275_1	chr4	22645569	22646048	+	0	NA	Intergenic	Intergenic	-47106	NR_102356	57733	Hs.653107	NM_020973	ENSG00000249948	GBA3	CBG|CBGL1|GLUC|KLRP	glucosylceramidase beta 3 (gene/pseudogene)	protein-coding	0.002088	0.345833	
chunk0173_95_1	chr6	143075903	143076434	+	0	NA	intron (NM_001286587, intron 2 of 6)	L1MD1|LINE|L1	15326	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.001883	0.317669	
chunk0081_112_1	chr17	39987681	39987903	+	0	NA	intron (NM_002809, intron 3 of 11)	intron (NM_002809, intron 3 of 11)	7024	NM_002809	5709	Hs.12970	NM_002809	ENSG00000108344	PSMD3	P58|RPN3|S3|TSTA2	proteasome 26S subunit, non-ATPase 3	protein-coding	0.013514	0.515695	
chunk0016_197_1	chr1	198656331	198657072	+	0	NA	intron (NR_052021, intron 2 of 2)	intron (NR_052021, intron 2 of 2)	17733	NM_080921	5788	Hs.654514	NM_002838	ENSG00000081237	PTPRC	B220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200	protein tyrosine phosphatase receptor type C	protein-coding	0.006748	0.374663	
chunk0198_478_1	chr8	145026904	145027103	+	0	NA	Intergenic	HERVK-int|LTR|ERVK	-24104	NR_023392	286101	Hs.367856	NR_023392		ZNF252P	ZNF252	zinc finger protein 252, pseudogene	pseudo	0.025126	0.460000	
chunk0205_337_1	chr9	113233075	113233301	+	0	NA	intron (NM_001859, intron 1 of 4)	MIR|SINE|MIR	11660	NM_001859	1317	Hs.532315	NM_001859	ENSG00000136868	SLC31A1	COPT1|CTR1	solute carrier family 31 member 1	protein-coding	0.004425	0.370044	
chunk0201_221_1	chr9	37422449	37422648	+	0	NA	promoter-TSS (NM_012203)	promoter-TSS (NM_012203)	-162	NM_012203	9380	Hs.155742	NM_012203	ENSG00000137106	GRHPR	GLXR|GLYD|PH2	glyoxylate and hydroxypyruvate reductase	protein-coding	0.085427	0.685000	
chunk0012_154_1	chr1	158098245	158098530	+	0	NA	3' UTR (NM_001286349, exon 13 of 13)	3' UTR (NM_001286349, exon 13 of 13)	42253	NR_033946	646268	Hs.506902	NR_033946	ENSG00000231666	LINC01704	-	long intergenic non-protein coding RNA 1704	ncRNA	0.007018	0.548951	158(AGGGACAGCTTGTTCT,-,0.00),159(GGGACAGCTTGTTCTT,+,0.00)
chunk0100_284_1	chr2	114067819	114068206	+	0	NA	Intergenic	Intergenic	-88028	NR_034130	100499194	Hs.662336	NR_034130		LOC100499194	-	uncharacterized LOC100499194	ncRNA	0.012920	0.440722	
chunk0059_217_1	chr14	33942873	33943127	+	0	NA	intron (NM_001308103, intron 1 of 4)	intron (NM_001308103, intron 1 of 4)	7826	NM_001308103	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.015748	0.403922	
chunk0015_308_1	chr1	189129928	189131033	+	0	NA	Intergenic	L1MB8|LINE|L1	1347149	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003620	0.312839	
chunk0182_80_1	chr7	92538336	92538589	+	0	NA	promoter-TSS (NR_026902)	promoter-TSS (NR_026902)	-13	NR_026902	84060	Hs.21590	NM_032120	ENSG00000127993	RBM48	C7orf64|HSPC304	RNA binding motif protein 48	protein-coding	0.007905	0.480315	
chunk0115_212_1	chr21	26903162	26903402	+	0	NA	Intergenic	Intergenic	-50679	NR_039916	100616243		NR_039916	ENSG00000266133	MIR4759	-	microRNA 4759	ncRNA	0.008333	0.385892	
chunk0197_435_1	chr8	127509638	127510228	+	0	NA	Intergenic	L2c|LINE|L2	-27794	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.001695	0.406091	
chunk0194_122_1	chr8	83972809	83973203	+	0	NA	Intergenic	Intergenic	-210212	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.007614	0.308861	
chunk0083_62_1	chr17	63838331	63839070	+	0	NA	intron (NM_001098426, intron 1 of 12)	intron (NM_001098426, intron 1 of 12)	4291	NM_001098426	6603	Hs.250581	NM_003077	ENSG00000108604	SMARCD2	BAF60B|CRACD2|PRO2451|Rsc6p|SGD2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2	protein-coding	0.010825	0.577027	387(TTGCACACACTGTCCC,-,0.00),388(TGCACACACTGTCCCT,+,0.00)
chunk0039_123_1	chr11	98056881	98057355	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-963858	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004219	0.378947	
chunk0170_303_1	chr6	115797033	115797245	+	0	NA	Intergenic	Intergenic	-241592	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.004717	0.483568	
chunk0137_346_1	chr4	25299840	25300331	+	0	NA	Intergenic	Intergenic	-12689	NM_024936	29063	Hs.278945	NM_024936	ENSG00000168228	ZCCHC4	HSPC052|ZGRF4	zinc finger CCHC-type containing 4	protein-coding	0.012220	0.434959	
chunk0058_358_1	chr14	28952656	28953371	+	0	NA	Intergenic	Intergenic	180309	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.001399	0.386872	395(AAGTTCACAATGTTCT,-,0.00),396(AGTTCACAATGTTCTT,+,0.00)
chunk0094_119_1	chr2	4519566	4520087	+	0	NA	Intergenic	Intergenic	136396	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.007678	0.354406	
chunk0134_158_1	chr3	177810049	177810730	+	0	NA	Intergenic	Intergenic	-6476	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.007342	0.334311	210(CAGCACAAACAGTTCC,-,0.00),211(AGCACAAACAGTTCCA,+,0.00)
chunk0015_229_1	chr1	187753686	187754214	+	0	NA	Intergenic	Intergenic	310322	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003788	0.372401	250(AAAGACACAGTGTACT,-,0.00),251(AAGACACAGTGTACTA,+,0.00)
chunk0056_80_1	chr13	79589859	79590098	+	0	NA	Intergenic	Intergenic	23251	NR_125772	103724388	Hs.434862	NR_125772	ENSG00000227676	LINC01068	-	long intergenic non-protein coding RNA 1068	ncRNA	0.012552	0.433333	
chunk0039_285_1	chr11	102635845	102636257	+	0	NA	Intergenic	L1MC4a|LINE|L1	-10719	NM_004771	9313	Hs.591946	NM_004771	ENSG00000137674	MMP20	AI2A2|MMP-20	matrix metallopeptidase 20	protein-coding	0.004854	0.358354	
chunk0109_340_1	chr20	9484556	9484954	+	0	NA	Intergenic	MER87B|LTR|ERV1	-29603	NM_001199897	24141	Hs.22920	NM_012261	ENSG00000125869	LAMP5	BAD-LAMP|BADLAMP|C20orf103|LAMP-5|UNC-46	lysosomal associated membrane protein family member 5	protein-coding	0.002513	0.411028	
chunk0138_238_1	chr4	39446860	39447059	+	0	NA	exon (NM_175737, exon 4 of 5)	exon (NM_175737, exon 4 of 5)	11628	NM_001024921	6133	Hs.412370	NM_000661	ENSG00000163682	RPL9	L9|NPC-A-16	ribosomal protein L9	protein-coding	0.115578	0.700000	
chunk0103_160_1	chr2	162559888	162560338	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-208823	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.013333	0.363636	245(CAGAACATCATGTTCC,-,0.00),246(AGAACATCATGTTCCC,+,0.00)
chunk0070_265_1	chr15	73984326	73984543	+	0	NA	intron (NM_001256675, intron 5 of 5)	intron (NM_001256675, intron 5 of 5)	7914	NM_001256673	9399	Hs.194816	NM_004809	ENSG00000067221	STOML1	SLP-1|STORP|hUNC-24	stomatin like 1	protein-coding	0.013825	0.532110	
chunk0182_245_1	chr7	97063741	97064496	+	0	NA	Intergenic	Intergenic	-39287	NM_005221	1749	Hs.99348	NM_005221	ENSG00000105880	DLX5	SHFM1D	distal-less homeobox 5	protein-coding	0.003974	0.325397	425(GGGTACATACAGTGCT,-,0.00),426(GGTACATACAGTGCTA,+,0.00)
chunk0111_291_1	chr20	31712418	31713093	+	0	NA	intron (NM_001191, intron 2 of 2)	intron (NM_001191, intron 2 of 2)	-8752	NR_131907	103021294		NR_131907	ENSG00000281376	ABALON	INXS	apoptotic BCL2L1-antisense long non-coding RNA	ncRNA	0.008889	0.483728	302(AGGGACACTATGTTCC,-,0.00),303(GGGACACTATGTTCCT,+,0.00)
chunk0186_5_1	chr7	135499052	135499449	+	0	NA	intron (NM_001008225, intron 1 of 10)	intron (NM_001008225, intron 1 of 10)	10877	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.002519	0.412060	
chunk0044_241_1	chr12	31721306	31721923	+	0	NA	intron (NM_001278412, intron 1 of 8)	intron (NM_001278412, intron 1 of 8)	7560	NM_001113402	196394	Hs.585084	NM_001113402	ENSG00000151743	AMN1	-	antagonist of mitotic exit network 1 homolog	protein-coding	0.003241	0.467638	
chunk0098_148_1	chr2	69683574	69683835	+	0	NA	Intergenic	Intergenic	-39859	NM_014911	22848	Hs.468878	NM_014911	ENSG00000115977	AAK1	-	AP2 associated kinase 1	protein-coding	0.000000	0.435115	
chunk0003_451_1	chr1	41474364	41474698	+	0	NA	Intergenic	MIR|SINE|MIR	10152	NM_001956	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.014970	0.522388	150(TAGTACTCAGTGTACT,-,0.00),151(AGTACTCAGTGTACTG,+,0.00)
chunk0053_115_1	chr13	29454947	29455394	+	0	NA	intron (NM_015233, intron 2 of 8)	L1MEf|LINE|L1	26530	NM_015233	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.008949	0.540179	
chunk0165_186_1	chr6	34416127	34416378	+	0	NA	intron (NM_001202470, intron 5 of 8)	intron (NM_001202470, intron 5 of 8)	9789	NM_001203245	6204	Hs.406620	NM_001014	ENSG00000124614	RPS10	DBA9|S10	ribosomal protein S10	protein-coding	0.003984	0.472222	
chunk0073_70_1	chr16	3695856	3696570	+	0	NA	intron (NM_016292, intron 1 of 17)	L1MC4a|LINE|L1	21384	NM_016292	10131	Hs.30345	NM_016292	ENSG00000126602	TRAP1	HSP 75|HSP75|HSP90L|TRAP-1	TNF receptor associated protein 1	protein-coding	0.023810	0.511888	
chunk0013_230_1	chr1	169568335	169568954	+	0	NA	intron (NM_000130, intron 3 of 24)	intron (NM_000130, intron 3 of 24)	17887	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.001616	0.319355	268(GAGCACAAGAAGTCCT,-,0.00),269(AGCACAAGAAGTCCTT,+,0.00)
chunk0032_60_1	chr11	2097270	2097526	+	0	NA	Intergenic	Intergenic	36811	NR_030158	619552		NR_030158	ENSG00000207805	MIR483	MIRN483|hsa-mir-483|mir-483	microRNA 483	ncRNA	0.050781	0.575875	68(AAGGACAAGCTGGTCT,-,0.00),69(AGGACAAGCTGGTCTT,+,0.00)
chunk0125_162_1	chr3	66492556	66493087	+	0	NA	intron (NM_015541, intron 1 of 18)	intron (NM_015541, intron 1 of 18)	7600	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.015066	0.415414	
chunk0162_347_1	chr6	7042289	7042934	+	0	NA	Intergenic	Intergenic	-64986	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.026357	0.486068	
chunk0190_126_1	chr8	30604441	30605153	+	0	NA	intron (NM_002095, intron 6 of 7)	intron (NM_002095, intron 6 of 7)	-33803	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.007022	0.340813	582(AAACACACAGTGTACT,-,0.00),583(AACACACAGTGTACTC,+,0.00)
chunk0102_221_1	chr2	148642896	148643161	+	0	NA	Intergenic	Intergenic	-1963	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.003774	0.454887	83(AAGAACTTCTTGTTCT,-,0.00),84(AGAACTTCTTGTTCTT,+,0.00)
chunk0056_245_1	chr13	89276101	89276616	+	0	NA	intron (NR_047025, intron 3 of 3)	intron (NR_047025, intron 3 of 3)	-39468	NR_131229	105616982	Hs.564527	NR_131229	ENSG00000232225	LINC01047	-	long intergenic non-protein coding RNA 1047	ncRNA	0.005825	0.325581	397(CAGGACACACTCTTCT,-,0.00),398(AGGACACACTCTTCTC,+,0.00)
chunk0133_82_1	chr3	167312242	167312698	+	0	NA	intron (NM_001199202, intron 16 of 20)	L1MC1|LINE|L1	67813	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.002193	0.365427	307(AGGAACTCTCTGTACT,-,0.00),308(GGAACTCTCTGTACTT,+,0.00)
chunk0199_298_1	chr9	6923875	6924556	+	0	NA	intron (NR_130707, intron 8 of 14)	intron (NR_130707, intron 8 of 14)	166574	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.007342	0.436950	
chunk0031_124_1	chr10	124763800	124764248	+	0	NA	intron (NM_212554, intron 5 of 6)	intron (NM_212554, intron 5 of 6)	-19663	NM_014661	9679	Hs.129195	NM_014661	ENSG00000189319	FAM53B	KIAA0140|bA12J10.2|smp	family with sequence similarity 53 member B	protein-coding	0.002232	0.318486	
chunk0145_23_1	chr4	143463610	143464097	+	0	NA	intron (NM_002039, intron 8 of 9)	intron (NM_002039, intron 8 of 9)	-49610	NM_003601	8467	Hs.558422	NM_003601	ENSG00000153147	SMARCA5	ISWI|SNF2H|WCRF135|hISWI|hSNF2H	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding	0.000000	0.319672	228(AAAAACATTCAGTTCT,-,0.00)
chunk0056_376_1	chr13	93143901	93144352	+	0	NA	Intergenic	Intergenic	-82699	NM_005708	10082	Hs.444329	NM_005708	ENSG00000183098	GPC6	OMIMD1	glypican 6	protein-coding	0.004435	0.400442	
chunk0206_88_1	chr9	120571754	120572219	+	0	NA	exon (NM_001272039, exon 2 of 35)	exon (NM_001272039, exon 2 of 35)	8184	NR_073557	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.006452	0.472103	
chunk0056_367_1	chr13	92677676	92677909	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	42163	NR_049776	100873969	Hs.577863	NR_046520	ENSG00000235984	GPC5-AS1	-	GPC5 antisense RNA 1	ncRNA	0.012876	0.508547	37(GAGGACAGTATGTGTT,-,0.00),38(AGGACAGTATGTGTTG,+,0.00),164(AGGAACTGGGTGTCCC,-,0.00),165(GGAACTGGGTGTCCCA,+,0.00)
chunk0017_459_1	chr1	214496076	214496462	+	0	NA	intron (NM_005401, intron 1 of 18)	intron (NM_005401, intron 1 of 18)	55412	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.010363	0.436693	
chunk0090_26_1	chr19	1110733	1110960	+	0	NA	exon (NM_001100122, exon 23 of 29).2	exon (NM_001100122, exon 23 of 29).2	6196	NM_001039848	2879	Hs.433951	NM_002085	ENSG00000167468	GPX4	GPx-4|GSHPx-4|MCSP|PHGPx|SMDS|snGPx|snPHGPx	glutathione peroxidase 4	protein-coding	0.035242	0.596491	86(TGGAACAGGGCGTTCT,-,0.00),87(GGAACAGGGCGTTCTG,+,0.00)
chunk0017_204_1	chr1	207794572	207795177	+	0	NA	3' UTR (NM_002389, exon 14 of 14)	3' UTR (NM_002389, exon 14 of 14)	7065	NR_029832	407026		NR_029832	ENSG00000284214	MIR29C	MIRN29C|miRNA29C|mir-29c	microRNA 29c	ncRNA	0.004959	0.372937	
chunk0162_265_1	chr6	5370491	5370748	+	0	NA	intron (NM_006567, intron 2 of 6)	intron (NM_006567, intron 2 of 6)	87456	NR_125848	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.003891	0.430233	128(AAGGACTGTGTGCTCT,-,0.00),129(AGGACTGTGTGCTCTG,+,0.00)
chunk0149_216_1	chr5	22059816	22060391	+	0	NA	intron (NM_004061, intron 5 of 14)	intron (NM_004061, intron 5 of 14)	-82249	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.001739	0.380208	
chunk0006_369_1	chr1	73203330	73203883	+	0	NA	Intergenic	L1M4c|LINE|L1	-102564	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.001808	0.324910	
chunk0070_347_1	chr15	75961313	75961764	+	0	NA	intron (NM_138573, intron 4 of 5)	intron (NM_138573, intron 4 of 5)	-28408	NR_003136									0.002217	0.309735	
chunk0182_367_1	chr7	99949637	99950335	+	0	NA	Intergenic	L1PA14|LINE|L1	-20366	NM_181538	349149	Hs.647524	NM_181538	ENSG00000176402	GJC3	CX29|CX30.2|CX31.3|GJE1	gap junction protein gamma 3	protein-coding	0.007163	0.373391	368(AGGAACAGACAGTTCC,-,0.00),369(GGAACAGACAGTTCCC,+,0.00)
chunk0033_187_1	chr11	16029836	16030454	+	0	NA	intron (NM_001145819, intron 12 of 15)	intron (NM_001145819, intron 12 of 15)	-60524	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.004854	0.292407	281(TTGTACATTGTGTTCT,-,0.00),282(TGTACATTGTGTTCTC,+,0.00)
chunk0154_250_1	chr5	81359932	81360266	+	0	NA	intron (NM_130767, intron 4 of 14)	intron (NM_130767, intron 4 of 14)	34070	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.005988	0.286567	
chunk0182_376_1	chr7	100081546	100081933	+	0	NA	promoter-TSS (NM_001278292)	promoter-TSS (NM_001278292)	25	NM_017715	7551	Hs.435302	NM_017715	ENSG00000166526	ZNF3	A8-51|HF.12|KOX25|PP838|Zfp113	zinc finger protein 3	protein-coding	0.087855	0.664948	
chunk0089_15_1	chr18	57659362	57659633	+	0	NA	intron (NM_005603, intron 22 of 27)	intron (NM_005603, intron 22 of 27)	29195	NM_001242804	100505549	Hs.660645	NM_001242804		LOC100505549	-	uncharacterized LOC100505549	protein-coding	0.018450	0.386029	44(AGGAACAAAATGTTTC,-,0.00)
chunk0042_133_1	chr12	3748188	3748796	+	0	NA	intron (NM_032680, intron 1 of 10)	intron (NM_032680, intron 1 of 10)	4708	NM_032680	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.006579	0.532020	
chunk0034_330_1	chr11	35390968	35391478	+	0	NA	intron (NM_001252652, intron 1 of 11)	MER58A|DNA|hAT-Charlie	28335	NM_004171	6506	Hs.502338	NM_004171	ENSG00000110436	SLC1A2	EAAT2|EIEE41|GLT-1|HBGT	solute carrier family 1 member 2	protein-coding	0.007843	0.420744	
chunk0183_305_1	chr7	107867924	107868744	+	0	NA	Intergenic	Intergenic	-22773	NM_001289752	1738	Hs.131711	NM_000108	ENSG00000091140	DLD	DLDD|DLDH|E3|GCSL|LAD|PHE3	dihydrolipoamide dehydrogenase	protein-coding	0.003659	0.343484	
chunk0133_156_1	chr3	169699372	169700079	+	0	NA	Intergenic	Intergenic	-35950	NM_001205194	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.014144	0.487288	358(GGGAACATTTTGATCT,-,0.00),359(GGAACATTTTGATCTT,+,0.00),393(GGCACTCCATGTCCAC,+,0.00)
chunk0111_355_1	chr20	33538623	33539407	+	0	NA	intron (NM_001032999, intron 1 of 10)	intron (NM_001032999, intron 1 of 10)	-23350	NM_005093	9139	Hs.153934	NM_005093	ENSG00000078699	CBFA2T2	EHT|MTGR1|ZMYND3|p85	CBFA2/RUNX1 partner transcriptional co-repressor 2	protein-coding	0.003827	0.364331	
chunk0190_85_1	chr8	30081063	30081558	+	0	NA	intron (NM_016127, intron 1 of 5)	intron (NM_016127, intron 1 of 5)	1898	NM_016127	51669	Hs.521487	NM_016127	ENSG00000133872	SARAF	FOAP-7|HSPC035|TMEM66|XTP3	store-operated calcium entry associated regulatory factor	protein-coding	0.016162	0.336694	
chunk0054_402_1	chr13	50458252	50458527	+	0	NA	intron (NR_109974, intron 4 of 6)	Helitron1Nb_Mam|RC|Helitron	69060	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.000000	0.297101	
chunk0031_110_1	chr10	124425577	124425984	+	0	NA	Intergenic	Intergenic	-6804	NM_000274	4942	Hs.523332	NM_000274	ENSG00000065154	OAT	GACR|HOGA|OATASE|OKT	ornithine aminotransferase	protein-coding	0.002457	0.247549	153(AAGATCAGTGTGTTTT,-,0.00)
chunk0010_393_1	chr1	119462379	119462714	+	0	NA	Intergenic	Intergenic	-44657	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.017910	0.485119	
chunk0080_336_1	chr17	32627913	32628901	+	0	NA	intron (NM_015194, intron 20 of 21)	intron (NM_015194, intron 20 of 21)	141320	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.004049	0.348837	
chunk0136_78_1	chr4	2223258	2223731	+	0	NA	intron (NM_181808, intron 3 of 25)	MER1B|DNA|hAT-Charlie	18670	NM_001303143	79441	Hs.665869	NM_024511	ENSG00000214367	HAUS3	C4orf15|IT1|dgt3	HAUS augmin like complex subunit 3	protein-coding	0.014799	0.485232	402(CTGTACAGCATGTACT,-,0.00),403(TGTACAGCATGTACTA,+,0.00)
chunk0067_14_1	chr15	40050209	40050527	+	0	NA	intron (NR_040060, intron 2 of 2)	intron (NR_040060, intron 2 of 2)	11057	NR_040059	100131089	Hs.386000	NR_040059	ENSG00000248508	SRP14-AS1	-	SRP14 antisense RNA1 (head to head)	ncRNA	0.003145	0.520376	102(GGGAACACACTGTTCT,-,0.00),103(GGAACACACTGTTCTC,+,0.00)
chunk0023_151_1	chr10	24229740	24230459	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	21308	NM_019590	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.008345	0.355556	
chunk0123_460_1	chr3	51359555	51359785	+	0	NA	intron (NM_004947, intron 46 of 52)	intron (NM_004947, intron 46 of 52)	-25567	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.013043	0.502165	
chunk0140_407_1	chr4	75660476	75661131	+	0	NA	intron (NM_203505, intron 2 of 11)	intron (NM_203505, intron 2 of 11)	12356	NM_012297	9908	Hs.303676	NM_012297	ENSG00000138757	G3BP2	-	G3BP stress granule assembly factor 2	protein-coding	0.003053	0.315549	294(TGGCCAGTGTGTTCTG,+,0.00)
chunk0140_173_1	chr4	69735469	69736094	+	0	NA	intron (NM_014465, intron 4 of 7)	L1MDa|LINE|L1	24931	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.008000	0.432907	191(TGGTACAGTATGTCCA,-,0.00),192(GGTACAGTATGTCCAG,+,0.00),429(AGCACTCACAGTACCT,+,0.00)
chunk0097_115_1	chr2	46366987	46367214	+	0	NA	intron (NM_001430, intron 6 of 15)	intron (NM_001430, intron 6 of 15)	-62090	NR_103805	101805491	Hs.304781	NR_103805	ENSG00000187600	LINC02583	-	long intergenic non-protein coding RNA 2583	ncRNA	0.000000	0.320175	
chunk0009_381_1	chr1	109970588	109970961	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	-13991	NM_001242673	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.000000	0.425134	
chunk0068_89_1	chr15	52071090	52071879	+	0	NA	Intergenic	Intergenic	41291	NM_001306168	10017	Hs.283672	NM_020396	ENSG00000137875	BCL2L10	BCL-B|Boo|Diva|bcl2-L-10	BCL2 like 10	protein-coding	0.015209	0.441772	278(GAGCACACTGTGTTTA,-,0.00)
chunk0118_336_1	chr22	35588133	35588429	+	0	NA	Intergenic	MIRb|SINE|MIR	29056	NM_005368	4151	Hs.517586	NM_005368	ENSG00000198125	MB	PVALB|myoglobgin	myoglobin	protein-coding	0.013514	0.478114	
chunk0146_390_1	chr4	168679652	168680222	+	0	NA	intron (NM_016081, intron 3 of 20)	intron (NM_016081, intron 3 of 20)	48320	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.008772	0.401051	
chunk0132_46_1	chr3	154885372	154886037	+	0	NA	Intergenic	L1MC1|LINE|L1	-193943	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.006015	0.328829	
chunk0065_157_1	chr15	25518561	25519093	+	0	NA	Intergenic	L1MD1|LINE|L1	-79799	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.009398	0.397749	
chunk0125_201_1	chr3	67038981	67039422	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	40898	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.006803	0.441176	
chunk0048_388_1	chr12	87146400	87146881	+	0	NA	Intergenic	L1PB1|LINE|L1	-307736	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.000000	0.373444	
chunk0117_248_1	chr22	23247081	23247593	+	0	NA	intron (NM_021574, intron 1 of 21)	intron (NM_021574, intron 1 of 21)	-15430	NR_033408	26226	Hs.729589	NR_033408	ENSG00000230701	FBXW4P1	FBW3|FBXW3|SHFM3P1	F-box and WD repeat domain containing 4 pseudogene 1	pseudo	0.015625	0.567251	
chunk0134_279_1	chr3	179701305	179701558	+	0	NA	intron (NM_003940, intron 4 of 20)	intron (NM_003940, intron 4 of 20)	48286	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.003953	0.444882	120(ATCACAATCTGTTCCT,+,0.00)
chunk0081_99_1	chr17	39787021	39787531	+	0	NA	intron (NM_001284514, intron 6 of 8)	intron (NM_001284514, intron 6 of 8)	-9051	NM_001284516	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.000000	0.371820	
chunk0149_335_1	chr5	26875189	26875422	+	0	NA	Intergenic	Intergenic	163277	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.004292	0.269231	
chunk0077_11_1	chr16	74781337	74781773	+	0	NA	Intergenic	L1ME1|LINE|L1	-6724	NM_024306	79152	Hs.461329	NM_024306	ENSG00000103089	FA2H	FAAH|FAH1|FAXDC1|SCS7|SPG35	fatty acid 2-hydroxylase	protein-coding	0.000000	0.331808	197(AAGGTCATTTTGTTCT,-,0.00),198(AGGTCATTTTGTTCTT,+,0.00)
chunk0016_170_1	chr1	197902642	197903088	+	0	NA	exon (NM_001024594, exon 1 of 3)	exon (NM_001024594, exon 1 of 3)	313	NM_001024594	388722	Hs.61329	NM_001024594	ENSG00000203724	C1orf53	-	chromosome 1 open reading frame 53	protein-coding	0.132287	0.729306	
chunk0141_69_1	chr4	77921542	77922260	+	0	NA	intron (NM_020236, intron 7 of 8)	Charlie4z|DNA|hAT-Charlie	59250	NM_020236	65008	Hs.532019	NM_020236	ENSG00000169288	MRPL1	BM022|L1MT|MRP-L1	mitochondrial ribosomal protein L1	protein-coding	0.006964	0.328234	
chunk0191_297_1	chr8	54326328	54326529	+	0	NA	Intergenic	Intergenic	-4258	NR_004385	26766		NR_004385	ENSG00000199212	RNU105C	E1-5|E1-6	RNA, U105C small nucleolar	snoRNA	0.009950	0.470297	
chunk0188_393_1	chr8	18636745	18637728	+	0	NA	intron (NM_015310, intron 10 of 15)	L1MC4a|LINE|L1	171659	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.009156	0.356707	
chunk0014_64_1	chr1	175918385	175918822	+	0	NA	Intergenic	MER67C|LTR|ERV1	41260	NR_125964	101928751		NR_125964	ENSG00000224718	LINC01657	-	long intergenic non-protein coding RNA 1657	ncRNA	0.004577	0.410959	
chunk0029_370_1	chr10	107966666	107967096	+	0	NA	intron (NR_125760, intron 4 of 4)	intron (NR_125760, intron 4 of 4)	102412	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.000000	0.373550	167(AATAACACCCTGTGCC,-,0.00),168(ATAACACCCTGTGCCC,+,0.00)
chunk0035_206_1	chr11	44716878	44717344	+	0	NA	Intergenic	Intergenic	-47315	NM_130783	90139	Hs.385634	NM_130783	ENSG00000157570	TSPAN18	TSPAN	tetraspanin 18	protein-coding	0.012876	0.417559	252(ATGAACTCGCTGTTCC,-,0.00),253(TGAACTCGCTGTTCCC,+,0.00)
chunk0087_16_1	chr18	30968755	30969189	+	0	NA	Intergenic	Intergenic	73843	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.000000	0.280460	182(AAGGGCAGCCTGTTCC,-,0.00),183(AGGGCAGCCTGTTCCA,+,0.00)
chunk0014_455_1	chr1	183991774	183992097	+	0	NA	intron (NM_001303421, intron 1 of 11)	intron (NM_001303421, intron 1 of 11)	45835	NM_001303420	23127	Hs.387995	NM_015101	ENSG00000198756	COLGALT2	C1orf17|ColGalT 2|GLT25D2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0.006192	0.456790	133(AGGAACACCGTGTGCT,-,0.00),134(GGAACACCGTGTGCTC,+,0.00)
chunk0207_233_1	chr9	131914058	131914534	+	0	NA	intron (NM_004269, intron 4 of 7)	MIRb|SINE|MIR	165591	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.008403	0.454927	
chunk0151_302_1	chr5	53034845	53035044	+	0	NA	intron (NR_073106, intron 2 of 29)	intron (NR_073106, intron 2 of 29)	45618	NM_002203	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.000000	0.355000	
chunk0040_443_1	chr11	121564241	121564610	+	0	NA	intron (NM_003105, intron 21 of 47)	intron (NM_003105, intron 21 of 47)	112222	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.002710	0.405405	
chunk0091_339_1	chr19	14496161	14496653	+	0	NA	promoter-TSS (NM_005716)	promoter-TSS (NM_005716)	-258	NM_202468	10755	Hs.655012	NM_005716	ENSG00000123159	GIPC1	C19orf3|GIPC|GLUT1CBP|Hs.6454|IIP-1|NIP|RGS19IP1|SEMCAP|SYNECTIIN|SYNECTIN|TIP-2	GIPC PDZ domain containing family member 1	protein-coding	0.083333	0.683570	
chunk0058_410_1	chr13	112414896	112415181	+	0	NA	intron (NM_145248, intron 5 of 6)	L1M1|LINE|L1	38701	NM_145248	122258	Hs.97592	NM_145248	ENSG00000153498	SPACA7	C13orf28	sperm acrosome associated 7	protein-coding	0.003509	0.472028	
chunk0177_294_1	chr7	25824888	25825145	+	0	NA	Intergenic	Intergenic	124970	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.000000	0.449612	78(CAGAACAGGATGTTCC,-,0.00),79(AGAACAGGATGTTCCA,+,0.00)
chunk0212_355_1	chrX	149288878	149289514	+	0	NA	Intergenic	Intergenic	216158	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.004717	0.496075	
chunk0167_47_1	chr6	55511072	55511628	+	0	NA	TTS (NR_109867)	TTS (NR_109867)	67864	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.008993	0.317774	
chunk0142_413_1	chr4	103131177	103131884	+	0	NA	intron (NM_001813, intron 42 of 48)	L1MC1|LINE|L1	-31663	NM_020139	56898	Hs.124696	NM_020139	ENSG00000164039	BDH2	DHRS6|EFA6R|PRO20933|SDR15C1|UCPA-OR|UNQ6308	3-hydroxybutyrate dehydrogenase 2	protein-coding	0.002829	0.329096	
chunk0185_456_1	chr7	135333301	135333616	+	0	NA	Intergenic	Intergenic	101479	NM_182489	346673	Hs.592279	NM_182489	ENSG00000146857	STRA8	-	stimulated by retinoic acid 8	protein-coding	0.006349	0.518987	276(AAGCACAGGCTGTGCT,-,0.00),277(AGCACAGGCTGTGCTC,+,0.00)
chunk0108_465_1	chr2	238602144	238602632	+	0	NA	Intergenic	Intergenic	-46889	NR_037809	151171	Hs.652076	NR_037809	ENSG00000225493	LINC01107	-	long intergenic non-protein coding RNA 1107	ncRNA	0.012295	0.404908	201(AAGACAGTGAGTGCTT,+,0.00)
chunk0195_5_1	chr8	92833102	92833379	+	0	NA	Intergenic	Intergenic	-47180	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.010830	0.377698	
chunk0071_201_1	chr15	83960030	83960655	+	0	NA	intron (NM_207517, intron 19 of 29)	intron (NM_207517, intron 19 of 29)	-119845	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.004800	0.386581	238(AGGAACACTGTGTCTT,-,0.00),239(GGAACACTGTGTCTTC,+,0.00)
chunk0096_191_1	chr2	30119674	30120321	+	0	NA	Intergenic	Intergenic	-26887	NM_001127400	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.006182	0.336420	
chunk0103_196_1	chr2	163667441	163668002	+	0	NA	intron (NM_018086, intron 2 of 2)	L2c|LINE|L2	68282	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.007130	0.419929	
chunk0153_435_1	chr5	76235372	76235770	+	0	NA	intron (NM_014979, intron 4 of 12)	intron (NM_014979, intron 4 of 12)	152157	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.005025	0.325815	
chunk0168_421_1	chr6	95528861	95529088	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	48477	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.403509	
chunk0116_440_1	chr21	43343000	43343629	+	0	NA	Intergenic	Intergenic	-11275	NR_103713	100126693	Hs.473952	NR_103713		LINC00322	C21orf136|NCRNA00322	long intergenic non-protein coding RNA 322	ncRNA	0.033386	0.619048	
chunk0144_280_1	chr4	137901012	137901576	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-187720	NR_038380	641364	Hs.570846	NR_038380	ENSG00000250033	SLC7A11-AS1	-	SLC7A11 antisense RNA 1	ncRNA	0.001773	0.357522	
chunk0083_263_1	chr17	68378404	68379170	+	0	NA	intron (NM_014960, intron 8 of 11)	intron (NM_014960, intron 8 of 11)	-34836	NM_001278433	5573	Hs.280342	NM_002734	ENSG00000108946	PRKAR1A	ACRDYS1|ADOHR|CAR|CNC|CNC1|PKR1|PPNAD1|PRKAR1|TSE1	protein kinase cAMP-dependent type I regulatory subunit alpha	protein-coding	0.020888	0.569752	
chunk0035_38_1	chr11	40894534	40895133	+	0	NA	intron (NM_020929, intron 1 of 4)	intron (NM_020929, intron 1 of 4)	564803	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005008	0.346667	
chunk0069_48_1	chr15	60722073	60722872	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	40903	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.005006	0.423750	522(AAGGACATCATGTCCA,-,0.00),523(AGGACATCATGTCCAC,+,0.00)
chunk0113_79_1	chr20	50661500	50661699	+	0	NA	intron (NM_001290268, intron 1 of 21)	intron (NM_001290268, intron 1 of 21)	16128	NR_111906	100506175	Hs.658270	NR_111906	ENSG00000234693	LOC100506175	-	uncharacterized LOC100506175	ncRNA	0.015075	0.510000	126(AGGAACACGCTGTCCC,-,0.00),127(GGAACACGCTGTCCCC,+,0.00)
chunk0050_406_1	chr12	109564071	109564471	+	0	NA	intron (NR_038118, intron 4 of 9)	MER20|DNA|hAT-Charlie	9282	NR_038118	326625	Hs.12106	NM_052845	ENSG00000139428	MMAB	ATR|CFAP23|cblB|cob	metabolism of cobalamin associated B	protein-coding	0.025000	0.493766	
chunk0159_74_1	chr5	137403873	137404444	+	0	NA	intron (NM_004598, intron 2 of 10)	MER102b|DNA|hAT-Charlie	95171	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.014011	0.449301	
chunk0132_325_1	chr3	161082131	161082561	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	22549	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.006977	0.452436	224(AAGAACAGCATGTTCC,-,0.00),225(AGAACAGCATGTTCCA,+,0.00)
chunk0115_401_1	chr21	30576191	30576688	+	0	NA	Intergenic	Intergenic	13958	NM_001164434	100288287	Hs.580880	NM_001164434	ENSG00000206106	KRTAP22-2	KAP22.2	keratin associated protein 22-2	protein-coding	0.010060	0.365462	233(ATGAACACAATGTGCC,-,0.00),234(TGAACACAATGTGCCT,+,0.00)
chunk0036_257_1	chr11	64917140	64917368	+	0	NA	promoter-TSS (NM_015104)	promoter-TSS (NM_015104)	-4	NM_015104	23130	Hs.370671	NM_015104	ENSG00000110046	ATG2A	-	autophagy related 2A	protein-coding	0.127193	0.729258	
chunk0047_355_1	chr12	74999958	75000201	+	0	NA	Intergenic	L1MA9|LINE|L1	209669	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.000000	0.319672	
chunk0032_294_1	chr11	9566100	9566330	+	0	NA	Intergenic	Intergenic	-7466	NM_003390	7465	Hs.249441	NM_003390	ENSG00000166483	WEE1	WEE1A|WEE1hu	WEE1 G2 checkpoint kinase	protein-coding	0.017391	0.467532	
chunk0029_269_1	chr10	103201666	103202109	+	0	NA	Intergenic	Intergenic	-8581	NM_012229	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.006772	0.335586	
chunk0156_337_1	chr5	111781897	111782633	+	0	NA	intron (NM_001142474, intron 2 of 3)	intron (NM_001142474, intron 2 of 3)	-24047	NM_001142476	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.004076	0.324288	359(GAGTACAAAAAGTTCT,-,0.00),360(AGTACAAAAAGTTCTG,+,0.00)
chunk0175_156_1	chr7	3870843	3871268	+	0	NA	intron (NM_152744, intron 5 of 44)	L1MCa|LINE|L1	-258630	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.007059	0.333333	
chunk0190_23_1	chr8	29158535	29159167	+	0	NA	intron (NM_015254, intron 13 of 39)	intron (NM_015254, intron 13 of 39)	104242	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.011076	0.402844	
chunk0108_115_1	chr2	229725539	229725952	+	0	NA	Intergenic	Intergenic	-11175	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.002421	0.367150	210(AAGGACAGCATGTCTC,-,0.00),211(AGGACAGCATGTCTCT,+,0.00)
chunk0110_55_1	chr20	10777737	10777936	+	0	NA	Intergenic	LTR16C|LTR|ERVL	24746	NR_110611	101929395	Hs.244862	NR_110611		LINC01752	-	long intergenic non-protein coding RNA 1752	ncRNA	0.015075	0.535000	
chunk0082_337_1	chr17	59751132	59751549	+	0	NA	intron (NM_030938, intron 5 of 11)	intron (NM_030938, intron 5 of 11)	-43742	NM_001015509	51651	Hs.12677	NM_016077	ENSG00000141378	PTRH2	BIT1|CFAP37|CGI-147|IMNEPD|PTH|PTH 2|PTH2	peptidyl-tRNA hydrolase 2	protein-coding	0.019185	0.435407	
chunk0097_32_1	chr2	42447361	42447560	+	0	NA	intron (NM_172344, intron 1 of 1)	L1ME4b|LINE|L1	46637	NM_133329	170850	Hs.352633	NM_133329	ENSG00000171126	KCNG3	KV10.1|KV6.3	potassium voltage-gated channel modifier subfamily G member 3	protein-coding	0.005025	0.365000	75(GGTGACACAGTGTTCC,-,0.00),76(GTGACACAGTGTTCCA,+,0.00)
chunk0142_163_1	chr4	95157505	95158047	+	0	NA	3' UTR (NM_001256794, exon 11 of 11)	3' UTR (NM_001256794, exon 11 of 11)	66285	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.000000	0.309392	
chunk0007_104_1	chr1	78866744	78867647	+	0	NA	Intergenic	MER77B|LTR|ERVL	139615	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.001107	0.378319	385(AGGAACACACTGTACC,-,0.00),386(GGAACACACTGTACCT,+,0.00)
chunk0142_406_1	chr4	102939070	102939316	+	0	NA	intron (NR_047515, intron 3 of 10)	L1PA15|LINE|L1	70215	NM_001008388	493856	Hs.444955	NM_001008388	ENSG00000145354	CISD2	ERIS|Miner1|NAF-1|WFS2|ZCD2	CDGSH iron sulfur domain 2	protein-coding	0.016260	0.348178	
chunk0066_106_1	chr15	29882175	29882680	+	0	NA	intron (NM_001301025, intron 2 of 28).2	intron (NM_001301025, intron 2 of 28).2	-59924	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.007921	0.405138	
chunk0064_19_1	chr14	89351361	89352201	+	0	NA	intron (NM_005197, intron 2 of 5)	intron (NM_005197, intron 2 of 5)	65329	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.015476	0.429251	
chunk0058_160_1	chr14	23286526	23286803	+	0	NA	promoter-TSS (NM_020834)	promoter-TSS (NM_020834)	-564	NM_020834	57594	Hs.632332	NM_020834	ENSG00000215271	HOMEZ	KIAA1443	homeobox and leucine zipper encoding	protein-coding	0.054152	0.593525	
chunk0088_55_1	chr18	44174320	44174670	+	0	NA	Intergenic	Intergenic	357202	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.002857	0.344729	102(ATGAACTGTCTGTTCT,-,0.00),103(TGAACTGTCTGTTCTG,+,0.00)
chunk0130_47_1	chr3	129314821	129315301	+	0	NA	3' UTR (NM_006026, exon 1 of 1)	3' UTR (NM_006026, exon 1 of 1)	-1210	NR_026991	339942	Hs.450096	NM_001025468		H1FX-AS1	C3orf47	H1FX antisense RNA 1	ncRNA	0.102083	0.665281	
chunk0003_130_1	chr1	32681485	32681860	+	0	NA	3' UTR (NM_005610, exon 12 of 12)	3' UTR (NM_005610, exon 12 of 12)	21088	NM_001161708	81493	Hs.712631	NM_030786	ENSG00000162520	SYNC	SYNC1|SYNCOILIN	syncoilin, intermediate filament protein	protein-coding	0.005333	0.428191	
chunk0114_298_1	chr21	16961966	16962347	+	0	NA	Intergenic	L1M2a|LINE|L1	371919	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.000000	0.335079	
chunk0050_413_1	chr12	109716758	109717018	+	0	NA	intron (NM_032829, intron 1 of 2)	MIRb|SINE|MIR	2506	NM_032829	84915	Hs.661785	NM_032829	ENSG00000139438	FAM222A	C12orf34	family with sequence similarity 222 member A	protein-coding	0.019231	0.521073	
chunk0020_3_1	chr1	231601893	231602629	+	0	NA	intron (NR_034037, intron 1 of 1)	intron (NR_034037, intron 1 of 1)	9829	NR_034037	100287814	Hs.25555	NR_034037	ENSG00000229228	LINC00582	-	long intergenic non-protein coding RNA 582	ncRNA	0.006793	0.370421	
chunk0022_9_1	chr10	7231697	7232169	+	0	NA	intron (NM_001018039, intron 9 of 20)	intron (NM_001018039, intron 9 of 20)	-45149	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.008475	0.401691	
chunk0152_443_1	chr5	66326231	66326732	+	0	NA	Intergenic	Intergenic	181646	NM_139168	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.003992	0.392430	301(AGGCAGACTGTGTTCC,-,0.00)
chunk0112_121_1	chr20	38460276	38460563	+	0	NA	Intergenic	MamGypLTR1a|LTR|Gypsy	11050	NR_002986	677837	Hs.16936	NR_002986	ENSG00000199266	SNORA60	ACA60	small nucleolar RNA, H/ACA box 60	snoRNA	0.006969	0.420139	
chunk0041_248_1	chr11	128843328	128843904	+	0	NA	intron (NM_153764, intron 1 of 1)	L2c|LINE|L2	-1082	NM_000220	3758	Hs.527830	NM_000220	ENSG00000151704	KCNJ1	KIR1.1|ROMK|ROMK1	potassium voltage-gated channel subfamily J member 1	protein-coding	0.003472	0.369151	
chunk0004_387_1	chr1	51889895	51890390	+	0	NA	Intergenic	L1MC4|LINE|L1	-11205	NM_002525	4898	Hs.584782	NM_002525	ENSG00000078618	NRDC	NRD1|hNRD1|hNRD2	nardilysin convertase	protein-coding	0.000000	0.368952	
chunk0138_189_1	chr4	38005052	38005661	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	44921	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.009852	0.450820	
chunk0098_371_1	chr2	78532118	78532451	+	0	NA	Intergenic	Intergenic	-241553	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.000000	0.308383	
chunk0113_260_1	chr20	56249214	56249423	+	0	NA	exon (NM_019888, exon 1 of 1)	exon (NM_019888, exon 1 of 1)	586	NM_019888	4159	Hs.248018	NM_019888	ENSG00000124089	MC3R	BMIQ9|MC3|MC3-R|OB20|OQTL	melanocortin 3 receptor	protein-coding	0.066986	0.580952	
chunk0025_132_1	chr10	52029097	52029805	+	0	NA	intron (NM_006258, intron 5 of 17)	intron (NM_006258, intron 5 of 17)	284677	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.005650	0.389281	
chunk0017_69_1	chr1	205563899	205564361	+	0	NA	Intergenic	Intergenic	-4854	NM_181644	148808	Hs.567714	NM_181644	ENSG00000174514	MFSD4A	MFSD4|UNQ3064	major facilitator superfamily domain containing 4A	protein-coding	0.010823	0.526998	
chunk0086_443_1	chr18	29161471	29162186	+	0	NA	Intergenic	Intergenic	-984382	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.001399	0.310056	
chunk0101_191_1	chr2	129605431	129605988	+	0	NA	Intergenic	Intergenic	-317468	NR_110285	101927924	Hs.570248	NR_110285	ENSG00000237574	LINC01856	-	long intergenic non-protein coding RNA 1856	ncRNA	0.008977	0.460573	
chunk0209_192_1	chrX	43865240	43865474	+	0	NA	intron (NM_000898, intron 1 of 14)	L1MB7|LINE|L1	17118	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.004274	0.391489	
chunk0077_325_1	chr16	82234197	82234829	+	0	NA	Intergenic	Intergenic	-64289	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.006329	0.330174	
chunk0174_244_1	chr6	160990203	160990472	+	0	NA	Intergenic	Intergenic	-1390	NM_006724	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.018587	0.344444	
chunk0005_129_1	chr1	57054819	57055423	+	0	NA	intron (NM_021080, intron 11 of 16)	intron (NM_021080, intron 11 of 16)	-88981	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.006623	0.419835	
chunk0021_156_1	chr10	4751581	4751780	+	0	NA	Intergenic	L1MEf|LINE|L1	-73610	NR_024475	100216001	Hs.634869	NR_024475	ENSG00000231298	MANCR	LINC00704	mitotically associated long non coding RNA	ncRNA	0.005025	0.270000	
chunk0093_385_1	chr19	56364933	56365288	+	0	NA	Intergenic	Intergenic	-2989	NR_003127	147947	Hs.467326	NM_194319	ENSG00000240225	ZNF542P	ZNF542	zinc finger protein 542, pseudogene	pseudo	0.008451	0.365169	157(AAGAACGCTTTGTTCT,-,0.00),158(AGAACGCTTTGTTCTT,+,0.00)
chunk0180_390_1	chr7	74635569	74636049	+	0	NA	Intergenic	Intergenic	-21856	NM_033000	2969	Hs.647041	NM_001518	ENSG00000263001	GTF2I	BAP135|BTKAP1|DIWS|GTFII-I|IB291|SPIN|TFII-I|WBS|WBSCR6	general transcription factor IIi	protein-coding	0.018750	0.492723	
chunk0105_112_1	chr2	184893970	184895082	+	0	NA	intron (NM_194250, intron 2 of 3)	intron (NM_194250, intron 2 of 3)	296160	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.018885	0.335130	
chunk0088_184_1	chr18	47413039	47413824	+	0	NA	Intergenic	Intergenic	32935	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.003822	0.484733	593(GGCCCATGCTGTTCCT,+,0.00)
chunk0038_268_1	chr11	89625189	89625452	+	0	NA	Intergenic	Intergenic	-33977	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.015209	0.416667	
chunk0055_127_1	chr13	57648974	57649315	+	0	NA	intron (NM_001040429, intron 1 of 3)	intron (NM_001040429, intron 1 of 3)	17489	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.002933	0.339181	
chunk0046_336_1	chr12	62889805	62890310	+	0	NA	intron (NM_020700, intron 1 of 9)	L1MC|LINE|L1	44828	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.009901	0.363636	
chunk0129_188_1	chr3	121109454	121109788	+	0	NA	intron (NM_014980, intron 5 of 27)	L1PA10|LINE|L1	59981	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.005988	0.364179	
chunk0077_46_1	chr16	75923041	75923543	+	0	NA	Intergenic	Intergenic	275555	NM_018975	54386	Hs.301419	NM_018975	ENSG00000166848	TERF2IP	DRIP5|RAP1	TERF2 interacting protein	protein-coding	0.001992	0.320080	
chunk0182_299_1	chr7	98409870	98410176	+	0	NA	Intergenic	(GTTTG)n|Simple_repeat|Simple_repeat	-8908	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.006536	0.351792	
chunk0204_309_1	chr9	100267351	100267551	+	0	NA	intron (NR_051962, intron 12 of 17)	intron (NR_051962, intron 12 of 17)	85120	NM_001161584	54881	Hs.494648	NM_017746	ENSG00000136891	TEX10	Ipi1|bA208F1.2	testis expressed 10	protein-coding	0.005000	0.388060	
chunk0164_214_1	chr6	22699237	22699953	+	0	NA	Intergenic	Intergenic	130146	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.005587	0.369596	365(GAAACAATGTGTACCT,+,0.00)
chunk0018_390_1	chr1	222531796	222532192	+	0	NA	exon (NM_024746, exon 6 of 9)	exon (NM_024746, exon 6 of 9)	16108	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.012626	0.380353	
chunk0119_122_1	chr22	42790755	42791037	+	0	NA	Intergenic	Intergenic	66506	NM_014570	26286	Hs.685225	NM_014570	ENSG00000242247	ARFGAP3	ARFGAP1	ADP ribosylation factor GTPase activating protein 3	protein-coding	0.014184	0.508834	98(CAGAACTCAGAGTCCC,-,0.00),99(AGAACTCAGAGTCCCT,+,0.00)
chunk0024_255_1	chr10	38918513	38918760	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	222040	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.012146	0.411290	
chunk0002_409_1	chr1	27490131	27490697	+	0	NA	promoter-TSS (NM_006990)	promoter-TSS (NM_006990)	-227	NM_001201404	10163	Hs.469244	NM_006990	ENSG00000158195	WASF2	IMD2|SCAR2|WASF4|WAVE2|dJ393P12.2	WASP family member 2	protein-coding	0.047703	0.550265	
chunk0186_407_1	chr7	145398831	145399133	+	0	NA	Intergenic	Intergenic	-562929	NM_022445	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.003311	0.435644	
chunk0110_184_1	chr20	14580542	14581075	+	0	NA	intron (NR_104193, intron 1 of 4)	intron (NR_104193, intron 1 of 4)	26424	NR_104193	140848	Hs.570367	NR_104193	ENSG00000227927	MACROD2-IT1	C20orf68|NCRNA00227|bA467D7.4	MACROD2 intronic transcript 1	ncRNA	0.005629	0.393258	
chunk0148_170_1	chr5	7333467	7333970	+	0	NA	Intergenic	Intergenic	-27004	NR_033906	442132	Hs.727388	NM_001034846		LOC442132	-	golgin A6 family-like 1 pseudogene	pseudo	0.007952	0.454365	
chunk0204_228_1	chr9	97567314	97567685	+	0	NA	intron (NM_001166116, intron 7 of 9)	MamRep38|DNA|hAT	65860	NM_003275	7111	Hs.404289	NM_003275	ENSG00000136842	TMOD1	D9S57E|ETMOD|TMOD	tropomodulin 1	protein-coding	0.008086	0.545699	
chunk0052_407_1	chr12	130961847	130962323	+	0	NA	intron (NM_198827, intron 2 of 24)	intron (NM_198827, intron 2 of 24)	8178	NM_198827	283383	Hs.719239	NM_198827	ENSG00000111452	ADGRD1	GPR133|PGR25	adhesion G protein-coupled receptor D1	protein-coding	0.023109	0.532495	
chunk0155_88_1	chr5	92242926	92243215	+	0	NA	Intergenic	Intergenic	-859738	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.006920	0.300000	
chunk0019_119_1	chr1	225412985	225413430	+	0	NA	intron (NM_002296, intron 7 of 13)	intron (NM_002296, intron 7 of 13)	14906	NM_002296	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.022472	0.461883	248(GGGACTGCGAGTACCT,+,0.00)
chunk0056_299_1	chr13	90766282	90766510	+	0	NA	Intergenic	Intergenic	160201	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.004386	0.310044	
chunk0073_38_1	chr16	2744800	2745012	+	0	NA	promoter-TSS (NR_027274)	promoter-TSS (NR_027274)	-109	NR_027274	100128788	Hs.311208	NR_027274	ENSG00000205913	SRRM2-AS1	-	SRRM2 antisense RNA 1	ncRNA	0.009434	0.563380	
chunk0171_132_1	chr6	122789599	122789912	+	0	NA	intron (NM_001286138, intron 1 of 6)	intron (NM_001286138, intron 1 of 6)	706	NM_001286138	10924	Hs.486357	NM_006714	ENSG00000172594	SMPDL3A	ASM3A|ASML3a|yR36GH4.1	sphingomyelin phosphodiesterase acid like 3A	protein-coding	0.063898	0.633758	
chunk0103_424_1	chr2	169764033	169764435	+	0	NA	Intergenic	L1MC5|LINE|L1	30388	NM_144711	151230	Hs.655150	NM_144711	ENSG00000213160	KLHL23	DITHP	kelch like family member 23	protein-coding	0.032338	0.464020	
chunk0030_14_1	chr10	110857534	110857925	+	0	NA	Intergenic	Intergenic	13175	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.017903	0.505102	
chunk0002_388_1	chr1	26900300	26900653	+	0	NA	promoter-TSS (NM_022078)	promoter-TSS (NM_022078)	-5	NM_022078	63906	Hs.10903	NM_022078	ENSG00000198746	GPATCH3	GPATC3	G-patch domain containing 3	protein-coding	0.067989	0.553672	
chunk0116_254_1	chr21	38810766	38811118	+	0	NA	intron (NM_001256295, intron 3 of 10)	intron (NM_001256295, intron 3 of 10)	5111	NM_005239	2114	Hs.644231	NM_005239	ENSG00000157557	ETS2	ETS2IT1	ETS proto-oncogene 2, transcription factor	protein-coding	0.014205	0.368272	
chunk0118_62_1	chr22	28376127	28376424	+	0	NA	intron (NM_001145418, intron 2 of 22)	intron (NM_001145418, intron 2 of 22)	-83594	NR_106713	102466081		NR_106713	ENSG00000276162	MIR5739	hsa-mir-5739	microRNA 5739	ncRNA	0.000000	0.365772	
chunk0116_409_1	chr21	42550673	42551023	+	0	NA	intron (NM_018964, intron 10 of 20)	L1MB8|LINE|L1	51216	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.002857	0.421652	
chunk0178_395_1	chr7	40726674	40726897	+	0	NA	intron (NM_024728, intron 13 of 14)	intron (NM_024728, intron 13 of 14)	253154	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.035874	0.504464	82(GGACACACACTGTACC,-,0.00),83(GACACACACTGTACCT,+,0.00)
chunk0112_297_1	chr20	44103951	44104424	+	0	NA	Intergenic	L2a|LINE|L2	83391	NM_175913	57158	Hs.441737	NM_020433	ENSG00000149596	JPH2	CMH17|JP-2|JP2	junctophilin 2	protein-coding	0.006342	0.453586	
chunk0079_167_1	chr17	13760874	13761073	+	0	NA	Intergenic	Intergenic	-159031	NM_006042	9955	Hs.462270	NM_006042	ENSG00000153976	HS3ST3A1	3-OST-3A|3OST3A1	heparan sulfate-glucosamine 3-sulfotransferase 3A1	protein-coding	0.010050	0.475000	
chunk0051_212_1	chr12	116544586	116545071	+	0	NA	Intergenic	Intergenic	11393	NR_027346	100287569	Hs.441601	NM_207436	ENSG00000196668	LINC00173	NCRNA00173	long intergenic non-protein coding RNA 173	ncRNA	0.010309	0.432099	
chunk0101_227_1	chr2	131105033	131105232	+	0	NA	5' UTR (NM_001267067, exon 1 of 6)	5' UTR (NM_001267067, exon 1 of 6)	285	NM_001267067	55041	Hs.469944	NM_017958	ENSG00000115762	PLEKHB2	EVT2	pleckstrin homology domain containing B2	protein-coding	0.045226	0.455000	
chunk0151_308_1	chr5	53337700	53337931	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-142619	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.008658	0.469828	
chunk0089_117_1	chr18	58569579	58569820	+	0	NA	intron (NM_052947, intron 4 of 12)	intron (NM_052947, intron 4 of 12)	-30921	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.000000	0.433884	
chunk0097_163_1	chr2	49298774	49299651	+	0	NA	Intergenic	L1PA6|LINE|L1	-144685	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.005701	0.498861	
chunk0045_385_1	chr12	52345644	52346137	+	0	NA	Intergenic	Intergenic	18732	NM_001300810	3891	Hs.182507	NM_002283	ENSG00000135443	KRT85	ECTD4|HB5|Hb-5|K85|KRTHB5|hHb5	keratin 85	protein-coding	0.000000	0.481781	
chunk0044_57_1	chr12	27727617	27727982	+	0	NA	intron (NM_001190864, intron 5 of 6)	MER2|DNA|TcMar-Tigger	17026	NM_021821	60488	Hs.714076	NM_021821	ENSG00000061794	MRPS35	HDCMD11P|MDS023|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding	0.005479	0.308743	
chunk0097_406_1	chr2	62478096	62478682	+	0	NA	Intergenic	Intergenic	28080	NM_198276	200728	Hs.308028	NM_198276	ENSG00000186889	TMEM17	-	transmembrane protein 17	protein-coding	0.005119	0.477002	
chunk0198_39_1	chr8	128309054	128309578	+	0	NA	Intergenic	Intergenic	159200	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.000000	0.405714	106(AGGAACAAGCTGTATC,-,0.00),107(GGAACAAGCTGTATCT,+,0.00)
chunk0142_32_1	chr4	90660909	90661175	+	0	NA	intron (NM_001145065, intron 6 of 10)	intron (NM_001145065, intron 6 of 10)	426011	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.003759	0.325843	
chunk0140_92_1	chr4	68303649	68303970	+	0	NA	Intergenic	MIR|SINE|MIR	46297	NM_133370	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.000000	0.257764	
chunk0177_186_1	chr7	23530383	23530587	+	0	NA	intron (NM_001282757, intron 1 of 8)	intron (NM_001282757, intron 1 of 8)	1556	NM_013293	29896	Hs.445652	NM_013293	ENSG00000164548	TRA2A	AWMS1|HSU53209	transformer 2 alpha homolog	protein-coding	0.019608	0.424390	
chunk0171_311_1	chr6	129398869	129399079	+	0	NA	intron (NM_001079823, intron 37 of 63)	intron (NM_001079823, intron 37 of 63)	311251	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.009524	0.374408	
chunk0173_303_1	chr6	148423704	148424032	+	0	NA	intron (NM_015278, intron 2 of 19)	intron (NM_015278, intron 2 of 19)	81275	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.015244	0.370821	160(TAGAACTTGCAGTTCC,-,0.00),161(AGAACTTGCAGTTCCT,+,0.00)
chunk0202_44_1	chr9	71234690	71235079	+	0	NA	Intergenic	Intergenic	-113286	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.007712	0.405128	
chunk0080_62_1	chr17	21968905	21969998	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	276928	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.020128	0.419561	
chunk0004_34_1	chr1	42606086	42606404	+	0	NA	intron (NM_001080850, intron 9 of 15)	Tigger2|DNA|TcMar-Tigger	-52132	NM_006347	10465	Hs.256639	NM_006347	ENSG00000171960	PPIH	CYP-20|CYPH|SnuCyp-20|USA-CYP	peptidylprolyl isomerase H	protein-coding	0.015723	0.376176	131(TAGTACACACTGTACT,-,0.00),132(AGTACACACTGTACTG,+,0.00)
chunk0084_338_1	chr17	81057310	81057888	+	0	NA	intron (NM_006340, intron 2 of 14)	intron (NM_006340, intron 2 of 14)	22452	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.024221	0.525043	338(GGTACGTTGTGTTCTT,+,0.00)
chunk0130_82_1	chr3	130689081	130689325	+	0	NA	intron (NM_014602, intron 14 of 19)	intron (NM_014602, intron 14 of 19)	57649	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.008197	0.424490	
chunk0211_297_1	chrX	122897151	122897451	+	0	NA	Intergenic	MIR|SINE|MIR	-286942	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.006667	0.378738	
chunk0193_126_1	chr8	74282870	74283071	+	0	NA	intron (NM_020647, intron 2 of 5)	intron (NM_020647, intron 2 of 5)	38357	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.000000	0.262376	
chunk0063_317_1	chr14	85128125	85129002	+	0	NA	Intergenic	L2a|LINE|L2	-265316	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005701	0.357631	162(AGGCACACAGTGTTTT,-,0.00),163(GGCACACAGTGTTTTC,+,0.00)
chunk0050_115_1	chr12	102023147	102023891	+	0	NA	intron (NM_016053, intron 6 of 6)	intron (NM_016053, intron 6 of 6)	38605	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.002688	0.362416	
chunk0179_446_1	chr7	52719711	52719943	+	0	NA	Intergenic	Intergenic	-315829	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008621	0.394850	
chunk0083_215_1	chr17	67020155	67020562	+	0	NA	intron (NM_014405, intron 2 of 3)	intron (NM_014405, intron 2 of 3)	-24178	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.031941	0.561275	
chunk0157_85_1	chr5	116553319	116553803	+	0	NA	intron (NM_001300780, intron 1 of 19)	intron (NM_001300780, intron 1 of 19)	21365	NM_020796	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.008264	0.480412	257(TAGAACACACTGTGCT,-,0.00),258(AGAACACACTGTGCTA,+,0.00)
chunk0208_69_1	chrX	12088285	12088862	+	0	NA	Intergenic	Intergenic	-49893	NM_014728	9758	Hs.657507	NM_014728	ENSG00000169933	FRMPD4	MRX104|PDZD10|PDZK10	FERM and PDZ domain containing 4	protein-coding	0.005199	0.394464	
chunk0024_93_1	chr10	34503708	34503923	+	0	NA	intron (NM_019619, intron 3 of 24)	intron (NM_019619, intron 3 of 24)	311510	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.004651	0.365741	107(GAATACACAGTGTGCC,-,0.00)
chunk0202_227_1	chr9	76415313	76415936	+	0	NA	Intergenic	Intergenic	17025	NR_026890	653162	Hs.655646	NR_026890		RPSAP9	LAMR1P9|RPSA_20_986	ribosomal protein SA pseudogene 9	pseudo	0.001605	0.395833	
chunk0054_408_1	chr13	50556506	50556919	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-29263	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.012107	0.456522	
chunk0073_265_1	chr16	12119378	12119941	+	0	NA	intron (NM_032167, intron 11 of 20)	intron (NM_032167, intron 11 of 20)	142925	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.008881	0.473404	
chunk0175_392_1	chr6	168388697	168389182	+	0	NA	Intergenic	Intergenic	-52212	NM_022138	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.035052	0.602881	
chunk0086_145_1	chr18	21306366	21306728	+	0	NA	intron (NM_001142966, intron 1 of 32)	intron (NM_001142966, intron 1 of 32)	64305	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.005525	0.366391	222(GAGAACAGCTTGCACT,-,0.00)
chunk0162_70_1	chr6	1761638	1762044	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	151395	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.009852	0.331695	
chunk0146_233_1	chr4	162150055	162150271	+	0	NA	intron (NM_001128427, intron 1 of 15)	intron (NM_001128427, intron 1 of 15)	13871	NM_001128428	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.004630	0.317972	
chunk0108_413_1	chr2	237540807	237541155	+	0	NA	intron (NM_001042467, intron 10 of 14)	intron (NM_001042467, intron 10 of 14)	-25593	NM_015893	51052	Hs.247710	NM_015893	ENSG00000071677	PRLH	PRH|PRRP	prolactin releasing hormone	protein-coding	0.020115	0.601719	
chunk0073_347_1	chr16	14656242	14656925	+	0	NA	intron (NM_016561, intron 5 of 7)	MIR|SINE|MIR	23772	NM_016561	51283	Hs.435556	NM_016561	ENSG00000103429	BFAR	BAR|RNF47	bifunctional apoptosis regulator	protein-coding	0.010249	0.482456	
chunk0209_356_1	chrX	53264659	53264861	+	0	NA	intron (NM_001111125, intron 2 of 14)	intron (NM_001111125, intron 2 of 14)	16854	NM_015075	23096	Hs.496138	NM_015075	ENSG00000124313	IQSEC2	BRAG1|IQ-ArfGEF|MRX1|MRX18|MRX78	IQ motif and Sec7 domain 2	protein-coding	0.004950	0.512315	120(AGGAACAAAATGTGCT,-,0.00),121(GGAACAAAATGTGCTC,+,0.00)
chunk0048_382_1	chr12	86498672	86499096	+	0	NA	intron (NM_013244, intron 1 of 6)	Tigger2b_Pri|DNA|TcMar-Tigger	340020	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.007075	0.343529	
chunk0066_165_1	chr15	32676285	32676547	+	0	NA	intron (NM_001144757, intron 2 of 5)	intron (NM_001144757, intron 2 of 5)	34747	NM_001144757	6447	Hs.156540	NM_003020	ENSG00000166922	SCG5	7B2|P7B2|SGNE1|SgV	secretogranin V	protein-coding	0.007634	0.433460	
chunk0059_25_1	chr14	29836576	29836775	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	91018	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005025	0.505000	
chunk0184_150_1	chr7	116170307	116170552	+	0	NA	Intergenic	LTR81AB|LTR|Gypsy	-40064	NM_015641	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.000000	0.357724	
chunk0074_411_1	chr16	35560027	35560353	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-53020	NR_034018	100130700	Hs.97712	NR_034018		TP53TG3HP	-	TP53 target 3 family member H, pseudogene	pseudo	0.003067	0.440367	
chunk0210_85_1	chrX	70923047	70923315	+	0	NA	Intergenic	L1ME4b|LINE|L1	7944	NM_001048164	84889	Hs.175220	NM_032803	ENSG00000165349	SLC7A3	ATRC3|CAT-3|CAT3	solute carrier family 7 member 3	protein-coding	0.011194	0.356877	
chunk0205_273_1	chr9	111464382	111464886	+	0	NA	intron (NM_001080398, intron 3 of 50)	L1ME3C|LINE|L1	20111	NM_001080398	23392	Hs.368255	NM_001080398	ENSG00000136813	ECPAS	ECM29|KIAA0368	Ecm29 proteasome adaptor and scaffold	protein-coding	0.005952	0.362376	
chunk0165_43_1	chr6	30078856	30079055	+	0	NA	Intergenic	Intergenic	-3104	NM_025236	80352	Hs.121178	NM_025236	ENSG00000204618	RNF39	HZF|HZFW|LIRF	ring finger protein 39	protein-coding	0.005025	0.450000	
chunk0025_311_1	chr10	57649775	57650657	+	0	NA	Intergenic	L1MA1|LINE|L1	-345657	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.009070	0.375991	
chunk0139_33_1	chr4	48422680	48423139	+	0	NA	3' UTR (NM_020846, exon 8 of 8)	3' UTR (NM_020846, exon 8 of 8)	-60434	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.004357	0.373913	
chunk0101_44_1	chr2	122643591	122644067	+	0	NA	Intergenic	Intergenic	888284	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.000000	0.345912	
chunk0188_230_1	chr8	12901679	12902030	+	0	NA	Intergenic	MER65B|LTR|ERV1	-43820	NM_020844	57604	Hs.202521	NM_020844	ENSG00000250305	TRMT9B	C8orf79|KIAA1456|TRM9L|hTRM9L	tRNA methyltransferase 9B (putative)	protein-coding	0.014245	0.446023	
chunk0055_291_1	chr13	65172755	65173012	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-693164	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.003891	0.348837	
chunk0181_438_1	chr7	90603318	90603763	+	0	NA	intron (NM_001287135, intron 1 of 14)	Tigger3a|DNA|TcMar-Tigger	7178	NM_001287135	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.004494	0.336323	206(AAGTACACTCTGTGAC,-,0.00)
chunk0027_172_1	chr10	74981805	74982397	+	0	NA	intron (NM_001256468, intron 11 of 17)	intron (NM_001256468, intron 11 of 17)	76413	NM_001003892	338599	Hs.535090	NM_001003892	ENSG00000188716	DUPD1	DUSP27|FMDSP	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.005068	0.376054	
chunk0105_118_1	chr2	185106814	185107404	+	0	NA	Intergenic	L1PA16|LINE|L1	508743	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.003390	0.360406	
chunk0038_262_1	chr11	89369334	89369718	+	0	NA	intron (NM_001300995, intron 12 of 16)	intron (NM_001300995, intron 12 of 16)	121215	NM_001291929	50507	Hs.371036	NM_016931	ENSG00000086991	NOX4	KOX|KOX-1|RENOX	NADPH oxidase 4	protein-coding	0.005208	0.342857	
chunk0076_445_1	chr16	73866504	73866980	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	348779	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.010504	0.436059	
chunk0002_440_1	chr1	28209682	28210189	+	0	NA	intron (NM_014280, intron 5 of 8)	intron (NM_014280, intron 5 of 8)	-15999	NM_001164721	5724	Hs.77542	NM_000952	ENSG00000169403	PTAFR	PAFR	platelet activating factor receptor	protein-coding	0.003945	0.442913	
chunk0100_410_1	chr2	119741092	119741401	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-18385	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.009709	0.470968	98(AAGCACAGTGTGTACT,-,0.00),99(AGCACAGTGTGTACTG,+,0.00)
chunk0204_340_1	chr9	101399621	101400452	+	0	NA	intron (NM_001278232, intron 2 of 2)	intron (NM_001278232, intron 2 of 2)	1182	NM_197977	7743	Hs.50123	NM_003452	ENSG00000136870	ZNF189	-	zinc finger protein 189	protein-coding	0.009627	0.442308	
chunk0153_133_1	chr5	68984811	68985327	+	0	NA	intron (NR_130778, intron 1 of 3)	L1MEi|LINE|L1	44858	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.005814	0.324952	
chunk0180_233_1	chr7	67438251	67438809	+	0	NA	Intergenic	Intergenic	102554	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.010753	0.493739	
chunk0189_146_1	chr8	22927741	22928133	+	0	NA	promoter-TSS (NM_144962)	promoter-TSS (NM_144962)	-29	NM_144962	157310	Hs.491242	NM_144962	ENSG00000134020	PEBP4	CORK-1|CORK1|GWTM1933|HEL-S-300|PEBP-4|PRO4408|hPEBP4	phosphatidylethanolamine binding protein 4	protein-coding	0.015306	0.605598	
chunk0168_281_1	chr6	90722562	90723219	+	0	NA	Intergenic	Intergenic	-135589	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.003044	0.326748	547(AGAAACATACTGTCCA,-,0.00),548(GAAACATACTGTCCAT,+,0.00)
chunk0018_233_1	chr1	219858899	219859282	+	0	NA	Intergenic	Intergenic	69561	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.007833	0.390625	
chunk0074_161_1	chr16	23390725	23391048	+	0	NA	intron (NM_153603, intron 16 of 16)	intron (NM_153603, intron 16 of 16)	62305	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.021672	0.521605	
chunk0171_138_1	chr6	123513125	123513528	+	0	NA	intron (NM_006073, intron 6 of 40)	intron (NM_006073, intron 6 of 40)	73722	NR_110844	101927990	Hs.660877	NR_110844		TRDN-AS1	HRAT13	TRDN antisense RNA 1	ncRNA	0.000000	0.356436	
chunk0096_44_1	chr2	26950166	26950441	+	0	NA	TTS (NM_001253724)	TTS (NM_001253724)	-20068	NM_012326	22924	Hs.515860	NM_012326	ENSG00000084764	MAPRE3	EB3|EBF3|EBF3-S|RP3	microtubule associated protein RP/EB family member 3	protein-coding	0.018182	0.507246	
chunk0014_153_1	chr1	178163430	178163903	+	0	NA	intron (NM_170692, intron 1 of 17)	L1MB7|LINE|L1	-69673	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.004228	0.316456	
chunk0167_82_1	chr6	56559502	56560057	+	0	NA	intron (NM_183380, intron 49 of 93)	intron (NM_183380, intron 49 of 93)	83117	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.003604	0.343525	
chunk0084_111_1	chr17	75780374	75780914	+	0	NA	promoter-TSS (NM_005324)	promoter-TSS (NM_005324)	-709	NM_005324	3021	Hs.180877	NM_005324	ENSG00000132475	H3F3B	H3.3B	H3 histone family member 3B	protein-coding	0.000000	0.330869	
chunk0126_209_1	chr3	78765531	78766110	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	253639	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.005181	0.355172	
chunk0174_450_1	chr6	166383389	166383623	+	0	NA	promoter-TSS (NM_016098)	promoter-TSS (NM_016098)	-493	NM_016098	51660	Hs.172755	NM_016098	ENSG00000060762	MPC1	BRP44L|CGI-129|MPYCD|SLC54A1	mitochondrial pyruvate carrier 1	protein-coding	0.111111	0.774468	
chunk0119_128_1	chr22	42892632	42892831	+	0	NA	intron (NM_001184970, intron 3 of 10)	intron (NM_001184970, intron 3 of 10)	-35329	NM_001142293	26286	Hs.685225	NM_014570	ENSG00000242247	ARFGAP3	ARFGAP1	ADP ribosylation factor GTPase activating protein 3	protein-coding	0.005025	0.580000	
chunk0108_406_1	chr2	237487340	237487683	+	0	NA	intron (NM_001042467, intron 1 of 14)	CpG	292	NM_001281473	79083	Hs.102406	NM_024101	ENSG00000115648	MLPH	SLAC2-A	melanophilin	protein-coding	0.064140	0.683140	247(GAGGACAGCGCGTTCC,-,0.00),248(AGGACAGCGCGTTCCC,+,0.00)
chunk0007_39_1	chr1	77702256	77702561	+	0	NA	intron (NM_015017, intron 22 of 24)	intron (NM_015017, intron 22 of 24)	-18981	NM_001308237	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.003279	0.316993	
chunk0064_304_1	chr14	95542552	95543118	+	0	NA	intron (NM_016417, intron 1 of 1)	intron (NM_016417, intron 1 of 1)	7849	NM_016417	51218	Hs.744943	NM_016417	ENSG00000182512	GLRX5	C14orf87|FLB4739|GRX5|PR01238|PRO1238|PRSA|SIDBA3|SPAHGC	glutaredoxin 5	protein-coding	0.008834	0.352734	471(GTCACAGAGTGTCCCT,+,0.00)
chunk0116_382_1	chr21	42230178	42230831	+	0	NA	intron (NM_207627, intron 3 of 15)	intron (NM_207627, intron 3 of 15)	10606	NM_207174	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.019908	0.432722	
chunk0126_328_1	chr3	81885548	81885747	+	0	NA	Intergenic	MER30|DNA|hAT-Charlie	-123848	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.020101	0.295000	
chunk0169_177_1	chr6	102267556	102268021	+	0	NA	Intergenic	L1PA7|LINE|L1	868803	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004301	0.347639	
chunk0169_403_1	chr6	108294699	108295097	+	0	NA	promoter-TSS (NM_145315)	promoter-TSS (NM_145315)	4	NM_145315	246269	Hs.259666	NM_145315	ENSG00000135537	AFG1L	AFG1|LACE1|c222389	AFG1 like ATPase	protein-coding	0.070352	0.621554	122(GGAGCTGCCTGTTCCG,+,0.00)
chunk0129_182_1	chr3	120966416	120967199	+	0	NA	intron (NM_014980, intron 3 of 27)	L1PA6|LINE|L1	58604	NM_001308330	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.010217	0.503827	
chunk0048_409_1	chr12	88186061	88186512	+	0	NA	intron (NM_181783, intron 10 of 13)	intron (NM_181783, intron 10 of 13)	43990	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.000000	0.367257	
chunk0046_62_1	chr12	55908910	55909730	+	0	NA	intron (NM_032345, intron 1 of 2)	L2b|LINE|L2	17805	NM_001143853	84305	Hs.505687	NM_032345	ENSG00000170473	PYM1	PYM|WIBG	PYM homolog 1, exon junction complex associated factor	protein-coding	0.008537	0.394641	
chunk0096_227_1	chr2	30639729	30640313	+	0	NA	intron (NM_001304446, intron 5 of 5)	intron (NM_001304446, intron 5 of 5)	167424	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.010274	0.411966	275(TGGTTCACACTGTCCT,-,0.00),276(GGTTCACACTGTCCTG,+,0.00)
chunk0048_254_1	chr12	81786875	81787121	+	0	NA	Intergenic	Intergenic	-27668	NM_003625	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.004065	0.242915	
chunk0052_92_1	chr13	22211991	22212264	+	0	NA	intron (NR_103810, intron 1 of 1)	intron (NR_103810, intron 1 of 1)	1842	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.032967	0.551095	
chunk0050_32_1	chr12	100195141	100195674	+	0	NA	Intergenic	Intergenic	-4680	NM_022496	64431	Hs.115088	NM_022496	ENSG00000075089	ACTR6	ARP6|CDA12|HSPC281|MSTP136|hARP6|hARPX	actin related protein 6	protein-coding	0.011257	0.440075	432(GACACTCACTGTTCCT,+,0.00)
chunk0044_134_1	chr12	29404005	29404576	+	0	NA	intron (NR_073172, intron 1 of 1)	intron (NR_073172, intron 1 of 1)	14996	NR_073170	101055625	Hs.569158	NR_073170	ENSG00000257599	OVCH1-AS1	-	OVCH1 antisense RNA 1	ncRNA	0.008757	0.444056	412(GGGCACAGGTTGTTCT,-,0.00),413(GGCACAGGTTGTTCTC,+,0.00)
chunk0037_35_1	chr11	70204541	70204787	+	0	NA	intron (NM_003824, intron 1 of 1)	intron (NM_003824, intron 1 of 1)	1501	NM_003824	8772	Hs.86131	NM_003824	ENSG00000168040	FADD	GIG3|MORT1	Fas associated via death domain	protein-coding	0.012195	0.445344	
chunk0133_392_1	chr3	174283832	174284047	+	0	NA	TTS (NM_014932)	TTS (NM_014932)	-363143	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004651	0.282407	
chunk0035_265_1	chr11	46514205	46514592	+	0	NA	intron (NM_001300731, intron 7 of 16)	intron (NM_001300731, intron 7 of 16)	-62509	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.002584	0.425258	
chunk0041_320_1	chr11	130115128	130115650	+	0	NA	intron (NM_001142278, intron 3 of 12)	intron (NM_001142278, intron 3 of 12)	-44398	NM_021978	6768	Hs.504315	NM_021978	ENSG00000149418	ST14	ARCI11|HAI|MT-SP1|MTSP1|PRSS14|SNC19|TADG15|TMPRSS14	suppression of tumorigenicity 14	protein-coding	0.005747	0.351816	
chunk0102_170_1	chr2	147487637	147488363	+	0	NA	Intergenic	Intergenic	-356517	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.005510	0.396149	365(AAGCACATAATGTGTC,-,0.00),415(AAGAACATTTAGTCCC,-,0.00),416(AGAACATTTAGTCCCA,+,0.00)
chunk0176_175_1	chr7	13709533	13710045	+	0	NA	Intergenic	Intergenic	276725	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.001953	0.343080	
chunk0186_92_1	chr7	137463375	137463574	+	0	NA	intron (NM_004717, intron 28 of 33)	intron (NM_004717, intron 28 of 33)	-119674	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.015075	0.520000	
chunk0157_23_1	chr5	115526462	115526876	+	0	NA	intron (NM_020177, intron 2 of 2)	intron (NM_020177, intron 2 of 2)	18225	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.007246	0.378313	
chunk0173_316_1	chr6	148620207	148620860	+	0	NA	Intergenic	L3|LINE|CR1	-126602	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.010720	0.412844	
chunk0069_447_1	chr15	68648934	68649501	+	0	NA	intron (NM_001190456, intron 2 of 11)	(TA)n|Simple_repeat|Simple_repeat	17229	NM_001190457	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.010582	0.315141	
chunk0035_347_1	chr11	48055624	48056293	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	-40824	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.019432	0.489552	
chunk0095_199_1	chr2	18313421	18313912	+	0	NA	Intergenic	L2c|LINE|L2	247027	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.002037	0.420732	221(AAGAACATTTAGTTCA,-,0.00),222(AGAACATTTAGTTCAT,+,0.00)
chunk0071_350_1	chr15	88496918	88497437	+	0	NA	Intergenic	Intergenic	29724	NM_176805	64963	Hs.111286	NM_022839	ENSG00000181991	MRPS11	HCC-2|MRP-S11|S11mt	mitochondrial ribosomal protein S11	protein-coding	0.023121	0.578846	407(GAGCACTGACTGTGCC,-,0.00),408(AGCACTGACTGTGCCA,+,0.00)
chunk0183_366_1	chr7	109163210	109163552	+	0	NA	Intergenic	Intergenic	-278794	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.000000	0.276968	
chunk0032_186_1	chr11	6252262	6252463	+	0	NA	Intergenic	Intergenic	-7312	NM_176875	887	Hs.203	NM_176875	ENSG00000110148	CCKBR	CCK-B|CCK2R|GASR	cholecystokinin B receptor	protein-coding	0.019900	0.475248	
chunk0183_377_1	chr7	109569559	109569949	+	0	NA	Intergenic	Intergenic	390459	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.327366	
chunk0165_60_1	chr6	30799202	30799487	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	31315	NR_130726	401247		NR_130726	ENSG00000214894	LINC00243	C6orf214|NCRNA00243	long intergenic non-protein coding RNA 243	ncRNA	0.010526	0.447552	
chunk0097_413_1	chr2	62778498	62778816	+	0	NA	intron (NM_001142614, intron 4 of 22)	intron (NM_001142614, intron 4 of 22)	71760	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.009434	0.338558	
chunk0196_17_1	chr8	101495126	101495820	+	0	NA	intron (NM_024915, intron 1 of 15)	intron (NM_024915, intron 1 of 15)	3033	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.014409	0.382734	324(AGGACATTTTGTCTTT,+,0.00)
chunk0041_242_1	chr11	128497188	128497461	+	0	NA	intron (NM_001143820, intron 3 of 9)	intron (NM_001143820, intron 3 of 9)	24986	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.007326	0.518248	
chunk0163_275_1	chr6	13448227	13448601	+	0	NA	intron (NM_018988, intron 1 of 1)	intron (NM_018988, intron 1 of 1)	23649	NR_038459	54438	Hs.484686	NM_018988	ENSG00000145990	GFOD1	ADG-90|C6orf114	glucose-fructose oxidoreductase domain containing 1	protein-coding	0.005348	0.458667	196(GAGCACAGCATGTTCT,-,0.00),197(AGCACAGCATGTTCTC,+,0.00)
chunk0161_259_1	chr5	172003535	172004246	+	0	NA	intron (NM_012300, intron 1 of 12)	intron (NM_012300, intron 1 of 12)	2983	NM_033644	23291	Hs.484138	NM_012300	ENSG00000072803	FBXW11	BTRC2|BTRCP2|FBW1B|FBXW1B|Fbw11|Hos	F-box and WD repeat domain containing 11	protein-coding	0.004219	0.342697	
chunk0078_224_1	chr17	6494632	6495116	+	0	NA	intron (NM_001165966, intron 3 of 18)	L1ME4b|LINE|L1	50459	NM_001195228	54478	Hs.592116	NM_019013	ENSG00000129195	PIMREG	CATS|FAM64A|RCS1	PICALM interacting mitotic regulator	protein-coding	0.002066	0.414433	395(AGGAACTGTGTGCTCC,-,0.00),396(GGAACTGTGTGCTCCC,+,0.00)
chunk0122_181_1	chr3	32630218	32630732	+	0	NA	Intergenic	Intergenic	-54670	NM_001256741	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.001946	0.407767	
chunk0059_83_1	chr14	30631953	30632184	+	0	NA	intron (NM_001283033, intron 3 of 21)	AluSz|SINE|Alu	9749	NM_001257376	23256	Hs.369168	NM_016106	ENSG00000092108	SCFD1	C14orf163|RA410|SLY1|SLY1P|STXBP1L2	sec1 family domain containing 1	protein-coding	0.012987	0.366379	
chunk0076_65_1	chr16	63007490	63007910	+	0	NA	Intergenic	L1MC1|LINE|L1	-970865	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.002381	0.334917	
chunk0210_23_1	chrX	67308396	67308746	+	0	NA	Intergenic	L1PB1|LINE|L1	-235461	NM_000044	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.002857	0.376068	
chunk0089_102_1	chr18	58417695	58418367	+	0	NA	Intergenic	L1ME4b|LINE|L1	-33043	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.010417	0.465082	
chunk0001_328_1	chr1	9544510	9544836	+	0	NA	intron (NM_032315, intron 1 of 6)	intron (NM_032315, intron 1 of 6)	5204	NM_032315	84275	Hs.568613	NM_032315	ENSG00000171612	SLC25A33	BMSC-MCP|PNC1	solute carrier family 25 member 33	protein-coding	0.015337	0.443425	
chunk0005_65_1	chr1	55606696	55607186	+	0	NA	Intergenic	Intergenic	381300	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.002041	0.397149	
chunk0152_289_1	chr5	61543697	61544187	+	0	NA	exon (NM_020928, exon 14 of 14)	exon (NM_020928, exon 14 of 14)	-93839	NM_173667									0.032653	0.523422	
chunk0010_157_1	chr1	115402524	115403167	+	0	NA	Intergenic	Intergenic	-64609	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.004666	0.444099	
chunk0119_96_1	chr22	41902831	41903457	+	0	NA	non-coding (NR_103834, exon 20 of 22)	non-coding (NR_103834, exon 20 of 22)	2200	NR_029507	407039		NR_029507	ENSG00000207932	MIR33A	MIR33|MIRN33|MIRN33A|hsa-mir-33|hsa-mir-33a|miR-33|miRNA33A|mir-33a	microRNA 33a	ncRNA	0.023962	0.641148	
chunk0001_209_1	chr1	7970913	7971675	+	0	NA	intron (NM_007262, intron 5 of 6)	intron (NM_007262, intron 5 of 6)	9640	NM_001123377	11315	Hs.419640	NM_007262	ENSG00000116288	PARK7	DJ-1|DJ1|GATD2|HEL-S-67p	Parkinsonism associated deglycase	protein-coding	0.020997	0.463958	
chunk0102_287_1	chr2	150494418	150494980	+	0	NA	Intergenic	Intergenic	-7004	NM_001254738	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.007117	0.380107	305(CAGTACATTTTGTTCA,-,0.00),306(AGTACATTTTGTTCAG,+,0.00)
chunk0030_369_1	chr10	119041651	119041893	+	0	NA	intron (NM_003750, intron 19 of 21)	intron (NM_003750, intron 19 of 21)	12056	NM_199461	340719	Hs.591918	NM_199461	ENSG00000188613	NANOS1	EC_Rep1a|NOS-1|NOS1|SPGF12|ZC2HC12A	nanos C2HC-type zinc finger 1	protein-coding	0.008264	0.386831	
chunk0086_289_1	chr18	23751629	23752084	+	0	NA	intron (NR_130106, intron 5 of 12)	LTR33|LTR|ERVL	62413	NR_130106	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.002198	0.489035	
chunk0159_244_1	chr5	141866160	141866464	+	0	NA	promoter-TSS (NM_001278615)	promoter-TSS (NM_001278615)	-110	NM_001278615	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.039474	0.609836	178(ATGAACTGTCTGTCCC,-,0.00),179(TGAACTGTCTGTCCCT,+,0.00)
chunk0113_294_1	chr20	57677604	57677861	+	0	NA	intron (NM_199171, intron 1 of 3)	L1MD2|LINE|L1	12892	NM_001255976	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.011673	0.410853	
chunk0012_398_1	chr1	163730321	163730672	+	0	NA	Intergenic	Intergenic	-307305	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.005698	0.423295	276(GTGGACTTTGTGTCCT,-,0.00),277(TGGACTTTGTGTCCTA,+,0.00)
chunk0177_79_1	chr7	21566027	21566446	+	0	NA	intron (NM_001277115, intron 6 of 81)	intron (NM_001277115, intron 6 of 81)	23021	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.011933	0.421429	
chunk0008_442_1	chr1	99614955	99615656	+	0	NA	intron (NR_031666, intron 1 of 4)	intron (NR_031666, intron 1 of 4)	-30570	NM_017734	54873	Hs.483993	NM_017734	ENSG00000099260	PALMD	C1orf11|PALML	palmdelphin	protein-coding	0.002853	0.404558	279(AGGAACAGTTTGTGTC,-,0.00),280(GGAACAGTTTGTGTCT,+,0.00)
chunk0032_260_1	chr11	8828955	8829253	+	0	NA	intron (NM_005418, intron 3 of 22)	(GT)n|Simple_repeat|Simple_repeat	-17769	NM_139157	6764	Hs.117715	NM_005418	ENSG00000166444	ST5	DENND2B|HTS1|p126	suppression of tumorigenicity 5	protein-coding	0.003356	0.498328	
chunk0043_132_1	chr12	15827780	15827982	+	0	NA	Intergenic	Intergenic	-38305	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.014851	0.369458	
chunk0141_38_1	chr4	77075881	77076144	+	0	NA	promoter-TSS (NM_006835)	promoter-TSS (NM_006835)	-40	NM_006835	10983	Hs.518827	NM_006835	ENSG00000118816	CCNI	CCNI1|CYC1|CYI	cyclin I	protein-coding	0.076046	0.571970	
chunk0084_77_1	chr17	75035104	75035531	+	0	NA	non-coding (NR_110835, exon 3 of 8)	non-coding (NR_110835, exon 3 of 8)	2750	NR_110835	23510	Hs.514468	NM_015353	ENSG00000180901	KCTD2	-	potassium channel tetramerization domain containing 2	protein-coding	0.058548	0.521028	
chunk0058_194_1	chr14	24396187	24396681	+	0	NA	Intergenic	LTR88b|LTR|Gypsy?	-2352	NM_025081	57523	Hs.288348	NM_025081	ENSG00000205978	NYNRIN	CGIN1|KIAA1305	NYN domain and retroviral integrase containing	protein-coding	0.008097	0.488889	268(GTGACAGGGTGTGCTC,+,0.00)
chunk0087_251_1	chr18	36904428	36904798	+	0	NA	intron (NM_020776, intron 5 of 9)	L1MEc|LINE|L1	-75397	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.000000	0.285714	
chunk0039_2_1	chr11	94885780	94885999	+	0	NA	Intergenic	AluJr4|SINE|Alu	87723	NM_016403	51503	Hs.503597	NM_016403	ENSG00000150316	CWC15	AD002|C11orf5|Cwf15|HSPC148|ORF5	CWC15 spliceosome associated protein homolog	protein-coding	0.000000	0.472727	72(CTGCACAGAGAGTCCC,-,0.00),73(TGCACAGAGAGTCCCA,+,0.00)
chunk0134_394_1	chr3	182967243	182967570	+	0	NA	intron (NM_001308101, intron 1 of 6)	intron (NM_001308101, intron 1 of 6)	13195	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.003058	0.332317	
chunk0017_213_1	chr1	207866731	207867509	+	0	NA	Intergenic	Intergenic	44218	NM_001773	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.014139	0.539153	249(AAGAACACCATGTTTA,-,0.00),250(AGAACACCATGTTTAT,+,0.00)
chunk0150_380_1	chr5	39400536	39401080	+	0	NA	intron (NM_001343, intron 1 of 14)	intron (NM_001343, intron 1 of 14)	24425	NM_001343	1601	Hs.696631	NM_001343	ENSG00000153071	DAB2	DOC-2|DOC2	DAB adaptor protein 2	protein-coding	0.007353	0.383486	
chunk0033_121_1	chr11	14543326	14543738	+	0	NA	intron (NM_148976, intron 2 of 10)	intron (NM_148976, intron 2 of 10)	-23087	NM_001143937	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.002427	0.297821	
chunk0104_428_1	chr2	180969196	180969557	+	0	NA	Intergenic	Intergenic	-11009	NM_182678	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.002770	0.342541	
chunk0018_364_1	chr1	221839908	221840240	+	0	NA	intron (NR_125989, intron 2 of 3)	intron (NR_125989, intron 2 of 3)	592	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.012048	0.531532	
chunk0158_21_1	chr5	125402901	125403158	+	0	NA	Intergenic	Intergenic	-90232	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.011673	0.341085	
chunk0067_270_1	chr15	46654800	46655276	+	0	NA	Intergenic	L1ME2|LINE|L1	-529168	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.002101	0.278826	
chunk0038_273_1	chr11	89649003	89649463	+	0	NA	Intergenic	L1M5|LINE|L1	-10064	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.013043	0.383948	
chunk0203_224_1	chr9	86983244	86983977	+	0	NA	intron (NR_049794, intron 3 of 6)	intron (NR_049794, intron 3 of 6)	34912	NR_049794	100506834	Hs.553987	NR_049794	ENSG00000226237	GAS1RR	LncRNA-Hh	GAS1 adjacent regulatory RNA	ncRNA	0.013643	0.403270	378(TGGTACACAATGTGCT,-,0.00),379(GGTACACAATGTGCTC,+,0.00)
chunk0177_379_1	chr7	26876841	26877281	+	0	NA	Intergenic	Intergenic	-12318	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.000000	0.328798	
chunk0063_302_1	chr14	84656696	84657447	+	0	NA	Intergenic	Intergenic	-736808	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.009321	0.363032	
chunk0068_456_1	chr15	59896585	59897156	+	0	NA	Intergenic	Intergenic	-107352	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.010508	0.424825	
chunk0160_344_1	chr5	160079183	160079841	+	0	NA	intron (NM_001267035, intron 2 of 2)	intron (NM_001267035, intron 2 of 2)	39933	NM_001130864	114825	Hs.744960	NM_052927	ENSG00000170234	PWWP2A	MST101	PWWP domain containing 2A	protein-coding	0.007599	0.365706	
chunk0122_355_1	chr3	37511335	37511787	+	0	NA	intron (NM_002207, intron 8 of 27)	intron (NM_002207, intron 8 of 27)	59239	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.013274	0.445916	
chunk0042_448_1	chr12	12425716	12425944	+	0	NA	intron (NM_058169, intron 2 of 3)	intron (NM_058169, intron 2 of 3)	68751	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.004386	0.406114	
chunk0140_418_1	chr4	75940327	75940856	+	0	NA	intron (NM_014435, intron 1 of 10)	CpG-21271	422	NM_014435	27163	Hs.437365	NM_014435	ENSG00000138744	NAAA	ASAHL|PLT	N-acylethanolamine acid amidase	protein-coding	0.102079	0.681132	
chunk0062_314_1	chr14	73149744	73150239	+	0	NA	intron (NM_000021, intron 3 of 11)	Charlie30a|DNA|hAT-Charlie	13556	NM_007318	5663	Hs.3260	NM_000021	ENSG00000080815	PSEN1	ACNINV3|AD3|FAD|PS-1|PS1|S182	presenilin 1	protein-coding	0.004040	0.324597	
chunk0201_287_1	chr9	39791396	39791601	+	0	NA	Intergenic	CpG	18661	NR_126046	389741	Hs.380240	NM_203448	ENSG00000278175	GLIDR	LINC01172|TCONS_00015562	glioblastoma down-regulated RNA	ncRNA	0.082927	0.640777	118(AGGGAGAGTCTGTACT,-,0.00)
chunk0137_401_1	chr4	27269068	27269431	+	0	NA	intron (NR_125921, intron 3 of 5)	L2a|LINE|L2	51770	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.008264	0.370879	
chunk0084_399_1	chr17	82145640	82145936	+	0	NA	intron (NM_198082, intron 14 of 16)	intron (NM_198082, intron 14 of 16)	-47558	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.020270	0.659933	
chunk0156_101_1	chr5	105074003	105074256	+	0	NA	Intergenic	LTR81|LTR|Gypsy	-25345	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.429134	
chunk0098_433_1	chr2	81880377	81881040	+	0	NA	Intergenic	Intergenic	-413762	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.367470	262(GGAACACAAAGATCTT,+,0.00)
chunk0087_6_1	chr18	30334590	30334849	+	0	NA	Intergenic	MER50|LTR|ERV1	35809	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.011583	0.446154	
chunk0052_168_1	chr13	24112208	24112912	+	0	NA	intron (NM_001286792, intron 3 of 14)	intron (NM_001286792, intron 3 of 14)	-48156	NM_001166271	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.005682	0.418440	5(TAAAACAGATTGTTCT,-,0.00),6(AAAACAGATTGTTCTC,+,0.00),392(ATGAACAAAATGTTCT,-,0.00),393(TGAACAAAATGTTCTT,+,0.00)
chunk0141_206_1	chr4	84461426	84461858	+	0	NA	Intergenic	L1ME1|LINE|L1	36592	NM_006168	4825	Hs.546270	NM_006168	ENSG00000163623	NKX6-1	NKX6.1|NKX6A	NK6 homeobox 1	protein-coding	0.009259	0.351039	
chunk0085_421_1	chr18	10537870	10538753	+	0	NA	intron (NM_003826, intron 5 of 11)	MER102b|DNA|hAT-Charlie	12435	NM_003826	8774	Hs.464622	NM_003826	ENSG00000134265	NAPG	GAMMASNAP	NSF attachment protein gamma	protein-coding	0.007928	0.378959	
chunk0044_48_1	chr12	27650308	27651097	+	0	NA	intron (NM_003622, intron 7 of 29)	intron (NM_003622, intron 7 of 29)	-45793	NM_001029874	387849	Hs.269836	NM_001029874	ENSG00000174236	REP15	RAB15EP	RAB15 effector protein	protein-coding	0.003802	0.329114	
chunk0079_389_1	chr17	18936519	18936757	+	0	NA	Intergenic	L1MB5|LINE|L1	-14038	NM_001282417	125206	Hs.462418	NM_152351	ENSG00000154025	SLC5A10	SGLT-5|SGLT5	solute carrier family 5 member 10	protein-coding	0.004202	0.376569	
chunk0169_280_1	chr6	105678168	105679066	+	0	NA	Intergenic	Intergenic	-275493	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.002227	0.340378	
chunk0005_445_1	chr1	63440581	63441301	+	0	NA	non-coding (NR_045147, exon 10 of 10)	non-coding (NR_045147, exon 10 of 10)	73351	NM_013339	29929	Hs.258501	NM_013339	ENSG00000088035	ALG6	CDG1C	ALG6 alpha-1,3-glucosyltransferase	protein-coding	0.005556	0.356449	165(AAAAACACAGAGTTCT,-,0.00)
chunk0072_344_1	chr15	99565751	99565958	+	0	NA	promoter-TSS (NM_005587)	promoter-TSS (NM_005587)	-74	NM_001130927	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.057971	0.586538	
chunk0180_364_1	chr7	73881410	73881610	+	0	NA	Intergenic	Intergenic	20351	NM_182504	135886	Hs.647026	NM_182504	ENSG00000175877	TMEM270	WBSCR28	transmembrane protein 270	protein-coding	0.015000	0.547264	
chunk0173_248_1	chr6	146923397	146924016	+	0	NA	intron (NR_034115, intron 7 of 10)	L1MEc|LINE|L1	-119882	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.004847	0.400000	
chunk0147_9_1	chr4	170599568	170599767	+	0	NA	Intergenic	L1M5|LINE|L1	373076	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.010050	0.320000	
chunk0108_172_1	chr2	231707907	231708256	+	0	NA	promoter-TSS (NM_001099285)	promoter-TSS (NM_001099285)	-444	NM_001099285	5757	Hs.459927	NM_002823	ENSG00000187514	PTMA	TMSA	prothymosin alpha	protein-coding	0.106017	0.748571	
chunk0186_168_1	chr7	139317886	139318556	+	0	NA	Intergenic	L1MEh|LINE|L1	-22138	NM_001244585	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.008955	0.450075	249(TAGGACAGTTTGTCTC,-,0.00),250(AGGACAGTTTGTCTCT,+,0.00)
chunk0091_392_1	chr19	16200567	16200768	+	0	NA	intron (NM_001130524, intron 1 of 12)	intron (NM_001130524, intron 1 of 12)	2813	NM_001130524	8907	Hs.71040	NM_032493	ENSG00000072958	AP1M1	AP47|CLAPM2|CLTNM|MU-1A	adaptor related protein complex 1 subunit mu 1	protein-coding	0.029851	0.524752	
chunk0049_19_1	chr12	89389945	89390494	+	0	NA	Intergenic	Intergenic	-37360	NM_022652	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.005464	0.387273	288(AGGTACAGCGTGTTCT,-,0.00),289(GGTACAGCGTGTTCTG,+,0.00)
chunk0209_139_1	chrX	41688102	41688342	+	0	NA	promoter-TSS (NM_005300)	promoter-TSS (NM_005300)	-751	NM_001097579	2857	Hs.495989	NM_005300	ENSG00000171659	GPR34	LYPSR1	G protein-coupled receptor 34	protein-coding	0.000000	0.294606	
chunk0095_138_1	chr2	16734803	16735298	+	0	NA	Intergenic	ORSL|DNA|hAT-Tip100	-69184	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.006061	0.441532	
chunk0002_75_1	chr1	14159574	14159829	+	0	NA	Intergenic	L1MA2|LINE|L1	410320	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.000000	0.507812	
chunk0090_430_1	chr18	79365577	79365926	+	0	NA	intron (NM_001306085, intron 26 of 28)	CpG	-30021	NM_006162	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.054441	0.602857	
chunk0146_364_1	chr4	168256139	168256994	+	0	NA	intron (NM_017631, intron 25 of 37)	LTR68|LTR|ERV1	62241	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.002339	0.371495	
chunk0025_199_1	chr10	53403831	53404241	+	0	NA	Intergenic	L1PBb|LINE|L1	-632336	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.007317	0.515815	
chunk0032_379_1	chr11	11336603	11336918	+	0	NA	intron (NM_198516, intron 7 of 10)	L2c|LINE|L2	16597	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.012698	0.433544	
chunk0201_90_1	chr9	34646926	34647125	+	0	NA	intron (NM_000155, intron 1 of 10)	intron (NM_000155, intron 1 of 10)	436	NM_000155	2592	Hs.522090	NM_000155	ENSG00000213930	GALT	-	galactose-1-phosphate uridylyltransferase	protein-coding	0.035176	0.625000	
chunk0100_286_1	chr2	114143641	114143965	+	0	NA	Intergenic	L2c|LINE|L2	-163819	NR_034130	100499194	Hs.662336	NR_034130		LOC100499194	-	uncharacterized LOC100499194	ncRNA	0.000000	0.390769	45(AAGGGCACACTGTTCC,-,0.00),46(AGGGCACACTGTTCCA,+,0.00),178(TGCTCAGAATGTTCCT,+,0.00)
chunk0012_156_1	chr1	158161520	158162048	+	0	NA	Intergenic	Intergenic	-18163	NM_001766	912	Hs.1799	NM_001766	ENSG00000158473	CD1D	CD1A|R3|R3G1	CD1d molecule	protein-coding	0.005682	0.378072	
chunk0119_37_1	chr22	40510643	40510842	+	0	NA	intron (NM_001282661, intron 3 of 13)	L2c|LINE|L2	-11058	NR_109965	101927257	Hs.662725	NR_109965	ENSG00000232564	MRTFA-AS1	-	MRTFA antisense RNA 1	ncRNA	0.005025	0.480000	
chunk0189_231_1	chr8	24457083	24458438	+	0	NA	intron (NM_003817, intron 3 of 21)	L1ME2z|LINE|L1	16764	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.005166	0.347345	
chunk0126_17_1	chr3	73542152	73542563	+	0	NA	intron (NR_121660, intron 1 of 1)	intron (NR_121660, intron 1 of 1)	19321	NM_001303140	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.009732	0.434466	
chunk0027_413_1	chr10	80615696	80616210	+	0	NA	intron (NM_207372, intron 6 of 6)	intron (NM_207372, intron 6 of 6)	75134	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.009728	0.390291	217(TAGAACATGGTGTCAT,-,0.00)
chunk0165_55_1	chr6	30617247	30617446	+	0	NA	promoter-TSS (NM_014046)	promoter-TSS (NM_014046)	-39	NM_002714	5514	Hs.106019	NM_002714	ENSG00000204569	PPP1R10	CAT53|FB19|PNUTS|PP1R10|R111|p99	protein phosphatase 1 regulatory subunit 10	protein-coding	0.090452	0.585000	
chunk0017_38_1	chr1	205121852	205122466	+	0	NA	promoter-TSS (NM_005057)	promoter-TSS (NM_005057)	-137	NM_005057	5929	Hs.519230	NM_005057	ENSG00000117222	RBBP5	RBQ3|SWD1	RB binding protein 5, histone lysine methyltransferase complex subunit	protein-coding	0.063518	0.531707	
chunk0026_227_1	chr10	65120043	65120462	+	0	NA	Intergenic	L1PA17|LINE|L1	294724	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.004773	0.302381	
chunk0106_392_1	chr2	207664150	207664558	+	0	NA	Intergenic	Intergenic	-39023	NM_001127395	151194	Hs.664764	NM_145280	ENSG00000144401	METTL21A	FAM119A|HCA557b|HSPA-KMT	methyltransferase like 21A	protein-coding	0.007353	0.361858	
chunk0148_24_1	chr5	600293	600858	+	0	NA	Intergenic	L1PA16|LINE|L1	11635	NR_103444	100996325	Hs.575249	NR_103444		LOC100996325	-	uncharacterized LOC100996325	ncRNA	0.026549	0.434629	
chunk0186_418_1	chr7	146491973	146492456	+	0	NA	intron (NM_014141, intron 1 of 23)	GA-rich|Low_complexity|Low_complexity	375853	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.010352	0.371901	
chunk0174_74_1	chr6	156046736	156047131	+	0	NA	Intergenic	Intergenic	100136	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.012658	0.457071	
chunk0052_418_1	chr12	131513230	131513776	+	0	NA	Intergenic	L2a|LINE|L2	166033	NR_103736	338797	Hs.592007	NM_001025466		LINC02370	-	long intergenic non-protein coding RNA 2370	ncRNA	0.007326	0.497258	
chunk0076_50_1	chr16	60984807	60985040	+	0	NA	Intergenic	Intergenic	70843	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.008584	0.380342	
chunk0197_442_1	chr8	127586074	127586490	+	0	NA	Intergenic	Intergenic	-104143	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.009615	0.477218	
chunk0155_140_1	chr5	93661843	93662757	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	-41512	NR_031754	100313887		NR_031754	ENSG00000284336	MIR2277	mir-2277	microRNA 2277	ncRNA	0.006565	0.370492	
chunk0143_201_1	chr4	113024464	113024672	+	0	NA	intron (NM_001127493, intron 2 of 46)	intron (NM_001127493, intron 2 of 46)	-25061	NM_020977	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.000000	0.344498	
chunk0141_213_1	chr4	84626559	84626962	+	0	NA	intron (NM_001263, intron 5 of 12)	L2b|LINE|L2	43856	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.017370	0.403465	
chunk0075_121_1	chr16	49733272	49733649	+	0	NA	intron (NM_001271620, intron 2 of 7)	intron (NM_001271620, intron 2 of 7)	89278	NM_015069	23090	Hs.443715	NM_015069	ENSG00000102935	ZNF423	Ebfaz|JBTS19|NPHP14|OAZ|Roaz|ZFP423|Zfp104|hOAZ	zinc finger protein 423	protein-coding	0.015915	0.394180	
chunk0160_401_1	chr5	163521006	163521632	+	0	NA	Intergenic	L1MC4|LINE|L1	15791	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.006390	0.417863	
chunk0137_344_1	chr4	25208087	25208468	+	0	NA	Intergenic	L2b|LINE|L2	-25754	NM_018323	55300	Hs.191701	NM_018323	ENSG00000038210	PI4K2B	PI4KIIB|PIK42B	phosphatidylinositol 4-kinase type 2 beta	protein-coding	0.000000	0.416230	
chunk0205_262_1	chr9	111240343	111240765	+	0	NA	Intergenic	Intergenic	30660	NR_106989	102465800		NR_106989	ENSG00000274263	MIR7702	hsa-mir-7702	microRNA 7702	ncRNA	0.004739	0.333333	
chunk0150_448_1	chr5	40649718	40650361	+	0	NA	Intergenic	MER21-int|LTR|ERVL	-29891	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.003110	0.434783	330(GGGAACACACTGTGCC,-,0.00),331(GGAACACACTGTGCCA,+,0.00)
chunk0026_44_1	chr10	60893132	60893713	+	0	NA	intron (NM_014836, intron 4 of 10)	intron (NM_014836, intron 4 of 10)	50853	NM_014836	9886	Hs.737374	NM_014836	ENSG00000072422	RHOBTB1	-	Rho related BTB domain containing 1	protein-coding	0.006885	0.365979	
chunk0056_232_1	chr13	88732398	88733028	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	191884	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.006349	0.340729	297(CAGAACAGATTGTACA,-,0.00),298(AGAACAGATTGTACAA,+,0.00)
chunk0196_454_1	chr8	116675119	116675390	+	0	NA	intron (NM_003756, intron 2 of 7)	Charlie25|DNA|hAT-Charlie	80569	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.003690	0.356618	
chunk0148_427_1	chr5	15350214	15350826	+	0	NA	Intergenic	Intergenic	-83960	NR_109944	101929454	Hs.453273	NR_109944		LINC02149	-	long intergenic non-protein coding RNA 2149	ncRNA	0.004902	0.381729	
chunk0171_199_1	chr6	125717961	125718594	+	0	NA	non-coding (NR_038906, exon 4 of 4)	non-coding (NR_038906, exon 4 of 4)	-31309	NM_012259	23493	Hs.144287	NM_012259	ENSG00000135547	HEY2	CHF1|GRIDLOCK|GRL|HERP1|HESR2|HRT2|bHLHb32	hes related family bHLH transcription factor with YRPW motif 2	protein-coding	0.006319	0.397476	
chunk0034_225_1	chr11	33168744	33169051	+	0	NA	intron (NR_034027, intron 1 of 3)	intron (NR_034027, intron 1 of 3)	7240	NR_034027	338739	Hs.423476	NR_034027	ENSG00000247151	CSTF3-DT	CSTF3-AS1	CSTF3 divergent transcript	ncRNA	0.009772	0.353896	
chunk0195_350_1	chr8	99611356	99611647	+	0	NA	intron (NM_152564, intron 33 of 61)	MIR|SINE|MIR	-74640	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.003436	0.284247	
chunk0136_352_1	chr3	195860367	195860916	+	0	NA	Intergenic	Intergenic	21754	NR_106887	102465977		NR_106887	ENSG00000276489	MIR6829	hsa-mir-6829	microRNA 6829	ncRNA	0.016393	0.490909	
chunk0196_328_1	chr8	112026506	112027116	+	0	NA	Intergenic	Intergenic	-616682	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.006557	0.337152	
chunk0158_383_1	chr5	134466156	134466985	+	0	NA	Intergenic	Intergenic	-31523	NR_105044	102546229		NR_105044		LOC102546229	-	uncharacterized LOC102546229	ncRNA	0.034982	0.622892	386(AAGGACGGGGTGTCCT,-,0.00),387(AGGACGGGGTGTCCTG,+,0.00)
chunk0072_8_1	chr16	335327	335572	+	0	NA	intron (NM_003502, intron 2 of 10)	(ACACAGC)n|Simple_repeat|Simple_repeat	17227	NM_181050	8312	Hs.592082	NM_003502	ENSG00000103126	AXIN1	AXIN|PPP1R49	axin 1	protein-coding	0.016327	0.491870	
chunk0165_184_1	chr6	34415196	34415425	+	0	NA	intron (NM_001202470, intron 5 of 8)	intron (NM_001202470, intron 5 of 8)	10731	NM_001203245	6204	Hs.406620	NM_001014	ENSG00000124614	RPS10	DBA9|S10	ribosomal protein S10	protein-coding	0.008734	0.430435	
chunk0102_90_1	chr2	143827583	143827994	+	0	NA	Intergenic	L2a|LINE|L2	-109279	NR_110237	101928386	Hs.668251	NR_110237	ENSG00000232377	LOC101928386	-	uncharacterized LOC101928386	ncRNA	0.002433	0.310680	
chunk0182_232_1	chr7	96595967	96596413	+	0	NA	Intergenic	Intergenic	68148	NR_038948	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.002242	0.436242	
chunk0079_402_1	chr17	19402020	19402715	+	0	NA	Intergenic	LTR54|LTR|ERV1	-8811	NM_007148	7732	Hs.189482	NM_007148	ENSG00000128482	RNF112	BFP|ZNF179	ring finger protein 112	protein-coding	0.002878	0.425287	
chunk0073_69_1	chr16	3678076	3678447	+	0	NA	intron (NM_001272049, intron 4 of 16)	MER3|DNA|hAT-Charlie	25322	NM_005223	1773	Hs.629638	NM_005223	ENSG00000213918	DNASE1	DNL1|DRNI	deoxyribonuclease 1	protein-coding	0.037736	0.491935	221(AGGAGCACAATGTCCC,-,0.00),222(GGAGCACAATGTCCCC,+,0.00)
chunk0176_331_1	chr7	17275873	17276661	+	0	NA	Intergenic	Intergenic	-22385	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.003807	0.389100	613(AGGCCCACACTGTGCC,-,0.00),614(GGCCCACACTGTGCCT,+,0.00)
chunk0040_289_1	chr11	117019438	117019637	+	0	NA	intron (NM_025164, intron 1 of 23)	intron (NM_025164, intron 1 of 23)	78878	NM_001281748	23387	Hs.167451	NM_025164	ENSG00000160584	SIK3	L19|QSK|SEMDK|SIK-3	SIK family kinase 3	protein-coding	0.005025	0.330000	
chunk0056_374_1	chr13	93118166	93118629	+	0	NA	Intergenic	Intergenic	73056	NR_126360	104326053	Hs.578064	NR_126360		LINC00363	TCONS_00021586	long intergenic non-protein coding RNA 363	ncRNA	0.006479	0.433190	
chunk0017_206_1	chr1	207812268	207812538	+	0	NA	Intergenic	Intergenic	-5976	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.022222	0.568266	
chunk0104_282_1	chr2	178271923	178272374	+	0	NA	intron (NM_001201482, intron 1 of 23)	intron (NM_001201482, intron 1 of 23)	-48096	NM_145739	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.004435	0.411504	202(AAGAACTTACTGTTCA,-,0.00),203(AGAACTTACTGTTCAG,+,0.00)
chunk0031_126_1	chr10	124823131	124823743	+	0	NA	intron (NM_032182, intron 4 of 8)	intron (NM_032182, intron 4 of 8)	21652	NM_032182	23172	Hs.280695	NM_032182	ENSG00000165660	ABRAXAS2	ABRO1|FAM175B|KIAA0157	abraxas 2, BRISC complex subunit	protein-coding	0.008170	0.362153	
chunk0187_210_1	chr7	151917866	151918782	+	0	NA	Intergenic	Intergenic	-38055	NR_033169	168391	Hs.647077	NM_145292	ENSG00000106648	GALNTL5	GALNACT19|GALNT15|GalNAc-T5L	polypeptide N-acetylgalactosaminyltransferase like 5	protein-coding	0.014192	0.482007	
chunk0097_172_1	chr2	49725120	49725319	+	0	NA	Intergenic	Intergenic	-570692	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.015075	0.415000	
chunk0208_265_1	chrX	21411742	21412393	+	0	NA	intron (NM_014927, intron 1 of 21)	intron (NM_014927, intron 1 of 21)	37649	NM_001168648	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.006144	0.403374	333(AAGAACAGGCAGTTAT,-,0.00)
chunk0013_325_1	chr1	171555718	171556165	+	0	NA	intron (NM_015172, intron 18 of 33)	L1PA6|LINE|L1	70414	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.008949	0.549107	
chunk0107_433_1	chr2	224846870	224847273	+	0	NA	intron (NM_014689, intron 19 of 55)	intron (NM_014689, intron 19 of 55)	99994	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.007444	0.366337	
chunk0011_9_1	chr1	125176301	125176607	+	0	NA	Intergenic	Intergenic	3657342	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.049020	0.358306	
chunk0067_369_1	chr15	48865290	48865489	+	0	NA	intron (NM_203349, intron 6 of 11)	intron (NM_203349, intron 6 of 11)	-12704	NM_014335	23741	Hs.255973	NM_014335	ENSG00000255302	EID1	C15orf3|CRI1|EID-1|IRO45620|PNAS-22|PTD014|RBP21	EP300 interacting inhibitor of differentiation 1	protein-coding	0.005025	0.375000	18(GAGAACACAGTGTCTT,-,0.00),19(AGAACACAGTGTCTTC,+,0.00)
chunk0160_8_1	chr5	148966146	148966893	+	0	NA	Intergenic	Intergenic	95890	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.008032	0.489305	393(TGGGACATTCTGTCCT,-,0.00),394(GGGACATTCTGTCCTT,+,0.00)
chunk0149_214_1	chr5	21814168	21814531	+	0	NA	intron (NM_004061, intron 9 of 14)	intron (NM_004061, intron 9 of 14)	-70105	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.002755	0.236264	
chunk0121_121_1	chr3	17481061	17481546	+	0	NA	intron (NM_014744, intron 3 of 21)	MER52A|LTR|ERV1	218717	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.024742	0.578189	325(AGGCACAAGCAGTACT,-,0.00),326(GGCACAAGCAGTACTC,+,0.00)
chunk0182_374_1	chr7	100022680	100022884	+	0	NA	intron (NM_001287054, intron 2 of 7)	MIRb|SINE|MIR	7210	NM_001287055	7586	Hs.615360	NM_003439	ENSG00000106261	ZKSCAN1	KOX18|PHZ-37|ZNF139|ZNF36|ZSCAN33	zinc finger with KRAB and SCAN domains 1	protein-coding	0.014706	0.487805	
chunk0173_320_1	chr6	148659104	148659753	+	0	NA	Intergenic	L1MA8|LINE|L1	-87707	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.004622	0.307692	
chunk0163_212_1	chr6	12033634	12034029	+	0	NA	intron (NM_002114, intron 2 of 8)	intron (NM_002114, intron 2 of 8)	21340	NM_002114	3096	Hs.567284	NM_002114	ENSG00000095951	HIVEP1	CIRIP|CRYBP1|GAAP|MBP-1|PRDII-BF1|Schnurri-1|ZAS1|ZNF40|ZNF40A	human immunodeficiency virus type I enhancer binding protein 1	protein-coding	0.005063	0.338384	
chunk0019_391_1	chr1	230227817	230228284	+	0	NA	intron (NM_001291866, intron 3 of 15)	L1ME3Cz|LINE|L1	160855	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.006424	0.352564	
chunk0140_412_1	chr4	75741019	75741254	+	0	NA	intron (NM_001290049, intron 1 of 25)	Tigger3b|DNA|TcMar-Tigger	16614	NM_001290049	8615	Hs.744877	NM_003715	ENSG00000138768	USO1	P115|TAP|VDP	USO1 vesicle transport factor	protein-coding	0.004255	0.360169	
chunk0053_341_1	chr13	34697943	34698304	+	0	NA	Intergenic	Intergenic	-57438	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.005540	0.359116	
chunk0004_419_1	chr1	52512360	52512932	+	0	NA	intron (NM_001009881, intron 3 of 29)	intron (NM_001009881, intron 3 of 29)	40444	NM_015269	23318	Hs.655407	NM_015269	ENSG00000134744	TUT4	PAPD3|TENT3A|ZCCHC11	terminal uridylyl transferase 4	protein-coding	0.003497	0.322862	
chunk0167_58_1	chr6	55895924	55896369	+	0	NA	Intergenic	Intergenic	-20569	NM_021073	653	Hs.296648	NM_021073	ENSG00000112175	BMP5	-	bone morphogenetic protein 5	protein-coding	0.006742	0.352018	
chunk0026_191_1	chr10	63629381	63629771	+	0	NA	Intergenic	Intergenic	108213	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.028205	0.473146	327(CTGAACTGCCTGTACC,-,0.00),328(TGAACTGCCTGTACCA,+,0.00)
chunk0202_319_1	chr9	78259890	78260203	+	0	NA	intron (NM_032171, intron 11 of 14)	L2a|LINE|L2	23971	NM_001098802	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.000000	0.334395	
chunk0015_35_1	chr1	184453484	184453881	+	0	NA	intron (NM_030806, intron 1 of 5)	intron (NM_030806, intron 1 of 5)	66666	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.005038	0.346734	
chunk0063_308_1	chr14	84840525	84840752	+	0	NA	Intergenic	Intergenic	-553241	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.004405	0.328947	
chunk0042_442_1	chr12	12397922	12398519	+	0	NA	intron (NM_058169, intron 2 of 3)	intron (NM_058169, intron 2 of 3)	41141	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.008375	0.387960	
chunk0046_159_1	chr12	58341705	58342118	+	0	NA	Intergenic	Intergenic	-249791	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.004843	0.376812	
chunk0162_459_1	chr5	180873368	180873982	+	0	NA	Intergenic	Intergenic	-12389	NM_001172638	643836	Hs.509227	NM_152283	ENSG00000196670	ZFP62	ZET|ZNF755	ZFP62 zinc finger protein	protein-coding	0.014658	0.512195	
chunk0075_297_1	chr16	54285992	54286191	+	0	NA	5' UTR (NM_024336, exon 1 of 4)	5' UTR (NM_024336, exon 1 of 4)	375	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.145729	0.785000	51(AAGGACATGGTGGCCC,-,0.00)
chunk0149_171_1	chr5	20651320	20651655	+	0	NA	Intergenic	L1PA8A|LINE|L1	-75614	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.005970	0.336310	
chunk0134_10_1	chr3	175397584	175398198	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	28351	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.003257	0.367480	103(GGGTACACCGTGTTTT,-,0.00),104(GGTACACCGTGTTTTA,+,0.00)
chunk0136_196_1	chr4	6917484	6918001	+	0	NA	intron (NM_020773, intron 1 of 13)	intron (NM_020773, intron 1 of 13)	7974	NM_020773	57533	Hs.518611	NM_020773	ENSG00000132405	TBC1D14	-	TBC1 domain family member 14	protein-coding	0.030948	0.555985	
chunk0040_429_1	chr11	121384807	121385388	+	0	NA	Intergenic	Intergenic	-67106	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.003442	0.403780	258(TAGAACATAAAGTTCC,-,0.00),259(AGAACATAAAGTTCCA,+,0.00)
chunk0054_417_1	chr13	50905137	50905560	+	0	NA	intron (NR_046552, intron 1 of 2)	L2b|LINE|L2	-4330	NM_001142279	79621	Hs.306291	NM_024570	ENSG00000136104	RNASEH2B	AGS2|DLEU8	ribonuclease H2 subunit B	protein-coding	0.007092	0.412736	
chunk0186_162_1	chr7	139270465	139270727	+	0	NA	intron (NM_173569, intron 8 of 17)	L1ME3D|LINE|L1	39111	NM_173569	254048	Hs.153458	NM_173569	ENSG00000157741	UBN2	-	ubinuclein 2	protein-coding	0.011450	0.456274	129(GGGTACACAGTGTTCC,-,0.00),130(GGTACACAGTGTTCCA,+,0.00)
chunk0091_398_1	chr19	16391919	16392138	+	0	NA	intron (NR_047665, intron 19 of 22)	intron (NR_047665, intron 19 of 22)	67188	NM_016270	10365	Hs.685136	NM_016270	ENSG00000127528	KLF2	LKLF	Kruppel like factor 2	protein-coding	0.004566	0.536364	
chunk0074_83_1	chr16	21638696	21638928	+	0	NA	intron (NM_001288660, intron 4 of 4)	L2c|LINE|L2	13854	NM_005849	10261	Hs.530902	NM_005849	ENSG00000140749	IGSF6	DORA	immunoglobulin superfamily member 6	protein-coding	0.008621	0.463519	77(GGGAACAGCATGTGCA,-,0.00),78(GGAACAGCATGTGCAA,+,0.00)
chunk0021_339_1	chr1	245997927	245998249	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	419324	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.009317	0.510836	
chunk0176_112_1	chr7	11858650	11858951	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-26602	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.013289	0.304636	
chunk0125_5_1	chr3	61739305	61739855	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	178011	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.000000	0.352087	
chunk0041_316_1	chr11	130089410	130089638	+	0	NA	intron (NM_001243299, intron 1 of 16)	intron (NM_001243299, intron 1 of 16)	18956	NM_001243299	334	Hs.370247	NM_001642	ENSG00000084234	APLP2	APLP-2|APPH|APPL2|CDEBP	amyloid beta precursor like protein 2	protein-coding	0.008772	0.458515	
chunk0016_90_1	chr1	194813042	194813503	+	0	NA	Intergenic	Intergenic	1508527	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.002169	0.320346	
chunk0200_210_1	chr9	20553646	20553944	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	-51453	NR_039685	100616441		NR_039685	ENSG00000264941	MIR4474	-	microRNA 4474	ncRNA	0.000000	0.307692	
chunk0069_57_1	chr15	60758171	60758727	+	0	NA	intron (NM_134261, intron 1 of 10)	CR1_Mam|LINE|CR1	76880	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.010791	0.441652	318(TAGGACATCCTGTCCA,-,0.00),319(AGGACATCCTGTCCAT,+,0.00)
chunk0148_287_1	chr5	11733432	11733905	+	0	NA	intron (NR_109988, intron 1 of 21)	intron (NR_109988, intron 1 of 21)	-144751	NM_001288715	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.002114	0.343882	
chunk0198_68_1	chr8	129939844	129940068	+	0	NA	promoter-TSS (NM_016623)	promoter-TSS (NM_016623)	-84	NM_016623	51571	Hs.126941	NM_016623	ENSG00000153310	FAM49B	BM-009|L1	family with sequence similarity 49 member B	protein-coding	0.102679	0.711111	
chunk0052_162_1	chr13	23969676	23970155	+	0	NA	Intergenic	L1ME4b|LINE|L1	-9711	NR_104595	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.008351	0.379167	
chunk0017_347_1	chr1	211785947	211786253	+	0	NA	intron (NM_014873, intron 4 of 7)	intron (NM_014873, intron 4 of 7)	44672	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.006536	0.397394	
chunk0195_201_1	chr8	96859917	96860582	+	0	NA	intron (NM_016134, intron 3 of 7)	intron (NM_016134, intron 3 of 7)	215022	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.003008	0.372372	
chunk0101_319_1	chr2	135576273	135576756	+	0	NA	intron (NM_001282799, intron 1 of 22)	L1MB8|LINE|L1	-9809	NM_001282800	23518	Hs.412462	NM_015361	ENSG00000048991	R3HDM1	R3HDM	R3H domain containing 1	protein-coding	0.006211	0.347107	
chunk0049_441_1	chr12	98535490	98535691	+	0	NA	TTS (NM_003276)	TTS (NM_003276)	-19364	NR_027157	100128191	Hs.594042	NR_027157	ENSG00000257167	TMPO-AS1	-	TMPO antisense RNA 1	ncRNA	0.000000	0.326733	158(AGAAACATGTTGTTCT,-,0.00),159(GAAACATGTTGTTCTG,+,0.00)
chunk0208_38_1	chrX	11367660	11368595	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-49441	NR_049865	100847063		NR_049865	ENSG00000263652	MIR548AX	-	microRNA 548ax	ncRNA	0.008556	0.410256	627(ATGCACACATTGTACT,-,0.00),628(TGCACACATTGTACTT,+,0.00)
chunk0058_286_1	chr14	26727429	26727872	+	0	NA	Intergenic	Charlie15b|DNA|hAT-Charlie	-81698	NR_110557	102724890	Hs.569381	NR_110556	ENSG00000257185	LINC02293	-	long intergenic non-protein coding RNA 2293	ncRNA	0.004515	0.308559	
chunk0121_297_1	chr3	23823733	23823970	+	0	NA	intron (NM_001202476, intron 2 of 4)	intron (NM_001202476, intron 2 of 4)	13408	NM_001202476	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.012658	0.394958	
chunk0001_322_1	chr1	9446545	9447175	+	0	NA	Intergenic	Intergenic	-17864	NR_104622	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.011111	0.494453	
chunk0117_303_1	chr22	24532053	24532453	+	0	NA	Intergenic	MER89-int|LTR|ERV1	23054	NM_001284254	83606	Hs.9850	NM_031444	ENSG00000138867	GUCD1	C22orf13|LLN4	guanylyl cyclase domain containing 1	protein-coding	0.007500	0.466334	
chunk0128_104_1	chr3	106065734	106066234	+	0	NA	Intergenic	L1MA1|LINE|L1	-196941	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.325349	
chunk0103_78_1	chr2	160575973	160576638	+	0	NA	Intergenic	X1_LINE|LINE|CR1	-82498	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.001504	0.415916	
chunk0124_439_1	chr3	61348753	61349154	+	0	NA	Intergenic	LTR33|LTR|ERVL	-97494	NM_001166243	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.004988	0.485075	
chunk0116_75_1	chr21	34674403	34674796	+	0	NA	intron (NM_053277, intron 1 of 5)	intron (NM_053277, intron 1 of 5)	5436	NM_053277	54102	Hs.473695	NM_053277	ENSG00000159212	CLIC6	CLIC1L	chloride intracellular channel 6	protein-coding	0.000000	0.281726	
chunk0100_426_1	chr2	120135842	120136318	+	0	NA	intron (NM_020909, intron 18 of 24)	L1MA3|LINE|L1	87328	NM_024121	79134	Hs.376722	NM_024121	ENSG00000226479	TMEM185B	FAM11B	transmembrane protein 185B	protein-coding	0.004202	0.308176	
chunk0193_460_1	chr8	81351356	81351934	+	0	NA	Intergenic	Intergenic	71162	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.000000	0.376511	
chunk0144_416_1	chr4	140450250	140450819	+	0	NA	intron (NM_001277353, intron 10 of 10)	MIR|SINE|MIR	-22873	NM_004362	1047	Hs.86368	NM_004362	ENSG00000153132	CLGN	-	calmegin	protein-coding	0.007030	0.357895	
chunk0043_138_1	chr12	16034171	16034432	+	0	NA	intron (NM_015954, intron 7 of 8)	L2b|LINE|L2	123129	NM_001300779	51071	Hs.39429	NM_015954	ENSG00000023697	DERA	CGI-26|DEOC	deoxyribose-phosphate aldolase	protein-coding	0.000000	0.416031	
chunk0027_115_1	chr10	74121840	74122176	+	0	NA	3' UTR (NM_012095, exon 9 of 9)	3' UTR (NM_012095, exon 9 of 9)	29060	NM_012095	26985	Hs.500104	NM_012095	ENSG00000185009	AP3M1	-	adaptor related protein complex 3 subunit mu 1	protein-coding	0.008929	0.367953	
chunk0159_450_1	chr5	148825966	148826235	+	0	NA	promoter-TSS (NM_000024)	promoter-TSS (NM_000024)	-493	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.044610	0.551852	
chunk0065_230_1	chr14	101005557	101006476	+	0	NA	Intergenic	Intergenic	12780	NR_003224	767612		NR_003224	ENSG00000200089	SNORD114-31	14q(II-31)	small nucleolar RNA, C/D box 114-31	snoRNA	0.019587	0.545652	
chunk0167_154_1	chr6	62620379	62621011	+	0	NA	Intergenic	L1ME1|LINE|L1	-334500	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.006329	0.328594	
chunk0071_5_1	chr15	78696408	78696860	+	0	NA	Intergenic	L1MA2|LINE|L1	-55389	NM_001256567	1143	Hs.624178	NM_000750	ENSG00000117971	CHRNB4	-	cholinergic receptor nicotinic beta 4 subunit	protein-coding	0.000000	0.350993	
chunk0131_385_1	chr3	152432116	152432367	+	0	NA	intron (NM_207294, intron 2 of 6)	intron (NM_207294, intron 2 of 6)	-91251	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.000000	0.341270	
chunk0001_240_1	chr1	8266589	8267116	+	0	NA	Intergenic	LTR24C|LTR|ERV1	-51233	NM_001080397	50651	Hs.463036	NM_001080397	ENSG00000162426	SLC45A1	DNB5|IDDNPF	solute carrier family 45 member 1	protein-coding	0.007590	0.348485	
chunk0094_255_1	chr2	7361045	7361335	+	0	NA	Intergenic	Intergenic	-60071	NR_038432	100506274	Hs.177930	NR_038432	ENSG00000229727	LOC100506274	-	uncharacterized LOC100506274	ncRNA	0.010345	0.463918	
chunk0079_408_1	chr17	19551531	19551815	+	0	NA	intron (NM_018242, intron 6 of 16)	intron (NM_018242, intron 6 of 16)	-5887	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.007042	0.487719	
chunk0182_238_1	chr7	96794140	96795106	+	0	NA	Intergenic	Intergenic	-84732	NM_006304	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.006211	0.374354	
chunk0083_334_1	chr17	70191235	70191550	+	0	NA	Intergenic	Intergenic	21857	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.006349	0.401899	
chunk0136_424_1	chr3	197555854	197556053	+	0	NA	promoter-TSS (NM_004051)	promoter-TSS (NM_004051)	34	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.130653	0.770000	
chunk0199_188_1	chr9	4696008	4696436	+	0	NA	intron (NM_017913, intron 3 of 6)	intron (NM_017913, intron 3 of 6)	16669	NM_017913	55664	Hs.666439	NM_017913	ENSG00000106993	CDC37L1	CDC37B|HARC	cell division cycle 37 like 1	protein-coding	0.004673	0.431235	
chunk0135_320_1	chr3	190044900	190045378	+	0	NA	intron (NM_001134418, intron 1 of 14)	L2a|LINE|L2	-75825	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.006276	0.375783	
chunk0179_56_1	chr7	43628901	43629505	+	0	NA	Intergenic	L1MDa|LINE|L1	46110	NM_004760	9263	Hs.709489	NM_004760	ENSG00000164543	STK17A	DRAK1	serine/threonine kinase 17a	protein-coding	0.006623	0.350413	
chunk0085_281_1	chr18	7904417	7904831	+	0	NA	intron (NM_001105244, intron 3 of 32)	L1MD2|LINE|L1	337308	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.004831	0.366265	
chunk0078_72_1	chr17	1590184	1590657	+	0	NA	intron (NM_001284498, intron 9 of 14)	intron (NM_001284498, intron 9 of 14)	14614	NM_001284499	124935	Hs.160550	NM_152346	ENSG00000167703	SLC43A2	LAT4	solute carrier family 43 member 2	protein-coding	0.023256	0.559072	
chunk0096_319_1	chr2	33291384	33291663	+	0	NA	intron (NM_000627, intron 15 of 29)	intron (NM_000627, intron 15 of 29)	-126993	NR_039628	100616136		NR_039628	ENSG00000283591	MIR4430	-	microRNA 4430	ncRNA	0.003584	0.392857	
chunk0136_358_1	chr3	195907764	195908148	+	0	NA	intron (NM_005781, intron 1 of 14)	intron (NM_005781, intron 1 of 14)	1053	NM_005781	10188	Hs.518513	NM_005781	ENSG00000061938	TNK2	ACK|ACK-1|ACK1|p21cdc42Hs	tyrosine kinase non receptor 2	protein-coding	0.033854	0.594805	
chunk0154_446_1	chr5	90415842	90416146	+	0	NA	Intergenic	LTR16|LTR|ERVL	5994	NR_105024	731157	Hs.551062	NR_105024	ENSG00000255647	LOC731157	-	uncharacterized LOC731157	ncRNA	0.009868	0.383607	
chunk0130_154_1	chr3	132347217	132347476	+	0	NA	intron (NM_001099, intron 7 of 9)	intron (NM_001099, intron 7 of 9)	29979	NM_001134194	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.003861	0.384615	
chunk0005_143_1	chr1	57639259	57639605	+	0	NA	intron (NM_021080, intron 3 of 16)	intron (NM_021080, intron 3 of 16)	-221111	NR_104362	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.002890	0.302594	
chunk0189_51_1	chr8	20015212	20015681	+	0	NA	Intergenic	Intergenic	76375	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.004264	0.334043	
chunk0210_124_1	chrX	73944138	73944361	+	0	NA	promoter-TSS (NR_024582)	promoter-TSS (NR_024582)	-75	NR_024582	554203	Hs.648316	NR_024582	ENSG00000225470	JPX	DCBALD06|ENOX|LINC00183|NCRNA00183	JPX transcript, XIST activator	ncRNA	0.089686	0.669643	
chunk0144_403_1	chr4	140305083	140305659	+	0	NA	intron (NR_033939, intron 2 of 4)	intron (NR_033939, intron 2 of 4)	-38072	NM_001153635	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.005208	0.421144	
chunk0144_166_1	chr4	131791218	131791417	+	0	NA	non-coding (NR_125884, exon 3 of 3)	non-coding (NR_125884, exon 3 of 3)	26479	NR_125883	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.005025	0.325000	
chunk0078_13_1	chr17	410075	410385	+	0	NA	promoter-TSS (NM_001013672)	promoter-TSS (NM_001013672)	-97	NM_001013672	400566	Hs.499607	NM_001013672	ENSG00000187624	C17orf97	CK20|LIAT1	chromosome 17 open reading frame 97	protein-coding	0.116129	0.655949	
chunk0196_240_1	chr8	108248186	108248969	+	0	NA	intron (NM_001568, intron 1 of 12)	CpG	153	NM_001568	3646	Hs.405590	NM_001568	ENSG00000104408	EIF3E	EIF3-P48|EIF3S6|INT6|eIF3-p46	eukaryotic translation initiation factor 3 subunit E	protein-coding	0.057471	0.520408	
chunk0007_68_1	chr1	78280730	78281113	+	0	NA	intron (NR_027310, intron 3 of 5)	intron (NR_027310, intron 3 of 5)	51322	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.005222	0.356771	224(AAATACAGCATGTCCT,-,0.00),225(AATACAGCATGTCCTA,+,0.00)
chunk0135_242_1	chr3	188691812	188692734	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	3492	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.005423	0.413868	19(GAGCACATTAAGTTCT,-,0.00),20(AGCACATTAAGTTCTT,+,0.00)
chunk0074_25_1	chr16	20388883	20389105	+	0	NA	intron (NM_174924, intron 2 of 11)	intron (NM_174924, intron 2 of 11)	15717	NM_174924	204474	Hs.376025	NM_174924	ENSG00000169340	PDILT	PDIA7	protein disulfide isomerase like, testis expressed	protein-coding	0.004505	0.426009	
chunk0091_156_1	chr19	7428046	7428462	+	0	NA	intron (NM_015318, intron 1 of 20)	intron (NM_015318, intron 1 of 20)	-11434	NM_001130955	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.016827	0.434053	
chunk0048_75_1	chr12	78895029	78895597	+	0	NA	intron (NM_001291901, intron 1 of 9)	intron (NM_001291901, intron 1 of 9)	30644	NM_001291901	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.001761	0.235501	
chunk0009_155_1	chr1	104991533	104992112	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	627113	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.006908	0.325862	224(CAGTACATACTGTACT,-,0.00),225(AGTACATACTGTACTA,+,0.00)
chunk0014_397_1	chr1	182887552	182888098	+	0	NA	non-coding (NR_033302, exon 29 of 29)	non-coding (NR_033302, exon 29 of 29)	48521	NM_001357	1660	Hs.191518	NM_001357	ENSG00000135829	DHX9	DDX9|LKP|NDH2|NDHII|RHA	DExH-box helicase 9	protein-coding	0.010989	0.316271	
chunk0117_316_1	chr22	24808912	24809118	+	0	NA	intron (NM_001039948, intron 2 of 25)	MIRb|SINE|MIR	2794	NM_001098498	129049	Hs.474397	NM_133454	ENSG00000167037	SGSM1	RUTBC2	small G protein signaling modulator 1	protein-coding	0.009709	0.473430	91(GAGAACACTGTGGCCC,-,0.00),92(AGAACACTGTGGCCCA,+,0.00)
chunk0087_300_1	chr18	39267962	39268311	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	354039	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.005731	0.297143	
chunk0023_385_1	chr10	30609372	30609712	+	0	NA	Intergenic	Intergenic	20176	NM_183058	119180	Hs.522610	NM_183058	ENSG00000151033	LYZL2	LYZD2	lysozyme like 2	protein-coding	0.000000	0.466276	
chunk0165_296_1	chr6	36558003	36558341	+	0	NA	Intergenic	L1ME4b|LINE|L1	-10656	NM_007271	11329	Hs.409578	NM_007271	ENSG00000112079	STK38	NDR|NDR1	serine/threonine kinase 38	protein-coding	0.005917	0.330383	
chunk0104_288_1	chr2	178363377	178363637	+	0	NA	intron (NM_001201482, intron 13 of 23)	intron (NM_001201482, intron 13 of 23)	43263	NM_145739	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.015385	0.513410	
chunk0141_347_1	chr4	87530858	87531170	+	0	NA	Intergenic	Intergenic	-1511	NM_001291976	8404	Hs.62886	NM_004684	ENSG00000152583	SPARCL1	MAST 9|MAST9|PIG33|SC1	SPARC like 1	protein-coding	0.012821	0.479233	
chunk0090_3_1	chr19	296082	296407	+	0	NA	Intergenic	Intergenic	-4809	NM_177526	8612	Hs.465506	NM_003712	ENSG00000141934	PLPP2	LPP2|PAP-2c|PAP2-g|PPAP2C	phospholipid phosphatase 2	protein-coding	0.015385	0.570552	
chunk0092_9_1	chr19	18506880	18507476	+	0	NA	intron (NM_006532, intron 1 of 11)	intron (NM_006532, intron 1 of 11)	14949	NM_006532	8178	Hs.515260	NM_006532	ENSG00000105656	ELL	C19orf17|ELL1|MEN|PPP1R68	elongation factor for RNA polymerase II	protein-coding	0.016779	0.551089	194(CAGCACTGGCTGTCCC,-,0.00),195(AGCACTGGCTGTCCCC,+,0.00),309(AGGAACACGCTCTTCT,-,0.00),310(GGAACACGCTCTTCTA,+,0.00),358(CTGCACAGTCTGTGCC,-,0.00),359(TGCACAGTCTGTGCCT,+,0.00)
chunk0118_159_1	chr22	30392991	30393379	+	0	NA	Intergenic	Intergenic	-3756	NM_001204204	23541	Hs.335614	NM_012429	ENSG00000100003	SEC14L2	C22orf6|SPF|TAP|TAP1	SEC14 like lipid binding 2	protein-coding	0.015464	0.580977	
chunk0054_176_1	chr13	44456768	44457358	+	0	NA	intron (NM_183422, intron 1 of 2)	Tigger9b|DNA|TcMar-Tigger	17238	NM_001243798	8848	Hs.436383	NM_006022	ENSG00000102804	TSC22D1	Ptg-2|TGFB1I4|TSC22	TSC22 domain family member 1	protein-coding	0.011864	0.338409	249(AAGTACAATCTGTTCC,-,0.00),250(AGTACAATCTGTTCCA,+,0.00)
chunk0054_167_1	chr13	44310836	44311504	+	0	NA	Intergenic	Intergenic	-62672	NM_001010897	387923	Hs.377972	NM_001010897	ENSG00000151778	SERP2	C13orf21|bA269C23.1	stress associated endoplasmic reticulum protein family member 2	protein-coding	0.004491	0.431988	
chunk0201_24_1	chr9	33162791	33163577	+	0	NA	intron (NM_001497, intron 1 of 5)	intron (NM_001497, intron 1 of 5)	-3764	NR_108109	101929639	Hs.545818	NR_108108	ENSG00000233554	B4GALT1-AS1	-	B4GALT1 antisense RNA 1	ncRNA	0.012723	0.518424	335(AAGTACACTCTGTCCT,-,0.00),336(AGTACACTCTGTCCTG,+,0.00)
chunk0051_346_1	chr12	120397998	120398724	+	0	NA	Intergenic	L2a|LINE|L2	-29181	NM_002442	4440	Hs.158311	NM_002442	ENSG00000135097	MSI1	-	musashi RNA binding protein 1	protein-coding	0.022039	0.550206	
chunk0155_109_1	chr5	92886371	92886737	+	0	NA	Intergenic	Intergenic	684789	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.008197	0.367847	
chunk0110_60_1	chr20	10848748	10848947	+	0	NA	Intergenic	Intergenic	60425	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.005025	0.435000	
chunk0036_130_1	chr11	61841734	61842018	+	0	NA	intron (NM_004265, intron 4 of 11)	intron (NM_004265, intron 4 of 11)	13843	NM_004265	9415	Hs.502745	NM_004265	ENSG00000134824	FADS2	D6D|DES6|FADSD6|LLCDL2|SLL0262|TU13	fatty acid desaturase 2	protein-coding	0.010563	0.445614	
chunk0095_132_1	chr2	16661471	16661844	+	0	NA	intron (NM_030797, intron 1 of 11)	intron (NM_030797, intron 1 of 11)	4209	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.010724	0.414439	
chunk0099_269_1	chr2	98122497	98122696	+	0	NA	intron (NM_144992, intron 5 of 27)	intron (NM_144992, intron 5 of 27)	35464	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.000000	0.400000	
chunk0212_181_1	chrX	132842695	132843245	+	0	NA	intron (NM_001077188, intron 3 of 5)	intron (NM_001077188, intron 3 of 5)	118425	NM_001077188	90161	Hs.385956	NM_147175	ENSG00000171004	HS6ST2	MRXSPM	heparan sulfate 6-O-sulfotransferase 2	protein-coding	0.005455	0.417423	
chunk0150_442_1	chr5	40552129	40552596	+	0	NA	Intergenic	Intergenic	-127568	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.010707	0.425214	
chunk0051_275_1	chr12	118098386	118098839	+	0	NA	intron (NM_019086, intron 1 of 8)	L2b|LINE|L2	5393	NM_019086	54621	Hs.187624	NM_019086	ENSG00000176834	VSIG10	-	V-set and immunoglobulin domain containing 10	protein-coding	0.006623	0.484581	
chunk0120_23_1	chr3	1991828	1992381	+	0	NA	Intergenic	Intergenic	-106762	NM_175607	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.005425	0.380866	
chunk0205_268_1	chr9	111443421	111443975	+	0	NA	intron (NM_001080398, intron 5 of 50)	intron (NM_001080398, intron 5 of 50)	41047	NM_001080398	23392	Hs.368255	NM_001080398	ENSG00000136813	ECPAS	ECM29|KIAA0368	Ecm29 proteasome adaptor and scaffold	protein-coding	0.007220	0.371171	204(TGGCACACAGTGTTCC,-,0.00),205(GGCACACAGTGTTCCT,+,0.00)
chunk0088_60_1	chr18	44253307	44253701	+	0	NA	Intergenic	L1PA6|LINE|L1	278193	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.007614	0.362025	
chunk0130_58_1	chr3	129781195	129781498	+	0	NA	intron (NM_001128224, intron 3 of 5)	L2a|LINE|L2	-92614	NR_033361									0.006601	0.398026	
chunk0133_339_1	chr3	172750681	172750912	+	0	NA	5' UTR (NM_001258315, exon 1 of 25)	5' UTR (NM_001258315, exon 1 of 25)	111	NM_001258316	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.056277	0.556034	
chunk0197_448_1	chr8	127823368	127823727	+	0	NA	intron (NR_003367, intron 1 of 8)	intron (NR_003367, intron 1 of 8)	27585	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.005571	0.455556	
chunk0100_194_1	chr2	111097417	111097886	+	0	NA	TTS (NR_122074)	TTS (NR_122074)	17937	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.002132	0.391489	
chunk0148_90_1	chr5	3486047	3486858	+	0	NA	intron (NR_033898, intron 2 of 4)	L1MB5|LINE|L1	17552	NR_104618	102467075	Hs.652949	NR_104618	ENSG00000250716	LINC01017	-	long intergenic non-protein coding RNA 1017	ncRNA	0.009864	0.418719	
chunk0106_398_1	chr2	207782259	207782458	+	0	NA	Intergenic	Intergenic	-12939	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.005025	0.500000	
chunk0008_380_1	chr1	96963057	96963306	+	0	NA	Intergenic	Intergenic	-132742	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.008032	0.396000	
chunk0138_245_1	chr4	39543886	39544520	+	0	NA	intron (NR_047679, intron 2 of 4)	LTR3B|LTR|ERVK	16364	NR_047679	100885776	Hs.640769	NR_047679	ENSG00000249348	UGDH-AS1	-	UGDH antisense RNA 1	ncRNA	0.015773	0.491339	
chunk0016_287_1	chr1	200891190	200891579	+	0	NA	promoter-TSS (NM_018265)	promoter-TSS (NM_018265)	-115	NM_018265	55765	Hs.518997	NM_018265	ENSG00000163362	INAVA	C1orf106	innate immunity activator	protein-coding	0.082262	0.633333	
chunk0027_32_1	chr10	72315579	72316028	+	0	NA	Intergenic	Intergenic	39346	NM_001002762	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.006682	0.508889	
chunk0059_331_1	chr14	36861681	36862041	+	0	NA	intron (NM_030631, intron 2 of 9)	intron (NM_030631, intron 2 of 9)	90530	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.002778	0.321330	272(ATGAACAGACAGTTCT,-,0.00),273(TGAACAGACAGTTCTC,+,0.00)
chunk0116_64_1	chr21	34121922	34122424	+	0	NA	intron (NM_032476, intron 1 of 2)	MER58A|DNA|hAT-Charlie	48650	NM_032476	64968	Hs.302742	NM_032476	ENSG00000243927	MRPS6	C21orf101|MRP-S6|RPMS6|S6mt	mitochondrial ribosomal protein S6	protein-coding	0.009960	0.457256	
chunk0025_373_1	chr10	59008396	59008887	+	0	NA	Intergenic	Intergenic	9123	NR_108046	100507008	Hs.170953	NR_108046		LINC00844	-	long intergenic non-protein coding RNA 844	ncRNA	0.006110	0.459350	256(CAGACCAGAGTGTTCT,-,0.00),257(AGACCAGAGTGTTCTA,+,0.00)
chunk0135_29_1	chr3	184805699	184806554	+	0	NA	Intergenic	Intergenic	-6017	NM_015303	23355	Hs.269263	NM_015303	ENSG00000156931	VPS8	KIAA0804	VPS8 subunit of CORVET complex	protein-coding	0.004678	0.399533	
chunk0142_264_1	chr4	99324933	99325443	+	0	NA	Intergenic	Intergenic	-3746	NM_000668	125	Hs.4	NM_000668	ENSG00000196616	ADH1B	ADH2|HEL-S-117	alcohol dehydrogenase 1B (class I), beta polypeptide	protein-coding	0.005882	0.352250	
chunk0043_368_1	chr12	24042058	24042481	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	-91237	NM_001261415	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.004728	0.280660	
chunk0187_2_1	chr8	274284	274803	+	0	NA	Intergenic	Intergenic	41993	NM_001287254	169270	Hs.591388	NM_173539	ENSG00000172748	ZNF596	-	zinc finger protein 596	protein-coding	0.021195	0.525000	
chunk0007_203_1	chr1	81401023	81401337	+	0	NA	Intergenic	L1MA5|LINE|L1	156522	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.006369	0.546032	
chunk0139_251_1	chr4	56260337	56260730	+	0	NA	intron (NM_020722, intron 2 of 10)	MLT2C1|LTR|ERVL	90338	NM_020722	57482	Hs.596667	NM_020722	ENSG00000109265	KIAA1211	CRAD	KIAA1211	protein-coding	0.010178	0.373096	
chunk0114_170_1	chr21	14367861	14368342	+	0	NA	Intergenic	Intergenic	15087	NM_006948	6782	Hs.352341	NM_006948	ENSG00000155304	HSPA13	STCH	heat shock protein family A (Hsp70) member 13	protein-coding	0.006237	0.363071	
chunk0085_122_1	chr18	2998661	2999298	+	0	NA	intron (NM_014646, intron 1 of 19)	intron (NM_014646, intron 1 of 19)	12968	NM_014646	9663	Hs.132342	NM_014646	ENSG00000101577	LPIN2	-	lipin 2	protein-coding	0.006279	0.373041	
chunk0185_119_1	chr7	126016016	126016616	+	0	NA	Intergenic	L1MC1|LINE|L1	-752025	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.001667	0.414309	235(AAGAACAGAATGTTCT,-,0.00),236(AGAACAGAATGTTCTG,+,0.00)
chunk0111_340_1	chr20	33165097	33165489	+	0	NA	Intergenic	ORSL-2b|DNA|hAT-Tip100	-2861	NM_080574	140683	Hs.125960	NM_080574	ENSG00000131050	BPIFA2	C20orf70|PSP|SPLUNC2|bA49G10.1	BPI fold containing family A member 2	protein-coding	0.005102	0.437659	
chunk0036_279_1	chr11	65357978	65358476	+	0	NA	TTS (NM_145719)	TTS (NM_145719)	3416	NM_145719	220359	Hs.632121	NM_145719	ENSG00000173825	TIGD3	-	tigger transposable element derived 3	protein-coding	0.012048	0.531062	210(AGGGACAGCGTGTGCA,-,0.00),211(GGGACAGCGTGTGCAG,+,0.00),243(AGGAGCACAGTGTGCT,-,0.00),244(GGAGCACAGTGTGCTG,+,0.00),265(GGGGGCAGGCAGTTCT,-,0.00),266(GGGGCAGGCAGTTCTG,+,0.00)
chunk0044_390_1	chr12	40090333	40090561	+	0	NA	intron (NM_052885, intron 1 of 9)	L3|LINE|CR1	15412	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.004386	0.305677	
chunk0117_436_1	chr21	46291537	46291767	+	0	NA	3' UTR (NM_001314026, exon 3 of 3)	3' UTR (NM_001314026, exon 3 of 3)	5322	NM_001314022	54059	Hs.474066	NM_058181	ENSG00000182362	YBEY	C21orf57	ybeY metalloendoribonuclease	protein-coding	0.013043	0.536797	
chunk0029_256_1	chr10	102982287	102982940	+	0	NA	intron (NM_199076, intron 1 of 6)	intron (NM_199076, intron 1 of 6)	64295	NM_017649	54805	Hs.643509	NM_017649	ENSG00000148842	CNNM2	ACDP2|HOMG6|HOMGSMR	cyclin and CBS domain divalent metal cation transport mediator 2	protein-coding	0.004594	0.371560	
chunk0032_193_1	chr11	6489047	6489636	+	0	NA	Intergenic	Intergenic	-7862	NM_012402	23647	Hs.75139	NM_012402	ENSG00000132254	ARFIP2	POR1	ADP ribosylation factor interacting protein 2	protein-coding	0.006791	0.444068	
chunk0175_169_1	chr7	4712590	4712919	+	0	NA	intron (NM_001037165, intron 1 of 8)	intron (NM_001037165, intron 1 of 8)	30455	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.021277	0.430303	
chunk0179_232_1	chr7	47969693	47969892	+	0	NA	intron (NM_004507, intron 5 of 7)	L1M8|LINE|L1	9833	NR_037917	3364	Hs.152983	NM_004507	ENSG00000136273	HUS1	hHUS1	HUS1 checkpoint clamp component	protein-coding	0.005025	0.395000	
chunk0082_402_1	chr17	60866632	60867042	+	0	NA	intron (NM_017679, intron 7 of 23)	intron (NM_017679, intron 7 of 23)	189026	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.002439	0.287105	
chunk0058_61_1	chr14	20636994	20637270	+	0	NA	Intergenic	L2|LINE|L2	4559	NM_001001968	341799	Hs.513132	NM_001001968	ENSG00000181803	OR6S1	OR14-37|OR6S1Q	olfactory receptor family 6 subfamily S member 1	protein-coding	0.003623	0.346570	
chunk0034_78_1	chr11	27205165	27205720	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	13326	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.007207	0.424460	
chunk0102_292_1	chr2	150605646	150606150	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-22999	NR_110247	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.007937	0.300990	
chunk0213_1_1	chrY	19518116	19518583	+	0	NA	Intergenic	L1PA8|LINE|L1	-15196	NR_033732	286554	Hs.211713	NM_173700	ENSG00000215580	BCORP1	BCORL2	BCL6 corepressor pseudogene 1	pseudo	0.004283	0.358974	
chunk0111_222_1	chr20	28898195	28898787	+	0	NA	Intergenic	(CCATT)n|Simple_repeat|Simple_repeat	-181899	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.008446	0.472175	
chunk0137_102_1	chr4	13484344	13484689	+	0	NA	promoter-TSS (NM_004249)	promoter-TSS (NM_004249)	-151	NM_001159601	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.095652	0.635838	
chunk0207_57_1	chrX	8654030	8654436	+	0	NA	intron (NM_000216, intron 2 of 13)	intron (NM_000216, intron 2 of 13)	77953	NM_000216	3730	Hs.521869	NM_000216	ENSG00000011201	ANOS1	ADMLX|HH1|HHA|KAL|KAL1|KALIG-1|KMS|WFDC19	anosmin 1	protein-coding	0.004926	0.407862	277(AAAGACAATCTGTGCT,-,0.00),278(AAGACAATCTGTGCTC,+,0.00)
chunk0200_195_1	chr9	19935535	19935811	+	0	NA	Intergenic	Intergenic	-148654	NM_001193288	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.014493	0.541516	
chunk0121_288_1	chr3	23600725	23600961	+	0	NA	Intergenic	MIRb|SINE|MIR	-205050	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.012712	0.464135	
chunk0096_439_1	chr2	38790279	38790735	+	0	NA	Intergenic	Intergenic	12322	NM_024775	79833	Hs.143818	NM_024775	ENSG00000152147	GEMIN6	-	gem nuclear organelle associated protein 6	protein-coding	0.004386	0.380744	262(AAGAACAAAATGTACA,-,0.00),263(AGAACAAAATGTACAC,+,0.00)
chunk0107_42_1	chr2	211181585	211182271	+	0	NA	Intergenic	Intergenic	564357	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.010204	0.419214	
chunk0156_402_1	chr5	113919851	113920190	+	0	NA	Intergenic	MER70A|LTR|ERVL	406326	NM_022828	64848	Hs.231942	NM_022828	ENSG00000047188	YTHDC2	CAHL|hYTHDC2	YTH domain containing 2	protein-coding	0.008850	0.491176	239(GAGCACAGGCTGTTCC,-,0.00),240(AGCACAGGCTGTTCCA,+,0.00)
chunk0091_387_1	chr19	16060481	16060718	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-6908	NM_001145160	7171	Hs.631618	NM_003290	ENSG00000167460	TPM4	HEL-S-108	tropomyosin 4	protein-coding	0.004219	0.386555	
chunk0133_419_1	chr3	174613203	174613544	+	0	NA	Intergenic	L1MA3|LINE|L1	-245948	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.002933	0.514620	156(CAGCACAGTGAGTTCC,-,0.00),157(AGCACAGTGAGTTCCT,+,0.00)
chunk0052_332_1	chr12	125990755	125991202	+	0	NA	Intergenic	L1ME4a|LINE|L1	-7604	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.000000	0.308036	
chunk0198_216_1	chr8	133883176	133883375	+	0	NA	Intergenic	Intergenic	-3221	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.005025	0.500000	
chunk0157_249_1	chr5	119810195	119810654	+	0	NA	Intergenic	Intergenic	180865	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.002179	0.347826	
chunk0150_49_1	chr5	31684662	31685170	+	0	NA	Intergenic	L2a|LINE|L2	-114008	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.007874	0.414538	
chunk0167_321_1	chr6	72255046	72255716	+	0	NA	intron (NM_001168407, intron 11 of 24)	intron (NM_001168407, intron 11 of 24)	38621	NM_001168410	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.005970	0.317437	346(CTGTACAAAATGTTCT,-,0.00),347(TGTACAAAATGTTCTA,+,0.00)
chunk0174_143_1	chr6	157596890	157597867	+	0	NA	intron (NM_024630, intron 3 of 8)	intron (NM_024630, intron 3 of 8)	68246	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.025589	0.503067	
chunk0107_247_1	chr2	217289802	217290287	+	0	NA	intron (NR_026597, intron 12 of 12)	intron (NR_026597, intron 12 of 12)	7311	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.004124	0.454733	
chunk0159_50_1	chr5	137214778	137215242	+	0	NA	intron (NM_004598, intron 3 of 10)	intron (NM_004598, intron 3 of 10)	284319	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.000000	0.350538	
chunk0046_280_1	chr12	61734602	61734907	+	0	NA	intron (NM_178539, intron 4 of 4)	intron (NM_178539, intron 4 of 4)	458085	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.000000	0.339869	
chunk0148_298_1	chr5	12262603	12263081	+	0	NA	Intergenic	Intergenic	-312015	NR_033383	404663	Hs.552273	NR_033383		LINC01194	CT49|TAG	long intergenic non-protein coding RNA 1194	ncRNA	0.006276	0.346555	
chunk0139_6_1	chr4	47851872	47852567	+	0	NA	intron (NR_103795, intron 21 of 23)	intron (NR_103795, intron 21 of 23)	-14113	NM_001278585	10699	Hs.518618	NM_006587	ENSG00000145244	CORIN	ATC2|CRN|Lrp4|PEE5|TMPRSS10	corin, serine peptidase	protein-coding	0.007194	0.331897	
chunk0003_10_1	chr1	28733783	28734075	+	0	NA	Intergenic	L2b|LINE|L2	-2692	NM_001173128	51441	Hs.532286	NM_016258	ENSG00000198492	YTHDF2	CAHL|HGRG8|NY-REN-2	YTH N6-methyladenosine RNA binding protein 2	protein-coding	0.023973	0.498294	82(CAGCACATGTTGTTCT,-,0.00),83(AGCACATGTTGTTCTT,+,0.00)
chunk0105_25_1	chr2	182077331	182077965	+	0	NA	intron (NM_001080545, intron 4 of 4)	intron (NM_001080545, intron 4 of 4)	91824	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.009464	0.379528	
chunk0107_365_1	chr2	222792002	222792321	+	0	NA	Intergenic	Intergenic	-68853	NM_004457	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.021944	0.496875	
chunk0153_378_1	chr5	74916749	74917255	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	-50164	NM_015566	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.007905	0.459566	
chunk0201_292_1	chr9	41042128	41042806	+	0	NA	intron (NR_002836, intron 4 of 8)	L1ME1|LINE|L1	32158	NR_002836	595135	Hs.571593	NR_002836	ENSG00000277778	PGM5P2	-	phosphoglucomutase 5 pseudogene 2	pseudo	0.007375	0.362297	
chunk0089_401_1	chr18	68180534	68181195	+	0	NA	Intergenic	L1MB5|LINE|L1	534252	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.013616	0.368580	
chunk0109_291_1	chr20	8245195	8245426	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	113045	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.000000	0.323276	
chunk0210_249_1	chrX	82945243	82945515	+	0	NA	Intergenic	Intergenic	-562882	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.007353	0.413919	
chunk0049_148_1	chr12	91915392	91915717	+	0	NA	Intergenic	L1MEd|LINE|L1	226159	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.003077	0.398773	218(AAGAACAGCAAGTACA,-,0.00),219(AGAACAGCAAGTACAG,+,0.00)
chunk0057_310_1	chr13	106558561	106558920	+	0	NA	intron (NM_018011, intron 2 of 3)	intron (NM_018011, intron 2 of 3)	9426	NM_018011	55082	Hs.508644	NM_018011	ENSG00000134884	ARGLU1	-	arginine and glutamate rich 1	protein-coding	0.000000	0.383333	168(AAGGACAACCTGTTCC,-,0.00),169(AGGACAACCTGTTCCT,+,0.00)
chunk0123_66_1	chr3	41251023	41251857	+	0	NA	intron (NM_017886, intron 35 of 36)	L1MEf|LINE|L1	51989	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005995	0.432335	
chunk0190_200_1	chr8	34481907	34482343	+	0	NA	Intergenic	Intergenic	-301796	NR_125746	103689844	Hs.590682	NR_125746	ENSG00000254344	LINC01288	TCONS_00014671	long intergenic non-protein coding RNA 1288	ncRNA	0.006881	0.352403	
chunk0075_288_1	chr16	53987994	53988656	+	0	NA	intron (NM_001080432, intron 8 of 8)	intron (NM_001080432, intron 8 of 8)	-51068	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.003021	0.346908	
chunk0168_37_1	chr6	78328670	78329183	+	0	NA	Intergenic	Intergenic	-538618	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.000000	0.354086	
chunk0027_290_1	chr10	77606879	77607108	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	30826	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.004367	0.521739	
chunk0164_113_1	chr6	20699498	20699906	+	0	NA	intron (NM_017774, intron 5 of 15)	intron (NM_017774, intron 5 of 15)	165245	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.007353	0.386308	
chunk0116_455_1	chr21	43859859	43860298	+	0	NA	Intergenic	MER41A|LTR|ERV1	-5157	NM_020132	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.015945	0.479545	
chunk0035_114_1	chr11	42552719	42553131	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-299235	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.004854	0.423729	
chunk0110_283_1	chr20	17605260	17605666	+	0	NA	intron (NM_001011546, intron 4 of 4)	intron (NM_001011546, intron 4 of 4)	35509	NM_001011546	11034	Hs.304192	NM_006870	ENSG00000125868	DSTN	ACTDP|ADF|HEL32|bA462D18.2	destrin, actin depolymerizing factor	protein-coding	0.009852	0.466830	
chunk0021_419_1	chr1	246938591	246939408	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-7575	NM_015446	25909	Hs.300887	NM_015446	ENSG00000153207	AHCTF1	ELYS|MST108|MSTP108|TMBS62	AT-hook containing transcription factor 1	protein-coding	0.009792	0.426650	368(AACACTCACTGTTCTC,+,0.00),492(AACACTCACTGTTCTC,+,0.00)
chunk0078_425_1	chr16	89394072	89394271	+	0	NA	intron (NM_001256182, intron 3 of 13)	intron (NM_001256182, intron 3 of 13)	-36747	NR_110931	101927817	Hs.667942	NR_110931		LOC101927817	-	uncharacterized LOC101927817	ncRNA	0.015075	0.615000	
chunk0025_81_1	chr10	50373593	50374141	+	0	NA	intron (NM_147156, intron 6 of 10)	intron (NM_147156, intron 6 of 10)	-125257	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.005474	0.335155	
chunk0089_344_1	chr18	65906267	65906951	+	0	NA	Intergenic	MER67C|LTR|ERV1	155688	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.007310	0.379562	
chunk0173_29_1	chr6	141999909	142000582	+	0	NA	Intergenic	L1MA4A|LINE|L1	88554	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.004458	0.313056	
chunk0210_351_1	chrX	96246021	96246229	+	0	NA	Intergenic	MIRb|SINE|MIR	91777	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.000000	0.344498	30(AGGTACAGTATGTTCT,-,0.00),31(GGTACAGTATGTTCTA,+,0.00)
chunk0156_389_1	chr5	113118465	113119211	+	0	NA	intron (NM_002387, intron 4 of 16)	intron (NM_002387, intron 4 of 16)	142128	NR_038352	167227	Hs.443875	NM_152624	ENSG00000172795	DCP2	NUDT20	decapping mRNA 2	protein-coding	0.014745	0.492637	316(GGAGACAGCCAGTTCC,-,0.00),317(GAGACAGCCAGTTCCG,+,0.00)
chunk0140_274_1	chr4	72169889	72170650	+	0	NA	Intergenic	L1PA17|LINE|L1	131137	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.006570	0.356955	
chunk0184_443_1	chr7	123198827	123199658	+	0	NA	intron (NM_022444, intron 1 of 14)	intron (NM_022444, intron 1 of 14)	729	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.001203	0.408654	
chunk0133_169_1	chr3	169943861	169944714	+	0	NA	non-coding (NR_027622, exon 2 of 2)	non-coding (NR_027622, exon 2 of 2)	22447	NR_024409	100128164	Hs.633070	NR_024409	ENSG00000239219	LOC100128164	-	four and a half LIM domains 1 pseudogene	pseudo	0.007034	0.359485	
chunk0082_389_1	chr17	60630328	60630873	+	0	NA	intron (NM_003620, intron 2 of 5)	intron (NM_003620, intron 2 of 5)	30417	NM_003620	8493	Hs.286073	NM_003620	ENSG00000170836	PPM1D	IDDGIP|PP2C-DELTA|WIP1	protein phosphatase, Mg2+/Mn2+ dependent 1D	protein-coding	0.011009	0.360806	
chunk0181_307_1	chr7	87220964	87221249	+	0	NA	Intergenic	Intergenic	-1391	NM_024315	79161	Hs.619593	NM_024315	ENSG00000135185	TMEM243	C7orf23|MM-TRAG|MMTRAG	transmembrane protein 243	protein-coding	0.042105	0.496503	
chunk0106_387_1	chr2	207579420	207579619	+	0	NA	intron (NM_134442, intron 8 of 8)	intron (NM_134442, intron 8 of 8)	45453	NM_145280	151194	Hs.664764	NM_145280	ENSG00000144401	METTL21A	FAM119A|HCA557b|HSPA-KMT	methyltransferase like 21A	protein-coding	0.010050	0.415000	
chunk0113_357_1	chr20	58993014	58994013	+	0	NA	exon (NM_198976, exon 12 of 15)	exon (NM_198976, exon 12 of 15)	12305	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.014014	0.499000	
chunk0059_118_1	chr14	31377937	31378477	+	0	NA	intron (NM_015473, intron 11 of 35)	MER58B|DNA|hAT-Charlie	42375	NM_015473	25938	Hs.744979	NM_015473	ENSG00000129493	HEATR5A	C14orf125	HEAT repeat containing 5A	protein-coding	0.001852	0.358595	
chunk0041_436_1	chr11	134497515	134498109	+	0	NA	intron (NR_033852, intron 5 of 5)	intron (NR_033852, intron 5 of 5)	61330	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.013468	0.546218	
chunk0198_203_1	chr8	133727949	133728420	+	0	NA	Intergenic	Intergenic	49168	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.010616	0.423729	
chunk0080_280_1	chr17	31186720	31187297	+	0	NA	intron (NM_001042492, intron 8 of 57)	HERVL-int|LTR|ERVL	92081	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.010399	0.510381	
chunk0037_231_1	chr11	75022962	75023161	+	0	NA	Intergenic	Intergenic	34156	NM_006656	10825	Hs.191074	NM_006656	ENSG00000162139	NEU3	SIAL3	neuraminidase 3	protein-coding	0.005025	0.550000	53(GAGGACTCCCAGTCCC,-,0.00),54(AGGACTCCCAGTCCCC,+,0.00)
chunk0202_439_1	chr9	82073628	82074043	+	0	NA	Intergenic	Intergenic	85063	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.000000	0.302885	
chunk0193_295_1	chr8	77813297	77813887	+	0	NA	Intergenic	Intergenic	362895	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.001695	0.353638	
chunk0004_339_1	chr1	50666800	50667261	+	0	NA	intron (NM_007051, intron 7 of 18)	intron (NM_007051, intron 7 of 18)	-243583	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.002169	0.415584	
chunk0211_91_1	chrX	110533531	110533837	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	13372	NR_002718	6998	Hs.592361	NR_002718	ENSG00000225366	TDGF1P3	CR-3|CRIPTO|CRIPTO-3|CRIPTO3|TDGF1|TDGF2|TDGF3	teratocarcinoma-derived growth factor 1 pseudogene 3	pseudo	0.003268	0.446254	
chunk0157_351_1	chr5	123000821	123001228	+	0	NA	intron (NM_014035, intron 4 of 6)	intron (NM_014035, intron 4 of 6)	35706	NM_000943	5480	Hs.110364	NM_000943	ENSG00000168938	PPIC	CYPC	peptidylprolyl isomerase C	protein-coding	0.004914	0.389706	
chunk0069_364_1	chr15	67148289	67148666	+	0	NA	intron (NM_001145103, intron 1 of 8)	intron (NM_001145103, intron 1 of 8)	10456	NM_001145103	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.007958	0.462963	
chunk0147_219_1	chr4	181063202	181063765	+	0	NA	TTS (NR_033918)	TTS (NR_033918)	95666	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.007105	0.326241	
chunk0140_332_1	chr4	73740394	73740912	+	0	NA	5' UTR (NM_000584, exon 1 of 4)	5' UTR (NM_000584, exon 1 of 4)	147	NM_000584	3576	Hs.624	NM_000584	ENSG00000169429	CXCL8	GCP-1|GCP1|IL8|LECT|LUCT|LYNAP|MDNCF|MONAP|NAF|NAP-1|NAP1	C-X-C motif chemokine ligand 8	protein-coding	0.011583	0.406551	
chunk0098_42_1	chr2	66466328	66466938	+	0	NA	intron (NM_002398, intron 7 of 12)	intron (NM_002398, intron 7 of 12)	-26303	NR_046625	100873998	Hs.734698	NR_046625	ENSG00000230749	MEIS1-AS2	MEIS1-AS1	MEIS1 antisense RNA 2	ncRNA	0.003279	0.402619	
chunk0145_1_1	chr4	142690179	142690458	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	156133	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.007168	0.382143	
chunk0127_236_1	chr3	96820366	96820625	+	0	NA	intron (NM_001080448, intron 1 of 17)	L2a|LINE|L2	5914	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.007722	0.361538	132(GGGAACATCTTGTCTT,-,0.00),133(GGAACATCTTGTCTTT,+,0.00)
chunk0054_337_1	chr13	49399730	49400480	+	0	NA	intron (NM_001079670, intron 3 of 10)	intron (NM_001079670, intron 3 of 10)	1433	NM_030925	81617	Hs.87159	NM_030925	ENSG00000102547	CAB39L	MO25-BETA|MO2L|bA103J18.3	calcium binding protein 39 like	protein-coding	0.001333	0.336884	
chunk0027_76_1	chr10	73332242	73332571	+	0	NA	intron (NM_145170, intron 8 of 27)	L1MCa|LINE|L1	26453	NM_145170	118491	Hs.591367	NM_145170	ENSG00000156042	CFAP70	TTC18	cilia and flagella associated protein 70	protein-coding	0.003040	0.415152	
chunk0047_222_1	chr12	71756597	71757011	+	0	NA	intron (NM_014999, intron 1 of 6)	MIR|SINE|MIR	1926	NM_014999	23011	Hs.524590	NM_014999	ENSG00000080371	RAB21	-	RAB21, member RAS oncogene family	protein-coding	0.002415	0.363855	
chunk0031_66_1	chr10	122911985	122912243	+	0	NA	intron (NM_001029888, intron 2 of 2)	intron (NM_001029888, intron 2 of 2)	1413	NM_001029888	118670	Hs.369829	NM_001029888	ENSG00000203795	FAM24A	-	family with sequence similarity 24 member A	protein-coding	0.011628	0.548263	
chunk0138_137_1	chr4	36882906	36883305	+	0	NA	Intergenic	Intergenic	358886	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.007519	0.342500	
chunk0065_179_1	chr15	26291611	26292137	+	0	NA	Intergenic	Intergenic	176061	NR_038851	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.015209	0.470588	
chunk0130_321_1	chr3	138007798	138008225	+	0	NA	intron (NM_001002026, intron 1 of 4)	intron (NM_001002026, intron 1 of 4)	-2153	NM_016369	51208	Hs.655324	NM_016369	ENSG00000066405	CLDN18	SFTA5|SFTPJ	claudin 18	protein-coding	0.002342	0.446262	
chunk0134_257_1	chr3	179421359	179421910	+	0	NA	intron (NM_021629, intron 2 of 9)	intron (NM_021629, intron 2 of 9)	29949	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.003630	0.340580	290(ATGGACAACTTGTTCC,-,0.00),291(TGGACAACTTGTTCCA,+,0.00)
chunk0053_180_1	chr13	30956689	30957235	+	0	NA	exon (NM_152325, exon 4 of 7)	exon (NM_152325, exon 4 of 7)	24265	NM_152325	122046	Hs.124463	NM_152325	ENSG00000175664	TEX26	C13orf26	testis expressed 26	protein-coding	0.016484	0.449726	
chunk0128_348_1	chr3	112440439	112440993	+	0	NA	Intergenic	L1PA16|LINE|L1	58845	NM_001085357	151888	Hs.445162	NM_181780	ENSG00000186265	BTLA	BTLA1|CD272	B and T lymphocyte associated	protein-coding	0.005415	0.353153	
chunk0048_455_1	chr12	88801156	88801640	+	0	NA	Intergenic	Intergenic	218294	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.002066	0.348454	
chunk0098_247_1	chr2	74856327	74856679	+	0	NA	intron (NM_000189, intron 2 of 17)	intron (NM_000189, intron 2 of 17)	23848	NM_000189	3099	Hs.406266	NM_000189	ENSG00000159399	HK2	HKII|HXK2	hexokinase 2	protein-coding	0.005682	0.439093	
chunk0048_64_1	chr12	78407030	78407611	+	0	NA	Intergenic	Intergenic	-456673	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.006885	0.331615	
chunk0124_319_1	chr3	58103054	58103343	+	0	NA	intron (NM_001164317, intron 9 of 46)	intron (NM_001164317, intron 9 of 46)	94798	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.024221	0.544828	100(TGGGTCAGGCTGTGCC,-,0.00),101(GGGTCAGGCTGTGCCC,+,0.00)
chunk0081_343_1	chr17	46922739	46922938	+	0	NA	promoter-TSS (NM_054022)	promoter-TSS (NM_054022)	-282	NM_001012511	9570	Hs.463278	NM_004287	ENSG00000108433	GOSR2	Bos1|EPM6|GS27	golgi SNAP receptor complex member 2	protein-coding	0.045226	0.510000	
chunk0171_81_1	chr6	121825124	121825444	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	389707	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.000000	0.348910	
chunk0063_144_1	chr14	79529566	79530296	+	0	NA	intron (NR_073547, intron 15 of 20)	intron (NR_073547, intron 15 of 20)	250592	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004110	0.337893	
chunk0126_255_1	chr3	79477185	79477714	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-30438	NR_037488	100500877		NR_037488	ENSG00000265193	MIR3923	-	microRNA 3923	ncRNA	0.001890	0.330189	
chunk0207_134_1	chr9	129320596	129321125	+	0	NA	promoter-TSS (NM_001012715)	promoter-TSS (NM_001012715)	-156	NM_001012715									0.062382	0.609434	158(GGGCACGTTCTGTTCC,-,0.00),159(GGCACGTTCTGTTCCC,+,0.00)
chunk0088_31_1	chr18	43820305	43820924	+	0	NA	Intergenic	L1PB1|LINE|L1	-542964	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.001616	0.350000	
chunk0039_210_1	chr11	101062153	101062424	+	0	NA	intron (NR_073143, intron 3 of 5)	intron (NR_073143, intron 3 of 5)	66775	NR_073143	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.000000	0.275735	
chunk0084_407_1	chr17	82233199	82233549	+	0	NA	intron (NM_001042423, intron 1 of 4)	intron (NM_001042423, intron 1 of 4)	1142	NM_001042423	9123	Hs.500761	NM_004207	ENSG00000141526	SLC16A3	MCT 3|MCT 4|MCT-3|MCT-4|MCT3|MCT4	solute carrier family 16 member 3	protein-coding	0.025714	0.618234	182(CAGAACATGCTGTGCT,-,0.00),183(AGAACATGCTGTGCTC,+,0.00)
chunk0024_322_1	chr10	43055233	43055439	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-21733	NM_020975	5979	Hs.350321	NM_000323	ENSG00000165731	RET	CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1	ret proto-oncogene	protein-coding	0.009709	0.434783	
chunk0188_94_1	chr8	8800238	8800676	+	0	NA	intron (NM_004225, intron 1 of 2)	MIR3|SINE|MIR	93164	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.004566	0.425968	
chunk0066_214_1	chr15	33893509	33894039	+	0	NA	intron (NM_020371, intron 2 of 5)	intron (NM_020371, intron 2 of 5)	-75114	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.005660	0.416196	342(GTGGTCACGGTGTTCC,-,0.00)
chunk0078_36_1	chr17	1001200	1001485	+	0	NA	3' UTR (NM_013337, exon 4 of 4)	3' UTR (NM_013337, exon 4 of 4)	4225	NM_013337	29928	Hs.745034	NM_013337	ENSG00000177370	TIMM22	TEX4|TIM22	translocase of inner mitochondrial membrane 22	protein-coding	0.014035	0.552448	
chunk0144_336_1	chr4	139126741	139127466	+	0	NA	intron (NM_201999, intron 2 of 8)	intron (NM_201999, intron 2 of 8)	12373	NM_201999	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.004138	0.402204	317(AAGGACAGAATGTCCA,-,0.00),318(AGGACAGAATGTCCAG,+,0.00),331(CAGATCAGTCTGTTCT,-,0.00),332(AGATCAGTCTGTTCTA,+,0.00),590(CAGAGCAGGATGTGCC,-,0.00),591(AGAGCAGGATGTGCCT,+,0.00)
chunk0110_31_1	chr20	10511953	10512388	+	0	NA	intron (NM_001009608, intron 2 of 7)	MER58A|DNA|hAT-Charlie	76867	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.002299	0.334862	
chunk0050_264_1	chr12	105960346	105960554	+	0	NA	Intergenic	Intergenic	179583	NM_014840	9891	Hs.524692	NM_014840	ENSG00000074590	NUAK1	ARK5	NUAK family kinase 1	protein-coding	0.004808	0.478469	
chunk0112_91_1	chr20	38065606	38066337	+	0	NA	intron (NM_021215, intron 5 of 6)	intron (NM_021215, intron 5 of 6)	32425	NM_021215	58490	Hs.278839	NM_021215	ENSG00000101413	RPRD1B	C20orf77|CREPT|K-H|Kub5-Hera|NET60|dJ1057B20.2	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.015048	0.420765	
chunk0139_349_1	chr4	60002770	60003378	+	0	NA	Intergenic	Intergenic	-919545	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.003289	0.348112	
chunk0105_83_1	chr2	183960496	183960695	+	0	NA	Intergenic	L1MA10|LINE|L1	-418380	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.010050	0.405000	3(TGGCTCAGCGTGTGCT,-,0.00),4(GGCTCAGCGTGTGCTT,+,0.00)
chunk0165_449_1	chr6	40714753	40715340	+	0	NA	Intergenic	Intergenic	-127582	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.006814	0.501701	
chunk0203_100_1	chr9	84274684	84275000	+	0	NA	Intergenic	Intergenic	65937	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.006329	0.425868	122(TGGCACACTGTGTCCT,-,0.00),123(GGCACACTGTGTCCTT,+,0.00)
chunk0101_439_1	chr2	139468726	139469081	+	0	NA	Intergenic	Intergenic	571579	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005634	0.356742	
chunk0161_84_1	chr5	167140761	167140991	+	0	NA	Intergenic	Intergenic	-143962	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.000000	0.393939	
chunk0012_34_1	chr1	155084995	155085306	+	0	NA	exon (NM_004952, exon 2 of 5)	exon (NM_004952, exon 2 of 5)	6278	NM_004952	1944	Hs.516656	NM_004952	ENSG00000143590	EFNA3	EFL2|EPLG3|Ehk1-L|LERK3	ephrin A3	protein-coding	0.086817	0.663462	
chunk0168_96_1	chr6	80058328	80058760	+	0	NA	Intergenic	Intergenic	-48083	NM_183050	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.006944	0.374134	132(TAGAACTGCAAGTTCT,-,0.00),133(AGAACTGCAAGTTCTA,+,0.00)
chunk0073_114_1	chr16	4679096	4679410	+	0	NA	intron (NM_001142291, intron 11 of 15)	intron (NM_001142291, intron 11 of 15)	7935	NR_106827	102466731		NR_106827	ENSG00000276641	MIR6769A	hsa-mir-6769a	microRNA 6769a	ncRNA	0.025478	0.571429	
chunk0098_365_1	chr2	78233884	78234433	+	0	NA	intron (NR_110288, intron 1 of 3)	intron (NR_110288, intron 1 of 3)	56573	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.007286	0.325455	
chunk0151_437_1	chr5	56013450	56013682	+	0	NA	Intergenic	Intergenic	18399	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.017241	0.472103	
chunk0024_240_1	chr10	38528129	38529649	+	0	NA	Intergenic	Intergenic	100743	NR_024497	399744	Hs.497951	NM_001013665		LINC00999	-	long intergenic non-protein coding RNA 999	ncRNA	0.023684	0.392505	
chunk0072_102_1	chr15	91099645	91099844	+	0	NA	promoter-TSS (NM_014848)	promoter-TSS (NM_014848)	-208	NM_001167580	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.065327	0.575000	
chunk0083_164_1	chr17	66003205	66003783	+	0	NA	intron (NM_001302891, intron 15 of 24)	intron (NM_001302891, intron 15 of 24)	-176951	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.005190	0.373057	
chunk0033_288_1	chr11	19659908	19660278	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	-53242	NM_001244963	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.008108	0.431267	
chunk0076_244_1	chr16	69189815	69190014	+	0	NA	intron (NM_006750, intron 1 of 6)	intron (NM_006750, intron 1 of 6)	2767	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.010050	0.355000	
chunk0033_428_1	chr11	25058534	25058733	+	0	NA	intron (NM_001009909, intron 10 of 11)	intron (NM_001009909, intron 10 of 11)	561663	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.360000	
chunk0186_338_1	chr7	143323957	143324399	+	0	NA	intron (NM_000083, intron 6 of 22)	intron (NM_000083, intron 6 of 22)	8052	NM_000083	1180	Hs.121483	NM_000083	ENSG00000188037	CLCN1	CLC1	chloride voltage-gated channel 1	protein-coding	0.004525	0.451467	
chunk0029_59_1	chr10	96540257	96540470	+	0	NA	intron (NM_020123, intron 9 of 14)	L3|LINE|CR1	-26437	NM_012465	7093	Hs.154296	NM_012465	ENSG00000095587	TLL2	-	tolloid like 2	protein-coding	0.009390	0.373832	
chunk0180_134_1	chr7	56060663	56061185	+	0	NA	TTS (NR_002957)	TTS (NR_002957)	454	NR_002957	677803	Hs.689706	NR_002957	ENSG00000207168	SNORA15	ACA15|SNORA15A	small nucleolar RNA, H/ACA box 15	snoRNA	0.001916	0.384321	
chunk0106_34_1	chr2	196096157	196096663	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-27598	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.007905	0.329389	
chunk0148_292_1	chr5	11854413	11854612	+	0	NA	intron (NR_109988, intron 1 of 21)	L2a|LINE|L2	49531	NM_001332	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.000000	0.325000	
chunk0155_381_1	chr5	98180800	98181001	+	0	NA	Intergenic	L1PB2|LINE|L1	-588395	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.004975	0.519802	
chunk0006_91_1	chr1	65150405	65150940	+	0	NA	intron (NM_001005353, intron 2 of 5)	intron (NM_001005353, intron 2 of 5)	2505	NM_013410	205	Hs.10862	NM_013410	ENSG00000162433	AK4	AK 4|AK3|AK3L1|AK3L2	adenylate kinase 4	protein-coding	0.011215	0.414179	
chunk0205_53_1	chr9	106450178	106450951	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-150364	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.001294	0.410853	375(TGGGACAGTCTGTGAC,-,0.00),376(GGGACAGTCTGTGACC,+,0.00)
chunk0132_258_1	chr3	158915790	158916001	+	0	NA	Intergenic	MER66-int|LTR|ERV1	113969	NR_110328	64747	Hs.58663	NM_022736	ENSG00000118855	MFSD1	SMAP4	major facilitator superfamily domain containing 1	protein-coding	0.014218	0.443396	
chunk0033_354_1	chr11	22981192	22981786	+	0	NA	Intergenic	L2c|LINE|L2	-121063	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.001684	0.322689	
chunk0092_219_1	chr19	31683956	31684454	+	0	NA	Intergenic	L1M5|LINE|L1	91924	NM_001205273	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.000000	0.272545	
chunk0020_40_1	chr1	232225184	232225558	+	0	NA	Intergenic	LTR39|LTR|ERV1	290237	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.005348	0.461333	
chunk0190_249_1	chr8	36935414	36935885	+	0	NA	exon (NM_001031836, exon 27 of 27)	exon (NM_001031836, exon 27 of 27)	151325	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.004246	0.411017	
chunk0052_338_1	chr12	126411249	126411487	+	0	NA	Intergenic	Intergenic	-31113	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.021008	0.476987	
chunk0153_234_1	chr5	72246981	72247319	+	0	NA	intron (NM_001286748, intron 4 of 11)	MER102c|DNA|hAT-Charlie	73107	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.008876	0.392330	
chunk0093_452_1	chr19	58580815	58581332	+	0	NA	intron (NR_026052, intron 1 of 1)	intron (NR_026052, intron 1 of 1)	5674	NR_026052	65996	Hs.541177	NM_023939	ENSG00000213753	CENPBD1P1	-	CENPB DNA-binding domains containing 1 pseudogene 1	pseudo	0.021277	0.515444	
chunk0108_264_1	chr2	234223804	234224396	+	0	NA	Intergenic	L1ME2|LINE|L1	173398	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.011824	0.333895	
chunk0090_310_1	chr18	75398133	75398657	+	0	NA	Intergenic	L1MC4|LINE|L1	29308	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.011450	0.358095	
chunk0157_200_1	chr5	119037481	119038039	+	0	NA	Intergenic	Intergenic	-33327	NM_005509	1657	Hs.181042	NM_005509	ENSG00000172869	DMXL1	-	Dmx like 1	protein-coding	0.014337	0.391771	
chunk0120_223_1	chr3	8138055	8138427	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-121934	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.013441	0.388740	
chunk0049_142_1	chr12	91833627	91833832	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	307984	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.004878	0.368932	
chunk0075_282_1	chr16	53893760	53894347	+	0	NA	intron (NM_001080432, intron 7 of 8)	intron (NM_001080432, intron 7 of 8)	-145340	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.003407	0.358844	
chunk0169_159_1	chr6	101912957	101913409	+	0	NA	intron (NM_001166247, intron 11 of 16)	intron (NM_001166247, intron 11 of 16)	514198	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.006637	0.306843	
chunk0192_340_1	chr8	67640847	67641370	+	0	NA	intron (NM_020361, intron 1 of 10)	MER52A|LTR|ERV1	105277	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.017208	0.543893	
chunk0212_309_1	chrX	142708027	142708675	+	0	NA	Intergenic	L1MC2|LINE|L1	-317567	NM_001009613	441525	Hs.535082	NM_001009613	ENSG00000189326	SPANXN4	CT11.9	SPANX family member N4	protein-coding	0.004630	0.366718	357(TGAAACAGAATGTCCT,-,0.00),358(GAAACAGAATGTCCTT,+,0.00)
chunk0066_171_1	chr15	32874604	32875150	+	0	NA	intron (NM_001103184, intron 12 of 16)	intron (NM_001103184, intron 12 of 16)	-156012	NR_109767	100131315	Hs.610545	NR_109767	ENSG00000259721	LOC100131315	-	uncharacterized LOC100131315	ncRNA	0.009158	0.367459	
chunk0018_134_1	chr1	218582839	218583124	+	0	NA	intron (NR_031644, intron 2 of 6)	L1ME2|LINE|L1	140355	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.000000	0.335664	
chunk0014_409_1	chr1	183052790	183053374	+	0	NA	intron (NM_002293, intron 1 of 27)	intron (NM_002293, intron 1 of 27)	29622	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.008562	0.338462	
chunk0153_372_1	chr5	74833405	74834027	+	0	NA	intron (NR_046462, intron 4 of 11)	intron (NR_046462, intron 4 of 11)	32671	NR_046462	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.003215	0.367576	
chunk0162_54_1	chr6	1325882	1326251	+	0	NA	Intergenic	Intergenic	13626	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.002710	0.443243	
chunk0193_1_1	chr8	70402043	70402461	+	0	NA	intron (NM_006540, intron 1 of 22)	CpG	1533	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.069378	0.651551	
chunk0199_221_1	chr9	5200861	5201126	+	0	NA	Intergenic	Intergenic	-15375	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.007547	0.338346	
chunk0043_362_1	chr12	23388969	23389535	+	0	NA	Intergenic	L1PA5|LINE|L1	195360	NM_178010	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.015901	0.527337	
chunk0098_28_1	chr2	65576781	65577307	+	0	NA	Intergenic	L2b|LINE|L2	-144522	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.017110	0.485769	
chunk0061_12_1	chr14	55599024	55599881	+	0	NA	intron (NM_001079521, intron 1 of 43)	intron (NM_001079521, intron 1 of 43)	19245	NR_073128	3895	Hs.509414	NM_004986	ENSG00000126777	KTN1	CG1|KNT|MU-RMS-40.19	kinectin 1	protein-coding	0.017503	0.406760	
chunk0085_128_1	chr18	3119719	3120274	+	0	NA	intron (NM_019856, intron 18 of 36)	intron (NM_019856, intron 18 of 36)	100112	NM_003803	8736	Hs.464469	NM_003803	ENSG00000101605	MYOM1	SKELEMIN	myomesin 1	protein-coding	0.016216	0.440647	
chunk0107_313_1	chr2	219597678	219597982	+	0	NA	promoter-TSS (NM_052902)	promoter-TSS (NM_052902)	-21	NM_052902	114790	Hs.22410	NM_052902	ENSG00000144589	STK11IP	LIP1|LKB1IP|STK11IP1	serine/threonine kinase 11 interacting protein	protein-coding	0.075658	0.609836	
chunk0052_461_1	chr12	132933265	132933464	+	0	NA	intron (NM_183238, intron 3 of 4)	MLT1F2|LTR|ERVL-MaLR	22918	NM_183238	100289635	Hs.29698	NM_183238	ENSG00000196458	ZNF605	-	zinc finger protein 605	protein-coding	0.015075	0.500000	
chunk0121_282_1	chr3	23573276	23573475	+	0	NA	intron (NM_152653, intron 5 of 5)	intron (NM_152653, intron 5 of 5)	-232518	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.005025	0.290000	
chunk0126_93_1	chr3	74861648	74862081	+	0	NA	Intergenic	Intergenic	-340724	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.343318	
chunk0005_74_1	chr1	55961923	55962379	+	0	NA	Intergenic	Intergenic	617433	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.002193	0.385120	
chunk0137_108_1	chr4	13733692	13734479	+	0	NA	intron (NR_121681, intron 2 of 3)	intron (NR_121681, intron 2 of 3)	78906	NR_121681	101929071	Hs.543714	NR_121681	ENSG00000250634	LINC01182	-	long intergenic non-protein coding RNA 1182	ncRNA	0.005083	0.413706	
chunk0161_277_1	chr5	172731365	172731738	+	0	NA	Intergenic	Intergenic	-23952	NM_001287812									0.026810	0.564171	
chunk0184_145_1	chr7	115805493	115806028	+	0	NA	Intergenic	Intergenic	162553	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.013084	0.393657	
chunk0156_408_1	chr5	114197050	114197755	+	0	NA	Intergenic	L1MB8|LINE|L1	-164917	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.002837	0.402266	
chunk0161_266_1	chr5	172414603	172414919	+	0	NA	intron (NM_001017995, intron 2 of 12)	intron (NM_001017995, intron 2 of 12)	39762	NM_001017995	285590	Hs.285666	NM_001017995	ENSG00000174705	SH3PXD2B	FAD49|FTHS|HOFI|KIAA1295|TKS4|TSK4	SH3 and PX domains 2B	protein-coding	0.028481	0.570978	
chunk0078_123_1	chr17	2965659	2966158	+	0	NA	promoter-TSS (NR_110818)	promoter-TSS (NR_110818)	-13	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.016032	0.564000	
chunk0111_228_1	chr20	29118776	29119111	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	38553	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.008955	0.458333	
chunk0182_56_1	chr7	91952021	91952590	+	0	NA	intron (NM_147185, intron 1 of 49)	L2c|LINE|L2	11430	NM_147185	10142	Hs.651221	NM_005751	ENSG00000127914	AKAP9	AKAP-9|AKAP350|AKAP450|CG-NAP|HYPERION|LQT11|MU-RMS-40.16A|PPP1R45|PRKA9|YOTIAO	A-kinase anchoring protein 9	protein-coding	0.005272	0.377193	
chunk0030_139_1	chr10	113679002	113679334	+	0	NA	promoter-TSS (NM_033338)	promoter-TSS (NM_033338)	6	NM_001267056	840	Hs.9216	NM_001227	ENSG00000165806	CASP7	CASP-7|CMH-1|ICE-LAP3|LICE2|MCH3	caspase 7	protein-coding	0.063253	0.600601	
chunk0166_441_1	chr6	52983802	52984001	+	0	NA	intron (NM_001512, intron 5 of 6)	intron (NM_001512, intron 5 of 6)	11479	NM_001512	2941	Hs.485557	NM_001512	ENSG00000170899	GSTA4	GSTA4-4|GTA4	glutathione S-transferase alpha 4	protein-coding	0.000000	0.365000	
chunk0042_141_1	chr12	3834707	3835217	+	0	NA	intron (NR_104461, intron 1 of 8)	L1M4a2|LINE|L1	38486	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.011765	0.465753	337(TGGAACACTGTGTACA,-,0.00),338(GGAACACTGTGTACAT,+,0.00)
chunk0015_146_1	chr1	186309669	186309876	+	0	NA	intron (NM_001303232, intron 6 of 11)	(TTTTG)n|Simple_repeat|Simple_repeat	13499	NM_001127709	10216	Hs.647723	NM_005807	ENSG00000116690	PRG4	CACP|HAPO|JCAP|MSF|SZP	proteoglycan 4	protein-coding	0.009662	0.365385	
chunk0003_394_1	chr1	39892537	39892760	+	0	NA	Intergenic	Intergenic	-9137	NR_132404	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.004484	0.388393	
chunk0102_298_1	chr2	150614029	150614554	+	0	NA	Intergenic	Intergenic	-14606	NR_110247	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.005714	0.385932	
chunk0111_309_1	chr20	32204185	32204508	+	0	NA	intron (NM_002657, intron 1 of 2)	intron (NM_002657, intron 1 of 2)	3397	NM_002657	5326	Hs.154104	NM_002657	ENSG00000126003	PLAGL2	ZNF900	PLAG1 like zinc finger 2	protein-coding	0.006192	0.478395	129(GAGAACATTACGTCCC,-,0.00),130(AGAACATTACGTCCCC,+,0.00)
chunk0012_387_1	chr1	163564899	163565208	+	0	NA	Intergenic	Intergenic	-141862	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.009709	0.429032	181(GGGAACATTCTGTTTC,-,0.00),182(GGAACATTCTGTTTCC,+,0.00)
chunk0104_121_1	chr2	173028583	173029166	+	0	NA	intron (NM_001282899, intron 22 of 27)	MIRc|SINE|MIR	-46963	NM_016653	51776	Hs.444451	NM_016653	ENSG00000091436	MAP3K20	AZK|CNM6|MLK7|MLT|MLTK|MLTKalpha|MLTKbeta|MRK|SFMMP|ZAK|mlklak|pk	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.008576	0.414384	
chunk0179_238_1	chr7	48088730	48088976	+	0	NA	promoter-TSS (NM_001287429)	promoter-TSS (NM_001287429)	250	NM_001287426	7378	Hs.488240	NM_003364	ENSG00000183696	UPP1	UDRPASE|UP|UPASE|UPP	uridine phosphorylase 1	protein-coding	0.056911	0.615385	
chunk0078_285_1	chr17	8034187	8034780	+	0	NA	Intergenic	Intergenic	-4557	NM_001039130	247	Hs.111256	NM_001141	ENSG00000179593	ALOX15B	15-LOX-2	arachidonate 15-lipoxygenase type B	protein-coding	0.005059	0.437710	
chunk0181_375_1	chr7	88868415	88868646	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	-72813	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.004329	0.383621	
chunk0183_359_1	chr7	108685538	108685948	+	0	NA	Intergenic	Intergenic	-115975	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.009756	0.347932	205(AGGAACATTTTGTTCT,-,0.00),206(GGAACATTTTGTTCTT,+,0.00)
chunk0024_328_1	chr10	43174942	43175436	+	0	NA	intron (NM_018590, intron 6 of 7)	MER58A|DNA|hAT-Charlie	36744	NM_018590	55454	Hs.657569	NM_018590	ENSG00000169826	CSGALNACT2	CHGN2|ChGn-2|GALNACT-2|GALNACT2|PRO0082|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding	0.012146	0.416162	
chunk0203_149_1	chr9	85591228	85591959	+	0	NA	intron (NM_001286715, intron 18 of 24)	intron (NM_001286715, intron 18 of 24)	150436	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.005472	0.346995	
chunk0067_139_1	chr15	43103445	43104119	+	0	NA	intron (NM_174916, intron 1 of 46)	intron (NM_174916, intron 1 of 46)	2306	NM_174916	197131	Hs.591121	NM_174916	ENSG00000159459	UBR1	JBS	ubiquitin protein ligase E3 component n-recognin 1	protein-coding	0.004451	0.364444	
chunk0188_20_1	chr8	6519131	6519415	+	0	NA	intron (NM_001147, intron 5 of 8)	Charlie1a|DNA|hAT-Charlie	43990	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.035211	0.508772	
chunk0103_225_1	chr2	164520215	164520921	+	0	NA	intron (NM_004490, intron 6 of 13)	L1PB1|LINE|L1	47982	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.002833	0.352192	
chunk0070_120_1	chr15	70725037	70725595	+	0	NA	intron (NM_018003, intron 1 of 18)	intron (NM_018003, intron 1 of 18)	-23035	NM_001008224	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.001792	0.352415	
chunk0125_267_1	chr3	69256138	69256429	+	0	NA	intron (NM_015123, intron 5 of 22)	intron (NM_015123, intron 5 of 22)	130021	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.003436	0.465753	
chunk0052_111_1	chr13	22816952	22817313	+	0	NA	Intergenic	Intergenic	81049	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.008310	0.328729	
chunk0107_306_1	chr2	219218641	219218870	+	0	NA	TTS (NM_024085)	TTS (NM_024085)	235	NM_005689	10058	Hs.107911	NM_005689	ENSG00000115657	ABCB6	ABC|LAN|MTABC3|PRP|umat	ATP binding cassette subfamily B member 6 (Langereis blood group)	protein-coding	0.122271	0.730435	
chunk0166_304_1	chr6	49542061	49542524	+	0	NA	Intergenic	Intergenic	-8108	NM_001145652	135398	Hs.722010	NM_153344	ENSG00000197261	C6orf141	-	chromosome 6 open reading frame 141	protein-coding	0.008639	0.349138	
chunk0206_219_1	chr9	123310884	123312255	+	0	NA	Intergenic	Intergenic	-42993	NM_001171137	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.012400	0.435131	1135(AGGAACTAAAAGTTCT,-,0.00)
chunk0008_49_1	chr1	89222691	89223174	+	0	NA	Intergenic	L1PA14|LINE|L1	-23982	NM_052941	115361	Hs.409925	NM_052941	ENSG00000162654	GBP4	Mpa2	guanylate binding protein 4	protein-coding	0.004141	0.336777	
chunk0075_428_1	chr16	57620238	57620699	+	0	NA	intron (NM_005682, intron 1 of 14)	intron (NM_005682, intron 1 of 14)	470	NM_005682	9289	Hs.513633	NM_005682	ENSG00000205336	ADGRG1	BFPP|BPPR|GPR56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding	0.043384	0.649351	
chunk0020_63_1	chr1	232568255	232568765	+	0	NA	Intergenic	Intergenic	-52902	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.000000	0.452055	
chunk0194_44_1	chr8	81972510	81972793	+	0	NA	Intergenic	Intergenic	-130365	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.007067	0.380282	110(AGGGACAGAGTGTCAT,-,0.00)
chunk0116_153_1	chr21	36505975	36506432	+	0	NA	intron (NM_001146077, intron 2 of 2)	L1ME4b|LINE|L1	-26113	NM_001146079	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.004376	0.399563	
chunk0076_450_1	chr16	74058789	74059017	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	156618	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.004386	0.414847	
chunk0186_111_1	chr7	138007681	138008317	+	0	NA	Intergenic	Intergenic	-5898	NM_001253775	64764	Hs.490273	NM_194071	ENSG00000182158	CREB3L2	BBF2H7	cAMP responsive element binding protein 3 like 2	protein-coding	0.007862	0.359498	
chunk0129_353_1	chr3	124887193	124887636	+	0	NA	promoter-TSS (NM_002213)	promoter-TSS (NM_002213)	-109	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.110609	0.754505	162(CGGCACACTCTGCCCC,-,0.00),163(GGCACACTCTGCCCCT,+,0.00)
chunk0176_161_1	chr7	13392375	13392808	+	0	NA	Intergenic	Intergenic	593923	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.004619	0.350230	
chunk0204_355_1	chr9	101648344	101648565	+	0	NA	intron (NM_133445, intron 3 of 8)	L1MA5A|LINE|L1	-53453	NM_147180	5535	Hs.151167	NM_147180	ENSG00000188386	PPP3R2	PPP3RL	protein phosphatase 3 regulatory subunit B, beta	protein-coding	0.000000	0.346847	
chunk0075_354_1	chr16	55937014	55937213	+	0	NA	intron (NM_001190158, intron 2 of 13)	L2c|LINE|L2	18918	NM_001190158	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.010050	0.460000	
chunk0037_51_1	chr11	70636161	70636510	+	0	NA	TTS (NR_046567)	TTS (NR_046567)	5241	NR_046567	100874198	Hs.656610	NR_046567	ENSG00000226627	SHANK2-AS1	-	SHANK2 antisense RNA 1	ncRNA	0.028653	0.451429	
chunk0033_282_1	chr11	19599377	19599696	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	24226	NR_039706	100616118		NR_039706	ENSG00000265210	MIR4486	-	microRNA 4486	ncRNA	0.009404	0.412500	
chunk0162_120_1	chr6	2846461	2846660	+	0	NA	Intergenic	Intergenic	-4511	NM_030666	1992	Hs.381167	NM_030666	ENSG00000021355	SERPINB1	EI|ELANH2|HEL-S-27|HEL57|LEI|M/NEI|MNEI|PI-2|PI2	serpin family B member 1	protein-coding	0.010050	0.410000	
chunk0046_420_1	chr12	64593346	64593821	+	0	NA	Intergenic	Intergenic	-16930	NM_178169	283349	Hs.643605	NM_178169	ENSG00000153179	RASSF3	RASSF5	Ras association domain family member 3	protein-coding	0.002105	0.405462	
chunk0051_15_1	chr12	111578778	111579352	+	0	NA	intron (NM_001310121, intron 1 of 25)	L1ME1|LINE|L1	20608	NM_001310123	6311	Hs.76253	NM_002973	ENSG00000204842	ATXN2	ATX2|SCA2|TNRC13	ataxin 2	protein-coding	0.003484	0.427826	
chunk0097_264_1	chr2	54545763	54546080	+	0	NA	intron (NM_003128, intron 2 of 35)	intron (NM_003128, intron 2 of 35)	-12473	NM_178313	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.003155	0.427673	
chunk0088_423_1	chr18	55192551	55192750	+	0	NA	Intergenic	Intergenic	-68344	NR_110743	101927229	Hs.638474	NR_110743	ENSG00000267013	LINC01929	-	long intergenic non-protein coding RNA 1929	ncRNA	0.005025	0.485000	81(AGGATCAGAGTGTGCT,-,0.00),82(GGATCAGAGTGTGCTG,+,0.00)
chunk0045_458_1	chr12	53788901	53789170	+	0	NA	Intergenic	Intergenic	-32001	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.003717	0.396296	
chunk0163_261_1	chr6	13038267	13038938	+	0	NA	intron (NM_030948, intron 4 of 14)	intron (NM_030948, intron 4 of 14)	256984	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.001490	0.382440	334(TAGCACTTGATGTTCT,-,0.00),335(AGCACTTGATGTTCTG,+,0.00)
chunk0040_150_1	chr11	113571400	113572038	+	0	NA	Intergenic	HAL1|LINE|L1	-96440	NM_016574	1813	Hs.73893	NM_000795	ENSG00000149295	DRD2	D2DR|D2R	dopamine receptor D2	protein-coding	0.009404	0.381847	
chunk0095_431_1	chr2	25079038	25079313	+	0	NA	intron (NM_014971, intron 1 of 22)	intron (NM_014971, intron 1 of 22)	37071	NM_014971	22979	Hs.4892	NM_014971	ENSG00000084710	EFR3B	KIAA0953	EFR3 homolog B	protein-coding	0.007273	0.485507	
chunk0174_445_1	chr6	166238208	166238427	+	0	NA	intron (NR_125862, intron 1 of 4)	intron (NR_125862, intron 1 of 4)	1348	NR_125862	101929297	Hs.434661	NR_125862	ENSG00000233365	LOC101929297	-	uncharacterized LOC101929297	ncRNA	0.000000	0.372727	
chunk0107_28_1	chr2	210410377	210410638	+	0	NA	intron (NR_110605, intron 1 of 5)	Tigger1|DNA|TcMar-Tigger	66198	NM_001136574	10314	Hs.13351	NM_006055	ENSG00000115365	LANCL1	GPR69A|p40	LanC like 1	protein-coding	0.007663	0.393130	
chunk0081_217_1	chr17	42623990	42624639	+	0	NA	Intergenic	Intergenic	-14887	NR_026697	162427	Hs.632262	NM_178126	ENSG00000141699	RETREG3	FAM134C	reticulophagy regulator family member 3	protein-coding	0.010786	0.472308	
chunk0016_292_1	chr1	201082293	201082698	+	0	NA	intron (NM_000069, intron 10 of 43)	L2c|LINE|L2	30071	NM_000069	779	Hs.1294	NM_000069	ENSG00000081248	CACNA1S	CACNL1A3|CCHL1A3|Cav1.1|HOKPP|HOKPP1|MHS5|TTPP1|hypoPP	calcium voltage-gated channel subunit alpha1 S	protein-coding	0.014815	0.453202	176(TTGCACACACTGTTCC,-,0.00),177(TGCACACACTGTTCCT,+,0.00)
chunk0174_65_1	chr6	155806351	155806833	+	0	NA	Intergenic	L1ME2|LINE|L1	-140205	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.000000	0.345756	
chunk0128_220_1	chr3	108103224	108103792	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-12420	NM_198793	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.008803	0.428822	
chunk0109_127_1	chr20	2890774	2890981	+	0	NA	intron (NM_080840, intron 1 of 22)	L2a|LINE|L2	17381	NM_080840	5786	Hs.269577	NM_002836	ENSG00000132670	PTPRA	HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA	protein tyrosine phosphatase receptor type A	protein-coding	0.004831	0.471154	
chunk0098_313_1	chr2	76484879	76485323	+	0	NA	Intergenic	Intergenic	-500864	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.009009	0.373034	
chunk0059_112_1	chr14	31164000	31164681	+	0	NA	intron (NM_015382, intron 10 of 42)	FLAM_A|SINE|Alu	43183	NM_015382	25831	Hs.708017	NM_015382	ENSG00000092148	HECTD1	EULIR	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.007342	0.375367	
chunk0094_17_1	chr2	1095098	1095537	+	0	NA	intron (NM_018968, intron 2 of 16)	MIRc|SINE|MIR	144449	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.004556	0.413636	
chunk0071_276_1	chr15	85725152	85725393	+	0	NA	intron (NM_007200, intron 26 of 36)	intron (NM_007200, intron 26 of 36)	33453	NR_120366	101929679	Hs.513112	NR_120366		LOC101929679	-	uncharacterized LOC101929679	ncRNA	0.008299	0.446281	105(AAGAACAGCCAGTACT,-,0.00),106(AGAACAGCCAGTACTA,+,0.00)
chunk0159_129_1	chr5	139062631	139063116	+	0	NA	intron (NM_001037633, intron 4 of 10)	intron (NM_001037633, intron 4 of 10)	135503	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.002062	0.469136	134(AGGACATGGTGAGCCT,+,0.00)
chunk0091_34_1	chr19	3556852	3557344	+	0	NA	intron (NM_001287529, intron 1 of 9)	CpG	486	NM_174983	126321	Hs.656901	NM_021731	ENSG00000161091	MFSD12	C19orf28|PP3501	major facilitator superfamily domain containing 12	protein-coding	0.093496	0.693712	
chunk0170_434_1	chr6	118844647	118845005	+	0	NA	intron (NM_017696, intron 7 of 11)	MamRTE1|LINE|RTE-BovB	-49251	NM_014034	25842	Hs.292316	NM_014034	ENSG00000111875	ASF1A	CGI-98|CIA|HSPC146	anti-silencing function 1A histone chaperone	protein-coding	0.008380	0.423398	
chunk0200_2_1	chr9	14424946	14425222	+	0	NA	Intergenic	Intergenic	-26101	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.010870	0.487365	
chunk0018_57_1	chr1	216621724	216621923	+	0	NA	intron (NM_001243505, intron 3 of 6)	intron (NM_001243505, intron 3 of 6)	101649	NM_001243518	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.440000	
chunk0107_87_1	chr2	213031026	213031439	+	0	NA	intron (NM_016260, intron 5 of 7)	L2b|LINE|L2	-104896	NR_039936	100616472		NR_039936	ENSG00000283637	MIR4776-2	mir-4776-2	microRNA 4776-2	ncRNA	0.016949	0.410628	
chunk0084_92_1	chr17	75393615	75394190	+	0	NA	intron (NM_203506, intron 1 of 4)	intron (NM_203506, intron 1 of 4)	11806	NM_002086	2885	Hs.444356	NM_002086	ENSG00000177885	GRB2	ASH|EGFRBP-GRB2|Grb3-3|MST084|MSTP084|NCKAP2	growth factor receptor bound protein 2	protein-coding	0.038261	0.626736	
chunk0009_88_1	chr1	101223820	101224201	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	12518	NR_104626	101928370	Hs.534209	NR_104626		LOC101928370	-	uncharacterized LOC101928370	ncRNA	0.002625	0.413613	189(GAGGACACAGTGTTCT,-,0.00),190(AGGACACAGTGTTCTC,+,0.00)
chunk0100_61_1	chr2	106364384	106364960	+	0	NA	Intergenic	Intergenic	-17442	NR_003506	285189	Hs.143436	NR_003506	ENSG00000240935	PLGLA	PLGLA1|PLGP2|PRGA	plasminogen like A (pseudogene)	pseudo	0.000000	0.310225	488(AAATACAGGATGTGCT,-,0.00),489(AATACAGGATGTGCTT,+,0.00)
chunk0205_174_1	chr9	108894207	108894909	+	0	NA	intron (NM_003640, intron 25 of 36)	intron (NM_003640, intron 25 of 36)	32330	NM_006687	10881	Hs.123530	NM_006687	ENSG00000187003	ACTL7A	-	actin like 7A	protein-coding	0.005698	0.394026	
chunk0128_342_1	chr3	112395117	112395337	+	0	NA	Intergenic	MER41C|LTR|ERV1	62158	NM_001004196	4345	Hs.79015	NM_005944	ENSG00000091972	CD200	MOX1|MOX2|MRC|OX-2	CD200 molecule	protein-coding	0.009091	0.416290	
chunk0038_45_1	chr11	82250713	82251052	+	0	NA	intron (NR_120571, intron 3 of 7)	intron (NR_120571, intron 3 of 7)	153031	NR_120571	101928989	Hs.145117	NR_120571	ENSG00000245832	MIR4300HG	-	MIR4300 host gene	ncRNA	0.005900	0.394118	224(TGACACAGTATGTTCT,-,0.00),225(GACACAGTATGTTCTC,+,0.00),286(TAGTACAGCCTGTGCT,-,0.00),287(AGTACAGCCTGTGCTA,+,0.00)
chunk0180_57_1	chr7	54796788	54797379	+	0	NA	intron (NR_110040, intron 2 of 2)	intron (NR_110040, intron 2 of 2)	37770	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.010152	0.413851	
chunk0187_195_1	chr7	151743552	151743957	+	0	NA	intron (NM_001040633, intron 3 of 15)	intron (NM_001040633, intron 3 of 15)	-7440	NM_001304527	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.022222	0.559113	208(GGGAGCAGCATGTCCT,-,0.00),209(GGAGCAGCATGTCCTG,+,0.00)
chunk0047_228_1	chr12	71818845	71819064	+	0	NA	Intergenic	Intergenic	-20753	NR_027449	64786	Hs.284630	NM_022771	ENSG00000121749	TBC1D15	RAB7-GAP	TBC1 domain family member 15	protein-coding	0.009132	0.345455	
chunk0146_134_1	chr4	159196316	159196852	+	0	NA	Intergenic	MIR|SINE|MIR	-67690	NR_037459	100500881		NR_037459	ENSG00000264105	MIR3688-1	MIR3688|mir-3688-1	microRNA 3688-1	ncRNA	0.013060	0.366853	336(AGAGCAGCATGTTCAG,+,0.00)
chunk0140_338_1	chr4	73839609	73840223	+	0	NA	Intergenic	L2c|LINE|L2	3360	NM_002993	6372	Hs.164021	NM_002993	ENSG00000124875	CXCL6	CKA-3|GCP-2|GCP2|SCYB6	C-X-C motif chemokine ligand 6	protein-coding	0.006515	0.336585	
chunk0190_351_1	chr8	39637338	39637762	+	0	NA	exon (NM_014237, exon 9 of 20)	exon (NM_014237, exon 9 of 20)	52982	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.004717	0.289412	
chunk0209_369_1	chrX	54029547	54029941	+	0	NA	intron (NM_001184897, intron 2 of 21)	MER45C|DNA|hAT-Tip100	13450	NM_001184898	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.017766	0.498734	
chunk0194_227_1	chr8	86258271	86258831	+	0	NA	Intergenic	Intergenic	-28176	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.001786	0.356506	
chunk0115_117_1	chr21	22999663	23000259	+	0	NA	Intergenic	Intergenic	-79323	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.003356	0.274707	
chunk0047_309_1	chr12	73955563	73955859	+	0	NA	Intergenic	LTR55|LTR|ERVL?	336920	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.003378	0.350168	
chunk0071_345_1	chr15	88316655	88316980	+	0	NA	Intergenic	L1ME1|LINE|L1	-60086	NM_001012338	4916	Hs.185701	NM_002530	ENSG00000140538	NTRK3	GP145-TrkC|TRKC|gp145(trkC)	neurotrophic receptor tyrosine kinase 3	protein-coding	0.006154	0.328221	
chunk0095_368_1	chr2	23408219	23408908	+	0	NA	intron (NM_052920, intron 1 of 13)	L1ME4a|LINE|L1	23136	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.013062	0.343478	
chunk0032_357_1	chr11	10558272	10558680	+	0	NA	3' UTR (NM_006691, exon 6 of 6)	3' UTR (NM_006691, exon 6 of 6)	10342	NM_006691	10894	Hs.655332	NM_006691	ENSG00000133800	LYVE1	CRSBP-1|HAR|LYVE-1|XLKD1	lymphatic vessel endothelial hyaluronan receptor 1	protein-coding	0.007353	0.366748	
chunk0069_390_1	chr15	67674523	67674753	+	0	NA	intron (NM_001206804, intron 13 of 21)	intron (NM_001206804, intron 13 of 21)	125634	NM_001206804	5607	Hs.114198	NM_002757	ENSG00000137764	MAP2K5	HsT17454|MAPKK5|MEK5|PRKMK5	mitogen-activated protein kinase kinase 5	protein-coding	0.008696	0.346320	
chunk0012_169_1	chr1	158547440	158547790	+	0	NA	exon (NM_001005189, exon 1 of 1)	exon (NM_001005189, exon 1 of 1)	490	NM_001005189	391112	Hs.553780	NM_001005189	ENSG00000197532	OR6Y1	OR1-11|OR6Y2	olfactory receptor family 6 subfamily Y member 1	protein-coding	0.008571	0.470085	
chunk0066_335_1	chr15	36791773	36792247	+	0	NA	intron (NM_032499, intron 11 of 11)	intron (NM_032499, intron 11 of 11)	26496	NR_027320	161635	Hs.659822	NR_027320		CSNK1A1P1	CSNK1A1P	casein kinase 1 alpha 1 pseudogene 1	pseudo	0.012658	0.437895	
chunk0196_93_1	chr8	102958570	102959265	+	0	NA	intron (NR_126339, intron 2 of 2)	intron (NR_126339, intron 2 of 2)	-62103	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.010072	0.432471	414(TGAAACATTCTGTACT,-,0.00),415(GAAACATTCTGTACTT,+,0.00)
chunk0152_237_1	chr5	60519248	60519813	+	0	NA	intron (NR_024617, intron 1 of 3)	intron (NR_024617, intron 1 of 3)	-31432	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.001770	0.363958	284(TGGCACAAGGTGTACT,-,0.00),285(GGCACAAGGTGTACTA,+,0.00)
chunk0036_394_1	chr11	67688883	67689388	+	0	NA	Intergenic	L1MB5|LINE|L1	-7921	NM_001031615	222	Hs.87539	NM_000695	ENSG00000132746	ALDH3B2	ALDH8	aldehyde dehydrogenase 3 family member B2	protein-coding	0.011881	0.482213	327(GGGCACACAGTGTTCT,-,0.00),328(GGCACACAGTGTTCTA,+,0.00)
chunk0052_77_1	chr13	21694784	21695187	+	0	NA	intron (NM_002010, intron 2 of 2)	intron (NM_002010, intron 2 of 2)	23909	NM_002010	2254	Hs.111	NM_002010	ENSG00000102678	FGF9	FGF-9|GAF|HBFG-9|HBGF-9|SYNS3	fibroblast growth factor 9	protein-coding	0.007444	0.418317	
chunk0086_237_1	chr18	22831595	22832066	+	0	NA	Intergenic	Intergenic	-44993	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.004246	0.438559	
chunk0068_119_1	chr15	52478623	52479007	+	0	NA	intron (NM_001142495, intron 1 of 39)	Tigger2|DNA|TcMar-Tigger	50235	NM_000259	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.007812	0.358442	
chunk0102_239_1	chr2	148956981	148957523	+	0	NA	intron (NR_111932, intron 3 of 19)	intron (NR_111932, intron 3 of 19)	9422	NR_111932	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.007380	0.383057	285(CAGAACACTGTGTAAC,-,0.00)
chunk0043_81_1	chr12	14461691	14462480	+	0	NA	intron (NM_001286514, intron 9 of 14)	intron (NM_001286514, intron 9 of 14)	77021	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.001267	0.298734	
chunk0179_299_1	chr7	50055363	50056024	+	0	NA	intron (NM_001159878, intron 4 of 7)	MIR|SINE|MIR	37571	NM_007009	11055	Hs.388841	NM_007009	ENSG00000042813	ZPBP	ZPBP1	zona pellucida binding protein	protein-coding	0.001513	0.315710	
chunk0007_342_1	chr1	84833033	84833493	+	0	NA	intron (NM_012152, intron 2 of 2)	intron (NM_012152, intron 2 of 2)	59950	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.008696	0.364425	
chunk0129_221_1	chr3	121848593	121848931	+	0	NA	intron (NM_018456, intron 2 of 5)	intron (NM_018456, intron 2 of 5)	13575	NM_018456	55840	Hs.477325	NM_018456	ENSG00000145088	EAF2	BM040|TRAITS|U19	ELL associated factor 2	protein-coding	0.002959	0.336283	
chunk0211_288_1	chrX	122385862	122386420	+	0	NA	Intergenic	Intergenic	-798102	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.001792	0.329159	
chunk0100_330_1	chr2	116665906	116666368	+	0	NA	Intergenic	L1MB7|LINE|L1	-1148542	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.008658	0.304536	
chunk0123_1_1	chr3	40042638	40043127	+	0	NA	intron (NM_015460, intron 2 of 16)	MER47B|DNA|TcMar-Tigger	-57129	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.004090	0.361224	
chunk0184_289_1	chr7	118844958	118845431	+	0	NA	Intergenic	L1MA8|LINE|L1	620536	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.002114	0.383966	
chunk0039_226_1	chr11	101599017	101599216	+	0	NA	Intergenic	L1M5|LINE|L1	-15188	NM_004621	7225	Hs.159003	NM_004621	ENSG00000137672	TRPC6	FSGS2|TRP6	transient receptor potential cation channel subfamily C member 6	protein-coding	0.005025	0.305000	
chunk0078_149_1	chr17	4123921	4124474	+	0	NA	intron (NM_015113, intron 1 of 54)	intron (NM_015113, intron 1 of 54)	-16892	NR_039973									0.010850	0.400722	288(GGAACTCACTGCGCTT,+,0.00)
chunk0028_28_1	chr10	82702474	82702952	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-469793	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.010460	0.377871	
chunk0007_220_1	chr1	81700887	81701193	+	0	NA	intron (NM_001297704, intron 1 of 20)	intron (NM_001297704, intron 1 of 20)	1270	NM_001297704	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.013072	0.381107	
chunk0122_340_1	chr3	37224971	37225212	+	0	NA	Intergenic	Intergenic	-18100	NM_002078	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.008299	0.483471	
chunk0181_131_1	chr7	80999112	80999576	+	0	NA	Intergenic	Intergenic	-79993	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.006466	0.462366	
chunk0165_283_1	chr6	36199552	36200148	+	0	NA	intron (NM_015695, intron 1 of 12)	L2a|LINE|L2	3077	NM_015695	27154	Hs.520096	NM_015695	ENSG00000096070	BRPF3	-	bromodomain and PHD finger containing 3	protein-coding	0.005034	0.386935	
chunk0020_310_1	chr1	237584228	237585385	+	0	NA	intron (NM_001035, intron 29 of 104)	AluJr|SINE|Alu	113687	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.006050	0.404145	
chunk0050_290_1	chr12	106689932	106690400	+	0	NA	intron (NM_032491, intron 3 of 13)	intron (NM_032491, intron 3 of 13)	-5466	NR_038912	100505978	Hs.662583	NR_038912	ENSG00000257711	LOC100505978	-	uncharacterized LOC100505978	ncRNA	0.006410	0.381663	
chunk0074_118_1	chr16	22614562	22615036	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	69101	NR_003676	653786	Hs.564945	NR_003676	ENSG00000257838	OTOAP1	-	OTOA pseudogene 1	pseudo	0.010549	0.435789	
chunk0083_190_1	chr17	66508730	66509536	+	0	NA	intron (NM_002737, intron 3 of 16)	MLT1H2|LTR|ERVL-MaLR	-92279	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.006203	0.474597	
chunk0114_24_1	chr21	7917028	7917295	+	0	NA	Intergenic	(ATTCCATTCC)n|Simple_repeat|Simple_repeat	-146613	NM_001282537	101928147	Hs.303798	NM_001282537	ENSG00000222018	FAM243A	C21orf140	family with sequence similarity 243 member A	protein-coding	0.014981	0.380597	
chunk0062_18_1	chr14	66507519	66507966	+	0	NA	5' UTR (NM_020806, exon 1 of 23)	5' UTR (NM_020806, exon 1 of 23)	335	NM_020806	10243	Hs.208765	NM_020806	ENSG00000171723	GPHN	GEPH|GPH|GPHRYN|HKPX1|MOCODC	gephyrin	protein-coding	0.082774	0.642857	
chunk0146_48_1	chr4	155597212	155597662	+	0	NA	Intergenic	Intergenic	-69273	NM_000856	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.002222	0.277162	
chunk0190_185_1	chr8	33421442	33421740	+	0	NA	intron (NM_032664, intron 3 of 4)	intron (NM_032664, intron 3 of 4)	51555	NM_032664	84750	Hs.458713	NM_032664	ENSG00000172728	FUT10	FUCTX	fucosyltransferase 10	protein-coding	0.016779	0.421405	
chunk0097_333_1	chr2	57626055	57626496	+	0	NA	Intergenic	Intergenic	-281376	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.006803	0.357466	
chunk0201_239_1	chr9	37733301	37733569	+	0	NA	intron (NM_014907, intron 10 of 15)	intron (NM_014907, intron 10 of 15)	-20368	NM_001286953	158234	Hs.655614	NM_144964	ENSG00000165275	TRMT10B	RG9MTD3|bA3J10.9	tRNA methyltransferase 10B	protein-coding	0.007463	0.416357	75(GGGAACACTAAGTACT,-,0.00),76(GGAACACTAAGTACTG,+,0.00)
chunk0070_405_1	chr15	77441097	77441629	+	0	NA	intron (NM_001304504, intron 1 of 9)	Charlie22a|DNA|hAT-Charlie	20712	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.003759	0.343340	
chunk0165_125_1	chr6	32983771	32984327	+	0	NA	Intergenic	Intergenic	10965	NM_001199456	6046	Hs.75243	NM_005104	ENSG00000204256	BRD2	BRD2-IT1|D6S113E|FSH|FSRG1|NAT|O27.1.1|RING3|RNF3	bromodomain containing 2	protein-coding	0.007194	0.421903	
chunk0041_29_1	chr12	754417	754616	+	0	NA	intron (NM_213655, intron 1 of 27)	intron (NM_213655, intron 1 of 27)	1593	NM_018979	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.025126	0.500000	
chunk0005_450_1	chr1	63487337	63488123	+	0	NA	intron (NM_014288, intron 3 of 8)	Tigger3a|DNA|TcMar-Tigger	35543	NM_001206739	23421	Hs.166539	NM_014288	ENSG00000142856	ITGB3BP	CENP-R|CENPR|HSU37139|NRIF3|TAP20	integrin subunit beta 3 binding protein	protein-coding	0.010178	0.349428	
chunk0042_236_1	chr12	6278099	6278812	+	0	NA	Intergenic	Intergenic	-31981	NM_018173	55200	Hs.631660	NM_018173	ENSG00000008323	PLEKHG6	MyoGEF	pleckstrin homology and RhoGEF domain containing G6	protein-coding	0.077139	0.663866	
chunk0002_397_1	chr1	27234570	27234778	+	0	NA	5' UTR (NM_001276252, exon 1 of 16)	5' UTR (NM_001276252, exon 1 of 16)	158	NM_001276252	23038	Hs.469154	NM_015023	ENSG00000142784	WDTC1	ADP|DCAF9	WD and tetratricopeptide repeats 1	protein-coding	0.105769	0.708134	
chunk0122_222_1	chr3	33637425	33637841	+	0	NA	intron (NM_015097, intron 8 of 38)	L2a|LINE|L2	21808	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.016827	0.393285	
chunk0079_337_1	chr17	17662462	17662838	+	0	NA	Intergenic	L2a|LINE|L2	15038	NR_131243	105371564	Hs.369680	NR_131243	ENSG00000223979	SMCR2	TCONS_00025215	Smith-Magenis syndrome chromosome region, candidate 2	ncRNA	0.023936	0.535809	
chunk0112_288_1	chr20	43849540	43850441	+	0	NA	Intergenic	Intergenic	-64862	NM_001098797	84969	Hs.26608	NM_032883	ENSG00000124191	TOX2	C20orf100|GCX-1|GCX1|dJ1108D11.2|dJ495O3.1	TOX high mobility group box family member 2	protein-coding	0.019978	0.441242	
chunk0013_384_1	chr1	172609472	172609838	+	0	NA	intron (NM_014283, intron 23 of 23)	intron (NM_014283, intron 23 of 23)	-49353	NM_000639	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.005464	0.354223	
chunk0099_59_1	chr2	84810539	84810853	+	0	NA	intron (NM_001370, intron 72 of 76)	intron (NM_001370, intron 72 of 76)	70549	NM_001277053	129293	Hs.469134	NM_001080824	ENSG00000186854	TRABD2A	C2orf89|TIKI1	TraB domain containing 2A	protein-coding	0.006369	0.555556	
chunk0006_354_1	chr1	72754690	72755114	+	0	NA	Intergenic	L1MD1|LINE|L1	-472308	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.002358	0.360000	
chunk0067_356_1	chr15	48538926	48539363	+	0	NA	intron (NM_000138, intron 6 of 65)	intron (NM_000138, intron 6 of 65)	106644	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.006865	0.420091	
chunk0064_148_1	chr14	91743102	91743779	+	0	NA	Intergenic	HAL1|LINE|L1	-11354	NM_024764	79820	Hs.131755	NM_024764	ENSG00000133962	CATSPERB	C14orf161|CatSper(beta)	cation channel sperm associated auxiliary subunit beta	protein-coding	0.005908	0.424779	
chunk0085_37_1	chr18	624294	624493	+	0	NA	intron (NM_014410, intron 3 of 8)	intron (NM_014410, intron 3 of 8)	7693	NM_199167	27098	Hs.732341	NM_014410	ENSG00000079101	CLUL1	RA337M	clusterin like 1	protein-coding	0.015075	0.350000	
chunk0162_405_1	chr5	179824857	179825156	+	0	NA	intron (NM_003900, intron 4 of 7)	intron (NM_003900, intron 4 of 7)	4164	NM_003900	8878	Hs.587290	NM_003900	ENSG00000161011	SQSTM1	A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B	sequestosome 1	protein-coding	0.010033	0.530000	
chunk0046_105_1	chr12	57175453	57175803	+	0	NA	exon (NM_002332, exon 23 of 89)	exon (NM_002332, exon 23 of 89)	-18876	NR_031597	100302201		NR_031597	ENSG00000221365	MIR1228	MIRN1228|hsa-mir-1228|mir-1228	microRNA 1228	ncRNA	0.028571	0.606838	
chunk0017_464_1	chr1	214573441	214573869	+	0	NA	Intergenic	Intergenic	-21974	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.014019	0.400932	215(AAGAACAATGTGAACC,-,0.00),216(AGAACAATGTGAACCT,+,0.00)
chunk0090_40_1	chr19	1409018	1409385	+	0	NA	intron (NM_018959, intron 1 of 11)	intron (NM_018959, intron 1 of 11)	1632	NM_018959	26528	Hs.222510	NM_018959	ENSG00000071626	DAZAP1	-	DAZ associated protein 1	protein-coding	0.027248	0.603261	
chunk0033_91_1	chr11	14125071	14125270	+	0	NA	intron (NM_006108, intron 5 of 15)	intron (NM_006108, intron 5 of 15)	162533	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.010050	0.500000	
chunk0127_49_1	chr3	88989670	88990042	+	0	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	-117668	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005376	0.340483	
chunk0023_452_1	chr10	32105911	32106219	+	0	NA	Intergenic	MIRc|SINE|MIR	-49622	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.003247	0.401294	
chunk0120_249_1	chr3	8803769	8803977	+	0	NA	Intergenic	L1MC1|LINE|L1	-34259	NM_000916	5021	Hs.2820	NM_000916	ENSG00000180914	OXTR	OT-R	oxytocin receptor	protein-coding	0.000000	0.301435	
chunk0028_306_1	chr10	91676756	91677338	+	0	NA	Intergenic	Intergenic	-43946	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.005155	0.377358	
chunk0170_18_1	chr6	109120144	109120631	+	0	NA	intron (NM_001083535, intron 3 of 12)	intron (NM_001083535, intron 3 of 12)	-8917	NM_173830	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.006160	0.360656	
chunk0022_219_1	chr10	13982980	13983515	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-91037	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.022430	0.445896	255(AGGCTCAATGTGTTCC,-,0.00),256(GGCTCAATGTGTTCCT,+,0.00)
chunk0006_428_1	chr1	76407369	76407755	+	0	NA	intron (NM_152996, intron 2 of 4)	intron (NM_152996, intron 2 of 4)	332858	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.000000	0.330749	
chunk0133_34_1	chr3	165966183	165966557	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-128905	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.002674	0.322667	
chunk0052_399_1	chr12	130793724	130794083	+	0	NA	intron (NM_001980, intron 9 of 9)	intron (NM_001980, intron 9 of 9)	45371	NM_001980	2054	Hs.437585	NM_001980	ENSG00000111450	STX2	EPIM|EPM|STX2A|STX2B|STX2C	syntaxin 2	protein-coding	0.011142	0.494444	
chunk0011_327_1	chr1	152086685	152087489	+	0	NA	exon (NM_001008536, exon 3 of 3)	exon (NM_001008536, exon 3 of 3)	1977	NM_001008536	126637	Hs.546477	NM_001008536	ENSG00000182898	TCHHL1	S100A17|THHL1	trichohyalin like 1	protein-coding	0.001244	0.436025	463(AGGATCATTGTGTTCA,-,0.00),464(GGATCATTGTGTTCAG,+,0.00)
chunk0138_444_1	chr4	46028760	46029328	+	0	NA	Intergenic	L1PB1|LINE|L1	95021	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.005282	0.340949	
chunk0209_187_1	chrX	43757282	43757568	+	0	NA	Intergenic	Intergenic	102518	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.000000	0.292683	
chunk0150_236_1	chr5	35997914	35998160	+	0	NA	intron (NM_001171873, intron 1 of 5)	PRIMA4-int|LTR|ERV1	2991	NM_001171873	133688	Hs.254699	NM_152404	ENSG00000145626	UGT3A1	-	UDP glycosyltransferase family 3 member A1	protein-coding	0.000000	0.421053	177(ATGAACAACCTGATCC,-,0.00)
chunk0119_421_1	chr22	49931050	49931344	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	12567	NM_001135101	79174	Hs.211282	NM_024324	ENSG00000184164	CRELD2	-	cysteine rich with EGF like domains 2	protein-coding	0.010204	0.542373	137(AGGAACTGAGTGTTTC,-,0.00),138(GGAACTGAGTGTTTCC,+,0.00)
chunk0018_48_1	chr1	216302889	216303412	+	0	NA	intron (NM_206933, intron 9 of 71)	intron (NM_206933, intron 9 of 71)	120246	NM_206933	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.001912	0.322519	
chunk0120_351_1	chr3	11504414	11504960	+	0	NA	intron (NM_001136031, intron 17 of 17)	HAL1|LINE|L1	64237	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.003663	0.402194	
chunk0124_227_1	chr3	56593464	56593910	+	0	NA	exon (NM_001141947, exon 9 of 18)	exon (NM_001141947, exon 9 of 18)	36531	NR_024460	285331	Hs.476399	NM_001012506	ENSG00000180376	CCDC66	-	coiled-coil domain containing 66	protein-coding	0.002242	0.373602	
chunk0004_392_1	chr1	51977261	51977501	+	0	NA	intron (NM_002867, intron 1 of 4)	L2b|LINE|L2	13383	NM_002867	5865	Hs.123072	NM_002867	ENSG00000169213	RAB3B	-	RAB3B, member RAS oncogene family	protein-coding	0.000000	0.477178	
chunk0076_74_1	chr16	63402996	63403209	+	0	NA	Intergenic	L1MB4|LINE|L1	-1366267	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.014085	0.383178	6(TTGAACATGTTGTCCC,-,0.00),7(TGAACATGTTGTCCCA,+,0.00)
chunk0140_399_1	chr4	75484874	75485391	+	0	NA	intron (NM_001009922, intron 7 of 7)	MER57A-int|LTR|ERV1	24164	NR_103725	25898	Hs.48297	NM_015436	ENSG00000163743	RCHY1	ARNIP|CHIMP|PIRH2|PRO1996|RNF199|ZCHY|ZNF363	ring finger and CHY zinc finger domain containing 1	protein-coding	0.003868	0.343629	
chunk0043_373_1	chr12	24294418	24294844	+	0	NA	intron (NM_152989, intron 3 of 17)	intron (NM_152989, intron 3 of 17)	71360	NR_120472	101928471	Hs.569156	NR_120472	ENSG00000256120	SOX5-AS1	-	SOX5 antisense RNA 1	ncRNA	0.011737	0.435597	
chunk0053_205_1	chr13	31949070	31949462	+	0	NA	intron (NR_027062, intron 2 of 3)	L2c|LINE|L2	-82034	NM_023037	10129	Hs.507669	NM_023037	ENSG00000073910	FRY	13CDNA73|214K23.2|C13orf14|CG003|bA207N4.2|bA37E23.1	FRY microtubule binding protein	protein-coding	0.002551	0.437659	212(AGGCACACAGTGTGCA,-,0.00),213(GGCACACAGTGTGCAT,+,0.00)
chunk0171_431_1	chr6	131631539	131632275	+	0	NA	Intergenic	Intergenic	-3668	NM_001270522	9439	Hs.29679	NM_004830	ENSG00000112282	MED23	ARC130|CRSP130|CRSP133|CRSP3|DRIP130|MRT18|SUR-2|SUR2	mediator complex subunit 23	protein-coding	0.005435	0.424695	436(AGGTACAGGTTGTTCT,-,0.00),437(GGTACAGGTTGTTCTG,+,0.00),476(AGGTACAGATTGTTCT,-,0.00),477(GGTACAGATTGTTCTA,+,0.00)
chunk0024_17_1	chr10	32985738	32985949	+	0	NA	Intergenic	Intergenic	-27478	NM_002211	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.004739	0.372642	
chunk0155_155_1	chr5	94100749	94101565	+	0	NA	intron (NR_028080, intron 1 of 8)	L1PA14|LINE|L1	10542	NM_001163417	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.011029	0.376989	
chunk0142_290_1	chr4	100143418	100143840	+	0	NA	Intergenic	Intergenic	-46404	NR_125924	101929353	Hs.147584	NR_125924	ENSG00000249710	LOC101929353	-	uncharacterized LOC101929353	ncRNA	0.004739	0.295508	
chunk0017_114_1	chr1	206036781	206037101	+	0	NA	Intergenic	Intergenic	-13032	NM_001910	1510	Hs.644082	NM_001910	ENSG00000196188	CTSE	CATE	cathepsin E	protein-coding	0.000000	0.457944	
chunk0058_4_1	chr14	18655997	18656215	+	0	NA	Intergenic	Intergenic	-22472	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.027523	0.328767	
chunk0198_220_1	chr8	133931335	133931764	+	0	NA	Intergenic	L1ME3|LINE|L1	45053	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006993	0.318605	250(GAAAACATCTTGTTCC,-,0.00),251(AAAACATCTTGTTCCC,+,0.00)
chunk0191_428_1	chr8	57832974	57833173	+	0	NA	Intergenic	L1M4a2|LINE|L1	-145285	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.000000	0.325000	
chunk0121_91_1	chr3	16490278	16490549	+	0	NA	intron (NM_015150, intron 2 of 9)	intron (NM_015150, intron 2 of 9)	23302	NM_015150	23180	Hs.98910	NM_015150	ENSG00000131378	RFTN1	MIG2|PIB10|PIG9|RAFTLIN	raftlin, lipid raft linker 1	protein-coding	0.007380	0.540441	
chunk0149_106_1	chr5	19022461	19022878	+	0	NA	Intergenic	MER83|LTR|ERV1	863603	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.009592	0.387560	
chunk0105_411_1	chr2	192876654	192877197	+	0	NA	Intergenic	Intergenic	127080	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.003683	0.329044	
chunk0021_34_1	chr10	849230	849738	+	0	NA	intron (NM_015155, intron 5 of 17)	L1MC3|LINE|L1	82221	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.011811	0.406680	
chunk0177_357_1	chr7	26659238	26659815	+	0	NA	Intergenic	Intergenic	20441	NM_001302625									0.005199	0.356401	
chunk0151_144_1	chr5	45784545	45784744	+	0	NA	Intergenic	MER50B|LTR|ERV1	-88526	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.010050	0.480000	178(AGGCACAGTGTGTTTA,-,0.00),179(GGCACAGTGTGTTTAG,+,0.00)
chunk0203_285_1	chr9	88871753	88871952	+	0	NA	Intergenic	Intergenic	-119011	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.030151	0.630000	
chunk0009_109_1	chr1	102602912	102603549	+	0	NA	Intergenic	HAL1M8|LINE|L1	505266	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.007849	0.363636	
chunk0181_318_1	chr7	87491619	87492347	+	0	NA	Intergenic	L1MDa|LINE|L1	-16280	NM_018850	5244	Hs.654403	NM_000443	ENSG00000005471	ABCB4	ABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3	ATP binding cassette subfamily B member 4	protein-coding	0.002747	0.445816	
chunk0205_45_1	chr9	105901464	105901973	+	0	NA	Intergenic	Intergenic	207193	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.007859	0.549020	232(GGGGTCAGTGTGTTCC,-,0.00),233(GGGTCAGTGTGTTCCT,+,0.00)
chunk0059_107_1	chr14	31065157	31065684	+	0	NA	intron (NM_001254728, intron 1 of 5)	L2c|LINE|L2	38777	NM_001254728	11154	Hs.293411	NM_007077	ENSG00000100478	AP4S1	AP47B|CLA20|CLAPS4|CPSQ6|SPG52	adaptor related protein complex 4 subunit sigma 1	protein-coding	0.009488	0.390152	
chunk0165_31_1	chr6	29904420	29904635	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	16767	NR_001434	3136	Hs.728808	NR_001434		HLA-H	HLAHP	major histocompatibility complex, class I, H (pseudogene)	pseudo	0.004651	0.430556	
chunk0139_41_1	chr4	48602662	48603778	+	0	NA	intron (NM_015030, intron 12 of 63)	intron (NM_015030, intron 12 of 63)	112968	NM_175619	326340	Hs.276457	NM_175619	ENSG00000182223	ZAR1	Z3CXXC6	zygote arrest 1	protein-coding	0.006272	0.358997	
chunk0074_331_1	chr16	31117739	31118615	+	0	NA	intron (NM_032188, intron 1 of 10)	intron (NM_032188, intron 1 of 10)	513	NM_032188	84148	Hs.533803	NM_032188	ENSG00000103510	KAT8	MOF|MYST1|ZC2HC8|hMOF	lysine acetyltransferase 8	protein-coding	0.050228	0.582668	675(CAGAACACACTGTGCC,-,0.00),676(AGAACACACTGTGCCC,+,0.00)
chunk0065_94_1	chr15	23882057	23882571	+	0	NA	Intergenic	L1MC3|LINE|L1	-92833	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.011673	0.386408	
chunk0081_202_1	chr17	42388604	42388880	+	0	NA	promoter-TSS (NM_213662)	promoter-TSS (NM_213662)	-247	NM_139276	6774	Hs.463059	NM_003150	ENSG00000168610	STAT3	ADMIO|ADMIO1|APRF|HIES	signal transducer and activator of transcription 3	protein-coding	0.054348	0.610108	
chunk0027_264_1	chr10	77305596	77306262	+	0	NA	intron (NM_001271518, intron 1 of 27)	UCON29|DNA|PiggyBac?	-44943	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.004505	0.464768	
chunk0013_252_1	chr1	169849515	169849908	+	0	NA	intron (NM_018186, intron 21 of 23)	intron (NM_018186, intron 21 of 23)	44248	NM_181093	57147	Hs.435560	NM_020423	ENSG00000000457	SCYL3	PACE-1|PACE1	SCY1 like pseudokinase 3	protein-coding	0.012723	0.383249	
chunk0117_29_1	chr22	11901095	11901961	+	0	NA	intron (NR_110761, intron 1 of 2)	L1MA5|LINE|L1	4122	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.005774	0.344867	
chunk0006_282_1	chr1	70587969	70588475	+	0	NA	Intergenic	Intergenic	-118231	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.005929	0.370809	
chunk0203_123_1	chr9	84992433	84992659	+	0	NA	intron (NM_001018064, intron 15 of 16)	intron (NM_001018064, intron 15 of 16)	322169	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.008850	0.471366	
chunk0110_449_1	chr20	21218670	21219127	+	0	NA	promoter-TSS (NR_109956)	promoter-TSS (NR_109956)	-609	NR_109956	101929591	Hs.656066	NR_109956	ENSG00000232712	KIZ-AS1	-	KIZ antisense RNA 1	ncRNA	0.008753	0.421397	
chunk0115_102_1	chr21	22609792	22609991	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-469393	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.010050	0.315000	
chunk0067_198_1	chr15	44868705	44869321	+	0	NA	Intergenic	L1PA6|LINE|L1	-87689	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.003247	0.392220	299(CTGAACAATCTGTTCC,-,0.00),300(TGAACAATCTGTTCCT,+,0.00)
chunk0090_63_1	chr19	2093250	2093905	+	0	NA	intron (NM_130807, intron 1 of 4)	AluSx|SINE|Alu	2693	NM_130807	126308	Hs.744938	NM_130807	ENSG00000172081	MOB3A	MOB-LAK|MOB1C|MOBKL2A|moblak	MOB kinase activator 3A	protein-coding	0.025954	0.541159	249(GGTCCAGCGTGTGCCT,+,0.00)
chunk0063_437_1	chr14	88708327	88708540	+	0	NA	intron (NM_183387, intron 10 of 42)	L2c|LINE|L2	84319	NM_183387	161436	Hs.325846	NM_183387	ENSG00000165521	EML5	EMAP-2|EMAP-5	EMAP like 5	protein-coding	0.000000	0.308411	
chunk0140_77_1	chr4	67616735	67616953	+	0	NA	3' UTR (NM_018227, exon 33 of 33)	3' UTR (NM_018227, exon 33 of 33)	58116	NM_012108	26228	Hs.435579	NM_012108	ENSG00000035720	STAP1	BRDG1|STAP-1	signal transducing adaptor family member 1	protein-coding	0.000000	0.255708	
chunk0031_1_1	chr10	121393128	121393754	+	0	NA	Intergenic	Intergenic	200526	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.004792	0.377990	
chunk0094_328_1	chr2	9031253	9031765	+	0	NA	Intergenic	Intergenic	-27762	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.000000	0.321637	
chunk0088_449_1	chr18	56764260	56764727	+	0	NA	intron (NM_052834, intron 16 of 26)	L1MA8|LINE|L1	113108	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.002141	0.305556	
chunk0145_66_1	chr4	145580936	145581524	+	0	NA	Intergenic	Intergenic	-38158	NM_172250	166785	Hs.452864	NM_172250	ENSG00000151611	MMAA	cblA	metabolism of cobalamin associated A	protein-coding	0.005102	0.392190	
chunk0195_276_1	chr8	98211312	98211570	+	0	NA	intron (NM_024759, intron 6 of 11)	intron (NM_024759, intron 6 of 11)	82952	NM_024759	79815	Hs.309489	NM_024759	ENSG00000104361	NIPAL2	NPAL2	NIPA like domain containing 2	protein-coding	0.003876	0.366795	
chunk0158_152_1	chr5	127515516	127516166	+	0	NA	Intergenic	L2a|LINE|L2	-1768	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.013846	0.443932	
chunk0199_353_1	chr9	12496715	12497081	+	0	NA	Intergenic	L1ME1|LINE|L1	-196488	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.002732	0.310627	
chunk0153_363_1	chr5	74521894	74522522	+	0	NA	intron (NR_126354, intron 1 of 2)	intron (NR_126354, intron 1 of 2)	14768	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.000000	0.406995	
chunk0034_352_1	chr11	35907894	35908611	+	0	NA	Intergenic	Intergenic	-35729	NM_174902	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.005579	0.387187	305(AGGAACACAGTGTCCC,-,0.00),306(GGAACACAGTGTCCCT,+,0.00),367(AAGAACTGCCAGTTCT,-,0.00),368(AGAACTGCCAGTTCTC,+,0.00)
chunk0094_454_1	chr2	11556819	11557572	+	0	NA	intron (NM_014668, intron 2 of 32)	intron (NM_014668, intron 2 of 32)	14470	NM_033090	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.007968	0.335544	185(GAGGACAAATTGTTCT,-,0.00),186(AGGACAAATTGTTCTC,+,0.00)
chunk0154_232_1	chr5	80877563	80878031	+	0	NA	TTS (NM_002439)	TTS (NM_002439)	-82892	NM_006909	5924	Hs.162129	NM_006909	ENSG00000113319	RASGRF2	GRF2|RAS-GRF2	Ras protein specific guanine nucleotide releasing factor 2	protein-coding	0.006410	0.537313	172(AGGAGCATTGTGTCCT,-,0.00),173(GGAGCATTGTGTCCTG,+,0.00)
chunk0124_44_1	chr3	52444866	52445065	+	0	NA	promoter-TSS (NM_020163)	promoter-TSS (NM_020163)	62	NM_020163	56920	Hs.59729	NM_020163	ENSG00000010319	SEMA3G	sem2	semaphorin 3G	protein-coding	0.040201	0.700000	
chunk0075_91_1	chr16	48338253	48338537	+	0	NA	intron (NM_031490, intron 12 of 14)	intron (NM_031490, intron 12 of 14)	-17290	NR_040677	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.000000	0.400000	
chunk0147_327_1	chr4	185195950	185196256	+	0	NA	intron (NM_020827, intron 1 of 4)	MER112|DNA|hAT-Charlie	7925	NM_020827	57587	Hs.535734	NM_020827	ENSG00000164323	CFAP97	KIAA1430|hmw	cilia and flagella associated protein 97	protein-coding	0.013072	0.364821	
chunk0136_225_1	chr4	8228556	8228977	+	0	NA	intron (NM_018986, intron 12 of 17)	intron (NM_018986, intron 12 of 17)	29433	NM_018986	54436	Hs.479116	NM_018986	ENSG00000125089	SH3TC1	-	SH3 domain and tetratricopeptide repeats 1	protein-coding	0.040380	0.630332	234(GGAGACAGGCAGTTCC,-,0.00),235(GAGACAGGCAGTTCCC,+,0.00),325(GAGCACTGAAAGTCCT,-,0.00),326(AGCACTGAAAGTCCTG,+,0.00)
chunk0130_253_1	chr3	135855807	135856295	+	0	NA	Intergenic	L1PB|LINE|L1	-109622	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.002049	0.374233	
chunk0031_295_1	chr10	128633289	128633666	+	0	NA	Intergenic	L1MC4a|LINE|L1	347527	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.005305	0.283069	
chunk0174_129_1	chr6	157382660	157383160	+	0	NA	intron (NM_024630, intron 1 of 8)	intron (NM_024630, intron 1 of 8)	1385	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.014000	0.419162	
chunk0050_333_1	chr12	107380160	107380374	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	61847	NM_001018072	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.018692	0.400000	
chunk0061_234_1	chr14	60686777	60687373	+	0	NA	Intergenic	Intergenic	37059	NM_017420	51804	Hs.97849	NM_017420	ENSG00000100625	SIX4	AREC3	SIX homeobox 4	protein-coding	0.001678	0.346734	
chunk0114_90_1	chr21	9309751	9309950	+	0	NA	Intergenic	AluSx|SINE|Alu	-180089	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.010050	0.480000	
chunk0193_66_1	chr8	73033054	73033389	+	0	NA	intron (NM_017489, intron 8 of 9)	intron (NM_017489, intron 8 of 9)	24359	NM_003218	7013	Hs.442707	NM_003218	ENSG00000147601	TERF1	PIN2|TRBF1|TRF|TRF1|hTRF1-AS|t-TRF1	telomeric repeat binding factor 1	protein-coding	0.005970	0.318452	
chunk0120_200_1	chr3	7160602	7161318	+	0	NA	intron (NM_000844, intron 2 of 9)	L2b|LINE|L2	-266943	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.005587	0.423989	331(TGGGACACAGTGTGTT,-,0.00),332(GGGACACAGTGTGTTC,+,0.00),333(GGACACAGTGTGTTCT,-,0.00),334(GACACAGTGTGTTCTC,+,0.00)
chunk0176_83_1	chr7	11497578	11497992	+	0	NA	intron (NM_015204, intron 6 of 26)	L1PA12|LINE|L1	334413	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.007246	0.448193	
chunk0137_117_1	chr4	14339607	14339959	+	0	NA	Intergenic	Intergenic	227815	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.005682	0.492918	
chunk0158_396_1	chr5	134632305	134632504	+	0	NA	intron (NM_001033503, intron 1 of 7)	intron (NM_001033503, intron 1 of 7)	439	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.025126	0.535000	
chunk0057_40_1	chr13	96173627	96173826	+	0	NA	intron (NM_153456, intron 1 of 1)	intron (NM_153456, intron 1 of 1)	82887	NM_153456	266722	Hs.171001	NM_153456	ENSG00000185352	HS6ST3	HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.000000	0.290000	
chunk0006_422_1	chr1	76143922	76144147	+	0	NA	intron (NM_152996, intron 1 of 4)	MIR|SINE|MIR	69330	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.000000	0.455752	
chunk0128_216_1	chr3	108060480	108060679	+	0	NA	intron (NM_198793, intron 4 of 8)	MLT1D|LTR|ERVL-MaLR	30509	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.005025	0.460000	
chunk0021_387_1	chr1	246566306	246567247	+	0	NA	promoter-TSS (NM_022366)	promoter-TSS (NM_022366)	439	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.073326	0.607219	
chunk0023_458_1	chr10	32332197	32332648	+	0	NA	intron (NM_001282391, intron 1 of 13)	MLT1F|LTR|ERVL-MaLR	14626	NM_001272019	80314	Hs.167805	NM_025209	ENSG00000120616	EPC1	Epl1	enhancer of polycomb homolog 1	protein-coding	0.006652	0.482301	
chunk0112_282_1	chr20	43657400	43657657	+	0	NA	Intergenic	CpG	-9491	NM_001278610	4605	Hs.179718	NM_002466	ENSG00000101057	MYBL2	B-MYB|BMYB	MYB proto-oncogene like 2	protein-coding	0.120623	0.720930	
chunk0210_223_1	chrX	82335332	82335796	+	0	NA	Intergenic	MER67C|LTR|ERV1	-1133622	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.006466	0.341935	
chunk0203_425_1	chr9	91059568	91059901	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	15398	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.003003	0.461078	138(AGGCACATCCTGTTCT,-,0.00),139(GGCACATCCTGTTCTC,+,0.00)
chunk0064_142_1	chr14	91604292	91605060	+	0	NA	intron (NM_024764, intron 22 of 26)	intron (NM_024764, intron 22 of 26)	-94196	NM_001284281	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.002604	0.479844	351(CAGGTCTGAGTGTTCC,-,0.00),381(CAGGACTGGATGTTCT,-,0.00),382(AGGACTGGATGTTCTG,+,0.00)
chunk0144_159_1	chr4	131071492	131071936	+	0	NA	Intergenic	MER92-int|LTR|ERV1	-693124	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.002252	0.253933	
chunk0059_175_1	chr14	32564497	32565252	+	0	NA	intron (NM_004274, intron 4 of 13)	intron (NM_004274, intron 4 of 13)	235601	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.002649	0.412698	273(TAGAACATCCTGTCTC,-,0.00),274(AGAACATCCTGTCTCC,+,0.00)
chunk0023_324_1	chr10	29223453	29223846	+	0	NA	Intergenic	Intergenic	-65412	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.012723	0.408629	
chunk0148_239_1	chr5	9587137	9587663	+	0	NA	Intergenic	Intergenic	38573	NR_003689	100113384		NR_003689		SNORD123	-	small nucleolar RNA, C/D box 123	snoRNA	0.001901	0.392789	
chunk0122_228_1	chr3	33679374	33679988	+	0	NA	intron (NM_015097, intron 6 of 38)	L1MC1|LINE|L1	-20240	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.001629	0.356098	
chunk0091_169_1	chr19	7804960	7805306	+	0	NA	Intergenic	L1M4|LINE|L1	17649	NR_002931	440508	Hs.568222	NR_002931		CLEC4GP1	-	C-type lectin domain family 4 member G pseudogene 1	pseudo	0.014451	0.449568	
chunk0004_156_1	chr1	45383292	45383872	+	0	NA	intron (NM_007170, intron 4 of 10)	intron (NM_007170, intron 4 of 10)	-43112	NM_001293192	4595	Hs.271353	NM_012222	ENSG00000132781	MUTYH	MYH	mutY DNA glycosylase	protein-coding	0.005172	0.364888	
chunk0069_233_1	chr15	64004671	64004921	+	0	NA	intron (NM_014326, intron 2 of 11)	intron (NM_014326, intron 2 of 11)	41526	NM_014326	23604	Hs.237886	NM_014326	ENSG00000035664	DAPK2	DRP-1|DRP1	death associated protein kinase 2	protein-coding	0.020000	0.498008	
chunk0060_146_1	chr14	45048397	45048638	+	0	NA	intron (NR_131765, intron 14 of 19)	MLT1E2|LTR|ERVL-MaLR	-35582	NM_017922	55015	Hs.274337	NM_017922	ENSG00000185246	PRPF39	-	pre-mRNA processing factor 39	protein-coding	0.000000	0.338843	
chunk0092_327_1	chr19	34881991	34882440	+	0	NA	Intergenic	LTR34|LTR|ERV1	16728	NR_046222	100652909	Hs.374015	NR_046222	ENSG00000271649	LINC00904	-	long intergenic non-protein coding RNA 904	ncRNA	0.006682	0.386667	
chunk0007_348_1	chr1	84845811	84846071	+	0	NA	intron (NM_012152, intron 2 of 2)	intron (NM_012152, intron 2 of 2)	47272	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.007692	0.413793	
chunk0009_52_1	chr1	100515769	100516551	+	0	NA	intron (NM_003672, intron 15 of 15)	intron (NM_003672, intron 15 of 15)	-22012	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.003836	0.335888	
chunk0108_76_1	chr2	227574566	227574850	+	0	NA	Intergenic	Intergenic	58612	NM_020161	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.010563	0.456140	
chunk0046_416_1	chr12	64452013	64452283	+	0	NA	promoter-TSS (NM_013254)	promoter-TSS (NM_013254)	88	NM_013254	29110	Hs.505874	NM_013254	ENSG00000183735	TBK1	FTDALS4|IIAE8|NAK|T2K	TANK binding kinase 1	protein-coding	0.162963	0.785978	
chunk0017_271_1	chr1	209713897	209714183	+	0	NA	intron (NM_181755, intron 5 of 6)	L2a|LINE|L2	9249	NM_005525	3290	Hs.195040	NM_005525	ENSG00000117594	HSD11B1	11-DH|11-beta-HSD1|CORTRD2|HDL|HSD11|HSD11B|HSD11L|SDR26C1	hydroxysteroid 11-beta dehydrogenase 1	protein-coding	0.000000	0.386760	
chunk0155_453_1	chr5	101716968	101717167	+	0	NA	Intergenic	Intergenic	579482	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.350000	
chunk0048_397_1	chr12	87953096	87953555	+	0	NA	Intergenic	Intergenic	76074	NM_152589	160419	Hs.112930	NM_152589	ENSG00000165805	C12orf50	-	chromosome 12 open reading frame 50	protein-coding	0.008715	0.391304	
chunk0026_439_1	chr10	71348085	71348284	+	0	NA	intron (NM_018344, intron 3 of 5)	L2b|LINE|L2	28931	NM_001174098	55315	Hs.438419	NM_018344	ENSG00000198246	SLC29A3	ENT3|HCLAP|HJCD|PHID	solute carrier family 29 member 3	protein-coding	0.015075	0.575000	
chunk0191_288_1	chr8	54064604	54065197	+	0	NA	intron (NM_001279359, intron 3 of 8)	MER30|DNA|hAT-Charlie	36654	NM_001279360	10434	Hs.744046	NM_006330	ENSG00000120992	LYPLA1	APT-1|APT1|LPL-I|LPL1|hAPT1	lysophospholipase 1	protein-coding	0.005059	0.356902	
chunk0168_128_1	chr6	82209948	82210221	+	0	NA	intron (NM_015525, intron 16 of 28)	intron (NM_015525, intron 16 of 28)	37670	NM_001300906	25998	Hs.306425	NM_015525	ENSG00000005700	IBTK	BTBD26|BTKI	inhibitor of Bruton tyrosine kinase	protein-coding	0.000000	0.317518	101(CAGAACATCCAGTACC,-,0.00),102(AGAACATCCAGTACCA,+,0.00)
chunk0014_75_1	chr1	176230150	176230476	+	0	NA	Intergenic	L1PA13|LINE|L1	-23069	NM_022457	64326	Hs.523744	NM_022457	ENSG00000143207	COP1	RFWD2|RNF200	COP1 E3 ubiquitin ligase	protein-coding	0.006135	0.559633	
chunk0149_165_1	chr5	20497195	20497839	+	0	NA	intron (NM_001291956, intron 1 of 14)	Tigger3a|DNA|TcMar-Tigger	78356	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006211	0.327132	361(AAGTACACGCTGTGAT,-,0.00)
chunk0118_177_1	chr22	30952486	30952791	+	0	NA	intron (NM_014941, intron 4 of 26)	intron (NM_014941, intron 4 of 26)	15859	NM_014941	22880	Hs.555918	NM_014941	ENSG00000133422	MORC2	CMT2Z|ZCW3|ZCWCC1	MORC family CW-type zinc finger 2	protein-coding	0.003279	0.424837	
chunk0175_387_1	chr6	168318047	168318495	+	0	NA	intron (NM_001286351, intron 1 of 5)	intron (NM_001286351, intron 1 of 5)	1483	NM_001286350	168002	Hs.673059	NM_214462	ENSG00000164488	DACT2	C6orf116|DAPPER2|DPR2|bA503C24.7	dishevelled binding antagonist of beta catenin 2	protein-coding	0.026786	0.523385	
chunk0159_445_1	chr5	148464884	148465410	+	0	NA	intron (NM_001040169, intron 5 of 5)	L1MC1|LINE|L1	81212	NM_001271723	81545	Hs.483772	NM_030793	ENSG00000145868	FBXO38	Fbx38|HMN2D|MOKA|SP329	F-box protein 38	protein-coding	0.003802	0.383302	
chunk0070_116_1	chr15	70616914	70617458	+	0	NA	TTS (NR_126481)	TTS (NR_126481)	1639	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.005515	0.434862	
chunk0203_36_1	chr9	83041613	83042208	+	0	NA	intron (NM_152573, intron 1 of 16)	intron (NM_152573, intron 1 of 16)	21218	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.003361	0.404362	
chunk0100_4_1	chr2	104481439	104481877	+	0	NA	intron (NR_015399, intron 1 of 3)	intron (NR_015399, intron 1 of 3)	28851	NR_110113	101927360	Hs.650324	NR_110113	ENSG00000234781	LINC01103	-	long intergenic non-protein coding RNA 1103	ncRNA	0.011416	0.476082	
chunk0080_403_1	chr17	35377509	35377781	+	0	NA	Intergenic	Intergenic	-3944	NM_001104588	91607	Hs.745059	NM_152270	ENSG00000172716	SLFN11	SLFN8/9	schlafen family member 11	protein-coding	0.025735	0.417582	98(AAGTACACTGAGTACT,-,0.00),99(AGTACACTGAGTACTT,+,0.00)
chunk0003_279_1	chr1	37070616	37070932	+	0	NA	Intergenic	Intergenic	-36531	NM_000831	2899	Hs.128848	NM_000831	ENSG00000163873	GRIK3	EAA5|GLR7|GLUR7|GluK3|GluR7a	glutamate ionotropic receptor kainate type subunit 3	protein-coding	0.009494	0.463722	
chunk0018_22_1	chr1	215528262	215528855	+	0	NA	Intergenic	Intergenic	-38834	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.006745	0.346801	
chunk0095_373_1	chr2	23478158	23478364	+	0	NA	intron (NM_052920, intron 2 of 13)	intron (NM_052920, intron 2 of 13)	92834	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.019417	0.550725	
chunk0099_256_1	chr2	97936177	97936516	+	0	NA	intron (NM_015348, intron 1 of 40)	L1M4|LINE|L1	59545	NM_015348	23505	Hs.469376	NM_015348	ENSG00000075568	TMEM131	CC28|PRO1048|RW1|YR-23	transmembrane protein 131	protein-coding	0.011799	0.491176	
chunk0153_73_1	chr5	67998606	67999244	+	0	NA	Intergenic	Intergenic	-190951	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.010972	0.500782	265(CAGCACAGAGTGTCAC,-,0.00),266(AGCACAGAGTGTCACT,+,0.00)
chunk0211_282_1	chrX	122273500	122273748	+	0	NA	Intergenic	Intergenic	902652	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.000000	0.377510	
chunk0015_51_1	chr1	184561983	184562706	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	175328	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.009682	0.383978	
chunk0081_208_1	chr17	42459935	42460134	+	0	NA	intron (NM_001130020, intron 1 of 20)	intron (NM_001130020, intron 1 of 20)	1190	NM_001130021	535	Hs.463074	NM_005177	ENSG00000033627	ATP6V0A1	ATP6N1|ATP6N1A|Stv1|VPP1|Vph1|a1	ATPase H+ transporting V0 subunit a1	protein-coding	0.020101	0.410000	12(CTGGACAGGCTGTGCC,-,0.00),13(TGGACAGGCTGTGCCT,+,0.00)
chunk0149_415_1	chr5	29475045	29475348	+	0	NA	Intergenic	Intergenic	-79220	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.006601	0.312500	
chunk0088_400_1	chr18	54470549	54471298	+	0	NA	Intergenic	Intergenic	110395	NM_001288982	162681	Hs.208701	NM_173529	ENSG00000166845	C18orf54	LAS2	chromosome 18 open reading frame 54	protein-coding	0.006676	0.322667	
chunk0129_197_1	chr3	121362631	121362893	+	0	NA	intron (NM_014980, intron 21 of 27)	L1MA1|LINE|L1	183244	NM_199420	10721	Hs.241517	NM_199420	ENSG00000051341	POLQ	PRO0327	DNA polymerase theta	protein-coding	0.000000	0.498099	
chunk0171_362_1	chr6	130708062	130708791	+	0	NA	Intergenic	L1MA9|LINE|L1	-118979	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.002743	0.405479	
chunk0013_258_1	chr1	170011234	170011623	+	0	NA	intron (NM_001204514, intron 11 of 20)	intron (NM_001204514, intron 11 of 20)	57487	NM_001204517	22920	Hs.433442	NM_014970	ENSG00000075945	KIFAP3	FLA3|KAP-1|KAP-3|KAP3|SMAP|Smg-GDS|dJ190I16.1	kinesin associated protein 3	protein-coding	0.000000	0.264103	
chunk0065_20_1	chr15	20340959	20341637	+	0	NA	Intergenic	(AGCCAGCCA)n|Simple_repeat|Simple_repeat	58554	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.008850	0.671576	
chunk0006_288_1	chr1	70773490	70773689	+	0	NA	intron (NR_125938, intron 5 of 6)	L1PA14|LINE|L1	67136	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.005025	0.535000	
chunk0108_290_1	chr2	234874481	234874749	+	0	NA	Intergenic	Intergenic	-77369	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.014925	0.531599	
chunk0118_416_1	chr22	38319234	38319774	+	0	NA	intron (NM_001289912, intron 5 of 14)	MIRb|SINE|MIR	-1420	NM_001894	1454	Hs.474833	NM_001894	ENSG00000213923	CSNK1E	CKIe|CKIepsilon|HCKIE	casein kinase 1 epsilon	protein-coding	0.012963	0.576710	
chunk0176_25_1	chr7	9036626	9036825	+	0	NA	Intergenic	Intergenic	-597545	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.010050	0.335000	
chunk0028_365_1	chr10	92731197	92731868	+	0	NA	Intergenic	L2b|LINE|L2	41608	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.008942	0.419643	386(TGGCACACAGTGTTTT,-,0.00),387(GGCACACAGTGTTTTA,+,0.00)
chunk0046_403_1	chr12	64222156	64222521	+	0	NA	promoter-TSS (NM_152440)	promoter-TSS (NM_152440)	-42	NM_001300940	144577	Hs.444671	NM_152440	ENSG00000174206	C12orf66	-	chromosome 12 open reading frame 66	protein-coding	0.104110	0.661202	
chunk0162_103_1	chr6	2608461	2608945	+	0	NA	Intergenic	Intergenic	25900	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.008264	0.389691	
chunk0046_166_1	chr12	58501949	58502259	+	0	NA	Intergenic	L2c|LINE|L2	-89598	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.009677	0.418006	142(CTGTACATAGAGTTCC,-,0.00)
chunk0162_466_1	chr5	181111742	181112278	+	0	NA	Intergenic	Intergenic	13294	NM_001258283	26693	Hs.742585	NM_001258283	ENSG00000185372	OR2V1	OR2V1P|OST265	olfactory receptor family 2 subfamily V member 1	protein-coding	0.011194	0.439479	
chunk0051_261_1	chr12	117533730	117534141	+	0	NA	intron (NM_173598, intron 10 of 19)	intron (NM_173598, intron 10 of 19)	-172133	NM_000620	4842	Hs.654410	NM_000620	ENSG00000089250	NOS1	IHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS	nitric oxide synthase 1	protein-coding	0.014599	0.529126	
chunk0158_158_1	chr5	127615709	127616341	+	0	NA	Intergenic	Intergenic	-32996	NM_001048252	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.004747	0.421801	
chunk0037_146_1	chr11	73439374	73439791	+	0	NA	intron (NM_001286050, intron 2 of 8)	intron (NM_001286050, intron 2 of 8)	62914	NM_032871	84957	Hs.533720	NM_032871	ENSG00000054967	RELT	AI3C|TNFRSF19L|TRLT	RELT TNF receptor	protein-coding	0.004796	0.401914	
chunk0146_22_1	chr4	155099565	155100292	+	0	NA	Intergenic	(TATC)n|Simple_repeat|Simple_repeat	-108701	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.006878	0.369505	269(GTGAACATAATGTCCC,-,0.00),270(TGAACATAATGTCCCC,+,0.00),395(AGACACAGACTGTTCT,-,0.00),396(GACACAGACTGTTCTA,+,0.00)
chunk0056_446_1	chr13	95212132	95212554	+	0	NA	intron (NM_001301830, intron 3 of 19)	intron (NM_001301830, intron 3 of 19)	89103	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.007109	0.349882	177(CAGAACGTAATGTGCC,-,0.00),178(AGAACGTAATGTGCCT,+,0.00)
chunk0028_247_1	chr10	90332444	90332643	+	0	NA	Intergenic	Intergenic	208262	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.010050	0.510000	
chunk0194_319_1	chr8	88324221	88324920	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	2918	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.002861	0.347143	
chunk0094_322_1	chr2	9000958	9001676	+	0	NA	intron (NM_138799, intron 1 of 12)	Tigger3b|DNA|TcMar-Tigger	2430	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.009749	0.392211	
chunk0057_63_1	chr13	97889756	97890147	+	0	NA	Intergenic	L2c|LINE|L2	-63724	NM_002271	3843	Hs.712598	NM_002271	ENSG00000065150	IPO5	IMB3|KPNB3|Pse1|RANBP5|imp5	importin 5	protein-coding	0.002558	0.464286	
chunk0139_323_1	chr4	58312773	58313398	+	0	NA	Intergenic	Intergenic	887213	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.004800	0.271565	
chunk0070_103_1	chr15	70368024	70368968	+	0	NA	Intergenic	L1PA6|LINE|L1	-247051	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.019068	0.503704	
chunk0165_423_1	chr6	39483023	39483582	+	0	NA	intron (NM_001289021, intron 12 of 21)	intron (NM_001289021, intron 12 of 21)	-51928	NM_001289024	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.003578	0.389286	
chunk0115_108_1	chr21	22782358	22782889	+	0	NA	Intergenic	L1MEf|LINE|L1	-296661	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.003766	0.296992	
chunk0067_192_1	chr15	44812051	44812426	+	0	NA	Intergenic	Intergenic	75876	NM_001301146	140691	Hs.745248	NM_080745	ENSG00000185880	TRIM69	HSD-34|HSD34|RNF36|Trif	tripartite motif containing 69	protein-coding	0.010667	0.513298	
chunk0163_15_1	chr6	7894285	7894976	+	0	NA	intron (NR_037616, intron 7 of 12)	Tigger1a_Art|DNA|TcMar-Tigger	15447	NM_001145549	81567	Hs.150837	NM_022085	ENSG00000239264	TXNDC5	ENDOPDI|ERP46|HCC-2|HCC2|PDIA15|STRF8|UNQ364	thioredoxin domain containing 5	protein-coding	0.014472	0.414740	
chunk0080_416_1	chr17	35716962	35717564	+	0	NA	exon (NM_001282, exon 20 of 21)	exon (NM_001282, exon 20 of 21)	-14397	NM_033315	91608	Hs.744994	NM_033315	ENSG00000270885	RASL10B	RRP17|VTS58635	RAS like family 10 member B	protein-coding	0.004983	0.436153	298(CAGGACATGCTGTACC,-,0.00),299(AGGACATGCTGTACCA,+,0.00)
chunk0034_424_1	chr11	38509896	38510673	+	0	NA	Intergenic	Intergenic	136072	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.002574	0.358612	346(GAAAACATACTGTGCT,-,0.00),347(AAAACATACTGTGCTC,+,0.00)
chunk0146_447_1	chr4	169901404	169901621	+	0	NA	Intergenic	Intergenic	74390	NR_037878	100506085	Hs.649173	NR_037878	ENSG00000248319	LINC02275	-	long intergenic non-protein coding RNA 2275	ncRNA	0.000000	0.389908	
chunk0090_326_1	chr18	75871534	75871867	+	0	NA	Intergenic	Intergenic	-251298	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.006006	0.422156	
chunk0062_147_1	chr14	69125524	69125879	+	0	NA	intron (NM_001284206, intron 1 of 8)	L1ME3Cz|LINE|L1	26898	NM_001284207	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.005634	0.292135	
chunk0114_287_1	chr21	16523847	16524323	+	0	NA	intron (NR_111004, intron 5 of 5)	MER34B|LTR|ERV1	-15004	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.008403	0.358491	
chunk0028_42_1	chr10	83111956	83112329	+	0	NA	Intergenic	L1PA13|LINE|L1	-879222	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.000000	0.350267	
chunk0004_398_1	chr1	52152695	52153014	+	0	NA	intron (NM_007324, intron 1 of 17)	ERV3-16A3_LTR|LTR|ERVL	10760	NM_007324	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.006270	0.409375	118(AAGTACATAGTGTATT,-,0.00)
chunk0065_386_1	chr14	104638044	104638452	+	0	NA	Intergenic	L1M5|LINE|L1	-33488	NM_001286389	388021	Hs.652298	NM_207379	ENSG00000258986	TMEM179	C14orf90|TMEM179A	transmembrane protein 179	protein-coding	0.019608	0.396088	
chunk0160_117_1	chr5	150843525	150844200	+	0	NA	Intergenic	Intergenic	-2661	NM_001145805	345611	Hs.519680	NM_001145805	ENSG00000237693	IRGM	IFI1|IRGM1|LRG-47|LRG47	immunity related GTPase M	protein-coding	0.010370	0.473373	240(ATGGACAGTCAGTACC,-,0.00),241(TGGACAGTCAGTACCC,+,0.00)
chunk0123_295_1	chr3	46598890	46599173	+	0	NA	Intergenic	Intergenic	-13404	NM_001195442	100132146	Hs.679623	NM_001195442	ENSG00000283473	FAM240A	-	family with sequence similarity 240 member A	protein-coding	0.010601	0.503521	
chunk0184_429_1	chr7	122941430	122941659	+	0	NA	Intergenic	Intergenic	54156	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.008734	0.330435	
chunk0198_348_1	chr8	140393763	140394437	+	0	NA	intron (NM_001160372, intron 7 of 22)	intron (NM_001160372, intron 7 of 22)	63662	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.017804	0.480000	283(AAGGACAGGCTGCTCC,-,0.00),284(AGGACAGGCTGCTCCA,+,0.00),300(AAGAACAAAATGTCCT,-,0.00),301(AGAACAAAATGTCCTC,+,0.00)
chunk0003_360_1	chr1	39348227	39348912	+	0	NA	intron (NM_012090, intron 35 of 92)	intron (NM_012090, intron 35 of 92)	-60935	NM_015038	643314	Hs.658760	NM_015038	ENSG00000127603	KIAA0754	-	KIAA0754	protein-coding	0.002920	0.427114	
chunk0197_236_1	chr8	123106861	123107524	+	0	NA	intron (NM_001145088, intron 8 of 19)	MER68|LTR|ERVL	34512	NM_001145088	93594	Hs.492716	NM_145647	ENSG00000156787	TBC1D31	Gm85|WDR67	TBC1 domain family member 31	protein-coding	0.009050	0.418675	
chunk0097_76_1	chr2	44465599	44465889	+	0	NA	intron (NM_024766, intron 3 of 10)	L1MA5A|LINE|L1	103840	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.003448	0.353952	
chunk0211_428_1	chrX	129361627	129361956	+	0	NA	Intergenic	Intergenic	161714	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.009119	0.403030	
chunk0134_130_1	chr3	177396638	177397130	+	0	NA	Intergenic	Intergenic	-45037	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.010163	0.387424	
chunk0142_333_1	chr4	101211085	101211860	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	29400	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.002581	0.391753	375(AAGCACAGTTTGCTCC,-,0.00),376(AGCACAGTTTGCTCCT,+,0.00)
chunk0058_330_1	chr14	28659368	28659882	+	0	NA	Intergenic	MER70B|LTR|ERVL	105694	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.011673	0.477670	322(GAGAACATCCTGTTCT,-,0.00),323(AGAACATCCTGTTCTC,+,0.00)
chunk0185_391_1	chr7	133430469	133430903	+	0	NA	intron (NM_001037126, intron 7 of 9)	L1MB7|LINE|L1	139805	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.002304	0.312644	
chunk0131_458_1	chr3	154122894	154123111	+	0	NA	exon (NM_001251963, exon 2 of 15)	exon (NM_001251963, exon 2 of 15)	1642	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.032258	0.518349	104(AAGAACAGAATGTCCC,-,0.00),105(AGAACAGAATGTCCCA,+,0.00)
chunk0091_419_1	chr19	16825236	16825808	+	0	NA	Intergenic	L2b|LINE|L2	-3865	NM_001297595	23309	Hs.13999	NM_015260	ENSG00000127511	SIN3B	-	SIN3 transcription regulator family member B	protein-coding	0.020979	0.499127	
chunk0167_253_1	chr6	69178313	69178664	+	0	NA	intron (NM_001704, intron 17 of 31)	L1PA16|LINE|L1	542748	NM_001704	577	Hs.13261	NM_001704	ENSG00000135298	ADGRB3	BAI3	adhesion G protein-coupled receptor B3	protein-coding	0.000000	0.338068	
chunk0138_250_1	chr4	39655742	39656330	+	0	NA	Intergenic	Intergenic	-17175	NM_174921	201895	Hs.205952	NM_174921	ENSG00000163683	SMIM14	C4orf34	small integral membrane protein 14	protein-coding	0.005102	0.359932	313(CAGAACACACAGTACT,-,0.00),314(AGAACACACAGTACTT,+,0.00)
chunk0189_35_1	chr8	19765306	19765866	+	0	NA	Intergenic	Intergenic	-51821	NM_018142	55174	Hs.512627	NM_018142	ENSG00000104613	INTS10	C8orf35|INT10	integrator complex subunit 10	protein-coding	0.010714	0.361854	286(GAGCACAGAGTGTCCA,-,0.00),287(AGCACAGAGTGTCCAG,+,0.00)
chunk0095_81_1	chr2	14881706	14881997	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	246760	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.003436	0.369863	
chunk0203_97_1	chr9	84254963	84255209	+	0	NA	Intergenic	Intergenic	85693	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.012195	0.400810	
chunk0170_147_1	chr6	111322012	111322597	+	0	NA	intron (NM_001286431, intron 29 of 34)	intron (NM_001286431, intron 29 of 34)	63025	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.006838	0.378840	
chunk0082_167_1	chr17	55779959	55780640	+	0	NA	Intergenic	Intergenic	29194	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.001468	0.379765	
chunk0156_176_1	chr5	107652485	107652754	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	18276	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.003717	0.314815	
chunk0191_422_1	chr8	57803114	57803618	+	0	NA	Intergenic	Intergenic	-174992	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.007937	0.338614	
chunk0128_203_1	chr3	107744295	107744797	+	0	NA	intron (NM_001276286, intron 7 of 16)	intron (NM_001276286, intron 7 of 16)	133522	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.005976	0.343936	
chunk0131_324_1	chr3	151112584	151113397	+	0	NA	intron (NM_053002, intron 1 of 42)	L2a|LINE|L2	26192	NM_053002	116931	Hs.744234	NM_053002	ENSG00000144893	MED12L	NOPAR|TNRC11L|TRALP|TRALPUSH	mediator complex subunit 12L	protein-coding	0.006150	0.385749	671(GGGAACAGACAGTGCA,-,0.00),672(GGAACAGACAGTGCAA,+,0.00)
chunk0196_287_1	chr8	109493980	109494428	+	0	NA	intron (NM_177531, intron 63 of 77)	L1MC4a|LINE|L1	-45496	NM_198120	9166	Hs.409368	NM_004215	ENSG00000147654	EBAG9	EB9|PDAF	estrogen receptor binding site associated antigen 9	protein-coding	0.008929	0.342984	31(TGGGACAGTAAGTACC,-,0.00),32(GGGACAGTAAGTACCT,+,0.00)
chunk0169_306_1	chr6	106069371	106069975	+	0	NA	Intergenic	Intergenic	-16647	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.014901	0.429752	316(TAATACAGTCTGTTCT,-,0.00),317(AATACAGTCTGTTCTT,+,0.00)
chunk0072_199_1	chr15	94560237	94560822	+	0	NA	Intergenic	Intergenic	204594	NM_001159644	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.008547	0.418089	
chunk0146_68_1	chr4	157004464	157005190	+	0	NA	Intergenic	Intergenic	-33433	NM_016205	56034	Hs.570855	NM_016205	ENSG00000145431	PDGFC	FALLOTEIN|SCDGF	platelet derived growth factor C	protein-coding	0.005510	0.332875	237(AAGTACAATGTGTTCT,-,0.00),238(AGTACAATGTGTTCTC,+,0.00),497(AAGTACACAGTGATCT,-,0.00),498(AGTACACAGTGATCTC,+,0.00)
chunk0150_38_1	chr5	31442440	31442778	+	0	NA	intron (NM_013235, intron 22 of 34)	intron (NM_013235, intron 22 of 34)	89566	NM_001100412	29102	Hs.97997	NM_013235	ENSG00000113360	DROSHA	ETOHI2|HSA242976|RANSE3L|RN3|RNASE3L|RNASEN	drosha ribonuclease III	protein-coding	0.005917	0.421829	
chunk0152_98_1	chr5	58317180	58317463	+	0	NA	Intergenic	Intergenic	142818	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.010601	0.415493	
chunk0108_303_1	chr2	235086516	235087131	+	0	NA	Intergenic	Intergenic	134839	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.017886	0.530844	324(TGGAACAGAATGTCCT,-,0.00),325(GGAACAGAATGTCCTG,+,0.00)
chunk0088_3_1	chr18	43034706	43035435	+	0	NA	intron (NM_001272077, intron 1 of 5)	MER31B|LTR|ERV1	80622	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.002743	0.391781	
chunk0064_164_1	chr14	92106466	92106790	+	0	NA	promoter-TSS (NR_028459)	promoter-TSS (NR_028459)	-7	NR_028469	4287	Hs.532632	NM_004993	ENSG00000066427	ATXN3	AT3|ATX3|JOS|MJD|MJD1|SCA3	ataxin 3	protein-coding	0.108025	0.683077	
chunk0017_448_1	chr1	214297350	214297549	+	0	NA	intron (NM_020197, intron 1 of 11)	intron (NM_020197, intron 1 of 11)	16227	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.020101	0.395000	
chunk0059_137_1	chr14	31927494	31928288	+	0	NA	Intergenic	L2a|LINE|L2	148808	NR_027263	84837	Hs.496755	NM_032751		ARHGAP5-AS1	C14orf128	ARHGAP5 antisense RNA 1 (head to head)	ncRNA	0.007557	0.413836	
chunk0045_294_1	chr12	50282823	50283022	+	0	NA	intron (NM_001113546, intron 1 of 10)	intron (NM_001113546, intron 1 of 10)	648	NM_001113546	51474	Hs.525419	NM_016357	ENSG00000050405	LIMA1	EPLIN|LDLCQ8|SREBP3	LIM domain and actin binding 1	protein-coding	0.040201	0.450000	
chunk0025_401_1	chr10	59456650	59457072	+	0	NA	Intergenic	Intergenic	-93958	NM_001143773	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.009479	0.434988	
chunk0074_301_1	chr16	29995637	29995836	+	0	NA	promoter-TSS (NM_173618)	promoter-TSS (NM_173618)	360	NM_003609	8479	Hs.567370	NM_003609	ENSG00000149929	HIRIP3	-	HIRA interacting protein 3	protein-coding	0.110553	0.600000	
chunk0086_98_1	chr18	13899721	13900090	+	0	NA	intron (NM_001291911, intron 1 of 1)	L1MA1|LINE|L1	15631	NM_000529	4158	Hs.248144	NM_000529	ENSG00000185231	MC2R	ACTHR	melanocortin 2 receptor	protein-coding	0.000000	0.318919	
chunk0081_232_1	chr17	42894086	42894594	+	0	NA	intron (NR_027254, intron 2 of 5)	intron (NR_027254, intron 2 of 5)	4394	NR_027254	388387	Hs.632257	NM_207388	ENSG00000213373	LINC00671	-	long intergenic non-protein coding RNA 671	ncRNA	0.015748	0.473477	
chunk0119_269_1	chr22	45974896	45975837	+	0	NA	intron (NM_058238, intron 1 of 3)	intron (NM_058238, intron 1 of 3)	1762	NM_058238	7477	Hs.512714	NM_058238	ENSG00000188064	WNT7B	-	Wnt family member 7B	protein-coding	0.048884	0.644374	
chunk0063_173_1	chr14	80394154	80394563	+	0	NA	intron (NR_038355, intron 6 of 8)	intron (NR_038355, intron 6 of 8)	-163304	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.004890	0.409756	
chunk0084_144_1	chr17	76506734	76506958	+	0	NA	Intergenic	Intergenic	-5419	NM_024599	79651	Hs.464157	NM_024599	ENSG00000129667	RHBDF2	RHBDL5|RHBDL6|TEC|TOC|TOCG|iRhom2	rhomboid 5 homolog 2	protein-coding	0.017857	0.608889	
chunk0115_132_1	chr21	23273004	23273698	+	0	NA	Intergenic	Intergenic	111484	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.002882	0.319424	
chunk0090_60_1	chr19	2065195	2065597	+	0	NA	Intergenic	L1MB7|LINE|L1	-14152	NM_017572	2872	Hs.515032	NM_017572	ENSG00000099875	MKNK2	GPRK7|MNK2	MAPK interacting serine/threonine kinase 2	protein-coding	0.034826	0.538462	
chunk0023_260_1	chr10	27646692	27646891	+	0	NA	Intergenic	MIR|SINE|MIR	-97824	NR_121652	101929202	Hs.568843	NR_121652		MKX-AS1	-	MKX antisense RNA 1	ncRNA	0.010050	0.435000	
chunk0131_79_1	chr3	143255546	143255818	+	0	NA	Intergenic	MIRb|SINE|MIR	-86564	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.003676	0.424908	
chunk0063_407_1	chr14	88241848	88242313	+	0	NA	intron (NM_021161, intron 2 of 6)	intron (NM_021161, intron 2 of 6)	28831	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.015054	0.437768	117(AAACACATGCTGTTCA,-,0.00)
chunk0160_199_1	chr5	154712555	154713308	+	0	NA	promoter-TSS (NM_015315)	promoter-TSS (NM_015315)	29	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.015936	0.579576	
chunk0098_159_1	chr2	70423248	70423785	+	0	NA	Intergenic	Intergenic	58124	NR_046798	100874273	Hs.682157	NR_046798	ENSG00000224606	TGFA-IT1	-	TGFA intronic transcript 1	ncRNA	0.001862	0.420074	
chunk0024_298_1	chr10	42301460	42301969	+	0	NA	Intergenic	Intergenic	66331	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.019646	0.392157	
chunk0087_426_1	chr18	42340377	42340721	+	0	NA	intron (NR_046174, intron 4 of 9)	L3|LINE|CR1	153881	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.002907	0.388406	
chunk0022_121_1	chr10	11539112	11539354	+	0	NA	intron (NM_014688, intron 2 of 14)	intron (NM_014688, intron 2 of 14)	-6953	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.000000	0.559671	
chunk0110_3_1	chr20	9564052	9564544	+	0	NA	intron (NM_020341, intron 6 of 10)	intron (NM_020341, intron 6 of 10)	-49300	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.000000	0.312373	
chunk0094_239_1	chr2	7023685	7024175	+	0	NA	intron (NM_014746, intron 6 of 8)	intron (NM_014746, intron 6 of 8)	53950	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.008163	0.380855	
chunk0112_9_1	chr20	35776595	35776923	+	0	NA	intron (NM_016436, intron 1 of 17)	MIR3|SINE|MIR	4758	NM_016436	51230	Hs.517044	NM_016436	ENSG00000025293	PHF20	C20orf104|GLEA2|HCA58|NZF|TDRD20A|TZP	PHD finger protein 20	protein-coding	0.009146	0.492401	
chunk0167_127_1	chr6	61792800	61793511	+	0	NA	intron (NM_152688, intron 6 of 8)	L1M5|LINE|L1	219052	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.004219	0.320225	305(GGGAACTTGCTGTACA,-,0.00)
chunk0080_135_1	chr17	27437377	27437848	+	0	NA	Intergenic	AluJb|SINE|Alu	19607	NR_033892	440419	Hs.385755	NR_033892	ENSG00000266433	TBC1D3P5	-	TBC1 domain family member 3 pseudogene 5	pseudo	0.002123	0.379237	
chunk0150_206_1	chr5	35129997	35130199	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	-11976	NM_001204318	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.009901	0.512315	
chunk0097_316_1	chr2	56444554	56444782	+	0	NA	Intergenic	LTR88a|LTR|Gypsy?	-258898	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.017544	0.497817	
chunk0187_383_1	chr7	157664803	157665146	+	0	NA	intron (NM_001308268, intron 13 of 22)	intron (NM_001308268, intron 13 of 22)	-90552	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.020408	0.540698	
chunk0194_397_1	chr8	91028213	91028528	+	0	NA	intron (NM_018710, intron 1 of 6)	ERVL-E-int|LTR|ERVL	12605	NM_018710	55529	Hs.202517	NM_018710	ENSG00000155099	PIP4P2	TMEM55A	phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2	protein-coding	0.006349	0.398734	
chunk0169_28_1	chr6	97033141	97033340	+	0	NA	intron (NM_001286254, intron 1 of 8)	Tigger1|DNA|TcMar-Tigger	23041	NM_001286254	114792	Hs.45056	NM_052904	ENSG00000186231	KLHL32	BKLHD5|KIAA1900|UG0030H05|dJ21F7.1	kelch like family member 32	protein-coding	0.005025	0.320000	
chunk0134_149_1	chr3	177700400	177700709	+	0	NA	intron (NR_047568, intron 3 of 3)	intron (NR_047568, intron 3 of 3)	-116311	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.012945	0.567742	227(TGGAACTCCTTGTGCT,-,0.00),228(GGAACTCCTTGTGCTC,+,0.00)
chunk0117_178_1	chr22	20858367	20858575	+	0	NA	promoter-TSS (NM_004782)	promoter-TSS (NM_004782)	341	NM_058004	5297	Hs.529438	NM_002650	ENSG00000241973	PI4KA	PI4K-ALPHA|PIK4CA|PMGYCHA|pi4K230	phosphatidylinositol 4-kinase alpha	protein-coding	0.081731	0.722488	
chunk0174_53_1	chr6	154908693	154908892	+	0	NA	Intergenic	Intergenic	55432	NR_036100	100422821		NR_036100	ENSG00000264814	MIR1273C	-	microRNA 1273c	ncRNA	0.000000	0.290000	
chunk0008_347_1	chr1	96028886	96029219	+	0	NA	Intergenic	MER52A|LTR|ERV1	36984	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.027027	0.622754	
chunk0169_87_1	chr6	99568457	99568943	+	0	NA	5' UTR (NM_005190, exon 1 of 12)	5' UTR (NM_005190, exon 1 of 12)	114	NM_001013399	892	Hs.430646	NM_005190	ENSG00000112237	CCNC	CycC|SRB11|hSRB11	cyclin C	protein-coding	0.090535	0.613963	
chunk0016_240_1	chr1	199901239	199902038	+	0	NA	Intergenic	MER87B|LTR|ERV1	-125964	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.001252	0.406250	
chunk0183_106_1	chr7	105304506	105304818	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	-5883	NM_001278273	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.009615	0.408946	
chunk0133_355_1	chr3	173395524	173395751	+	0	NA	Intergenic	CpG	-2811	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.118943	0.684211	
chunk0068_221_1	chr15	55257177	55257701	+	0	NA	intron (NM_183234, intron 1 of 6)	intron (NM_183234, intron 1 of 6)	12847	NM_183234	5873	Hs.654978	NM_004580	ENSG00000069974	RAB27A	GS2|HsT18676|RAB27|RAM	RAB27A, member RAS oncogene family	protein-coding	0.001908	0.470476	
chunk0131_379_1	chr3	152270052	152270617	+	0	NA	promoter-TSS (NR_027037)	promoter-TSS (NR_027037)	-708	NR_027037	401093	Hs.725347	NR_027037	ENSG00000229619	MBNL1-AS1	-	MBNL1 antisense RNA 1	ncRNA	0.017699	0.445230	324(GTGGACACTATGTCCC,-,0.00),325(TGGACACTATGTCCCT,+,0.00)
chunk0013_110_1	chr1	167876407	167877003	+	0	NA	intron (NM_001167749, intron 9 of 29)	MLT1H2|LTR|ERVL-MaLR	37521	NM_001167749	55811	Hs.320892	NM_018417	ENSG00000143199	ADCY10	HCA2|HEL-S-7a|SAC|SACI|Sacy|hsAC	adenylate cyclase 10	protein-coding	0.003356	0.443886	
chunk0053_235_1	chr13	32628673	32629063	+	0	NA	intron (NM_015032, intron 1 of 34)	L1ME3G|LINE|L1	42441	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.007692	0.317136	
chunk0047_398_1	chr12	75755987	75756566	+	0	NA	Intergenic	Intergenic	-244638	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.003454	0.332759	
chunk0171_401_1	chr6	131233950	131234614	+	0	NA	intron (NM_016377, intron 7 of 7)	L2b|LINE|L2	-15877	NM_138633	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.006024	0.381955	
chunk0129_119_1	chr3	119826751	119827266	+	0	NA	intron (NM_001146156, intron 10 of 10)	intron (NM_001146156, intron 10 of 10)	44298	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.007767	0.430233	
chunk0116_319_1	chr21	41045497	41046471	+	0	NA	Intergenic	Intergenic	102080	NR_024100	284835	Hs.106234	NR_024100	ENSG00000226496	LINC00323	C21orf130|NCRNA00323|PRED42	long intergenic non-protein coding RNA 323	ncRNA	0.018480	0.483077	558(AAGAACAGAGTGTGCT,-,0.00),559(AGAACAGAGTGTGCTG,+,0.00)
chunk0067_88_1	chr15	41922724	41923066	+	0	NA	intron (NR_120332, intron 1 of 3)	Kanga1c|DNA|TcMar-Tc2	1478	NR_120332	101928363	Hs.680195	NR_120332		EHD4-AS1	-	EHD4 antisense RNA 1	ncRNA	0.011696	0.413994	
chunk0128_390_1	chr3	113929906	113930317	+	0	NA	intron (NM_001172105, intron 5 of 12)	MamRTE1|LINE|RTE-BovB	-17790	NM_173570	254887	Hs.21902	NM_173570	ENSG00000184307	ZDHHC23	DHHC-23|NIDD	zinc finger DHHC-type containing 23	protein-coding	0.002433	0.305825	
chunk0042_213_1	chr12	6070990	6071190	+	0	NA	intron (NM_000552, intron 10 of 51)	intron (NM_000552, intron 10 of 51)	53580	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.015000	0.517413	
chunk0067_27_1	chr15	40367184	40367885	+	0	NA	exon (NM_033510, exon 8 of 8)	exon (NM_033510, exon 8 of 8)	9299	NM_033510	85455	Hs.355645	NM_033510	ENSG00000140323	DISP2	C15orf36|DISPB|HsT16908|LINC00594	dispatched RND transporter family member 2	protein-coding	0.034237	0.622507	228(AAGTACAGCCTGCTCT,-,0.00),229(AGTACAGCCTGCTCTT,+,0.00),387(CAGGACACGGTGTACC,-,0.00),388(AGGACACGGTGTACCC,+,0.00)
chunk0089_373_1	chr18	67255646	67256104	+	0	NA	Intergenic	L1M5|LINE|L1	174291	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.004367	0.278867	
chunk0211_9_1	chrX	107683040	107683511	+	0	NA	Intergenic	Intergenic	33206	NM_001015881	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.004246	0.504237	256(CAGGACAATCAGTACT,-,0.00),257(AGGACAATCAGTACTC,+,0.00)
chunk0151_418_1	chr5	55657174	55657959	+	0	NA	intron (NR_047649, intron 6 of 13)	intron (NR_047649, intron 6 of 13)	35487	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.005096	0.319338	
chunk0158_210_1	chr5	128218620	128218861	+	0	NA	Intergenic	Intergenic	134949	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.004149	0.367769	19(ATTACAGGATGTTCTC,+,0.00),193(ATGAACAATTTGTTCC,-,0.00),194(TGAACAATTTGTTCCT,+,0.00)
chunk0020_184_1	chr1	234723540	234724847	+	0	NA	intron (NR_038856, intron 1 of 2)	intron (NR_038856, intron 1 of 2)	151	NR_038856	100506810	Hs.586634	NR_038856	ENSG00000227630	LINC01132	-	long intergenic non-protein coding RNA 1132	ncRNA	0.019128	0.489297	
chunk0149_136_1	chr5	19889591	19890075	+	0	NA	intron (NM_001167667, intron 2 of 12)	intron (NM_001167667, intron 2 of 12)	-3561	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002066	0.307216	
chunk0026_388_1	chr10	69650094	69650755	+	0	NA	Intergenic	Intergenic	20177	NM_145306	219738	Hs.522992	NM_145306	ENSG00000171224	FAM241B	C10orf35	family with sequence similarity 241 member B	protein-coding	0.006051	0.551360	
chunk0140_243_1	chr4	71300288	71300494	+	0	NA	intron (NM_001098484, intron 3 of 25)	intron (NM_001098484, intron 3 of 25)	-38662	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.014563	0.565217	
chunk0114_255_1	chr21	16098432	16098787	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	27495	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.000000	0.297753	
chunk0030_88_1	chr10	112360404	112361272	+	0	NA	Intergenic	Intergenic	-4243	NR_028134	390003	Hs.534691	NR_028134	ENSG00000243316	GUCY2GP	GUCY2G	guanylate cyclase 2G, pseudogene	pseudo	0.014977	0.479862	329(GAGCACACCGCGTACT,-,0.00),330(AGCACACCGCGTACTC,+,0.00)
chunk0106_181_1	chr2	201219828	201220298	+	0	NA	3' UTR (NM_001230, exon 8 of 8)	3' UTR (NM_001230, exon 8 of 8)	-13380	NM_001080124	841	Hs.599762	NM_001228	ENSG00000064012	CASP8	ALPS2B|CAP4|Casp-8|FLICE|MACH|MCH5	caspase 8	protein-coding	0.008511	0.401274	
chunk0205_65_1	chr9	106670362	106670572	+	0	NA	intron (NR_104145, intron 5 of 6)	intron (NR_104145, intron 5 of 6)	54409	NR_104145	100996590	Hs.147110	NR_104145	ENSG00000234323	LINC01505	-	long intergenic non-protein coding RNA 1505	ncRNA	0.004762	0.417062	
chunk0093_186_1	chr19	49097589	49098132	+	0	NA	intron (NM_003089, intron 4 of 9)	intron (NM_003089, intron 4 of 9)	12720	NM_001301069	6625	Hs.467097	NM_003089	ENSG00000104852	SNRNP70	RNPU1Z|RPU1|SNRP70|Snp1|U1-70K|U170K|U1AP|U1RNP	small nuclear ribonucleoprotein U1 subunit 70	protein-coding	0.007366	0.511029	59(AGGGTCATTATGTGCT,-,0.00),60(GGGTCATTATGTGCTG,+,0.00)
chunk0201_328_1	chr9	63816867	63817413	+	0	NA	Intergenic	Intergenic	-2434	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.038462	0.581353	
chunk0173_406_1	chr6	150748239	150748613	+	0	NA	intron (NM_001029884, intron 3 of 16)	intron (NM_001029884, intron 3 of 16)	-117253	NM_015440	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.005348	0.338667	
chunk0178_352_1	chr7	38825862	38826710	+	0	NA	intron (NM_080631, intron 4 of 27)	L1M6|LINE|L1	82914	NM_080631	27072	Hs.592184	NM_014396	ENSG00000006715	VPS41	HVPS41|HVSP41|hVps41p	VPS41 subunit of HOPS complex	protein-coding	0.003538	0.402827	432(GAGATCTGCCTGTTCT,-,0.00),433(AGATCTGCCTGTTCTG,+,0.00)
chunk0212_398_1	chrX	150931451	150931720	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-32769	NM_001242614	83692	Hs.522805	NM_031462	ENSG00000102181	CD99L2	CD99B|MIC2L1	CD99 molecule like 2	protein-coding	0.003717	0.396296	
chunk0141_448_1	chr4	89229555	89229997	+	0	NA	Intergenic	Intergenic	78234	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.006787	0.363431	
chunk0023_379_1	chr10	30437290	30437504	+	0	NA	5' UTR (NM_005204, exon 2 of 9)	5' UTR (NM_005204, exon 2 of 9)	3376	NM_001244134	1326	Hs.432453	NM_005204	ENSG00000107968	MAP3K8	AURA2|COT|EST|ESTF|MEKK8|TPL2|Tpl-2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding	0.018692	0.437209	
chunk0021_355_1	chr1	246262152	246262475	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	155099	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.012384	0.345679	
chunk0017_380_1	chr1	212147307	212147728	+	0	NA	Intergenic	Intergenic	69904	NR_036068	100422947		NR_036068	ENSG00000264358	MIR3122	mir-3122	microRNA 3122	ncRNA	0.009501	0.504739	
chunk0096_75_1	chr2	27829852	27830366	+	0	NA	intron (NM_022128, intron 6 of 7)	L1MEi|LINE|L1	58392	NM_145330	9553	Hs.515879	NM_004891	ENSG00000243147	MRPL33	C2orf1|L33mt|MRP-L33|RPL33L	mitochondrial ribosomal protein L33	protein-coding	0.007782	0.466019	
chunk0097_303_1	chr2	55887454	55887977	+	0	NA	intron (NM_001039349, intron 4 of 10)	intron (NM_001039349, intron 4 of 10)	36448	NM_001039349	2202	Hs.76224	NM_004105	ENSG00000115380	EFEMP1	DHRD|DRAD|FBLN3|FBNL|FIBL-3|MLVT|MTLV|S1-5	EGF containing fibulin extracellular matrix protein 1	protein-coding	0.009560	0.360687	
chunk0201_209_1	chr9	37195972	37196566	+	0	NA	intron (NM_032226, intron 2 of 8)	intron (NM_032226, intron 2 of 8)	75671	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.003367	0.332773	239(GGGTCACTCTGTCCAG,+,0.00)
chunk0070_435_1	chr15	78140341	78140705	+	0	NA	Intergenic	Intergenic	-8854	NM_005530	3419	Hs.591110	NM_005530	ENSG00000166411	IDH3A	-	isocitrate dehydrogenase (NAD(+)) 3 alpha	protein-coding	0.000000	0.443836	
chunk0210_157_1	chrX	77649730	77650330	+	0	NA	intron (NM_138270, intron 14 of 33)	L1M5|LINE|L1	136239	NM_138270	546	Hs.533526	NM_000489	ENSG00000085224	ATRX	JMS|MRX52|RAD54|RAD54L|XH2|XNP|ZNF-HX	ATRX chromatin remodeler	protein-coding	0.005000	0.344426	
chunk0030_27_1	chr10	111136910	111137906	+	0	NA	Intergenic	Intergenic	60376	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.011044	0.406219	289(GAGCCCACTCTGTGCC,-,0.00),290(AGCCCACTCTGTGCCT,+,0.00)
chunk0151_168_1	chr5	49666133	49666592	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	775038	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.016746	0.408115	
chunk0138_331_1	chr4	41590568	41590906	+	0	NA	intron (NM_001112717, intron 3 of 25)	intron (NM_001112717, intron 3 of 25)	-22035	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.008876	0.486726	
chunk0042_206_1	chr12	6004912	6005366	+	0	NA	intron (NM_000552, intron 34 of 51)	L1MC4a|LINE|L1	-58907	NM_001278597	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.000000	0.314286	
chunk0054_131_1	chr13	43516458	43516875	+	0	NA	intron (NM_001242863, intron 2 of 16)	intron (NM_001242863, intron 2 of 16)	67814	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.002398	0.416268	
chunk0174_174_1	chr6	158808238	158808964	+	0	NA	intron (NM_003379, intron 1 of 12)	MIR1_Amn|SINE|MIR	-9378	NR_102425	101409257	Hs.571207	NR_102425	ENSG00000233893	EZR-AS1	-	EZR antisense RNA 1	ncRNA	0.011019	0.452545	
chunk0166_263_1	chr6	47682266	47682515	+	0	NA	exon (NM_153839, exon 7 of 11)	exon (NM_153839, exon 7 of 11)	-16163	NM_153838	221393	Hs.150131	NM_153838	ENSG00000153294	ADGRF4	GPR115|PGR18	adhesion G protein-coupled receptor F4	protein-coding	0.016064	0.524000	
chunk0130_127_1	chr3	131645015	131645313	+	0	NA	intron (NM_130808, intron 7 of 15)	intron (NM_130808, intron 7 of 15)	-142148	NM_007208	11222	Hs.205163	NM_007208	ENSG00000114686	MRPL3	COXPD9|MRL3|RPML3	mitochondrial ribosomal protein L3	protein-coding	0.006711	0.367893	
chunk0079_307_1	chr17	17120342	17121354	+	0	NA	intron (NM_015134, intron 3 of 22)	intron (NM_015134, intron 3 of 22)	78088	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.008893	0.511352	136(AGGAGCAGGGTGTGCT,-,0.00),137(GGAGCAGGGTGTGCTC,+,0.00)
chunk0208_442_1	chrX	30886191	30886420	+	0	NA	intron (NM_152787, intron 1 of 10)	intron (NM_152787, intron 1 of 10)	3089	NM_152787	257397	Hs.188256	NM_152787	ENSG00000157625	TAB3	MAP3K7IP3|NAP1	TGF-beta activated kinase 1 (MAP3K7) binding protein 3	protein-coding	0.008734	0.282609	
chunk0119_370_1	chr22	47605390	47606020	+	0	NA	Intergenic	L2b|LINE|L2	25864	NR_033377	400932	Hs.561058	NM_001001693	ENSG00000205634	LINC00898	-	long intergenic non-protein coding RNA 898	ncRNA	0.026984	0.562599	
chunk0048_319_1	chr12	83202544	83203174	+	0	NA	Intergenic	Intergenic	515704	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.007937	0.320127	
chunk0124_64_1	chr3	52979943	52980480	+	0	NA	intron (NM_016329, intron 1 of 20)	Tigger2|DNA|TcMar-Tigger	65862	NM_016329	51460	Hs.343679	NM_016329	ENSG00000163935	SFMBT1	RU1|SFMBT|hSFMBT	Scm like with four mbt domains 1	protein-coding	0.007449	0.306691	
chunk0087_194_1	chr18	35745975	35746174	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	91505	NM_020474	2589	Hs.514806	NM_020474	ENSG00000141429	GALNT1	GALNAC-T1	polypeptide N-acetylgalactosaminyltransferase 1	protein-coding	0.015075	0.430000	
chunk0046_135_1	chr12	57839754	57840019	+	0	NA	intron (NM_005730, intron 1 of 7)	MIR|SINE|MIR	7078	NM_005730	10106	Hs.524530	NM_005730	ENSG00000175215	CTDSP2	OS4|PSR2|SCP2	CTD small phosphatase 2	protein-coding	0.003774	0.402256	
chunk0162_435_1	chr5	180494057	180494529	+	0	NA	promoter-TSS (NM_001303241)	promoter-TSS (NM_001303241)	-106	NM_001303241	57472	Hs.608380	NM_015455	ENSG00000113300	CNOT6	CCR4|Ccr4a	CCR4-NOT transcription complex subunit 6	protein-coding	0.122881	0.714588	
chunk0090_43_1	chr19	1533548	1533747	+	0	NA	intron (NM_001243079, intron 12 of 13)	intron (NM_001243079, intron 12 of 13)	9573	NM_001243079	126520	Hs.195352	NM_001011716	ENSG00000185988	PLK5	PLK-5|PLK5P|SgK384ps	polo like kinase 5	protein-coding	0.010050	0.585000	
chunk0028_336_1	chr10	92105374	92105895	+	0	NA	intron (NM_001178137, intron 7 of 9)	intron (NM_001178137, intron 7 of 9)	137645	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.005758	0.396552	
chunk0027_248_1	chr10	77125337	77125622	+	0	NA	intron (NM_001014797, intron 5 of 28)	L2a|LINE|L2	-15352	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.014035	0.534965	
chunk0145_46_1	chr4	144837309	144837508	+	0	NA	Intergenic	L1PA6|LINE|L1	-191389	NR_037595	646576	Hs.632595	NR_037595	ENSG00000248890	HHIP-AS1	-	HHIP antisense RNA 1	ncRNA	0.020101	0.535000	
chunk0049_190_1	chr12	92963663	92964294	+	0	NA	Intergenic	Intergenic	-34647	NM_003566	8411	Hs.567367	NM_003566	ENSG00000102189	EEA1	MST105|MSTP105|ZFYVE2	early endosome antigen 1	protein-coding	0.017433	0.386076	
chunk0157_157_1	chr5	117880753	117881724	+	0	NA	intron (NR_104997, intron 1 of 2)	intron (NR_104997, intron 1 of 2)	150877	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.004119	0.348765	
chunk0003_224_1	chr1	35542547	35542873	+	0	NA	intron (NM_024874, intron 2 of 20)	intron (NM_024874, intron 2 of 20)	14726	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.003067	0.376147	
chunk0018_68_1	chr1	217089507	217090107	+	0	NA	promoter-TSS (NM_001243506)	promoter-TSS (NM_001243506)	47	NM_001243505	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.070000	0.574043	
chunk0196_90_1	chr8	102917582	102918273	+	0	NA	intron (NR_126339, intron 2 of 2)	L1ME4b|LINE|L1	53656	NR_126339	100506753	Hs.602901	NR_126338		AZIN1-AS1	-	AZIN1 antisense RNA 1	ncRNA	0.005789	0.426301	
chunk0051_289_1	chr12	118289367	118289868	+	0	NA	intron (NM_016281, intron 1 of 20)	intron (NM_016281, intron 1 of 20)	83328	NM_016281	51347	Hs.644420	NM_016281	ENSG00000135090	TAOK3	DPK|JIK|MAP3K18|hKFC-A	TAO kinase 3	protein-coding	0.011976	0.358566	
chunk0041_178_1	chr11	126223863	126224107	+	0	NA	intron (NM_024556, intron 1 of 8)	intron (NM_024556, intron 1 of 8)	12261	NM_024556	79607	Hs.276315	NM_024556	ENSG00000197798	FAM118B	-	family with sequence similarity 118 member B	protein-coding	0.008197	0.351020	150(GTTACAGGGTGTTCTT,+,0.00)
chunk0102_454_1	chr2	158357468	158358212	+	0	NA	intron (NM_001301685, intron 2 of 6)	intron (NM_001301685, intron 2 of 6)	98913	NM_138803	130940	Hs.668597	NM_138803	ENSG00000153237	CCDC148	-	coiled-coil domain containing 148	protein-coding	0.005376	0.304698	
chunk0086_207_1	chr18	22455402	22455931	+	0	NA	Intergenic	MIRb|SINE|MIR	-37751	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.003781	0.411321	
chunk0047_156_1	chr12	69751638	69752033	+	0	NA	intron (NM_175623, intron 1 of 10)	L1MC5a|LINE|L1	12445	NR_103520	117177	Hs.258209	NM_022456	ENSG00000127328	RAB3IP	RABIN3|RABIN8	RAB3A interacting protein	protein-coding	0.002532	0.295455	
chunk0187_21_1	chr8	664690	665061	+	0	NA	intron (NM_207332, intron 5 of 5)	intron (NM_207332, intron 5 of 5)	66364	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.005391	0.338710	
chunk0209_453_1	chrX	66029636	66029854	+	0	NA	intron (NM_001184831, intron 2 of 5)	intron (NM_001184831, intron 2 of 5)	10380	NM_001184831	11326	Hs.8904	NM_007268	ENSG00000155659	VSIG4	CRIg|Z39IG	V-set and immunoglobulin domain containing 4	protein-coding	0.018349	0.383562	
chunk0001_287_1	chr1	8787275	8787474	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	30266	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.005025	0.380000	
chunk0044_348_1	chr12	38628937	38629582	+	0	NA	Intergenic	Intergenic	276359	NM_153634	144402	Hs.40910	NM_153634	ENSG00000139117	CPNE8	-	copine 8	protein-coding	0.006202	0.342105	
chunk0102_209_1	chr2	148416361	148416889	+	0	NA	intron (NM_018328, intron 5 of 14)	L1PB3|LINE|L1	-228366	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.001894	0.427221	362(TAGTACACATTGTACT,-,0.00),363(AGTACACATTGTACTC,+,0.00)
chunk0055_47_1	chr13	52341263	52341635	+	0	NA	non-coding (NR_120400, exon 3 of 3)	non-coding (NR_120400, exon 3 of 3)	7154	NR_120400	103191607		NR_120400	ENSG00000271564	LINC02333	-	long intergenic non-protein coding RNA 2333	ncRNA	0.005376	0.461126	
chunk0124_455_1	chr3	61615550	61615967	+	0	NA	intron (NM_002841, intron 1 of 29)	L1MC4|LINE|L1	54189	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.002398	0.368421	280(TAGAACAAGAAGTTCC,-,0.00),281(AGAACAAGAAGTTCCA,+,0.00)
chunk0064_414_1	chr14	99571450	99572005	+	0	NA	intron (NM_001144995, intron 1 of 5)	intron (NM_001144995, intron 1 of 5)	32663	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.014414	0.546763	
chunk0108_316_1	chr2	235491369	235491925	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-2442	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.010791	0.499102	
chunk0177_26_1	chr7	20621737	20622337	+	0	NA	intron (NM_001163941, intron 1 of 27)	intron (NM_001163941, intron 1 of 27)	6415	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.008333	0.327787	264(AAGAACACAACGTGCT,-,0.00),265(AGAACACAACGTGCTT,+,0.00)
chunk0100_300_1	chr2	115223717	115224042	+	0	NA	intron (NM_001004360, intron 1 of 25)	L1ME4a|LINE|L1	61772	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.009231	0.325153	
chunk0213_11_1	chrY	20502911	20503237	+	0	NA	intron (NR_001542, intron 2 of 5)	L1M1|LINE|L1	16154	NR_001542	246119	Hs.461175	NR_001542	ENSG00000229236	TTTY10	NCRNA00133|TTY10	testis-specific transcript, Y-linked 10	ncRNA	0.003067	0.308869	
chunk0040_98_1	chr11	111707116	111707663	+	0	NA	intron (NM_015191, intron 8 of 14)	intron (NM_015191, intron 8 of 14)	59056	NM_001177563	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.012797	0.397810	322(AAGCACTCTGTGTCCT,-,0.00),323(AGCACTCTGTGTCCTT,+,0.00)
chunk0179_343_1	chr7	50749666	50750227	+	0	NA	intron (NM_001001555, intron 2 of 16)	intron (NM_001001555, intron 2 of 16)	-17593	NM_001001549	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.008913	0.437722	211(AAGCACAGTTTGTACT,-,0.00),212(AGCACAGTTTGTACTT,+,0.00)
chunk0025_344_1	chr10	58120895	58121632	+	0	NA	Intergenic	L1M5|LINE|L1	146671	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.006784	0.318428	651(AAGAACACAGTGTACC,-,0.00),652(AGAACACAGTGTACCT,+,0.00)
chunk0197_265_1	chr8	123625129	123625861	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	27455	NM_001081675	340359	Hs.450252	NM_001081675	ENSG00000175946	KLHL38	C8ORFK36	kelch like family member 38	protein-coding	0.012295	0.399727	392(AGGCAGAGACTGTGCC,-,0.00)
chunk0079_86_1	chr17	11878932	11879700	+	0	NA	intron (NM_001372, intron 53 of 68)	intron (NM_001372, intron 53 of 68)	-3586	NM_004662	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.001302	0.269181	
chunk0026_440_1	chr10	71377395	71377798	+	0	NA	Intergenic	Intergenic	-19338	NM_001171931	64072	Hs.656032	NM_022124	ENSG00000107736	CDH23	CDHR23|PITA5|USH1D	cadherin related 23	protein-coding	0.059553	0.574257	
chunk0205_445_1	chr9	115443978	115444406	+	0	NA	Intergenic	Intergenic	300047	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.004673	0.333333	194(AGGCACATAGTGTACT,-,0.00),195(GGCACATAGTGTACTA,+,0.00)
chunk0058_6_1	chr14	18660576	18660775	+	0	NA	Intergenic	Intergenic	-27041	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.030151	0.530000	
chunk0199_391_1	chr9	13250298	13250880	+	0	NA	intron (NM_003829, intron 1 of 45)	intron (NM_003829, intron 1 of 45)	28975	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.001718	0.324185	
chunk0143_35_1	chr4	106836058	106836479	+	0	NA	Intergenic	Intergenic	200028	NM_014421	27123	Hs.211869	NM_014421	ENSG00000155011	DKK2	DKK-2	dickkopf WNT signaling pathway inhibitor 2	protein-coding	0.000000	0.281991	
chunk0047_392_1	chr12	75545959	75546613	+	0	NA	Intergenic	Intergenic	-34648	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.006116	0.358779	380(AAAGACATTGTGTTCT,-,0.00),381(AAGACATTGTGTTCTA,+,0.00)
chunk0200_21_1	chr9	14700305	14701012	+	0	NA	Intergenic	L2c|LINE|L2	-7176	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.002829	0.419492	
chunk0105_189_1	chr2	187569067	187569392	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-14737	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.003077	0.337423	
chunk0130_291_1	chr3	136630707	136631531	+	0	NA	intron (NM_005862, intron 1 of 33)	L1MC1|LINE|L1	121284	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.004854	0.336970	
chunk0193_325_1	chr8	78876598	78876806	+	0	NA	Intergenic	L1PA8A|LINE|L1	-71179	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.004808	0.478469	
chunk0152_346_1	chr5	62607036	62607235	+	0	NA	intron (NM_016338, intron 29 of 29)	intron (NM_016338, intron 29 of 29)	28400	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.000000	0.425000	
chunk0205_143_1	chr9	108213102	108213418	+	0	NA	Intergenic	Intergenic	642735	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.003165	0.362776	
chunk0117_172_1	chr22	20499663	20500118	+	0	NA	Intergenic	Intergenic	-4007	NM_032775	84861	Hs.517419	NM_032775	ENSG00000099910	KLHL22	KELCHL	kelch like family member 22	protein-coding	0.015385	0.504386	
chunk0197_206_1	chr8	122587729	122588037	+	0	NA	Intergenic	Arthur1B|DNA|hAT-Tip100	-19239	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.009740	0.446602	
chunk0050_316_1	chr12	107079308	107079874	+	0	NA	intron (NM_004075, intron 1 of 12)	L2b|LINE|L2	14266	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.001767	0.393298	
chunk0188_124_1	chr8	9136236	9136589	+	0	NA	3' UTR (NM_024607, exon 2 of 2)	3' UTR (NM_024607, exon 2 of 2)	14298	NM_024607	79660	Hs.458513	NM_024607	ENSG00000173281	PPP1R3B	GL|PPP1R4|PTG	protein phosphatase 1 regulatory subunit 3B	protein-coding	0.005666	0.358757	
chunk0020_296_1	chr1	237217214	237217484	+	0	NA	intron (NM_001035, intron 1 of 104)	intron (NM_001035, intron 1 of 104)	174947	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.007407	0.357934	
chunk0155_187_1	chr5	94508528	94508844	+	0	NA	intron (NM_001145678, intron 5 of 20)	intron (NM_001145678, intron 5 of 20)	109918	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.009494	0.444795	
chunk0134_100_1	chr3	176920932	176921259	+	0	NA	Intergenic	Intergenic	-104094	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.009174	0.402439	
chunk0152_275_1	chr5	61299329	61299703	+	0	NA	Intergenic	Intergenic	-32757	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.008021	0.432000	210(GGAACTGGGTGTTTTG,+,0.00)
chunk0026_382_1	chr10	69430832	69431417	+	0	NA	Intergenic	L1MEj|LINE|L1	-14206	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.013675	0.411263	
chunk0066_377_1	chr15	38817617	38817986	+	0	NA	Intergenic	Intergenic	121203	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.021680	0.505405	
chunk0029_128_1	chr10	98586788	98586991	+	0	NA	intron (NM_001166246, intron 9 of 12)	MIRb|SINE|MIR	-139926	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.019704	0.450980	100(GGGCCAGATTGTTCTG,+,0.00)
chunk0058_300_1	chr14	26960778	26961099	+	0	NA	Intergenic	Intergenic	52296	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.009346	0.326087	
chunk0007_364_1	chr1	84947573	84947788	+	0	NA	intron (NM_153259, intron 6 of 13)	L1M2|LINE|L1	49442	NM_153259	255231	Hs.591446	NM_153259	ENSG00000153898	MCOLN2	TRP-ML2|TRPML2	mucolipin 2	protein-coding	0.009302	0.546296	
chunk0151_412_1	chr5	55635114	55635570	+	0	NA	intron (NM_001282429, intron 12 of 14)	MIRb|SINE|MIR	57711	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.002193	0.369803	
chunk0016_328_1	chr1	201760719	201761299	+	0	NA	intron (NM_001167738, intron 1 of 26)	intron (NM_001167738, intron 1 of 26)	21174	NM_001167738	89796	Hs.585374	NM_020443	ENSG00000134369	NAV1	POMFIL3|STEERIN1|UNC53H1	neuron navigator 1	protein-coding	0.006897	0.387263	
chunk0015_350_1	chr1	190175331	190175619	+	0	NA	intron (NM_199051, intron 6 of 7)	intron (NM_199051, intron 6 of 7)	302154	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.010417	0.301038	
chunk0128_233_1	chr3	108392367	108392656	+	0	NA	intron (NM_014981, intron 37 of 41)	intron (NM_014981, intron 37 of 41)	80726	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.000000	0.424138	
chunk0055_82_1	chr13	53873150	53873384	+	0	NA	intron (NR_047488, intron 5 of 5)	intron (NR_047488, intron 5 of 5)	57848	NR_047488	100861552	Hs.224691	NR_047488	ENSG00000261517	LINC00558	-	long intergenic non-protein coding RNA 558	ncRNA	0.004274	0.395745	
chunk0173_32_1	chr6	142088948	142089147	+	0	NA	promoter-TSS (NM_002511)	promoter-TSS (NM_002511)	-248	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.050251	0.580000	
chunk0124_153_1	chr3	54873505	54873797	+	0	NA	TTS (NR_046666)	TTS (NR_046666)	27604	NR_046666	100874237	Hs.570583	NR_046666	ENSG00000243715	CACNA2D3-AS1	-	CACNA2D3 antisense RNA 1	ncRNA	0.023973	0.453925	204(CTGCACAAATTGTTCT,-,0.00),205(TGCACAAATTGTTCTC,+,0.00)
chunk0016_454_1	chr1	204206546	204206854	+	0	NA	intron (NM_198447, intron 1 of 4)	intron (NM_198447, intron 1 of 4)	7392	NM_198447	127845	Hs.532401	NM_198447	ENSG00000174567	GOLT1A	CGI-141|GOT1|HMFN1187|YMR292W|hGOT1b	golgi transport 1A	protein-coding	0.012987	0.375405	
chunk0081_238_1	chr17	42940493	42940834	+	0	NA	Intergenic	Intergenic	23835	NM_001261434	80755	Hs.317403	NM_001261434	ENSG00000266967	AARSD1	-	alanyl-tRNA synthetase domain containing 1	protein-coding	0.005865	0.423977	114(CTGAACAATGAGTTCT,-,0.00),115(TGAACAATGAGTTCTG,+,0.00),203(AAGTGCAGCGTGTGCT,-,0.00),204(AGTGCAGCGTGTGCTC,+,0.00)
chunk0088_430_1	chr18	55579473	55579805	+	0	NA	intron (NM_003199, intron 3 of 19)	intron (NM_003199, intron 3 of 19)	6480	NM_001306207	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.006024	0.354354	144(AAACACACCATGTTCC,-,0.00),145(AACACACCATGTTCCT,+,0.00)
chunk0001_24_1	chr1	1258946	1259412	+	0	NA	intron (NM_194315, intron 4 of 7)	CpG	-12457	NM_001014980	388581	Hs.197613	NM_001014980	ENSG00000184163	C1QTNF12	C1QDC2|CTRP12|FAM132A	C1q and TNF related 12	protein-coding	0.060086	0.580300	
chunk0079_375_1	chr17	18088801	18089093	+	0	NA	intron (NM_001388, intron 1 of 12)	L2b|LINE|L2	1080	NM_001388	1819	Hs.78582	NM_001388	ENSG00000108591	DRG2	-	developmentally regulated GTP binding protein 2	protein-coding	0.003425	0.515358	
chunk0065_23_1	chr15	20398299	20398879	+	0	NA	Intergenic	Intergenic	107591	NR_036432	283755	Hs.608918	NM_001024682	ENSG00000180229	HERC2P3	D15F37S4	hect domain and RLD 2 pseudogene 3	pseudo	0.008621	0.373494	
chunk0184_261_1	chr7	118233790	118234571	+	0	NA	intron (NM_019644, intron 1 of 6)	intron (NM_019644, intron 1 of 6)	9522	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.005122	0.310742	
chunk0017_442_1	chr1	214228980	214229334	+	0	NA	Intergenic	Intergenic	-52065	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.008475	0.422535	168(AGGAACACAGAGTGCC,-,0.00),169(GGAACACAGAGTGCCT,+,0.00)
chunk0174_211_1	chr6	160338005	160338240	+	0	NA	Intergenic	Intergenic	-10251	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.008511	0.508475	
chunk0193_46_1	chr8	71987022	71987357	+	0	NA	intron (NR_033652, intron 4 of 4)	L1ME3G|LINE|L1	88395	NM_007332	8989	Hs.716816	NM_007332	ENSG00000104321	TRPA1	ANKTM1|FEPS|FEPS1	transient receptor potential cation channel subfamily A member 1	protein-coding	0.002985	0.303571	
chunk0042_265_1	chr12	6853517	6854327	+	0	NA	intron (NM_003481, intron 1 of 19)	intron (NM_003481, intron 1 of 19)	1795	NM_003481	8078	Hs.631661	NM_003481	ENSG00000111667	USP5	ISOT	ubiquitin specific peptidase 5	protein-coding	0.007407	0.456227	329(CAGTACACACTGTTCC,-,0.00),330(AGTACACACTGTTCCT,+,0.00)
chunk0069_216_1	chr15	63538873	63539458	+	0	NA	intron (NR_046342, intron 4 of 15)	intron (NR_046342, intron 4 of 15)	34654	NR_046341	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.006838	0.360068	303(CAGAACTGTGTGTTTC,-,0.00),304(AGAACTGTGTGTTTCT,+,0.00)
chunk0197_38_1	chr8	118099005	118099353	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	12640	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.002874	0.392550	
chunk0008_213_1	chr1	93672093	93672507	+	0	NA	intron (NM_003567, intron 2 of 11)	intron (NM_003567, intron 2 of 11)	9070	NM_001261409	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.004831	0.462651	
chunk0162_133_1	chr6	3125361	3125661	+	0	NA	intron (NR_026649, intron 2 of 7)	intron (NR_026649, intron 2 of 7)	7135	NM_001302777	670	Hs.10136	NM_004332	ENSG00000137274	BPHL	BPH-RP|MCNAA|VACVASE	biphenyl hydrolase like	protein-coding	0.003333	0.411960	
chunk0046_433_1	chr12	64794061	64794355	+	0	NA	Intergenic	HAL1|LINE|L1	-30364	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.003401	0.400000	
chunk0178_196_1	chr7	34471442	34471809	+	0	NA	intron (NR_033665, intron 2 of 3)	L1MA4A|LINE|L1	-186614	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.002725	0.562500	
chunk0005_268_1	chr1	59831519	59831718	+	0	NA	intron (NM_015888, intron 3 of 21)	L1ME1|LINE|L1	16757	NM_015888	51361	Hs.378836	NM_015888	ENSG00000134709	HOOK1	HK1	hook microtubule tethering protein 1	protein-coding	0.010050	0.445000	
chunk0192_156_1	chr8	62222620	62223024	+	0	NA	Intergenic	L1MA9|LINE|L1	-26120	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.004950	0.365432	
chunk0164_241_1	chr6	23303279	23303529	+	0	NA	Intergenic	Intergenic	733955	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.004000	0.378486	
chunk0183_415_1	chr7	110758933	110759543	+	0	NA	intron (NM_032549, intron 5 of 5)	L2c|LINE|L2	-331768	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.008197	0.379705	
chunk0012_181_1	chr1	159314033	159314241	+	0	NA	exon (NM_001004467, exon 1 of 1)	exon (NM_001004467, exon 1 of 1)	522	NM_001004467	441911	Hs.553833	NM_001004467	ENSG00000196266	OR10J3	OR1-25|OR10J3P	olfactory receptor family 10 subfamily J member 3	protein-coding	0.004808	0.507177	
chunk0024_292_1	chr10	42087825	42088024	+	0	NA	Intergenic	Intergenic	280121	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.070352	0.395000	
chunk0100_251_1	chr2	113068465	113068870	+	0	NA	intron (NM_173161, intron 1 of 4)	intron (NM_173161, intron 1 of 4)	697	NM_173161	84639	Hs.306974	NM_032556	ENSG00000136697	IL1F10	FIL1-theta|FKSG75|IL-1HY2|IL-38|IL1-theta|IL1HY2	interleukin 1 family member 10	protein-coding	0.000000	0.349754	
chunk0045_186_1	chr12	47245720	47246117	+	0	NA	Intergenic	Intergenic	-29475	NR_026544	100233209	Hs.657722	NR_026544	ENSG00000247774	PCED1B-AS1	-	PCED1B antisense RNA 1	ncRNA	0.005038	0.329146	
chunk0203_257_1	chr9	87640422	87640663	+	0	NA	intron (NM_001288730, intron 8 of 25)	intron (NM_001288730, intron 8 of 25)	-85517	NM_001912	1514	Hs.731507	NM_001912	ENSG00000135047	CTSL	CATL|CTSL1|MEP	cathepsin L	protein-coding	0.016598	0.541322	
chunk0110_430_1	chr20	20778514	20778749	+	0	NA	Intergenic	Intergenic	-66008	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.004255	0.271186	
chunk0057_60_1	chr13	97575858	97576463	+	0	NA	Intergenic	L1ME3G|LINE|L1	141939	NM_021033	5911	Hs.508480	NM_021033	ENSG00000125249	RAP2A	K-REV|KREV|RAP2|RbBP-30	RAP2A, member of RAS oncogene family	protein-coding	0.004959	0.311881	306(ATTACAGTATGTTCCT,+,0.00)
chunk0070_133_1	chr15	70876350	70876902	+	0	NA	intron (NM_001284357, intron 2 of 16)	intron (NM_001284357, intron 2 of 16)	15807	NM_020147	56906	Hs.591123	NM_020147	ENSG00000129028	THAP10	-	THAP domain containing 10	protein-coding	0.003623	0.415913	256(TAGTACTGCCAGTTCT,-,0.00),257(AGTACTGCCAGTTCTT,+,0.00)
chunk0154_329_1	chr5	85217002	85217482	+	0	NA	Intergenic	Intergenic	-832375	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.002083	0.311850	
chunk0115_138_1	chr21	23425880	23426243	+	0	NA	Intergenic	Intergenic	-41226	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.002755	0.340659	155(AGGAGCAAAATGTCCT,-,0.00),156(GGAGCAAAATGTCCTT,+,0.00)
chunk0042_347_1	chr12	10066881	10067452	+	0	NA	Intergenic	Intergenic	31899	NM_001297750	51267	Hs.29549	NM_016511	ENSG00000150048	CLEC1A	CLEC-1|CLEC1	C-type lectin domain family 1 member A	protein-coding	0.001751	0.312937	
chunk0037_5_1	chr11	68857584	68857813	+	0	NA	Intergenic	L1ME4b|LINE|L1	-15767	NM_001031847	1374	Hs.503043	NM_001876	ENSG00000110090	CPT1A	CPT1|CPT1-L|L-CPT1	carnitine palmitoyltransferase 1A	protein-coding	0.008734	0.439130	
chunk0186_317_1	chr7	143046513	143046719	+	0	NA	Intergenic	Intergenic	-5725	NM_001001667	346517	Hs.554721	NM_001001667	ENSG00000225781	OR6V1	GPR138	olfactory receptor family 6 subfamily V member 1	protein-coding	0.000000	0.410628	
chunk0087_30_1	chr18	31157401	31157600	+	0	NA	exon (NM_004948, exon 3 of 17)	exon (NM_004948, exon 3 of 17)	5356	NM_024421	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.015075	0.440000	
chunk0100_349_1	chr2	117396959	117397165	+	0	NA	Intergenic	L1MCb|LINE|L1	-417617	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.009709	0.415459	
chunk0008_206_1	chr1	93538832	93539039	+	0	NA	intron (NM_001164473, intron 10 of 16)	intron (NM_001164473, intron 10 of 16)	46227	NM_001308251	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.014493	0.302885	
chunk0176_367_1	chr7	18414891	18415184	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-80709	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.017065	0.428571	
chunk0176_376_1	chr7	18549230	18549682	+	0	NA	intron (NM_001204147, intron 1 of 9)	L1MD2|LINE|L1	40179	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.002212	0.324503	
chunk0164_359_1	chr6	25557921	25558681	+	0	NA	intron (NM_017640, intron 29 of 36)	intron (NM_017640, intron 29 of 36)	-93900	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.002632	0.329829	
chunk0028_62_1	chr10	83330693	83331047	+	0	NA	Intergenic	L1MB7|LINE|L1	-808559	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.405634	168(AGGGACAGAGTGTTCT,-,0.00),169(GGGACAGAGTGTTCTG,+,0.00)
chunk0060_5_1	chr14	39060639	39061117	+	0	NA	intron (NM_006364, intron 13 of 19)	intron (NM_006364, intron 13 of 19)	42355	NM_006364	10484	Hs.272927	NM_006364	ENSG00000100934	SEC23A	CLSD|hSec23A	Sec23 homolog A, coat complex II component	protein-coding	0.002092	0.319415	
chunk0026_409_1	chr10	70233416	70233921	+	0	NA	promoter-TSS (NM_021129)	promoter-TSS (NM_021129)	-234	NM_021129	5464	Hs.437403	NM_021129	ENSG00000180817	PPA1	HEL-S-66p|IOPPP|PP|PP1|SID6-8061	pyrophosphatase (inorganic) 1	protein-coding	0.071287	0.618577	
chunk0150_347_1	chr5	38653429	38653730	+	0	NA	intron (NR_103554, intron 7 of 8)	intron (NR_103554, intron 7 of 8)	-58174	NM_002310	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.006645	0.473510	111(GGGGACAAACAGTGCC,-,0.00),112(GGGACAAACAGTGCCC,+,0.00),147(AAGAACACACTGATCT,-,0.00),148(AGAACACACTGATCTT,+,0.00)
chunk0041_172_1	chr11	126129883	126130435	+	0	NA	Intergenic	Intergenic	-66867	NM_016952	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.009058	0.509946	
chunk0026_254_1	chr10	66572661	66573116	+	0	NA	intron (NM_001127384, intron 10 of 17)	intron (NM_001127384, intron 10 of 17)	-353146	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.004396	0.392544	
chunk0166_215_1	chr6	46881468	46881844	+	0	NA	intron (NM_001098518, intron 7 of 20)	intron (NM_001098518, intron 7 of 20)	-21815	NR_110658	101926962	Hs.680113	NR_110658		LOC101926962	-	uncharacterized LOC101926962	ncRNA	0.000000	0.381963	
chunk0193_11_1	chr8	70493215	70493663	+	0	NA	Intergenic	ERVL-int|LTR|ERVL	22305	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.006696	0.463252	
chunk0078_130_1	chr17	3512915	3513200	+	0	NA	3' UTR (NM_001258205, exon 18 of 18)	3' UTR (NM_001258205, exon 18 of 18)	37055	NM_000049	443	Hs.171142	NM_000049	ENSG00000108381	ASPA	ACY2|ASP	aspartoacylase	protein-coding	0.038596	0.510490	
chunk0022_297_1	chr10	15527039	15527247	+	0	NA	intron (NM_001291494, intron 27 of 28)	intron (NM_001291494, intron 27 of 28)	-156084	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.009615	0.344498	
chunk0200_383_1	chr9	26782675	26783434	+	0	NA	Intergenic	Intergenic	109774	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.005270	0.343421	
chunk0102_322_1	chr2	151717178	151717714	+	0	NA	exon (NM_001164508, exon 10 of 182)	exon (NM_001164508, exon 10 of 182)	17041	NM_001164507	4703	Hs.588655	NM_004543	ENSG00000183091	NEB	NEB177D|NEM2	nebulin	protein-coding	0.007463	0.368715	
chunk0052_317_1	chr12	125095421	125095778	+	0	NA	intron (NM_023928, intron 5 of 17)	intron (NM_023928, intron 5 of 17)	30220	NM_023928	65985	Hs.656073	NM_023928	ENSG00000081760	AACS	ACSF1|SUR-5	acetoacetyl-CoA synthetase	protein-coding	0.016807	0.569832	202(CAGAACAGCCTCTTCT,-,0.00),203(AGAACAGCCTCTTCTC,+,0.00)
chunk0118_433_1	chr22	38681723	38681968	+	0	NA	promoter-TSS (NM_020243)	promoter-TSS (NM_020243)	-104	NM_020243	56993	Hs.595072	NM_020243	ENSG00000100216	TOMM22	1C9-2|MST065|MSTP065|TOM22	translocase of outer mitochondrial membrane 22	protein-coding	0.106122	0.695122	
chunk0080_433_1	chr17	35988105	35988501	+	0	NA	intron (NR_027921, intron 4 of 7)	intron (NR_027921, intron 4 of 7)	-1575	NM_032962	6358	Hs.272493	NM_004166	ENSG00000276409	CCL14	CC-1|CC-3|CKB1|HCC-1|HCC-1(1-74)|HCC-1/HCC-3|HCC-3|MCIF|NCC-2|NCC2|SCYA14|SCYL2|SY14	C-C motif chemokine ligand 14	protein-coding	0.000000	0.337531	
chunk0135_32_1	chr3	185076354	185076644	+	0	NA	Intergenic	Intergenic	76515	NM_001025266	285382	Hs.245793	NM_001025266	ENSG00000187068	C3orf70	-	chromosome 3 open reading frame 70	protein-coding	0.017241	0.443299	146(GTGTACTCACTGTCCT,-,0.00),147(TGTACTCACTGTCCTA,+,0.00)
chunk0153_70_1	chr5	67928319	67928525	+	0	NA	Intergenic	L1ME1|LINE|L1	135209	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.000000	0.236715	
chunk0173_115_1	chr6	143622197	143622541	+	0	NA	intron (NM_001100166, intron 1 of 11)	L2c|LINE|L2	14189	NM_014721	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.011628	0.501449	154(AAGTACTGTGTGTTCC,-,0.00),155(AGTACTGTGTGTTCCT,+,0.00)
chunk0138_462_1	chr4	47691849	47692345	+	0	NA	intron (NM_001278585, intron 5 of 19)	intron (NM_001278585, intron 5 of 19)	39428	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.002016	0.366197	
chunk0189_345_1	chr8	26693643	26694078	+	0	NA	Intergenic	Intergenic	115455	NM_001244604	1808	Hs.593187	NM_001386	ENSG00000092964	DPYSL2	CRMP-2|CRMP2|DHPRP2|DRP-2|DRP2|N2A3|ULIP-2|ULIP2	dihydropyrimidinase like 2	protein-coding	0.009195	0.403670	268(GGGTACATGCTGTCCT,-,0.00),269(GGTACATGCTGTCCTC,+,0.00)
chunk0027_320_1	chr10	78211816	78212521	+	0	NA	Intergenic	MIRb|SINE|MIR	-36457	NR_038985	100132987	Hs.55047	NR_038985	ENSG00000230417	LINC00856	-	long intergenic non-protein coding RNA 856	ncRNA	0.012766	0.555241	
chunk0008_38_1	chr1	88864747	88865270	+	0	NA	intron (NM_001514, intron 2 of 6)	intron (NM_001514, intron 2 of 6)	26610	NM_001514	2959	Hs.481852	NM_001514	ENSG00000137947	GTF2B	TF2B|TFIIB	general transcription factor IIB	protein-coding	0.005736	0.356870	
chunk0040_275_1	chr11	116774027	116774469	+	0	NA	Intergenic	L1MA9|LINE|L1	-1250	NM_001159736	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.004525	0.318284	
chunk0050_303_1	chr12	106791331	106791849	+	0	NA	intron (NM_018157, intron 2 of 8)	intron (NM_018157, intron 2 of 8)	-16759	NR_040246	100287944	Hs.742087	NR_040246	ENSG00000257545	LOC100287944	-	uncharacterized LOC100287944	ncRNA	0.007722	0.341040	
chunk0212_392_1	chrX	150672359	150672925	+	0	NA	3' UTR (NM_000252, exon 15 of 15)	3' UTR (NM_000252, exon 15 of 15)	-20722	NM_001306144	8776	Hs.347187	NM_003828	ENSG00000063601	MTMR1	-	myotubularin related protein 1	protein-coding	0.014134	0.356261	
chunk0141_442_1	chr4	89065792	89066099	+	0	NA	Intergenic	ERV24B_Prim-int|LTR|ERV1	-8750	NM_014883	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.006515	0.337662	
chunk0197_213_1	chr8	122708141	122708340	+	0	NA	Intergenic	L2|LINE|L2	-14134	NR_126348	104266958	Hs.575540	NR_126348	ENSG00000253819	LINC01151	-	long intergenic non-protein coding RNA 1151	ncRNA	0.000000	0.480000	
chunk0087_286_1	chr18	38796610	38797393	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	825174	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.003831	0.353316	
chunk0065_85_1	chr15	23671010	23671515	+	0	NA	Intergenic	Intergenic	16041	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.003960	0.367589	
chunk0036_72_1	chr11	59784913	59785137	+	0	NA	intron (NM_004177, intron 2 of 10)	MIRc|SINE|MIR	25847	NM_017840	54948	Hs.530734	NM_017840	ENSG00000166902	MRPL16	L16mt|MRP-L16|PNAS-111	mitochondrial ribosomal protein L16	protein-coding	0.000000	0.346667	
chunk0201_322_1	chr9	63327251	63327600	+	0	NA	intron (NR_002817, intron 2 of 3)	intron (NR_002817, intron 2 of 3)	6854	NR_026558	441432	Hs.743215	NR_026558		AQP7P3	AQPap-3	aquaporin 7 pseudogene 3	pseudo	0.008596	0.500000	
chunk0006_9_1	chr1	63880770	63881197	+	0	NA	intron (NM_001083592, intron 1 of 6)	L4_C_Mam|LINE|RTE-X	106964	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.004684	0.387850	
chunk0178_358_1	chr7	38882518	38882717	+	0	NA	intron (NM_080631, intron 2 of 27)	L2a|LINE|L2	26583	NM_080631	27072	Hs.592184	NM_014396	ENSG00000006715	VPS41	HVPS41|HVSP41|hVps41p	VPS41 subunit of HOPS complex	protein-coding	0.000000	0.430000	
chunk0169_247_1	chr6	105257299	105257754	+	0	NA	Intergenic	Intergenic	-77543	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.000000	0.326754	
chunk0120_230_1	chr3	8282527	8283003	+	0	NA	intron (NR_033378, intron 3 of 3)	intron (NR_033378, intron 3 of 3)	218893	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.000000	0.387841	
chunk0109_321_1	chr20	9162438	9162768	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	-54787	NM_182797	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.009091	0.296073	
chunk0176_80_1	chr7	11478064	11478296	+	0	NA	intron (NM_015204, intron 7 of 26)	intron (NM_015204, intron 7 of 26)	354018	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.000000	0.433476	
chunk0027_242_1	chr10	77041616	77042045	+	0	NA	intron (NM_001014797, intron 14 of 28)	intron (NM_001014797, intron 14 of 28)	-99001	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.009324	0.504651	192(TAGAACGGCTTGTGCT,-,0.00),193(AGAACGGCTTGTGCTT,+,0.00)
chunk0192_398_1	chr8	68875179	68875896	+	0	NA	Intergenic	Intergenic	228653	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.005579	0.324513	137(CAGGACACCGAGTACC,-,0.00),138(AGGACACCGAGTACCA,+,0.00),353(TGAGACACACTGTCCC,-,0.00),354(GAGACACACTGTCCCT,+,0.00)
chunk0093_294_1	chr19	52395485	52395770	+	0	NA	non-coding (NR_125345, exon 5 of 7)	non-coding (NR_125345, exon 5 of 7)	2130	NR_125345	102724105	Hs.188680	NR_125345	ENSG00000269834	ZNF528-AS1	-	ZNF528 antisense RNA 1	ncRNA	0.014035	0.503497	
chunk0057_43_1	chr13	96292589	96292835	+	0	NA	intron (NM_153456, intron 1 of 1)	intron (NM_153456, intron 1 of 1)	-134517	NR_039723	100616137		NR_039723	ENSG00000283487	MIR4501	-	microRNA 4501	ncRNA	0.000000	0.311741	
chunk0167_291_1	chr6	70709975	70710294	+	0	NA	intron (NM_001281440, intron 1 of 10)	Tigger3b|DNA|TcMar-Tigger	41604	NM_001281440	60682	Hs.485717	NM_021940	ENSG00000112305	SMAP1	SMAP-1	small ArfGAP 1	protein-coding	0.012539	0.428125	
chunk0036_13_1	chr11	58199199	58199961	+	0	NA	Intergenic	Intergenic	4601	NM_001004459	219958	Hs.553644	NM_001004459	ENSG00000197887	OR1S2	OR11-231	olfactory receptor family 1 subfamily S member 2	protein-coding	0.002625	0.326343	
chunk0185_353_1	chr7	132305494	132305861	+	0	NA	intron (NM_020911, intron 3 of 31)	intron (NM_020911, intron 3 of 31)	270887	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.024523	0.535326	
chunk0053_95_1	chr13	28545670	28546260	+	0	NA	Intergenic	Intergenic	-50837	NM_001160030	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.005085	0.426396	
chunk0148_328_1	chr5	14131618	14132347	+	0	NA	Intergenic	Intergenic	-11738	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.019204	0.456164	277(AAGATCACATTGTACT,-,0.00),278(AGATCACATTGTACTT,+,0.00),601(TTGCACTGGGTGTCCT,-,0.00),602(TGCACTGGGTGTCCTC,+,0.00)
chunk0169_365_1	chr6	107071582	107071877	+	0	NA	intron (NM_001080450, intron 4 of 4)	L1ME1|LINE|L1	42703	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.016949	0.371622	137(CAGTACACAAAGTACT,-,0.00),138(AGTACACAAAGTACTC,+,0.00)
chunk0190_157_1	chr8	31260084	31260622	+	0	NA	Intergenic	L1ME3A|LINE|L1	-226638	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.007435	0.276438	
chunk0115_311_1	chr21	28550024	28550823	+	0	NA	Intergenic	Intergenic	11105	NR_026553	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.002503	0.315000	
chunk0208_448_1	chrX	31993581	31993963	+	0	NA	intron (NM_004010, intron 44 of 78)	intron (NM_004010, intron 44 of 78)	161697	NM_004023	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.007853	0.357702	
chunk0142_316_1	chr4	100779574	100780548	+	0	NA	Intergenic	L1M5|LINE|L1	-104948	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.001027	0.318974	
chunk0189_267_1	chr8	25312077	25312864	+	0	NA	intron (NM_024940, intron 13 of 51)	intron (NM_024940, intron 13 of 51)	-32932	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.015248	0.414975	
chunk0040_346_1	chr11	118544698	118544993	+	0	NA	3' UTR (NM_001168618, exon 12 of 12)	3' UTR (NM_001168618, exon 12 of 12)	-13751	NR_120576	101929089	Hs.666633	NR_120572	ENSG00000255435	LOC101929089	-	uncharacterized LOC101929089	ncRNA	0.006780	0.537162	
chunk0087_160_1	chr18	34806641	34806981	+	0	NA	intron (NM_032975, intron 6 of 21)	intron (NM_032975, intron 6 of 21)	-11151	NM_001198943	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.002941	0.390029	
chunk0094_292_1	chr2	8458826	8459208	+	0	NA	Intergenic	Intergenic	124775	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.005236	0.436031	187(AGGAACATCACGTCCT,-,0.00),188(GGAACATCACGTCCTT,+,0.00)
chunk0165_3_1	chr6	28569814	28570157	+	0	NA	Intergenic	Intergenic	17350	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.002915	0.334302	
chunk0117_413_1	chr21	45814103	45814306	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	22215	NR_038876	100129027	Hs.689591	NR_038876	ENSG00000205424	LOC100129027	-	uncharacterized LOC100129027	ncRNA	0.009852	0.450980	
chunk0187_451_1	chr7	159179536	159179885	+	0	NA	Intergenic	Intergenic	-34753	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.022923	0.482857	
chunk0045_379_1	chr12	52217261	52217583	+	0	NA	intron (NR_027358, intron 3 of 4)	intron (NR_027358, intron 3 of 4)	6492	NR_027358	283404	Hs.662443	NR_027358	ENSG00000258279	LINC00592	-	long intergenic non-protein coding RNA 592	ncRNA	0.015528	0.585139	
chunk0049_164_1	chr12	92146128	92146524	+	0	NA	promoter-TSS (NM_001731)	promoter-TSS (NM_001731)	-429	NM_001731	694	Hs.255935	NM_001731	ENSG00000133639	BTG1	APRO2	BTG anti-proliferation factor 1	protein-coding	0.080808	0.644836	
chunk0207_104_1	chr9	128607562	128608199	+	0	NA	exon (NM_001195532, exon 32 of 55)	exon (NM_001195532, exon 32 of 55)	48970	NM_052844	89891	Hs.495240	NM_052844	ENSG00000119333	WDR34	DIC5|FAP133|SRTD11|bA216B9.3	WD repeat domain 34	protein-coding	0.021978	0.547022	
chunk0032_151_1	chr11	4777708	4777982	+	0	NA	Intergenic	L1ME3A|LINE|L1	-7928	NM_001004752	256892		NM_001004752	ENSG00000280021	OR51F1	OR11-21|OR51F1P	olfactory receptor family 51 subfamily F member 1 (gene/pseudogene)	protein-coding	0.003650	0.334545	
chunk0084_437_1	chr17	82751693	82752130	+	0	NA	promoter-TSS (NM_005993).2	promoter-TSS (NM_005993).2	-153	NM_005993	6904	Hs.464391	NM_005993	ENSG00000141556	TBCD	PEBAT|SSD-1|tfcD	tubulin folding cofactor D	protein-coding	0.135011	0.757991	
chunk0173_178_1	chr6	144696766	144697469	+	0	NA	intron (NM_007124, intron 51 of 73)	intron (NM_007124, intron 51 of 73)	291462	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.005690	0.308239	
chunk0115_199_1	chr21	26206227	26206526	+	0	NA	Intergenic	MER41C|LTR|ERV1	-35248	NM_001136131	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.013378	0.326667	
chunk0108_242_1	chr2	233756695	233757192	+	0	NA	intron (NM_019093, intron 1 of 4)	intron (NM_019093, intron 1 of 4)	-1598	NR_037696	100286922	Hs.124112	NR_037694	ENSG00000178836	LOC100286922	-	DnaJ heat shock protein family (Hsp40) member B3 pseudogene	pseudo	0.006036	0.439759	
chunk0146_39_1	chr4	155445219	155445817	+	0	NA	Intergenic	Intergenic	-68548	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.003344	0.295492	
chunk0081_299_1	chr17	45148622	45148928	+	0	NA	5' UTR (NM_006460, exon 1 of 1)	5' UTR (NM_006460, exon 1 of 1)	1458	NM_006460	10614	Hs.586945	NM_006460	ENSG00000186834	HEXIM1	CLP1|EDG1|HIS1|MAQ1	HEXIM P-TEFb complex subunit 1	protein-coding	0.049020	0.599349	
chunk0054_86_1	chr13	42537348	42537970	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-25077	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.003215	0.341894	
chunk0134_97_1	chr3	176812103	176812669	+	0	NA	Intergenic	Intergenic	4615	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.000000	0.395062	
chunk0059_444_1	chr14	38839847	38840158	+	0	NA	intron (NR_039982, intron 2 of 4)	L1M6|LINE|L1	76880	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.003215	0.381410	
chunk0123_46_1	chr3	40992583	40993104	+	0	NA	Intergenic	L1ME1|LINE|L1	-206608	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005758	0.312261	
chunk0154_343_1	chr5	86175007	86175438	+	0	NA	Intergenic	Intergenic	-107222	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.002320	0.368056	
chunk0105_80_1	chr2	183909694	183909993	+	0	NA	Intergenic	L1MD1|LINE|L1	-469132	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.360000	
chunk0101_254_1	chr2	132646400	132646891	+	0	NA	TTS (NM_001508)	TTS (NM_001508)	24263	NM_144586	116372	Hs.432395	NM_144586	ENSG00000150551	LYPD1	LYPDC1|PHTS	LY6/PLAUR domain containing 1	protein-coding	0.018330	0.416667	
chunk0101_409_1	chr2	139087014	139087263	+	0	NA	Intergenic	L1MA7|LINE|L1	189814	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.008032	0.328000	
chunk0038_143_1	chr11	84367322	84367522	+	0	NA	intron (NM_001142699, intron 7 of 27)	MER58A|DNA|hAT-Charlie	-50083	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.015000	0.417910	
chunk0151_173_1	chr5	50286825	50287190	+	0	NA	Intergenic	Intergenic	154393	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.002740	0.355191	
chunk0151_407_1	chr5	55601082	55601622	+	0	NA	Intergenic	Intergenic	-66274	NM_003711	8611	Hs.696231	NM_003711	ENSG00000067113	PLPP1	LLP1a|LPP1|PAP-2a|PAP2|PPAP2A	phospholipid phosphatase 1	protein-coding	0.016667	0.451017	
chunk0031_11_1	chr10	121572932	121573260	+	0	NA	intron (NM_022970, intron 2 of 17)	intron (NM_022970, intron 2 of 17)	20871	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.027439	0.446809	
chunk0009_192_1	chr1	105915306	105915712	+	0	NA	Intergenic	Intergenic	-296574	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004926	0.356265	
chunk0127_38_1	chr3	88737471	88737766	+	0	NA	Intergenic	Intergenic	-369906	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003390	0.543919	
chunk0057_55_1	chr13	97466655	97467216	+	0	NA	3' UTR (NM_021033, exon 2 of 2)	3' UTR (NM_021033, exon 2 of 2)	32714	NM_021033	5911	Hs.508480	NM_021033	ENSG00000125249	RAP2A	K-REV|KREV|RAP2|RbBP-30	RAP2A, member of RAS oncogene family	protein-coding	0.005348	0.339858	
chunk0057_184_1	chr13	102731867	102732066	+	0	NA	exon (NM_001146197, exon 4 of 4)	exon (NM_001146197, exon 4 of 4)	27106	NM_001146197	643677	Hs.368382	NM_001146197	ENSG00000175820	CCDC168	C13orf40	coiled-coil domain containing 168	protein-coding	0.020101	0.370000	86(TGGAACAATCCGTTCT,-,0.00),87(GGAACAATCCGTTCTT,+,0.00)
chunk0161_235_1	chr5	171390161	171390367	+	0	NA	intron (NM_002520, intron 2 of 10)	intron (NM_002520, intron 2 of 10)	2560	NM_002520	4869	Hs.557550	NM_002520	ENSG00000181163	NPM1	B23|NPM	nucleophosmin 1	protein-coding	0.000000	0.371981	
chunk0105_245_1	chr2	188628420	188628755	+	0	NA	Intergenic	Intergenic	161517	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.002985	0.446429	146(AGGGACAGAGTGTGCC,-,0.00),147(GGGACAGAGTGTGCCC,+,0.00)
chunk0144_87_1	chr4	128179635	128179978	+	0	NA	intron (NM_018078, intron 15 of 19)	intron (NM_018078, intron 15 of 19)	109023	NM_006320	10424	Hs.507910	NM_006320	ENSG00000164040	PGRMC2	DG6|PMBP	progesterone receptor membrane component 2	protein-coding	0.002915	0.281977	
chunk0035_380_1	chr11	55262930	55263634	+	0	NA	intron (NM_024114, intron 1 of 5)	Tigger3a|DNA|TcMar-Tigger	1100	NM_024114	79097	Hs.195715	NM_024114	ENSG00000150244	TRIM48	RNF101	tripartite motif containing 48	protein-coding	0.014205	0.409929	312(TAGAACACGCTGTACA,-,0.00),313(AGAACACGCTGTACAG,+,0.00)
chunk0099_128_1	chr2	86105853	86106337	+	0	NA	promoter-TSS (NM_017952)	promoter-TSS (NM_017952)	60	NM_015425	25885	Hs.531818	NM_015425	ENSG00000068654	POLR1A	A190|AFDCIN|RPA1|RPA194|RPO1-4|RPO14	RNA polymerase I subunit A	protein-coding	0.068182	0.523711	
chunk0144_28_1	chr4	125013833	125014191	+	0	NA	Intergenic	L2a|LINE|L2	-301280	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.002793	0.462396	82(GGGAACAGCAAGTGCA,-,0.00),83(GGAACAGCAAGTGCAA,+,0.00)
chunk0178_78_1	chr7	30437813	30438038	+	0	NA	intron (NM_006092, intron 9 of 13)	intron (NM_006092, intron 9 of 13)	40852	NM_006092	10392	Hs.405153	NM_006092	ENSG00000106100	NOD1	CARD4|CLR7.1|NLRC1	nucleotide binding oligomerization domain containing 1	protein-coding	0.026667	0.575221	
chunk0185_221_1	chr7	129074047	129074277	+	0	NA	Intergenic	LTR105_Mam|LTR|ERVL	18939	NR_002187	286016	Hs.369665	NR_002187	ENSG00000230359	TPI1P2	-	triosephosphate isomerase 1 pseudogene 2	pseudo	0.004348	0.497835	
chunk0181_337_1	chr7	88146565	88147155	+	0	NA	intron (NM_021721, intron 17 of 27)	intron (NM_021721, intron 17 of 27)	-69800	NR_120517	102723885	Hs.489040	NR_120517		LOC102723885	-	uncharacterized LOC102723885	ncRNA	0.003390	0.387479	
chunk0116_44_1	chr21	33650984	33651247	+	0	NA	intron (NM_001001132, intron 1 of 29)	intron (NM_001001132, intron 1 of 29)	8637	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.019011	0.571970	
chunk0194_153_1	chr8	84715886	84716246	+	0	NA	intron (NM_001287244, intron 1 of 7)	intron (NM_001287244, intron 1 of 7)	10139	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005556	0.329640	239(TAAACACATTGTTCTT,+,0.00)
chunk0198_233_1	chr8	134133086	134133533	+	0	NA	Intergenic	Intergenic	246813	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.002237	0.343750	
chunk0202_254_1	chr9	76827821	76828192	+	0	NA	intron (NM_015225, intron 4 of 18)	L2c|LINE|L2	63570	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.008086	0.365591	
chunk0155_369_1	chr5	97482780	97483221	+	0	NA	Intergenic	LTR33|LTR|ERVL	-21696	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.002268	0.400452	
chunk0063_418_1	chr14	88465674	88466271	+	0	NA	3' UTR (NM_007039, exon 19 of 19)	3' UTR (NM_007039, exon 19 of 19)	80328	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.006700	0.307692	
chunk0109_253_1	chr20	6616637	6616840	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-151360	NM_001200	650	Hs.73853	NM_001200	ENSG00000125845	BMP2	BDA2|BMP2A|SSFSC	bone morphogenetic protein 2	protein-coding	0.000000	0.446078	
chunk0040_218_1	chr11	114243861	114244253	+	0	NA	intron (NM_006006, intron 5 of 6)	intron (NM_006006, intron 5 of 6)	-51756	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.020408	0.506361	
chunk0066_7_1	chr15	26901960	26902159	+	0	NA	intron (NM_001165037, intron 6 of 10)	L1MD3|LINE|L1	34933	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.005025	0.360000	
chunk0168_256_1	chr6	89067867	89068210	+	0	NA	Intergenic	Intergenic	-12672	NM_006813	10957	Hs.75969	NM_006813	ENSG00000146278	PNRC1	B4-2|PNAS-145|PROL2|PRR2	proline rich nuclear receptor coactivator 1	protein-coding	0.000000	0.354651	
chunk0140_302_1	chr4	72974555	72975187	+	0	NA	Intergenic	Intergenic	94888	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.011076	0.366509	
chunk0051_443_1	chr12	123217446	123217810	+	0	NA	intron (NM_022782, intron 6 of 23)	intron (NM_022782, intron 6 of 23)	15610	NR_103517	10198	Hs.577404	NM_022782	ENSG00000051825	MPHOSPH9	MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding	0.008242	0.356164	
chunk0206_297_1	chr9	124673786	124674446	+	0	NA	intron (NR_038975, intron 1 of 1)	MIRb|SINE|MIR	15680	NR_038975	100379345	Hs.660412	NR_038975	ENSG00000224020	MIR181A2HG	-	MIR181A2 host gene	ncRNA	0.006061	0.375189	
chunk0127_206_1	chr3	96393346	96393939	+	0	NA	Intergenic	L1ME1|LINE|L1	33678	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.006745	0.286195	331(AGTTCTGACTGTTCTT,+,0.00)
chunk0002_191_1	chr1	19426990	19427748	+	0	NA	intron (NM_001313932, intron 1 of 4)	MamRep434|DNA|TcMar-Tigger	57338	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.019789	0.466403	547(GGGAACAGTTTGTGCT,-,0.00),548(GGAACAGTTTGTGCTG,+,0.00)
chunk0090_296_1	chr18	75131883	75132452	+	0	NA	Intergenic	Intergenic	73346	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.024605	0.419298	
chunk0105_376_1	chr2	192144419	192144942	+	0	NA	intron (NM_016192, intron 4 of 9)	intron (NM_016192, intron 4 of 9)	50253	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.003824	0.314885	
chunk0105_367_1	chr2	191961494	191961696	+	0	NA	intron (NM_016192, intron 7 of 9)	intron (NM_016192, intron 7 of 9)	-114315	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.004950	0.310345	
chunk0079_131_1	chr17	12681484	12681965	+	0	NA	intron (NR_104605, intron 2 of 2)	intron (NR_104605, intron 2 of 2)	15834	NM_001146312	93649	Hs.462257	NM_153604	ENSG00000141052	MYOCD	MYCD	myocardin	protein-coding	0.014553	0.491701	198(AAGAACAGTGTGTACC,-,0.00),199(AGAACAGTGTGTACCT,+,0.00),286(GAGCTCACCTTGTTCC,-,0.00),287(AGCTCACCTTGTTCCT,+,0.00)
chunk0004_228_1	chr1	47013218	47013524	+	0	NA	Intergenic	MIRb|SINE|MIR	-10197	NM_178033	260293	Hs.439760	NM_178033	ENSG00000186377	CYP4X1	CYPIVX1	cytochrome P450 family 4 subfamily X member 1	protein-coding	0.009804	0.403909	
chunk0159_174_1	chr5	140036199	140036539	+	0	NA	intron (NM_004883, intron 1 of 9)	intron (NM_004883, intron 1 of 9)	6930	NM_013983	9542	Hs.408515	NM_004883	ENSG00000158458	NRG2	DON1|HRG2|NTAK	neuregulin 2	protein-coding	0.005882	0.363636	161(GGGTACAGAATGTCCT,-,0.00),162(GGTACAGAATGTCCTT,+,0.00)
chunk0045_79_1	chr12	45785128	45785347	+	0	NA	intron (NM_152641, intron 3 of 20)	MIRb|SINE|MIR	55400	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.000000	0.336364	60(GAGCACAGAGTGCCCT,-,0.00),61(AGCACAGAGTGCCCTA,+,0.00)
chunk0050_248_1	chr12	105401232	105401625	+	0	NA	Intergenic	Intergenic	70792	NM_001145199	387882	Hs.368938	NM_207376	ENSG00000235162	C12orf75	AGD3|OCC-1|OCC1	chromosome 12 open reading frame 75	protein-coding	0.007634	0.375635	
chunk0192_339_1	chr8	67620856	67621245	+	0	NA	intron (NM_020361, intron 2 of 10)	MER68|LTR|ERVL	125335	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.000000	0.430769	
chunk0029_96_1	chr10	97336903	97337598	+	0	NA	Intergenic	MIRc|SINE|MIR	-2549	NM_012083	23401	Hs.140720	NM_012083	ENSG00000181274	FRAT2	FRAT-2	FRAT regulator of WNT signaling pathway 2	protein-coding	0.008633	0.479885	205(CAGAACAGGTTGTACA,-,0.00),206(AGAACAGGTTGTACAA,+,0.00)
chunk0210_393_1	chrX	97936044	97936709	+	0	NA	Intergenic	Intergenic	-371841	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.003008	0.384384	
chunk0052_302_1	chr12	124742020	124742423	+	0	NA	Intergenic	Intergenic	121752	NM_005505	949	Hs.731377	NM_005505	ENSG00000073060	SCARB1	CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1	scavenger receptor class B member 1	protein-coding	0.027295	0.537129	
chunk0120_157_1	chr3	5484046	5484427	+	0	NA	Intergenic	L1MA10|LINE|L1	-233981	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.007874	0.363874	
chunk0023_294_1	chr10	28761694	28762293	+	0	NA	intron (NR_120652, intron 2 of 3)	intron (NR_120652, intron 2 of 3)	18343	NR_120652	101929218	Hs.224866	NR_120652		LINC01517	-	long intergenic non-protein coding RNA 1517	ncRNA	0.008347	0.336667	
chunk0122_398_1	chr3	38001279	38001878	+	0	NA	exon (NM_015873, exon 11 of 19)	exon (NM_015873, exon 11 of 19)	7991	NM_015873	50853	Hs.103665	NM_015873	ENSG00000136059	VILL	-	villin like	protein-coding	0.016694	0.606667	291(CAGTACATCCTGTACC,-,0.00),292(AGTACATCCTGTACCT,+,0.00)
chunk0060_201_1	chr14	48129845	48130044	+	0	NA	Intergenic	Intergenic	-334930	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.000000	0.245000	
chunk0097_242_1	chr2	53609952	53610587	+	0	NA	Intergenic	Intergenic	-157523	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.000000	0.361635	
chunk0043_401_1	chr12	25635937	25636222	+	0	NA	intron (NM_001145727, intron 1 of 7)	L1PB1|LINE|L1	12483	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.000000	0.367133	
chunk0053_314_1	chr13	34147701	34148275	+	0	NA	Intergenic	LTR33A|LTR|ERVL	329919	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.003484	0.483478	
chunk0209_381_1	chrX	54419714	54420327	+	0	NA	Intergenic	L2c|LINE|L2	-20400	NM_058163	90121	Hs.522662	NM_058163	ENSG00000158526	TSR2	DBA14|DT1P1A10|WGG1	TSR2 ribosome maturation factor	protein-coding	0.004894	0.400651	410(GGGAACAGATTGTTCC,-,0.00),411(GGAACAGATTGTTCCC,+,0.00)
chunk0086_218_1	chr18	22556583	22556817	+	0	NA	Intergenic	Intergenic	-138785	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.008547	0.565957	
chunk0048_44_1	chr12	78086164	78086814	+	0	NA	intron (NM_014903, intron 12 of 38)	intron (NM_014903, intron 12 of 38)	255200	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.000000	0.307220	
chunk0158_226_1	chr5	128956077	128956656	+	0	NA	Intergenic	Intergenic	-9151	NM_014031	28965	Hs.49765	NM_014031	ENSG00000113396	SLC27A6	ACSVL2|FACVL2|FATP6|VLCS-H1	solute carrier family 27 member 6	protein-coding	0.006908	0.346552	259(GAGGACTCAGTGTCCT,-,0.00),260(AGGACTCAGTGTCCTC,+,0.00)
chunk0126_427_1	chr3	86909453	86910060	+	0	NA	Intergenic	MER121|DNA|hAT?	81351	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.004942	0.305921	264(AAGAACACGCTGTTCC,-,0.00),265(AGAACACGCTGTTCCT,+,0.00)
chunk0159_53_1	chr5	137218957	137219465	+	0	NA	intron (NM_004598, intron 3 of 10)	intron (NM_004598, intron 3 of 10)	280118	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.003937	0.438114	211(AAATACACTGTGTTCT,-,0.00),212(AATACACTGTGTTCTT,+,0.00)
chunk0135_178_1	chr3	188065000	188065254	+	0	NA	Intergenic	Intergenic	-88746	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.007874	0.345098	
chunk0101_382_1	chr2	138520180	138520481	+	0	NA	intron (NM_001001664, intron 1 of 10)	intron (NM_001001664, intron 1 of 10)	18550	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.006645	0.331126	
chunk0076_268_1	chr16	69448752	69449179	+	0	NA	intron (NM_030579, intron 3 of 4)	intron (NM_030579, intron 3 of 4)	24370	NM_030579	80777	Hs.461131	NM_030579	ENSG00000103018	CYB5B	CYB5-M|CYPB5M|OMB5	cytochrome b5 type B	protein-coding	0.002342	0.411215	
chunk0064_190_1	chr14	92726335	92726833	+	0	NA	intron (NM_001008530, intron 3 of 14)	intron (NM_001008530, intron 3 of 14)	22118	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.016064	0.567134	206(AGGAGCTCCCTGTTCT,-,0.00),207(GGAGCTCCCTGTTCTT,+,0.00)
chunk0058_16_1	chr14	19344394	19344721	+	0	NA	Intergenic	Intergenic	-6883	NR_110526	503639	Hs.659013	NM_001013701		DUXAP10	-	double homeobox A pseudogene 10	pseudo	0.012232	0.487805	178(AGAAACATCATGTTCC,-,0.00),179(GAAACATCATGTTCCT,+,0.00)
chunk0157_393_1	chr5	124124979	124125178	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	313442	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005025	0.435000	
chunk0097_320_1	chr2	57046044	57046902	+	0	NA	Intergenic	Intergenic	-860703	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.004662	0.369034	240(AAGAACACACTGTGTT,-,0.00),241(AGAACACACTGTGTTC,+,0.00),242(GAACACACTGTGTTCT,-,0.00),243(AACACACTGTGTTCTA,+,0.00)
chunk0033_9_1	chr11	12386879	12387084	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	9502	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.009756	0.451456	
chunk0003_72_1	chr1	31308025	31308665	+	0	NA	intron (NM_001282566, intron 1 of 6)	intron (NM_001282566, intron 1 of 6)	11363	NM_001282572	51538	Hs.524094	NM_016505	ENSG00000121766	ZCCHC17	HSPC251|PS1D|pNO40	zinc finger CCHC-type containing 17	protein-coding	0.003125	0.385335	
chunk0063_168_1	chr14	80300161	80300748	+	0	NA	intron (NR_038355, intron 2 of 8)	intron (NR_038355, intron 2 of 8)	-69400	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.005111	0.318027	
chunk0045_260_1	chr12	49473819	49474465	+	0	NA	intron (NM_001293286, intron 2 of 12)	intron (NM_001293286, intron 2 of 12)	-65015	NM_001314030	23416	Hs.64064	NM_012284	ENSG00000135519	KCNH3	BEC1|ELK2|Kv12.2	potassium voltage-gated channel subfamily H member 3	protein-coding	0.006192	0.350850	
chunk0013_126_1	chr1	168073884	168074508	+	0	NA	intron (NM_001017977, intron 18 of 18)	intron (NM_001017977, intron 18 of 18)	62240	NM_001267612	23432	Hs.271809	NM_007369	ENSG00000143147	GPR161	RE2	G protein-coupled receptor 161	protein-coding	0.000000	0.308800	294(AGGGACATATAGTCCC,-,0.00),295(GGGACATATAGTCCCT,+,0.00)
chunk0031_325_1	chr10	129257544	129257935	+	0	NA	Intergenic	Intergenic	-209445	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.012788	0.392857	
chunk0030_140_1	chr10	113679568	113680382	+	0	NA	exon (NM_001267057, exon 1 of 7)	exon (NM_001267057, exon 1 of 7)	306	NM_033339	840	Hs.9216	NM_001227	ENSG00000165806	CASP7	CASP-7|CMH-1|ICE-LAP3|LICE2|MCH3	caspase 7	protein-coding	0.085995	0.662577	
chunk0049_414_1	chr12	97426010	97426663	+	0	NA	Intergenic	Intergenic	-38685	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.009188	0.368502	
chunk0067_52_1	chr15	40845573	40845778	+	0	NA	intron (NM_181642, intron 2 of 10)	intron (NM_181642, intron 2 of 10)	1230	NM_001032367	6692	Hs.233950	NM_003710	ENSG00000166145	SPINT1	HAI|HAI1|MANSC2	serine peptidase inhibitor, Kunitz type 1	protein-coding	0.000000	0.587379	
chunk0043_8_1	chr12	12855151	12855588	+	0	NA	Intergenic	Intergenic	-20108	NR_003932	387841	Hs.631728	NR_003932	ENSG00000234498	RPL13AP20	RPL13A_9_1211	ribosomal protein L13a pseudogene 20	pseudo	0.011442	0.383562	239(GGGATCAAGATGTTCT,-,0.00),240(GGATCAAGATGTTCTC,+,0.00)
chunk0078_257_1	chr17	7266673	7267312	+	0	NA	Intergenic	L2a|LINE|L2	-3799	NM_001185022	1366	Hs.513915	NM_001307	ENSG00000181885	CLDN7	CEPTRL2|CLDN-7|CPETRL2|Hs.84359|claudin-1	claudin 7	protein-coding	0.004695	0.404687	148(TTGTACAGTCTGTTCT,-,0.00),149(TGTACAGTCTGTTCTC,+,0.00)
chunk0069_348_1	chr15	66600265	66600693	+	0	NA	intron (NR_110372, intron 1 of 4)	intron (NR_110372, intron 1 of 4)	18289	NR_110372	102723165	Hs.636703	NR_110372	ENSG00000259471	LINC01169	-	long intergenic non-protein coding RNA 1169	ncRNA	0.014019	0.564103	
chunk0035_448_1	chr11	57667290	57667826	+	0	NA	promoter-TSS (NM_015457)	promoter-TSS (NM_015457)	-444	NM_015457	25921	Hs.27239	NM_015457	ENSG00000156599	ZDHHC5	DHHC5|ZNF375	zinc finger DHHC-type containing 5	protein-coding	0.061567	0.515829	
chunk0007_233_1	chr1	82064691	82065187	+	0	NA	Intergenic	L2b|LINE|L2	264542	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.002016	0.402414	
chunk0148_17_1	chr5	348522	349002	+	0	NA	intron (NM_020731, intron 2 of 11)	L1ME1|LINE|L1	44586	NM_001242412	57491	Hs.50823	NM_020731	ENSG00000286169	AHRR	AHH|AHHR|bHLHe77	aryl-hydrocarbon receptor repressor	protein-coding	0.014583	0.442827	
chunk0132_110_1	chr3	155869758	155870327	+	0	NA	promoter-TSS (NM_003875)	promoter-TSS (NM_003875)	-494	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.017575	0.482456	
chunk0144_313_1	chr4	138655054	138655791	+	0	NA	Intergenic	Intergenic	345711	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.002714	0.371274	
chunk0100_323_1	chr2	116490109	116490315	+	0	NA	Intergenic	MLT1B-int|LTR|ERVL-MaLR	-1324467	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.000000	0.400966	158(AAGAACAGAATGTGTC,-,0.00),159(AGAACAGAATGTGTCT,+,0.00)
chunk0155_270_1	chr5	95960845	95961126	+	0	NA	intron (NM_012081, intron 1 of 11)	CpG	-1016	NR_130776	101929710		NR_130776	ENSG00000251314	LOC101929710	-	uncharacterized LOC101929710	ncRNA	0.067616	0.645390	116(GAGTACACCGTGTGCC,-,0.00),117(AGTACACCGTGTGCCC,+,0.00),163(GAGCACACAGTGTGTC,-,0.00),164(AGCACACAGTGTGTCC,+,0.00)
chunk0117_406_1	chr21	45638439	45638718	+	0	NA	Intergenic	Intergenic	-96107	NM_001205206	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.007168	0.435714	
chunk0018_39_1	chr1	215636998	215637622	+	0	NA	intron (NM_206933, intron 69 of 71)	MER5A|DNA|hAT-Charlie	69918	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.012821	0.462400	
chunk0128_364_1	chr3	113135998	113136210	+	0	NA	Intergenic	Intergenic	31627	NR_110823	101929717	Hs.638426	NR_110823	ENSG00000243795	LINC02044	-	long intergenic non-protein coding RNA 2044	ncRNA	0.014151	0.497653	109(CAGCACAGCCAGTCCC,-,0.00),110(AGCACAGCCAGTCCCT,+,0.00)
chunk0117_163_1	chr22	20216938	20217251	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	10762	NR_026919	150197	Hs.635544	NM_152508	ENSG00000236499	LINC00896	-	long intergenic non-protein coding RNA 896	ncRNA	0.012780	0.464968	
chunk0163_289_1	chr6	14025714	14026230	+	0	NA	Intergenic	L2c|LINE|L2	-91284	NM_001251901	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.001938	0.429400	
chunk0179_202_1	chr7	47371070	47371664	+	0	NA	intron (NM_022748, intron 16 of 30)	MIRb|SINE|MIR	210777	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.005051	0.499160	
chunk0082_432_1	chr17	61503939	61504320	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	47683	NM_018488	9496	Hs.143907	NM_018488	ENSG00000121075	TBX4	ICPPS|SPS	T-box transcription factor 4	protein-coding	0.007874	0.384817	
chunk0092_297_1	chr19	34233160	34233472	+	0	NA	Intergenic	Intergenic	-21235	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.016026	0.511182	
chunk0123_11_1	chr3	40262880	40263152	+	0	NA	intron (NR_033965, intron 2 of 2)	MER31B|LTR|ERV1	-46666	NM_005875	10289	Hs.315230	NM_005875	ENSG00000114784	EIF1B	GC20	eukaryotic translation initiation factor 1B	protein-coding	0.000000	0.435897	
chunk0056_99_1	chr13	82436142	82437106	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-1209641	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.000000	0.356477	650(GAGGACAAAATGTCCA,-,0.00),651(AGGACAAAATGTCCAT,+,0.00)
chunk0137_132_1	chr4	15149853	15150502	+	0	NA	intron (NR_125911, intron 2 of 5)	intron (NR_125911, intron 2 of 5)	147503	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.010786	0.524615	
chunk0134_425_1	chr3	183408809	183409091	+	0	NA	intron (NM_015078, intron 1 of 29)	intron (NM_015078, intron 1 of 29)	19319	NM_015078	23101	Hs.208267	NM_015078	ENSG00000053524	MCF2L2	ARHGEF22	MCF.2 cell line derived transforming sequence-like 2	protein-coding	0.000000	0.342756	
chunk0098_62_1	chr2	66850878	66851168	+	0	NA	Intergenic	Intergenic	-53413	NR_110169	101060019	Hs.116425	NR_110169	ENSG00000230525	LINC01799	-	long intergenic non-protein coding RNA 1799	ncRNA	0.013793	0.405498	
chunk0156_432_1	chr5	114565669	114566368	+	0	NA	intron (NR_130785, intron 3 of 12)	intron (NR_130785, intron 3 of 12)	132488	NM_170775	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.010014	0.404286	
chunk0096_254_1	chr2	31313977	31314471	+	0	NA	Intergenic	L1MC1|LINE|L1	80210	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.002024	0.379798	
chunk0126_24_1	chr3	73593258	73593457	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-23842	NM_001303139	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.005025	0.295000	
chunk0060_350_1	chr14	52158139	52158785	+	0	NA	Intergenic	L1PA6|LINE|L1	-89234	NM_007361	22795	Hs.369840	NM_007361	ENSG00000087303	NID2	NID-2	nidogen 2	protein-coding	0.007740	0.516229	
chunk0151_92_1	chr5	42891009	42891489	+	0	NA	Intergenic	L1MC5a|LINE|L1	-79327	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.004167	0.316008	
chunk0134_285_1	chr3	179837389	179837887	+	0	NA	intron (NM_001256750, intron 8 of 14)	intron (NM_001256750, intron 8 of 14)	-60556	NR_110059	101928790	Hs.667247	NR_110059	ENSG00000244302	PEX5L-AS2	-	PEX5L antisense RNA 2	ncRNA	0.008032	0.392786	
chunk0039_158_1	chr11	98876343	98876736	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-144437	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.007634	0.398477	
chunk0199_119_1	chr9	3525587	3526011	+	0	NA	5' UTR (NM_134428, exon 1 of 18)	5' UTR (NM_134428, exon 1 of 18)	202	NM_001282116	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.056604	0.595294	
chunk0142_320_1	chr4	100859159	100859737	+	0	NA	Intergenic	L1PBb|LINE|L1	-184335	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.005190	0.295337	184(TTGAACTGGATGTCCT,-,0.00),185(TGAACTGGATGTCCTT,+,0.00)
chunk0096_388_1	chr2	37472813	37473133	+	0	NA	Intergenic	Intergenic	128363	NM_012413	25797	Hs.79033	NM_012413	ENSG00000115828	QPCT	GCT|QC|sQC	glutaminyl-peptide cyclotransferase	protein-coding	0.006250	0.370717	
chunk0099_122_1	chr2	86046926	86047452	+	0	NA	exon (NM_015425, exon 19 of 34)	exon (NM_015425, exon 19 of 34)	-23321	NR_026984									0.011407	0.438330	
chunk0058_323_1	chr14	27739769	27740241	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-106727	NR_130461	100422830		NR_130461	ENSG00000264657	MIR3171	-	microRNA 3171	ncRNA	0.000000	0.376321	
chunk0065_124_1	chr15	24857033	24857419	+	0	NA	intron (NM_022805, intron 1 of 11)	intron (NM_022805, intron 1 of 11)	675	NM_022805	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.012953	0.335917	
chunk0170_404_1	chr6	117682053	117682397	+	0	NA	intron (NM_138459, intron 1 of 4)	intron (NM_138459, intron 1 of 4)	6771	NM_138459	116150	Hs.289008	NM_138459	ENSG00000153989	NUS1	C6orf68|CDG1AA|MGC:7199|MRD55|NgBR|TANGO14	NUS1 dehydrodolichyl diphosphate synthase subunit	protein-coding	0.005814	0.443478	
chunk0073_442_1	chr16	19323053	19323537	+	0	NA	Intergenic	MLT2F|LTR|ERVL	37512	NM_001256720	728276	Hs.632180	NM_001256720	ENSG00000261210	CLEC19A	-	C-type lectin domain containing 19A	protein-coding	0.014463	0.478351	
chunk0001_170_1	chr1	6701664	6702033	+	0	NA	promoter-TSS (NM_018198)	promoter-TSS (NM_018198)	58	NM_018198	55735	Hs.462640	NM_018198	ENSG00000007923	DNAJC11	dJ126A5.1	DnaJ heat shock protein family (Hsp40) member C11	protein-coding	0.121951	0.724324	
chunk0170_259_1	chr6	113819484	113819724	+	0	NA	Intergenic	Intergenic	-37731	NM_002356	4082	Hs.519909	NM_002356	ENSG00000277443	MARCKS	80K-L|MACS|PKCSL|PRKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.008333	0.398340	
chunk0154_217_1	chr5	80624023	80624236	+	0	NA	Intergenic	Intergenic	-1605	NR_125754	103689917	Hs.740035	NR_125754	ENSG00000251221	LINC01337	TCONS_00009713	long intergenic non-protein coding RNA 1337	ncRNA	0.009390	0.392523	
chunk0027_316_1	chr10	78111129	78111487	+	0	NA	Intergenic	LTR81B|LTR|Gypsy	77548	NM_001142284	6229	Hs.280130	NM_001026	ENSG00000138326	RPS24	DBA3|S24|eS24	ribosomal protein S24	protein-coding	0.002793	0.459610	
chunk0140_229_1	chr4	71150874	71151456	+	0	NA	Intergenic	MER3|DNA|hAT-Charlie	-36121	NM_001098484	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.003436	0.367067	291(ATCACAGAATGTTCTG,+,0.00)
chunk0124_397_1	chr3	59739780	59740446	+	0	NA	Intergenic	L1ME3B|LINE|L1	-690124	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.006006	0.332834	
chunk0004_222_1	chr1	46858188	46858567	+	0	NA	intron (NR_002788, intron 9 of 11)	intron (NR_002788, intron 9 of 11)	42098	NR_002788	163720	Hs.591431	NR_002788	ENSG00000154198	CYP4Z2P	-	cytochrome P450 family 4 subfamily Z member 2, pseudogene	pseudo	0.002639	0.326316	191(TGGAACATTATGTGCA,-,0.00),192(GGAACATTATGTGCAT,+,0.00)
chunk0057_296_1	chr13	106336664	106337143	+	0	NA	Intergenic	Intergenic	-39660	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.014614	0.341667	
chunk0131_186_1	chr3	148025301	148025500	+	0	NA	Intergenic	Intergenic	604073	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.010050	0.445000	
chunk0106_355_1	chr2	206865853	206866389	+	0	NA	Intergenic	L2c|LINE|L2	-73433	NM_173077	130749	Hs.684103	NM_173077	ENSG00000144410	CPO	-	carboxypeptidase O	protein-coding	0.003731	0.337058	
chunk0095_8_1	chr2	11830620	11830916	+	0	NA	Intergenic	Intergenic	6218	NR_036226	100422996		NR_036226	ENSG00000265172	MIR4262	-	microRNA 4262	ncRNA	0.016892	0.377104	
chunk0142_242_1	chr4	98860763	98861813	+	0	NA	Intergenic	L2a|LINE|L2	67804	NM_001130678	1977	Hs.13211	NM_001968	ENSG00000151247	EIF4E	AUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding	0.002857	0.348240	
chunk0146_104_1	chr4	158782930	158783181	+	0	NA	intron (NM_020840, intron 1 of 16)	intron (NM_020840, intron 1 of 16)	14025	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.003984	0.392857	
chunk0062_404_1	chr14	74963772	74964131	+	0	NA	Intergenic	Intergenic	-8187	NM_002632	5228	Hs.252820	NM_002632	ENSG00000119630	PGF	D12S1900|PGFL|PIGF|PLGF|PlGF-2|SHGC-10760	placental growth factor	protein-coding	0.011142	0.541667	218(AGAAACTGAGTGTTCT,-,0.00),219(GAAACTGAGTGTTCTA,+,0.00)
chunk0137_311_1	chr4	24478324	24478820	+	0	NA	Intergenic	Intergenic	41718	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.008065	0.438632	
chunk0207_39_1	chrX	5985632	5986026	+	0	NA	intron (NM_181332, intron 3 of 5)	L1ME3B|LINE|L1	241374	NM_001282146	57502	Hs.21107	NM_020742	ENSG00000146938	NLGN4X	ASPGX2|AUTSX2|HLNX|HNL4X|NLGN4	neuroligin 4 X-linked	protein-coding	0.010152	0.313924	
chunk0063_412_1	chr14	88385359	88385653	+	0	NA	promoter-TSS (NM_018418)	promoter-TSS (NM_018418)	-138	NM_001040428	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.068027	0.627119	
chunk0108_248_1	chr2	233933732	233933999	+	0	NA	intron (NM_024080, intron 3 of 25)	intron (NM_024080, intron 3 of 25)	16467	NM_024080	79054	Hs.366053	NM_024080	ENSG00000144481	TRPM8	LTRPC6|LTrpC-6|TRPP8|trp-p8	transient receptor potential cation channel subfamily M member 8	protein-coding	0.000000	0.503731	
chunk0188_23_1	chr8	6532021	6532551	+	0	NA	intron (NM_001118888, intron 1 of 7)	intron (NM_001118888, intron 1 of 7)	30977	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.016981	0.418079	277(AGGGACACCGTGTGCT,-,0.00),278(GGGACACCGTGTGCTT,+,0.00)
chunk0165_430_1	chr6	39724797	39725087	+	0	NA	intron (NM_145027, intron 1 of 22)	intron (NM_145027, intron 1 of 22)	463	NM_145027	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.058621	0.542955	
chunk0139_330_1	chr4	58811248	58811835	+	0	NA	Intergenic	L1MA3|LINE|L1	1385669	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003407	0.340136	
chunk0197_69_1	chr8	118878387	118879168	+	0	NA	Intergenic	Intergenic	73367	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.002561	0.314578	
chunk0136_395_1	chr3	197010952	197011315	+	0	NA	intron (NM_005929, intron 9 of 15)	intron (NM_005929, intron 9 of 15)	8227	NR_038285	100507057	Hs.666451	NR_038285	ENSG00000228109	MELTF-AS1	MFI2-AS1	MELTF antisense RNA 1	ncRNA	0.038567	0.637363	229(CAGCACAGCGTGTGCT,-,0.00),230(AGCACAGCGTGTGCTG,+,0.00)
chunk0059_250_1	chr14	35064272	35064578	+	0	NA	intron (NM_173607, intron 2 of 4)	intron (NM_173607, intron 2 of 4)	-16656	NR_110415	101927178	Hs.617139	NR_110415	ENSG00000151327	LOC101927178	-	uncharacterized LOC101927178	ncRNA	0.016340	0.400651	
chunk0118_371_1	chr22	36453257	36453456	+	0	NA	Intergenic	Intergenic	28284	NM_012473	25828	Hs.211929	NM_012473	ENSG00000100348	TXN2	COXPD29|MT-TRX|MTRX|TRX2|TXN	thioredoxin 2	protein-coding	0.000000	0.475000	
chunk0166_334_1	chr6	50183115	50183399	+	0	NA	Intergenic	L1M5|LINE|L1	-134606	NM_001037498	245915	Hs.571092	NM_001037498	ENSG00000180872	DEFB112	DEFB-12	defensin beta 112	protein-coding	0.007042	0.294737	
chunk0107_336_1	chr2	221184042	221184432	+	0	NA	Intergenic	Intergenic	388121	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.000000	0.327366	195(AAGAACTTAATGTACT,-,0.00),196(AGAACTTAATGTACTT,+,0.00)
chunk0160_138_1	chr5	151363127	151363428	+	0	NA	Intergenic	L1M3f|LINE|L1	-15687	NM_181776	153201	Hs.483877	NM_181776	ENSG00000186335	SLC36A2	PAT2|TRAMD1	solute carrier family 36 member 2	protein-coding	0.003322	0.493377	
chunk0044_216_1	chr12	31265024	31265562	+	0	NA	Intergenic	Intergenic	-59023	NR_026806	79857	Hs.534485	NM_024799	ENSG00000177340	FLJ13224	-	uncharacterized LOC79857	ncRNA	0.013011	0.385900	
chunk0092_121_1	chr19	27793812	27794193	+	0	NA	promoter-TSS (NR_027301)	promoter-TSS (NR_027301)	-62	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.068241	0.609948	
chunk0048_191_1	chr12	81120552	81120973	+	0	NA	intron (NM_024560, intron 2 of 15)	intron (NM_024560, intron 2 of 15)	-37626	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.000000	0.260664	
chunk0028_159_1	chr10	86992856	86993287	+	0	NA	intron (NM_133447, intron 4 of 11)	intron (NM_133447, intron 4 of 11)	22330	NM_133447	119385	Hs.511787	NM_133447		AGAP11	-	ArfGAP with GTPase domain, ankyrin repeat and PH domain 11	protein-coding	0.004640	0.312500	
chunk0094_298_1	chr2	8500250	8501032	+	0	NA	Intergenic	Intergenic	83151	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.014066	0.496807	
chunk0100_16_1	chr2	105071063	105071456	+	0	NA	intron (NM_182640, intron 2 of 10)	MIRb|SINE|MIR	31685	NR_110227	101927492	Hs.469537	NR_110227	ENSG00000231851	UTAT33	-	uncharacterized LOC101927492	ncRNA	0.002545	0.279188	
chunk0041_115_1	chr11	124960806	124961371	+	0	NA	intron (NM_025004, intron 4 of 15)	L2a|LINE|L2	6967	NM_025004	80071	Hs.287555	NM_025004	ENSG00000149548	CCDC15	-	coiled-coil domain containing 15	protein-coding	0.003540	0.310954	
chunk0126_287_1	chr3	80234423	80235055	+	0	NA	Intergenic	L2c|LINE|L2	-466830	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.011076	0.398104	
chunk0117_32_1	chr22	11926517	11926844	+	0	NA	intron (NR_110761, intron 2 of 2)	L1PA12|LINE|L1	29274	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.012232	0.542683	
chunk0009_198_1	chr1	105956354	105956998	+	0	NA	Intergenic	MER70A|LTR|ERVL	-337741	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.006211	0.387597	281(TGGAACAGGATGTCCT,-,0.00),282(GGAACAGGATGTCCTG,+,0.00)
chunk0166_272_1	chr6	48086012	48086366	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	-17500	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.008475	0.326761	
chunk0090_55_1	chr19	2007169	2007592	+	0	NA	intron (NM_017797, intron 1 of 8)	MER58A|DNA|hAT-Charlie	8323	NM_017797	55643	Hs.465543	NM_017797	ENSG00000133243	BTBD2	-	BTB domain containing 2	protein-coding	0.014184	0.457547	
chunk0168_59_1	chr6	79113868	79114110	+	0	NA	Intergenic	HAL1|LINE|L1	-35695	NM_017934	55023	Hs.511817	NM_017934	ENSG00000146247	PHIP	BRWD2|DCAF14|DIDOD|WDR11|ndrp	pleckstrin homology domain interacting protein	protein-coding	0.000000	0.423868	
chunk0149_241_1	chr5	23495489	23496000	+	0	NA	Intergenic	Intergenic	-11865	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.000000	0.263672	
chunk0175_181_1	chr7	5358754	5359179	+	0	NA	intron (NM_001080495, intron 15 of 29)	intron (NM_001080495, intron 15 of 29)	64580	NM_001080495	84629	Hs.520638	NM_001013722	ENSG00000182095	TNRC18	CAGL79|TNRC18A	trinucleotide repeat containing 18	protein-coding	0.007059	0.441315	
chunk0095_401_1	chr2	24329547	24330100	+	0	NA	intron (NM_019595, intron 1 of 38)	intron (NM_019595, intron 1 of 38)	30705	NM_019595	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.007233	0.333935	1(CAGGCCACTGTGTCCT,-,0.00),2(AGGCCACTGTGTCCTG,+,0.00)
chunk0080_371_1	chr17	33283916	33284496	+	0	NA	intron (NM_001094, intron 1 of 9)	MamRep434|DNA|TcMar-Tigger	8782	NM_183377	40	Hs.368417	NM_001094	ENSG00000108684	ASIC2	ACCN|ACCN1|ASIC2a|BNC1|BNaC1|MDEG|hBNaC1	acid sensing ion channel subunit 2	protein-coding	0.013793	0.406196	
chunk0093_79_1	chr19	40726304	40726790	+	0	NA	intron (NM_025194, intron 2 of 6)	MER58A|DNA|hAT-Charlie	9444	NM_025194	80271	Hs.515415	NM_025194	ENSG00000086544	ITPKC	IP3-3KC|IP3KC	inositol-trisphosphate 3-kinase C	protein-coding	0.010288	0.441478	
chunk0046_371_1	chr12	63346101	63346420	+	0	NA	Intergenic	L1ME2|LINE|L1	-193450	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.003135	0.340625	
chunk0007_390_1	chr1	85403401	85404450	+	0	NA	intron (NM_001134445, intron 2 of 6)	intron (NM_001134445, intron 2 of 6)	61281	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.004766	0.326667	
chunk0202_388_1	chr9	81070780	81071151	+	0	NA	Intergenic	Intergenic	618570	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.016173	0.379032	
chunk0159_211_1	chr5	140647760	140648004	+	0	NA	promoter-TSS (NM_001185012)	promoter-TSS (NM_001185012)	38	NR_037428	100500820		NR_037428	ENSG00000284325	MIR3655	-	microRNA 3655	ncRNA	0.053279	0.518367	
chunk0035_442_1	chr11	57515065	57515491	+	0	NA	promoter-TSS (NM_001198810)	promoter-TSS (NM_001198810)	-393	NM_001198810	8501	Hs.591952	NM_003627	ENSG00000149150	SLC43A1	LAT3|PB39|POV1|R00504	solute carrier family 43 member 1	protein-coding	0.084507	0.641686	
chunk0174_45_1	chr6	154613038	154613398	+	0	NA	Intergenic	Intergenic	-102599	NM_173515	154043	Hs.16064	NM_173515	ENSG00000153721	CNKSR3	CNK3|CNK3/IPCEF1|MAGI1	CNKSR family member 3	protein-coding	0.025000	0.479224	
chunk0054_375_1	chr13	49993766	49993995	+	0	NA	non-coding (NR_002612, exon 9 of 11)	non-coding (NR_002612, exon 9 of 11)	2621	NR_037407	100500908		NR_037407	ENSG00000264864	MIR3613	-	microRNA 3613	ncRNA	0.008734	0.439130	
chunk0095_344_1	chr2	20862957	20863348	+	0	NA	Intergenic	L1MC4|LINE|L1	-40022	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.010230	0.369898	
chunk0044_203_1	chr12	30807444	30807717	+	0	NA	Intergenic	L1M3f|LINE|L1	11899	NR_040245	100287314	Hs.355210	NR_040245		LINC00941	lncRNA-MUF	long intergenic non-protein coding RNA 941	ncRNA	0.007326	0.448905	
chunk0126_90_1	chr3	74780509	74780973	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-259601	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002155	0.363441	
chunk0061_70_1	chr14	56648993	56649192	+	0	NA	3' UTR (NM_017799, exon 16 of 16)	3' UTR (NM_017799, exon 16 of 16)	69299	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.010050	0.475000	
chunk0015_5_1	chr1	184078820	184079353	+	0	NA	Intergenic	Intergenic	27435	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.001876	0.374532	325(AAGAACTGCTTGTACT,-,0.00),326(AGAACTGCTTGTACTC,+,0.00)
chunk0054_246_1	chr13	46164434	46165061	+	0	NA	intron (NM_002298, intron 1 of 15)	intron (NM_002298, intron 1 of 15)	17577	NM_002298	3936	Hs.381099	NM_002298	ENSG00000136167	LCP1	CP64|HEL-S-37|L-PLASTIN|LC64P|LPL|PLS2	lymphocyte cytosolic protein 1	protein-coding	0.001595	0.375796	
chunk0201_17_1	chr9	33070313	33070984	+	0	NA	intron (NM_018225, intron 3 of 11)	L1MA3|LINE|L1	6068	NM_018225	55234	Hs.655351	NM_018225	ENSG00000122692	SMU1	BWD|SMU-1|fSAP57	SMU1 DNA replication regulator and spliceosomal factor	protein-coding	0.005961	0.370536	
chunk0144_42_1	chr4	125843164	125843725	+	0	NA	Intergenic	L1MDb|LINE|L1	336185	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.005348	0.362989	
chunk0179_329_1	chr7	50601159	50601431	+	0	NA	intron (NM_001001549, intron 13 of 14)	L1MC5a|LINE|L1	-35838	NM_001082971	1644	Hs.359698	NM_000790	ENSG00000132437	DDC	AADC	dopa decarboxylase	protein-coding	0.003676	0.366300	
chunk0030_109_1	chr10	112761812	112762038	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-61571	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.013274	0.348018	
chunk0069_220_1	chr15	63655946	63656222	+	0	NA	intron (NM_003922, intron 49 of 77)	intron (NM_003922, intron 49 of 77)	-55257	NR_034080	100130855	Hs.631163	NR_034080	ENSG00000259248	USP3-AS1	-	USP3 antisense RNA 1	ncRNA	0.010870	0.397112	
chunk0100_41_1	chr2	105644228	105644747	+	0	NA	Intergenic	MIRc|SINE|MIR	-33928	NR_038891	285000	Hs.737917	NR_038891		LOC285000	-	uncharacterized LOC285000	ncRNA	0.028902	0.450000	
chunk0204_34_1	chr9	92623817	92624161	+	0	NA	intron (NM_022755, intron 11 of 12)	MER6B|DNA|TcMar-Tigger	5939	NR_036505	100128361	Hs.660395	NR_036505		LOC100128361	-	uncharacterized LOC100128361	ncRNA	0.008721	0.440580	155(TAGTACACTAAGTCCT,-,0.00),156(AGTACACTAAGTCCTC,+,0.00)
chunk0111_339_1	chr20	33150991	33151374	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	-16972	NM_080574	140683	Hs.125960	NM_080574	ENSG00000131050	BPIFA2	C20orf70|PSP|SPLUNC2|bA49G10.1	BPI fold containing family A member 2	protein-coding	0.007833	0.419271	189(AAGAGCACTGTGTCCT,-,0.00),190(AGAGCACTGTGTCCTG,+,0.00)
chunk0082_438_1	chr17	61568656	61569006	+	0	NA	Intergenic	Intergenic	22371	NM_199290	342538	Hs.591178	NM_199290	ENSG00000253506	NACA2	ANAC|NACAL	nascent polypeptide associated complex subunit alpha 2	protein-coding	0.011429	0.404558	
chunk0036_224_1	chr11	63862872	63863268	+	0	NA	intron (NM_001039469, intron 1 of 18)	intron (NM_001039469, intron 1 of 18)	24142	NM_001163296	2011	Hs.567261	NM_004954	ENSG00000072518	MARK2	EMK-1|EMK1|PAR-1|Par-1b|Par1b	microtubule affinity regulating kinase 2	protein-coding	0.010101	0.486146	
chunk0179_208_1	chr7	47538684	47539320	+	0	NA	intron (NM_022748, intron 1 of 30)	intron (NM_022748, intron 1 of 30)	43142	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.007862	0.445840	
chunk0089_362_1	chr18	66972099	66972302	+	0	NA	Intergenic	Intergenic	-109384	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.004926	0.411765	
chunk0186_308_1	chr7	142927117	142927805	+	0	NA	intron (NM_019841, intron 7 of 14).2	MSTA|LTR|ERVL-MaLR	6262	NM_019841	56302	Hs.283369	NM_019841	ENSG00000127412	TRPV5	CAT2|ECAC1|OTRPC3	transient receptor potential cation channel subfamily V member 5	protein-coding	0.008721	0.441219	
chunk0076_262_1	chr16	69395166	69395376	+	0	NA	Intergenic	L1ME4b|LINE|L1	-9283	NM_005652	7014	Hs.63335	NM_005652	ENSG00000132604	TERF2	TRBF2|TRF2	telomeric repeat binding factor 2	protein-coding	0.004762	0.331754	
chunk0144_247_1	chr4	135457565	135457937	+	0	NA	Intergenic	HAL1b|LINE|L1	430342	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.005376	0.281501	
chunk0194_64_1	chr8	82409322	82409521	+	0	NA	Intergenic	L1M5|LINE|L1	-567135	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.300000	
chunk0011_297_1	chr1	151553498	151553989	+	0	NA	intron (NM_001126337, intron 1 of 11)	L1ME3A|LINE|L1	7947	NR_030280	693139		NR_030280	ENSG00000207606	MIR554	MIRN554|hsa-mir-554	microRNA 554	ncRNA	0.012220	0.418699	
chunk0188_85_1	chr8	8555215	8555799	+	0	NA	Intergenic	Intergenic	-146649	NM_194284	137075	Hs.183617	NM_194284	ENSG00000253958	CLDN23	CLDNL|hCG1646163	claudin 23	protein-coding	0.008562	0.451282	
chunk0052_229_1	chr13	25620046	25620352	+	0	NA	intron (NM_001313741, intron 24 of 35)	L1MEd|LINE|L1	151425	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.003268	0.423453	
chunk0205_50_1	chr9	106149960	106150462	+	0	NA	Intergenic	L2a|LINE|L2	-450717	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.001992	0.337972	
chunk0097_248_1	chr2	53744753	53745168	+	0	NA	intron (NM_145863, intron 2 of 8)	intron (NM_145863, intron 2 of 8)	-22832	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.002410	0.307692	151(TAAAACATTCTGTTCT,-,0.00),152(AAAACATTCTGTTCTT,+,0.00)
chunk0122_392_1	chr3	37892904	37893180	+	0	NA	intron (NM_001008392, intron 1 of 7)	intron (NM_001008392, intron 1 of 7)	30864	NM_005808	10217	Hs.475963	NM_005808	ENSG00000144677	CTDSPL	C3orf8|HYA22|PSR1|RBSP3|SCP3	CTD small phosphatase like	protein-coding	0.007246	0.501805	
chunk0152_212_1	chr5	60291685	60292754	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-195494	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.006548	0.313084	734(AATACATATTGTTCTT,+,0.00)
chunk0186_229_1	chr7	140531112	140531406	+	0	NA	intron (NM_015689, intron 12 of 17)	intron (NM_015689, intron 12 of 17)	-51690	NR_117084	23608	Hs.744883	NM_013446	ENSG00000133606	MKRN1	RNF61	makorin ring finger protein 1	protein-coding	0.006803	0.338983	
chunk0062_341_1	chr14	73644861	73645146	+	0	NA	5' UTR (NM_031427, exon 1 of 8)	5' UTR (NM_031427, exon 1 of 8)	128	NM_031427	83544	Hs.271270	NM_031427	ENSG00000119661	DNAL1	C14orf168|CILD16|LC1	dynein axonemal light chain 1	protein-coding	0.087719	0.653846	
chunk0020_43_1	chr1	232282993	232283582	+	0	NA	Intergenic	Intergenic	232321	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.011885	0.393220	
chunk0008_69_1	chr1	89727229	89727607	+	0	NA	Intergenic	L2b|LINE|L2	-93596	NM_001134479	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.002646	0.453826	148(TAGCACATACTGTTCT,-,0.00),149(AGCACATACTGTTCTA,+,0.00)
chunk0098_336_1	chr2	77065368	77065567	+	0	NA	intron (NM_001282924, intron 3 of 3)	L2c|LINE|L2	79502	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.005025	0.285000	
chunk0199_469_1	chr9	14344229	14344551	+	0	NA	intron (NM_001190738, intron 1 of 8)	intron (NM_001190738, intron 1 of 8)	-30344	NM_001190737	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.015528	0.504644	
chunk0153_204_1	chr5	71783318	71783857	+	0	NA	Intergenic	Intergenic	64424	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.022263	0.409259	
chunk0055_154_1	chr13	60027515	60027985	+	0	NA	intron (NR_109838, intron 3 of 4)	intron (NR_109838, intron 3 of 4)	14447	NR_051994	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004255	0.305732	
chunk0117_115_1	chr22	18001298	18001881	+	0	NA	intron (NM_015241, intron 1 of 31)	CpG	-20628	NR_030378	693233		NR_030378	ENSG00000207780	MIR648	MIRN648|hsa-mir-648	microRNA 648	ncRNA	0.090909	0.652397	
chunk0156_361_1	chr5	112545462	112545760	+	0	NA	Intergenic	Intergenic	-82825	NR_104672	102467214	Hs.124613	NR_104672		LINC02200	-	long intergenic non-protein coding RNA 2200	ncRNA	0.010067	0.484950	
chunk0102_17_1	chr2	141499358	141499578	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	632233	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.018182	0.389140	
chunk0063_162_1	chr14	80231639	80232120	+	0	NA	promoter-TSS (NM_000793)	promoter-TSS (NM_000793)	-825	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.004158	0.336100	256(GGGGACACCATGATCT,-,0.00),257(GGGACACCATGATCTC,+,0.00)
chunk0041_32_1	chr12	817952	818300	+	0	NA	intron (NM_213655, intron 2 of 27)	L1MB5|LINE|L1	65203	NM_018979	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.002874	0.303725	188(CAGAACACTCTGTGCC,-,0.00),189(AGAACACTCTGTGCCC,+,0.00)
chunk0037_350_1	chr11	77566751	77567347	+	0	NA	Intergenic	L1MA3|LINE|L1	-4040	NR_130930	646029	Hs.609654	NM_001039908		LOC646029	-	uncharacterized LOC646029	ncRNA	0.008389	0.345059	
chunk0027_303_1	chr10	77881139	77881561	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	45240	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.007109	0.503546	
chunk0144_365_1	chr4	139876734	139876933	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	211065	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.010050	0.540000	
chunk0185_197_1	chr7	128427358	128427608	+	0	NA	Intergenic	MER119|DNA|hAT-Charlie	-17496	NM_001304521	3614	Hs.654401	NM_000883	ENSG00000106348	IMPDH1	IMPD|IMPD1|IMPDH-I|LCA11|RP10|sWSS2608	inosine monophosphate dehydrogenase 1	protein-coding	0.016000	0.450199	
chunk0072_311_1	chr15	98796688	98796993	+	0	NA	intron (NM_001291858, intron 2 of 20)	L2a|LINE|L2	12414	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.016393	0.444444	
chunk0190_393_1	chr8	40155977	40156661	+	0	NA	Intergenic	Intergenic	2851	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.005848	0.313869	
chunk0133_181_1	chr3	170180944	170181143	+	0	NA	intron (NM_024947, intron 1 of 14)	intron (NM_024947, intron 1 of 14)	706	NM_001308116	80012	Hs.529592	NM_024947	ENSG00000173889	PHC3	EDR3|HPH3	polyhomeotic homolog 3	protein-coding	0.035176	0.505000	58(GAAACAGTAAGTTCTG,+,0.00)
chunk0093_379_1	chr19	56283334	56283563	+	0	NA	Intergenic	MIRb|SINE|MIR	-55158	NM_024303	79149	Hs.177688	NM_024303	ENSG00000131848	ZSCAN5A	ZNF495|ZSCAN5	zinc finger and SCAN domain containing 5A	protein-coding	0.017467	0.400000	74(GAGCACAGAGAGTTCA,-,0.00),75(AGCACAGAGAGTTCAT,+,0.00)
chunk0091_355_1	chr19	15283659	15283892	+	0	NA	Intergenic	Intergenic	-3324	NM_058243	23476	Hs.187763	NM_014299	ENSG00000141867	BRD4	CAP|HUNK1|HUNKI|MCAP	bromodomain containing 4	protein-coding	0.021459	0.525641	
chunk0010_85_1	chr1	113434403	113435007	+	0	NA	intron (NM_152900, intron 1 of 20)	L2c|LINE|L2	43852	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.001656	0.337190	
chunk0005_273_1	chr1	59917375	59917574	+	0	NA	intron (NM_000775, intron 1 of 8)	MIR|SINE|MIR	9277	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.005025	0.390000	
chunk0050_320_1	chr12	107114741	107115184	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-21105	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.002257	0.371622	
chunk0082_361_1	chr17	60198554	60198761	+	0	NA	intron (NM_032582, intron 26 of 33)	intron (NM_032582, intron 26 of 33)	32988	NR_002999	677681		NR_002999	ENSG00000252577	SCARNA20	ACA66	small Cajal body-specific RNA 20	ncRNA	0.004831	0.341346	
chunk0014_439_1	chr1	183719369	183719695	+	0	NA	intron (NM_001297669, intron 2 of 18)	intron (NM_001297669, intron 2 of 18)	-66219	NM_203454	403314	Hs.97335	NM_203454	ENSG00000173627	APOBEC4	C1orf169	apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4	protein-coding	0.006135	0.477064	
chunk0056_202_1	chr13	85783016	85783656	+	0	NA	Intergenic	Intergenic	16012	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.004687	0.329173	
chunk0023_357_1	chr10	29917047	29917782	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	142145	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.009524	0.406250	
chunk0052_144_1	chr13	23778766	23779501	+	0	NA	intron (NM_005932, intron 16 of 18)	L1M2|LINE|L1	-109756	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.005442	0.380435	
chunk0156_318_1	chr5	111092115	111092646	+	0	NA	exon (NM_139281, exon 1 of 23)	exon (NM_139281, exon 1 of 23)	208	NM_139281	134430	Hs.533237	NM_139281	ENSG00000134987	WDR36	GLC1G|TA-WDRP|TAWDRP|UTP21	WD repeat domain 36	protein-coding	0.075330	0.584586	
chunk0011_422_1	chr1	154468736	154469160	+	0	NA	3' UTR (NM_000565, exon 10 of 10)	3' UTR (NM_000565, exon 10 of 10)	33102	NM_001010846	126669	Hs.591481	NM_001010846	ENSG00000169291	SHE	-	Src homology 2 domain containing E	protein-coding	0.018868	0.552941	
chunk0009_187_1	chr1	105818177	105818585	+	0	NA	Intergenic	Intergenic	-199446	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004902	0.383863	
chunk0150_114_1	chr5	32889016	32889559	+	0	NA	Intergenic	L2a|LINE|L2	-58156	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.003683	0.375000	
chunk0126_298_1	chr3	80696334	80696638	+	0	NA	Intergenic	Intergenic	-297382	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.003289	0.413115	
chunk0049_278_1	chr12	93863152	93863401	+	0	NA	Intergenic	Intergenic	-125453	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.020080	0.532000	
chunk0115_81_1	chr21	22115663	22116250	+	0	NA	intron (NR_038400, intron 5 of 5)	intron (NR_038400, intron 5 of 5)	17339	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.005111	0.346939	
chunk0059_189_1	chr14	32809428	32809653	+	0	NA	intron (NM_004274, intron 12 of 13)	intron (NM_004274, intron 12 of 13)	-129713	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.004444	0.429204	
chunk0179_99_1	chr7	44748648	44748847	+	0	NA	promoter-TSS (NM_031449)	promoter-TSS (NM_031449)	181	NM_001300959	83637	Hs.77978	NM_031449	ENSG00000122515	ZMIZ2	NET27|TRAFIP20|ZIMP7|hZIMP7	zinc finger MIZ-type containing 2	protein-coding	0.135678	0.790000	
chunk0183_214_1	chr7	106500103	106500500	+	0	NA	Intergenic	Intergenic	160887	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.012594	0.351759	
chunk0180_348_1	chr7	73528185	73528798	+	0	NA	Intergenic	Intergenic	-6206	NM_032408	9031	Hs.743372	NM_023005	ENSG00000009954	BAZ1B	WBSCR10|WBSCR9|WSTF	bromodomain adjacent to zinc finger domain 1B	protein-coding	0.014682	0.426710	
chunk0072_368_1	chr15	99943617	99943816	+	0	NA	Intergenic	L1MA9|LINE|L1	-136789	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.020101	0.550000	
chunk0173_264_1	chr6	147179595	147180408	+	0	NA	intron (NR_034115, intron 1 of 10)	L3|LINE|CR1	21076	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.006150	0.342752	
chunk0102_93_1	chr2	143994991	143995425	+	0	NA	intron (NM_001006636, intron 7 of 11)	intron (NM_001006636, intron 7 of 11)	58141	NR_110237	101928386	Hs.668251	NR_110237	ENSG00000232377	LOC101928386	-	uncharacterized LOC101928386	ncRNA	0.004608	0.337931	252(CTGTACAGTATGTACT,-,0.00),253(TGTACAGTATGTACTT,+,0.00)
chunk0186_144_1	chr7	138831095	138831573	+	0	NA	TTS (NM_001164665)	TTS (NM_001164665)	-33138	NM_130840	50617	Hs.98967	NM_020632	ENSG00000105929	ATP6V0A4	A4|ATP6N1B|ATP6N2|RDRTA2|RTA1C|RTADR|STV1|VPH1|VPP2	ATPase H+ transporting V0 subunit a4	protein-coding	0.010460	0.373695	162(AAGTACTGGGTGTTCT,-,0.00),163(AGTACTGGGTGTTCTC,+,0.00)
chunk0100_33_1	chr2	105315906	105316474	+	0	NA	intron (NM_004257, intron 1 of 11)	L1ME2|LINE|L1	13524	NM_004257	9392	Hs.446350	NM_004257	ENSG00000135966	TGFBRAP1	TRAP-1|TRAP1|VPS3	transforming growth factor beta receptor associated protein 1	protein-coding	0.015845	0.372583	289(AGGGACACAGTGAACT,-,0.00),290(GGGACACAGTGAACTT,+,0.00)
chunk0182_202_1	chr7	95986195	95986606	+	0	NA	intron (NM_001278421, intron 7 of 15)	intron (NM_001278421, intron 7 of 15)	213894	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.009732	0.456311	
chunk0204_392_1	chr9	102414289	102414809	+	0	NA	Intergenic	Intergenic	-105088	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.007692	0.339731	
chunk0079_432_1	chr17	19948007	19948545	+	0	NA	intron (NM_007202, intron 4 of 14)	L1MDb|LINE|L1	29580	NM_007202	11216	Hs.642676	NM_007202	ENSG00000108599	AKAP10	AKAP-10|D-AKAP-2|D-AKAP2|PRKA10	A-kinase anchoring protein 10	protein-coding	0.009294	0.437848	243(AGAACTTGCAGTACCT,+,0.00)
chunk0184_98_1	chr7	113376899	113377379	+	0	NA	Intergenic	Intergenic	-258557	NR_015442									0.000000	0.313929	
chunk0176_301_1	chr7	16822034	16822743	+	0	NA	Intergenic	Intergenic	-17274	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.005642	0.367606	
chunk0129_456_1	chr3	128282390	128282651	+	0	NA	intron (NM_021937, intron 4 of 6)	intron (NM_021937, intron 4 of 6)	129063	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.026820	0.480916	
chunk0017_236_1	chr1	208178109	208178521	+	0	NA	intron (NM_025179, intron 3 of 31)	intron (NM_025179, intron 3 of 31)	66005	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.004854	0.493947	155(ATGTACACAATGTGCA,-,0.00)
chunk0008_271_1	chr1	94676588	94677110	+	0	NA	intron (NR_104131, intron 4 of 4)	intron (NR_104131, intron 4 of 4)	69051	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.011494	0.483748	386(GTGGACACAGTGTCCC,-,0.00),387(TGGACACAGTGTCCCC,+,0.00)
chunk0117_76_1	chr22	17117100	17117680	+	0	NA	3' UTR (NM_001163079, exon 2 of 2)	3' UTR (NM_001163079, exon 2 of 2)	3933	NM_031890	27439	Hs.209577	NM_031890	ENSG00000183307	TMEM121B	CECR6	transmembrane protein 121B	protein-coding	0.008621	0.564544	222(AAGCACAGATTGTGCA,-,0.00),223(AGCACAGATTGTGCAT,+,0.00)
chunk0018_348_1	chr1	221579141	221579609	+	0	NA	Intergenic	L1MEc|LINE|L1	157525	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.012821	0.349680	
chunk0147_288_1	chr4	184331354	184331804	+	0	NA	Intergenic	LTR82B|LTR|ERVL	22398	NR_040108	728175	Hs.590107	NR_040108	ENSG00000180712	LINC02363	-	long intergenic non-protein coding RNA 2363	ncRNA	0.008889	0.432373	163(TGGTACAACCAGTTCT,-,0.00),164(GGTACAACCAGTTCTG,+,0.00)
chunk0132_1_1	chr3	154169534	154169733	+	0	NA	intron (NM_015595, intron 6 of 14)	Tigger17a|DNA|TcMar-Tigger	48273	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.010050	0.385000	
chunk0039_451_1	chr11	108467319	108467518	+	0	NA	intron (NM_152587, intron 1 of 8)	intron (NM_152587, intron 1 of 8)	113	NM_152587	160140	Hs.653180	NM_152587	ENSG00000166323	C11orf65	-	chromosome 11 open reading frame 65	protein-coding	0.060302	0.555000	
chunk0107_403_1	chr2	223981446	223982107	+	0	NA	intron (NM_006216, intron 6 of 8)	intron (NM_006216, intron 6 of 8)	24372	NM_022915	65080	Hs.203559	NM_022915	ENSG00000135900	MRPL44	COXPD16|L44MT|MRP-L44	mitochondrial ribosomal protein L44	protein-coding	0.007564	0.391239	
chunk0107_177_1	chr2	215759394	215760134	+	0	NA	intron (NR_037195, intron 1 of 9)	intron (NR_037195, intron 1 of 9)	41721	NR_132383	105373869	Hs.152812	NR_132383		LINC01614	LCAL4	long intergenic non-protein coding RNA 1614	ncRNA	0.002703	0.379217	
chunk0087_4_1	chr18	30217208	30218342	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-81135	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.002646	0.385903	
chunk0107_166_1	chr2	215423335	215423837	+	0	NA	intron (NM_001306131, intron 8 of 44)	intron (NM_001306131, intron 8 of 44)	12482	NM_212476	2335	Hs.203717	NM_002026	ENSG00000115414	FN1	CIG|ED-B|FINC|FN|FNZ|GFND|GFND2|LETS|MSF|SMDCF	fibronectin 1	protein-coding	0.005976	0.419483	
chunk0044_68_1	chr12	27906345	27907085	+	0	NA	Intergenic	LTR8A|LTR|ERV1	63246	NM_198964	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.001351	0.408907	
chunk0139_160_1	chr4	53773507	53774099	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	77902	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.003378	0.458685	
chunk0124_388_1	chr3	59654275	59654506	+	0	NA	Intergenic	Intergenic	-604401	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.012987	0.439655	
chunk0047_169_1	chr12	70243247	70243448	+	0	NA	promoter-TSS (NM_001199303)	promoter-TSS (NM_001199303)	13	NR_120459	101928062	Hs.568059	NR_120459	ENSG00000257815	LINC01481	-	long intergenic non-protein coding RNA 1481	ncRNA	0.099502	0.658416	
chunk0209_109_1	chrX	40173922	40174378	+	0	NA	intron (NM_001123383, intron 1 of 14)	intron (NM_001123383, intron 1 of 14)	3179	NM_001123383	54880	Hs.659681	NM_017745	ENSG00000183337	BCOR	ANOP2|MAA2|MCOPS2	BCL6 corepressor	protein-coding	0.035088	0.542670	
chunk0016_255_1	chr1	200118671	200119147	+	0	NA	intron (NM_205860, intron 6 of 7)	intron (NM_205860, intron 6 of 7)	76084	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.004202	0.410901	
chunk0133_340_1	chr3	172874612	172874820	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	124031	NM_001258316	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.009615	0.377990	
chunk0078_394_1	chr16	88122163	88122493	+	0	NA	Intergenic	CpG	-21343	NR_120310	400553	Hs.592071	NR_120310	ENSG00000205037	LOC400553	-	uncharacterized LOC400553	ncRNA	0.060606	0.598187	
chunk0085_370_1	chr18	9477279	9477861	+	0	NA	intron (NM_006788, intron 1 of 9)	intron (NM_006788, intron 1 of 9)	2038	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.003436	0.363636	
chunk0090_400_1	chr18	78406988	78407348	+	0	NA	Intergenic	Intergenic	-413441	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.022222	0.506925	228(GTGTACACAGTGTGCC,-,0.00),229(TGTACACAGTGTGCCC,+,0.00)
chunk0149_7_1	chr5	15757720	15758043	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-142879	NR_109945	101929472	Hs.662664	NR_109945		CTD-2350J17.1	-	uncharacterized LOC101929472	ncRNA	0.024768	0.450617	
chunk0014_319_1	chr1	181358772	181359639	+	0	NA	Intergenic	L2c|LINE|L2	122817	NR_046249	100287948	Hs.742594	NR_046249	ENSG00000179452	LINC01699	GM140	long intergenic non-protein coding RNA 1699	ncRNA	0.006920	0.437788	
chunk0201_93_1	chr9	34688664	34688934	+	0	NA	TTS (NM_006274)	TTS (NM_006274)	2478	NM_006274	6363	Hs.50002	NM_006274	ENSG00000172724	CCL19	CKb11|ELC|MIP-3b|MIP3B|SCYA19	C-C motif chemokine ligand 19	protein-coding	0.000000	0.464945	
chunk0189_201_1	chr8	23795237	23795720	+	0	NA	Intergenic	Intergenic	59329	NM_003155	6781	Hs.25590	NM_003155	ENSG00000159167	STC1	STC	stanniocalcin 1	protein-coding	0.012422	0.450413	
chunk0005_45_1	chr1	54904427	54905241	+	0	NA	Intergenic	Intergenic	-17586	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.002457	0.408589	481(AGGGACACACAGTCCT,-,0.00),482(GGGACACACAGTCCTC,+,0.00)
chunk0212_419_1	chrX	152843695	152844094	+	0	NA	intron (NM_001129765, intron 2 of 8)	intron (NM_001129765, intron 2 of 8)	12927	NM_001129765	50814	Hs.57698	NM_015922	ENSG00000147383	NSDHL	H105E3|SDR31E1|XAP104	NAD(P) dependent steroid dehydrogenase-like	protein-coding	0.015038	0.480000	
chunk0145_384_1	chr4	151691624	151691936	+	0	NA	intron (NM_004564, intron 9 of 12)	intron (NM_004564, intron 9 of 12)	69243	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.019231	0.495208	
chunk0041_290_1	chr11	129458855	129459191	+	0	NA	Intergenic	Intergenic	83037	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.020833	0.525223	
chunk0092_428_1	chr19	38111906	38112315	+	0	NA	intron (NM_015073, intron 8 of 21)	intron (NM_015073, intron 8 of 21)	112140	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.024450	0.512195	
chunk0187_152_1	chr7	150016759	150017187	+	0	NA	Intergenic	LTR47B3|LTR|ERVL	-143111	NR_027040	401431	Hs.556998	NM_001008745	ENSG00000204934	ATP6V0E2-AS1	-	ATP6V0E2 antisense RNA 1	ncRNA	0.004673	0.454545	
chunk0083_19_1	chr17	63035840	63036559	+	0	NA	intron (NM_025185, intron 1 of 24)	L1ME1|LINE|L1	26662	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.002782	0.322222	224(GAGTTCATTGTGTGCT,-,0.00),225(AGTTCATTGTGTGCTC,+,0.00),601(CTGCACTGTCTGTTCT,-,0.00),602(TGCACTGTCTGTTCTG,+,0.00)
chunk0114_240_1	chr21	15992286	15992689	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-78035	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.004963	0.433168	
chunk0200_396_1	chr9	27078492	27079129	+	0	NA	Intergenic	Intergenic	-30331	NM_000459	7010	Hs.89640	NM_000459	ENSG00000120156	TEK	CD202B|GLC3E|TIE-2|TIE2|VMCM|VMCM1	TEK receptor tyrosine kinase	protein-coding	0.001570	0.368339	
chunk0098_416_1	chr2	80205362	80205940	+	0	NA	intron (NM_004389, intron 7 of 17)	intron (NM_004389, intron 7 of 17)	98711	NM_178839	347730	Hs.591580	NM_178839	ENSG00000162951	LRRTM1	-	leucine rich repeat transmembrane neuronal 1	protein-coding	0.005190	0.331606	
chunk0057_449_1	chr13	110801841	110802277	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	68249	NR_027701	283487	Hs.245390	NM_178514	ENSG00000255874	LINC00346	C13orf29|NCRNA00346	long intergenic non-protein coding RNA 346	ncRNA	0.016055	0.414188	
chunk0143_231_1	chr4	114276109	114276446	+	0	NA	Intergenic	Intergenic	-296555	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.000000	0.316568	
chunk0096_397_1	chr2	37674126	37674551	+	0	NA	Intergenic	Intergenic	-1803	NM_001270436	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.004706	0.455399	
chunk0036_149_1	chr11	62236137	62236576	+	0	NA	Intergenic	Intergenic	-5896	NM_006551	10647	Hs.204096	NM_006551	ENSG00000124935	SCGB1D2	LIPB|LPHB|LPNB	secretoglobin family 1D member 2	protein-coding	0.006834	0.354545	
chunk0020_31_1	chr1	232038802	232039087	+	0	NA	non-coding (NR_028393, exon 16 of 16)	non-coding (NR_028393, exon 16 of 16)	113110	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.010526	0.444056	
chunk0022_91_1	chr10	9305191	9305393	+	0	NA	Intergenic	Intergenic	-9699	NR_120635	101928272	Hs.650697	NR_120635		LOC101928272	-	uncharacterized LOC101928272	ncRNA	0.000000	0.339901	
chunk0032_452_1	chr10	133265703	133266252	+	0	NA	intron (NM_001109, intron 21 of 22)	L1MC4a|LINE|L1	10926	NM_001109	101	Hs.501574	NM_001109	ENSG00000151651	ADAM8	CD156|CD156a|MS2	ADAM metallopeptidase domain 8	protein-coding	0.023679	0.545455	
chunk0122_34_1	chr3	27971383	27971824	+	0	NA	Intergenic	Intergenic	-137467	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.004535	0.386878	
chunk0120_94_1	chr3	4300859	4301095	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-2327	NM_006515	6419	Hs.475300	NM_006515	ENSG00000170364	SETMAR	METNASE|Mar1	SET domain and mariner transposase fusion gene	protein-coding	0.000000	0.329114	
chunk0092_354_1	chr19	35469384	35469728	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	19841	NM_005306	2867	Hs.248056	NM_005306	ENSG00000126262	FFAR2	FFA2R|GPR43	free fatty acid receptor 2	protein-coding	0.005814	0.382609	177(ATCACAGAGTGTACTT,+,0.00)
chunk0148_255_1	chr5	10302006	10302291	+	0	NA	intron (NM_138809, intron 1 of 5)	intron (NM_138809, intron 1 of 5)	5908	NM_138809	134147	Hs.192586	NM_138809	ENSG00000164237	CMBL	JS-1	carboxymethylenebutenolidase homolog	protein-coding	0.021053	0.500000	
chunk0021_340_1	chr1	245999433	246000246	+	0	NA	intron (NM_001167740, intron 5 of 11)	MIRc|SINE|MIR	417573	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.008610	0.367322	
chunk0045_193_1	chr12	47393150	47393375	+	0	NA	Intergenic	Intergenic	-28993	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.008889	0.442478	
chunk0195_51_1	chr8	93509830	93510078	+	0	NA	intron (NR_033858, intron 7 of 10)	intron (NR_033858, intron 7 of 10)	190479	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.004032	0.401606	
chunk0099_281_1	chr2	98379177	98379462	+	0	NA	intron (NM_001298, intron 3 of 7)	intron (NM_001298, intron 3 of 7)	33164	NM_001079878	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.010526	0.520979	
chunk0212_169_1	chrX	132520149	132520614	+	0	NA	Intergenic	L1MC4|LINE|L1	-30413	NM_001170704	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.006452	0.334764	
chunk0144_135_1	chr4	129714605	129714902	+	0	NA	Intergenic	Intergenic	56725	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.000000	0.218121	
chunk0147_422_1	chr4	187354867	187355085	+	0	NA	intron (NR_038931, intron 1 of 4)	intron (NR_038931, intron 1 of 4)	150637	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.009174	0.497717	
chunk0063_332_1	chr14	85300061	85300689	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-93504	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.001592	0.448331	
chunk0161_18_1	chr5	165699773	165700252	+	0	NA	Intergenic	Intergenic	1226358	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.002088	0.279167	284(CAAAACAAGGTGTGCC,-,0.00)
chunk0198_22_1	chr8	128117524	128117850	+	0	NA	Intergenic	Intergenic	-32429	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.003067	0.388379	
chunk0047_419_1	chr12	76092317	76092517	+	0	NA	Intergenic	L1MC3|LINE|L1	-7384	NM_139207	4673	Hs.524599	NM_004537	ENSG00000187109	NAP1L1	NAP1|NAP1L|NRP	nucleosome assembly protein 1 like 1	protein-coding	0.005000	0.457711	
chunk0185_188_1	chr7	128259794	128259993	+	0	NA	Intergenic	LTR8|LTR|ERV1	18615	NM_000230	3952	Hs.194236	NM_000230	ENSG00000174697	LEP	LEPD|OB|OBS	leptin	protein-coding	0.010050	0.490000	
chunk0142_29_1	chr4	90572966	90573165	+	0	NA	intron (NM_001145065, intron 5 of 10)	L1MA6|LINE|L1	338034	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.005025	0.550000	
chunk0070_378_1	chr15	76477387	76477597	+	0	NA	intron (NM_020843, intron 23 of 30)	L1M5|LINE|L1	-109155	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.000000	0.345972	
chunk0156_131_1	chr5	106801997	106802663	+	0	NA	Intergenic	Intergenic	208684	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.007508	0.329835	
chunk0076_174_1	chr16	67445398	67445743	+	0	NA	intron (NM_004691, intron 2 of 7)	intron (NM_004691, intron 2 of 7)	14437	NM_000196	3291	Hs.1376	NM_000196	ENSG00000176387	HSD11B2	AME|AME1|HSD11K|HSD2|SDR9C3	hydroxysteroid 11-beta dehydrogenase 2	protein-coding	0.008696	0.609827	
chunk0021_222_1	chr10	6255349	6256047	+	0	NA	Intergenic	Intergenic	52821	NM_004566	5209	Hs.195471	NM_004566	ENSG00000170525	PFKFB3	IPFK2|PFK2|iPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding	0.035817	0.523605	351(GGGAACTCCATGTTCT,-,0.00),352(GGAACTCCATGTTCTG,+,0.00)
chunk0098_403_1	chr2	79833351	79833974	+	0	NA	intron (NM_004389, intron 3 of 17)	intron (NM_004389, intron 3 of 17)	32921	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.003210	0.344551	
chunk0041_76_1	chr11	124094074	124094378	+	0	NA	Intergenic	Intergenic	-21178	NM_001130142	4013	Hs.152944	NM_014622	ENSG00000110002	VWA5A	BCSC-1|BCSC1|LOH11CR2A	von Willebrand factor A domain containing 5A	protein-coding	0.023026	0.478689	
chunk0098_177_1	chr2	71187845	71188483	+	0	NA	3' UTR (NM_020459, exon 4 of 4)	3' UTR (NM_020459, exon 4 of 4)	38939	NM_020459	400961	Hs.416735	NM_020459	ENSG00000124374	PAIP2B	-	poly(A) binding protein interacting protein 2B	protein-coding	0.014107	0.449139	
chunk0098_166_1	chr2	70641214	70641639	+	0	NA	Intergenic	Intergenic	-87411	NM_003236	7039	Hs.170009	NM_003236	ENSG00000163235	TGFA	TFGA	transforming growth factor alpha	protein-coding	0.014118	0.490610	
chunk0194_75_1	chr8	82662875	82663558	+	0	NA	Intergenic	L1PA16|LINE|L1	-740542	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.011713	0.520468	
chunk0011_288_1	chr1	151459446	151459892	+	0	NA	promoter-TSS (NM_001194937)	promoter-TSS (NM_001194937)	-204	NM_015100	23126	Hs.489873	NM_015100	ENSG00000143442	POGZ	MRD37|WHSUS|ZNF280E|ZNF635|ZNF635m	pogo transposable element derived with ZNF domain	protein-coding	0.033632	0.494407	
chunk0084_243_1	chr17	78789559	78790041	+	0	NA	Intergenic	Intergenic	-7458	NM_017456	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.020747	0.484472	
chunk0207_220_1	chr9	131678463	131678843	+	0	NA	intron (NM_001304275, intron 1 of 23)	intron (NM_001304275, intron 1 of 23)	31189	NM_198679	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.010526	0.498688	
chunk0177_452_1	chr7	28168867	28169431	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-11308	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.007092	0.387611	
chunk0112_327_1	chr20	44945248	44945570	+	0	NA	intron (NM_006809, intron 5 of 6)	MLT1G|LTR|ERVL-MaLR	15064	NM_006809	10953	Hs.517066	NM_006809	ENSG00000025772	TOMM34	HTOM34P|TOM34|URCC3	translocase of outer mitochondrial membrane 34	protein-coding	0.018634	0.479876	
chunk0151_399_1	chr5	55498366	55498949	+	0	NA	intron (NR_103485, intron 1 of 6)	intron (NR_103485, intron 1 of 6)	10269	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.006861	0.357877	
chunk0004_181_1	chr1	46024301	46024883	+	0	NA	intron (NM_015112, intron 15 of 28)	intron (NM_015112, intron 15 of 28)	108116	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.000000	0.440823	
chunk0121_219_1	chr3	21809887	21810086	+	0	NA	Intergenic	L1MDb|LINE|L1	-58662	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.000000	0.315000	
chunk0111_169_1	chr20	25237690	25238206	+	0	NA	Intergenic	L1ME3|LINE|L1	-10122	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.011628	0.502901	205(GGGAACAGGATGTGCT,-,0.00),206(GGAACAGGATGTGCTC,+,0.00)
chunk0131_357_1	chr3	151843285	151843625	+	0	NA	intron (NR_110202, intron 1 of 3)	intron (NR_110202, intron 1 of 3)	29382	NM_001086	13	Hs.506908	NM_001086	ENSG00000114771	AADAC	CES5A1|DAC	arylacetamide deacetylase	protein-coding	0.002941	0.384164	
chunk0151_77_1	chr5	42677577	42677776	+	0	NA	intron (NM_001242403, intron 3 of 9)	MER30|DNA|hAT-Charlie	-79142	NM_001134848	100129792	Hs.745017	NM_001134848	ENSG00000198865	CCDC152	CH5400	coiled-coil domain containing 152	protein-coding	0.015075	0.400000	
chunk0175_340_1	chr6	167426128	167426516	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-41812	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.012887	0.408740	
chunk0055_321_1	chr13	68662913	68663662	+	0	NA	Intergenic	MIRc|SINE|MIR	222038	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.005340	0.252000	
chunk0051_237_1	chr12	117022561	117022876	+	0	NA	intron (NM_012174, intron 8 of 10)	intron (NM_012174, intron 8 of 10)	-35381	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.006349	0.420886	
chunk0092_282_1	chr19	33580366	33580984	+	0	NA	Intergenic	Intergenic	-41280	NM_001127895	64377	Hs.165724	NM_022467	ENSG00000124302	CHST8	GALNAC4ST1|GalNAc4ST|PSS3	carbohydrate sulfotransferase 8	protein-coding	0.022654	0.589661	
chunk0038_74_1	chr11	83118504	83118807	+	0	NA	Intergenic	Intergenic	-38440	NM_015885	51585	Hs.128959	NM_015885	ENSG00000165494	PCF11	-	PCF11 cleavage and polyadenylation factor subunit	protein-coding	0.003300	0.447368	
chunk0166_414_1	chr6	52503976	52504208	+	0	NA	intron (NM_012288, intron 10 of 10)	intron (NM_012288, intron 10 of 10)	72972	NM_012288	9697	Hs.520182	NM_012288	ENSG00000065308	TRAM2	-	translocation associated membrane protein 2	protein-coding	0.017241	0.618026	
chunk0042_114_1	chr12	3248134	3248848	+	0	NA	intron (NM_001168320, intron 2 of 7)	intron (NM_001168320, intron 2 of 7)	-132858	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.004202	0.454545	296(CTGGACTTAATGTTCC,-,0.00),297(TGGACTTAATGTTCCT,+,0.00)
chunk0206_354_1	chr9	125675054	125675283	+	0	NA	intron (NM_001006618, intron 1 of 7)	intron (NM_001006618, intron 1 of 7)	32066	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.000000	0.386957	
chunk0013_66_1	chr1	167372457	167373505	+	0	NA	intron (NM_001198786, intron 5 of 14)	intron (NM_001198786, intron 5 of 14)	43937	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.003817	0.327931	
chunk0200_158_1	chr9	18393541	18394391	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-80115	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.005882	0.406580	
chunk0020_283_1	chr1	236673489	236673765	+	0	NA	Intergenic	MIRb|SINE|MIR	-12827	NM_001278343	88	Hs.498178	NM_001103	ENSG00000077522	ACTN2	CMD1AA|CMH23	actinin alpha 2	protein-coding	0.003623	0.368231	
chunk0146_348_1	chr4	166281868	166282696	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	409024	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.001208	0.314837	
chunk0077_1_1	chr16	74446899	74447115	+	0	NA	TTS (NM_012201)	TTS (NM_012201)	-25537	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.032407	0.576037	
chunk0211_327_1	chrX	123988878	123989147	+	0	NA	intron (NM_001282418, intron 2 of 33)	intron (NM_001282418, intron 2 of 33)	27306	NM_001042751	10735	Hs.496710	NM_006603	ENSG00000101972	STAG2	NEDXCF|SA-2|SA2|SCC3B|bA517O1.1	stromal antigen 2	protein-coding	0.003717	0.407407	
chunk0094_90_1	chr2	4032079	4032299	+	0	NA	Intergenic	L1PA16|LINE|L1	-58157	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.009091	0.321267	
chunk0206_428_1	chr9	127740361	127740768	+	0	NA	intron (NM_001252334, intron 9 of 11)	MIRb|SINE|MIR	-5215	NM_001252021	27433	Hs.444106	NM_130459	ENSG00000160404	TOR2A	TORP1	torsin family 2 member A	protein-coding	0.017199	0.490196	292(GGGAACTTGTTGTTCT,-,0.00),293(GGAACTTGTTGTTCTT,+,0.00)
chunk0085_269_1	chr18	7722130	7722725	+	0	NA	intron (NM_001105244, intron 1 of 32)	L1M4|LINE|L1	155111	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.001681	0.323826	
chunk0020_125_1	chr1	233497765	233498191	+	0	NA	Intergenic	LTR35B|LTR|ERV1	-116026	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.011737	0.433255	
chunk0199_89_1	chr9	2653677	2654331	+	0	NA	3' UTR (NM_001018056, exon 18 of 18)	3' UTR (NM_001018056, exon 18 of 18)	-31631	NR_015375	401491	Hs.416043	NR_015375	ENSG00000236404	VLDLR-AS1	linc-VLDLR|lincRNA-VLDLR	VLDLR antisense RNA 1	ncRNA	0.012232	0.386260	
chunk0105_137_1	chr2	186129908	186130528	+	0	NA	Intergenic	Intergenic	-43901	NR_110218	101927217	Hs.130011	NR_110218	ENSG00000237877	LINC01473	-	long intergenic non-protein coding RNA 1473	ncRNA	0.001613	0.370370	
chunk0114_209_1	chr21	15472035	15472634	+	0	NA	Intergenic	Intergenic	-257691	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.011686	0.408333	236(CTGAACATTATGTCCA,-,0.00),237(TGAACATTATGTCCAG,+,0.00)
chunk0161_147_1	chr5	168696708	168696938	+	0	NA	intron (NM_003062, intron 27 of 35)	intron (NM_003062, intron 27 of 35)	-10104	NR_130737	101927969	Hs.661903	NR_130737		LOC101927969	-	uncharacterized LOC101927969	ncRNA	0.004348	0.484848	
chunk0079_361_1	chr17	17941995	17942420	+	0	NA	intron (NM_001033551, intron 1 of 13)	MIRc|SINE|MIR	30263	NM_001033551	146691	Hs.462379	NM_144678	ENSG00000175662	TOM1L2	-	target of myb1 like 2 membrane trafficking protein	protein-coding	0.004706	0.429577	245(AAGATCAGCATGTTCT,-,0.00),246(AGATCAGCATGTTCTT,+,0.00)
chunk0026_153_1	chr10	62463093	62463352	+	0	NA	intron (NM_199451, intron 4 of 7)	intron (NM_199451, intron 4 of 7)	-57226	NM_199452	22891	Hs.22653	NM_014951	ENSG00000138311	ZNF365	Su48|UAN|ZNF365D	zinc finger protein 365	protein-coding	0.011583	0.438462	
chunk0206_288_1	chr9	124406915	124407349	+	0	NA	intron (NM_002799, intron 4 of 7)	intron (NM_002799, intron 4 of 7)	8341	NM_002799	5695	Hs.213470	NM_002799	ENSG00000136930	PSMB7	Z	proteasome subunit beta 7	protein-coding	0.009217	0.367816	
chunk0089_311_1	chr18	63861791	63862289	+	0	NA	Intergenic	L1M5|LINE|L1	-25665	NM_002575	5055	Hs.594481	NM_002575	ENSG00000197632	SERPINB2	HsT1201|PAI|PAI-2|PAI2|PLANH2	serpin family B member 2	protein-coding	0.006024	0.286573	
chunk0042_271_1	chr12	6963078	6963316	+	0	NA	promoter-TSS (NR_029682)	promoter-TSS (NR_029682)	-502	NR_029779	406985		NR_029779	ENSG00000207713	MIR200C	MIRN200C|mir-200c	microRNA 200c	ncRNA	0.046218	0.686192	
chunk0019_353_1	chr1	229558824	229559111	+	0	NA	promoter-TSS (NM_012089)	promoter-TSS (NM_012089)	-272	NM_012089	23456	Hs.17614	NM_012089	ENSG00000135776	ABCB10	EST20237|M-ABC2|MTABC2	ATP binding cassette subfamily B member 10	protein-coding	0.118467	0.722222	
chunk0015_267_1	chr1	188225993	188226479	+	0	NA	Intergenic	L1MA3|LINE|L1	782608	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.002058	0.332649	
chunk0069_104_1	chr15	61561181	61561432	+	0	NA	Intergenic	L2|LINE|L2	-332003	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.007968	0.432540	
chunk0015_276_1	chr1	188548052	188548883	+	0	NA	Intergenic	L1MA3|LINE|L1	1104839	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007220	0.314904	
chunk0114_328_1	chr21	17498616	17498846	+	0	NA	Intergenic	Intergenic	-14175	NM_001207065	1525	Hs.627078	NM_001338	ENSG00000154639	CXADR	CAR|CAR4/6|HCAR	CXADR Ig-like cell adhesion molecule	protein-coding	0.008696	0.393939	
chunk0155_139_1	chr5	93605880	93606489	+	0	NA	Intergenic	Intergenic	14604	NR_031754	100313887		NR_031754	ENSG00000284336	MIR2277	mir-2277	microRNA 2277	ncRNA	0.011494	0.373770	
chunk0036_100_1	chr11	61120949	61121382	+	0	NA	intron (NM_014207, intron 5 of 10)	intron (NM_014207, intron 5 of 10)	18707	NM_014207	921	Hs.58685	NM_014207	ENSG00000110448	CD5	LEU1|T1	CD5 molecule	protein-coding	0.013857	0.559908	161(CAGCACGATCTGTCCC,-,0.00)
chunk0095_102_1	chr2	15307330	15307731	+	0	NA	intron (NR_052013, intron 40 of 50)	intron (NR_052013, intron 40 of 50)	253818	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.002494	0.335821	
chunk0097_29_1	chr2	42382329	42382626	+	0	NA	Intergenic	Intergenic	-21261	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.020202	0.506711	95(AGGAACACAGTGTTTC,-,0.00),96(GGAACACAGTGTTTCC,+,0.00)
chunk0041_333_1	chr11	130535118	130535891	+	0	NA	Intergenic	Intergenic	86530	NM_139055	170689	Hs.534221	NM_139055	ENSG00000166106	ADAMTS15	-	ADAM metallopeptidase with thrombospondin type 1 motif 15	protein-coding	0.020699	0.452196	
chunk0171_117_1	chr6	122533380	122534034	+	0	NA	intron (NM_001270393, intron 3 of 7)	intron (NM_001270393, intron 3 of 7)	61790	NM_001270393	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.006116	0.352672	
chunk0159_262_1	chr5	142187209	142187920	+	0	NA	Intergenic	Intergenic	78805	NM_030571	80762	Hs.9788	NM_030571	ENSG00000131507	NDFIP1	N4WBP5	Nedd4 family interacting protein 1	protein-coding	0.005626	0.471910	
chunk0120_20_1	chr3	1529634	1530070	+	0	NA	Intergenic	Intergenic	437194	NM_014461	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.009174	0.327231	
chunk0181_176_1	chr7	82985132	82985597	+	0	NA	intron (NM_014510, intron 3 of 19)	L4_A_Mam|LINE|RTE-X	177517	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.002151	0.388412	
chunk0209_140_1	chrX	41960013	41960488	+	0	NA	Intergenic	L2a|LINE|L2	-37216	NM_001126055	8573	Hs.495984	NM_003688	ENSG00000147044	CASK	CAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK	calcium/calmodulin dependent serine protein kinase	protein-coding	0.004211	0.451681	
chunk0184_346_1	chr7	120741355	120742026	+	0	NA	intron (NM_012281, intron 3 of 5)	intron (NM_012281, intron 3 of 5)	116433	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.008942	0.334821	
chunk0148_93_1	chr5	3556097	3556670	+	0	NA	Intergenic	L1MC1|LINE|L1	-20289	NR_033898	285577	Hs.582442	NR_033898	ENSG00000248118	LINC01019	-	long intergenic non-protein coding RNA 1019	ncRNA	0.001745	0.315331	
chunk0187_158_1	chr7	150367870	150368271	+	0	NA	promoter-TSS (NM_001099696)	promoter-TSS (NM_001099696)	-720	NM_001099695	29803	Hs.647086	NM_013400	ENSG00000214022	REPIN1	AP4|RIP60|ZNF464|Zfp464	replication initiator 1	protein-coding	0.039900	0.487562	
chunk0133_228_1	chr3	171261530	171261831	+	0	NA	intron (NM_001161560, intron 2 of 31)	L2a|LINE|L2	-154921	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.006645	0.370861	
chunk0032_324_1	chr11	10066209	10066892	+	0	NA	intron (NM_030962, intron 2 of 39)	L1MEc|LINE|L1	227408	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.008785	0.324561	
chunk0011_354_1	chr1	152514118	152514357	+	0	NA	promoter-TSS (NM_019060)	promoter-TSS (NM_019060)	-265	NM_019060	54544	Hs.110196	NM_019060	ENSG00000169509	CRCT1	C1orf42|NICE-1|NICE1	cysteine rich C-terminal 1	protein-coding	0.004184	0.520833	140(AGGTACAAACAGTGCC,-,0.00),141(GGTACAAACAGTGCCC,+,0.00)
chunk0072_362_1	chr15	99772363	99772830	+	0	NA	Intergenic	Intergenic	34331	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.004283	0.414530	
chunk0079_438_1	chr17	20081241	20081469	+	0	NA	intron (NM_001243439, intron 1 of 14)	intron (NM_001243439, intron 1 of 14)	-5667	NM_152904	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.017544	0.524017	
chunk0182_208_1	chr7	96300208	96300670	+	0	NA	intron (NR_027662, intron 1 of 16)	MIRb|SINE|MIR	21708	NM_014251	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.000000	0.382289	
chunk0082_312_1	chr17	59127122	59127419	+	0	NA	intron (NM_182620, intron 2 of 3)	FLAM_C|SINE|Alu	10602	NR_030411	768216		NR_030411	ENSG00000211514	MIR454	MIRN454|hsa-mir-454|mir-454	microRNA 454	ncRNA	0.003367	0.348993	
chunk0128_57_1	chr3	104889135	104889866	+	0	NA	Intergenic	Intergenic	-477213	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.004104	0.321038	374(CAGTACTGCATGTTCT,-,0.00),375(AGTACTGCATGTTCTA,+,0.00)
chunk0056_329_1	chr13	91168040	91168600	+	0	NA	intron (NR_047004, intron 2 of 3)	MIRb|SINE|MIR	43378	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.008929	0.409982	
chunk0066_241_1	chr15	34450798	34451440	+	0	NA	Intergenic	Intergenic	-13653	NR_027409	23015	Hs.182982	NM_181077	ENSG00000175265	GOLGA8A	GM88|GOLGA8B	golgin A8 family member A	protein-coding	0.006231	0.345257	
chunk0018_220_1	chr1	219580126	219580371	+	0	NA	Intergenic	Intergenic	348403	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.012245	0.406504	
chunk0182_329_1	chr7	99082986	99083475	+	0	NA	intron (NM_020429, intron 1 of 18)	L1MB7|LINE|L1	60890	NM_020429	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.006135	0.336735	
chunk0011_428_1	chr1	154567974	154568298	+	0	NA	intron (NM_000748, intron 1 of 5)	intron (NM_000748, intron 1 of 5)	355	NM_000748	1141	Hs.2306	NM_000748	ENSG00000160716	CHRNB2	EFNL3|nAChRB2	cholinergic receptor nicotinic beta 2 subunit	protein-coding	0.074074	0.704615	
chunk0156_312_1	chr5	110909961	110910381	+	0	NA	Intergenic	Intergenic	-159909	NR_045089	85480	Hs.389874	NM_033035	ENSG00000145777	TSLP	-	thymic stromal lymphopoietin	protein-coding	0.000000	0.318290	
chunk0126_292_1	chr3	80420578	80420924	+	0	NA	Intergenic	Intergenic	-573117	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.008671	0.371758	
chunk0006_327_1	chr1	71782039	71782709	+	0	NA	intron (NM_173808, intron 2 of 6)	MLT1A0|LTR|ERVL-MaLR	54638	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005970	0.397914	345(TAGGACAGAATGTGTC,-,0.00),346(AGGACAGAATGTGTCT,+,0.00)
chunk0056_208_1	chr13	86080640	86080934	+	0	NA	Intergenic	L1MC5|LINE|L1	-281439	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.006803	0.298305	
chunk0061_103_1	chr14	57714300	57714698	+	0	NA	intron (NM_001306087, intron 1 of 7)	intron (NM_001306087, intron 1 of 7)	151375	NM_001206920	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.002513	0.353383	
chunk0063_111_1	chr14	79077103	79077485	+	0	NA	intron (NR_073547, intron 14 of 20)	intron (NR_073547, intron 14 of 20)	-202045	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.013089	0.386423	198(GAGCACACGGTGTGTT,-,0.00),199(AGCACACGGTGTGTTT,+,0.00)
chunk0152_261_1	chr5	60996366	60996636	+	0	NA	intron (NM_174889, intron 1 of 3)	L1MA1|LINE|L1	51372	NM_174889	91942	Hs.591757	NM_174889	ENSG00000164182	NDUFAF2	B17.2L|MC1DN10|MMTN|NDUFA12L|mimitin	NADH:ubiquinone oxidoreductase complex assembly factor 2	protein-coding	0.011111	0.523985	
chunk0078_10_1	chr17	369495	370099	+	0	NA	Intergenic	L2b|LINE|L2	-16955	NM_001190411	9501	Hs.651925	NM_006987	ENSG00000181031	RPH3AL	NOC2	rabphilin 3A like (without C2 domains)	protein-coding	0.014901	0.482645	
chunk0120_386_1	chr3	12294972	12295363	+	0	NA	intron (NM_138711, intron 1 of 7)	intron (NM_138711, intron 1 of 7)	6230	NM_138711	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.007673	0.336735	
chunk0049_334_1	chr12	94889344	94890158	+	0	NA	Intergenic	Intergenic	55297	NR_036685	160313	Hs.527883	NR_036685	ENSG00000216306	KRT19P2	KRT19P5	keratin 19 pseudogene 2	pseudo	0.006143	0.428221	377(AGGAACTCTCTGTCCT,-,0.00),378(GGAACTCTCTGTCCTT,+,0.00)
chunk0198_48_1	chr8	128492823	128493146	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	71695	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.000000	0.354938	
chunk0025_117_1	chr10	51397696	51398026	+	0	NA	intron (NM_006258, intron 2 of 17)	intron (NM_006258, intron 2 of 17)	98288	NR_030336	693190		NR_030336	ENSG00000207813	MIR605	MIRN605|hsa-mir-605|mir-605	microRNA 605	ncRNA	0.003030	0.407855	
chunk0018_342_1	chr1	221525852	221526078	+	0	NA	Intergenic	Intergenic	-189669	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.004425	0.431718	
chunk0093_193_1	chr19	49229479	49229802	+	0	NA	Intergenic	LTR40c|LTR|ERVL	71881	NM_001195227	54795	Hs.467101	NM_017636	ENSG00000130529	TRPM4	LTrpC4|PFHB1B|TRPM4B|hTRPM4	transient receptor potential cation channel subfamily M member 4	protein-coding	0.006192	0.506173	
chunk0147_282_1	chr4	184287876	184288128	+	0	NA	Intergenic	Intergenic	65975	NR_040108	728175	Hs.590107	NR_040108	ENSG00000180712	LINC02363	-	long intergenic non-protein coding RNA 2363	ncRNA	0.007937	0.509881	
chunk0087_330_1	chr18	40016440	40016739	+	0	NA	Intergenic	Intergenic	-49697	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.003344	0.276667	
chunk0153_120_1	chr5	68648844	68649272	+	0	NA	Intergenic	Intergenic	356490	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.007009	0.400932	20(AAGAACAGTGTGAGCT,-,0.00),21(AGAACAGTGTGAGCTG,+,0.00)
chunk0190_179_1	chr8	33065380	33065613	+	0	NA	Intergenic	Intergenic	343663	NM_001159996	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.004292	0.448718	
chunk0030_381_1	chr10	119332742	119333269	+	0	NA	intron (NM_005308, intron 2 of 15)	L2a|LINE|L2	-44967	NR_039829	100616398		NR_039829	ENSG00000265719	MIR4681	-	microRNA 4681	ncRNA	0.007590	0.403409	
chunk0086_261_1	chr18	23453042	23453241	+	0	NA	5' UTR (NM_003831, exon 1 of 13)	5' UTR (NM_003831, exon 1 of 13)	318	NM_003831	8780	Hs.445511	NM_003831	ENSG00000101782	RIOK3	SUDD	RIO kinase 3	protein-coding	0.065327	0.680000	
chunk0073_141_1	chr16	6583523	6584156	+	0	NA	intron (NM_018723, intron 2 of 15)	intron (NM_018723, intron 2 of 15)	-189970	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.007899	0.345426	
chunk0074_245_1	chr16	27585126	27585473	+	0	NA	intron (NM_015202, intron 2 of 27)	L1MA2|LINE|L1	35152	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.011527	0.399425	
chunk0195_231_1	chr8	97447423	97448093	+	0	NA	Intergenic	MamRep38|DNA|hAT	-1261	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.010448	0.445604	367(CTGTACAGAGTGTACC,-,0.00),368(TGTACAGAGTGTACCA,+,0.00)
chunk0191_327_1	chr8	55955118	55955373	+	0	NA	intron (NM_001111097, intron 8 of 12)	intron (NM_001111097, intron 8 of 12)	75418	NM_001111097	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.019608	0.468750	130(CGGCACATACTGAGCC,-,0.00)
chunk0163_150_1	chr6	10949834	10950664	+	0	NA	intron (NM_001040274, intron 23 of 29)	L1MEd|LINE|L1	3840	NR_125851	101928191	Hs.638939	NR_125851		LOC101928191	-	uncharacterized LOC101928191	ncRNA	0.007229	0.341757	
chunk0040_261_1	chr11	116058830	116059223	+	0	NA	Intergenic	L1M5|LINE|L1	-298826	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.002545	0.304569	
chunk0145_258_1	chr4	148943587	148943969	+	0	NA	Intergenic	Intergenic	-210517	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.000000	0.349869	295(AAGATCTGGATGTTCC,-,0.00)
chunk0188_223_1	chr8	12802325	12802752	+	0	NA	intron (NR_102423, intron 1 of 1)	intron (NR_102423, intron 1 of 1)	8295	NR_102423	101409254	Hs.571476	NR_102423	ENSG00000255494	LINC00681	-	long intergenic non-protein coding RNA 681	ncRNA	0.000000	0.345794	
chunk0061_116_1	chr14	58367349	58367834	+	0	NA	intron (NM_023000, intron 23 of 23)	L2c|LINE|L2	-28335	NM_207377	387990	Hs.592307	NM_207377	ENSG00000196860	TOMM20L	UNQ9438	translocase of outer mitochondrial membrane 20 like	protein-coding	0.006186	0.405350	213(TGGAACAGTGTGTACC,-,0.00),214(GGAACAGTGTGTACCC,+,0.00)
chunk0110_40_1	chr20	10573413	10573981	+	0	NA	intron (NM_001009608, intron 4 of 7)	intron (NM_001009608, intron 4 of 7)	75998	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.003521	0.362039	
chunk0092_288_1	chr19	33946845	33947332	+	0	NA	Intergenic	Intergenic	150242	NM_024076	79047	Hs.221873	NM_024076	ENSG00000153885	KCTD15	-	potassium channel tetramerization domain containing 15	protein-coding	0.004107	0.463115	
chunk0146_220_1	chr4	161829962	161830348	+	0	NA	intron (NM_001128427, intron 4 of 15)	intron (NM_001128427, intron 4 of 15)	-192578	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.322997	
chunk0119_59_1	chr22	40951055	40951371	+	0	NA	promoter-TSS (NM_014248)	promoter-TSS (NM_014248)	-134	NM_014248	9978	Hs.474949	NM_014248	ENSG00000100387	RBX1	BA554C12.1|RNF75|ROC1	ring-box 1	protein-coding	0.120253	0.753943	
chunk0188_185_1	chr8	11489394	11490103	+	0	NA	Intergenic	L1M4a1|LINE|L1	-4264	NM_001715	640	Hs.146591	NM_001715	ENSG00000136573	BLK	MODY11	BLK proto-oncogene, Src family tyrosine kinase	protein-coding	0.005642	0.336620	
chunk0009_14_1	chr1	100000464	100000945	+	0	NA	intron (NM_001271684, intron 3 of 5)	U6|snRNA|snRNA	30268	NM_001271685	23443	Hs.448979	NM_012243	ENSG00000117620	SLC35A3	AMRS	solute carrier family 35 member A3	protein-coding	0.000000	0.315353	274(AAGCACTGCCTGTGCT,-,0.00),275(AGCACTGCCTGTGCTT,+,0.00)
chunk0064_215_1	chr14	93280397	93280596	+	0	NA	intron (NM_001289133, intron 1 of 8)	intron (NM_001289133, intron 1 of 8)	52596	NM_001289133	55727	Hs.525549	NM_018167	ENSG00000011114	BTBD7	FUP1	BTB domain containing 7	protein-coding	0.005025	0.295000	
chunk0083_441_1	chr17	72666715	72667100	+	0	NA	intron (NM_001159770, intron 7 of 9)	intron (NM_001159770, intron 7 of 9)	-26435	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.010390	0.474093	
chunk0128_134_1	chr3	106610716	106611009	+	0	NA	Intergenic	Intergenic	629776	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.003413	0.323129	
chunk0102_255_1	chr2	149354872	149355077	+	0	NA	intron (NM_194317, intron 1 of 4)	intron (NM_194317, intron 1 of 4)	24459	NM_194317	130574	Hs.21929	NM_194317	ENSG00000187123	LYPD6	-	LY6/PLAUR domain containing 6	protein-coding	0.004878	0.359223	
chunk0010_185_1	chr1	115933703	115933993	+	0	NA	intron (NR_125970, intron 2 of 4)	MLT1H2|LTR|ERVL-MaLR	14472	NR_125969	101928995	Hs.559119	NR_125969	ENSG00000228127	LINC01649	-	long intergenic non-protein coding RNA 1649	ncRNA	0.003448	0.419244	
chunk0176_250_1	chr7	16184438	16184809	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-25863	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.000000	0.317204	184(AGGCACATGCTGTTTA,-,0.00)
chunk0124_254_1	chr3	56889026	56889335	+	0	NA	intron (NM_001128615, intron 3 of 12)	intron (NM_001128615, intron 3 of 12)	27291	NM_001289698	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.019417	0.467742	
chunk0071_146_1	chr15	82849510	82849716	+	0	NA	3' UTR (NM_004839, exon 9 of 9)	3' UTR (NM_004839, exon 9 of 9)	39985	NM_001080435	123720	Hs.377360	NM_001080435	ENSG00000156232	WHAMM	WHAMM1|WHDC1	WASP homolog associated with actin, golgi membranes and microtubules	protein-coding	0.048544	0.550725	
chunk0094_24_1	chr2	1358762	1359064	+	0	NA	intron (NM_018968, intron 16 of 16)	L1MB1|LINE|L1	-54548	NM_001206745	7173	Hs.467554	NM_000547	ENSG00000115705	TPO	MSA|TDH2A|TPX	thyroid peroxidase	protein-coding	0.000000	0.363036	
chunk0169_371_1	chr6	107228720	107229199	+	0	NA	intron (NM_020381, intron 4 of 7)	Eulor6C|DNA?|DNA?	-114527	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.002088	0.291667	
chunk0175_228_1	chr7	6290406	6290646	+	0	NA	Intergenic	Intergenic	-17915	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.008333	0.531120	64(TGGGACAGGATGTCCA,-,0.00),65(GGGACAGGATGTCCAC,+,0.00)
chunk0108_29_1	chr2	226564415	226565053	+	0	NA	Intergenic	Intergenic	94059	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.006270	0.447574	349(AAGAACACAATGTTTA,-,0.00)
chunk0043_108_1	chr12	15158139	15158442	+	0	NA	intron (NM_032918, intron 2 of 4)	AluJo|SINE|Alu	6367	NR_046559	100873980	Hs.569154	NR_046559	ENSG00000255660	RERG-AS1	-	RERG antisense RNA 1	ncRNA	0.009901	0.411184	190(TGGAACACAGTGTTAT,-,0.00),191(GGAACACAGTGTTATG,+,0.00)
chunk0146_342_1	chr4	166127575	166127889	+	0	NA	Intergenic	Intergenic	254474	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.000000	0.361905	206(CAGAACATTATGATCC,-,0.00),207(AGAACATTATGATCCA,+,0.00)
chunk0084_317_1	chr17	80592272	80592471	+	0	NA	intron (NM_020761, intron 1 of 33)	L2|LINE|L2	47546	NM_001163034	57521	Hs.133044	NM_020761	ENSG00000141564	RPTOR	KOG1|Mip1	regulatory associated protein of MTOR complex 1	protein-coding	0.020101	0.530000	
chunk0065_200_1	chr14	100075213	100075810	+	0	NA	intron (NM_016337, intron 1 of 13)	intron (NM_016337, intron 1 of 13)	10097	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.013400	0.536789	
chunk0003_425_1	chr1	40911370	40911578	+	0	NA	Intergenic	MER41C|LTR|ERV1	-49128	NM_133467	163732	Hs.355820	NM_133467	ENSG00000179862	CITED4	-	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4	protein-coding	0.004808	0.349282	138(AGGAACATCCTGTTCT,-,0.00),139(GGAACATCCTGTTCTA,+,0.00)
chunk0010_223_1	chr1	116292749	116293569	+	0	NA	Intergenic	Intergenic	-80014	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.006098	0.455542	
chunk0109_47_1	chr20	833544	833907	+	0	NA	promoter-TSS (NM_001289146)	promoter-TSS (NM_001289146)	28	NM_001289145	83541	Hs.574822	NM_031424	ENSG00000125898	FAM110A	C20orf55|F10|bA371L19.3	family with sequence similarity 110 member A	protein-coding	0.096419	0.708791	
chunk0209_52_1	chrX	36865949	36866510	+	0	NA	Intergenic	Intergenic	-142130	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.001783	0.361210	
chunk0070_372_1	chr15	76349739	76349942	+	0	NA	intron (NM_020843, intron 30 of 30)	intron (NM_020843, intron 30 of 30)	13116	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.000000	0.460784	
chunk0008_114_1	chr1	91559717	91560329	+	0	NA	Intergenic	Intergenic	58915	NM_001134420	8317	Hs.533573	NM_003503	ENSG00000097046	CDC7	CDC7L1|HsCDC7|Hsk1|huCDC7	cell division cycle 7	protein-coding	0.001634	0.401305	301(ATGTACATAGAGTTCC,-,0.00),302(TGTACATAGAGTTCCT,+,0.00)
chunk0063_338_1	chr14	85356899	85357763	+	0	NA	Intergenic	L2b|LINE|L2	-36548	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005787	0.343353	380(AGGCACACTTTGTTCT,-,0.00),381(GGCACACTTTGTTCTA,+,0.00)
chunk0162_234_1	chr6	4738478	4738982	+	0	NA	intron (NR_026590, intron 3 of 8)	L1ME3Cz|LINE|L1	32571	NR_026590									0.017857	0.401980	326(TGGAACAATATGTGCA,-,0.00),327(GGAACAATATGTGCAG,+,0.00)
chunk0185_182_1	chr7	128138222	128138694	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	56597	NR_030324	693178		NR_030324	ENSG00000207588	MIR593	MIRN593|hsa-mir-593	microRNA 593	ncRNA	0.004237	0.338266	
chunk0147_428_1	chr4	187412361	187412995	+	0	NA	intron (NR_038931, intron 1 of 4)	intron (NR_038931, intron 1 of 4)	92935	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.011041	0.352756	
chunk0138_25_1	chr4	30967777	30968325	+	0	NA	intron (NM_001173523, intron 2 of 2)	intron (NM_001173523, intron 2 of 2)	-203093	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.001825	0.353370	381(GAGCAGACACTGTTCC,-,0.00)
chunk0107_105_1	chr2	214011487	214011686	+	0	NA	intron (NR_047659, intron 14 of 17)	MER58A|DNA|hAT-Charlie	253519	NR_039640	100616375		NR_039640	ENSG00000265734	MIR4438	-	microRNA 4438	ncRNA	0.005025	0.355000	
chunk0058_33_1	chr14	20055468	20055885	+	0	NA	Intergenic	Intergenic	-4369	NM_001004717	122742	Hs.553574	NM_001004717	ENSG00000176246	OR4L1	OR14-28|OR4L2P	olfactory receptor family 4 subfamily L member 1	protein-coding	0.002398	0.330144	
chunk0134_13_1	chr3	175404034	175404363	+	0	NA	intron (NM_207015, intron 5 of 13)	MIRb|SINE|MIR	34658	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.000000	0.372727	
chunk0201_255_1	chr9	38154993	38155192	+	0	NA	Intergenic	Intergenic	-85879	NM_003028	6461	Hs.521482	NM_003028	ENSG00000107338	SHB	bA3J10.2	SH2 domain containing adaptor protein B	protein-coding	0.010050	0.525000	
chunk0203_279_1	chr9	88771127	88771772	+	0	NA	Intergenic	L1MC3|LINE|L1	-25544	NR_036252	100423015		NR_036252	ENSG00000265873	MIR4289	-	microRNA 4289	ncRNA	0.001550	0.286378	216(TTGGACTTGGTGTTCC,-,0.00),217(TGGACTTGGTGTTCCC,+,0.00)
chunk0125_146_1	chr3	66271796	66272414	+	0	NA	intron (NM_001164796, intron 4 of 8)	MIRb|SINE|MIR	51363	NR_028475	115286	Hs.379386	NM_173471	ENSG00000144741	SLC25A26	COXPD28|SAMC	solute carrier family 25 member 26	protein-coding	0.003236	0.318255	
chunk0003_36_1	chr1	30250405	30250930	+	0	NA	Intergenic	Intergenic	-213055	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.017143	0.473384	
chunk0134_72_1	chr3	176376448	176377232	+	0	NA	Intergenic	Intergenic	-138263	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.001276	0.336306	
chunk0104_9_1	chr2	170345780	170346000	+	0	NA	intron (NR_110576, intron 1 of 3)	MLT1C|LTR|ERVL-MaLR	5053	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.004545	0.475113	
chunk0177_458_1	chr7	28573155	28573584	+	0	NA	intron (NM_182899, intron 4 of 9)	intron (NM_182899, intron 4 of 9)	-112612	NM_001011666	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.009324	0.448837	
chunk0021_309_1	chr1	244936085	244936311	+	0	NA	Intergenic	Intergenic	-33671	NM_032328	84288	Hs.134857	NM_032328	ENSG00000203666	EFCAB2	CFAP200|DRC8	EF-hand calcium binding domain 2	protein-coding	0.008850	0.370044	
chunk0122_387_1	chr3	37853733	37854101	+	0	NA	intron (NR_110532, intron 1 of 5)	intron (NR_110532, intron 1 of 5)	7863	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.019022	0.569106	79(AGAAACAGGCAGTGCC,-,0.00)
chunk0035_141_1	chr11	42870477	42870872	+	0	NA	Intergenic	Intergenic	398695	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.007595	0.366162	
chunk0016_93_1	chr1	195005410	195005609	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	1576972	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005025	0.405000	
chunk0011_282_1	chr1	151403309	151403909	+	0	NA	3' UTR (NM_207171, exon 17 of 17)	3' UTR (NM_207171, exon 17 of 17)	4044	NM_002796	5692	Hs.89545	NM_002796	ENSG00000159377	PSMB4	HN3|HsN3|PRAAS3|PROS-26|PROS26	proteasome subunit beta 4	protein-coding	0.008333	0.405990	
chunk0192_169_1	chr8	62657691	62658333	+	0	NA	intron (NR_130764, intron 3 of 6)	intron (NR_130764, intron 3 of 6)	-319849	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.010903	0.423017	
chunk0021_228_1	chr10	6334639	6335198	+	0	NA	intron (NR_040079, intron 5 of 5)	L2a|LINE|L2	8374	NR_040079	399715		NR_040079	ENSG00000215244	LINC02649	-	long intergenic non-protein coding RNA 2649	ncRNA	0.007156	0.441071	
chunk0028_420_1	chr10	93495469	93495877	+	0	NA	promoter-TSS (NM_001127182)	promoter-TSS (NM_001127182)	-939	NM_001127182	55165	Hs.14559	NM_018131	ENSG00000138180	CEP55	C10orf3|CT111|MARCH|URCC6	centrosomal protein 55	protein-coding	0.022059	0.437653	
chunk0080_313_1	chr17	31878096	31878540	+	0	NA	exon (NM_018428, exon 13 of 19)	exon (NM_018428, exon 13 of 19)	-19011	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.011261	0.424719	
chunk0190_386_1	chr8	40104239	40104923	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-48887	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.008772	0.381022	
chunk0115_368_1	chr21	30199885	30200522	+	0	NA	Intergenic	Intergenic	11580	NR_038855	266919	Hs.561028	NR_038855	ENSG00000227342	LINC00307	D21S2091E|NCRNA00307	long intergenic non-protein coding RNA 307	ncRNA	0.006279	0.302508	
chunk0014_227_1	chr1	179831264	179831701	+	0	NA	Intergenic	Intergenic	46324	NM_145034	163590	Hs.571797	NM_022347	ENSG00000169905	TOR1AIP2	IFRG15|LULL1|NET9	torsin 1A interacting protein 2	protein-coding	0.011442	0.465753	
chunk0128_48_1	chr3	104761139	104761407	+	0	NA	Intergenic	Intergenic	-605440	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.007463	0.408922	
chunk0095_117_1	chr2	15759241	15759705	+	0	NA	Intergenic	MER97a|DNA|hAT-Tip100	68691	NR_110201	101926966	Hs.502835	NR_110201	ENSG00000231031	LINC01804	-	long intergenic non-protein coding RNA 1804	ncRNA	0.002155	0.309677	
chunk0170_84_1	chr6	110042597	110042948	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	64516	NM_005284	2830	Hs.46332	NM_005284	ENSG00000146360	GPR6	-	G protein-coupled receptor 6	protein-coding	0.014245	0.522727	298(AGGTACAGATAGTTCT,-,0.00),299(GGTACAGATAGTTCTA,+,0.00)
chunk0165_326_1	chr6	37244504	37244721	+	0	NA	intron (NM_001286401, intron 1 of 2)	intron (NM_001286401, intron 1 of 2)	13025	NM_145316	221468	Hs.520101	NM_145316	ENSG00000172738	TMEM217	C6orf128|dJ355M6.2	transmembrane protein 217	protein-coding	0.004608	0.394495	
chunk0072_81_1	chr15	90598018	90598330	+	0	NA	intron (NM_001042574, intron 3 of 14)	intron (NM_001042574, intron 3 of 14)	-62060	NR_120371	101929765	Hs.615348	NR_120371	ENSG00000245479	LINC01585	-	long intergenic non-protein coding RNA 1585	ncRNA	0.019231	0.584665	113(CAGAACACAGAGTTCC,-,0.00),114(AGAACACAGAGTTCCA,+,0.00)
chunk0064_278_1	chr14	95157266	95157734	+	0	NA	promoter-TSS (NM_177438)	promoter-TSS (NM_177438)	-78	NM_177438	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.141026	0.763326	
chunk0182_343_1	chr7	99438897	99439149	+	0	NA	promoter-TSS (NM_006693)	promoter-TSS (NM_006693)	83	NM_001081559	10898	Hs.489287	NM_006693	ENSG00000160917	CPSF4	CPSF30|NAR|NEB-1|NEB1	cleavage and polyadenylation specific factor 4	protein-coding	0.134921	0.739130	
chunk0056_343_1	chr13	91524917	91525200	+	0	NA	intron (NM_004466, intron 2 of 7)	intron (NM_004466, intron 2 of 7)	126439	NM_004466	2262	Hs.655675	NM_004466	ENSG00000179399	GPC5	-	glypican 5	protein-coding	0.010601	0.316901	
chunk0120_179_1	chr3	6182930	6183277	+	0	NA	Intergenic	Intergenic	622346	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.002882	0.318966	
chunk0156_86_1	chr5	104498433	104498810	+	0	NA	Intergenic	L2|LINE|L2	-600853	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.002653	0.359788	
chunk0036_97_1	chr11	60956309	60956630	+	0	NA	Intergenic	Intergenic	-4684	NR_027391	51296	Hs.237856	NM_016582	ENSG00000110446	SLC15A3	OCTP|PHT2|PTR3	solute carrier family 15 member 3	protein-coding	0.009346	0.518634	
chunk0023_193_1	chr10	25119315	25119660	+	0	NA	intron (NR_120649, intron 3 of 7)	L1ME4a|LINE|L1	6429	NR_120649	101929025	Hs.553324	NR_120649	ENSG00000231422	LINC01516	-	long intergenic non-protein coding RNA 1516	ncRNA	0.023188	0.427746	
chunk0029_421_1	chr10	109983602	109983909	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-22213	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.009772	0.392857	
chunk0162_363_1	chr6	7194691	7194915	+	0	NA	intron (NM_001003698, intron 6 of 11)	intron (NM_001003698, intron 6 of 11)	86950	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.004464	0.400000	
chunk0160_81_1	chr5	149938289	149938587	+	0	NA	intron (NM_000440, intron 1 of 21)	intron (NM_000440, intron 1 of 21)	-5461	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.006711	0.474916	
chunk0069_68_1	chr15	60871202	60871505	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	189784	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.003300	0.401316	
chunk0044_39_1	chr12	27491232	27491705	+	0	NA	intron (NM_001145010, intron 6 of 8)	intron (NM_001145010, intron 6 of 8)	24658	NM_001145010	341346	Hs.282121	NM_001145010	ENSG00000165935	SMCO2	C12orf70	single-pass membrane protein with coiled-coil domains 2	protein-coding	0.006342	0.343882	
chunk0198_57_1	chr8	128657793	128658228	+	0	NA	Intergenic	Intergenic	-93331	NR_121673	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.002299	0.385321	
chunk0011_91_1	chr1	145785780	145786070	+	0	NA	intron (NM_014455, intron 2 of 8)	intron (NM_014455, intron 2 of 8)	-38144	NM_006468	10623	Hs.515768	NM_006468	ENSG00000186141	POLR3C	RPC3|RPC62	RNA polymerase III subunit C	protein-coding	0.006897	0.367698	
chunk0111_34_1	chr20	22211899	22212393	+	0	NA	Intergenic	L1MB3|LINE|L1	70655	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.002024	0.349495	
chunk0002_439_1	chr1	28172649	28173235	+	0	NA	intron (NM_001164723, intron 1 of 2)	MIRc|SINE|MIR	4002	NM_001164723	5724	Hs.77542	NM_000952	ENSG00000169403	PTAFR	PAFR	platelet activating factor receptor	protein-coding	0.015358	0.475298	
chunk0062_84_1	chr14	67898268	67898814	+	0	NA	intron (NM_133509, intron 7 of 10)	L1MA10|LINE|L1	78762	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.003663	0.352834	
chunk0033_327_1	chr11	21649776	21650528	+	0	NA	Intergenic	MER3|DNA|hAT-Charlie	-543024	NM_213599	203859	Hs.154329	NM_213599	ENSG00000171714	ANO5	GDD1|LGMD2L|LGMDR12|TMEM16E	anoctamin 5	protein-coding	0.001330	0.285525	
chunk0186_437_1	chr7	147033868	147034200	+	0	NA	intron (NM_014141, intron 3 of 23)	MER66D|LTR|ERV1	63575	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.006024	0.417417	
chunk0118_313_1	chr22	35085479	35086174	+	0	NA	3' UTR (NM_001303508, exon 5 of 5)	3' UTR (NM_001303508, exon 5 of 5)	19690	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.012950	0.538793	105(AAACACAGCCTGTCCC,-,0.00),106(AACACAGCCTGTCCCA,+,0.00)
chunk0127_114_1	chr3	90246792	90247040	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	1139392	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004032	0.365462	
chunk0188_351_1	chr8	17904133	17904764	+	0	NA	Intergenic	MIR|SINE|MIR	-8910	NM_201552	2267	Hs.491143	NM_004467	ENSG00000104760	FGL1	HFREP1|HP-041|HPS|LFIRE-1|LFIRE1	fibrinogen like 1	protein-coding	0.004754	0.436709	
chunk0135_290_1	chr3	189482816	189483300	+	0	NA	Intergenic	L1MC3|LINE|L1	-148369	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.008264	0.383505	
chunk0067_155_1	chr15	43808414	43808947	+	0	NA	intron (NM_005926, intron 7 of 8)	intron (NM_005926, intron 7 of 8)	8259	NM_016400	25764	Hs.730672	NM_016400	ENSG00000242028	HYPK	C15orf63|HSPC136	huntingtin interacting protein K	protein-coding	0.009381	0.398876	
chunk0196_292_1	chr8	109581015	109581447	+	0	NA	intron (NM_017786, intron 6 of 8)	L2c|LINE|L2	40605	NM_001278938	9166	Hs.409368	NM_004215	ENSG00000147654	EBAG9	EB9|PDAF	estrogen receptor binding site associated antigen 9	protein-coding	0.002315	0.434180	166(AGAAACAGCTTGTTCT,-,0.00),167(GAAACAGCTTGTTCTT,+,0.00)
chunk0115_431_1	chr21	31847238	31847907	+	0	NA	Intergenic	Intergenic	-25743	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.008969	0.413433	
chunk0122_419_1	chr3	38983240	38983522	+	0	NA	Intergenic	Intergenic	-29730	NM_001287223	11280	Hs.591657	NM_014139	ENSG00000168356	SCN11A	FEPS3|HSAN7|NAV1.9|NaN|PN5|SCN12A|SNS-2	sodium voltage-gated channel alpha subunit 11	protein-coding	0.000000	0.441696	
chunk0020_449_1	chr1	242228869	242229507	+	0	NA	intron (NM_001195812, intron 3 of 8)	intron (NM_001195812, intron 3 of 8)	220294	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.006270	0.322379	
chunk0137_373_1	chr4	26175878	26176117	+	0	NA	Intergenic	Intergenic	-143713	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.008368	0.425000	
chunk0123_252_1	chr3	45807769	45808043	+	0	NA	Intergenic	Intergenic	-11363	NM_022405	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.007299	0.425455	
chunk0057_31_1	chr13	95703109	95703395	+	0	NA	intron (NM_006260, intron 1 of 11)	Tigger17a|DNA|TcMar-Tigger	26113	NM_006260	5611	Hs.59214	NM_006260	ENSG00000102580	DNAJC3	ACPHD|ERdj6|HP58|P58|P58IPK|PRKRI	DnaJ heat shock protein family (Hsp40) member C3	protein-coding	0.003497	0.376307	
chunk0117_264_1	chr22	23828691	23829046	+	0	NA	intron (NM_003073, intron 7 of 8)	intron (NM_003073, intron 7 of 8)	10144	NM_198440	91319	Hs.593679	NM_198440	ENSG00000099958	DERL3	C22orf14|IZP6|LLN2|derlin-3	derlin 3	protein-coding	0.011268	0.587079	190(GAGAACAGCCTGTTCC,-,0.00),191(AGAACAGCCTGTTCCC,+,0.00)
chunk0190_20_1	chr8	28925187	28925773	+	0	NA	intron (NM_024567, intron 2 of 10)	intron (NM_024567, intron 2 of 10)	34772	NM_024567	79618	Hs.563560	NM_024567	ENSG00000147421	HMBOX1	HNF1LA|HOT1|PBHNF	homeobox containing 1	protein-coding	0.001706	0.350937	333(AAGCACATAGAGTTCT,-,0.00),334(AGCACATAGAGTTCTA,+,0.00)
chunk0062_205_1	chr14	70067752	70068177	+	0	NA	intron (NM_033262, intron 2 of 7)	intron (NM_033262, intron 2 of 7)	12253	NM_182936	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.011765	0.509390	247(ATGCACACAGCGTTCC,-,0.00)
chunk0106_309_1	chr2	205161123	205161339	+	0	NA	intron (NM_205863, intron 11 of 21)	intron (NM_205863, intron 11 of 21)	-521269	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.009259	0.368664	
chunk0164_7_1	chr6	17700535	17700798	+	0	NA	intron (NM_005124, intron 1 of 21)	intron (NM_005124, intron 1 of 21)	6168	NM_001278209	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.003802	0.359848	
chunk0207_216_1	chr9	131502854	131503053	+	0	NA	promoter-TSS (NM_007171)	promoter-TSS (NM_007171)	51	NM_001077365	10585	Hs.522449	NM_007171	ENSG00000130714	POMT1	LGMD2K|LGMDR11|MDDGA1|MDDGB1|MDDGC1|RT	protein O-mannosyltransferase 1	protein-coding	0.155779	0.755000	
chunk0082_307_1	chr17	59101061	59101306	+	0	NA	intron (NM_001005207, intron 2 of 24)	intron (NM_001005207, intron 2 of 24)	5722	NM_001005207	4591	Hs.579079	NM_015294	ENSG00000108395	TRIM37	MUL|POB1|TEF3	tripartite motif containing 37	protein-coding	0.000000	0.361789	
chunk0078_279_1	chr17	7959469	7960053	+	0	NA	Intergenic	L2|LINE|L2	27637	NM_053051	116840	Hs.348012	NM_053051	ENSG00000170037	CNTROB	LIP8|PP1221	centrobin, centriole duplication and spindle assembly protein	protein-coding	0.003425	0.389744	321(AAGATCAGTGTGTTCC,-,0.00),322(AGATCAGTGTGTTCCA,+,0.00)
chunk0007_134_1	chr1	79233924	79234296	+	0	NA	Intergenic	Intergenic	-227300	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.002688	0.356568	
chunk0105_250_1	chr2	188772942	188773457	+	0	NA	intron (NM_052952, intron 1 of 1)	Tigger3a|DNA|TcMar-Tigger	16905	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.001942	0.335271	
chunk0066_136_1	chr15	31274422	31274744	+	0	NA	Intergenic	Intergenic	-43736	NM_001243538	283710	Hs.591097	NM_001243538		LOC283710	-	uncharacterized LOC283710	protein-coding	0.015528	0.455108	
chunk0212_34_1	chrY	11177141	11177470	+	0	NA	Intergenic	Intergenic	1244285	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.018237	0.563636	
chunk0141_49_1	chr4	77415444	77416324	+	0	NA	Intergenic	L1PA16|LINE|L1	-95869	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.000000	0.360953	
chunk0170_205_1	chr6	112472157	112472799	+	0	NA	Intergenic	Intergenic	125148	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.004673	0.356143	
chunk0046_28_1	chr12	54444163	54444667	+	0	NA	intron (NR_120487, intron 3 of 3)	intron (NR_120487, intron 3 of 3)	24630	NR_120488	102724050	Hs.670941	NR_120486	ENSG00000258137	LOC102724050	-	uncharacterized LOC102724050	ncRNA	0.000000	0.380198	
chunk0129_89_1	chr3	119257684	119257883	+	0	NA	intron (NR_046574, intron 3 of 3)	LTR2|LTR|ERV1	-16878	NM_003778	8702	Hs.13225	NM_003778	ENSG00000121578	B4GALT4	B4Gal-T4|beta4Gal-T4	beta-1,4-galactosyltransferase 4	protein-coding	0.025126	0.500000	
chunk0014_44_1	chr1	175162472	175162837	+	0	NA	intron (NM_001162893, intron 4 of 4)	intron (NM_001162893, intron 4 of 4)	30159	NM_001162895	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.005479	0.448087	
chunk0096_153_1	chr2	29233612	29234039	+	0	NA	intron (NM_004304, intron 13 of 28)	L2c|LINE|L2	118399	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.009368	0.420561	
chunk0173_76_1	chr6	142683024	142683490	+	0	NA	Intergenic	Intergenic	-45368	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.010730	0.413276	
chunk0073_236_1	chr16	11496734	11497310	+	0	NA	Intergenic	Intergenic	31762	NR_110907	101927131	Hs.569654	NR_110907	ENSG00000262999	LOC101927131	-	uncharacterized LOC101927131	ncRNA	0.020833	0.537262	
chunk0132_66_1	chr3	155174492	155174691	+	0	NA	intron (NM_000902, intron 22 of 22)	intron (NM_000902, intron 22 of 22)	-66354	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.005025	0.275000	
chunk0046_87_1	chr12	56469324	56469523	+	0	NA	exon (NM_207344, exon 2 of 2)	exon (NM_207344, exon 2 of 2)	906	NM_207344	283377	Hs.128676	NM_207344	ENSG00000176422	SPRYD4	-	SPRY domain containing 4	protein-coding	0.020101	0.580000	
chunk0025_102_1	chr10	50596649	50596930	+	0	NA	intron (NM_147156, intron 1 of 10)	MIRb|SINE|MIR	27188	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.000000	0.432624	
chunk0039_383_1	chr11	107019027	107019375	+	0	NA	promoter-TSS (NM_000855)	promoter-TSS (NM_000855)	-756	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.068966	0.638968	
chunk0155_198_1	chr5	94801069	94801458	+	0	NA	intron (NM_024717, intron 17 of 22)	L2a|LINE|L2	182577	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.002571	0.320513	
chunk0183_71_1	chr7	104259796	104260090	+	0	NA	Intergenic	Intergenic	-51896	NM_181747	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.000000	0.355932	
chunk0053_18_1	chr13	26499332	26499531	+	0	NA	Intergenic	MIRb|SINE|MIR	-58272	NM_006646	10810	Hs.618732	NM_006646	ENSG00000132970	WASF3	Brush-1|SCAR3|WAVE3	WASP family member 3	protein-coding	0.010050	0.545000	
chunk0151_332_1	chr5	53822149	53822422	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	129314	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.007326	0.459854	
chunk0207_203_1	chr9	131185535	131185786	+	0	NA	intron (NM_005085, intron 24 of 35)	intron (NM_005085, intron 24 of 35)	60099	NM_005085	8021	Hs.654530	NM_005085	ENSG00000126883	NUP214	CAIN|CAN	nucleoporin 214	protein-coding	0.007968	0.361111	
chunk0080_87_1	chr17	26594762	26595039	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	699096	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.028881	0.420863	
chunk0091_309_1	chr19	12919393	12919720	+	0	NA	promoter-TSS (NR_049880)	promoter-TSS (NR_049880)	-284	NM_001105578	256126	Hs.655173	NM_001105578	ENSG00000161860	SYCE2	CESC1	synaptonemal complex central element protein 2	protein-coding	0.073394	0.576220	
chunk0192_387_1	chr8	68712236	68712929	+	0	NA	intron (NM_052958, intron 9 of 13)	L1PB1|LINE|L1	-381091	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.001443	0.342939	
chunk0005_211_1	chr1	59144371	59144923	+	0	NA	intron (NR_027120, intron 1 of 2)	MIRc|SINE|MIR	2160	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.000000	0.367089	
chunk0109_58_1	chr20	1337384	1337859	+	0	NA	intron (NR_040047, intron 1 of 2)	intron (NR_040047, intron 1 of 2)	-8386	NM_080489	27111	Hs.657015	NM_015685	ENSG00000125775	SDCBP2	SITAC|SITAC18|ST-2|ST2	syndecan binding protein 2	protein-coding	0.010526	0.407563	
chunk0195_146_1	chr8	95156464	95157045	+	0	NA	TTS (NM_024613)	TTS (NM_024613)	23033	NM_024613	79666	Hs.29724	NM_024613	ENSG00000175895	PLEKHF2	EAPF|PHAFIN2|ZFYVE18	pleckstrin homology and FYVE domain containing 2	protein-coding	0.003442	0.353952	
chunk0031_252_1	chr10	127133549	127134156	+	0	NA	intron (NM_001290223, intron 27 of 51)	intron (NM_001290223, intron 27 of 51)	62306	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.003295	0.391447	329(CTGCACATGCAGTGCC,-,0.00),330(TGCACATGCAGTGCCT,+,0.00)
chunk0091_228_1	chr19	10396946	10397454	+	0	NA	intron (NM_007065, intron 1 of 7)	L2a|LINE|L2	6338	NR_031592	100302213		NR_031592	ENSG00000284268	MIR1181	MIRN1181|hsa-mir-1181	microRNA 1181	ncRNA	0.019685	0.491159	
chunk0098_420_1	chr2	80482875	80483210	+	0	NA	intron (NM_004389, intron 9 of 17)	intron (NM_004389, intron 9 of 17)	169663	NM_001282599	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.000000	0.419643	281(GTGAACATTTTGTACC,-,0.00),282(TGAACATTTTGTACCT,+,0.00)
chunk0122_169_1	chr3	32317083	32317416	+	0	NA	intron (NM_178868, intron 1 of 3)	MIR|SINE|MIR	-74422	NM_138410	112616	Hs.440494	NM_138410	ENSG00000153551	CMTM7	CKLFSF7	CKLF like MARVEL transmembrane domain containing 7	protein-coding	0.003003	0.383234	
chunk0139_194_1	chr4	54586287	54586575	+	0	NA	Intergenic	Intergenic	-71497	NM_000222	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.006944	0.442907	
chunk0166_190_1	chr6	46217572	46217899	+	0	NA	Intergenic	Intergenic	-46725	NM_001290073	59084	Hs.35198	NM_021572	ENSG00000112796	ENPP5	NPP-5|NPP5	ectonucleotide pyrophosphatase/phosphodiesterase family member 5	protein-coding	0.012232	0.411585	232(AGGGACACTCTGTACC,-,0.00),233(GGGACACTCTGTACCA,+,0.00)
chunk0036_36_1	chr11	58750175	58750554	+	0	NA	Intergenic	L1PA6|LINE|L1	-18390	NM_005838	10249	Hs.145384	NM_005838	ENSG00000149124	GLYAT	ACGNAT|CAT|GAT	glycine-N-acyltransferase	protein-coding	0.005277	0.505263	
chunk0080_28_1	chr17	21043948	21044339	+	0	NA	Intergenic	Intergenic	-1104	NM_015276	23326	Hs.462492	NM_015276	ENSG00000124422	USP22	USP3L	ubiquitin specific peptidase 22	protein-coding	0.025575	0.461735	
chunk0045_357_1	chr12	51904956	51905297	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-2292	NM_000020	94	Hs.591026	NM_000020	ENSG00000139567	ACVRL1	ACVRLK1|ALK-1|ALK1|HHT|HHT2|ORW2|SKR3|TSR-I	activin A receptor like type 1	protein-coding	0.000000	0.482456	
chunk0084_302_1	chr17	80030707	80031159	+	0	NA	intron (NM_019020, intron 1 of 11)	intron (NM_019020, intron 1 of 11)	4925	NM_019020	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.035398	0.607064	
chunk0071_231_1	chr15	85047736	85047935	+	0	NA	intron (NM_002605, intron 1 of 21)	MamSINE1|SINE|tRNA-RTE	65861	NM_173454	5151	Hs.9333	NM_002605	ENSG00000073417	PDE8A	HsT19550	phosphodiesterase 8A	protein-coding	0.005025	0.350000	
chunk0075_327_1	chr16	54649765	54650263	+	0	NA	Intergenic	MIRc|SINE|MIR	278764	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.016064	0.452906	
chunk0147_91_1	chr4	173243961	173244170	+	0	NA	intron (NM_017423, intron 1 of 11)	MER58A|DNA|hAT-Charlie	-24095	NR_036093	100422849		NR_036093	ENSG00000221296	MIR548T	-	microRNA 548t	ncRNA	0.009569	0.485714	
chunk0160_373_1	chr5	161192796	161193649	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-254596	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.005862	0.401639	
chunk0174_268_1	chr6	161395102	161395489	+	0	NA	intron (NM_013988, intron 6 of 8)	L1ME4b|LINE|L1	-121220	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.012920	0.404639	
chunk0153_405_1	chr5	75363843	75364069	+	0	NA	Intergenic	Intergenic	26788	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.017699	0.511013	
chunk0211_219_1	chrX	118584039	118584637	+	0	NA	intron (NM_144658, intron 14 of 52)	L1ME2|LINE|L1	88429	NM_144658	139818	Hs.368203	NM_144658	ENSG00000147251	DOCK11	ACG|ZIZ2|bB128O4.1	dedicator of cytokinesis 11	protein-coding	0.006689	0.360601	291(TGTACTCAGTGTTCTT,+,0.00)
chunk0047_34_1	chr12	66571555	66572267	+	0	NA	intron (NM_021150, intron 2 of 23)	intron (NM_021150, intron 2 of 23)	107234	NM_021150	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.007022	0.417952	
chunk0184_218_1	chr7	117384541	117384982	+	0	NA	exon (NM_001301822, exon 5 of 12)	exon (NM_001301822, exon 5 of 12)	42762	NM_001301821	136991	Hs.352412	NM_130768	ENSG00000154438	ASZ1	ALP1|ANKL1|C7orf7|CT1.19|GASZ|Orf3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding	0.004535	0.316742	
chunk0024_427_1	chr10	46040110	46040390	+	0	NA	intron (NM_002443, intron 1 of 3)	intron (NM_002443, intron 1 of 3)	6019	NM_138634	4477	Hs.255462	NM_002443	ENSG00000263639	MSMB	HPC13|IGBF|MSP|MSPB|PN44|PRPS|PSP|PSP-94|PSP57|PSP94	microseminoprotein beta	protein-coding	0.003571	0.384342	
chunk0118_28_1	chr22	26703243	26703803	+	0	NA	intron (NR_110543, intron 1 of 5)	L1MD3|LINE|L1	30680	NR_110543	102724827	Hs.642767	NR_110543		MIATNB	-	MIAT neighbor	ncRNA	0.003571	0.390374	
chunk0118_87_1	chr22	29030724	29031017	+	0	NA	intron (NR_046851, intron 2 of 2)	intron (NR_046851, intron 2 of 2)	606	NR_046851	100874123	Hs.674708	NR_046851	ENSG00000177993	ZNRF3-AS1	-	ZNRF3 antisense RNA 1	ncRNA	0.051195	0.683673	
chunk0077_66_1	chr16	76908768	76909237	+	0	NA	Intergenic	Intergenic	40066	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.000000	0.310638	
chunk0019_221_1	chr1	227290297	227290781	+	0	NA	intron (NM_014826, intron 1 of 34)	intron (NM_014826, intron 1 of 34)	27586	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.000000	0.313402	
chunk0050_436_1	chr12	110320657	110320911	+	0	NA	intron (NM_170665, intron 5 of 19)	intron (NM_170665, intron 5 of 19)	39557	NM_001681	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.011811	0.388235	
chunk0173_290_1	chr6	148258599	148259384	+	0	NA	Intergenic	Intergenic	-83602	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.011465	0.430025	
chunk0007_57_1	chr1	77983887	77984295	+	0	NA	Intergenic	MER57E1|LTR|ERV1	-4886	NM_003902	8880	Hs.567380	NM_003902	ENSG00000162613	FUBP1	FBP|FUBP|hDH V	far upstream element binding protein 1	protein-coding	0.002451	0.376528	
chunk0013_1_1	chr1	165643040	165643457	+	0	NA	intron (NM_004528, intron 1 of 5)	L1ME4a|LINE|L1	12375	NM_004528	4259	Hs.191734	NM_004528	ENSG00000143198	MGST3	GST-III	microsomal glutathione S-transferase 3	protein-coding	0.002398	0.284689	
chunk0101_153_1	chr2	128217665	128218167	+	0	NA	Intergenic	Intergenic	100681	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.007968	0.425447	
chunk0087_61_1	chr18	31633524	31633784	+	0	NA	intron (NM_004775, intron 5 of 8)	L2a|LINE|L2	41887	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.011538	0.486590	
chunk0183_335_1	chr7	108290284	108290825	+	0	NA	intron (NM_001193582, intron 3 of 30)	intron (NM_001193582, intron 3 of 30)	-50384	NM_001037132	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.005545	0.341328	
chunk0054_432_1	chr13	51282315	51282662	+	0	NA	3' UTR (NM_001242312, exon 4 of 4)	3' UTR (NM_001242312, exon 4 of 4)	-58544	NM_001101320	647174	Hs.685891	NM_001101320	ENSG00000253309	SERPINE3	-	serpin family E member 3	protein-coding	0.011527	0.497126	
chunk0194_254_1	chr8	86618753	86619215	+	0	NA	intron (NM_019098, intron 13 of 17)	intron (NM_019098, intron 13 of 17)	104557	NM_003909	8895	Hs.191219	NM_003909	ENSG00000085719	CPNE3	CPN3|PRO1071	copine 3	protein-coding	0.017316	0.460043	
chunk0057_125_1	chr13	99473379	99474028	+	0	NA	Intergenic	Intergenic	25603	NR_110731	102725509	Hs.648968	NR_110731		LINC01232	TCONS_00021520	long intergenic non-protein coding RNA 1232	ncRNA	0.015408	0.453846	
chunk0137_81_1	chr4	13066311	13066524	+	0	NA	Intergenic	Intergenic	417948	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.000000	0.476636	
chunk0154_99_1	chr5	78174515	78174735	+	0	NA	intron (NM_003664, intron 11 of 26)	L1PA6|LINE|L1	120130	NM_001271769	8546	Hs.532091	NM_003664	ENSG00000132842	AP3B1	ADTB3|ADTB3A|HPS|HPS2|PE	adaptor related protein complex 3 subunit beta 1	protein-coding	0.013636	0.552036	
chunk0198_134_1	chr8	132490239	132490753	+	0	NA	Intergenic	Intergenic	-9739	NM_004519	3786	Hs.374023	NM_004519	ENSG00000184156	KCNQ3	BFNC2|EBN2|KV7.3	potassium voltage-gated channel subfamily Q member 3	protein-coding	0.011673	0.425243	
chunk0012_340_1	chr1	162578790	162579577	+	0	NA	intron (NM_003115, intron 3 of 9)	intron (NM_003115, intron 3 of 9)	17677	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.005083	0.333756	
chunk0030_155_1	chr10	113945733	113945932	+	0	NA	Intergenic	Intergenic	91200	NM_198514	374354	Hs.369924	NM_198514	ENSG00000196865	NHLRC2	FINCA	NHL repeat containing 2	protein-coding	0.015075	0.450000	
chunk0188_249_1	chr8	14394863	14395105	+	0	NA	intron (NM_139167, intron 2 of 7)	MIR|SINE|MIR	458526	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.004132	0.333333	
chunk0163_237_1	chr6	12331334	12331649	+	0	NA	Intergenic	Intergenic	41195	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.003175	0.443038	
chunk0140_437_1	chr4	76197972	76198980	+	0	NA	intron (NM_005506, intron 1 of 11)	intron (NM_005506, intron 1 of 11)	15423	NM_005506	950	Hs.349656	NM_005506	ENSG00000138760	SCARB2	AMRF|CD36L2|EPM4|HLGP85|LGP85|LIMP-2|LIMPII|SR-BII	scavenger receptor class B member 2	protein-coding	0.007937	0.452924	
chunk0110_310_1	chr20	18466755	18467026	+	0	NA	promoter-TSS (NR_104209)	promoter-TSS (NR_104209)	295	NM_001099407	55184	Hs.472225	NM_018152	ENSG00000089091	DZANK1	ANKRD64|C20orf12|C20orf84	double zinc ribbon and ankyrin repeat domains 1	protein-coding	0.077491	0.665441	
chunk0131_193_1	chr3	148538045	148538372	+	0	NA	Intergenic	MIRb|SINE|MIR	-159663	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.000000	0.304878	173(CAAAACAGATTGTTCT,-,0.00),174(AAAACAGATTGTTCTG,+,0.00)
chunk0010_249_1	chr1	116481446	116481667	+	0	NA	Intergenic	Intergenic	-2730	NR_125973	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.009050	0.531532	
chunk0118_306_1	chr22	35052849	35053330	+	0	NA	Intergenic	Intergenic	-13047	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.012474	0.441909	
chunk0017_49_1	chr1	205317494	205318031	+	0	NA	intron (NM_030952, intron 1 of 6)	intron (NM_030952, intron 1 of 6)	4029	NM_030952	81788	Hs.497512	NM_030952	ENSG00000163545	NUAK2	SNARK	NUAK family kinase 2	protein-coding	0.009311	0.576208	
chunk0125_231_1	chr3	68215600	68215995	+	0	NA	intron (NM_213609, intron 2 of 4)	L1MC3|LINE|L1	211581	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.005063	0.366162	
chunk0039_21_1	chr11	95647008	95647834	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	142369	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.003632	0.353083	533(GAGAACTTAATGTTCC,-,0.00),534(AGAACTTAATGTTCCC,+,0.00)
chunk0001_292_1	chr1	8890090	8890573	+	0	NA	Intergenic	Alu|SINE|Alu	-11239	NM_001428	2023	Hs.517145	NM_001428	ENSG00000074800	ENO1	ENO1L1|HEL-S-17|MPB1|NNE|PPH	enolase 1	protein-coding	0.018634	0.469008	
chunk0159_273_1	chr5	142370629	142370970	+	0	NA	intron (NR_120664, intron 3 of 3)	intron (NR_120664, intron 3 of 3)	45506	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.002933	0.362573	
chunk0149_305_1	chr5	25796832	25797031	+	0	NA	Intergenic	LTR57-int|LTR|ERVL	-956348	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.005025	0.490000	
chunk0155_356_1	chr5	97224196	97224536	+	0	NA	Intergenic	Intergenic	-41065	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.000000	0.299120	
chunk0012_222_1	chr1	160201708	160202465	+	0	NA	TTS (NM_001231)	TTS (NM_001231)	-3233	NM_003768	8682	Hs.517216	NM_003768	ENSG00000162734	PEA15	HMAT1|HUMMAT1H|MAT1|MAT1H|PEA-15|PED|PED-PEA15|PED/PEA15	proliferation and apoptosis adaptor protein 15	protein-coding	0.005284	0.480211	405(GAGAACAGAGAGTGCT,-,0.00),406(AGAACAGAGAGTGCTA,+,0.00),671(CAGCACAGTCTGTTAT,-,0.00),672(AGCACAGTCTGTTATT,+,0.00)
chunk0202_153_1	chr9	73598037	73598236	+	0	NA	Intergenic	Intergenic	446405	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.005025	0.370000	
chunk0109_154_1	chr20	3847170	3847655	+	0	NA	intron (NM_001206491, intron 1 of 5)	intron (NM_001206491, intron 1 of 5)	613	NR_037921	57506	Hs.570362	NM_020746	ENSG00000088888	MAVS	CARDIF|IPS-1|IPS1|VISA	mitochondrial antiviral signaling protein	protein-coding	0.059794	0.600823	315(GGGAACACTCTGTCAC,-,0.00),316(GGAACACTCTGTCACC,+,0.00)
chunk0130_67_1	chr3	129908134	129908816	+	0	NA	non-coding (NR_037893, exon 3 of 3)	non-coding (NR_037893, exon 3 of 3)	14604	NR_037893	100507032	Hs.529562	NR_037893	ENSG00000271270	TMCC1-AS1	-	TMCC1 antisense RNA 1 (head to head)	ncRNA	0.007331	0.434846	
chunk0176_137_1	chr7	12715573	12716220	+	0	NA	Intergenic	Intergenic	28610	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.015456	0.456790	362(CAGAACACTTTGTCCT,-,0.00),363(AGAACACTTTGTCCTT,+,0.00)
chunk0035_236_1	chr11	45933091	45933992	+	0	NA	3' UTR (NM_001101802, exon 18 of 18)	3' UTR (NM_001101802, exon 18 of 18)	10865	NM_001300721	120071	Hs.86543	NM_152312	ENSG00000165905	LARGE2	GYLTL1B|PP5656	LARGE xylosyl- and glucuronyltransferase 2	protein-coding	0.021088	0.508869	
chunk0022_288_1	chr10	15461798	15461997	+	0	NA	Intergenic	Intergenic	-90838	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.020101	0.535000	
chunk0135_76_1	chr3	185994726	185994930	+	0	NA	Intergenic	L2b|LINE|L2	34859	NR_033752	344887	Hs.128803	NR_033752	ENSG00000171658	NMRAL2P	NMRAL1P1	NmrA like redox sensor 2, pseudogene	pseudo	0.004902	0.473171	
chunk0168_269_1	chr6	90009100	90009573	+	0	NA	intron (NM_021813, intron 5 of 8)	intron (NM_021813, intron 5 of 8)	114867	NM_032602	84694	Hs.334499	NM_032602	ENSG00000135355	GJA10	CX62	gap junction protein alpha 10	protein-coding	0.002114	0.354430	
chunk0089_199_1	chr18	60007565	60007935	+	0	NA	Intergenic	L1ME1|LINE|L1	107790	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.005405	0.334232	
chunk0208_49_1	chrX	11458279	11458526	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-30617	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.008097	0.471774	
chunk0149_366_1	chr5	28067064	28067290	+	0	NA	Intergenic	L1PA13|LINE|L1	594885	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.008850	0.533040	
chunk0149_377_1	chr5	28313742	28314308	+	0	NA	Intergenic	Intergenic	-612845	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.001767	0.294533	273(AGAAACTCAGTGTTCT,-,0.00)
chunk0048_439_1	chr12	88546433	88546942	+	0	NA	intron (NM_000899, intron 1 of 9)	L2a|LINE|L2	33786	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.007859	0.356863	
chunk0022_428_1	chr10	19296703	19297008	+	0	NA	intron (NM_001142308, intron 21 of 39)	L4_A_Mam|LINE|RTE-X	248084	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.000000	0.284314	
chunk0172_276_1	chr6	137644922	137645139	+	0	NA	Intergenic	L1MA4A|LINE|L1	-20616	NR_125867	102723649	Hs.129235	NR_125867		LOC102723649	-	uncharacterized LOC102723649	ncRNA	0.004608	0.316514	
chunk0080_247_1	chr17	30333482	30334104	+	0	NA	intron (NM_206832, intron 1 of 6)	intron (NM_206832, intron 1 of 6)	254	NM_206832	388364	Hs.371005	NM_206832	ENSG00000182271	TMIGD1	TMIGD|UNQ9372	transmembrane and immunoglobulin domain containing 1	protein-coding	0.008039	0.415730	
chunk0138_411_1	chr4	43851150	43851372	+	0	NA	Intergenic	LTR62|LTR|ERVL	-165600	NR_131959	100506827	Hs.156197	NR_131958	ENSG00000251350	LINC02475	LVCAT1	long intergenic non-protein coding RNA 2475	ncRNA	0.000000	0.417040	
chunk0044_104_1	chr12	28603657	28604214	+	0	NA	Intergenic	Intergenic	346735	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.003591	0.333333	254(CAGAACACTGTGAGCT,-,0.00),255(AGAACACTGTGAGCTT,+,0.00)
chunk0003_149_1	chr1	33036865	33037075	+	0	NA	promoter-TSS (NM_001199199)	promoter-TSS (NM_001199199)	-59	NM_001199199	204	Hs.470907	NM_001625	ENSG00000004455	AK2	ADK2	adenylate kinase 2	protein-coding	0.090476	0.625592	
chunk0123_258_1	chr3	45879632	45879875	+	0	NA	intron (NM_001276378, intron 2 of 11)	L1MC1|LINE|L1	-6751	NM_001256369	10803	Hs.225946	NM_006641	ENSG00000173585	CCR9	CC-CKR-9|CDw199|GPR-9-6|GPR28	C-C motif chemokine receptor 9	protein-coding	0.008230	0.372951	133(AGGAACTCTCTGTACC,-,0.00),134(GGAACTCTCTGTACCT,+,0.00)
chunk0192_34_1	chr8	58648745	58648944	+	0	NA	intron (NM_003580, intron 1 of 30)	MSTB-int|LTR|ERVL-MaLR	10563	NM_001144772	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.015075	0.520000	
chunk0019_197_1	chr1	226815022	226815596	+	0	NA	Intergenic	Intergenic	-55263	NM_012486	5664	Hs.25363	NM_000447	ENSG00000143801	PSEN2	AD3L|AD4|CMD1V|PS2|STM2	presenilin 2	protein-coding	0.013937	0.506087	
chunk0004_355_1	chr1	51487638	51488137	+	0	NA	intron (NM_001981, intron 1 of 24)	intron (NM_001981, intron 1 of 24)	31436	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.002004	0.346000	129(AAGTACACCCTGTGCT,-,0.00),130(AGTACACCCTGTGCTG,+,0.00)
chunk0053_147_1	chr13	30188774	30189108	+	0	NA	Intergenic	Intergenic	-80066	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.005988	0.379104	
chunk0202_455_1	chr9	82560252	82560829	+	0	NA	Intergenic	Intergenic	502588	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.012132	0.456747	
chunk0056_217_1	chr13	88115931	88116576	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-26614	NR_131919	105370306	Hs.560133	NR_131919	ENSG00000231019	LINC00373	-	long intergenic non-protein coding RNA 373	ncRNA	0.006202	0.369969	
chunk0026_397_1	chr10	69757807	69758416	+	0	NA	Intergenic	Intergenic	-43777	NM_001130103	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.013136	0.542623	406(GGCACTGTGTGTGCAG,+,0.00)
chunk0106_222_1	chr2	202566318	202566874	+	0	NA	3' UTR (NM_001204, exon 13 of 13)	3' UTR (NM_001204, exon 13 of 13)	-68582	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.003597	0.308797	
chunk0157_20_1	chr5	115490429	115491191	+	0	NA	Intergenic	Intergenic	54084	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.002625	0.494102	348(GAGAACACTCAGCCCT,-,0.00),349(AGAACACTCAGCCCTC,+,0.00)
chunk0092_91_1	chr19	22122135	22122579	+	0	NA	Intergenic	Intergenic	69909	NM_033468	113835	Hs.283900	NM_033468	ENSG00000197134	ZNF257	BMZF-4|BMZF4	zinc finger protein 257	protein-coding	0.009009	0.406742	
chunk0162_315_1	chr6	6689568	6689837	+	0	NA	Intergenic	Intergenic	-66876	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.003717	0.455556	
chunk0155_192_1	chr5	94654280	94654679	+	0	NA	intron (NM_032290, intron 8 of 20)	intron (NM_032290, intron 8 of 20)	35793	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.000000	0.302500	
chunk0017_141_1	chr1	206635557	206635756	+	0	NA	5' UTR (NM_003582, exon 1 of 3)	5' UTR (NM_003582, exon 1 of 3)	120	NM_001004023	8444	Hs.164267	NM_003582	ENSG00000143479	DYRK3	DYRK5|RED|REDK|hYAK3-2	dual specificity tyrosine phosphorylation regulated kinase 3	protein-coding	0.120603	0.740000	
chunk0194_388_1	chr8	90934541	90935433	+	0	NA	intron (NM_022351, intron 9 of 12)	intron (NM_022351, intron 9 of 12)	50270	NM_001190972	100127983	Hs.733266	NM_001190972	ENSG00000253250	C8orf88	-	chromosome 8 open reading frame 88	protein-coding	0.002242	0.350504	295(AGGGACAAGATGTCCA,-,0.00),296(GGGACAAGATGTCCAT,+,0.00)
chunk0101_64_1	chr2	123494143	123494817	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-530807	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.004451	0.425185	398(TAGAACTGCCTGTACC,-,0.00),399(AGAACTGCCTGTACCT,+,0.00)
chunk0057_423_1	chr13	110014699	110015436	+	0	NA	Intergenic	Intergenic	-38218	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.013569	0.397019	340(CAGTACACTCTGTGCT,-,0.00),341(AGTACACTCTGTGCTT,+,0.00)
chunk0025_108_1	chr10	51074535	51074922	+	0	NA	exon (NM_006258, exon 1 of 18)	exon (NM_006258, exon 1 of 18)	254	NM_006258	5592	Hs.407535	NM_006258	ENSG00000185532	PRKG1	AAT8|PKG|PKG1|PRKG1B|PRKGR1B|cGK|cGK 1|cGK1|cGKI|cGKI-BETA|cGKI-alpha	protein kinase cGMP-dependent 1	protein-coding	0.082687	0.644330	
chunk0165_63_1	chr6	30907840	30908185	+	0	NA	promoter-TSS (NM_001517)	promoter-TSS (NM_001517)	-188	NM_001517	2968	Hs.485070	NM_001517	ENSG00000213780	GTF2H4	P52|TFB2|TFIIH	general transcription factor IIH subunit 4	protein-coding	0.078261	0.604046	
chunk0070_315_1	chr15	75389114	75389702	+	0	NA	intron (NM_001145358, intron 16 of 20)	intron (NM_001145358, intron 16 of 20)	-20781	NM_006715	4123	Hs.26232	NM_006715	ENSG00000140400	MAN2C1	MAN6A8|MANA|MANA1	mannosidase alpha class 2C member 1	protein-coding	0.010204	0.455008	
chunk0161_434_1	chr5	178474466	178475129	+	0	NA	intron (NM_173465, intron 2 of 28)	L2a|LINE|L2	115758	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.010558	0.405120	
chunk0118_247_1	chr22	32780570	32780802	+	0	NA	intron (NM_003490, intron 5 of 12)	MIR|SINE|MIR	-20130	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.004310	0.429185	153(CTGAACTTCCTGTGCC,-,0.00),154(TGAACTTCCTGTGCCT,+,0.00)
chunk0030_453_1	chr10	121076585	121077280	+	0	NA	Intergenic	Intergenic	-225753	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.008633	0.482759	
chunk0047_387_1	chr12	75489201	75489668	+	0	NA	intron (NM_006851, intron 2 of 5)	L2a|LINE|L2	8701	NM_006851	11010	Hs.205558	NM_006851	ENSG00000139278	GLIPR1	CRISP7|GLIPR|RTVP1	GLI pathogenesis related 1	protein-coding	0.004283	0.435897	73(CAGGTCTCTCTGTTCT,-,0.00),74(AGGTCTCTCTGTTCTT,+,0.00)
chunk0172_345_1	chr6	138888800	138889052	+	0	NA	intron (NM_001195037, intron 18 of 20)	intron (NM_001195037, intron 18 of 20)	92815	NM_001195037	345930	Hs.660603	NM_001077706	ENSG00000203734	ECT2L	ARHGEF32|C6orf91|FBXO49|LFDH|dJ509I19.2|dJ509I19.3|dJ509I19.5	epithelial cell transforming 2 like	protein-coding	0.000000	0.268775	
chunk0036_285_1	chr11	65428980	65429317	+	0	NA	non-coding (NR_131012, exon 1 of 1)	non-coding (NR_131012, exon 1 of 1)	6350	NR_131012	283131	Hs.523789	NR_002802	ENSG00000245532	NEAT1	LINC00084|NCRNA00084|TncRNA|VINC	nuclear paraspeckle assembly transcript 1	ncRNA	0.008902	0.343195	64(GATGACAGGATGTTCC,-,0.00),65(ATGACAGGATGTTCCC,+,0.00)
chunk0106_340_1	chr2	206415195	206415751	+	0	NA	Intergenic	L1P2|LINE|L1	-28171	NM_003812	8745	Hs.370287	NM_003812	ENSG00000114948	ADAM23	MDC-3|MDC3	ADAM metallopeptidase domain 23	protein-coding	0.008993	0.515260	
chunk0189_5_1	chr8	19438410	19439032	+	0	NA	intron (NM_001130518, intron 6 of 9)	MER58A|DNA|hAT-Charlie	124745	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.006431	0.385233	
chunk0151_111_1	chr5	43483731	43484256	+	0	NA	promoter-TSS (NM_022483)	promoter-TSS (NM_022483)	-103	NM_022483	64417	Hs.732093	NM_022483	ENSG00000151881	TMEM267	C5orf28	transmembrane protein 267	protein-coding	0.078095	0.610266	
chunk0153_103_1	chr5	68419452	68419667	+	0	NA	Intergenic	Intergenic	126991	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.004651	0.337963	
chunk0118_42_1	chr22	27792524	27792766	+	0	NA	intron (NM_002430, intron 1 of 1)	intron (NM_002430, intron 1 of 1)	8853	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.024793	0.465021	
chunk0101_455_1	chr2	140143581	140143780	+	0	NA	Intergenic	Intergenic	443005	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.305000	
chunk0180_203_1	chr7	66348709	66349130	+	0	NA	intron (NM_003596, intron 3 of 5)	intron (NM_003596, intron 3 of 5)	51489	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.009501	0.372038	258(TGGAACTGTCAGTACT,-,0.00),259(GGAACTGTCAGTACTA,+,0.00)
chunk0024_287_1	chr10	42073616	42074003	+	0	NA	Intergenic	Intergenic	294236	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.043928	0.363402	
chunk0064_272_1	chr14	95042813	95043048	+	0	NA	Intergenic	L1MD2|LINE|L1	90573	NM_001195573	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.008511	0.402542	139(CAGAACATTCTGTATC,-,0.00),140(AGAACATTCTGTATCT,+,0.00)
chunk0115_362_1	chr21	29865215	29865845	+	0	NA	intron (NM_175611, intron 1 of 15)	intron (NM_175611, intron 1 of 15)	74434	NM_175611	2897	Hs.664641	NM_000830	ENSG00000171189	GRIK1	EAA3|EEA3|GLR5|GLUR5|GluK1|gluR-5	glutamate ionotropic receptor kainate type subunit 1	protein-coding	0.004762	0.302694	
chunk0018_203_1	chr1	219368562	219369299	+	0	NA	Intergenic	Intergenic	193961	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.002714	0.337398	
chunk0080_42_1	chr17	21256839	21257341	+	0	NA	Intergenic	Intergenic	-3824	NM_152914	256302	Hs.654713	NM_152914	ENSG00000274180	NATD1	C17orf103|Gtlf3b	N-acetyltransferase domain containing 1	protein-coding	0.015936	0.433400	
chunk0202_64_1	chr9	71719562	71720077	+	0	NA	intron (NM_001135820, intron 11 of 22)	intron (NM_001135820, intron 11 of 22)	49065	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.011650	0.393411	255(GGAGACATACTGTTCT,-,0.00),256(GAGACATACTGTTCTA,+,0.00)
chunk0171_108_1	chr6	122147497	122147882	+	0	NA	Intergenic	Intergenic	-251862	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.010390	0.347150	
chunk0005_174_1	chr1	58621635	58621940	+	0	NA	Intergenic	Intergenic	-44293	NM_002353	4070	Hs.23582	NM_002353	ENSG00000184292	TACSTD2	EGP-1|EGP1|GA733-1|GA7331|GP50|M1S1|TROP2	tumor associated calcium signal transducer 2	protein-coding	0.000000	0.486928	
chunk0093_357_1	chr19	55526609	55526835	+	0	NA	Intergenic	Intergenic	9572	NM_001101401	646643	Hs.532676	NM_001101401	ENSG00000187550	SBK2	SGK069	SH3 domain binding kinase family member 2	protein-coding	0.035398	0.506608	
chunk0209_88_1	chrX	39238382	39238671	+	0	NA	Intergenic	Intergenic	88836	NR_038968	286442	Hs.638478	NR_038968	ENSG00000235304	LINC01281	-	long intergenic non-protein coding RNA 1281	ncRNA	0.006920	0.500000	
chunk0152_15_1	chr5	56356657	56356940	+	0	NA	Intergenic	Intergenic	-123439	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.010601	0.390845	
chunk0059_376_1	chr14	37369396	37369887	+	0	NA	intron (NM_001195296, intron 12 of 14)	intron (NM_001195296, intron 12 of 14)	171728	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.010183	0.371951	
chunk0126_239_1	chr3	79337869	79338529	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-73528	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.001515	0.266263	
chunk0059_367_1	chr14	37329462	37330014	+	0	NA	intron (NM_001195296, intron 11 of 14)	intron (NM_001195296, intron 11 of 14)	131825	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.001812	0.311031	
chunk0098_280_1	chr2	75680121	75680608	+	0	NA	intron (NM_001201334, intron 11 of 16)	intron (NM_001201334, intron 11 of 16)	30242	NM_001201334	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.002053	0.340164	
chunk0210_386_1	chrX	97628372	97628730	+	0	NA	Intergenic	Intergenic	-64016	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.002793	0.392758	
chunk0034_395_1	chr11	36766855	36767265	+	0	NA	Intergenic	Intergenic	-168781	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.004878	0.335766	265(TGGTACAACTTGTTCT,-,0.00),266(GGTACAACTTGTTCTT,+,0.00)
chunk0158_195_1	chr5	127988030	127988265	+	0	NA	Intergenic	Intergenic	94927	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.004255	0.432203	
chunk0064_334_1	chr14	96515496	96515839	+	0	NA	intron (NM_001293628, intron 1 of 21)	L4_A_Mam|LINE|RTE-X	12802	NM_001293628	10914	Hs.253726	NM_032632	ENSG00000090060	PAPOLA	PAP|PAP-alpha	poly(A) polymerase alpha	protein-coding	0.005831	0.334302	
chunk0143_146_1	chr4	109921356	109921576	+	0	NA	intron (NM_001963, intron 1 of 23)	intron (NM_001963, intron 1 of 23)	8582	NM_001178130	1950	Hs.419815	NM_001963	ENSG00000138798	EGF	HOMG4|URG	epidermal growth factor	protein-coding	0.000000	0.402715	93(CAGGACATTCAGTACA,-,0.00),94(AGGACATTCAGTACAC,+,0.00)
chunk0169_433_1	chr6	108707246	108707865	+	0	NA	Intergenic	Intergenic	-44099	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.008078	0.432258	
chunk0005_53_1	chr1	55149552	55150081	+	0	NA	intron (NM_015306, intron 16 of 67)	Kanga11a|DNA|TcMar-Tc2	65550	NM_015306	23358	Hs.477009	NM_015306	ENSG00000162402	USP24	-	ubiquitin specific peptidase 24	protein-coding	0.001890	0.364151	
chunk0090_283_1	chr18	74916679	74917366	+	0	NA	intron (NM_001146189, intron 6 of 6)	intron (NM_001146189, intron 6 of 6)	286059	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.013100	0.398256	
chunk0180_216_1	chr7	67021112	67021521	+	0	NA	intron (NM_018264, intron 6 of 15)	intron (NM_018264, intron 6 of 15)	24511	NM_018264	55253	Hs.520917	NM_018264	ENSG00000198874	TYW1	RSAFD1|TYW1A|YPL207W	tRNA-yW synthesizing protein 1 homolog	protein-coding	0.014670	0.460976	
chunk0040_15_1	chr11	108797687	108797998	+	0	NA	intron (NM_004398, intron 13 of 17)	intron (NM_004398, intron 13 of 17)	132817	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.009646	0.442308	
chunk0061_54_1	chr14	56399418	56399618	+	0	NA	Intergenic	Intergenic	-180275	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.010000	0.427861	168(TGGCACAGAGTGTGCA,-,0.00),169(GGCACAGAGTGTGCAA,+,0.00)
chunk0096_455_1	chr2	39933068	39933400	+	0	NA	intron (NR_038441, intron 2 of 4)	MLT1H|LTR|ERVL-MaLR	15600	NR_038441	100128590	Hs.744988	NR_038441	ENSG00000227028	SLC8A1-AS1	-	SLC8A1 antisense RNA 1	ncRNA	0.006024	0.405405	
chunk0070_73_1	chr15	69951526	69951972	+	0	NA	Intergenic	L1ME4b|LINE|L1	116515	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.004484	0.364653	
chunk0128_447_1	chr3	115126286	115126485	+	0	NA	intron (NM_015642, intron 1 of 9)	L1ME3F|LINE|L1	20895	NM_015642	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.005025	0.355000	
chunk0156_246_1	chr5	108766533	108767011	+	0	NA	intron (NM_001308028, intron 1 of 17)	intron (NM_001308028, intron 1 of 17)	17845	NM_001308028	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.004184	0.394572	
chunk0090_125_1	chr18	71807453	71808079	+	0	NA	Intergenic	Intergenic	-25540	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.003195	0.306220	232(AAGAACAACATGTTCT,-,0.00),233(AGAACAACATGTTCTC,+,0.00)
chunk0065_185_1	chr15	26627985	26628559	+	0	NA	intron (NR_103801, intron 1 of 6)	Tigger1|DNA|TcMar-Tigger	906	NM_001191321	2562	Hs.302352	NM_000814	ENSG00000166206	GABRB3	ECA5|EIEE43	gamma-aminobutyric acid type A receptor beta3 subunit	protein-coding	0.005226	0.408696	
chunk0054_438_1	chr13	51386160	51386412	+	0	NA	intron (NM_001306091, intron 9 of 19)	intron (NM_001306091, intron 9 of 19)	-37647	NR_049878	100847003		NR_049878	ENSG00000266072	MIR5693	-	microRNA 5693	ncRNA	0.003968	0.339921	112(AGGTACTGTATGTTCT,-,0.00),113(GGTACTGTATGTTCTC,+,0.00)
chunk0146_203_1	chr4	161364572	161364834	+	0	NA	Intergenic	Intergenic	-658030	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.011450	0.338403	
chunk0014_191_1	chr1	178888030	178888333	+	0	NA	intron (NM_001286247, intron 13 of 18)	intron (NM_001286247, intron 13 of 18)	-17101	NM_004673	9068	Hs.591474	NM_004673	ENSG00000116194	ANGPTL1	ANG3|ANGPT3|ARP1|AngY|UNQ162|dJ595C2.2	angiopoietin like 1	protein-coding	0.006601	0.292763	
chunk0071_51_1	chr15	80099953	80100210	+	0	NA	intron (NM_001242919, intron 1 of 5)	intron (NM_001242919, intron 1 of 5)	1665	NM_001242919	54469	Hs.596679	NM_019006	ENSG00000086666	ZFAND6	AWP1|ZA20D3|ZFAND5B	zinc finger AN1-type containing 6	protein-coding	0.003891	0.321705	
chunk0022_282_1	chr10	15251096	15251383	+	0	NA	intron (NM_001010924, intron 4 of 7)	intron (NM_001010924, intron 4 of 7)	-82529	NM_001308295	9397	Hs.60339	NM_004808	ENSG00000152465	NMT2	-	N-myristoyltransferase 2	protein-coding	0.003484	0.437500	
chunk0141_141_1	chr4	81328017	81328270	+	0	NA	Intergenic	Intergenic	-113026	NM_001282485	5593	Hs.232044	NM_006259	ENSG00000138669	PRKG2	PKG2|PRKGR2|cGK2|cGKII	protein kinase cGMP-dependent 2	protein-coding	0.003953	0.267717	
chunk0076_45_1	chr16	60006518	60006723	+	0	NA	intron (NR_110917, intron 1 of 3)	intron (NR_110917, intron 1 of 3)	151267	NR_110917	101927580	Hs.552235	NR_110917	ENSG00000261807	LINC02141	-	long intergenic non-protein coding RNA 2141	ncRNA	0.004878	0.286408	
chunk0113_324_1	chr20	58421030	58421449	+	0	NA	intron (NM_001195677, intron 2 of 2)	intron (NM_001195677, intron 2 of 2)	32120	NM_001195677	9217	Hs.182625	NM_004738	ENSG00000124164	VAPB	ALS8|VAMP-B|VAP-B	VAMP associated protein B and C	protein-coding	0.009547	0.380952	
chunk0081_56_1	chr17	38585114	38585685	+	0	NA	intron (NM_025248, intron 1 of 18)	intron (NM_025248, intron 1 of 18)	20531	NM_025248	80725	Hs.448872	NM_025248	ENSG00000277363	SRCIN1	P140|SNIP	SRC kinase signaling inhibitor 1	protein-coding	0.014011	0.582168	306(AAGCACACGGTGTGCT,-,0.00),307(AGCACACGGTGTGCTT,+,0.00)
chunk0012_228_1	chr1	160315204	160315777	+	0	NA	intron (NM_001098398, intron 8 of 32)	L1MA4|LINE|L1	-1775	NR_002190	474338	Hs.621179	NR_002190		SUMO1P3	-	SUMO1 pseudogene 3	pseudo	0.006981	0.475610	
chunk0194_440_1	chr8	92507058	92507533	+	0	NA	Intergenic	Intergenic	148199	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.002105	0.329832	
chunk0144_371_1	chr4	139921682	139921994	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	232241	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.012821	0.504792	
chunk0165_40_1	chr6	30051402	30052150	+	0	NA	intron (NR_026751, intron 3 of 5).8	L1MA4A|LINE|L1	9408	NR_026751	80862	Hs.653168	NR_026751	ENSG00000204623	ZNRD1ASP	C6orf12|HCG8|HCGVIII|HCGVIII-1|HTEX4|NCRNA00171|TCTEX4|ZNRD1-AS|ZNRD1-AS1|ZNRD1AS|ZNRD1AS1	zinc ribbon domain containing 1 antisense, pseudogene	pseudo	0.009358	0.353805	
chunk0082_375_1	chr17	60466073	60466593	+	0	NA	exon (NM_001282476, exon 4 of 12)	exon (NM_001282476, exon 4 of 12)	43829	NM_181707	124773	Hs.129312	NM_181707	ENSG00000141371	C17orf64	-	chromosome 17 open reading frame 64	protein-coding	0.003846	0.355086	
chunk0139_30_1	chr4	48405268	48405631	+	0	NA	intron (NM_020846, intron 6 of 7)	HAL1M8|LINE|L1	63853	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.002755	0.318681	
chunk0070_12_1	chr15	68899987	68900431	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-30291	NR_033672	79400	Hs.657932	NM_024505	ENSG00000255346	NOX5	-	NADPH oxidase 5	protein-coding	0.006757	0.413483	
chunk0049_215_1	chr12	93234600	93235189	+	0	NA	intron (NR_040096, intron 2 of 4)	intron (NR_040096, intron 2 of 4)	60528	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.005093	0.454237	
chunk0188_200_1	chr8	11853926	11854458	+	0	NA	intron (NM_001908, intron 1 of 9)	intron (NM_001908, intron 1 of 9)	13945	NM_147783	1508	Hs.520898	NM_001908	ENSG00000164733	CTSB	APPS|CPSB|RECEUP	cathepsin B	protein-coding	0.026316	0.557223	
chunk0111_387_1	chr20	34089887	34090243	+	0	NA	intron (NM_001316363, intron 8 of 8)	intron (NM_001316363, intron 8 of 8)	22291	NM_001316363	8894	Hs.429180	NM_003908	ENSG00000125977	EIF2S2	EIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta	eukaryotic translation initiation factor 2 subunit beta	protein-coding	0.014045	0.481793	
chunk0012_309_1	chr1	162257724	162258392	+	0	NA	intron (NM_001164757, intron 2 of 9)	L2c|LINE|L2	-84488	NR_030283	693141		NR_030283	ENSG00000207729	MIR556	MIRN556|hsa-mir-556|mir-556	microRNA 556	ncRNA	0.005988	0.437967	
chunk0181_408_1	chr7	90132926	90133244	+	0	NA	intron (NR_110029, intron 2 of 2)	intron (NR_110029, intron 2 of 2)	13685	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.003145	0.329154	241(AGAGACTGTCTGTCCC,-,0.00),242(GAGACTGTCTGTCCCC,+,0.00)
chunk0124_75_1	chr3	53155640	53156175	+	0	NA	Intergenic	(CACTGCT)n|Simple_repeat|Simple_repeat	-5300	NM_006254	5580	Hs.155342	NM_006254	ENSG00000163932	PRKCD	ALPS3|CVID9|MAY1|PKCD|nPKC-delta	protein kinase C delta	protein-coding	0.014953	0.582090	
chunk0091_222_1	chr19	10183966	10184295	+	0	NA	intron (NM_001379, intron 1 of 39)	intron (NM_001379, intron 1 of 39)	10949	NM_001130823	1786	Hs.202672	NM_001379	ENSG00000130816	DNMT1	ADCADN|AIM|CXXC9|DNMT|HSN1E|MCMT|m.HsaI	DNA methyltransferase 1	protein-coding	0.009119	0.542424	
chunk0046_365_1	chr12	63192503	63192775	+	0	NA	Intergenic	Intergenic	-39829	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.000000	0.494505	
chunk0037_267_1	chr11	75653552	75653751	+	0	NA	intron (NM_207577, intron 1 of 2)	intron (NM_207577, intron 1 of 2)	14783	NM_033063	4135	Hs.585540	NM_033063	ENSG00000171533	MAP6	MAP6-N|MTAP6|N-STOP|STOP	microtubule associated protein 6	protein-coding	0.000000	0.300000	
chunk0068_182_1	chr15	54626863	54627448	+	0	NA	3' UTR (NM_001080534, exon 31 of 31)	3' UTR (NM_001080534, exon 31 of 31)	569878	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.005128	0.348123	
chunk0038_450_1	chr11	94800395	94800856	+	0	NA	intron (NM_130847, intron 3 of 12)	intron (NM_130847, intron 3 of 12)	32283	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.002169	0.419913	
chunk0105_301_1	chr2	190170318	190170949	+	0	NA	intron (NM_001042521, intron 2 of 2)	intron (NM_001042521, intron 2 of 2)	-10230	NM_001042519	84281	Hs.389311	NM_032321	ENSG00000187699	C2orf88	smAKAP	chromosome 2 open reading frame 88	protein-coding	0.004754	0.376582	
chunk0031_258_1	chr10	127227216	127227415	+	0	NA	intron (NM_001290223, intron 27 of 51)	intron (NM_001290223, intron 27 of 51)	-31157	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.015075	0.565000	
chunk0191_219_1	chr8	52467035	52467378	+	0	NA	Intergenic	Intergenic	-57327	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.017493	0.476744	
chunk0138_161_1	chr4	37670243	37670637	+	0	NA	intron (NM_001085399, intron 1 of 6)	intron (NM_001085399, intron 1 of 6)	15937	NM_001085400	768211	Hs.283378	NM_001085399	ENSG00000181826	RELL1	-	RELT like 1	protein-coding	0.002538	0.356962	
chunk0054_361_1	chr13	49690129	49690508	+	0	NA	intron (NR_103802, intron 1 of 4)	intron (NR_103802, intron 1 of 4)	1169	NM_001278636	84650	Hs.433278	NM_032565	ENSG00000123179	EBPL	EBRP	EBP like	protein-coding	0.015831	0.357895	
chunk0097_436_1	chr2	63981592	63982139	+	0	NA	exon (NM_016516, exon 3 of 23)	exon (NM_016516, exon 3 of 23)	37215	NM_001005739	51542	Hs.48499	NM_016516	ENSG00000143952	VPS54	HCC8|PPP1R164|SLP-8p|VPS54L|WR|hVps54L	VPS54 subunit of GARP complex	protein-coding	0.007313	0.350365	
chunk0205_74_1	chr9	106942452	106942800	+	0	NA	intron (NM_021224, intron 7 of 12)	intron (NM_021224, intron 7 of 12)	79529	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.008621	0.372493	
chunk0084_229_1	chr17	78670184	78670408	+	0	NA	Intergenic	Intergenic	-38239	NR_110848	101928710	Hs.464224	NR_110848	ENSG00000267123	SCAT1	LINC02081|XLOC_012582	S-phase cancer associated transcript 1	ncRNA	0.040179	0.577778	41(TGGGACTTCCTGTTCT,-,0.00),42(GGGACTTCCTGTTCTT,+,0.00)
chunk0125_51_1	chr3	63937871	63938455	+	0	NA	intron (NM_001177387, intron 3 of 12)	intron (NM_001177387, intron 3 of 12)	-29581	NM_001128149	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.006849	0.372650	
chunk0043_117_1	chr12	15536345	15536547	+	0	NA	intron (NM_030667, intron 12 of 26)	L2a|LINE|L2	-9898	NM_030671	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.004950	0.502463	
chunk0184_212_1	chr7	117280156	117280693	+	0	NA	intron (NM_003391, intron 4 of 4)	L2b|LINE|L2	42865	NR_024047	7472	Hs.567356	NM_003391	ENSG00000105989	WNT2	INT1L1|IRP	Wnt family member 2	protein-coding	0.009311	0.460967	
chunk0173_333_1	chr6	148887205	148888240	+	0	NA	intron (NM_005715, intron 2 of 7)	Charlie18a|DNA|hAT-Charlie	76962	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.008696	0.449807	
chunk0084_308_1	chr17	80131023	80131664	+	0	NA	Intergenic	L1MB7|LINE|L1	15840	NM_014740	9775	Hs.389649	NM_014740	ENSG00000141543	EIF4A3	DDX48|Fal1|MUK34|NMP265|NUK34|RCPS|eIF-4A-III|eIF4A-III|eIF4AIII	eukaryotic translation initiation factor 4A3	protein-coding	0.010920	0.383178	
chunk0037_345_1	chr11	77400793	77401820	+	0	NA	intron (NM_001128620, intron 1 of 15)	intron (NM_001128620, intron 1 of 15)	72757	NM_001128620	5058	Hs.435714	NM_002576	ENSG00000149269	PAK1	IDDMSSD|PAKalpha	p21 (RAC1) activated kinase 1	protein-coding	0.006816	0.427043	
chunk0107_280_1	chr2	218310877	218311245	+	0	NA	intron (NM_015488, intron 2 of 9)	Tigger3a|DNA|TcMar-Tigger	-12118	NM_022572	25953	Hs.98475	NM_015488	ENSG00000127838	PNKD	BRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|TAHCCP2	PNKD metallo-beta-lactamase domain containing	protein-coding	0.005435	0.428184	
chunk0174_262_1	chr6	161165004	161165447	+	0	NA	intron (NM_020133, intron 3 of 8)	intron (NM_020133, intron 3 of 8)	-3243	NR_024277	79992	Hs.664873	NM_024929	ENSG00000279355	AGPAT4-IT1	C6orf59|NCRNA00241	AGPAT4 intronic transcript 1	ncRNA	0.011287	0.459459	
chunk0083_28_1	chr17	63212087	63212655	+	0	NA	intron (NM_025185, intron 5 of 24)	intron (NM_025185, intron 5 of 24)	202834	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.001761	0.335677	
chunk0039_257_1	chr11	102279840	102280238	+	0	NA	Intergenic	Intergenic	-37411	NM_182962	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.030151	0.388471	
chunk0174_101_1	chr6	156854729	156855087	+	0	NA	intron (NM_017519, intron 2 of 18)	intron (NM_017519, intron 2 of 18)	-75177	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.002793	0.342618	
chunk0026_269_1	chr10	67021827	67022175	+	0	NA	intron (NR_111909, intron 2 of 2)	intron (NR_111909, intron 2 of 2)	9735	NR_111909	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.008621	0.363897	
chunk0159_337_1	chr5	143931462	143931693	+	0	NA	Intergenic	L1MA2|LINE|L1	119416	NM_021182	57824	Hs.158320	NM_021182	ENSG00000158497	HMHB1	HB-1|HB-1Y|HLA-HB1	histocompatibility minor HB-1	protein-coding	0.008658	0.495690	
chunk0164_364_1	chr6	25634551	25634968	+	0	NA	Intergenic	Intergenic	-17442	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.007194	0.406699	177(AAGCACATTCTGAACC,-,0.00),178(AGCACATTCTGAACCT,+,0.00)
chunk0188_1_1	chr8	6272705	6273156	+	0	NA	Intergenic	Intergenic	133618	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.011086	0.380531	
chunk0135_84_1	chr3	186124707	186125074	+	0	NA	Intergenic	Intergenic	-15778	NM_004454	2119	Hs.43697	NM_004454	ENSG00000244405	ETV5	ERM	ETS variant 5	protein-coding	0.010899	0.470109	333(AAACACATTCTGTCCT,-,0.00),334(AACACATTCTGTCCTC,+,0.00)
chunk0109_339_1	chr20	9436086	9436413	+	0	NA	intron (NM_001172646, intron 28 of 37)	Tigger4b|DNA|TcMar-Tigger	-78109	NM_001199897	24141	Hs.22920	NM_012261	ENSG00000125869	LAMP5	BAD-LAMP|BADLAMP|C20orf103|LAMP-5|UNC-46	lysosomal associated membrane protein family member 5	protein-coding	0.003058	0.320122	
chunk0069_106_1	chr15	61633838	61634431	+	0	NA	Intergenic	Intergenic	-404831	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.006745	0.367003	245(CTGGACATGGTGTTCT,-,0.00),246(TGGACATGGTGTTCTC,+,0.00)
chunk0050_18_1	chr12	99701186	99701664	+	0	NA	intron (NM_152788, intron 8 of 25)	L1MA3|LINE|L1	53675	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.004184	0.338205	
chunk0122_321_1	chr3	37053300	37053798	+	0	NA	3' UTR (NM_001134369, exon 15 of 15)	3' UTR (NM_001134369, exon 15 of 15)	59772	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.012048	0.390782	
chunk0138_202_1	chr4	38621046	38622299	+	0	NA	intron (NR_026804, intron 6 of 7)	AluSx1|SINE|Alu	-42497	NM_016531	51274	Hs.298658	NM_016531	ENSG00000109787	KLF3	BKLF	Kruppel like factor 3	protein-coding	0.015164	0.460128	941(CAGAACACGGTGTCCT,-,0.00),942(AGAACACGGTGTCCTG,+,0.00)
chunk0010_1_1	chr1	111768004	111768252	+	0	NA	TTS (NM_007204)	TTS (NM_007204)	-12331	NM_198926	55924	Hs.193406	NM_019099	ENSG00000197852	INKA2	C1orf183|FAM212B	inka box actin regulator 2	protein-coding	0.000000	0.373494	
chunk0003_195_1	chr1	34709900	34710269	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-40390	NR_030278	693137		NR_030278	ENSG00000207941	MIR552	MIRN552|hsa-mir-552	microRNA 552	ncRNA	0.002710	0.451351	289(CAGCACTTCCAGTTCC,-,0.00)
chunk0198_359_1	chr8	140790878	140791125	+	0	NA	intron (NM_001316342, intron 11 of 32)	intron (NM_001316342, intron 11 of 32)	-58348	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.008097	0.383065	
chunk0038_318_1	chr11	91586106	91586620	+	0	NA	Intergenic	Intergenic	-717161	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.000000	0.374757	
chunk0089_443_1	chr18	70252397	70252604	+	0	NA	Intergenic	Intergenic	-36401	NM_004232	9306	Hs.44439	NM_004232	ENSG00000170677	SOCS6	CIS-4|CIS4|HSPC060|SOCS-4|SOCS-6|SOCS4|SSI4|STAI4|STATI4	suppressor of cytokine signaling 6	protein-coding	0.000000	0.259615	
chunk0015_332_1	chr1	189762166	189762417	+	0	NA	Intergenic	LTR1A2|LTR|ERV1	715338	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.015936	0.484127	150(TGGTACAGGGTGTTCT,-,0.00),151(GGTACAGGGTGTTCTT,+,0.00)
chunk0163_373_1	chr6	16128591	16128887	+	0	NA	promoter-TSS (NM_013262)	promoter-TSS (NM_013262)	-347	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.067568	0.572391	
chunk0206_192_1	chr9	122975151	122975725	+	0	NA	intron (NM_012197, intron 2 of 25)	intron (NM_012197, intron 2 of 25)	34429	NM_012197	23637	Hs.271341	NM_012197	ENSG00000011454	RABGAP1	GAPCENA|TBC1D11	RAB GTPase activating protein 1	protein-coding	0.005226	0.384348	45(AAGCACAAAGTGTCCC,-,0.00),46(AGCACAAAGTGTCCCT,+,0.00),247(TGGAACATTTTGTCCT,-,0.00),248(GGAACATTTTGTCCTT,+,0.00)
chunk0147_198_1	chr4	177793766	177794089	+	0	NA	intron (NR_028342, intron 2 of 5)	intron (NR_028342, intron 2 of 5)	65170	NR_028342	285501	Hs.722466	NM_001085490	ENSG00000231171	LINC01098	-	long intergenic non-protein coding RNA 1098	ncRNA	0.009288	0.354938	
chunk0060_77_1	chr14	42023412	42023938	+	0	NA	Intergenic	Charlie1b|DNA|hAT-Charlie	416114	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.003802	0.292220	
chunk0087_225_1	chr18	36195302	36195994	+	0	NA	intron (NM_017947, intron 2 of 14)	intron (NM_017947, intron 2 of 14)	8131	NM_017947	55034	Hs.405028	NM_017947	ENSG00000075643	MOCOS	HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding	0.004335	0.471861	194(GGGTCATTCTGTACTG,+,0.00)
chunk0160_237_1	chr5	155755326	155755580	+	0	NA	Intergenic	Intergenic	-571304	NM_172244	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.000000	0.360784	
chunk0129_240_1	chr3	122063808	122064229	+	0	NA	intron (NM_001206925, intron 1 of 5)	intron (NM_001206925, intron 1 of 5)	8656	NM_001206924	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.007126	0.438389	
chunk0108_147_1	chr2	230932442	230932930	+	0	NA	Intergenic	Intergenic	-7460	NM_005683	9290	Hs.114545	NM_005683	ENSG00000135898	GPR55	LPIR1	G protein-coupled receptor 55	protein-coding	0.020492	0.511247	329(AGGCACACCCTGTTCT,-,0.00),330(GGCACACCCTGTTCTA,+,0.00)
chunk0011_356_1	chr1	152666732	152667304	+	0	NA	Intergenic	Intergenic	3607	NM_178430	353141	Hs.490225	NM_178430	ENSG00000187223	LCE2D	LEP12|SPRL1A	late cornified envelope 2D	protein-coding	0.001748	0.469459	344(AGGAACATCCTGCCCA,-,0.00)
chunk0031_179_1	chr10	125633398	125633996	+	0	NA	Intergenic	Intergenic	49447	NM_001128202	387718	Hs.148259	NM_001128202	ENSG00000175018	TEX36	C10orf122|bA383C5.1	testis expressed 36	protein-coding	0.023411	0.422371	
chunk0033_155_1	chr11	15600678	15601124	+	0	NA	Intergenic	MIRb|SINE|MIR	-42984	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.004484	0.440716	
chunk0065_66_1	chr15	23107227	23107751	+	0	NA	Intergenic	L1MC4|LINE|L1	29333	NM_001001413	283767	Hs.531569	NM_001001413	ENSG00000273976	GOLGA6L1	-	golgin A6 family like 1	protein-coding	0.001908	0.380952	
chunk0158_149_1	chr5	127479108	127480190	+	0	NA	Intergenic	(TTATTT)n|Simple_repeat|Simple_repeat	-37960	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.001848	0.309326	
chunk0087_183_1	chr18	35517690	35518035	+	0	NA	Intergenic	Intergenic	-19871	NM_194281	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.002899	0.468208	154(AAGAACACAGTGTTCC,-,0.00),155(AGAACACAGTGTTCCA,+,0.00)
chunk0094_197_1	chr2	6332724	6333093	+	0	NA	Intergenic	L1PA6|LINE|L1	42514	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.005420	0.494595	
chunk0034_349_1	chr11	35901221	35902024	+	0	NA	Intergenic	L1MC4a|LINE|L1	-42359	NM_174902	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.003736	0.318408	
chunk0180_335_1	chr7	72924880	72925102	+	0	NA	intron (NM_001257190, intron 4 of 15)	CpG	29772	NR_033323	260294	Hs.510927	NM_148936	ENSG00000106133	NSUN5P2	NOL1R2|NSUN5C|WBSCR20B|WBSCR20C	NSUN5 pseudogene 2	pseudo	0.139640	0.645740	
chunk0067_327_1	chr15	48271478	48271830	+	0	NA	intron (NM_001184832, intron 19 of 26)	intron (NM_001184832, intron 19 of 26)	-59770	NM_001025248	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.005682	0.337110	
chunk0126_188_1	chr3	78328887	78329096	+	0	NA	Intergenic	Intergenic	690468	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004785	0.380952	
chunk0049_336_1	chr12	94954121	94954676	+	0	NA	Intergenic	Intergenic	49315	NM_001258338	55967	Hs.506374	NM_018838	ENSG00000184752	NDUFA12	B17.2|DAP13|MC1DN23	NADH:ubiquinone oxidoreductase subunit A12	protein-coding	0.001802	0.437050	256(CAGGACTCTGTGTTCC,-,0.00),257(AGGACTCTGTGTTCCC,+,0.00)
chunk0120_384_1	chr3	12276925	12277260	+	0	NA	Intergenic	L1MB7|LINE|L1	-10758	NM_005037	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.008955	0.416667	
chunk0085_64_1	chr18	1253802	1254204	+	0	NA	Intergenic	LTR101_Mam|LTR|ERVL	105626	NR_023927	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.007463	0.379653	
chunk0129_322_1	chr3	124107473	124108032	+	0	NA	intron (NM_003947, intron 1 of 33)	intron (NM_003947, intron 1 of 33)	13041	NM_003947	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.005367	0.498214	
chunk0133_67_1	chr3	166901226	166901479	+	0	NA	Intergenic	Intergenic	478931	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.000000	0.322835	
chunk0119_388_1	chr22	48428292	48428676	+	0	NA	Intergenic	Intergenic	-60976	NM_001082967	25817	Hs.436854	NM_015381	ENSG00000219438	TAFA5	FAM19A5|QLLK5208|TAFA-5|UNQ5208	TAFA chemokine like family member 5	protein-coding	0.023438	0.485714	
chunk0172_77_1	chr6	134428641	134428860	+	0	NA	TTS (NR_125852)	TTS (NR_125852)	-8966	NR_038217	154092	Hs.223718	NR_038216		LINC01010	-	long intergenic non-protein coding RNA 1010	ncRNA	0.031963	0.545455	
chunk0028_190_1	chr10	88570342	88570704	+	0	NA	intron (NM_001031709, intron 4 of 6)	intron (NM_001031709, intron 4 of 6)	12802	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.005525	0.380165	
chunk0072_237_1	chr15	95924157	95924439	+	0	NA	Intergenic	Intergenic	-401630	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.010638	0.540636	
chunk0134_210_1	chr3	178558646	178558868	+	0	NA	promoter-TSS (NM_005832)	promoter-TSS (NM_005832)	57	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.009009	0.439462	
chunk0189_173_1	chr8	23516948	23517211	+	0	NA	Intergenic	Intergenic	-11771	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.003802	0.424242	
chunk0018_335_1	chr1	221393977	221394683	+	0	NA	Intergenic	Intergenic	-58034	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.008499	0.405941	
chunk0016_119_1	chr1	196353201	196353904	+	0	NA	intron (NM_198503, intron 14 of 27)	intron (NM_198503, intron 14 of 27)	228929	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005690	0.345170	
chunk0045_31_1	chr12	44078356	44078585	+	0	NA	intron (NM_001286212, intron 3 of 6)	intron (NM_001286212, intron 3 of 6)	242609	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.017467	0.456522	
chunk0029_319_1	chr10	104340150	104340355	+	0	NA	Intergenic	L2c|LINE|L2	-1759	NM_001272013	85450	Hs.523252	NM_033397	ENSG00000148841	ITPRIP	DANGER|KIAA1754|bA127L20|bA127L20.2	inositol 1,4,5-trisphosphate receptor interacting protein	protein-coding	0.009756	0.451456	
chunk0145_94_1	chr4	145965405	145966021	+	0	NA	Intergenic	L1PA7|LINE|L1	-26753	NM_001306215	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.004870	0.371151	198(AGTACATTGTGTCTTT,+,0.00)
chunk0059_299_1	chr14	35944394	35944647	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	118129	NM_032352	84312	Hs.525299	NM_032352	ENSG00000100916	BRMS1L	BRMS1	BRMS1 like transcriptional repressor	protein-coding	0.000000	0.271654	
chunk0081_444_1	chr17	49101284	49101754	+	0	NA	Intergenic	Intergenic	-30941	NM_001159388	124872	Hs.374679	NM_153446	ENSG00000167080	B4GALNT2	B4GALT|GALGT2	beta-1,4-N-acetyl-galactosaminyltransferase 2	protein-coding	0.002128	0.477707	320(AAGGTCATTTTGTTCC,-,0.00),321(AGGTCATTTTGTTCCT,+,0.00)
chunk0020_193_1	chr1	234894272	234894720	+	0	NA	Intergenic	Intergenic	69503	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.008929	0.412027	
chunk0121_155_1	chr3	19256234	19256601	+	0	NA	intron (NM_144633, intron 2 of 15)	LTR89|LTR|ERVL?	58514	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.008174	0.421196	98(CAGACCATTGTGTCCT,-,0.00),99(AGACCATTGTGTCCTT,+,0.00)
chunk0123_179_1	chr3	44175043	44175442	+	0	NA	Intergenic	Intergenic	61030	NR_029700	406929		NR_029700	ENSG00000207954	MIR138-1	MIRN138-1|mir-138-1	microRNA 138-1	ncRNA	0.005013	0.350000	
chunk0205_246_1	chr9	110194296	110194594	+	0	NA	Intergenic	MER4C|LTR|ERV1	13688	NM_001012993	401546	Hs.125608	NM_001012993	ENSG00000188959	C9orf152	bA470J20.2	chromosome 9 open reading frame 152	protein-coding	0.006711	0.381271	
chunk0055_34_1	chr13	52025500	52026065	+	0	NA	intron (NM_001004127, intron 3 of 3)	intron (NM_001004127, intron 3 of 3)	1091	NM_021645	9724	Hs.512963	NM_021645	ENSG00000253797	UTP14C	2700066J21Rik|KIAA0266|UTP14B	UTP14C small subunit processome component	protein-coding	0.003540	0.427562	
chunk0173_84_1	chr6	142829875	142830219	+	0	NA	intron (NM_006734, intron 2 of 9)	intron (NM_006734, intron 2 of 9)	115154	NM_006734	3097	Hs.510172	NM_006734	ENSG00000010818	HIVEP2	HIV-EP2|MBP-2|MIBP1|MRD43|SHN2|ZAS2|ZNF40B	human immunodeficiency virus type I enhancer binding protein 2	protein-coding	0.000000	0.307246	
chunk0013_351_1	chr1	172225719	172226616	+	0	NA	intron (NM_001136127, intron 14 of 19)	L1ME3G|LINE|L1	-81332	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.002230	0.318486	718(CAGGACATATTGTACT,-,0.00),719(AGGACATATTGTACTA,+,0.00)
chunk0193_386_1	chr8	80330815	80331014	+	0	NA	Intergenic	Intergenic	89525	NR_049894	100847056		NR_049894	ENSG00000265588	MIR5708	-	microRNA 5708	ncRNA	0.005025	0.485000	
chunk0155_91_1	chr5	92308168	92308954	+	0	NA	Intergenic	Intergenic	-925229	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.326557	
chunk0083_313_1	chr17	69485961	69486672	+	0	NA	intron (NM_002758, intron 1 of 11)	intron (NM_002758, intron 1 of 11)	71619	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.005626	0.404494	
chunk0081_301_1	chr17	45158312	45158784	+	0	NA	Intergenic	Intergenic	-1626	NM_001303437	124790	Hs.56382	NM_144608	ENSG00000168517	HEXIM2	L3	HEXIM P-TEFb complex subunit 2	protein-coding	0.004237	0.391121	
chunk0074_232_1	chr16	27203327	27203666	+	0	NA	promoter-TSS (NM_001145348)	promoter-TSS (NM_001145348)	10	NM_024773	79831	Hs.145717	NM_024773	ENSG00000155666	KDM8	JMJD5	lysine demethylase 8	protein-coding	0.073746	0.582353	
chunk0092_192_1	chr19	30556624	30556823	+	0	NA	intron (NM_014717, intron 4 of 4)	intron (NM_014717, intron 4 of 4)	184330	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.005025	0.415000	
chunk0124_256_1	chr3	56955414	56956035	+	0	NA	intron (NR_046572, intron 2 of 2)	intron (NR_046572, intron 2 of 2)	15684	NR_046572	100874200	Hs.549631	NR_046572	ENSG00000240198	ARHGEF3-AS1	-	ARHGEF3 antisense RNA 1	ncRNA	0.008052	0.463023	240(AAGCACACCCTGCCCT,-,0.00),241(AGCACACCCTGCCCTA,+,0.00)
chunk0057_357_1	chr13	108643543	108644000	+	0	NA	intron (NM_001198950, intron 1 of 34)	L1ME1|LINE|L1	14548	NM_001198950	23026	Hs.656587	NM_015011	ENSG00000041515	MYO16	MYAP3|MYR8|Myo16b|NYAP3|PPP1R107	myosin XVI	protein-coding	0.004376	0.362445	
chunk0048_122_1	chr12	79847320	79847880	+	0	NA	intron (NM_001244990, intron 3 of 24)	L2a|LINE|L2	66311	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.001786	0.317291	
chunk0146_335_1	chr4	165873246	165873679	+	0	NA	5' UTR (NM_001204760, exon 1 of 10)	5' UTR (NM_001204760, exon 1 of 10)	204	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.103926	0.679724	
chunk0137_237_1	chr4	20403832	20404471	+	0	NA	intron (NM_001289135, intron 4 of 35)	intron (NM_001289135, intron 4 of 35)	11962	NR_037876	100505893	Hs.665305	NR_037876	ENSG00000248228	SLIT2-IT1	-	SLIT2 intronic transcript 1	ncRNA	0.004695	0.334375	
chunk0021_67_1	chr10	1324697	1325408	+	0	NA	intron (NM_018702, intron 3 of 9)	intron (NM_018702, intron 3 of 9)	165284	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.023910	0.516854	508(GTGGACACAGAGTCCT,-,0.00),509(TGGACACAGAGTCCTC,+,0.00)
chunk0019_170_1	chr1	226134996	226135438	+	0	NA	Intergenic	L2b|LINE|L2	51505	NM_022735	64746	Hs.520207	NM_022735	ENSG00000182827	ACBD3	GCP60|GOCAP1|GOLPH1|PAP7	acyl-CoA binding domain containing 3	protein-coding	0.045249	0.598194	
chunk0179_107_1	chr7	45007062	45007643	+	0	NA	intron (NM_001167934, intron 1 of 8)	intron (NM_001167934, intron 1 of 8)	7164	NM_031443	83605	Hs.148272	NM_031443	ENSG00000136280	CCM2	C7orf22|OSM|PP10187	CCM2 scaffold protein	protein-coding	0.012048	0.441581	
chunk0034_251_1	chr11	34274867	34275071	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	83039	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.029412	0.600000	
chunk0148_119_1	chr5	5174983	5175182	+	0	NA	intron (NM_139056, intron 3 of 22)	L1M1|LINE|L1	34752	NM_139056	170690	Hs.661915	NM_139056	ENSG00000145536	ADAMTS16	ADAMTS16s	ADAM metallopeptidase with thrombospondin type 1 motif 16	protein-coding	0.010050	0.485000	
chunk0051_368_1	chr12	121403760	121403999	+	0	NA	intron (NM_194271, intron 2 of 6)	intron (NM_194271, intron 2 of 6)	3761	NM_194271	80196	Hs.292804	NM_025126	ENSG00000170633	RNF34	CARP-1|CARP1|RFI|RIF|RIFF|hRFI	ring finger protein 34	protein-coding	0.008368	0.300000	
chunk0204_58_1	chr9	93365573	93365776	+	0	NA	Intergenic	Intergenic	-19260	NM_001098808	445577	Hs.575636	NM_001098808	ENSG00000204352	C9orf129	bA165J3.3	chromosome 9 open reading frame 129	protein-coding	0.009852	0.573529	
chunk0038_131_1	chr11	84106583	84106976	+	0	NA	intron (NM_001142699, intron 9 of 27)	intron (NM_001142699, intron 9 of 27)	166501	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.398477	
chunk0163_81_1	chr6	9418322	9418739	+	0	NA	Intergenic	UCON27|Unknown|Unknown	766321	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.002398	0.339713	
chunk0007_359_1	chr1	84936595	84937207	+	0	NA	intron (NM_153259, intron 11 of 13)	MIRb|SINE|MIR	-43688	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.004902	0.370310	
chunk0074_374_1	chr16	34592760	34593489	+	0	NA	Intergenic	Intergenic	-433088	NR_038368									0.039781	0.364384	
chunk0162_236_1	chr6	4770290	4770658	+	0	NA	intron (NR_026590, intron 3 of 8)	MIR|SINE|MIR	-5972	NM_004824	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.008152	0.349593	
chunk0008_116_1	chr1	91579704	91580305	+	0	NA	Intergenic	Intergenic	78896	NM_001134420	8317	Hs.533573	NM_003503	ENSG00000097046	CDC7	CDC7L1|HsCDC7|Hsk1|huCDC7	cell division cycle 7	protein-coding	0.008319	0.378738	
chunk0062_76_1	chr14	67702272	67702746	+	0	NA	intron (NM_152443, intron 1 of 8)	LTR57-int|LTR|ERVL	623	NM_152443	145226	Hs.415322	NM_152443	ENSG00000139988	RDH12	LCA13|RP53|SDR7C2	retinol dehydrogenase 12	protein-coding	0.000000	0.265263	
chunk0011_198_1	chr1	149996062	149996337	+	0	NA	intron (NM_020205, intron 1 of 11)	intron (NM_020205, intron 1 of 11)	14538	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.007273	0.438406	161(CAGGTCACACTGTCCA,-,0.00),162(AGGTCACACTGTCCAG,+,0.00)
chunk0075_155_1	chr16	51550173	51550374	+	0	NA	Intergenic	Intergenic	-212246	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.004975	0.386139	
chunk0198_241_1	chr8	134356520	134357030	+	0	NA	Intergenic	Intergenic	-241296	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.003922	0.305284	
chunk0208_234_1	chrX	19623769	19624046	+	0	NA	intron (NM_001184960, intron 3 of 12)	intron (NM_001184960, intron 3 of 12)	47094	NM_001184960	30011	Hs.726365	NM_031892	ENSG00000147010	SH3KBP1	AGMX2|CD2BP3|CIN85|GIG10|HSB-1|HSB1|IMD61|MIG18	SH3 domain containing kinase binding protein 1	protein-coding	0.003610	0.345324	
chunk0144_148_1	chr4	130109959	130110532	+	0	NA	Intergenic	Intergenic	-338767	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.001745	0.348432	
chunk0018_71_1	chr1	217107696	217107906	+	0	NA	intron (NM_001134285, intron 1 of 8)	intron (NM_001134285, intron 1 of 8)	-17947	NM_001243505	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.312796	
chunk0166_105_1	chr6	43874423	43874622	+	0	NA	Intergenic	Intergenic	-16506	NR_024478	100132354	Hs.376232	NR_024478		LINC01512	HI-LNC77	long intergenic non-protein coding RNA 1512	ncRNA	0.010050	0.565000	
chunk0042_405_1	chr12	11615673	11615872	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-34082	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.000000	0.450000	
chunk0193_20_1	chr8	70667613	70668393	+	0	NA	intron (NM_016027, intron 1 of 6)	intron (NM_016027, intron 1 of 6)	1209	NM_016027	51110	Hs.118554	NM_016027	ENSG00000147592	LACTB2	CGI-83	lactamase beta 2	protein-coding	0.005128	0.373880	324(CAAGACAGACTGTACC,-,0.00),325(AAGACAGACTGTACCC,+,0.00)
chunk0141_378_1	chr4	88177781	88178082	+	0	NA	intron (NM_001257386, intron 1 of 15)	L1MA4|LINE|L1	-19072	NM_004827	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.013289	0.480132	
chunk0120_252_1	chr3	8910014	8910345	+	0	NA	intron (NM_020165, intron 9 of 12)	HAL1|LINE|L1	53296	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.006042	0.394578	
chunk0004_291_1	chr1	48878517	48879059	+	0	NA	intron (NM_032785, intron 5 of 13)	intron (NM_032785, intron 5 of 13)	-101819	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.009225	0.419890	
chunk0097_147_1	chr2	48116237	48116653	+	0	NA	Intergenic	Intergenic	-198211	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.004808	0.417266	
chunk0034_6_1	chr11	25918939	25919533	+	0	NA	Intergenic	Intergenic	-269887	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.008418	0.332773	
chunk0105_56_1	chr2	183316893	183317459	+	0	NA	Intergenic	L2c|LINE|L2	192821	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.003534	0.356261	
chunk0180_71_1	chr7	54935497	54936044	+	0	NA	Intergenic	Intergenic	-83262	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.005484	0.392336	
chunk0093_423_1	chr19	57804985	57805422	+	0	NA	Intergenic	LTR10C|LTR|ERV1	9710	NM_024762	79818	Hs.560727	NM_024762	ENSG00000178935	ZNF552	-	zinc finger protein 552	protein-coding	0.016018	0.420091	
chunk0175_67_1	chr7	2073981	2074245	+	0	NA	intron (NM_003550, intron 11 of 18)	intron (NM_003550, intron 11 of 18)	-133563	NM_001304525	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.041667	0.573585	
chunk0045_283_1	chr12	50021553	50022170	+	0	NA	intron (NM_013277, intron 1 of 18)	intron (NM_013277, intron 1 of 18)	3663	NM_013277	29127	Hs.505469	NM_013277	ENSG00000161800	RACGAP1	CYK4|HsCYK-4|ID-GAP|MgcRacGAP	Rac GTPase activating protein 1	protein-coding	0.003241	0.357605	
chunk0079_143_1	chr17	13134173	13134671	+	0	NA	Intergenic	Intergenic	-116358	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.006024	0.424850	332(GAGCACTCTGTGTCCT,-,0.00),333(AGCACTCTGTGTCCTA,+,0.00)
chunk0208_372_1	chrX	27512660	27512859	+	0	NA	Intergenic	L1MA6|LINE|L1	-49418	NR_002784									0.000000	0.290000	
chunk0192_253_1	chr8	65807884	65808296	+	0	NA	intron (NM_001242318, intron 1 of 12)	MER63A|DNA|hAT-Blackjack	-18996	NM_002603	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.002427	0.394673	271(AGGAACATTCAGTGCT,-,0.00),272(GGAACATTCAGTGCTA,+,0.00)
chunk0156_74_1	chr5	103703516	103703974	+	0	NA	Intergenic	Intergenic	-140944	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.006550	0.346405	
chunk0177_326_1	chr7	26374517	26375067	+	0	NA	TTS (NM_013322)	TTS (NM_013322)	10467	NM_001199838	29887	Hs.741316	NM_013322	ENSG00000086300	SNX10	OPTB8	sorting nexin 10	protein-coding	0.005455	0.299456	
chunk0142_18_1	chr4	90347171	90347466	+	0	NA	intron (NM_001145065, intron 3 of 10)	(TCTA)n|Simple_repeat|Simple_repeat	112287	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.000000	0.310811	
chunk0066_48_1	chr15	28102874	28103498	+	0	NA	Intergenic	L1MC1|LINE|L1	-3874	NM_001300984	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.016026	0.409600	
chunk0185_298_1	chr7	131157767	131158493	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	48034	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.017906	0.474553	704(GTGTACATACTGTGCT,-,0.00),705(TGTACATACTGTGCTT,+,0.00)
chunk0051_431_1	chr12	122926018	122926217	+	0	NA	intron (NM_203444, intron 11 of 11)	L1MB5|LINE|L1	-29952	NM_024667	79720	Hs.507162	NM_024667	ENSG00000139722	VPS37B	-	VPS37B subunit of ESCRT-I	protein-coding	0.005025	0.430000	
chunk0173_205_1	chr6	145380213	145380682	+	0	NA	Intergenic	L1M4|LINE|L1	-354422	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.002132	0.336170	
chunk0045_125_1	chr12	46340478	46341000	+	0	NA	Intergenic	L1PB1|LINE|L1	32123	NM_001307936	54407	Hs.221847	NM_018976	ENSG00000134294	SLC38A2	ATA2|PRO1068|SAT2|SNAT2	solute carrier family 38 member 2	protein-coding	0.003831	0.363289	
chunk0150_116_1	chr5	32934355	32934580	+	0	NA	Intergenic	Intergenic	-12976	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.008889	0.477876	
chunk0079_445_1	chr17	20190572	20191555	+	0	NA	intron (NM_001033554, intron 1 of 5)	L1MC1|LINE|L1	35069	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.007121	0.417683	
chunk0055_387_1	chr13	73365623	73365898	+	0	NA	Intergenic	Intergenic	-198484	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.014545	0.391304	
chunk0088_324_1	chr18	50982161	50983190	+	0	NA	intron (NM_018696, intron 2 of 3)	intron (NM_018696, intron 2 of 3)	14658	NM_018696	55520	Hs.657360	NM_018696	ENSG00000141642	ELAC1	D29	elaC ribonuclease Z 1	protein-coding	0.008746	0.416505	844(TGGAACATTTTGTTTT,-,0.00),845(GGAACATTTTGTTTTC,+,0.00)
chunk0066_22_1	chr15	27412449	27412819	+	0	NA	intron (NM_033223, intron 5 of 9)	intron (NM_033223, intron 5 of 9)	-251315	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.013514	0.393531	
chunk0093_125_1	chr19	45210648	45211229	+	0	NA	Intergenic	AluJr|SINE|Alu	23273	NM_138568	90332	Hs.337557	NM_138568	ENSG00000283632	EXOC3L2	XTP7	exocyst complex component 3 like 2	protein-coding	0.012048	0.486254	
chunk0017_372_1	chr1	212060778	212061231	+	0	NA	intron (NM_016448, intron 5 of 14)	L1MA4A|LINE|L1	-8953	NR_026911	100131205	Hs.126774	NR_026911	ENSG00000220749	RPL21P28	RPL21_8_160	ribosomal protein L21 pseudogene 28	pseudo	0.006623	0.381057	
chunk0052_146_1	chr13	23788454	23788961	+	0	NA	intron (NM_005932, intron 16 of 18)	intron (NM_005932, intron 16 of 18)	-100182	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.003945	0.407480	
chunk0186_146_1	chr7	138961119	138961394	+	0	NA	intron (NM_020910, intron 1 of 19)	intron (NM_020910, intron 1 of 19)	20062	NM_001164665	57670	Hs.605380	NM_020910	ENSG00000122778	KIAA1549	-	KIAA1549	protein-coding	0.010909	0.485507	
chunk0073_73_1	chr16	3795355	3795711	+	0	NA	intron (NM_001079846, intron 3 of 29)	intron (NM_001079846, intron 3 of 29)	-77936	NM_001272049	10131	Hs.30345	NM_016292	ENSG00000126602	TRAP1	HSP 75|HSP75|HSP90L|TRAP-1	TNF receptor associated protein 1	protein-coding	0.008427	0.392157	
chunk0088_458_1	chr18	57276665	57276875	+	0	NA	Intergenic	Intergenic	-75720	NM_015879	51046	Hs.23172	NM_015879	ENSG00000177511	ST8SIA3	SIAT8C|ST8SiaIII	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.009524	0.355450	
chunk0081_250_1	chr17	43251585	43251827	+	0	NA	TTS (NR_002716).5	TTS (NR_002716).5	313	NR_002716	6066		NR_002716	ENSG00000274585	RNU2-1	RNU2|U2	RNA, U2 small nuclear 1	snRNA	0.078512	0.588477	
chunk0147_192_1	chr4	177567839	177568200	+	0	NA	Intergenic	Intergenic	-125516	NM_000027	175	Hs.207776	NM_000027	ENSG00000038002	AGA	AGU|ASRG|GA	aspartylglucosaminidase	protein-coding	0.022161	0.417127	
chunk0043_15_1	chr12	12947025	12947229	+	0	NA	intron (NM_018654, intron 1 of 2)	intron (NM_018654, intron 1 of 2)	3257	NM_018654	55507	Hs.644599	NM_018654	ENSG00000111291	GPRC5D	-	G protein-coupled receptor class C group 5 member D	protein-coding	0.009804	0.443902	
chunk0005_389_1	chr1	62144352	62144561	+	0	NA	intron (NM_176877, intron 41 of 42)	L3|LINE|CR1	-50346	NM_019079	54596	Hs.685462	NM_019079	ENSG00000240563	L1TD1	ECAT11	LINE1 type transposase domain containing 1	protein-coding	0.004785	0.419048	
chunk0183_216_1	chr7	106611883	106612123	+	0	NA	Intergenic	L2a|LINE|L2	49185	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.008333	0.410788	
chunk0015_461_1	chr1	192631715	192632113	+	0	NA	Intergenic	Intergenic	-4224	NM_002927	6003	Hs.497220	NM_002927	ENSG00000127074	RGS13	-	regulator of G protein signaling 13	protein-coding	0.000000	0.310777	
chunk0035_315_1	chr11	47269722	47269987	+	0	NA	promoter-TSS (NM_130476)	promoter-TSS (NM_130476)	206	NM_130474	8567	Hs.82548	NM_003682	ENSG00000110514	MADD	DENN|IG20|RAB3GEP	MAP kinase activating death domain	protein-coding	0.094340	0.665414	
chunk0145_20_1	chr4	143412341	143412714	+	0	NA	intron (NM_002039, intron 1 of 9)	L2c|LINE|L2	69067	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.008043	0.377005	
chunk0024_353_1	chr10	43628130	43629196	+	0	NA	promoter-TSS (NR_038867)	promoter-TSS (NR_038867)	-154	NR_038867	414201	Hs.666576	NR_038867	ENSG00000223910	ZNF32-AS3	C10orf44|ZNF32-OT1|bA402L1.3	ZNF32 antisense RNA 3	ncRNA	0.005629	0.428304	
chunk0110_458_1	chr20	21310023	21310284	+	0	NA	intron (NM_012255, intron 1 of 29)	L1ME1|LINE|L1	6849	NM_012255	22803	Hs.255932	NM_012255	ENSG00000088930	XRN2	-	5'-3' exoribonuclease 2	protein-coding	0.007663	0.335878	
chunk0073_12_1	chr16	2047273	2047562	+	0	NA	promoter-TSS (NM_001077183)	promoter-TSS (NM_001077183)	449	NM_002528	4913	Hs.66196	NM_002528	ENSG00000065057	NTHL1	FAP3|NTH1|OCTS3|hNTH1	nth like DNA glycosylase 1	protein-coding	0.048443	0.620690	104(GAGGACAGCAAGTTCA,-,0.00),105(AGGACAGCAAGTTCAC,+,0.00)
chunk0075_453_1	chr16	58369709	58369908	+	0	NA	Intergenic	Intergenic	-22586	NM_001126129	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.015075	0.385000	
chunk0017_234_1	chr1	208075401	208075677	+	0	NA	intron (NM_025179, intron 12 of 31)	L1MC4a|LINE|L1	-164201	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.003623	0.350181	
chunk0115_150_1	chr21	23671903	23672292	+	0	NA	Intergenic	Intergenic	-287262	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.010283	0.407692	
chunk0127_54_1	chr3	89155173	89155617	+	0	NA	intron (NM_005233, intron 2 of 16)	MIRb|SINE|MIR	47871	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.002252	0.287640	
chunk0207_71_1	chrX	9164985	9165184	+	0	NA	Intergenic	L1ME2z|LINE|L1	-130957	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.005025	0.370000	
chunk0110_324_1	chr20	19047852	19048313	+	0	NA	Intergenic	Intergenic	-164564	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.008677	0.482684	319(AGGACATGGTCTTCCT,+,0.00)
chunk0116_128_1	chr21	36163295	36164066	+	0	NA	promoter-TSS (NM_005128)	promoter-TSS (NM_005128)	-861	NM_005128	9980	Hs.204575	NM_005128	ENSG00000142197	DOP1B	21orf5|C21orf5|DOPEY2	DOP1 leucine zipper like protein B	protein-coding	0.014267	0.426166	
chunk0166_403_1	chr6	52012972	52013558	+	0	NA	intron (NM_138694, intron 34 of 66)	L3|LINE|CR1	74360	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.001706	0.391823	302(AGGAACACACTGTTTT,-,0.00),303(GGAACACACTGTTTTC,+,0.00)
chunk0034_300_1	chr11	34944458	34944732	+	0	NA	intron (NM_001166158, intron 2 of 5)	intron (NM_001166158, intron 2 of 5)	2758	NR_039836	100616437		NR_039836	ENSG00000251862	MIR1343	-	microRNA 1343	ncRNA	0.003650	0.290909	152(AAGTACTTTCTGTACT,-,0.00),153(AGTACTTTCTGTACTG,+,0.00)
chunk0107_164_1	chr2	215397907	215398133	+	0	NA	intron (NM_001306131, intron 21 of 44)	intron (NM_001306131, intron 21 of 44)	38048	NM_212476	2335	Hs.203717	NM_002026	ENSG00000115414	FN1	CIG|ED-B|FINC|FN|FNZ|GFND|GFND2|LETS|MSF|SMDCF	fibronectin 1	protein-coding	0.000000	0.383260	
chunk0166_166_1	chr6	45827852	45828574	+	0	NA	Intergenic	MIR3|SINE|MIR	109384	NR_045674	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.015235	0.423237	273(CAGGACAAATTGTGCT,-,0.00),274(AGGACAAATTGTGCTC,+,0.00)
chunk0158_100_1	chr5	126700617	126701139	+	0	NA	Intergenic	MIR|SINE|MIR	69156	NM_207408	389320	Hs.177983	NM_207408	ENSG00000196900	TEX43	C5orf48|Tseg7	testis expressed 43	protein-coding	0.011494	0.422562	
chunk0129_328_1	chr3	124552222	124552706	+	0	NA	intron (NM_001024660, intron 33 of 59)	intron (NM_001024660, intron 33 of 59)	-32195	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.012397	0.465979	
chunk0166_177_1	chr6	46062028	46062819	+	0	NA	intron (NM_001114086, intron 1 of 5)	intron (NM_001114086, intron 1 of 5)	17925	NM_001114086	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.006321	0.419192	
chunk0062_333_1	chr14	73413613	73414034	+	0	NA	intron (NM_001005743, intron 1 of 12)	intron (NM_001005743, intron 1 of 12)	44757	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.014252	0.421801	
chunk0076_417_1	chr16	72924915	72925414	+	0	NA	intron (NM_006885, intron 3 of 9)	intron (NM_006885, intron 3 of 9)	123211	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.026052	0.508000	188(TTGTACAATCTGTGCT,-,0.00),189(TGTACAATCTGTGCTT,+,0.00)
chunk0104_27_1	chr2	170679423	170680205	+	0	NA	Intergenic	Intergenic	34753	NR_027433	440925	Hs.668461	NM_001013712	ENSG00000222033	LINC01124	-	long intergenic non-protein coding RNA 1124	ncRNA	0.012788	0.401022	
chunk0177_40_1	chr7	20916840	20918088	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	82033	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.009615	0.369095	
chunk0078_396_1	chr16	88510196	88510732	+	0	NA	intron (NM_153813, intron 3 of 9)	intron (NM_153813, intron 3 of 9)	41546	NR_049821	100847057		NR_049821	ENSG00000263456	MIR5189	mir-5189	microRNA 5189	ncRNA	0.024254	0.599628	
chunk0047_253_1	chr12	72456250	72456449	+	0	NA	intron (NM_013381, intron 3 of 18)	intron (NM_013381, intron 3 of 18)	-182840	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.000000	0.405000	
chunk0097_18_1	chr2	42084105	42084690	+	0	NA	Intergenic	Intergenic	36376	NM_138370	91461	Hs.408542	NM_138370	ENSG00000162878	PKDCC	SGK493|Vlk	protein kinase domain containing, cytoplasmic	protein-coding	0.011966	0.510239	393(TGGATCACCCTGTCCT,-,0.00),394(GGATCACCCTGTCCTT,+,0.00)
chunk0205_307_1	chr9	112404295	112404977	+	0	NA	intron (NM_032303, intron 2 of 10)	intron (NM_032303, intron 2 of 10)	24727	NM_032303	84263	Hs.59486	NM_032303	ENSG00000119471	HSDL2	C9orf99|SDR13C1	hydroxysteroid dehydrogenase like 2	protein-coding	0.011730	0.420205	
chunk0104_88_1	chr2	172088552	172089328	+	0	NA	3' UTR (NM_001038493, exon 2 of 2)	3' UTR (NM_001038493, exon 2 of 2)	3460	NM_001038493	1745	Hs.407015	NM_178120	ENSG00000144355	DLX1	-	distal-less homeobox 1	protein-coding	0.030928	0.459459	354(AGGAACGCACTGTTCA,-,0.00),355(GGAACGCACTGTTCAA,+,0.00)
chunk0189_92_1	chr8	21458149	21458413	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	160042	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.011364	0.430189	
chunk0179_175_1	chr7	46908677	46909329	+	0	NA	Intergenic	Intergenic	673141	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.001534	0.422665	578(CTGGACAAGGTGTTCA,-,0.00),579(TGGACAAGGTGTTCAT,+,0.00)
chunk0077_185_1	chr16	79712031	79712588	+	0	NA	Intergenic	Intergenic	-58162	NR_104660	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.010772	0.439068	214(AGGGACTTTGTGTTCC,-,0.00),215(GGGACTTTGTGTTCCC,+,0.00)
chunk0142_147_1	chr4	94935884	94936207	+	0	NA	intron (NM_001203, intron 2 of 12)	intron (NM_001203, intron 2 of 12)	-60187	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.006192	0.333333	212(TGGAACATTTTGTGCT,-,0.00),213(GGAACATTTTGTGCTA,+,0.00)
chunk0015_338_1	chr1	189841792	189842276	+	0	NA	Intergenic	L1MA8|LINE|L1	635595	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004132	0.311340	
chunk0121_453_1	chr3	26874612	26874837	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	251915	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.017778	0.482301	
chunk0206_198_1	chr9	123028383	123028650	+	0	NA	intron (NM_012197, intron 13 of 25)	intron (NM_012197, intron 13 of 25)	-5127	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.003745	0.417910	183(GAGAACAGCGTGTACT,-,0.00),184(AGAACAGCGTGTACTC,+,0.00)
chunk0145_386_1	chr4	151760802	151761114	+	0	NA	promoter-TSS (NM_004564)	promoter-TSS (NM_004564)	65	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.064103	0.597444	
chunk0138_329_1	chr4	41575199	41576069	+	0	NA	intron (NM_001112717, intron 3 of 25)	intron (NM_001112717, intron 3 of 25)	-37138	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.005747	0.355913	320(GAGAACACTCTGTACT,-,0.00),321(AGAACACTCTGTACTT,+,0.00),724(TGGAACTATTTGTTCT,-,0.00),725(GGAACTATTTGTTCTC,+,0.00)
chunk0061_271_1	chr14	61491142	61491760	+	0	NA	intron (NM_006255, intron 10 of 13)	intron (NM_006255, intron 10 of 13)	78743	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.003236	0.426494	
chunk0054_129_1	chr13	43494311	43494627	+	0	NA	intron (NM_001242863, intron 2 of 16)	intron (NM_001242863, intron 2 of 16)	45617	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.009494	0.340694	
chunk0170_333_1	chr6	116255237	116255701	+	0	NA	Intergenic	Intergenic	-1371	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.010776	0.389247	218(AAGGACAATGTGTCCA,-,0.00),219(AGGACAATGTGTCCAG,+,0.00)
chunk0040_117_1	chr11	112175476	112175675	+	0	NA	promoter-TSS (NM_001256400)	promoter-TSS (NM_001256400)	90	NM_001256398	83875	Hs.728325	NM_031938	ENSG00000197580	BCO2	B-DIOX-II|BCDO2	beta-carotene oxygenase 2	protein-coding	0.010050	0.450000	
chunk0092_356_1	chr19	35495337	35495779	+	0	NA	Intergenic	Intergenic	-5027	NM_207392	388533	Hs.112457	NM_207392	ENSG00000188508	KRTDAP	KDAP|UNQ467	keratinocyte differentiation associated protein	protein-coding	0.045249	0.620767	
chunk0154_112_1	chr5	78696681	78697227	+	0	NA	Intergenic	L1MD2|LINE|L1	-48129	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.001832	0.396709	
chunk0038_312_1	chr11	91366180	91366805	+	0	NA	Intergenic	Intergenic	-497290	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.008000	0.400958	231(CAGGACAGACCGTACT,-,0.00),232(AGGACAGACCGTACTT,+,0.00)
chunk0077_223_1	chr16	80248632	80249041	+	0	NA	intron (NR_120307, intron 2 of 5)	MER53|DNA|hAT	-291898	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.000000	0.329268	
chunk0112_381_1	chr20	46260651	46260862	+	0	NA	intron (NM_021248, intron 1 of 11)	intron (NM_021248, intron 1 of 11)	47742	NM_021248	64405	Hs.472861	NM_021248	ENSG00000149654	CDH22	C20orf25|dJ998H6.1	cadherin 22	protein-coding	0.009479	0.547170	
chunk0056_83_1	chr13	79865055	79865416	+	0	NA	Intergenic	Intergenic	-7351	NR_120413	101927195	Hs.342412	NR_120413	ENSG00000229175	LINC00382	TCONS_00021500	long intergenic non-protein coding RNA 382	ncRNA	0.008310	0.364641	
chunk0098_414_1	chr2	80018245	80018444	+	0	NA	intron (NM_004389, intron 7 of 17)	intron (NM_004389, intron 7 of 17)	-151761	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.015075	0.380000	
chunk0079_65_1	chr17	11205230	11205717	+	0	NA	Intergenic	L2c|LINE|L2	-35950	NM_001173462	388336	Hs.592124	NM_175903	ENSG00000188803	SHISA6	-	shisa family member 6	protein-coding	0.014374	0.395492	172(ATAACACTTTGTTCCG,+,0.00)
chunk0138_208_1	chr4	38728609	38729160	+	0	NA	Intergenic	Intergenic	54106	NM_001017388	81793	Hs.120551	NM_030956	ENSG00000174123	TLR10	CD290	toll like receptor 10	protein-coding	0.007260	0.510870	
chunk0178_330_1	chr7	38291593	38292314	+	0	NA	Intergenic	Intergenic	-18306	NM_001003806	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.005548	0.441828	
chunk0093_31_1	chr19	39332388	39332587	+	0	NA	intron (NM_004877, intron 4 of 6)	L1MD|LINE|L1	3599	NM_004877	9535	Hs.5210	NM_004877	ENSG00000130755	GMFG	GMF-GAMMA	glia maturation factor gamma	protein-coding	0.020101	0.385000	
chunk0212_253_1	chrX	139063234	139063978	+	0	NA	intron (NM_001139501, intron 2 of 7)	L1MEd|LINE|L1	141417	NM_001139500	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.004032	0.332886	
chunk0027_434_1	chr10	81007846	81008189	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	467198	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.002915	0.380814	
chunk0119_254_1	chr22	45809328	45809928	+	0	NA	intron (NM_001167621, intron 9 of 10)	intron (NM_001167621, intron 9 of 10)	49104	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.005000	0.349418	
chunk0032_40_1	chr11	1238929	1239218	+	0	NA	intron (NM_002458, intron 26 of 48)	intron (NM_002458, intron 26 of 48)	16008	NM_002458	727897	Hs.523395	NM_002458	ENSG00000117983	MUC5B	MG1|MUC-5B|MUC5|MUC9	mucin 5B, oligomeric mucus/gel-forming	protein-coding	0.051903	0.631034	
chunk0025_261_1	chr10	55369419	55369663	+	0	NA	Intergenic	Intergenic	-229449	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.004098	0.285714	
chunk0050_147_1	chr12	102646013	102646389	+	0	NA	Intergenic	L2c|LINE|L2	-165556	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.002660	0.374005	
chunk0141_372_1	chr4	88078830	88079029	+	0	NA	Intergenic	L1ME4a|LINE|L1	71282	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.005025	0.285000	
chunk0063_345_1	chr14	85407112	85407570	+	0	NA	intron (NR_102738, intron 1 of 1)	intron (NR_102738, intron 1 of 1)	13426	NR_102738	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.006550	0.403050	96(AAGAACAGTTTGTGTC,-,0.00),97(AGAACAGTTTGTGTCT,+,0.00)
chunk0064_159_1	chr14	91963326	91963871	+	0	NA	Intergenic	Intergenic	-15896	NM_006329	10516	Hs.332708	NM_006329	ENSG00000140092	FBLN5	ADCL2|ARCL1A|ARMD3|DANCE|EVEC|FIBL-5|HNARMD|UP50	fibulin 5	protein-coding	0.014679	0.338828	307(GAGTACAGTACGTTCC,-,0.00),308(AGTACAGTACGTTCCC,+,0.00)
chunk0076_176_1	chr16	67451736	67452264	+	0	NA	intron (NM_004691, intron 2 of 7)	intron (NM_004691, intron 2 of 7)	20867	NM_000196	3291	Hs.1376	NM_000196	ENSG00000176387	HSD11B2	AME|AME1|HSD11K|HSD2|SDR9C3	hydroxysteroid 11-beta dehydrogenase 2	protein-coding	0.003788	0.570888	
chunk0083_247_1	chr17	67779193	67779736	+	0	NA	Intergenic	Intergenic	38794	NR_003706	100124536	Hs.693446	NR_003706	ENSG00000200394	SNORA38B	-	small nucleolar RNA, H/ACA box 38B	snoRNA	0.018416	0.534926	307(TAGGACTCCATGTGCT,-,0.00),308(AGGACTCCATGTGCTC,+,0.00)
chunk0144_142_1	chr4	129841184	129841962	+	0	NA	Intergenic	Intergenic	-70095	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.001285	0.304236	
chunk0011_192_1	chr1	149899310	149899743	+	0	NA	promoter-TSS (NM_016074)	promoter-TSS (NM_016074)	-76	NM_016074	51027	Hs.13880	NM_016074	ENSG00000178096	BOLA1	CGI-143	bolA family member 1	protein-coding	0.046189	0.541475	
chunk0187_10_1	chr8	555506	555998	+	0	NA	Intergenic	MER31A|LTR|ERV1	-9971	NM_175075	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.004065	0.466531	
chunk0102_119_1	chr2	144869277	144869930	+	0	NA	intron (NR_033870, intron 2 of 4)	intron (NR_033870, intron 2 of 4)	201636	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.006126	0.399083	
chunk0135_277_1	chr3	189342996	189343654	+	0	NA	Intergenic	Intergenic	-102731	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.003040	0.383915	
chunk0185_292_1	chr7	131067016	131067405	+	0	NA	intron (NR_109854, intron 2 of 5)	intron (NR_109854, intron 2 of 5)	39820	NR_024153	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.017995	0.484615	
chunk0213_20_1	chrY	21672350	21672894	+	0	NA	Intergenic	Intergenic	-77956	NR_001537	83868	Hs.615432	NR_001537	ENSG00000184991	TTTY13	NCRNA00136|TTY13	testis-specific transcript, Y-linked 13	ncRNA	0.018382	0.392661	
chunk0083_365_1	chr17	70933649	70934191	+	0	NA	Intergenic	Intergenic	268259	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.016605	0.344383	
chunk0033_453_1	chr11	25631920	25632572	+	0	NA	Intergenic	Intergenic	-556877	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.001534	0.326187	
chunk0035_12_1	chr11	40186521	40186849	+	0	NA	intron (NM_020929, intron 3 of 4)	intron (NM_020929, intron 3 of 4)	106445	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.021341	0.477204	
chunk0073_315_1	chr16	14182478	14182830	+	0	NA	intron (NM_001308142, intron 3 of 16)	L1MC4|LINE|L1	111340	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.005682	0.388102	236(TGGGACATCTTGTGCC,-,0.00),237(GGGACATCTTGTGCCG,+,0.00)
chunk0005_402_1	chr1	62500709	62501204	+	0	NA	intron (NM_001272001, intron 36 of 47)	AluJr|SINE|Alu	64244	NM_003368	7398	Hs.35086	NM_003368	ENSG00000162607	USP1	UBP	ubiquitin specific peptidase 1	protein-coding	0.012121	0.467742	236(GAGAACAGCTTGAGCC,-,0.00),237(AGAACAGCTTGAGCCC,+,0.00)
chunk0098_164_1	chr2	70524238	70524437	+	0	NA	intron (NM_001099691, intron 1 of 5)	intron (NM_001099691, intron 1 of 5)	29301	NM_001308158	7039	Hs.170009	NM_003236	ENSG00000163235	TGFA	TFGA	transforming growth factor alpha	protein-coding	0.015075	0.535000	
chunk0208_378_1	chrX	28016932	28017180	+	0	NA	Intergenic	Intergenic	-35607	NM_001017930	139425	Hs.447365	NM_001017930	ENSG00000226372	DCAF8L1	WDR42B	DDB1 and CUL4 associated factor 8 like 1	protein-coding	0.004032	0.429719	166(TAGTGCAGGATGTTCC,-,0.00),167(AGTGCAGGATGTTCCC,+,0.00)
chunk0023_400_1	chr10	30991639	30991838	+	0	NA	intron (NM_001143766, intron 1 of 7)	intron (NM_001143766, intron 1 of 7)	7779	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.000000	0.475000	
chunk0063_276_1	chr14	84203942	84204388	+	0	NA	Intergenic	Intergenic	-1189714	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.002242	0.340045	
chunk0124_59_1	chr3	52856737	52857092	+	0	NA	intron (NM_198563, intron 1 of 8)	intron (NM_198563, intron 1 of 8)	-10362	NR_107031	102465866		NR_107031	ENSG00000275789	MIR8064	hsa-mir-8064	microRNA 8064	ncRNA	0.014085	0.477528	
chunk0171_261_1	chr6	127422744	127423148	+	0	NA	Intergenic	Intergenic	36444	NM_014702	9729	Hs.319247	NM_014702	ENSG00000189367	KIAA0408	-	KIAA0408	protein-coding	0.000000	0.340741	
chunk0009_121_1	chr1	103004470	103005041	+	0	NA	intron (NM_080630, intron 16 of 64)	intron (NM_080630, intron 16 of 64)	103741	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.003503	0.277972	
chunk0111_253_1	chr20	30667480	30667679	+	0	NA	Intergenic	L1MA5|LINE|L1	-264117	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.010050	0.370000	
chunk0181_211_1	chr7	84553494	84554188	+	0	NA	intron (NR_110079, intron 2 of 2)	intron (NR_110079, intron 2 of 2)	21365	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.002882	0.330935	
chunk0183_203_1	chr7	106401518	106401987	+	0	NA	Intergenic	L1ME3G|LINE|L1	-116560	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.002132	0.329787	
chunk0078_158_1	chr17	4220615	4220938	+	0	NA	intron (NR_047571, intron 2 of 23)	intron (NR_047571, intron 2 of 23)	43071	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.018576	0.462963	146(AAGGACAGTGTGTGCT,-,0.00),147(AGGACAGTGTGTGCTG,+,0.00)
chunk0150_103_1	chr5	32624715	32624917	+	0	NA	Intergenic	Intergenic	39317	NM_006713	10923	Hs.229641	NM_006713	ENSG00000113387	SUB1	P15|PC4|p14	SUB1 regulator of transcription	protein-coding	0.000000	0.339901	
chunk0177_63_1	chr7	21202155	21202504	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-225742	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.002865	0.480000	
chunk0201_119_1	chr9	35338632	35338860	+	0	NA	intron (NM_006377, intron 10 of 38)	intron (NM_006377, intron 10 of 38)	-68009	NR_003581	158381	Hs.575661	NR_003581	ENSG00000179766	ATP8B5P	FetA	ATPase phospholipid transporting 8B5, pseudogene	pseudo	0.008772	0.475983	
chunk0127_120_1	chr3	93839036	93839970	+	0	NA	Intergenic	Intergenic	134578	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.002141	0.321925	
chunk0089_145_1	chr18	58975454	58975963	+	0	NA	intron (NM_018181, intron 8 of 10)	intron (NM_018181, intron 8 of 10)	-59971	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.021611	0.425490	
chunk0108_18_1	chr2	226220738	226221021	+	0	NA	Intergenic	Intergenic	78085	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.000000	0.334507	
chunk0149_233_1	chr5	23285137	23285489	+	0	NA	Intergenic	Intergenic	-222296	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.000000	0.192635	
chunk0051_362_1	chr12	121294443	121294642	+	0	NA	intron (NM_006549, intron 1 of 16)	intron (NM_006549, intron 1 of 16)	2211	NM_172226	10645	Hs.297343	NM_006549	ENSG00000110931	CAMKK2	CAMKK|CAMKKB	calcium/calmodulin dependent protein kinase kinase 2	protein-coding	0.005025	0.510000	
chunk0140_146_1	chr4	69309979	69310839	+	0	NA	Intergenic	LTR10C|LTR|ERV1	29910	NM_001207004	54490	Hs.653154	NM_053039	ENSG00000135226	UGT2B28	-	UDP glucuronosyltransferase family 2 member B28	protein-coding	0.008140	0.373984	
chunk0166_416_1	chr6	52543182	52543891	+	0	NA	intron (NM_012288, intron 1 of 10)	intron (NM_012288, intron 1 of 10)	33528	NM_012288	9697	Hs.520182	NM_012288	ENSG00000065308	TRAM2	-	translocation associated membrane protein 2	protein-coding	0.005642	0.373239	280(CAGAACAAAATGTTTT,-,0.00),281(AGAACAAAATGTTTTT,+,0.00)
chunk0042_116_1	chr12	3267095	3267434	+	0	NA	intron (NM_001168320, intron 2 of 7)	intron (NM_001168320, intron 2 of 7)	-114085	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.014749	0.505882	204(AGGAACACAAAGTGCT,-,0.00),205(GGAACACAAAGTGCTC,+,0.00)
chunk0168_397_1	chr6	94550913	94551250	+	0	NA	Intergenic	Intergenic	843998	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.002967	0.322485	
chunk0206_356_1	chr9	125743968	125744503	+	0	NA	intron (NR_122032, intron 1 of 1)	intron (NR_122032, intron 1 of 1)	1694	NR_122032	51145	Hs.104671	NM_016158		LOC51145	-	uncharacterized LOC51145	ncRNA	0.007477	0.408582	
chunk0182_25_1	chr7	91416399	91416834	+	0	NA	Intergenic	Intergenic	152148	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.004598	0.392202	
chunk0056_25_1	chr13	77280242	77280524	+	0	NA	intron (NM_015057, intron 3 of 82)	intron (NM_015057, intron 3 of 82)	46659	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.000000	0.332155	132(AAGAACATGCTGTCCA,-,0.00),133(AGAACATGCTGTCCAA,+,0.00)
chunk0085_153_1	chr18	3529742	3529984	+	0	NA	intron (NM_001308390, intron 8 of 10)	intron (NM_001308390, intron 8 of 10)	63613	NR_110429	100505592	Hs.635114	NR_110428	ENSG00000266835	GAPLINC	LINC01540	gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNA	ncRNA	0.008264	0.378601	
chunk0048_128_1	chr12	79874577	79875048	+	0	NA	intron (NM_001244990, intron 2 of 24)	MIRb|SINE|MIR	39099	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.000000	0.366525	226(AGGTACTCATTGTTCC,-,0.00),227(GGTACTCATTGTTCCC,+,0.00)
chunk0022_139_1	chr10	11898381	11898605	+	0	NA	Intergenic	Intergenic	-3783	NR_038222	219731	Hs.576787	NR_038222	ENSG00000225778	PROSER2-AS1	-	PROSER2 antisense RNA 1	ncRNA	0.022321	0.542222	
chunk0015_111_1	chr1	185175539	185176123	+	0	NA	intron (NM_017673, intron 5 of 18)	intron (NM_017673, intron 5 of 18)	18672	NM_017673	54823	Hs.134183	NM_017673	ENSG00000116668	SWT1	C1orf26|HsSwt1	SWT1 RNA endoribonuclease homolog	protein-coding	0.008562	0.372650	
chunk0188_295_1	chr8	15702098	15702835	+	0	NA	intron (NM_006765, intron 6 of 10)	L3|LINE|CR1	162379	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.004071	0.369919	
chunk0090_357_1	chr18	76822322	76822676	+	0	NA	promoter-TSS (NR_040024)	promoter-TSS (NR_040024)	-108	NM_001306089	7776	Hs.719137	NM_007345	ENSG00000130856	ZNF236	ZNF236A|ZNF236B	zinc finger protein 236	protein-coding	0.180791	0.814085	
chunk0069_165_1	chr15	62727993	62728683	+	0	NA	intron (NM_015059, intron 25 of 55)	L1ME3A|LINE|L1	81027	NM_015059	83660	Hs.569438	NM_015059	ENSG00000171914	TLN2	ILWEQ	talin 2	protein-coding	0.011594	0.413893	300(TGGTACATACAGTGCT,-,0.00),301(GGTACATACAGTGCTT,+,0.00)
chunk0092_198_1	chr19	30664011	30664758	+	0	NA	Intergenic	Intergenic	291991	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.008032	0.465241	
chunk0008_405_1	chr1	98058223	98058638	+	0	NA	Intergenic	Intergenic	-8737	NR_046105	400765	Hs.451802	NM_001001688	ENSG00000225206	MIR137HG	-	MIR137 host gene	ncRNA	0.004819	0.346154	
chunk0136_33_1	chr4	986448	986647	+	0	NA	promoter-TSS (NM_000203)	promoter-TSS (NM_000203)	-450	NR_110313	3425	Hs.89560	NM_000203	ENSG00000127415	IDUA	IDA|MPS1	iduronidase alpha-L-	protein-coding	0.015075	0.385000	
chunk0127_405_1	chr3	102457355	102457899	+	0	NA	intron (NM_175056, intron 4 of 10)	intron (NM_175056, intron 4 of 10)	22612	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.003676	0.326606	
chunk0052_231_1	chr13	25709133	25709438	+	0	NA	intron (NM_001313741, intron 25 of 35)	intron (NM_001313741, intron 25 of 35)	240511	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.006557	0.392157	
chunk0015_399_1	chr1	190997571	190998346	+	0	NA	Intergenic	Intergenic	373068	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.001290	0.305412	
chunk0172_274_1	chr6	137589131	137589388	+	0	NA	Intergenic	L1PB4|LINE|L1	-76387	NR_125867	102723649	Hs.129235	NR_125867		LOC102723649	-	uncharacterized LOC102723649	ncRNA	0.003891	0.593023	
chunk0073_378_1	chr16	15874052	15874525	+	0	NA	intron (NR_130757, intron 1 of 2)	intron (NR_130757, intron 1 of 2)	14361	NM_001304500	123811	Hs.514179	NM_144600	ENSG00000133393	FOPNL	C16orf63|FOR20|PHSECRG2	FGFR1OP N-terminal like	protein-coding	0.006342	0.354430	
chunk0044_106_1	chr12	28770293	28770492	+	0	NA	Intergenic	Intergenic	-378611	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.000000	0.360000	
chunk0046_19_1	chr12	54273929	54274358	+	0	NA	intron (NM_012117, intron 1 of 4)	intron (NM_012117, intron 1 of 4)	5988	NM_012117	23468	Hs.349283	NM_012117	ENSG00000094916	CBX5	HEL25|HP1|HP1A	chromobox 5	protein-coding	0.004662	0.397674	
chunk0206_139_1	chr9	121094449	121094648	+	0	NA	intron (NM_007018, intron 2 of 41)	MSTD|LTR|ERVL-MaLR	6252	NM_007018	11064	Hs.653263	NM_007018	ENSG00000119397	CNTRL	CEP1|CEP110|FAN|bA165P4.1	centriolin	protein-coding	0.005025	0.450000	
chunk0067_219_1	chr15	45154846	45155243	+	0	NA	intron (NM_017434, intron 28 of 34)	intron (NM_017434, intron 28 of 34)	25050	NM_175940	53905	Hs.272813	NM_017434	ENSG00000137857	DUOX1	LNOX1|NOXEF1|THOX1	dual oxidase 1	protein-coding	0.007557	0.547739	102(AGGGACAGTGTGGTCC,-,0.00),103(GGGACAGTGTGGTCCT,+,0.00),212(GAGTACAGCCTGTCAT,-,0.00),213(AGTACAGCCTGTCATT,+,0.00)
chunk0191_453_1	chr8	58056878	58057300	+	0	NA	intron (NM_147189, intron 3 of 4)	intron (NM_147189, intron 3 of 4)	62535	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.016588	0.529551	
chunk0149_364_1	chr5	27907248	27907561	+	0	NA	Intergenic	L2a|LINE|L2	435112	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.000000	0.328025	
chunk0132_351_1	chr3	161411953	161412880	+	0	NA	Intergenic	Intergenic	-14011	NR_102265	101243545	Hs.737526	NR_102265	ENSG00000240567	LINC02067	-	long intergenic non-protein coding RNA 2067	ncRNA	0.007551	0.383621	
chunk0060_332_1	chr14	51534813	51535153	+	0	NA	intron (NM_001042481, intron 1 of 14)	intron (NM_001042481, intron 1 of 14)	45862	NM_001042481	122786	Hs.434914	NM_152330	ENSG00000139926	FRMD6	C14orf31|EX1|Willin|c14_5320	FERM domain containing 6	protein-coding	0.008824	0.466276	
chunk0028_414_1	chr10	93431393	93431674	+	0	NA	intron (NM_013451, intron 3 of 53)	intron (NM_013451, intron 3 of 53)	50784	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.014235	0.482270	
chunk0116_37_1	chr21	33415461	33415829	+	0	NA	intron (NM_005534, intron 2 of 6)	intron (NM_005534, intron 2 of 6)	12749	NM_005534	3460	Hs.634632	NM_005534	ENSG00000159128	IFNGR2	AF-1|IFGR2|IFNGT1|IMD28	interferon gamma receptor 2	protein-coding	0.002717	0.365854	
chunk0145_179_1	chr4	147642738	147642937	+	0	NA	exon (NM_001304458, exon 9 of 11)	exon (NM_001304458, exon 9 of 11)	25449	NM_018241	55751	Hs.203896	NM_018241	ENSG00000164168	TMEM184C	TMEM34	transmembrane protein 184C	protein-coding	0.005025	0.415000	87(GAGTACGTTCTGTTCC,-,0.00),88(AGTACGTTCTGTTCCT,+,0.00)
chunk0167_222_1	chr6	66699179	66699501	+	0	NA	Intergenic	Intergenic	911461	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.000000	0.303406	
chunk0177_310_1	chr7	26060879	26061189	+	0	NA	Intergenic	Intergenic	-91193	NM_004289	9603	Hs.404741	NM_004289	ENSG00000050344	NFE2L3	NRF3	nuclear factor, erythroid 2 like 3	protein-coding	0.000000	0.401929	
chunk0187_360_1	chr7	157318432	157318754	+	0	NA	Intergenic	Intergenic	-18423	NM_005494	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.018634	0.547988	
chunk0208_315_1	chrX	23919861	23920143	+	0	NA	intron (NM_001169574, intron 5 of 8)	L1M1|LINE|L1	11996	NM_001169574	254158	Hs.351265	NM_152761	ENSG00000165182	CXorf58	-	chromosome X open reading frame 58	protein-coding	0.010638	0.533569	
chunk0129_17_1	chr3	117053618	117053964	+	0	NA	Intergenic	Intergenic	132360	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.345821	
chunk0186_231_1	chr7	140638611	140638978	+	0	NA	Intergenic	L2b|LINE|L2	-34359	NM_052853	90956	Hs.744886	NM_052853	ENSG00000133597	ADCK2	AARF	aarF domain containing kinase 2	protein-coding	0.019074	0.551630	103(TTGCACATTCTGTTCT,-,0.00),104(TGCACATTCTGTTCTT,+,0.00)
chunk0168_455_1	chr6	95951340	95951854	+	0	NA	Intergenic	L2a|LINE|L2	-64372	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.363107	
chunk0201_391_1	chr9	69120481	69120897	+	0	NA	promoter-TSS (NM_001170414)	promoter-TSS (NM_001170414)	-575	NM_001170414	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.043269	0.577938	
chunk0172_332_1	chr6	138469201	138469509	+	0	NA	intron (NM_020464, intron 3 of 6)	intron (NM_020464, intron 3 of 6)	30087	NM_001144060	57224	Hs.652741	NM_020464	ENSG00000135540	NHSL1	C6orf63	NHS like 1	protein-coding	0.029221	0.436893	
chunk0027_18_1	chr10	72130203	72130901	+	0	NA	intron (NM_001198800, intron 8 of 9)	intron (NM_001198800, intron 8 of 9)	-41520	NM_001134434	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.004298	0.344778	
chunk0070_49_1	chr15	69561234	69561810	+	0	NA	promoter-TSS (NR_026979)	promoter-TSS (NR_026979)	-198	NR_026979	145837	Hs.410126	NR_026979		DRAIC	-	downregulated RNA in cancer, inhibitor of cell invasion and migration	ncRNA	0.024306	0.504333	
chunk0051_373_1	chr12	121602890	121603213	+	0	NA	Intergenic	Intergenic	6522	NR_049838	100847078		NR_049838	ENSG00000265470	MIR548AQ	-	microRNA 548aq	ncRNA	0.018576	0.339506	
chunk0189_418_1	chr8	27854239	27854450	+	0	NA	Intergenic	Intergenic	-16249	NM_001278945	55872	Hs.104741	NM_018492	ENSG00000168078	PBK	CT84|HEL164|Nori-3|SPK|TOPK	PDZ binding kinase	protein-coding	0.009479	0.443396	
chunk0029_227_1	chr10	102421252	102421451	+	0	NA	intron (NM_024326, intron 1 of 3)	CpG-3312	-1417	NM_001270965	5662	Hs.154658	NM_002779	ENSG00000059915	PSD	EFA6|EFA6A|PSD1|TYL	pleckstrin and Sec7 domain containing	protein-coding	0.090452	0.685000	
chunk0109_392_1	chr2	240173274	240173763	+	0	NA	Intergenic	Intergenic	-32862	NM_148961	150677	Hs.148586	NM_148961	ENSG00000178602	OTOS	OTOSP	otospiralin	protein-coding	0.008180	0.336735	
chunk0131_31_1	chr3	142327654	142328261	+	0	NA	intron (NM_001282857, intron 37 of 40)	L1PB4|LINE|L1	-102350	NM_001039547	256356	Hs.135904	NM_152776	ENSG00000175066	GK5	-	glycerol kinase 5	protein-coding	0.003295	0.353618	
chunk0060_274_1	chr14	50344804	50345271	+	0	NA	exon (NM_004196, exon 3 of 9)	exon (NM_004196, exon 3 of 9)	32708	NM_015684	27109	Hs.438489	NM_015684	ENSG00000125375	DMAC2L	ATP5S|ATPW|FB|HSU79253	distal membrane arm assembly complex 2 like	protein-coding	0.008565	0.378205	
chunk0079_50_1	chr17	10698440	10699061	+	0	NA	intron (NM_020233, intron 1 of 3)	intron (NM_020233, intron 1 of 3)	1140	NM_020233	56985	Hs.47668	NM_020233	ENSG00000170222	ADPRM	C17orf48|MDS006|NBLA03831	ADP-ribose/CDP-alcohol diphosphatase, manganese dependent	protein-coding	0.016103	0.382637	244(CGGAACATAGTGTTAC,-,0.00),245(GGAACATAGTGTTACC,+,0.00)
chunk0054_143_1	chr13	43772113	43772446	+	0	NA	intron (NM_017993, intron 1 of 16)	intron (NM_017993, intron 1 of 16)	14701	NM_017993	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.003003	0.347305	
chunk0014_421_1	chr1	183306585	183306902	+	0	NA	intron (NM_015039, intron 1 of 10)	intron (NM_015039, intron 1 of 10)	-1869	NM_170706	23057	Hs.497123	NM_015039	ENSG00000157064	NMNAT2	C1orf15|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.009464	0.415094	
chunk0212_321_1	chrX	143932267	143932971	+	0	NA	Intergenic	L1PB2|LINE|L1	48548	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.001420	0.312057	
chunk0161_436_1	chr5	178505930	178506271	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	84455	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.029326	0.581871	
chunk0105_446_1	chr2	195021962	195022588	+	0	NA	Intergenic	Intergenic	291680	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.003195	0.357257	
chunk0038_86_1	chr11	83335430	83335866	+	0	NA	Intergenic	Intergenic	-49241	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.004587	0.443936	
chunk0199_209_1	chr9	4985293	4985510	+	0	NA	5' UTR (NM_004972, exon 1 of 25)	5' UTR (NM_004972, exon 1 of 25)	156	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.124424	0.761468	
chunk0178_61_1	chr7	30165442	30166053	+	0	NA	Intergenic	Intergenic	30811	NM_152793	222166	Hs.200100	NM_152793	ENSG00000180354	MTURN	C7orf41|Ells1	maturin, neural progenitor differentiation regulator homolog	protein-coding	0.004910	0.400327	
chunk0141_363_1	chr4	88041517	88041996	+	0	NA	intron (NM_000297, intron 4 of 14)	MER68|LTR|ERVL	34109	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.006263	0.495833	
chunk0029_44_1	chr10	96294567	96294915	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-9587	NM_004088	1791	Hs.534206	NM_004088	ENSG00000107447	DNTT	TDT	DNA nucleotidylexotransferase	protein-coding	0.008621	0.418338	
chunk0059_232_1	chr14	34275249	34275786	+	0	NA	Intergenic	Intergenic	186745	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.005587	0.353160	
chunk0081_137_1	chr17	40560383	40560614	+	0	NA	promoter-TSS (NM_001301718)	promoter-TSS (NM_001301718)	-104	NM_001301718	1236	Hs.370036	NM_001838	ENSG00000126353	CCR7	BLR2|CC-CKR-7|CCR-7|CD197|CDw197|CMKBR7|EBI1	C-C motif chemokine receptor 7	protein-coding	0.025974	0.556034	
chunk0188_66_1	chr8	8289068	8289658	+	0	NA	Intergenic	Intergenic	60793	NR_024363	286042	Hs.656318	NR_024361	ENSG00000173295	FAM86B3P	-	family with sequence similarity 86, member A pseudogene	pseudo	0.011864	0.397631	
chunk0045_449_1	chr12	53623463	53623672	+	0	NA	intron (NM_006856, intron 1 of 11)	intron (NM_006856, intron 1 of 11)	2429	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.009569	0.361905	
chunk0139_352_1	chr4	60103634	60104213	+	0	NA	Intergenic	L1MC5a|LINE|L1	-818696	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.003454	0.317241	
chunk0165_452_1	chr6	40836104	40836355	+	0	NA	Intergenic	Intergenic	187051	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.015936	0.404762	133(AGTCCATGATGTTCTT,+,0.00)
chunk0041_84_1	chr11	124301226	124301623	+	0	NA	Intergenic	Intergenic	9342	NM_001002917	283159	Hs.504211	NM_001002917	ENSG00000196341	OR8D1	JCG9|OR8D3|OST004|PDJ9J14	olfactory receptor family 8 subfamily D member 1	protein-coding	0.002519	0.276382	
chunk0048_96_1	chr12	79316759	79317462	+	0	NA	intron (NM_001291901, intron 7 of 9)	intron (NM_001291901, intron 7 of 9)	-102147	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.014225	0.377841	
chunk0197_54_1	chr8	118562478	118562716	+	0	NA	intron (NR_109794, intron 2 of 4)	L2|LINE|L2	-58404	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.016807	0.389121	
chunk0005_167_1	chr1	58541482	58541944	+	0	NA	intron (NM_145243, intron 1 of 8)	intron (NM_145243, intron 1 of 8)	5086	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.004329	0.343413	
chunk0005_176_1	chr1	58686993	58687949	+	0	NA	intron (NM_001085487, intron 6 of 19)	intron (NM_001085487, intron 6 of 19)	12604	NM_001085487	114803	Hs.744921	NM_001085487	ENSG00000162601	MYSM1	2A-DUB|2ADUB|BMFS4	Myb like, SWIRM and MPN domains 1	protein-coding	0.010460	0.411703	
chunk0023_125_1	chr10	23795815	23796218	+	0	NA	intron (NM_001098500, intron 1 of 18)	LTR39|LTR|ERV1	101270	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.002481	0.403465	
chunk0059_374_1	chr14	37367580	37368131	+	0	NA	intron (NM_001195296, intron 11 of 14)	intron (NM_001195296, intron 11 of 14)	169942	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.009074	0.327899	246(TAGTACAGTTAGTGCT,-,0.00),247(AGTACAGTTAGTGCTA,+,0.00)
chunk0034_41_1	chr11	26847186	26847922	+	0	NA	Intergenic	Intergenic	-125527	NM_178498	159963	Hs.148907	NM_178498	ENSG00000148942	SLC5A12	SMCT2	solute carrier family 5 member 12	protein-coding	0.005435	0.396201	357(TGAACTCTTTGTGCTT,+,0.00)
chunk0102_391_1	chr2	154782284	154782919	+	0	NA	intron (NM_002239, intron 2 of 2)	intron (NM_002239, intron 2 of 2)	84020	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.007874	0.355346	
chunk0154_107_1	chr5	78510316	78510828	+	0	NA	intron (NM_005779, intron 3 of 4)	intron (NM_005779, intron 3 of 4)	138253	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.052734	0.606238	
chunk0038_307_1	chr11	90945347	90945608	+	0	NA	Intergenic	Intergenic	-76275	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.007663	0.309160	
chunk0115_237_1	chr21	27398435	27398866	+	0	NA	Intergenic	Intergenic	-323729	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.011601	0.363426	
chunk0143_144_1	chr4	109915903	109916212	+	0	NA	intron (NM_001963, intron 1 of 23)	intron (NM_001963, intron 1 of 23)	3173	NM_001178130	1950	Hs.419815	NM_001963	ENSG00000138798	EGF	HOMG4|URG	epidermal growth factor	protein-coding	0.012945	0.429032	
chunk0104_109_1	chr2	172798859	172799516	+	0	NA	intron (NM_007023, intron 3 of 30)	MIR|SINE|MIR	-22400	NM_001100397	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.009132	0.419453	
chunk0203_158_1	chr9	85814681	85815638	+	0	NA	intron (NR_029410, intron 1 of 8)	intron (NR_029410, intron 1 of 8)	9157	NR_029410	389765	Hs.715986	NR_029410		LOC389765	-	kinesin family member 27 pseudogene	pseudo	0.002090	0.400835	
chunk0010_66_1	chr1	113056888	113057463	+	0	NA	intron (NR_103777, intron 1 of 2)	intron (NR_103777, intron 1 of 2)	15927	NR_103777	100996251	Hs.382067	NR_103777	ENSG00000238198	LRIG2-DT	-	LRIG2 divergent transcript	ncRNA	0.006957	0.444444	
chunk0064_336_1	chr14	96565535	96565785	+	0	NA	3' UTR (NM_001293632, exon 20 of 20)	3' UTR (NM_001293632, exon 20 of 20)	62795	NM_001293628	10914	Hs.253726	NM_032632	ENSG00000090060	PAPOLA	PAP|PAP-alpha	poly(A) polymerase alpha	protein-coding	0.008000	0.342629	
chunk0146_214_1	chr4	161708000	161708241	+	0	NA	intron (NM_001128427, intron 6 of 15)	intron (NM_001128427, intron 6 of 15)	-314613	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004149	0.359504	
chunk0108_434_1	chr2	237939299	237939630	+	0	NA	Intergenic	L1MC3|LINE|L1	-27481	NM_001278307	140739	Hs.471785	NM_080678	ENSG00000184182	UBE2F	NCE2	ubiquitin conjugating enzyme E2 F (putative)	protein-coding	0.000000	0.367470	
chunk0170_264_1	chr6	113883865	113884270	+	0	NA	Intergenic	Intergenic	-10720	NR_038863	285758	Hs.359399	NR_038863	ENSG00000227502	LINC01268	ROCKI	long intergenic non-protein coding RNA 1268	ncRNA	0.000000	0.371921	
chunk0082_244_1	chr17	57412334	57412578	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	111141	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.008197	0.379592	
chunk0035_378_1	chr11	50270856	50271074	+	0	NA	Intergenic	Intergenic	27497	NR_003034	441601	Hs.144683	NR_003034	ENSG00000255042	LOC441601	-	septin 7 pseudogene	pseudo	0.009174	0.378995	
chunk0208_12_1	chrX	10709239	10709563	+	0	NA	intron (NM_033290, intron 1 of 9)	intron (NM_033290, intron 1 of 9)	-31662	NM_001098624	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.009259	0.384615	
chunk0211_155_1	chrX	114097197	114097396	+	0	NA	Intergenic	Intergenic	-159078	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.005025	0.385000	
chunk0022_198_1	chr10	13508365	13509128	+	0	NA	Intergenic	L2c|LINE|L2	-5770	NM_152751	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.017038	0.434555	
chunk0071_437_1	chr15	89940037	89940620	+	0	NA	Intergenic	L1MA8|LINE|L1	-27338	NM_001199058	100526783		NM_001199058	ENSG00000250021	ARPIN-AP3S2	ARPIN|C15orf38|C15orf38-AP3S2	ARPIN-AP3S2 readthrough	protein-coding	0.008576	0.378425	
chunk0116_96_1	chr21	35067622	35068038	+	0	NA	Intergenic	Intergenic	-18532	NM_001754	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.002404	0.366906	
chunk0092_139_1	chr19	28169927	28170153	+	0	NA	Intergenic	Intergenic	-376100	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.004425	0.511013	
chunk0156_244_1	chr5	108696866	108697486	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	31085	NR_046368	100652853	Hs.133009	NR_046368	ENSG00000272523	LINC01023	HP07349	long intergenic non-protein coding RNA 1023	ncRNA	0.004839	0.368760	
chunk0024_221_1	chr10	37841194	37841913	+	0	NA	intron (NM_001267605, intron 3 of 6)	L1MC3|LINE|L1	16083	NM_001267605	57209	Hs.528423	NM_021045	ENSG00000198105	ZNF248	bA162G10.3	zinc finger protein 248	protein-coding	0.002782	0.340278	
chunk0020_357_1	chr1	239576597	239577116	+	0	NA	Intergenic	Intergenic	-52217	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.009634	0.409615	282(AAGCACACACTGTGCT,-,0.00),283(AGCACACACTGTGCTA,+,0.00)
chunk0152_102_1	chr5	58408068	58408619	+	0	NA	Intergenic	Intergenic	51796	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.001815	0.380435	244(CTGAACACTCTGTTCT,-,0.00),245(TGAACACTCTGTTCTC,+,0.00)
chunk0113_326_1	chr20	58481007	58481206	+	0	NA	intron (NR_130908, intron 1 of 1)	intron (NR_130908, intron 1 of 1)	33832	NM_001304787	164284	Hs.119286	NM_153360	ENSG00000198768	APCDD1L	-	APC down-regulated 1 like	protein-coding	0.015075	0.505000	
chunk0074_299_1	chr16	29906540	29906795	+	0	NA	TTS (NM_181718)	TTS (NM_181718)	5841	NM_181718	253982	Hs.655761	NM_181718	ENSG00000174939	ASPHD1	-	aspartate beta-hydroxylase domain containing 1	protein-coding	0.027451	0.566406	
chunk0208_73_1	chrX	12848274	12848766	+	0	NA	Intergenic	Intergenic	-18563	NM_016562	51284	Hs.659215	NM_016562	ENSG00000196664	TLR7	TLR7-like	toll like receptor 7	protein-coding	0.002033	0.332657	
chunk0131_125_1	chr3	144169787	144170000	+	0	NA	Intergenic	HAL1|LINE|L1	196568	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.364486	
chunk0117_205_1	chr22	21851638	21852015	+	0	NA	intron (NM_138957, intron 1 of 7)	L1ME3D|LINE|L1	15854	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.002653	0.314815	
chunk0051_81_1	chr12	113865313	113865522	+	0	NA	intron (NM_001146699, intron 21 of 24)	L2a|LINE|L2	-91734	NR_110026	100506465	Hs.211461	NR_110025	ENSG00000249550	LINC01234	LCAL84|onco-lncRNA-32	long intergenic non-protein coding RNA 1234	ncRNA	0.004785	0.461905	
chunk0163_368_1	chr6	15949279	15949578	+	0	NA	Intergenic	Intergenic	-179658	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.006689	0.480000	
chunk0062_264_1	chr14	71692488	71692820	+	0	NA	intron (NM_001284245, intron 10 of 20)	intron (NM_001284245, intron 10 of 20)	105083	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.012048	0.483483	
chunk0055_419_1	chr13	74979034	74980123	+	0	NA	Intergenic	Intergenic	260803	NR_027466	647288	Hs.567920	NR_027466	ENSG00000214249	CTAGE11P	-	CTAGE family member 11, pseudogene	pseudo	0.007346	0.346789	842(ATGGACATCTTGTTCC,-,0.00),843(TGGACATCTTGTTCCT,+,0.00)
chunk0187_279_1	chr7	155415420	155416029	+	0	NA	Intergenic	Intergenic	-42405	NM_001427	2020	Hs.134989	NM_001427	ENSG00000164778	EN2	-	engrailed homeobox 2	protein-coding	0.008210	0.408197	294(AGGCTCACTCTGTACC,-,0.00),295(GGCTCACTCTGTACCT,+,0.00)
chunk0155_422_1	chr5	100242971	100243191	+	0	NA	Intergenic	MLT1F1-int|LTR|ERVL-MaLR	145173	NR_027503	100133050	Hs.534796	NR_027503		LOC100133050	-	glucuronidase beta pseudogene	pseudo	0.004545	0.330317	130(GAGTACATAATGATCT,-,0.00),131(AGTACATAATGATCTC,+,0.00)
chunk0197_120_1	chr8	119937309	119937940	+	0	NA	intron (NM_022783, intron 3 of 8)	LTR40a|LTR|ERVL	63969	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.004754	0.419304	
chunk0036_2_1	chr11	57838922	57839781	+	0	NA	Intergenic	L1MC2|LINE|L1	77589	NM_001206883	1500	Hs.166011	NM_001331	ENSG00000198561	CTNND1	BCDS2|CAS|CTNND|P120CAS|P120CTN|p120|p120(CAS)|p120(CTN)	catenin delta 1	protein-coding	0.003492	0.332558	
chunk0018_214_1	chr1	219521200	219521819	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	346540	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.006462	0.408065	323(AGGAACTGCCTGTACT,-,0.00),324(GGAACTGCCTGTACTC,+,0.00)
chunk0057_193_1	chr13	102969944	102970238	+	0	NA	Intergenic	Intergenic	89992	NR_026965	121952	Hs.660773	NR_026965	ENSG00000250878	METTL21EP	METTL21CP1	methyltransferase like 21E, pseudogene	pseudo	0.010204	0.400000	
chunk0034_16_1	chr11	26048053	26048809	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-140692	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.011905	0.422721	
chunk0118_19_1	chr22	25696988	25697471	+	0	NA	intron (NM_005160, intron 13 of 20)	L3|LINE|CR1	-44924	NM_032608	84700	Hs.417959	NM_032608	ENSG00000133454	MYO18B	KFS4	myosin XVIIIB	protein-coding	0.002070	0.400826	67(GAGACAGACAGTCCCT,+,0.00)
chunk0017_363_1	chr1	211947748	211948324	+	0	NA	intron (NM_001199811, intron 17 of 19)	LTR22B|LTR|ERVK	-87517	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.003472	0.383016	484(TTGAACATTTTGTGCC,-,0.00),485(TGAACATTTTGTGCCC,+,0.00)
chunk0028_164_1	chr10	87092798	87092997	+	0	NA	intron (NM_005271, intron 1 of 12)	intron (NM_005271, intron 1 of 12)	2122	NM_005271	2746	Hs.500409	NM_005271	ENSG00000148672	GLUD1	GDH|GDH1|GLUD	glutamate dehydrogenase 1	protein-coding	0.010050	0.395000	
chunk0117_84_1	chr22	17230210	17230832	+	0	NA	Intergenic	Intergenic	-8667	NM_001282227	51816	Hs.170310	NM_017424	ENSG00000093072	ADA2	ADGF|CECR1|IDGFL|PAN|SNEDS|VAIHS	adenosine deaminase 2	protein-coding	0.022508	0.473515	
chunk0210_252_1	chrX	83004676	83005195	+	0	NA	Intergenic	Intergenic	-503326	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.000000	0.334615	
chunk0077_351_1	chr16	83765707	83766056	+	0	NA	intron (NM_001220488, intron 12 of 14)	intron (NM_001220488, intron 12 of 14)	38095	NR_120308	102724163		NR_120308	ENSG00000260228	LOC102724163	-	uncharacterized LOC102724163	ncRNA	0.005731	0.397143	
chunk0169_148_1	chr6	101608770	101609052	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	209926	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.409894	
chunk0194_59_1	chr8	82334955	82335259	+	0	NA	Intergenic	Intergenic	-492821	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.321311	
chunk0174_337_1	chr6	163955564	163955763	+	0	NA	Intergenic	Intergenic	541020	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.000000	0.360000	32(GTGTACATCATGTACC,-,0.00),33(TGTACATCATGTACCC,+,0.00)
chunk0112_155_1	chr20	39152775	39153100	+	0	NA	Intergenic	Intergenic	71811	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.003077	0.466258	
chunk0125_437_1	chr3	72725618	72725873	+	0	NA	Intergenic	Intergenic	122702	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.011765	0.468750	
chunk0173_180_1	chr6	144789815	144790014	+	0	NA	intron (NM_007124, intron 61 of 73)	MIRb|SINE|MIR	384259	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.000000	0.340000	
chunk0095_261_1	chr2	19600979	19601298	+	0	NA	Intergenic	Intergenic	-242527	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.003135	0.446875	
chunk0037_332_1	chr11	77140792	77141009	+	0	NA	intron (NM_001127179, intron 2 of 26)	intron (NM_001127179, intron 2 of 26)	12630	NM_001127180	4647	Hs.370421	NM_000260	ENSG00000137474	MYO7A	DFNA11|DFNB2|MYOVIIA|MYU7A|NSRD2|USH1B	myosin VIIA	protein-coding	0.004608	0.449541	
chunk0030_219_1	chr10	114719136	114719578	+	0	NA	Intergenic	Intergenic	-34702	NM_001003408	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.006787	0.406321	
chunk0158_425_1	chr5	135207103	135207534	+	0	NA	intron (NM_001277348, intron 3 of 5)	L1ME3G|LINE|L1	40859	NR_037895	340073	Hs.434422	NR_037895	ENSG00000249647	C5orf66-AS2	-	C5orf66 antisense RNA 2	ncRNA	0.009281	0.458333	
chunk0123_94_1	chr3	42079709	42080178	+	0	NA	Intergenic	Intergenic	-11311	NM_001042646	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.017058	0.485106	
chunk0163_431_1	chr6	17259429	17259771	+	0	NA	Intergenic	Intergenic	-21978	NM_001143942	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.008772	0.379009	
chunk0076_389_1	chr16	72416077	72416429	+	0	NA	intron (NR_126330, intron 7 of 13)	L1ME3B|LINE|L1	-243803	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.000000	0.297450	
chunk0157_252_1	chr5	119876469	119876982	+	0	NA	Intergenic	Intergenic	247166	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.000000	0.359922	
chunk0097_434_1	chr2	63888161	63888504	+	0	NA	intron (NM_001001521, intron 8 of 9)	MER6A|DNA|TcMar-Tigger	46452	NM_006759	7360	Hs.516217	NM_006759	ENSG00000169764	UGP2	UDPG|UDPGP|UDPGP2|UGP1|UGPP1|UGPP2|pHC379	UDP-glucose pyrophosphorylase 2	protein-coding	0.002915	0.348837	
chunk0179_118_1	chr7	45554149	45554788	+	0	NA	Intergenic	L1MA9|LINE|L1	-19672	NM_001281768	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.006260	0.360938	317(AAGGACAGTCTGTTTA,-,0.00),318(AGGACAGTCTGTTTAA,+,0.00)
chunk0080_19_1	chr17	20965374	20965954	+	0	NA	intron (NR_123730, intron 5 of 5)	L1PA16|LINE|L1	27144	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.001724	0.356282	255(CTGAACAGGGAGTTCT,-,0.00),256(TGAACAGGGAGTTCTT,+,0.00)
chunk0047_321_1	chr12	74293809	74294074	+	0	NA	Intergenic	Intergenic	-1310	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.045283	0.582707	
chunk0130_222_1	chr3	134222855	134223304	+	0	NA	intron (NM_002958, intron 1 of 14)	intron (NM_002958, intron 1 of 14)	27665	NM_002958	6259	Hs.654562	NM_002958	ENSG00000163785	RYK	D3S3195|JTK5|JTK5A|RYK1	receptor like tyrosine kinase	protein-coding	0.008909	0.451111	227(AGGCACATGCTGTCTT,-,0.00),228(GGCACATGCTGTCTTC,+,0.00),264(AAGAACACTATGTTTT,-,0.00),265(AGAACACTATGTTTTT,+,0.00)
chunk0139_284_1	chr4	57130201	57130559	+	0	NA	intron (NR_034081, intron 1 of 4)	L1MC1|LINE|L1	-19995	NM_001553	3490	Hs.479808	NM_001553	ENSG00000163453	IGFBP7	AGM|FSTL2|IBP-7|IGFBP-7|IGFBP-7v|IGFBPRP1|MAC25|PSF|RAMSVPS|TAF	insulin like growth factor binding protein 7	protein-coding	0.002793	0.398329	
chunk0068_298_1	chr15	57117871	57118435	+	0	NA	intron (NM_003205, intron 5 of 19)	intron (NM_003205, intron 5 of 19)	-101277	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.001773	0.362832	
chunk0098_190_1	chr2	72102907	72103125	+	0	NA	Intergenic	Intergenic	44846	NM_019885	56603	Hs.91546	NM_019885	ENSG00000003137	CYP26B1	CYP26A2|P450RAI-2|P450RAI2|RHFCA	cytochrome P450 family 26 subfamily B member 1	protein-coding	0.000000	0.378995	
chunk0076_408_1	chr16	72773095	72773818	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-108447	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.004149	0.393646	
chunk0139_424_1	chr4	64167213	64167422	+	0	NA	Intergenic	Intergenic	242143	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.000000	0.366667	
chunk0052_51_1	chr13	20994005	20994209	+	0	NA	intron (NM_014572, intron 2 of 7)	intron (NM_014572, intron 2 of 7)	-44679	NR_104058	101930748	Hs.637638	NR_104058	ENSG00000233780	LINC00367	-	long intergenic non-protein coding RNA 367	ncRNA	0.000000	0.443902	
chunk0190_384_1	chr8	40085585	40086246	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-67553	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.004539	0.362538	416(ATTACACACTGTCCCC,+,0.00)
chunk0034_323_1	chr11	35304315	35304990	+	0	NA	intron (NM_001195728, intron 6 of 11)	intron (NM_001195728, intron 6 of 11)	114906	NM_004171	6506	Hs.502338	NM_004171	ENSG00000110436	SLC1A2	EAAT2|EIEE41|GLT-1|HBGT	solute carrier family 1 member 2	protein-coding	0.004444	0.420118	
chunk0118_441_1	chr22	39019966	39020215	+	0	NA	Intergenic	AluSq2|SINE|Alu	-1023	NM_152426	140564	Hs.629775	NM_152426	ENSG00000243811	APOBEC3D	A3D|APOBEC3DE|APOBEC3E|ARP6	apolipoprotein B mRNA editing enzyme catalytic subunit 3D	protein-coding	0.012048	0.480000	
chunk0042_120_1	chr12	3349863	3350062	+	0	NA	Intergenic	Intergenic	-31387	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.010050	0.490000	
chunk0166_420_1	chr6	52569996	52570395	+	0	NA	intron (NM_012288, intron 1 of 10)	intron (NM_012288, intron 1 of 10)	6869	NM_012288	9697	Hs.520182	NM_012288	ENSG00000065308	TRAM2	-	translocation associated membrane protein 2	protein-coding	0.002506	0.400000	
chunk0158_123_1	chr5	127003920	127004680	+	0	NA	intron (NM_178450, intron 1 of 4)	intron (NM_178450, intron 1 of 4)	26508	NM_178450	115123	Hs.132441	NM_178450	ENSG00000173926	MARCH3	MARCH-III|RNF173	membrane associated ring-CH-type finger 3	protein-coding	0.006579	0.428384	
chunk0113_40_1	chr20	49895547	49895971	+	0	NA	Intergenic	Intergenic	17980	NM_001135773	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.011792	0.451765	
chunk0139_358_1	chr4	60286670	60287301	+	0	NA	Intergenic	L1P3|LINE|L1	-635634	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.006339	0.349684	
chunk0165_458_1	chr6	40973894	40974394	+	0	NA	intron (NR_110873, intron 1 of 5)	L1PREC2|LINE|L1	49136	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.006000	0.359281	
chunk0176_56_1	chr7	11211739	11212246	+	0	NA	Intergenic	Intergenic	238120	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.001972	0.322835	
chunk0181_45_1	chr7	79903602	79903830	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-231108	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.004386	0.366812	
chunk0060_461_1	chr14	55241564	55242172	+	0	NA	Intergenic	L1MC4|LINE|L1	-29435	NM_017943	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.008224	0.422003	286(AGGAACATTTTGTACT,-,0.00),287(GGAACATTTTGTACTG,+,0.00)
chunk0158_285_1	chr5	131774900	131775357	+	0	NA	intron (NM_001008738, intron 1 of 16)	intron (NM_001008738, intron 1 of 16)	21935	NM_133372	96459	Hs.591273	NM_133372	ENSG00000217128	FNIP1	-	folliculin interacting protein 1	protein-coding	0.008753	0.316594	
chunk0160_150_1	chr5	151489274	151489524	+	0	NA	3' UTR (NM_078483, exon 11 of 11)	3' UTR (NM_078483, exon 11 of 11)	32749	NR_106752	102465246		NR_106752	ENSG00000276622	MIR6499	hsa-mir-6499|mir-6499	microRNA 6499	ncRNA	0.032000	0.537849	
chunk0104_140_1	chr2	173432878	173433080	+	0	NA	Intergenic	Intergenic	78146	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.014851	0.408867	
chunk0147_139_1	chr4	174614000	174614276	+	0	NA	Intergenic	Intergenic	-91240	NM_001256305	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.003623	0.353791	
chunk0121_381_1	chr3	25195685	25196163	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	21592	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.004184	0.294363	
chunk0056_411_1	chr13	94215341	94215879	+	0	NA	intron (NM_005708, intron 4 of 8)	intron (NM_005708, intron 4 of 8)	-27619	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.000000	0.304267	
chunk0199_240_1	chr9	5499964	5500459	+	0	NA	Intergenic	LTR46-int|LTR|ERV1	-10334	NM_025239	80380	Hs.532279	NM_025239	ENSG00000197646	PDCD1LG2	B7DC|Btdc|CD273|PD-L2|PDCD1L2|PDL2|bA574F11.2	programmed cell death 1 ligand 2	protein-coding	0.010101	0.481855	
chunk0040_108_1	chr11	111918818	111919047	+	0	NA	promoter-TSS (NM_080659)	promoter-TSS (NM_080659)	55	NM_080659	91894	Hs.97013	NM_080659	ENSG00000149300	C11orf52	-	chromosome 11 open reading frame 52	protein-coding	0.030568	0.552174	
chunk0046_304_1	chr12	62272132	62272636	+	0	NA	intron (NM_006313, intron 1 of 20)	intron (NM_006313, intron 1 of 20)	12025	NR_106740	102465133		NR_106740	ENSG00000284360	MIR6125	hsa-mir-6125|mir-6125	microRNA 6125	ncRNA	0.000000	0.293069	
chunk0112_453_1	chr20	48812067	48812660	+	0	NA	intron (NM_020820, intron 1 of 39)	intron (NM_020820, intron 1 of 39)	15520	NM_020820	57580	Hs.153310	NM_020820	ENSG00000124126	PREX1	P-REX1	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	protein-coding	0.003373	0.316498	
chunk0182_411_1	chr7	100942368	100942868	+	0	NA	Intergenic	Intergenic	-6802	NM_005960	4584	Hs.703577	NM_005960	ENSG00000169894	MUC3A	MUC-3A|MUC3	mucin 3A, cell surface associated	protein-coding	0.014000	0.381238	
chunk0013_185_1	chr1	169070586	169070866	+	0	NA	intron (NR_104091, intron 1 of 4)	intron (NR_104091, intron 1 of 4)	16279	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.003571	0.423488	
chunk0072_150_1	chr15	92797018	92797427	+	0	NA	TTS (NR_033769)	TTS (NR_033769)	1738	NR_033769	728619	Hs.684129	NR_033769		ASB9P1	-	ankyrin repeat and SOCS box containing 9 pseudogene 1	pseudo	0.004890	0.382927	
chunk0127_116_1	chr3	90259865	90260350	+	0	NA	Intergenic	Intergenic	1152583	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.002062	0.312757	
chunk0080_441_1	chr17	36705254	36705886	+	0	NA	Intergenic	G-rich|Low_complexity|Low_complexity	103974	NM_024864	79922	Hs.194864	NM_024864	ENSG00000278619	MRM1	-	mitochondrial rRNA methyltransferase 1	protein-coding	0.020570	0.513428	
chunk0138_217_1	chr4	38906897	38907325	+	0	NA	intron (NR_033290, intron 4 of 12)	intron (NR_033290, intron 4 of 12)	39079	NR_030300	693159		NR_030300	ENSG00000207944	MIR574	MIR574-3p|MIRN574|hsa-mir-574|mir-574	microRNA 574	ncRNA	0.011682	0.456876	
chunk0024_197_1	chr10	36321570	36321891	+	0	NA	Intergenic	L1PA15|LINE|L1	543428	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.006231	0.329193	
chunk0044_415_1	chr12	41519638	41520149	+	0	NA	intron (NM_001164595, intron 5 of 9)	intron (NM_001164595, intron 5 of 9)	82154	NM_013377	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.009785	0.433594	
chunk0148_391_1	chr5	14788247	14788780	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	37499	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.007505	0.425094	
chunk0117_277_1	chr22	24195665	24196038	+	0	NA	Intergenic	LTR48B|LTR|ERV1	14375	NM_019601	56241	Hs.131819	NM_019601	ENSG00000099994	SUSD2	BK65A6.2|W5C5	sushi domain containing 2	protein-coding	0.000000	0.430481	
chunk0192_321_1	chr8	67085622	67085920	+	0	NA	intron (NM_001291339, intron 1 of 25)	intron (NM_001291339, intron 1 of 25)	1923	NM_001291339	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.000000	0.304348	
chunk0155_282_1	chr5	96088045	96088405	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	9087	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.008333	0.429363	
chunk0202_370_1	chr9	80556661	80556860	+	0	NA	Intergenic	Intergenic	581737	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.000000	0.310000	
chunk0131_423_1	chr3	153305210	153305888	+	0	NA	Intergenic	Intergenic	143337	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.004425	0.396171	
chunk0167_228_1	chr6	67291961	67292626	+	0	NA	Intergenic	Intergenic	-763058	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.007519	0.339339	
chunk0060_338_1	chr14	51651227	51651759	+	0	NA	promoter-TSS (NM_152330)	promoter-TSS (NM_152330)	251	NR_037676	145438	Hs.645410	NR_037676	ENSG00000273888	FRMD6-AS1	C14orf82	FRMD6 antisense RNA 1	ncRNA	0.105263	0.718574	
chunk0142_434_1	chr4	105014345	105014544	+	0	NA	Intergenic	Intergenic	-131431	NM_017628	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.000000	0.365000	
chunk0066_134_1	chr15	31214849	31215090	+	0	NA	Intergenic	Intergenic	15878	NM_001243538	283710	Hs.591097	NM_001243538		LOC283710	-	uncharacterized LOC283710	protein-coding	0.012448	0.607438	
chunk0018_171_1	chr1	219022008	219022220	+	0	NA	intron (NR_031644, intron 6 of 6)	L1MA3|LINE|L1	151674	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.004717	0.492958	
chunk0207_214_1	chr9	131469357	131469844	+	0	NA	intron (NM_013318, intron 12 of 30)	intron (NM_013318, intron 12 of 30)	-16065	NR_003050	692093		NR_003050	ENSG00000231587	SNORD62B	U62|U62B	small nucleolar RNA, C/D box 62B	snoRNA	0.012320	0.504098	180(AGGCACTGGGAGTGCC,-,0.00),216(CAGCTCAGGATGTGCT,-,0.00),217(AGCTCAGGATGTGCTG,+,0.00)
chunk0167_309_1	chr6	71479193	71479648	+	0	NA	Intergenic	Intergenic	58393	NR_121615	102724000	Hs.145785	NR_121615		LINC01626	-	long intergenic non-protein coding RNA 1626	ncRNA	0.004396	0.383772	246(TAGGACTTTGTGTTCC,-,0.00),247(AGGACTTTGTGTTCCT,+,0.00)
chunk0064_62_1	chr14	90052814	90053541	+	0	NA	Intergenic	L1ME2z|LINE|L1	-8588	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.006878	0.379121	
chunk0039_130_1	chr11	98307559	98307784	+	0	NA	Intergenic	Intergenic	-713305	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.349558	
chunk0180_171_1	chr7	65375738	65376018	+	0	NA	intron (NM_001287534, intron 1 of 1)	intron (NM_001287534, intron 1 of 1)	2079	NM_152626	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.025000	0.526690	
chunk0089_429_1	chr18	69949613	69950145	+	0	NA	intron (NM_006566, intron 1 of 6)	(CA)n|Simple_repeat|Simple_repeat	-2026	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.011278	0.457786	
chunk0189_412_1	chr8	27740237	27741079	+	0	NA	intron (NM_001304529, intron 5 of 6)	L2a|LINE|L2	31995	NR_130761	55246	Hs.445512	NM_018246	ENSG00000147419	CCDC25	-	coiled-coil domain containing 25	protein-coding	0.003563	0.408066	
chunk0109_398_1	chr2	240280610	240280986	+	0	NA	Intergenic	L1MA3|LINE|L1	-140142	NM_148961	150677	Hs.148586	NM_148961	ENSG00000178602	OTOS	OTOSP	otospiralin	protein-coding	0.005319	0.328912	
chunk0073_234_1	chr16	11394848	11395128	+	0	NA	Intergenic	Intergenic	49550	NR_130754	116028	Hs.347524	NM_152308	ENSG00000175643	RMI2	BLAP18|C16orf75	RecQ mediated genome instability 2	protein-coding	0.014286	0.508897	214(AAGCACAATGTGATCT,-,0.00),215(AGCACAATGTGATCTT,+,0.00)
chunk0172_338_1	chr6	138664074	138664537	+	0	NA	Intergenic	L2c|LINE|L2	-27363	NR_033896	441172	Hs.92290	NR_033896		FLJ46906	-	uncharacterized LOC441172	ncRNA	0.008639	0.409483	
chunk0153_271_1	chr5	72879549	72880030	+	0	NA	intron (NM_153188, intron 9 of 24)	intron (NM_153188, intron 9 of 24)	1198	NR_039968	100616152		NR_039968	ENSG00000263593	MIR4804	-	microRNA 4804	ncRNA	0.012474	0.419087	
chunk0211_453_1	chrX	130108537	130108836	+	0	NA	intron (NM_001127197, intron 1 of 8)	intron (NM_001127197, intron 1 of 8)	1814	NM_001421	2000	Hs.271940	NM_001421	ENSG00000102034	ELF4	ELFR|MEF	E74 like ETS transcription factor 4	protein-coding	0.010033	0.563333	
chunk0141_315_1	chr4	87156512	87156891	+	0	NA	Intergenic	L1MEd|LINE|L1	63567	NM_001292003	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.005277	0.344737	166(CAGAACAGGAAGTCCC,-,0.00),167(AGAACAGGAAGTCCCC,+,0.00)
chunk0019_287_1	chr1	228769865	228770350	+	0	NA	Intergenic	Intergenic	35030	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.020619	0.520576	
chunk0031_20_1	chr10	121844057	121844275	+	0	NA	intron (NM_001001976, intron 8 of 11)	AluJo|SINE|Alu	83897	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.013761	0.447489	
chunk0038_375_1	chr11	93437451	93437958	+	0	NA	exon (NM_181645, exon 14 of 14)	exon (NM_181645, exon 14 of 14)	105676	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.005917	0.358268	
chunk0016_391_1	chr1	202974795	202975052	+	0	NA	Intergenic	Intergenic	-7647	NM_016243	51706	Hs.334832	NM_016243	ENSG00000159348	CYB5R1	B5R.1|B5R1|B5R2|NQO3A2|humb5R2	cytochrome b5 reductase 1	protein-coding	0.007782	0.410853	
chunk0195_144_1	chr8	95143319	95143927	+	0	NA	intron (NM_024613, intron 1 of 1)	L2c|LINE|L2	9902	NM_024613	79666	Hs.29724	NM_024613	ENSG00000175895	PLEKHF2	EAPF|PHAFIN2|ZFYVE18	pleckstrin homology and FYVE domain containing 2	protein-coding	0.016447	0.426929	
chunk0154_175_1	chr5	80016834	80017462	+	0	NA	intron (NM_001306213, intron 2 of 22)	L4_B_Mam|LINE|RTE-X	-18151	NM_003248	7060	Hs.211426	NM_003248	ENSG00000113296	THBS4	TSP-4|TSP4	thrombospondin 4	protein-coding	0.003185	0.311606	
chunk0025_15_1	chr10	47389614	47390048	+	0	NA	Intergenic	L1MB4|LINE|L1	-5558	NM_153034	118738	Hs.27788	NM_153034	ENSG00000265763	ZNF488	-	zinc finger protein 488	protein-coding	0.006912	0.372414	
chunk0113_63_1	chr20	50427905	50428104	+	0	NA	Intergenic	Intergenic	-82317	NM_002827	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.015075	0.520000	
chunk0049_159_1	chr12	92043069	92043578	+	0	NA	intron (NR_132341, intron 1 of 4)	MIR3|SINE|MIR	98390	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.003929	0.398039	
chunk0169_142_1	chr6	101456716	101457343	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	58044	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.315287	337(AGGAACACCATGGCCT,-,0.00),338(GGAACACCATGGCCTT,+,0.00)
chunk0107_190_1	chr2	216132765	216133167	+	0	NA	intron (NM_021141, intron 10 of 20)	intron (NM_021141, intron 10 of 20)	23669	NM_021141	7520	Hs.388739	NM_021141	ENSG00000079246	XRCC5	KARP-1|KARP1|KU80|KUB2|Ku86|NFIV	X-ray repair cross complementing 5	protein-coding	0.000000	0.404467	
chunk0146_171_1	chr4	160318806	160319689	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	1051401	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.005663	0.420814	
chunk0210_258_1	chrX	83935897	83936580	+	0	NA	Intergenic	L1PB4|LINE|L1	75112	NM_001271680	1538	Hs.444230	NM_021118	ENSG00000183035	CYLC1	CYCL1	cylicin 1	protein-coding	0.002928	0.346491	
chunk0139_196_1	chr4	54772285	54773301	+	0	NA	Intergenic	L2a|LINE|L2	114865	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.007874	0.406096	
chunk0185_239_1	chr7	129855226	129855724	+	0	NA	intron (NM_182697, intron 3 of 4)	intron (NM_182697, intron 3 of 4)	-80461	NR_029615	406959		NR_029615	ENSG00000207691	MIR183	MIRN183|miR-183|miRNA183	microRNA 183	ncRNA	0.012048	0.364729	
chunk0151_345_1	chr5	54310626	54310898	+	0	NA	promoter-TSS (NM_019087)	promoter-TSS (NM_019087)	-189	NM_019087	54622	Hs.659125	NM_019087	ENSG00000185305	ARL15	ARFRP2	ADP ribosylation factor like GTPase 15	protein-coding	0.077206	0.630037	
chunk0128_241_1	chr3	108430217	108430642	+	0	NA	intron (NM_014981, intron 27 of 41)	intron (NM_014981, intron 27 of 41)	98893	NM_014981	22989	Hs.731060	NM_014981	ENSG00000144821	MYH15	-	myosin heavy chain 15	protein-coding	0.004706	0.312207	
chunk0130_228_1	chr3	134382035	134382371	+	0	NA	Intergenic	Intergenic	-6786	NM_001278683	51421	Hs.426312	NM_016201	ENSG00000114019	AMOTL2	LCCP	angiomotin like 2	protein-coding	0.008929	0.551929	
chunk0011_139_1	chr1	147242140	147242639	+	0	NA	promoter-TSS (NM_024568)	promoter-TSS (NM_024568)	-252	NM_001256337	9557	Hs.191164	NM_004284	ENSG00000131778	CHD1L	ALC1|CHDL	chromodomain helicase DNA binding protein 1 like	protein-coding	0.058116	0.530000	131(AAGAACAGTTTGATCT,-,0.00),132(AGAACAGTTTGATCTT,+,0.00)
chunk0189_162_1	chr8	23225133	23225406	+	0	NA	promoter-TSS (NM_003844)	promoter-TSS (NM_003844)	48	NR_033928	389641	Hs.591835	NR_033928	ENSG00000246582	LOC389641	-	uncharacterized LOC389641	ncRNA	0.069597	0.642336	
chunk0179_112_1	chr7	45093300	45093568	+	0	NA	Intergenic	L1MB8|LINE|L1	-4540	NM_001146334	23148	Hs.96633	NM_001146334	ENSG00000136274	NACAD	-	NAC alpha domain containing	protein-coding	0.014925	0.327138	
chunk0151_267_1	chr5	52492049	52492248	+	0	NA	Intergenic	Intergenic	-295792	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.005025	0.445000	
chunk0101_269_1	chr2	133644334	133644707	+	0	NA	Intergenic	Intergenic	-76060	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.002681	0.368984	
chunk0019_90_1	chr1	224543254	224543549	+	0	NA	Intergenic	MER21C|LTR|ERVL	-73076	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.010169	0.452703	
chunk0157_258_1	chr5	119989315	119989514	+	0	NA	Intergenic	L1PA7|LINE|L1	359855	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.005025	0.355000	
chunk0130_309_1	chr3	137020221	137020907	+	0	NA	Intergenic	Intergenic	62699	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.007289	0.377001	
chunk0079_129_1	chr17	12672922	12673426	+	0	NA	intron (NR_104605, intron 2 of 2)	intron (NR_104605, intron 2 of 2)	7284	NM_001146312	93649	Hs.462257	NM_153604	ENSG00000141052	MYOCD	MYCD	myocardin	protein-coding	0.005952	0.354455	
chunk0037_338_1	chr11	77316961	77317187	+	0	NA	Intergenic	Intergenic	-29656	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.004425	0.365639	
chunk0066_57_1	chr15	28456871	28457172	+	0	NA	intron (NR_031672, intron 1 of 2)	intron (NR_031672, intron 1 of 2)	30530	NR_039732	100616223		NR_039732	ENSG00000276941	MIR4509-1	-	microRNA 4509-1	ncRNA	0.036545	0.688742	
chunk0093_449_1	chr19	58513936	58514297	+	0	NA	exon (NM_001316978, exon 3 of 3)	exon (NM_001316978, exon 3 of 3)	-2051	NM_012254	10998	Hs.292177	NM_012254	ENSG00000083807	SLC27A5	ACSB|ACSVL6|BACS|BAL|FACVL3|FATP-5|FATP5|VLACSR|VLCS-H2|VLCSH2	solute carrier family 27 member 5	protein-coding	0.127424	0.715470	
chunk0190_252_1	chr8	36978231	36978662	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	194122	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.006961	0.395833	
chunk0050_434_1	chr12	110306357	110306783	+	0	NA	intron (NM_170665, intron 5 of 19)	L1PA17|LINE|L1	25343	NM_001681	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.007042	0.409836	244(GAGAACAGACAGTATT,-,0.00),245(AGAACAGACAGTATTT,+,0.00)
chunk0152_108_1	chr5	58466907	58467228	+	0	NA	Intergenic	Intergenic	-6928	NM_006622	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.009346	0.484472	
chunk0041_266_1	chr11	129100164	129100871	+	0	NA	intron (NM_001142685, intron 4 of 21)	L1MB3|LINE|L1	-76324	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.007072	0.566384	
chunk0141_73_1	chr4	78052669	78053378	+	0	NA	Intergenic	L1ME3G|LINE|L1	-4547	NM_001166133	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.008463	0.347887	
chunk0091_67_1	chr19	4939421	4939828	+	0	NA	intron (NM_001048201, intron 5 of 16)	intron (NM_001048201, intron 5 of 16)	6937	NR_039902	100616337		NR_039902	ENSG00000263409	MIR4747	mir-4747	microRNA 4747	ncRNA	0.012285	0.519608	214(TAGGTCAGTGTGTTCC,-,0.00),215(AGGTCAGTGTGTTCCC,+,0.00)
chunk0041_277_1	chr11	129319088	129319613	+	0	NA	Intergenic	Intergenic	-56636	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.005714	0.406844	260(TTAAACAGGCTGTCCC,-,0.00),261(TAAACAGGCTGTCCCT,+,0.00)
chunk0200_360_1	chr9	25646717	25647141	+	0	NA	Intergenic	MIRb|SINE|MIR	31929	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.004717	0.378824	
chunk0022_192_1	chr10	13448321	13448520	+	0	NA	intron (NM_152751, intron 7 of 8)	intron (NM_152751, intron 7 of 8)	54556	NM_001100912	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.015075	0.525000	
chunk0014_281_1	chr1	180544041	180544409	+	0	NA	Intergenic	Intergenic	-14749	NR_125716	148756		NR_125716	ENSG00000236719	OVAAL	LINC01131|OVAL	ovarian adenocarcinoma amplified long non-coding RNA	ncRNA	0.010870	0.544715	
chunk0162_141_1	chr6	3178673	3179136	+	0	NA	Intergenic	Intergenic	16863	NR_038295	100507194	Hs.678053	NR_038295	ENSG00000230269	LINC02525	-	long intergenic non-protein coding RNA 2525	ncRNA	0.019438	0.536638	
chunk0171_15_1	chr6	119854524	119854908	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-160463	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.000000	0.329870	158(TAGTACAAGTTGTGCT,-,0.00),159(AGTACAAGTTGTGCTT,+,0.00)
chunk0035_372_1	chr11	49284944	49285276	+	0	NA	Intergenic	Intergenic	-76440	NM_001193471	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.000000	0.357357	
chunk0054_445_1	chr13	51412404	51413274	+	0	NA	intron (NM_012141, intron 4 of 17)	intron (NM_012141, intron 4 of 17)	40300	NM_012141	26512	Hs.439440	NM_012141	ENSG00000102786	INTS6	DBI-1|DDX26|DDX26A|DICE1|HDB|INT6|Notchl2	integrator complex subunit 6	protein-coding	0.005747	0.374282	
chunk0209_9_1	chrX	35056539	35056847	+	0	NA	Intergenic	Intergenic	113897	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.006494	0.365696	122(AAAACAACGTGTGCCT,+,0.00)
chunk0080_304_1	chr17	31738203	31738449	+	0	NA	Intergenic	L2a|LINE|L2	120981	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.028455	0.461538	
chunk0086_108_1	chr18	14170203	14170762	+	0	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-8615	NR_040113	440482	Hs.632352	NM_001029999		ANKRD20A5P	ANKRD20A5	ankyrin repeat domain 20 family member A5, pseudogene	pseudo	0.008945	0.571429	
chunk0001_188_1	chr1	7339894	7340430	+	0	NA	intron (NM_015215, intron 5 of 22)	MER58A|DNA|hAT-Charlie	-431107	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.005597	0.461825	
chunk0070_141_1	chr15	71071437	71071921	+	0	NA	Intergenic	LTR40a|LTR|ERVL	43821	NM_001102658	196993	Hs.646533	NM_001102658	ENSG00000225362	CT62	-	cancer/testis antigen 62	protein-coding	0.002066	0.420619	
chunk0042_54_1	chr12	1830982	1831366	+	0	NA	exon (NM_001039029, exon 4 of 5)	exon (NM_001039029, exon 4 of 5)	10907	NM_001163926	654429	Hs.585579	NM_001039029	ENSG00000166159	LRTM2	-	leucine rich repeats and transmembrane domains 2	protein-coding	0.049479	0.633766	
chunk0193_179_1	chr8	75123570	75124390	+	0	NA	Intergenic	Intergenic	123826	NM_001286777	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.006098	0.401949	
chunk0191_155_1	chr8	49071978	49072232	+	0	NA	promoter-TSS (NM_001256597)	promoter-TSS (NM_001256597)	-236	NM_001007176	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.027559	0.560784	
chunk0155_428_1	chr5	100551602	100552096	+	0	NA	intron (NM_198507, intron 1 of 2)	MLT1C|LTR|ERVL-MaLR	16544	NM_198507	345757	Hs.356108	NM_198507	ENSG00000174132	FAM174A	HGS_RE408|NS5ATP6|TMEM157|UNQ1912	family with sequence similarity 174 member A	protein-coding	0.008097	0.393939	
chunk0118_304_1	chr22	35033896	35034193	+	0	NA	Intergenic	MIR|SINE|MIR	-32092	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.010101	0.520134	
chunk0119_75_1	chr22	41280261	41280484	+	0	NA	intron (NM_001278651, intron 3 of 16)	intron (NM_001278651, intron 3 of 16)	5645	NM_001278651	5905	Hs.183800	NM_002883	ENSG00000100401	RANGAP1	Fug1|RANGAP|SD	Ran GTPase activating protein 1	protein-coding	0.000000	0.540179	
chunk0172_111_1	chr6	135033212	135033646	+	0	NA	intron (NM_001145158, intron 3 of 16)	intron (NM_001145158, intron 3 of 16)	21469	NM_001145158	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.006912	0.413793	
chunk0204_47_1	chr9	92911604	92912329	+	0	NA	Intergenic	Intergenic	29399	NR_111003	642943	Hs.643602	NR_111003		LOC642943	-	SPATA31 subfamily A pseudogene	pseudo	0.006897	0.420110	
chunk0156_450_1	chr5	114906965	114907233	+	0	NA	Intergenic	THE1D|LTR|ERVL-MaLR	-133686	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.453532	
chunk0065_295_1	chr14	102699523	102699764	+	0	NA	intron (NM_015156, intron 3 of 11)	intron (NM_015156, intron 3 of 11)	-77836	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.004149	0.413223	
chunk0168_153_1	chr6	83194747	83194979	+	0	NA	promoter-TSS (NM_001199917)	promoter-TSS (NM_001199917)	-927	NM_001199917	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.008621	0.309013	
chunk0137_150_1	chr4	15701287	15701549	+	0	NA	Intergenic	Intergenic	-1532	NM_004334	683	Hs.720344	NM_004334	ENSG00000109743	BST1	CD157	bone marrow stromal cell antigen 1	protein-coding	0.007634	0.368821	
chunk0123_386_1	chr3	48740189	48740783	+	0	NA	Intergenic	Intergenic	-23208	NM_001146179	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.006734	0.512605	292(GAGTACACAGTGACCT,-,0.00),293(AGTACACAGTGACCTT,+,0.00)
chunk0035_234_1	chr11	45880001	45880465	+	0	NA	intron (NM_021117, intron 11 of 11)	intron (NM_021117, intron 11 of 11)	-5263	NM_005456	9479	Hs.234249	NM_005456	ENSG00000121653	MAPK8IP1	IB1|JIP-1|JIP1|PRKM8IP	mitogen-activated protein kinase 8 interacting protein 1	protein-coding	0.008621	0.447312	272(AGGCGCACTCTGTCCT,-,0.00),273(GGCGCACTCTGTCCTT,+,0.00)
chunk0104_52_1	chr2	171370029	171370385	+	0	NA	intron (NM_024770, intron 2 of 9)	intron (NM_024770, intron 2 of 9)	-64044	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.000000	0.313725	
chunk0017_315_1	chr1	211258522	211258790	+	0	NA	promoter-TSS (NM_001136225)	promoter-TSS (NM_001136225)	-710	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.029851	0.483271	
chunk0155_354_1	chr5	97142416	97142615	+	0	NA	exon (NM_153234, exon 1 of 6)	exon (NM_153234, exon 1 of 6)	301	NM_153234	167410	Hs.656702	NM_153234	ENSG00000145721	LIX1	C5orf11|Lft	limb and CNS expressed 1	protein-coding	0.010050	0.440000	
chunk0202_269_1	chr9	77063634	77064223	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	44273	NM_001013735	442425	Hs.553843	NM_001013735	ENSG00000204612	FOXB2	bA159H20.4	forkhead box B2	protein-coding	0.010187	0.401695	
chunk0164_233_1	chr6	23191444	23192110	+	0	NA	Intergenic	L1MCc|LINE|L1	622328	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.001502	0.380810	
chunk0109_156_1	chr20	3898526	3898964	+	0	NA	intron (NM_153640, intron 1 of 6)	intron (NM_153640, intron 1 of 6)	8929	NM_153640	80025	Hs.114180	NM_024960	ENSG00000125779	PANK2	C20orf48|HARP|HSS|NBIA1|PKAN	pantothenate kinase 2	protein-coding	0.006849	0.332574	
chunk0056_161_1	chr13	84464464	84464959	+	0	NA	intron (NR_046871, intron 3 of 6)	intron (NR_046871, intron 3 of 6)	-318943	NR_132852	106635542		NR_132852		SNORA107	-	small nucleolar RNA, H/ACA box 107	snoRNA	0.006061	0.336694	223(CAGGACAGATAGTACC,-,0.00),224(AGGACAGATAGTACCT,+,0.00)
chunk0002_37_1	chr1	12485517	12485983	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-21496	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.008584	0.436831	
chunk0183_220_1	chr7	106672168	106672877	+	0	NA	Intergenic	L1PA6|LINE|L1	-11334	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.009873	0.501408	
chunk0098_215_1	chr2	73110565	73110764	+	0	NA	intron (NM_015470, intron 1 of 4)	intron (NM_015470, intron 1 of 4)	2354	NM_015470	26056	Hs.24557	NM_015470	ENSG00000135631	RAB11FIP5	GAF1|RIP11|pp75	RAB11 family interacting protein 5	protein-coding	0.000000	0.465000	59(CAAGACAGGCTGTTCT,-,0.00),60(AAGACAGGCTGTTCTT,+,0.00)
chunk0172_168_1	chr6	136096062	136096261	+	0	NA	intron (NM_018945, intron 2 of 12)	intron (NM_018945, intron 2 of 12)	154150	NM_138419	113115	Hs.121536	NM_138419	ENSG00000146410	MTFR2	DUFD1|FAM54A	mitochondrial fission regulator 2	protein-coding	0.010050	0.495000	
chunk0080_148_1	chr17	27840672	27841178	+	0	NA	Intergenic	MER57A1|LTR|ERV1	-40396	NM_000625	4843	Hs.709191	NM_000625	ENSG00000007171	NOS2	HEP-NOS|INOS|NOS|NOS2A	nitric oxide synthase 2	protein-coding	0.001976	0.364892	
chunk0045_55_1	chr12	45292692	45293367	+	0	NA	intron (NM_001142678, intron 1 of 19)	intron (NM_001142678, intron 1 of 19)	346	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.004444	0.390533	
chunk0182_118_1	chr7	94110264	94110463	+	0	NA	Intergenic	Intergenic	-105985	NM_005868	10282	Hs.489132	NM_005868	ENSG00000105829	BET1	HBET1	Bet1 golgi vesicular membrane trafficking protein	protein-coding	0.010050	0.385000	70(AAGGACAGGCTGTTCT,-,0.00),71(AGGACAGGCTGTTCTG,+,0.00)
chunk0068_24_1	chr15	50856488	50856852	+	0	NA	Intergenic	Intergenic	-52002	NM_007347	23431	Hs.413366	NM_007347	ENSG00000081014	AP4E1	CPSQ4|SPG51|STUT1	adaptor related protein complex 4 subunit epsilon 1	protein-coding	0.010989	0.441096	
chunk0110_26_1	chr20	10469768	10469967	+	0	NA	intron (NM_001009608, intron 2 of 7)	intron (NM_001009608, intron 2 of 7)	34564	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.030151	0.460000	
chunk0109_387_1	chr2	240076088	240076441	+	0	NA	Intergenic	Intergenic	-30192	NM_173351	150681	Hs.626616	NM_173351	ENSG00000178586	OR6B3	OR6B3P|OR6B3Q	olfactory receptor family 6 subfamily B member 3	protein-coding	0.000000	0.409605	
chunk0056_118_1	chr13	83002405	83002711	+	0	NA	Intergenic	Intergenic	879835	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.013072	0.345277	
chunk0040_401_1	chr11	120525735	120526221	+	0	NA	intron (NM_014619, intron 1 of 20)	MIRc|SINE|MIR	14232	NM_014619	2900	Hs.538738	NM_014619	ENSG00000149403	GRIK4	EAA1|GRIK|GluK4|KA1	glutamate ionotropic receptor kainate type subunit 4	protein-coding	0.016461	0.466119	
chunk0188_126_1	chr8	9150459	9150697	+	0	NA	5' UTR (NM_024607, exon 1 of 2)	5' UTR (NM_024607, exon 1 of 2)	132	NM_024607	79660	Hs.458513	NM_024607	ENSG00000173281	PPP1R3B	GL|PPP1R4|PTG	protein phosphatase 1 regulatory subunit 3B	protein-coding	0.088235	0.682008	
chunk0063_201_1	chr14	81219221	81219424	+	0	NA	intron (NM_201595, intron 1 of 8)	intron (NM_201595, intron 1 of 8)	1630	NM_015859	2957	Hs.592334	NM_015859	ENSG00000165417	GTF2A1	TF2A1|TFIIA|TFIIA-42|TFIIAL	general transcription factor IIA subunit 1	protein-coding	0.054187	0.553922	
chunk0197_459_1	chr8	127891763	127892436	+	0	NA	intron (NR_003367, intron 2 of 8)	intron (NR_003367, intron 2 of 8)	56624	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.008915	0.507418	446(GTTACATGCTGTTCTC,+,0.00)
chunk0037_418_1	chr11	79926776	79927123	+	0	NA	Intergenic	L2b|LINE|L2	-486298	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.002882	0.393678	
chunk0123_157_1	chr3	43465051	43465655	+	0	NA	intron (NM_018075, intron 11 of 12)	Tigger3c|DNA|TcMar-Tigger	-113391	NR_046757	100873954	Hs.600984	NR_046757		SNRK-AS1	-	SNRK antisense RNA 1	ncRNA	0.000000	0.365289	
chunk0192_58_1	chr8	59959268	59959467	+	0	NA	Intergenic	Intergenic	322028	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.005025	0.290000	
chunk0152_344_1	chr5	62575901	62576361	+	0	NA	intron (NM_016338, intron 27 of 29)	intron (NM_016338, intron 27 of 29)	-2604	NM_181506	100130733	Hs.721348	NM_181506	ENSG00000186105	LRRC70	SLRN	leucine rich repeat containing 70	protein-coding	0.008696	0.405640	
chunk0088_26_1	chr18	43789440	43790221	+	0	NA	Intergenic	Intergenic	-512180	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.005122	0.347826	
chunk0169_19_1	chr6	96779184	96779383	+	0	NA	Intergenic	Intergenic	58194	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.000000	0.350000	
chunk0039_360_1	chr11	106009186	106009432	+	0	NA	3' UTR (NM_032424, exon 3 of 3)	3' UTR (NM_032424, exon 3 of 3)	12918	NM_032424	84437	Hs.266782	NM_032424	ENSG00000170903	MSANTD4	KIAA1826	Myb/SANT DNA binding domain containing 4 with coiled-coils	protein-coding	0.004065	0.372470	
chunk0025_207_1	chr10	53596160	53596533	+	0	NA	Intergenic	Intergenic	-824646	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.005362	0.374332	
chunk0165_151_1	chr6	33721481	33722008	+	0	NA	TTS (NM_001142883)	TTS (NM_001142883)	-9993	NM_032340	84300	Hs.732448	NM_032340	ENSG00000137288	UQCC2	C6orf125|C6orf126|Cbp6|M19|MC3DN7|MNF1|bA6B20.2	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding	0.017078	0.428030	299(TAGAACTGTTTGTTCT,-,0.00),300(AGAACTGTTTGTTCTT,+,0.00)
chunk0078_21_1	chr17	767190	767420	+	0	NA	intron (NM_016080, intron 8 of 8)	L2a|LINE|L2	-14968	NM_018146	55178	Hs.182729	NM_018146	ENSG00000171861	MRM3	RMTL1|RNMTL1	mitochondrial rRNA methyltransferase 3	protein-coding	0.008696	0.385281	
chunk0044_71_1	chr12	27971975	27972255	+	0	NA	promoter-TSS (NM_002820)	promoter-TSS (NM_002820)	-132	NM_002820	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.003571	0.298932	
chunk0060_168_1	chr14	45447138	45447743	+	0	NA	Intergenic	L1MA4A|LINE|L1	-194038	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.001653	0.328383	
chunk0193_230_1	chr8	76620294	76620660	+	0	NA	intron (NR_024360, intron 2 of 3)	intron (NR_024360, intron 2 of 3)	-60803	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.008197	0.370572	
chunk0118_148_1	chr22	29971159	29971420	+	0	NA	intron (NM_021090, intron 3 of 19)	intron (NM_021090, intron 3 of 19)	-35760	NR_106876	102466742		NR_106876	ENSG00000275818	MIR6818	hsa-mir-6818	microRNA 6818	ncRNA	0.007663	0.335878	178(AAAACATACAGTTCTC,+,0.00)
chunk0124_269_1	chr3	57354975	57355610	+	0	NA	intron (NM_001291661, intron 59 of 73)	L1MC4a|LINE|L1	-62610	NM_001142733	142686	Hs.665154	NM_130387	ENSG00000239388	ASB14	-	ankyrin repeat and SOCS box containing 14	protein-coding	0.000000	0.317610	35(GGGAACACAGAGATCC,-,0.00),36(GGAACACAGAGATCCT,+,0.00)
chunk0057_379_1	chr13	109240481	109240743	+	0	NA	Intergenic	Intergenic	-73309	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.007634	0.349810	
chunk0091_291_1	chr19	12365862	12366158	+	0	NA	promoter-TSS (NM_030824)	promoter-TSS (NM_030824)	-349	NM_030824	79973	Hs.253193	NM_030824	ENSG00000198342	ZNF442	-	zinc finger protein 442	protein-coding	0.016892	0.579125	
chunk0075_52_1	chr16	47524138	47524424	+	0	NA	intron (NM_001031835, intron 7 of 31)	intron (NM_001031835, intron 7 of 31)	62982	NM_001031835	5257	Hs.78060	NM_000293	ENSG00000102893	PHKB	-	phosphorylase kinase regulatory subunit beta	protein-coding	0.006993	0.337979	
chunk0122_47_1	chr3	28468708	28469252	+	0	NA	intron (NM_001040432, intron 4 of 9)	L1MA2|LINE|L1	-106298	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.000000	0.315596	
chunk0160_289_1	chr5	158023311	158023651	+	0	NA	Intergenic	L2b|LINE|L2	-164306	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.020588	0.475073	
chunk0057_79_1	chr13	98451533	98452055	+	0	NA	3' UTR (NM_001032296, exon 11 of 11)	3' UTR (NM_001032296, exon 11 of 11)	70331	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.021073	0.529637	
chunk0195_229_1	chr8	97390112	97390541	+	0	NA	intron (NR_125390, intron 2 of 2)	Charlie9|DNA|hAT-Charlie	56171	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.009324	0.344186	
chunk0036_210_1	chr11	63558564	63558763	+	0	NA	intron (NM_017878, intron 2 of 3)	intron (NM_017878, intron 2 of 3)	4720	NM_017878	54979	Hs.272805	NM_017878	ENSG00000133328	PLAAT2	HRASLS2|PLA1/2-2|PLAAT-2	phospholipase A and acyltransferase 2	protein-coding	0.015075	0.600000	
chunk0178_194_1	chr7	34380171	34380567	+	0	NA	intron (NR_033664, intron 4 of 4)	MER57A-int|LTR|ERV1	-277870	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.002525	0.342569	
chunk0014_122_1	chr1	177451072	177451388	+	0	NA	Intergenic	LTR16A|LTR|ERVL	99644	NR_126001	102724661	Hs.146628	NR_126001		LINC01645	-	long intergenic non-protein coding RNA 1645	ncRNA	0.006329	0.400631	
chunk0069_214_1	chr15	63519863	63520235	+	0	NA	intron (NR_046342, intron 1 of 15)	L1MC4|LINE|L1	15538	NR_046341	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.010753	0.369973	
chunk0040_8_1	chr11	108620912	108621252	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-27344	NM_001308019	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.002941	0.313783	
chunk0024_188_1	chr10	36146861	36147679	+	0	NA	Intergenic	Intergenic	368968	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.001222	0.352869	
chunk0033_140_1	chr11	15441622	15441885	+	0	NA	Intergenic	Intergenic	-202132	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.003802	0.428030	
chunk0208_133_1	chrX	15606607	15607605	+	0	NA	intron (NR_126564, intron 1 of 1)	LTR10C|LTR|ERV1	4225	NR_126564	104798195	Hs.131674	NR_126564	ENSG00000225833	GS1-594A7.3	-	uncharacterized LOC104798195	ncRNA	0.005010	0.344344	407(ATGTACTTTATGTTCT,-,0.00),408(TGTACTTTATGTTCTT,+,0.00)
chunk0195_308_1	chr8	98781984	98782666	+	0	NA	intron (NM_001256312, intron 3 of 12)	intron (NM_001256312, intron 3 of 12)	43346	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.011730	0.477306	414(ATCACAGCCTGTACCT,+,0.00)
chunk0070_380_1	chr15	76552773	76552972	+	0	NA	intron (NM_020843, intron 22 of 30)	L1PA15|LINE|L1	-33775	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.020101	0.530000	
chunk0068_427_1	chr15	59482648	59482977	+	0	NA	intron (NM_152450, intron 3 of 8)	intron (NM_152450, intron 3 of 8)	44639	NM_152450	145773	Hs.531168	NM_152450	ENSG00000157470	FAM81A	-	family with sequence similarity 81 member A	protein-coding	0.012158	0.412121	
chunk0171_207_1	chr6	125877296	125877611	+	0	NA	intron (NM_001122842, intron 4 of 15)	intron (NM_001122842, intron 4 of 15)	-41771	NM_001199622	135112	Hs.171426	NM_181782	ENSG00000111912	NCOA7	ERAP140|ESNA1|NCOA7-AS|Nbla00052|Nbla10993|TLDC4|dJ187J11.3	nuclear receptor coactivator 7	protein-coding	0.000000	0.471519	
chunk0136_349_1	chr3	195850819	195851131	+	0	NA	Intergenic	MIRb|SINE|MIR	31420	NR_106887	102465977		NR_106887	ENSG00000276489	MIR6829	hsa-mir-6829	microRNA 6829	ncRNA	0.016026	0.492013	
chunk0196_197_1	chr8	106340701	106341170	+	0	NA	intron (NM_001198533, intron 1 of 16)	intron (NM_001198533, intron 1 of 16)	70757	NM_018002	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.004264	0.306383	
chunk0072_289_1	chr15	98611750	98612152	+	0	NA	Intergenic	Intergenic	-36588	NM_000875	3480	Hs.643120	NM_000875	ENSG00000140443	IGF1R	CD221|IGFIR|IGFR|JTK13	insulin like growth factor 1 receptor	protein-coding	0.007463	0.444169	
chunk0120_11_1	chr3	1106161	1106705	+	0	NA	intron (NM_014461, intron 1 of 22)	intron (NM_014461, intron 1 of 22)	13775	NM_014461	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.005515	0.328440	
chunk0011_270_1	chr1	151156150	151156531	+	0	NA	promoter-TSS (NM_024575)	promoter-TSS (NM_024575)	-289	NM_001204848	100534012	Hs.732060	NM_001204848	ENSG00000163156	TNFAIP8L2-SCNM1	SCNM1	TNFAIP8L2-SCNM1 readthrough	protein-coding	0.002625	0.463351	97(GTGACAGTCTGTGCTC,+,0.00)
chunk0183_39_1	chr7	103784713	103785479	+	0	NA	intron (NM_005045, intron 3 of 64)	intron (NM_005045, intron 3 of 64)	204420	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.001305	0.312907	
chunk0087_352_1	chr18	40890484	40890761	+	0	NA	Intergenic	L2a|LINE|L2	629975	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.003610	0.255396	
chunk0045_184_1	chr12	47193847	47194111	+	0	NA	intron (NM_001281429, intron 2 of 2)	intron (NM_001281429, intron 2 of 2)	6167	NR_039847	100616486		NR_039847	ENSG00000263838	MIR4698	-	microRNA 4698	ncRNA	0.003788	0.509434	
chunk0079_244_1	chr17	16069379	16069792	+	0	NA	intron (NM_006311, intron 31 of 45)	intron (NM_006311, intron 31 of 45)	-69893	NM_001042697	125150	Hs.593985	NM_001042697	ENSG00000214941	ZSWIM7	SWS1	zinc finger SWIM-type containing 7	protein-coding	0.012107	0.376812	
chunk0008_204_1	chr1	93501791	93502468	+	0	NA	intron (NM_017737, intron 2 of 14)	intron (NM_017737, intron 2 of 14)	53998	NM_017737	54874	Hs.134060	NM_017737	ENSG00000137942	FNBP1L	C1orf39|TOCA1	formin binding protein 1 like	protein-coding	0.001477	0.296460	305(AAGAACTGAATGTACA,-,0.00),306(AGAACTGAATGTACAG,+,0.00)
chunk0057_260_1	chr13	105513334	105513777	+	0	NA	Intergenic	Intergenic	-7874	NR_040247	282706	Hs.558713	NR_040247	ENSG00000232307	DAOA-AS1	DAOA-AS|DAOAAS|G30	DAOA antisense RNA 1	ncRNA	0.009029	0.362613	
chunk0124_370_1	chr3	59258937	59259146	+	0	NA	Intergenic	Intergenic	-209052	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.004785	0.476190	76(AAGCACAGGCTGTACA,-,0.00),77(AGCACAGGCTGTACAT,+,0.00)
chunk0119_64_1	chr22	41022315	41022694	+	0	NA	Intergenic	CpG	51217	NR_132979	106635682		NR_132979		SNORD140	-	small nucleolar RNA, C/D box 140	snoRNA	0.094987	0.705263	
chunk0176_374_1	chr7	18526481	18526686	+	0	NA	intron (NM_001204147, intron 1 of 9)	intron (NM_001204147, intron 1 of 9)	17306	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.000000	0.364078	36(GGGAACATCTAGTTCT,-,0.00),37(GGAACATCTAGTTCTT,+,0.00)
chunk0056_331_1	chr13	91211469	91211906	+	0	NA	promoter-TSS (NR_047004)	promoter-TSS (NR_047004)	11	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.009153	0.433790	
chunk0008_459_1	chr1	99785374	99785890	+	0	NA	Intergenic	Intergenic	-19839	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.001938	0.344294	
chunk0170_178_1	chr6	111818606	111818894	+	0	NA	intron (NM_002037, intron 2 of 13)	intron (NM_002037, intron 2 of 13)	54702	NM_002037	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.006944	0.446367	
chunk0153_69_1	chr5	67926293	67926692	+	0	NA	Intergenic	L1M5|LINE|L1	133279	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.002506	0.295000	
chunk0015_173_1	chr1	186756033	186756322	+	0	NA	Intergenic	Intergenic	-72723	NM_001311193	5321	Hs.497200	NM_024420	ENSG00000116711	PLA2G4A	GURDP|PLA2G4|cPLA2|cPLA2-alpha	phospholipase A2 group IVA	protein-coding	0.013841	0.424138	
chunk0061_38_1	chr14	56028368	56028910	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-89736	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.005535	0.462247	
chunk0112_88_1	chr20	38034560	38034759	+	0	NA	intron (NM_021215, intron 1 of 6)	MIRb|SINE|MIR	1113	NM_021215	58490	Hs.278839	NM_021215	ENSG00000101413	RPRD1B	C20orf77|CREPT|K-H|Kub5-Hera|NET60|dJ1057B20.2	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.005025	0.480000	
chunk0085_388_1	chr18	9887891	9888543	+	0	NA	TTS (NM_001098529)	TTS (NM_001098529)	2491	NM_032243	84203	Hs.98712	NM_032243	ENSG00000168454	TXNDC2	SPTRX|SPTRX1	thioredoxin domain containing 2	protein-coding	0.012270	0.395100	
chunk0015_407_1	chr1	191135263	191135813	+	0	NA	Intergenic	L1MCa|LINE|L1	510648	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.003636	0.362976	
chunk0107_215_1	chr2	216740989	216741253	+	0	NA	Intergenic	Intergenic	-45572	NM_000599	3488	Hs.607212	NM_000599	ENSG00000115461	IGFBP5	IBP5	insulin like growth factor binding protein 5	protein-coding	0.011364	0.475472	
chunk0128_7_1	chr3	103623752	103624337	+	0	NA	Intergenic	L1MA4|LINE|L1	-99928	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.005128	0.320819	
chunk0145_393_1	chr4	152411674	152412266	+	0	NA	intron (NM_033632, intron 1 of 11)	intron (NM_033632, intron 1 of 11)	-29458	NM_001013415	55294	Hs.561245	NM_018315	ENSG00000109670	FBXW7	AGO|CDC4|FBW6|FBW7|FBX30|FBXO30|FBXW6|SEL-10|SEL10|hAgo|hCdc4	F-box and WD repeat domain containing 7	protein-coding	0.005068	0.322091	
chunk0058_457_1	chr13	113992925	113993217	+	0	NA	intron (NM_007368, intron 21 of 23)	intron (NM_007368, intron 21 of 23)	-64080	NR_047495	100861555	Hs.353773	NR_047495	ENSG00000260910	LINC00565	-	long intergenic non-protein coding RNA 565	ncRNA	0.006849	0.385666	
chunk0104_381_1	chr2	180328694	180329229	+	0	NA	Intergenic	L1MA2|LINE|L1	-321908	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.001869	0.416045	184(AAGCACTCACAGTACC,-,0.00),185(AGCACTCACAGTACCT,+,0.00)
chunk0176_232_1	chr7	15779612	15779902	+	0	NA	Intergenic	L1MEg|LINE|L1	91379	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.003448	0.274914	
chunk0062_178_1	chr14	69658361	69658756	+	0	NA	5' UTR (NM_014734, exon 2 of 6)	5' UTR (NM_014734, exon 2 of 6)	46965	NM_014734	9766	Hs.440025	NM_014734	ENSG00000100647	SUSD6	DRAGO|KIAA0247	sushi domain containing 6	protein-coding	0.022785	0.452020	
chunk0137_289_1	chr4	23906886	23907500	+	0	NA	Intergenic	Intergenic	-17116	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.013029	0.400000	
chunk0086_8_1	chr18	11995629	11995996	+	0	NA	intron (NM_014214, intron 1 of 7)	intron (NM_014214, intron 1 of 7)	14384	NM_014214	3613	Hs.743311	NM_014214	ENSG00000141401	IMPA2	-	inositol monophosphatase 2	protein-coding	0.008174	0.502717	249(AAGAACTCTGTGTACC,-,0.00),250(AGAACTCTGTGTACCT,+,0.00)
chunk0152_8_1	chr5	56275570	56275769	+	0	NA	Intergenic	Intergenic	-42310	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.005025	0.400000	
chunk0181_273_1	chr7	86240901	86241352	+	0	NA	Intergenic	HAL1|LINE|L1	-402788	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.006652	0.382743	181(AAGTACACAGTGTTCT,-,0.00),182(AGTACACAGTGTTCTG,+,0.00)
chunk0033_52_1	chr11	13332072	13332436	+	0	NA	intron (NM_001178, intron 3 of 19)	intron (NM_001178, intron 3 of 19)	54527	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.002747	0.463014	
chunk0205_438_1	chr9	115326202	115326955	+	0	NA	intron (NM_017418, intron 4 of 7)	intron (NM_017418, intron 4 of 7)	184760	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.006640	0.399204	
chunk0120_46_1	chr3	2869801	2870468	+	0	NA	intron (NM_001206955, intron 7 of 23)	intron (NM_001206955, intron 7 of 23)	-22081	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.001499	0.351796	
chunk0159_402_1	chr5	147512615	147513057	+	0	NA	Intergenic	Intergenic	-2780	NM_001197294	1809	Hs.519659	NM_001387	ENSG00000113657	DPYSL3	CRMP-4|CRMP4|DRP-3|DRP3|LCRMP|ULIP|ULIP-1	dihydropyrimidinase like 3	protein-coding	0.006787	0.406321	
chunk0001_197_1	chr1	7702849	7703273	+	0	NA	intron (NM_015215, intron 11 of 22)	intron (NM_015215, intron 11 of 22)	-68208	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.016509	0.515294	
chunk0198_366_1	chr8	140983645	140983856	+	0	NA	intron (NM_153831, intron 1 of 31)	intron (NM_153831, intron 1 of 31)	17563	NM_005607	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.004739	0.438679	
chunk0198_377_1	chr8	141195979	141196252	+	0	NA	TTS (NM_014957)	TTS (NM_014957)	32459	NM_001286648	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.007326	0.423358	
chunk0087_284_1	chr18	38770598	38770797	+	0	NA	Intergenic	Intergenic	851478	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.000000	0.355000	
chunk0061_206_1	chr14	60298896	60299547	+	0	NA	TTS (NM_177952)	TTS (NM_177952)	49973	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.003072	0.346626	
chunk0164_48_1	chr6	18835565	18835889	+	0	NA	Intergenic	Intergenic	263943	NR_030312	693125		NR_030312	ENSG00000207775	MIR548A1	MIRN548A1	microRNA 548a-1	ncRNA	0.000000	0.400000	
chunk0178_426_1	chr7	41145784	41146261	+	0	NA	Intergenic	Intergenic	44418	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.004193	0.443515	
chunk0155_121_1	chr5	93053564	93053837	+	0	NA	Intergenic	Intergenic	517643	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.003663	0.255474	
chunk0049_280_1	chr12	93898692	93898903	+	0	NA	Intergenic	LTR39|LTR|ERV1	-160974	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.004739	0.391509	
chunk0156_50_1	chr5	103093724	103094135	+	0	NA	intron (NM_017676, intron 7 of 7)	intron (NM_017676, intron 7 of 7)	26209	NM_017676	54826	Hs.24088	NM_017676	ENSG00000145723	GIN1	GIN-1|TGIN1|ZH2C2	gypsy retrotransposon integrase 1	protein-coding	0.002433	0.305825	177(TAGTACTGAATGTGCT,-,0.00),178(AGTACTGAATGTGCTC,+,0.00)
chunk0172_418_1	chr6	140319233	140319555	+	0	NA	Intergenic	Intergenic	114142	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.006211	0.356037	
chunk0115_443_1	chr21	32200001	32200243	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	78943	NM_018944	54069	Hs.190518	NM_018944	ENSG00000159055	MIS18A	B28|C21orf45|C21orf46|FASP1|MIS18alpha|hMis18alpha	MIS18 kinetochore protein A	protein-coding	0.020661	0.448560	
chunk0011_369_1	chr1	153395192	153395579	+	0	NA	Intergenic	Intergenic	-4197	NM_002964	6279	Hs.416073	NM_002964	ENSG00000143546	S100A8	60B8AG|CAGA|CFAG|CGLA|CP-10|L1Ag|MA387|MIF|MRP8|NIF|P8	S100 calcium binding protein A8	protein-coding	0.015504	0.559278	
chunk0070_448_1	chr15	78429417	78430041	+	0	NA	Intergenic	L2c|LINE|L2	-8447	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.006410	0.424000	
chunk0211_27_1	chrX	107972288	107972731	+	0	NA	Intergenic	MIRb|SINE|MIR	9861	NM_031273	56156	Hs.333130	NM_031273	ENSG00000170925	TEX13B	TGC3B|TSGA5	testis expressed 13B	protein-coding	0.000000	0.355856	
chunk0031_157_1	chr10	125165398	125165907	+	0	NA	Intergenic	L2b|LINE|L2	-4597	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.005894	0.433333	
chunk0189_332_1	chr8	26391740	26392011	+	0	NA	intron (NM_004331, intron 2 of 5)	L2c|LINE|L2	8868	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.011070	0.408088	24(GATCACAGACTGTTCT,-,0.00),25(ATCACAGACTGTTCTT,+,0.00)
chunk0120_325_1	chr3	10460037	10460773	+	0	NA	intron (NM_001001331, intron 1 of 22)	intron (NM_001001331, intron 1 of 22)	45179	NM_001001331	491	Hs.268942	NM_001683	ENSG00000157087	ATP2B2	PMCA2|PMCA2a|PMCA2i	ATPase plasma membrane Ca2+ transporting 2	protein-coding	0.004076	0.549525	
chunk0064_105_1	chr14	91105738	91105997	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-8146	NM_001286472	80017	Hs.309849	NM_024952	ENSG00000133943	DGLUCY	C14orf159	D-glutamate cyclase	protein-coding	0.007722	0.392308	
chunk0093_296_1	chr19	52558729	52559092	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-11363	NM_018260	55762	Hs.235167	NM_018260	ENSG00000167562	ZNF701	-	zinc finger protein 701	protein-coding	0.008264	0.453297	
chunk0147_270_1	chr4	183765134	183765529	+	0	NA	Intergenic	Intergenic	-32691	NR_132761	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.022785	0.436869	
chunk0065_110_1	chr15	24621589	24621951	+	0	NA	Intergenic	L1PA13|LINE|L1	-53624	NM_018958	23742	Hs.649663	NM_018958	ENSG00000185823	NPAP1	C15orf2	nuclear pore associated protein 1	protein-coding	0.008287	0.564738	
chunk0162_448_1	chr5	180666547	180667051	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-17175	NM_182925	2324	Hs.646917	NM_002020	ENSG00000037280	FLT4	FLT-4|FLT41|LMPH1A|LMPHM1|PCL|VEGFR-3|VEGFR3	fms related tyrosine kinase 4	protein-coding	0.021825	0.461386	
chunk0040_344_1	chr11	118523822	118524149	+	0	NA	3' UTR (NM_001197104, exon 36 of 36)	3' UTR (NM_001197104, exon 36 of 36)	-3510	NM_001080441	143941	Hs.653449	NM_001080441	ENSG00000172425	TTC36	HBP21	tetratricopeptide repeat domain 36	protein-coding	0.012232	0.460366	
chunk0142_314_1	chr4	100679469	100679901	+	0	NA	Intergenic	Intergenic	-4572	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.000000	0.404157	191(AAGAAGATGCTGTGCC,-,0.00)
chunk0043_218_1	chr12	19792397	19792899	+	0	NA	Intergenic	L1ME3D|LINE|L1	-222037	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.001992	0.302187	
chunk0205_361_1	chr9	113592505	113593210	+	0	NA	intron (NM_001276260, intron 3 of 6)	MIR|SINE|MIR	-1063	NM_144489	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.015603	0.464589	187(TGGCCAGGCTGTTCTC,+,0.00)
chunk0060_418_1	chr14	53327563	53327815	+	0	NA	Intergenic	HAL1|LINE|L1	174335	NR_110062	101927620		NR_110062	ENSG00000258731	LOC101927620	-	uncharacterized LOC101927620	ncRNA	0.000000	0.335968	
chunk0152_401_1	chr5	64912130	64912755	+	0	NA	intron (NM_001297644, intron 11 of 12)	L1ME3B|LINE|L1	143524	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.000000	0.337061	
chunk0119_455_1	chr22	50396819	50397571	+	0	NA	intron (NM_001242900, intron 3 of 22)	intron (NM_001242900, intron 3 of 22)	53878	NM_001242899	9701	Hs.449098	NM_014678	ENSG00000100239	PPP6R2	KIAA0685|PP6R2|SAP190|SAPS2	protein phosphatase 6 regulatory subunit 2	protein-coding	0.007979	0.499336	
chunk0189_274_1	chr8	25359697	25360422	+	0	NA	intron (NM_024940, intron 28 of 51)	intron (NM_024940, intron 28 of 51)	14657	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.013793	0.477961	309(GTGGACAGGATGTGCC,-,0.00),310(TGGACAGGATGTGCCG,+,0.00)
chunk0136_300_1	chr3	195095172	195095371	+	0	NA	intron (NR_104188, intron 1 of 3)	intron (NR_104188, intron 1 of 3)	683	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.050251	0.545000	
chunk0064_403_1	chr14	99403257	99403882	+	0	NA	intron (NM_032233, intron 11 of 12)	intron (NM_032233, intron 11 of 12)	77320	NM_032233	84193	Hs.510407	NM_032233	ENSG00000183576	SETD3	C14orf154|hSETD3	SET domain containing 3, actin histidine methyltransferase	protein-coding	0.008000	0.408946	429(AGGAACATTTTGTGTT,-,0.00)
chunk0055_339_1	chr13	69681554	69681928	+	0	NA	Intergenic	Intergenic	-425472	NR_002717	6315	Hs.676453	NR_002717		ATXN8OS	KLHL1AS|NCRNA00003|SCA8	ATXN8 opposite strand lncRNA	ncRNA	0.000000	0.298667	
chunk0012_291_1	chr1	162060965	162061342	+	0	NA	Intergenic	Intergenic	-8638	NM_001164757	9722	Hs.731942	NM_014697	ENSG00000198929	NOS1AP	6330408P19Rik|CAPON	nitric oxide synthase 1 adaptor protein	protein-coding	0.002653	0.330688	
chunk0081_245_1	chr17	42990077	42990313	+	0	NA	intron (NM_173079, intron 3 of 4)	L2b|LINE|L2	-8234	NM_000988	6155	Hs.514196	NM_000988	ENSG00000131469	RPL27	DBA16|L27	ribosomal protein L27	protein-coding	0.000000	0.324895	
chunk0195_302_1	chr8	98735722	98736397	+	0	NA	intron (NM_006281, intron 4 of 10)	L1M5|LINE|L1	89612	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.000000	0.332840	
chunk0209_219_1	chrX	44841407	44841673	+	0	NA	Intergenic	L2c|LINE|L2	-2463	NM_022076	63904	Hs.534478	NM_022076	ENSG00000189037	DUSP21	LMWDSP21	dual specificity phosphatase 21	protein-coding	0.011278	0.374532	
chunk0169_304_1	chr6	106056406	106056979	+	0	NA	Intergenic	Intergenic	-29628	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.003490	0.409408	208(AGGAACTACTTGTGCT,-,0.00),209(GGAACTACTTGTGCTT,+,0.00)
chunk0168_75_1	chr6	79663273	79663649	+	0	NA	intron (NM_031469, intron 1 of 3)	L1PA6|LINE|L1	32178	NM_031469	83699	Hs.302772	NM_031469	ENSG00000198478	SH3BGRL2	-	SH3 domain binding glutamate rich protein like 2	protein-coding	0.010638	0.501326	
chunk0014_128_1	chr1	177611079	177611494	+	0	NA	Intergenic	MIRb|SINE|MIR	-89238	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.004819	0.425481	
chunk0095_218_1	chr2	18762726	18763098	+	0	NA	Intergenic	Intergenic	-173332	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.002688	0.364611	
chunk0127_70_1	chr3	89408337	89408797	+	0	NA	intron (NM_005233, intron 9 of 16)	intron (NM_005233, intron 9 of 16)	301043	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.008696	0.331887	
chunk0189_111_1	chr8	22122798	22123421	+	0	NA	intron (NM_018411, intron 6 of 17)	intron (NM_018411, intron 6 of 17)	7943	NM_018411	55806	Hs.272367	NM_005144	ENSG00000168453	HR	ALUNC|AU|HSA277165|HYPT4|MUHH|MUHH1	HR lysine demethylase and nuclear receptor corepressor	protein-coding	0.020867	0.490385	
chunk0212_154_1	chrX	132060645	132061337	+	0	NA	intron (NM_001042452, intron 2 of 9)	intron (NM_001042452, intron 2 of 9)	37383	NM_001042452	51765	Hs.444247	NM_016542	ENSG00000134602	STK26	MASK|MST4	serine/threonine kinase 26	protein-coding	0.010116	0.414141	449(AGGCACACATTGTTTT,-,0.00),450(GGCACACATTGTTTTT,+,0.00)
chunk0131_60_1	chr3	142844146	142844738	+	0	NA	intron (NM_013363, intron 3 of 8)	L1ME2z|LINE|L1	44761	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.005068	0.370995	
chunk0119_153_1	chr22	43088911	43089259	+	0	NA	intron (NR_027779, intron 1 of 11)	CpG	343	NM_012263	25809	Hs.660298	NM_012263	ENSG00000100271	TTLL1	C22orf7|HS323M22B	tubulin tyrosine ligase like 1	protein-coding	0.077586	0.561605	
chunk0005_337_1	chr1	61142789	61143422	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	60797	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.014218	0.449527	
chunk0126_353_1	chr3	82887939	82888419	+	0	NA	Intergenic	Intergenic	-1126380	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.002083	0.370062	
chunk0151_5_1	chr5	40775312	40775873	+	0	NA	intron (NM_206907, intron 2 of 9)	L2a|LINE|L2	-19622	NM_012382	23548	Hs.348915	NM_012382	ENSG00000113638	TTC33	OSRF	tetratricopeptide repeat domain 33	protein-coding	0.001783	0.357651	
chunk0061_347_1	chr14	63662818	63663132	+	0	NA	Intergenic	MER52A|LTR|ERV1	-21052	NM_001258272	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.022293	0.606349	
chunk0132_124_1	chr3	156025151	156025419	+	0	NA	Intergenic	L2c|LINE|L2	-95263	NM_172160	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.007463	0.375465	
chunk0111_58_1	chr20	22744766	22745275	+	0	NA	Intergenic	Intergenic	-137503	NR_109883	101929685	Hs.563018	NR_109883	ENSG00000237396	LNCNEF	LINC01384|lncRNA-NEF	lncRNA neighboring enhancer of FOXA2	ncRNA	0.001965	0.419608	
chunk0061_265_1	chr14	61430127	61430820	+	0	NA	intron (NM_006255, intron 2 of 13)	L1P3|LINE|L1	109030	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.005772	0.410663	
chunk0103_41_1	chr2	159268224	159268423	+	0	NA	intron (NM_001128213, intron 5 of 10)	intron (NM_001128213, intron 5 of 10)	18229	NM_152528	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.000000	0.355000	
chunk0084_146_1	chr17	76557297	76557703	+	0	NA	promoter-TSS (NR_038111)	promoter-TSS (NR_038111)	-264	NR_038109	100507246	Hs.288215	NR_038108	ENSG00000163597	SNHG16	Nbla10727|Nbla12061|ncRAN	small nucleolar RNA host gene 16	ncRNA	0.044335	0.570025	187(AGGGACAAACTGTGTT,-,0.00),188(GGGACAAACTGTGTTG,+,0.00)
chunk0087_358_1	chr18	41162109	41162945	+	0	NA	Intergenic	(CAAA)n|Simple_repeat|Simple_repeat	358070	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.007177	0.385902	357(AGGTTCACTCTGTCCC,-,0.00),358(GGTTCACTCTGTCCCA,+,0.00)
chunk0081_376_1	chr17	47983444	47984244	+	0	NA	Intergenic	Intergenic	12888	NM_001278198	80279	Hs.20157	NM_025197	ENSG00000108465	CDK5RAP3	C53|HSF-27|IC53|LZAP|MST016|OK/SW-cl.114|PP1553	CDK5 regulatory subunit associated protein 3	protein-coding	0.016250	0.513109	
chunk0164_22_1	chr6	18062803	18063241	+	0	NA	Intergenic	L1MEg|LINE|L1	59598	NM_198586	378884	Hs.348351	NM_198586	ENSG00000187566	NHLRC1	EPM2A|EPM2B|MALIN|bA204B7.2	NHL repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.004566	0.375854	
chunk0081_367_1	chr17	47893514	47894063	+	0	NA	Intergenic	Intergenic	-2362	NM_003110	6668	Hs.514276	NM_003110	ENSG00000167182	SP2	-	Sp2 transcription factor	protein-coding	0.010929	0.467273	
chunk0071_317_1	chr15	86555219	86556303	+	0	NA	intron (NM_152336, intron 20 of 23)	MIRc|SINE|MIR	-238793	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.005535	0.383410	
chunk0141_133_1	chr4	80977802	80978342	+	0	NA	Intergenic	Intergenic	-52893	NM_001201	651	Hs.387411	NM_001201	ENSG00000152785	BMP3	BMP-3A	bone morphogenetic protein 3	protein-coding	0.005556	0.386322	
chunk0203_451_1	chr9	91460850	91461334	+	0	NA	Intergenic	Intergenic	-36466	NM_001290000	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.004132	0.331959	
chunk0150_204_1	chr5	35045084	35045468	+	0	NA	intron (NM_001306173, intron 1 of 12)	intron (NM_001306173, intron 1 of 12)	2859	NM_001306173	64902	Hs.34494	NM_031900	ENSG00000113492	AGXT2	AGT2|BAIBA|DAIBAT	alanine--glyoxylate aminotransferase 2	protein-coding	0.002604	0.324675	
chunk0154_83_1	chr5	77791549	77791845	+	0	NA	Intergenic	Intergenic	-15336	NM_001297738	6902	Hs.291212	NM_004607	ENSG00000171530	TBCA	-	tubulin folding cofactor A	protein-coding	0.003378	0.397306	41(GGACACATTGTGTTCT,-,0.00),42(GACACATTGTGTTCTT,+,0.00)
chunk0023_43_1	chr10	21254820	21255026	+	0	NA	Intergenic	Charlie17b|DNA|hAT-Charlie	80621	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.004854	0.541063	
chunk0163_311_1	chr6	14689066	14689437	+	0	NA	Intergenic	Intergenic	-403797	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.002695	0.403226	
chunk0082_129_1	chr17	55285535	55285964	+	0	NA	intron (NM_002126, intron 2 of 3)	intron (NM_002126, intron 2 of 3)	20789	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.020979	0.483721	
chunk0056_112_1	chr13	82794722	82795130	+	0	NA	Intergenic	MER21C|LTR|ERVL	1087467	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.007353	0.342298	
chunk0027_95_1	chr10	73715692	73716141	+	0	NA	intron (NR_026592, intron 9 of 11)	intron (NR_026592, intron 9 of 11)	14598	NR_026592	729096	Hs.709171	NR_026592	ENSG00000271816	BMS1P4	BMS1LP4	BMS1 pseudogene 4	pseudo	0.002227	0.388889	
chunk0106_127_1	chr2	199295020	199295372	+	0	NA	intron (NM_015265, intron 11 of 11)	intron (NM_015265, intron 11 of 11)	162900	NM_001172509	23314	Hs.516617	NM_015265	ENSG00000119042	SATB2	GLSS	SATB homeobox 2	protein-coding	0.005682	0.305949	
chunk0068_90_1	chr15	52076967	52077263	+	0	NA	Intergenic	Intergenic	35660	NM_001306168	10017	Hs.283672	NM_020396	ENSG00000137875	BCL2L10	BCL-B|Boo|Diva|bcl2-L-10	BCL2 like 10	protein-coding	0.010135	0.478114	65(GGGAACAGCGAGTCCT,-,0.00),66(GGAACAGCGAGTCCTG,+,0.00)
chunk0137_429_1	chr4	28314008	28314808	+	0	NA	Intergenic	Intergenic	-505174	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.002500	0.350811	
chunk0198_305_1	chr8	138318043	138318299	+	0	NA	intron (NM_015912, intron 2 of 19)	intron (NM_015912, intron 2 of 19)	178651	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.007812	0.369650	
chunk0092_270_1	chr19	33293115	33293572	+	0	NA	Intergenic	Intergenic	9221	NM_001287424	1050	Hs.76171	NM_004364	ENSG00000245848	CEBPA	C/EBP-alpha|CEBP	CCAAT enhancer binding protein alpha	protein-coding	0.017505	0.434498	
chunk0182_112_1	chr7	93592470	93592707	+	0	NA	Intergenic	MIRb|SINE|MIR	-17858	NM_001742	799	Hs.489127	NM_001742	ENSG00000004948	CALCR	CRT|CT-R|CTR|CTR1	calcitonin receptor	protein-coding	0.000000	0.344538	
chunk0156_129_1	chr5	106730657	106730940	+	0	NA	Intergenic	L1PREC2|LINE|L1	280216	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.010601	0.602113	
chunk0080_142_1	chr17	27531428	27531645	+	0	NA	intron (NM_014238, intron 2 of 20)	intron (NM_014238, intron 2 of 20)	59526	NM_014238	8844	Hs.133534	NM_014238	ENSG00000141068	KSR1	KSR|RSU2	kinase suppressor of ras 1	protein-coding	0.013825	0.610092	
chunk0183_104_1	chr7	105255481	105255689	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	13492	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.009615	0.387560	
chunk0100_457_1	chr2	121128796	121129311	+	0	NA	Intergenic	Intergenic	156149	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.013592	0.476744	
chunk0081_80_1	chr17	39327126	39327728	+	0	NA	intron (NM_001184906, intron 2 of 13)	L1MC4|LINE|L1	74229	NM_032875	84961	Hs.462946	NM_032875	ENSG00000108306	FBXL20	Fbl2|Fbl20	F-box and leucine rich repeat protein 20	protein-coding	0.009967	0.351575	319(AGGGACAGAATGAACC,-,0.00),320(GGGACAGAATGAACCC,+,0.00)
chunk0085_254_1	chr18	7585703	7585942	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	18506	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.008368	0.450000	95(CAGGACAGAGTGTTCA,-,0.00),96(AGGACAGAGTGTTCAT,+,0.00)
chunk0187_130_1	chr7	149205963	149206415	+	0	NA	intron (NM_003575, intron 2 of 7)	L2a|LINE|L2	10727	NM_003575	8427	Hs.729056	NM_003575	ENSG00000170265	ZNF282	HUB1	zinc finger protein 282	protein-coding	0.028761	0.479029	
chunk0085_409_1	chr18	10398120	10398681	+	0	NA	Intergenic	Intergenic	15970	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.007130	0.382562	
chunk0173_341_1	chr6	149021842	149022572	+	0	NA	intron (NM_005715, intron 7 of 7)	intron (NM_005715, intron 7 of 7)	-57523	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.020548	0.447332	
chunk0130_181_1	chr3	133459337	133460202	+	0	NA	intron (NM_003571, intron 4 of 6)	intron (NM_003571, intron 4 of 6)	59774	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.011561	0.445727	
chunk0105_299_1	chr2	190169685	190170117	+	0	NA	intron (NM_001042521, intron 2 of 2)	intron (NM_001042521, intron 2 of 2)	-10962	NM_001042519	84281	Hs.389311	NM_032321	ENSG00000187699	C2orf88	smAKAP	chromosome 2 open reading frame 88	protein-coding	0.009259	0.401848	193(GGTACAGGTTGTTTTG,+,0.00)
chunk0193_393_1	chr8	80435958	80436267	+	0	NA	Intergenic	L2c|LINE|L2	-49507	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.003236	0.487097	
chunk0118_142_1	chr22	29917435	29917958	+	0	NA	intron (NM_021090, intron 1 of 19)	intron (NM_021090, intron 1 of 19)	34527	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.003824	0.324427	
chunk0149_134_1	chr5	19863209	19863566	+	0	NA	intron (NM_001167667, intron 2 of 12)	MER45C|DNA|hAT-Tip100	22885	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.008403	0.446927	
chunk0155_297_1	chr5	96314421	96314788	+	0	NA	intron (NR_130776, intron 2 of 4)	L2c|LINE|L2	117555	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.005450	0.402174	
chunk0020_186_1	chr1	234751210	234751712	+	0	NA	Intergenic	Intergenic	27419	NR_038856	100506810	Hs.586634	NR_038856	ENSG00000227630	LINC01132	-	long intergenic non-protein coding RNA 1132	ncRNA	0.003984	0.441352	
chunk0060_162_1	chr14	45327456	45327952	+	0	NA	Intergenic	Intergenic	-74302	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.002016	0.354125	
chunk0125_317_1	chr3	70840564	70840987	+	0	NA	Intergenic	Intergenic	224148	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.004728	0.379717	
chunk0174_417_1	chr6	165805877	165806242	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-143959	NM_001130690	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.019178	0.442623	
chunk0006_27_1	chr1	64042531	64043171	+	0	NA	intron (NM_001083592, intron 2 of 6)	intron (NM_001083592, intron 2 of 6)	69354	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.012500	0.447738	327(GTGAACAGAATGTTCT,-,0.00),328(TGAACAGAATGTTCTC,+,0.00)
chunk0206_369_1	chr9	125934320	125934805	+	0	NA	intron (NM_001134778, intron 4 of 8)	intron (NM_001134778, intron 4 of 8)	186363	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.333333	
chunk0171_275_1	chr6	127768676	127769243	+	0	NA	intron (NM_001010923, intron 4 of 5)	intron (NM_001010923, intron 4 of 5)	132122	NM_001010923	387357	Hs.661756	NM_001010923	ENSG00000172673	THEMIS	C6orf190|C6orf207|GASP|SPOT|TSEPA	thymocyte selection associated	protein-coding	0.008818	0.343310	
chunk0173_259_1	chr6	147133506	147133933	+	0	NA	intron (NR_034115, intron 3 of 10)	L1MA9|LINE|L1	-25206	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.009368	0.338785	
chunk0070_442_1	chr15	78260912	78261414	+	0	NA	Intergenic	MER67A|LTR|ERV1	-2982	NM_018602	55466	Hs.513053	NM_018602	ENSG00000140403	DNAJA4	MST104|MSTP104|PRO1472	DnaJ heat shock protein family (Hsp40) member A4	protein-coding	0.005976	0.381710	
chunk0026_59_1	chr10	61111079	61111430	+	0	NA	Intergenic	Intergenic	94979	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.000000	0.383523	129(ATGAACACACTGGTCT,-,0.00),130(TGAACACACTGGTCTC,+,0.00)
chunk0189_338_1	chr8	26460147	26460736	+	0	NA	Intergenic	L1ME1|LINE|L1	53526	NM_007257	10687	Hs.591838	NM_007257	ENSG00000240694	PNMA2	MA2|MM2|RGAG2	PNMA family member 2	protein-coding	0.015280	0.415254	360(AGGAACACGATGTCCA,-,0.00),361(GGAACACGATGTCCAT,+,0.00)
chunk0173_404_1	chr6	150712290	150712851	+	0	NA	intron (NM_001029884, intron 2 of 16)	intron (NM_001029884, intron 2 of 16)	112707	NM_001029884	57480	Hs.189781	NM_001029884	ENSG00000120278	PLEKHG1	ARHGEF41	pleckstrin homology and RhoGEF domain containing G1	protein-coding	0.003565	0.387900	
chunk0172_412_1	chr6	140105929	140106136	+	0	NA	Intergenic	L1MCa|LINE|L1	-99220	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.019324	0.490385	90(AAGAACAGAATGTTCT,-,0.00),91(AGAACAGAATGTTCTG,+,0.00)
chunk0072_429_1	chr15	101208737	101209372	+	0	NA	intron (NM_014918, intron 2 of 2)	L1MC4|LINE|L1	42878	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.003150	0.356918	
chunk0068_287_1	chr15	56968836	56969220	+	0	NA	intron (NM_003205, intron 3 of 19)	MER4A1_|LTR|ERV1	50393	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.002604	0.415584	
chunk0037_162_1	chr11	73676126	73676610	+	0	NA	3' UTR (NM_001243719, exon 8 of 8)	3' UTR (NM_001243719, exon 8 of 8)	27678	NM_001130036	58473	Hs.445489	NM_021200	ENSG00000021300	PLEKHB1	KPL1|PHR1|PHRET1	pleckstrin homology domain containing B1	protein-coding	0.004132	0.325773	
chunk0056_462_1	chr13	95281316	95281575	+	0	NA	intron (NM_001105515, intron 1 of 20)	intron (NM_001105515, intron 1 of 20)	20001	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.003861	0.396154	
chunk0028_272_1	chr10	90938004	90938799	+	0	NA	Intergenic	Intergenic	-8899	NR_131214	105378427		NR_131214		XLOC_008559	-	uncharacterized LOC105378427	ncRNA	0.011321	0.442211	
chunk0063_350_1	chr14	85478999	85479350	+	0	NA	Intergenic	Intergenic	-50970	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.005698	0.369318	
chunk0060_412_1	chr14	53148702	53149158	+	0	NA	intron (NM_030637, intron 1 of 11)	MIR|SINE|MIR	4398	NM_001160147	80821	Hs.125525	NM_030637	ENSG00000100523	DDHD1	PA-PLA1|PAPLA1|SPG28	DDHD domain containing 1	protein-coding	0.002193	0.336980	
chunk0184_117_1	chr7	113789939	113790344	+	0	NA	Intergenic	Intergenic	128886	NM_002711	5506	Hs.458309	NM_002711	ENSG00000154415	PPP1R3A	GM|PP1G|PPP1R3	protein phosphatase 1 regulatory subunit 3A	protein-coding	0.009877	0.458128	
chunk0087_196_1	chr18	35767382	35767991	+	0	NA	Intergenic	L1MB8|LINE|L1	113117	NM_020474	2589	Hs.514806	NM_020474	ENSG00000141429	GALNT1	GALNAC-T1	polypeptide N-acetylgalactosaminyltransferase 1	protein-coding	0.006568	0.332787	
chunk0047_58_1	chr12	67496561	67497225	+	0	NA	Intergenic	Intergenic	-23189	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.004518	0.374436	
chunk0042_204_1	chr12	5944768	5944973	+	0	NA	intron (NM_001278597, intron 1 of 25)	intron (NM_001278597, intron 1 of 25)	389	NM_001278596	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.029268	0.495146	
chunk0174_167_1	chr6	158574862	158575428	+	0	NA	intron (NM_020823, intron 2 of 16)	MLT2B4|LTR|ERVL	-34562	NR_106981	102465694		NR_106981	ENSG00000278571	MIR7161	hsa-mir-7161	microRNA 7161	ncRNA	0.005300	0.446208	
chunk0174_176_1	chr6	159047819	159048051	+	0	NA	Intergenic	Intergenic	-2783	NM_054114	117289	Hs.529984	NM_054114	ENSG00000164691	TAGAP	ARHGAP47|FKSG15|IDDM21|TAGAP1	T cell activation RhoGTPase activating protein	protein-coding	0.017241	0.454936	60(AAGGACAGTGAGTTCC,-,0.00),61(AGGACAGTGAGTTCCG,+,0.00),81(GGGGACTGTGAGTTCT,-,0.00),82(GGGACTGTGAGTTCTA,+,0.00)
chunk0166_159_1	chr6	45535856	45536084	+	0	NA	intron (NM_001278478, intron 5 of 5)	intron (NM_001278478, intron 5 of 5)	113393	NM_001278478	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.013158	0.432314	
chunk0046_142_1	chr12	58092891	58093372	+	0	NA	Intergenic	MER39|LTR|ERV1	151469	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.004158	0.410788	
chunk0191_88_1	chr8	47637565	47638331	+	0	NA	intron (NM_001080394, intron 10 of 19)	L1MC3|LINE|L1	100216	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.002611	0.353325	298(AGGAACAGAGAGCTCC,-,0.00)
chunk0017_133_1	chr1	206558363	206558706	+	0	NA	intron (NM_182665, intron 1 of 4)	intron (NM_182665, intron 1 of 4)	1370	NM_182665	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.005831	0.465116	
chunk0160_429_1	chr5	164501213	164501827	+	0	NA	intron (NR_105065, intron 2 of 3)	L2b|LINE|L2	31241	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.004886	0.351220	
chunk0075_109_1	chr16	48878880	48879477	+	0	NA	Intergenic	Intergenic	-268969	NM_153029	9683	Hs.511839	NM_153029	ENSG00000102921	N4BP1	-	NEDD4 binding protein 1	protein-coding	0.005025	0.469900	
chunk0158_13_1	chr5	125233654	125233883	+	0	NA	intron (NR_109882, intron 4 of 5)	intron (NR_109882, intron 4 of 5)	196937	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.004367	0.386957	
chunk0179_411_1	chr7	51666357	51666576	+	0	NA	Intergenic	Intergenic	-349648	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.013699	0.477273	
chunk0003_226_1	chr1	35598564	35598976	+	0	NA	TTS (NM_001199780)	TTS (NM_001199780)	25400	NM_178548	339488	Hs.567844	NM_178548	ENSG00000116819	TFAP2E	AP2E	transcription factor AP-2 epsilon	protein-coding	0.002427	0.360775	210(AGGATCATAGTGTTCC,-,0.00),211(GGATCATAGTGTTCCA,+,0.00)
chunk0025_275_1	chr10	56203538	56204024	+	0	NA	Intergenic	L1PA5|LINE|L1	157492	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.004115	0.234086	
chunk0154_25_1	chr5	76926104	76926717	+	0	NA	Intergenic	Intergenic	-26445	NM_001882	1393	Hs.115617	NM_001882	ENSG00000145708	CRHBP	CRF-BP|CRFBP	corticotropin releasing hormone binding protein	protein-coding	0.004894	0.451140	
chunk0163_138_1	chr6	10690450	10691077	+	0	NA	intron (NM_001145020, intron 1 of 4)	intron (NM_001145020, intron 1 of 4)	3843	NR_026737	347744	Hs.61389	NM_001145020	ENSG00000137434	C6orf52	-	chromosome 6 open reading frame 52	protein-coding	0.006380	0.375796	
chunk0090_260_1	chr18	74367961	74368191	+	0	NA	Intergenic	Intergenic	-41372	NR_131977	101927606	Hs.623809	NR_131977	ENSG00000259779	LINC01922	-	long intergenic non-protein coding RNA 1922	ncRNA	0.017391	0.562771	
chunk0108_314_1	chr2	235478626	235478825	+	0	NA	Intergenic	MIRb|SINE|MIR	-15364	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.020101	0.430000	
chunk0023_60_1	chr10	21965311	21966043	+	0	NA	intron (NM_022365, intron 1 of 11)	MER41C|LTR|ERV1	38044	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.005464	0.377899	
chunk0085_382_1	chr18	9804030	9804974	+	0	NA	intron (NM_006868, intron 3 of 6)	intron (NM_006868, intron 3 of 6)	-81224	NM_001098529	84203	Hs.98712	NM_032243	ENSG00000168454	TXNDC2	SPTRX|SPTRX1	thioredoxin domain containing 2	protein-coding	0.016949	0.521693	225(GGGGACAGGCTGCTCT,-,0.00),226(GGGACAGGCTGCTCTG,+,0.00),346(AGGCACTGTCTGTGCC,-,0.00),347(GGCACTGTCTGTGCCT,+,0.00)
chunk0047_154_1	chr12	69740157	69740418	+	0	NA	intron (NM_175623, intron 1 of 10)	intron (NM_175623, intron 1 of 10)	897	NR_103520	117177	Hs.258209	NM_022456	ENSG00000127328	RAB3IP	RABIN3|RABIN8	RAB3A interacting protein	protein-coding	0.007663	0.343511	
chunk0102_456_1	chr2	158376391	158376595	+	0	NA	intron (NM_001301685, intron 1 of 6)	intron (NM_001301685, intron 1 of 6)	80260	NM_138803	130940	Hs.668597	NM_138803	ENSG00000153237	CCDC148	-	coiled-coil domain containing 148	protein-coding	0.000000	0.278049	
chunk0083_371_1	chr17	71112199	71112817	+	0	NA	intron (NR_104152, intron 3 of 3)	intron (NR_104152, intron 3 of 3)	89671	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.008091	0.376414	
chunk0205_432_1	chr9	115199165	115199935	+	0	NA	intron (NM_017418, intron 1 of 7)	AluSq2|SINE|Alu	57732	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.009091	0.425422	
chunk0159_408_1	chr5	147756559	147757085	+	0	NA	intron (NM_001270941, intron 1 of 21)	intron (NM_001270941, intron 1 of 21)	26026	NM_014790	9832	Hs.740461	NM_014790	ENSG00000176049	JAKMIP2	JAMIP2|NECC1	janus kinase and microtubule interacting protein 2	protein-coding	0.000000	0.407970	177(ATAAACAGCCTGTGCT,-,0.00),178(TAAACAGCCTGTGCTC,+,0.00)
chunk0092_369_1	chr19	36034681	36035534	+	0	NA	3' UTR (NM_152658, exon 4 of 4)	3' UTR (NM_152658, exon 4 of 4)	-2212	NM_015526	25999	Hs.466539	NM_015526	ENSG00000105270	CLIP3	CLIPR-59|CLIPR59|RSNL1	CAP-Gly domain containing linker protein 3	protein-coding	0.016413	0.542155	
chunk0129_93_1	chr3	119413540	119413961	+	0	NA	intron (NM_020754, intron 11 of 11)	intron (NM_020754, intron 11 of 11)	49932	NR_073506	55254	Hs.594171	NM_018266	ENSG00000176142	TMEM39A	-	transmembrane protein 39A	protein-coding	0.007126	0.428910	
chunk0077_124_1	chr16	78392712	78393011	+	0	NA	intron (NM_016373, intron 6 of 8)	intron (NM_016373, intron 6 of 8)	293448	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.030100	0.486667	
chunk0135_341_1	chr3	190344999	190345213	+	0	NA	Intergenic	Intergenic	-22660	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.000000	0.404651	
chunk0013_23_1	chr1	166177648	166177934	+	0	NA	Intergenic	Intergenic	-11070	NM_001017961	149297	Hs.22930	NM_001017961	ENSG00000188859	FAM78B	-	family with sequence similarity 78 member B	protein-coding	0.010490	0.456446	
chunk0062_172_1	chr14	69531143	69531897	+	0	NA	Intergenic	Intergenic	43363	NM_001271507	56936	Hs.458319	NM_020181	ENSG00000267909	CCDC177	C14orf162|PLPL	coiled-coil domain containing 177	protein-coding	0.005305	0.380132	241(AAGCTCACTATGTACC,-,0.00),242(AGCTCACTATGTACCT,+,0.00),666(CAGGACTGACTGTGCC,-,0.00),667(AGGACTGACTGTGCCA,+,0.00)
chunk0093_55_1	chr19	40253638	40254056	+	0	NA	intron (NM_001243028, intron 3 of 12)	L1MC5|LINE|L1	-27157	NM_024877	79935	Hs.631603	NM_024877	ENSG00000105219	CNTD2	CCNP	cyclin N-terminal domain containing 2	protein-coding	0.016746	0.424821	
chunk0158_72_1	chr5	126326458	126327020	+	0	NA	Intergenic	L1ME4b|LINE|L1	-33357	NM_001146319	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.001779	0.287744	
chunk0121_109_1	chr3	17296489	17297059	+	0	NA	intron (NM_014744, intron 14 of 21)	intron (NM_014744, intron 14 of 21)	363578	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.000000	0.345009	
chunk0103_16_1	chr2	158997528	158997851	+	0	NA	intron (NM_001145909, intron 1 of 26)	L1MC3|LINE|L1	29055	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.009288	0.398148	
chunk0025_346_1	chr10	58148872	58149301	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	118848	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.009324	0.365116	
chunk0176_238_1	chr7	15885787	15886105	+	0	NA	Intergenic	Intergenic	197568	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.000000	0.347962	152(AAGAACAATTTGTTCC,-,0.00),153(AGAACAATTTGTTCCT,+,0.00)
chunk0033_27_1	chr11	12822637	12822843	+	0	NA	intron (NM_021961, intron 3 of 12)	intron (NM_021961, intron 3 of 12)	148318	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.009709	0.434783	
chunk0206_187_1	chr9	122888644	122888936	+	0	NA	intron (NM_001100588, intron 4 of 20)	L1MC5a|LINE|L1	-8471	NR_003071	692206	Hs.693253	NR_003071	ENSG00000212447	SNORD90	HBII-295	small nucleolar RNA, C/D box 90	snoRNA	0.006849	0.368601	
chunk0123_393_1	chr3	48862321	48862520	+	0	NA	intron (NM_000387, intron 5 of 8)	intron (NM_000387, intron 5 of 8)	14483	NR_109997	100506637	Hs.634259	NR_109996	ENSG00000224424	PRKAR2A-AS1	-	PRKAR2A antisense RNA 1	ncRNA	0.005025	0.555000	
chunk0151_201_1	chr5	50710703	50711252	+	0	NA	intron (NM_024615, intron 2 of 25)	intron (NM_024615, intron 2 of 25)	44039	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.003643	0.330909	
chunk0153_213_1	chr5	71974191	71974686	+	0	NA	Intergenic	Intergenic	-132853	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.004040	0.427419	244(AGGAACAAAATGTCCC,-,0.00),245(GGAACAAAATGTCCCC,+,0.00)
chunk0185_24_1	chr7	124126110	124126721	+	0	NA	Intergenic	Intergenic	-92946	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.004910	0.370915	
chunk0079_74_1	chr17	11531752	11532099	+	0	NA	intron (NM_001173462, intron 3 of 4)	L1MA7|LINE|L1	-66506	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.005764	0.310345	176(CAAAACACTTTGTGCC,-,0.00)
chunk0065_126_1	chr15	24877879	24878078	+	0	NA	intron (NM_022805, intron 1 of 11)	intron (NM_022805, intron 1 of 11)	21427	NM_022805	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.020101	0.410000	
chunk0082_143_1	chr17	55446806	55447147	+	0	NA	Intergenic	(TTTA)n|Simple_repeat|Simple_repeat	-24996	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.005865	0.391813	
chunk0170_163_1	chr6	111566888	111567200	+	0	NA	intron (NM_147200, intron 7 of 9)	intron (NM_147200, intron 7 of 9)	316	NM_001164283	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.032051	0.536741	255(AAGCACAACGTGTCCC,-,0.00),256(AGCACAACGTGTCCCA,+,0.00)
chunk0180_113_1	chr7	55420521	55421022	+	0	NA	intron (NM_018697, intron 6 of 8)	intron (NM_018697, intron 6 of 8)	55323	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.005988	0.392430	
chunk0015_168_1	chr1	186674548	186674775	+	0	NA	exon (NM_000963, exon 10 of 10)	exon (NM_000963, exon 10 of 10)	5766	NM_000963	5743	Hs.196384	NM_000963	ENSG00000073756	PTGS2	COX-2|COX2|GRIPGHS|PGG/HS|PGHS-2|PHS-2|hCox-2	prostaglandin-endoperoxide synthase 2	protein-coding	0.013216	0.478070	
chunk0090_186_1	chr18	72965338	72965679	+	0	NA	Intergenic	Intergenic	-97933	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.017595	0.441520	
chunk0195_317_1	chr8	98924077	98924394	+	0	NA	intron (NM_001256312, intron 1 of 12)	intron (NM_001256312, intron 1 of 12)	18336	NM_001256312	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.006309	0.399371	
chunk0002_281_1	chr1	22472540	22473002	+	0	NA	intron (NM_001083621, intron 2 of 18)	intron (NM_001083621, intron 2 of 18)	20920	NM_001083621	9923	Hs.418966	NM_014870	ENSG00000184677	ZBTB40	ZNF923	zinc finger and BTB domain containing 40	protein-coding	0.004329	0.451404	247(AAGAGCAGTGTGTCCT,-,0.00),248(AGAGCAGTGTGTCCTG,+,0.00)
chunk0181_268_1	chr7	86162420	86163043	+	0	NA	Intergenic	L1PA8A|LINE|L1	-481183	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.003210	0.365385	
chunk0131_184_1	chr3	147758873	147759072	+	0	NA	Intergenic	Intergenic	337645	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.005025	0.360000	
chunk0212_47_1	chrY	11310190	11310449	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1111271	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.007722	0.457692	
chunk0071_302_1	chr15	86101135	86101729	+	0	NA	intron (NR_120368, intron 3 of 5)	L1MA4A|LINE|L1	15285	NR_120368	101929701	Hs.132570	NR_120368	ENSG00000260477	LINC01584	-	long intergenic non-protein coding RNA 1584	ncRNA	0.008418	0.297479	
chunk0165_26_1	chr6	29705956	29706731	+	0	NA	Intergenic	L1MC5|LINE|L1	-16997	NM_001098478	3134	Hs.519972	NM_018950	ENSG00000204642	HLA-F	CDA12|HLA-5.4|HLA-CDA12|HLAF	major histocompatibility complex, class I, F	protein-coding	0.005161	0.408505	614(AGGGACAAAATGTTTT,-,0.00),615(GGGACAAAATGTTTTT,+,0.00)
chunk0097_95_1	chr2	45821814	45822340	+	0	NA	intron (NM_005400, intron 1 of 14)	intron (NM_005400, intron 1 of 14)	170173	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.017110	0.497154	246(GGGTGCAGAATGTTCT,-,0.00),247(GGTGCAGAATGTTCTG,+,0.00)
chunk0093_43_1	chr19	39726160	39726468	+	0	NA	Intergenic	Intergenic	11715	NM_001828	1178	Hs.889	NM_001828	ENSG00000105205	CLC	GAL10|Gal-10|LGALS10|LGALS10A|LPPL_HUMAN	Charcot-Leyden crystal galectin	protein-coding	0.000000	0.495146	
chunk0057_294_1	chr13	106293165	106293364	+	0	NA	Intergenic	Intergenic	-83299	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.005025	0.290000	
chunk0142_235_1	chr4	98538072	98538391	+	0	NA	intron (NM_005723, intron 1 of 7)	intron (NM_005723, intron 1 of 7)	120430	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.003135	0.487500	
chunk0088_151_1	chr18	46333514	46333713	+	0	NA	promoter-TSS (NR_046357)	promoter-TSS (NR_046357)	-611	NM_001256758	494470	Hs.501114	NM_152470	ENSG00000141622	RNF165	ARKL2|Ark2C|RNF111L2	ring finger protein 165	protein-coding	0.085427	0.640000	
chunk0171_218_1	chr6	126123162	126123672	+	0	NA	Intergenic	Intergenic	136987	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.007843	0.403131	212(AGGAACACAGTGCGCT,-,0.00),213(GGAACACAGTGCGCTG,+,0.00)
chunk0011_14_1	chr1	143184637	143185088	+	0	NA	Intergenic	(ATCGAATGGA)n|Simple_repeat|Simple_repeat	237730	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.057650	0.373894	
chunk0069_71_1	chr15	60934655	60935169	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	253343	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.001946	0.427184	233(CTGCACTGCCTGTTCC,-,0.00),234(TGCACTGCCTGTTCCT,+,0.00)
chunk0133_127_1	chr3	168881768	168882213	+	0	NA	Intergenic	Intergenic	-19955	NR_109989	100507661	Hs.65918	NR_109989	ENSG00000242268	LINC02082	-	long intergenic non-protein coding RNA 2082	ncRNA	0.006742	0.374439	
chunk0101_59_1	chr2	123171000	123171433	+	0	NA	Intergenic	Intergenic	-854071	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.002309	0.317972	
chunk0128_305_1	chr3	111518127	111518358	+	0	NA	Intergenic	Intergenic	-23837	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.004329	0.336207	
chunk0062_163_1	chr14	69388558	69389055	+	0	NA	intron (NM_004450, intron 2 of 3)	intron (NM_004450, intron 2 of 3)	9498	NM_004450	2079	Hs.509791	NM_004450	ENSG00000100632	ERH	DROER	ERH mRNA splicing and mitosis factor	protein-coding	0.010060	0.367470	
chunk0022_270_1	chr10	15084407	15084738	+	0	NA	intron (NM_001039844, intron 1 of 3)	MER51A|LTR|ERV1	4204	NM_001039844	414149		NM_001039844	ENSG00000176244	ACBD7	bA455B2.2	acyl-CoA binding domain containing 7	protein-coding	0.018127	0.442771	
chunk0144_19_1	chr4	124868506	124868705	+	0	NA	Intergenic	Intergenic	-155873	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.010050	0.335000	
chunk0187_257_1	chr7	154837190	154837454	+	0	NA	intron (NM_001290252, intron 14 of 23)	(CACA)n|Simple_repeat|Simple_repeat	-91195	NR_024476	100132707	Hs.586358	NR_024476	ENSG00000214106	PAXIP1-AS2	PAXIP1OS	PAXIP1 antisense RNA 2	ncRNA	0.026515	0.479245	
chunk0146_106_1	chr4	158796191	158797047	+	0	NA	intron (NM_020840, intron 1 of 16)	intron (NM_020840, intron 1 of 16)	27589	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.008178	0.411902	443(TAGGACAGTGAGTACT,-,0.00),444(AGGACAGTGAGTACTT,+,0.00)
chunk0062_406_1	chr14	75040573	75040843	+	0	NA	intron (NM_014381, intron 4 of 11)	intron (NM_014381, intron 4 of 11)	10824	NM_014381	27030	Hs.436650	NM_014381	ENSG00000119684	MLH3	HNPCC7	mutL homolog 3	protein-coding	0.003704	0.391144	
chunk0044_214_1	chr12	31206049	31206404	+	0	NA	Intergenic	Intergenic	-118090	NR_026806	79857	Hs.534485	NM_024799	ENSG00000177340	FLJ13224	-	uncharacterized LOC79857	ncRNA	0.005634	0.463483	
chunk0107_334_1	chr2	221001363	221001900	+	0	NA	Intergenic	Intergenic	570727	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.005587	0.347584	
chunk0166_336_1	chr6	50849794	50850046	+	0	NA	Intergenic	Intergenic	31194	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.055556	0.525692	
chunk0006_109_1	chr1	65503878	65504410	+	0	NA	intron (NM_001003680, intron 2 of 19)	L1MC3|LINE|L1	-21545	NM_001198688	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.009398	0.380863	
chunk0037_173_1	chr11	74003919	74004201	+	0	NA	intron (NM_003356, intron 5 of 6)	intron (NM_003356, intron 5 of 6)	5177	NM_022803	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.017730	0.540636	145(ATGCACTGTTTGTCCC,-,0.00)
chunk0068_170_1	chr15	54168086	54168737	+	0	NA	intron (NM_001080534, intron 3 of 30)	intron (NM_001080534, intron 3 of 30)	155507	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.013825	0.303681	
chunk0037_407_1	chr11	79686747	79687519	+	0	NA	Intergenic	Intergenic	-246482	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.006477	0.452781	292(CAGAACAGTCAGTGCT,-,0.00),293(AGAACAGTCAGTGCTC,+,0.00)
chunk0009_282_1	chr1	107593495	107594240	+	0	NA	intron (NM_006113, intron 25 of 26)	(TAGAAG)n|Simple_repeat|Simple_repeat	94637	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002685	0.348525	
chunk0174_402_1	chr6	165556489	165556791	+	0	NA	intron (NM_001130690, intron 1 of 21)	intron (NM_001130690, intron 1 of 21)	105460	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.003311	0.372937	171(AAATACATTCTGTACC,-,0.00),172(AATACATTCTGTACCT,+,0.00)
chunk0055_398_1	chr13	74131217	74131448	+	0	NA	intron (NM_007249, intron 1 of 7)	intron (NM_007249, intron 1 of 7)	2597	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.012987	0.461207	
chunk0185_427_1	chr7	134708627	134709267	+	0	NA	Intergenic	MIRc|SINE|MIR	62168	NM_001293085	669	Hs.198365	NM_001724	ENSG00000172331	BPGM	DPGM|ECYT8	bisphosphoglycerate mutase	protein-coding	0.003125	0.368175	
chunk0025_218_1	chr10	53873149	53873582	+	0	NA	intron (NM_001142769, intron 28 of 35)	intron (NM_001142769, intron 28 of 35)	734592	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.004619	0.368664	
chunk0107_272_1	chr2	217865177	217865879	+	0	NA	intron (NM_001308023, intron 15 of 29)	intron (NM_001308023, intron 15 of 29)	35100	NR_106867	102465485		NR_106867	ENSG00000275458	MIR6809	hsa-mir-6809	microRNA 6809	ncRNA	0.004274	0.509246	
chunk0211_52_1	chrX	109458208	109458676	+	0	NA	intron (NM_001522, intron 3 of 19)	MIRb|SINE|MIR	23614	NM_001522	2986	Hs.123074	NM_001522	ENSG00000101890	GUCY2F	CYGF|GC-F|GUC2DL|GUC2F|RETGC-2|ROS-GC2	guanylate cyclase 2F, retinal	protein-coding	0.002137	0.392324	
chunk0094_182_1	chr2	6068137	6068533	+	0	NA	Intergenic	Intergenic	86357	NR_026833	400940	Hs.378814	NM_207479		LOC400940	-	uncharacterized LOC400940	ncRNA	0.005051	0.370277	
chunk0125_302_1	chr3	70071947	70072666	+	0	NA	Intergenic	Intergenic	72562	NR_110000	101927152	Hs.382046	NR_110000	ENSG00000240405	SAMMSON	LINC01212	survival associated mitochondrial melanoma specific oncogenic non-coding RNA	ncRNA	0.022253	0.384722	
chunk0202_59_1	chr9	71654281	71654534	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	114477	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.015810	0.366142	
chunk0210_11_1	chrX	66899799	66900040	+	0	NA	Intergenic	MIRb|SINE|MIR	-260621	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.000000	0.363636	
chunk0115_289_1	chr21	28226252	28227111	+	0	NA	intron (NR_126012, intron 1 of 5)	L1MC4|LINE|L1	1986	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.006985	0.401163	132(GTGTACAGTGTGTGCT,-,0.00),133(TGTACAGTGTGTGCTT,+,0.00)
chunk0196_353_1	chr8	114589790	114590312	+	0	NA	Intergenic	Intergenic	1077961	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.001916	0.332696	287(CAGGACACTCTGTCCA,-,0.00),288(AGGACACTCTGTCCAG,+,0.00)
chunk0139_225_1	chr4	55122213	55122767	+	0	NA	intron (NM_002253, intron 1 of 29)	intron (NM_002253, intron 1 of 29)	3105	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.003610	0.351351	
chunk0016_89_1	chr1	194623674	194623926	+	0	NA	Intergenic	Intergenic	1319055	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.007937	0.300395	
chunk0020_79_1	chr1	232707048	232707669	+	0	NA	Intergenic	Intergenic	35357	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.003221	0.363344	274(TTGAACATGTTGTGCC,-,0.00),275(TGAACATGTTGTGCCC,+,0.00)
chunk0211_140_1	chrX	112876648	112876847	+	0	NA	Intergenic	Intergenic	-35932	NM_133265	154796	Hs.528051	NM_133265	ENSG00000126016	AMOT	-	angiomotin	protein-coding	0.000000	0.340000	
chunk0066_390_1	chr15	39031278	39031568	+	0	NA	Intergenic	Intergenic	-219246	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.010345	0.398625	
chunk0136_16_1	chr4	125710	126114	+	0	NA	intron (NM_001289930, intron 1 of 3)	intron (NM_001289930, intron 1 of 3)	1436	NR_110529	255403	Hs.636638	NM_001039127	ENSG00000250312	ZNF718	-	zinc finger protein 718	protein-coding	0.017327	0.555556	160(AAGCACACGCAGTGCC,-,0.00),161(AGCACACGCAGTGCCC,+,0.00)
chunk0168_388_1	chr6	94044980	94045769	+	0	NA	Intergenic	Intergenic	338291	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.012674	0.389873	297(TGAGACAGAATGTTCC,-,0.00),298(GAGACAGAATGTTCCT,+,0.00)
chunk0035_435_1	chr11	57431184	57431669	+	0	NA	Intergenic	Intergenic	-3846	NM_017611	29015	Hs.99962	NM_014096	ENSG00000134802	SLC43A3	EEG1|ENBT1|FOAP-13|PRO1659|SEEEG-1	solute carrier family 43 member 3	protein-coding	0.012371	0.467078	
chunk0075_27_1	chr16	46906819	46907113	+	0	NA	exon (NM_133443, exon 5 of 12)	exon (NM_133443, exon 5 of 12)	21852	NM_001142466	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.034014	0.596610	
chunk0075_88_1	chr16	48287272	48287746	+	0	NA	intron (NM_031490, intron 8 of 14)	L1M4|LINE|L1	43342	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.002110	0.416842	
chunk0189_77_1	chr8	20968160	20968538	+	0	NA	intron (NR_130774, intron 4 of 4)	intron (NR_130774, intron 4 of 4)	-5637	NR_033894	286114	Hs.651884	NR_033894	ENSG00000253199	LINC02153	-	long intergenic non-protein coding RNA 2153	ncRNA	0.005291	0.393140	148(AGGGACTGACTGTGTC,-,0.00)
chunk0061_69_1	chr14	56608779	56609349	+	0	NA	intron (NM_017799, intron 5 of 15)	intron (NM_017799, intron 5 of 15)	29271	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.007018	0.415061	
chunk0095_346_1	chr2	20913507	20913977	+	0	NA	Intergenic	Intergenic	-90612	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.008511	0.475584	
chunk0051_132_1	chr12	115491682	115492345	+	0	NA	Intergenic	L2c|LINE|L2	656641	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.009050	0.432229	
chunk0153_38_1	chr5	67160049	67160682	+	0	NA	intron (NM_001290226, intron 24 of 26)	(TTGTAT)n|Simple_repeat|Simple_repeat	36424	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.006319	0.400631	
chunk0023_55_1	chr10	21823533	21823958	+	0	NA	intron (NM_022365, intron 8 of 11)	MER30|DNA|hAT-Charlie	179976	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.007059	0.347418	
chunk0092_187_1	chr19	30360141	30360523	+	0	NA	Intergenic	Intergenic	-12061	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.026178	0.454308	
chunk0176_299_1	chr7	16812768	16813478	+	0	NA	Intergenic	Intergenic	-8009	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.005634	0.338959	
chunk0191_109_1	chr8	48177969	48178638	+	0	NA	Intergenic	Intergenic	169868	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.002990	0.362687	
chunk0210_46_1	chrX	68416716	68416915	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	16642	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.000000	0.425000	100(TTGCACAGCCTGTTTT,-,0.00)
chunk0113_3_1	chr20	49200631	49200830	+	0	NA	Intergenic	L1MC3|LINE|L1	-12363	NM_004602	6780	Hs.596704	NM_004602	ENSG00000124214	STAU1	PPP1R150|STAU	staufen double-stranded RNA binding protein 1	protein-coding	0.000000	0.455000	
chunk0095_275_1	chr2	19887546	19888248	+	0	NA	Intergenic	Intergenic	14086	NM_001008237	130502	Hs.591547	NM_001008237	ENSG00000183891	TTC32	-	tetratricopeptide repeat domain 32	protein-coding	0.015670	0.473684	
chunk0054_244_1	chr13	46142840	46143714	+	0	NA	intron (NM_002298, intron 12 of 15)	intron (NM_002298, intron 12 of 15)	-38201	NM_001872	1361	Hs.512937	NM_001872	ENSG00000080618	CPB2	CPU|PCPB|TAFI	carboxypeptidase B2	protein-coding	0.006865	0.395429	
chunk0014_96_1	chr1	176696058	176696709	+	0	NA	intron (NM_020318, intron 7 of 22)	intron (NM_020318, intron 7 of 22)	233212	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.009217	0.452454	376(GGTACTGGTTGTGCTT,+,0.00)
chunk0100_395_1	chr2	119242589	119242870	+	0	NA	intron (NM_018234, intron 2 of 5)	MIR|SINE|MIR	6342	NR_046721	100874111	Hs.704682	NR_046721	ENSG00000229867	STEAP3-AS1	-	STEAP3 antisense RNA 1	ncRNA	0.017794	0.500000	
chunk0147_14_1	chr4	170674852	170675177	+	0	NA	Intergenic	Intergenic	-365588	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.009231	0.380368	
chunk0108_95_1	chr2	228613821	228614357	+	0	NA	Intergenic	Intergenic	-432444	NM_001142644	80309	Hs.436306	NM_030623	ENSG00000153820	SPHKAP	SKIP	SPHK1 interactor, AKAP domain containing	protein-coding	0.005597	0.374302	
chunk0175_127_1	chr7	3370150	3370452	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	68853	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.003311	0.386139	145(CAGTACAGGGTGTACC,-,0.00),146(AGTACAGGGTGTACCA,+,0.00)
chunk0043_207_1	chr12	19517915	19518847	+	0	NA	3' UTR (NM_153207, exon 8 of 8)	3' UTR (NM_153207, exon 8 of 8)	77800	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.007511	0.319400	
chunk0093_60_1	chr19	40349403	40349602	+	0	NA	promoter-TSS (NM_001256440)	promoter-TSS (NM_001256440)	-975	NM_001256440	126526	Hs.631557	NM_178830	ENSG00000160392	C19orf47	-	chromosome 19 open reading frame 47	protein-coding	0.030151	0.530000	
chunk0060_173_1	chr14	46074321	46074520	+	0	NA	intron (NR_102701, intron 1 of 5)	L1M5|LINE|L1	10261	NR_102701	100506412	Hs.207545	NR_102699	ENSG00000258700	LINC00871	-	long intergenic non-protein coding RNA 871	ncRNA	0.015075	0.275000	
chunk0170_413_1	chr6	118031803	118032277	+	0	NA	intron (NM_001029858, intron 1 of 7)	intron (NM_001029858, intron 1 of 7)	124514	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.006329	0.385263	
chunk0050_235_1	chr12	105182252	105182769	+	0	NA	intron (NM_018171, intron 17 of 20)	L1PA7|LINE|L1	50895	NM_001251905	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.003868	0.380309	276(AGGAACAGGTTGTTCA,-,0.00),277(GGAACAGGTTGTTCAG,+,0.00)
chunk0031_393_1	chr10	131144919	131145511	+	0	NA	intron (NM_174937, intron 7 of 11)	intron (NM_174937, intron 7 of 11)	49997	NR_120623	101927489	Hs.659317	NR_120623	ENSG00000230098	TCERG1L-AS1	-	TCERG1L antisense RNA 1	ncRNA	0.008446	0.397976	245(TAGGACAAACTGTGCC,-,0.00),246(AGGACAAACTGTGCCT,+,0.00)
chunk0010_110_1	chr1	114235903	114236283	+	0	NA	Intergenic	Intergenic	-82243	NM_001270805	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.007895	0.454068	
chunk0180_106_1	chr7	55336534	55336743	+	0	NA	Intergenic	MER67C|LTR|ERV1	-28810	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.004785	0.428571	
chunk0130_355_1	chr3	138799745	138800255	+	0	NA	Intergenic	L2b|LINE|L2	-40641	NM_006219	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.007843	0.454012	325(TTGTACATGCTGTTCT,-,0.00),326(TGTACATGCTGTTCTT,+,0.00)
chunk0112_140_1	chr20	38604691	38605384	+	0	NA	intron (NM_001164431, intron 1 of 14)	intron (NM_001164431, intron 1 of 14)	3103	NM_001164431	343578		NM_001164431	ENSG00000124143	ARHGAP40	C20orf95|dJ1100H13.4	Rho GTPase activating protein 40	protein-coding	0.005772	0.399135	
chunk0072_443_1	chr15	101616617	101616833	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	35666	NM_025141	80213	Hs.288912	NM_025141	ENSG00000184277	TM2D3	BLP2	TM2 domain containing 3	protein-coding	0.032407	0.502304	
chunk0015_418_1	chr1	191480935	191481292	+	0	NA	Intergenic	LTR38|LTR|ERV1	-677349	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.011204	0.382682	
chunk0064_280_1	chr14	95188984	95189258	+	0	NA	3' UTR (NM_024734, exon 13 of 13)	3' UTR (NM_024734, exon 13 of 13)	-31111	NM_030621	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.007299	0.367273	
chunk0138_99_1	chr4	36000858	36001509	+	0	NA	Intergenic	MER54A|LTR|ERVL	-242933	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004608	0.427914	
chunk0174_389_1	chr6	165250871	165251093	+	0	NA	Intergenic	Intergenic	58640	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.004505	0.376682	
chunk0149_48_1	chr5	16627714	16628040	+	0	NA	intron (NR_109946, intron 3 of 3)	L1MC5a|LINE|L1	-10819	NM_001034850	54463	Hs.481704	NM_019000	ENSG00000154153	RETREG1	FAM134B|JK-1|JK1	reticulophagy regulator 1	protein-coding	0.006135	0.370031	
chunk0121_88_1	chr3	16448461	16448958	+	0	NA	intron (NM_015150, intron 2 of 9)	intron (NM_015150, intron 2 of 9)	65006	NM_015150	23180	Hs.98910	NM_015150	ENSG00000131378	RFTN1	MIG2|PIB10|PIG9|RAFTLIN	raftlin, lipid raft linker 1	protein-coding	0.012072	0.445783	
chunk0038_432_1	chr11	94638550	94639389	+	0	NA	Intergenic	Intergenic	71661	NM_152431	143689	Hs.660188	NM_152431	ENSG00000134627	PIWIL4	HIWI2|MIWI2	piwi like RNA-mediated gene silencing 4	protein-coding	0.008343	0.433333	
chunk0157_325_1	chr5	122009950	122010501	+	0	NA	intron (NM_152546, intron 4 of 7)	intron (NM_152546, intron 4 of 7)	48264	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.003630	0.364130	296(AAGTACATGGAGTTCT,-,0.00),297(AGTACATGGAGTTCTA,+,0.00)
chunk0160_443_1	chr5	164857597	164857907	+	0	NA	Intergenic	Intergenic	387473	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.000000	0.382637	
chunk0143_243_1	chr4	114692936	114693365	+	0	NA	Intergenic	L2a|LINE|L2	36391	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.006993	0.341860	
chunk0055_156_1	chr13	60035192	60035497	+	0	NA	intron (NR_109838, intron 3 of 4)	intron (NR_109838, intron 3 of 4)	22041	NR_051994	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.006557	0.346405	
chunk0076_337_1	chr16	71456605	71457289	+	0	NA	intron (NM_001304492, intron 1 of 4)	intron (NM_001304492, intron 1 of 4)	5276	NM_145911	7571	Hs.656643	NM_145911	ENSG00000167377	ZNF23	KOX16|ZNF359|ZNF612|Zfp612	zinc finger protein 23	protein-coding	0.011696	0.491971	
chunk0047_47_1	chr12	67047715	67048027	+	0	NA	Intergenic	L1ME4c|LINE|L1	48413	NR_120490	102724421	Hs.135774	NR_120490	ENSG00000257083	LOC102724421	-	uncharacterized LOC102724421	ncRNA	0.003205	0.319489	
chunk0146_113_1	chr4	158841527	158841737	+	0	NA	intron (NM_020840, intron 7 of 16)	LTR75|LTR|ERVL	72602	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.004762	0.464455	
chunk0021_127_1	chr10	3783805	3784343	+	0	NA	intron (NR_027653, intron 1 of 3)	intron (NR_027653, intron 1 of 3)	1207	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.031599	0.499072	
chunk0078_451_1	chr16	89926430	89926671	+	0	NA	intron (NM_006086, intron 1 of 3)	CpG	3271	NM_006086	10381	Hs.511743	NM_006086	ENSG00000258947	TUBB3	CDCBM|CDCBM1|CFEOM3|CFEOM3A|FEOM3|TUBB4|beta-4	tubulin beta 3 class III	protein-coding	0.087137	0.669421	
chunk0178_160_1	chr7	33825556	33825811	+	0	NA	Intergenic	Intergenic	-79228	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.003922	0.437500	
chunk0009_428_1	chr1	111110285	111110568	+	0	NA	Intergenic	L1MA4|LINE|L1	-29201	NM_001007794	10390	Hs.363572	NM_006090	ENSG00000134255	CEPT1	-	choline/ethanolamine phosphotransferase 1	protein-coding	0.000000	0.507042	
chunk0210_325_1	chrX	93722641	93723028	+	0	NA	Intergenic	Intergenic	48821	NM_173698	286499	Hs.110069	NM_173698	ENSG00000179083	FAM133A	CT115	family with sequence similarity 133 member A	protein-coding	0.002584	0.453608	
chunk0146_415_1	chr4	169103939	169104654	+	0	NA	intron (NM_020870, intron 11 of 11)	intron (NM_020870, intron 11 of 11)	-93979	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.004196	0.458101	
chunk0062_115_1	chr14	68415414	68415619	+	0	NA	intron (NM_133509, intron 9 of 10)	L2c|LINE|L2	378398	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.009756	0.436893	
chunk0108_235_1	chr2	233721447	233721646	+	0	NA	intron (NM_007120, intron 1 of 4)	intron (NM_007120, intron 1 of 4)	2754	NM_007120	54657	Hs.554822	NM_007120	ENSG00000244474	UGT1A4	GNT1|HUG-BR2|UDPGT|UDPGT 1-4|UGT-1A|UGT-1D|UGT1|UGT1-01|UGT1-04|UGT1.1|UGT1.4|UGT1A|UGT1A1|UGT1A4S|UGT1D|hUG-BR1	UDP glucuronosyltransferase family 1 member A4	protein-coding	0.000000	0.315000	154(AGGAACAATTTGTTCC,-,0.00),155(GGAACAATTTGTTCCT,+,0.00)
chunk0203_383_1	chr9	90420784	90421509	+	0	NA	intron (NR_109795, intron 1 of 2)	MER76-int|LTR|ERVL	12343	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.011034	0.506887	501(AGGCACACCCTGTTCC,-,0.00),502(GGCACACCCTGTTCCA,+,0.00)
chunk0190_11_1	chr8	28823890	28824438	+	0	NA	intron (NR_026826, intron 4 of 14)	intron (NR_026826, intron 4 of 14)	65751	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.005474	0.411658	
chunk0085_75_1	chr18	1680236	1680435	+	0	NA	Intergenic	Intergenic	-320706	NR_023926	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.000000	0.320000	
chunk0092_14_1	chr19	18629766	18630138	+	0	NA	Intergenic	L2a|LINE|L2	-7076	NM_018316	55295	Hs.250632	NM_018316	ENSG00000167487	KLHL26	-	kelch like family member 26	protein-coding	0.021505	0.517426	249(TAGAACATTCTGTCCC,-,0.00),250(AGAACATTCTGTCCCC,+,0.00)
chunk0160_145_1	chr5	151463214	151463762	+	0	NA	intron (NM_001308151, intron 2 of 8)	MIR|SINE|MIR	15892	NM_078483	206358	Hs.269004	NM_078483	ENSG00000123643	SLC36A1	Dct1|LYAAT1|PAT1|TRAMD3	solute carrier family 36 member 1	protein-coding	0.003650	0.422587	
chunk0153_347_1	chr5	74328311	74328544	+	0	NA	TTS (NR_105010)	TTS (NR_105010)	5941	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.000000	0.431624	
chunk0047_82_1	chr12	67992694	67993487	+	0	NA	intron (NR_104125, intron 1 of 3)	intron (NR_104125, intron 1 of 3)	3645	NR_104125	100885789	Hs.439832	NR_104124	ENSG00000255733	IFNG-AS1	GS1-410F4.2|NEST|Tmevpg1	IFNG antisense RNA 1	ncRNA	0.006305	0.343829	
chunk0104_155_1	chr2	174052719	174053069	+	0	NA	Intergenic	Intergenic	-87192	NM_003111	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.008571	0.367521	
chunk0119_397_1	chr22	48938403	48938978	+	0	NA	Intergenic	Intergenic	71920	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.019130	0.515625	
chunk0179_25_1	chr7	42887747	42888240	+	0	NA	Intergenic	MER54B|LTR|ERVL	24097	NM_024054	79020	Hs.698120	NM_024054	ENSG00000136197	C7orf25	-	chromosome 7 open reading frame 25	protein-coding	0.032454	0.518219	
chunk0103_349_1	chr2	168086757	168087410	+	0	NA	intron (NM_013233, intron 10 of 17)	intron (NM_013233, intron 10 of 17)	-145939	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.009188	0.440367	308(AGGAACACTCTGTCCT,-,0.00),309(GGAACACTCTGTCCTG,+,0.00)
chunk0018_165_1	chr1	218930437	218931039	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	243050	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.011628	0.417910	
chunk0144_304_1	chr4	138450743	138451318	+	0	NA	Intergenic	Intergenic	141319	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.005217	0.399306	
chunk0207_106_1	chr9	128772140	128772466	+	0	NA	promoter-TSS (NM_006336)	promoter-TSS (NM_006336)	-369	NM_006336	10444	Hs.147950	NM_006336	ENSG00000160445	ZER1	C9orf60|ZYG|ZYG11BL	zyg-11 related cell cycle regulator	protein-coding	0.061350	0.623853	
chunk0049_177_1	chr12	92349589	92350062	+	0	NA	Intergenic	HAL1|LINE|L1	-71706	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.002114	0.343882	
chunk0049_166_1	chr12	92191166	92191538	+	0	NA	Intergenic	Intergenic	-45455	NM_001731	694	Hs.255935	NM_001731	ENSG00000133639	BTG1	APRO2	BTG anti-proliferation factor 1	protein-coding	0.005376	0.353887	
chunk0191_52_1	chr8	46490809	46491483	+	0	NA	Intergenic	LTR3A|LTR|ERVK	-349740	NR_027013	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.005935	0.435556	
chunk0207_463_1	chr9	138133544	138133790	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-16446	NR_027156	643224	Hs.551805	NR_027156		TUBBP5	-	tubulin beta pseudogene 5	pseudo	0.020325	0.473684	
chunk0049_403_1	chr12	96946481	96947040	+	0	NA	intron (NM_001135175, intron 13 of 14)	intron (NM_001135175, intron 13 of 14)	39294	NM_001135175	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.007156	0.360714	210(AGGTGCAGTGTGTTCT,-,0.00),211(GGTGCAGTGTGTTCTG,+,0.00)
chunk0084_51_1	chr17	74301389	74301615	+	0	NA	intron (NM_023036, intron 8 of 13)	intron (NM_023036, intron 8 of 13)	-24710	NM_153209	124602	Hs.372773	NM_153209	ENSG00000196169	KIF19	KIF19A	kinesin family member 19	protein-coding	0.013274	0.568282	
chunk0101_256_1	chr2	133263120	133263491	+	0	NA	intron (NM_207481, intron 4 of 17)	intron (NM_207481, intron 4 of 17)	-2890	NR_110294	101928161	Hs.661917	NR_110294	ENSG00000226953	NCKAP5-AS2	-	NCKAP5 antisense RNA 2	ncRNA	0.000000	0.362903	
chunk0125_229_1	chr3	68072565	68073140	+	0	NA	intron (NM_213609, intron 2 of 4)	intron (NM_213609, intron 2 of 4)	68636	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.008696	0.388889	
chunk0006_140_1	chr1	66253683	66254229	+	0	NA	intron (NM_001037340, intron 2 of 14)	intron (NM_001037340, intron 2 of 14)	-78152	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.003663	0.321755	
chunk0147_187_1	chr4	177322112	177322785	+	0	NA	intron (NM_018248, intron 1 of 9)	intron (NM_018248, intron 1 of 9)	12611	NM_018248	55247	Hs.405467	NM_018248	ENSG00000109674	NEIL3	FGP2|FPG2|NEI3|ZGRF3|hFPG2|hNEI3	nei like DNA glycosylase 3	protein-coding	0.011887	0.359050	
chunk0003_210_1	chr1	35288709	35289049	+	0	NA	intron (NM_005095, intron 1 of 29)	intron (NM_005095, intron 1 of 29)	19912	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.000000	0.378299	
chunk0170_115_1	chr6	110662550	110662888	+	0	NA	intron (NM_015076, intron 4 of 12)	intron (NM_015076, intron 4 of 12)	-151902	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.000000	0.315634	
chunk0004_67_1	chr1	43349103	43349334	+	0	NA	intron (NM_005373, intron 9 of 11)	CpG-1006	-9737	NM_001255	991	Hs.524947	NM_001255	ENSG00000117399	CDC20	CDC20A|bA276H19.3|p55CDC	cell division cycle 20	protein-coding	0.077922	0.724138	
chunk0094_188_1	chr2	6182137	6182401	+	0	NA	Intergenic	Intergenic	193153	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.007576	0.369811	
chunk0064_420_1	chr14	99615984	99616438	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-11821	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.013216	0.421978	217(AGGTACATGCTGTACA,-,0.00),218(GGTACATGCTGTACAG,+,0.00)
chunk0083_433_1	chr17	72610731	72611435	+	0	NA	intron (NR_033876, intron 3 of 4)	intron (NR_033876, intron 3 of 4)	-18279	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.008523	0.397163	
chunk0136_323_1	chr3	195406408	195406797	+	0	NA	intron (NM_012287, intron 1 of 22)	AluJr|SINE|Alu	36486	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.002571	0.387179	
chunk0077_85_1	chr16	77414599	77415365	+	0	NA	intron (NM_199355, intron 3 of 22)	intron (NM_199355, intron 3 of 22)	20132	NM_199355	170692	Hs.188746	NM_139054	ENSG00000140873	ADAMTS18	ADAMTS21|KNO2|MMCAT	ADAM metallopeptidase with thrombospondin type 1 motif 18	protein-coding	0.003916	0.371578	337(AGGCACATAATGTGCT,-,0.00),338(GGCACATAATGTGCTC,+,0.00)
chunk0125_308_1	chr3	70723012	70723584	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	341625	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.006993	0.364747	
chunk0048_281_1	chr12	82510357	82510565	+	0	NA	Intergenic	Intergenic	-151656	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.000000	0.325359	
chunk0153_265_1	chr5	72839402	72839625	+	0	NA	intron (NM_002270, intron 1 of 24)	intron (NM_002270, intron 1 of 24)	-8590	NM_153188	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.000000	0.281250	
chunk0107_278_1	chr2	218217125	218217331	+	0	NA	promoter-TSS (NM_005731)	promoter-TSS (NM_005731)	134	NM_152862	10109	Hs.529303	NM_005731	ENSG00000163466	ARPC2	ARC34|PNAS-139|PRO2446|p34-Arc	actin related protein 2/3 complex subunit 2	protein-coding	0.111650	0.729469	
chunk0199_255_1	chr9	6004753	6005054	+	0	NA	intron (NM_001017969, intron 1 of 7)	intron (NM_001017969, intron 1 of 7)	-2923	NR_039811	100616288		NR_039811	ENSG00000263575	MIR4665	mir-4665	microRNA 4665	ncRNA	0.006645	0.347682	
chunk0025_212_1	chr10	53699681	53700103	+	0	NA	Intergenic	Intergenic	908065	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.007109	0.366430	
chunk0123_230_1	chr3	45418435	45418823	+	0	NA	intron (NM_015340, intron 5 of 21)	MER58A|DNA|hAT-Charlie	30046	NM_015340	23395	Hs.526975	NM_015340	ENSG00000011376	LARS2	HLASA|LEURS|PRLTS4|mtLeuRS	leucyl-tRNA synthetase 2, mitochondrial	protein-coding	0.007732	0.421594	
chunk0131_296_1	chr3	150588285	150589105	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-14584	NM_016275	51714	Hs.369052	NM_016275	ENSG00000198843	SELENOT	SELT	selenoprotein T	protein-coding	0.003659	0.410475	
chunk0149_447_1	chr5	29853705	29854300	+	0	NA	Intergenic	Intergenic	-458026	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.003361	0.322148	
chunk0057_186_1	chr13	102823282	102823639	+	0	NA	intron (NM_017693, intron 7 of 10)	MIRb|SINE|MIR	16314	NM_001204425	100533467	Hs.258429	NM_001204425	ENSG00000134899	BIVM-ERCC5	ERCC5-202	BIVM-ERCC5 readthrough	protein-coding	0.002801	0.396648	
chunk0095_207_1	chr2	18498256	18498839	+	0	NA	Intergenic	Intergenic	62146	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.003431	0.323630	
chunk0045_60_1	chr12	45340781	45341101	+	0	NA	intron (NM_001142679, intron 3 of 19)	intron (NM_001142679, intron 3 of 19)	48258	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.000000	0.295950	
chunk0021_291_1	chr1	244604942	244605141	+	0	NA	intron (NM_001130957, intron 17 of 21)	intron (NM_001130957, intron 17 of 21)	-48007	NR_123735	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.020101	0.545000	
chunk0185_90_1	chr7	125484611	125485309	+	0	NA	Intergenic	L1MC2|LINE|L1	-220669	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.004298	0.323319	
chunk0041_259_1	chr11	129018138	129018544	+	0	NA	intron (NM_001142685, intron 10 of 21)	intron (NM_001142685, intron 10 of 21)	5852	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.004926	0.329238	
chunk0161_242_1	chr5	171610580	171611127	+	0	NA	Intergenic	L2a|LINE|L2	-175019	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.016453	0.468978	
chunk0194_269_1	chr8	87017481	87017938	+	0	NA	intron (NM_173538, intron 4 of 10)	MER4B-int|LTR|ERV1	151261	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.006565	0.301310	
chunk0209_327_1	chrX	50565632	50566186	+	0	NA	Intergenic	Intergenic	-95171	NM_001013742	139189	Hs.38132	NM_001013742	ENSG00000274588	DGKK	-	diacylglycerol kinase kappa	protein-coding	0.009025	0.445045	274(AAGAACAGCCTGTTCT,-,0.00),275(AGAACAGCCTGTTCTC,+,0.00)
chunk0043_346_1	chr12	23005395	23005769	+	0	NA	Intergenic	L1ME1|LINE|L1	-170054	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.005348	0.341333	
chunk0035_133_1	chr11	42772624	42773103	+	0	NA	Intergenic	Intergenic	496506	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.010438	0.479167	
chunk0028_215_1	chr10	89475478	89476040	+	0	NA	intron (NM_213606, intron 2 of 7)	intron (NM_213606, intron 2 of 7)	19768	NR_120614	101926906	Hs.568874	NR_120614	ENSG00000234452	SLC16A12-AS1	-	SLC16A12 antisense RNA 1	ncRNA	0.007117	0.380107	
chunk0134_195_1	chr3	178357391	178357888	+	0	NA	Intergenic	L1MA7|LINE|L1	-61562	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.002012	0.289157	
chunk0071_229_1	chr15	85016454	85016747	+	0	NA	intron (NM_002605, intron 1 of 21)	L1MC5|LINE|L1	34626	NM_173454	5151	Hs.9333	NM_002605	ENSG00000073417	PDE8A	HsT19550	phosphodiesterase 8A	protein-coding	0.000000	0.329932	
chunk0109_169_1	chr20	4149626	4150082	+	0	NA	intron (NM_175842, intron 1 of 8)	intron (NM_175842, intron 1 of 8)	1075	NM_001270691	54498	Hs.433337	NM_175839	ENSG00000088826	SMOX	C20orf16|PAO|PAO-1|PAO1|PAOH|PAOH1|SMO	spermine oxidase	protein-coding	0.046053	0.632385	
chunk0105_374_1	chr2	192123882	192125023	+	0	NA	intron (NM_016192, intron 4 of 9)	intron (NM_016192, intron 4 of 9)	70481	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.001753	0.397548	758(AGAAACAGACTGTACA,-,0.00),759(GAAACAGACTGTACAC,+,0.00)
chunk0161_320_1	chr5	173567474	173568043	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	-11876	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.014060	0.384211	
chunk0171_212_1	chr6	126025477	126026011	+	0	NA	intron (NM_001031712, intron 12 of 12)	intron (NM_001031712, intron 12 of 12)	39314	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.000000	0.302804	
chunk0159_167_1	chr5	139655978	139656304	+	0	NA	intron (NM_016463, intron 1 of 2)	intron (NM_016463, intron 1 of 2)	7425	NM_016463	51523	Hs.189119	NM_016463	ENSG00000171604	CXXC5	CF5|HSPC195|RINF|WID	CXXC finger protein 5	protein-coding	0.027607	0.639144	
chunk0159_176_1	chr5	140123462	140123661	+	0	NA	Intergenic	Intergenic	-2375	NM_001007189	492311	Hs.696360	NM_001007189	ENSG00000182700	IGIP	C5orf53	IgA inducing protein	protein-coding	0.000000	0.245000	
chunk0050_95_1	chr12	101877276	101877537	+	0	NA	promoter-TSS (NM_018370)	promoter-TSS (NM_018370)	79	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.118774	0.694656	
chunk0181_262_1	chr7	85927314	85927568	+	0	NA	Intergenic	MER68|LTR|ERVL	-716473	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.003937	0.419608	
chunk0132_23_1	chr3	154547540	154547739	+	0	NA	Intergenic	L1M5|LINE|L1	-117924	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.010050	0.315000	
chunk0090_294_1	chr18	75070736	75071009	+	0	NA	Intergenic	Intergenic	134641	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.010989	0.445255	
chunk0071_308_1	chr15	86179584	86180092	+	0	NA	intron (NM_152336, intron 4 of 23)	L1ME1|LINE|L1	37827	NM_152336	123624	Hs.31795	NM_152336	ENSG00000273540	AGBL1	CCP4|FECD8	ATP/GTP binding protein like 1	protein-coding	0.003937	0.308448	
chunk0031_230_1	chr10	126558744	126559407	+	0	NA	Intergenic	Intergenic	-37634	NM_001004298	118611	Hs.587663	NM_001004298	ENSG00000154493	C10orf90	FATS|bA422P15.2	chromosome 10 open reading frame 90	protein-coding	0.003017	0.430723	
chunk0038_438_1	chr11	94674080	94674566	+	0	NA	Intergenic	Intergenic	-94019	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.008230	0.486653	234(AAGCACAGGCTGTGCT,-,0.00),235(AGCACAGGCTGTGCTG,+,0.00)
chunk0023_296_1	chr10	28773971	28774501	+	0	NA	intron (NR_120652, intron 2 of 3)	HAL1ME|LINE|L1	21814	NR_038376	100507605	Hs.119207	NR_038374	ENSG00000235824	LINC00837	-	long intergenic non-protein coding RNA 837	ncRNA	0.003774	0.418079	
chunk0095_98_1	chr2	15275038	15275365	+	0	NA	intron (NR_052013, intron 44 of 50)	intron (NR_052013, intron 44 of 50)	286147	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.012232	0.378049	
chunk0082_65_1	chr17	51408631	51409138	+	0	NA	Intergenic	Intergenic	72169	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.007890	0.391732	
chunk0164_57_1	chr6	19281859	19282513	+	0	NA	Intergenic	Intergenic	-101706	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.006116	0.401527	
chunk0115_429_1	chr21	31826636	31827098	+	0	NA	Intergenic	MER49|LTR|ERV1	-46448	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.006494	0.403888	54(GGGCACTCAGTGTGCA,-,0.00),55(GGCACTCAGTGTGCAG,+,0.00),298(TAGAACATGCTGTATT,-,0.00),299(AGAACATGCTGTATTC,+,0.00)
chunk0111_82_1	chr20	23249259	23249868	+	0	NA	Intergenic	Intergenic	-101173	NM_013248	29107	Hs.516933	NM_013248	ENSG00000132661	NXT1	MTR2|P15	nuclear transport factor 2 like export factor 1	protein-coding	0.008210	0.431148	
chunk0151_350_1	chr5	54389966	54390165	+	0	NA	intron (NR_126379, intron 1 of 4)	intron (NR_126379, intron 1 of 4)	-65536	NM_006308	8988	Hs.41707	NM_006308	ENSG00000169271	HSPB3	DHMN2C|HMN2C|HSPL27	heat shock protein family B (small) member 3	protein-coding	0.005025	0.420000	
chunk0062_32_1	chr14	67032296	67032648	+	0	NA	intron (NM_001024218, intron 9 of 21)	L1MB2|LINE|L1	-156921	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.002841	0.518414	
chunk0097_235_1	chr2	53314544	53314908	+	0	NA	Intergenic	Intergenic	-453066	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.002747	0.328767	
chunk0102_89_1	chr2	143561700	143562153	+	0	NA	intron (NM_018460, intron 11 of 13)	intron (NM_018460, intron 11 of 13)	-375141	NR_110237	101928386	Hs.668251	NR_110237	ENSG00000232377	LOC101928386	-	uncharacterized LOC101928386	ncRNA	0.013245	0.352423	
chunk0015_412_1	chr1	191279435	191279885	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	654770	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.004444	0.427938	240(AAGGACACTGTGTTCT,-,0.00),241(AGGACACTGTGTTCTC,+,0.00)
chunk0133_291_1	chr3	172140627	172141120	+	0	NA	intron (NM_022763, intron 3 of 25)	(TTATAT)n|Simple_repeat|Simple_repeat	100319	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.008114	0.398785	
chunk0156_65_1	chr5	103466549	103466845	+	0	NA	Intergenic	Intergenic	75288	NR_104670	102467212	Hs.641885	NR_104670	ENSG00000248757	LINC02115	-	long intergenic non-protein coding RNA 2115	ncRNA	0.000000	0.323232	123(AAGGGCTGTGTGTCCT,-,0.00)
chunk0158_224_1	chr5	128695870	128696154	+	0	NA	Intergenic	LTR50|LTR|ERVL	-157970	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.000000	0.428070	
chunk0142_95_1	chr4	94271367	94271572	+	0	NA	intron (NM_001128430, intron 11 of 23)	intron (NM_001128430, intron 11 of 23)	18175	NM_001254949	56916	Hs.410406	NM_020159	ENSG00000163104	SMARCAD1	ADERM|BASNS|ETL1|HEL1|HRZ	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding	0.000000	0.325243	
chunk0140_35_1	chr4	66273313	66273707	+	0	NA	Intergenic	MER129|LTR?|LTR?	-3314	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.002538	0.326582	
chunk0182_175_1	chr7	95597177	95597402	+	0	NA	promoter-TSS (NM_002612)	promoter-TSS (NM_002612)	-676	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.022222	0.384956	
chunk0039_10_1	chr11	95119504	95119861	+	0	NA	intron (NM_015036, intron 1 of 1)	L1MA2|LINE|L1	29872	NM_015036	23052	Hs.167115	NM_015036	ENSG00000149218	ENDOD1	-	endonuclease domain containing 1	protein-coding	0.002801	0.547486	
chunk0170_32_1	chr6	109313231	109313489	+	0	NA	Intergenic	Intergenic	19057	NR_028595	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.011628	0.513514	
chunk0172_92_1	chr6	134640935	134641158	+	0	NA	Intergenic	Intergenic	-101041	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.000000	0.410714	
chunk0011_187_1	chr1	149615750	149616224	+	0	NA	intron (NR_111950, intron 1 of 8)	intron (NR_111950, intron 1 of 8)	8975	NR_111951	57234	Hs.456578	NR_046135	ENSG00000277147	LINC00869	FAM91A2	long intergenic non-protein coding RNA 869	ncRNA	0.027426	0.437895	
chunk0009_422_1	chr1	110856304	110856690	+	0	NA	Intergenic	Intergenic	-14702	NM_001040033	963	Hs.443057	NM_000560	ENSG00000143119	CD53	MOX44|TSPAN25	CD53 molecule	protein-coding	0.005181	0.452196	
chunk0044_171_1	chr12	30027729	30027973	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-243092	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.000000	0.355102	
chunk0098_278_1	chr2	75582920	75583398	+	0	NA	Intergenic	L1MA3|LINE|L1	-13437	NM_032181	84141	Hs.302346	NM_032181	ENSG00000115363	EVA1A	FAM176A|TMEM166	eva-1 homolog A, regulator of programmed cell death	protein-coding	0.002092	0.344468	
chunk0013_124_1	chr1	168026956	168027184	+	0	NA	intron (NM_018442, intron 11 of 19)	L2|LINE|L2	28410	NR_031702	100313835		NR_031702	ENSG00000221545	MIR1255B2	MIR1255B-2|MIRN1255B2|hsa-mir-1255b-2	microRNA 1255b-2	ncRNA	0.008772	0.393013	
chunk0056_175_1	chr13	85332486	85332900	+	0	NA	Intergenic	Intergenic	-30910	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.000000	0.325301	
chunk0114_391_1	chr20	63209796	63210414	+	0	NA	intron (NM_017798, intron 3 of 4)	Tigger3b|DNA|TcMar-Tigger	6081	NM_017798	54915	Hs.744852	NM_017798	ENSG00000149658	YTHDF1	C20orf21	YTH N6-methyladenosine RNA binding protein 1	protein-coding	0.011327	0.479806	
chunk0018_415_1	chr1	222674454	222674880	+	0	NA	intron (NM_022831, intron 7 of 9)	intron (NM_022831, intron 7 of 9)	30364	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.002347	0.304450	
chunk0042_70_1	chr12	2049905	2050356	+	0	NA	TTS (NR_046768)	TTS (NR_046768)	1778	NR_046768	100874369	Hs.208723	NR_046768	ENSG00000256257	CACNA1C-IT2	-	CACNA1C intronic transcript 2	ncRNA	0.006652	0.429204	
chunk0212_82_1	chrY	11659869	11660117	+	0	NA	Intergenic	Intergenic	761597	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.020161	0.393574	
chunk0207_113_1	chr9	128862307	128862919	+	0	NA	intron (NM_001287390, intron 1 of 14)	intron (NM_001287390, intron 1 of 14)	19462	NM_001287390	883	Hs.495250	NM_004059	ENSG00000171097	KYAT1	CCBL1|GTK|KAT1|KATI	kynurenine aminotransferase 1	protein-coding	0.013072	0.510604	286(GGGCACTGCCAGTTCT,-,0.00),287(GGCACTGCCAGTTCTC,+,0.00)
chunk0006_52_1	chr1	64536205	64536739	+	0	NA	intron (NM_001293274, intron 1 of 25)	UCON37|Unknown|Unknown	30558	NM_001293274	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.013109	0.388785	
chunk0168_382_1	chr6	93990041	93990455	+	0	NA	Intergenic	L1MA5|LINE|L1	283165	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.007246	0.351807	
chunk0117_404_1	chr21	45568337	45569068	+	0	NA	Intergenic	L1MC3|LINE|L1	-26231	NM_001205206	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.012312	0.441257	202(TAGAACATCTTGTACT,-,0.00),203(AGAACATCTTGTACTA,+,0.00)
chunk0190_46_1	chr8	29377639	29378314	+	0	NA	Intergenic	Intergenic	-27226	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.010370	0.392012	
chunk0128_377_1	chr3	113390286	113390570	+	0	NA	intron (NM_018338, intron 15 of 20)	L1MA3|LINE|L1	-13570	NR_046728	100874029	Hs.599665	NR_046728	ENSG00000243849	CFAP44-AS1	WDR52-AS1	CFAP44 antisense RNA 1	ncRNA	0.000000	0.343860	
chunk0117_259_1	chr22	23521658	23522146	+	0	NA	Intergenic	CpG	-16200	NR_109832	101978785	Hs.575107	NR_109832		PCAT14	-	prostate cancer associated transcript 14	ncRNA	0.106557	0.699387	111(AAGAACAGTTTGTCTT,-,0.00),112(AGAACAGTTTGTCTTT,+,0.00)
chunk0029_439_1	chr10	110214056	110214256	+	0	NA	intron (NM_001008541, intron 1 of 4)	MIR3|SINE|MIR	3925	NM_001008541	4601	Hs.602078	NM_005962	ENSG00000119950	MXI1	MAD2|MXD2|MXI|bHLHc11	MAX interactor 1, dimerization protein	protein-coding	0.010000	0.427861	
chunk0128_366_1	chr3	113231923	113232234	+	0	NA	intron (NM_001301861, intron 2 of 19)	intron (NM_001301861, intron 2 of 19)	19581	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.000000	0.525641	
chunk0045_43_1	chr12	44948763	44949095	+	0	NA	Intergenic	Intergenic	-35001	NM_001145110	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.042169	0.570571	
chunk0201_89_1	chr9	34637524	34638136	+	0	NA	promoter-TSS (NM_005866)	promoter-TSS (NM_005866)	-4	NM_001282206	10280	Hs.522087	NM_005866	ENSG00000147955	SIGMAR1	ALS16|DSMA2|OPRS1|SIG-1R|SR-BP|SR-BP1|SRBP|hSigmaR1|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding	0.096405	0.690049	
chunk0156_445_1	chr5	114822759	114823037	+	0	NA	Intergenic	Intergenic	-49485	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.387097	
chunk0002_421_1	chr1	27789533	27789980	+	0	NA	intron (NM_177424, intron 2 of 8)	intron (NM_177424, intron 2 of 8)	16573	NM_177424	23673	Hs.523855	NM_177424	ENSG00000117758	STX12	STX13|STX14	syntaxin 12	protein-coding	0.008949	0.435268	142(GAGGACACAGTGTCCT,-,0.00),143(AGGACACAGTGTCCTT,+,0.00)
chunk0073_133_1	chr16	5024535	5025193	+	0	NA	TTS (NM_016256)	TTS (NM_016256)	-8838	NR_038913	100507589	Hs.729936	NR_038913		NAGPA-AS1	-	NAGPA antisense RNA 1	ncRNA	0.016717	0.497724	
chunk0211_109_1	chrX	111441629	111441828	+	0	NA	Intergenic	MIRb|SINE|MIR	-29496	NM_178153	1641	Hs.34780	NM_000555	ENSG00000077279	DCX	DBCN|DC|LISX|SCLH|XLIS	doublecortin	protein-coding	0.005025	0.405000	
chunk0200_257_1	chr9	21686630	21687001	+	0	NA	Intergenic	Intergenic	-115821	NM_002451	4507	Hs.193268	NM_002451	ENSG00000099810	MTAP	BDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fus	methylthioadenosine phosphorylase	protein-coding	0.005391	0.338710	
chunk0204_321_1	chr9	100588981	100589344	+	0	NA	TTS (NM_001018116)	TTS (NM_001018116)	11083	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.016529	0.467033	
chunk0116_281_1	chr21	39798972	39799764	+	0	NA	intron (NM_001080444, intron 8 of 8)	intron (NM_001080444, intron 8 of 8)	53961	NM_001080444	150084	Hs.422120	NM_001080444	ENSG00000183067	IGSF5	GSF5|JAM4	immunoglobulin superfamily member 5	protein-coding	0.013889	0.510719	
chunk0103_251_1	chr2	164980785	164981470	+	0	NA	Intergenic	Intergenic	-25602	NM_001199148	151258	Hs.658702	NM_173512	ENSG00000169507	SLC38A11	AVT2	solute carrier family 38 member 11	protein-coding	0.005839	0.374636	
chunk0191_140_1	chr8	48790554	48790950	+	0	NA	Intergenic	Intergenic	-55441	NR_024605	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.015152	0.448363	
chunk0096_256_1	chr2	31319531	31320230	+	0	NA	Intergenic	Intergenic	85866	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.007153	0.440000	359(AGGAACAGGGTGTACA,-,0.00),360(GGAACAGGGTGTACAC,+,0.00)
chunk0144_441_1	chr4	141127860	141128312	+	0	NA	intron (NM_020724, intron 1 of 6)	intron (NM_020724, intron 1 of 6)	5376	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.008850	0.419426	160(TGGAACACCCTGTTTC,-,0.00),161(GGAACACCCTGTTTCA,+,0.00)
chunk0082_445_1	chr17	61947378	61947755	+	0	NA	intron (NM_005121, intron 28 of 29)	intron (NM_005121, intron 28 of 29)	-19550	NR_026641									0.007958	0.354497	
chunk0038_153_1	chr11	84671407	84671778	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	251829	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.008086	0.413978	
chunk0067_150_1	chr15	43305993	43306210	+	0	NA	Intergenic	L2c|LINE|L2	-3846	NM_052955	116179	Hs.164661	NM_052955	ENSG00000159495	TGM7	TGMZ	transglutaminase 7	protein-coding	0.000000	0.412844	69(CAGGACAGTATGTTCT,-,0.00),70(AGGACAGTATGTTCTG,+,0.00)
chunk0033_362_1	chr11	23084706	23085149	+	0	NA	Intergenic	Intergenic	-224501	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.004515	0.371622	
chunk0101_244_1	chr2	131604365	131605204	+	0	NA	intron (NR_033885, intron 5 of 5)	Zaphod2|DNA|hAT-Tip100	8010	NR_033885	440915	Hs.631267	NM_001017421		POTEKP	ACT|ACTBL3|POTE2delta|POTEK	POTE ankyrin domain family member K, pseudogene	pseudo	0.003576	0.395238	509(TAGAACAAGGTGCTCT,-,0.00),510(AGAACAAGGTGCTCTG,+,0.00)
chunk0182_182_1	chr7	95628635	95629147	+	0	NA	Intergenic	Intergenic	-32278	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.003906	0.395712	
chunk0135_295_1	chr3	189593429	189593816	+	0	NA	Intergenic	L1MA9|LINE|L1	-37805	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.002584	0.329897	
chunk0034_233_1	chr11	33701632	33702093	+	0	NA	Intergenic	MIR|SINE|MIR	-1122	NM_001166692	100131378	Hs.709466	NM_001166692	ENSG00000205177	C11orf91	-	chromosome 11 open reading frame 91	protein-coding	0.004338	0.441558	
chunk0059_209_1	chr14	33705515	33705995	+	0	NA	intron (NM_022123, intron 5 of 10)	intron (NM_022123, intron 5 of 10)	-3182	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.014583	0.363825	
chunk0097_384_1	chr2	61678990	61679571	+	0	NA	Intergenic	LTR26B|LTR|ERV1	-140997	NM_003400	7514	Hs.370770	NM_003400	ENSG00000082898	XPO1	CRM-1|CRM1|emb|exp1	exportin 1	protein-coding	0.013769	0.417526	
chunk0009_207_1	chr1	106127121	106127701	+	0	NA	Intergenic	MER97b|DNA|hAT-Tip100	-508476	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.005172	0.330465	
chunk0056_182_1	chr13	85413125	85413420	+	0	NA	intron (NR_046989, intron 1 of 3)	intron (NR_046989, intron 1 of 3)	49669	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.003390	0.334459	
chunk0059_328_1	chr14	36833402	36833644	+	0	NA	intron (NM_030631, intron 2 of 9)	intron (NM_030631, intron 2 of 9)	118868	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.004132	0.349794	
chunk0028_100_1	chr10	84291419	84291946	+	0	NA	non-coding (NR_038220, exon 5 of 6)	non-coding (NR_038220, exon 5 of 6)	11702	NR_038220	170425	Hs.434131	NR_038220	ENSG00000229404	LINC00858	CRCAL-2	long intergenic non-protein coding RNA 858	ncRNA	0.000000	0.439394	
chunk0013_333_1	chr1	171721212	171721563	+	0	NA	intron (NM_003762, intron 3 of 7)	L1PA5|LINE|L1	20852	NM_003762	8674	Hs.6651	NM_003762	ENSG00000117533	VAMP4	VAMP-4|VAMP24	vesicle associated membrane protein 4	protein-coding	0.002849	0.315341	
chunk0187_441_1	chr7	158910130	158910426	+	0	NA	intron (NM_018051, intron 11 of 24)	intron (NM_018051, intron 11 of 24)	53700	NM_018051	55112	Hs.389945	NM_018051	ENSG00000126870	WDR60	FAP163|SRPS6|SRTD8	WD repeat domain 60	protein-coding	0.040541	0.582492	
chunk0020_116_1	chr1	233312023	233312545	+	0	NA	Intergenic	L1MC4a|LINE|L1	-15484	NM_032435	84451	Hs.547779	NM_032435	ENSG00000143674	MAP3K21	MLK4|dJ862P8.3	mitogen-activated protein kinase kinase kinase 21	protein-coding	0.005747	0.340344	
chunk0122_146_1	chr3	32045156	32045954	+	0	NA	Intergenic	Intergenic	-60956	NM_015141	23171	Hs.82432	NM_015141	ENSG00000152642	GPD1L	GPD1-L	glycerol-3-phosphate dehydrogenase 1 like	protein-coding	0.006266	0.435544	
chunk0014_262_1	chr1	180167638	180168170	+	0	NA	intron (NM_001004128, intron 2 of 12)	intron (NM_001004128, intron 2 of 12)	13071	NM_001004128	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.009398	0.553471	237(CAGGGCACTCTGTTCC,-,0.00),238(AGGGCACTCTGTTCCT,+,0.00)
chunk0199_374_1	chr9	12908992	12909405	+	0	NA	Intergenic	LTR8|LTR|ERV1	63435	NR_132976	106635615		NR_132976		SNORD137	-	small nucleolar RNA, C/D box 137	snoRNA	0.007264	0.449275	
chunk0130_111_1	chr3	131386386	131386841	+	0	NA	non-coding (NR_033268, exon 2 of 2)	non-coding (NR_033268, exon 2 of 2)	4832	NR_033268	131870	Hs.282050	NM_152395	ENSG00000198585	NUDT16	-	nudix hydrolase 16	protein-coding	0.006593	0.484649	211(AGCACATTTTGTTTCT,+,0.00)
chunk0032_141_1	chr11	4681709	4682026	+	0	NA	exon (NM_030774, exon 2 of 2)	exon (NM_030774, exon 2 of 2)	15979	NM_030774	81285	Hs.501758	NM_030774	ENSG00000167332	OR51E2	HPRAJ|OR51E3P|OR52A2|PSGR	olfactory receptor family 51 subfamily E member 2	protein-coding	0.015773	0.503145	
chunk0040_139_1	chr11	112566212	112566576	+	0	NA	Intergenic	L2a|LINE|L2	-10592	NR_104155	387810	Hs.512255	NR_104155	ENSG00000255484	LINC02764	-	long intergenic non-protein coding RNA 2764	ncRNA	0.005495	0.446575	
chunk0083_396_1	chr17	71788300	71788550	+	0	NA	Intergenic	Intergenic	237554	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.012000	0.350598	
chunk0107_425_1	chr2	224772480	224772861	+	0	NA	intron (NM_014689, intron 53 of 55)	LTR33|LTR|ERVL	174395	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.005249	0.450262	
chunk0104_132_1	chr2	173230183	173230470	+	0	NA	intron (NM_016653, intron 12 of 19)	intron (NM_016653, intron 12 of 19)	51710	NR_033882	339751	Hs.570083	NR_033882	ENSG00000238133	MAP3K20-AS1	MLK7-AS1	MAP3K20 antisense RNA 1	ncRNA	0.013937	0.423611	
chunk0212_51_1	chrY	11312099	11312553	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1109264	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.002203	0.446154	
chunk0060_309_1	chr14	50954475	50954737	+	0	NA	Intergenic	Intergenic	-10076	NM_001163940	5836	Hs.282417	NM_002863	ENSG00000100504	PYGL	GSD6	glycogen phosphorylase L	protein-coding	0.011450	0.425856	
chunk0189_181_1	chr8	23570030	23570954	+	0	NA	intron (NM_016612, intron 3 of 3)	intron (NM_016612, intron 3 of 3)	41642	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.011905	0.443243	
chunk0192_231_1	chr8	65460292	65460491	+	0	NA	Intergenic	Intergenic	102275	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.000000	0.380000	
chunk0167_338_1	chr6	72589126	72589325	+	0	NA	Intergenic	Intergenic	-32618	NM_001160133	56479	Hs.445324	NM_019842	ENSG00000185760	KCNQ5	Kv7.5|MRD46	potassium voltage-gated channel subfamily Q member 5	protein-coding	0.000000	0.350000	
chunk0202_244_1	chr9	76715394	76715791	+	0	NA	intron (NM_015225, intron 6 of 18)	intron (NM_015225, intron 6 of 18)	-23177	NM_001308050	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.007557	0.349246	
chunk0100_136_1	chr2	108719100	108719606	+	0	NA	promoter-TSS (NM_006267)	promoter-TSS (NM_006267)	-128	NM_006267	5903	Hs.199561	NM_006267	ENSG00000153201	RANBP2	ADANE|ANE1|IIAE3|NUP358|TRP1|TRP2	RAN binding protein 2	protein-coding	0.086957	0.570020	
chunk0024_112_1	chr10	34699759	34700278	+	0	NA	intron (NM_019619, intron 1 of 24)	intron (NM_019619, intron 1 of 24)	115307	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.005780	0.401923	
chunk0138_292_1	chr4	40941885	40942154	+	0	NA	intron (NM_004307, intron 7 of 17)	intron (NM_004307, intron 7 of 17)	-84827	NM_001166053	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.007435	0.440741	
chunk0060_228_1	chr14	49479138	49479855	+	0	NA	Intergenic	L2c|LINE|L2	106920	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.009763	0.417827	162(TTGCACATTCTGTTCT,-,0.00),163(TGCACATTCTGTTCTC,+,0.00)
chunk0043_428_1	chr12	25992701	25992970	+	0	NA	intron (NM_001164747, intron 1 of 5)	intron (NM_001164747, intron 1 of 5)	19080	NM_001164747	11228	Hs.696433	NM_007211	ENSG00000123094	RASSF8	C12orf2|HOJ1	Ras association domain family member 8	protein-coding	0.011152	0.437037	
chunk0209_289_1	chrX	48165281	48165600	+	0	NA	Intergenic	AluSg|SINE|Alu	31323	NM_175723	6758	Hs.166198	NM_021015	ENSG00000165583	SSX5	-	SSX family member 5	protein-coding	0.025078	0.500000	
chunk0088_12_1	chr18	43194396	43195031	+	0	NA	Intergenic	Intergenic	-79021	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.331761	327(GAGAACAAGCTGATCT,-,0.00),328(AGAACAAGCTGATCTA,+,0.00)
chunk0126_83_1	chr3	74717395	74717596	+	0	NA	Intergenic	L1ME1|LINE|L1	-196355	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.267327	
chunk0010_277_1	chr1	117336576	117336792	+	0	NA	Intergenic	MamGyp-int|LTR|Gypsy	-30779	NM_006699	10905	Hs.435938	NM_006699	ENSG00000198162	MAN1A2	MAN1B	mannosidase alpha class 1A member 2	protein-coding	0.004630	0.456221	
chunk0095_288_1	chr2	20164356	20164579	+	0	NA	Intergenic	Intergenic	60699	NM_002997	6382	Hs.224607	NM_002997	ENSG00000115884	SDC1	CD138|SDC|SYND1|syndecan	syndecan 1	protein-coding	0.013453	0.535714	
chunk0010_266_1	chr1	116932130	116932419	+	0	NA	intron (NM_020440, intron 1 of 8)	intron (NM_020440, intron 1 of 8)	22351	NM_020440	5738	Hs.418093	NM_020440	ENSG00000134247	PTGFRN	CD315|CD9P-1|EWI-F|FPRP|SMAP-6	prostaglandin F2 receptor inhibitor	protein-coding	0.010381	0.365517	
chunk0003_105_1	chr1	32104122	32104673	+	0	NA	Intergenic	Intergenic	-3646	NM_012316	23633	Hs.470588	NM_012316	ENSG00000025800	KPNA6	IPOA7|KPNA7	karyopherin subunit alpha 6	protein-coding	0.009074	0.460145	483(AGGAAGATACTGTTCC,-,0.00),484(GGAAGATACTGTTCCT,+,0.00)
chunk0110_73_1	chr20	10976625	10977213	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-67647	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.006803	0.382003	
chunk0191_373_1	chr8	56987989	56988499	+	0	NA	intron (NM_017813, intron 1 of 4)	intron (NM_017813, intron 1 of 4)	5627	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.003922	0.367906	
chunk0107_36_1	chr2	211067227	211067756	+	0	NA	Intergenic	L2a|LINE|L2	449920	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.005671	0.362264	
chunk0178_216_1	chr7	35570835	35571459	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	124015	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.011218	0.404800	
chunk0172_309_1	chr6	138188600	138188838	+	0	NA	intron (NM_020340, intron 2 of 33)	intron (NM_020340, intron 2 of 33)	26803	NM_020340	57221	Hs.194408	NM_020340	ENSG00000112379	ARFGEF3	A7322|BIG3|C6orf92|KIAA1244|PPP1R33|dJ171N11.1	ARFGEF family member 3	protein-coding	0.004202	0.485356	
chunk0088_73_1	chr18	44645725	44646076	+	0	NA	Intergenic	L1ME4a|LINE|L1	-34273	NM_001130110	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.002849	0.329545	
chunk0069_196_1	chr15	63349530	63349941	+	0	NA	intron (NM_206925, intron 2 of 9)	intron (NM_206925, intron 2 of 9)	32375	NM_206925	771	Hs.210995	NM_001218	ENSG00000074410	CA12	CA-XII|CAXII|HsT18816|T18816	carbonic anhydrase 12	protein-coding	0.014599	0.451456	
chunk0071_387_1	chr15	89162798	89162997	+	0	NA	intron (NM_007011, intron 9 of 14)	L2a|LINE|L2	58794	NM_000326	6017	Hs.1933	NM_000326	ENSG00000140522	RLBP1	CRALBP	retinaldehyde binding protein 1	protein-coding	0.005025	0.450000	
chunk0188_266_1	chr8	14817310	14817509	+	0	NA	intron (NM_139167, intron 1 of 7)	L1MA6|LINE|L1	36101	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.010050	0.500000	
chunk0188_277_1	chr8	15494598	15494959	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-45309	NM_178234	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.008310	0.392265	
chunk0168_375_1	chr6	93919452	93919679	+	0	NA	Intergenic	MER119|DNA|hAT-Charlie	212482	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.004405	0.403509	
chunk0111_51_1	chr20	22578527	22578892	+	0	NA	promoter-TSS (NR_001558)	promoter-TSS (NR_001558)	-67	NR_001558	140828	Hs.9842	NR_001558	ENSG00000259974	LINC00261	ALIEN|C20orf56|DEANR1|FALCOR|HCCDR1|NCRNA00261|TCONS_00027846|onco-lncRNA-17	long intergenic non-protein coding RNA 261	ncRNA	0.049315	0.445355	
chunk0073_324_1	chr16	14418712	14419278	+	0	NA	Intergenic	Intergenic	-48729	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.015901	0.493827	262(GGGAACATTGTGGACT,-,0.00)
chunk0103_48_1	chr2	159399698	159400341	+	0	NA	intron (NM_001289975, intron 16 of 35)	Tigger15a|DNA|TcMar-Tigger	-113220	NM_001128212	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.007776	0.333851	
chunk0087_171_1	chr18	35054363	35054928	+	0	NA	intron (NR_046177, intron 1 of 6)	intron (NR_046177, intron 1 of 6)	12995	NR_046177	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.019469	0.404594	271(CAGGACATCCTGTGAT,-,0.00)
chunk0201_137_1	chr9	35747055	35747601	+	0	NA	intron (NM_020944, intron 1 of 16)	intron (NM_020944, intron 1 of 16)	1900	NM_020944	57704	Hs.443134	NM_020944	ENSG00000070610	GBA2	AD035|NLGase|SPG46	glucosylceramidase beta 2	protein-coding	0.000000	0.484461	
chunk0108_384_1	chr2	237005623	237006179	+	0	NA	Intergenic	Intergenic	-79540	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.016187	0.387792	262(AGAAACATCGTGTTCT,-,0.00),263(GAAACATCGTGTTCTA,+,0.00)
chunk0078_42_1	chr17	1097081	1097372	+	0	NA	intron (NM_001092, intron 2 of 21)	intron (NM_001092, intron 2 of 21)	11874	NM_001092	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.034364	0.575342	
chunk0173_295_1	chr6	148343512	148343834	+	0	NA	intron (NM_015278, intron 1 of 19)	intron (NM_015278, intron 1 of 19)	1080	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.003106	0.371517	
chunk0161_20_1	chr5	165723942	165724194	+	0	NA	Intergenic	Intergenic	1202302	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.011905	0.379447	
chunk0075_362_1	chr16	56246144	56246574	+	0	NA	TTS (NR_037499)	TTS (NR_037499)	839	NR_037499	100500891		NR_037499	ENSG00000265281	MIR3935	-	microRNA 3935	ncRNA	0.018605	0.540603	
chunk0185_208_1	chr7	128727253	128727599	+	0	NA	intron (NR_104243, intron 7 of 8)	L2c|LINE|L2	-11866	NM_001199673	813	Hs.7753	NM_001219	ENSG00000128595	CALU	-	calumenin	protein-coding	0.011561	0.489914	
chunk0185_329_1	chr7	131844037	131844299	+	0	NA	Intergenic	Intergenic	-66052	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.019084	0.505703	
chunk0004_201_1	chr1	46613067	46613448	+	0	NA	exon (NM_145279, exon 2 of 4)	exon (NM_145279, exon 2 of 4)	1876	NM_145279	148932	Hs.632401	NM_145279	ENSG00000142961	MOB3C	MOB1E|MOBKL2C	MOB kinase activator 3C	protein-coding	0.057743	0.615183	208(CGGAACGTCTTGTCCT,-,0.00),209(GGAACGTCTTGTCCTT,+,0.00)
chunk0130_338_1	chr3	138666664	138666922	+	0	NA	intron (NM_001256045, intron 8 of 12)	L2a|LINE|L2	40828	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.003876	0.409266	
chunk0022_117_1	chr10	11454787	11455036	+	0	NA	Intergenic	MIR3|SINE|MIR	77369	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.012048	0.528000	
chunk0193_29_1	chr8	71059030	71059601	+	0	NA	Intergenic	Intergenic	297196	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.008757	0.400350	
chunk0097_252_1	chr2	53938282	53938481	+	0	NA	intron (NM_014614, intron 4 of 46)	intron (NM_014614, intron 4 of 46)	32459	NM_014614	23198	Hs.413801	NM_014614	ENSG00000068878	PSME4	PA200	proteasome activator subunit 4	protein-coding	0.005025	0.380000	4(TGGAACACAGAGTCCT,-,0.00),5(GGAACACAGAGTCCTC,+,0.00)
chunk0169_130_1	chr6	101129852	101130107	+	0	NA	Intergenic	Intergenic	-248607	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.003922	0.335938	
chunk0120_147_1	chr3	5219611	5220334	+	0	NA	TTS (NM_014674)	TTS (NM_014674)	30283	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.004149	0.328729	
chunk0098_425_1	chr2	81097366	81097594	+	0	NA	Intergenic	L1ME1|LINE|L1	369466	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.004386	0.314410	
chunk0037_309_1	chr11	76772539	76772834	+	0	NA	Intergenic	Intergenic	-9627	NM_001258210	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.023729	0.466216	
chunk0083_158_1	chr17	65963746	65964010	+	0	NA	intron (NM_001302891, intron 15 of 24)	intron (NM_001302891, intron 15 of 24)	-137335	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.007576	0.377358	
chunk0178_203_1	chr7	34600005	34600297	+	0	NA	intron (NR_033664, intron 2 of 4)	MIR|SINE|MIR	-58088	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.017123	0.395904	
chunk0006_373_1	chr1	73457148	73457372	+	0	NA	Intergenic	Intergenic	151090	NR_110676	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.000000	0.315556	
chunk0011_108_1	chr1	145999618	145999882	+	0	NA	Intergenic	Intergenic	-3119	NM_006472	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.000000	0.445283	
chunk0061_423_1	chr14	65184059	65184423	+	0	NA	Intergenic	Intergenic	38106	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.005495	0.498630	
chunk0037_228_1	chr11	74982222	74982664	+	0	NA	Intergenic	LTR40c|LTR|ERVL	-6462	NM_006656	10825	Hs.191074	NM_006656	ENSG00000162139	NEU3	SIAL3	neuraminidase 3	protein-coding	0.009050	0.474041	
chunk0187_304_1	chr7	156299584	156300054	+	0	NA	Intergenic	L1ME1|LINE|L1	145769	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.004255	0.276008	
chunk0045_271_1	chr12	49735476	49735883	+	0	NA	Intergenic	Harlequin-int|LTR|ERV1	-5831	NM_003217	7009	Hs.743965	NM_003217	ENSG00000139644	TMBIM6	BAXI1|BI-1|TEGT	transmembrane BAX inhibitor motif containing 6	protein-coding	0.012285	0.411765	
chunk0161_386_1	chr5	176944234	176944770	+	0	NA	intron (NM_016290, intron 9 of 14)	intron (NM_016290, intron 9 of 14)	-45170	NM_002115	3101	Hs.411695	NM_002115	ENSG00000160883	HK3	HKIII|HXK3	hexokinase 3	protein-coding	0.003731	0.387337	251(AAGGACAGCATGTCCT,-,0.00),252(AGGACAGCATGTCCTA,+,0.00)
chunk0086_139_1	chr18	21265313	21265792	+	0	NA	intron (NM_001142966, intron 1 of 32)	intron (NM_001142966, intron 1 of 32)	23310	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.004175	0.329167	319(GGAGACAAGGTGTTCT,-,0.00),320(GAGACAAGGTGTTCTT,+,0.00)
chunk0096_244_1	chr2	31188047	31189010	+	0	NA	intron (NM_001145122, intron 13 of 21)	intron (NM_001145122, intron 13 of 21)	29017	NM_001145122	440854	Hs.468059	NM_001145122	ENSG00000214711	CAPN14	-	calpain 14	protein-coding	0.008307	0.464730	
chunk0088_315_1	chr18	50791931	50792439	+	0	NA	Intergenic	Intergenic	27879	NM_001127175	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.005906	0.343811	
chunk0149_300_1	chr5	25638411	25638711	+	0	NA	Intergenic	L1MEi|LINE|L1	-797978	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.006667	0.308970	
chunk0012_267_1	chr1	161749864	161750078	+	0	NA	exon (NM_007240, exon 1 of 6)	exon (NM_007240, exon 1 of 6)	203	NM_007240	11266	Hs.416216	NM_007240	ENSG00000081721	DUSP12	DUSP1|YVH1	dual specificity phosphatase 12	protein-coding	0.084112	0.655814	
chunk0167_111_1	chr6	57275089	57275922	+	0	NA	Intergenic	AluSz6|SINE|Alu	-12159	NR_109774	100506188	Hs.485640	NR_109774		LOC100506188	-	uncharacterized LOC100506188	ncRNA	0.009604	0.430456	
chunk0012_276_1	chr1	161864684	161864974	+	0	NA	intron (NM_007348, intron 14 of 15)	intron (NM_007348, intron 14 of 15)	98585	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.000000	0.371134	
chunk0078_365_1	chr16	87369345	87369640	+	0	NA	intron (NM_001282683, intron 2 of 9)	L1MB3|LINE|L1	14301	NM_024735	79791	Hs.567582	NM_024735	ENSG00000103264	FBXO31	FBX14|FBXO14|Fbx31|MRT45|pp2386	F-box protein 31	protein-coding	0.023729	0.483108	
chunk0110_315_1	chr20	18641048	18641649	+	0	NA	intron (NM_080820, intron 4 of 5)	L1MB3|LINE|L1	53436	NM_080820	92675	Hs.659442	NM_080820	ENSG00000125821	DTD1	C20orf88|DTD|DUE-B|DUEB|HARS2|pqn-68	D-aminoacyl-tRNA deacylase 1	protein-coding	0.009983	0.377076	
chunk0069_358_1	chr15	66931936	66933094	+	0	NA	Intergenic	Intergenic	-133342	NM_005902	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.016408	0.490940	
chunk0035_458_1	chr11	57799314	57799679	+	0	NA	intron (NM_001085461, intron 6 of 18)	intron (NM_001085461, intron 6 of 18)	37734	NM_001206883	1500	Hs.166011	NM_001331	ENSG00000198561	CTNND1	BCDS2|CAS|CTNND|P120CAS|P120CTN|p120|p120(CAS)|p120(CTN)	catenin delta 1	protein-coding	0.000000	0.461749	
chunk0107_97_1	chr2	213372776	213373134	+	0	NA	intron (NR_047659, intron 10 of 17)	intron (NR_047659, intron 10 of 17)	88576	NM_024532	79582	Hs.743365	NM_024532	ENSG00000144451	SPAG16	PF20|WDR29	sperm associated antigen 16	protein-coding	0.000000	0.323120	
chunk0078_247_1	chr17	7106250	7106686	+	0	NA	intron (NM_001201352, intron 7 of 8)	MADE2|DNA|TcMar-Mariner	7842	NM_080914	433	Hs.654440	NM_001181	ENSG00000161944	ASGR2	ASGP-R2|ASGPR2|CLEC4H2|HBXBP|HL-2	asialoglycoprotein receptor 2	protein-coding	0.025229	0.418764	
chunk0012_345_1	chr1	162614402	162614737	+	0	NA	Intergenic	L1ME4c|LINE|L1	-17869	NM_001014796	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.008955	0.282738	
chunk0030_150_1	chr10	113849724	113850583	+	0	NA	exon (NM_014881, exon 2 of 9)	exon (NM_014881, exon 2 of 9)	4063	NM_014881	9937	Hs.1560	NM_014881	ENSG00000198924	DCLRE1A	PSO2|SNM1|SNM1A	DNA cross-link repair 1A	protein-coding	0.015134	0.406977	
chunk0098_36_1	chr2	66041659	66041890	+	0	NA	Intergenic	Intergenic	316554	NR_039938	100616464		NR_039938	ENSG00000264525	MIR4778	-	microRNA 4778	ncRNA	0.000000	0.448276	136(AGTACAGGCTCTTCCT,+,0.00)
chunk0043_282_1	chr12	21336563	21337163	+	0	NA	intron (NM_134431, intron 2 of 15)	intron (NM_134431, intron 2 of 15)	-1965	NM_021094	6579	Hs.46440	NM_005075	ENSG00000084453	SLCO1A2	OATP|OATP-A|OATP1A2|SLC21A3	solute carrier organic anion transporter family member 1A2	protein-coding	0.008333	0.357737	
chunk0020_103_1	chr1	232982645	232983130	+	0	NA	Intergenic	Intergenic	32263	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.006186	0.454733	
chunk0047_51_1	chr12	67270768	67271059	+	0	NA	intron (NM_018448, intron 1 of 14)	intron (NM_018448, intron 1 of 14)	1632	NM_018448	55832	Hs.546407	NM_018448	ENSG00000111530	CAND1	TIP120|TIP120A	cullin associated and neddylation dissociated 1	protein-coding	0.010309	0.291096	
chunk0069_424_1	chr15	68107139	68107643	+	0	NA	intron (NM_016166, intron 2 of 13)	intron (NM_016166, intron 2 of 13)	53157	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.000000	0.332673	
chunk0177_141_1	chr7	22675535	22675734	+	0	NA	Intergenic	MIR|SINE|MIR	-10101	NR_122075	401312	Hs.583393	NR_122075	ENSG00000105889	LOC401312	-	uncharacterized LOC401312	ncRNA	0.015075	0.470000	
chunk0057_120_1	chr13	99363623	99364010	+	0	NA	intron (NM_001144072, intron 7 of 8)	intron (NM_001144072, intron 7 of 8)	7685	NR_030353	693208		NR_030353	ENSG00000207719	MIR623	MIRN623|hsa-mir-623	microRNA 623	ncRNA	0.005168	0.358247	
chunk0164_323_1	chr6	25138263	25138626	+	0	NA	promoter-TSS (NR_002174)	promoter-TSS (NR_002174)	-52	NR_027626	8418	Hs.484918	NR_002174	ENSG00000168405	CMAHP	CMAH|CSAH	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	pseudo	0.013774	0.478022	
chunk0036_420_1	chr11	68296547	68296746	+	0	NA	Intergenic	Intergenic	-15963	NM_001291902	4041	Hs.6347	NM_002335	ENSG00000162337	LRP5	BMND1|EVR1|EVR4|HBM|LR3|LRP-5|LRP-7|LRP7|OPPG|OPS|OPTA1|PCLD4|VBCH2	LDL receptor related protein 5	protein-coding	0.015075	0.555000	
chunk0080_360_1	chr17	32951323	32951836	+	0	NA	Intergenic	Intergenic	23669	NM_015544	26022	Hs.3447	NM_015544	ENSG00000006042	TMEM98	TADA1	transmembrane protein 98	protein-coding	0.003899	0.511673	
chunk0106_345_1	chr2	206745087	206745721	+	0	NA	intron (NR_104261, intron 7 of 9)	intron (NR_104261, intron 7 of 9)	-19984	NM_014929	22868	Hs.5930	NM_014929	ENSG00000118246	FASTKD2	KIAA0971	FAST kinase domains 2	protein-coding	0.001577	0.348031	320(AAGATCATAGTGTTCA,-,0.00),321(AGATCATAGTGTTCAT,+,0.00)
chunk0052_321_1	chr12	125374907	125375329	+	0	NA	intron (NM_052907, intron 2 of 8)	intron (NM_052907, intron 2 of 8)	48502	NM_052907	114795	Hs.524838	NM_052907	ENSG00000139364	TMEM132B	-	transmembrane protein 132B	protein-coding	0.002370	0.378251	203(TAGCACACAATGTACT,-,0.00),204(AGCACACAATGTACTA,+,0.00)
chunk0095_282_1	chr2	20104792	20105358	+	0	NA	Intergenic	Intergenic	-53047	NM_014713	9741	Hs.467807	NM_014713	ENSG00000068697	LAPTM4A	HUMORF13|LAPTM4|MBNT|Mtrp	lysosomal protein transmembrane 4 alpha	protein-coding	0.015901	0.516755	
chunk0069_284_1	chr15	65160767	65161506	+	0	NA	intron (NM_006660, intron 6 of 13)	intron (NM_006660, intron 6 of 13)	24089	NM_006660	10845	Hs.113823	NM_006660	ENSG00000166855	CLPX	EPP2	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding	0.004060	0.350000	
chunk0070_310_1	chr15	75176405	75176742	+	0	NA	Intergenic	Intergenic	-25307	NM_015492	56905	Hs.17936	NM_015492	ENSG00000167173	C15orf39	-	chromosome 15 open reading frame 39	protein-coding	0.008902	0.553254	160(CAGGACAGAATGTTCC,-,0.00),161(AGGACAGAATGTTCCA,+,0.00)
chunk0089_9_1	chr18	57445287	57446057	+	0	NA	intron (NM_004852, intron 1 of 1)	intron (NM_004852, intron 1 of 1)	9987	NM_004852	9480	Hs.194725	NM_004852	ENSG00000119547	ONECUT2	OC-2|OC2	one cut homeobox 2	protein-coding	0.010390	0.422827	
chunk0200_304_1	chr9	22964841	22965199	+	0	NA	Intergenic	MER57B2|LTR|ERV1	318820	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.002793	0.381616	
chunk0020_405_1	chr1	240906511	240906743	+	0	NA	intron (NM_001282773, intron 4 of 15)	intron (NM_001282773, intron 4 of 15)	-225645	NR_036069	100422856		NR_036069	ENSG00000265831	MIR3123	mir-3123	microRNA 3123	ncRNA	0.000000	0.437768	
chunk0033_431_1	chr11	25138250	25138741	+	0	NA	Intergenic	Intergenic	641525	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004073	0.278455	
chunk0062_249_1	chr14	71466128	71466732	+	0	NA	Intergenic	Intergenic	-21431	NR_027046	145474	Hs.658241	NR_027046		LOC145474	-	uncharacterized LOC145474	ncRNA	0.004967	0.388430	
chunk0142_252_1	chr4	98984689	98984948	+	0	NA	Intergenic	Intergenic	-10819	NM_015143	23173	Hs.480364	NM_015143	ENSG00000164024	METAP1	MAP1A|MetAP1A	methionyl aminopeptidase 1	protein-coding	0.000000	0.515385	
chunk0205_397_1	chr9	114558547	114558757	+	0	NA	Intergenic	MER92B|LTR|ERV1	-29062	NM_004888	9550	Hs.388654	NM_004888	ENSG00000136888	ATP6V1G1	ATP6G|ATP6G1|ATP6GL|ATP6J|Vma10	ATPase H+ transporting V1 subunit G1	protein-coding	0.004762	0.379147	
chunk0172_222_1	chr6	136983707	136984083	+	0	NA	intron (NR_027994, intron 2 of 2)	MER45R|DNA|hAT-Tip100	9336	NR_027994	100294720	Hs.520412	NR_027994	ENSG00000225391	NHEG1	-	neuroblastoma highly expressed 1	ncRNA	0.005319	0.498674	
chunk0016_137_1	chr1	197170423	197170919	+	0	NA	intron (NM_194314, intron 9 of 9)	MamRep605|LTR?|LTR?	-23977	NM_001206846	259266	Hs.121028	NM_018136	ENSG00000066279	ASPM	ASP|Calmbp1|MCPH5	abnormal spindle microtubule assembly	protein-coding	0.000000	0.362173	196(GGAACATGGTGACCAT,+,0.00)
chunk0202_450_1	chr9	82424717	82424916	+	0	NA	Intergenic	Intergenic	436044	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.000000	0.425000	
chunk0004_350_1	chr1	51139997	51140197	+	0	NA	intron (NM_001136508, intron 3 of 4)	intron (NM_001136508, intron 3 of 4)	37863	NM_001136508	284546	Hs.176177	NM_001136508	ENSG00000204006	C1orf185	-	chromosome 1 open reading frame 185	protein-coding	0.015000	0.358209	
chunk0060_340_1	chr14	52003203	52004055	+	0	NA	intron (NM_016039, intron 6 of 7)	intron (NM_016039, intron 6 of 7)	14119	NM_016039	51637	Hs.534457	NM_016039	ENSG00000087302	RTRAF	C14orf166|CGI-99|CGI99|CLE|CLE7|LCRP369|RLLM1|hCLE|hCLE1	RNA transcription, translation and transport factor	protein-coding	0.009390	0.371630	346(AAGTACAGACTGTCCT,-,0.00),347(AGTACAGACTGTCCTC,+,0.00)
chunk0156_269_1	chr5	109484980	109485443	+	0	NA	Intergenic	Intergenic	-75237	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.017279	0.484914	
chunk0029_337_1	chr10	105990218	105990516	+	0	NA	Intergenic	L1MA4A|LINE|L1	-170034	NR_120625	101927549	Hs.556885	NR_120625		LINC02627	-	long intergenic non-protein coding RNA 2627	ncRNA	0.010067	0.588629	
chunk0073_452_1	chr16	19434647	19434891	+	0	NA	intron (NM_001308161, intron 2 of 20)	MIRb|SINE|MIR	17073	NM_001261841	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.000000	0.387755	
chunk0093_271_1	chr19	51539950	51540228	+	0	NA	Intergenic	L1MA7|LINE|L1	-8233	NM_001177549	946	Hs.720304	NM_001245	ENSG00000105492	SIGLEC6	CD327|CD33L|CD33L1|CD33L2|CDW327|OBBP1	sialic acid binding Ig like lectin 6	protein-coding	0.007194	0.369176	
chunk0078_306_1	chr17	8287639	8288285	+	0	NA	promoter-TSS (NM_016492)	promoter-TSS (NM_016492)	-689	NM_001177801	29098	Hs.408233	NM_016492	ENSG00000108961	RANGRF	HSPC165|HSPC236|MOG1|RANGNRF	RAN guanine nucleotide release factor	protein-coding	0.024768	0.506955	
chunk0118_360_1	chr22	36351901	36352437	+	0	NA	intron (NM_002473, intron 1 of 40)	intron (NM_002473, intron 1 of 40)	35898	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.031716	0.562384	
chunk0082_269_1	chr17	57910101	57910412	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	-6867	NM_001292025	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.006431	0.448718	
chunk0167_274_1	chr6	70371494	70371730	+	0	NA	Intergenic	Intergenic	-22590	NR_125857	101928353		NR_125857		EVADR	-	uncharacterized LOC101928353	ncRNA	0.000000	0.312236	
chunk0106_276_1	chr2	204052203	204052500	+	0	NA	Intergenic	Intergenic	115603	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.003367	0.385906	
chunk0084_47_1	chr17	74192882	74193374	+	0	NA	Intergenic	L2c|LINE|L2	-10528	NM_001035258	6169	Hs.380953	NM_000999	ENSG00000172809	RPL38	L38	ribosomal protein L38	protein-coding	0.008130	0.501014	
chunk0072_219_1	chr15	95662933	95663250	+	0	NA	Intergenic	Intergenic	229998	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.003155	0.349057	
chunk0050_384_1	chr12	108926473	108927218	+	0	NA	intron (NM_018711, intron 11 of 15)	LTR40a|LTR|ERVL	46764	NM_001917	1610	Hs.113227	NM_001917	ENSG00000110887	DAO	DAAO|DAMOX|OXDA	D-amino acid oxidase	protein-coding	0.004027	0.391421	
chunk0046_279_1	chr12	61664074	61664342	+	0	NA	Intergenic	L1PA8A|LINE|L1	528631	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.003731	0.531599	
chunk0109_317_1	chr20	9121878	9122310	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	53040	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.009259	0.284065	
chunk0056_188_1	chr13	85639881	85640349	+	0	NA	Intergenic	Intergenic	159233	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.000000	0.353945	
chunk0090_54_1	chr19	1997891	1998272	+	0	NA	intron (NM_017797, intron 1 of 8)	(CACT)n|Simple_repeat|Simple_repeat	17622	NM_017797	55643	Hs.465543	NM_017797	ENSG00000133243	BTBD2	-	BTB domain containing 2	protein-coding	0.013123	0.439791	
chunk0166_2_1	chr6	41330073	41330526	+	0	NA	Intergenic	L1ME3G|LINE|L1	-5491	NM_001199509	9436	Hs.194721	NM_004828	ENSG00000096264	NCR2	CD336|LY95|NK-p44|NKP44|dJ149M18.1	natural cytotoxicity triggering receptor 2	protein-coding	0.004415	0.334802	
chunk0059_322_1	chr14	36597659	36598173	+	0	NA	Intergenic	Intergenic	-15335	NM_014360	26257	Hs.234763	NM_014360	ENSG00000136327	NKX2-8	NKX2.8|NKX2H|Nkx2-9	NK2 homeobox 8	protein-coding	0.011673	0.444660	
chunk0158_190_1	chr5	127924616	127924930	+	0	NA	Intergenic	Intergenic	158301	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.003185	0.406349	
chunk0085_131_1	chr18	3148228	3148497	+	0	NA	intron (NM_019856, intron 13 of 36)	L1ME1|LINE|L1	71746	NM_003803	8736	Hs.464469	NM_003803	ENSG00000101605	MYOM1	SKELEMIN	myomesin 1	protein-coding	0.007435	0.355556	
chunk0164_16_1	chr6	17928434	17928991	+	0	NA	intron (NM_022113, intron 2 of 38)	intron (NM_022113, intron 2 of 38)	58911	NM_022113	63971	Hs.94499	NM_022113	ENSG00000137177	KIF13A	RBKIN|bA500C11.2	kinesin family member 13A	protein-coding	0.001795	0.365591	
chunk0042_193_1	chr12	5260625	5260959	+	0	NA	Intergenic	L2c|LINE|L2	-17641	NR_120477	101929584	Hs.436529	NR_120476	ENSG00000256115	LINC02443	-	long intergenic non-protein coding RNA 2443	ncRNA	0.002994	0.414925	
chunk0192_51_1	chr8	59030431	59030712	+	0	NA	intron (NM_014729, intron 1 of 8)	intron (NM_014729, intron 1 of 8)	88637	NM_014729	9760	Hs.491805	NM_014729	ENSG00000198846	TOX	TOX1	thymocyte selection associated high mobility group box	protein-coding	0.021352	0.404255	
chunk0034_390_1	chr11	36638521	36639109	+	0	NA	intron (NM_001276722, intron 4 of 5)	intron (NM_001276722, intron 4 of 5)	-40536	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.005102	0.368421	
chunk0145_29_1	chr4	143615064	143615580	+	0	NA	intron (NM_001168235, intron 5 of 7)	intron (NM_001168235, intron 5 of 7)	55850	NR_003675	441046	Hs.135705	NM_001011539	ENSG00000236296	GUSBP5	GYPELOC441046	GUSB pseudogene 5	pseudo	0.005814	0.417795	
chunk0098_285_1	chr2	75773363	75774020	+	0	NA	Intergenic	Intergenic	-62706	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.006088	0.407295	
chunk0159_319_1	chr5	143425564	143426128	+	0	NA	intron (NM_001018075, intron 1 of 8)	L1MB7|LINE|L1	9666	NM_001018074	2908	Hs.122926	NM_000176	ENSG00000113580	NR3C1	GCCR|GCR|GCRST|GR|GRL	nuclear receptor subfamily 3 group C member 1	protein-coding	0.005319	0.352212	
chunk0033_368_1	chr11	23236599	23237338	+	0	NA	Intergenic	Intergenic	182222	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.004060	0.322973	
chunk0132_264_1	chr3	159184400	159184671	+	0	NA	intron (NM_001042706, intron 1 of 3)	L2a|LINE|L2	-88712	NM_001197108	29970	Hs.134665	NM_014575	ENSG00000151967	SCHIP1	SCHIP-1	schwannomin interacting protein 1	protein-coding	0.000000	0.330882	
chunk0001_161_1	chr1	6352753	6353083	+	0	NA	intron (NM_007274, intron 1 of 8)	AluSx|SINE|Alu	6026	NM_181866	11332	Hs.126137	NM_007274	ENSG00000097021	ACOT7	ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH	acyl-CoA thioesterase 7	protein-coding	0.030303	0.459215	104(AAGCACTTCATGTTCC,-,0.00),105(AGCACTTCATGTTCCT,+,0.00)
chunk0117_66_1	chr22	16959201	16959673	+	0	NA	Intergenic	Intergenic	48785	NM_001037814	128954	Hs.434113	NM_001037814	ENSG00000215568	GAB4	-	GRB2 associated binding protein family member 4	protein-coding	0.012712	0.490486	
chunk0078_87_1	chr17	1999487	1999816	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	25694	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.018237	0.539394	
chunk0196_411_1	chr8	115998212	115998854	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	326526	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.004673	0.368585	188(CAGGTCACAATGTCCC,-,0.00),189(AGGTCACAATGTCCCT,+,0.00)
chunk0184_14_1	chr7	111784689	111785192	+	0	NA	intron (NM_014705, intron 32 of 51)	intron (NM_014705, intron 32 of 51)	-23565	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.000000	0.371032	
chunk0003_416_1	chr1	40391710	40392198	+	0	NA	intron (NM_001198978, intron 1 of 9)	intron (NM_001198978, intron 1 of 9)	-1391	NM_001198979	64744	Hs.15200	NM_022733	ENSG00000084070	SMAP2	SMAP1L	small ArfGAP2	protein-coding	0.002049	0.378323	170(AAGAACTGAATGTCCC,-,0.00),171(AGAACTGAATGTCCCC,+,0.00)
chunk0013_290_1	chr1	171083413	171083668	+	0	NA	Intergenic	Intergenic	-7337	NM_001002294	2328	Hs.445350	NM_006894	ENSG00000007933	FMO3	FMOII|TMAU|dJ127D3.1	flavin containing dimethylaniline monoxygenase 3	protein-coding	0.015686	0.492188	
chunk0173_1_1	chr6	141005385	141005907	+	0	NA	Intergenic	Intergenic	321832	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.000000	0.311663	
chunk0101_450_1	chr2	140041764	140041963	+	0	NA	Intergenic	Intergenic	544822	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.295000	
chunk0108_258_1	chr2	234064927	234065281	+	0	NA	intron (NM_006944, intron 4 of 7)	L1MB7|LINE|L1	14402	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.008475	0.343662	
chunk0147_102_1	chr4	173425935	173426396	+	0	NA	Intergenic	MER53|DNA|hAT	-26699	NM_007281	11341	Hs.7122	NM_007281	ENSG00000164106	SCRG1	SCRG-1	stimulator of chondrogenesis 1	protein-coding	0.004338	0.435065	273(TGGTACTGTCTGTACT,-,0.00),274(GGTACTGTCTGTACTA,+,0.00)
chunk0115_327_1	chr21	28874344	28874543	+	0	NA	intron (NR_047510, intron 6 of 6)	ERVL-B4-int|LTR|ERVL	10930	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.005025	0.515000	
chunk0028_149_1	chr10	86775107	86775382	+	0	NA	intron (NM_004329, intron 1 of 12)	intron (NM_004329, intron 1 of 12)	18605	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.014545	0.409420	
chunk0014_268_1	chr1	180301548	180302119	+	0	NA	intron (NM_032360, intron 7 of 7)	Tigger2b_Pri|DNA|TcMar-Tigger	-27152	NR_037642	100527964	Hs.496545	NR_037642	ENSG00000230124	LHX4-AS1	-	LHX4 antisense RNA 1	ncRNA	0.008757	0.379371	338(CAGAACAGTATGTACT,-,0.00),339(AGAACAGTATGTACTA,+,0.00)
chunk0078_28_1	chr17	855513	855899	+	0	NA	intron (NM_022463, intron 1 of 7)	L4_A_Mam|LINE|RTE-X	8405	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.005181	0.447028	
chunk0049_210_1	chr12	93166852	93167115	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-7383	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.003802	0.348485	
chunk0188_205_1	chr8	12133451	12133803	+	0	NA	exon (NM_001256869, exon 1 of 1)	exon (NM_001256869, exon 1 of 1)	382	NM_001256869	392197	Hs.741132	NM_001256869	ENSG00000226430	USP17L7	-	ubiquitin specific peptidase 17 like family member 7	protein-coding	0.017045	0.526912	
chunk0054_256_1	chr13	46260865	46261082	+	0	NA	intron (NM_001282460, intron 7 of 9)	intron (NM_001282460, intron 7 of 9)	36871	NR_047493	100861554	Hs.90866	NR_047493	ENSG00000261097	LINC00563	-	long intergenic non-protein coding RNA 563	ncRNA	0.004608	0.376147	
chunk0127_357_1	chr3	101441352	101441599	+	0	NA	intron (NM_001077203, intron 4 of 22)	L1M2|LINE|L1	71766	NM_001077203	57337	Hs.529551	NM_020654	ENSG00000138468	SENP7	-	SUMO specific peptidase 7	protein-coding	0.008097	0.580645	
chunk0103_22_1	chr2	159045628	159046001	+	0	NA	intron (NM_001145909, intron 2 of 26)	intron (NM_001145909, intron 2 of 26)	77180	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.013405	0.336898	
chunk0118_279_1	chr22	33803685	33804390	+	0	NA	intron (NM_133642, intron 1 of 14)	intron (NM_133642, intron 1 of 14)	79051	NR_038950	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.009929	0.426346	
chunk0134_336_1	chr3	182136103	182136589	+	0	NA	Intergenic	Intergenic	183982	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.002058	0.398357	
chunk0092_108_1	chr19	23556442	23556873	+	0	NA	Intergenic	HERVK22-int|LTR|ERVK	130558	NM_138330	171392	Hs.264345	NM_138330	ENSG00000197372	ZNF675	TBZF|TIZ	zinc finger protein 675	protein-coding	0.004640	0.416667	
chunk0151_67_1	chr5	42520040	42520630	+	0	NA	intron (NM_001242400, intron 2 of 10)	intron (NM_001242400, intron 2 of 10)	-27708	NM_001242402	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.001695	0.404399	
chunk0087_214_1	chr18	36053460	36053813	+	0	NA	intron (NM_001303412, intron 1 of 8)	L1MB5|LINE|L1	13958	NM_001303411	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.011331	0.347458	
chunk0075_431_1	chr16	57635653	57636056	+	0	NA	intron (NM_001145772, intron 1 of 14)	MIR|SINE|MIR	-3441	NM_001290144	9289	Hs.513633	NM_005682	ENSG00000205336	ADGRG1	BFPP|BPPR|GPR56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding	0.024814	0.594059	
chunk0038_64_1	chr11	83019898	83020157	+	0	NA	intron (NM_001286060, intron 1 of 4)	MER52A|LTR|ERV1	14542	NM_001286059	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.011583	0.584615	104(CAGGACTGCATGTTCC,-,0.00),105(AGGACTGCATGTTCCA,+,0.00)
chunk0002_45_1	chr1	12615263	12615546	+	0	NA	intron (NM_004753, intron 1 of 5)	intron (NM_004753, intron 1 of 5)	2327	NM_004753	9249	Hs.289347	NM_004753	ENSG00000162496	DHRS3	DD83.1|RDH17|Rsdr1|SDR1|SDR16C1|retSDR1	dehydrogenase/reductase 3	protein-coding	0.021201	0.478873	
chunk0168_307_1	chr6	91864337	91864615	+	0	NA	Intergenic	Intergenic	-174048	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.007194	0.362007	
chunk0156_370_1	chr5	112762336	112763214	+	0	NA	intron (NM_001127510, intron 3 of 16)	intron (NM_001127510, intron 3 of 16)	24916	NM_001127510	324	Hs.158932	NM_000038	ENSG00000134982	APC	BTPS2|DP2|DP2.5|DP3|GS|PPP1R46	APC regulator of WNT signaling pathway	protein-coding	0.001139	0.336746	
chunk0204_35_1	chr9	92624761	92624960	+	0	NA	intron (NM_022755, intron 11 of 12)	L1ME3|LINE|L1	6810	NR_036505	100128361	Hs.660395	NR_036505		LOC100128361	-	uncharacterized LOC100128361	ncRNA	0.005025	0.340000	
chunk0077_264_1	chr16	80980989	80981676	+	0	NA	intron (NM_020188, intron 3 of 3)	intron (NM_020188, intron 3 of 3)	-25166	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.001456	0.341570	
chunk0065_180_1	chr15	26311714	26311981	+	0	NA	Intergenic	Intergenic	196034	NR_038851	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.007491	0.347015	78(GAATACAGTGTGTTCC,-,0.00),79(AATACAGTGTGTTCCA,+,0.00)
chunk0013_76_1	chr1	167594575	167595176	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-35362	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.011647	0.398671	
chunk0150_193_1	chr5	34771312	34771894	+	0	NA	intron (NM_001145520, intron 3 of 17)	intron (NM_001145520, intron 3 of 17)	-30715	NR_106988									0.003436	0.396226	
chunk0209_429_1	chrX	59487488	59487687	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-1576954	NM_007156	7789	Hs.550094	NM_007156	ENSG00000198205	ZXDA	ZNF896	zinc finger X-linked duplicated A	protein-coding	0.006579	0.464052	
chunk0142_384_1	chr4	102393366	102393568	+	0	NA	Intergenic	L1MC5|LINE|L1	-47969	NM_001135146	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.009901	0.349754	
chunk0043_288_1	chr12	21374411	21374832	+	0	NA	intron (NM_134431, intron 1 of 15)	intron (NM_134431, intron 1 of 15)	1753	NM_000415	3375	Hs.46835	NM_000415	ENSG00000121351	IAPP	DAP|IAP	islet amyloid polypeptide	protein-coding	0.007126	0.308057	
chunk0090_120_1	chr18	71682509	71683125	+	0	NA	Intergenic	Intergenic	99409	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.008117	0.372771	
chunk0051_155_1	chr12	115835436	115835974	+	0	NA	Intergenic	L1MA4|LINE|L1	312949	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.014870	0.463822	
chunk0125_34_1	chr3	62416012	62416756	+	0	NA	intron (NM_003716, intron 28 of 29)	intron (NM_003716, intron 28 of 29)	-42869	NM_018008	55079	Hs.241523	NM_018008	ENSG00000153266	FEZF2	FEZ|FEZL|FKSG36|TOF|ZFP312|ZNF312	FEZ family zinc finger 2	protein-coding	0.008065	0.412081	
chunk0003_166_1	chr1	33470916	33471276	+	0	NA	Intergenic	Intergenic	-1535	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.013889	0.396122	
chunk0095_354_1	chr2	21646832	21647290	+	0	NA	Intergenic	Intergenic	63591	NR_038837	645949	Hs.456782	NR_038837	ENSG00000229621	LINC01822	-	long intergenic non-protein coding RNA 1822	ncRNA	0.006550	0.422658	232(GAGAACATTTTGTCCC,-,0.00),233(AGAACATTTTGTCCCT,+,0.00)
chunk0183_4_1	chr7	102415817	102416584	+	0	NA	intron (NR_038967, intron 8 of 8)	intron (NR_038967, intron 8 of 8)	-10345	NR_031669	100313829		NR_031669	ENSG00000221510	MIR548O	MIRN548O	microRNA 548o	ncRNA	0.020860	0.502604	448(TAGTACAGAGCGTTCT,-,0.00),449(AGTACAGAGCGTTCTC,+,0.00)
chunk0003_403_1	chr1	40037714	40038282	+	0	NA	Intergenic	Intergenic	-2585	NM_006367	10487	Hs.370581	NM_006367	ENSG00000131236	CAP1	CAP|CAP1-PEN	cyclase associated actin cytoskeleton regulatory protein 1	protein-coding	0.008803	0.455185	
chunk0001_411_1	chr1	11058879	11059292	+	0	NA	intron (NM_003132, intron 2 of 7)	CpG	949	NM_003132	6723	Hs.76244	NM_003132	ENSG00000116649	SRM	PAPT|SPDSY|SPS1|SRML1	spermidine synthase	protein-coding	0.055690	0.659420	
chunk0183_293_1	chr7	107779634	107779844	+	0	NA	exon (NM_000111, exon 12 of 21)	exon (NM_000111, exon 12 of 21)	23494	NM_000111	1811	Hs.1650	NM_000111	ENSG00000091138	SLC26A3	CLD|DRA	solute carrier family 26 member 3	protein-coding	0.009524	0.383886	
chunk0069_352_1	chr15	66649447	66650817	+	0	NA	intron (NR_110372, intron 1 of 4)	L2b|LINE|L2	-52204	NM_005585	4091	Hs.153863	NM_005585	ENSG00000137834	SMAD6	AOVD2|HsT17432|MADH6|MADH7	SMAD family member 6	protein-coding	0.008759	0.522247	
chunk0025_91_1	chr10	50542914	50543309	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	80866	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.000000	0.409091	
chunk0068_343_1	chr15	57740895	57741596	+	0	NA	Intergenic	Intergenic	34724	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.004280	0.340456	399(TGGAACATCTTGTTCT,-,0.00),400(GGAACATCTTGTTCTT,+,0.00)
chunk0037_340_1	chr11	77362903	77363207	+	0	NA	intron (NM_001128620, intron 5 of 15)	intron (NM_001128620, intron 5 of 15)	-75637	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.000000	0.367213	
chunk0168_86_1	chr6	79872148	79872703	+	0	NA	Intergenic	Intergenic	-60179	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.003604	0.372302	
chunk0124_50_1	chr3	52609490	52609862	+	0	NA	exon (NM_018313, exon 17 of 30)	exon (NM_018313, exon 17 of 30)	73071	NM_001124767	440957	Hs.660577	NM_001124767	ENSG00000168273	SMIM4	C3orf78	small integral membrane protein 4	protein-coding	0.013441	0.436997	
chunk0031_436_1	chr10	132489121	132489626	+	0	NA	Intergenic	Intergenic	44163	NM_173541									0.031683	0.636364	
chunk0055_144_1	chr13	59764036	59764246	+	0	NA	intron (NM_001258366, intron 26 of 26)	intron (NM_001258366, intron 26 of 26)	-248577	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004762	0.402844	119(TAGAACACCTTGCTCC,-,0.00),120(AGAACACCTTGCTCCT,+,0.00)
chunk0094_175_1	chr2	5678337	5678536	+	0	NA	intron (NR_110580, intron 2 of 4)	intron (NR_110580, intron 2 of 4)	12682	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.000000	0.410000	
chunk0075_368_1	chr16	56373107	56373659	+	0	NA	intron (NM_001144, intron 10 of 13)	L1MC1|LINE|L1	52155	NM_001144	267	Hs.295137	NM_001144	ENSG00000159461	AMFR	GP78|RNF45	autocrine motility factor receptor	protein-coding	0.014493	0.481013	130(CAGGGCACACTGTTCT,-,0.00),131(AGGGCACACTGTTCTT,+,0.00),414(CAGTACATCATGTTCA,-,0.00),415(AGTACATCATGTTCAA,+,0.00)
chunk0026_74_1	chr10	61294184	61294925	+	0	NA	Intergenic	Intergenic	-158085	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.008097	0.424528	420(AAGAACTGCATGTTCC,-,0.00),421(AGAACTGCATGTTCCA,+,0.00)
chunk0105_93_1	chr2	184335667	184336092	+	0	NA	Intergenic	Intergenic	-43096	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.016471	0.338028	212(CAGAACATACAGTTTT,-,0.00),213(AGAACATACAGTTTTC,+,0.00)
chunk0213_29_1	chrY	56734674	56734926	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	-219455	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.047619	0.391304	
chunk0091_345_1	chr19	14554216	14554747	+	0	NA	intron (NM_138501, intron 1 of 12)	intron (NM_138501, intron 1 of 12)	17596	NM_004146	4713	Hs.532853	NM_004146	ENSG00000099795	NDUFB7	B18|CI-B18	NADH:ubiquinone oxidoreductase subunit B7	protein-coding	0.020716	0.597744	
chunk0161_94_1	chr5	167310162	167310631	+	0	NA	intron (NM_001122679, intron 1 of 28)	intron (NM_001122679, intron 1 of 28)	25558	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.008529	0.348936	
chunk0174_227_1	chr6	160454266	160455078	+	0	NA	Intergenic	Intergenic	56452	NR_028093	80350	Hs.654503	NM_024492	ENSG00000213071	LPAL2	APOA2|APOAL|APOARGC|apo(a)rg-C	lipoprotein(a) like 2, pseudogene	pseudo	0.008621	0.364084	
chunk0107_123_1	chr2	214559965	214560680	+	0	NA	intron (NM_001080500, intron 3 of 3)	intron (NM_001080500, intron 3 of 3)	50140	NR_047698	100885780	Hs.665982	NR_047698	ENSG00000224257	VWC2L-IT1	-	VWC2L intronic transcript 1	ncRNA	0.005594	0.332402	
chunk0061_31_1	chr14	55889081	55889729	+	0	NA	Intergenic	Intergenic	-92731	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.009259	0.386749	
chunk0112_81_1	chr20	37989533	37990214	+	0	NA	intron (NM_014657, intron 8 of 8)	L4_A_Mam|LINE|RTE-X	43595	NM_014657	9675	Hs.655481	NM_014657	ENSG00000101407	TTI1	KIAA0406|smg-10	TELO2 interacting protein 1	protein-coding	0.010279	0.463343	504(AGGTACTTCCTGTACC,-,0.00),505(GGTACTTCCTGTACCA,+,0.00)
chunk0110_363_1	chr20	19808621	19808820	+	0	NA	Intergenic	Intergenic	-77801	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.030151	0.585000	
chunk0085_318_1	chr18	8333934	8334439	+	0	NA	intron (NM_001105244, intron 22 of 32)	intron (NM_001105244, intron 22 of 32)	32848	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.009901	0.537549	
chunk0074_17_1	chr16	19868542	19868741	+	0	NA	intron (NM_001304771, intron 2 of 3)	intron (NM_001304771, intron 2 of 3)	16270	NM_016235	51704	Hs.148685	NM_016235	ENSG00000167191	GPRC5B	RAIG-2|RAIG2	G protein-coupled receptor class C group 5 member B	protein-coding	0.010050	0.565000	
chunk0148_137_1	chr5	5954815	5955064	+	0	NA	Intergenic	Intergenic	382353	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.004016	0.580000	
chunk0041_66_1	chr11	123639654	123639954	+	0	NA	intron (NM_018400, intron 3 of 5)	L2c|LINE|L2	14803	NM_001040151	55800	Hs.4865	NM_018400	ENSG00000166257	SCN3B	ATFB16|BRGDA7|HSA243396|SCNB3	sodium voltage-gated channel beta subunit 3	protein-coding	0.010000	0.352159	
chunk0091_267_1	chr19	11356044	11356379	+	0	NA	intron (NM_001170635, intron 1 of 9)	intron (NM_001170635, intron 1 of 9)	825	NM_001170635	64748	Hs.6846	NM_022737	ENSG00000105520	PLPPR2	LPPR2|PRG4	phospholipid phosphatase related 2	protein-coding	0.014925	0.511905	
chunk0078_313_1	chr17	8355238	8355437	+	0	NA	Intergenic	Intergenic	5204	NR_024447	100128288	Hs.549913	NR_024447		LOC100128288	-	uncharacterized LOC100128288	ncRNA	0.000000	0.295000	
chunk0037_222_1	chr11	74912004	74912417	+	0	NA	intron (NM_001270380, intron 8 of 14)	intron (NM_001270380, intron 8 of 14)	36977	NM_001270381	143570	Hs.370145	NM_182969	ENSG00000166435	XRRA1	-	X-ray radiation resistance associated 1	protein-coding	0.002421	0.408213	
chunk0135_1_1	chr3	184011413	184011795	+	0	NA	TTS (NR_046570)	TTS (NR_046570)	5266	NR_046570	100873982	Hs.570696	NR_046570	ENSG00000223882	ABCC5-AS1	-	ABCC5 antisense RNA 1	ncRNA	0.005236	0.389034	
chunk0194_65_1	chr8	82409539	82409756	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-567361	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.004608	0.344037	
chunk0144_257_1	chr4	136670217	136670605	+	0	NA	Intergenic	Intergenic	-756731	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.005155	0.367609	282(AAGATCAGAATGTGCT,-,0.00),283(AGATCAGAATGTGCTC,+,0.00)
chunk0140_321_1	chr4	73462836	73463357	+	0	NA	Intergenic	L1MA7|LINE|L1	-18649	NM_001133	173	Hs.168718	NM_001133	ENSG00000079557	AFM	ALB2|ALBA|ALF	afamin	protein-coding	0.013436	0.408046	
chunk0083_152_1	chr17	65896881	65897350	+	0	NA	intron (NM_001302891, intron 18 of 24)	intron (NM_001302891, intron 18 of 24)	-70572	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.378723	
chunk0103_447_1	chr2	170218351	170218963	+	0	NA	intron (NR_045684, intron 6 of 34)	Charlie29a|DNA|hAT-Charlie	40512	NM_001083615	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.003268	0.344209	
chunk0011_102_1	chr1	145964438	145964673	+	0	NA	promoter-TSS (NM_032305)	promoter-TSS (NM_032305)	27	NM_001039888	284615	Hs.620591	NM_001039888	ENSG00000272031	ANKRD34A	ANKRD34	ankyrin repeat domain 34A	protein-coding	0.068085	0.588983	
chunk0104_311_1	chr2	179214610	179215089	+	0	NA	intron (NM_178123, intron 1 of 17)	L1PA6|LINE|L1	49774	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.006263	0.383333	253(CTGAACATCCTGCTCC,-,0.00),254(TGAACATCCTGCTCCT,+,0.00),337(AAAGACACAATGTACC,-,0.00)
chunk0032_49_1	chr11	1670532	1670874	+	0	NA	Intergenic	Intergenic	5104	NR_026643	387742	Hs.567908	NM_001014374	ENSG00000205866	FAM99A	-	family with sequence similarity 99 member A	ncRNA	0.000000	0.556851	
chunk0200_441_1	chr9	30490202	30490542	+	0	NA	Intergenic	Intergenic	-81918	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.014706	0.381232	
chunk0047_231_1	chr12	71889618	71890159	+	0	NA	intron (NM_001146213, intron 5 of 16)	L1PA15|LINE|L1	-38905	NR_024072	729633	Hs.716256	NR_024072		MRS2P2	-	MRS2 pseudogene 2	pseudo	0.007394	0.387454	
chunk0050_252_1	chr12	105733638	105733974	+	0	NA	intron (NR_110109, intron 3 of 4)	MER58A|DNA|hAT-Charlie	27032	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.002976	0.418398	
chunk0046_360_1	chr12	63047130	63047575	+	0	NA	Intergenic	MER126|DNA|DNA	105458	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.004494	0.347534	
chunk0071_34_1	chr15	79706692	79706956	+	0	NA	Intergenic	L1MA4|LINE|L1	190173	NR_037654	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.003788	0.343396	
chunk0130_332_1	chr3	138247839	138248041	+	0	NA	intron (NM_001267042, intron 11 of 20)	intron (NM_001267042, intron 11 of 20)	60692	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.009901	0.325123	
chunk0062_351_1	chr14	73754925	73755296	+	0	NA	intron (NM_001043318, intron 1 of 11)	intron (NM_001043318, intron 1 of 11)	-3637	NR_039727	100616158		NR_039727	ENSG00000264741	MIR4505	mir-4505	microRNA 4505	ncRNA	0.018868	0.586022	
chunk0097_258_1	chr2	54333994	54334727	+	0	NA	intron (NM_001100396, intron 1 of 4)	intron (NM_001100396, intron 1 of 4)	3426	NM_001100396	129852	Hs.732626	NM_173486	ENSG00000177994	C2orf73	-	chromosome 2 open reading frame 73	protein-coding	0.006821	0.311989	
chunk0009_275_1	chr1	107501103	107501462	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	187222	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.011142	0.438889	
chunk0040_192_1	chr11	114110941	114111375	+	0	NA	intron (NM_006006, intron 2 of 6)	(GT)n|Simple_repeat|Simple_repeat	50592	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.016129	0.367816	178(GGGACGTGATGTACTT,+,0.00)
chunk0088_234_1	chr18	48475918	48476666	+	0	NA	Intergenic	Intergenic	-62764	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.005348	0.439252	
chunk0104_199_1	chr2	175785962	175786528	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	216100	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.007067	0.412698	
chunk0084_154_1	chr17	76688768	76689128	+	0	NA	promoter-TSS (NR_130928)	promoter-TSS (NR_130928)	-61	NR_130928	439921	Hs.250723	NM_198530	ENSG00000182534	MXRA7	-	matrix remodeling associated 7	protein-coding	0.027778	0.545706	
chunk0098_149_1	chr2	69772941	69773510	+	0	NA	intron (NM_001153, intron 1 of 12)	intron (NM_001153, intron 1 of 12)	31230	NM_001153	307	Hs.422986	NM_001153	ENSG00000196975	ANXA4	ANX4|HEL-S-274|P32.5|PAP-II|PIG28|PP4-X|ZAP36	annexin A4	protein-coding	0.007030	0.405263	
chunk0038_397_1	chr11	93648058	93648465	+	0	NA	Intergenic	Intergenic	-13389	NM_033395	85459	Hs.458418	NM_033395	ENSG00000166004	CEP295	KIAA1731	centrosomal protein 295	protein-coding	0.004914	0.453431	
chunk0057_116_1	chr13	99313950	99314317	+	0	NA	exon (NM_177967, exon 3 of 7)	exon (NM_177967, exon 3 of 7)	-6638	NM_004951	1880	Hs.784	NM_004951	ENSG00000169508	GPR183	EBI2|hEBI2	G protein-coupled receptor 183	protein-coding	0.002725	0.320652	
chunk0102_301_1	chr2	150836523	150836859	+	0	NA	Intergenic	L2c|LINE|L2	207794	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.002976	0.400593	
chunk0036_416_1	chr11	68192079	68192701	+	0	NA	intron (NM_001300909, intron 1 of 8)	L2a|LINE|L2	20927	NM_016028	51111	Hs.632120	NM_016028	ENSG00000110066	KMT5B	CGI-85|CGI85|MRD51|SUV420H1	lysine methyltransferase 5B	protein-coding	0.003215	0.407705	
chunk0154_197_1	chr5	80247102	80247698	+	0	NA	intron (NM_178276, intron 1 of 12)	intron (NM_178276, intron 1 of 12)	8682	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.008389	0.437186	
chunk0202_74_1	chr9	71766700	71767446	+	0	NA	intron (NM_001135820, intron 1 of 22)	intron (NM_001135820, intron 1 of 22)	1811	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.009383	0.435074	
chunk0088_372_1	chr18	54105554	54105882	+	0	NA	Intergenic	Intergenic	116694	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.003049	0.340426	64(TGGGACTCCCTGTTCA,-,0.00),65(GGGACTCCCTGTTCAG,+,0.00)
chunk0020_54_1	chr1	232525710	232526210	+	0	NA	Intergenic	Intergenic	-10352	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.008000	0.461078	
chunk0199_299_1	chr9	6929235	6929555	+	0	NA	intron (NR_130707, intron 8 of 14)	intron (NR_130707, intron 8 of 14)	171754	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.000000	0.308411	
chunk0110_234_1	chr20	16284058	16284420	+	0	NA	intron (NM_001199865, intron 24 of 24)	MER65B|LTR|ERV1	289195	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.011050	0.493113	
chunk0028_285_1	chr10	91341324	91341640	+	0	NA	intron (NR_024467, intron 4 of 4)	LTR39|LTR|ERV1	-68803	NR_104291	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.006329	0.438486	188(AGGAACTGAGAGTCCC,-,0.00),189(GGAACTGAGAGTCCCG,+,0.00)
chunk0017_458_1	chr1	214484578	214484834	+	0	NA	intron (NM_005401, intron 1 of 18)	intron (NM_005401, intron 1 of 18)	66975	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.003906	0.431907	
chunk0129_238_1	chr3	122013799	122014436	+	0	NA	intron (NM_175924, intron 1 of 6)	intron (NM_175924, intron 1 of 6)	8163	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.004710	0.347962	
chunk0062_223_1	chr14	71036390	71036846	+	0	NA	intron (NM_001308160, intron 17 of 33)	Tigger3c|DNA|TcMar-Tigger	129213	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.008772	0.371991	
chunk0079_59_1	chr17	10967907	10968404	+	0	NA	Intergenic	L1PA16|LINE|L1	-130054	NM_001101387	644139	Hs.553909	NM_001101387	ENSG00000233670	PIRT	-	phosphoinositide interacting regulator of transient receptor potential channels	protein-coding	0.000000	0.399598	280(GGAACATTGAGTACAT,+,0.00)
chunk0085_246_1	chr18	7394294	7394621	+	0	NA	Intergenic	Intergenic	163318	NM_001105581	339291	Hs.647588	NM_001105581	ENSG00000206422	LRRC30	-	leucine rich repeat containing 30	protein-coding	0.018349	0.445122	295(AAGAACACGGAGATCC,-,0.00),296(AGAACACGGAGATCCT,+,0.00)
chunk0198_479_1	chr8	145029199	145029826	+	0	NA	Intergenic	HERVK14C-int|LTR|ERVK	-22926	NM_023080	65265	Hs.169615	NM_023080	ENSG00000182307	C8orf33	-	chromosome 8 open reading frame 33	protein-coding	0.014354	0.409236	
chunk0002_53_1	chr1	13619800	13620328	+	0	NA	Intergenic	Intergenic	34592	NM_001006624	10630	Hs.468675	NM_006474	ENSG00000162493	PDPN	AGGRUS|GP36|GP40|Gp38|HT1A-1|OTS8|PA2.26|T1A|T1A-2|T1A2|TI1A	podoplanin	protein-coding	0.017045	0.434783	254(AAGCACAGCGTGTTCT,-,0.00),255(AGCACAGCGTGTTCTA,+,0.00),297(TAGTACAGACAGTCCT,-,0.00),298(AGTACAGACAGTCCTA,+,0.00)
chunk0133_267_1	chr3	171901975	171902329	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-1412	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.011299	0.459155	
chunk0133_276_1	chr3	172029898	172030396	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-9481	NM_022763	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.000000	0.406814	
chunk0114_245_1	chr21	16021667	16022115	+	0	NA	Intergenic	L2c|LINE|L2	-48631	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.004464	0.367483	
chunk0062_185_1	chr14	69713598	69714331	+	0	NA	3' UTR (NM_014734, exon 6 of 6)	3' UTR (NM_014734, exon 6 of 6)	-53148	NM_001039465	6430	Hs.632326	NM_006925	ENSG00000100650	SRSF5	HRS|SFRS5|SRP40	serine and arginine rich splicing factor 5	protein-coding	0.009550	0.457766	
chunk0201_301_1	chr9	41230585	41231018	+	0	NA	Intergenic	Intergenic	-2954	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.004619	0.345622	
chunk0203_313_1	chr9	89474118	89474557	+	0	NA	intron (NM_006378, intron 1 of 17)	intron (NM_006378, intron 1 of 17)	5359	NM_006378	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.013667	0.429545	
chunk0190_18_1	chr8	28921774	28922138	+	0	NA	intron (NM_024567, intron 2 of 10)	intron (NM_024567, intron 2 of 10)	31248	NM_024567	79618	Hs.563560	NM_024567	ENSG00000147421	HMBOX1	HNF1LA|HOT1|PBHNF	homeobox containing 1	protein-coding	0.000000	0.350685	
chunk0109_302_1	chr20	8815750	8816486	+	0	NA	intron (NM_182734, intron 32 of 32)	intron (NM_182734, intron 32 of 32)	-15067	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.000000	0.327001	
chunk0023_271_1	chr10	27960549	27961141	+	0	NA	intron (NM_001290020, intron 10 of 19)	intron (NM_001290020, intron 10 of 19)	21072	NM_001290021	55130	Hs.127530	NM_018076	ENSG00000169126	ARMC4	CILD23	armadillo repeat containing 4	protein-coding	0.011824	0.374368	
chunk0181_128_1	chr7	80924267	80924602	+	0	NA	Intergenic	Intergenic	-5083	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.008955	0.389881	
chunk0041_295_1	chr11	129587184	129587498	+	0	NA	Intergenic	Intergenic	29928	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.015924	0.415873	
chunk0193_436_1	chr8	81010657	81010893	+	0	NA	intron (NM_018440, intron 3 of 8)	intron (NM_018440, intron 3 of 8)	101293	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.004237	0.438819	62(CAGTACACTTTGTTCA,-,0.00),63(AGTACACTTTGTTCAG,+,0.00)
chunk0006_431_1	chr1	76481548	76481905	+	0	NA	intron (NM_152996, intron 3 of 4)	intron (NM_152996, intron 3 of 4)	-385775	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.000000	0.337989	113(CAGCACTATGTGTTCT,-,0.00),114(AGCACTATGTGTTCTT,+,0.00)
chunk0114_367_1	chr21	20023137	20023471	+	0	NA	Intergenic	Intergenic	779804	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005988	0.364179	
chunk0114_376_1	chr20	62955783	62956198	+	0	NA	intron (NM_001302643, intron 2 of 13)	intron (NM_001302643, intron 2 of 13)	3343	NM_001302643	63910	Hs.512686	NM_022082	ENSG00000101194	SLC17A9	C20orf59|POROK8|VNUT	solute carrier family 17 member 9	protein-coding	0.024096	0.612981	
chunk0058_359_1	chr14	28959268	28959528	+	0	NA	Intergenic	L1PA7|LINE|L1	186694	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.003846	0.337165	188(ATGAACAGACTCTTCT,-,0.00)
chunk0065_266_1	chr14	101842979	101843572	+	0	NA	intron (NM_001161725, intron 3 of 15)	intron (NM_001161725, intron 3 of 15)	33472	NM_002719	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.005059	0.446128	
chunk0165_73_1	chr6	31186158	31186910	+	0	NA	Intergenic	LTR2B|LTR|ERV1	-8635	NR_026816	100130889	Hs.670091	NM_001134284		PSORS1C3	NCRNA00196	psoriasis susceptibility 1 candidate 3	ncRNA	0.025266	0.476760	
chunk0138_239_1	chr4	39514922	39515468	+	0	NA	intron (NM_001184701, intron 1 of 10)	intron (NM_001184701, intron 1 of 10)	12403	NM_001184701	7358	Hs.572518	NM_003359	ENSG00000109814	UGDH	GDH|UDP-GlcDH|UDPGDH|UGD	UDP-glucose 6-dehydrogenase	protein-coding	0.007326	0.380256	
chunk0065_277_1	chr14	102185353	102185727	+	0	NA	intron (NM_001242418, intron 1 of 2)	MIRc|SINE|MIR	45688	NM_001242416	91833	Hs.36859	NM_144574	ENSG00000140153	WDR20	DMR	WD repeat domain 20	protein-coding	0.021390	0.474667	
chunk0101_74_1	chr2	123738693	123739173	+	0	NA	Intergenic	L1MB4|LINE|L1	-286354	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.002083	0.384615	
chunk0170_223_1	chr6	113310566	113311003	+	0	NA	Intergenic	L1ME5|LINE|L1	339291	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.004577	0.317352	
chunk0084_58_1	chr17	74514018	74514998	+	0	NA	Intergenic	(TGACAGG)n|Simple_repeat|Simple_repeat	16966	NM_174892	124599	Hs.313343	NM_174892	ENSG00000178789	CD300LB	CD300b|CLM-7|CLM7|CMRF35-A2|IREM-3|IREM3|TREM-5|TREM5	CD300 molecule like family member b	protein-coding	0.010204	0.476045	
chunk0162_40_1	chr6	1088488	1088981	+	0	NA	intron (NR_027115, intron 1 of 4)	intron (NR_027115, intron 1 of 4)	12598	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.010142	0.390688	
chunk0085_375_1	chr18	9576081	9576421	+	0	NA	intron (NM_001042388, intron 10 of 19)	intron (NM_001042388, intron 10 of 19)	38356	NM_001042388	9989	Hs.743236	NM_005134	ENSG00000154845	PPP4R1	MEG1|PP4(Rmeg)|PP4R1	protein phosphatase 4 regulatory subunit 1	protein-coding	0.005882	0.348974	
chunk0090_405_1	chr18	78788856	78789156	+	0	NA	Intergenic	Intergenic	-191269	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.010000	0.348837	
chunk0077_333_1	chr16	82488129	82488350	+	0	NA	Intergenic	Intergenic	-138555	NM_001220489	1012	Hs.654386	NM_001257	ENSG00000140945	CDH13	CDHH|P105	cadherin 13	protein-coding	0.027149	0.563063	
chunk0147_117_1	chr4	174246893	174247483	+	0	NA	intron (NM_012180, intron 3 of 5)	intron (NM_012180, intron 3 of 5)	-26790	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.003390	0.338409	
chunk0003_280_1	chr1	37374282	37374818	+	0	NA	Intergenic	L1ME2|LINE|L1	99893	NR_038842	728431	Hs.380738	NR_038842	ENSG00000233621	LINC01137	-	long intergenic non-protein coding RNA 1137	ncRNA	0.011194	0.428305	174(TAGAACACTTTGTCCT,-,0.00),175(AGAACACTTTGTCCTT,+,0.00)
chunk0170_185_1	chr6	112018961	112019531	+	0	NA	Intergenic	Intergenic	-34829	NR_125354	8838	Hs.558428	NM_003880	ENSG00000112761	CCN6	LIBC|PPAC|PPD|WISP-3|WISP3	cellular communication network factor 6	protein-coding	0.015789	0.411559	304(TAGAGCATTGTGTACT,-,0.00),305(AGAGCATTGTGTACTG,+,0.00)
chunk0016_250_1	chr1	200084635	200085190	+	0	NA	intron (NM_205860, intron 5 of 7)	intron (NM_205860, intron 5 of 7)	42087	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.016216	0.383094	
chunk0133_345_1	chr3	172945854	172946318	+	0	NA	intron (NM_031955, intron 6 of 10)	L1M1|LINE|L1	195182	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.002155	0.513978	
chunk0111_146_1	chr20	25029010	25029359	+	0	NA	intron (NM_032501, intron 3 of 13)	L1MB2|LINE|L1	3522	NM_001252676	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.002865	0.297143	
chunk0008_357_1	chr1	96511066	96511308	+	0	NA	Intergenic	Intergenic	-137062	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.008264	0.485597	
chunk0171_428_1	chr6	131628089	131628322	+	0	NA	promoter-TSS (NM_004830)	promoter-TSS (NM_004830)	34	NM_015979	9439	Hs.29679	NM_004830	ENSG00000112282	MED23	ARC130|CRSP130|CRSP133|CRSP3|DRIP130|MRT18|SUR-2|SUR2	mediator complex subunit 23	protein-coding	0.085837	0.645299	
chunk0178_220_1	chr7	35616919	35617557	+	0	NA	Intergenic	Intergenic	77924	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.007837	0.433490	
chunk0124_65_1	chr3	52982715	52982973	+	0	NA	intron (NM_016329, intron 1 of 20)	Tigger2|DNA|TcMar-Tigger	63229	NM_016329	51460	Hs.343679	NM_016329	ENSG00000163935	SFMBT1	RU1|SFMBT|hSFMBT	Scm like with four mbt domains 1	protein-coding	0.007752	0.359073	
chunk0168_312_1	chr6	92117625	92118060	+	0	NA	Intergenic	(AAAC)n|Simple_repeat|Simple_repeat	-427414	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.000000	0.344037	
chunk0203_306_1	chr9	89351661	89352139	+	0	NA	intron (NM_001282690, intron 14 of 16)	HAL1|LINE|L1	33049	NM_001282690	79048	Hs.59804	NM_024077	ENSG00000187742	SECISBP2	SBP2	SECIS binding protein 2	protein-coding	0.008368	0.486430	
chunk0208_452_1	chrX	32957321	32957706	+	0	NA	intron (NM_004010, intron 2 of 78)	intron (NM_004010, intron 2 of 78)	170914	NM_004010	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.002597	0.339378	
chunk0080_10_1	chr17	20928649	20929123	+	0	NA	Intergenic	L2a|LINE|L2	-9634	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.014768	0.410526	
chunk0021_267_1	chr1	243834263	243834728	+	0	NA	intron (NM_181690, intron 1 of 13)	intron (NM_181690, intron 1 of 13)	8787	NM_005465	10000	Hs.498292	NM_005465	ENSG00000117020	AKT3	MPPH|MPPH2|PKB-GAMMA|PKBG|PRKBG|RAC-PK-gamma|RAC-gamma|STK-2	AKT serine/threonine kinase 3	protein-coding	0.015054	0.390558	272(GAGTACACACTGTACT,-,0.00),273(AGTACACACTGTACTT,+,0.00)
chunk0068_208_1	chr15	55083189	55083931	+	0	NA	Intergenic	Intergenic	113473	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.005391	0.379542	
chunk0021_276_1	chr1	244254158	244254586	+	0	NA	Intergenic	Intergenic	-98263	NM_001012970	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.018692	0.484848	
chunk0061_400_1	chr14	64666973	64667172	+	0	NA	Intergenic	Intergenic	-37336	NM_001308147	26030	Hs.509637	NM_015549	ENSG00000126822	PLEKHG3	ARHGEF43|KIAA0599	pleckstrin homology and RhoGEF domain containing G3	protein-coding	0.000000	0.440000	
chunk0157_147_1	chr5	117645404	117645915	+	0	NA	Intergenic	L1ME1|LINE|L1	-84702	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.003914	0.363281	
chunk0112_362_1	chr20	45465087	45465842	+	0	NA	Intergenic	Intergenic	-4290	NM_006103	10406	Hs.2719	NM_006103	ENSG00000101443	WFDC2	EDDM4|HE4|WAP5|dJ461P17.6	WAP four-disulfide core domain 2	protein-coding	0.002649	0.402116	
chunk0171_354_1	chr6	130369249	130369550	+	0	NA	intron (NM_001258276, intron 1 of 1)	intron (NM_001258276, intron 1 of 1)	3118	NM_001258276	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.009967	0.417219	
chunk0136_447_1	chr3	197977095	197977903	+	0	NA	intron (NR_026786, intron 5 of 16)	intron (NR_026786, intron 5 of 16)	17299	NR_026786	89782	Hs.518540	NM_033029	ENSG00000185621	LMLN	GP63|INV|IX14|LMNL1|MSP	leishmanolysin like peptidase	protein-coding	0.014851	0.306551	
chunk0131_271_1	chr3	150157925	150158626	+	0	NA	Intergenic	Intergenic	-80244	NR_110168	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.005706	0.427350	
chunk0068_329_1	chr15	57597532	57597731	+	0	NA	intron (NR_104371, intron 1 of 16)	intron (NR_104371, intron 1 of 16)	5727	NM_001285900	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.010050	0.485000	84(GGGCACATTGTGTGCC,-,0.00),85(GGCACATTGTGTGCCT,+,0.00)
chunk0116_211_1	chr21	37574498	37574716	+	0	NA	Intergenic	Intergenic	154307	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.013761	0.557078	
chunk0194_50_1	chr8	82043866	82044105	+	0	NA	Intergenic	Intergenic	-201699	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.345833	
chunk0178_342_1	chr7	38749783	38750005	+	0	NA	intron (NM_080631, intron 21 of 27)	AluJr4|SINE|Alu	-62805	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.013514	0.381166	
chunk0024_175_1	chr10	35766052	35766302	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-12125	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.012000	0.410359	
chunk0155_15_1	chr5	90887238	90887725	+	0	NA	intron (NR_003149, intron 83 of 89)	L2a|LINE|L2	328681	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.004107	0.381148	
chunk0205_64_1	chr9	106640189	106640885	+	0	NA	intron (NR_104145, intron 3 of 6)	L1ME2|LINE|L1	24479	NR_104145	100996590	Hs.147110	NR_104145	ENSG00000234323	LINC01505	-	long intergenic non-protein coding RNA 1505	ncRNA	0.000000	0.348637	
chunk0153_423_1	chr5	75827002	75827779	+	0	NA	Intergenic	L1ME3C|LINE|L1	-109902	NM_001099271	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.000000	0.339332	
chunk0113_141_1	chr20	52152969	52153226	+	0	NA	exon (NM_199426, exon 6 of 6)	exon (NM_199426, exon 6 of 6)	38888	NM_022088	55734	Hs.473082	NM_018197	ENSG00000020256	ZFP64	ZNF338	ZFP64 zinc finger protein	protein-coding	0.046693	0.585271	
chunk0141_324_1	chr4	87298351	87298762	+	0	NA	Intergenic	Intergenic	2027	NR_049891	100847027		NR_049891	ENSG00000263981	MIR5705	-	microRNA 5705	ncRNA	0.004866	0.398058	
chunk0118_10_1	chr22	25601672	25602278	+	0	NA	intron (NM_005160, intron 1 of 20)	L1ME2|LINE|L1	37081	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.003300	0.326194	269(TAGGACAGACTGTCCA,-,0.00),270(AGGACAGACTGTCCAT,+,0.00)
chunk0144_130_1	chr4	129386708	129387105	+	0	NA	Intergenic	Intergenic	290779	NM_001099783	132321	Hs.567679	NM_173487	ENSG00000151470	C4orf33	-	chromosome 4 open reading frame 33	protein-coding	0.005038	0.389447	
chunk0052_253_1	chr12	123533107	123533390	+	0	NA	exon (NM_178314, exon 1 of 7)	exon (NM_178314, exon 1 of 7)	470	NM_178314	353116	Hs.530315	NM_178314	ENSG00000188026	RILPL1	GOSPEL|RLP1	Rab interacting lysosomal protein like 1	protein-coding	0.113074	0.697183	
chunk0148_250_1	chr5	10208502	10209148	+	0	NA	Intergenic	L1MC4|LINE|L1	41084	NM_199133	134145	Hs.481569	NM_199133	ENSG00000150756	ATPSCKMT	FAM173B|JS-2|hFAM173B	ATP synthase c subunit lysine N-methyltransferase	protein-coding	0.004644	0.329212	
chunk0141_458_1	chr4	89454232	89454525	+	0	NA	Intergenic	Intergenic	-146368	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.003413	0.357143	174(AGTCACATTCTGTTCT,-,0.00),175(GTCACATTCTGTTCTA,+,0.00)
chunk0021_345_1	chr1	246052261	246052557	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	365003	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.013514	0.387205	114(TAGTACAAGATGTACT,-,0.00),115(AGTACAAGATGTACTT,+,0.00)
chunk0175_276_1	chr7	7562621	7563095	+	0	NA	intron (NR_110084, intron 2 of 4)	intron (NR_110084, intron 2 of 4)	3207	NR_110084	101927391	Hs.223837	NR_110084		LOC101927391	-	uncharacterized LOC101927391	ncRNA	0.004219	0.397895	408(AAGAACATCCTGGCCA,-,0.00)
chunk0036_166_1	chr11	62538912	62539134	+	0	NA	intron (NM_024060, intron 1 of 5)	intron (NM_024060, intron 1 of 5)	7837	NM_024060	79026	Hs.502756	NM_001620	ENSG00000124942	AHNAK	AHNAKRS|PM227	AHNAK nucleoprotein	protein-coding	0.031532	0.551570	
chunk0057_103_1	chr13	98984067	98984645	+	0	NA	intron (NM_001130049, intron 1 of 32)	intron (NM_001130049, intron 1 of 32)	-6272	NM_001130048	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.003460	0.392055	
chunk0203_28_1	chr9	82919221	82920029	+	0	NA	Intergenic	Intergenic	143503	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002475	0.336218	
chunk0036_177_1	chr11	62621177	62621577	+	0	NA	intron (NM_001288721, intron 1 of 5)	L2a|LINE|L2	798	NM_012200	26229	Hs.502759	NM_012200	ENSG00000149541	B3GAT3	GLCATI|JDSCD|glcUAT-I	beta-1,3-glucuronyltransferase 3	protein-coding	0.012500	0.453865	
chunk0036_403_1	chr11	68082412	68083107	+	0	NA	intron (NM_001277, intron 2 of 11)	intron (NM_001277, intron 2 of 11)	37965	NR_106811	102465451		NR_106811	ENSG00000275022	MIR6753	hsa-mir-6753	microRNA 6753	ncRNA	0.017266	0.364943	
chunk0185_217_1	chr7	128911575	128911774	+	0	NA	promoter-TSS (NM_001135914)	promoter-TSS (NM_001135914)	-955	NM_199349	375616	Hs.371746	NM_199349	ENSG00000135253	KCP	CRIM2|KCP1|NET67	kielin cysteine rich BMP regulator	protein-coding	0.015075	0.575000	
chunk0026_450_1	chr10	71589938	71590648	+	0	NA	intron (NM_001171931, intron 9 of 24)	intron (NM_001171931, intron 9 of 24)	-78373	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.014085	0.483826	
chunk0074_209_1	chr16	25258029	25258647	+	0	NA	promoter-TSS (NM_001012981)	promoter-TSS (NM_001012981)	-804	NM_001012981	342357	Hs.513451	NM_001012981	ENSG00000155592	ZKSCAN2	ZNF694|ZSCAN31|ZSCAN34	zinc finger with KRAB and SCAN domains 2	protein-coding	0.066343	0.652666	168(AGGGACACGGCGTTCC,-,0.00),169(GGGACACGGCGTTCCG,+,0.00)
chunk0119_361_1	chr22	47469945	47470168	+	0	NA	intron (NR_109967, intron 1 of 2)	intron (NR_109967, intron 1 of 2)	17055	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.000000	0.392857	
chunk0053_386_1	chr13	36146500	36147176	+	0	NA	Intergenic	MIRb|SINE|MIR	-15461	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.005917	0.367799	
chunk0095_91_1	chr2	15187821	15188027	+	0	NA	intron (NR_052013, intron 48 of 50)	intron (NR_052013, intron 48 of 50)	373424	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.009709	0.463768	110(AGGTACACACAGTTCT,-,0.00),111(GGTACACACAGTTCTG,+,0.00)
chunk0139_415_1	chr4	63814398	63814665	+	0	NA	Intergenic	L1PA13|LINE|L1	594929	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.011236	0.544776	141(GGGGACAGGCTGCACT,-,0.00),142(GGGACAGGCTGCACTC,+,0.00)
chunk0165_315_1	chr6	37102341	37102609	+	0	NA	Intergenic	Intergenic	-67671	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.018657	0.624535	199(CTGAACATCCTGACCC,-,0.00)
chunk0126_161_1	chr3	77692275	77692729	+	0	NA	Intergenic	Intergenic	594490	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.000000	0.320879	
chunk0117_295_1	chr22	24500422	24500875	+	0	NA	intron (NM_016327, intron 2 of 9)	intron (NM_016327, intron 2 of 9)	5365	NM_016327	51733	Hs.731656	NM_016327	ENSG00000100024	UPB1	BUP1	beta-ureidopropionase 1	protein-coding	0.028698	0.535242	
chunk0022_108_1	chr10	10114634	10114841	+	0	NA	Intergenic	L1PA16|LINE|L1	56015	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.004831	0.394231	
chunk0162_63_1	chr6	1577520	1578061	+	0	NA	Intergenic	Intergenic	-27741	NR_125804	101927703	Hs.607964	NR_125804		FOXCUT	LINC01379|TCONS_00011636	FOXC1 upstream transcript	ncRNA	0.027726	0.490775	296(AGGAACACTGAGTCCT,-,0.00),297(GGAACACTGAGTCCTG,+,0.00)
chunk0152_192_1	chr5	59840346	59840827	+	0	NA	intron (NM_001165899, intron 3 of 16)	L3|LINE|CR1	53208	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.006237	0.443983	
chunk0197_357_1	chr8	125648204	125648541	+	0	NA	Intergenic	LTR33A_|LTR|ERVL	216163	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.011869	0.470414	
chunk0086_192_1	chr18	22098522	22098907	+	0	NA	Intergenic	Intergenic	70254	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.007792	0.401554	
chunk0175_345_1	chr6	167491304	167491883	+	0	NA	Intergenic	L2b|LINE|L2	-107083	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.010363	0.458621	
chunk0011_117_1	chr1	146792826	146793133	+	0	NA	intron (NR_103556, intron 37 of 45)	intron (NR_103556, intron 37 of 45)	-145566	NM_001278141	149013	Hs.666981	NM_001278141	ENSG00000268043	NBPF12	COAS1|KIAA1245	NBPF member 12	protein-coding	0.009772	0.490260	
chunk0044_358_1	chr12	39236931	39237403	+	0	NA	Intergenic	Intergenic	206223	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.006356	0.342495	
chunk0209_443_1	chrX	64458264	64458728	+	0	NA	Intergenic	L1PA13|LINE|L1	-63043	NM_017677	55613	Hs.442892	NM_017677	ENSG00000102043	MTMR8	-	myotubularin related protein 8	protein-coding	0.004310	0.320430	
chunk0124_445_1	chr3	61531557	61531888	+	0	NA	Intergenic	LTR102_Mam|LTR|ERVL	-29847	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.006042	0.445783	
chunk0136_22_1	chr4	617742	617969	+	0	NA	Intergenic	MER70B|LTR|ERVL	-7719	NM_001145291	5158	Hs.623810	NM_000283	ENSG00000133256	PDE6B	CSNB3|CSNBAD2|GMP-PDEbeta|PDEB|RP40|rd1	phosphodiesterase 6B	protein-coding	0.026432	0.578947	126(TAGGGCAGGATGTCCC,-,0.00),127(AGGGCAGGATGTCCCA,+,0.00)
chunk0047_146_1	chr12	69688882	69689572	+	0	NA	promoter-TSS (NM_152439)	promoter-TSS (NM_152439)	50	NM_152439	144453	Hs.280782	NM_032735	ENSG00000127325	BEST3	VMD2L3	bestrophin 3	protein-coding	0.018841	0.490593	266(CTGAACTTCCTGTTCT,-,0.00),267(TGAACTTCCTGTTCTT,+,0.00),664(GGGGACAAGATGTACC,-,0.00),665(GGGACAAGATGTACCT,+,0.00)
chunk0102_444_1	chr2	157946945	157947245	+	0	NA	Intergenic	Intergenic	-48084	NM_001135098	151531	Hs.128427	NM_173355	ENSG00000007001	UPP2	UDRPASE2|UP2|UPASE2	uridine phosphorylase 2	protein-coding	0.003333	0.348837	
chunk0136_48_1	chr4	1211525	1212294	+	0	NA	3' UTR (NM_001328, exon 9 of 9)	3' UTR (NM_001328, exon 9 of 9)	1789	NR_104331	285463	Hs.707614	NR_104331	ENSG00000280927	CTBP1-AS	PCAT10	CTBP1 antisense RNA	ncRNA	0.045514	0.522078	
chunk0109_308_1	chr20	8837475	8837734	+	0	NA	intron (NM_182734, intron 32 of 32)	ERVL-B4-int|LTR|ERVL	6419	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.000000	0.426923	
chunk0157_18_1	chr5	115453551	115453750	+	0	NA	Intergenic	Intergenic	91244	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.005025	0.475000	
chunk0009_212_1	chr1	106267928	106268458	+	0	NA	Intergenic	Intergenic	-649258	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.009434	0.372881	
chunk0121_373_1	chr3	25037556	25037922	+	0	NA	Intergenic	L2c|LINE|L2	-136593	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.430518	250(AAGTACAAGGTGTCCT,-,0.00),251(AGTACAAGGTGTCCTT,+,0.00)
chunk0159_227_1	chr5	141148392	141149375	+	0	NA	Intergenic	Intergenic	-1139	NM_018939	56130	Hs.283085	NM_018939	ENSG00000113211	PCDHB6	PCDH-BETA6	protocadherin beta 6	protein-coding	0.006104	0.341463	283(AGGAACAGTGTGTTCC,-,0.00),284(GGAACAGTGTGTTCCC,+,0.00),780(TTGGACTTGGTGTTCT,-,0.00),781(TGGACTTGGTGTTCTT,+,0.00)
chunk0071_169_1	chr15	83123473	83123971	+	0	NA	intron (NM_023003, intron 6 of 9)	intron (NM_023003, intron 6 of 9)	16150	NM_023003	53346	Hs.513094	NM_023003	ENSG00000136404	TM6SF1	-	transmembrane 6 superfamily member 1	protein-coding	0.002008	0.352705	
chunk0124_143_1	chr3	54613296	54613961	+	0	NA	intron (NM_018398, intron 9 of 37)	intron (NM_018398, intron 9 of 37)	26229	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.007519	0.435435	
chunk0209_145_1	chrX	42025792	42026269	+	0	NA	Intergenic	Intergenic	-102996	NM_001126055	8573	Hs.495984	NM_003688	ENSG00000147044	CASK	CAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK	calcium/calmodulin dependent serine protein kinase	protein-coding	0.008386	0.364017	
chunk0164_6_1	chr6	17678936	17679309	+	0	NA	intron (NM_005124, intron 2 of 21)	L1MA4|LINE|L1	27712	NM_001278209	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.002681	0.262032	
chunk0109_229_1	chr20	5868804	5869003	+	0	NA	Intergenic	L2b|LINE|L2	-42425	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.000000	0.530000	132(GGGAACAATATGTGCA,-,0.00),133(GGAACAATATGTGCAA,+,0.00)
chunk0028_97_1	chr10	84270706	84271174	+	0	NA	Intergenic	Intergenic	-9040	NR_038220	170425	Hs.434131	NR_038220	ENSG00000229404	LINC00858	CRCAL-2	long intergenic non-protein coding RNA 858	ncRNA	0.002137	0.388060	
chunk0043_91_1	chr12	14724187	14724422	+	0	NA	Intergenic	Intergenic	-27719	NM_004963	2984	Hs.524278	NM_004963	ENSG00000070019	GUCY2C	DIAR6|GC-C|GUC2C|MECIL|MUCIL|STAR	guanylate cyclase 2C	protein-coding	0.000000	0.516949	
chunk0194_129_1	chr8	84205698	84206053	+	0	NA	intron (NM_001100391, intron 1 of 8)	MLT1B|LTR|ERVL-MaLR	21010	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.000000	0.435393	
chunk0115_219_1	chr21	27042475	27042812	+	0	NA	Intergenic	L2c|LINE|L2	-75523	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.005935	0.319527	
chunk0036_105_1	chr11	61286103	61286302	+	0	NA	intron (NM_152718, intron 5 of 19)	MIR|SINE|MIR	9114	NM_152718	220001	Hs.60640	NM_152718	ENSG00000167992	VWCE	URG11|VWC1	von Willebrand factor C and EGF domains	protein-coding	0.015075	0.550000	
chunk0167_399_1	chr6	75062004	75062347	+	0	NA	Intergenic	Intergenic	143732	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.000000	0.340116	97(GAGAACACACTGTGCC,-,0.00),98(AGAACACACTGTGCCT,+,0.00)
chunk0143_34_1	chr4	106816021	106816507	+	0	NA	Intergenic	Intergenic	220032	NM_014421	27123	Hs.211869	NM_014421	ENSG00000155011	DKK2	DKK-2	dickkopf WNT signaling pathway inhibitor 2	protein-coding	0.004115	0.392197	
chunk0158_414_1	chr5	134935709	134936120	+	0	NA	intron (NM_032151, intron 2 of 3)	intron (NM_032151, intron 2 of 3)	7875	NR_039666									0.012165	0.385922	
chunk0196_83_1	chr8	102807225	102807686	+	0	NA	Intergenic	Intergenic	56745	NM_148174	51582	Hs.459106	NM_015878	ENSG00000155096	AZIN1	AZI|AZI1|AZIA1|OAZI|OAZIN|ODC1L	antizyme inhibitor 1	protein-coding	0.034707	0.614719	
chunk0103_57_1	chr2	159712385	159712632	+	0	NA	promoter-TSS (NM_001282806)	promoter-TSS (NM_001282806)	51	NM_001282805	64844	Hs.529272	NM_022826	ENSG00000136536	MARCH7	AXO|AXOT|MARCH-VII|RNF177	membrane associated ring-CH-type finger 7	protein-coding	0.105263	0.689516	
chunk0032_236_1	chr11	7652613	7652827	+	0	NA	intron (NM_003621, intron 23 of 23)	intron (NM_003621, intron 23 of 23)	20171	NM_001302827	51700	Hs.414362	NM_016229	ENSG00000166394	CYB5R2	B5R.2	cytochrome b5 reductase 2	protein-coding	0.014019	0.506977	115(AGGAACTCCCAGTTCA,-,0.00),116(GGAACTCCCAGTTCAT,+,0.00)
chunk0173_66_1	chr6	142569487	142569750	+	0	NA	intron (NR_027312, intron 1 of 2)	intron (NR_027312, intron 1 of 2)	68218	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.000000	0.356061	
chunk0148_301_1	chr5	12467757	12468336	+	0	NA	Intergenic	L1PREC2|LINE|L1	-106811	NR_033383	404663	Hs.552273	NR_033383		LINC01194	CT49|TAG	long intergenic non-protein coding RNA 1194	ncRNA	0.006908	0.560345	
chunk0025_288_1	chr10	56786955	56787194	+	0	NA	Intergenic	Intergenic	-425801	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.300000	
chunk0132_76_1	chr3	155233105	155233804	+	0	NA	Intergenic	Intergenic	-7491	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.004292	0.415714	326(AGGCACTGACTGTTCC,-,0.00),327(GGCACTGACTGTTCCC,+,0.00)
chunk0152_356_1	chr5	63683668	63683928	+	0	NA	Intergenic	Intergenic	278494	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.015385	0.352490	136(TAGGACTAATTGTTCT,-,0.00),137(AGGACTAATTGTTCTG,+,0.00)
chunk0184_270_1	chr7	118529103	118529684	+	0	NA	Intergenic	(TCTATTA)n|Simple_repeat|Simple_repeat	304735	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.001721	0.309278	
chunk0015_222_1	chr1	187705699	187706381	+	0	NA	Intergenic	Intergenic	262412	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008798	0.351391	
chunk0205_153_1	chr9	108473180	108473933	+	0	NA	Intergenic	Intergenic	382439	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.010624	0.438992	
chunk0094_112_1	chr2	4274012	4274304	+	0	NA	Intergenic	Intergenic	-300126	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.003425	0.341297	
chunk0183_61_1	chr7	104141942	104142654	+	0	NA	intron (NM_002553, intron 12 of 13)	L1M1|LINE|L1	65749	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.002809	0.302945	115(CAGAACAGAAAGTCCA,-,0.00),116(AGAACAGAAAGTCCAG,+,0.00)
chunk0139_113_1	chr4	52498368	52498815	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	158001	NM_001134223	64854	Hs.7966	NM_022832	ENSG00000109189	USP46	-	ubiquitin specific peptidase 46	protein-coding	0.000000	0.388393	183(AAGAACATTCTGAACT,-,0.00),184(AGAACATTCTGAACTG,+,0.00)
chunk0075_373_1	chr16	56487363	56487872	+	0	NA	intron (NM_031885, intron 15 of 16)	L1M5|LINE|L1	32479	NM_031885	583	Hs.333738	NM_031885	ENSG00000125124	BBS2	BBS|RP74	Bardet-Biedl syndrome 2	protein-coding	0.005894	0.317647	
chunk0153_125_1	chr5	68843992	68844375	+	0	NA	Intergenic	Intergenic	185744	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.005222	0.390625	134(AAGAACACCACGTACT,-,0.00),135(AGAACACCACGTACTA,+,0.00)
chunk0192_146_1	chr8	62034194	62034928	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-214381	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.001362	0.302041	
chunk0160_327_1	chr5	159518367	159518803	+	0	NA	Intergenic	Intergenic	-52309	NR_027110	285627	Hs.552766	NR_027110	ENSG00000253298	LINC01845	-	long intergenic non-protein coding RNA 1845	ncRNA	0.009174	0.478261	
chunk0164_251_1	chr6	23442078	23442306	+	0	NA	Intergenic	Intergenic	-683994	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.000000	0.393013	
chunk0090_116_1	chr18	71490573	71491200	+	0	NA	Intergenic	Intergenic	88070	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.006380	0.371019	
chunk0180_183_1	chr7	65928747	65929002	+	0	NA	intron (NM_001284342, intron 1 of 1)	L1ME1|LINE|L1	53440	NM_001293104	2990	Hs.255230	NM_000181	ENSG00000169919	GUSB	BG|MPS7	glucuronidase beta	protein-coding	0.000000	0.378906	
chunk0168_131_1	chr6	82787776	82788298	+	0	NA	Intergenic	Intergenic	277804	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.000000	0.340344	
chunk0195_387_1	chr8	100231052	100231251	+	0	NA	intron (NM_003114, intron 14 of 18)	intron (NM_003114, intron 14 of 18)	72108	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.010050	0.315000	
chunk0002_211_1	chr1	19619735	19620231	+	0	NA	intron (NR_033758, intron 2 of 4)	intron (NR_033758, intron 2 of 4)	12176	NR_077246	644068	Hs.660760	NR_077246		RPS14P3	RPS14_1_16	ribosomal protein S14 pseudogene 3	pseudo	0.002016	0.390342	
chunk0110_378_1	chr20	19981602	19982091	+	0	NA	intron (NM_018993, intron 7 of 10)	intron (NM_018993, intron 7 of 10)	-35444	NM_016100	51126	Hs.368783	NM_016100	ENSG00000173418	NAA20	NAT3|NAT3P|NAT5|NAT5P|dJ1002M8.1	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding	0.008180	0.467347	
chunk0033_81_1	chr11	13954557	13955086	+	0	NA	Intergenic	Intergenic	-7816	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.005671	0.435849	
chunk0149_16_1	chr5	15902029	15902444	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-32946	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.014458	0.459135	191(GGAACAGGATGTTTAC,+,0.00)
chunk0153_283_1	chr5	73178496	73178906	+	0	NA	Intergenic	Intergenic	5505	NM_153217	134288	Hs.508588	NM_153217	ENSG00000164325	TMEM174	-	transmembrane protein 174	protein-coding	0.007317	0.340633	
chunk0042_357_1	chr12	10254370	10254688	+	0	NA	Intergenic	L1PREC2|LINE|L1	41639	NM_031412	23710	Hs.524250	NM_031412	ENSG00000139112	GABARAPL1	APG8-LIKE|APG8L|ATG8|ATG8B|ATG8L|GEC1	GABA type A receptor associated protein like 1	protein-coding	0.022013	0.448276	
chunk0046_394_1	chr12	63893398	63893597	+	0	NA	intron (NM_020762, intron 1 of 21)	intron (NM_020762, intron 1 of 21)	48736	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.005025	0.390000	
chunk0180_225_1	chr7	67193130	67193609	+	0	NA	intron (NM_018264, intron 14 of 15)	intron (NM_018264, intron 14 of 15)	-78972	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.014614	0.435417	
chunk0079_256_1	chr17	16141504	16142099	+	0	NA	intron (NM_006311, intron 11 of 45)	intron (NM_006311, intron 11 of 45)	52838	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.000000	0.332215	323(AAGAACACACAGTTCC,-,0.00),324(AGAACACACAGTTCCA,+,0.00)
chunk0017_452_1	chr1	214331995	214332289	+	0	NA	exon (NM_020197, exon 10 of 12)	exon (NM_020197, exon 10 of 12)	50920	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.013605	0.494915	103(TTGCACATGATGTACC,-,0.00),104(TGCACATGATGTACCA,+,0.00)
chunk0113_49_1	chr20	50137910	50138240	+	0	NA	intron (NR_027889, intron 3 of 6)	L1MC3|LINE|L1	15723	NM_001162505	387521	Hs.744839	NM_199129	ENSG00000240849	TMEM189	KUA	transmembrane protein 189	protein-coding	0.006061	0.441088	210(GGGGACTCTCTGTACT,-,0.00),211(GGGACTCTCTGTACTA,+,0.00)
chunk0203_365_1	chr9	89933526	89934040	+	0	NA	Intergenic	Intergenic	-35633	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.009728	0.446602	
chunk0001_25_1	chr1	1272591	1272866	+	0	NA	intron (NM_194315, intron 1 of 7)	intron (NM_194315, intron 1 of 7)	1126	NM_194457	118424	Hs.191987	NM_058167	ENSG00000160087	UBE2J2	NCUBE-2|NCUBE2|PRO2121	ubiquitin conjugating enzyme E2 J2	protein-coding	0.043636	0.608696	
chunk0131_114_1	chr3	144053111	144053324	+	0	NA	Intergenic	Intergenic	79892	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.252336	
chunk0018_183_1	chr1	219213557	219214274	+	0	NA	Intergenic	L1MEc|LINE|L1	38946	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.005579	0.314763	
chunk0006_362_1	chr1	72945191	72945681	+	0	NA	Intergenic	Intergenic	-360734	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.008163	0.370672	
chunk0171_288_1	chr6	128254105	128254367	+	0	NA	intron (NM_001291983, intron 2 of 18)	intron (NM_001291983, intron 2 of 18)	226371	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.007634	0.292776	
chunk0174_319_1	chr6	163175785	163176164	+	0	NA	intron (NM_001080378, intron 5 of 5)	intron (NM_001080378, intron 5 of 5)	16028	NR_122120	729658	Hs.728991	NR_122120		PACRG-AS3	-	PACRG antisense RNA 3	ncRNA	0.007916	0.410526	151(AAGCACAGTTTGTGTT,-,0.00),152(AGCACAGTTTGTGTTT,+,0.00)
chunk0149_41_1	chr5	16547319	16548023	+	0	NA	intron (NM_001034850, intron 3 of 8)	intron (NM_001034850, intron 3 of 8)	-38673	NM_019000	54463	Hs.481704	NM_019000	ENSG00000154153	RETREG1	FAM134B|JK-1|JK1	reticulophagy regulator 1	protein-coding	0.011364	0.344681	
chunk0211_368_1	chrX	126061751	126062156	+	0	NA	Intergenic	L1M1|LINE|L1	-47809	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.004938	0.347291	
chunk0003_420_1	chr1	40783184	40783799	+	0	NA	promoter-TSS (NM_004700)	promoter-TSS (NM_004700)	-521	NM_004700	9132	Hs.473058	NM_004700	ENSG00000117013	KCNQ4	DFNA2|DFNA2A|KV7.4	potassium voltage-gated channel subfamily Q member 4	protein-coding	0.092683	0.691558	266(CGGGACACTGCGTCCC,-,0.00),267(GGGACACTGCGTCCCT,+,0.00)
chunk0112_431_1	chr20	47506536	47506773	+	0	NA	intron (NM_001174087, intron 1 of 22)	intron (NM_001174087, intron 1 of 22)	4797	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.004219	0.386555	
chunk0048_174_1	chr12	80858421	80859058	+	0	NA	intron (NM_004664, intron 2 of 5)	intron (NM_004664, intron 2 of 5)	-26110	NR_030348	693202		NR_030348	ENSG00000207763	MIR617	MIRN617|hsa-mir-617	microRNA 617	ncRNA	0.001570	0.333856	
chunk0121_81_1	chr3	16056275	16056515	+	0	NA	Intergenic	L2b|LINE|L2	-118282	NM_054110	117248	Hs.411308	NM_054110	ENSG00000131386	GALNT15	GALNACT15|GALNT13|GALNT7|GALNTL2|PIH5|pp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.008333	0.473029	125(TTGTACATGTTGTTCT,-,0.00),126(TGTACATGTTGTTCTT,+,0.00)
chunk0184_369_1	chr7	121212981	121213700	+	0	NA	intron (NM_001105533, intron 15 of 17)	MIRb|SINE|MIR	-112027	NM_016087	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.002782	0.373611	
chunk0025_422_1	chr10	59839235	59839434	+	0	NA	intron (NM_005436, intron 2 of 8)	intron (NM_005436, intron 2 of 8)	67322	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.005025	0.400000	
chunk0145_436_1	chr4	153358731	153359474	+	0	NA	intron (NM_001253861, intron 4 of 6)	L1MC2|LINE|L1	14453	NM_032117	84057	Hs.294088	NM_032117	ENSG00000121211	MND1	GAJ	meiotic nuclear divisions 1	protein-coding	0.012113	0.341398	196(AAGTACAGAGAGTTCC,-,0.00),197(AGTACAGAGAGTTCCC,+,0.00)
chunk0176_255_1	chr7	16277919	16278923	+	0	NA	intron (NM_001101417, intron 4 of 8)	intron (NM_001101417, intron 4 of 8)	67935	NR_038947	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.001992	0.361194	746(AAGTACATTGTGTTCC,-,0.00),747(AGTACATTGTGTTCCT,+,0.00)
chunk0010_180_1	chr1	115841717	115842174	+	0	NA	promoter-TSS (NM_005599)	promoter-TSS (NM_005599)	-819	NM_005599	4808	Hs.46296	NM_005599	ENSG00000177551	NHLH2	HEN2|NSCL2|bHLHa34	nescient helix-loop-helix 2	protein-coding	0.008753	0.351528	
chunk0028_36_1	chr10	82915857	82916255	+	0	NA	intron (NM_001010848, intron 4 of 8)	intron (NM_001010848, intron 4 of 8)	-683136	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.002513	0.335840	
chunk0090_103_1	chr18	70946186	70946602	+	0	NA	Intergenic	L1M1|LINE|L1	-295537	NM_001278515									0.002404	0.316547	
chunk0127_193_1	chr3	96034513	96034882	+	0	NA	Intergenic	L1MC1|LINE|L1	-325267	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.005420	0.340541	
chunk0064_210_1	chr14	93040392	93040745	+	0	NA	intron (NM_001142594, intron 3 of 10)	intron (NM_001142594, intron 3 of 10)	-26884	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.014164	0.624294	
chunk0074_322_1	chr16	30775742	30776146	+	0	NA	3' UTR (NM_001286572, exon 20 of 20)	3' UTR (NM_001286572, exon 20 of 20)	11258	NM_001080417	23361	Hs.301094	NM_001080417	ENSG00000102870	ZNF629	ZNF|ZNF65	zinc finger protein 629	protein-coding	0.121287	0.708642	
chunk0044_352_1	chr12	38892009	38892628	+	0	NA	intron (NM_153634, intron 1 of 19)	intron (NM_153634, intron 1 of 19)	13300	NM_153634	144402	Hs.40910	NM_153634	ENSG00000139117	CPNE8	-	copine 8	protein-coding	0.006462	0.411290	
chunk0164_349_1	chr6	25447127	25448318	+	0	NA	intron (NM_017640, intron 5 of 36)	intron (NM_017640, intron 5 of 36)	168294	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.003359	0.430369	
chunk0188_180_1	chr8	11357003	11357202	+	0	NA	intron (NR_001578, intron 2 of 8)	intron (NR_001578, intron 2 of 8)	-11300	NR_026814	83656	Hs.583896	NM_054017	ENSG00000184608	FAM167A-AS1	C8orf12	FAM167A antisense RNA 1	ncRNA	0.010050	0.455000	
chunk0100_359_1	chr2	117684775	117684974	+	0	NA	Intergenic	Intergenic	-129805	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.005025	0.440000	
chunk0137_327_1	chr4	24804856	24805578	+	0	NA	TTS (NM_173463)	TTS (NM_173463)	9754	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.011080	0.479945	
chunk0080_394_1	chr17	35030637	35031211	+	0	NA	intron (NR_037713, intron 1 of 6)	intron (NR_037713, intron 1 of 6)	32816	NM_001017368	117584	Hs.13680	NM_057178	ENSG00000092871	RFFL	CARP-2|CARP2|FRING|RIFIFYLIN|RNF189|RNF34L	ring finger and FYVE like domain containing E3 ubiquitin protein ligase	protein-coding	0.003484	0.420870	
chunk0086_198_1	chr18	22243441	22243930	+	0	NA	Intergenic	Intergenic	74248	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.006135	0.406122	
chunk0130_77_1	chr3	130538155	130538777	+	0	NA	Intergenic	MIR|SINE|MIR	-21868	NM_001102608	131873	Hs.591282	NM_001102608	ENSG00000206384	COL6A6	-	collagen type VI alpha 6 chain	protein-coding	0.003215	0.375602	341(AAGAAGATACTGTGCC,-,0.00)
chunk0030_237_1	chr10	115020564	115020933	+	0	NA	Intergenic	L2c|LINE|L2	26091	NR_120677	102724589		NR_120677	ENSG00000236799	LINC02626	-	long intergenic non-protein coding RNA 2626	ncRNA	0.005420	0.391892	
chunk0163_155_1	chr6	11024539	11024949	+	0	NA	intron (NM_017770, intron 1 of 7)	intron (NM_017770, intron 1 of 7)	-19014	NR_038963	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.002439	0.355231	
chunk0196_25_1	chr8	101539794	101540083	+	0	NA	intron (NM_024915, intron 1 of 15)	L2a|LINE|L2	47498	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.013841	0.424138	156(AAGAACATTATGTCAC,-,0.00)
chunk0022_102_1	chr10	10015045	10015309	+	0	NA	Intergenic	L1MB2|LINE|L1	-43545	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.000000	0.369811	
chunk0146_183_1	chr4	160827383	160828262	+	0	NA	Intergenic	L2a|LINE|L2	-1194911	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.001138	0.281818	
chunk0041_1_1	chr12	53645	53888	+	0	NA	Intergenic	L3|LINE|CR1	-13117	NM_001170738	440073	Hs.536319	NM_015232	ENSG00000120645	IQSEC3	-	IQ motif and Sec7 domain 3	protein-coding	0.016461	0.459016	
chunk0162_326_1	chr6	6780223	6780574	+	0	NA	Intergenic	Intergenic	-157572	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.028490	0.443182	244(CAGAACTCTCAGTTCC,-,0.00),245(AGAACTCTCAGTTCCA,+,0.00)
chunk0190_147_1	chr8	30945517	30945794	+	0	NA	Intergenic	Intergenic	87146	NM_013357	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.010830	0.359712	
chunk0075_81_1	chr16	48229929	48230438	+	0	NA	intron (NM_033151, intron 2 of 28)	L2b|LINE|L2	2088	NM_033151	85320	Hs.652267	NM_032583	ENSG00000121270	ABCC11	EWWD|MRP8|WW	ATP binding cassette subfamily C member 11	protein-coding	0.009823	0.484314	
chunk0185_343_1	chr7	132146777	132147414	+	0	NA	intron (NM_020911, intron 27 of 31)	intron (NM_020911, intron 27 of 31)	236875	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.017268	0.445141	
chunk0028_425_1	chr10	93702540	93702751	+	0	NA	promoter-TSS (NM_145246)	promoter-TSS (NM_145246)	-73	NM_145246	118924	Hs.586650	NM_145246	ENSG00000148690	FRA10AC1	C10orf4|F26C11.1-like|FRA10A	FRA10A associated CGG repeat 1	protein-coding	0.104265	0.660377	
chunk0153_31_1	chr5	67118712	67119120	+	0	NA	intron (NM_001290226, intron 11 of 26)	intron (NM_001290226, intron 11 of 26)	77873	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.002451	0.381418	
chunk0112_368_1	chr20	45621276	45621734	+	0	NA	intron (NM_147198, intron 1 of 4)	MER68|LTR|ERVL	-8241	NM_080753	140832	Hs.199380	NM_080753	ENSG00000180305	WFDC10A	C20orf146|WAP10|dJ688G8.3	WAP four-disulfide core domain 10A	protein-coding	0.000000	0.385621	
chunk0027_252_1	chr10	77157319	77157628	+	0	NA	intron (NM_001014797, intron 5 of 28)	intron (NM_001014797, intron 5 of 28)	16642	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.009709	0.303226	
chunk0092_117_1	chr19	27581603	27581861	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-211735	NR_110689	101927151	Hs.567934	NR_110687	ENSG00000267575	LOC101927151	-	uncharacterized LOC101927151	ncRNA	0.007752	0.420849	
chunk0208_324_1	chrX	24482006	24482387	+	0	NA	intron (NM_005391, intron 1 of 10)	MIRb|SINE|MIR	16969	NM_005391	5165	Hs.296031	NM_005391	ENSG00000067992	PDK3	CMTX6|GS1-358P8.4	pyruvate dehydrogenase kinase 3	protein-coding	0.010499	0.434555	222(GGAGACAGAGTGTTCC,-,0.00),223(GAGACAGAGTGTTCCT,+,0.00)
chunk0033_373_1	chr11	23463461	23464087	+	0	NA	Intergenic	L1MDa|LINE|L1	-44584	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.007987	0.358852	
chunk0085_86_1	chr18	2406572	2406796	+	0	NA	Intergenic	Intergenic	164819	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.000000	0.377778	
chunk0040_356_1	chr11	118779475	118779835	+	0	NA	exon (NM_004397, exon 4 of 14)	exon (NM_004397, exon 4 of 14)	11293	NM_001257191	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.005556	0.335180	
chunk0148_444_1	chr4	189881182	189881566	+	0	NA	promoter-TSS (NR_132380)	promoter-TSS (NR_132380)	-141	NR_132380	105377617	Hs.662618	NR_132380	ENSG00000250666	LINC01596	-	long intergenic non-protein coding RNA 1596	ncRNA	0.039062	0.529870	
chunk0168_318_1	chr6	92294298	92294630	+	0	NA	Intergenic	Intergenic	-604036	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.003012	0.327327	
chunk0208_458_1	chrX	34467251	34467953	+	0	NA	Intergenic	L1MC3|LINE|L1	189686	NM_031442	83604	Hs.8769	NM_031442	ENSG00000147027	TMEM47	BCMP1|TM4SF10|VAB-9	transmembrane protein 47	protein-coding	0.007123	0.321479	365(AAGTACATCCAGTACC,-,0.00),366(AGTACATCCAGTACCC,+,0.00)
chunk0201_250_1	chr9	37911710	37911915	+	0	NA	Intergenic	Intergenic	-7459	NR_024873	92014	Hs.634120	NM_033412	ENSG00000122696	SLC25A51	CG7943|MCART1	solute carrier family 25 member 51	protein-coding	0.000000	0.480583	
chunk0065_84_1	chr15	23658568	23658774	+	0	NA	Intergenic	L1MA8|LINE|L1	-10825	NM_019066	54551	Hs.141496	NM_019066	ENSG00000254585	MAGEL2	NDNL1|PWLS|SHFYNG|nM15	MAGE family member L2	protein-coding	0.009709	0.328502	
chunk0107_100_1	chr2	213801468	213801688	+	0	NA	intron (NR_047659, intron 12 of 17)	intron (NR_047659, intron 12 of 17)	43511	NR_039640	100616375		NR_039640	ENSG00000265734	MIR4438	-	microRNA 4438	ncRNA	0.004545	0.384615	
chunk0014_273_1	chr1	180381213	180381472	+	0	NA	intron (NM_032360, intron 6 of 7)	L1MA4A|LINE|L1	57048	NR_036067	100423032		NR_036067	ENSG00000265435	MIR3121	mir-3121	microRNA 3121	ncRNA	0.011583	0.357692	
chunk0001_83_1	chr1	2640258	2640546	+	0	NA	TTS (NM_001242672)	TTS (NM_001242672)	-7360	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.020833	0.615917	125(AAGAACAAGCTGTTCT,-,0.00),126(AGAACAAGCTGTTCTC,+,0.00)
chunk0141_452_1	chr4	89410872	89411425	+	0	NA	Intergenic	Intergenic	-103138	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.009042	0.411552	412(GGCACATTTTGTTTTT,+,0.00)
chunk0165_363_1	chr6	38159883	38160127	+	0	NA	Intergenic	Arthur1B|DNA|hAT-Tip100	340474	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.032787	0.493878	91(TGGAACAGGGAGTACC,-,0.00),92(GGAACAGGGAGTACCG,+,0.00)
chunk0070_326_1	chr15	75526980	75527618	+	0	NA	intron (NM_002833, intron 1 of 12)	intron (NM_002833, intron 1 of 12)	51992	NM_002833	5780	Hs.445775	NM_002833	ENSG00000169410	PTPN9	MEG2|PTPMEG2	protein tyrosine phosphatase non-receptor type 9	protein-coding	0.006270	0.417840	
chunk0016_301_1	chr1	201307825	201308054	+	0	NA	intron (NM_001005337, intron 2 of 13)	intron (NM_001005337, intron 2 of 13)	24487	NM_001005337	5317	Hs.497350	NM_000299	ENSG00000081277	PKP1	B6P	plakophilin 1	protein-coding	0.026201	0.556522	
chunk0077_76_1	chr16	77183130	77183426	+	0	NA	Intergenic	L1ME1|LINE|L1	-7641	NM_001286640	22879	Hs.513743	NM_014940	ENSG00000103111	MON1B	HSRG1|SAND2|SRG1	MON1 homolog B, secretory trafficking associated	protein-coding	0.003378	0.350168	
chunk0177_236_1	chr7	24589770	24590271	+	0	NA	intron (NM_001303037, intron 1 of 11)	MER20B|DNA|hAT-Charlie	16674	NM_001303037	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.001996	0.354582	
chunk0169_257_1	chr6	105326125	105326750	+	0	NA	intron (NM_002726, intron 9 of 14)	intron (NM_002726, intron 9 of 14)	76687	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.006400	0.442492	
chunk0178_348_1	chr7	38773198	38773871	+	0	NA	intron (NM_080631, intron 11 of 27)	intron (NM_080631, intron 11 of 27)	-86445	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.002972	0.360534	
chunk0029_101_1	chr10	97475961	97476395	+	0	NA	intron (NM_001289404, intron 7 of 29)	intron (NM_001289404, intron 7 of 29)	22431	NM_001289404	64210	Hs.500721	NM_022362	ENSG00000155229	MMS19	CIAO4|MET18|MMS19L|hMMS19	MMS19 homolog, cytosolic iron-sulfur assembly component	protein-coding	0.002304	0.432184	
chunk0055_437_1	chr13	75566630	75566998	+	0	NA	exon (NM_006002, exon 4 of 9)	exon (NM_006002, exon 4 of 9)	17064	NM_006002	7347	Hs.162241	NM_006002	ENSG00000118939	UCHL3	UCH-L3	ubiquitin C-terminal hydrolase L3	protein-coding	0.000000	0.319783	
chunk0183_30_1	chr7	103487323	103487922	+	0	NA	intron (NM_005045, intron 60 of 64)	intron (NM_005045, intron 60 of 64)	-41445	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.010017	0.366667	
chunk0111_35_1	chr20	22213239	22213687	+	0	NA	Intergenic	Intergenic	69338	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.008929	0.425390	
chunk0108_325_1	chr2	235607691	235608139	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	102164	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.035714	0.489978	
chunk0006_132_1	chr1	65948870	65949176	+	0	NA	intron (NM_002600, intron 3 of 16)	ERV3-16A3_I-int|LTR|ERVL	35778	NM_001297441	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.009804	0.442997	121(AGGGACAAAATGTTCT,-,0.00),122(GGGACAAAATGTTCTA,+,0.00)
chunk0067_145_1	chr15	43190212	43190552	+	0	NA	exon (NM_012142, exon 6 of 11)	exon (NM_012142, exon 6 of 11)	5114	NR_045999	23582	Hs.36794	NM_012142	ENSG00000166946	CCNDBP1	DIP1|GCIP|HHM	cyclin D1 binding protein 1	protein-coding	0.002941	0.392962	
chunk0116_262_1	chr21	39038744	39038987	+	0	NA	Intergenic	MER44A|DNA|TcMar-Tigger	-61091	NR_109962	101928435	Hs.385528	NR_109962	ENSG00000232837	LINC01700	-	long intergenic non-protein coding RNA 1700	ncRNA	0.012346	0.336066	
chunk0140_82_1	chr4	67780474	67780802	+	0	NA	Intergenic	Intergenic	-24552	NM_001012763	2798	Hs.407587	NM_000406	ENSG00000109163	GNRHR	GNRHR1|GRHR|HH7|LHRHR|LRHR	gonadotropin releasing hormone receptor	protein-coding	0.006098	0.419453	
chunk0196_107_1	chr8	103099082	103099281	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-41512	NM_024812	79870	Hs.533446	NM_024812	ENSG00000164929	BAALC	-	BAALC binder of MAP3K1 and KLF4	protein-coding	0.000000	0.420000	
chunk0171_297_1	chr6	128503207	128503625	+	0	NA	intron (NM_001291981, intron 1 of 32).2	intron (NM_001291981, intron 1 of 32).2	17258	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.009569	0.372315	106(AAGTACATTTTGTGCC,-,0.00),107(AGTACATTTTGTGCCC,+,0.00)
chunk0097_11_1	chr2	41560613	41561222	+	0	NA	Intergenic	Intergenic	-316638	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.003284	0.359016	
chunk0182_353_1	chr7	99616846	99617210	+	0	NA	promoter-TSS (NM_145115)	promoter-TSS (NM_145115)	80	NM_145115	221785	Hs.446297	NM_145115	ENSG00000197037	ZSCAN25	ZNF498	zinc finger and SCAN domain containing 25	protein-coding	0.104396	0.682192	
chunk0125_339_1	chr3	71068983	71069182	+	0	NA	intron (NM_032682, intron 7 of 20)	intron (NM_032682, intron 7 of 20)	-4159	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.000000	0.350000	154(GAAAACACTGAGTTCT,-,0.00),155(AAAACACTGAGTTCTC,+,0.00)
chunk0154_182_1	chr5	80128906	80129477	+	0	NA	intron (NR_126061, intron 11 of 13)	intron (NR_126061, intron 11 of 13)	-45526	NR_109930	101929215		NR_109930	ENSG00000249825	CTD-2201I18.1	-	uncharacterized LOC101929215	ncRNA	0.008757	0.437063	
chunk0178_104_1	chr7	30778123	30778649	+	0	NA	intron (NM_032222, intron 1 of 17)	intron (NM_032222, intron 1 of 17)	6969	NM_032222	84182	Hs.660192	NM_032222	ENSG00000106125	MINDY4	AQP-1|AQP1|C7orf67|CHIP28|FAM188B	MINDY lysine 48 deubiquitinase 4	protein-coding	0.017110	0.428843	
chunk0038_382_1	chr11	93495594	93496010	+	0	NA	intron (NM_020179, intron 2 of 2)	intron (NM_020179, intron 2 of 2)	47578	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.002404	0.410072	
chunk0112_311_1	chr20	44517555	44518108	+	0	NA	intron (NM_006811, intron 1 of 9)	L2c|LINE|L2	4254	NM_006811	10955	Hs.272168	NM_006811	ENSG00000132824	SERINC3	AIGP1|DIFF33|SBBI99|TDE|TDE1|TMS-1	serine incorporator 3	protein-coding	0.007233	0.406137	
chunk0195_398_1	chr8	100334993	100335248	+	0	NA	intron (NM_001280539, intron 1 of 10)	intron (NM_001280539, intron 1 of 10)	1098	NM_001280539	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003922	0.277344	
chunk0170_85_1	chr6	110069626	110069825	+	0	NA	Intergenic	L2a|LINE|L2	91469	NM_005284	2830	Hs.46332	NM_005284	ENSG00000146360	GPR6	-	G protein-coupled receptor 6	protein-coding	0.010050	0.455000	
chunk0174_439_1	chr6	166096632	166096985	+	0	NA	Intergenic	L1PA13|LINE|L1	71861	NM_001270484	6862	Hs.389457	NM_003181	ENSG00000164458	TBXT	SAVA|T|TFT	T-box transcription factor T	protein-coding	0.000000	0.330508	
chunk0057_70_1	chr13	98225119	98225645	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	16858	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.028517	0.453510	
chunk0168_361_1	chr6	93406831	93407312	+	0	NA	intron (NM_004440, intron 3 of 16)	intron (NM_004440, intron 3 of 16)	12511	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.002079	0.290456	
chunk0145_316_1	chr4	150537284	150537703	+	0	NA	intron (NM_001199282, intron 40 of 56)	L1PA16|LINE|L1	-44432	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.004773	0.373810	
chunk0056_353_1	chr13	92034929	92035489	+	0	NA	intron (NM_004466, intron 6 of 7)	AluYh3|SINE|Alu	316998	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.026786	0.438503	
chunk0021_5_1	chr10	227281	227622	+	0	NA	intron (NM_006624, intron 4 of 14)	intron (NM_006624, intron 4 of 14)	47457	NM_001202467	10771	Hs.292265	NM_006624	ENSG00000015171	ZMYND11	BRAM1|BS69|MRD30	zinc finger MYND-type containing 11	protein-coding	0.000000	0.342105	
chunk0087_165_1	chr18	34929150	34929378	+	0	NA	Intergenic	Intergenic	-47664	NM_001143826	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.004386	0.410480	
chunk0014_45_1	chr1	175169236	175169757	+	0	NA	intron (NM_001162895, intron 1 of 2)	intron (NM_001162895, intron 1 of 2)	23317	NM_001162895	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.005758	0.419540	
chunk0096_143_1	chr2	29005813	29006012	+	0	NA	intron (NM_199280, intron 6 of 19)	(GT)n|Simple_repeat|Simple_repeat	24614	NM_199280	165186	Hs.525977	NM_199280	ENSG00000189350	TOGARAM2	FAM179A	TOG array regulator of axonemal microtubules 2	protein-coding	0.015075	0.475000	
chunk0005_319_1	chr1	60765062	60765471	+	0	NA	intron (NR_110628, intron 1 of 5)	MER58A|DNA|hAT-Charlie	60318	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.019560	0.419512	
chunk0212_35_1	chrY	11279876	11280075	+	0	NA	Intergenic	Intergenic	1141615	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.010050	0.315000	
chunk0093_213_1	chr19	49766031	49766282	+	0	NA	promoter-TSS (NM_130787)	promoter-TSS (NM_130787)	-767	NM_014203	160	Hs.467125	NM_014203	ENSG00000196961	AP2A1	ADTAA|AP2-ALPHA|CLAPA1	adaptor related protein complex 2 subunit alpha 1	protein-coding	0.027888	0.436508	
chunk0210_95_1	chrX	71290753	71291440	+	0	NA	intron (NM_007363, intron 3 of 11)	intron (NM_007363, intron 3 of 11)	7904	NM_007363	4841	Hs.533282	NM_007363	ENSG00000147140	NONO	MRXS34|NMT55|NRB54|P54|P54NRB|PPP1R114	non-POU domain containing octamer binding	protein-coding	0.005822	0.385174	239(AGTACAGGTTGCTCTG,+,0.00)
chunk0091_201_1	chr19	8921974	8922207	+	0	NA	intron (NM_024690, intron 10 of 83)	intron (NM_024690, intron 10 of 83)	59252	NM_024690	94025	Hs.432676	NM_024690	ENSG00000181143	MUC16	CA125	mucin 16, cell surface associated	protein-coding	0.017167	0.568376	
chunk0150_186_1	chr5	34576967	34577210	+	0	NA	Intergenic	Intergenic	-79240	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.016461	0.413934	
chunk0105_322_1	chr2	190919027	190919656	+	0	NA	intron (NM_014905, intron 7 of 17)	intron (NM_014905, intron 7 of 17)	38520	NM_014905	2744	Hs.116448	NM_014905	ENSG00000115419	GLS	AAD20|CASGID|EIEE71|GAC|GAM|GDPAG|GLS1|KGA	glutaminase	protein-coding	0.001590	0.317460	
chunk0025_297_1	chr10	57131449	57131960	+	0	NA	Intergenic	Intergenic	172855	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.013699	0.345703	
chunk0055_317_1	chr13	68357389	68357645	+	0	NA	Intergenic	Intergenic	527808	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.007812	0.315175	
chunk0169_10_1	chr6	96537745	96538082	+	0	NA	intron (NM_015323, intron 9 of 18)	intron (NM_015323, intron 9 of 18)	16087	NM_015323	23376	Hs.149367	NM_015323	ENSG00000014123	UFL1	KIAA0776|Maxer|NLBP|RCAD	UFM1 specific ligase 1	protein-coding	0.014837	0.372781	
chunk0108_46_1	chr2	226799844	226800263	+	0	NA	Intergenic	CpG	-1263	NM_005544	3667	Hs.471508	NM_005544	ENSG00000169047	IRS1	HIRS-1	insulin receptor substrate 1	protein-coding	0.116945	0.752381	
chunk0209_237_1	chrX	45302559	45302909	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-101833	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.000000	0.307692	
chunk0024_83_1	chr10	34405870	34406138	+	0	NA	intron (NM_001184790, intron 4 of 22)	intron (NM_001184790, intron 4 of 22)	409321	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.379182	
chunk0119_312_1	chr22	46660897	46661259	+	0	NA	intron (NM_015124, intron 3 of 17)	intron (NM_015124, intron 3 of 17)	34317	NM_015124	23151	Hs.475150	NM_015124	ENSG00000075240	GRAMD4	DIP	GRAM domain containing 4	protein-coding	0.016575	0.504132	
chunk0207_78_1	chrX	9320886	9321508	+	0	NA	Intergenic	Intergenic	-142098	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.016077	0.423756	
chunk0063_291_1	chr14	84432515	84432981	+	0	NA	Intergenic	Intergenic	-961131	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.404711	
chunk0197_294_1	chr8	124425432	124425734	+	0	NA	Intergenic	Intergenic	-25224	NM_017956	55039	Hs.9925	NM_017956	ENSG00000183665	TRMT12	TRM12|TYW2	tRNA methyltransferase 12 homolog	protein-coding	0.013245	0.471947	121(ATGGACACATTGTTCC,-,0.00),122(TGGACACATTGTTCCC,+,0.00)
chunk0153_43_1	chr5	67248571	67249305	+	0	NA	Intergenic	Intergenic	-52149	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.004087	0.419048	317(CAGTACACACTGTACT,-,0.00),318(AGTACACACTGTACTT,+,0.00)
chunk0123_242_1	chr3	45641178	45641377	+	0	NA	intron (NM_014240, intron 2 of 7)	intron (NM_014240, intron 2 of 7)	46446	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.000000	0.420000	
chunk0019_208_1	chr1	227001896	227002389	+	0	NA	intron (NM_014826, intron 33 of 34)	MER46C|DNA|TcMar-Tigger	61905	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.008114	0.319838	
chunk0157_95_1	chr5	116720436	116721007	+	0	NA	Intergenic	Intergenic	41488	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.001751	0.340909	
chunk0105_240_1	chr2	188516248	188516602	+	0	NA	intron (NM_001252669, intron 4 of 8)	HAL1|LINE|L1	218933	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.000000	0.315493	
chunk0035_385_1	chr11	55474291	55474774	+	0	NA	Intergenic	MIR|SINE|MIR	-79775	NM_001001920	81309		NM_001001920	ENSG00000181939	OR4C15	OR11-127|OR11-134	olfactory receptor family 4 subfamily C member 15	protein-coding	0.004141	0.388430	
chunk0161_230_1	chr5	171110243	171110530	+	0	NA	intron (NM_022897, intron 14 of 27)	intron (NM_022897, intron 14 of 27)	-198898	NM_021025	30012	Hs.249125	NM_021025	ENSG00000164438	TLX3	HOX11L2|RNX	T cell leukemia homeobox 3	protein-coding	0.010453	0.381944	
chunk0026_129_1	chr10	62048060	62048516	+	0	NA	promoter-TSS (NM_001244638)	promoter-TSS (NM_001244638)	-923	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.006579	0.415755	
chunk0100_7_1	chr2	104682275	104682772	+	0	NA	Intergenic	Intergenic	75196	NR_038231	284998	Hs.410180	NR_038231	ENSG00000234177	LINC01114	PANCAT	long intergenic non-protein coding RNA 1114	ncRNA	0.010060	0.383534	
chunk0130_92_1	chr3	130812054	130812385	+	0	NA	Intergenic	L2a|LINE|L2	-38306	NM_001199182	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.000000	0.331325	
chunk0132_32_1	chr3	154718322	154718633	+	0	NA	Intergenic	Intergenic	-288762	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.003215	0.371795	
chunk0019_329_1	chr1	229208601	229209237	+	0	NA	Intergenic	MER70A|LTR|ERVL	-34118	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.004717	0.442700	358(AAGGACATCCTGCTCT,-,0.00),359(AGGACATCCTGCTCTT,+,0.00)
chunk0031_320_1	chr10	129169194	129169445	+	0	NA	Intergenic	Intergenic	-297865	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.015936	0.547619	
chunk0045_265_1	chr12	49593597	49593984	+	0	NA	intron (NR_027450, intron 5 of 6)	AluJr|SINE|Alu	11837	NR_027450	84070	Hs.524406	NM_032130	ENSG00000135436	FAM186B	C12orf25	family with sequence similarity 186 member B	protein-coding	0.002584	0.350515	
chunk0143_392_1	chr4	123116378	123116850	+	0	NA	intron (NM_145207, intron 14 of 15)	intron (NM_145207, intron 14 of 15)	193544	NM_145207	166378	Hs.709648	NM_145207	ENSG00000145375	SPATA5	AFG2|EHLMRS|SPAF	spermatogenesis associated 5	protein-coding	0.002119	0.361522	
chunk0190_235_1	chr8	36212511	36212735	+	0	NA	Intergenic	Intergenic	-502303	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.000000	0.391111	
chunk0104_373_1	chr2	180180562	180181178	+	0	NA	Intergenic	Intergenic	-173817	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.008117	0.361426	
chunk0108_11_1	chr2	226053546	226053970	+	0	NA	Intergenic	Intergenic	-89036	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.002358	0.301176	
chunk0062_23_1	chr14	66884135	66884734	+	0	NA	intron (NM_001024218, intron 5 of 21)	MIR|SINE|MIR	-304959	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.005008	0.353333	357(TAGCACATCTTGTTCC,-,0.00),358(AGCACATCTTGTTCCA,+,0.00)
chunk0013_172_1	chr1	168842921	168843283	+	0	NA	Intergenic	Intergenic	56161	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.005525	0.396694	
chunk0038_254_1	chr11	88508140	88508397	+	0	NA	non-coding (NR_049724, exon 1 of 6)	non-coding (NR_049724, exon 1 of 6)	3692	NR_049724	100873989	Hs.616625	NR_049724	ENSG00000255082	GRM5-AS1	-	GRM5 antisense RNA 1	ncRNA	0.019455	0.387597	
chunk0165_133_1	chr6	33329053	33329368	+	0	NA	Intergenic	Intergenic	-6194	NM_001254717	1616	Hs.336916	NM_001350	ENSG00000204209	DAXX	BING2|DAP6|EAP1|SMIM40	death domain associated protein	protein-coding	0.015873	0.585443	
chunk0097_325_1	chr2	57160920	57161394	+	0	NA	Intergenic	LTR40c|LTR|ERVL	-746494	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.004219	0.429474	234(AAGCACACACTGTTCT,-,0.00),235(AGCACACACTGTTCTA,+,0.00)
chunk0101_143_1	chr2	127615564	127616032	+	0	NA	intron (NM_001080527, intron 25 of 46)	HERVK3-int|LTR|ERVK	-30066	NM_001161416	2840	Hs.46453	NM_005291	ENSG00000144230	GPR17	-	G protein-coupled receptor 17	protein-coding	0.025641	0.486141	
chunk0034_134_1	chr11	28616370	28616722	+	0	NA	Intergenic	Intergenic	-138998	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.008523	0.413598	
chunk0093_206_1	chr19	49580450	49580868	+	0	NA	promoter-TSS (NM_015953)	promoter-TSS (NM_015953)	-87	NM_001270960	51070	Hs.7236	NM_015953	ENSG00000142546	NOSIP	CGI-25	nitric oxide synthase interacting protein	protein-coding	0.052632	0.546539	
chunk0158_334_1	chr5	133154743	133154977	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	102890	NM_002154	3308	Hs.90093	NM_002154	ENSG00000170606	HSPA4	APG-2|HEL-S-5a|HS24/P52|HSPH2|RY|hsp70|hsp70RY	heat shock protein family A (Hsp70) member 4	protein-coding	0.008547	0.421277	
chunk0078_371_1	chr16	87474664	87475002	+	0	NA	intron (NM_015144, intron 1 of 12)	L1ME2z|LINE|L1	17021	NM_015144	23174	Hs.156231	NM_015144	ENSG00000140948	ZCCHC14	BDG-29|BDG29	zinc finger CCHC-type containing 14	protein-coding	0.014793	0.533923	
chunk0103_364_1	chr2	168278379	168279098	+	0	NA	Intergenic	Intergenic	-31143	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.009736	0.370833	347(TAGTACATTCTGTTTC,-,0.00),348(AGTACATTCTGTTTCT,+,0.00)
chunk0002_268_1	chr1	21760953	21761620	+	0	NA	intron (NM_001032730, intron 1 of 10)	intron (NM_001032730, intron 1 of 10)	21909	NM_032236	84196	Hs.467524	NM_032236	ENSG00000090686	USP48	RAP1GA1|USP31	ubiquitin specific peptidase 48	protein-coding	0.007496	0.398204	
chunk0195_156_1	chr8	95517631	95518212	+	0	NA	intron (NR_038207, intron 2 of 2)	intron (NR_038207, intron 2 of 2)	-248687	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.001721	0.410653	
chunk0031_242_1	chr10	126840772	126840971	+	0	NA	Intergenic	Intergenic	-64538	NM_001290223	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.010050	0.470000	
chunk0015_181_1	chr1	187172285	187172484	+	0	NA	intron (NR_126347, intron 1 of 3)	L1PB4|LINE|L1	79542	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.000000	0.465000	
chunk0156_59_1	chr5	103377987	103378216	+	0	NA	Intergenic	Intergenic	118744	NM_001316968	90355	Hs.482976	NM_033211	ENSG00000181751	C5orf30	-	chromosome 5 open reading frame 30	protein-coding	0.000000	0.356522	94(GGGTACATAGTGTACC,-,0.00),95(GGTACATAGTGTACCA,+,0.00)
chunk0112_138_1	chr20	38599596	38600123	+	0	NA	Intergenic	Intergenic	-2075	NM_001164431	343578		NM_001164431	ENSG00000124143	ARHGAP40	C20orf95|dJ1100H13.4	Rho GTPase activating protein 40	protein-coding	0.020873	0.541667	
chunk0061_296_1	chr14	61652930	61653159	+	0	NA	intron (NR_039985, intron 2 of 2)	L2a|LINE|L2	-42357	NM_001530	3091	Hs.597216	NM_001530	ENSG00000100644	HIF1A	HIF-1-alpha|HIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78	hypoxia inducible factor 1 subunit alpha	protein-coding	0.017467	0.500000	
chunk0045_347_1	chr12	51472037	51472411	+	0	NA	intron (NM_001039960, intron 14 of 24)	intron (NM_001039960, intron 14 of 24)	47107	NM_001258403	9498	Hs.4749	NM_004858	ENSG00000050438	SLC4A8	NBC3|NDCBE	solute carrier family 4 member 8	protein-coding	0.008021	0.394667	127(TAGGACACTCTGGTCC,-,0.00),128(AGGACACTCTGGTCCT,+,0.00)
chunk0042_186_1	chr12	5063158	5063448	+	0	NA	Intergenic	Intergenic	19384	NM_002234	3741	Hs.150208	NM_002234	ENSG00000130037	KCNA5	ATFB7|HCK1|HK2|HPCN1|KV1.5|PCN1	potassium voltage-gated channel subfamily A member 5	protein-coding	0.003448	0.405498	
chunk0082_59_1	chr17	51348909	51349188	+	0	NA	Intergenic	Intergenic	12333	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.003584	0.414286	
chunk0077_32_1	chr16	75318102	75318478	+	0	NA	intron (NM_006324, intron 5 of 6)	intron (NM_006324, intron 5 of 6)	-50237	NM_001170715	9564	Hs.479747	NM_014567	ENSG00000050820	BCAR1	CAS|CAS1|CASS1|CRKAS|P130Cas	BCAR1 scaffold protein, Cas family member	protein-coding	0.015957	0.490716	
chunk0126_462_1	chr3	87595697	87596318	+	0	NA	Intergenic	Intergenic	-319420	NM_001122757	5449	Hs.591654	NM_000306	ENSG00000064835	POU1F1	CPHD1|GHF-1|PIT1|POU1F1a|Pit-1	POU class 1 homeobox 1	protein-coding	0.006441	0.360129	341(AGAACTGAACGTTCTC,+,0.00)
chunk0158_272_1	chr5	131368215	131368592	+	0	NA	intron (NM_001038702, intron 2 of 4)	L1ME3Cz|LINE|L1	104394	NM_001038702	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.005305	0.394180	
chunk0029_408_1	chr10	109907781	109908474	+	0	NA	intron (NR_030724, intron 1 of 18)	intron (NR_030724, intron 1 of 18)	15426	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.015873	0.426513	
chunk0066_323_1	chr15	36420812	36421163	+	0	NA	Intergenic	Intergenic	-158616	NM_001130010	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.000000	0.292614	
chunk0086_187_1	chr18	22044436	22045029	+	0	NA	Intergenic	Intergenic	124236	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.006745	0.498316	362(CAGAACTTCTTGTCCT,-,0.00),363(AGAACTTCTTGTCCTC,+,0.00)
chunk0010_404_1	chr1	119565336	119565535	+	0	NA	non-coding (NR_033781, exon 1 of 1)	non-coding (NR_033781, exon 1 of 1)	1555	NR_033781	128102	Hs.681806	NR_033781		HSD3BP4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 4	pseudo	0.010050	0.355000	
chunk0097_46_1	chr2	43279383	43279867	+	0	NA	intron (NR_073394, intron 34 of 35)	MER58A|DNA|hAT-Charlie	52414	NR_027251	100129726	Hs.194480	NM_178529	ENSG00000279873	LINC01126	-	long intergenic non-protein coding RNA 1126	ncRNA	0.014463	0.410309	
chunk0010_259_1	chr1	116652759	116653189	+	0	NA	intron (NM_001007237, intron 2 of 10)	intron (NM_001007237, intron 2 of 10)	13982	NM_001542	3321	Hs.171057	NM_001542	ENSG00000143061	IGSF3	EWI-3|LCDD|V8	immunoglobulin superfamily member 3	protein-coding	0.006977	0.466357	
chunk0102_189_1	chr2	147679450	147679910	+	0	NA	Intergenic	Intergenic	-164837	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002174	0.373102	
chunk0191_132_1	chr8	48699443	48699800	+	0	NA	Intergenic	Intergenic	35690	NM_024593	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.022409	0.592179	
chunk0048_262_1	chr12	82005715	82006169	+	0	NA	Intergenic	Intergenic	52223	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.004405	0.443956	
chunk0129_56_1	chr3	117497721	117498022	+	0	NA	Intergenic	Intergenic	576440	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.003322	0.400662	
chunk0028_72_1	chr10	83700526	83700733	+	0	NA	Intergenic	LTR81A|LTR|Gypsy	-438800	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.375000	
chunk0152_187_1	chr5	59799608	59799835	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-31109	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004405	0.377193	
chunk0109_144_1	chr20	3477749	3478141	+	0	NA	intron (NM_139322, intron 1 of 24)	intron (NM_139322, intron 1 of 24)	6927	NM_139321	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.002551	0.335878	
chunk0155_346_1	chr5	97012830	97013648	+	0	NA	intron (NM_175920, intron 11 of 17)	L2b|LINE|L2	54787	NM_175920	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.004890	0.367521	
chunk0202_143_1	chr9	73484548	73484747	+	0	NA	Intergenic	L1ME3B|LINE|L1	332916	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.290000	
chunk0186_82_1	chr7	137301488	137301955	+	0	NA	intron (NM_002825, intron 1 of 4)	A-rich|Low_complexity|Low_complexity	42079	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.010707	0.346154	
chunk0208_151_1	chrX	16125435	16126326	+	0	NA	intron (NM_005314, intron 1 of 2)	intron (NM_005314, intron 1 of 2)	2579	NM_005314	2925	Hs.567282	NM_005314	ENSG00000126010	GRPR	BB2|BB2R	gastrin releasing peptide receptor	protein-coding	0.008979	0.430493	133(AGGAACAAACAGTCCT,-,0.00),134(GGAACAAACAGTCCTC,+,0.00)
chunk0087_415_1	chr18	42214196	42214396	+	0	NA	intron (NR_046174, intron 2 of 9)	L1PBa|LINE|L1	27628	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.015000	0.363184	
chunk0194_244_1	chr8	86394915	86395449	+	0	NA	intron (NM_007013, intron 5 of 24)	intron (NM_007013, intron 5 of 24)	52417	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.011236	0.368224	
chunk0132_115_1	chr3	155933332	155933625	+	0	NA	intron (NM_003875, intron 13 of 15)	intron (NM_003875, intron 13 of 15)	62942	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.006826	0.367347	
chunk0153_60_1	chr5	67698543	67699193	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-94345	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.000000	0.310292	291(AAGTACTTTATGTTCC,-,0.00),292(AGTACTTTATGTTCCT,+,0.00)
chunk0008_294_1	chr1	94963004	94963333	+	0	NA	non-coding (NR_033998, exon 4 of 4)	non-coding (NR_033998, exon 4 of 4)	35140	NR_033998	729970	Hs.297988	NR_033998	ENSG00000235501	LOC729970	-	hCG2028352-like	ncRNA	0.021277	0.418182	
chunk0211_138_1	chrX	112865243	112865956	+	0	NA	Intergenic	Intergenic	-24784	NM_133265	154796	Hs.528051	NM_133265	ENSG00000126016	AMOT	-	angiomotin	protein-coding	0.008415	0.417367	
chunk0188_404_1	chr8	18753411	18754020	+	0	NA	intron (NM_015310, intron 9 of 15)	Tigger15a|DNA|TcMar-Tigger	55180	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.004926	0.355738	
chunk0133_5_1	chr3	165212524	165213233	+	0	NA	intron (NR_125764, intron 1 of 5)	intron (NR_125764, intron 1 of 5)	5918	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.002821	0.325352	325(AAGAACAGTTTGTTCT,-,0.00),326(AGAACAGTTTGTTCTC,+,0.00)
chunk0030_145_1	chr10	113735932	113736251	+	0	NA	Intergenic	Intergenic	-15363	NM_001193435	79949	Hs.228320	NM_024889	ENSG00000148735	PLEKHS1	C10orf81|HEL185	pleckstrin homology domain containing S1	protein-coding	0.006270	0.496875	
chunk0188_259_1	chr8	14762343	14763011	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	90833	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.002994	0.324365	
chunk0186_47_1	chr7	136195162	136195556	+	0	NA	Intergenic	L1MA4A|LINE|L1	-217903	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.000000	0.339241	
chunk0197_186_1	chr8	121324690	121325365	+	0	NA	Intergenic	L2c|LINE|L2	-314319	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.000000	0.377219	
chunk0017_151_1	chr1	206823869	206824068	+	0	NA	intron (NM_153758, intron 1 of 5)	intron (NM_153758, intron 1 of 5)	-4909	NM_013371	29949	Hs.661017	NM_013371	ENSG00000142224	IL19	IL-10C|MDA1|NG.1|ZMDA1	interleukin 19	protein-coding	0.015075	0.490000	
chunk0101_65_1	chr2	123505750	123506486	+	0	NA	Intergenic	L1ME1|LINE|L1	-519169	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.001359	0.302578	
chunk0178_39_1	chr7	29503313	29503531	+	0	NA	intron (NM_001293077, intron 3 of 4)	intron (NM_001293077, intron 3 of 4)	19606	NM_001293081	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.004587	0.502283	155(TAGAACAGGATGACCC,-,0.00),156(AGAACAGGATGACCCA,+,0.00)
chunk0077_406_1	chr16	84994604	84995149	+	0	NA	intron (NM_001145548, intron 2 of 8)	intron (NM_001145548, intron 2 of 8)	16659	NM_001145548	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.016514	0.448718	
chunk0004_276_1	chr1	48421260	48421534	+	0	NA	intron (NM_019073, intron 3 of 12)	intron (NM_019073, intron 3 of 12)	50811	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.000000	0.240000	
chunk0004_267_1	chr1	48265061	48265444	+	0	NA	Intergenic	(ATTTT)n|Simple_repeat|Simple_repeat	42567	NM_001135181	200010	Hs.37890	NM_001011547	ENSG00000117834	SLC5A9	SGLT4	solute carrier family 5 member 9	protein-coding	0.005222	0.286458	
chunk0172_355_1	chr6	139078769	139079101	+	0	NA	Intergenic	Intergenic	50253	NM_021243	58527	Hs.600861	NM_021243	ENSG00000146386	ABRACL	C6orf115|Costars|HSPC280|PRO2013	ABRA C-terminal like	protein-coding	0.003012	0.396396	
chunk0113_380_1	chr20	59899766	59900056	+	0	NA	intron (NM_014258, intron 17 of 43)	intron (NM_014258, intron 17 of 43)	32243	NM_014258	10388	Hs.202676	NM_014258	ENSG00000196074	SYCP2	SCP-2|SCP2	synaptonemal complex protein 2	protein-coding	0.000000	0.295533	
chunk0127_379_1	chr3	102055144	102055793	+	0	NA	Intergenic	Intergenic	114609	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.004622	0.333846	
chunk0118_257_1	chr22	33070106	33070437	+	0	NA	Intergenic	L2b|LINE|L2	-11880	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.006042	0.409639	
chunk0030_443_1	chr10	120917607	120918388	+	0	NA	Intergenic	Intergenic	-66818	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.012804	0.478261	265(CAGGACATTTTGTTCT,-,0.00),266(AGGACATTTTGTTCTT,+,0.00)
chunk0081_89_1	chr17	39617931	39618130	+	0	NA	Intergenic	CpG	-8894	NM_032192	84152	Hs.286192	NM_032192	ENSG00000131771	PPP1R1B	DARPP-32|DARPP32	protein phosphatase 1 regulatory inhibitor subunit 1B	protein-coding	0.115578	0.725000	125(GGAAACAGCTTGTGCC,-,0.00)
chunk0132_413_1	chr3	164374178	164374498	+	0	NA	Intergenic	Intergenic	-202782	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.283489	
chunk0105_454_1	chr2	195129507	195130029	+	0	NA	Intergenic	Intergenic	399173	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.001916	0.336520	111(ATGTACATAGAGTCCT,-,0.00),269(AAGAACACACTGTGTA,-,0.00),270(AGAACACACTGTGTAT,+,0.00)
chunk0193_303_1	chr8	78006766	78007368	+	0	NA	Intergenic	Intergenic	-509034	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.006645	0.346600	
chunk0191_311_1	chr8	55458496	55458706	+	0	NA	intron (NM_052898, intron 2 of 2)	LTR1E|LTR|ERV1	-3280	NR_027765	100133234	Hs.729852	NR_027765	ENSG00000248522	SBF1P1	-	SET binding factor 1 pseudogene 1	pseudo	0.009524	0.516588	
chunk0105_209_1	chr2	187924015	187924880	+	0	NA	Intergenic	LTR38A1|LTR|ERV1	363244	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.002312	0.406467	
chunk0114_137_1	chr21	10025629	10025908	+	0	NA	Intergenic	L2a|LINE|L2	-204707	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.321429	
chunk0052_47_1	chr13	20905051	20905378	+	0	NA	Intergenic	Intergenic	-2440	NM_022459	64328	Hs.507452	NM_022459	ENSG00000132953	XPO4	exp4	exportin 4	protein-coding	0.006116	0.362805	
chunk0003_159_1	chr1	33339118	33339689	+	0	NA	intron (NM_198040, intron 8 of 13)	intron (NM_198040, intron 8 of 13)	-6911	NR_037400	100500853		NR_037400	ENSG00000284154	MIR3605	mir-3605	microRNA 3605	ncRNA	0.010508	0.500000	
chunk0198_395_1	chr8	141418970	141419626	+	0	NA	Intergenic	Intergenic	-2090	NM_007079	11156	Hs.43666	NM_007079	ENSG00000184489	PTP4A3	PRL-3|PRL-R|PRL3	protein tyrosine phosphatase 4A3	protein-coding	0.016768	0.602740	
chunk0080_257_1	chr17	30500466	30500671	+	0	NA	intron (NM_001007024, intron 6 of 8)	L1M5|LINE|L1	23160	NM_001007025	9527	Hs.462680	NM_004871	ENSG00000108587	GOSR1	GOLIM2|GOS-28|GOS28|GOS28/P28|GS28|P28	golgi SNAP receptor complex member 1	protein-coding	0.000000	0.339806	
chunk0084_321_1	chr17	80683781	80684169	+	0	NA	intron (NM_020761, intron 3 of 33)	intron (NM_020761, intron 3 of 33)	121657	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.025773	0.501285	
chunk0029_389_1	chr10	109571342	109572119	+	0	NA	Intergenic	L1ME4b|LINE|L1	351823	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.005148	0.353470	390(TGAAACATTATGTCCC,-,0.00),391(GAAACATTATGTCCCT,+,0.00)
chunk0168_432_1	chr6	95636779	95637200	+	0	NA	Intergenic	MER52D|LTR|ERV1	59492	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.028504	0.627962	
chunk0126_118_1	chr3	75669166	75669677	+	0	NA	Intergenic	CpG	-2860	NR_040005	401074	Hs.528540	NR_040004	ENSG00000242516	LINC00960	-	long intergenic non-protein coding RNA 960	ncRNA	0.091977	0.712891	472(CGGGACTTTGTGTTCC,-,0.00),473(GGGACTTTGTGTTCCC,+,0.00)
chunk0120_314_1	chr3	10224836	10225071	+	0	NA	intron (NM_001570, intron 9 of 12)	intron (NM_001570, intron 9 of 12)	-23540	NM_014760	9797	Hs.475401	NM_014760	ENSG00000157014	TATDN2	-	TatD DNase domain containing 2	protein-coding	0.004255	0.500000	
chunk0019_202_1	chr1	226938734	226939132	+	0	NA	Intergenic	MER4C|LTR|ERV1	-1304	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.020101	0.388471	
chunk0150_294_1	chr5	37389731	37389996	+	0	NA	intron (NM_018034, intron 3 of 17)	intron (NM_018034, intron 3 of 17)	10553	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.003774	0.394737	
chunk0202_445_1	chr9	82208810	82209514	+	0	NA	Intergenic	L1M1|LINE|L1	220390	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.002841	0.368794	
chunk0119_318_1	chr22	46742841	46743350	+	0	NA	Intergenic	Intergenic	-4840	NM_022766	64781	Hs.200668	NM_022766	ENSG00000100422	CERK	LK4|dA59H18.2|dA59H18.3|hCERK	ceramide kinase	protein-coding	0.011788	0.537255	
chunk0004_345_1	chr1	50950426	50951031	+	0	NA	intron (NM_007051, intron 1 of 18)	intron (NM_007051, intron 1 of 18)	9536	NM_007051	11124	Hs.530402	NM_007051	ENSG00000185104	FAF1	CGI-03|HFAF1s|UBXD12|UBXN3A|hFAF1	Fas associated factor 1	protein-coding	0.008264	0.412541	
chunk0134_280_1	chr3	179709415	179709677	+	0	NA	intron (NM_003940, intron 6 of 20)	intron (NM_003940, intron 6 of 20)	56401	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.007634	0.387833	
chunk0022_344_1	chr10	16896792	16897357	+	0	NA	intron (NM_001081, intron 54 of 66)	L1MDb|LINE|L1	-79620	NM_012425	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.005310	0.342756	409(GATACAACGTGTTCTT,+,0.00)
chunk0123_248_1	chr3	45759924	45760176	+	0	NA	intron (NM_020208, intron 9 of 10)	intron (NM_020208, intron 9 of 10)	36493	NM_020208	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.019841	0.525692	182(AGGAACATTCTGTTCT,-,0.00),183(GGAACATTCTGTTCTA,+,0.00)
chunk0099_167_1	chr2	88613997	88614209	+	0	NA	intron (NM_004836, intron 1 of 16)	L2a|LINE|L2	10826	NM_001313915	9451	Hs.591589	NM_004836	ENSG00000172071	EIF2AK3	PEK|PERK|WRS	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding	0.004717	0.427230	107(AGGAACACAATGTCCC,-,0.00),108(GGAACACAATGTCCCC,+,0.00)
chunk0190_95_1	chr8	30157233	30157866	+	0	NA	intron (NM_006571, intron 1 of 6)	L1PB4|LINE|L1	1252	NM_006571	10671	Hs.158427	NM_006571	ENSG00000104671	DCTN6	WS-3|WS3|p27	dynactin subunit 6	protein-coding	0.011058	0.402208	
chunk0152_14_1	chr5	56350738	56351144	+	0	NA	Intergenic	Intergenic	-117582	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.004926	0.393120	
chunk0146_78_1	chr4	157322262	157322705	+	0	NA	intron (NM_001083619, intron 6 of 15)	intron (NM_001083619, intron 6 of 15)	101815	NM_001083620	2891	Hs.32763	NM_000826	ENSG00000120251	GRIA2	GLUR2|GLURB|GluA2|GluR-K2|HBGR2	glutamate ionotropic receptor AMPA type subunit 2	protein-coding	0.004515	0.331081	
chunk0033_199_1	chr11	16746825	16747385	+	0	NA	intron (NM_014267, intron 2 of 4)	MamSINE1|SINE|tRNA-RTE	8504	NM_014267	10944	Hs.368226	NM_014267	ENSG00000110696	C11orf58	IMAGE145052|SMAP	chromosome 11 open reading frame 58	protein-coding	0.008929	0.385027	
chunk0093_347_1	chr19	55014502	55014814	+	0	NA	exon (NM_001083899, exon 8 of 8).10	exon (NM_001083899, exon 8 of 8).10	23606	NM_001083899	51206	Hs.661752	NM_016363	ENSG00000088053	GP6	BDPLT11|GPIV|GPVI	glycoprotein VI platelet	protein-coding	0.016026	0.565495	
chunk0107_224_1	chr2	216954898	216955117	+	0	NA	Intergenic	L1PREC2|LINE|L1	84235	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.004566	0.381818	
chunk0050_11_1	chr12	99658445	99659030	+	0	NA	intron (NM_152788, intron 8 of 25)	MIRb|SINE|MIR	10987	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.000000	0.324232	
chunk0051_52_1	chr12	112367852	112368139	+	0	NA	intron (NM_001109662, intron 1 of 75)	intron (NM_001109662, intron 1 of 75)	14097	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.006969	0.295139	
chunk0073_26_1	chr16	2340799	2341019	+	0	NA	promoter-TSS (NM_001089)	promoter-TSS (NM_001089)	-13	NR_003574	650655	Hs.376281	NR_003574	ENSG00000238098	ABCA17P	ABCA17	ATP binding cassette subfamily A member 17, pseudogene	pseudo	0.136364	0.764706	
chunk0041_110_1	chr11	124882303	124883129	+	0	NA	Intergenic	Intergenic	15219	NM_019055	54538	Hs.524121	NM_019055	ENSG00000154133	ROBO4	ECSM4|MRB	roundabout guidance receptor 4	protein-coding	0.013317	0.518742	418(TGGCCCAGACTGTCCT,-,0.00),419(GGCCCAGACTGTCCTG,+,0.00)
chunk0055_243_1	chr13	63018572	63019167	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	-211510	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.006723	0.325503	
chunk0006_138_1	chr1	66169482	66169681	+	0	NA	intron (NM_001037340, intron 1 of 14)	intron (NM_001037340, intron 1 of 14)	-118863	NR_123718	101927139	Hs.127908	NR_123718	ENSG00000227466	LOC101927139	-	uncharacterized LOC101927139	ncRNA	0.020101	0.445000	
chunk0086_14_1	chr18	12212644	12212924	+	0	NA	intron (NR_049896, intron 3 of 4)	intron (NR_049896, intron 3 of 4)	12005	NR_049896	497259	Hs.451609	NR_049896		C18orf61	-	uncharacterized LOC497259	ncRNA	0.000000	0.345196	
chunk0199_446_1	chr9	14043065	14043343	+	0	NA	Intergenic	Intergenic	115233	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.003597	0.430108	
chunk0131_69_1	chr3	142960011	142960535	+	0	NA	TTS (NM_198504)	TTS (NM_198504)	3063	NM_198504	344838	Hs.408385	NM_198504	ENSG00000188582	PAQR9	-	progestin and adipoQ receptor family member 9	protein-coding	0.003817	0.424762	
chunk0181_421_1	chr7	90277207	90277602	+	0	NA	intron (NM_001039706, intron 11 of 22)	intron (NM_001039706, intron 11 of 22)	32230	NM_001039706	79846	Hs.521014	NM_024788	ENSG00000105792	CFAP69	C7orf63|FAP69|SPGF24	cilia and flagella associated protein 69	protein-coding	0.005063	0.275253	
chunk0090_70_1	chr19	2483987	2484666	+	0	NA	Intergenic	Intergenic	8201	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.013255	0.486765	333(CAGCACAGACAGTTTC,-,0.00)
chunk0173_126_1	chr6	143689069	143689317	+	0	NA	intron (NM_001100164, intron 1 of 12)	L2a|LINE|L2	11228	NM_001100165	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.020161	0.485944	
chunk0045_206_1	chr12	47788697	47789179	+	0	NA	intron (NM_001308090, intron 18 of 24)	intron (NM_001308090, intron 18 of 24)	15754	NM_017842	55652	Hs.438867	NM_017842	ENSG00000211584	SLC48A1	HRG-1|HRG1|hHRG-1	solute carrier family 48 member 1	protein-coding	0.014523	0.443064	
chunk0195_392_1	chr8	100266264	100266531	+	0	NA	intron (NM_183419, intron 5 of 9)	intron (NM_183419, intron 5 of 9)	36862	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003745	0.305970	
chunk0066_16_1	chr15	27235424	27235717	+	0	NA	intron (NM_033223, intron 3 of 9)	MER34C_|LTR|ERV1	-74251	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.010239	0.404762	
chunk0142_46_1	chr4	91110478	91110723	+	0	NA	intron (NM_001145065, intron 10 of 10)	L2c|LINE|L2	875569	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.004082	0.341463	
chunk0059_255_1	chr14	35117156	35117494	+	0	NA	intron (NM_017917, intron 1 of 12)	intron (NM_017917, intron 1 of 12)	-4996	NM_001256678	9692	Hs.458487	NM_014672	ENSG00000100890	PRORP	KIAA0391|MRPP3	protein only RNase P catalytic subunit	protein-coding	0.005917	0.418879	167(TGGTACACAGTGTTCT,-,0.00),168(GGTACACAGTGTTCTT,+,0.00)
chunk0136_390_1	chr3	196807664	196808089	+	0	NA	exon (NM_002577, exon 7 of 15)	exon (NM_002577, exon 7 of 15)	-59980	NM_152699	205564	Hs.240770	NM_152699	ENSG00000119231	SENP5	-	SUMO specific peptidase 5	protein-coding	0.004706	0.354460	
chunk0012_201_1	chr1	160024938	160025385	+	0	NA	Intergenic	MIR|SINE|MIR	6832	NM_145167	93183	Hs.552810	NM_145167	ENSG00000143315	PIGM	GPI-MT-I	phosphatidylinositol glycan anchor biosynthesis class M	protein-coding	0.002237	0.341518	
chunk0139_335_1	chr4	59321247	59321746	+	0	NA	Intergenic	LTR86A2|LTR|ERVL	-1601123	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.006012	0.340000	
chunk0064_2_1	chr14	89176000	89176782	+	0	NA	intron (NM_005197, intron 5 of 5)	intron (NM_005197, intron 5 of 5)	240719	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.008951	0.412516	
chunk0038_388_1	chr11	93541895	93542494	+	0	NA	intron (NM_020179, intron 1 of 2)	intron (NM_020179, intron 1 of 2)	1186	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.015025	0.486667	
chunk0194_450_1	chr8	92605537	92605892	+	0	NA	intron (NR_125827, intron 3 of 4)	MIRb|SINE|MIR	49780	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.014085	0.441011	
chunk0121_199_1	chr3	20909246	20909770	+	0	NA	Intergenic	Intergenic	-496218	NR_002311	391518	Hs.543226	NR_002311		VENTXP7	HPX42|VENTX1	VENT homeobox pseudogene 7	pseudo	0.007634	0.350476	
chunk0018_78_1	chr1	217228391	217229250	+	0	NA	Intergenic	Intergenic	-91065	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.005821	0.370930	454(GGGAACAGTCTGTTTT,-,0.00),455(GGAACAGTCTGTTTTG,+,0.00)
chunk0141_151_1	chr4	81601299	81601537	+	0	NA	Intergenic	Intergenic	-129490	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.004202	0.397490	
chunk0076_44_1	chr16	59965622	59966019	+	0	NA	intron (NR_110917, intron 1 of 3)	LTR10C|LTR|ERV1	110467	NR_110917	101927580	Hs.552235	NR_110917	ENSG00000261807	LINC02141	-	long intergenic non-protein coding RNA 2141	ncRNA	0.012594	0.391960	
chunk0069_225_1	chr15	63778411	63778851	+	0	NA	intron (NM_003922, intron 1 of 77)	L1MC4|LINE|L1	55317	NM_003922	8925	Hs.210385	NM_003922	ENSG00000103657	HERC1	MDFPMR|p532|p619	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding	0.011364	0.328798	
chunk0008_186_1	chr1	93171595	93172276	+	0	NA	intron (NR_030761, intron 1 of 4)	L1MEd|LINE|L1	8754	NM_001167830	50999	Hs.482873	NM_016040	ENSG00000117500	TMED5	CGI-100|p24g2|p28	transmembrane p24 trafficking protein 5	protein-coding	0.004405	0.340176	
chunk0113_448_1	chr20	62838179	62838508	+	0	NA	intron (NM_001853, intron 30 of 31)	Tigger3a|DNA|TcMar-Tigger	-6223	NM_080750	100132911		NM_080750		DPH3P1	C20orf143|DPH3B|ZCSL1	diphthamide biosynthesis 3 pseudogene 1	protein-coding	0.036474	0.557576	
chunk0069_183_1	chr15	63093441	63093747	+	0	NA	Intergenic	Intergenic	-28206	NM_032857	114294	Hs.410388	NM_032857	ENSG00000103642	LACTB	G24|MRPL56	lactamase beta	protein-coding	0.009804	0.488599	
chunk0050_46_1	chr12	100849362	100849768	+	0	NA	intron (NM_001286615, intron 1 of 27)	L1ME4b|LINE|L1	-52081	NM_001286616	121601	Hs.58785	NM_178826	ENSG00000151572	ANO4	TMEM16D	anoctamin 4	protein-coding	0.009852	0.351351	
chunk0029_402_1	chr10	109632382	109633606	+	0	NA	Intergenic	MER4-int|LTR|ERV1	290559	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.002451	0.322449	
chunk0023_69_1	chr10	22110954	22111293	+	0	NA	Intergenic	Intergenic	98860	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.008850	0.400000	
chunk0066_41_1	chr15	27792615	27793004	+	0	NA	intron (NM_001300984, intron 22 of 22)	intron (NM_001300984, intron 22 of 22)	306503	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.025707	0.576923	
chunk0167_173_1	chr6	63492407	63493054	+	0	NA	Intergenic	Intergenic	-79282	NM_003463	7803	Hs.227777	NM_003463	ENSG00000112245	PTP4A1	HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1	protein tyrosine phosphatase 4A1	protein-coding	0.006182	0.375000	291(CAGAACAGCATGTACT,-,0.00),292(AGAACAGCATGTACTC,+,0.00)
chunk0142_11_1	chr4	89868853	89869052	+	0	NA	Intergenic	Intergenic	-25949	NM_007351	22915	Hs.268107	NM_007351	ENSG00000138722	MMRN1	ECM|EMILIN4|GPIa*|MMRN	multimerin 1	protein-coding	0.000000	0.285000	
chunk0126_331_1	chr3	82043841	82044502	+	0	NA	Intergenic	Intergenic	-282372	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.009077	0.364048	
chunk0040_14_1	chr11	108754999	108755354	+	0	NA	intron (NM_004398, intron 13 of 17)	intron (NM_004398, intron 13 of 17)	90151	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.005634	0.404494	
chunk0096_445_1	chr2	39379667	39380152	+	0	NA	intron (NM_003618, intron 1 of 33)	intron (NM_003618, intron 1 of 33)	57403	NM_003618	8491	Hs.655750	NM_003618	ENSG00000011566	MAP4K3	GLK|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.000000	0.333333	244(CTGTACACAATGTACT,-,0.00),245(TGTACACAATGTACTC,+,0.00)
chunk0036_336_1	chr11	66718015	66718904	+	0	NA	intron (NM_006946, intron 2 of 36)	intron (NM_006946, intron 2 of 36)	2940	NM_006946	6712	Hs.26915	NM_006946	ENSG00000173898	SPTBN2	GTRAP41|SCA5|SCAR14	spectrin beta, non-erythrocytic 2	protein-coding	0.035996	0.622472	322(GTCACACTGTGTCCTG,+,0.00)
chunk0183_426_1	chr7	111012181	111012693	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	-78569	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.005859	0.284600	
chunk0007_395_1	chr1	85481776	85482107	+	0	NA	intron (NM_001134445, intron 2 of 6)	intron (NM_001134445, intron 2 of 6)	-16735	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.009063	0.490964	
chunk0051_140_1	chr12	115714004	115714235	+	0	NA	Intergenic	Charlie18a|DNA|hAT-Charlie	434535	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.008658	0.370690	
chunk0045_213_1	chr12	47949659	47950072	+	0	NA	Intergenic	L2b|LINE|L2	-13682	NM_001143841	79022	Hs.596726	NM_024056	ENSG00000134291	TMEM106C	-	transmembrane protein 106C	protein-coding	0.026634	0.538647	
chunk0058_7_1	chr14	18667868	18668076	+	0	NA	Intergenic	Intergenic	-34338	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.014423	0.545455	179(TGGGACACTCTGCTCT,-,0.00),180(GGGACACTCTGCTCTG,+,0.00)
chunk0009_261_1	chr1	107419633	107419832	+	0	NA	intron (NM_001312688, intron 6 of 7)	intron (NM_001312688, intron 6 of 7)	268772	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.000000	0.370000	
chunk0205_75_1	chr9	106964850	106965296	+	0	NA	intron (NM_021224, intron 7 of 12)	intron (NM_021224, intron 7 of 12)	101976	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.006726	0.427293	
chunk0050_325_1	chr12	107159292	107159930	+	0	NA	Intergenic	Intergenic	-65754	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.006270	0.417840	
chunk0091_350_1	chr19	15123960	15124346	+	0	NA	intron (NM_006844, intron 2 of 15)	intron (NM_006844, intron 2 of 15)	1646	NM_006844	10994	Hs.78880	NM_006844	ENSG00000105135	ILVBL	209L8|AHAS|HACL1L|ILV2H	ilvB acetolactate synthase like	protein-coding	0.007772	0.591731	177(TGGCACAGACTGTGCC,-,0.00),178(GGCACAGACTGTGCCG,+,0.00)
chunk0139_71_1	chr4	49107336	49107567	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	120809	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.017316	0.413793	
chunk0006_311_1	chr1	71427798	71428156	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	346653	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.002793	0.415042	
chunk0075_199_1	chr16	52496233	52496906	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	50325	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.008915	0.344214	598(ATGAACAGTTAGTGCC,-,0.00),599(TGAACAGTTAGTGCCC,+,0.00)
chunk0013_178_1	chr1	168913568	168914165	+	0	NA	intron (NR_104091, intron 3 of 4)	intron (NR_104091, intron 3 of 4)	126925	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.008375	0.438127	327(GGGAACAGCAAGTACC,-,0.00),328(GGAACAGCAAGTACCT,+,0.00)
chunk0083_383_1	chr17	71517682	71518237	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-315780	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.009009	0.406475	
chunk0193_316_1	chr8	78544524	78544920	+	0	NA	intron (NR_125389, intron 2 of 2)	intron (NR_125389, intron 2 of 2)	13781	NR_125389	101927003	Hs.614849	NR_125389	ENSG00000254266	PKIA-AS1	-	PKIA antisense RNA 1	ncRNA	0.005051	0.309824	
chunk0144_360_1	chr4	139817774	139817990	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	152114	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.000000	0.534562	85(TGCTCACTGTGTTCCT,+,0.00)
chunk0087_106_1	chr18	32539705	32540171	+	0	NA	Intergenic	Intergenic	28275	NR_003558	441818	Hs.549773	NR_003558	ENSG00000260389	WBP11P1	HsT3017	WW domain binding protein 11 pseudogene 1	pseudo	0.006438	0.355460	
chunk0037_355_1	chr11	77695609	77695903	+	0	NA	intron (NM_016578, intron 7 of 15)	L1MD3|LINE|L1	-57950	NM_001311200	1207	Hs.430733	NM_001293	ENSG00000074201	CLNS1A	CLCI|CLNS1B|ICln	chloride nucleotide-sensitive channel 1A	protein-coding	0.003401	0.393220	
chunk0035_26_1	chr11	40481041	40481422	+	0	NA	intron (NM_020929, intron 2 of 4)	intron (NM_020929, intron 2 of 4)	-188101	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005249	0.311518	
chunk0061_184_1	chr14	60151847	60152051	+	0	NA	intron (NM_016029, intron 4 of 6)	intron (NM_016029, intron 4 of 6)	13544	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.014706	0.502439	
chunk0098_224_1	chr2	73739151	73739350	+	0	NA	Intergenic	MER70-int|LTR|ERVL	-1860	NM_016058	51002	Hs.157401	NM_016058	ENSG00000144034	TPRKB	CGI-121|CGI121|GAMOS5	TP53RK binding protein	protein-coding	0.015075	0.455000	
chunk0176_17_1	chr7	8290899	8291376	+	0	NA	intron (NR_125740, intron 3 of 5)	intron (NR_125740, intron 3 of 5)	-28525	NM_001276478	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.006289	0.399582	
chunk0077_413_1	chr16	85137175	85137820	+	0	NA	intron (NR_033984, intron 1 of 2)	CpG	347	NR_033984	400548	Hs.592054	NR_033984	ENSG00000278214	LINC02139	-	long intergenic non-protein coding RNA 2139	ncRNA	0.044961	0.674923	
chunk0157_235_1	chr5	119530024	119530573	+	0	NA	intron (NM_000414, intron 21 of 23)	intron (NM_000414, intron 21 of 23)	77801	NM_001292028	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.009107	0.269091	
chunk0042_294_1	chr12	7704543	7704742	+	0	NA	Intergenic	AluSx4|SINE|Alu	-6812	NM_199286	359787	Hs.131358	NM_199286	ENSG00000187569	DPPA3	Pgc7|STELLA	developmental pluripotency associated 3	protein-coding	0.000000	0.445000	
chunk0022_401_1	chr10	18195080	18196091	+	0	NA	intron (NM_001167945, intron 2 of 13)	intron (NM_001167945, intron 2 of 13)	54772	NM_001167945	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.010880	0.429842	
chunk0158_278_1	chr5	131552873	131553371	+	0	NA	intron (NM_016340, intron 5 of 27)	L1MCc|LINE|L1	82114	NM_001164386	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.000000	0.400802	
chunk0135_126_1	chr3	187132773	187133115	+	0	NA	intron (NM_052969, intron 1 of 2)	L1MCc|LINE|L1	6531	NM_052969	116832	Hs.647900	NM_052969	ENSG00000163923	RPL39L	L39-2|RPL39L1	ribosomal protein L39 like	protein-coding	0.000000	0.437318	
chunk0099_417_1	chr2	102442813	102443502	+	0	NA	intron (NM_003853, intron 7 of 11)	intron (NM_003853, intron 7 of 11)	10868	NR_039930	100616157		NR_039930	ENSG00000264764	MIR4772	mir-4772	microRNA 4772	ncRNA	0.014514	0.392754	
chunk0163_88_1	chr6	9480117	9480828	+	0	NA	Intergenic	Intergenic	828263	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.008439	0.339888	357(AGAGCAGGTTGTGCTT,+,0.00)
chunk0112_132_1	chr20	38554912	38555435	+	0	NA	intron (NM_020336, intron 22 of 29)	MIRc|SINE|MIR	-26022	NM_001018082	149685	Hs.368028	NM_174906	ENSG00000182035	ADIG	SMAF1	adipogenin	protein-coding	0.003824	0.385496	
chunk0124_74_1	chr3	53150146	53150739	+	0	NA	Intergenic	Intergenic	-10765	NM_006254	5580	Hs.155342	NM_006254	ENSG00000163932	PRKCD	ALPS3|CVID9|MAY1|PKCD|nPKC-delta	protein kinase C delta	protein-coding	0.005059	0.510101	285(GGGGACATTTTGTGCT,-,0.00),286(GGGACATTTTGTGCTC,+,0.00)
chunk0076_227_1	chr16	68732124	68732361	+	0	NA	Intergenic	Intergenic	-5050	NM_004360	999	Hs.461086	NM_004360	ENSG00000039068	CDH1	Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO	cadherin 1	protein-coding	0.008439	0.609244	
chunk0026_50_1	chr10	60955944	60956563	+	0	NA	intron (NR_024554, intron 2 of 11)	Tigger3b|DNA|TcMar-Tigger	-11978	NM_001242359	9886	Hs.737374	NM_014836	ENSG00000072422	RHOBTB1	-	Rho related BTB domain containing 1	protein-coding	0.003231	0.346774	
chunk0025_121_1	chr10	51675144	51675505	+	0	NA	intron (NM_006258, intron 3 of 17)	intron (NM_006258, intron 3 of 17)	24271	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.000000	0.334254	
chunk0196_175_1	chr8	105910193	105910429	+	0	NA	intron (NR_125796, intron 2 of 7)	intron (NR_125796, intron 2 of 7)	150192	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.000000	0.324895	39(AAGAGCAAAGTGTCCT,-,0.00),40(AGAGCAAAGTGTCCTC,+,0.00)
chunk0115_9_1	chr21	20353294	20354000	+	0	NA	Intergenic	Intergenic	449461	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005666	0.343706	370(AATAACATGCTGTCCT,-,0.00),371(ATAACATGCTGTCCTT,+,0.00)
chunk0067_443_1	chr15	50164414	50164917	+	0	NA	Intergenic	L1M1|LINE|L1	-17531	NM_001159629	11001	Hs.11729	NM_003645	ENSG00000140284	SLC27A2	ACSVL1|FACVL1|FATP2|HsT17226|VLACS|VLCS|hFACVL1	solute carrier family 27 member 2	protein-coding	0.001988	0.496032	
chunk0203_433_1	chr9	91237647	91238000	+	0	NA	intron (NM_001306190, intron 5 of 8)	intron (NM_001306190, intron 5 of 8)	124101	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.005666	0.358757	
chunk0002_262_1	chr1	21338187	21338510	+	0	NA	intron (NM_001113348, intron 1 of 18)	intron (NM_001113348, intron 1 of 18)	7193	NM_001113348	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.006192	0.500000	
chunk0202_50_1	chr9	71285174	71285801	+	0	NA	Intergenic	Intergenic	-163889	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.014354	0.452229	
chunk0129_446_1	chr3	128127071	128127505	+	0	NA	Intergenic	Intergenic	-3460	NM_003707	8607	Hs.272822	NM_003707	ENSG00000175792	RUVBL1	ECP-54|ECP54|INO80H|NMP 238|NMP238|PONTIN|Pontin52|RVB1|TIH1|TIP49|TIP49A	RuvB like AAA ATPase 1	protein-coding	0.009217	0.452874	
chunk0016_80_1	chr1	194081491	194081708	+	0	NA	Intergenic	MIRb|SINE|MIR	776854	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.000000	0.325688	101(TGGATCATTCTGTGCT,-,0.00),102(GGATCATTCTGTGCTC,+,0.00)
chunk0103_390_1	chr2	168876744	168877129	+	0	NA	intron (NM_020675, intron 4 of 6)	intron (NM_020675, intron 4 of 6)	13498	NM_020675	57405	Hs.421956	NM_020675	ENSG00000152253	SPC25	AD024|SPBC25|hSpc25	SPC25 component of NDC80 kinetochore complex	protein-coding	0.002597	0.329016	
chunk0197_79_1	chr8	119112293	119112770	+	0	NA	Intergenic	Intergenic	45346	NM_006438	10584	Hs.176615	NM_006438	ENSG00000184374	COLEC10	3MC3|CL-34|CLL1	collectin subfamily member 10	protein-coding	0.006289	0.357741	
chunk0018_424_1	chr1	222785061	222785261	+	0	NA	Intergenic	Intergenic	-29928	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.000000	0.373134	
chunk0055_308_1	chr13	66353639	66354033	+	0	NA	intron (NM_203487, intron 4 of 4)	intron (NM_203487, intron 4 of 4)	135586	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.005076	0.313924	
chunk0023_265_1	chr10	27738623	27739112	+	0	NA	intron (NM_173576, intron 3 of 6)	intron (NM_173576, intron 3 of 6)	-5748	NR_121652	101929202	Hs.568843	NR_121652		MKX-AS1	-	MKX antisense RNA 1	ncRNA	0.006135	0.346939	
chunk0104_368_1	chr2	180141535	180142064	+	0	NA	Intergenic	L2c|LINE|L2	-134746	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.003781	0.358491	
chunk0155_212_1	chr5	95072142	95072448	+	0	NA	intron (NM_024717, intron 1 of 22)	intron (NM_024717, intron 1 of 22)	9571	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.000000	0.387622	120(GAGTACAGTAAGTCCT,-,0.00),121(AGTACAGTAAGTCCTA,+,0.00)
chunk0039_441_1	chr11	108124743	108125044	+	0	NA	intron (NM_000019, intron 1 of 11)	L2a|LINE|L2	3362	NM_000019	38	Hs.232375	NM_000019	ENSG00000075239	ACAT1	ACAT|MAT|T2|THIL	acetyl-CoA acetyltransferase 1	protein-coding	0.016611	0.400662	
chunk0065_341_1	chr14	103543658	103544173	+	0	NA	Intergenic	Intergenic	14743	NM_152307	115708	Hs.525610	NM_152307	ENSG00000166166	TRMT61A	C14orf172|GCD14|Gcd14p|TRM61|hTRM61	tRNA methyltransferase 61A	protein-coding	0.023301	0.653101	282(AGGCACGGGGTGTGCT,-,0.00),283(GGCACGGGGTGTGCTG,+,0.00)
chunk0033_138_1	chr11	15349224	15349537	+	0	NA	Intergenic	Intergenic	200278	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.003195	0.490446	
chunk0134_416_1	chr3	183275489	183275723	+	0	NA	intron (NM_015078, intron 15 of 29)	AluJo|SINE|Alu	22362	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.004274	0.395745	
chunk0052_154_1	chr13	23835982	23836798	+	0	NA	intron (NM_005932, intron 13 of 18)	intron (NM_005932, intron 13 of 18)	-52499	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.004902	0.312118	
chunk0141_385_1	chr4	88281501	88282037	+	0	NA	intron (NM_152542, intron 1 of 6)	intron (NM_152542, intron 1 of 6)	3062	NM_152542	152926	Hs.43744	NM_152542	ENSG00000163644	PPM1K	BDP|MSUDMV|PP2Ckappa|PP2Cm|PTMP|UG0882E07	protein phosphatase, Mg2+/Mn2+ dependent 1K	protein-coding	0.011194	0.398510	
chunk0019_217_1	chr1	227154473	227155364	+	0	NA	intron (NM_014826, intron 6 of 34)	L1MEd|LINE|L1	163207	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.004489	0.308296	
chunk0105_17_1	chr2	182000742	182001277	+	0	NA	intron (NM_001080545, intron 2 of 4)	intron (NM_001080545, intron 2 of 4)	15185	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.003738	0.382463	
chunk0002_273_1	chr1	21937712	21938010	+	0	NA	promoter-TSS (NM_005529)	promoter-TSS (NM_005529)	-564	NM_001291860	3339	Hs.562227	NM_005529	ENSG00000142798	HSPG2	HSPG|PLC|PRCAN|SJA|SJS|SJS1	heparan sulfate proteoglycan 2	protein-coding	0.050336	0.561873	
chunk0164_33_1	chr6	18362095	18362633	+	0	NA	Intergenic	Intergenic	-24986	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.003717	0.397032	
chunk0085_361_1	chr18	9352839	9353117	+	0	NA	intron (NM_020648, intron 2 of 4)	Tigger3a|DNA|TcMar-Tigger	18211	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.000000	0.318996	
chunk0180_358_1	chr7	73758444	73759062	+	0	NA	Intergenic	Intergenic	11517	NM_001306	1365	Hs.647023	NM_001306	ENSG00000165215	CLDN3	C7orf1|CPE-R2|CPETR2|HRVP1|RVP1	claudin 3	protein-coding	0.008091	0.555735	287(AGGTACTATCTGTTCT,-,0.00),288(GGTACTATCTGTTCTT,+,0.00)
chunk0186_154_1	chr7	139117655	139118089	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-8153	NM_024625	56829	Hs.133512	NM_020119	ENSG00000105939	ZC3HAV1	ARTD13|FLB6421|PARP13|ZAP|ZC3H2|ZC3HDC2	zinc finger CCCH-type containing, antiviral 1	protein-coding	0.004608	0.411494	
chunk0006_199_1	chr1	67588266	67588728	+	0	NA	Intergenic	Intergenic	-96680	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.015152	0.395248	209(CAGCACTCCGTGTTCT,-,0.00),210(AGCACTCCGTGTTCTT,+,0.00)
chunk0075_311_1	chr16	54429030	54429434	+	0	NA	Intergenic	L2a|LINE|L2	-142766	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.009901	0.469136	
chunk0139_171_1	chr4	53963737	53964206	+	0	NA	Intergenic	Intergenic	23311	NR_027153	402176	Hs.452943	NM_001011538		RPL21P44	RPL21_17_477	ribosomal protein L21 pseudogene 44	pseudo	0.006397	0.365957	
chunk0099_389_1	chr2	101710253	101710822	+	0	NA	intron (NM_145686, intron 2 of 30)	L2a|LINE|L2	12461	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.005272	0.405263	
chunk0205_388_1	chr9	114385344	114385877	+	0	NA	intron (NM_030767, intron 1 of 21)	intron (NM_030767, intron 1 of 21)	8795	NM_030767	80709	Hs.494895	NM_030767	ENSG00000106948	AKNA	-	AT-hook transcription factor	protein-coding	0.016886	0.548689	241(AGGAACATCCTGTCTT,-,0.00),242(GGAACATCCTGTCTTC,+,0.00)
chunk0186_58_1	chr7	136652470	136652696	+	0	NA	Intergenic	Intergenic	-216069	NM_001006627	1129	Hs.535891	NM_000739	ENSG00000181072	CHRM2	HM2	cholinergic receptor muscarinic 2	protein-coding	0.004425	0.370044	
chunk0158_215_1	chr5	128349267	128349573	+	0	NA	exon (NM_001999, exon 23 of 65)	exon (NM_001999, exon 23 of 65)	188622	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.016340	0.439739	
chunk0144_10_1	chr4	124747115	124747694	+	0	NA	Intergenic	Intergenic	-34672	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.003454	0.324138	317(AAGAACAAAGTGTCAC,-,0.00)
chunk0146_196_1	chr4	161332574	161332865	+	0	NA	Intergenic	Intergenic	-690014	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.003436	0.270548	
chunk0030_429_1	chr10	120453464	120453861	+	0	NA	Intergenic	Intergenic	-3292	NM_001030059	196051	Hs.40479	NM_001030059	ENSG00000203805	PLPP4	DPPL2|PPAPDC1|PPAPDC1A	phospholipid phosphatase 4	protein-coding	0.005038	0.467337	227(TGGAACAGGATGGCCC,-,0.00),228(GGAACAGGATGGCCCC,+,0.00)
chunk0128_395_1	chr3	113975506	113975931	+	0	NA	intron (NM_020817, intron 16 of 16)	L2a|LINE|L2	27817	NM_173570	254887	Hs.21902	NM_173570	ENSG00000184307	ZDHHC23	DHHC-23|NIDD	zinc finger DHHC-type containing 23	protein-coding	0.002353	0.392019	
chunk0101_50_1	chr2	123051190	123052025	+	0	NA	Intergenic	Intergenic	-973680	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.001198	0.314593	
chunk0071_392_1	chr15	89301421	89301802	+	0	NA	intron (NM_018193, intron 26 of 36)	intron (NM_018193, intron 26 of 36)	25199	NR_106824	102466983		NR_106824	ENSG00000275101	MIR6766	hsa-mir-6766	microRNA 6766	ncRNA	0.005249	0.374346	
chunk0029_176_1	chr10	100648818	100649390	+	0	NA	Intergenic	Intergenic	-86605	NM_001304569	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.012238	0.376963	
chunk0130_412_1	chr3	140595204	140595900	+	0	NA	Intergenic	Intergenic	-82472	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.004310	0.437590	296(CAGAACAGCTTGTACT,-,0.00),297(AGAACAGCTTGTACTC,+,0.00)
chunk0193_248_1	chr8	76901239	76901733	+	0	NA	Intergenic	L1PA6|LINE|L1	65364	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004049	0.494949	
chunk0092_344_1	chr19	35249984	35250277	+	0	NA	intron (NM_205834, intron 1 of 9)	MIRc|SINE|MIR	1474	NM_001260490	51599	Hs.466507	NM_015925	ENSG00000105699	LSR	ILDR3|LISCH7	lipolysis stimulated lipoprotein receptor	protein-coding	0.027304	0.568027	201(AGGAACAATGTGTGCC,-,0.00),202(GGAACAATGTGTGCCA,+,0.00)
chunk0029_167_1	chr10	99927099	99927762	+	0	NA	intron (NR_024130, intron 1 of 4)	MIRb|SINE|MIR	221	NR_024130	100188954	Hs.656104	NR_024130		DNMBP-AS1	NCRNA00093	DNMBP antisense RNA 1	ncRNA	0.012066	0.423193	469(ATTACACAGTGTTCCC,+,0.00)
chunk0190_314_1	chr8	38528308	38528513	+	0	NA	exon (NM_207412, exon 1 of 3)	exon (NM_207412, exon 1 of 3)	252	NM_001303531	389649	Hs.546586	NM_207412	ENSG00000196166	C8orf86	-	chromosome 8 open reading frame 86	protein-coding	0.039024	0.553398	122(TGGAACTGCCTGTTCT,-,0.00),123(GGAACTGCCTGTTCTT,+,0.00)
chunk0196_118_1	chr8	103519878	103520322	+	0	NA	intron (NM_001100117, intron 1 of 23)	MIRb|SINE|MIR	19352	NM_001100117	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.002252	0.352809	
chunk0032_442_1	chr10	132967533	132967807	+	0	NA	intron (NR_046231, intron 1 of 2)	LTR1A2|LTR|ERV1	2136	NR_046231	399829	Hs.252872	NR_046231	ENSG00000240707	LINC01168	-	long intergenic non-protein coding RNA 1168	ncRNA	0.036496	0.585455	
chunk0016_376_1	chr1	202592661	202593285	+	0	NA	3' UTR (NM_001136504, exon 9 of 9)	3' UTR (NM_001136504, exon 9 of 9)	50480	NM_001136504	127833	Hs.25422	NM_177402	ENSG00000143858	SYT2	CMS7|MYSPC|SytII	synaptotagmin 2	protein-coding	0.000000	0.456000	
chunk0104_431_1	chr2	181003417	181003937	+	0	NA	intron (NM_001278554, intron 3 of 5)	intron (NM_001278554, intron 3 of 5)	22553	NM_001278554	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.003846	0.297505	
chunk0031_316_1	chr10	129096586	129096832	+	0	NA	Intergenic	Intergenic	-370475	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.012195	0.457490	
chunk0053_230_1	chr13	32412658	32412899	+	0	NA	intron (NM_052818, intron 1 of 4)	intron (NM_052818, intron 1 of 4)	15400	NM_001286459	90634	Hs.732118	NM_052818	ENSG00000139597	N4BP2L1	CG018	NEDD4 binding protein 2 like 1	protein-coding	0.012448	0.388430	
chunk0206_8_1	chr9	115649935	115650396	+	0	NA	Intergenic	Intergenic	94074	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.019523	0.504329	254(GAGGACAACATGTTCC,-,0.00),255(AGGACAACATGTTCCC,+,0.00)
chunk0016_245_1	chr1	200016762	200017305	+	0	NA	Intergenic	Intergenic	-10569	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005525	0.426471	338(CAGGACACACTGACCT,-,0.00),339(AGGACACACTGACCTT,+,0.00)
chunk0133_350_1	chr3	173148156	173148397	+	0	NA	Intergenic	L1MA1|LINE|L1	-7008	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.004149	0.388430	
chunk0127_186_1	chr3	95689941	95690268	+	0	NA	Intergenic	Intergenic	-6911	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.012232	0.359756	
chunk0167_162_1	chr6	62736707	62737524	+	0	NA	Intergenic	Intergenic	-450920	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.002448	0.224939	
chunk0012_5_1	chr1	154723825	154724324	+	0	NA	intron (NM_170782, intron 5 of 7)	intron (NM_170782, intron 5 of 7)	-96094	NM_001025107	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.014028	0.434000	
chunk0085_438_1	chr18	11005496	11005905	+	0	NA	intron (NM_022068, intron 2 of 51)	intron (NM_022068, intron 2 of 51)	143062	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.014670	0.504878	181(AGGGACTTTTTGTGCT,-,0.00),182(GGGACTTTTTGTGCTG,+,0.00)
chunk0151_291_1	chr5	52878341	52878913	+	0	NA	intron (NM_181501, intron 6 of 28)	intron (NM_181501, intron 6 of 28)	90325	NM_181501	3672	Hs.644352	NM_181501	ENSG00000213949	ITGA1	CD49a|VLA1	integrin subunit alpha 1	protein-coding	0.008741	0.369983	
chunk0123_303_1	chr3	46959354	46959553	+	0	NA	intron (NM_001277074, intron 1 of 6)	intron (NM_001277074, intron 1 of 6)	17048	NR_102269	151903	Hs.631918	NM_144716	ENSG00000160799	CCDC12	-	coiled-coil domain containing 12	protein-coding	0.025126	0.545000	
chunk0061_43_1	chr14	56168115	56168502	+	0	NA	intron (NM_021255, intron 1 of 5)	L1MA1|LINE|L1	49933	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.002584	0.538660	
chunk0080_130_1	chr17	27321439	27322029	+	0	NA	Intergenic	Intergenic	27654	NM_015626	26118	Hs.446017	NM_015626	ENSG00000109046	WSB1	SWIP1|WSB-1	WD repeat and SOCS box containing 1	protein-coding	0.008475	0.472081	
chunk0197_379_1	chr8	126926806	126927274	+	0	NA	Intergenic	Intergenic	-86114	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.008547	0.396588	241(CTGCACATTTTGTACC,-,0.00),242(TGCACATTTTGTACCC,+,0.00)
chunk0130_162_1	chr3	132662384	132662612	+	0	NA	intron (NM_024818, intron 1 of 11)	L2c|LINE|L2	2202	NM_024818	79876	Hs.170737	NM_024818	ENSG00000081307	UBA5	EIEE44|SCAR24|THIFP1|UBE1DC1	ubiquitin like modifier activating enzyme 5	protein-coding	0.000000	0.314410	
chunk0194_74_1	chr8	82649755	82650032	+	0	NA	Intergenic	L1MA3|LINE|L1	-753865	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003610	0.338129	
chunk0049_195_1	chr12	93019395	93019973	+	0	NA	intron (NR_040096, intron 3 of 4)	Tigger12c|DNA|TcMar-Tigger	-90353	NM_003566	8411	Hs.567367	NM_003566	ENSG00000102189	EEA1	MST105|MSTP105|ZFYVE2	early endosome antigen 1	protein-coding	0.010381	0.447323	168(CAGCACAAGCTGTTTT,-,0.00),169(AGCACAAGCTGTTTTC,+,0.00)
chunk0046_130_1	chr12	57543882	57544146	+	0	NA	intron (NM_001261412, intron 2 of 13)	intron (NM_001261412, intron 2 of 13)	3317	NM_006400	10540	Hs.289123	NM_006400	ENSG00000175203	DCTN2	DCTN50|DYNAMITIN|HEL-S-77|RBP50	dynactin subunit 2	protein-coding	0.003788	0.411321	
chunk0001_118_1	chr1	4144393	4144784	+	0	NA	Intergenic	(TCA)n|Simple_repeat|Simple_repeat	203976	NR_040065	728716	Hs.668359	NR_040065		LINC01346	-	long intergenic non-protein coding RNA 1346	ncRNA	0.005115	0.433673	
chunk0189_309_1	chr8	26096179	26096795	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-51363	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.006494	0.414911	257(AAGAACAAGCTGTCTC,-,0.00),258(AGAACAAGCTGTCTCT,+,0.00)
chunk0060_181_1	chr14	46608569	46609047	+	0	NA	Intergenic	L1PA15|LINE|L1	43017	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.004184	0.369520	306(AGAACACGCAGTGTTT,+,0.00)
chunk0088_133_1	chr18	45820424	45820641	+	0	NA	Intergenic	Intergenic	-5048	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.009217	0.582569	
chunk0119_375_1	chr22	47689502	47690149	+	0	NA	intron (NR_122046, intron 6 of 8)	L1MB5|LINE|L1	58151	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.007728	0.427469	
chunk0095_121_1	chr2	15894426	15894776	+	0	NA	Intergenic	Intergenic	-25798	NR_125783	103752554	Hs.269571	NR_125783	ENSG00000223850	MYCNUT	MYCNUN|lncUSMycN	MYCN upstream transcript	ncRNA	0.017143	0.384615	
chunk0177_442_1	chr7	28036725	28037277	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-143456	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.003623	0.464738	
chunk0014_211_1	chr1	179303240	179303888	+	0	NA	intron (NM_001252511, intron 2 of 14)	intron (NM_001252511, intron 2 of 14)	9850	NM_001252511	6646	Hs.445588	NM_003101	ENSG00000057252	SOAT1	ACACT|ACAT|ACAT-1|ACAT1|SOAT|STAT	sterol O-acyltransferase 1	protein-coding	0.007716	0.357473	
chunk0148_367_1	chr5	14627201	14627564	+	0	NA	Intergenic	L1MA9|LINE|L1	25000	NR_132980	106635683		NR_132980		SNORD141A	-	small nucleolar RNA, C/D box 141A	snoRNA	0.000000	0.348901	134(GTGTACAACATGTTCT,-,0.00),135(TGTACAACATGTTCTG,+,0.00)
chunk0096_50_1	chr2	27119132	27119454	+	0	NA	promoter-TSS (NM_006569)	promoter-TSS (NM_006569)	-166	NM_001166240	10669	Hs.159525	NM_006569	ENSG00000138028	CGREF1	CGR11	cell growth regulator with EF-hand domain 1	protein-coding	0.055901	0.532508	
chunk0084_253_1	chr17	79020259	79020643	+	0	NA	intron (NR_040018, intron 1 of 2)	intron (NR_040018, intron 1 of 2)	-2483	NM_153372	114897	Hs.201398	NM_030968	ENSG00000173918	C1QTNF1	CTRP1|GIP|ZSIG37	C1q and TNF related 1	protein-coding	0.018229	0.496104	106(ATGACATGCTGTGCTT,+,0.00),247(GGGCACAGAACGTGCT,-,0.00),248(GGCACAGAACGTGCTG,+,0.00)
chunk0153_296_1	chr5	73424328	73424990	+	0	NA	Intergenic	Intergenic	23868	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.007553	0.398190	
chunk0070_430_1	chr15	78041689	78042106	+	0	NA	intron (NM_015079, intron 3 of 12)	MIR|SINE|MIR	35755	NM_144572	23102	Hs.567426	NM_015079	ENSG00000167202	TBC1D2B	-	TBC1 domain family member 2B	protein-coding	0.007194	0.397129	
chunk0138_90_1	chr4	35593768	35594205	+	0	NA	Intergenic	MIR|SINE|MIR	-650130	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.002288	0.347032	
chunk0110_133_1	chr20	13513361	13513870	+	0	NA	intron (NM_017714, intron 10 of 13)	intron (NM_017714, intron 10 of 13)	125321	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.001965	0.405882	
chunk0067_429_1	chr15	49925467	49926270	+	0	NA	intron (NR_073596, intron 16 of 27)	intron (NR_073596, intron 16 of 27)	187448	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.003736	0.364428	
chunk0123_316_1	chr3	47265547	47265765	+	0	NA	intron (NM_182902, intron 8 of 20)	intron (NM_182902, intron 8 of 20)	-17184	NM_025010	23276	Hs.517946	NM_025010	ENSG00000114648	KLHL18	-	kelch like family member 18	protein-coding	0.009174	0.552511	
chunk0075_138_1	chr16	50205311	50205630	+	0	NA	intron (NM_001040284, intron 2 of 12)	intron (NM_001040284, intron 2 of 12)	52552	NM_001040284	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.000000	0.312500	
chunk0034_447_1	chr11	39567894	39568213	+	0	NA	Intergenic	Intergenic	725077	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.362500	27(TGCACTGGATGTGCTC,+,0.00)
chunk0021_350_1	chr1	246171263	246171851	+	0	NA	intron (NM_001167740, intron 5 of 11)	Tigger3c|DNA|TcMar-Tigger	245855	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.005102	0.392190	353(CTGTACAGTATGTTCT,-,0.00),354(TGTACAGTATGTTCTT,+,0.00)
chunk0031_303_1	chr10	128800479	128800859	+	0	NA	Intergenic	MLT2D|LTR|ERVL	514719	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.005263	0.435696	
chunk0092_401_1	chr19	37371339	37371628	+	0	NA	intron (NM_032453, intron 1 of 4)	intron (NM_032453, intron 1 of 4)	326	NM_032453	84503	Hs.590940	NM_032453	ENSG00000189164	ZNF527	-	zinc finger protein 527	protein-coding	0.024221	0.468966	
chunk0026_65_1	chr10	61149940	61150175	+	0	NA	Intergenic	L1ME3A|LINE|L1	133782	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.004255	0.355932	
chunk0140_58_1	chr4	66907334	66907565	+	0	NA	Intergenic	L1ME1|LINE|L1	514551	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.000000	0.375000	
chunk0143_339_1	chr4	121519316	121519860	+	0	NA	Intergenic	Intergenic	-138562	NM_198179	84109	Hs.368977	NM_198179	ENSG00000186867	QRFPR	AQ27|GPR103|SP9155	pyroglutamylated RFamide peptide receptor	protein-coding	0.007353	0.447706	96(GGGAGCACTGTGTTCC,-,0.00),97(GGAGCACTGTGTTCCC,+,0.00)
chunk0028_224_1	chr10	89642267	89642751	+	0	NA	intron (NM_148977, intron 1 of 6)	intron (NM_148977, intron 1 of 6)	1382	NM_138316	53354	Hs.163555	NM_138316	ENSG00000152782	PANK1	PANK	pantothenate kinase 1	protein-coding	0.006198	0.352577	
chunk0207_352_1	chr9	135170001	135170221	+	0	NA	Intergenic	(TGTG)n|Simple_repeat|Simple_repeat	-11498	NR_046107	401557	Hs.640138	NR_046107		LOC401557	-	uncharacterized LOC401557	ncRNA	0.031818	0.515837	
chunk0140_154_1	chr4	69398604	69399006	+	0	NA	Intergenic	Intergenic	97103	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.004975	0.347395	
chunk0026_445_1	chr10	71505530	71506242	+	0	NA	intron (NM_001171931, intron 3 of 24)	L1MB5|LINE|L1	6034	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.012640	0.424965	
chunk0163_109_1	chr6	10127350	10127612	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-284837	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.000000	0.433460	
chunk0034_22_1	chr11	26219401	26220342	+	0	NA	intron (NM_001313726, intron 1 of 27)	MER70A|LTR|ERVL	30748	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.004251	0.414013	546(CAGAACTTCTTGTTCT,-,0.00),547(AGAACTTCTTGTTCTA,+,0.00)
chunk0206_344_1	chr9	125550759	125550964	+	0	NA	intron (NM_001006618, intron 6 of 7)	intron (NM_001006618, intron 6 of 7)	156373	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.004878	0.339806	
chunk0197_260_1	chr8	123541805	123542186	+	0	NA	promoter-TSS (NM_001242463)	promoter-TSS (NM_001242463)	-742	NM_001242463	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.018373	0.536649	
chunk0003_336_1	chr1	38951092	38951363	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-9397	NM_017821	54933	Hs.524626	NM_017821	ENSG00000158315	RHBDL2	RRP2	rhomboid like 2	protein-coding	0.025830	0.408088	
chunk0200_148_1	chr9	18207671	18208635	+	0	NA	Intergenic	MIRb|SINE|MIR	-265928	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.008299	0.382383	
chunk0196_331_1	chr8	112389997	112390418	+	0	NA	intron (NM_198123, intron 36 of 70)	MLT1L|LTR|ERVL-MaLR	-253286	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.009501	0.412322	229(AGGGACATTCTGTTTT,-,0.00),230(GGGACATTCTGTTTTA,+,0.00)
chunk0043_297_1	chr12	21828719	21829155	+	0	NA	intron (NM_020297, intron 29 of 37)	intron (NM_020297, intron 29 of 37)	-54116	NM_004982	3764	Hs.102308	NM_004982	ENSG00000121361	KCNJ8	KIR6.1|uKATP-1	potassium voltage-gated channel subfamily J member 8	protein-coding	0.018349	0.377574	
chunk0184_192_1	chr7	116873653	116873914	+	0	NA	intron (NM_006136, intron 1 of 9)	intron (NM_006136, intron 1 of 9)	11274	NM_006136	830	Hs.446123	NM_006136	ENSG00000198898	CAPZA2	CAPPA2|CAPZ	capping actin protein of muscle Z-line subunit alpha 2	protein-coding	0.003831	0.416031	203(AGGTACATTCTGTACC,-,0.00),204(GGTACATTCTGTACCA,+,0.00)
chunk0093_69_1	chr19	40612287	40612594	+	0	NA	intron (NM_001042545, intron 15 of 29)	intron (NM_001042545, intron 15 of 29)	11069	NM_001042545	8425	Hs.466766	NM_003573	ENSG00000090006	LTBP4	ARCL1C|LTBP-4|LTBP4L|LTBP4S	latent transforming growth factor beta binding protein 4	protein-coding	0.000000	0.496753	
chunk0062_124_1	chr14	68475620	68476358	+	0	NA	intron (NM_133509, intron 10 of 10)	L2a|LINE|L2	317925	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.002710	0.355886	300(AAGAACTTCATGTTCT,-,0.00),301(AGAACTTCATGTTCTT,+,0.00)
chunk0198_457_1	chr8	144391094	144391337	+	0	NA	exon (NM_174922, exon 6 of 15)	exon (NM_174922, exon 6 of 15)	3015	NR_030635	100126351		NR_030635	ENSG00000284310	MIR939	MIRN939|hsa-mir-939|mir-939	microRNA 939	ncRNA	0.020576	0.622951	
chunk0100_305_1	chr2	115503133	115503779	+	0	NA	intron (NM_001178037, intron 4 of 25)	intron (NM_001178037, intron 4 of 25)	341349	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.009288	0.357032	
chunk0208_26_1	chrX	11075368	11075658	+	0	NA	Intergenic	MIR|SINE|MIR	-35773	NM_001171991	3052	Hs.211571	NM_005333	ENSG00000004961	HCCS	CCHL|LSDMCA1|MCOPS7|MLS	holocytochrome c synthase	protein-coding	0.003448	0.343643	
chunk0191_199_1	chr8	51884642	51885089	+	0	NA	intron (NM_052937, intron 1 of 5)	LTR41|LTR|ERVL	14321	NM_052937	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.002237	0.430804	316(TAGCACTCTCTGTACT,-,0.00),317(AGCACTCTCTGTACTT,+,0.00)
chunk0131_347_1	chr3	151572794	151573491	+	0	NA	Intergenic	L1PA6|LINE|L1	-7147	NR_049818	100847036		NR_049818	ENSG00000264330	MIR5186	-	microRNA 5186	ncRNA	0.007174	0.383954	
chunk0176_209_1	chr7	14761268	14761946	+	0	NA	intron (NM_145695, intron 1 of 23)	intron (NM_145695, intron 1 of 23)	79843	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.005900	0.440353	
chunk0176_454_1	chr7	20130027	20130240	+	0	NA	intron (NR_110114, intron 1 of 5)	intron (NR_110114, intron 1 of 5)	10293	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.000000	0.462617	66(CAGCACATTCTGTCTT,-,0.00),67(AGCACATTCTGTCTTT,+,0.00)
chunk0109_437_1	chr2	241370583	241371072	+	0	NA	intron (NM_014808, intron 1 of 26)	intron (NM_014808, intron 1 of 26)	14578	NM_001282983	9855	Hs.726316	NM_014808	ENSG00000006607	FARP2	FIR|FRG|PLEKHC3	FERM, ARH/RhoGEF and pleckstrin domain protein 2	protein-coding	0.008180	0.365306	
chunk0099_402_1	chr2	101999848	102000199	+	0	NA	intron (NR_048564, intron 1 of 8)	intron (NR_048564, intron 1 of 8)	1061	NR_048564	7850	Hs.25333	NM_004633	ENSG00000115590	IL1R2	CD121b|CDw121b|IL-1R-2|IL-1RT-2|IL-1RT2|IL1R2c|IL1RB	interleukin 1 receptor type 2	protein-coding	0.019943	0.392045	
chunk0134_166_1	chr3	177921618	177922079	+	0	NA	Intergenic	L1MA7|LINE|L1	104983	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.006508	0.305195	
chunk0058_366_1	chr14	29052105	29052315	+	0	NA	Intergenic	Intergenic	279506	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.004762	0.331754	
chunk0058_377_1	chr14	29340907	29341287	+	0	NA	Intergenic	Intergenic	568393	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.000000	0.309711	
chunk0092_8_1	chr19	18500956	18501187	+	0	NA	intron (NM_006532, intron 1 of 11)	intron (NM_006532, intron 1 of 11)	21056	NM_006532	8178	Hs.515260	NM_006532	ENSG00000105656	ELL	C19orf17|ELL1|MEN|PPP1R68	elongation factor for RNA polymerase II	protein-coding	0.034632	0.599138	
chunk0038_75_1	chr11	83126892	83127462	+	0	NA	Intergenic	Intergenic	-29918	NM_015885	51585	Hs.128959	NM_015885	ENSG00000165494	PCF11	-	PCF11 cleavage and polyadenylation factor subunit	protein-coding	0.012281	0.395797	159(GAAAACATTTTGTTCC,-,0.00),160(AAAACATTTTGTTCCA,+,0.00)
chunk0065_259_1	chr14	101749409	101749708	+	0	NA	Intergenic	L1PA6|LINE|L1	-12240	NM_001161725	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.003344	0.520000	
chunk0179_182_1	chr7	47026516	47027094	+	0	NA	Intergenic	MIR|SINE|MIR	555339	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.012111	0.452504	
chunk0065_404_1	chr14	105316870	105317485	+	0	NA	intron (NM_001100913, intron 1 of 24)	L1ME3E|LINE|L1	-1600	NM_001242786	2972	Hs.424484	NM_001519	ENSG00000185024	BRF1	BRF|BRF-1|CFDS|GTF3B|HEL-S-76p|TAF3B2|TAF3C|TAFIII90|TF3B90|TFIIIB90|hBRF	BRF1 RNA polymerase III transcription initiation factor subunit	protein-coding	0.037398	0.560065	412(GTGGACATCGTGTGCC,-,0.00),413(TGGACATCGTGTGCCA,+,0.00)
chunk0170_124_1	chr6	110712743	110712995	+	0	NA	intron (NM_015076, intron 2 of 12)	intron (NM_015076, intron 2 of 12)	-101752	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.007937	0.415020	148(GAGACATACTGTTCAT,+,0.00)
chunk0039_304_1	chr11	103043913	103044183	+	0	NA	Intergenic	Intergenic	48167	NM_032299	84259	Hs.503716	NM_032299	ENSG00000137692	DCUN1D5	SCCRO5	defective in cullin neddylation 1 domain containing 5	protein-coding	0.003704	0.391144	
chunk0196_112_1	chr8	103278307	103278842	+	0	NA	Intergenic	Intergenic	-19859	NM_001164615	8323	Hs.591863	NM_003506	ENSG00000164930	FZD6	FZ-6|FZ6|HFZ6|NDNC10	frizzled class receptor 6	protein-coding	0.000000	0.313433	276(CAGAACACACTGCACT,-,0.00),277(AGAACACACTGCACTG,+,0.00)
chunk0032_448_1	chr10	133121701	133121902	+	0	NA	intron (NM_001291085, intron 2 of 3)	(GT)n|Simple_repeat|Simple_repeat	19555	NM_001291085	84435	Hs.435183	NM_032422	ENSG00000197177	ADGRA1	GPR123	adhesion G protein-coupled receptor A1	protein-coding	0.034826	0.559406	
chunk0086_270_1	chr18	23612174	23612906	+	0	NA	intron (NM_173505, intron 8 of 9)	intron (NM_173505, intron 8 of 9)	-25923	NM_000271	4864	Hs.464779	NM_000271	ENSG00000141458	NPC1	NPC|POGZ|SLC65A1	NPC intracellular cholesterol transporter 1	protein-coding	0.013661	0.454297	
chunk0209_150_1	chrX	42560971	42561301	+	0	NA	Intergenic	Intergenic	217099	NR_002191									0.009091	0.377644	
chunk0135_110_1	chr3	186916057	186916363	+	0	NA	Intergenic	Intergenic	-14316	NM_173216	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.016340	0.482085	
chunk0157_314_1	chr5	121961924	121962123	+	0	NA	promoter-TSS (NM_152546)	promoter-TSS (NM_152546)	62	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.070352	0.570000	
chunk0017_26_1	chr1	204536336	204536949	+	0	NA	intron (NM_001278518, intron 5 of 6)	intron (NM_001278518, intron 5 of 6)	20263	NM_001278516	4194	Hs.497492	NM_002393	ENSG00000198625	MDM4	HDMX|MDMX|MRP1	MDM4 regulator of p53	protein-coding	0.006525	0.319218	
chunk0094_83_1	chr2	3783814	3784289	+	0	NA	intron (NM_001287444, intron 9 of 10)	L1M5|LINE|L1	80459	NM_001287444	728597	Hs.304233	NM_001287444	ENSG00000214866	DCDC2C	-	doublecortin domain containing 2C	protein-coding	0.000000	0.275210	
chunk0015_355_1	chr1	190251832	190252154	+	0	NA	intron (NM_199051, intron 4 of 7)	intron (NM_199051, intron 4 of 7)	225636	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.284830	133(AAAACATTGAGTTCTT,+,0.00)
chunk0193_242_1	chr8	76818323	76818522	+	0	NA	intron (NM_024721, intron 4 of 10)	intron (NM_024721, intron 4 of 10)	-135147	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.015075	0.335000	
chunk0127_294_1	chr3	97957619	97957972	+	0	NA	intron (NM_153182, intron 4 of 9)	intron (NM_153182, intron 4 of 9)	14656	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.019830	0.466102	
chunk0090_459_1	chr18	80176633	80177033	+	0	NA	intron (NR_028340, intron 2 of 2)	intron (NR_028340, intron 2 of 2)	28909	NR_028339	100130522	Hs.352602	NM_001145731	ENSG00000267270	PARD6G-AS1	-	PARD6G antisense RNA 1	ncRNA	0.037500	0.518703	
chunk0107_13_1	chr2	210170163	210170672	+	0	NA	intron (NM_001307976, intron 1 of 13)	intron (NM_001307976, intron 1 of 13)	953	NM_001307976	151050	Hs.282260	NM_152519	ENSG00000144445	KANSL1L	C2orf67|MSL1v2	KAT8 regulatory NSL complex subunit 1 like	protein-coding	0.025540	0.439216	
chunk0048_273_1	chr12	82358469	82358699	+	0	NA	promoter-TSS (NM_032230)	promoter-TSS (NM_032230)	87	NM_032230	84190	Hs.506222	NM_032230	ENSG00000127720	METTL25	C12orf26	methyltransferase like 25	protein-coding	0.056522	0.614719	
chunk0058_305_1	chr14	27073495	27073956	+	0	NA	Intergenic	Intergenic	165083	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.002169	0.350649	
chunk0187_148_1	chr7	149727173	149727372	+	0	NA	intron (NM_032534, intron 11 of 16)	intron (NM_032534, intron 11 of 16)	12261	NM_001290187	84626	Hs.299560	NM_032534	ENSG00000133619	KRBA1	-	KRAB-A domain containing 1	protein-coding	0.015075	0.610000	
chunk0205_382_1	chr9	114112990	114113729	+	0	NA	Intergenic	Intergenic	-14302	NM_138424	113220	Hs.28149	NM_138424	ENSG00000136883	KIF12	-	kinesin family member 12	protein-coding	0.014885	0.556757	317(GAGGACACCAAGTTCC,-,0.00),318(AGGACACCAAGTTCCC,+,0.00)
chunk0152_270_1	chr5	61246054	61246374	+	0	NA	Intergenic	Intergenic	-83739	NM_001048249	643155	Hs.508479	NM_001048249	ENSG00000188725	SMIM15	C5orf43	small integral membrane protein 15	protein-coding	0.006250	0.476636	
chunk0096_129_1	chr2	28661377	28662019	+	0	NA	Intergenic	Intergenic	-90050	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.007788	0.477449	351(GGAGACATTCTGTTCT,-,0.00),352(GAGACATTCTGTTCTG,+,0.00)
chunk0019_343_1	chr1	229380113	229380392	+	0	NA	Intergenic	Intergenic	-37311	NM_145257	126731	Hs.585011	NM_145257	ENSG00000154429	CCSAP	C1orf96|CSAP	centriole, cilia and spindle associated protein	protein-coding	0.021505	0.532143	242(CAGAACGGGTTGTTCC,-,0.00),243(AGAACGGGTTGTTCCC,+,0.00)
chunk0021_201_1	chr10	5834218	5834787	+	0	NA	Intergenic	L2b|LINE|L2	-20953	NM_001494	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.014060	0.508772	
chunk0023_213_1	chr10	25549221	25549500	+	0	NA	intron (NM_020752, intron 5 of 10)	intron (NM_020752, intron 5 of 10)	-102352	NR_108067	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.003584	0.342857	
chunk0203_371_1	chr9	90020321	90020558	+	0	NA	TTS (NR_038882)	TTS (NR_038882)	3096	NR_036253	100422963		NR_036253	ENSG00000263967	MIR4290	-	microRNA 4290	ncRNA	0.012658	0.445378	59(TGGTGCAGGCTGTTCC,-,0.00),60(GGTGCAGGCTGTTCCT,+,0.00)
chunk0119_86_1	chr22	41512737	41513144	+	0	NA	intron (NM_001098, intron 4 of 17)	intron (NM_001098, intron 4 of 17)	31549	NM_001018052	171568	Hs.712617	NM_138338	ENSG00000100413	POLR3H	RPC22.9|RPC8	RNA polymerase III subunit H	protein-coding	0.022113	0.578431	
chunk0085_432_1	chr18	10750595	10751046	+	0	NA	intron (NM_022068, intron 26 of 51)	intron (NM_022068, intron 26 of 51)	8829	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.006652	0.407080	
chunk0026_143_1	chr10	62293603	62293827	+	0	NA	Intergenic	Intergenic	-24852	NM_145307	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.004464	0.346667	
chunk0137_9_1	chr4	10649821	10650237	+	0	NA	intron (NM_052964, intron 2 of 18)	intron (NM_052964, intron 2 of 18)	34733	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.000000	0.304556	194(ATGAACAAAGTGTACA,-,0.00),195(TGAACAAAGTGTACAT,+,0.00)
chunk0107_72_1	chr2	212282559	212283224	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	143469	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.004511	0.385886	
chunk0150_379_1	chr5	39392631	39393138	+	0	NA	intron (NM_001343, intron 3 of 14)	intron (NM_001343, intron 3 of 14)	-28331	NM_001737	735	Hs.654443	NM_001737	ENSG00000113600	C9	ARMD15|C9D	complement C9	protein-coding	0.013807	0.381890	
chunk0066_6_1	chr15	26900938	26901759	+	0	NA	intron (NM_001165037, intron 6 of 10)	L1MD3|LINE|L1	34222	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.006090	0.346715	
chunk0193_320_1	chr8	78615376	78615633	+	0	NA	Intergenic	Intergenic	-50543	NM_016010	51101	Hs.271876	NM_016010	ENSG00000104427	ZC2HC1A	C8orf70|CGI-62|FAM164A	zinc finger C2HC-type containing 1A	protein-coding	0.000000	0.360465	
chunk0131_206_1	chr3	148843664	148843863	+	0	NA	intron (NM_001871, intron 6 of 10)	intron (NM_001871, intron 6 of 10)	15962	NM_001871	1360	Hs.477891	NM_001871	ENSG00000153002	CPB1	CPB|PASP|PCPB	carboxypeptidase B1	protein-coding	0.005025	0.365000	
chunk0100_366_1	chr2	117958142	117958663	+	0	NA	exon (NM_019044, exon 12 of 24)	exon (NM_019044, exon 12 of 24)	55761	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.011516	0.431034	
chunk0167_168_1	chr6	63140685	63141382	+	0	NA	Intergenic	L1M1|LINE|L1	178944	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.002869	0.438395	
chunk0095_297_1	chr2	20282901	20283210	+	0	NA	exon (NM_001282791, exon 12 of 20)	exon (NM_001282791, exon 12 of 20)	44331	NM_001282791	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.006472	0.454839	
chunk0045_69_1	chr12	45623834	45624033	+	0	NA	Intergenic	Intergenic	103988	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.000000	0.440000	163(AGGAACAATGTGTTCT,-,0.00),164(GGAACAATGTGTTCTC,+,0.00)
chunk0117_126_1	chr22	19089363	19089620	+	0	NA	intron (NM_005137, intron 1 of 9)	intron (NM_005137, intron 1 of 9)	32963	NM_001184781	9993	Hs.517357	NM_005137	ENSG00000070413	DGCR2	DGS-C|IDD|LAN|SEZ-12	DiGeorge syndrome critical region gene 2	protein-coding	0.035019	0.565891	
chunk0163_52_1	chr6	8767895	8768192	+	0	NA	intron (NR_038980, intron 3 of 4)	intron (NR_038980, intron 3 of 4)	115834	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.003367	0.335570	
chunk0040_369_1	chr11	118919848	118920123	+	0	NA	Intergenic	Intergenic	-9081	NM_182557	283149	Hs.414740	NM_182557	ENSG00000186174	BCL9L	B9L|BCL9-2|DLNB11	BCL9 like	protein-coding	0.014545	0.565217	
chunk0155_218_1	chr5	95304652	95305110	+	0	NA	Intergenic	MIRc|SINE|MIR	-20306	NM_024717	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.004367	0.339869	
chunk0103_233_1	chr2	164693318	164693892	+	0	NA	intron (NM_001278460, intron 12 of 13)	intron (NM_001278460, intron 12 of 13)	-5828	NR_033309	100337591	Hs.664357	NR_033309	ENSG00000206869	SNORA70F	U70F	small nucleolar RNA, H/ACA box 70F	snoRNA	0.000000	0.281739	
chunk0208_385_1	chrX	28741341	28741902	+	0	NA	intron (NM_014271, intron 1 of 10)	intron (NM_014271, intron 1 of 10)	154057	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.003565	0.318505	
chunk0195_339_1	chr8	99391986	99392198	+	0	NA	intron (NM_152564, intron 21 of 61)	LTR40a|LTR|ERVL	144638	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.014151	0.422535	
chunk0055_302_1	chr13	66301527	66301937	+	0	NA	Intergenic	Intergenic	83482	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.000000	0.299270	
chunk0110_435_1	chr20	20827098	20827517	+	0	NA	Intergenic	Intergenic	-114684	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.019093	0.526190	204(AAGAACATTCTGGACC,-,0.00)
chunk0073_151_1	chr16	6629030	6629616	+	0	NA	intron (NM_018723, intron 2 of 15)	intron (NM_018723, intron 2 of 15)	-144486	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.010239	0.349233	
chunk0091_5_1	chr19	2576223	2576422	+	0	NA	intron (NM_052847, intron 2 of 4)	intron (NM_052847, intron 2 of 4)	-54393	NR_107004	102465838		NR_107004	ENSG00000277904	MIR7850	hsa-mir-7850	microRNA 7850	ncRNA	0.055276	0.655000	105(CTGCACACGGTGTGCT,-,0.00),106(TGCACACGGTGTGCTG,+,0.00)
chunk0067_289_1	chr15	47437091	47437478	+	0	NA	intron (NM_001198999, intron 2 of 19)	intron (NM_001198999, intron 2 of 19)	253078	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.000000	0.353093	
chunk0013_406_1	chr1	173053831	173054447	+	0	NA	Intergenic	MIRb|SINE|MIR	-3176	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.003247	0.358185	
chunk0132_178_1	chr3	156958302	156958804	+	0	NA	intron (NM_001004316, intron 6 of 12)	intron (NM_001004316, intron 6 of 12)	-131328	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.003984	0.417495	
chunk0144_394_1	chr4	140184153	140184352	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-30173	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.005025	0.450000	
chunk0169_279_1	chr6	105609523	105609926	+	0	NA	Intergenic	Intergenic	-206600	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.029777	0.519802	
chunk0207_196_1	chr9	131068038	131068574	+	0	NA	intron (NM_006059, intron 15 of 27)	intron (NM_006059, intron 15 of 27)	-28170	NR_033701	83543	Hs.4944	NM_031426	ENSG00000126878	AIF1L	C9orf58|IBA2	allograft inflammatory factor 1 like	protein-coding	0.020522	0.623836	307(AGGCACATTGTGCCCT,-,0.00),308(GGCACATTGTGCCCTT,+,0.00)
chunk0011_344_1	chr1	152227336	152227541	+	0	NA	Intergenic	Intergenic	-3242	NM_001009931	388697	Hs.490162	NM_001009931	ENSG00000197915	HRNR	FLG3|S100A16|S100a18	hornerin	protein-coding	0.000000	0.412621	
chunk0175_201_1	chr7	5997246	5997705	+	0	NA	intron (NR_003085, intron 6 of 14)	intron (NR_003085, intron 6 of 14)	11631	NR_003085									0.015251	0.400000	
chunk0180_352_1	chr7	73665209	73665614	+	0	NA	Intergenic	L2b|LINE|L2	-2433	NM_001077621	155382	Hs.647037	NM_152560	ENSG00000176428	VPS37D	WBSCR24	VPS37D subunit of ESCRT-I	protein-coding	0.007407	0.438424	
chunk0043_121_1	chr12	15627394	15628049	+	0	NA	intron (NM_004447, intron 18 of 20)	intron (NM_004447, intron 18 of 20)	81377	NM_030668	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.006107	0.347561	
chunk0042_260_1	chr12	6688965	6689434	+	0	NA	5' UTR (NM_133476, exon 1 of 10)	5' UTR (NM_133476, exon 1 of 10)	176	NM_133476	171017	Hs.103315	NM_133476	ENSG00000126746	ZNF384	CAGH1|CAGH1A|CIZ|ERDA2|NMP4|NP|TNRC1	zinc finger protein 384	protein-coding	0.100213	0.717021	
chunk0126_107_1	chr3	75099790	75100259	+	0	NA	Intergenic	L1MA3|LINE|L1	-114452	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.000000	0.331915	
chunk0027_11_1	chr10	72097825	72098293	+	0	NA	intron (NM_001198800, intron 9 of 9)	intron (NM_001198800, intron 9 of 9)	-9027	NM_001134434	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.012821	0.411514	
chunk0158_263_1	chr5	131159946	131160698	+	0	NA	intron (NR_024611, intron 2 of 2)	intron (NR_024611, intron 2 of 2)	5026	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.006649	0.420983	
chunk0014_174_1	chr1	178407348	178407684	+	0	NA	intron (NM_170692, intron 4 of 17)	intron (NM_170692, intron 4 of 17)	66045	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.002976	0.311573	
chunk0079_370_1	chr17	18055470	18056070	+	0	NA	intron (NM_024052, intron 3 of 5)	AluJr|SINE|Alu	16473	NM_024052	79018	Hs.187422	NM_024052	ENSG00000141034	GID4	C17orf39|VID2|VID24	GID complex subunit 4 homolog	protein-coding	0.016667	0.457571	
chunk0066_251_1	chr15	34684198	34684803	+	0	NA	Intergenic	MER63B|DNA|hAT-Blackjack	70081	NM_020660	57369	Hs.283816	NM_020660	ENSG00000159248	GJD2	CX36|GJA9	gap junction protein delta 2	protein-coding	0.004959	0.417492	
chunk0088_435_1	chr18	55732154	55732644	+	0	NA	Intergenic	Intergenic	-96406	NM_001243226	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.002041	0.405295	233(GAGAACAAGCTGTTTC,-,0.00),234(AGAACAAGCTGTTTCT,+,0.00)
chunk0131_38_1	chr3	142500766	142501774	+	0	NA	intron (NM_001184, intron 30 of 46)	intron (NM_001184, intron 30 of 46)	-53208	NM_001282859	54464	Hs.435103	NM_019001	ENSG00000114127	XRN1	SEP1	5'-3' exoribonuclease 1	protein-coding	0.003968	0.353816	
chunk0033_132_1	chr11	14892285	14892600	+	0	NA	promoter-TSS (NM_024514)	promoter-TSS (NM_024514)	-237	NM_024514	120227	Hs.371427	NM_024514	ENSG00000186104	CYP2R1	-	cytochrome P450 family 2 subfamily R member 1	protein-coding	0.050794	0.579114	
chunk0071_156_1	chr15	82919205	82920025	+	0	NA	intron (NM_199330, intron 1 of 8)	intron (NM_199330, intron 1 of 8)	33109	NM_004839	9455	Hs.578443	NM_004839	ENSG00000103942	HOMER2	ACPD|CPD|DFNA68|HOMER-2|VESL-2	homer scaffold protein 2	protein-coding	0.009756	0.416565	144(AAGGACAGGTTGGCCT,-,0.00)
chunk0094_25_1	chr2	1462577	1462841	+	0	NA	intron (NM_175722, intron 6 of 14)	intron (NM_175722, intron 6 of 14)	48301	NM_175721	7173	Hs.467554	NM_000547	ENSG00000115705	TPO	MSA|TDH2A|TPX	thyroid peroxidase	protein-coding	0.011364	0.358491	
chunk0044_183_1	chr12	30335974	30336422	+	0	NA	Intergenic	Intergenic	341046	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.006696	0.454343	
chunk0183_160_1	chr7	105972957	105973161	+	0	NA	intron (NM_001301161, intron 1 of 17)	intron (NM_001301161, intron 1 of 17)	9848	NM_152750	222256	Hs.150120	NM_152750	ENSG00000128536	CDHR3	CDH28	cadherin related family member 3	protein-coding	0.009804	0.507317	
chunk0102_245_1	chr2	149027765	149028279	+	0	NA	Intergenic	Intergenic	-10445	NM_001317003	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.011673	0.444660	
chunk0176_240_1	chr7	16026247	16026459	+	0	NA	Intergenic	Intergenic	-184133	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.009434	0.338028	
chunk0032_380_1	chr11	11345027	11345336	+	0	NA	intron (NM_198516, intron 6 of 10)	intron (NM_198516, intron 6 of 10)	8176	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.006472	0.541935	
chunk0083_451_1	chr17	73187330	73187573	+	0	NA	Intergenic	Intergenic	-5583	NM_018714	9382	Hs.103555	NM_018714	ENSG00000166685	COG1	CDG2G|LDLB	component of oligomeric golgi complex 1	protein-coding	0.012346	0.463115	
chunk0011_401_1	chr1	154186770	154187359	+	0	NA	TTS (NR_103460)	TTS (NR_103460)	-3815	NM_001043353	7170	Hs.535581	NM_152263	ENSG00000143549	TPM3	CAPM1|CFTD|HEL-189|HEL-S-82p|NEM1|OK/SW-cl.5|TM-5|TM3|TM30|TM30nm|TM5|TPM3nu|TPMsk3|TRK|hscp30	tropomyosin 3	protein-coding	0.005093	0.401695	
chunk0013_413_1	chr1	173172143	173172567	+	0	NA	Intergenic	Intergenic	33203	NM_001297562	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.002358	0.512941	
chunk0044_225_1	chr12	31388524	31389059	+	0	NA	intron (NM_001308339, intron 22 of 22)	intron (NM_001308339, intron 22 of 22)	-62566	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.005607	0.358209	
chunk0200_142_1	chr9	18040401	18040687	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-433537	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.006993	0.418118	
chunk0211_199_1	chrX	117947381	117947716	+	0	NA	intron (NM_001168303, intron 1 of 6)	Tigger10|DNA|TcMar-Tigger	26190	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.002985	0.312500	
chunk0066_349_1	chr15	37969466	37970053	+	0	NA	Intergenic	L1PA15|LINE|L1	35152	NM_152453	145942	Hs.179646	NM_152453	ENSG00000166069	TMCO5A	TMCO5	transmembrane and coiled-coil domains 5A	protein-coding	0.001704	0.375850	303(AAGAACATGCAGTACT,-,0.00),304(AGAACATGCAGTACTT,+,0.00)
chunk0014_53_1	chr1	175340784	175341289	+	0	NA	intron (NM_003285, intron 18 of 22)	intron (NM_003285, intron 18 of 22)	-147943	NM_001162894	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.005941	0.446640	
chunk0077_178_1	chr16	79644694	79644950	+	0	NA	Intergenic	Intergenic	-44097	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.007812	0.377432	
chunk0179_188_1	chr7	47153518	47153718	+	0	NA	Intergenic	Intergenic	428526	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.020000	0.462687	
chunk0027_46_1	chr10	72787919	72788477	+	0	NA	intron (NR_073062, intron 3 of 9)	intron (NR_073062, intron 3 of 9)	67169	NR_039823	100616286		NR_039823	ENSG00000266719	MIR4676	-	microRNA 4676	ncRNA	0.014337	0.449016	
chunk0145_248_1	chr4	148788007	148788269	+	0	NA	Intergenic	Intergenic	-345618	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.000000	0.372624	
chunk0176_322_1	chr7	17046805	17047172	+	0	NA	Intergenic	(TCCTATG)n|Simple_repeat|Simple_repeat	-164999	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.013624	0.361413	
chunk0078_135_1	chr17	3668238	3668897	+	0	NA	promoter-TSS (NM_031298)	promoter-TSS (NM_031298)	112	NM_014604	30851	Hs.12956	NM_014604	ENSG00000213977	TAX1BP3	TIP-1|TIP1	Tax1 binding protein 3	protein-coding	0.113809	0.700000	
chunk0201_80_1	chr9	34503212	34503846	+	0	NA	intron (NM_001281428, intron 12 of 19)	intron (NM_001281428, intron 12 of 19)	19510	NM_198573	375704	Hs.522085	NM_198573	ENSG00000168913	ENHO	C9orf165|UNQ470	energy homeostasis associated	protein-coding	0.001577	0.513386	
chunk0099_408_1	chr2	102131527	102131980	+	0	NA	intron (NM_001288706, intron 1 of 11)	L1MEc|LINE|L1	-11023	NM_000877	3554	Hs.701982	NM_000877	ENSG00000115594	IL1R1	CD121A|D2S1473|IL-1R-alpha|IL1R|IL1RA|P80	interleukin 1 receptor type 1	protein-coding	0.011038	0.345815	
chunk0205_254_1	chr9	110743022	110743318	+	0	NA	intron (NM_001166281, intron 6 of 11)	intron (NM_001166281, intron 6 of 11)	74399	NM_005592	4593	Hs.521653	NM_005592	ENSG00000030304	MUSK	CMS9|FADS|FADS1	muscle associated receptor tyrosine kinase	protein-coding	0.016892	0.447811	
chunk0152_369_1	chr5	64320480	64320708	+	0	NA	intron (NM_001113561, intron 5 of 7)	HAL1ME|LINE|L1	154750	NM_178532	285671	Hs.657843	NM_178532	ENSG00000164197	RNF180	RINES	ring finger protein 180	protein-coding	0.004386	0.327511	
chunk0205_409_1	chr9	114804452	114804894	+	0	NA	intron (NM_005118, intron 1 of 3)	intron (NM_005118, intron 1 of 3)	1455	NM_005118	9966	Hs.23349	NM_005118	ENSG00000181634	TNFSF15	TL1|TL1A|TNLG1B|VEGI|VEGI192A	TNF superfamily member 15	protein-coding	0.011312	0.483070	
chunk0139_214_1	chr4	55015776	55016365	+	0	NA	Intergenic	Intergenic	109525	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.006791	0.359322	262(AAGAACATTGTGTTCT,-,0.00),263(AGAACATTGTGTTCTG,+,0.00)
chunk0102_367_1	chr2	152780963	152781491	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	63334	NR_024526	151188	Hs.643580	NM_152522	ENSG00000177917	ARL6IP6	AIP-6|AIP6|PFAAP1	ADP ribosylation factor like GTPase 6 interacting protein 6	protein-coding	0.007576	0.459357	
chunk0086_369_1	chr18	26090484	26091020	+	0	NA	promoter-TSS (NM_005637)	promoter-TSS (NM_005637)	-105	NM_005637	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.089552	0.681564	
chunk0030_289_1	chr10	117222974	117223173	+	0	NA	Intergenic	Intergenic	-18000	NM_003054	6571	Hs.596992	NM_003054	ENSG00000165646	SLC18A2	PKDYS2|SVAT|SVMT|VAT2|VMAT2	solute carrier family 18 member A2	protein-coding	0.010050	0.480000	
chunk0153_55_1	chr5	67635867	67636627	+	0	NA	Intergenic	Intergenic	-156966	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.003947	0.467806	
chunk0076_319_1	chr16	70582517	70583038	+	0	NA	intron (NM_001172771, intron 1 of 6)	intron (NM_001172771, intron 1 of 6)	2882	NM_001172771	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.011516	0.530651	
chunk0005_191_1	chr1	58922174	58922830	+	0	NA	Intergenic	Intergenic	-97974	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.021341	0.508371	288(CAGAACAAGCTGTTTC,-,0.00),289(AGAACAAGCTGTTTCA,+,0.00)
chunk0098_72_1	chr2	67277363	67277772	+	0	NA	intron (NR_110564, intron 3 of 4)	intron (NR_110564, intron 3 of 4)	-62248	NR_038844	644838	Hs.145561	NR_038844	ENSG00000236780	LINC01829	-	long intergenic non-protein coding RNA 1829	ncRNA	0.012225	0.482927	202(CAGAACAGGGAGTTCT,-,0.00),203(AGAACAGGGAGTTCTT,+,0.00)
chunk0199_56_1	chr9	1966560	1966941	+	0	NA	Intergenic	Intergenic	-48469	NM_001289397	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.005249	0.350785	
chunk0041_126_1	chr11	125039596	125040162	+	0	NA	intron (NM_025004, intron 15 of 15)	intron (NM_025004, intron 15 of 15)	-23238	NM_001145290	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.012367	0.403880	
chunk0162_3_1	chr6	264557	265073	+	0	NA	Intergenic	L1MB4|LINE|L1	-27242	NM_001286555	56940	Hs.29106	NM_020185	ENSG00000112679	DUSP22	JKAP|JSP-1|JSP1|LMW-DSP2|LMWDSP2|MKP-x|MKPX|VHX	dual specificity phosphatase 22	protein-coding	0.003876	0.315280	
chunk0160_9_1	chr5	148976811	148977092	+	0	NA	Intergenic	Intergenic	85458	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.003559	0.425532	
chunk0153_184_1	chr5	71625030	71625507	+	0	NA	intron (NM_022132, intron 6 of 16)	intron (NM_022132, intron 6 of 16)	37980	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.000000	0.366109	225(CTGAACTCAGTGTTCT,-,0.00),226(TGAACTCAGTGTTCTG,+,0.00)
chunk0042_379_1	chr12	10636062	10636528	+	0	NA	intron (NM_018423, intron 2 of 10)	intron (NM_018423, intron 2 of 10)	-22686	NM_018048	55110	Hs.104650	NM_018048	ENSG00000111196	MAGOHB	MGN2|mago|magoh	mago homolog B, exon junction complex subunit	protein-coding	0.006438	0.402570	
chunk0101_129_1	chr2	127143848	127144480	+	0	NA	Intergenic	MIR|SINE|MIR	-36837	NM_139351	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.014241	0.477093	246(AGGAACGCTGTGTACC,-,0.00),247(GGAACGCTGTGTACCA,+,0.00)
chunk0114_301_1	chr21	16978493	16978762	+	0	NA	Intergenic	LTR41|LTR|ERVL	388390	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.011152	0.544444	
chunk0079_269_1	chr17	16215550	16215813	+	0	NA	promoter-TSS (NM_006311)	promoter-TSS (NM_006311)	-121	NM_006311	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.114068	0.738636	
chunk0151_127_1	chr5	43909261	43909519	+	0	NA	Intergenic	L1P2|LINE|L1	-306160	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.015504	0.501931	
chunk0169_360_1	chr6	106782348	106782869	+	0	NA	intron (NR_033557, intron 1 of 6)	intron (NR_033557, intron 1 of 6)	-1517	NR_030314	693172		NR_030314	ENSG00000207577	MIR587	MIRN587|hsa-mir-587	microRNA 587	ncRNA	0.017274	0.503831	
chunk0001_112_1	chr1	3767632	3768016	+	0	NA	intron (NM_152492, intron 10 of 11)	MIR|SINE|MIR	-4937	NM_001288583	388588	Hs.22047	NM_001163724	ENSG00000235169	SMIM1	Vel	small integral membrane protein 1 (Vel blood group)	protein-coding	0.018229	0.537662	
chunk0039_19_1	chr11	95590008	95590619	+	0	NA	Intergenic	Intergenic	199477	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.016367	0.444444	122(GGGAACAAACTGTGCT,-,0.00),123(GGAACAAACTGTGCTG,+,0.00)
chunk0130_168_1	chr3	133077727	133077935	+	0	NA	intron (NM_001136469, intron 2 of 5)	intron (NM_001136469, intron 2 of 5)	39543	NM_023943	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.014423	0.502392	
chunk0035_151_1	chr11	43062525	43063041	+	0	NA	Intergenic	Intergenic	206586	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.001938	0.402321	
chunk0116_273_1	chr21	39313639	39313976	+	0	NA	promoter-TSS (NM_033656)	promoter-TSS (NM_033656)	-21	NM_033656	54014	Hs.627139	NM_018963	ENSG00000185658	BRWD1	C21orf107|DCAF19|N143|WDR9|WRD9	bromodomain and WD repeat domain containing 1	protein-coding	0.121662	0.724852	
chunk0189_222_1	chr8	24386295	24386602	+	0	NA	intron (NM_001145272, intron 1 of 12)	L5|LINE|RTE-X	2163	NM_001145271	27299	Hs.521459	NM_014479	ENSG00000134028	ADAMDEC1	M12.219	ADAM like decysin 1	protein-coding	0.006515	0.392857	
chunk0102_80_1	chr2	143294008	143294453	+	0	NA	intron (NM_018460, intron 6 of 13)	intron (NM_018460, intron 6 of 13)	164900	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.002247	0.327354	
chunk0133_201_1	chr3	170809875	170810263	+	0	NA	Intergenic	Intergenic	60187	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.002577	0.370180	
chunk0131_213_1	chr3	149004641	149005215	+	0	NA	intron (NM_004130, intron 4 of 7)	Charlie17a|DNA|hAT-Charlie	13520	NM_004130	2992	Hs.477892	NM_004130	ENSG00000163754	GYG1	GSD15|GYG	glycogenin 1	protein-coding	0.006969	0.413913	
chunk0167_418_1	chr6	75480537	75480813	+	0	NA	intron (NR_110608, intron 1 of 1)	intron (NR_110608, intron 1 of 1)	13154	NM_001289987	27145	Hs.201488	NM_015687	ENSG00000118407	FILIP1	FILIP	filamin A interacting protein 1	protein-coding	0.000000	0.379061	
chunk0207_358_1	chr9	135309229	135309456	+	0	NA	Intergenic	Intergenic	-33907	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.026432	0.631579	
chunk0120_235_1	chr3	8444278	8444805	+	0	NA	intron (NR_033378, intron 3 of 3)	intron (NR_033378, intron 3 of 3)	57117	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.022770	0.490530	
chunk0051_27_1	chr12	111900039	111900277	+	0	NA	non-coding (NR_036636, exon 1 of 1)	non-coding (NR_036636, exon 1 of 1)	1095	NR_036636	8759	Hs.661708	NR_036636		ADAM1A	ADAM1|ADAM1P|FTNAP|Ftna|PH-30a	ADAM metallopeptidase domain 1A (pseudogene)	pseudo	0.016807	0.502092	
chunk0018_284_1	chr1	220709499	220709698	+	0	NA	Intergenic	MER21B|LTR|ERVL	19312	NM_024709	79762	Hs.519839	NM_024709	ENSG00000162817	C1orf115	-	chromosome 1 open reading frame 115	protein-coding	0.010050	0.470000	
chunk0072_9_1	chr16	379347	379820	+	0	NA	intron (NM_021259, intron 1 of 12)	intron (NM_021259, intron 1 of 12)	2367	NM_021259	58986	Hs.288940	NM_021259	ENSG00000129925	TMEM8A	GPI-PLA2|M83|PGAP6|TMEM6|TMEM8	transmembrane protein 8A	protein-coding	0.023256	0.658228	190(AGGACCACGGTGTCCC,-,0.00),191(GGACCACGGTGTCCCG,+,0.00)
chunk0003_62_1	chr1	31170768	31171115	+	0	NA	Intergenic	Intergenic	68946	NM_024522	79570	Hs.470259	NM_024522	ENSG00000084628	NKAIN1	FAM77C	sodium/potassium transporting ATPase interacting 1	protein-coding	0.008646	0.571839	
chunk0070_3_1	chr15	68787447	68788195	+	0	NA	exon (NM_006305, exon 2 of 7)	exon (NM_006305, exon 2 of 7)	14104	NR_036197	100422971		NR_036197	ENSG00000265195	MIR4312	-	microRNA 4312	ncRNA	0.028075	0.512684	
chunk0075_132_1	chr16	50182162	50182935	+	0	NA	intron (NM_001040284, intron 2 of 12)	intron (NM_001040284, intron 2 of 12)	29630	NM_001040284	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.006468	0.334625	
chunk0023_206_1	chr10	25343294	25343779	+	0	NA	intron (NM_020752, intron 2 of 10)	intron (NM_020752, intron 2 of 10)	-167260	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.002062	0.318930	
chunk0207_424_1	chr9	137250095	137250536	+	0	NA	promoter-TSS (NM_001256700)	promoter-TSS (NM_001256700)	-946	NM_001256701	441476	Hs.372640	NM_001004353	ENSG00000197768	STPG3	C9orf173	sperm-tail PG-rich repeat containing 3	protein-coding	0.029478	0.606335	220(AAGTACACTCTGTTCC,-,0.00),221(AGTACACTCTGTTCCA,+,0.00)
chunk0201_376_1	chr9	68803529	68803954	+	0	NA	intron (NM_003558, intron 2 of 15)	intron (NM_003558, intron 2 of 15)	23693	NM_138333	116224	Hs.655572	NM_138333	ENSG00000187866	FAM122A	C9orf42	family with sequence similarity 122A	protein-coding	0.007059	0.460094	
chunk0051_88_1	chr12	114527296	114527517	+	0	NA	Intergenic	Intergenic	-118964	NM_000192	6910	Hs.381715	NM_000192	ENSG00000089225	TBX5	HOS	T-box transcription factor 5	protein-coding	0.000000	0.418919	
chunk0138_24_1	chr4	30875056	30875362	+	0	NA	intron (NM_032457, intron 1 of 2)	MLT1B|LTR|ERVL-MaLR	154794	NM_002589	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.016340	0.420195	
chunk0201_367_1	chr9	68631929	68632199	+	0	NA	Intergenic	Intergenic	-73350	NM_003558	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.000000	0.450185	
chunk0189_340_1	chr8	26606863	26607131	+	0	NA	intron (NM_001244604, intron 3 of 13)	L1ME4a|LINE|L1	28592	NM_001244604	1808	Hs.593187	NM_001386	ENSG00000092964	DPYSL2	CRMP-2|CRMP2|DHPRP2|DRP-2|DRP2|N2A3|ULIP-2|ULIP2	dihydropyrimidinase like 2	protein-coding	0.007463	0.345725	
chunk0027_325_1	chr10	78328066	78328427	+	0	NA	Intergenic	L1MA4A|LINE|L1	60918	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.008310	0.549724	
chunk0156_382_1	chr5	112957305	112957795	+	0	NA	Intergenic	Intergenic	-19160	NM_001242377	167227	Hs.443875	NM_152624	ENSG00000172795	DCP2	NUDT20	decapping mRNA 2	protein-coding	0.004082	0.336049	
chunk0022_275_1	chr10	15123746	15124133	+	0	NA	intron (NM_001308295, intron 9 of 12)	intron (NM_001308295, intron 9 of 12)	-26620	NM_153244	221060	Hs.567777	NM_153244		RPP38-DT	C10orf111	RPP38 divergent transcript	ncRNA	0.007752	0.378866	
chunk0128_300_1	chr3	111423041	111423342	+	0	NA	Intergenic	L1PB3|LINE|L1	-118888	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.000000	0.350993	
chunk0159_128_1	chr5	139061287	139061574	+	0	NA	intron (NM_001037633, intron 4 of 10)	intron (NM_001037633, intron 4 of 10)	136946	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.010453	0.527778	82(AAGGACAGGATGTCCT,-,0.00),83(AGGACAGGATGTCCTC,+,0.00)
chunk0004_274_1	chr1	48405287	48405901	+	0	NA	intron (NM_019073, intron 5 of 12)	MLT1F1|LTR|ERVL-MaLR	66614	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.004886	0.391870	
chunk0077_259_1	chr16	80934608	80934864	+	0	NA	Intergenic	L2b|LINE|L2	-42140	NR_131947	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.007812	0.478599	
chunk0197_184_1	chr8	121322688	121323057	+	0	NA	Intergenic	L1M5|LINE|L1	-316474	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.008130	0.294595	
chunk0063_181_1	chr14	80587900	80588664	+	0	NA	intron (NM_152446, intron 18 of 23)	intron (NM_152446, intron 18 of 23)	351258	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.002618	0.341176	
chunk0031_95_1	chr10	123744646	123745002	+	0	NA	TTS (NM_198148)	TTS (NM_198148)	78469	NM_153442	2849	Hs.12751	NM_153442	ENSG00000154478	GPR26	-	G protein-coupled receptor 26	protein-coding	0.008427	0.380952	
chunk0105_456_1	chr2	195156503	195156879	+	0	NA	Intergenic	L1ME3A|LINE|L1	426096	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.007979	0.294430	
chunk0121_429_1	chr3	25916277	25916752	+	0	NA	Intergenic	Intergenic	-42819	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.002105	0.369748	
chunk0178_415_1	chr7	41045575	41045871	+	0	NA	Intergenic	Intergenic	-55881	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.003378	0.531987	
chunk0058_233_1	chr14	25470372	25470843	+	0	NA	Intergenic	Intergenic	-420310	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.002123	0.307203	
chunk0082_382_1	chr17	60501719	60501967	+	0	NA	intron (NM_006380, intron 1 of 12)	intron (NM_006380, intron 1 of 12)	24397	NM_001282476	10513	Hs.84084	NM_006380	ENSG00000062725	APPBP2	APP-BP2|HS.84084|PAT1	amyloid beta precursor protein binding protein 2	protein-coding	0.008065	0.417671	
chunk0133_162_1	chr3	169817216	169817699	+	0	NA	Intergenic	L1M1|LINE|L1	-4465	NM_001080460	344657	Hs.319484	NM_001080460	ENSG00000188306	LRRIQ4	LRRC64	leucine rich repeats and IQ motif containing 4	protein-coding	0.004141	0.328512	
chunk0207_410_1	chr9	136969111	136969310	+	0	NA	Intergenic	Intergenic	-8294	NM_000954	5730	Hs.446429	NM_000954	ENSG00000107317	PTGDS	L-PGDS|LPGDS|PDS|PGD2|PGDS|PGDS2	prostaglandin D2 synthase	protein-coding	0.020101	0.695000	
chunk0054_153_1	chr13	44075246	44075463	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	-35195	NR_104065	101929212	Hs.534877	NR_104064	ENSG00000227258	SMIM2-AS1	C13orf44-AS1|C3orf81-AS1	SMIM2 antisense RNA 1	ncRNA	0.009217	0.412844	
chunk0183_196_1	chr7	106327767	106328942	+	0	NA	Intergenic	MamGypLTR1d|LTR|Gypsy	-43162	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.009362	0.386905	
chunk0076_281_1	chr16	69615904	69616162	+	0	NA	intron (NM_138713, intron 2 of 14)	intron (NM_138713, intron 2 of 14)	50067	NM_006599	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.011628	0.505792	
chunk0191_443_1	chr8	57968000	57968816	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-9950	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.001225	0.318237	
chunk0004_332_1	chr1	50462902	50463306	+	0	NA	intron (NM_007051, intron 18 of 18)	MER68|LTR|ERVL	-39657	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.004950	0.414815	
chunk0202_432_1	chr9	81851455	81851856	+	0	NA	Intergenic	Intergenic	-61782	NR_026851	347127	Hs.215235	NM_198509	ENSG00000240632	SPATA31D5P	FAM75D5|FAM75D5P	SPATA31 subfamily D member 5, pseudogene	pseudo	0.012469	0.427861	225(AGGACCAAAGTGTTCT,-,0.00),226(GGACCAAAGTGTTCTC,+,0.00)
chunk0003_263_1	chr1	36269073	36269827	+	0	NA	intron (NM_005119, intron 2 of 11)	intron (NM_005119, intron 2 of 11)	-36943	NM_001162530	79729	Hs.524496	NM_024676	ENSG00000214193	SH3D21	C1orf113	SH3 domain containing 21	protein-coding	0.006631	0.439735	
chunk0047_308_1	chr12	73907458	73907971	+	0	NA	Intergenic	Intergenic	384917	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.007797	0.305447	
chunk0168_445_1	chr6	95809027	95809474	+	0	NA	Intergenic	L1PA15|LINE|L1	-206719	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.002237	0.330357	
chunk0099_174_1	chr2	89787251	89787454	+	0	NA	Intergenic	Intergenic	974982	NR_039635	100616399		NR_039635	ENSG00000265510	MIR4436A	mir-4436a	microRNA 4436a	ncRNA	0.034483	0.362745	
chunk0022_346_1	chr10	16957817	16958016	+	0	NA	intron (NM_001081, intron 31 of 66)	(A)n|Simple_repeat|Simple_repeat	-140462	NM_012425	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.005025	0.295000	
chunk0194_307_1	chr8	88099645	88100019	+	0	NA	intron (NM_005941, intron 6 of 9)	intron (NM_005941, intron 6 of 9)	-225764	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.002674	0.333333	
chunk0120_316_1	chr3	10283727	10283926	+	0	NA	promoter-TSS (NR_026829)	promoter-TSS (NR_026829)	-593	NR_026829	84657	Hs.302131	NM_001039102	ENSG00000231177	LINC00852	C3orf42|GHRL-AS2|GHRLOS2|NAG73	long intergenic non-protein coding RNA 852	ncRNA	0.015075	0.510000	
chunk0065_172_1	chr15	25892179	25892522	+	0	NA	Intergenic	Intergenic	-10010	NR_040082	100128714	Hs.587854	NR_040082	ENSG00000206187	LINC02346	-	long intergenic non-protein coding RNA 2346	ncRNA	0.008746	0.441860	164(GAGCACAGGCTGTGCC,-,0.00),165(AGCACAGGCTGTGCCA,+,0.00)
chunk0047_229_1	chr12	71844616	71844826	+	0	NA	intron (NR_027449, intron 1 of 15)	L2c|LINE|L2	5014	NM_001146213	64786	Hs.284630	NM_022771	ENSG00000121749	TBC1D15	RAB7-GAP	TBC1 domain family member 15	protein-coding	0.004762	0.369668	
chunk0113_133_1	chr20	51750259	51750594	+	0	NA	intron (NM_006045, intron 1 of 27)	intron (NM_006045, intron 1 of 27)	17985	NM_006045	10079	Hs.649234	NM_006045	ENSG00000054793	ATP9A	ATPIIA	ATPase phospholipid transporting 9A (putative)	protein-coding	0.017910	0.529762	
chunk0025_187_1	chr10	53225088	53225571	+	0	NA	Intergenic	L1MA4|LINE|L1	-453629	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.004141	0.371901	
chunk0150_296_1	chr5	37429670	37429993	+	0	NA	intron (NM_018034, intron 5 of 17)	L1ME1|LINE|L1	50521	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.000000	0.314815	
chunk0024_208_1	chr10	36755186	36755735	+	0	NA	Intergenic	L1MC3|LINE|L1	-370397	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.001821	0.354545	
chunk0175_412_1	chr6	168788502	168788935	+	0	NA	Intergenic	HAL1|LINE|L1	347567	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.009238	0.405530	
chunk0019_83_1	chr1	224502950	224503830	+	0	NA	Intergenic	Intergenic	-69091	NM_001115113	80232	Hs.497873	NM_025160	ENSG00000162923	WDR26	CDW2|GID7|MIP2|SKDEAS	WD repeat domain 26	protein-coding	0.019318	0.564132	228(TAGAACACAATGTACT,-,0.00),229(AGAACACAATGTACTA,+,0.00)
chunk0185_462_1	chr7	135463837	135464177	+	0	NA	intron (NM_001008225, intron 1 of 10)	L1PA14|LINE|L1	46120	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.002941	0.360704	
chunk0168_65_1	chr6	79325649	79326170	+	0	NA	Intergenic	L1MD|LINE|L1	-12525	NR_130915	80078		NR_130915	ENSG00000286042	LCAL1	onco-lncRNA-27	lung cancer associated lncRNA 1	ncRNA	0.007678	0.354406	
chunk0154_292_1	chr5	83085091	83085456	+	0	NA	intron (NM_022550, intron 1 of 7)	intron (NM_022550, intron 1 of 7)	7775	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.005479	0.360656	
chunk0040_297_1	chr11	117148263	117148632	+	0	NA	intron (NR_110282, intron 1 of 2)	MIR|SINE|MIR	4163	NM_001309431	5049	Hs.728488	NM_002572	ENSG00000168092	PAFAH1B2	HEL-S-303	platelet activating factor acetylhydrolase 1b catalytic subunit 2	protein-coding	0.008130	0.432432	
chunk0024_329_1	chr10	43184064	43184514	+	0	NA	3' UTR (NM_018590, exon 8 of 8)	3' UTR (NM_018590, exon 8 of 8)	45450	NM_001282862	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.002222	0.323725	
chunk0067_138_1	chr15	43082149	43082650	+	0	NA	intron (NM_174916, intron 3 of 46)	intron (NM_174916, intron 3 of 46)	23689	NM_174916	197131	Hs.591121	NM_174916	ENSG00000159459	UBR1	JBS	ubiquitin protein ligase E3 component n-recognin 1	protein-coding	0.003992	0.320717	
chunk0127_60_1	chr3	89256802	89257098	+	0	NA	intron (NM_005233, intron 3 of 16)	intron (NM_005233, intron 3 of 16)	149426	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003378	0.309764	
chunk0206_218_1	chr9	123309550	123309892	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-41145	NM_001171137	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.002924	0.428571	
chunk0160_109_1	chr5	150753589	150753937	+	0	NA	intron (NM_016221, intron 2 of 12)	intron (NM_016221, intron 2 of 12)	4757	NM_001135644	51164	Hs.675564	NM_016221	ENSG00000132912	DCTN4	DYN4|P62	dynactin subunit 4	protein-coding	0.008621	0.386819	
chunk0075_429_1	chr16	57622784	57623021	+	0	NA	intron (NM_005682, intron 1 of 14)	intron (NM_005682, intron 1 of 14)	2904	NM_005682	9289	Hs.513633	NM_005682	ENSG00000205336	ADGRG1	BFPP|BPPR|GPR56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding	0.021097	0.617647	142(AGGGACAGGGTGACCC,-,0.00),143(GGGACAGGGTGACCCT,+,0.00)
chunk0143_154_1	chr4	110097228	110097738	+	0	NA	intron (NM_001130721, intron 3 of 4)	intron (NM_001130721, intron 3 of 4)	101132	NM_001130721	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.005882	0.375734	
chunk0071_82_1	chr15	80761836	80762120	+	0	NA	Intergenic	Intergenic	-17365	NM_001293298	57214	Hs.459088	NM_018689	ENSG00000103888	CEMIP	CCSP1|HYBID|KIAA1199|TMEM2L	cell migration inducing hyaluronidase 1	protein-coding	0.010563	0.540351	
chunk0041_85_1	chr11	124339896	124340155	+	0	NA	Intergenic	Intergenic	-19828	NM_001002918	283160	Hs.504212	NM_001002918	ENSG00000279116	OR8D2	JCG2	olfactory receptor family 8 subfamily D member 2 (gene/pseudogene)	protein-coding	0.011583	0.476923	
chunk0173_124_1	chr6	143652928	143653166	+	0	NA	intron (NM_001100166, intron 1 of 11)	intron (NM_001100166, intron 1 of 11)	-24918	NM_001100164	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.008403	0.502092	
chunk0045_459_1	chr12	53797857	53798403	+	0	NA	Intergenic	Intergenic	-41096	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.000000	0.394881	
chunk0139_342_1	chr4	59630028	59630707	+	0	NA	Intergenic	Intergenic	-1292252	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.008837	0.330882	
chunk0165_442_1	chr6	40409136	40409678	+	0	NA	intron (NM_020737, intron 2 of 2)	MIRb|SINE|MIR	30983	NR_024015									0.011070	0.438306	
chunk0187_371_1	chr7	157492905	157493500	+	0	NA	intron (NR_110157, intron 2 of 3)	intron (NR_110157, intron 2 of 3)	26971	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.008403	0.481544	281(TGGCACTGAGAGTTCC,-,0.00),282(GGCACTGAGAGTTCCT,+,0.00)
chunk0117_23_1	chr22	11356140	11356556	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-394819	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.004808	0.366906	
chunk0029_45_1	chr10	96352607	96353266	+	0	NA	intron (NM_001284321, intron 1 of 4)	intron (NM_001284321, intron 1 of 4)	4223	NM_001284326	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.007587	0.463636	
chunk0194_86_1	chr8	82953826	82954301	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-449695	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.002105	0.365546	8(GAGCACTTTATGTTCC,-,0.00),9(AGCACTTTATGTTCCC,+,0.00)
chunk0074_391_1	chr16	35367765	35367964	+	0	NA	intron (NR_027079, intron 1 of 8)	BSR/Beta|Satellite|Satellite	4333	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.005025	0.455000	
chunk0209_431_1	chrX	62740095	62740450	+	0	NA	Intergenic	HERVK-int|LTR|ERVK	611067	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.002817	0.337079	
chunk0012_92_1	chr1	156289652	156290423	+	0	NA	intron (NM_032323, intron 3 of 3)	MIRb|SINE|MIR	5652	NM_001256609	112770	Hs.202522	NM_144580	ENSG00000198715	GLMP	C1orf85|NCU-G1	glycosylated lysosomal membrane protein	protein-coding	0.001297	0.388601	
chunk0197_55_1	chr8	118591348	118591788	+	0	NA	intron (NR_109794, intron 1 of 4)	intron (NR_109794, intron 1 of 4)	-29433	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.000000	0.297052	
chunk0072_109_1	chr15	91346939	91347229	+	0	NA	Intergenic	Intergenic	-116255	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.000000	0.412371	
chunk0007_16_1	chr1	77342744	77343276	+	0	NA	intron (NM_012093, intron 6 of 13)	L2a|LINE|L2	60408	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.000000	0.367730	
chunk0091_173_1	chr19	7995222	7995812	+	0	NA	intron (NM_001419, intron 1 of 5)	MER58A|DNA|hAT-Charlie	10128	NM_001419	1994	Hs.184492	NM_001419	ENSG00000066044	ELAVL1	ELAV1|HUR|Hua|MelG	ELAV like RNA binding protein 1	protein-coding	0.008475	0.382403	
chunk0108_393_1	chr2	237099650	237099880	+	0	NA	TTS (NM_198189)	TTS (NM_198189)	14324	NM_198189	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.000000	0.376623	157(GGTACAAGATGTCCAG,+,0.00)
chunk0199_301_1	chr9	6996458	6996887	+	0	NA	intron (NR_130707, intron 13 of 14)	intron (NR_130707, intron 13 of 14)	239031	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.009324	0.362791	140(AAGGACAAGCCGTGCT,-,0.00)
chunk0175_162_1	chr7	4189056	4189281	+	0	NA	intron (NM_001079653, intron 9 of 19)	intron (NM_001079653, intron 9 of 19)	59483	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.040000	0.513274	108(GGGAGCTGGCTGTCCC,-,0.00),109(GGAGCTGGCTGTCCCT,+,0.00)
chunk0100_390_1	chr2	118546579	118546976	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	56189	NR_110272	101927709	Hs.274529	NR_110272		LOC101927709	-	uncharacterized LOC101927709	ncRNA	0.012594	0.412060	256(ATGAACACCCAGTTCA,-,0.00),257(TGAACACCCAGTTCAT,+,0.00)
chunk0023_70_1	chr10	22131945	22132384	+	0	NA	Intergenic	L1ME4c|LINE|L1	77819	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.000000	0.295455	
chunk0036_272_1	chr11	65150764	65151282	+	0	NA	Intergenic	Intergenic	-16491	NM_032431	84447	Hs.75859	NM_032431	ENSG00000162298	SYVN1	DER3|HRD1	synoviolin 1	protein-coding	0.013514	0.585742	
chunk0008_184_1	chr1	93129456	93129905	+	0	NA	intron (NM_007358, intron 11 of 14)	intron (NM_007358, intron 11 of 14)	50445	NM_007358	22823	Hs.31016	NM_007358	ENSG00000143033	MTF2	M96|PCL2|TDRD19A|dJ976O13.2	metal response element binding transcription factor 2	protein-coding	0.000000	0.320000	
chunk0095_270_1	chr2	19799696	19801002	+	0	NA	Intergenic	Intergenic	-68505	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.010720	0.498852	1102(TAGATCACAATGTACT,-,0.00),1103(AGATCACAATGTACTT,+,0.00)
chunk0185_112_1	chr7	125758445	125758774	+	0	NA	Intergenic	L1M2|LINE|L1	-494318	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.000000	0.357576	
chunk0102_299_1	chr2	150789562	150789970	+	0	NA	Intergenic	Intergenic	160869	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.000000	0.308068	148(AGGAACAAAGTGAACT,-,0.00),149(GGAACAAAGTGAACTT,+,0.00)
chunk0011_212_1	chr1	150121292	150121539	+	0	NA	intron (NM_007259, intron 14 of 14)	intron (NM_007259, intron 14 of 14)	-28019	NM_001304722	51177	Hs.438824	NM_016274	ENSG00000023902	PLEKHO1	CKIP-1|CKIP1|JBP|OC120	pleckstrin homology domain containing O1	protein-coding	0.000000	0.391129	103(GAACACATGCTGTCCT,-,0.00),104(AACACATGCTGTCCTA,+,0.00)
chunk0082_254_1	chr17	57550138	57550826	+	0	NA	intron (NM_138962, intron 7 of 13)	intron (NM_138962, intron 7 of 13)	-26885	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.021802	0.460087	387(AAGAACACGATGTCTC,-,0.00),388(AGAACACGATGTCTCT,+,0.00)
chunk0183_358_1	chr7	108658447	108658733	+	0	NA	Intergenic	Intergenic	-88822	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.013986	0.383275	
chunk0082_409_1	chr17	60950213	60950904	+	0	NA	intron (NM_017679, intron 14 of 23)	AluJo|SINE|Alu	272747	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.004342	0.342486	
chunk0111_308_1	chr20	32111310	32111667	+	0	NA	intron (NM_014742, intron 1 of 17)	L2a|LINE|L2	1982	NM_014742	9777	Hs.654665	NM_014742	ENSG00000101337	TM9SF4	dJ836N17.2	transmembrane 9 superfamily member 4	protein-coding	0.005602	0.407821	
chunk0007_41_1	chr1	77745292	77745699	+	0	NA	5' UTR (NM_201626, exon 2 of 22)	5' UTR (NM_201626, exon 2 of 22)	14384	NM_015017	23032	Hs.480597	NM_015017	ENSG00000077254	USP33	VDU1	ubiquitin specific peptidase 33	protein-coding	0.009828	0.399510	
chunk0035_430_1	chr11	57306205	57306683	+	0	NA	intron (NM_033396, intron 6 of 11)	intron (NM_033396, intron 6 of 11)	18495	NM_033396	85456	Hs.530730	NM_033396	ENSG00000149115	TNKS1BP1	TAB182	tankyrase 1 binding protein 1	protein-coding	0.023013	0.440501	
chunk0020_347_1	chr1	239306518	239306854	+	0	NA	Intergenic	Intergenic	-322387	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.014881	0.335312	
chunk0156_409_1	chr5	114245881	114246566	+	0	NA	Intergenic	Intergenic	-116096	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.004380	0.316327	
chunk0096_432_1	chr2	38460271	38460972	+	0	NA	intron (NR_110259, intron 4 of 4)	L2c|LINE|L2	55119	NR_110259	101929596	Hs.537341	NR_110259		LINC02613	-	long intergenic non-protein coding RNA 2613	ncRNA	0.005706	0.374644	
chunk0156_254_1	chr5	109036991	109037584	+	0	NA	intron (NM_001308028, intron 11 of 17)	intron (NM_001308028, intron 11 of 17)	112681	NM_001308031	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.005059	0.340067	155(AAGTACATGCTGTGCT,-,0.00),156(AGTACATGCTGTGCTC,+,0.00)
chunk0137_109_1	chr4	13750626	13750998	+	0	NA	intron (NR_121681, intron 2 of 3)	intron (NR_121681, intron 2 of 3)	95633	NR_121681	101929071	Hs.543714	NR_121681	ENSG00000250634	LINC01182	-	long intergenic non-protein coding RNA 1182	ncRNA	0.002688	0.426273	
chunk0036_334_1	chr11	66694866	66695065	+	0	NA	intron (NM_006946, intron 20 of 36)	LTR41C|LTR|ERVL	-17044	NM_001286135	83759	Hs.618713	NM_031492	ENSG00000173914	RBM4B	RBM30|RBM4L|ZCCHC15|ZCCHC21B|ZCRB3B	RNA binding motif protein 4B	protein-coding	0.015075	0.550000	
chunk0030_138_1	chr10	113626134	113626503	+	0	NA	intron (NM_001261463, intron 20 of 41)	intron (NM_001261463, intron 20 of 41)	37752	NM_198060	4892	Hs.268788	NM_006175	ENSG00000197893	NRAP	N-RAP	nebulin related anchoring protein	protein-coding	0.005420	0.454054	173(TGAGACAGCCTGTTCC,-,0.00),174(GAGACAGCCTGTTCCA,+,0.00)
chunk0122_317_1	chr3	37040742	37040965	+	0	NA	intron (NM_001167618, intron 14 of 18)	intron (NM_001167618, intron 14 of 18)	47076	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.008969	0.495536	
chunk0132_404_1	chr3	164129555	164130235	+	0	NA	Intergenic	Intergenic	41661	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.270191	
chunk0127_43_1	chr3	88896725	88897303	+	0	NA	Intergenic	Intergenic	-210510	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.298791	
chunk0067_311_1	chr15	47897839	47898040	+	0	NA	Intergenic	Intergenic	-51703	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.009950	0.376238	
chunk0157_242_1	chr5	119718952	119719505	+	0	NA	Intergenic	Intergenic	89669	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.001808	0.357401	323(AGGAACATTAAGTACT,-,0.00),324(GGAACATTAAGTACTT,+,0.00)
chunk0092_218_1	chr19	31674785	31675405	+	0	NA	Intergenic	Intergenic	82814	NM_001205273	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.017742	0.404187	
chunk0193_314_1	chr8	78522294	78522684	+	0	NA	intron (NM_181839, intron 1 of 2)	intron (NM_181839, intron 1 of 2)	6388	NM_181839	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.002564	0.306905	
chunk0132_259_1	chr3	159031210	159031817	+	0	NA	Intergenic	Intergenic	-37739	NM_001197113	100505385	Hs.134665	NM_001197113	ENSG00000283154	IQCJ-SCHIP1	-	IQCJ-SCHIP1 readthrough	protein-coding	0.008237	0.342105	
chunk0190_248_1	chr8	36899164	36899659	+	0	NA	intron (NM_001031836, intron 19 of 26)	intron (NM_001031836, intron 19 of 26)	115087	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.004040	0.358871	225(CAGAACACTCTGCTCA,-,0.00),226(AGAACACTCTGCTCAC,+,0.00)
chunk0049_100_1	chr12	90877609	90878299	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-40069	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.004348	0.445731	
chunk0188_115_1	chr8	9073146	9073424	+	0	NA	Intergenic	Intergenic	24840	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.017986	0.405018	
chunk0207_160_1	chr9	130068363	130068955	+	0	NA	intron (NM_001287346, intron 1 of 16)	intron (NM_001287346, intron 1 of 16)	14953	NM_020960	57720	Hs.512461	NM_020960	ENSG00000148358	GPR107	GCDRP|LUSTR1|bA138E2.2	G protein-coupled receptor 107	protein-coding	0.011824	0.384486	365(CAAAACAGTATGTCCT,-,0.00),366(AAAACAGTATGTCCTC,+,0.00)
chunk0052_339_1	chr12	126474621	126475028	+	0	NA	Intergenic	L1MC3|LINE|L1	32343	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.004914	0.377451	
chunk0123_95_1	chr3	42123149	42123437	+	0	NA	intron (NM_001042646, intron 1 of 15)	intron (NM_001042646, intron 1 of 15)	-25942	NM_001265609	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.010417	0.519031	
chunk0015_291_1	chr1	188763660	188763895	+	0	NA	Intergenic	L1MC3|LINE|L1	1320149	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004255	0.334746	
chunk0192_302_1	chr8	66762884	66763524	+	0	NA	intron (NM_001033578, intron 1 of 16)	L1MC5|LINE|L1	4801	NR_002734	26255	Hs.647156	NR_002734	ENSG00000213005	PTTG3P	PTTG3|rcPTTG1	pituitary tumor-transforming 3, pseudogene	pseudo	0.006250	0.346334	
chunk0002_337_1	chr1	24770196	24770636	+	0	NA	intron (NM_013943, intron 1 of 5)	intron (NM_013943, intron 1 of 5)	25147	NM_013943	25932	Hs.440544	NM_013943	ENSG00000169504	CLIC4	CLIC4L|H1|MTCLIC|huH1|p64H1	chloride intracellular channel 4	protein-coding	0.002273	0.335601	262(GAGATCAGCCAGTGCT,-,0.00),263(AGATCAGCCAGTGCTT,+,0.00)
chunk0033_429_1	chr11	25094006	25094451	+	0	NA	Intergenic	MER92C|LTR|ERV1	597258	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004494	0.446188	238(AGGAACACTCTGTTTT,-,0.00),239(GGAACACTCTGTTTTG,+,0.00)
chunk0042_296_1	chr12	7727613	7728141	+	0	NA	Intergenic	Intergenic	16423	NM_199286	359787	Hs.131358	NM_199286	ENSG00000187569	DPPA3	Pgc7|STELLA	developmental pluripotency associated 3	protein-coding	0.009470	0.410208	
chunk0087_104_1	chr18	32488574	32488814	+	0	NA	Intergenic	Intergenic	-18210	NM_001242409	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.008333	0.373444	
chunk0021_162_1	chr10	5071786	5071985	+	0	NA	intron (NM_001253908, intron 1 of 8)	MER67A|LTR|ERV1	-22491	NM_003739	8644	Hs.78183	NM_003739	ENSG00000196139	AKR1C3	DD3|DDX|HA1753|HAKRB|HAKRe|HSD17B5|PGFS|hluPGFS	aldo-keto reductase family 1 member C3	protein-coding	0.015075	0.460000	
chunk0079_397_1	chr17	19313413	19314527	+	0	NA	intron (NM_014964, intron 7 of 10)	intron (NM_014964, intron 7 of 10)	-7709	NR_048576	100874018	Hs.621672	NR_048576	ENSG00000235397	EPN2-AS1	-	EPN2 antisense RNA 1	ncRNA	0.011670	0.496861	
chunk0098_226_1	chr2	73853630	73854123	+	0	NA	intron (NM_213622, intron 7 of 9)	L1ME3B|LINE|L1	24878	NM_213622	10617	Hs.469018	NM_006463	ENSG00000124356	STAMBP	AMSH|MICCAP	STAM binding protein	protein-coding	0.010142	0.408907	
chunk0061_186_1	chr14	60156335	60156736	+	0	NA	intron (NM_016029, intron 1 of 6)	MIR3|SINE|MIR	8958	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.000000	0.328358	
chunk0099_53_1	chr2	84518500	84519195	+	0	NA	intron (NM_001370, intron 2 of 76)	intron (NM_001370, intron 2 of 76)	2392	NM_001370	1768	Hs.249972	NM_001370	ENSG00000115423	DNAH6	DNHL1|Dnahc6|HL-2|HL2	dynein axonemal heavy chain 6	protein-coding	0.010072	0.380747	
chunk0204_437_1	chr9	103963707	103964182	+	0	NA	Intergenic	Intergenic	-35765	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.004211	0.321429	
chunk0210_242_1	chrX	82757451	82758126	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-750473	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.007407	0.381657	358(TGGAACTCAATGTTCT,-,0.00),359(GGAACTCAATGTTCTT,+,0.00)
chunk0083_130_1	chr17	65417673	65417872	+	0	NA	Intergenic	Intergenic	-39769	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.015075	0.465000	
chunk0212_308_1	chrX	142684761	142685072	+	0	NA	Intergenic	Intergenic	-341002	NM_001009613	441525	Hs.535082	NM_001009613	ENSG00000189326	SPANXN4	CT11.9	SPANX family member N4	protein-coding	0.000000	0.326923	
chunk0008_55_1	chr1	89423013	89423548	+	0	NA	intron (NR_003133, intron 4 of 4)	intron (NR_003133, intron 4 of 4)	15601	NR_003133	400759	Hs.661968	NR_003133	ENSG00000225492	GBP1P1	-	guanylate binding protein 1 pseudogene 1	pseudo	0.009346	0.421642	
chunk0120_303_1	chr3	9976283	9976754	+	0	NA	intron (NM_018447, intron 3 of 7)	L3|LINE|CR1	10320	NM_018447	55831	Hs.475392	NM_018447	ENSG00000125037	EMC3	POB|TMEM111	ER membrane protein complex subunit 3	protein-coding	0.006369	0.459746	
chunk0084_387_1	chr17	82030471	82030748	+	0	NA	exon (NM_144999, exon 17 of 17)	exon (NM_144999, exon 17 of 17)	-1047	NM_001316307	5881	Hs.45002	NM_005052	ENSG00000169750	RAC3	-	Rac family small GTPase 3	protein-coding	0.097473	0.712230	
chunk0201_299_1	chr9	41229346	41230281	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-3942	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.006652	0.541528	
chunk0041_23_1	chr12	559629	559934	+	0	NA	intron (NM_173593, intron 19 of 19)	intron (NM_173593, intron 19 of 19)	50632	NM_001294345	4815	Hs.655804	NM_016533	ENSG00000171840	NINJ2	-	ninjurin 2	protein-coding	0.026230	0.565359	33(TGGTACACCGTGTACC,-,0.00),34(GGTACACCGTGTACCA,+,0.00)
chunk0135_124_1	chr3	187069684	187069895	+	0	NA	intron (NM_003032, intron 4 of 6)	L2c|LINE|L2	47912	NM_003032	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.000000	0.448113	124(GGGTACACACTGTACT,-,0.00),125(GGTACACACTGTACTA,+,0.00)
chunk0064_285_1	chr14	95265308	95265880	+	0	NA	intron (NM_024734, intron 1 of 12)	intron (NM_024734, intron 1 of 12)	54314	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.010490	0.441536	261(TGGCACAGTGCGTGCT,-,0.00),262(GGCACAGTGCGTGCTA,+,0.00)
chunk0006_443_1	chr1	76751788	76752235	+	0	NA	Intergenic	Intergenic	-115490	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.004474	0.348214	
chunk0112_145_1	chr20	38731450	38731649	+	0	NA	Intergenic	Intergenic	7087	NM_080552	140679	Hs.179080	NM_080552	ENSG00000101438	SLC32A1	VGAT|VIAAT	solute carrier family 32 member 1	protein-coding	0.055276	0.645000	
chunk0130_350_1	chr3	138752049	138752296	+	0	NA	intron (NM_006219, intron 2 of 21)	intron (NM_006219, intron 2 of 21)	7187	NM_006219	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.008097	0.334677	
chunk0050_230_1	chr12	105000965	105001507	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	14916	NM_152318	121053	Hs.295563	NM_152318	ENSG00000151131	C12orf45	-	chromosome 12 open reading frame 45	protein-coding	0.005535	0.355433	331(AAGAACATATTGTTAT,-,0.00)
chunk0114_56_1	chr21	8875424	8875638	+	0	NA	Intergenic	Intergenic	-111468	NR_128711	103504731		NR_128711	ENSG00000264462	MIR3648-2	hsa-mir-3648-2	microRNA 3648-2	ncRNA	0.009346	0.353488	
chunk0169_158_1	chr6	101880951	101881169	+	0	NA	intron (NM_001166247, intron 10 of 16)	intron (NM_001166247, intron 10 of 16)	482075	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.237443	
chunk0057_69_1	chr13	98214772	98215211	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	6467	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.013667	0.463636	
chunk0199_250_1	chr9	5799306	5799797	+	0	NA	intron (NM_024896, intron 11 of 14)	intron (NM_024896, intron 11 of 14)	33530	NM_024896	79956	Hs.591078	NM_024896	ENSG00000099219	ERMP1	FXNA|KIAA1815|bA207C16.3	endoplasmic reticulum metallopeptidase 1	protein-coding	0.010183	0.398374	
chunk0206_212_1	chr9	123208710	123208998	+	0	NA	intron (NR_033234, intron 1 of 18)	L1MEc|LINE|L1	59710	NM_018387	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.003472	0.477509	
chunk0085_50_1	chr18	820892	821168	+	0	NA	Intergenic	Intergenic	-8704	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.007246	0.339350	
chunk0086_121_1	chr18	14947439	14947821	+	0	NA	intron (NR_104164, intron 1 of 3)	intron (NR_104164, intron 1 of 3)	1363	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.005236	0.469974	
chunk0067_132_1	chr15	42919912	42920262	+	0	NA	intron (NM_173500, intron 1 of 14)	intron (NM_173500, intron 1 of 14)	722	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.045714	0.521368	
chunk0064_425_1	chr14	99847063	99847432	+	0	NA	intron (NM_004434, intron 1 of 21)	L1ME1|LINE|L1	53839	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.016260	0.327027	114(GAGAACATACTCTTCC,-,0.00),115(AGAACATACTCTTCCC,+,0.00)
chunk0203_142_1	chr9	85532597	85532834	+	0	NA	Intergenic	LTR40a|LTR|ERVL	209314	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.000000	0.386555	
chunk0010_413_1	chr1	119631397	119631745	+	0	NA	intron (NM_001080470, intron 1 of 2)	CpG	16196	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.077586	0.719198	152(AGGGACGGCCAGTTCC,-,0.00)
chunk0124_318_1	chr3	58096971	58097191	+	0	NA	intron (NM_001164317, intron 6 of 46)	intron (NM_001164317, intron 6 of 46)	88681	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.004545	0.497738	177(GAATACAGACTGTACT,-,0.00),178(AATACAGACTGTACTC,+,0.00)
chunk0170_110_1	chr6	110643305	110643561	+	0	NA	intron (NM_015076, intron 4 of 12)	L1MA3|LINE|L1	-166792	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.003906	0.326848	
chunk0080_451_1	chr17	36989202	36989582	+	0	NA	exon (NM_012138, exon 7 of 12)	exon (NM_012138, exon 7 of 12)	40517	NM_012138	26574	Hs.195740	NM_012138	ENSG00000275700	AATF	BFR2|CHE-1|CHE1|DED	apoptosis antagonizing transcription factor	protein-coding	0.015789	0.433071	172(CAGCTCAGCCTGTCCC,-,0.00),173(AGCTCAGCCTGTCCCA,+,0.00)
chunk0154_298_1	chr5	83124722	83124980	+	0	NA	intron (NM_022550, intron 3 of 7)	intron (NM_022550, intron 3 of 7)	47353	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.003876	0.366795	
chunk0161_46_1	chr5	166045133	166045553	+	0	NA	Intergenic	Intergenic	881027	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004762	0.308789	
chunk0006_145_1	chr1	66279717	66279918	+	0	NA	intron (NM_001037340, intron 5 of 14)	MLT2C1|LTR|ERVL	-52291	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.004975	0.396040	79(AGGCACAATATGTTCT,-,0.00),80(GGCACAATATGTTCTT,+,0.00)
chunk0180_160_1	chr7	64908171	64908595	+	0	NA	intron (NM_021148, intron 1 of 3)	L1PA11|LINE|L1	5141	NM_021148	10793	Hs.520889	NM_021148	ENSG00000198039	ZNF273	HZF9	zinc finger protein 273	protein-coding	0.007075	0.430588	
chunk0175_418_1	chr6	168877913	168878195	+	0	NA	Intergenic	Intergenic	284247	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.028369	0.561837	
chunk0188_413_1	chr8	18883427	18883633	+	0	NA	intron (NM_015310, intron 2 of 15)	intron (NM_015310, intron 2 of 15)	-74635	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.000000	0.333333	
chunk0118_451_1	chr22	39529068	39529401	+	0	NA	non-coding (NR_130151, exon 5 of 5)	non-coding (NR_130151, exon 5 of 5)	3621	NM_194326	91582	Hs.526933	NM_194326	ENSG00000187051	RPS19BP1	AROS|S19BP	ribosomal protein S19 binding protein 1	protein-coding	0.033033	0.589820	
chunk0020_38_1	chr1	232207409	232207724	+	0	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	281732	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.006349	0.392405	
chunk0022_98_1	chr10	9754853	9755056	+	0	NA	Intergenic	Intergenic	-303768	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.009852	0.495098	
chunk0150_55_1	chr5	31845196	31845854	+	0	NA	intron (NM_178140, intron 1 of 23)	intron (NM_178140, intron 1 of 23)	46601	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.007599	0.418816	
chunk0018_160_1	chr1	218833922	218834199	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	339728	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.014440	0.359712	
chunk0178_106_1	chr7	30809045	30809248	+	0	NA	intron (NR_037598, intron 7 of 19)	Harlequin-int|LTR|ERV1	37729	NM_032222	84182	Hs.660192	NM_032222	ENSG00000106125	MINDY4	AQP-1|AQP1|C7orf67|CHIP28|FAM188B	MINDY lysine 48 deubiquitinase 4	protein-coding	0.004926	0.367647	
chunk0178_463_1	chr7	42221334	42221587	+	0	NA	intron (NM_000168, intron 2 of 14)	(CACA)n|Simple_repeat|Simple_repeat	15559	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.015810	0.511811	
chunk0145_314_1	chr4	150498413	150498961	+	0	NA	intron (NM_001199282, intron 40 of 56)	intron (NM_001199282, intron 40 of 56)	-83238	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.003650	0.278689	
chunk0202_361_1	chr9	80334973	80335519	+	0	NA	Intergenic	L1MC1|LINE|L1	360223	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.003663	0.305302	
chunk0137_52_1	chr4	11611978	11612209	+	0	NA	Intergenic	Intergenic	-183180	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.000000	0.357759	
chunk0155_401_1	chr5	98977752	98978336	+	0	NA	Intergenic	Intergenic	48910	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.003425	0.408547	
chunk0160_140_1	chr5	151408567	151409099	+	0	NA	Intergenic	Intergenic	-28159	NM_001308151	206358	Hs.269004	NM_078483	ENSG00000123643	SLC36A1	Dct1|LYAAT1|PAT1|TRAMD3	solute carrier family 36 member 1	protein-coding	0.005639	0.386492	
chunk0129_137_1	chr3	120244272	120244471	+	0	NA	promoter-TSS (NM_001168271)	promoter-TSS (NM_001168271)	-76	NM_001168271	165829	Hs.333358	NM_153002	ENSG00000175697	GPR156	GABABL|PGR28	G protein-coupled receptor 156	protein-coding	0.015075	0.495000	
chunk0108_230_1	chr2	233597517	233597993	+	0	NA	Intergenic	L1M5|LINE|L1	-19890	NM_019076	54576	Hs.554822	NM_019076	ENSG00000242366	UGT1A8	GNT1|UDPGT|UDPGT 1-8|UGT-1A|UGT-1H|UGT1|UGT1-01|UGT1-08|UGT1.1|UGT1.8|UGT1A|UGT1A1|UGT1A8S|UGT1H|hUG-BR1	UDP glucuronosyltransferase family 1 member A8	protein-coding	0.002101	0.385744	
chunk0146_410_1	chr4	169069971	169070400	+	0	NA	Intergenic	Intergenic	-59868	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.013986	0.434884	
chunk0062_110_1	chr14	68307491	68307793	+	0	NA	intron (NM_133509, intron 8 of 10)	intron (NM_133509, intron 8 of 10)	486272	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.003311	0.396040	
chunk0101_438_1	chr2	139465755	139466230	+	0	NA	Intergenic	Intergenic	568668	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.010526	0.378151	247(AAGCTCACACTGTACT,-,0.00),248(AGCTCACACTGTACTA,+,0.00)
chunk0181_44_1	chr7	79797635	79797985	+	0	NA	Intergenic	Intergenic	-337014	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.005714	0.350427	
chunk0139_348_1	chr4	59936892	59937190	+	0	NA	Intergenic	Intergenic	-985578	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.006711	0.274247	
chunk0165_448_1	chr6	40619494	40619693	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-32129	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.000000	0.460000	
chunk0004_461_1	chr1	53663533	53663903	+	0	NA	intron (NM_147193, intron 1 of 9)	intron (NM_147193, intron 1 of 9)	70486	NM_147193	148979	Hs.306691	NM_147193	ENSG00000174332	GLIS1	-	GLIS family zinc finger 1	protein-coding	0.024324	0.595687	234(CAGGACAAAACGTTCC,-,0.00)
chunk0012_173_1	chr1	158844272	158844711	+	0	NA	intron (NM_002432, intron 4 of 6)	intron (NM_002432, intron 4 of 6)	13113	NM_002432	4332	Hs.153837	NM_002432	ENSG00000163563	MNDA	PYHIN3	myeloid cell nuclear differentiation antigen	protein-coding	0.009112	0.445455	
chunk0115_88_1	chr21	22325162	22325944	+	0	NA	Intergenic	L2a|LINE|L2	226936	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.006394	0.330779	510(AAGAGCTCCCTGTGCT,-,0.00)
chunk0059_119_1	chr14	31395694	31396384	+	0	NA	intron (NM_015473, intron 4 of 35)	MIRb|SINE|MIR	24543	NM_015473	25938	Hs.744979	NM_015473	ENSG00000129493	HEATR5A	C14orf125	HEAT repeat containing 5A	protein-coding	0.008696	0.448625	
chunk0082_388_1	chr17	60606165	60606435	+	0	NA	intron (NM_003620, intron 1 of 5)	L1MB4|LINE|L1	6117	NM_003620	8493	Hs.286073	NM_003620	ENSG00000170836	PPM1D	IDDGIP|PP2C-DELTA|WIP1	protein phosphatase, Mg2+/Mn2+ dependent 1D	protein-coding	0.000000	0.357934	
chunk0183_284_1	chr7	107617096	107617935	+	0	NA	intron (NM_001008405, intron 7 of 7)	intron (NM_001008405, intron 7 of 7)	36756	NM_001008405	55973	Hs.303787	NM_018844	ENSG00000075790	BCAP29	BAP29	B cell receptor associated protein 29	protein-coding	0.003576	0.325000	
chunk0012_407_1	chr1	164075489	164075953	+	0	NA	Intergenic	L1MC4|LINE|L1	-483639	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.000000	0.290323	
chunk0091_92_1	chr19	5630045	5630535	+	0	NA	intron (NR_037699, intron 2 of 18)	L1ME3G|LINE|L1	7255	NM_001201339	6294	Hs.728802	NM_002967	ENSG00000160633	SAFB	HAP|HET|SAB-B1|SAF-B|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding	0.020408	0.366599	
chunk0016_299_1	chr1	201266356	201267057	+	0	NA	Intergenic	HAL1b|LINE|L1	-16746	NM_000299	5317	Hs.497350	NM_000299	ENSG00000081277	PKP1	B6P	plakophilin 1	protein-coding	0.004280	0.408832	
chunk0185_331_1	chr7	131934121	131934824	+	0	NA	intron (NR_110836, intron 5 of 5)	MER5A|DNA|hAT-Charlie	24252	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.007112	0.454545	395(AAGCACTGACTGTTCT,-,0.00),396(AGCACTGACTGTTCTA,+,0.00)
chunk0064_36_1	chr14	89586651	89587291	+	0	NA	intron (NM_001085471, intron 1 of 6)	MLT2D|LTR|ERVL	10755	NR_024620	29018	Hs.673124	NM_014099	ENSG00000259073	FOXN3-AS2	PRO1768	FOXN3 antisense RNA 2	ncRNA	0.012500	0.441498	
chunk0058_390_1	chr13	111051147	111051418	+	0	NA	Intergenic	(CACA)n|Simple_repeat|Simple_repeat	-44556	NR_120415	101927802	Hs.559193	NR_120415		LINC00368	-	long intergenic non-protein coding RNA 368	ncRNA	0.007380	0.503676	
chunk0181_227_1	chr7	85226688	85227061	+	0	NA	Intergenic	Intergenic	-104943	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.008043	0.304813	
chunk0134_190_1	chr3	178301233	178301504	+	0	NA	Intergenic	Intergenic	-117833	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.011070	0.305147	
chunk0142_393_1	chr4	102596323	102597054	+	0	NA	intron (NM_003998, intron 14 of 23)	intron (NM_003998, intron 14 of 23)	95359	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.006840	0.367486	
chunk0009_117_1	chr1	102766116	102766714	+	0	NA	Intergenic	Intergenic	342081	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.001672	0.327212	
chunk0150_184_1	chr5	34532468	34532804	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	-123692	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.011905	0.433234	
chunk0159_122_1	chr5	138800994	138801396	+	0	NA	intron (NM_001290307, intron 3 of 18)	Tigger2b_Pri|DNA|TcMar-Tigger	47799	NM_001903	1495	Hs.445981	NM_001903	ENSG00000044115	CTNNA1	CAP102|MDPT2	catenin alpha 1	protein-coding	0.009950	0.349876	200(TAGTACAGTGTGTACT,-,0.00),201(AGTACAGTGTGTACTA,+,0.00)
chunk0198_323_1	chr8	139854945	139855260	+	0	NA	intron (NM_001160372, intron 21 of 22)	intron (NM_001160372, intron 21 of 22)	-152046	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.022222	0.484177	
chunk0163_9_1	chr6	7725520	7725831	+	0	NA	Intergenic	Intergenic	-1103	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.025723	0.445513	
chunk0065_178_1	chr15	26156952	26157372	+	0	NA	Intergenic	Intergenic	41349	NR_038851	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.014286	0.396675	74(TGGAACAAAATGTCCC,-,0.00),75(GGAACAAAATGTCCCC,+,0.00)
chunk0081_17_1	chr17	37299542	37300138	+	0	NA	promoter-TSS (NM_198837)	promoter-TSS (NM_198837)	-73	NM_198838	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.013423	0.425461	
chunk0020_206_1	chr1	235006702	235006962	+	0	NA	Intergenic	Intergenic	-42833	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.007692	0.417625	
chunk0094_217_1	chr2	6654214	6654476	+	0	NA	Intergenic	L3|LINE|CR1	-3826	NR_110497	102800314	Hs.258100	NR_110497	ENSG00000236172	MIR7515HG	-	MIR7515 host gene	ncRNA	0.007634	0.406844	
chunk0044_61_1	chr12	27780565	27780853	+	0	NA	exon (NM_020782, exon 1 of 3)	exon (NM_020782, exon 1 of 3)	455	NM_020782	57542	Hs.505104	NM_020782	ENSG00000087448	KLHL42	Ctb9|KLHDC5	kelch like family member 42	protein-coding	0.062500	0.671280	
chunk0128_349_1	chr3	112540196	112540404	+	0	NA	intron (NM_022488, intron 7 of 11)	intron (NM_022488, intron 7 of 11)	21663	NM_001278712	64422	Hs.477126	NM_022488	ENSG00000144848	ATG3	APG3|APG3-LIKE|APG3L|PC3-96	autophagy related 3	protein-coding	0.000000	0.354067	
chunk0043_270_1	chr12	20883283	20883554	+	0	NA	exon (NM_019844, exon 13 of 16)	exon (NM_019844, exon 13 of 16)	72714	NM_019844	28234	Hs.504966	NM_019844	ENSG00000111700	SLCO1B3	HBLRR|LST-2|LST-3TM13|LST3|OATP-8|OATP1B3|OATP8|SLC21A8	solute carrier organic anion transporter family member 1B3	protein-coding	0.000000	0.290441	
chunk0015_127_1	chr1	185490583	185491139	+	0	NA	Intergenic	L1ME4a|LINE|L1	137627	NR_110793	101929093	Hs.535227	NR_110793	ENSG00000228309	LINC01350	GS1-204I12.1	long intergenic non-protein coding RNA 1350	ncRNA	0.008993	0.375224	269(AAGTACTCCATGTTCA,-,0.00),270(AGTACTCCATGTTCAC,+,0.00)
chunk0197_296_1	chr8	124447602	124448327	+	0	NA	Intergenic	Intergenic	-2843	NM_017956	55039	Hs.9925	NM_017956	ENSG00000183665	TRMT12	TRM12|TYW2	tRNA methyltransferase 12 homolog	protein-coding	0.005517	0.409091	
chunk0184_91_1	chr7	113331296	113331497	+	0	NA	Intergenic	L1PA8A|LINE|L1	-212814	NR_015442									0.034826	0.579208	
chunk0202_438_1	chr9	82064464	82064937	+	0	NA	Intergenic	AluSc|SINE|Alu	75928	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.025370	0.470464	
chunk0047_302_1	chr12	73798651	73798931	+	0	NA	Intergenic	Intergenic	493840	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.000000	0.323843	
chunk0209_362_1	chrX	53639530	53640086	+	0	NA	intron (NM_031407, intron 7 of 83)	MIRb|SINE|MIR	46921	NM_031407	10075	Hs.136905	NM_031407	ENSG00000086758	HUWE1	ARF-BP1|HECTH9|HSPC272|Ib772|LASU1|MRXST|MULE|URE-B1|UREB1	HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.350090	
chunk0123_235_1	chr3	45546961	45547620	+	0	NA	intron (NM_015340, intron 21 of 21)	intron (NM_015340, intron 21 of 21)	-37745	NR_048543	100885795	Hs.641094	NR_048543		LARS2-AS1	-	LARS2 antisense RNA 1	ncRNA	0.019727	0.515152	
chunk0155_8_1	chr5	90855447	90855737	+	0	NA	intron (NR_003149, intron 81 of 89)	intron (NR_003149, intron 81 of 89)	296792	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.000000	0.395189	132(CTGGACAAGATGTTCC,-,0.00),133(TGGACAAGATGTTCCC,+,0.00)
chunk0101_361_1	chr2	137975508	137975943	+	0	NA	intron (NM_006895, intron 2 of 5)	intron (NM_006895, intron 2 of 5)	11487	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.004598	0.353211	
chunk0130_201_1	chr3	133742609	133743180	+	0	NA	Intergenic	Intergenic	-3239	NM_001063	7018	Hs.518267	NM_001063	ENSG00000091513	TF	HEL-S-71p|PRO1557|PRO2086|TFQTL1	transferrin	protein-coding	0.008757	0.473776	
chunk0174_96_1	chr6	156816391	156816956	+	0	NA	intron (NM_017519, intron 1 of 18)	intron (NM_017519, intron 1 of 18)	-36942	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.012389	0.448763	293(GGGTACAGAGTGTTCT,-,0.00),294(GGTACAGAGTGTTCTA,+,0.00)
chunk0147_218_1	chr4	180870492	180870969	+	0	NA	Intergenic	L1PB1|LINE|L1	288419	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.006289	0.370293	
chunk0084_34_1	chr17	73860501	73861037	+	0	NA	Intergenic	Intergenic	-32232	NR_027146	283982	Hs.464079	NM_182564		LINC00469	C17orf54	long intergenic non-protein coding RNA 469	ncRNA	0.016791	0.445065	249(TGGCTCACAGTGTTCC,-,0.00),250(GGCTCACAGTGTTCCT,+,0.00)
chunk0056_170_1	chr13	85228110	85228309	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-80152	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.000000	0.390000	
chunk0021_168_1	chr10	5301337	5301786	+	0	NA	Intergenic	Intergenic	-63452	NM_053049	114131	Hs.511775	NM_053049	ENSG00000178473	UCN3	SCP|SPC|UCNIII	urocortin 3	protein-coding	0.006682	0.391111	161(CAGAGCATTGTGTACC,-,0.00),162(AGAGCATTGTGTACCT,+,0.00)
chunk0068_107_1	chr15	52331540	52331944	+	0	NA	intron (NM_001142495, intron 32 of 39)	intron (NM_001142495, intron 32 of 39)	-35944	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.012376	0.461728	
chunk0124_131_1	chr3	54353892	54354477	+	0	NA	intron (NM_018398, intron 3 of 37)	intron (NM_018398, intron 3 of 37)	231518	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.011966	0.394198	
chunk0054_64_1	chr13	41944711	41945297	+	0	NA	intron (NM_015058, intron 2 of 44)	L1M4|LINE|L1	16081	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.005119	0.398637	
chunk0009_467_1	chr1	111705354	111705816	+	0	NA	intron (NM_001010935, intron 7 of 8)	intron (NM_001010935, intron 7 of 8)	33839	NM_019099	55924	Hs.193406	NM_019099	ENSG00000197852	INKA2	C1orf183|FAM212B	inka box actin regulator 2	protein-coding	0.000000	0.336933	
chunk0133_418_1	chr3	174590996	174591721	+	0	NA	Intergenic	Intergenic	-267963	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.005517	0.391185	
chunk0034_136_1	chr11	28713886	28714541	+	0	NA	Intergenic	Intergenic	-236665	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.003053	0.324695	536(TAGAACAGTGTGTCTC,-,0.00),537(AGAACAGTGTGTCTCA,+,0.00)
chunk0190_242_1	chr8	36836865	36837117	+	0	NA	intron (NM_001031836, intron 14 of 26)	intron (NM_001031836, intron 14 of 26)	52667	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.003968	0.399209	
chunk0038_256_1	chr11	88567511	88567710	+	0	NA	exon (NM_000842, exon 8 of 9)	exon (NM_000842, exon 8 of 9)	63034	NR_049724	100873989	Hs.616625	NR_049724	ENSG00000255082	GRM5-AS1	-	GRM5 antisense RNA 1	ncRNA	0.010050	0.475000	
chunk0092_212_1	chr19	31541048	31541346	+	0	NA	Intergenic	L1PB|LINE|L1	-46992	NM_001278575	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.006711	0.404682	
chunk0106_92_1	chr2	197170026	197170577	+	0	NA	intron (NM_001195144, intron 2 of 27)	MER103C|DNA|hAT-Charlie	132218	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.005445	0.409420	219(AGAAACACGGTGTTCA,-,0.00),220(GAAACACGGTGTTCAA,+,0.00)
chunk0136_7_1	chr4	40566	41606	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-12199	NM_001286054	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.008654	0.451489	
chunk0182_170_1	chr7	95560691	95560907	+	0	NA	Intergenic	Intergenic	35814	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.009259	0.391705	
chunk0169_152_1	chr6	101729900	101730406	+	0	NA	intron (NM_001166247, intron 6 of 16)	intron (NM_001166247, intron 6 of 16)	331168	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001976	0.309665	
chunk0103_377_1	chr2	168632752	168633115	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	49990	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.019284	0.450549	225(TGGTTCACTCTGTCCC,-,0.00),226(GGTTCACTCTGTCCCT,+,0.00)
chunk0176_89_1	chr7	11580930	11581465	+	0	NA	intron (NM_015204, intron 4 of 26)	(ATT)n|Simple_repeat|Simple_repeat	251001	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.001869	0.274254	
chunk0103_366_1	chr2	168286621	168287177	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-39304	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.005396	0.360862	
chunk0151_355_1	chr5	54604011	54604527	+	0	NA	Intergenic	L1MB4|LINE|L1	86506	NM_052870	112574	Hs.432755	NM_052870	ENSG00000178996	SNX18	SH3PX2|SH3PXD3B|SNAG1	sorting nexin 18	protein-coding	0.007752	0.357834	
chunk0153_379_1	chr5	74954181	74954523	+	0	NA	Intergenic	Intergenic	76547	NM_016591	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.005848	0.527697	
chunk0190_320_1	chr8	38791468	38791936	+	0	NA	intron (NM_001146216, intron 2 of 12)	intron (NM_001146216, intron 2 of 12)	4498	NM_001122824	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.010684	0.413646	
chunk0042_184_1	chr12	5047611	5048110	+	0	NA	Intergenic	Intergenic	3941	NM_002234	3741	Hs.150208	NM_002234	ENSG00000130037	KCNA5	ATFB7|HCK1|HK2|HPCN1|KV1.5|PCN1	potassium voltage-gated channel subfamily A member 5	protein-coding	0.014028	0.480000	
chunk0122_243_1	chr3	34197008	34197514	+	0	NA	Intergenic	L1ME2|LINE|L1	398690	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.001976	0.364892	
chunk0200_371_1	chr9	26329830	26330439	+	0	NA	Intergenic	Intergenic	263459	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.004926	0.454098	323(CAGAACACCATGTGAC,-,0.00)
chunk0020_213_1	chr1	235237153	235237745	+	0	NA	intron (NM_031371, intron 8 of 22)	intron (NM_031371, intron 8 of 22)	-47333	NR_039908	100616224		NR_039908	ENSG00000263439	MIR4753	mir-4753	microRNA 4753	ncRNA	0.005068	0.318718	
chunk0031_235_1	chr10	126583052	126583380	+	0	NA	Intergenic	Intergenic	-61775	NM_001004298	118611	Hs.587663	NM_001004298	ENSG00000154493	C10orf90	FATS|bA422P15.2	chromosome 10 open reading frame 90	protein-coding	0.009146	0.358663	
chunk0212_302_1	chrX	142063206	142063405	+	0	NA	Intergenic	L1PB|LINE|L1	141985	NM_016249	51438	Hs.123536	NM_016249	ENSG00000046774	MAGEC2	CT10|HCA587|MAGEE1	MAGE family member C2	protein-coding	0.005025	0.360000	
chunk0071_47_1	chr15	79935849	79936137	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-12239	NR_037652	400410	Hs.729127	NM_001100879	ENSG00000180953	ST20	HCCS-1	suppressor of tumorigenicity 20	protein-coding	0.006944	0.453287	185(AGGCACATCCTGTACA,-,0.00),186(GGCACATCCTGTACAG,+,0.00)
chunk0050_393_1	chr12	109158970	109159527	+	0	NA	intron (NM_001093, intron 1 of 51)	intron (NM_001093, intron 1 of 51)	19851	NM_001093	32	Hs.234898	NM_001093	ENSG00000076555	ACACB	ACC2|ACCB|HACC275	acetyl-CoA carboxylase beta	protein-coding	0.017953	0.460573	
chunk0153_79_1	chr5	68087807	68088330	+	0	NA	Intergenic	MamTip3|DNA|hAT-Tip100	-101808	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.005736	0.425573	
chunk0082_440_1	chr17	61779999	61780384	+	0	NA	intron (NM_032043, intron 13 of 19)	intron (NM_032043, intron 13 of 19)	83368	NM_032043	83990	Hs.128903	NM_032043	ENSG00000136492	BRIP1	BACH1|FANCJ|OF	BRCA1 interacting protein C-terminal helicase 1	protein-coding	0.002597	0.334197	
chunk0010_406_1	chr1	119576304	119577054	+	0	NA	Intergenic	L1PA6|LINE|L1	12799	NR_033781	128102	Hs.681806	NR_033781		HSD3BP4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 4	pseudo	0.004000	0.372836	531(AAAGACACAATGTACC,-,0.00)
chunk0161_11_1	chr5	165591801	165592197	+	0	NA	Intergenic	Intergenic	1121720	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.005051	0.340050	
chunk0175_168_1	chr7	4700753	4701120	+	0	NA	intron (NM_001037165, intron 1 of 8)	intron (NM_001037165, intron 1 of 8)	18637	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.016349	0.532609	
chunk0070_151_1	chr15	71146563	71147200	+	0	NA	intron (NM_024817, intron 1 of 16)	intron (NM_024817, intron 1 of 16)	5432	NM_024817	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.006279	0.445141	358(TAGAACATTCTGTACC,-,0.00),359(AGAACATTCTGTACCC,+,0.00)
chunk0042_55_1	chr12	1871199	1871435	+	0	NA	intron (NM_172364, intron 18 of 37)	(GT)n|Simple_repeat|Simple_repeat	47387	NM_172364	93589	Hs.13768	NM_172364	ENSG00000151062	CACNA2D4	RCD4	calcium voltage-gated channel auxiliary subunit alpha2delta 4	protein-coding	0.012712	0.493671	
chunk0180_410_1	chr7	75945297	75945592	+	0	NA	intron (NM_000941, intron 1 of 15)	intron (NM_000941, intron 1 of 15)	1661	NR_002955	677801	Hs.689708	NR_002955	ENSG00000201643	SNORA14A	ACA14a	small nucleolar RNA, H/ACA box 14A	snoRNA	0.010169	0.429054	
chunk0191_145_1	chr8	48850389	48851047	+	0	NA	Intergenic	Intergenic	70722	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.003040	0.376328	
chunk0113_435_1	chr20	62391300	62391543	+	0	NA	exon (NM_031215, exon 9 of 10)	exon (NM_031215, exon 9 of 10)	4356	NM_001024	6227	Hs.190968	NM_001024	ENSG00000171858	RPS21	HLDF|S21	ribosomal protein S21	protein-coding	0.049383	0.643443	
chunk0109_146_1	chr20	3556880	3557079	+	0	NA	intron (NM_001207047, intron 6 of 24)	intron (NM_001207047, intron 6 of 24)	85961	NM_139321	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.005025	0.415000	
chunk0100_233_1	chr2	112303207	112303422	+	0	NA	exon (NM_198581, exon 3 of 12)	exon (NM_198581, exon 3 of 12)	27713	NM_198581	376940	Hs.190477	NM_198581	ENSG00000188177	ZC3H6	ZC3HDC6	zinc finger CCCH-type containing 6	protein-coding	0.004651	0.351852	
chunk0194_375_1	chr8	90012513	90013089	+	0	NA	intron (NM_001359, intron 1 of 9)	intron (NM_001359, intron 1 of 9)	11449	NM_001359	1666	Hs.492212	NM_001359	ENSG00000104325	DECR1	DECR|NADPH|SDR18C1	2,4-dienoyl-CoA reductase 1	protein-coding	0.006944	0.414211	
chunk0195_58_1	chr8	93674324	93674577	+	0	NA	intron (NR_033858, intron 3 of 10)	intron (NR_033858, intron 3 of 10)	25983	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.011858	0.456693	80(AAGAACACAGTGTGTC,-,0.00),81(AGAACACAGTGTGTCT,+,0.00)
chunk0155_344_1	chr5	96984897	96985238	+	0	NA	intron (NM_175920, intron 2 of 17)	intron (NM_175920, intron 2 of 17)	26615	NM_175920	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.002933	0.385965	
chunk0064_97_1	chr14	90981683	90982004	+	0	NA	intron (NM_182398, intron 2 of 12)	Charlie24|DNA|hAT-Charlie	78806	NM_004755	9252	Hs.510225	NM_004755	ENSG00000100784	RPS6KA5	MSK1|MSPK1|RLPK	ribosomal protein S6 kinase A5	protein-coding	0.006231	0.357143	
chunk0099_211_1	chr2	95004233	95004700	+	0	NA	Intergenic	Intergenic	-21189	NM_022438	4118	Hs.80395	NM_002371	ENSG00000172005	MAL	MVP17|VIP17	mal, T cell differentiation protein	protein-coding	0.017131	0.570513	
chunk0168_143_1	chr6	83051749	83052320	+	0	NA	intron (NM_198920, intron 3 of 9)	L2c|LINE|L2	13807	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.003503	0.430070	
chunk0137_140_1	chr4	15375951	15376401	+	0	NA	intron (NM_001135171, intron 1 of 2)	intron (NM_001135171, intron 1 of 2)	1625	NM_001135171	114905	Hs.153714	NM_031911	ENSG00000163145	C1QTNF7	CTRP7|ZACRP7	C1q and TNF related 7	protein-coding	0.013333	0.401330	183(GTGACACAATGTTCCC,+,0.00)
chunk0043_369_1	chr12	24082225	24082545	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	-130036	NR_030625	100126320		NR_030625	ENSG00000216192	MIR920	MIRN920|hsa-mir-920	microRNA 920	ncRNA	0.003125	0.333333	
chunk0076_421_1	chr16	72952946	72953313	+	0	NA	intron (NM_001164766, intron 1 of 8)	intron (NM_001164766, intron 1 of 8)	95246	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.013624	0.388587	
chunk0156_440_1	chr5	114702259	114703238	+	0	NA	intron (NR_130785, intron 1 of 12)	intron (NR_130785, intron 1 of 12)	70665	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.006129	0.373469	
chunk0160_52_1	chr5	149613885	149614728	+	0	NA	intron (NM_001001669, intron 4 of 12)	L1ME3G|LINE|L1	32734	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.008304	0.452607	305(CTGAACAACTTGTACC,-,0.00),306(TGAACAACTTGTACCT,+,0.00)
chunk0194_246_1	chr8	86414389	86414887	+	0	NA	intron (NM_007013, intron 9 of 24)	intron (NM_007013, intron 9 of 24)	71873	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.362725	
chunk0030_132_1	chr10	113461104	113461463	+	0	NA	Intergenic	L1MEh|LINE|L1	-89548	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.005571	0.494444	154(CAGAACATCTTGTTTC,-,0.00),155(AGAACATCTTGTTTCT,+,0.00)
chunk0162_151_1	chr6	3380379	3380578	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	64535	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.010050	0.360000	
chunk0171_14_1	chr6	119757428	119757772	+	0	NA	Intergenic	L1PA17|LINE|L1	-257579	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.002907	0.397101	
chunk0004_111_1	chr1	44402339	44402580	+	0	NA	Intergenic	Intergenic	-2829	NM_018150	55182	Hs.456557	NM_018150	ENSG00000187147	RNF220	C1orf164	ring finger protein 220	protein-coding	0.004149	0.388430	
chunk0022_207_1	chr10	13808201	13808453	+	0	NA	intron (NM_018027, intron 4 of 24)	intron (NM_018027, intron 4 of 24)	221388	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.015873	0.399209	
chunk0121_289_1	chr3	23612387	23612719	+	0	NA	Intergenic	Intergenic	-193340	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.024096	0.486486	263(TAGAACGCAATGTGCT,-,0.00),264(AGAACGCAATGTGCTC,+,0.00)
chunk0188_406_1	chr8	18774221	18774886	+	0	NA	intron (NM_015310, intron 8 of 15)	intron (NM_015310, intron 8 of 15)	34342	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.010526	0.405405	235(CAATACATCGTGTTCC,-,0.00),236(AATACATCGTGTTCCT,+,0.00),354(TGGTACAGCCTGTTCC,-,0.00),355(GGTACAGCCTGTTCCT,+,0.00)
chunk0072_52_1	chr16	1421148	1421347	+	0	NA	promoter-TSS (NM_001272051)	promoter-TSS (NM_001272051)	-447	NM_001272051	283951	Hs.58373	NM_001010878	ENSG00000174109	C16orf91	CCSMST1|URLC5|gs103	chromosome 16 open reading frame 91	protein-coding	0.060302	0.505000	
chunk0125_47_1	chr3	63932827	63933252	+	0	NA	intron (NM_001177387, intron 3 of 12)	intron (NM_001177387, intron 3 of 12)	34640	NM_001177387	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.002353	0.392019	
chunk0188_163_1	chr8	10760995	10761453	+	0	NA	Intergenic	Intergenic	-30650	NM_031439	83595	Hs.709543	NM_031439	ENSG00000171056	SOX7	-	SRY-box transcription factor 7	protein-coding	0.026201	0.498911	
chunk0178_113_1	chr7	30970349	30971132	+	0	NA	intron (NM_000823, intron 4 of 12)	intron (NM_000823, intron 4 of 12)	6719	NM_000823	2692	Hs.767	NM_000823	ENSG00000106128	GHRHR	GHRFR|GRFR|IGHD1B|IGHD4	growth hormone releasing hormone receptor	protein-coding	0.008940	0.545918	395(GGATACATTGTGTTCC,-,0.00),396(GATACATTGTGTTCCC,+,0.00)
chunk0174_37_1	chr6	154415424	154416034	+	0	NA	intron (NM_173515, intron 9 of 12)	intron (NM_173515, intron 9 of 12)	-58963	NM_015553	26034	Hs.146100	NM_015553	ENSG00000074706	IPCEF1	PIP3-E	interaction protein for cytohesin exchange factors 1	protein-coding	0.008197	0.418985	
chunk0048_337_1	chr12	84137320	84137531	+	0	NA	Intergenic	L1ME1|LINE|L1	775404	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.004739	0.301887	
chunk0018_410_1	chr1	222652334	222652871	+	0	NA	intron (NM_198551, intron 13 of 27)	intron (NM_198551, intron 13 of 27)	8299	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.003724	0.392193	
chunk0035_3_1	chr11	39776869	39777525	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	515933	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.009146	0.388128	326(TGGGACACACCGTTCC,-,0.00),327(GGGACACACCGTTCCC,+,0.00),421(AGGGTCACTGTGTACC,-,0.00)
chunk0008_296_1	chr1	94993785	94994195	+	0	NA	intron (NR_131032, intron 2 of 2)	intron (NR_131032, intron 2 of 2)	65962	NR_033998	729970	Hs.297988	NR_033998	ENSG00000235501	LOC729970	-	hCG2028352-like	ncRNA	0.012195	0.445255	
chunk0024_217_1	chr10	37561145	37561794	+	0	NA	Intergenic	Intergenic	41462	NM_001190489	100288485	Hs.727092	NM_001190489	ENSG00000256892	MTRNR2L7	HN7	MT-RNR2 like 7	protein-coding	0.004622	0.372308	
chunk0090_206_1	chr18	73318684	73319209	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-5995	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.007619	0.361217	
chunk0157_316_1	chr5	121970102	121970491	+	0	NA	intron (NM_152546, intron 1 of 7)	intron (NM_152546, intron 1 of 7)	8335	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.005141	0.315385	
chunk0054_397_1	chr13	50412229	50412598	+	0	NA	intron (NR_109974, intron 3 of 6)	intron (NR_109974, intron 3 of 6)	115036	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.002710	0.359459	
chunk0127_296_1	chr3	98185168	98185616	+	0	NA	Intergenic	HUERS-P3b-int|LTR|ERV1	16692	NM_001005515	403274	Hs.554713	NM_001005515	ENSG00000233412	OR5H15	-	olfactory receptor family 5 subfamily H member 15	protein-coding	0.000000	0.400891	226(AAGAACAGCTTGTCCT,-,0.00),227(AGAACAGCTTGTCCTT,+,0.00)
chunk0184_428_1	chr7	122919740	122920029	+	0	NA	Intergenic	Intergenic	-33125	NM_017954	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.000000	0.344828	
chunk0002_101_1	chr1	15222839	15223292	+	0	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	-24207	NM_052929	114827	Hs.659997	NM_052929	ENSG00000142621	FHAD1	-	forkhead associated phosphopeptide binding domain 1	protein-coding	0.006623	0.477974	
chunk0045_70_1	chr12	45632695	45633241	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	94953	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.012821	0.440585	
chunk0037_291_1	chr11	76112986	76113333	+	0	NA	intron (NM_003369, intron 13 of 14)	HAL1|LINE|L1	93371	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.000000	0.353448	
chunk0193_235_1	chr8	76689808	76690511	+	0	NA	intron (NM_024721, intron 1 of 10)	intron (NM_024721, intron 1 of 10)	-6884	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.004267	0.328125	
chunk0166_13_1	chr6	41623352	41623783	+	0	NA	Intergenic	L2c|LINE|L2	-13610	NM_001300804	4188	Hs.520119	NM_005586	ENSG00000112559	MDFI	I-MF|I-mfa	MyoD family inhibitor	protein-coding	0.011601	0.465278	
chunk0042_43_1	chr12	1649276	1649728	+	0	NA	Intergenic	Intergenic	10878	NR_037422	100500816		NR_037422	ENSG00000266043	MIR3649	-	microRNA 3649	ncRNA	0.008850	0.474614	
chunk0039_365_1	chr11	106121344	106122036	+	0	NA	Intergenic	LTR36|LTR|ERV1	-43952	NM_152433	143879	Hs.101949	NM_152433	ENSG00000182359	KBTBD3	BKLHD3	kelch repeat and BTB domain containing 3	protein-coding	0.011561	0.435786	
chunk0140_392_1	chr4	75306533	75306867	+	0	NA	Intergenic	Intergenic	-47376	NR_033964	441025	Hs.407667	NR_033964	ENSG00000251383	LINC02483	-	long intergenic non-protein coding RNA 2483	ncRNA	0.008982	0.373134	
chunk0004_399_1	chr1	52158274	52158483	+	0	NA	intron (NM_007324, intron 1 of 17)	ERV3-16A3_I-int|LTR|ERVL	16284	NM_007324	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.004785	0.495238	
chunk0021_92_1	chr10	2587500	2588030	+	0	NA	Intergenic	Intergenic	-272691	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.001887	0.338983	
chunk0007_6_1	chr1	77179387	77180177	+	0	NA	intron (NM_005482, intron 3 of 10)	intron (NM_005482, intron 3 of 10)	39665	NM_005482	10026	Hs.178305	NM_005482	ENSG00000142892	PIGK	GPI8	phosphatidylinositol glycan anchor biosynthesis class K	protein-coding	0.002532	0.340076	
chunk0146_286_1	chr4	164149952	164150305	+	0	NA	intron (NM_001166373, intron 1 of 7)	intron (NM_001166373, intron 1 of 7)	47583	NM_012403	23520	Hs.661161	NM_012403		ANP32C	PP32R1	acidic nuclear phosphoprotein 32 family member C	protein-coding	0.002833	0.293785	
chunk0166_72_1	chr6	43086848	43087071	+	0	NA	intron (NM_001270398, intron 1 of 19)	MER91A|DNA|hAT-Tip100	10145	NM_001270398	5754	Hs.90572	NM_002821	ENSG00000112655	PTK7	CCK-4|CCK4	protein tyrosine kinase 7 (inactive)	protein-coding	0.000000	0.459821	
chunk0039_247_1	chr11	102158255	102158609	+	0	NA	intron (NM_001282098, intron 2 of 6)	MER5A1|DNA|hAT-Charlie	45992	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.005650	0.400000	
chunk0117_124_1	chr22	19060192	19060538	+	0	NA	intron (NR_033674, intron 4 of 8)	intron (NR_033674, intron 4 of 8)	-11990	NR_024157	25786	Hs.720269	NR_024157	ENSG00000273311	DGCR11	DGS-D	DiGeorge syndrome critical region gene 11	ncRNA	0.017341	0.527378	
chunk0128_323_1	chr3	111913954	111914479	+	0	NA	intron (NM_145753, intron 3 of 16)	L1ME3G|LINE|L1	54495	NM_001134439	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.005714	0.338403	
chunk0131_204_1	chr3	148734484	148734811	+	0	NA	intron (NM_031850, intron 3 of 3)	intron (NM_031850, intron 3 of 3)	4467	NM_032049	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.006116	0.387195	
chunk0135_85_1	chr3	186302777	186303107	+	0	NA	intron (NM_001346, intron 3 of 24)	intron (NM_001346, intron 3 of 24)	59292	NM_001346	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.009091	0.501511	
chunk0173_23_1	chr6	141734611	141735075	+	0	NA	Intergenic	Intergenic	353956	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.002155	0.326882	
chunk0209_81_1	chrX	38371664	38371906	+	0	NA	intron (NM_000531, intron 3 of 9)	intron (NM_000531, intron 3 of 9)	19302	NM_000531	5009	Hs.117050	NM_000531	ENSG00000036473	OTC	OCTD	ornithine carbamoyltransferase	protein-coding	0.004132	0.390947	117(AAGAACATTTTGCTCT,-,0.00),118(AGAACATTTTGCTCTT,+,0.00)
chunk0188_172_1	chr8	11134091	11134421	+	0	NA	intron (NM_173683, intron 1 of 2)	L2c|LINE|L2	67110	NM_173683	286046	Hs.657083	NM_173683	ENSG00000171044	XKR6	C8orf21|C8orf5|C8orf7|XRG6	XK related 6	protein-coding	0.003030	0.429003	
chunk0106_168_1	chr2	200786183	200786940	+	0	NA	intron (NR_001557, intron 29 of 30)	intron (NR_001557, intron 29 of 30)	-24985	NM_001207067	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.003963	0.331135	
chunk0131_459_1	chr3	154126600	154127168	+	0	NA	intron (NM_015595, intron 3 of 14)	Tigger3b|DNA|TcMar-Tigger	5524	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.005282	0.386643	
chunk0091_418_1	chr19	16734584	16734862	+	0	NA	intron (NM_001007525, intron 3 of 18)	AluJr|SINE|Alu	14747	NM_001007525	284434	Hs.406014	NM_001007525	ENSG00000188039	NWD1	-	NACHT and WD repeat domain containing 1	protein-coding	0.007194	0.473118	
chunk0112_429_1	chr20	47484511	47484976	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	-17114	NM_006534	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.010753	0.366953	
chunk0081_328_1	chr17	46189830	46190341	+	0	NA	intron (NM_001193465, intron 2 of 15)	intron (NM_001193465, intron 2 of 15)	2715	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.013699	0.402344	
chunk0009_102_1	chr1	102238345	102239194	+	0	NA	Intergenic	L1ME3A|LINE|L1	-241535	NM_001288823	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.003534	0.344706	
chunk0092_98_1	chr19	23115304	23115551	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-1548	NM_001277403	100129543	Hs.427120	NM_001277403	ENSG00000183850	ZNF730	-	zinc finger protein 730	protein-coding	0.016194	0.423387	
chunk0162_385_1	chr6	7561475	7562004	+	0	NA	intron (NM_001008844, intron 4 of 23)	intron (NM_001008844, intron 4 of 23)	20102	NM_004415	1832	Hs.519873	NM_004415	ENSG00000096696	DSP	DCWHKTA|DP	desmoplakin	protein-coding	0.017013	0.462264	298(TAGAACAATGTGTTTT,-,0.00),299(AGAACAATGTGTTTTA,+,0.00)
chunk0081_454_1	chr17	49353679	49354048	+	0	NA	intron (NM_014897, intron 1 of 5)	intron (NM_014897, intron 1 of 5)	-7302	NR_110884	102724596	Hs.559253	NR_110882	ENSG00000248714	LOC102724596	-	uncharacterized LOC102724596	ncRNA	0.002710	0.362162	
chunk0006_289_1	chr1	70840194	70840510	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	133899	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.000000	0.324921	
chunk0013_404_1	chr1	173009380	173009761	+	0	NA	Intergenic	MIR|SINE|MIR	41393	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.002625	0.376963	169(TGGTACACTAAGTGCT,-,0.00),170(GGTACACTAAGTGCTA,+,0.00)
chunk0182_287_1	chr7	98251904	98252482	+	0	NA	promoter-TSS (NM_015395)	promoter-TSS (NM_015395)	58	NM_015395	25851	Hs.592281	NM_015395	ENSG00000205356	TECPR1	-	tectonin beta-propeller repeat containing 1	protein-coding	0.112457	0.732297	
chunk0105_89_1	chr2	184081041	184081602	+	0	NA	Intergenic	L1MEc|LINE|L1	-297654	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.003565	0.359431	
chunk0012_412_1	chr1	164166437	164167051	+	0	NA	Intergenic	L1PA6|LINE|L1	-392616	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.014658	0.474797	
chunk0088_442_1	chr18	56501829	56502149	+	0	NA	Intergenic	Intergenic	136700	NR_024546	9352	Hs.114412	NM_004786	ENSG00000091164	TXNL1	HEL-S-114|TRP32|TXL-1|TXNL|Txl	thioredoxin like 1	protein-coding	0.009375	0.426791	270(GTAACATGGTGTTCCA,+,0.00)
chunk0130_5_1	chr3	128346564	128347092	+	0	NA	intron (NM_021937, intron 5 of 6)	Cheshire|DNA|hAT-Charlie	-116766	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.005682	0.362949	
chunk0011_346_1	chr1	152316822	152317276	+	0	NA	intron (NM_002016, intron 1 of 2)	L2|LINE|L2	3590	NR_103778	339400	Hs.23783	NR_103778	ENSG00000237975	FLG-AS1	-	FLG antisense RNA 1	ncRNA	0.000000	0.404396	232(ATAAACAGTCTGTGCT,-,0.00),233(TAAACAGTCTGTGCTC,+,0.00)
chunk0129_250_1	chr3	122202807	122203256	+	0	NA	intron (NM_001178065, intron 1 of 6)	L1ME3E|LINE|L1	18697	NM_001178065	846	Hs.435615	NM_000388	ENSG00000036828	CASR	CAR|EIG8|FHH|FIH|GPRC2A|HHC|HHC1|HYPOC1|NSHPT|PCAR1|hCasR	calcium sensing receptor	protein-coding	0.006682	0.388889	
chunk0175_92_1	chr7	2733259	2733487	+	0	NA	intron (NM_001293092, intron 2 of 2)	intron (NM_001293092, intron 2 of 2)	29767	NM_001282440	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.048246	0.572052	
chunk0115_109_1	chr21	22815688	22815887	+	0	NA	Intergenic	Intergenic	-263497	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.005025	0.295000	
chunk0004_77_1	chr1	43607932	43608641	+	0	NA	intron (NM_130440, intron 20 of 32)	intron (NM_130440, intron 20 of 32)	-41840	NM_014663	9682	Hs.155983	NM_014663	ENSG00000066135	KDM4A	JHDM3A|JMJD2|JMJD2A|TDRD14A	lysine demethylase 4A	protein-coding	0.008463	0.543662	
chunk0104_237_1	chr2	176604078	176604372	+	0	NA	Intergenic	Intergenic	-3173	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.000000	0.328814	
chunk0094_202_1	chr2	6408399	6408948	+	0	NA	Intergenic	Intergenic	-33251	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.003643	0.365455	
chunk0154_239_1	chr5	80990056	80990255	+	0	NA	intron (NM_006909, intron 1 of 26)	intron (NM_006909, intron 1 of 26)	-29248	NR_105015	102524628	Hs.737159	NR_105015	ENSG00000251450	RASGRF2-AS1	-	RASGRF2 antisense RNA 1	ncRNA	0.010050	0.420000	
chunk0007_251_1	chr1	82686879	82687266	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	297850	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.002584	0.420103	
chunk0194_318_1	chr8	88298129	88298552	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	29148	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.009456	0.384434	
chunk0014_176_1	chr1	178449266	178449540	+	0	NA	intron (NM_170692, intron 9 of 17)	intron (NM_170692, intron 9 of 17)	-63674	NM_001170724	84066	Hs.534501	NM_032126	ENSG00000240021	TEX35	C1orf49|TSC24	testis expressed 35	protein-coding	0.003650	0.360000	
chunk0014_167_1	chr1	178330816	178331298	+	0	NA	intron (NM_170692, intron 3 of 17)	MIR|SINE|MIR	-10414	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.006224	0.393375	
chunk0056_90_1	chr13	81695649	81696097	+	0	NA	Intergenic	Intergenic	-468890	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.002232	0.374165	
chunk0042_60_1	chr12	1979964	1980287	+	0	NA	intron (NM_152640, intron 3 of 8)	L1ME3|LINE|L1	24386	NM_152640	196513	Hs.130934	NM_152640	ENSG00000151065	DCP1B	DCP1	decapping mRNA 1B	protein-coding	0.003096	0.354938	
chunk0191_289_1	chr8	54087803	54088006	+	0	NA	intron (NM_001279358, intron 2 of 8)	LTR10C|LTR|ERV1	13650	NM_001279360	10434	Hs.744046	NM_006330	ENSG00000120992	LYPLA1	APT-1|APT1|LPL-I|LPL1|hAPT1	lysophospholipase 1	protein-coding	0.019704	0.426471	
chunk0168_129_1	chr6	82263222	82263670	+	0	NA	Intergenic	Intergenic	-15692	NM_015525	25998	Hs.306425	NM_015525	ENSG00000005700	IBTK	BTBD26|BTKI	inhibitor of Bruton tyrosine kinase	protein-coding	0.006696	0.396437	267(GGGGACAGAGTGTCAC,-,0.00),268(GGGACAGAGTGTCACT,+,0.00)
chunk0026_438_1	chr10	71342120	71342781	+	0	NA	intron (NR_033414, intron 2 of 3)	intron (NR_033414, intron 2 of 3)	23197	NM_001174098	55315	Hs.438419	NM_018344	ENSG00000198246	SLC29A3	ENT3|HCLAP|HJCD|PHID	solute carrier family 29 member 3	protein-coding	0.010590	0.483384	
chunk0143_82_1	chr4	108236982	108237579	+	0	NA	Intergenic	Intergenic	65160	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.005025	0.354515	
chunk0167_5_1	chr6	53439728	53440252	+	0	NA	Intergenic	Intergenic	-90811	NM_021814	60481	Hs.520189	NM_021814	ENSG00000012660	ELOVL5	HELO1|SCA38|dJ483K16.1	ELOVL fatty acid elongase 5	protein-coding	0.005725	0.302857	355(AAGAACTGTTTGTGCT,-,0.00),356(AGAACTGTTTGTGCTC,+,0.00)
chunk0124_246_1	chr3	56812956	56813328	+	0	NA	intron (NM_001128615, intron 4 of 12)	AmnSINE2|SINE|tRNA-Deu	-11175	NM_019555	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.000000	0.404826	
chunk0012_162_1	chr1	158197139	158197711	+	0	NA	Intergenic	L1MA4|LINE|L1	17478	NM_001766	912	Hs.1799	NM_001766	ENSG00000158473	CD1D	CD1A|R3|R3G1	CD1d molecule	protein-coding	0.012238	0.380454	286(TTGAACAGCATGTCCT,-,0.00),287(TGAACAGCATGTCCTG,+,0.00)
chunk0200_135_1	chr9	17644379	17644754	+	0	NA	intron (NM_003026, intron 1 of 8)	L1PA7|LINE|L1	65612	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.010667	0.375000	137(GGTACACTGTGTGTTC,+,0.00)
chunk0179_292_1	chr7	49754158	49754379	+	0	NA	Intergenic	MER53|DNA|hAT	-19393	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.301802	91(AAGTACAGGATGTCCT,-,0.00),92(AGTACAGGATGTCCTG,+,0.00)
chunk0180_30_1	chr7	54000936	54001169	+	0	NA	Intergenic	Intergenic	-189121	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.004292	0.393162	
chunk0034_241_1	chr11	34105456	34105976	+	0	NA	5' UTR (NM_024662, exon 1 of 29)	5' UTR (NM_024662, exon 1 of 29)	152	NM_001144030	55226	Hs.577281	NM_024662	ENSG00000135372	NAT10	ALP|Kre33|NET43	N-acetyltransferase 10	protein-coding	0.073077	0.608445	
chunk0195_47_1	chr8	93436079	93436528	+	0	NA	intron (NR_033858, intron 7 of 10)	intron (NR_033858, intron 7 of 10)	264130	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.006682	0.457778	
chunk0043_187_1	chr12	18878197	18878641	+	0	NA	Intergenic	L2c|LINE|L2	140308	NM_033328	93661	Hs.131288	NM_033328	ENSG00000177938	CAPZA3	CAPPA3|Gsg3|HEL-S-86	capping actin protein of muscle Z-line subunit alpha 3	protein-coding	0.006757	0.348315	
chunk0205_256_1	chr9	110744417	110744896	+	0	NA	intron (NM_001166281, intron 6 of 11)	L1MA9|LINE|L1	75885	NM_005592	4593	Hs.521653	NM_005592	ENSG00000030304	MUSK	CMS9|FADS|FADS1	muscle associated receptor tyrosine kinase	protein-coding	0.004175	0.358333	
chunk0121_145_1	chr3	18883493	18883804	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-264877	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.003215	0.320513	166(TAGTACATAGTGTACT,-,0.00),167(AGTACATAGTGTACTA,+,0.00)
chunk0212_317_1	chrX	143694902	143695159	+	0	NA	Intergenic	Intergenic	25638	NM_001009615	494119		NM_001009615	ENSG00000268988	SPANXN2	CT11.7|SPANX-N2	SPANX family member N2	protein-coding	0.003891	0.337209	
chunk0044_330_1	chr12	38175484	38175960	+	0	NA	Intergenic	Intergenic	-141033	NM_001013620	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.010504	0.429769	
chunk0032_133_1	chr11	4503278	4503522	+	0	NA	Intergenic	Intergenic	14521	NM_001005171	390036	Hs.553726	NM_001005171	ENSG00000196778	OR52K1	OR11-8	olfactory receptor family 52 subfamily K member 1	protein-coding	0.008197	0.542857	
chunk0029_211_1	chr10	101961653	101962106	+	0	NA	intron (NM_024541, intron 20 of 25)	intron (NM_024541, intron 20 of 25)	94296	NM_024541	79591	Hs.16004	NM_024541	ENSG00000120029	ARMH3	C10orf76	armadillo like helical domain containing 3	protein-coding	0.004415	0.394273	271(AGGGACAGGATGTACC,-,0.00),272(GGGACAGGATGTACCA,+,0.00)
chunk0135_23_1	chr3	184519722	184520158	+	0	NA	Intergenic	L1M5|LINE|L1	36978	NR_046593	100874079	Hs.574899	NR_046593	ENSG00000230215	LINC01840	EIF2B5-AS1	long intergenic non-protein coding RNA 1840	ncRNA	0.009174	0.347826	
chunk0041_124_1	chr11	125037070	125037476	+	0	NA	intron (NM_025004, intron 13 of 15)	L1M1|LINE|L1	-25844	NM_001145290	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.002463	0.388206	
chunk0173_85_1	chr6	142844748	142845435	+	0	NA	intron (NM_006734, intron 1 of 9)	intron (NM_006734, intron 1 of 9)	100110	NM_006734	3097	Hs.510172	NM_006734	ENSG00000010818	HIVEP2	HIV-EP2|MBP-2|MIBP1|MRD43|SHN2|ZAS2|ZNF40B	human immunodeficiency virus type I enhancer binding protein 2	protein-coding	0.005822	0.389535	
chunk0187_433_1	chr7	158732976	158733803	+	0	NA	3' UTR (NM_020728, exon 22 of 22)	3' UTR (NM_020728, exon 22 of 22)	-28558	NM_017760	54892	Hs.18616	NM_017760	ENSG00000146918	NCAPG2	3KS|CAP-G2|CAPG2|LUZP5|MTB|hCAP-G2	non-SMC condensin II complex subunit G2	protein-coding	0.008464	0.352657	292(AAGGACAACGTGTACC,-,0.00),293(AGGACAACGTGTACCT,+,0.00)
chunk0102_374_1	chr2	153469295	153469852	+	0	NA	Intergenic	Intergenic	9235	NM_019845	56475	Hs.100890	NM_019845	ENSG00000177519	RPRM	REPRIMO	reprimo, TP53 dependent G2 arrest mediator homolog	protein-coding	0.007181	0.392473	
chunk0124_375_1	chr3	59409289	59409780	+	0	NA	Intergenic	Intergenic	-359545	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.004073	0.380081	
chunk0055_35_1	chr13	52032491	52032831	+	0	NA	3' UTR (NM_021645, exon 2 of 2)	3' UTR (NM_021645, exon 2 of 2)	7970	NM_021645	9724	Hs.512963	NM_021645	ENSG00000253797	UTP14C	2700066J21Rik|KIAA0266|UTP14B	UTP14C small subunit processome component	protein-coding	0.002941	0.390029	187(GTCACAGGATGTTCTG,+,0.00)
chunk0125_58_1	chr3	64072069	64072620	+	0	NA	intron (NR_045697, intron 1 of 2)	L2a|LINE|L2	4380	NR_045697	100652759	Hs.731187	NR_045697	ENSG00000241111	PRICKLE2-AS1	-	PRICKLE2 antisense RNA 1	ncRNA	0.005445	0.449275	
chunk0095_14_1	chr2	12153858	12154256	+	0	NA	intron (NR_110196, intron 2 of 5)	L1MC1|LINE|L1	-45073	NR_037452	100500884		NR_037452	ENSG00000264089	MIR3681	-	microRNA 3681	ncRNA	0.002513	0.368421	79(AAGTACAGAGAGTTCC,-,0.00),80(AGTACAGAGAGTTCCC,+,0.00)
chunk0119_450_1	chr22	50362835	50363116	+	0	NA	intron (NM_001242900, intron 1 of 22)	intron (NM_001242900, intron 1 of 22)	19658	NM_001242899	9701	Hs.449098	NM_014678	ENSG00000100239	PPP6R2	KIAA0685|PP6R2|SAP190|SAPS2	protein phosphatase 6 regulatory subunit 2	protein-coding	0.010676	0.460993	
chunk0125_154_1	chr3	66450749	66450948	+	0	NA	intron (NM_015541, intron 3 of 18)	intron (NM_015541, intron 3 of 18)	49573	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.000000	0.470000	
chunk0026_361_1	chr10	69124965	69125173	+	0	NA	intron (NM_001035260, intron 1 of 7)	intron (NM_001035260, intron 1 of 7)	917	NM_001035260	9559	Hs.499925	NM_004896	ENSG00000122958	VPS26A	HB58|Hbeta58|PEP8A|VPS26	VPS26, retromer complex component A	protein-coding	0.024038	0.492823	
chunk0079_153_1	chr17	13225605	13225877	+	0	NA	Intergenic	Intergenic	-207677	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.003676	0.380952	
chunk0065_115_1	chr15	24680316	24680637	+	0	NA	3' UTR (NM_018958, exon 1 of 1)	3' UTR (NM_018958, exon 1 of 1)	5082	NM_018958	23742	Hs.649663	NM_018958	ENSG00000185823	NPAP1	C15orf2	nuclear pore associated protein 1	protein-coding	0.000000	0.456522	153(CTGCACATACAGTTCT,-,0.00),154(TGCACATACAGTTCTC,+,0.00)
chunk0147_275_1	chr4	183961002	183961420	+	0	NA	intron (NM_020225, intron 1 of 3)	intron (NM_020225, intron 1 of 3)	55855	NM_020225	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.019139	0.460621	
chunk0172_291_1	chr6	137838193	137838544	+	0	NA	intron (NR_049793, intron 3 of 3)	L1PB1|LINE|L1	-28820	NM_001270508	7128	Hs.211600	NM_006290	ENSG00000118503	TNFAIP3	A20|AISBL|OTUD7C|TNFA1P2	TNF alpha induced protein 3	protein-coding	0.005698	0.355114	
chunk0206_98_1	chr9	120728925	120729124	+	0	NA	Intergenic	Intergenic	-14537	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.010050	0.395000	
chunk0157_303_1	chr5	121162996	121163476	+	0	NA	Intergenic	Intergenic	-159314	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.002083	0.257796	
chunk0136_366_1	chr3	196073243	196073473	+	0	NA	intron (NM_001313966, intron 2 of 16)	AluJb|SINE|Alu	8732	NM_003234	7037	Hs.529618	NM_003234	ENSG00000072274	TFRC	CD71|IMD46|T9|TFR|TFR1|TR|TRFR|p90	transferrin receptor	protein-coding	0.021739	0.497835	
chunk0180_286_1	chr7	70032031	70032398	+	0	NA	intron (NM_015570, intron 2 of 18)	intron (NM_015570, intron 2 of 18)	433295	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.008174	0.331522	
chunk0064_100_1	chr14	91055239	91055495	+	0	NA	intron (NM_182398, intron 1 of 12)	L1MB8|LINE|L1	5282	NM_004755	9252	Hs.510225	NM_004755	ENSG00000100784	RPS6KA5	MSK1|MSPK1|RLPK	ribosomal protein S6 kinase A5	protein-coding	0.000000	0.334630	
chunk0120_320_1	chr3	10356103	10356340	+	0	NA	intron (NM_001001331, intron 14 of 22)	MIR3|SINE|MIR	25992	NR_036084	100422933		NR_036084	ENSG00000264534	MIR378B	-	microRNA 378b	ncRNA	0.016878	0.478992	18(AAGAACTACTTGTCCT,-,0.00),19(AGAACTACTTGTCCTT,+,0.00)
chunk0192_243_1	chr8	65644850	65645054	+	0	NA	intron (NM_001145839, intron 1 of 6)	CpG	299	NM_001145839	9650	Hs.584788	NM_014637	ENSG00000066855	MTFR1	CHPPR|FAM54A2	mitochondrial fission regulator 1	protein-coding	0.088235	0.682927	
chunk0109_231_1	chr20	5906650	5906878	+	0	NA	Intergenic	Intergenic	-4564	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.008772	0.423581	
chunk0174_128_1	chr6	157323378	157323640	+	0	NA	5' UTR (NM_018452, exon 1 of 4)	5' UTR (NM_018452, exon 1 of 4)	750	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.076336	0.642586	
chunk0156_75_1	chr5	103708759	103709036	+	0	NA	Intergenic	Intergenic	-146096	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.000000	0.305755	
chunk0144_158_1	chr4	131023649	131023848	+	0	NA	Intergenic	Intergenic	-741090	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.005025	0.320000	
chunk0133_92_1	chr3	167748354	167748784	+	0	NA	intron (NM_005025, intron 1 of 8)	intron (NM_005025, intron 1 of 8)	12846	NM_005025	5274	Hs.478153	NM_005025	ENSG00000163536	SERPINI1	PI12|neuroserpin	serpin family I member 1	protein-coding	0.011628	0.396752	
chunk0147_346_1	chr4	185591647	185592193	+	0	NA	intron (NM_003603, intron 21 of 22)	(ACAAA)n|Simple_repeat|Simple_repeat	-56362	NM_001114107	27295	Hs.701364	NM_014476	ENSG00000154553	PDLIM3	ALP	PDZ and LIM domain 3	protein-coding	0.010989	0.424132	
chunk0103_7_1	chr2	158828946	158829360	+	0	NA	Intergenic	Intergenic	33836	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.004831	0.409639	
chunk0106_418_1	chr2	208043496	208043856	+	0	NA	Intergenic	MER97c|DNA|hAT-Tip100	-18116	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.013889	0.407202	
chunk0141_430_1	chr4	88822911	88823666	+	0	NA	promoter-TSS (NM_001265579)	promoter-TSS (NM_001265579)	73	NM_001265580	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.017219	0.481481	
chunk0148_238_1	chr5	9582115	9582415	+	0	NA	Intergenic	Intergenic	33438	NR_003689	100113384		NR_003689		SNORD123	-	small nucleolar RNA, C/D box 123	snoRNA	0.003333	0.451827	
chunk0122_229_1	chr3	33719191	33719511	+	0	NA	Intergenic	Intergenic	-1138	NM_015097	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.000000	0.352025	122(AAGCACACTGTGTTTA,-,0.00),123(AGCACACTGTGTTTAT,+,0.00)
chunk0111_317_1	chr20	32307021	32307517	+	0	NA	intron (NM_004798, intron 1 of 8)	L1MC1|LINE|L1	29618	NM_004798	9371	Hs.369670	NM_004798	ENSG00000101350	KIF3B	FLA8|HH0048|KLP-11	kinesin family member 3B	protein-coding	0.006048	0.356137	
chunk0075_145_1	chr16	50487401	50487834	+	0	NA	Intergenic	Intergenic	-60713	NM_033119	85407	Hs.187578	NM_033119	ENSG00000140807	NKD1	Naked1	NKD inhibitor of WNT signaling pathway 1	protein-coding	0.009238	0.317972	
chunk0186_392_1	chr7	144607248	144607880	+	0	NA	intron (NM_022445, intron 6 of 8)	L2a|LINE|L2	-197337	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.001582	0.319115	
chunk0052_392_1	chr12	130639958	130640351	+	0	NA	Intergenic	Intergenic	-122289	NM_015347	23504	Hs.657441	NM_015347	ENSG00000060709	RIMBP2	PPP1R133|RBP2|RIM-BP2	RIMS binding protein 2	protein-coding	0.022901	0.479695	263(GGGGACAATGTGTACC,-,0.00),264(GGGACAATGTGTACCT,+,0.00)
chunk0201_374_1	chr9	68740646	68740891	+	0	NA	intron (NM_001278253, intron 1 of 13)	intron (NM_001278253, intron 1 of 13)	35354	NM_001278253	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.012245	0.406504	
chunk0071_58_1	chr15	80287432	80287866	+	0	NA	intron (NR_033833, intron 2 of 2)	intron (NR_033833, intron 2 of 2)	-35388	NR_120317									0.002304	0.347126	
chunk0120_242_1	chr3	8567753	8568275	+	0	NA	3' UTR (NM_014583, exon 6 of 6)	3' UTR (NM_014583, exon 6 of 6)	-3768	NR_024065	29931	Hs.433151	NM_013343		LINC00312	ERR-10|ERR10|LMCD1DN|LOH3CR2A|NAG-7|NAG7|NCRNA00312	long intergenic non-protein coding RNA 312	ncRNA	0.011494	0.414914	
chunk0150_43_1	chr5	31534520	31534933	+	0	NA	intron (NM_018356, intron 2 of 8)	MER58A|DNA|hAT-Charlie	2460	NM_018356	55322	Hs.519246	NM_018356	ENSG00000082213	C5orf22	-	chromosome 5 open reading frame 22	protein-coding	0.000000	0.400966	
chunk0049_123_1	chr12	91462888	91463389	+	0	NA	Intergenic	Intergenic	-280014	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.007984	0.390438	
chunk0023_204_1	chr10	25318917	25319473	+	0	NA	intron (NM_020752, intron 2 of 10)	L2c|LINE|L2	-142919	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.003597	0.398564	
chunk0207_426_1	chr9	137269175	137269643	+	0	NA	intron (NM_015456, intron 10 of 12)	intron (NM_015456, intron 10 of 12)	-8419	NM_017723	54863	Hs.495541	NM_017723	ENSG00000198113	TOR4A	C9orf167	torsin family 4 member A	protein-coding	0.032051	0.515991	
chunk0099_45_1	chr2	84160433	84161074	+	0	NA	Intergenic	Intergenic	-129929	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.001560	0.451713	367(AGGAACAGTCTGTCCA,-,0.00),368(GGAACAGTCTGTCCAG,+,0.00)
chunk0181_319_1	chr7	87674938	87675148	+	0	NA	intron (NM_001134406, intron 2 of 9)	L1PA13|LINE|L1	38280	NM_000927	5243	Hs.489033	NM_000927	ENSG00000085563	ABCB1	ABC20|CD243|CLCS|GP170|MDR1|P-GP|PGY1	ATP binding cassette subfamily B member 1	protein-coding	0.009524	0.559242	
chunk0171_369_1	chr6	130933761	130934265	+	0	NA	intron (NM_001199388, intron 3 of 17)	intron (NM_001199388, intron 3 of 17)	66754	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.011905	0.435644	
chunk0021_173_1	chr10	5467869	5468349	+	0	NA	Intergenic	Intergenic	21558	NR_073040	10276	Hs.25155	NM_005863	ENSG00000173848	NET1	ARHGEF8|NET1A	neuroepithelial cell transforming 1	protein-coding	0.006250	0.528067	
chunk0061_260_1	chr14	61397630	61397865	+	0	NA	intron (NM_006255, intron 2 of 13)	intron (NM_006255, intron 2 of 13)	76304	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.008511	0.381356	
chunk0081_322_1	chr17	46109613	46110216	+	0	NA	intron (NM_001193465, intron 3 of 15)	intron (NM_001193465, intron 3 of 15)	82886	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.003317	0.380795	286(AAGTACATTTTGTTCT,-,0.00),287(AGTACATTTTGTTCTG,+,0.00)
chunk0127_55_1	chr3	89162776	89163025	+	0	NA	intron (NM_005233, intron 2 of 16)	LTR16A|LTR|ERVL	55376	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.012048	0.476000	
chunk0018_426_1	chr1	222804835	222805354	+	0	NA	Intergenic	Intergenic	-9995	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.005780	0.425000	
chunk0194_312_1	chr8	88243836	88244409	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	83366	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.013962	0.329268	
chunk0159_37_1	chr5	137013279	137013641	+	0	NA	intron (NM_004598, intron 6 of 10)	MER103C|DNA|hAT-Charlie	485869	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.008287	0.380165	
chunk0052_156_1	chr13	23853064	23853447	+	0	NA	intron (NM_005932, intron 10 of 18)	Tigger3b|DNA|TcMar-Tigger	-35634	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.002611	0.346354	
chunk0017_3_1	chr1	204314218	204314647	+	0	NA	intron (NM_014935, intron 1 of 22)	intron (NM_014935, intron 1 of 22)	45497	NM_014935	22874	Hs.253146	NM_014935	ENSG00000143850	PLEKHA6	PEPP-3|PEPP3	pleckstrin homology domain containing A6	protein-coding	0.011655	0.516279	
chunk0065_413_1	chr14	105733448	105733991	+	0	NA	Intergenic	Intergenic	-60912	NR_046211	2003	Hs.744419	NR_046211		ELK2AP	ELK2|ELK2.1|ELK2P1	ETS transcription factor ELK2A, pseudogene	pseudo	0.018416	0.505515	
chunk0183_78_1	chr7	104624031	104624437	+	0	NA	intron (NM_199000, intron 1 of 2)	intron (NM_199000, intron 1 of 2)	179858	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.014778	0.383292	27(AAGAAGACGATGTTCC,-,0.00),28(AGAAGACGATGTTCCT,+,0.00)
chunk0134_414_1	chr3	183253572	183253876	+	0	NA	intron (NM_032047, intron 1 of 1)	CpG	480	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.098684	0.626230	
chunk0067_199_1	chr15	44893410	44894170	+	0	NA	Intergenic	L1PA6|LINE|L1	-62912	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.006579	0.373193	390(AGGAACAGGTTGTTCA,-,0.00),391(GGAACAGGTTGTTCAG,+,0.00)
chunk0088_448_1	chr18	56710306	56710895	+	0	NA	intron (NM_015285, intron 12 of 27)	intron (NM_015285, intron 12 of 27)	59215	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.008489	0.301695	
chunk0081_240_1	chr17	42946775	42947144	+	0	NA	Intergenic	Intergenic	17539	NM_001261434	80755	Hs.317403	NM_001261434	ENSG00000266967	AARSD1	-	alanyl-tRNA synthetase domain containing 1	protein-coding	0.005420	0.400000	208(GAACACACTCTGTTCT,-,0.00),209(AACACACTCTGTTCTT,+,0.00)
chunk0046_21_1	chr12	54356245	54356636	+	0	NA	intron (NR_120486, intron 1 of 3)	intron (NR_120486, intron 1 of 3)	2749	NR_120486	102724050	Hs.670941	NR_120486	ENSG00000258137	LOC102724050	-	uncharacterized LOC102724050	ncRNA	0.007673	0.497449	184(GGGAACAGTATGATCC,-,0.00),185(GGAACAGTATGATCCA,+,0.00)
chunk0020_69_1	chr1	232664904	232665618	+	0	NA	Intergenic	L1MEg|LINE|L1	77454	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.002801	0.332867	
chunk0147_207_1	chr4	179643619	179643818	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	1515431	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.005025	0.385000	
chunk0136_305_1	chr3	195164346	195164709	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	16656	NR_102710	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.002755	0.546703	
chunk0025_369_1	chr10	58640161	58640481	+	0	NA	intron (NM_001080512, intron 2 of 20)	intron (NM_001080512, intron 2 of 20)	-74694	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.003125	0.323988	
chunk0146_194_1	chr4	161248004	161248271	+	0	NA	Intergenic	L1M4|LINE|L1	-774596	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.343284	
chunk0032_435_1	chr10	132746348	132746925	+	0	NA	intron (NM_005539, intron 9 of 15)	intron (NM_005539, intron 9 of 15)	39397	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.032929	0.532872	284(TGGCACACAGCGTTCC,-,0.00),285(GGCACACAGCGTTCCC,+,0.00)
chunk0051_9_1	chr12	111503202	111503569	+	0	NA	intron (NM_001310121, intron 14 of 25)	MIR|SINE|MIR	68523	NM_001291424	10019	Hs.506784	NM_005475	ENSG00000111252	SH2B3	IDDM20|LNK	SH2B adaptor protein 3	protein-coding	0.002725	0.364130	
chunk0207_30_1	chrX	3697280	3697479	+	0	NA	intron (NM_005044, intron 1 of 8)	AluJb|SINE|Alu	16255	NM_005044	5613	Hs.390788	NM_005044	ENSG00000183943	PRKX	PKX1	protein kinase X-linked	protein-coding	0.005025	0.465000	
chunk0142_157_1	chr4	95093926	95094474	+	0	NA	intron (NM_001256794, intron 1 of 10)	intron (NM_001256794, intron 1 of 10)	2709	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.009124	0.351548	
chunk0049_36_1	chr12	89762793	89763383	+	0	NA	Intergenic	Intergenic	54133	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.005085	0.331641	
chunk0121_443_1	chr3	26375058	26375257	+	0	NA	Intergenic	L1PREC2|LINE|L1	-247652	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.005025	0.375000	
chunk0080_383_1	chr17	34346729	34347278	+	0	NA	Intergenic	Intergenic	-9449	NM_005408	6357	Hs.414629	NM_005408	ENSG00000181374	CCL13	CKb10|MCP-4|NCC-1|NCC1|SCYA13|SCYL1	C-C motif chemokine ligand 13	protein-coding	0.010929	0.356364	
chunk0036_263_1	chr11	65095967	65096271	+	0	NA	promoter-TSS (NR_073519)	promoter-TSS (NR_073519)	4	NM_013265	738	Hs.277517	NM_013265	ENSG00000149823	VPS51	ANG2|ANG3|C11orf2|C11orf3|FFR	VPS51 subunit of GARP complex	protein-coding	0.049342	0.619672	
chunk0128_41_1	chr3	104599032	104599701	+	0	NA	Intergenic	Intergenic	-767347	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.008969	0.386567	
chunk0068_331_1	chr15	57610168	57610584	+	0	NA	intron (NR_104371, intron 2 of 16)	intron (NR_104371, intron 2 of 16)	18472	NM_001285900	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.021635	0.508393	
chunk0175_407_1	chr6	168650376	168651100	+	0	NA	exon (NM_001166412, exon 10 of 13)	exon (NM_001166412, exon 10 of 13)	209587	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.026243	0.470345	
chunk0092_346_1	chr19	35322950	35323293	+	0	NA	Intergenic	AluSq2|SINE|Alu	-6045	NM_001278417	933	Hs.579691	NM_001771	ENSG00000012124	CD22	SIGLEC-2|SIGLEC2	CD22 molecule	protein-coding	0.023324	0.462209	
chunk0187_135_1	chr7	149421928	149422640	+	0	NA	Intergenic	Intergenic	38678	NM_015694	27153	Hs.38512	NM_015694	ENSG00000196453	ZNF777	-	zinc finger protein 777	protein-coding	0.088483	0.674614	
chunk0029_174_1	chr10	100442579	100442882	+	0	NA	Intergenic	L2a|LINE|L2	-20325	NM_003393	7479	Hs.421281	NM_003393	ENSG00000075290	WNT8B	-	Wnt family member 8B	protein-coding	0.006601	0.427632	
chunk0184_422_1	chr7	122808107	122809260	+	0	NA	intron (NM_017954, intron 1 of 29)	MamGypsy2-I|LTR|Gypsy	78076	NM_001009571	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.002602	0.342288	321(AAGAACATGAAGTCCT,-,0.00),322(AGAACATGAAGTCCTG,+,0.00),857(TAGGACTATATGTTCC,-,0.00),858(AGGACTATATGTTCCT,+,0.00)
chunk0118_383_1	chr22	36840247	36840886	+	0	NA	Intergenic	L1ME4b|LINE|L1	-20422	NM_000631	4689	Hs.474781	NM_000631	ENSG00000100365	NCF4	CGD3|NCF|P40PHOX|SH3PXD4	neutrophil cytosolic factor 4	protein-coding	0.007825	0.431250	
chunk0127_184_1	chr3	95613261	95613463	+	0	NA	Intergenic	Intergenic	69831	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.004950	0.300493	
chunk0091_412_1	chr19	16660849	16661081	+	0	NA	promoter-TSS (NM_024074)	promoter-TSS (NM_024074)	-162	NM_024074	79041	Hs.436068	NM_024074	ENSG00000072954	TMEM38A	TRIC-A|TRICA	transmembrane protein 38A	protein-coding	0.107759	0.755365	48(CAGAACAGGCAGCTCC,-,0.00),49(AGAACAGGCAGCTCCC,+,0.00)
chunk0047_243_1	chr12	72255169	72255511	+	0	NA	non-coding (NR_026837, exon 2 of 2)	non-coding (NR_026837, exon 2 of 2)	-17409	NM_013381	29953	Hs.199814	NM_013381	ENSG00000072657	TRHDE	PAP-II|PGPEP2|TRH-DE	thyrotropin releasing hormone degrading enzyme	protein-coding	0.014620	0.451895	
chunk0200_433_1	chr9	29790599	29791216	+	0	NA	Intergenic	L1ME2|LINE|L1	-577907	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.008104	0.305825	
chunk0188_178_1	chr8	11343150	11343812	+	0	NA	intron (NR_001578, intron 1 of 8)	intron (NR_001578, intron 1 of 8)	3844	NR_001578	157739	Hs.583896	NR_001578	ENSG00000154316	TDH	SDR14E1P	L-threonine dehydrogenase (pseudogene)	pseudo	0.006042	0.339367	
chunk0106_162_1	chr2	200708425	200708751	+	0	NA	intron (NR_001557, intron 1 of 30)	intron (NR_001557, intron 1 of 30)	12865	NR_001557									0.006135	0.422018	
chunk0092_275_1	chr19	33357512	33357754	+	0	NA	Intergenic	L1M5|LINE|L1	-16036	NM_001806	1054	Hs.429666	NM_001806	ENSG00000153879	CEBPG	GPE1BP|IG/EBP-1	CCAAT enhancer binding protein gamma	protein-coding	0.000000	0.370370	148(GGGGCTGTCTGTTCTG,+,0.00)
chunk0031_314_1	chr10	129068961	129069705	+	0	NA	Intergenic	Intergenic	-397851	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.008065	0.441611	
chunk0198_300_1	chr8	138111262	138111600	+	0	NA	Intergenic	MIR|SINE|MIR	385391	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.008876	0.380531	
chunk0172_127_1	chr6	135251584	135252013	+	0	NA	Intergenic	Intergenic	12638	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.009324	0.430233	
chunk0069_61_1	chr15	60818791	60819115	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	137384	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.009259	0.449231	
chunk0016_232_1	chr1	199730237	199730459	+	0	NA	Intergenic	Intergenic	-297254	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.004505	0.318386	
chunk0011_98_1	chr1	145891921	145892534	+	0	NA	3' UTR (NM_001303041, exon 26 of 26)	3' UTR (NM_001303041, exon 26 of 26)	-6361	NM_001280799	148741	Hs.710624	NM_144698	ENSG00000198483	ANKRD35	-	ankyrin repeat domain 35	protein-coding	0.009788	0.514658	54(AGGTACACCCAGTCCT,-,0.00),55(GGTACACCCAGTCCTC,+,0.00)
chunk0191_429_1	chr8	57844859	57845611	+	0	NA	Intergenic	Intergenic	-133123	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.003989	0.383798	
chunk0128_16_1	chr3	103889134	103889450	+	0	NA	Intergenic	L3|LINE|CR1	-365176	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.283912	
chunk0177_435_1	chr7	27969156	27969355	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	-211202	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.015075	0.470000	
chunk0018_194_1	chr1	219306172	219306586	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	131410	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.000000	0.356627	
chunk0027_393_1	chr10	80078460	80078832	+	0	NA	promoter-TSS (NM_001270374)	promoter-TSS (NM_001270374)	0	NM_025125	80195	Hs.169982	NM_025125	ENSG00000133678	TMEM254	C10orf57|bA369J21.6	transmembrane protein 254	protein-coding	0.075269	0.640751	
chunk0185_107_1	chr7	125651200	125651743	+	0	NA	Intergenic	L1MB3|LINE|L1	-387180	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.001842	0.323529	292(AGGTACACAGAGTACT,-,0.00),293(GGTACACAGAGTACTA,+,0.00)
chunk0201_238_1	chr9	37700715	37701343	+	0	NA	intron (NM_014907, intron 2 of 15)	intron (NM_014907, intron 2 of 15)	49974	NM_014907	22844	Hs.163990	NM_014907	ENSG00000070601	FRMPD1	FRMD2	FERM and PDZ domain containing 1	protein-coding	0.006369	0.402226	
chunk0208_430_1	chrX	29999726	30000242	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-215574	NM_002364	4113	Hs.113824	NM_002364	ENSG00000099399	MAGEB2	CT3.2|DAM6|MAGE-XP-2	MAGE family member B2	protein-coding	0.007752	0.342360	
chunk0033_443_1	chr11	25401101	25401641	+	0	NA	Intergenic	Intergenic	-787752	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.000000	0.329020	
chunk0148_374_1	chr5	14657373	14657907	+	0	NA	Intergenic	Intergenic	-5258	NR_132981	106635684		NR_132981		SNORD141B	-	small nucleolar RNA, C/D box 141B	snoRNA	0.000000	0.308411	
chunk0084_169_1	chr17	77377362	77377742	+	0	NA	intron (NM_001113494, intron 1 of 10)	intron (NM_001113494, intron 1 of 10)	1469	NM_001113494	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.036842	0.553806	
chunk0137_88_1	chr4	13234817	13235338	+	0	NA	Intergenic	L1PB3|LINE|L1	249288	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.001919	0.304598	
chunk0074_119_1	chr16	22620025	22620224	+	0	NA	Intergenic	Charlie24|DNA|hAT-Charlie	74426	NR_003676	653786	Hs.564945	NR_003676	ENSG00000257838	OTOAP1	-	OTOA pseudogene 1	pseudo	0.030151	0.465000	
chunk0193_95_1	chr8	73631329	73631955	+	0	NA	intron (NM_001164383, intron 1 of 9)	intron (NM_001164383, intron 1 of 9)	115285	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.003195	0.344498	264(CTACACAGACTGTTCT,-,0.00),265(TACACAGACTGTTCTG,+,0.00)
chunk0120_248_1	chr3	8801580	8802157	+	0	NA	Intergenic	L1MB8|LINE|L1	-32254	NM_000916	5021	Hs.2820	NM_000916	ENSG00000180914	OXTR	OT-R	oxytocin receptor	protein-coding	0.001733	0.287197	
chunk0061_379_1	chr14	64144382	64144886	+	0	NA	intron (NM_182914, intron 83 of 115)	L1ME4c|LINE|L1	-49509	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.007937	0.318812	419(GTGCACAGAGTGTTCA,-,0.00),420(TGCACAGAGTGTTCAA,+,0.00)
chunk0063_355_1	chr14	85587199	85587873	+	0	NA	intron (NM_013231, intron 1 of 1)	intron (NM_013231, intron 1 of 1)	57392	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.011869	0.370370	
chunk0141_3_1	chr4	76563369	76564004	+	0	NA	intron (NM_020859, intron 2 of 10)	intron (NM_020859, intron 2 of 10)	-9882	NR_039654	100616299		NR_039654	ENSG00000263445	MIR4450	mir-4450	microRNA 4450	ncRNA	0.009449	0.463836	235(GAAAACATAATGTTCT,-,0.00),236(AAAACATAATGTTCTT,+,0.00)
chunk0050_157_1	chr12	103241114	103241816	+	0	NA	intron (NR_103526, intron 10 of 10)	intron (NR_103526, intron 10 of 10)	89623	NR_126333	101929058	Hs.171310	NR_126333	ENSG00000257860	LOC101929058	-	uncharacterized LOC101929058	ncRNA	0.004274	0.391181	
chunk0039_87_1	chr11	97211954	97212308	+	0	NA	Intergenic	Intergenic	-705254	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.008475	0.374648	
chunk0159_96_1	chr5	138198499	138199342	+	0	NA	intron (NM_004661, intron 6 of 15)	intron (NM_004661, intron 6 of 15)	14423	NM_004661	8697	Hs.73625	NM_004661	ENSG00000094880	CDC23	ANAPC8|APC8|CUT23	cell division cycle 23	protein-coding	0.004745	0.407583	
chunk0122_302_1	chr3	36568122	36568332	+	0	NA	Intergenic	L1PA7|LINE|L1	171634	NM_033403	85443	Hs.631907	NM_033403	ENSG00000163673	DCLK3	CLR|DCAMKL3|DCDC3C|DCK3	doublecortin like kinase 3	protein-coding	0.004762	0.341232	22(GAGAACTGTTTGTTCT,-,0.00),23(AGAACTGTTTGTTCTT,+,0.00)
chunk0197_43_1	chr8	118365590	118366419	+	0	NA	intron (NR_109794, intron 4 of 4)	L2b|LINE|L2	-254185	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.007238	0.393976	174(CAGAACAGTCTGTTCC,-,0.00),175(AGAACAGTCTGTTCCT,+,0.00)
chunk0153_294_1	chr5	73406743	73407119	+	0	NA	Intergenic	Intergenic	41596	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.007979	0.440318	153(CAGGACAGCCAGTTTC,-,0.00),154(AGGACAGCCAGTTTCC,+,0.00)
chunk0052_398_1	chr12	130765121	130765519	+	0	NA	Intergenic	Intergenic	73954	NM_001980	2054	Hs.437585	NM_001980	ENSG00000111450	STX2	EPIM|EPM|STX2A|STX2B|STX2C	syntaxin 2	protein-coding	0.017588	0.426065	
chunk0182_427_1	chr7	101352196	101352742	+	0	NA	Intergenic	MER134|DNA?|DNA?	-10351	NM_001278563	136227	Hs.654854	NM_133457	ENSG00000160963	COL26A1	EMI6|EMID2|EMU2|SH2B	collagen type XXVI alpha 1 chain	protein-coding	0.012821	0.468007	
chunk0008_60_1	chr1	89489445	89489842	+	0	NA	Intergenic	L1M1|LINE|L1	-35195	NM_001134476	23507	Hs.482017	NM_015350	ENSG00000197147	LRRC8B	TA-LRRP|TALRRP	leucine rich repeat containing 8 VRAC subunit B	protein-coding	0.005038	0.505025	
chunk0123_314_1	chr3	47164055	47164321	+	0	NA	promoter-TSS (NM_014159)	promoter-TSS (NM_014159)	-182	NR_033373	285352	Hs.570631	NR_033373		KIF9-AS1	-	KIF9 antisense RNA 1	ncRNA	0.109023	0.711610	
chunk0006_429_1	chr1	76434081	76434329	+	0	NA	intron (NM_152996, intron 3 of 4)	intron (NM_152996, intron 3 of 4)	359501	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.004032	0.429719	
chunk0212_243_1	chrX	137568314	137568708	+	0	NA	intron (NM_003413, intron 1 of 2)	intron (NM_003413, intron 1 of 2)	2324	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.048223	0.531646	
chunk0091_162_1	chr19	7535661	7535957	+	0	NA	exon (NM_001166114, exon 1 of 32)	exon (NM_001166114, exon 1 of 32)	106	NM_001166114	10908	Hs.631863	NM_006702	ENSG00000032444	PNPLA6	BNHS|LNMS|NTE|NTEMND|OMCS|SPG39|iPLA2delta|sws	patatin like phospholipase domain containing 6	protein-coding	0.118243	0.696970	
chunk0106_412_1	chr2	207971060	207971407	+	0	NA	intron (NM_001080475, intron 3 of 7)	intron (NM_001080475, intron 3 of 7)	54327	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.002882	0.367816	
chunk0148_232_1	chr5	9431821	9432266	+	0	NA	intron (NM_003966, intron 2 of 22)	intron (NM_003966, intron 2 of 22)	-79290	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.011236	0.448430	
chunk0029_53_1	chr10	96423607	96424298	+	0	NA	intron (NM_012465, intron 5 of 20)	L1MA2|LINE|L1	-64587	NM_033207	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.001447	0.348266	
chunk0056_427_1	chr13	94850688	94851099	+	0	NA	intron (NR_110754, intron 2 of 4)	intron (NR_110754, intron 2 of 4)	89952	NR_110754	101927284	Hs.551673	NR_110754		LOC101927284	-	uncharacterized LOC101927284	ncRNA	0.004866	0.417476	293(AAGGACATTCTGACCT,-,0.00),294(AGGACATTCTGACCTG,+,0.00)
chunk0028_226_1	chr10	89645362	89645561	+	0	NA	5' UTR (NM_148977, exon 1 of 7)	5' UTR (NM_148977, exon 1 of 7)	111	NM_148977	53354	Hs.163555	NM_138316	ENSG00000152782	PANK1	PANK	pantothenate kinase 1	protein-coding	0.060302	0.530000	
chunk0039_28_1	chr11	95717342	95717869	+	0	NA	Intergenic	MIRb|SINE|MIR	72185	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.001898	0.367424	
chunk0083_257_1	chr17	68294531	68295115	+	0	NA	intron (NM_001267727, intron 1 of 11)	intron (NM_001267727, intron 1 of 11)	3328	NM_001267727	22901	Hs.437249	NM_014960	ENSG00000141337	ARSG	USH4	arylsulfatase G	protein-coding	0.011986	0.492308	262(TGGTACAGGTAGTTCT,-,0.00),263(GGTACAGGTAGTTCTG,+,0.00)
chunk0144_152_1	chr4	130473292	130473945	+	0	NA	Intergenic	L1M4b|LINE|L1	-702140	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.003063	0.264526	
chunk0171_270_1	chr6	127656140	127656693	+	0	NA	Intergenic	Intergenic	79242	NM_001010905	352999	Hs.226268	NM_001010905	ENSG00000184530	C6orf58	LEG1	chromosome 6 open reading frame 58	protein-coding	0.005425	0.324910	
chunk0003_334_1	chr1	38875053	38875494	+	0	NA	exon (NM_030772, exon 2 of 2)	exon (NM_030772, exon 2 of 2)	-1895	NM_012333	26292	Hs.591506	NM_012333	ENSG00000214114	MYCBP	AMY-1	MYC binding protein	protein-coding	0.002268	0.350679	
chunk0102_238_1	chr2	148879192	148879494	+	0	NA	intron (NM_004522, intron 1 of 25)	intron (NM_004522, intron 1 of 25)	4120	NM_004522	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.006623	0.343234	
chunk0206_346_1	chr9	125580816	125581109	+	0	NA	intron (NM_001006618, intron 5 of 7)	L1MD2|LINE|L1	126272	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.010239	0.384354	
chunk0049_97_1	chr12	90858043	90858609	+	0	NA	Intergenic	MER61F|LTR|ERV1	-59697	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.005300	0.428571	
chunk0140_156_1	chr4	69408291	69408965	+	0	NA	Intergenic	Intergenic	87280	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.002967	0.343704	
chunk0012_168_1	chr1	158507065	158507552	+	0	NA	Intergenic	L1M1|LINE|L1	27430	NM_001004472	343406	Hs.451913	NM_001004472	ENSG00000198965	OR10R2	OR1-8|OR10R2Q	olfactory receptor family 10 subfamily R member 2	protein-coding	0.004107	0.493852	
chunk0053_11_1	chr13	26228203	26228454	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-5957	NM_005977	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.007968	0.500000	
chunk0189_67_1	chr8	20630328	20630527	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-323206	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.010050	0.360000	
chunk0061_79_1	chr14	56701806	56702406	+	0	NA	Intergenic	L1MD1|LINE|L1	103557	NR_073036	5015	Hs.288655	NM_021728	ENSG00000165588	OTX2	CPHD6|MCOPS5	orthodenticle homeobox 2	protein-coding	0.011667	0.359401	
chunk0133_407_1	chr3	174392476	174392998	+	0	NA	Intergenic	MER41D|LTR|ERV1	-466584	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.000000	0.365201	
chunk0192_317_1	chr8	67062000	67062517	+	0	NA	promoter-TSS (NM_006837)	promoter-TSS (NM_006837)	69	NM_006837	10987	Hs.491912	NM_006837	ENSG00000121022	COPS5	CSN5|JAB1|MOV-34|SGN5	COP9 signalosome subunit 5	protein-coding	0.042553	0.471042	252(GAGAACATCTTGTCTC,-,0.00)
chunk0062_126_1	chr14	68506738	68507860	+	0	NA	intron (NM_133509, intron 10 of 10)	intron (NM_133509, intron 10 of 10)	286615	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.012478	0.470169	
chunk0085_143_1	chr18	3261705	3261907	+	0	NA	promoter-TSS (NM_001144944)	promoter-TSS (NM_001144944)	24	NR_130143	104968399	Hs.464472	NR_130143	ENSG00000264235	LOC104968399	-	uncharacterized LOC104968399	ncRNA	0.113861	0.719212	
chunk0026_432_1	chr10	71196618	71197058	+	0	NA	Intergenic	LTR32|LTR|ERVL	-15697	NM_001244889	219699	Hs.522997	NM_170744	ENSG00000107731	UNC5B	UNC5H2|p53RDL1	unc-5 netrin receptor B	protein-coding	0.009091	0.512472	364(TGGGACAGGCTGTGTC,-,0.00),365(GGGACAGGCTGTGTCT,+,0.00)
chunk0003_272_1	chr1	36419359	36419856	+	0	NA	intron (NM_145047, intron 8 of 9)	MIRc|SINE|MIR	-21648	NM_032881	84967	Hs.603131	NM_032881	ENSG00000181817	LSM10	MST074|MSTP074	LSM10, U7 small nuclear RNA associated	protein-coding	0.008048	0.385542	
chunk0044_4_1	chr12	26832548	26832840	+	0	NA	exon (NM_002223, exon 1 of 57)	exon (NM_002223, exon 1 of 57)	504	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.102740	0.686007	184(AGGGACACGATGTCCC,-,0.00),185(GGGACACGATGTCCCC,+,0.00)
chunk0129_301_1	chr3	123627366	123628293	+	0	NA	intron (NM_053027, intron 29 of 32)	intron (NM_053027, intron 29 of 32)	-7146	NM_053031	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.003236	0.386853	520(CAGTACAGCCTGTTAC,-,0.00),521(AGTACAGCCTGTTACT,+,0.00)
chunk0078_148_1	chr17	4010643	4011201	+	0	NA	intron (NM_015113, intron 52 of 54)	intron (NM_015113, intron 52 of 54)	-46458	NM_174956	489	Hs.513870	NM_005173	ENSG00000074370	ATP2A3	SERCA3	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3	protein-coding	0.005376	0.409660	
chunk0176_456_1	chr7	20138455	20138683	+	0	NA	3' UTR (NM_182762, exon 7 of 7)	3' UTR (NM_182762, exon 7 of 7)	1857	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.004386	0.292576	
chunk0111_243_1	chr20	29831501	29831805	+	0	NA	Intergenic	Intergenic	-48731	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.013158	0.459016	
chunk0115_52_1	chr21	21340609	21341314	+	0	NA	intron (NM_004540, intron 8 of 17)	intron (NM_004540, intron 8 of 17)	342646	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.002837	0.291785	
chunk0044_293_1	chr12	32773223	32773847	+	0	NA	Intergenic	Intergenic	-17582	NM_001040436	51067	Hs.505231	NM_015936	ENSG00000139131	YARS2	CGI-04|MLASA2|MT-TYRRS|TYRRS	tyrosyl-tRNA synthetase 2	protein-coding	0.009615	0.443200	
chunk0087_68_1	chr18	31931260	31931459	+	0	NA	exon (NM_014939, exon 2 of 29)	exon (NM_014939, exon 2 of 29)	11769	NM_014939	22878	Hs.202001	NM_014939	ENSG00000153339	TRAPPC8	GSG1|HsT2706|KIAA1012|TRS85	trafficking protein particle complex 8	protein-coding	0.015075	0.405000	
chunk0090_265_1	chr18	74500887	74501439	+	0	NA	intron (NM_018235, intron 2 of 11)	intron (NM_018235, intron 2 of 11)	1575	NM_001168499	55748	Hs.149185	NM_018235	ENSG00000133313	CNDP2	CN2|CPGL|HEL-S-13|HsT2298|PEPA	carnosine dipeptidase 2	protein-coding	0.025362	0.470163	
chunk0162_26_1	chr6	884502	885140	+	0	NA	Intergenic	Intergenic	16323	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.007837	0.411581	
chunk0147_98_1	chr4	173380121	173380320	+	0	NA	Intergenic	L1MB5|LINE|L1	9278	NM_003864	8819	Hs.591715	NM_003864	ENSG00000164105	SAP30	-	Sin3A associated protein 30	protein-coding	0.005025	0.340000	
chunk0170_126_1	chr6	110817707	110818006	+	0	NA	intron (NM_001287215, intron 1 of 8)	intron (NM_001287215, intron 1 of 8)	-1971	NM_001300964	23097	Hs.744895	NM_015076	ENSG00000155111	CDK19	CDC2L6|CDK11|bA346C16.3	cyclin dependent kinase 19	protein-coding	0.006689	0.373333	252(TAGAACAGCATGTACA,-,0.00),253(AGAACAGCATGTACAT,+,0.00)
chunk0039_306_1	chr11	103103528	103103727	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-5804	NM_001377	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.000000	0.425000	
chunk0025_270_1	chr10	55915022	55915336	+	0	NA	Intergenic	Intergenic	316189	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.009554	0.365079	
chunk0065_406_1	chr14	105420942	105421148	+	0	NA	intron (NM_001203258, intron 1 of 20)	intron (NM_001203258, intron 1 of 20)	1196	NM_001203258	9112	Hs.525629	NM_004689	ENSG00000182979	MTA1	-	metastasis associated 1	protein-coding	0.048544	0.661836	86(CAGAACACTCTGTGTC,-,0.00),87(AGAACACTCTGTGTCT,+,0.00)
chunk0211_289_1	chrX	122503468	122504705	+	0	NA	Intergenic	L1PA16|LINE|L1	-680157	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.003234	0.331987	
chunk0134_164_1	chr3	177898007	177898468	+	0	NA	non-coding (NR_110826, exon 3 of 3)	non-coding (NR_110826, exon 3 of 3)	81372	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.002169	0.435065	
chunk0184_288_1	chr7	118830477	118830842	+	0	NA	Intergenic	L1MB7|LINE|L1	606001	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.005479	0.355191	
chunk0118_21_1	chr22	25849077	25849369	+	0	NA	intron (NM_032608, intron 20 of 43)	intron (NM_032608, intron 20 of 43)	107070	NM_032608	84700	Hs.417959	NM_032608	ENSG00000133454	MYO18B	KFS4	myosin XVIIIB	protein-coding	0.023973	0.522184	124(AGGGTCAGGGTGTCCC,-,0.00),125(GGGTCAGGGTGTCCCG,+,0.00)
chunk0007_300_1	chr1	84174510	84175018	+	0	NA	intron (NM_001300915, intron 2 of 11)	intron (NM_001300915, intron 2 of 11)	-6868	NM_001242862	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.003937	0.282908	
chunk0049_72_1	chr12	90305516	90306243	+	0	NA	Intergenic	Intergenic	596924	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.005502	0.355769	
chunk0088_141_1	chr18	46051912	46052455	+	0	NA	intron (NM_024430, intron 1 of 14)	intron (NM_024430, intron 1 of 14)	20101	NM_024430	9050	Hs.567384	NM_024430	ENSG00000152229	PSTPIP2	MAYP	proline-serine-threonine phosphatase interacting protein 2	protein-coding	0.011050	0.466912	
chunk0148_56_1	chr5	1870343	1870542	+	0	NA	Intergenic	Intergenic	12324	NM_016358	50805	Hs.196927	NM_016358	ENSG00000113430	IRX4	IRXA3	iroquois homeobox 4	protein-coding	0.020101	0.565000	
chunk0123_434_1	chr3	50314394	50314635	+	0	NA	Intergenic	Intergenic	-2133	NM_153281	3373	Hs.75619	NM_033159	ENSG00000114378	HYAL1	HYAL-1|LUCA1|MPS9|NAT6	hyaluronidase 1	protein-coding	0.008299	0.508264	124(GGAAACACCATGTCCC,-,0.00),125(GAAACACCATGTCCCT,+,0.00)
chunk0197_31_1	chr8	118061156	118061774	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	50354	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.004854	0.376414	
chunk0050_20_1	chr12	99731961	99732640	+	0	NA	intron (NM_152788, intron 8 of 25)	L1ME1|LINE|L1	84550	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.001473	0.322059	
chunk0167_345_1	chr6	72805852	72806080	+	0	NA	intron (NM_019842, intron 1 of 13)	L1MA3|LINE|L1	161787	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.008772	0.366812	
chunk0008_283_1	chr1	94783204	94783632	+	0	NA	intron (NR_104131, intron 1 of 4)	intron (NR_104131, intron 1 of 4)	36863	NR_104131	101928079	Hs.596857	NR_104131	ENSG00000224081	SLC44A3-AS1	LINC01057|XLOC_000303	SLC44A3 antisense RNA 1	ncRNA	0.002336	0.517483	
chunk0097_94_1	chr2	45741590	45741956	+	0	NA	intron (NM_005400, intron 1 of 14)	intron (NM_005400, intron 1 of 14)	89869	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.010929	0.569482	147(TAGTACAGCCTGTGCT,-,0.00),148(AGTACAGCCTGTGCTG,+,0.00)
chunk0041_200_1	chr11	126585794	126586025	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	-66869	NR_120532	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.034632	0.487069	
chunk0083_10_1	chr17	62805934	62806187	+	0	NA	intron (NM_001288780, intron 1 of 10)	intron (NM_001288780, intron 1 of 10)	593	NM_001100875	162333	Hs.665663	NM_152598	ENSG00000173838	MARCH10	MARCH-X|RNF190	membrane associated ring-CH-type finger 10	protein-coding	0.011858	0.318898	
chunk0174_281_1	chr6	161798959	161799478	+	0	NA	intron (NM_013988, intron 3 of 8)	intron (NM_013988, intron 3 of 8)	-525143	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.009634	0.461538	
chunk0200_306_1	chr9	23101012	23101283	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	454947	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.003690	0.411765	154(ATGACATAATGTTCTT,+,0.00)
chunk0106_332_1	chr2	205971974	205972490	+	0	NA	Intergenic	Intergenic	113950	NM_017759	54891	Hs.445036	NM_017759	ENSG00000114933	INO80D	-	INO80 complex subunit D	protein-coding	0.001938	0.419729	
chunk0168_450_1	chr6	95883119	95884238	+	0	NA	Intergenic	Intergenic	-132291	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.003575	0.316071	
chunk0045_116_1	chr12	46246426	46247338	+	0	NA	intron (NM_001077484, intron 1 of 16)	L1PA6|LINE|L1	19613	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.009868	0.479737	
chunk0009_401_1	chr1	110292404	110293032	+	0	NA	intron (NR_036595, intron 2 of 3)	MIR3|SINE|MIR	46453	NR_036595	440600	Hs.649375	NR_036595	ENSG00000227963	RBM15-AS1	AS-RBM15	RBM15 antisense RNA 1	ncRNA	0.009554	0.478537	317(AGGGACAGCAAGTTCT,-,0.00),318(GGGACAGCAAGTTCTT,+,0.00)
chunk0156_153_1	chr5	107384237	107384657	+	0	NA	intron (NM_001962, intron 4 of 4)	intron (NM_001962, intron 4 of 4)	286448	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.011905	0.451306	
chunk0208_310_1	chrX	23888216	23888557	+	0	NA	intron (NR_026545, intron 1 of 7)	intron (NR_026545, intron 1 of 7)	19554	NM_024122	79135	Hs.495851	NM_024122	ENSG00000184831	APOO	FAM121B|MIC26|MICOS26|Mic23|My025	apolipoprotein O	protein-coding	0.002933	0.380117	
chunk0189_291_1	chr8	25766106	25766406	+	0	NA	Intergenic	Intergenic	278868	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.013333	0.458472	
chunk0095_198_1	chr2	18309362	18309736	+	0	NA	Intergenic	Intergenic	251144	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.000000	0.322667	
chunk0110_141_1	chr20	13610917	13611538	+	0	NA	intron (NM_017714, intron 4 of 13)	intron (NM_017714, intron 4 of 13)	27709	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.003221	0.331190	
chunk0209_199_1	chrX	43956010	43956611	+	0	NA	intron (NM_000266, intron 2 of 2)	intron (NM_000266, intron 2 of 2)	17365	NM_000266	4693	Hs.522615	NM_000266	ENSG00000124479	NDP	EVR2|FEVR|ND	norrin cystine knot growth factor NDP	protein-coding	0.001664	0.370432	
chunk0054_382_1	chr13	50217216	50217779	+	0	NA	intron (NR_109974, intron 2 of 6)	L1MB7|LINE|L1	45479	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.000000	0.324468	370(TGAACTGTGTGTTCAC,+,0.00)
chunk0025_139_1	chr10	52146850	52147505	+	0	NA	intron (NM_006258, intron 8 of 17)	intron (NM_006258, intron 8 of 17)	166951	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.003053	0.361280	
chunk0127_400_1	chr3	102363002	102363262	+	0	NA	Intergenic	L1M2c|LINE|L1	-71883	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.007692	0.513410	
chunk0012_111_1	chr1	156751851	156752050	+	0	NA	promoter-TSS (NM_004494)	promoter-TSS (NM_004494)	-199	NM_004494	3068	Hs.743948	NM_004494	ENSG00000143321	HDGF	HMG1L2	heparin binding growth factor	protein-coding	0.150754	0.780000	
chunk0167_276_1	chr6	70392513	70393006	+	0	NA	Intergenic	HAL1b|LINE|L1	-1443	NR_125857	101928353		NR_125857		EVADR	-	uncharacterized LOC101928353	ncRNA	0.004057	0.297571	
chunk0138_182_1	chr4	37967875	37968074	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	7539	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.015075	0.315000	
chunk0167_267_1	chr6	69792241	69793046	+	0	NA	intron (NM_018368, intron 1 of 15)	Charlie1b|DNA|hAT-Charlie	4514	NM_018368	55788	Hs.271643	NM_018368	ENSG00000168216	LMBRD1	C6orf209|LMBD1|MAHCF|NESI	LMBR1 domain containing 1	protein-coding	0.002484	0.363524	
chunk0022_261_1	chr10	14859898	14860345	+	0	NA	intron (NM_016299, intron 10 of 13)	L1MC|LINE|L1	-18662	NM_001193424	79723	Hs.554883	NM_024670	ENSG00000152455	SUV39H2	KMT1B	suppressor of variegation 3-9 homolog 2	protein-coding	0.002237	0.305804	
chunk0200_87_1	chr9	16484816	16485260	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-208725	NR_073471									0.006757	0.408989	
chunk0107_2_1	chr2	209642917	209643355	+	0	NA	intron (NM_031845, intron 3 of 11)	intron (NM_031845, intron 3 of 11)	63457	NM_031845	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.002283	0.334852	222(TAGAACTGTCTGTGCC,-,0.00),223(AGAACTGTCTGTGCCG,+,0.00),271(GGCACATAGTGTATTT,+,0.00)
chunk0035_40_1	chr11	40935534	40936076	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	523831	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001845	0.313076	
chunk0155_117_1	chr5	92970515	92970901	+	0	NA	Intergenic	Intergenic	600635	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.005181	0.330749	
chunk0096_86_1	chr2	27985596	27985987	+	0	NA	intron (NM_199191, intron 3 of 11)	L2b|LINE|L2	-10576	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.007673	0.326531	
chunk0132_266_1	chr3	159264079	159264615	+	0	NA	TTS (NM_001042706)	TTS (NM_001042706)	-8900	NM_001197108	29970	Hs.134665	NM_014575	ENSG00000151967	SCHIP1	SCHIP-1	schwannomin interacting protein 1	protein-coding	0.007463	0.372439	
chunk0200_28_1	chr9	14849189	14849905	+	0	NA	intron (NM_144966, intron 7 of 37)	intron (NM_144966, intron 7 of 37)	61448	NM_144966	158326	Hs.50850	NM_144966	ENSG00000164946	FREM1	BNAR|C9orf143|C9orf145|C9orf154|MOTA|TILRR|TRIGNO2	FRAS1 related extracellular matrix 1	protein-coding	0.011173	0.398884	
chunk0032_73_1	chr11	2612760	2613166	+	0	NA	non-coding (NR_002728, exon 1 of 1)	non-coding (NR_002728, exon 1 of 1)	87035	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.004926	0.398034	
chunk0105_119_1	chr2	185148934	185149344	+	0	NA	Intergenic	MIR|SINE|MIR	550773	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.007317	0.328467	
chunk0176_391_1	chr7	18821031	18821327	+	0	NA	intron (NM_178425, intron 16 of 24)	MLT1A1|LTR|ERVL-MaLR	296493	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.010135	0.447811	61(AGGGACACTGTGTCCT,-,0.00),62(GGGACACTGTGTCCTT,+,0.00)
chunk0132_277_1	chr3	159763104	159763417	+	0	NA	intron (NM_001197108, intron 1 of 6)	CpG	5352	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.076677	0.630573	
chunk0196_343_1	chr8	114292772	114293163	+	0	NA	Intergenic	Intergenic	-855954	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.005115	0.293367	
chunk0023_120_1	chr10	23419597	23420082	+	0	NA	Intergenic	Intergenic	-19430	NM_001145373	220213	Hs.499042	NM_001145373	ENSG00000165312	OTUD1	DUBA7|OTDC1	OTU deubiquitinase 1	protein-coding	0.004124	0.353909	
chunk0032_12_1	chr11	644480	644752	+	0	NA	exon (NM_001293634, exon 11 of 11)	exon (NM_001293634, exon 11 of 11)	7311	NM_000797	1815	Hs.99922	NM_000797	ENSG00000069696	DRD4	D4DR	dopamine receptor D4	protein-coding	0.036765	0.641026	
chunk0179_90_1	chr7	44608753	44610029	+	0	NA	intron (NM_001003941, intron 1 of 8)	AluJb|SINE|Alu	2869	NM_001003941	4967	Hs.488181	NM_002541	ENSG00000105953	OGDH	AKGDH|E1k|OGDC	oxoglutarate dehydrogenase	protein-coding	0.013323	0.388410	
chunk0002_402_1	chr1	27348959	27349572	+	0	NA	intron (NM_032872, intron 6 of 14)	intron (NM_032872, intron 6 of 14)	7273	NM_032872	84958	Hs.469175	NM_032872	ENSG00000142765	SYTL1	JFC1|SLP1	synaptotagmin like 1	protein-coding	0.048940	0.644951	
chunk0119_129_1	chr22	42905741	42906171	+	0	NA	intron (NM_001184970, intron 2 of 10)	intron (NM_001184970, intron 2 of 10)	41085	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.006977	0.582367	
chunk0182_292_1	chr7	98295884	98296432	+	0	NA	intron (NM_018842, intron 12 of 13)	intron (NM_018842, intron 12 of 13)	14491	NM_015379	25798	Hs.567438	NM_015379	ENSG00000164713	BRI3	I3	brain protein I3	protein-coding	0.031022	0.566485	
chunk0204_302_1	chr9	100131915	100132521	+	0	NA	intron (NM_014425, intron 3 of 16)	L2c|LINE|L2	32998	NM_014425	27130	Hs.558477	NM_014425	ENSG00000119509	INVS	INV|NPH2|NPHP2	inversin	protein-coding	0.003300	0.337727	
chunk0135_185_1	chr3	188170958	188171465	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	-7332	NR_024413	401105	Hs.679026	NM_207488	ENSG00000279891	FLJ42393	AVPC1948	uncharacterized LOC401105	ncRNA	0.005917	0.407480	
chunk0058_57_1	chr14	20597919	20598311	+	0	NA	intron (NR_122043, intron 3 of 4)	intron (NR_122043, intron 3 of 4)	-7292	NM_001024822	493901	Hs.729466	NM_001024822	ENSG00000258436	RNASE12	HEL-S-85p|RAI1	ribonuclease A family member 12 (inactive)	protein-coding	0.015306	0.511450	144(CAGAACAAGCTGTTCC,-,0.00),145(AGAACAAGCTGTTCCT,+,0.00)
chunk0126_329_1	chr3	82021693	82021892	+	0	NA	Intergenic	Intergenic	-259993	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.005025	0.330000	
chunk0003_414_1	chr1	40338987	40339186	+	0	NA	Intergenic	MIRb|SINE|MIR	-21819	NM_001852	1298	Hs.418012	NM_001852	ENSG00000049089	COL9A2	DJ39G22.4|EDM2|MED|STL5	collagen type IX alpha 2 chain	protein-coding	0.010050	0.465000	
chunk0131_54_1	chr3	142740193	142740658	+	0	NA	intron (NM_003304, intron 2 of 11)	intron (NM_003304, intron 2 of 11)	16001	NM_003304	7220	Hs.250687	NM_003304	ENSG00000144935	TRPC1	HTRP-1|TRP1	transient receptor potential cation channel subfamily C member 1	protein-coding	0.002151	0.384120	
chunk0019_112_1	chr1	225138232	225138517	+	0	NA	intron (NM_001373, intron 26 of 83)	L1PA11|LINE|L1	208713	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.010526	0.566434	
chunk0187_42_1	chr8	1449549	1449882	+	0	NA	Intergenic	Intergenic	-51651	NM_004745	9228	Hs.113287	NM_004745	ENSG00000198010	DLGAP2	C8orf68|DAP2|ERICH1-AS1|SAPAP2	DLG associated protein 2	protein-coding	0.039039	0.634731	
chunk0126_208_1	chr3	78756578	78756777	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	262782	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.005025	0.350000	
chunk0192_437_1	chr8	69719682	69720127	+	0	NA	intron (NM_001146009, intron 3 of 7)	HERV1_LTRd|LTR|ERV1	113265	NM_001146009	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.022472	0.419283	
chunk0094_99_1	chr2	4195350	4195939	+	0	NA	Intergenic	Intergenic	-221612	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.006791	0.306780	
chunk0178_171_1	chr7	34078251	34078537	+	0	NA	intron (NM_133468, intron 12 of 15)	intron (NM_133468, intron 12 of 15)	173483	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.010490	0.327526	150(CAGCACACCATGTTTC,-,0.00),151(AGCACACCATGTTTCT,+,0.00)
chunk0058_134_1	chr14	22770956	22771231	+	0	NA	exon (NM_005015, exon 8 of 10)	exon (NM_005015, exon 8 of 10)	4571	NM_005015	5018	Hs.151134	NM_005015	ENSG00000155463	OXA1L	OXA1	OXA1L mitochondrial inner membrane protein	protein-coding	0.014545	0.485507	132(CAGTACGCACTGTACT,-,0.00),133(AGTACGCACTGTACTT,+,0.00)
chunk0164_395_1	chr6	26288074	26288548	+	0	NA	Intergenic	LTR3|LTR|ERVK	-2812	NM_003543	8365	Hs.591790	NM_003543	ENSG00000158406	HIST1H4H	H4/h|H4FH	histone cluster 1 H4 family member h	protein-coding	0.014768	0.450526	
chunk0101_86_1	chr2	124163863	124164235	+	0	NA	intron (NM_130773, intron 1 of 23)	intron (NM_130773, intron 1 of 23)	138762	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.005376	0.369973	
chunk0054_409_1	chr13	50568077	50568627	+	0	NA	Intergenic	L1MC|LINE|L1	-40903	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.005455	0.301270	
chunk0039_433_1	chr11	107963110	107963680	+	0	NA	TTS (NM_017516)	TTS (NM_017516)	34920	NM_017516	54734	Hs.354906	NM_017516	ENSG00000179331	RAB39A	RAB39	RAB39A, member RAS oncogene family	protein-coding	0.014035	0.397548	
chunk0113_372_1	chr20	59320078	59320308	+	0	NA	intron (NM_207032, intron 2 of 4)	intron (NM_207032, intron 2 of 4)	19766	NM_207033	1908	Hs.1408	NM_000114	ENSG00000124205	EDN3	ET-3|ET3|HSCR4|PPET3|WS4B	endothelin 3	protein-coding	0.030435	0.506494	
chunk0001_343_1	chr1	9782155	9782611	+	0	NA	intron (NM_001009566, intron 1 of 18)	intron (NM_001009566, intron 1 of 18)	42143	NM_014944	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.002193	0.286652	
chunk0197_125_1	chr8	119978027	119978227	+	0	NA	intron (NM_022783, intron 4 of 8)	intron (NM_022783, intron 4 of 8)	104472	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.015000	0.482587	
chunk0177_73_1	chr7	21374568	21375078	+	0	NA	Intergenic	L1ME4c|LINE|L1	-53248	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.000000	0.260274	
chunk0117_200_1	chr22	21807865	21808118	+	0	NA	intron (NM_138957, intron 1 of 7)	intron (NM_138957, intron 1 of 7)	59689	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.003953	0.401575	
chunk0077_266_1	chr16	80991106	80991379	+	0	NA	intron (NM_020188, intron 2 of 3)	L1MC3|LINE|L1	-15256	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.007326	0.408759	
chunk0004_173_1	chr1	45856064	45856917	+	0	NA	intron (NM_015112, intron 3 of 28)	intron (NM_015112, intron 3 of 28)	52877	NM_015112	23139	Hs.319481	NM_015112	ENSG00000086015	MAST2	MAST205|MTSSK	microtubule associated serine/threonine kinase 2	protein-coding	0.008206	0.364169	
chunk0197_283_1	chr8	124145502	124145843	+	0	NA	intron (NR_103547, intron 1 of 4)	intron (NR_103547, intron 1 of 4)	25850	NR_103547	157376	Hs.662360	NM_182525	ENSG00000253868	FER1L6-AS2	C8orf78	FER1L6 antisense RNA 2	ncRNA	0.008798	0.523392	
chunk0202_307_1	chr9	78003454	78004273	+	0	NA	intron (NM_002072, intron 1 of 6)	intron (NM_002072, intron 1 of 6)	27586	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.017094	0.458537	
chunk0184_297_1	chr7	119472392	119472741	+	0	NA	Intergenic	Intergenic	434809	NR_131960	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.014327	0.462857	
chunk0043_192_1	chr12	19129007	19129664	+	0	NA	promoter-TSS (NM_001190860)	promoter-TSS (NM_001190860)	-357	NM_001190860	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.073059	0.527356	
chunk0177_12_1	chr7	20475003	20475494	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-140374	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.012220	0.347561	
chunk0142_386_1	chr4	102420426	102420960	+	0	NA	Intergenic	Intergenic	-75195	NM_001135146	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.001873	0.385047	
chunk0145_147_1	chr4	147049194	147049405	+	0	NA	Intergenic	L2a|LINE|L2	-103417	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.009479	0.410377	
chunk0012_338_1	chr1	162568639	162569351	+	0	NA	intron (NM_003115, intron 2 of 9)	intron (NM_003115, intron 2 of 9)	7489	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.005618	0.382889	
chunk0211_150_1	chrX	113793925	113794654	+	0	NA	intron (NR_131204, intron 1 of 2)	intron (NR_131204, intron 1 of 2)	143929	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.006859	0.330137	330(CAGAACAGAGTGTCTT,-,0.00),331(AGAACAGAGTGTCTTA,+,0.00)
chunk0023_54_1	chr10	21755335	21755632	+	0	NA	Intergenic	Tigger4b|DNA|TcMar-Tigger	220838	NM_001195626	8028	Hs.30385	NM_004641	ENSG00000078403	MLLT10	AF10	MLLT10 histone lysine methyltransferase DOT1L cofactor	protein-coding	0.023569	0.426174	
chunk0095_356_1	chr2	22591969	22592169	+	0	NA	Intergenic	L1PA10|LINE|L1	55590	NR_110577	102723362	Hs.502887	NR_110577	ENSG00000233587	LINC01884	-	long intergenic non-protein coding RNA 1884	ncRNA	0.020000	0.388060	
chunk0115_381_1	chr21	30319630	30319892	+	0	NA	exon (NM_203405, exon 1 of 1)	exon (NM_203405, exon 1 of 1)	528	NM_203405	388818	Hs.28704	NM_203405	ENSG00000197683	KRTAP26-1	-	keratin associated protein 26-1	protein-coding	0.030534	0.551331	
chunk0009_344_1	chr1	109370610	109370937	+	0	NA	intron (NM_002959, intron 1 of 19)	L2c|LINE|L2	22584	NM_001205228	6272	Hs.485195	NM_002959	ENSG00000134243	SORT1	Gp95|LDLCQ6|NT3|NTR3	sortilin 1	protein-coding	0.000000	0.371951	162(TGGTACTCCCTGTGCC,-,0.00),163(GGTACTCCCTGTGCCT,+,0.00)
chunk0073_40_1	chr16	2829853	2830277	+	0	NA	promoter-TSS (NM_145252)	promoter-TSS (NM_145252)	-107	NM_145252	124220	Hs.105887	NM_145252	ENSG00000162078	ZG16B	EECP|HRPE773|JCLN2|PAUF|PRO1567	zymogen granule protein 16B	protein-coding	0.030660	0.632941	
chunk0031_434_1	chr10	132482228	132482552	+	0	NA	Intergenic	L1M5|LINE|L1	37180	NM_173541									0.012346	0.403077	154(AGGAACAGAACGTTCC,-,0.00),155(GGAACAGAACGTTCCA,+,0.00)
chunk0166_285_1	chr6	48400142	48400341	+	0	NA	Intergenic	L2a|LINE|L2	-331552	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.000000	0.425000	
chunk0193_18_1	chr8	70616365	70616877	+	0	NA	intron (NR_038881, intron 1 of 3)	intron (NR_038881, intron 1 of 3)	8044	NR_038881	286190	Hs.662204	NR_038881	ENSG00000246366	LACTB2-AS1	-	LACTB2 antisense RNA 1	ncRNA	0.005859	0.405458	
chunk0091_332_1	chr19	14017836	14018220	+	0	NA	Intergenic	L1MB3|LINE|L1	-10120	NM_080864	117579	Hs.352155	NM_080864	ENSG00000171136	RLN3	H3|RXN3|ZINS4|insl7	relaxin 3	protein-coding	0.018229	0.485714	198(GAAGACAAAATGTTCT,-,0.00),199(AAGACAAAATGTTCTG,+,0.00)
chunk0200_313_1	chr9	23255304	23255559	+	0	NA	Intergenic	Intergenic	416968	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.003922	0.347656	
chunk0151_309_1	chr5	53338211	53338630	+	0	NA	Intergenic	L2c|LINE|L2	-142014	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.002387	0.376190	235(GAGTACAGTGTGATCC,-,0.00),236(AGTACAGTGTGATCCA,+,0.00)
chunk0143_253_1	chr4	115655680	115656155	+	0	NA	Intergenic	L1MC3|LINE|L1	-542041	NM_022569	64579	Hs.591700	NM_022569	ENSG00000138653	NDST4	N-HSST|N-HSST 4|NDST-4|NHSST4	N-deacetylase and N-sulfotransferase 4	protein-coding	0.004211	0.285714	
chunk0202_86_1	chr9	71960688	71961062	+	0	NA	intron (NM_182505, intron 2 of 3)	intron (NM_182505, intron 2 of 3)	49368	NM_182505	138241	Hs.534190	NM_182505	ENSG00000155621	C9orf85	-	chromosome 9 open reading frame 85	protein-coding	0.021390	0.469333	
chunk0186_387_1	chr7	144499777	144500196	+	0	NA	intron (NM_001042482, intron 7 of 7)	L1M5|LINE|L1	-89759	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.004773	0.288095	
chunk0116_408_1	chr21	42535787	42536082	+	0	NA	intron (NM_018964, intron 6 of 20)	intron (NM_018964, intron 6 of 20)	36302	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.013559	0.527027	199(GACACAGGATGTGCTG,+,0.00)
chunk0101_307_1	chr2	135150869	135151103	+	0	NA	intron (NM_001172435, intron 18 of 24)	L2c|LINE|L2	98721	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.000000	0.404255	
chunk0151_228_1	chr5	51024384	51025166	+	0	NA	Intergenic	L2a|LINE|L2	-54588	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.003836	0.333333	260(AAGTACATGGTGTGTT,-,0.00)
chunk0158_420_1	chr5	135135462	135135903	+	0	NA	intron (NM_001277348, intron 2 of 5)	intron (NM_001277348, intron 2 of 5)	-95635	NR_105050	101927953	Hs.436898	NR_105049	ENSG00000249082	C5orf66-AS1	Epist	C5orf66 antisense RNA 1	ncRNA	0.015873	0.567873	
chunk0078_441_1	chr16	89534909	89535235	+	0	NA	intron (NM_003119, intron 9 of 16)	L1MD3|LINE|L1	-25585	NM_001243130	6137	Hs.410817	NM_000977	ENSG00000167526	RPL13	BBC1|D16S444E|D16S44E|L13	ribosomal protein L13	protein-coding	0.015337	0.535168	
chunk0035_63_1	chr11	41533896	41534104	+	0	NA	Intergenic	Intergenic	-74364	NM_001258419	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.478469	
chunk0166_123_1	chr6	44570164	44570382	+	0	NA	Intergenic	Intergenic	134632	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.013761	0.557078	135(TAGTACTGGCTGTTCT,-,0.00),136(AGTACTGGCTGTTCTC,+,0.00)
chunk0072_453_1	chr15	101824637	101825298	+	0	NA	Intergenic	Intergenic	6780	NM_001001674	390649	Hs.554589	NM_001001674	ENSG00000182854	OR4F15	-	olfactory receptor family 4 subfamily F member 15	protein-coding	0.013616	0.392749	
chunk0112_150_1	chr20	38980072	38980614	+	0	NA	intron (NR_033905, intron 3 of 21)	MIR|SINE|MIR	18005	NM_021931	60625	Hs.444520	NM_021931	ENSG00000101452	DHX35	C20orf15|DDX35|KAIA0875	DEAH-box helicase 35	protein-coding	0.000000	0.338858	
chunk0173_185_1	chr6	144915274	144915848	+	0	NA	Intergenic	L1PB3|LINE|L1	509906	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.003484	0.318261	
chunk0012_461_1	chr1	165372164	165372681	+	0	NA	Intergenic	Intergenic	-15707	NM_177398	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.009671	0.362934	
chunk0091_274_1	chr19	11581929	11582481	+	0	NA	Intergenic	AluJb|SINE|Alu	-3219	NM_001111035	54	Hs.1211	NM_001611	ENSG00000102575	ACP5	HPAP|TRACP5a|TRACP5b|TRAP|TrATPase	acid phosphatase 5, tartrate resistant	protein-coding	0.009058	0.448463	369(GAGAACTTACTGTTCT,-,0.00),370(AGAACTTACTGTTCTC,+,0.00)
chunk0032_315_1	chr11	9931249	9931460	+	0	NA	intron (NM_030962, intron 16 of 39)	L1PA6|LINE|L1	92212	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.014218	0.533019	
chunk0142_20_1	chr4	90391664	90391993	+	0	NA	intron (NM_001145065, intron 3 of 10)	intron (NM_001145065, intron 3 of 10)	156797	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.000000	0.293939	
chunk0093_405_1	chr19	57088530	57088729	+	0	NA	Intergenic	Intergenic	-31512	NM_020903	57663	Hs.515632	NM_020903	ENSG00000131864	USP29	HOM-TES-84/86	ubiquitin specific peptidase 29	protein-coding	0.015075	0.560000	143(GAGAACAGGCTGAACA,-,0.00),144(AGAACAGGCTGAACAG,+,0.00)
chunk0084_339_1	chr17	81063598	81064048	+	0	NA	intron (NM_006340, intron 3 of 14)	intron (NM_006340, intron 3 of 14)	28676	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.017778	0.580931	
chunk0173_223_1	chr6	145968570	145969324	+	0	NA	Intergenic	Intergenic	-4850	NM_173082	257218	Hs.723297	NM_173082	ENSG00000146414	SHPRH	bA545I5.2	SNF2 histone linker PHD RING helicase	protein-coding	0.002653	0.368212	
chunk0128_33_1	chr3	104426766	104427290	+	0	NA	Intergenic	Intergenic	-902912	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.007634	0.409524	229(AAGCACAGGCTGTACA,-,0.00),230(AGCACAGGCTGTACAA,+,0.00)
chunk0068_411_1	chr15	59074913	59075487	+	0	NA	intron (NM_001270529, intron 6 of 13)	Tigger1|DNA|TcMar-Tigger	-29885	NM_004701	9133	Hs.194698	NM_004701	ENSG00000157456	CCNB2	HsT17299	cyclin B2	protein-coding	0.003484	0.328696	368(AAGCACTAAATGTGCC,-,0.00),369(AGCACTAAATGTGCCT,+,0.00)
chunk0060_67_1	chr14	41901059	41901496	+	0	NA	intron (NM_152447, intron 5 of 5)	intron (NM_152447, intron 5 of 5)	293716	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.006865	0.296804	
chunk0044_410_1	chr12	41072449	41072734	+	0	NA	TTS (NM_001843)	TTS (NM_001843)	-115857	NM_001164595	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.007018	0.346154	
chunk0106_461_1	chr2	209433919	209434328	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	10076	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.004890	0.326829	
chunk0014_337_1	chr1	182197601	182197997	+	0	NA	Intergenic	Intergenic	116262	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.010101	0.435768	134(CGGCACACTCTGAACC,-,0.00)
chunk0093_103_1	chr19	43641502	43641701	+	0	NA	Intergenic	Intergenic	-1762	NM_145296	199731	Hs.370984	NM_145296	ENSG00000105767	CADM4	IGSF4C|NECL4|Necl-4|TSLL2|synCAM4	cell adhesion molecule 4	protein-coding	0.005025	0.575000	
chunk0006_150_1	chr1	66300252	66300472	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-31746	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.013636	0.493213	
chunk0212_437_1	chrX	154305707	154306304	+	0	NA	intron (NM_001145933, intron 2 of 12)	intron (NM_001145933, intron 2 of 12)	948	NM_001145934	8277	Hs.102866	NM_012253	ENSG00000007350	TKTL1	TKR|TKT2	transketolase like 1	protein-coding	0.016750	0.515050	278(AAGTACACTGTGTCCC,-,0.00),279(AGTACACTGTGTCCCG,+,0.00)
chunk0013_180_1	chr1	168960100	168960630	+	0	NA	intron (NR_104091, intron 3 of 4)	intron (NR_104091, intron 3 of 4)	126640	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.001887	0.333333	
chunk0065_76_1	chr15	23546044	23546742	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	15738	NR_039731	100616275		NR_039731	ENSG00000265673	MIR4508	mir-4508	microRNA 4508	ncRNA	0.007163	0.420601	
chunk0072_155_1	chr15	92841225	92841492	+	0	NA	Intergenic	Intergenic	-41485	NR_037600	100507217	Hs.622504	NR_037600		LINC01578	-	long intergenic non-protein coding RNA 1578	ncRNA	0.003745	0.399254	
chunk0101_246_1	chr2	131674121	131674788	+	0	NA	Intergenic	Intergenic	37429	NR_108087	101927994	Hs.635757	NR_108087	ENSG00000224559	LINC01087	-	long intergenic non-protein coding RNA 1087	ncRNA	0.019490	0.423653	322(AGGAACATGATGTTCC,-,0.00),323(GGAACATGATGTTCCT,+,0.00)
chunk0005_128_1	chr1	57011671	57011870	+	0	NA	intron (NM_021080, intron 14 of 16)	MIRb|SINE|MIR	-45630	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.010050	0.380000	
chunk0045_405_1	chr12	52907085	52907706	+	0	NA	intron (NM_001256293, intron 1 of 8)	intron (NM_001256293, intron 1 of 8)	-2311	NM_002273	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.009662	0.572347	
chunk0187_313_1	chr7	156466368	156466786	+	0	NA	Intergenic	Intergenic	-20989	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.026316	0.451074	
chunk0117_351_1	chr21	44297562	44297942	+	0	NA	3' UTR (NM_000383, exon 14 of 14)	3' UTR (NM_000383, exon 14 of 14)	-2282	NM_001002021	5211	Hs.255093	NM_002626	ENSG00000141959	PFKL	ATP-PFK|PFK-B|PFK-L	phosphofructokinase, liver type	protein-coding	0.042105	0.606299	
chunk0126_202_1	chr3	78613338	78613729	+	0	NA	intron (NM_133631, intron 26 of 28)	intron (NM_133631, intron 26 of 28)	405926	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.005115	0.400510	
chunk0153_357_1	chr5	74416710	74416933	+	0	NA	intron (NR_126354, intron 2 of 2)	MIR|SINE|MIR	94335	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.000000	0.375000	
chunk0042_283_1	chr12	7304822	7305205	+	0	NA	intron (NM_001080454, intron 1 of 12)	intron (NM_001080454, intron 1 of 12)	681	NM_001080454	341392	Hs.450804	NM_001080454	ENSG00000215009	ACSM4	-	acyl-CoA synthetase medium chain family member 4	protein-coding	0.005222	0.408854	
chunk0104_145_1	chr2	173631382	173631663	+	0	NA	Intergenic	Intergenic	276689	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.000000	0.297872	
chunk0085_74_1	chr18	1577849	1578448	+	0	NA	Intergenic	L2c|LINE|L2	-218519	NR_023926	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.008347	0.410000	
chunk0199_376_1	chr9	13027192	13027391	+	0	NA	Intergenic	Intergenic	-54658	NR_132976	106635615		NR_132976		SNORD137	-	small nucleolar RNA, C/D box 137	snoRNA	0.005025	0.460000	
chunk0204_229_1	chr9	97640325	97640671	+	0	NA	intron (NM_002486, intron 1 of 22)	intron (NM_002486, intron 1 of 22)	-6818	NM_139246	158427	Hs.723236	NM_139246	ENSG00000136925	TSTD2	C9orf97	thiosulfate sulfurtransferase like domain containing 2	protein-coding	0.005780	0.394813	
chunk0199_367_1	chr9	12816778	12817207	+	0	NA	intron (NM_203403, intron 1 of 1)	intron (NM_203403, intron 1 of 1)	-2603	NR_125775	101929467	Hs.586443	NR_125775	ENSG00000235448	LURAP1L-AS1	-	LURAP1L antisense RNA 1	ncRNA	0.011655	0.397674	
chunk0160_155_1	chr5	151709395	151709660	+	0	NA	Intergenic	LTR9D|LTR|ERV1	-22473	NM_001309444	6678	Hs.111779	NM_003118	ENSG00000113140	SPARC	BM-40|OI17|ON	secreted protein acidic and cysteine rich	protein-coding	0.018868	0.462406	
chunk0122_144_1	chr3	31958676	31958882	+	0	NA	intron (NM_017784, intron 1 of 11)	MER58A|DNA|hAT-Charlie	-22995	NM_001137674	344787	Hs.585139	NM_001137674	ENSG00000197385	ZNF860	-	zinc finger protein 860	protein-coding	0.004854	0.420290	
chunk0061_193_1	chr14	60222965	60223255	+	0	NA	Intergenic	Intergenic	-22642	NM_177952	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.006897	0.491409	
chunk0020_114_1	chr1	233299444	233299643	+	0	NA	Intergenic	Intergenic	-3830	NM_014801	80003	Hs.370605	NM_014801	ENSG00000135749	PCNX2	PCNXL2	pecanex 2	protein-coding	0.005025	0.465000	
chunk0102_56_1	chr2	142822183	142822486	+	0	NA	Intergenic	Intergenic	-55292	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.006601	0.328947	103(AAGTACACTATGTGCT,-,0.00),104(AGTACACTATGTGCTT,+,0.00)
chunk0056_298_1	chr13	90757831	90758513	+	0	NA	Intergenic	Intergenic	168425	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.002933	0.333821	
chunk0133_77_1	chr3	167105262	167105486	+	0	NA	Intergenic	LTR80A|LTR|ERVL	274909	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.004464	0.386667	
chunk0172_67_1	chr6	134329838	134330296	+	0	NA	Intergenic	Intergenic	-12009	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.002183	0.300654	
chunk0129_189_1	chr3	121116491	121116773	+	0	NA	intron (NM_014980, intron 6 of 27)	intron (NM_014980, intron 6 of 27)	66992	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.000000	0.296820	
chunk0083_394_1	chr17	71656987	71657656	+	0	NA	Intergenic	L1MEi|LINE|L1	368658	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.005979	0.400000	
chunk0182_298_1	chr7	98400471	98400870	+	0	NA	intron (NM_018842, intron 1 of 13)	G-rich|Low_complexity|Low_complexity	445	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.050125	0.682500	
chunk0042_125_1	chr12	3378966	3379353	+	0	NA	Intergenic	L2a|LINE|L2	-2190	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.015504	0.469072	
chunk0103_359_1	chr2	168220960	168221662	+	0	NA	intron (NM_013233, intron 1 of 17)	intron (NM_013233, intron 1 of 17)	26284	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.008547	0.366999	
chunk0116_389_1	chr21	42330908	42331348	+	0	NA	Intergenic	L2a|LINE|L2	-15532	NM_003226	7033	Hs.82961	NM_003226	ENSG00000160180	TFF3	ITF|P1B|TFI	trefoil factor 3	protein-coding	0.006818	0.376417	
chunk0067_81_1	chr15	41666389	41666794	+	0	NA	intron (NM_001080541, intron 1 of 22)	L1PA17|LINE|L1	6179	NM_001164273	23269	Hs.187569	NM_001080541	ENSG00000174197	MGA	MAD5|MXD5	MAX dimerization protein MGA	protein-coding	0.007407	0.325123	
chunk0098_195_1	chr2	72308466	72308884	+	0	NA	intron (NM_015189, intron 20 of 21)	intron (NM_015189, intron 20 of 21)	-160813	NM_001277742	56603	Hs.91546	NM_019885	ENSG00000003137	CYP26B1	CYP26A2|P450RAI-2|P450RAI2|RHFCA	cytochrome P450 family 26 subfamily B member 1	protein-coding	0.000000	0.329356	
chunk0002_408_1	chr1	27487976	27488286	+	0	NA	intron (NM_001201404, intron 1 of 7)	intron (NM_001201404, intron 1 of 7)	2056	NM_006990	10163	Hs.469244	NM_006990	ENSG00000158195	WASF2	IMD2|SCAR2|WASF4|WAVE2|dJ393P12.2	WASP family member 2	protein-coding	0.006452	0.401929	
chunk0145_18_1	chr4	143399299	143399636	+	0	NA	intron (NM_002039, intron 1 of 9)	intron (NM_002039, intron 1 of 9)	56007	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.002967	0.360947	
chunk0179_24_1	chr7	42851881	42852482	+	0	NA	Intergenic	Intergenic	59909	NM_024054	79020	Hs.698120	NM_024054	ENSG00000136197	C7orf25	-	chromosome 7 open reading frame 25	protein-coding	0.004992	0.448505	
chunk0076_96_1	chr16	65208092	65208487	+	0	NA	Intergenic	Intergenic	-31716	NR_110918	101927650	Hs.634008	NR_110918	ENSG00000259847	LINC02126	-	long intergenic non-protein coding RNA 2126	ncRNA	0.005063	0.345960	
chunk0202_246_1	chr9	76792872	76793684	+	0	NA	intron (NM_015225, intron 6 of 18)	intron (NM_015225, intron 6 of 18)	28842	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.004926	0.386224	
chunk0186_34_1	chr7	136033129	136033852	+	0	NA	Intergenic	Intergenic	-56034	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.005533	0.415746	408(TAGTACATAGTGTTCC,-,0.00),409(AGTACATAGTGTTCCG,+,0.00)
chunk0106_338_1	chr2	206343737	206344364	+	0	NA	Intergenic	MER54A|LTR|ERVL	69022	NM_001285549	57683	Hs.110489	NM_020923	ENSG00000204186	ZDBF2	Slx9	zinc finger DBF-type containing 2	protein-coding	0.004785	0.480892	
chunk0086_91_1	chr18	13759961	13760616	+	0	NA	3' UTR (NM_003799, exon 12 of 12)	3' UTR (NM_003799, exon 12 of 12)	33628	NM_003799	8731	Hs.592347	NM_003799	ENSG00000101654	RNMT	CMT1|CMT1c|MET|Met|RG7MT1|cm1p|hCMT1|hMet	RNA guanine-7 methyltransferase	protein-coding	0.003053	0.330793	
chunk0168_244_1	chr6	88260551	88260823	+	0	NA	Intergenic	Intergenic	-94639	NM_001160258	1268	Hs.75110	NM_016083	ENSG00000118432	CNR1	CANN6|CB-R|CB1|CB1A|CB1K5|CB1R|CNR	cannabinoid receptor 1	protein-coding	0.000000	0.443223	
chunk0048_402_1	chr12	87965577	87965776	+	0	NA	Intergenic	Intergenic	63723	NM_152589	160419	Hs.112930	NM_152589	ENSG00000165805	C12orf50	-	chromosome 12 open reading frame 50	protein-coding	0.000000	0.365000	
chunk0043_356_1	chr12	23186775	23187469	+	0	NA	intron (NR_120471, intron 2 of 4)	intron (NR_120471, intron 2 of 4)	11486	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.001441	0.402878	330(CAAAACACTGTGTGCC,-,0.00),331(AAAACACTGTGTGCCA,+,0.00)
chunk0030_373_1	chr10	119240988	119241187	+	0	NA	intron (NM_005308, intron 1 of 15)	MIRc|SINE|MIR	33402	NM_005308	2869	Hs.524625	NM_005308	ENSG00000198873	GRK5	FP2025|GPRK5	G protein-coupled receptor kinase 5	protein-coding	0.040201	0.565000	
chunk0150_31_1	chr5	31095828	31096099	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-97692	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.003690	0.363971	
chunk0010_264_1	chr1	116900722	116901116	+	0	NA	Intergenic	Intergenic	-9004	NM_020440	5738	Hs.418093	NM_020440	ENSG00000134247	PTGFRN	CD315|CD9P-1|EWI-F|FPRP|SMAP-6	prostaglandin F2 receptor inhibitor	protein-coding	0.017766	0.432911	
chunk0097_20_1	chr2	42222417	42222787	+	0	NA	intron (NM_019063, intron 1 of 22)	MER58B|DNA|hAT-Charlie	-52371	NR_110584	102723824	Hs.639826	NR_110584		LOC102723824	-	uncharacterized LOC102723824	ncRNA	0.002703	0.345013	
chunk0052_34_1	chr13	20701460	20701858	+	0	NA	Intergenic	Intergenic	-1684	NM_138284	53342	Hs.655142	NM_138284	ENSG00000172458	IL17D	IL-17D	interleukin 17D	protein-coding	0.007538	0.401003	171(GGGAACACGATGAGCC,-,0.00),172(GGAACACGATGAGCCT,+,0.00)
chunk0133_399_1	chr3	174333653	174334141	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	-413101	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004098	0.400818	
chunk0201_56_1	chr9	33888958	33889364	+	0	NA	intron (NM_017811, intron 2 of 4)	intron (NM_017811, intron 2 of 4)	45203	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.002463	0.348894	
chunk0054_388_1	chr13	50320182	50320733	+	0	NA	intron (NR_109974, intron 2 of 6)	L2b|LINE|L2	148439	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.001815	0.369565	
chunk0039_135_1	chr11	98451356	98452072	+	0	NA	Intergenic	L1MC1|LINE|L1	-569262	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004190	0.316597	
chunk0188_264_1	chr8	14800915	14801278	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	52414	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.008264	0.326923	
chunk0166_36_1	chr6	42138698	42139469	+	0	NA	intron (NM_001164446, intron 1 of 4)	intron (NM_001164446, intron 1 of 4)	3894	NM_001164446	647024	Hs.444277	NM_001164446	ENSG00000188112	C6orf132	bA7K24.2	chromosome 6 open reading frame 132	protein-coding	0.009079	0.465026	
chunk0149_457_1	chr5	30028286	30028828	+	0	NA	Intergenic	Intergenic	-632581	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.007380	0.344383	
chunk0036_190_1	chr11	63024074	63024273	+	0	NA	Intergenic	Intergenic	-8328	NM_001184736	9376	Hs.266223	NM_004254	ENSG00000149452	SLC22A8	OAT3	solute carrier family 22 member 8	protein-coding	0.040201	0.555000	
chunk0202_375_1	chr9	80643746	80644530	+	0	NA	Intergenic	Intergenic	669115	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.006378	0.383439	
chunk0073_326_1	chr16	14424537	14425109	+	0	NA	Intergenic	Intergenic	-54557	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.015734	0.514834	
chunk0161_252_1	chr5	171883681	171884249	+	0	NA	intron (NM_012300, intron 6 of 12)	L1MC1|LINE|L1	98093	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.001761	0.346221	
chunk0169_383_1	chr6	107622330	107622600	+	0	NA	intron (NM_018013, intron 5 of 6)	L3|LINE|CR1	109931	NM_001286409	256380	Hs.486109	NM_198081	ENSG00000146285	SCML4	dJ47M23.1	Scm polycomb group protein like 4	protein-coding	0.003704	0.416974	
chunk0001_217_1	chr1	8048820	8049192	+	0	NA	Intergenic	Intergenic	-22673	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.000000	0.308311	
chunk0187_28_1	chr8	717313	717800	+	0	NA	intron (NM_001303100, intron 1 of 5)	intron (NM_001303100, intron 1 of 5)	13683	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.018480	0.508197	
chunk0062_66_1	chr14	67550961	67551594	+	0	NA	intron (NM_020715, intron 2 of 28)	MER94|DNA|hAT-Blackjack	17986	NM_020715	57475	Hs.594236	NM_020715	ENSG00000054690	PLEKHH1	-	pleckstrin homology, MyTH4 and FERM domain containing H1	protein-coding	0.006319	0.427445	
chunk0108_386_1	chr2	237020131	237020506	+	0	NA	Intergenic	Intergenic	-65123	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.005333	0.377660	241(GTTACAGAATGTTCTC,+,0.00)
chunk0189_127_1	chr8	22383127	22384254	+	0	NA	intron (NM_001135153, intron 1 of 8)	intron (NM_001135153, intron 1 of 8)	16153	NM_001135153	23516	Hs.491232	NM_015359	ENSG00000104635	SLC39A14	HCIN|HMNDYT2|LZT-Hs4|NET34|ZIP14|cig19	solute carrier family 39 member 14	protein-coding	0.015972	0.554965	385(TGAACAGTCTGCACTC,+,0.00),393(CTGCACTCTCTGTCCT,-,0.00),394(TGCACTCTCTGTCCTT,+,0.00)
chunk0091_338_1	chr19	14443552	14443982	+	0	NA	intron (NM_213560, intron 3 of 21)	intron (NM_213560, intron 3 of 21)	3493	NM_213560	5585	Hs.466044	NM_002741	ENSG00000123143	PKN1	DBK|PAK-1|PAK1|PKN|PKN-ALPHA|PRK1|PRKCL1	protein kinase N1	protein-coding	0.023256	0.554524	
chunk0074_89_1	chr16	22017756	22018014	+	0	NA	intron (NM_001164579, intron 1 of 2)	intron (NM_001164579, intron 1 of 2)	9750	NM_001164579	730094	Hs.498890	NM_173501	ENSG00000185716	MOSMO	ATTHOG|BC030336|C16orf52	modulator of smoothened	protein-coding	0.007752	0.366795	
chunk0018_61_1	chr1	216766827	216767433	+	0	NA	intron (NM_001243513, intron 1 of 7)	MIR3|SINE|MIR	38237	NM_001243514	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.006601	0.360791	
chunk0194_361_1	chr8	89719593	89720127	+	0	NA	intron (NR_125822, intron 4 of 4)	intron (NR_125822, intron 4 of 4)	37851	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.003745	0.317757	249(AAGAACATGTTGTACC,-,0.00),250(AGAACATGTTGTACCA,+,0.00)
chunk0187_87_1	chr8	3523516	3524108	+	0	NA	intron (NM_033225, intron 10 of 69)	(CA)n|Simple_repeat|Simple_repeat	-795361	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.018581	0.494098	
chunk0021_399_1	chr1	246631236	246632035	+	0	NA	intron (NM_152609, intron 3 of 10)	intron (NM_152609, intron 3 of 10)	65298	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.002503	0.317500	
chunk0051_219_1	chr12	116636706	116637371	+	0	NA	Intergenic	Intergenic	77657	NM_001085481	643246	Hs.356061	NM_001085481	ENSG00000258102	MAP1LC3B2	ATG8G	microtubule associated protein 1 light chain 3 beta 2	protein-coding	0.013534	0.409910	
chunk0041_351_1	chr11	130762611	130763429	+	0	NA	Intergenic	Intergenic	90064	NM_001271983	283171	Hs.376151	NM_001271983		C11orf44	-	chromosome 11 open reading frame 44	protein-coding	0.023227	0.532357	
chunk0151_340_1	chr5	54222238	54222680	+	0	NA	intron (NM_019087, intron 1 of 4)	intron (NM_019087, intron 1 of 4)	88114	NM_019087	54622	Hs.659125	NM_019087	ENSG00000185305	ARL15	ARFRP2	ADP ribosylation factor like GTPase 15	protein-coding	0.009050	0.406321	
chunk0004_92_1	chr1	43793014	43793530	+	0	NA	intron (NM_174963, intron 3 of 12)	L1MA3|LINE|L1	-45350	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.005814	0.348162	
chunk0034_7_1	chr11	25926403	25926647	+	0	NA	Intergenic	Intergenic	-262598	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.004098	0.387755	
chunk0200_42_1	chr9	15211304	15211892	+	0	NA	intron (NM_001168341, intron 2 of 17)	intron (NM_001168341, intron 2 of 17)	38602	NM_001168342	158219	Hs.563630	NM_152574	ENSG00000155158	TTC39B	C9orf52	tetratricopeptide repeat domain 39B	protein-coding	0.008503	0.417657	289(CAGAACAAAATGTTCC,-,0.00),290(AGAACAAAATGTTCCA,+,0.00)
chunk0100_57_1	chr2	106277393	106277945	+	0	NA	Intergenic	LTR48B|LTR|ERV1	-83330	NM_025076	80146	Hs.469561	NM_025076	ENSG00000115652	UXS1	SDR6E1|UGD	UDP-glucuronate decarboxylase 1	protein-coding	0.010870	0.446655	
chunk0140_34_1	chr4	66226600	66226999	+	0	NA	Intergenic	L1ME3|LINE|L1	-50025	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.005013	0.282500	
chunk0019_331_1	chr1	229221208	229222010	+	0	NA	Intergenic	Intergenic	-46808	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.007481	0.468244	
chunk0206_15_1	chr9	115689543	115690245	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	54345	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.001425	0.332859	
chunk0089_27_1	chr18	57797252	57797563	+	0	NA	intron (NM_005603, intron 1 of 27)	intron (NM_005603, intron 1 of 27)	5688	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.009646	0.496795	
chunk0154_170_1	chr5	79708987	79709524	+	0	NA	intron (NM_153610, intron 1 of 12)	L1M5|LINE|L1	19419	NM_153610	202333	Hs.482625	NM_153610	ENSG00000164309	CMYA5	C5orf10|SPRYD2|TRIM76	cardiomyopathy associated 5	protein-coding	0.003724	0.362454	
chunk0132_205_1	chr3	157336630	157337053	+	0	NA	intron (NM_001167911, intron 9 of 12)	MER58A|DNA|hAT-Charlie	-99950	NM_002852	5806	Hs.591286	NM_002852	ENSG00000163661	PTX3	TNFAIP5|TSG-14	pentraxin 3	protein-coding	0.004728	0.349057	
chunk0213_18_1	chrY	21631047	21631436	+	0	NA	Intergenic	Intergenic	-36575	NR_001537	83868	Hs.615432	NR_001537	ENSG00000184991	TTTY13	NCRNA00136|TTY13	testis-specific transcript, Y-linked 13	ncRNA	0.010283	0.397436	
chunk0026_131_1	chr10	62098471	62098670	+	0	NA	Intergenic	Intergenic	49359	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.010050	0.455000	
chunk0067_373_1	chr15	48935830	48936102	+	0	NA	intron (NM_203349, intron 1 of 11)	L2c|LINE|L2	27478	NM_203349	399694	Hs.642615	NM_203349	ENSG00000185634	SHC4	RaLP|SHCD	SHC adaptor protein 4	protein-coding	0.003676	0.340659	
chunk0038_370_1	chr11	93374178	93374923	+	0	NA	intron (NM_181645, intron 7 of 13)	L1PB1|LINE|L1	43833	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.001342	0.345845	348(TTGAACAGGGTGTTCT,-,0.00),349(TGAACAGGGTGTTCTT,+,0.00)
chunk0042_31_1	chr12	1484294	1484530	+	0	NA	intron (NM_001301248, intron 18 of 18)	L1ME4b|LINE|L1	-16079	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.012712	0.371308	
chunk0076_37_1	chr16	59729267	59729634	+	0	NA	Intergenic	L1PA13|LINE|L1	25741	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.008174	0.551630	
chunk0183_225_1	chr7	106862760	106862959	+	0	NA	Intergenic	Intergenic	-2419	NM_001282426	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.000000	0.440000	
chunk0200_247_1	chr9	21083319	21083908	+	0	NA	Intergenic	L1ME3A|LINE|L1	-5650	NM_002176	3456	Hs.93177	NM_002176	ENSG00000171855	IFNB1	IFB|IFF|IFN-beta|IFNB	interferon beta 1	protein-coding	0.001698	0.276271	
chunk0108_20_1	chr2	226352821	226353520	+	0	NA	Intergenic	Intergenic	210376	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.008584	0.430000	
chunk0043_198_1	chr12	19282219	19282684	+	0	NA	intron (NM_019012, intron 10 of 25)	intron (NM_019012, intron 10 of 25)	77126	NM_001256787	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.000000	0.293991	
chunk0137_155_1	chr4	15821388	15821739	+	0	NA	intron (NR_132660, intron 2 of 6)	L1PA10|LINE|L1	43298	NM_001775	952	Hs.479214	NM_001775	ENSG00000004468	CD38	ADPRC 1|ADPRC1	CD38 molecule	protein-coding	0.002849	0.318182	
chunk0187_306_1	chr7	156310075	156310533	+	0	NA	Intergenic	L1MA9|LINE|L1	135284	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.010917	0.437908	215(CTGAACATCATGTTCT,-,0.00),216(TGAACATCATGTTCTC,+,0.00),399(AGTACAGACAGCTCTT,+,0.00)
chunk0150_283_1	chr5	37040534	37040796	+	0	NA	intron (NM_015384, intron 34 of 45)	L1ME3Cz|LINE|L1	163906	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.000000	0.315589	
chunk0161_384_1	chr5	176941389	176941697	+	0	NA	intron (NM_016290, intron 10 of 14)	intron (NM_016290, intron 10 of 14)	-42211	NM_002115	3101	Hs.411695	NM_002115	ENSG00000160883	HK3	HKIII|HXK3	hexokinase 3	protein-coding	0.000000	0.271845	
chunk0156_455_1	chr5	114969526	114970200	+	0	NA	Intergenic	L1MC4a|LINE|L1	-196450	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.010386	0.368889	
chunk0030_81_1	chr10	112322232	112322490	+	0	NA	intron (NR_028134, intron 12 of 18)	intron (NR_028134, intron 12 of 18)	-22673	NR_106772	102465427		NR_106772	ENSG00000283688	MIR6715B	hsa-mir-6715b	microRNA 6715b	ncRNA	0.007752	0.463320	
chunk0113_378_1	chr20	59826262	59826947	+	0	NA	intron (NM_080672, intron 8 of 12)	intron (NM_080672, intron 8 of 12)	105394	NM_183246	116154	Hs.473218	NM_080672	ENSG00000087495	PHACTR3	C20orf101|H17739|PPP1R123|SCAPIN1|SCAPININ	phosphatase and actin regulator 3	protein-coding	0.011679	0.586006	252(GGGCACATGCTGTCCT,-,0.00),253(GGCACATGCTGTCCTC,+,0.00),336(CTGTACACACTGTCCT,-,0.00),337(TGTACACACTGTCCTC,+,0.00),415(CTGCACACACAGTCCT,-,0.00),416(TGCACACACAGTCCTG,+,0.00),620(GAGAACAGAAAGTGCC,-,0.00),621(AGAACAGAAAGTGCCT,+,0.00)
chunk0012_274_1	chr1	161824394	161825314	+	0	NA	intron (NM_007348, intron 9 of 15)	L2c|LINE|L2	58610	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.005435	0.383279	315(AAAAACTGTGTGTTCT,-,0.00),316(AAAACTGTGTGTTCTT,+,0.00)
chunk0175_399_1	chr6	168549066	168549265	+	0	NA	exon (NM_001166412, exon 7 of 13)	exon (NM_001166412, exon 7 of 13)	108014	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.015075	0.375000	
chunk0091_461_1	chr19	18183737	18183936	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-9394	NM_032683	84769	Hs.515254	NM_032683	ENSG00000254858	MPV17L2	FKSG24	MPV17 mitochondrial inner membrane protein like 2	protein-coding	0.000000	0.285000	
chunk0032_363_1	chr11	10777469	10777985	+	0	NA	intron (NM_014633, intron 24 of 24)	intron (NM_014633, intron 24 of 24)	23881	NR_004403	692223	Hs.723086	NR_004403	ENSG00000238622	SNORD97	U97	small nucleolar RNA, C/D box 97	snoRNA	0.013566	0.450677	
chunk0093_116_1	chr19	44615964	44616165	+	0	NA	intron (NM_001205280, intron 1 of 4)	intron (NM_001205280, intron 1 of 4)	2434	NM_001205280	147710	Hs.512509	NM_001205280	ENSG00000216588	IGSF23	-	immunoglobulin superfamily member 23	protein-coding	0.014925	0.420792	
chunk0163_327_1	chr6	15073444	15074066	+	0	NA	Intergenic	Intergenic	-172220	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.008039	0.468700	
chunk0144_451_1	chr4	141896727	141897008	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	260271	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.010676	0.379433	
chunk0096_246_1	chr2	31194084	31194534	+	0	NA	intron (NM_001145122, intron 9 of 21)	L2c|LINE|L2	23236	NM_001145122	440854	Hs.468059	NM_001145122	ENSG00000214711	CAPN14	-	calpain 14	protein-coding	0.008889	0.470067	163(AGGCACTGTTTGTCCT,-,0.00),164(GGCACTGTTTGTCCTG,+,0.00),222(TGTACATGAAGTTCCT,+,0.00)
chunk0103_241_1	chr2	164826570	164826951	+	0	NA	intron (NM_001278458, intron 2 of 16)	intron (NM_001278458, intron 2 of 16)	-13989	NR_110574	101929633	Hs.570267	NR_110574		LOC101929633	-	uncharacterized LOC101929633	ncRNA	0.005249	0.395288	
chunk0132_84_1	chr3	155370169	155370926	+	0	NA	Intergenic	Intergenic	-76847	NR_037902									0.000000	0.431398	512(GGGCACACACTGATCA,-,0.00),513(GGCACACACTGATCAG,+,0.00)
chunk0191_150_1	chr8	48921586	48922064	+	0	NA	promoter-TSS (NM_003068)	promoter-TSS (NM_003068)	-385	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.066946	0.607516	
chunk0150_125_1	chr5	33228252	33228478	+	0	NA	Intergenic	Intergenic	-212331	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.013274	0.370044	
chunk0054_440_1	chr13	51389742	51390241	+	0	NA	intron (NM_001306091, intron 7 of 19)	intron (NM_001306091, intron 7 of 19)	-41352	NR_049878	100847003		NR_049878	ENSG00000266072	MIR5693	-	microRNA 5693	ncRNA	0.006012	0.286000	
chunk0021_77_1	chr10	1549646	1550281	+	0	NA	intron (NR_033387, intron 1 of 1)	intron (NR_033387, intron 1 of 1)	23333	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.020472	0.520440	
chunk0096_375_1	chr2	36821240	36821475	+	0	NA	Intergenic	Intergenic	124667	NM_001177971	5212	Hs.137415	NM_053276	ENSG00000205221	VIT	VIT1	vitrin	protein-coding	0.004255	0.419492	
chunk0012_332_1	chr1	162548288	162548674	+	0	NA	Intergenic	Intergenic	-13025	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.010363	0.423773	159(GAGAAGACACTGTTCC,-,0.00),160(AGAAGACACTGTTCCT,+,0.00)
chunk0008_423_1	chr1	98717456	98718010	+	0	NA	intron (NR_033716, intron 8 of 8)	intron (NR_033716, intron 8 of 8)	56053	NM_015976	51375	Hs.197015	NM_015976	ENSG00000162627	SNX7	-	sorting nexin 7	protein-coding	0.009025	0.365766	
chunk0200_365_1	chr9	25699710	25700250	+	0	NA	Intergenic	L2a|LINE|L2	-21122	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.003704	0.345656	
chunk0117_249_1	chr22	23278896	23279239	+	0	NA	intron (NM_021574, intron 8 of 21)	MIRb|SINE|MIR	16300	NR_033408	26226	Hs.729589	NR_033408	ENSG00000230701	FBXW4P1	FBW3|FBXW3|SHFM3P1	F-box and WD repeat domain containing 4 pseudogene 1	pseudo	0.014577	0.540698	
chunk0134_278_1	chr3	179688848	179689316	+	0	NA	intron (NM_003940, intron 2 of 20)	intron (NM_003940, intron 2 of 20)	35937	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.010684	0.407249	
chunk0110_49_1	chr20	10658510	10659193	+	0	NA	intron (NM_000214, intron 3 of 25)	intron (NM_000214, intron 3 of 25)	-9156	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.017570	0.441520	
chunk0048_389_1	chr12	87215608	87215881	+	0	NA	Intergenic	Intergenic	-376840	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.000000	0.313869	
chunk0035_326_1	chr11	47521276	47521808	+	0	NA	intron (NM_001172639, intron 1 of 15)	MIR|SINE|MIR	2446	NM_001172639	10658	Hs.595333	NM_006560	ENSG00000149187	CELF1	BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50	CUGBP Elav-like family member 1	protein-coding	0.000000	0.320826	
chunk0069_426_1	chr15	68187571	68188136	+	0	NA	3' UTR (NM_016166, exon 14 of 14)	3' UTR (NM_016166, exon 14 of 14)	18257	NM_001031733	91860	Hs.709550	NM_033429	ENSG00000129007	CALML4	NY-BR-20	calmodulin like 4	protein-coding	0.014159	0.409894	
chunk0101_131_1	chr2	127226556	127227032	+	0	NA	Intergenic	Intergenic	-21027	NM_001001665	339761	Hs.407639	NM_001001665	ENSG00000186684	CYP27C1	-	cytochrome P450 family 27 subfamily C member 1	protein-coding	0.018908	0.480084	
chunk0150_400_1	chr5	39863652	39864009	+	0	NA	Intergenic	Intergenic	-188461	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.014006	0.374302	
chunk0004_168_1	chr1	45680850	45681289	+	0	NA	intron (NM_021639, intron 2 of 12)	intron (NM_021639, intron 2 of 12)	5561	NM_021639	60313	Hs.238432	NM_021639	ENSG00000159592	GPBP1L1	SP192	GC-rich promoter binding protein 1 like 1	protein-coding	0.002278	0.329545	
chunk0155_108_1	chr5	92850898	92851293	+	0	NA	Intergenic	Intergenic	720248	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.005063	0.368687	
chunk0209_132_1	chrX	41152316	41152710	+	0	NA	intron (NM_001039591, intron 13 of 44)	intron (NM_001039591, intron 13 of 44)	66878	NM_001039591	8239	Hs.77578	NM_004652	ENSG00000124486	USP9X	DFFRX|FAF|FAM|MRX99|MRXS99F	ubiquitin specific peptidase 9 X-linked	protein-coding	0.000000	0.359494	
chunk0127_423_1	chr3	102635137	102635355	+	0	NA	Intergenic	Intergenic	200231	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.264840	
chunk0011_261_1	chr1	150937039	150937411	+	0	NA	intron (NM_001243491, intron 3 of 8)	L1MB2|LINE|L1	10886	NM_001145415	9869	Hs.643565	NM_012432	ENSG00000143379	SETDB1	ESET|H3-K9-HMTase4|KG1T|KMT1E|TDRD21	SET domain bifurcated histone lysine methyltransferase 1	protein-coding	0.013441	0.412869	
chunk0114_238_1	chr21	15988057	15988586	+	0	NA	Intergenic	Intergenic	-82201	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.001890	0.354717	
chunk0170_295_1	chr6	115351824	115352310	+	0	NA	Intergenic	Intergenic	-686664	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.000000	0.279261	
chunk0003_190_1	chr1	34014706	34015029	+	0	NA	intron (NM_052896, intron 3 of 69)	intron (NM_052896, intron 3 of 69)	145911	NR_038372	402779	Hs.666207	NR_038372	ENSG00000231163	CSMD2-AS1	-	CSMD2 antisense RNA 1	ncRNA	0.000000	0.453704	
chunk0071_253_1	chr15	85414349	85414853	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	33985	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.001984	0.340594	219(AGGTACAGAGTGTTCC,-,0.00),220(GGTACAGAGTGTTCCT,+,0.00)
chunk0118_158_1	chr22	30383144	30383765	+	0	NA	intron (NM_001017981, intron 5 of 8)	MIRb|SINE|MIR	3859	NM_001017981	200312	Hs.592194	NM_001017981	ENSG00000099999	RNF215	-	ring finger protein 215	protein-coding	0.016103	0.588424	
chunk0032_372_1	chr11	11034717	11035015	+	0	NA	Intergenic	L1MD2|LINE|L1	176649	NR_034137	729013	Hs.726427	NR_034137	ENSG00000247271	ZBED5-AS1	-	ZBED5 antisense RNA 1	ncRNA	0.006711	0.408027	
chunk0129_80_1	chr3	118097868	118098211	+	0	NA	Intergenic	Intergenic	-845037	NR_046230	100506765	Hs.660823	NR_046230	ENSG00000239877	IGSF11-AS1	-	IGSF11 antisense RNA 1	ncRNA	0.005831	0.383721	
chunk0152_428_1	chr5	65968952	65969449	+	0	NA	intron (NM_018695, intron 1 of 24)	intron (NM_018695, intron 1 of 24)	-23627	NR_028474	100303749	Hs.608060	NR_028474		LOC100303749	-	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene	pseudo	0.012072	0.331325	
chunk0082_397_1	chr17	60790363	60790739	+	0	NA	intron (NM_017679, intron 6 of 23)	intron (NM_017679, intron 6 of 23)	112740	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.000000	0.297082	213(TGGCACACCATGTACA,-,0.00),214(GGCACACCATGTACAG,+,0.00)
chunk0068_25_1	chr15	50858753	50859151	+	0	NA	Intergenic	L2a|LINE|L2	-49720	NM_007347	23431	Hs.413366	NM_007347	ENSG00000081014	AP4E1	CPSQ4|SPG51|STUT1	adaptor related protein complex 4 subunit epsilon 1	protein-coding	0.002513	0.421053	205(GAGTACAGTATGTGCC,-,0.00),206(AGTACAGTATGTGCCT,+,0.00)
chunk0041_223_1	chr11	127766146	127766692	+	0	NA	Intergenic	Intergenic	495349	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.003663	0.352834	246(GAGCACATCCTGTCCC,-,0.00),247(AGCACATCCTGTCCCT,+,0.00)
chunk0085_450_1	chr18	11267983	11268786	+	0	NA	Intergenic	Intergenic	-119622	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.011208	0.347015	
chunk0106_399_1	chr2	207787818	207788122	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-18551	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.013158	0.495082	
chunk0175_111_1	chr7	3242232	3242437	+	0	NA	Intergenic	Intergenic	-59114	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.480583	
chunk0185_161_1	chr7	127755721	127755962	+	0	NA	intron (NM_014390, intron 10 of 23)	intron (NM_014390, intron 10 of 23)	103693	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.016598	0.380165	
chunk0064_13_1	chr14	89312933	89313303	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	103992	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.010811	0.444744	
chunk0045_54_1	chr12	45260000	45260557	+	0	NA	intron (NM_001142679, intron 1 of 19)	intron (NM_001142679, intron 1 of 19)	-32405	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.005386	0.431900	52(TAGAACATACTGCACT,-,0.00),53(AGAACATACTGCACTG,+,0.00)
chunk0086_354_1	chr18	25836673	25837215	+	0	NA	Intergenic	Intergenic	253703	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.003690	0.480663	
chunk0080_158_1	chr17	28097850	28098352	+	0	NA	intron (NM_016231, intron 1 of 10)	MIR3|SINE|MIR	55439	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.007968	0.337972	
chunk0041_185_1	chr11	126351363	126351800	+	0	NA	intron (NR_033839, intron 1 of 1)	MLT1A0|LTR|ERVL-MaLR	4006	NR_033839	399972	Hs.585206	NR_033839		GSEC	DCPS-AS1|ST3GAL4-AS1	G-quadruplex forming sequence containing lncRNA	ncRNA	0.013730	0.465753	
chunk0053_258_1	chr13	33065341	33065713	+	0	NA	3' UTR (NM_004795, exon 5 of 5)	3' UTR (NM_004795, exon 5 of 5)	49094	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.002688	0.310992	
chunk0005_37_1	chr1	54881033	54881547	+	0	NA	intron (NM_014762, intron 2 of 8)	L1PA13|LINE|L1	5958	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.007782	0.388350	
chunk0126_217_1	chr3	78823908	78824274	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	195368	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002732	0.340599	
chunk0197_449_1	chr8	127847466	127847880	+	0	NA	intron (NR_003367, intron 1 of 8)	L1MC4a|LINE|L1	51711	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.009662	0.443373	
chunk0158_416_1	chr5	135014369	135014626	+	0	NA	Intergenic	Intergenic	-18783	NM_001277348									0.019455	0.534884	
chunk0156_397_1	chr5	113666644	113667524	+	0	NA	Intergenic	L1PB1|LINE|L1	153390	NM_022828	64848	Hs.231942	NM_022828	ENSG00000047188	YTHDC2	CAHL|hYTHDC2	YTH domain containing 2	protein-coding	0.012500	0.341657	
chunk0133_338_1	chr3	172750182	172750594	+	0	NA	promoter-TSS (NM_001258315)	promoter-TSS (NM_001258315)	-297	NM_001258315	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.031553	0.481840	
chunk0027_20_1	chr10	72243701	72244054	+	0	NA	Intergenic	L2c|LINE|L2	-26743	NR_045564	51008	Hs.500007	NM_015947	ENSG00000138303	ASCC1	ASC1p50|CGI-18|SMABF2|p50	activating signal cointegrator 1 complex subunit 1	protein-coding	0.025496	0.542373	187(GGGAACAGCATGTGCA,-,0.00),188(GGAACAGCATGTGCAA,+,0.00)
chunk0086_428_1	chr18	28013116	28013776	+	0	NA	intron (NM_001308176, intron 2 of 14)	intron (NM_001308176, intron 2 of 14)	23139	NM_001308176	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.003030	0.328290	
chunk0096_318_1	chr2	33197456	33197874	+	0	NA	intron (NM_000627, intron 3 of 29)	intron (NM_000627, intron 3 of 29)	63068	NM_001166266	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.007177	0.391408	
chunk0136_359_1	chr3	195914756	195915258	+	0	NA	Intergenic	Intergenic	-5998	NM_005781	10188	Hs.518513	NM_005781	ENSG00000061938	TNK2	ACK|ACK-1|ACK1|p21cdc42Hs	tyrosine kinase non receptor 2	protein-coding	0.019920	0.570577	186(GAGAACAGACTGTGCC,-,0.00),187(AGAACAGACTGTGCCT,+,0.00)
chunk0090_114_1	chr18	71369094	71369532	+	0	NA	Intergenic	Intergenic	209643	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.004566	0.323462	289(AGGAACAAAGTGTGCT,-,0.00),290(GGAACAAAGTGTGCTC,+,0.00)
chunk0116_167_1	chr21	36754651	36754954	+	0	NA	intron (NM_001242785, intron 11 of 11)	intron (NM_001242785, intron 11 of 11)	55669	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.019802	0.394737	
chunk0116_176_1	chr21	36823064	36823581	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	124189	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.015474	0.384170	324(AGGAACAGTCAGTTCA,-,0.00),325(GGAACAGTCAGTTCAA,+,0.00)
chunk0202_131_1	chr9	73221971	73222407	+	0	NA	Intergenic	Intergenic	70458	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.002294	0.347826	
chunk0056_239_1	chr13	89061805	89062193	+	0	NA	Intergenic	L1PA16|LINE|L1	-173292	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.002577	0.498715	
chunk0022_15_1	chr10	7494046	7494768	+	0	NA	Intergenic	Intergenic	-82921	NM_001029880	57713	Hs.407983	NM_001018039	ENSG00000198879	SFMBT2	-	Scm like with four mbt domains 2	protein-coding	0.012465	0.479945	649(GGCACTTTGTGTGCAT,+,0.00)
chunk0129_376_1	chr3	125670173	125670606	+	0	NA	Intergenic	Intergenic	-74852	NM_022776	114885	Hs.477440	NM_022776	ENSG00000144909	OSBPL11	ORP-11|ORP11|OSBP12|TCCCIA00292	oxysterol binding protein like 11	protein-coding	0.000000	0.329493	
chunk0044_30_1	chr12	27303247	27303649	+	0	NA	intron (NM_015000, intron 3 of 13)	intron (NM_015000, intron 3 of 13)	-29406	NM_001248004	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.004975	0.451613	
chunk0018_330_1	chr1	221343183	221344185	+	0	NA	Intergenic	MIRc|SINE|MIR	-7388	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.003992	0.378863	684(GAGCACACTCTGCTCT,-,0.00),685(AGCACACTCTGCTCTC,+,0.00)
chunk0125_253_1	chr3	69090623	69091141	+	0	NA	intron (NM_006407, intron 1 of 2)	intron (NM_006407, intron 1 of 2)	5943	NM_006407	10550	Hs.518060	NM_006407	ENSG00000144746	ARL6IP5	DERP11|GTRAP3-18|HSPC127|JWA|PRAF3|Yip6b|addicsin|hp22|jmx	ADP ribosylation factor like GTPase 6 interacting protein 5	protein-coding	0.017375	0.481696	
chunk0182_239_1	chr7	96800773	96801169	+	0	NA	Intergenic	Intergenic	-91080	NM_006304	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.005051	0.423174	
chunk0048_417_1	chr12	88266853	88268238	+	0	NA	Intergenic	Intergenic	125249	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.003610	0.353535	1055(ATGTACAAAGTGTTCT,-,0.00),1056(TGTACAAAGTGTTCTG,+,0.00),1084(CAGAACAATGAGTACT,-,0.00),1085(AGAACAATGAGTACTG,+,0.00)
chunk0006_237_1	chr1	68931514	68931855	+	0	NA	Intergenic	L2c|LINE|L2	-434463	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.002933	0.394737	
chunk0134_215_1	chr3	178618025	178618613	+	0	NA	intron (NM_001278911, intron 1 of 4)	MIRb|SINE|MIR	59619	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.005102	0.339559	288(CGGCTCACAGTGTGCC,-,0.00)
chunk0028_195_1	chr10	88814638	88814953	+	0	NA	intron (NM_001128215, intron 4 of 8)	intron (NM_001128215, intron 4 of 8)	12065	NM_001128215	340654	Hs.55118	NM_001128215	ENSG00000173239	LIPM	LIPL3|bA304I5.1	lipase family member M	protein-coding	0.009524	0.373418	
chunk0087_342_1	chr18	40259696	40259895	+	0	NA	Intergenic	L1MB7|LINE|L1	193509	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.010050	0.320000	
chunk0039_371_1	chr11	106372158	106372549	+	0	NA	Intergenic	Intergenic	120946	NR_120551	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.005115	0.298469	
chunk0199_189_1	chr9	4712984	4713414	+	0	NA	intron (NM_016282, intron 4 of 4)	intron (NM_016282, intron 4 of 4)	13028	NM_001199856	50808	Hs.732022	NM_016282	ENSG00000147853	AK3	AK3L1|AK6|AKL3L|AKL3L1|FIX	adenylate kinase 3	protein-coding	0.002326	0.359629	
chunk0180_330_1	chr7	72731929	72732128	+	0	NA	intron (NM_001145440, intron 8 of 13)	L1M2|LINE|L1	34125	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.005025	0.315000	
chunk0097_179_1	chr2	50078948	50079353	+	0	NA	intron (NM_001135659, intron 20 of 23)	L1MC4a|LINE|L1	268606	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.009877	0.332512	
chunk0104_289_1	chr2	178407167	178407432	+	0	NA	Intergenic	MER89|LTR|ERV1	-6360	NR_110204	101927027	Hs.715694	NR_110204	ENSG00000223960	CHROMR	CHROME|PRKRA-AS1	cholesterol induced regulator of metabolism RNA	ncRNA	0.015094	0.492481	
chunk0049_224_1	chr12	93428664	93429073	+	0	NA	intron (NM_003348, intron 1 of 3)	intron (NM_003348, intron 1 of 3)	13382	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.012225	0.451220	209(AAGCACAGTCAGTGCT,-,0.00),210(AGCACAGTCAGTGCTG,+,0.00)
chunk0021_111_1	chr10	3287887	3288351	+	0	NA	Intergenic	Intergenic	-30576	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.045259	0.524731	
chunk0023_103_1	chr10	22959156	22959706	+	0	NA	exon (NM_001282746, exon 6 of 17)	exon (NM_001282746, exon 6 of 17)	31407	NM_001282746	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.003636	0.324864	
chunk0154_287_1	chr5	82720858	82721181	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-119136	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.006192	0.444444	
chunk0027_386_1	chr10	79726661	79727001	+	0	NA	intron (NR_120613, intron 6 of 6)	Tigger3c|DNA|TcMar-Tigger	23604	NM_001278495	729262	Hs.742755	NM_001278495	ENSG00000188199	NUTM2B	FAM22B|bA119F19.1	NUT family member 2B	protein-coding	0.002941	0.360704	
chunk0033_150_1	chr11	15503067	15503590	+	0	NA	Intergenic	L2c|LINE|L2	-140557	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.000000	0.408397	
chunk0067_362_1	chr15	48637373	48638024	+	0	NA	intron (NM_000138, intron 2 of 65)	L2c|LINE|L2	8090	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.007680	0.406442	
chunk0131_116_1	chr3	144096812	144097536	+	0	NA	Intergenic	Intergenic	123849	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.004144	0.471724	
chunk0087_220_1	chr18	36112835	36113194	+	0	NA	intron (NM_001099406, intron 6 of 7)	intron (NM_001099406, intron 6 of 7)	16380	NM_012319	25800	Hs.79136	NM_012319	ENSG00000141424	SLC39A6	LIV-1|ZIP6	solute carrier family 39 member 6	protein-coding	0.005571	0.341667	
chunk0133_461_1	chr3	175310090	175310457	+	0	NA	intron (NM_207015, intron 4 of 13)	intron (NM_207015, intron 4 of 13)	-39177	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.002725	0.255435	
chunk0048_167_1	chr12	80827381	80827644	+	0	NA	intron (NM_004664, intron 4 of 5)	intron (NM_004664, intron 4 of 5)	5117	NR_030348	693202		NR_030348	ENSG00000207763	MIR617	MIRN617|hsa-mir-617	microRNA 617	ncRNA	0.003802	0.340909	
chunk0091_77_1	chr19	5046244	5046778	+	0	NA	intron (NM_015015, intron 5 of 22)	intron (NM_015015, intron 5 of 22)	77398	NM_015015	23030	Hs.654816	NM_015015	ENSG00000127663	KDM4B	JMJD2B|TDRD14B	lysine demethylase 4B	protein-coding	0.026217	0.581308	96(CAGCTCAGCCTGTGCC,-,0.00),97(AGCTCAGCCTGTGCCT,+,0.00)
chunk0195_321_1	chr8	98978081	98978280	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	33777	NM_053001	116039	Hs.253247	NM_053001	ENSG00000164920	OSR2	-	odd-skipped related transciption factor 2	protein-coding	0.005025	0.535000	
chunk0048_176_1	chr12	80916364	80917130	+	0	NA	intron (NM_004664, intron 1 of 5)	L2c|LINE|L2	19086	NR_030349	693203		NR_030349	ENSG00000208022	MIR618	MIRN618|hsa-mir-618|mir-618	microRNA 618	ncRNA	0.001305	0.400261	
chunk0191_237_1	chr8	52940316	52940746	+	0	NA	exon (NM_005285, exon 1 of 1)	exon (NM_005285, exon 1 of 1)	623	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.104651	0.696056	
chunk0141_63_1	chr4	77715638	77716100	+	0	NA	3' UTR (NM_001286790, exon 12 of 12)	3' UTR (NM_001286790, exon 12 of 12)	103521	NM_001286790	246175	Hs.592519	NM_144571	ENSG00000138767	CNOT6L	CCR4b	CCR4-NOT transcription complex subunit 6 like	protein-coding	0.004329	0.341253	
chunk0152_282_1	chr5	61446747	61447254	+	0	NA	intron (NM_020928, intron 1 of 13)	LOR1-int|LTR|ERV1	114727	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.003945	0.393701	342(AAGAACATCATGTACT,-,0.00),343(AGAACATCATGTACTA,+,0.00)
chunk0160_381_1	chr5	161308975	161309295	+	0	NA	intron (NM_000813, intron 9 of 9)	L1PA13|LINE|L1	238989	NM_000813	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.006250	0.330218	
chunk0089_109_1	chr18	58544251	58544918	+	0	NA	intron (NM_052947, intron 4 of 12)	intron (NM_052947, intron 4 of 12)	-56036	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.005997	0.411677	
chunk0147_261_1	chr4	183621614	183622260	+	0	NA	Intergenic	L1MC4|LINE|L1	37282	NM_152682	201965	Hs.133337	NM_152682	ENSG00000182552	RWDD4	FAM28A|RWDD4A	RWD domain containing 4	protein-coding	0.006192	0.378671	
chunk0118_396_1	chr22	37807981	37808421	+	0	NA	TTS (NM_005318)	TTS (NM_005318)	296	NM_001171690	23464	Hs.54609	NM_014291	ENSG00000100116	GCAT	KBL	glycine C-acetyltransferase	protein-coding	0.079545	0.614512	
chunk0017_40_1	chr1	205175433	205175925	+	0	NA	intron (NM_199462, intron 2 of 11)	intron (NM_199462, intron 2 of 11)	35920	NM_015375	25778	Hs.6874	NM_015375	ENSG00000133059	DSTYK	CAKUT1|DustyPK|HDCMD38P|RIP5|RIPK5|SPG23	dual serine/threonine and tyrosine protein kinase	protein-coding	0.010163	0.427992	
chunk0146_330_1	chr4	165729214	165729694	+	0	NA	intron (NR_121676, intron 3 of 5)	intron (NR_121676, intron 3 of 5)	13617	NR_121677	101928131	Hs.406479	NR_121677		LOC101928131	-	uncharacterized LOC101928131	ncRNA	0.008333	0.313929	
chunk0149_395_1	chr5	28862114	28862467	+	0	NA	Intergenic	Intergenic	-64580	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.000000	0.395480	
chunk0081_93_1	chr17	39662506	39662835	+	0	NA	intron (NM_001165937, intron 14 of 14)	intron (NM_001165937, intron 14 of 14)	-2676	NM_003673	8557	Hs.77628	NM_003673	ENSG00000173991	TCAP	CMD1N|CMH25|LGMD2G|LGMDR7|T-cap|TELE|telethonin	titin-cap	protein-coding	0.012158	0.654545	129(AGGCCCAGCATGTTCT,-,0.00),130(GGCCCAGCATGTTCTT,+,0.00)
chunk0030_362_1	chr10	118737928	118738128	+	0	NA	intron (NM_153810, intron 1 of 8)	intron (NM_153810, intron 1 of 8)	17218	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.000000	0.383085	
chunk0001_202_1	chr1	7844537	7844747	+	0	NA	3' UTR (NM_001289864, exon 22 of 22)	3' UTR (NM_001289864, exon 22 of 22)	8402	NM_006786	10911	Hs.715862	NM_006786	ENSG00000049247	UTS2	PRO1068|U-II|UCN2|UII	urotensin 2	protein-coding	0.023810	0.412322	
chunk0145_434_1	chr4	153276970	153277379	+	0	NA	TTS (NM_001302692)	TTS (NM_001302692)	19815	NM_001302694	23321	Hs.435711	NM_015271	ENSG00000109654	TRIM2	CMT2R|RNF86	tripartite motif containing 2	protein-coding	0.007335	0.451220	
chunk0136_241_1	chr4	9979234	9979609	+	0	NA	intron (NM_020041, intron 5 of 11)	L2a|LINE|L2	42069	NM_020041	56606	Hs.444612	NM_020041	ENSG00000109667	SLC2A9	GLUT9|GLUTX|UAQTL2|URATv1	solute carrier family 2 member 9	protein-coding	0.016000	0.515957	
chunk0072_381_1	chr15	100283654	100283875	+	0	NA	intron (NM_139057, intron 3 of 21)	intron (NM_139057, intron 3 of 21)	58214	NM_139057	170691	Hs.513200	NM_139057	ENSG00000140470	ADAMTS17	WMS4	ADAM metallopeptidase with thrombospondin type 1 motif 17	protein-coding	0.004525	0.504505	123(AGGGACAGGTTGTTCC,-,0.00),124(GGGACAGGTTGTTCCT,+,0.00)
chunk0203_19_1	chr9	82810952	82811237	+	0	NA	Intergenic	MER41A|LTR|ERV1	252034	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.003509	0.465035	
chunk0043_139_1	chr12	16042621	16042939	+	0	NA	Intergenic	Intergenic	131608	NM_001300779	51071	Hs.39429	NM_015954	ENSG00000023697	DERA	CGI-26|DEOC	deoxyribose-phosphate aldolase	protein-coding	0.003145	0.369906	
chunk0080_396_1	chr17	35087278	35088210	+	0	NA	intron (NR_037713, intron 1 of 6)	intron (NR_037713, intron 1 of 6)	1585	NR_037713	117584	Hs.13680	NM_057178	ENSG00000092871	RFFL	CARP-2|CARP2|FRING|RIFIFYLIN|RNF189|RNF34L	ring finger and FYVE like domain containing E3 ubiquitin protein ligase	protein-coding	0.013948	0.406217	
chunk0119_65_1	chr22	41044991	41045439	+	0	NA	Intergenic	L1ME4b|LINE|L1	28506	NR_132979	106635682		NR_132979		SNORD140	-	small nucleolar RNA, C/D box 140	snoRNA	0.017857	0.363029	
chunk0133_111_1	chr3	168091282	168091911	+	0	NA	intron (NM_001308155, intron 1 of 14)	intron (NM_001308155, intron 1 of 14)	4329	NM_014498	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.004769	0.353968	
chunk0068_83_1	chr15	52006620	52006975	+	0	NA	Intergenic	Intergenic	-12417	NM_002748	5597	Hs.411847	NM_002748	ENSG00000069956	MAPK6	ERK3|HsT17250|PRKM6|p97MAPK	mitogen-activated protein kinase 6	protein-coding	0.002817	0.404494	247(AGGTACAGACAGTCCC,-,0.00),248(GGTACAGACAGTCCCT,+,0.00)
chunk0008_449_1	chr1	99685560	99685897	+	0	NA	intron (NM_017734, intron 3 of 7)	MamRTE1|LINE|RTE-BovB	27225	NR_031666	100302152		NR_031666	ENSG00000221669	MIR548N	MIRN548N|hsa-mir-548n	microRNA 548n	ncRNA	0.011869	0.500000	
chunk0175_338_1	chr6	167275029	167275248	+	0	NA	Intergenic	Intergenic	-16177	NM_018974	54346	Hs.567508	NM_018974	ENSG00000112494	UNC93A	Unc-93A|dJ366N23.1|dJ366N23.2	unc-93 homolog A	protein-coding	0.013699	0.550000	
chunk0026_246_1	chr10	66376476	66377114	+	0	NA	intron (NM_001127384, intron 12 of 17)	intron (NM_001127384, intron 12 of 17)	-549239	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.004702	0.314554	
chunk0117_185_1	chr22	21108571	21109024	+	0	NA	intron (NR_037566, intron 1 of 5)	L1ME2|LINE|L1	5781	NR_037566	400892	Hs.745077	NM_207474		BCRP2	BCR-2|BCR2|BCRL2	BCR pseudogene 2	pseudo	0.006623	0.310573	
chunk0005_96_1	chr1	56437844	56438280	+	0	NA	Intergenic	Intergenic	141522	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.004587	0.441648	
chunk0058_447_1	chr13	113816836	113817187	+	0	NA	intron (NR_044995, intron 1 of 4)	intron (NR_044995, intron 1 of 4)	1401	NR_044995	650669	Hs.369201	NM_001039799		GAS6-AS1	-	GAS6 antisense RNA 1	ncRNA	0.034188	0.559659	
chunk0121_150_1	chr3	19072869	19073385	+	0	NA	Intergenic	L1MC2|LINE|L1	-75398	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.001938	0.336557	
chunk0023_116_1	chr10	23304484	23304762	+	0	NA	Intergenic	L1M3a|LINE|L1	40220	NM_153714	256815	Hs.132442	NM_153714	ENSG00000179133	C10orf67	C10orf115|LINC01552	chromosome 10 open reading frame 67	protein-coding	0.007194	0.573477	
chunk0010_333_1	chr1	118332411	118333066	+	0	NA	Intergenic	L2c|LINE|L2	-147513	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.006107	0.378049	339(GGGACTATTTGTTCCC,+,0.00)
chunk0124_438_1	chr3	61320748	61320991	+	0	NA	Intergenic	Intergenic	-69410	NM_001166243	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.004115	0.290984	
chunk0173_200_1	chr6	145266988	145267872	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-467439	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.006787	0.427119	
chunk0013_266_1	chr1	170113737	170114205	+	0	NA	Intergenic	Intergenic	-32076	NM_001136107	149281	Hs.553612	NM_001136107	ENSG00000203740	METTL11B	C1orf184|HOMT1B|NTM1B	methyltransferase like 11B	protein-coding	0.006410	0.351812	197(GACACAGTGTGTACCC,+,0.00)
chunk0159_281_1	chr5	142590874	142591370	+	0	NA	Intergenic	Intergenic	23039	NM_033137	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.012097	0.436620	225(GGTAACAGGATGTCCT,-,0.00),226(GTAACAGGATGTCCTC,+,0.00)
chunk0013_277_1	chr1	170531797	170532196	+	0	NA	promoter-TSS (NM_001146039)	promoter-TSS (NM_001146039)	-126	NM_152281	92344	Hs.183702	NM_152281	ENSG00000120370	GORAB	GO|NTKLBP1|SCYL1BP1	golgin, RAB6 interacting	protein-coding	0.047619	0.577500	
chunk0045_120_1	chr12	46264573	46264909	+	0	NA	intron (NM_001278387, intron 1 of 17)	L1PB3|LINE|L1	1754	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.002976	0.353116	148(TAGTACACATTGTACC,-,0.00),149(AGTACACATTGTACCC,+,0.00)
chunk0040_428_1	chr11	121357882	121358309	+	0	NA	Intergenic	Intergenic	65227	NM_001024956	6309	Hs.287749	NM_006918	ENSG00000109929	SC5D	ERG3|S5DES|SC5DL	sterol-C5-desaturase	protein-coding	0.014052	0.429907	
chunk0162_324_1	chr6	6758815	6759352	+	0	NA	Intergenic	Intergenic	-136257	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.024209	0.542751	
chunk0063_228_1	chr14	81610658	81611502	+	0	NA	intron (NR_110074, intron 1 of 2)	intron (NR_110074, intron 1 of 2)	11981	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.003555	0.362130	
chunk0103_136_1	chr2	162083891	162085068	+	0	NA	Intergenic	MER34D|LTR|ERV1	-9937	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.001699	0.391341	
chunk0119_445_1	chr22	50141732	50142378	+	0	NA	intron (NM_001164105, intron 15 of 25)	intron (NM_001164105, intron 15 of 25)	-5000	NM_001164106	54456	Hs.62880	NM_018995	ENSG00000073146	MOV10L1	CHAMP|DJ402G11.8	Mov10 like RISC complex RNA helicase 1	protein-coding	0.017028	0.429675	
chunk0004_418_1	chr1	52448899	52449364	+	0	NA	intron (NM_001009881, intron 20 of 29)	(TC)n|Simple_repeat|Simple_repeat	44584	NM_032864	84950	Hs.5301	NM_032284	ENSG00000134748	PRPF38A	PRP38A|Prp38	pre-mRNA processing factor 38A	protein-coding	0.008602	0.394850	
chunk0084_392_1	chr17	82110176	82110622	+	0	NA	intron (NM_198082, intron 16 of 16)	intron (NM_198082, intron 16 of 16)	-12169	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.011211	0.442953	
chunk0058_22_1	chr14	19881161	19881499	+	0	NA	Intergenic	Intergenic	5062	NM_001005501	390431	Hs.551345	NM_001005501	ENSG00000165762	OR4K2	OR14-15	olfactory receptor family 4 subfamily K member 2	protein-coding	0.008876	0.342183	
chunk0040_354_1	chr11	118765230	118765454	+	0	NA	exon (NM_004397, exon 6 of 14)	exon (NM_004397, exon 6 of 14)	25606	NM_001257191	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.004464	0.400000	
chunk0148_446_1	chr4	189970626	189971128	+	0	NA	Intergenic	Intergenic	30058	NM_004477	2483	Hs.203772	NM_004477	ENSG00000109536	FRG1	FRG1A|FSG1	FSHD region gene 1	protein-coding	0.013944	0.479125	291(AGGCACAGTGTGCTCC,-,0.00),292(GGCACAGTGTGCTCCT,+,0.00)
chunk0202_318_1	chr9	78258365	78258600	+	0	NA	intron (NM_032171, intron 11 of 14)	HAL1ME|LINE|L1	22407	NM_001098802	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.000000	0.330508	
chunk0063_309_1	chr14	84875343	84875742	+	0	NA	Intergenic	Intergenic	-518337	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005013	0.347500	
chunk0079_382_1	chr17	18314913	18315244	+	0	NA	promoter-TSS (NM_004618)	promoter-TSS (NM_004618)	-71	NM_004618	7156	Hs.592115	NM_004618	ENSG00000177302	TOP3A	MGRISCE2|PEOB5|TOP3|ZGRF7	DNA topoisomerase III alpha	protein-coding	0.078550	0.629518	
chunk0076_128_1	chr16	66695839	66696308	+	0	NA	intron (NM_181521, intron 1 of 3)	CpG	634	NM_181521	146223	Hs.643961	NM_178818	ENSG00000183723	CMTM4	CKLFSF4	CKLF like MARVEL transmembrane domain containing 4	protein-coding	0.074627	0.680851	
chunk0070_324_1	chr15	75493695	75494304	+	0	NA	intron (NM_002833, intron 7 of 12)	MER58A|DNA|hAT-Charlie	-38216	NM_001145357	25942	Hs.513039	NM_015477	ENSG00000169375	SIN3A	WITKOS	SIN3 transcription regulator family member A	protein-coding	0.013136	0.329508	
chunk0139_104_1	chr4	51877007	51877449	+	0	NA	intron (NM_001287755, intron 4 of 10)	intron (NM_001287755, intron 4 of 10)	33649	NM_001287755	23142	Hs.605388	NM_015115	ENSG00000109184	DCUN1D4	-	defective in cullin neddylation 1 domain containing 4	protein-coding	0.006787	0.401806	
chunk0158_403_1	chr5	134731517	134731952	+	0	NA	Intergenic	Intergenic	-6746	NM_001745	819	Hs.529846	NM_001745	ENSG00000164615	CAMLG	CAML|GET2	calcium modulating ligand	protein-coding	0.006897	0.332569	
chunk0034_377_1	chr11	36317857	36318610	+	0	NA	intron (NM_001160167, intron 1 of 8)	Tigger3a|DNA|TcMar-Tigger	22058	NM_001160167	79899	Hs.19987	NM_024841	ENSG00000135362	PRR5L	PROTOR2	proline rich 5 like	protein-coding	0.007968	0.350133	
chunk0158_177_1	chr5	127754163	127755049	+	0	NA	Intergenic	Intergenic	101591	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.005643	0.394589	
chunk0042_400_1	chr12	11182865	11183445	+	0	NA	Intergenic	Intergenic	3782	NM_181429	353164	Hs.553716	NM_181429	ENSG00000186136	TAS2R42	T2R24|T2R42|T2R55|TAS2R55	taste 2 receptor member 42	protein-coding	0.000000	0.414802	
chunk0166_100_1	chr6	43813115	43813616	+	0	NA	Intergenic	L2b|LINE|L2	41380	NM_001287044	7422	Hs.73793	NM_003376	ENSG00000112715	VEGFA	MVCD1|VEGF|VPF	vascular endothelial growth factor A	protein-coding	0.011976	0.482072	230(AGGGACAGTGTGTACA,-,0.00),231(GGGACAGTGTGTACAA,+,0.00)
chunk0091_399_1	chr19	16400349	16400603	+	0	NA	TTS (NM_001258376)	TTS (NM_001258376)	71536	NM_021235	58513	Hs.654639	NM_021235	ENSG00000127527	EPS15L1	EPS15R	epidermal growth factor receptor pathway substrate 15 like 1	protein-coding	0.011811	0.411765	
chunk0175_461_1	chr6	170480333	170480713	+	0	NA	Intergenic	Intergenic	72806	NM_002793	5689	Hs.352768	NM_002793	ENSG00000008018	PSMB1	HC5|PMSB1|PSC5	proteasome subunit beta 1	protein-coding	0.007895	0.503937	
chunk0108_179_1	chr2	232182955	232183734	+	0	NA	intron (NR_046476, intron 9 of 20)	L1MB7|LINE|L1	10691	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.006418	0.401282	
chunk0070_458_1	chr15	78541064	78541480	+	0	NA	intron (NM_002789, intron 1 of 8)	intron (NM_002789, intron 1 of 8)	867	NM_002789	5685	Hs.251531	NM_002789	ENSG00000041357	PSMA4	HC9|HsT17706|PSC9	proteasome subunit alpha 4	protein-coding	0.014423	0.455635	
chunk0021_338_1	chr1	245986525	245987241	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	430529	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.016760	0.407252	140(AAGAACAGGAAGTCTC,-,0.00)
chunk0115_453_1	chr21	32539579	32539812	+	0	NA	Intergenic	Intergenic	45840	NM_144659	140290	Hs.728804	NM_018277	ENSG00000242220	TCP10L	C21orf77|PRED77|TCP10A-1|TCP10A-2	t-complex 10 like	protein-coding	0.008584	0.538462	
chunk0185_411_1	chr7	134261370	134262108	+	0	NA	intron (NM_144648, intron 19 of 19)	MER58A|DNA|hAT-Charlie	55336	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.004065	0.366712	
chunk0124_361_1	chr3	58778177	58778558	+	0	NA	intron (NM_198463, intron 14 of 15)	L1MA4A|LINE|L1	-46104	NR_110820	101929238	Hs.683953	NR_110820	ENSG00000242428	C3orf67-AS1	-	C3orf67 antisense RNA 1	ncRNA	0.010499	0.562827	
chunk0075_150_1	chr16	50931243	50931630	+	0	NA	intron (NR_039672, intron 2 of 6)	intron (NR_039672, intron 2 of 6)	52663	NR_039672	100616347		NR_039672	ENSG00000265226	MIR548AI	-	microRNA 548ai	ncRNA	0.002584	0.363402	
chunk0158_105_1	chr5	126801421	126802022	+	0	NA	intron (NM_005573, intron 1 of 10)	intron (NM_005573, intron 1 of 10)	24568	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.001664	0.355482	
chunk0178_71_1	chr7	30319554	30320117	+	0	NA	intron (NM_147128, intron 1 of 4)	intron (NM_147128, intron 1 of 4)	-29945	NR_037513	100500883		NR_037513	ENSG00000283237	MIR550B1	-	microRNA 550b-1	ncRNA	0.005329	0.359929	
chunk0007_33_1	chr1	77655414	77655668	+	0	NA	intron (NM_001308237, intron 1 of 13)	MLT1A0|LTR|ERVL-MaLR	27117	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.003937	0.427451	
chunk0196_329_1	chr8	112074192	112074441	+	0	NA	Intergenic	L1M2|LINE|L1	-569177	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.008032	0.532000	
chunk0084_156_1	chr17	76901619	76901916	+	0	NA	intron (NM_198955, intron 2 of 15)	intron (NM_198955, intron 2 of 15)	29120	NM_198955	146664	Hs.144531	NM_144677	ENSG00000167889	MGAT5B	GnT-IX|GnT-VB	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B	protein-coding	0.013468	0.526846	
chunk0088_236_1	chr18	48494004	48494269	+	0	NA	Intergenic	Intergenic	-44920	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.000000	0.432331	
chunk0196_208_1	chr8	106617696	106618072	+	0	NA	intron (NM_001198532, intron 2 of 15)	intron (NM_001198532, intron 2 of 15)	-39924	NM_181354	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.015957	0.429708	
chunk0115_155_1	chr21	23977303	23977755	+	0	NA	Intergenic	Intergenic	343848	NR_109963	101927869	Hs.555591	NR_109963	ENSG00000224832	LINC01689	-	long intergenic non-protein coding RNA 1689	ncRNA	0.004425	0.353201	
chunk0057_114_1	chr13	99224184	99224521	+	0	NA	intron (NR_026644, intron 1 of 8)	MLT1B|LTR|ERVL-MaLR	23443	NR_026644	337867	Hs.508545	NM_177967	ENSG00000134882	UBAC2	PHGDHL1	UBA domain containing 2	protein-coding	0.008902	0.396450	
chunk0096_312_1	chr2	33144093	33144428	+	0	NA	intron (NM_000627, intron 1 of 29)	intron (NM_000627, intron 1 of 29)	9663	NM_001166266	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.011940	0.458333	
chunk0018_4_1	chr1	214846163	214846493	+	0	NA	Intergenic	Intergenic	-159214	NM_001017424	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.015152	0.422961	
chunk0035_310_1	chr11	47242659	47242951	+	0	NA	exon (NM_001302492, exon 9 of 10)	exon (NM_001302492, exon 9 of 10)	-5495	NM_001251934	10062	Hs.438863	NM_005693	ENSG00000025434	NR1H3	LXR-a|LXRA|RLD-1	nuclear receptor subfamily 1 group H member 3	protein-coding	0.037671	0.621160	
chunk0069_410_1	chr15	67944027	67944284	+	0	NA	Intergenic	Intergenic	-104110	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.027237	0.596899	
chunk0168_74_1	chr6	79645757	79646097	+	0	NA	intron (NM_031469, intron 1 of 3)	intron (NM_031469, intron 1 of 3)	14644	NM_031469	83699	Hs.302772	NM_031469	ENSG00000198478	SH3BGRL2	-	SH3 domain binding glutamate rich protein like 2	protein-coding	0.002941	0.384164	
chunk0135_249_1	chr3	188881286	188881485	+	0	NA	3' UTR (NM_005578, exon 11 of 11)	3' UTR (NM_005578, exon 11 of 11)	66254	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.000000	0.385000	
chunk0058_48_1	chr14	20343359	20343758	+	0	NA	promoter-TSS (NR_002312)	promoter-TSS (NR_002312)	-56	NM_001042618	10038	Hs.409412	NM_005484	ENSG00000129484	PARP2	ADPRT2|ADPRTL2|ADPRTL3|ARTD2|PARP-2|pADPRT-2	poly(ADP-ribose) polymerase 2	protein-coding	0.085213	0.595000	
chunk0083_279_1	chr17	68614754	68615216	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-13169	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.008658	0.388769	
chunk0081_255_1	chr17	43336908	43337425	+	0	NA	Intergenic	HERVK13-int|LTR|ERVK	-36935	NR_002716	6066		NR_002716	ENSG00000274585	RNU2-1	RNU2|U2	RNA, U2 small nuclear 1	snRNA	0.009671	0.382239	
chunk0092_261_1	chr19	33081016	33081350	+	0	NA	5' UTR (NM_018025, exon 1 of 20)	5' UTR (NM_018025, exon 1 of 20)	303	NM_018025	55094	Hs.466436	NM_018025	ENSG00000076650	GPATCH1	ECGP|GPATC1	G-patch domain containing 1	protein-coding	0.086826	0.677612	
chunk0180_4_1	chr7	52977678	52978141	+	0	NA	Intergenic	Intergenic	-57747	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.004320	0.327586	
chunk0013_205_1	chr1	169426021	169426700	+	0	NA	intron (NM_001300968, intron 2 of 6)	intron (NM_001300968, intron 2 of 6)	1114	NM_021179	57821	Hs.567557	NM_021179	ENSG00000117477	CCDC181	C1orf114	coiled-coil domain containing 181	protein-coding	0.010309	0.344118	
chunk0126_343_1	chr3	82477553	82477790	+	0	NA	Intergenic	Intergenic	-715872	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.012658	0.420168	
chunk0061_357_1	chr14	63726640	63727411	+	0	NA	intron (NM_030791, intron 1 of 2)	intron (NM_030791, intron 1 of 2)	1070	NM_030791	81537	Hs.24678	NM_030791	ENSG00000126821	SGPP1	SPP-1|SPPase1	sphingosine-1-phosphate phosphatase 1	protein-coding	0.028534	0.432642	564(GAGAACTCCGAGTTCT,-,0.00),565(AGAACTCCGAGTTCTT,+,0.00),688(GAGGGCATGCTGTACT,-,0.00),689(AGGGCATGCTGTACTC,+,0.00)
chunk0093_120_1	chr19	44741927	44742296	+	0	NA	Intergenic	Intergenic	-6610	NM_005178	602	Hs.31210	NM_005178	ENSG00000069399	BCL3	BCL4|D19S37	BCL3 transcription coactivator	protein-coding	0.027100	0.627027	
chunk0015_67_1	chr1	184705166	184706005	+	0	NA	intron (NM_025191, intron 18 of 19)	intron (NM_025191, intron 18 of 19)	49322	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.003576	0.332143	
chunk0119_143_1	chr22	42978223	42978731	+	0	NA	intron (NM_001184970, intron 1 of 10)	MIRb|SINE|MIR	-18596	NM_001184971	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.015748	0.465619	
chunk0153_193_1	chr5	71703018	71703450	+	0	NA	Intergenic	Intergenic	-15929	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.016204	0.547344	243(TGGACGCTCTGTGCCT,+,0.00)
chunk0026_86_1	chr10	61454587	61454885	+	0	NA	intron (NR_120643, intron 1 of 5)	L4_A_Mam|LINE|RTE-X	-1286	NM_178505	219623	Hs.623955	NM_178505	ENSG00000196932	TMEM26	-	transmembrane protein 26	protein-coding	0.010067	0.464883	
chunk0079_440_1	chr17	20178157	20178457	+	0	NA	intron (NM_001033554, intron 1 of 5)	intron (NM_001033554, intron 1 of 5)	22313	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.010000	0.445183	
chunk0110_236_1	chr20	16293688	16293960	+	0	NA	intron (NM_001199865, intron 24 of 24)	HAL1|LINE|L1	279610	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.007353	0.501832	
chunk0010_76_1	chr1	113255161	113255605	+	0	NA	Intergenic	Intergenic	-49130	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.013514	0.435955	
chunk0212_144_1	chrX	131820641	131820899	+	0	NA	intron (NR_026975, intron 2 of 12)	L2a|LINE|L2	9873	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.003876	0.316602	
chunk0113_363_1	chr20	59097717	59098389	+	0	NA	Intergenic	Intergenic	-55207	NM_001256403	51012	Hs.656865	NM_016045	ENSG00000101166	PRELID3B	C20orf45|SLMO2|dJ543J19.5	PRELI domain containing 3B	protein-coding	0.007440	0.375929	
chunk0131_405_1	chr3	152880592	152881290	+	0	NA	Intergenic	Intergenic	46248	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.001433	0.343348	473(AGAACAGTGTCTACCT,+,0.00)
chunk0133_274_1	chr3	172012816	172013213	+	0	NA	Intergenic	Intergenic	-26614	NM_022763	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.000000	0.379397	
chunk0032_378_1	chr11	11251463	11251879	+	0	NA	Intergenic	L2a|LINE|L2	101686	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.004808	0.470024	
chunk0059_89_1	chr14	30842402	30842842	+	0	NA	Intergenic	Intergenic	-31913	NM_004086	1690	Hs.21016	NM_004086	ENSG00000100473	COCH	COCH-5B2|COCH5B2|DFNA9|DFNB110	cochlin	protein-coding	0.000000	0.340136	
chunk0210_29_1	chrX	67633093	67633614	+	0	NA	intron (NM_001011645, intron 1 of 7)	L1PA15|LINE|L1	64512	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.001919	0.363985	
chunk0013_84_1	chr1	167663240	167663439	+	0	NA	intron (NM_052862, intron 1 of 6)	intron (NM_052862, intron 1 of 6)	33102	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.010050	0.595000	
chunk0114_232_1	chr21	15959449	15960057	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-110769	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.008224	0.338259	226(CAGAACATTCAGTTCT,-,0.00),227(AGAACATTCAGTTCTG,+,0.00)
chunk0155_102_1	chr5	92514614	92515234	+	0	NA	Intergenic	LTR23|LTR|ERV1	1056419	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.334944	
chunk0140_169_1	chr4	69718810	69719376	+	0	NA	Intergenic	Intergenic	41619	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.003534	0.350970	
chunk0025_198_1	chr10	53372974	53373239	+	0	NA	Intergenic	L1PA6|LINE|L1	-601406	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.357143	
chunk0077_180_1	chr16	79664425	79664787	+	0	NA	Intergenic	Intergenic	-63881	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.002762	0.468320	225(TAGGACACTCTGTTAC,-,0.00),226(AGGACACTCTGTTACT,+,0.00)
chunk0004_162_1	chr1	45551191	45551436	+	0	NA	intron (NM_001202413, intron 2 of 9)	MIRb|SINE|MIR	530	NM_001202414	10327	Hs.474584	NM_006066	ENSG00000117448	AKR1A1	ALDR1|ALR|ARM|DD3|HEL-S-6	aldo-keto reductase family 1 member A1	protein-coding	0.024490	0.463415	
chunk0179_170_1	chr7	46886666	46886982	+	0	NA	Intergenic	Intergenic	695320	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.012658	0.482650	
chunk0086_422_1	chr18	27057228	27057969	+	0	NA	intron (NM_031422, intron 2 of 5)	intron (NM_031422, intron 2 of 5)	127740	NM_001256316	83539	Hs.44584	NM_031422	ENSG00000154080	CHST9	GALNAC4ST-2|GalNAc4ST2	carbohydrate sulfotransferase 9	protein-coding	0.013495	0.433962	373(GAGCACAGCGAGTACT,-,0.00),374(AGCACAGCGAGTACTG,+,0.00)
chunk0031_18_1	chr10	121835126	121835802	+	0	NA	intron (NM_001001976, intron 10 of 11)	L1MC5|LINE|L1	92599	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.004438	0.360414	
chunk0157_29_1	chr5	115588831	115589170	+	0	NA	intron (NM_001164469, intron 3 of 3)	LTR67B|LTR|ERVL	-13155	NR_109875	101927100	Hs.745340	NR_109874		LOC101927100	-	uncharacterized LOC101927100	ncRNA	0.002950	0.400000	
chunk0053_252_1	chr13	32984624	32985336	+	0	NA	Intergenic	L2b|LINE|L2	-31453	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.009831	0.416550	
chunk0134_263_1	chr3	179463095	179463298	+	0	NA	Intergenic	Intergenic	-11613	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.019704	0.431373	
chunk0026_307_1	chr10	68018276	68018681	+	0	NA	intron (NM_022079, intron 8 of 25)	L1M5|LINE|L1	-7595	NR_131184	100009667		NR_131184		POU5F1P5	Oct4-pg5	POU class 5 homeobox 1 pseudogene 5	pseudo	0.004938	0.266010	
chunk0203_441_1	chr9	91341457	91341895	+	0	NA	intron (NM_001698, intron 3 of 9)	L2a|LINE|L2	20248	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.009132	0.403189	
chunk0127_31_1	chr3	88617707	88618140	+	0	NA	Intergenic	Intergenic	-468057	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.002309	0.364055	232(TAGGACAAAATGTGCC,-,0.00),233(AGGACAAAATGTGCCT,+,0.00)
chunk0099_262_1	chr2	98056557	98057187	+	0	NA	Intergenic	Intergenic	-30260	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.017460	0.450079	
chunk0067_431_1	chr15	49946709	49947106	+	0	NA	intron (NR_073596, intron 15 of 27)	MER54B|LTR|ERVL	166409	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.007557	0.472362	
chunk0208_40_1	chrX	11382993	11383371	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	44603	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.010582	0.379947	
chunk0143_321_1	chr4	119676028	119676401	+	0	NA	Intergenic	Intergenic	-47388	NM_001083	8654	Hs.647971	NM_001083	ENSG00000138735	PDE5A	CGB-PDE|CN5A|PDE5	phosphodiesterase 5A	protein-coding	0.008043	0.350267	
chunk0080_152_1	chr17	27975385	27975677	+	0	NA	Intergenic	Intergenic	-67131	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.010274	0.508532	
chunk0186_419_1	chr7	146557662	146557896	+	0	NA	intron (NM_014141, intron 1 of 23)	LTR82B|LTR|ERVL	441418	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.000000	0.340426	
chunk0002_417_1	chr1	27631225	27631493	+	0	NA	intron (NM_005248, intron 1 of 12)	intron (NM_005248, intron 1 of 12)	3857	NM_005248	2268	Hs.1422	NM_005248	ENSG00000000938	FGR	SRC2|c-fgr|c-src2|p55-Fgr|p55c-fgr|p58-Fgr|p58c-fgr	FGR proto-oncogene, Src family tyrosine kinase	protein-coding	0.014925	0.535316	191(AGACACAGGATGTCCT,-,0.00),192(GACACAGGATGTCCTG,+,0.00)
chunk0021_274_1	chr1	244176171	244176781	+	0	NA	Intergenic	Intergenic	123271	NM_006352	10472	Hs.69997	NM_006352	ENSG00000179456	ZBTB18	C2H2-171|MRD22|RP58|TAZ-1|ZNF238	zinc finger and BTB domain containing 18	protein-coding	0.013115	0.392799	
chunk0166_149_1	chr6	45095903	45096107	+	0	NA	intron (NM_181356, intron 5 of 12)	intron (NM_181356, intron 5 of 12)	101765	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.009804	0.312195	123(AGGGACGCTATGTTCC,-,0.00),124(GGGACGCTATGTTCCA,+,0.00)
chunk0046_152_1	chr12	58202822	58203445	+	0	NA	Intergenic	MIRc|SINE|MIR	261471	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.006421	0.384615	
chunk0162_452_1	chr5	180825906	180826413	+	0	NA	Intergenic	L2a|LINE|L2	-4798	NR_027183	729678	Hs.348292	NR_027183	ENSG00000245060	LINC00847	-	long intergenic non-protein coding RNA 847	ncRNA	0.003945	0.470472	
chunk0202_312_1	chr9	78167418	78167617	+	0	NA	Intergenic	Intergenic	-68558	NM_032171	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.010050	0.460000	
chunk0023_405_1	chr10	31076971	31077374	+	0	NA	Intergenic	Intergenic	-45235	NR_026560	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.002481	0.358911	
chunk0154_427_1	chr5	89238152	89238384	+	0	NA	Intergenic	Intergenic	-334163	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.012931	0.330472	
chunk0203_304_1	chr9	89328101	89328377	+	0	NA	intron (NM_001282690, intron 4 of 16)	Tigger3b|DNA|TcMar-Tigger	9388	NM_001282690	79048	Hs.59804	NM_024077	ENSG00000187742	SECISBP2	SBP2	SECIS binding protein 2	protein-coding	0.018116	0.342960	
chunk0063_222_1	chr14	81537395	81537824	+	0	NA	Intergenic	Intergenic	-3748	NM_001244984	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.004662	0.367442	
chunk0073_310_1	chr16	14172995	14173194	+	0	NA	intron (NM_001308142, intron 3 of 16)	intron (NM_001308142, intron 3 of 16)	101780	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.005025	0.355000	
chunk0040_422_1	chr11	121268684	121269429	+	0	NA	Intergenic	Intergenic	-23623	NM_006918	6309	Hs.287749	NM_006918	ENSG00000109929	SC5D	ERG3|S5DES|SC5DL	sterol-C5-desaturase	protein-coding	0.005369	0.388740	
chunk0104_429_1	chr2	181002953	181003261	+	0	NA	intron (NM_001278554, intron 3 of 5)	intron (NM_001278554, intron 3 of 5)	21983	NM_001278554	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.003247	0.336570	
chunk0171_356_1	chr6	130583768	130584120	+	0	NA	Intergenic	Intergenic	146827	NM_052913	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.005682	0.334278	
chunk0132_180_1	chr3	157052826	157053073	+	0	NA	Intergenic	Charlie2b|DNA|hAT-Charlie	-36932	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.000000	0.241935	
chunk0083_360_1	chr17	70617550	70618091	+	0	NA	Intergenic	Intergenic	448285	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.011091	0.466790	
chunk0021_332_1	chr1	245706362	245706776	+	0	NA	Intergenic	Intergenic	551584	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.014493	0.445783	
chunk0105_391_1	chr2	192457634	192457833	+	0	NA	Intergenic	Intergenic	-262800	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.005025	0.275000	
chunk0176_119_1	chr7	12007578	12008256	+	0	NA	Intergenic	Intergenic	-175719	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.004425	0.340206	
chunk0109_35_1	chr20	571260	571584	+	0	NA	Intergenic	Charlie4a|DNA|hAT-Charlie	-27584	NM_001895	1457	Hs.644056	NM_001895	ENSG00000101266	CSNK2A1	CK2A1|CKII|Cka1|Cka2|OCNDS	casein kinase 2 alpha 1	protein-coding	0.003086	0.356923	
chunk0173_249_1	chr6	146980553	146981114	+	0	NA	intron (NR_034115, intron 6 of 10)	intron (NR_034115, intron 6 of 10)	-177009	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.001783	0.377224	
chunk0070_452_1	chr15	78455924	78456309	+	0	NA	intron (NM_004136, intron 2 of 21)	MLT1F|LTR|ERVL-MaLR	17940	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.005195	0.414508	
chunk0090_271_1	chr18	74616941	74617183	+	0	NA	Intergenic	Intergenic	-13901	NM_001146189	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.020661	0.489712	
chunk0052_169_1	chr13	24127180	24127426	+	0	NA	intron (NM_001286792, intron 3 of 14)	LTR33|LTR|ERVL	-33413	NM_001166271	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.004065	0.578947	
chunk0207_330_1	chr9	134299985	134300192	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-26375	NM_002957	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.009662	0.557692	
chunk0063_340_1	chr14	85360625	85360837	+	0	NA	Intergenic	MIRb|SINE|MIR	-33148	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.305164	
chunk0206_261_1	chr9	123923311	123923929	+	0	NA	intron (NM_024820, intron 1 of 20)	intron (NM_024820, intron 1 of 20)	6518	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.008091	0.418417	
chunk0028_2_1	chr10	81925766	81926031	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	48211	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.003774	0.409774	
chunk0012_77_1	chr1	155815728	155816229	+	0	NA	intron (NM_001282858, intron 7 of 31)	intron (NM_001282858, intron 7 of 31)	-32146	NR_132767	106633816		NR_132767		SCARNA26B	-	small Cajal body-specific RNA 26B	ncRNA	0.007984	0.344622	
chunk0079_388_1	chr17	18921850	18922119	+	0	NA	intron (NM_001243936, intron 7 of 9)	L1MB5|LINE|L1	-28692	NM_001282417	125206	Hs.462418	NM_152351	ENSG00000154025	SLC5A10	SGLT-5|SGLT5	solute carrier family 5 member 10	protein-coding	0.007435	0.396296	99(AAGAACACCCTGCACC,-,0.00),100(AGAACACCCTGCACCC,+,0.00)
chunk0178_335_1	chr7	38316881	38317103	+	0	NA	Intergenic	Intergenic	-24585	NR_040085	100506776	Hs.173034	NR_040085	ENSG00000281103	TRG-AS1	TCRGV	T cell receptor gamma locus antisense RNA 1	ncRNA	0.009009	0.408072	
chunk0076_122_1	chr16	66651985	66652357	+	0	NA	intron (NM_181521, intron 1 of 3)	intron (NM_181521, intron 1 of 3)	44536	NM_181521	146223	Hs.643961	NM_178818	ENSG00000183723	CMTM4	CKLFSF4	CKLF like MARVEL transmembrane domain containing 4	protein-coding	0.016129	0.530831	
chunk0086_288_1	chr18	23743419	23743618	+	0	NA	intron (NR_130106, intron 2 of 12)	intron (NR_130106, intron 2 of 12)	54075	NR_130106	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.000000	0.445000	106(GAGGACAGGCTGTACC,-,0.00),107(AGGACAGGCTGTACCA,+,0.00)
chunk0030_368_1	chr10	119025211	119025569	+	0	NA	Intergenic	Intergenic	-4326	NM_199461	340719	Hs.591918	NM_199461	ENSG00000188613	NANOS1	EC_Rep1a|NOS-1|NOS1|SPGF12|ZC2HC12A	nanos C2HC-type zinc finger 1	protein-coding	0.016760	0.607242	
chunk0169_451_1	chr6	108782472	108783075	+	0	NA	Intergenic	Intergenic	31119	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.018242	0.443709	
chunk0135_351_1	chr3	190448923	190449207	+	0	NA	intron (NM_207316, intron 1 of 4)	intron (NM_207316, intron 1 of 4)	811	NM_207316	131920	Hs.335321	NM_207316	ENSG00000198398	TMEM207	UNQ846	transmembrane protein 207	protein-coding	0.007042	0.329825	
chunk0008_400_1	chr1	97525538	97525911	+	0	NA	intron (NM_000110, intron 12 of 22)	intron (NM_000110, intron 12 of 22)	-271197	NR_046591	100873933	Hs.568669	NR_046591	ENSG00000235777	DPYD-AS2	-	DPYD antisense RNA 2	ncRNA	0.016086	0.425134	
chunk0012_399_1	chr1	163744141	163744534	+	0	NA	Intergenic	L1MA2|LINE|L1	-321146	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.002545	0.406091	
chunk0069_160_1	chr15	62545364	62546136	+	0	NA	Intergenic	Intergenic	99431	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.002591	0.457956	
chunk0188_290_1	chr8	15656883	15657312	+	0	NA	intron (NM_006765, intron 3 of 10)	MLT1A1-int|LTR|ERVL-MaLR	117010	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.002331	0.427907	
chunk0139_39_1	chr4	48592252	48592537	+	0	NA	intron (NM_015030, intron 16 of 63)	Charlie7|DNA|hAT-Charlie	102142	NM_175619	326340	Hs.276457	NM_175619	ENSG00000182223	ZAR1	Z3CXXC6	zygote arrest 1	protein-coding	0.000000	0.325175	
chunk0165_49_1	chr6	30213980	30214186	+	0	NA	promoter-TSS (NM_001242783).2	promoter-TSS (NM_001242783).2	-589	NM_003449	7726	Hs.485041	NM_003449	ENSG00000234127	TRIM26	AFP|RNF95|ZNF173	tripartite motif containing 26	protein-coding	0.067961	0.608696	
chunk0101_312_1	chr2	135173586	135173815	+	0	NA	Intergenic	Intergenic	121435	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.008734	0.578261	
chunk0029_273_1	chr10	103428173	103428647	+	0	NA	intron (NM_014976, intron 21 of 35)	intron (NM_014976, intron 21 of 35)	23995	NR_046344	51063	Hs.241545	NM_015916	ENSG00000138172	CALHM2	FAM26B	calcium homeostasis modulator family member 2	protein-coding	0.014768	0.364211	
chunk0001_329_1	chr1	9553515	9554205	+	0	NA	intron (NM_032315, intron 2 of 6)	intron (NM_032315, intron 2 of 6)	14391	NM_032315	84275	Hs.568613	NM_032315	ENSG00000171612	SLC25A33	BMSC-MCP|PNC1	solute carrier family 25 member 33	protein-coding	0.014493	0.428365	320(CTGCACACCCTGTACC,-,0.00),321(TGCACACCCTGTACCG,+,0.00)
chunk0062_1_1	chr14	66001022	66001528	+	0	NA	Intergenic	Intergenic	-485096	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.000000	0.408284	
chunk0146_4_1	chr4	154836921	154837245	+	0	NA	Intergenic	HERVK22-int|LTR|ERVK	55578	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.015432	0.476923	
chunk0142_179_1	chr4	95651833	95652263	+	0	NA	Intergenic	Intergenic	-102838	NM_003728	8633	Hs.388565	NM_003728	ENSG00000182168	UNC5C	UNC5H3	unc-5 netrin receptor C	protein-coding	0.000000	0.352668	
chunk0053_384_1	chr13	36091640	36092283	+	0	NA	intron (NM_004734, intron 3 of 17)	L2b|LINE|L2	39416	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.006221	0.374224	
chunk0208_63_1	chrX	11715937	11716582	+	0	NA	Intergenic	Intergenic	-41900	NM_078629	10943	Hs.655288	NM_006800	ENSG00000005302	MSL3	MSL3L1	MSL complex subunit 3	protein-coding	0.007752	0.340557	
chunk0127_125_1	chr3	93973722	93973924	+	0	NA	5' UTR (NM_001314077, exon 1 of 16)	5' UTR (NM_001314077, exon 1 of 16)	258	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.173267	0.788177	
chunk0154_24_1	chr5	76919032	76919381	+	0	NA	intron (NM_130772, intron 4 of 4)	L1MC1|LINE|L1	-33649	NM_001882	1393	Hs.115617	NM_001882	ENSG00000145708	CRHBP	CRF-BP|CRFBP	corticotropin releasing hormone binding protein	protein-coding	0.000000	0.385714	
chunk0089_140_1	chr18	58942519	58943150	+	0	NA	intron (NM_018181, intron 6 of 10)	Charlie29a|DNA|hAT-Charlie	80005	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.007924	0.422468	
chunk0175_332_1	chr6	167216325	167216736	+	0	NA	Intergenic	Intergenic	45937	NM_001145121	401285		NM_001013683	ENSG00000166984	TCP10L2	-	t-complex 10 like 2	protein-coding	0.024331	0.512136	
chunk0024_99_1	chr10	34538253	34539097	+	0	NA	intron (NM_019619, intron 2 of 24)	intron (NM_019619, intron 2 of 24)	276650	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.013033	0.428402	273(TGGGACATGCAGTTCC,-,0.00),274(GGGACATGCAGTTCCA,+,0.00)
chunk0127_283_1	chr3	97870074	97870619	+	0	NA	intron (NM_153605, intron 3 of 21)	L1PA15|LINE|L1	48306	NM_153605	131544	Hs.733378	NM_153605	ENSG00000080200	CRYBG3	DKFZp667G2110|vlAKAP	crystallin beta-gamma domain containing 3	protein-coding	0.005505	0.358974	
chunk0211_237_1	chrX	119060528	119061085	+	0	NA	Intergenic	L1MA9|LINE|L1	84474	NM_001289109	79836	Hs.144266	NM_024778	ENSG00000175556	LONRF3	RNF127	LON peptidase N-terminal domain and ring finger 3	protein-coding	0.003591	0.344086	
chunk0102_446_1	chr2	158189241	158189946	+	0	NA	intron (NM_001301684, intron 9 of 11)	MER103C|DNA|hAT-Charlie	22943	NR_038850	554201	Hs.570262	NR_038850	ENSG00000227480	CCDC148-AS1	-	CCDC148 antisense RNA 1	ncRNA	0.001418	0.352691	375(GAGGACTTAGTGTGCT,-,0.00),376(AGGACTTAGTGTGCTT,+,0.00)
chunk0047_144_1	chr12	69682193	69682392	+	0	NA	TTS (NM_001282616)	TTS (NM_001282616)	6985	NM_152439	144453	Hs.280782	NM_032735	ENSG00000127325	BEST3	VMD2L3	bestrophin 3	protein-coding	0.000000	0.360000	
chunk0170_1_1	chr6	108934679	108935223	+	0	NA	intron (NM_001286609, intron 10 of 16)	MIR|SINE|MIR	-10848	NR_104137	101929716		NR_104137		ARMC2-AS1	-	ARMC2 antisense RNA 1	ncRNA	0.007353	0.297248	
chunk0173_230_1	chr6	146373368	146374014	+	0	NA	intron (NM_001278064, intron 5 of 7)	L1MA1|LINE|L1	-170001	NM_006834	10981	Hs.287714	NM_006834	ENSG00000118508	RAB32	-	RAB32, member RAS oncogene family	protein-coding	0.006192	0.403400	
chunk0098_21_1	chr2	65416918	65417551	+	0	NA	intron (NM_181784, intron 1 of 5)	intron (NM_181784, intron 1 of 5)	15288	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.006319	0.487382	
chunk0181_75_1	chr7	80280090	80280682	+	0	NA	Intergenic	Intergenic	94053	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.001689	0.296796	
chunk0068_245_1	chr15	55954241	55954942	+	0	NA	intron (NM_006154, intron 2 of 28)	AluSp|SINE|Alu	-37460	NM_001284338	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.014265	0.415954	
chunk0088_347_1	chr18	51721681	51721880	+	0	NA	Intergenic	Intergenic	329738	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.010050	0.430000	
chunk0096_101_1	chr2	28233362	28233939	+	0	NA	intron (NM_199191, intron 7 of 11)	intron (NM_199191, intron 7 of 11)	-26689	NR_120504	100505736	Hs.659540	NR_120504		LOC100505736	-	uncharacterized LOC100505736	ncRNA	0.008666	0.403114	
chunk0047_412_1	chr12	75921974	75922400	+	0	NA	Intergenic	Intergenic	109589	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.007042	0.433255	
chunk0091_243_1	chr19	10726248	10726707	+	0	NA	intron (NM_001005360, intron 1 of 20)	intron (NM_001005360, intron 1 of 20)	8073	NR_030368	693223		NR_030368	ENSG00000207972	MIR638	MIRN638|hsa-mir-638	microRNA 638	ncRNA	0.021786	0.482609	230(AGGCACGCCCTGTTCC,-,0.00),231(GGCACGCCCTGTTCCC,+,0.00)
chunk0169_195_1	chr6	102703727	102704001	+	0	NA	Intergenic	Intergenic	1304879	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.283636	
chunk0088_265_1	chr18	49167065	49167296	+	0	NA	intron (NM_017653, intron 13 of 16)	intron (NM_017653, intron 13 of 16)	-117412	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.000000	0.336207	150(ATGAACACTCTGTTTT,-,0.00),151(TGAACACTCTGTTTTG,+,0.00)
chunk0139_134_1	chr4	53454179	53454538	+	0	NA	intron (NM_030917, intron 16 of 17)	Tigger3a|DNA|TcMar-Tigger	-45719	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.002786	0.344444	
chunk0012_317_1	chr1	162318685	162319153	+	0	NA	intron (NM_001164757, intron 4 of 9)	L2|LINE|L2	-23627	NR_030283	693141		NR_030283	ENSG00000207729	MIR556	MIRN556|hsa-mir-556|mir-556	microRNA 556	ncRNA	0.002137	0.501066	
chunk0192_168_1	chr8	62529405	62530234	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	280877	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.004825	0.434940	
chunk0078_215_1	chr17	6054284	6054989	+	0	NA	Intergenic	Intergenic	-15978	NM_015253	23302	Hs.370166	NM_015253	ENSG00000179314	WSCD1	-	WSC domain containing 1	protein-coding	0.008511	0.488669	
chunk0005_256_1	chr1	59743440	59743965	+	0	NA	intron (NM_001244714, intron 12 of 13)	intron (NM_001244714, intron 12 of 13)	-10406	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.001905	0.401141	178(CAGCACATCATGTGCC,-,0.00),179(AGCACATCATGTGCCT,+,0.00)
chunk0166_130_1	chr6	44720886	44721462	+	0	NA	Intergenic	Intergenic	285533	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.003472	0.337955	
chunk0042_430_1	chr12	12167695	12168290	+	0	NA	intron (NM_002336, intron 7 of 22)	intron (NM_002336, intron 7 of 22)	56040	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.003361	0.322148	
chunk0121_212_1	chr3	21705054	21706051	+	0	NA	intron (NM_024697, intron 1 of 7)	intron (NM_024697, intron 1 of 7)	45772	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.006018	0.392786	
chunk0172_58_1	chr6	134175716	134176210	+	0	NA	promoter-TSS (NM_001143678)	promoter-TSS (NM_001143678)	-31	NM_001143678	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.040486	0.511111	
chunk0009_373_1	chr1	109927875	109928465	+	0	NA	intron (NM_000757, intron 8 of 8)	intron (NM_000757, intron 8 of 8)	17559	NM_000757	1435	Hs.173894	NM_000757	ENSG00000184371	CSF1	CSF-1|MCSF	colony stimulating factor 1	protein-coding	0.011864	0.560068	258(GGGAACAAAGCGTCCT,-,0.00),259(GGAACAAAGCGTCCTG,+,0.00)
chunk0151_392_1	chr5	55399055	55399448	+	0	NA	intron (NM_015360, intron 20 of 26)	intron (NM_015360, intron 20 of 26)	91503	NM_015360	23517	Hs.274531	NM_015360	ENSG00000039123	MTREX	Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118	Mtr4 exosome RNA helicase	protein-coding	0.002545	0.390863	180(TAGGACATAATGTGCA,-,0.00),181(AGGACATAATGTGCAA,+,0.00)
chunk0068_367_1	chr15	58046922	58047159	+	0	NA	intron (NM_003888, intron 1 of 12)	intron (NM_003888, intron 1 of 12)	18883	NM_001206897	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.004219	0.432773	
chunk0068_376_1	chr15	58247978	58248508	+	0	NA	Intergenic	Intergenic	110034	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.016981	0.495292	
chunk0021_308_1	chr1	244925177	244925390	+	0	NA	Intergenic	HAL1|LINE|L1	-44586	NM_032328	84288	Hs.134857	NM_032328	ENSG00000203666	EFCAB2	CFAP200|DRC8	EF-hand calcium binding domain 2	protein-coding	0.009390	0.331776	
chunk0177_204_1	chr7	23956667	23957185	+	0	NA	Intergenic	LTR107_Mam|LTR|LTR	246600	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.011583	0.475915	
chunk0176_197_1	chr7	14092116	14092708	+	0	NA	Intergenic	Intergenic	-100987	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.003378	0.382799	
chunk0191_207_1	chr8	52093931	52094464	+	0	NA	Intergenic	Intergenic	-195011	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.005629	0.483146	
chunk0141_60_1	chr4	77650911	77651192	+	0	NA	Intergenic	Intergenic	139298	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.003559	0.365248	
chunk0089_139_1	chr18	58935594	58935960	+	0	NA	intron (NM_018181, intron 5 of 10)	intron (NM_018181, intron 5 of 10)	72948	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.000000	0.318801	
chunk0008_3_1	chr1	87075620	87075819	+	0	NA	intron (NM_012262, intron 2 of 6)	intron (NM_012262, intron 2 of 6)	-54046	NR_026988	339524	Hs.306423	NM_207357	ENSG00000267272	LINC01140	-	long intergenic non-protein coding RNA 1140	ncRNA	0.000000	0.350000	
chunk0111_162_1	chr20	25190243	25190926	+	0	NA	intron (NR_109994, intron 1 of 5)	intron (NR_109994, intron 1 of 5)	-5119	NM_001114089	955	Hs.500375	NM_001247	ENSG00000197586	ENTPD6	CD39L2|IL-6SAG|IL6ST2|NTPDase-6|dJ738P15.3	ectonucleoside triphosphate diphosphohydrolase 6	protein-coding	0.005857	0.453216	
chunk0188_303_1	chr8	16402948	16403290	+	0	NA	Intergenic	L1M5|LINE|L1	-210328	NM_138716	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.011696	0.311953	
chunk0172_154_1	chr6	135764959	135765453	+	0	NA	Intergenic	L1ME1|LINE|L1	-86490	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.002024	0.292929	
chunk0099_244_1	chr2	97728279	97728534	+	0	NA	intron (NM_001079, intron 4 of 13)	intron (NM_001079, intron 4 of 13)	-6000	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.015686	0.523438	
chunk0129_25_1	chr3	117141820	117142454	+	0	NA	Intergenic	Intergenic	220706	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001577	0.415748	
chunk0017_43_1	chr1	205211234	205211808	+	0	NA	promoter-TSS (NM_015375)	promoter-TSS (NM_015375)	78	NM_015375	25778	Hs.6874	NM_015375	ENSG00000133059	DSTYK	CAKUT1|DustyPK|HDCMD38P|RIP5|RIPK5|SPG23	dual serine/threonine and tyrosine protein kinase	protein-coding	0.104530	0.699130	
chunk0065_242_1	chr14	101315397	101316036	+	0	NA	Intergenic	LTR10A|LTR|ERV1	92206	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.009390	0.428125	306(AAGTACAATGAGTTCT,-,0.00),307(AGTACAATGAGTTCTG,+,0.00)
chunk0155_311_1	chr5	96591365	96591815	+	0	NA	intron (NR_130776, intron 4 of 4)	LTR24B|LTR|ERV1	-70447	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.008889	0.363636	
chunk0081_90_1	chr17	39632632	39632847	+	0	NA	intron (NM_032192, intron 4 of 6)	intron (NM_032192, intron 4 of 6)	4241	NM_001242464	84152	Hs.286192	NM_032192	ENSG00000131771	PPP1R1B	DARPP-32|DARPP32	protein phosphatase 1 regulatory inhibitor subunit 1B	protein-coding	0.023256	0.611111	
chunk0001_232_1	chr1	8182161	8182962	+	0	NA	Intergenic	Intergenic	-26111	NR_125998	102724539	Hs.516816	NR_125998	ENSG00000227634	LINC01714	-	long intergenic non-protein coding RNA 1714	ncRNA	0.018727	0.405237	
chunk0006_98_1	chr1	65170441	65171040	+	0	NA	intron (NM_001005353, intron 2 of 5)	intron (NM_001005353, intron 2 of 5)	22573	NM_013410	205	Hs.10862	NM_013410	ENSG00000162433	AK4	AK 4|AK3|AK3L1|AK3L2	adenylate kinase 4	protein-coding	0.013356	0.423333	
chunk0013_95_1	chr1	167701538	167702063	+	0	NA	intron (NM_052862, intron 6 of 6)	intron (NM_052862, intron 6 of 6)	-20150	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.003810	0.471483	
chunk0125_291_1	chr3	69930396	69930647	+	0	NA	intron (NM_198159, intron 2 of 9)	L2a|LINE|L2	-6079	NM_198178	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.007968	0.460317	
chunk0145_404_1	chr4	152760885	152761281	+	0	NA	Intergenic	Intergenic	18681	NM_145720	201798	Hs.301243	NM_145720	ENSG00000169989	TIGD4	-	tigger transposable element derived 4	protein-coding	0.005051	0.332494	
chunk0066_358_1	chr15	38264865	38265508	+	0	NA	intron (NM_152594, intron 1 of 6)	MIR|SINE|MIR	12335	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.004666	0.322981	461(AGAACTTTTAGTTCTT,+,0.00)
chunk0004_144_1	chr1	45018650	45018978	+	0	NA	exon (NM_020883, exon 14 of 14)	exon (NM_020883, exon 14 of 14)	6681	NM_000374	7389	Hs.78601	NM_000374	ENSG00000126088	UROD	PCT|UPD	uroporphyrinogen decarboxylase	protein-coding	0.024390	0.562310	
chunk0043_109_1	chr12	15184544	15184743	+	0	NA	intron (NM_032918, intron 2 of 4)	intron (NM_032918, intron 2 of 4)	32720	NR_046559	100873980	Hs.569154	NR_046559	ENSG00000255660	RERG-AS1	-	RERG antisense RNA 1	ncRNA	0.020101	0.405000	65(GGGAACACAGTGTGTT,-,0.00),66(GGAACACAGTGTGTTT,+,0.00)
chunk0131_133_1	chr3	144438052	144438251	+	0	NA	Intergenic	L1PBa|LINE|L1	464826	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.005025	0.580000	13(GAGCACAGCCTCTCCT,-,0.00),14(AGCACAGCCTCTCCTT,+,0.00)
chunk0024_56_1	chr10	33836010	33836232	+	0	NA	Intergenic	Intergenic	-63441	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.004505	0.372197	
chunk0120_115_1	chr3	4688463	4688903	+	0	NA	intron (NM_002222, intron 30 of 57)	intron (NM_002222, intron 30 of 57)	62907	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.009091	0.442177	216(AGGAACAGCTTGTTCT,-,0.00),217(GGAACAGCTTGTTCTT,+,0.00)
chunk0163_297_1	chr6	14251023	14251295	+	0	NA	Intergenic	MIRb|SINE|MIR	34295	NR_108097	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.007353	0.362637	
chunk0175_308_1	chr6	166624315	166624693	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	2734	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.010582	0.464380	49(CAGTACTTTGTGTCCT,-,0.00),50(AGTACTTTGTGTCCTA,+,0.00)
chunk0066_424_1	chr15	39593660	39593959	+	0	NA	intron (NM_003246, intron 19 of 21)	intron (NM_003246, intron 19 of 21)	12730	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.000000	0.470000	
chunk0085_262_1	chr18	7642157	7642356	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	74940	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.010050	0.410000	146(GAGAACTATTTGTTCT,-,0.00),147(AGAACTATTTGTTCTC,+,0.00)
chunk0027_85_1	chr10	73576158	73577051	+	0	NA	promoter-TSS (NM_152586)	promoter-TSS (NM_152586)	-929	NM_152586	159195	Hs.657355	NM_152586	ENSG00000166348	USP54	C10orf29|bA137L10.3|bA137L10.4	ubiquitin specific peptidase 54	protein-coding	0.004479	0.373602	546(AGGAACTGAAAGTTCC,-,0.00),547(GGAACTGAAAGTTCCT,+,0.00)
chunk0198_194_1	chr8	133529849	133530179	+	0	NA	intron (NM_003033, intron 2 of 8)	L2a|LINE|L2	41926	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.015152	0.483384	
chunk0154_93_1	chr5	78060312	78060867	+	0	NA	intron (NM_003664, intron 22 of 26)	intron (NM_003664, intron 22 of 26)	102342	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.007207	0.332734	104(AAGGACAAAATGTTTC,-,0.00),105(AGGACAAAATGTTTCT,+,0.00)
chunk0039_420_1	chr11	107750732	107751368	+	0	NA	Intergenic	L1MC4a|LINE|L1	-38989	NM_003063	6588	Hs.334629	NM_003063	ENSG00000170290	SLN	-	sarcolipin	protein-coding	0.020440	0.397174	
chunk0010_303_1	chr1	117857477	117857771	+	0	NA	Intergenic	MIR|SINE|MIR	72055	NM_017686	54834	Hs.310809	NM_017686	ENSG00000196505	GDAP2	MACROD3|SCAR27	ganglioside induced differentiation associated protein 2	protein-coding	0.006803	0.383051	
chunk0124_408_1	chr3	60488208	60488484	+	0	NA	intron (NM_001166243, intron 5 of 9)	intron (NM_001166243, intron 5 of 9)	129524	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.010870	0.400722	
chunk0210_172_1	chrX	78327117	78327411	+	0	NA	intron (NM_001282188, intron 1 of 3)	intron (NM_001282188, intron 1 of 3)	427	NM_001282187	10800	Hs.733809	NM_006639	ENSG00000173198	CYSLTR1	CYSLT1|CYSLT1R|CYSLTR|HMTMF81	cysteinyl leukotriene receptor 1	protein-coding	0.006803	0.386441	
chunk0055_350_1	chr13	70297971	70298504	+	0	NA	Intergenic	Intergenic	-189744	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.009381	0.350187	
chunk0083_224_1	chr17	67246698	67246971	+	0	NA	Intergenic	Intergenic	-1631	NM_014877	9931	Hs.370140	NM_014877	ENSG00000198265	HELZ	DHRC|DRHC|HUMORF5	helicase with zinc finger	protein-coding	0.032967	0.594891	
chunk0011_429_1	chr1	154607865	154608254	+	0	NA	5' UTR (NM_015841, exon 1 of 15)	5' UTR (NM_015841, exon 1 of 15)	189	NM_015840	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.110540	0.666667	
chunk0061_385_1	chr14	64432104	64432878	+	0	NA	intron (NM_005956, intron 15 of 27)	L1ME1|LINE|L1	-33008	NM_004857	9495	Hs.656683	NM_004857	ENSG00000179841	AKAP5	AKAP75|AKAP79|H21	A-kinase anchoring protein 5	protein-coding	0.006460	0.369032	
chunk0202_101_1	chr9	72396658	72396959	+	0	NA	Intergenic	Intergenic	-31561	NM_001102421	7763	Hs.406096	NM_006007	ENSG00000107372	ZFAND5	ZA20D2|ZFAND5A|ZNF216	zinc finger AN1-type containing 5	protein-coding	0.009967	0.377483	
chunk0056_454_1	chr13	95238929	95239238	+	0	NA	intron (NM_001105515, intron 3 of 20)	L1MC5|LINE|L1	62363	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.000000	0.267742	
chunk0191_98_1	chr8	47825451	47826070	+	0	NA	intron (NM_006904, intron 63 of 85)	intron (NM_006904, intron 63 of 85)	-87596	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.004847	0.374194	520(TGTACACTCAGTGCTC,+,0.00)
chunk0056_209_1	chr13	86082022	86082221	+	0	NA	Intergenic	L2a|LINE|L2	-282773	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.005025	0.390000	
chunk0135_230_1	chr3	188624158	188624822	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-55824	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.006024	0.412030	
chunk0037_154_1	chr11	73598010	73598293	+	0	NA	promoter-TSS (NM_015159)	promoter-TSS (NM_015159)	38	NM_015159	23201	Hs.475334	NM_015159	ENSG00000054965	FAM168A	KIAA0280|TCRP1	family with sequence similarity 168 member A	protein-coding	0.120141	0.742958	
chunk0079_439_1	chr17	20165079	20165639	+	0	NA	intron (NM_001033554, intron 1 of 5)	L1PA10|LINE|L1	9365	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.012500	0.438503	
chunk0044_33_1	chr12	27366600	27366846	+	0	NA	intron (NM_001248003, intron 1 of 14)	L1ME4c|LINE|L1	33869	NM_001248003	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.000000	0.303644	
chunk0018_300_1	chr1	220906968	220907240	+	0	NA	Intergenic	Intergenic	-26964	NR_046901	100873924	Hs.645593	NR_046901	ENSG00000257551	HLX-AS1	-	HLX antisense RNA 1	ncRNA	0.007353	0.501832	
chunk0107_21_1	chr2	210215049	210215554	+	0	NA	intron (NM_001608, intron 4 of 10)	intron (NM_001608, intron 4 of 10)	10190	NM_001608	33	Hs.471277	NM_001608	ENSG00000115361	ACADL	ACAD4|LCAD	acyl-CoA dehydrogenase long chain	protein-coding	0.003960	0.418972	
chunk0081_287_1	chr17	44674108	44674620	+	0	NA	3' UTR (NM_001145080, exon 8 of 8)	3' UTR (NM_001145080, exon 8 of 8)	15433	NM_001099225	124808	Hs.579115	NM_144609	ENSG00000180329	CCDC43	-	coiled-coil domain containing 43	protein-coding	0.005859	0.309942	
chunk0182_209_1	chr7	96303194	96303401	+	0	NA	intron (NR_027662, intron 1 of 16)	intron (NR_027662, intron 1 of 16)	18850	NM_014251	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.004831	0.427885	
chunk0204_399_1	chr9	102564198	102564529	+	0	NA	intron (NR_103830, intron 1 of 4)	intron (NR_103830, intron 1 of 4)	44726	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.003021	0.292169	180(CAGCACATGCCGTGCC,-,0.00),181(AGCACATGCCGTGCCA,+,0.00)
chunk0112_275_1	chr20	43410998	43411285	+	0	NA	Intergenic	L1P4|LINE|L1	-46723	NR_034009	6431	Hs.684950	NM_006275	ENSG00000124193	SRSF6	B52|HEL-S-91|SFRS6|SRP55	serine and arginine rich splicing factor 6	protein-coding	0.006969	0.378472	
chunk0111_412_1	chr20	34627591	34627790	+	0	NA	intron (NM_080476, intron 6 of 11)	intron (NM_080476, intron 6 of 11)	49595	NM_080476	128869	Hs.253319	NM_080476	ENSG00000101464	PIGU	CDC91L1|GAB1	phosphatidylinositol glycan anchor biosynthesis class U	protein-coding	0.020101	0.405000	
chunk0188_316_1	chr8	17256421	17256620	+	0	NA	intron (NM_001145152, intron 1 of 10)	L1MA4|LINE|L1	9628	NM_152415	137492	Hs.343873	NM_152415	ENSG00000155975	VPS37A	HCRP1|PQBP2|SPG53	VPS37A subunit of ESCRT-I	protein-coding	0.015075	0.355000	
chunk0059_182_1	chr14	32640736	32641051	+	0	NA	intron (NM_004274, intron 7 of 13)	A-rich|Low_complexity|Low_complexity	-298360	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.000000	0.338608	
chunk0157_172_1	chr5	118174988	118175390	+	0	NA	intron (NR_104997, intron 2 of 2)	Tigger3a|DNA|TcMar-Tigger	-107385	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.004975	0.302730	206(CTGTACAGCATGTTCT,-,0.00),207(TGTACAGCATGTTCTT,+,0.00)
chunk0205_421_1	chr9	115029092	115029383	+	0	NA	intron (NM_002160, intron 25 of 27)	intron (NM_002160, intron 25 of 27)	89020	NM_002160	3371	Hs.143250	NM_002160	ENSG00000041982	TNC	150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C	tenascin C	protein-coding	0.010309	0.397260	
chunk0190_178_1	chr8	33001269	33001565	+	0	NA	Intergenic	Intergenic	279584	NM_001159996	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.010135	0.400673	
chunk0115_187_1	chr21	26122764	26123358	+	0	NA	intron (NM_001136131, intron 1 of 15)	intron (NM_001136131, intron 1 of 15)	17329	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.006734	0.310924	
chunk0010_316_1	chr1	118069653	118070295	+	0	NA	intron (NM_206996, intron 17 of 48)	L2a|LINE|L2	115251	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.003115	0.381026	
chunk0100_68_1	chr2	106574987	106575467	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-106882	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.006250	0.419958	
chunk0009_81_1	chr1	101025407	101025658	+	0	NA	promoter-TSS (NR_109849)	promoter-TSS (NR_109849)	274	NM_001077395	51611	Hs.440776	NM_015958	ENSG00000117543	DPH5	AD-018|CGI-30|HSPC143|NPD015	diphthamide biosynthesis 5	protein-coding	0.023904	0.452381	
chunk0120_465_1	chr22	50628284	50628503	+	0	NA	promoter-TSS (NM_001085425)	promoter-TSS (NM_001085425)	-220	NM_001085427	410	Hs.88251	NM_000487	ENSG00000100299	ARSA	ASA|MLD	arylsulfatase A	protein-coding	0.109589	0.700000	
chunk0145_341_1	chr4	150961651	150962081	+	0	NA	intron (NM_001199282, intron 2 of 56)	MIR|SINE|MIR	53401	NM_001199282	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.004651	0.364269	133(GAGAACAGAAAGTCCA,-,0.00),134(AGAACAGAAAGTCCAC,+,0.00)
chunk0101_101_1	chr2	125086526	125086932	+	0	NA	Intergenic	Intergenic	1061442	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.007389	0.341523	
chunk0017_60_1	chr1	205492211	205492485	+	0	NA	Intergenic	Intergenic	-12208	NM_002596	5129	Hs.445402	NM_002596	ENSG00000117266	CDK18	PCTAIRE|PCTAIRE3|PCTK3	cyclin dependent kinase 18	protein-coding	0.000000	0.549091	
chunk0114_329_1	chr21	17522924	17523402	+	0	NA	intron (NM_001207065, intron 1 of 2)	intron (NM_001207065, intron 1 of 2)	10257	NM_001207064	1525	Hs.627078	NM_001338	ENSG00000154639	CXADR	CAR|CAR4/6|HCAR	CXADR Ig-like cell adhesion molecule	protein-coding	0.004184	0.419624	210(AGGCACATCCTGTTAC,-,0.00)
chunk0150_430_1	chr5	40410913	40411331	+	0	NA	Intergenic	Intergenic	-268808	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.007177	0.412888	
chunk0186_181_1	chr7	139609741	139609960	+	0	NA	intron (NM_001113239, intron 9 of 14)	L1ME4b|LINE|L1	85922	NM_001080511	154790	Hs.57806	NM_001080511	ENSG00000236279	CLEC2L	-	C-type lectin domain family 2 member L	protein-coding	0.013699	0.354545	
chunk0209_102_1	chrX	39953872	39954176	+	0	NA	Intergenic	Intergenic	116463	NR_039763	100616251		NR_039763	ENSG00000263972	MIR1587	-	microRNA 1587	ncRNA	0.032895	0.563934	
chunk0139_57_1	chr4	48796297	48796554	+	0	NA	Intergenic	L2a|LINE|L2	-16126	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.003891	0.387597	120(GGCACAGTCTCTGCCT,+,0.00)
chunk0047_162_1	chr12	69842480	69842909	+	0	NA	intron (NM_182530, intron 1 of 24)	intron (NM_182530, intron 1 of 24)	17371	NM_182530	196446	Hs.253773	NM_182530	ENSG00000166268	MYRFL	C12orf15|C12orf28|bcm1377	myelin regulatory factor like	protein-coding	0.004662	0.430233	
chunk0212_412_1	chrX	152038537	152039063	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-64121	NM_004961	2564	Hs.22785	NM_004961	ENSG00000102287	GABRE	-	gamma-aminobutyric acid type A receptor epsilon subunit	protein-coding	0.003802	0.339658	
chunk0052_181_1	chr13	24209811	24210461	+	0	NA	intron (NM_153023, intron 1 of 11)	L1MA8|LINE|L1	44303	NR_046531	100874231	Hs.577998	NR_046531	ENSG00000227213	SPATA13-AS1	-	SPATA13 antisense RNA 1	ncRNA	0.007692	0.373272	
chunk0211_275_1	chrX	122026578	122027081	+	0	NA	Intergenic	Intergenic	655857	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.003976	0.412698	
chunk0014_312_1	chr1	181153041	181153240	+	0	NA	Intergenic	Intergenic	-21344	NR_125966	101928973	Hs.637822	NR_125966	ENSG00000237292	LINC01732	-	long intergenic non-protein coding RNA 1732	ncRNA	0.040201	0.590000	
chunk0129_83_1	chr3	118430148	118430675	+	0	NA	Intergenic	L1PA15|LINE|L1	-512665	NR_046230	100506765	Hs.660823	NR_046230	ENSG00000239877	IGSF11-AS1	-	IGSF11 antisense RNA 1	ncRNA	0.000000	0.359848	
chunk0204_77_1	chr9	93893834	93894164	+	0	NA	Intergenic	Intergenic	61327	NM_021570	56033	Hs.164960	NM_021570	ENSG00000131668	BARX1	-	BARX homeobox 1	protein-coding	0.021212	0.586103	
chunk0187_159_1	chr7	150368536	150368825	+	0	NA	promoter-TSS (NM_001099696)	promoter-TSS (NM_001099696)	-110	NM_001099695	29803	Hs.647086	NM_013400	ENSG00000214022	REPIN1	AP4|RIP60|ZNF464|Zfp464	replication initiator 1	protein-coding	0.110727	0.751724	
chunk0122_92_1	chr3	30258763	30259299	+	0	NA	Intergenic	Intergenic	-324875	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.003731	0.413408	
chunk0007_194_1	chr1	81032965	81033164	+	0	NA	Intergenic	Intergenic	391777	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.010050	0.420000	
chunk0066_196_1	chr15	33252125	33252359	+	0	NA	Intergenic	Intergenic	-4687	NR_046005	100652857	Hs.439998	NR_046005		TMCO5B	-	transmembrane and coiled-coil domains 5B (pseudogene)	pseudo	0.000000	0.382979	
chunk0064_10_1	chr14	89247688	89248073	+	0	NA	intron (NM_001085471, intron 4 of 6)	L2a|LINE|L2	169230	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.005195	0.440415	
chunk0133_229_1	chr3	171263058	171263641	+	0	NA	intron (NM_001161560, intron 2 of 31)	intron (NM_001161560, intron 2 of 31)	-156590	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.001715	0.363014	
chunk0037_58_1	chr11	70769196	70769776	+	0	NA	intron (NM_012309, intron 13 of 24)	intron (NM_012309, intron 13 of 24)	-93304	NR_073536	220070	Hs.326766	NM_145308	ENSG00000171671	SHANK2-AS3	C11orf76	SHANK2 antisense RNA 3	ncRNA	0.029310	0.557659	
chunk0033_212_1	chr11	17128920	17129261	+	0	NA	intron (NM_002645, intron 12 of 31)	intron (NM_002645, intron 12 of 31)	40717	NM_002645	5286	Hs.175343	NM_002645	ENSG00000011405	PIK3C2A	CPK|OCSKD|PI3-K-C2(ALPHA)|PI3-K-C2A|PI3K-C2-alpha|PI3K-C2alpha	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha	protein-coding	0.005865	0.391813	
chunk0090_448_1	chr18	79887049	79887592	+	0	NA	intron (NM_012283, intron 1 of 1)	intron (NM_012283, intron 1 of 1)	23652	NM_012283	26251	Hs.247905	NM_012283	ENSG00000178342	KCNG2	KCNF2|KV6.2	potassium voltage-gated channel modifier subfamily G member 2	protein-coding	0.027624	0.623162	305(CAGGACACACTGGGCT,-,0.00),306(AGGACACACTGGGCTC,+,0.00)
chunk0207_251_1	chr9	132086578	132087124	+	0	NA	Intergenic	L2c|LINE|L2	-6964	NM_001253882	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.007326	0.495430	
chunk0032_459_1	chr10	133562376	133563057	+	0	NA	intron (NM_130784, intron 2 of 13)	MER4-int|LTR|ERV1	2918	NM_001143763	93426	Hs.553795	NM_130784	ENSG00000171772	SYCE1	C10orf94|CT76|POF12|SPGF15	synaptonemal complex central element protein 1	protein-coding	0.005874	0.395894	
chunk0192_418_1	chr8	69508243	69508750	+	0	NA	intron (NM_015170, intron 3 of 22)	intron (NM_015170, intron 3 of 22)	15703	NM_001128206	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.011834	0.352362	
chunk0057_442_1	chr13	110560819	110561087	+	0	NA	intron (NM_017817, intron 1 of 1)	MIR|SINE|MIR	784	NM_017817	55647	Hs.743563	NM_017817	ENSG00000139832	RAB20	-	RAB20, member RAS oncogene family	protein-coding	0.029851	0.498141	84(GGGAACACTCTGTGCC,-,0.00),85(GGAACACTCTGTGCCT,+,0.00)
chunk0095_140_1	chr2	16740039	16740657	+	0	NA	Intergenic	Intergenic	-74482	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.004854	0.483037	
chunk0027_23_1	chr10	72248387	72249321	+	0	NA	Intergenic	Intergenic	-25065	NM_019058	54541	Hs.744875	NM_019058	ENSG00000168209	DDIT4	Dig2|REDD-1|REDD1	DNA damage inducible transcript 4	protein-coding	0.020343	0.531551	594(GAGAACATTGTGTTCT,-,0.00),595(AGAACATTGTGTTCTG,+,0.00)
chunk0032_204_1	chr11	7348255	7348638	+	0	NA	intron (NM_175733, intron 3 of 6)	intron (NM_175733, intron 3 of 6)	96496	NM_175733	143425	Hs.177193	NM_175733	ENSG00000170743	SYT9	-	synaptotagmin 9	protein-coding	0.007833	0.434896	
chunk0065_248_1	chr14	101481161	101481477	+	0	NA	Intergenic	Intergenic	-73397	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.018987	0.533123	
chunk0117_157_1	chr22	19962567	19963322	+	0	NA	promoter-TSS (NR_039918)	promoter-TSS (NR_039918)	397	NM_007310	1312	Hs.370408	NM_000754	ENSG00000093010	COMT	HEL-S-98n	catechol-O-methyltransferase	protein-coding	0.027815	0.630952	593(GGGCACAGGATGTGTT,-,0.00)
chunk0055_201_1	chr13	61934800	61935357	+	0	NA	Intergenic	Intergenic	94470	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.010772	0.313620	
chunk0137_369_1	chr4	26141659	26142494	+	0	NA	Intergenic	Intergenic	-177634	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.009581	0.467703	
chunk0030_8_1	chr10	110837370	110837953	+	0	NA	3' UTR (NM_001134363, exon 14 of 14)	3' UTR (NM_001134363, exon 14 of 14)	33243	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.005146	0.457192	240(CTGTACATTCTGTCCT,-,0.00),241(TGTACATTCTGTCCTC,+,0.00)
chunk0014_131_1	chr1	177621549	177622113	+	0	NA	Intergenic	Intergenic	-78693	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.005319	0.366372	
chunk0091_317_1	chr19	13051659	13051907	+	0	NA	intron (NM_001271043, intron 2 of 10)	intron (NM_001271043, intron 2 of 10)	27202	NM_001271043	4784	Hs.257970	NM_002501	ENSG00000008441	NFIX	CTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2	nuclear factor I X	protein-coding	0.044355	0.622490	
chunk0078_263_1	chr17	7613398	7614150	+	0	NA	promoter-TSS (NM_001289114)	promoter-TSS (NM_001289114)	-290	NM_001289114	6462	Hs.632235	NM_001040	ENSG00000129214	SHBG	ABP|SBP|TEBG	sex hormone binding globulin	protein-coding	0.014628	0.450199	
chunk0162_79_1	chr6	1838584	1839136	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	228414	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.009058	0.374322	
chunk0018_251_1	chr1	220206144	220206367	+	0	NA	intron (NM_012414, intron 7 of 34)	intron (NM_012414, intron 7 of 34)	-5579	NR_002994	677818	Hs.730572	NR_002994	ENSG00000222370	SNORA36B	ACA36b	small nucleolar RNA, H/ACA box 36B	snoRNA	0.004484	0.299107	
chunk0161_126_1	chr5	168136351	168136623	+	0	NA	intron (NM_001080428, intron 9 of 24)	intron (NM_001080428, intron 9 of 24)	95885	NR_109894	101927862	Hs.659376	NR_109894	ENSG00000253978	CTB-178M22.2	-	uncharacterized LOC101927862	ncRNA	0.011029	0.483516	
chunk0198_286_1	chr8	135589579	135590070	+	0	NA	intron (NM_006558, intron 6 of 8)	intron (NM_006558, intron 6 of 8)	132359	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.012220	0.365854	
chunk0159_370_1	chr5	145909849	145910261	+	0	NA	Intergenic	Intergenic	-26508	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.024272	0.433414	
chunk0057_380_1	chr13	109278446	109278645	+	0	NA	Intergenic	MIR|SINE|MIR	-111242	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.000000	0.305000	
chunk0012_243_1	chr1	160935578	160935777	+	0	NA	intron (NR_110695, intron 3 of 5)	intron (NR_110695, intron 3 of 5)	3212	NR_110695	101928372		NR_110695	ENSG00000198358	LOC101928372	-	uncharacterized LOC101928372	ncRNA	0.020101	0.570000	
chunk0075_218_1	chr16	52725479	52725820	+	0	NA	Intergenic	MIRb|SINE|MIR	-118674	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.002933	0.400585	
chunk0206_429_1	chr9	127758632	127758831	+	0	NA	intron (NM_001252334, intron 3 of 11)	intron (NM_001252334, intron 3 of 11)	-3427	NM_001142533	10044	Hs.306412	NM_005489	ENSG00000095370	SH2D3C	CHAT|NSP3|PRO34088|SHEP1	SH2 domain containing 3C	protein-coding	0.000000	0.495000	
chunk0124_402_1	chr3	59895946	59896304	+	0	NA	intron (NM_001166243, intron 8 of 9)	L2a|LINE|L2	721745	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.008380	0.409471	
chunk0164_183_1	chr6	22037578	22037874	+	0	NA	intron (NR_015410, intron 7 of 11)	intron (NR_015410, intron 7 of 11)	109467	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.013514	0.410774	
chunk0061_26_1	chr14	55803101	55803439	+	0	NA	Intergenic	MIRc|SINE|MIR	-6596	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.000000	0.418879	
chunk0180_251_1	chr7	69232650	69233110	+	0	NA	Intergenic	Intergenic	364615	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.019565	0.483731	
chunk0103_415_1	chr2	169565694	169566319	+	0	NA	intron (NR_104020, intron 3 of 13)	L1MA1|LINE|L1	7915	NR_104020	79675	Hs.529276	NM_024622	ENSG00000138399	FASTKD1	-	FAST kinase domains 1	protein-coding	0.006400	0.383387	
chunk0110_213_1	chr20	15337095	15337534	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	140456	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.006834	0.318182	143(AAGAACAGTTTGTGTT,-,0.00),144(AGAACAGTTTGTGTTT,+,0.00)
chunk0211_207_1	chrX	118207873	118208359	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	-90776	NM_001168301	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.002058	0.392197	
chunk0199_161_1	chr9	4334509	4334798	+	0	NA	Intergenic	Intergenic	-34618	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.010381	0.527586	
chunk0153_151_1	chr5	69299659	69300200	+	0	NA	intron (NM_001297697, intron 9 of 12).2	intron (NM_001297697, intron 9 of 12).2	32787	NM_176816	202243	Hs.654850	NM_176816	ENSG00000183323	CCDC125	KENAE	coiled-coil domain containing 125	protein-coding	0.014787	0.464945	
chunk0005_59_1	chr1	55447528	55447913	+	0	NA	Intergenic	Intergenic	222079	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.005195	0.370466	
chunk0070_79_1	chr15	70093556	70093989	+	0	NA	intron (NM_020908, intron 4 of 19)	intron (NM_020908, intron 4 of 19)	1013	NM_001282982	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.016166	0.474654	
chunk0146_349_1	chr4	166714901	166715182	+	0	NA	Intergenic	Intergenic	519385	NM_001204353	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.000000	0.340426	
chunk0047_418_1	chr12	76032154	76032407	+	0	NA	promoter-TSS (NM_007350)	promoter-TSS (NM_007350)	-504	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.102767	0.606299	67(GAGGACATCGTGTCTT,-,0.00),68(AGGACATCGTGTCTTC,+,0.00)
chunk0185_189_1	chr7	128323213	128323481	+	0	NA	intron (NM_001166135, intron 9 of 14)	intron (NM_001166135, intron 9 of 14)	-15584	NR_046216	55131	Hs.274263	NM_018077	ENSG00000106344	RBM28	ANES	RNA binding motif protein 28	protein-coding	0.003731	0.382900	
chunk0030_401_1	chr10	119942705	119943475	+	0	NA	non-coding (NR_037771, exon 18 of 18)	non-coding (NR_037771, exon 18 of 18)	-15423	NR_039830	100616322		NR_039830	ENSG00000265370	MIR4682	-	microRNA 4682	ncRNA	0.010390	0.425422	
chunk0023_435_1	chr10	31864394	31864797	+	0	NA	intron (NM_001270696, intron 3 of 17)	intron (NM_001270696, intron 3 of 17)	44331	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.004963	0.321782	
chunk0070_379_1	chr15	76533010	76533829	+	0	NA	intron (NM_020843, intron 22 of 30)	Tigger3a|DNA|TcMar-Tigger	-53228	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.006105	0.363415	
chunk0018_6_1	chr1	215060070	215060374	+	0	NA	intron (NM_001017424, intron 1 of 6)	intron (NM_001017424, intron 1 of 6)	-22995	NM_014217	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.019737	0.537705	
chunk0006_346_1	chr1	72519511	72519903	+	0	NA	Intergenic	Intergenic	-237113	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.005102	0.284987	
chunk0198_30_1	chr8	128177012	128177463	+	0	NA	Intergenic	Intergenic	27121	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.011086	0.424779	170(GTAACATCCTGTTCCT,+,0.00)
chunk0029_74_1	chr10	96684379	96684676	+	0	NA	intron (NM_152309, intron 2 of 16)	intron (NM_152309, intron 2 of 16)	35995	NM_152309	118788	Hs.310456	NM_152309	ENSG00000155629	PIK3AP1	BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.006734	0.513423	126(CTGTACAATGTGTTCC,-,0.00),127(TGTACAATGTGTTCCA,+,0.00)
chunk0160_270_1	chr5	157335671	157336360	+	0	NA	intron (NM_001037333, intron 21 of 30)	intron (NM_001037333, intron 21 of 30)	9706	NM_001001343	408263	Hs.437066	NM_001001343	ENSG00000172568	FNDC9	C5orf40	fibronectin type III domain containing 9	protein-coding	0.011611	0.460870	252(AAGCACTAAATGTTCT,-,0.00),253(AGCACTAAATGTTCTT,+,0.00)
chunk0120_406_1	chr3	12647999	12648340	+	0	NA	intron (NM_002880, intron 1 of 16)	intron (NM_002880, intron 1 of 16)	16032	NM_002880	5894	Hs.159130	NM_002880	ENSG00000132155	RAF1	CMD1NN|CRAF|NS5|Raf-1|c-Raf	Raf-1 proto-oncogene, serine/threonine kinase	protein-coding	0.005865	0.304094	
chunk0205_281_1	chr9	111605147	111605760	+	0	NA	intron (NR_034087, intron 2 of 2)	L1MC4|LINE|L1	-5598	NM_001146108	22949	Hs.584864	NM_012212	ENSG00000106853	PTGR1	LTB4DH|PGR1|ZADH3	prostaglandin reductase 1	protein-coding	0.011419	0.408795	301(AGGAACAGAGTGTCTA,-,0.00),302(GGAACAGAGTGTCTAC,+,0.00)
chunk0108_124_1	chr2	229835540	229836100	+	0	NA	intron (NM_001284214, intron 6 of 41)	intron (NM_001284214, intron 6 of 41)	44308	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.005357	0.344029	
chunk0040_9_1	chr11	108649109	108649360	+	0	NA	Intergenic	L1M1|LINE|L1	-15791	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.000000	0.317460	
chunk0042_3_1	chr12	1050007	1050690	+	0	NA	intron (NR_027949, intron 2 of 15)	intron (NR_027949, intron 2 of 15)	22600	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.010249	0.415205	
chunk0162_379_1	chr6	7479927	7480126	+	0	NA	Intergenic	Intergenic	-61611	NM_001008844	1832	Hs.519873	NM_004415	ENSG00000096696	DSP	DCWHKTA|DP	desmoplakin	protein-coding	0.025126	0.490000	
chunk0128_410_1	chr3	114624002	114624354	+	0	NA	promoter-TSS (NM_001164347)	promoter-TSS (NM_001164347)	28	NM_001164347	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.008523	0.427762	220(GAGTTCACAGTGTTCC,-,0.00),221(AGTTCACAGTGTTCCA,+,0.00)
chunk0121_218_1	chr3	21803563	21804253	+	0	NA	Intergenic	Intergenic	-52584	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.001449	0.312590	
chunk0081_427_1	chr17	48802089	48802539	+	0	NA	intron (NM_001130918, intron 3 of 15)	Tigger19a|DNA|TcMar-Tigger	-7990	NM_173623	284076	Hs.91930	NM_173623	ENSG00000170703	TTLL6	TTL.6	tubulin tyrosine ligase like 6	protein-coding	0.004444	0.390244	
chunk0151_398_1	chr5	55480944	55481231	+	0	NA	intron (NM_003711, intron 1 of 5)	intron (NM_003711, intron 1 of 5)	27839	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.006969	0.354167	
chunk0077_314_1	chr16	82040315	82040514	+	0	NA	intron (NM_002153, intron 1 of 4)	intron (NM_002153, intron 1 of 4)	5161	NM_002153	3294	Hs.162795	NM_002153	ENSG00000086696	HSD17B2	EDH17B2|HSD17|SDR9C2	hydroxysteroid 17-beta dehydrogenase 2	protein-coding	0.005025	0.375000	
chunk0207_300_1	chr9	133347995	133348243	+	0	NA	promoter-TSS (NM_181491)	promoter-TSS (NM_181491)	37	NM_133640	6837	Hs.78354	NM_006752	ENSG00000148297	MED22	MED24|SRB6|SURF5|surf-5	mediator complex subunit 22	protein-coding	0.104839	0.606426	
chunk0058_68_1	chr14	20893899	20894524	+	0	NA	Intergenic	L2a|LINE|L2	2808	NM_002935	6037	Hs.73839	NM_002935	ENSG00000169397	RNASE3	ECP|RAF1|RNS3	ribonuclease A family member 3	protein-coding	0.009600	0.426518	
chunk0192_162_1	chr8	62440193	62440513	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	191411	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.003125	0.355140	
chunk0006_275_1	chr1	70354922	70355232	+	0	NA	promoter-TSS (NM_030816)	promoter-TSS (NM_030816)	267	NM_001031693	11147	Hs.142245	NM_007071	ENSG00000197568	HHLA3	-	HERV-H LTR-associating 3	protein-coding	0.048387	0.508039	
chunk0112_207_1	chr20	40468659	40469348	+	0	NA	Intergenic	Intergenic	220237	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.007257	0.378261	
chunk0034_71_1	chr11	27177175	27177745	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	41308	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.008772	0.499124	
chunk0180_6_1	chr7	52983285	52983530	+	0	NA	Intergenic	L1MCa|LINE|L1	-52249	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008163	0.333333	
chunk0072_270_1	chr15	96835478	96835708	+	0	NA	Intergenic	Intergenic	52186	NM_001304805									0.008696	0.346320	
chunk0171_27_1	chr6	120314734	120314979	+	0	NA	Intergenic	Intergenic	299677	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.008163	0.276423	
chunk0194_176_1	chr8	85029471	85029670	+	0	NA	Intergenic	Intergenic	-77518	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.005025	0.370000	
chunk0194_167_1	chr8	84853340	84854013	+	0	NA	intron (NM_001100393, intron 5 of 8)	UCON105|Unknown|Unknown	147749	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004458	0.345697	274(CTGAGCAGTCTGTGCT,-,0.00),275(TGAGCAGTCTGTGCTC,+,0.00)
chunk0039_280_1	chr11	102527178	102527775	+	0	NA	intron (NM_002423, intron 3 of 5)	intron (NM_002423, intron 3 of 5)	3271	NM_002423	4316	Hs.2256	NM_002423	ENSG00000137673	MMP7	MMP-7|MPSL1|PUMP-1	matrix metallopeptidase 7	protein-coding	0.010050	0.384615	
chunk0109_345_1	chr2	238801968	238802234	+	0	NA	Intergenic	Intergenic	-45931	NM_001271893	117581	Hs.422585	NM_057179	ENSG00000233608	TWIST2	AMS|BBRSAY|DERMO1|FFDD3|SETLSS|bHLHa39	twist family bHLH transcription factor 2	protein-coding	0.018797	0.441948	
chunk0014_318_1	chr1	181347868	181348192	+	0	NA	Intergenic	Intergenic	111642	NR_046249	100287948	Hs.742594	NR_046249	ENSG00000179452	LINC01699	GM140	long intergenic non-protein coding RNA 1699	ncRNA	0.018519	0.523077	
chunk0022_443_1	chr10	19675607	19675806	+	0	NA	intron (NM_001142308, intron 36 of 39)	intron (NM_001142308, intron 36 of 39)	52844	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.005025	0.300000	
chunk0041_157_1	chr11	125917023	125917223	+	0	NA	exon (NM_013264, exon 9 of 12)	exon (NM_013264, exon 9 of 12)	12757	NM_013264	29118	Hs.420263	NM_013264	ENSG00000109832	DDX25	GRTH	DEAD-box helicase 25	protein-coding	0.025000	0.467662	
chunk0212_418_1	chrX	152806393	152806621	+	0	NA	Intergenic	Intergenic	24250	NM_004344	1069	Hs.82794	NM_004344	ENSG00000147400	CETN2	CALT|CEN2	centrin 2	protein-coding	0.004386	0.410480	
chunk0152_9_1	chr5	56279935	56280293	+	0	NA	Intergenic	Intergenic	-46755	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.005587	0.467967	
chunk0114_202_1	chr21	15377707	15378128	+	0	NA	Intergenic	L2a|LINE|L2	-313112	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.007126	0.407583	
chunk0146_6_1	chr4	154890601	154891204	+	0	NA	Intergenic	LTR16C|LTR|ERVL	109397	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.001658	0.375828	
chunk0007_286_1	chr1	83901561	83901947	+	0	NA	intron (NM_024686, intron 18 of 20)	intron (NM_024686, intron 18 of 20)	-40758	NR_119375	101927587	Hs.621230	NR_119375	ENSG00000233008	LINC01725	-	long intergenic non-protein coding RNA 1725	ncRNA	0.010363	0.377261	
chunk0095_109_1	chr2	15499836	15500282	+	0	NA	intron (NR_052013, intron 11 of 50)	intron (NR_052013, intron 11 of 50)	61289	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.006726	0.308725	
chunk0124_389_1	chr3	59660837	59661251	+	0	NA	Intergenic	Intergenic	-611055	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.012077	0.368675	
chunk0047_168_1	chr12	70072085	70072670	+	0	NA	Intergenic	Intergenic	-170617	NM_014515	4848	Hs.133350	NM_014515	ENSG00000111596	CNOT2	CDC36|HSPC131|NOT2|NOT2H	CCR4-NOT transcription complex subunit 2	protein-coding	0.006838	0.353242	255(TAGGACTTCCTGTTCA,-,0.00),256(AGGACTTCCTGTTCAA,+,0.00)
chunk0197_430_1	chr8	127493695	127494199	+	0	NA	Intergenic	Intergenic	-11808	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.005952	0.366337	
chunk0209_108_1	chrX	40169207	40169567	+	0	NA	intron (NM_001123383, intron 1 of 14)	intron (NM_001123383, intron 1 of 14)	7942	NM_001123383	54880	Hs.659681	NM_017745	ENSG00000183337	BCOR	ANOP2|MAA2|MCOPS2	BCL6 corepressor	protein-coding	0.036111	0.432133	
chunk0191_346_1	chr8	56387421	56388039	+	0	NA	intron (NR_103832, intron 2 of 3)	intron (NR_103832, intron 2 of 3)	2980	NR_103832	442388	Hs.632065	NM_001145251	ENSG00000253542	SDR16C6P	SDR16C6	short chain dehydrogenase/reductase family 16C member 6, pseudogene	pseudo	0.009709	0.434572	408(GAGAACAGCTTGTGCA,-,0.00),409(AGAACAGCTTGTGCAA,+,0.00)
chunk0165_69_1	chr6	31129099	31129565	+	0	NA	intron (NM_014068, intron 2 of 5).4	intron (NM_014068, intron 2 of 5).4	-8857	NM_001264	1041	Hs.310958	NM_001264	ENSG00000204539	CDSN	HTSS|HTSS1|HYPT2|PSS|PSS1|S	corneodesmosin	protein-coding	0.008584	0.447537	
chunk0171_88_1	chr6	121879078	121879426	+	0	NA	Intergenic	Charlie1b|DNA|hAT-Charlie	443675	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.002874	0.338109	
chunk0030_344_1	chr10	118458926	118459584	+	0	NA	Intergenic	Intergenic	102147	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.012158	0.409712	
chunk0073_184_1	chr16	8959902	8960171	+	0	NA	intron (NM_003470, intron 1 of 30)	intron (NM_003470, intron 1 of 30)	3448	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.018587	0.466667	
chunk0036_148_1	chr11	62208370	62208968	+	0	NA	promoter-TSS (NM_002407)	promoter-TSS (NM_002407)	1	NM_002407	4246	Hs.97644	NM_002407	ENSG00000124939	SCGB2A1	LPHC|LPNC|MGB2|UGB3	secretoglobin family 2A member 1	protein-coding	0.013378	0.517529	
chunk0192_412_1	chr8	69151024	69151313	+	0	NA	Intergenic	Tigger10|DNA|TcMar-Tigger	-46978	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.006920	0.324138	
chunk0133_302_1	chr3	172245950	172246627	+	0	NA	intron (NM_022763, intron 4 of 25)	intron (NM_022763, intron 4 of 25)	202168	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.014771	0.407080	
chunk0159_269_1	chr5	142301227	142301518	+	0	NA	Intergenic	Intergenic	16950	NR_131221	100642175	Hs.684549	NR_131221		SPRY4-IT1	SPRIGHTLY	SPRY4 intronic transcript 1	ncRNA	0.003436	0.417808	
chunk0026_337_1	chr10	68446142	68446672	+	0	NA	non-coding (NR_102264, exon 8 of 22)	non-coding (NR_102264, exon 8 of 22)	25566	NM_001080449	1763	Hs.532446	NM_001080449	ENSG00000138346	DNA2	DNA2L|hDNA2	DNA replication helicase/nuclease 2	protein-coding	0.003774	0.395480	263(CAGAACAACCTGTGCA,-,0.00),264(AGAACAACCTGTGCAA,+,0.00)
chunk0090_442_1	chr18	79629577	79630613	+	0	NA	Intergenic	Intergenic	-49706	NM_004715	9150	Hs.465490	NM_004715	ENSG00000060069	CTDP1	CCFDN|FCP1	CTD phosphatase subunit 1	protein-coding	0.032819	0.501446	470(AAGTACAAACTGACCC,-,0.00),471(AGTACAAACTGACCCT,+,0.00)
chunk0033_218_1	chr11	17275274	17275860	+	0	NA	Intergenic	MIRb|SINE|MIR	-1172	NM_005013	4925	Hs.654599	NM_005013	ENSG00000070081	NUCB2	HEL-S-109|NEFA	nucleobindin 2	protein-coding	0.008532	0.407155	207(GGGCACACAGAGTCCA,-,0.00),208(GGCACACAGAGTCCAG,+,0.00)
chunk0193_259_1	chr8	76971991	76972203	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-5247	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004717	0.568075	
chunk0191_275_1	chr8	53723663	53723862	+	0	NA	intron (NM_015941, intron 13 of 13)	intron (NM_015941, intron 13 of 13)	119280	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.025126	0.555000	
chunk0105_353_1	chr2	191638062	191638644	+	0	NA	Intergenic	Intergenic	-39719	NM_001254736	64859	Hs.591610	NM_022837	ENSG00000173559	NABP1	OBFC2A|SOSS-B2|SSB2	nucleic acid binding protein 1	protein-coding	0.008591	0.420240	
chunk0067_401_1	chr15	49255664	49256377	+	0	NA	intron (NM_001001556, intron 5 of 9)	intron (NM_001001556, intron 5 of 9)	86004	NM_002044	2585	Hs.122006	NM_002044	ENSG00000156958	GALK2	GK2	galactokinase 2	protein-coding	0.004208	0.323529	
chunk0110_38_1	chr20	10558483	10558910	+	0	NA	intron (NM_001009608, intron 3 of 7)	intron (NM_001009608, intron 3 of 7)	90999	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.016393	0.399533	
chunk0109_267_1	chr20	8050735	8051352	+	0	NA	Intergenic	Intergenic	-31214	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.011345	0.419094	342(GAGAACATCCTGTCAC,-,0.00)
chunk0028_451_1	chr10	94482668	94483322	+	0	NA	intron (NM_015188, intron 3 of 12)	L1MA2|LINE|L1	-62772	NM_001289068	3070	Hs.463677	NM_018063	ENSG00000119969	HELLS	ICF4|LSH|Nbla10143|PASG|SMARCA6	helicase, lymphoid specific	protein-coding	0.007645	0.416794	
chunk0109_276_1	chr20	8099424	8099951	+	0	NA	Intergenic	Intergenic	-32578	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.000000	0.354167	
chunk0208_43_1	chrX	11421766	11422340	+	0	NA	intron (NR_109776, intron 1 of 14)	L2b|LINE|L2	5732	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.006969	0.420870	533(AGGGACAGCAAGTACA,-,0.00)
chunk0071_127_1	chr15	81621962	81622161	+	0	NA	Intergenic	L1MC3|LINE|L1	-247984	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.010050	0.345000	
chunk0168_273_1	chr6	90368785	90369432	+	0	NA	Intergenic	Intergenic	56366	NR_039671	100616109		NR_039671	ENSG00000266760	MIR4464	mir-4464	microRNA 4464	ncRNA	0.012365	0.415123	329(AGAGACACTGTGTGCT,-,0.00),330(GAGACACTGTGTGCTG,+,0.00)
chunk0092_429_1	chr19	38164950	38165656	+	0	NA	intron (NM_015073, intron 15 of 21)	MLT1L|LTR|ERVL-MaLR	58947	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.014164	0.509194	
chunk0158_135_1	chr5	127311449	127311657	+	0	NA	intron (NM_001308119, intron 2 of 14)	intron (NM_001308119, intron 2 of 14)	20789	NM_001308121	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.004808	0.416268	
chunk0111_418_1	chr20	34791308	34791659	+	0	NA	intron (NM_014071, intron 2 of 14)	intron (NM_014071, intron 2 of 14)	34147	NM_001242539	23054	Hs.368971	NM_014071	ENSG00000198646	NCOA6	AIB3|ASC2|NRC|PRIP|RAP250|TRBP	nuclear receptor coactivator 6	protein-coding	0.005698	0.411932	
chunk0082_319_1	chr17	59289776	59290358	+	0	NA	Intergenic	Intergenic	-41625	NM_001005404	388403	Hs.463613	NM_001005404	ENSG00000175155	YPEL2	FKSG4	yippee like 2	protein-coding	0.010309	0.420240	
chunk0056_322_1	chr13	91096145	91096811	+	0	NA	Intergenic	Charlie2b|DNA|hAT-Charlie	-6861	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.003003	0.262369	
chunk0064_394_1	chr14	99226704	99227223	+	0	NA	intron (NM_022898, intron 2 of 2)	intron (NM_022898, intron 2 of 2)	44750	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.005780	0.398077	
chunk0118_210_1	chr22	31813025	31813806	+	0	NA	intron (NR_110988, intron 20 of 38)	intron (NR_110988, intron 20 of 38)	58553	NM_001136029	9681	Hs.435022	NM_014662	ENSG00000100150	DEPDC5	DEP.5|FFEVF|FFEVF1	DEP domain containing 5	protein-coding	0.008963	0.404092	
chunk0049_279_1	chr12	93865568	93865859	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-127890	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.000000	0.356164	
chunk0059_188_1	chr14	32774151	32774648	+	0	NA	intron (NM_004274, intron 12 of 13)	intron (NM_004274, intron 12 of 13)	-164854	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.006036	0.341365	
chunk0034_335_1	chr11	35458946	35459510	+	0	NA	intron (NM_015430, intron 6 of 11)	intron (NM_015430, intron 6 of 11)	-39165	NM_001252652	6506	Hs.502338	NM_004171	ENSG00000110436	SLC1A2	EAAT2|EIEE41|GLT-1|HBGT	solute carrier family 1 member 2	protein-coding	0.005319	0.415929	244(GGTACACTATGTCTTT,+,0.00),308(GAAACTGCCTGTGCCT,+,0.00)
chunk0154_255_1	chr5	81558259	81558760	+	0	NA	intron (NM_001256733, intron 4 of 15)	L2a|LINE|L2	-164340	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.001996	0.362550	
chunk0196_238_1	chr8	108242444	108243307	+	0	NA	intron (NM_001568, intron 1 of 12)	L1ME3A|LINE|L1	5855	NM_001568	3646	Hs.405590	NM_001568	ENSG00000104408	EIF3E	EIF3-P48|EIF3S6|INT6|eIF3-p46	eukaryotic translation initiation factor 3 subunit E	protein-coding	0.006952	0.353009	
chunk0122_407_1	chr3	38189708	38190147	+	0	NA	intron (NM_005109, intron 2 of 17)	L2c|LINE|L2	24392	NM_005109	9943	Hs.475970	NM_005109	ENSG00000172939	OXSR1	OSR1	oxidative stress responsive kinase 1	protein-coding	0.000000	0.425000	187(AAGCACACAATGTACT,-,0.00),188(AGCACACAATGTACTA,+,0.00)
chunk0162_260_1	chr6	5231683	5232232	+	0	NA	intron (NM_020408, intron 1 of 2)	intron (NM_020408, intron 1 of 2)	28993	NR_104417	57128	Hs.387755	NM_020408	ENSG00000214113	LYRM4	C6orf149|CGI-203|COXPD19|ISD11	LYR motif containing 4	protein-coding	0.007286	0.352727	
chunk0025_88_1	chr10	50510535	50511161	+	0	NA	intron (NM_147156, intron 3 of 10)	L1MC4a|LINE|L1	113129	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.004792	0.330144	394(AAGCACATTATGTATT,-,0.00)
chunk0122_173_1	chr3	32405666	32406150	+	0	NA	intron (NM_181472, intron 1 of 3)	intron (NM_181472, intron 1 of 3)	14237	NM_181472	112616	Hs.440494	NM_138410	ENSG00000153551	CMTM7	CKLFSF7	CKLF like MARVEL transmembrane domain containing 7	protein-coding	0.008264	0.408247	
chunk0126_299_1	chr3	80705085	80705391	+	0	NA	Intergenic	THE1B-int|LTR|ERVL-MaLR	-288630	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.013072	0.540717	
chunk0210_178_1	chrX	79230172	79230664	+	0	NA	Intergenic	L1MA2|LINE|L1	59446	NM_032553	84636	Hs.326713	NM_032553	ENSG00000147138	GPR174	FKSG79|GPCR17|LYPSR3	G protein-coupled receptor 174	protein-coding	0.010163	0.292089	
chunk0156_319_1	chr5	111243506	111243785	+	0	NA	intron (NM_001744, intron 1 of 10)	intron (NM_001744, intron 1 of 10)	19396	NM_001744	814	Hs.438801	NM_001744	ENSG00000152495	CAMK4	CaMK IV|CaMK-GR|CaMKIV|caMK	calcium/calmodulin dependent protein kinase IV	protein-coding	0.007168	0.432143	
chunk0182_322_1	chr7	99013397	99013596	+	0	NA	TTS (NM_001244580)	TTS (NM_001244580)	331	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.045226	0.595000	
chunk0073_55_1	chr16	3305327	3305526	+	0	NA	promoter-TSS (NM_153028)	promoter-TSS (NM_153028)	13	NM_033208	91151	Hs.161287	NM_033208	ENSG00000140993	TIGD7	Sancho	tigger transposable element derived 7	protein-coding	0.075377	0.655000	
chunk0094_446_1	chr2	11508349	11508806	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-25539	NM_014668	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.021882	0.451965	
chunk0056_240_1	chr13	89100225	89100438	+	0	NA	Intergenic	Intergenic	-134960	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.004695	0.341121	
chunk0067_8_1	chr15	39974986	39975187	+	0	NA	intron (NM_001013703, intron 11 of 38)	MIRb|SINE|MIR	40962	NM_001013703	440275	Hs.656673	NM_001013703	ENSG00000128829	EIF2AK4	GCN2|PVOD2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding	0.014925	0.450495	
chunk0176_221_1	chr7	15011489	15012090	+	0	NA	Intergenic	L2a|LINE|L2	-170339	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.008319	0.420266	
chunk0199_411_1	chr9	13586515	13586872	+	0	NA	Intergenic	Intergenic	-155364	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.014006	0.365922	
chunk0190_172_1	chr8	32353664	32354073	+	0	NA	intron (NM_013962, intron 1 of 4)	L1ME1|LINE|L1	-86878	NR_047475	100874286	Hs.147060	NR_047475	ENSG00000254049	NRG1-IT3	-	NRG1 intronic transcript 3	ncRNA	0.009780	0.375610	
chunk0157_178_1	chr5	118529851	118530286	+	0	NA	intron (NR_104610, intron 1 of 9)	intron (NR_104610, intron 1 of 9)	32049	NR_104610	101927280	Hs.543951	NR_104610		LINC02208	HRAT56	long intergenic non-protein coding RNA 2208	ncRNA	0.006897	0.362385	
chunk0110_206_1	chr20	15109502	15109865	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	-87175	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.013774	0.370879	164(GAGTACAAAATGTTCT,-,0.00),165(AGTACAAAATGTTCTG,+,0.00)
chunk0182_240_1	chr7	96937558	96937977	+	0	NA	Intergenic	Intergenic	-68211	NM_005222	1750	Hs.249196	NM_005222	ENSG00000006377	DLX6	-	distal-less homeobox 6	protein-coding	0.004773	0.369048	139(GGGCACTTTGTGTCCC,-,0.00),140(GGCACTTTGTGTCCCA,+,0.00)
chunk0070_260_1	chr15	73734732	73734931	+	0	NA	TTS (NM_001303254)	TTS (NM_001303254)	16644	NM_001039614	388135	Hs.40794	NM_001039614	ENSG00000205363	INSYN1	C15orf59	inhibitory synaptic factor 1	protein-coding	0.015075	0.485000	
chunk0103_165_1	chr2	162596656	162597035	+	0	NA	intron (NM_033272, intron 2 of 15)	L1MA7|LINE|L1	-172091	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.000000	0.336842	
chunk0198_410_1	chr8	142403105	142403546	+	0	NA	promoter-TSS (NM_001291931)	promoter-TSS (NM_001291931)	-76	NM_145003	203062	Hs.370931	NM_145003	ENSG00000171045	TSNARE1	-	t-SNARE domain containing 1	protein-coding	0.145125	0.764706	
chunk0031_259_1	chr10	127244090	127244367	+	0	NA	intron (NM_001290223, intron 27 of 51)	MER53|DNA|hAT	-48070	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.003610	0.330935	
chunk0191_218_1	chr8	52426816	52427355	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	-17206	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.009276	0.457407	
chunk0033_275_1	chr11	19234804	19235334	+	0	NA	intron (NM_001256371, intron 4 of 12)	intron (NM_001256371, intron 4 of 12)	5891	NM_024680	79733	Hs.523526	NM_024680	ENSG00000129173	E2F8	E2F-8	E2F transcription factor 8	protein-coding	0.026415	0.391714	
chunk0073_43_1	chr16	2904906	2905114	+	0	NA	Intergenic	CpG	-6969	NM_020912	84256	Hs.655321	NM_020912	ENSG00000059122	FLYWCH1	-	FLYWCH-type zinc finger 1	protein-coding	0.091346	0.688995	
chunk0185_245_1	chr7	130070143	130070517	+	0	NA	promoter-TSS (NM_014997)	promoter-TSS (NM_014997)	-179	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.056150	0.546667	
chunk0165_347_1	chr6	37966722	37967315	+	0	NA	intron (NM_021943, intron 2 of 5)	L1MC4|LINE|L1	147487	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.001686	0.329966	
chunk0141_296_1	chr4	86942111	86942853	+	0	NA	intron (NM_001166693, intron 1 of 20)	intron (NM_001166693, intron 1 of 20)	7480	NM_001166693	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.004043	0.371467	
chunk0116_438_1	chr21	43287779	43288635	+	0	NA	Intergenic	Intergenic	43832	NR_103713	100126693	Hs.473952	NR_103713		LINC00322	C21orf136|NCRNA00322	long intergenic non-protein coding RNA 322	ncRNA	0.023364	0.494749	
chunk0105_221_1	chr2	188129540	188130220	+	0	NA	intron (NR_126396, intron 2 of 2)	L2c|LINE|L2	157811	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.007353	0.328928	
chunk0101_337_1	chr2	136637311	136637730	+	0	NA	Intergenic	Intergenic	-128042	NM_001316349	80731	Hs.68533	NM_001080427	ENSG00000144229	THSD7B	-	thrombospondin type 1 domain containing 7B	protein-coding	0.004773	0.402381	
chunk0035_60_1	chr11	41513053	41513376	+	0	NA	Intergenic	L1MC4|LINE|L1	-53578	NM_001258419	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.283951	
chunk0122_162_1	chr3	32240140	32240655	+	0	NA	intron (NM_178868, intron 1 of 3)	intron (NM_178868, intron 1 of 3)	1718	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.015534	0.463178	
chunk0014_246_1	chr1	180043836	180044538	+	0	NA	intron (NM_014810, intron 21 of 37)	intron (NM_014810, intron 21 of 37)	89414	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.000000	0.321479	436(TAGAACAGTGTGTGCC,-,0.00),437(AGAACAGTGTGTGCCC,+,0.00)
chunk0123_341_1	chr3	47772759	47773148	+	0	NA	intron (NM_003074, intron 1 of 27)	intron (NM_003074, intron 1 of 27)	8962	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.012853	0.400000	
chunk0189_253_1	chr8	25141319	25141748	+	0	NA	Intergenic	Intergenic	-43239	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.011655	0.481395	
chunk0207_41_1	chrX	6001951	6002399	+	0	NA	intron (NM_181332, intron 3 of 5)	intron (NM_181332, intron 3 of 5)	225028	NM_001282146	57502	Hs.21107	NM_020742	ENSG00000146938	NLGN4X	ASPGX2|AUTSX2|HLNX|HNL4X|NLGN4	neuroligin 4 X-linked	protein-coding	0.006696	0.432071	219(TAGAACTCCTTGTCCC,-,0.00),220(AGAACTCCTTGTCCCT,+,0.00)
chunk0063_392_1	chr14	87093664	87094046	+	0	NA	Intergenic	Intergenic	188077	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.010471	0.375979	
chunk0014_375_1	chr1	182661316	182662213	+	0	NA	intron (NM_001102450, intron 5 of 6)	intron (NM_001102450, intron 5 of 6)	11168	NM_001102450	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.001115	0.407572	298(CAGGACTTAATGTTCC,-,0.00),299(AGGACTTAATGTTCCA,+,0.00)
chunk0211_212_1	chrX	118277430	118278028	+	0	NA	Intergenic	L1ME4b|LINE|L1	-68344	NM_001184965	54521	Hs.98510	NM_019045	ENSG00000131725	WDR44	RAB11BP|RPH11|SYM-4	WD repeat domain 44	protein-coding	0.001672	0.347245	
chunk0093_435_1	chr19	58305436	58306151	+	0	NA	Intergenic	LTR3|LTR|ERVK	-21226	NM_181846	342945	Hs.388162	NM_181846	ENSG00000182318	ZSCAN22	HKR2|ZNF50	zinc finger and SCAN domain containing 22	protein-coding	0.041958	0.557263	
chunk0084_309_1	chr17	80169940	80170220	+	0	NA	promoter-TSS (NR_047566)	promoter-TSS (NR_047566)	88	NR_047566	79092	Hs.675480	NM_024110	ENSG00000141527	CARD14	BIMP2|CARMA2|PRP|PSORS2|PSS1	caspase recruitment domain family member 14	protein-coding	0.039286	0.622776	
chunk0045_133_1	chr12	46403019	46403580	+	0	NA	intron (NR_125381, intron 2 of 2)	intron (NR_125381, intron 2 of 2)	19192	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.005348	0.384342	
chunk0175_317_1	chr6	166673975	166674281	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	-46890	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.009804	0.390879	
chunk0011_145_1	chr1	147437125	147437423	+	0	NA	intron (NR_038423, intron 3 of 3)	LTR51|LTR|ERV1	80601	NR_038423	100289211	Hs.323484	NR_038423	ENSG00000278811	LINC00624	-	long intergenic non-protein coding RNA 624	ncRNA	0.010067	0.411371	
chunk0033_346_1	chr11	22923082	22924092	+	0	NA	Intergenic	Intergenic	-63161	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.001980	0.381800	
chunk0047_92_1	chr12	68612709	68613064	+	0	NA	intron (NM_001251917, intron 1 of 5)	intron (NM_001251917, intron 1 of 5)	2047	NM_015646	5908	Hs.369920	NM_015646	ENSG00000127314	RAP1B	K-REV|RAL1B	RAP1B, member of RAS oncogene family	protein-coding	0.011268	0.342697	
chunk0070_186_1	chr15	71868160	71868359	+	0	NA	intron (NM_006901, intron 32 of 41)	MLT1E2|LTR|ERVL-MaLR	57711	NM_016346	10002	Hs.187354	NM_014249	ENSG00000278570	NR2E3	ESCS|PNR|RNR|RP37|rd7	nuclear receptor subfamily 2 group E member 3	protein-coding	0.005025	0.455000	
chunk0128_30_1	chr3	104266066	104266601	+	0	NA	Intergenic	L1MA4A|LINE|L1	-742217	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.001869	0.354478	
chunk0084_228_1	chr17	78651345	78651695	+	0	NA	Intergenic	L1ME3G|LINE|L1	-19463	NR_110848	101928710	Hs.464224	NR_110848	ENSG00000267123	SCAT1	LINC02081|XLOC_012582	S-phase cancer associated transcript 1	ncRNA	0.005714	0.321937	
chunk0185_367_1	chr7	132881153	132881624	+	0	NA	intron (NM_017812, intron 5 of 7)	intron (NM_017812, intron 5 of 7)	153527	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.006369	0.351695	200(CAGAACTAAATGTACT,-,0.00),201(AGAACTAAATGTACTT,+,0.00)
chunk0190_406_1	chr8	40378331	40378715	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	225055	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.010417	0.438961	
chunk0099_74_1	chr2	85249344	85249662	+	0	NA	intron (NM_031283, intron 3 of 11)	intron (NM_031283, intron 3 of 11)	78793	NM_001206844	10618	Hs.593382	NM_006464	ENSG00000152291	TGOLN2	TGN38|TGN46|TGN48|TGN51|TTGN2	trans-golgi network protein 2	protein-coding	0.006289	0.485893	
chunk0144_195_1	chr4	133682209	133682408	+	0	NA	Intergenic	L1M2|LINE|L1	519440	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005025	0.500000	
chunk0185_376_1	chr7	133059693	133060247	+	0	NA	intron (NM_017812, intron 2 of 7)	L2b|LINE|L2	22098	NM_017812	54927	Hs.655010	NM_017812	ENSG00000106554	CHCHD3	MICOS19|MINOS3|Mic19|PPP1R22	coiled-coil-helix-coiled-coil-helix domain containing 3	protein-coding	0.010830	0.414414	528(AAACACACACAGTTCT,-,0.00)
chunk0007_160_1	chr1	79875521	79875798	+	0	NA	Intergenic	L1PA15|LINE|L1	-660096	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.014440	0.604317	
chunk0058_104_1	chr14	21724250	21724862	+	0	NA	Intergenic	L1MA8|LINE|L1	59473	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.009804	0.414356	
chunk0107_451_1	chr2	225632059	225632508	+	0	NA	intron (NM_020864, intron 5 of 5)	intron (NM_020864, intron 5 of 5)	231397	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.006682	0.435556	
chunk0039_403_1	chr11	107457754	107457953	+	0	NA	promoter-TSS (NM_152434)	promoter-TSS (NM_152434)	-7	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.075377	0.515000	
chunk0039_166_1	chr11	99350184	99350553	+	0	NA	intron (NM_014361, intron 2 of 24)	L1ME2z|LINE|L1	-205777	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.008130	0.305405	
chunk0010_320_1	chr1	118110761	118111272	+	0	NA	intron (NM_206996, intron 4 of 48)	MIRb|SINE|MIR	74209	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.000000	0.371094	
chunk0039_177_1	chr11	100273260	100273595	+	0	NA	intron (NM_014361, intron 18 of 24)	L1PA13|LINE|L1	-414249	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.023881	0.592262	135(TAGTACAGTCTGCTCC,-,0.00),136(AGTACAGTCTGCTCCC,+,0.00)
chunk0004_437_1	chr1	53092005	53092333	+	0	NA	intron (NM_001287595, intron 7 of 10)	intron (NM_001287595, intron 7 of 10)	29956	NM_001199081	127435	Hs.586141	NM_153703	ENSG00000174348	PODN	PCAN|SLRR5A	podocan	protein-coding	0.030488	0.613982	
chunk0116_361_1	chr21	41605703	41605902	+	0	NA	Intergenic	Intergenic	-73500	NR_024367	54090	Hs.570442	NR_024367		LINC00111	C21orf21|NCRNA00111	long intergenic non-protein coding RNA 111	ncRNA	0.035176	0.620000	
chunk0136_415_1	chr3	197401956	197402333	+	0	NA	Intergenic	Intergenic	-102872	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.015915	0.391534	
chunk0117_230_1	chr22	22824232	22824496	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	1588	NR_030755	723778		NR_030755	ENSG00000284049	MIR650	MIRN650|hsa-mir-650	microRNA 650	ncRNA	0.007576	0.309434	
chunk0176_353_1	chr7	17881861	17882469	+	0	NA	intron (NM_015132, intron 5 of 25)	intron (NM_015132, intron 5 of 25)	58343	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.006579	0.348112	
chunk0037_82_1	chr11	71433068	71433467	+	0	NA	Intergenic	Intergenic	-9913	NR_038862	399923	Hs.128191	NM_001001680	ENSG00000172900	FLJ42102	-	uncharacterized LOC399923	ncRNA	0.010025	0.565000	152(GGGAACAGAATGCTCT,-,0.00),153(GGAACAGAATGCTCTC,+,0.00),215(TGGATCACCCTGTTCT,-,0.00),216(GGATCACCCTGTTCTC,+,0.00)
chunk0188_242_1	chr8	13637301	13637888	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	70751	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.006814	0.372449	
chunk0112_212_1	chr20	40476500	40476699	+	0	NA	Intergenic	Intergenic	212641	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.010050	0.405000	93(CAGAACATATTGTCCC,-,0.00),94(AGAACATATTGTCCCA,+,0.00)
chunk0038_281_1	chr11	89728328	89728657	+	0	NA	Intergenic	L1PA15-16|LINE|L1	18193	NM_001271942	390231	Hs.723112	NM_001146162	ENSG00000214414	TRIM77	TRIM77P	tripartite motif containing 77	protein-coding	0.006079	0.506061	162(GAGTACACAATGTTCC,-,0.00),163(AGTACACAATGTTCCC,+,0.00)
chunk0146_323_1	chr4	165626708	165627326	+	0	NA	Intergenic	Intergenic	-57622	NR_121676	101928151	Hs.639858	NR_121676	ENSG00000249500	LINC01179	-	long intergenic non-protein coding RNA 1179	ncRNA	0.008091	0.392569	380(TGTACAGGCTGTTTTC,+,0.00)
chunk0001_299_1	chr1	9070436	9070837	+	0	NA	promoter-TSS (NM_001135585)	promoter-TSS (NM_001135585)	-808	NM_001135585	6518	Hs.530003	NM_003039	ENSG00000142583	SLC2A5	GLUT-5|GLUT5	solute carrier family 2 member 5	protein-coding	0.017456	0.517413	
chunk0012_308_1	chr1	162240605	162240817	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	83604	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.009434	0.375587	
chunk0010_242_1	chr1	116454832	116455409	+	0	NA	non-coding (NR_125973, exon 3 of 4)	non-coding (NR_125973, exon 3 of 4)	23706	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.010399	0.541522	
chunk0137_187_1	chr4	17740864	17741459	+	0	NA	intron (NM_015688, intron 1 of 17)	L2a|LINE|L2	40351	NM_015688	27146	Hs.744951	NM_015688	ENSG00000047662	FAM184B	-	family with sequence similarity 184 member B	protein-coding	0.015126	0.426174	
chunk0089_192_1	chr18	59957363	59958117	+	0	NA	Intergenic	L1MB4|LINE|L1	57780	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.007958	0.362914	
chunk0210_115_1	chrX	72381707	72382413	+	0	NA	intron (NR_051952, intron 8 of 9)	intron (NR_051952, intron 8 of 9)	-74873	NM_001144886	4435	Hs.40403	NM_004143	ENSG00000125931	CITED1	MSG1	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1	protein-coding	0.004249	0.445545	
chunk0128_286_1	chr3	110925913	110926163	+	0	NA	Intergenic	Intergenic	143921	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.016000	0.486056	
chunk0021_317_1	chr1	245242950	245243430	+	0	NA	intron (NM_018012, intron 2 of 14)	L1ME3Cz|LINE|L1	88205	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.004167	0.397089	
chunk0206_443_1	chr9	128016818	128017490	+	0	NA	Intergenic	L1MC3|LINE|L1	-36621	NM_001035254	399665	Hs.535972	NM_203305	ENSG00000167106	FAM102A	C9orf132|EEIG1|SYM-3A|bA203J24.7	family with sequence similarity 102 member A	protein-coding	0.007440	0.398217	
chunk0051_297_1	chr12	118559976	118560341	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	183605	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.021918	0.491803	
chunk0012_229_1	chr1	160320059	160320344	+	0	NA	intron (NM_001098398, intron 8 of 32)	L1MA4|LINE|L1	2936	NR_002190	474338	Hs.621179	NR_002190		SUMO1P3	-	SUMO1 pseudogene 3	pseudo	0.010526	0.339161	
chunk0136_165_1	chr4	6172280	6172537	+	0	NA	intron (NM_001099433, intron 1 of 20)	intron (NM_001099433, intron 1 of 20)	22211	NM_001306133	152789	Hs.479066	NM_144720	ENSG00000152969	JAKMIP1	Gababrbp|JAMIP1|MARLIN1	janus kinase and microtubule interacting protein 1	protein-coding	0.011673	0.558140	
chunk0035_43_1	chr11	41041083	41041316	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	418437	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.004292	0.358974	
chunk0129_411_1	chr3	126956464	126956708	+	0	NA	intron (NM_032343, intron 6 of 7)	intron (NM_032343, intron 6 of 7)	-32008	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.028689	0.522449	
chunk0069_33_1	chr15	60488568	60489097	+	0	NA	3' UTR (NM_134262, exon 10 of 10)	3' UTR (NM_134262, exon 10 of 10)	9654	NR_120340	101928784	Hs.655155	NR_120339	ENSG00000245534	RORA-AS1	-	RORA antisense RNA 1	ncRNA	0.007561	0.349057	
chunk0075_275_1	chr16	53817893	53818303	+	0	NA	intron (NM_001080432, intron 2 of 8)	intron (NM_001080432, intron 2 of 8)	114135	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.002439	0.291971	
chunk0007_410_1	chr1	85816231	85816779	+	0	NA	intron (NM_152890, intron 47 of 59)	intron (NM_152890, intron 47 of 59)	-108072	NM_017953	54680	Hs.5111	NM_017953	ENSG00000117174	ZNHIT6	BCD1|C1orf181|NY-BR-75	zinc finger HIT-type containing 6	protein-coding	0.001825	0.329690	
chunk0180_323_1	chr7	72152706	72153044	+	0	NA	intron (NM_001017440, intron 2 of 5)	intron (NM_001017440, intron 2 of 5)	184348	NM_001017440	83698	Hs.592750	NM_031468	ENSG00000183166	CALN1	CABP8	calneuron 1	protein-coding	0.005917	0.445428	189(AGGCACTGTTTGTCCC,-,0.00),190(GGCACTGTTTGTCCCC,+,0.00)
chunk0017_296_1	chr1	210558303	210558520	+	0	NA	intron (NM_001170580, intron 9 of 11)	intron (NM_001170580, intron 9 of 11)	229115	NM_001170580	55733	Hs.58650	NM_018194	ENSG00000054392	HHAT	MART2|SKI1|Skn	hedgehog acyltransferase	protein-coding	0.004608	0.454128	74(AGGGGCACCCTGTGCT,-,0.00),75(GGGGCACCCTGTGCTT,+,0.00)
chunk0114_217_1	chr21	15639238	15639437	+	0	NA	Intergenic	Intergenic	-90688	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.010050	0.500000	
chunk0073_60_1	chr16	3459944	3460149	+	0	NA	intron (NM_001083600, intron 1 of 6)	intron (NM_001083600, intron 1 of 6)	2054	NM_024845	79903	Hs.513296	NM_024845	ENSG00000122390	NAA60	HAT4|NAT15|NatF|hNaa60	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding	0.019512	0.485437	
chunk0032_70_1	chr11	2375685	2376362	+	0	NA	promoter-TSS (NM_001297649)	promoter-TSS (NM_001297649)	-154	NM_001297649	975	Hs.54457	NM_004356	ENSG00000110651	CD81	CVID6|S5.7|TAPA1|TSPAN28	CD81 molecule	protein-coding	0.019202	0.491150	5(AAGGACACAGTGTGCA,-,0.00),6(AGGACACAGTGTGCAT,+,0.00)
chunk0195_127_1	chr8	94959784	94960373	+	0	NA	Intergenic	Intergenic	-10691	NM_001135733	94241	Hs.492261	NM_033285	ENSG00000164938	TP53INP1	SIP|TP53DINP1|TP53INP1A|TP53INP1B|Teap|p53DINP1	tumor protein p53 inducible nuclear protein 1	protein-coding	0.015280	0.423729	
chunk0039_416_1	chr11	107689601	107689814	+	0	NA	Intergenic	Intergenic	22354	NM_003063	6588	Hs.334629	NM_003063	ENSG00000170290	SLN	-	sarcolipin	protein-coding	0.009390	0.443925	
chunk0120_172_1	chr3	5890786	5891100	+	0	NA	Intergenic	Intergenic	-640688	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.006369	0.384127	
chunk0095_27_1	chr2	12781702	12782396	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	44682	NR_036072	100422986		NR_036072	ENSG00000264370	MIR3125	mir-3125	microRNA 3125	ncRNA	0.004323	0.385612	
chunk0027_124_1	chr10	74214484	74214732	+	0	NA	intron (NM_001202449, intron 2 of 9)	intron (NM_001202449, intron 2 of 9)	38119	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.004032	0.365462	114(TTCACAGTCTGTTCCT,+,0.00)
chunk0210_465_1	chrX	107536305	107536946	+	0	NA	intron (NM_032428, intron 5 of 15)	L1MD2|LINE|L1	9196	NR_046750	100874122	Hs.600967	NR_046750	ENSG00000227610	FRMPD3-AS1	-	FRMPD3 antisense RNA 1	ncRNA	0.010920	0.378505	
chunk0134_441_1	chr3	183689013	183689300	+	0	NA	Intergenic	L1M4|LINE|L1	-8662	NM_018023	55689	Hs.632575	NM_018023	ENSG00000163872	YEATS2	-	YEATS domain containing 2	protein-coding	0.003484	0.343750	
chunk0179_93_1	chr7	44622275	44622690	+	0	NA	intron (NM_001003941, intron 1 of 8)	intron (NM_001003941, intron 1 of 8)	15960	NM_001003941	4967	Hs.488181	NM_002541	ENSG00000105953	OGDH	AKGDH|E1k|OGDC	oxoglutarate dehydrogenase	protein-coding	0.002410	0.355769	
chunk0009_368_1	chr1	109869687	109870269	+	0	NA	Intergenic	Intergenic	-40633	NM_172210	1435	Hs.173894	NM_000757	ENSG00000184371	CSF1	CSF-1|MCSF	colony stimulating factor 1	protein-coding	0.012027	0.409949	195(AGGGACTGGCAGTTCC,-,0.00),196(GGGACTGGCAGTTCCA,+,0.00)
chunk0203_263_1	chr9	87816060	87816440	+	0	NA	Intergenic	L1MA6|LINE|L1	-28495	NR_033405	1518	Hs.726015	NR_033405		CTSLP8	CTSL1P8	cathepsin L pseudogene 8	pseudo	0.005263	0.370079	
chunk0002_432_1	chr1	28073813	28074209	+	0	NA	intron (NM_001282560, intron 1 of 16)	intron (NM_001282560, intron 1 of 16)	14626	NR_104214	2140	Hs.185774	NM_001990	ENSG00000158161	EYA3	-	EYA transcriptional coactivator and phosphatase 3	protein-coding	0.002525	0.267003	
chunk0142_85_1	chr4	93907561	93908137	+	0	NA	Intergenic	Intergenic	78922	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.003472	0.285962	196(AAGCACTCAATGTGCT,-,0.00),197(AGCACTCAATGTGCTA,+,0.00)
chunk0100_39_1	chr2	105610946	105611158	+	0	NA	promoter-TSS (NR_038891)	promoter-TSS (NR_038891)	-493	NR_038891	285000	Hs.737917	NR_038891		LOC285000	-	uncharacterized LOC285000	ncRNA	0.023585	0.464789	
chunk0147_145_1	chr4	174925682	174926067	+	0	NA	intron (NM_014269, intron 2 of 4)	intron (NM_014269, intron 2 of 4)	7516	NM_001130704	11086	Hs.126838	NM_014269	ENSG00000168594	ADAM29	CT73|svph1	ADAM metallopeptidase domain 29	protein-coding	0.005195	0.347150	
chunk0060_82_1	chr14	42168576	42169077	+	0	NA	Intergenic	L1PA7|LINE|L1	561265	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.003992	0.342629	
chunk0111_92_1	chr20	23544874	23545189	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	23718	NM_080610	128821	Hs.121554	NM_080610	ENSG00000101435	CST9L	CTES7B|bA218C14.1	cystatin 9 like	protein-coding	0.003175	0.512658	
chunk0126_238_1	chr3	79247734	79247933	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-163894	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.000000	0.410000	
chunk0075_346_1	chr16	55389501	55389826	+	0	NA	Intergenic	Intergenic	65104	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.012308	0.512270	
chunk0192_407_1	chr8	69025588	69026713	+	0	NA	intron (NR_039986, intron 2 of 4)	intron (NR_039986, intron 2 of 4)	78040	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.002667	0.330373	
chunk0192_173_1	chr8	62728976	62729533	+	0	NA	intron (NR_130764, intron 3 of 6)	L1MC|LINE|L1	-248607	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.010772	0.351254	
chunk0095_88_1	chr2	15079698	15080083	+	0	NA	Intergenic	L2b|LINE|L2	444799	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.012987	0.422280	
chunk0123_404_1	chr3	48966168	48966682	+	0	NA	intron (NM_006321, intron 5 of 15)	intron (NM_006321, intron 5 of 15)	-23483	NM_177938	54681	Hs.654944	NM_017732	ENSG00000178467	P4HTM	EGLN4|HIFPH4|P4H-TM|PH-4|PH4|PHD4	prolyl 4-hydroxylase, transmembrane	protein-coding	0.005837	0.388350	
chunk0096_337_1	chr2	35461233	35462332	+	0	NA	Intergenic	Intergenic	-9623	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.003640	0.324545	
chunk0123_259_1	chr3	45942083	45942496	+	0	NA	intron (NM_024513, intron 14 of 17)	MIRb|SINE|MIR	-1192	NM_006564	10663	Hs.34526	NM_006564	ENSG00000172215	CXCR6	BONZO|CD186|STRL33|TYMSTR	C-X-C motif chemokine receptor 6	protein-coding	0.007264	0.509662	
chunk0020_442_1	chr1	242108193	242108424	+	0	NA	intron (NM_001195812, intron 6 of 8)	intron (NM_001195812, intron 6 of 8)	-109225	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.021645	0.525862	
chunk0122_412_1	chr3	38354739	38355475	+	0	NA	intron (NM_005108, intron 2 of 18)	MLT1H|LTR|ERVL-MaLR	8347	NM_005108	9942	Hs.659985	NM_005108	ENSG00000093217	XYLB	-	xylulokinase	protein-coding	0.006793	0.439620	
chunk0132_95_1	chr3	155628775	155629249	+	0	NA	intron (NM_014996, intron 1 of 21)	MIRb|SINE|MIR	47304	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.006329	0.345263	
chunk0198_160_1	chr8	133143893	133144315	+	0	NA	Intergenic	Intergenic	-41038	NM_001282965	6503	Hs.75367	NM_006748	ENSG00000155926	SLA	SLA1|SLAP	Src like adaptor	protein-coding	0.004739	0.423168	
chunk0048_438_1	chr12	88541659	88541927	+	0	NA	intron (NM_000899, intron 2 of 9)	intron (NM_000899, intron 2 of 9)	38680	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.011194	0.356877	132(CAGTACAAAGTGTTCA,-,0.00),133(AGTACAAAGTGTTCAA,+,0.00)
chunk0041_230_1	chr11	128400672	128400871	+	0	NA	Intergenic	Intergenic	121539	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.010050	0.295000	
chunk0006_218_1	chr1	68327418	68327896	+	0	NA	Intergenic	Intergenic	-95056	NM_024911	79971	Hs.647659	NM_024911	ENSG00000116729	WLS	C1orf139|EVI|GPR177|MRP|mig-14	Wnt ligand secretion mediator	protein-coding	0.006276	0.382046	241(TGGAACAATATGTTCT,-,0.00),242(GGAACAATATGTTCTT,+,0.00)
chunk0078_272_1	chr17	7889115	7889466	+	0	NA	intron (NM_001005273, intron 1 of 39)	intron (NM_001005273, intron 1 of 39)	439	NM_001005273	1107	Hs.25601	NM_005852	ENSG00000170004	CHD3	Mi-2a|Mi2-ALPHA|SNIBCPS|ZFH	chromodomain helicase DNA binding protein 3	protein-coding	0.005698	0.607955	
chunk0083_13_1	chr17	62860907	62861112	+	0	NA	Intergenic	Intergenic	-52628	NM_001288779	162333	Hs.665663	NM_152598	ENSG00000173838	MARCH10	MARCH-X|RNF190	membrane associated ring-CH-type finger 10	protein-coding	0.004878	0.461165	
chunk0098_451_1	chr2	82330016	82330303	+	0	NA	Intergenic	Intergenic	-526644	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.003484	0.375000	
chunk0200_336_1	chr9	24210603	24210971	+	0	NA	Intergenic	MER54A|LTR|ERVL	334889	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.002717	0.447154	
chunk0003_148_1	chr1	33010867	33011620	+	0	NA	TTS (NM_001625)	TTS (NM_001625)	25668	NM_001625	204	Hs.470907	NM_001625	ENSG00000004455	AK2	ADK2	adenylate kinase 2	protein-coding	0.005312	0.466844	
chunk0181_382_1	chr7	89376147	89376764	+	0	NA	Intergenic	L1PB2|LINE|L1	-580738	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.003241	0.349515	
chunk0106_302_1	chr2	204672322	204672664	+	0	NA	intron (NM_205863, intron 1 of 21)	MER5C1|DNA|hAT-Charlie	126700	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.000000	0.314869	
chunk0157_32_1	chr5	115648622	115649032	+	0	NA	intron (NR_104674, intron 3 of 4)	LTR40c|LTR|ERVL	-22648	NM_181836	51014	Hs.642817	NM_181836	ENSG00000134970	TMED7	CGI-109|p24g3|p24gamma3|p27	transmembrane p24 trafficking protein 7	protein-coding	0.002439	0.416058	212(GAGGACTGGCTGTTCC,-,0.00),213(AGGACTGGCTGTTCCC,+,0.00)
chunk0009_431_1	chr1	111150768	111151445	+	0	NA	intron (NM_001007794, intron 2 of 8)	MER4E1|LTR|ERV1	-10890	NM_178454	128338	Hs.485606	NM_178454	ENSG00000156171	DRAM2	CORD21|PRO180|TMEM77|WWFQ154	DNA damage regulated autophagy modulator 2	protein-coding	0.017725	0.429204	
chunk0092_443_1	chr19	38683716	38684384	+	0	NA	intron (NM_004924, intron 1 of 20)	intron (NM_004924, intron 1 of 20)	36423	NM_004924	81	Hs.270291	NM_004924	ENSG00000130402	ACTN4	ACTININ-4|FSGS|FSGS1	actinin alpha 4	protein-coding	0.008982	0.512706	
chunk0124_167_1	chr3	55268589	55268788	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	212710	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.005025	0.355000	
chunk0124_176_1	chr3	55397322	55397600	+	0	NA	Intergenic	L2a|LINE|L2	83937	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.003597	0.455197	
chunk0190_413_1	chr8	40703819	40704188	+	0	NA	intron (NM_001135731, intron 3 of 5)	intron (NM_001135731, intron 3 of 5)	193821	NM_001135731	79698	Hs.591850	NM_024645	ENSG00000165061	ZMAT4	-	zinc finger matrin-type 4	protein-coding	0.008130	0.402703	
chunk0083_72_1	chr17	64107790	64108169	+	0	NA	intron (NM_001433, intron 1 of 21)	intron (NM_001433, intron 1 of 21)	22163	NM_001433	2081	Hs.133982	NM_001433	ENSG00000178607	ERN1	IRE1|IRE1P|IRE1a|hIRE1p	endoplasmic reticulum to nucleus signaling 1	protein-coding	0.007916	0.405263	
chunk0078_334_1	chr17	8707489	8707765	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	37209	NM_144681	146849	Hs.121438	NM_144681	ENSG00000161973	CCDC42	CCDC42A	coiled-coil domain containing 42	protein-coding	0.018116	0.447653	
chunk0019_250_1	chr1	227606143	227606552	+	0	NA	intron (NM_178549, intron 2 of 3)	LTR5B|LTR|ERVK	42828	NM_178549	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.024450	0.478049	184(GGGAACGTACTGTGCC,-,0.00),185(GGAACGTACTGTGCCC,+,0.00)
chunk0212_92_1	chrY	12729613	12730192	+	0	NA	intron (NM_004654, intron 7 of 45)	L1M4c|LINE|L1	28671	NM_004654	8287	Hs.598540	NM_004654	ENSG00000114374	USP9Y	DFFRY|SPGFY2	ubiquitin specific peptidase 9 Y-linked	protein-coding	0.005181	0.436207	435(AGGCTCAAGCTGTTCT,-,0.00),436(GGCTCAAGCTGTTCTC,+,0.00)
chunk0210_32_1	chrX	67646847	67647600	+	0	NA	intron (NM_001011645, intron 2 of 7)	intron (NM_001011645, intron 2 of 7)	78382	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.000000	0.377984	
chunk0034_171_1	chr11	31012645	31013166	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-20219	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.003839	0.289272	
chunk0094_56_1	chr2	3226532	3226731	+	0	NA	intron (NM_003310, intron 4 of 8)	L1MA9|LINE|L1	-100605	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.010050	0.395000	
chunk0047_407_1	chr12	75863278	75863630	+	0	NA	Intergenic	LTR90A|LTR|LTR	168322	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.011364	0.348442	
chunk0047_173_1	chr12	70549623	70550097	+	0	NA	intron (NM_001109754, intron 21 of 33)	intron (NM_001109754, intron 21 of 33)	59984	NM_001206971	5787	Hs.201030	NM_002837	ENSG00000127329	PTPRB	HPTP-BETA|HPTPB|PTPB|R-PTP-BETA|VEPTP	protein tyrosine phosphatase receptor type B	protein-coding	0.010549	0.423158	395(TGGACTGTGAGTTCTT,+,0.00)
chunk0062_11_1	chr14	66246602	66247047	+	0	NA	Intergenic	Intergenic	-239547	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.000000	0.352018	
chunk0181_440_1	chr7	90618665	90618864	+	0	NA	intron (NM_001287135, intron 2 of 14)	intron (NM_001287135, intron 2 of 14)	22402	NM_001287135	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.000000	0.345000	
chunk0188_248_1	chr8	14334846	14335261	+	0	NA	intron (NM_139167, intron 2 of 7)	intron (NM_139167, intron 2 of 7)	518457	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.007229	0.377404	
chunk0092_145_1	chr19	28289482	28290057	+	0	NA	Intergenic	Intergenic	437925	NR_110759	100420587	Hs.569956	NR_110759	ENSG00000283403	LOC100420587	-	SHC binding and spindle associated 1 pseudogene	pseudo	0.013913	0.486111	
chunk0187_336_1	chr7	156753580	156753854	+	0	NA	intron (NM_022458, intron 9 of 16)	L2a|LINE|L2	109916	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.018248	0.541818	102(ATGGACACAATGTACC,-,0.00),103(TGGACACAATGTACCC,+,0.00)
chunk0160_14_1	chr5	149016957	149017434	+	0	NA	intron (NM_024577, intron 12 of 16)	L2a|LINE|L2	45214	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.008386	0.393305	
chunk0053_126_1	chr13	29782137	29782377	+	0	NA	intron (NM_007106, intron 1 of 4)	intron (NM_007106, intron 1 of 4)	68426	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.000000	0.352697	
chunk0128_194_1	chr3	107599100	107599391	+	0	NA	intron (NM_001276286, intron 2 of 16)	intron (NM_001276286, intron 2 of 16)	76309	NM_001142568	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.010309	0.452055	142(CAGTACTGTCTGTGCT,-,0.00),143(AGTACTGTCTGTGCTT,+,0.00)
chunk0080_226_1	chr17	29789395	29789606	+	0	NA	intron (NM_001282129, intron 3 of 15)	MLT1A-int|LTR|ERVL-MaLR	-28068	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.009479	0.466981	
chunk0117_393_1	chr21	45421401	45422116	+	0	NA	intron (NR_028082, intron 2 of 2)	intron (NR_028082, intron 2 of 2)	3282	NR_028082	378832	Hs.517353	NM_199175	ENSG00000183535	COL18A1-AS1	C21orf123|NCRNA00175|PRED80	COL18A1 antisense RNA 1	ncRNA	0.029371	0.587989	
chunk0034_214_1	chr11	32829543	32830187	+	0	NA	promoter-TSS (NM_024081)	promoter-TSS (NM_024081)	-70	NM_024081	79056	Hs.471695	NM_024081	ENSG00000135378	PRRG4	PRGP4|TMG4	proline rich and Gla domain 4	protein-coding	0.099379	0.706977	
chunk0018_16_1	chr1	215279698	215280111	+	0	NA	Intergenic	Intergenic	196687	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.007264	0.442029	
chunk0165_213_1	chr6	35034971	35035360	+	0	NA	intron (NM_015245, intron 11 of 23)	L2b|LINE|L2	106245	NM_001093728									0.020566	0.530769	
chunk0020_380_1	chr1	239883186	239884125	+	0	NA	intron (NM_000740, intron 4 of 4)	MIR|SINE|MIR	16217	NR_046582	100873984	Hs.199475	NR_046582	ENSG00000234601	CHRM3-AS1	-	CHRM3 antisense RNA 1	ncRNA	0.005325	0.372340	610(AAGAACAAAATGTCTC,-,0.00),611(AGAACAAAATGTCTCC,+,0.00)
chunk0074_188_1	chr16	24783467	24784090	+	0	NA	intron (NM_014494, intron 5 of 24)	intron (NM_014494, intron 5 of 24)	54050	NM_014494	27327	Hs.655057	NM_014494	ENSG00000090905	TNRC6A	CAGH26|FAME6|GW1|GW182|TNRC6	trinucleotide repeat containing adaptor 6A	protein-coding	0.014446	0.371795	
chunk0118_226_1	chr22	32153082	32153600	+	0	NA	intron (NM_001010859, intron 2 of 8)	L1MC|LINE|L1	5915	NM_001010859	150297	Hs.426551	NM_001010859	ENSG00000205856	C22orf42	dJ90G24.6	chromosome 22 open reading frame 42	protein-coding	0.000000	0.300578	
chunk0033_98_1	chr11	14235082	14235590	+	0	NA	intron (NM_006108, intron 6 of 15)	L2a|LINE|L2	123149	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.017717	0.532417	
chunk0072_14_1	chr16	443436	443635	+	0	NA	intron (NM_014700, intron 1 of 13)	intron (NM_014700, intron 1 of 13)	17867	NM_014700	9727	Hs.531642	NM_014700	ENSG00000090565	RAB11FIP3	CART1|FIP3-Rab11|Rab11-FIP3	RAB11 family interacting protein 3	protein-coding	0.025126	0.435000	
chunk0180_16_1	chr7	53408257	53408779	+	0	NA	Intergenic	L1M5|LINE|L1	372862	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.001916	0.256214	
chunk0061_151_1	chr14	59633849	59634261	+	0	NA	intron (NM_021136, intron 3 of 8)	L2a|LINE|L2	-3241	NM_206852	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.007282	0.397094	
chunk0022_289_1	chr10	15462421	15462854	+	0	NA	Intergenic	Intergenic	-91578	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.013857	0.389401	
chunk0170_11_1	chr6	109036529	109037059	+	0	NA	intron (NM_014454, intron 1 of 9)	intron (NM_014454, intron 1 of 9)	-27239	NM_001199933	27244	Hs.591336	NM_014454	ENSG00000080546	SESN1	PA26|SEST1	sestrin 1	protein-coding	0.007547	0.355932	
chunk0121_207_1	chr3	21531216	21531768	+	0	NA	intron (NM_024697, intron 3 of 7)	L1MC1|LINE|L1	-11297	NR_046731	100874216	Hs.661720	NR_046731	ENSG00000225542	ZNF385D-AS1	-	ZNF385D antisense RNA 1	ncRNA	0.007246	0.358047	
chunk0168_268_1	chr6	89941201	89941887	+	0	NA	intron (NM_021813, intron 7 of 8)	intron (NM_021813, intron 7 of 8)	47075	NM_032602	84694	Hs.334499	NM_032602	ENSG00000135355	GJA10	CX62	gap junction protein alpha 10	protein-coding	0.020408	0.483261	307(CAGGACAAACAGTTCC,-,0.00),308(AGGACAAACAGTTCCT,+,0.00)
chunk0089_198_1	chr18	59983948	59984147	+	0	NA	Intergenic	L1ME3C|LINE|L1	84087	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.015075	0.410000	
chunk0149_225_1	chr5	22605704	22606218	+	0	NA	intron (NM_004061, intron 1 of 14)	intron (NM_004061, intron 1 of 14)	247661	NM_004061	1010	Hs.113684	NM_004061	ENSG00000154162	CDH12	CDHB	cadherin 12	protein-coding	0.003891	0.535922	
chunk0010_248_1	chr1	116475997	116476908	+	0	NA	intron (NR_125973, intron 1 of 3)	intron (NR_125973, intron 1 of 3)	2374	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.008782	0.483553	537(GGGAACATGCTGTGCC,-,0.00),538(GGAACATGCTGTGCCC,+,0.00)
chunk0175_243_1	chr7	6562291	6562549	+	0	NA	Intergenic	L1MC|LINE|L1	-10984	NM_001145118	392862	Hs.512174	NM_001145118	ENSG00000215045	GRID2IP	DELPHILIN	Grid2 interacting protein	protein-coding	0.003876	0.420849	
chunk0013_314_1	chr1	171387296	171387664	+	0	NA	Intergenic	Intergenic	48584	NR_002719	7151	Hs.661092	NR_002719		TOP1P1	-	DNA topoisomerase I pseudogene 1	pseudo	0.002717	0.327913	
chunk0112_218_1	chr20	40673508	40673707	+	0	NA	Intergenic	Intergenic	15633	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.000000	0.490000	
chunk0149_183_1	chr5	21194059	21194266	+	0	NA	Intergenic	Intergenic	-265318	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.000000	0.336538	
chunk0153_26_1	chr5	67069594	67070143	+	0	NA	intron (NM_001290226, intron 2 of 26)	intron (NM_001290226, intron 2 of 26)	65248	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.009107	0.427273	50(GAAAACAGGTTGTCCT,-,0.00),51(AAAACAGGTTGTCCTG,+,0.00)
chunk0199_25_1	chr9	656587	656946	+	0	NA	intron (NM_001256877, intron 2 of 12)	intron (NM_001256877, intron 2 of 12)	-50040	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.011142	0.416667	153(AAGCAGAGAATGTTCT,-,0.00)
chunk0029_244_1	chr10	102724706	102725325	+	0	NA	intron (NM_178858, intron 1 of 11)	L1MCb|LINE|L1	10474	NM_178858	118980	Hs.44070	NM_178858	ENSG00000156398	SFXN2	SLC56A2	sideroflexin 2	protein-coding	0.003231	0.391935	256(CTGGACATGATGTACC,-,0.00),257(TGGACATGATGTACCC,+,0.00)
chunk0207_323_1	chr9	134211042	134211257	+	0	NA	Intergenic	Intergenic	-46585	NR_023344	100151684	Hs.545589	NR_023344	ENSG00000221676	RNU6ATAC	RNU6ATAC1|U6ATAC	RNA, U6atac small nuclear (U12-dependent splicing)	snRNA	0.037209	0.606481	
chunk0016_99_1	chr1	195245673	195246212	+	0	NA	Intergenic	Intergenic	1336539	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.003711	0.261111	
chunk0084_340_1	chr17	81065614	81066447	+	0	NA	intron (NM_006340, intron 3 of 14)	intron (NM_006340, intron 3 of 14)	30883	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.024010	0.607914	151(GGTACAACGTGTACAC,+,0.00)
chunk0068_189_1	chr15	54805512	54806132	+	0	NA	Intergenic	Intergenic	391211	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.000000	0.367150	
chunk0122_168_1	chr3	32304363	32304987	+	0	NA	intron (NM_178868, intron 1 of 3)	intron (NM_178868, intron 1 of 3)	65996	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.001603	0.368000	
chunk0116_432_1	chr21	43011423	43011694	+	0	NA	intron (NM_004571, intron 4 of 10)	intron (NM_004571, intron 4 of 10)	37048	NM_001286258	5316	Hs.431043	NM_004571	ENSG00000160199	PKNOX1	PREP1|pkonx1c	PBX/knotted 1 homeobox 1	protein-coding	0.018450	0.529412	
chunk0210_163_1	chrX	77949764	77950340	+	0	NA	intron (NR_104109, intron 1 of 9)	intron (NR_104109, intron 1 of 9)	19586	NM_001029891	441531	Hs.632822	NM_001029891	ENSG00000226784	PGAM4	PGAM-B|PGAM1|PGAM3|dJ1000K24.1	phosphoglycerate mutase family member 4	protein-coding	0.003472	0.419411	
chunk0210_406_1	chrX	100464370	100464734	+	0	NA	Intergenic	L1ME3G|LINE|L1	-54279	NM_020766	57526	Hs.4993	NM_020766	ENSG00000165194	PCDH19	EFMR|EIEE9	protocadherin 19	protein-coding	0.000000	0.309589	
chunk0091_308_1	chr19	12890549	12890921	+	0	NA	promoter-TSS (NR_102317)	promoter-TSS (NR_102317)	-394	NR_102317	2639	Hs.532699	NM_000159	ENSG00000105607	GCDH	ACAD5|GCD	glutaryl-CoA dehydrogenase	protein-coding	0.024194	0.493298	
chunk0070_294_1	chr15	74663996	74664902	+	0	NA	intron (NM_025083, intron 3 of 6)	intron (NM_025083, intron 3 of 6)	31596	NM_001142443	80153	Hs.96852	NM_025083	ENSG00000179151	EDC3	LSM16|MRT50|YJDC|YJEFN2|hYjeF_N2-15q23	enhancer of mRNA decapping 3	protein-coding	0.004415	0.417861	
chunk0060_47_1	chr14	41288735	41289120	+	0	NA	Intergenic	L1PA15|LINE|L1	-318634	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.007792	0.536269	
chunk0081_170_1	chr17	41378756	41379142	+	0	NA	intron (NM_021013, intron 6 of 6)	intron (NM_021013, intron 6 of 6)	3435	NM_021013	3885	Hs.296942	NM_021013	ENSG00000131737	KRT34	HA4|Ha-4|KRTHA4|hHa4	keratin 34	protein-coding	0.020725	0.542636	
chunk0147_443_1	chr4	187618689	187619232	+	0	NA	intron (NR_110436, intron 2 of 2)	intron (NR_110436, intron 2 of 2)	53681	NR_110436	100506272	Hs.508163	NR_110436	ENSG00000250590	LINC02492	-	long intergenic non-protein coding RNA 2492	ncRNA	0.003683	0.386029	
chunk0143_127_1	chr4	109501125	109501542	+	0	NA	intron (NM_001300813, intron 7 of 24)	Tigger3|DNA|TcMar-Tigger	12635	NR_030302	693161		NR_030302	ENSG00000207988	MIR576	MIRN576|hsa-mir-576	microRNA 576	ncRNA	0.011990	0.375598	
chunk0084_222_1	chr17	78387854	78388445	+	0	NA	intron (NR_111989, intron 1 of 8)	intron (NR_111989, intron 1 of 8)	9531	NR_111989	9489	Hs.654671	NM_024419	ENSG00000087157	PGS1	-	phosphatidylglycerophosphate synthase 1	protein-coding	0.015228	0.478041	
chunk0204_111_1	chr9	94885855	94886422	+	0	NA	intron (NM_032823, intron 5 of 14)	intron (NM_032823, intron 5 of 14)	76176	NR_031755	100313780		NR_031755	ENSG00000252153	MIR2278	mir-2278	microRNA 2278	ncRNA	0.007055	0.369718	
chunk0134_19_1	chr3	175484572	175485294	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	115393	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.002770	0.348548	
chunk0028_21_1	chr10	82467043	82467381	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-234292	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.005917	0.389381	
chunk0064_360_1	chr14	97217090	97217468	+	0	NA	Intergenic	Intergenic	-241537	NR_110166	101929241	Hs.650839	NR_110165	ENSG00000246084	LINC02325	-	long intergenic non-protein coding RNA 2325	ncRNA	0.015873	0.414248	
chunk0058_39_1	chr14	20179351	20179723	+	0	NA	Intergenic	Intergenic	-17799	NM_001005503	390439	Hs.554582	NM_001005503	ENSG00000196832	OR11G2	OR14-34	olfactory receptor family 11 subfamily G member 2	protein-coding	0.016129	0.495979	
chunk0021_243_1	chr1	242945314	242945811	+	0	NA	Intergenic	Intergenic	156182	NR_029401	731275	Hs.722350	NR_029401	ENSG00000214837	LINC01347	-	long intergenic non-protein coding RNA 1347	ncRNA	0.010060	0.475904	
chunk0174_269_1	chr6	161404238	161404607	+	0	NA	intron (NM_013988, intron 6 of 8)	intron (NM_013988, intron 6 of 8)	-130347	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.010840	0.418919	160(CTGGACAGTCTGTCCA,-,0.00),161(TGGACAGTCTGTCCAA,+,0.00)
chunk0166_257_1	chr6	47535179	47535696	+	0	NA	intron (NM_012120, intron 3 of 17)	intron (NM_012120, intron 3 of 17)	57648	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.000000	0.310811	
chunk0019_301_1	chr1	228881769	228882255	+	0	NA	Intergenic	Intergenic	146935	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.006173	0.476386	
chunk0052_355_1	chr12	127114972	127115629	+	0	NA	Intergenic	Intergenic	-54903	NR_104646	101927592	Hs.385663	NR_104646	ENSG00000249345	LINC02405	-	long intergenic non-protein coding RNA 2405	ncRNA	0.009132	0.378419	
chunk0172_47_1	chr6	134051749	134052212	+	0	NA	intron (NM_145176, intron 1 of 4)	intron (NM_145176, intron 1 of 4)	671	NM_145176	154091	Hs.486508	NM_145176	ENSG00000146411	SLC2A12	GLUT12|GLUT8	solute carrier family 2 member 12	protein-coding	0.017279	0.398707	
chunk0132_235_1	chr3	158487878	158488112	+	0	NA	intron (NM_001271834, intron 6 of 8)	Kanga1a|DNA|TcMar-Tc2	83071	NR_104147	100996447	Hs.369810	NR_104147	ENSG00000243150	LOC100996447	-	uncharacterized LOC100996447	ncRNA	0.008547	0.404255	
chunk0026_101_1	chr10	61793636	61794241	+	0	NA	Intergenic	Intergenic	-107316	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.001653	0.343234	
chunk0025_52_1	chr10	49496016	49496251	+	0	NA	intron (NM_000124, intron 7 of 20)	L2c|LINE|L2	28148	NM_170753	267004	Hs.49063	NM_170753	ENSG00000225830	PGBD3	-	piggyBac transposable element derived 3	protein-coding	0.017021	0.508475	
chunk0162_294_1	chr6	6405425	6405993	+	0	NA	intron (NR_026970, intron 4 of 7)	intron (NR_026970, intron 4 of 7)	-85018	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.000000	0.314587	
chunk0184_219_1	chr7	117442861	117443091	+	0	NA	Intergenic	MIRb|SINE|MIR	-15453	NM_001301822	136991	Hs.352412	NM_130768	ENSG00000154438	ASZ1	ALP1|ANKL1|C7orf7|CT1.19|GASZ|Orf3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding	0.004348	0.376623	
chunk0111_407_1	chr20	34525763	34526367	+	0	NA	intron (NM_001281728, intron 2 of 4)	intron (NM_001281728, intron 2 of 4)	9681	NM_001281727	83658	Hs.593920	NM_014183	ENSG00000125971	DYNLRB1	BITH|BLP|DNCL2A|DNLC2A|ROBLD1	dynein light chain roadblock-type 1	protein-coding	0.021523	0.525620	
chunk0003_142_1	chr1	32981312	32982150	+	0	NA	Intergenic	MIR|SINE|MIR	-16918	NM_001127361	127544	Hs.591504	NM_153341	ENSG00000116514	RNF19B	IBRDC3|NKLAM	ring finger protein 19B	protein-coding	0.005967	0.426698	
chunk0100_104_1	chr2	108260710	108261103	+	0	NA	intron (NM_001008743, intron 5 of 6)	(GTTT)n|Simple_repeat|Simple_repeat	13711	NM_001008743	442038		NM_001008743	ENSG00000196228	SULT1C3	ST1C3	sulfotransferase family 1C member 3	protein-coding	0.005089	0.342640	
chunk0106_308_1	chr2	204948298	204948876	+	0	NA	intron (NM_205863, intron 2 of 21)	intron (NM_205863, intron 2 of 21)	402794	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.006920	0.371330	
chunk0165_38_1	chr6	30050878	30051297	+	0	NA	intron (NR_026751, intron 3 of 5).8	L1MB7|LINE|L1	10097	NR_026751	80862	Hs.653168	NR_026751	ENSG00000204623	ZNRD1ASP	C6orf12|HCG8|HCGVIII|HCGVIII-1|HTEX4|NCRNA00171|TCTEX4|ZNRD1-AS|ZNRD1-AS1|ZNRD1AS|ZNRD1AS1	zinc ribbon domain containing 1 antisense, pseudogene	pseudo	0.004773	0.316667	
chunk0139_48_1	chr4	48681248	48681471	+	0	NA	intron (NM_015030, intron 3 of 63)	intron (NM_015030, intron 3 of 63)	98940	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.022422	0.397321	
chunk0111_173_1	chr20	25273455	25274065	+	0	NA	intron (NM_002862, intron 4 of 19)	intron (NM_002862, intron 4 of 19)	25690	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.022951	0.504092	283(CGGAACAGCTTGTCTT,-,0.00),284(GGAACAGCTTGTCTTC,+,0.00)
chunk0128_426_1	chr3	114906778	114907404	+	0	NA	intron (NM_001164343, intron 2 of 11)	intron (NM_001164343, intron 2 of 11)	-6469	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.007987	0.323764	
chunk0017_55_1	chr1	205365930	205366318	+	0	NA	Intergenic	Intergenic	-7128	NR_038425	284576	Hs.585440	NR_038425	ENSG00000226235	LEMD1-AS1	-	LEMD1 antisense RNA 1	ncRNA	0.012887	0.501285	239(GTGAACAAAATGTACC,-,0.00),240(TGAACAAAATGTACCA,+,0.00)
chunk0156_227_1	chr5	108282490	108283110	+	0	NA	intron (NM_001163315, intron 4 of 8)	L1PB4|LINE|L1	99298	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.001613	0.302738	
chunk0192_92_1	chr8	61331100	61331652	+	0	NA	intron (NM_173519, intron 2 of 5)	HAL1|LINE|L1	43410	NM_173519	157807	Hs.591874	NM_173519	ENSG00000177182	CLVS1	C6orf212L|CRALBPL|RLBP1L1	clavesin 1	protein-coding	0.001812	0.347197	
chunk0006_212_1	chr1	67880072	67880655	+	0	NA	intron (NR_040077, intron 1 of 9)	intron (NR_040077, intron 1 of 9)	-46891	NM_018841	55970	Hs.431101	NM_018841	ENSG00000172380	GNG12	-	G protein subunit gamma 12	protein-coding	0.005146	0.416096	
chunk0190_32_1	chr8	29240213	29240913	+	0	NA	intron (NM_015254, intron 2 of 39)	intron (NM_015254, intron 2 of 39)	22530	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.012857	0.376605	
chunk0062_325_1	chr14	73368024	73368342	+	0	NA	intron (NM_001005743, intron 2 of 12)	intron (NM_001005743, intron 2 of 12)	90397	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.012579	0.366771	
chunk0122_418_1	chr3	38960718	38961207	+	0	NA	Intergenic	Intergenic	-7311	NM_001287223	11280	Hs.591657	NM_014139	ENSG00000168356	SCN11A	FEPS3|HSAN7|NAV1.9|NaN|PN5|SCN12A|SNS-2	sodium voltage-gated channel alpha subunit 11	protein-coding	0.006135	0.471429	
chunk0082_227_1	chr17	57281134	57281720	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	24414	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.022184	0.487223	
chunk0025_140_1	chr10	52156396	52156889	+	0	NA	intron (NM_006258, intron 8 of 17)	intron (NM_006258, intron 8 of 17)	157486	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.006085	0.319838	
chunk0114_343_1	chr21	17796109	17796370	+	0	NA	intron (NM_017447, intron 3 of 4)	intron (NM_017447, intron 3 of 4)	-3730	NR_038871	246312	Hs.473425	NR_038870	ENSG00000240770	C21orf91-OT1	D21S2089E|NCRNA00285	C21orf91 overlapping transcript 1	ncRNA	0.003831	0.358779	
chunk0210_413_1	chrX	100864949	100865260	+	0	NA	intron (NM_007052, intron 2 of 12)	intron (NM_007052, intron 2 of 12)	9241	NM_007052	27035	Hs.592227	NM_007052	ENSG00000007952	NOX1	GP91-2|MOX1|NOH-1|NOH1	NADPH oxidase 1	protein-coding	0.003215	0.413462	
chunk0088_69_1	chr18	44541436	44542280	+	0	NA	intron (NR_131768, intron 1 of 4)	intron (NR_131768, intron 1 of 4)	10079	NR_131768	105667213	Hs.135737	NR_131768		LINC01601	-	long intergenic non-protein coding RNA 1601	ncRNA	0.004739	0.345562	
chunk0170_325_1	chr6	116153109	116153308	+	0	NA	intron (NM_152729, intron 6 of 11)	intron (NM_152729, intron 6 of 11)	-27075	NM_000493	1300	Hs.520339	NM_000493	ENSG00000123500	COL10A1	-	collagen type X alpha 1 chain	protein-coding	0.000000	0.215000	
chunk0182_17_1	chr7	91263171	91263618	+	0	NA	Intergenic	Intergenic	-1074	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.038031	0.459821	
chunk0155_199_1	chr5	94891229	94891476	+	0	NA	intron (NM_024717, intron 11 of 22)	intron (NM_024717, intron 11 of 22)	190514	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.012146	0.379032	120(GGGCACGTTGTGTTCC,-,0.00),121(GGCACGTTGTGTTCCT,+,0.00)
chunk0204_461_1	chr9	104675239	104675495	+	0	NA	Intergenic	Intergenic	-19055	NM_001004484	286365	Hs.553683	NM_001004484	ENSG00000179055	OR13D1	OR9-15	olfactory receptor family 13 subfamily D member 1	protein-coding	0.003906	0.291829	
chunk0127_3_1	chr3	87766614	87767199	+	0	NA	Intergenic	L1MB8|LINE|L1	-215670	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.006838	0.431741	
chunk0105_197_1	chr2	187710614	187711125	+	0	NA	Intergenic	Intergenic	-156377	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.332031	
chunk0133_243_1	chr3	171532196	171532395	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-71887	NM_001161563	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.000000	0.385000	
chunk0199_83_1	chr9	2500553	2501271	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-120881	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.004178	0.363004	
chunk0136_113_1	chr4	3354567	3354766	+	0	NA	intron (NM_198229, intron 3 of 17)	L1ME3B|LINE|L1	-15331	NM_198227	6002	Hs.527061	NM_002926	ENSG00000159788	RGS12	-	regulator of G protein signaling 12	protein-coding	0.015075	0.400000	
chunk0037_47_1	chr11	70436459	70437093	+	0	NA	TTS (NM_001184740)	TTS (NM_001184740)	38270	NM_001184740	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.036278	0.500787	372(TAAAACACTCTGTGCT,-,0.00),373(AAAACACTCTGTGCTT,+,0.00)
chunk0002_361_1	chr1	26067207	26067523	+	0	NA	exon (NM_032588, exon 1 of 9)	exon (NM_032588, exon 1 of 9)	269	NM_032588	84676	Hs.279709	NM_032588	ENSG00000158022	TRIM63	IRF|MURF1|MURF2|RNF28|SMRZ	tripartite motif containing 63	protein-coding	0.015823	0.542587	154(CGGCACAGGTTGTGCT,-,0.00),155(GGCACAGGTTGTGCTG,+,0.00)
chunk0085_273_1	chr18	7755983	7756350	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	188850	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.002725	0.391304	
chunk0126_374_1	chr3	84105971	84106632	+	0	NA	Intergenic	Intergenic	763274	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.004539	0.365559	
chunk0120_178_1	chr3	6125405	6125818	+	0	NA	Intergenic	HAL1M8|LINE|L1	679838	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.004843	0.408213	
chunk0174_370_1	chr6	164819847	164820664	+	0	NA	intron (NR_131926, intron 1 of 3)	L1MA2|LINE|L1	1808	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.006120	0.337408	
chunk0093_133_1	chr19	46030812	46031105	+	0	NA	Intergenic	LTR14|LTR|ERVK	-7660	NM_005091	8993	Hs.137583	NM_005091	ENSG00000008438	PGLYRP1	PGLYRP|PGRP|PGRP-S|PGRPS|TAG7|TNFSF3L	peptidoglycan recognition protein 1	protein-coding	0.013652	0.445578	
chunk0165_206_1	chr6	34684569	34684811	+	0	NA	intron (NM_022758, intron 1 of 3)	intron (NM_022758, intron 1 of 3)	12160	NM_024294	64771	Hs.643498	NM_022758	ENSG00000196821	ILRUN	C6orf106|FP852|dJ391O22.4	inflammation and lipid regulator with UBA-like and NBR1-like domains	protein-coding	0.008264	0.374486	
chunk0212_407_1	chrX	151985846	151986485	+	0	NA	Intergenic	Intergenic	-11486	NM_004961	2564	Hs.22785	NM_004961	ENSG00000102287	GABRE	-	gamma-aminobutyric acid type A receptor epsilon subunit	protein-coding	0.009390	0.514062	
chunk0087_390_1	chr18	41842918	41843226	+	0	NA	Intergenic	L2c|LINE|L2	-112126	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.003247	0.385113	160(TGGCACAGCCTGTTCT,-,0.00),161(GGCACAGCCTGTTCTA,+,0.00)
chunk0212_173_1	chrX	132611554	132611899	+	0	NA	Intergenic	Intergenic	-55916	NR_046691	100874102	Hs.619341	NR_046691	ENSG00000235849	HS6ST2-AS1	-	HS6ST2 antisense RNA 1	ncRNA	0.008696	0.349711	219(CAGCACATGCAGTTCT,-,0.00),220(AGCACATGCAGTTCTG,+,0.00)
chunk0062_46_1	chr14	67281570	67282021	+	0	NA	intron (NM_022474, intron 3 of 14)	intron (NM_022474, intron 3 of 14)	40500	NM_001256550	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.002217	0.307522	
chunk0146_16_1	chr4	155055435	155056370	+	0	NA	Intergenic	L1MB7|LINE|L1	-152727	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.003209	0.338675	
chunk0135_157_1	chr3	187780959	187781650	+	0	NA	Intergenic	MIRb|SINE|MIR	-35579	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.007236	0.423410	
chunk0076_256_1	chr16	69262223	69262662	+	0	NA	intron (NM_006750, intron 3 of 6)	intron (NM_006750, intron 3 of 6)	-48942	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.020501	0.345455	
chunk0064_279_1	chr14	95168785	95169078	+	0	NA	intron (NR_015415, intron 3 of 3)	L2c|LINE|L2	-10921	NM_030621	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.003413	0.421769	167(GGGCACAGAGTGTTCC,-,0.00),168(GGCACAGAGTGTTCCA,+,0.00),190(AGGAACAGCATGCCCA,-,0.00)
chunk0171_140_1	chr6	123518992	123519474	+	0	NA	intron (NM_006073, intron 5 of 40)	intron (NM_006073, intron 5 of 40)	79629	NR_110844	101927990	Hs.660877	NR_110844		TRDN-AS1	HRAT13	TRDN antisense RNA 1	ncRNA	0.004149	0.474120	
chunk0051_121_1	chr12	115297771	115298172	+	0	NA	Intergenic	L1MC3|LINE|L1	-613807	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.009975	0.440299	
chunk0049_394_1	chr12	96452192	96452815	+	0	NA	Intergenic	L1PA17|LINE|L1	-37068	NM_001306084	144535	Hs.382121	NM_198520	ENSG00000188596	CFAP54	C12orf55|C12orf63	cilia and flagella associated protein 54	protein-coding	0.003210	0.339744	
chunk0121_98_1	chr3	16892243	16892824	+	0	NA	intron (NM_001144382, intron 1 of 5)	intron (NM_001144382, intron 1 of 5)	7574	NM_001144382	23228	Hs.202010	NM_015184	ENSG00000154822	PLCL2	PLCE2	phospholipase C like 2	protein-coding	0.003442	0.336770	
chunk0156_44_1	chr5	102794616	102795022	+	0	NA	Intergenic	Intergenic	-71004	NR_033440	5066	Hs.369430	NM_000919	ENSG00000145730	PAM	PAL|PHM	peptidylglycine alpha-amidating monooxygenase	protein-coding	0.004926	0.390663	
chunk0046_226_1	chr12	59941822	59942447	+	0	NA	Intergenic	Intergenic	252797	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.004800	0.327476	
chunk0066_78_1	chr15	29401605	29402122	+	0	NA	intron (NM_015307, intron 1 of 10)	L1ME4b|LINE|L1	-132047	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.013540	0.364865	
chunk0137_14_1	chr4	10773058	10773484	+	0	NA	Intergenic	Intergenic	-88509	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.009390	0.416862	
chunk0138_89_1	chr4	35563668	35564227	+	0	NA	Intergenic	Intergenic	-680169	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.005367	0.260714	
chunk0033_207_1	chr11	16955170	16955592	+	0	NA	intron (NM_175058, intron 3 of 22)	L2c|LINE|L2	59035	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.002370	0.413712	
chunk0204_338_1	chr9	101388502	101389209	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-3850	NM_001701	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.002829	0.300847	231(AAGACTGTGTGTTCCC,+,0.00)
chunk0180_41_1	chr7	54484938	54485539	+	0	NA	Intergenic	L2c|LINE|L2	-57087	NM_001301009	222008	Hs.335933	NM_182546	ENSG00000170419	VSTM2A	VSTM2	V-set and transmembrane domain containing 2A	protein-coding	0.006656	0.431894	
chunk0017_184_1	chr1	207316366	207316987	+	0	NA	Intergenic	Intergenic	-4796	NM_001300902	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.001610	0.409968	
chunk0009_362_1	chr1	109741744	109742062	+	0	NA	promoter-TSS (NR_024537)	promoter-TSS (NR_024537)	-865	NM_000849	2947	Hs.2006	NM_000849	ENSG00000134202	GSTM3	GST5|GSTB|GSTM3-3|GTM3	glutathione S-transferase mu 3	protein-coding	0.006289	0.485893	
chunk0200_62_1	chr9	15723160	15723380	+	0	NA	intron (NM_173550, intron 12 of 25)	intron (NM_173550, intron 12 of 25)	170171	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.009091	0.429864	
chunk0178_359_1	chr7	39017033	39017308	+	0	NA	intron (NM_007252, intron 2 of 10)	L2b|LINE|L2	39161	NM_001166018	11281	Hs.137106	NM_007252	ENSG00000106536	POU6F2	RPF-1|WT5|WTSL	POU class 6 homeobox 2	protein-coding	0.003636	0.355072	
chunk0083_285_1	chr17	68689958	68690444	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	62047	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.014403	0.367556	
chunk0005_370_1	chr1	61638356	61638832	+	0	NA	Intergenic	Intergenic	-15648	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.010504	0.396226	199(AAGTACAGGATGTACT,-,0.00),200(AGTACAGGATGTACTT,+,0.00)
chunk0061_324_1	chr14	63016257	63016657	+	0	NA	intron (NM_172375, intron 2 of 9)	intron (NM_172375, intron 2 of 9)	28781	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.002500	0.336658	
chunk0039_62_1	chr11	96302910	96303380	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-38293	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.004255	0.341826	
chunk0157_333_1	chr5	122434100	122434860	+	0	NA	intron (NR_131761, intron 6 of 12)	intron (NR_131761, intron 6 of 12)	43391	NR_131761	9627	Hs.426463	NM_005460	ENSG00000064692	SNCAIP	SYPH1|Sph1	synuclein alpha interacting protein	protein-coding	0.007895	0.387648	
chunk0064_130_1	chr14	91395979	91396714	+	0	NA	intron (NM_001080414, intron 3 of 29)	intron (NM_001080414, intron 3 of 29)	21498	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.032653	0.480978	
chunk0083_123_1	chr17	65035176	65035600	+	0	NA	intron (NM_001282425, intron 2 of 3)	L1ME4a|LINE|L1	20386	NM_001282425	10672	Hs.515018	NM_006572	ENSG00000120063	GNA13	G13	G protein subunit alpha 13	protein-coding	0.004717	0.334118	
chunk0063_387_1	chr14	86767174	86767431	+	0	NA	Intergenic	Intergenic	-138476	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.003891	0.333333	
chunk0085_45_1	chr18	770402	770816	+	0	NA	intron (NM_005433, intron 1 of 11)	L1MEc|LINE|L1	41717	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.000000	0.419277	
chunk0023_372_1	chr10	30213267	30213587	+	0	NA	intron (NR_120653, intron 1 of 2)	intron (NR_120653, intron 1 of 2)	1575	NR_120653	101929279	Hs.559153	NR_120653		LOC101929279	-	uncharacterized LOC101929279	ncRNA	0.006250	0.426791	
chunk0109_201_1	chr20	5119614	5119900	+	0	NA	non-coding (NR_028370, exon 1 of 1)	non-coding (NR_028370, exon 1 of 1)	171	NR_028370	100302739	Hs.744934	NR_028370		PCNA-AS1	PCNA-AS|PCNAAS	PCNA antisense RNA 1	ncRNA	0.073427	0.613240	
chunk0037_253_1	chr11	75509151	75509463	+	0	NA	intron (NM_030792, intron 1 of 16)	intron (NM_030792, intron 1 of 16)	16247	NM_030792	81544	Hs.503297	NM_030792	ENSG00000158555	GDPD5	GDE2|PP1665	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding	0.009615	0.555911	
chunk0113_54_1	chr20	50165955	50166349	+	0	NA	Intergenic	Intergenic	-6418	NR_109943	101927541	Hs.570391	NR_109943	ENSG00000231742	LINC01273	-	long intergenic non-protein coding RNA 1273	ncRNA	0.032995	0.554430	
chunk0048_312_1	chr12	83097141	83097847	+	0	NA	intron (NM_152588, intron 11 of 11)	intron (NM_152588, intron 11 of 11)	410339	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.007082	0.359264	
chunk0159_59_1	chr5	137279748	137280045	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	219433	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.003367	0.489933	
chunk0208_449_1	chrX	32226313	32226771	+	0	NA	intron (NM_004010, intron 43 of 78)	L2c|LINE|L2	-71073	NM_004022	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.002183	0.348584	166(CAGTACACTATGTACC,-,0.00),167(AGTACACTATGTACCT,+,0.00)
chunk0148_208_1	chr5	8612911	8613641	+	0	NA	Intergenic	Intergenic	152351	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.005479	0.436389	116(GGGATCATGGTGTCCC,-,0.00),117(GGATCATGGTGTCCCT,+,0.00)
chunk0107_152_1	chr2	215178979	215179582	+	0	NA	Intergenic	L1MA4A|LINE|L1	-40852	NM_173076	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.004975	0.321192	
chunk0003_19_1	chr1	29111102	29111476	+	0	NA	intron (NM_203342, intron 18 of 20)	intron (NM_203342, intron 18 of 20)	11212	NM_001171868	399474	Hs.712722	NM_001003682	ENSG00000253304	TMEM200B	TTMB	transmembrane protein 200B	protein-coding	0.016043	0.416000	149(GAGCACAGAAAGTCCT,-,0.00),150(AGCACAGAAAGTCCTA,+,0.00)
chunk0087_447_1	chr18	42633454	42634149	+	0	NA	intron (NR_046174, intron 7 of 9)	intron (NR_046174, intron 7 of 9)	447133	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.001439	0.316092	
chunk0210_333_1	chrX	95023843	95024422	+	0	NA	Intergenic	Intergenic	39094	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.005181	0.324138	211(AGGAACTGTATGTACT,-,0.00),212(GGAACTGTATGTACTT,+,0.00)
chunk0030_117_1	chr10	112831923	112832450	+	0	NA	Intergenic	Intergenic	8690	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.036053	0.526515	
chunk0150_40_1	chr5	31482212	31482561	+	0	NA	intron (NM_013235, intron 15 of 34)	intron (NM_013235, intron 15 of 34)	49789	NM_001100412	29102	Hs.97997	NM_013235	ENSG00000113360	DROSHA	ETOHI2|HSA242976|RANSE3L|RN3|RNASE3L|RNASEN	drosha ribonuclease III	protein-coding	0.005731	0.440000	
chunk0122_338_1	chr3	37179059	37179601	+	0	NA	Intergenic	Intergenic	-2970	NM_017724	9209	Hs.740522	NM_006309	ENSG00000093167	LRRFIP2	HUFI-2	LRR binding FLII interacting protein 2	protein-coding	0.003690	0.340700	260(CTGGTCATACTGTTCC,-,0.00)
chunk0135_386_1	chr3	191263388	191263985	+	0	NA	Intergenic	Intergenic	51153	NM_198184	344901	Hs.526794	NM_198184	ENSG00000188729	OSTN	MUSCLIN	osteocrin	protein-coding	0.001675	0.334448	275(AGTACAATGTGATCTT,+,0.00)
chunk0069_323_1	chr15	65970911	65971110	+	0	NA	intron (NM_032445, intron 7 of 22)	L2c|LINE|L2	-69223	NR_036196	100422905		NR_036196	ENSG00000263512	MIR4311	-	microRNA 4311	ncRNA	0.020101	0.465000	
chunk0035_423_1	chr11	57251075	57251532	+	0	NA	Intergenic	Intergenic	-13850	NM_005161	187	Hs.438311	NM_005161	ENSG00000134817	APLNR	AGTRL1|APJ|APJR|HG11	apelin receptor	protein-coding	0.004376	0.469432	
chunk0056_93_1	chr13	81987868	81988147	+	0	NA	Intergenic	MER67C|LTR|ERV1	-761024	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.003584	0.360714	
chunk0092_237_1	chr19	32692222	32692784	+	0	NA	exon (NM_001105570, exon 1 of 3)	exon (NM_001105570, exon 1 of 3)	542	NM_001105570	390916	Hs.203961	NM_001105570	ENSG00000213965	NUDT19	RP2	nudix hydrolase 19	protein-coding	0.094306	0.712256	
chunk0087_22_1	chr18	31011251	31011809	+	0	NA	intron (NM_024423, intron 9 of 16)	L3|LINE|CR1	31285	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.012545	0.398927	
chunk0192_77_1	chr8	60752881	60753080	+	0	NA	intron (NM_017780, intron 2 of 37)	intron (NM_017780, intron 2 of 37)	11721	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.000000	0.360000	
chunk0008_326_1	chr1	95332604	95333326	+	0	NA	Intergenic	Intergenic	98810	NR_103484	25950	Hs.483512	NM_015485	ENSG00000122481	RWDD3	RSUME	RWD domain containing 3	protein-coding	0.004155	0.408022	282(CAGAACACTCTGTACA,-,0.00),283(AGAACACTCTGTACAG,+,0.00)
chunk0089_187_1	chr18	59899314	59899761	+	0	NA	promoter-TSS (NM_021127)	promoter-TSS (NM_021127)	-423	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.038031	0.540179	
chunk0137_192_1	chr4	17810329	17810591	+	0	NA	promoter-TSS (NM_022346)	promoter-TSS (NM_022346)	298	NM_017741	54876	Hs.614787	NM_017741	ENSG00000163257	DCAF16	C4orf30	DDB1 and CUL4 associated factor 16	protein-coding	0.099237	0.665399	
chunk0033_15_1	chr11	12448424	12448668	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	71067	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.012295	0.497959	
chunk0200_105_1	chr9	16817471	16817856	+	0	NA	intron (NM_017637, intron 1 of 6)	intron (NM_017637, intron 1 of 6)	53125	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.005195	0.388601	
chunk0002_318_1	chr1	24201844	24202327	+	0	NA	intron (NR_027087, intron 1 of 2)	intron (NR_027087, intron 1 of 2)	1845	NR_027087	284632	Hs.638906	NR_027087	ENSG00000230023	LINC02800	-	long intergenic non-protein coding RNA 2800	ncRNA	0.002070	0.491736	
chunk0103_214_1	chr2	163917323	163917932	+	0	NA	Intergenic	Intergenic	-181624	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.008210	0.281967	
chunk0126_56_1	chr3	74339947	74340357	+	0	NA	intron (NM_020872, intron 10 of 21)	MER2|DNA|TcMar-Tigger	180988	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002439	0.343066	
chunk0110_271_1	chr20	17369349	17369561	+	0	NA	intron (NM_002594, intron 5 of 11)	(CA)n|Simple_repeat|Simple_repeat	142503	NM_001201529	5126	Hs.315186	NM_002594	ENSG00000125851	PCSK2	NEC 2|NEC-2|NEC2|PC2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding	0.009434	0.483568	
chunk0102_202_1	chr2	148016847	148017412	+	0	NA	intron (NM_001190879, intron 1 of 14)	L1ME3B|LINE|L1	3608	NM_001190882	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.005310	0.309187	
chunk0204_418_1	chr9	102964999	102965523	+	0	NA	Intergenic	L1MA7|LINE|L1	-30050	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.003817	0.348571	
chunk0180_33_1	chr7	54247802	54248104	+	0	NA	Intergenic	Intergenic	-45532	NR_004422									0.003311	0.273927	
chunk0100_348_1	chr2	117355372	117355763	+	0	NA	Intergenic	L2c|LINE|L2	-459112	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.005115	0.405612	
chunk0088_271_1	chr18	49259691	49260091	+	0	NA	intron (NM_017653, intron 11 of 16)	(AATA)n|Simple_repeat|Simple_repeat	200818	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.007500	0.294264	
chunk0171_381_1	chr6	131065714	131065986	+	0	NA	Intergenic	Intergenic	-2528	NM_001199388	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.007353	0.461538	
chunk0189_82_1	chr8	21249672	21249919	+	0	NA	Intergenic	MIRc|SINE|MIR	-48444	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.000000	0.366935	
chunk0104_98_1	chr2	172351182	172351381	+	0	NA	Intergenic	Intergenic	-76073	NM_001316306	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.015075	0.580000	
chunk0018_33_1	chr1	215612371	215612752	+	0	NA	intron (NM_016121, intron 15 of 17)	intron (NM_016121, intron 15 of 17)	45169	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.007874	0.358639	
chunk0032_103_1	chr11	3700260	3700825	+	0	NA	intron (NM_016320, intron 24 of 32)	intron (NM_016320, intron 24 of 32)	-29158	NM_001303035	57053	Hs.732806	NM_020402	ENSG00000129749	CHRNA10	-	cholinergic receptor nicotinic alpha 10 subunit	protein-coding	0.005310	0.376325	
chunk0187_177_1	chr7	150918960	150919366	+	0	NA	Intergenic	L1MC3|LINE|L1	36666	NM_001204798	3757	Hs.647099	NM_000238	ENSG00000055118	KCNH2	ERG-1|ERG1|H-ERG|HERG|HERG1|Kv11.1|LQT2|SQT1	potassium voltage-gated channel subfamily H member 2	protein-coding	0.027094	0.415233	
chunk0022_150_1	chr10	12405229	12406104	+	0	NA	intron (NM_020397, intron 1 of 9)	MamRep434|DNA|TcMar-Tigger	56123	NM_153498	57118	Hs.600547	NM_020397	ENSG00000183049	CAMK1D	CKLiK|CaM-K1|CaMKID	calcium/calmodulin dependent protein kinase ID	protein-coding	0.022857	0.425799	
chunk0045_315_1	chr12	50722468	50722832	+	0	NA	intron (NM_173602, intron 26 of 37)	intron (NM_173602, intron 26 of 37)	-41356	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.013736	0.493151	
chunk0187_403_1	chr7	157962028	157962868	+	0	NA	intron (NM_001308268, intron 11 of 22)	intron (NM_001308268, intron 11 of 22)	107863	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.023810	0.458977	446(GAGGACACCCTGATCC,-,0.00),447(AGGACACCCTGATCCA,+,0.00)
chunk0007_293_1	chr1	84020275	84020561	+	0	NA	Intergenic	MER101B|LTR|ERV1	-21268	NM_024686	79739	Hs.445826	NM_024686	ENSG00000137941	TTLL7	-	tubulin tyrosine ligase like 7	protein-coding	0.010490	0.439024	
chunk0122_461_1	chr3	39962690	39963211	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	-137061	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.009597	0.392720	
chunk0009_132_1	chr1	104469917	104470339	+	0	NA	Intergenic	Intergenic	397105	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.002370	0.304965	
chunk0204_168_1	chr9	95919114	95919459	+	0	NA	intron (NM_001010895, intron 6 of 13)	intron (NM_001010895, intron 6 of 13)	-43309	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.008696	0.375723	
chunk0091_144_1	chr19	7197315	7198085	+	0	NA	intron (NM_001079817, intron 2 of 20)	(GT)n|Simple_repeat|Simple_repeat	96602	NM_001079817	3643	Hs.465744	NM_000208	ENSG00000171105	INSR	CD220|HHF5	insulin receptor	protein-coding	0.029870	0.581064	
chunk0072_192_1	chr15	94275506	94275901	+	0	NA	Intergenic	Intergenic	-22498	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.005063	0.297980	
chunk0055_345_1	chr13	70218543	70218950	+	0	NA	Intergenic	Intergenic	-110253	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.007371	0.306373	
chunk0211_261_1	chrX	121002584	121003181	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	-17098	NM_001080139	728049	Hs.729566	NM_001080139	ENSG00000230347	CT47A8	CT47.8	cancer/testis antigen family 47 member A8	protein-coding	0.003350	0.257525	
chunk0154_328_1	chr5	85057989	85058264	+	0	NA	Intergenic	Intergenic	-673259	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.003636	0.297101	
chunk0055_267_1	chr13	63629538	63630127	+	0	NA	Intergenic	Intergenic	-107603	NR_002171	283491	Hs.363054	NR_002171		OR7E156P	-	olfactory receptor family 7 subfamily E member 156 pseudogene	pseudo	0.003396	0.330508	
chunk0187_416_1	chr7	158331884	158332112	+	0	NA	intron (NM_130842, intron 1 of 21)	intron (NM_130842, intron 1 of 21)	200815	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.035088	0.524017	
chunk0020_141_1	chr1	233704581	233705481	+	0	NA	Intergenic	Intergenic	80879	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.003333	0.392897	421(GAAAACAGTATGTTCT,-,0.00),422(AAAACAGTATGTTCTG,+,0.00)
chunk0038_128_1	chr11	84054080	84054345	+	0	NA	intron (NM_001142699, intron 11 of 27)	intron (NM_001142699, intron 11 of 27)	219068	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003774	0.330827	
chunk0017_400_1	chr1	212596191	212596390	+	0	NA	intron (NM_001030287, intron 1 of 3)	intron (NM_001030287, intron 1 of 3)	-12338	NM_001674	467	Hs.460	NM_001674	ENSG00000162772	ATF3	-	activating transcription factor 3	protein-coding	0.010050	0.380000	
chunk0122_111_1	chr3	30871821	30872020	+	0	NA	intron (NM_207359, intron 1 of 14)	intron (NM_207359, intron 1 of 14)	22741	NM_207359	339896	Hs.657052	NM_207359	ENSG00000144644	GADL1	ADC|CSADC|HuADC|HuCSADC	glutamate decarboxylase like 1	protein-coding	0.000000	0.340000	
chunk0146_33_1	chr4	155405031	155405666	+	0	NA	Intergenic	Intergenic	-28378	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.007874	0.301887	327(ATAACAGCATGTTCTT,+,0.00)
chunk0150_63_1	chr5	32095188	32095457	+	0	NA	intron (NM_178140, intron 20 of 23)	intron (NM_178140, intron 20 of 23)	78997	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.022305	0.470370	99(CAGAACACGGCGTTCT,-,0.00),100(AGAACACGGCGTTCTT,+,0.00)
chunk0104_207_1	chr2	175923745	175924229	+	0	NA	TTS (NM_001305011)	TTS (NM_001305011)	78358	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.000000	0.270103	
chunk0130_146_1	chr3	132267404	132268082	+	0	NA	Intergenic	L2c|LINE|L2	-49624	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.007375	0.418262	343(CAAGACACAGTGTTCT,-,0.00),344(AAGACACAGTGTTCTC,+,0.00)
chunk0173_386_1	chr6	150047723	150048312	+	0	NA	Intergenic	Intergenic	21049	NM_024518	79465	Hs.15422	NM_024518	ENSG00000131019	ULBP3	N2DL-3|NKG2DL3|RAET1N	UL16 binding protein 3	protein-coding	0.005093	0.376271	305(GAAAACATGCTGTACT,-,0.00),306(AAAACATGCTGTACTT,+,0.00)
chunk0139_233_1	chr4	55356930	55357609	+	0	NA	intron (NM_024592, intron 1 of 4)	L2a|LINE|L2	11048	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.010309	0.480882	476(CAGAACAGCATGTTCT,-,0.00),477(AGAACAGCATGTTCTT,+,0.00)
chunk0193_84_1	chr8	73497855	73498435	+	0	NA	intron (NM_001164380, intron 13 of 14)	intron (NM_001164380, intron 13 of 14)	78071	NR_038406	100128126	Hs.679921	NR_038406	ENSG00000253302	STAU2-AS1	-	STAU2 antisense RNA 1	ncRNA	0.003448	0.345955	173(CAGGACACATTGTGTT,-,0.00),174(AGGACACATTGTGTTT,+,0.00)
chunk0093_363_1	chr19	55670339	55670629	+	0	NA	intron (NM_001012478, intron 11 of 11)	intron (NM_001012478, intron 11 of 11)	-4711	NM_001130072	29924	Hs.279953	NM_013333	ENSG00000063245	EPN1	-	epsin 1	protein-coding	0.044828	0.611684	
chunk0005_269_1	chr1	59864898	59865185	+	0	NA	intron (NM_015888, intron 17 of 21)	MIRb|SINE|MIR	50180	NM_015888	51361	Hs.378836	NM_015888	ENSG00000134709	HOOK1	HK1	hook microtubule tethering protein 1	protein-coding	0.003484	0.416667	
chunk0032_116_1	chr11	3894969	3895525	+	0	NA	intron (NM_001277961, intron 1 of 11)	intron (NM_001277961, intron 1 of 11)	39185	NR_039835	100616453		NR_039835	ENSG00000284525	MIR4687	-	microRNA 4687	ncRNA	0.016187	0.490126	187(GAGCACTTGGTGTTCT,-,0.00),188(AGCACTTGGTGTTCTC,+,0.00)
chunk0090_236_1	chr18	73756114	73756920	+	0	NA	Intergenic	L2a|LINE|L2	391247	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.031017	0.529120	272(TAGGACACCATGTCCA,-,0.00),273(AGGACACCATGTCCAT,+,0.00)
chunk0134_142_1	chr3	177602917	177603589	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	161332	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.004464	0.417533	
chunk0075_15_1	chr16	46831088	46831437	+	0	NA	promoter-TSS (NM_001001436)	promoter-TSS (NM_001001436)	-100	NM_001001436	388272	Hs.406551	NM_001001436	ENSG00000155330	C16orf87	-	chromosome 16 open reading frame 87	protein-coding	0.134670	0.734286	
chunk0058_342_1	chr14	28847787	28848098	+	0	NA	Intergenic	L1PA6|LINE|L1	75238	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.000000	0.391026	
chunk0079_191_1	chr17	14217850	14218576	+	0	NA	Intergenic	Intergenic	18620	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.001377	0.335626	
chunk0045_73_1	chr12	45695059	45695331	+	0	NA	Intergenic	MER57B2|LTR|ERV1	32726	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.003676	0.417582	134(AGGCACAGACTGTTCA,-,0.00),135(GGCACAGACTGTTCAA,+,0.00)
chunk0145_266_1	chr4	149025296	149025883	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-128706	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.003407	0.425170	
chunk0193_205_1	chr8	75972988	75973284	+	0	NA	Intergenic	Intergenic	433168	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.003378	0.235690	
chunk0164_196_1	chr6	22380377	22380644	+	0	NA	Intergenic	Intergenic	-77657	NM_001163558	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.000000	0.425373	
chunk0042_40_1	chr12	1581468	1581694	+	0	NA	intron (NM_152441, intron 1 of 1)	intron (NM_152441, intron 1 of 1)	12584	NM_152441	144699	Hs.367956	NM_152441	ENSG00000171823	FBXL14	Fbl14	F-box and leucine rich repeat protein 14	protein-coding	0.030973	0.524229	
chunk0105_188_1	chr2	187567907	187568301	+	0	NA	Intergenic	Intergenic	-13612	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.301266	
chunk0112_261_1	chr20	42531568	42531878	+	0	NA	intron (NM_133170, intron 7 of 31)	intron (NM_133170, intron 7 of 31)	-153760	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.012903	0.491961	126(AAGGACTCCCAGTGCT,-,0.00),127(AGGACTCCCAGTGCTC,+,0.00)
chunk0142_223_1	chr4	97912296	97912523	+	0	NA	intron (NM_174952, intron 8 of 10)	L1PA10|LINE|L1	230831	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.008811	0.412281	
chunk0058_220_1	chr14	25055109	25055385	+	0	NA	Intergenic	Intergenic	-4950	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.014493	0.400722	
chunk0181_397_1	chr7	89760592	89760791	+	0	NA	Intergenic	L1MB7|LINE|L1	-358709	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.010050	0.555000	
chunk0116_312_1	chr21	40643166	40643955	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	-12793	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.005070	0.437975	
chunk0051_428_1	chr12	122887949	122888882	+	0	NA	intron (NM_024667, intron 1 of 3)	intron (NM_024667, intron 1 of 3)	7750	NM_024667	79720	Hs.507162	NM_024667	ENSG00000139722	VPS37B	-	VPS37B subunit of ESCRT-I	protein-coding	0.017149	0.443255	
chunk0198_293_1	chr8	135798735	135799238	+	0	NA	Intergenic	Intergenic	341521	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.007952	0.343254	
chunk0095_155_1	chr2	17106312	17106943	+	0	NA	Intergenic	Intergenic	411812	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.003170	0.435127	
chunk0029_129_1	chr10	98612809	98613598	+	0	NA	intron (NM_001166246, intron 9 of 12)	intron (NM_001166246, intron 9 of 12)	-166240	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.007605	0.432911	
chunk0043_453_1	chr12	26711091	26711475	+	0	NA	intron (NM_002223, intron 8 of 56)	intron (NM_002223, intron 8 of 56)	121915	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.013021	0.407792	122(CTGAACAAGCTGTTCC,-,0.00),123(TGAACAAGCTGTTCCA,+,0.00)
chunk0060_253_1	chr14	50025748	50026020	+	0	NA	intron (NR_131171, intron 6 of 8)	MLT1F2|LTR|ERVL-MaLR	-18364	NR_126498	283551	Hs.292580	NM_001012706	ENSG00000214900	LINC01588	C14orf182	long intergenic non-protein coding RNA 1588	ncRNA	0.000000	0.501832	
chunk0004_243_1	chr1	47329025	47329286	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-4642	NR_046394	51727	Hs.731647	NM_016308	ENSG00000162368	CMPK1	CK|CMK|CMPK|UMK|UMP-CMPK|UMPK	cytidine/uridine monophosphate kinase 1	protein-coding	0.003831	0.427481	
chunk0142_185_1	chr4	96147505	96148024	+	0	NA	Intergenic	Intergenic	307676	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.003854	0.353846	
chunk0077_147_1	chr16	78894867	78895255	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	705664	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.025773	0.413882	
chunk0131_234_1	chr3	149369187	149369420	+	0	NA	3' UTR (NM_014220, exon 5 of 5)	3' UTR (NM_014220, exon 5 of 5)	-8475	NR_109810	100874091	Hs.549633	NR_046650	ENSG00000240541	TM4SF1-AS1	-	TM4SF1 antisense RNA 1	ncRNA	0.000000	0.371795	
chunk0173_20_1	chr6	141481544	141482096	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	606979	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.005435	0.356239	327(GGGGACGTTCTGTGCT,-,0.00),328(GGGACGTTCTGTGCTG,+,0.00)
chunk0084_181_1	chr17	77614523	77614817	+	0	NA	Intergenic	L1MB5|LINE|L1	67729	NR_040050	100507351	Hs.514518	NR_040050		LOC100507351	-	uncharacterized LOC100507351	ncRNA	0.013605	0.461017	
chunk0045_12_1	chr12	42996690	42997462	+	0	NA	Intergenic	Intergenic	-350578	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.005181	0.335058	
chunk0079_44_1	chr17	10499899	10500343	+	0	NA	intron (NM_005963, intron 28 of 39)	intron (NM_005963, intron 28 of 39)	18421	NM_005963	4619	Hs.689619	NM_005963	ENSG00000109061	MYH1	HEL71|MYHSA1|MYHa|MyHC-2X/D|MyHC-2x	myosin heavy chain 1	protein-coding	0.006757	0.368539	
chunk0044_349_1	chr12	38886048	38886504	+	0	NA	intron (NM_153634, intron 1 of 19)	MIR|SINE|MIR	19342	NM_153634	144402	Hs.40910	NM_153634	ENSG00000139117	CPNE8	-	copine 8	protein-coding	0.000000	0.396061	
chunk0164_352_1	chr6	25455155	25455354	+	0	NA	intron (NM_017640, intron 8 of 36)	intron (NM_017640, intron 8 of 36)	175826	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.015075	0.335000	
chunk0128_61_1	chr3	104954253	104954541	+	0	NA	Intergenic	L1MC3|LINE|L1	-412316	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006944	0.297578	
chunk0003_304_1	chr1	37676456	37676881	+	0	NA	Intergenic	Intergenic	13927	NM_001303030	54955	Hs.272673	NM_017850	ENSG00000116922	C1orf109	-	chromosome 1 open reading frame 109	protein-coding	0.018824	0.436620	149(CTGGACAAAATGTGCC,-,0.00),150(TGGACAAAATGTGCCT,+,0.00)
chunk0102_208_1	chr2	148254897	148255254	+	0	NA	intron (NM_018328, intron 4 of 14)	HERVL18-int|LTR|ERVL	-233471	NM_181742	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.011204	0.516760	
chunk0100_342_1	chr2	117060626	117060855	+	0	NA	Intergenic	Intergenic	-753939	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.008734	0.300000	
chunk0204_412_1	chr9	102848640	102849075	+	0	NA	Intergenic	Intergenic	-146454	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.004598	0.288991	
chunk0066_225_1	chr15	34015684	34016062	+	0	NA	intron (NM_020371, intron 1 of 5)	intron (NM_020371, intron 1 of 5)	23229	NM_020371	57099	Hs.555966	NM_020371	ENSG00000169857	AVEN	PDCD12	apoptosis and caspase activation inhibitor	protein-coding	0.021164	0.427441	
chunk0152_327_1	chr5	62156028	62156241	+	0	NA	Intergenic	Intergenic	-150028	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.009390	0.336449	
chunk0111_399_1	chr20	34263940	34264667	+	0	NA	intron (NM_001672, intron 2 of 2)	Tigger2b_Pri|DNA|TcMar-Tigger	3938	NM_001672	434	Hs.659995	NM_001672	ENSG00000101440	ASIP	AGSW|AGTI|AGTIL|ASP|SHEP9	agouti signaling protein	protein-coding	0.006878	0.340659	323(CAGTACATACTGTACT,-,0.00),324(AGTACATACTGTACTA,+,0.00)
chunk0086_327_1	chr18	24444499	24445042	+	0	NA	intron (NM_018439, intron 7 of 10)	MER53|DNA|hAT	-15859	NM_021624	59340	Hs.287388	NM_021624	ENSG00000134489	HRH4	AXOR35|BG26|GPCR105|GPRv53|H4|H4R|HH4R	histamine receptor H4	protein-coding	0.001842	0.369485	
chunk0102_329_1	chr2	151828441	151828796	+	0	NA	promoter-TSS (NM_012097)	promoter-TSS (NM_012097)	-123	NM_012097	26225	Hs.470233	NM_012097	ENSG00000162980	ARL5A	ARFLP5|ARL5	ADP ribosylation factor like GTPase 5A	protein-coding	0.078873	0.606742	
chunk0137_198_1	chr4	17961033	17961683	+	0	NA	intron (NM_001166139, intron 4 of 6)	intron (NM_001166139, intron 4 of 6)	60502	NM_153686	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.000000	0.308756	
chunk0041_179_1	chr11	126231624	126232496	+	0	NA	intron (NM_024556, intron 2 of 8)	intron (NM_024556, intron 2 of 8)	20336	NM_024556	79607	Hs.276315	NM_024556	ENSG00000197798	FAM118B	-	family with sequence similarity 118 member B	protein-coding	0.008028	0.356243	
chunk0043_155_1	chr12	16461287	16461726	+	0	NA	Intergenic	Intergenic	108089	NM_145764	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.004556	0.318182	
chunk0161_1_1	chr5	165250894	165251305	+	0	NA	Intergenic	L2c|LINE|L2	780820	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.007299	0.429612	
chunk0066_183_1	chr15	33117666	33117917	+	0	NA	intron (NM_001277313, intron 4 of 20)	intron (NM_001277313, intron 4 of 20)	-49759	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.003984	0.357143	
chunk0026_402_1	chr10	70055223	70055644	+	0	NA	intron (NM_018649, intron 1 of 8)	FLAM_C|SINE|Alu	2832	NM_018649	55506	Hs.499953	NM_018649	ENSG00000099284	H2AFY2	macroH2A2	H2A histone family member Y2	protein-coding	0.007126	0.393365	
chunk0035_31_1	chr11	40659539	40659800	+	0	NA	intron (NM_020929, intron 1 of 4)	MER52A|LTR|ERV1	-366539	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003831	0.488550	
chunk0069_41_1	chr15	60571746	60572296	+	0	NA	intron (NM_134260, intron 1 of 11)	intron (NM_134260, intron 1 of 11)	20487	NM_134262	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.003636	0.397459	
chunk0202_176_1	chr9	74160305	74160661	+	0	NA	Intergenic	Intergenic	-211048	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.005618	0.358543	
chunk0145_205_1	chr4	147929942	147930293	+	0	NA	intron (NM_024605, intron 13 of 22)	L2b|LINE|L2	147522	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.005698	0.375000	
chunk0073_125_1	chr16	4876699	4877100	+	0	NA	exon (NM_001079514, exon 16 of 18)	exon (NM_001079514, exon 16 of 18)	28519	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.022444	0.569652	
chunk0155_373_1	chr5	97576962	97577300	+	0	NA	intron (NR_105028, intron 2 of 3)	intron (NR_105028, intron 2 of 3)	72435	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.005917	0.330383	
chunk0100_220_1	chr2	111957641	111958201	+	0	NA	intron (NM_006343, intron 4 of 18)	intron (NM_006343, intron 4 of 18)	59307	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.010714	0.434938	325(GGGAACATCCTGTTAC,-,0.00),326(GGAACATCCTGTTACT,+,0.00)
chunk0083_97_1	chr17	64506786	64507108	+	0	NA	promoter-TSS (NM_004396)	promoter-TSS (NM_004396)	211	NM_001316990	90799	Hs.569713	NM_138363	ENSG00000258890	CEP95	CCDC45	centrosomal protein 95	protein-coding	0.108696	0.622291	
chunk0168_174_1	chr6	84007388	84007763	+	0	NA	Intergenic	Intergenic	-26126	NM_138409	112609	Hs.370055	NM_138409	ENSG00000135324	MRAP2	C6orf117|bA51G5.2	melanocortin 2 receptor accessory protein 2	protein-coding	0.002667	0.369681	
chunk0116_131_1	chr21	36188047	36188623	+	0	NA	intron (NM_005128, intron 2 of 36)	intron (NM_005128, intron 2 of 36)	23794	NM_005128	9980	Hs.204575	NM_005128	ENSG00000142197	DOP1B	21orf5|C21orf5|DOPEY2	DOP1 leucine zipper like protein B	protein-coding	0.012153	0.507799	
chunk0135_94_1	chr3	186426057	186426541	+	0	NA	Intergenic	Intergenic	-64065	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.010331	0.422680	
chunk0099_445_1	chr2	103349215	103349462	+	0	NA	Intergenic	L1MD2|LINE|L1	587307	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.012146	0.362903	
chunk0073_283_1	chr16	12811208	12811803	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-7618	NM_001099455	55313	Hs.460002	NM_018340	ENSG00000103381	CPPED1	CSTP1	calcineurin like phosphoesterase domain containing 1	protein-coding	0.008403	0.453020	249(CAGAACAATTTGTCCT,-,0.00),250(AGAACAATTTGTCCTA,+,0.00)
chunk0001_446_1	chr1	11759322	11759586	+	0	NA	Intergenic	MIRc|SINE|MIR	-2739	NM_001010881	284498	Hs.585415	NM_001010881		C1orf167	-	chromosome 1 open reading frame 167	protein-coding	0.003788	0.426415	
chunk0212_77_1	chrY	11534031	11534246	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	887452	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.023256	0.375000	
chunk0039_336_1	chr11	104444373	104444622	+	0	NA	Intergenic	Intergenic	164805	NR_120585	102723895	Hs.48803	NR_120585	ENSG00000256422	LINC02552	-	long intergenic non-protein coding RNA 2552	ncRNA	0.004016	0.360000	
chunk0065_436_1	chr14	106426018	106426475	+	0	NA	Intergenic	L1P4|LINE|L1	-56193	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.008753	0.316594	
chunk0006_261_1	chr1	69631669	69632065	+	0	NA	Intergenic	L2a|LINE|L2	-128308	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.002525	0.372796	
chunk0159_256_1	chr5	142058225	142058463	+	0	NA	Intergenic	L1ME2|LINE|L1	-45289	NM_005471	10007	Hs.633853	NM_005471	ENSG00000113552	GNPDA1	GNP1|GNPDA|GNPI|GPI|HLN	glucosamine-6-phosphate deaminase 1	protein-coding	0.004202	0.343096	
chunk0144_210_1	chr4	134264709	134265406	+	0	NA	Intergenic	(TTGT)n|Simple_repeat|Simple_repeat	-63309	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005739	0.277937	
chunk0193_266_1	chr8	77066073	77066351	+	0	NA	Intergenic	Intergenic	-65168	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.010791	0.362007	
chunk0093_73_1	chr19	40645857	40646269	+	0	NA	Intergenic	L1ME4a|LINE|L1	44059	NM_001289980	9253	Hs.326953	NM_004756	ENSG00000105245	NUMBL	CAG3A|CTG3a|NBL|NUMB-R|NUMBLIKE|NUMBR|TNRC23	NUMB like endocytic adaptor protein	protein-coding	0.014563	0.418886	
chunk0143_67_1	chr4	108045705	108046140	+	0	NA	Intergenic	Intergenic	56208	NM_001184705	3033	Hs.438289	NM_005327	ENSG00000138796	HADH	HAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHAD	hydroxyacyl-CoA dehydrogenase	protein-coding	0.006897	0.506881	
chunk0007_330_1	chr1	84688505	84688950	+	0	NA	intron (NM_014021, intron 1 of 14)	intron (NM_014021, intron 1 of 14)	1741	NM_001166417	117178	Hs.22587	NM_014021	ENSG00000117155	SSX2IP	ADIP|hMsd1	SSX family member 2 interacting protein	protein-coding	0.013483	0.401345	201(TAGAACATAATGTGCT,-,0.00),202(AGAACATAATGTGCTT,+,0.00)
chunk0145_84_1	chr4	145878760	145879279	+	0	NA	intron (NM_178835, intron 4 of 14)	intron (NM_178835, intron 4 of 14)	59941	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.005780	0.444231	
chunk0104_275_1	chr2	178124955	178125585	+	0	NA	intron (NM_152945, intron 8 of 9)	L2c|LINE|L2	12846	NM_152945	129831	Hs.377257	NM_152945	ENSG00000155636	RBM45	DRB1|RB-1	RNA binding motif protein 45	protein-coding	0.000000	0.351823	
chunk0190_333_1	chr8	39025486	39026164	+	0	NA	exon (NM_003816, exon 10 of 22)	exon (NM_003816, exon 10 of 22)	28839	NR_027638	8754	Hs.591852	NM_003816	ENSG00000168615	ADAM9	CORD9|MCMP|MDC9|Mltng	ADAM metallopeptidase domain 9	protein-coding	0.007375	0.335788	356(GGGAACAGTGTGTTCA,-,0.00),357(GGAACAGTGTGTTCAA,+,0.00)
chunk0136_71_1	chr4	1940245	1940460	+	0	NA	3' UTR (NM_007331, exon 11 of 11)	3' UTR (NM_007331, exon 11 of 11)	-34284	NR_003004	677770	Hs.676951	NR_003004	ENSG00000249784	SCARNA22	ACA11	small Cajal body-specific RNA 22	ncRNA	0.000000	0.370370	
chunk0177_405_1	chr7	27440241	27440703	+	0	NA	Intergenic	Intergenic	-175502	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.006494	0.377970	
chunk0061_452_1	chr14	65943203	65943477	+	0	NA	Intergenic	MIRb|SINE|MIR	472238	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.000000	0.400000	119(TGGAACAGGCTGTTAT,-,0.00),120(GGAACAGGCTGTTATT,+,0.00)
chunk0141_449_1	chr4	89245230	89245942	+	0	NA	3' UTR (NM_198281, exon 2 of 2)	3' UTR (NM_198281, exon 2 of 2)	62424	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.002809	0.367461	332(AGGGACAGCCTGTTCT,-,0.00),333(GGGACAGCCTGTTCTA,+,0.00)
chunk0122_274_1	chr3	35529227	35529926	+	0	NA	Intergenic	L1MC1|LINE|L1	-109598	NM_001267616	10777	Hs.475902	NM_016300	ENSG00000172995	ARPP21	ARPP-21|R3HDM3|RCS|TARPP	cAMP regulated phosphoprotein 21	protein-coding	0.011445	0.421429	
chunk0023_378_1	chr10	30414126	30414325	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	-19796	NM_005204	1326	Hs.432453	NM_005204	ENSG00000107968	MAP3K8	AURA2|COT|EST|ESTF|MEKK8|TPL2|Tpl-2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding	0.005025	0.395000	
chunk0185_137_1	chr7	127107801	127108089	+	0	NA	intron (NR_028041, intron 1 of 10)	intron (NR_028041, intron 1 of 10)	-49761	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.013889	0.463668	
chunk0201_208_1	chr9	37184886	37185245	+	0	NA	intron (NM_032226, intron 2 of 8)	intron (NM_032226, intron 2 of 8)	64467	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.011142	0.383333	
chunk0045_363_1	chr12	51997208	51997472	+	0	NA	TTS (NM_020328)	TTS (NM_020328)	-9605	NM_181711	160622	Hs.407202	NM_181711	ENSG00000161835	GRASP	TAMALIN	general receptor for phosphoinositides 1 associated scaffold protein	protein-coding	0.011364	0.464151	
chunk0009_311_1	chr1	108342135	108342617	+	0	NA	Intergenic	L1PA14|LINE|L1	-98295	NM_001143989	148545	Hs.511849	NM_152488	ENSG00000196427	NBPF4	-	NBPF member 4	protein-coding	0.020747	0.416149	
chunk0127_310_1	chr3	99176405	99177016	+	0	NA	Intergenic	Intergenic	-275021	NM_080927	131566	Hs.203691	NM_080927	ENSG00000057019	DCBLD2	CLCP1|ESDN	discoidin, CUB and LCCL domain containing 2	protein-coding	0.004910	0.313725	
chunk0053_66_1	chr13	28185257	28185753	+	0	NA	intron (NM_175854, intron 4 of 18)	intron (NM_175854, intron 4 of 18)	-46331	NR_029383	100288730	Hs.123191	NR_029383		PAN3-AS1	-	PAN3 antisense RNA 1	ncRNA	0.006048	0.311871	
chunk0099_65_1	chr2	84925892	84926221	+	0	NA	Intergenic	MER91C|DNA|hAT-Tip100	20417	NM_021103	9168	Hs.446574	NM_021103	ENSG00000034510	TMSB10	MIG12|TB10	thymosin beta 10	protein-coding	0.066869	0.633333	
chunk0049_257_1	chr12	93719553	93720088	+	0	NA	intron (NR_110093, intron 2 of 2)	L1MC1|LINE|L1	18003	NR_110092	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.001869	0.302239	
chunk0078_414_1	chr16	89240852	89241069	+	0	NA	Intergenic	Intergenic	23257	NM_182531	197320	Hs.647385	NM_182531	ENSG00000170100	ZNF778	-	zinc finger protein 778	protein-coding	0.073733	0.614679	
chunk0097_223_1	chr2	52073701	52073982	+	0	NA	Intergenic	Intergenic	628774	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.007117	0.297872	
chunk0072_356_1	chr15	99760028	99760619	+	0	NA	Intergenic	MIR|SINE|MIR	-26879	NM_001284421	145748	Hs.562568	NM_152449	ENSG00000183060	LYSMD4	-	LysM domain containing 4	protein-coding	0.015228	0.391892	
chunk0179_17_1	chr7	42610697	42611112	+	0	NA	Intergenic	Intergenic	95543	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.004819	0.367788	
chunk0042_326_1	chr12	9673611	9673810	+	0	NA	intron (NM_001197319, intron 1 of 2)	L1PA10|LINE|L1	4002	NM_013269	29121	Hs.268326	NM_013269	ENSG00000069493	CLEC2D	CLAX|LLT1|OCIL	C-type lectin domain family 2 member D	protein-coding	0.010050	0.550000	
chunk0122_332_1	chr3	37137820	37138539	+	0	NA	intron (NM_017724, intron 3 of 13)	intron (NM_017724, intron 3 of 13)	36426	NM_006309	9209	Hs.740522	NM_006309	ENSG00000093167	LRRFIP2	HUFI-2	LRR binding FLII interacting protein 2	protein-coding	0.006954	0.372222	
chunk0098_396_1	chr2	79781811	79782100	+	0	NA	intron (NM_004389, intron 3 of 17)	intron (NM_004389, intron 3 of 17)	84628	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.000000	0.296552	
chunk0079_227_1	chr17	15414961	15415483	+	0	NA	Intergenic	Intergenic	52389	NM_001204477	284040	Hs.164595	NM_173622	ENSG00000239704	CDRT4	-	CMT1A duplicated region transcript 4	protein-coding	0.019157	0.562141	221(GGGCACGGCATGTGCC,-,0.00),222(GGCACGGCATGTGCCT,+,0.00),274(AAGCACACAGTGCCCT,-,0.00),275(AGCACACAGTGCCCTC,+,0.00)
chunk0197_40_1	chr8	118195669	118195868	+	0	NA	non-coding (NR_109794, exon 5 of 5)	non-coding (NR_109794, exon 5 of 5)	-83949	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.000000	0.455000	
chunk0110_464_1	chr20	21564404	21564885	+	0	NA	Intergenic	Intergenic	-5380	NR_109880	101929625	Hs.542413	NR_109880		LINC01727	-	long intergenic non-protein coding RNA 1727	ncRNA	0.031185	0.518672	229(AAGTACTGCCTGTGCC,-,0.00),230(AGTACTGCCTGTGCCC,+,0.00)
chunk0020_49_1	chr1	232322310	232323007	+	0	NA	Intergenic	Intergenic	192950	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.002869	0.446991	
chunk0101_176_1	chr2	129284938	129285400	+	0	NA	Intergenic	L1MD2|LINE|L1	-11278	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.002165	0.339093	
chunk0101_167_1	chr2	128867577	128868146	+	0	NA	non-coding (NR_110278, exon 3 of 3)	non-coding (NR_110278, exon 3 of 3)	3261	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.012302	0.461404	
chunk0107_158_1	chr2	215232884	215233417	+	0	NA	Intergenic	L1ME3D|LINE|L1	-78806	NM_004044	471	Hs.90280	NM_004044	ENSG00000138363	ATIC	AICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding	0.001876	0.337079	
chunk0068_444_1	chr15	59689620	59690079	+	0	NA	promoter-TSS (NM_004330)	promoter-TSS (NM_004330)	-406	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.045752	0.460870	
chunk0200_416_1	chr9	27560256	27560458	+	0	NA	TTS (NM_145005)	TTS (NM_145005)	13136	NM_018325	203228	Hs.493639	NM_018325	ENSG00000147894	C9orf72	ALSFTD|DENND9|DENNL72|FTDALS|FTDALS1	C9orf72-SMCR8 complex subunit	protein-coding	0.009901	0.320197	
chunk0210_290_1	chrX	85860799	85861143	+	0	NA	TTS (NM_000390)	TTS (NM_000390)	25191	NR_031710	100302171		NR_031710	ENSG00000283435	MIR1321	MIRN1321|hsa-mir-1321	microRNA 1321	ncRNA	0.002907	0.362319	
chunk0104_346_1	chr2	179848164	179848783	+	0	NA	intron (NM_152520, intron 1 of 9)	intron (NM_152520, intron 1 of 9)	12435	NR_031659	100302172		NR_031659	ENSG00000221240	MIR1258	MIRN1258|hsa-mir-1258|mir-1258	microRNA 1258	ncRNA	0.006462	0.388710	
chunk0048_318_1	chr12	83168028	83168710	+	0	NA	Intergenic	Intergenic	481214	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.002933	0.360176	381(TGGGACATTGAGTTCC,-,0.00),382(GGGACATTGAGTTCCC,+,0.00)
chunk0111_77_1	chr20	23100164	23100834	+	0	NA	Intergenic	Intergenic	-14159	NM_012072	22918	Hs.97199	NM_012072	ENSG00000125810	CD93	C1QR1|C1qR(P)|C1qRP|CDw93|ECSM3|MXRA4|dJ737E23.1	CD93 molecule	protein-coding	0.011940	0.514158	
chunk0015_321_1	chr1	189410142	189410415	+	0	NA	Intergenic	Intergenic	1067351	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.357664	
chunk0011_237_1	chr1	150555550	150555793	+	0	NA	intron (NM_019032, intron 8 of 18)	intron (NM_019032, intron 8 of 18)	3742	NR_036211	100422997		NR_036211	ENSG00000264553	MIR4257	-	microRNA 4257	ncRNA	0.024691	0.500000	
chunk0163_91_1	chr6	9559618	9560016	+	0	NA	Intergenic	L2c|LINE|L2	-852501	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.002513	0.340852	
chunk0078_164_1	chr17	4237214	4237578	+	0	NA	intron (NM_001257999, intron 2 of 24)	intron (NM_001257999, intron 2 of 24)	26451	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.005495	0.279452	
chunk0093_315_1	chr19	53773097	53773514	+	0	NA	Intergenic	Intergenic	10961	NR_030222	574500		NR_030222	ENSG00000284362	MIR519A2	MIRN519A-2|MIRN519A2|mir-519a-2	microRNA 519a-2	ncRNA	0.011990	0.394737	
chunk0032_405_1	chr11	11841903	11842146	+	0	NA	5' UTR (NM_001282659, exon 1 of 28)	5' UTR (NM_001282659, exon 1 of 28)	601	NM_017944	55031	Hs.577256	NM_017944	ENSG00000170242	USP47	TRFP	ubiquitin specific peptidase 47	protein-coding	0.115226	0.700820	
chunk0189_47_1	chr8	19987243	19987648	+	0	NA	Intergenic	MER63C|DNA|hAT-Blackjack	48374	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.007407	0.325123	
chunk0150_326_1	chr5	38309705	38309904	+	0	NA	intron (NM_152403, intron 1 of 21)	intron (NM_152403, intron 1 of 21)	-18818	NR_046219	100852408	Hs.570954	NR_046219	ENSG00000248730	EGFLAM-AS4	-	EGFLAM antisense RNA 4	ncRNA	0.010050	0.455000	97(GGGGACAGCCAGTCCA,-,0.00),98(GGGACAGCCAGTCCAC,+,0.00)
chunk0027_351_1	chr10	78672699	78673225	+	0	NA	Intergenic	L1PA11|LINE|L1	394486	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.007605	0.426945	
chunk0207_33_1	chrX	4309789	4309988	+	0	NA	Intergenic	Intergenic	323684	NR_110390	101928201	Hs.586488	NR_110390	ENSG00000236513	LOC101928201	-	uncharacterized LOC101928201	ncRNA	0.005025	0.320000	
chunk0063_34_1	chr14	76784707	76785070	+	0	NA	intron (NR_104183, intron 1 of 2)	intron (NR_104183, intron 1 of 2)	1836	NR_104184	100506603	Hs.673984	NR_104183	ENSG00000258301	VASH1-AS1	-	VASH1 antisense RNA 1	ncRNA	0.008264	0.576923	
chunk0057_236_1	chr13	104431852	104432259	+	0	NA	Intergenic	Intergenic	1006855	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.002457	0.330882	
chunk0124_337_1	chr3	58300141	58300340	+	0	NA	Intergenic	MER53|DNA|hAT	-6005	NR_049758	11102	Hs.446320	NM_007042	ENSG00000163684	RPP14	P14	ribonuclease P/MRP subunit p14	protein-coding	0.005025	0.350000	
chunk0157_76_1	chr5	116442322	116442671	+	0	NA	Intergenic	Intergenic	-5002	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.008596	0.485714	
chunk0109_350_1	chr2	238882872	238883529	+	0	NA	intron (NM_001271893, intron 1 of 1)	intron (NM_001271893, intron 1 of 1)	35168	NM_057179	117581	Hs.422585	NM_057179	ENSG00000233608	TWIST2	AMS|BBRSAY|DERMO1|FFDD3|SETLSS|bHLHa39	twist family bHLH transcription factor 2	protein-coding	0.024353	0.524316	
chunk0068_301_1	chr15	57149165	57149550	+	0	NA	intron (NM_003205, intron 5 of 19)	intron (NM_003205, intron 5 of 19)	-70073	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.000000	0.344560	319(TAGAGCAGTTTGTTCT,-,0.00),320(AGAGCAGTTTGTTCTA,+,0.00)
chunk0117_179_1	chr22	20858662	20859185	+	0	NA	promoter-TSS (NM_004782)	promoter-TSS (NM_004782)	-81	NM_004782	9342	Hs.108002	NM_004782	ENSG00000099940	SNAP29	CEDNIK|SNAP-29	synaptosome associated protein 29	protein-coding	0.141491	0.750000	
chunk0175_437_1	chr6	169722937	169723260	+	0	NA	intron (NM_133325, intron 1 of 11)	intron (NM_133325, intron 1 of 11)	912	NM_018288	55274	Hs.435933	NM_018288	ENSG00000130024	PHF10	BAF45A|XAP135	PHD finger protein 10	protein-coding	0.055728	0.524691	
chunk0137_356_1	chr4	25730862	25731647	+	0	NA	Intergenic	Intergenic	74790	NM_001177999	10568	Hs.479372	NM_006424	ENSG00000157765	SLC34A2	NAPI-3B|NAPI-IIb|NPTIIb	solute carrier family 34 member 2	protein-coding	0.007643	0.394402	
chunk0058_348_1	chr14	28881003	28881354	+	0	NA	Intergenic	Intergenic	108474	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.005698	0.321023	153(GGGAACATAGTGCTCA,-,0.00),154(GGAACATAGTGCTCAC,+,0.00)
chunk0123_180_1	chr3	44237771	44238327	+	0	NA	Intergenic	Intergenic	-3837	NM_001145030	375337	Hs.132125	NM_001145030	ENSG00000173769	TOPAZ1	C3orf77	testis and ovary specific PAZ domain containing 1	protein-coding	0.005396	0.447038	
chunk0200_166_1	chr9	18972228	18972855	+	0	NA	intron (NM_001287049, intron 1 of 3)	intron (NM_001287049, intron 1 of 3)	60717	NM_153707	158297	Hs.731593	NM_153707	ENSG00000155875	SAXO1	C9orf138|FAM154A	stabilizer of axonemal microtubules 1	protein-coding	0.006380	0.410828	
chunk0173_94_1	chr6	143048169	143048514	+	0	NA	Intergenic	L1MC2|LINE|L1	-10759	NR_038987	100507489	Hs.486645	NR_038987		LINC01277	-	long intergenic non-protein coding RNA 1277	ncRNA	0.008696	0.346821	
chunk0151_419_1	chr5	55681565	55682065	+	0	NA	intron (NM_173514, intron 3 of 15)	MER58A|DNA|hAT-Charlie	11238	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.012000	0.423154	
chunk0083_36_1	chr17	63356340	63356539	+	0	NA	intron (NM_025185, intron 12 of 24)	intron (NM_025185, intron 12 of 24)	84407	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.005025	0.440000	
chunk0200_403_1	chr9	27289548	27290049	+	0	NA	intron (NM_001161585, intron 4 of 6)	intron (NM_001161585, intron 4 of 6)	-7005	NR_026679	158035	Hs.201554	NR_026679	ENSG00000283945	LINC00032	C9orf14|NCRNA00032	long intergenic non-protein coding RNA 32	ncRNA	0.009980	0.372510	279(GTGTACAGTCTGTTCT,-,0.00),280(TGTACAGTCTGTTCTC,+,0.00)
chunk0155_81_1	chr5	91906508	91906723	+	0	NA	Intergenic	L1MC4|LINE|L1	-523283	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.328704	
chunk0019_189_1	chr1	226671299	226671851	+	0	NA	intron (NR_103784, intron 1 of 1)	L2a|LINE|L2	3493	NR_103784	100506443	Hs.664293	NR_103784		ITPKB-IT1	-	ITPKB intronic transcript 1	ncRNA	0.010870	0.495479	
chunk0073_31_1	chr16	2602845	2603324	+	0	NA	promoter-TSS (NR_015441)	promoter-TSS (NR_015441)	-300	NR_015441	652276	Hs.720448	NR_015441	ENSG00000215154	LOC652276	-	potassium channel tetramerization domain containing 5 pseudogene	pseudo	0.031315	0.402083	
chunk0198_330_1	chr8	140012483	140012726	+	0	NA	intron (NM_001160372, intron 18 of 22)	MIR|SINE|MIR	-309548	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.028807	0.561475	
chunk0210_76_1	chrX	70156879	70157473	+	0	NA	intron (NM_001551, intron 6 of 6)	L1ME3A|LINE|L1	-20307	NM_198512	347516	Hs.454355	NM_198512	ENSG00000184210	DGAT2L6	DC3	diacylglycerol O-acyltransferase 2 like 6	protein-coding	0.005051	0.366387	
chunk0012_144_1	chr1	157472303	157472553	+	0	NA	Intergenic	Intergenic	80092	NM_031281	83416	Hs.415950	NM_031281	ENSG00000143297	FCRL5	BXMAS1|CD307|CD307e|FCRH5|IRTA2|PRO820	Fc receptor like 5	protein-coding	0.012000	0.426295	
chunk0016_202_1	chr1	198689079	198689594	+	0	NA	intron (NR_052021, intron 2 of 2)	intron (NR_052021, intron 2 of 2)	50368	NM_080921	5788	Hs.654514	NM_002838	ENSG00000081237	PTPRC	B220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200	protein tyrosine phosphatase receptor type C	protein-coding	0.007767	0.327519	
chunk0164_284_1	chr6	24549890	24550392	+	0	NA	intron (NM_001168377, intron 18 of 18)	intron (NM_001168377, intron 18 of 18)	33086	NM_001252328	9856	Hs.26441	NM_014809	ENSG00000137261	KIAA0319	AAVR|DYLX2|DYX2|NMIG	KIAA0319	protein-coding	0.013944	0.463221	
chunk0096_167_1	chr2	29598288	29598689	+	0	NA	intron (NM_004304, intron 3 of 28)	intron (NM_004304, intron 3 of 28)	323123	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.004988	0.393035	33(CGGTACAGAGAGTACT,-,0.00),34(GGTACAGAGAGTACTT,+,0.00),177(TAAAACAGCTTGTTCT,-,0.00),178(AAAACAGCTTGTTCTT,+,0.00)
chunk0096_176_1	chr2	29759695	29760181	+	0	NA	intron (NM_004304, intron 1 of 28)	intron (NM_004304, intron 1 of 28)	161673	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.008230	0.398357	
chunk0101_417_1	chr2	139206745	139207005	+	0	NA	Intergenic	L2b|LINE|L2	309551	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.007692	0.360153	
chunk0087_48_1	chr18	31420900	31421367	+	0	NA	intron (NR_110788, intron 1 of 3)	intron (NR_110788, intron 1 of 3)	5855	NR_110788	101927718	Hs.625473	NR_110788	ENSG00000266729	DSG1-AS1	-	DSG1 antisense RNA 1	ncRNA	0.002141	0.279915	
chunk0103_171_1	chr2	162732963	162733205	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-35852	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.008264	0.411523	
chunk0051_422_1	chr12	122688149	122688744	+	0	NA	Intergenic	Intergenic	14911	NM_177551	338442	Hs.524812	NM_177551	ENSG00000182782	HCAR2	GPR109A|HCA2|HM74a|HM74b|NIACR1|PUMAG|Puma-g	hydroxycarboxylic acid receptor 2	protein-coding	0.010084	0.466443	283(GAGAACATCCTGTACT,-,0.00),284(AGAACATCCTGTACTG,+,0.00)
chunk0110_114_1	chr20	12388893	12389304	+	0	NA	Intergenic	Intergenic	471233	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.007299	0.441748	172(TGGGCCAGCGTGTTCC,-,0.00),173(GGGCCAGCGTGTTCCT,+,0.00),218(TGGTACATTGTGTTCC,-,0.00),219(GGTACATTGTGTTCCC,+,0.00)
chunk0168_53_1	chr6	78774841	78775285	+	0	NA	Intergenic	Intergenic	-92481	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.002252	0.406742	98(GAGAACAGAATGTTTT,-,0.00),99(AGAACAGAATGTTTTG,+,0.00)
chunk0149_78_1	chr5	17269200	17269489	+	0	NA	intron (NM_006317, intron 1 of 1)	intron (NM_006317, intron 1 of 1)	51783	NM_006317	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.013841	0.417241	
chunk0169_226_1	chr6	104499541	104499790	+	0	NA	Intergenic	Intergenic	360254	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.008032	0.356000	
chunk0120_264_1	chr3	9149538	9149837	+	0	NA	intron (NM_001033117, intron 1 of 21)	MLT1H|LTR|ERVL-MaLR	-42806	NR_121663	101927416	Hs.475364	NR_121663	ENSG00000228723	SRGAP3-AS2	-	SRGAP3 antisense RNA 2	ncRNA	0.010033	0.516667	
chunk0017_449_1	chr1	214316650	214316880	+	0	NA	intron (NM_020197, intron 3 of 11)	intron (NM_020197, intron 3 of 11)	35543	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.017391	0.432900	
chunk0108_223_1	chr2	233533902	233534375	+	0	NA	intron (NM_018218, intron 9 of 30)	intron (NM_018218, intron 9 of 30)	31452	NM_018218	55230	Hs.96513	NM_018218	ENSG00000085982	USP40	-	ubiquitin specific peptidase 40	protein-coding	0.004228	0.358650	
chunk0204_162_1	chr9	95875864	95876146	+	0	NA	promoter-TSS (NR_023389)	promoter-TSS (NR_023389)	-28	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.099291	0.689046	
chunk0072_198_1	chr15	94485527	94485726	+	0	NA	Intergenic	L1MA4A|LINE|L1	129691	NM_001159644	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.005025	0.560000	
chunk0021_437_1	chr1	247930269	247930903	+	0	NA	Intergenic	Intergenic	-6443	NM_175911	284521	Hs.372936	NM_175911	ENSG00000196071	OR2L13	OR2L14	olfactory receptor family 2 subfamily L member 13	protein-coding	0.006309	0.325984	
chunk0009_138_1	chr1	104671507	104672021	+	0	NA	Intergenic	Intergenic	598741	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.013619	0.366990	
chunk0074_221_1	chr16	25915344	25915554	+	0	NA	intron (NM_006040, intron 1 of 1)	intron (NM_006040, intron 1 of 1)	-109788	NR_036146	100422923		NR_036146	ENSG00000265005	MIR548W	-	microRNA 548w	ncRNA	0.004762	0.308057	
chunk0154_240_1	chr5	81060464	81060724	+	0	NA	intron (NM_006909, intron 2 of 26)	L2a|LINE|L2	-99687	NR_105015	102524628	Hs.737159	NR_105015	ENSG00000251450	RASGRF2-AS1	-	RASGRF2 antisense RNA 1	ncRNA	0.003846	0.348659	
chunk0089_14_1	chr18	57621733	57622082	+	0	NA	promoter-TSS (NM_004539)	promoter-TSS (NM_004539)	38	NM_004539	4677	Hs.465224	NM_004539	ENSG00000134440	NARS	ASNRS|NARS1	asparaginyl-tRNA synthetase	protein-coding	0.100287	0.642857	
chunk0098_158_1	chr2	70228911	70229540	+	0	NA	intron (NM_022173, intron 4 of 12)	intron (NM_022173, intron 4 of 12)	19422	NM_022173	7072	Hs.413123	NM_022037	ENSG00000116001	TIA1	TIA-1|WDM	TIA1 cytotoxic granule associated RNA binding protein	protein-coding	0.006359	0.326984	151(GTGAACGCTGTGTGCT,-,0.00)
chunk0138_119_1	chr4	36339911	36340659	+	0	NA	intron (NM_001170700, intron 8 of 8)	intron (NM_001170700, intron 8 of 8)	56263	NM_001170700	401124	Hs.363407	NM_001136536	ENSG00000197057	DTHD1	-	death domain containing 1	protein-coding	0.002674	0.383178	
chunk0044_251_1	chr12	32010527	32011056	+	0	NA	Intergenic	Intergenic	51372	NM_018169	55196	Hs.445129	NM_018169	ENSG00000174718	RESF1	C12orf35|GET|KIAA1551|UTA2-1	retroelement silencing factor 1	protein-coding	0.003781	0.416981	
chunk0040_327_1	chr11	118274097	118274562	+	0	NA	Intergenic	Intergenic	-9793	NM_005797	10205	Hs.116651	NM_005797	ENSG00000149573	MPZL2	DFNB111|EVA|EVA1	myelin protein zero like 2	protein-coding	0.004301	0.403433	
chunk0054_319_1	chr13	48980329	48980528	+	0	NA	intron (NM_001278438, intron 1 of 25)	Tigger15a|DNA|TcMar-Tigger	3819	NM_001278438	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.000000	0.375000	
chunk0094_238_1	chr2	7012796	7012995	+	0	NA	intron (NM_014746, intron 3 of 8)	intron (NM_014746, intron 3 of 8)	64985	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.005025	0.450000	
chunk0191_261_1	chr8	53401496	53401992	+	0	NA	Intergenic	Intergenic	-150047	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.002016	0.293763	
chunk0182_255_1	chr7	97215629	97215927	+	0	NA	Intergenic	L1PA6|LINE|L1	99185	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.016779	0.561873	
chunk0048_131_1	chr12	79899901	79900188	+	0	NA	intron (NM_001244990, intron 2 of 24)	L2c|LINE|L2	13867	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.000000	0.336806	
chunk0139_390_1	chr4	62138498	62138802	+	0	NA	intron (NR_110595, intron 2 of 7)	LTR28C|LTR|ERV1	23115	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.006579	0.540984	
chunk0162_357_1	chr6	7156352	7156612	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	48629	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.003846	0.452107	82(GGGAACACTGTGCCCT,-,0.00),83(GGAACACTGTGCCCTT,+,0.00)
chunk0188_29_1	chr8	6566538	6566763	+	0	NA	intron (NM_024596, intron 12 of 13)	intron (NM_024596, intron 12 of 13)	-3387	NM_001147	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.048889	0.566372	
chunk0107_396_1	chr2	223863710	223863909	+	0	NA	Intergenic	Intergenic	-26207	NM_001039569	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.005025	0.325000	
chunk0136_335_1	chr3	195696087	195696490	+	0	NA	intron (NR_122105, intron 2 of 4)	L1PA7|LINE|L1	-3113	NR_030296	693155		NR_030296	ENSG00000207650	MIR570	MIRN570|hsa-mir-570	microRNA 570	ncRNA	0.009926	0.361386	
chunk0147_237_1	chr4	182642736	182643287	+	0	NA	intron (NM_001080477, intron 5 of 27)	intron (NM_001080477, intron 5 of 27)	274466	NM_001012732	1635	Hs.183850	NM_001921	ENSG00000129187	DCTD	-	dCMP deaminase	protein-coding	0.005445	0.297101	290(GAGAACTCTGTGTTCC,-,0.00),291(AGAACTCTGTGTTCCT,+,0.00)
chunk0083_425_1	chr17	72432688	72432887	+	0	NA	intron (NR_036488, intron 1 of 3)	intron (NR_036488, intron 1 of 3)	160017	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.005025	0.385000	
chunk0004_317_1	chr1	49638841	49639150	+	0	NA	intron (NM_032785, intron 3 of 13)	intron (NM_032785, intron 3 of 13)	-166910	NR_046839	100874313	Hs.551277	NR_046839	ENSG00000225623	AGBL4-IT1	-	AGBL4 intronic transcript 1	ncRNA	0.012945	0.470968	
chunk0047_77_1	chr12	67761241	67761493	+	0	NA	Intergenic	Intergenic	-31892	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.015873	0.430830	
chunk0186_228_1	chr7	140484986	140485334	+	0	NA	Intergenic	LTR29|LTR|ERV1	-5591	NR_117084	23608	Hs.744883	NM_013446	ENSG00000133606	MKRN1	RNF61	makorin ring finger protein 1	protein-coding	0.005747	0.406877	
chunk0132_434_1	chr3	165039196	165039669	+	0	NA	intron (NM_001041, intron 19 of 47)	intron (NM_001041, intron 19 of 47)	39063	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.002114	0.267932	
chunk0028_396_1	chr10	93106600	93107005	+	0	NA	Intergenic	Intergenic	32912	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.007407	0.426108	
chunk0201_343_1	chr9	65432304	65432530	+	0	NA	Intergenic	Intergenic	-147208	NM_001126334	653427	Hs.714683	NM_001126334	ENSG00000204779	FOXD4L5	bA15J10.2	forkhead box D4 like 5	protein-coding	0.008850	0.515419	
chunk0046_195_1	chr12	58905208	58905589	+	0	NA	intron (NM_001136051, intron 3 of 18)	intron (NM_001136051, intron 3 of 18)	14148	NM_001136051	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.007874	0.324607	
chunk0058_216_1	chr14	24982347	24982988	+	0	NA	intron (NM_014178, intron 1 of 5)	intron (NM_014178, intron 1 of 5)	66333	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.012480	0.392523	
chunk0026_417_1	chr10	70462806	70463005	+	0	NA	Intergenic	Intergenic	-15903	NM_014431	27143	Hs.202351	NM_014431	ENSG00000107719	PALD1	KIAA1274|PALD	phosphatase domain containing paladin 1	protein-coding	0.005025	0.600000	
chunk0049_130_1	chr12	91613361	91613943	+	0	NA	Intergenic	Intergenic	-430528	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.008591	0.384220	258(AAGGTCATGGTGTTCT,-,0.00),259(AGGTCATGGTGTTCTG,+,0.00)
chunk0151_387_1	chr5	55322343	55322542	+	0	NA	exon (NM_015360, exon 2 of 27)	exon (NM_015360, exon 2 of 27)	14694	NM_015360	23517	Hs.274531	NM_015360	ENSG00000039123	MTREX	Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118	Mtr4 exosome RNA helicase	protein-coding	0.005025	0.320000	
chunk0052_309_1	chr12	124916963	124917610	+	0	NA	Intergenic	Intergenic	1739	NR_049820	100847004		NR_049820	ENSG00000265345	MIR5188	mir-5188	microRNA 5188	ncRNA	0.024730	0.509259	
chunk0192_332_1	chr8	67331662	67331920	+	0	NA	intron (NM_006421, intron 1 of 38)	intron (NM_006421, intron 1 of 38)	11886	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.000000	0.339768	
chunk0153_458_1	chr5	76424745	76425065	+	0	NA	intron (NM_006633, intron 1 of 35)	intron (NM_006633, intron 1 of 35)	21650	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.006250	0.498442	182(GGAGACAGGCTGTGCC,-,0.00),183(GAGACAGGCTGTGCCC,+,0.00)
chunk0054_191_1	chr13	44887035	44887539	+	0	NA	Intergenic	Intergenic	-77657	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.005952	0.435644	246(TTGCACAGGGTGTTCT,-,0.00),247(TGCACAGGGTGTTCTC,+,0.00)
chunk0116_375_1	chr21	42057016	42057215	+	0	NA	Intergenic	Intergenic	-5844	NM_001199528	89766	Hs.242520	NM_173568	ENSG00000177398	UMODL1	-	uromodulin like 1	protein-coding	0.020101	0.480000	
chunk0101_389_1	chr2	138656173	138656583	+	0	NA	Intergenic	Intergenic	123863	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.004878	0.408759	211(CAGAACATTGTGTCTT,-,0.00),212(AGAACATTGTGTCTTT,+,0.00)
chunk0186_309_1	chr7	142949461	142949836	+	0	NA	intron (NM_000420, intron 10 of 18)	L2a|LINE|L2	10142	NM_178829	135927	Hs.239676	NM_178829	ENSG00000165131	LLCFC1	C7orf34|ctm-1	LLLL and CFNLAS motif containing 1	protein-coding	0.005333	0.348404	
chunk0204_173_1	chr9	96031266	96031874	+	0	NA	Intergenic	Intergenic	-9815	NR_024129	100188953	Hs.434310	NR_024129	ENSG00000225194	LINC00092	NCRNA00092	long intergenic non-protein coding RNA 92	ncRNA	0.009868	0.538588	
chunk0185_250_1	chr7	130110698	130111313	+	0	NA	intron (NM_014997, intron 2 of 9)	intron (NM_014997, intron 2 of 9)	40496	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.006504	0.290584	
chunk0129_175_1	chr3	120869062	120869629	+	0	NA	Intergenic	Intergenic	-38858	NM_014980	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.003527	0.352113	
chunk0087_134_1	chr18	33781279	33781874	+	0	NA	Intergenic	Intergenic	202999	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.000000	0.427852	
chunk0208_31_1	chrX	11239305	11239773	+	0	NA	intron (NR_109776, intron 3 of 14)	intron (NR_109776, intron 3 of 14)	26436	NM_013423	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.002137	0.383795	
chunk0141_423_1	chr4	88631696	88632227	+	0	NA	intron (NM_014606, intron 3 of 25)	L1MEf|LINE|L1	39538	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.005650	0.409774	
chunk0168_45_1	chr6	78512365	78512798	+	0	NA	Intergenic	L2a|LINE|L2	-354963	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.000000	0.304147	
chunk0099_50_1	chr2	84481202	84481532	+	0	NA	Intergenic	Intergenic	-21905	NM_003849	8802	Hs.270428	NM_003849	ENSG00000163541	SUCLG1	GALPHA|MTDPS9|SUCLA1	succinate-CoA ligase alpha subunit	protein-coding	0.003030	0.371601	
chunk0204_407_1	chr9	102819582	102819895	+	0	NA	Intergenic	Intergenic	-175573	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.000000	0.292994	
chunk0011_150_1	chr1	147540805	147541066	+	0	NA	promoter-TSS (NM_004326)	promoter-TSS (NM_004326)	-566	NM_004326	607	Hs.415209	NM_004326	ENSG00000116128	BCL9	LGS	BCL9 transcription coactivator	protein-coding	0.019157	0.511450	
chunk0212_338_1	chrX	146077152	146077525	+	0	NA	Intergenic	Intergenic	-49466	NR_030581	100126341		NR_030581	ENSG00000216056	MIR891A	MIRN891A	microRNA 891a	ncRNA	0.013405	0.387701	
chunk0171_453_1	chr6	132210311	132210510	+	0	NA	Intergenic	L1PA16|LINE|L1	76432	NR_038981	100507254	Hs.103070	NR_038981	ENSG00000228495	LINC01013	-	long intergenic non-protein coding RNA 1013	ncRNA	0.005025	0.565000	
chunk0120_333_1	chr3	10811947	10812770	+	0	NA	Intergenic	X6A_LINE|LINE|CR1	-3874	NM_014229	6538	Hs.655078	NM_014229	ENSG00000132164	SLC6A11	GAT-3|GAT3|GAT4	solute carrier family 6 member 11	protein-coding	0.004860	0.438107	
chunk0014_438_1	chr1	183684762	183685404	+	0	NA	intron (NM_001297670, intron 1 of 17)	intron (NM_001297670, intron 1 of 17)	-31770	NM_203454	403314	Hs.97335	NM_203454	ENSG00000173627	APOBEC4	C1orf169	apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4	protein-coding	0.012461	0.419907	
chunk0113_116_1	chr20	51478283	51478671	+	0	NA	intron (NM_001136021, intron 3 of 10)	intron (NM_001136021, intron 3 of 10)	-25500	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.010309	0.457584	
chunk0093_378_1	chr19	56205314	56205598	+	0	NA	Intergenic	Intergenic	-12404	NM_001080456	342933	Hs.132130	NM_001080456	ENSG00000197213	ZSCAN5B	ZNF371|ZNF495B	zinc finger and SCAN domain containing 5B	protein-coding	0.014085	0.357895	
chunk0192_274_1	chr8	66113237	66113461	+	0	NA	Intergenic	CpG	-13694	NM_184085	84675	Hs.85524	NM_033058	ENSG00000147573	TRIM55	MURF-2|RNF29|muRF2	tripartite motif containing 55	protein-coding	0.075893	0.586667	
chunk0131_315_1	chr3	150826285	150826484	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	-62908	NM_005067	6478	Hs.477959	NM_005067	ENSG00000181788	SIAH2	hSiah2	siah E3 ubiquitin protein ligase 2	protein-coding	0.005025	0.530000	
chunk0027_223_1	chr10	76254635	76255068	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	472090	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.009238	0.417051	334(TGAACTCAATGTACTT,+,0.00)
chunk0203_164_1	chr9	86036684	86036937	+	0	NA	intron (NM_177937, intron 6 of 9)	L1MB7|LINE|L1	62785	NM_016548	51280	Hs.494337	NM_016548	ENSG00000135052	GOLM1	C9orf155|GOLPH2|GP73|HEL46|PSEC0257|bA379P1.3	golgi membrane protein 1	protein-coding	0.015810	0.440945	
chunk0050_200_1	chr12	104097970	104098371	+	0	NA	intron (NM_013320, intron 12 of 14)	intron (NM_013320, intron 12 of 14)	-27105	NR_106988									0.004988	0.355721	
chunk0029_65_1	chr10	96572940	96573393	+	0	NA	intron (NM_020123, intron 2 of 14)	intron (NM_020123, intron 2 of 14)	13886	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.011038	0.332599	255(AGAGACATAATGTTCC,-,0.00),256(GAGACATAATGTTCCA,+,0.00)
chunk0033_261_1	chr11	18704188	18704398	+	0	NA	TTS (NM_173588)	TTS (NM_173588)	5558	NM_153347	144110	Hs.502100	NM_153347	ENSG00000151117	TMEM86A	-	transmembrane protein 86A	protein-coding	0.009524	0.507109	
chunk0029_445_1	chr10	110313738	110313940	+	0	NA	Intergenic	Intergenic	-8890	NM_005871	10285	Hs.632093	NM_005871	ENSG00000119953	SMNDC1	SMNR|SPF30|TDRD16C	survival motor neuron domain containing 1	protein-coding	0.009901	0.438424	110(AGTCACATCCTGTTCT,-,0.00),111(GTCACATCCTGTTCTT,+,0.00)
chunk0187_420_1	chr7	158539745	158540119	+	0	NA	intron (NM_130843, intron 1 of 21)	intron (NM_130843, intron 1 of 21)	1844	NM_001308268	5799	Hs.490789	NM_002847	ENSG00000155093	PTPRN2	IA-2beta|IAR|ICAAR|PTPRP|R-PTP-N2	protein tyrosine phosphatase receptor type N2	protein-coding	0.029412	0.626667	
chunk0149_358_1	chr5	27738660	27738859	+	0	NA	Intergenic	Intergenic	266467	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.000000	0.295000	
chunk0199_331_1	chr9	9724232	9724543	+	0	NA	intron (NM_002839, intron 7 of 45)	intron (NM_002839, intron 7 of 45)	866369	NR_121599	101929407	Hs.649971	NR_121599		PTPRD-AS1	-	PTPRD antisense RNA 1	ncRNA	0.003215	0.339744	
chunk0102_343_1	chr2	152302157	152302548	+	0	NA	Intergenic	Intergenic	-32885	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.000000	0.318878	
chunk0209_344_1	chrX	52979718	52979938	+	0	NA	intron (NM_001242492, intron 1 of 4)	intron (NM_001242492, intron 1 of 4)	15644	NM_001242490	29057	Hs.6451	NM_014138	ENSG00000268350	FAM156A	PRO0659|TMEM29	family with sequence similarity 156 member A	protein-coding	0.009091	0.425339	97(GGGAACATTGTGTCCT,-,0.00),98(GGAACATTGTGTCCTT,+,0.00)
chunk0163_282_1	chr6	13701689	13702102	+	0	NA	intron (NM_005493, intron 1 of 13)	intron (NM_005493, intron 1 of 13)	9669	NM_005493	10048	Hs.708182	NM_005493	ENSG00000010017	RANBP9	BPM-L|BPM90|RANBPM|RanBP7	RAN binding protein 9	protein-coding	0.014528	0.437198	206(AAGAACAGTCTGTACT,-,0.00),207(AGAACAGTCTGTACTC,+,0.00)
chunk0149_424_1	chr5	29565999	29566465	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-170256	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004292	0.342612	
chunk0123_266_1	chr3	46036455	46036926	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	-9203	NM_005283	2829	Hs.128375	NM_005283	ENSG00000173578	XCR1	CCXCR1|GPR5	X-C motif chemokine receptor 1	protein-coding	0.002123	0.275424	254(CAGAACAAAATGATCT,-,0.00),255(AGAACAAAATGATCTT,+,0.00)
chunk0167_51_1	chr6	55522309	55522775	+	0	NA	intron (NM_019036, intron 4 of 9)	intron (NM_019036, intron 4 of 9)	56672	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.004292	0.319058	204(AGGAACTGAGAGTTCC,-,0.00),205(GGAACTGAGAGTTCCT,+,0.00)
chunk0023_73_1	chr10	22173450	22174039	+	0	NA	Intergenic	HAL1b|LINE|L1	36239	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.003396	0.347458	
chunk0202_389_1	chr9	81122210	81122427	+	0	NA	Intergenic	MER52A|LTR|ERV1	567217	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.000000	0.472477	
chunk0032_120_1	chr11	4040574	4040954	+	0	NA	intron (NM_001277961, intron 3 of 11)	intron (NM_001277961, intron 3 of 11)	-53930	NM_001033	6240	Hs.445705	NM_001033	ENSG00000167325	RRM1	R1|RIR1|RR1	ribonucleotide reductase catalytic subunit M1	protein-coding	0.000000	0.440945	
chunk0044_323_1	chr12	34232832	34233708	+	0	NA	Intergenic	Intergenic	210989	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.010274	0.466363	
chunk0023_12_1	chr10	20895467	20896193	+	0	NA	intron (NM_006393, intron 2 of 27)	intron (NM_006393, intron 2 of 27)	1772	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.006887	0.392022	
chunk0074_353_1	chr16	33947267	33947467	+	0	NA	Intergenic	L1ME2|LINE|L1	177990	NR_130772	104644205	Hs.742548	NR_130771		ENPP7P13	DUNQU1	ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 13	pseudo	0.005000	0.308458	
chunk0041_386_1	chr11	132499478	132500184	+	0	NA	intron (NM_001012393, intron 4 of 7)	intron (NM_001012393, intron 4 of 7)	215529	NR_046820	100874281		NR_046820		NTM-IT	NTM-IT3	NTM intronic transcript	ncRNA	0.008499	0.429986	
chunk0165_271_1	chr6	35952292	35952543	+	0	NA	intron (NM_052961, intron 17 of 19)	MER134|DNA?|DNA?	-31237	NR_034069	6732	Hs.443861	NM_003137	ENSG00000096063	SRPK1	SFRSK1	SRSF protein kinase 1	protein-coding	0.007968	0.373016	
chunk0200_280_1	chr9	22335630	22335978	+	0	NA	Intergenic	Intergenic	-111037	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.002874	0.406877	
chunk0106_437_1	chr2	208495986	208496448	+	0	NA	Intergenic	L2c|LINE|L2	89387	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.006494	0.382289	236(AGGAACAATCTGTTTT,-,0.00),237(GGAACAATCTGTTTTC,+,0.00)
chunk0148_217_1	chr5	8839131	8840098	+	0	NA	promoter-TSS (NR_109932)	promoter-TSS (NR_109932)	-118	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.025853	0.495868	840(GAGTACAGGCTGATCC,-,0.00),841(AGTACAGGCTGATCCA,+,0.00)
chunk0198_61_1	chr8	129352615	129353333	+	0	NA	non-coding (NR_130918, exon 3 of 3)	non-coding (NR_130918, exon 3 of 3)	-111734	NR_033916	728724	Hs.49902	NR_033916	ENSG00000229140	LINC00977	-	long intergenic non-protein coding RNA 977	ncRNA	0.009749	0.439499	357(AGGCACAATCTGTTCA,-,0.00),358(GGCACAATCTGTTCAG,+,0.00),400(AGACACACTCTGTACT,-,0.00),401(GACACACTCTGTACTT,+,0.00)
chunk0014_361_1	chr1	182410429	182411045	+	0	NA	intron (NR_034131, intron 3 of 3)	ERVL-E-int|LTR|ERVL	3116	NR_034131	388719	Hs.508989	NM_001010899	ENSG00000203729	LINC00272	C1orf120|NCRNA00272	long intergenic non-protein coding RNA 272	ncRNA	0.001623	0.400324	
chunk0111_338_1	chr20	33070322	33070590	+	0	NA	intron (NM_182658, intron 11 of 14)	MIRc|SINE|MIR	-11056	NM_182519	149954	Hs.38961	NM_182519	ENSG00000186191	BPIFB4	C20orf186|LPLUNC4|RY2G5|dJ726C3.5	BPI fold containing family B member 4	protein-coding	0.026119	0.516729	
chunk0082_439_1	chr17	61723121	61723706	+	0	NA	intron (NM_032043, intron 16 of 19)	intron (NM_032043, intron 16 of 19)	-132211	NM_199290	342538	Hs.591178	NM_199290	ENSG00000253506	NACA2	ANAC|NACAL	nascent polypeptide associated complex subunit alpha 2	protein-coding	0.000000	0.353242	
chunk0179_209_1	chr7	47575895	47576568	+	0	NA	intron (NM_022748, intron 1 of 30)	intron (NM_022748, intron 1 of 30)	5913	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.013373	0.544510	
chunk0177_54_1	chr7	21049248	21049492	+	0	NA	Intergenic	Intergenic	213939	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.008197	0.518367	
chunk0137_139_1	chr4	15374681	15375054	+	0	NA	intron (NM_001135171, intron 1 of 2)	(TC)n|Simple_repeat|Simple_repeat	316	NM_001135171	114905	Hs.153714	NM_031911	ENSG00000163145	C1QTNF7	CTRP7|ZACRP7	C1q and TNF related 7	protein-coding	0.018767	0.449198	
chunk0036_304_1	chr11	66002102	66002303	+	0	NA	promoter-TSS (NM_001242486)	promoter-TSS (NM_001242486)	-36	NM_001242483	84285	Hs.425178	NM_032325	ENSG00000175376	EIF1AD	OBELIX|haponin	eukaryotic translation initiation factor 1A domain containing	protein-coding	0.069652	0.608911	
chunk0047_111_1	chr12	68890656	68891299	+	0	NA	intron (NM_001005502, intron 2 of 8)	intron (NM_001005502, intron 2 of 8)	42222	NM_198320	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.012442	0.454969	
chunk0179_328_1	chr7	50600626	50600885	+	0	NA	intron (NM_001001549, intron 13 of 14)	L1M|LINE|L1	-35298	NM_001082971	1644	Hs.359698	NM_000790	ENSG00000132437	DDC	AADC	dopa decarboxylase	protein-coding	0.007722	0.438462	
chunk0030_108_1	chr10	112735302	112735692	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-87999	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.005128	0.337596	
chunk0176_182_1	chr7	13859373	13859683	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	126986	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.003226	0.389068	
chunk0045_372_1	chr12	52111373	52111609	+	0	NA	Intergenic	SATR2|Satellite|Satellite	17922	NR_120440	26628	Hs.524431	NR_120438	ENSG00000257542	OR7E47P	OR7E141	olfactory receptor family 7 subfamily E member 47 pseudogene	pseudo	0.016949	0.409283	
chunk0103_335_1	chr2	167795732	167796325	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-22644	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.005059	0.324916	
chunk0121_261_1	chr3	23142143	23142342	+	0	NA	Intergenic	L1PA16|LINE|L1	-61051	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005025	0.430000	13(AAGTACTGCATGTTCT,-,0.00),14(AGTACTGCATGTTCTC,+,0.00)
chunk0019_80_1	chr1	224360461	224360660	+	0	NA	exon (NM_001277198, exon 2 of 5)	exon (NM_001277198, exon 2 of 5)	3749	NM_001277197	29097	Hs.445890	NM_014184	ENSG00000143771	CNIH4	CNIH-4|CNIH2|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding	0.000000	0.280000	
chunk0028_158_1	chr10	86934733	86935030	+	0	NA	TTS (NM_024756)	TTS (NM_024756)	22787	NM_024756	79812	Hs.524479	NM_024756	ENSG00000173269	MMRN2	EMILIN-3|EMILIN3|ENDOGLYX-1	multimerin 2	protein-coding	0.016835	0.416107	
chunk0158_247_1	chr5	130801853	130802340	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	363252	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.004107	0.413934	
chunk0126_446_1	chr3	87161377	87162076	+	0	NA	Intergenic	Intergenic	64551	NR_039958	100616161		NR_039958	ENSG00000264119	MIR4795	-	microRNA 4795	ncRNA	0.004292	0.412857	372(AAGAACATAATGATCT,-,0.00),373(AGAACATAATGATCTG,+,0.00)
chunk0211_15_1	chrX	107726731	107727200	+	0	NA	intron (NM_198057, intron 1 of 2)	Mam_R4|LINE|Dong-R4	-9904	NM_004089	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.012793	0.461702	
chunk0031_266_1	chr10	127694468	127694838	+	0	NA	Intergenic	LTR50|LTR|ERVL	-42621	NM_207426	399823	Hs.449674	NM_207426	ENSG00000186766	FOXI2	-	forkhead box I2	protein-coding	0.024324	0.501348	
chunk0108_249_1	chr2	233941021	233941400	+	0	NA	intron (NM_024080, intron 5 of 25)	LTR31|LTR|ERV1	23812	NM_024080	79054	Hs.366053	NM_024080	ENSG00000144481	TRPM8	LTRPC6|LTrpC-6|TRPP8|trp-p8	transient receptor potential cation channel subfamily M member 8	protein-coding	0.013193	0.410526	
chunk0067_108_1	chr15	42438340	42438936	+	0	NA	exon (NM_022473, exon 9 of 19)	exon (NM_022473, exon 9 of 19)	18929	NM_001284306	64397	Hs.511143	NM_022473	ENSG00000103994	ZNF106	SH3BP3|ZFP106|ZNF474	zinc finger protein 106	protein-coding	0.001678	0.351759	
chunk0127_63_1	chr3	89332115	89332540	+	0	NA	intron (NM_005233, intron 3 of 16)	intron (NM_005233, intron 3 of 16)	224803	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.007059	0.394366	71(TAGGACATACAGTTCC,-,0.00),72(AGGACATACAGTTCCT,+,0.00)
chunk0017_423_1	chr1	213111110	213111876	+	0	NA	intron (NM_001287219, intron 5 of 14)	intron (NM_001287219, intron 5 of 14)	60260	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.003916	0.298566	
chunk0177_120_1	chr7	22332273	22332795	+	0	NA	intron (NM_012294, intron 1 of 25)	intron (NM_012294, intron 1 of 25)	24380	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.005747	0.382409	224(GAGAACAGGATGTTCT,-,0.00),225(AGAACAGGATGTTCTT,+,0.00)
chunk0057_141_1	chr13	99908145	99908433	+	0	NA	non-coding (NR_104592, exon 10 of 10)	non-coding (NR_104592, exon 10 of 10)	48876	NR_120421	101927437	Hs.619936	NR_120421		LOC101927437	-	uncharacterized LOC101927437	ncRNA	0.006944	0.512111	
chunk0045_234_1	chr12	48545582	48545954	+	0	NA	Intergenic	L1MCb|LINE|L1	20136	NM_001005203	341568	Hs.524373	NM_001005203	ENSG00000284723	OR8S1	-	olfactory receptor family 8 subfamily S member 1	protein-coding	0.000000	0.418231	
chunk0147_150_1	chr4	175623691	175624251	+	0	NA	Intergenic	Intergenic	163705	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.010714	0.351159	
chunk0013_147_1	chr1	168560241	168561007	+	0	NA	Intergenic	L1MC3|LINE|L1	-15849	NM_002995	6375	Hs.546295	NM_002995	ENSG00000143184	XCL1	ATAC|LPTN|LTN|SCM-1|SCM-1a|SCM1|SCM1A|SCYC1	X-C motif chemokine ligand 1	protein-coding	0.001305	0.359844	
chunk0101_402_1	chr2	138881375	138881849	+	0	NA	Intergenic	Intergenic	-15712	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.004219	0.362105	
chunk0008_310_1	chr1	95133670	95133992	+	0	NA	intron (NM_001199691, intron 1 of 7)	L2b|LINE|L2	15908	NM_001199691	100527978	Hs.483512	NM_001199691	ENSG00000271092	TLCD4-RWDD3	TMEM56-RWDD3	TLCD4-RWDD3 readthrough	protein-coding	0.000000	0.448916	
chunk0117_20_1	chr22	11302398	11302749	+	0	NA	Intergenic	Intergenic	-341044	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.017094	0.463068	
chunk0047_461_1	chr12	76876004	76876496	+	0	NA	intron (NM_001300965, intron 1 of 5)	intron (NM_001300965, intron 1 of 5)	2790	NM_001300965	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.006098	0.377282	
chunk0016_217_1	chr1	199045739	199045961	+	0	NA	intron (NR_126351, intron 2 of 2)	L1PA16|LINE|L1	-26886	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.009009	0.466368	
chunk0209_401_1	chrX	55646477	55646811	+	0	NA	Intergenic	Intergenic	23244	NM_198451	139628	Hs.364260	NM_198451	ENSG00000189299	FOXR2	FOXN6	forkhead box R2	protein-coding	0.008982	0.435821	174(GGGAACATTGTGTTCT,-,0.00),175(GGAACATTGTGTTCTT,+,0.00)
chunk0081_292_1	chr17	45038884	45039217	+	0	NA	intron (NM_001288654, intron 1 of 4)	intron (NM_001288654, intron 1 of 4)	12467	NM_001288655	79877	Hs.463148	NM_024819	ENSG00000172992	DCAKD	-	dephospho-CoA kinase domain containing	protein-coding	0.015015	0.550898	
chunk0212_111_1	chrY	19337172	19337454	+	0	NA	Intergenic	L1P3|LINE|L1	165840	NR_002923	286554	Hs.211713	NM_173700	ENSG00000215580	BCORP1	BCORL2	BCL6 corepressor pseudogene 1	pseudo	0.007092	0.332155	172(ATGAACAATTTGTCCT,-,0.00),173(TGAACAATTTGTCCTA,+,0.00)
chunk0189_154_1	chr8	23033888	23034164	+	0	NA	intron (NR_027140, intron 1 of 8)	L1MA7|LINE|L1	-34203	NR_038873	286059	Hs.306673	NR_038873	ENSG00000246130	LOC286059	-	TNF receptor superfamily member 10d pseudogene	pseudo	0.003623	0.375451	217(GGGCACACAATGTACA,-,0.00),218(GGCACACAATGTACAA,+,0.00)
chunk0043_381_1	chr12	24840486	24840819	+	0	NA	intron (NM_001178092, intron 5 of 8)	intron (NM_001178092, intron 5 of 8)	61736	NM_001178094	586	Hs.438993	NM_005504	ENSG00000060982	BCAT1	BCATC|BCT1|ECA39|MECA39|PNAS121|PP18	branched chain amino acid transaminase 1	protein-coding	0.000000	0.356287	
chunk0032_54_1	chr11	1791846	1792095	+	0	NA	Intergenic	L1MEc|LINE|L1	-27978	NM_001909	1509	Hs.654447	NM_001909	ENSG00000117984	CTSD	CLN10|CPSD|HEL-S-130P	cathepsin D	protein-coding	0.004016	0.352000	
chunk0072_139_1	chr15	92665109	92665413	+	0	NA	Intergenic	Intergenic	-9460	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.026316	0.442623	
chunk0009_199_1	chr1	106007164	106007991	+	0	NA	Intergenic	L1MC1|LINE|L1	-388642	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001209	0.330918	
chunk0130_51_1	chr3	129423851	129424599	+	0	NA	intron (NM_207307, intron 1 of 8)	intron (NM_207307, intron 1 of 8)	4426	NM_207307	90288	Hs.652347	NM_207307	ENSG00000172771	EFCAB12	C3orf25	EF-hand calcium binding domain 12	protein-coding	0.005348	0.487316	
chunk0034_165_1	chr11	30775927	30776418	+	0	NA	Intergenic	L2c|LINE|L2	-189789	NM_001145399	744	Hs.289795	NM_001584	ENSG00000066382	MPPED2	239FB|C11orf8	metallophosphoesterase domain containing 2	protein-coding	0.006110	0.378049	
chunk0091_437_1	chr19	17097625	17098111	+	0	NA	intron (NM_004145, intron 1 of 39)	MER58A|DNA|hAT-Charlie	22087	NM_004145	4650	Hs.123198	NM_004145	ENSG00000099331	MYO9B	CELIAC4|MYR5	myosin IXB	protein-coding	0.014403	0.482546	232(ATTACAGTCTGTGCCT,+,0.00)
chunk0077_434_1	chr16	85570419	85570670	+	0	NA	Intergenic	Intergenic	-40879	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.035857	0.551587	
chunk0085_211_1	chr18	6719618	6720054	+	0	NA	Intergenic	MIRb|SINE|MIR	-114597	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.004587	0.377574	
chunk0128_330_1	chr3	111978894	111979192	+	0	NA	non-coding (NR_073571, exon 1 of 3)	non-coding (NR_073571, exon 1 of 3)	167	NR_073571	55347	Hs.477115	NM_018394	ENSG00000144827	ABHD10	-	abhydrolase domain containing 10	protein-coding	0.093960	0.648829	
chunk0096_389_1	chr2	37585225	37585447	+	0	NA	Intergenic	Intergenic	86863	NM_001270438	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.000000	0.457399	
chunk0015_253_1	chr1	188030543	188031097	+	0	NA	Intergenic	Intergenic	587192	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003610	0.297297	
chunk0205_122_1	chr9	107858131	107858400	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-368545	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.007435	0.381481	
chunk0170_258_1	chr6	113746645	113746846	+	0	NA	Intergenic	Intergenic	-96670	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.014925	0.410891	67(AAGGACACGATGATCC,-,0.00),68(AGGACACGATGATCCC,+,0.00)
chunk0075_261_1	chr16	53476336	53476618	+	0	NA	intron (NM_005611, intron 17 of 21)	L1MB5|LINE|L1	26827	NM_001012398	64400	Hs.380897	NM_022476	ENSG00000166971	AKTIP	FT1|FTS	AKT interacting protein	protein-coding	0.000000	0.318021	106(GAGAACAGTGTGTATT,-,0.00),107(AGAACAGTGTGTATTC,+,0.00)
chunk0149_196_1	chr5	21589230	21589863	+	0	NA	TTS (NR_027026)	TTS (NR_027026)	130066	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.004739	0.339117	
chunk0142_200_1	chr4	97250602	97251039	+	0	NA	Intergenic	L2b|LINE|L2	-116106	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.006865	0.340183	
chunk0026_176_1	chr10	63313975	63314312	+	0	NA	intron (NM_032776, intron 2 of 25)	L1PB1|LINE|L1	-44920	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.002967	0.378698	
chunk0026_167_1	chr10	63259435	63259875	+	0	NA	intron (NM_001282948, intron 2 of 24)	intron (NM_001282948, intron 2 of 24)	9568	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.000000	0.344671	
chunk0048_375_1	chr12	86349194	86349603	+	0	NA	intron (NM_013244, intron 2 of 6)	L1MEg|LINE|L1	475103	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.004890	0.429268	
chunk0019_376_1	chr1	229905012	229905435	+	0	NA	Intergenic	L1ME1|LINE|L1	-152566	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.016548	0.405660	
chunk0112_15_1	chr20	35953867	35954170	+	0	NA	exon (NM_016558, exon 3 of 3)	exon (NM_016558, exon 3 of 3)	608	NM_033630	51282	Hs.584909	NM_016558	ENSG00000171222	SCAND1	RAZ1|SDP1	SCAN domain containing 1	protein-coding	0.112211	0.726974	
chunk0039_159_1	chr11	98888198	98888397	+	0	NA	Intergenic	L1MC1|LINE|L1	-132679	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.010050	0.355000	
chunk0199_118_1	chr9	3517457	3517833	+	0	NA	intron (NM_134428, intron 1 of 17)	intron (NM_134428, intron 1 of 17)	8356	NM_001282116	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.000000	0.395225	
chunk0097_351_1	chr2	59654897	59655116	+	0	NA	Intergenic	Intergenic	437298	NR_110219	101927285	Hs.570209	NR_110219	ENSG00000222030	LINC01793	-	long intergenic non-protein coding RNA 1793	ncRNA	0.013699	0.445455	
chunk0140_309_1	chr4	73068055	73068427	+	0	NA	intron (NM_001297733, intron 1 of 5)	intron (NM_001297733, intron 1 of 5)	1518	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.005376	0.327078	
chunk0209_8_1	chrX	34998530	34999038	+	0	NA	Intergenic	Intergenic	55988	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.007874	0.339882	
chunk0158_42_1	chr5	125791653	125792103	+	0	NA	Intergenic	ERV24_Prim-int|LTR|ERV1	298617	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.004444	0.396896	
chunk0163_354_1	chr6	15579283	15579552	+	0	NA	intron (NM_001271667, intron 7 of 9)	L1MA5|LINE|L1	83641	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.011152	0.381481	
chunk0004_302_1	chr1	49021479	49021843	+	0	NA	intron (NM_032785, intron 5 of 13)	MLT1A0|LTR|ERVL-MaLR	-235750	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.005495	0.402740	
chunk0117_386_1	chr21	45225675	45226436	+	0	NA	non-coding (NR_073200, exon 13 of 13)	non-coding (NR_073200, exon 13 of 13)	61841	NM_133635	23275	Hs.592164	NM_015227	ENSG00000186866	POFUT2	C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding	0.022339	0.465879	151(AAGGGCATTGTGTTCC,-,0.00),152(AGGGCATTGTGTTCCG,+,0.00)
chunk0023_315_1	chr10	29098977	29099330	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-189908	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.002833	0.418079	
chunk0202_402_1	chr9	81454627	81455011	+	0	NA	Intergenic	Intergenic	234716	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.010417	0.438961	
chunk0104_218_1	chr2	176346559	176346926	+	0	NA	Intergenic	L1ME3E|LINE|L1	77347	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.000000	0.315217	
chunk0155_362_1	chr5	97326832	97327385	+	0	NA	Intergenic	Intergenic	-143807	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.003617	0.294224	
chunk0019_245_1	chr1	227527214	227527738	+	0	NA	Intergenic	L1PB1|LINE|L1	-36043	NR_102302	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.001908	0.352381	
chunk0047_338_1	chr12	74610626	74611136	+	0	NA	Intergenic	Intergenic	73110	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.005882	0.354207	
chunk0087_57_1	chr18	31583310	31583963	+	0	NA	Intergenic	L3|LINE|CR1	-8131	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.007657	0.458716	
chunk0080_195_1	chr17	29110866	29111353	+	0	NA	intron (NM_203318, intron 17 of 40)	L2a|LINE|L2	-35500	NM_004740	9220	Hs.462590	NM_004740	ENSG00000221995	TIAF1	MAJN|SPR210	TGFB1-induced anti-apoptotic factor 1	protein-coding	0.010267	0.491803	
chunk0163_428_1	chr6	17218057	17218511	+	0	NA	Intergenic	Intergenic	-63294	NM_001143942	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.008811	0.439560	
chunk0194_337_1	chr8	89012382	89013071	+	0	NA	Intergenic	Intergenic	-685238	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.005806	0.336232	388(AAGTACTTGGTGTCCC,-,0.00),389(AGTACTTGGTGTCCCA,+,0.00)
chunk0111_111_1	chr20	23827511	23827790	+	0	NA	promoter-TSS (NM_001322)	promoter-TSS (NM_001322)	-975	NM_001322	1470	Hs.669305	NM_001322	ENSG00000170369	CST2	-	cystatin SA	protein-coding	0.010753	0.407143	174(TGTACAGTCCGTTCCT,+,0.00)
chunk0174_59_1	chr6	155251444	155251904	+	0	NA	intron (NM_001010927, intron 8 of 12)	intron (NM_001010927, intron 8 of 12)	-12339	NM_001001346	49861	Hs.567491	NM_001001346	ENSG00000171217	CLDN20	-	claudin 20	protein-coding	0.013043	0.427332	231(ATGAACACAGTGTCCT,-,0.00),232(TGAACACAGTGTCCTC,+,0.00)
chunk0181_153_1	chr7	82036771	82036995	+	0	NA	intron (NM_000722, intron 11 of 38)	intron (NM_000722, intron 11 of 38)	27706	NR_110077	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.008929	0.395556	
chunk0073_400_1	chr16	16091334	16091923	+	0	NA	intron (NM_004996, intron 19 of 30)	L2a|LINE|L2	131843	NM_001171	368	Hs.442182	NM_001171	ENSG00000091262	ABCC6	ABC34|ARA|EST349056|GACI2|MLP1|MOAT-E|MOATE|MRP6|PXE|PXE1|URG7	ATP binding cassette subfamily C member 6	protein-coding	0.001698	0.520339	266(GGGAACAGCCAGTACA,-,0.00),267(GGAACAGCCAGTACAA,+,0.00)
chunk0059_221_1	chr14	34122034	34122531	+	0	NA	Intergenic	Intergenic	-171204	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.006036	0.425703	304(CAAGACACACTGTCCC,-,0.00),305(AAGACACACTGTCCCT,+,0.00)
chunk0010_436_1	chr1	119948435	119948812	+	0	NA	intron (NM_024408, intron 16 of 33)	intron (NM_024408, intron 16 of 33)	-52099	NM_021794	11085	Hs.283011	NM_021794	ENSG00000134249	ADAM30	svph4	ADAM metallopeptidase domain 30	protein-coding	0.010610	0.518519	
chunk0145_180_1	chr4	147684147	147684426	+	0	NA	promoter-TSS (NM_001304458)	promoter-TSS (NM_001304458)	-56	NM_001304458	90826	Hs.591692	NM_138364	ENSG00000164169	PRMT9	PRMT10	protein arginine methyltransferase 9	protein-coding	0.103943	0.646429	
chunk0179_240_1	chr7	48110197	48110748	+	0	NA	Intergenic	Intergenic	21218	NR_109837	7378	Hs.488240	NM_003364	ENSG00000183696	UPP1	UDRPASE|UP|UPASE|UPP	uridine phosphorylase 1	protein-coding	0.012704	0.472826	
chunk0038_96_1	chr11	83482841	83483074	+	0	NA	intron (NM_001142699, intron 22 of 27)	intron (NM_001142699, intron 22 of 27)	-196550	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.004292	0.401709	17(AAGAACATAAAGTACA,-,0.00),18(AGAACATAAAGTACAT,+,0.00)
chunk0158_87_1	chr5	126536890	126537197	+	0	NA	Intergenic	L1MC4|LINE|L1	58347	NM_001201377	501	Hs.483239	NM_001182	ENSG00000164904	ALDH7A1	ATQ1|EPD|PDE	aldehyde dehydrogenase 7 family member A1	protein-coding	0.009772	0.431818	143(TGGAACATCTTGTGCC,-,0.00),144(GGAACATCTTGTGCCA,+,0.00)
chunk0109_5_1	chr20	143293	143836	+	0	NA	intron (NM_030931, intron 1 of 1)	L1ME4a|LINE|L1	1011	NM_030931	81623	Hs.124211	NM_030931	ENSG00000125788	DEFB126	C20orf8|DEFB-26|DEFB26|HBD26|bA530N10.1|hBD-26	defensin beta 126	protein-coding	0.001842	0.283088	
chunk0201_217_1	chr9	37260106	37260321	+	0	NA	intron (NM_032226, intron 2 of 8)	MER45R|DNA|hAT-Tip100	139615	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.009302	0.509259	
chunk0062_384_1	chr14	74675151	74675350	+	0	NA	intron (NM_001039479, intron 8 of 19)	intron (NM_001039479, intron 8 of 19)	37854	NM_001039479	9870	Hs.497417	NM_014821	ENSG00000119682	AREL1	FIEL1|KIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.340000	
chunk0163_288_1	chr6	13961039	13961356	+	0	NA	intron (NM_001165033, intron 1 of 1)	intron (NM_001165033, intron 1 of 1)	36004	NM_001165033	221687	Hs.111164	NM_152737	ENSG00000180537	RNF182	-	ring finger protein 182	protein-coding	0.009464	0.317610	
chunk0053_1_1	chr13	26019966	26020593	+	0	NA	3' UTR (NM_016529, exon 37 of 37)	3' UTR (NM_016529, exon 37 of 37)	30781	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.011164	0.433121	
chunk0113_405_1	chr20	61115344	61115660	+	0	NA	Intergenic	L2a|LINE|L2	36438	NR_109919	100506470	Hs.125674	NR_109919	ENSG00000229606	LINC01718	-	long intergenic non-protein coding RNA 1718	ncRNA	0.006329	0.441640	
chunk0080_2_1	chr17	20735517	20736307	+	0	NA	intron (NR_073509, intron 11 of 11)	intron (NR_073509, intron 11 of 11)	23466	NR_073509	100287072	Hs.676308	NR_073509		LOC100287072	-	ribosomal protein S6 kinase B1 pseudogene	pseudo	0.007595	0.375474	
chunk0131_363_1	chr3	151971599	151971964	+	0	NA	Intergenic	(TCATT)n|Simple_repeat|Simple_repeat	-43606	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.000000	0.330601	
chunk0100_203_1	chr2	111247771	111248054	+	0	NA	Intergenic	Intergenic	73174	NR_039636	100616341		NR_039636	ENSG00000266139	MIR4435-2	mir-4435-2	microRNA 4435-2	ncRNA	0.010601	0.397887	
chunk0181_455_1	chr7	90763059	90763434	+	0	NA	intron (NM_001287136, intron 3 of 13)	L1MCa|LINE|L1	53430	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.010667	0.420213	
chunk0092_150_1	chr19	28860809	28861021	+	0	NA	Intergenic	Intergenic	-104216	NR_027318	148145	Hs.112651	NR_027318	ENSG00000267339	LINC00906	-	long intergenic non-protein coding RNA 906	ncRNA	0.000000	0.549296	
chunk0149_352_1	chr5	27413765	27414491	+	0	NA	Intergenic	L1MC3|LINE|L1	-58164	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.002755	0.320495	
chunk0035_449_1	chr11	57667966	57668319	+	0	NA	5' UTR (NM_015457, exon 1 of 12)	5' UTR (NM_015457, exon 1 of 12)	140	NM_015457	25921	Hs.27239	NM_015457	ENSG00000156599	ZDHHC5	DHHC5|ZNF375	zinc finger DHHC-type containing 5	protein-coding	0.130312	0.723164	
chunk0030_102_1	chr10	112631530	112631921	+	0	NA	intron (NM_145206, intron 5 of 7)	intron (NM_145206, intron 5 of 7)	-2445	NR_036177	100422909		NR_036177	ENSG00000264763	MIR4295	-	microRNA 4295	ncRNA	0.012788	0.426020	
chunk0179_322_1	chr7	50527253	50527852	+	0	NA	intron (NM_001242889, intron 4 of 12)	L2a|LINE|L2	-4207	NR_033845	100129427	Hs.680434	NR_033845	ENSG00000226122	DDC-AS1	-	DDC antisense RNA 1	ncRNA	0.008347	0.375000	
chunk0169_210_1	chr6	102972342	102972855	+	0	NA	Intergenic	Intergenic	1573613	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001949	0.278210	
chunk0118_2_1	chr22	25311280	25311586	+	0	NA	Intergenic	Intergenic	-6824	NR_029395	91353	Hs.651077	NM_001013618		IGLL3P	16.1|IGLL3	immunoglobulin lambda like polypeptide 3, pseudogene	pseudo	0.006536	0.439739	
chunk0133_144_1	chr3	169291541	169291926	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-143999	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.000000	0.339378	
chunk0176_188_1	chr7	13899208	13899803	+	0	NA	intron (NR_120445, intron 14 of 14)	intron (NR_120445, intron 14 of 14)	87009	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.008403	0.340604	
chunk0096_408_1	chr2	38026941	38027276	+	0	NA	intron (NM_144713, intron 10 of 10)	intron (NM_144713, intron 10 of 10)	9233	NR_102712	101410544	Hs.591566	NR_102712		RMDN2-AS1	-	RMDN2 antisense RNA 1	ncRNA	0.005970	0.416667	
chunk0085_174_1	chr18	5237886	5238209	+	0	NA	promoter-TSS (NR_015389)	promoter-TSS (NR_015389)	-18	NR_026849	147525	Hs.657197	NM_152471		LINC00526	C18orf18|HsT959	long intergenic non-protein coding RNA 526	ncRNA	0.111455	0.691358	
chunk0078_190_1	chr17	4908809	4909187	+	0	NA	Intergenic	Intergenic	-5924	NM_000080	1145	Hs.654535	NM_000080	ENSG00000108556	CHRNE	ACHRE|CMS1D|CMS1E|CMS2A|CMS4A|CMS4B|CMS4C|FCCMS|SCCMS	cholinergic receptor nicotinic epsilon subunit	protein-coding	0.023810	0.530343	
chunk0089_369_1	chr18	67120864	67121519	+	0	NA	Intergenic	L1M4|LINE|L1	39607	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.000000	0.375000	
chunk0006_15_1	chr1	63916468	63916755	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	142592	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.000000	0.434028	144(CTGTACACTTTGTTCC,-,0.00),145(TGTACACTTTGTTCCT,+,0.00)
chunk0048_307_1	chr12	82880070	82880548	+	0	NA	intron (NM_152588, intron 2 of 11)	intron (NM_152588, intron 2 of 11)	193154	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004184	0.369520	370(TGCACTGAATGTGCCT,+,0.00)
chunk0161_66_1	chr5	166567720	166568198	+	0	NA	Intergenic	L1M5|LINE|L1	358411	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004184	0.286013	
chunk0068_137_1	chr15	52875020	52875438	+	0	NA	Intergenic	Intergenic	-85217	NM_004498	3175	Hs.555318	NM_004498	ENSG00000169856	ONECUT1	HNF-6|HNF6|HNF6A	one cut homeobox 1	protein-coding	0.002392	0.384248	
chunk0135_179_1	chr3	188076355	188076565	+	0	NA	Intergenic	Intergenic	-77413	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.009524	0.559242	77(CGGCACAGAGTGTTCT,-,0.00),78(GGCACAGAGTGTTCTG,+,0.00)
chunk0102_217_1	chr2	148516508	148516936	+	0	NA	Intergenic	Intergenic	-128269	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.004673	0.296037	
chunk0095_381_1	chr2	23679386	23679975	+	0	NA	intron (NM_052920, intron 5 of 13)	L2c|LINE|L2	247434	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.015280	0.503390	352(GAGCACAAGTTGTTCT,-,0.00),353(AGCACAAGTTGTTCTG,+,0.00)
chunk0086_219_1	chr18	22579479	22579967	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	-161808	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.014344	0.529652	
chunk0052_222_1	chr13	25496439	25497052	+	0	NA	intron (NM_001313741, intron 2 of 35)	intron (NM_001313741, intron 2 of 35)	27971	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.008157	0.392508	301(AGGAACAATTTGTTCT,-,0.00),302(GGAACAATTTGTTCTC,+,0.00)
chunk0124_101_1	chr3	53614334	53614825	+	0	NA	intron (NM_000720, intron 3 of 48)	LTR41|LTR|ERVL	119530	NM_001128840	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.012220	0.487805	
chunk0060_321_1	chr14	51366127	51366347	+	0	NA	TTS (NR_038358)	TTS (NR_038358)	32844	NR_038358	283553	Hs.325752	NR_038358	ENSG00000258479	LINC00640	-	long intergenic non-protein coding RNA 640	ncRNA	0.009091	0.561086	
chunk0064_257_1	chr14	94636632	94637152	+	0	NA	Intergenic	Intergenic	-3833	NR_015340	388007	Hs.527795	NR_015340	ENSG00000187483	SERPINA13P	SERPINA13|UNQ6121	serpin family A member 13, pseudogene	pseudo	0.001923	0.374280	
chunk0199_462_1	chr9	14251278	14251939	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	62438	NM_005596	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.012103	0.468278	
chunk0167_231_1	chr6	67350682	67351206	+	0	NA	Intergenic	L2b|LINE|L2	-704407	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.007634	0.308571	231(AGGCACAGTGCGTACC,-,0.00)
chunk0084_355_1	chr17	81343019	81343293	+	0	NA	Intergenic	CpG	-12482	NM_178520	284186	Hs.364191	NM_178520		TMEM105	-	TMEM105 long non-coding RNA	ncRNA	0.080292	0.640000	134(AGGGACTCTCCGTTCT,-,0.00),135(GGGACTCTCCGTTCTC,+,0.00)
chunk0036_19_1	chr11	58391818	58392258	+	0	NA	Intergenic	Intergenic	11371	NM_001005469	441608	Hs.553826	NM_001005469	ENSG00000172769	OR5B3	OR11-239|OR5B13|OST129	olfactory receptor family 5 subfamily B member 3	protein-coding	0.004545	0.340136	
chunk0034_106_1	chr11	27716084	27716722	+	0	NA	intron (NM_170731, intron 1 of 1)	intron (NM_170731, intron 1 of 1)	3344	NM_001143807	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.004702	0.333333	254(TAGTACGCAATGTTCT,-,0.00),255(AGTACGCAATGTTCTT,+,0.00)
chunk0050_249_1	chr12	105454818	105455174	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	124360	NM_001145199	387882	Hs.368938	NM_207376	ENSG00000235162	C12orf75	AGD3|OCC-1|OCC1	chromosome 12 open reading frame 75	protein-coding	0.005618	0.456583	178(GAGGACACAGCGTTCT,-,0.00),179(AGGACACAGCGTTCTT,+,0.00)
chunk0166_360_1	chr6	51453833	51454058	+	0	NA	Intergenic	Intergenic	-167925	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.008889	0.469027	
chunk0158_306_1	chr5	132365901	132366305	+	0	NA	promoter-TSS (NR_037500)	promoter-TSS (NR_037500)	-504	NR_037500	100500865		NR_037500	ENSG00000263597	MIR3936	mir-3936	microRNA 3936	ncRNA	0.007426	0.392593	154(GAGAACACAAAGTTCT,-,0.00),155(AGAACACAAAGTTCTT,+,0.00)
chunk0192_338_1	chr8	67581492	67581913	+	0	NA	intron (NM_020361, intron 2 of 10)	intron (NM_020361, intron 2 of 10)	164683	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.004751	0.398104	196(TTGGACTGGCTGTCCC,-,0.00),197(TGGACTGGCTGTCCCC,+,0.00)
chunk0142_351_1	chr4	101756124	101756671	+	0	NA	Intergenic	Intergenic	-34210	NM_001127507	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.003656	0.423358	245(AAGCACAGCCAGTACA,-,0.00),246(AGCACAGCCAGTACAT,+,0.00)
chunk0119_273_1	chr22	46018689	46019203	+	0	NA	Intergenic	L2c|LINE|L2	12330	NR_027240	730668	Hs.640071	NR_027240	ENSG00000280424	LOC730668	-	dynein heavy chain -like pseudogene	pseudo	0.000000	0.390291	
chunk0152_219_1	chr5	60329843	60330340	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-157622	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.004024	0.363454	
chunk0186_222_1	chr7	140143886	140144865	+	0	NA	intron (NM_030647, intron 1 of 19)	L1M4|LINE|L1	32566	NM_030647	80853	Hs.308710	NM_030647	ENSG00000006459	KDM7A	JHDM1D	lysine demethylase 7A	protein-coding	0.008172	0.384694	372(AAGAAGAGTCTGTTCT,-,0.00),373(AGAAGAGTCTGTTCTA,+,0.00)
chunk0165_464_1	chr6	41287748	41288000	+	0	NA	Intergenic	L1M6|LINE|L1	-1155	NM_001242589	54210	Hs.283022	NM_018643	ENSG00000124731	TREM1	CD354|TREM-1	triggering receptor expressed on myeloid cells 1	protein-coding	0.000000	0.300395	116(AAGAACATTATGACCC,-,0.00),117(AGAACATTATGACCCT,+,0.00)
chunk0212_274_1	chrX	139759124	139759528	+	0	NA	intron (NM_001010986, intron 22 of 28)	L2a|LINE|L2	-51104	NM_001171876	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.007426	0.422222	
chunk0063_169_1	chr14	80304207	80304648	+	0	NA	intron (NR_038355, intron 2 of 8)	intron (NR_038355, intron 2 of 8)	-73373	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.009070	0.398190	
chunk0052_340_1	chr12	126499053	126499377	+	0	NA	Intergenic	Intergenic	56734	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.009259	0.421538	
chunk0017_283_1	chr1	209856443	209856669	+	0	NA	3' UTR (NM_014388, exon 12 of 12)	3' UTR (NM_014388, exon 12 of 12)	28589	NM_014388	27042	Hs.194754	NM_014388	ENSG00000117597	UTP25	C1orf107|DEF|DIEXF|DJ434O14.5	UTP25 small subunit processor component	protein-coding	0.013274	0.471366	
chunk0150_310_1	chr5	37900523	37901108	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	27390	NM_001278094	100861519	Hs.536820	NM_001278094		GDNF-AS1	GDNFOS	GDNF antisense RNA 1	ncRNA	0.003419	0.426621	376(TGGACCAGCCTGTTCT,-,0.00),377(GGACCAGCCTGTTCTA,+,0.00)
chunk0097_200_1	chr2	50718119	50718769	+	0	NA	intron (NM_001135659, intron 5 of 23)	intron (NM_001135659, intron 5 of 23)	-22182	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.007692	0.360983	
chunk0048_86_1	chr12	79163042	79163700	+	0	NA	intron (NM_001135805, intron 4 of 11)	intron (NM_001135805, intron 4 of 11)	117718	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.007599	0.429439	255(GAGAACATTCTCTTCC,-,0.00),256(AGAACATTCTCTTCCT,+,0.00),407(GGGGTCACTATGTGCC,-,0.00)
chunk0014_432_1	chr1	183543518	183543883	+	0	NA	intron (NM_001174061, intron 13 of 21)	intron (NM_001174061, intron 13 of 21)	46904	NM_000433	4688	Hs.587558	NM_000433	ENSG00000116701	NCF2	NCF-2|NOXA2|P67-PHOX|P67PHOX	neutrophil cytosolic factor 2	protein-coding	0.005479	0.404372	
chunk0041_94_1	chr11	124629619	124630250	+	0	NA	intron (NM_032811, intron 5 of 8)	intron (NM_032811, intron 5 of 8)	-6564	NR_106988									0.007924	0.294304	
chunk0093_372_1	chr19	55955924	55956961	+	0	NA	intron (NM_001317000, intron 3 of 9)	AluSx|SINE|Alu	8610	NM_176811	126205	Hs.446925	NM_176811	ENSG00000179709	NLRP8	CLR19.2|NALP8|NOD16|PAN4	NLR family pyrin domain containing 8	protein-coding	0.019286	0.491329	
chunk0114_99_1	chr21	9341919	9342320	+	0	NA	Intergenic	MER52A|LTR|ERV1	-212358	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.019950	0.614428	
chunk0186_340_1	chr7	143325243	143325694	+	0	NA	intron (NR_046453, intron 7 of 21)	intron (NR_046453, intron 7 of 21)	9342	NM_000083	1180	Hs.121483	NM_000083	ENSG00000188037	CLCN1	CLC1	chloride voltage-gated channel 1	protein-coding	0.004435	0.367257	
chunk0208_423_1	chrX	29808728	29809193	+	0	NA	intron (NM_014271, intron 6 of 10)	L1MEd|LINE|L1	234682	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.002151	0.347639	
chunk0031_205_1	chr10	125886110	125886345	+	0	NA	Intergenic	L2a|LINE|L2	-4912	NM_018180	55760	Hs.370292	NM_018180	ENSG00000089876	DHX32	DDX32|DHLP1	DEAH-box helicase 32 (putative)	protein-coding	0.008511	0.453390	30(TGGAACTTGGTGTTCA,-,0.00),31(GGAACTTGGTGTTCAC,+,0.00)
chunk0212_332_1	chrX	144672091	144672441	+	0	NA	Intergenic	Intergenic	-575321	NM_001009614	494118		NM_001009614	ENSG00000203923	SPANXN1	CT11.6	SPANX family member N1	protein-coding	0.000000	0.316239	
chunk0042_310_1	chr12	7990749	7991441	+	0	NA	Intergenic	Intergenic	-41668	NM_018416	55810	Hs.120844	NM_018416	ENSG00000065970	FOXJ2	FHX	forkhead box J2	protein-coding	0.014451	0.408369	
chunk0128_293_1	chr3	110961295	110961527	+	0	NA	Intergenic	L1MCa|LINE|L1	108548	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.004310	0.334764	
chunk0034_113_1	chr11	27990782	27991002	+	0	NA	Intergenic	Intergenic	-65923	NR_030341	693195		NR_030341	ENSG00000207874	MIR610	MIRN610|hsa-mir-610	microRNA 610	ncRNA	0.000000	0.285068	
chunk0199_112_1	chr9	3417908	3418212	+	0	NA	intron (NM_001282116, intron 1 of 16)	intron (NM_001282116, intron 1 of 16)	-22464	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.000000	0.318033	123(TGAGCATTCTGTGCTT,+,0.00)
chunk0154_17_1	chr5	76690956	76691667	+	0	NA	intron (NM_006633, intron 30 of 35)	intron (NM_006633, intron 30 of 35)	-21092	NR_028375	100302746		NR_028375		NCRUPAR	NCRNA00193|ncR-uPAR	non-protein coding RNA, upstream of F2R/PAR1	ncRNA	0.009845	0.424157	
chunk0089_270_1	chr18	62739895	62740397	+	0	NA	intron (NM_194449, intron 1 of 16)	intron (NM_194449, intron 1 of 16)	24707	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.009960	0.417495	
chunk0012_437_1	chr1	164891586	164892083	+	0	NA	Intergenic	Intergenic	-117193	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.000000	0.445783	
chunk0165_114_1	chr6	32881528	32881918	+	0	NA	Intergenic	L1MD1|LINE|L1	-12453	NR_037178	100294145	Hs.559456	NR_037177		LOC100294145	-	uncharacterized LOC100294145	ncRNA	0.000000	0.365729	
chunk0140_340_1	chr4	73895224	73895969	+	0	NA	Intergenic	MER50|LTR|ERV1	26204	NR_046035	2919	Hs.789	NM_001511	ENSG00000163739	CXCL1	FSP|GRO1|GROa|MGSA|MGSA-a|NAP-3|SCYB1	C-X-C motif chemokine ligand 1	protein-coding	0.009396	0.454424	418(AAGCACAGTGTGTTCC,-,0.00),419(AGCACAGTGTGTTCCC,+,0.00)
chunk0073_449_1	chr16	19396243	19397036	+	0	NA	Intergenic	HERVK14C-int|LTR|ERVK	-13900	NM_001308161	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.015132	0.414358	
chunk0185_301_1	chr7	131203922	131204197	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	93963	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.007273	0.420290	
chunk0047_274_1	chr12	73061975	73062215	+	0	NA	Intergenic	L1MB1|LINE|L1	-97095	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.302905	
chunk0099_129_1	chr2	86191283	86191568	+	0	NA	intron (NM_001100170, intron 1 of 14)	MLT2C2|LTR|ERVL	1683	NR_039939	100616159		NR_039939	ENSG00000265420	MIR4779	-	microRNA 4779	ncRNA	0.000000	0.472028	
chunk0205_128_1	chr9	108053462	108054215	+	0	NA	Intergenic	Intergenic	-564118	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.019920	0.465517	
chunk0151_34_1	chr5	41832811	41833782	+	0	NA	intron (NM_000436, intron 7 of 16)	L1M1|LINE|L1	-36734	NR_046635	100874002	Hs.375537	NR_046635	ENSG00000248668	OXCT1-AS1	-	OXCT1 antisense RNA 1	ncRNA	0.002060	0.339506	
chunk0125_67_1	chr3	64268419	64269130	+	0	NA	Intergenic	Intergenic	-43319	NM_198859	166336	Hs.148105	NM_198859	ENSG00000163637	PRICKLE2	EPM5	prickle planar cell polarity protein 2	protein-coding	0.008439	0.422753	
chunk0016_343_1	chr1	201983225	201983457	+	0	NA	intron (NM_020216, intron 1 of 10)	CpG	703	NM_020216	6051	Hs.497391	NM_020216	ENSG00000176393	RNPEP	AP-B|APB	arginyl aminopeptidase	protein-coding	0.068966	0.630901	
chunk0020_236_1	chr1	235802363	235802918	+	0	NA	intron (NM_001301365, intron 8 of 52)	L2b|LINE|L2	50420	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.003604	0.357914	
chunk0004_229_1	chr1	47030967	47031584	+	0	NA	intron (NM_178033, intron 2 of 11)	intron (NM_178033, intron 2 of 11)	7707	NM_178033	260293	Hs.439760	NM_178033	ENSG00000186377	CYP4X1	CYPIVX1	cytochrome P450 family 4 subfamily X member 1	protein-coding	0.004862	0.438511	
chunk0120_76_1	chr3	3582553	3582846	+	0	NA	Intergenic	Intergenic	-216738	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.006826	0.438776	
chunk0175_144_1	chr7	3576137	3576663	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	274952	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.013308	0.421252	
chunk0069_6_1	chr15	60035342	60035900	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	31399	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.005376	0.339893	
chunk0149_284_1	chr5	25255092	25255571	+	0	NA	Intergenic	Intergenic	-414748	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.002088	0.325000	
chunk0163_422_1	chr6	17151665	17152372	+	0	NA	Intergenic	Intergenic	49760	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.005658	0.395480	572(CAGCACACGCTGTCCC,-,0.00),573(AGCACACGCTGTCCCC,+,0.00)
chunk0029_143_1	chr10	99338860	99339532	+	0	NA	intron (NM_020348, intron 1 of 10)	intron (NM_020348, intron 1 of 10)	10097	NM_020348	26507	Hs.274579	NM_020348	ENSG00000119946	CNNM1	ACDP1|CLP-1	cyclin and CBS domain divalent metal cation transport mediator 1	protein-coding	0.002976	0.432392	
chunk0202_408_1	chr9	81529624	81529905	+	0	NA	Intergenic	Intergenic	159771	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.000000	0.347518	
chunk0127_326_1	chr3	100234860	100235059	+	0	NA	Intergenic	Intergenic	-25858	NM_001199198	55773	Hs.477003	NM_018309	ENSG00000036054	TBC1D23	NS4ATP1|PCH11	TBC1 domain family member 23	protein-coding	0.005025	0.340000	
chunk0050_351_1	chr12	107751551	107751914	+	0	NA	exon (NM_012406, exon 5 of 12)	exon (NM_012406, exon 5 of 12)	9405	NM_012406	11108	Hs.506655	NM_012406	ENSG00000110851	PRDM4	PFM1	PR/SET domain 4	protein-coding	0.016529	0.541209	
chunk0063_419_1	chr14	88468160	88468384	+	0	NA	intron (NM_007039, intron 18 of 18)	intron (NM_007039, intron 18 of 18)	82628	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.013393	0.515556	
chunk0054_227_1	chr13	45537842	45538401	+	0	NA	Intergenic	L2a|LINE|L2	73226	NM_031431	83548	Hs.507948	NM_031431	ENSG00000136152	COG3	SEC34	component of oligomeric golgi complex 3	protein-coding	0.010733	0.480357	243(CAGCACTTGCTGTTCC,-,0.00),244(AGCACTTGCTGTTCCC,+,0.00)
chunk0040_219_1	chr11	114281139	114281959	+	0	NA	Intergenic	L2c|LINE|L2	-14264	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.006098	0.459196	
chunk0047_332_1	chr12	74418164	74418428	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-119475	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.003788	0.400000	
chunk0155_368_1	chr5	97453544	97453743	+	0	NA	Intergenic	Intergenic	-51053	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.010050	0.335000	
chunk0130_231_1	chr3	134485674	134485884	+	0	NA	promoter-TSS (NM_025180)	promoter-TSS (NM_025180)	46	NM_001042383	80254	Hs.443301	NM_025180	ENSG00000182923	CEP63	SCKL6	centrosomal protein 63	protein-coding	0.076190	0.611374	
chunk0062_252_1	chr14	71536965	71537337	+	0	NA	intron (NM_001284245, intron 1 of 20)	intron (NM_001284245, intron 1 of 20)	7839	NM_001284245	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.008065	0.399464	
chunk0004_308_1	chr1	49248341	49248597	+	0	NA	intron (NM_032785, intron 3 of 13)	MIR|SINE|MIR	-8942	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.000000	0.365759	
chunk0192_111_1	chr8	61689739	61690352	+	0	NA	promoter-TSS (NM_020164)	promoter-TSS (NM_020164)	-196	NM_032467	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.003263	0.403909	297(TGGAACAAACTGTGCT,-,0.00),298(GGAACAAACTGTGCTG,+,0.00)
chunk0070_193_1	chr15	72060618	72061074	+	0	NA	intron (NM_006901, intron 1 of 41)	L1M1|LINE|L1	-53412	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.006579	0.509847	
chunk0085_53_1	chr18	845221	845539	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-33054	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.012579	0.429467	
chunk0100_216_1	chr2	111944737	111945418	+	0	NA	intron (NM_006343, intron 3 of 18)	intron (NM_006343, intron 3 of 18)	46463	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.007342	0.372434	
chunk0002_246_1	chr1	21019218	21019473	+	0	NA	intron (NM_001198801, intron 4 of 34)	intron (NM_001198801, intron 4 of 34)	-30913	NR_031657	100302155		NR_031657	ENSG00000221808	MIR1256	MIRN1256|hsa-mir-1256	microRNA 1256	ncRNA	0.007843	0.304688	
chunk0173_179_1	chr6	144783223	144783653	+	0	NA	intron (NM_007124, intron 60 of 73)	intron (NM_007124, intron 60 of 73)	377783	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.000000	0.296984	
chunk0067_102_1	chr15	42282841	42283377	+	0	NA	intron (NM_001301410, intron 4 of 4)	MLT1A|LTR|ERVL-MaLR	8941	NM_198141	2595	Hs.730806	NM_198141	ENSG00000214013	GANC	-	glucosidase alpha, neutral C	protein-coding	0.011194	0.430168	
chunk0115_198_1	chr21	26166758	26167476	+	0	NA	intron (NM_001136131, intron 1 of 15)	intron (NM_001136131, intron 1 of 15)	3703	NM_000484	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.001393	0.385257	
chunk0028_152_1	chr10	86849721	86850016	+	0	NA	intron (NM_004329, intron 2 of 12)	intron (NM_004329, intron 2 of 12)	93229	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.006780	0.375000	
chunk0023_363_1	chr10	30013650	30014086	+	0	NA	3' UTR (NM_020848, exon 4 of 4)	3' UTR (NM_020848, exon 4 of 4)	45691	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.013761	0.480549	
chunk0054_44_1	chr13	41295135	41295694	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-15791	NM_001110798	79612	Hs.512914	NM_018527	ENSG00000172766	NAA16	NARG1L	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	protein-coding	0.001789	0.341071	
chunk0024_232_1	chr10	38487510	38487709	+	0	NA	Intergenic	Intergenic	59463	NR_024497	399744	Hs.497951	NM_001013665		LINC00999	-	long intergenic non-protein coding RNA 999	ncRNA	0.030151	0.405000	
chunk0045_378_1	chr12	52192281	52192535	+	0	NA	promoter-TSS (NM_001081492)	promoter-TSS (NM_001081492)	-408	NM_001081492	144501	Hs.140978	NM_182507	ENSG00000167767	KRT80	KB20	keratin 80	protein-coding	0.019685	0.537255	
chunk0210_264_1	chrX	84162414	84162726	+	0	NA	intron (NM_014496, intron 2 of 21)	intron (NM_014496, intron 2 of 21)	25365	NM_014496	27330	Hs.234478	NM_014496	ENSG00000072133	RPS6KA6	PP90RSK4|RSK-4|RSK4|S6K-alpha-6|p90RSK6	ribosomal protein S6 kinase A6	protein-coding	0.000000	0.357827	
chunk0123_84_1	chr3	41937477	41937953	+	0	NA	intron (NM_017886, intron 3 of 36)	intron (NM_017886, intron 3 of 36)	24453	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.008403	0.262055	
chunk0164_78_1	chr6	19892256	19892782	+	0	NA	Intergenic	Intergenic	55149	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.019011	0.449715	
chunk0166_279_1	chr6	48273541	48273919	+	0	NA	Intergenic	Intergenic	-205041	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.000000	0.390501	
chunk0174_256_1	chr6	161122171	161122380	+	0	NA	Intergenic	L1PB1|LINE|L1	39707	NR_024277	79992	Hs.664873	NM_024929	ENSG00000279355	AGPAT4-IT1	C6orf59|NCRNA00241	AGPAT4 intronic transcript 1	ncRNA	0.009569	0.328571	
chunk0046_2_1	chr12	53954275	53954519	+	0	NA	promoter-TSS (NM_173860)	promoter-TSS (NM_173860)	-533	NM_173860	3228	Hs.381267	NM_173860	ENSG00000123407	HOXC12	HOC3F|HOX3|HOX3F	homeobox C12	protein-coding	0.024590	0.408163	
chunk0178_136_1	chr7	32816587	32816786	+	0	NA	Intergenic	L3|LINE|CR1	-9616	NR_132360	102724668	Hs.636806	NR_132360		DPY19L1P2	THC1072510	DPY19L1 pseudogene 2	pseudo	0.010050	0.425000	
chunk0044_16_1	chr12	27095174	27095642	+	0	NA	Intergenic	Intergenic	-12886	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.006410	0.464819	
chunk0001_56_1	chr1	2043881	2044293	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-6383	NM_002744	5590	Hs.496255	NM_002744	ENSG00000067606	PRKCZ	PKC-ZETA|PKC2	protein kinase C zeta	protein-coding	0.009709	0.530266	
chunk0141_125_1	chr4	80137641	80137965	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	-47467	NM_020226	56978	Hs.373642	NM_020226	ENSG00000152784	PRDM8	EPM10|KMT8D|PFM5	PR/SET domain 8	protein-coding	0.006173	0.366154	102(GAGGACATTGTGTTCT,-,0.00),103(AGGACATTGTGTTCTA,+,0.00)
chunk0155_431_1	chr5	100647549	100648326	+	0	NA	Intergenic	Intergenic	112632	NM_198507	345757	Hs.356108	NM_198507	ENSG00000174132	FAM174A	HGS_RE408|NS5ATP6|TMEM157|UNQ1912	family with sequence similarity 174 member A	protein-coding	0.012870	0.417738	531(CAGAACTGGCTGTTCT,-,0.00),532(AGAACTGGCTGTTCTT,+,0.00)
chunk0081_298_1	chr17	45147747	45147946	+	0	NA	5' UTR (NM_006460, exon 1 of 1)	5' UTR (NM_006460, exon 1 of 1)	529	NM_006460	10614	Hs.586945	NM_006460	ENSG00000186834	HEXIM1	CLP1|EDG1|HIS1|MAQ1	HEXIM P-TEFb complex subunit 1	protein-coding	0.065327	0.485000	
chunk0129_107_1	chr3	119677316	119677576	+	0	NA	promoter-TSS (NM_005694)	promoter-TSS (NM_005694)	-50	NM_005694	10063	Hs.534383	NM_005694	ENSG00000138495	COX17	-	cytochrome c oxidase copper chaperone COX17	protein-coding	0.069231	0.559387	94(AAGTACAGGAAGTCCT,-,0.00),95(AGTACAGGAAGTCCTG,+,0.00)
chunk0108_200_1	chr2	232550405	232550608	+	0	NA	promoter-TSS (NM_001276337)	promoter-TSS (NM_001276337)	67	NR_049797	100847037		NR_049797	ENSG00000284407	MIR5001	mir-5001	microRNA 5001	ncRNA	0.093596	0.691176	
chunk0017_31_1	chr1	204882255	204882902	+	0	NA	intron (NM_001005389, intron 1 of 15)	L2a|LINE|L2	53924	NM_001160332	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.007728	0.450617	
chunk0157_264_1	chr5	120081267	120081675	+	0	NA	Intergenic	Intergenic	-382807	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.002451	0.312958	
chunk0024_374_1	chr10	44540678	44540940	+	0	NA	Intergenic	L1PA16|LINE|L1	-155712	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.003817	0.338403	
chunk0076_370_1	chr16	72092635	72093138	+	0	NA	promoter-TSS (NM_014003)	promoter-TSS (NM_014003)	754	NM_017853	54957	Hs.134406	NM_017853	ENSG00000140830	TXNL4B	DLP|Dim2	thioredoxin like 4B	protein-coding	0.017893	0.452381	275(AGGCACAGGGAGTTCC,-,0.00),276(GGCACAGGGAGTTCCT,+,0.00)
chunk0002_375_1	chr1	26531791	26532104	+	0	NA	intron (NM_002953, intron 1 of 21)	intron (NM_002953, intron 1 of 21)	2189	NM_002953	6195	Hs.149957	NM_002953	ENSG00000117676	RPS6KA1	HU-1|MAPKAPK1A|RSK|RSK1|p90Rsk	ribosomal protein S6 kinase A1	protein-coding	0.025559	0.630573	
chunk0116_307_1	chr21	40606393	40606688	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	24227	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.006780	0.445946	
chunk0007_225_1	chr1	81752745	81753194	+	0	NA	intron (NM_001297704, intron 1 of 20)	intron (NM_001297704, intron 1 of 20)	-47428	NM_012302	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.002227	0.322222	
chunk0163_139_1	chr6	10697905	10698767	+	0	NA	intron (NM_017906, intron 2 of 9)	intron (NM_017906, intron 2 of 9)	3381	NM_017906	55003	Hs.310231	NM_017906	ENSG00000111845	PAK1IP1	MAK11|PIP1|WDR84|bA421M1.5|hPIP1	PAK1 interacting protein 1	protein-coding	0.010441	0.449594	
chunk0003_306_1	chr1	37779915	37780445	+	0	NA	Intergenic	Intergenic	-13922	NM_001113482	149175	Hs.534562	NM_152496	ENSG00000185090	MANEAL	-	mannosidase endo-alpha like	protein-coding	0.005660	0.410546	
chunk0188_147_1	chr8	9678597	9679303	+	0	NA	intron (NM_003747, intron 3 of 26)	intron (NM_003747, intron 3 of 26)	-62722	NR_030327	693182		NR_030327	ENSG00000207701	MIR597	MIRN597|hsa-mir-597|mir-597	microRNA 597	ncRNA	0.002833	0.268741	
chunk0007_183_1	chr1	80679615	80680093	+	0	NA	Intergenic	Intergenic	38567	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.002092	0.365344	258(GAGTACAGAGTGCCCT,-,0.00),259(AGTACAGAGTGCCCTG,+,0.00)
chunk0194_273_1	chr8	87166288	87166878	+	0	NA	intron (NM_173538, intron 4 of 10)	L2|LINE|L2	300135	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.005085	0.397631	
chunk0039_272_1	chr11	102448582	102448944	+	0	NA	intron (NM_052932, intron 2 of 4)	intron (NM_052932, intron 2 of 4)	4281	NM_052932	114908	Hs.503709	NM_052932	ENSG00000152558	TMEM123	KCT3|PORIMIN|PORMIN	transmembrane protein 123	protein-coding	0.000000	0.366391	
chunk0087_241_1	chr18	36670924	36671150	+	0	NA	intron (NM_001281739, intron 11 of 23)	L1MEc|LINE|L1	-7619	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.000000	0.392070	68(GGGAACAGGCAGTACT,-,0.00),69(GGAACAGGCAGTACTC,+,0.00)
chunk0121_108_1	chr3	17257405	17257638	+	0	NA	intron (NM_014744, intron 16 of 21)	intron (NM_014744, intron 16 of 21)	324325	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.000000	0.324786	
chunk0168_167_1	chr6	83859325	83859699	+	0	NA	promoter-TSS (NM_016230)	promoter-TSS (NM_016230)	-139	NM_016230	51167	Hs.5741	NM_016230	ENSG00000065615	CYB5R4	NCB5OR|cb5/cb5R|dJ676J13.1	cytochrome b5 reductase 4	protein-coding	0.053476	0.517333	
chunk0137_282_1	chr4	23853717	23854049	+	0	NA	intron (NM_013261, intron 2 of 12)	MIR|SINE|MIR	36194	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.006024	0.390390	
chunk0089_297_1	chr18	63422569	63422804	+	0	NA	promoter-TSS (NM_004869)	promoter-TSS (NM_004869)	-167	NM_004869	9525	Hs.126550	NM_004869	ENSG00000119541	VPS4B	MIG1|SKD1|SKD1B|VPS4-2	vacuolar protein sorting 4 homolog B	protein-coding	0.072340	0.639831	
chunk0133_51_1	chr3	166484712	166485335	+	0	NA	Intergenic	Intergenic	-647558	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.003210	0.283654	
chunk0051_192_1	chr12	116275821	116276121	+	0	NA	intron (NM_015335, intron 1 of 30)	intron (NM_015335, intron 1 of 30)	1215	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.026667	0.372093	
chunk0202_174_1	chr9	73905491	73905747	+	0	NA	Intergenic	Intergenic	-465912	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.000000	0.346304	236(AAGAACACAGTGTGTA,-,0.00),237(AGAACACAGTGTGTAT,+,0.00)
chunk0109_407_1	chr2	240561050	240561302	+	0	NA	promoter-TSS (NM_001308375)	promoter-TSS (NM_001308375)	-66	NM_001308375	51281	Hs.656615	NM_016552	ENSG00000144504	ANKMY1	ZMYND13	ankyrin repeat and MYND domain containing 1	protein-coding	0.083333	0.695652	
chunk0099_432_1	chr2	102812903	102813441	+	0	NA	intron (NM_144632, intron 4 of 4)	intron (NM_144632, intron 4 of 4)	51141	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.009294	0.385900	
chunk0159_254_1	chr5	142013795	142014129	+	0	NA	promoter-TSS (NM_005471)	promoter-TSS (NM_005471)	-907	NM_005471	10007	Hs.633853	NM_005471	ENSG00000113552	GNPDA1	GNP1|GNPDA|GNPI|GPI|HLN	glucosamine-6-phosphate deaminase 1	protein-coding	0.017964	0.465672	
chunk0067_261_1	chr15	45811718	45812460	+	0	NA	Intergenic	MER51B|LTR|ERV1	177349	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.010782	0.433378	
chunk0066_330_1	chr15	36612235	36612686	+	0	NA	intron (NM_001290232, intron 1 of 10)	MLT1J|LTR|ERVL-MaLR	17591	NM_001290232	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.011086	0.442478	
chunk0134_433_1	chr3	183490027	183490583	+	0	NA	3' UTR (NM_130446, exon 7 of 7)	3' UTR (NM_130446, exon 7 of 7)	42654	NR_038301	100505687	Hs.551751	NR_038301	ENSG00000240024	LINC00888	-	long intergenic non-protein coding RNA 888	ncRNA	0.014388	0.425494	
chunk0159_409_1	chr5	147826274	147826638	+	0	NA	intron (NM_003122, intron 4 of 4)	intron (NM_003122, intron 4 of 4)	12775	NM_003122	6690	Hs.407856	NM_003122	ENSG00000164266	SPINK1	PCTT|PSTI|Spink3|TATI|TCP	serine peptidase inhibitor, Kazal type 1	protein-coding	0.005495	0.361644	
chunk0092_368_1	chr19	35999170	35999556	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	4175	NM_001042631	644096	Hs.356460	NM_001042631	ENSG00000205138	SDHAF1	LYRM8	succinate dehydrogenase complex assembly factor 1	protein-coding	0.007772	0.550388	
chunk0193_264_1	chr8	77033898	77034353	+	0	NA	Intergenic	Intergenic	-33081	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.006593	0.405702	168(AAGGACAGTATGTGCC,-,0.00),169(AGGACAGTATGTGCCG,+,0.00)
chunk0001_444_1	chr1	11737080	11737821	+	0	NA	intron (NM_001040195, intron 1 of 3)	intron (NM_001040195, intron 1 of 3)	1365	NM_001040195	57085	Hs.464438	NM_020350	ENSG00000177674	AGTRAP	ATRAP	angiotensin II receptor associated protein	protein-coding	0.008097	0.463612	
chunk0199_99_1	chr9	2853417	2854031	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-9594	NM_014878	9933	Hs.493309	NM_014878	ENSG00000080608	PUM3	HA-8|HLA-HA8|KIAA0020|PEN|PUF-A|PUF6|XTP5	pumilio RNA binding family member 3	protein-coding	0.004886	0.373984	
chunk0065_434_1	chr14	106332015	106332493	+	0	NA	Intergenic	Intergenic	44580	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.002092	0.308977	
chunk0010_147_1	chr1	115143192	115143804	+	0	NA	Intergenic	MIRb|SINE|MIR	-53998	NM_005725	10100	Hs.310458	NM_005725	ENSG00000134198	TSPAN2	NET3|TSN2|TSPAN-2	tetraspanin 2	protein-coding	0.003268	0.417618	
chunk0039_334_1	chr11	104355679	104355889	+	0	NA	Intergenic	Intergenic	103193	NR_106987									0.000000	0.398104	
chunk0055_111_1	chr13	56894140	56894585	+	0	NA	Intergenic	MER50|LTR|ERV1	-246556	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.011236	0.439462	272(CAGATCAGCCTGTTCT,-,0.00),273(AGATCAGCCTGTTCTC,+,0.00)
chunk0016_25_1	chr1	192905406	192905852	+	0	NA	Intergenic	Intergenic	42628	NR_126003	102724954	Hs.243488	NR_126003		LINC01032	-	long intergenic non-protein coding RNA 1032	ncRNA	0.000000	0.319911	
chunk0072_428_1	chr15	101193334	101193533	+	0	NA	intron (NM_014918, intron 2 of 2)	intron (NM_014918, intron 2 of 2)	58499	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.020101	0.585000	
chunk0046_100_1	chr12	56934303	56935087	+	0	NA	promoter-TSS (NM_148897)	promoter-TSS (NM_148897)	-290	NM_148897	121214	Hs.380178	NM_148897	ENSG00000170426	SDR9C7	ARCI13|RDHS|SDR-O|SDRO	short chain dehydrogenase/reductase family 9C member 7	protein-coding	0.005102	0.501911	
chunk0122_276_1	chr3	35538631	35538928	+	0	NA	Intergenic	L2a|LINE|L2	-100395	NM_001267616	10777	Hs.475902	NM_016300	ENSG00000172995	ARPP21	ARPP-21|R3HDM3|RCS|TARPP	cAMP regulated phosphoprotein 21	protein-coding	0.016835	0.345638	82(GAAAACAGAATGTTCT,-,0.00),83(AAAACAGAATGTTCTG,+,0.00)
chunk0122_267_1	chr3	35213158	35213703	+	0	NA	intron (NR_110817, intron 2 of 3)	L1MB8|LINE|L1	180593	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.007339	0.336996	
chunk0173_258_1	chr6	147081156	147081473	+	0	NA	intron (NR_034115, intron 4 of 10)	intron (NR_034115, intron 4 of 10)	-77611	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.006309	0.377358	
chunk0088_103_1	chr18	45010231	45010742	+	0	NA	intron (NM_015559, intron 4 of 5)	intron (NM_015559, intron 4 of 5)	-40320	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.005871	0.351562	
chunk0011_362_1	chr1	153084406	153084658	+	0	NA	Intergenic	L1PA13|LINE|L1	9996	NM_001024209	6704	Hs.568518	NM_001024209	ENSG00000203785	SPRR2E	-	small proline rich protein 2E	protein-coding	0.000000	0.517787	
chunk0076_397_1	chr16	72560499	72560828	+	0	NA	intron (NR_126330, intron 2 of 13)	intron (NR_126330, intron 2 of 13)	104346	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.003040	0.360606	
chunk0032_271_1	chr11	9083974	9084521	+	0	NA	intron (NM_020974, intron 2 of 21)	L1MC4a|LINE|L1	6132	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.003656	0.383212	
chunk0003_87_1	chr1	31704602	31705138	+	0	NA	promoter-TSS (NM_001856)	promoter-TSS (NM_001856)	-703	NM_001856	1307	Hs.368921	NM_001856	ENSG00000084636	COL16A1	447AA|FP1572	collagen type XVI alpha 1 chain	protein-coding	0.026119	0.523277	
chunk0096_53_1	chr2	27273175	27273414	+	0	NA	Intergenic	L2a|LINE|L2	-2127	NM_001303127	285126	Hs.116303	NM_173650	ENSG00000163793	DNAJC5G	CSP-gamma	DnaJ heat shock protein family (Hsp40) member C5 gamma	protein-coding	0.012552	0.525000	98(GGGAACACGATGTTTT,-,0.00),99(GGAACACGATGTTTTC,+,0.00)
chunk0078_416_1	chr16	89261494	89262147	+	0	NA	Intergenic	L1M4|LINE|L1	44117	NM_182531	197320	Hs.647385	NM_182531	ENSG00000170100	ZNF778	-	zinc finger protein 778	protein-coding	0.021440	0.506116	
chunk0005_455_1	chr1	63555324	63556082	+	0	NA	intron (NM_032437, intron 9 of 13)	L1MA8|LINE|L1	6723	NR_002771	79469	Hs.659291	NR_002771		DLEU2L	BCMSUNL	deleted in lymphocytic leukemia 2 like	ncRNA	0.002639	0.416337	
chunk0070_400_1	chr15	77116105	77116690	+	0	NA	intron (NM_024776, intron 7 of 7)	intron (NM_024776, intron 7 of 7)	-45169	NM_005724	10099	Hs.744863	NM_005724	ENSG00000140391	TSPAN3	TM4-A|TM4SF8|TSPAN-3	tetraspanin 3	protein-coding	0.005128	0.378840	
chunk0138_93_1	chr4	35761885	35762346	+	0	NA	Intergenic	L1P4b|LINE|L1	-482001	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004338	0.359307	
chunk0110_103_1	chr20	11811648	11812074	+	0	NA	intron (NR_110635, intron 1 of 1)	intron (NR_110635, intron 1 of 1)	58854	NR_110635	728450	Hs.560990	NR_110635	ENSG00000228422	LINC00687	C20orf61|dJ1012F16.1	long intergenic non-protein coding RNA 687	ncRNA	0.004695	0.297424	
chunk0101_174_1	chr2	129100908	129101660	+	0	NA	Intergenic	Intergenic	172607	NR_122041	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.009309	0.440903	
chunk0042_324_1	chr12	9354575	9354840	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-12757	NR_120479	101930452	Hs.734183	NR_120479	ENSG00000260423	LINC02367	-	long intergenic non-protein coding RNA 2367	ncRNA	0.003774	0.372180	167(CAGAACTCATTGTACT,-,0.00),168(AGAACTCATTGTACTT,+,0.00)
chunk0083_195_1	chr17	66571763	66572109	+	0	NA	intron (NM_002737, intron 3 of 16)	intron (NM_002737, intron 3 of 16)	-155082	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.017341	0.452450	
chunk0050_295_1	chr12	106760717	106760928	+	0	NA	intron (NM_032491, intron 13 of 13)	intron (NM_032491, intron 13 of 13)	-13799	NM_018157	55188	Hs.131306	NM_018157	ENSG00000111785	RIC8B	RIC8|hSyn	RIC8 guanine nucleotide exchange factor B	protein-coding	0.000000	0.386792	
chunk0031_333_1	chr10	129453460	129453659	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-13625	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.005025	0.415000	
chunk0092_431_1	chr19	38196227	38196573	+	0	NA	intron (NM_015073, intron 18 of 21)	intron (NM_015073, intron 18 of 21)	27850	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.020231	0.628242	
chunk0009_443_1	chr1	111406033	111406778	+	0	NA	Intergenic	LTR41|LTR|ERVL	-16554	NR_029429	441897	Hs.568387	NR_029429	ENSG00000227179	PGCP1	-	progastricsin pseudogene 1	pseudo	0.005369	0.410188	
chunk0160_354_1	chr5	160343046	160343281	+	0	NA	Intergenic	MIR|SINE|MIR	-3571	NR_131769	79616	Hs.14070	NM_024565	ENSG00000135083	CCNJL	-	cyclin J like	protein-coding	0.008511	0.398305	177(AAGCACACAGTGTTTC,-,0.00),178(AGCACACAGTGTTTCA,+,0.00)
chunk0122_345_1	chr3	37293470	37294255	+	0	NA	intron (NM_002078, intron 5 of 23)	Tigger3a|DNA|TcMar-Tigger	50671	NM_001172713	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.010191	0.368957	
chunk0042_458_1	chr12	12546411	12546897	+	0	NA	intron (NM_030640, intron 1 of 6)	intron (NM_030640, intron 1 of 6)	15860	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.002058	0.377823	
chunk0166_158_1	chr6	45446050	45446282	+	0	NA	intron (NM_001278478, intron 3 of 5)	intron (NM_001278478, intron 3 of 5)	23589	NM_001278478	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.021552	0.463519	
chunk0143_309_1	chr4	118969359	118969918	+	0	NA	intron (NM_133477, intron 1 of 4)	intron (NM_133477, intron 1 of 4)	80797	NM_133477	171024	Hs.655519	NM_133477	ENSG00000172403	SYNPO2	-	synaptopodin 2	protein-coding	0.008945	0.355357	
chunk0104_344_1	chr2	179806039	179806466	+	0	NA	intron (NM_152520, intron 1 of 9)	L1M5|LINE|L1	54656	NR_031659	100302172		NR_031659	ENSG00000221240	MIR1258	MIRN1258|hsa-mir-1258|mir-1258	microRNA 1258	ncRNA	0.000000	0.315421	
chunk0068_446_1	chr15	59725262	59725767	+	0	NA	Intergenic	Intergenic	-36071	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.007921	0.337945	
chunk0200_414_1	chr9	27539418	27540133	+	0	NA	Intergenic	Intergenic	-9923	NM_024761	79817	Hs.369022	NM_024761	ENSG00000120162	MOB3B	C9orf35|MOB1D|MOBKL2B	MOB kinase activator 3B	protein-coding	0.006993	0.444134	420(AGGGACTTTCTGTTCA,-,0.00),421(GGGACTTTCTGTTCAG,+,0.00)
chunk0137_428_1	chr4	28278576	28279127	+	0	NA	Intergenic	Intergenic	-540731	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.001815	0.398551	250(AAGTACAGTCTGTCCT,-,0.00),251(AGTACAGTCTGTCCTG,+,0.00)
chunk0198_183_1	chr8	133412719	133413177	+	0	NA	Intergenic	L1M3|LINE|L1	-115644	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.004367	0.313725	
chunk0161_223_1	chr5	170946562	170947226	+	0	NA	intron (NM_022897, intron 12 of 27)	Tigger17a|DNA|TcMar-Tigger	85012	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.003012	0.314286	
chunk0078_166_1	chr17	4246070	4246431	+	0	NA	intron (NR_047571, intron 1 of 23)	intron (NR_047571, intron 1 of 23)	17597	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.011080	0.361878	
chunk0118_100_1	chr22	29267903	29268391	+	0	NA	promoter-TSS (NM_012265)	promoter-TSS (NM_012265)	138	NM_013986	2130	Hs.374477	NM_005243	ENSG00000182944	EWSR1	EWS|EWS-FLI1|bK984G1.4	EWS RNA binding protein 1	protein-coding	0.100410	0.640082	
chunk0078_177_1	chr17	4643642	4644068	+	0	NA	Intergenic	L1ME4b|LINE|L1	-2190	NM_001140	246	Hs.73809	NM_001140	ENSG00000161905	ALOX15	12-LOX|15-LOX|15-LOX-1|LOG15	arachidonate 15-lipoxygenase	protein-coding	0.011737	0.440281	
chunk0078_403_1	chr16	88760547	88761090	+	0	NA	intron (NM_001142864, intron 1 of 50)	intron (NM_001142864, intron 1 of 50)	18051	NR_120387	339059	Hs.449817	NR_120387	ENSG00000182376	LOC339059	-	uncharacterized LOC339059	ncRNA	0.040516	0.652574	
chunk0101_53_1	chr2	123116209	123116712	+	0	NA	Intergenic	L1PA15|LINE|L1	-908827	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.011928	0.349206	
chunk0084_291_1	chr17	79925111	79925405	+	0	NA	intron (NR_110850, intron 1 of 5)	MIRb|SINE|MIR	1467	NR_110850	101928766	Hs.630666	NR_110850	ENSG00000262585	LINC01979	-	long intergenic non-protein coding RNA 1979	ncRNA	0.034014	0.606780	
chunk0161_185_1	chr5	169864407	169864884	+	0	NA	intron (NM_001129891, intron 3 of 3)	MIRc|SINE|MIR	116095	NM_001129891	100131897	Hs.721917	NM_001129891	ENSG00000204767	INSYN2B	C5orf57|FAM196B	inhibitory synaptic factor family member 2B	protein-coding	0.004193	0.418410	
chunk0137_354_1	chr4	25702604	25702900	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	46288	NM_001177999	10568	Hs.479372	NM_006424	ENSG00000157765	SLC34A2	NAPI-3B|NAPI-IIb|NPTIIb	solute carrier family 34 member 2	protein-coding	0.003378	0.316498	184(GAGGACATTATGTCCA,-,0.00),185(AGGACATTATGTCCAA,+,0.00)
chunk0055_461_1	chr13	76466109	76466477	+	0	NA	Intergenic	Intergenic	420112	NM_138444	115207	Hs.644125	NM_138444	ENSG00000178695	KCTD12	C13orf2|PFET1|PFETIN	potassium channel tetramerization domain containing 12	protein-coding	0.002717	0.398374	
chunk0177_271_1	chr7	25456772	25457227	+	0	NA	Intergenic	Intergenic	-228513	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.015385	0.442982	
chunk0197_452_1	chr8	127852410	127852993	+	0	NA	intron (NR_003367, intron 1 of 8)	MIRb|SINE|MIR	56739	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.013722	0.500000	
chunk0093_49_1	chr19	40225876	40226472	+	0	NA	intron (NM_024877, intron 1 of 4)	CpG	516	NM_024877	79935	Hs.631603	NM_024877	ENSG00000105219	CNTD2	CCNP	cyclin N-terminal domain containing 2	protein-coding	0.058725	0.582915	
chunk0155_150_1	chr5	93797329	93797528	+	0	NA	intron (NR_028080, intron 6 of 8)	intron (NR_028080, intron 6 of 8)	-55825	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.000000	0.295000	
chunk0082_128_1	chr17	55169655	55170067	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-95099	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.000000	0.317191	
chunk0079_281_1	chr17	16468249	16468989	+	0	NA	intron (NR_027176, intron 6 of 6)	L1MB3|LINE|L1	23572	NM_001113567	388341	Hs.25425	NM_207387	ENSG00000181350	LRRC75A	C17orf76|FAM211A	leucine rich repeat containing 75A	protein-coding	0.012162	0.472335	548(GAGGACAGCTTGAGCC,-,0.00)
chunk0045_141_1	chr12	46457168	46457433	+	0	NA	intron (NR_125378, intron 3 of 3)	intron (NR_125378, intron 3 of 3)	73193	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.015094	0.315789	
chunk0200_164_1	chr9	18887964	18888231	+	0	NA	intron (NM_001040272, intron 24 of 28)	intron (NM_001040272, intron 24 of 28)	145161	NM_153707	158297	Hs.731593	NM_153707	ENSG00000155875	SAXO1	C9orf138|FAM154A	stabilizer of axonemal microtubules 1	protein-coding	0.000000	0.470149	
chunk0002_74_1	chr1	14142440	14142725	+	0	NA	Intergenic	Intergenic	393201	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.021053	0.468531	
chunk0175_51_1	chr7	1532638	1533155	+	0	NA	intron (NM_002360, intron 1 of 2)	intron (NM_002360, intron 1 of 2)	2164	NM_002360	7975	Hs.520612	NM_002360	ENSG00000198517	MAFK	NFE2U|P18	MAF bZIP transcription factor K	protein-coding	0.042553	0.534749	
chunk0085_408_1	chr18	10314151	10315349	+	0	NA	Intergenic	Intergenic	99620	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.013356	0.494579	1028(AAATACATTCTGTTCC,-,0.00),1029(AATACATTCTGTTCCC,+,0.00)
chunk0096_174_1	chr2	29724012	29724579	+	0	NA	intron (NM_004304, intron 1 of 28)	intron (NM_004304, intron 1 of 28)	197316	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.007055	0.387324	
chunk0090_378_1	chr18	77262523	77263326	+	0	NA	intron (NM_001480, intron 2 of 2)	intron (NM_001480, intron 2 of 2)	12872	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.003736	0.388060	
chunk0061_40_1	chr14	56133621	56133984	+	0	NA	intron (NM_021255, intron 1 of 5)	intron (NM_021255, intron 1 of 5)	15427	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.005510	0.478022	
chunk0057_372_1	chr13	109104801	109105258	+	0	NA	intron (NM_001198950, intron 28 of 34)	L2a|LINE|L2	62274	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.021882	0.480349	
chunk0124_262_1	chr3	57122858	57123236	+	0	NA	intron (NM_017563, intron 1 of 12)	intron (NM_017563, intron 1 of 12)	42328	NM_017563	54756	Hs.150725	NM_017563	ENSG00000144730	IL17RD	HH18|IL-17RD|IL17RLM|SEF	interleukin 17 receptor D	protein-coding	0.002646	0.461741	
chunk0012_146_1	chr1	157683210	157683800	+	0	NA	intron (NM_052939, intron 10 of 14)	intron (NM_052939, intron 10 of 14)	17352	NM_052939	115352	Hs.292449	NM_052939	ENSG00000160856	FCRL3	CD307c|FCRH3|IFGP3|IRTA3|SPAP2	Fc receptor like 3	protein-coding	0.001695	0.443316	
chunk0105_298_1	chr2	190143294	190143551	+	0	NA	intron (NM_001042521, intron 1 of 2)	L2c|LINE|L2	5662	NM_001042521	84281	Hs.389311	NM_032321	ENSG00000187699	C2orf88	smAKAP	chromosome 2 open reading frame 88	protein-coding	0.003891	0.410853	41(TGGAACATGCCGTTCC,-,0.00),42(GGAACATGCCGTTCCC,+,0.00)
chunk0178_22_1	chr7	29328087	29328457	+	0	NA	intron (NM_001293070, intron 2 of 13)	intron (NM_001293070, intron 2 of 13)	-119302	NR_120522	102724484	Hs.638665	NR_120522		LOC102724484	-	uncharacterized LOC102724484	ncRNA	0.013514	0.393531	
chunk0144_72_1	chr4	127774061	127774332	+	0	NA	TTS (NM_031291)	TTS (NM_031291)	-8102	NM_014278	22824	Hs.135554	NM_014278	ENSG00000164070	HSPA4L	APG-1|HSPH3|Osp94	heat shock protein family A (Hsp70) member 4 like	protein-coding	0.000000	0.264706	
chunk0136_220_1	chr4	8115893	8116349	+	0	NA	intron (NM_032432, intron 1 of 15)	MLT1G1|LTR|ERVL-MaLR	42711	NM_001130087	84448	Hs.233404	NM_032432	ENSG00000163995	ABLIM2	-	actin binding LIM protein family member 2	protein-coding	0.024123	0.553611	
chunk0202_53_1	chr9	71367635	71367834	+	0	NA	Intergenic	Intergenic	-246136	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.010050	0.380000	
chunk0114_112_1	chr21	9586581	9586780	+	0	NA	Intergenic	(TGGTGA)n|Simple_repeat|Simple_repeat	234381	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.015075	0.425000	
chunk0120_266_1	chr3	9194421	9195130	+	0	NA	TTS (NR_121663)	TTS (NR_121663)	2282	NR_121664	101927416	Hs.475364	NR_121663	ENSG00000228723	SRGAP3-AS2	-	SRGAP3 antisense RNA 2	ncRNA	0.007052	0.490141	394(GAGAACACTGTGCCCT,-,0.00),395(AGAACACTGTGCCCTG,+,0.00)
chunk0169_224_1	chr6	104414807	104415072	+	0	NA	Intergenic	Intergenic	444980	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.421053	
chunk0020_73_1	chr1	232679374	232679719	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	63169	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.014493	0.341040	
chunk0120_277_1	chr3	9402531	9402784	+	0	NA	intron (NM_001292043, intron 1 of 24)	intron (NM_001292043, intron 1 of 24)	4957	NM_001080517	55209	Hs.288164	NM_018187	ENSG00000168137	SETD5	-	SET domain containing 5	protein-coding	0.007905	0.401575	
chunk0016_83_1	chr1	194245932	194246392	+	0	NA	Intergenic	Intergenic	941417	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.002174	0.331887	
chunk0160_282_1	chr5	157877649	157877969	+	0	NA	Intergenic	L1MB7|LINE|L1	-18634	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.006250	0.408100	
chunk0104_8_1	chr2	170341776	170341975	+	0	NA	intron (NR_110576, intron 3 of 3)	intron (NR_110576, intron 3 of 3)	9068	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.005025	0.360000	
chunk0178_447_1	chr7	41978388	41978601	+	0	NA	intron (NM_000168, intron 11 of 14)	intron (NM_000168, intron 11 of 14)	258525	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.014085	0.546729	
chunk0147_362_1	chr4	185811845	185812220	+	0	NA	promoter-TSS (NM_001145671)	promoter-TSS (NM_001145671)	224	NM_003603	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.018667	0.484043	
chunk0055_338_1	chr13	69314322	69314543	+	0	NA	intron (NR_125752, intron 3 of 3)	intron (NR_125752, intron 3 of 3)	92086	NR_125752	103689913	Hs.585628	NR_125752	ENSG00000235221	LINC00383	LINC00401	long intergenic non-protein coding RNA 383	ncRNA	0.009050	0.346847	
chunk0014_129_1	chr1	177613224	177613503	+	0	NA	Intergenic	L1MA6|LINE|L1	-87161	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.007168	0.589286	
chunk0135_258_1	chr3	189052093	189052568	+	0	NA	Intergenic	L1PB1|LINE|L1	-104691	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.004211	0.386555	191(ATGAACAGACAGTTCT,-,0.00),192(TGAACAGACAGTTCTC,+,0.00)
chunk0209_218_1	chrX	44726125	44726580	+	0	NA	Intergenic	Intergenic	-117651	NM_022076	63904	Hs.534478	NM_022076	ENSG00000189037	DUSP21	LMWDSP21	dual specificity phosphatase 21	protein-coding	0.004396	0.353070	
chunk0086_381_1	chr18	26468944	26469282	+	0	NA	intron (NM_001142730, intron 3 of 4)	intron (NM_001142730, intron 3 of 4)	46118	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.005917	0.454277	128(CAGAACACCCTGTACT,-,0.00),129(AGAACACCCTGTACTG,+,0.00)
chunk0074_90_1	chr16	22026481	22027053	+	0	NA	intron (NM_001164579, intron 1 of 2)	intron (NM_001164579, intron 1 of 2)	18632	NM_001164579	730094	Hs.498890	NM_173501	ENSG00000185716	MOSMO	ATTHOG|BC030336|C16orf52	modulator of smoothened	protein-coding	0.010490	0.338569	273(ATGAACTCTATGTCCT,-,0.00),274(TGAACTCTATGTCCTT,+,0.00)
chunk0021_51_1	chr10	1049445	1049644	+	0	NA	promoter-TSS (NM_004508)	promoter-TSS (NM_004508)	-423	NM_004508	3422	Hs.283652	NM_004508	ENSG00000067064	IDI1	IPP1|IPPI1	isopentenyl-diphosphate delta isomerase 1	protein-coding	0.080402	0.640000	
chunk0136_342_1	chr3	195727456	195728130	+	0	NA	intron (NM_020790, intron 4 of 5)	intron (NM_020790, intron 4 of 5)	6911	NM_020790	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.010386	0.496296	
chunk0072_282_1	chr15	98018807	98019572	+	0	NA	Intergenic	Intergenic	58486	NM_183376	91947	Hs.6093	NM_183376	ENSG00000140450	ARRDC4	-	arrestin domain containing 4	protein-coding	0.009150	0.402089	
chunk0195_340_1	chr8	99445757	99446299	+	0	NA	intron (NM_152564, intron 23 of 61)	MER58A|DNA|hAT-Charlie	90702	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.000000	0.333333	
chunk0196_444_1	chr8	116571891	116572304	+	0	NA	Intergenic	Intergenic	183726	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.004843	0.446860	206(CAGGTCACCATGTGCT,-,0.00),207(AGGTCACCATGTGCTC,+,0.00)
chunk0107_394_1	chr2	223841322	223841939	+	0	NA	Intergenic	Intergenic	-4028	NM_001039569	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.006483	0.427184	271(AAGTACAGTGTGTTAC,-,0.00)
chunk0168_417_1	chr6	95367916	95368122	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	209432	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.371981	
chunk0020_12_1	chr1	231683872	231684125	+	0	NA	intron (NM_001164556, intron 1 of 4)	intron (NM_001164556, intron 1 of 4)	57183	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.003953	0.535433	
chunk0059_170_1	chr14	32451013	32451717	+	0	NA	intron (NM_004274, intron 2 of 13)	intron (NM_004274, intron 2 of 13)	122092	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.001420	0.310638	
chunk0184_27_1	chr7	112043480	112043787	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	162774	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.003257	0.379870	129(AAGAACACACTGTTCC,-,0.00),130(AGAACACACTGTTCCA,+,0.00)
chunk0061_326_1	chr14	63093543	63093846	+	0	NA	Intergenic	MER21B|LTR|ERVL	-48456	NM_172375	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.006601	0.381579	
chunk0143_340_1	chr4	121572606	121572844	+	0	NA	Intergenic	L1PA7|LINE|L1	124267	NM_001154	308	Hs.480653	NM_001154	ENSG00000164111	ANXA5	ANX5|ENX2|HEL-S-7|PP4|RPRGL3	annexin A5	protein-coding	0.004202	0.376569	
chunk0017_357_1	chr1	211912149	211912473	+	0	NA	Intergenic	Intergenic	-81539	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.003086	0.375385	
chunk0028_279_1	chr10	91034561	91035029	+	0	NA	Intergenic	L1MC1|LINE|L1	-11013	NR_047467	100874184	Hs.512240	NR_047467		LINC00502	-	long intergenic non-protein coding RNA 502	ncRNA	0.012821	0.445629	
chunk0037_169_1	chr11	73869210	73869444	+	0	NA	Intergenic	Intergenic	-7372	NM_001267806	80227	Hs.525017	NM_025155	ENSG00000175575	PAAF1	PAAF|Rpn14|WDR71	proteasomal ATPase associated factor 1	protein-coding	0.004274	0.463830	
chunk0139_7_1	chr4	47853241	47853659	+	0	NA	intron (NR_103795, intron 21 of 23)	MIRb|SINE|MIR	-15344	NM_001278585	10699	Hs.518618	NM_006587	ENSG00000145244	CORIN	ATC2|CRN|Lrp4|PEE5|TMPRSS10	corin, serine peptidase	protein-coding	0.000000	0.326969	
chunk0109_92_1	chr20	2133329	2133537	+	0	NA	intron (NM_080836, intron 3 of 3)	intron (NM_080836, intron 3 of 3)	31551	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.000000	0.454545	
chunk0072_422_1	chr15	100999449	101000115	+	0	NA	intron (NM_024652, intron 6 of 33)	intron (NM_024652, intron 6 of 33)	80567	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.006006	0.328336	
chunk0102_83_1	chr2	143334950	143335334	+	0	NA	intron (NM_018460, intron 6 of 13)	MER103C|DNA|hAT-Charlie	205812	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.002604	0.368831	
chunk0046_149_1	chr12	58171850	58172258	+	0	NA	Intergenic	Intergenic	230392	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.007353	0.413203	
chunk0120_205_1	chr3	7325340	7325930	+	0	NA	intron (NM_000844, intron 4 of 9)	intron (NM_000844, intron 4 of 9)	209649	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.005085	0.406091	301(CAGCACAACCAGTGCC,-,0.00),302(AGCACAACCAGTGCCA,+,0.00),370(CAGAACAGCATGTCTA,-,0.00),371(AGAACAGCATGTCTAT,+,0.00)
chunk0015_34_1	chr1	184442618	184442873	+	0	NA	intron (NM_030806, intron 1 of 5)	intron (NM_030806, intron 1 of 5)	55729	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.308594	147(GGATACATTCTGTGCT,-,0.00),148(GATACATTCTGTGCTG,+,0.00)
chunk0099_361_1	chr2	100785937	100786326	+	0	NA	Intergenic	Intergenic	-34020	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.012853	0.430769	
chunk0115_91_1	chr21	22395330	22395693	+	0	NA	Intergenic	Intergenic	296894	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.000000	0.230769	
chunk0043_219_1	chr12	19795625	19796076	+	0	NA	Intergenic	L2a|LINE|L2	-218835	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.011086	0.404867	
chunk0060_419_1	chr14	53432439	53432638	+	0	NA	Intergenic	Intergenic	279184	NR_110062	101927620		NR_110062	ENSG00000258731	LOC101927620	-	uncharacterized LOC101927620	ncRNA	0.005025	0.525000	
chunk0053_351_1	chr13	34933377	34933667	+	0	NA	Intergenic	Intergenic	-8765	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.000000	0.371134	
chunk0160_422_1	chr5	164296680	164296963	+	0	NA	Intergenic	Intergenic	170581	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.024735	0.531690	
chunk0075_102_1	chr16	48492814	48493116	+	0	NA	Intergenic	Intergenic	-107647	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.016556	0.438944	155(GTCACAGCATGTTCCT,+,0.00)
chunk0084_127_1	chr17	76162507	76162731	+	0	NA	exon (NM_052916, exon 9 of 19)	exon (NM_052916, exon 9 of 19)	-21320	NM_001454	2302	Hs.651204	NM_001454	ENSG00000129654	FOXJ1	FKHL13|HFH-4|HFH4	forkhead box J1	protein-coding	0.008929	0.440000	140(AAGGACAGGCTGTCTC,-,0.00),141(AGGACAGGCTGTCTCT,+,0.00)
chunk0031_290_1	chr10	128438740	128438977	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	152908	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.012658	0.483193	
chunk0204_5_1	chr9	91630769	91631283	+	0	NA	Intergenic	L2b|LINE|L2	-5225	NR_037472	100500821		NR_037472	ENSG00000266855	MIR3910-1	mir-3910-1	microRNA 3910-1	ncRNA	0.005837	0.363107	
chunk0135_384_1	chr3	191243496	191243695	+	0	NA	intron (NM_198184, intron 2 of 2)	L1MA9|LINE|L1	31062	NM_198184	344901	Hs.526794	NM_198184	ENSG00000188729	OSTN	MUSCLIN	osteocrin	protein-coding	0.005025	0.310000	107(GTGTACAGTATGTTCT,-,0.00),108(TGTACAGTATGTTCTG,+,0.00)
chunk0023_236_1	chr10	26925450	26925949	+	0	NA	Intergenic	L1MC2|LINE|L1	16302	NR_026795	387644	Hs.529965	NR_026795	ENSG00000283709	FAM238C	C10orf51|LINC00202|LINC00202-1|NCRNA00202|bB27G4.1	family with sequence similarity 238 member C	ncRNA	0.002004	0.326000	
chunk0123_76_1	chr3	41604784	41605091	+	0	NA	intron (NM_017886, intron 31 of 36)	LTR102_Mam|LTR|ERVL	357231	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.003257	0.379870	
chunk0064_383_1	chr14	98909283	98909826	+	0	NA	Intergenic	MIR|SINE|MIR	197941	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.014733	0.459559	
chunk0164_426_1	chr6	27388611	27389073	+	0	NA	promoter-TSS (NM_001076781)	promoter-TSS (NM_001076781)	97	NM_001076781	346157	Hs.651176	NM_001013719	ENSG00000124613	ZNF391	dJ153G14.3	zinc finger protein 391	protein-coding	0.064935	0.609071	
chunk0120_84_1	chr3	3694211	3694862	+	0	NA	Intergenic	Intergenic	-104901	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.004608	0.372699	
chunk0178_48_1	chr7	29798642	29799274	+	0	NA	Intergenic	Intergenic	-7596	NM_001080529	644150	Hs.380698	NM_001080529	ENSG00000122574	WIPF3	CR16	WAS/WASL interacting protein family member 3	protein-coding	0.007911	0.489731	364(AGAACTTCCTGCTCTC,+,0.00)
chunk0020_363_1	chr1	239696151	239696635	+	0	NA	intron (NM_000740, intron 3 of 4)	MIR|SINE|MIR	22726	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.006198	0.377320	
chunk0098_10_1	chr2	65136260	65136872	+	0	NA	Intergenic	Intergenic	-6265	NM_015543	5861	Hs.310645	NM_004161	ENSG00000138069	RAB1A	RAB1|YPT1	RAB1A, member RAS oncogene family	protein-coding	0.001634	0.430669	
chunk0022_81_1	chr10	8948847	8949306	+	0	NA	Intergenic	Intergenic	51087	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.006536	0.363043	
chunk0093_141_1	chr19	46378212	46378532	+	0	NA	intron (NM_001204284, intron 4 of 11)	L1ME2|LINE|L1	31378	NM_006247	5536	Hs.654604	NM_006247	ENSG00000011485	PPP5C	PP5|PPP5|PPT	protein phosphatase 5 catalytic subunit	protein-coding	0.003125	0.330218	
chunk0170_179_1	chr6	111838630	111838956	+	0	NA	intron (NM_002037, intron 2 of 13)	intron (NM_002037, intron 2 of 13)	34659	NM_002037	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.009202	0.379205	85(AAGAACACCATCTTCC,-,0.00),86(AGAACACCATCTTCCT,+,0.00)
chunk0106_146_1	chr2	200259519	200260271	+	0	NA	Intergenic	L2c|LINE|L2	-45986	NM_001282743	26010	Hs.120323	NM_015535	ENSG00000196141	SPATS2L	DNAPTP6|SGNP	spermatogenesis associated serine rich 2 like	protein-coding	0.011968	0.386454	
chunk0103_216_1	chr2	163987049	163987765	+	0	NA	Intergenic	Intergenic	-251404	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.009777	0.377964	
chunk0096_211_1	chr2	30502918	30503616	+	0	NA	intron (NM_001304445, intron 3 of 7)	MER66C|LTR|ERV1	56041	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.004298	0.410587	
chunk0014_50_1	chr1	175232227	175232969	+	0	NA	Intergenic	L2c|LINE|L2	-39505	NM_001162894	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.008086	0.394347	374(ATGCACTTCCTGTCCC,-,0.00),375(TGCACTTCCTGTCCCT,+,0.00)
chunk0058_71_1	chr14	21024885	21025143	+	0	NA	promoter-TSS (NM_001282216)	promoter-TSS (NM_001282216)	12	NM_001282214	57447	Hs.525205	NM_016250	ENSG00000165795	NDRG2	SYLD	NDRG family member 2	protein-coding	0.116279	0.764479	
chunk0049_451_1	chr12	98944937	98945507	+	0	NA	intron (NM_001204067, intron 4 of 11)	AluJb|SINE|Alu	-50326	NM_001204081	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.010526	0.453590	
chunk0078_105_1	chr17	2374764	2375370	+	0	NA	intron (NM_001098509, intron 16 of 22)	intron (NM_001098509, intron 16 of 22)	25897	NM_020310	4335	Hs.626579	NM_020310	ENSG00000070444	MNT	MAD6|MXD6|ROX|bHLHd3	MAX network transcriptional repressor	protein-coding	0.016502	0.505766	280(CTGAACACTCAGTACT,-,0.00),281(TGAACACTCAGTACTG,+,0.00)
chunk0201_83_1	chr9	34545934	34546133	+	0	NA	Intergenic	HAL1b|LINE|L1	-21979	NR_024369	415056	Hs.734229	NR_024369		CNTFR-AS1	-	CNTFR antisense RNA 1	ncRNA	0.005025	0.410000	
chunk0149_160_1	chr5	20409515	20409764	+	0	NA	intron (NM_001291956, intron 1 of 14)	L1MB2|LINE|L1	166234	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.276000	
chunk0099_438_1	chr2	103057067	103057319	+	0	NA	Intergenic	Intergenic	295162	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.000000	0.296443	
chunk0066_293_1	chr15	35443361	35443696	+	0	NA	intron (NM_080650, intron 5 of 8)	LTR68|LTR|ERV1	-71164	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.000000	0.416667	
chunk0177_114_1	chr7	22213256	22213496	+	0	NA	intron (NM_012294, intron 9 of 25)	intron (NM_012294, intron 9 of 25)	143538	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.000000	0.360996	
chunk0051_198_1	chr12	116366266	116366738	+	0	NA	Intergenic	Intergenic	61816	NR_039683	100616309		NR_039683	ENSG00000264037	MIR4472-2	-	microRNA 4472-2	ncRNA	0.025424	0.560254	
chunk0142_1_1	chr4	89497884	89498298	+	0	NA	Intergenic	Intergenic	-190081	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.007246	0.327711	246(AGAACACAATGTTTAC,+,0.00)
chunk0066_4_1	chr15	26888839	26889107	+	0	NA	intron (NM_001165037, intron 6 of 10)	intron (NM_001165037, intron 6 of 10)	21847	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.029851	0.542751	
chunk0187_164_1	chr7	150685443	150686129	+	0	NA	promoter-TSS (NM_015660)	promoter-TSS (NM_015660)	80	NM_015660	26157	Hs.647071	NM_015660	ENSG00000106560	GIMAP2	HIMAP2|IAN12|IMAP2	GTPase, IMAP family member 2	protein-coding	0.014577	0.388646	
chunk0121_102_1	chr3	17065458	17065689	+	0	NA	intron (NM_001144382, intron 4 of 5)	L3|LINE|CR1	132377	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.004329	0.435345	
chunk0062_179_1	chr14	69669807	69670070	+	0	NA	intron (NM_014734, intron 2 of 5)	intron (NM_014734, intron 2 of 5)	58345	NM_014734	9766	Hs.440025	NM_014734	ENSG00000100647	SUSD6	DRAGO|KIAA0247	sushi domain containing 6	protein-coding	0.007605	0.428030	
chunk0074_24_1	chr16	20363115	20363493	+	0	NA	intron (NM_174924, intron 9 of 11)	FLAM_A|SINE|Alu	-10426	NM_001278614	7369	Hs.654425	NM_003361	ENSG00000169344	UMOD	ADMCKD2|FJHN|HNFJ|HNFJ1|MCKD2|THGP|THP	uromodulin	protein-coding	0.002646	0.379947	
chunk0135_252_1	chr3	188939977	188940551	+	0	NA	Intergenic	Intergenic	7375	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.006969	0.426087	51(AAGGACATGATGTCAT,-,0.00)
chunk0091_146_1	chr19	7331213	7331431	+	0	NA	Intergenic	(CAT)n|Simple_repeat|Simple_repeat	-37020	NM_000208	3643	Hs.465744	NM_000208	ENSG00000171105	INSR	CD220|HHF5	insulin receptor	protein-coding	0.004587	0.415525	
chunk0048_74_1	chr12	78889789	78890167	+	0	NA	intron (NM_001291901, intron 1 of 9)	intron (NM_001291901, intron 1 of 9)	25309	NM_001291901	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.000000	0.311346	
chunk0089_121_1	chr18	58654136	58654335	+	0	NA	Intergenic	L1M2|LINE|L1	-17151	NM_173844	10892	Hs.601217	NM_006785	ENSG00000172175	MALT1	IMD12|MLT|MLT1|PCASP1	MALT1 paracaspase	protein-coding	0.000000	0.350000	
chunk0209_212_1	chrX	44686257	44686808	+	0	NA	Intergenic	L2a|LINE|L2	-143557	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.005445	0.356884	
chunk0101_211_1	chr2	130260501	130260890	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-62234	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.010283	0.461538	
chunk0103_203_1	chr2	163714980	163715306	+	0	NA	intron (NM_018086, intron 2 of 2)	intron (NM_018086, intron 2 of 2)	20860	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.012270	0.431193	
chunk0195_309_1	chr8	98782986	98783388	+	0	NA	intron (NM_001256312, intron 3 of 12)	Tigger1|DNA|TcMar-Tigger	42484	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004975	0.330025	
chunk0083_2_1	chr17	62387541	62387925	+	0	NA	intron (NM_001144933, intron 5 of 11)	intron (NM_001144933, intron 5 of 11)	7180	NM_173503	146779	Hs.152670	NM_173503	ENSG00000172421	EFCAB3	-	EF-hand calcium binding domain 3	protein-coding	0.005208	0.350649	
chunk0055_332_1	chr13	68995042	68995270	+	0	NA	Intergenic	Intergenic	-109831	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.000000	0.279476	
chunk0110_405_1	chr20	20462228	20462602	+	0	NA	intron (NM_020343, intron 37 of 39)	intron (NM_020343, intron 37 of 39)	94294	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.008021	0.445333	
chunk0050_1_1	chr12	99029855	99030061	+	0	NA	intron (NM_001204067, intron 4 of 11)	MIRc|SINE|MIR	-63401	NR_110095	101928937	Hs.555499	NR_110095	ENSG00000258039	LOC101928937	-	uncharacterized LOC101928937	ncRNA	0.004854	0.449275	
chunk0141_357_1	chr4	87911137	87911573	+	0	NA	Intergenic	Intergenic	-64295	NM_001251829	6696	Hs.313	NM_000582	ENSG00000118785	SPP1	BNSP|BSPI|ETA-1|OPN	secreted phosphoprotein 1	protein-coding	0.009174	0.400458	156(CAGAACACACTGTCTT,-,0.00),157(AGAACACACTGTCTTC,+,0.00)
chunk0160_288_1	chr5	158001227	158001649	+	0	NA	Intergenic	Intergenic	-142263	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.002370	0.382979	
chunk0188_18_1	chr8	6477423	6477873	+	0	NA	intron (NM_024596, intron 10 of 13)	intron (NM_024596, intron 10 of 13)	71056	NM_001172574	79648	Hs.593807	NM_024596	ENSG00000147316	MCPH1	BRIT1|MCT	microcephalin 1	protein-coding	0.004444	0.321508	
chunk0094_367_1	chr2	9668693	9669316	+	0	NA	Intergenic	Intergenic	-37949	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.006421	0.480769	
chunk0094_376_1	chr2	9900547	9900962	+	0	NA	intron (NM_005680, intron 8 of 14)	L2|LINE|L2	-50909	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.004819	0.406250	
chunk0009_145_1	chr1	104884162	104884674	+	0	NA	Intergenic	Intergenic	734517	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.003906	0.343080	241(AAGAACAAAGTGTCCC,-,0.00),242(AGAACAAAGTGTCCCT,+,0.00)
chunk0114_118_1	chr21	9664082	9664349	+	0	NA	Intergenic	LTR12C|LTR|ERV1	156846	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.014981	0.660448	
chunk0195_228_1	chr8	97340661	97341022	+	0	NA	intron (NR_125390, intron 2 of 2)	L1PA11|LINE|L1	-62893	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.011080	0.422652	
chunk0177_464_1	chr7	28663437	28663980	+	0	NA	intron (NM_182899, intron 4 of 9)	intron (NM_182899, intron 4 of 9)	-22273	NM_001011666	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.005525	0.404412	
chunk0102_25_1	chr2	141582205	141582495	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	549351	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.010345	0.391753	
chunk0171_327_1	chr6	129845728	129845927	+	0	NA	exon (NM_001010876, exon 2 of 5)	exon (NM_001010876, exon 2 of 5)	15444	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.005025	0.395000	
chunk0175_231_1	chr7	6385524	6385849	+	0	NA	intron (NM_006908, intron 1 of 5)	intron (NM_006908, intron 1 of 5)	11191	NM_006908	5879	Hs.413812	NM_006908	ENSG00000136238	RAC1	MIG5|MRD48|Rac-1|TC-25|p21-Rac1	Rac family small GTPase 1	protein-coding	0.009231	0.377301	
chunk0094_245_1	chr2	7119639	7120403	+	0	NA	Intergenic	Intergenic	-42141	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.009162	0.428758	480(AAGTACAGTGTGTTCA,-,0.00),481(AGTACAGTGTGTTCAC,+,0.00)
chunk0108_295_1	chr2	234989278	234989613	+	0	NA	intron (NM_014521, intron 1 of 5)	intron (NM_014521, intron 1 of 5)	37461	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.020896	0.529762	
chunk0032_114_1	chr11	3879999	3880204	+	0	NA	intron (NM_001277961, intron 1 of 11)	MIRb|SINE|MIR	24039	NR_039835	100616453		NR_039835	ENSG00000284525	MIR4687	-	microRNA 4687	ncRNA	0.000000	0.475728	
chunk0173_384_1	chr6	149993343	149993850	+	0	NA	Intergenic	L1PA16|LINE|L1	11548	NR_024045	646024	Hs.560537	NR_024045	ENSG00000218358	RAET1K	-	retinoic acid early transcript 1K pseudogene	pseudo	0.003945	0.362205	
chunk0136_348_1	chr3	195839688	195840046	+	0	NA	Intergenic	Intergenic	-27894	NM_018406	4585	Hs.369646	NM_004532	ENSG00000145113	MUC4	ASGP|HSA276359|MUC-4	mucin 4, cell surface associated	protein-coding	0.019553	0.610028	195(CAGGACACACTGTCCT,-,0.00),196(AGGACACACTGTCCTC,+,0.00)
chunk0072_288_1	chr15	98597489	98597701	+	0	NA	Intergenic	Intergenic	-50944	NM_000875	3480	Hs.643120	NM_000875	ENSG00000140443	IGF1R	CD221|IGFIR|IGFR|JTK13	insulin like growth factor 1 receptor	protein-coding	0.009434	0.488263	
chunk0003_42_1	chr1	30675523	30676151	+	0	NA	Intergenic	L1ME4b|LINE|L1	-42935	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.003185	0.341812	
chunk0119_337_1	chr22	46986983	46987666	+	0	NA	intron (NM_014346, intron 9 of 12)	intron (NM_014346, intron 9 of 12)	-71282	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.013177	0.412281	
chunk0130_144_1	chr3	132257500	132257925	+	0	NA	Intergenic	L1MB7|LINE|L1	-59655	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.014118	0.389671	
chunk0088_405_1	chr18	54623475	54623724	+	0	NA	Intergenic	Intergenic	32440	NM_173629	284254	Hs.376146	NM_173629	ENSG00000178690	DYNAP	C18orf26	dynactin associated protein	protein-coding	0.004016	0.320000	
chunk0145_264_1	chr4	148978401	148978893	+	0	NA	Intergenic	MIR|SINE|MIR	-175648	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.006098	0.363083	
chunk0197_458_1	chr8	127884331	127884977	+	0	NA	intron (NR_003367, intron 1 of 8)	L1ME3A|LINE|L1	64069	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.012384	0.432767	
chunk0056_119_1	chr13	83060947	83061148	+	0	NA	Intergenic	Intergenic	821346	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.316832	100(TGGAACACTCTGTTCC,-,0.00),101(GGAACACTCTGTTCCT,+,0.00)
chunk0082_122_1	chr17	55154191	55154390	+	0	NA	intron (NM_178509, intron 17 of 17)	MLT1J2|LTR|ERVL-MaLR	-110670	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.005025	0.445000	
chunk0019_299_1	chr1	228877277	228877878	+	0	NA	Intergenic	Intergenic	142500	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.003328	0.347176	
chunk0090_234_1	chr18	73733251	73733977	+	0	NA	Intergenic	Intergenic	408673	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.005510	0.394773	
chunk0094_80_1	chr2	3651958	3652544	+	0	NA	Intergenic	Intergenic	-5945	NM_018436	55821	Hs.97899	NM_018436	ENSG00000151360	ALLC	ALC	allantoicase	protein-coding	0.039249	0.540034	
chunk0147_431_1	chr4	187478191	187478572	+	0	NA	intron (NR_038931, intron 1 of 4)	intron (NR_038931, intron 1 of 4)	27232	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.023622	0.374346	
chunk0022_373_1	chr10	17536500	17536746	+	0	NA	Intergenic	Intergenic	80751	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.004065	0.473684	
chunk0132_29_1	chr3	154705935	154706538	+	0	NA	Intergenic	L1M5|LINE|L1	-276521	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.006633	0.302980	
chunk0138_255_1	chr4	39858257	39858667	+	0	NA	intron (NM_001100399, intron 26 of 32)	L1M4|LINE|L1	119494	NM_001100399	23244	Hs.331431	NM_015200	ENSG00000121892	PDS5A	PIG54|SCC-112|SCC112	PDS5 cohesin associated factor A	protein-coding	0.000000	0.330900	205(AAGAACAGTCTCTTCA,-,0.00)
chunk0172_169_1	chr6	136158368	136158904	+	0	NA	intron (NM_018945, intron 8 of 12)	intron (NM_018945, intron 8 of 12)	91675	NM_138419	113115	Hs.121536	NM_138419	ENSG00000146410	MTFR2	DUFD1|FAM54A	mitochondrial fission regulator 2	protein-coding	0.009328	0.469274	
chunk0107_10_1	chr2	210028951	210029210	+	0	NA	promoter-TSS (NR_110291)	promoter-TSS (NR_110291)	-842	NR_110291	101928020	Hs.635556	NR_110291		LOC101928020	-	uncharacterized LOC101928020	ncRNA	0.011583	0.307692	
chunk0164_194_1	chr6	22363182	22363624	+	0	NA	Intergenic	Intergenic	-60550	NM_001163558	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.002262	0.419865	
chunk0156_122_1	chr5	106495512	106495754	+	0	NA	Intergenic	L1MD2|LINE|L1	515381	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.000000	0.304527	
chunk0058_335_1	chr14	28679054	28679565	+	0	NA	Intergenic	L1M4|LINE|L1	86010	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.001957	0.302734	
chunk0159_388_1	chr5	146507235	146507924	+	0	NA	intron (NM_006706, intron 19 of 21)	intron (NM_006706, intron 19 of 21)	8534	NM_194251	134391	Hs.483732	NM_194251	ENSG00000173250	GPR151	GALR4|GALRL|GPCR|GPCR-2037|PGR7	G protein-coupled receptor 151	protein-coding	0.008708	0.349275	
chunk0134_135_1	chr3	177479256	177479466	+	0	NA	intron (NR_047568, intron 1 of 3)	intron (NR_047568, intron 1 of 3)	37440	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.019048	0.369668	
chunk0137_422_1	chr4	28149764	28150232	+	0	NA	Intergenic	Intergenic	-669584	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.006410	0.371002	
chunk0006_117_1	chr1	65641068	65641751	+	0	NA	Intergenic	Intergenic	115720	NM_001198687	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.005857	0.279240	
chunk0057_378_1	chr13	109231324	109231699	+	0	NA	Intergenic	MIR3|SINE|MIR	-64208	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.002667	0.369681	
chunk0003_365_1	chr1	39386920	39387155	+	0	NA	intron (NM_012090, intron 51 of 92)	MIRc|SINE|MIR	-22467	NM_015038	643314	Hs.658760	NM_015038	ENSG00000127603	KIAA0754	-	KIAA0754	protein-coding	0.012766	0.372881	
chunk0025_327_1	chr10	57870091	57870562	+	0	NA	Intergenic	Intergenic	397608	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.002123	0.341102	
chunk0105_292_1	chr2	189922377	189922999	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-138317	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.006431	0.394864	171(CAGTACTTGCTGTACT,-,0.00),172(AGTACTTGCTGTACTT,+,0.00)
chunk0206_362_1	chr9	125857824	125858058	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	109742	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.323404	
chunk0060_169_1	chr14	45466685	45467566	+	0	NA	Intergenic	LTR85a|LTR|Gypsy?	-213723	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.001135	0.411565	
chunk0029_438_1	chr10	110141281	110141587	+	0	NA	Intergenic	Intergenic	-66171	NM_130439	4601	Hs.602078	NM_005962	ENSG00000119950	MXI1	MAD2|MXD2|MXI|bHLHc11	MAX interactor 1, dimerization protein	protein-coding	0.003268	0.423453	
chunk0200_190_1	chr9	19642246	19642689	+	0	NA	intron (NM_020344, intron 1 of 9)	intron (NM_020344, intron 1 of 9)	144552	NM_020344	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.006772	0.448198	
chunk0022_362_1	chr10	17284548	17284953	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-54765	NR_108061	100507347	Hs.740502	NR_108060	ENSG00000229124	VIM-AS1	-	VIM antisense RNA 1	ncRNA	0.002469	0.359606	99(AAGAACACTGTGATCA,-,0.00),100(AGAACACTGTGATCAA,+,0.00),226(GGTACAAACTGTTTCT,+,0.00)
chunk0065_147_1	chr15	25386097	25386622	+	0	NA	intron (NM_130838, intron 1 of 9)	L1MC1|LINE|L1	19147	NM_130838	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.001905	0.374525	200(TAGTACATCATGTCCA,-,0.00),201(AGTACATCATGTCCAA,+,0.00)
chunk0010_434_1	chr1	119867562	119868375	+	0	NA	Intergenic	AluY|SINE|Alu	-23088	NM_001047980	343505		NM_001047980		NBPF7	-	NBPF member 7	protein-coding	0.011070	0.460688	303(GAGCACATCCTGTACC,-,0.00),304(AGCACATCCTGTACCA,+,0.00)
chunk0001_137_1	chr1	5597903	5598527	+	0	NA	Intergenic	Intergenic	34144	NR_039612									0.014423	0.518400	
chunk0191_102_1	chr8	48029440	48029854	+	0	NA	intron (NM_003350, intron 1 of 3)	intron (NM_003350, intron 1 of 3)	21212	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.002415	0.359036	185(AAGTACAGACAGTGCA,-,0.00),186(AGTACAGACAGTGCAT,+,0.00)
chunk0014_65_1	chr1	176000257	176000469	+	0	NA	intron (NM_001001740, intron 14 of 18)	L1M1|LINE|L1	-31823	NR_002998	677679		NR_002998	ENSG00000252906	SCARNA3	HBI-100	small Cajal body-specific RNA 3	ncRNA	0.004717	0.366197	
chunk0051_139_1	chr12	115692936	115693464	+	0	NA	Intergenic	Intergenic	455454	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.007576	0.436673	
chunk0111_276_1	chr20	31187133	31187363	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-70416	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.017391	0.389610	
chunk0136_216_1	chr4	7757688	7758195	+	0	NA	TTS (NM_001134647)	TTS (NM_001134647)	3851	NR_026892	84740	Hs.663029	NM_032654	ENSG00000272620	AFAP1-AS1	AFAP1-AS|AFAP1AS	AFAP1 antisense RNA 1	ncRNA	0.023669	0.476378	471(GAGGACACGCTGCTCA,-,0.00),472(AGGACACGCTGCTCAC,+,0.00)
chunk0090_363_1	chr18	76978770	76978983	+	0	NA	TTS (NM_002385)	TTS (NM_002385)	38223	NM_001025081	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.051643	0.500000	
chunk0028_10_1	chr10	82256646	82257028	+	0	NA	intron (NM_001165973, intron 2 of 10)	intron (NM_001165973, intron 2 of 10)	-23917	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.005236	0.381201	211(GGGAACATTATGTCTC,-,0.00),212(GGAACATTATGTCTCT,+,0.00)
chunk0085_176_1	chr18	5245888	5246611	+	0	NA	non-coding (NR_015389, exon 3 of 3)	non-coding (NR_015389, exon 3 of 3)	8149	NR_015389	339290	Hs.643553	NR_015389	ENSG00000263753	LINC00667	-	long intergenic non-protein coding RNA 667	ncRNA	0.002766	0.383978	
chunk0044_395_1	chr12	40634598	40635441	+	0	NA	Intergenic	Intergenic	-57423	NM_001843	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.004745	0.434834	
chunk0092_81_1	chr19	21071297	21071508	+	0	NA	Intergenic	L1PA17|LINE|L1	-10745	NR_117088	148206	Hs.729186	NM_182515	ENSG00000160352	ZNF714	-	zinc finger protein 714	protein-coding	0.000000	0.353774	
chunk0085_167_1	chr18	3773139	3773741	+	0	NA	intron (NM_001308390, intron 2 of 10)	intron (NM_001308390, intron 2 of 10)	71918	NM_001242766	9229	Hs.594640	NM_004746	ENSG00000170579	DLGAP1	DAP-1|DAP-1-ALPHA|DAP-1-BETA|DAP1|DLGAP1A|DLGAP1B|GKAP|SAPAP1	DLG associated protein 1	protein-coding	0.004983	0.343284	315(AGGAACAAAATGTTTT,-,0.00),316(GGAACAAAATGTTTTC,+,0.00)
chunk0111_345_1	chr20	33251887	33252278	+	0	NA	Intergenic	Intergenic	16086	NM_130852	51297	Hs.211092	NM_016583	ENSG00000198183	BPIFA1	LUNX|NASG|PLUNC|SPLUNC1|SPURT|bA49G10.5	BPI fold containing family A member 1	protein-coding	0.007673	0.494898	
chunk0075_117_1	chr16	49272595	49273027	+	0	NA	Intergenic	Intergenic	9020	NM_004352	869	Hs.458423	NM_004352	ENSG00000102924	CBLN1	-	cerebellin 1 precursor	protein-coding	0.002315	0.427252	
chunk0145_333_1	chr4	150771771	150772570	+	0	NA	intron (NM_001199282, intron 34 of 56)	ERVL-B4-int|LTR|ERVL	190245	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.003755	0.441250	
chunk0133_146_1	chr3	169305452	169306127	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-158055	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.004444	0.355030	349(ATGGACTCTTTGTTCT,-,0.00)
chunk0182_391_1	chr7	100409075	100409525	+	0	NA	intron (NM_017984, intron 9 of 17)	intron (NM_017984, intron 9 of 17)	-19490	NM_001194990	56257	Hs.178011	NM_019606	ENSG00000146834	MEPCE	BCDIN3	methylphosphate capping enzyme	protein-coding	0.011111	0.445676	240(AAGGACACTGAGTGCT,-,0.00),241(AGGACACTGAGTGCTA,+,0.00)
chunk0153_63_1	chr5	67814427	67814966	+	0	NA	Intergenic	Intergenic	21483	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.005566	0.351852	
chunk0114_175_1	chr21	14830320	14830906	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-187506	NM_001256579	388813	Hs.334177	NM_001256579		LOC388813	-	uncharacterized protein ENSP00000383407-like	protein-coding	0.005119	0.405451	
chunk0184_109_1	chr7	113491321	113491660	+	0	NA	Intergenic	Intergenic	-372908	NR_015442									0.002950	0.350000	
chunk0026_211_1	chr10	64109277	64110002	+	0	NA	Intergenic	Intergenic	588276	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.002759	0.389807	333(ATGTACACTGTGTACT,-,0.00),334(TGTACACTGTGTACTA,+,0.00)
chunk0206_373_1	chr9	126082648	126082984	+	0	NA	Intergenic	Intergenic	193099	NR_121584	101929116	Hs.382124	NR_121584	ENSG00000228392	LOC101929116	-	uncharacterized LOC101929116	ncRNA	0.026786	0.540059	
chunk0211_108_1	chrX	111253219	111253574	+	0	NA	intron (NM_014289, intron 3 of 12)	intron (NM_014289, intron 3 of 12)	17150	NM_014289	827	Hs.496593	NM_014289	ENSG00000077274	CAPN6	CANPX|CAPNX|CalpM|DJ914P14.1	calpain 6	protein-coding	0.002817	0.401685	
chunk0188_434_1	chr8	19128353	19128692	+	0	NA	Intergenic	Intergenic	-114836	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.002950	0.435294	
chunk0023_141_1	chr10	24034503	24035124	+	0	NA	intron (NM_001098500, intron 2 of 18)	intron (NM_001098500, intron 2 of 18)	-173978	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.014493	0.517685	
chunk0067_15_1	chr15	40055339	40055779	+	0	NA	intron (NR_040060, intron 2 of 2)	intron (NR_040060, intron 2 of 2)	16248	NR_040059	100131089	Hs.386000	NR_040059	ENSG00000248508	SRP14-AS1	-	SRP14 antisense RNA1 (head to head)	ncRNA	0.011364	0.600907	
chunk0163_192_1	chr6	11655666	11656118	+	0	NA	Intergenic	Intergenic	117665	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.019912	0.432671	
chunk0029_361_1	chr10	107618354	107618750	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	450741	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.002525	0.329975	
chunk0076_153_1	chr16	67240790	67241370	+	0	NA	intron (NM_013241, intron 1 of 21)	intron (NM_013241, intron 1 of 21)	6442	NM_013241	29109	Hs.95231	NM_013241	ENSG00000135723	FHOD1	FHOS	formin homology 2 domain containing 1	protein-coding	0.005172	0.616179	
chunk0116_450_1	chr21	43712239	43712548	+	0	NA	Intergenic	Intergenic	-6704	NM_003681	8566	Hs.284491	NM_003681	ENSG00000160209	PDXK	C21orf124|C21orf97|HEL-S-1a|PKH|PNK|PRED79	pyridoxal kinase	protein-coding	0.025890	0.516129	
chunk0016_161_1	chr1	197738658	197738864	+	0	NA	intron (NM_001300858, intron 2 of 15)	L1MEc|LINE|L1	36732	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.000000	0.342995	
chunk0027_295_1	chr10	77624509	77624741	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	13194	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.000000	0.334764	
chunk0190_205_1	chr8	35501719	35501939	+	0	NA	intron (NM_080872, intron 1 of 16)	intron (NM_080872, intron 1 of 16)	208491	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.004545	0.321267	
chunk0057_315_1	chr13	106727516	106727856	+	0	NA	Intergenic	Intergenic	73806	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.005882	0.407625	
chunk0062_20_1	chr14	66536654	66536857	+	0	NA	intron (NM_001024218, intron 1 of 21)	L1ME3|LINE|L1	29348	NM_020806	10243	Hs.208765	NM_020806	ENSG00000171723	GPHN	GEPH|GPH|GPHRYN|HKPX1|MOCODC	gephyrin	protein-coding	0.000000	0.318627	
chunk0070_423_1	chr15	77921577	77921982	+	0	NA	intron (NR_027024, intron 4 of 17)	intron (NR_027024, intron 4 of 17)	5067	NR_027024	645752	Hs.546408	NR_027024		LOC645752	-	golgin A6 family member A pseudogene	pseudo	0.007407	0.532020	
chunk0165_103_1	chr6	32387048	32387454	+	0	NA	Intergenic	Intergenic	-3259	NR_044996	414764	Hs.57692	NR_044996	ENSG00000225914	HCG23	dJ1077I5.3	HLA complex group 23	ncRNA	0.014778	0.496314	
chunk0110_120_1	chr20	12937046	12937518	+	0	NA	promoter-TSS (NR_109872)	promoter-TSS (NR_109872)	-319	NR_109872	102606466	Hs.602196	NR_109872		LOC102606466	-	uncharacterized LOC102606466	ncRNA	0.008475	0.401691	
chunk0209_98_1	chrX	39813748	39813947	+	0	NA	Intergenic	Intergenic	-23714	NR_039763	100616251		NR_039763	ENSG00000263972	MIR1587	-	microRNA 1587	ncRNA	0.015075	0.540000	
chunk0148_411_1	chr5	14947317	14947681	+	0	NA	Intergenic	Intergenic	-75721	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.002747	0.449315	
chunk0106_231_1	chr2	202634674	202634906	+	0	NA	promoter-TSS (NM_173511)	promoter-TSS (NM_173511)	-388	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.107759	0.669528	
chunk0093_236_1	chr19	50804653	50804878	+	0	NA	promoter-TSS (NM_199250)	promoter-TSS (NM_199250)	88	NM_001290154	84798	Hs.256301	NM_032712	ENSG00000167747	C19orf48	-	chromosome 19 open reading frame 48	protein-coding	0.066667	0.557522	
chunk0115_428_1	chr21	31781832	31782151	+	0	NA	Intergenic	L2b|LINE|L2	-49873	NM_020706	57466	Hs.17255	NM_020706	ENSG00000156304	SCAF4	SFRS15|SRA4	SR-related CTD associated factor 4	protein-coding	0.009404	0.512500	
chunk0193_76_1	chr8	73293930	73294427	+	0	NA	promoter-TSS (NM_172037)	promoter-TSS (NM_172037)	-424	NM_172037	157506	Hs.244940	NM_172037	ENSG00000121039	RDH10	SDR16C4	retinol dehydrogenase 10	protein-coding	0.090543	0.670683	
chunk0158_304_1	chr5	132363393	132363777	+	0	NA	intron (NR_110997, intron 3 of 7)	L2a|LINE|L2	2014	NR_037500	100500865		NR_037500	ENSG00000263597	MIR3936	mir-3936	microRNA 3936	ncRNA	0.010417	0.423377	
chunk0107_360_1	chr2	222713172	222713371	+	0	NA	Intergenic	Intergenic	41533	NM_058165	116255	Hs.344090	NM_058165	ENSG00000124003	MOGAT1	DGAT2L|DGAT2L1|MGAT1	monoacylglycerol O-acyltransferase 1	protein-coding	0.010050	0.460000	
chunk0170_20_1	chr6	109182650	109183108	+	0	NA	Intergenic	Intergenic	53575	NM_173830	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.008734	0.394336	
chunk0121_117_1	chr3	17420785	17420997	+	0	NA	intron (NM_014744, intron 4 of 21)	intron (NM_014744, intron 4 of 21)	279129	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.000000	0.380282	
chunk0088_120_1	chr18	45720540	45721221	+	0	NA	Intergenic	Intergenic	-3243	NM_001308279	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.010279	0.435484	361(AGGAACATTCTGTTCC,-,0.00),362(GGAACATTCTGTTCCA,+,0.00)
chunk0189_392_1	chr8	27478897	27479817	+	0	NA	promoter-TSS (NM_001282455)	promoter-TSS (NM_001282455)	-61	NM_000742	1135	Hs.57718	NM_000742	ENSG00000120903	CHRNA2	-	cholinergic receptor nicotinic alpha 2 subunit	protein-coding	0.017391	0.560261	326(AGGCTCACGCTGTTCT,-,0.00),327(GGCTCACGCTGTTCTC,+,0.00)
chunk0037_387_1	chr11	78801431	78801778	+	0	NA	intron (NM_001098816, intron 15 of 33)	intron (NM_001098816, intron 15 of 33)	-226740	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.002882	0.482759	
chunk0046_285_1	chr12	62015018	62015640	+	0	NA	intron (NM_178539, intron 1 of 4)	L2a|LINE|L2	177510	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.000000	0.332263	
chunk0063_253_1	chr14	82724822	82725112	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-1101906	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.006897	0.481100	
chunk0109_418_1	chr2	241126186	241126766	+	0	NA	exon (NM_001252120, exon 11 of 19)	exon (NM_001252120, exon 11 of 19)	23028	NM_001252122	23178	Hs.397891	NM_015148	ENSG00000115687	PASK	PASKIN|STK37	PAS domain containing serine/threonine kinase	protein-coding	0.044828	0.581756	
chunk0014_445_1	chr1	183827745	183828361	+	0	NA	intron (NM_001297672, intron 2 of 16)	intron (NM_001297672, intron 2 of 16)	22972	NM_001297671	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.006494	0.341977	
chunk0040_453_1	chr11	121688419	121688845	+	0	NA	Intergenic	MER33|DNA|hAT-Charlie	236429	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.004695	0.360656	
chunk0112_108_1	chr20	38380727	38381228	+	0	NA	Intergenic	Intergenic	34566	NM_004139	3929	Hs.154078	NM_004139	ENSG00000129988	LBP	BPIFD2	lipopolysaccharide binding protein	protein-coding	0.015968	0.486056	
chunk0185_446_1	chr7	134970389	134970697	+	0	NA	3' UTR (NM_033140, exon 12 of 12)	3' UTR (NM_033140, exon 12 of 12)	-15965	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.006494	0.307443	
chunk0046_123_1	chr12	57355823	57356273	+	0	NA	Intergenic	L1ME1|LINE|L1	-45585	NM_014925	22864	Hs.443673	NM_014925	ENSG00000179912	R3HDM2	CAG6|PR01365	R3H domain containing 2	protein-coding	0.000000	0.341463	
chunk0162_423_1	chr5	180081483	180082047	+	0	NA	Intergenic	L1ME4c|LINE|L1	-9647	NM_018434	55819	Hs.484363	NM_018434	ENSG00000113269	RNF130	G1RZFP|GOLIATH|GP	ring finger protein 130	protein-coding	0.010638	0.437168	
chunk0165_116_1	chr6	32909130	32909629	+	0	NA	Intergenic	L2b|LINE|L2	15203	NR_037177	100294145	Hs.559456	NR_037177		LOC100294145	-	uncharacterized LOC100294145	ncRNA	0.006012	0.340000	313(AGGTACAGTCTGTCTC,-,0.00),314(GGTACAGTCTGTCTCC,+,0.00)
chunk0020_372_1	chr1	239803993	239804192	+	0	NA	intron (NM_000740, intron 3 of 4)	intron (NM_000740, intron 3 of 4)	-84973	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.005025	0.410000	
chunk0048_450_1	chr12	88720667	88721335	+	0	NA	Intergenic	Intergenic	-140528	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.005988	0.330344	
chunk0152_453_1	chr5	66441823	66442022	+	0	NA	Intergenic	Intergenic	69682	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.005025	0.295000	
chunk0088_54_1	chr18	44170092	44170573	+	0	NA	Intergenic	Intergenic	361365	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.000000	0.358921	
chunk0095_327_1	chr2	20636335	20636927	+	0	NA	intron (NM_022460, intron 4 of 6)	MER112|DNA|hAT-Charlie	14473	NM_022460	64342	Hs.531785	NM_022460	ENSG00000118960	HS1BP3	ETM2|HS1-BP3	HCLS1 binding protein 3	protein-coding	0.016892	0.456998	
chunk0091_231_1	chr19	10421945	10422537	+	0	NA	intron (NM_001111307, intron 1 of 14)	intron (NM_001111307, intron 1 of 14)	1584	NM_001111307	5141	Hs.89901	NM_006202	ENSG00000065989	PDE4A	DPDE2|PDE4|PDE46	phosphodiesterase 4A	protein-coding	0.011824	0.510961	314(TGGAACAGTCTGTGCT,-,0.00),315(GGAACAGTCTGTGCTC,+,0.00)
chunk0148_161_1	chr5	6636208	6637002	+	0	NA	intron (NM_001047, intron 1 of 4)	intron (NM_001047, intron 1 of 4)	3218	NM_001047	6715	Hs.552	NM_001047	ENSG00000145545	SRD5A1	S5AR 1	steroid 5 alpha-reductase 1	protein-coding	0.012594	0.540881	
chunk0053_223_1	chr13	32253818	32254262	+	0	NA	intron (NM_023037, intron 50 of 60)	intron (NM_023037, intron 50 of 60)	57914	NM_001136571	646799	Hs.569254	NM_001136571	ENSG00000189167	ZAR1L	Z3CXXC7|ZAR2	zygote arrest 1 like	protein-coding	0.020270	0.386517	
chunk0193_290_1	chr8	77589114	77589540	+	0	NA	Intergenic	Intergenic	138630	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.004695	0.365340	
chunk0097_66_1	chr2	44170386	44170758	+	0	NA	intron (NM_177969, intron 1 of 4)	intron (NM_177969, intron 1 of 4)	1769	NM_177969	5495	Hs.416769	NM_002706	ENSG00000138032	PPM1B	PP2C-beta|PP2C-beta-X|PP2CB|PP2CBETA|PPC2BETAX	protein phosphatase, Mg2+/Mn2+ dependent 1B	protein-coding	0.008065	0.345845	184(AGTCACAGTATGTTCT,-,0.00),185(GTCACAGTATGTTCTA,+,0.00)
chunk0080_285_1	chr17	31274221	31274752	+	0	NA	intron (NM_001042492, intron 36 of 57)	intron (NM_001042492, intron 36 of 57)	22876	NM_002544	4974	Hs.113874	NM_002544	ENSG00000126861	OMG	OMGP	oligodendrocyte myelin glycoprotein	protein-coding	0.003766	0.351504	
chunk0209_207_1	chrX	44223985	44224316	+	0	NA	intron (NM_025184, intron 11 of 14)	intron (NM_025184, intron 11 of 14)	119527	NM_025184	80258	Hs.521953	NM_025184	ENSG00000183690	EFHC2	MRX74|dJ1158H2.1	EF-hand domain containing 2	protein-coding	0.003021	0.355422	
chunk0047_276_1	chr12	73094107	73094454	+	0	NA	Intergenic	THE1B-int|LTR|ERVL-MaLR	-64910	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.005764	0.517241	
chunk0024_80_1	chr10	34334889	34335368	+	0	NA	intron (NM_001184791, intron 15 of 20)	intron (NM_001184791, intron 15 of 20)	480197	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.008351	0.310417	
chunk0149_286_1	chr5	25331737	25331936	+	0	NA	Intergenic	MER52D|LTR|ERV1	-491253	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.010050	0.595000	
chunk0068_56_1	chr15	51708048	51708247	+	0	NA	intron (NM_001165257, intron 9 of 10)	intron (NM_001165257, intron 9 of 10)	26794	NM_013243	29106	Hs.232618	NM_013243	ENSG00000104112	SCG3	SGIII	secretogranin III	protein-coding	0.010050	0.450000	
chunk0169_72_1	chr6	99050146	99050644	+	0	NA	Intergenic	Intergenic	-74214	NR_039672	100616347		NR_039672	ENSG00000265226	MIR548AI	-	microRNA 548ai	ncRNA	0.010040	0.318637	
chunk0020_234_1	chr1	235771224	235771759	+	0	NA	intron (NM_001301365, intron 19 of 52)	intron (NM_001301365, intron 19 of 52)	81569	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.003738	0.285448	
chunk0153_40_1	chr5	67216691	67217061	+	0	NA	Intergenic	Intergenic	-20087	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.002703	0.396226	
chunk0033_117_1	chr11	14520388	14520840	+	0	NA	promoter-TSS (NM_002786)	promoter-TSS (NM_002786)	-169	NM_001143937	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.066372	0.554084	
chunk0019_238_1	chr1	227399238	227399939	+	0	NA	Intergenic	L1MC1|LINE|L1	-81463	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.005706	0.398860	
chunk0118_285_1	chr22	33852011	33852232	+	0	NA	intron (NM_133642, intron 1 of 14)	intron (NM_133642, intron 1 of 14)	68307	NM_004737	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.004525	0.396396	
chunk0161_200_1	chr5	170518255	170518881	+	0	NA	intron (NM_001278339, intron 1 of 7)	intron (NM_001278339, intron 1 of 7)	14532	NM_001278340	30820	Hs.484111	NM_014592	ENSG00000182132	KCNIP1	KCHIP1|VABP	potassium voltage-gated channel interacting protein 1	protein-coding	0.011182	0.468900	282(AGACACAGGCTGTTCT,-,0.00),283(GACACAGGCTGTTCTC,+,0.00)
chunk0168_408_1	chr6	94970897	94971377	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	606314	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.004167	0.378378	
chunk0121_467_1	chr3	27289571	27290187	+	0	NA	intron (NM_199347, intron 20 of 24)	intron (NM_199347, intron 20 of 24)	-73356	NM_001031741	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.003247	0.361426	
chunk0109_168_1	chr20	4116023	4116382	+	0	NA	Intergenic	L1MC5a|LINE|L1	-32577	NM_175840	54498	Hs.433337	NM_175839	ENSG00000088826	SMOX	C20orf16|PAO|PAO-1|PAO1|PAOH|PAOH1|SMO	spermine oxidase	protein-coding	0.002786	0.363889	270(TGGAACATGATGTTCT,-,0.00),271(GGAACATGATGTTCTA,+,0.00)
chunk0206_81_1	chr9	120386408	120386699	+	0	NA	Intergenic	Intergenic	-141503	NR_029604	406939		NR_029604	ENSG00000207814	MIR147A	MIR147|MIRN147|hsa-mir-147a	microRNA 147a	ncRNA	0.020619	0.445205	
chunk0127_324_1	chr3	100151955	100152198	+	0	NA	intron (NM_032359, intron 2 of 9)	MLT1B-int|LTR|ERVL-MaLR	-33748	NR_028357	644444	Hs.652353	NR_028357	ENSG00000235156	TMEM30CP	CDC50C|TMEM30C	transmembrane protein 30C, pseudogene	pseudo	0.004115	0.426230	
chunk0158_441_1	chr5	135686206	135686578	+	0	NA	Intergenic	L2c|LINE|L2	-32457	NR_027127	340074	Hs.434633	NR_027127	ENSG00000251045	SLC25A48-AS1	LINC01959	SLC25A48 antisense RNA 1	ncRNA	0.010753	0.463807	
chunk0078_420_1	chr16	89302597	89303072	+	0	NA	intron (NR_045839, intron 5 of 9)	intron (NR_045839, intron 5 of 9)	-18299	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.021053	0.487395	256(AAGGACATGGTGTTCA,-,0.00),257(AGGACATGGTGTTCAA,+,0.00)
chunk0071_228_1	chr15	84937074	84937409	+	0	NA	intron (NM_001287762, intron 14 of 17)	L1ME4c|LINE|L1	-43272	NM_001243137	5151	Hs.9333	NM_002605	ENSG00000073417	PDE8A	HsT19550	phosphodiesterase 8A	protein-coding	0.014925	0.416667	
chunk0110_54_1	chr20	10769228	10769524	+	0	NA	Intergenic	Intergenic	16286	NR_110611	101929395	Hs.244862	NR_110611		LINC01752	-	long intergenic non-protein coding RNA 1752	ncRNA	0.000000	0.424242	
chunk0002_244_1	chr1	20784695	20785182	+	0	NA	intron (NM_016287, intron 1 of 12)	intron (NM_016287, intron 1 of 12)	1750	NM_016287	50809	Hs.142442	NM_016287	ENSG00000127483	HP1BP3	HP1-BP74|HP1BP74	heterochromatin protein 1 binding protein 3	protein-coding	0.024641	0.471311	
chunk0036_42_1	chr11	58989106	58989573	+	0	NA	intron (NR_033853, intron 4 of 5)	L1PA6|LINE|L1	46090	NM_001220496	92292	Hs.38085	NM_080661	ENSG00000166840	GLYATL1	GATF-C|GNAT	glycine-N-acyltransferase like 1	protein-coding	0.004283	0.489316	
chunk0183_33_1	chr7	103672957	103673403	+	0	NA	intron (NM_005045, intron 11 of 64)	L1MEh|LINE|L1	-227003	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.000000	0.279642	
chunk0024_245_1	chr10	38835687	38835887	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	139191	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.015000	0.383085	
chunk0006_102_1	chr1	65378049	65378248	+	0	NA	intron (NM_014787, intron 4 of 18)	L2c|LINE|L2	-42300	NM_001198683	54741	Hs.23581	NM_017526	ENSG00000213625	LEPROT	LEPR|OB-RGRP|OBRGRP|VPS55	leptin receptor overlapping transcript	protein-coding	0.000000	0.485000	
chunk0113_271_1	chr20	56604406	56605124	+	0	NA	Intergenic	L1MC5a|LINE|L1	-24537	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.019499	0.520167	
chunk0098_360_1	chr2	77664451	77665022	+	0	NA	Intergenic	Intergenic	-142360	NM_024993	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.003503	0.298951	
chunk0100_214_1	chr2	111927418	111928082	+	0	NA	intron (NM_006343, intron 1 of 18)	intron (NM_006343, intron 1 of 18)	29136	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.007530	0.454135	385(GAGGGCATGATGTCCT,-,0.00),386(AGGGCATGATGTCCTG,+,0.00)
chunk0059_287_1	chr14	35683906	35684366	+	0	NA	intron (NM_001283043, intron 20 of 41)	intron (NM_001283043, intron 20 of 41)	125090	NM_001283044	253959	Hs.113150	NM_014990	ENSG00000174373	RALGAPA1	GARNL1|GRIPE|RalGAPalpha1|TULIP1|p240	Ral GTPase activating protein catalytic alpha subunit 1	protein-coding	0.010870	0.355748	
chunk0210_266_1	chrX	84175856	84176414	+	0	NA	intron (NM_014496, intron 1 of 21)	intron (NM_014496, intron 1 of 21)	11800	NM_014496	27330	Hs.234478	NM_014496	ENSG00000072133	RPS6KA6	PP90RSK4|RSK-4|RSK4|S6K-alpha-6|p90RSK6	ribosomal protein S6 kinase A6	protein-coding	0.000000	0.341682	
chunk0203_105_1	chr9	84494895	84495326	+	0	NA	Intergenic	L1ME1|LINE|L1	-126612	NM_022127	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.004640	0.347222	
chunk0030_15_1	chr10	110916396	110916828	+	0	NA	intron (NM_001195304, intron 2 of 4)	intron (NM_001195304, intron 2 of 4)	2324	NM_001195306	92482	Hs.232543	NM_001195304	ENSG00000214413	BBIP1	BBIP10|BBS18|NCRNA00081|bA348N5.3	BBSome interacting protein 1	protein-coding	0.002315	0.383372	
chunk0210_277_1	chrX	84648064	84648584	+	0	NA	Intergenic	L2a|LINE|L2	-145845	NM_144657	139324	Hs.559546	NM_144657	ENSG00000165259	HDX	CXorf43|D030011N01Rik	highly divergent homeobox	protein-coding	0.007692	0.333973	
chunk0009_289_1	chr1	107682422	107683061	+	0	NA	intron (NM_006113, intron 19 of 26)	intron (NM_006113, intron 19 of 26)	5763	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.004695	0.345313	
chunk0125_309_1	chr3	70737968	70738272	+	0	NA	Intergenic	Intergenic	326803	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.006579	0.429508	
chunk0178_134_1	chr7	32552343	32552953	+	0	NA	intron (NM_015060, intron 6 of 15)	AluJb|SINE|Alu	57222	NM_015060	23080	Hs.128056	NM_015060	ENSG00000105778	AVL9	KIAA0241	AVL9 cell migration associated	protein-coding	0.004918	0.382979	405(AGAGACAAGGTGTCCC,-,0.00),406(GAGACAAGGTGTCCCT,+,0.00)
chunk0058_171_1	chr14	23640524	23640744	+	0	NA	intron (NM_182908, intron 4 of 8)	intron (NM_182908, intron 4 of 8)	4270	NM_005794	10202	Hs.272499	NM_005794	ENSG00000100867	DHRS2	HEP27|SDR25C1	dehydrogenase/reductase 2	protein-coding	0.009091	0.497738	
chunk0134_371_1	chr3	182739112	182739311	+	0	NA	Intergenic	Intergenic	-54292	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.005025	0.455000	
chunk0107_279_1	chr2	218272668	218273044	+	0	NA	TTS (NM_001077399)	TTS (NM_001077399)	2464	NM_001077399	25953	Hs.98475	NM_015488	ENSG00000127838	PNKD	BRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|TAHCCP2	PNKD metallo-beta-lactamase domain containing	protein-coding	0.018617	0.578249	357(CAGAGCTCAGTGTTCC,-,0.00)
chunk0174_254_1	chr6	161062556	161063265	+	0	NA	intron (NM_006724, intron 3 of 25)	L1M8|LINE|L1	71183	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.001410	0.288732	
chunk0021_146_1	chr10	4197056	4197527	+	0	NA	Intergenic	Intergenic	46621	NR_108040	100652988	Hs.433011	NR_108040		LINC00702	-	long intergenic non-protein coding RNA 702	ncRNA	0.006369	0.381356	218(AAGAACAGGATGTGCT,-,0.00),219(AGAACAGGATGTGCTT,+,0.00)
chunk0174_409_1	chr6	165646886	165647503	+	0	NA	intron (NM_006661, intron 1 of 22)	intron (NM_006661, intron 1 of 22)	14906	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.011345	0.438511	
chunk0126_250_1	chr3	79377753	79378478	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-33612	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.006897	0.421488	
chunk0024_376_1	chr10	44632979	44633344	+	0	NA	Intergenic	AluJb|SINE|Alu	-248064	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.008219	0.393443	
chunk0157_277_1	chr5	120439585	120439954	+	0	NA	Intergenic	MER57C1|LTR|ERV1	-24509	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.008130	0.351351	
chunk0157_266_1	chr5	120083981	120084681	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-379947	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.001429	0.362340	
chunk0085_417_1	chr18	10518742	10518966	+	0	NA	Intergenic	Intergenic	-7022	NM_003826	8774	Hs.464622	NM_003826	ENSG00000134265	NAPG	GAMMASNAP	NSF attachment protein gamma	protein-coding	0.013393	0.497778	186(GAGAACGTCATGTTCC,-,0.00),187(AGAACGTCATGTTCCA,+,0.00)
chunk0057_73_1	chr13	98297155	98297399	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	88753	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.012295	0.469388	
chunk0024_367_1	chr10	44253658	44254112	+	0	NA	Intergenic	Intergenic	-38865	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.008811	0.485714	
chunk0125_228_1	chr3	67992328	67992822	+	0	NA	intron (NM_001252216, intron 1 of 4)	intron (NM_001252216, intron 1 of 4)	983	NM_001252216	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.000000	0.357576	
chunk0115_282_1	chr21	28180481	28180797	+	0	NA	intron (NR_126012, intron 3 of 5)	intron (NR_126012, intron 3 of 5)	48028	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.009494	0.328076	
chunk0131_141_1	chr3	145745570	145746017	+	0	NA	Intergenic	Intergenic	415702	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.000000	0.285714	
chunk0120_180_1	chr3	6283522	6283809	+	0	NA	Intergenic	L1PA16|LINE|L1	521784	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.006969	0.517361	
chunk0174_388_1	chr6	165249254	165250070	+	0	NA	Intergenic	L1ME2|LINE|L1	59960	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.007353	0.386781	
chunk0115_422_1	chr21	31529283	31529612	+	0	NA	intron (NM_003253, intron 1 of 28)	intron (NM_003253, intron 1 of 28)	29530	NM_003253	7074	Hs.517228	NM_003253	ENSG00000156299	TIAM1	TIAM-1	T cell lymphoma invasion and metastasis 1	protein-coding	0.003040	0.372727	
chunk0132_436_1	chr3	165095597	165095913	+	0	NA	Intergenic	Intergenic	-17260	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.000000	0.328076	
chunk0118_36_1	chr22	27456925	27457440	+	0	NA	Intergenic	Intergenic	344316	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.011650	0.478682	197(GGATCATTATGTACTT,+,0.00)
chunk0058_214_1	chr14	24965833	24966147	+	0	NA	intron (NM_014178, intron 2 of 5)	intron (NM_014178, intron 2 of 5)	83010	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.003185	0.434921	
chunk0087_136_1	chr18	33802850	33803365	+	0	NA	Intergenic	Intergenic	224530	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.005825	0.465116	
chunk0004_35_1	chr1	42658119	42658851	+	0	NA	exon (NM_006347, exon 1 of 10)	exon (NM_006347, exon 1 of 10)	108	NM_006347	10465	Hs.256639	NM_006347	ENSG00000171960	PPIH	CYP-20|CYPH|SnuCyp-20|USA-CYP	peptidylprolyl isomerase H	protein-coding	0.060109	0.611187	
chunk0015_419_1	chr1	191515393	191515700	+	0	NA	Intergenic	Intergenic	-642916	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.003257	0.308442	
chunk0202_45_1	chr9	71254559	71254906	+	0	NA	Intergenic	Intergenic	-133134	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.000000	0.281609	
chunk0090_315_1	chr18	75522855	75523148	+	0	NA	Intergenic	Intergenic	-95298	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.010239	0.377551	
chunk0011_81_1	chr1	145206894	145207512	+	0	NA	intron (NR_111954, intron 1 of 3)	intron (NR_111954, intron 1 of 3)	8868	NR_111956	103091866	Hs.271249	NR_111954	ENSG00000272419	LINC01145	-	long intergenic non-protein coding RNA 1145	ncRNA	0.021036	0.405493	
chunk0160_91_1	chr5	150092174	150092384	+	0	NA	intron (NM_005211, intron 1 of 21)	intron (NM_005211, intron 1 of 21)	-5639	NM_001288705	1436	Hs.586219	NM_005211	ENSG00000182578	CSF1R	C-FMS|CD115|CSF-1R|CSFR|FIM2|FMS|HDLS|M-CSF-R	colony stimulating factor 1 receptor	protein-coding	0.000000	0.355450	
chunk0100_171_1	chr2	109548242	109548522	+	0	NA	intron (NR_047585, intron 7 of 8)	intron (NR_047585, intron 7 of 8)	65824	NM_178584	151011	Hs.469615	NM_144710	ENSG00000186522	SEPTIN10	SEPT10	septin 10	protein-coding	0.017857	0.419929	
chunk0036_87_1	chr11	60844756	60845041	+	0	NA	intron (NM_024098, intron 1 of 3)	L2a|LINE|L2	2942	NM_024098	79080	Hs.4253	NM_024098	ENSG00000110104	CCDC86	-	coiled-coil domain containing 86	protein-coding	0.000000	0.430070	
chunk0156_96_1	chr5	104817090	104817622	+	0	NA	Intergenic	Intergenic	-282118	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.001880	0.339587	
chunk0142_66_1	chr4	92789530	92789969	+	0	NA	intron (NM_001286838, intron 2 of 14)	L1MEd|LINE|L1	485350	NM_001510	2895	Hs.162727	NM_001510	ENSG00000152208	GRID2	GluD2|SCAR18	glutamate ionotropic receptor delta type subunit 2	protein-coding	0.006834	0.302273	
chunk0192_276_1	chr8	66124139	66124338	+	0	NA	Intergenic	Intergenic	-2805	NM_184085	84675	Hs.85524	NM_033058	ENSG00000147573	TRIM55	MURF-2|RNF29|muRF2	tripartite motif containing 55	protein-coding	0.025126	0.495000	
chunk0009_429_1	chr1	111133548	111133978	+	0	NA	intron (NM_178454, intron 2 of 8)	intron (NM_178454, intron 2 of 8)	-5864	NM_001007794	10390	Hs.363572	NM_006090	ENSG00000134255	CEPT1	-	choline/ethanolamine phosphotransferase 1	protein-coding	0.002326	0.392111	
chunk0112_102_1	chr20	38209062	38209384	+	0	NA	Intergenic	Intergenic	-43925	NM_198951	7052	Hs.517033	NM_004613	ENSG00000198959	TGM2	TG(C)|TGC	transglutaminase 2	protein-coding	0.009317	0.554180	
chunk0116_244_1	chr21	38592832	38593266	+	0	NA	intron (NR_111949, intron 1 of 4)	intron (NR_111949, intron 1 of 4)	-8104	NM_001243429	2078	Hs.473819	NM_004449	ENSG00000157554	ERG	erg-3|p55	ETS transcription factor ERG	protein-coding	0.013825	0.452874	
chunk0189_398_1	chr8	27499470	27500018	+	0	NA	intron (NM_001256483, intron 1 of 17)	MLT1B|LTR|ERVL-MaLR	8576	NM_001256484	2053	Hs.212088	NM_001979	ENSG00000120915	EPHX2	ABHD20|CEH|SEH	epoxide hydrolase 2	protein-coding	0.003650	0.422587	
chunk0026_53_1	chr10	61029451	61029986	+	0	NA	Intergenic	MIRb|SINE|MIR	13443	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.009346	0.416045	
chunk0070_31_1	chr15	69343192	69343518	+	0	NA	intron (NM_001104554, intron 2 of 8)	Kanga2_a|DNA|TcMar-Tc2	28952	NM_001104554	54852	Hs.591096	NM_017705	ENSG00000137819	PAQR5	MPRG	progestin and adipoQ receptor family member 5	protein-coding	0.006135	0.412844	102(AGGGTCACTGTGTTCC,-,0.00),103(GGGTCACTGTGTTCCT,+,0.00)
chunk0131_49_1	chr3	142691506	142691917	+	0	NA	intron (NM_002670, intron 10 of 15)	intron (NM_002670, intron 10 of 15)	-32713	NM_001251845	7220	Hs.250687	NM_003304	ENSG00000144935	TRPC1	HTRP-1|TRP1	transient receptor potential cation channel subfamily C member 1	protein-coding	0.007299	0.303398	
chunk0109_412_1	chr2	240982795	240983069	+	0	NA	Intergenic	Intergenic	-15481	NR_033841	200772	Hs.647893	NR_033841	ENSG00000233392	LOC200772	-	uncharacterized LOC200772	ncRNA	0.018248	0.636364	
chunk0203_403_1	chr9	90706208	90706649	+	0	NA	Intergenic	L1MB1|LINE|L1	-63323	NM_017594	54769	Hs.165636	NM_017594	ENSG00000165023	DIRAS2	Di-Ras2	DIRAS family GTPase 2	protein-coding	0.004535	0.411765	
chunk0082_96_1	chr17	54409238	54409437	+	0	NA	Intergenic	L2c|LINE|L2	-491354	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.015075	0.405000	
chunk0161_351_1	chr5	174623840	174624197	+	0	NA	Intergenic	L2a|LINE|L2	-100554	NM_002449	4488	Hs.89404	NM_002449	ENSG00000120149	MSX2	CRS2|FPP|HOX8|MSH|PFM|PFM1	msh homeobox 2	protein-coding	0.019608	0.452514	
chunk0080_36_1	chr17	21200582	21200781	+	0	NA	intron (NM_003876, intron 1 of 1)	intron (NM_003876, intron 1 of 1)	13914	NM_003876	8834	Hs.592945	NM_003876	ENSG00000178307	TMEM11	C17orf35|PM1|PMI	transmembrane protein 11	protein-coding	0.020101	0.570000	
chunk0172_34_1	chr6	133975655	133975993	+	0	NA	intron (NM_004865, intron 1 of 6)	L1ME3E|LINE|L1	22661	NM_004865	9519	Hs.486507	NM_004865	ENSG00000028839	TBPL1	MGC:8389|MGC:9620|STUD|TLF|TLP|TRF2	TATA-box binding protein like 1	protein-coding	0.002959	0.324484	
chunk0036_28_1	chr11	58573815	58574389	+	0	NA	intron (NM_001143995, intron 1 of 8)	intron (NM_001143995, intron 1 of 8)	1815	NM_004811	9404	Hs.125474	NM_004811	ENSG00000110031	LPXN	LDPL	leupaxin	protein-coding	0.008711	0.433043	
chunk0210_205_1	chrX	80697346	80697910	+	0	NA	intron (NM_153252, intron 25 of 40)	L1PA17|LINE|L1	112106	NM_153252	254065	Hs.147027	NM_153252	ENSG00000165288	BRWD3	BRODL|MRX93	bromodomain and WD repeat domain containing 3	protein-coding	0.010638	0.407080	
chunk0181_370_1	chr7	88784068	88784742	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	11312	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.005935	0.394074	
chunk0052_67_1	chr13	21372429	21373074	+	0	NA	non-coding (NR_104487, exon 13 of 13)	non-coding (NR_104487, exon 13 of 13)	-27892	NR_103841	100652865	Hs.659198	NR_103840		LINC00539	LINC00422	long intergenic non-protein coding RNA 539	ncRNA	0.001550	0.284830	
chunk0176_298_1	chr7	16810541	16810840	+	0	NA	Intergenic	Intergenic	-5576	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.016722	0.370000	
chunk0129_99_1	chr3	119536611	119537257	+	0	NA	intron (NM_005191, intron 4 of 6)	Tigger3a|DNA|TcMar-Tigger	22700	NM_005191	941	Hs.838	NM_005191	ENSG00000121594	CD80	B7|B7-1|B7.1|BB1|CD28LG|CD28LG1|LAB7	CD80 molecule	protein-coding	0.007740	0.367852	
chunk0186_67_1	chr7	137084076	137084275	+	0	NA	intron (NR_046103, intron 1 of 3)	MIR|SINE|MIR	80166	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.005025	0.375000	
chunk0059_24_1	chr14	29822200	29822730	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	105228	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005660	0.352166	
chunk0117_252_1	chr22	23390372	23390612	+	0	NA	TTS (NR_003950)	TTS (NR_003950)	-8366	NR_037839	649264	Hs.600549	NR_037839		CES5AP1	-	carboxylesterase 5A pseudogene 1	pseudo	0.004167	0.381743	
chunk0210_84_1	chrX	70479993	70480341	+	0	NA	intron (NM_021120, intron 10 of 18)	intron (NM_021120, intron 10 of 18)	-24173	NR_109801	100873930	Hs.571699	NR_046586	ENSG00000231651	DLG3-AS1	-	DLG3 antisense RNA 1	ncRNA	0.005747	0.461318	
chunk0106_51_1	chr2	196280019	196280420	+	0	NA	intron (NM_020760, intron 14 of 28)	intron (NM_020760, intron 14 of 28)	20195	NR_110226	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.000000	0.350746	358(TGGAACAGAATGTTTC,-,0.00),359(GGAACAGAATGTTTCA,+,0.00),378(GGAACTCTATGTACAT,+,0.00)
chunk0022_368_1	chr10	17445238	17445483	+	0	NA	intron (NM_001004470, intron 2 of 7)	intron (NM_001004470, intron 2 of 7)	8895	NM_001004470	338596	Hs.677766	NM_001004470	ENSG00000148488	ST8SIA6	SIA8F|SIAT8-F|SIAT8F|ST8SIA-VI|ST8SiaVI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding	0.012245	0.398374	
chunk0123_264_1	chr3	46021217	46021416	+	0	NA	exon (NM_005283, exon 3 of 3)	exon (NM_005283, exon 3 of 3)	6171	NM_001024644	2829	Hs.128375	NM_005283	ENSG00000173578	XCR1	CCXCR1|GPR5	X-C motif chemokine receptor 1	protein-coding	0.060302	0.590000	
chunk0149_426_1	chr5	29649982	29650666	+	0	NA	Intergenic	L1MA5|LINE|L1	-254348	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004386	0.309489	
chunk0211_102_1	chrX	110941885	110942420	+	0	NA	Intergenic	Intergenic	-2133	NM_001128167	5063	Hs.593599	NM_002578	ENSG00000077264	PAK3	ARA|MRX30|MRX47|OPHN3|PAK-3|PAK3beta|bPAK|beta-PAK	p21 (RAC1) activated kinase 3	protein-coding	0.001869	0.416045	262(TGGAACAGGGAGTCCC,-,0.00),263(GGAACAGGGAGTCCCT,+,0.00)
chunk0080_425_1	chr17	35808974	35809665	+	0	NA	promoter-TSS (NM_003487)	promoter-TSS (NM_003487)	-136	NM_003487	8148	Hs.402752	NM_003487	ENSG00000270647	TAF15	Npl3|RBP56|TAF2N|TAFII68	TATA-box binding protein associated factor 15	protein-coding	0.078148	0.592486	
chunk0179_456_1	chr7	52782061	52782855	+	0	NA	Intergenic	Intergenic	-253198	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.015113	0.350943	
chunk0163_198_1	chr6	11763548	11763927	+	0	NA	intron (NM_032744, intron 3 of 5)	intron (NM_032744, intron 3 of 5)	15310	NM_032744	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.005277	0.431579	
chunk0126_301_1	chr3	80762787	80763052	+	0	NA	Intergenic	Intergenic	-230949	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.011321	0.312030	
chunk0152_155_1	chr5	59361529	59362028	+	0	NA	intron (NM_001165899, intron 3 of 16)	L2c|LINE|L2	-4877	NM_001197219	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002004	0.372000	
chunk0145_290_1	chr4	149911958	149912211	+	0	NA	Intergenic	Intergenic	-166190	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.007905	0.409449	
chunk0041_384_1	chr11	131998104	131998406	+	0	NA	intron (NM_001144058, intron 1 of 7)	intron (NM_001144058, intron 1 of 7)	87437	NM_001144059	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.016556	0.491749	
chunk0124_273_1	chr3	57522754	57523351	+	0	NA	intron (NM_198564, intron 4 of 11)	intron (NM_198564, intron 4 of 11)	21292	NM_001291661	201625	Hs.201378	NM_178504	ENSG00000174844	DNAH12	DHC3|DLP12|DLP3|DNAH12L|DNAH7L|DNAHC12|DNAHC3|DNHD2|HDHC3|HL-19|HL19	dynein axonemal heavy chain 12	protein-coding	0.006700	0.392977	
chunk0102_411_1	chr2	156498183	156498751	+	0	NA	intron (NM_001083112, intron 3 of 16)	intron (NM_001083112, intron 3 of 16)	62079	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.008803	0.432337	
chunk0209_275_1	chrX	47058938	47059670	+	0	NA	3' UTR (NM_001077445, exon 11 of 11)	3' UTR (NM_001077445, exon 11 of 11)	-19051	NM_001282849	9104	Hs.77854	NM_004683	ENSG00000130988	RGN	GNL|HEL-S-41|RC|SMP30	regucalcin	protein-coding	0.002732	0.403820	
chunk0086_155_1	chr18	21526522	21526968	+	0	NA	Intergenic	Intergenic	73987	NM_052911	114799	Hs.464733	NM_052911	ENSG00000141446	ESCO1	A930014I12Rik|CTF|ECO1|EFO1|ESO1	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.004484	0.389262	
chunk0034_39_1	chr11	26715062	26715536	+	0	NA	intron (NM_178498, intron 1 of 14)	intron (NM_178498, intron 1 of 14)	6728	NM_178498	159963	Hs.148907	NM_178498	ENSG00000148942	SLC5A12	SMCT2	solute carrier family 5 member 12	protein-coding	0.002110	0.440000	
chunk0036_306_1	chr11	66004511	66004836	+	0	NA	TTS (NM_001143985)	TTS (NM_001143985)	-2507	NM_001242483	84285	Hs.425178	NM_032325	ENSG00000175376	EIF1AD	OBELIX|haponin	eukaryotic translation initiation factor 1A domain containing	protein-coding	0.012308	0.478528	
chunk0158_19_1	chr5	125354541	125355068	+	0	NA	intron (NR_109882, intron 5 of 5)	L1PB1|LINE|L1	-138457	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.000000	0.314394	
chunk0043_327_1	chr12	22593871	22594413	+	0	NA	Intergenic	L3|LINE|CR1	-31000	NM_018638	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.003690	0.362799	
chunk0054_421_1	chr13	50966590	50966789	+	0	NA	intron (NM_001142279, intron 9 of 9)	intron (NM_001142279, intron 9 of 9)	-55977	NR_046552	100874255	Hs.741501	NR_046552		RNASEH2B-AS1	-	RNASEH2B antisense RNA 1	ncRNA	0.010050	0.425000	
chunk0162_283_1	chr6	5839314	5839705	+	0	NA	Intergenic	Intergenic	-144237	NR_110842	101927950	Hs.571136	NR_110842	ENSG00000270174	LOC101927950	-	uncharacterized LOC101927950	ncRNA	0.023018	0.540816	
chunk0174_440_1	chr6	166173201	166173449	+	0	NA	Intergenic	Intergenic	-4656	NM_003181	6862	Hs.389457	NM_003181	ENSG00000164458	TBXT	SAVA|T|TFT	T-box transcription factor T	protein-coding	0.016129	0.538153	112(CAGAACATGCTGTGAT,-,0.00)
chunk0096_45_1	chr2	26982401	26982778	+	0	NA	intron (NM_012326, intron 1 of 6)	intron (NM_012326, intron 1 of 6)	12218	NM_012326	22924	Hs.515860	NM_012326	ENSG00000084764	MAPRE3	EB3|EBF3|EBF3-S|RP3	microtubule associated protein RP/EB family member 3	protein-coding	0.002653	0.462963	
chunk0091_51_1	chr19	4713398	4713743	+	0	NA	intron (NM_139159, intron 4 of 21)	intron (NM_139159, intron 4 of 21)	10273	NM_139159	91039	Hs.515081	NM_139159	ENSG00000142002	DPP9	DP9|DPLP9|DPP IX|DPRP-2|DPRP2	dipeptidyl peptidase 9	protein-coding	0.060870	0.656069	
chunk0118_97_1	chr22	29151418	29151711	+	0	NA	intron (NM_032045, intron 9 of 9)	intron (NM_032045, intron 9 of 9)	-54348	NM_133455	129080	Hs.289106	NM_133455	ENSG00000186998	EMID1	EMI5|EMU1	EMI domain containing 1	protein-coding	0.017065	0.459184	
chunk0125_340_1	chr3	71077067	71077708	+	0	NA	intron (NM_032682, intron 7 of 20)	intron (NM_032682, intron 7 of 20)	-12464	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.012480	0.423676	
chunk0162_125_1	chr6	2932143	2932477	+	0	NA	Intergenic	Intergenic	-28998	NM_004155	5272	Hs.104879	NM_004155	ENSG00000170542	SERPINB9	CAP-3|CAP3|PI-9|PI9	serpin family B member 9	protein-coding	0.017964	0.534328	
chunk0090_12_1	chr19	556027	556338	+	0	NA	Intergenic	Intergenic	12148	NM_005317	3004	Hs.465511	NM_005317	ENSG00000197540	GZMM	LMET1|MET1	granzyme M	protein-coding	0.025723	0.608974	230(TGGGACACGCAGTGCC,-,0.00),231(GGGACACGCAGTGCCC,+,0.00)
chunk0031_264_1	chr10	127479667	127479923	+	0	NA	Intergenic	Intergenic	-69554	NM_001030013	594857	Hs.643423	NM_001030013	ENSG00000214285	NPS	-	neuropeptide S	protein-coding	0.000000	0.381323	
chunk0103_342_1	chr2	168059929	168060205	+	0	NA	intron (NM_013233, intron 14 of 17)	intron (NM_013233, intron 14 of 17)	-118923	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.007246	0.335740	115(AGAACACGGTGATCAC,+,0.00)
chunk0081_188_1	chr17	41930082	41930741	+	0	NA	promoter-TSS (NM_031421)	promoter-TSS (NM_031421)	-212	NM_031421	83538	Hs.201134	NM_031421	ENSG00000204815	TTC25	-	tetratricopeptide repeat domain 25	protein-coding	0.051593	0.533333	
chunk0147_81_1	chr4	173053925	173054206	+	0	NA	Intergenic	Intergenic	-114688	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.003559	0.308511	
chunk0164_410_1	chr6	26745442	26745675	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-85806	NM_001242798	79692	Hs.126280	NM_024639	ENSG00000181315	ZNF322	HCG12|ZNF322A|ZNF388|ZNF489	zinc finger protein 322	protein-coding	0.042918	0.534188	
chunk0140_67_1	chr4	67360590	67360946	+	0	NA	Intergenic	L1M4b|LINE|L1	61232	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.000000	0.282913	
chunk0190_277_1	chr8	37682813	37683161	+	0	NA	Intergenic	Intergenic	-12764	NM_025069	80139	Hs.288042	NM_025069	ENSG00000183779	ZNF703	NLZ1|ZEPPO1|ZNF503L|ZPO1	zinc finger protein 703	protein-coding	0.008621	0.475645	
chunk0036_313_1	chr11	66127302	66127812	+	0	NA	intron (NM_018026, intron 1 of 23)	intron (NM_018026, intron 1 of 23)	57204	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.017647	0.473581	
chunk0090_73_1	chr19	2491445	2491688	+	0	NA	Intergenic	Intergenic	15441	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.028807	0.540984	
chunk0156_37_1	chr5	102617830	102618319	+	0	NA	TTS (NR_047462)	TTS (NR_047462)	36706	NR_047462	100861468	Hs.519483	NR_047462	ENSG00000250958	LINC00492	-	long intergenic non-protein coding RNA 492	ncRNA	0.002045	0.359184	
chunk0204_350_1	chr9	101543968	101544349	+	0	NA	intron (NM_019592, intron 5 of 19)	X7A_LINE|LINE|CR1	10309	NM_019592	56254	Hs.729085	NM_019592	ENSG00000155827	RNF20	BRE1|BRE1A|hBRE1	ring finger protein 20	protein-coding	0.005249	0.356021	
chunk0102_161_1	chr2	147284754	147285496	+	0	NA	Intergenic	L2b|LINE|L2	-559392	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002695	0.333782	
chunk0076_455_1	chr16	74321159	74321530	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	24569	NM_002811	5713	Hs.440604	NM_002811	ENSG00000103035	PSMD7	MOV34|P40|Rpn8|S12	proteasome 26S subunit, non-ATPase 7	protein-coding	0.005391	0.508065	
chunk0027_1_1	chr10	71717487	71718340	+	0	NA	intron (NM_001168390, intron 1 of 1)	intron (NM_001168390, intron 1 of 1)	1908	NM_001164375	414152	Hs.568788	NM_001164375	ENSG00000214688	C10orf105	-	chromosome 10 open reading frame 105	protein-coding	0.014068	0.502342	
chunk0070_283_1	chr15	74548010	74548490	+	0	NA	intron (NM_001307939, intron 2 of 8)	intron (NM_001307939, intron 2 of 8)	7073	NM_001307939	10620	Hs.647642	NM_006465	ENSG00000179361	ARID3B	BDP|DRIL2	AT-rich interaction domain 3B	protein-coding	0.010417	0.467775	146(AAGAACTGAGTGTTCC,-,0.00),147(AGAACTGAGTGTTCCT,+,0.00)
chunk0025_219_1	chr10	53878843	53879264	+	0	NA	intron (NM_001142769, intron 28 of 35)	intron (NM_001142769, intron 28 of 35)	728904	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.009501	0.348341	
chunk0184_52_1	chr7	112282744	112283091	+	0	NA	intron (NM_021994, intron 1 of 11)	MIR|SINE|MIR	76329	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.000000	0.393678	
chunk0012_231_1	chr1	160343743	160343945	+	0	NA	promoter-TSS (NM_004371)	promoter-TSS (NM_004371)	-280	NM_004371	1314	Hs.162121	NM_004371	ENSG00000122218	COPA	AILJK|HEP-COP|alpha-COP	coatomer protein complex subunit alpha	protein-coding	0.034653	0.482759	
chunk0189_156_1	chr8	23070605	23070804	+	0	NA	intron (NR_038873, intron 1 of 2)	LTR12C|LTR|ERV1	-1517	NM_003842	8795	Hs.521456	NM_003842	ENSG00000120889	TNFRSF10B	CD262|DR5|KILLER|KILLER/DR5|TRAIL-R2|TRAILR2|TRICK2|TRICK2A|TRICK2B|TRICKB|ZTNFR9	TNF receptor superfamily member 10b	protein-coding	0.060302	0.590000	
chunk0070_125_1	chr15	70752259	70752513	+	0	NA	intron (NM_018003, intron 1 of 18)	intron (NM_018003, intron 1 of 18)	11125	NM_018003	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.007874	0.407843	54(AAGATCAGAGTGTACT,-,0.00),55(AGATCAGAGTGTACTG,+,0.00)
chunk0139_305_1	chr4	57681826	57682325	+	0	NA	Intergenic	Intergenic	256203	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.010020	0.410000	308(TAGAGCAGCTTGTTCT,-,0.00),309(AGAGCAGCTTGTTCTG,+,0.00)
chunk0082_37_1	chr17	50909099	50909788	+	0	NA	Intergenic	Intergenic	-41465	NM_001243877	10140	Hs.703321	NM_005749	ENSG00000141232	TOB1	APRO5|APRO6|PIG49|TOB|TROB|TROB1	transducer of ERBB2, 1	protein-coding	0.018868	0.553623	331(GGGAACACAAAGTACC,-,0.00),332(GGAACACAAAGTACCT,+,0.00)
chunk0165_405_1	chr6	38900174	38900676	+	0	NA	intron (NM_001206927, intron 62 of 92)	L1ME3A|LINE|L1	52682	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.003984	0.363817	
chunk0080_97_1	chr17	26879155	26879636	+	0	NA	Intergenic	AluYj4|SINE|Alu	414601	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.008316	0.452282	
chunk0049_21_1	chr12	89507574	89507894	+	0	NA	intron (NM_172240, intron 2 of 11)	intron (NM_172240, intron 2 of 11)	17072	NM_003774	8693	Hs.25130	NM_003774	ENSG00000257594	GALNT4	GALNAC-T4|GALNACT4	polypeptide N-acetylgalactosaminyltransferase 4	protein-coding	0.003125	0.380062	
chunk0149_194_1	chr5	21447200	21448066	+	0	NA	Intergenic	L1MC2|LINE|L1	-11847	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.005774	0.405998	
chunk0151_321_1	chr5	53598934	53599544	+	0	NA	intron (NM_002495, intron 1 of 4)	L1M2|LINE|L1	38604	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.001639	0.306056	
chunk0071_340_1	chr15	88004353	88004858	+	0	NA	intron (NM_001007156, intron 14 of 15)	CR1_Mam|LINE|CR1	-248125	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.005941	0.418972	221(AAGAACACATTGTCCT,-,0.00),222(AGAACACATTGTCCTG,+,0.00)
chunk0055_77_1	chr13	53562321	53562971	+	0	NA	Intergenic	L1ME1|LINE|L1	-252773	NR_047488	100861552	Hs.224691	NR_047488	ENSG00000261517	LINC00558	-	long intergenic non-protein coding RNA 558	ncRNA	0.004615	0.322581	
chunk0077_436_1	chr16	85594834	85595294	+	0	NA	Intergenic	Intergenic	-16359	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.030435	0.618221	
chunk0015_169_1	chr1	186678740	186679062	+	0	NA	intron (NM_000963, intron 3 of 9)	intron (NM_000963, intron 3 of 9)	1526	NM_000963	5743	Hs.196384	NM_000963	ENSG00000073756	PTGS2	COX-2|COX2|GRIPGHS|PGG/HS|PGHS-2|PHS-2|hCox-2	prostaglandin-endoperoxide synthase 2	protein-coding	0.003106	0.352941	
chunk0050_66_1	chr12	101431639	101432057	+	0	NA	Intergenic	Intergenic	-24028	NM_001301068	400	Hs.372616	NM_001177	ENSG00000120805	ARL1	ARFL1	ADP ribosylation factor like GTPase 1	protein-coding	0.011962	0.415274	
chunk0194_262_1	chr8	86865304	86865754	+	0	NA	promoter-TSS (NM_173538)	promoter-TSS (NM_173538)	-919	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.006667	0.514412	
chunk0076_64_1	chr16	62016506	62016884	+	0	NA	intron (NM_001796, intron 2 of 11)	intron (NM_001796, intron 2 of 11)	20140	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.002646	0.411609	
chunk0039_263_1	chr11	102320779	102320978	+	0	NA	intron (NM_182962, intron 1 of 9)	Charlie8|DNA|hAT-Charlie	3428	NM_001165	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.000000	0.455000	59(CAGAACAGTCAGTCCC,-,0.00),60(AGAACAGTCAGTCCCA,+,0.00)
chunk0161_249_1	chr5	171774199	171774868	+	0	NA	Intergenic	Intergenic	-11339	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.017937	0.535821	
chunk0026_174_1	chr10	63297618	63297955	+	0	NA	intron (NM_032776, intron 2 of 25)	LTR2752|LTR|ERV1	-28563	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.017804	0.594675	
chunk0193_333_1	chr8	79289328	79289956	+	0	NA	Intergenic	Intergenic	-321172	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.001592	0.346582	
chunk0105_239_1	chr2	188508773	188509014	+	0	NA	intron (NM_001252669, intron 4 of 8)	MIRb|SINE|MIR	211401	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.004149	0.396694	
chunk0114_107_1	chr21	9541368	9541857	+	0	NA	Intergenic	Intergenic	279449	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.004090	0.379592	
chunk0061_310_1	chr14	61988122	61988804	+	0	NA	Intergenic	Intergenic	-7360	NM_031914	83851	Hs.404139	NM_031914	ENSG00000139973	SYT16	CHR14SYT|SYT14L|Strep14|syt14r	synaptotagmin 16	protein-coding	0.004399	0.335286	
chunk0048_244_1	chr12	81600614	81601110	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-2491	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.006048	0.305835	
chunk0203_416_1	chr9	90939261	90939712	+	0	NA	Intergenic	Intergenic	112066	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.011086	0.440265	
chunk0163_356_1	chr6	15662202	15662532	+	0	NA	intron (NR_036448, intron 1 of 9)	CpG	691	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.100000	0.703927	
chunk0128_183_1	chr3	107408805	107409086	+	0	NA	Intergenic	Intergenic	-21985	NR_110039	101929607	Hs.252565	NR_110039	ENSG00000273125	LINC01990	-	long intergenic non-protein coding RNA 1990	ncRNA	0.007117	0.585106	
chunk0168_402_1	chr6	94703009	94703561	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	874166	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.007246	0.367089	
chunk0066_61_1	chr15	28820158	28820418	+	0	NA	intron (NR_037599, intron 10 of 13)	L1M7|LINE|L1	28387	NR_047567	728310	Hs.589351	NM_001365371	ENSG00000261649	GOLGA6L7	GOLGA6L7P	golgin A6 family like 7	protein-coding	0.000000	0.340996	
chunk0137_91_1	chr4	13331620	13332253	+	0	NA	Intergenic	Intergenic	152429	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.006319	0.487382	
chunk0023_49_1	chr10	21634976	21635340	+	0	NA	intron (NM_001195626, intron 7 of 21)	HAL1M8|LINE|L1	100513	NM_001195626	8028	Hs.30385	NM_004641	ENSG00000078403	MLLT10	AF10	MLLT10 histone lysine methyltransferase DOT1L cofactor	protein-coding	0.005495	0.427397	
chunk0019_232_1	chr1	227372643	227373308	+	0	NA	Intergenic	Intergenic	-54850	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.004511	0.403904	
chunk0154_89_1	chr5	77997331	77997739	+	0	NA	Intergenic	Intergenic	39288	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.004902	0.391198	
chunk0037_34_1	chr11	70183510	70183765	+	0	NA	intron (NM_018043, intron 24 of 25)	intron (NM_018043, intron 24 of 25)	-19526	NM_003824	8772	Hs.86131	NM_003824	ENSG00000168040	FADD	GIG3|MORT1	Fas associated via death domain	protein-coding	0.011765	0.570312	
chunk0201_118_1	chr9	35293572	35294114	+	0	NA	intron (NM_006377, intron 7 of 38)	intron (NM_006377, intron 7 of 38)	-112912	NR_003581	158381	Hs.575661	NR_003581	ENSG00000179766	ATP8B5P	FetA	ATPase phospholipid transporting 8B5, pseudogene	pseudo	0.001845	0.386740	
chunk0123_172_1	chr3	44052221	44052554	+	0	NA	Intergenic	Intergenic	-61825	NR_029700	406929		NR_029700	ENSG00000207954	MIR138-1	MIRN138-1|mir-138-1	microRNA 138-1	ncRNA	0.012012	0.458084	
chunk0055_92_1	chr13	54929875	54930145	+	0	NA	Intergenic	Intergenic	-244444	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.000000	0.324723	
chunk0036_433_1	chr11	68469170	68469397	+	0	NA	intron (NM_001164161, intron 1 of 23)	MER58A|DNA|hAT-Charlie	8565	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.000000	0.434211	
chunk0208_79_1	chrX	12988968	12989204	+	0	NA	Intergenic	Intergenic	13979	NM_021109	7114	Hs.437277	NM_021109	ENSG00000205542	TMSB4X	FX|PTMB4|TB4X|TMSB4	thymosin beta 4 X-linked	protein-coding	0.008475	0.421941	
chunk0105_170_1	chr2	187102511	187103128	+	0	NA	Intergenic	Intergenic	-253649	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.006483	0.333333	
chunk0074_239_1	chr16	27528182	27528739	+	0	NA	intron (NM_001286242, intron 6 of 36)	L2b|LINE|L2	21470	NM_001286242	2975	Hs.371718	NM_001520	ENSG00000077235	GTF3C1	TFIIIC|TFIIIC220|TFIIICalpha	general transcription factor IIIC subunit 1	protein-coding	0.019749	0.449821	
chunk0161_124_1	chr5	168047554	168047953	+	0	NA	intron (NM_001122679, intron 6 of 28)	intron (NM_001122679, intron 6 of 28)	184619	NR_109894	101927862	Hs.659376	NR_109894	ENSG00000253978	CTB-178M22.2	-	uncharacterized LOC101927862	ncRNA	0.005013	0.517500	
chunk0198_284_1	chr8	135576992	135577486	+	0	NA	intron (NM_006558, intron 5 of 8)	L1MC3|LINE|L1	119774	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.004049	0.335354	
chunk0078_159_1	chr17	4230084	4230536	+	0	NA	intron (NR_047571, intron 2 of 23)	intron (NR_047571, intron 2 of 23)	33537	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.004425	0.423841	
chunk0096_273_1	chr2	31922459	31923055	+	0	NA	intron (NM_001137602, intron 2 of 7)	L1PA15|LINE|L1	87907	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.011745	0.385260	
chunk0130_317_1	chr3	137765879	137766347	+	0	NA	3' UTR (NM_004189, exon 1 of 1)	3' UTR (NM_004189, exon 1 of 1)	1821	NM_004189	8403	Hs.248184	NM_004189	ENSG00000168875	SOX14	SOX28	SRY-box transcription factor 14	protein-coding	0.008547	0.345416	
chunk0022_138_1	chr10	11868069	11868297	+	0	NA	intron (NM_153256, intron 3 of 3)	intron (NM_153256, intron 3 of 3)	26527	NR_038222	219731	Hs.576787	NR_038222	ENSG00000225778	PROSER2-AS1	-	PROSER2 antisense RNA 1	ncRNA	0.008772	0.353712	
chunk0047_5_1	chr12	65052071	65052608	+	0	NA	intron (NM_007191, intron 9 of 9)	intron (NM_007191, intron 9 of 9)	69227	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.007449	0.451673	
chunk0063_82_1	chr14	77746216	77746783	+	0	NA	intron (NM_012245, intron 3 of 13)	intron (NM_012245, intron 3 of 13)	-14331	NM_174943	283579	Hs.375834	NM_174943	ENSG00000197734	C14orf178	-	chromosome 14 open reading frame 178	ncRNA	0.005291	0.341549	
chunk0032_347_1	chr11	10326368	10326785	+	0	NA	intron (NR_103765, intron 1 of 3)	intron (NR_103765, intron 1 of 3)	18263	NR_103765	100130460	Hs.501890	NR_103765		CAND1.11	-	uncharacterized LOC100130460	ncRNA	0.004796	0.502392	
chunk0176_287_1	chr7	16719155	16719627	+	0	NA	Intergenic	Intergenic	-34335	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.002119	0.367865	241(AAGAACATTAAGTACT,-,0.00),242(AGAACATTAAGTACTA,+,0.00)
chunk0092_199_1	chr19	30895887	30896096	+	0	NA	Intergenic	Intergenic	453293	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.014354	0.433333	
chunk0103_39_1	chr2	159209963	159210322	+	0	NA	intron (NM_001145909, intron 19 of 26)	intron (NM_001145909, intron 19 of 26)	23307	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.019499	0.511111	141(AGGTACAAGCTGTTCT,-,0.00),142(GGTACAAGCTGTTCTC,+,0.00)
chunk0094_301_1	chr2	8539740	8540303	+	0	NA	Intergenic	Intergenic	43771	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.017762	0.597518	
chunk0148_112_1	chr5	4862481	4862782	+	0	NA	Intergenic	Intergenic	89150	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.003322	0.317881	
chunk0200_263_1	chr9	21945632	21945971	+	0	NA	Intergenic	L1PREC2|LINE|L1	-21338	NR_024274	51198	Hs.721053	NM_016349		CDKN2A-DT	C9orf53|CDKN2A-AS1|bA149I2.3	CDKN2A divergent transcript	ncRNA	0.005900	0.511765	
chunk0019_56_1	chr1	224182370	224182593	+	0	NA	promoter-TSS (NM_003676)	promoter-TSS (NM_003676)	-727	NM_003676	8560	Hs.299878	NM_003676	ENSG00000143753	DEGS1	DEGS|DEGS-1|DES1|Des-1|FADS7|HLD18|MIG15|MLD	delta 4-desaturase, sphingolipid 1	protein-coding	0.026906	0.392857	86(GTGCACAGCATGTTCT,-,0.00),87(TGCACAGCATGTTCTT,+,0.00)
chunk0067_346_1	chr15	48481326	48482149	+	0	NA	exon (NM_000138, exon 32 of 66)	exon (NM_000138, exon 32 of 66)	149569	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.006075	0.325243	
chunk0068_238_1	chr15	55825257	55825894	+	0	NA	Intergenic	Intergenic	-82456	NM_173814	283659	Hs.130957	NM_173814	ENSG00000166450	PRTG	IGDCC5	protogenin	protein-coding	0.009419	0.409091	332(AGGCACACCATGCTCC,-,0.00),333(GGCACACCATGCTCCT,+,0.00)
chunk0102_118_1	chr2	144705159	144705460	+	0	NA	intron (NR_033870, intron 1 of 4)	intron (NR_033870, intron 1 of 4)	37342	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.006645	0.430464	
chunk0005_440_1	chr1	63362010	63362728	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-5221	NM_013339	29929	Hs.258501	NM_013339	ENSG00000088035	ALG6	CDG1C	ALG6 alpha-1,3-glucosyltransferase	protein-coding	0.002786	0.367177	
chunk0108_126_1	chr2	229848352	229848893	+	0	NA	intron (NM_004238, intron 3 of 40)	HAL1|LINE|L1	31506	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.005545	0.367159	
chunk0133_35_1	chr3	166013827	166014370	+	0	NA	Intergenic	Intergenic	-176633	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.001842	0.312500	
chunk0119_408_1	chr22	49534339	49534680	+	0	NA	intron (NR_110523, intron 1 of 4)	intron (NR_110523, intron 1 of 4)	8957	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.041056	0.532164	145(TGGAACGCGGTGTTCT,-,0.00),146(GGAACGCGGTGTTCTC,+,0.00)
chunk0037_392_1	chr11	78954083	78954737	+	0	NA	intron (NM_001098816, intron 6 of 33)	MER113|DNA|hAT-Charlie	-379546	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.004587	0.444275	
chunk0023_442_1	chr10	31961266	31961714	+	0	NA	Intergenic	MER50-int|LTR|ERV1	-32614	NM_001270697	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.008929	0.456570	
chunk0169_123_1	chr6	100934486	100935006	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-53374	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.003846	0.370441	
chunk0120_259_1	chr3	9059529	9059810	+	0	NA	intron (NM_001033117, intron 6 of 21)	intron (NM_001033117, intron 6 of 21)	-96194	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.035587	0.531915	
chunk0120_404_1	chr3	12631588	12631856	+	0	NA	intron (NM_002880, intron 1 of 16)	MER91A|DNA|hAT-Tip100	32479	NM_002880	5894	Hs.159130	NM_002880	ENSG00000132155	RAF1	CMD1NN|CRAF|NS5|Raf-1|c-Raf	Raf-1 proto-oncogene, serine/threonine kinase	protein-coding	0.003731	0.416357	
chunk0140_291_1	chr4	72502187	72502744	+	0	NA	intron (NM_014243, intron 3 of 21)	L1PA15-16|LINE|L1	66334	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.003591	0.338710	
chunk0208_379_1	chrX	28168562	28168847	+	0	NA	Intergenic	Intergenic	-187255	NM_001017930	139425	Hs.447365	NM_001017930	ENSG00000226372	DCAF8L1	WDR42B	DDB1 and CUL4 associated factor 8 like 1	protein-coding	0.000000	0.314685	
chunk0213_32_1	chrY	56839284	56839572	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-114827	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.006944	0.442907	
chunk0194_53_1	chr8	82130648	82130847	+	0	NA	Intergenic	L1PB1|LINE|L1	-288461	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.505000	
chunk0077_316_1	chr16	82059828	82060324	+	0	NA	intron (NM_002153, intron 1 of 4)	intron (NM_002153, intron 1 of 4)	24823	NM_002153	3294	Hs.162795	NM_002153	ENSG00000086696	HSD17B2	EDH17B2|HSD17|SDR9C2	hydroxysteroid 17-beta dehydrogenase 2	protein-coding	0.004032	0.400402	
chunk0008_26_1	chr1	87885295	87885643	+	0	NA	Intergenic	Intergenic	-513814	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.002874	0.383954	
chunk0122_350_1	chr3	37349314	37350231	+	0	NA	intron (NM_002078, intron 21 of 23)	intron (NM_002078, intron 21 of 23)	-36497	NM_178344	339883	Hs.475945	NM_178339	ENSG00000198590	C3orf35	APRG1	chromosome 3 open reading frame 35	protein-coding	0.006543	0.407407	541(TTGTACACAGTGTTCT,-,0.00),542(TGTACACAGTGTTCTT,+,0.00)
chunk0087_366_1	chr18	41460945	41461300	+	0	NA	Intergenic	Intergenic	59475	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.002817	0.308989	
chunk0193_413_1	chr8	80697892	80698407	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	176632	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.005825	0.432171	
chunk0191_401_1	chr8	57544364	57544840	+	0	NA	Intergenic	MIR|SINE|MIR	200815	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.014706	0.404612	
chunk0067_275_1	chr15	46993535	46993734	+	0	NA	Intergenic	L1PA8A|LINE|L1	-190572	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.005025	0.315000	
chunk0132_303_1	chr3	160238408	160238864	+	0	NA	Intergenic	MIR|SINE|MIR	13000	NM_001168214	401097	Hs.729755	NM_001168214	ENSG00000180044	C3orf80	-	chromosome 3 open reading frame 80	protein-coding	0.010965	0.420131	
chunk0144_100_1	chr4	128525808	128526007	+	0	NA	Intergenic	Intergenic	97891	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.005025	0.315000	
chunk0071_181_1	chr15	83511723	83511966	+	0	NA	intron (NM_001301109, intron 4 of 11)	Tigger19a|DNA|TcMar-Tigger	64616	NR_125370	6457	Hs.270055	NM_003027	ENSG00000140600	SH3GL3	CNSA3|EEN-B2|HsT19371|SH3D2C|SH3P13	SH3 domain containing GRB2 like 3, endophilin A3	protein-coding	0.012346	0.536885	
chunk0026_262_1	chr10	66860438	66861061	+	0	NA	intron (NM_001127384, intron 7 of 17)	intron (NM_001127384, intron 7 of 17)	-65285	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.003210	0.387821	
chunk0046_72_1	chr12	56013517	56013904	+	0	NA	Intergenic	Intergenic	-7195	NM_022465	64375	Hs.553221	NM_022465	ENSG00000123411	IKZF4	EOS|ZNFN1A4	IKAROS family zinc finger 4	protein-coding	0.010336	0.497423	
chunk0066_286_1	chr15	35308522	35309286	+	0	NA	Intergenic	Intergenic	63460	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.005236	0.354248	
chunk0099_307_1	chr2	99336414	99336654	+	0	NA	promoter-TSS (NM_005783)	promoter-TSS (NM_005783)	-137	NM_005783	10190	Hs.536122	NM_005783	ENSG00000115514	TXNDC9	APACD|PHLP3	thioredoxin domain containing 9	protein-coding	0.083333	0.618257	
chunk0155_145_1	chr5	93717243	93717478	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	24243	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.008511	0.415254	
chunk0194_174_1	chr8	84949008	84949280	+	0	NA	Intergenic	Intergenic	-157944	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.007353	0.509158	
chunk0191_344_1	chr8	56212055	56212351	+	0	NA	promoter-TSS (NM_002655)	intron (NM_024300, intron 1 of 4)	447	NM_001011669	79145	Hs.436913	NM_024300	ENSG00000170791	CHCHD7	COX23	coiled-coil-helix-coiled-coil-helix domain containing 7	protein-coding	0.074324	0.639731	
chunk0151_58_1	chr5	42470778	42471403	+	0	NA	intron (NM_001242401, intron 1 of 10)	intron (NM_001242401, intron 1 of 10)	46098	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.001600	0.373802	
chunk0021_35_1	chr10	853138	853337	+	0	NA	intron (NM_015155, intron 5 of 17)	Tigger1|DNA|TcMar-Tigger	78468	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.000000	0.340000	
chunk0205_227_1	chr9	109903157	109903885	+	0	NA	intron (NM_053016, intron 3 of 6)	intron (NM_053016, intron 3 of 6)	123224	NM_053016	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.010989	0.471879	418(GGGAACAAGGAGTTCA,-,0.00),419(GGAACAAGGAGTTCAG,+,0.00)
chunk0201_331_1	chr9	63817650	63818301	+	0	NA	Intergenic	CpG	-1599	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.052227	0.650307	
chunk0172_392_1	chr6	139643781	139643989	+	0	NA	Intergenic	MIRb|SINE|MIR	-127188	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.004808	0.421053	
chunk0131_442_1	chr3	153906302	153906799	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-214453	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.004024	0.371486	
chunk0159_153_1	chr5	139332042	139332429	+	0	NA	TTS (NM_001194955)	TTS (NM_001194955)	-9597	NM_016480	51247	Hs.396644	NM_016480	ENSG00000120727	PAIP2	PAIP-2|PAIP2A	poly(A) binding protein interacting protein 2	protein-coding	0.002584	0.432990	
chunk0198_352_1	chr8	140479599	140480283	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-21362	NM_031466	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.023392	0.494891	236(GGGAACAGCGTGTTCT,-,0.00),237(GGAACAGCGTGTTCTT,+,0.00)
chunk0193_406_1	chr8	80581602	80582110	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	95643	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.003937	0.481336	
chunk0006_401_1	chr1	75574716	75575015	+	0	NA	intron (NM_001130058, intron 1 of 23)	intron (NM_001130058, intron 1 of 23)	36249	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.000000	0.386667	
chunk0132_316_1	chr3	160755015	160755498	+	0	NA	promoter-TSS (NM_139245)	promoter-TSS (NM_139245)	-952	NM_139245	151742	Hs.389027	NM_139245	ENSG00000163590	PPM1L	PP2C-epsilon|PP2CE|PPM1-LIKE	protein phosphatase, Mg2+/Mn2+ dependent 1L	protein-coding	0.080745	0.636364	
chunk0193_163_1	chr8	74740668	74741233	+	0	NA	intron (NR_033830, intron 4 of 5)	Tigger17c|DNA|TcMar-Tigger	35257	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.007080	0.339223	
chunk0138_209_1	chr4	38797452	38797814	+	0	NA	exon (NM_003263, exon 4 of 4)	exon (NM_003263, exon 4 of 4)	7158	NM_003263	7096	Hs.621817	NM_003263	ENSG00000174125	TLR1	CD281|TIL|TIL. LPRS5|rsc786	toll like receptor 1	protein-coding	0.005525	0.338843	
chunk0138_454_1	chr4	47517670	47518191	+	0	NA	intron (NM_020453, intron 3 of 22)	intron (NM_020453, intron 3 of 22)	32537	NM_020453	57205	Hs.437241	NM_020453	ENSG00000145246	ATP10D	ATPVD	ATPase phospholipid transporting 10D (putative)	protein-coding	0.001919	0.287356	
chunk0162_43_1	chr6	1131669	1132321	+	0	NA	Intergenic	Intergenic	-30663	NR_027115	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.012270	0.468606	
chunk0022_311_1	chr10	15851794	15852421	+	0	NA	intron (NM_024948, intron 1 of 14)	L2c|LINE|L2	8413	NM_024948	80013	Hs.158870	NM_024948	ENSG00000148481	MINDY3	C10orf97|CARP|DERP5|FAM188A|MST126|MSTP126|my042	MINDY lysine 48 deubiquitinase 3	protein-coding	0.004785	0.383758	323(TAGCACAACCAGTACT,-,0.00),324(AGCACAACCAGTACTT,+,0.00)
chunk0206_199_1	chr9	123048325	123048859	+	0	NA	intron (NM_012197, intron 13 of 25)	intron (NM_012197, intron 13 of 25)	14949	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.005618	0.321495	
chunk0090_435_1	chr18	79517417	79517616	+	0	NA	intron (NM_172387, intron 9 of 9)	intron (NM_172387, intron 9 of 9)	117242	NM_001278672	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.055276	0.560000	
chunk0077_303_1	chr16	81604985	81605301	+	0	NA	intron (NM_030629, intron 1 of 20)	intron (NM_030629, intron 1 of 20)	-6205	NR_106759	102465251		NR_106759	ENSG00000275109	MIR6504	hsa-mir-6504	microRNA 6504	ncRNA	0.018987	0.514196	
chunk0076_75_1	chr16	63463289	63464032	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-1426825	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.004038	0.408602	
chunk0054_128_1	chr13	43478078	43478463	+	0	NA	intron (NM_001127615, intron 3 of 16)	intron (NM_001127615, intron 3 of 16)	29418	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.010390	0.316062	
chunk0060_392_1	chr14	52852760	52853476	+	0	NA	Intergenic	Intergenic	-61450	NM_198066	64841	Hs.478025	NM_198066	ENSG00000100522	GNPNAT1	GNA1|GNPNAT|Gpnat1	glucosamine-phosphate N-acetyltransferase 1	protein-coding	0.005587	0.362622	
chunk0138_328_1	chr4	41533716	41533983	+	0	NA	intron (NM_001112717, intron 3 of 25)	L2c|LINE|L2	-78923	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.007491	0.451493	
chunk0202_273_1	chr9	77142417	77142857	+	0	NA	Intergenic	Intergenic	-34808	NM_033305	23230	Hs.459790	NM_015186	ENSG00000197969	VPS13A	CHAC|CHOREIN	vacuolar protein sorting 13 homolog A	protein-coding	0.002273	0.317460	
chunk0097_126_1	chr2	46732081	46732293	+	0	NA	intron (NM_144949, intron 1 of 1)	Tigger9b|DNA|TcMar-Tigger	32977	NM_144949	9655	Hs.468426	NM_014011	ENSG00000171150	SOCS5	CIS6|CISH6|Cish5|SOCS-5	suppressor of cytokine signaling 5	protein-coding	0.004717	0.399061	
chunk0031_172_1	chr10	125591710	125592349	+	0	NA	Intergenic	MER124|DNA?|DNA?	17658	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.018779	0.450000	
chunk0088_204_1	chr18	47950193	47950418	+	0	NA	Intergenic	Intergenic	-19159	NM_001003652	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.004444	0.367257	
chunk0064_396_1	chr14	99274713	99274912	+	0	NA	Intergenic	CpG	-3099	NM_001282237	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.050251	0.650000	
chunk0005_388_1	chr1	62038991	62039205	+	0	NA	intron (NM_176877, intron 30 of 42)	intron (NM_176877, intron 30 of 42)	-39688	NR_036058	100422902		NR_036058	ENSG00000263908	MIR3116-1	-	microRNA 3116-1	ncRNA	0.004673	0.451163	58(GGGAACATTATGATCC,-,0.00),59(GGAACATTATGATCCA,+,0.00)
chunk0167_317_1	chr6	72095667	72095973	+	0	NA	intron (NM_014989, intron 2 of 33)	intron (NM_014989, intron 2 of 33)	-116991	NM_001168408	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.003268	0.384365	156(GTGTACTCTGTGTCCT,-,0.00)
chunk0053_85_1	chr13	28415847	28416276	+	0	NA	intron (NM_001159920, intron 10 of 12)	MIRb|SINE|MIR	79067	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.004662	0.448837	
chunk0179_391_1	chr7	51350178	51350926	+	0	NA	Intergenic	Intergenic	-33734	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.009358	0.407210	
chunk0013_320_1	chr1	171465396	171466049	+	0	NA	Intergenic	MER50|LTR|ERV1	-19805	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.003063	0.452599	434(GAGACTGCCTGTCCCT,+,0.00)
chunk0099_86_1	chr2	85421234	85422044	+	0	NA	Intergenic	L2b|LINE|L2	-7565	NM_001256139	822	Hs.516155	NM_001747	ENSG00000042493	CAPG	AFCP|HEL-S-66|MCP	capping actin protein, gelsolin like	protein-coding	0.017284	0.533909	550(GGGGCCAGGATGTTCC,-,0.00),551(GGGCCAGGATGTTCCA,+,0.00)
chunk0187_215_1	chr7	151932689	151932888	+	0	NA	Intergenic	Intergenic	-23591	NR_033169	168391	Hs.647077	NM_145292	ENSG00000106648	GALNTL5	GALNACT19|GALNT15|GalNAc-T5L	polypeptide N-acetylgalactosaminyltransferase like 5	protein-coding	0.040201	0.545000	
chunk0124_45_1	chr3	52468801	52469365	+	0	NA	intron (NM_001276293, intron 3 of 12)	L1MC|LINE|L1	13575	NM_001276293	11188	Hs.435290	NM_007184	ENSG00000010322	NISCH	I-1|IR1|IRAS|hIRAS	nischarin	protein-coding	0.008865	0.412389	288(AAGGACACCCTGTCTC,-,0.00),289(AGGACACCCTGTCTCC,+,0.00)
chunk0208_260_1	chrX	21150874	21151347	+	0	NA	Intergenic	Intergenic	-223308	NM_014927	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.002114	0.360759	335(CAGCACTGCCAGTTCT,-,0.00),336(AGCACTGCCAGTTCTT,+,0.00)
chunk0175_35_1	chr7	867064	867570	+	0	NA	intron (NM_001130965, intron 16 of 18)	intron (NM_001130965, intron 16 of 18)	-9237	NM_015949	51608	Hs.107387	NM_015949	ENSG00000239857	GET4	C7orf20|CEE|CGI-20|TRC35	guided entry of tail-anchored proteins factor 4	protein-coding	0.033597	0.599606	277(CGGCACAGTCTGTGTC,-,0.00),278(GGCACAGTCTGTGTCA,+,0.00)
chunk0177_265_1	chr7	25385151	25385489	+	0	NA	Intergenic	Intergenic	-156834	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.017751	0.474926	
chunk0102_331_1	chr2	151853037	151853541	+	0	NA	intron (NM_001005746, intron 12 of 13)	intron (NM_001005746, intron 12 of 13)	-24794	NM_012097	26225	Hs.470233	NM_012097	ENSG00000162980	ARL5A	ARFLP5|ARL5	ADP ribosylation factor like GTPase 5A	protein-coding	0.005952	0.378218	
chunk0199_343_1	chr9	11314020	11314458	+	0	NA	Intergenic	L1MC|LINE|L1	701033	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.004566	0.255125	
chunk0212_5_1	chrY	5967922	5968122	+	0	NA	Intergenic	Intergenic	275588	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.005000	0.417910	
chunk0176_90_1	chr7	11592691	11593476	+	0	NA	intron (NM_015204, intron 3 of 26)	intron (NM_015204, intron 3 of 26)	239115	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.011465	0.370229	689(GGGGACACCATGTCAT,-,0.00)
chunk0184_381_1	chr7	121447573	121448293	+	0	NA	Intergenic	Intergenic	-51565	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.006944	0.393897	
chunk0042_385_1	chr12	10717236	10717676	+	0	NA	intron (NM_003651, intron 3 of 9)	intron (NM_003651, intron 3 of 9)	5898	NM_003651	8531	Hs.221889	NM_003651	ENSG00000060138	YBX3	CSDA|CSDA1|DBPA|ZONAB	Y-box binding protein 3	protein-coding	0.006818	0.374150	
chunk0013_242_1	chr1	169671926	169672194	+	0	NA	Intergenic	Intergenic	36796	NR_029467	6402	Hs.728756	NM_000655	ENSG00000188404	SELL	CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1	selectin L	protein-coding	0.003731	0.390335	89(GAAGACAGCATGTGCT,-,0.00),90(AAGACAGCATGTGCTT,+,0.00)
chunk0059_292_1	chr14	35826676	35827046	+	0	NA	intron (NM_032352, intron 1 of 9)	(CGGGG)n|Simple_repeat|Simple_repeat	470	NM_032352	84312	Hs.525299	NM_032352	ENSG00000100916	BRMS1L	BRMS1	BRMS1 like transcriptional repressor	protein-coding	0.081081	0.695418	
chunk0110_459_1	chr20	21314121	21314404	+	0	NA	intron (NM_012255, intron 1 of 29)	L1MB8|LINE|L1	10958	NM_012255	22803	Hs.255932	NM_012255	ENSG00000088930	XRN2	-	5'-3' exoribonuclease 2	protein-coding	0.007067	0.327465	
chunk0197_26_1	chr8	117991929	117992457	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	119626	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.005682	0.421550	
chunk0101_273_1	chr2	133674226	133675091	+	0	NA	Intergenic	Intergenic	-106198	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.018497	0.443418	
chunk0034_220_1	chr11	32982684	32983074	+	0	NA	Intergenic	L2a|LINE|L2	-32985	NM_001077242	91614	Hs.280990	NM_139160	ENSG00000121690	DEPDC7	TR2|dJ85M6.4	DEP domain containing 7	protein-coding	0.005128	0.468031	
chunk0205_44_1	chr9	105893374	105893943	+	0	NA	Intergenic	Intergenic	199133	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.001757	0.470175	200(GTGCACTGACTGTTCT,-,0.00),201(TGCACTGACTGTTCTC,+,0.00)
chunk0081_197_1	chr17	42325814	42326263	+	0	NA	intron (NM_003150, intron 15 of 23)	intron (NM_003150, intron 15 of 23)	37982	NM_001288720	6776	Hs.437058	NM_003152	ENSG00000126561	STAT5A	MGF|STAT5	signal transducer and activator of transcription 5A	protein-coding	0.017817	0.457778	
chunk0129_208_1	chr3	121739576	121740127	+	0	NA	intron (NM_001256488, intron 1 of 20)	L1MD2|LINE|L1	9916	NM_001256488	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.003630	0.342391	
chunk0141_379_1	chr4	88196592	88197180	+	0	NA	intron (NM_001257386, intron 1 of 15)	L1MCa|LINE|L1	34436	NM_001257386	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.006803	0.400679	262(CAGAACATTCTGTTCT,-,0.00),263(AGAACATTCTGTTCTC,+,0.00)
chunk0143_355_1	chr4	121995809	121996451	+	0	NA	Intergenic	Intergenic	-44376	NM_001130698	7222	Hs.150981	NM_003305	ENSG00000138741	TRPC3	SCA41|TRP3	transient receptor potential cation channel subfamily C member 3	protein-coding	0.003115	0.402799	
chunk0023_448_1	chr10	32095105	32095527	+	0	NA	Intergenic	Intergenic	-38873	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.000000	0.472813	
chunk0112_8_1	chr20	35771661	35772111	+	0	NA	promoter-TSS (NM_016436)	promoter-TSS (NM_016436)	-115	NM_016436	51230	Hs.517044	NM_016436	ENSG00000025293	PHF20	C20orf104|GLEA2|HCA58|NZF|TDRD20A|TZP	PHD finger protein 20	protein-coding	0.091111	0.645233	149(GGGGACTTCGTGTTCC,-,0.00),150(GGGACTTCGTGTTCCT,+,0.00)
chunk0166_383_1	chr6	51704987	51705223	+	0	NA	intron (NM_138694, intron 60 of 66)	MamRep488|DNA|hAT-Tip100	83235	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.004237	0.421941	148(GTGGACATTATGTTCC,-,0.00),149(TGGACATTATGTTCCC,+,0.00)
chunk0061_3_1	chr14	55423380	55423579	+	0	NA	intron (NM_199047, intron 6 of 6)	intron (NM_199047, intron 6 of 6)	-11621	NM_014924	22863	Hs.414809	NM_014924	ENSG00000126775	ATG14	ATG14L|BARKOR|KIAA0831	autophagy related 14	protein-coding	0.010050	0.415000	
chunk0186_127_1	chr7	138237923	138238319	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	114363	NR_039678	100616226		NR_039678	ENSG00000284028	MIR4468	-	microRNA 4468	ncRNA	0.012626	0.355164	
chunk0119_402_1	chr22	49302379	49302959	+	0	NA	Intergenic	CpG	240797	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.063793	0.574871	
chunk0037_398_1	chr11	79216063	79216299	+	0	NA	intron (NM_001098816, intron 2 of 33)	L2b|LINE|L2	185928	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.000000	0.485232	
chunk0002_129_1	chr1	16608235	16608744	+	0	NA	intron (NM_017940, intron 2 of 28)	intron (NM_017940, intron 2 of 28)	5116	NM_017940	55672	Hs.467587	NM_017940	ENSG00000219481	NBPF1	AB13|AB14|AB23|AD2|NBG|NBPF	NBPF member 1	protein-coding	0.013752	0.513725	422(AAGAGCACACAGTGCT,-,0.00),423(AGAGCACACAGTGCTT,+,0.00)
chunk0102_112_1	chr2	144542010	144542563	+	0	NA	intron (NR_110570, intron 1 of 2)	intron (NR_110570, intron 1 of 2)	20418	NR_110570	101928455	Hs.333693	NR_110570		LINC01412	-	long intergenic non-protein coding RNA 1412	ncRNA	0.003617	0.386282	
chunk0193_32_1	chr8	71322353	71322926	+	0	NA	intron (NM_172060, intron 2 of 15)	intron (NM_172060, intron 2 of 15)	33872	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.008726	0.391986	218(GAGTACAAGGAGTCCT,-,0.00),219(AGTACAAGGAGTCCTG,+,0.00)
chunk0052_127_1	chr13	23499874	23500145	+	0	NA	Intergenic	L1MC3|LINE|L1	30497	NR_038995	100506697	Hs.50118	NR_038995	ENSG00000232977	LINC00327	NCRNA00327	long intergenic non-protein coding RNA 327	ncRNA	0.011070	0.397059	
chunk0128_78_1	chr3	105387888	105388195	+	0	NA	intron (NM_001627, intron 1 of 15)	intron (NM_001627, intron 1 of 15)	21328	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.292208	
chunk0180_457_1	chr7	77499099	77499430	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-38192	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.003021	0.352410	
chunk0064_152_1	chr14	91815386	91815702	+	0	NA	intron (NM_001128596, intron 1 of 11)	intron (NM_001128596, intron 1 of 11)	-11610	NR_106988									0.006329	0.334385	111(AAGAACTTCATGTCCA,-,0.00)
chunk0144_149_1	chr4	130238111	130238396	+	0	NA	Intergenic	Intergenic	-466775	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.007018	0.314685	
chunk0152_27_1	chr5	56815225	56815566	+	0	NA	5' UTR (NM_005921, exon 1 of 20)	5' UTR (NM_005921, exon 1 of 20)	322	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.137830	0.801170	
chunk0086_88_1	chr18	13608712	13608941	+	0	NA	intron (NM_181481, intron 3 of 5)	intron (NM_181481, intron 3 of 5)	-2288	NR_039752	100616130		NR_039752	ENSG00000263527	MIR4526	mir-4526	microRNA 4526	ncRNA	0.021834	0.421739	
chunk0005_409_1	chr1	62593914	62594447	+	0	NA	intron (NM_001272001, intron 14 of 47)	intron (NM_001272001, intron 14 of 47)	-3307	NM_014495	27329	Hs.209153	NM_014495	ENSG00000132855	ANGPTL3	ANG-5|ANGPT5|ANL3|FHBL2	angiopoietin like 3	protein-coding	0.005629	0.312734	
chunk0107_130_1	chr2	214749062	214749341	+	0	NA	intron (NR_104216, intron 6 of 9)	L2a|LINE|L2	60510	NR_104212	580	Hs.591642	NM_000465	ENSG00000138376	BARD1	-	BRCA1 associated RING domain 1	protein-coding	0.003584	0.478571	103(GGGAACATCTAGTTCC,-,0.00),104(GGAACATCTAGTTCCT,+,0.00)
chunk0005_254_1	chr1	59716882	59717531	+	0	NA	intron (NM_001244714, intron 12 of 13)	intron (NM_001244714, intron 12 of 13)	16090	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.007704	0.400000	
chunk0171_9_1	chr6	119628625	119629248	+	0	NA	Intergenic	Intergenic	-137634	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.011236	0.347756	
chunk0159_64_1	chr5	137307019	137307235	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	192202	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.004630	0.382488	
chunk0113_69_1	chr20	50519456	50519853	+	0	NA	intron (NM_001278618, intron 1 of 8)	intron (NM_001278618, intron 1 of 8)	9333	NM_001278618	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.012594	0.432161	188(TGGTACATGCTGTTTT,-,0.00),189(GGTACATGCTGTTTTA,+,0.00)
chunk0205_191_1	chr9	109098735	109099292	+	0	NA	intron (NM_032012, intron 3 of 17)	intron (NM_032012, intron 3 of 17)	20932	NM_032012	23731	Hs.308074	NM_032012	ENSG00000106771	TMEM245	C9orf5|CG-2|CG2	transmembrane protein 245	protein-coding	0.007181	0.440860	
chunk0177_206_1	chr7	23981553	23982298	+	0	NA	Intergenic	L1M6|LINE|L1	271599	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.005369	0.364611	348(TTGTACAGTCTGTTCT,-,0.00),349(TGTACAGTCTGTTCTC,+,0.00),420(AAGAACAGCCTGTACA,-,0.00),421(AGAACAGCCTGTACAG,+,0.00)
chunk0017_260_1	chr1	209517713	209518186	+	0	NA	Intergenic	Intergenic	-65751	NM_020439	57172	Hs.199068	NM_020439	ENSG00000008118	CAMK1G	CLICK3|CLICKIII|VWS1|dJ272L16.1	calcium/calmodulin dependent protein kinase IG	protein-coding	0.004228	0.485232	
chunk0029_131_1	chr10	98652933	98653454	+	0	NA	intron (NM_001166246, intron 6 of 12)	L1MCa|LINE|L1	-206230	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.000000	0.319923	
chunk0055_407_1	chr13	74366533	74367119	+	0	NA	Intergenic	Intergenic	-52347	NR_047005	100874151	Hs.564552	NR_047005	ENSG00000226240	LINC00381	-	long intergenic non-protein coding RNA 381	ncRNA	0.010239	0.422487	
chunk0152_88_1	chr5	58189935	58190295	+	0	NA	Intergenic	Intergenic	-67774	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.000000	0.357341	
chunk0086_27_1	chr18	12437782	12437981	+	0	NA	Intergenic	Intergenic	17692	NM_001142406	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.015075	0.520000	
chunk0131_380_1	chr3	152298582	152299217	+	0	NA	promoter-TSS (NM_207295)	promoter-TSS (NM_207295)	-506	NM_207297	4154	Hs.201858	NM_021038	ENSG00000152601	MBNL1	EXP|MBNL	muscleblind like splicing regulator 1	protein-coding	0.017323	0.435535	237(AGGAGCAGGCTGTTCA,-,0.00),238(GGAGCAGGCTGTTCAG,+,0.00)
chunk0001_245_1	chr1	8343164	8343857	+	0	NA	intron (NM_001080397, intron 8 of 8)	intron (NM_001080397, intron 8 of 8)	25425	NM_001080397	50651	Hs.463036	NM_001080397	ENSG00000162426	SLC45A1	DNB5|IDDNPF	solute carrier family 45 member 1	protein-coding	0.046176	0.619597	435(TGAACTCCCTGTGCAT,+,0.00)
chunk0172_156_1	chr6	135799026	135799545	+	0	NA	Intergenic	L1MEc|LINE|L1	-52411	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.005780	0.451923	
chunk0164_293_1	chr6	24733915	24734628	+	0	NA	Intergenic	AluJo|SINE|Alu	-15096	NM_030939	81688	Hs.744857	NM_030939	ENSG00000112308	C6orf62	Nbla00237|XTP12|dJ30M3.2	chromosome 6 open reading frame 62	protein-coding	0.002805	0.413165	
chunk0042_26_1	chr12	1425009	1425559	+	0	NA	intron (NR_027946, intron 17 of 18)	intron (NR_027946, intron 17 of 18)	-75207	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.000000	0.417423	
chunk0145_163_1	chr4	147220888	147221391	+	0	NA	Intergenic	Intergenic	123578	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.005964	0.327381	
chunk0145_406_1	chr4	152779804	152780168	+	0	NA	promoter-TSS (NM_001287432)	promoter-TSS (NM_001287432)	49	NM_001025595	27236	Hs.416089	NM_014447	ENSG00000164144	ARFIP1	HSU52521	ADP ribosylation factor interacting protein 1	protein-coding	0.079670	0.652055	
chunk0109_111_1	chr20	2544225	2544817	+	0	NA	intron (NM_080751, intron 2 of 19)	MER110-int|LTR|ERV1	7914	NM_080751	117532	Hs.352626	NM_080751	ENSG00000149488	TMC2	C20orf145	transmembrane channel like 2	protein-coding	0.001689	0.404722	
chunk0197_385_1	chr8	127018486	127018976	+	0	NA	intron (NR_045262, intron 1 of 1)	intron (NR_045262, intron 1 of 1)	5577	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.002041	0.389002	
chunk0067_98_1	chr15	42230797	42231072	+	0	NA	intron (NM_015497, intron 12 of 19)	intron (NM_015497, intron 12 of 19)	-22608	NM_015289	23339	Hs.88025	NM_015289	ENSG00000166887	VPS39	TLP|VAM6|hVam6p	VPS39 subunit of HOPS complex	protein-coding	0.007273	0.355072	
chunk0099_246_1	chr2	97782112	97782336	+	0	NA	intron (NM_015348, intron 31 of 40)	L1MD1|LINE|L1	47818	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.008929	0.564444	
chunk0025_9_1	chr10	47202316	47202611	+	0	NA	Intergenic	Intergenic	-97761	NM_004962	2662	Hs.2171	NM_004962	ENSG00000266524	GDF10	BIP|BMP-3b|BMP3B	growth differentiation factor 10	protein-coding	0.003390	0.331081	
chunk0155_443_1	chr5	101537645	101537936	+	0	NA	Intergenic	L1PA13|LINE|L1	-634505	NM_175052	7903	Hs.308628	NM_005668	ENSG00000113532	ST8SIA4	PST|PST1|SIAT8D|ST8SIA-IV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding	0.013746	0.571918	
chunk0173_46_1	chr6	142307859	142308521	+	0	NA	intron (NM_020455, intron 1 of 25)	MIRb|SINE|MIR	6271	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.003021	0.372549	
chunk0115_121_1	chr21	23090225	23090986	+	0	NA	Intergenic	Intergenic	11321	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.002628	0.329396	
chunk0060_156_1	chr14	45118544	45119034	+	0	NA	intron (NM_002013, intron 5 of 6)	intron (NM_002013, intron 5 of 6)	7914	NR_003691	100113389	Hs.712501	NR_003691	ENSG00000239043	SNORD127	-	small nucleolar RNA, C/D box 127	snoRNA	0.012245	0.405295	
chunk0007_358_1	chr1	84914067	84914376	+	0	NA	Intergenic	Intergenic	-21008	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.003236	0.370968	148(ATGGACATAGTGTGCA,-,0.00),149(TGGACATAGTGTGCAT,+,0.00)
chunk0051_369_1	chr12	121413876	121414348	+	0	NA	intron (NM_194271, intron 2 of 6)	intron (NM_194271, intron 2 of 6)	13994	NM_194271	80196	Hs.292804	NM_025126	ENSG00000170633	RNF34	CARP-1|CARP1|RFI|RIF|RIFF|hRFI	ring finger protein 34	protein-coding	0.004237	0.331924	
chunk0004_146_1	chr1	45169024	45169230	+	0	NA	intron (NM_020883, intron 1 of 13)	intron (NM_020883, intron 1 of 13)	37451	NM_020883	57643	Hs.656613	NM_020883	ENSG00000162415	ZSWIM5	-	zinc finger SWIM-type containing 5	protein-coding	0.009709	0.381643	91(CAACACATCATGTTCC,-,0.00),92(AACACATCATGTTCCT,+,0.00)
chunk0183_41_1	chr7	103842550	103842872	+	0	NA	intron (NM_005045, intron 2 of 64)	intron (NM_005045, intron 2 of 64)	146805	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.003106	0.325077	
chunk0141_79_1	chr4	78512458	78512782	+	0	NA	intron (NM_025074, intron 64 of 73)	intron (NM_025074, intron 64 of 73)	-38968	NM_005139	306	Hs.480042	NM_005139	ENSG00000138772	ANXA3	ANX3	annexin A3	protein-coding	0.003086	0.360000	
chunk0030_207_1	chr10	114519229	114519525	+	0	NA	intron (NM_001003407, intron 6 of 21)	intron (NM_001003407, intron 6 of 21)	7549	NM_006720	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.016892	0.501684	
chunk0001_376_1	chr1	10379083	10379491	+	0	NA	3' UTR (NM_015074, exon 47 of 47)	3' UTR (NM_015074, exon 47 of 47)	-19705	NM_001304451	5226	Hs.464071	NM_002631	ENSG00000142657	PGD	6PGD	phosphogluconate dehydrogenase	protein-coding	0.022059	0.501222	225(CTGGACTGTCTGTTCA,-,0.00),226(TGGACTGTCTGTTCAT,+,0.00)
chunk0007_424_1	chr1	86515814	86516072	+	0	NA	Intergenic	Intergenic	-31133	NM_012128	22802	Hs.567422	NM_012128	ENSG00000016602	CLCA4	CaCC|CaCC2	chloride channel accessory 4	protein-coding	0.003876	0.447876	
chunk0066_426_1	chr15	39622801	39623260	+	0	NA	intron (NM_152597, intron 10 of 11)	intron (NM_152597, intron 10 of 11)	41951	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.006536	0.417391	
chunk0177_38_1	chr7	20906395	20907217	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	71375	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.003650	0.346294	
chunk0022_132_1	chr10	11776139	11776529	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	33977	NM_024693	79746	Hs.22242	NM_024693	ENSG00000134463	ECHDC3	-	enoyl-CoA hydratase domain containing 3	protein-coding	0.007692	0.406650	
chunk0014_74_1	chr1	176193945	176194488	+	0	NA	intron (NM_001001740, intron 1 of 18)	L1ME1|LINE|L1	13028	NM_001286644	64326	Hs.523744	NM_022457	ENSG00000143207	COP1	RFWD2|RNF200	COP1 E3 ubiquitin ligase	protein-coding	0.007366	0.363971	
chunk0028_257_1	chr10	90589534	90590195	+	0	NA	Intergenic	Intergenic	-49059	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.006051	0.435045	
chunk0034_348_1	chr11	35847468	35847731	+	0	NA	Intergenic	Intergenic	-96382	NM_174902	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.003802	0.518939	
chunk0158_148_1	chr5	127461363	127461889	+	0	NA	TTS (NM_001256545)	TTS (NM_001256545)	-55983	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.005703	0.379507	
chunk0023_380_1	chr10	30496720	30496945	+	0	NA	Intergenic	Intergenic	62811	NM_001244134	1326	Hs.432453	NM_005204	ENSG00000107968	MAP3K8	AURA2|COT|EST|ESTF|MEKK8|TPL2|Tpl-2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding	0.008889	0.451327	
chunk0087_305_1	chr18	39341039	39341357	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	280977	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.000000	0.373041	
chunk0145_413_1	chr4	152831879	152832423	+	0	NA	intron (NM_001025595, intron 2 of 8)	L1ME3|LINE|L1	52214	NM_001025595	27236	Hs.416089	NM_014447	ENSG00000164144	ARFIP1	HSU52521	ADP ribosylation factor interacting protein 1	protein-coding	0.005515	0.372477	
chunk0024_137_1	chr10	35056028	35056394	+	0	NA	intron (NM_001198778, intron 4 of 20)	L2a|LINE|L2	18119	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.002732	0.359673	
chunk0083_226_1	chr17	67381737	67382288	+	0	NA	intron (NM_181671, intron 1 of 9)	MIRc|SINE|MIR	4731	NM_181671	26207	Hs.591185	NM_012417	ENSG00000154217	PITPNC1	M-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1	phosphatidylinositol transfer protein cytoplasmic 1	protein-coding	0.012704	0.420290	
chunk0168_101_1	chr6	80171887	80172184	+	0	NA	intron (NM_000056, intron 6 of 10)	L1ME2z|LINE|L1	65408	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.000000	0.345638	
chunk0009_150_1	chr1	104933748	104934212	+	0	NA	Intergenic	LTR2752|LTR|ERV1	684955	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.019397	0.572043	
chunk0050_126_1	chr12	102114242	102114570	+	0	NA	intron (NM_024057, intron 1 of 8)	intron (NM_024057, intron 1 of 8)	4177	NM_024057	79023	Hs.444276	NM_024057	ENSG00000075188	NUP37	MCPH24|p37	nucleoporin 37	protein-coding	0.003049	0.382979	
chunk0005_382_1	chr1	61836568	61837183	+	0	NA	intron (NM_176877, intron 17 of 42)	intron (NM_176877, intron 17 of 42)	94398	NM_176877	10207	Hs.478125	NM_005799	ENSG00000132849	PATJ	Cipp|INADL|InaD-like|hINADL	PATJ crumbs cell polarity complex component	protein-coding	0.004878	0.358766	313(CAGAACAAAAAGTACT,-,0.00),314(AGAACAAAAAGTACTG,+,0.00)
chunk0192_5_1	chr8	58191443	58192107	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	80326	NR_105005	101929528	Hs.563551	NR_105005	ENSG00000253281	LOC101929528	-	uncharacterized LOC101929528	ncRNA	0.004518	0.398496	
chunk0147_199_1	chr4	177809836	177810284	+	0	NA	intron (NR_028342, intron 2 of 5)	intron (NR_028342, intron 2 of 5)	81303	NR_028342	285501	Hs.722466	NM_001085490	ENSG00000231171	LINC01098	-	long intergenic non-protein coding RNA 1098	ncRNA	0.008929	0.354120	
chunk0196_245_1	chr8	108517405	108517915	+	0	NA	Intergenic	L1MA10|LINE|L1	74036	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.005882	0.338552	
chunk0188_314_1	chr8	17246355	17246577	+	0	NA	promoter-TSS (NM_152415)	promoter-TSS (NM_152415)	412	NM_054026	29883	Hs.587465	NM_013354	ENSG00000198791	CNOT7	CAF-1|CAF1|Caf1a|hCAF-1	CCR4-NOT transcription complex subunit 7	protein-coding	0.058559	0.627803	
chunk0193_115_1	chr8	74177482	74178116	+	0	NA	Intergenic	Intergenic	143528	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.011041	0.392126	328(AAGAACTTCATGTTCT,-,0.00),329(AGAACTTCATGTTCTC,+,0.00)
chunk0178_364_1	chr7	39308806	39309102	+	0	NA	intron (NM_007252, intron 5 of 10)	intron (NM_007252, intron 5 of 10)	97392	NR_046711	100861520	Hs.571292	NR_046711	ENSG00000224122	POU6F2-AS1	-	POU6F2 antisense RNA 1	ncRNA	0.027027	0.525253	
chunk0027_460_1	chr10	81814283	81815039	+	0	NA	Intergenic	L1MD|LINE|L1	-60653	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.005291	0.338177	
chunk0067_207_1	chr15	44990410	44990810	+	0	NA	Intergenic	L1M5|LINE|L1	-32494	NM_003104	6652	Hs.878	NM_003104	ENSG00000140263	SORD	HEL-S-95n|RDH|SDH|SORD1|XDH	sorbitol dehydrogenase	protein-coding	0.002500	0.359102	
chunk0182_456_1	chr7	102121638	102121933	+	0	NA	intron (NM_001202546, intron 7 of 21)	MIRc|SINE|MIR	-163277	NM_020979	10603	Hs.489448	NM_020979	ENSG00000160999	SH2B2	APS	SH2B adaptor protein 2	protein-coding	0.013559	0.493243	
chunk0196_376_1	chr8	115296362	115296962	+	0	NA	Intergenic	Intergenic	371350	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.006667	0.376040	
chunk0048_50_1	chr12	78099863	78100181	+	0	NA	intron (NM_014903, intron 12 of 38)	intron (NM_014903, intron 12 of 38)	268733	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.006289	0.307210	
chunk0196_367_1	chr8	115163977	115164351	+	0	NA	Intergenic	L1MB3|LINE|L1	503848	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.005348	0.370667	
chunk0010_314_1	chr1	118059288	118059977	+	0	NA	intron (NM_206996, intron 18 of 48)	L1M1|LINE|L1	125593	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.001451	0.279710	
chunk0150_26_1	chr5	30837884	30838501	+	0	NA	Intergenic	Intergenic	-355463	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.008104	0.389968	
chunk0129_202_1	chr3	121648534	121648969	+	0	NA	intron (NM_001292041, intron 3 of 12)	intron (NM_001292041, intron 3 of 12)	12197	NM_001292041	3059	Hs.14601	NM_005335	ENSG00000180353	HCLS1	CTTNL|HS1|lckBP1|p75	hematopoietic cell-specific Lyn substrate 1	protein-coding	0.009195	0.424312	
chunk0016_118_1	chr1	196118113	196118351	+	0	NA	Intergenic	L1PA17|LINE|L1	464249	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.025210	0.372385	
chunk0003_371_1	chr1	39544293	39544861	+	0	NA	intron (NR_003929, intron 6 of 8)	L1MC4|LINE|L1	15121	NR_003929	728448	Hs.472508	NR_003929	ENSG00000243970	PPIEL	PPIEP1	peptidylprolyl isomerase E like pseudogene	pseudo	0.007042	0.376098	
chunk0112_344_1	chr20	45114660	45115013	+	0	NA	intron (NM_145652, intron 1 of 3)	intron (NM_145652, intron 1 of 3)	336	NM_145652	149708	Hs.375031	NM_145652	ENSG00000175121	WFDC5	PRG5|WAP1|dJ211D12.5	WAP four-disulfide core domain 5	protein-coding	0.025496	0.533898	
chunk0013_248_1	chr1	169764886	169765592	+	0	NA	Intergenic	L1MD2|LINE|L1	29681	NM_033418	92342	Hs.33922	NM_033418	ENSG00000171806	METTL18	AsTP2|C1orf156|HPM1	methyltransferase like 18	protein-coding	0.007082	0.332390	
chunk0029_318_1	chr10	104331235	104332037	+	0	NA	intron (NM_001272013, intron 1 of 1)	intron (NM_001272013, intron 1 of 1)	2269	NM_033397	85450	Hs.523252	NM_033397	ENSG00000148841	ITPRIP	DANGER|KIAA1754|bA127L20|bA127L20.2	inositol 1,4,5-trisphosphate receptor interacting protein	protein-coding	0.012469	0.516812	160(GAGAACAGTATGTTAT,-,0.00),161(AGAACAGTATGTTATG,+,0.00)
chunk0135_325_1	chr3	190114966	190115747	+	0	NA	intron (NM_001134418, intron 1 of 14)	intron (NM_001134418, intron 1 of 14)	-5608	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.002561	0.345269	
chunk0126_189_1	chr3	78420799	78421021	+	0	NA	Intergenic	Intergenic	598549	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.443946	
chunk0098_130_1	chr2	69082474	69083124	+	0	NA	intron (NM_053034, intron 8 of 14)	intron (NM_053034, intron 8 of 14)	-20883	NR_036073	100423030		NR_036073	ENSG00000266649	MIR3126	mir-3126	microRNA 3126	ncRNA	0.016923	0.466974	
chunk0141_260_1	chr4	86306836	86307401	+	0	NA	intron (NM_138980, intron 2 of 13)	intron (NM_138980, intron 2 of 13)	53104	NM_138982	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.005310	0.376325	
chunk0183_16_1	chr7	103130193	103130706	+	0	NA	intron (NM_001122838, intron 1 of 4)	MIRb|SINE|MIR	11954	NR_026660	100129424	Hs.720729	NR_026660		RPL19P12	RPL19_4_829	ribosomal protein L19 pseudogene 12	pseudo	0.009747	0.428016	321(AGGTACATAATGTACT,-,0.00),322(GGTACATAATGTACTT,+,0.00)
chunk0176_24_1	chr7	8612527	8613088	+	0	NA	intron (NM_152745, intron 2 of 2)	intron (NM_152745, intron 2 of 2)	178852	NM_152745	30010	Hs.487564	NM_152745	ENSG00000122584	NXPH1	NPH1|Nbla00697	neurexophilin 1	protein-coding	0.001783	0.348754	
chunk0030_98_1	chr10	112440402	112440866	+	0	NA	exon (NM_001303134, exon 5 of 11)	exon (NM_001303134, exon 5 of 11)	6325	NM_022494	64429	Hs.196990	NM_022494	ENSG00000023041	ZDHHC6	DHHC-6|ZNF376	zinc finger DHHC-type containing 6	protein-coding	0.015086	0.384946	
chunk0079_96_1	chr17	12075930	12076370	+	0	NA	intron (NM_001281435, intron 3 of 11)	intron (NM_001281435, intron 3 of 11)	-5749	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.002273	0.403628	
chunk0109_338_1	chr20	9423624	9424240	+	0	NA	exon (NM_182797, exon 25 of 36)	exon (NM_182797, exon 25 of 36)	-90426	NM_001199897	24141	Hs.22920	NM_012261	ENSG00000125869	LAMP5	BAD-LAMP|BADLAMP|C20orf103|LAMP-5|UNC-46	lysosomal associated membrane protein family member 5	protein-coding	0.012987	0.369530	
chunk0170_157_1	chr6	111508669	111509204	+	0	NA	intron (NR_034109, intron 1 of 1)	intron (NR_034109, intron 1 of 1)	-25221	NM_001286432	5980	Hs.232021	NM_002912	ENSG00000009413	REV3L	POLZ|REV3	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding	0.007477	0.416045	
chunk0102_462_1	chr2	158694142	158694341	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-101076	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.005025	0.235000	
chunk0131_448_1	chr3	154077665	154078185	+	0	NA	intron (NR_037901, intron 2 of 3)	MamRep434|DNA|TcMar-Tigger	-43078	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.007692	0.337812	234(GAGAACAGCTTGTTCC,-,0.00),235(AGAACAGCTTGTTCCT,+,0.00)
chunk0167_243_1	chr6	67676783	67677652	+	0	NA	Intergenic	L2c|LINE|L2	-378134	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.001151	0.335632	
chunk0040_27_1	chr11	110207363	110207955	+	0	NA	intron (NM_001260496, intron 6 of 7)	MER58B|DNA|hAT-Charlie	89053	NM_001260496	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.005068	0.344013	
chunk0063_47_1	chr14	76947050	76947253	+	0	NA	Intergenic	Intergenic	81548	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.034483	0.617647	
chunk0172_398_1	chr6	139773056	139773330	+	0	NA	intron (NR_038399, intron 1 of 2)	intron (NR_038399, intron 1 of 2)	2120	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.003650	0.309091	
chunk0089_91_1	chr18	58337077	58337856	+	0	NA	intron (NM_001144967, intron 13 of 30)	intron (NM_001144967, intron 13 of 30)	-113608	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.012837	0.442308	20(CAGGACAAGGTGACCC,-,0.00),21(AGGACAAGGTGACCCC,+,0.00),472(AGGTACACATTGTGCC,-,0.00),473(GGTACACATTGTGCCA,+,0.00)
chunk0149_61_1	chr5	16894676	16894881	+	0	NA	intron (NM_012334, intron 1 of 40)	intron (NM_012334, intron 1 of 40)	41498	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.009756	0.529126	
chunk0026_268_1	chr10	67000754	67000974	+	0	NA	intron (NR_111911, intron 1 of 6)	intron (NR_111911, intron 1 of 6)	11289	NR_111911	101928961	Hs.687014	NR_111911		LOC101928961	-	uncharacterized LOC101928961	ncRNA	0.009091	0.371041	
chunk0060_398_1	chr14	53004019	53004531	+	0	NA	Intergenic	Intergenic	-53178	NM_001135000	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.009766	0.321637	
chunk0122_201_1	chr3	33069894	33070275	+	0	NA	intron (NM_000404, intron 2 of 15)	L1PA15|LINE|L1	26717	NM_001136238	643853	Hs.443031	NM_001039770	ENSG00000188167	TMPPE	-	transmembrane protein with metallophosphoesterase domain	protein-coding	0.005249	0.384817	
chunk0066_194_1	chr15	33233912	33234715	+	0	NA	Intergenic	Intergenic	13242	NR_046005	100652857	Hs.439998	NR_046005		TMCO5B	-	transmembrane and coiled-coil domains 5B (pseudogene)	pseudo	0.009963	0.440299	
chunk0057_435_1	chr13	110480577	110481675	+	0	NA	intron (NM_001846, intron 31 of 47)	intron (NM_001846, intron 31 of 47)	27053	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.020036	0.523203	276(GGAGACACACTGTTCT,-,0.00),277(GAGACACACTGTTCTT,+,0.00),302(GAGACACACAGTTCTG,+,0.00),331(GGAGACACACTGTTCT,-,0.00),332(GAGACACACTGTTCTG,+,0.00),361(GGAGACACACTGTTCT,-,0.00),362(GAGACACACTGTTCTG,+,0.00),392(GAGACACACAGTTCTG,+,0.00),421(GGAGACACACTGTTCT,-,0.00),422(GAGACACACTGTTCTG,+,0.00),452(GAGACACACAGTTCTG,+,0.00),481(GGAGACACACTGTTCT,-,0.00),482(GAGACACACTGTTCTG,+,0.00),511(GGAGACACACTGTTCT,-,0.00),512(GAGACACACTGTTCTG,+,0.00),542(GAGACACACAGTTCTG,+,0.00),571(GGAGACACACTGTTCT,-,0.00),572(GAGACACACTGTTCTG,+,0.00),601(GGAGACACACTGTTCT,-,0.00),602(GAGACACACTGTTCTG,+,0.00),632(GAGACACACAGTTCTG,+,0.00),661(GGAGACACACTGTTCT,-,0.00),662(GAGACACACTGTTCTG,+,0.00),691(GGAGACACACTGTTCT,-,0.00),692(GAGACACACTGTTCTG,+,0.00),721(GGAGACACACTGTTCT,-,0.00),722(GAGACACACTGTTCTG,+,0.00),751(GGAGACACACTGTTCT,-,0.00),752(GAGACACACTGTTCTG,+,0.00),781(GGAGACACACTGTTCT,-,0.00),782(GAGACACACTGTTCTG,+,0.00),811(GGAGACACACTGTTCT,-,0.00),812(GAGACACACTGTTCTG,+,0.00),841(GGAGACACACTGTTCT,-,0.00),842(GAGACACACTGTTCTG,+,0.00),902(GAGACACACAGTTCTG,+,0.00),931(GGAGACACACTGTTCT,-,0.00),932(GAGACACACTGTTCTG,+,0.00),991(GGAGACACACTGTTCT,-,0.00),992(GAGACACACTGTTCTG,+,0.00),1021(GGAGACACACTGTTCT,-,0.00),1022(GAGACACACTGTTCTG,+,0.00),1051(GGAGACACACTGTTCT,-,0.00),1052(GAGACACACTGTTCTG,+,0.00),1082(GAGACACACAGTTCTG,+,0.00)
chunk0054_122_1	chr13	43280822	43281041	+	0	NA	intron (NM_001127615, intron 12 of 16)	intron (NM_001127615, intron 12 of 16)	167766	NR_047013	100874159	Hs.633241	NR_047013		LINC00400	-	long intergenic non-protein coding RNA 400	ncRNA	0.000000	0.409091	
chunk0104_117_1	chr2	172931487	172931703	+	0	NA	intron (NM_001282901, intron 1 of 24)	intron (NM_001282901, intron 1 of 24)	3390	NM_001282901	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.009259	0.460829	
chunk0187_263_1	chr7	155051978	155052177	+	0	NA	Intergenic	Intergenic	-18247	NM_024012	3361	Hs.65791	NM_024012	ENSG00000157219	HTR5A	5-HT5A	5-hydroxytryptamine receptor 5A	protein-coding	0.010050	0.465000	
chunk0039_190_1	chr11	100837385	100837593	+	0	NA	intron (NM_152432, intron 3 of 23)	LTR43B|LTR|ERV1	-149534	NR_133571	100128386	Hs.635125	NR_133571	ENSG00000248027	LOC100128386	-	uncharacterized LOC100128386	ncRNA	0.004808	0.397129	
chunk0135_46_1	chr3	185537278	185537761	+	0	NA	intron (NM_139248, intron 1 of 9)	intron (NM_139248, intron 1 of 9)	15062	NM_139248	200879	Hs.68864	NM_139248	ENSG00000163898	LIPH	AH|ARWH2|HYPT7|LAH2|LPDLR|PLA1B|mPA-PLA1	lipase H	protein-coding	0.016563	0.458678	
chunk0062_157_1	chr14	69289474	69289848	+	0	NA	intron (NM_001168368, intron 1 of 14)	intron (NM_001168368, intron 1 of 14)	29697	NM_001168368	57452	Hs.21035	NM_020692	ENSG00000100626	GALNT16	GALNACT16|GALNTL1|GalNAc-T16	polypeptide N-acetylgalactosaminyltransferase 16	protein-coding	0.018717	0.549333	
chunk0196_80_1	chr8	102616627	102617281	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	37010	NR_103759	7071	Hs.435001	NM_005655	ENSG00000155090	KLF10	EGR-alpha|EGRA|TIEG|TIEG1	Kruppel like factor 10	protein-coding	0.004587	0.409160	
chunk0148_331_1	chr5	14212821	14213250	+	0	NA	intron (NM_007118, intron 1 of 56)	intron (NM_007118, intron 1 of 56)	69315	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.009324	0.411628	
chunk0198_358_1	chr8	140762640	140762888	+	0	NA	intron (NM_001316342, intron 14 of 32)	intron (NM_001316342, intron 14 of 32)	-30111	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.004032	0.377510	
chunk0154_119_1	chr5	78740275	78740911	+	0	NA	Intergenic	L2a|LINE|L2	-91768	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.003145	0.394035	
chunk0029_375_1	chr10	108090837	108091116	+	0	NA	Intergenic	L1M1|LINE|L1	-21683	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.007168	0.539286	
chunk0053_124_1	chr13	29743187	29743572	+	0	NA	Intergenic	Intergenic	107304	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.036364	0.546632	
chunk0016_175_1	chr1	198079460	198080112	+	0	NA	Intergenic	MER61E|LTR|ERV1	-77192	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.001534	0.436447	
chunk0102_107_1	chr2	144406227	144406705	+	0	NA	intron (NM_001171653, intron 3 of 8)	L2a|LINE|L2	-73932	NM_001284235	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.006276	0.413361	295(AAGAGCAGCATGTGCA,-,0.00)
chunk0095_9_1	chr2	11872785	11873005	+	0	NA	Intergenic	Intergenic	-35909	NR_036226	100422996		NR_036226	ENSG00000265172	MIR4262	-	microRNA 4262	ncRNA	0.009091	0.425339	
chunk0152_109_1	chr5	58481390	58481794	+	0	NA	Intergenic	Intergenic	-9843	NM_001304431	202309	Hs.547697	NM_152687	ENSG00000175857	GAPT	C5orf29	GRB2 binding adaptor protein, transmembrane	protein-coding	0.004950	0.533333	
chunk0051_187_1	chr12	116176953	116177407	+	0	NA	intron (NM_015335, intron 2 of 30)	L1ME3A|LINE|L1	-28526	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.008811	0.373626	
chunk0149_330_1	chr5	26648910	26649572	+	0	NA	Intergenic	MER87|LTR|ERV1	389341	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.006042	0.371041	
chunk0119_417_1	chr22	49797660	49798196	+	0	NA	exon (NM_001304809, exon 6 of 13)	exon (NM_001304809, exon 6 of 13)	27972	NM_001304809	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.042910	0.497207	297(TAGAACACGGTGTCCC,-,0.00),298(AGAACACGGTGTCCCT,+,0.00)
chunk0034_216_1	chr11	32899168	32899786	+	0	NA	intron (NM_001076786, intron 1 of 12)	L2b|LINE|L2	6299	NM_001076786	79832	Hs.369368	NM_024774	ENSG00000060749	QSER1	-	glutamine and serine rich 1	protein-coding	0.000000	0.400646	260(TGGAACAATGAGTACT,-,0.00),261(GGAACAATGAGTACTA,+,0.00)
chunk0128_196_1	chr3	107622099	107622616	+	0	NA	intron (NM_001276286, intron 2 of 16)	L1ME1|LINE|L1	99421	NM_001142568	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.011605	0.359073	
chunk0080_224_1	chr17	29744546	29745173	+	0	NA	intron (NM_001282129, intron 3 of 15)	intron (NM_001282129, intron 3 of 15)	16573	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.007974	0.372611	
chunk0137_297_1	chr4	24010430	24011119	+	0	NA	Intergenic	Intergenic	-120697	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.008708	0.373913	
chunk0187_272_1	chr7	155276747	155277215	+	0	NA	Intergenic	Intergenic	-20795	NM_198337	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.014957	0.524520	
chunk0139_241_1	chr4	55528298	55528954	+	0	NA	intron (NM_004898, intron 1 of 22)	intron (NM_004898, intron 1 of 22)	17306	NM_001267843	9575	Hs.436975	NM_004898	ENSG00000134852	CLOCK	KAT13D|bHLHe8	clock circadian regulator	protein-coding	0.006098	0.394216	
chunk0055_412_1	chr13	74633654	74633888	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	80928	NR_034025	338864	Hs.97408	NR_034024	ENSG00000236678	LINC00347	-	long intergenic non-protein coding RNA 347	ncRNA	0.004274	0.446809	
chunk0097_110_1	chr2	46134438	46135432	+	0	NA	intron (NM_005400, intron 11 of 14)	intron (NM_005400, intron 11 of 14)	-162467	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.012072	0.453266	290(GTGGTCACTCTGTCCT,-,0.00),291(TGGTCACTCTGTCCTG,+,0.00)
chunk0105_427_1	chr2	193293554	193294109	+	0	NA	Intergenic	L1ME2z|LINE|L1	543986	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.005405	0.316547	
chunk0020_133_1	chr1	233623440	233623645	+	0	NA	promoter-TSS (NR_039625)	promoter-TSS (NR_039625)	-610	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.019512	0.364078	
chunk0193_178_1	chr8	74938134	74938775	+	0	NA	Intergenic	L1MA2|LINE|L1	-46019	NM_031461	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.001560	0.333333	
chunk0031_115_1	chr10	124632089	124632776	+	0	NA	intron (NM_014661, intron 4 of 4)	intron (NM_014661, intron 4 of 4)	-71596	NR_120630	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.033479	0.581395	
chunk0151_82_1	chr5	42811816	42812259	+	0	NA	promoter-TSS (NM_005410)	promoter-TSS (NM_005410)	-115	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.011287	0.430180	
chunk0111_350_1	chr20	33401069	33401642	+	0	NA	intron (NM_001278167, intron 1 of 13)	CpG	214	NM_001278168	51654	Hs.435952	NM_016082	ENSG00000101391	CDK5RAP1	C20orf34|C42|CGI-05|HSPC167	CDK5 regulatory subunit associated protein 1	protein-coding	0.075044	0.608014	263(TGAACACCGTGCGCTT,+,0.00)
chunk0201_107_1	chr9	35038019	35038591	+	0	NA	Intergenic	Intergenic	-2790	NM_001040411	138724	Hs.148250	NM_203299	ENSG00000174038	C9orf131	-	chromosome 9 open reading frame 131	protein-coding	0.006993	0.431065	
chunk0210_259_1	chrX	83966247	83966849	+	0	NA	Intergenic	L1M2|LINE|L1	105422	NM_001271680	1538	Hs.444230	NM_021118	ENSG00000183035	CYLC1	CYCL1	cylicin 1	protein-coding	0.003322	0.323383	
chunk0144_123_1	chr4	128879676	128880216	+	0	NA	Intergenic	Intergenic	68102	NM_001287443	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.003704	0.321627	331(AGGAACATGCTGTGAT,-,0.00),332(GGAACATGCTGTGATT,+,0.00)
chunk0185_238_1	chr7	129497707	129497906	+	0	NA	Intergenic	L2c|LINE|L2	-4673	NM_001195243	100287482	Hs.178144	NM_001195243	ENSG00000240204	SMKR1	-	small lysine rich protein 1	protein-coding	0.005025	0.465000	
chunk0116_445_1	chr21	43352176	43352792	+	0	NA	Intergenic	MER57F|LTR|ERV1	9865	NR_131902	101928399	Hs.517319	NR_131902	ENSG00000237989	LINC01679	TCONS_00029157	long intergenic non-protein coding RNA 1679	ncRNA	0.017857	0.453809	
chunk0153_430_1	chr5	76163202	76163683	+	0	NA	intron (NM_014979, intron 2 of 12)	intron (NM_014979, intron 2 of 12)	80028	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.006237	0.421162	
chunk0049_158_1	chr12	92030536	92031130	+	0	NA	intron (NR_132341, intron 1 of 4)	intron (NR_132341, intron 1 of 4)	110880	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.005051	0.396639	300(AAGAACAGGATGTTCT,-,0.00),301(AGAACAGGATGTTCTG,+,0.00)
chunk0004_231_1	chr1	47052296	47052933	+	0	NA	Intergenic	Intergenic	-14874	NM_178134	199974	Hs.176588	NM_178134	ENSG00000186160	CYP4Z1	CYP4A20	cytochrome P450 family 4 subfamily Z member 1	protein-coding	0.000000	0.289969	
chunk0079_128_1	chr17	12650818	12651182	+	0	NA	Intergenic	Intergenic	-14890	NM_153604	93649	Hs.462257	NM_153604	ENSG00000141052	MYOCD	MYCD	myocardin	protein-coding	0.021978	0.361644	115(AAGAACAGGCTGTGCT,-,0.00),116(AGAACAGGCTGTGCTT,+,0.00)
chunk0147_311_1	chr4	184902071	184902438	+	0	NA	Intergenic	Intergenic	-2793	NR_039976	100506229	Hs.378150	NR_039975		LINC01093	-	long intergenic non-protein coding RNA 1093	ncRNA	0.010899	0.434783	
chunk0136_104_1	chr4	3112956	3113330	+	0	NA	intron (NM_002111, intron 6 of 66)	intron (NM_002111, intron 6 of 66)	-38629	NR_045414	100750326	Hs.575112	NR_045414		HTT-AS	HTT-AS1|HTTAS	HTT antisense RNA	ncRNA	0.005348	0.400000	301(AAGCTCACCGTGTGCT,-,0.00),302(AGCTCACCGTGTGCTG,+,0.00)
chunk0101_268_1	chr2	133566221	133566627	+	0	NA	intron (NM_207481, intron 1 of 17)	intron (NM_207481, intron 1 of 17)	2036	NM_207363	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.009852	0.449631	
chunk0108_460_1	chr2	238435753	238436379	+	0	NA	intron (NM_001040445, intron 3 of 4)	L1MEd|LINE|L1	9081	NM_001040445	51665	Hs.516788	NM_016114	ENSG00000065802	ASB1	ASB-1	ankyrin repeat and SOCS box containing 1	protein-coding	0.036741	0.470494	
chunk0093_448_1	chr19	58499491	58499690	+	0	NA	exon (NM_012254, exon 7 of 10)	exon (NM_012254, exon 7 of 10)	12475	NM_012254	10998	Hs.292177	NM_012254	ENSG00000083807	SLC27A5	ACSB|ACSVL6|BACS|BAL|FACVL3|FATP-5|FATP5|VLACSR|VLCS-H2|VLCSH2	solute carrier family 27 member 5	protein-coding	0.110553	0.665000	
chunk0169_100_1	chr6	100518588	100518981	+	0	NA	intron (NM_006828, intron 37 of 41)	intron (NM_006828, intron 37 of 41)	-55109	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.002545	0.342640	
chunk0008_151_1	chr1	92411765	92412188	+	0	NA	Intergenic	Intergenic	71823	NM_001127215	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.007092	0.431604	
chunk0037_339_1	chr11	77357321	77358145	+	0	NA	intron (NM_001128620, intron 6 of 15)	MIRc|SINE|MIR	-70315	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.003641	0.381818	
chunk0178_233_1	chr7	35800834	35801374	+	0	NA	promoter-TSS (NR_120511)	promoter-TSS (NR_120511)	118	NM_001011553	989	Hs.191346	NM_001788	ENSG00000122545	SEPTIN7	CDC10|CDC3|NBLA02942|SEPT7|SEPT7A	septin 7	protein-coding	0.100000	0.658041	
chunk0162_296_1	chr6	6433997	6434337	+	0	NA	intron (NR_026970, intron 4 of 7)	L1ME4b|LINE|L1	-113476	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.008824	0.348974	
chunk0107_257_1	chr2	217375009	217375588	+	0	NA	intron (NR_026597, intron 8 of 12)	intron (NR_026597, intron 8 of 12)	92565	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.006908	0.427586	
chunk0123_32_1	chr3	40690947	40691611	+	0	NA	Intergenic	Intergenic	166401	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.015060	0.532331	
chunk0198_78_1	chr8	130081911	130082282	+	0	NA	TTS (NR_045385)	TTS (NR_045385)	2672	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.000000	0.411290	223(CTGGACAGAATGTTCT,-,0.00),224(TGGACAGAATGTTCTG,+,0.00)
chunk0141_186_1	chr4	83317235	83317591	+	0	NA	intron (NM_001166498, intron 4 of 10)	intron (NM_001166498, intron 4 of 10)	17400	NM_001199830	10855	Hs.44227	NM_006665	ENSG00000173083	HPSE	HPA|HPA1|HPR1|HPSE1|HSE1	heparanase	protein-coding	0.005618	0.414566	
chunk0063_58_1	chr14	77076115	77076819	+	0	NA	promoter-TSS (NR_110553)	promoter-TSS (NR_110553)	-276	NR_110553	102724190	Hs.562528	NR_110553	ENSG00000258819	LINC02289	-	long intergenic non-protein coding RNA 2289	ncRNA	0.014205	0.495035	328(AAGAACTCCTTGTCCC,-,0.00),329(AGAACTCCTTGTCCCG,+,0.00)
chunk0060_339_1	chr14	51975028	51975375	+	0	NA	Intergenic	Intergenic	-14309	NM_016039	51637	Hs.534457	NM_016039	ENSG00000087302	RTRAF	C14orf166|CGI-99|CGI99|CLE|CLE7|LCRP369|RLLM1|hCLE|hCLE1	RNA transcription, translation and transport factor	protein-coding	0.002882	0.370690	254(AGGCACAGAGTGTTTT,-,0.00),255(GGCACAGAGTGTTTTT,+,0.00)
chunk0077_320_1	chr16	82150608	82150972	+	0	NA	intron (NM_005792, intron 3 of 4)	intron (NM_005792, intron 3 of 4)	19434	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.002747	0.389041	
chunk0206_132_1	chr9	121021145	121021772	+	0	NA	intron (NM_001735, intron 11 of 40)	intron (NM_001735, intron 11 of 40)	28818	NM_001735	727	Hs.494997	NM_001735	ENSG00000106804	C5	C5D|C5a|C5b|CPAMD4|ECLZB	complement C5	protein-coding	0.007974	0.394904	319(GAGTACACATTGTCCT,-,0.00),320(AGTACACATTGTCCTA,+,0.00)
chunk0192_201_1	chr8	64327426	64327893	+	0	NA	intron (NR_125826, intron 1 of 4)	L2a|LINE|L2	40899	NR_125826	102724623	Hs.586375	NR_125826	ENSG00000253554	LINC01414	-	long intergenic non-protein coding RNA 1414	ncRNA	0.006424	0.446581	
chunk0015_392_1	chr1	190764190	190764592	+	0	NA	intron (NR_033922, intron 2 of 4)	intron (NR_033922, intron 2 of 4)	139501	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.009950	0.297767	
chunk0128_358_1	chr3	113064098	113064643	+	0	NA	Intergenic	Intergenic	-44662	NM_015412	25871	Hs.591288	NM_015412	ENSG00000163608	NEPRO	C3orf17|NET17	nucleolus and neural progenitor protein	protein-coding	0.005505	0.380952	295(AGGAACACTTCGTCCC,-,0.00)
chunk0048_445_1	chr12	88633971	88634567	+	0	NA	Intergenic	LTR57|LTR|ERVL	-53796	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.001678	0.443886	
chunk0145_172_1	chr4	147353443	147353684	+	0	NA	Intergenic	Intergenic	-8846	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.008299	0.475207	
chunk0126_80_1	chr3	74704661	74705421	+	0	NA	Intergenic	Intergenic	-183901	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.005263	0.342970	445(AGGGACACTGTGTGTT,-,0.00),446(GGGACACTGTGTGTTG,+,0.00)
chunk0019_446_1	chr1	231326040	231326651	+	0	NA	Intergenic	Intergenic	11527	NM_175876	149371	Hs.356198	NM_175876	ENSG00000116903	EXOC8	EXO84|Exo84p|SEC84	exocyst complex component 8	protein-coding	0.003273	0.341503	
chunk0110_70_1	chr20	10961682	10962480	+	0	NA	Intergenic	Intergenic	-52809	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.005013	0.379224	210(TTGAACACCATGTTCA,-,0.00),211(TGAACACCATGTTCAT,+,0.00)
chunk0003_135_1	chr1	32759391	32759810	+	0	NA	intron (NM_020888, intron 1 of 6)	intron (NM_020888, intron 1 of 6)	-6034	NM_001198973	57648	Hs.591502	NM_020888	ENSG00000162522	KIAA1522	-	KIAA1522	protein-coding	0.014320	0.538095	
chunk0058_165_1	chr14	23328593	23329092	+	0	NA	Intergenic	L2c|LINE|L2	8654	NM_004643	8106	Hs.707712	NM_004643	ENSG00000100836	PABPN1	OPMD|PAB2|PABII|PABP-2|PABP2	poly(A) binding protein nuclear 1	protein-coding	0.014028	0.406000	300(CAGGACAAACTGTTCC,-,0.00),301(AGGACAAACTGTTCCT,+,0.00)
chunk0109_399_1	chr2	240308990	240309296	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-126555	NM_002081	2817	Hs.328232	NM_002081	ENSG00000063660	GPC1	glypican	glypican 1	protein-coding	0.003268	0.400651	
chunk0077_242_1	chr16	80718248	80718447	+	0	NA	intron (NM_152342, intron 1 of 6)	intron (NM_152342, intron 1 of 6)	85931	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.000000	0.315000	
chunk0134_365_1	chr3	182685848	182686461	+	0	NA	Intergenic	Intergenic	-107349	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.008157	0.333876	
chunk0089_354_1	chr18	66687589	66687832	+	0	NA	Intergenic	MER41-int|LTR|ERV1	-83572	NR_073130	28513	Hs.42771	NM_021153	ENSG00000071991	CDH19	CDH7|CDH7L2	cadherin 19	protein-coding	0.012346	0.459016	
chunk0200_278_1	chr9	22301176	22301911	+	0	NA	Intergenic	Intergenic	-145298	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.008163	0.350543	
chunk0172_339_1	chr6	138755204	138755458	+	0	NA	intron (NM_001242740, intron 2 of 3)	intron (NM_001242740, intron 2 of 3)	-18189	NM_015439	25901	Hs.412019	NM_015439	ENSG00000024862	CCDC28A	C6orf80|CCRL1AP	coiled-coil domain containing 28A	protein-coding	0.003937	0.360784	
chunk0143_181_1	chr4	112113049	112113311	+	0	NA	Intergenic	HAL1|LINE|L1	-32217	NM_152400	132720	Hs.23439	NM_152400	ENSG00000174749	FAM241A	C4orf32	family with sequence similarity 241 member A	protein-coding	0.007634	0.368821	
chunk0108_110_1	chr2	229612466	229613158	+	0	NA	intron (NM_139072, intron 1 of 12)	intron (NM_139072, intron 1 of 12)	101758	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.014451	0.408369	155(TGGAACATGCTGGGCT,-,0.00),156(GGAACATGCTGGGCTC,+,0.00)
chunk0159_397_1	chr5	147278235	147278512	+	0	NA	intron (NM_145001, intron 3 of 6)	intron (NM_145001, intron 3 of 6)	43357	NM_145001	202374	Hs.585069	NM_145001	ENSG00000169302	STK32A	YANK1	serine/threonine kinase 32A	protein-coding	0.007220	0.348921	
chunk0047_350_1	chr12	74980385	74981147	+	0	NA	Intergenic	Intergenic	228982	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.006562	0.346003	
chunk0129_217_1	chr3	121827802	121828005	+	0	NA	intron (NM_001023571, intron 4 of 11)	intron (NM_001023571, intron 4 of 11)	7176	NM_001023570	9657	Hs.604110	NM_001023570	ENSG00000173226	IQCB1	NPHP5|PIQ|SLSN5	IQ motif containing B1	protein-coding	0.000000	0.308824	
chunk0161_85_1	chr5	167142873	167143294	+	0	NA	Intergenic	Intergenic	-141755	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.007126	0.409953	
chunk0119_167_1	chr22	43297539	43298405	+	0	NA	intron (NM_173050, intron 3 of 21)	intron (NM_173050, intron 3 of 21)	45416	NM_173050	80274	Hs.133995	NM_152514	ENSG00000159307	SCUBE1	-	signal peptide, CUB domain and EGF like domain containing 1	protein-coding	0.020785	0.538639	
chunk0205_319_1	chr9	112756758	112757118	+	0	NA	intron (NM_001012994, intron 1 of 8)	L1MA9|LINE|L1	6084	NM_001012994	401548	Hs.522350	NM_001012994	ENSG00000148158	SNX30	ATG24A	sorting nexin family member 30	protein-coding	0.008333	0.362881	
chunk0012_35_1	chr1	155105779	155106080	+	0	NA	Intergenic	L2a|LINE|L2	-21944	NM_004428	1942	Hs.516664	NM_004428	ENSG00000169242	EFNA1	B61|ECKLG|EFL1|EPLG1|LERK-1|LERK1|TNFAIP4	ephrin A1	protein-coding	0.009967	0.536424	122(GAGAACACAGTGTGCA,-,0.00),123(AGAACACAGTGTGCAT,+,0.00)
chunk0165_204_1	chr6	34650876	34651080	+	0	NA	intron (NM_024294, intron 2 of 4)	intron (NM_024294, intron 2 of 4)	45872	NM_024294	64771	Hs.643498	NM_022758	ENSG00000196821	ILRUN	C6orf106|FP852|dJ391O22.4	inflammation and lipid regulator with UBA-like and NBR1-like domains	protein-coding	0.000000	0.395122	
chunk0010_95_1	chr1	113780320	113780793	+	0	NA	intron (NM_018364, intron 2 of 6)	intron (NM_018364, intron 2 of 6)	-21401	NM_006608	10745	Hs.655824	NM_006608	ENSG00000116793	PHTF1	PHTF	putative homeodomain transcription factor 1	protein-coding	0.008457	0.337553	
chunk0139_359_1	chr4	60290321	60290542	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-632188	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.009050	0.382883	
chunk0099_318_1	chr2	99675622	99675870	+	0	NA	intron (NM_001025108, intron 10 of 23)	intron (NM_001025108, intron 10 of 23)	-185728	NM_016316	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.012097	0.497992	100(AGGAACTGTCTGTACT,-,0.00),101(GGAACTGTCTGTACTT,+,0.00)
chunk0045_442_1	chr12	53585716	53586113	+	0	NA	intron (NM_006856, intron 2 of 11)	intron (NM_006856, intron 2 of 11)	40082	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.005038	0.419598	221(AGGTACAGTATGTTCA,-,0.00),222(GGTACAGTATGTTCAA,+,0.00)
chunk0165_459_1	chr6	41083005	41083482	+	0	NA	intron (NM_002505, intron 3 of 9)	intron (NM_002505, intron 3 of 9)	10275	NM_021705	4800	Hs.10441	NM_002505	ENSG00000001167	NFYA	CBF-A|CBF-B|HAP2|NF-YA	nuclear transcription factor Y subunit alpha	protein-coding	0.000000	0.341004	
chunk0059_239_1	chr14	34548677	34549388	+	0	NA	Intergenic	AluJo|SINE|Alu	2318	NR_004430	26871		NR_004430	ENSG00000206652	RNU1-1	HSD1|HU1-1|RNU1|RNU1A|RNU1A3|RNU1G4|Rnu1a1|U1|U1A1	RNA, U1 small nuclear 1	snRNA	0.019691	0.476124	500(AGGAAGATAGTGTCCC,-,0.00)
chunk0148_175_1	chr5	7649112	7649951	+	0	NA	intron (NM_020546, intron 4 of 24)	intron (NM_020546, intron 4 of 24)	201959	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.002384	0.410714	481(AAGGCCAGAGTGTACC,-,0.00)
chunk0009_237_1	chr1	106879463	106879788	+	0	NA	Intergenic	L1M1|LINE|L1	-177020	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.009231	0.552147	
chunk0076_254_1	chr16	69259954	69260385	+	0	NA	exon (NM_006750, exon 3 of 7)	exon (NM_006750, exon 3 of 7)	-51215	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.009281	0.453704	124(AGGAACACGTTGATCC,-,0.00),125(GGAACACGTTGATCCT,+,0.00)
chunk0109_77_1	chr20	1901941	1902140	+	0	NA	intron (NM_080792, intron 2 of 8)	intron (NM_080792, intron 2 of 8)	6860	NM_001040023	140885	Hs.581021	NM_080792	ENSG00000198053	SIRPA	BIT|CD172A|MFR|MYD-1|P84|PTPNS1|SHPS1|SIRP	signal regulatory protein alpha	protein-coding	0.030151	0.440000	60(AGGTACACGATGTGCT,-,0.00),61(GGTACACGATGTGCTC,+,0.00),76(CGGCACAGGCTGAGCC,-,0.00),77(GGCACAGGCTGAGCCT,+,0.00)
chunk0049_396_1	chr12	96770135	96770733	+	0	NA	intron (NM_001306084, intron 60 of 67)	L1M6|LINE|L1	-136789	NM_001135177	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.003344	0.447412	
chunk0078_62_1	chr17	1469248	1469570	+	0	NA	intron (NM_001080779, intron 25 of 31)	intron (NM_001080779, intron 25 of 31)	-13142	NM_016823	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.059006	0.517028	
chunk0018_395_1	chr1	222600034	222600826	+	0	NA	Intergenic	Intergenic	10471	NR_110614	100506161	Hs.553851	NR_110613	ENSG00000225265	TAF1A-AS1	-	TAF1A antisense RNA 1	ncRNA	0.001263	0.354351	
chunk0196_189_1	chr8	106133565	106134112	+	0	NA	Intergenic	Intergenic	-73335	NR_125797	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.003656	0.324818	
chunk0072_297_1	chr15	98746241	98746609	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-38001	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.010870	0.468835	239(TAGCACACCTTGTACA,-,0.00),240(AGCACACCTTGTACAC,+,0.00)
chunk0036_371_1	chr11	67312566	67312985	+	0	NA	TTS (NM_017857)	TTS (NM_017857)	-5064	NR_024469	100130987	Hs.664585	NR_024469		LOC100130987	-	uncharacterized LOC100130987	ncRNA	0.026253	0.545238	
chunk0028_130_1	chr10	85181302	85181583	+	0	NA	Intergenic	Intergenic	17463	NR_120668	101929624	Hs.588831	NR_120667	ENSG00000237267	LINC01519	-	long intergenic non-protein coding RNA 1519	ncRNA	0.003559	0.446809	
chunk0011_311_1	chr1	151885473	151885793	+	0	NA	intron (NM_053055, intron 4 of 5)	intron (NM_053055, intron 4 of 5)	24252	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.003125	0.380062	
chunk0013_303_1	chr1	171250879	171251600	+	0	NA	intron (NM_001282693, intron 1 of 8)	LTR22B|LTR|ERVK	2768	NM_002021	2326	Hs.1424	NM_002021	ENSG00000010932	FMO1	-	flavin containing dimethylaniline monoxygenase 1	protein-coding	0.033287	0.463989	
chunk0094_137_1	chr2	4942634	4942863	+	0	NA	Intergenic	L2a|LINE|L2	-286526	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.013100	0.413043	
chunk0081_353_1	chr17	47588079	47588307	+	0	NA	intron (NM_006310, intron 9 of 22)	intron (NM_006310, intron 9 of 22)	57115	NM_006310	9520	Hs.443837	NM_006310	ENSG00000141279	NPEPPS	AAP-S|MP100|PSA	aminopeptidase puromycin sensitive	protein-coding	0.026316	0.349345	
chunk0098_257_1	chr2	75153316	75153783	+	0	NA	intron (NM_001058, intron 1 of 4)	intron (NM_001058, intron 1 of 4)	45970	NM_001058	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.002141	0.420940	
chunk0048_65_1	chr12	78662871	78663453	+	0	NA	Intergenic	Intergenic	-200831	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.006873	0.384220	422(AGGCAGAGACTGTTCT,-,0.00),423(GGCAGAGACTGTTCTT,+,0.00)
chunk0007_78_1	chr1	78374629	78375179	+	0	NA	Intergenic	L2b|LINE|L2	-116139	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.003636	0.411978	
chunk0046_224_1	chr12	59843316	59843686	+	0	NA	Intergenic	Intergenic	154164	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.008108	0.388140	
chunk0123_115_1	chr3	42424058	42424979	+	0	NA	Intergenic	Intergenic	-13916	NM_144634	131375	Hs.234895	NM_144634	ENSG00000157093	LYZL4	LYC4|LYZA	lysozyme like 4	protein-coding	0.008686	0.401302	
chunk0147_138_1	chr4	174579262	174579661	+	0	NA	Intergenic	Intergenic	-56563	NM_001256305	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.010025	0.375000	
chunk0055_162_1	chr13	60347527	60348102	+	0	NA	Intergenic	Intergenic	-48643	NM_001146071	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.005217	0.380208	
chunk0040_109_1	chr11	111946701	111946921	+	0	NA	intron (NM_001037954, intron 1 of 19)	intron (NM_001037954, intron 1 of 19)	9608	NM_001037954	85458	Hs.655626	NM_033425	ENSG00000150764	DIXDC1	CCD1	DIX domain containing 1	protein-coding	0.009091	0.466063	
chunk0122_5_1	chr3	27329314	27329988	+	0	NA	intron (NM_199347, intron 6 of 24)	intron (NM_199347, intron 6 of 24)	39809	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.007418	0.422222	259(AGGAACAACCAGTTCT,-,0.00),260(GGAACAACCAGTTCTT,+,0.00)
chunk0197_151_1	chr8	120418902	120419466	+	0	NA	intron (NM_014078, intron 5 of 6)	MIR|SINE|MIR	-26214	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.003546	0.283186	
chunk0104_102_1	chr2	172461738	172462065	+	0	NA	intron (NM_000210, intron 1 of 25)	intron (NM_000210, intron 1 of 25)	34346	NM_001079818	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.003058	0.490854	
chunk0126_245_1	chr3	79358306	79358774	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-53187	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.008547	0.351812	
chunk0049_152_1	chr12	91934351	91934615	+	0	NA	Intergenic	Intergenic	207230	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.007576	0.343396	
chunk0169_149_1	chr6	101631170	101631481	+	0	NA	intron (NM_001166247, intron 3 of 16)	intron (NM_001166247, intron 3 of 16)	232340	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.333333	
chunk0031_163_1	chr10	125303539	125304089	+	0	NA	Intergenic	L1MB7|LINE|L1	-142759	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.009091	0.366606	
chunk0124_53_1	chr3	52810932	52811612	+	0	NA	Intergenic	L2c|LINE|L2	-12663	NR_046615	100873993	Hs.602700	NR_046615	ENSG00000239799	ITIH4-AS1	-	ITIH4 antisense RNA 1	ncRNA	0.016176	0.572687	353(TAGCACACAGTGTCCT,-,0.00),354(AGCACACAGTGTCCTG,+,0.00),381(GGGCGCATGCTGTTCC,-,0.00),382(GGCGCATGCTGTTCCC,+,0.00)
chunk0031_406_1	chr10	131908110	131908763	+	0	NA	intron (NR_033191, intron 2 of 9)	intron (NR_033191, intron 2 of 9)	7792	NM_001291310	55844	Hs.380372	NM_018461	ENSG00000175470	PPP2R2D	B55D|B55delta|MDS026	protein phosphatase 2 regulatory subunit Bdelta	protein-coding	0.012251	0.426606	
chunk0105_90_1	chr2	184261456	184261655	+	0	NA	Intergenic	Intergenic	-117420	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.290000	
chunk0153_3_1	chr5	66703457	66703937	+	0	NA	intron (NM_198828, intron 1 of 5)	intron (NM_198828, intron 1 of 5)	107349	NM_001290228	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.002083	0.392931	
chunk0185_232_1	chr7	129360896	129361257	+	0	NA	intron (NM_001130720, intron 1 of 16)	MER5A1|DNA|hAT-Charlie	-7047	NM_001130723	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.005540	0.345304	
chunk0121_401_1	chr3	25478389	25478612	+	0	NA	intron (NM_001290216, intron 2 of 7)	MamRep137|DNA|TcMar-Tigger	20190	NM_001290217	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.013453	0.522321	
chunk0123_413_1	chr3	49357557	49357894	+	0	NA	exon (NM_000581, exon 2 of 2)	exon (NM_000581, exon 2 of 2)	633	NM_000581	2876	Hs.76686	NM_000581	ENSG00000233276	GPX1	GPXD|GSHPX1	glutathione peroxidase 1	protein-coding	0.071217	0.579882	
chunk0134_87_1	chr3	176674439	176674767	+	0	NA	Intergenic	L2|LINE|L2	-39071	NR_109968	100505547	Hs.253350	NR_109968		LINC01208	-	long intergenic non-protein coding RNA 1208	ncRNA	0.009146	0.352584	
chunk0045_380_1	chr12	52228388	52228655	+	0	NA	Intergenic	Intergenic	-4649	NM_005556	3855	Hs.411501	NM_005556	ENSG00000135480	KRT7	CK7|K2C7|K7|SCL	keratin 7	protein-coding	0.007491	0.399254	
chunk0141_294_1	chr4	86860772	86861193	+	0	NA	Intergenic	L1ME1|LINE|L1	-11719	NM_197965	345274	Hs.452996	NM_197965	ENSG00000145283	SLC10A6	SOAT	solute carrier family 10 member 6	protein-coding	0.002375	0.350711	
chunk0075_8_1	chr16	46762436	46763070	+	0	NA	intron (NM_001308301, intron 1 of 11)	intron (NM_001308301, intron 1 of 11)	493	NM_001308301	91807	Hs.130465	NM_182493	ENSG00000140795	MYLK3	MLCK|MLCK2|caMLCK	myosin light chain kinase 3	protein-coding	0.012618	0.439370	
chunk0208_186_1	chrX	17166535	17166804	+	0	NA	Intergenic	Intergenic	-208751	NM_198270	4810	Hs.201623	NM_198270	ENSG00000188158	NHS	CTRCT40|CXN|SCML1	NHS actin remodeling regulator	protein-coding	0.003717	0.440741	120(CAGAACATTGTGTGCC,-,0.00),121(AGAACATTGTGTGCCT,+,0.00)
chunk0148_107_1	chr5	4516280	4516773	+	0	NA	Intergenic	Intergenic	-256955	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.010142	0.419028	
chunk0087_7_1	chr18	30695068	30695487	+	0	NA	Intergenic	L1PA13|LINE|L1	347538	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.002387	0.559524	335(AAGGTCTGCCTGTGCC,-,0.00)
chunk0035_79_1	chr11	41934050	41934647	+	0	NA	Intergenic	Intergenic	219780	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.003350	0.386288	
chunk0189_169_1	chr8	23421346	23421790	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-17359	NM_002318	4017	Hs.626637	NM_002318	ENSG00000134013	LOXL2	LOR|LOR2|WS9-14	lysyl oxidase like 2	protein-coding	0.022523	0.442697	
chunk0113_38_1	chr20	49868447	49868718	+	0	NA	intron (NR_048540, intron 8 of 11)	intron (NR_048540, intron 8 of 11)	45157	NM_001135773	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.000000	0.466912	109(AGGACATTCTCTTCCT,+,0.00)
chunk0190_259_1	chr8	37109902	37111300	+	0	NA	Intergenic	L1PREC2|LINE|L1	326277	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.001431	0.370979	
chunk0030_218_1	chr10	114697322	114697537	+	0	NA	Intergenic	Intergenic	-12774	NM_001003408	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.032558	0.620370	
chunk0093_442_1	chr19	58381052	58381362	+	0	NA	promoter-TSS (NR_049780)	promoter-TSS (NR_049780)	-185	NM_138466	116412	Hs.222236	NM_138466	ENSG00000152475	ZNF837	-	zinc finger protein 837	protein-coding	0.090323	0.588424	
chunk0178_390_1	chr7	40418031	40418416	+	0	NA	intron (NM_024728, intron 9 of 14)	intron (NM_024728, intron 9 of 14)	283247	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.000000	0.370466	
chunk0185_374_1	chr7	133006819	133007223	+	0	NA	intron (NM_017812, intron 3 of 7)	HAL1b|LINE|L1	27894	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.004950	0.293827	
chunk0190_404_1	chr8	40370954	40371601	+	0	NA	Intergenic	LTR82A|LTR|ERVL	217809	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.010819	0.381173	291(CAGAACAGTGTGATCT,-,0.00),292(AGAACAGTGTGATCTT,+,0.00)
chunk0117_46_1	chr22	12601810	12602009	+	0	NA	Intergenic	CpG	704503	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.070352	0.590000	
chunk0079_122_1	chr17	12536084	12536549	+	0	NA	Intergenic	MIRb|SINE|MIR	-13652	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.006452	0.388412	
chunk0130_302_1	chr3	136976669	136976868	+	0	NA	intron (NM_144717, intron 1 of 6)	L1MA4A|LINE|L1	18903	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.005025	0.490000	
chunk0070_184_1	chr15	71833839	71834041	+	0	NA	intron (NM_006901, intron 39 of 41)	L1ME3B|LINE|L1	23392	NM_016346	10002	Hs.187354	NM_014249	ENSG00000278570	NR2E3	ESCS|PNR|RNR|RP37|rd7	nuclear receptor subfamily 2 group E member 3	protein-coding	0.000000	0.261084	
chunk0101_262_1	chr2	133438164	133438605	+	0	NA	intron (NM_207481, intron 3 of 17)	intron (NM_207481, intron 3 of 17)	130076	NM_207363	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.004535	0.357466	
chunk0132_248_1	chr3	158699480	158699986	+	0	NA	intron (NM_206963, intron 4 of 5)	intron (NM_206963, intron 4 of 5)	-27040	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.009881	0.447732	
chunk0070_55_1	chr15	69591870	69592322	+	0	NA	promoter-TSS (NR_126438)	promoter-TSS (NR_126438)	-104	NR_126438	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.002212	0.410596	
chunk0089_288_1	chr18	63157582	63158019	+	0	NA	intron (NM_000633, intron 2 of 2)	intron (NM_000633, intron 2 of 2)	161580	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.018307	0.417808	
chunk0039_164_1	chr11	99139626	99140067	+	0	NA	intron (NM_001243270, intron 1 of 23)	intron (NM_001243270, intron 1 of 23)	118870	NM_014361	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004535	0.242081	185(AAAAACTTTCTGTCCT,-,0.00),186(AAAACTTTCTGTCCTT,+,0.00)
chunk0022_199_1	chr10	13556776	13557056	+	0	NA	Intergenic	HAL1|LINE|L1	-30023	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.003571	0.313167	
chunk0134_306_1	chr3	180837168	180837784	+	0	NA	intron (NR_109986, intron 2 of 13)	L1PA12|LINE|L1	32702	NR_109986	101928882	Hs.734668	NR_109986	ENSG00000285336	LOC101928882	-	uncharacterized LOC101928882	ncRNA	0.006494	0.341977	
chunk0184_155_1	chr7	116220301	116220888	+	0	NA	intron (NM_015641, intron 1 of 6)	MIR|SINE|MIR	-2357	NM_152829	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.005111	0.375850	
chunk0058_463_1	chr13	114318878	114319214	+	0	NA	intron (NM_001164145, intron 1 of 2)	intron (NM_001164145, intron 1 of 2)	4556	NM_001164145	283489	Hs.7542	NM_032436	ENSG00000198824	CHAMP1	C13orf8|CAMP|CHAMP|MRD40|ZNF828	chromosome alignment maintaining phosphoprotein 1	protein-coding	0.000000	0.364985	
chunk0026_273_1	chr10	67114898	67115304	+	0	NA	intron (NM_001127384, intron 7 of 17)	intron (NM_001127384, intron 7 of 17)	102835	NR_111909	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.004926	0.402948	
chunk0092_138_1	chr19	28140623	28140829	+	0	NA	Intergenic	MER4C|LTR|ERV1	-346786	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.014563	0.405797	
chunk0058_106_1	chr14	21734475	21735061	+	0	NA	Intergenic	Intergenic	69685	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.011945	0.362862	245(CTGTACAAGGTGTTCT,-,0.00),246(TGTACAAGGTGTTCTA,+,0.00)
chunk0005_75_1	chr1	55965791	55966289	+	0	NA	Intergenic	Intergenic	613544	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.010040	0.356713	244(TGGGACATGAAGTTCT,-,0.00),245(GGGACATGAAGTTCTA,+,0.00)
chunk0066_160_1	chr15	32256515	32256734	+	0	NA	intron (NR_038253, intron 2 of 7)	L1MC5a|LINE|L1	86053	NR_026771	26082	Hs.652128	NR_026771	ENSG00000225930	LINC02249	DKFZP434L187	long intergenic non-protein coding RNA 2249	ncRNA	0.018265	0.377273	
chunk0075_401_1	chr16	56923889	56924247	+	0	NA	Intergenic	L1MB5|LINE|L1	-8022	NM_001010989	9709	Hs.146393	NM_014685	ENSG00000051108	HERPUD1	HERP|Mif1|SUP	homocysteine inducible ER protein with ubiquitin like domain 1	protein-coding	0.005587	0.398329	
chunk0160_121_1	chr5	150910335	150910838	+	0	NA	Intergenic	L1MEc|LINE|L1	-5603	NM_001172831	91975	Hs.134885	NM_052860	ENSG00000145908	ZNF300	-	zinc finger protein 300	protein-coding	0.007952	0.347222	
chunk0121_8_1	chr3	14460666	14460905	+	0	NA	intron (NM_001134367, intron 6 of 14)	intron (NM_001134367, intron 6 of 14)	58209	NM_003043	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.025105	0.608333	
chunk0168_337_1	chr6	92746131	92746415	+	0	NA	Intergenic	Intergenic	673309	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.010563	0.333333	
chunk0024_301_1	chr10	42427155	42427705	+	0	NA	intron (NR_103829, intron 5 of 8)	intron (NR_103829, intron 5 of 8)	44810	NR_103829	414194	Hs.568048	NR_103829	ENSG00000182632	CCNYL2	C10orf21|CCNYL2P|bA178A10.2	cyclin Y like 2 (pseudogene)	pseudo	0.005455	0.333938	
chunk0015_156_1	chr1	186513039	186513290	+	0	NA	Intergenic	Intergenic	-52056	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.000000	0.539683	
chunk0149_4_1	chr5	15657850	15658139	+	0	NA	intron (NM_012304, intron 2 of 3)	MLT1N2|LTR|ERVL-MaLR	-42992	NR_109945	101929472	Hs.662664	NR_109945		CTD-2350J17.1	-	uncharacterized LOC101929472	ncRNA	0.003460	0.400000	
chunk0113_206_1	chr20	53737925	53738801	+	0	NA	Intergenic	Intergenic	137346	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.026256	0.462942	
chunk0041_11_1	chr12	339446	339886	+	0	NA	intron (NM_001042603, intron 10 of 27)	intron (NM_001042603, intron 10 of 27)	-49684	NM_001130147	84318	Hs.631656	NM_032358	ENSG00000120647	CCDC77	-	coiled-coil domain containing 77	protein-coding	0.004545	0.344671	
chunk0100_165_1	chr2	109322094	109322520	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	-8682	NR_036224	100423027		NR_036224	ENSG00000265965	MIR4266	-	microRNA 4266	ncRNA	0.014085	0.475410	
chunk0177_69_1	chr7	21366012	21366671	+	0	NA	Intergenic	Intergenic	-61730	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.007587	0.371212	
chunk0193_172_1	chr8	74830623	74831091	+	0	NA	intron (NM_015886, intron 2 of 5)	intron (NM_015886, intron 2 of 5)	6320	NM_015886	51050	Hs.98558	NM_015886	ENSG00000137558	PI15	CRISP8|P24TI|P25TI	peptidase inhibitor 15	protein-coding	0.014957	0.390192	
chunk0162_55_1	chr6	1337753	1338183	+	0	NA	Intergenic	L3|LINE|CR1	25528	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.009302	0.392111	
chunk0084_67_1	chr17	74758172	74758794	+	0	NA	intron (NM_004252, intron 1 of 5)	intron (NM_004252, intron 1 of 5)	9870	NR_037409	100500847		NR_037409	ENSG00000284186	MIR3615	mir-3615	microRNA 3615	ncRNA	0.030547	0.613162	
chunk0083_210_1	chr17	66956931	66957432	+	0	NA	Intergenic	Intergenic	-7683	NM_014405	27092	Hs.514423	NM_014405	ENSG00000075461	CACNG4	-	calcium voltage-gated channel auxiliary subunit gamma 4	protein-coding	0.015968	0.372510	
chunk0010_235_1	chr1	116409044	116409740	+	0	NA	intron (NR_024125, intron 1 of 2)	intron (NR_024125, intron 1 of 2)	9167	NR_024126	84852	Hs.664752	NM_032766	ENSG00000203865	ATP1A1-AS1	ATP1A1OS|C1orf203	ATP1A1 antisense RNA 1	ncRNA	0.012931	0.502152	
chunk0074_298_1	chr16	29863230	29863724	+	0	NA	promoter-TSS (NM_001286586)	promoter-TSS (NM_001286586)	-189	NM_001286585	10423	Hs.121549	NM_006319	ENSG00000103502	CDIPT	PIS|PIS1	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	protein-coding	0.042510	0.549495	
chunk0003_433_1	chr1	41129149	41129675	+	0	NA	intron (NM_001031694, intron 6 of 15)	L1MB3|LINE|L1	30521	NM_001172222	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.007605	0.383302	
chunk0202_262_1	chr9	76943063	76943417	+	0	NA	Intergenic	Intergenic	-37153	NM_015225	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.011299	0.447887	313(GGAACGCTTTGTGCTT,+,0.00)
chunk0144_97_1	chr4	128450583	128450869	+	0	NA	intron (NR_125882, intron 1 of 8)	intron (NR_125882, intron 1 of 8)	22710	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.006993	0.449477	0(GGAACAGAAAGTGCTT,+,0.00)
chunk0048_143_1	chr12	80141502	80141754	+	0	NA	Intergenic	Intergenic	-67825	NM_173591	283310	Hs.723594	NM_173591	ENSG00000165899	OTOGL	C12orf64|DFNB84B	otogelin like	protein-coding	0.003968	0.403162	
chunk0055_418_1	chr13	74929397	74929762	+	0	NA	Intergenic	L1MB7|LINE|L1	310802	NR_027466	647288	Hs.567920	NR_027466	ENSG00000214249	CTAGE11P	-	CTAGE family member 11, pseudogene	pseudo	0.005479	0.327869	
chunk0187_278_1	chr7	155380736	155381337	+	0	NA	Intergenic	Intergenic	-13103	NR_103545	338436	Hs.521326	NR_103545	ENSG00000204960	BLACE	-	B cell acute lymphoblastic leukemia expressed	ncRNA	0.023295	0.481728	
chunk0152_140_1	chr5	59127786	59127985	+	0	NA	intron (NM_006203, intron 5 of 14)	intron (NM_006203, intron 5 of 14)	-88373	NM_001197222	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.030151	0.530000	58(AAGGACTCCCCGTTCC,-,0.00),59(AGGACTCCCCGTTCCT,+,0.00)
chunk0128_284_1	chr3	110909631	110910088	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	160100	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.000000	0.344978	
chunk0040_52_1	chr11	111137722	111138449	+	0	NA	Intergenic	Mam_R4|LINE|Dong-R4	-117897	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.001376	0.318681	
chunk0163_369_1	chr6	15953357	15953570	+	0	NA	Intergenic	Intergenic	-175623	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.004695	0.439252	
chunk0199_329_1	chr9	8768993	8769482	+	0	NA	intron (NM_002839, intron 11 of 45)	intron (NM_002839, intron 11 of 45)	-35291	NM_130391	5789	Hs.446083	NM_002839	ENSG00000153707	PTPRD	HPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA	protein tyrosine phosphatase receptor type D	protein-coding	0.010225	0.338776	
chunk0204_276_1	chr9	98358145	98358561	+	0	NA	intron (NM_005458, intron 13 of 18)	L1ME3D|LINE|L1	-102632	NM_018421	55357	Hs.371016	NM_018421	ENSG00000095383	TBC1D2	PARIS-1|PARIS1|TBC1D2A	TBC1 domain family member 2	protein-coding	0.007212	0.525180	
chunk0051_14_1	chr12	111560026	111560673	+	0	NA	intron (NM_001310121, intron 1 of 25)	MER2|DNA|TcMar-Tigger	39324	NM_001310123	6311	Hs.76253	NM_002973	ENSG00000204842	ATXN2	ATX2|SCA2|TNRC13	ataxin 2	protein-coding	0.009274	0.399691	
chunk0085_101_1	chr18	2741743	2741967	+	0	NA	intron (NM_015295, intron 28 of 47)	L2|LINE|L2	85968	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.004464	0.444444	
chunk0086_52_1	chr18	12954709	12954908	+	0	NA	intron (NM_001013437, intron 2 of 8)	L1MB7|LINE|L1	6824	NM_001013437	81929	Hs.301048	NM_031216	ENSG00000085415	SEH1L	SEC13L|SEH1A|SEH1B|Seh1	SEH1 like nucleoporin	protein-coding	0.005025	0.365000	
chunk0033_8_1	chr11	12381861	12382475	+	0	NA	intron (NM_018222, intron 1 of 12)	Tigger2b_Pri|DNA|TcMar-Tigger	4689	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.014658	0.352846	287(TGGTACAGTATGTACT,-,0.00),288(GGTACAGTATGTACTA,+,0.00)
chunk0039_414_1	chr11	107540952	107541151	+	0	NA	intron (NM_138775, intron 7 of 11)	intron (NM_138775, intron 7 of 11)	24684	NM_138775	91801	Hs.503763	NM_138775	ENSG00000137760	ALKBH8	ABH8|TRM9|TRMT9|TRMT9A	alkB homolog 8, tRNA methyltransferase	protein-coding	0.000000	0.370000	
chunk0199_208_1	chr9	4984349	4984661	+	0	NA	promoter-TSS (NM_004972)	promoter-TSS (NM_004972)	-740	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.070513	0.654952	
chunk0017_294_1	chr1	210419304	210419803	+	0	NA	intron (NM_001170580, intron 7 of 11)	intron (NM_001170580, intron 7 of 11)	90257	NM_001170580	55733	Hs.58650	NM_018194	ENSG00000054392	HHAT	MART2|SKI1|Skn	hedgehog acyltransferase	protein-coding	0.008016	0.416000	247(CAGATCAAGCTGTTCC,-,0.00),248(AGATCAAGCTGTTCCC,+,0.00)
chunk0125_355_1	chr3	71242230	71242566	+	0	NA	intron (NM_032682, intron 5 of 20)	intron (NM_032682, intron 5 of 20)	2767	NM_001244814	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.011905	0.415430	
chunk0045_448_1	chr12	53603795	53604362	+	0	NA	intron (NM_006856, intron 1 of 11)	intron (NM_006856, intron 1 of 11)	21918	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.001764	0.362676	
chunk0127_26_1	chr3	88564588	88564882	+	0	NA	Intergenic	Intergenic	-414869	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.003401	0.318644	
chunk0058_113_1	chr14	22057053	22057385	+	0	NA	Intergenic	L1PA16|LINE|L1	392136	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.009036	0.345345	
chunk0050_460_1	chr12	111070911	111071390	+	0	NA	intron (NM_015267, intron 1 of 21)	L1MC1|LINE|L1	37126	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.006263	0.366667	
chunk0032_69_1	chr11	2325680	2326125	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	23889	NM_139022	10077	Hs.271954	NM_005705	ENSG00000064201	TSPAN32	ART1|PHEMX|PHMX|TSSC6	tetraspanin 32	protein-coding	0.008989	0.486547	
chunk0104_108_1	chr2	172722500	172722823	+	0	NA	TTS (NR_026995)	TTS (NR_026995)	-13136	NM_007023	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.003096	0.404321	
chunk0073_79_1	chr16	3868680	3869137	+	0	NA	intron (NM_001079846, intron 1 of 29)	intron (NM_001079846, intron 1 of 29)	11212	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.015317	0.530568	
chunk0055_168_1	chr13	60509666	60510196	+	0	NA	intron (NM_030794, intron 9 of 13)	intron (NM_030794, intron 9 of 13)	112638	NM_001146070	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.005660	0.365348	
chunk0203_159_1	chr9	85834434	85834981	+	0	NA	intron (NR_029410, intron 5 of 8)	MER68|LTR|ERVL	28705	NR_029410	389765	Hs.715986	NR_029410		LOC389765	-	kinesin family member 27 pseudogene	pseudo	0.003656	0.430657	
chunk0113_213_1	chr20	53814649	53814891	+	0	NA	Intergenic	Intergenic	60939	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.008264	0.386831	
chunk0075_344_1	chr16	55369156	55369355	+	0	NA	Intergenic	Intergenic	44696	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.020101	0.370000	
chunk0041_46_1	chr11	123046510	123046764	+	0	NA	Intergenic	L2c|LINE|L2	11519	NR_003125	85391		NR_003125	ENSG00000200879	SNORD14E	-	small nucleolar RNA, C/D box 14E	snoRNA	0.003937	0.513725	118(TGGAACATGCTGTTCC,-,0.00),119(GGAACATGCTGTTCCC,+,0.00)
chunk0100_415_1	chr2	119810199	119810676	+	0	NA	intron (NM_002830, intron 2 of 26)	L1ME3B|LINE|L1	50806	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.004193	0.313808	
chunk0129_343_1	chr3	124837798	124838182	+	0	NA	intron (NM_002213, intron 5 of 14)	intron (NM_002213, intron 5 of 14)	49315	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.015625	0.490909	
chunk0204_345_1	chr9	101449259	101449646	+	0	NA	Intergenic	CpG	-13672	NM_000035	229	Hs.530274	NM_000035	ENSG00000136872	ALDOB	ALDB|ALDO2	aldolase, fructose-bisphosphate B	protein-coding	0.067183	0.634021	200(GGAACGGACTGATCCT,+,0.00)
chunk0183_251_1	chr7	107162791	107163259	+	0	NA	Intergenic	Intergenic	-5936	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.000000	0.321962	
chunk0076_440_1	chr16	73480530	73480760	+	0	NA	Intergenic	Intergenic	93840	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.004348	0.554113	35(GAGGGCAGAATGTGCC,-,0.00),36(AGGGCAGAATGTGCCT,+,0.00)
chunk0156_421_1	chr5	114374454	114374882	+	0	NA	intron (NM_001278204, intron 2 of 6)	intron (NM_001278204, intron 2 of 6)	12349	NM_021614	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.009346	0.331002	
chunk0194_45_1	chr8	81990407	81991019	+	0	NA	Intergenic	L1PA6|LINE|L1	-148427	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.026144	0.548124	591(CGGTACAGTCTGTCAC,-,0.00)
chunk0116_143_1	chr21	36347440	36347885	+	0	NA	intron (NM_015358, intron 8 of 16)	L2b|LINE|L2	27473	NM_015358	23515	Hs.421150	NM_015358	ENSG00000159256	MORC3	NXP2|ZCW5|ZCWCC3	MORC family CW-type zinc finger 3	protein-coding	0.004494	0.414798	
chunk0024_444_1	chr10	46558560	46559111	+	0	NA	Intergenic	L2b|LINE|L2	-2764	NM_014696	9721	Hs.523375	NM_014696	ENSG00000204175	GPRIN2	GRIN2|KIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding	0.009074	0.521739	
chunk0029_86_1	chr10	97109699	97110262	+	0	NA	intron (NM_003061, intron 4 of 36)	intron (NM_003061, intron 4 of 36)	7224	NR_038330	100505540	Hs.568878	NR_038330	ENSG00000234855	SLIT1-AS1	-	SLIT1 antisense RNA 1	ncRNA	0.012433	0.485816	423(GAGGACATTCTGTGCC,-,0.00),424(AGGACATTCTGTGCCT,+,0.00)
chunk0002_65_1	chr1	13871436	13871819	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	122246	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.005222	0.375000	
chunk0145_178_1	chr4	147636930	147637131	+	0	NA	TTS (NM_001304458)	TTS (NM_001304458)	19642	NM_018241	55751	Hs.203896	NM_018241	ENSG00000164168	TMEM184C	TMEM34	transmembrane protein 184C	protein-coding	0.004975	0.351485	
chunk0155_289_1	chr5	96173116	96173435	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	94137	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.006270	0.368750	
chunk0038_44_1	chr11	82250141	82250410	+	0	NA	intron (NR_120571, intron 3 of 7)	intron (NR_120571, intron 3 of 7)	153638	NR_120571	101928989	Hs.145117	NR_120571	ENSG00000245832	MIR4300HG	-	MIR4300 host gene	ncRNA	0.007435	0.340741	
chunk0163_270_1	chr6	13332394	13332699	+	0	NA	Intergenic	Intergenic	-3963	NM_001143966	51256	Hs.484678	NM_016495	ENSG00000145979	TBC1D7	MGCPH|PIG51|TBC7	TBC1 domain family member 7	protein-coding	0.006557	0.421569	
chunk0123_406_1	chr3	49132392	49132654	+	0	NA	exon (NM_002292, exon 2 of 32)	exon (NM_002292, exon 2 of 32)	643	NM_002292	3913	Hs.439726	NM_002292	ENSG00000172037	LAMB2	LAMS|NPHS5	laminin subunit beta 2	protein-coding	0.034351	0.642586	75(GTCACACCCTGTCCCC,+,0.00)
chunk0128_352_1	chr3	112984348	112984942	+	0	NA	Intergenic	MER68|LTR|ERVL	-6308	NM_138485	29083	Hs.127496	NM_014170	ENSG00000163607	GTPBP8	HSPC135	GTP binding protein 8 (putative)	protein-coding	0.003367	0.393277	
chunk0164_61_1	chr6	19376896	19377415	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-196675	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.003854	0.330769	
chunk0056_89_1	chr13	81326905	81327316	+	0	NA	Intergenic	Intergenic	-100127	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.002433	0.347087	
chunk0200_334_1	chr9	24132202	24132733	+	0	NA	Intergenic	Intergenic	-306402	NM_004432	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.003766	0.368421	223(GAGGACAAGGTGTCCA,-,0.00),224(AGGACAAGGTGTCCAG,+,0.00)
chunk0182_89_1	chr7	92795410	92795935	+	0	NA	intron (NM_001145306, intron 2 of 7)	intron (NM_001145306, intron 2 of 7)	38245	NM_001259	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.001905	0.325095	232(GAGAACTAACTGTGCC,-,0.00),233(AGAACTAACTGTGCCA,+,0.00)
chunk0206_138_1	chr9	121090389	121090945	+	0	NA	intron (NM_007018, intron 2 of 41)	MER58A|DNA|hAT-Charlie	2371	NM_007018	11064	Hs.653263	NM_007018	ENSG00000119397	CNTRL	CEP1|CEP110|FAN|bA165P4.1	centriolin	protein-coding	0.008993	0.371634	
chunk0190_341_1	chr8	39218390	39218589	+	0	NA	intron (NM_145004, intron 12 of 24).2	L1MA3|LINE|L1	-96174	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.005025	0.555000	
chunk0015_398_1	chr1	190950619	190950912	+	0	NA	Intergenic	Intergenic	325875	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.003413	0.353741	156(TAGGTCAGCATGTCCT,-,0.00),157(AGGTCAGCATGTCCTT,+,0.00)
chunk0073_379_1	chr16	15899733	15900082	+	0	NA	Intergenic	Intergenic	-11258	NM_001304498	123811	Hs.514179	NM_144600	ENSG00000133393	FOPNL	C16orf63|FOR20|PHSECRG2	FGFR1OP N-terminal like	protein-coding	0.008596	0.525714	
chunk0167_302_1	chr6	71365842	71366054	+	0	NA	Intergenic	Intergenic	11083	NR_029598	407032		NR_029598	ENSG00000199094	MIR30C2	MIRN30C2|mir-30c-2	microRNA 30c-2	ncRNA	0.000000	0.272300	
chunk0071_355_1	chr15	88638700	88639266	+	0	NA	5' UTR (NM_002201, exon 1 of 4)	5' UTR (NM_002201, exon 1 of 4)	240	NM_002201	3669	Hs.459265	NM_002201	ENSG00000172183	ISG20	CD25|HEM45	interferon stimulated exonuclease gene 20	protein-coding	0.044170	0.643739	
chunk0170_393_1	chr6	117387410	117387663	+	0	NA	intron (NM_002944, intron 13 of 42)	intron (NM_002944, intron 13 of 42)	38319	NM_002944	6098	Hs.1041	NM_002944	ENSG00000047936	ROS1	MCF3|ROS|c-ros-1	ROS proto-oncogene 1, receptor tyrosine kinase	protein-coding	0.003953	0.322835	
chunk0151_47_1	chr5	42360111	42360553	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	-63443	NM_000163	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.004525	0.354402	246(GGGGACTGTTTGTACT,-,0.00),247(GGGACTGTTTGTACTA,+,0.00)
chunk0020_435_1	chr1	241840249	241840506	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-7814	NM_130398	9156	Hs.498248	NM_003686	ENSG00000174371	EXO1	HEX1|hExoI	exonuclease 1	protein-coding	0.015564	0.449612	
chunk0092_311_1	chr19	34457860	34458323	+	0	NA	intron (NM_005499, intron 12 of 16)	intron (NM_005499, intron 12 of 16)	-23884	NM_001080436	126374	Hs.585010	NM_001080436	ENSG00000142279	WTIP	-	WT1 interacting protein	protein-coding	0.017279	0.409483	
chunk0105_287_1	chr2	189836854	189837053	+	0	NA	intron (NR_110332, intron 6 of 12)	intron (NR_110332, intron 6 of 12)	-52582	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.010050	0.340000	
chunk0067_218_1	chr15	45148798	45149179	+	0	NA	intron (NM_017434, intron 22 of 34)	intron (NM_017434, intron 22 of 34)	18994	NM_175940	53905	Hs.272813	NM_017434	ENSG00000137857	DUOX1	LNOX1|NOXEF1|THOX1	dual oxidase 1	protein-coding	0.002625	0.549738	
chunk0033_401_1	chr11	24567689	24568083	+	0	NA	intron (NM_001252008, intron 1 of 11)	L1M4b|LINE|L1	70916	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.291139	
chunk0031_413_1	chr10	132162805	132163068	+	0	NA	intron (NM_001105521, intron 18 of 23)	intron (NM_001105521, intron 18 of 23)	-23974	NM_006426	10570	Hs.100058	NM_006426	ENSG00000151640	DPYSL4	CRMP3|DRP-4|ULIP4	dihydropyrimidinase like 4	protein-coding	0.015209	0.625000	
chunk0089_422_1	chr18	69752800	69753204	+	0	NA	intron (NM_152721, intron 6 of 7)	LTR40a|LTR|ERVL	194851	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.004950	0.451852	
chunk0117_11_1	chr22	11066422	11066744	+	0	NA	Intergenic	REP522|Satellite|telo	-105054	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.046584	0.631579	
chunk0102_175_1	chr2	147518200	147518791	+	0	NA	Intergenic	Intergenic	-326022	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.381757	
chunk0183_6_1	chr7	102812051	102812346	+	0	NA	TTS (NM_001287150)	TTS (NM_001287150)	63246	NM_001145269	222234	Hs.202543	NM_147194	ENSG00000222011	FAM185A	-	family with sequence similarity 185 member A	protein-coding	0.013559	0.354730	
chunk0016_107_1	chr1	195894268	195894658	+	0	NA	Intergenic	MER70A|LTR|ERVL	688018	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.002564	0.447570	305(TAGGACATCCTGTTCT,-,0.00),306(AGGACATCCTGTTCTG,+,0.00)
chunk0174_64_1	chr6	155621388	155621917	+	0	NA	Intergenic	Intergenic	-165749	NM_015718	50508	Hs.247776	NM_015718	ENSG00000074771	NOX3	GP91-3|MOX-2	NADPH oxidase 3	protein-coding	0.001890	0.311321	
chunk0096_262_1	chr2	31528721	31529349	+	0	NA	intron (NM_000348, intron 4 of 4)	intron (NM_000348, intron 4 of 4)	51936	NM_000348	6716	Hs.458345	NM_000348	ENSG00000277893	SRD5A2	-	steroid 5 alpha-reductase 2	protein-coding	0.015924	0.446741	
chunk0078_336_1	chr17	8837480	8837822	+	0	NA	intron (NR_110865, intron 5 of 19)	intron (NR_110865, intron 5 of 19)	30026	NR_110865	146850	Hs.255809	NM_001010855	ENSG00000276231	PIK3R6	C17orf38|HsT41028|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase regulatory subunit 6	protein-coding	0.011696	0.533528	
chunk0062_393_1	chr14	74796410	74796741	+	0	NA	intron (NM_019589, intron 4 of 20)	L2c|LINE|L2	33209	NM_019589	56252	Hs.531111	NM_019589	ENSG00000119596	YLPM1	C14orf170|PPP1R169|ZAP113|ZAP3	YLP motif containing 1	protein-coding	0.000000	0.337349	
chunk0212_201_1	chrX	134570476	134570888	+	0	NA	intron (NM_001316889, intron 1 of 1)	intron (NM_001316889, intron 1 of 1)	20658	NR_038998	100506757	Hs.130961	NR_038998		LINC00629	LINC00629A|LINC00629B|LINC00629C|LINC00629D	long intergenic non-protein coding RNA 629	ncRNA	0.007282	0.426150	187(GGTACACAGCGTCCTG,+,0.00)
chunk0091_35_1	chr19	3603411	3603616	+	0	NA	intron (NM_201636, intron 1 of 3)	intron (NM_201636, intron 1 of 3)	3320	NM_001060	6915	Hs.442530	NM_001060	ENSG00000006638	TBXA2R	BDPLT13|TXA2-R	thromboxane A2 receptor	protein-coding	0.053659	0.631068	81(GGGACAAGGCGTTCCT,+,0.00)
chunk0121_344_1	chr3	24628374	24628869	+	0	NA	Intergenic	Intergenic	-107186	NR_039955									0.000000	0.300403	
chunk0189_419_1	chr8	27869197	27869782	+	0	NA	TTS (NM_173833)	TTS (NM_173833)	16627	NR_036249	100422828		NR_036249	ENSG00000265847	MIR4287	-	microRNA 4287	ncRNA	0.008547	0.467577	
chunk0143_208_1	chr4	113522083	113522686	+	0	NA	intron (NM_172114, intron 8 of 17)	intron (NM_172114, intron 8 of 17)	239543	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.003317	0.375828	
chunk0042_304_1	chr12	7907024	7907486	+	0	NA	Intergenic	Intergenic	-16059	NM_001286237	144195	Hs.655169	NM_153449	ENSG00000173262	SLC2A14	GLUT14|SLC2A3P3	solute carrier family 2 member 14	protein-coding	0.008658	0.457883	
chunk0160_408_1	chr5	163791146	163791946	+	0	NA	Intergenic	Intergenic	286018	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.005000	0.372035	
chunk0008_19_1	chr1	87554000	87554662	+	0	NA	Intergenic	Intergenic	-182676	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.003021	0.407240	
chunk0075_128_1	chr16	50098637	50098881	+	0	NA	intron (NM_182922, intron 12 of 14)	intron (NM_182922, intron 12 of 14)	32789	NM_182922	55027	Hs.733027	NM_017939	ENSG00000155393	HEATR3	SYO1	HEAT repeat containing 3	protein-coding	0.012295	0.220408	
chunk0107_363_1	chr2	222786065	222786807	+	0	NA	Intergenic	Intergenic	-74578	NM_004457	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.014825	0.403769	235(CAGGACATTTTGTACC,-,0.00),236(AGGACATTTTGTACCC,+,0.00)
chunk0052_411_1	chr12	131237071	131237706	+	0	NA	Intergenic	Intergenic	72377	NR_026670	116437	Hs.675497	NR_026670	ENSG00000204603	LINC01257	-	long intergenic non-protein coding RNA 1257	ncRNA	0.014173	0.473270	341(GAGGACACGTTGTCTC,-,0.00),342(AGGACACGTTGTCTCT,+,0.00)
chunk0191_37_1	chr8	43082567	43082772	+	0	NA	intron (NR_033698, intron 5 of 7)	intron (NR_033698, intron 5 of 7)	-10837	NM_032237	84197	Hs.491646	NM_032237	ENSG00000185900	POMK	MDDGA12|MDDGC12|SGK196	protein O-mannose kinase	protein-coding	0.014634	0.412621	
chunk0165_100_1	chr6	32274168	32274648	+	0	NA	Intergenic	Intergenic	-50341	NM_004557	4855	Hs.436100	NM_004557	ENSG00000204301	NOTCH4	INT3	notch receptor 4	protein-coding	0.004167	0.338877	160(GGAAACATTGTGTACT,-,0.00),161(GAAACATTGTGTACTT,+,0.00)
chunk0070_420_1	chr15	77817393	77818048	+	0	NA	intron (NM_001301186, intron 1 of 5)	intron (NM_001301186, intron 1 of 5)	1804	NM_001301191	84894	Hs.656765	NM_032808	ENSG00000169783	LINGO1	LERN1|LRRN6A|MRT64|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding	0.015267	0.530488	
chunk0150_441_1	chr5	40548540	40548889	+	0	NA	Intergenic	Intergenic	-131216	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.002865	0.325714	51(GAGCACACATAGTTCC,-,0.00),52(AGCACACATAGTTCCA,+,0.00)
chunk0043_312_1	chr12	22209126	22210042	+	0	NA	intron (NM_003034, intron 4 of 4)	L1ME3G|LINE|L1	125130	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.005459	0.339149	
chunk0110_123_1	chr20	13018016	13018778	+	0	NA	intron (NM_018327, intron 1 of 11)	intron (NM_018327, intron 1 of 11)	9418	NM_018327	55304	Hs.425023	NM_018327	ENSG00000172296	SPTLC3	C20orf38|LCB 3|LCB2B|LCB3|SPT 3|SPT3|SPTLC2L|dJ718P11|dJ718P11.1|hLCB2b	serine palmitoyltransferase long chain base subunit 3	protein-coding	0.001312	0.334207	
chunk0212_182_1	chrX	132862620	132863060	+	0	NA	intron (NM_001077188, intron 3 of 5)	intron (NM_001077188, intron 3 of 5)	98555	NM_001077188	90161	Hs.385956	NM_147175	ENSG00000171004	HS6ST2	MRXSPM	heparan sulfate 6-O-sulfotransferase 2	protein-coding	0.006818	0.392290	
chunk0203_449_1	chr9	91433228	91433467	+	0	NA	Intergenic	MIR|SINE|MIR	-8721	NM_001290000	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.004184	0.387500	
chunk0007_84_1	chr1	78490922	78491279	+	0	NA	promoter-TSS (NM_001039585)	promoter-TSS (NM_001039585)	57	NM_000959	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.103641	0.689944	
chunk0067_439_1	chr15	50006132	50006774	+	0	NA	intron (NR_073596, intron 8 of 27)	intron (NR_073596, intron 8 of 27)	106863	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.006231	0.345257	
chunk0143_329_1	chr4	120009496	120010076	+	0	NA	Intergenic	Intergenic	57072	NM_002358	4085	Hs.591697	NM_002358	ENSG00000164109	MAD2L1	HSMAD2|MAD2	mitotic arrest deficient 2 like 1	protein-coding	0.005172	0.425129	376(GGGACATCGAGTGCAT,+,0.00)
chunk0076_150_1	chr16	67192085	67192429	+	0	NA	promoter-TSS (NM_001950)	promoter-TSS (NM_001950)	92	NM_001950	1874	Hs.108371	NM_001950	ENSG00000205250	E2F4	E2F-4	E2F transcription factor 4	protein-coding	0.098837	0.724638	
chunk0110_285_1	chr20	17646148	17646613	+	0	NA	intron (NM_001042576, intron 4 of 25)	MER102a|DNA|hAT-Charlie	35903	NM_004587	6238	Hs.472213	NM_004587	ENSG00000125844	RRBP1	ES/130|ES130|RRp|hES	ribosome binding protein 1	protein-coding	0.021505	0.523605	
chunk0002_155_1	chr1	18058711	18059630	+	0	NA	Intergenic	Intergenic	-6487	NR_125946	101927876	Hs.522954	NR_125946	ENSG00000261781	LINC01654	-	long intergenic non-protein coding RNA 1654	ncRNA	0.013058	0.526087	631(AGGAAGAATCTGTTCT,-,0.00)
chunk0186_411_1	chr7	146128419	146128978	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	12337	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.003578	0.289286	
chunk0194_14_1	chr8	81524710	81525160	+	0	NA	TTS (NM_001105281)	TTS (NM_001105281)	6380	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.013333	0.345898	
chunk0116_453_1	chr21	43786534	43787452	+	0	NA	Intergenic	CpG	-2544	NM_003683	8568	Hs.110757	NM_003683	ENSG00000160214	RRP1	D21S2056E|NNP-1|NOP52|RRP1A	ribosomal RNA processing 1	protein-coding	0.056645	0.576714	
chunk0024_154_1	chr10	35432754	35432953	+	0	NA	intron (NM_001282853, intron 2 of 10)	intron (NM_001282853, intron 2 of 10)	95979	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.000000	0.330000	104(GGGCTCAGTGTGTTCC,-,0.00),105(GGCTCAGTGTGTTCCT,+,0.00)
chunk0162_420_1	chr5	180071935	180072354	+	0	NA	promoter-TSS (NM_001280801)	promoter-TSS (NM_001280801)	-26	NM_018434	55819	Hs.484363	NM_018434	ENSG00000113269	RNF130	G1RZFP|GOLIATH|GP	ring finger protein 130	protein-coding	0.119332	0.723810	152(CGGAACACAAAGTCCC,-,0.00),153(GGAACACAAAGTCCCT,+,0.00)
chunk0192_188_1	chr8	63244512	63244810	+	0	NA	Intergenic	L2a|LINE|L2	75658	NM_001277814	253943	Hs.491861	NM_152758	ENSG00000185728	YTHDF3	-	YTH N6-methyladenosine RNA binding protein 3	protein-coding	0.006711	0.391304	
chunk0173_359_1	chr6	149332792	149333363	+	0	NA	intron (NM_015093, intron 1 of 8)	L2c|LINE|L2	14777	NM_015093	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.012259	0.365385	
chunk0088_285_1	chr18	49560530	49560986	+	0	NA	Intergenic	CpG	-1273	NM_001308006	9388	Hs.465102	NM_006033	ENSG00000101670	LIPG	EDL|EL|PRO719	lipase G, endothelial type	protein-coding	0.065789	0.590810	127(AGGGACAAAGCGTGCT,-,0.00),128(GGGACAAAGCGTGCTC,+,0.00)
chunk0189_238_1	chr8	24576071	24576506	+	0	NA	Intergenic	Intergenic	-27670	NR_125808	101929294	Hs.637673	NR_125808		LOC101929294	-	uncharacterized LOC101929294	ncRNA	0.011494	0.408257	
chunk0072_408_1	chr15	100893734	100894305	+	0	NA	exon (NM_000693, exon 6 of 13)	exon (NM_000693, exon 6 of 13)	14327	NM_000693	220	Hs.459538	NM_000693	ENSG00000184254	ALDH1A3	ALDH1A6|ALDH6|MCOP8|RALDH3	aldehyde dehydrogenase 1 family member A3	protein-coding	0.019264	0.524476	274(GGGAACACCATGGTCC,-,0.00),275(GGAACACCATGGTCCT,+,0.00)
chunk0068_387_1	chr15	58528740	58528986	+	0	NA	intron (NM_000236, intron 1 of 8)	intron (NM_000236, intron 1 of 8)	-30128	NR_120338	101928694	Hs.655781	NR_120338	ENSG00000259293	LIPC-AS1	-	LIPC antisense RNA 1	ncRNA	0.008130	0.514170	
chunk0040_450_1	chr11	121649740	121650268	+	0	NA	Intergenic	L2a|LINE|L2	197801	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.015152	0.485822	
chunk0182_51_1	chr7	91910803	91911497	+	0	NA	Intergenic	L2a|LINE|L2	-29725	NM_005751	10142	Hs.651221	NM_005751	ENSG00000127914	AKAP9	AKAP-9|AKAP350|AKAP450|CG-NAP|HYPERION|LQT11|MU-RMS-40.16A|PPP1R45|PRKA9|YOTIAO	A-kinase anchoring protein 9	protein-coding	0.005764	0.407194	252(GAGAACACTAAGTGCA,-,0.00),253(AGAACACTAAGTGCAC,+,0.00)
chunk0028_372_1	chr10	92799757	92800175	+	0	NA	Intergenic	Intergenic	-34747	NM_001013848	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.011962	0.367542	
chunk0140_161_1	chr4	69561046	69561299	+	0	NA	Intergenic	L1M1|LINE|L1	-35158	NM_001297616	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.015810	0.283465	
chunk0172_56_1	chr6	134166671	134167272	+	0	NA	Intergenic	Intergenic	7925	NM_005627	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.004992	0.410299	
chunk0080_54_1	chr17	21667128	21667957	+	0	NA	Intergenic	Intergenic	-24981	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.007238	0.473494	719(GGGGACACTGAGTGCA,-,0.00),720(GGGACACTGAGTGCAG,+,0.00)
chunk0102_67_1	chr2	142944157	142944601	+	0	NA	intron (NM_001032998, intron 4 of 11)	intron (NM_001032998, intron 4 of 11)	66753	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.002252	0.346067	
chunk0045_158_1	chr12	46633605	46633816	+	0	NA	intron (NR_125377, intron 3 of 3)	L1MC1|LINE|L1	192287	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.004739	0.372642	
chunk0059_412_1	chr14	37864869	37865436	+	0	NA	Intergenic	Intergenic	269953	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.010582	0.478873	
chunk0094_47_1	chr2	2867904	2868178	+	0	NA	Intergenic	Intergenic	257985	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.021898	0.487273	
chunk0013_33_1	chr1	166698450	166698653	+	0	NA	Intergenic	L1ME4b|LINE|L1	94635	NR_002925	116123	Hs.348539	NM_138784	ENSG00000215834	FMO9P	-	flavin containing dimethylaniline monoxygenase 9, pseudogene	pseudo	0.000000	0.318627	
chunk0121_128_1	chr3	17805468	17806054	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-64854	NM_014744	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.003413	0.471891	
chunk0050_171_1	chr12	103827894	103828161	+	0	NA	intron (NM_001031701, intron 1 of 13)	L3|LINE|CR1	13170	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.003745	0.414179	
chunk0176_338_1	chr7	17558811	17559717	+	0	NA	promoter-TSS (NR_110013)	promoter-TSS (NR_110013)	-355	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.005519	0.392503	
chunk0200_193_1	chr9	19918604	19918814	+	0	NA	Intergenic	Intergenic	-131690	NM_001193288	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.004762	0.507109	
chunk0003_326_1	chr1	38440975	38441409	+	0	NA	Intergenic	L1MEc|LINE|L1	-226425	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.004608	0.402299	
chunk0206_370_1	chr9	125951905	125952261	+	0	NA	intron (NM_001134778, intron 5 of 8)	intron (NM_001134778, intron 5 of 8)	203884	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.310924	
chunk0154_35_1	chr5	77057572	77058102	+	0	NA	intron (NM_018046, intron 11 of 13)	MER70A|LTR|ERVL	22734	NR_003014	677828	Hs.693249	NR_003014	ENSG00000238961	SNORA47	HBI-115	small nucleolar RNA, H/ACA box 47	snoRNA	0.003774	0.453861	236(AAGGACATCCTGTTTC,-,0.00),237(AGGACATCCTGTTTCC,+,0.00)
chunk0038_15_1	chr11	80921023	80921887	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-158652	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.004630	0.353757	455(AAGAACATAAAGTACA,-,0.00),456(AGAACATAAAGTACAT,+,0.00)
chunk0099_9_1	chr2	82731778	82732290	+	0	NA	Intergenic	LTR33|LTR|ERVL	-124769	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007812	0.360624	
chunk0007_205_1	chr1	81414406	81414730	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	143134	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.030864	0.486154	113(CAGAACAGGATGTGCT,-,0.00),114(AGAACAGGATGTGCTG,+,0.00)
chunk0034_23_1	chr11	26228037	26228398	+	0	NA	intron (NM_001313726, intron 1 of 27)	intron (NM_001313726, intron 1 of 27)	39094	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.008310	0.386740	16(AGAGACAGTGTGTGCT,-,0.00),17(GAGACAGTGTGTGCTA,+,0.00),242(TAGTACAATCTGTTCT,-,0.00),243(AGTACAATCTGTTCTA,+,0.00)
chunk0146_434_1	chr4	169508761	169509170	+	0	NA	intron (NM_001199397, intron 19 of 35)	intron (NM_001199397, intron 19 of 35)	103662	NM_001199400	4750	Hs.481181	NM_012224	ENSG00000137601	NEK1	ALS24|NY-REN-55|SRPS2|SRPS2A|SRTD6	NIMA related kinase 1	protein-coding	0.002445	0.365854	
chunk0062_134_1	chr14	68672785	68673547	+	0	NA	Intergenic	Intergenic	120748	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.006562	0.397117	698(ATGCACATACTGTACA,-,0.00),699(TGCACATACTGTACAC,+,0.00)
chunk0108_214_1	chr2	233372279	233372514	+	0	NA	intron (NM_152879, intron 1 of 29)	intron (NM_152879, intron 1 of 29)	-15758	NM_003648	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.004255	0.385593	
chunk0090_360_1	chr18	76895344	76895543	+	0	NA	intron (NM_001306089, intron 10 of 30)	intron (NM_001306089, intron 10 of 30)	71283	NM_007345	7776	Hs.719137	NM_007345	ENSG00000130856	ZNF236	ZNF236A|ZNF236B	zinc finger protein 236	protein-coding	0.025126	0.530000	
chunk0032_195_1	chr11	6603415	6603869	+	0	NA	promoter-TSS (NM_001278442)	promoter-TSS (NM_001278442)	8	NM_015324	23378	Hs.652255	NM_015324	ENSG00000132275	RRP8	KIAA0409|NML	ribosomal RNA processing 8	protein-coding	0.112335	0.718681	
chunk0004_89_1	chr1	43783685	43783896	+	0	NA	intron (NM_001270465, intron 2 of 7)	intron (NM_001270465, intron 2 of 7)	-54832	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.014218	0.566038	
chunk0191_96_1	chr8	47763972	47764282	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-25963	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.019355	0.549839	
chunk0044_95_1	chr12	28443091	28443866	+	0	NA	intron (NM_018318, intron 7 of 11)	(TTCA)n|Simple_repeat|Simple_repeat	186278	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.002581	0.319588	
chunk0033_128_1	chr11	14676049	14676728	+	0	NA	intron (NM_000922, intron 1 of 15)	Tigger3c|DNA|TcMar-Tigger	32665	NM_000922	5140	Hs.445711	NM_000922	ENSG00000152270	PDE3B	HcGIP1|cGIPDE1	phosphodiesterase 3B	protein-coding	0.007364	0.348529	
chunk0184_65_1	chr7	112467804	112468214	+	0	NA	non-coding (NR_120333, exon 8 of 12)	non-coding (NR_120333, exon 8 of 12)	-12844	NM_001134468	286006	Hs.396189	NM_182597	ENSG00000181016	LSMEM1	C7orf53	leucine rich single-pass membrane protein 1	protein-coding	0.009756	0.379562	
chunk0062_57_1	chr14	67442597	67442845	+	0	NA	promoter-TSS (NR_049879)	promoter-TSS (NR_049879)	-791	NR_049879	100847064		NR_049879	ENSG00000265993	MIR5694	-	microRNA 5694	ncRNA	0.008065	0.497992	
chunk0093_152_1	chr19	46967703	46968162	+	0	NA	intron (NM_004491, intron 2 of 5)	L2c|LINE|L2	49256	NM_004491	2909	Hs.509447	NM_004491	ENSG00000160007	ARHGAP35	GRF-1|GRLF1|P190-A|P190A|p190ARhoGAP|p190RhoGAP	Rho GTPase activating protein 35	protein-coding	0.019608	0.515217	
chunk0020_10_1	chr1	231674308	231674841	+	0	NA	intron (NM_001164556, intron 1 of 4)	intron (NM_001164556, intron 1 of 4)	47759	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.003752	0.380150	353(GGGTACACAGAGTACC,-,0.00),354(GGTACACAGAGTACCT,+,0.00)
chunk0098_363_1	chr2	78000656	78000945	+	0	NA	intron (NR_110288, intron 1 of 3)	intron (NR_110288, intron 1 of 3)	-45774	NR_024342	100170221	Hs.717311	NR_024342		SNAR-H	snaR-2	small NF90 (ILF3) associated RNA H	snRNA	0.006920	0.275862	
chunk0081_276_1	chr17	44076626	44077313	+	0	NA	TTS (NM_138387)	TTS (NM_138387)	6239	NR_028581	92579	Hs.294005	NM_138387	ENSG00000141349	G6PC3	SCN4|UGRP	glucose-6-phosphatase catalytic subunit 3	protein-coding	0.007278	0.543605	364(AAGCACACTATGAACC,-,0.00)
chunk0178_386_1	chr7	40282800	40283304	+	0	NA	intron (NM_024728, intron 8 of 14)	L1MA7|LINE|L1	148076	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.005952	0.372277	
chunk0115_176_1	chr21	25735097	25735310	+	0	NA	5' UTR (NM_002040, exon 1 of 10)	5' UTR (NM_002040, exon 1 of 10)	185	NM_002040	2551	Hs.473470	NM_002040	ENSG00000154727	GABPA	E4TF1-60|E4TF1A|NFT2|NRF2|NRF2A|RCH04A07	GA binding protein transcription factor subunit alpha	protein-coding	0.051643	0.504673	
chunk0095_318_1	chr2	20468918	20469327	+	0	NA	Intergenic	Intergenic	22051	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.014670	0.458537	
chunk0049_442_1	chr12	98596036	98596289	+	0	NA	intron (NM_002635, intron 3 of 7)	intron (NM_002635, intron 3 of 7)	2537	NM_005888	5250	Hs.290404	NM_002635	ENSG00000075415	SLC25A3	OK/SW-cl.48|PHC|PTP	solute carrier family 25 member 3	protein-coding	0.003953	0.366142	
chunk0055_239_1	chr13	62858538	62858971	+	0	NA	Intergenic	Intergenic	-51395	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.004619	0.304147	
chunk0012_391_1	chr1	163585803	163586347	+	0	NA	Intergenic	Intergenic	-162884	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.009191	0.357798	
chunk0081_345_1	chr17	47188862	47189171	+	0	NA	intron (NM_001114091, intron 1 of 18)	CpG	296	NM_001114091	996	Hs.463295	NM_001256	ENSG00000004897	CDC27	ANAPC3|APC3|CDC27Hs|D0S1430E|D17S978E|H-NUC|HNUC|NUC2	cell division cycle 27	protein-coding	0.071197	0.625806	
chunk0105_77_1	chr2	183872161	183872901	+	0	NA	Intergenic	MER67C|LTR|ERV1	-506444	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.002703	0.360324	396(AGGAAGATAGTGTCCC,-,0.00)
chunk0014_109_1	chr1	176813429	176813978	+	0	NA	intron (NM_020318, intron 21 of 22)	L1PA11|LINE|L1	215742	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.001821	0.327273	
chunk0001_321_1	chr1	9436134	9436814	+	0	NA	Intergenic	Intergenic	-7478	NR_104622	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.005882	0.458150	348(CAGTACACGATGTACA,-,0.00),349(AGTACACGATGTACAA,+,0.00)
chunk0126_253_1	chr3	79414816	79415148	+	0	NA	intron (NR_110133, intron 1 of 2)	intron (NR_110133, intron 1 of 2)	3255	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.006024	0.417417	
chunk0084_175_1	chr17	77508438	77508637	+	0	NA	Intergenic	Intergenic	33294	NM_001113495	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.000000	0.500000	
chunk0100_66_1	chr2	106561333	106561773	+	0	NA	Intergenic	Intergenic	-93208	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.020455	0.560091	
chunk0142_171_1	chr4	95336680	95337366	+	0	NA	intron (NM_003728, intron 1 of 15)	intron (NM_003728, intron 1 of 15)	212187	NM_003728	8633	Hs.388565	NM_003728	ENSG00000182168	UNC5C	UNC5H3	unc-5 netrin receptor C	protein-coding	0.002915	0.333333	
chunk0018_434_1	chr1	222911848	222912516	+	0	NA	intron (NM_032890, intron 2 of 9)	intron (NM_032890, intron 2 of 9)	97093	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.002994	0.378176	
chunk0176_111_1	chr7	11781343	11781760	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	50647	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.009592	0.373206	
chunk0105_399_1	chr2	192566093	192566948	+	0	NA	Intergenic	L1MC3|LINE|L1	-183325	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.001170	0.314252	
chunk0193_293_1	chr8	77653964	77654685	+	0	NA	Intergenic	Intergenic	203627	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.006935	0.333795	
chunk0047_182_1	chr12	70711662	70712291	+	0	NA	intron (NM_130846, intron 2 of 9)	intron (NM_130846, intron 2 of 9)	42632	NM_130846	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.006359	0.368254	
chunk0085_354_1	chr18	9136353	9136613	+	0	NA	promoter-TSS (NM_001083625)	promoter-TSS (NM_001083625)	237	NR_110772	101927275	Hs.656442	NR_110771	ENSG00000266053	NDUFV2-AS1	-	NDUFV2 antisense RNA 1	ncRNA	0.076923	0.647510	
chunk0193_4_1	chr8	70468967	70469511	+	0	NA	Intergenic	Intergenic	-1895	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.003676	0.337615	
chunk0173_241_1	chr6	146860894	146861476	+	0	NA	intron (NR_034115, intron 7 of 10)	intron (NR_034115, intron 7 of 10)	-57361	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.005155	0.409949	
chunk0046_54_1	chr12	55420596	55420843	+	0	NA	Intergenic	L1PA14|LINE|L1	-5535	NM_001005183	390326	Hs.553764	NM_001005183	ENSG00000185821	OR6C76	-	olfactory receptor family 6 subfamily C member 76	protein-coding	0.000000	0.548387	
chunk0186_161_1	chr7	139252889	139253239	+	0	NA	intron (NM_173569, intron 3 of 17)	intron (NM_173569, intron 3 of 17)	21579	NM_173569	254048	Hs.153458	NM_173569	ENSG00000157741	UBN2	-	ubinuclein 2	protein-coding	0.002857	0.330484	
chunk0006_37_1	chr1	64340492	64341286	+	0	NA	Intergenic	L2b|LINE|L2	-129904	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.005038	0.427673	290(AGGACACTGTGTTTAT,+,0.00)
chunk0206_269_1	chr9	124064063	124064491	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	52667	NM_004789	9355	Hs.696425	NM_004789	ENSG00000106689	LHX2	LH2|hLhx2	LIM homeobox 2	protein-coding	0.009346	0.361305	
chunk0178_20_1	chr7	29291195	29291692	+	0	NA	intron (NM_001293072, intron 1 of 12)	intron (NM_001293072, intron 1 of 12)	-82473	NR_120522	102724484	Hs.638665	NR_120522		LOC102724484	-	uncharacterized LOC102724484	ncRNA	0.008048	0.397590	311(GTGGTCAGACTGTTCC,-,0.00),312(TGGTCAGACTGTTCCC,+,0.00)
chunk0144_70_1	chr4	127708880	127709493	+	0	NA	intron (NM_015693, intron 13 of 15)	LTR16|LTR|ERVL	-21214	NM_031291	83447	Hs.149030	NM_031291	ENSG00000151475	SLC25A31	AAC4|ANT 4|ANT4|SFEC35kDa	solute carrier family 25 member 31	protein-coding	0.009788	0.438111	
chunk0048_453_1	chr12	88749474	88749683	+	0	NA	Intergenic	Intergenic	-169105	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.000000	0.309524	
chunk0061_42_1	chr14	56149214	56149498	+	0	NA	intron (NM_021255, intron 1 of 5)	intron (NM_021255, intron 1 of 5)	30981	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.010563	0.378947	
chunk0118_120_1	chr22	29517309	29518179	+	0	NA	intron (NM_001002877, intron 16 of 20)	intron (NM_001002877, intron 16 of 20)	35911	NM_001002878	8563	Hs.75361	NM_003678	ENSG00000100296	THOC5	C22orf19|Fmip|PK1.3|fSAP79	THO complex 5	protein-coding	0.010345	0.486797	
chunk0166_141_1	chr6	44917437	44917782	+	0	NA	intron (NM_181356, intron 12 of 12)	intron (NM_181356, intron 12 of 12)	280161	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.005797	0.407514	
chunk0042_441_1	chr12	12368717	12368962	+	0	NA	intron (NM_058169, intron 2 of 3)	(TTAT)n|Simple_repeat|Simple_repeat	11760	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.008163	0.369919	
chunk0078_423_1	chr16	89352425	89352685	+	0	NA	intron (NM_001256182, intron 3 of 13)	intron (NM_001256182, intron 3 of 13)	31422	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.011538	0.578544	
chunk0026_192_1	chr10	63664280	63664663	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	143108	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.013055	0.343750	
chunk0034_85_1	chr11	27396111	27396750	+	0	NA	intron (NM_018490, intron 2 of 17)	intron (NM_018490, intron 2 of 17)	-33182	NM_080654	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.006260	0.437500	
chunk0150_304_1	chr5	37717650	37717932	+	0	NA	intron (NM_018034, intron 13 of 17)	intron (NM_018034, intron 13 of 17)	117031	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.017730	0.420495	
chunk0156_108_1	chr5	105491614	105492160	+	0	NA	Intergenic	Intergenic	392413	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.297989	
chunk0053_342_1	chr13	34708753	34709424	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	-68403	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.002981	0.345238	
chunk0140_411_1	chr4	75726573	75726901	+	0	NA	intron (NM_001290049, intron 1 of 25)	intron (NM_001290049, intron 1 of 25)	2215	NM_001290049	8615	Hs.744877	NM_003715	ENSG00000138768	USO1	P115|TAP|VDP	USO1 vesicle transport factor	protein-coding	0.009146	0.392097	
chunk0137_408_1	chr4	27827240	27827650	+	0	NA	Intergenic	Intergenic	609966	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.000000	0.313869	
chunk0019_392_1	chr1	230308038	230308430	+	0	NA	Intergenic	Intergenic	117694	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.020408	0.539440	
chunk0082_108_1	chr17	54783894	54784093	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-116698	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.000000	0.345000	
chunk0104_421_1	chr2	180867043	180867504	+	0	NA	intron (NR_104320, intron 3 of 3)	L1M1|LINE|L1	-113112	NM_182678	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.006508	0.350649	
chunk0149_172_1	chr5	20694028	20694273	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-118277	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004082	0.418699	
chunk0037_56_1	chr11	70753017	70753659	+	0	NA	intron (NM_012309, intron 13 of 24)	L1MEf|LINE|L1	-91498	NM_133266	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.010903	0.356143	
chunk0198_205_1	chr8	133740162	133740613	+	0	NA	Intergenic	L2b|LINE|L2	36965	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.004435	0.484513	198(AGACACACCTTGTTCC,-,0.00),199(GACACACCTTGTTCCT,+,0.00)
chunk0092_370_1	chr19	36121821	36122064	+	0	NA	intron (NM_001281, intron 4 of 5)	CpG-14326	6114	NM_001300971	1155	Hs.31053	NM_001281	ENSG00000105254	TBCB	CG22|CKAP1|CKAPI	tubulin folding cofactor B	protein-coding	0.078189	0.655738	
chunk0184_143_1	chr7	115773058	115773356	+	0	NA	Intergenic	Intergenic	195106	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.006711	0.351171	
chunk0137_389_1	chr4	26975407	26976051	+	0	NA	intron (NM_020860, intron 3 of 11)	L1PA6|LINE|L1	115038	NM_001169117	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.013975	0.527132	
chunk0097_171_1	chr2	49701363	49701948	+	0	NA	Intergenic	Intergenic	-547128	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.011966	0.365188	
chunk0021_119_1	chr10	3551543	3552068	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	233110	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.026667	0.507605	216(AAGTACAGATTGTACC,-,0.00),217(AGTACAGATTGTACCA,+,0.00)
chunk0078_125_1	chr17	2995270	2995476	+	0	NA	exon (NM_001100398, exon 12 of 24)	exon (NM_001100398, exon 12 of 24)	-29478	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.038835	0.531401	
chunk0121_122_1	chr3	17498294	17498565	+	0	NA	intron (NM_014744, intron 3 of 21)	intron (NM_014744, intron 3 of 21)	201591	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.007380	0.301471	
chunk0098_73_1	chr2	67289108	67289513	+	0	NA	TTS (NR_110564)	TTS (NR_110564)	-73991	NR_038844	644838	Hs.145561	NR_038844	ENSG00000236780	LINC01829	-	long intergenic non-protein coding RNA 1829	ncRNA	0.002469	0.364532	320(GGTCCATTCTGTCCTT,+,0.00)
chunk0148_67_1	chr5	2118259	2118713	+	0	NA	Intergenic	Intergenic	193715	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.015419	0.479121	
chunk0041_136_1	chr11	125267224	125267423	+	0	NA	intron (NM_022062, intron 2 of 12)	intron (NM_022062, intron 2 of 12)	102660	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.020101	0.540000	
chunk0078_283_1	chr17	8031890	8032401	+	0	NA	Intergenic	FLAM_A|SINE|Alu	-6895	NM_001039130	247	Hs.111256	NM_001141	ENSG00000179593	ALOX15B	15-LOX-2	arachidonate 15-lipoxygenase type B	protein-coding	0.007828	0.406250	
chunk0059_418_1	chr14	38039366	38039586	+	0	NA	Intergenic	Intergenic	-168523	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.013636	0.384615	
chunk0111_188_1	chr20	25390900	25391172	+	0	NA	promoter-TSS (NM_015600)	promoter-TSS (NM_015600)	-54	NM_001042472	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.091912	0.736264	
chunk0098_12_1	chr2	65300992	65301481	+	0	NA	Intergenic	Intergenic	65561	NM_001128210	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.028630	0.530612	
chunk0123_61_1	chr3	41217108	41217468	+	0	NA	intron (NM_001098209, intron 1 of 15)	L2a|LINE|L2	17837	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.002778	0.385042	
chunk0008_304_1	chr1	95042090	95042828	+	0	NA	intron (NM_001305242, intron 2 of 4)	HAL1|LINE|L1	-19137	NR_132786	101928098	Hs.730090	NR_132786	ENSG00000230427	LOC101928098	-	uncharacterized LOC101928098	ncRNA	0.008130	0.415426	177(AAGCACTCATTGTCCT,-,0.00),178(AGCACTCATTGTCCTT,+,0.00)
chunk0164_406_1	chr6	26596703	26596972	+	0	NA	promoter-TSS (NM_013375)	promoter-TSS (NM_013375)	-106	NM_013375	29777	Hs.254406	NM_013375	ENSG00000146109	ABT1	Esf2|hABT1	activator of basal transcription 1	protein-coding	0.066914	0.581481	
chunk0166_49_1	chr6	42749142	42749471	+	0	NA	Intergenic	L1MA4|LINE|L1	-3160	NM_003192	6903	Hs.75064	NM_003192	ENSG00000124659	TBCC	CFC	tubulin folding cofactor C	protein-coding	0.003040	0.390909	
chunk0124_270_1	chr3	57412629	57413098	+	0	NA	intron (NM_001291661, intron 39 of 73)	L1MC1|LINE|L1	-120181	NM_001142733	142686	Hs.665154	NM_130387	ENSG00000239388	ASB14	-	ankyrin repeat and SOCS box containing 14	protein-coding	0.006397	0.361702	
chunk0009_75_1	chr1	100983629	100984188	+	0	NA	Intergenic	Intergenic	41898	NM_001077395	51611	Hs.440776	NM_015958	ENSG00000117543	DPH5	AD-018|CGI-30|HSPC143|NPD015	diphthamide biosynthesis 5	protein-coding	0.005367	0.375000	
chunk0048_155_1	chr12	80585083	80585721	+	0	NA	intron (NM_001145026, intron 25 of 44)	L2a|LINE|L2	-122227	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.001567	0.413146	
chunk0026_356_1	chr10	68901389	68901866	+	0	NA	intron (NM_024045, intron 1 of 14)	CpG	349	NM_024045	79009	Hs.522984	NM_024045	ENSG00000107625	DDX50	GU2|GUB|RH-II/GuB|mcdrh	DExD-box helicase 50	protein-coding	0.048218	0.592050	138(GGGAACTGTCTGTCCC,-,0.00),139(GGAACTGTCTGTCCCT,+,0.00)
chunk0145_293_1	chr4	149997859	149998542	+	0	NA	Intergenic	Intergenic	-80074	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.005857	0.444444	
chunk0044_235_1	chr12	31587968	31588368	+	0	NA	intron (NM_001308339, intron 1 of 22)	L2a|LINE|L2	-1755	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.005000	0.491272	
chunk0039_379_1	chr11	106819520	106819826	+	0	NA	intron (NM_001256424, intron 4 of 8)	Tigger1|DNA|TcMar-Tigger	198772	NM_000855	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.000000	0.325733	
chunk0199_181_1	chr9	4639335	4639927	+	0	NA	intron (NM_001039395, intron 3 of 10)	intron (NM_001039395, intron 3 of 10)	-22663	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.006757	0.382799	330(AAGAACTCAATGTTCT,-,0.00),331(AGAACTCAATGTTCTT,+,0.00)
chunk0107_315_1	chr2	219771968	219772515	+	0	NA	Intergenic	Intergenic	134324	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.014625	0.417883	
chunk0061_87_1	chr14	57004484	57004683	+	0	NA	Intergenic	MIR3|SINE|MIR	191400	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.005025	0.405000	36(GAGAACTGGGAGTTCT,-,0.00),37(AGAACTGGGAGTTCTA,+,0.00)
chunk0093_396_1	chr19	56846379	56847087	+	0	NA	intron (NR_024059, intron 1 of 1)	L1MEi|LINE|L1	5831	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.004237	0.301834	
chunk0147_370_1	chr4	185912671	185913480	+	0	NA	intron (NM_001270771, intron 1 of 23)	intron (NM_001270771, intron 1 of 23)	43641	NM_021069	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.008653	0.351852	
chunk0003_63_1	chr1	31187535	31188152	+	0	NA	intron (NM_024522, intron 2 of 6)	intron (NM_024522, intron 2 of 6)	52044	NM_024522	79570	Hs.470259	NM_024522	ENSG00000084628	NKAIN1	FAM77C	sodium/potassium transporting ATPase interacting 1	protein-coding	0.017828	0.525890	
chunk0185_169_1	chr7	127891866	127892332	+	0	NA	intron (NM_014390, intron 13 of 23)	intron (NM_014390, intron 13 of 23)	-105410	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.008584	0.466809	
chunk0039_79_1	chr11	97068717	97068916	+	0	NA	Intergenic	L1PA11|LINE|L1	-561939	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.005025	0.490000	
chunk0120_225_1	chr3	8145692	8146165	+	0	NA	Intergenic	Intergenic	-129621	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.010571	0.405063	
chunk0043_318_1	chr12	22318798	22319392	+	0	NA	intron (NM_003034, intron 1 of 4)	MIRb|SINE|MIR	15619	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.003367	0.366387	
chunk0205_261_1	chr9	110992341	110992805	+	0	NA	intron (NM_057159, intron 1 of 4)	L1ME1|LINE|L1	45512	NM_057159	1902	Hs.126667	NM_001401	ENSG00000198121	LPAR1	EDG2|GPR26|Gpcr26|LPA1|Mrec1.3|VZG1|edg-2|rec.1.3|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.002155	0.326882	
chunk0017_190_1	chr1	207323396	207323829	+	0	NA	intron (NR_125349, intron 2 of 10)	intron (NR_125349, intron 2 of 10)	2140	NM_001300904	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.006928	0.329493	
chunk0027_335_1	chr10	78491626	78491900	+	0	NA	Intergenic	L1MD1|LINE|L1	224435	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.021898	0.560000	
chunk0189_374_1	chr8	27316307	27316698	+	0	NA	intron (NM_173174, intron 3 of 35)	L1M5|LINE|L1	5020	NM_173174	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.007673	0.377551	
chunk0160_402_1	chr5	163527022	163527591	+	0	NA	Intergenic	HAL1|LINE|L1	21778	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.003515	0.384211	
chunk0084_107_1	chr17	75764491	75765042	+	0	NA	intron (NM_000154, intron 1 of 7)	CpG	433	NM_000154	2584	Hs.407966	NM_000154	ENSG00000108479	GALK1	GALK|GK1|HEL-S-19	galactokinase 1	protein-coding	0.078040	0.688406	314(GGGAACAGCCTGTCCC,-,0.00),315(GGAACAGCCTGTCCCG,+,0.00)
chunk0143_202_1	chr4	113064099	113064591	+	0	NA	intron (NM_020977, intron 1 of 44)	intron (NM_020977, intron 1 of 44)	14716	NM_001148	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.006098	0.415822	
chunk0120_183_1	chr3	6709135	6709653	+	0	NA	intron (NR_110123, intron 2 of 3)	AluSz|SINE|Alu	96055	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.011583	0.344894	
chunk0063_444_1	chr14	88961080	88961613	+	0	NA	Intergenic	Intergenic	137193	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.007505	0.443820	
chunk0177_2_1	chr7	20304400	20305018	+	0	NA	intron (NR_110117, intron 3 of 4)	MER67A|LTR|ERV1	8001	NR_110117	101927769	Hs.256080	NR_110117	ENSG00000226097	LOC101927769	-	uncharacterized LOC101927769	ncRNA	0.011327	0.420032	
chunk0207_434_1	chr9	137390455	137390896	+	0	NA	intron (NR_104598, intron 2 of 10)	intron (NR_104598, intron 2 of 10)	32587	NR_104598	54932	Hs.495553	NM_017820	ENSG00000187609	EXD3	mut-7	exonuclease 3'-5' domain containing 3	protein-coding	0.031746	0.542986	33(GATAACAGTATGTTCT,-,0.00),34(ATAACAGTATGTTCTG,+,0.00)
chunk0040_244_1	chr11	115198278	115198659	+	0	NA	intron (NM_001301045, intron 7 of 10)	intron (NM_001301045, intron 7 of 10)	306055	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.023622	0.416230	
chunk0101_139_1	chr2	127476180	127476579	+	0	NA	Intergenic	L1MB3|LINE|L1	50132	NM_017969	55677	Hs.469879	NM_017969	ENSG00000163166	IWS1	-	interacts with SUPT6H, CTD assembly factor 1	protein-coding	0.005013	0.332500	
chunk0061_306_1	chr14	61863210	61863704	+	0	NA	Intergenic	L1MC1|LINE|L1	101100	NM_003082	6617	Hs.179312	NM_003082	ENSG00000023608	SNAPC1	PTFgamma|SNAP43	small nuclear RNA activating complex polypeptide 1	protein-coding	0.008097	0.365657	
chunk0011_269_1	chr1	151137594	151137831	+	0	NA	exon (NM_001178061, exon 10 of 20)	exon (NM_001178061, exon 10 of 20)	8952	NM_001178061	10500	Hs.516316	NM_030913	ENSG00000143434	SEMA6C	SEMAY|m-SemaY|m-SemaY2	semaphorin 6C	protein-coding	0.012658	0.554622	
chunk0109_90_1	chr20	2102014	2102690	+	0	NA	intron (NM_080836, intron 1 of 3)	CpG	470	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.093195	0.649926	
chunk0072_402_1	chr15	100759767	100760815	+	0	NA	Intergenic	Intergenic	-119401	NM_001293815	220	Hs.459538	NM_000693	ENSG00000184254	ALDH1A3	ALDH1A6|ALDH6|MCOP8|RALDH3	aldehyde dehydrogenase 1 family member A3	protein-coding	0.015267	0.495710	
chunk0211_37_1	chrX	108488295	108488977	+	0	NA	intron (NM_033380, intron 1 of 50)	L1ME4b|LINE|L1	48792	NM_000495	1287	Hs.369089	NM_000495	ENSG00000188153	COL4A5	ASLN|ATS|ATS1|CA54	collagen type IV alpha 5 chain	protein-coding	0.001466	0.317716	570(AGGAACACTTTGTGTT,-,0.00),571(GGAACACTTTGTGTTT,+,0.00)
chunk0151_137_1	chr5	44697911	44698494	+	0	NA	Intergenic	Intergenic	110591	NR_109864	100506674	Hs.575213	NR_109862		MRPS30-DT	BRCAT54	MRPS30 divergent transcript	ncRNA	0.005146	0.301370	
chunk0058_66_1	chr14	20774372	20775049	+	0	NA	Intergenic	Intergenic	6283	NM_022360	64184	Hs.525202	NM_022360	ENSG00000181552	EDDM3B	EP3B|FAM12B|HE3-BETA|HE3B|RAM2	epididymal protein 3B	protein-coding	0.008863	0.417404	
chunk0049_380_1	chr12	95879367	95879589	+	0	NA	intron (NM_182496, intron 12 of 15)	intron (NM_182496, intron 12 of 15)	20547	NM_003095	6636	Hs.105465	NM_003095	ENSG00000139343	SNRPF	SMF|Sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding	0.022523	0.367713	
chunk0079_8_1	chr17	9217293	9217692	+	0	NA	intron (NM_004822, intron 5 of 6)	intron (NM_004822, intron 5 of 6)	-38374	NR_110828	101928266	Hs.639880	NR_110828	ENSG00000262966	LOC101928266	-	uncharacterized LOC101928266	ncRNA	0.010025	0.432500	
chunk0073_414_1	chr16	18801386	18801609	+	0	NA	promoter-TSS (NM_001313858)	promoter-TSS (NM_001313858)	-127	NM_001313858	23204	Hs.634882	NM_015161	ENSG00000170540	ARL6IP1	AIP1|ARL6IP|ARMER|SPG61	ADP ribosylation factor like GTPase 6 interacting protein 1	protein-coding	0.089686	0.669643	
chunk0192_182_1	chr8	63128828	63129465	+	0	NA	Intergenic	Intergenic	39296	NR_102684	101410533	Hs.163027	NR_102684	ENSG00000270673	YTHDF3-AS1	-	YTHDF3 antisense RNA 1 (head to head)	ncRNA	0.014129	0.394984	
chunk0074_407_1	chr16	35516477	35516934	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	-9535	NR_034018	100130700	Hs.97712	NR_034018		TP53TG3HP	-	TP53 target 3 family member H, pseudogene	pseudo	0.000000	0.406114	
chunk0107_73_1	chr2	212464198	212464617	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	-38047	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.004773	0.285714	
chunk0193_330_1	chr8	79096364	79097026	+	0	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-291172	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.006042	0.348416	
chunk0007_277_1	chr1	83715115	83715447	+	0	NA	intron (NR_119375, intron 2 of 2)	MIRb|SINE|MIR	145265	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.003012	0.393393	
chunk0187_193_1	chr7	151721696	151722059	+	0	NA	intron (NM_001040633, intron 3 of 15)	L2c|LINE|L2	14437	NM_001304527	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.013774	0.505495	
chunk0025_307_1	chr10	57638475	57638994	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-334175	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.005780	0.380769	
chunk0091_391_1	chr19	16143535	16143811	+	0	NA	non-coding (NR_111904, exon 3 of 6)	non-coding (NR_111904, exon 3 of 6)	9645	NR_111904	84941	Hs.631617	NM_032855	ENSG00000196684	HSH2D	ALX|HSH2	hematopoietic SH2 domain containing	protein-coding	0.028986	0.617329	
chunk0108_171_1	chr2	231568739	231569161	+	0	NA	Intergenic	Intergenic	-23914	NM_152614	165100	Hs.98104	NM_152614	ENSG00000177673	TEX44	C2orf57	testis expressed 44	protein-coding	0.007109	0.565012	180(CAGATCATCCAGTTCT,-,0.00),181(AGATCATCCAGTTCTT,+,0.00)
chunk0171_86_1	chr6	121866616	121867135	+	0	NA	Intergenic	MER34B|LTR|ERV1	431298	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.001927	0.396154	130(GGGAACACTCTGTCTC,-,0.00),131(GGAACACTCTGTCTCA,+,0.00)
chunk0181_81_1	chr7	80319271	80319836	+	0	NA	Intergenic	MER31-int|LTR|ERV1	54886	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.003540	0.284452	
chunk0032_2_1	chr11	240337	240817	+	0	NA	intron (NM_002817, intron 2 of 12)	intron (NM_002817, intron 2 of 12)	3769	NM_002817	5719	Hs.134688	NM_002817	ENSG00000185627	PSMD13	HSPC027|Rpn9|S11|p40.5	proteasome 26S subunit, non-ATPase 13	protein-coding	0.002083	0.357588	
chunk0124_369_1	chr3	59249197	59249701	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-199460	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.007937	0.415842	
chunk0185_419_1	chr7	134467841	134468670	+	0	NA	Intergenic	Intergenic	-9119	NM_001628	231	Hs.521212	NM_001628	ENSG00000085662	AKR1B1	ADR|ALDR1|ALR2|AR	aldo-keto reductase family 1 member B	protein-coding	0.015682	0.459036	
chunk0071_343_1	chr15	88119735	88120060	+	0	NA	intron (NM_002530, intron 13 of 18)	intron (NM_002530, intron 13 of 18)	-132833	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.009231	0.481595	247(AGGGACACTCTGTTCC,-,0.00),248(GGGACACTCTGTTCCA,+,0.00)
chunk0057_279_1	chr13	105991310	105991599	+	0	NA	Intergenic	L2c|LINE|L2	284624	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.003460	0.362069	
chunk0159_289_1	chr5	142753083	142753845	+	0	NA	intron (NR_110558, intron 1 of 3)	intron (NR_110558, intron 1 of 3)	7864	NR_110558	101926975	Hs.638583	NR_110558	ENSG00000236714	LINC01844	-	long intergenic non-protein coding RNA 1844	ncRNA	0.005249	0.456094	317(TTGAACAGAATGTACC,-,0.00),318(TGAACAGAATGTACCG,+,0.00)
chunk0094_82_1	chr2	3779614	3779840	+	0	NA	intron (NM_001287444, intron 9 of 10)	intron (NM_001287444, intron 9 of 10)	76135	NM_001287444	728597	Hs.304233	NM_001287444	ENSG00000214866	DCDC2C	-	doublecortin domain containing 2C	protein-coding	0.026549	0.506608	
chunk0083_114_1	chr17	64751277	64751980	+	0	NA	intron (NR_026899, intron 11 of 12)	intron (NR_026899, intron 11 of 12)	-29131	NR_106728	102464831		NR_106728	ENSG00000278581	MIR6080	hsa-mir-6080	microRNA 6080	ncRNA	0.008535	0.390625	382(AAGTACATTACGTCCT,-,0.00)
chunk0068_34_1	chr15	51060010	51060729	+	0	NA	intron (NM_001311175, intron 1 of 1)	MARNA|DNA|TcMar-Mariner	34336	NM_001311175	388121	Hs.306343	NM_207381	ENSG00000183578	TNFAIP8L3	TIPE3	TNF alpha induced protein 8 like 3	protein-coding	0.006954	0.433333	
chunk0086_244_1	chr18	22999477	23000108	+	0	NA	intron (NM_002894, intron 14 of 18)	L2c|LINE|L2	65916	NM_203291	5932	Hs.546282	NM_002894	ENSG00000101773	RBBP8	COM1|CTIP|JWDS|RIM|SAE2|SCKL2	RB binding protein 8, endonuclease	protein-coding	0.007924	0.337025	
chunk0098_315_1	chr2	76655190	76655681	+	0	NA	Intergenic	L1MC1|LINE|L1	-330530	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.002037	0.296748	
chunk0082_102_1	chr17	54698873	54699534	+	0	NA	Intergenic	Intergenic	-201488	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.006051	0.368580	256(AAGGACATCAAGTGCA,-,0.00),257(AGGACATCAAGTGCAT,+,0.00)
chunk0107_12_1	chr2	210147617	210147816	+	0	NA	intron (NM_001307976, intron 2 of 13)	intron (NM_001307976, intron 2 of 13)	23654	NM_001307976	151050	Hs.282260	NM_152519	ENSG00000144445	KANSL1L	C2orf67|MSL1v2	KAT8 regulatory NSL complex subunit 1 like	protein-coding	0.000000	0.295000	
chunk0156_102_1	chr5	105139266	105139620	+	0	NA	Intergenic	Intergenic	39969	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.005650	0.312676	
chunk0152_244_1	chr5	60758356	60758565	+	0	NA	intron (NM_024930, intron 7 of 8)	intron (NM_024930, intron 7 of 8)	-58294	NM_018369	55789	Hs.482233	NM_018369	ENSG00000035499	DEPDC1B	BRCC3|XTP1	DEP domain containing 1B	protein-coding	0.004785	0.295238	
chunk0096_139_1	chr2	28760399	28760617	+	0	NA	intron (NM_206876, intron 2 of 8)	Tigger3c|DNA|TcMar-Tigger	8748	NM_002709	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.000000	0.388128	21(AAGCACATTGTGTTAC,-,0.00)
chunk0050_214_1	chr12	104355167	104355411	+	0	NA	Intergenic	Intergenic	51557	NM_001008394	493861	Hs.659857	NM_001008394	ENSG00000255150	EID3	NS4EB|NSE4B|NSMCE4B	EP300 interacting inhibitor of differentiation 3	protein-coding	0.008197	0.420408	
chunk0110_36_1	chr20	10553993	10554679	+	0	NA	intron (NM_001009608, intron 2 of 7)	L1ME2|LINE|L1	95359	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.005831	0.352256	326(TGGCACAATTTGTTCT,-,0.00),327(GGCACAATTTGTTCTC,+,0.00)
chunk0213_4_1	chrY	19565228	19565732	+	0	NA	Intergenic	L1MB5|LINE|L1	-1878	NR_045128	246126	Hs.522863	NM_001005852	ENSG00000131002	TXLNGY	CYorf15A|CYorf15B|TXLNG2P	taxilin gamma pseudogene, Y-linked	pseudo	0.003968	0.354455	
chunk0197_304_1	chr8	124525619	124526111	+	0	NA	intron (NR_027427, intron 1 of 12)	intron (NR_027427, intron 1 of 12)	13223	NM_001146160	83940	Hs.170568	NM_032026	ENSG00000147687	TATDN1	CDA11	TatD DNase domain containing 1	protein-coding	0.006098	0.367140	
chunk0026_198_1	chr10	63692606	63692837	+	0	NA	Intergenic	Intergenic	171358	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.004329	0.383621	180(ATGAACAAAATGTTCC,-,0.00),181(TGAACAAAATGTTCCA,+,0.00)
chunk0020_394_1	chr1	240527643	240527919	+	0	NA	intron (NM_022469, intron 1 of 1)	MIRc|SINE|MIR	84381	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.010870	0.335740	
chunk0063_301_1	chr14	84650138	84650667	+	0	NA	Intergenic	L1PA7|LINE|L1	-743477	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003781	0.350943	
chunk0150_19_1	chr5	30580938	30581449	+	0	NA	Intergenic	Intergenic	-612462	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.005871	0.341797	
chunk0171_307_1	chr6	129217423	129217828	+	0	NA	intron (NM_001079823, intron 12 of 63)	intron (NM_001079823, intron 12 of 63)	334484	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.000000	0.334975	
chunk0072_389_1	chr15	100516807	100517502	+	0	NA	intron (NM_001290341, intron 3 of 13)	MIRb|SINE|MIR	27132	NM_001290342	204219	Hs.662371	NM_178842	ENSG00000154227	CERS3	ARCI9|LASS3	ceramide synthase 3	protein-coding	0.007194	0.462644	
chunk0043_131_1	chr12	15819788	15820477	+	0	NA	Intergenic	(AT)n|Simple_repeat|Simple_repeat	-30556	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.005806	0.376812	
chunk0011_370_1	chr1	153577850	153578188	+	0	NA	Intergenic	Intergenic	-12189	NM_005978	6273	Hs.516484	NM_005978	ENSG00000196754	S100A2	CAN19|S100L	S100 calcium binding protein A2	protein-coding	0.014793	0.519174	
chunk0093_158_1	chr19	47510097	47510386	+	0	NA	intron (NR_038456, intron 1 of 11)	intron (NR_038456, intron 1 of 11)	5017	NR_038456	8775	Hs.126938	NM_003827	ENSG00000105402	NAPA	SNAPA	NSF attachment protein alpha	protein-coding	0.024221	0.555172	266(CAGAACACCCTCTGCC,-,0.00)
chunk0141_190_1	chr4	83506363	83506812	+	0	NA	Intergenic	HERVH48-int|LTR|ERV1	-21450	NM_139076	84142	Hs.334772	NM_139076	ENSG00000163322	ABRAXAS1	ABRA1|CCDC98|FAM175A	abraxas 1, BRCA1 A complex subunit	protein-coding	0.017817	0.495556	
chunk0003_40_1	chr1	30664047	30664964	+	0	NA	Intergenic	Intergenic	-54267	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.022901	0.575163	
chunk0016_67_1	chr1	193542034	193542255	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	237399	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.004525	0.454955	
chunk0079_344_1	chr17	17734643	17734863	+	0	NA	intron (NM_030665, intron 2 of 5)	intron (NM_030665, intron 2 of 5)	31549	NR_130894	100861516	Hs.624874	NR_130894	ENSG00000237328	RAI1-AS1	-	RAI1 antisense RNA 1	ncRNA	0.036364	0.565611	
chunk0125_343_1	chr3	71110835	71111231	+	0	NA	intron (NM_032682, intron 7 of 20)	intron (NM_032682, intron 7 of 20)	19908	NM_001244815	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.010101	0.425693	
chunk0162_280_1	chr6	5756758	5757024	+	0	NA	intron (NM_006567, intron 6 of 6)	intron (NM_006567, intron 6 of 6)	-61619	NR_110842	101927950	Hs.571136	NR_110842	ENSG00000270174	LOC101927950	-	uncharacterized LOC101927950	ncRNA	0.011278	0.411985	
chunk0014_140_1	chr1	177898196	177898540	+	0	NA	Intergenic	Intergenic	71547	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.026163	0.417391	
chunk0025_86_1	chr10	50438530	50438738	+	0	NA	intron (NM_147156, intron 5 of 10)	MLT1F2|LTR|ERVL-MaLR	185343	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.004808	0.435407	
chunk0103_223_1	chr2	164407513	164407925	+	0	NA	Intergenic	L1MC3|LINE|L1	160831	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.002427	0.297821	149(GAGAACATCTTGTGCA,-,0.00),150(AGAACATCTTGTGCAG,+,0.00)
chunk0195_329_1	chr8	99076057	99076472	+	0	NA	intron (NR_047582, intron 4 of 8)	L1M2|LINE|L1	62998	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.002410	0.314904	
chunk0110_425_1	chr20	20743394	20744417	+	0	NA	Intergenic	Intergenic	-31282	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.018573	0.493164	
chunk0163_53_1	chr6	8793147	8793571	+	0	NA	Intergenic	Intergenic	141150	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.018868	0.432941	188(GAGTACGCAGTGTGCT,-,0.00),189(AGTACGCAGTGTGCTG,+,0.00)
chunk0069_314_1	chr15	65759815	65760255	+	0	NA	intron (NM_005848, intron 2 of 31)	L1ME4a|LINE|L1	32258	NM_001144823	10260	Hs.654567	NM_005848	ENSG00000174485	DENND4A	IRLB|MYCPBP	DENN domain containing 4A	protein-coding	0.004545	0.306122	
chunk0211_96_1	chrX	110703537	110704099	+	0	NA	intron (NM_001143983, intron 4 of 9)	intron (NM_001143983, intron 4 of 9)	92030	NM_145234	91851	Hs.496587	NM_145234	ENSG00000101938	CHRDL1	CHL|MGC1|MGCN|NRLN1|VOPT|dA141H5.1	chordin like 1	protein-coding	0.007117	0.419183	
chunk0147_269_1	chr4	183764392	183764708	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-33472	NR_132761	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.012658	0.561514	164(CGGGACAGGATGTGCT,-,0.00),165(GGGACAGGATGTGCTT,+,0.00)
chunk0070_280_1	chr15	74505911	74506234	+	0	NA	Intergenic	Intergenic	-35105	NM_006465	10620	Hs.647642	NM_006465	ENSG00000179361	ARID3B	BDP|DRIL2	AT-rich interaction domain 3B	protein-coding	0.015480	0.533951	
chunk0116_155_1	chr21	36508803	36509381	+	0	NA	intron (NM_001146077, intron 2 of 2)	MamTip3|DNA|hAT-Tip100	-29002	NM_001146079	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.019031	0.512953	
chunk0036_310_1	chr11	66113871	66114073	+	0	NA	intron (NM_018026, intron 1 of 23)	L1ME3G|LINE|L1	43619	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.009901	0.394089	
chunk0164_413_1	chr6	27020288	27020595	+	0	NA	promoter-TSS (NR_026776)	promoter-TSS (NR_026776)	-135	NR_026776	100270746	Hs.590428	NR_026776		LOC100270746	-	uncharacterized LOC100270746	ncRNA	0.048860	0.474026	
chunk0049_448_1	chr12	98877399	98877840	+	0	NA	intron (NM_001204067, intron 4 of 11)	intron (NM_001204067, intron 4 of 11)	17277	NM_001204080	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.006803	0.325792	
chunk0129_355_1	chr3	124923727	124924039	+	0	NA	intron (NM_033049, intron 2 of 11)	intron (NM_033049, intron 2 of 11)	10868	NM_033049	56667	Hs.5940	NM_033049	ENSG00000173702	MUC13	DRCC1|MUC-13	mucin 13, cell surface associated	protein-coding	0.000000	0.428115	
chunk0118_116_1	chr22	29378051	29378258	+	0	NA	intron (NM_145730, intron 1 of 20)	intron (NM_145730, intron 1 of 20)	10429	NM_001127	162	Hs.368794	NM_001127	ENSG00000100280	AP1B1	ADTB1|AP105A|BAM22|CLAPB2	adaptor related protein complex 1 subunit beta 1	protein-coding	0.014493	0.490385	
chunk0098_378_1	chr2	79117489	79118004	+	0	NA	Intergenic	Intergenic	-2712	NM_002909	5967	Hs.49407	NM_002909	ENSG00000115386	REG1A	ICRF|P19|PSP|PSPS|PSPS1|PTP|REG	regenerating family member 1 alpha	protein-coding	0.000000	0.317829	
chunk0170_22_1	chr6	109196320	109197243	+	0	NA	Intergenic	Intergenic	-39833	NM_001277339	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.005417	0.372294	
chunk0088_100_1	chr18	44989849	44990248	+	0	NA	intron (NM_015559, intron 4 of 5)	L1ME3E|LINE|L1	-19882	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.012531	0.310000	
chunk0162_177_1	chr6	3702881	3703082	+	0	NA	Intergenic	Intergenic	49031	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.009950	0.475248	
chunk0077_33_1	chr16	75342352	75342597	+	0	NA	intron (NM_006324, intron 5 of 6)	intron (NM_006324, intron 5 of 6)	-74421	NM_001170715	9564	Hs.479747	NM_014567	ENSG00000050820	BCAR1	CAS|CAS1|CASS1|CRKAS|P130Cas	BCAR1 scaffold protein, Cas family member	protein-coding	0.000000	0.434959	
chunk0108_71_1	chr2	227475648	227476051	+	0	NA	intron (NM_001135189, intron 1 of 11)	intron (NM_001135189, intron 1 of 11)	3677	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.009926	0.356436	
chunk0122_182_1	chr3	32648183	32648462	+	0	NA	Intergenic	Intergenic	-36823	NM_001256741	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.010753	0.435714	
chunk0114_291_1	chr21	16603748	16604353	+	0	NA	intron (NR_027790, intron 7 of 7)	intron (NR_027790, intron 7 of 7)	13813	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.004959	0.336634	
chunk0162_403_1	chr5	179821412	179821850	+	0	NA	intron (NM_003900, intron 1 of 7)	CpG	789	NM_003900	8878	Hs.587290	NM_003900	ENSG00000161011	SQSTM1	A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B	sequestosome 1	protein-coding	0.093607	0.669704	
chunk0046_103_1	chr12	57111823	57112391	+	0	NA	promoter-TSS (NM_001178081)	promoter-TSS (NM_001178081)	-694	NM_003153	6778	Hs.524518	NM_003153	ENSG00000166888	STAT6	D12S1644|IL-4-STAT|STAT6B|STAT6C	signal transducer and activator of transcription 6	protein-coding	0.017606	0.539543	
chunk0041_241_1	chr11	128491639	128492519	+	0	NA	intron (NM_001143820, intron 3 of 9)	intron (NM_001143820, intron 3 of 9)	30231	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.007955	0.414302	777(AGTCCAGGCTGTGCCC,+,0.00)
chunk0015_56_1	chr1	184608600	184609012	+	0	NA	intron (NM_030806, intron 5 of 5)	intron (NM_030806, intron 5 of 5)	146101	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.009709	0.513317	
chunk0056_146_1	chr13	83765714	83766312	+	0	NA	Intergenic	Intergenic	116380	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.005017	0.363940	248(AGGGACAGAGTGTTCC,-,0.00),249(GGGACAGAGTGTTCCT,+,0.00)
chunk0062_22_1	chr14	66540050	66540438	+	0	NA	intron (NM_001024218, intron 1 of 21)	MLT1I|LTR|ERVL-MaLR	32837	NM_020806	10243	Hs.208765	NM_020806	ENSG00000171723	GPHN	GEPH|GPH|GPHRYN|HKPX1|MOCODC	gephyrin	protein-coding	0.002577	0.424165	157(GGGCCATGCTGTTCTT,+,0.00)
chunk0023_396_1	chr10	30921316	30921935	+	0	NA	intron (NM_182755, intron 3 of 7)	L1M7|LINE|L1	77892	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.006462	0.367742	252(AGGCACACAGTGTCCT,-,0.00),253(GGCACACAGTGTCCTT,+,0.00)
chunk0165_285_1	chr6	36334964	36335163	+	0	NA	intron (NM_001010903, intron 1 of 11)	intron (NM_001010903, intron 1 of 11)	1822	NM_001010903	389384	Hs.162104	NM_001010903	ENSG00000189325	BNIP5	C6orf222	BCL2 interacting protein 5	protein-coding	0.015075	0.480000	
chunk0080_116_1	chr17	27136695	27136894	+	0	NA	Intergenic	L1ME2|LINE|L1	157202	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.000000	0.305000	
chunk0034_124_1	chr11	28288921	28289489	+	0	NA	intron (NM_001113528, intron 4 of 6)	intron (NM_001113528, intron 4 of 6)	180954	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.001761	0.342707	
chunk0203_31_1	chr9	82991788	82992172	+	0	NA	intron (NM_152573, intron 15 of 16)	L2a|LINE|L2	71148	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.007812	0.381818	
chunk0185_387_1	chr7	133399709	133399938	+	0	NA	intron (NM_001037126, intron 7 of 9)	intron (NM_001037126, intron 7 of 9)	108942	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.000000	0.434783	
chunk0140_25_1	chr4	65661476	65662026	+	0	NA	intron (NM_001281765, intron 1 of 17)	intron (NM_001281765, intron 1 of 17)	-8210	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.001818	0.415608	
chunk0070_403_1	chr15	77417598	77418149	+	0	NA	intron (NM_024776, intron 1 of 7)	intron (NM_024776, intron 1 of 7)	2231	NM_024776	79834	Hs.9587	NM_024776	ENSG00000173517	PEAK1	SGK269	pseudopodium enriched atypical kinase 1	protein-coding	0.007260	0.347826	
chunk0036_63_1	chr11	59617622	59618278	+	0	NA	Intergenic	L1MC5a|LINE|L1	-1806	NM_002556	5007	Hs.597091	NM_002556	ENSG00000110048	OSBP	OSBP1	oxysterol binding protein	protein-coding	0.003049	0.363775	
chunk0070_177_1	chr15	71653957	71654427	+	0	NA	intron (NM_001286429, intron 1 of 11)	MER58A|DNA|hAT-Charlie	37347	NR_120346	101929173	Hs.680593	NR_120346		THSD4-AS2	-	THSD4 antisense RNA 2	ncRNA	0.008511	0.369427	
chunk0110_100_1	chr20	11544053	11544299	+	0	NA	Intergenic	Intergenic	-270793	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.008130	0.368421	
chunk0182_146_1	chr7	95049010	95049736	+	0	NA	intron (NM_001166160, intron 2 of 19)	L1MC1|LINE|L1	139475	NM_001166162	55607	Hs.21816	NM_017650	ENSG00000158528	PPP1R9A	NRB1|NRBI|Neurabin-I	protein phosphatase 1 regulatory subunit 9A	protein-coding	0.002755	0.389271	
chunk0167_93_1	chr6	56991717	56992143	+	0	NA	intron (NM_152731, intron 2 of 6)	intron (NM_152731, intron 2 of 6)	36955	NM_152731	221336	Hs.582993	NM_152731	ENSG00000151917	BEND6	C6orf65	BEN domain containing 6	protein-coding	0.007042	0.374707	130(AGGTACTTCTTGTCCT,-,0.00),131(GGTACTTCTTGTCCTT,+,0.00)
chunk0070_166_1	chr15	71411938	71412579	+	0	NA	intron (NM_024817, intron 6 of 16)	intron (NM_024817, intron 6 of 16)	-134944	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.017161	0.464174	
chunk0133_391_1	chr3	174234374	174234683	+	0	NA	intron (NM_014932, intron 4 of 6)	MER50|LTR|ERV1	-313732	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.006472	0.429032	
chunk0160_417_1	chr5	164172937	164173181	+	0	NA	Intergenic	L2a|LINE|L2	294343	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.004098	0.400000	
chunk0084_112_1	chr17	75855309	75855565	+	0	NA	promoter-TSS (NM_012478)	promoter-TSS (NM_012478)	-17	NM_012478	23558	Hs.514489	NM_012478	ENSG00000132471	WBP2	DFNB107|GRAMD6|WBP-2	WW domain binding protein 2	protein-coding	0.058594	0.571984	
chunk0193_61_1	chr8	72795983	72796379	+	0	NA	intron (NM_004770, intron 2 of 2)	intron (NM_004770, intron 2 of 2)	64136	NR_110656	101926908	Hs.680588	NR_110656	ENSG00000253726	LOC101926908	-	uncharacterized LOC101926908	ncRNA	0.007576	0.370277	
chunk0143_217_1	chr4	113658904	113659412	+	0	NA	intron (NM_172114, intron 3 of 17)	intron (NM_172114, intron 3 of 17)	102769	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.005906	0.359528	
chunk0039_186_1	chr11	100753116	100753315	+	0	NA	intron (NM_152432, intron 1 of 23)	L1PBa|LINE|L1	-65260	NR_133571	100128386	Hs.635125	NR_133571	ENSG00000248027	LOC100128386	-	uncharacterized LOC100128386	ncRNA	0.010050	0.590000	
chunk0200_357_1	chr9	25537903	25538586	+	0	NA	Intergenic	Intergenic	140614	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.004392	0.368421	
chunk0204_221_1	chr9	97468588	97469141	+	0	NA	intron (NM_014290, intron 8 of 16)	intron (NM_014290, intron 8 of 16)	-32316	NM_001166116	7111	Hs.404289	NM_003275	ENSG00000136842	TMOD1	D9S57E|ETMOD|TMOD	tropomodulin 1	protein-coding	0.005425	0.471119	
chunk0186_83_1	chr7	137320996	137321424	+	0	NA	intron (NM_002825, intron 1 of 4)	intron (NM_002825, intron 1 of 4)	22590	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.009346	0.410256	
chunk0202_198_1	chr9	75231004	75231521	+	0	NA	Intergenic	Intergenic	142780	NM_012383	26578	Hs.494192	NM_012383	ENSG00000134996	OSTF1	OSF|SH3P2|bA235O14.1	osteoclast stimulating factor 1	protein-coding	0.005803	0.422780	
chunk0028_12_1	chr10	82392343	82392542	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-159522	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.005025	0.340000	
chunk0074_162_1	chr16	23393139	23393435	+	0	NA	exon (NM_153603, exon 15 of 17)	exon (NM_153603, exon 15 of 17)	59904	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.027027	0.488215	186(AGGGACATGATGTACT,-,0.00),187(GGGACATGATGTACTG,+,0.00)
chunk0116_381_1	chr21	42183922	42184121	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-15668	NM_207627	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.020101	0.495000	
chunk0103_351_1	chr2	168092393	168093024	+	0	NA	intron (NM_013233, intron 10 of 17)	intron (NM_013233, intron 10 of 17)	-151564	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.012678	0.393987	
chunk0184_129_1	chr7	114935158	114935458	+	0	NA	intron (NM_001166345, intron 2 of 4)	intron (NM_001166345, intron 2 of 4)	13154	NM_001166345	29969	Hs.741413	NM_199072	ENSG00000135272	MDFIC	HIC|MDFIC1	MyoD family inhibitor domain containing	protein-coding	0.000000	0.265781	
chunk0131_158_1	chr3	146429317	146429516	+	0	NA	Intergenic	MST-int|LTR|ERVL-MaLR	39885	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.010050	0.455000	
chunk0038_261_1	chr11	89147214	89147752	+	0	NA	Intergenic	Intergenic	-30389	NM_000372	7299	Hs.503555	NM_000372	ENSG00000077498	TYR	ATN|CMM8|OCA1|OCA1A|OCAIA|SHEP3	tyrosinase	protein-coding	0.001859	0.361781	
chunk0134_430_1	chr3	183465816	183466368	+	0	NA	Intergenic	Intergenic	18441	NR_038301	100505687	Hs.551751	NR_038301	ENSG00000240024	LINC00888	-	long intergenic non-protein coding RNA 888	ncRNA	0.016304	0.329114	
chunk0059_92_1	chr14	30898746	30899400	+	0	NA	intron (NM_001083893, intron 16 of 17)	L2a|LINE|L2	-9265	NR_038356	100506071	Hs.729195	NR_038356	ENSG00000258525	LOC100506071	-	uncharacterized LOC100506071	ncRNA	0.001529	0.374046	
chunk0027_171_1	chr10	74960412	74961189	+	0	NA	intron (NM_001256468, intron 4 of 17)	MIRb|SINE|MIR	97714	NM_001003892	338599	Hs.535090	NM_001003892	ENSG00000188716	DUPD1	DUSP27|FMDSP	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.003861	0.368895	
chunk0066_333_1	chr15	36667913	36668340	+	0	NA	intron (NM_032499, intron 6 of 11)	intron (NM_032499, intron 6 of 11)	73257	NM_001290232	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.000000	0.336449	
chunk0191_122_1	chr8	48371715	48371919	+	0	NA	Intergenic	Intergenic	-179750	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.000000	0.346341	
chunk0137_167_1	chr4	16140921	16141403	+	0	NA	Intergenic	Intergenic	-57162	NM_001145848	8842	Hs.614734	NM_006017	ENSG00000007062	PROM1	AC133|CD133|CORD12|MCDR2|MSTP061|PROML1|RP41|STGD4	prominin 1	protein-coding	0.000000	0.453416	274(GTGAACAGTGTGTGTC,-,0.00),275(TGAACAGTGTGTGTCT,+,0.00)
chunk0168_282_1	chr6	90723314	90723682	+	0	NA	Intergenic	Intergenic	-136197	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.005435	0.314363	
chunk0137_176_1	chr4	17463712	17464082	+	0	NA	Intergenic	MER67A|LTR|ERV1	48337	NM_001306140	5860	Hs.75438	NM_000320	ENSG00000151552	QDPR	DHPR|HDHPR|PKU2|SDR33C1	quinoid dihydropteridine reductase	protein-coding	0.002703	0.474394	
chunk0117_359_1	chr21	44764717	44765294	+	0	NA	Intergenic	Intergenic	36831	NM_001202489	7327	Hs.529420	NM_003343	ENSG00000184787	UBE2G2	UBC7	ubiquitin conjugating enzyme E2 G2	protein-coding	0.020797	0.624567	
chunk0128_277_1	chr3	110754353	110754567	+	0	NA	Intergenic	Intergenic	315499	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.004673	0.455814	
chunk0028_73_1	chr10	83729371	83729686	+	0	NA	Intergenic	Intergenic	-409901	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.316456	
chunk0128_266_1	chr3	110507564	110508112	+	0	NA	Intergenic	L1PB1|LINE|L1	562121	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.000000	0.344262	
chunk0003_310_1	chr1	37810887	37811300	+	0	NA	3' UTR (NM_005955, exon 11 of 11)	3' UTR (NM_005955, exon 11 of 11)	-2900	NM_024640	79693	Hs.301564	NM_024640	ENSG00000196449	YRDC	DRIP3|IRIP|SUA5	yrdC N6-threonylcarbamoyltransferase domain containing	protein-coding	0.007264	0.456522	215(AGGAACAATCTGTTCC,-,0.00),216(GGAACAATCTGTTCCT,+,0.00)
chunk0149_32_1	chr5	16350794	16351220	+	0	NA	Intergenic	LTR47B3|LTR|ERVL	90095	NR_104625	101929505	Hs.639360	NR_104625	ENSG00000248150	LINC02150	-	long intergenic non-protein coding RNA 2150	ncRNA	0.007042	0.430913	
chunk0174_429_1	chr6	166032759	166033266	+	0	NA	Intergenic	L1M4a2|LINE|L1	-44973	NR_026860	90632	Hs.31917	NR_026860	ENSG00000112541	LINC00473	C6orf176|LNC473|bA142J11.1	long intergenic non-protein coding RNA 473	ncRNA	0.011834	0.500000	
chunk0101_356_1	chr2	137937365	137937587	+	0	NA	Intergenic	Intergenic	-9544	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.009009	0.461883	
chunk0125_329_1	chr3	71025571	71025832	+	0	NA	intron (NM_032682, intron 11 of 20)	intron (NM_032682, intron 11 of 20)	39222	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.003831	0.339695	
chunk0018_147_1	chr1	218672530	218673065	+	0	NA	intron (NR_031644, intron 3 of 6)	intron (NR_031644, intron 3 of 6)	230171	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.007477	0.365672	265(GGGTACAGTCTGTCTT,-,0.00),266(GGTACAGTCTGTCTTC,+,0.00)
chunk0107_378_1	chr2	223219997	223220855	+	0	NA	Intergenic	Intergenic	168496	NM_080671	23704	Hs.348522	NM_080671	ENSG00000152049	KCNE4	MIRP3	potassium voltage-gated channel subfamily E regulatory subunit 4	protein-coding	0.011655	0.448196	441(ATGACAGCTTGTTCCC,+,0.00)
chunk0160_167_1	chr5	152526063	152526279	+	0	NA	Intergenic	L1MEd|LINE|L1	-120892	NM_020167	56923	Hs.731911	NM_020167	ENSG00000132911	NMUR2	FM-4|FM4|NMU-R2|NMU2R|TGR-1|TGR1	neuromedin U receptor 2	protein-coding	0.004630	0.396313	
chunk0025_312_1	chr10	57689782	57690132	+	0	NA	Intergenic	Intergenic	-385398	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.008571	0.370370	
chunk0160_176_1	chr5	153613902	153614190	+	0	NA	intron (NM_001258020, intron 3 of 16)	L2a|LINE|L2	121874	NM_001258021	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.017361	0.515571	
chunk0069_95_1	chr15	61328102	61328301	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-98898	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.005025	0.385000	
chunk0136_223_1	chr4	8175245	8175814	+	0	NA	Intergenic	MIRb|SINE|MIR	-16697	NM_032432	84448	Hs.233404	NM_032432	ENSG00000163995	ABLIM2	-	actin binding LIM protein family member 2	protein-coding	0.022847	0.507018	
chunk0209_44_1	chrX	36621609	36622227	+	0	NA	Intergenic	L1ME2|LINE|L1	-181626	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.004854	0.303716	
chunk0023_158_1	chr10	24264397	24264734	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	-11120	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.005935	0.366864	
chunk0153_247_1	chr5	72503113	72503408	+	0	NA	intron (NM_152625, intron 1 of 4)	intron (NM_152625, intron 1 of 4)	4162	NM_152625	167465	Hs.224794	NM_152625	ENSG00000178175	ZNF366	DC-SCRIPT|DCSCRIPT	zinc finger protein 366	protein-coding	0.010169	0.324324	200(GAGAACATCCAGTGCT,-,0.00),201(AGAACATCCAGTGCTG,+,0.00)
chunk0119_297_1	chr22	46348044	46348403	+	0	NA	intron (NM_001282783, intron 3 of 9)	intron (NM_001282783, intron 3 of 9)	12822	NM_001282782	55687	Hs.439524	NM_018006	ENSG00000100416	TRMU	LCAL3|MTO2|MTU1|TRMT|TRMT1	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	protein-coding	0.019499	0.500000	205(TAGAACACTGTGTGCC,-,0.00),206(AGAACACTGTGTGCCC,+,0.00)
chunk0009_388_1	chr1	110019689	110020195	+	0	NA	intron (NM_001242673, intron 15 of 16)	intron (NM_001242673, intron 15 of 16)	-11635	NM_001270768	85369	Hs.584996	NM_033088	ENSG00000143093	STRIP1	FAM40A|FAR11A	striatin interacting protein 1	protein-coding	0.001976	0.398422	
chunk0036_40_1	chr11	58926197	58926789	+	0	NA	Intergenic	HERVK22-int|LTR|ERVK	-1136	NM_001220494	92292	Hs.38085	NM_080661	ENSG00000166840	GLYATL1	GATF-C|GNAT	glycine-N-acyltransferase like 1	protein-coding	0.011824	0.389545	
chunk0203_283_1	chr9	88816583	88816999	+	0	NA	Intergenic	Intergenic	-70886	NR_036252	100423015		NR_036252	ENSG00000265873	MIR4289	-	microRNA 4289	ncRNA	0.007212	0.553957	153(AGGAACAAGGTGTGCC,-,0.00),154(GGAACAAGGTGTGCCA,+,0.00)
chunk0057_10_1	chr13	95541213	95541722	+	0	NA	intron (NM_182848, intron 1 of 4)	intron (NM_182848, intron 1 of 4)	-7557	NR_046533	100874194	Hs.569229	NR_046533	ENSG00000223392	CLDN10-AS1	-	CLDN10 antisense RNA 1	ncRNA	0.005894	0.427451	
chunk0006_122_1	chr1	65758132	65758681	+	0	NA	Intergenic	MER49|LTR|ERV1	-34104	NM_001037341	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.001821	0.396364	
chunk0095_86_1	chr2	15041544	15041930	+	0	NA	Intergenic	Intergenic	406646	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.015544	0.498708	
chunk0180_147_1	chr7	58033110	58033309	+	0	NA	Intergenic	Intergenic	583032	NM_001159279	441234	Hs.533121	NM_001159279	ENSG00000182111	ZNF716	-	zinc finger protein 716	protein-coding	0.035176	0.330000	
chunk0203_125_1	chr9	85118024	85118356	+	0	NA	Intergenic	Intergenic	447813	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.009036	0.363363	
chunk0144_459_1	chr4	142277169	142277681	+	0	NA	intron (NM_001101669, intron 9 of 25)	L1PB1|LINE|L1	569026	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.005859	0.354776	
chunk0179_35_1	chr7	43204392	43204723	+	0	NA	intron (NM_015052, intron 2 of 29)	L2b|LINE|L2	53662	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.003021	0.412651	
chunk0103_249_1	chr2	164956425	164957004	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-1189	NM_001199148	151258	Hs.658702	NM_173512	ENSG00000169507	SLC38A11	AVT2	solute carrier family 38 member 11	protein-coding	0.005181	0.327586	
chunk0195_343_1	chr8	99483696	99484021	+	0	NA	intron (NM_152564, intron 25 of 61)	MER91C|DNA|hAT-Tip100	52872	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.003077	0.349693	226(AAGGACATGATGGCCC,-,0.00)
chunk0144_204_1	chr4	133910283	133910482	+	0	NA	Intergenic	L1PBa|LINE|L1	291366	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005025	0.535000	
chunk0140_83_1	chr4	67928815	67929025	+	0	NA	intron (NM_001114387, intron 5 of 9)	intron (NM_001114387, intron 5 of 9)	34594	NM_001114387	339967	Hs.450110	NM_182606	ENSG00000187054	TMPRSS11A	ECRG1	transmembrane serine protease 11A	protein-coding	0.019048	0.383886	
chunk0028_315_1	chr10	91798177	91798415	+	0	NA	promoter-TSS (NM_025235)	promoter-TSS (NM_025235)	-5	NR_108071	100507633	Hs.291528	NR_108070	ENSG00000228701	TNKS2-AS1	-	TNKS2 antisense RNA 1 (head to head)	ncRNA	0.109244	0.631799	
chunk0186_25_1	chr7	135930513	135930905	+	0	NA	intron (NM_001128619, intron 3 of 3)	L2a|LINE|L2	46747	NM_145808	136319	Hs.602015	NM_145808	ENSG00000105887	MTPN	GCDP|V-1	myotrophin	protein-coding	0.012755	0.468193	
chunk0202_356_1	chr9	79990507	79990926	+	0	NA	intron (NR_121212, intron 3 of 4)	UCON105|Unknown|Unknown	15693	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.002387	0.361905	320(GGGGTCAGAGTGTTCT,-,0.00),321(GGGTCAGAGTGTTCTC,+,0.00)
chunk0058_295_1	chr14	26867098	26867689	+	0	NA	Intergenic	Intergenic	-5740	NR_110041	101927081	Hs.97955	NR_110041	ENSG00000257612	MIR4307HG	-	MIR4307 host gene	ncRNA	0.010152	0.359797	
chunk0162_416_1	chr5	179978458	179979192	+	0	NA	intron (NM_018434, intron 4 of 8)	intron (NM_018434, intron 4 of 8)	36572	NR_029885	442908		NR_029885	ENSG00000198995	MIR340	MIRN340|hsa-mir-340|mir-340	microRNA 340	ncRNA	0.006812	0.420408	
chunk0060_446_1	chr14	54789494	54789751	+	0	NA	3' UTR (NM_001161576, exon 11 of 11)	3' UTR (NM_001161576, exon 11 of 11)	34834	NM_001161577	23034	Hs.98259	NM_015589	ENSG00000020577	SAMD4A	SAMD4|SMAUG|SMAUG1|SMG|SMGA	sterile alpha motif domain containing 4A	protein-coding	0.011673	0.368217	
chunk0024_82_1	chr10	34356361	34356833	+	0	NA	intron (NM_019619, intron 14 of 24)	intron (NM_019619, intron 14 of 24)	458728	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.331924	
chunk0043_246_1	chr12	20339092	20339297	+	0	NA	Intergenic	Intergenic	-30051	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.004878	0.364078	
chunk0169_70_1	chr6	99032459	99032833	+	0	NA	Intergenic	Intergenic	-84640	NM_001278716	26235	Hs.536850	NM_012160	ENSG00000112234	FBXL4	FBL4|FBL5|MTDPS13	F-box and leucine rich repeat protein 4	protein-coding	0.005348	0.413333	292(GAGTACAGTGTGTCAC,-,0.00)
chunk0004_456_1	chr1	53526523	53526971	+	0	NA	intron (NM_147193, intron 4 of 9)	intron (NM_147193, intron 4 of 9)	67348	NM_033067	63948	Hs.131654	NM_033067	ENSG00000143006	DMRTB1	-	DMRT like family B with proline rich C-terminal 1	protein-coding	0.046875	0.603563	
chunk0181_362_1	chr7	88661844	88662503	+	0	NA	Intergenic	L1MC3|LINE|L1	-97195	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.007587	0.321212	
chunk0118_103_1	chr22	29281965	29282384	+	0	NA	intron (NM_001163286, intron 5 of 15)	intron (NM_001163286, intron 5 of 15)	14165	NM_013986	2130	Hs.374477	NM_005243	ENSG00000182944	EWSR1	EWS|EWS-FLI1|bK984G1.4	EWS RNA binding protein 1	protein-coding	0.014320	0.354762	
chunk0132_33_1	chr3	154758029	154758667	+	0	NA	Intergenic	Intergenic	-321299	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.007837	0.305164	
chunk0127_304_1	chr3	98733792	98734519	+	0	NA	intron (NM_001271145, intron 1 of 9)	intron (NM_001271145, intron 1 of 9)	1451	NM_001271145	10402	Hs.148716	NM_006100	ENSG00000064225	ST3GAL6	SIAT10|ST3GALVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding	0.026135	0.450549	
chunk0090_394_1	chr18	77733804	77734044	+	0	NA	Intergenic	Intergenic	259803	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.016667	0.531120	
chunk0019_339_1	chr1	229319889	229320354	+	0	NA	TTS (NM_145257)	TTS (NM_145257)	15739	NM_006542	10638	Hs.296169	NM_006542	ENSG00000213029	SPHAR	-	S-phase response (cyclin related)	protein-coding	0.010753	0.431330	
chunk0096_198_1	chr2	30203182	30203474	+	0	NA	Intergenic	Intergenic	-28203	NM_030915	81606	Hs.567598	NM_030915	ENSG00000213626	LBH	-	LBH regulator of WNT signaling pathway	protein-coding	0.010274	0.539249	
chunk0078_400_1	chr16	88738851	88739101	+	0	NA	non-coding (NR_103774, exon 3 of 3)	non-coding (NR_103774, exon 3 of 3)	-3791	NR_120387	339059	Hs.449817	NR_120387	ENSG00000182376	LOC339059	-	uncharacterized LOC339059	ncRNA	0.028000	0.637450	
chunk0071_208_1	chr15	84032494	84033064	+	0	NA	intron (NM_207517, intron 28 of 29)	L1ME3G|LINE|L1	-47408	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.000000	0.290718	
chunk0105_274_1	chr2	189541701	189541900	+	0	NA	Intergenic	Intergenic	39011	NM_014585	30061	Hs.643005	NM_014585	ENSG00000138449	SLC40A1	FPN1|HFE4|IREG1|MST079|MSTP079|MTP1|SLC11A3	solute carrier family 40 member 1	protein-coding	0.010050	0.445000	
chunk0161_220_1	chr5	170890579	170891286	+	0	NA	intron (NM_022897, intron 3 of 27)	FRAM|SINE|Alu	29050	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.004243	0.327684	
chunk0052_25_1	chr13	20476358	20476770	+	0	NA	intron (NM_015974, intron 3 of 7)	intron (NM_015974, intron 3 of 7)	-42718	NR_039721	100616304		NR_039721	ENSG00000263978	MIR4499	-	microRNA 4499	ncRNA	0.024272	0.486683	
chunk0124_187_1	chr3	55609698	55609900	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	49670	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.009901	0.408867	
chunk0164_172_1	chr6	21955377	21956008	+	0	NA	intron (NR_015410, intron 5 of 11)	intron (NR_015410, intron 5 of 11)	191501	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.014263	0.382911	
chunk0100_1_1	chr2	103656649	103657110	+	0	NA	Intergenic	L2c|LINE|L2	751453	NR_037885	100287010	Hs.694603	NR_037885		LOC100287010	-	uncharacterized LOC100287010	ncRNA	0.004338	0.346320	
chunk0159_145_1	chr5	139177890	139178848	+	0	NA	intron (NM_022464, intron 1 of 9)	intron (NM_022464, intron 1 of 9)	20007	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.003132	0.474453	
chunk0070_416_1	chr15	77507951	77508156	+	0	NA	Intergenic	Intergenic	87402	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.014634	0.524272	
chunk0123_330_1	chr3	47473350	47473885	+	0	NA	intron (NM_012235, intron 1 of 22)	intron (NM_012235, intron 1 of 22)	2338	NM_012235	22937	Hs.531789	NM_012235	ENSG00000114650	SCAP	-	SREBF chaperone	protein-coding	0.009346	0.440299	
chunk0209_227_1	chrX	45052695	45052952	+	0	NA	intron (NR_111960, intron 9 of 27)	AluJr|SINE|Alu	148078	NM_176819	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.027237	0.519380	
chunk0021_391_1	chr1	246597325	246597577	+	0	NA	intron (NM_152609, intron 2 of 10)	L1MB7|LINE|L1	31114	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.019841	0.415020	
chunk0105_332_1	chr2	191092944	191093740	+	0	NA	intron (NM_003151, intron 3 of 23)	L1PA6|LINE|L1	57918	NM_003151	6775	Hs.80642	NM_003151	ENSG00000138378	STAT4	SLEB11	signal transducer and activator of transcription 4	protein-coding	0.007538	0.505646	
chunk0051_211_1	chr12	116529073	116529434	+	0	NA	Intergenic	Intergenic	-4169	NR_027345	100287569	Hs.441601	NM_207436	ENSG00000196668	LINC00173	NCRNA00173	long intergenic non-protein coding RNA 173	ncRNA	0.019391	0.425414	
chunk0053_203_1	chr13	31945948	31946675	+	0	NA	intron (NR_027062, intron 2 of 3)	intron (NR_027062, intron 2 of 3)	-84989	NM_023037	10129	Hs.507669	NM_023037	ENSG00000073910	FRY	13CDNA73|214K23.2|C13orf14|CG003|bA207N4.2|bA37E23.1	FRY microtubule binding protein	protein-coding	0.006878	0.344780	
chunk0161_342_1	chr5	174104038	174104668	+	0	NA	intron (NM_015980, intron 4 of 4)	intron (NM_015980, intron 4 of 4)	58749	NM_015980	51617	Hs.559412	NM_015980	ENSG00000170091	NSG2	CALY3|HMP19	neuronal vesicle trafficking associated 2	protein-coding	0.014286	0.508716	
chunk0159_443_1	chr5	148398245	148398855	+	0	NA	intron (NM_030793, intron 2 of 21)	intron (NM_030793, intron 2 of 21)	14615	NM_001271723	81545	Hs.483772	NM_030793	ENSG00000145868	FBXO38	Fbx38|HMN2D|MOKA|SP329	F-box protein 38	protein-coding	0.004918	0.335516	305(GGGAGCAGAATGTCCC,-,0.00),306(GGAGCAGAATGTCCCT,+,0.00)
chunk0029_9_1	chr10	95360289	95360787	+	0	NA	intron (NM_001290298, intron 16 of 25)	MER57C2|LTR|ERV1	-69390	NM_020992	9124	Hs.368525	NM_020992	ENSG00000107438	PDLIM1	CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1	PDZ and LIM domain 1	protein-coding	0.000000	0.444890	
chunk0073_190_1	chr16	9020773	9021242	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-57523	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.008529	0.425532	
chunk0119_121_1	chr22	42682185	42682758	+	0	NA	Intergenic	LTR50|LTR|ERVL	-33072	NM_000398	1727	Hs.561064	NM_000398	ENSG00000100243	CYB5R3	B5R|DIA1	cytochrome b5 reductase 3	protein-coding	0.013962	0.541812	105(ATGGACACAGTGATCC,-,0.00),106(TGGACACAGTGATCCT,+,0.00)
chunk0001_253_1	chr1	8412319	8412977	+	0	NA	intron (NM_001042682, intron 2 of 12)	intron (NM_001042682, intron 2 of 12)	11039	NM_001042682	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.009119	0.418816	
chunk0113_2_1	chr20	49199963	49200391	+	0	NA	Intergenic	L1MC3|LINE|L1	-11810	NM_004602	6780	Hs.596704	NM_004602	ENSG00000124214	STAU1	PPP1R150|STAU	staufen double-stranded RNA binding protein 1	protein-coding	0.016355	0.433566	
chunk0094_58_1	chr2	3343014	3343464	+	0	NA	intron (NM_003310, intron 2 of 8)	intron (NM_003310, intron 2 of 8)	34643	NM_003310	7260	Hs.502770	NM_003310	ENSG00000032389	EIPR1	EIPR-1|TSSC1	EARP complex and GARP complex interacting protein 1	protein-coding	0.026667	0.527716	
chunk0095_375_1	chr2	23549152	23549382	+	0	NA	intron (NM_052920, intron 2 of 13)	intron (NM_052920, intron 2 of 13)	163840	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.013043	0.528139	
chunk0211_122_1	chrX	112247546	112248058	+	0	NA	intron (NM_001004308, intron 2 of 2)	intron (NM_001004308, intron 2 of 2)	164777	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.005859	0.405458	
chunk0138_144_1	chr4	37008265	37008464	+	0	NA	Intergenic	LTR18C|LTR|ERVL	233627	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.010050	0.470000	
chunk0126_321_1	chr3	81601457	81602296	+	0	NA	intron (NM_000158, intron 7 of 15)	L2b|LINE|L2	159923	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004768	0.319048	
chunk0051_174_1	chr12	116080749	116081161	+	0	NA	intron (NM_015335, intron 4 of 30)	MER119|DNA|hAT-Charlie	67699	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.004854	0.341404	
chunk0043_307_1	chr12	22168887	22169516	+	0	NA	Intergenic	L1ME1|LINE|L1	123025	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.003180	0.363492	
chunk0202_192_1	chr9	74906711	74907259	+	0	NA	Intergenic	L1ME5|LINE|L1	-18891	NM_017662	140803	Hs.272225	NM_017662	ENSG00000119121	TRPM6	CHAK2|HMGX|HOMG|HOMG1|HSH	transient receptor potential cation channel subfamily M member 6	protein-coding	0.000000	0.289617	272(ATGAACATGAAGTGCC,-,0.00),273(TGAACATGAAGTGCCC,+,0.00)
chunk0084_118_1	chr17	75999849	76000428	+	0	NA	promoter-TSS (NM_001258)	promoter-TSS (NM_001258)	-768	NM_001258	1018	Hs.706766	NM_001258	ENSG00000250506	CDK3	-	cyclin dependent kinase 3	protein-coding	0.043178	0.598276	
chunk0183_436_1	chr7	111169676	111170131	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	78897	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.004396	0.335526	
chunk0018_18_1	chr1	215365217	215365416	+	0	NA	Intergenic	L1P2|LINE|L1	-202076	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.010050	0.545000	
chunk0039_294_1	chr11	102811178	102811563	+	0	NA	intron (NR_038390, intron 4 of 7)	intron (NR_038390, intron 4 of 7)	-13135	NM_002421	4312	Hs.83169	NM_002421	ENSG00000196611	MMP1	CLG|CLGN	matrix metallopeptidase 1	protein-coding	0.005195	0.354922	
chunk0022_269_1	chr10	15037764	15037986	+	0	NA	Intergenic	Intergenic	-6021	NM_001039702	55301	Hs.24309	NM_018324	ENSG00000152463	OLAH	AURA1|SAST|TE2|THEDC1	oleoyl-ACP hydrolase	protein-coding	0.018018	0.493274	
chunk0168_288_1	chr6	90858826	90859512	+	0	NA	Intergenic	Intergenic	-271868	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.013120	0.427948	
chunk0058_1_1	chr14	16093234	16093514	+	0	NA	Intergenic	SAR|Satellite|Satellite	-2507743	NM_001013354	440153	Hs.534880	NM_001013354	ENSG00000257115	OR11H12	-	olfactory receptor family 11 subfamily H member 12	protein-coding	0.003571	0.224199	
chunk0024_47_1	chr10	33676972	33677262	+	0	NA	Intergenic	Intergenic	95563	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.013793	0.412371	
chunk0155_455_1	chr5	101729534	101730239	+	0	NA	Intergenic	Intergenic	566663	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.005674	0.382436	
chunk0066_290_1	chr15	35412185	35412804	+	0	NA	intron (NM_080650, intron 5 of 8)	L1MC1|LINE|L1	-40130	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.006462	0.350000	
chunk0017_414_1	chr1	213050950	213051161	+	0	NA	promoter-TSS (NM_001287218)	promoter-TSS (NM_001287218)	-178	NM_012424	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.061611	0.584906	
chunk0153_87_1	chr5	68201723	68202316	+	0	NA	Intergenic	Intergenic	12143	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.008432	0.405724	
chunk0033_96_1	chr11	14151040	14151239	+	0	NA	intron (NM_006108, intron 6 of 15)	L3|LINE|CR1	188502	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.015075	0.465000	
chunk0180_18_1	chr7	53540913	53541112	+	0	NA	Intergenic	Intergenic	270919	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.020101	0.390000	
chunk0153_28_1	chr5	67095240	67095742	+	0	NA	intron (NM_001290226, intron 4 of 26)	intron (NM_001290226, intron 4 of 26)	90871	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.009960	0.407555	
chunk0149_163_1	chr5	20441639	20442115	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	133996	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002101	0.289308	
chunk0040_74_1	chr11	111326657	111327168	+	0	NA	Intergenic	Intergenic	-20845	NR_039712	100616330		NR_039712	ENSG00000264032	MIR4491	mir-4491	microRNA 4491	ncRNA	0.009785	0.478516	
chunk0149_406_1	chr5	29152796	29153117	+	0	NA	intron (NR_130777, intron 3 of 8).2	intron (NR_130777, intron 3 of 8).2	9453	NR_130777	101929660	Hs.171348	NR_130777		LINC02109	-	long intergenic non-protein coding RNA 2109	ncRNA	0.000000	0.310559	
chunk0176_399_1	chr7	18996390	18996801	+	0	NA	3' UTR (NM_178423, exon 26 of 26)	3' UTR (NM_178423, exon 26 of 26)	121077	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.007299	0.351942	
chunk0131_152_1	chr3	146117521	146117978	+	0	NA	intron (NM_000935, intron 3 of 18)	L2a|LINE|L2	43746	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.004376	0.412664	
chunk0095_246_1	chr2	19235261	19235692	+	0	NA	Intergenic	Intergenic	-112953	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.004640	0.423611	135(AGGTACACTGTGAGCT,-,0.00),136(GGTACACTGTGAGCTG,+,0.00)
chunk0089_337_1	chr18	65756702	65757016	+	0	NA	intron (NM_004361, intron 1 of 11)	intron (NM_004361, intron 1 of 11)	5938	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.003185	0.326984	
chunk0009_409_1	chr1	110450368	110450567	+	0	NA	promoter-TSS (NM_032414)	promoter-TSS (NM_032414)	-699	NM_032414	84432	Hs.514793	NM_032414	ENSG00000143125	PROK1	EGVEGF|PK1|PRK1	prokineticin 1	protein-coding	0.005025	0.535000	
chunk0210_183_1	chrX	79632187	79632426	+	0	NA	Intergenic	L1ME3F|LINE|L1	-264754	NM_004867	9452	Hs.17109	NM_004867	ENSG00000078596	ITM2A	BRICD2A|E25A	integral membrane protein 2A	protein-coding	0.000000	0.383333	
chunk0112_122_1	chr20	38472649	38472887	+	0	NA	promoter-TSS (NM_001282917)	promoter-TSS (NM_001282917)	-38	NM_001282918	57148	Hs.598850	NM_020336	ENSG00000170471	RALGAPB	KIAA1219|RalGAPbeta	Ral GTPase activating protein non-catalytic beta subunit	protein-coding	0.105042	0.644351	
chunk0076_237_1	chr16	69026391	69026590	+	0	NA	intron (NM_024562, intron 16 of 17)	intron (NM_024562, intron 16 of 17)	-79074	NM_001199280	3038	Hs.592069	NM_005329	ENSG00000103044	HAS3	-	hyaluronan synthase 3	protein-coding	0.005025	0.495000	
chunk0176_77_1	chr7	11391639	11391913	+	0	NA	intron (NM_015204, intron 22 of 26)	L1PA7|LINE|L1	417904	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.018248	0.563636	
chunk0009_254_1	chr1	107094552	107095067	+	0	NA	Intergenic	Intergenic	38164	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.000000	0.325581	
chunk0155_64_1	chr5	91577722	91578276	+	0	NA	Intergenic	Intergenic	-194667	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.007220	0.367568	
chunk0209_191_1	chrX	43860901	43861305	+	0	NA	intron (NM_000898, intron 1 of 14)	L2a|LINE|L2	21372	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.014851	0.402469	
chunk0059_407_1	chr14	37778088	37778378	+	0	NA	intron (NM_001310135, intron 16 of 32)	L1PA15|LINE|L1	183034	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.010345	0.577320	
chunk0139_11_1	chr4	47911409	47911760	+	0	NA	intron (NR_103795, intron 2 of 23)	intron (NR_103795, intron 2 of 23)	-2643	NR_125879	101927157	Hs.134190	NR_125879		LOC101927157	-	uncharacterized LOC101927157	ncRNA	0.014245	0.377841	296(CAGCACTACCTGTACT,-,0.00),297(AGCACTACCTGTACTT,+,0.00)
chunk0025_131_1	chr10	51998205	51998618	+	0	NA	intron (NM_006258, intron 5 of 17)	L1MEd|LINE|L1	-298816	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.002421	0.323671	
chunk0012_119_1	chr1	156960645	156961156	+	0	NA	intron (NM_198236, intron 14 of 40)	intron (NM_198236, intron 14 of 40)	-24656	NR_030527	768220		NR_030527	ENSG00000211581	MIR765	MIRN765|hsa-mir-765|mir-765	microRNA 765	ncRNA	0.007828	0.458984	42(CGGCACAGGCAGTTTT,-,0.00),43(GGCACAGGCAGTTTTT,+,0.00)
chunk0157_183_1	chr5	118651631	118652216	+	0	NA	Intergenic	Intergenic	55735	NR_104998	102467225	Hs.582523	NR_104998	ENSG00000249128	LINC02215	-	long intergenic non-protein coding RNA 2215	ncRNA	0.003419	0.343003	418(CAGAACATCATGCTCT,-,0.00),419(AGAACATCATGCTCTC,+,0.00)
chunk0088_149_1	chr18	46256021	46256368	+	0	NA	intron (NM_145055, intron 4 of 4)	intron (NM_145055, intron 4 of 4)	-78030	NM_001256758	494470	Hs.501114	NM_152470	ENSG00000141622	RNF165	ARKL2|Ark2C|RNF111L2	ring finger protein 165	protein-coding	0.002882	0.341954	
chunk0031_4_1	chr10	121401281	121401663	+	0	NA	Intergenic	L1MD1|LINE|L1	192495	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.000000	0.365535	
chunk0207_147_1	chr9	129656675	129657261	+	0	NA	Intergenic	Intergenic	-8673	NM_016307	51450	Hs.660115	NM_016307	ENSG00000167157	PRRX2	PMX2|PRX2	paired related homeobox 2	protein-coding	0.015358	0.514480	
chunk0063_137_1	chr14	79459819	79460620	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	180880	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.008739	0.352868	436(AAATACATAATGTTCC,-,0.00),437(AATACATAATGTTCCC,+,0.00)
chunk0050_335_1	chr12	107450576	107450813	+	0	NA	intron (NM_001018072, intron 1 of 16)	LTR29|LTR|ERV1	-130163	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.008439	0.504202	
chunk0121_37_1	chr3	15263929	15264421	+	0	NA	intron (NM_001018009, intron 4 of 8)	intron (NM_001018009, intron 4 of 8)	9991	NR_046084	100505696	Hs.745026	NR_046084	ENSG00000224660	SH3BP5-AS1	-	SH3BP5 antisense RNA 1	ncRNA	0.004065	0.395538	243(ATTACAGGGTGTCCTG,+,0.00)
chunk0031_293_1	chr10	128464473	128464700	+	0	NA	Intergenic	Intergenic	178636	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.004405	0.578947	
chunk0094_154_1	chr2	5207590	5208014	+	0	NA	Intergenic	Tigger6b|DNA|TcMar-Tigger	483316	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.002358	0.265882	
chunk0157_225_1	chr5	119417864	119418380	+	0	NA	Intergenic	Intergenic	-34321	NM_001292027	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.007752	0.404255	
chunk0174_289_1	chr6	162219666	162220022	+	0	NA	intron (NM_013987, intron 3 of 10)	intron (NM_013987, intron 3 of 10)	-507288	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.002809	0.330532	
chunk0153_306_1	chr5	73541342	73541980	+	0	NA	Intergenic	Intergenic	24025	NM_023039	57763	Hs.239154	NM_023039	ENSG00000164331	ANKRA2	ANKRA	ankyrin repeat family A member 2	protein-coding	0.009404	0.405321	350(TGGAACACGTTGTTTC,-,0.00),351(GGAACACGTTGTTTCA,+,0.00)
chunk0098_234_1	chr2	74109674	74109984	+	0	NA	Intergenic	L3|LINE|CR1	38083	NM_001035505	388962	Hs.61472	NM_212552	ENSG00000163170	BOLA3	MMDS2	bolA family member 3	protein-coding	0.016129	0.469453	
chunk0014_27_1	chr1	174604144	174604371	+	0	NA	intron (NM_014857, intron 13 of 20)	L1M1|LINE|L1	156183	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.004405	0.486842	
chunk0027_214_1	chr10	76086953	76087506	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	304468	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.014467	0.476534	301(CAGAACTGTTTGTTCT,-,0.00),302(AGAACTGTTTGTTCTG,+,0.00)
chunk0057_394_1	chr13	109537181	109537967	+	0	NA	Intergenic	Intergenic	136878	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.019084	0.411690	
chunk0171_318_1	chr6	129662032	129662387	+	0	NA	intron (NM_033515, intron 1 of 14)	intron (NM_033515, intron 1 of 14)	48016	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.005634	0.443820	237(AAGGACAGGCTGCTCT,-,0.00),238(AGGACAGGCTGCTCTT,+,0.00)
chunk0168_422_1	chr6	95530296	95530778	+	0	NA	Intergenic	MER67D|LTR|ERV1	46914	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.004149	0.399586	
chunk0012_469_1	chr1	165629836	165630477	+	0	NA	promoter-TSS (NM_004528)	promoter-TSS (NM_004528)	-717	NM_004528	4259	Hs.191734	NM_004528	ENSG00000143198	MGST3	GST-III	microsomal glutathione S-transferase 3	protein-coding	0.021841	0.471963	
chunk0181_368_1	chr7	88748205	88748404	+	0	NA	Intergenic	Intergenic	-11064	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.010050	0.405000	
chunk0035_190_1	chr11	44202713	44202912	+	0	NA	intron (NM_001178083, intron 10 of 14)	MIRb|SINE|MIR	106615	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.000000	0.425000	
chunk0071_202_1	chr15	83991199	83991645	+	0	NA	intron (NM_207517, intron 23 of 29)	MamRep605|LTR?|LTR?	-88765	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.008969	0.456376	292(CAGAACACTCTGTCCC,-,0.00),293(AGAACACTCTGTCCCT,+,0.00)
chunk0165_36_1	chr6	29977162	29977361	+	0	NA	intron (NR_028032, intron 1 of 2)	CpG	2146	NR_028032	10255	Hs.656251	NM_005844	ENSG00000204625	HCG9	HCGIX|HCGIX4	HLA complex group 9	ncRNA	0.065327	0.590000	
chunk0084_331_1	chr17	81018332	81018748	+	0	NA	Intergenic	Intergenic	16179	NR_026857	440465	Hs.448889	NM_001004336	ENSG00000226137	BAIAP2-DT	BAIAP2-AS1|lnc-BAIAP2	BAIAP2 divergent transcript	ncRNA	0.036058	0.563549	51(AAGGGCAGCTTGTCCT,-,0.00),52(AGGGCAGCTTGTCCTC,+,0.00)
chunk0128_205_1	chr3	107824412	107825153	+	0	NA	Intergenic	Intergenic	53286	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.008097	0.442049	
chunk0022_370_1	chr10	17465694	17466273	+	0	NA	Intergenic	MIRc|SINE|MIR	-11728	NM_001004470	338596	Hs.677766	NM_001004470	ENSG00000148488	ST8SIA6	SIA8F|SIAT8-F|SIAT8F|ST8SIA-VI|ST8SiaVI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding	0.012090	0.422414	
chunk0187_357_1	chr7	157255314	157255742	+	0	NA	intron (NM_014671, intron 21 of 22)	intron (NM_014671, intron 21 of 22)	-81488	NM_005494	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.009346	0.347319	189(AAGGTCACGTTGTCCC,-,0.00),190(AGGTCACGTTGTCCCC,+,0.00)
chunk0068_419_1	chr15	59170107	59170684	+	0	NA	TTS (NR_031750)	TTS (NR_031750)	867	NR_031750	100313886		NR_031750	ENSG00000253030	MIR2116	mir-2116	microRNA 2116	ncRNA	0.015598	0.510381	
chunk0014_88_1	chr1	176567082	176568046	+	0	NA	intron (NM_020318, intron 2 of 22)	L2c|LINE|L2	104393	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.004149	0.378238	
chunk0105_338_1	chr2	191249439	191250036	+	0	NA	intron (NM_001130158, intron 1 of 30)	intron (NM_001130158, intron 1 of 30)	4209	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.000000	0.433110	
chunk0123_4_1	chr3	40087564	40088009	+	0	NA	intron (NM_001284425, intron 3 of 15)	intron (NM_001284425, intron 3 of 15)	-12225	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.004494	0.468610	
chunk0185_34_1	chr7	124330784	124331245	+	0	NA	Intergenic	L1MC4|LINE|L1	21082	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.004338	0.337662	
chunk0075_96_1	chr16	48441701	48442287	+	0	NA	Intergenic	Intergenic	-56676	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.008532	0.497445	103(GAGGACAGAATGGGCT,-,0.00),104(AGGACAGAATGGGCTC,+,0.00)
chunk0054_8_1	chr13	40352376	40352884	+	0	NA	intron (NR_024506, intron 5 of 5)	intron (NR_024506, intron 5 of 5)	128376	NR_024507	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.019685	0.524558	121(AGGAACAGGACGTTCT,-,0.00),122(GGAACAGGACGTTCTA,+,0.00)
chunk0161_348_1	chr5	174491850	174492450	+	0	NA	intron (NR_125806, intron 2 of 5)	intron (NR_125806, intron 2 of 5)	155796	NR_125806	101928176	Hs.436014	NR_125806	ENSG00000249306	LINC01411	-	long intergenic non-protein coding RNA 1411	ncRNA	0.010000	0.457571	
chunk0033_37_1	chr11	13030658	13031387	+	0	NA	Intergenic	Intergenic	21599	NM_001080521	644943	Hs.134650	NM_001080521	ENSG00000189431	RASSF10	-	Ras association domain family member 10	protein-coding	0.005487	0.479452	
chunk0153_313_1	chr5	73663427	73663877	+	0	NA	intron (NM_001080479, intron 1 of 36)	intron (NM_001080479, intron 1 of 36)	37494	NM_001177693	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.004444	0.361419	
chunk0151_301_1	chr5	53031783	53032145	+	0	NA	intron (NR_073106, intron 2 of 29)	intron (NR_073106, intron 2 of 29)	42638	NM_002203	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.008287	0.410468	195(AAGAACAATCTGAGCT,-,0.00),196(AGAACAATCTGAGCTC,+,0.00)
chunk0085_91_1	chr18	2583112	2583372	+	0	NA	intron (NM_006101, intron 6 of 16)	intron (NM_006101, intron 6 of 16)	11731	NM_006101	10403	Hs.414407	NM_006101	ENSG00000080986	NDC80	HEC|HEC1|HsHec1|KNTC2|TID3|hsNDC80	NDC80 kinetochore complex component	protein-coding	0.000000	0.363985	
chunk0002_381_1	chr1	26702897	26703352	+	0	NA	intron (NM_139135, intron 1 of 19)	intron (NM_139135, intron 1 of 19)	7093	NM_139135	8289	Hs.468972	NM_006015	ENSG00000117713	ARID1A	B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1	AT-rich interaction domain 1A	protein-coding	0.000000	0.359649	
chunk0145_61_1	chr4	145343386	145343676	+	0	NA	Intergenic	L1MCa|LINE|L1	-138268	NM_005900	4086	Hs.604588	NM_005900	ENSG00000170365	SMAD1	BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1	SMAD family member 1	protein-coding	0.006897	0.436426	163(CAGAACATTCTGTTCT,-,0.00),164(AGAACATTCTGTTCTT,+,0.00)
chunk0114_127_1	chr21	9800898	9801310	+	0	NA	intron (NR_038377, intron 3 of 5)	intron (NR_038377, intron 3 of 5)	19957	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.004854	0.503632	
chunk0078_449_1	chr16	89816799	89816998	+	0	NA	promoter-TSS (NM_000135)	promoter-TSS (NM_000135)	-241	NM_000135	2175	Hs.744083	NM_000135	ENSG00000187741	FANCA	FA|FA-H|FA1|FAA|FACA|FAH|FANCH	FA complementation group A	protein-coding	0.120603	0.700000	
chunk0164_178_1	chr6	21986641	21987156	+	0	NA	intron (NR_015410, intron 6 of 11)	intron (NR_015410, intron 6 of 11)	160295	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.011650	0.428295	258(GGGAACATCGTGTCCA,-,0.00),259(GGAACATCGTGTCCAG,+,0.00)
chunk0173_136_1	chr6	143774159	143775129	+	0	NA	intron (NM_001100166, intron 7 of 11)	intron (NM_001100166, intron 7 of 11)	-68727	NM_032860	84946	Hs.185675	NM_032860	ENSG00000135521	LTV1	C6orf93|dJ468K18.4	LTV1 ribosome biogenesis factor	protein-coding	0.003093	0.430484	
chunk0074_418_1	chr16	35846756	35847470	+	0	NA	Intergenic	AluSx1|SINE|Alu	100561	NR_033985	400533	Hs.499135	NR_033985	ENSG00000261122	LINC02167	-	long intergenic non-protein coding RNA 2167	ncRNA	0.007003	0.379021	
chunk0055_298_1	chr13	65628169	65628492	+	0	NA	Intergenic	Intergenic	-237717	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.006192	0.293210	
chunk0181_431_1	chr7	90445045	90445706	+	0	NA	Intergenic	Intergenic	42041	NM_001185072	9069	Hs.731917	NM_012129	ENSG00000157224	CLDN12	-	claudin 12	protein-coding	0.009077	0.371601	
chunk0025_318_1	chr10	57731266	57731617	+	0	NA	Intergenic	Intergenic	-426882	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.000000	0.343750	
chunk0107_372_1	chr2	222915540	222915774	+	0	NA	intron (NM_004457, intron 4 of 16)	intron (NM_004457, intron 4 of 16)	54643	NM_203372	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.008547	0.319149	
chunk0139_325_1	chr4	58359754	58359953	+	0	NA	Intergenic	MER52A|LTR|ERV1	933981	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.015075	0.535000	70(CTGGACAAGATGTACT,-,0.00),71(TGGACAAGATGTACTG,+,0.00)
chunk0165_425_1	chr6	39602731	39603434	+	0	NA	intron (NM_145027, intron 6 of 22)	intron (NM_145027, intron 6 of 22)	122323	NM_145027	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.005690	0.407670	346(ATGAACTGTTTGTTCT,-,0.00),347(TGAACTGTTTGTTCTA,+,0.00)
chunk0146_18_1	chr4	155056551	155056841	+	0	NA	Intergenic	MIR|SINE|MIR	-151933	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.010345	0.405498	
chunk0115_389_1	chr21	30443145	30443682	+	0	NA	Intergenic	Intergenic	3085	NM_181623	254950	Hs.553654	NM_181623	ENSG00000186970	KRTAP15-1	KAP15.1	keratin associated protein 15-1	protein-coding	0.000000	0.405204	
chunk0196_253_1	chr8	108623003	108623595	+	0	NA	Intergenic	Intergenic	164242	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.001689	0.364250	
chunk0178_179_1	chr7	34198200	34198966	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	293672	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.005222	0.425033	308(TGGAACATGCTGTCTC,-,0.00),309(GGAACATGCTGTCTCC,+,0.00),387(AAGTACACTCTGTTCA,-,0.00),388(AGTACACTCTGTTCAC,+,0.00)
chunk0149_413_1	chr5	29431442	29432034	+	0	NA	Intergenic	L1ME3B|LINE|L1	-35762	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.008446	0.296796	464(TGTACTGGATGTCCTT,+,0.00)
chunk0054_401_1	chr13	50441506	50441977	+	0	NA	intron (NR_109974, intron 4 of 6)	MIRb|SINE|MIR	85708	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.004246	0.394068	
chunk0121_96_1	chr3	16775503	16776220	+	0	NA	Intergenic	Intergenic	-109098	NM_001144382	23228	Hs.202010	NM_015184	ENSG00000154822	PLCL2	PLCE2	phospholipase C like 2	protein-coding	0.005579	0.371866	
chunk0044_314_1	chr12	33581660	33582186	+	0	NA	Intergenic	Intergenic	-142104	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.009506	0.349146	
chunk0066_76_1	chr15	29346162	29346464	+	0	NA	intron (NM_015307, intron 2 of 10)	intron (NM_015307, intron 2 of 10)	-76497	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.019868	0.557756	156(GGGGACTGCTTGTTCT,-,0.00),157(GGGACTGCTTGTTCTA,+,0.00)
chunk0005_150_1	chr1	58118927	58119417	+	0	NA	intron (NM_021080, intron 1 of 16)	MER46C|DNA|TcMar-Tigger	131367	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.002041	0.360489	
chunk0009_382_1	chr1	109978844	109979276	+	0	NA	Intergenic	Intergenic	-5705	NM_001242673	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.006944	0.450346	
chunk0170_48_1	chr6	109453771	109453978	+	0	NA	intron (NM_001159291, intron 2 of 23)	intron (NM_001159291, intron 2 of 23)	2113	NM_001159291	64780	Hs.33476	NM_022765	ENSG00000135596	MICAL1	MICAL|MICAL-1|NICAL	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding	0.043478	0.677885	
chunk0006_128_1	chr1	65921305	65922025	+	0	NA	intron (NM_002600, intron 3 of 16)	MER58A|DNA|hAT-Charlie	8420	NM_001297441	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.006944	0.361997	592(TGGGACTGTGTGTTCT,-,0.00),593(GGGACTGTGTGTTCTA,+,0.00)
chunk0127_19_1	chr3	88224562	88224900	+	0	NA	Intergenic	Intergenic	-74865	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.008876	0.333333	
chunk0051_53_1	chr12	112368482	112368693	+	0	NA	intron (NM_001109662, intron 1 of 75)	L1ME4a|LINE|L1	13505	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.000000	0.254717	
chunk0090_10_1	chr19	528634	528894	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-2969	NM_004359	997	Hs.514997	NM_004359	ENSG00000099804	CDC34	E2-CDC34|UBC3|UBCH3|UBE2R1	cell division cycle 34	protein-coding	0.030769	0.567050	
chunk0028_363_1	chr10	92712012	92712598	+	0	NA	Intergenic	Intergenic	22381	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.011945	0.390119	
chunk0153_433_1	chr5	76231030	76231528	+	0	NA	intron (NM_014979, intron 4 of 12)	L1MA7|LINE|L1	147865	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.006024	0.340681	
chunk0073_215_1	chr16	10601847	10602302	+	0	NA	Intergenic	Intergenic	-21358	NM_001424	2013	Hs.531561	NM_001424	ENSG00000213853	EMP2	XMP	epithelial membrane protein 2	protein-coding	0.008791	0.583333	225(GAGAACATCCAGTTCC,-,0.00),226(AGAACATCCAGTTCCC,+,0.00)
chunk0100_110_1	chr2	108367735	108368208	+	0	NA	Intergenic	Intergenic	-9994	NM_006588	27233	Hs.312644	NM_006588	ENSG00000198075	SULT1C4	SULT1C|SULT1C2	sulfotransferase family 1C member 4	protein-coding	0.002114	0.341772	
chunk0213_30_1	chrY	56742606	56742846	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	-211529	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.004167	0.419087	
chunk0002_140_1	chr1	17098322	17098632	+	0	NA	intron (NM_007365, intron 3 of 15)	intron (NM_007365, intron 3 of 15)	20976	NM_007365	11240	Hs.33455	NM_007365	ENSG00000117115	PADI2	PAD-H19|PAD2|PDI2	peptidyl arginine deiminase 2	protein-coding	0.016129	0.395498	
chunk0105_418_1	chr2	192971050	192971550	+	0	NA	Intergenic	Intergenic	221455	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.000000	0.279441	
chunk0154_51_1	chr5	77186833	77187447	+	0	NA	Intergenic	Kanga1c|DNA|TcMar-Tc2	-23741	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.001629	0.380488	223(ATGTACACAGTGTACA,-,0.00)
chunk0063_367_1	chr14	85870762	85871450	+	0	NA	Intergenic	L1MB8|LINE|L1	-63572	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.002907	0.284470	
chunk0063_376_1	chr14	86247983	86248349	+	0	NA	Intergenic	L1ME3A|LINE|L1	313488	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.002732	0.329700	
chunk0080_70_1	chr17	21991729	21992042	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	299362	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.003195	0.385350	
chunk0132_323_1	chr3	161031041	161031433	+	0	NA	intron (NM_139245, intron 2 of 3)	intron (NM_139245, intron 2 of 3)	73658	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.002551	0.422392	
chunk0025_361_1	chr10	58509151	58509954	+	0	NA	Intergenic	L2a|LINE|L2	-3592	NM_001080512	80114	Hs.100261	NM_001080512	ENSG00000122870	BICC1	BICC|CYSRD	BicC family RNA binding protein 1	protein-coding	0.000000	0.370647	
chunk0084_411_1	chr17	82288023	82288326	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-14432	NR_110578	1453	Hs.631725	NM_001893	ENSG00000141551	CSNK1D	ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID	casein kinase 1 delta	protein-coding	0.033003	0.585526	
chunk0174_150_1	chr6	157824085	157824284	+	0	NA	intron (NM_016224, intron 1 of 17)	intron (NM_016224, intron 1 of 17)	1013	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.045226	0.470000	
chunk0126_154_1	chr3	76949446	76949874	+	0	NA	Intergenic	Intergenic	-90483	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.021028	0.468531	
chunk0207_235_1	chr9	131943253	131944005	+	0	NA	intron (NM_001253881, intron 3 of 6)	intron (NM_001253881, intron 3 of 6)	136258	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.021277	0.444887	262(AGGAACAGTGTGCTCC,-,0.00),263(GGAACAGTGTGCTCCC,+,0.00),299(GTTACACTCTGTTCTG,+,0.00)
chunk0040_445_1	chr11	121568026	121568281	+	0	NA	intron (NM_003105, intron 22 of 47)	AluJo|SINE|Alu	115950	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.011765	0.500000	
chunk0141_272_1	chr4	86443441	86443904	+	0	NA	intron (NM_002753, intron 1 of 13)	L1MCa|LINE|L1	9458	NM_002753	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.017279	0.450431	
chunk0096_14_1	chr2	26073315	26073883	+	0	NA	intron (NM_016131, intron 1 of 5)	LTR33B|LTR|ERVL	39739	NM_016131	10890	Hs.467960	NM_016131	ENSG00000084733	RAB10	-	RAB10, member RAS oncogene family	protein-coding	0.005282	0.416520	
chunk0063_245_1	chr14	82387479	82388189	+	0	NA	Intergenic	Intergenic	-764773	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.005634	0.371308	445(GAGTACAGAATGTACA,-,0.00),446(AGTACAGAATGTACAA,+,0.00),508(TGAACAACTTGTTCAT,+,0.00)
chunk0122_197_1	chr3	33019141	33019375	+	0	NA	intron (NM_000404, intron 12 of 15)	intron (NM_000404, intron 12 of 15)	67684	NM_005508	1233	Hs.184926	NM_005508	ENSG00000183813	CCR4	CC-CKR-4|CD194|CKR4|CMKBR4|ChemR13|HGCN:14099|K5-5	C-C motif chemokine receptor 4	protein-coding	0.008547	0.336170	
chunk0093_21_1	chr2	284994	285629	+	0	NA	intron (NM_001002919, intron 4 of 5)	intron (NM_001002919, intron 4 of 5)	2997	NM_001002919	285016	Hs.355207	NM_001002919	ENSG00000189292	ALKAL2	AUGA|FAM150B|PRO1097|RGPG542	ALK and LTK ligand 2	protein-coding	0.020472	0.443396	
chunk0142_415_1	chr4	103152479	103153009	+	0	NA	intron (NM_001813, intron 25 of 48)	L1ME1|LINE|L1	45665	NM_001813	1062	Hs.75573	NM_001813	ENSG00000138778	CENPE	CENP-E|KIF10|MCPH13|PPP1R61	centromere protein E	protein-coding	0.009434	0.342750	
chunk0066_115_1	chr15	30172962	30173267	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-22922	NR_026771	26082	Hs.652128	NR_026771	ENSG00000225930	LINC02249	DKFZP434L187	long intergenic non-protein coding RNA 2249	ncRNA	0.003279	0.513072	
chunk0119_354_1	chr22	47337138	47337462	+	0	NA	Intergenic	LTR33B|LTR|ERVL	149811	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.012346	0.492308	
chunk0120_424_1	chr3	13053058	13053738	+	0	NA	intron (NM_001134382, intron 1 of 13)	intron (NM_001134382, intron 1 of 13)	19719	NM_001134382	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.026471	0.550661	344(CAGAACACCCTGTGCT,-,0.00),345(AGAACACCCTGTGCTT,+,0.00)
chunk0135_366_1	chr3	190731909	190732315	+	0	NA	Intergenic	MER61B|LTR|ERV1	130564	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.009852	0.425061	
chunk0205_98_1	chr9	107438393	107438848	+	0	NA	intron (NR_121581, intron 4 of 7)	intron (NR_121581, intron 4 of 7)	27965	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.006593	0.480263	
chunk0068_339_1	chr15	57692670	57693213	+	0	NA	intron (NR_104367, intron 14 of 15)	intron (NR_104367, intron 14 of 15)	-13580	NM_015532	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.003683	0.343750	
chunk0135_377_1	chr3	191002365	191002847	+	0	NA	Intergenic	Intergenic	124676	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.000000	0.354037	
chunk0155_75_1	chr5	91802903	91803274	+	0	NA	Intergenic	LTR28C|LTR|ERV1	-419756	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.002695	0.545699	
chunk0108_463_1	chr2	238588451	238588650	+	0	NA	Intergenic	Intergenic	-33051	NR_037809	151171	Hs.652076	NR_037809	ENSG00000225493	LINC01107	-	long intergenic non-protein coding RNA 1107	ncRNA	0.005025	0.480000	
chunk0083_347_1	chr17	70300351	70300891	+	0	NA	Intergenic	L1MCc|LINE|L1	131086	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.003704	0.321627	
chunk0119_428_1	chr22	50007042	50007355	+	0	NA	intron (NM_001001694, intron 3 of 14)	L1MEc|LINE|L1	5428	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.006390	0.388535	
chunk0044_434_1	chr12	42235357	42235889	+	0	NA	3' UTR (NM_001190980, exon 3 of 3)	3' UTR (NM_001190980, exon 3 of 3)	2664	NM_001190977	10138	Hs.649195	NM_005748	ENSG00000015153	YAF2	-	YY1 associated factor 2	protein-coding	0.001880	0.407129	261(AGGAACACAGTGTCCC,-,0.00),262(GGAACACAGTGTCCCT,+,0.00)
chunk0063_80_1	chr14	77744841	77745197	+	0	NA	intron (NM_012245, intron 3 of 13)	intron (NM_012245, intron 3 of 13)	-15811	NM_174943	283579	Hs.375834	NM_174943	ENSG00000197734	C14orf178	-	chromosome 14 open reading frame 178	ncRNA	0.005618	0.380952	
chunk0168_297_1	chr6	91373269	91373816	+	0	NA	Intergenic	L1PA7|LINE|L1	-148118	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.010969	0.377737	
chunk0089_167_1	chr18	59144955	59145679	+	0	NA	intron (NM_033280, intron 1 of 5)	MER58A|DNA|hAT-Charlie	5460	NM_033280	90701	Hs.45107	NM_033280	ENSG00000166562	SEC11C	SEC11L3|SPC21|SPCS4C	SEC11 homolog C, signal peptidase complex subunit	protein-coding	0.008287	0.440000	
chunk0089_176_1	chr18	59656203	59656426	+	0	NA	intron (NM_133459, intron 2 of 10)	intron (NM_133459, intron 2 of 10)	41098	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.000000	0.308036	
chunk0206_256_1	chr9	123799537	123800121	+	0	NA	intron (NM_024820, intron 2 of 20)	intron (NM_024820, intron 2 of 20)	130309	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.008562	0.353846	
chunk0180_95_1	chr7	55140902	55141177	+	0	NA	intron (NM_201283, intron 1 of 9)	intron (NM_201283, intron 1 of 9)	47910	NR_047551	100507500	Hs.720489	NR_047551	ENSG00000224057	EGFR-AS1	-	EGFR antisense RNA 1	ncRNA	0.000000	0.445652	
chunk0149_333_1	chr5	26836916	26837509	+	0	NA	Intergenic	Intergenic	201370	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.001686	0.269360	
chunk0051_262_1	chr12	117678833	117679032	+	0	NA	intron (NM_173598, intron 4 of 19)	intron (NM_173598, intron 4 of 19)	289291	NM_173598	283455	Hs.375836	NM_173598	ENSG00000171435	KSR2	-	kinase suppressor of ras 2	protein-coding	0.005025	0.505000	
chunk0079_117_1	chr17	12421176	12421733	+	0	NA	Intergenic	Intergenic	-128514	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.016158	0.408602	
chunk0048_109_1	chr12	79504269	79504468	+	0	NA	Intergenic	L1PREC2|LINE|L1	85111	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.005025	0.545000	
chunk0162_62_1	chr6	1552188	1552777	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-53049	NR_125804	101927703	Hs.607964	NR_125804		FOXCUT	LINC01379|TCONS_00011636	FOXC1 upstream transcript	ncRNA	0.006791	0.440678	312(AAGTACATTATGTGCC,-,0.00),313(AGTACATTATGTGCCT,+,0.00)
chunk0193_194_1	chr8	75750504	75750703	+	0	NA	Intergenic	Intergenic	210635	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.015075	0.350000	
chunk0127_142_1	chr3	94284516	94285101	+	0	NA	Intergenic	Intergenic	-221585	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.006838	0.389078	
chunk0136_23_1	chr4	673430	673629	+	0	NA	intron (NR_033743, intron 1 of 2)	CpG	809	NM_007100	521	Hs.85539	NM_007100	ENSG00000169020	ATP5ME	ATP5I|ATP5K	ATP synthase membrane subunit e	protein-coding	0.050251	0.560000	
chunk0067_191_1	chr15	44798182	44798865	+	0	NA	Intergenic	Intergenic	62161	NM_001301146	140691	Hs.745248	NM_080745	ENSG00000185880	TRIM69	HSD-34|HSD34|RNF36|Trif	tripartite motif containing 69	protein-coding	0.001464	0.339181	
chunk0126_58_1	chr3	74342446	74342985	+	0	NA	intron (NM_020872, intron 10 of 21)	intron (NM_020872, intron 10 of 21)	178425	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.005566	0.331481	
chunk0056_35_1	chr13	77312771	77313216	+	0	NA	intron (NM_015057, intron 1 of 82)	L1MEf|LINE|L1	14049	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.002247	0.278027	
chunk0188_395_1	chr8	18651621	18652105	+	0	NA	intron (NM_015310, intron 10 of 15)	intron (NM_015310, intron 10 of 15)	157032	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.006198	0.414433	
chunk0003_3_1	chr1	28537515	28537714	+	0	NA	intron (NM_001048194, intron 10 of 10)	intron (NM_001048194, intron 10 of 10)	-15403	NM_017846	54952	Hs.533626	NM_017846	ENSG00000180098	TRNAU1AP	PRO1902|SECP43|TRSPAP1	tRNA selenocysteine 1 associated protein 1	protein-coding	0.005025	0.535000	
chunk0111_353_1	chr20	33532801	33533124	+	0	NA	intron (NM_001032999, intron 1 of 10)	intron (NM_001032999, intron 1 of 10)	-29403	NM_005093	9139	Hs.153934	NM_005093	ENSG00000078699	CBFA2T2	EHT|MTGR1|ZMYND3|p85	CBFA2/RUNX1 partner transcriptional co-repressor 2	protein-coding	0.006192	0.395062	229(CTGAACAAACAGTGCT,-,0.00),230(TGAACAAACAGTGCTT,+,0.00)
chunk0025_438_1	chr10	60123324	60123602	+	0	NA	intron (NM_001204403, intron 26 of 43)	intron (NM_001204403, intron 26 of 43)	17553	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.007194	0.415771	76(AAGTACACACTGGCCT,-,0.00),77(AGTACACACTGGCCTT,+,0.00)
chunk0181_311_1	chr7	87344308	87344915	+	0	NA	intron (NR_015381, intron 1 of 2)	MER46C|DNA|TcMar-Tigger	881	NR_015381	11257	Hs.274329	NM_007233	ENSG00000182165	TP53TG1	LINC00096|NCRNA00096|P53TG1|P53TG1-D|TP53AP1	TP53 target 1	ncRNA	0.004942	0.314145	
chunk0055_90_1	chr13	54890965	54891482	+	0	NA	Intergenic	Intergenic	-283231	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.005803	0.328185	
chunk0069_147_1	chr15	62455411	62455760	+	0	NA	Intergenic	Intergenic	112556	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.022923	0.511429	
chunk0020_130_1	chr1	233602238	233602453	+	0	NA	Intergenic	L2a|LINE|L2	-11659	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.000000	0.416667	
chunk0010_395_1	chr1	119472181	119472682	+	0	NA	Intergenic	HUERS-P2-int|LTR|ERV1	-34772	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.003992	0.442231	
chunk0091_89_1	chr19	5605578	5605777	+	0	NA	intron (NM_014649, intron 9 of 20)	L1MEc|LINE|L1	17250	NM_014649	9667	Hs.655392	NM_014649	ENSG00000130254	SAFB2	-	scaffold attachment factor B2	protein-coding	0.010050	0.500000	
chunk0074_338_1	chr16	31400392	31400647	+	0	NA	intron (NM_005353, intron 5 of 29)	intron (NM_005353, intron 5 of 29)	7207	NM_005353	3681	Hs.679163	NM_005353	ENSG00000156886	ITGAD	ADB2|CD11D	integrin subunit alpha D	protein-coding	0.015686	0.546875	
chunk0104_96_1	chr2	172299792	172300269	+	0	NA	Intergenic	Intergenic	-127324	NM_001316306	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.008386	0.397490	
chunk0018_95_1	chr1	217639335	217639598	+	0	NA	intron (NM_138796, intron 1 of 10)	L1MEj|LINE|L1	8142	NM_138796	128153	Hs.171130	NM_138796	ENSG00000162814	SPATA17	IQCH|MSRG-11|MSRG11	spermatogenesis associated 17	protein-coding	0.007605	0.295455	
chunk0196_47_1	chr8	101870254	101870598	+	0	NA	intron (NM_001040629, intron 3 of 6)	intron (NM_001040629, intron 3 of 6)	-79215	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.002907	0.353623	
chunk0140_175_1	chr4	69756050	69756664	+	0	NA	intron (NM_014465, intron 1 of 7)	MLT2B4|LTR|ERVL	4355	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.003257	0.347967	
chunk0161_104_1	chr5	167389798	167390313	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	105217	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.011650	0.343023	
chunk0129_309_1	chr3	123798618	123798817	+	0	NA	intron (NM_053025, intron 3 of 33)	intron (NM_053025, intron 3 of 33)	85585	NM_053028	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.015075	0.540000	70(GGGAACATCTAGTCCC,-,0.00),71(GGAACATCTAGTCCCT,+,0.00)
chunk0028_133_1	chr10	85431023	85431251	+	0	NA	TTS (NR_120669)	TTS (NR_120669)	1635	NR_120669	101929646	Hs.116129	NR_120669		LINC02647	-	long intergenic non-protein coding RNA 2647	ncRNA	0.004386	0.475983	
chunk0017_334_1	chr1	211541304	211542376	+	0	NA	Intergenic	Intergenic	36917	NM_021194	7779	Hs.519469	NM_021194	ENSG00000170385	SLC30A1	ZNT1|ZRC1	solute carrier family 30 member 1	protein-coding	0.006530	0.495806	214(GGAGACATGGTGTTCT,-,0.00),215(GAGACATGGTGTTCTC,+,0.00)
chunk0116_109_1	chr21	35501842	35502209	+	0	NA	intron (NR_073512, intron 1 of 2)	intron (NR_073512, intron 1 of 2)	78739	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.013624	0.407609	
chunk0176_92_1	chr7	11610620	11611254	+	0	NA	intron (NM_015204, intron 2 of 26)	intron (NM_015204, intron 2 of 26)	221261	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.003155	0.286614	
chunk0145_30_1	chr4	143626004	143626485	+	0	NA	intron (NM_001168235, intron 3 of 7)	L2a|LINE|L2	66772	NR_003675	441046	Hs.135705	NM_001011539	ENSG00000236296	GUSBP5	GYPELOC441046	GUSB pseudogene 5	pseudo	0.006237	0.431535	
chunk0186_175_1	chr7	139369751	139370128	+	0	NA	intron (NM_016019, intron 1 of 9)	intron (NM_016019, intron 1 of 9)	10093	NM_001270643	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.005305	0.359788	
chunk0089_417_1	chr18	69259435	69259646	+	0	NA	Intergenic	Intergenic	-141508	NM_152721	220164	Hs.278285	NM_152721	ENSG00000206052	DOK6	DOK5L|HsT3226	docking protein 6	protein-coding	0.004739	0.382075	
chunk0034_200_1	chr11	32304474	32305187	+	0	NA	Intergenic	Intergenic	125987	NM_001198552	7490	Hs.591980	NM_000378	ENSG00000184937	WT1	AWT1|GUD|NPHS4|WAGR|WIT-2|WT33	WT1 transcription factor	protein-coding	0.002805	0.434174	
chunk0052_175_1	chr13	24194612	24194927	+	0	NA	intron (NM_153023, intron 1 of 11)	intron (NM_153023, intron 1 of 11)	32353	NR_031753	100313842		NR_031753	ENSG00000252695	MIR2276	-	microRNA 2276	ncRNA	0.019048	0.382911	
chunk0211_281_1	chrX	122272037	122272323	+	0	NA	Intergenic	Intergenic	901208	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.003497	0.358885	
chunk0129_228_1	chr3	121958506	121958804	+	0	NA	Intergenic	L1M1|LINE|L1	63625	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.000000	0.331104	
chunk0119_282_1	chr22	46069705	46070055	+	0	NA	Intergenic	Intergenic	-15736	NM_018280	55267	Hs.567529	NM_018280		PRR34	C22orf26	PRR34 long non-coding RNA	protein-coding	0.031429	0.544160	
chunk0066_32_1	chr15	27629615	27629948	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-468462	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.009009	0.556886	
chunk0017_272_1	chr1	209734270	209734710	+	0	NA	exon (NM_005525, exon 6 of 6)	exon (NM_005525, exon 6 of 6)	-21542	NM_025228	80342	Hs.147434	NM_025228	ENSG00000009790	TRAF3IP3	T3JAM	TRAF3 interacting protein 3	protein-coding	0.004545	0.444444	
chunk0086_65_1	chr18	13076930	13077251	+	0	NA	intron (NM_032142, intron 30 of 44)	intron (NM_032142, intron 30 of 44)	85728	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.018692	0.416149	
chunk0055_287_1	chr13	64720488	64720831	+	0	NA	Intergenic	L1P3|LINE|L1	-876534	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.002915	0.380814	
chunk0088_224_1	chr18	48356897	48357677	+	0	NA	Intergenic	Intergenic	-181769	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.014103	0.544174	
chunk0001_47_1	chr1	1847264	1847625	+	0	NA	intron (NM_002074, intron 1 of 11)	Tigger2|DNA|TcMar-Tigger	43673	NM_002074	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.005540	0.444751	
chunk0183_316_1	chr7	108018125	108018338	+	0	NA	Intergenic	Intergenic	-14872	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.000000	0.490654	
chunk0093_383_1	chr19	56355325	56356068	+	0	NA	Intergenic	Intergenic	-12403	NR_003127	147947	Hs.467326	NM_194319	ENSG00000240225	ZNF542P	ZNF542	zinc finger protein 542, pseudogene	pseudo	0.001346	0.313172	
chunk0173_377_1	chr6	149750077	149750304	+	0	NA	intron (NM_001252051, intron 1 of 6)	intron (NM_001252051, intron 1 of 6)	495	NM_001252051	5110	Hs.279257	NM_005389	ENSG00000120265	PCMT1	PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase	protein-coding	0.083700	0.684211	
chunk0030_191_1	chr10	114280017	114280322	+	0	NA	intron (NM_001272046, intron 8 of 13)	intron (NM_001272046, intron 8 of 13)	40915	NM_001272046	340706	Hs.197741	NM_198496	ENSG00000165816	VWA2	AMACO|CCSP-2|CCSP2|NET42	von Willebrand factor A domain containing 2	protein-coding	0.006557	0.460784	
chunk0013_300_1	chr1	171224142	171224687	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-24057	NM_001282694	2326	Hs.1424	NM_002021	ENSG00000010932	FMO1	-	flavin containing dimethylaniline monoxygenase 1	protein-coding	0.007339	0.358974	226(ATGTACTTTATGTTCT,-,0.00),227(TGTACTTTATGTTCTT,+,0.00)
chunk0081_350_1	chr17	47297879	47298082	+	0	NA	intron (NM_000212, intron 10 of 14)	intron (NM_000212, intron 10 of 14)	25633	NR_110881	102724508	Hs.661005	NR_110880	ENSG00000263293	THCAT158	-	thyroid cancer-associated transcript 158	ncRNA	0.000000	0.362745	
chunk0145_286_1	chr4	149750620	149751023	+	0	NA	Intergenic	Intergenic	-327453	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.002481	0.282178	
chunk0061_371_1	chr14	64112725	64113511	+	0	NA	intron (NM_182914, intron 65 of 115)	intron (NM_182914, intron 65 of 115)	-17993	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.019084	0.454892	
chunk0138_229_1	chr4	39231922	39232121	+	0	NA	intron (NM_025132, intron 18 of 36)	intron (NM_025132, intron 18 of 36)	49617	NM_025132	57728	Hs.438482	NM_025132	ENSG00000157796	WDR19	ATD5|CED4|DYF-2|IFT144|NPHP13|ORF26|Oseg6|PWDMP|SRTD5	WD repeat domain 19	protein-coding	0.010050	0.275000	
chunk0170_233_1	chr6	113466477	113466864	+	0	NA	Intergenic	Intergenic	183405	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.010336	0.360825	
chunk0193_426_1	chr8	80814975	80815432	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	59578	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.006565	0.318777	
chunk0015_238_1	chr1	187802268	187802964	+	0	NA	Intergenic	Intergenic	358988	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004310	0.335725	
chunk0152_445_1	chr5	66333206	66333405	+	0	NA	Intergenic	Intergenic	178299	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.005025	0.485000	
chunk0200_294_1	chr9	22829130	22829698	+	0	NA	Intergenic	Intergenic	183214	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.003521	0.388401	313(AAGCACACAAAGTTCT,-,0.00),314(AGCACACAAAGTTCTT,+,0.00)
chunk0054_108_1	chr13	42861084	42861497	+	0	NA	intron (NR_126388, intron 2 of 2)	intron (NR_126388, intron 2 of 2)	11454	NR_126388	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.007264	0.376812	
chunk0086_445_1	chr18	29307678	29307880	+	0	NA	Intergenic	Intergenic	-991131	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.004950	0.310345	
chunk0105_168_1	chr2	187092298	187093062	+	0	NA	Intergenic	Intergenic	-243510	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.002618	0.309804	395(ATGTACTGTATGTGCT,-,0.00)
chunk0124_192_1	chr3	55629084	55629940	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	29957	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.007009	0.443407	
chunk0077_323_1	chr16	82195988	82196467	+	0	NA	Intergenic	Merlin1_HS|DNA|Merlin	-26003	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.002088	0.381250	
chunk0038_212_1	chr11	86499652	86499935	+	0	NA	intron (NM_001014811, intron 4 of 13)	MIRc|SINE|MIR	125057	NM_021827	60494	Hs.144913	NM_021827	ENSG00000149201	CCDC81	-	coiled-coil domain containing 81	protein-coding	0.010601	0.461268	
chunk0112_281_1	chr20	43632499	43632986	+	0	NA	intron (NM_001303458, intron 10 of 13)	L4_A_Mam|LINE|RTE-X	-34277	NM_001278610	4605	Hs.179718	NM_002466	ENSG00000101057	MYBL2	B-MYB|BMYB	MYB proto-oncogene like 2	protein-coding	0.008214	0.403689	
chunk0169_116_1	chr6	100800911	100801481	+	0	NA	intron (NM_006828, intron 5 of 41)	intron (NM_006828, intron 5 of 41)	80176	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.003509	0.318739	
chunk0108_113_1	chr2	229685441	229686078	+	0	NA	intron (NM_139072, intron 1 of 12)	L2b|LINE|L2	28811	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.012559	0.456113	
chunk0046_70_1	chr12	55997514	55997760	+	0	NA	TTS (NM_002868)	TTS (NM_002868)	378	NM_001032386	6821	Hs.558403	NM_000456	ENSG00000139531	SUOX	-	sulfite oxidase	protein-coding	0.020325	0.562753	
chunk0078_296_1	chr17	8151711	8152116	+	0	NA	intron (NM_002616, intron 1 of 22)	CpG	522	NM_002616	5187	Hs.445534	NM_002616	ENSG00000179094	PER1	PER|RIGUI|hPER	period circadian regulator 1	protein-coding	0.044444	0.613300	200(GGGAACGGGATGTTCT,-,0.00),201(GGAACGGGATGTTCTA,+,0.00)
chunk0101_14_1	chr2	121476230	121476629	+	0	NA	intron (NM_015282, intron 8 of 38)	intron (NM_015282, intron 8 of 38)	-54451	NR_023343	100151683	Hs.689638	NR_023343	ENSG00000264229	RNU4ATAC	MOPD1|RFMN|RNU4ATAC1|TALS|U4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	snRNA	0.007519	0.455000	
chunk0181_138_1	chr7	81367507	81367715	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	258605	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.004808	0.478469	
chunk0165_13_1	chr6	28751031	28751494	+	0	NA	Intergenic	L1MDa|LINE|L1	112415	NR_033379	401242	Hs.448285	NR_033379	ENSG00000225595	LINC01623	-	long intergenic non-protein coding RNA 1623	ncRNA	0.006479	0.310345	
chunk0144_54_1	chr4	126785848	126786178	+	0	NA	Intergenic	Intergenic	-846919	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.003030	0.244713	
chunk0074_111_1	chr16	22297694	22298597	+	0	NA	intron (NM_001258035, intron 1 of 19)	intron (NM_001258035, intron 1 of 19)	770	NM_001258034	55718	Hs.460298	NM_018119	ENSG00000058600	POLR3E	RPC5|SIN	RNA polymerase III subunit E	protein-coding	0.059801	0.574115	
chunk0142_165_1	chr4	95250633	95251269	+	0	NA	intron (NM_003728, intron 4 of 15)	intron (NM_003728, intron 4 of 15)	159460	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.009434	0.376766	
chunk0175_456_1	chr6	170306382	170306633	+	0	NA	promoter-TSS (NM_001286381)	promoter-TSS (NM_001286381)	-215	NM_032448	84498	Hs.369522	NM_032448	ENSG00000112584	FAM120B	CCPG|KIAA1838|PGCC1|SAN1|dJ894D12.1	family with sequence similarity 120B	protein-coding	0.123506	0.714286	
chunk0127_148_1	chr3	94418314	94418759	+	0	NA	Intergenic	L1PA15|LINE|L1	-355313	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.004494	0.542601	
chunk0203_60_1	chr9	83431624	83432600	+	0	NA	intron (NM_001244959, intron 1 of 14)	intron (NM_001244959, intron 1 of 14)	35630	NM_001244960	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.008197	0.498465	302(GAGGACACTTAGTTCA,-,0.00)
chunk0115_101_1	chr21	22554380	22554658	+	0	NA	Intergenic	(TTTAC)n|Simple_repeat|Simple_repeat	455902	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.003597	0.268817	
chunk0149_290_1	chr5	25427287	25427764	+	0	NA	Intergenic	Intergenic	-586942	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.000000	0.286611	
chunk0066_406_1	chr15	39314445	39314744	+	0	NA	Intergenic	Intergenic	63925	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.000000	0.340000	
chunk0142_106_1	chr4	94429072	94429271	+	0	NA	Intergenic	Intergenic	-22686	NM_001256425	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.000000	0.430000	
chunk0064_49_1	chr14	89793591	89793825	+	0	NA	Intergenic	Intergenic	160849	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.004274	0.510638	
chunk0051_268_1	chr12	117861041	117861342	+	0	NA	intron (NM_173598, intron 1 of 19)	L1ME4b|LINE|L1	107032	NM_173598	283455	Hs.375836	NM_173598	ENSG00000171435	KSR2	-	kinase suppressor of ras 2	protein-coding	0.006645	0.417219	
chunk0007_404_1	chr1	85543772	85544369	+	0	NA	intron (NM_001134445, intron 1 of 6)	Tigger8|DNA|TcMar-Tigger	34293	NM_001134445	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.003350	0.369565	
chunk0058_460_1	chr13	114097223	114097528	+	0	NA	intron (NM_007368, intron 1 of 23)	intron (NM_007368, intron 1 of 23)	35245	NM_007368	22821	Hs.593075	NM_007368	ENSG00000185989	RASA3	GAP1IP4BP|GAPIII	RAS p21 protein activator 3	protein-coding	0.036066	0.526144	
chunk0205_275_1	chr9	111481810	111482304	+	0	NA	intron (NM_001080398, intron 3 of 50)	L1MB3|LINE|L1	2688	NM_001080398	23392	Hs.368255	NM_001080398	ENSG00000136813	ECPAS	ECM29|KIAA0368	Ecm29 proteasome adaptor and scaffold	protein-coding	0.022267	0.426263	92(AGGGACAGAAAGTACA,-,0.00)
chunk0007_259_1	chr1	82997202	82997807	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-11296	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.008264	0.412541	342(AGGAACAAGGTGTGCA,-,0.00),343(GGAACAAGGTGTGCAG,+,0.00)
chunk0074_274_1	chr16	28505019	28505348	+	0	NA	intron (NM_145659, intron 1 of 4)	intron (NM_145659, intron 1 of 4)	1651	NM_145659	246778	Hs.528111	NM_145659	ENSG00000197272	IL27	IL-27|IL-27A|IL27A|IL27p28|IL30|p28	interleukin 27	protein-coding	0.009119	0.560606	119(GGGCACACCATGTTCT,-,0.00),120(GGCACACCATGTTCTG,+,0.00)
chunk0030_227_1	chr10	114822961	114823194	+	0	NA	intron (NM_020940, intron 1 of 16)	intron (NM_020940, intron 1 of 16)	1333	NM_001135051	57700	Hs.192619	NM_020940	ENSG00000151553	FAM160B1	KIAA1600|bA106M7.3	family with sequence similarity 160 member B1	protein-coding	0.000000	0.329060	
chunk0187_294_1	chr7	155919097	155919453	+	0	NA	Intergenic	Intergenic	-43357	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.033708	0.588235	
chunk0041_7_1	chr12	304893	305092	+	0	NA	intron (NM_001042603, intron 24 of 27)	intron (NM_001042603, intron 24 of 27)	-42119	NM_016615	6540	Hs.504398	NM_016615	ENSG00000010379	SLC6A13	GAT-2|GAT2|GAT3	solute carrier family 6 member 13	protein-coding	0.020101	0.400000	
chunk0048_140_1	chr12	80051213	80051489	+	0	NA	Intergenic	L1MA4A|LINE|L1	-115896	NM_001244990	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.003623	0.368231	
chunk0152_143_1	chr5	59207905	59208428	+	0	NA	intron (NM_006203, intron 2 of 14)	AluSx1|SINE|Alu	67953	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.013384	0.429389	
chunk0050_113_1	chr12	102021696	102021895	+	0	NA	intron (NM_016053, intron 6 of 6)	intron (NM_016053, intron 6 of 6)	40329	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.005025	0.390000	
chunk0130_17_1	chr3	128423556	128423944	+	0	NA	Intergenic	L1MB7|LINE|L1	-39844	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.005155	0.442159	163(GGGGACAGGGTGTTCT,-,0.00),164(GGGACAGGGTGTTCTA,+,0.00)
chunk0003_430_1	chr1	41045813	41046719	+	0	NA	intron (NM_001031694, intron 12 of 15)	intron (NM_001031694, intron 12 of 15)	-24511	NM_144990	200172	Hs.194609	NM_144990	ENSG00000171790	SLFNL1	-	schlafen like 1	protein-coding	0.013245	0.509372	
chunk0202_187_1	chr9	74631244	74631720	+	0	NA	intron (NM_006914, intron 2 of 9)	intron (NM_006914, intron 2 of 9)	-132929	NR_125791	103752585	Hs.635501	NR_125791		RORB-AS1	-	RORB antisense RNA 1	ncRNA	0.004202	0.354298	
chunk0006_281_1	chr1	70549642	70549952	+	0	NA	Intergenic	L1MCa|LINE|L1	138579	NM_001902	1491	Hs.19904	NM_001902	ENSG00000116761	CTH	-	cystathionine gamma-lyase	protein-coding	0.000000	0.372990	
chunk0013_251_1	chr1	169829228	169829575	+	0	NA	exon (NM_018186, exon 13 of 24)	exon (NM_018186, exon 13 of 24)	33992	NM_018186	55732	Hs.443551	NM_018186	ENSG00000000460	C1orf112	-	chromosome 1 open reading frame 112	protein-coding	0.002882	0.376437	
chunk0125_99_1	chr3	65479889	65480351	+	0	NA	intron (NM_015520, intron 3 of 24)	intron (NM_015520, intron 3 of 24)	-413696	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.010823	0.388769	
chunk0081_201_1	chr17	42387050	42387440	+	0	NA	intron (NM_139276, intron 1 of 23)	intron (NM_139276, intron 1 of 23)	1142	NM_213662	6774	Hs.463059	NM_003150	ENSG00000168610	STAT3	ADMIO|ADMIO1|APRF|HIES	signal transducer and activator of transcription 3	protein-coding	0.010256	0.414322	
chunk0083_213_1	chr17	66968783	66969509	+	0	NA	intron (NM_014405, intron 1 of 3)	intron (NM_014405, intron 1 of 3)	4282	NM_014405	27092	Hs.514423	NM_014405	ENSG00000075461	CACNG4	-	calcium voltage-gated channel auxiliary subunit gamma 4	protein-coding	0.009642	0.517194	
chunk0025_432_1	chr10	59991493	59992223	+	0	NA	Intergenic	Intergenic	-30945	NR_024340	283025	Hs.522955	NM_001017982	ENSG00000235931	LINC01553	C10orf40	long intergenic non-protein coding RNA 1553	ncRNA	0.005479	0.391245	357(AGGAACTGTCTGTACT,-,0.00),358(GGAACTGTCTGTACTG,+,0.00)
chunk0086_143_1	chr18	21284422	21284975	+	0	NA	intron (NM_001142966, intron 1 of 32)	L1MB7|LINE|L1	42456	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.007233	0.370036	209(GTGAACATCGTGTACA,-,0.00)
chunk0055_24_1	chr13	51912089	51912402	+	0	NA	Intergenic	L2a|LINE|L2	50264	NM_031290	83446	Hs.120573	NM_031290	ENSG00000123171	CCDC70	-	coiled-coil domain containing 70	protein-coding	0.028754	0.496815	131(GAGCACAGTGTGTGCA,-,0.00),132(AGCACAGTGTGTGCAG,+,0.00)
chunk0073_263_1	chr16	12036941	12037388	+	0	NA	intron (NM_032167, intron 4 of 20)	MER58A|DNA|hAT-Charlie	60430	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.024609	0.531250	
chunk0045_383_1	chr12	52327567	52327869	+	0	NA	Intergenic	Intergenic	-6320	NM_002282	3889	Hs.720768	NM_002282	ENSG00000170523	KRT83	EKVP5|HB3|Hb-3|KRTHB3|MNLIX	keratin 83	protein-coding	0.013245	0.537954	
chunk0123_410_1	chr3	49183672	49184056	+	0	NA	intron (NM_001080528, intron 2 of 3)	L1MD1|LINE|L1	7994	NM_001080528	646498		NM_001080528	ENSG00000236980	C3orf84	-	chromosome 3 open reading frame 84	protein-coding	0.002604	0.345455	
chunk0208_272_1	chrX	21713743	21713942	+	0	NA	intron (NM_014332, intron 4 of 4)	intron (NM_014332, intron 4 of 4)	44318	NR_045617	23676	Hs.86492	NM_014332	ENSG00000091482	SMPX	DFN6|DFNX4	small muscle protein X-linked	protein-coding	0.000000	0.300000	
chunk0021_456_1	chr1	248917841	248918143	+	0	NA	exon (NM_170725, exon 3 of 3)	exon (NM_170725, exon 3 of 3)	11749	NM_001017434	267002	Hs.602037	NM_170725	ENSG00000185220	PGBD2	-	piggyBac transposable element derived 2	protein-coding	0.019868	0.518152	
chunk0185_398_1	chr7	133863553	133863917	+	0	NA	intron (NM_021807, intron 11 of 17)	intron (NM_021807, intron 11 of 17)	-38847	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.000000	0.394521	
chunk0031_160_1	chr10	125282474	125283119	+	0	NA	Intergenic	L3b|LINE|CR1	-121741	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.010853	0.510836	
chunk0173_305_1	chr6	148488423	148488739	+	0	NA	intron (NM_015278, intron 8 of 19)	L1MB3|LINE|L1	145988	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.009494	0.372240	
chunk0105_412_1	chr2	192885562	192885769	+	0	NA	Intergenic	Intergenic	135820	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.014493	0.408654	
chunk0161_39_1	chr5	165876274	165877038	+	0	NA	Intergenic	L2a|LINE|L2	1049714	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.001309	0.385621	
chunk0012_89_1	chr1	156225408	156225848	+	0	NA	exon (NM_001199654, exon 2 of 5)	exon (NM_001199654, exon 2 of 5)	12640	NM_001199653	11243	Hs.530479	NM_007221	ENSG00000160783	PMF1	-	polyamine modulated factor 1	protein-coding	0.011364	0.469388	
chunk0192_353_1	chr8	68032772	68033352	+	0	NA	intron (NM_025170, intron 6 of 23)	intron (NM_025170, intron 6 of 23)	80694	NM_025170	80243	Hs.169943	NM_024870	ENSG00000046889	PREX2	DEP.2|DEPDC2|P-REX2|PPP1R129	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 2	protein-coding	0.006897	0.397590	
chunk0177_226_1	chr7	24345399	24345666	+	0	NA	Intergenic	L1ME3C|LINE|L1	61344	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.000000	0.305970	
chunk0206_59_1	chr9	118966020	118966463	+	0	NA	Intergenic	MIR|SINE|MIR	403220	NM_014618	1620	Hs.532316	NM_014618	ENSG00000078725	BRINP1	DBC1|DBCCR1|FAM5A	BMP/retinoic acid inducible neural specific 1	protein-coding	0.009029	0.369369	
chunk0147_256_1	chr4	183443659	183444025	+	0	NA	promoter-TSS (NM_017632)	promoter-TSS (NM_017632)	-794	NM_017632	55602	Hs.592508	NM_017632	ENSG00000168564	CDKN2AIP	CARF	CDKN2A interacting protein	protein-coding	0.032787	0.487738	
chunk0013_6_1	chr1	165696551	165696801	+	0	NA	intron (NM_000696, intron 1 of 10)	intron (NM_000696, intron 1 of 10)	1987	NM_000696	223	Hs.2533	NM_000696	ENSG00000143149	ALDH9A1	ALDH4|ALDH7|ALDH9|E3|TMABADH	aldehyde dehydrogenase 9 family member A1	protein-coding	0.000000	0.378486	
chunk0198_341_1	chr8	140208982	140209546	+	0	NA	intron (NM_001160372, intron 17 of 22)	L2b|LINE|L2	248498	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.023050	0.492035	440(AGGAACAGGCCGTCCC,-,0.00),441(GGAACAGGCCGTCCCC,+,0.00)
chunk0119_422_1	chr22	49933267	49933466	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	14736	NM_001135101	79174	Hs.211282	NM_024324	ENSG00000184164	CRELD2	-	cysteine rich with EGF like domains 2	protein-coding	0.015075	0.605000	45(AGGAACATGCTGTTCT,-,0.00),46(GGAACATGCTGTTCTA,+,0.00)
chunk0002_109_1	chr1	15642135	15642670	+	0	NA	intron (NM_032341, intron 5 of 9)	intron (NM_032341, intron 5 of 9)	-17467	NM_006511	6248	Hs.239459	NM_006511	ENSG00000215695	RSC1A1	RS1	regulator of solute carriers 1	protein-coding	0.011215	0.412313	
chunk0101_187_1	chr2	129452619	129453021	+	0	NA	Intergenic	L1MD2|LINE|L1	-178929	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.004975	0.270471	
chunk0087_11_1	chr18	30818560	30819100	+	0	NA	Intergenic	L1ME3A|LINE|L1	223985	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.003704	0.349353	
chunk0162_336_1	chr6	6897346	6897686	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-210081	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.002941	0.463343	
chunk0211_421_1	chrX	129118580	129119105	+	0	NA	Intergenic	Intergenic	404663	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.009524	0.334601	
chunk0077_16_1	chr16	75016871	75017339	+	0	NA	intron (NM_032268, intron 1 of 4)	intron (NM_032268, intron 1 of 4)	18088	NM_032268	84937	Hs.427284	NM_032268	ENSG00000186187	ZNRF1	NIN283	zinc and ring finger 1	protein-coding	0.000000	0.341151	
chunk0028_435_1	chr10	93896965	93897659	+	0	NA	intron (NM_153226, intron 1 of 2)	intron (NM_153226, intron 1 of 2)	3339	NM_153226	159371	Hs.632085	NM_153226	ENSG00000176273	SLC35G1	C10orf60|POST|TMEM20	solute carrier family 35 member G1	protein-coding	0.005764	0.434532	
chunk0178_393_1	chr7	40570216	40570637	+	0	NA	intron (NM_001193312, intron 11 of 12)	L2c|LINE|L2	409513	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.002375	0.407583	178(GAGAACAGCATGAGCT,-,0.00),179(AGAACAGCATGAGCTG,+,0.00)
chunk0037_299_1	chr11	76356232	76356431	+	0	NA	intron (NR_130898, intron 4 of 5)	intron (NR_130898, intron 4 of 5)	24634	NR_130898	5612	Hs.503315	NM_004705	ENSG00000137492	THAP12	DAP4|P52rIPK|PRKRIR|THAP0	THAP domain containing 12	protein-coding	0.010050	0.500000	
chunk0171_432_1	chr6	131651824	131652812	+	0	NA	intron (NR_133007, intron 3 of 23)	intron (NR_133007, intron 3 of 23)	15083	NM_005021	5169	Hs.486489	NM_005021	ENSG00000154269	ENPP3	B10|CD203c|NPP3|PD-IBETA|PDNP3	ectonucleotide pyrophosphatase/phosphodiesterase 3	protein-coding	0.007085	0.427705	473(AAGCTCACAGTGTACC,-,0.00),474(AGCTCACAGTGTACCT,+,0.00)
chunk0103_124_1	chr2	161802889	161803323	+	0	NA	intron (NM_001178016, intron 3 of 26)	intron (NM_001178016, intron 3 of 26)	178771	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.002304	0.324138	
chunk0019_419_1	chr1	230770593	230770963	+	0	NA	intron (NM_016452, intron 6 of 18)	intron (NM_016452, intron 6 of 18)	23363	NM_016452	10753	Hs.498021	NM_006615	ENSG00000135773	CAPN9	GC36|nCL-4	calpain 9	protein-coding	0.008108	0.528302	
chunk0004_391_1	chr1	51956447	51956725	+	0	NA	intron (NM_002867, intron 2 of 4)	L2b|LINE|L2	34178	NM_002867	5865	Hs.123072	NM_002867	ENSG00000169213	RAB3B	-	RAB3B, member RAS oncogene family	protein-coding	0.003597	0.480287	
chunk0132_41_1	chr3	154801255	154801676	+	0	NA	Intergenic	Intergenic	-278182	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.011876	0.379147	
chunk0151_189_1	chr5	50505231	50506045	+	0	NA	Intergenic	Intergenic	-64238	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.006143	0.402454	
chunk0105_162_1	chr2	186840772	186841246	+	0	NA	intron (NM_182521, intron 3 of 8)	intron (NM_182521, intron 3 of 8)	8161	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.002110	0.256842	
chunk0198_404_1	chr8	141853108	141853374	+	0	NA	Intergenic	Intergenic	-66928	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.026316	0.588015	140(GAGTGCATCCTGTGCC,-,0.00)
chunk0170_390_1	chr6	117170082	117170597	+	0	NA	Intergenic	Intergenic	-95219	NM_182645	245806	Hs.99324	NM_153453	ENSG00000170162	VGLL2	VGL2|VITO1	vestigial like family member 2	protein-coding	0.000000	0.292636	
chunk0124_198_1	chr3	55730938	55731515	+	0	NA	intron (NR_132749, intron 14 of 17)	intron (NR_132749, intron 14 of 17)	-71757	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.003466	0.455017	
chunk0038_218_1	chr11	86706102	86706824	+	0	NA	Intergenic	Intergenic	-33827	NM_001161586	10873	Hs.199743	NM_006680	ENSG00000151376	ME3	NADP-ME	malic enzyme 3	protein-coding	0.004155	0.424620	
chunk0122_221_1	chr3	33591128	33591426	+	0	NA	intron (NM_015097, intron 21 of 38)	intron (NM_015097, intron 21 of 38)	68164	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.006711	0.424749	
chunk0054_102_1	chr13	42790495	42790809	+	0	NA	3' UTR (NM_182508, exon 4 of 4)	3' UTR (NM_182508, exon 4 of 4)	9102	NM_182508	144809	Hs.16970	NM_182508	ENSG00000179813	FAM216B	C13orf30	family with sequence similarity 216 member B	protein-coding	0.000000	0.400000	
chunk0078_184_1	chr17	4705419	4705851	+	0	NA	TTS (NR_103482)	TTS (NR_103482)	-1298	NM_001278241	27043	Hs.744899	NM_014389	ENSG00000141456	PELP1	MNAR|P160	proline, glutamate and leucine rich protein 1	protein-coding	0.018519	0.406467	
chunk0194_139_1	chr8	84386944	84387307	+	0	NA	intron (NM_001100392, intron 2 of 9)	MIRb|SINE|MIR	202260	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.011019	0.357143	
chunk0133_456_1	chr3	175232846	175233568	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	37889	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.004155	0.319502	
chunk0163_273_1	chr6	13413498	13413898	+	0	NA	intron (NM_018988, intron 1 of 1)	intron (NM_018988, intron 1 of 1)	-5561	NM_001242630	54438	Hs.484686	NM_018988	ENSG00000145990	GFOD1	ADG-90|C6orf114	glucose-fructose oxidoreductase domain containing 1	protein-coding	0.005000	0.516209	210(TGGGACAGCCTGTGCT,-,0.00),211(GGGACAGCCTGTGCTG,+,0.00)
chunk0184_244_1	chr7	117711505	117711852	+	0	NA	exon (NM_033427, exon 23 of 23)	exon (NM_033427, exon 23 of 23)	161829	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.000000	0.402299	
chunk0123_160_1	chr3	43475024	43475419	+	0	NA	intron (NM_018075, intron 11 of 12)	L1MC|LINE|L1	-123259	NR_046757	100873954	Hs.600984	NR_046757		SNRK-AS1	-	SNRK antisense RNA 1	ncRNA	0.007595	0.345960	
chunk0207_95_1	chrX	9640017	9640216	+	0	NA	intron (NM_001139468, intron 3 of 17)	intron (NM_001139468, intron 3 of 17)	125849	NM_000273	4935	Hs.74124	NM_000273	ENSG00000101850	GPR143	NYS6|OA1	G protein-coupled receptor 143	protein-coding	0.010050	0.340000	
chunk0196_82_1	chr8	102685427	102685920	+	0	NA	Intergenic	Intergenic	-29771	NM_005655	7071	Hs.435001	NM_005655	ENSG00000155090	KLF10	EGR-alpha|EGRA|TIEG|TIEG1	Kruppel like factor 10	protein-coding	0.010142	0.491903	
chunk0203_43_1	chr9	83069153	83069823	+	0	NA	Intergenic	L1ME1|LINE|L1	-6360	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002985	0.345753	
chunk0032_226_1	chr11	7585568	7586193	+	0	NA	intron (NM_003621, intron 3 of 23)	intron (NM_003621, intron 3 of 23)	-11306	NM_001256568	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.004800	0.431310	
chunk0067_44_1	chr15	40775753	40776060	+	0	NA	intron (NM_018163, intron 6 of 10)	intron (NM_018163, intron 6 of 10)	5945	NM_001130448	643338	Hs.631715	NM_001130448	ENSG00000188277	C15orf62	-	chromosome 15 open reading frame 62	protein-coding	0.009772	0.561688	142(GGGCACAAAGTGTCCC,-,0.00),143(GGCACAAAGTGTCCCA,+,0.00)
chunk0117_7_1	chr22	10717001	10717295	+	0	NA	Intergenic	Intergenic	244381	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.030612	0.413559	
chunk0059_77_1	chr14	30596579	30597068	+	0	NA	intron (NM_001308097, intron 5 of 13)	intron (NM_001308097, intron 5 of 13)	-25431	NM_182835	23256	Hs.369168	NM_016106	ENSG00000092108	SCFD1	C14orf163|RA410|SLY1|SLY1P|STXBP1L2	sec1 family domain containing 1	protein-coding	0.004090	0.351020	
chunk0026_369_1	chr10	69330540	69330861	+	0	NA	intron (NM_000188, intron 1 of 17)	MER39|LTR|ERV1	11853	NM_000188	3098	Hs.370365	NM_000188	ENSG00000156515	HK1	HK|HK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1|RP79|hexokinase	hexokinase 1	protein-coding	0.003115	0.444099	
chunk0159_237_1	chr5	141711434	141711944	+	0	NA	Intergenic	Intergenic	-29456	NM_022481	64411	Hs.726187	NM_022481	ENSG00000120318	ARAP3	CENTD3|DRAG1	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	protein-coding	0.017647	0.563601	
chunk0200_186_1	chr9	19420968	19421320	+	0	NA	intron (NM_001010887, intron 1 of 5)	Tigger3a|DNA|TcMar-Tigger	12217	NM_001010887	340485	Hs.41379	NM_001010887	ENSG00000177076	ACER2	ALKCDase2|ASAH3L	alkaline ceramidase 2	protein-coding	0.000000	0.356941	
chunk0132_16_1	chr3	154450569	154451196	+	0	NA	Intergenic	Intergenic	-21167	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.007974	0.310510	
chunk0181_132_1	chr7	81000134	81000473	+	0	NA	Intergenic	Intergenic	-80952	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.005900	0.344118	
chunk0083_38_1	chr17	63432380	63432839	+	0	NA	3' UTR (NM_001017916, exon 6 of 6)	3' UTR (NM_001017916, exon 6 of 6)	8237	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.019608	0.502174	
chunk0065_457_1	chr14	106846020	106846721	+	0	NA	Intergenic	L1PBb|LINE|L1	4629	NR_049827	100847062		NR_049827	ENSG00000265929	MIR5195	-	microRNA 5195	ncRNA	0.005706	0.316239	369(TTGGACAGAATGTTCT,-,0.00),370(TGGACAGAATGTTCTG,+,0.00)
chunk0039_357_1	chr11	105750855	105751231	+	0	NA	intron (NM_001112812, intron 2 of 9)	intron (NM_001112812, intron 2 of 9)	140359	NM_001112812	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.005319	0.318302	
chunk0062_390_1	chr14	74774025	74774238	+	0	NA	intron (NM_019589, intron 1 of 20)	MER47B|DNA|TcMar-Tigger	10765	NM_019589	56252	Hs.531111	NM_019589	ENSG00000119596	YLPM1	C14orf170|PPP1R169|ZAP113|ZAP3	YLP motif containing 1	protein-coding	0.004695	0.364486	
chunk0019_169_1	chr1	226133239	226133483	+	0	NA	Intergenic	Intergenic	53361	NM_022735	64746	Hs.520207	NM_022735	ENSG00000182827	ACBD3	GCP60|GOCAP1|GOLPH1|PAP7	acyl-CoA binding domain containing 3	protein-coding	0.020492	0.546939	
chunk0096_187_1	chr2	29908676	29909191	+	0	NA	intron (NM_004304, intron 1 of 28)	intron (NM_004304, intron 1 of 28)	12678	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.001942	0.397287	227(AGGAAGAGACTGTACT,-,0.00),228(GGAAGAGACTGTACTT,+,0.00)
chunk0087_46_1	chr18	31369287	31370054	+	0	NA	intron (NR_110788, intron 1 of 3)	L1ME2|LINE|L1	-7107	NM_177986	147409	Hs.407618	NM_177986	ENSG00000175065	DSG4	CDGF13|CDHF13|HYPT6|LAH	desmoglein 4	protein-coding	0.003911	0.321615	
chunk0035_263_1	chr11	46512870	46513281	+	0	NA	intron (NM_001300731, intron 7 of 16)	intron (NM_001300731, intron 7 of 16)	-61186	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.007299	0.400485	
chunk0176_407_1	chr7	19310672	19310957	+	0	NA	Intergenic	Intergenic	-165393	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.021053	0.412587	105(GGGACCAGAGTGTGCC,-,0.00),106(GGACCAGAGTGTGCCC,+,0.00)
chunk0077_41_1	chr16	75599831	75600050	+	0	NA	non-coding (NR_036460, exon 11 of 11)	non-coding (NR_036460, exon 11 of 11)	23383	NR_036460									0.004566	0.368182	
chunk0164_264_1	chr6	23649896	23650703	+	0	NA	Intergenic	Intergenic	-475887	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.008674	0.381188	393(GAGTACAGGATGAGCT,-,0.00),394(AGTACAGGATGAGCTG,+,0.00)
chunk0092_59_1	chr19	20082964	20083487	+	0	NA	intron (NM_007138, intron 1 of 3)	LTR5_Hs|LTR|ERVK	5231	NM_007138	7643	Hs.55304	NM_007138	ENSG00000213988	ZNF90	HTF9	zinc finger protein 90	protein-coding	0.019120	0.461832	
chunk0167_17_1	chr6	53679733	53679952	+	0	NA	Intergenic	Intergenic	-14134	NM_001003760	401265	Hs.131064	NM_001003760	ENSG00000124743	KLHL31	BKLHD6|KBTBD1|KLHL|bA345L23.2	kelch like family member 31	protein-coding	0.036530	0.572727	
chunk0134_310_1	chr3	180863593	180864097	+	0	NA	intron (NR_109986, intron 1 of 13)	L1MB8|LINE|L1	6333	NR_109986	101928882	Hs.734668	NR_109986	ENSG00000285336	LOC101928882	-	uncharacterized LOC101928882	ncRNA	0.007937	0.376238	
chunk0072_337_1	chr15	99273013	99273212	+	0	NA	intron (NM_001284400, intron 2 of 8)	intron (NM_001284400, intron 2 of 8)	15587	NR_073383	7190	Hs.656611	NR_073383	ENSG00000259706	HSP90B2P	GRP94P1|GRP94b|HSP|HSPCP2|TRA1P1|TRAP1	heat shock protein 90 beta family member 2, pseudogene	pseudo	0.005025	0.355000	
chunk0149_76_1	chr5	17261300	17261878	+	0	NA	intron (NM_006317, intron 1 of 1)	intron (NM_006317, intron 1 of 1)	44028	NM_006317	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.010381	0.385147	
chunk0048_52_1	chr12	78221012	78221330	+	0	NA	Intergenic	Intergenic	389882	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.003145	0.354232	
chunk0129_222_1	chr3	121892032	121892231	+	0	NA	Intergenic	Intergenic	-2193	NM_001145998	6565	Hs.518089	NM_021082	ENSG00000163406	SLC15A2	PEPT2	solute carrier family 15 member 2	protein-coding	0.000000	0.385000	
chunk0040_143_1	chr11	113322650	113323060	+	0	NA	intron (NM_017868, intron 2 of 21)	L2b|LINE|L2	8326	NM_017868	54970	Hs.288772	NM_017868	ENSG00000149292	TTC12	TPARM	tetratricopeptide repeat domain 12	protein-coding	0.002439	0.401460	
chunk0108_165_1	chr2	231365143	231365797	+	0	NA	intron (NM_001271466, intron 22 of 23)	intron (NM_001271466, intron 22 of 23)	2762	NR_039937	100616317		NR_039937	ENSG00000263641	MIR4777	-	microRNA 4777	ncRNA	0.030581	0.526718	
chunk0013_349_1	chr1	172186528	172187195	+	0	NA	intron (NM_001136127, intron 14 of 19)	intron (NM_001136127, intron 14 of 19)	-42026	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.002999	0.419162	
chunk0204_182_1	chr9	96139685	96139888	+	0	NA	Intergenic	Intergenic	-23375	NR_132344	158434	Hs.381771	NM_001256408	ENSG00000275465	LOC158434	-	uncharacterized LOC158434	ncRNA	0.019704	0.416667	
chunk0169_405_1	chr6	108348538	108349117	+	0	NA	intron (NM_145315, intron 3 of 12)	intron (NM_145315, intron 3 of 12)	53933	NM_145315	246269	Hs.259666	NM_145315	ENSG00000135537	AFG1L	AFG1|LACE1|c222389	AFG1 like ATPase	protein-coding	0.001727	0.346552	
chunk0011_256_1	chr1	150836305	150836534	+	0	NA	exon (NM_001197325, exon 6 of 21)	exon (NM_001197325, exon 6 of 21)	-27978	NM_000396	1513	Hs.632466	NM_000396	ENSG00000143387	CTSK	CTS02|CTSO|CTSO1|CTSO2|PKND|PYCD	cathepsin K	protein-coding	0.013100	0.443478	
chunk0076_443_1	chr16	73776864	73777109	+	0	NA	Intergenic	Intergenic	390181	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.020408	0.426829	66(ATGCACATTGTGTACC,-,0.00),67(TGCACATTGTGTACCT,+,0.00)
chunk0191_281_1	chr8	53815375	53815896	+	0	NA	intron (NM_015941, intron 5 of 13)	Charlie7|DNA|hAT-Charlie	27407	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.001919	0.383142	
chunk0168_121_1	chr6	82014967	82015444	+	0	NA	Intergenic	L3|LINE|CR1	-201013	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.004193	0.422594	
chunk0116_140_1	chr21	36274115	36274497	+	0	NA	intron (NM_005128, intron 27 of 36)	L2a|LINE|L2	-45883	NM_015358	23515	Hs.421150	NM_015358	ENSG00000159256	MORC3	NXP2|ZCW5|ZCWCC3	MORC family CW-type zinc finger 3	protein-coding	0.010471	0.409922	84(CAGTACAGTGTGTATT,-,0.00),85(AGTACAGTGTGTATTG,+,0.00)
chunk0114_67_1	chr21	9099916	9100165	+	0	NA	intron (NR_038329, intron 2 of 2)	CER|Satellite|Satellite	29721	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.012048	0.472000	
chunk0113_210_1	chr20	53786093	53786421	+	0	NA	Intergenic	Intergenic	89452	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.009146	0.398176	
chunk0087_325_1	chr18	39946809	39947066	+	0	NA	Intergenic	Intergenic	-119349	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.399225	
chunk0160_337_1	chr5	159982118	159982700	+	0	NA	Intergenic	Intergenic	-26691	NM_003314	7265	Hs.519718	NM_003314	ENSG00000113312	TTC1	TPR1	tetratricopeptide repeat domain 1	protein-coding	0.003436	0.442539	
chunk0129_340_1	chr3	124781733	124782333	+	0	NA	intron (NM_002213, intron 10 of 14)	intron (NM_002213, intron 10 of 14)	49594	NR_036088	100422864		NR_036088	ENSG00000265981	MIR544B	-	microRNA 544b	ncRNA	0.006667	0.442596	
chunk0007_341_1	chr1	84826895	84828118	+	0	NA	intron (NM_012152, intron 2 of 2)	intron (NM_012152, intron 2 of 2)	65707	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.005724	0.392157	257(GTGTACAATGTGTGCC,-,0.00),258(TGTACAATGTGTGCCT,+,0.00),979(AAGAACACACAGTTCA,-,0.00),980(AGAACACACAGTTCAT,+,0.00)
chunk0078_55_1	chr17	1433794	1434362	+	0	NA	intron (NM_005206, intron 2 of 2)	MER58B|DNA|hAT-Charlie	22189	NM_005206	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.012324	0.437610	
chunk0050_106_1	chr12	101981263	101981902	+	0	NA	Intergenic	Intergenic	80542	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.003130	0.343750	
chunk0017_278_1	chr1	209787636	209787986	+	0	NA	3' UTR (NM_006147, exon 9 of 9)	3' UTR (NM_006147, exon 9 of 9)	-3081	NM_152485	148304	Hs.497642	NM_152485	ENSG00000162757	C1orf74	URLC4	chromosome 1 open reading frame 74	protein-coding	0.002857	0.444444	
chunk0069_18_1	chr15	60374574	60375149	+	0	NA	intron (NM_001002857, intron 4 of 13)	intron (NM_001002857, intron 4 of 13)	23125	NM_001136015	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.012174	0.486111	
chunk0151_376_1	chr5	55181997	55182277	+	0	NA	Intergenic	Intergenic	-8960	NM_001170402	166979	Hs.669184	NM_152623	ENSG00000164287	CDC20B	G6VTS76519	cell division cycle 20B	protein-coding	0.003571	0.370107	179(AGTGCATGATGTTCTT,+,0.00)
chunk0151_367_1	chr5	54915267	54916100	+	0	NA	Intergenic	LTR40A1|LTR|ERVL	69903	NM_007036	11082	Hs.129944	NM_007036	ENSG00000164283	ESM1	endocan	endothelial cell specific molecule 1	protein-coding	0.003601	0.394484	
chunk0134_63_1	chr3	176185242	176185503	+	0	NA	Intergenic	Intergenic	-329731	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.003831	0.267176	4(AGGAACATAGTGTACT,-,0.00),5(GGAACATAGTGTACTA,+,0.00)
chunk0128_341_1	chr3	112314548	112314897	+	0	NA	Intergenic	MER4C|LTR|ERV1	-18347	NM_005944	4345	Hs.79015	NM_005944	ENSG00000091972	CD200	MOX1|MOX2|MRC|OX-2	CD200 molecule	protein-coding	0.005731	0.368571	
chunk0079_108_1	chr17	12277838	12278484	+	0	NA	Intergenic	UCON55|DNA|TcMar-Tigger	196262	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.006192	0.421947	
chunk0130_328_1	chr3	138227472	138227767	+	0	NA	intron (NM_001282342, intron 4 of 19)	intron (NM_001282342, intron 4 of 19)	40371	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.003390	0.381757	
chunk0136_124_1	chr4	3720302	3720720	+	0	NA	Intergenic	Intergenic	-42656	NR_034136	100133461	Hs.554274	NR_034136	ENSG00000250632	LINC02171	-	long intergenic non-protein coding RNA 2171	ncRNA	0.019139	0.465394	
chunk0061_433_1	chr14	65467997	65468335	+	0	NA	intron (NM_004480, intron 2 of 9)	OldhAT1|DNA|hAT-Ac	-2936	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.017751	0.410029	
chunk0123_30_1	chr3	40644050	40644508	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	119401	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.000000	0.398693	
chunk0005_443_1	chr1	63421014	63421213	+	0	NA	intron (NM_013339, intron 12 of 14)	L2a|LINE|L2	53523	NM_013339	29929	Hs.258501	NM_013339	ENSG00000088035	ALG6	CDG1C	ALG6 alpha-1,3-glucosyltransferase	protein-coding	0.005025	0.325000	
chunk0190_352_1	chr8	39638594	39638970	+	0	NA	intron (NM_014237, intron 10 of 19)	intron (NM_014237, intron 10 of 19)	54214	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.002660	0.244032	
chunk0154_146_1	chr5	79375704	79376278	+	0	NA	3' UTR (NM_004272, exon 9 of 9)	3' UTR (NM_004272, exon 9 of 9)	137845	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.006969	0.332174	
chunk0130_454_1	chr3	141412288	141412788	+	0	NA	intron (NM_001080412, intron 7 of 7)	intron (NM_001080412, intron 7 of 7)	-74509	NM_001303246	5922	Hs.98445	NM_006506	ENSG00000155903	RASA2	GAP1M	RAS p21 protein activator 2	protein-coding	0.010000	0.397206	170(CAGAACAGTCTGTTCT,-,0.00),171(AGAACAGTCTGTTCTT,+,0.00)
chunk0038_346_1	chr11	92911482	92911681	+	0	NA	Intergenic	Intergenic	-58042	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.005025	0.525000	
chunk0157_358_1	chr5	123340194	123340726	+	0	NA	Intergenic	Intergenic	83132	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.009398	0.356473	
chunk0130_209_1	chr3	133944785	133945709	+	0	NA	exon (NM_005630, exon 10 of 14)	exon (NM_005630, exon 10 of 14)	-15435	NM_025041	80111	Hs.287691	NM_025041	ENSG00000174640	C3orf36	-	chromosome 3 open reading frame 36	ncRNA	0.017316	0.536216	462(TAGAACTTGATGTGCT,-,0.00),463(AGAACTTGATGTGCTG,+,0.00)
chunk0059_111_1	chr14	31159866	31160139	+	0	NA	intron (NM_015382, intron 10 of 42)	intron (NM_015382, intron 10 of 42)	47521	NM_015382	25831	Hs.708017	NM_015382	ENSG00000092148	HECTD1	EULIR	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.018315	0.361314	
chunk0201_127_1	chr9	35489559	35489758	+	0	NA	promoter-TSS (NM_014806)	promoter-TSS (NM_014806)	-294	NM_014806	9853	Hs.493796	NM_014806	ENSG00000198853	RUSC2	Iporin|MRT61	RUN and SH3 domain containing 2	protein-coding	0.035176	0.615000	
chunk0078_43_1	chr17	1115130	1115524	+	0	NA	intron (NM_021962, intron 2 of 22).2	L2b|LINE|L2	-6227	NM_001092	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.012690	0.554430	
chunk0210_424_1	chrX	102534463	102534694	+	0	NA	Intergenic	L1M1|LINE|L1	-15387	NR_002216	55999	Hs.454283	NR_002216	ENSG00000196970	NXF4	-	nuclear RNA export factor 4 pseudogene	pseudo	0.008658	0.379310	
chunk0027_165_1	chr10	74897135	74897528	+	0	NA	intron (NM_001256468, intron 3 of 17)	intron (NM_001256468, intron 3 of 17)	70918	NM_001256468	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.010178	0.467005	
chunk0212_197_1	chrX	134241465	134241767	+	0	NA	intron (NM_001101357, intron 1 of 1)	intron (NM_001101357, intron 1 of 1)	4569	NM_001101357	347475	Hs.679431	NM_001101357	ENSG00000203952	CCDC160	-	coiled-coil domain containing 160	protein-coding	0.003311	0.399340	141(GAGGACTACTTGTCCT,-,0.00)
chunk0122_353_1	chr3	37477326	37477531	+	0	NA	intron (NM_002207, intron 3 of 27)	intron (NM_002207, intron 3 of 27)	25106	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.004878	0.519417	
chunk0151_245_1	chr5	51510575	51510870	+	0	NA	Intergenic	Intergenic	-127390	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.000000	0.358108	134(CAGCTCATTCTGTCCC,-,0.00),135(AGCTCATTCTGTCCCA,+,0.00)
chunk0009_455_1	chr1	111612606	111612836	+	0	NA	Intergenic	Intergenic	-4403	NR_034126	100129269	Hs.689728	NR_034126		LINC01160	-	long intergenic non-protein coding RNA 1160	ncRNA	0.008696	0.294372	
chunk0203_184_1	chr9	86369155	86369628	+	0	NA	Intergenic	LTR26|LTR|ERV1	-14904	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.002114	0.386076	297(GAGAACAAGCTGGCCT,-,0.00)
chunk0085_297_1	chr18	8023348	8023798	+	0	NA	intron (NM_001105244, intron 7 of 32)	intron (NM_001105244, intron 7 of 32)	343461	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.000000	0.308204	
chunk0203_55_1	chr9	83146413	83146660	+	0	NA	Intergenic	Intergenic	-83408	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.012146	0.362903	
chunk0118_204_1	chr22	31653367	31653645	+	0	NA	Intergenic	Intergenic	-22682	NM_014338	23761	Hs.420559	NM_014338	ENSG00000241878	PISD	DJ858B16|PSD|PSDC|PSSC|dJ858B16.2	phosphatidylserine decarboxylase	protein-coding	0.007194	0.433692	
chunk0118_459_1	chr22	39813069	39813278	+	0	NA	intron (NM_152512, intron 5 of 6)	intron (NM_152512, intron 5 of 6)	80617	NM_152512	150350	Hs.474869	NM_152512	ENSG00000176177	ENTHD1	CACNA1I|dJ370M22.3	ENTH domain containing 1	protein-coding	0.014354	0.466667	
chunk0009_64_1	chr1	100860550	100860938	+	0	NA	Intergenic	Intergenic	34435	NM_001261440	2135	Hs.357637	NM_001439	ENSG00000162694	EXTL2	EXTR2	exostosin like glycosyltransferase 2	protein-coding	0.002577	0.416452	
chunk0033_281_1	chr11	19401178	19401648	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	50689	NM_001111018	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.010638	0.352442	
chunk0105_407_1	chr2	192769997	192770471	+	0	NA	intron (NR_002769, intron 2 of 2)	intron (NR_002769, intron 2 of 2)	20389	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.002110	0.301053	
chunk0151_80_1	chr5	42787814	42788153	+	0	NA	intron (NM_001134848, intron 6 of 8)	L1PA17|LINE|L1	23939	NM_005410	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.002950	0.361765	
chunk0095_432_1	chr2	25079543	25080139	+	0	NA	intron (NM_014971, intron 1 of 22)	intron (NM_014971, intron 1 of 22)	37737	NM_014971	22979	Hs.4892	NM_014971	ENSG00000084710	EFR3B	KIAA0953	EFR3 homolog B	protein-coding	0.010067	0.370184	
chunk0155_409_1	chr5	99275632	99275845	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	-258252	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.004695	0.500000	
chunk0002_27_1	chr1	12407196	12407927	+	0	NA	intron (NM_018156, intron 62 of 68)	intron (NM_018156, intron 62 of 68)	-99685	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.009576	0.374317	
chunk0036_430_1	chr11	68406885	68407236	+	0	NA	intron (NM_001291902, intron 9 of 22)	intron (NM_001291902, intron 9 of 22)	-53658	NM_001164164	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.022792	0.394886	
chunk0183_320_1	chr7	108049963	108050316	+	0	NA	intron (NM_007356, intron 26 of 33)	MER58A|DNA|hAT-Charlie	-46780	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.008499	0.420904	
chunk0195_99_1	chr8	94444150	94445048	+	0	NA	intron (NM_001205262, intron 3 of 3)	MER67B|LTR|ERV1	-7647	NM_001205263	25788	Hs.30561	NM_006550	ENSG00000197275	RAD54B	RDH54	RAD54 homolog B	protein-coding	0.002227	0.384872	
chunk0069_434_1	chr15	68352528	68352727	+	0	NA	intron (NM_001004439, intron 7 of 29)	MamTip1|DNA|hAT-Tip100	74824	NM_015322	10116	Hs.362733	NM_015322	ENSG00000169018	FEM1B	F1A-ALPHA|F1AA|FEM1-beta	fem-1 homolog B	protein-coding	0.010050	0.390000	28(GAAAACAGGATGTGCC,-,0.00),29(AAAACAGGATGTGCCA,+,0.00)
chunk0035_334_1	chr11	47947093	47947609	+	0	NA	Intergenic	Intergenic	-33207	NM_001098503	5795	Hs.318547	NM_002843	ENSG00000149177	PTPRJ	CD148|DEP1|HPTPeta|R-PTP-ETA|SCC1	protein tyrosine phosphatase receptor type J	protein-coding	0.017442	0.526112	
chunk0123_286_1	chr3	46405386	46405943	+	0	NA	intron (NR_125406, intron 1 of 3)	intron (NR_125406, intron 1 of 3)	1395	NR_125406	102724297	Hs.622021	NR_125406		LOC102724297	-	uncharacterized LOC102724297	ncRNA	0.014363	0.510753	
chunk0200_260_1	chr9	21816756	21816999	+	0	NA	intron (NM_002451, intron 3 of 7)	intron (NM_002451, intron 3 of 7)	14241	NM_002451	4507	Hs.193268	NM_002451	ENSG00000099810	MTAP	BDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fus	methylthioadenosine phosphorylase	protein-coding	0.004115	0.327869	
chunk0102_127_1	chr2	145026957	145027669	+	0	NA	intron (NR_033870, intron 3 of 4)	intron (NR_033870, intron 3 of 4)	359346	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.009831	0.366059	
chunk0014_381_1	chr1	182707103	182707617	+	0	NA	Intergenic	Intergenic	-34428	NM_033345	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.009728	0.462136	
chunk0052_112_1	chr13	22841782	22842060	+	0	NA	Intergenic	Intergenic	56260	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.007194	0.455197	
chunk0041_366_1	chr11	131329086	131329295	+	0	NA	Intergenic	Intergenic	-41286	NM_001048209	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.014354	0.533333	
chunk0053_104_1	chr13	28823042	28823523	+	0	NA	Intergenic	Intergenic	-104269	NM_001135919	283537	Hs.117167	NM_181785	ENSG00000139508	SLC46A3	FKSG16	solute carrier family 46 member 3	protein-coding	0.010395	0.408714	
chunk0041_377_1	chr11	131851956	131852193	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	-58744	NM_016522	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.025316	0.554622	160(AGGGACAGAGTGTTCT,-,0.00),161(GGGACAGAGTGTTCTA,+,0.00)
chunk0084_83_1	chr17	75148487	75148813	+	0	NA	exon (NM_016185, exon 2 of 5)	exon (NM_016185, exon 2 of 5)	4643	NM_001288610	51155	Hs.532803	NM_016185	ENSG00000189159	JPT1	ARM2|HN1|HN1A	Jupiter microtubule associated homolog 1	protein-coding	0.003067	0.422018	96(AGGCCATTTTGTTCTT,+,0.00)
chunk0183_242_1	chr7	107069186	107069796	+	0	NA	intron (NM_002736, intron 1 of 10)	intron (NM_002736, intron 1 of 10)	24758	NM_002736	5577	Hs.433068	NM_002736	ENSG00000005249	PRKAR2B	PRKAR2|RII-BETA	protein kinase cAMP-dependent type II regulatory subunit beta	protein-coding	0.009836	0.386252	292(TAGTACATTGTGTCCT,-,0.00),293(AGTACATTGTGTCCTT,+,0.00)
chunk0152_129_1	chr5	58894737	58894936	+	0	NA	Intergenic	Intergenic	105096	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.015075	0.475000	
chunk0111_197_1	chr20	25754695	25754898	+	0	NA	Intergenic	Intergenic	41446	NR_027061	728882	Hs.682103	NR_026714		FAM182B	-	family with sequence similarity 182 member B	ncRNA	0.009852	0.323529	
chunk0096_270_1	chr2	31916791	31917515	+	0	NA	intron (NM_015955, intron 5 of 8)	intron (NM_015955, intron 5 of 8)	93511	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.009669	0.328276	332(CAGAGCATCATGTACT,-,0.00),333(AGAGCATCATGTACTT,+,0.00)
chunk0166_442_1	chr6	52990397	52990596	+	0	NA	intron (NM_001512, intron 2 of 6)	intron (NM_001512, intron 2 of 6)	4884	NM_001512	2941	Hs.485557	NM_001512	ENSG00000170899	GSTA4	GSTA4-4|GTA4	glutathione S-transferase alpha 4	protein-coding	0.005025	0.510000	118(CTGATCAGCCTGTTCC,-,0.00),119(TGATCAGCCTGTTCCT,+,0.00)
chunk0042_142_1	chr12	3842560	3842969	+	0	NA	intron (NR_104461, intron 1 of 8)	intron (NR_104461, intron 1 of 8)	30684	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.009780	0.351220	
chunk0046_459_1	chr12	64966834	64967501	+	0	NA	intron (NR_033988, intron 2 of 2)	L1PB|LINE|L1	83393	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.001499	0.341317	
chunk0199_340_1	chr9	11106799	11107280	+	0	NA	Intergenic	L1M1|LINE|L1	493833	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.006237	0.383817	
chunk0046_204_1	chr12	59055440	59055721	+	0	NA	Intergenic	MamRep137|DNA|TcMar-Tigger	-135042	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.000000	0.382979	
chunk0013_323_1	chr1	171521472	171522048	+	0	NA	intron (NM_015172, intron 6 of 33)	intron (NM_015172, intron 6 of 33)	36233	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.003472	0.360485	
chunk0004_119_1	chr1	44631953	44632167	+	0	NA	intron (NM_018150, intron 5 of 14)	CpG	42548	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.144860	0.776744	
chunk0208_263_1	chrX	21401563	21401978	+	0	NA	intron (NM_014927, intron 1 of 21)	intron (NM_014927, intron 1 of 21)	27352	NM_001168648	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.002410	0.341346	
chunk0140_112_1	chr4	68670489	68671006	+	0	NA	promoter-TSS (NM_001076)	promoter-TSS (NM_001076)	29	NM_001076	7366	Hs.150207	NM_001076	ENSG00000196620	UGT2B15	HLUG4|UDPGT 2B8|UDPGT2B15|UDPGTH3|UGT2B8	UDP glucuronosyltransferase family 2 member B15	protein-coding	0.005803	0.355212	
chunk0040_129_1	chr11	112357494	112357779	+	0	NA	intron (NR_126004, intron 2 of 3)	intron (NR_126004, intron 2 of 3)	86887	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.003509	0.538462	32(GAGAACACTGAGATCC,-,0.00)
chunk0134_40_1	chr3	175721995	175722890	+	0	NA	intron (NM_207015, intron 11 of 13)	intron (NM_207015, intron 11 of 13)	53891	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.004469	0.328125	
chunk0054_117_1	chr13	42924163	42924780	+	0	NA	intron (NM_001002264, intron 7 of 12)	intron (NM_001002264, intron 7 of 12)	-51727	NR_126389	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.014587	0.428803	298(CAGCACACGCAGTTCT,-,0.00),299(AGCACACGCAGTTCTG,+,0.00)
chunk0104_122_1	chr2	173038052	173038773	+	0	NA	intron (NM_001282899, intron 26 of 27)	intron (NM_001282899, intron 26 of 27)	-37425	NM_016653	51776	Hs.444451	NM_016653	ENSG00000091436	MAP3K20	AZK|CNM6|MLK7|MLT|MLTK|MLTKalpha|MLTKbeta|MRK|SFMMP|ZAK|mlklak|pk	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.006935	0.398892	
chunk0190_284_1	chr8	37762588	37763084	+	0	NA	intron (NM_007198, intron 1 of 7)	CpG	253	NM_007198	11212	Hs.304792	NM_007198	ENSG00000147471	PLPBP	EPVB6D|PROSC	pyridoxal phosphate binding protein	protein-coding	0.094758	0.674044	
chunk0176_412_1	chr7	19329905	19330223	+	0	NA	Intergenic	Intergenic	-184643	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.003145	0.373041	189(TGGAACAGGCTGTACT,-,0.00),190(GGAACAGGCTGTACTT,+,0.00)
chunk0199_222_1	chr9	5264087	5264369	+	0	NA	Intergenic	L1PB4|LINE|L1	32809	NM_002195	3641	Hs.418506	NM_002195	ENSG00000120211	INSL4	EPIL|PLACENTIN	insulin like 4	protein-coding	0.003546	0.325088	
chunk0165_224_1	chr6	35332295	35332783	+	0	NA	Intergenic	L1P2|LINE|L1	-10019	NM_006238	5467	Hs.696032	NM_006238	ENSG00000112033	PPARD	FAAR|NR1C2|NUC1|NUCI|NUCII|PPARB	peroxisome proliferator activated receptor delta	protein-coding	0.010246	0.552147	
chunk0070_159_1	chr15	71291568	71291994	+	0	NA	intron (NM_024817, intron 5 of 16)	intron (NM_024817, intron 5 of 16)	-102722	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.002347	0.437939	
chunk0052_462_1	chr12	132982950	132983337	+	0	NA	Intergenic	Intergenic	-3205	NM_019591	7574	Hs.489608	NM_019591	ENSG00000198393	ZNF26	HEL-179|KOX20	zinc finger protein 26	protein-coding	0.031008	0.463918	27(TAGAACATCCAGTACA,-,0.00),61(TAGAACATCCAGTGCA,-,0.00),62(AGAACATCCAGTGCAA,+,0.00),95(CAGAACATCCAGTACA,-,0.00),129(TAGAACATCCAGTTCA,-,0.00),130(AGAACATCCAGTTCAA,+,0.00),163(TAGAACATCCAGTACA,-,0.00),197(TAGAACATCCAGTGCA,-,0.00),198(AGAACATCCAGTGCAA,+,0.00),231(TAGAACATCCAGTGCA,-,0.00),232(AGAACATCCAGTGCAA,+,0.00),265(TAGAACATCCAGTGCA,-,0.00),266(AGAACATCCAGTGCAA,+,0.00),299(TAGAACATCCAGTGCA,-,0.00),300(AGAACATCCAGTGCAA,+,0.00),333(TAGAACATCCAGTGCA,-,0.00),334(AGAACATCCAGTGCAA,+,0.00)
chunk0034_185_1	chr11	31560820	31561537	+	0	NA	intron (NM_019040, intron 3 of 9)	intron (NM_019040, intron 3 of 9)	51449	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.004184	0.352368	188(AAGTACACTCTGTGAT,-,0.00)
chunk0059_338_1	chr14	36967712	36968395	+	0	NA	intron (NM_030631, intron 1 of 9)	L2b|LINE|L2	-15662	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.011713	0.464912	
chunk0210_196_1	chrX	80309110	80309627	+	0	NA	intron (NR_110646, intron 2 of 5)	MER68|LTR|ERVL	25950	NR_110646	101060146	Hs.546064	NR_110646	ENSG00000278530	CHMP1B2P	-	charged multivesicular body protein 1B2, pseudogene	pseudo	0.001934	0.399614	
chunk0139_258_1	chr4	56496272	56496590	+	0	NA	intron (NM_001267722, intron 15 of 16)	HAL1|LINE|L1	-8778	NM_206919	132946	Hs.444449	NM_206919	ENSG00000196503	ARL9	-	ADP ribosylation factor like GTPase 9	protein-coding	0.000000	0.307210	
chunk0099_219_1	chr2	96093803	96094025	+	0	NA	Intergenic	Intergenic	22331	NM_000682	151	Hs.247686	NM_000682	ENSG00000274286	ADRA2B	ADRA2L1|ADRA2RL1|ADRARL1|ALPHA2BAR|FAME2|alpha-2BAR	adrenoceptor alpha 2B	protein-coding	0.018018	0.443946	127(CAGAAGACTCTGTTCT,-,0.00),128(AGAAGACTCTGTTCTC,+,0.00)
chunk0076_429_1	chr16	73020208	73020778	+	0	NA	intron (NM_006885, intron 1 of 9)	intron (NM_006885, intron 1 of 9)	27882	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.021053	0.436077	
chunk0078_60_1	chr17	1460224	1460635	+	0	NA	Intergenic	Intergenic	-4162	NM_016823	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.017032	0.524272	281(AGAGACTGCCTGTTCC,-,0.00)
chunk0043_361_1	chr12	23380814	23381244	+	0	NA	Intergenic	L1PA17|LINE|L1	203583	NM_178010	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.004651	0.341067	
chunk0205_218_1	chr9	109568511	109568764	+	0	NA	Intergenic	L1PA15|LINE|L1	-57092	NR_037493	100500898		NR_037493	ENSG00000263861	MIR3927	-	microRNA 3927	ncRNA	0.003953	0.570866	
chunk0110_13_1	chr20	10030309	10030630	+	0	NA	intron (NR_040710, intron 3 of 4)	intron (NR_040710, intron 3 of 4)	-4530	NM_198798	63926	Hs.70903	NM_022096	ENSG00000132623	ANKEF1	ANKRD5	ankyrin repeat and EF-hand domain containing 1	protein-coding	0.006231	0.369565	132(AAGAACAACGTGTACT,-,0.00),133(AGAACAACGTGTACTT,+,0.00)
chunk0088_72_1	chr18	44641230	44641487	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-38815	NM_001130110	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.007782	0.437984	
chunk0049_141_1	chr12	91817382	91817982	+	0	NA	Intergenic	Intergenic	324031	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.003333	0.424293	
chunk0179_51_1	chr7	43547589	43548291	+	0	NA	intron (NM_015052, intron 26 of 29)	Tigger2|DNA|TcMar-Tigger	-25398	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.007123	0.335704	424(TAGTACAGTATGTACT,-,0.00),425(AGTACAGTATGTACTA,+,0.00)
chunk0073_334_1	chr16	14505947	14506427	+	0	NA	intron (NM_002582, intron 21 of 23)	L1MC4|LINE|L1	124084	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.004167	0.361746	
chunk0089_408_1	chr18	68483630	68483988	+	0	NA	Intergenic	Intergenic	231307	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.011173	0.295265	
chunk0141_215_1	chr4	84634754	84635268	+	0	NA	intron (NM_001263, intron 7 of 12)	intron (NM_001263, intron 7 of 12)	52107	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.001946	0.297087	
chunk0031_30_1	chr10	122026685	122027075	+	0	NA	intron (NM_001291877, intron 2 of 19)	L1MC1|LINE|L1	37706	NM_206862	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.015385	0.375959	
chunk0200_379_1	chr9	26503885	26504166	+	0	NA	Intergenic	Intergenic	388803	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.000000	0.297872	
chunk0066_172_1	chr15	32967753	32968076	+	0	NA	intron (NM_001103184, intron 4 of 16)	intron (NM_001103184, intron 4 of 16)	100118	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.000000	0.361111	
chunk0109_298_1	chr20	8447590	8448270	+	0	NA	intron (NM_015192, intron 3 of 31)	intron (NM_015192, intron 3 of 31)	315665	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.002941	0.427313	
chunk0192_221_1	chr8	65305091	65305721	+	0	NA	Intergenic	L2a|LINE|L2	-125066	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.007937	0.372425	264(GAAACAATTTGTTCTT,+,0.00)
chunk0155_382_1	chr5	98259435	98259780	+	0	NA	Intergenic	L1M1|LINE|L1	-509688	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.002899	0.494220	
chunk0167_328_1	chr6	72372469	72372931	+	0	NA	intron (NM_001168411, intron 1 of 5)	intron (NM_001168411, intron 1 of 5)	5970	NM_001168411	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.006494	0.371490	119(AGGGACATACAGTACT,-,0.00),120(GGGACATACAGTACTT,+,0.00)
chunk0148_291_1	chr5	11850472	11851042	+	0	NA	intron (NR_109988, intron 1 of 21)	intron (NR_109988, intron 1 of 21)	53286	NM_001332	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.007018	0.330998	272(AAGTACATTTTGTACT,-,0.00),273(AGTACATTTTGTACTA,+,0.00)
chunk0169_54_1	chr6	97987131	97987662	+	0	NA	Intergenic	L2a|LINE|L2	-37135	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.003766	0.298872	
chunk0194_198_1	chr8	85551715	85552271	+	0	NA	Intergenic	Intergenic	-87078	NR_121630	100996348	Hs.606624	NR_121630	ENSG00000253549	CA3-AS1	-	CA3 antisense RNA 1	ncRNA	0.005396	0.317774	
chunk0117_377_1	chr21	45117208	45117495	+	0	NA	intron (NM_015834, intron 1 of 12)	intron (NM_015834, intron 1 of 12)	42773	NM_001160230	104	Hs.474018	NM_001112	ENSG00000197381	ADARB1	ADAR2|DRABA2|DRADA2|RED1	adenosine deaminase RNA specific B1	protein-coding	0.010453	0.451389	
chunk0117_366_1	chr21	44938936	44939349	+	0	NA	promoter-TSS (NM_001316988)	promoter-TSS (NM_001316988)	-555	NM_001316988	85395	Hs.410830	NM_058190	ENSG00000160256	FAM207A	C21orf70|PRED56	family with sequence similarity 207 member A	protein-coding	0.026634	0.557971	
chunk0077_300_1	chr16	81584101	81584603	+	0	NA	intron (NM_030629, intron 1 of 20)	L2a|LINE|L2	-26996	NR_106759	102465251		NR_106759	ENSG00000275109	MIR6504	hsa-mir-6504	microRNA 6504	ncRNA	0.019920	0.463221	
chunk0207_314_1	chr9	133892222	133892478	+	0	NA	intron (NM_001134398, intron 2 of 29)	intron (NM_001134398, intron 2 of 29)	99974	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.007812	0.568093	
chunk0088_13_1	chr18	43195261	43196014	+	0	NA	Intergenic	Intergenic	-79945	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.002656	0.338196	
chunk0167_209_1	chr6	65344654	65345092	+	0	NA	intron (NM_198283, intron 8 of 9)	LTR80A|LTR|ERVL	43455	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.002283	0.298405	
chunk0073_272_1	chr16	12338012	12338617	+	0	NA	intron (NM_032167, intron 15 of 20)	intron (NM_032167, intron 15 of 20)	361580	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.023140	0.504950	295(AAGTACACTCTGTTCA,-,0.00),296(AGTACACTCTGTTCAG,+,0.00)
chunk0008_148_1	chr1	92315508	92315811	+	0	NA	intron (NM_024813, intron 6 of 12)	X7A_LINE|LINE|CR1	-16650	NM_053274	11146	Hs.49105	NM_007070	ENSG00000174842	GLMN	FAP|FAP48|FAP68|FKBPAP|GLML|GVM|VMGLOM	glomulin, FKBP associated protein	protein-coding	0.006601	0.312500	
chunk0106_456_1	chr2	209408704	209408903	+	0	NA	Intergenic	L1MB7|LINE|L1	-15244	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.010050	0.300000	
chunk0110_72_1	chr20	10970053	10970470	+	0	NA	Intergenic	Intergenic	-60989	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.002398	0.399522	
chunk0027_415_1	chr10	80624929	80625303	+	0	NA	intron (NM_207372, intron 6 of 6)	L1ME3E|LINE|L1	84297	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.008021	0.333333	
chunk0159_150_1	chr5	139301533	139302053	+	0	NA	intron (NM_001194956, intron 1 of 13)	intron (NM_001194956, intron 1 of 13)	8043	NM_001194956	9782	Hs.268939	NM_018834	ENSG00000015479	MATR3	ALS21|MPD2|VCPDM	matrin 3	protein-coding	0.019231	0.410749	
chunk0193_160_1	chr8	74727852	74728053	+	0	NA	intron (NR_033830, intron 4 of 5)	intron (NR_033830, intron 4 of 5)	22259	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.009950	0.420792	6(AAGGACTTTGTGTACA,-,0.00),7(AGGACTTTGTGTACAT,+,0.00)
chunk0060_238_1	chr14	49658608	49659078	+	0	NA	intron (NM_002692, intron 10 of 18)	Tigger3b|DNA|TcMar-Tigger	-23613	NM_001083908	55172	Hs.231761	NM_018139	ENSG00000165506	DNAAF2	C14orf104|CILD10|KTU|PF13	dynein axonemal assembly factor 2	protein-coding	0.004255	0.375796	
chunk0090_130_1	chr18	71861963	71862525	+	0	NA	Intergenic	L1ME2z|LINE|L1	-80018	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.003559	0.303730	
chunk0062_364_1	chr14	73944352	73945562	+	0	NA	intron (NM_152445, intron 2 of 8)	intron (NM_152445, intron 2 of 8)	-4977	NM_182480	51004	Hs.131555	NM_182476	ENSG00000119723	COQ6	CGI-10|CGI10|COQ10D6	coenzyme Q6, monooxygenase	protein-coding	0.015702	0.509496	242(AGGCACAGGCTGTGCC,-,0.00),243(GGCACAGGCTGTGCCC,+,0.00)
chunk0163_268_1	chr6	13309916	13310335	+	0	NA	intron (NM_001258457, intron 4 of 6)	L1MC5|LINE|L1	-14539	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.000000	0.352381	
chunk0187_379_1	chr7	157630353	157630738	+	0	NA	intron (NM_001308268, intron 14 of 22)	intron (NM_001308268, intron 14 of 22)	-56123	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.036364	0.518135	146(AACACACCGTGTGCCC,+,0.00)
chunk0045_451_1	chr12	53625873	53626506	+	0	NA	promoter-TSS (NM_001206683)	promoter-TSS (NM_001206683)	-193	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.067930	0.634069	
chunk0021_89_1	chr10	2348529	2348864	+	0	NA	Intergenic	L1ME3B|LINE|L1	-33622	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.008955	0.351190	
chunk0095_438_1	chr2	25190417	25191091	+	0	NA	Intergenic	L2a|LINE|L2	-13559	NR_132378	106144568	Hs.580474	NR_132378	ENSG00000230452	LINC01381	DADOT	long intergenic non-protein coding RNA 1381	ncRNA	0.007418	0.365926	
chunk0145_160_1	chr4	147152909	147153316	+	0	NA	Intergenic	Intergenic	191605	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.009828	0.316176	
chunk0049_49_1	chr12	89949444	89949715	+	0	NA	Intergenic	Intergenic	240624	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.003690	0.290441	
chunk0074_399_1	chr16	35420885	35421201	+	0	NA	Intergenic	Intergenic	57512	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.009494	0.444795	
chunk0209_439_1	chrX	63560839	63561192	+	0	NA	promoter-TSS (NR_015353)	promoter-TSS (NR_015353)	-22	NR_015353	92249	Hs.31532	NR_015353	ENSG00000235437	LINC01278	-	long intergenic non-protein coding RNA 1278	ncRNA	0.033994	0.559322	
chunk0158_26_1	chr5	125478606	125479065	+	0	NA	Intergenic	Intergenic	-14426	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.008715	0.406522	
chunk0164_290_1	chr6	24632574	24632845	+	0	NA	intron (NM_001168374, intron 1 of 21)	intron (NM_001168374, intron 1 of 21)	13312	NM_001168375	9856	Hs.26441	NM_014809	ENSG00000137261	KIAA0319	AAVR|DYLX2|DYX2|NMIG	KIAA0319	protein-coding	0.003690	0.411765	
chunk0040_50_1	chr11	110855155	110855632	+	0	NA	Intergenic	Intergenic	-142204	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.002096	0.397490	
chunk0012_456_1	chr1	165192335	165193199	+	0	NA	Intergenic	Intergenic	163474	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.004630	0.425434	601(TGGAACACAAAGTGCT,-,0.00),602(GGAACACAAAGTGCTG,+,0.00)
chunk0186_118_1	chr7	138089536	138089884	+	0	NA	intron (NM_001190906, intron 2 of 7)	Penelope1_Vert|LINE|Penelope	13278	NM_001190907	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.008621	0.378223	221(AGAAACAGTGTGTGCA,-,0.00),222(GAAACAGTGTGTGCAG,+,0.00)
chunk0058_126_1	chr14	22334619	22334827	+	0	NA	Intergenic	Intergenic	254514	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.009615	0.550239	
chunk0176_168_1	chr7	13543531	13543814	+	0	NA	Intergenic	L1ME3|LINE|L1	442842	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.003534	0.292254	
chunk0082_344_1	chr17	59845349	59846049	+	0	NA	Intergenic	Intergenic	4433	NR_029493	406991	Hs.444569	NR_029493	ENSG00000284190	MIR21	MIRN21|hsa-mir-21|miR-21|miRNA21	microRNA 21	ncRNA	0.004286	0.388017	245(AAGCACATCATGTATT,-,0.00)
chunk0196_58_1	chr8	102175709	102176018	+	0	NA	Intergenic	Intergenic	50431	NR_049859	100847001		NR_049859	ENSG00000266756	MIR5680	-	microRNA 5680	ncRNA	0.006472	0.438710	131(CAGCACTGGAAGTTCC,-,0.00),132(AGCACTGGAAGTTCCT,+,0.00)
chunk0150_148_1	chr5	33721676	33722287	+	0	NA	intron (NM_030955, intron 3 of 23)	intron (NM_030955, intron 3 of 23)	170038	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.006547	0.405229	
chunk0077_6_1	chr16	74510642	74510883	+	0	NA	intron (NM_001145666, intron 1 of 25)	L2b|LINE|L2	-89292	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.004149	0.429752	67(GAGTACATACTGTGTT,-,0.00),68(AGTACATACTGTGTTC,+,0.00)
chunk0020_257_1	chr1	236289619	236289818	+	0	NA	Intergenic	Intergenic	-7679	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.005025	0.385000	
chunk0089_389_1	chr18	67866740	67867106	+	0	NA	intron (NR_033921, intron 3 of 4)	intron (NR_033921, intron 3 of 4)	-350193	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.002732	0.365123	
chunk0197_142_1	chr8	120310272	120310724	+	0	NA	intron (NM_021110, intron 37 of 47)	intron (NM_021110, intron 37 of 47)	-134900	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.004425	0.434879	
chunk0155_440_1	chr5	101305535	101305778	+	0	NA	Intergenic	Intergenic	-402371	NM_175052	7903	Hs.308628	NM_005668	ENSG00000113532	ST8SIA4	PST|PST1|SIAT8D|ST8SIA-IV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding	0.000000	0.356557	
chunk0075_421_1	chr16	57420925	57421374	+	0	NA	Intergenic	L1MA4A|LINE|L1	16382	NM_002987	6361	Hs.546294	NM_002987	ENSG00000102970	CCL17	A-152E5.3|ABCD-2|SCYA17|TARC	C-C motif chemokine ligand 17	protein-coding	0.013363	0.420000	
chunk0123_194_1	chr3	44386449	44386717	+	0	NA	intron (NM_001282915, intron 5 of 10)	MER52A|LTR|ERV1	48131	NM_173826	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.007463	0.631970	
chunk0052_118_1	chr13	23212725	23213155	+	0	NA	intron (NM_000231, intron 2 of 7)	intron (NM_000231, intron 2 of 7)	32019	NM_000231	6445	Hs.37167	NM_000231	ENSG00000102683	SGCG	35DAG|A4|DAGA4|DMDA|DMDA1|LGMD2C|LGMDR5|MAM|SCARMD2|SCG3|gamma-SG	sarcoglycan gamma	protein-coding	0.009302	0.433875	
chunk0023_21_1	chr10	21002002	21002473	+	0	NA	intron (NM_213569, intron 3 of 6)	intron (NM_213569, intron 3 of 6)	-104635	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.012739	0.322034	265(CAGAACTTCGTGTCCT,-,0.00),266(AGAACTTCGTGTCCTA,+,0.00)
chunk0192_197_1	chr8	64301017	64301994	+	0	NA	intron (NR_125826, intron 1 of 4)	intron (NR_125826, intron 1 of 4)	67053	NR_125826	102724623	Hs.586375	NR_125826	ENSG00000253554	LINC01414	-	long intergenic non-protein coding RNA 1414	ncRNA	0.002047	0.314928	
chunk0076_289_1	chr16	69840251	69840805	+	0	NA	intron (NM_007014, intron 6 of 24)	intron (NM_007014, intron 6 of 24)	1791	NM_001270453	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.012635	0.454054	394(GGGTACGCTGTGTTCT,-,0.00),395(GGTACGCTGTGTTCTT,+,0.00)
chunk0140_331_1	chr4	73704655	73704934	+	0	NA	Intergenic	Intergenic	-35712	NM_000584	3576	Hs.624	NM_000584	ENSG00000169429	CXCL8	GCP-1|GCP1|IL8|LECT|LUCT|LYNAP|MDNCF|MONAP|NAF|NAP-1|NAP1	C-X-C motif chemokine ligand 8	protein-coding	0.014337	0.457143	
chunk0019_34_1	chr1	223815185	223815741	+	0	NA	intron (NM_001031685, intron 2 of 17)	intron (NM_001031685, intron 2 of 17)	30509	NM_001031685	7159	Hs.523968	NM_005426	ENSG00000143514	TP53BP2	53BP2|ASPP2|BBP|P53BP2|PPP1R13A	tumor protein p53 binding protein 2	protein-coding	0.005396	0.448833	
chunk0157_352_1	chr5	123068512	123068711	+	0	NA	Intergenic	Intergenic	-20535	NM_001136239	93166	Hs.135118	NM_001136239	ENSG00000061455	PRDM6	KMT8C|PDA3|PRISM	PR/SET domain 6	protein-coding	0.000000	0.410000	
chunk0148_127_1	chr5	5372421	5372847	+	0	NA	Intergenic	Intergenic	-50039	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.004695	0.442623	
chunk0161_68_1	chr5	166595716	166595989	+	0	NA	Intergenic	L2b|LINE|L2	330518	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.003663	0.328467	
chunk0119_91_1	chr22	41832795	41833234	+	0	NA	promoter-TSS (NR_103834)	promoter-TSS (NR_103834)	-65	NR_103834	6721	Hs.443258	NM_004599	ENSG00000198911	SREBF2	SREBP-2|SREBP2|bHLHd2	sterol regulatory element binding transcription factor 2	protein-coding	0.109339	0.690909	
chunk0190_358_1	chr8	39728585	39729088	+	0	NA	intron (NM_014237, intron 19 of 19)	intron (NM_014237, intron 19 of 19)	109453	NM_001278114	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.001988	0.295635	
chunk0030_319_1	chr10	118042542	118043007	+	0	NA	intron (NM_014904, intron 1 of 4)	intron (NM_014904, intron 1 of 4)	3829	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.002151	0.324034	
chunk0175_89_1	chr7	2702275	2702772	+	0	NA	intron (NM_001284355, intron 2 of 5)	intron (NM_001284355, intron 2 of 5)	14321	NM_001284355	155185	Hs.42221	NM_133463	ENSG00000174945	AMZ1	-	archaelysin family metallopeptidase 1	protein-coding	0.030181	0.604418	
chunk0196_154_1	chr8	104639519	104639787	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-50629	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.003731	0.479554	
chunk0130_322_1	chr3	138019532	138020013	+	0	NA	intron (NM_016369, intron 1 of 4)	intron (NM_016369, intron 1 of 4)	9608	NM_016369	51208	Hs.655324	NM_016369	ENSG00000066405	CLDN18	SFTA5|SFTPJ	claudin 18	protein-coding	0.000000	0.437759	293(GGGAACACTGAGTTCC,-,0.00),294(GGAACACTGAGTTCCT,+,0.00)
chunk0079_102_1	chr17	12115001	12115380	+	0	NA	intron (NM_001281435, intron 8 of 11)	intron (NM_001281435, intron 8 of 11)	33291	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.005277	0.326316	
chunk0139_384_1	chr4	61509920	61510391	+	0	NA	intron (NM_015236, intron 1 of 22)	L1PA16|LINE|L1	13034	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.006369	0.343220	
chunk0068_398_1	chr15	58680984	58681455	+	0	NA	intron (NM_001110, intron 3 of 15)	intron (NM_001110, intron 3 of 15)	12388	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.010616	0.355932	
chunk0166_380_1	chr6	51694586	51695099	+	0	NA	intron (NM_138694, intron 60 of 66)	intron (NM_138694, intron 60 of 66)	72972	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.003899	0.392996	201(ATAAACAGACTGTGCT,-,0.00),202(TAAACAGACTGTGCTG,+,0.00)
chunk0190_424_1	chr8	41401445	41402385	+	0	NA	Intergenic	Intergenic	-88647	NM_001174124	51125	Hs.654773	NM_016099	ENSG00000147533	GOLGA7	GCP16|GOLGA3AP1|GOLGA7A|HSPC041	golgin A7	protein-coding	0.006383	0.432519	
chunk0048_88_1	chr12	79201930	79202328	+	0	NA	intron (NM_001135805, intron 4 of 11)	intron (NM_001135805, intron 4 of 11)	156476	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.000000	0.333333	
chunk0210_352_1	chrX	96308366	96308655	+	0	NA	Intergenic	L1MC2|LINE|L1	29392	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.000000	0.327586	
chunk0031_426_1	chr10	132407881	132408250	+	0	NA	intron (NM_138499, intron 2 of 2)	intron (NM_138499, intron 2 of 2)	10867	NM_138499	170394	Hs.527751	NM_138499	ENSG00000171813	PWWP2B	PWWP2|bA432J24.1|pp8607	PWWP domain containing 2B	protein-coding	0.040650	0.640541	
chunk0077_251_1	chr16	80870801	80871262	+	0	NA	intron (NR_131948, intron 1 of 2)	L1PA10|LINE|L1	21565	NR_131948	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.004338	0.363636	
chunk0055_170_1	chr13	60517585	60518407	+	0	NA	intron (NM_030794, intron 10 of 13)	MER5C1|DNA|hAT-Charlie	120703	NM_001146070	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.002433	0.428919	766(AGGGACACACTGTCCT,-,0.00),767(GGGACACACTGTCCTC,+,0.00)
chunk0037_374_1	chr11	78261214	78261521	+	0	NA	intron (NM_012296, intron 2 of 9)	intron (NM_012296, intron 2 of 9)	72555	NM_020798	57558	Hs.531249	NM_020798	ENSG00000118369	USP35	-	ubiquitin specific peptidase 35	protein-coding	0.013029	0.444805	
chunk0063_189_1	chr14	80727358	80727845	+	0	NA	intron (NM_152446, intron 18 of 23)	L1PA15|LINE|L1	211939	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.004107	0.350410	
chunk0121_421_1	chr3	25845525	25846204	+	0	NA	Intergenic	Intergenic	27831	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.005891	0.347059	300(GAAAACAACATGTTCT,-,0.00),301(AAAACAACATGTTCTT,+,0.00)
chunk0130_240_1	chr3	135056106	135056461	+	0	NA	intron (NM_004441, intron 3 of 15)	intron (NM_004441, intron 3 of 15)	261026	NM_004441	2047	Hs.116092	NM_004441	ENSG00000154928	EPHB1	ELK|EPHT2|Hek6|NET	EPH receptor B1	protein-coding	0.019718	0.567416	
chunk0178_157_1	chr7	33581061	33581613	+	0	NA	intron (NM_014451, intron 19 of 20)	intron (NM_014451, intron 19 of 20)	-323574	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.007246	0.367089	118(CAAGACACTGTGTACT,-,0.00),119(AAGACACTGTGTACTT,+,0.00)
chunk0187_79_1	chr8	2967730	2968000	+	0	NA	intron (NM_033225, intron 57 of 69)	intron (NM_033225, intron 57 of 69)	-239414	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.011111	0.416974	
chunk0135_7_1	chr3	184112785	184112990	+	0	NA	Intergenic	Intergenic	12708	NM_198314	285242	Hs.449179	NM_182589	ENSG00000186038	HTR3E	5-HT3-E|5-HT3E|5-HT3c1	5-hydroxytryptamine receptor 3E	protein-coding	0.009756	0.451456	
chunk0074_77_1	chr16	21552693	21552923	+	0	NA	Intergenic	Intergenic	-32364	NR_002594	387254	Hs.448808	NR_002594		SLC7A5P2	IMAA|MMAA	solute carrier family 7 member 5 pseudogene 2	pseudo	0.034783	0.567100	
chunk0174_237_1	chr6	160812228	160812599	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	110220	NM_000301	5340	Hs.143436	NM_000301	ENSG00000122194	PLG	-	plasminogen	protein-coding	0.002695	0.397849	
chunk0051_273_1	chr12	118057899	118058303	+	0	NA	intron (NM_001278557, intron 1 of 8)	intron (NM_001278557, intron 1 of 8)	3110	NM_018639	55884	Hs.506985	NM_018639	ENSG00000176871	WSB2	SBA2	WD repeat and SOCS box containing 2	protein-coding	0.007426	0.441975	145(TGGATCAGGGTGTTCT,-,0.00),146(GGATCAGGGTGTTCTA,+,0.00)
chunk0041_305_1	chr11	129828442	129828678	+	0	NA	intron (NM_138788, intron 1 of 5)	intron (NM_138788, intron 1 of 5)	12714	NM_138788	120224	Hs.504301	NM_138788	ENSG00000151715	TMEM45B	-	transmembrane protein 45B	protein-coding	0.012712	0.481013	
chunk0077_349_1	chr16	83715199	83715510	+	0	NA	intron (NM_001220488, intron 11 of 14)	intron (NM_001220488, intron 11 of 14)	88622	NR_120308	102724163		NR_120308	ENSG00000260228	LOC102724163	-	uncharacterized LOC102724163	ncRNA	0.019293	0.458333	
chunk0066_178_1	chr15	33037021	33037265	+	0	NA	intron (NM_001103184, intron 2 of 16)	intron (NM_001103184, intron 2 of 16)	30889	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.004098	0.363265	123(CAGAACTCACAGTTCT,-,0.00),124(AGAACTCACAGTTCTT,+,0.00)
chunk0109_292_1	chr20	8250516	8250901	+	0	NA	intron (NM_015192, intron 2 of 31)	L2c|LINE|L2	118443	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.002597	0.360104	
chunk0131_21_1	chr3	142132899	142133193	+	0	NA	intron (NM_001178138, intron 1 of 13)	L1MEd|LINE|L1	16498	NM_001178138	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.003401	0.274576	
chunk0060_374_1	chr14	52545433	52546140	+	0	NA	intron (NM_001160047, intron 1 of 20)	intron (NM_001160047, intron 1 of 20)	6797	NM_001160047	57544	Hs.532609	NM_020784	ENSG00000087301	TXNDC16	ERp90|KIAA1344	thioredoxin domain containing 16	protein-coding	0.008487	0.375706	399(AGAGACATGCTGTCCT,-,0.00),400(GAGACATGCTGTCCTC,+,0.00)
chunk0201_291_1	chr9	41019171	41019466	+	0	NA	intron (NR_002836, intron 8 of 8)	intron (NR_002836, intron 8 of 8)	26981	NR_034006	100132352	Hs.231861	NR_034006		FRG1HP	-	FSHD region gene 1 family member H, pseudogene	pseudo	0.006780	0.405405	
chunk0172_232_1	chr6	137076468	137077180	+	0	NA	Intergenic	Intergenic	-31644	NM_001278723	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.008427	0.446003	380(AATCACATACTGTTCC,-,0.00),381(ATCACATACTGTTCCT,+,0.00)
chunk0016_127_1	chr1	196977201	196977685	+	0	NA	promoter-TSS (NM_030787)	promoter-TSS (NM_030787)	-94	NM_030787	81494	Hs.282594	NM_030787	ENSG00000134389	CFHR5	CFHL5|CFHR5D|FHR-5|FHR5	complement factor H related 5	protein-coding	0.010331	0.373196	
chunk0212_221_1	chrX	136057543	136057999	+	0	NA	Intergenic	Intergenic	72344	NM_001042537	10479	Hs.62185	NM_006359	ENSG00000198689	SLC9A6	MRSA|NHE6	solute carrier family 9 member A6	protein-coding	0.008772	0.343545	
chunk0181_199_1	chr7	83663014	83663284	+	0	NA	Intergenic	Intergenic	-13986	NM_012431	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.007407	0.509225	
chunk0156_8_1	chr5	102010503	102011335	+	0	NA	Intergenic	Intergenic	285630	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.003606	0.290516	
chunk0067_319_1	chr15	48002736	48003171	+	0	NA	Intergenic	Intergenic	-118019	NM_205850	283652	Hs.710240	NM_205850	ENSG00000188467	SLC24A5	JSX|NCKX5|OCA6|SHEP4	solute carrier family 24 member 5	protein-coding	0.002299	0.410550	
chunk0103_85_1	chr2	160613801	160614000	+	0	NA	Intergenic	Intergenic	-120093	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.000000	0.360000	
chunk0043_432_1	chr12	26113105	26113623	+	0	NA	Intergenic	Intergenic	11706	NM_030762	79365	Hs.177841	NM_030762	ENSG00000123095	BHLHE41	BHLHB3|DEC2|SHARP1|hDEC2	basic helix-loop-helix family member e41	protein-coding	0.013514	0.412331	271(TGGCACTCACTGTGCC,-,0.00),272(GGCACTCACTGTGCCA,+,0.00)
chunk0116_88_1	chr21	34736583	34737541	+	0	NA	intron (NR_024351, intron 1 of 5)	L1ME4b|LINE|L1	120	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.005219	0.399374	272(AGATCAGTTTGTTCAT,+,0.00)
chunk0060_232_1	chr14	49598772	49599050	+	0	NA	non-coding (NR_037792, exon 1 of 6)	non-coding (NR_037792, exon 1 of 6)	214	NR_037792	122769	Hs.451090	NM_152329	ENSG00000165501	LRR1	4-1BBLRR|LRR-1|PPIL5	leucine rich repeat protein 1	protein-coding	0.089928	0.645161	
chunk0008_142_1	chr1	92080331	92080774	+	0	NA	5' UTR (NM_183242, exon 1 of 9)	5' UTR (NM_183242, exon 1 of 9)	247	NM_183242	284697	Hs.676102	NM_183242	ENSG00000189195	BTBD8	-	BTB domain containing 8	protein-coding	0.074492	0.637387	
chunk0052_331_1	chr12	125981744	125982183	+	0	NA	intron (NR_034132, intron 1 of 5)	MER61F|LTR|ERV1	1411	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.009112	0.456818	
chunk0073_278_1	chr16	12501707	12502096	+	0	NA	intron (NM_032167, intron 19 of 20)	intron (NM_032167, intron 19 of 20)	-218420	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.000000	0.435897	
chunk0172_374_1	chr6	139304410	139304909	+	0	NA	Intergenic	Intergenic	-12588	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.008016	0.404000	
chunk0039_193_1	chr11	100875469	100876067	+	0	NA	intron (NM_152432, intron 4 of 23)	intron (NM_152432, intron 4 of 23)	-116312	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.013378	0.487479	
chunk0187_260_1	chr7	154930255	154930514	+	0	NA	intron (NR_024476, intron 2 of 7)	intron (NR_024476, intron 2 of 7)	1867	NR_024477	100132707	Hs.586358	NR_024476	ENSG00000214106	PAXIP1-AS2	PAXIP1OS	PAXIP1 antisense RNA 2	ncRNA	0.011583	0.450000	128(AAGAACACCATGTTCC,-,0.00),129(AGAACACCATGTTCCT,+,0.00)
chunk0208_215_1	chrX	18558710	18559204	+	0	NA	intron (NM_001037343, intron 4 of 21)	intron (NM_001037343, intron 4 of 21)	113146	NM_000330	6247	Hs.715725	NM_000330	ENSG00000102104	RS1	RS|XLRS1	retinoschisin 1	protein-coding	0.006073	0.456566	228(GGGAACAGGCTGTGCT,-,0.00),229(GGAACAGGCTGTGCTT,+,0.00)
chunk0033_421_1	chr11	24837006	24837587	+	0	NA	intron (NM_001252010, intron 5 of 9)	intron (NM_001252010, intron 5 of 9)	340326	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.005164	0.324742	
chunk0186_331_1	chr7	143172352	143172919	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-10784	NM_176881	259285	Hs.553660	NM_176881	ENSG00000236398	TAS2R39	T2R39|T2R57	taste 2 receptor member 39	protein-coding	0.010582	0.380282	401(AGGTCTGAATGTTCCT,+,0.00)
chunk0083_69_1	chr17	64087679	64088249	+	0	NA	intron (NM_001433, intron 2 of 21)	intron (NM_001433, intron 2 of 21)	42178	NM_001433	2081	Hs.133982	NM_001433	ENSG00000178607	ERN1	IRE1|IRE1P|IRE1a|hIRE1p	endoplasmic reticulum to nucleus signaling 1	protein-coding	0.008772	0.444834	
chunk0116_27_1	chr21	33121642	33121900	+	0	NA	intron (NR_109961, intron 1 of 2)	intron (NR_109961, intron 1 of 2)	1929	NR_109961	101928107	Hs.382669	NR_109961	ENSG00000226527	LOC101928107	-	uncharacterized LOC101928107	ncRNA	0.031008	0.540541	147(AGGAACAGGCAGTTAT,-,0.00)
chunk0155_388_1	chr5	98565561	98565760	+	0	NA	Intergenic	Intergenic	-203635	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.005025	0.350000	135(AAGGACATTCTGCACT,-,0.00),136(AGGACATTCTGCACTG,+,0.00)
chunk0177_210_1	chr7	24074980	24075204	+	0	NA	Intergenic	Intergenic	-209096	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.008929	0.413333	
chunk0102_291_1	chr2	150574524	150575081	+	0	NA	Intergenic	L2a|LINE|L2	-2581	NR_110241	101929260	Hs.732324	NR_110241	ENSG00000236049	LINC01920	-	long intergenic non-protein coding RNA 1920	ncRNA	0.007181	0.374552	
chunk0133_89_1	chr3	167734843	167735072	+	0	NA	promoter-TSS (NM_001122752)	promoter-TSS (NM_001122752)	-94	NM_145859	11235	Hs.478150	NM_007217	ENSG00000114209	PDCD10	CCM3|TFAR15	programmed cell death 10	protein-coding	0.082969	0.613043	
chunk0190_196_1	chr8	33566487	33566908	+	0	NA	intron (NM_024787, intron 1 of 5)	CpG	431	NM_024787	79845	Hs.151237	NM_024787	ENSG00000133874	RNF122	-	ring finger protein 122	protein-coding	0.090261	0.677725	
chunk0038_207_1	chr11	86372583	86373118	+	0	NA	Intergenic	Intergenic	-1886	NM_001156474	60494	Hs.144913	NM_021827	ENSG00000149201	CCDC81	-	coiled-coil domain containing 81	protein-coding	0.000000	0.328358	
chunk0144_405_1	chr4	140310339	140310746	+	0	NA	intron (NR_033939, intron 2 of 4)	intron (NR_033939, intron 2 of 4)	-32901	NM_001153635	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.007371	0.433824	
chunk0082_401_1	chr17	60856656	60857502	+	0	NA	intron (NM_017679, intron 7 of 23)	intron (NM_017679, intron 7 of 23)	179268	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.001182	0.296340	379(GTAACAGATTGTTCTG,+,0.00)
chunk0059_274_1	chr14	35390962	35391315	+	0	NA	Intergenic	MIRb|SINE|MIR	13616	NM_020529	4792	Hs.81328	NM_020529	ENSG00000100906	NFKBIA	EDAID2|IKBA|MAD-3|NFKBI	NFKB inhibitor alpha	protein-coding	0.005666	0.488701	73(GGGAACAGGAAGTTTT,-,0.00)
chunk0104_128_1	chr2	173160572	173160942	+	0	NA	intron (NM_133646, intron 2 of 11)	intron (NM_133646, intron 2 of 11)	84920	NM_133646	51776	Hs.444451	NM_016653	ENSG00000091436	MAP3K20	AZK|CNM6|MLK7|MLT|MLTK|MLTKalpha|MLTKbeta|MRK|SFMMP|ZAK|mlklak|pk	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.013514	0.425876	
chunk0179_231_1	chr7	47951438	47951755	+	0	NA	Intergenic	Intergenic	-3122	NM_138295	168507	Hs.195979	NM_138295	ENSG00000158683	PKD1L1	HTX8|PRO19563	polycystin 1 like 1, transient receptor potential channel interacting	protein-coding	0.000000	0.393082	
chunk0210_284_1	chrX	84907727	84907926	+	0	NA	Intergenic	Intergenic	-26325	NR_024062	100131816	Hs.460809	NM_178567	ENSG00000229547	UBE2DNL	-	ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)	pseudo	0.015075	0.480000	
chunk0156_401_1	chr5	113886138	113886870	+	0	NA	Intergenic	Intergenic	372810	NM_022828	64848	Hs.231942	NM_022828	ENSG00000047188	YTHDC2	CAHL|hYTHDC2	YTH domain containing 2	protein-coding	0.004098	0.334243	
chunk0140_118_1	chr4	68815479	68816166	+	0	NA	promoter-TSS (NM_001075)	promoter-TSS (NM_001075)	-171	NM_001075	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.004367	0.328488	
chunk0064_236_1	chr14	94215121	94215924	+	0	NA	intron (NM_058237, intron 3 of 24).2	intron (NM_058237, intron 3 of 24).2	41210	NM_058237	57718	Hs.259599	NM_020958	ENSG00000119698	PPP4R4	CFAP14|KIAA1622|PP4R4	protein phosphatase 4 regulatory subunit 4	protein-coding	0.002491	0.299751	340(CAGATCATGATGTTCC,-,0.00),341(AGATCATGATGTTCCA,+,0.00)
chunk0137_101_1	chr4	13470361	13470865	+	0	NA	intron (NM_001017979, intron 3 of 6)	intron (NM_001017979, intron 3 of 6)	13752	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.000000	0.384158	246(GAAACATCCAGTCCTT,+,0.00)
chunk0115_337_1	chr21	29145918	29146592	+	0	NA	intron (NM_001286624, intron 1 of 3)	intron (NM_001286624, intron 1 of 3)	696	NM_001286624	56911	Hs.222802	NM_020152	ENSG00000156265	MAP3K7CL	C21orf7|HC21ORF7|TAK1L|TAKL|TAKL-1|TAKL-2|TAKL-4	MAP3K7 C-terminal like	protein-coding	0.008902	0.398519	342(AAGTACAGTGTGTTCC,-,0.00),343(AGTACAGTGTGTTCCC,+,0.00)
chunk0042_148_1	chr12	3853775	3853991	+	0	NA	intron (NR_104461, intron 1 of 8)	L1PA6|LINE|L1	19565	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.004630	0.364055	
chunk0166_448_1	chr6	53140159	53140946	+	0	NA	intron (NM_003643, intron 2 of 5)	intron (NM_003643, intron 2 of 5)	8274	NM_003643	8521	Hs.23589	NM_003643	ENSG00000137270	GCM1	GCMA|hGCMa	glial cells missing transcription factor 1	protein-coding	0.001271	0.399746	471(AGGAACAAAATGATCC,-,0.00)
chunk0085_121_1	chr18	2979413	2979744	+	0	NA	intron (NM_014646, intron 1 of 19)	intron (NM_014646, intron 1 of 19)	32369	NM_014646	9663	Hs.132342	NM_014646	ENSG00000101577	LPIN2	-	lipin 2	protein-coding	0.006042	0.334337	
chunk0139_252_1	chr4	56296588	56296950	+	0	NA	intron (NM_020722, intron 3 of 10)	intron (NM_020722, intron 3 of 10)	90739	NM_001286671	132949	Hs.104347	NM_181806	ENSG00000157426	AASDH	ACSF4|LYS2|NRPS1098|NRPS998	aminoadipate-semialdehyde dehydrogenase	protein-coding	0.008287	0.498623	
chunk0086_50_1	chr18	12882960	12883426	+	0	NA	intron (NM_001207013, intron 1 of 10)	L1ME1|LINE|L1	1142	NM_001207013	5771	Hs.654527	NM_002828	ENSG00000175354	PTPN2	PTN2|PTPT|TC-PTP|TCELLPTP|TCPTP	protein tyrosine phosphatase non-receptor type 2	protein-coding	0.042918	0.496788	143(CGGAACACCGTGCCCC,-,0.00),144(GGAACACCGTGCCCCC,+,0.00)
chunk0044_18_1	chr12	27133117	27133396	+	0	NA	Intergenic	Intergenic	-50734	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.000000	0.442857	
chunk0094_253_1	chr2	7328724	7329262	+	0	NA	Intergenic	Intergenic	-92268	NR_038432	100506274	Hs.177930	NR_038432	ENSG00000229727	LOC100506274	-	uncharacterized LOC100506274	ncRNA	0.005576	0.395176	280(TGGAACAGGAAGTACC,-,0.00),281(GGAACAGGAAGTACCA,+,0.00)
chunk0205_212_1	chr9	109331441	109331780	+	0	NA	Intergenic	Intergenic	-10646	NM_019114	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.008850	0.600000	
chunk0001_58_1	chr1	2085096	2085403	+	0	NA	intron (NM_001242874, intron 1 of 14)	intron (NM_001242874, intron 1 of 14)	11263	NM_001242874	5590	Hs.496255	NM_002744	ENSG00000067606	PRKCZ	PKC-ZETA|PKC2	protein kinase C zeta	protein-coding	0.042345	0.571429	
chunk0013_41_1	chr1	166944689	166944939	+	0	NA	intron (NM_199351, intron 3 of 9)	L2c|LINE|L2	30510	NM_199351	387597	Hs.444835	NM_199351	ENSG00000143195	ILDR2	C1orf32|dJ782G3.1	immunoglobulin like domain containing receptor 2	protein-coding	0.012000	0.478088	
chunk0141_263_1	chr4	86331134	86331862	+	0	NA	intron (NM_138980, intron 2 of 13)	intron (NM_138980, intron 2 of 13)	28724	NM_138982	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.006868	0.379973	456(GAGCACAAGGTGTTCC,-,0.00),457(AGCACAAGGTGTTCCT,+,0.00)
chunk0098_133_1	chr2	69286405	69286726	+	0	NA	Intergenic	L1ME3F|LINE|L1	100689	NM_002056	2673	Hs.580300	NM_002056	ENSG00000198380	GFPT1	CMS12|CMSTA1|GFA|GFAT|GFAT 1|GFAT1|GFAT1m|GFPT|GFPT1L|MSLG	glutamine--fructose-6-phosphate transaminase 1	protein-coding	0.003115	0.388199	
chunk0157_284_1	chr5	120681732	120682135	+	0	NA	intron (NM_001308088, intron 3 of 3)	L1MCc|LINE|L1	150469	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.000000	0.346535	
chunk0132_6_1	chr3	154225294	154226046	+	0	NA	intron (NM_015595, intron 10 of 14)	intron (NM_015595, intron 10 of 14)	98827	NM_001114397	170506	Hs.446270	NM_020865	ENSG00000174953	DHX36	DDX36|G4R1|MLEL1|RHAU	DEAH-box helicase 36	protein-coding	0.005319	0.304117	
chunk0176_418_1	chr7	19379525	19379787	+	0	NA	Intergenic	Intergenic	-234235	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.000000	0.357414	
chunk0184_74_1	chr7	112651467	112651785	+	0	NA	intron (NR_110158, intron 5 of 7)	L1MA9|LINE|L1	29245	NR_110158	101928012	Hs.521131	NR_110158	ENSG00000223646	LOC101928012	-	uncharacterized LOC101928012	ncRNA	0.000000	0.300940	
chunk0061_135_1	chr14	59215326	59215694	+	0	NA	intron (NM_001270520, intron 1 of 24)	intron (NM_001270520, intron 1 of 24)	26847	NM_001270520	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.016304	0.514905	
chunk0152_50_1	chr5	57435519	57435997	+	0	NA	Intergenic	Intergenic	47051	NM_001017992	345651	Hs.482167	NM_001017992	ENSG00000169067	ACTBL2	ACT	actin beta like 2	protein-coding	0.002092	0.377871	
chunk0199_228_1	chr9	5364321	5364640	+	0	NA	intron (NM_018465, intron 3 of 5)	L1MC3|LINE|L1	-24607	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.003135	0.415625	149(CAGCACAGAGTGAACC,-,0.00),150(AGCACAGAGTGAACCT,+,0.00)
chunk0031_194_1	chr10	125756099	125756746	+	0	NA	intron (NR_110858, intron 25 of 25)	L1MCc|LINE|L1	-4362	NR_120633	101927983	Hs.634269	NR_120633	ENSG00000236991	EDRF1-AS1	-	EDRF1 antisense RNA 1	ncRNA	0.013910	0.358025	
chunk0102_355_1	chr2	152550411	152550625	+	0	NA	intron (NM_052905, intron 4 of 25)	MIR3|SINE|MIR	166943	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.004673	0.381395	
chunk0169_271_1	chr6	105553203	105553581	+	0	NA	Intergenic	Intergenic	-150268	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.013228	0.451187	
chunk0094_34_1	chr2	1751023	1751375	+	0	NA	Intergenic	Intergenic	-6652	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.031250	0.569405	
chunk0064_315_1	chr14	95886666	95886943	+	0	NA	intron (NR_038861, intron 1 of 1)	intron (NR_038861, intron 1 of 1)	10032	NR_038861	100507043	Hs.455955	NR_038861	ENSG00000250366	TUNAR	HI-LNC78|LINC00617|TUNA	TCL1 upstream neural differentiation-associated RNA	ncRNA	0.010830	0.557554	152(ATGGACAGTTTGTCCT,-,0.00),153(TGGACAGTTTGTCCTC,+,0.00)
chunk0175_454_1	chr6	170251113	170251410	+	0	NA	Intergenic	Intergenic	11308	NR_002787	154449	Hs.447751	NR_002787	ENSG00000230960	LOC154449	-	uncharacterized LOC154449	ncRNA	0.013468	0.456376	146(TGGAACGGATTGTTCC,-,0.00),147(GGAACGGATTGTTCCT,+,0.00)
chunk0175_209_1	chr7	6028505	6029272	+	0	NA	intron (NM_001134335, intron 12 of 14)	intron (NM_001134335, intron 12 of 14)	-2488	NM_001271700	100310846	Hs.744468	NM_001271700	ENSG00000157999	ANKRD61	-	ankyrin repeat domain 61	protein-coding	0.009126	0.401042	
chunk0143_112_1	chr4	108774823	108775256	+	0	NA	Intergenic	Intergenic	-11960	NM_001146627	64850	Hs.106576	NM_031279	ENSG00000164089	ETNPPL	AGXT2L1	ethanolamine-phosphate phospho-lyase	protein-coding	0.004619	0.400922	
chunk0084_217_1	chr17	78226820	78227122	+	0	NA	Intergenic	Intergenic	-4339	NM_001204211	283999	Hs.632228	NM_001145529	ENSG00000204278	TMEM235	ARGM1	transmembrane protein 235	protein-coding	0.033113	0.584158	
chunk0039_400_1	chr11	107383488	107384072	+	0	NA	intron (NM_152434, intron 12 of 17)	(AATA)n|Simple_repeat|Simple_repeat	74066	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.000000	0.317949	
chunk0065_300_1	chr14	102727453	102727705	+	0	NA	3' UTR (NM_015156, exon 12 of 12)	3' UTR (NM_015156, exon 12 of 12)	-49900	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.023810	0.450593	
chunk0010_323_1	chr1	118111341	118111838	+	0	NA	intron (NM_206996, intron 4 of 48)	(AC)n|Simple_repeat|Simple_repeat	73636	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.014085	0.399598	
chunk0171_65_1	chr6	121448897	121449100	+	0	NA	3' UTR (NM_000165, exon 2 of 2)	3' UTR (NM_000165, exon 2 of 2)	13421	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.000000	0.313725	
chunk0187_296_1	chr7	156073223	156073720	+	0	NA	Intergenic	Intergenic	110839	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.016097	0.572289	
chunk0175_328_1	chr6	167031066	167031753	+	0	NA	intron (NM_194429, intron 9 of 11)	L2c|LINE|L2	32092	NM_001278690	11116	Hs.487175	NM_007045	ENSG00000213066	FGFR1OP	FOP	FGFR1 oncogene partner	protein-coding	0.008734	0.457849	219(TGGAACACACTGTCCC,-,0.00),220(GGAACACACTGTCCCC,+,0.00)
chunk0007_406_1	chr1	85551302	85551922	+	0	NA	intron (NM_001134445, intron 1 of 6)	L2b|LINE|L2	26751	NM_001134445	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.004839	0.423510	
chunk0066_404_1	chr15	39275302	39275699	+	0	NA	Intergenic	Intergenic	24831	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.010076	0.502513	
chunk0146_242_1	chr4	162282779	162283727	+	0	NA	Intergenic	L1ME1|LINE|L1	-119219	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.007384	0.339305	
chunk0091_17_1	chr19	3057260	3057627	+	0	NA	intron (NM_198970, intron 3 of 6)	intron (NM_198970, intron 3 of 6)	4930	NM_198970	166	Hs.515053	NM_001130	ENSG00000104964	TLE5	AES|AES-1|AES-2|ESP1|GRG|GRG5|Grg-5	TLE family member 5, transcriptional modulator	protein-coding	0.057221	0.687500	
chunk0066_259_1	chr15	34829033	34829479	+	0	NA	Intergenic	L1MEd|LINE|L1	-33530	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.002242	0.328859	
chunk0007_163_1	chr1	79966475	79966842	+	0	NA	Intergenic	Intergenic	-569097	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.005450	0.323370	
chunk0040_361_1	chr11	118818457	118819005	+	0	NA	Intergenic	Intergenic	-27468	NM_004397	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.000000	0.346084	243(TAAAACACAGTGTTCC,-,0.00),244(AAAACACAGTGTTCCT,+,0.00)
chunk0145_358_1	chr4	151215261	151215613	+	0	NA	intron (NM_001009555, intron 2 of 20)	intron (NM_001009555, intron 2 of 20)	11071	NM_001009555	152503	Hs.744983	NM_001009555	ENSG00000109686	SH3D19	EBP|EVE1|Eve-1|Kryn|SH3P19	SH3 domain containing 19	protein-coding	0.002841	0.405099	
chunk0206_440_1	chr9	127978285	127978568	+	0	NA	intron (NM_001035254, intron 1 of 10)	intron (NM_001035254, intron 1 of 10)	2107	NM_001035254	399665	Hs.535972	NM_203305	ENSG00000167106	FAM102A	C9orf132|EEIG1|SYM-3A|bA203J24.7	family with sequence similarity 102 member A	protein-coding	0.028269	0.542254	
chunk0025_445_1	chr10	60186562	60187090	+	0	NA	exon (NM_001204404, exon 17 of 44)	exon (NM_001204404, exon 17 of 44)	-45810	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.020833	0.431002	
chunk0074_345_1	chr16	31573695	31573905	+	0	NA	Intergenic	L1MA3|LINE|L1	-4276	NR_027011	440359	Hs.650902	NR_027011		YBX3P1	CSDAP1	Y-box binding protein 3 pseudogene 1	pseudo	0.009524	0.374408	
chunk0137_262_1	chr4	22041646	22041986	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-93065	NM_147182	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.002941	0.354839	
chunk0191_227_1	chr8	52753731	52754725	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-39762	NM_001083617	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.002012	0.341709	
chunk0128_172_1	chr3	107282071	107282346	+	0	NA	intron (NR_028302, intron 1 of 3)	intron (NR_028302, intron 1 of 3)	41516	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.003636	0.333333	
chunk0073_159_1	chr16	7974429	7975049	+	0	NA	Intergenic	L2c|LINE|L2	615099	NR_110736	283953	Hs.150849	NM_001146336	ENSG00000232258	TMEM114	-	transmembrane protein 114	protein-coding	0.024194	0.441224	
chunk0081_92_1	chr17	39661071	39661270	+	0	NA	intron (NM_001165937, intron 13 of 14)	intron (NM_001165937, intron 13 of 14)	-4176	NM_003673	8557	Hs.77628	NM_003673	ENSG00000173991	TCAP	CMD1N|CMH25|LGMD2G|LGMDR7|T-cap|TELE|telethonin	titin-cap	protein-coding	0.015075	0.600000	79(GGGTACAGCATGTACA,-,0.00),80(GGTACAGCATGTACAG,+,0.00)
chunk0203_79_1	chr9	83894329	83894628	+	0	NA	intron (NM_017576, intron 5 of 17)	MER68|LTR|ERVL	26987	NM_017576	55582	Hs.697514	NM_017576	ENSG00000165115	KIF27	-	kinesin family member 27	protein-coding	0.003344	0.426667	
chunk0193_284_1	chr8	77512954	77513603	+	0	NA	Intergenic	Intergenic	62581	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.003082	0.352308	
chunk0092_388_1	chr19	36528956	36529155	+	0	NA	promoter-TSS (NM_001166037)	promoter-TSS (NM_001166037)	-709	NM_001166038	339324	Hs.18103	NM_001012756	ENSG00000254004	ZNF260	OZRF1|PEX1|ZFP260	zinc finger protein 260	protein-coding	0.035176	0.515000	
chunk0146_320_1	chr4	165463555	165463897	+	0	NA	intron (NM_001873, intron 1 of 8)	MIRb|SINE|MIR	77484	NR_030304	693163		NR_030304	ENSG00000207559	MIR578	MIRN578|hsa-mir-578	microRNA 578	ncRNA	0.005848	0.335277	
chunk0021_454_1	chr1	248874306	248874522	+	0	NA	Intergenic	Intergenic	-15298	NM_017865	55657	Hs.377705	NM_017865	ENSG00000171163	ZNF692	AREBP|Zfp692	zinc finger protein 692	protein-coding	0.037037	0.451613	
chunk0191_44_1	chr8	43220009	43220227	+	0	NA	Intergenic	Intergenic	-72324	NM_001002920	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.009174	0.534247	
chunk0122_287_1	chr3	36147479	36148207	+	0	NA	Intergenic	Intergenic	-232644	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.006868	0.417010	225(GAGAACATTGTGTGCA,-,0.00),226(AGAACATTGTGTGCAA,+,0.00)
chunk0203_379_1	chr9	90345265	90345687	+	0	NA	intron (NR_109795, intron 2 of 2)	intron (NR_109795, intron 2 of 2)	88013	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.021327	0.491726	160(AAGGTCACTGTGTGCC,-,0.00),161(AGGTCACTGTGTGCCT,+,0.00)
chunk0076_138_1	chr16	66988244	66988572	+	0	NA	promoter-TSS (NM_173815)	promoter-TSS (NM_173815)	-181	NM_173815	283848	Hs.346947	NM_173815	ENSG00000172824	CES4A	CES6|CES8	carboxylesterase 4A	protein-coding	0.021341	0.537994	
chunk0003_26_1	chr1	29453356	29453587	+	0	NA	Intergenic	L2b|LINE|L2	-103357	NR_110758	101928460	Hs.434659	NR_110758	ENSG00000230523	LINC01756	-	long intergenic non-protein coding RNA 1756	ncRNA	0.012987	0.551724	187(TGGGACAGAGTGTGCC,-,0.00),188(GGGACAGAGTGTGCCT,+,0.00)
chunk0070_334_1	chr15	75625657	75625922	+	0	NA	5' UTR (NM_005701, exon 1 of 9)	5' UTR (NM_005701, exon 1 of 9)	316	NM_001042581	10073	Hs.21577	NM_005701	ENSG00000169371	SNUPN	KPNBL|RNUT1|Snurportin1	snurportin 1	protein-coding	0.086792	0.669173	
chunk0150_371_1	chr5	39074423	39074641	+	0	NA	promoter-TSS (NM_152756)	promoter-TSS (NM_152756)	-124	NM_152756	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.137615	0.780822	
chunk0161_415_1	chr5	177998560	177999636	+	0	NA	Intergenic	Intergenic	-2856	NM_006261	5626	Hs.158301	NM_006261	ENSG00000175325	PROP1	CPHD2|PROP-1	PROP paired-like homeobox 1	protein-coding	0.006506	0.497679	756(AGCACACTGTGCTCAT,+,0.00),1045(CAGGACAGTCTGACCT,-,0.00),1046(AGGACAGTCTGACCTC,+,0.00)
chunk0177_224_1	chr7	24239206	24239629	+	0	NA	Intergenic	Intergenic	-44771	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.000000	0.301887	
chunk0025_65_1	chr10	49841593	49842242	+	0	NA	intron (NR_130169, intron 13 of 16)	intron (NR_130169, intron 13 of 16)	-79538	NM_001143997	55753	Hs.17860	NM_018245	ENSG00000197444	OGDHL	-	oxoglutarate dehydrogenase like	protein-coding	0.016949	0.409231	196(AAGTACATCTTGTACA,-,0.00)
chunk0113_13_1	chr20	49418051	49418560	+	0	NA	intron (NM_004975, intron 1 of 1)	MamRep4096|DNA|hAT-Tip100	64339	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.011788	0.384314	
chunk0011_382_1	chr1	153777610	153778083	+	0	NA	exon (NM_024330, exon 4 of 10)	exon (NM_024330, exon 4 of 10)	2554	NM_024330	11000	Hs.438723	NM_024330	ENSG00000143554	SLC27A3	ACSVL3|FATP3|VLCS-3	solute carrier family 27 member 3	protein-coding	0.019027	0.590717	
chunk0040_438_1	chr11	121478447	121478822	+	0	NA	intron (NM_003105, intron 3 of 47)	intron (NM_003105, intron 3 of 47)	26431	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.029333	0.476064	
chunk0190_160_1	chr8	31353666	31354231	+	0	NA	Intergenic	Intergenic	-285804	NM_013962	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.005310	0.402827	311(AAGAACTAAATGTTCA,-,0.00),312(AGAACTAAATGTTCAG,+,0.00)
chunk0063_238_1	chr14	82180284	82180515	+	0	NA	Intergenic	Intergenic	-557338	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.008658	0.413793	
chunk0162_334_1	chr6	6812462	6813088	+	0	NA	Intergenic	MIR|SINE|MIR	-189949	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.006390	0.395534	
chunk0132_395_1	chr3	163897703	163897902	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	273754	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.010050	0.375000	18(TAGAACATACTGTACT,-,0.00),19(AGAACATACTGTACTA,+,0.00)
chunk0147_254_1	chr4	183417297	183417850	+	0	NA	Intergenic	Intergenic	-27063	NM_017632	55602	Hs.592508	NM_017632	ENSG00000168564	CDKN2AIP	CARF	CDKN2A interacting protein	protein-coding	0.019892	0.483755	
chunk0090_451_1	chr18	79941688	79942281	+	0	NA	intron (NM_025078, intron 3 of 5)	intron (NM_025078, intron 3 of 5)	9669	NM_025078	80148	Hs.288284	NM_025078	ENSG00000122490	SLC66A2	PQLC1	solute carrier family 66 member 2	protein-coding	0.025295	0.535354	244(AGGCACAAACCGTTCT,-,0.00),245(GGCACAAACCGTTCTC,+,0.00)
chunk0070_272_1	chr15	74149004	74149412	+	0	NA	Intergenic	L1MD|LINE|L1	18806	NM_020851	57611	Hs.254775	NM_020851	ENSG00000167178	ISLR2	LINX	immunoglobulin superfamily containing leucine rich repeat 2	protein-coding	0.022059	0.364303	
chunk0028_442_1	chr10	93982129	93982684	+	0	NA	Intergenic	L1M5|LINE|L1	-11583	NM_016341	51196	Hs.655033	NM_016341	ENSG00000138193	PLCE1	NPHS3|PLCE|PPLC	phospholipase C epsilon 1	protein-coding	0.001802	0.347122	285(GGTACAGTATGTCTCC,+,0.00)
chunk0058_23_1	chr14	19906112	19906319	+	0	NA	Intergenic	Intergenic	-14392	NM_001005483	79317	Hs.554585	NM_001005483	ENSG00000176281	OR4K5	OR14-16	olfactory receptor family 4 subfamily K member 5	protein-coding	0.004831	0.442308	
chunk0125_175_1	chr3	66606937	66607268	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-106681	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.003021	0.460843	
chunk0189_250_1	chr8	25074368	25074567	+	0	NA	Intergenic	MamGypLTR1b|LTR|Gypsy	-110305	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.000000	0.370000	
chunk0103_126_1	chr2	161933601	161933800	+	0	NA	intron (NM_001178016, intron 15 of 26)	L1MA8|LINE|L1	140842	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.005025	0.475000	
chunk0095_50_1	chr2	13654580	13654836	+	0	NA	Intergenic	Intergenic	-647695	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.000000	0.365759	
chunk0096_121_1	chr2	28617424	28617995	+	0	NA	intron (NM_001170585, intron 43 of 56)	intron (NM_001170585, intron 43 of 56)	121638	NM_153021	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.005254	0.494755	
chunk0078_186_1	chr17	4731333	4731730	+	0	NA	exon (NM_001305000, exon 1 of 3)	exon (NM_001305000, exon 1 of 3)	123	NM_001001683	400569	Hs.513885	NM_001001683	ENSG00000161920	MED11	HSPC296	mediator complex subunit 11	protein-coding	0.080605	0.610553	
chunk0205_8_1	chr9	104931201	104931620	+	0	NA	Intergenic	Intergenic	-3164	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.004773	0.371429	
chunk0064_12_1	chr14	89305155	89305580	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	111743	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.021176	0.420188	
chunk0133_209_1	chr3	170941424	170942438	+	0	NA	Intergenic	L1ME2z|LINE|L1	-33294	NM_020390	56648	Hs.164144	NM_020390	ENSG00000163577	EIF5A2	EIF-5A2|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding	0.001972	0.328079	
chunk0133_454_1	chr3	175207763	175208367	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	63031	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.009934	0.357025	
chunk0193_352_1	chr8	79899848	79900062	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-28218	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.004673	0.465116	
chunk0198_406_1	chr8	141874163	141874442	+	0	NA	Intergenic	Intergenic	-87989	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.010753	0.567857	
chunk0122_90_1	chr3	30171401	30171827	+	0	NA	Intergenic	Intergenic	-237458	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.000000	0.365340	
chunk0198_163_1	chr8	133184784	133185158	+	0	NA	Intergenic	Intergenic	-6068	NM_001204870	8840	Hs.492974	NM_003882	ENSG00000104415	CCN4	WISP1|WISP1-OT1|WISP1-UT1|WISP1c|WISP1i|WISP1tc	cellular communication network factor 4	protein-coding	0.008021	0.538667	
chunk0120_30_1	chr3	2372238	2372620	+	0	NA	intron (NM_001206955, intron 2 of 23)	intron (NM_001206955, intron 2 of 23)	133600	NM_001206955	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.002618	0.336815	
chunk0159_362_1	chr5	145815109	145815447	+	0	NA	intron (NM_182960, intron 5 of 7)	MLT1A|LTR|ERVL-MaLR	20091	NM_182960	153768	Hs.314261	NM_138492	ENSG00000186314	PRELID2	-	PRELI domain containing 2	protein-coding	0.002959	0.389381	
chunk0015_245_1	chr1	187961308	187961821	+	0	NA	Intergenic	Intergenic	517936	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.328794	256(GAGAACATAGTGTGCT,-,0.00),257(AGAACATAGTGTGCTT,+,0.00)
chunk0006_44_1	chr1	64477083	64477316	+	0	NA	intron (NM_020925, intron 1 of 26)	intron (NM_020925, intron 1 of 26)	6406	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.004292	0.384615	
chunk0032_224_1	chr11	7554992	7556151	+	0	NA	intron (NM_003621, intron 2 of 23)	intron (NM_003621, intron 2 of 23)	-41615	NM_001256568	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.008628	0.423276	831(TGGAACTATGTGTTCC,-,0.00),832(GGAACTATGTGTTCCT,+,0.00)
chunk0184_246_1	chr7	117901189	117901601	+	0	NA	Intergenic	MIR|SINE|MIR	-27888	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.007282	0.438257	
chunk0161_165_1	chr5	169197311	169197654	+	0	NA	intron (NM_003062, intron 3 of 35)	intron (NM_003062, intron 3 of 35)	66212	NR_030311	693170		NR_030311	ENSG00000207619	MIR585	MIRN585|hsa-mir-585|mir-585	microRNA 585	ncRNA	0.002915	0.453488	177(TGAGACATGCTGTTCT,-,0.00),178(GAGACATGCTGTTCTC,+,0.00)
chunk0206_388_1	chr9	126918971	126919361	+	0	NA	intron (NM_001190729, intron 1 of 17)	intron (NM_001190729, intron 1 of 17)	4392	NM_014636	9649	Hs.432842	NM_014636	ENSG00000136828	RALGPS1	RALGEF2|RALGPS1A	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.000000	0.358056	
chunk0089_211_1	chr18	61037358	61037943	+	0	NA	Intergenic	Intergenic	-452892	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.001709	0.325939	
chunk0200_184_1	chr9	19404506	19405070	+	0	NA	Intergenic	Intergenic	-4139	NM_001010887	340485	Hs.41379	NM_001010887	ENSG00000177076	ACER2	ALKCDase2|ASAH3L	alkaline ceramidase 2	protein-coding	0.003546	0.437168	
chunk0209_122_1	chrX	40784753	40785259	+	0	NA	Intergenic	LTR67B|LTR|ERVL	48190	NR_027761	100132831	Hs.729923	NR_027761		LOC100132831	-	A20-binding inhibitor of NF-kappaB activation 2 pseudogene	pseudo	0.007905	0.398422	
chunk0042_371_1	chr12	10541579	10542002	+	0	NA	Intergenic	L1M5|LINE|L1	58045	NR_028045	10748	Hs.159297	NM_006611		KLRA1P	KLRA1|KLRAP1|LY49L|Ly-49L|Ly49	killer cell lectin like receptor A1, pseudogene	pseudo	0.004728	0.297170	
chunk0127_433_1	chr3	102952902	102953142	+	0	NA	Intergenic	Intergenic	518007	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.004167	0.352697	
chunk0019_253_1	chr1	227708546	227708949	+	0	NA	Intergenic	Intergenic	-11040	NR_036753	401983	Hs.681816	NR_036753		ZNF847P	gm127	zinc finger protein 847, pseudogene	pseudo	0.017370	0.373762	
chunk0101_121_1	chr2	126634209	126634815	+	0	NA	Intergenic	Intergenic	-21423	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.019802	0.461285	320(AGGAACACCGTGGACT,-,0.00)
chunk0114_309_1	chr21	17118592	17119080	+	0	NA	Intergenic	MER70B|LTR|ERVL	-320054	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.002049	0.429448	
chunk0145_196_1	chr4	147855776	147855976	+	0	NA	intron (NM_024605, intron 4 of 22)	intron (NM_024605, intron 4 of 22)	73281	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.005000	0.417910	50(GGGGACATACTGTCCT,-,0.00),51(GGGACATACTGTCCTG,+,0.00)
chunk0185_58_1	chr7	124765711	124766015	+	0	NA	5' UTR (NM_005302, exon 1 of 2)	5' UTR (NM_005302, exon 1 of 2)	162	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.108553	0.708197	
chunk0079_261_1	chr17	16170765	16171209	+	0	NA	intron (NM_001190438, intron 1 of 18)	intron (NM_001190438, intron 1 of 18)	23652	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.015766	0.328090	
chunk0064_73_1	chr14	90153737	90154474	+	0	NA	intron (NM_022054, intron 1 of 1)	intron (NM_022054, intron 1 of 1)	92340	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.004071	0.521680	
chunk0164_266_1	chr6	23653008	23653294	+	0	NA	Intergenic	Intergenic	-473035	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.000000	0.376307	
chunk0181_145_1	chr7	81615761	81615960	+	0	NA	intron (NR_126026, intron 2 of 8)	L2c|LINE|L2	10356	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.005025	0.405000	
chunk0190_410_1	chr8	40559882	40560378	+	0	NA	intron (NM_001135731, intron 5 of 5)	intron (NM_001135731, intron 5 of 5)	337694	NM_001135731	79698	Hs.591850	NM_024645	ENSG00000165061	ZMAT4	-	zinc finger matrin-type 4	protein-coding	0.004032	0.368209	
chunk0015_367_1	chr1	190452064	190452619	+	0	NA	intron (NM_199051, intron 2 of 7)	intron (NM_199051, intron 2 of 7)	25288	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.010811	0.329137	
chunk0092_440_1	chr19	38375565	38376387	+	0	NA	intron (NM_002812, intron 1 of 6)	MIR|SINE|MIR	1426	NM_002812	5714	Hs.78466	NM_002812	ENSG00000099341	PSMD8	HEL-S-91n|HIP6|HYPF|Nin1p|Rpn12|S14|p31	proteasome 26S subunit, non-ATPase 8	protein-coding	0.010949	0.517618	348(AGGCACTGAGTGTCCC,-,0.00),349(GGCACTGAGTGTCCCT,+,0.00)
chunk0015_376_1	chr1	190515980	190516352	+	0	NA	Intergenic	Intergenic	37615	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.005376	0.284182	
chunk0120_286_1	chr3	9749720	9749919	+	0	NA	promoter-TSS (NM_016819)	promoter-TSS (NM_016819)	-125	NM_016827	4968	Hs.380271	NM_002542	ENSG00000114026	OGG1	HMMH|HOGG1|MUTM|OGH1	8-oxoguanine DNA glycosylase	protein-coding	0.090452	0.660000	
chunk0160_262_1	chr5	157019413	157019793	+	0	NA	Intergenic	L1MC1|LINE|L1	38638	NM_012206	26762	Hs.129711	NM_012206	ENSG00000113249	HAVCR1	CD365|HAVCR|HAVCR-1|KIM-1|KIM1|TIM|TIM-1|TIM1|TIMD-1|TIMD1	hepatitis A virus cellular receptor 1	protein-coding	0.000000	0.338583	
chunk0180_320_1	chr7	71899358	71899969	+	0	NA	intron (NM_001017440, intron 4 of 5)	intron (NM_001017440, intron 4 of 5)	437560	NM_001017440	83698	Hs.592750	NM_031468	ENSG00000183166	CALN1	CABP8	calneuron 1	protein-coding	0.014730	0.349673	
chunk0152_361_1	chr5	63770774	63771349	+	0	NA	Intergenic	L1MEc|LINE|L1	191231	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.003478	0.378472	
chunk0007_413_1	chr1	85959692	85959929	+	0	NA	intron (NM_152890, intron 24 of 59)	intron (NM_152890, intron 24 of 59)	196628	NM_152890	255631	Hs.659516	NM_152890	ENSG00000171502	COL24A1	-	collagen type XXIV alpha 1 chain	protein-coding	0.004219	0.302521	
chunk0205_401_1	chr9	114619094	114619824	+	0	NA	intron (NM_153045, intron 2 of 8)	intron (NM_153045, intron 2 of 8)	8033	NM_153045	203197	Hs.522357	NM_153045	ENSG00000157693	TMEM268	C9orf91	transmembrane protein 268	protein-coding	0.019178	0.439124	292(GAGGACTTGCTGTTCT,-,0.00),293(AGGACTTGCTGTTCTC,+,0.00)
chunk0087_230_1	chr18	36350855	36351149	+	0	NA	intron (NM_001281739, intron 1 of 23)	intron (NM_001281739, intron 1 of 23)	53306	NM_001281739	80206	Hs.436636	NM_025135	ENSG00000134775	FHOD3	FHOS2|Formactin2	formin homology 2 domain containing 3	protein-coding	0.010204	0.433898	
chunk0185_154_1	chr7	127702319	127702563	+	0	NA	exon (NM_014390, exon 6 of 24)	exon (NM_014390, exon 6 of 24)	50293	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.016393	0.489796	
chunk0022_75_1	chr10	8821053	8821664	+	0	NA	Intergenic	Intergenic	-76631	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.011457	0.330065	
chunk0030_281_1	chr10	116831919	116832140	+	0	NA	Intergenic	Intergenic	-17483	NM_001242699	387712	Hs.693248	NM_001242699	ENSG00000188316	ENO4	C10orf134	enolase 4	protein-coding	0.040724	0.477477	
chunk0018_242_1	chr1	219988918	219989250	+	0	NA	intron (NM_004446, intron 18 of 31)	intron (NM_004446, intron 18 of 31)	57574	NM_004446	2058	Hs.497788	NM_004446	ENSG00000136628	EPRS	EARS|GLUPRORS|HLD15|PARS|PIG32|QARS|QPRS	glutamyl-prolyl-tRNA synthetase	protein-coding	0.000000	0.288288	
chunk0005_199_1	chr1	59057292	59057506	+	0	NA	intron (NR_110626, intron 2 of 2)	intron (NR_110626, intron 2 of 2)	36923	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.009346	0.493023	
chunk0076_311_1	chr16	70346687	70347041	+	0	NA	promoter-TSS (NM_018332)	promoter-TSS (NM_018332)	-57	NM_018332	55308	Hs.656037	NM_018332	ENSG00000168872	DDX19A	DDX19-DDX19L|DDX19L	DEAD-box helicase 19A	protein-coding	0.104520	0.625352	
chunk0200_55_1	chr9	15576376	15576875	+	0	NA	intron (NM_173550, intron 3 of 25)	intron (NM_173550, intron 3 of 25)	23526	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.016032	0.440000	
chunk0202_121_1	chr9	72985699	72986220	+	0	NA	Intergenic	Intergenic	-32642	NM_000689	216	Hs.76392	NM_000689	ENSG00000165092	ALDH1A1	ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1	aldehyde dehydrogenase 1 family member A1	protein-coding	0.005758	0.333333	
chunk0056_229_1	chr13	88659679	88659920	+	0	NA	Intergenic	L1PA8|LINE|L1	118970	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.000000	0.409091	
chunk0082_212_1	chr17	57034823	57035122	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-10506	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.000000	0.443333	
chunk0083_459_1	chr17	73224717	73225138	+	0	NA	intron (NM_001098832, intron 2 of 3)	(ACAGG)n|Simple_repeat|Simple_repeat	2790	NM_001289412	84923	Hs.741276	NM_032837	ENSG00000133193	FAM104A	-	family with sequence similarity 104 member A	protein-coding	0.004751	0.518957	
chunk0072_262_1	chr15	96335987	96336637	+	0	NA	intron (NM_021005, intron 2 of 2)	intron (NM_021005, intron 2 of 2)	2972	NM_001145157	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.015385	0.445469	294(GAGACACACAGTTCCG,+,0.00)
chunk0015_80_1	chr1	184823014	184823290	+	0	NA	intron (NM_052966, intron 8 of 13)	intron (NM_052966, intron 8 of 13)	-68245	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.007246	0.429603	
chunk0011_409_1	chr1	154337299	154338048	+	0	NA	exon (NM_001005855, exon 12 of 12)	exon (NM_001005855, exon 12 of 12)	9873	NM_020452	57198	Hs.435700	NM_020452	ENSG00000143515	ATP8B2	ATPID	ATPase phospholipid transporting 8B2	protein-coding	0.013351	0.457333	
chunk0204_298_1	chr9	100049337	100050101	+	0	NA	intron (NM_015051, intron 4 of 11)	L1MD2|LINE|L1	49333	NM_015051	23071	Hs.154023	NM_015051	ENSG00000023318	ERP44	PDIA10|TXNDC4	endoplasmic reticulum protein 44	protein-coding	0.005236	0.304575	
chunk0182_308_1	chr7	98548209	98548461	+	0	NA	Intergenic	Intergenic	-68950	NM_002523	4885	Hs.3281	NM_002523	ENSG00000106236	NPTX2	NARP|NP-II|NP2	neuronal pentraxin 2	protein-coding	0.000000	0.462451	
chunk0083_204_1	chr17	66702485	66702798	+	0	NA	intron (NM_002737, intron 8 of 16)	L1MA9|LINE|L1	-84431	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.000000	0.328025	
chunk0056_308_1	chr13	90899865	90900546	+	0	NA	intron (NR_027039, intron 4 of 5)	intron (NR_027039, intron 4 of 5)	26392	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.002937	0.341642	283(AGGAACACATTGCTCT,-,0.00),284(GGAACACATTGCTCTA,+,0.00)
chunk0050_104_1	chr12	101966338	101966855	+	0	NA	Intergenic	Intergenic	89269	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.001934	0.351351	321(TAGAACATTGTGAACT,-,0.00),322(AGAACATTGTGAACTC,+,0.00)
chunk0119_192_1	chr22	44638926	44639429	+	0	NA	Intergenic	Intergenic	-13758	NR_044991	414351	Hs.572878	NR_044991		LINC00229	C22orf10|NCRNA00229|dJ474I12.C22.2	long intergenic non-protein coding RNA 229	ncRNA	0.047714	0.591270	236(GAGCACACGCTGTTCC,-,0.00),237(AGCACACGCTGTTCCT,+,0.00)
chunk0066_341_1	chr15	37219144	37219897	+	0	NA	Intergenic	Intergenic	-118221	NM_002399	4212	Hs.510989	NM_002399	ENSG00000134138	MEIS2	CPCMR|HsT18361|MRG1	Meis homeobox 2	protein-coding	0.005312	0.401857	
chunk0211_191_1	chrX	117522863	117523500	+	0	NA	Intergenic	Intergenic	450557	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.001570	0.416928	530(CAGCTCAAACTGTTCC,-,0.00),531(AGCTCAAACTGTTCCT,+,0.00)
chunk0018_320_1	chr1	221289265	221289482	+	0	NA	Intergenic	Intergenic	46923	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.009217	0.394495	
chunk0182_229_1	chr7	96548639	96549008	+	0	NA	Intergenic	Intergenic	-45300	NM_001201450	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.016260	0.405405	
chunk0006_227_1	chr1	68544557	68545353	+	0	NA	Intergenic	Intergenic	-47734	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.007538	0.356336	
chunk0203_260_1	chr9	87778908	87779299	+	0	NA	intron (NR_027917, intron 3 of 4)	Tigger3b|DNA|TcMar-Tigger	6188	NR_027917	392360	Hs.690450	NM_001023564	ENSG00000188029	CTSL3P	CTSL3|HCTSL-s	cathepsin L family member 3, pseudogene	pseudo	0.002558	0.410714	
chunk0147_440_1	chr4	187515016	187515469	+	0	NA	Intergenic	Intergenic	-9629	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.006623	0.332599	
chunk0081_173_1	chr17	41536948	41537420	+	0	NA	Intergenic	Intergenic	-8795	NM_002276	3880	Hs.654568	NM_002276	ENSG00000171345	KRT19	CK19|K19|K1CS	keratin 19	protein-coding	0.002119	0.549683	
chunk0101_297_1	chr2	134815738	134816080	+	0	NA	Intergenic	Intergenic	-22707	NM_138326	130013	Hs.655728	NM_138326	ENSG00000153086	ACMSD	-	aminocarboxymuconate semialdehyde decarboxylase	protein-coding	0.002924	0.443149	
chunk0141_336_1	chr4	87419366	87420282	+	0	NA	Intergenic	Intergenic	-2752	NM_001248011	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.006550	0.418757	169(GAGATCTGGCTGTCCC,-,0.00)
chunk0112_227_1	chr20	41034362	41034657	+	0	NA	intron (NM_003286, intron 2 of 20)	intron (NM_003286, intron 2 of 20)	5687	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.006780	0.435811	80(GTGGACAGTATGTGCT,-,0.00),81(TGGACAGTATGTGCTG,+,0.00)
chunk0151_299_1	chr5	52947028	52947576	+	0	NA	intron (NM_181501, intron 27 of 28)	intron (NM_181501, intron 27 of 28)	-42024	NR_073104	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.005474	0.340619	248(AAGAACTCAATGTTCC,-,0.00),249(AGAACTCAATGTTCCA,+,0.00)
chunk0184_86_1	chr7	113119578	113120176	+	0	NA	Intergenic	Intergenic	-1295	NR_015442									0.013378	0.332220	
chunk0178_325_1	chr7	38254951	38255291	+	0	NA	Intergenic	Intergenic	18526	NM_001003799	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.000000	0.346041	
chunk0076_132_1	chr16	66737351	66737932	+	0	NA	intron (NM_001286157, intron 3 of 11)	intron (NM_001286157, intron 3 of 11)	13981	NM_001286157	1783	Hs.369068	NM_006141	ENSG00000135720	DYNC1LI2	DNCLI2|LIC2	dynein cytoplasmic 1 light intermediate chain 2	protein-coding	0.012048	0.453608	186(AAGAACATGCTGTTTC,-,0.00),187(AGAACATGCTGTTTCC,+,0.00)
chunk0121_319_1	chr3	24254325	24254710	+	0	NA	intron (NM_000461, intron 2 of 9)	MARNA|DNA|TcMar-Mariner	103193	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.000000	0.388601	
chunk0162_278_1	chr6	5712576	5713313	+	0	NA	intron (NM_006567, intron 6 of 6)	intron (NM_006567, intron 6 of 6)	-17672	NR_110842	101927950	Hs.571136	NR_110842	ENSG00000270174	LOC101927950	-	uncharacterized LOC101927950	ncRNA	0.010855	0.468835	444(ATGTACAGTGTGTGCC,-,0.00),445(TGTACAGTGTGTGCCC,+,0.00)
chunk0063_374_1	chr14	86141896	86142237	+	0	NA	Intergenic	Intergenic	207388	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.005865	0.432749	
chunk0084_343_1	chr17	81142750	81143134	+	0	NA	intron (NM_001080395, intron 1 of 13)	intron (NM_001080395, intron 1 of 13)	-9634	NR_031652	100302229		NR_031652	ENSG00000221025	MIR1250	MIRN1250|hsa-mir-1250|mir-1250	microRNA 1250	ncRNA	0.049479	0.646753	235(AGGCACAGCGTGGCCT,-,0.00),236(GGCACAGCGTGGCCTG,+,0.00)
chunk0207_320_1	chr9	134165085	134165471	+	0	NA	promoter-TSS (NR_023344)	promoter-TSS (NR_023344)	-714	NR_023344	100151684	Hs.545589	NR_023344	ENSG00000221676	RNU6ATAC	RNU6ATAC1|U6ATAC	RNA, U6atac small nuclear (U12-dependent splicing)	snRNA	0.103627	0.671835	
chunk0118_69_1	chr22	28640565	28641059	+	0	NA	intron (NM_001145418, intron 1 of 22)	L1MB7|LINE|L1	39053	NM_001145418	23331	Hs.387856	NM_015281	ENSG00000100154	TTC28	TPRBK	tetratricopeptide repeat domain 28	protein-coding	0.004049	0.327273	
chunk0197_371_1	chr8	126558362	126558661	+	0	NA	promoter-TSS (NM_174911)	promoter-TSS (NM_174911)	-45	NM_174911	157638	Hs.124951	NM_174911	ENSG00000168672	LRATD2	BCMP101|FAM84B|NSE2	LRAT domain containing 2	protein-coding	0.107023	0.696667	
chunk0007_115_1	chr1	78975976	78976301	+	0	NA	intron (NM_022159, intron 2 of 14)	L1MEc|LINE|L1	30672	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.000000	0.377301	
chunk0154_437_1	chr5	90289215	90290011	+	0	NA	intron (NR_120601, intron 1 of 5)	L1MB8|LINE|L1	458	NR_120601	101929495	Hs.346679	NR_120601		LINC01339	-	long intergenic non-protein coding RNA 1339	ncRNA	0.005025	0.355082	
chunk0012_17_1	chr1	154885250	154885697	+	0	NA	Intergenic	L2c|LINE|L2	-15195	NM_001204087	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.011186	0.430804	
chunk0080_69_1	chr17	21988530	21988849	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	296166	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.021944	0.415625	
chunk0148_355_1	chr5	14543413	14543993	+	0	NA	Intergenic	Intergenic	-38079	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.003448	0.423408	
chunk0028_448_1	chr10	94415909	94416393	+	0	NA	intron (NM_015188, intron 1 of 12)	intron (NM_015188, intron 1 of 12)	13722	NM_015188	23232	Hs.500598	NM_015188	ENSG00000108239	TBC1D12	-	TBC1 domain family member 12	protein-coding	0.002066	0.348454	283(AGTTCAGGATGTACTT,+,0.00)
chunk0021_240_1	chr1	242506608	242506879	+	0	NA	intron (NM_152666, intron 2 of 10)	intron (NM_152666, intron 2 of 10)	17953	NM_152666	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.022140	0.496324	
chunk0126_156_1	chr3	77073164	77073524	+	0	NA	intron (NM_001290065, intron 1 of 26)	intron (NM_001290065, intron 1 of 26)	-24668	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.005556	0.321330	
chunk0211_44_1	chrX	108572577	108573593	+	0	NA	intron (NM_033380, intron 8 of 50)	L2a|LINE|L2	133241	NM_000495	1287	Hs.369089	NM_000495	ENSG00000188153	COL4A5	ASLN|ATS|ATS1|CA54	collagen type IV alpha 5 chain	protein-coding	0.003937	0.347099	269(AAGAACTGCATGCTCT,-,0.00)
chunk0140_99_1	chr4	68386986	68387621	+	0	NA	Intergenic	MIR|SINE|MIR	-37197	NM_001031732	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.012598	0.492138	
chunk0142_39_1	chr4	90943028	90943479	+	0	NA	intron (NM_001145065, intron 9 of 10)	intron (NM_001145065, intron 9 of 10)	708222	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.008869	0.331858	
chunk0157_160_1	chr5	117965478	117965677	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	235216	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.005025	0.375000	
chunk0064_363_1	chr14	97644408	97644616	+	0	NA	intron (NR_033943, intron 3 of 3)	intron (NR_033943, intron 3 of 3)	42146	NR_033943	100129345	Hs.23632	NR_033943	ENSG00000197176	LINC02291	-	long intergenic non-protein coding RNA 2291	ncRNA	0.004808	0.430622	109(AAGGACAAAATGTGCC,-,0.00),110(AGGACAAAATGTGCCA,+,0.00)
chunk0198_32_1	chr8	128209828	128210427	+	0	NA	Intergenic	Intergenic	60011	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.011686	0.405000	
chunk0123_78_1	chr3	41606612	41607207	+	0	NA	intron (NM_017886, intron 31 of 36)	L1MA5|LINE|L1	355259	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.005042	0.340604	
chunk0104_439_1	chr2	181272370	181272763	+	0	NA	intron (NR_130784, intron 3 of 4)	Tigger3b|DNA|TcMar-Tigger	33086	NR_039637	100616213		NR_039637	ENSG00000266705	MIR4437	mir-4437	microRNA 4437	ncRNA	0.002545	0.345178	
chunk0164_84_1	chr6	20126121	20126374	+	0	NA	intron (NM_001080480, intron 7 of 12)	intron (NM_001080480, intron 7 of 12)	86217	NM_001080480	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.007905	0.405512	
chunk0120_426_1	chr3	13154657	13155406	+	0	NA	Intergenic	L1M4|LINE|L1	-81914	NM_001134382	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.005340	0.318667	
chunk0020_383_1	chr1	239892459	239893532	+	0	NA	intron (NM_000740, intron 4 of 4)	MIR|SINE|MIR	6877	NR_046582	100873984	Hs.199475	NR_046582	ENSG00000234601	CHRM3-AS1	-	CHRM3 antisense RNA 1	ncRNA	0.002796	0.376164	348(AAGGACATAATGTGCC,-,0.00),349(AGGACATAATGTGCCA,+,0.00)
chunk0202_297_1	chr9	77855128	77855533	+	0	NA	intron (NM_002072, intron 2 of 6)	intron (NM_002072, intron 2 of 6)	176119	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.009877	0.320197	
chunk0165_210_1	chr6	34958761	34959174	+	0	NA	intron (NM_015245, intron 1 of 23)	L2b|LINE|L2	69706	NM_015245	23294	Hs.656492	NM_015245	ENSG00000064999	ANKS1A	ANKS1	ankyrin repeat and sterile alpha motif domain containing 1A	protein-coding	0.007264	0.446860	
chunk0188_41_1	chr8	6642501	6643051	+	0	NA	intron (NR_125386, intron 1 of 4)	Charlie5|DNA|hAT-Charlie	-20556	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.012727	0.424682	287(GAGAACTGAATGTTTC,-,0.00)
chunk0146_248_1	chr4	162457525	162458132	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-293794	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.013180	0.381579	
chunk0062_7_1	chr14	66119096	66119744	+	0	NA	Intergenic	Intergenic	-366951	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.009259	0.437596	631(TGCCCAGCCTGTTCCT,+,0.00)
chunk0117_390_1	chr21	45411809	45412349	+	0	NA	intron (NM_130445, intron 2 of 42)	intron (NM_130445, intron 2 of 42)	-2014	NR_052004	100874236	Hs.589901	NR_052004	ENSG00000224574	COL18A1-AS2	-	COL18A1 antisense RNA 2	ncRNA	0.042593	0.499076	
chunk0044_436_1	chr12	42281300	42281686	+	0	NA	Intergenic	Intergenic	42366	NR_107005	102467003		NR_107005	ENSG00000278520	MIR7851	hsa-mir-7851	microRNA 7851	ncRNA	0.010363	0.428941	
chunk0143_118_1	chr4	109412664	109413296	+	0	NA	Intergenic	Intergenic	-20792	NM_001042734	10427	Hs.292472	NM_006323	ENSG00000138802	SEC24B	SEC24	SEC24 homolog B, COPII coat complex component	protein-coding	0.003165	0.375987	
chunk0208_62_1	chrX	11560117	11560442	+	0	NA	intron (NR_109776, intron 1 of 14)	MER58A|DNA|hAT-Charlie	105422	NM_013427	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.006154	0.343558	
chunk0178_46_1	chr7	29770084	29770611	+	0	NA	Intergenic	Intergenic	-36207	NM_001080529	644150	Hs.380698	NM_001080529	ENSG00000122574	WIPF3	CR16	WAS/WASL interacting protein family member 3	protein-coding	0.013283	0.452652	280(AAGAACATTCTGTACT,-,0.00),281(AGAACATTCTGTACTT,+,0.00)
chunk0206_409_1	chr9	127424015	127424426	+	0	NA	promoter-TSS (NM_007135)	promoter-TSS (NM_007135)	-154	NM_001286697	7633	Hs.522399	NM_007135	ENSG00000196152	ZNF79	pT7	zinc finger protein 79	protein-coding	0.075426	0.577670	
chunk0089_174_1	chr18	59579548	59580076	+	0	NA	intron (NM_133459, intron 2 of 10)	intron (NM_133459, intron 2 of 10)	117600	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.015152	0.451796	258(TGGCACATGCTGACCT,-,0.00),259(GGCACATGCTGACCTG,+,0.00)
chunk0206_254_1	chr9	123784521	123784821	+	0	NA	intron (NM_024820, intron 3 of 20)	intron (NM_024820, intron 3 of 20)	145467	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.003333	0.358804	
chunk0127_135_1	chr3	94100132	94100450	+	0	NA	intron (NM_022072, intron 5 of 5)	L1MA7|LINE|L1	-37068	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.006289	0.363636	173(AAGGACATTCTGTTAT,-,0.00),174(AGGACATTCTGTTATT,+,0.00)
chunk0124_422_1	chr3	61117210	61117723	+	0	NA	intron (NM_001166243, intron 2 of 9)	intron (NM_001166243, intron 2 of 9)	133993	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.009747	0.394942	
chunk0024_419_1	chr10	45653185	45653582	+	0	NA	intron (NR_104256, intron 2 of 6)	L1PA16|LINE|L1	19349	NM_001282905	93550	Hs.89029	NM_174890	ENSG00000172671	ZFAND4	ANUBL1	zinc finger AN1-type containing 4	protein-coding	0.002519	0.351759	
chunk0085_369_1	chr18	9461586	9462070	+	0	NA	Intergenic	HAL1|LINE|L1	-13704	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.002066	0.350515	
chunk0193_196_1	chr8	75785102	75785301	+	0	NA	Intergenic	MER52A|LTR|ERV1	245233	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.010050	0.615000	
chunk0130_89_1	chr3	130796530	130796980	+	0	NA	Intergenic	L1M4c|LINE|L1	-49903	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.004444	0.334812	
chunk0181_443_1	chr7	90688876	90689153	+	0	NA	intron (NM_001287135, intron 2 of 14)	intron (NM_001287135, intron 2 of 14)	-20384	NM_012395	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.003610	0.482014	
chunk0006_191_1	chr1	67561764	67562071	+	0	NA	Intergenic	Intergenic	-123260	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.013029	0.542208	
chunk0047_170_1	chr12	70400059	70400659	+	0	NA	intron (NM_014505, intron 2 of 2)	intron (NM_014505, intron 2 of 2)	34077	NM_014505	27345	Hs.525529	NM_014505	ENSG00000135643	KCNMB4	-	potassium calcium-activated channel subfamily M regulatory beta subunit 4	protein-coding	0.006667	0.347754	
chunk0149_180_1	chr5	21171028	21171479	+	0	NA	Intergenic	Intergenic	-288227	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.000000	0.296460	
chunk0175_240_1	chr7	6482328	6482674	+	0	NA	intron (NM_006854, intron 1 of 4)	Tigger15a|DNA|TcMar-Tigger	1717	NM_006854	11014	Hs.654552	NM_006854	ENSG00000136240	KDELR2	ELP-1|ERD2.2	KDEL endoplasmic reticulum protein retention receptor 2	protein-coding	0.011561	0.414986	
chunk0055_221_1	chr13	62432064	62432841	+	0	NA	Intergenic	Intergenic	220170	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.006435	0.330334	351(CAAAACAAAATGTCCT,-,0.00),352(AAAACAAAATGTCCTT,+,0.00)
chunk0198_465_1	chr8	144669766	144670263	+	0	NA	intron (NM_001308208, intron 1 of 10)	L1MB5|LINE|L1	15798	NM_001308208	80728	Hs.148988	NM_025251	ENSG00000147799	ARHGAP39	CrGAP|Vilse	Rho GTPase activating protein 39	protein-coding	0.030181	0.457831	
chunk0092_382_1	chr19	36378751	36379012	+	0	NA	intron (NM_020917, intron 1 of 4)	CpG	322	NM_020917	57677	Hs.35524	NM_020917	ENSG00000142065	ZFP14	ZNF531	ZFP14 zinc finger protein	protein-coding	0.061303	0.572519	
chunk0105_5_1	chr2	181698300	181698509	+	0	NA	Intergenic	L2c|LINE|L2	-17739	NM_002500	4760	Hs.574626	NM_002500	ENSG00000162992	NEUROD1	BETA2|BHF-1|MODY6|NEUROD|bHLHa3	neuronal differentiation 1	protein-coding	0.000000	0.419048	
chunk0034_66_1	chr11	27159381	27159650	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	59253	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.007435	0.411111	66(AGGAACAGCATGTCTC,-,0.00),67(GGAACAGCATGTCTCA,+,0.00)
chunk0137_268_1	chr4	22479901	22480450	+	0	NA	intron (NM_145290, intron 1 of 18)	L1M5|LINE|L1	35879	NM_145290	166647	Hs.99195	NM_145290	ENSG00000152990	ADGRA3	GPR125|PGR21|TEM5L	adhesion G protein-coupled receptor A3	protein-coding	0.014572	0.425455	
chunk0187_184_1	chr7	151299497	151299959	+	0	NA	Intergenic	(TGTGTG)n|Simple_repeat|Simple_repeat	-22583	NM_003078	6604	Hs.647067	NM_003078	ENSG00000082014	SMARCD3	BAF60C|CRACD3|Rsc6p	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding	0.015152	0.477322	
chunk0128_178_1	chr3	107382633	107383257	+	0	NA	promoter-TSS (NR_126332)	promoter-TSS (NR_126332)	-786	NR_126332	101929579	Hs.552750	NR_126332		LOC101929579	-	uncharacterized LOC101929579	ncRNA	0.006410	0.400000	
chunk0010_41_1	chr1	112721919	112722414	+	0	NA	intron (NM_001004440, intron 1 of 4)	intron (NM_001004440, intron 1 of 4)	1599	NM_182759	284467	Hs.439116	NM_182759	ENSG00000184599	TAFA3	FAM19A3|TAFA-3	TAFA chemokine like family member 3	protein-coding	0.016162	0.592742	191(GGGGACAAGGTGTGCC,-,0.00),192(GGGACAAGGTGTGCCT,+,0.00)
chunk0065_349_1	chr14	103627043	103627421	+	0	NA	Intergenic	L2a|LINE|L2	-1956	NM_005552	3831	Hs.20107	NM_005552	ENSG00000126214	KLC1	KLC|KNS2|KNS2A	kinesin light chain 1	protein-coding	0.018519	0.477573	
chunk0145_352_1	chr4	151153502	151154067	+	0	NA	intron (NM_001009555, intron 9 of 20)	intron (NM_001009555, intron 9 of 20)	21768	NM_001128924	152503	Hs.744983	NM_001009555	ENSG00000109686	SH3D19	EBP|EVE1|Eve-1|Kryn|SH3P19	SH3 domain containing 19	protein-coding	0.012389	0.379859	260(CAGTACTGAATGTTCT,-,0.00),261(AGTACTGAATGTTCTG,+,0.00)
chunk0018_248_1	chr1	220164469	220165014	+	0	NA	exon (NM_012414, exon 27 of 35)	exon (NM_012414, exon 27 of 35)	35878	NR_031705	100302234		NR_031705	ENSG00000281696	MIR664A	MIR664|MIRN664|hsa-mir-664|hsa-mir-664a|mir-664a	microRNA 664a	ncRNA	0.003670	0.338828	
chunk0171_143_1	chr6	123658772	123659333	+	0	NA	Intergenic	L2c|LINE|L2	-21959	NM_001251987	10345	Hs.144744	NM_006073	ENSG00000186439	TRDN	CPVT5|TDN|TRISK	triadin	protein-coding	0.003565	0.368327	
chunk0147_388_1	chr4	186654071	186654333	+	0	NA	intron (NM_005245, intron 3 of 26)	intron (NM_005245, intron 3 of 26)	69631	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.011450	0.456274	
chunk0176_201_1	chr7	14670589	14670934	+	0	NA	intron (NM_145695, intron 12 of 23)	L1MA9|LINE|L1	170689	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.000000	0.341040	
chunk0191_191_1	chr8	51722168	51722428	+	0	NA	intron (NM_144651, intron 1 of 22)	LTR1F1|LTR|ERV1	87147	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.015385	0.590038	
chunk0043_50_1	chr12	13561962	13562166	+	0	NA	3' UTR (NM_000834, exon 13 of 13)	3' UTR (NM_000834, exon 13 of 13)	-185319	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.014706	0.463415	
chunk0008_371_1	chr1	96820060	96820684	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	97734	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.003205	0.337600	
chunk0017_336_1	chr1	211578382	211578691	+	0	NA	exon (NM_021194, exon 1 of 2)	exon (NM_021194, exon 1 of 2)	221	NM_021194	7779	Hs.519469	NM_021194	ENSG00000170385	SLC30A1	ZNT1|ZRC1	solute carrier family 30 member 1	protein-coding	0.116505	0.716129	
chunk0069_29_1	chr15	60454615	60455350	+	0	NA	intron (NM_024611, intron 8 of 15)	intron (NM_024611, intron 8 of 15)	24178	NM_024611	79664	Hs.200943	NM_024611	ENSG00000128915	ICE2	BRCC1|NARG2	interactor of little elongation complex ELL subunit 2	protein-coding	0.008163	0.376359	327(GAGAACATGCAGTCCA,-,0.00),328(AGAACATGCAGTCCAA,+,0.00)
chunk0094_387_1	chr2	9981038	9981380	+	0	NA	intron (NM_198182, intron 8 of 15)	intron (NM_198182, intron 8 of 15)	29546	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.014620	0.501458	16(AGGAACAAAGTGTGCC,-,0.00),17(GGAACAAAGTGTGCCC,+,0.00),242(AGGGACAGTGTGTTTC,-,0.00),243(GGGACAGTGTGTTTCC,+,0.00)
chunk0125_107_1	chr3	65592101	65592502	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-301515	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.000000	0.365672	
chunk0087_393_1	chr18	41850744	41851274	+	0	NA	Intergenic	Intergenic	-104189	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.005660	0.370998	
chunk0159_431_1	chr5	148147537	148148141	+	0	NA	Intergenic	Intergenic	-20707	NM_001001325	408187	Hs.553815	NM_001001325	ENSG00000196800	SPINK14	SPINK5L2	serine peptidase inhibitor, Kazal type 14 (putative)	protein-coding	0.008278	0.370248	
chunk0065_251_1	chr14	101495768	101496368	+	0	NA	Intergenic	Intergenic	59608	NR_002770	64150	Hs.525597	NR_002770	ENSG00000258498	DIO3OS	C14orf134|DIO3-AS1|DIO3-OS|NCRNA00041	DIO3 opposite strand upstream RNA	ncRNA	0.016667	0.479201	
chunk0093_130_1	chr19	45742865	45743516	+	0	NA	intron (NM_001310124, intron 3 of 14)	intron (NM_001310124, intron 3 of 14)	9939	NM_001310124	388553	Hs.721835	NM_001310124	ENSG00000237452	BHMG1	HMGDC	basic helix-loop-helix and HMG-box containing 1	protein-coding	0.009217	0.460123	323(AGGTTCACCCTGTGCT,-,0.00),324(GGTTCACCCTGTGCTT,+,0.00)
chunk0160_268_1	chr5	157304145	157304344	+	0	NA	exon (NM_014376, exon 8 of 31)	exon (NM_014376, exon 8 of 31)	34902	NM_014376	26999	Hs.519702	NM_014376	ENSG00000055163	CYFIP2	EIEE65|PIR121	cytoplasmic FMR1 interacting protein 2	protein-coding	0.020101	0.560000	174(GAGAACAAGATGTACC,-,0.00),175(AGAACAAGATGTACCT,+,0.00)
chunk0174_373_1	chr6	164881522	164882180	+	0	NA	Intergenic	L1MDa|LINE|L1	-59788	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.006079	0.385432	
chunk0156_218_1	chr5	108135231	108135827	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	246569	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.005034	0.370184	
chunk0097_104_1	chr2	46031035	46031495	+	0	NA	intron (NM_005400, intron 10 of 14)	intron (NM_005400, intron 10 of 14)	-266137	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.013043	0.425163	
chunk0163_101_1	chr6	9649013	9649268	+	0	NA	Intergenic	L1MEf|LINE|L1	-763178	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003922	0.417969	
chunk0161_113_1	chr5	167551299	167552030	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	-203272	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.002736	0.378415	468(AGGGGCACAGTGTTCA,-,0.00),469(GGGGCACAGTGTTCAT,+,0.00)
chunk0089_53_1	chr18	58117994	58118227	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	-31223	NM_001144969	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.004292	0.452991	
chunk0056_302_1	chr13	90798116	90798589	+	0	NA	Intergenic	Intergenic	128245	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.008457	0.388186	
chunk0007_32_1	chr1	77635026	77635225	+	0	NA	intron (NM_015534, intron 4 of 14)	intron (NM_015534, intron 4 of 14)	47533	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.000000	0.375000	
chunk0196_339_1	chr8	113950457	113950910	+	0	NA	Intergenic	L1MD1|LINE|L1	-513670	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.002208	0.354626	
chunk0153_148_1	chr5	69217769	69218110	+	0	NA	intron (NM_033281, intron 1 of 3)	CpG	193	NM_033281	92259	Hs.631971	NM_033281	ENSG00000134056	MRPS36	DC47|MRP-S36	mitochondrial ribosomal protein S36	protein-coding	0.105572	0.657895	
chunk0180_248_1	chr7	68938974	68939272	+	0	NA	Intergenic	Intergenic	658372	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.003356	0.448161	
chunk0167_89_1	chr6	56855060	56855259	+	0	NA	intron (NM_001144769, intron 3 of 96)	intron (NM_001144769, intron 3 of 96)	-3243	NM_001144770	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.000000	0.340000	
chunk0072_268_1	chr15	96723818	96724098	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	57696	NR_102754	100652749	Hs.303588	NR_102753	ENSG00000259282	SPATA8-AS1	-	SPATA8 antisense RNA 1 (head to head)	ncRNA	0.010714	0.427046	
chunk0198_115_1	chr8	131836247	131836553	+	0	NA	Intergenic	LTR78B|LTR|ERV1	-67709	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.000000	0.482085	
chunk0100_23_1	chr2	105175258	105175879	+	0	NA	Intergenic	Intergenic	-66175	NM_007227	11250	Hs.590903	NM_007227	ENSG00000135973	GPR45	PSP24|PSP24(ALPHA)|PSP24A	G protein-coupled receptor 45	protein-coding	0.011272	0.495177	410(GGGCACTCAGTGTCCT,-,0.00),411(GGCACTCAGTGTCCTC,+,0.00)
chunk0204_292_1	chr9	99421414	99421821	+	0	NA	Intergenic	MIR3|SINE|MIR	-46360	NR_102271	100996569	Hs.745280	NR_102270	ENSG00000271086	NAMA	-	non-protein coding RNA, associated with MAP kinase pathway and growth arrest	ncRNA	0.009828	0.426471	130(TGGGACTCAATGTTCT,-,0.00),131(GGGACTCAATGTTCTC,+,0.00)
chunk0182_302_1	chr7	98448570	98449237	+	0	NA	Intergenic	Intergenic	-47788	NM_018842	55971	Hs.656063	NM_018842	ENSG00000006453	BAIAP2L1	IRTKS	BAI1 associated protein 2 like 1	protein-coding	0.013493	0.479042	100(AGAAGACAATGTCCTT,+,0.00),398(AAGCACAAAATGTTCC,-,0.00),399(AGCACAAAATGTTCCT,+,0.00)
chunk0049_378_1	chr12	95835975	95836181	+	0	NA	Intergenic	Intergenic	-22853	NM_003095	6636	Hs.105465	NM_003095	ENSG00000139343	SNRPF	SMF|Sm-F|snRNP-F	small nuclear ribonucleoprotein polypeptide F	protein-coding	0.000000	0.280193	
chunk0168_14_1	chr6	76861541	76861918	+	0	NA	Intergenic	Intergenic	601674	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.005305	0.439153	129(AGGAACACCTTGAGCT,-,0.00),130(GGAACACCTTGAGCTT,+,0.00)
chunk0082_218_1	chr17	57120677	57121280	+	0	NA	3' UTR (NM_003488, exon 11 of 11)	3' UTR (NM_003488, exon 11 of 11)	35204	NM_001242902	8165	Hs.463506	NM_003488	ENSG00000121057	AKAP1	AKAP|AKAP121|AKAP149|AKAP84|D-AKAP1|PPP1R43|PRKA1|SAKAP84|TDRD17	A-kinase anchoring protein 1	protein-coding	0.000000	0.394040	
chunk0183_314_1	chr7	107996283	107996535	+	0	NA	intron (NM_002291, intron 4 of 33)	intron (NM_002291, intron 4 of 33)	6950	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.019841	0.375494	184(AAGCACAACTTGTGCA,-,0.00)
chunk0129_67_1	chr3	117618195	117618444	+	0	NA	Intergenic	L1PA16|LINE|L1	696888	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.008032	0.360000	
chunk0210_410_1	chrX	100709385	100709653	+	0	NA	intron (NM_080737, intron 1 of 18)	AluSz|SINE|Alu	22015	NM_080737	94121	Hs.592224	NM_080737	ENSG00000102362	SYTL4	SLP4	synaptotagmin like 4	protein-coding	0.014925	0.468401	
chunk0200_296_1	chr9	22884602	22884887	+	0	NA	Intergenic	L1PA5|LINE|L1	238544	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.010526	0.377622	102(GAGTACAGAATGTTCT,-,0.00),103(AGTACAGAATGTTCTT,+,0.00)
chunk0067_421_1	chr15	49807635	49807989	+	0	NA	Intergenic	Intergenic	186783	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.000000	0.323944	
chunk0065_6_1	chr15	19961851	19962306	+	0	NA	Intergenic	Intergenic	-320666	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.004396	0.333333	
chunk0179_144_1	chr7	46163052	46163522	+	0	NA	Intergenic	Intergenic	-242015	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.010638	0.511677	57(AAGGACACCAAGTCCT,-,0.00),58(AGGACACCAAGTCCTG,+,0.00)
chunk0145_284_1	chr4	149738536	149738735	+	0	NA	Intergenic	Intergenic	-339639	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.000000	0.470000	
chunk0041_390_1	chr11	132764889	132765498	+	0	NA	intron (NM_001012393, intron 2 of 7)	intron (NM_001012393, intron 2 of 7)	177949	NM_002545	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.019704	0.465574	
chunk0025_143_1	chr10	52252265	52252821	+	0	NA	intron (NM_006258, intron 10 of 17)	intron (NM_006258, intron 10 of 17)	61585	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.005396	0.359066	
chunk0086_432_1	chr18	28156157	28157075	+	0	NA	intron (NM_001792, intron 1 of 15)	intron (NM_001792, intron 1 of 15)	20830	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.001089	0.460283	
chunk0133_322_1	chr3	172516903	172517149	+	0	NA	TTS (NM_001190943)	TTS (NM_001190943)	6449	NM_001190943	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.012195	0.502024	
chunk0122_24_1	chr3	27710895	27711492	+	0	NA	Intergenic	L1MC5|LINE|L1	11522	NM_001278183	8320	Hs.591663	NM_005442	ENSG00000163508	EOMES	TBR2	eomesodermin	protein-coding	0.008375	0.351171	
chunk0092_254_1	chr19	33029829	33030318	+	0	NA	intron (NM_033103, intron 2 of 14)	MER68|LTR|ERVL	34845	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.016360	0.487755	
chunk0092_409_1	chr19	37655081	37655280	+	0	NA	5' UTR (NM_014898, exon 1 of 6)	5' UTR (NM_014898, exon 1 of 6)	232	NM_014898	22835	Hs.668737	NM_014898	ENSG00000120784	ZFP30	ZNF745	ZFP30 zinc finger protein	protein-coding	0.080402	0.655000	
chunk0050_39_1	chr12	100574222	100574429	+	0	NA	intron (NM_001303130, intron 1 of 8)	intron (NM_001303130, intron 1 of 8)	664	NM_174942	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.028986	0.500000	
chunk0052_99_1	chr13	22458035	22458347	+	0	NA	Intergenic	Intergenic	247906	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.016026	0.460064	
chunk0172_189_1	chr6	136600904	136601429	+	0	NA	intron (NM_005923, intron 20 of 29)	intron (NM_005923, intron 20 of 29)	-27948	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.003810	0.378327	
chunk0046_69_1	chr12	55977727	55977986	+	0	NA	intron (NM_001252037, intron 1 of 4)	intron (NM_001252037, intron 1 of 4)	3845	NM_001252037	5869	Hs.157659	NM_002868	ENSG00000111540	RAB5B	-	RAB5B, member RAS oncogene family	protein-coding	0.011583	0.423077	
chunk0096_297_1	chr2	32618572	32618950	+	0	NA	3' UTR (NM_016252, exon 74 of 74)	3' UTR (NM_016252, exon 74 of 74)	-9259	NM_001193509	55622	Hs.468125	NM_017735	ENSG00000018699	TTC27	-	tetratricopeptide repeat domain 27	protein-coding	0.000000	0.345646	227(CAGTACATTCTGTACC,-,0.00),228(AGTACATTCTGTACCT,+,0.00)
chunk0114_222_1	chr21	15759743	15759942	+	0	NA	intron (NM_013396, intron 1 of 23)	intron (NM_013396, intron 1 of 23)	29817	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.010050	0.365000	
chunk0078_294_1	chr17	8138707	8138981	+	0	NA	Intergenic	Intergenic	6227	NR_106943	102465532		NR_106943	ENSG00000284117	MIR6883	hsa-mir-6883	microRNA 6883	ncRNA	0.076642	0.545455	
chunk0085_270_1	chr18	7729890	7730251	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	162754	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.005540	0.339779	
chunk0029_155_1	chr10	99443545	99444228	+	0	NA	Intergenic	L1ME3G|LINE|L1	-13113	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.005857	0.330409	
chunk0157_410_1	chr5	124573452	124574131	+	0	NA	Intergenic	Intergenic	-135271	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.014728	0.401471	
chunk0195_112_1	chr8	94725121	94725527	+	0	NA	intron (NM_181787, intron 1 of 18)	intron (NM_181787, intron 1 of 18)	5449	NM_181787	286148	Hs.567828	NM_181787	ENSG00000156162	DPY19L4	-	dpy-19 like 4	protein-coding	0.000000	0.336609	161(AGGAACACTCTGTACT,-,0.00),162(GGAACACTCTGTACTT,+,0.00)
chunk0124_288_1	chr3	57696939	57697272	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-4016	NM_152678	201627	Hs.91085	NM_152678	ENSG00000174839	DENND6A	AFI1A|FAM116A	DENN domain containing 6A	protein-coding	0.000000	0.449102	
chunk0016_355_1	chr1	202254475	202254716	+	0	NA	intron (NM_001017404, intron 4 of 15)	intron (NM_001017404, intron 4 of 15)	40440	NM_001017404	59352	Hs.497402	NM_021636	ENSG00000133067	LGR6	GPCR|VTS20631	leucine rich repeat containing G protein-coupled receptor 6	protein-coding	0.004149	0.466942	
chunk0003_385_1	chr1	39850417	39851092	+	0	NA	intron (NR_132407, intron 1 of 7)	intron (NR_132407, intron 1 of 7)	32757	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.002963	0.394970	
chunk0189_301_1	chr8	26000375	26001166	+	0	NA	intron (NM_022659, intron 6 of 15)	MER124|DNA?|DNA?	44354	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.011378	0.415404	
chunk0060_189_1	chr14	47012529	47012763	+	0	NA	intron (NM_182830, intron 8 of 16)	MIRb|SINE|MIR	330600	NM_182830	161357	Hs.436380	NM_182830	ENSG00000139915	MDGA2	MAMDC1|c14_5286	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.000000	0.336170	
chunk0095_129_1	chr2	16514368	16514727	+	0	NA	Intergenic	MER124|DNA?|DNA?	151319	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.000000	0.422222	
chunk0206_382_1	chr9	126725573	126726249	+	0	NA	Intergenic	L1ME3C|LINE|L1	-79095	NM_001135776	23099	Hs.355581	NM_014007	ENSG00000169155	ZBTB43	ZBTB22B|ZNF-X|ZNF297B	zinc finger and BTB domain containing 43	protein-coding	0.010355	0.376662	
chunk0014_219_1	chr1	179484625	179485236	+	0	NA	intron (NR_073544, intron 17 of 25)	L1PA13|LINE|L1	91022	NM_014625	7827	Hs.412710	NM_014625	ENSG00000116218	NPHS2	PDCN|SRN1	NPHS2 stomatin family member, podocin	protein-coding	0.008183	0.571895	
chunk0031_78_1	chr10	123144762	123145228	+	0	NA	Intergenic	Intergenic	-3127	NM_005519	3167	Hs.444756	NM_005519	ENSG00000188816	HMX2	H6L|Nkx5-2	H6 family homeobox 2	protein-coding	0.030043	0.573876	227(AGGAACTGAGTGTTCC,-,0.00),228(GGAACTGAGTGTTCCT,+,0.00)
chunk0147_75_1	chr4	172982145	172982553	+	0	NA	intron (NM_001034845, intron 10 of 12)	intron (NM_001034845, intron 10 of 12)	-186404	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.004902	0.459658	
chunk0012_328_1	chr1	162500743	162501211	+	0	NA	exon (NM_001184763, exon 3 of 8)	exon (NM_001184763, exon 3 of 8)	3172	NM_175866	127933	Hs.127310	NM_144624	ENSG00000152332	UHMK1	KIS|KIST|P-CIP2	U2AF homology motif kinase 1	protein-coding	0.004274	0.385928	254(GATACAGAATGTACCT,+,0.00)
chunk0181_429_1	chr7	90412551	90413122	+	0	NA	exon (NM_012129, exon 3 of 3)	exon (NM_012129, exon 3 of 3)	9502	NM_001185072	9069	Hs.731917	NM_012129	ENSG00000157224	CLDN12	-	claudin 12	protein-coding	0.019264	0.538462	
chunk0185_82_1	chr7	125373852	125374324	+	0	NA	intron (NR_110188, intron 8 of 8)	intron (NR_110188, intron 8 of 8)	-109797	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.002119	0.348837	
chunk0062_366_1	chr14	73977924	73978245	+	0	NA	intron (NM_001249, intron 6 of 15)	intron (NM_001249, intron 6 of 15)	-27670	NM_152445	145483	Hs.550547	NM_152445	ENSG00000156050	FAM161B	C14orf44|c14_5547	FAM161 centrosomal protein B	protein-coding	0.003115	0.369565	
chunk0022_382_1	chr10	17603371	17604036	+	0	NA	intron (NM_014241, intron 3 of 6)	intron (NM_014241, intron 3 of 6)	13671	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.003008	0.333333	
chunk0082_275_1	chr17	57946552	57947131	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	8482	NM_001271875	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.015544	0.501724	
chunk0139_20_1	chr4	48287125	48287605	+	0	NA	Intergenic	L1MD1|LINE|L1	-17568	NM_003215	7006	Hs.479670	NM_003215	ENSG00000135605	TEC	PSCTK4	tec protein tyrosine kinase	protein-coding	0.002083	0.284823	
chunk0071_462_1	chr15	90400043	90400298	+	0	NA	intron (NM_003870, intron 2 of 37)	intron (NM_003870, intron 2 of 37)	11929	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.007843	0.347656	
chunk0188_300_1	chr8	15943389	15943588	+	0	NA	Intergenic	Intergenic	249303	NM_138715	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.000000	0.420000	
chunk0012_209_1	chr1	160102072	160102409	+	0	NA	Intergenic	Intergenic	-3412	NM_001206665	93185	Hs.332012	NM_052868	ENSG00000162729	IGSF8	CD316|CD81P3|EWI-2|EWI2|KCT-4|LIR-D1|PGRL	immunoglobulin superfamily member 8	protein-coding	0.011869	0.434911	
chunk0144_271_1	chr4	137515480	137516011	+	0	NA	Intergenic	Intergenic	16753	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.001883	0.293233	
chunk0001_398_1	chr1	10745895	10746366	+	0	NA	intron (NM_001079843, intron 2 of 20)	MIR1_Amn|SINE|MIR	50546	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.036093	0.565678	235(GAGGACATACTGTTCC,-,0.00),236(AGGACATACTGTTCCC,+,0.00)
chunk0081_412_1	chr17	48573432	48573640	+	0	NA	intron (NM_002146, intron 1 of 3)	intron (NM_002146, intron 1 of 3)	912	NM_002146	3213	Hs.654560	NM_002146	ENSG00000120093	HOXB3	HOX2|HOX2G|Hox-2.7	homeobox B3	protein-coding	0.024038	0.535885	
chunk0198_178_1	chr8	133356190	133356602	+	0	NA	Intergenic	Intergenic	-59092	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.012136	0.530266	
chunk0065_323_1	chr14	103148585	103149045	+	0	NA	Intergenic	Intergenic	22488	NM_006291	7127	Hs.525607	NM_006291	ENSG00000185215	TNFAIP2	B94|EXOC3L3	TNF alpha induced protein 2	protein-coding	0.030435	0.490239	
chunk0039_423_1	chr11	107825808	107826372	+	0	NA	intron (NM_017515, intron 1 of 7)	L1MC5|LINE|L1	33098	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.007092	0.353982	
chunk0033_191_1	chr11	16225968	16226763	+	0	NA	intron (NM_001145819, intron 4 of 15)	(TTGTTT)n|Simple_repeat|Simple_repeat	176502	NM_017508	55553	Hs.368226	NM_017508	ENSG00000110693	SOX6	HSSOX6|SOXD	SRY-box transcription factor 6	protein-coding	0.003774	0.364322	
chunk0082_346_1	chr17	59853335	59853571	+	0	NA	Intergenic	L2c|LINE|L2	12187	NR_029493	406991	Hs.444569	NR_029493	ENSG00000284190	MIR21	MIRN21|hsa-mir-21|miR-21|miRNA21	microRNA 21	ncRNA	0.029661	0.476793	
chunk0010_300_1	chr1	117753454	117753822	+	0	NA	Intergenic	L2c|LINE|L2	147656	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.010870	0.490515	198(GGGAACAGCATGTGAT,-,0.00)
chunk0134_324_1	chr3	181850886	181851330	+	0	NA	Intergenic	Intergenic	-101256	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.009009	0.364045	
chunk0090_383_1	chr18	77374021	77374542	+	0	NA	Intergenic	Intergenic	124229	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.021113	0.394636	238(GAGAACAAACAGTTCT,-,0.00),239(AGAACAAACAGTTCTG,+,0.00)
chunk0180_316_1	chr7	71282714	71283059	+	0	NA	intron (NM_022479, intron 1 of 10)	intron (NM_022479, intron 1 of 10)	-24788	NR_037479	100500920		NR_037479	ENSG00000283278	MIR3914-2	-	microRNA 3914-2	ncRNA	0.008696	0.528902	
chunk0058_124_1	chr14	22333936	22334464	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	255037	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.018939	0.357278	
chunk0085_187_1	chr18	6150258	6150697	+	0	NA	intron (NM_173464, intron 13 of 19)	intron (NM_173464, intron 13 of 19)	-106267	NR_110765	101927150		NR_110765		L3MBTL4-AS1	-	L3MBTL4 antisense RNA 1	ncRNA	0.009112	0.384091	
chunk0123_196_1	chr3	44396368	44397019	+	0	NA	intron (NM_001282915, intron 7 of 10)	intron (NM_001282915, intron 7 of 10)	58241	NM_173826	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.010753	0.365031	
chunk0037_80_1	chr11	71296609	71297006	+	0	NA	Intergenic	L1MC1|LINE|L1	-72011	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.000000	0.402010	
chunk0131_130_1	chr3	144386452	144386844	+	0	NA	Intergenic	Intergenic	413323	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.005102	0.358779	
chunk0156_346_1	chr5	111914951	111915528	+	0	NA	intron (NR_046678, intron 1 of 3)	LTR16A2|LTR|ERVL	2731	NR_046678	100873948	Hs.147716	NR_046678	ENSG00000250095	NREP-AS1	-	NREP antisense RNA 1	ncRNA	0.001733	0.430796	206(GGGAACTGGAAGTGCC,-,0.00),207(GGAACTGGAAGTGCCT,+,0.00)
chunk0155_59_1	chr5	91503098	91503620	+	0	NA	Intergenic	Intergenic	-120027	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.007663	0.304015	
chunk0016_181_1	chr1	198144150	198144527	+	0	NA	Intergenic	L2c|LINE|L2	-12640	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.000000	0.306878	
chunk0187_60_1	chr8	1946811	1947509	+	0	NA	intron (NM_001308152, intron 26 of 27).2	intron (NM_001308152, intron 26 of 27).2	-24237	NR_126346	104266957	Hs.734498	NR_126346	ENSG00000253696	KBTBD11-OT1	-	KBTBD11 overlapping transcript 1	ncRNA	0.032951	0.513591	
chunk0084_329_1	chr17	80930124	80930414	+	0	NA	intron (NM_020761, intron 24 of 33)	(CTCAG)n|Simple_repeat|Simple_repeat	-61572	NM_024591	79643	Hs.514560	NM_024591	ENSG00000176108	CHMP6	VPS20	charged multivesicular body protein 6	protein-coding	0.000000	0.594502	
chunk0029_381_1	chr10	108721688	108722460	+	0	NA	Intergenic	L1PA17|LINE|L1	-652781	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.003886	0.345408	
chunk0128_32_1	chr3	104318483	104318698	+	0	NA	Intergenic	L1M1|LINE|L1	-794474	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.013953	0.361111	
chunk0084_208_1	chr17	78174374	78174901	+	0	NA	3' UTR (NM_003258, exon 7 of 7)	3' UTR (NM_003258, exon 7 of 7)	6047	NM_004710	9144	Hs.464210	NM_004710	ENSG00000108639	SYNGR2	-	synaptogyrin 2	protein-coding	0.030361	0.636364	
chunk0203_294_1	chr9	89021169	89021556	+	0	NA	intron (NM_016848, intron 11 of 11)	intron (NM_016848, intron 11 of 11)	29953	NM_005226	1903	Hs.585118	NM_005226	ENSG00000213694	S1PR3	EDG-3|EDG3|LPB3|S1P3	sphingosine-1-phosphate receptor 3	protein-coding	0.005168	0.505155	
chunk0193_78_1	chr8	73312387	73312969	+	0	NA	non-coding (NR_125388, exon 6 of 6)	non-coding (NR_125388, exon 6 of 6)	18076	NM_172037	157506	Hs.244940	NM_172037	ENSG00000121039	RDH10	SDR16C4	retinol dehydrogenase 10	protein-coding	0.013746	0.403087	
chunk0046_347_1	chr12	62957215	62957999	+	0	NA	Intergenic	Intergenic	-22722	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.002551	0.356688	
chunk0190_426_1	chr8	41442469	41443125	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-47765	NM_001174124	51125	Hs.654773	NM_016099	ENSG00000147533	GOLGA7	GCP16|GOLGA3AP1|GOLGA7A|HSPC041	golgin A7	protein-coding	0.010671	0.398782	
chunk0037_245_1	chr11	75411887	75412367	+	0	NA	intron (NM_001256802, intron 6 of 6)	intron (NM_001256802, intron 6 of 6)	7706	NR_000025	114599	Hs.689080	NR_000025	ENSG00000207445	SNORD15B	RNU15B|U15B	small nucleolar RNA, C/D box 15B	snoRNA	0.002083	0.484407	
chunk0107_380_1	chr2	223230273	223230739	+	0	NA	Intergenic	L1M6|LINE|L1	178576	NM_080671	23704	Hs.348522	NM_080671	ENSG00000152049	KCNE4	MIRP3	potassium voltage-gated channel subfamily E regulatory subunit 4	protein-coding	0.008584	0.411135	210(AAGCACAGAGTGTTTT,-,0.00),211(AGCACAGAGTGTTTTA,+,0.00)
chunk0184_312_1	chr7	120199128	120199653	+	0	NA	Intergenic	Intergenic	-74278	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.001905	0.351711	
chunk0173_233_1	chr6	146547243	146547604	+	0	NA	intron (NM_006834, intron 1 of 2)	intron (NM_006834, intron 1 of 2)	3731	NM_006834	10981	Hs.287714	NM_006834	ENSG00000118508	RAB32	-	RAB32, member RAS oncogene family	protein-coding	0.000000	0.320442	204(GGGAACAGTCTGCTCT,-,0.00),205(GGAACAGTCTGCTCTG,+,0.00)
chunk0053_415_1	chr13	37104559	37104904	+	0	NA	exon (NM_145203, exon 1 of 1)	exon (NM_145203, exon 1 of 1)	933	NM_145203	122011	Hs.512897	NM_145203	ENSG00000180138	CSNK1A1L	CK1	casein kinase 1 alpha 1 like	protein-coding	0.026087	0.421965	
chunk0209_96_1	chrX	39627372	39627788	+	0	NA	Intergenic	Intergenic	-33636	NR_037501	100500822		NR_037501	ENSG00000263730	MIR3937	-	microRNA 3937	ncRNA	0.014423	0.527578	123(CAGAACAATCTGTCAC,-,0.00)
chunk0139_386_1	chr4	61640113	61640442	+	0	NA	intron (NM_015236, intron 2 of 22)	intron (NM_015236, intron 2 of 22)	143156	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.006079	0.360606	192(CAGAACAGATCGTTCT,-,0.00),193(AGAACAGATCGTTCTC,+,0.00)
chunk0037_376_1	chr11	78348806	78349522	+	0	NA	intron (NM_080491, intron 1 of 9)	L1ME1|LINE|L1	-7284	NM_012296	9846	Hs.429434	NM_012296	ENSG00000033327	GAB2	-	GRB2 associated binding protein 2	protein-coding	0.004190	0.384937	137(GTGTACATACTGTACT,-,0.00),138(TGTACATACTGTACTC,+,0.00)
chunk0037_367_1	chr11	78155896	78156761	+	0	NA	intron (NR_102281, intron 2 of 2)	L1ME4b|LINE|L1	16535	NR_102280	100289388	Hs.628183	NM_203432	ENSG00000246174	KCTD21-AS1	-	KCTD21 antisense RNA 1	ncRNA	0.010405	0.423788	
chunk0046_265_1	chr12	61052904	61053358	+	0	NA	Intergenic	Intergenic	1139708	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.002203	0.342857	
chunk0017_159_1	chr1	206998820	206999487	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-28528	NM_001122979	83953	Hs.145519	NM_032029	ENSG00000162897	FCAMR	CD351|FCA/MR|FKSG87	Fc fragment of IgA and IgM receptor	protein-coding	0.002999	0.363772	
chunk0151_238_1	chr5	51183567	51184011	+	0	NA	Intergenic	Intergenic	-199335	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.002252	0.382022	
chunk0166_133_1	chr6	44789887	44790142	+	0	NA	Intergenic	UCON26|Unknown|Unknown	354373	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.015686	0.492188	
chunk0042_433_1	chr12	12202152	12202351	+	0	NA	intron (NM_002336, intron 3 of 22)	intron (NM_002336, intron 3 of 22)	64626	NM_002336	4040	Hs.584775	NM_002336	ENSG00000070018	LRP6	ADCAD2|STHAG7	LDL receptor related protein 6	protein-coding	0.015075	0.470000	
chunk0127_371_1	chr3	101900868	101901324	+	0	NA	Intergenic	MER67D|LTR|ERV1	-39763	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.006579	0.415755	
chunk0054_261_1	chr13	46421460	46421805	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	-31590	NM_001286761	80183	Hs.98117	NM_025113	ENSG00000102445	RUBCNL	C13orf18|KIAA0226L|PACER	rubicon like autophagy enhancer	protein-coding	0.005797	0.427746	175(CTGGACAGTATGTACT,-,0.00),176(TGGACAGTATGTACTT,+,0.00)
chunk0105_201_1	chr2	187743664	187743960	+	0	NA	Intergenic	L1ME3A|LINE|L1	-189320	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.272727	
chunk0194_288_1	chr8	87494796	87495257	+	0	NA	Intergenic	L1MC1|LINE|L1	379042	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.002169	0.303030	
chunk0011_75_1	chr1	144412553	144412808	+	0	NA	TTS (NR_104076)	TTS (NR_104076)	104	NR_104076	101954267		NR_104076	ENSG00000207205	RNVU1-15	RNU1-121|RNU1-66|RNVU1-16|vU1.15|vU1.16	RNA, variant U1 small nuclear 15	snRNA	0.058824	0.539062	
chunk0053_165_1	chr13	30673835	30674172	+	0	NA	Intergenic	tRNA-Asn-AAC|tRNA|tRNA	-39475	NM_001204406	241	Hs.507658	NM_001629	ENSG00000132965	ALOX5AP	FLAP	arachidonate 5-lipoxygenase activating protein	protein-coding	0.086053	0.568047	119(AAGCACTGACCGTCCC,-,0.00),120(AGCACTGACCGTCCCT,+,0.00)
chunk0125_112_1	chr3	65660202	65660557	+	0	NA	intron (NM_015520, intron 1 of 24)	L2b|LINE|L2	-233437	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.011268	0.393258	187(AAGTACAAGATGTTCT,-,0.00),188(AGTACAAGATGTTCTG,+,0.00)
chunk0099_155_1	chr2	87532025	87532536	+	0	NA	Intergenic	Intergenic	76825	NR_024205	112597	Hs.652166	NR_024204	ENSG00000222041	CYTOR	C2orf59|LINC00152|NCRNA00152	cytoskeleton regulator RNA	ncRNA	0.009785	0.417969	
chunk0007_178_1	chr1	80594032	80594341	+	0	NA	intron (NR_125940, intron 2 of 3)	L1PB1|LINE|L1	-47101	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.009709	0.493548	
chunk0025_129_1	chr10	51910912	51911149	+	0	NA	intron (NM_006258, intron 5 of 17)	intron (NM_006258, intron 5 of 17)	-211435	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.000000	0.344538	
chunk0080_265_1	chr17	30916126	30916431	+	0	NA	Intergenic	Intergenic	-5458	NM_018404	55803	Hs.514063	NM_018404	ENSG00000184060	ADAP2	CENTA2|HSA272195|cent-b	ArfGAP with dual PH domains 2	protein-coding	0.003279	0.375817	
chunk0172_245_1	chr6	137210215	137210809	+	0	NA	intron (NM_000416, intron 1 of 6)	intron (NM_000416, intron 1 of 6)	8918	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.003367	0.374790	
chunk0047_287_1	chr12	73475861	73476450	+	0	NA	Intergenic	LTR40a|LTR|ERVL	316965	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.010187	0.354237	
chunk0036_385_1	chr11	67637453	67637975	+	0	NA	intron (NM_005995, intron 1 of 7)	LTR10C|LTR|ERV1	1846	NM_005995	347853	Hs.454480	NM_005995	ENSG00000167800	TBX10	TBX13|TBX7	T-box transcription factor 10	protein-coding	0.011494	0.380497	
chunk0212_90_1	chrY	12528446	12528995	+	0	NA	Intergenic	Intergenic	-107130	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.007286	0.514545	
chunk0106_240_1	chr2	203035842	203036258	+	0	NA	intron (NM_001114132, intron 2 of 54)	MIR|SINE|MIR	21171	NM_001114132	65065	Hs.648846	NM_198945	ENSG00000144426	NBEAL1	A530083I02Rik|ALS2CR16|ALS2CR17	neurobeachin like 1	protein-coding	0.002404	0.340528	
chunk0103_110_1	chr2	161415586	161415814	+	0	NA	promoter-TSS (NM_006593)	promoter-TSS (NM_006593)	-409	NM_006593	10716	Hs.210862	NM_006593	ENSG00000136535	TBR1	IDDAS|TBR-1|TES-56	T-box brain transcription factor 1	protein-coding	0.035088	0.528384	
chunk0150_433_1	chr5	40429801	40430147	+	0	NA	Intergenic	Intergenic	-249956	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.005780	0.432277	
chunk0049_12_1	chr12	89316474	89317172	+	0	NA	Intergenic	Intergenic	36036	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.005731	0.434907	
chunk0172_376_1	chr6	139318401	139318719	+	0	NA	Intergenic	L1MEg|LINE|L1	-26489	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.003145	0.354232	
chunk0172_367_1	chr6	139247524	139248048	+	0	NA	intron (NM_153235, intron 8 of 9)	intron (NM_153235, intron 8 of 9)	44285	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.003817	0.316190	
chunk0095_143_1	chr2	16817669	16818481	+	0	NA	Intergenic	Intergenic	-152209	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.006158	0.387454	
chunk0049_73_1	chr12	90333417	90333809	+	0	NA	Intergenic	Intergenic	-584410	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.005102	0.353690	
chunk0149_266_1	chr5	24073078	24073711	+	0	NA	intron (NR_131245, intron 4 of 4)	MER70A|LTR|ERVL	122046	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.007899	0.421136	
chunk0149_277_1	chr5	24551840	24552223	+	0	NA	intron (NM_006727, intron 2 of 11)	intron (NM_006727, intron 2 of 11)	92945	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.000000	0.273438	
chunk0006_319_1	chr1	71565204	71565675	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	271573	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.000000	0.408898	
chunk0075_191_1	chr16	52389834	52390257	+	0	NA	Intergenic	L1MA6|LINE|L1	156849	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.007092	0.351415	
chunk0182_317_1	chr7	98943984	98944184	+	0	NA	intron (NM_003496, intron 31 of 70)	intron (NM_003496, intron 31 of 70)	62387	NR_132754	106633801		NR_132754		SCARNA28	ZL1	small Cajal body-specific RNA 28	ncRNA	0.010000	0.447761	
chunk0109_188_1	chr20	4937385	4937947	+	0	NA	intron (NM_005116, intron 2 of 16)	MIRb|SINE|MIR	63833	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.005338	0.444050	
chunk0026_297_1	chr10	67819850	67820137	+	0	NA	intron (NM_201262, intron 2 of 2)	L2b|LINE|L2	18186	NM_021800	56521	Hs.260720	NM_021800	ENSG00000108176	DNAJC12	HPANBH4|JDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding	0.010453	0.493056	
chunk0106_322_1	chr2	205630557	205630913	+	0	NA	Intergenic	Intergenic	-51765	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.005618	0.400560	338(GAGGCCAGGATGTTCT,-,0.00),339(AGGCCAGGATGTTCTG,+,0.00)
chunk0090_21_1	chr19	934897	935477	+	0	NA	intron (NM_005224, intron 3 of 8)	intron (NM_005224, intron 3 of 8)	9150	NM_005224	1820	Hs.501296	NM_005224	ENSG00000116017	ARID3A	BRIGHT|DRIL1|DRIL3|E2FBP1	AT-rich interaction domain 3A	protein-coding	0.051724	0.664372	
chunk0157_30_1	chr5	115625783	115625982	+	0	NA	5' UTR (NM_001164469, exon 1 of 4)	5' UTR (NM_001164469, exon 1 of 4)	297	NM_001164469	100302736		NM_001164468	ENSG00000251201	TMED7-TICAM2	MyD88-4|TICAM-2|TICAM2|TIRAP3|TIRP|TRAM	TMED7-TICAM2 readthrough	protein-coding	0.120603	0.705000	
chunk0008_135_1	chr1	91896244	91896443	+	0	NA	intron (NM_001195684, intron 2 of 17)	intron (NM_001195684, intron 2 of 17)	9659	NM_001195684	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.000000	0.430000	
chunk0162_215_1	chr6	4241597	4241973	+	0	NA	Intergenic	L1PA11|LINE|L1	-51756	NR_125874	102724096	Hs.571140	NR_125874		LOC102724096	-	uncharacterized LOC102724096	ncRNA	0.005319	0.440318	
chunk0123_358_1	chr3	48218581	48218970	+	0	NA	Intergenic	MIRc|SINE|MIR	-4572	NM_004345	820	Hs.51120	NM_004345	ENSG00000164047	CAMP	CAP-18|CAP18|CRAMP|FALL-39|FALL39|HSD26|LL37	cathelicidin antimicrobial peptide	protein-coding	0.012853	0.476923	
chunk0022_254_1	chr10	14653714	14653917	+	0	NA	intron (NM_001282695, intron 2 of 5)	intron (NM_001282695, intron 2 of 5)	-49397	NM_001282697	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.019704	0.450980	
chunk0060_245_1	chr14	49893800	49894158	+	0	NA	exon (NM_001663, exon 2 of 2)	exon (NM_001663, exon 2 of 2)	961	NM_001663	382	Hs.525330	NM_001663	ENSG00000165527	ARF6	-	ADP ribosylation factor 6	protein-coding	0.069832	0.573816	
chunk0192_24_1	chr8	58480314	58480814	+	0	NA	Intergenic	Intergenic	19597	NM_000780	1581	Hs.1644	NM_000780	ENSG00000167910	CYP7A1	CP7A|CYP7|CYPVII	cytochrome P450 family 7 subfamily A member 1	protein-coding	0.006000	0.417166	
chunk0043_445_1	chr12	26493499	26493878	+	0	NA	intron (NM_002223, intron 39 of 56)	L1MA5|LINE|L1	298115	NM_005086	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.007916	0.365789	
chunk0004_255_1	chr1	47793523	47793953	+	0	NA	intron (NM_001194986, intron 4 of 6)	intron (NM_001194986, intron 4 of 6)	203152	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.002326	0.489559	
chunk0022_409_1	chr10	18403104	18403585	+	0	NA	intron (NM_001167945, intron 3 of 13)	intron (NM_001167945, intron 3 of 13)	2760	NM_201570	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.012474	0.369295	
chunk0043_65_1	chr12	14208054	14208306	+	0	NA	Intergenic	LTR108a_Mam|LTR|ERVL	-157452	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.003968	0.411067	
chunk0093_257_1	chr19	51066830	51067347	+	0	NA	Intergenic	LTR37A|LTR|ERV1	-1978	NM_015596	26085	Hs.165296	NM_015596	ENSG00000167759	KLK13	KLK-L4|KLKL4	kallikrein related peptidase 13	protein-coding	0.003868	0.388031	
chunk0059_276_1	chr14	35398166	35398753	+	0	NA	Intergenic	Intergenic	6295	NM_020529	4792	Hs.81328	NM_020529	ENSG00000100906	NFKBIA	EDAID2|IKBA|MAD-3|NFKBI	NFKB inhibitor alpha	protein-coding	0.005111	0.445578	
chunk0126_339_1	chr3	82186233	82186498	+	0	NA	Intergenic	Intergenic	-424566	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.011321	0.548872	
chunk0059_267_1	chr14	35297652	35298013	+	0	NA	intron (NM_001282232, intron 1 of 6)	intron (NM_001282232, intron 1 of 6)	5515	NM_001282232	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.005540	0.378453	
chunk0098_380_1	chr2	79171647	79172124	+	0	NA	Intergenic	L1MA4|LINE|L1	-12131	NM_138937	5068	Hs.567312	NM_002580	ENSG00000172016	REG3A	HIP|HIP/PAP|INGAP|PAP|PAP-H|PAP1|PBCGF|REG-III|REG3	regenerating family member 3 alpha	protein-coding	0.000000	0.322176	
chunk0071_112_1	chr15	81303922	81304127	+	0	NA	intron (NM_001172128, intron 16 of 18)	intron (NM_001172128, intron 16 of 18)	7111	NM_004513	3603	Hs.459095	NM_004513	ENSG00000172349	IL16	LCF|NIL16|PRIL16|prIL-16	interleukin 16	protein-coding	0.014634	0.514563	
chunk0027_104_1	chr10	73999346	73999559	+	0	NA	intron (NM_003373, intron 1 of 20)	intron (NM_003373, intron 1 of 20)	1338	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.009390	0.504673	
chunk0032_13_1	chr11	665271	665667	+	0	NA	intron (NM_001293634, intron 8 of 10)	intron (NM_001293634, intron 8 of 10)	28164	NM_000797	1815	Hs.99922	NM_000797	ENSG00000069696	DRD4	D4DR	dopamine receptor D4	protein-coding	0.020202	0.455919	43(GAGGACAGGGTGTCAC,-,0.00)
chunk0081_162_1	chr17	40978597	40979023	+	0	NA	exon (NM_182497, exon 8 of 9)	exon (NM_182497, exon 8 of 9)	8325	NM_182497	125115	Hs.534929	NM_182497	ENSG00000204889	KRT40	CK-40|K40|KA36	keratin 40	protein-coding	0.025822	0.498829	
chunk0196_398_1	chr8	115894945	115895332	+	0	NA	Intergenic	Intergenic	-226110	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.002584	0.278351	
chunk0119_139_1	chr22	42955265	42955539	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	4479	NM_001184971	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.018248	0.447273	
chunk0107_448_1	chr2	225449114	225449509	+	0	NA	intron (NM_020864, intron 2 of 5)	MIRb|SINE|MIR	48425	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.005063	0.310606	
chunk0187_43_1	chr8	1565889	1566288	+	0	NA	intron (NM_001277161, intron 3 of 10)	intron (NM_001277161, intron 3 of 10)	55576	NR_103863	100507435	Hs.667133	NR_103863	ENSG00000253267	DLGAP2-AS1	-	DLGAP2 antisense RNA 1	ncRNA	0.017544	0.400000	
chunk0192_427_1	chr8	69619615	69619941	+	0	NA	intron (NR_132437, intron 6 of 16)	LTR1B|LTR|ERV1	26878	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.024540	0.559633	
chunk0183_95_1	chr7	105083142	105083358	+	0	NA	intron (NM_018682, intron 12 of 25)	Tigger2|DNA|TcMar-Tigger	69060	NM_018682	55904	Hs.592262	NM_018682	ENSG00000005483	KMT2E	HDCMC04P|MLL5|NKp44L	lysine methyltransferase 2E	protein-coding	0.004630	0.391705	
chunk0210_286_1	chrX	85598231	85598444	+	0	NA	Intergenic	L1PB1|LINE|L1	-218594	NM_024921	79983	Hs.267038	NM_024921	ENSG00000124429	POF1B	POF|POF2B	POF1B actin binding protein	protein-coding	0.004695	0.331776	
chunk0209_37_1	chrX	36259987	36260186	+	0	NA	intron (NM_001304548, intron 49 of 63)	L1PA16|LINE|L1	180206	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.000000	0.380000	
chunk0128_115_1	chr3	106342325	106342854	+	0	NA	Intergenic	Intergenic	-473546	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.005671	0.369811	
chunk0146_316_1	chr4	165385472	165386044	+	0	NA	promoter-TSS (NR_030304)	promoter-TSS (NR_030304)	-484	NR_030304	693163		NR_030304	ENSG00000207559	MIR578	MIRN578|hsa-mir-578	microRNA 578	ncRNA	0.006993	0.424084	259(AGGAACAAAGTGTGCA,-,0.00),260(GGAACAAAGTGTGCAT,+,0.00)
chunk0060_80_1	chr14	42120813	42121012	+	0	NA	Intergenic	L1PB1|LINE|L1	513351	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.005025	0.345000	
chunk0111_90_1	chr20	23404063	23404561	+	0	NA	intron (NR_104266, intron 1 of 10)	intron (NR_104266, intron 1 of 10)	17207	NM_001283026	63908	Hs.269471	NM_022080	ENSG00000125814	NAPB	SNAP-BETA|SNAPB	NSF attachment protein beta	protein-coding	0.008032	0.450902	
chunk0009_269_1	chr1	107474992	107475575	+	0	NA	intron (NM_001312688, intron 7 of 7)	intron (NM_001312688, intron 7 of 7)	213221	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.000000	0.392123	
chunk0121_191_1	chr3	20565315	20565688	+	0	NA	Intergenic	L1MC1|LINE|L1	223033	NR_110814	101927829	Hs.639381	NR_110814	ENSG00000231304	LOC101927829	-	uncharacterized LOC101927829	ncRNA	0.008043	0.352941	
chunk0061_142_1	chr14	59375746	59376225	+	0	NA	Intergenic	L1MC1|LINE|L1	89356	NM_022571	64582	Hs.647573	NM_022571	ENSG00000181619	GPR135	HUMNPIIY20	G protein-coupled receptor 135	protein-coding	0.004175	0.366667	
chunk0141_159_1	chr4	82084905	82085104	+	0	NA	Intergenic	Intergenic	288992	NM_002138	3184	Hs.480073	NM_002138	ENSG00000138668	HNRNPD	AUF1|AUF1A|HNRPD|P37|hnRNPD0	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.000000	0.420000	
chunk0143_175_1	chr4	111037710	111037951	+	0	NA	Intergenic	Intergenic	-177183	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.016598	0.413223	
chunk0094_169_1	chr2	5489767	5490506	+	0	NA	Intergenic	L1MA3|LINE|L1	200982	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.006766	0.390541	
chunk0115_262_1	chr21	27805885	27806686	+	0	NA	Intergenic	Intergenic	83906	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.007491	0.356608	
chunk0059_345_1	chr14	37048012	37048312	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	-95771	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.010000	0.382060	
chunk0013_395_1	chr1	172879485	172879816	+	0	NA	Intergenic	L1PA16|LINE|L1	171313	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.003021	0.328313	
chunk0024_387_1	chr10	44850148	44850765	+	0	NA	intron (NR_033842, intron 2 of 7)	intron (NR_033842, intron 2 of 7)	-60860	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.009724	0.540453	531(CTGAACACATTGTGCA,-,0.00)
chunk0180_303_1	chr7	70502089	70502390	+	0	NA	intron (NM_015570, intron 5 of 18)	intron (NM_015570, intron 5 of 18)	-630298	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.019934	0.476821	
chunk0157_286_1	chr5	120749696	120750119	+	0	NA	Intergenic	Intergenic	218443	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.007092	0.294811	
chunk0073_62_1	chr16	3500833	3501132	+	0	NA	promoter-TSS (NM_015041)	promoter-TSS (NM_015041)	37	NM_015041	23059	Hs.155995	NM_015041	ENSG00000103351	CLUAP1	CFAP22|FAP22|IFT38	clusterin associated protein 1	protein-coding	0.110368	0.660000	
chunk0002_9_1	chr1	12184071	12184584	+	0	NA	intron (NM_001066, intron 1 of 9)	intron (NM_001066, intron 1 of 9)	-7386	NR_039775	100616438		NR_039775	ENSG00000263676	MIR4632	-	microRNA 4632	ncRNA	0.009747	0.591440	
chunk0032_72_1	chr11	2600825	2601029	+	0	NA	intron (NM_181798, intron 10 of 15)	L1MC4|LINE|L1	99071	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.014706	0.434146	101(AGGCACACAGTGTATC,-,0.00),102(GGCACACAGTGTATCT,+,0.00)
chunk0064_372_1	chr14	98374245	98374646	+	0	NA	Intergenic	Intergenic	-337168	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.022444	0.490050	
chunk0136_126_1	chr4	3745835	3746034	+	0	NA	Intergenic	L1MC4|LINE|L1	-20635	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.025126	0.445000	
chunk0063_299_1	chr14	84643423	84643951	+	0	NA	Intergenic	Intergenic	-750192	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.007576	0.368620	
chunk0118_38_1	chr22	27686889	27687357	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	114375	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.012821	0.469083	
chunk0120_160_1	chr3	5497613	5498370	+	0	NA	Intergenic	Intergenic	-247736	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.002642	0.428760	
chunk0143_107_1	chr4	108664854	108665277	+	0	NA	intron (NM_001267818, intron 4 of 4)	intron (NM_001267818, intron 4 of 4)	14480	NM_021227	58505	Hs.445803	NM_021227	ENSG00000198856	OSTC	DC2	oligosaccharyltransferase complex non-catalytic subunit	protein-coding	0.007092	0.419811	
chunk0084_202_1	chr17	78114766	78115468	+	0	NA	intron (NM_001127198, intron 18 of 19)	intron (NM_001127198, intron 18 of 19)	-3318	NR_040071	100131096	Hs.635442	NR_040071	ENSG00000204282	TNRC6C-AS1	TMC6|lnc	TNRC6C antisense RNA 1	ncRNA	0.031339	0.625889	351(TGGGACAGTGTGTACT,-,0.00),352(GGGACAGTGTGTACTA,+,0.00)
chunk0071_331_1	chr15	87565146	87565442	+	0	NA	Intergenic	MIR|SINE|MIR	-11635	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.000000	0.414141	
chunk0151_374_1	chr5	55033187	55033386	+	0	NA	intron (NM_002104, intron 4 of 4)	intron (NM_002104, intron 4 of 4)	9007	NM_002104	3003	Hs.277937	NM_002104	ENSG00000113088	GZMK	TRYP2	granzyme K	protein-coding	0.005025	0.305000	
chunk0075_227_1	chr16	52878743	52879474	+	0	NA	Intergenic	Intergenic	-175925	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.006840	0.393443	
chunk0160_273_1	chr5	157523818	157524238	+	0	NA	intron (NM_033274, intron 5 of 22)	intron (NM_033274, intron 5 of 22)	51795	NM_033274	8728	Hs.483944	NM_023038	ENSG00000135074	ADAM19	FKSG34|MADDAM|MLTNB	ADAM metallopeptidase domain 19	protein-coding	0.009524	0.532067	
chunk0174_368_1	chr6	164740213	164740707	+	0	NA	Intergenic	MLT1J1-int|LTR|ERVL-MaLR	81603	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.006073	0.393939	230(AAGGACACACTGTTTT,-,0.00),231(AGGACACACTGTTTTT,+,0.00)
chunk0211_319_1	chrX	123803349	123804008	+	0	NA	Intergenic	Intergenic	-56134	NM_001204401	331	Hs.356076	NM_001167	ENSG00000101966	XIAP	API3|BIRC4|IAP-3|ILP1|MIHA|XLP2|hIAP-3|hIAP3	X-linked inhibitor of apoptosis	protein-coding	0.007587	0.437879	
chunk0004_93_1	chr1	43830944	43831190	+	0	NA	intron (NM_174963, intron 5 of 12)	MIRc|SINE|MIR	-7555	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.000000	0.376518	
chunk0154_144_1	chr5	79357355	79357930	+	0	NA	Intergenic	MER65-int|LTR|ERV1	121540	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.003478	0.354167	
chunk0116_9_1	chr21	32719056	32719346	+	0	NA	intron (NM_001160302, intron 2 of 31)	MER119|DNA|hAT-Charlie	8738	NM_001160302	8867	Hs.473632	NM_003895	ENSG00000159082	SYNJ1	EIEE53|INPP5G|PARK20	synaptojanin 1	protein-coding	0.006897	0.419244	
chunk0130_456_1	chr3	141455751	141456204	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	-31070	NM_001303246	5922	Hs.98445	NM_006506	ENSG00000155903	RASA2	GAP1M	RAS p21 protein activator 2	protein-coding	0.019868	0.515419	
chunk0195_175_1	chr8	96168891	96169090	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-8198	NM_001001557	392255	Hs.492277	NM_001001557	ENSG00000156466	GDF6	BMP-13|BMP13|CDMP2|KFM|KFS|KFS1|KFSL|SGM1|SYNS4	growth differentiation factor 6	protein-coding	0.000000	0.355000	
chunk0026_121_1	chr10	62004995	62005392	+	0	NA	intron (NM_032199, intron 4 of 9)	MIRb|SINE|MIR	-44018	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.002519	0.447236	
chunk0025_50_1	chr10	49419042	49419348	+	0	NA	Intergenic	MIRc|SINE|MIR	-23179	NM_001276451	644168	Hs.534530	NM_001080520	ENSG00000165606	DRGX	DRG11|PRRXL1	dorsal root ganglia homeobox	protein-coding	0.013072	0.537459	
chunk0019_321_1	chr1	229171832	229172242	+	0	NA	Intergenic	Intergenic	2764	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.009756	0.445255	
chunk0072_273_1	chr15	96881866	96882354	+	0	NA	Intergenic	Intergenic	98703	NM_001304805									0.002049	0.343558	
chunk0149_84_1	chr5	17312462	17312661	+	0	NA	Intergenic	Intergenic	74749	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.015075	0.430000	
chunk0189_137_1	chr8	22564654	22565033	+	0	NA	promoter-TSS (NM_001018003)	promoter-TSS (NM_001018003)	-823	NM_001018003	10174	Hs.528572	NM_005775	ENSG00000120896	SORBS3	SCAM-1|SCAM1|SH3D4	sorbin and SH3 domain containing 3	protein-coding	0.031662	0.576316	
chunk0206_75_1	chr9	119973954	119974493	+	0	NA	Intergenic	MIRb|SINE|MIR	39163	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.005566	0.437037	
chunk0121_44_1	chr3	15460673	15460903	+	0	NA	intron (NM_080539, intron 11 of 15)	intron (NM_080539, intron 11 of 15)	33231	NM_033083	85403	Hs.716733	NM_033083	ENSG00000144597	EAF1	-	ELL associated factor 1	protein-coding	0.000000	0.411255	
chunk0049_363_1	chr12	95578728	95579254	+	0	NA	Intergenic	Intergenic	-27501	NM_032147	84101	Hs.646421	NM_032147	ENSG00000136014	USP44	-	ubiquitin specific peptidase 44	protein-coding	0.007605	0.428843	
chunk0207_303_1	chr9	133423171	133423467	+	0	NA	intron (NR_024514, intron 2 of 17)	intron (NR_024514, intron 2 of 17)	1319	NM_139026	11093	Hs.131433	NM_139025	ENSG00000160323	ADAMTS13	ADAM-TS13|ADAMTS-13|C9orf8|VWFCP|vWF-CP	ADAM metallopeptidase with thrombospondin type 1 motif 13	protein-coding	0.010135	0.525253	
chunk0151_232_1	chr5	51048097	51048730	+	0	NA	Intergenic	MIRc|SINE|MIR	-78226	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.001580	0.359621	
chunk0091_454_1	chr19	17945093	17945313	+	0	NA	Intergenic	Intergenic	-6099	NM_002248	3780	Hs.158173	NM_002248	ENSG00000105642	KCNN1	KCa2.1|SK1|SKCA1|hSK1	potassium calcium-activated channel subfamily N member 1	protein-coding	0.004545	0.597285	
chunk0091_209_1	chr19	9622533	9622915	+	0	NA	intron (NR_122038, intron 1 of 3)	LTR10C|LTR|ERV1	1242	NR_122038	284385	Hs.651747	NM_001242812	ENSG00000267106	ZNF561-AS1	C19orf82	ZNF561 antisense RNA 1 (head to head)	ncRNA	0.005236	0.407311	
chunk0076_199_1	chr16	68023006	68023622	+	0	NA	5' UTR (NM_001271763, exon 1 of 15)	5' UTR (NM_001271763, exon 1 of 15)	370	NM_001271762	54920	Hs.534460	NM_017803	ENSG00000167264	DUS2	DUS2L|SMM1|URLC8	dihydrouridine synthase 2	protein-coding	0.087662	0.633712	
chunk0192_287_1	chr8	66459463	66460042	+	0	NA	intron (NM_144650, intron 12 of 13)	intron (NM_144650, intron 12 of 13)	27269	NM_144650	137872	Hs.720023	NM_144650	ENSG00000147576	ADHFE1	ADH8|HMFT2263|HOT	alcohol dehydrogenase iron containing 1	protein-coding	0.006908	0.400000	
chunk0142_68_1	chr4	93155971	93156468	+	0	NA	intron (NM_001286838, intron 3 of 14)	intron (NM_001286838, intron 3 of 14)	-672708	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.010060	0.311245	206(TGGAACACAGTGTTAT,-,0.00),207(GGAACACAGTGTTATA,+,0.00)
chunk0005_311_1	chr1	60582745	60583124	+	0	NA	Intergenic	L1MEd|LINE|L1	242650	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.002639	0.305263	
chunk0128_413_1	chr3	114711652	114711980	+	0	NA	intron (NM_001164344, intron 1 of 7)	L2a|LINE|L2	31709	NR_039959	100616166		NR_039959	ENSG00000264623	MIR4796	mir-4796	microRNA 4796	ncRNA	0.009146	0.343465	
chunk0036_26_1	chr11	58458584	58458843	+	0	NA	Intergenic	L1MA8|LINE|L1	-18540	NM_001004733	390191	Hs.553754	NM_001004733	ENSG00000172362	OR5B12	OR11-241|OR5B12P|OR5B16|OST743	olfactory receptor family 5 subfamily B member 12	protein-coding	0.000000	0.330769	
chunk0082_98_1	chr17	54459727	54460165	+	0	NA	Intergenic	Intergenic	-440745	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.004566	0.325740	
chunk0203_186_1	chr9	86380597	86381113	+	0	NA	Intergenic	L1PA4|LINE|L1	-26368	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.009690	0.392650	144(AGGAACAGGTTGTTCA,-,0.00),145(GGAACAGGTTGTTCAG,+,0.00)
chunk0091_328_1	chr19	13774200	13774560	+	0	NA	promoter-TSS (NM_014047)	promoter-TSS (NM_014047)	-63	NM_014047	28974	Hs.231616	NM_014047	ENSG00000104979	C19orf53	HSPC023|LYDG10	chromosome 19 open reading frame 53	protein-coding	0.061111	0.495845	
chunk0175_17_1	chr7	332899	333098	+	0	NA	Intergenic	CpG	42828	NM_001195127	100288524	Hs.702860	NM_001195127	ENSG00000248767	WI2-2373I1.2	-	forkhead box L1-like	ncRNA	0.080402	0.730000	
chunk0158_3_1	chr5	125151186	125151602	+	0	NA	intron (NR_109882, intron 2 of 5)	intron (NR_109882, intron 2 of 5)	114563	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.004808	0.374101	
chunk0039_31_1	chr11	95789555	95789872	+	0	NA	promoter-TSS (NM_001243776)	promoter-TSS (NM_001243776)	77	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.107256	0.710692	
chunk0001_392_1	chr1	10661859	10662147	+	0	NA	intron (NM_001079843, intron 5 of 20)	(AC)n|Simple_repeat|Simple_repeat	134673	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.017361	0.429066	
chunk0121_227_1	chr3	21855351	21856187	+	0	NA	Intergenic	Intergenic	-101370	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.001196	0.338112	
chunk0159_373_1	chr5	145968898	145969294	+	0	NA	intron (NM_152550, intron 2 of 9)	intron (NM_152550, intron 2 of 9)	32533	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.002525	0.332494	
chunk0149_205_1	chr5	21660690	21661071	+	0	NA	Intergenic	Intergenic	201400	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.002625	0.311518	
chunk0118_206_1	chr22	31720965	31721164	+	0	NA	intron (NM_173566, intron 3 of 8)	intron (NM_173566, intron 3 of 8)	29070	NM_173566	253143	Hs.438906	NM_173566	ENSG00000183530	PRR14L	C22orf30	proline rich 14 like	protein-coding	0.005025	0.370000	
chunk0095_445_1	chr2	25492045	25492259	+	0	NA	intron (NM_001256303, intron 9 of 19)	intron (NM_001256303, intron 9 of 19)	-149562	NM_175629	1788	Hs.515840	NM_022552	ENSG00000119772	DNMT3A	DNMT3A2|M.HsaIIIA|TBRS	DNA methyltransferase 3 alpha	protein-coding	0.014019	0.362791	164(TAGAACTCTGTGTCCT,-,0.00),165(AGAACTCTGTGTCCTA,+,0.00)
chunk0139_94_1	chr4	49577162	49577597	+	0	NA	Intergenic	HSAT5|Satellite|Satellite	590737	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.004598	0.525229	
chunk0043_143_1	chr12	16224150	16224715	+	0	NA	exon (NM_001170798, exon 6 of 9)	exon (NM_001170798, exon 6 of 9)	53253	NM_001170798	729025	Hs.692712	NM_001170798	ENSG00000188991	SLC15A5	-	solute carrier family 15 member 5	protein-coding	0.007080	0.371025	220(AGGTTCAGTATGTTCT,-,0.00),221(GGTTCAGTATGTTCTA,+,0.00)
chunk0069_436_1	chr15	68359664	68360210	+	0	NA	intron (NM_001004439, intron 5 of 29)	intron (NM_001004439, intron 5 of 29)	72216	NM_001004439	22801	Hs.436416	NM_012211	ENSG00000137809	ITGA11	HsT18964	integrin subunit alpha 11	protein-coding	0.009158	0.389397	
chunk0168_369_1	chr6	93715858	93716078	+	0	NA	intron (NR_015362, intron 1 of 9)	L1MA9|LINE|L1	8885	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.009091	0.524887	
chunk0171_50_1	chr6	121008342	121008765	+	0	NA	Intergenic	L2a|LINE|L2	325947	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.000000	0.370283	
chunk0008_433_1	chr1	99446944	99447226	+	0	NA	Intergenic	L1ME1|LINE|L1	40719	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.017730	0.342756	
chunk0134_452_1	chr3	183968663	183969129	+	0	NA	intron (NM_005688, intron 11 of 29)	L2c|LINE|L2	-37442	NR_046570	100873982	Hs.570696	NR_046570	ENSG00000223882	ABCC5-AS1	-	ABCC5 antisense RNA 1	ncRNA	0.008584	0.434690	
chunk0075_44_1	chr16	47416616	47417036	+	0	NA	intron (NM_030790, intron 6 of 17)	MSTB|LTR|ERVL-MaLR	44448	NM_030790	81533	Hs.42217	NM_030790	ENSG00000129636	ITFG1	2310047C21Rik|CDA08|LNKN-1|TIP	integrin alpha FG-GAP repeat containing 1	protein-coding	0.002381	0.406176	
chunk0124_91_1	chr3	53485742	53486347	+	0	NA	Intergenic	Intergenic	-9005	NM_000720	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.004959	0.367987	
chunk0041_364_1	chr11	131121939	131122145	+	0	NA	Intergenic	Intergenic	-205555	NM_001301089	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.009709	0.560386	
chunk0183_235_1	chr7	106991076	106991628	+	0	NA	Intergenic	Intergenic	-53381	NM_002736	5577	Hs.433068	NM_002736	ENSG00000005249	PRKAR2B	PRKAR2|RII-BETA	protein kinase cAMP-dependent type II regulatory subunit beta	protein-coding	0.000000	0.426763	
chunk0024_34_1	chr10	33334311	33334520	+	0	NA	non-coding (NR_045259, exon 1 of 16)	non-coding (NR_045259, exon 1 of 16)	490	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.095694	0.638095	
chunk0194_354_1	chr8	89476539	89477118	+	0	NA	Intergenic	L2a|LINE|L2	280883	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.003454	0.325862	
chunk0163_337_1	chr6	15408917	15409647	+	0	NA	intron (NM_001267040, intron 2 of 17)	intron (NM_001267040, intron 2 of 17)	160427	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.009589	0.413133	218(TAGAACACTGTGTTCT,-,0.00),219(AGAACACTGTGTTCTA,+,0.00)
chunk0021_17_1	chr10	454806	455305	+	0	NA	intron (NM_014974, intron 3 of 36)	intron (NM_014974, intron 3 of 36)	-172969	NR_106988									0.012024	0.476000	272(CAGAAGAGAATGTTCC,-,0.00),273(AGAAGAGAATGTTCCT,+,0.00),434(AGGAACAGTGAGTCCC,-,0.00),435(GGAACAGTGAGTCCCT,+,0.00)
chunk0150_135_1	chr5	33439106	33439356	+	0	NA	Intergenic	Intergenic	-1465	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.012000	0.354582	
chunk0012_240_1	chr1	160817939	160818428	+	0	NA	intron (NM_001261456, intron 5 of 9)	intron (NM_001261456, intron 5 of 9)	22109	NM_001033667	4063	Hs.403857	NM_002348	ENSG00000122224	LY9	CD229|SLAMF3|hly9|mLY9	lymphocyte antigen 9	protein-coding	0.020450	0.483673	
chunk0080_206_1	chr17	29379186	29379684	+	0	NA	Intergenic	Intergenic	-11227	NR_039749	100616122		NR_039749	ENSG00000284162	MIR4523	-	microRNA 4523	ncRNA	0.016064	0.402806	
chunk0164_180_1	chr6	22001226	22001791	+	0	NA	intron (NR_015410, intron 6 of 11)	L3|LINE|CR1	145685	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.003540	0.446996	
chunk0194_428_1	chr8	92481670	92482273	+	0	NA	Intergenic	L2b|LINE|L2	173523	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.001658	0.408940	336(GGGAACATCTTGTCCT,-,0.00),337(GGAACATCTTGTCCTT,+,0.00)
chunk0111_24_1	chr20	21994114	21994697	+	0	NA	Intergenic	MIRb|SINE|MIR	-59685	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.005146	0.381849	
chunk0208_159_1	chrX	16195151	16195571	+	0	NA	Intergenic	Intergenic	27880	NM_001277307	645864	Hs.632792	NM_001277307	ENSG00000182798	MAGEB17	-	MAGE family member B17	protein-coding	0.002381	0.323040	
chunk0162_263_1	chr6	5293107	5293333	+	0	NA	intron (NM_006567, intron 1 of 6)	L2c|LINE|L2	31869	NM_006567	10667	Hs.484547	NM_006567	ENSG00000145982	FARS2	COXPD14|FARS1|HSPC320|PheRS|SPG77|mtPheRS	phenylalanyl-tRNA synthetase 2, mitochondrial	protein-coding	0.008850	0.453744	
chunk0107_442_1	chr2	225086252	225086692	+	0	NA	Intergenic	HAL1ME|LINE|L1	-43859	NM_014689	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.004545	0.453515	
chunk0087_157_1	chr18	34757626	34757847	+	0	NA	intron (NM_032975, intron 3 of 21)	intron (NM_032975, intron 3 of 21)	1760	NM_001391	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.013575	0.328829	
chunk0046_206_1	chr12	59072808	59073344	+	0	NA	Intergenic	Intergenic	-152538	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.005597	0.376164	
chunk0044_29_1	chr12	27293298	27293885	+	0	NA	intron (NM_015000, intron 1 of 13)	intron (NM_015000, intron 1 of 13)	-39263	NM_001248004	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.006814	0.421769	
chunk0122_170_1	chr3	32354500	32355235	+	0	NA	intron (NM_178868, intron 1 of 3)	intron (NM_178868, intron 1 of 3)	-36804	NM_138410	112616	Hs.440494	NM_138410	ENSG00000153551	CMTM7	CKLFSF7	CKLF like MARVEL transmembrane domain containing 7	protein-coding	0.010884	0.422554	
chunk0204_239_1	chr9	97954818	97955438	+	0	NA	Intergenic	Intergenic	-10213	NM_018437	55363	Hs.176626	NM_018437	ENSG00000136929	HEMGN	CT155|EDAG|EDAG-1|NDR	hemogen	protein-coding	0.001613	0.418680	368(AAGAACATTTTGTGCT,-,0.00),369(AGAACATTTTGTGCTT,+,0.00)
chunk0031_284_1	chr10	128255065	128255855	+	0	NA	Intergenic	Intergenic	-30490	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.008861	0.422250	541(GTGCACACAATGTACT,-,0.00),542(TGCACACAATGTACTT,+,0.00)
chunk0135_390_1	chr3	191296132	191296734	+	0	NA	intron (NM_198152, intron 4 of 8)	L2b|LINE|L2	-32652	NM_174908	152137	Hs.478682	NM_174908	ENSG00000152492	CCDC50	C3orf6|DFNA44|YMER	coiled-coil domain containing 50	protein-coding	0.003322	0.393035	
chunk0081_168_1	chr17	41264521	41265183	+	0	NA	promoter-TSS (NM_001277331)	promoter-TSS (NM_001277331)	-526	NM_001277331	100507608		NM_001277331	ENSG00000212659	KRTAP9-6	KAP9.6|KRTAP9.6|KRTAP9L2	keratin associated protein 9-6	protein-coding	0.009063	0.457014	257(TAGCACACATTGTGCT,-,0.00),258(AGCACACATTGTGCTG,+,0.00)
chunk0184_131_1	chr7	115271226	115271906	+	0	NA	Intergenic	Intergenic	-40211	NR_126407	104355291		NR_126407	ENSG00000233607	LINC01392	-	long intergenic non-protein coding RNA 1392	ncRNA	0.004412	0.374449	
chunk0065_16_1	chr15	20340256	20340730	+	0	NA	Intergenic	(AGCCAGCCA)n|Simple_repeat|Simple_repeat	57749	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.018987	0.665263	
chunk0200_60_1	chr9	15704532	15704797	+	0	NA	intron (NM_173550, intron 11 of 25)	intron (NM_173550, intron 11 of 25)	151565	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.011321	0.342105	
chunk0196_392_1	chr8	115804091	115804955	+	0	NA	Intergenic	Intergenic	-135495	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.011574	0.332948	374(TGGTACATAGTGTGCA,-,0.00),375(GGTACATAGTGTGCAC,+,0.00)
chunk0071_118_1	chr15	81398607	81399148	+	0	NA	intron (NR_120365, intron 6 of 6)	intron (NR_120365, intron 6 of 6)	-24800	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.009242	0.411439	
chunk0188_251_1	chr8	14408124	14408501	+	0	NA	intron (NM_139167, intron 2 of 7)	intron (NM_139167, intron 2 of 7)	445198	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.013263	0.415344	
chunk0166_435_1	chr6	52909446	52909789	+	0	NA	promoter-TSS (NM_000847)	promoter-TSS (NM_000847)	81	NM_000847	2940	Hs.102484	NM_000847	ENSG00000174156	GSTA3	GSTA3-3|GTA3	glutathione S-transferase alpha 3	protein-coding	0.008746	0.392442	94(AAGAACATAAAGTACT,-,0.00),95(AGAACATAAAGTACTC,+,0.00)
chunk0157_194_1	chr5	118937462	118937661	+	0	NA	intron (NM_173666, intron 3 of 5)	MER73|LTR|ERVL	-37025	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.005025	0.425000	
chunk0165_226_1	chr6	35368813	35369012	+	0	NA	intron (NM_001171819, intron 2 of 6)	intron (NM_001171819, intron 2 of 6)	26354	NM_177435	5467	Hs.696032	NM_006238	ENSG00000112033	PPARD	FAAR|NR1C2|NUC1|NUCI|NUCII|PPARB	peroxisome proliferator activated receptor delta	protein-coding	0.000000	0.445000	
chunk0212_427_1	chrX	153361929	153362150	+	0	NA	Intergenic	MER49|LTR|ERV1	27884	NM_001080485	10838	Hs.348963	NM_020636	ENSG00000063587	ZNF275	-	zinc finger protein 275	protein-coding	0.000000	0.414414	
chunk0145_78_1	chr4	145739880	145740105	+	0	NA	Intergenic	Intergenic	59788	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.022222	0.477876	
chunk0070_263_1	chr15	73919821	73920223	+	0	NA	non-coding (NR_040068, exon 2 of 3)	non-coding (NR_040068, exon 2 of 3)	-6426	NM_005576	4016	Hs.65436	NM_005576	ENSG00000129038	LOXL1	LOL|LOXL	lysyl oxidase like 1	protein-coding	0.012438	0.478908	
chunk0080_213_1	chr17	29568765	29569003	+	0	NA	intron (NM_138349, intron 1 of 6)	CpG-10923	163	NM_138349	90313	Hs.514050	NM_138349	ENSG00000167543	TP53I13	DSCP1	tumor protein p53 inducible protein 13	protein-coding	0.096639	0.698745	155(GGGACGCGGAGTTCTT,+,0.00)
chunk0115_268_1	chr21	27974263	27974462	+	0	NA	Intergenic	Intergenic	-39001	NR_027246	246705	Hs.505079	NM_145180	ENSG00000178457	LINC00314	C21orf94|NCRNA00314	long intergenic non-protein coding RNA 314	ncRNA	0.005025	0.370000	
chunk0014_327_1	chr1	182029343	182029727	+	0	NA	Intergenic	L2b|LINE|L2	32177	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.039062	0.597403	
chunk0010_251_1	chr1	116556570	116556887	+	0	NA	intron (NR_026665, intron 1 of 5)	intron (NR_026665, intron 1 of 5)	3383	NR_039621	100616384		NR_039621	ENSG00000264419	MIR548AC	-	microRNA 548ac	ncRNA	0.018927	0.509434	
chunk0051_101_1	chr12	114813221	114813760	+	0	NA	Intergenic	Intergenic	-129326	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.018553	0.444444	
chunk0053_113_1	chr13	29450940	29451521	+	0	NA	intron (NM_015233, intron 2 of 8)	L1MD|LINE|L1	22590	NM_015233	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.003442	0.328179	
chunk0092_75_1	chr19	20675197	20675799	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-13902	NM_145297	199777	Hs.657001	NM_145297	ENSG00000188171	ZNF626	-	zinc finger protein 626	protein-coding	0.003322	0.394693	191(AAGTACAATGAGTTCT,-,0.00),192(AGTACAATGAGTTCTG,+,0.00)
chunk0085_14_1	chr18	291241	291698	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-23410	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.015317	0.325328	
chunk0210_194_1	chrX	80274514	80274811	+	0	NA	intron (NR_110646, intron 5 of 5)	L1PA7|LINE|L1	60656	NR_110646	101060146	Hs.546064	NR_110646	ENSG00000278530	CHMP1B2P	-	charged multivesicular body protein 1B2, pseudogene	pseudo	0.003367	0.426174	
chunk0061_148_1	chr14	59483857	59484343	+	0	NA	promoter-TSS (NM_001098625)	promoter-TSS (NM_001098625)	255	NM_144581	112849	Hs.729061	NM_144581	ENSG00000126790	L3HYPDH	C14orf149	trans-L-3-hydroxyproline dehydratase	protein-coding	0.117284	0.710472	
chunk0046_38_1	chr12	54796561	54797219	+	0	NA	Intergenic	Intergenic	-57625	NM_058173	118430	Hs.348419	NM_058173	ENSG00000172551	MUCL1	SBEM	mucin like 1	protein-coding	0.003040	0.400607	277(AAACACTGTGTGTTCT,-,0.00),278(AACACTGTGTGTTCTC,+,0.00),298(AGGAGCAGCATGTCCT,-,0.00),299(GGAGCAGCATGTCCTT,+,0.00)
chunk0050_68_1	chr12	101459761	101460217	+	0	NA	Intergenic	LTR33|LTR|ERVL	-16890	NM_152323	121599	Hs.577097	NM_152323	ENSG00000166211	SPIC	SPI-C	Spi-C transcription factor	protein-coding	0.008772	0.505470	
chunk0212_24_1	chrY	10757080	10757285	+	0	NA	Intergenic	(CCATT)n|Simple_repeat|Simple_repeat	846384	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.004878	0.466019	
chunk0007_172_1	chr1	80278338	80279444	+	0	NA	Intergenic	Intergenic	-256864	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000904	0.292683	
chunk0048_9_1	chr12	76991137	76991771	+	0	NA	Intergenic	Intergenic	74126	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.004732	0.360630	
chunk0125_118_1	chr3	65808242	65808884	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-85253	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.010903	0.447900	
chunk0194_282_1	chr8	87365308	87366153	+	0	NA	intron (NM_173538, intron 10 of 10)	intron (NM_173538, intron 10 of 10)	499282	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.001183	0.291962	
chunk0120_410_1	chr3	12829379	12829677	+	0	NA	intron (NM_012298, intron 11 of 12)	L1ME3G|LINE|L1	10922	NM_001007074	6161	Hs.265174	NM_000994	ENSG00000144713	RPL32	L32|PP9932	ribosomal protein L32	protein-coding	0.013423	0.411371	
chunk0128_406_1	chr3	114451421	114451925	+	0	NA	intron (NM_001164343, intron 8 of 11)	intron (NM_001164343, intron 8 of 11)	-1920	NR_121661	101929754	Hs.614195	NR_121661	ENSG00000242290	ZBTB20-AS5	-	ZBTB20 antisense RNA 5	ncRNA	0.017857	0.396040	
chunk0137_273_1	chr4	22560797	22561238	+	0	NA	Intergenic	Intergenic	-44963	NM_145290	166647	Hs.99195	NM_145290	ENSG00000152990	ADGRA3	GPR125|PGR21|TEM5L	adhesion G protein-coupled receptor A3	protein-coding	0.006803	0.280543	
chunk0123_352_1	chr3	48064489	48065063	+	0	NA	intron (NM_030885, intron 1 of 3)	Tigger3c|DNA|TcMar-Tigger	24503	NM_002375	4134	Hs.517949	NM_002375	ENSG00000047849	MAP4	-	microtubule associated protein 4	protein-coding	0.005226	0.405217	
chunk0027_39_1	chr10	72449825	72450279	+	0	NA	intron (NM_006077, intron 8 of 11)	L2c|LINE|L2	73934	NM_001195519	10367	Hs.524367	NM_006077	ENSG00000107745	MICU1	CALC|CBARA1|EFHA3|MPXPS|ara CALC	mitochondrial calcium uptake 1	protein-coding	0.011013	0.417582	
chunk0156_207_1	chr5	108085478	108085695	+	0	NA	intron (NM_001163315, intron 6 of 8)	MER39|LTR|ERV1	296512	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.013825	0.500000	85(CTGAACACTGTGTGCC,-,0.00),86(TGAACACTGTGTGCCG,+,0.00)
chunk0057_21_1	chr13	95604163	95604580	+	0	NA	intron (NM_198968, intron 14 of 22)	intron (NM_198968, intron 14 of 22)	40335	NM_014934	22873	Hs.656580	NM_014934	ENSG00000134874	DZIP1	DZIP|DZIPt1	DAZ interacting zinc finger protein 1	protein-coding	0.021583	0.538278	
chunk0117_364_1	chr21	44911053	44911252	+	0	NA	intron (NM_001127491, intron 1 of 15)	(AC)n|Simple_repeat|Simple_repeat	9810	NM_001303238	3689	Hs.375957	NM_000211	ENSG00000160255	ITGB2	CD18|LAD|LCAMB|LFA-1|MAC-1|MF17|MFI7	integrin subunit beta 2	protein-coding	0.025126	0.500000	
chunk0190_30_1	chr8	29225581	29226054	+	0	NA	intron (NM_015254, intron 2 of 39)	intron (NM_015254, intron 2 of 39)	37276	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.008457	0.417722	
chunk0062_305_1	chr14	73083331	73083860	+	0	NA	intron (NM_021239, intron 5 of 18)	intron (NM_021239, intron 5 of 18)	25082	NM_021239	58517	Hs.531106	NM_021239	ENSG00000119707	RBM25	NET52|RED120|RNPC7|S164|Snu71|fSAP94	RNA binding motif protein 25	protein-coding	0.003781	0.309434	330(TAGCACTCTTTGTCCT,-,0.00),331(AGCACTCTTTGTCCTC,+,0.00)
chunk0201_181_1	chr9	36258853	36259152	+	0	NA	promoter-TSS (NM_001190384)	promoter-TSS (NM_001190384)	-503	NM_001190384	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.033445	0.550000	
chunk0185_47_1	chr7	124663058	124663269	+	0	NA	Intergenic	Intergenic	102862	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.000000	0.316038	75(AGGGAGACACTGTCCC,-,0.00),76(GGGAGACACTGTCCCT,+,0.00)
chunk0111_427_1	chr20	35049639	35050351	+	0	NA	intron (NM_199368, intron 5 of 18)	intron (NM_199368, intron 5 of 18)	42820	NM_015638	26133	Hs.168073	NM_015638	ENSG00000100991	TRPC4AP	C20orf188|PPP1R158|TRRP4AP|TRUSS	transient receptor potential cation channel subfamily C member 4 associated protein	protein-coding	0.007022	0.375877	
chunk0109_182_1	chr20	4770727	4771009	+	0	NA	Intergenic	Intergenic	-30200	NR_024267	149830	Hs.126516	NM_177549	ENSG00000180259	PRNT	M8	prion locus lncRNA, testis expressed	ncRNA	0.007092	0.367491	
chunk0106_328_1	chr2	205800424	205800624	+	0	NA	Intergenic	Intergenic	118024	NM_201264	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.005000	0.512438	94(CAGGACACACTGCACC,-,0.00),95(AGGACACACTGCACCT,+,0.00)
chunk0105_350_1	chr2	191415211	191415410	+	0	NA	intron (NM_001130158, intron 29 of 30)	intron (NM_001130158, intron 29 of 30)	169782	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.000000	0.385000	
chunk0038_401_1	chr11	93697570	93698169	+	0	NA	exon (NM_033395, exon 15 of 30)	exon (NM_033395, exon 15 of 30)	-23645	NR_002569	619383	Hs.660668	NR_002569	ENSG00000254911	SCARNA9	Z32|mgU2-19/30	small Cajal body-specific RNA 9	ncRNA	0.006678	0.416667	292(AGAAGAGTATGTTCCG,+,0.00)
chunk0106_209_1	chr2	202408279	202408863	+	0	NA	intron (NM_001204, intron 1 of 12)	intron (NM_001204, intron 1 of 12)	32244	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.003425	0.341880	
chunk0207_316_1	chr9	133932302	133932680	+	0	NA	intron (NM_001134398, intron 2 of 29)	intron (NM_001134398, intron 2 of 29)	59833	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.034392	0.490765	
chunk0106_454_1	chr2	209391897	209392314	+	0	NA	Intergenic	Intergenic	-31942	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.000000	0.370813	
chunk0167_456_1	chr6	76418647	76419160	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-346225	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.003899	0.437743	
chunk0082_207_1	chr17	56926710	56927334	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-12974	NM_005082	7706	Hs.528952	NM_005082	ENSG00000121060	TRIM25	EFP|RNF147|Z147|ZNF147	tripartite motif containing 25	protein-coding	0.004808	0.371200	
chunk0181_289_1	chr7	86939168	86939598	+	0	NA	intron (NM_001291990, intron 6 of 21)	intron (NM_001291990, intron 6 of 21)	26592	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.006977	0.392111	
chunk0010_6_1	chr1	111856897	111857668	+	0	NA	promoter-TSS (NR_046783)	promoter-TSS (NR_046783)	-377	NR_046783	100874295	Hs.738190	NR_046783	ENSG00000232558	KCND3-IT1	-	KCND3 intronic transcript 1	ncRNA	0.025940	0.527202	490(CAGGACGAAGTGTTCC,-,0.00),491(AGGACGAAGTGTTCCT,+,0.00)
chunk0044_320_1	chr12	34048590	34048815	+	0	NA	Intergenic	L1PB1|LINE|L1	26421	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.013333	0.557522	
chunk0032_123_1	chr11	4182164	4182444	+	0	NA	Intergenic	Intergenic	-4848	NR_047550	100506082	Hs.445705	NR_047550	ENSG00000254480	LINC02749	-	long intergenic non-protein coding RNA 2749	ncRNA	0.003571	0.608541	186(AGGTGCAGCCTGTGCC,-,0.00),187(GGTGCAGCCTGTGCCT,+,0.00)
chunk0163_176_1	chr6	11299126	11299509	+	0	NA	intron (NM_001142393, intron 2 of 7)	L1PA6|LINE|L1	-66635	NM_006403	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.018277	0.539062	
chunk0163_167_1	chr6	11175675	11176189	+	0	NA	Intergenic	L2b|LINE|L2	56750	NM_182966	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.003891	0.380583	
chunk0138_51_1	chr4	31536641	31537294	+	0	NA	Intergenic	L1M2|LINE|L1	365823	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.004594	0.298165	
chunk0150_365_1	chr5	39055419	39055783	+	0	NA	intron (NM_001285439, intron 2 of 38)	L2a|LINE|L2	18807	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.002747	0.369863	
chunk0189_80_1	chr8	21123301	21123550	+	0	NA	Intergenic	L1ME1|LINE|L1	149439	NR_033894	286114	Hs.651884	NR_033894	ENSG00000253199	LINC02153	-	long intergenic non-protein coding RNA 2153	ncRNA	0.008032	0.360000	
chunk0102_340_1	chr2	152298653	152298961	+	0	NA	Intergenic	L1MC1|LINE|L1	-36430	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.003247	0.343042	
chunk0032_285_1	chr11	9416781	9417555	+	0	NA	intron (NM_006391, intron 6 of 24)	intron (NM_006391, intron 6 of 24)	-11598	NR_002962	677808	Hs.689720	NR_002962	ENSG00000201998	SNORA23	ACA23	small nucleolar RNA, H/ACA box 23	snoRNA	0.002584	0.305806	
chunk0176_345_1	chr7	17759307	17759564	+	0	NA	Intergenic	L1PB3|LINE|L1	181073	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.000000	0.387597	166(AAGAACACCCTGTTCA,-,0.00),167(AGAACACCCTGTTCAA,+,0.00)
chunk0085_192_1	chr18	6478625	6479108	+	0	NA	Intergenic	Intergenic	-32550	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.006211	0.373967	219(TAGAACATCCTGTCCT,-,0.00),220(AGAACATCCTGTCCTC,+,0.00)
chunk0041_134_1	chr11	125222912	125223240	+	0	NA	intron (NM_022062, intron 1 of 12)	intron (NM_022062, intron 1 of 12)	58413	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.006098	0.443769	
chunk0164_404_1	chr6	26544405	26544915	+	0	NA	intron (NM_006353, intron 1 of 1)	L1ME3D|LINE|L1	6316	NM_006353	10473	Hs.236774	NM_006353	ENSG00000182952	HMGN4	HMG17L3|NHC	high mobility group nucleosomal binding domain 4	protein-coding	0.000000	0.350294	
chunk0008_306_1	chr1	95072787	95073030	+	0	NA	promoter-TSS (NM_001305242)	promoter-TSS (NM_001305242)	43	NM_001305242	199857	Hs.408927	NM_144988	ENSG00000172339	ALG14	CMS15	ALG14 UDP-N-acetylglucosaminyltransferase subunit	protein-coding	0.090535	0.594262	
chunk0176_267_1	chr7	16426030	16426287	+	0	NA	Intergenic	L1MC1|LINE|L1	-4836	NM_001101426	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.003891	0.325581	
chunk0183_147_1	chr7	105830450	105830842	+	0	NA	intron (NM_020725, intron 2 of 11)	intron (NM_020725, intron 2 of 11)	45939	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.002551	0.470738	
chunk0044_242_1	chr12	31731751	31732262	+	0	NA	Intergenic	Intergenic	-2832	NM_001278412	196394	Hs.585084	NM_001113402	ENSG00000151743	AMN1	-	antagonist of mitotic exit network 1 homolog	protein-coding	0.007828	0.398438	234(AAGAACAAGATGTTCC,-,0.00),235(AGAACAAGATGTTCCT,+,0.00),264(GAAAACAGGATGTTCT,-,0.00),265(AAAACAGGATGTTCTT,+,0.00)
chunk0164_259_1	chr6	23547801	23548000	+	0	NA	Intergenic	Intergenic	-578286	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.000000	0.415000	
chunk0200_125_1	chr9	17362068	17362346	+	0	NA	intron (NM_017738, intron 12 of 25)	intron (NM_017738, intron 12 of 25)	-216747	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.003597	0.369176	
chunk0069_303_1	chr15	65541167	65541646	+	0	NA	intron (NM_016395, intron 1 of 10)	MER90a|LTR|ERV1	10917	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.006263	0.362500	
chunk0035_403_1	chr11	56715948	56716726	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	15949	NM_001013358	504191		NM_001013358		OR9G9	OR9G1	olfactory receptor family 9 subfamily G member 9	protein-coding	0.006427	0.335045	
chunk0111_292_1	chr20	31719746	31720201	+	0	NA	intron (NM_001191, intron 2 of 2)	intron (NM_001191, intron 2 of 2)	-1534	NR_131907	103021294		NR_131907	ENSG00000281376	ABALON	INXS	apoptotic BCL2L1-antisense long non-coding RNA	ncRNA	0.002198	0.495614	
chunk0002_219_1	chr1	19776269	19776675	+	0	NA	intron (NM_181719, intron 4 of 15)	L2b|LINE|L2	23445	NM_181719	255104	Hs.466729	NM_181719	ENSG00000162542	TMCO4	-	transmembrane and coiled-coil domains 4	protein-coding	0.017241	0.466830	
chunk0026_428_1	chr10	70900095	70900778	+	0	NA	Intergenic	L1M5|LINE|L1	-11650	NM_000281	5092	Hs.3192	NM_000281	ENSG00000166228	PCBD1	DCOH|PCBD|PCD|PHS	pterin-4 alpha-carbinolamine dehydratase 1	protein-coding	0.007321	0.349415	
chunk0168_139_1	chr6	83008607	83009085	+	0	NA	intron (NM_198920, intron 8 of 9)	intron (NM_198920, intron 8 of 9)	56995	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.002092	0.359081	
chunk0035_166_1	chr11	43792791	43793159	+	0	NA	intron (NM_016142, intron 3 of 10)	L2a|LINE|L2	-87832	NM_139178	221120	Hs.720708	NM_139178	ENSG00000166199	ALKBH3	ABH3|DEPC-1|DEPC1|PCA1|hABH3	alkB homolog 3, alpha-ketoglutaratedependent dioxygenase	protein-coding	0.005435	0.376694	
chunk0096_91_1	chr2	28011883	28012432	+	0	NA	intron (NM_199191, intron 4 of 11)	intron (NM_199191, intron 4 of 11)	15790	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.003643	0.345455	
chunk0102_222_1	chr2	148645034	148645633	+	0	NA	intron (NM_015630, intron 1 of 13)	CpG	342	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.091820	0.601667	
chunk0200_283_1	chr9	22379054	22379694	+	0	NA	Intergenic	Intergenic	-67467	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.009375	0.405616	
chunk0022_397_1	chr10	17980666	17981382	+	0	NA	intron (NM_001282733, intron 5 of 12)	intron (NM_001282733, intron 5 of 12)	29185	NM_001282734	221074	Hs.350895	NM_152725	ENSG00000148482	SLC39A12	LZT-Hs8|ZIP-12|bA570F3.1	solute carrier family 39 member 12	protein-coding	0.008380	0.380753	
chunk0025_450_1	chr10	60282761	60283357	+	0	NA	intron (NM_001204403, intron 2 of 43)	L2a|LINE|L2	106817	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.008389	0.376884	
chunk0206_455_1	chr9	128378560	128378759	+	0	NA	intron (NM_030914, intron 2 of 4)	L2b|LINE|L2	7340	NM_030914	81605	Hs.495229	NM_030914	ENSG00000167118	URM1	C9orf74	ubiquitin related modifier 1	protein-coding	0.015075	0.485000	
chunk0019_154_1	chr1	225834353	225835005	+	0	NA	intron (NM_001291163, intron 3 of 8)	intron (NM_001291163, intron 3 of 8)	9378	NM_000120	2052	Hs.89649	NM_000120	ENSG00000143819	EPHX1	EPHX|EPOX|HYL1|MEH	epoxide hydrolase 1	protein-coding	0.013804	0.488515	
chunk0074_350_1	chr16	33491345	33491950	+	0	NA	Intergenic	Intergenic	4588	NR_033866	390705	Hs.278513	NR_033866		LOC390705	-	protein phosphatase 2 regulatory subunit B'', beta pseudogene	pseudo	0.008264	0.663366	
chunk0150_247_1	chr5	36273782	36274023	+	0	NA	intron (NM_145000, intron 1 of 13)	MER57B2|LTR|ERV1	28007	NM_145000	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.004149	0.380165	
chunk0196_34_1	chr8	101583285	101584330	+	0	NA	intron (NM_024915, intron 7 of 15)	intron (NM_024915, intron 7 of 15)	91367	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.003828	0.389101	
chunk0122_239_1	chr3	33855972	33856763	+	0	NA	intron (NM_001162429, intron 15 of 17)	L1M7|LINE|L1	57796	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.011378	0.412879	
chunk0185_253_1	chr7	130127183	130127484	+	0	NA	intron (NM_014997, intron 7 of 9)	intron (NM_014997, intron 7 of 9)	56824	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.009967	0.397351	
chunk0156_15_1	chr5	102068908	102069422	+	0	NA	Intergenic	Intergenic	227384	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.007782	0.394175	
chunk0204_170_1	chr9	95980845	95981363	+	0	NA	intron (NM_020207, intron 17 of 18)	intron (NM_020207, intron 17 of 18)	40651	NR_024129	100188953	Hs.434310	NR_024129	ENSG00000225194	LINC00092	NCRNA00092	long intergenic non-protein coding RNA 92	ncRNA	0.007722	0.335260	
chunk0088_195_1	chr18	47587595	47588021	+	0	NA	Intergenic	Intergenic	207312	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.004695	0.489461	
chunk0115_211_1	chr21	26887214	26887837	+	0	NA	Intergenic	Intergenic	-42116	NM_006988	9510	Hs.643357	NM_006988	ENSG00000154734	ADAMTS1	C3-C5|METH1	ADAM metallopeptidase with thrombospondin type 1 motif 1	protein-coding	0.006421	0.432692	307(CAGCTCACTTTGTTCC,-,0.00)
chunk0137_45_1	chr4	11496867	11497591	+	0	NA	Intergenic	Intergenic	-68316	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.000000	0.353103	
chunk0093_394_1	chr19	56747654	56748067	+	0	NA	Intergenic	Intergenic	-17462	NR_110744	101929059	Hs.607132	NR_110744	ENSG00000286125	ZIM2-AS1	ZIM2as	ZIM2 antisense RNA 1	ncRNA	0.016949	0.471014	
chunk0192_298_1	chr8	66689790	66690079	+	0	NA	intron (NM_001204173, intron 2 of 18)	LTR40c|LTR|ERVL	22382	NM_019607	56260	Hs.661238	NM_019607	ENSG00000213865	C8orf44	-	chromosome 8 open reading frame 44	ncRNA	0.006920	0.448276	
chunk0019_58_1	chr1	224186699	224187114	+	0	NA	intron (NM_003676, intron 1 of 2)	intron (NM_003676, intron 1 of 2)	3698	NM_003676	8560	Hs.299878	NM_003676	ENSG00000143753	DEGS1	DEGS|DEGS-1|DES1|Des-1|FADS7|HLD18|MIG15|MLD	delta 4-desaturase, sphingolipid 1	protein-coding	0.007229	0.394231	
chunk0133_93_1	chr3	167754392	167754591	+	0	NA	intron (NM_005025, intron 1 of 8)	intron (NM_005025, intron 1 of 8)	18768	NM_005025	5274	Hs.478153	NM_005025	ENSG00000163536	SERPINI1	PI12|neuroserpin	serpin family I member 1	protein-coding	0.000000	0.285000	
chunk0206_64_1	chr9	119802680	119802886	+	0	NA	Intergenic	Intergenic	-132277	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.014563	0.497585	
chunk0179_317_1	chr7	50502163	50502730	+	0	NA	intron (NM_001082971, intron 7 of 14)	intron (NM_001082971, intron 7 of 14)	-29313	NR_033845	100129427	Hs.680434	NR_033845	ENSG00000226122	DDC-AS1	-	DDC antisense RNA 1	ncRNA	0.015873	0.556338	302(CAGGACATTCAGTTCT,-,0.00),303(AGGACATTCAGTTCTT,+,0.00)
chunk0150_42_1	chr5	31491141	31491604	+	0	NA	intron (NM_013235, intron 12 of 34)	MIR|SINE|MIR	40803	NM_001100412	29102	Hs.97997	NM_013235	ENSG00000113360	DROSHA	ETOHI2|HSA242976|RANSE3L|RN3|RNASE3L|RNASEN	drosha ribonuclease III	protein-coding	0.002160	0.331897	
chunk0040_246_1	chr11	115264141	115264573	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	240166	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.002315	0.374134	190(GAGAACTGTTTGTCCA,-,0.00),278(TGGCACATTCAGTTCT,-,0.00),279(GGCACATTCAGTTCTA,+,0.00)
chunk0148_309_1	chr5	13052405	13052970	+	0	NA	Intergenic	Intergenic	384828	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003540	0.335689	
chunk0142_216_1	chr4	97707974	97708173	+	0	NA	intron (NM_174952, intron 10 of 10)	intron (NM_174952, intron 10 of 10)	341147	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.005025	0.330000	
chunk0095_74_1	chr2	14572551	14573098	+	0	NA	Intergenic	Intergenic	-59862	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.003656	0.348540	
chunk0082_15_1	chr17	50309459	50309831	+	0	NA	Intergenic	Intergenic	-21790	NR_125805	103752589	Hs.612913	NR_125805	ENSG00000251179	TMEM92-AS1	TCONS_00025237|lncRNA-508851	TMEM92 antisense RNA 1	ncRNA	0.000000	0.353887	
chunk0189_376_1	chr8	27323121	27323429	+	0	NA	5' UTR (NM_173174, exon 5 of 36)	5' UTR (NM_173174, exon 5 of 36)	873	NM_004103	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.006494	0.459547	
chunk0050_203_1	chr12	104138089	104138366	+	0	NA	promoter-TSS (NM_006166)	promoter-TSS (NM_006166)	35	NM_006166	4801	Hs.84928	NM_006166	ENSG00000120837	NFYB	CBF-A|CBF-B|HAP3|NF-YB	nuclear transcription factor Y subunit beta	protein-coding	0.126354	0.723022	
chunk0212_292_1	chrX	140967137	140967470	+	0	NA	Intergenic	MIRc|SINE|MIR	-35288	NM_032461	728695	Hs.434105	NM_032461	ENSG00000227234	SPANXB1	B1|CT11.2|SPANX-B|SPANXB|SPANXB2|SPANXF1|SPANXF2	SPANX family member B1	protein-coding	0.006006	0.428144	
chunk0197_313_1	chr8	124742019	124742387	+	0	NA	Intergenic	Intergenic	-13696	NM_001282971	9788	Hs.336994	NM_014751	ENSG00000170873	MTSS1	MIM|MIMA|MIMB	MTSS I-BAR domain containing 1	protein-coding	0.008152	0.398374	
chunk0189_245_1	chr8	24928653	24929070	+	0	NA	Intergenic	MER41D|LTR|ERV1	13919	NM_001105541	4741	Hs.458657	NM_005382	ENSG00000104722	NEFM	NEF3|NF-M|NFM	neurofilament medium	protein-coding	0.000000	0.380383	131(CATAACAGTGTGTGCT,-,0.00),132(ATAACAGTGTGTGCTT,+,0.00)
chunk0008_28_1	chr1	87904459	87905125	+	0	NA	Intergenic	Intergenic	-533137	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.003003	0.370315	
chunk0059_5_1	chr14	29692482	29692850	+	0	NA	intron (NM_002742, intron 2 of 17)	intron (NM_002742, intron 2 of 17)	235027	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.002717	0.352304	159(GGAAACATTATGTACC,-,0.00),160(GAAACATTATGTACCC,+,0.00)
chunk0071_161_1	chr15	82999951	83000522	+	0	NA	intron (NM_001160115, intron 3 of 4)	MamRep605|LTR?|LTR?	11405	NR_027650	123207	Hs.352541	NM_144597	ENSG00000169609	C15orf40	-	chromosome 15 open reading frame 40	protein-coding	0.008757	0.465035	217(AGGGACAGAATGTTCT,-,0.00),218(GGGACAGAATGTTCTC,+,0.00)
chunk0135_447_1	chr3	194160971	194161526	+	0	NA	Intergenic	Intergenic	25106	NM_005524	3280	Hs.250666	NM_005524	ENSG00000114315	HES1	HES-1|HHL|HRY|bHLHb39	hes family bHLH transcription factor 1	protein-coding	0.012613	0.552158	473(AAGATCAGGCTGTGCC,-,0.00),474(AGATCAGGCTGTGCCG,+,0.00)
chunk0169_347_1	chr6	106553756	106554153	+	0	NA	intron (NM_001624, intron 14 of 19)	intron (NM_001624, intron 14 of 19)	42099	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.012594	0.492462	
chunk0008_87_1	chr1	90761342	90761650	+	0	NA	Intergenic	Intergenic	-44259	NM_020063	343472	Hs.451956	NM_020063	ENSG00000143032	BARHL2	-	BarH like homeobox 2	protein-coding	0.012987	0.472492	
chunk0117_57_1	chr22	15633002	15633886	+	0	NA	Intergenic	Intergenic	-56582	NM_001136213	23784	Hs.581075	NM_001004053	ENSG00000198062	POTEH	A26C3|ACTBL1|CT104.7|POTE22	POTE ankyrin domain family member H	protein-coding	0.007919	0.338983	
chunk0109_221_1	chr20	5767598	5768226	+	0	NA	intron (NM_001303477, intron 2 of 3)	intron (NM_001303477, intron 2 of 3)	17525	NM_152504	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.011146	0.494436	
chunk0103_1_1	chr2	158724239	158724747	+	0	NA	Intergenic	Intergenic	-70824	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.015748	0.538310	
chunk0039_60_1	chr11	96241525	96241841	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-99755	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.012658	0.425868	
chunk0171_450_1	chr6	132020351	132020703	+	0	NA	Intergenic	Intergenic	-69149	NM_001901	1490	Hs.410037	NM_001901	ENSG00000118523	CCN2	CTGF|HCS24|IGFBP8|NOV2	cellular communication network factor 2	protein-coding	0.005682	0.422096	
chunk0081_111_1	chr17	39981362	39981726	+	0	NA	intron (NM_002809, intron 1 of 11)	intron (NM_002809, intron 1 of 11)	776	NM_002809	5709	Hs.12970	NM_002809	ENSG00000108344	PSMD3	P58|RPN3|S3|TSTA2	proteasome 26S subunit, non-ATPase 3	protein-coding	0.016484	0.484932	
chunk0083_103_1	chr17	64589117	64589453	+	0	NA	intron (NM_022739, intron 5 of 18)	intron (NM_022739, intron 5 of 18)	72983	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.000000	0.287834	
chunk0005_431_1	chr1	63002229	63002714	+	0	NA	Intergenic	Intergenic	218365	NM_178221	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.006186	0.374486	
chunk0016_228_1	chr1	199581581	199582244	+	0	NA	Intergenic	Intergenic	-445690	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.012066	0.396084	390(AAGTACAGTCTGGTCT,-,0.00),391(AGTACAGTCTGGTCTC,+,0.00)
chunk0072_45_1	chr16	1197304	1197559	+	0	NA	intron (NM_021098, intron 5 of 34)	intron (NM_021098, intron 5 of 34)	27823	NM_012467	25823	Hs.592076	NM_012467	ENSG00000116176	TPSG1	PRSS31|TMT|trpA	tryptase gamma 1	protein-coding	0.031373	0.554688	
chunk0061_441_1	chr14	65675410	65675814	+	0	NA	intron (NR_038167, intron 7 of 8)	intron (NR_038167, intron 7 of 8)	204510	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.017327	0.424691	
chunk0021_93_1	chr10	2656922	2657196	+	0	NA	Intergenic	Intergenic	-341985	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.036496	0.472727	
chunk0026_282_1	chr10	67373973	67374629	+	0	NA	intron (NM_001291133, intron 6 of 8)	MER58A|DNA|hAT-Charlie	29109	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.006098	0.308980	
chunk0142_203_1	chr4	97337260	97337497	+	0	NA	Intergenic	L1PA10|LINE|L1	-29548	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.000000	0.563025	
chunk0066_277_1	chr15	35129282	35129592	+	0	NA	Intergenic	Intergenic	-107889	NR_003144	723972	Hs.631698	NR_003144	ENSG00000259516	ANP32AP1	-	acidic nuclear phosphoprotein 32 family member A pseudogene 1	pseudo	0.006452	0.366559	190(AGGAACATTCTGGTCC,-,0.00),191(GGAACATTCTGGTCCT,+,0.00)
chunk0058_200_1	chr14	24725512	24725766	+	0	NA	Intergenic	Intergenic	-91413	NM_004131	3002	Hs.1051	NM_004131	ENSG00000100453	GZMB	C11|CCPI|CGL-1|CGL1|CSP-B|CSPB|CTLA1|CTSGL1|HLP|SECT	granzyme B	protein-coding	0.007874	0.466667	
chunk0051_408_1	chr12	122111073	122111568	+	0	NA	intron (NM_014938, intron 1 of 16)	intron (NM_014938, intron 1 of 16)	32592	NM_014938	22877	Hs.437153	NM_014938	ENSG00000175727	MLXIP	MIR|MONDOA|bHLHe36	MLX interacting protein	protein-coding	0.002020	0.368952	
chunk0007_264_1	chr1	83024921	83025165	+	0	NA	Intergenic	Intergenic	-38835	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.004098	0.387755	
chunk0173_22_1	chr6	141561199	141561598	+	0	NA	Intergenic	Intergenic	527401	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.007519	0.377500	
chunk0045_10_1	chr12	42976475	42976989	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-330234	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.005837	0.398058	307(CAGAGCACACTGTGCT,-,0.00),308(AGAGCACACTGTGCTC,+,0.00),309(GAGCACACTGTGCTCT,-,0.00),310(AGCACACTGTGCTCTC,+,0.00)
chunk0128_333_1	chr3	112035746	112036187	+	0	NA	Intergenic	Intergenic	-3652	NR_026734	344805	Hs.435490	NM_001042575	ENSG00000176040	TMPRSS7	-	transmembrane serine protease 7	protein-coding	0.006803	0.334842	
chunk0073_166_1	chr16	8240581	8241353	+	0	NA	Intergenic	Intergenic	348871	NR_110736	283953	Hs.150849	NM_001146336	ENSG00000232258	TMEM114	-	transmembrane protein 114	protein-coding	0.006477	0.338939	
chunk0211_439_1	chrX	129613436	129613736	+	0	NA	Intergenic	Intergenic	41370	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.000000	0.352159	
chunk0086_246_1	chr18	23178857	23179056	+	0	NA	intron (NM_138375, intron 1 of 9)	intron (NM_138375, intron 1 of 9)	23131	NM_138375	91768	Hs.11108	NM_138375	ENSG00000134508	CABLES1	CABL1|CABLES|HsT2563|IK3-1	Cdk5 and Abl enzyme substrate 1	protein-coding	0.020101	0.440000	
chunk0073_403_1	chr16	16836910	16837296	+	0	NA	Intergenic	L1MB2|LINE|L1	457858	NM_001282507	101059938	Hs.634612	NM_001282507	ENSG00000214967	NPIPA7	NPIPA8	nuclear pore complex interacting protein family member A7	protein-coding	0.002591	0.423773	
chunk0143_25_1	chr4	106056518	106057096	+	0	NA	intron (NM_001163435, intron 25 of 25)	LTR84b|LTR|ERVL	-34329	NR_125928	101929577	Hs.631131	NR_125928	ENSG00000249635	LOC101929577	-	uncharacterized LOC101929577	ncRNA	0.000000	0.343696	
chunk0160_45_1	chr5	149572217	149572599	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-9164	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.002618	0.365535	
chunk0202_91_1	chr9	72293117	72293714	+	0	NA	Intergenic	Intergenic	-12021	NR_110952	100507540	Hs.54957	NR_110952	ENSG00000225434	LINC01504	-	long intergenic non-protein coding RNA 1504	ncRNA	0.006700	0.354515	
chunk0184_438_1	chr7	123077176	123077388	+	0	NA	Intergenic	Intergenic	-81582	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.004717	0.431925	
chunk0083_116_1	chr17	64920942	64921141	+	0	NA	Intergenic	MER21B|LTR|ERVL	-1561	NM_001303255	374819	Hs.551962	NM_199340	ENSG00000176809	LRRC37A3	LRRC37|LRRC37A	leucine rich repeat containing 37 member A3	protein-coding	0.010050	0.405000	
chunk0104_44_1	chr2	171154337	171154707	+	0	NA	intron (NM_001136554, intron 1 of 20)	MIR3|SINE|MIR	6378	NM_012290	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.002703	0.393531	
chunk0098_49_1	chr2	66496579	66497230	+	0	NA	intron (NM_002398, intron 7 of 12)	intron (NM_002398, intron 7 of 12)	-56574	NR_046625	100873998	Hs.734698	NR_046625	ENSG00000230749	MEIS1-AS2	MEIS1-AS1	MEIS1 antisense RNA 2	ncRNA	0.007680	0.406442	
chunk0197_306_1	chr8	124526255	124526954	+	0	NA	intron (NR_027427, intron 1 of 12)	intron (NR_027427, intron 1 of 12)	12484	NM_001146160	83940	Hs.170568	NM_032026	ENSG00000147687	TATDN1	CDA11	TatD DNase domain containing 1	protein-coding	0.008584	0.360000	
chunk0050_216_1	chr12	104524192	104524508	+	0	NA	intron (NM_018413, intron 1 of 2)	intron (NM_018413, intron 1 of 2)	-67283	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.006329	0.403785	
chunk0020_396_1	chr1	240596724	240597727	+	0	NA	intron (NM_022469, intron 1 of 1)	intron (NM_022469, intron 1 of 1)	14937	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.017946	0.440239	
chunk0193_225_1	chr8	76605327	76605716	+	0	NA	Intergenic	L2a|LINE|L2	-75759	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.000000	0.351282	155(AAGGTCTGCCTGTGCT,-,0.00),156(AGGTCTGCCTGTGCTT,+,0.00)
chunk0166_12_1	chr6	41584740	41585065	+	0	NA	intron (NM_001012427, intron 4 of 16)	intron (NM_001012427, intron 4 of 16)	-13821	NR_039784	100616178		NR_039784	ENSG00000266494	MIR4641	-	microRNA 4641	ncRNA	0.024615	0.625767	
chunk0042_42_1	chr12	1594656	1594872	+	0	NA	promoter-TSS (NM_152441)	promoter-TSS (NM_152441)	-599	NM_152441	144699	Hs.367956	NM_152441	ENSG00000171823	FBXL14	Fbl14	F-box and leucine rich repeat protein 14	protein-coding	0.180556	0.811060	
chunk0054_212_1	chr13	45250632	45251239	+	0	NA	intron (NM_004128, intron 5 of 7)	intron (NM_004128, intron 5 of 7)	-49895	NM_198404	386618	Hs.23406	NM_198404	ENSG00000180332	KCTD4	bA321C24.3	potassium channel tetramerization domain containing 4	protein-coding	0.004942	0.348684	336(GAGAACTTTTTGTACT,-,0.00),337(AGAACTTTTTGTACTT,+,0.00)
chunk0099_27_1	chr2	83196346	83196600	+	0	NA	Intergenic	Intergenic	339670	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.003937	0.329412	
chunk0104_227_1	chr2	176446106	176446474	+	0	NA	Intergenic	Intergenic	154762	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.008152	0.409214	
chunk0100_351_1	chr2	117502010	117502834	+	0	NA	Intergenic	Intergenic	-312257	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.008495	0.389091	312(AAGGACAGCTTGTTCA,-,0.00),313(AGGACAGCTTGTTCAT,+,0.00)
chunk0038_108_1	chr11	83707917	83708662	+	0	NA	intron (NM_001142699, intron 18 of 27)	L2a|LINE|L2	-25864	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004027	0.321716	324(TAGAACACAAAGTACC,-,0.00),325(AGAACACAAAGTACCT,+,0.00)
chunk0092_64_1	chr19	20309886	20310431	+	0	NA	Intergenic	LTR10C|LTR|ERV1	89196	NR_036053	100302179		NR_036053	ENSG00000238517	MIR1270	MIR1270-1|MIR1270-2|MIRN1270|hsa-mir-1270|hsa-mir-1270-1|mir-1270	microRNA 1270	ncRNA	0.018349	0.402930	267(AAGAACATAAAGTCCA,-,0.00),268(AGAACATAAAGTCCAT,+,0.00)
chunk0177_285_1	chr7	25710938	25711530	+	0	NA	Intergenic	L1MC|LINE|L1	238752	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.003378	0.355818	
chunk0042_247_1	chr12	6384886	6385360	+	0	NA	exon (NM_002342, exon 3 of 10)	exon (NM_002342, exon 3 of 10)	1090	NM_002342	4055	Hs.1116	NM_002342	ENSG00000111321	LTBR	D12S370|LT-BETA-R|TNF-R-III|TNFCR|TNFR-RP|TNFR2-RP|TNFR3|TNFRSF3	lymphotoxin beta receptor	protein-coding	0.042194	0.633684	
chunk0079_346_1	chr17	17774173	17774723	+	0	NA	intron (NM_030665, intron 2 of 5)	intron (NM_030665, intron 2 of 5)	5081	NR_024007	140771	Hs.352643	NM_144774	ENSG00000226746	SMCR5	NCRNA00034	Smith-Magenis syndrome chromosome region, candidate 5	ncRNA	0.029091	0.582577	158(AGGTACTCGGTGTTCT,-,0.00),159(GGTACTCGGTGTTCTT,+,0.00)
chunk0161_171_1	chr5	169328144	169328588	+	0	NA	Intergenic	L1ME1|LINE|L1	-27237	NM_001271946	6586	Hs.552087	NM_003062	ENSG00000184347	SLIT3	MEGF5|SLIL2|SLIT1|Slit-3|slit2	slit guidance ligand 3	protein-coding	0.004505	0.343820	
chunk0099_88_1	chr2	85482465	85482695	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	47785	NM_198482	284948	Hs.209542	NM_198482	ENSG00000152292	SH2D6	-	SH2 domain containing 6	protein-coding	0.013043	0.450216	
chunk0190_61_1	chr8	29738293	29738926	+	0	NA	intron (NR_026765, intron 1 of 3)	intron (NR_026765, intron 1 of 3)	9500	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.007899	0.405363	
chunk0154_229_1	chr5	80820273	80820774	+	0	NA	intron (NM_002439, intron 20 of 23)	L2c|LINE|L2	-140166	NM_006909	5924	Hs.162129	NM_006909	ENSG00000113319	RASGRF2	GRF2|RAS-GRF2	Ras protein specific guanine nucleotide releasing factor 2	protein-coding	0.001996	0.320717	
chunk0208_280_1	chrX	21884938	21885430	+	0	NA	3' UTR (NM_015884, exon 11 of 11)	3' UTR (NM_015884, exon 11 of 11)	29197	NM_206923	404281	Hs.673601	NM_206923	ENSG00000230797	YY2	ZNF631	YY2 transcription factor	protein-coding	0.010163	0.328600	
chunk0174_311_1	chr6	162760000	162760319	+	0	NA	intron (NM_152410, intron 2 of 6)	LTR16A1|LTR|ERVL	32189	NM_001080379	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.015674	0.481250	
chunk0197_87_1	chr8	119213967	119214412	+	0	NA	intron (NM_052886, intron 1 of 3)	intron (NM_052886, intron 1 of 3)	5818	NM_052886	114569	Hs.201083	NM_052886	ENSG00000147676	MAL2	-	mal, T cell differentiation protein 2 (gene/pseudogene)	protein-coding	0.002247	0.390135	199(ATGCACATGCAGTACT,-,0.00),200(TGCACATGCAGTACTT,+,0.00)
chunk0101_91_1	chr2	124193873	124194151	+	0	NA	intron (NM_130773, intron 1 of 23)	intron (NM_130773, intron 1 of 23)	168725	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.014388	0.516129	
chunk0042_365_1	chr12	10395705	10396037	+	0	NA	intron (NM_001199805, intron 4 of 12)	LTR41C|LTR|ERVL	-5817	NM_007360	22914	Hs.387787	NM_007360	ENSG00000213809	KLRK1	CD314|D12S2489E|KLR|NKG2-D|NKG2D	killer cell lectin like receptor K1	protein-coding	0.015060	0.459459	
chunk0112_439_1	chr20	47711056	47711410	+	0	NA	intron (NM_198596, intron 3 of 20)	MIR|SINE|MIR	74831	NM_018837	55959	Hs.162016	NM_018837	ENSG00000196562	SULF2	HSULF-2	sulfatase 2	protein-coding	0.028249	0.574648	127(AGGAACACGCTGTTCC,-,0.00),128(GGAACACGCTGTTCCT,+,0.00)
chunk0001_34_1	chr1	1406949	1407198	+	0	NA	intron (NM_017971, intron 1 of 3)	CpG-95	240	NM_017971	55052	Hs.182698	NM_017971	ENSG00000242485	MRPL20	L20mt|MRP-L20	mitochondrial ribosomal protein L20	protein-coding	0.096386	0.652000	
chunk0079_275_1	chr17	16398324	16398808	+	0	NA	Intergenic	Intergenic	-16976	NM_016113	51393	Hs.279746	NM_016113	ENSG00000187688	TRPV2	VRL|VRL-1|VRL1	transient receptor potential cation channel subfamily V member 2	protein-coding	0.014463	0.463918	
chunk0184_361_1	chr7	121022023	121022470	+	0	NA	intron (NM_001105533, intron 2 of 17)	intron (NM_001105533, intron 2 of 17)	32855	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.000000	0.316964	
chunk0008_313_1	chr1	95172955	95173268	+	0	NA	intron (NR_125949, intron 3 of 3)	intron (NR_125949, intron 3 of 3)	55188	NM_001199691	100527978	Hs.483512	NM_001199691	ENSG00000271092	TLCD4-RWDD3	TMEM56-RWDD3	TLCD4-RWDD3 readthrough	protein-coding	0.000000	0.308917	
chunk0199_127_1	chr9	3716205	3716921	+	0	NA	Intergenic	L1M1|LINE|L1	48477	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.004190	0.333333	
chunk0197_28_1	chr8	117998989	117999234	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	112708	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.008163	0.341463	
chunk0173_447_1	chr6	151689353	151690202	+	0	NA	promoter-TSS (NM_001122742)	promoter-TSS (NM_001122742)	-719	NM_001122742	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.005889	0.351765	
chunk0134_151_1	chr3	177706655	177706854	+	0	NA	intron (NR_047568, intron 3 of 3)	LTR88b|LTR|Gypsy?	-110111	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.005025	0.475000	
chunk0197_42_1	chr8	118283490	118283689	+	0	NA	intron (NR_109794, intron 4 of 4)	intron (NR_109794, intron 4 of 4)	-171770	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.005025	0.445000	
chunk0182_437_1	chr7	101608613	101609280	+	0	NA	Intergenic	Intergenic	20350	NM_138403	93408	Hs.247831	NM_138403	ENSG00000106436	MYL10	MYLC2PL|PLRLC	myosin light chain 10	protein-coding	0.016492	0.598802	
chunk0048_219_1	chr12	81427558	81427944	+	0	NA	intron (NM_001220478, intron 3 of 28)	intron (NM_001220478, intron 3 of 28)	-58337	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.007772	0.297158	
chunk0066_84_1	chr15	29707332	29707628	+	0	NA	intron (NM_175610, intron 24 of 26)	intron (NM_175610, intron 24 of 26)	114068	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.027027	0.555556	
chunk0006_439_1	chr1	76587196	76587645	+	0	NA	intron (NM_152996, intron 3 of 4)	intron (NM_152996, intron 3 of 4)	-280081	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.020045	0.502222	
chunk0138_231_1	chr4	39320376	39320847	+	0	NA	exon (NM_001204747, exon 9 of 25)	exon (NM_001204747, exon 9 of 25)	45770	NM_001204747	5981	Hs.507475	NM_002913	ENSG00000035928	RFC1	A1|CANVAS|MHCBFB|PO-GA|RECC1|RFC|RFC140	replication factor C subunit 1	protein-coding	0.000000	0.338983	
chunk0042_306_1	chr12	7932983	7933509	+	0	NA	intron (NM_006931, intron 2 of 9)	intron (NM_006931, intron 2 of 9)	3050	NM_006931	6515	Hs.419240	NM_006931	ENSG00000059804	SLC2A3	GLUT3	solute carrier family 2 member 3	protein-coding	0.028517	0.462998	188(AAGAACAGACTGTTAC,-,0.00),189(AGAACAGACTGTTACA,+,0.00)
chunk0166_363_1	chr6	51463283	51463510	+	0	NA	Intergenic	Intergenic	-158474	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.004405	0.346491	
chunk0192_292_1	chr8	66531052	66532017	+	0	NA	Intergenic	Intergenic	38278	NM_152765	254778	Hs.268869	NM_152765	ENSG00000169085	VXN	C8orf46	vexin	protein-coding	0.008290	0.401656	661(AAAACAAATTGTTCTG,+,0.00)
chunk0024_156_1	chr10	35452284	35452636	+	0	NA	intron (NM_001282853, intron 2 of 10)	intron (NM_001282853, intron 2 of 10)	115586	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.002841	0.342776	
chunk0015_301_1	chr1	188876033	188876509	+	0	NA	Intergenic	Intergenic	1432643	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008403	0.297694	
chunk0171_244_1	chr6	127132434	127133071	+	0	NA	intron (NM_032784, intron 1 of 4)	intron (NM_032784, intron 1 of 4)	13849	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.001570	0.335423	
chunk0037_137_1	chr11	73140661	73141184	+	0	NA	intron (NM_014824, intron 1 of 19)	intron (NM_014824, intron 1 of 19)	1176	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.045889	0.562977	
chunk0029_52_1	chr10	96416481	96416936	+	0	NA	intron (NM_012465, intron 7 of 20)	intron (NM_012465, intron 7 of 20)	-57343	NM_033207	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.013187	0.489035	
chunk0128_76_1	chr3	105387135	105387497	+	0	NA	intron (NM_001627, intron 1 of 15)	intron (NM_001627, intron 1 of 15)	20603	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.005525	0.363636	
chunk0028_236_1	chr10	89911140	89911339	+	0	NA	Intergenic	L1PA13|LINE|L1	46134	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.015075	0.595000	
chunk0201_228_1	chr9	37515793	37516151	+	0	NA	exon (NM_012166, exon 10 of 11)	exon (NM_012166, exon 10 of 11)	30037	NM_001282766	64425	Hs.591087	NM_022490	ENSG00000137054	POLR1E	PAF53|PRAF1	RNA polymerase I subunit E	protein-coding	0.030726	0.557103	
chunk0208_420_1	chrX	29675283	29675498	+	0	NA	intron (NM_014271, intron 6 of 10)	intron (NM_014271, intron 6 of 10)	101112	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.004651	0.416667	
chunk0186_343_1	chr7	143370335	143370786	+	0	NA	Intergenic	MER41A|LTR|ERV1	-7813	NM_001278297	9715	Hs.648908	NM_014690	ENSG00000159784	FAM131B	-	family with sequence similarity 131 member B	protein-coding	0.017738	0.466814	
chunk0178_252_1	chr7	36261092	36261511	+	0	NA	intron (NM_030636, intron 3 of 7)	intron (NM_030636, intron 3 of 7)	105872	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.004773	0.445238	
chunk0076_81_1	chr16	63764922	63765136	+	0	NA	Intergenic	Intergenic	1357108	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.004673	0.316279	
chunk0198_471_1	chr8	144828471	144828670	+	0	NA	intron (NM_003416, intron 1 of 4)	L2c|LINE|L2	1052	NM_001282796	7553	Hs.493218	NM_003416	ENSG00000147789	ZNF7	HF.16|KOX4|zf30	zinc finger protein 7	protein-coding	0.015075	0.520000	
chunk0086_86_1	chr18	13549207	13549671	+	0	NA	intron (NM_181481, intron 3 of 5)	intron (NM_181481, intron 3 of 5)	-61675	NR_039752	100616130		NR_039752	ENSG00000263527	MIR4526	mir-4526	microRNA 4526	ncRNA	0.010776	0.453763	
chunk0177_425_1	chr7	27784264	27784823	+	0	NA	intron (NM_001206901, intron 5 of 16)	intron (NM_001206901, intron 5 of 16)	44448	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.007156	0.369643	
chunk0150_313_1	chr5	38022741	38022955	+	0	NA	Intergenic	Intergenic	149423	NM_001278094	100861519	Hs.536820	NM_001278094		GDNF-AS1	GDNFOS	GDNF antisense RNA 1	ncRNA	0.018692	0.451163	
chunk0201_309_1	chr9	42940887	42941195	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	152641	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.006494	0.446602	196(TGGAACAACCTGTGCT,-,0.00),197(GGAACAACCTGTGCTC,+,0.00)
chunk0120_293_1	chr3	9890429	9890765	+	0	NA	promoter-TSS (NM_032492)	promoter-TSS (NM_032492)	10	NM_032492	84522	Hs.24054	NM_032492	ENSG00000171135	JAGN1	GL009|SCN6	jagunal homolog 1	protein-coding	0.104167	0.667656	
chunk0030_37_1	chr10	111525620	111526154	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	448855	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.000000	0.345794	
chunk0032_97_1	chr11	3634405	3634643	+	0	NA	intron (NR_002720, intron 3 of 6)	intron (NR_002720, intron 3 of 6)	7792	NM_053017	116969	Hs.125680	NM_053017	ENSG00000167311	ART5	ARTC5	ADP-ribosyltransferase 5	protein-coding	0.004202	0.468619	
chunk0148_340_1	chr5	14341067	14341352	+	0	NA	intron (NM_007118, intron 11 of 56)	intron (NM_007118, intron 11 of 56)	197489	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.003509	0.412587	
chunk0023_279_1	chr10	28285829	28286116	+	0	NA	Intergenic	Intergenic	3378	NR_107053	102465880		NR_107053	ENSG00000275036	MIR8086	hsa-mir-8086	microRNA 8086	ncRNA	0.010453	0.357639	
chunk0021_255_1	chr1	243411302	243411974	+	0	NA	intron (NM_006642, intron 13 of 17)	L1ME1|LINE|L1	65462	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.008929	0.402675	
chunk0017_280_1	chr1	209801857	209802779	+	0	NA	intron (NM_006147, intron 1 of 8)	intron (NM_006147, intron 1 of 8)	3857	NM_006147	3664	Hs.591415	NM_006147	ENSG00000117595	IRF6	LPS|OFC6|PIT|PPS|PPS1|VWS|VWS1	interferon regulatory factor 6	protein-coding	0.006508	0.438787	
chunk0052_343_1	chr12	126528992	126529224	+	0	NA	Intergenic	Intergenic	86627	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.000000	0.321888	
chunk0092_153_1	chr19	29329617	29329838	+	0	NA	intron (NR_040029, intron 9 of 9)	intron (NR_040029, intron 9 of 9)	-116498	NM_006003	7386	Hs.743307	NM_006003	ENSG00000169021	UQCRFS1	RIP1|RIS1|RISP|UQCR5	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding	0.013575	0.540541	
chunk0085_198_1	chr18	6556360	6556670	+	0	NA	intron (NR_120518, intron 2 of 5)	MIR|SINE|MIR	45099	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.006452	0.334405	
chunk0053_71_1	chr13	28299773	28300023	+	0	NA	TTS (NM_002019)	TTS (NM_002019)	-160724	NR_029383	100288730	Hs.123191	NR_029383		PAN3-AS1	-	PAN3 antisense RNA 1	ncRNA	0.000000	0.370518	
chunk0073_105_1	chr16	4538651	4538850	+	0	NA	promoter-TSS (NM_001199056)	promoter-TSS (NM_001199056)	65	NM_001199056	29965	Hs.654653	NM_013399	ENSG00000089486	CDIP1	C16orf5|CDIP|I1|LITAFL	cell death inducing p53 target 1	protein-coding	0.105528	0.710000	
chunk0100_200_1	chr2	111185535	111186048	+	0	NA	Intergenic	Intergenic	64877	NM_001204106	10018	Hs.469658	NM_006538	ENSG00000153094	BCL2L11	BAM|BIM|BOD	BCL2 like 11	protein-coding	0.019493	0.529183	223(GGGAACTAAGTGTTCT,-,0.00),224(GGAACTAAGTGTTCTG,+,0.00)
chunk0199_291_1	chr9	6675274	6675565	+	0	NA	Intergenic	Intergenic	-29727	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.013746	0.445205	
chunk0145_183_1	chr4	147760115	147760414	+	0	NA	intron (NM_024605, intron 1 of 22)	MIRc|SINE|MIR	-22331	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.013378	0.416667	
chunk0042_87_1	chr12	2570236	2570849	+	0	NA	intron (NM_001129846, intron 13 of 45)	intron (NM_001129846, intron 13 of 45)	101678	NR_046579	100874235	Hs.667644	NR_046579	ENSG00000256271	CACNA1C-AS2	-	CACNA1C antisense RNA 2	ncRNA	0.016313	0.426710	
chunk0025_244_1	chr10	54503813	54504287	+	0	NA	intron (NM_001142773, intron 2 of 31)	intron (NM_001142773, intron 2 of 31)	103907	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.006329	0.378947	201(AAGAACTGTTAGTTCT,-,0.00),202(AGAACTGTTAGTTCTT,+,0.00)
chunk0197_365_1	chr8	126189025	126189857	+	0	NA	Intergenic	Intergenic	-136054	NR_125421	101927657	Hs.552133	NR_125421	ENSG00000244791	LOC101927657	-	uncharacterized LOC101927657	ncRNA	0.004808	0.357743	
chunk0136_66_1	chr4	1899543	1900260	+	0	NA	promoter-TSS (NM_133334)	promoter-TSS (NM_133334)	-725	NM_133334	7468	Hs.113876	NM_007331	ENSG00000109685	NSD2	KMT3F|KMT3G|MMSET|REIIBP|TRX5|WHS|WHSC1	nuclear receptor binding SET domain protein 2	protein-coding	0.005579	0.481894	563(GGGCACATTCTGAGCC,-,0.00),564(GGCACATTCTGAGCCT,+,0.00)
chunk0170_136_1	chr6	111045718	111046138	+	0	NA	TTS (NR_002932)	TTS (NR_002932)	1626	NR_002932	442245	Hs.551627	NR_002932		GSTM2P1	-	glutathione S-transferase mu 2 pseudogene 1	pseudo	0.002381	0.313539	
chunk0067_96_1	chr15	42107446	42107756	+	0	NA	Intergenic	Intergenic	-13047	NM_178034	283748	Hs.380225	NM_178034	ENSG00000159337	PLA2G4D	cPLA2delta	phospholipase A2 group IVD	protein-coding	0.025806	0.504823	
chunk0093_10_1	chr2	95803	96288	+	0	NA	Intergenic	L1PA7|LINE|L1	-49457	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.000000	0.384774	311(CTGAACAACCTGTTCC,-,0.00),312(TGAACAACCTGTTCCT,+,0.00),395(AAAGACACAATGTACC,-,0.00)
chunk0066_205_1	chr15	33729432	33729631	+	0	NA	intron (NM_001036, intron 47 of 103)	intron (NM_001036, intron 47 of 103)	-239357	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.015075	0.445000	
chunk0152_307_1	chr5	61809818	61810286	+	0	NA	Intergenic	Intergenic	-74354	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.002137	0.445629	
chunk0051_389_1	chr12	121888268	121888879	+	0	NA	promoter-TSS (NM_002813)	promoter-TSS (NM_002813)	38	NM_001171993	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.072013	0.570261	
chunk0104_191_1	chr2	175097103	175097833	+	0	NA	exon (NM_001256090, exon 12 of 15)	exon (NM_001256090, exon 12 of 15)	70241	NR_030630	100126350		NR_030630	ENSG00000215973	MIR933	MIRN933|hsa-mir-933|mir-933	microRNA 933	ncRNA	0.006849	0.363885	
chunk0020_152_1	chr1	233940474	233940917	+	0	NA	intron (NM_173508, intron 2 of 7)	intron (NM_173508, intron 2 of 7)	35983	NM_173508	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.004515	0.353604	
chunk0102_228_1	chr2	148713721	148713920	+	0	NA	intron (NM_015630, intron 2 of 13)	Tigger3b|DNA|TcMar-Tigger	68829	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.000000	0.380000	113(AGGTACACTCTGTGAT,-,0.00)
chunk0003_324_1	chr1	38314565	38315007	+	0	NA	Intergenic	L1MC3|LINE|L1	-100019	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.004525	0.302483	
chunk0173_48_1	chr6	142313393	142313847	+	0	NA	intron (NM_020455, intron 2 of 25)	intron (NM_020455, intron 2 of 25)	11701	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.004405	0.360440	
chunk0197_247_1	chr8	123391936	123392260	+	0	NA	intron (NM_014109, intron 1 of 27)	intron (NM_014109, intron 1 of 27)	4367	NM_014109	29028	Hs.370834	NM_014109	ENSG00000156802	ATAD2	ANCCA|CT137|PRO2000	ATPase family AAA domain containing 2	protein-coding	0.006173	0.406154	
chunk0147_64_1	chr4	172712616	172713099	+	0	NA	intron (NR_125894, intron 1 of 2)	MIR|SINE|MIR	14021	NR_125894	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.002070	0.345041	424(AGGTACACAGTGCTCC,-,0.00),425(GGTACACAGTGCTCCC,+,0.00)
chunk0111_298_1	chr20	31879599	31879836	+	0	NA	intron (NM_001008409, intron 2 of 14)	intron (NM_001008409, intron 2 of 14)	9015	NM_001008409	164395	Hs.712915	NM_001008409	ENSG00000131044	TTLL9	C20orf125	tubulin tyrosine ligase like 9	protein-coding	0.067511	0.642857	
chunk0108_216_1	chr2	233391129	233391634	+	0	NA	intron (NM_003648, intron 2 of 28)	L1ME4a|LINE|L1	3227	NM_003648	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.003960	0.347826	
chunk0146_436_1	chr4	169593056	169593643	+	0	NA	intron (NM_001199399, intron 5 of 32)	MER58A|DNA|hAT-Charlie	19278	NM_001199400	4750	Hs.481181	NM_012224	ENSG00000137601	NEK1	ALS24|NY-REN-55|SRPS2|SRPS2A|SRTD6	NIMA related kinase 1	protein-coding	0.001704	0.362245	
chunk0087_94_1	chr18	32405576	32405992	+	0	NA	intron (NM_001242409, intron 1 of 5)	MLT1J1|LTR|ERVL-MaLR	64700	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.004808	0.419664	
chunk0078_193_1	chr17	5184561	5185018	+	0	NA	intron (NM_032530, intron 1 of 1)	LTR41C|LTR|ERVL	7094	NM_032530	84622	Hs.658402	NM_032530	ENSG00000180626	ZNF594	-	zinc finger protein 594	protein-coding	0.008753	0.425764	
chunk0026_422_1	chr10	70803710	70804058	+	0	NA	Intergenic	Intergenic	-12064	NM_003901	8879	Hs.499984	NM_003901	ENSG00000166224	SGPL1	NPHS14|S1PL|SPL	sphingosine-1-phosphate lyase 1	protein-coding	0.005747	0.398281	
chunk0098_141_1	chr2	69650303	69650502	+	0	NA	Intergenic	L2a|LINE|L2	-6557	NM_014911	22848	Hs.468878	NM_014911	ENSG00000115977	AAK1	-	AP2 associated kinase 1	protein-coding	0.000000	0.350000	
chunk0003_458_1	chr1	41688920	41689408	+	0	NA	intron (NM_001127714, intron 1 of 7)	L2c|LINE|L2	-204481	NR_126098	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.022541	0.478528	
chunk0086_307_1	chr18	24051120	24051795	+	0	NA	intron (NM_001135993, intron 1 of 13)	intron (NM_001135993, intron 1 of 13)	-35997	NR_110796	102724246	Hs.569872	NR_110796	ENSG00000264745	TTC39C-AS1	-	TTC39C antisense RNA 1	ncRNA	0.013333	0.477811	
chunk0187_31_1	chr8	848842	849163	+	0	NA	intron (NR_073397, intron 2 of 3)	intron (NR_073397, intron 2 of 3)	111397	NR_073397	9228	Hs.113287	NM_004745	ENSG00000198010	DLGAP2	C8orf68|DAP2|ERICH1-AS1|SAPAP2	DLG associated protein 2	protein-coding	0.049844	0.521739	
chunk0044_248_1	chr12	31868970	31869265	+	0	NA	Intergenic	Intergenic	-76876	NM_001013699	440093	Hs.448697	NM_001013699	ENSG00000188375	H3F3C	H3.5	H3 histone family member 3C	protein-coding	0.003390	0.435811	
chunk0001_387_1	chr1	10596945	10597289	+	0	NA	intron (NM_004565, intron 3 of 8)	intron (NM_004565, intron 3 of 8)	122171	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.023256	0.463768	131(CAGCACAGTCTGTAAC,-,0.00)
chunk0180_436_1	chr7	76568808	76569108	+	0	NA	intron (NR_029411, intron 2 of 2)	L4_A_Mam|LINE|RTE-X	19617	NR_029411	100133091	Hs.712837	NR_029411	ENSG00000205485	LOC100133091	-	uncharacterized LOC100133091	ncRNA	0.000000	0.308970	
chunk0040_307_1	chr11	117367900	117368136	+	0	NA	intron (NM_014956, intron 8 of 32)	intron (NM_014956, intron 8 of 32)	40163	NM_014956	22897	Hs.504009	NM_014956	ENSG00000110274	CEP164	NPHP15	centrosomal protein 164	protein-coding	0.008475	0.341772	
chunk0178_384_1	chr7	40273725	40274240	+	0	NA	intron (NM_001193312, intron 7 of 12)	LTR80A|LTR|ERVL	139006	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.003883	0.350775	
chunk0008_42_1	chr1	88979698	88980350	+	0	NA	3' UTR (NM_001162536, exon 3 of 3)	3' UTR (NM_001162536, exon 3 of 3)	12936	NM_019610	494115	Hs.481898	NM_019610	ENSG00000213516	RBMXL1	RBM1	RBMX like 1	protein-coding	0.003067	0.376723	
chunk0081_274_1	chr17	43864385	43864623	+	0	NA	TTS (NM_145273)	TTS (NM_145273)	17356	NM_001168322	146894	Hs.147313	NM_145273	ENSG00000161649	CD300LG	CLM-9|CLM9|NEPMUCIN|TREM-4|TREM4	CD300 molecule like family member g	protein-coding	0.004202	0.560669	80(AGGCACTGTGTGTGCC,-,0.00),81(GGCACTGTGTGTGCCA,+,0.00)
chunk0083_405_1	chr17	71993537	71994166	+	0	NA	Intergenic	L1P4e|LINE|L1	32128	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.009539	0.511111	
chunk0094_339_1	chr2	9262565	9262775	+	0	NA	intron (NM_003887, intron 1 of 27)	intron (NM_003887, intron 1 of 27)	55905	NM_003887	8853	Hs.555902	NM_003887	ENSG00000151693	ASAP2	AMAP2|CENTB3|DDEF2|PAG3|PAP|Pap-alpha|SHAG1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding	0.004762	0.464455	
chunk0070_190_1	chr15	72033210	72033735	+	0	NA	intron (NM_006901, intron 2 of 41)	L1ME1|LINE|L1	-80786	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.005714	0.306084	144(CAGTACATAATGTACT,-,0.00),145(AGTACATAATGTACTA,+,0.00)
chunk0005_362_1	chr1	61391707	61392165	+	0	NA	intron (NM_001145511, intron 7 of 10)	intron (NM_001145511, intron 7 of 10)	-138418	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.008734	0.440087	
chunk0108_203_1	chr2	232655172	232655851	+	0	NA	intron (NM_001308395, intron 2 of 4)	intron (NM_001308395, intron 2 of 4)	22014	NM_001308395	80303	Hs.516769	NM_025202	ENSG00000115468	EFHD1	MST133|MSTP133|PP3051|SWS2	EF-hand domain family member D1	protein-coding	0.010309	0.495588	
chunk0088_2_1	chr18	43002884	43003198	+	0	NA	intron (NM_001272077, intron 2 of 5)	MLT1D|LTR|ERVL-MaLR	112651	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.003185	0.457143	
chunk0076_373_1	chr16	72188263	72188976	+	0	NA	Intergenic	Intergenic	-16169	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.012623	0.459384	370(AGGTACAGTGTGTGCC,-,0.00),371(GGTACAGTGTGTGCCA,+,0.00)
chunk0115_174_1	chr21	25582674	25583252	+	0	NA	non-coding (NR_024092, exon 1 of 1)	non-coding (NR_024092, exon 1 of 1)	261	NR_024092	282566	Hs.384586	NR_024092	ENSG00000260583	LINC00515	C21orf71|PRED21	long intergenic non-protein coding RNA 515	ncRNA	0.006920	0.416235	
chunk0043_74_1	chr12	14408666	14408865	+	0	NA	intron (NM_181352, intron 1 of 14)	intron (NM_181352, intron 1 of 14)	23701	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.000000	0.285000	
chunk0210_61_1	chrX	69425076	69425276	+	0	NA	Intergenic	Charlie17a|DNA|hAT-Charlie	-80059	NM_015686	27112	Hs.87619	NM_015686	ENSG00000130054	FAM155B	CXorf63|TED|TMEM28|bB57D9.1	family with sequence similarity 155 member B	protein-coding	0.005000	0.522388	
chunk0139_157_1	chr4	53734271	53734858	+	0	NA	TTS (NR_125918)	TTS (NR_125918)	38663	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.006814	0.343537	310(GAGCACACCATGACCC,-,0.00)
chunk0030_96_1	chr10	112427580	112427871	+	0	NA	3' UTR (NM_016234, exon 21 of 21)	3' UTR (NM_016234, exon 21 of 21)	19234	NM_022494	64429	Hs.196990	NM_022494	ENSG00000023041	ZDHHC6	DHHC-6|ZNF376	zinc finger DHHC-type containing 6	protein-coding	0.000000	0.359589	
chunk0081_332_1	chr17	46286728	46286980	+	0	NA	Intergenic	Intergenic	-8277	NM_014834	9884	Hs.579108	NM_014834	ENSG00000176681	LRRC37A	LRRC37	leucine rich repeat containing 37A	protein-coding	0.003968	0.387352	
chunk0032_36_1	chr11	1090935	1091230	+	0	NA	intron (NM_002457, intron 26 of 59)	(CATG)n|Simple_repeat|Simple_repeat	16207	NM_002457	4583	Hs.315	NM_002457		MUC2	MLP|MUC-2|SMUC	mucin 2, oligomeric mucus/gel-forming	protein-coding	0.030508	0.530405	48(GAGCACACAGTGTACA,-,0.00),49(AGCACACAGTGTACAC,+,0.00)
chunk0162_190_1	chr6	3865327	3865535	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	16033	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.009615	0.459330	
chunk0205_117_1	chr9	107819633	107820303	+	0	NA	Intergenic	Intergenic	-330248	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.016418	0.427720	
chunk0018_436_1	chr1	222916149	222916532	+	0	NA	intron (NM_032890, intron 2 of 9)	intron (NM_032890, intron 2 of 9)	101251	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.007833	0.432292	
chunk0049_435_1	chr12	98265005	98265341	+	0	NA	Intergenic	L2b|LINE|L2	191972	NR_033801	121456	Hs.620643	NR_033801	ENSG00000227825	SLC9A7P1	-	solute carrier family 9 member 7 pseudogene 1	pseudo	0.002976	0.338279	
chunk0045_394_1	chr12	52650879	52651314	+	0	NA	intron (NM_000423, intron 1 of 8)	intron (NM_000423, intron 1 of 8)	1079	NM_000423	3849	Hs.707	NM_000423	ENSG00000172867	KRT2	CK-2e|K2e|KRT2A|KRT2E|KRTE	keratin 2	protein-coding	0.013793	0.451835	
chunk0126_169_1	chr3	77917370	77917727	+	0	NA	Intergenic	LTR24C|LTR|ERV1	819536	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.008403	0.343575	
chunk0116_219_1	chr21	37658903	37659466	+	0	NA	intron (NM_002240, intron 3 of 3)	intron (NM_002240, intron 3 of 3)	238884	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.010657	0.471631	317(CAGATCATGTTGTTCC,-,0.00)
chunk0085_356_1	chr18	9221309	9221946	+	0	NA	intron (NM_015208, intron 7 of 12)	intron (NM_015208, intron 7 of 12)	84064	NM_001204056	23253	Hs.464585	NM_015208	ENSG00000101745	ANKRD12	ANCO-2|ANCO1|GAC-1|Nbla00144	ankyrin repeat domain 12	protein-coding	0.007849	0.368339	
chunk0008_365_1	chr1	96703291	96703959	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-17980	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.001497	0.399103	424(CAGGACTTATTGTACC,-,0.00),425(AGGACTTATTGTACCT,+,0.00)
chunk0200_423_1	chr9	28713264	28713573	+	0	NA	intron (NM_001258282, intron 2 of 6)	MLT1J1|LTR|ERVL-MaLR	5887	NM_152570	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.009709	0.370968	
chunk0113_149_1	chr20	52591455	52591918	+	0	NA	Intergenic	Intergenic	-29152	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.008639	0.435345	
chunk0159_199_1	chr5	140400688	140400887	+	0	NA	Intergenic	CpG	-1027	NM_024668	54882	Hs.594084	NM_017747	ENSG00000131503	ANKHD1	MASK|MASK1|PP2500|VBARP	ankyrin repeat and KH domain containing 1	protein-coding	0.105528	0.675000	
chunk0026_288_1	chr10	67697936	67698150	+	0	NA	Intergenic	Intergenic	-1852	NM_013266	29119	Hs.21375	NM_013266	ENSG00000183230	CTNNA3	ARVD13|VR22	catenin alpha 3	protein-coding	0.004673	0.432558	
chunk0140_343_1	chr4	73917962	73918440	+	0	NA	Intergenic	Intergenic	48809	NR_046035	2919	Hs.789	NM_001511	ENSG00000163739	CXCL1	FSP|GRO1|GROa|MGSA|MGSA-a|NAP-3|SCYB1	C-X-C motif chemokine ligand 1	protein-coding	0.004184	0.384134	
chunk0051_402_1	chr12	122068169	122068369	+	0	NA	Intergenic	Intergenic	-10459	NM_014938	22877	Hs.437153	NM_014938	ENSG00000175727	MLXIP	MIR|MONDOA|bHLHe36	MLX interacting protein	protein-coding	0.015000	0.477612	
chunk0109_197_1	chr20	5096653	5096888	+	0	NA	Intergenic	Intergenic	16317	NM_001009923	29058	Hs.472024	NM_014145	ENSG00000089063	TMEM230	C20orf30|HSPC274|dJ1116H23.2.1	transmembrane protein 230	protein-coding	0.008511	0.504237	131(AGGAACATGGTGTCCT,-,0.00),132(GGAACATGGTGTCCTG,+,0.00)
chunk0172_137_1	chr6	135327142	135327765	+	0	NA	intron (NM_017651, intron 23 of 27)	intron (NM_017651, intron 23 of 27)	88293	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.008026	0.445513	
chunk0128_290_1	chr3	110946696	110947364	+	0	NA	Intergenic	L1M2|LINE|L1	122929	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.002994	0.297459	
chunk0067_37_1	chr15	40511688	40511887	+	0	NA	Intergenic	CpG	20763	NR_002208	359821	Hs.678598	NR_002208		MRPL42P5	-	mitochondrial ribosomal protein L42 pseudogene 5	pseudo	0.140704	0.765000	
chunk0042_313_1	chr12	8350960	8351441	+	0	NA	Intergenic	L1M2|LINE|L1	39552	NR_024420	389634	Hs.434403	NM_001012988	ENSG00000226091	LINC00937	-	long intergenic non-protein coding RNA 937	ncRNA	0.010395	0.334025	
chunk0089_273_1	chr18	62768153	62768760	+	0	NA	intron (NM_194449, intron 1 of 16)	intron (NM_194449, intron 1 of 16)	53017	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.004942	0.353618	222(AAGTACAGCATGAACT,-,0.00),223(AGTACAGCATGAACTT,+,0.00)
chunk0016_222_1	chr1	199439504	199440025	+	0	NA	Intergenic	L1MA3|LINE|L1	-420800	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.005758	0.323755	
chunk0158_310_1	chr5	132450585	132450920	+	0	NA	intron (NR_045116, intron 3 of 3)	L1ME3G|LINE|L1	39979	NR_045116									0.002985	0.315476	
chunk0150_306_1	chr5	37738660	37739094	+	0	NA	intron (NM_018034, intron 17 of 17)	intron (NM_018034, intron 17 of 17)	95945	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.004608	0.340230	
chunk0097_216_1	chr2	51438147	51438356	+	0	NA	Intergenic	L1MC2|LINE|L1	-405715	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.009569	0.338095	
chunk0058_249_1	chr14	25667703	25668110	+	0	NA	Intergenic	Intergenic	-617609	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004914	0.345588	
chunk0194_297_1	chr8	87895954	87896270	+	0	NA	Intergenic	Intergenic	-22044	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.003165	0.362776	
chunk0135_48_1	chr3	185629954	185630288	+	0	NA	3' UTR (NM_021627, exon 17 of 17)	3' UTR (NM_021627, exon 17 of 17)	43878	NM_021627	59343	Hs.401388	NM_021627	ENSG00000163904	SENP2	AXAM2|SMT3IP2	SUMO specific peptidase 2	protein-coding	0.008982	0.402985	
chunk0107_141_1	chr2	214919436	214919662	+	0	NA	intron (NR_110292, intron 2 of 3)	L1MB3|LINE|L1	109320	NR_110292	101928103	Hs.665619	NR_110292	ENSG00000229267	SNHG31	-	small nucleolar RNA host gene 31	ncRNA	0.004425	0.392070	
chunk0053_335_1	chr13	34432207	34432406	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	208379	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.005025	0.350000	
chunk0047_298_1	chr12	73657985	73658489	+	0	NA	Intergenic	LTR44|LTR|ERV1	499047	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.001984	0.324752	
chunk0060_137_1	chr14	44939065	44939264	+	0	NA	intron (NM_001308112, intron 2 of 4)	MSTD-int|LTR|ERVL-MaLR	21968	NM_001308112	54813	Hs.550906	NM_017658	ENSG00000179454	KLHL28	BTBD5	kelch like family member 28	protein-coding	0.000000	0.540000	
chunk0015_444_1	chr1	191939821	191940200	+	0	NA	Intergenic	L1PA7|LINE|L1	-218452	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.005277	0.378947	
chunk0029_140_1	chr10	99293299	99293782	+	0	NA	Intergenic	Intergenic	-35559	NM_020348	26507	Hs.274579	NM_020348	ENSG00000119946	CNNM1	ACDP1|CLP-1	cyclin and CBS domain divalent metal cation transport mediator 1	protein-coding	0.004141	0.293388	237(AAGAACATTTTGTTCT,-,0.00),238(AGAACATTTTGTTCTT,+,0.00)
chunk0177_97_1	chr7	21945770	21946274	+	0	NA	promoter-TSS (NM_001127371)	promoter-TSS (NM_001127371)	-98	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.105159	0.702970	
chunk0184_432_1	chr7	123011842	123012283	+	0	NA	Intergenic	MIR|SINE|MIR	-16362	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.004535	0.341629	
chunk0187_125_1	chr7	149147366	149147807	+	0	NA	5' UTR (NM_170686, exon 1 of 6)	5' UTR (NM_170686, exon 1 of 6)	118	NM_170686	57541	Hs.632032	NM_020781	ENSG00000197024	ZNF398	P51|P71|ZER6	zinc finger protein 398	protein-coding	0.154195	0.791855	
chunk0008_247_1	chr1	94406347	94406943	+	0	NA	Intergenic	Intergenic	-11732	NM_002858	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.008389	0.405360	
chunk0016_340_1	chr1	201861594	201861958	+	0	NA	intron (NM_018085, intron 13 of 23)	intron (NM_018085, intron 13 of 23)	-1597	NR_106797	102466724		NR_106797	ENSG00000277681	MIR6739	hsa-mir-6739	microRNA 6739	ncRNA	0.008242	0.383562	
chunk0054_346_1	chr13	49528431	49529040	+	0	NA	3' UTR (NM_001040444, exon 11 of 11)	3' UTR (NM_001040444, exon 11 of 11)	32343	NM_001040444	51131	Hs.369039	NM_001040443	ENSG00000136147	PHF11	APY|BCAP|IGEL|IGER|IGHER|NY-REN-34|NYREN34	PHD finger protein 11	protein-coding	0.004926	0.367213	
chunk0196_419_1	chr8	116113012	116113528	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	211789	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.005814	0.408124	
chunk0179_229_1	chr7	47906860	47907064	+	0	NA	intron (NM_138295, intron 9 of 56)	intron (NM_138295, intron 9 of 56)	41512	NM_138295	168507	Hs.195979	NM_138295	ENSG00000158683	PKD1L1	HTX8|PRO19563	polycystin 1 like 1, transient receptor potential channel interacting	protein-coding	0.009804	0.360976	
chunk0138_146_1	chr4	37054991	37055440	+	0	NA	Intergenic	Intergenic	186776	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.006682	0.344444	
chunk0057_158_1	chr13	100533759	100533958	+	0	NA	promoter-TSS (NM_033110)	promoter-TSS (NM_033110)	-56	NM_033110	87769	Hs.350868	NM_033110	ENSG00000134864	GGACT	A2LD1	gamma-glutamylamine cyclotransferase	protein-coding	0.040201	0.575000	
chunk0036_324_1	chr11	66347743	66347999	+	0	NA	promoter-TSS (NM_006876)	promoter-TSS (NM_006876)	-181	NM_006876	11041	Hs.8526	NM_006876	ENSG00000174684	B4GAT1	B3GN-T1|B3GNT1|B3GNT6|BETA3GNTI|MDDGA13|iGAT|iGNT	beta-1,4-glucuronyltransferase 1	protein-coding	0.160156	0.758755	
chunk0179_308_1	chr7	50342733	50343063	+	0	NA	intron (NM_001291840, intron 2 of 2)	intron (NM_001291840, intron 2 of 2)	23850	NM_001291840	10320	Hs.435949	NM_006060	ENSG00000185811	IKZF1	CVID13|Hs.54452|IK1|IKAROS|LYF1|LyF-1|PPP1R92|PRO0758|ZNFN1A1	IKAROS family zinc finger 1	protein-coding	0.021212	0.501511	125(GGAGACAGCGTGTGCT,-,0.00),126(GAGACAGCGTGTGCTC,+,0.00),162(GAGTACACCATGATCC,-,0.00)
chunk0030_128_1	chr10	113341819	113342164	+	0	NA	Intergenic	L2|LINE|L2	-208840	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.005797	0.534682	
chunk0028_141_1	chr10	86630478	86630853	+	0	NA	Intergenic	L1M5|LINE|L1	-23892	NM_033282	94233	Hs.283922	NM_033282	ENSG00000122375	OPN4	MOP	opsin 4	protein-coding	0.005333	0.351064	
chunk0035_420_1	chr11	57121574	57122183	+	0	NA	Intergenic	MER21C|LTR|ERVL	-59869	NM_001005210	219527	Hs.199853	NM_001005210	ENSG00000183908	LRRC55	-	leucine rich repeat containing 55	protein-coding	0.004926	0.450820	
chunk0051_167_1	chr12	116010081	116010352	+	0	NA	intron (NM_015335, intron 9 of 30)	intron (NM_015335, intron 9 of 30)	138438	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.003690	0.400735	
chunk0069_320_1	chr15	65892637	65892836	+	0	NA	TTS (NM_004663)	TTS (NM_004663)	23277	NM_001206836	8766	Hs.321541	NM_004663	ENSG00000103769	RAB11A	YL8	RAB11A, member RAS oncogene family	protein-coding	0.000000	0.475000	
chunk0079_212_1	chr17	14794403	14794641	+	0	NA	Intergenic	L2b|LINE|L2	-236453	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.004202	0.384937	
chunk0158_63_1	chr5	126104917	126105348	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-74445	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.002320	0.405093	
chunk0051_176_1	chr12	116108691	116109122	+	0	NA	intron (NM_015335, intron 3 of 30)	intron (NM_015335, intron 3 of 30)	39748	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.000000	0.312500	223(AGGTACATGGTGTCCT,-,0.00),224(GGTACATGGTGTCCTG,+,0.00)
chunk0204_24_1	chr9	92332708	92333282	+	0	NA	intron (NM_001012267, intron 2 of 7)	intron (NM_001012267, intron 2 of 7)	-7401	NM_017948	55035	Hs.442199	NM_017948	ENSG00000198000	NOL8	C9orf34|NOP132|bA62C3.3|bA62C3.4	nucleolar protein 8	protein-coding	0.003484	0.389565	
chunk0017_416_1	chr1	213070306	213070907	+	0	NA	intron (NM_001136138, intron 1 of 13)	MER57B1|LTR|ERV1	19373	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.003328	0.328904	
chunk0046_271_1	chr12	61282975	61283553	+	0	NA	Intergenic	Intergenic	909575	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.005190	0.390328	
chunk0007_290_1	chr1	83998589	83998889	+	0	NA	intron (NM_024686, intron 1 of 20)	CpG	411	NM_024686	79739	Hs.445826	NM_024686	ENSG00000137941	TTLL7	-	tubulin tyrosine ligase like 7	protein-coding	0.063333	0.644518	
chunk0103_66_1	chr2	159946279	159946809	+	0	NA	3' UTR (NM_001007267, exon 27 of 27)	3' UTR (NM_001007267, exon 27 of 27)	-41788	NM_001198760	100526664	Hs.153563	NM_001198759	ENSG00000248672	LY75-CD302	CD205|CLEC13B|DEC-205|LY75|Ly-75|gp200-MR6	LY75-CD302 readthrough	protein-coding	0.001887	0.333333	245(GTGAACACAAAGTTCC,-,0.00),246(TGAACACAAAGTTCCA,+,0.00)
chunk0022_153_1	chr10	12512754	12513066	+	0	NA	intron (NM_020397, intron 1 of 9)	intron (NM_020397, intron 1 of 9)	-65843	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.025641	0.485623	
chunk0041_447_1	chr11	134823892	134824199	+	0	NA	Intergenic	Intergenic	387563	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.016287	0.512987	
chunk0039_296_1	chr11	102835589	102835894	+	0	NA	TTS (NM_002422)	TTS (NM_002422)	7948	NM_002422	4314	Hs.375129	NM_002422	ENSG00000149968	MMP3	CHDS6|MMP-3|SL-1|STMY|STMY1|STR1	matrix metallopeptidase 3	protein-coding	0.006557	0.424837	
chunk0125_25_1	chr3	62159698	62160302	+	0	NA	intron (NM_002841, intron 7 of 29)	intron (NM_002841, intron 7 of 29)	158947	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.011589	0.424793	285(TAGCACAGAATGTTCA,-,0.00),286(AGCACAGAATGTTCAT,+,0.00)
chunk0127_365_1	chr3	101779622	101780504	+	0	NA	intron (NM_001134456, intron 1 of 7)	intron (NM_001134456, intron 1 of 7)	621	NM_001134456	91775	Hs.595933	NM_145037	ENSG00000144815	NXPE3	FAM55C|MST115|MSTP115	neurexophilin and PC-esterase domain family member 3	protein-coding	0.029478	0.481314	
chunk0044_303_1	chr12	32920443	32921083	+	0	NA	Intergenic	Intergenic	-23917	NM_004572	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.014063	0.375975	
chunk0069_242_1	chr15	64117988	64118242	+	0	NA	intron (NM_148955, intron 2 of 12)	intron (NM_148955, intron 2 of 12)	22231	NM_001242933	6642	Hs.188634	NM_003099	ENSG00000028528	SNX1	HsT17379|VPS5	sorting nexin 1	protein-coding	0.003937	0.403922	
chunk0149_404_1	chr5	29011271	29011775	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-53721	NR_109948	101929645	Hs.531878	NR_109948		LOC101929645	-	uncharacterized LOC101929645	ncRNA	0.001984	0.259406	
chunk0129_291_1	chr3	123497964	123498222	+	0	NA	intron (NM_198402, intron 6 of 6)	intron (NM_198402, intron 6 of 6)	-49548	NM_183357	111	Hs.593292	NM_183357	ENSG00000173175	ADCY5	AC5|FDFM	adenylate cyclase 5	protein-coding	0.003876	0.494208	
chunk0041_22_1	chr12	539155	539705	+	0	NA	intron (NM_173593, intron 3 of 19)	intron (NM_173593, intron 3 of 19)	70983	NM_001294345	4815	Hs.655804	NM_016533	ENSG00000171840	NINJ2	-	ninjurin 2	protein-coding	0.009091	0.448276	
chunk0037_250_1	chr11	75454508	75455274	+	0	NA	intron (NM_030792, intron 6 of 16)	intron (NM_030792, intron 6 of 16)	-24262	NM_001039548	283212	Hs.292451	NM_173583	ENSG00000149243	KLHL35	-	kelch like family member 35	protein-coding	0.016971	0.494133	451(TGGAACACTCTGAGCT,-,0.00),452(GGAACACTCTGAGCTC,+,0.00)
chunk0083_120_1	chr17	65022701	65023388	+	0	NA	intron (NM_001282425, intron 2 of 3)	Cheshire|DNA|hAT-Charlie	32730	NM_001282425	10672	Hs.515018	NM_006572	ENSG00000120063	GNA13	G13	G protein subunit alpha 13	protein-coding	0.008734	0.399709	
chunk0156_261_1	chr5	109278853	109279139	+	0	NA	Intergenic	Intergenic	130978	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.006993	0.411150	
chunk0064_133_1	chr14	91403923	91404204	+	0	NA	intron (NM_001080414, intron 3 of 29)	intron (NM_001080414, intron 3 of 29)	13781	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.010676	0.510638	
chunk0093_279_1	chr19	51799489	51799688	+	0	NA	intron (NM_002030, intron 1 of 1)	intron (NM_002030, intron 1 of 1)	4430	NM_002030	2359	Hs.445466	NM_002030	ENSG00000187474	FPR3	FML2_HUMAN|FMLP-R-II|FMLPY|FPRH1|FPRH2|FPRL2|RMLP-R-I	formyl peptide receptor 3	protein-coding	0.030151	0.535000	
chunk0050_220_1	chr12	104677789	104678063	+	0	NA	intron (NM_001173982, intron 2 of 2)	L2a|LINE|L2	86293	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.000000	0.498182	
chunk0144_265_1	chr4	137187992	137188254	+	0	NA	Intergenic	L1MC5a|LINE|L1	344375	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.007634	0.323194	
chunk0212_239_1	chrX	137369086	137369577	+	0	NA	Intergenic	Intergenic	-196856	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.000000	0.335366	
chunk0086_312_1	chr18	24215362	24216264	+	0	NA	intron (NM_001242508, intron 5 of 15)	intron (NM_001242508, intron 5 of 15)	56419	NM_018030	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.009978	0.375415	248(AAGAACTCCGTGTCCC,-,0.00),249(AGAACTCCGTGTCCCC,+,0.00)
chunk0052_329_1	chr12	125908038	125908325	+	0	NA	Intergenic	Intergenic	75193	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.003484	0.378472	
chunk0186_208_1	chr7	139878961	139879598	+	0	NA	intron (NM_001314028, intron 3 of 12)	intron (NM_001314028, intron 3 of 12)	50126	NM_001061	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.010989	0.421630	
chunk0210_330_1	chrX	94698159	94698558	+	0	NA	Intergenic	PABL_B|LTR|ERV1	364868	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.010025	0.385000	224(GGGAACACTTTGTCCA,-,0.00),225(GGAACACTTTGTCCAC,+,0.00)
chunk0076_362_1	chr16	71861245	71861576	+	0	NA	intron (NM_001201556, intron 6 of 6)	intron (NM_001201556, intron 6 of 6)	15419	NM_001137675	342371	Hs.743239	NM_001137675	ENSG00000224470	ATXN1L	BOAT|BOAT1	ataxin 1 like	protein-coding	0.009063	0.493976	180(AAGGACACAACGTTCC,-,0.00),181(AGGACACAACGTTCCA,+,0.00)
chunk0144_347_1	chr4	139534623	139534973	+	0	NA	intron (NM_001306200, intron 2 of 2)	intron (NM_001306200, intron 2 of 2)	21971	NM_001306200	80854	Hs.480792	NM_030648	ENSG00000145391	SETD7	KMT7|SET7|SET7/9|SET9	SET domain containing 7, histone lysine methyltransferase	protein-coding	0.011429	0.418803	
chunk0141_403_1	chr4	88523665	88523864	+	0	NA	promoter-TSS (NM_032906)	promoter-TSS (NM_032906)	37	NM_001042616	84992	Hs.26136	NM_001042616	ENSG00000255072	PIGY	HPMRS6|PIG-Y	phosphatidylinositol glycan anchor biosynthesis class Y	protein-coding	0.095477	0.725000	
chunk0143_411_1	chr4	123386441	123387072	+	0	NA	Intergenic	Kanga1a|DNA|TcMar-Tc2	-10039	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.014263	0.422468	
chunk0198_76_1	chr8	130073373	130073909	+	0	NA	intron (NM_001247996, intron 28 of 30)	L2|LINE|L2	11127	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.020522	0.484171	197(AGGAACTGACAGTGCA,-,0.00),243(AAGTACATAGCGTTCC,-,0.00),244(AGTACATAGCGTTCCA,+,0.00)
chunk0141_177_1	chr4	82721930	82722129	+	0	NA	intron (NM_001037582, intron 1 of 4)	intron (NM_001037582, intron 1 of 4)	31401	NR_030301	693160		NR_030301	ENSG00000207746	MIR575	MIRN575|hsa-mir-575	microRNA 575	ncRNA	0.005025	0.460000	
chunk0098_236_1	chr2	74486984	74487183	+	0	NA	intron (NR_027749, intron 2 of 11)	L2a|LINE|L2	-3853	NM_032779	84865	Hs.430199	NM_032779	ENSG00000135637	CCDC142	-	coiled-coil domain containing 142	protein-coding	0.000000	0.470000	
chunk0204_427_1	chr9	103265964	103266687	+	0	NA	intron (NR_121578, intron 5 of 9)	L1MD|LINE|L1	58708	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.008299	0.330110	
chunk0052_208_1	chr13	25214428	25215065	+	0	NA	Intergenic	MER51E|LTR|ERV1	33414	NR_120427	102723318	Hs.549877	NR_120427		LINC01053	-	long intergenic non-protein coding RNA 1053	ncRNA	0.007849	0.420063	257(AGGCACAGCCAGTTCT,-,0.00),258(GGCACAGCCAGTTCTA,+,0.00)
chunk0097_348_1	chr2	58842499	58842922	+	0	NA	intron (NR_033873, intron 2 of 13)	intron (NR_033873, intron 2 of 13)	321957	NR_033873	400955	Hs.503210	NR_033873	ENSG00000233723	LINC01122	-	long intergenic non-protein coding RNA 1122	ncRNA	0.007092	0.393868	
chunk0002_327_1	chr1	24384573	24385265	+	0	NA	intron (NM_178122, intron 2 of 7)	MIRb|SINE|MIR	28853	NM_178122	90529	Hs.403187	NM_178122	ENSG00000001460	STPG1	C1orf201|MAPO2	sperm tail PG-rich repeat containing 1	protein-coding	0.014451	0.497835	
chunk0122_292_1	chr3	36175500	36175713	+	0	NA	Intergenic	L1M1|LINE|L1	-204881	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.004695	0.509346	
chunk0186_329_1	chr7	143155124	143155711	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	23336	NM_002652	5304	Hs.99949	NM_002652	ENSG00000159763	PIP	GCDFP-15|GCDFP15|GPIP4	prolactin induced protein	protein-coding	0.005111	0.411565	
chunk0071_25_1	chr15	79097851	79098292	+	0	NA	Intergenic	L1MC|LINE|L1	-7198	NM_002891	5923	Hs.459035	NM_002891	ENSG00000058335	RASGRF1	CDC25|CDC25L|GNRP|GRF1|GRF55|H-GRF55|PP13187|ras-GRF1	Ras protein specific guanine nucleotide releasing factor 1	protein-coding	0.002268	0.305430	
chunk0062_241_1	chr14	71372352	71372846	+	0	NA	Intergenic	Intergenic	-25738	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.008097	0.341414	181(ATGTACATTCTGTCCT,-,0.00),182(TGTACATTCTGTCCTA,+,0.00)
chunk0172_250_1	chr6	137261199	137261999	+	0	NA	Intergenic	Intergenic	-42169	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.007500	0.397004	
chunk0106_255_1	chr2	203585704	203585904	+	0	NA	Intergenic	Intergenic	-50469	NM_203365	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.010000	0.422886	
chunk0113_285_1	chr20	57061069	57061277	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-152523	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.028846	0.488038	169(CAGGACATTATGTTTT,-,0.00),170(AGGACATTATGTTTTT,+,0.00)
chunk0154_317_1	chr5	83945805	83946004	+	0	NA	intron (NM_001278642, intron 9 of 9)	intron (NM_001278642, intron 9 of 9)	-224827	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.015075	0.355000	
chunk0027_216_1	chr10	76161971	76162211	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	379330	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.004167	0.360996	
chunk0124_297_1	chr3	57865059	57865258	+	0	NA	intron (NM_001304420, intron 11 of 21)	intron (NM_001304420, intron 11 of 21)	-24756	NM_001311179	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.005025	0.355000	
chunk0057_396_1	chr13	109570260	109570917	+	0	NA	Intergenic	MIRc|SINE|MIR	-157686	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.010654	0.434650	
chunk0038_117_1	chr11	83941144	83941433	+	0	NA	intron (NM_001142699, intron 14 of 27)	intron (NM_001142699, intron 14 of 27)	-258863	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003460	0.317241	
chunk0047_239_1	chr12	72207163	72207530	+	0	NA	Intergenic	Intergenic	-65403	NM_013381	29953	Hs.199814	NM_013381	ENSG00000072657	TRHDE	PAP-II|PGPEP2|TRH-DE	thyrotropin releasing hormone degrading enzyme	protein-coding	0.000000	0.366848	
chunk0113_123_1	chr20	51543394	51543703	+	0	NA	promoter-TSS (NM_012340)	promoter-TSS (NM_012340)	-829	NM_173091	4773	Hs.744148	NM_012340	ENSG00000101096	NFATC2	NFAT1|NFATP	nuclear factor of activated T cells 2	protein-coding	0.019417	0.529032	
chunk0153_441_1	chr5	76342512	76342711	+	0	NA	intron (NM_001297716, intron 12 of 12)	intron (NM_001297716, intron 12 of 12)	-60644	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.000000	0.550000	
chunk0040_312_1	chr11	117717736	117718374	+	0	NA	intron (NM_020693, intron 3 of 32)	intron (NM_020693, intron 3 of 32)	79206	NM_020693	57453	Hs.659513	NM_020693	ENSG00000177103	DSCAML1	DSCAM2	DS cell adhesion molecule like 1	protein-coding	0.026646	0.569640	
chunk0073_420_1	chr16	19076860	19077505	+	0	NA	intron (NM_016138, intron 4 of 5)	MER58A|DNA|hAT-Charlie	9265	NM_001190983	10229	Hs.157113	NM_016138	ENSG00000167186	COQ7	CAT5|CLK-1|CLK1|COQ10D8	coenzyme Q7, hydroxylase	protein-coding	0.015504	0.445820	
chunk0062_359_1	chr14	73877826	73878090	+	0	NA	intron (NM_001146155, intron 5 of 9)	AluJr4|SINE|Alu	-8657	NM_021188	57862	Hs.270869	NM_021188	ENSG00000119725	ZNF410	APA-1|APA1	zinc finger protein 410	protein-coding	0.011364	0.467925	
chunk0142_342_1	chr4	101324716	101325096	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	5508	NR_031656	100302193		NR_031656	ENSG00000221265	MIR1255A	MIRN1255A|hsa-mir-1255a	microRNA 1255a	ncRNA	0.005263	0.356955	
chunk0163_408_1	chr6	16799814	16800396	+	0	NA	Intergenic	Intergenic	-38615	NM_001128164	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.006873	0.368782	
chunk0115_45_1	chr21	21249529	21249963	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	251431	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.006912	0.319540	
chunk0140_208_1	chr4	70594837	70595156	+	0	NA	intron (NM_016519, intron 2 of 12)	intron (NM_016519, intron 2 of 12)	2738	NM_016519	258	Hs.272396	NM_016519	ENSG00000178522	AMBN	AI1F	ameloblastin	protein-coding	0.006270	0.406250	138(AAGTACACTTTGTTCT,-,0.00),139(AGTACACTTTGTTCTG,+,0.00)
chunk0099_140_1	chr2	86562903	86563284	+	0	NA	intron (NM_001198954, intron 3 of 7)	CpG	404	NR_036454	51652	Hs.591582	NM_016079	ENSG00000115561	CHMP3	CGI-149|NEDF|VPS24	charged multivesicular body protein 3	protein-coding	0.083990	0.649215	
chunk0141_416_1	chr4	88612169	88612665	+	0	NA	intron (NM_014606, intron 3 of 25)	intron (NM_014606, intron 3 of 25)	19994	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.002016	0.410463	242(CAGCACACAGAGTTCT,-,0.00),243(AGCACACAGAGTTCTA,+,0.00)
chunk0083_54_1	chr17	63675986	63676339	+	0	NA	intron (NM_203351, intron 7 of 16)	intron (NM_203351, intron 7 of 16)	23997	NM_030576	80774	Hs.591166	NM_030576	ENSG00000136490	LIMD2	-	LIM domain containing 2	protein-coding	0.005666	0.497175	
chunk0143_161_1	chr4	110352294	110352493	+	0	NA	Intergenic	Intergenic	-123680	NM_001977	2028	Hs.435765	NM_001977	ENSG00000138792	ENPEP	APA|CD249|gp160	glutamyl aminopeptidase	protein-coding	0.005025	0.320000	
chunk0060_250_1	chr14	49961761	49962877	+	0	NA	Intergenic	Intergenic	-4080	NR_106724	102464828		NR_106724	ENSG00000278038	MIR6076	hsa-mir-6076	microRNA 6076	ncRNA	0.018817	0.430618	
chunk0058_185_1	chr14	24116313	24116512	+	0	NA	intron (NR_028100, intron 1 of 13)	AluJo|SINE|Alu	1127	NM_181357	80344	Hs.525251	NM_025230	ENSG00000100897	DCAF11	GL014|PRO2389|WDR23	DDB1 and CUL4 associated factor 11	protein-coding	0.010050	0.480000	65(GGGCTCACTGTGTTCC,-,0.00),66(GGCTCACTGTGTTCCC,+,0.00)
chunk0074_5_1	chr16	19582378	19582953	+	0	NA	intron (NM_001300743, intron 7 of 27)	intron (NM_001300743, intron 7 of 27)	27250	NM_001300743	57020	Hs.654964	NM_020314	ENSG00000103544	VPS35L	C16orf62	VPS35 endosomal protein sorting factor like	protein-coding	0.017391	0.427083	
chunk0004_240_1	chr1	47266934	47267528	+	0	NA	intron (NM_001282938, intron 16 of 18)	L2a|LINE|L2	-34896	NM_001290406	6886	Hs.705618	NM_003189	ENSG00000162367	TAL1	SCL|TCL5|bHLHa17|tal-1	TAL bHLH transcription factor 1, erythroid differentiation factor	protein-coding	0.003367	0.416807	240(ATAACACCTTGTTCCC,+,0.00)
chunk0159_138_1	chr5	139146784	139147488	+	0	NA	intron (NM_022464, intron 1 of 9)	intron (NM_022464, intron 1 of 9)	51240	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.002841	0.421277	
chunk0205_102_1	chr9	107504373	107505202	+	0	NA	Intergenic	Intergenic	-15067	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.008444	0.443373	
chunk0198_290_1	chr8	135641082	135641831	+	0	NA	intron (NM_006558, intron 7 of 8)	intron (NM_006558, intron 7 of 8)	183991	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.004005	0.398667	
chunk0170_359_1	chr6	116773796	116774401	+	0	NA	Intergenic	Intergenic	-8375	NM_001085480	221303	Hs.126712	NM_001085480	ENSG00000183807	FAM162B	C6orf189|bA86F4.2	family with sequence similarity 162 member B	protein-coding	0.001653	0.374587	314(GAGATCACAATGTTCT,-,0.00),315(AGATCACAATGTTCTA,+,0.00)
chunk0142_220_1	chr4	97809423	97809728	+	0	NA	intron (NM_174952, intron 9 of 10)	MLT1E3|LTR|ERVL-MaLR	333665	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.006557	0.392157	
chunk0096_288_1	chr2	32372764	32373122	+	0	NA	intron (NM_016252, intron 1 of 73)	L1ME1|LINE|L1	15915	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.005587	0.359331	
chunk0058_223_1	chr14	25081555	25082059	+	0	NA	Intergenic	Intergenic	-31510	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.009921	0.388119	
chunk0126_387_1	chr3	84863122	84863585	+	0	NA	non-coding (NR_033860, exon 5 of 21)	non-coding (NR_033860, exon 5 of 21)	6222	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.004320	0.342672	
chunk0117_22_1	chr22	11341947	11342262	+	0	NA	Intergenic	L1P1|LINE|L1	-380575	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.006349	0.512658	
chunk0203_193_1	chr9	86417986	86418651	+	0	NA	Intergenic	Intergenic	-63831	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.006015	0.301802	
chunk0209_421_1	chrX	57108220	57108706	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	13083	NM_001006681	474343	Hs.460717	NM_001006681	ENSG00000186787	SPIN2B	SPIN-2|SPIN-2B|SPIN2_duplicate|TDRD26|dJ323P24.2	spindlin family member 2B	protein-coding	0.008230	0.400411	194(GAGAACTGGATGTGCA,-,0.00),195(AGAACTGGATGTGCAC,+,0.00)
chunk0053_171_1	chr13	30835414	30835993	+	0	NA	Intergenic	Intergenic	32497	NR_047012	100874158	Hs.577982	NR_047012	ENSG00000237879	LINC00398	-	long intergenic non-protein coding RNA 398	ncRNA	0.020725	0.484483	
chunk0101_422_1	chr2	139255400	139255997	+	0	NA	Intergenic	L1MD1|LINE|L1	358374	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.008375	0.344482	326(AAAGACTGAATGTTCT,-,0.00),327(AAGACTGAATGTTCTC,+,0.00),402(TAGGACAGGAAGTTCT,-,0.00),403(AGGACAGGAAGTTCTA,+,0.00)
chunk0051_417_1	chr12	122400470	122400669	+	0	NA	TTS (NR_045382)	TTS (NR_045382)	5027	NR_045382	100507066	Hs.624253	NR_045382		CLIP1-AS1	-	CLIP1 antisense RNA 1	ncRNA	0.030151	0.520000	
chunk0131_10_1	chr3	141797213	141797977	+	0	NA	intron (NM_139209, intron 2 of 3)	CpG	19394	NM_139209	131890	Hs.680654	NM_139209	ENSG00000114124	GRK7	GPRK7	G protein-coupled receptor kinase 7	protein-coding	0.058901	0.596078	
chunk0001_419_1	chr1	11152023	11152632	+	0	NA	intron (NM_004958, intron 30 of 57)	intron (NM_004958, intron 30 of 57)	8429	NR_046600	100873935	Hs.679133	NR_046600	ENSG00000225602	MTOR-AS1	-	MTOR antisense RNA 1	ncRNA	0.016420	0.465574	
chunk0196_169_1	chr8	105786238	105787049	+	0	NA	intron (NR_125796, intron 5 of 7)	intron (NR_125796, intron 5 of 7)	273860	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.007398	0.338670	
chunk0010_33_1	chr1	112530041	112530653	+	0	NA	intron (NM_017744, intron 14 of 14)	intron (NM_017744, intron 14 of 14)	21599	NM_024494	7482	Hs.258575	NM_004185	ENSG00000134245	WNT2B	WNT13	Wnt family member 2B	protein-coding	0.009804	0.404568	
chunk0149_341_1	chr5	26932295	26932888	+	0	NA	intron (NM_016279, intron 2 of 11)	L1MCa|LINE|L1	105991	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.005059	0.276094	
chunk0147_397_1	chr4	186726981	186727495	+	0	NA	Intergenic	Intergenic	-3405	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.054475	0.487379	
chunk0136_295_1	chr3	195001974	195002712	+	0	NA	Intergenic	Intergenic	-92245	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.008130	0.504736	267(GACACACTGTGTGCTT,+,0.00),555(GTGCACACACTGTGCC,-,0.00),556(TGCACACACTGTGCCC,+,0.00)
chunk0059_350_1	chr14	37200453	37200764	+	0	NA	intron (NM_138731, intron 1 of 13)	MER57E1|LTR|ERV1	2695	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.003215	0.358974	
chunk0019_82_1	chr1	224427437	224427706	+	0	NA	intron (NM_001115113, intron 3 of 13)	intron (NM_001115113, intron 3 of 13)	6728	NM_025160	80232	Hs.497873	NM_025160	ENSG00000162923	WDR26	CDW2|GID7|MIP2|SKDEAS	WD repeat domain 26	protein-coding	0.000000	0.392593	
chunk0107_236_1	chr2	217110107	217110492	+	0	NA	Intergenic	Intergenic	-172434	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.002597	0.370466	
chunk0166_234_1	chr6	47130668	47131024	+	0	NA	Intergenic	Intergenic	-88483	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.005618	0.420168	
chunk0093_360_1	chr19	55581905	55582424	+	0	NA	Intergenic	L1ME4b|LINE|L1	-1319	NM_152600	163033	Hs.112529	NM_152600	ENSG00000218891	ZNF579	-	zinc finger protein 579	protein-coding	0.007707	0.411538	
chunk0188_33_1	chr8	6582977	6583763	+	0	NA	intron (NM_024596, intron 12 of 13)	intron (NM_024596, intron 12 of 13)	-20107	NM_001147	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.016539	0.419314	
chunk0139_230_1	chr4	55336253	55336528	+	0	NA	Intergenic	Intergenic	-9831	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.010909	0.405797	
chunk0017_403_1	chr1	212665407	212665797	+	0	NA	Intergenic	Intergenic	34383	NM_018664	55509	Hs.62919	NM_018664	ENSG00000123685	BATF3	JDP1|JUNDM1|SNFT	basic leucine zipper ATF-like transcription factor 3	protein-coding	0.053846	0.667519	
chunk0017_166_1	chr1	207025512	207025953	+	0	NA	intron (NM_001083924, intron 1 of 2)	Tigger19a|DNA|TcMar-Tigger	7024	NM_001083924	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.002268	0.373303	
chunk0177_100_1	chr7	21954701	21954915	+	0	NA	Intergenic	Intergenic	-8884	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.009346	0.367442	
chunk0017_177_1	chr1	207058953	207059152	+	0	NA	intron (NM_001018053, intron 2 of 14)	intron (NM_001018053, intron 2 of 14)	5777	NM_006212	5208	Hs.282702	NM_006212	ENSG00000123836	PFKFB2	PFK-2/FBPase-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding	0.010050	0.480000	38(CAGGACAGAATGTTCC,-,0.00),39(AGGACAGAATGTTCCT,+,0.00)
chunk0071_83_1	chr15	80768080	80768547	+	0	NA	Intergenic	MIR|SINE|MIR	-11030	NM_001293298	57214	Hs.459088	NM_018689	ENSG00000103888	CEMIP	CCSP1|HYBID|KIAA1199|TMEM2L	cell migration inducing hyaluronidase 1	protein-coding	0.006424	0.358974	
chunk0024_339_1	chr10	43225536	43225786	+	0	NA	intron (NM_145313, intron 1 of 12)	intron (NM_145313, intron 1 of 12)	4078	NM_001282862	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.008000	0.557769	108(AGGAACACGATGTCCA,-,0.00),109(GGAACACGATGTCCAC,+,0.00)
chunk0055_182_1	chr13	61463403	61463605	+	0	NA	Intergenic	Intergenic	-47982	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.004950	0.320197	
chunk0097_220_1	chr2	51742739	51743292	+	0	NA	Intergenic	Intergenic	-710479	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.003617	0.346570	
chunk0118_114_1	chr22	29361635	29361864	+	0	NA	intron (NM_145730, intron 3 of 20)	L2c|LINE|L2	26834	NM_001127	162	Hs.368794	NM_001127	ENSG00000100280	AP1B1	ADTB1|AP105A|BAM22|CLAPB2	adaptor related protein complex 1 subunit beta 1	protein-coding	0.004367	0.456522	
chunk0127_313_1	chr3	99685606	99685905	+	0	NA	intron (NM_001850, intron 2 of 4)	intron (NM_001850, intron 2 of 4)	47159	NM_001850	1295	Hs.654548	NM_001850	ENSG00000144810	COL8A1	C3orf7	collagen type VIII alpha 1 chain	protein-coding	0.000000	0.310000	
chunk0054_98_1	chr13	42737280	42737743	+	0	NA	Intergenic	Intergenic	-44039	NM_182508	144809	Hs.16970	NM_182508	ENSG00000179813	FAM216B	C13orf30	family with sequence similarity 216 member B	protein-coding	0.008639	0.325431	
chunk0045_360_1	chr12	51984666	51985209	+	0	NA	intron (NM_004302, intron 5 of 8)	intron (NM_004302, intron 5 of 8)	-22008	NM_181711	160622	Hs.407202	NM_181711	ENSG00000161835	GRASP	TAMALIN	general receptor for phosphoinositides 1 associated scaffold protein	protein-coding	0.009208	0.443015	
chunk0208_403_1	chrX	29211040	29211509	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	-363004	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.004264	0.378723	
chunk0031_225_1	chr10	126288632	126288858	+	0	NA	intron (NM_001288973, intron 2 of 22)	intron (NM_001288973, intron 2 of 22)	99813	NM_001288975	8038	Hs.594351	NM_003474	ENSG00000148848	ADAM12	ADAM12-OT1|CAR10|MCMP|MCMPMltna|MLTN|MLTNA	ADAM metallopeptidase domain 12	protein-coding	0.022124	0.585903	
chunk0208_166_1	chrX	16589273	16589603	+	0	NA	3' UTR (NM_175859, exon 19 of 19)	3' UTR (NM_175859, exon 19 of 19)	37647	NR_039762	100616428		NR_039762	ENSG00000265144	MIR548AM	-	microRNA 548am	ncRNA	0.006061	0.429003	
chunk0174_199_1	chr6	160137097	160137787	+	0	NA	intron (NM_153187, intron 6 of 9)	intron (NM_153187, intron 6 of 9)	15611	NM_003057	6580	Hs.117367	NM_003057	ENSG00000175003	SLC22A1	HOCT1|OCT1|oct1_cds	solute carrier family 22 member 1	protein-coding	0.018841	0.562952	351(AGGTTCAGTGTGTCCT,-,0.00),352(GGTTCAGTGTGTCCTG,+,0.00)
chunk0017_105_1	chr1	205939579	205940022	+	0	NA	intron (NM_052934, intron 1 of 20)	intron (NM_052934, intron 1 of 20)	3660	NM_134325	115019	Hs.164073	NM_052934	ENSG00000174502	SLC26A9	-	solute carrier family 26 member 9	protein-coding	0.009029	0.542793	
chunk0087_179_1	chr18	35474792	35475083	+	0	NA	intron (NM_194281, intron 4 of 4)	L1MCa|LINE|L1	22712	NM_001308064	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.006873	0.356164	
chunk0060_301_1	chr14	50838418	50838675	+	0	NA	Intergenic	LTR33|LTR|ERVL	-7425	NM_016350	51199	Hs.310429	NM_016350	ENSG00000100503	NIN	SCKL7	ninein	protein-coding	0.003891	0.523256	235(GGCACATCCTGGTCCT,+,0.00)
chunk0122_298_1	chr3	36312931	36313285	+	0	NA	Intergenic	LTR101_Mam|LTR|ERVL	-67379	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.002825	0.315493	
chunk0023_394_1	chr10	30896933	30897496	+	0	NA	intron (NM_001143766, intron 5 of 7)	Tigger8|DNA|TcMar-Tigger	102303	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.000000	0.351064	
chunk0152_318_1	chr5	62005044	62005310	+	0	NA	Intergenic	Intergenic	-269479	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.003759	0.393258	
chunk0053_214_1	chr13	32060767	32061106	+	0	NA	intron (NM_023037, intron 1 of 60)	intron (NM_023037, intron 1 of 60)	-29297	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.005900	0.450000	101(ATGAACAGTCTGCCCT,-,0.00),102(TGAACAGTCTGCCCTG,+,0.00)
chunk0113_36_1	chr20	49850618	49851030	+	0	NA	exon (NM_001260491, exon 7 of 16)	exon (NM_001260491, exon 7 of 16)	38111	NR_048538	23315	Hs.444202	NM_015266	ENSG00000197818	SLC9A8	NHE-8|NHE8	solute carrier family 9 member A8	protein-coding	0.007282	0.368039	
chunk0056_144_1	chr13	83730676	83731530	+	0	NA	Intergenic	Intergenic	151290	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.008197	0.361404	
chunk0014_9_1	chr1	174239400	174239695	+	0	NA	intron (NM_014857, intron 4 of 20)	L2a|LINE|L2	80133	NM_014857	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.006780	0.331081	
chunk0192_239_1	chr8	65556534	65556777	+	0	NA	intron (NR_033893, intron 1 of 4)	MIRb|SINE|MIR	6011	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.016461	0.372951	
chunk0210_293_1	chrX	86214628	86214857	+	0	NA	intron (NM_001139514, intron 1 of 11)	intron (NM_001139514, intron 1 of 11)	-48226	NM_001139515	117154	Hs.86603	NM_053281	ENSG00000126733	DACH2	-	dachshund family transcription factor 2	protein-coding	0.004367	0.339130	152(TGGAACTGAATGTTCT,-,0.00),153(GGAACTGAATGTTCTT,+,0.00)
chunk0052_202_1	chr13	25084062	25084437	+	0	NA	Intergenic	L1ME4b|LINE|L1	-11889	NM_030979	5042	Hs.458280	NM_030979	ENSG00000151846	PABPC3	PABP3|PABPL3|tPABP	poly(A) binding protein cytoplasmic 3	protein-coding	0.002667	0.382979	
chunk0037_444_1	chr11	80394129	80394386	+	0	NA	Intergenic	Intergenic	368546	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.007782	0.364341	
chunk0186_202_1	chr7	139792315	139792779	+	0	NA	intron (NM_001166254, intron 3 of 14)	intron (NM_001166254, intron 3 of 14)	14299	NM_001166254	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.002155	0.449462	
chunk0039_55_1	chr11	96207457	96207715	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-133852	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.007752	0.467181	
chunk0101_282_1	chr2	134101732	134102337	+	0	NA	Intergenic	MER92-int|LTR|ERV1	-25091	NR_037450	100500878		NR_037450	ENSG00000263813	MIR3679	mir-3679	microRNA 3679	ncRNA	0.001653	0.323432	246(GAGAACACTTTGTTCT,-,0.00),247(AGAACACTTTGTTCTC,+,0.00)
chunk0182_144_1	chr7	94932657	94933232	+	0	NA	intron (NM_001166160, intron 2 of 19)	intron (NM_001166160, intron 2 of 19)	23046	NM_001166162	55607	Hs.21816	NM_017650	ENSG00000158528	PPP1R9A	NRB1|NRBI|Neurabin-I	protein phosphatase 1 regulatory subunit 9A	protein-coding	0.003478	0.336806	240(TGGAACAGAGTGAACC,-,0.00),241(GGAACAGAGTGAACCA,+,0.00)
chunk0025_74_1	chr10	50237130	50237405	+	0	NA	intron (NM_019893, intron 3 of 19)	MLT1F|LTR|ERVL-MaLR	11343	NM_019893	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.007273	0.456522	
chunk0209_281_1	chrX	47215609	47216314	+	0	NA	TTS (NM_003334)	TTS (NM_003334)	-2168	NM_033018	5127	Hs.496068	NM_006201	ENSG00000102225	CDK16	PCTAIRE|PCTAIRE1|PCTGAIRE|PCTK1	cyclin dependent kinase 16	protein-coding	0.014184	0.505666	450(TAGCTCAACCTGTTCT,-,0.00),451(AGCTCAACCTGTTCTG,+,0.00),483(ATCACAGCCTGTGCCC,+,0.00)
chunk0034_126_1	chr11	28464328	28464551	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	13109	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.000000	0.388393	
chunk0080_114_1	chr17	27085153	27085912	+	0	NA	Intergenic	L1M2|LINE|L1	208464	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.003953	0.326316	420(GAGGACAGCATGACCC,-,0.00),421(AGGACAGCATGACCCT,+,0.00)
chunk0158_326_1	chr5	132887324	132887631	+	0	NA	intron (NM_014423, intron 17 of 20)	intron (NM_014423, intron 17 of 20)	13811	NM_052971	116842	Hs.337588	NM_052971	ENSG00000164406	LEAP2	LEAP-2	liver enriched antimicrobial peptide 2	protein-coding	0.003257	0.379870	
chunk0117_48_1	chr22	12627585	12627812	+	0	NA	Intergenic	Intergenic	730292	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.008811	0.473684	
chunk0180_29_1	chr7	53880525	53880753	+	0	NA	Intergenic	Intergenic	-68708	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.008772	0.515284	
chunk0204_90_1	chr9	94288227	94288426	+	0	NA	intron (NM_001301275, intron 2 of 4)	intron (NM_001301275, intron 2 of 4)	29060	NM_001301275	169841	Hs.387623	NM_003448	ENSG00000175787	ZNF169	-	zinc finger protein 169	protein-coding	0.020101	0.490000	
chunk0066_180_1	chr15	33109722	33110178	+	0	NA	intron (NM_001277313, intron 4 of 20)	L2b|LINE|L2	-41918	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.008772	0.319475	
chunk0096_428_1	chr2	38421810	38422059	+	0	NA	Intergenic	Intergenic	-44644	NR_024191									0.004016	0.488000	
chunk0030_122_1	chr10	113116317	113116718	+	0	NA	intron (NM_001146283, intron 5 of 12)	intron (NM_001146283, intron 5 of 12)	71162	NR_132769	106635520		NR_132769		SNORA87	-	small nucleolar RNA, H/ACA box 87	snoRNA	0.007481	0.308458	
chunk0179_302_1	chr7	50078490	50078981	+	0	NA	intron (NM_007009, intron 3 of 7)	L1P4|LINE|L1	14529	NM_007009	11055	Hs.388841	NM_007009	ENSG00000042813	ZPBP	ZPBP1	zona pellucida binding protein	protein-coding	0.002037	0.317073	
chunk0168_198_1	chr6	85517220	85517452	+	0	NA	intron (NM_001297614, intron 22 of 27)	L2c|LINE|L2	67752	NM_002526	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.004310	0.373391	
chunk0089_268_1	chr18	62717308	62717569	+	0	NA	intron (NM_194449, intron 1 of 16)	intron (NM_194449, intron 1 of 16)	1999	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.015326	0.438931	
chunk0195_161_1	chr8	95653666	95654052	+	0	NA	intron (NR_038205, intron 2 of 2)	intron (NR_038205, intron 2 of 2)	294489	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.002591	0.390181	118(CAGCACACCTTGTTCT,-,0.00),119(AGCACACCTTGTTCTT,+,0.00),292(GAGATCAATCTGTTCC,-,0.00),293(AGATCAATCTGTTCCT,+,0.00)
chunk0048_327_1	chr12	83805835	83806360	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	1106732	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.007619	0.385932	
chunk0090_158_1	chr18	72472811	72473270	+	0	NA	Intergenic	Intergenic	71448	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.002179	0.380435	
chunk0126_34_1	chr3	73725670	73725975	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-100901	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.006557	0.401961	
chunk0040_131_1	chr11	112472255	112472980	+	0	NA	Intergenic	Intergenic	-9615	NR_120559	101928823	Hs.126118	NR_120559	ENSG00000254968	LINC02763	-	long intergenic non-protein coding RNA 2763	ncRNA	0.016552	0.395317	
chunk0036_452_1	chr11	68651651	68652263	+	0	NA	Intergenic	Intergenic	-32518	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.034314	0.597064	276(GGGGACACAGAGTCCC,-,0.00),277(GGGACACAGAGTCCCA,+,0.00)
chunk0032_149_1	chr11	4752248	4752507	+	0	NA	Intergenic	Intergenic	17540	NM_001004752	256892		NM_001004752	ENSG00000280021	OR51F1	OR11-21|OR51F1P	olfactory receptor family 51 subfamily F member 1 (gene/pseudogene)	protein-coding	0.019305	0.480769	
chunk0092_397_1	chr19	37218180	37218608	+	0	NA	Intergenic	Intergenic	-7845	NM_152279	92285	Hs.390568	NM_152279	ENSG00000245680	ZNF585B	SZFP41	zinc finger protein 585B	protein-coding	0.044393	0.564103	
chunk0072_53_1	chr16	1532271	1532951	+	0	NA	intron (NM_001256541, intron 1 of 3)	intron (NM_001256541, intron 1 of 3)	-1046	NM_024600	79652	Hs.459652	NM_024600	ENSG00000131634	TMEM204	C16orf30|CLP24	transmembrane protein 204	protein-coding	0.033824	0.594714	343(CAGGACTCTCTGTCCC,-,0.00),344(AGGACTCTCTGTCCCA,+,0.00)
chunk0057_152_1	chr13	100322935	100323323	+	0	NA	intron (NM_001127692, intron 15 of 22)	MER58A|DNA|hAT-Charlie	157886	NR_047686	100885777	Hs.662554	NR_047686		PCCA-AS1	-	PCCA antisense RNA 1	ncRNA	0.002577	0.383033	
chunk0153_19_1	chr5	66993455	66993690	+	0	NA	intron (NM_001290226, intron 1 of 26)	L2c|LINE|L2	10582	NR_111908	101928794	Hs.672435	NR_111908		MAST4-AS1	-	MAST4 antisense RNA 1	ncRNA	0.000000	0.466102	180(AGGAACAGGATGTGCA,-,0.00),181(GGAACAGGATGTGCAA,+,0.00)
chunk0161_71_1	chr5	166710264	166710613	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	215932	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005731	0.402857	
chunk0119_14_1	chr22	40133122	40133373	+	0	NA	intron (NM_001024843, intron 3 of 23)	intron (NM_001024843, intron 3 of 23)	-44678	NM_001162501	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.003984	0.333333	
chunk0069_248_1	chr15	64400543	64400933	+	0	NA	intron (NM_016213, intron 4 of 12)	intron (NM_016213, intron 4 of 12)	12934	NM_016213	9325	Hs.500340	NM_016213	ENSG00000103671	TRIP4	ASC-1|ASC1|HsT17391|MDCDC|SMABF1|ZC2HC5	thyroid hormone receptor interactor 4	protein-coding	0.005128	0.347826	
chunk0144_213_1	chr4	134360487	134360938	+	0	NA	Intergenic	Intergenic	-158964	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.002217	0.300885	
chunk0059_201_1	chr14	33454755	33455277	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-253921	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.011494	0.435946	
chunk0012_255_1	chr1	161367883	161368082	+	0	NA	promoter-TSS (NM_001013625)	promoter-TSS (NM_001013625)	-99	NM_001013625	257177	Hs.534593	NM_001013625	ENSG00000188931	CFAP126	C1orf192|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding	0.015075	0.435000	
chunk0078_357_1	chr16	87281422	87281751	+	0	NA	intron (NR_104667, intron 3 of 4)	L1M4|LINE|L1	10866	NR_104667	101928682	Hs.149004	NR_104667	ENSG00000261697	LOC101928682	-	uncharacterized LOC101928682	ncRNA	0.003040	0.324242	
chunk0137_174_1	chr4	17232784	17233299	+	0	NA	Intergenic	Intergenic	-46984	NR_125919	101929123	Hs.638913	NR_125919	ENSG00000250819	LINC02493	-	long intergenic non-protein coding RNA 2493	ncRNA	0.003883	0.457364	242(AGGAACAGAGTGTCCT,-,0.00),243(GGAACAGAGTGTCCTA,+,0.00)
chunk0018_29_1	chr1	215567870	215568698	+	0	NA	intron (NM_016121, intron 1 of 17)	intron (NM_016121, intron 1 of 17)	892	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.020531	0.472859	485(TAGGACAGTGTGTCCA,-,0.00),486(AGGACAGTGTGTCCAG,+,0.00)
chunk0128_264_1	chr3	110399192	110399587	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	670570	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.010127	0.340909	
chunk0076_431_1	chr16	73047526	73047783	+	0	NA	intron (NM_006885, intron 1 of 9)	intron (NM_006885, intron 1 of 9)	721	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.046693	0.631783	
chunk0163_389_1	chr6	16431710	16431954	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	193252	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.024590	0.416327	
chunk0171_74_1	chr6	121593204	121593403	+	0	NA	Intergenic	L3|LINE|CR1	157726	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.005025	0.410000	
chunk0155_370_1	chr5	97501167	97501953	+	0	NA	Intergenic	Intergenic	-3136	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.005089	0.376112	
chunk0154_243_1	chr5	81272393	81272851	+	0	NA	intron (NR_034122, intron 1 of 3)	L1PB1|LINE|L1	28947	NR_034123	100131067	Hs.655855	NR_034121	ENSG00000247572	CKMT2-AS1	-	CKMT2 antisense RNA 1	ncRNA	0.008734	0.339869	
chunk0101_354_1	chr2	137929612	137929994	+	0	NA	Intergenic	Intergenic	-1871	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.010471	0.430809	329(AGGAACAGGCTGGCCC,-,0.00),330(GGAACAGGCTGGCCCT,+,0.00)
chunk0195_411_1	chr8	100654255	100654693	+	0	NA	Intergenic	Intergenic	-4809	NM_152628	169166	Hs.567758	NM_152628	ENSG00000174226	SNX31	-	sorting nexin 31	protein-coding	0.013699	0.487472	
chunk0204_287_1	chr9	99136552	99137168	+	0	NA	intron (NM_001306210, intron 3 of 8)	intron (NM_001306210, intron 3 of 8)	31771	NM_004612	7046	Hs.494622	NM_004612	ENSG00000106799	TGFBR1	AAT5|ACVRLK4|ALK-5|ALK5|ESS1|LDS1|LDS1A|LDS2A|MSSE|SKR4|TBR-i|TBRI|TGFR-1|tbetaR-I	transforming growth factor beta receptor 1	protein-coding	0.006494	0.340357	343(AGGAACATGATGTACA,-,0.00),344(GGAACATGATGTACAC,+,0.00)
chunk0081_399_1	chr17	48258392	48259018	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-35642	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.001597	0.342903	
chunk0108_220_1	chr2	233495218	233495604	+	0	NA	intron (NM_018218, intron 23 of 30)	intron (NM_018218, intron 23 of 30)	70179	NM_018218	55230	Hs.96513	NM_018218	ENSG00000085982	USP40	-	ubiquitin specific peptidase 40	protein-coding	0.005181	0.325581	
chunk0101_428_1	chr2	139290291	139291026	+	0	NA	Intergenic	Intergenic	393334	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.006803	0.334239	321(CAAGACACTTTGTTCC,-,0.00),322(AAGACACTTTGTTCCA,+,0.00)
chunk0127_28_1	chr3	88581694	88582108	+	0	NA	Intergenic	Intergenic	-432035	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.000000	0.368675	
chunk0116_327_1	chr21	41250436	41250951	+	0	NA	intron (NM_138991, intron 6 of 7)	intron (NM_138991, intron 6 of 7)	-65454	NM_182832									0.015534	0.436047	
chunk0177_149_1	chr7	22859962	22860206	+	0	NA	Intergenic	Intergenic	3471	NR_003075	692210		NR_003075	ENSG00000221740	SNORD93	HBII-336	small nucleolar RNA, C/D box 93	snoRNA	0.008197	0.367347	
chunk0141_105_1	chr4	79514787	79515301	+	0	NA	intron (NR_038826, intron 3 of 3)	intron (NR_038826, intron 3 of 3)	22451	NR_038826	100506035	Hs.507664	NR_038826	ENSG00000250334	LINC00989	-	long intergenic non-protein coding RNA 989	ncRNA	0.009728	0.378641	
chunk0137_53_1	chr4	11623474	11624009	+	0	NA	Intergenic	Intergenic	-194828	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.007477	0.389925	
chunk0166_378_1	chr6	51613519	51614207	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-8007	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.004360	0.384615	
chunk0165_2_1	chr6	28525166	28525413	+	0	NA	promoter-TSS (NM_003996)	promoter-TSS (NM_003996)	-723	NM_003996	2880	Hs.248129	NM_001509	ENSG00000224586	GPX5	EGLP|GPx-5|GSHPx-5|HEL-S-75p	glutathione peroxidase 5	protein-coding	0.016194	0.415323	
chunk0113_97_1	chr20	50929324	50929690	+	0	NA	intron (NM_015339, intron 1 of 4)	intron (NM_015339, intron 1 of 4)	-1477	NR_110008	101927631	Hs.301898	NR_110007	ENSG00000259456	ADNP-AS1	-	ADNP antisense RNA 1	ncRNA	0.021858	0.498638	184(AAGCACATCCTGTTCT,-,0.00),185(AGCACATCCTGTTCTA,+,0.00)
chunk0067_122_1	chr15	42706983	42707560	+	0	NA	intron (NM_020759, intron 26 of 32)	L1ME5|LINE|L1	29948	NM_138477	146059	Hs.599232	NM_138477	ENSG00000140326	CDAN1	CDA1|CDAI|CDAN1A|DLT|PRO1295	codanin 1	protein-coding	0.010399	0.356401	
chunk0064_435_1	chr14	99940779	99941371	+	0	NA	3' UTR (NM_001008707, exon 23 of 23)	3' UTR (NM_001008707, exon 23 of 23)	-124339	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.016892	0.399663	
chunk0055_188_1	chr13	61600506	61601092	+	0	NA	Intergenic	Intergenic	-185277	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.003413	0.337308	
chunk0029_27_1	chr10	95817194	95817467	+	0	NA	intron (NM_001312654, intron 2 of 9)	intron (NM_001312654, intron 2 of 9)	61414	NM_001164182	953	Hs.576612	NM_001776	ENSG00000138185	ENTPD1	ATPDase|CD39|NTPDase-1|SPG64	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding	0.003663	0.529197	
chunk0139_393_1	chr4	62419459	62419658	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-257793	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.005025	0.450000	
chunk0072_174_1	chr15	93656029	93656335	+	0	NA	Intergenic	Intergenic	-200378	NR_120321	101927153	Hs.371900	NR_120321		LINC02207	-	long intergenic non-protein coding RNA 2207	ncRNA	0.006536	0.407166	
chunk0152_131_1	chr5	58922867	58923228	+	0	NA	Intergenic	Intergenic	76885	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.024931	0.516575	
chunk0108_342_1	chr2	235924534	235925176	+	0	NA	intron (NM_014914, intron 11 of 16)	LTR40a|LTR|ERVL	243154	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.017134	0.514774	
chunk0144_206_1	chr4	134065114	134065852	+	0	NA	Intergenic	L1PA15|LINE|L1	136265	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005420	0.330176	
chunk0120_61_1	chr3	3137512	3137917	+	0	NA	intron (NM_001302946, intron 3 of 7)	HAL1|LINE|L1	10798	NM_001302946	51095	Hs.732725	NM_016000	ENSG00000072756	TRNT1	CCA1|CGI-47|MtCCA|RPEM|SIFD	tRNA nucleotidyl transferase 1	protein-coding	0.014815	0.344828	
chunk0029_88_1	chr10	97135933	97136317	+	0	NA	intron (NM_003061, intron 4 of 36)	L1MC1|LINE|L1	33369	NR_038330	100505540	Hs.568878	NR_038330	ENSG00000234855	SLIT1-AS1	-	SLIT1 antisense RNA 1	ncRNA	0.015625	0.503896	
chunk0167_119_1	chr6	60818838	60819236	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-755066	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.000000	0.343358	
chunk0041_48_1	chr11	123122315	123122647	+	0	NA	intron (NM_024769, intron 1 of 6)	intron (NM_024769, intron 1 of 6)	-60146	NM_153201	3312	Hs.180414	NM_006597	ENSG00000109971	HSPA8	HEL-33|HEL-S-72p|HSC54|HSC70|HSC71|HSP71|HSP73|HSPA10|LAP-1|LAP1|NIP71	heat shock protein family A (Hsp70) member 8	protein-coding	0.021084	0.459459	
chunk0043_244_1	chr12	20276842	20277041	+	0	NA	Intergenic	L1M4b|LINE|L1	-92304	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.010050	0.505000	
chunk0060_444_1	chr14	54537625	54538533	+	0	NA	exon (NM_006568, exon 6 of 6)	exon (NM_006568, exon 6 of 6)	28210	NM_006568	10668	Hs.59106	NM_006568	ENSG00000100532	CGRRF1	CGR19|RNF197	cell growth regulator with ring finger domain 1	protein-coding	0.005507	0.339934	
chunk0140_202_1	chr4	70453096	70453466	+	0	NA	intron (NM_001145006, intron 1 of 3)	L1M1|LINE|L1	-18677	NM_001145007	4589	Hs.631946	NM_152291	ENSG00000171195	MUC7	MG2	mucin 7, secreted	protein-coding	0.002703	0.506739	115(CAGGACAGCCAGTTCC,-,0.00),116(AGGACAGCCAGTTCCC,+,0.00)
chunk0168_356_1	chr6	93337743	93337979	+	0	NA	intron (NM_004440, intron 5 of 16)	intron (NM_004440, intron 5 of 16)	81721	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.004237	0.409283	67(AGGAACAGCTTGCTCT,-,0.00),68(GGAACAGCTTGCTCTT,+,0.00)
chunk0163_402_1	chr6	16755872	16756118	+	0	NA	intron (NM_000332, intron 1 of 8)	intron (NM_000332, intron 1 of 8)	5495	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.012195	0.279352	
chunk0206_397_1	chr9	127089497	127090091	+	0	NA	intron (NM_012098, intron 4 of 4)	intron (NM_012098, intron 4 of 4)	32971	NM_012098	23452	Hs.653262	NM_012098	ENSG00000136859	ANGPTL2	ARP2|HARP	angiopoietin like 2	protein-coding	0.011785	0.512605	266(AAGGACAAGCAGTTCA,-,0.00),267(AGGACAAGCAGTTCAG,+,0.00)
chunk0004_454_1	chr1	53512064	53512579	+	0	NA	intron (NM_147193, intron 7 of 9)	intron (NM_147193, intron 7 of 9)	52922	NM_033067	63948	Hs.131654	NM_033067	ENSG00000143006	DMRTB1	-	DMRT like family B with proline rich C-terminal 1	protein-coding	0.013592	0.434109	
chunk0202_354_1	chr9	79962334	79963047	+	0	NA	intron (NR_121213, intron 1 of 2)	intron (NR_121213, intron 1 of 2)	-12333	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.002805	0.386555	684(AGAAACTTGCTGTTCC,-,0.00)
chunk0155_269_1	chr5	95956891	95957256	+	0	NA	intron (NM_012081, intron 1 of 11)	intron (NM_012081, intron 1 of 11)	-4928	NR_130776	101929710		NR_130776	ENSG00000251314	LOC101929710	-	uncharacterized LOC101929710	ncRNA	0.000000	0.357923	
chunk0037_301_1	chr11	76367890	76368537	+	0	NA	intron (NR_130898, intron 1 of 5)	intron (NR_130898, intron 1 of 5)	12752	NR_130898	5612	Hs.503315	NM_004705	ENSG00000137492	THAP12	DAP4|P52rIPK|PRKRIR|THAP0	THAP domain containing 12	protein-coding	0.004637	0.325617	
chunk0162_414_1	chr5	179912459	179913088	+	0	NA	Intergenic	Intergenic	-4917	NM_198868	23061	Hs.155829	NM_015043	ENSG00000197226	TBC1D9B	GRAMD9B	TBC1 domain family member 9B	protein-coding	0.022258	0.546032	
chunk0040_318_1	chr11	117985124	117985356	+	0	NA	Intergenic	LTR38C|LTR|ERV1	-1151	NM_001558	3587	Hs.504035	NM_001558	ENSG00000110324	IL10RA	CD210|CD210a|CDW210A|HIL-10R|IL-10R1|IL10R	interleukin 10 receptor subunit alpha	protein-coding	0.030172	0.467811	
chunk0123_225_1	chr3	45398165	45398586	+	0	NA	intron (NM_015340, intron 3 of 21)	intron (NM_015340, intron 3 of 21)	9792	NM_015340	23395	Hs.526975	NM_015340	ENSG00000011376	LARS2	HLASA|LEURS|PRLTS4|mtLeuRS	leucyl-tRNA synthetase 2, mitochondrial	protein-coding	0.014252	0.369668	
chunk0004_328_1	chr1	50154461	50154812	+	0	NA	intron (NM_021952, intron 2 of 6)	intron (NM_021952, intron 2 of 6)	45020	NM_001294348	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.005698	0.377841	
chunk0127_306_1	chr3	98783948	98784672	+	0	NA	intron (NM_001271147, intron 6 of 9)	intron (NM_001271147, intron 6 of 9)	51606	NM_001271145	10402	Hs.148716	NM_006100	ENSG00000064225	ST3GAL6	SIAT10|ST3GALVI	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	protein-coding	0.009669	0.438621	
chunk0090_396_1	chr18	77865972	77866278	+	0	NA	Intergenic	L1MD2|LINE|L1	127602	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.032680	0.563518	
chunk0070_414_1	chr15	77495905	77496443	+	0	NA	Intergenic	Intergenic	75523	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.016729	0.517625	290(CAGTTCATTGTGTTCT,-,0.00),291(AGTTCATTGTGTTCTT,+,0.00)
chunk0091_93_1	chr19	5631988	5632316	+	0	NA	intron (NR_037699, intron 2 of 18)	intron (NR_037699, intron 2 of 18)	9117	NM_001201339	6294	Hs.728802	NM_002967	ENSG00000160633	SAFB	HAP|HET|SAB-B1|SAF-B|SAF-B1|SAFB1	scaffold attachment factor B	protein-coding	0.003049	0.367781	
chunk0105_345_1	chr2	191318017	191318462	+	0	NA	intron (NM_001130158, intron 3 of 30)	L2b|LINE|L2	72711	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.002247	0.399103	
chunk0131_394_1	chr3	152793820	152794458	+	0	NA	Intergenic	L2b|LINE|L2	-40554	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.004702	0.345853	599(AAGAACATGGTGTTTA,-,0.00)
chunk0035_280_1	chr11	46690503	46690941	+	0	NA	intron (NM_004308, intron 3 of 12)	L2c|LINE|L2	9943	NM_004308	392	Hs.138860	NM_004308	ENSG00000175220	ARHGAP1	CDC42GAP|RHOGAP|RHOGAP1|p50rhoGAP	Rho GTPase activating protein 1	protein-coding	0.011416	0.473804	
chunk0172_444_1	chr6	140921286	140921601	+	0	NA	Intergenic	Intergenic	237629	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.009524	0.354430	
chunk0099_109_1	chr2	85742541	85742922	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-11055	NM_032827	84913	Hs.135569	NM_032827	ENSG00000168874	ATOH8	HATH6|bHLHa21	atonal bHLH transcription factor 8	protein-coding	0.023622	0.554974	
chunk0205_108_1	chr9	107604239	107604466	+	0	NA	Intergenic	L2c|LINE|L2	-114632	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.004405	0.429825	150(GGGAACATCATGATCT,-,0.00),151(GGAACATCATGATCTA,+,0.00)
chunk0159_132_1	chr5	139079414	139079613	+	0	NA	intron (NM_001037633, intron 4 of 10)	intron (NM_001037633, intron 4 of 10)	118863	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.000000	0.385000	126(AAGTACAGAATGTGCT,-,0.00),127(AGTACAGAATGTGCTG,+,0.00)
chunk0198_333_1	chr8	140034654	140034912	+	0	NA	intron (NM_001160372, intron 17 of 22)	MIRb|SINE|MIR	-331727	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.011628	0.494208	20(AGGCTCATACTGTGCT,-,0.00),21(GGCTCATACTGTGCTC,+,0.00)
chunk0144_38_1	chr4	125655100	125655640	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	148111	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.005556	0.419593	
chunk0185_321_1	chr7	131472043	131472596	+	0	NA	intron (NM_001145354, intron 17 of 18)	intron (NM_001145354, intron 17 of 18)	84298	NM_001018111	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.000000	0.321300	313(CAAGACAGTTTGTTCT,-,0.00),314(AAGACAGTTTGTTCTT,+,0.00)
chunk0200_400_1	chr9	27199956	27200419	+	0	NA	intron (NM_001290077, intron 11 of 21)	L1ME3Cz|LINE|L1	82606	NR_026679	158035	Hs.201554	NR_026679	ENSG00000283945	LINC00032	C9orf14|NCRNA00032	long intergenic non-protein coding RNA 32	ncRNA	0.002160	0.321121	
chunk0172_112_1	chr6	135054512	135054742	+	0	NA	intron (NM_001145158, intron 1 of 16)	CpG	271	NM_001145158	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.056522	0.562771	
chunk0207_178_1	chr9	130695309	130695550	+	0	NA	intron (NM_014285, intron 1 of 8)	intron (NM_014285, intron 1 of 8)	1669	NR_104230	23404	Hs.654643	NM_014285	ENSG00000130713	EXOSC2	RRP4|Rrp4p|SHRF|hRrp4p|p7	exosome component 2	protein-coding	0.024896	0.516529	102(AGGAACACGTTGTTCT,-,0.00),103(GGAACACGTTGTTCTT,+,0.00)
chunk0045_224_1	chr12	48151100	48151299	+	0	NA	intron (NM_024095, intron 3 of 3)	intron (NM_024095, intron 3 of 3)	6395	NM_024095	140461	Hs.432699	NM_024095	ENSG00000177981	ASB8	PP14212	ankyrin repeat and SOCS box containing 8	protein-coding	0.005025	0.445000	
chunk0173_104_1	chr6	143267743	143268172	+	0	NA	intron (NM_001286587, intron 4 of 6)	Charlie19a|DNA|hAT-Charlie	174720	NM_001286259	134637	Hs.709561	NM_182503	ENSG00000189007	ADAT2	DEADC1|TAD2|dJ20N2|dJ20N2.1	adenosine deaminase tRNA specific 2	protein-coding	0.004662	0.413953	
chunk0131_13_1	chr3	141884131	141884782	+	0	NA	intron (NM_001679, intron 1 of 6)	MLT2A1|LTR|ERVL	7828	NM_001679	483	Hs.477789	NM_001679	ENSG00000069849	ATP1B3	ATPB-3|CD298	ATPase Na+/K+ transporting subunit beta 3	protein-coding	0.004608	0.424847	
chunk0056_162_1	chr13	84668448	84669228	+	0	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-114816	NR_132852	106635542		NR_132852		SNORA107	-	small nucleolar RNA, H/ACA box 107	snoRNA	0.006410	0.366197	
chunk0012_90_1	chr1	156281490	156281801	+	0	NA	intron (NM_015327, intron 1 of 21)	intron (NM_015327, intron 1 of 21)	1184	NM_015327	23381	Hs.516837	NM_015327	ENSG00000198952	SMG5	EST1B|LPTS-RP1|LPTSRP1|SMG-5	SMG5 nonsense mediated mRNA decay factor	protein-coding	0.016077	0.455128	
chunk0125_245_1	chr3	68925783	68926024	+	0	NA	intron (NM_001005527, intron 1 of 5)	L1ME4a|LINE|L1	6707	NM_001005527	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.024896	0.500000	
chunk0010_30_1	chr1	112474368	112474711	+	0	NA	intron (NM_001291880, intron 1 of 4)	L1MEc|LINE|L1	7998	NM_004185	7482	Hs.258575	NM_004185	ENSG00000134245	WNT2B	WNT13	Wnt family member 2B	protein-coding	0.017493	0.404070	
chunk0163_361_1	chr6	15760953	15761425	+	0	NA	Intergenic	Intergenic	-98131	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.004237	0.367865	
chunk0166_459_1	chr6	53302072	53302493	+	0	NA	intron (NM_001242828, intron 1 of 8)	intron (NM_001242828, intron 1 of 8)	25289	NR_049866	100847075		NR_049866	ENSG00000264056	MIR5685	-	microRNA 5685	ncRNA	0.009501	0.459716	
chunk0162_142_1	chr6	3219573	3220032	+	0	NA	Intergenic	MIR3|SINE|MIR	7932	NM_178012	347733	Hs.300701	NM_178012	ENSG00000137285	TUBB2B	CDCBM7|PMGYSA|bA506K6.1	tubulin beta 2B class IIb	protein-coding	0.010893	0.428261	
chunk0046_442_1	chr12	64836706	64837234	+	0	NA	intron (NM_015279, intron 6 of 11)	intron (NM_015279, intron 6 of 11)	12398	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.003788	0.396975	
chunk0107_206_1	chr2	216596173	216596823	+	0	NA	intron (NR_110392, intron 2 of 3)	intron (NR_110392, intron 2 of 3)	10440	NR_110392	101928232	Hs.694592	NR_110392		LINC01280	-	long intergenic non-protein coding RNA 1280	ncRNA	0.013846	0.405530	
chunk0206_319_1	chr9	125196361	125196582	+	0	NA	Intergenic	Intergenic	-4071	NM_001174152	10244	Hs.19012	NM_005833	ENSG00000136933	RABEPK	RAB9P40|bA65N13.1|p40	Rab9 effector protein with kelch motifs	protein-coding	0.013575	0.481982	
chunk0014_282_1	chr1	180550815	180551053	+	0	NA	Intergenic	Intergenic	-8040	NR_125716	148756		NR_125716	ENSG00000236719	OVAAL	LINC01131|OVAL	ovarian adenocarcinoma amplified long non-coding RNA	ncRNA	0.012605	0.330544	
chunk0022_191_1	chr10	13437164	13437473	+	0	NA	Intergenic	Intergenic	65658	NM_001100912	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.035599	0.506452	
chunk0188_30_1	chr8	6577188	6577406	+	0	NA	intron (NM_024596, intron 12 of 13)	intron (NM_024596, intron 12 of 13)	-14034	NM_001147	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.018349	0.529680	
chunk0103_325_1	chr2	167720861	167721529	+	0	NA	Intergenic	Intergenic	-97477	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.002994	0.375187	
chunk0060_112_1	chr14	43567783	43568564	+	0	NA	Intergenic	Intergenic	939123	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.002561	0.342711	
chunk0139_200_1	chr4	54808785	54809344	+	0	NA	Intergenic	L1PA6|LINE|L1	151136	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.003578	0.410714	316(AGGAACAACCAGTACC,-,0.00),317(GGAACAACCAGTACCA,+,0.00)
chunk0125_376_1	chr3	71545295	71545916	+	0	NA	intron (NM_032682, intron 2 of 20)	intron (NM_032682, intron 2 of 20)	-2048	NM_001244816	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.003221	0.305466	
chunk0125_367_1	chr3	71395340	71395922	+	0	NA	intron (NM_032682, intron 3 of 20)	L2a|LINE|L2	-90871	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.005155	0.415094	
chunk0132_196_1	chr3	157235885	157236525	+	0	NA	Intergenic	AluSz6|SINE|Alu	-75445	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.006250	0.393136	
chunk0160_129_1	chr5	151234888	151235264	+	0	NA	Intergenic	Intergenic	-10983	NM_015621	26112	Hs.655336	NM_015621	ENSG00000198624	CCDC69	-	coiled-coil domain containing 69	protein-coding	0.029255	0.554377	
chunk0183_341_1	chr7	108399663	108400301	+	0	NA	intron (NM_001193582, intron 1 of 30)	intron (NM_001193582, intron 1 of 30)	56415	NM_001193584	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.009404	0.348983	
chunk0075_254_1	chr16	53448924	53449495	+	0	NA	intron (NM_005611, intron 4 of 21)	intron (NM_005611, intron 4 of 21)	14770	NM_005611	5934	Hs.513609	NM_005611	ENSG00000103479	RBL2	P130|Rb2	RB transcriptional corepressor like 2	protein-coding	0.005254	0.356643	
chunk0208_135_1	chrX	15616377	15616896	+	0	NA	intron (NR_126564, intron 1 of 1)	Plat_L3|LINE|CR1	13755	NR_126564	104798195	Hs.131674	NR_126564	ENSG00000225833	GS1-594A7.3	-	uncharacterized LOC104798195	ncRNA	0.009634	0.448077	
chunk0195_189_1	chr8	96619672	96619903	+	0	NA	Intergenic	Intergenic	-25440	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.004329	0.383621	69(AGGAACTAGGTGTCCA,-,0.00),70(GGAACTAGGTGTCCAC,+,0.00),126(AGGCACAGAAAGTGCT,-,0.00),127(GGCACAGAAAGTGCTC,+,0.00)
chunk0131_72_1	chr3	142983215	142983998	+	0	NA	intron (NR_125393, intron 2 of 4)	L1ME4b|LINE|L1	17861	NR_034032	100289361	Hs.599649	NR_034032	ENSG00000268129	LOC100289361	-	uncharacterized LOC100289361	ncRNA	0.007663	0.415816	
chunk0024_309_1	chr10	42662861	42663208	+	0	NA	Intergenic	L1MA9|LINE|L1	-24197	NM_001305036	7582	Hs.435774	NM_006955	ENSG00000196693	ZNF33B	KOX2|KOX31|ZNF11B	zinc finger protein 33B	protein-coding	0.008646	0.324713	
chunk0127_62_1	chr3	89311539	89311983	+	0	NA	intron (NM_005233, intron 3 of 16)	intron (NM_005233, intron 3 of 16)	204237	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004505	0.373034	
chunk0112_75_1	chr20	37846136	37846964	+	0	NA	intron (NM_030877, intron 13 of 15)	MIRb|SINE|MIR	-56547	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.012077	0.490953	
chunk0089_450_1	chr18	70304406	70305110	+	0	NA	intron (NM_004232, intron 1 of 1)	L1M4|LINE|L1	15857	NM_004232	9306	Hs.44439	NM_004232	ENSG00000170677	SOCS6	CIS-4|CIS4|HSPC060|SOCS-4|SOCS-6|SOCS4|SSI4|STAI4|STATI4	suppressor of cytokine signaling 6	protein-coding	0.015625	0.387234	459(AGGAACTCTTTGTCCA,-,0.00)
chunk0049_54_1	chr12	90027083	90027504	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	318338	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.000000	0.424171	
chunk0068_291_1	chr15	57033742	57034048	+	0	NA	intron (NM_003205, intron 3 of 19)	intron (NM_003205, intron 3 of 19)	115260	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.003268	0.345277	
chunk0189_161_1	chr8	23218704	23218999	+	0	NA	intron (NM_003844, intron 1 of 9)	MIR|SINE|MIR	6316	NM_003844	8797	Hs.213467	NM_003844	ENSG00000104689	TNFRSF10A	APO2|CD261|DR4|TRAILR-1|TRAILR1	TNF receptor superfamily member 10a	protein-coding	0.006780	0.456081	
chunk0158_43_1	chr5	125800767	125801440	+	0	NA	Intergenic	Intergenic	307842	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.004458	0.373887	
chunk0190_251_1	chr8	36936562	36937225	+	0	NA	TTS (NM_001031836)	TTS (NM_001031836)	152569	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.001508	0.296687	
chunk0209_269_1	chrX	46812289	46812922	+	0	NA	Intergenic	L2a|LINE|L2	-24307	NM_006915	6102	Hs.44766	NM_006915	ENSG00000102218	RP2	DELXp11.3|NM23-H10|NME10|TBCCD2|XRP2	RP2 activator of ARL3 GTPase	protein-coding	0.006319	0.433754	
chunk0047_209_1	chr12	71576412	71576955	+	0	NA	intron (NM_003667, intron 13 of 17)	intron (NM_003667, intron 13 of 17)	-87214	NM_031435	83591	Hs.245798	NM_031435	ENSG00000173451	THAP2	-	THAP domain containing 2	protein-coding	0.009208	0.487132	
chunk0071_245_1	chr15	85395297	85395545	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	14805	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.008065	0.349398	
chunk0047_454_1	chr12	76645895	76646142	+	0	NA	Intergenic	MER52A|LTR|ERV1	-86209	NM_020841	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.012146	0.580645	
chunk0009_37_1	chr1	100412950	100413618	+	0	NA	intron (NM_003672, intron 4 of 15)	intron (NM_003672, intron 4 of 15)	60817	NM_003672	8556	Hs.127411	NM_003672	ENSG00000079335	CDC14A	DFNB105|DFNB32|DFNB35|cdc14|hCDC14	cell division cycle 14A	protein-coding	0.008982	0.384155	307(GAGAACAACCAGTTCC,-,0.00),308(AGAACAACCAGTTCCT,+,0.00)
chunk0095_268_1	chr2	19777488	19777898	+	0	NA	Intergenic	Intergenic	-91161	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.002439	0.435523	
chunk0167_197_1	chr6	64504498	64504972	+	0	NA	intron (NM_001142800, intron 26 of 42)	intron (NM_001142800, intron 26 of 42)	-796683	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.006329	0.427368	
chunk0163_438_1	chr6	17395104	17395470	+	0	NA	intron (NM_006366, intron 1 of 12)	MER58B|DNA|hAT-Charlie	1782	NM_006366	10486	Hs.132902	NM_006366	ENSG00000112186	CAP2	-	cyclase associated actin cytoskeleton regulatory protein 2	protein-coding	0.002732	0.351499	
chunk0140_238_1	chr4	71248890	71249178	+	0	NA	intron (NM_001098484, intron 2 of 25)	intron (NM_001098484, intron 2 of 25)	61748	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.003472	0.377163	
chunk0064_116_1	chr14	91265777	91266348	+	0	NA	Intergenic	LTR29|LTR|ERV1	-12182	NM_003485	8111	Hs.8882	NM_003485	ENSG00000119714	GPR68	AI2A6|GPR12A|OGR1	G protein-coupled receptor 68	protein-coding	0.007005	0.386364	
chunk0029_192_1	chr10	101385961	101386302	+	0	NA	intron (NM_003939, intron 1 of 13)	intron (NM_003939, intron 1 of 13)	32098	NM_033637	8945	Hs.643802	NM_003939	ENSG00000166167	BTRC	BETA-TRCP|FBW1A|FBXW1|FBXW1A|FWD1|bTrCP|bTrCP1|betaTrCP	beta-transducin repeat containing E3 ubiquitin protein ligase	protein-coding	0.000000	0.368421	99(CAGAACATCCTGTTCT,-,0.00),100(AGAACATCCTGTTCTC,+,0.00)
chunk0188_286_1	chr8	15598597	15599189	+	0	NA	intron (NM_006765, intron 1 of 10)	L1MC1|LINE|L1	58806	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.001689	0.362563	
chunk0098_213_1	chr2	73084178	73084653	+	0	NA	intron (NM_015470, intron 3 of 4)	intron (NM_015470, intron 3 of 4)	-12579	NM_144579	94097	Hs.368171	NM_144579	ENSG00000144040	SFXN5	BBG-TCC|SLC56A5	sideroflexin 5	protein-coding	0.006316	0.510504	
chunk0169_141_1	chr6	101454336	101454619	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	55492	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.007067	0.422535	
chunk0077_424_1	chr16	85349339	85350191	+	0	NA	Intergenic	Intergenic	-43440	NR_049816	100847022		NR_049816	ENSG00000266307	MIR5093	-	microRNA 5093	ncRNA	0.031690	0.600234	
chunk0107_38_1	chr2	211088250	211088840	+	0	NA	Intergenic	Intergenic	470974	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.003390	0.373942	366(GGGAACAGTATGTCCT,-,0.00),367(GGAACAGTATGTCCTA,+,0.00)
chunk0081_317_1	chr17	46018054	46018726	+	0	NA	intron (NM_001123067, intron 9 of 10).3	MamRep434|DNA|TcMar-Tigger	19140	NM_001007532	246744	Hs.661831	NM_001007532	ENSG00000256762	STH	MAPTIT	saitohin	protein-coding	0.008929	0.454681	
chunk0016_392_1	chr1	203027565	203027908	+	0	NA	intron (NM_001304331, intron 1 of 29)	intron (NM_001304331, intron 1 of 29)	1215	NM_001304331	8497	Hs.153648	NM_015053	ENSG00000143847	PPFIA4	-	PTPRF interacting protein alpha 4	protein-coding	0.011662	0.473837	
chunk0128_320_1	chr3	111869577	111870233	+	0	NA	intron (NM_001134439, intron 1 of 17)	intron (NM_001134439, intron 1 of 17)	10184	NM_001134439	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.001524	0.418569	
chunk0205_132_1	chr9	108087776	108088259	+	0	NA	Intergenic	Intergenic	-598297	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.010352	0.473140	
chunk0159_108_1	chr5	138559987	138560283	+	0	NA	TTS (NR_002913)	TTS (NR_002913)	975	NR_002913	26785		NR_002913	ENSG00000206989	SNORD63	RNU63|SNORD63A|U63	small nucleolar RNA, C/D box 63	snoRNA	0.013514	0.471380	
chunk0200_3_1	chr9	14445185	14445465	+	0	NA	Intergenic	L1ME3D|LINE|L1	-46342	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.000000	0.277580	
chunk0103_46_1	chr2	159358668	159359088	+	0	NA	intron (NM_001289975, intron 26 of 35)	L1PA7|LINE|L1	-72079	NM_001128212	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.009524	0.382423	
chunk0121_409_1	chr3	25623989	25625483	+	0	NA	exon (NM_001068, exon 19 of 36)	exon (NM_001068, exon 19 of 36)	39636	NM_001068	7155	Hs.475733	NM_001068	ENSG00000077097	TOP2B	TOPIIB|top2beta	DNA topoisomerase II beta	protein-coding	0.007363	0.343813	
chunk0077_358_1	chr16	84086383	84086689	+	0	NA	intron (NM_003791, intron 9 of 22)	intron (NM_003791, intron 9 of 22)	30407	NM_003791	8720	Hs.75890	NM_003791	ENSG00000140943	MBTPS1	PCSK8|S1P|SEDKF|SKI-1	membrane bound transcription factor peptidase, site 1	protein-coding	0.032680	0.605863	229(AGGCCCACAGTGTTCC,-,0.00),230(GGCCCACAGTGTTCCC,+,0.00)
chunk0074_146_1	chr16	23163939	23164376	+	0	NA	Intergenic	HAL1|LINE|L1	-14887	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.006865	0.378995	
chunk0125_80_1	chr3	64578331	64578755	+	0	NA	intron (NM_182920, intron 28 of 39)	MIRb|SINE|MIR	17197	NR_110150	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.007075	0.390588	188(AGGACAGTCAGACCTG,+,0.00)
chunk0091_24_1	chr19	3336499	3337443	+	0	NA	Intergenic	Intergenic	-22592	NM_001245005	4782	Hs.170131	NM_005597	ENSG00000141905	NFIC	CTF|CTF5|NF-I|NFI	nuclear factor I C	protein-coding	0.020127	0.598942	413(GAGGACACGTTGTACC,-,0.00),414(AGGACACGTTGTACCA,+,0.00)
chunk0121_254_1	chr3	23039432	23039737	+	0	NA	Intergenic	Intergenic	-163709	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.006557	0.415033	
chunk0120_323_1	chr3	10428329	10428925	+	0	NA	intron (NM_001001331, intron 2 of 22)	intron (NM_001001331, intron 2 of 22)	-34065	NR_030614	100126334		NR_030614	ENSG00000216135	MIR885	MIRN885|hsa-mir-885|mir-885	microRNA 885	ncRNA	0.016779	0.532663	282(GGAGACACAATGTTCC,-,0.00),283(GAGACACAATGTTCCC,+,0.00)
chunk0014_428_1	chr1	183472318	183472837	+	0	NA	promoter-TSS (NR_040063)	promoter-TSS (NR_040063)	206	NM_201569	9887	Hs.591463	NM_014837	ENSG00000116698	SMG7	C1orf16|EST1C|SGA56M	SMG7 nonsense mediated mRNA decay factor	protein-coding	0.098266	0.726923	
chunk0075_382_1	chr16	56681909	56682599	+	0	NA	promoter-TSS (NM_005952)	promoter-TSS (NM_005952)	-216	NM_005952	4501	Hs.374950	NM_005952	ENSG00000187193	MT1X	MT-1l|MT1	metallothionein 1X	protein-coding	0.068116	0.633864	
chunk0135_104_1	chr3	186687313	186687665	+	0	NA	Intergenic	Intergenic	21537	NM_000412	3273	Hs.1498	NM_000412	ENSG00000113905	HRG	HPRG|HRGP|THPH11	histidine rich glycoprotein	protein-coding	0.019886	0.456091	
chunk0108_364_1	chr2	236586053	236586253	+	0	NA	Intergenic	MIRb|SINE|MIR	16416	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.020000	0.407960	
chunk0090_210_1	chr18	73363112	73363656	+	0	NA	Intergenic	L1MB5|LINE|L1	38443	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.003676	0.322936	
chunk0157_300_1	chr5	121100983	121101358	+	0	NA	Intergenic	L1MC1|LINE|L1	-221380	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.000000	0.332447	
chunk0180_172_1	chr7	65384763	65385061	+	0	NA	intron (NM_001287534, intron 1 of 1)	intron (NM_001287534, intron 1 of 1)	11113	NM_152626	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.006711	0.347826	
chunk0212_328_1	chrX	144032165	144032407	+	0	NA	Intergenic	Intergenic	148215	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.000000	0.271605	
chunk0064_103_1	chr14	91087137	91088227	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-26331	NM_001286472	80017	Hs.309849	NM_024952	ENSG00000133943	DGLUCY	C14orf159	D-glutamate cyclase	protein-coding	0.010092	0.432631	339(ATGTACTTTATGTTCT,-,0.00),340(TGTACTTTATGTTCTT,+,0.00)
chunk0179_461_1	chr7	52878545	52878950	+	0	NA	Intergenic	Intergenic	-156909	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.002469	0.221675	
chunk0014_354_1	chr1	182347107	182347479	+	0	NA	Intergenic	HAL1M8|LINE|L1	-33232	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.013441	0.498660	
chunk0201_398_1	chr9	69155503	69155945	+	0	NA	intron (NM_001170414, intron 2 of 21)	intron (NM_001170414, intron 2 of 21)	-18331	NM_004817	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.006787	0.469526	
chunk0153_272_1	chr5	72883963	72884322	+	0	NA	intron (NM_153188, intron 11 of 24)	L1MB8|LINE|L1	5551	NR_039968	100616152		NR_039968	ENSG00000263593	MIR4804	-	microRNA 4804	ncRNA	0.011142	0.436111	
chunk0027_233_1	chr10	76433383	76433582	+	0	NA	intron (NR_131178, intron 7 of 7)	intron (NR_131178, intron 7 of 7)	-454562	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.020101	0.540000	110(GAGCACGGCCTGTCCT,-,0.00),111(AGCACGGCCTGTCCTG,+,0.00)
chunk0119_453_1	chr22	50391383	50391690	+	0	NA	intron (NM_001242900, intron 2 of 22)	AluJr|SINE|Alu	48219	NM_001242899	9701	Hs.449098	NM_014678	ENSG00000100239	PPP6R2	KIAA0685|PP6R2|SAP190|SAPS2	protein phosphatase 6 regulatory subunit 2	protein-coding	0.009772	0.396104	
chunk0212_209_1	chrX	135404185	135404539	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	7933	NR_104652	100506790	Hs.161358	NR_104652	ENSG00000229015	LOC100506790	-	uncharacterized LOC100506790	ncRNA	0.000000	0.428169	
chunk0079_150_1	chr17	13187786	13188056	+	0	NA	Intergenic	L1M5|LINE|L1	-169857	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.003704	0.309963	
chunk0049_120_1	chr12	91435146	91435849	+	0	NA	Intergenic	Intergenic	-252373	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.001422	0.419034	
chunk0155_281_1	chr5	96036481	96037257	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	-42269	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.002577	0.357786	436(GAGAGCAAACTGTTCT,-,0.00),437(AGAGCAAACTGTTCTC,+,0.00)
chunk0084_446_1	chr17	82889454	82890003	+	0	NA	intron (NM_005993, intron 16 of 38)	intron (NM_005993, intron 16 of 38)	-49673	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.029144	0.490909	
chunk0186_238_1	chr7	140836700	140836907	+	0	NA	intron (NM_004333, intron 2 of 17)	L2a|LINE|L2	87961	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.000000	0.360577	
chunk0132_424_1	chr3	164635530	164635729	+	0	NA	Intergenic	Intergenic	195851	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.000000	0.275000	
chunk0106_24_1	chr2	195840600	195840867	+	0	NA	intron (NM_018897, intron 47 of 64)	L1MEf|LINE|L1	183605	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.000000	0.287313	215(AATACACTGTGTTCAT,+,0.00)
chunk0210_300_1	chrX	87515596	87516206	+	0	NA	Intergenic	Intergenic	-1811	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.001639	0.360065	
chunk0059_51_1	chr14	30028107	30028586	+	0	NA	Intergenic	L1PA11|LINE|L1	-100653	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.010438	0.379167	
chunk0115_445_1	chr21	32241026	32241823	+	0	NA	Intergenic	Intergenic	37641	NM_018944	54069	Hs.190518	NM_018944	ENSG00000159055	MIS18A	B28|C21orf45|C21orf46|FASP1|MIS18alpha|hMis18alpha	MIS18 kinetochore protein A	protein-coding	0.010038	0.384712	497(AGGAACATGGAGTTCC,-,0.00),498(GGAACATGGAGTTCCT,+,0.00)
chunk0087_124_1	chr18	33421338	33421912	+	0	NA	intron (NM_001308126, intron 1 of 22)	intron (NM_001308126, intron 1 of 22)	18456	NM_001308126	374864	Hs.115461	NM_198995	ENSG00000166960	CCDC178	C18orf34	coiled-coil domain containing 178	protein-coding	0.006969	0.370435	
chunk0141_433_1	chr4	88863955	88864170	+	0	NA	intron (NM_014883, intron 6 of 23)	intron (NM_014883, intron 6 of 23)	-40701	NM_001015045	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.013953	0.296296	
chunk0190_349_1	chr8	39365297	39365557	+	0	NA	intron (NR_001448, intron 8 of 14)	L1MB7|LINE|L1	50764	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.000000	0.337165	
chunk0130_197_1	chr3	133661479	133662099	+	0	NA	5' UTR (NM_007027, exon 1 of 28)	5' UTR (NM_007027, exon 1 of 28)	104	NM_007027	11073	Hs.593379	NM_007027	ENSG00000163781	TOPBP1	Dpb11|TOP2BP1	DNA topoisomerase II binding protein 1	protein-coding	0.079032	0.637681	
chunk0098_206_1	chr2	72718814	72719446	+	0	NA	intron (NM_015189, intron 5 of 21)	L1M4a2|LINE|L1	106918	NM_015189	23233	Hs.303454	NM_015189	ENSG00000144036	EXOC6B	SEC15B|SEC15L2|SEMDJL3	exocyst complex component 6B	protein-coding	0.006329	0.391785	
chunk0073_371_1	chr16	15550986	15551513	+	0	NA	intron (NM_001142469, intron 2 of 5)	intron (NM_001142469, intron 2 of 5)	48983	NM_001142469	89927	Hs.401798	NM_033201	ENSG00000166780	BMERB1	C16orf45|MINP	bMERB domain containing 1	protein-coding	0.017078	0.492424	264(CAGTACTGTGTGTACC,-,0.00),265(AGTACTGTGTGTACCC,+,0.00)
chunk0153_334_1	chr5	74104327	74105079	+	0	NA	Intergenic	Intergenic	203622	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.006649	0.381142	210(ATGGACATCCTGTCTC,-,0.00),451(GAGGACAAACTGTGCT,-,0.00),452(AGGACAAACTGTGCTC,+,0.00)
chunk0052_238_1	chr13	25958977	25959277	+	0	NA	intron (NM_001313741, intron 32 of 35)	intron (NM_001313741, intron 32 of 35)	91933	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.000000	0.465116	
chunk0033_254_1	chr11	18384257	18384687	+	0	NA	Intergenic	Intergenic	-3315	NR_036116	100423016		NR_036116	ENSG00000264603	MIR3159	-	microRNA 3159	ncRNA	0.004651	0.494200	
chunk0132_358_1	chr3	161558288	161558770	+	0	NA	Intergenic	Intergenic	61721	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.010373	0.492754	258(CAGGTCAGGTTGTGCT,-,0.00),259(AGGTCAGGTTGTGCTG,+,0.00)
chunk0092_319_1	chr19	34661267	34661828	+	0	NA	Intergenic	L1ME3B|LINE|L1	15674	NR_045208	100130342	Hs.679909	NR_045208		SCGB2B3P	C2B|SCGB4A3P	secretoglobin family 2B member 3, pseudogene	pseudo	0.007130	0.386121	
chunk0037_112_1	chr11	72358910	72359436	+	0	NA	intron (NM_001258393, intron 3 of 14)	intron (NM_001258393, intron 3 of 14)	75511	NM_001258394	81570	Hs.523877	NM_030813	ENSG00000162129	CLPB	ANKCLB|HSP78|MEGCANN|MGCA7|SKD3	ClpB homolog, mitochondrial AAA ATPase chaperonin	protein-coding	0.011407	0.449715	
chunk0106_427_1	chr2	208279194	208279917	+	0	NA	intron (NM_015040, intron 5 of 41)	L1PA16|LINE|L1	13288	NM_015040	200576	Hs.744997	NM_015040	ENSG00000115020	PIKFYVE	CFD|FAB1|HEL37|PIP5K|PIP5K3|ZFYVE29	phosphoinositide kinase, FYVE-type zinc finger containing	protein-coding	0.004149	0.335635	
chunk0115_65_1	chr21	21518462	21518992	+	0	NA	intron (NM_004540, intron 16 of 17)	L2a|LINE|L2	218592	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.003774	0.291902	
chunk0161_377_1	chr5	176695115	176695427	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	47884	NM_012171	26262	Hs.532129	NM_012171	ENSG00000048140	TSPAN17	FBX23|FBXO23|TM4SF17	tetraspanin 17	protein-coding	0.012821	0.543131	
chunk0203_151_1	chr9	85614285	85614978	+	0	NA	intron (NM_001286715, intron 16 of 24)	intron (NM_001286715, intron 16 of 24)	127398	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.005772	0.299712	
chunk0161_366_1	chr5	176040550	176040874	+	0	NA	Intergenic	Intergenic	21343	NR_103794	100996385	Hs.382347	NR_103794	ENSG00000248469	LOC100996385	-	uncharacterized LOC100996385	ncRNA	0.027778	0.563077	
chunk0111_209_1	chr20	26517015	26517264	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-307906	NR_040095	284801	Hs.370699	NR_040095	ENSG00000227195	MIR663AHG	-	MIR663A host gene	ncRNA	0.032129	0.412000	
chunk0009_96_1	chr1	101816968	101817187	+	0	NA	intron (NR_110212, intron 4 of 6)	intron (NR_110212, intron 4 of 6)	30003	NR_110212	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.000000	0.304545	
chunk0138_5_1	chr4	30282707	30283164	+	0	NA	Intergenic	Intergenic	-437473	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.006565	0.388646	
chunk0100_157_1	chr2	109187265	109187842	+	0	NA	intron (NM_001099289, intron 1 of 9)	Tigger3a|DNA|TcMar-Tigger	-45965	NR_036223	100422863		NR_036223	ENSG00000264934	MIR4265	-	microRNA 4265	ncRNA	0.008666	0.413495	
chunk0078_385_1	chr16	87854298	87854628	+	0	NA	intron (NM_003486, intron 1 of 9)	intron (NM_003486, intron 1 of 9)	15031	NM_003486	8140	Hs.513797	NM_003486	ENSG00000103257	SLC7A5	4F2LC|CD98|D16S469E|E16|LAT1|MPE16	solute carrier family 7 member 5	protein-coding	0.012121	0.480363	
chunk0164_147_1	chr6	21367388	21368167	+	0	NA	Intergenic	(TTGTACACTT)n|Simple_repeat|Simple_repeat	144115	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.006418	0.443590	
chunk0182_412_1	chr7	100957972	100958463	+	0	NA	exon (NM_005960, exon 2 of 12)	exon (NM_005960, exon 2 of 12)	8797	NM_005960	4584	Hs.703577	NM_005960	ENSG00000169894	MUC3A	MUC-3A|MUC3	mucin 3A, cell surface associated	protein-coding	0.018330	0.526423	
chunk0003_294_1	chr1	37507782	37508409	+	0	NA	intron (NR_073092, intron 4 of 8)	intron (NR_073092, intron 4 of 8)	6724	NR_073092	64769	Hs.17118	NM_022756	ENSG00000163875	MEAF6	C1orf149|CENP-28|EAF6|NY-SAR-91	MYST/Esa1 associated factor 6	protein-coding	0.011164	0.366242	
chunk0137_129_1	chr4	15144317	15144562	+	0	NA	intron (NR_125911, intron 2 of 5)	UCON4|Unknown|Unknown	141765	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.012245	0.434959	
chunk0199_321_1	chr9	7483875	7484448	+	0	NA	Intergenic	L1PA10|LINE|L1	315638	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.003490	0.348432	
chunk0118_442_1	chr22	39128604	39128822	+	0	NA	Intergenic	Intergenic	23820	NM_175709	23492	Hs.356416	NM_175709	ENSG00000100307	CBX7	-	chromobox 7	protein-coding	0.013761	0.547945	
chunk0085_109_1	chr18	2774470	2775072	+	0	NA	intron (NM_015295, intron 41 of 47)	intron (NM_015295, intron 41 of 47)	-72259	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.008306	0.447761	256(TGACACACAATGTTCT,-,0.00),257(GACACACAATGTTCTT,+,0.00)
chunk0096_9_1	chr2	25966472	25966671	+	0	NA	intron (NM_002254, intron 1 of 7)	intron (NM_002254, intron 1 of 7)	16003	NM_002254	3797	Hs.21611	NM_002254	ENSG00000084731	KIF3C	-	kinesin family member 3C	protein-coding	0.015075	0.520000	
chunk0015_175_1	chr1	186854076	186854323	+	0	NA	intron (NM_001311193, intron 1 of 15)	intron (NM_001311193, intron 1 of 15)	25299	NM_024420	5321	Hs.497200	NM_024420	ENSG00000116711	PLA2G4A	GURDP|PLA2G4|cPLA2|cPLA2-alpha	phospholipase A2 group IVA	protein-coding	0.012146	0.350806	
chunk0187_430_1	chr7	158682413	158682954	+	0	NA	intron (NR_104054, intron 11 of 30)	intron (NR_104054, intron 11 of 30)	22148	NR_104054	54892	Hs.18616	NM_017760	ENSG00000146918	NCAPG2	3KS|CAP-G2|CAPG2|LUZP5|MTB|hCAP-G2	non-SMC condensin II complex subunit G2	protein-coding	0.000000	0.317343	
chunk0174_117_1	chr6	157157312	157157545	+	0	NA	intron (NM_017519, intron 8 of 18)	intron (NM_017519, intron 8 of 18)	166831	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.025751	0.529915	
chunk0032_130_1	chr11	4484032	4484660	+	0	NA	Intergenic	L2|LINE|L2	-4533	NM_001005171	390036	Hs.553726	NM_001005171	ENSG00000196778	OR52K1	OR11-8	olfactory receptor family 52 subfamily K member 1	protein-coding	0.006369	0.406995	219(TGGAACTTTGTGTACT,-,0.00),220(GGAACTTTGTGTACTT,+,0.00)
chunk0044_333_1	chr12	38261251	38261590	+	0	NA	Intergenic	L1M2b|LINE|L1	-55335	NM_001013620	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.005900	0.550000	
chunk0184_176_1	chr7	116538032	116538496	+	0	NA	intron (NM_001172895, intron 2 of 2)	intron (NM_001172895, intron 2 of 2)	11906	NM_001172897	857	Hs.74034	NM_001753	ENSG00000105974	CAV1	BSCL3|CGL3|LCCNS|MSTP085|PPH3|VIP21	caveolin 1	protein-coding	0.006466	0.380645	
chunk0184_167_1	chr7	116316996	116317742	+	0	NA	Intergenic	Intergenic	-30642	NR_130922	102724434	Hs.667624	NR_130921	ENSG00000237870	LOC102724434	-	uncharacterized LOC102724434	ncRNA	0.009383	0.423025	434(CAAGACAGACAGTTCT,-,0.00),435(AAGACAGACAGTTCTT,+,0.00)
chunk0043_262_1	chr12	20716977	20717652	+	0	NA	intron (NM_017435, intron 7 of 14)	intron (NM_017435, intron 7 of 14)	21849	NM_017435	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.001481	0.303254	204(AGGCTCATTATGTGCC,-,0.00)
chunk0149_434_1	chr5	29717825	29718037	+	0	NA	Intergenic	L1MA1|LINE|L1	-321955	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.009434	0.319249	
chunk0023_72_1	chr10	22168248	22168855	+	0	NA	Intergenic	Intergenic	41432	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.004942	0.315789	
chunk0188_194_1	chr8	11769468	11769807	+	0	NA	promoter-TSS (NM_001135748)	promoter-TSS (NM_001135748)	-26	NM_001135746	252969	Hs.293818	NM_145043	ENSG00000154328	NEIL2	NEH2|NEI2	nei like DNA glycosylase 2	protein-coding	0.088496	0.720588	
chunk0020_226_1	chr1	235504766	235505294	+	0	NA	promoter-TSS (NM_152490)	promoter-TSS (NM_152490)	-549	NM_001277155	148789	Hs.498143	NM_152490	ENSG00000162885	B3GALNT2	B3GalNAc-T2|MDDGA11	beta-1,3-N-acetylgalactosaminyltransferase 2	protein-coding	0.079545	0.646503	
chunk0175_170_1	chr7	4714093	4714512	+	0	NA	intron (NM_001037165, intron 1 of 8)	AluSz|SINE|Alu	32003	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.021480	0.490476	
chunk0004_239_1	chr1	47262858	47263296	+	0	NA	exon (NM_001048166, exon 15 of 17)	exon (NM_001048166, exon 15 of 17)	-30742	NM_001290406	6886	Hs.705618	NM_003189	ENSG00000162367	TAL1	SCL|TCL5|bHLHa17|tal-1	TAL bHLH transcription factor 1, erythroid differentiation factor	protein-coding	0.000000	0.394077	
chunk0069_264_1	chr15	64636737	64637421	+	0	NA	intron (NM_015042, intron 2 of 8)	L1ME3A|LINE|L1	66202	NM_001301302	4947	Hs.744924	NM_002537	ENSG00000180304	OAZ2	AZ2	ornithine decarboxylase antizyme 2	protein-coding	0.004386	0.367883	
chunk0147_319_1	chr4	184977941	184978569	+	0	NA	Intergenic	Intergenic	-39815	NR_039660	100616111		NR_039660	ENSG00000263458	MIR4455	-	microRNA 4455	ncRNA	0.014331	0.383148	
chunk0140_232_1	chr4	71189507	71190030	+	0	NA	intron (NM_001098484, intron 1 of 25)	intron (NM_001098484, intron 1 of 25)	2482	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.009560	0.393130	
chunk0163_432_1	chr6	17271651	17271887	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-9809	NM_001143942	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.012712	0.510549	
chunk0036_260_1	chr11	64954248	64954562	+	0	NA	intron (NM_001037225, intron 4 of 10)	intron (NM_001037225, intron 4 of 10)	17686	NM_001037225	283129	Hs.567793	NM_001037225	ENSG00000168070	MAJIN	C11orf85	membrane anchored junction protein	protein-coding	0.015924	0.463492	
chunk0008_159_1	chr1	92653449	92653890	+	0	NA	intron (NM_005665, intron 11 of 17)	L1PB4|LINE|L1	138735	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.002268	0.529412	
chunk0037_331_1	chr11	77075527	77075773	+	0	NA	intron (NM_004055, intron 1 of 12)	intron (NM_004055, intron 1 of 12)	8705	NM_004055	726	Hs.248153	NM_004055	ENSG00000149260	CAPN5	ADNIV|HTRA3|VRNI|nCL-3	calpain 5	protein-coding	0.008130	0.530364	
chunk0063_99_1	chr14	78586673	78586926	+	0	NA	intron (NM_004796, intron 1 of 16)	intron (NM_004796, intron 1 of 16)	183068	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.019763	0.480315	38(GTGTACACCCTGTCCC,-,0.00),39(TGTACACCCTGTCCCC,+,0.00)
chunk0193_395_1	chr8	80487269	80487618	+	0	NA	exon (NM_023929, exon 1 of 7)	exon (NM_023929, exon 1 of 7)	1230	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.085960	0.665714	
chunk0130_221_1	chr3	134166523	134166911	+	0	NA	intron (NM_002958, intron 13 of 14)	intron (NM_002958, intron 13 of 14)	84027	NM_002958	6259	Hs.654562	NM_002958	ENSG00000163785	RYK	D3S3195|JTK5|JTK5A|RYK1	receptor like tyrosine kinase	protein-coding	0.005155	0.383033	282(CAGGACAGCAAGTGCT,-,0.00),283(AGGACAGCAAGTGCTC,+,0.00)
chunk0121_440_1	chr3	26135911	26136182	+	0	NA	Intergenic	L2a|LINE|L2	-262351	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.007380	0.312500	
chunk0054_237_1	chr13	45812851	45813453	+	0	NA	intron (NM_198849, intron 1 of 1)	intron (NM_198849, intron 1 of 1)	38559	NM_198849	283514	Hs.368483	NM_198849	ENSG00000215475	SIAH3	-	siah E3 ubiquitin protein ligase family member 3	protein-coding	0.009967	0.547264	280(GGGAACATGGTGAGCC,-,0.00),281(GGAACATGGTGAGCCT,+,0.00),324(GGGAACATGGTGAGCC,-,0.00),325(GGAACATGGTGAGCCT,+,0.00),368(GGGAACATGGTGAGCC,-,0.00),369(GGAACATGGTGAGCCT,+,0.00)
chunk0154_77_1	chr5	77525325	77525568	+	0	NA	Intergenic	L2c|LINE|L2	-32939	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.000000	0.418033	
chunk0047_322_1	chr12	74309975	74310344	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-17528	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.002710	0.348649	
chunk0077_352_1	chr16	83779807	83780346	+	0	NA	exon (NM_001257, exon 12 of 14)	exon (NM_001257, exon 12 of 14)	23900	NR_120308	102724163		NR_120308	ENSG00000260228	LOC102724163	-	uncharacterized LOC102724163	ncRNA	0.014842	0.405556	
chunk0161_305_1	chr5	173411110	173411371	+	0	NA	Intergenic	Intergenic	63785	NR_107023	102465862		NR_107023	ENSG00000274994	MIR8056	hsa-mir-8056	microRNA 8056	ncRNA	0.011494	0.557252	
chunk0091_90_1	chr19	5620959	5621766	+	0	NA	exon (NM_014649, exon 2 of 21)	exon (NM_014649, exon 2 of 21)	1565	NM_014649	9667	Hs.655392	NM_014649	ENSG00000130254	SAFB2	-	scaffold attachment factor B2	protein-coding	0.022305	0.483911	235(AGGGACACCGAGTACC,-,0.00),236(GGGACACCGAGTACCA,+,0.00),481(GGGCACACACTGTTCC,-,0.00),482(GGCACACACTGTTCCT,+,0.00)
chunk0210_251_1	chrX	82987318	82987517	+	0	NA	Intergenic	MIRb|SINE|MIR	-520844	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.005025	0.355000	
chunk0156_289_1	chr5	109999930	110000579	+	0	NA	Intergenic	L2b|LINE|L2	117072	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.001541	0.390769	
chunk0146_178_1	chr4	160737089	160737468	+	0	NA	Intergenic	Intergenic	-1285455	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.005277	0.271053	
chunk0055_89_1	chr13	54764629	54764879	+	0	NA	Intergenic	L1ME3|LINE|L1	-409700	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.004000	0.386454	
chunk0089_244_1	chr18	62166770	62167233	+	0	NA	intron (NM_176787, intron 1 of 30)	L1PA8|LINE|L1	20055	NM_012327	23556	Hs.157031	NM_012327	ENSG00000197563	PIGN	MCAHS|MCAHS1|MCD4|MDC4|PIG-N	phosphatidylinositol glycan anchor biosynthesis class N	protein-coding	0.010799	0.407328	
chunk0012_427_1	chr1	164668298	164668877	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	106054	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.025907	0.484483	
chunk0016_398_1	chr1	203162722	203163362	+	0	NA	intron (NM_001048230, intron 2 of 2)	intron (NM_001048230, intron 2 of 2)	12772	NM_004997	4608	Hs.927	NM_004997	ENSG00000133055	MYBPH	-	myosin binding protein H	protein-coding	0.010937	0.500780	
chunk0099_139_1	chr2	86519461	86519795	+	0	NA	intron (NR_036454, intron 1 of 3)	intron (NR_036454, intron 1 of 3)	43869	NR_036454	51652	Hs.591582	NM_016079	ENSG00000115561	CHMP3	CGI-149|NEDF|VPS24	charged multivesicular body protein 3	protein-coding	0.000000	0.286567	
chunk0010_194_1	chr1	116008640	116008896	+	0	NA	intron (NM_018420, intron 2 of 11)	MIRc|SINE|MIR	-31492	NR_125970	101928977	Hs.627914	NR_125970		LOC101928977	-	uncharacterized LOC101928977	ncRNA	0.007812	0.513619	
chunk0159_102_1	chr5	138461673	138462056	+	0	NA	Intergenic	Intergenic	-3628	NM_001964	1958	Hs.326035	NM_001964	ENSG00000120738	EGR1	AT225|G0S30|KROX-24|NGFI-A|TIS8|ZIF-268|ZNF225	early growth response 1	protein-coding	0.018277	0.507812	
chunk0205_138_1	chr9	108172398	108172685	+	0	NA	Intergenic	L1PB1|LINE|L1	-682821	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.000000	0.329861	
chunk0198_303_1	chr8	138260198	138260406	+	0	NA	intron (NM_015912, intron 4 of 19)	LTR22B2|LTR|ERVK	236520	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.024038	0.464115	
chunk0029_198_1	chr10	101529956	101530419	+	0	NA	intron (NM_033637, intron 6 of 14)	intron (NM_033637, intron 6 of 14)	58083	NM_001308382	27343	Hs.523230	NM_013274	ENSG00000166169	POLL	BETAN|POLKAPPA	DNA polymerase lambda	protein-coding	0.006479	0.426724	
chunk0082_289_1	chr17	58352062	58352366	+	0	NA	promoter-TSS (NM_003168)	promoter-TSS (NM_003168)	24	NR_073470	6827	Hs.439481	NM_003168	ENSG00000213246	SUPT4H1	SPT4|SPT4H|SUPT4H|Supt4a	SPT4 homolog, DSIF elongation factor subunit	protein-coding	0.085526	0.659016	
chunk0118_380_1	chr22	36628221	36628420	+	0	NA	intron (NM_006078, intron 1 of 3)	intron (NM_006078, intron 1 of 3)	74325	NM_006078	10369	Hs.146766	NM_006078	ENSG00000166862	CACNG2	MRD10	calcium voltage-gated channel auxiliary subunit gamma 2	protein-coding	0.005025	0.405000	
chunk0106_287_1	chr2	204202181	204202811	+	0	NA	Intergenic	L2b|LINE|L2	265748	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.001587	0.381933	
chunk0113_257_1	chr20	56157886	56158256	+	0	NA	Intergenic	Intergenic	-90661	NM_019888	4159	Hs.248018	NM_019888	ENSG00000124089	MC3R	BMIQ9|MC3|MC3-R|OB20|OQTL	melanocortin 3 receptor	protein-coding	0.010811	0.463612	
chunk0200_430_1	chr9	29637845	29638136	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	-424990	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.000000	0.328767	
chunk0139_249_1	chr4	56126709	56126921	+	0	NA	Intergenic	Intergenic	29386	NR_106988									0.004717	0.352113	
chunk0164_18_1	chr6	17961249	17961918	+	0	NA	intron (NM_001243423, intron 2 of 2)	L4_A_Mam|LINE|RTE-X	26040	NM_022113	63971	Hs.94499	NM_022113	ENSG00000137177	KIF13A	RBKIN|bA500C11.2	kinesin family member 13A	protein-coding	0.005979	0.397015	356(AAGGACAGAAAGATCC,-,0.00),357(AGGACAGAAAGATCCT,+,0.00)
chunk0012_24_1	chr1	154961817	154962105	+	0	NA	promoter-TSS (NM_138300)	promoter-TSS (NM_138300)	-179	NM_138300	90780	Hs.533597	NM_138300	ENSG00000163348	PYGO2	1190004M21Rik	pygopus family PHD finger 2	protein-coding	0.145833	0.775087	
chunk0110_21_1	chr20	10315079	10315440	+	0	NA	Intergenic	Intergenic	-95753	NR_040710	100131208	Hs.658178	NR_040710	ENSG00000227906	SNAP25-AS1	-	SNAP25 antisense RNA 1	ncRNA	0.013850	0.461326	
chunk0050_364_1	chr12	107925796	107926119	+	0	NA	Intergenic	Intergenic	-22186	NR_037629	728739	Hs.741995	NR_037629		LOC728739	-	programmed cell death 2 pseudogene	pseudo	0.006192	0.469136	172(CAGAACACAATGTCCT,-,0.00),173(AGAACACAATGTCCTG,+,0.00)
chunk0021_170_1	chr10	5360392	5360905	+	0	NA	Intergenic	MER34A1|LTR|ERV1	-4365	NM_053049	114131	Hs.511775	NM_053049	ENSG00000178473	UCN3	SCP|SPC|UCNIII	urocortin 3	protein-coding	0.011696	0.426070	
chunk0056_168_1	chr13	85044124	85044323	+	0	NA	Intergenic	Intergenic	103834	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.010050	0.380000	
chunk0024_340_1	chr10	43260234	43260690	+	0	NA	intron (NM_145313, intron 1 of 12)	intron (NM_145313, intron 1 of 12)	6457	NM_145313	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.028509	0.669584	
chunk0070_148_1	chr15	71098805	71099303	+	0	NA	Intergenic	Intergenic	16446	NM_001102658	196993	Hs.646533	NM_001102658	ENSG00000225362	CT62	-	cancer/testis antigen 62	protein-coding	0.002008	0.382766	
chunk0182_168_1	chr7	95550037	95550753	+	0	NA	Intergenic	Intergenic	46218	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.011173	0.461646	314(GGGAACACGCCGTTCT,-,0.00),315(GGAACACGCCGTTCTC,+,0.00)
chunk0033_388_1	chr11	24252355	24253037	+	0	NA	Intergenic	Intergenic	-244274	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004399	0.363104	358(TGGCACATGTAGTTCT,-,0.00),359(GGCACATGTAGTTCTT,+,0.00)
chunk0132_284_1	chr3	159937495	159937888	+	0	NA	intron (NR_108088, intron 9 of 9)	intron (NR_108088, intron 9 of 9)	-51145	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.007634	0.390863	
chunk0141_135_1	chr4	81111547	81112193	+	0	NA	intron (NM_001282483, intron 9 of 13)	intron (NM_001282483, intron 9 of 13)	42287	NM_001282481	5593	Hs.232044	NM_006259	ENSG00000138669	PRKG2	PKG2|PRKGR2|cGK2|cGKII	protein kinase cGMP-dependent 2	protein-coding	0.007740	0.358578	
chunk0137_50_1	chr4	11591469	11591923	+	0	NA	Intergenic	Intergenic	-162783	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.011013	0.380220	216(AGCACTCTTTGTACTC,+,0.00),280(GGGCACATCATGTTCA,-,0.00),281(GGCACATCATGTTCAG,+,0.00)
chunk0115_143_1	chr21	23480411	23481309	+	0	NA	Intergenic	L1M5|LINE|L1	-96025	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.002227	0.282536	
chunk0098_265_1	chr2	75303277	75303671	+	0	NA	Intergenic	HAL1|LINE|L1	-103955	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.002538	0.367089	
chunk0155_421_1	chr5	100212945	100213427	+	0	NA	Intergenic	Intergenic	175068	NR_027503	100133050	Hs.534796	NR_027503		LOC100133050	-	glucuronidase beta pseudogene	pseudo	0.002075	0.438923	232(GGGAACAAGATGTTCC,-,0.00),233(GGAACAAGATGTTCCT,+,0.00)
chunk0075_440_1	chr16	57971435	57971678	+	0	NA	promoter-TSS (NM_001286130)	promoter-TSS (NM_001286130)	-440	NM_001135639	1258	Hs.147062	NM_001297	ENSG00000070729	CNGB1	CNCG2|CNCG3L|CNCG4|CNG4|CNGB1B|GAR1|GARP|GARP2|RCNC2|RCNCb|RCNCbeta|RP45	cyclic nucleotide gated channel beta 1	protein-coding	0.012346	0.614754	
chunk0081_243_1	chr17	42984406	42984964	+	0	NA	intron (NM_173079, intron 1 of 4)	intron (NM_173079, intron 1 of 4)	4120	NM_173079	146923	Hs.632255	NM_173079	ENSG00000198863	RUNDC1	-	RUN domain containing 1	protein-coding	0.007168	0.398927	
chunk0064_405_1	chr14	99475045	99475647	+	0	NA	intron (NM_032233, intron 1 of 12)	intron (NM_032233, intron 1 of 12)	5543	NM_032233	84193	Hs.510407	NM_032233	ENSG00000183576	SETD3	C14orf154|hSETD3	SET domain containing 3, actin histidine methyltransferase	protein-coding	0.016611	0.427861	
chunk0001_181_1	chr1	7198646	7199486	+	0	NA	intron (NM_015215, intron 4 of 22)	L2a|LINE|L2	413742	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.028571	0.587396	
chunk0154_399_1	chr5	88496763	88497134	+	0	NA	Intergenic	MIRb|SINE|MIR	-57858	NR_105021	102546226	Hs.535810	NR_105021	ENSG00000250156	LINC02060	-	long intergenic non-protein coding RNA 2060	ncRNA	0.002695	0.395161	
chunk0124_219_1	chr3	56209231	56209446	+	0	NA	intron (NR_132749, intron 3 of 17)	L2a|LINE|L2	259025	NR_132749	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.000000	0.527778	
chunk0210_6_1	chrX	66847510	66848262	+	0	NA	Intergenic	L1MA1|LINE|L1	-208588	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.002660	0.358566	
chunk0024_222_1	chr10	37857589	37857808	+	0	NA	promoter-TSS (NM_021045)	promoter-TSS (NM_021045)	-62	NM_001267606	57209	Hs.528423	NM_021045	ENSG00000198105	ZNF248	bA162G10.3	zinc finger protein 248	protein-coding	0.109589	0.677273	
chunk0104_397_1	chr2	180609495	180609818	+	0	NA	Intergenic	MIR|SINE|MIR	-82448	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.003096	0.373457	
chunk0066_314_1	chr15	35765028	35765568	+	0	NA	intron (NR_038251, intron 2 of 2)	intron (NR_038251, intron 2 of 2)	-161558	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.005556	0.345656	
chunk0144_236_1	chr4	134953051	134953532	+	0	NA	Intergenic	Intergenic	-751543	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.014553	0.377593	
chunk0060_118_1	chr14	43779238	43779526	+	0	NA	Intergenic	Intergenic	727914	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.003472	0.377163	
chunk0044_76_1	chr12	28072110	28072843	+	0	NA	Intergenic	L1MA8|LINE|L1	-100493	NM_002820	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.006821	0.346049	
chunk0162_148_1	chr6	3334533	3334927	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	75802	NM_001135750	389362	Hs.207069	NM_001128591	ENSG00000180822	PSMG4	C6orf86|PAC4|bA506K6.2	proteasome assembly chaperone 4	protein-coding	0.017766	0.473418	
chunk0126_355_1	chr3	82927617	82928492	+	0	NA	Intergenic	Intergenic	-1166255	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.005714	0.335616	
chunk0088_21_1	chr18	43484808	43485140	+	0	NA	Intergenic	LTR18B|LTR|ERVL	-207324	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.006024	0.489489	
chunk0039_310_1	chr11	103316948	103317221	+	0	NA	intron (NM_001377, intron 80 of 88)	intron (NM_001377, intron 80 of 88)	207653	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.003663	0.375912	
chunk0148_156_1	chr5	6590450	6591029	+	0	NA	Intergenic	L1ME4b|LINE|L1	7463	NR_024424	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.008636	0.412069	
chunk0065_410_1	chr14	105617186	105617759	+	0	NA	Intergenic	(TCACA)n|Simple_repeat|Simple_repeat	-3644	NR_107059	102466889		NR_107059	ENSG00000277030	MIR8071-2	hsa-mir-8071-2	microRNA 8071-2	ncRNA	0.012216	0.500000	
chunk0014_288_1	chr1	180615370	180616172	+	0	NA	Intergenic	L2b|LINE|L2	-16239	NM_004736	9213	Hs.227656	NM_004736	ENSG00000143324	XPR1	IBGC6|SLC53A1|SYG1|X3	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.007481	0.399751	
chunk0182_418_1	chr7	101117504	101117850	+	0	NA	Intergenic	Intergenic	-9412	NM_000602	5054	Hs.414795	NM_000602	ENSG00000106366	SERPINE1	PAI|PAI-1|PAI1|PLANH1	serpin family E member 1	protein-coding	0.017341	0.573487	
chunk0204_93_1	chr9	94397625	94398324	+	0	NA	intron (NM_032558, intron 1 of 11)	L1MC3|LINE|L1	23423	NM_032558	84641	Hs.555996	NM_032558	ENSG00000148110	MFSD14B	HIATL1	major facilitator superfamily domain containing 14B	protein-coding	0.005722	0.384286	
chunk0011_319_1	chr1	151972904	151973233	+	0	NA	Intergenic	Intergenic	21170	NM_002966	6281	Hs.143873	NM_002966	ENSG00000197747	S100A10	42C|ANX2L|ANX2LG|CAL1L|CLP11|Ca[1]|GP11|P11|p10	S100 calcium binding protein A10	protein-coding	0.006079	0.439394	
chunk0085_140_1	chr18	3255132	3255595	+	0	NA	TTS (NR_130143)	TTS (NR_130143)	3150	NM_001303049	10627	Hs.190086	NM_006471	ENSG00000101608	MYL12A	HEL-S-24|MLC-2B|MLCB|MRCL3|MRLC3|MYL2B	myosin light chain 12A	protein-coding	0.006479	0.377155	
chunk0028_69_1	chr10	83677686	83678062	+	0	NA	Intergenic	LTR41|LTR|ERVL	-461555	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.007979	0.466844	122(AAGGACAGCAAGTTCT,-,0.00),123(AGGACAGCAAGTTCTC,+,0.00)
chunk0053_7_1	chr13	26179416	26179777	+	0	NA	intron (NM_183045, intron 5 of 5)	MER70B|LTR|ERVL	42161	NM_183044	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.005540	0.508287	
chunk0123_457_1	chr3	51356274	51357152	+	0	NA	intron (NM_004947, intron 43 of 52)	MIRb|SINE|MIR	-28524	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.007973	0.502844	
chunk0040_101_1	chr11	111786819	111787079	+	0	NA	intron (NM_024740, intron 14 of 14)	intron (NM_024740, intron 14 of 14)	-20504	NM_181700	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.000000	0.367816	
chunk0072_50_1	chr16	1297032	1297769	+	0	NA	Intergenic	MER4D|LTR|ERV1	-11753	NM_194261	7329	Hs.302903	NM_003345	ENSG00000103275	UBE2I	C358B7.1|P18|UBC9	ubiquitin conjugating enzyme E2 I	protein-coding	0.006784	0.440379	
chunk0037_118_1	chr11	72752372	72752571	+	0	NA	promoter-TSS (NM_001040118)	promoter-TSS (NM_001040118)	-82	NM_001040118	116985	Hs.503165	NM_015242	ENSG00000186635	ARAP1	CENTD2	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	protein-coding	0.090452	0.770000	
chunk0056_418_1	chr13	94444871	94445270	+	0	NA	intron (NM_001922, intron 6 of 7)	intron (NM_001922, intron 6 of 7)	34612	NM_001129889	1638	Hs.301865	NM_001922	ENSG00000080166	DCT	TRP-2|TYRP2	dopachrome tautomerase	protein-coding	0.000000	0.377500	
chunk0111_322_1	chr20	32330159	32330707	+	0	NA	intron (NM_004798, intron 8 of 8)	intron (NM_004798, intron 8 of 8)	-27911	NM_001164603	171023	Hs.374043	NM_015338	ENSG00000171456	ASXL1	BOPS|MDS	ASXL transcriptional regulator 1	protein-coding	0.009124	0.402550	
chunk0043_268_1	chr12	20830207	20830907	+	0	NA	intron (NM_019844, intron 3 of 15)	MER4C|LTR|ERV1	19853	NM_019844	28234	Hs.504966	NM_019844	ENSG00000111700	SLCO1B3	HBLRR|LST-2|LST-3TM13|LST3|OATP-8|OATP1B3|OATP8|SLC21A8	solute carrier organic anion transporter family member 1B3	protein-coding	0.001429	0.350927	320(GTGAACATAGAGTACC,-,0.00),321(TGAACATAGAGTACCT,+,0.00)
chunk0165_451_1	chr6	40732780	40733545	+	0	NA	Intergenic	L1ME2z|LINE|L1	-145698	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.007843	0.368146	
chunk0007_303_1	chr1	84225484	84225794	+	0	NA	intron (NM_182948, intron 9 of 9)	L1MA4A|LINE|L1	44007	NM_001242862	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.003226	0.511254	
chunk0065_160_1	chr15	25560343	25560795	+	0	NA	Intergenic	Intergenic	-121541	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.008850	0.408389	
chunk0013_78_1	chr1	167617282	167617859	+	0	NA	Intergenic	Intergenic	-12667	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.008666	0.493080	308(GGGAACAAAGTGTTCC,-,0.00),309(GGAACAAAGTGTTCCA,+,0.00)
chunk0059_231_1	chr14	34253817	34254607	+	0	NA	Intergenic	Intergenic	208050	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.007595	0.369153	
chunk0006_75_1	chr1	64935593	64935920	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	30748	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.009174	0.466463	
chunk0179_274_1	chr7	49429137	49429836	+	0	NA	Intergenic	Intergenic	-344175	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.010014	0.424286	
chunk0025_273_1	chr10	56139148	56139991	+	0	NA	Intergenic	Intergenic	221704	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.008304	0.356635	
chunk0135_39_1	chr3	185341606	185342089	+	0	NA	intron (NM_001242317, intron 2 of 12)	MER58A|DNA|hAT-Charlie	-21201	NM_004721	9175	Hs.591306	NM_004721	ENSG00000073803	MAP3K13	LZK|MEKK13|MLK	mitogen-activated protein kinase kinase kinase 13	protein-coding	0.004141	0.419421	
chunk0044_290_1	chr12	32747147	32747757	+	0	NA	intron (NM_001040436, intron 4 of 4)	intron (NM_001040436, intron 4 of 4)	8501	NM_001040436	51067	Hs.505231	NM_015936	ENSG00000139131	YARS2	CGI-04|MLASA2|MT-TYRRS|TYRRS	tyrosyl-tRNA synthetase 2	protein-coding	0.009836	0.397709	
chunk0122_17_1	chr3	27496357	27496677	+	0	NA	Intergenic	Intergenic	-12097	NM_001258379	9497	Hs.250072	NM_003615	ENSG00000033867	SLC4A7	NBC2|NBC3|NBCN1|SBC2|SLC4A6	solute carrier family 4 member 7	protein-coding	0.003125	0.467290	246(AGGTACAATCTGTGCT,-,0.00),247(GGTACAATCTGTGCTT,+,0.00)
chunk0029_356_1	chr10	107533045	107533714	+	0	NA	Intergenic	Intergenic	-368671	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.016442	0.411940	538(TAGCACACACAGTGCC,-,0.00),539(AGCACACACAGTGCCT,+,0.00)
chunk0076_401_1	chr16	72644711	72645420	+	0	NA	intron (NR_126330, intron 1 of 13)	intron (NR_126330, intron 1 of 13)	19944	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.002821	0.332394	
chunk0003_186_1	chr1	33746703	33747003	+	0	NA	intron (NM_052896, intron 13 of 69)	intron (NM_052896, intron 13 of 69)	-113622	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.003333	0.411960	224(AGAAACATACTGTGCT,-,0.00),225(GAAACATACTGTGCTG,+,0.00)
chunk0016_156_1	chr1	197633447	197633674	+	0	NA	intron (NM_001300858, intron 10 of 15)	LTR41|LTR|ERVL	141933	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.000000	0.535088	
chunk0118_448_1	chr22	39399745	39399985	+	0	NA	intron (NM_006116, intron 1 of 10)	CpG	111	NM_153497	10454	Hs.507681	NM_006116	ENSG00000100324	TAB1	3'-Tab1|MAP3K7IP1	TGF-beta activated kinase 1 (MAP3K7) binding protein 1	protein-coding	0.062500	0.692946	
chunk0111_240_1	chr20	29478386	29478701	+	0	NA	Intergenic	Intergenic	-61582	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.012698	0.465190	140(AGGAACACACTGTGCC,-,0.00),141(GGAACACACTGTGCCT,+,0.00)
chunk0036_379_1	chr11	67521227	67521451	+	0	NA	intron (NM_016366, intron 3 of 6)	L2a|LINE|L2	2089	NM_016366	51475	Hs.278984	NM_016366	ENSG00000167791	CABP2	DFNB93	calcium binding protein 2	protein-coding	0.008929	0.440000	64(TGCACGTGCTGTTCCT,+,0.00)
chunk0196_181_1	chr8	105989580	105990214	+	0	NA	intron (NR_125797, intron 1 of 4)	MER67D|LTR|ERV1	70606	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.006309	0.404724	565(TAGCTCACCCTGTGCT,-,0.00),566(AGCTCACCCTGTGCTT,+,0.00)
chunk0168_88_1	chr6	79913434	79913726	+	0	NA	Intergenic	Intergenic	34018	NM_022726	6785	Hs.101915	NM_022726	ENSG00000118402	ELOVL4	ADMD|CT118|ISQMR|SCA34|STGD2|STGD3	ELOVL fatty acid elongase 4	protein-coding	0.006849	0.477816	
chunk0114_419_1	chr20	64102713	64103088	+	0	NA	Intergenic	CpG	3931	NM_005286	2832	Hs.248118	NM_005286	ENSG00000125522	NPBWR2	GPR8	neuropeptides B and W receptor 2	protein-coding	0.058667	0.627660	275(AGGGACAGCTTGTTCT,-,0.00),276(GGGACAGCTTGTTCTT,+,0.00)
chunk0210_349_1	chrX	96222246	96222852	+	0	NA	Intergenic	Intergenic	115353	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.008251	0.393740	282(AAGAACTTAATGTTCC,-,0.00),283(AGAACTTAATGTTCCA,+,0.00)
chunk0105_35_1	chr2	182774153	182774432	+	0	NA	intron (NM_018981, intron 22 of 23)	L1PA6|LINE|L1	58251	NR_073367	54431	Hs.516632	NM_018981	ENSG00000077232	DNAJC10	ERdj5|JPDI|MTHr|PDIA19	DnaJ heat shock protein family (Hsp40) member C10	protein-coding	0.017921	0.528571	
chunk0107_265_1	chr2	217510762	217510961	+	0	NA	intron (NR_026597, intron 2 of 12)	L1MC4|LINE|L1	228128	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.015075	0.370000	
chunk0153_278_1	chr5	72949371	72949885	+	0	NA	Intergenic	Intergenic	-6353	NM_001146032	115548	Hs.165762	NM_138782	ENSG00000157107	FCHO2	-	FCH domain only 2	protein-coding	0.000000	0.433010	238(TGGTACACTGTGTTCT,-,0.00),239(GGTACACTGTGTTCTG,+,0.00)
chunk0052_374_1	chr12	128839329	128840223	+	0	NA	Intergenic	L1ME4a|LINE|L1	-13658	NR_133646	144423	Hs.655668	NM_144669	ENSG00000151948	GLT1D1	-	glycosyltransferase 1 domain containing 1	protein-coding	0.020134	0.482682	462(ATGTACAGGGTGTTTC,-,0.00)
chunk0172_331_1	chr6	138451612	138452286	+	0	NA	intron (NM_020464, intron 3 of 6)	MIRb|SINE|MIR	-16655	NR_036099	100423001		NR_036099	ENSG00000266555	MIR3145	mir-3145	microRNA 3145	ncRNA	0.000000	0.368889	280(AAAAACAGTGTGTACC,-,0.00),281(AAAACAGTGTGTACCA,+,0.00),356(GAGAACAGAATGACCC,-,0.00),357(AGAACAGAATGACCCA,+,0.00)
chunk0143_189_1	chr4	112277233	112277490	+	0	NA	3' UTR (NM_052864, exon 2 of 2)	3' UTR (NM_052864, exon 2 of 2)	8542	NM_052864	92610	Hs.310640	NM_052864	ENSG00000145365	TIFA	T2BP|T6BP|TIFAA	TRAF interacting protein with forkhead associated domain	protein-coding	0.007782	0.391473	
chunk0036_79_1	chr11	60625152	60625566	+	0	NA	intron (NR_026946, intron 2 of 6)	L1MA9|LINE|L1	9608	NR_026946	283197	Hs.372650	NM_174939	ENSG00000181995	LINC00301	C11orf64|NCRNA00301	long intergenic non-protein coding RNA 301	ncRNA	0.007246	0.351807	
chunk0201_392_1	chr9	69122863	69123062	+	0	NA	intron (NM_001170414, intron 1 of 21)	intron (NM_001170414, intron 1 of 21)	1698	NM_001170414	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.020101	0.475000	
chunk0180_178_1	chr7	65719175	65719439	+	0	NA	TTS (NR_027392)	TTS (NR_027392)	31617	NR_103527	441242	Hs.373941	NM_001013464	ENSG00000272693	LOC441242	-	uncharacterized LOC441242	ncRNA	0.003788	0.430189	
chunk0033_440_1	chr11	25337523	25338089	+	0	NA	Intergenic	L1MC1|LINE|L1	840836	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.005300	0.322751	
chunk0208_433_1	chrX	30144263	30144725	+	0	NA	Intergenic	L1ME4a|LINE|L1	-71064	NM_002364	4113	Hs.113824	NM_002364	ENSG00000099399	MAGEB2	CT3.2|DAM6|MAGE-XP-2	MAGE family member B2	protein-coding	0.000000	0.334773	
chunk0186_374_1	chr7	144117074	144117519	+	0	NA	Intergenic	Intergenic	7713	NM_001005480	442361	Hs.553841	NM_001005480	ENSG00000221989	OR2A2	OR2A17P|OR2A2P|OR7-11|OST008	olfactory receptor family 2 subfamily A member 2	protein-coding	0.004494	0.340807	
chunk0212_322_1	chrX	143938153	143938438	+	0	NA	Intergenic	L1MA2|LINE|L1	54224	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.003509	0.356643	
chunk0057_210_1	chr13	103883211	103883466	+	0	NA	Intergenic	Intergenic	458138	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.023529	0.507812	
chunk0190_300_1	chr8	38089972	38090211	+	0	NA	Intergenic	HERV1_I-int|LTR|ERV1	-15402	NM_004674	9070	Hs.521530	NM_004674	ENSG00000129691	ASH2L	ASH2|ASH2L1|ASH2L2|Bre2	ASH2 like, histone lysine methyltransferase complex subunit	protein-coding	0.008368	0.454167	
chunk0075_388_1	chr16	56773552	56774185	+	0	NA	intron (NM_014669, intron 3 of 21)	intron (NM_014669, intron 3 of 21)	-7924	NM_001242795	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.004739	0.367508	381(AAGGACATAGTGTTCA,-,0.00),382(AGGACATAGTGTTCAA,+,0.00)
chunk0017_135_1	chr1	206607017	206607318	+	0	NA	intron (NM_006893, intron 4 of 14)	intron (NM_006893, intron 4 of 14)	5384	NM_006893	1939	Hs.497581	NM_006893	ENSG00000143486	EIF2D	HCA56|LGTN	eukaryotic translation initiation factor 2D	protein-coding	0.009967	0.317881	107(CAGATCTGTGTGTTCT,-,0.00),108(AGATCTGTGTGTTCTT,+,0.00)
chunk0014_422_1	chr1	183375660	183376024	+	0	NA	intron (NM_015039, intron 1 of 10)	intron (NM_015039, intron 1 of 10)	42657	NM_015039	23057	Hs.497123	NM_015039	ENSG00000157064	NMNAT2	C1orf15|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.002747	0.397260	180(TGGCACTGTGTGTTCA,-,0.00),181(GGCACTGTGTGTTCAT,+,0.00),225(TAGAACAACCTGTGCT,-,0.00),226(AGAACAACCTGTGCTG,+,0.00)
chunk0168_27_1	chr6	77521153	77521482	+	0	NA	Intergenic	L1PA7|LINE|L1	-57914	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.003040	0.345455	148(CTGAACAACCTGTTCC,-,0.00),149(TGAACAACCTGTTCCT,+,0.00)
chunk0027_390_1	chr10	79925963	79926411	+	0	NA	intron (NR_033857, intron 5 of 5)	intron (NR_033857, intron 5 of 5)	6009	NR_002724	8512	Hs.733579	NR_002724	ENSG00000242600	MBL1P	COLEC3P|MBL1P1	mannose binding lectin 1, pseudogene	pseudo	0.015625	0.550111	
chunk0060_331_1	chr14	51491799	51492341	+	0	NA	intron (NM_001042481, intron 1 of 14)	intron (NM_001042481, intron 1 of 14)	2949	NM_001042481	122786	Hs.434914	NM_152330	ENSG00000139926	FRMD6	C14orf31|EX1|Willin|c14_5320	FERM domain containing 6	protein-coding	0.005535	0.482505	
chunk0120_41_1	chr3	2827557	2827756	+	0	NA	intron (NM_001206955, intron 6 of 23)	intron (NM_001206955, intron 6 of 23)	-64559	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.005025	0.310000	
chunk0157_349_1	chr5	122937907	122938221	+	0	NA	intron (NM_014035, intron 2 of 6)	intron (NM_014035, intron 2 of 6)	92599	NM_014035	28966	Hs.483200	NM_014035	ENSG00000064652	SNX24	PRO1284|SBBI31	sorting nexin 24	protein-coding	0.012739	0.561905	
chunk0198_316_1	chr8	139758156	139758535	+	0	NA	intron (NM_001160372, intron 21 of 22)	intron (NM_001160372, intron 21 of 22)	-55289	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.018470	0.560526	
chunk0088_383_1	chr18	54263968	54264594	+	0	NA	Intergenic	Intergenic	-5198	NM_007195	11201	Hs.438533	NM_007195	ENSG00000101751	POLI	RAD30B|RAD3OB|eta2	DNA polymerase iota	protein-coding	0.004792	0.389155	
chunk0068_127_1	chr15	52653435	52654150	+	0	NA	intron (NM_019600, intron 2 of 12)	L2c|LINE|L2	-1742	NM_001286495	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.006993	0.350559	
chunk0091_287_1	chr19	11964818	11965173	+	0	NA	promoter-TSS (NM_001012753)	promoter-TSS (NM_001012753)	-59	NM_001012753	284390	Hs.646386	NM_001012753	ENSG00000197054	ZNF763	ZNF|ZNF440L	zinc finger protein 763	protein-coding	0.036620	0.567416	
chunk0041_68_1	chr11	123655364	123655757	+	0	NA	promoter-TSS (NM_001040151)	promoter-TSS (NM_001040151)	-953	NM_018400	55800	Hs.4865	NM_018400	ENSG00000166257	SCN3B	ATFB16|BRGDA7|HSA243396|SCNB3	sodium voltage-gated channel beta subunit 3	protein-coding	0.017812	0.451777	206(AGTAACAGAATGTCCC,-,0.00),207(GTAACAGAATGTCCCC,+,0.00)
chunk0192_209_1	chr8	65043904	65044445	+	0	NA	Intergenic	Intergenic	136166	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.003697	0.313653	
chunk0192_454_1	chr8	70221209	70221544	+	0	NA	intron (NM_006540, intron 2 of 22)	intron (NM_006540, intron 2 of 22)	-150049	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.002985	0.348214	196(AAGTACACTGTGTTCC,-,0.00),197(AGTACACTGTGTTCCA,+,0.00)
chunk0181_98_1	chr7	80466058	80466306	+	0	NA	intron (NM_001102386, intron 5 of 7)	MamRep605|LTR?|LTR?	45744	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.008065	0.449799	
chunk0186_232_1	chr7	140651884	140652129	+	0	NA	Intergenic	Intergenic	-21147	NM_052853	90956	Hs.744886	NM_052853	ENSG00000133597	ADCK2	AARF	aarF domain containing kinase 2	protein-coding	0.016327	0.548780	
chunk0212_240_1	chrX	137379857	137380395	+	0	NA	Intergenic	Intergenic	-186061	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.009294	0.324675	259(CAGCTCAGTGTGTTCT,-,0.00),260(AGCTCAGTGTGTTCTC,+,0.00)
chunk0148_398_1	chr5	14842678	14843076	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	-16865	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.005025	0.461153	188(GAGAACACAATGTTCT,-,0.00),189(AGAACACAATGTTCTG,+,0.00)
chunk0106_90_1	chr2	197168759	197169170	+	0	NA	intron (NM_001195144, intron 2 of 27)	L2b|LINE|L2	133555	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.012165	0.504854	238(CAGAACATTGTGCACC,-,0.00),239(AGAACATTGTGCACCT,+,0.00)
chunk0167_221_1	chr6	66647214	66647509	+	0	NA	Intergenic	L1M3e|LINE|L1	859482	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.013559	0.537162	
chunk0076_8_1	chr16	58592411	58592919	+	0	NA	intron (NR_049763, intron 2 of 49)	intron (NR_049763, intron 2 of 49)	-32734	NR_002980	677830	Hs.677515	NR_002980	ENSG00000281910	SNORA50A	ACA50|SNORA50|SNORA76A	small nucleolar RNA, H/ACA box 50A	snoRNA	0.005906	0.426326	
chunk0107_347_1	chr2	221688484	221689229	+	0	NA	Intergenic	Intergenic	-114654	NM_001304536	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.008054	0.341823	298(TACACACCGTGTTCTC,+,0.00)
chunk0046_380_1	chr12	63495852	63496215	+	0	NA	Intergenic	Intergenic	172541	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.000000	0.291209	
chunk0192_328_1	chr8	67202362	67203039	+	0	NA	intron (NM_006421, intron 36 of 38)	intron (NM_006421, intron 36 of 38)	118852	NM_001291339	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.011817	0.417404	
chunk0093_224_1	chr19	50088568	50088859	+	0	NA	Intergenic	L1MC2|LINE|L1	3896	NR_024214	100169951	Hs.723094	NR_024214		SNAR-A3	-	small NF90 (ILF3) associated RNA A3	snRNA	0.010309	0.359589	
chunk0115_129_1	chr21	23252641	23252953	+	0	NA	Intergenic	Intergenic	132038	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.003205	0.255591	
chunk0150_62_1	chr5	32027936	32028490	+	0	NA	intron (NM_178140, intron 5 of 23)	intron (NM_178140, intron 5 of 23)	-92054	NR_036241	100422874		NR_036241	ENSG00000266243	MIR4279	-	microRNA 4279	ncRNA	0.014440	0.443243	310(AGTCACAGTGTGTTCC,-,0.00),311(GTCACAGTGTGTTCCA,+,0.00)
chunk0028_347_1	chr10	92231238	92231478	+	0	NA	intron (NM_001178137, intron 2 of 9)	intron (NM_001178137, intron 2 of 9)	11921	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.000000	0.390041	183(CAGAACACTTTGTACA,-,0.00),184(AGAACACTTTGTACAC,+,0.00)
chunk0194_219_1	chr8	86165000	86165777	+	0	NA	Intergenic	L2a|LINE|L2	64987	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.001287	0.419023	
chunk0034_258_1	chr11	34407314	34407695	+	0	NA	Intergenic	Intergenic	-31421	NM_001752	847	Hs.502302	NM_001752	ENSG00000121691	CAT	-	catalase	protein-coding	0.002625	0.460733	214(TGGTGCATCCTGTTCT,-,0.00),215(GGTGCATCCTGTTCTT,+,0.00)
chunk0139_185_1	chr4	54305885	54306173	+	0	NA	Intergenic	L1PB1|LINE|L1	76932	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.006944	0.359862	
chunk0051_361_1	chr12	121237558	121237856	+	0	NA	TTS (NM_172216)	TTS (NM_172216)	27846	NR_046373	5025	Hs.321709	NM_002560	ENSG00000135124	P2RX4	P2X4|P2X4R	purinergic receptor P2X 4	protein-coding	0.010067	0.404682	
chunk0005_8_1	chr1	54058394	54058705	+	0	NA	intron (NR_130900, intron 2 of 4)	intron (NR_130900, intron 2 of 4)	4470	NR_039942	100616315		NR_039942	ENSG00000283749	MIR4781	mir-4781	microRNA 4781	ncRNA	0.016077	0.445513	
chunk0196_355_1	chr8	114667431	114667895	+	0	NA	Intergenic	L1M4a2|LINE|L1	1000349	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004310	0.301075	
chunk0137_65_1	chr4	11890897	11891412	+	0	NA	Intergenic	L1MB8|LINE|L1	-332297	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.007767	0.284884	
chunk0066_95_1	chr15	29784453	29784995	+	0	NA	intron (NM_175610, intron 2 of 26)	HAL1M8|LINE|L1	36824	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.014760	0.364641	
chunk0094_222_1	chr2	6750751	6751281	+	0	NA	intron (NR_038369, intron 1 of 5)	intron (NR_038369, intron 1 of 5)	19295	NR_038369	400941	Hs.446195	NM_001001695	ENSG00000205837	LINC00487	-	long intergenic non-protein coding RNA 487	ncRNA	0.005660	0.403013	
chunk0206_44_1	chr9	117406027	117406226	+	0	NA	intron (NM_014010, intron 1 of 21)	intron (NM_014010, intron 1 of 21)	8913	NM_014010	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.010050	0.460000	
chunk0091_170_1	chr19	7833346	7833657	+	0	NA	intron (NM_145245, intron 1 of 18)	intron (NM_145245, intron 1 of 18)	3226	NM_145245	115704	Hs.26870	NM_145245	ENSG00000142459	EVI5L	-	ecotropic viral integration site 5 like	protein-coding	0.028939	0.570513	
chunk0181_212_1	chr7	84583315	84583724	+	0	NA	intron (NR_110080, intron 3 of 3)	intron (NR_110080, intron 3 of 3)	51043	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.009780	0.334146	
chunk0081_308_1	chr17	45579818	45580074	+	0	NA	Intergenic	Intergenic	21916	NR_026901	644172	Hs.448859	NR_026901		MAPK8IP1P2	-	mitogen-activated protein kinase 8 interacting protein 1 pseudogene 2	pseudo	0.011719	0.509728	
chunk0112_409_1	chr20	47126112	47126429	+	0	NA	intron (NM_172110, intron 9 of 13)	intron (NM_172110, intron 9 of 13)	-40697	NR_037410	100500814		NR_037410	ENSG00000264901	MIR3616	mir-3616	microRNA 3616	ncRNA	0.041009	0.581761	
chunk0159_117_1	chr5	138659789	138660562	+	0	NA	Intergenic	MIR|SINE|MIR	-84546	NM_004134	3313	Hs.184233	NM_004134	ENSG00000113013	HSPA9	CRP40|CSA|EVPLS|GRP-75|GRP75|HEL-S-124m|HSPA9B|MOT|MOT2|MTHSP75|PBP74|SAAN|SIDBA4	heat shock protein family A (Hsp70) member 9	protein-coding	0.005175	0.428941	
chunk0171_262_1	chr6	127432027	127432380	+	0	NA	Intergenic	Intergenic	27187	NM_014702	9729	Hs.319247	NM_014702	ENSG00000189367	KIAA0408	-	KIAA0408	protein-coding	0.000000	0.355932	241(AAGAACAGTGTGTGCT,-,0.00),242(AGAACAGTGTGTGCTG,+,0.00)
chunk0112_254_1	chr20	42074860	42075574	+	0	NA	3' UTR (NM_007050, exon 31 of 31)	3' UTR (NM_007050, exon 31 of 31)	-456723	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.004202	0.467133	
chunk0006_388_1	chr1	74739250	74739450	+	0	NA	intron (NR_027962, intron 3 of 5)	L2a|LINE|L2	-5942	NM_001889	1429	Hs.83114	NM_001889	ENSG00000116791	CRYZ	-	crystallin zeta	protein-coding	0.005000	0.388060	
chunk0065_30_1	chr15	20644355	20644656	+	0	NA	Intergenic	L1MC3|LINE|L1	82156	NR_027411	729786	Hs.592025	NR_027411	ENSG00000181984	GOLGA8CP	GOLGA8C	golgin A8 family member C, pseudogene	pseudo	0.003322	0.311258	
chunk0037_175_1	chr11	74035150	74035803	+	0	NA	intron (NM_015531, intron 30 of 30)	L2c|LINE|L2	-26239	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.003063	0.405199	
chunk0109_119_1	chr20	2769942	2770141	+	0	NA	Intergenic	Intergenic	30605	NM_019609	56265	Hs.659346	NM_019609	ENSG00000088882	CPXM1	CPX1|CPXM	carboxypeptidase X, M14 family member 1	protein-coding	0.015075	0.580000	
chunk0030_59_1	chr10	111925919	111926516	+	0	NA	Intergenic	Intergenic	257562	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.008375	0.404682	295(CAGGACAGAGAGTTCC,-,0.00),296(AGGACAGAGAGTTCCT,+,0.00)
chunk0013_424_1	chr1	173427529	173427966	+	0	NA	intron (NR_125960, intron 1 of 1)	Tigger3a|DNA|TcMar-Tigger	33615	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.009153	0.351598	180(ATCACAGAGTGTACTT,+,0.00)
chunk0081_229_1	chr17	42804873	42805592	+	0	NA	intron (NM_173478, intron 3 of 6)	L2c|LINE|L2	6396	NM_173478	124817	Hs.12272	NM_173478	ENSG00000176563	CNTD1	CNTD|COSA1	cyclin N-terminal domain containing 1	protein-coding	0.001391	0.420833	
chunk0176_35_1	chr7	9591880	9592551	+	0	NA	Intergenic	L1PA15|LINE|L1	-42055	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.001490	0.345238	
chunk0005_401_1	chr1	62490916	62491223	+	0	NA	intron (NM_001272001, intron 40 of 47)	MIR|SINE|MIR	54357	NM_003368	7398	Hs.35086	NM_003368	ENSG00000162607	USP1	UBP	ubiquitin specific peptidase 1	protein-coding	0.006515	0.344156	
chunk0138_350_1	chr4	41859130	41859603	+	0	NA	Intergenic	Intergenic	23245	NR_104143	101927074	Hs.611425	NR_104143	ENSG00000245870	LINC00682	-	long intergenic non-protein coding RNA 682	ncRNA	0.008457	0.402954	
chunk0189_25_1	chr8	19682217	19682416	+	0	NA	intron (NR_024040, intron 1 of 9)	intron (NR_024040, intron 1 of 9)	267	NM_018371	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.015075	0.520000	
chunk0133_287_1	chr3	172132624	172133203	+	0	NA	intron (NM_022763, intron 2 of 25)	intron (NM_022763, intron 2 of 25)	92359	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.008636	0.327586	
chunk0021_90_1	chr10	2374282	2374481	+	0	NA	Intergenic	Intergenic	-59307	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.025126	0.455000	
chunk0018_115_1	chr1	218319306	218319819	+	0	NA	intron (NM_016052, intron 4 of 4)	L1MC5a|LINE|L1	-25772	NM_003238	7042	Hs.133379	NM_003238	ENSG00000092969	TGFB2	G-TSF|LDS4|TGF-beta2	transforming growth factor beta 2	protein-coding	0.005848	0.391051	236(TGGGACAGGATGTCCA,-,0.00),237(GGGACAGGATGTCCAG,+,0.00)
chunk0166_70_1	chr6	43009124	43009480	+	0	NA	intron (NM_001270476, intron 11 of 15)	intron (NM_001270476, intron 11 of 15)	4578	NM_014623	4201	Hs.278362	NM_014623	ENSG00000124733	MEA1	HYS|MEA	male-enhanced antigen 1	protein-coding	0.016854	0.551821	
chunk0058_230_1	chr14	25303982	25304250	+	0	NA	Intergenic	L1PREC2|LINE|L1	-253819	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.007463	0.379182	
chunk0185_291_1	chr7	131061865	131062103	+	0	NA	intron (NR_109854, intron 2 of 5)	LTR87|LTR|ERVL?	45046	NR_024153	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.012605	0.439331	
chunk0051_438_1	chr12	123132821	123133020	+	0	NA	Intergenic	L1MB4|LINE|L1	-22431	NM_001300801	57605	Hs.272759	NM_020845	ENSG00000090975	PITPNM2	NIR-3|NIR3|RDGB2|RDGBA2	phosphatidylinositol transfer protein membrane associated 2	protein-coding	0.010050	0.405000	
chunk0131_224_1	chr3	149248823	149249051	+	0	NA	Intergenic	Intergenic	-26892	NM_000096	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.008772	0.371179	
chunk0016_339_1	chr1	201851498	201851981	+	0	NA	intron (NM_018085, intron 4 of 23)	intron (NM_018085, intron 4 of 23)	-11634	NR_106797	102466724		NR_106797	ENSG00000277681	MIR6739	hsa-mir-6739	microRNA 6739	ncRNA	0.008282	0.347107	
chunk0099_198_1	chr2	92081195	92081441	+	0	NA	Intergenic	Intergenic	140185	NR_027714	440888	Hs.730239	NM_001032412		ACTR3BP2	FKSG73	ACTR3B pseudogene 2	pseudo	0.032520	0.348178	
chunk0205_199_1	chr9	109245435	109245943	+	0	NA	intron (NM_018424, intron 14 of 15)	intron (NM_018424, intron 14 of 15)	75275	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.015748	0.453831	193(GAGAACACAGAGATCC,-,0.00)
chunk0045_13_1	chr12	43004914	43005525	+	0	NA	Intergenic	Intergenic	-358721	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.014730	0.410131	595(AAACACATAATGTTCT,-,0.00),596(AACACATAATGTTCTG,+,0.00)
chunk0029_139_1	chr10	99292270	99292469	+	0	NA	Intergenic	L2a|LINE|L2	-36730	NM_020348	26507	Hs.274579	NM_020348	ENSG00000119946	CNNM1	ACDP1|CLP-1	cyclin and CBS domain divalent metal cation transport mediator 1	protein-coding	0.000000	0.355000	
chunk0062_165_1	chr14	69411234	69411531	+	0	NA	intron (NM_001252150, intron 1 of 6)	intron (NM_001252150, intron 1 of 6)	12714	NM_001252148	55334	Hs.432690	NM_018375	ENSG00000029364	SLC39A9	ZIP-9|ZIP9	solute carrier family 39 member 9	protein-coding	0.003367	0.379195	
chunk0190_16_1	chr8	28883728	28884193	+	0	NA	intron (NM_018250, intron 1 of 16)	intron (NM_018250, intron 1 of 16)	5955	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.002151	0.388412	
chunk0117_104_1	chr22	17761152	17761354	+	0	NA	intron (NM_001244567, intron 1 of 5)	intron (NM_001244567, intron 1 of 5)	3006	NR_036168	100423025		NR_036168	ENSG00000264757	MIR3198-1	MIR3198|mir-3198-1	microRNA 3198-1	ncRNA	0.009901	0.399015	
chunk0128_303_1	chr3	111484842	111485129	+	0	NA	Intergenic	Intergenic	-57094	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.006969	0.388889	
chunk0075_75_1	chr16	48126889	48127740	+	0	NA	intron (NM_033226, intron 9 of 28)	intron (NM_033226, intron 9 of 28)	19456	NM_033226	94160	Hs.410111	NM_033226	ENSG00000140798	ABCC12	MRP9	ATP binding cassette subfamily C member 12	protein-coding	0.014101	0.488263	
chunk0211_409_1	chrX	128855941	128856707	+	0	NA	Intergenic	Intergenic	667181	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.003916	0.338983	
chunk0004_298_1	chr1	48939075	48939548	+	0	NA	intron (NM_032785, intron 5 of 13)	intron (NM_032785, intron 5 of 13)	-162342	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.006342	0.432489	248(AGGCACAGCCTGTACT,-,0.00),249(GGCACAGCCTGTACTG,+,0.00)
chunk0045_72_1	chr12	45690904	45691386	+	0	NA	Intergenic	Intergenic	36776	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.006224	0.354037	
chunk0025_262_1	chr10	55409765	55410012	+	0	NA	Intergenic	L1ME5|LINE|L1	-189102	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.008097	0.338710	
chunk0137_445_1	chr4	29113747	29114091	+	0	NA	Intergenic	Intergenic	294337	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.011628	0.298551	
chunk0090_226_1	chr18	73625864	73627108	+	0	NA	Intergenic	Intergenic	301545	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.005627	0.412851	
chunk0184_408_1	chr7	122537147	122537442	+	0	NA	intron (NM_017954, intron 8 of 29)	(ACAA)n|Simple_repeat|Simple_repeat	161860	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.000000	0.260135	
chunk0156_145_1	chr5	107253843	107254388	+	0	NA	Intergenic	Intergenic	-243101	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.007339	0.404762	
chunk0170_165_1	chr6	111653970	111654586	+	0	NA	Intergenic	Intergenic	-48004	NM_147686	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.006494	0.392220	
chunk0082_145_1	chr17	55454744	55455398	+	0	NA	Intergenic	L1ME4a|LINE|L1	-33091	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.009174	0.389313	251(GAGAACTATCTGTGCA,-,0.00),252(AGAACTATCTGTGCAC,+,0.00)
chunk0003_260_1	chr1	36248530	36248980	+	0	NA	intron (NM_005119, intron 1 of 11)	intron (NM_005119, intron 1 of 11)	24339	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.008889	0.427938	
chunk0197_336_1	chr8	125231376	125231648	+	0	NA	intron (NM_173685, intron 5 of 7)	L2b|LINE|L2	139671	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.000000	0.377289	
chunk0206_227_1	chr9	123327701	123328267	+	0	NA	Intergenic	Intergenic	-28183	NM_173689	286204	Hs.568340	NM_173689	ENSG00000148204	CRB2	FSGS9|VMCKD	crumbs cell polarity complex component 2	protein-coding	0.017668	0.537919	
chunk0107_69_1	chr2	212229000	212229211	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	197255	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.000000	0.396226	
chunk0074_51_1	chr16	20851582	20851869	+	0	NA	Intergenic	Intergenic	-45252	NM_001142725	112479	Hs.248437	NM_080663	ENSG00000196678	ERI2	EXOD1|ZGRF5	ERI1 exoribonuclease family member 2	protein-coding	0.003484	0.503472	153(CTGCACACTCTGTTCT,-,0.00),154(TGCACACTCTGTTCTT,+,0.00)
chunk0011_191_1	chr1	149885701	149886052	+	0	NA	3' UTR (NM_003528, exon 1 of 1)	3' UTR (NM_003528, exon 1 of 1)	806	NM_003528	8349	Hs.2178	NM_003528	ENSG00000184678	HIST2H2BE	GL105|H2B|H2B.1|H2BFQ|H2BGL105|H2BQ	histone cluster 2 H2B family member e	protein-coding	0.051282	0.539773	
chunk0084_56_1	chr17	74444460	74444689	+	0	NA	intron (NM_018653, intron 3 of 3)	intron (NM_018653, intron 3 of 3)	10877	NM_018653	55890	Hs.446438	NM_018653	ENSG00000170412	GPRC5C	RAIG-3|RAIG3	G protein-coupled receptor class C group 5 member C	protein-coding	0.034934	0.626087	
chunk0191_440_1	chr8	57940312	57940556	+	0	NA	Intergenic	Intergenic	-37924	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.004098	0.400000	
chunk0180_115_1	chr7	55431663	55432576	+	0	NA	3' UTR (NM_018697, exon 9 of 9)	3' UTR (NM_018697, exon 9 of 9)	66671	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.007667	0.420131	436(AAGCACTGGCAGTTCC,-,0.00),437(AGCACTGGCAGTTCCA,+,0.00),719(AGAAACATAATGTTCT,-,0.00),720(GAAACATAATGTTCTA,+,0.00)
chunk0021_287_1	chr1	244424805	244425467	+	0	NA	intron (NM_001126, intron 4 of 12)	intron (NM_001126, intron 4 of 12)	26998	NM_001126	159	Hs.498313	NM_001126	ENSG00000035687	ADSS	ADEH|ADSS 2|ADSS2	adenylosuccinate synthase	protein-coding	0.001511	0.380090	
chunk0143_245_1	chr4	114705020	114705577	+	0	NA	Intergenic	Intergenic	48539	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.005386	0.362007	225(CAGAGCAGGCTGTTCC,-,0.00),226(AGAGCAGGCTGTTCCA,+,0.00),256(CAGAGCATGCTGTTCA,-,0.00),257(AGAGCATGCTGTTCAT,+,0.00)
chunk0061_272_1	chr14	61514011	61514470	+	0	NA	intron (NM_006255, intron 10 of 13)	intron (NM_006255, intron 10 of 13)	55954	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.010893	0.469565	218(GAGTTCACTGTGTCCT,-,0.00),219(AGTTCACTGTGTCCTG,+,0.00)
chunk0092_44_1	chr19	19408547	19408856	+	0	NA	intron (NM_017660, intron 1 of 11)	intron (NM_017660, intron 1 of 11)	22868	NM_017660	54815	Hs.118964	NM_017660	ENSG00000167491	GATAD2A	p66alpha	GATA zinc finger domain containing 2A	protein-coding	0.012945	0.406452	135(GAGTGCATACTGTGCC,-,0.00),136(AGTGCATACTGTGCCT,+,0.00),260(AAGGACACTGTGACCT,-,0.00),261(AGGACACTGTGACCTG,+,0.00)
chunk0160_445_1	chr5	164873335	164873692	+	0	NA	Intergenic	L1MC1|LINE|L1	403234	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.002801	0.391061	
chunk0122_454_1	chr3	39850500	39850883	+	0	NA	intron (NM_015460, intron 1 of 16)	MamRep434|DNA|TcMar-Tigger	41031	NR_104316	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.002611	0.325521	
chunk0146_115_1	chr4	158858420	158858790	+	0	NA	intron (NM_020840, intron 8 of 16)	intron (NM_020840, intron 8 of 16)	89575	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.010811	0.345013	
chunk0062_415_1	chr14	75150019	75150624	+	0	NA	intron (NM_006827, intron 2 of 4)	intron (NM_006827, intron 2 of 4)	-23246	NM_033116	91754	Hs.7200	NM_033116	ENSG00000119638	NEK9	APUG|LCCS10|NC|NERCC|NERCC1	NIMA related kinase 9	protein-coding	0.008264	0.400990	
chunk0190_41_1	chr8	29349530	29349807	+	0	NA	promoter-TSS (NM_057158)	promoter-TSS (NM_057158)	-863	NM_057158	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.083032	0.600719	
chunk0133_90_1	chr3	167735361	167735717	+	0	NA	promoter-TSS (NM_001122752)	promoter-TSS (NM_001122752)	-105	NM_001122752	5274	Hs.478153	NM_005025	ENSG00000163536	SERPINI1	PI12|neuroserpin	serpin family I member 1	protein-coding	0.039326	0.661064	
chunk0128_316_1	chr3	111781921	111782510	+	0	NA	intron (NM_001134437, intron 1 of 17)	intron (NM_001134437, intron 1 of 17)	49735	NM_001134437	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.005093	0.394915	375(AAGGACATTACGTTCC,-,0.00),376(AGGACATTACGTTCCT,+,0.00)
chunk0207_163_1	chr9	130189814	130190492	+	0	NA	intron (NM_014286, intron 1 of 7)	intron (NM_014286, intron 1 of 7)	-10440	NM_001128826	23413	Hs.642946	NM_014286	ENSG00000107130	NCS1	FLUP|FREQ	neuronal calcium sensor 1	protein-coding	0.007375	0.416789	
chunk0049_103_1	chr12	90923579	90923778	+	0	NA	intron (NR_038868, intron 1 of 4)	LTR16|LTR|ERVL	5655	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.000000	0.480000	
chunk0207_406_1	chr9	136952576	136952806	+	0	NA	intron (NM_178536, intron 1 of 5)	intron (NM_178536, intron 1 of 5)	375	NM_178536	286256	Hs.440519	NM_178536	ENSG00000184925	LCN12	-	lipocalin 12	protein-coding	0.034783	0.670996	128(AGGGTCACCATGTCCC,-,0.00),129(GGGTCACCATGTCCCT,+,0.00)
chunk0210_323_1	chrX	93473780	93474079	+	0	NA	Intergenic	L1PA16|LINE|L1	199754	NM_004538	4675	Hs.21365	NM_004538	ENSG00000186310	NAP1L3	MB20|NPL3	nucleosome assembly protein 1 like 3	protein-coding	0.000000	0.336667	
chunk0112_382_1	chr20	46337985	46338184	+	0	NA	Intergenic	Intergenic	26374	NM_173073	51006	Hs.593344	NM_015945	ENSG00000080189	SLC35C2	BA394O2.1|C20orf5|CGI-15|OVCOV1	solute carrier family 35 member C2	protein-coding	0.030151	0.655000	
chunk0154_111_1	chr5	78648137	78648355	+	0	NA	intron (NM_005779, intron 1 of 4)	CpG	579	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.133028	0.707763	67(GAGGAGACGCTGTTCC,-,0.00),68(AGGAGACGCTGTTCCC,+,0.00)
chunk0005_344_1	chr1	61184376	61184575	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	69043	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.005025	0.420000	
chunk0050_233_1	chr12	105077568	105078012	+	0	NA	intron (NM_001034173, intron 1 of 22)	intron (NM_001034173, intron 1 of 22)	6773	NR_027752	160428	Hs.42572	NM_001034173	ENSG00000136010	ALDH1L2	mtFDH	aldehyde dehydrogenase 1 family member L2	protein-coding	0.009009	0.444944	419(CGGCACAGAGTGCCCC,-,0.00),420(GGCACAGAGTGCCCCA,+,0.00)
chunk0061_334_1	chr14	63335059	63335898	+	0	NA	Intergenic	L1PB1|LINE|L1	-16599	NM_145171	122876	Hs.375028	NM_145171	ENSG00000179600	GPHB5	B5|GPB5|ZLUT1	glycoprotein hormone subunit beta 5	protein-coding	0.001192	0.332143	
chunk0059_146_1	chr14	32092530	32093088	+	0	NA	exon (NM_001030055, exon 2 of 7)	exon (NM_001030055, exon 2 of 7)	15520	NM_001173	394	Hs.592313	NM_001173	ENSG00000100852	ARHGAP5	GFI2|RhoGAP5|p190-B|p190BRhoGAP	Rho GTPase activating protein 5	protein-coding	0.010753	0.393560	
chunk0170_415_1	chr6	118199072	118199660	+	0	NA	intron (NM_001029858, intron 2 of 7)	intron (NM_001029858, intron 2 of 7)	291840	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.003401	0.354839	67(TAGGACATCCTGTTCT,-,0.00),68(AGGACATCCTGTTCTA,+,0.00)
chunk0013_196_1	chr1	169224769	169224968	+	0	NA	intron (NR_104229, intron 10 of 12)	L2c|LINE|L2	118159	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.010050	0.350000	
chunk0006_440_1	chr1	76603116	76603432	+	0	NA	intron (NM_152996, intron 3 of 4)	L1ME3E|LINE|L1	-264227	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.003165	0.347003	
chunk0130_353_1	chr3	138767904	138768103	+	0	NA	Intergenic	MER52A|LTR|ERV1	-8644	NM_006219	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.020101	0.495000	
chunk0143_376_1	chr4	122602492	122602918	+	0	NA	Intergenic	Intergenic	-16278	NR_104126	100996941	Hs.439487	NR_104126	ENSG00000227145	IL21-AS1	-	IL21 antisense RNA 1	ncRNA	0.014085	0.386417	
chunk0143_367_1	chr4	122246971	122247332	+	0	NA	intron (NM_015312, intron 32 of 83)	intron (NM_015312, intron 32 of 83)	76548	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.002770	0.312155	
chunk0120_300_1	chr3	9970019	9970605	+	0	NA	intron (NM_018447, intron 6 of 7)	intron (NM_018447, intron 6 of 7)	16526	NM_018447	55831	Hs.475392	NM_018447	ENSG00000125037	EMC3	POB|TMEM111	ER membrane protein complex subunit 3	protein-coding	0.003413	0.388416	
chunk0097_390_1	chr2	61959026	61959346	+	0	NA	intron (NM_152516, intron 1 of 2)	L1MC|LINE|L1	53518	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.009375	0.302181	
chunk0003_79_1	chr1	31471711	31471910	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-28275	NR_034112	149086	Hs.729905	NR_034112	ENSG00000260386	LDC1P	LINC01225	leucine decarboxylase 1, pseudogene	pseudo	0.005025	0.435000	
chunk0174_108_1	chr6	156955621	156956130	+	0	NA	intron (NM_017519, intron 4 of 18)	intron (NM_017519, intron 4 of 18)	-176144	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.011788	0.521569	
chunk0064_120_1	chr14	91290788	91291524	+	0	NA	intron (NM_001080414, intron 23 of 29)	intron (NM_001080414, intron 23 of 29)	-37276	NM_003485	8111	Hs.8882	NM_003485	ENSG00000119714	GPR68	AI2A6|GPR12A|OGR1	G protein-coupled receptor 68	protein-coding	0.020380	0.496608	
chunk0083_133_1	chr17	65485782	65486052	+	0	NA	Intergenic	Intergenic	28376	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.018519	0.542435	
chunk0036_186_1	chr11	62879582	62880059	+	0	NA	intron (NM_001012662, intron 3 of 11)	intron (NM_001012662, intron 3 of 11)	-1052	NM_001013251	6520	Hs.502769	NM_002394	ENSG00000168003	SLC3A2	4F2|4F2HC|4T2HC|CD98|CD98HC|MDU1|NACAE	solute carrier family 3 member 2	protein-coding	0.006289	0.516736	188(AGGAACAAGGAGTTCC,-,0.00),189(GGAACAAGGAGTTCCT,+,0.00)
chunk0018_32_1	chr1	215607656	215607855	+	0	NA	intron (NM_016121, intron 13 of 17)	intron (NM_016121, intron 13 of 17)	40363	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.000000	0.300000	
chunk0001_355_1	chr1	9901637	9902406	+	0	NA	intron (NM_020248, intron 1 of 5)	intron (NM_020248, intron 1 of 5)	8237	NM_001012329	56998	Hs.463759	NM_020248	ENSG00000178585	CTNNBIP1	ICAT	catenin beta interacting protein 1	protein-coding	0.016905	0.533766	358(AGGAACACTGTGTGCT,-,0.00),359(GGAACACTGTGTGCTT,+,0.00)
chunk0003_379_1	chr1	39700865	39701483	+	0	NA	Intergenic	LTR46|LTR|ERV1	-9464	NM_016257	51440	Hs.743975	NM_016257	ENSG00000116983	HPCAL4	HLP4	hippocalcin like 4	protein-coding	0.021036	0.499192	
chunk0095_273_1	chr2	19835800	19836493	+	0	NA	Intergenic	Intergenic	-32708	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.012987	0.510086	
chunk0100_393_1	chr2	119129912	119130169	+	0	NA	Intergenic	Intergenic	28855	NM_182528	165257	Hs.433493	NM_182528	ENSG00000144119	C1QL2	C1QTNF10|CTRP10	complement C1q like 2	protein-coding	0.031128	0.472868	
chunk0149_147_1	chr5	20174623	20175083	+	0	NA	intron (NM_001291956, intron 2 of 14)	intron (NM_001291956, intron 2 of 14)	-186609	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.013043	0.284165	
chunk0189_83_1	chr8	21252837	21253266	+	0	NA	Intergenic	Intergenic	-45188	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.006993	0.437209	
chunk0033_75_1	chr11	13786645	13787112	+	0	NA	Intergenic	LTR50|LTR|ERVL	118219	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.008565	0.512821	140(TAGAACGGCCTGTGCT,-,0.00),141(AGAACGGCCTGTGCTC,+,0.00)
chunk0211_382_1	chrX	127127545	127128104	+	0	NA	Intergenic	Intergenic	308060	NM_001122716	100130613	Hs.130370	NM_001122716	ENSG00000183631	PRR32	CXorf64	proline rich 32	protein-coding	0.008945	0.355357	
chunk0126_181_1	chr3	78141560	78141821	+	0	NA	Intergenic	L2a|LINE|L2	877769	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003831	0.309160	
chunk0192_17_1	chr8	58453895	58454667	+	0	NA	Intergenic	Intergenic	43017	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.005181	0.333765	
chunk0099_356_1	chr2	100415678	100415890	+	0	NA	intron (NM_004854, intron 1 of 6)	Tigger3a|DNA|TcMar-Tigger	1884	NM_004854	9486	Hs.516370	NM_004854	ENSG00000115526	CHST10	HNK-1ST|HNK1ST	carbohydrate sulfotransferase 10	protein-coding	0.014151	0.356808	
chunk0067_59_1	chr15	40944831	40945166	+	0	NA	Intergenic	Intergenic	-8440	NM_024111	79094	Hs.155569	NM_024111	ENSG00000128965	CHAC1	-	ChaC glutathione specific gamma-glutamylcyclotransferase 1	protein-coding	0.008955	0.479167	
chunk0041_104_1	chr11	124823678	124824019	+	0	NA	intron (NR_103862, intron 4 of 4)	MER50|LTR|ERV1	23420	NR_103862	100507283	Hs.564177	NR_103862	ENSG00000245498	LOC100507283	-	uncharacterized LOC100507283	ncRNA	0.008798	0.482456	
chunk0119_381_1	chr22	48244883	48245082	+	0	NA	Intergenic	Intergenic	-29382	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.055276	0.600000	
chunk0143_80_1	chr4	108206388	108206898	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	34523	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.003922	0.418787	
chunk0017_371_1	chr1	212035223	212035476	+	0	NA	promoter-TSS (NM_001286230)	promoter-TSS (NM_001286230)	-204	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.051383	0.547244	
chunk0008_336_1	chr1	95604783	95605056	+	0	NA	Intergenic	Intergenic	94803	NR_110621	100996635	Hs.639548	NR_110621	ENSG00000228971	LINC02607	-	long intergenic non-protein coding RNA 2607	ncRNA	0.010989	0.383212	
chunk0098_69_1	chr2	66981130	66981329	+	0	NA	Intergenic	Intergenic	-58739	NR_110600	102724321	Hs.146803	NR_110600	ENSG00000232688	LINC01628	-	long intergenic non-protein coding RNA 1628	ncRNA	0.010050	0.335000	
chunk0042_62_1	chr12	2009241	2009633	+	0	NA	Intergenic	Intergenic	-4926	NM_152640	196513	Hs.130934	NM_152640	ENSG00000151065	DCP1B	DCP1	decapping mRNA 1B	protein-coding	0.000000	0.333333	
chunk0092_227_1	chr19	32359451	32359670	+	0	NA	intron (NM_001136156, intron 4 of 6)	intron (NM_001136156, intron 4 of 6)	13952	NM_001136156	22847	Hs.205392	NM_014910	ENSG00000168813	ZNF507	-	zinc finger protein 507	protein-coding	0.013699	0.404545	
chunk0087_23_1	chr18	31034332	31035138	+	0	NA	intron (NM_024423, intron 1 of 16)	L1MB7|LINE|L1	8080	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.007444	0.311029	
chunk0168_109_1	chr6	80527362	80528133	+	0	NA	Intergenic	Intergenic	421120	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.010376	0.363990	
chunk0007_248_1	chr1	82678438	82679079	+	0	NA	Intergenic	Intergenic	306164	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.007800	0.370717	
chunk0127_159_1	chr3	94600056	94600256	+	0	NA	Intergenic	L1PB1|LINE|L1	-338107	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.353234	
chunk0182_92_1	chr7	92802234	92802974	+	0	NA	intron (NM_001145306, intron 2 of 7)	intron (NM_001145306, intron 2 of 7)	31313	NM_001259	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.005405	0.360324	
chunk0172_175_1	chr6	136361322	136361878	+	0	NA	intron (NM_001198619, intron 11 of 17)	intron (NM_001198619, intron 11 of 17)	-71749	NM_001077440	9774	Hs.486542	NM_014739	ENSG00000029363	BCLAF1	BTF|bK211L9.1	BCL2 associated transcription factor 1	protein-coding	0.017986	0.448833	227(AGGGTCACAGTGTTCT,-,0.00),228(GGGTCACAGTGTTCTG,+,0.00)
chunk0180_32_1	chr7	54201524	54201777	+	0	NA	non-coding (NR_004422, exon 1 of 1)	non-coding (NR_004422, exon 1 of 1)	771	NR_004422									0.000000	0.492126	
chunk0106_170_1	chr2	200797246	200797687	+	0	NA	intron (NR_110275, intron 2 of 3)	intron (NR_110275, intron 2 of 3)	-14080	NM_001207067	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.011338	0.452489	
chunk0104_64_1	chr2	171587039	171587396	+	0	NA	Intergenic	Intergenic	64861	NM_001127383	79901	Hs.221941	NM_024843	ENSG00000071967	CYBRD1	CYB561A2|DCYTB|FRRS3	cytochrome b reductase 1	protein-coding	0.014006	0.410615	
chunk0193_457_1	chr8	81314502	81314829	+	0	NA	Intergenic	Intergenic	34182	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.009174	0.344512	
chunk0065_194_1	chr14	100032106	100032399	+	0	NA	Intergenic	Intergenic	-33162	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.003413	0.404762	
chunk0198_320_1	chr8	139777030	139777685	+	0	NA	intron (NM_001160372, intron 21 of 22)	intron (NM_001160372, intron 21 of 22)	-74301	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.010687	0.443598	358(GGGAACAGAGCGTGCC,-,0.00),359(GGAACAGAGCGTGCCT,+,0.00)
chunk0058_393_1	chr13	111247506	111248188	+	0	NA	intron (NM_001113513, intron 7 of 19)	MER58A|DNA|hAT-Charlie	61021	NM_001113513	8874	Hs.508738	NM_003899	ENSG00000102606	ARHGEF7	BETA-PIX|COOL-1|COOL1|Nbla10314|P50|P50BP|P85|P85COOL1|P85SPR|PAK3|PIXB	Rho guanine nucleotide exchange factor 7	protein-coding	0.016129	0.437775	233(GGCACGTGCTGTACTT,+,0.00)
chunk0145_457_1	chr4	153847453	153848095	+	0	NA	Intergenic	Intergenic	-58698	NM_003013	6423	Hs.481022	NM_003013	ENSG00000145423	SFRP2	FRP-2|SARP1|SDF-5	secreted frizzled related protein 2	protein-coding	0.004673	0.384137	
chunk0099_192_1	chr2	90392275	90392722	+	0	NA	Intergenic	Intergenic	1267451	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.042506	0.375000	
chunk0211_440_1	chrX	129625771	129626251	+	0	NA	Intergenic	L1PA17|LINE|L1	28945	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.002083	0.338877	
chunk0142_390_1	chr4	102560966	102561192	+	0	NA	intron (NM_003998, intron 5 of 23)	L2b|LINE|L2	59750	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.000000	0.400881	174(AAGGTCATTCTGTCCT,-,0.00),175(AGGTCATTCTGTCCTT,+,0.00)
chunk0028_213_1	chr10	89445037	89445707	+	0	NA	intron (NM_213606, intron 3 of 7)	L1PA6|LINE|L1	-10619	NR_120614	101926906	Hs.568874	NR_120614	ENSG00000234452	SLC16A12-AS1	-	SLC16A12 antisense RNA 1	ncRNA	0.011940	0.509687	
chunk0157_16_1	chr5	115418969	115419180	+	0	NA	Intergenic	Intergenic	-122313	NM_001040440	153733	Hs.436121	NM_152549	ENSG00000164221	CCDC112	MBC1	coiled-coil domain containing 112	protein-coding	0.014218	0.448113	
chunk0134_193_1	chr3	178320629	178321019	+	0	NA	Intergenic	Intergenic	-98377	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.007692	0.491049	
chunk0051_432_1	chr12	122926538	122926764	+	0	NA	intron (NM_203444, intron 11 of 11)	AluJr|SINE|Alu	-30486	NM_024667	79720	Hs.507162	NM_024667	ENSG00000139722	VPS37B	-	VPS37B subunit of ESCRT-I	protein-coding	0.004425	0.418502	149(GAGACCAGCCTGTTCA,-,0.00),150(AGACCAGCCTGTTCAA,+,0.00)
chunk0195_80_1	chr8	94089452	94089718	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	119002	NM_004063	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.000000	0.389513	
chunk0021_24_1	chr10	546890	547459	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	94604	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.017575	0.515789	
chunk0172_107_1	chr6	134950228	134950497	+	0	NA	promoter-TSS (NM_170771)	promoter-TSS (NM_170771)	-240	NM_022568	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.007435	0.385185	
chunk0071_189_1	chr15	83663050	83663891	+	0	NA	intron (NM_207517, intron 2 of 29)	intron (NM_207517, intron 2 of 29)	9384	NM_001301110	57188	Hs.459162	NM_207517	ENSG00000156218	ADAMTSL3	ADAMTSL-3	ADAMTS like 3	protein-coding	0.011891	0.446556	
chunk0151_99_1	chr5	43208693	43209228	+	0	NA	intron (NR_072980, intron 1 of 3)	intron (NR_072980, intron 1 of 3)	16108	NR_072980	167359	Hs.25845	NM_153361	ENSG00000177453	NIM1K	NIM1	NIM1 serine/threonine protein kinase	protein-coding	0.003738	0.395522	
chunk0150_336_1	chr5	38561505	38562201	+	0	NA	intron (NR_103553, intron 1 of 2)	intron (NR_103553, intron 1 of 2)	-4292	NR_037423	100500824		NR_037423	ENSG00000265304	MIR3650	-	microRNA 3650	ncRNA	0.008621	0.428981	
chunk0207_32_1	chrX	4287000	4287316	+	0	NA	Intergenic	Intergenic	346414	NR_110390	101928201	Hs.586488	NR_110390	ENSG00000236513	LOC101928201	-	uncharacterized LOC101928201	ncRNA	0.000000	0.324921	
chunk0198_242_1	chr8	134503978	134504234	+	0	NA	intron (NM_001174158, intron 13 of 13)	intron (NM_001174158, intron 13 of 13)	-93965	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.015625	0.494163	
chunk0210_16_1	chrX	66914932	66915150	+	0	NA	Intergenic	Intergenic	-275743	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.000000	0.415525	
chunk0030_256_1	chr10	115669547	115669868	+	0	NA	intron (NM_207303, intron 26 of 28)	intron (NM_207303, intron 26 of 28)	576342	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.000000	0.341615	
chunk0043_273_1	chr12	20953728	20954221	+	0	NA	Intergenic	L1PA7|LINE|L1	-61722	NM_001009562	338821	Hs.729117	NM_001009562	ENSG00000205754	SLCO1B7	LST-3|LST-3TM12|LST3|SLC21A21	solute carrier organic anion transporter family member 1B7 (putative)	protein-coding	0.002028	0.370445	245(CTGAACAACATGTTCC,-,0.00),246(TGAACAACATGTTCCT,+,0.00)
chunk0053_305_1	chr13	33870482	33870681	+	0	NA	intron (NM_181558, intron 8 of 8)	intron (NM_181558, intron 8 of 8)	52512	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.005025	0.485000	
chunk0175_427_1	chr6	169028362	169028609	+	0	NA	Intergenic	L1MC4|LINE|L1	133816	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.008097	0.487903	109(TTGAACATGATGTTCT,-,0.00),110(TGAACATGATGTTCTG,+,0.00)
chunk0124_327_1	chr3	58149864	58150717	+	0	NA	intron (NM_001164317, intron 39 of 46)	intron (NM_001164317, intron 39 of 46)	60713	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.025791	0.504684	
chunk0004_292_1	chr1	48915361	48915617	+	0	NA	intron (NM_032785, intron 5 of 13)	L2c|LINE|L2	-138520	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.007812	0.412451	
chunk0132_78_1	chr3	155239349	155239555	+	0	NA	Intergenic	L1PA15|LINE|L1	-1493	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.000000	0.536232	
chunk0025_268_1	chr10	55864409	55864620	+	0	NA	Intergenic	Intergenic	265524	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.004739	0.268868	
chunk0180_163_1	chr7	64997486	64997884	+	0	NA	intron (NM_001007253, intron 1 of 1)	HERV3-int|LTR|ERV1	-6649	NM_015852	51351	Hs.250693	NM_015852	ENSG00000152926	ZNF117	H-plk|HPF9	zinc finger protein 117	protein-coding	0.010050	0.516291	
chunk0094_228_1	chr2	6938924	6939183	+	0	NA	intron (NM_014746, intron 1 of 8)	L1MB7|LINE|L1	-20371	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.003861	0.380769	200(GAGAACTCTATGTTCA,-,0.00),201(AGAACTCTATGTTCAA,+,0.00)
chunk0195_367_1	chr8	99929599	99929992	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-35781	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.002545	0.337563	
chunk0112_440_1	chr20	47894664	47895611	+	0	NA	Intergenic	D20S16|Satellite|Satellite	-88089	NR_109942	101060004	Hs.129970	NR_109942		LINC01523	-	long intergenic non-protein coding RNA 1523	ncRNA	0.035903	0.565401	
chunk0180_406_1	chr7	75882998	75883197	+	0	NA	intron (NM_001040456, intron 2 of 3)	intron (NM_001040456, intron 2 of 3)	4098	NM_001040457	57414	Hs.488827	NM_020684	ENSG00000005486	RHBDD2	NPD007|RHBDL7	rhomboid domain containing 2	protein-coding	0.010050	0.540000	
chunk0089_74_1	chr18	58223543	58224286	+	0	NA	intron (NM_001144966, intron 1 of 29)	intron (NM_001144966, intron 1 of 29)	2392	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.021534	0.490591	
chunk0048_121_1	chr12	79841446	79841733	+	0	NA	intron (NM_001244990, intron 4 of 24)	intron (NM_001244990, intron 4 of 24)	72322	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.006969	0.340278	
chunk0195_376_1	chr8	100038703	100039229	+	0	NA	exon (NM_015668, exon 14 of 28)	exon (NM_015668, exon 14 of 28)	-14882	NR_031675									0.007605	0.326376	307(AAGTACACACTGTTCT,-,0.00),308(AGTACACACTGTTCTT,+,0.00)
chunk0040_337_1	chr11	118396927	118397646	+	0	NA	3' UTR (NM_004788, exon 20 of 20)	3' UTR (NM_004788, exon 20 of 20)	-4103	NR_033759	10632	Hs.486360	NM_006476	ENSG00000167283	ATP5MG	ATP5JG|ATP5L	ATP synthase membrane subunit g	protein-coding	0.002782	0.355556	
chunk0170_113_1	chr6	110655940	110656947	+	0	NA	intron (NM_015076, intron 4 of 12)	Tigger16b|DNA|TcMar-Tigger	-158178	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.004965	0.341270	
chunk0154_332_1	chr5	85422997	85423265	+	0	NA	Intergenic	Intergenic	-859313	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.003731	0.315985	91(GAGAACATCGTGTTTT,-,0.00),92(AGAACATCGTGTTTTG,+,0.00)
chunk0125_189_1	chr3	66737682	66738063	+	0	NA	Intergenic	Intergenic	-237451	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.007874	0.390052	
chunk0136_325_1	chr3	195443017	195443216	+	0	NA	promoter-TSS (NM_012287)	promoter-TSS (NM_012287)	-28	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.110553	0.740000	
chunk0197_62_1	chr8	118691353	118691654	+	0	NA	intron (NR_038210, intron 3 of 4)	L1PB3|LINE|L1	-69508	NR_109794	401474	Hs.359393	NM_207506	ENSG00000177570	SAMD12	-	sterile alpha motif domain containing 12	protein-coding	0.000000	0.284768	
chunk0094_309_1	chr2	8804024	8804401	+	0	NA	intron (NM_020738, intron 7 of 29)	intron (NM_020738, intron 7 of 29)	33413	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.005305	0.407407	
chunk0199_253_1	chr9	5843455	5844161	+	0	NA	Intergenic	Intergenic	-10727	NM_024896	79956	Hs.591078	NM_024896	ENSG00000099219	ERMP1	FXNA|KIAA1815|bA207C16.3	endoplasmic reticulum metallopeptidase 1	protein-coding	0.012748	0.451202	674(TAGACACCCTGTCCTG,+,0.00)
chunk0153_263_1	chr5	72821466	72822026	+	0	NA	intron (NM_002270, intron 1 of 24)	intron (NM_002270, intron 1 of 24)	5155	NM_002270	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.005357	0.365419	
chunk0034_252_1	chr11	34316710	34317101	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	41103	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.010230	0.461735	226(AAGAACAGAAAGATCT,-,0.00),227(AGAACAGAAAGATCTG,+,0.00)
chunk0175_24_1	chr7	624890	625180	+	0	NA	intron (NM_001164758, intron 4 of 10)	L1MC|LINE|L1	21637	NR_110055	101926963	Hs.521338	NR_110054		LOC101926963	-	uncharacterized LOC101926963	ncRNA	0.003448	0.343643	
chunk0146_413_1	chr4	169093110	169093759	+	0	NA	TTS (NM_020870)	TTS (NM_020870)	-83117	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.001541	0.326154	
chunk0047_17_1	chr12	65495346	65495545	+	0	NA	intron (NR_120431, intron 3 of 3)	intron (NR_120431, intron 3 of 3)	146927	NR_120432	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.005025	0.545000	
chunk0062_113_1	chr14	68349870	68350335	+	0	NA	intron (NM_133509, intron 8 of 10)	intron (NM_133509, intron 8 of 10)	443812	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.010753	0.377682	
chunk0108_233_1	chr2	233700188	233700502	+	0	NA	intron (NM_205862, intron 2 of 5)	intron (NM_205862, intron 2 of 5)	7479	NM_001072	54578	Hs.554822	NM_001072	ENSG00000167165	UGT1A6	GNT1|HLUGP|HLUGP1|UDPGT|UDPGT 1-6|UGT-1A|UGT-1C|UGT-1E|UGT1|UGT1-01|UGT1-03|UGT1-05|UGT1.1|UGT1.3|UGT1.5|UGT1A|UGT1A1|UGT1A3|UGT1A5|UGT1A6S|UGT1C|UGT1E|UGT1F|hUG-BR1	UDP glucuronosyltransferase family 1 member A6	protein-coding	0.003185	0.380952	
chunk0055_456_1	chr13	75836346	75837072	+	0	NA	intron (NM_001306080, intron 19 of 30)	intron (NM_001306080, intron 19 of 30)	-34329	NM_001257995	729420	Hs.586820	NM_001257995		LMO7DN	C13orf45	LMO7 downstream neighbor	protein-coding	0.008264	0.394773	
chunk0177_257_1	chr7	25271330	25271709	+	0	NA	Intergenic	Intergenic	-43033	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.000000	0.321053	
chunk0120_6_1	chr3	424428	425207	+	0	NA	Intergenic	Intergenic	-39022	NR_110739	101927193	Hs.677744	NR_110739	ENSG00000234661	CHL1-AS1	-	CHL1 antisense RNA 1	ncRNA	0.002567	0.369231	
chunk0168_52_1	chr6	78676151	78677196	+	0	NA	Intergenic	L1PA6|LINE|L1	-190871	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.013397	0.500956	51(ATGACAGACTGTACCG,+,0.00)
chunk0104_153_1	chr2	174024721	174025132	+	0	NA	Intergenic	Intergenic	-59224	NM_003111	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.019465	0.461165	
chunk0169_236_1	chr6	105051573	105051789	+	0	NA	intron (NM_001004317, intron 3 of 3)	L2a|LINE|L2	84665	NM_147147	11149	Hs.221660	NM_007073	ENSG00000112276	BVES	CARICK|HBVES|LGMD2X|LGMDR25|POP1|POPDC1	blood vessel epicardial substance	protein-coding	0.004630	0.354839	
chunk0069_76_1	chr15	61029891	61030122	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	199297	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.004329	0.482759	
chunk0160_143_1	chr5	151453816	151454555	+	0	NA	intron (NM_001308150, intron 1 of 10)	intron (NM_001308150, intron 1 of 10)	6589	NM_078483	206358	Hs.269004	NM_078483	ENSG00000123643	SLC36A1	Dct1|LYAAT1|PAT1|TRAMD3	solute carrier family 36 member 1	protein-coding	0.004060	0.372973	361(TTGGACTTTGTGTTCT,-,0.00),362(TGGACTTTGTGTTCTG,+,0.00)
chunk0074_231_1	chr16	27193547	27194288	+	0	NA	Intergenic	Intergenic	-9569	NM_024773	79831	Hs.145717	NM_024773	ENSG00000155666	KDM8	JMJD5	lysine demethylase 8	protein-coding	0.012146	0.469003	335(GAGACCAGGTTGTTCC,-,0.00),336(AGACCAGGTTGTTCCC,+,0.00)
chunk0018_163_1	chr1	218895283	218895815	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	278239	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.007519	0.386492	
chunk0081_302_1	chr17	45296795	45297088	+	0	NA	intron (NM_003954, intron 1 of 15)	L2a|LINE|L2	20123	NM_003954	9020	Hs.404183	NM_003954	ENSG00000006062	MAP3K14	FTDCR1B|HS|HSNIK|NIK	mitogen-activated protein kinase kinase kinase 14	protein-coding	0.003413	0.445578	
chunk0195_245_1	chr8	97652085	97652831	+	0	NA	intron (NM_178812, intron 1 of 11)	L2a|LINE|L2	8279	NM_178812	92140	Hs.377155	NM_178812	ENSG00000147649	MTDH	3D3|AEG-1|AEG1|LYRIC|LYRIC/3D3	metadherin	protein-coding	0.008043	0.361446	
chunk0117_39_1	chr22	12174316	12174543	+	0	NA	Intergenic	Intergenic	277023	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.017621	0.473684	
chunk0006_382_1	chr1	74432256	74432817	+	0	NA	intron (NM_015978, intron 17 of 24)	intron (NM_015978, intron 17 of 24)	-144894	NR_121671	101927320	Hs.662589	NR_121670	ENSG00000234497	ERICH3-AS1	-	ERICH3 antisense RNA 1	ncRNA	0.005348	0.396797	
chunk0178_460_1	chr7	42152556	42152930	+	0	NA	intron (NM_000168, intron 2 of 14)	intron (NM_000168, intron 2 of 14)	84276	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.013369	0.421333	
chunk0018_406_1	chr1	222642388	222642899	+	0	NA	intron (NM_198551, intron 6 of 27)	L1MC5|LINE|L1	-1660	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.001957	0.328125	
chunk0049_405_1	chr12	96996486	96996951	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	89252	NM_001135175	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.006452	0.412017	234(AGGATCTCACTGTTCT,-,0.00),235(GGATCTCACTGTTCTC,+,0.00)
chunk0188_410_1	chr8	18868496	18869024	+	0	NA	intron (NM_015310, intron 3 of 15)	intron (NM_015310, intron 3 of 15)	-59865	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.007576	0.379962	
chunk0181_218_1	chr7	84763873	84764465	+	0	NA	Intergenic	Intergenic	231693	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.000000	0.279933	
chunk0078_151_1	chr17	4136257	4136704	+	0	NA	intron (NM_015113, intron 1 of 54)	MIR|SINE|MIR	-4609	NR_039973									0.022371	0.491071	
chunk0115_50_1	chr21	21286747	21287113	+	0	NA	intron (NM_004540, intron 4 of 17)	intron (NM_004540, intron 4 of 17)	288615	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.005464	0.291553	
chunk0137_143_1	chr4	15649967	15650679	+	0	NA	intron (NM_012161, intron 1 of 10)	intron (NM_012161, intron 1 of 10)	5089	NM_001193535	26234	Hs.643433	NM_012161	ENSG00000118564	FBXL5	FBL4|FBL5|FLR1	F-box and leucine rich repeat protein 5	protein-coding	0.008427	0.354839	
chunk0161_7_1	chr5	165348255	165348705	+	0	NA	Intergenic	L2c|LINE|L2	878201	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.000000	0.403548	
chunk0116_121_1	chr21	36044045	36044519	+	0	NA	intron (NR_040087, intron 5 of 10)	MER58C|DNA|hAT-Charlie	16082	NM_001007261	54093	Hs.606200	NM_017438	ENSG00000185917	SETD4	C21orf18|C21orf27	SET domain containing 4	protein-coding	0.023207	0.469474	
chunk0156_443_1	chr5	114778674	114779118	+	0	NA	Intergenic	Intergenic	-5483	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.346067	
chunk0026_9_1	chr10	60473512	60474027	+	0	NA	intron (NM_001204403, intron 2 of 43)	Charlie16a|DNA|hAT-Charlie	-83893	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005825	0.410853	
chunk0184_389_1	chr7	121609953	121610804	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-214010	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.003525	0.406103	423(AAGTACATGCTGTTAC,-,0.00)
chunk0073_135_1	chr16	5398227	5398528	+	0	NA	Intergenic	(TGTGTG)n|Simple_repeat|Simple_repeat	217873	NR_110902	101926950	Hs.613285	NR_110902	ENSG00000260338	LINC01570	-	long intergenic non-protein coding RNA 1570	ncRNA	0.009967	0.483444	
chunk0100_230_1	chr2	112284114	112284368	+	0	NA	intron (NM_198581, intron 1 of 11)	intron (NM_198581, intron 1 of 11)	8640	NM_198581	376940	Hs.190477	NM_198581	ENSG00000188177	ZC3H6	ZC3HDC6	zinc finger CCCH-type containing 6	protein-coding	0.000000	0.329412	
chunk0158_55_1	chr5	125975979	125976634	+	0	NA	Intergenic	Intergenic	-203271	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.003053	0.339939	
chunk0028_38_1	chr10	82928597	82929027	+	0	NA	intron (NM_001010848, intron 4 of 8)	intron (NM_001010848, intron 4 of 8)	-695892	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.002326	0.403712	
chunk0110_451_1	chr20	21241393	21241797	+	0	NA	intron (NM_001163022, intron 10 of 11)	intron (NM_001163022, intron 10 of 11)	-23306	NR_109956	101929591	Hs.656066	NR_109956	ENSG00000232712	KIZ-AS1	-	KIZ antisense RNA 1	ncRNA	0.017327	0.449383	
chunk0180_413_1	chr7	76049207	76049561	+	0	NA	TTS (NR_104165)	TTS (NR_104165)	1365	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.016949	0.456338	151(AAGTACATTAAGTACC,-,0.00),152(AGTACATTAAGTACCT,+,0.00)
chunk0007_320_1	chr1	84479208	84479711	+	0	NA	exon (NM_025065, exon 1 of 9)	exon (NM_025065, exon 1 of 9)	222	NM_025065	80135	Hs.481202	NM_025065	ENSG00000117133	RPF1	BXDC5	ribosome production factor 1 homolog	protein-coding	0.081511	0.587302	
chunk0082_443_1	chr17	61906399	61906685	+	0	NA	intron (NM_020748, intron 8 of 24)	Tigger6a|DNA|TcMar-Tigger	21474	NM_020748	57508	Hs.279646	NM_020748	ENSG00000108506	INTS2	INT2|KIAA1287	integrator complex subunit 2	protein-coding	0.006993	0.379791	232(GAGGACTGTATGTACA,-,0.00)
chunk0039_326_1	chr11	104315498	104315729	+	0	NA	Intergenic	Intergenic	63022	NR_106987									0.008658	0.370690	
chunk0170_106_1	chr6	110621423	110621737	+	0	NA	intron (NM_015076, intron 11 of 12)	intron (NM_015076, intron 11 of 12)	-144939	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.009554	0.466667	102(GGGAACACAGTGTTCC,-,0.00),103(GGAACACAGTGTTCCC,+,0.00)
chunk0065_426_1	chr14	106071009	106071613	+	0	NA	Intergenic	L1MA9|LINE|L1	-99042	NR_002224	8755	Hs.662288	NR_002224	ENSG00000271968	ADAM6	C14orf96|tMDCIV	ADAM metallopeptidase domain 6 (pseudogene)	pseudo	0.004967	0.320661	
chunk0093_13_1	chr2	145497	145888	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-99104	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.000000	0.346939	
chunk0088_451_1	chr18	57089104	57089303	+	0	NA	Intergenic	Intergenic	-17084	NR_048536	100885779	Hs.565136	NR_048536	ENSG00000258609	LINC-ROR	ROR|lincRNA-RoR|lincRNA-ST8SIA3	long intergenic non-protein coding RNA, regulator of reprogramming	ncRNA	0.020101	0.410000	
chunk0066_235_1	chr15	34224824	34225339	+	0	NA	promoter-TSS (NM_001286420)	promoter-TSS (NM_001286420)	84	NM_016454	51234	Hs.250905	NM_016454	ENSG00000128463	EMC4	PIG17|TMEM85	ER membrane protein complex subunit 4	protein-coding	0.040777	0.558140	
chunk0036_294_1	chr11	65570131	65570363	+	0	NA	promoter-TSS (NM_006396)	promoter-TSS (NM_006396)	166	NR_038923	254100	Hs.595927	NR_038923		SSSCA1-AS1	-	SSSCA1 antisense RNA 1 (head to head)	ncRNA	0.094828	0.665236	
chunk0212_17_1	chrY	8656009	8656541	+	0	NA	Intergenic	Intergenic	27603	NR_001550	252950	Hs.522852	NR_001550		TTTY18	NCRNA00143	testis-specific transcript, Y-linked 18	ncRNA	0.001880	0.424015	259(TGGAACTCTGTGTTCT,-,0.00),260(GGAACTCTGTGTTCTT,+,0.00)
chunk0069_290_1	chr15	65286804	65287166	+	0	NA	promoter-TSS (NM_001316943)	promoter-TSS (NM_001316943)	-142	NM_001316943	54956	Hs.30634	NM_017851	ENSG00000138617	PARP16	ARTD15|C15orf30|pART15	poly(ADP-ribose) polymerase family member 16	protein-coding	0.140884	0.776860	
chunk0188_160_1	chr8	10628931	10629238	+	0	NA	intron (NM_178857, intron 1 of 3)	intron (NM_178857, intron 1 of 3)	26023	NM_178857	94137	Hs.33538	NM_178857	ENSG00000183638	RP1L1	DCDC4B	RP1 like 1	protein-coding	0.013029	0.490260	
chunk0179_399_1	chr7	51557325	51557674	+	0	NA	Intergenic	L1PA6|LINE|L1	-240681	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.005731	0.502857	
chunk0146_406_1	chr4	169014641	169015701	+	0	NA	Intergenic	Intergenic	-4854	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.009434	0.409048	302(CAGGACATAATGTTCT,-,0.00),303(AGGACATAATGTTCTA,+,0.00),684(GAGAACTCAGTGTTCC,-,0.00),685(AGAACTCAGTGTTCCT,+,0.00)
chunk0062_106_1	chr14	68267737	68267988	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	448083	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.003984	0.353175	
chunk0144_49_1	chr4	126569822	126570340	+	0	NA	Intergenic	Intergenic	1062822	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.005792	0.368015	
chunk0007_242_1	chr1	82484938	82485821	+	0	NA	Intergenic	Intergenic	499543	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.006795	0.382353	
chunk0146_163_1	chr4	160037712	160038329	+	0	NA	Intergenic	L1MB1|LINE|L1	770174	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.000000	0.326861	
chunk0086_337_1	chr18	24799516	24800104	+	0	NA	Intergenic	L2b|LINE|L2	171628	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.008503	0.439728	
chunk0133_427_1	chr3	174855679	174855942	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-3511	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.000000	0.333333	
chunk0102_339_1	chr2	152175696	152176161	+	0	NA	promoter-TSS (NM_005843)	promoter-TSS (NM_005843)	64	NM_005843	10254	Hs.17200	NM_005843	ENSG00000115145	STAM2	Hbp|STAM2A|STAM2B	signal transducing adaptor molecule 2	protein-coding	0.105376	0.673820	
chunk0079_237_1	chr17	15928805	15929058	+	0	NA	Intergenic	L2a|LINE|L2	-15986	NM_000676	136	Hs.167046	NM_000676	ENSG00000170425	ADORA2B	ADORA2	adenosine A2b receptor	protein-coding	0.011858	0.551181	
chunk0112_388_1	chr20	46714506	46714769	+	0	NA	intron (NM_030777, intron 1 of 4)	intron (NM_030777, intron 1 of 4)	4997	NM_030777	81031	Hs.305971	NM_030777	ENSG00000197496	SLC2A10	ATORS|ATS|GLUT10	solute carrier family 2 member 10	protein-coding	0.030418	0.598485	
chunk0179_77_1	chr7	44298840	44299399	+	0	NA	intron (NM_172084, intron 1 of 15)	L1MB4|LINE|L1	26512	NM_172078	816	Hs.351887	NM_001220	ENSG00000058404	CAMK2B	CAM2|CAMK2|CAMKB|MRD54	calcium/calmodulin dependent protein kinase II beta	protein-coding	0.001789	0.360714	
chunk0182_407_1	chr7	100874873	100875219	+	0	NA	promoter-TSS (NM_001128852)	promoter-TSS (NM_001128852)	-33	NM_001128854	51593	Hs.111801	NM_015908	ENSG00000087087	SRRT	ARS2|ASR2|serrate	serrate, RNA effector molecule	protein-coding	0.124277	0.665706	
chunk0067_256_1	chr15	45750451	45750763	+	0	NA	Intergenic	L1ME3A|LINE|L1	115867	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.000000	0.415335	
chunk0008_62_1	chr1	89579474	89579679	+	0	NA	intron (NM_015350, intron 3 of 5)	intron (NM_015350, intron 3 of 5)	20863	NM_015350	23507	Hs.482017	NM_015350	ENSG00000197147	LRRC8B	TA-LRRP|TALRRP	leucine rich repeat containing 8 VRAC subunit B	protein-coding	0.000000	0.354369	
chunk0085_88_1	chr18	2532865	2533642	+	0	NA	Intergenic	MLT1E2-int|LTR|ERVL-MaLR	38250	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.003861	0.393316	360(AGGGTCAGAGTGTTCA,-,0.00),361(GGGTCAGAGTGTTCAG,+,0.00)
chunk0186_299_1	chr7	142868084	142868791	+	0	NA	intron (NR_104001, intron 13 of 18)	intron (NR_104001, intron 13 of 18)	5681	NM_001280795	2051	Hs.380089	NM_004445	ENSG00000106123	EPHB6	HEP	EPH receptor B6	protein-coding	0.036775	0.622881	
chunk0042_336_1	chr12	9836914	9837126	+	0	NA	intron (NM_016523, intron 3 of 5)	L1MB5|LINE|L1	9539	NR_120305	51348	Hs.183125	NM_016523	ENSG00000150045	KLRF1	CLEC5C|NKp80	killer cell lectin like receptor F1	protein-coding	0.004717	0.300469	
chunk0122_322_1	chr3	37056975	37057390	+	0	NA	intron (NM_017724, intron 11 of 13)	intron (NM_017724, intron 11 of 13)	63405	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.000000	0.463942	140(AAGCTCACTTTGTTCT,-,0.00)
chunk0022_319_1	chr10	16300630	16301071	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-136093	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.011338	0.364253	
chunk0206_191_1	chr9	122954309	122954670	+	0	NA	intron (NM_012197, intron 1 of 25)	intron (NM_012197, intron 1 of 25)	13480	NM_012197	23637	Hs.271341	NM_012197	ENSG00000011454	RABGAP1	GAPCENA|TBC1D11	RAB GTPase activating protein 1	protein-coding	0.000000	0.350829	
chunk0052_299_1	chr12	124720532	124721462	+	0	NA	Intergenic	Intergenic	142976	NM_005505	949	Hs.731377	NM_005505	ENSG00000073060	SCARB1	CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1	scavenger receptor class B member 1	protein-coding	0.020430	0.493018	
chunk0015_331_1	chr1	189714979	189715213	+	0	NA	Intergenic	MER92A|LTR|ERV1	762533	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.370213	
chunk0011_227_1	chr1	150362850	150363157	+	0	NA	Intergenic	L2a|LINE|L2	-1108	NM_001297674	23248	Hs.213666	NM_015203	ENSG00000163125	RPRD2	HSPC099|KIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding	0.048860	0.487013	30(TTGCACTTGCTGTTCC,-,0.00),31(TGCACTTGCTGTTCCT,+,0.00)
chunk0037_107_1	chr11	72247007	72247558	+	0	NA	Intergenic	Intergenic	-3106	NM_005169	401	Hs.731115	NM_005169	ENSG00000165462	PHOX2A	ARIX|CFEOM2|FEOM2|NCAM2|PMX2A	paired like homeobox 2A	protein-coding	0.009074	0.507246	
chunk0056_407_1	chr13	94157682	94158278	+	0	NA	intron (NR_046535, intron 3 of 3)	L2|LINE|L2	30011	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.003356	0.430486	299(AAGAACACAGAGTACC,-,0.00),300(AGAACACAGAGTACCC,+,0.00)
chunk0136_11_1	chr4	58994	59256	+	0	NA	intron (NM_001286053, intron 1 of 1)	intron (NM_001286053, intron 1 of 1)	5840	NM_001286053	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.003817	0.463878	
chunk0120_349_1	chr3	11478870	11479391	+	0	NA	intron (NM_001136031, intron 17 of 17)	intron (NM_001136031, intron 17 of 17)	89794	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.001919	0.352490	
chunk0111_17_1	chr20	21985780	21986104	+	0	NA	Intergenic	Intergenic	-68148	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.000000	0.301538	
chunk0165_383_1	chr6	38408589	38408820	+	0	NA	intron (NM_001172418, intron 5 of 10)	intron (NM_001172418, intron 5 of 10)	187363	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.004329	0.331897	
chunk0020_210_1	chr1	235129765	235130100	+	0	NA	promoter-TSS (NM_014765)	promoter-TSS (NM_014765)	-991	NM_014765	9804	Hs.533192	NM_014765	ENSG00000173726	TOMM20	MAS20|MOM19|TOM20	translocase of outer mitochondrial membrane 20	protein-coding	0.002985	0.419643	
chunk0050_390_1	chr12	109093519	109093815	+	0	NA	promoter-TSS (NM_001205179)	promoter-TSS (NM_001205179)	-179	NM_001205180	121642	Hs.374458	NM_001001655	ENSG00000189046	ALKBH2	ABH2	alkB homolog 2, alpha-ketoglutarate dependent dioxygenase	protein-coding	0.054054	0.609428	
chunk0190_323_1	chr8	38829401	38830038	+	0	NA	intron (NM_001122824, intron 3 of 10)	intron (NM_001122824, intron 3 of 10)	42515	NM_001122824	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.006279	0.445141	
chunk0034_384_1	chr11	36467796	36468402	+	0	NA	Intergenic	Intergenic	42214	NM_004620	7189	Hs.444172	NM_004620	ENSG00000175104	TRAF6	MGC:3310|RNF85	TNF receptor associated factor 6	protein-coding	0.003300	0.520593	
chunk0158_184_1	chr5	127884951	127885604	+	0	NA	Intergenic	Intergenic	197797	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.001531	0.420489	
chunk0185_127_1	chr7	126450692	126451016	+	0	NA	intron (NR_028041, intron 9 of 10)	L2a|LINE|L2	607330	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.006173	0.393846	
chunk0097_233_1	chr2	53211161	53211696	+	0	NA	Intergenic	Intergenic	-508813	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.003738	0.412313	241(ATGAACATACTGTGCT,-,0.00),242(TGAACATACTGTGCTG,+,0.00)
chunk0201_339_1	chr9	64117864	64118812	+	0	NA	Intergenic	L1MB7|LINE|L1	101388	NR_033856	644316	Hs.632789	NR_033856		FLJ43315	-	asparagine synthetase pseudogene	pseudo	0.004219	0.316122	
chunk0014_91_1	chr1	176593478	176593840	+	0	NA	intron (NM_020318, intron 2 of 22)	intron (NM_020318, intron 2 of 22)	130488	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.005525	0.432507	
chunk0041_39_1	chr12	932683	933085	+	0	NA	intron (NR_123713, intron 3 of 13)	intron (NR_123713, intron 3 of 13)	192	NM_001297420	5893	Hs.410355	NM_134422	ENSG00000002016	RAD52	-	RAD52 homolog, DNA repair protein	protein-coding	0.037313	0.468983	
chunk0210_41_1	chrX	68274851	68275473	+	0	NA	intron (NM_002547, intron 4 of 24)	intron (NM_002547, intron 4 of 24)	158295	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.003215	0.359551	
chunk0114_34_1	chr21	8219825	8220282	+	0	NA	intron (NR_003287, intron 1 of 2)	CpG	6165	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.037199	0.526201	
chunk0126_309_1	chr3	81102234	81102633	+	0	NA	Intergenic	L2a|LINE|L2	108565	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.007519	0.307500	
chunk0189_175_1	chr8	23529845	23530350	+	0	NA	intron (NM_016612, intron 1 of 3)	intron (NM_016612, intron 1 of 3)	1247	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.029703	0.541502	
chunk0032_10_1	chr11	576136	576560	+	0	NA	promoter-TSS (NM_001286583).2	promoter-TSS (NM_001286583).2	-98	NM_001286582	57661	Hs.325838	NM_020901	ENSG00000070047	PHRF1	PPP1R125|RNF221	PHD and ring finger domains 1	protein-coding	0.099057	0.668235	
chunk0125_250_1	chr3	68995405	68995638	+	0	NA	intron (NR_103826, intron 8 of 15)	intron (NR_103826, intron 8 of 15)	18373	NR_103826	285203	Hs.518059	NM_173654	ENSG00000163378	EOGT	AER61|AOS4|C3orf64|EOGT1	EGF domain specific O-linked N-acetylglucosamine transferase	protein-coding	0.008584	0.555556	
chunk0027_134_1	chr10	74388924	74389151	+	0	NA	intron (NM_001123, intron 4 of 10)	L1MEc|LINE|L1	140287	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.000000	0.460526	80(GGGCACACCTTGTTTC,-,0.00),81(GGCACACCTTGTTTCT,+,0.00)
chunk0179_92_1	chr7	44617205	44617521	+	0	NA	intron (NM_001003941, intron 1 of 8)	intron (NM_001003941, intron 1 of 8)	10841	NM_001003941	4967	Hs.488181	NM_002541	ENSG00000105953	OGDH	AKGDH|E1k|OGDC	oxoglutarate dehydrogenase	protein-coding	0.006329	0.413249	
chunk0018_333_1	chr1	221382179	221382897	+	0	NA	Intergenic	Intergenic	-46242	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.002786	0.383866	
chunk0002_422_1	chr1	27830757	27831033	+	0	NA	promoter-TSS (NM_002713)	promoter-TSS (NM_002713)	81	NM_002713	5511	Hs.533474	NM_002713	ENSG00000117751	PPP1R8	ARD-1|ARD1|NIPP-1|NIPP1|PRO2047	protein phosphatase 1 regulatory subunit 8	protein-coding	0.079710	0.631769	
chunk0126_228_1	chr3	78932135	78932937	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	86923	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004988	0.318804	
chunk0102_419_1	chr2	156844274	156844568	+	0	NA	Intergenic	Intergenic	408033	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.006803	0.254237	
chunk0135_203_1	chr3	188283106	188283591	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	57943	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.006186	0.425926	67(TAGGTCAGAATGTGCC,-,0.00),68(AGGTCAGAATGTGCCA,+,0.00)
chunk0086_417_1	chr18	27012329	27012920	+	0	NA	intron (NM_031422, intron 4 of 5)	intron (NM_031422, intron 4 of 5)	-146872	NM_001650	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.003384	0.337838	
chunk0144_442_1	chr4	141135327	141135593	+	0	NA	Intergenic	L1MC4|LINE|L1	-1998	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.007519	0.419476	55(AAGTACAGAGTGAGCC,-,0.00),56(AGTACAGAGTGAGCCC,+,0.00),164(GGGACAGTCTGAACAT,+,0.00)
chunk0007_29_1	chr1	77602030	77602614	+	0	NA	intron (NM_001308237, intron 4 of 13)	intron (NM_001308237, intron 4 of 13)	80336	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.001712	0.338462	
chunk0087_223_1	chr18	36129269	36129961	+	0	NA	promoter-TSS (NM_001242878)	promoter-TSS (NM_001242878)	-221	NM_001099406	25800	Hs.79136	NM_012319	ENSG00000141424	SLC39A6	LIV-1|ZIP6	solute carrier family 39 member 6	protein-coding	0.102601	0.683983	
chunk0110_396_1	chr20	20360488	20360996	+	0	NA	TTS (NM_015585)	TTS (NM_015585)	-7379	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.009843	0.436149	
chunk0204_240_1	chr9	97981117	97981331	+	0	NA	Intergenic	Intergenic	-1983	NM_006401	10541	Hs.730654	NM_006401	ENSG00000136938	ANP32B	APRIL|PHAPI2|SSP29	acidic nuclear phosphoprotein 32 family member B	protein-coding	0.018692	0.497674	128(AAGAACGGACAGTGCC,-,0.00),129(AGAACGGACAGTGCCG,+,0.00)
chunk0035_42_1	chr11	41029587	41029912	+	0	NA	intron (NM_001258419, intron 1 of 6)	L2b|LINE|L2	429887	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.012308	0.346626	
chunk0033_153_1	chr11	15595286	15595870	+	0	NA	Intergenic	MER57C2|LTR|ERV1	-48307	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.015411	0.442735	
chunk0154_162_1	chr5	79527526	79527725	+	0	NA	Intergenic	MIR|SINE|MIR	-13789	NM_004272	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.000000	0.325000	
chunk0089_65_1	chr18	58186078	58186661	+	0	NA	intron (NM_001144967, intron 2 of 30)	intron (NM_001144967, intron 2 of 30)	-9021	NM_001144970	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.013722	0.438356	
chunk0172_83_1	chr6	134480598	134480797	+	0	NA	intron (NR_038219, intron 4 of 4)	intron (NR_038219, intron 4 of 4)	-1800	NR_125852	101928231	Hs.634168	NR_125852		CT69	-	cancer/testis associated transcript 69	ncRNA	0.000000	0.360000	
chunk0149_95_1	chr5	18574681	18574970	+	0	NA	Intergenic	Intergenic	-1187515	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.006920	0.358621	
chunk0040_176_1	chr11	114036384	114037038	+	0	NA	Intergenic	Intergenic	-22998	NM_006006	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.029052	0.502290	346(AAAACAGAAAGTTCCT,+,0.00)
chunk0023_100_1	chr10	22781417	22781692	+	0	NA	Intergenic	L2b|LINE|L2	-66980	NM_005028	5305	Hs.57079	NM_005028	ENSG00000150867	PIP4K2A	PI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK	phosphatidylinositol-5-phosphate 4-kinase type 2 alpha	protein-coding	0.007273	0.380435	
chunk0087_185_1	chr18	35582834	35583381	+	0	NA	Intergenic	L2a|LINE|L2	-8630	NR_039771	100616257		NR_039771	ENSG00000283514	MIR3975	-	microRNA 3975	ncRNA	0.012797	0.427007	268(GGAGACACAATGTCCT,-,0.00),269(GAGACACAATGTCCTT,+,0.00)
chunk0180_333_1	chr7	72753856	72754065	+	0	NA	intron (NM_001145440, intron 7 of 13)	Tigger1|DNA|TcMar-Tigger	56057	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.014354	0.409524	
chunk0109_89_1	chr20	2088614	2089044	+	0	NA	Intergenic	MIR|SINE|MIR	-13053	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.004651	0.417633	
chunk0168_381_1	chr6	93964298	93964529	+	0	NA	Intergenic	Intergenic	257330	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.000000	0.379310	
chunk0195_137_1	chr8	95100584	95101623	+	0	NA	Intergenic	Intergenic	-27921	NR_132986	105375650	Hs.665518	NR_132986	ENSG00000245080	MIR3150BHG	-	MIR3150B host gene	ncRNA	0.009625	0.404808	526(CAATACATTGTGTTCT,-,0.00),527(AATACATTGTGTTCTT,+,0.00)
chunk0071_250_1	chr15	85405364	85405977	+	0	NA	intron (NM_007200, intron 1 of 36)	MIRb|SINE|MIR	25054	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.009788	0.405537	
chunk0100_179_1	chr2	110747763	110747969	+	0	NA	intron (NM_001142807, intron 1 of 17)	intron (NM_001142807, intron 1 of 17)	15293	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.000000	0.507246	
chunk0183_277_1	chr7	107580912	107581529	+	0	NA	intron (NM_001008405, intron 1 of 7)	intron (NM_001008405, intron 1 of 7)	461	NM_001008405	55973	Hs.303787	NM_018844	ENSG00000075790	BCAP29	BAP29	B cell receptor associated protein 29	protein-coding	0.014587	0.315534	
chunk0173_216_1	chr6	145588495	145589005	+	0	NA	Intergenic	Intergenic	-146119	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.001961	0.334638	71(CAGCACTCATTGTTCT,-,0.00),72(AGCACTCATTGTTCTA,+,0.00)
chunk0003_193_1	chr1	34113677	34113876	+	0	NA	intron (NM_052896, intron 1 of 69)	L1MB2|LINE|L1	51498	NM_001281956	114784	Hs.656915	NM_052896	ENSG00000121904	CSMD2	dJ1007G16.1|dJ1007G16.2|dJ947L8.1	CUB and Sushi multiple domains 2	protein-coding	0.000000	0.395000	
chunk0035_247_1	chr11	46252341	46252741	+	0	NA	Intergenic	Intergenic	-25097	NM_052854	90993	Hs.405961	NM_052854	ENSG00000157613	CREB3L1	OASIS|OI16	cAMP responsive element binding protein 3 like 1	protein-coding	0.010000	0.493766	
chunk0114_392_1	chr20	63230966	63231185	+	0	NA	Intergenic	LTR1A2|LTR|ERV1	-4808	NM_139317	79444	Hs.256126	NM_022161	ENSG00000101197	BIRC7	KIAP|LIVIN|ML-IAP|MLIAP|RNF50	baculoviral IAP repeat containing 7	protein-coding	0.050228	0.613636	
chunk0078_324_1	chr17	8588764	8589390	+	0	NA	intron (NM_001256095, intron 4 of 41)	intron (NM_001256095, intron 4 of 41)	41684	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.009585	0.344498	
chunk0089_445_1	chr18	70272927	70273557	+	0	NA	Intergenic	Intergenic	-15659	NM_004232	9306	Hs.44439	NM_004232	ENSG00000170677	SOCS6	CIS-4|CIS4|HSPC060|SOCS-4|SOCS-6|SOCS4|SSI4|STAI4|STATI4	suppressor of cytokine signaling 6	protein-coding	0.003175	0.397781	
chunk0150_166_1	chr5	34036887	34037287	+	0	NA	intron (NR_037951, intron 1 of 8)	intron (NR_037951, intron 1 of 8)	6179	NM_181435	114899	Hs.171929	NM_030945	ENSG00000082196	C1QTNF3	C1ATNF3|CORCS|CORS|CORS-26|CORS26|CTRP3	C1q and TNF related 3	protein-coding	0.007500	0.346633	
chunk0150_177_1	chr5	34487274	34487751	+	0	NA	Intergenic	L3|LINE|CR1	-168816	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.018868	0.445607	
chunk0201_419_1	chr9	69610076	69610990	+	0	NA	intron (NM_001163, intron 1 of 12)	MER65-int|LTR|ERV1	61826	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.001094	0.379235	
chunk0161_359_1	chr5	175446024	175446484	+	0	NA	Intergenic	AluSx1|SINE|Alu	-2094	NM_000794	1812	Hs.2624	NM_000794	ENSG00000184845	DRD1	DADR|DRD1A	dopamine receptor D1	protein-coding	0.028261	0.472885	196(CAGCACAAACTGTACT,-,0.00),197(AGCACAAACTGTACTT,+,0.00)
chunk0163_375_1	chr6	16168573	16169208	+	0	NA	Intergenic	THE1C|LTR|ERVL-MaLR	27334	NR_039782	100616269		NR_039782	ENSG00000263712	MIR4639	-	microRNA 4639	ncRNA	0.006299	0.441824	
chunk0150_403_1	chr5	39901883	39902147	+	0	NA	Intergenic	Intergenic	-150276	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.003788	0.305660	
chunk0205_81_1	chr9	107067723	107068060	+	0	NA	intron (NR_126029, intron 3 of 4)	MER57B2|LTR|ERV1	35097	NR_126029	340512	Hs.432529	NR_126029	ENSG00000230782	LOC340512	-	uncharacterized LOC340512	ncRNA	0.011869	0.431953	
chunk0093_97_1	chr19	43352153	43352393	+	0	NA	Intergenic	L2b|LINE|L2	-1386	NM_020406	57126	Hs.232165	NM_020406	ENSG00000204936	CD177	HNA-2a|HNA2A|NB1|NB1 GP|PRV-1|PRV1	CD177 molecule	protein-coding	0.012500	0.402490	
chunk0166_116_1	chr6	44482647	44483124	+	0	NA	Intergenic	MIRb|SINE|MIR	47244	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.008386	0.560669	
chunk0042_416_1	chr12	11754367	11754713	+	0	NA	intron (NM_001987, intron 2 of 7)	MIR3|SINE|MIR	104686	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.008671	0.394813	
chunk0049_70_1	chr12	90300558	90300893	+	0	NA	Intergenic	Intergenic	591770	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.000000	0.297619	224(AAGAACTACCTGTACT,-,0.00),225(AGAACTACCTGTACTA,+,0.00)
chunk0163_246_1	chr6	12468401	12468688	+	0	NA	Intergenic	Intergenic	178248	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.006969	0.357639	
chunk0096_327_1	chr2	33719060	33719391	+	0	NA	intron (NR_126403, intron 1 of 5)	intron (NR_126403, intron 1 of 5)	8992	NR_003143	151325	Hs.528847	NM_207329	ENSG00000239649	MYADML	-	myeloid associated differentiation marker like (pseudogene)	pseudo	0.006042	0.313253	
chunk0048_354_1	chr12	85301212	85301624	+	0	NA	exon (NM_006982, exon 4 of 4)	exon (NM_006982, exon 4 of 4)	21160	NM_006982	8092	Hs.41683	NM_006982	ENSG00000180318	ALX1	CART1|FND3|HEL23	ALX homeobox 1	protein-coding	0.019417	0.406780	
chunk0050_22_1	chr12	99883939	99884716	+	0	NA	intron (NM_152788, intron 1 of 25)	L1ME1|LINE|L1	100327	NM_152788	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.001287	0.320051	
chunk0083_12_1	chr17	62830657	62830887	+	0	NA	Intergenic	L1MC3|LINE|L1	-22391	NM_001288779	162333	Hs.665663	NM_152598	ENSG00000173838	MARCH10	MARCH-X|RNF190	membrane associated ring-CH-type finger 10	protein-coding	0.000000	0.406926	
chunk0200_326_1	chr9	23683091	23683356	+	0	NA	Intergenic	Intergenic	-10824	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.007547	0.436090	
chunk0157_33_1	chr5	115738810	115739302	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	-66404	NR_104674	102467217	Hs.147738	NR_104674		LOC102467217	-	uncharacterized LOC102467217	ncRNA	0.006098	0.359026	
chunk0008_105_1	chr1	91338460	91338669	+	0	NA	intron (NM_001017975, intron 20 of 38)	L1PA14|LINE|L1	66305	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.009569	0.590476	
chunk0015_411_1	chr1	191174953	191175373	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	550273	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.007143	0.401425	
chunk0133_292_1	chr3	172156644	172156843	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	116189	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.010050	0.345000	
chunk0035_365_1	chr11	49180240	49180489	+	0	NA	intron (NM_001014986, intron 7 of 17)	intron (NM_001014986, intron 7 of 17)	28306	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.012048	0.368000	
chunk0048_428_1	chr12	88417487	88417972	+	0	NA	Intergenic	Intergenic	162744	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.010309	0.393004	
chunk0085_453_1	chr18	11508743	11509045	+	0	NA	Intergenic	L1ME1|LINE|L1	18846	NR_110778	101927433	Hs.331210	NR_110778	ENSG00000267252	LINC01255	-	long intergenic non-protein coding RNA 1255	ncRNA	0.006623	0.330033	
chunk0022_439_1	chr10	19613819	19614493	+	0	NA	intron (NM_001142308, intron 35 of 39)	MIR|SINE|MIR	114394	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.004451	0.391111	299(ATGAACTGGTTGTTCT,-,0.00),300(TGAACTGGTTGTTCTT,+,0.00)
chunk0041_220_1	chr11	127658522	127658880	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	387631	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.013966	0.387187	
chunk0052_446_1	chr12	132494135	132494721	+	0	NA	intron (NM_001142641, intron 1 of 16)	intron (NM_001142641, intron 1 of 16)	3857	NM_001142641	57666	Hs.411138	NM_001142641	ENSG00000112787	FBRSL1	-	fibrosin like 1	protein-coding	0.018771	0.586031	286(CAGAACAGGTTGTGCC,-,0.00),287(AGAACAGGTTGTGCCG,+,0.00)
chunk0142_22_1	chr4	90462057	90462376	+	0	NA	intron (NM_001145065, intron 4 of 10)	MLT2C1|LTR|ERVL	227185	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.006270	0.309375	
chunk0187_63_1	chr8	1998462	1998976	+	0	NA	intron (NM_014867, intron 1 of 1)	intron (NM_014867, intron 1 of 1)	24841	NM_014867	9920	Hs.5333	NM_014867	ENSG00000176595	KBTBD11	KLHDC7C	kelch repeat and BTB domain containing 11	protein-coding	0.013619	0.479612	230(GAGACAGCCAGTTCTC,+,0.00)
chunk0150_416_1	chr5	40306810	40307513	+	0	NA	Intergenic	Intergenic	254870	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.002845	0.330966	
chunk0045_285_1	chr12	50055436	50055843	+	0	NA	Intergenic	MIRb|SINE|MIR	-1998	NM_001095	41	Hs.274361	NM_001095	ENSG00000110881	ASIC1	ACCN2|ASIC|BNaC2	acid sensing ion channel subunit 1	protein-coding	0.014742	0.473039	
chunk0201_169_1	chr9	36099653	36100295	+	0	NA	intron (NM_001316345, intron 12 of 22)	L1ME2|LINE|L1	-36562	NR_104638	152007	Hs.493819	NM_022343	ENSG00000122694	GLIPR2	C9orf19|GAPR-1|GAPR1	GLI pathogenesis related 2	protein-coding	0.003115	0.377916	
chunk0004_24_1	chr1	42314032	42314611	+	0	NA	intron (NM_001198850, intron 1 of 12)	AluSq2|SINE|Alu	20644	NM_001198851	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.010363	0.465517	
chunk0084_238_1	chr17	78736663	78737453	+	0	NA	intron (NM_004762, intron 1 of 12)	intron (NM_004762, intron 1 of 12)	-13308	NM_001292018	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.021519	0.472819	
chunk0060_25_1	chr14	39853520	39853739	+	0	NA	Intergenic	L1ME2z|LINE|L1	-421129	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.004566	0.390909	
chunk0181_261_1	chr7	85866826	85867087	+	0	NA	Intergenic	L1PA10|LINE|L1	-745025	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.011494	0.564885	
chunk0088_158_1	chr18	46676082	46676493	+	0	NA	Intergenic	Intergenic	-19254	NM_144612	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.024331	0.468447	
chunk0045_123_1	chr12	46328790	46329457	+	0	NA	Intergenic	MLT1I-int|LTR|ERVL-MaLR	43739	NM_001307936	54407	Hs.221847	NM_018976	ENSG00000134294	SLC38A2	ATA2|PRO1068|SAT2|SNAT2	solute carrier family 38 member 2	protein-coding	0.000000	0.341317	367(GGACACATCATGTTCC,-,0.00),368(GACACATCATGTTCCT,+,0.00)
chunk0171_211_1	chr6	125991563	125992153	+	0	NA	intron (NM_001031712, intron 1 of 12)	intron (NM_001031712, intron 1 of 12)	5428	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.003390	0.351946	
chunk0178_295_1	chr7	37541161	37541360	+	0	NA	Intergenic	Intergenic	-91934	NM_001206480	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.020101	0.555000	
chunk0129_154_1	chr3	120567137	120567404	+	0	NA	Intergenic	Intergenic	-29011	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.014981	0.369403	
chunk0115_450_1	chr21	32475904	32476362	+	0	NA	intron (NM_058187, intron 4 of 7)	L1MC|LINE|L1	63696	NM_001286556	59271	Hs.208358	NM_058187	ENSG00000166979	EVA1C	B18|B19|C21orf63|C21orf64|FAM176C|PRED34|SUE21	eva-1 homolog C	protein-coding	0.006550	0.366013	
chunk0112_397_1	chr20	46831670	46832182	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-62698	NM_005244	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.005859	0.477583	
chunk0075_153_1	chr16	51402868	51403194	+	0	NA	intron (NR_039672, intron 6 of 6)	intron (NR_039672, intron 6 of 6)	-251759	NM_002968	6299	Hs.135787	NM_002968	ENSG00000103449	SALL1	HEL-S-89|HSAL1|Sal-1|TBS|ZNF794	spalt like transcription factor 1	protein-coding	0.009202	0.348624	
chunk0103_384_1	chr2	168691274	168691560	+	0	NA	intron (NM_001256126, intron 5 of 10)	intron (NM_001256126, intron 5 of 10)	95012	NR_045786	100861402	Hs.506829	NR_045786	ENSG00000227617	CERS6-AS1	-	CERS6 antisense RNA 1	ncRNA	0.003497	0.449477	201(AGGTACACTGAGTTCA,-,0.00),202(GGTACACTGAGTTCAG,+,0.00)
chunk0073_42_1	chr16	2861178	2861884	+	0	NA	Intergenic	L1PB4|LINE|L1	-3361	NM_022119	64063	Hs.459709	NM_022119	ENSG00000005001	PRSS22	BSSP-4|SP001LA|hBSSP-4	serine protease 22	protein-coding	0.014164	0.439887	
chunk0207_290_1	chr9	133088991	133089687	+	0	NA	Intergenic	MER51E|LTR|ERV1	6800	NR_001275	1057	Hs.654361	NR_001275	ENSG00000170827	CELP	CELL|cell1|cell2|cell3	carboxyl ester lipase pseudogene	pseudo	0.014368	0.533716	325(AGGTACAGCCCGTTCA,-,0.00),326(GGTACAGCCCGTTCAC,+,0.00)
chunk0015_161_1	chr1	186558691	186558976	+	0	NA	Intergenic	(CAAA)n|Simple_repeat|Simple_repeat	-97725	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.000000	0.360140	
chunk0151_208_1	chr5	50760764	50761048	+	0	NA	intron (NM_024615, intron 5 of 25)	intron (NM_024615, intron 5 of 25)	93968	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.000000	0.315789	
chunk0158_400_1	chr5	134685939	134686192	+	0	NA	intron (NM_001252231, intron 9 of 12)	intron (NM_001252231, intron 9 of 12)	37280	NM_001252231	10802	Hs.595540	NM_021982	ENSG00000113615	SEC24A	-	SEC24 homolog A, COPII coat complex component	protein-coding	0.003953	0.311024	
chunk0042_177_1	chr12	4735915	4736450	+	0	NA	intron (NM_017417, intron 2 of 10)	L1M4b|LINE|L1	15596	NM_017417	26290	Hs.511985	NM_017417	ENSG00000130035	GALNT8	GALNAC-T8	polypeptide N-acetylgalactosaminyltransferase 8	protein-coding	0.001869	0.432836	
chunk0166_103_1	chr6	43849861	43850260	+	0	NA	Intergenic	Intergenic	-40968	NR_024478	100132354	Hs.376232	NR_024478		LINC01512	HI-LNC77	long intergenic non-protein coding RNA 1512	ncRNA	0.015038	0.462500	
chunk0042_403_1	chr12	11556106	11556741	+	0	NA	non-coding (NR_033890, exon 6 of 8)	non-coding (NR_033890, exon 6 of 8)	8393	NR_033890	338817	Hs.733066	NR_033890	ENSG00000247157	LINC01252	-	long intergenic non-protein coding RNA 1252	ncRNA	0.011024	0.449686	367(GAAGACAGACTGTTCC,-,0.00),368(AAGACAGACTGTTCCC,+,0.00)
chunk0172_25_1	chr6	132964962	132965196	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-50751	NR_039664									0.004274	0.391489	
chunk0116_428_1	chr21	42973732	42974394	+	0	NA	promoter-TSS (NM_001286258)	promoter-TSS (NM_001286258)	-447	NM_004571	5316	Hs.431043	NM_004571	ENSG00000160199	PKNOX1	PREP1|pkonx1c	PBX/knotted 1 homeobox 1	protein-coding	0.072508	0.672700	
chunk0051_312_1	chr12	119621821	119622280	+	0	NA	intron (NM_001136534, intron 1 of 2)	intron (NM_001136534, intron 1 of 2)	28591	NM_001136534	387890	Hs.530965	NM_001136534	ENSG00000224982	TMEM233	DSPB2|IFITMD2	transmembrane protein 233	protein-coding	0.004357	0.360870	
chunk0105_231_1	chr2	188324119	188324583	+	0	NA	intron (NR_045563, intron 2 of 12)	intron (NR_045563, intron 2 of 12)	26859	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.000000	0.324731	215(GGGAACATGCTGTTAC,-,0.00),216(GGAACATGCTGTTACT,+,0.00)
chunk0021_292_1	chr1	244662473	244663206	+	0	NA	intron (NR_123736, intron 1 of 3)	L2a|LINE|L2	9791	NR_123736	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.002729	0.350136	475(TAGAACAAGCAGTACC,-,0.00),476(AGAACAAGCAGTACCA,+,0.00)
chunk0101_327_1	chr2	135993942	135994487	+	0	NA	intron (NR_110199, intron 1 of 3)	intron (NR_110199, intron 1 of 3)	-8530	NM_001293312	1615	Hs.503787	NM_001349	ENSG00000115866	DARS	HBSL|aspRS	aspartyl-tRNA synthetase	protein-coding	0.007339	0.388278	
chunk0086_167_1	chr18	21740653	21741025	+	0	NA	promoter-TSS (NM_020774)	promoter-TSS (NM_020774)	-490	NM_020774	57534	Hs.140903	NM_020774	ENSG00000101752	MIB1	DIP-1|DIP1|LVNC7|MIB|ZZANK2|ZZZ6	mindbomb E3 ubiquitin protein ligase 1	protein-coding	0.096774	0.667560	
chunk0073_247_1	chr16	11705402	11705601	+	0	NA	intron (NM_001303447, intron 5 of 12)	intron (NM_001303447, intron 5 of 12)	37068	NM_003498	8303	Hs.618526	NM_003498	ENSG00000184602	SNN	-	stannin	protein-coding	0.010050	0.430000	
chunk0097_48_1	chr2	43389715	43390253	+	0	NA	intron (NR_073394, intron 27 of 35)	L2c|LINE|L2	162773	NR_027251	100129726	Hs.194480	NM_178529	ENSG00000279873	LINC01126	-	long intergenic non-protein coding RNA 1126	ncRNA	0.007435	0.432282	
chunk0209_256_1	chrX	46290267	46290842	+	0	NA	Intergenic	L1MA8|LINE|L1	37120	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.001739	0.296875	296(TAGGACATCCAGTACT,-,0.00),297(AGGACATCCAGTACTA,+,0.00)
chunk0086_176_1	chr18	21853952	21854368	+	0	NA	intron (NM_020774, intron 18 of 20)	intron (NM_020774, intron 18 of 20)	-22754	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.007212	0.376499	
chunk0177_10_1	chr7	20381514	20381904	+	0	NA	intron (NM_002214, intron 5 of 13)	intron (NM_002214, intron 5 of 13)	-49947	NR_110120	101927811	Hs.285724	NR_110119	ENSG00000271133	LOC101927811	-	uncharacterized LOC101927811	ncRNA	0.035897	0.419437	
chunk0146_333_1	chr4	165839988	165840246	+	0	NA	Intergenic	Intergenic	-33141	NM_001204760	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.003876	0.436293	
chunk0076_117_1	chr16	66550120	66550408	+	0	NA	promoter-TSS (NM_001172643)	promoter-TSS (NM_001172643)	27	NM_001172643	7084	Hs.512619	NM_004614	ENSG00000166548	TK2	MTDPS2|MTTK|PEOB3|SCA31	thymidine kinase 2	protein-coding	0.048611	0.525952	
chunk0139_23_1	chr4	48329109	48329810	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-12137	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.001427	0.376068	
chunk0194_9_1	chr8	81449515	81450037	+	0	NA	Intergenic	Intergenic	-2292	NM_002677	5375	Hs.571512	NM_002677	ENSG00000147588	PMP2	CMT1G|FABP8|M-FABP|MP2|P2	peripheral myelin protein 2	protein-coding	0.003831	0.349904	
chunk0188_330_1	chr8	17614243	17614624	+	0	NA	intron (NM_006207, intron 3 of 6)	intron (NM_006207, intron 3 of 6)	38000	NM_006207	5157	Hs.458573	NM_006207	ENSG00000104213	PDGFRL	PDGRL|PRLTS	platelet derived growth factor receptor like	protein-coding	0.013123	0.397906	
chunk0012_239_1	chr1	160789337	160789633	+	0	NA	Intergenic	Intergenic	-6589	NM_002348	4063	Hs.403857	NM_002348	ENSG00000122224	LY9	CD229|SLAMF3|hly9|mLY9	lymphocyte antigen 9	protein-coding	0.016892	0.478114	
chunk0048_282_1	chr12	82524639	82524867	+	0	NA	Intergenic	Intergenic	-162402	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004386	0.362445	150(ATGCACACCGTGTTCT,-,0.00),151(TGCACACCGTGTTCTG,+,0.00)
chunk0152_176_1	chr5	59652434	59652702	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	51135	NR_030308	693167		NR_030308	ENSG00000202601	MIR582	MIRN582|hsa-mir-582	microRNA 582	ncRNA	0.007463	0.327138	
chunk0059_35_1	chr14	29897125	29897325	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	30468	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005000	0.228856	
chunk0129_58_1	chr3	117563146	117563505	+	0	NA	Intergenic	L2a|LINE|L2	641894	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002786	0.383333	
chunk0117_342_1	chr21	43979475	43980009	+	0	NA	intron (NM_020132, intron 8 of 9)	L1MEd|LINE|L1	-32583	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.014981	0.491589	
chunk0063_217_1	chr14	81473059	81473368	+	0	NA	3' UTR (NM_005065, exon 21 of 21)	3' UTR (NM_005065, exon 21 of 21)	-23056	NR_109999	100506700	Hs.116304	NR_109999	ENSG00000258675	LINC02308	-	long intergenic non-protein coding RNA 2308	ncRNA	0.003236	0.332258	
chunk0054_429_1	chr13	51125615	51125862	+	0	NA	intron (NR_102431, intron 1 of 4)	L2a|LINE|L2	46484	NR_102432	647166	Hs.195052	NM_001351589	ENSG00000226792	C13orf42	LINC00371|LINC00372	chromosome 13 open reading frame 42	protein-coding	0.004049	0.455645	
chunk0010_330_1	chr1	118321516	118321834	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-136450	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.003145	0.344828	
chunk0197_105_1	chr8	119753318	119753892	+	0	NA	intron (NM_003184, intron 22 of 25)	intron (NM_003184, intron 22 of 25)	79229	NM_003184	6873	Hs.122752	NM_003184	ENSG00000064313	TAF2	CIF150|MRT40|TAF2B|TAFII150	TATA-box binding protein associated factor 2	protein-coding	0.001742	0.295652	
chunk0142_447_1	chr4	105458841	105459233	+	0	NA	intron (NM_006903, intron 1 of 10)	L2a|LINE|L2	15033	NM_176866	27068	Hs.654957	NM_006903	ENSG00000138777	PPA2	HSPC124|SCFAI|SCFI|SID6-306	pyrophosphatase (inorganic) 2	protein-coding	0.002551	0.335878	
chunk0066_147_1	chr15	31405612	31405837	+	0	NA	intron (NM_001302461, intron 1 of 1).2	HAL1ME|LINE|L1	78869	NM_001302461	51621	Hs.376443	NM_015995	ENSG00000169926	KLF13	BTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel like factor 13	protein-coding	0.013333	0.513274	
chunk0121_153_1	chr3	19192305	19193050	+	0	NA	intron (NM_144633, intron 1 of 15)	intron (NM_144633, intron 1 of 15)	44152	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.004027	0.309651	
chunk0098_114_1	chr2	68470712	68471132	+	0	NA	intron (NM_173545, intron 1 of 9)	intron (NM_173545, intron 1 of 9)	3363	NM_173545	200558	Hs.720369	NM_173545	ENSG00000169621	APLF	APFL|C2orf13|PALF|Xip1|ZCCHH1	aprataxin and PNKP like factor	protein-coding	0.004762	0.399050	
chunk0202_327_1	chr9	78468224	78468431	+	0	NA	Intergenic	Intergenic	171252	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.014493	0.471154	
chunk0073_365_1	chr16	15404848	15405301	+	0	NA	intron (NM_001128423, intron 2 of 3)	L1MC4|LINE|L1	9320	NM_001128423	255027	Hs.720673	NM_173803	ENSG00000156968	MPV17L	M-LPH|MLPH1|MLPH2|MPV17L1	MPV17 mitochondrial inner membrane protein like	protein-coding	0.011038	0.469163	225(CATGACAGCGTGTTCC,-,0.00),226(ATGACAGCGTGTTCCA,+,0.00)
chunk0175_292_1	chr7	7780931	7781313	+	0	NA	intron (NM_001302350, intron 3 of 4)	L1ME3A|LINE|L1	-62515	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.002618	0.313316	
chunk0004_427_1	chr1	52697964	52698180	+	0	NA	intron (NM_023077, intron 1 of 2)	CpG	294	NM_023077	65260	Hs.349905	NM_023077	ENSG00000162377	COA7	C1orf163|RESA1|SCAN3|SELRC1	cytochrome c oxidase assembly factor 7 (putative)	protein-coding	0.083333	0.645161	
chunk0083_315_1	chr17	69498597	69498998	+	0	NA	intron (NM_002758, intron 1 of 11)	MER54B|LTR|ERVL	84100	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.017456	0.519900	
chunk0117_220_1	chr22	22548363	22548598	+	0	NA	exon (NM_206956, exon 6 of 6)	exon (NM_206956, exon 6 of 6)	9274	NM_001291719	23532	Hs.30743	NM_006115	ENSG00000185686	PRAME	CT130|MAPE|OIP-4|OIP4	preferentially expressed antigen in melanoma	protein-coding	0.025532	0.576271	
chunk0199_47_1	chr9	1462670	1463179	+	0	NA	Intergenic	MIRc|SINE|MIR	412304	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.003929	0.433333	
chunk0041_348_1	chr11	130744050	130744583	+	0	NA	Intergenic	Intergenic	71360	NM_001271983	283171	Hs.376151	NM_001271983		C11orf44	-	chromosome 11 open reading frame 44	protein-coding	0.005629	0.329588	
chunk0004_287_1	chr1	48836647	48837025	+	0	NA	intron (NM_032785, intron 6 of 13)	L2b|LINE|L2	-59867	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.005291	0.271768	
chunk0197_166_1	chr8	120842905	120843104	+	0	NA	Intergenic	Intergenic	-30935	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.010050	0.430000	
chunk0061_414_1	chr14	65032030	65032744	+	0	NA	intron (NM_001202558, intron 7 of 12)	intron (NM_001202558, intron 7 of 12)	-12301	NR_039855	100616490		NR_039855	ENSG00000266531	MIR4706	mir-4706	microRNA 4706	ncRNA	0.016807	0.455944	580(AAGCGCATACTGTGCT,-,0.00),581(AGCGCATACTGTGCTG,+,0.00)
chunk0197_177_1	chr8	121151445	121151781	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-339544	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.008929	0.412463	
chunk0114_398_1	chr20	63575814	63576103	+	0	NA	Intergenic	Intergenic	-1719	NM_001037335	85441	Hs.517180	NM_033405	ENSG00000130589	HELZ2	PDIP-1|PRIC285	helicase with zinc finger 2	protein-coding	0.024221	0.544828	157(GTGGACACACAGTTCC,-,0.00),158(TGGACACACAGTTCCA,+,0.00),177(CAGAACAGAGAGTCCA,-,0.00),178(AGAACAGAGAGTCCAG,+,0.00)
chunk0077_225_1	chr16	80299534	80299879	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-241028	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.020290	0.500000	
chunk0065_61_1	chr15	22968463	22968842	+	0	NA	intron (NM_001287810, intron 1 of 31)	intron (NM_001287810, intron 1 of 31)	11767	NM_001287810	23191	Hs.26704	NM_014608	ENSG00000273749	CYFIP1	P140SRA-1|SHYC|SRA-1|SRA1	cytoplasmic FMR1 interacting protein 1	protein-coding	0.010554	0.465789	
chunk0098_271_1	chr2	75480980	75481868	+	0	NA	Intergenic	Intergenic	-42644	NR_110281	101927884	Hs.671110	NR_110281	ENSG00000231172	LOC101927884	-	uncharacterized LOC101927884	ncRNA	0.006757	0.402700	
chunk0078_452_1	chr16	89972692	89972891	+	0	NA	promoter-TSS (NM_145039)	promoter-TSS (NM_145039)	41	NM_145039	92806	Hs.513832	NM_145039	ENSG00000177946	CENPBD1	-	CENPB DNA-binding domain containing 1	protein-coding	0.135678	0.775000	
chunk0073_306_1	chr16	14139457	14140115	+	0	NA	intron (NM_001308142, intron 2 of 16)	L1M4|LINE|L1	68472	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.004559	0.376328	300(ATGAACACACTGTGCT,-,0.00),301(TGAACACACTGTGCTA,+,0.00),579(ATGAACTGTATGTCCA,-,0.00),580(TGAACTGTATGTCCAT,+,0.00)
chunk0113_360_1	chr20	59073724	59074343	+	0	NA	Intergenic	Intergenic	-31187	NM_001256403	51012	Hs.656865	NM_016045	ENSG00000101166	PRELID3B	C20orf45|SLMO2|dJ543J19.5	PRELI domain containing 3B	protein-coding	0.006462	0.379032	
chunk0054_289_1	chr13	47935902	47936462	+	0	NA	Intergenic	L1ME4a|LINE|L1	-3560	NR_047492	100861549	Hs.660978	NR_047492	ENSG00000260388	LINC00562	-	long intergenic non-protein coding RNA 562	ncRNA	0.003571	0.333333	430(AGAACATTATGTTTAT,+,0.00)
chunk0128_436_1	chr3	114980333	114980532	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	-79810	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.000000	0.250000	
chunk0133_298_1	chr3	172203763	172204298	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	163476	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.016822	0.440299	
chunk0032_394_1	chr11	11614935	11615202	+	0	NA	intron (NM_198516, intron 1 of 10)	intron (NM_198516, intron 1 of 10)	6946	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.003745	0.376866	
chunk0029_369_1	chr10	107759656	107760168	+	0	NA	Intergenic	Intergenic	309381	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.007812	0.343080	
chunk0156_237_1	chr5	108371261	108371659	+	0	NA	intron (NM_001163315, intron 1 of 8)	MER58A|DNA|hAT-Charlie	10638	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.005025	0.383459	
chunk0062_335_1	chr14	73432110	73432621	+	0	NA	intron (NM_001005743, intron 1 of 12)	L1M5|LINE|L1	26215	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.007828	0.308594	
chunk0071_444_1	chr15	90095682	90095939	+	0	NA	intron (NM_002168, intron 1 of 10)	intron (NM_002168, intron 1 of 10)	4811	NM_001289910	3418	Hs.596461	NM_002168	ENSG00000182054	IDH2	D2HGA2|ICD-M|IDH|IDHM|IDP|IDPM|mNADP-IDH	isocitrate dehydrogenase (NADP(+)) 2, mitochondrial	protein-coding	0.003891	0.496124	
chunk0045_36_1	chr12	44368464	44368936	+	0	NA	intron (NM_001286211, intron 6 of 6)	intron (NM_001286211, intron 6 of 6)	506961	NM_001145109	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.002119	0.334038	
chunk0036_357_1	chr11	66934952	66935321	+	0	NA	promoter-TSS (NR_036121)	promoter-TSS (NR_036121)	-630	NR_036121	100423029		NR_036121	ENSG00000266423	MIR3163	-	microRNA 3163	ncRNA	0.013550	0.456757	
chunk0134_260_1	chr3	179432082	179432926	+	0	NA	intron (NM_021629, intron 1 of 9)	intron (NM_021629, intron 1 of 9)	19079	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.004739	0.401183	
chunk0106_239_1	chr2	203030478	203030895	+	0	NA	intron (NM_001114132, intron 2 of 54)	intron (NM_001114132, intron 2 of 54)	15807	NM_001114132	65065	Hs.648846	NM_198945	ENSG00000144426	NBEAL1	A530083I02Rik|ALS2CR16|ALS2CR17	neurobeachin like 1	protein-coding	0.004796	0.394737	
chunk0148_419_1	chr5	15026893	15027386	+	0	NA	Intergenic	Intergenic	-155361	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.012170	0.475709	
chunk0082_237_1	chr17	57340625	57341165	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	83882	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.011111	0.567468	
chunk0097_22_1	chr2	42283746	42284146	+	0	NA	intron (NM_019063, intron 8 of 22)	L1ME4b|LINE|L1	77270	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.010000	0.349127	
chunk0155_37_1	chr5	91110587	91111156	+	0	NA	intron (NR_003149, intron 87 of 89)	intron (NR_003149, intron 87 of 89)	203531	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.008787	0.389474	
chunk0024_355_1	chr10	43778093	43779039	+	0	NA	Intergenic	Intergenic	11851	NR_002726	10151	Hs.632956	NR_002726		HNRNPA3P1	D10S102|FBRNP|HNRPA3|HNRPA3P1	heterogeneous nuclear ribonucleoprotein A3 pseudogene 1	pseudo	0.005285	0.376980	306(TGGAACACTATGTTCA,-,0.00),307(GGAACACTATGTTCAG,+,0.00),686(GGGAACAACGTGACCC,-,0.00),687(GGAACAACGTGACCCC,+,0.00)
chunk0178_1_1	chr7	28916928	28917142	+	0	NA	Intergenic	L1ME3A|LINE|L1	41378	NM_014817	9865	Hs.744120	NM_014817	ENSG00000255690	TRIL	-	TLR4 interactor with leucine rich repeats	protein-coding	0.009346	0.306977	
chunk0144_448_1	chr4	141830468	141830905	+	0	NA	Intergenic	ERV24_Prim-int|LTR|ERV1	194090	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.002288	0.335616	
chunk0103_258_1	chr2	165417703	165417955	+	0	NA	Intergenic	L1PB1|LINE|L1	-51818	NM_001172173	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.015873	0.474308	
chunk0002_354_1	chr1	25826731	25826930	+	0	NA	intron (NM_001099627, intron 5 of 6)	intron (NM_001099627, intron 5 of 6)	-3224	NR_024498	646471	Hs.727271	NR_024498		LOC646471	-	uncharacterized LOC646471	ncRNA	0.020101	0.570000	123(CGTAACAGGCTGTTCC,-,0.00),124(GTAACAGGCTGTTCCT,+,0.00)
chunk0035_313_1	chr11	47248716	47249078	+	0	NA	promoter-TSS (NM_001302492)	promoter-TSS (NM_001302492)	-1	NM_001130102	10062	Hs.438863	NM_005693	ENSG00000025434	NR1H3	LXR-a|LXRA|RLD-1	nuclear receptor subfamily 1 group H member 3	protein-coding	0.085635	0.622590	
chunk0116_288_1	chr21	40225049	40225248	+	0	NA	intron (NR_073202, intron 11 of 32)	intron (NR_073202, intron 11 of 32)	-12717	NR_039917	100616148		NR_039917	ENSG00000263973	MIR4760	-	microRNA 4760	ncRNA	0.005025	0.465000	
chunk0204_454_1	chr9	104498363	104498562	+	0	NA	Intergenic	L2b|LINE|L2	-5801	NM_001004485	138805	Hs.553602	NM_001004485	ENSG00000186881	OR13F1	OR9-6	olfactory receptor family 13 subfamily F member 1	protein-coding	0.020101	0.395000	
chunk0126_222_1	chr3	78845907	78846416	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	173298	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003929	0.349020	
chunk0006_397_1	chr1	75423508	75424026	+	0	NA	intron (NM_001130058, intron 2 of 23)	intron (NM_001130058, intron 2 of 23)	187347	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.015444	0.398844	
chunk0073_87_1	chr16	4095424	4095629	+	0	NA	intron (NM_001116, intron 2 of 10)	intron (NM_001116, intron 2 of 10)	20659	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.014634	0.388350	
chunk0146_76_1	chr4	157246857	157247558	+	0	NA	intron (NM_001083619, intron 2 of 15)	intron (NM_001083619, intron 2 of 15)	26539	NM_001083620	2891	Hs.32763	NM_000826	ENSG00000120251	GRIA2	GLUR2|GLURB|GluA2|GluR-K2|HBGR2	glutamate ionotropic receptor AMPA type subunit 2	protein-coding	0.001427	0.368946	266(CTGAACACATTGTGCT,-,0.00),267(TGAACACATTGTGCTC,+,0.00)
chunk0182_399_1	chr7	100648405	100648630	+	0	NA	intron (NM_016188, intron 7 of 13)	intron (NM_016188, intron 7 of 13)	-6967	NM_003227	7036	Hs.544932	NM_003227	ENSG00000106327	TFR2	HFE3|TFRC2	transferrin receptor 2	protein-coding	0.022222	0.579646	
chunk0075_455_1	chr16	58389997	58390449	+	0	NA	Intergenic	Intergenic	-2171	NM_001126129	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.000000	0.315673	
chunk0164_314_1	chr6	25033377	25034036	+	0	NA	intron (NM_001286446, intron 1 of 13)	L1MC4a|LINE|L1	8462	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.000000	0.337879	
chunk0184_101_1	chr7	113402688	113403344	+	0	NA	Intergenic	Intergenic	-284434	NR_015442									0.004573	0.353120	
chunk0073_28_1	chr16	2388657	2389375	+	0	NA	intron (NR_003574, intron 8 of 16)	intron (NR_003574, intron 8 of 16)	-40378	NM_001761	899	Hs.1973	NM_001761	ENSG00000162063	CCNF	FBX1|FBXO1	cyclin F	protein-coding	0.004178	0.479833	
chunk0200_63_1	chr9	15727817	15728071	+	0	NA	exon (NM_173550, exon 15 of 26)	exon (NM_173550, exon 15 of 26)	174845	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.000000	0.407843	
chunk0002_428_1	chr1	27971637	27972210	+	0	NA	3' UTR (NM_001990, exon 18 of 18)	3' UTR (NM_001990, exon 18 of 18)	12461	NM_018053	55113	Hs.55024	NM_018053	ENSG00000158156	XKR8	XRG8|hXkr8	XK related 8	protein-coding	0.006981	0.468641	191(GAGAGCACTGTGTTCC,-,0.00),192(AGAGCACTGTGTTCCC,+,0.00)
chunk0026_219_1	chr10	64650591	64650790	+	0	NA	Intergenic	MIR|SINE|MIR	-174838	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.000000	0.350000	
chunk0204_328_1	chr9	101088443	101089017	+	0	NA	intron (NM_207299, intron 1 of 7)	intron (NM_207299, intron 1 of 7)	59981	NM_207299	54886	Hs.382683	NM_017753	ENSG00000148123	PLPPR1	LPPR1|PRG-3	phospholipid phosphatase related 1	protein-coding	0.003484	0.311304	
chunk0166_405_1	chr6	52059919	52060211	+	0	NA	intron (NM_138694, intron 14 of 66)	intron (NM_138694, intron 14 of 66)	27560	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.003425	0.416382	
chunk0095_45_1	chr2	13560583	13561186	+	0	NA	Intergenic	Intergenic	-553871	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.001658	0.329470	
chunk0153_190_1	chr5	71665055	71665309	+	0	NA	Intergenic	Intergenic	-53981	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.007874	0.415686	
chunk0119_140_1	chr22	42962856	42963538	+	0	NA	intron (NM_001184970, intron 1 of 10)	L2b|LINE|L2	-3316	NM_001184971	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.016129	0.537335	
chunk0174_344_1	chr6	164203752	164204281	+	0	NA	Intergenic	L1ME4c|LINE|L1	618047	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.005671	0.369811	
chunk0093_123_1	chr19	44859006	44859544	+	0	NA	intron (NM_002856, intron 1 of 5)	intron (NM_002856, intron 1 of 5)	13139	NM_002856	5819	Hs.655455	NM_002856	ENSG00000130202	NECTIN2	CD112|HVEB|PRR2|PVRL2|PVRR2	nectin cell adhesion molecule 2	protein-coding	0.016729	0.530612	
chunk0154_168_1	chr5	79668447	79668969	+	0	NA	intron (NM_001297744, intron 12 of 15)	intron (NM_001297744, intron 12 of 15)	-21128	NM_153610	202333	Hs.482625	NM_153610	ENSG00000164309	CMYA5	C5orf10|SPRYD2|TRIM76	cardiomyopathy associated 5	protein-coding	0.001916	0.342256	256(AGGTACATTCTGGTCT,-,0.00)
chunk0045_425_1	chr12	53321537	53321802	+	0	NA	promoter-TSS (NM_015665)	promoter-TSS (NM_015665)	-41	NM_001173466	8086	Hs.369144	NM_015665	ENSG00000094914	AAAS	AAA|AAASb|ADRACALA|ADRACALIN|ALADIN|GL003	aladin WD repeat nucleoporin	protein-coding	0.090566	0.593985	
chunk0038_368_1	chr11	93359456	93359747	+	0	NA	intron (NM_181645, intron 4 of 13)	L1MDa|LINE|L1	28884	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.000000	0.414384	
chunk0171_174_1	chr6	125023938	125024316	+	0	NA	intron (NM_152553, intron 3 of 8)	intron (NM_152553, intron 3 of 8)	40763	NR_104440	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.005291	0.364116	
chunk0005_108_1	chr1	56625778	56626234	+	0	NA	Intergenic	L2a|LINE|L2	-19311	NM_006252	5563	Hs.437039	NM_006252	ENSG00000162409	PRKAA2	AMPK|AMPK2|AMPKa2|PRKAA	protein kinase AMP-activated catalytic subunit alpha 2	protein-coding	0.006579	0.326039	
chunk0142_48_1	chr4	91258282	91258627	+	0	NA	intron (NM_001145065, intron 10 of 10)	intron (NM_001145065, intron 10 of 10)	1018848	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.000000	0.323699	95(CAGAACACCCTCTTCC,-,0.00),96(AGAACACCCTCTTCCT,+,0.00)
chunk0093_285_1	chr19	51983241	51983905	+	0	NA	intron (NM_021632, intron 1 of 4)	LTR5B|LTR|ERVK	3253	NM_021632	59348	Hs.407694	NM_021632	ENSG00000256683	ZNF350	ZBRK1|ZFQR	zinc finger protein 350	protein-coding	0.012048	0.455639	
chunk0114_156_1	chr21	10478663	10478862	+	0	NA	intron (NM_182484, intron 6 of 8)	intron (NM_182484, intron 6 of 8)	-42752	NM_001290224	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.015075	0.375000	
chunk0117_348_1	chr21	44063411	44063740	+	0	NA	exon (NM_003274, exon 7 of 23)	exon (NM_003274, exon 7 of 23)	-43752	NM_005049	5822	Hs.449076	NM_005049	ENSG00000241945	PWP2	EHOC-17|PWP2H|UTP1	PWP2 small subunit processome component	protein-coding	0.030395	0.536364	
chunk0134_379_1	chr3	182810535	182810938	+	0	NA	intron (NM_014616, intron 1 of 29)	intron (NM_014616, intron 1 of 29)	17233	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.007444	0.331683	216(GAGTACTGTCTGTACT,-,0.00),217(AGTACTGTCTGTACTG,+,0.00)
chunk0094_181_1	chr2	6060152	6060684	+	0	NA	Intergenic	Intergenic	78440	NR_026833	400940	Hs.378814	NM_207479		LOC400940	-	uncharacterized LOC400940	ncRNA	0.007519	0.365854	
chunk0149_235_1	chr5	23336822	23337101	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-170648	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.007168	0.360714	152(TTGGACATTATGTGCC,-,0.00),153(TGGACATTATGTGCCA,+,0.00)
chunk0018_76_1	chr1	217169923	217170122	+	0	NA	Intergenic	L1MD2|LINE|L1	-32267	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.310000	101(TGGTACAGGGAGTTCC,-,0.00),102(GGTACAGGGAGTTCCT,+,0.00)
chunk0118_236_1	chr22	32502171	32502810	+	0	NA	Intergenic	Intergenic	27253	NM_001257990	25793	Hs.5912	NM_012179	ENSG00000100225	FBXO7	FBX|FBX07|FBX7|PARK15|PKPS	F-box protein 7	protein-coding	0.009390	0.490625	351(AAGGACACTGTGTGCT,-,0.00),352(AGGACACTGTGTGCTC,+,0.00)
chunk0146_290_1	chr4	164753959	164754340	+	0	NA	promoter-TSS (NR_038834)	promoter-TSS (NR_038834)	18	NR_038834									0.010499	0.397906	
chunk0119_52_1	chr22	40757282	40757682	+	0	NA	Intergenic	L2c|LINE|L2	56476	NR_039923	100616283		NR_039923	ENSG00000266594	MIR4766	mir-4766	microRNA 4766	ncRNA	0.005000	0.391521	
chunk0188_293_1	chr8	15684120	15684543	+	0	NA	intron (NM_006765, intron 6 of 10)	L1PA17|LINE|L1	144244	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.009456	0.544811	
chunk0104_75_1	chr2	171830285	171830563	+	0	NA	intron (NR_047549, intron 7 of 16)	intron (NR_047549, intron 7 of 16)	63882	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.003597	0.301075	
chunk0050_48_1	chr12	100915082	100915629	+	0	NA	intron (NM_178826, intron 2 of 26)	intron (NM_178826, intron 2 of 26)	13709	NM_001286616	121601	Hs.58785	NM_178826	ENSG00000151572	ANO4	TMEM16D	anoctamin 4	protein-coding	0.000000	0.366788	
chunk0085_155_1	chr18	3567490	3567781	+	0	NA	intron (NM_001308390, intron 6 of 10)	intron (NM_001308390, intron 6 of 10)	-26479	NR_024101	649446	Hs.19872	NM_001039796		DLGAP1-AS1	HsT914	DLGAP1 antisense RNA 1	ncRNA	0.006873	0.369863	
chunk0160_74_1	chr5	149886700	149886913	+	0	NA	intron (NM_000440, intron 13 of 21)	intron (NM_000440, intron 13 of 21)	46171	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.004695	0.448598	
chunk0062_71_1	chr14	67633341	67633713	+	0	NA	intron (NM_001172, intron 2 of 7)	intron (NM_001172, intron 2 of 7)	13665	NM_001172	384	Hs.226007	NM_001172	ENSG00000081181	ARG2	-	arginase 2	protein-coding	0.010753	0.439678	212(CTGGACACTCTGTTCC,-,0.00),213(TGGACACTCTGTTCCC,+,0.00)
chunk0188_4_1	chr8	6274690	6275126	+	0	NA	Intergenic	Intergenic	131640	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.016055	0.512586	
chunk0008_177_1	chr1	92943020	92943240	+	0	NA	intron (NM_001252273, intron 1 of 4)	intron (NM_001252273, intron 1 of 4)	18392	NM_001252273	388650	Hs.180946	NM_001006605	ENSG00000154511	DIPK1A	FAM69A	divergent protein kinase domain 1A	protein-coding	0.004545	0.339367	
chunk0171_53_1	chr6	121161703	121162473	+	0	NA	intron (NM_152730, intron 22 of 31)	L1PA11|LINE|L1	172412	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.003896	0.363165	
chunk0191_397_1	chr8	57503164	57503573	+	0	NA	Intergenic	L1MDa|LINE|L1	159581	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.002445	0.287805	
chunk0010_293_1	chr1	117592428	117592627	+	0	NA	Intergenic	Intergenic	13243	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.015075	0.470000	
chunk0154_418_1	chr5	89047256	89047663	+	0	NA	Intergenic	Intergenic	-143354	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.002457	0.321078	
chunk0053_136_1	chr13	29923662	29924442	+	0	NA	intron (NR_047501, intron 1 of 1)	intron (NR_047501, intron 1 of 1)	2599	NR_047501	100861573	Hs.585619	NR_047501	ENSG00000224405	LINC00572	-	long intergenic non-protein coding RNA 572	ncRNA	0.012821	0.501921	
chunk0010_4_1	chr1	111822802	111823085	+	0	NA	intron (NM_172198, intron 2 of 6)	MIRb|SINE|MIR	33962	NR_046783	100874295	Hs.738190	NR_046783	ENSG00000232558	KCND3-IT1	-	KCND3 intronic transcript 1	ncRNA	0.024735	0.443662	
chunk0183_205_1	chr7	106413363	106413786	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-128382	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.007092	0.431604	209(GTTACACGCTGTTCCC,+,0.00)
chunk0127_280_1	chr3	97824003	97824374	+	0	NA	intron (NM_153605, intron 1 of 21)	intron (NM_153605, intron 1 of 21)	2148	NM_153605	131544	Hs.733378	NM_153605	ENSG00000080200	CRYBG3	DKFZp667G2110|vlAKAP	crystallin beta-gamma domain containing 3	protein-coding	0.005391	0.336022	200(TAGTACTGAATGTCCC,-,0.00),201(AGTACTGAATGTCCCA,+,0.00)
chunk0113_279_1	chr20	56821353	56821850	+	0	NA	Intergenic	L2a|LINE|L2	192299	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.024145	0.485944	
chunk0111_255_1	chr20	30812900	30813183	+	0	NA	Intergenic	Intergenic	-409579	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.045936	0.507042	
chunk0108_22_1	chr2	226519710	226520207	+	0	NA	Intergenic	Intergenic	138835	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.008048	0.409639	
chunk0175_298_1	chr7	7859832	7860298	+	0	NA	intron (NM_001302349, intron 3 of 3)	intron (NM_001302349, intron 3 of 3)	-108678	NM_138426	113263	Hs.131673	NM_138426	ENSG00000106415	GLCCI1	FAM117C|GCTR|GIG18|TSSN1	glucocorticoid induced 1	protein-coding	0.002146	0.282655	239(AAGGACATCTTGTACC,-,0.00),240(AGGACATCTTGTACCC,+,0.00)
chunk0163_307_1	chr6	14598204	14598911	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-313103	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.007072	0.418079	
chunk0080_236_1	chr17	30098910	30099367	+	0	NA	intron (NM_198529, intron 22 of 22)	L1MB7|LINE|L1	-17669	NM_032141	84081	Hs.462663	NM_032141	ENSG00000126653	NSRP1	CCDC55|HSPC095|NSrp70	nuclear speckle splicing regulatory protein 1	protein-coding	0.004376	0.384279	
chunk0180_76_1	chr7	54987703	54988191	+	0	NA	Intergenic	L2c|LINE|L2	-31085	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.004098	0.347648	
chunk0089_143_1	chr18	58952939	58953308	+	0	NA	intron (NM_018181, intron 7 of 10)	intron (NM_018181, intron 7 of 10)	-82556	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.008130	0.367568	
chunk0033_455_1	chr11	25671104	25671575	+	0	NA	Intergenic	L1MB4|LINE|L1	-517784	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.006369	0.343220	
chunk0200_40_1	chr9	15189572	15189831	+	0	NA	intron (NM_152574, intron 12 of 19)	intron (NM_152574, intron 12 of 19)	60499	NM_001168342	158219	Hs.563630	NM_152574	ENSG00000155158	TTC39B	C9orf52	tetratricopeptide repeat domain 39B	protein-coding	0.019305	0.434615	77(GAAAACACACTGTTCA,-,0.00),78(AAAACACACTGTTCAA,+,0.00)
chunk0088_152_1	chr18	46366924	46367275	+	0	NA	intron (NM_001256758, intron 1 of 5)	intron (NM_001256758, intron 1 of 5)	32875	NM_152470	494470	Hs.501114	NM_152470	ENSG00000141622	RNF165	ARKL2|Ark2C|RNF111L2	ring finger protein 165	protein-coding	0.017094	0.460227	
chunk0174_8_1	chr6	152295775	152296006	+	0	NA	intron (NM_033071, intron 92 of 145)	intron (NM_033071, intron 92 of 145)	-84640	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.017316	0.413793	
chunk0144_380_1	chr4	140059232	140059567	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	94680	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.002985	0.401786	
chunk0155_96_1	chr5	92369222	92369616	+	0	NA	Intergenic	Intergenic	-986087	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.005076	0.387342	
chunk0035_87_1	chr11	42025208	42025892	+	0	NA	Intergenic	L1MA9|LINE|L1	228140	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.004386	0.345985	
chunk0083_363_1	chr17	70871315	70871758	+	0	NA	Intergenic	Intergenic	330643	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.002257	0.337838	
chunk0108_447_1	chr2	238243978	238244662	+	0	NA	3' UTR (NM_022817, exon 23 of 23)	3' UTR (NM_022817, exon 23 of 23)	-4196	NM_018645	55502	Hs.42949	NM_018645	ENSG00000144485	HES6	C-HAIRY1|HES-6|bHLHb41|bHLHc23	hes family bHLH transcription factor 6	protein-coding	0.008772	0.344526	
chunk0132_183_1	chr3	157070854	157071162	+	0	NA	Intergenic	Intergenic	-18873	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.012987	0.478964	115(TAAAACAGACAGTTCT,-,0.00),116(AAAACAGACAGTTCTG,+,0.00)
chunk0084_232_1	chr17	78717630	78717951	+	0	NA	promoter-TSS (NM_001292019)	promoter-TSS (NM_001292019)	-758	NM_001292019	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.034268	0.521739	142(AGGACCACACTGTCCT,-,0.00),143(GGACCACACTGTCCTA,+,0.00)
chunk0073_313_1	chr16	14181568	14181802	+	0	NA	intron (NM_001308142, intron 3 of 16)	intron (NM_001308142, intron 3 of 16)	110371	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.004274	0.306383	
chunk0071_301_1	chr15	86094841	86095040	+	0	NA	intron (NR_120368, intron 3 of 5)	MER21C|LTR|ERVL	21777	NR_120368	101929701	Hs.132570	NR_120368	ENSG00000260477	LINC01584	-	long intergenic non-protein coding RNA 1584	ncRNA	0.010050	0.450000	
chunk0183_84_1	chr7	104883717	104884234	+	0	NA	intron (NM_199000, intron 2 of 2)	intron (NM_199000, intron 2 of 2)	42670	NR_027374	723809	Hs.124316	NR_027374	ENSG00000225329	LHFPL3-AS2	-	LHFPL3 antisense RNA 2	ncRNA	0.025145	0.501931	
chunk0132_225_1	chr3	158077553	158077847	+	0	NA	Intergenic	Intergenic	28463	NM_001163678	6474	Hs.55967	NM_003030	ENSG00000168779	SHOX2	OG12|OG12X|SHOT	short stature homeobox 2	protein-coding	0.000000	0.291525	
chunk0035_28_1	chr11	40486615	40486957	+	0	NA	intron (NM_020929, intron 2 of 4)	intron (NM_020929, intron 2 of 4)	-193656	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005848	0.294461	
chunk0209_59_1	chrX	37327865	37328140	+	0	NA	Intergenic	Intergenic	-21273	NM_001173486	5638	Hs.190341	NM_000950	ENSG00000130962	PRRG1	PRGP1	proline rich and Gla domain 1	protein-coding	0.003636	0.268116	
chunk0197_416_1	chr8	127330169	127330807	+	0	NA	intron (NR_117099, intron 2 of 3)	intron (NR_117099, intron 2 of 3)	-69911	NR_109834	101805488	Hs.745578	NR_109834	ENSG00000280997	CCAT2	LINC00873|NCCP1	colon cancer associated transcript 2	ncRNA	0.006270	0.444444	
chunk0061_164_1	chr14	59794649	59795230	+	0	NA	intron (NM_021136, intron 1 of 8)	MLT1J|LTR|ERVL-MaLR	75900	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.000000	0.357388	
chunk0116_422_1	chr21	42731244	42732071	+	0	NA	intron (NM_001001584, intron 3 of 17)	intron (NM_001001584, intron 3 of 17)	77905	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.026602	0.550725	394(GAGAACACCGTGTTCT,-,0.00),395(AGAACACCGTGTTCTG,+,0.00)
chunk0051_318_1	chr12	119728053	119728843	+	0	NA	intron (NM_007174, intron 27 of 46)	L1MC1|LINE|L1	-14724	NR_031589	100302274		NR_031589	ENSG00000283768	MIR1178	MIRN1178|hsa-mir-1178	microRNA 1178	ncRNA	0.008861	0.426043	328(GGGAACTCTCTGTGCT,-,0.00),329(GGAACTCTCTGTGCTT,+,0.00)
chunk0177_394_1	chr7	27120827	27121291	+	0	NA	promoter-TSS (NR_122069)	promoter-TSS (NR_122069)	-860	NR_122069	285943	Hs.714774	NR_122069		HOXA-AS2	HOXA3as	HOXA cluster antisense RNA 2	ncRNA	0.010776	0.468817	
chunk0212_255_1	chrX	139195169	139195587	+	0	NA	intron (NM_001139501, intron 2 of 7)	intron (NM_001139501, intron 2 of 7)	9645	NM_001139500	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.016746	0.412888	59(AGGAGCACCTTGTCCT,-,0.00),60(GGAGCACCTTGTCCTG,+,0.00),89(GGCTCACATTGTTCCC,+,0.00)
chunk0021_298_1	chr1	244705680	244706435	+	0	NA	non-coding (NR_123735, exon 5 of 5)	non-coding (NR_123735, exon 5 of 5)	53009	NR_123736	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.011921	0.435185	
chunk0063_343_1	chr14	85401211	85401863	+	0	NA	intron (NR_102738, intron 1 of 1)	intron (NR_102738, intron 1 of 1)	7622	NR_102738	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003067	0.373660	
chunk0084_374_1	chr17	81727375	81728024	+	0	NA	Intergenic	Intergenic	15463	NM_001270953	1468	Hs.548187	NM_012140	ENSG00000183048	SLC25A10	DIC	solute carrier family 25 member 10	protein-coding	0.033898	0.527692	
chunk0207_333_1	chr9	134363495	134363870	+	0	NA	intron (NM_002957, intron 1 of 9)	intron (NM_002957, intron 1 of 9)	-15613	NM_001291920	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.040000	0.672872	200(GAGCACTGCCTGTGCT,-,0.00),201(AGCACTGCCTGTGCTG,+,0.00)
chunk0091_239_1	chr19	10670147	10670618	+	0	NA	intron (NM_001137673, intron 1 of 17)	intron (NM_001137673, intron 1 of 17)	16121	NM_017620	3609	Hs.465885	NM_004516	ENSG00000129351	ILF3	CBTF|DRBF|DRBP76|MMP4|MPHOSPH4|MPP4|MPP4110|NF-AT-90|NF110|NF110b|NF90|NF90a|NF90b|NF90c|NF90ctv|NFAR|NFAR-1|NFAR-2|NFAR110|NFAR2|NFAR90|TCP110|TCP80	interleukin enhancer binding factor 3	protein-coding	0.002123	0.364407	
chunk0110_152_1	chr20	13739212	13739953	+	0	NA	intron (NM_016649, intron 9 of 13)	intron (NM_016649, intron 9 of 13)	45304	NM_016649	51575	Hs.369284	NM_016649	ENSG00000089048	ESF1	ABTAP|C20orf6|HDCMC28P|bA526K24.1	ESF1 nucleolar pre-rRNA processing protein homolog	protein-coding	0.005398	0.358491	386(AAGAACTACTTGTTCT,-,0.00),387(AGAACTACTTGTTCTA,+,0.00)
chunk0016_419_1	chr1	203429056	203429551	+	0	NA	Intergenic	LTR22A|LTR|ERVK	-46452	NM_201348	5549	Hs.632481	NM_002725	ENSG00000188783	PRELP	MST161|MSTP161|SLRR2A	proline and arginine rich end leucine rich repeat protein	protein-coding	0.020202	0.506048	
chunk0049_204_1	chr12	93145217	93145464	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-29026	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.012146	0.375000	
chunk0135_342_1	chr3	190345391	190345848	+	0	NA	Intergenic	MIR3|SINE|MIR	-23173	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.006565	0.384279	
chunk0023_123_1	chr10	23766377	23766616	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	71750	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.004184	0.300000	
chunk0169_442_1	chr6	108763752	108764467	+	0	NA	intron (NR_033376, intron 3 of 4)	L2a|LINE|L2	12455	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.013986	0.474860	
chunk0205_431_1	chr9	115156112	115156788	+	0	NA	intron (NM_017418, intron 1 of 7)	intron (NM_017418, intron 1 of 7)	14632	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.001479	0.353028	
chunk0023_285_1	chr10	28529550	28529849	+	0	NA	intron (NR_033805, intron 1 of 2)	L2a|LINE|L2	2655	NR_033805	220906	Hs.403253	NR_033805		WAC-AS1	-	WAC antisense RNA 1 (head to head)	ncRNA	0.003344	0.400000	
chunk0087_200_1	chr18	35797727	35798125	+	0	NA	Intergenic	L3|LINE|CR1	107000	NR_029616	406963		NR_029616	ENSG00000207797	MIR187	MIRN187|miR-187|miRNA187	microRNA 187	ncRNA	0.005025	0.423559	
chunk0191_64_1	chr8	47101176	47101723	+	0	NA	Intergenic	L2c|LINE|L2	-87858	NR_037168	100287846	Hs.21550	NR_037168		LOC100287846	-	uncharacterized LOC100287846	ncRNA	0.003656	0.388686	
chunk0165_396_1	chr6	38813363	38814045	+	0	NA	intron (NM_001206927, intron 24 of 92)	intron (NM_001206927, intron 24 of 92)	98363	NM_001206927	1769	Hs.520106	NM_001371	ENSG00000124721	DNAH8	ATPase|hdhc9	dynein axonemal heavy chain 8	protein-coding	0.007331	0.364568	
chunk0141_247_1	chr4	85032462	85032947	+	0	NA	Intergenic	MER51B|LTR|ERV1	65886	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.000000	0.407407	
chunk0117_216_1	chr22	22318801	22319117	+	0	NA	non-coding (NR_027293, exon 9 of 11)	non-coding (NR_027293, exon 9 of 11)	20861	NR_027293	96610	Hs.449601	NM_080926		BMS1P20	IGL|IGLV|IGLV1	BMS1 pseudogene 20	pseudo	0.006329	0.536278	
chunk0196_222_1	chr8	107427358	107427578	+	0	NA	intron (NM_001146, intron 1 of 8)	intron (NM_001146, intron 1 of 8)	70587	NM_001199859	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.004545	0.479638	
chunk0002_91_1	chr1	14700448	14700788	+	0	NA	intron (NM_015209, intron 1 of 7)	intron (NM_015209, intron 1 of 7)	101901	NM_015209	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.005882	0.436950	
chunk0179_412_1	chr7	51681084	51681299	+	0	NA	Intergenic	Intergenic	-364373	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.023256	0.472222	
chunk0135_220_1	chr3	188541852	188542651	+	0	NA	intron (NM_001167671, intron 5 of 10)	MIRc|SINE|MIR	26415	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.005006	0.325000	
chunk0102_34_1	chr2	141834703	141835426	+	0	NA	intron (NM_018557, intron 1 of 90)	intron (NM_018557, intron 1 of 90)	296637	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.004149	0.353591	
chunk0182_338_1	chr7	99260446	99260645	+	0	NA	Intergenic	MIR|SINE|MIR	-12756	NR_002147	84176	Hs.621401	NR_002147		MYH16	MHC20|MYH16P|MYH5	myosin heavy chain 16 pseudogene	pseudo	0.000000	0.465000	
chunk0083_234_1	chr17	67510898	67511494	+	0	NA	intron (NM_181671, intron 1 of 9)	L1ME3G|LINE|L1	-39611	NR_030385	693131		NR_030385	ENSG00000263690	MIR548D2	MIRN548D2	microRNA 548d-2	ncRNA	0.011745	0.353434	
chunk0142_57_1	chr4	92004845	92005185	+	0	NA	Intergenic	L1PA10|LINE|L1	272287	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.002941	0.343109	
chunk0033_397_1	chr11	24511527	24511883	+	0	NA	intron (NM_001252008, intron 1 of 11)	intron (NM_001252008, intron 1 of 11)	14735	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.014045	0.288515	
chunk0050_134_1	chr12	102394197	102394568	+	0	NA	Intergenic	MIRb|SINE|MIR	84269	NM_001111284	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.002695	0.400538	
chunk0170_171_1	chr6	111669334	111669763	+	0	NA	intron (NM_153048, intron 10 of 10)	intron (NM_153048, intron 10 of 10)	50514	NM_153047	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.009324	0.423256	
chunk0079_429_1	chr17	19937472	19937981	+	0	NA	intron (NM_007202, intron 8 of 14)	MIR3|SINE|MIR	40130	NM_007202	11216	Hs.642676	NM_007202	ENSG00000108599	AKAP10	AKAP-10|D-AKAP-2|D-AKAP2|PRKA10	A-kinase anchoring protein 10	protein-coding	0.003929	0.350980	
chunk0044_32_1	chr12	27338035	27338409	+	0	NA	intron (NM_001248003, intron 1 of 14)	intron (NM_001248003, intron 1 of 14)	5368	NM_001248003	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.002674	0.389333	
chunk0096_219_1	chr2	30576197	30576661	+	0	NA	intron (NM_001304446, intron 5 of 5)	intron (NM_001304446, intron 5 of 5)	129203	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.006466	0.350538	
chunk0136_258_1	chr4	10347215	10347717	+	0	NA	Intergenic	Intergenic	109942	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.009960	0.395626	349(GTGGACAGTCTGTTTC,-,0.00),350(TGGACAGTCTGTTTCC,+,0.00)
chunk0027_447_1	chr10	81269905	81270642	+	0	NA	Intergenic	MIR|SINE|MIR	-605041	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.009498	0.405149	
chunk0186_56_1	chr7	136402573	136403112	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-425386	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.009276	0.385185	
chunk0133_239_1	chr3	171416799	171417412	+	0	NA	intron (NR_027767, intron 1 of 2)	intron (NR_027767, intron 1 of 2)	43303	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.003263	0.317590	
chunk0152_408_1	chr5	65066792	65067312	+	0	NA	Intergenic	Intergenic	298134	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.003846	0.391555	318(GAGTACAGACTGATCA,-,0.00),319(AGTACAGACTGATCAT,+,0.00)
chunk0198_436_1	chr8	143597423	143597756	+	0	NA	promoter-TSS (NM_001289950)	promoter-TSS (NM_001289950)	86	NM_001130053	1936	Hs.333388	NM_001960	ENSG00000104529	EEF1D	EF-1D|EF1D|FP1047	eukaryotic translation elongation factor 1 delta	protein-coding	0.141141	0.757485	
chunk0043_211_1	chr12	19608022	19608464	+	0	NA	Intergenic	Intergenic	167662	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.004525	0.349887	
chunk0041_203_1	chr11	126633564	126634345	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	-18824	NR_120532	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.010243	0.456522	
chunk0176_51_1	chr7	11031011	11031403	+	0	NA	intron (NR_033435, intron 6 of 15)	intron (NR_033435, intron 6 of 15)	57335	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.000000	0.277354	
chunk0060_411_1	chr14	53127007	53127609	+	0	NA	intron (NM_030637, intron 1 of 11)	intron (NM_030637, intron 1 of 11)	26020	NM_001160147	80821	Hs.125525	NM_030637	ENSG00000100523	DDHD1	PA-PLA1|PAPLA1|SPG28	DDHD domain containing 1	protein-coding	0.004983	0.339967	
chunk0122_93_1	chr3	30310862	30311061	+	0	NA	Intergenic	Intergenic	-295541	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.005025	0.410000	
chunk0120_33_1	chr3	2541987	2542427	+	0	NA	intron (NM_001206955, intron 2 of 23)	intron (NM_001206955, intron 2 of 23)	303378	NM_001206955	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.000000	0.403628	
chunk0205_368_1	chr9	113767752	113768159	+	0	NA	Intergenic	Intergenic	-108327	NM_133374	114991	Hs.349208	NM_133374	ENSG00000157657	ZNF618	FP13169|NEDD10	zinc finger protein 618	protein-coding	0.000000	0.446078	378(TAGGACACTGTGATCT,-,0.00),379(AGGACACTGTGATCTG,+,0.00)
chunk0008_280_1	chr1	94757796	94758251	+	0	NA	intron (NR_104131, intron 1 of 4)	intron (NR_104131, intron 1 of 4)	-12123	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.010989	0.500000	
chunk0138_345_1	chr4	41690750	41691294	+	0	NA	intron (NM_001112717, intron 24 of 25)	intron (NM_001112717, intron 24 of 25)	57948	NM_003924	8929	Hs.87202	NM_003924	ENSG00000109132	PHOX2B	CCHS|NBLST2|NBPhox|PMX2B	paired like homeobox 2B	protein-coding	0.001838	0.385321	
chunk0054_145_1	chr13	43784520	43784899	+	0	NA	intron (NM_017993, intron 1 of 16)	intron (NM_017993, intron 1 of 16)	2271	NM_017993	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.000000	0.334211	217(AACACACAGTGTACTC,+,0.00)
chunk0016_387_1	chr1	202889159	202889402	+	0	NA	promoter-TSS (NM_002871)	promoter-TSS (NM_002871)	-23	NM_002871	5877	Hs.90875	NM_002871	ENSG00000183155	RABIF	MSS4|RASGFR3|RASGRF3	RAB interacting factor	protein-coding	0.061728	0.577869	
chunk0095_174_1	chr2	17662562	17663221	+	0	NA	TTS (NM_001142286)	TTS (NM_001142286)	90938	NM_024624	79677	Hs.526728	NM_024624	ENSG00000163029	SMC6	SMC-6|SMC6L1|hSMC6	structural maintenance of chromosomes 6	protein-coding	0.003035	0.345455	
chunk0003_357_1	chr1	39170979	39171476	+	0	NA	intron (NM_012090, intron 1 of 92)	(TG)n|Simple_repeat|Simple_repeat	87060	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.008048	0.381526	
chunk0086_408_1	chr18	26765416	26765919	+	0	NA	Intergenic	Intergenic	-62029	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.005964	0.464286	119(AGGAACAGCCAGTGCC,-,0.00),120(GGAACAGCCAGTGCCA,+,0.00)
chunk0052_56_1	chr13	21033304	21034020	+	0	NA	intron (NM_014572, intron 2 of 7)	intron (NM_014572, intron 2 of 7)	27921	NM_014572	26524	Hs.78960	NM_014572	ENSG00000150457	LATS2	KPM	large tumor suppressor kinase 2	protein-coding	0.011173	0.423989	342(GAGTACAATTTGTTCC,-,0.00),343(AGTACAATTTGTTCCA,+,0.00)
chunk0029_187_1	chr10	101091685	101092401	+	0	NA	intron (NR_130722, intron 2 of 2)	intron (NR_130722, intron 2 of 2)	30801	NM_030929	81621	Hs.534859	NM_030929	ENSG00000107821	KAZALD1	BONO1|FKSG28|FKSG40|IGFBP-rP10	Kazal type serine peptidase inhibitor domain 1	protein-coding	0.012570	0.449093	452(AAGCACAGAGTGACCC,-,0.00),453(AGCACAGAGTGACCCT,+,0.00)
chunk0127_177_1	chr3	95353973	95354374	+	0	NA	Intergenic	Intergenic	329020	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.014963	0.335821	192(GAGCTCAACGTGTTCC,-,0.00),193(AGCTCAACGTGTTCCT,+,0.00)
chunk0082_150_1	chr17	55513729	55514034	+	0	NA	Intergenic	Intergenic	-91901	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.006557	0.379085	
chunk0127_166_1	chr3	94893278	94893926	+	0	NA	Intergenic	LTR24|LTR|ERV1	-44661	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.006173	0.383667	
chunk0172_411_1	chr6	140088162	140088573	+	0	NA	intron (NR_121622, intron 3 of 3)	intron (NR_121622, intron 3 of 3)	-97106	NR_121624	103352541	Hs.582647	NR_121624		LOC103352541	-	uncharacterized LOC103352541	ncRNA	0.007299	0.339806	
chunk0155_128_1	chr5	93207326	93207777	+	0	NA	Intergenic	Intergenic	363792	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.013304	0.380531	
chunk0138_267_1	chr4	40200812	40201157	+	0	NA	intron (NM_001278362, intron 2 of 3)	intron (NM_001278362, intron 2 of 3)	4077	NM_001278359	399	Hs.654594	NM_004310	ENSG00000168421	RHOH	ARHH|TTF	ras homolog family member H	protein-coding	0.020290	0.393064	
chunk0138_276_1	chr4	40482018	40482319	+	0	NA	intron (NM_001098634, intron 2 of 6)	intron (NM_001098634, intron 2 of 6)	19951	NR_039966	100616274		NR_039966	ENSG00000263642	MIR4802	-	microRNA 4802	ncRNA	0.009967	0.427152	106(TGGAACAGCATGTGCT,-,0.00),107(GGAACAGCATGTGCTA,+,0.00)
chunk0127_403_1	chr3	102431272	102431471	+	0	NA	Intergenic	Intergenic	-3644	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.305000	99(AAGTACATGGTGTGTT,-,0.00),100(AGTACATGGTGTGTTT,+,0.00)
chunk0114_339_1	chr21	17738067	17738522	+	0	NA	Intergenic	Intergenic	54215	NR_038870	246312	Hs.473425	NR_038870	ENSG00000240770	C21orf91-OT1	D21S2089E|NCRNA00285	C21orf91 overlapping transcript 1	ncRNA	0.015385	0.372807	
chunk0070_441_1	chr15	78221202	78221998	+	0	NA	intron (NM_001199377, intron 1 of 13)	LTR5B|LTR|ERVK	13107	NM_015162	23205	Hs.655760	NM_015162	ENSG00000103740	ACSBG1	BG|BG1|BGM|GR-LACS|LPD	acyl-CoA synthetase bubblegum family member 1	protein-coding	0.017588	0.465496	545(CAGTACATCGTGTCCC,-,0.00),546(AGTACATCGTGTCCCT,+,0.00)
chunk0150_420_1	chr5	40365854	40366434	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-313786	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.003448	0.342513	
chunk0056_461_1	chr13	95277549	95277954	+	0	NA	intron (NM_001105515, intron 1 of 20)	intron (NM_001105515, intron 1 of 20)	23695	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.012346	0.490148	174(GAGAACAGCAAGTGCT,-,0.00),175(AGAACAGCAAGTGCTG,+,0.00)
chunk0109_456_1	chr2	241891808	241892195	+	0	NA	intron (NR_110220, intron 2 of 3)	intron (NR_110220, intron 2 of 3)	10638	NR_110220	101927289	Hs.130180	NR_110220	ENSG00000233806	LINC01237	-	long intergenic non-protein coding RNA 1237	ncRNA	0.020672	0.487113	
chunk0064_70_1	chr14	90136834	90137297	+	0	NA	intron (NM_022054, intron 1 of 1)	intron (NM_022054, intron 1 of 1)	75300	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.010799	0.413793	
chunk0037_161_1	chr11	73675498	73675968	+	0	NA	TTS (NM_001243719)	TTS (NM_001243719)	27043	NM_001130036	58473	Hs.445489	NM_021200	ENSG00000021300	PLEKHB1	KPL1|PHR1|PHRET1	pleckstrin homology domain containing B1	protein-coding	0.002128	0.339703	
chunk0129_82_1	chr3	118163047	118163484	+	0	NA	Intergenic	L1P2|LINE|L1	-779811	NR_046230	100506765	Hs.660823	NR_046230	ENSG00000239877	IGSF11-AS1	-	IGSF11 antisense RNA 1	ncRNA	0.009153	0.525114	
chunk0051_246_1	chr12	117143323	117143599	+	0	NA	TTS (NM_015002)	TTS (NM_015002)	43994	NR_120464	101928244	Hs.742266	NR_120464		TESC-AS1	-	TESC antisense RNA 1 (head to head)	ncRNA	0.018116	0.393502	
chunk0168_453_1	chr6	95910308	95910915	+	0	NA	Intergenic	Intergenic	-105358	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.003295	0.305921	
chunk0156_150_1	chr5	107314324	107315012	+	0	NA	Intergenic	Intergenic	-303654	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.004360	0.375907	
chunk0204_17_1	chr9	91837967	91838388	+	0	NA	intron (NM_004560, intron 1 of 8)	intron (NM_004560, intron 1 of 8)	111985	NM_004560	4920	Hs.98255	NM_004560	ENSG00000169071	ROR2	BDB|BDB1|NTRKR2	receptor tyrosine kinase like orphan receptor 2	protein-coding	0.014252	0.436019	
chunk0042_420_1	chr12	11829756	11830280	+	0	NA	intron (NM_001987, intron 2 of 7)	intron (NM_001987, intron 2 of 7)	180164	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.011450	0.491429	
chunk0166_120_1	chr6	44558702	44559188	+	0	NA	Intergenic	Intergenic	123304	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.004115	0.509240	241(GAGGACAGTTTGTTCT,-,0.00),242(AGGACAGTTTGTTCTC,+,0.00)
chunk0076_108_1	chr16	66435206	66435405	+	0	NA	intron (NM_001197224, intron 1 of 4)	MIRb|SINE|MIR	8008	NM_001136106	146227	Hs.97805	NM_001136106	ENSG00000166546	BEAN1	BEAN|SCA31	brain expressed associated with NEDD4 1	protein-coding	0.000000	0.505000	
chunk0070_304_1	chr15	74913165	74913502	+	0	NA	Intergenic	Intergenic	-6212	NM_020447	57184	Hs.367690	NM_020447	ENSG00000178761	FAM219B	C15orf17	family with sequence similarity 219 member B	protein-coding	0.005935	0.396450	
chunk0200_310_1	chr9	23226989	23227733	+	0	NA	Intergenic	Intergenic	445038	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.004032	0.323490	478(AAGAACACGCTGGCCT,-,0.00),479(AGAACACGCTGGCCTT,+,0.00)
chunk0104_440_1	chr2	181485427	181485870	+	0	NA	intron (NM_000885, intron 9 of 27)	intron (NM_000885, intron 9 of 27)	28756	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.006772	0.349099	
chunk0148_387_1	chr5	14767833	14768257	+	0	NA	intron (NM_054027, intron 2 of 11)	intron (NM_054027, intron 2 of 11)	55351	NR_046285	100130744	Hs.660550	NR_046285		LOC100130744	-	uncharacterized LOC100130744	ncRNA	0.014151	0.395294	
chunk0143_250_1	chr4	114890979	114891178	+	0	NA	intron (NM_022569, intron 6 of 13)	intron (NM_022569, intron 6 of 13)	222798	NM_022569	64579	Hs.591700	NM_022569	ENSG00000138653	NDST4	N-HSST|N-HSST 4|NDST-4|NHSST4	N-deacetylase and N-sulfotransferase 4	protein-coding	0.005025	0.395000	
chunk0160_450_1	chr5	165051234	165051563	+	0	NA	Intergenic	L1MC3|LINE|L1	581119	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.006079	0.339394	
chunk0181_15_1	chr7	77738921	77739172	+	0	NA	intron (NM_198467, intron 2 of 7)	intron (NM_198467, intron 2 of 7)	-41701	NR_038361	100505854	Hs.72451	NR_038361	ENSG00000214293	APTR	RSBN1L-AS1	Alu-mediated CDKN1A/p21 transcriptional regulator	ncRNA	0.007968	0.384921	
chunk0060_161_1	chr14	45253346	45253854	+	0	NA	promoter-TSS (NM_018353)	promoter-TSS (NM_018353)	-198	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.066929	0.552063	347(AAGAACATTTTGTTCT,-,0.00),348(AGAACATTTTGTTCTT,+,0.00)
chunk0041_216_1	chr11	127230046	127230370	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-40862	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.006173	0.350769	
chunk0165_158_1	chr6	33799452	33799668	+	0	NA	intron (NM_001184698, intron 2 of 4)	intron (NM_001184698, intron 2 of 4)	4456	NM_001184698	4295	Hs.2813	NM_002418	ENSG00000096395	MLN	-	motilin	protein-coding	0.004630	0.428571	185(GGGAACTCAGAGTCCC,-,0.00),186(GGAACTCAGAGTCCCT,+,0.00)
chunk0040_408_1	chr11	121048858	121049421	+	0	NA	intron (NM_152715, intron 3 of 7)	L2c|LINE|L2	25035	NM_152715	219899	Hs.504136	NM_152715	ENSG00000154114	TBCEL	El|LRRC35	tubulin folding cofactor E like	protein-coding	0.005329	0.342199	
chunk0037_411_1	chr11	79807411	79807902	+	0	NA	Intergenic	Intergenic	-367005	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.004073	0.414634	
chunk0015_25_1	chr1	184368054	184368471	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-18754	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.002398	0.435407	
chunk0162_304_1	chr6	6565100	6565463	+	0	NA	intron (NR_026970, intron 2 of 7)	intron (NR_026970, intron 2 of 7)	-23420	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.008264	0.467033	
chunk0063_208_1	chr14	81382354	81383069	+	0	NA	intron (NM_033104, intron 3 of 5)	intron (NM_033104, intron 3 of 5)	44501	NM_033104	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.012587	0.382682	
chunk0163_312_1	chr6	14696496	14696941	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-411264	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.004494	0.363229	
chunk0019_291_1	chr1	228804883	228805504	+	0	NA	Intergenic	Intergenic	70116	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.014493	0.464630	
chunk0053_241_1	chr13	32663700	32664022	+	0	NA	intron (NM_015032, intron 6 of 34)	L1PB3|LINE|L1	77434	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.000000	0.380805	
chunk0045_100_1	chr12	46126474	46126673	+	0	NA	Intergenic	Intergenic	-135955	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.005025	0.450000	
chunk0058_20_1	chr14	19771333	19771639	+	0	NA	Intergenic	LTR27E|LTR|ERV1	-8837	NM_001005500	441670	Hs.553829	NM_001005500	ENSG00000176299	OR4M1	OR14-7	olfactory receptor family 4 subfamily M member 1	protein-coding	0.016340	0.521173	
chunk0044_115_1	chr12	29053553	29054164	+	0	NA	Intergenic	L1ME2|LINE|L1	-95145	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.003273	0.321895	
chunk0140_56_1	chr4	66676233	66676704	+	0	NA	Intergenic	L1M5|LINE|L1	399644	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.004246	0.309322	
chunk0080_141_1	chr17	27506290	27506774	+	0	NA	intron (NM_014238, intron 2 of 20)	intron (NM_014238, intron 2 of 20)	34522	NM_014238	8844	Hs.133534	NM_014238	ENSG00000141068	KSR1	KSR|RSU2	kinase suppressor of ras 1	protein-coding	0.018595	0.488660	
chunk0063_329_1	chr14	85235937	85236245	+	0	NA	Intergenic	L2c|LINE|L2	-157788	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.009740	0.378641	
chunk0182_111_1	chr7	93407103	93407437	+	0	NA	Intergenic	Intergenic	75585	NR_030388	724023		NR_030388	ENSG00000208014	MIR653	MIRN653|hsa-mir-653|mir-653	microRNA 653	ncRNA	0.000000	0.486567	
chunk0006_455_1	chr1	77051433	77051756	+	0	NA	intron (NM_030965, intron 4 of 4)	MIR|SINE|MIR	-8549	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.003096	0.453704	
chunk0072_450_1	chr15	101717360	101717664	+	0	NA	intron (NM_152334, intron 3 of 18)	MLT1J2|LTR|ERVL-MaLR	6930	NM_152334	123283	Hs.657163	NM_152334	ENSG00000185418	TARSL2	-	threonyl-tRNA synthetase like 2	protein-coding	0.006579	0.422951	
chunk0095_53_1	chr2	13682698	13683336	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-676004	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.004702	0.405321	
chunk0112_153_1	chr20	38999862	39000715	+	0	NA	intron (NR_033905, intron 8 of 21)	L2c|LINE|L2	37950	NM_021931	60625	Hs.444520	NM_021931	ENSG00000101452	DHX35	C20orf15|DDX35|KAIA0875	DEAH-box helicase 35	protein-coding	0.004689	0.456674	
chunk0075_397_1	chr16	56914243	56914596	+	0	NA	3' UTR (NM_000339, exon 26 of 26)	3' UTR (NM_000339, exon 26 of 26)	10155	NR_106923	102466752		NR_106923	ENSG00000283471	MIR6863	hsa-mir-6863	microRNA 6863	ncRNA	0.016997	0.457627	
chunk0197_280_1	chr8	124089063	124089280	+	0	NA	intron (NM_001039112, intron 33 of 40)	L1MA3|LINE|L1	-48389	NR_040044	439941	Hs.683919	NM_001038706	ENSG00000181171	FER1L6-AS1	C8orf54	FER1L6 antisense RNA 1	ncRNA	0.009217	0.500000	
chunk0004_170_1	chr1	45822748	45822984	+	0	NA	intron (NM_015112, intron 1 of 28)	LTR78B|LTR|ERV1	19253	NM_015112	23139	Hs.319481	NM_015112	ENSG00000086015	MAST2	MAST205|MTSSK	microtubule associated serine/threonine kinase 2	protein-coding	0.004237	0.438819	117(AAATACAAGCTGTTCC,-,0.00),118(AATACAAGCTGTTCCC,+,0.00)
chunk0175_239_1	chr7	6479097	6479628	+	0	NA	intron (NM_006854, intron 1 of 4)	AluJb|SINE|Alu	4856	NM_006854	11014	Hs.654552	NM_006854	ENSG00000136240	KDELR2	ELP-1|ERD2.2	KDEL endoplasmic reticulum protein retention receptor 2	protein-coding	0.022599	0.498120	
chunk0039_430_1	chr11	107893414	107893623	+	0	NA	Intergenic	Intergenic	-34330	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.004785	0.380952	
chunk0131_285_1	chr3	150317603	150317834	+	0	NA	intron (NR_110187, intron 1 of 1)	intron (NR_110187, intron 1 of 1)	6029	NR_110186	101928022	Hs.555199	NR_110186		LINC01214	-	long intergenic non-protein coding RNA 1214	ncRNA	0.008658	0.409483	
chunk0001_340_1	chr1	9668090	9668598	+	0	NA	intron (NM_005026, intron 1 of 23)	MIR|SINE|MIR	-13758	NR_027045	644997	Hs.568595	NM_001045478	ENSG00000179840	PIK3CD-AS1	C1orf200	PIK3CD antisense RNA 1	ncRNA	0.007874	0.388998	
chunk0050_57_1	chr12	101098310	101098516	+	0	NA	intron (NM_001286616, intron 20 of 26)	intron (NM_001286616, intron 20 of 26)	111825	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.000000	0.381643	
chunk0057_195_1	chr13	103194990	103195324	+	0	NA	Intergenic	MIRb|SINE|MIR	-128311	NM_000452	6555	Hs.194783	NM_000452	ENSG00000125255	SLC10A2	ASBT|IBAT|ISBT|NTCP2|PBAM	solute carrier family 10 member 2	protein-coding	0.002994	0.426866	
chunk0142_134_1	chr4	94694578	94695023	+	0	NA	Intergenic	Intergenic	62733	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.004494	0.414798	
chunk0066_434_1	chr15	39693684	39694329	+	0	NA	intron (NM_152597, intron 10 of 11)	L1MA7|LINE|L1	88832	NM_152597	161835	Hs.129598	NM_152597	ENSG00000150667	FSIP1	HSD10	fibrous sheath interacting protein 1	protein-coding	0.000000	0.311146	342(AAGACCACACTGTACC,-,0.00),343(AGACCACACTGTACCC,+,0.00)
chunk0007_436_1	chr1	86793057	86793622	+	0	NA	Intergenic	Intergenic	88769	NM_016009	51100	Hs.136309	NM_016009	ENSG00000097033	SH3GLB1	Bif-1|CGI-61|PPP1R70|dJ612B15.2	SH3 domain containing GRB2 like, endophilin B1	protein-coding	0.001770	0.434629	
chunk0101_219_1	chr2	130816822	130817277	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	60758	NM_001105195	205147	Hs.369289	NM_152698	ENSG00000178171	AMER3	FAM123C	APC membrane recruitment protein 3	protein-coding	0.006593	0.394737	
chunk0024_181_1	chr10	35979032	35979571	+	0	NA	Intergenic	L1ME1|LINE|L1	200999	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.003711	0.329630	263(CTGTACATTCTGTTCT,-,0.00),264(TGTACATTCTGTTCTC,+,0.00)
chunk0179_162_1	chr7	46603550	46604304	+	0	NA	Intergenic	Intergenic	-682655	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.018568	0.455629	434(GAGAACATTGCGTACC,-,0.00),435(AGAACATTGCGTACCC,+,0.00),515(GGGGCTGTGTGTTCTT,+,0.00)
chunk0001_222_1	chr1	8061324	8061727	+	0	NA	Intergenic	Intergenic	-35192	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.000000	0.435644	
chunk0121_397_1	chr3	25424677	25424876	+	0	NA	intron (NM_001290300, intron 1 of 7)	intron (NM_001290300, intron 1 of 7)	-3487	NM_001290266	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.020101	0.460000	
chunk0134_186_1	chr3	178217538	178217738	+	0	NA	Intergenic	Intergenic	-201563	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.010000	0.442786	
chunk0058_386_1	chr14	29555821	29556487	+	0	NA	Intergenic	Intergenic	371539	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.016517	0.400300	
chunk0208_87_1	chrX	13369667	13369940	+	0	NA	Intergenic	Intergenic	34562	NR_045260	100133123	Hs.449499	NR_045260	ENSG00000226985	LINC01203	-	long intergenic non-protein coding RNA 1203	ncRNA	0.003663	0.383212	
chunk0017_42_1	chr1	205188226	205188731	+	0	NA	intron (NM_199462, intron 1 of 11)	Tigger3c|DNA|TcMar-Tigger	23121	NM_015375	25778	Hs.6874	NM_015375	ENSG00000133059	DSTYK	CAKUT1|DustyPK|HDCMD38P|RIP5|RIPK5|SPG23	dual serine/threonine and tyrosine protein kinase	protein-coding	0.005941	0.341897	
chunk0099_270_1	chr2	98216557	98217013	+	0	NA	intron (NM_144992, intron 13 of 27)	MIRb|SINE|MIR	-129370	NM_001298	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.008772	0.518600	
chunk0026_327_1	chr10	68260248	68260488	+	0	NA	Intergenic	Intergenic	-28255	NM_145178	220202	Hs.175396	NM_145178	ENSG00000179774	ATOH7	Math5|NCRNA|PHPVAR|RNANC|bHLHa13	atonal bHLH transcription factor 7	protein-coding	0.012500	0.564315	
chunk0106_292_1	chr2	204418138	204418677	+	0	NA	Intergenic	L1ME1|LINE|L1	-127386	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.001855	0.331481	
chunk0148_34_1	chr5	835961	836429	+	0	NA	intron (NM_024786, intron 6 of 12)	L1MEd|LINE|L1	14791	NM_024786	79844	Hs.654874	NM_024786	ENSG00000188818	ZDHHC11	ZNF399	zinc finger DHHC-type containing 11	protein-coding	0.014957	0.449893	
chunk0019_127_1	chr1	225533212	225533411	+	0	NA	intron (NM_001008493, intron 3 of 14)	intron (NM_001008493, intron 3 of 14)	-104456	NM_194442	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.005025	0.380000	
chunk0137_244_1	chr4	20604148	20604362	+	0	NA	intron (NM_001289135, intron 32 of 35)	intron (NM_001289135, intron 32 of 35)	75980	NR_029631	407000		NR_029631	ENSG00000207732	MIR218-1	MIRN218-1|mir-218-1	microRNA 218-1	ncRNA	0.000000	0.274419	57(CTGTACAGTATGTTCA,-,0.00),58(TGTACAGTATGTTCAA,+,0.00)
chunk0092_439_1	chr19	38336477	38336676	+	0	NA	intron (NM_021185, intron 1 of 28)	intron (NM_021185, intron 1 of 28)	773	NM_021185	57828	Hs.324335	NM_021185	ENSG00000099338	CATSPERG	C19orf15	cation channel sperm associated auxiliary subunit gamma	protein-coding	0.085427	0.715000	
chunk0108_57_1	chr2	227180098	227180610	+	0	NA	intron (NM_000091, intron 1 of 51)	intron (NM_000091, intron 1 of 51)	15789	NM_000091	1285	Hs.570065	NM_000091	ENSG00000169031	COL4A3	ATS2|ATS3	collagen type IV alpha 3 chain	protein-coding	0.017578	0.491228	267(GAGTACTGTCTGTGCC,-,0.00),268(AGTACTGTCTGTGCCT,+,0.00)
chunk0153_414_1	chr5	75570295	75570625	+	0	NA	intron (NM_016218, intron 4 of 14)	MER58A|DNA|hAT-Charlie	-41016	NM_001276713	728780	Hs.370455	NM_001271529	ENSG00000189045	ANKDD1B	-	ankyrin repeat and death domain containing 1B	protein-coding	0.006061	0.323263	
chunk0211_455_1	chrX	130166882	130167230	+	0	NA	Intergenic	L2b|LINE|L2	-1169	NM_004208	9131	Hs.424932	NM_004208	ENSG00000156709	AIFM1	AIF|CMT2D|CMTX4|COWCK|COXPD6|DFNX5|NADMR|NAMSD|PDCD8	apoptosis inducing factor mitochondria associated 1	protein-coding	0.017241	0.375358	
chunk0178_66_1	chr7	30253540	30253794	+	0	NA	Intergenic	L2b|LINE|L2	-30640	NM_147128	223082	Hs.263912	NM_147128	ENSG00000180233	ZNRF2	RNF202	zinc and ring finger 2	protein-coding	0.011811	0.458824	
chunk0017_87_1	chr1	205744061	205744307	+	0	NA	intron (NM_022731, intron 1 of 6)	intron (NM_022731, intron 1 of 6)	6060	NM_022731	64710	Hs.213061	NM_022731	ENSG00000069275	NUCKS1	JC7|NUCKS	nuclear casein kinase and cyclin dependent kinase substrate 1	protein-coding	0.008130	0.396761	
chunk0119_88_1	chr22	41674274	41674524	+	0	NA	3' UTR (NM_005008, exon 4 of 4)	3' UTR (NM_005008, exon 4 of 4)	14510	NM_001003796	4809	Hs.182255	NM_005008	ENSG00000100138	SNU13	15.5K|FA-1|FA1|NHP2L1|NHPX|OTK27|SNRNP15-5|SPAG12|SSFA1	small nuclear ribonucleoprotein 13	protein-coding	0.016000	0.486056	
chunk0010_61_1	chr1	113027076	113027423	+	0	NA	intron (NR_103777, intron 2 of 2)	MIRb|SINE|MIR	45853	NR_103777	100996251	Hs.382067	NR_103777	ENSG00000238198	LRIG2-DT	-	LRIG2 divergent transcript	ncRNA	0.014409	0.471264	
chunk0055_119_1	chr13	57394319	57394779	+	0	NA	Intergenic	L2|LINE|L2	227352	NM_001130405	729240	Hs.525056	NM_001130405	ENSG00000229665	PRR20C	PRR20|PRR20A|PRR20B|PRR20D|PRR20E	proline rich 20C	protein-coding	0.000000	0.364425	
chunk0146_264_1	chr4	162848287	162848526	+	0	NA	Intergenic	Intergenic	245222	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.000000	0.491667	129(AAGCACAGTGTGTCAC,-,0.00),130(AGCACAGTGTGTCACT,+,0.00)
chunk0131_425_1	chr3	153331849	153332165	+	0	NA	Intergenic	Intergenic	-152488	NM_001101337									0.000000	0.321767	
chunk0189_331_1	chr8	26390989	26391466	+	0	NA	intron (NM_004331, intron 1 of 5)	intron (NM_004331, intron 1 of 5)	8220	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.004193	0.410042	
chunk0034_46_1	chr11	26891861	26892288	+	0	NA	Intergenic	L1PA16|LINE|L1	-102007	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.007026	0.397196	218(AAATACAGCATGTTCT,-,0.00),219(AATACAGCATGTTCTC,+,0.00)
chunk0023_97_1	chr10	22655216	22656027	+	0	NA	intron (NM_005028, intron 1 of 9)	intron (NM_005028, intron 1 of 9)	58953	NM_005028	5305	Hs.57079	NM_005028	ENSG00000150867	PIP4K2A	PI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK	phosphatidylinositol-5-phosphate 4-kinase type 2 alpha	protein-coding	0.013564	0.433498	
chunk0032_279_1	chr11	9116003	9116510	+	0	NA	Intergenic	L1ME3A|LINE|L1	21893	NR_027713	283102	Hs.689472	NR_027713	ENSG00000213538	KRT8P41	-	keratin 8 pseudogene 41	pseudo	0.007890	0.379921	
chunk0005_117_1	chr1	56765324	56765941	+	0	NA	intron (NM_001004303, intron 5 of 19)	L1MDa|LINE|L1	54064	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.003241	0.457929	
chunk0057_2_1	chr13	95438178	95438699	+	0	NA	intron (NM_182848, intron 1 of 4)	intron (NM_182848, intron 1 of 4)	4839	NM_001160100	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.003839	0.469349	
chunk0100_386_1	chr2	118301327	118301571	+	0	NA	Intergenic	L2b|LINE|L2	212975	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.000000	0.355102	
chunk0197_420_1	chr8	127341527	127342073	+	0	NA	intron (NR_117099, intron 3 of 3)	L2a|LINE|L2	-58599	NR_109834	101805488	Hs.745578	NR_109834	ENSG00000280997	CCAT2	LINC00873|NCCP1	colon cancer associated transcript 2	ncRNA	0.003663	0.393053	
chunk0155_122_1	chr5	93058735	93059039	+	0	NA	Intergenic	Intergenic	512456	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.367213	
chunk0119_27_1	chr22	40276337	40277016	+	0	NA	intron (NM_001024843, intron 9 of 23)	intron (NM_001024843, intron 9 of 23)	-69824	NM_001123378	158	Hs.75527	NM_000026	ENSG00000239900	ADSL	AMPS|ASASE|ASL	adenylosuccinate lyase	protein-coding	0.004418	0.372059	
chunk0187_310_1	chr7	156451618	156451933	+	0	NA	Intergenic	L1M5|LINE|L1	-6187	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.006349	0.319620	
chunk0013_225_1	chr1	169529357	169529719	+	0	NA	intron (NM_000130, intron 16 of 24)	intron (NM_000130, intron 16 of 24)	-43568	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.008287	0.410468	
chunk0056_274_1	chr13	90304626	90305300	+	0	NA	Intergenic	Intergenic	73781	NR_030754	693207		NR_030754	ENSG00000283783	MIR622	MIRN622|hsa-mir-622	microRNA 622	ncRNA	0.000000	0.282963	
chunk0040_389_1	chr11	119749768	119750325	+	0	NA	Intergenic	Intergenic	20463	NR_120587	102724301	Hs.637640	NR_120587	ENSG00000254854	LOC102724301	-	uncharacterized LOC102724301	ncRNA	0.008977	0.516129	505(GGGCACAGGCTGGGCT,-,0.00),506(GGCACAGGCTGGGCTT,+,0.00)
chunk0043_53_1	chr12	13730074	13730696	+	0	NA	intron (NM_000834, intron 3 of 12)	intron (NM_000834, intron 3 of 12)	249703	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.011254	0.396469	319(TGGTACTCTTTGTTCC,-,0.00),320(GGTACTCTTTGTTCCA,+,0.00)
chunk0118_49_1	chr22	27894720	27895155	+	0	NA	intron (NM_001284277, intron 6 of 10)	intron (NM_001284277, intron 6 of 10)	24277	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.002299	0.334862	
chunk0177_360_1	chr7	26689999	26690528	+	0	NA	intron (NM_001303468, intron 10 of 12)	intron (NM_001303468, intron 10 of 12)	51178	NM_001302625									0.001890	0.347170	
chunk0017_306_1	chr1	211187359	211187723	+	0	NA	Intergenic	L1MC4|LINE|L1	-53426	NM_002238	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.005495	0.317808	
chunk0067_269_1	chr15	46060272	46060651	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	425721	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.002639	0.428947	158(AAGCACTGGATGTGCT,-,0.00),159(AGCACTGGATGTGCTG,+,0.00)
chunk0013_183_1	chr1	169031712	169031911	+	0	NA	intron (NR_104091, intron 3 of 4)	intron (NR_104091, intron 3 of 4)	55194	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.015075	0.520000	
chunk0006_153_1	chr1	66316380	66316891	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-15473	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.000000	0.359375	
chunk0112_455_1	chr20	48928917	48929686	+	0	NA	intron (NM_006420, intron 1 of 38)	intron (NM_006420, intron 1 of 38)	7563	NM_006420	10564	Hs.62578	NM_006420	ENSG00000124198	ARFGEF2	BIG2|PVNH2|dJ1164I10.1	ADP ribosylation factor guanine nucleotide exchange factor 2	protein-coding	0.003901	0.412987	
chunk0182_274_1	chr7	98136013	98136441	+	0	NA	intron (NM_014916, intron 1 of 13)	L1MD3|LINE|L1	29342	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.011682	0.440559	
chunk0083_378_1	chr17	71402607	71402806	+	0	NA	Intergenic	Intergenic	-200527	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.015075	0.475000	
chunk0044_413_1	chr12	41272051	41272393	+	0	NA	intron (NM_001164595, intron 3 of 9)	intron (NM_001164595, intron 3 of 9)	83774	NM_001164595	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.000000	0.259475	
chunk0093_100_1	chr19	43427054	43427365	+	0	NA	Intergenic	Intergenic	12326	NM_001130011	83639	Hs.97978	NM_031451	ENSG00000131126	TEX101	CT131|GTPR867|NYD-SP8|PRO1884|SGRG|SPATA44|TES101RP	testis expressed 101	protein-coding	0.000000	0.317308	
chunk0135_348_1	chr3	190395610	190395900	+	0	NA	intron (NM_006580, intron 1 of 4)	intron (NM_006580, intron 1 of 4)	7883	NM_006580	10686	Hs.251391	NM_006580	ENSG00000113946	CLDN16	HOMG3|PCLN1	claudin 16	protein-coding	0.003448	0.271478	
chunk0195_250_1	chr8	97765377	97765576	+	0	NA	Intergenic	L2b|LINE|L2	-10105	NM_018407	55353	Hs.492314	NM_018407	ENSG00000104341	LAPTM4B	LAPTM4beta|LC27	lysosomal protein transmembrane 4 beta	protein-coding	0.005025	0.505000	
chunk0097_134_1	chr2	47191975	47192260	+	0	NA	TTS (NR_110208)	TTS (NR_110208)	-15181	NM_001305625	805	Hs.468442	NM_001743	ENSG00000143933	CALM2	CALM|CALML2|CAM1|CAM3|CAMC|CAMII|CAMIII|LQT15|PHKD|PHKD2|caM	calmodulin 2	protein-coding	0.014035	0.479021	
chunk0163_131_1	chr6	10572875	10573429	+	0	NA	intron (NM_001491, intron 1 of 2)	intron (NM_001491, intron 1 of 2)	-12608	NM_145655	2651	Hs.519884	NM_001491	ENSG00000111846	GCNT2	CCAT|CTRCT13|GCNT2C|GCNT5|IGNT|II|NACGT1|NAGCT1|ULG3|bA360O19.2|bA421M1.1	glucosaminyl (N-acetyl) transferase 2 (I blood group)	protein-coding	0.014440	0.376577	
chunk0136_252_1	chr4	10174239	10174554	+	0	NA	Intergenic	MER9B|LTR|ERVK	-57447	NM_017491	9948	Hs.128548	NM_005112	ENSG00000071127	WDR1	AIP1|HEL-S-52|NORI-1	WD repeat domain 1	protein-coding	0.003175	0.455696	157(AGGCACAGGCAGCTCC,-,0.00),158(GGCACAGGCAGCTCCT,+,0.00)
chunk0038_81_1	chr11	83207460	83207714	+	0	NA	intron (NR_125355, intron 3 of 5)	intron (NR_125355, intron 3 of 5)	13848	NM_001300977	338699	Hs.503438	NM_182603	ENSG00000137494	ANKRD42	PPP1R79|SARP	ankyrin repeat domain 42	protein-coding	0.000000	0.341176	
chunk0158_125_1	chr5	127022896	127023172	+	0	NA	intron (NM_178450, intron 1 of 4)	intron (NM_178450, intron 1 of 4)	7774	NM_178450	115123	Hs.132441	NM_178450	ENSG00000173926	MARCH3	MARCH-III|RNF173	membrane associated ring-CH-type finger 3	protein-coding	0.007246	0.415162	
chunk0056_332_1	chr13	91226273	91226590	+	0	NA	Intergenic	L1MB4|LINE|L1	-14733	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.003155	0.374214	
chunk0196_309_1	chr8	110018675	110018874	+	0	NA	Intergenic	L1M1|LINE|L1	-44044	NM_014379	27012	Hs.13285	NM_014379	ENSG00000164794	KCNV1	HNKA|KCNB3|KV2.3|KV8.1	potassium voltage-gated channel modifier subfamily V member 1	protein-coding	0.005025	0.575000	
chunk0208_247_1	chrX	20221729	20222348	+	0	NA	intron (NM_004586, intron 2 of 21)	MER58A|DNA|hAT-Charlie	44594	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.008078	0.406452	
chunk0196_228_1	chr8	107614339	107615032	+	0	NA	Intergenic	Intergenic	-116630	NM_001146	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.004329	0.344380	356(CAGCACACAGTGTTCT,-,0.00),357(AGCACACAGTGTTCTA,+,0.00)
chunk0042_280_1	chr12	7206085	7206548	+	0	NA	intron (NM_001131023, intron 10 of 15)	MER58B|DNA|hAT-Charlie	15954	NM_000319	5830	Hs.567327	NM_000319	ENSG00000139197	PEX5	PBD2A|PBD2B|PTS1-BP|PTS1R|PXR1|RCDP5	peroxisomal biogenesis factor 5	protein-coding	0.012959	0.351293	
chunk0087_249_1	chr18	36843368	36844151	+	0	NA	intron (NM_020776, intron 3 of 9)	intron (NM_020776, intron 3 of 9)	-14543	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.007663	0.372449	664(GTGGACAGTCAGTTCC,-,0.00),665(TGGACAGTCAGTTCCT,+,0.00)
chunk0179_418_1	chr7	51786211	51786888	+	0	NA	Intergenic	L1ME5|LINE|L1	-469731	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.002954	0.331858	
chunk0158_283_1	chr5	131684449	131684653	+	0	NA	intron (NM_001008738, intron 10 of 16)	intron (NM_001008738, intron 10 of 16)	-49315	NM_001164389	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.004902	0.302439	
chunk0080_49_1	chr17	21636876	21637458	+	0	NA	Intergenic	Intergenic	-55356	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.010309	0.324185	
chunk0184_337_1	chr7	120653911	120654380	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	203978	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.006397	0.351064	
chunk0044_406_1	chr12	41052251	41052953	+	0	NA	intron (NM_175038, intron 21 of 21)	intron (NM_175038, intron 21 of 21)	-135846	NM_001164595	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.002849	0.280228	
chunk0162_19_1	chr6	796265	796899	+	0	NA	Intergenic	Intergenic	-71916	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.006309	0.321260	417(AGCACAAGGTGCTCTG,+,0.00)
chunk0090_195_1	chr18	73101770	73101988	+	0	NA	Intergenic	MIR|SINE|MIR	162619	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.009174	0.296804	
chunk0127_105_1	chr3	90080834	90081375	+	0	NA	Intergenic	Intergenic	973580	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.001848	0.369004	
chunk0044_163_1	chr12	29921064	29921483	+	0	NA	Intergenic	Intergenic	-136514	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.007160	0.466667	148(GGGAACACTGTGTTCA,-,0.00),149(GGAACACTGTGTTCAT,+,0.00)
chunk0150_280_1	chr5	37002116	37002939	+	0	NA	intron (NM_015384, intron 14 of 45)	intron (NM_015384, intron 14 of 45)	125768	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.001215	0.344660	
chunk0129_47_1	chr3	117431370	117431909	+	0	NA	Intergenic	Intergenic	510208	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.007421	0.312963	
chunk0164_235_1	chr6	23257289	23257702	+	0	NA	Intergenic	L1PA5|LINE|L1	688046	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.004843	0.371981	170(GGTACATTGTGTCTTT,+,0.00)
chunk0141_87_1	chr4	78652276	78652744	+	0	NA	intron (NR_038306, intron 2 of 2)	intron (NR_038306, intron 2 of 2)	6516	NR_038305	100505702	Hs.235795	NR_038303		LINC01094	-	long intergenic non-protein coding RNA 1094	ncRNA	0.002137	0.415778	
chunk0039_3_1	chr11	94971089	94971407	+	0	NA	intron (NM_016403, intron 3 of 6)	intron (NM_016403, intron 3 of 6)	2364	NM_016403	51503	Hs.503597	NM_016403	ENSG00000150316	CWC15	AD002|C11orf5|Cwf15|HSPC148|ORF5	CWC15 spliceosome associated protein homolog	protein-coding	0.006289	0.347962	
chunk0028_114_1	chr10	84460579	84460778	+	0	NA	intron (NM_001284243, intron 3 of 7)	L1ME1|LINE|L1	35496	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.000000	0.315000	
chunk0065_4_1	chr15	19640104	19640482	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-642451	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.010582	0.353562	
chunk0134_294_1	chr3	180063639	180064239	+	0	NA	Intergenic	L2c|LINE|L2	-26886	NM_001256750	51555	Hs.235331	NM_016559	ENSG00000114757	PEX5L	PEX5R|PEX5RP|PXR2|PXR2B|TRIP8b	peroxisomal biogenesis factor 5 like	protein-coding	0.003333	0.344426	
chunk0017_313_1	chr1	211237520	211237935	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-21639	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.019277	0.463942	
chunk0043_174_1	chr12	17194034	17194809	+	0	NA	Intergenic	MLT1A1-int|LTR|ERVL-MaLR	205674	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.009032	0.364691	
chunk0115_74_1	chr21	21897340	21898054	+	0	NA	Intergenic	Intergenic	150712	NR_109958	101927821	Hs.334181	NR_109958	ENSG00000233997	LINC01425	-	long intergenic non-protein coding RNA 1425	ncRNA	0.005602	0.345455	
chunk0152_389_1	chr5	64654607	64654819	+	0	NA	Intergenic	L1MC|LINE|L1	-35595	NM_001164442	100132916	Hs.591776	NM_001164442	ENSG00000145642	SHISAL2B	FAM159B	shisa like 2B	protein-coding	0.004717	0.314554	
chunk0070_19_1	chr15	69052481	69053119	+	0	NA	intron (NM_001184780, intron 14 of 15)	LTR106_Mam|LTR|LTR	-28050	NR_026949	283673	Hs.177927	NM_173610	ENSG00000212766	EWSAT1	LINC00277|NCRNA00277|TMEM84	Ewing sarcoma associated transcript 1	ncRNA	0.006270	0.306729	
chunk0179_168_1	chr7	46774493	46775011	+	0	NA	Intergenic	Intergenic	807392	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.001931	0.400771	244(CAGAACAACTTGTTCC,-,0.00),245(AGAACAACTTGTTCCC,+,0.00)
chunk0001_228_1	chr1	8116701	8117166	+	0	NA	Intergenic	Intergenic	-90600	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.012903	0.429185	
chunk0105_146_1	chr2	186463245	186463503	+	0	NA	Intergenic	Intergenic	-22784	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.003876	0.312741	
chunk0023_36_1	chr10	21194490	21194715	+	0	NA	Intergenic	Zaphod2|DNA|hAT-Tip100	20300	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.004444	0.424779	
chunk0161_136_1	chr5	168424163	168424425	+	0	NA	intron (NM_001161661, intron 11 of 22)	intron (NM_001161661, intron 11 of 22)	-62164	NM_002887	5917	Hs.654907	NM_002887	ENSG00000113643	RARS	ArgRS|DALRD1|HLD9	arginyl-tRNA synthetase	protein-coding	0.000000	0.403042	153(CAGGTCATCCTGTGCT,-,0.00),154(AGGTCATCCTGTGCTA,+,0.00)
chunk0159_344_1	chr5	144156613	144156901	+	0	NA	Intergenic	Intergenic	13957	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.003472	0.328720	
chunk0068_67_1	chr15	51888315	51888571	+	0	NA	intron (NM_014547, intron 4 of 9)	intron (NM_014547, intron 4 of 9)	35677	NR_109775	100422556	Hs.664788	NR_109775		LOC100422556	-	LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene	pseudo	0.011719	0.431907	
chunk0113_394_1	chr20	60071861	60072379	+	0	NA	3' UTR (NM_001302815, exon 4 of 4)	3' UTR (NM_001302815, exon 4 of 4)	-15566	NR_109918	729296	Hs.534781	NR_109916		LOC729296	-	uncharacterized LOC729296	ncRNA	0.003861	0.315992	
chunk0012_298_1	chr1	162168165	162168611	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	11281	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.017937	0.516779	
chunk0199_58_1	chr9	2145434	2146063	+	0	NA	intron (NM_003070, intron 27 of 33)	intron (NM_003070, intron 27 of 33)	-11932	NM_001289398	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.009539	0.407937	225(TTGGACTTAGTGTTCC,-,0.00),226(TGGACTTAGTGTTCCA,+,0.00)
chunk0014_121_1	chr1	177445005	177445563	+	0	NA	Intergenic	Intergenic	93698	NR_126001	102724661	Hs.146628	NR_126001		LINC01645	-	long intergenic non-protein coding RNA 1645	ncRNA	0.003584	0.372093	229(AAGAACAGTTAGTGCC,-,0.00),230(AGAACAGTTAGTGCCT,+,0.00)
chunk0001_309_1	chr1	9269238	9269463	+	0	NA	3' UTR (NM_004285, exon 5 of 5)	3' UTR (NM_004285, exon 5 of 5)	-23532	NM_025106	80176	Hs.8261	NM_025106	ENSG00000171621	SPSB1	SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding	0.044444	0.606195	
chunk0102_387_1	chr2	154653510	154653955	+	0	NA	Intergenic	Intergenic	-44849	NM_002239	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.002247	0.302691	
chunk0124_9_1	chr3	51538423	51538831	+	0	NA	Intergenic	CpG	-2953	NM_015106	23132	Hs.105399	NM_015106	ENSG00000164080	RAD54L2	ARIP4|HSPC325|SRISNF2L	RAD54 like 2	protein-coding	0.115196	0.679707	
chunk0086_389_1	chr18	26580211	26580708	+	0	NA	intron (NM_001258222, intron 1 of 4)	intron (NM_001258222, intron 1 of 4)	11076	NR_107024	102466874		NR_107024	ENSG00000276221	MIR8057	hsa-mir-8057	microRNA 8057	ncRNA	0.014085	0.483936	237(GGGCACACTCTGTTCA,-,0.00),238(GGCACACTCTGTTCAC,+,0.00)
chunk0030_269_1	chr10	116427644	116428132	+	0	NA	promoter-TSS (NM_001011709)	promoter-TSS (NM_001011709)	-24	NM_001011709	119548	Hs.276724	NM_001011709	ENSG00000203837	PNLIPRP3	-	pancreatic lipase related protein 3	protein-coding	0.004098	0.298569	
chunk0081_437_1	chr17	48928953	48929198	+	0	NA	TTS (NM_023079)	TTS (NM_023079)	15717	NM_007241	11267	Hs.127249	NM_007241	ENSG00000159210	SNF8	Dot3|EAP30|VPS22	SNF8 subunit of ESCRT-II	protein-coding	0.008163	0.418699	
chunk0199_154_1	chr9	4264144	4264865	+	0	NA	intron (NM_001042413, intron 2 of 10)	L2a|LINE|L2	35531	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.004161	0.403047	277(GTAACACGATGTCCTT,+,0.00),428(AGGACATAATGCACTT,+,0.00)
chunk0153_164_1	chr5	71012727	71013025	+	0	NA	exon (NM_004536, exon 4 of 17).3	exon (NM_004536, exon 4 of 17).3	12238	NM_004536	4671	Hs.646951	NM_004536	ENSG00000249437	NAIP	BIRC1|NLRB1|psiNAIP	NLR family apoptosis inhibitory protein	protein-coding	0.013423	0.444816	
chunk0180_264_1	chr7	69616690	69617240	+	0	NA	intron (NM_015570, intron 1 of 18)	L2a|LINE|L2	18046	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.001818	0.368421	278(AGGCACAGGAAGTACC,-,0.00),279(GGCACAGGAAGTACCA,+,0.00)
chunk0072_244_1	chr15	96029281	96029541	+	0	NA	Intergenic	Intergenic	-296517	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.000000	0.363985	
chunk0173_348_1	chr6	149061872	149062463	+	0	NA	intron (NM_005715, intron 7 of 7)	intron (NM_005715, intron 7 of 7)	-97483	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.003384	0.391892	294(ATAACATAATGTTCTT,+,0.00)
chunk0076_102_1	chr16	65809669	65810133	+	0	NA	Intergenic	Intergenic	-233601	NR_027755	283867	Hs.444774	NM_001101346	ENSG00000261742	LINC00922	-	long intergenic non-protein coding RNA 922	ncRNA	0.015086	0.434409	
chunk0091_292_1	chr19	12395611	12396214	+	0	NA	intron (NM_001080821, intron 1 of 3)	L1MB4|LINE|L1	5362	NM_001080821	90576	Hs.546637	NM_203381	ENSG00000196466	ZNF799	HIT-40|ZNF842	zinc finger protein 799	protein-coding	0.001658	0.372517	
chunk0169_380_1	chr6	107416223	107416741	+	0	NA	intron (NM_020381, intron 1 of 7)	intron (NM_020381, intron 1 of 7)	43093	NM_020381	57107	Hs.745008	NM_020381	ENSG00000164494	PDSS2	C6orf210|COQ10D3|COQ1B|DLP1|bA59I9.3|hDLP1	decaprenyl diphosphate synthase subunit 2	protein-coding	0.005792	0.360308	
chunk0154_173_1	chr5	80015658	80016193	+	0	NA	intron (NM_001306213, intron 2 of 22)	MamRep605|LTR?|LTR?	-19374	NM_003248	7060	Hs.211426	NM_003248	ENSG00000113296	THBS4	TSP-4|TSP4	thrombospondin 4	protein-coding	0.007477	0.481343	
chunk0158_31_1	chr5	125590255	125590805	+	0	NA	intron (NR_109887, intron 3 of 3)	intron (NR_109887, intron 3 of 3)	97269	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.003636	0.388385	
chunk0034_11_1	chr11	26017301	26017873	+	0	NA	Intergenic	LTR39|LTR|ERV1	-171536	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.001748	0.376963	
chunk0128_29_1	chr3	104236138	104236424	+	0	NA	Intergenic	L1MA6|LINE|L1	-712165	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.358885	
chunk0154_407_1	chr5	88725728	88726025	+	0	NA	intron (NM_001193348, intron 7 of 7)	intron (NM_001193348, intron 7 of 7)	-41073	NR_015436	645323	Hs.12827	NR_015436	ENSG00000245526	LINC00461	ECONEXIN|EyeLinc1|VISC	long intergenic non-protein coding RNA 461	ncRNA	0.006734	0.359060	
chunk0023_425_1	chr10	31631299	31631539	+	0	NA	Intergenic	Intergenic	277507	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.008333	0.531120	
chunk0163_318_1	chr6	14775415	14776029	+	0	NA	Intergenic	Intergenic	-470253	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.001629	0.400000	
chunk0084_299_1	chr17	80024340	80024667	+	0	NA	intron (NM_019020, intron 1 of 11)	(CA)n|Simple_repeat|Simple_repeat	11355	NM_019020	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.009174	0.493902	
chunk0108_134_1	chr2	230350878	230351298	+	0	NA	intron (NM_138402, intron 2 of 18)	intron (NM_138402, intron 2 of 18)	23908	NM_001308163	93349	Hs.589661	NM_138402	ENSG00000185404	SP140L	-	SP140 nuclear body protein like	protein-coding	0.002381	0.396675	
chunk0104_254_1	chr2	177607228	177607509	+	0	NA	Intergenic	Intergenic	11598	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.007117	0.351064	
chunk0177_279_1	chr7	25618785	25619206	+	0	NA	Intergenic	Intergenic	330991	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.004751	0.402844	
chunk0063_202_1	chr14	81261508	81261707	+	0	NA	3' UTR (NM_001256430, exon 8 of 8)	3' UTR (NM_001256430, exon 8 of 8)	-40376	NM_201595	2957	Hs.592334	NM_015859	ENSG00000165417	GTF2A1	TF2A1|TFIIA|TFIIA-42|TFIIAL	general transcription factor IIA subunit 1	protein-coding	0.005025	0.365000	
chunk0151_343_1	chr5	54296347	54296822	+	0	NA	intron (NM_019087, intron 1 of 4)	L2c|LINE|L2	13989	NM_019087	54622	Hs.659125	NM_019087	ENSG00000185305	ARL15	ARFRP2	ADP ribosylation factor like GTPase 15	protein-coding	0.006316	0.525210	
chunk0160_244_1	chr5	156572898	156573497	+	0	NA	intron (NM_000337, intron 4 of 8)	intron (NM_000337, intron 4 of 8)	246440	NM_000337	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.003339	0.351667	268(AAGCACATACTGTACT,-,0.00),269(AGCACATACTGTACTT,+,0.00)
chunk0122_255_1	chr3	34890236	34891037	+	0	NA	intron (NR_110817, intron 2 of 3)	MER58B|DNA|hAT-Charlie	503387	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.001248	0.334165	
chunk0104_409_1	chr2	180722593	180722950	+	0	NA	intron (NR_104320, intron 1 of 3)	MLT1K|LTR|ERVL-MaLR	30667	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.005602	0.466480	172(TGGGACAGAGTGAACC,-,0.00),173(GGGACAGAGTGAACCC,+,0.00)
chunk0061_416_1	chr14	65047684	65047883	+	0	NA	intron (NM_001202558, intron 10 of 12)	intron (NM_001202558, intron 10 of 12)	3095	NR_039855	100616490		NR_039855	ENSG00000266531	MIR4706	mir-4706	microRNA 4706	ncRNA	0.010050	0.450000	
chunk0110_10_1	chr20	9940927	9941386	+	0	NA	Intergenic	Intergenic	-45177	NR_109861	101929371	Hs.619265	NR_109861		PARAL1	-	PPARG activating RBM14 associated lncRNA 1	ncRNA	0.000000	0.360870	
chunk0063_161_1	chr14	80158427	80158774	+	0	NA	Intergenic	HAL1|LINE|L1	-52819	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.011527	0.413793	160(CGGTACACAGTGATCT,-,0.00),161(GGTACACAGTGATCTT,+,0.00)
chunk0156_362_1	chr5	112593857	112594585	+	0	NA	Intergenic	Intergenic	-34215	NR_104672	102467214	Hs.124613	NR_104672		LINC02200	-	long intergenic non-protein coding RNA 2200	ncRNA	0.008242	0.419753	
chunk0140_250_1	chr4	71391372	71391743	+	0	NA	intron (NM_001098484, intron 6 of 25)	intron (NM_001098484, intron 6 of 25)	52504	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.000000	0.293011	
chunk0009_44_1	chr1	100462643	100463035	+	0	NA	exon (NM_033313, exon 9 of 11)	exon (NM_033313, exon 9 of 11)	-75333	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.030612	0.458015	
chunk0170_342_1	chr6	116315025	116315384	+	0	NA	intron (NM_001080976, intron 1 of 5)	MIR|SINE|MIR	35084	NM_001080976	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.000000	0.386111	152(CTGAACATTATGTGCC,-,0.00),153(TGAACATTATGTGCCA,+,0.00)
chunk0133_182_1	chr3	170181559	170181758	+	0	NA	promoter-TSS (NM_024947)	promoter-TSS (NM_024947)	91	NM_001308116	80012	Hs.529592	NM_024947	ENSG00000173889	PHC3	EDR3|HPH3	polyhomeotic homolog 3	protein-coding	0.060302	0.610000	
chunk0151_25_1	chr5	41755556	41756224	+	0	NA	intron (NM_000436, intron 14 of 16)	L1M4|LINE|L1	-114140	NR_046635	100874002	Hs.375537	NR_046635	ENSG00000248668	OXCT1-AS1	-	OXCT1 antisense RNA 1	ncRNA	0.001497	0.315396	
chunk0062_220_1	chr14	70966972	70967442	+	0	NA	intron (NM_001308160, intron 3 of 33)	intron (NM_001308160, intron 3 of 33)	59802	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.004255	0.318471	
chunk0206_122_1	chr9	120942000	120943176	+	0	NA	Intergenic	Intergenic	-13415	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.008503	0.442651	
chunk0095_389_1	chr2	23913951	23914438	+	0	NA	intron (NR_125717, intron 1 of 28)	intron (NR_125717, intron 1 of 28)	12920	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.006160	0.364754	
chunk0071_446_1	chr15	90138455	90138991	+	0	NA	Intergenic	L3|LINE|CR1	-36169	NM_002168	3418	Hs.596461	NM_002168	ENSG00000182054	IDH2	D2HGA2|ICD-M|IDH|IDHM|IDP|IDPM|mNADP-IDH	isocitrate dehydrogenase (NADP(+)) 2, mitochondrial	protein-coding	0.011194	0.502793	268(AGACACAGGATGTACT,-,0.00)
chunk0016_253_1	chr1	200111233	200111821	+	0	NA	intron (NM_205860, intron 6 of 7)	intron (NM_205860, intron 6 of 7)	68702	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.011905	0.388795	228(TGGTGCACTCTGTTCC,-,0.00),229(GGTGCACTCTGTTCCT,+,0.00),315(GGGACTGAAAGTCCTG,+,0.00)
chunk0086_211_1	chr18	22485581	22486372	+	0	NA	Intergenic	Intergenic	-68061	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.007585	0.433081	
chunk0124_109_1	chr3	53842740	53843246	+	0	NA	intron (NM_018397, intron 1 of 8)	intron (NM_018397, intron 1 of 8)	3400	NM_018397	55349	Hs.126688	NM_018397	ENSG00000016391	CHDH	-	choline dehydrogenase	protein-coding	0.015810	0.522682	
chunk0083_141_1	chr17	65742608	65743081	+	0	NA	intron (NR_126542, intron 2 of 5)	intron (NR_126542, intron 2 of 5)	83699	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.008457	0.417722	
chunk0060_329_1	chr14	51481609	51482101	+	0	NA	intron (NR_051990, intron 2 of 2)	intron (NR_051990, intron 2 of 2)	-7266	NM_001042481	122786	Hs.434914	NM_152330	ENSG00000139926	FRMD6	C14orf31|EX1|Willin|c14_5320	FERM domain containing 6	protein-coding	0.008130	0.411765	
chunk0076_261_1	chr16	69385944	69386241	+	0	NA	promoter-TSS (NM_005652)	promoter-TSS (NM_005652)	-104	NM_005652	7014	Hs.63335	NM_005652	ENSG00000132604	TERF2	TRBF2|TRF2	telomeric repeat binding factor 2	protein-coding	0.094276	0.627517	
chunk0128_434_1	chr3	114967170	114967691	+	0	NA	intron (NM_001164343, intron 2 of 11)	intron (NM_001164343, intron 2 of 11)	-66808	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.005758	0.337165	
chunk0143_56_1	chr4	107711917	107712550	+	0	NA	intron (NM_005443, intron 1 of 11)	intron (NM_005443, intron 1 of 11)	8030	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.004739	0.386435	314(GGGACTATCTGTTCAT,+,0.00)
chunk0200_452_1	chr9	31365518	31365717	+	0	NA	Intergenic	Intergenic	-957163	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.005025	0.370000	
chunk0167_239_1	chr6	67563545	67564201	+	0	NA	Intergenic	Intergenic	-491478	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.007622	0.292237	
chunk0088_10_1	chr18	43183144	43183580	+	0	NA	Intergenic	Intergenic	-67670	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.361556	
chunk0050_241_1	chr12	105269892	105270420	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	-33926	NM_001251904	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.001894	0.353497	165(GAAACATCTTGTTCCT,+,0.00)
chunk0160_312_1	chr5	159177392	159177808	+	0	NA	intron (NM_144726, intron 4 of 10)	intron (NM_144726, intron 4 of 10)	30048	NM_001199382	153830	Hs.349306	NM_144726	ENSG00000145860	RNF145	-	ring finger protein 145	protein-coding	0.002404	0.335731	
chunk0025_176_1	chr10	52933623	52933884	+	0	NA	Intergenic	Intergenic	-162053	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.328244	
chunk0003_125_1	chr1	32501789	32502503	+	0	NA	Intergenic	L1MC4|LINE|L1	-36999	NM_001040441	653121	Hs.546479	NM_144621	ENSG00000160062	ZBTB8A	BOZF1|ZBTB8|ZNF916A	zinc finger and BTB domain containing 8A	protein-coding	0.015406	0.436364	310(CGGCACAAGATGTTCC,-,0.00),311(GGCACAAGATGTTCCA,+,0.00)
chunk0142_359_1	chr4	101887905	101888795	+	0	NA	intron (NM_017935, intron 5 of 16)	intron (NM_017935, intron 5 of 16)	74524	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.008989	0.350168	
chunk0122_391_1	chr3	37864056	37864550	+	0	NA	intron (NM_001008392, intron 1 of 7)	intron (NM_001008392, intron 1 of 7)	2125	NM_005808	10217	Hs.475963	NM_005808	ENSG00000144677	CTDSPL	C3orf8|HYA22|PSR1|RBSP3|SCP3	CTD small phosphatase like	protein-coding	0.004049	0.458586	
chunk0060_208_1	chr14	48814386	48815075	+	0	NA	Intergenic	L1M3f|LINE|L1	771686	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.008708	0.413043	
chunk0204_456_1	chr9	104529559	104530299	+	0	NA	Intergenic	Intergenic	-2720	NM_001001919	138804	Hs.553601	NM_001001919	ENSG00000148136	OR13C4	HSHTPCRX17|HTPCRX17|OR2K1|OR37F|OR9-7	olfactory receptor family 13 subfamily C member 4	protein-coding	0.006757	0.376518	
chunk0008_414_1	chr1	98393617	98393816	+	0	NA	Intergenic	Intergenic	183005	NR_046088	729987	Hs.683961	NR_046088	ENSG00000226053	LINC01776	-	long intergenic non-protein coding RNA 1776	ncRNA	0.005025	0.365000	
chunk0053_57_1	chr13	27957063	27957324	+	0	NA	Intergenic	Intergenic	11987	NR_002162	432369	Hs.574118	NR_002162		ATP5F1EP2	ATP5EP2	ATP synthase F1 subunit epsilon pseudogene 2	pseudo	0.007663	0.389313	
chunk0046_234_1	chr12	60237565	60237789	+	0	NA	Intergenic	L1PA7|LINE|L1	548340	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.008929	0.360000	
chunk0015_217_1	chr1	187579564	187580076	+	0	NA	Intergenic	Intergenic	136192	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.009766	0.391813	
chunk0094_127_1	chr2	4631326	4631840	+	0	NA	intron (NR_034134, intron 4 of 4)	L1MEb|LINE|L1	24639	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.007782	0.310680	233(AGGAACATCCTGAACC,-,0.00),234(GGAACATCCTGAACCT,+,0.00)
chunk0002_356_1	chr1	25889685	25890229	+	0	NA	intron (NM_001145454, intron 4 of 4)	L2a|LINE|L2	16196	NM_203401	3925	Hs.209983	NM_005563	ENSG00000117632	STMN1	C1orf215|LAP18|Lag|OP18|PP17|PP19|PR22|SMN	stathmin 1	protein-coding	0.007353	0.506422	243(AGGAACACACTGCACC,-,0.00),244(GGAACACACTGCACCT,+,0.00)
chunk0089_361_1	chr18	66968196	66968587	+	0	NA	Intergenic	Intergenic	-113193	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.002558	0.267857	
chunk0174_275_1	chr6	161618897	161619340	+	0	NA	intron (NM_013988, intron 4 of 8)	intron (NM_013988, intron 4 of 8)	-345043	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.018059	0.436937	
chunk0107_405_1	chr2	224041913	224042438	+	0	NA	Intergenic	Intergenic	-2856	NM_006216	5270	Hs.38449	NM_006216	ENSG00000135919	SERPINE2	GDN|GDNPF|PI-7|PI7|PN-1|PN1|PNI	serpin family E member 2	protein-coding	0.007619	0.441065	
chunk0087_295_1	chr18	38991748	38992405	+	0	NA	Intergenic	Intergenic	630099	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.003044	0.329787	
chunk0147_128_1	chr4	174396403	174397084	+	0	NA	Intergenic	(ATAT)n|Simple_repeat|Simple_repeat	-27052	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.007342	0.303519	
chunk0059_229_1	chr14	34243549	34243762	+	0	NA	Intergenic	Intergenic	218607	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.004695	0.443925	
chunk0046_372_1	chr12	63439939	63440176	+	0	NA	Intergenic	Intergenic	228517	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.004219	0.348739	
chunk0174_346_1	chr6	164220147	164220392	+	0	NA	Intergenic	Intergenic	601794	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.004082	0.341463	
chunk0125_446_1	chr3	72835606	72835923	+	0	NA	intron (NM_018130, intron 4 of 10)	intron (NM_018130, intron 4 of 10)	12683	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.015773	0.465409	
chunk0116_192_1	chr21	37066366	37066944	+	0	NA	intron (NM_153682, intron 4 of 4)	intron (NM_153682, intron 4 of 4)	-2589	NR_131189	105372795	Hs.528019	NR_131189		LOC105372795	-	uncharacterized LOC105372795	ncRNA	0.005190	0.317789	271(GAGTACACAATGATCC,-,0.00),272(AGTACACAATGATCCT,+,0.00)
chunk0181_117_1	chr7	80768895	80769309	+	0	NA	intron (NM_006379, intron 12 of 17)	L1MA4|LINE|L1	122449	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.000000	0.291566	
chunk0028_120_1	chr10	84632822	84633359	+	0	NA	Intergenic	MER41C|LTR|ERV1	207908	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.011173	0.394052	
chunk0129_392_1	chr3	126355749	126356491	+	0	NA	intron (NM_014079, intron 1 of 2)	CpG	1273	NM_014079	28999	Hs.272215	NM_014079	ENSG00000163884	KLF15	KKLF	Kruppel like factor 15	protein-coding	0.053908	0.651413	230(GGGGACACGCTGTTCC,-,0.00),231(GGGACACGCTGTTCCG,+,0.00)
chunk0009_227_1	chr1	106673490	106674041	+	0	NA	Intergenic	L1ME3A|LINE|L1	-382880	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.000000	0.309783	
chunk0171_176_1	chr6	125141251	125141711	+	0	NA	Intergenic	Intergenic	-12248	NM_001300994	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.010870	0.357918	
chunk0035_441_1	chr11	57514339	57514654	+	0	NA	intron (NM_003627, intron 1 of 14)	CpG	389	NM_001198810	8501	Hs.591952	NM_003627	ENSG00000149150	SLC43A1	LAT3|PB39|POV1|R00504	solute carrier family 43 member 1	protein-coding	0.053968	0.648734	
chunk0069_341_1	chr15	66482461	66482822	+	0	NA	intron (NM_002755, intron 6 of 10)	L2b|LINE|L2	14393	NR_039737	100616149		NR_039737	ENSG00000266589	MIR4512	-	microRNA 4512	ncRNA	0.011080	0.549724	182(AGGGACAAGGTGTCTC,-,0.00),183(GGGACAAGGTGTCTCT,+,0.00)
chunk0194_27_1	chr8	81682453	81682999	+	0	NA	intron (NM_001144879, intron 1 of 7)	intron (NM_001144879, intron 1 of 7)	3628	NM_005536	3612	Hs.656694	NM_005536	ENSG00000133731	IMPA1	IMP|IMPA|MRT59	inositol monophosphatase 1	protein-coding	0.003663	0.396709	224(CAGAACTAGATGTTCT,-,0.00),225(AGAACTAGATGTTCTC,+,0.00)
chunk0078_63_1	chr17	1491503	1491827	+	0	NA	promoter-TSS (NM_033375)	promoter-TSS (NM_033375)	13	NM_033375	4641	Hs.286226	NM_033375	ENSG00000197879	MYO1C	MMI-beta|MMIb|NMI|myr2	myosin IC	protein-coding	0.169753	0.849231	
chunk0159_212_1	chr5	140700829	140701116	+	0	NA	intron (NM_144723, intron 2 of 5)	intron (NM_144723, intron 2 of 5)	525	NM_144723	153527	Hs.350194	NM_144723	ENSG00000146007	ZMAT2	Ptg-12|Snu23	zinc finger matrin-type 2	protein-coding	0.041812	0.510417	
chunk0179_350_1	chr7	50813084	50813290	+	0	NA	Intergenic	Intergenic	-19725	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.004854	0.478261	
chunk0161_447_1	chr5	178749369	178750033	+	0	NA	Intergenic	Intergenic	-18999	NM_005649	6940	Hs.484324	NM_005649	ENSG00000169131	ZNF354A	EZNF|HEL104|HKL1|KID-1|KID1|TCF17	zinc finger protein 354A	protein-coding	0.013554	0.392481	278(CAGCACAACCAGTACT,-,0.00),279(AGCACAACCAGTACTG,+,0.00)
chunk0026_453_1	chr10	71603029	71603629	+	0	NA	intron (NM_001171931, intron 9 of 24)	intron (NM_001171931, intron 9 of 24)	-91409	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.018333	0.590682	
chunk0105_437_1	chr2	193937374	193937741	+	0	NA	Intergenic	Intergenic	-406712	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.002725	0.301630	
chunk0020_285_1	chr1	236929221	236929423	+	0	NA	Intergenic	Intergenic	75096	NM_001276687	645745	Hs.632513	NM_001039954	ENSG00000244020	MT1HL1	MT1P2	metallothionein 1H like 1	protein-coding	0.000000	0.334975	
chunk0080_372_1	chr17	33294093	33294292	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-1204	NM_183377	40	Hs.368417	NM_001094	ENSG00000108684	ASIC2	ACCN|ACCN1|ASIC2a|BNC1|BNaC1|MDEG|hBNaC1	acid sensing ion channel subunit 2	protein-coding	0.005025	0.550000	
chunk0095_402_1	chr2	24368374	24368777	+	0	NA	Intergenic	L2a|LINE|L2	-8047	NM_147152	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.000000	0.321782	
chunk0069_259_1	chr15	64558419	64558818	+	0	NA	intron (NM_015042, intron 1 of 8)	L2b|LINE|L2	59198	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.340000	
chunk0069_404_1	chr15	67915603	67915802	+	0	NA	Intergenic	Intergenic	-75657	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.010050	0.470000	
chunk0028_54_1	chr10	83222282	83222592	+	0	NA	Intergenic	MER52-int|LTR|ERV1	-916992	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.016129	0.543408	30(AAGAACACCTTGTTCT,-,0.00),31(AGAACACCTTGTTCTG,+,0.00)
chunk0035_304_1	chr11	47106893	47107153	+	0	NA	intron (NM_024113, intron 3 of 8)	intron (NM_024113, intron 3 of 8)	70102	NM_032389	84364	Hs.436204	NM_032389	ENSG00000149182	ARFGAP2	IRZ|NBLA10535|ZFP289|ZNF289	ADP ribosylation factor GTPase activating protein 2	protein-coding	0.015385	0.528736	
chunk0192_119_1	chr8	61740301	61740500	+	0	NA	Intergenic	L1MEd|LINE|L1	25612	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.000000	0.295000	
chunk0118_372_1	chr22	36523124	36523338	+	0	NA	exon (NM_003753, exon 6 of 15)	exon (NM_003753, exon 6 of 15)	5999	NM_003753	8664	Hs.55682	NM_003753	ENSG00000100353	EIF3D	EIF3S7|eIF3-p66|eIF3-zeta	eukaryotic translation initiation factor 3 subunit D	protein-coding	0.009346	0.372093	
chunk0209_440_1	chrX	63784264	63784520	+	0	NA	intron (NM_001173479, intron 1 of 8)	intron (NM_001173479, intron 1 of 8)	1154	NM_001173479	23229	Hs.54697	NM_015185	ENSG00000131089	ARHGEF9	COLLYBISTIN|EIEE8|HPEM-2|PEM-2|PEM2	Cdc42 guanine nucleotide exchange factor 9	protein-coding	0.000000	0.498054	
chunk0187_324_1	chr7	156639930	156640185	+	0	NA	promoter-TSS (NM_001184996)	promoter-TSS (NM_001184996)	597	NR_026865	100506380	Hs.647014	NM_032625	ENSG00000182648	LINC01006	C7orf13|MY040	long intergenic non-protein coding RNA 1006	ncRNA	0.090196	0.640625	
chunk0171_417_1	chr6	131467761	131468011	+	0	NA	Intergenic	L1PA15|LINE|L1	-105318	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.004000	0.422311	
chunk0053_134_1	chr13	29873022	29873271	+	0	NA	non-coding (NR_046510, exon 2 of 2)	non-coding (NR_046510, exon 2 of 2)	15259	NR_046510	100874059	Hs.569261	NR_046510	ENSG00000224329	LINC00297	NCRNA00297	long intergenic non-protein coding RNA 297	ncRNA	0.000000	0.376000	
chunk0173_171_1	chr6	144411318	144412123	+	0	NA	intron (NM_007124, intron 2 of 73)	intron (NM_007124, intron 2 of 73)	6065	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.009938	0.404467	
chunk0090_149_1	chr18	72339383	72340062	+	0	NA	Intergenic	Intergenic	204766	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.000000	0.348529	
chunk0080_234_1	chr17	30092703	30093091	+	0	NA	exon (NM_198529, exon 22 of 23)	exon (NM_198529, exon 22 of 23)	-23910	NM_032141	84081	Hs.462663	NM_032141	ENSG00000126653	NSRP1	CCDC55|HSPC095|NSrp70	nuclear speckle splicing regulatory protein 1	protein-coding	0.000000	0.326478	
chunk0084_80_1	chr17	75132924	75133407	+	0	NA	Intergenic	AluJo|SINE|Alu	-1370	NR_045513	30833	Hs.67201	NM_014595	ENSG00000125458	NT5C	DNT|DNT1|HEL74|P5N2|PN-I|PN-II|UMPH2|cdN|dNT-1	5', 3'-nucleotidase, cytosolic	protein-coding	0.010352	0.506198	101(AAGAACATGCTGAACT,-,0.00),102(AGAACATGCTGAACTG,+,0.00)
chunk0103_94_1	chr2	161217942	161218392	+	0	NA	intron (NM_004180, intron 4 of 7)	intron (NM_004180, intron 4 of 7)	-26572	NR_110164	100996579	Hs.660929	NR_110163	ENSG00000227403	LINC01806	-	long intergenic non-protein coding RNA 1806	ncRNA	0.006667	0.359202	
chunk0048_192_1	chr12	81143025	81143457	+	0	NA	exon (NM_024560, exon 5 of 16)	exon (NM_024560, exon 5 of 16)	-15147	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.011574	0.390300	
chunk0149_320_1	chr5	26451191	26451726	+	0	NA	Intergenic	Intergenic	587124	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.009346	0.365672	242(ATAACACAATGTGCTC,+,0.00)
chunk0187_458_1	chr7	159318592	159319357	+	0	NA	Intergenic	Intergenic	-174017	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.005229	0.407311	
chunk0003_31_1	chr1	29706229	29706759	+	0	NA	Intergenic	MER41C|LTR|ERV1	331118	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.015094	0.467043	
chunk0092_122_1	chr19	27806628	27806827	+	0	NA	TTS (NR_110690)	TTS (NR_110690)	-12787	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.045226	0.490000	
chunk0207_180_1	chr9	130710488	130711073	+	0	NA	Intergenic	Intergenic	-3101	NM_007313	25	Hs.431048	NM_005157	ENSG00000097007	ABL1	ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-abl	ABL proto-oncogene 1, non-receptor tyrosine kinase	protein-coding	0.011966	0.395904	
chunk0098_405_1	chr2	79873805	79874004	+	0	NA	intron (NM_004389, intron 5 of 17)	AluJr|SINE|Alu	-7321	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.000000	0.460000	
chunk0037_329_1	chr11	77060946	77061543	+	0	NA	Intergenic	L1MC4a|LINE|L1	-5701	NM_004055	726	Hs.248153	NM_004055	ENSG00000149260	CAPN5	ADNIV|HTRA3|VRNI|nCL-3	calpain 5	protein-coding	0.006700	0.369565	
chunk0064_347_1	chr14	96708235	96708711	+	0	NA	Intergenic	(AGT)n|Simple_repeat|Simple_repeat	-88874	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.016807	0.467505	
chunk0050_359_1	chr12	107798406	107798636	+	0	NA	Intergenic	L1MA6|LINE|L1	24136	NM_203436	121549	Hs.149910	NM_203436	ENSG00000187855	ASCL4	HASH4|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding	0.000000	0.350649	
chunk0063_411_1	chr14	88356466	88357158	+	0	NA	Intergenic	Intergenic	-28832	NM_001040428	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.010116	0.395382	224(TAGCACTTATTGTCCT,-,0.00),225(AGCACTTATTGTCCTG,+,0.00)
chunk0037_208_1	chr11	74546669	74547053	+	0	NA	Intergenic	LTR32|LTR|ERVL	-45669	NR_046409	10714	Hs.82502	NM_006591	ENSG00000077514	POLD3	P66|P68|PPP1R128	DNA polymerase delta 3, accessory subunit	protein-coding	0.018229	0.503896	
chunk0040_211_1	chr11	114163895	114164333	+	0	NA	intron (NM_006006, intron 3 of 6)	intron (NM_006006, intron 3 of 6)	103548	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.018265	0.446469	221(CAGTACACTGTGTGCT,-,0.00),222(AGTACACTGTGTGCTC,+,0.00)
chunk0021_182_1	chr10	5554179	5555010	+	0	NA	Intergenic	Intergenic	-28348	NR_120496	100132159	Hs.239600	NR_120496		CALML3-AS1	-	CALML3 antisense RNA 1	ncRNA	0.015644	0.508413	
chunk0061_166_1	chr14	59822153	59822751	+	0	NA	intron (NM_021136, intron 1 of 8)	L1PA14|LINE|L1	48387	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.000000	0.337229	
chunk0084_245_1	chr17	78831849	78832449	+	0	NA	intron (NM_025090, intron 4 of 19)	intron (NM_025090, intron 4 of 19)	8738	NM_025090	57602	Hs.464243	NM_025090	ENSG00000055483	USP36	DUB1	ubiquitin specific peptidase 36	protein-coding	0.015000	0.437604	
chunk0061_177_1	chr14	59936788	59937378	+	0	NA	intron (NR_075071, intron 6 of 32)	L2c|LINE|L2	17370	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.003390	0.363790	
chunk0178_223_1	chr7	35658574	35659152	+	0	NA	intron (NM_022373, intron 5 of 8)	intron (NM_022373, intron 5 of 8)	36299	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.001730	0.338515	
chunk0142_241_1	chr4	98771912	98772111	+	0	NA	Intergenic	Intergenic	-113350	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.005025	0.400000	
chunk0130_239_1	chr3	135012156	135012576	+	0	NA	intron (NM_004441, intron 3 of 15)	intron (NM_004441, intron 3 of 15)	217109	NM_004441	2047	Hs.116092	NM_004441	ENSG00000154928	EPHB1	ELK|EPHT2|Hek6|NET	EPH receptor B1	protein-coding	0.007143	0.479810	177(AAGCACAGCCAGTCCT,-,0.00),178(AGCACAGCCAGTCCTC,+,0.00)
chunk0161_22_1	chr5	165757687	165758145	+	0	NA	Intergenic	Intergenic	1168454	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.008734	0.413943	
chunk0084_376_1	chr17	81793405	81793654	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-10603	NM_000160	2642	Hs.208	NM_000160	ENSG00000215644	GCGR	GGR|GL-R	glucagon receptor	protein-coding	0.032129	0.504000	
chunk0052_250_1	chr12	123445931	123446316	+	0	NA	Intergenic	MamRep488|DNA|hAT-Tip100	-9390	NM_145058	196383	Hs.488173	NM_145058	ENSG00000150977	RILPL2	RLP2	Rab interacting lysosomal protein like 2	protein-coding	0.010390	0.440415	
chunk0045_195_1	chr12	47407422	47407854	+	0	NA	Intergenic	Intergenic	-43369	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.006944	0.374134	
chunk0185_228_1	chr7	129283223	129283974	+	0	NA	intron (NM_001130720, intron 1 of 16)	intron (NM_001130720, intron 1 of 16)	58584	NM_001130720	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.000000	0.325798	
chunk0177_396_1	chr7	27171490	27171904	+	0	NA	non-coding (NR_046609, exon 3 of 3)	non-coding (NR_046609, exon 3 of 3)	-2134	NR_029911	442920		NR_029911	ENSG00000283745	MIR196B	MIRN196B|miR-196b|miRNA196B	microRNA 196b	ncRNA	0.033816	0.544578	
chunk0078_40_1	chr17	1030835	1031118	+	0	NA	intron (NM_001092, intron 15 of 21)	intron (NM_001092, intron 15 of 21)	865	NM_001256847	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.045936	0.633803	
chunk0074_317_1	chr16	30599452	30600244	+	0	NA	Intergenic	MER77|LTR|ERVL	9980	NR_104166	115509	Hs.454685	NM_138447	ENSG00000156853	ZNF689	TIPUH1	zinc finger protein 689	protein-coding	0.011364	0.433796	
chunk0132_330_1	chr3	161098661	161098936	+	0	NA	intron (NM_001038628, intron 6 of 7)	L3|LINE|CR1	6097	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.003636	0.394928	
chunk0153_420_1	chr5	75694293	75694506	+	0	NA	intron (NM_152408, intron 5 of 10)	L1MA7|LINE|L1	18056	NM_152408	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.000000	0.257009	
chunk0073_441_1	chr16	19284453	19284652	+	0	NA	Intergenic	Intergenic	-1231	NM_001256720	728276	Hs.632180	NM_001256720	ENSG00000261210	CLEC19A	-	C-type lectin domain containing 19A	protein-coding	0.000000	0.505000	
chunk0185_309_1	chr7	131357163	131358014	+	0	NA	intron (NM_013255, intron 1 of 17)	L1MC3|LINE|L1	29752	NM_013255	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.007051	0.380282	303(GAGTACTCTCAGTTCT,-,0.00),304(AGTACTCTCAGTTCTT,+,0.00)
chunk0093_2_1	chr2	22689	23211	+	0	NA	Intergenic	L1PA14|LINE|L1	23638	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.000000	0.365201	
chunk0114_58_1	chr21	8881046	8881450	+	0	NA	Intergenic	L1MB7|LINE|L1	-105751	NR_128711	103504731		NR_128711	ENSG00000264462	MIR3648-2	hsa-mir-3648-2	microRNA 3648-2	ncRNA	0.009901	0.348148	
chunk0081_146_1	chr17	40764685	40764884	+	0	NA	Intergenic	Intergenic	7375	NM_181539	353288	Hs.592133	NM_181539	ENSG00000186393	KRT26	CK26|K25|K25IRS2|K26|KRT25B	keratin 26	protein-coding	0.000000	0.410000	
chunk0186_250_1	chr7	141006203	141007045	+	0	NA	intron (NM_053035, intron 2 of 2)	intron (NM_053035, intron 2 of 2)	8055	NM_016071	51650	Hs.416207	NM_016071	ENSG00000090263	MRPS33	CGI-139|MRP-S33|PTD003|S33mt	mitochondrial ribosomal protein S33	protein-coding	0.011876	0.432977	
chunk0045_2_1	chr12	42865137	42865942	+	0	NA	Intergenic	Intergenic	-219041	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.004969	0.367246	384(TTGTACAGCCTGTTCT,-,0.00),385(TGTACAGCCTGTTCTC,+,0.00)
chunk0027_136_1	chr10	74421258	74421549	+	0	NA	intron (NM_001202450, intron 6 of 9)	L1MC3|LINE|L1	107921	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.003436	0.369863	
chunk0165_279_1	chr6	36092894	36093337	+	0	NA	intron (NM_001315, intron 8 of 11)	intron (NM_001315, intron 8 of 11)	-37369	NR_072996	5603	Hs.178695	NM_002754	ENSG00000156711	MAPK13	MAPK 13|MAPK-13|PRKM13|SAPK4|p38delta	mitogen-activated protein kinase 13	protein-coding	0.002257	0.378378	
chunk0038_237_1	chr11	87122848	87123340	+	0	NA	intron (NM_001168724, intron 4 of 13)	MER58B|DNA|hAT-Charlie	85250	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.006098	0.381339	
chunk0138_77_1	chr4	34922355	34922853	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-882711	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.006024	0.336673	
chunk0147_122_1	chr4	174255669	174256254	+	0	NA	intron (NM_012180, intron 3 of 5)	intron (NM_012180, intron 3 of 5)	-27716	NM_001040157	80817	Hs.555989	NM_030633	ENSG00000164118	CEP44	KIAA1712|PS1TP3	centrosomal protein 44	protein-coding	0.010256	0.356655	
chunk0144_435_1	chr4	140963702	140964310	+	0	NA	intron (NM_020724, intron 2 of 6)	intron (NM_020724, intron 2 of 6)	169456	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.001645	0.311987	
chunk0158_357_1	chr5	133753784	133754702	+	0	NA	Intergenic	Intergenic	-141711	NM_015082	23105	Hs.483390	NM_015082	ENSG00000053108	FSTL4	-	follistatin like 4	protein-coding	0.004357	0.361262	588(AAGATCAAAATGTCCT,-,0.00)
chunk0014_369_1	chr1	182602854	182603053	+	0	NA	intron (NM_002928, intron 2 of 4)	intron (NM_002928, intron 2 of 4)	1460	NM_002928	6004	Hs.413297	NM_002928	ENSG00000143333	RGS16	A28-RGS14|A28-RGS14P|RGS-R	regulator of G protein signaling 16	protein-coding	0.015075	0.510000	
chunk0153_280_1	chr5	73039056	73039559	+	0	NA	intron (NM_001146032, intron 9 of 24)	intron (NM_001146032, intron 9 of 24)	-81254	NM_173490	134285	Hs.162246	NM_173490	ENSG00000157111	TMEM171	PRP2	transmembrane protein 171	protein-coding	0.000000	0.376984	
chunk0180_180_1	chr7	65882398	65883105	+	0	NA	intron (NM_001284342, intron 1 of 1)	intron (NM_001284342, intron 1 of 1)	9481	NM_173517	154807	Hs.427232	NM_173517	ENSG00000196715	VKORC1L1	-	vitamin K epoxide reductase complex subunit 1 like 1	protein-coding	0.005658	0.272599	315(AAGCACATTCAGTACT,-,0.00),316(AGCACATTCAGTACTA,+,0.00)
chunk0093_195_1	chr19	49295370	49295902	+	0	NA	intron (NM_014037, intron 7 of 11)	intron (NM_014037, intron 7 of 11)	13232	NR_036209	100422979		NR_036209	ENSG00000265407	MIR4324	mir-4324	microRNA 4324	ncRNA	0.001880	0.362101	
chunk0064_206_1	chr14	93011682	93011881	+	0	NA	intron (NM_001142594, intron 4 of 10)	intron (NM_001142594, intron 4 of 10)	-55671	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.015075	0.565000	
chunk0066_29_1	chr15	27583783	27584287	+	0	NA	Intergenic	L1M4|LINE|L1	-422716	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.003968	0.346535	274(AAGGACAGTCTGTTCA,-,0.00),275(AGGACAGTCTGTTCAA,+,0.00)
chunk0115_307_1	chr21	28538958	28539547	+	0	NA	promoter-TSS (NR_026553)	promoter-TSS (NR_026553)	-66	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.005093	0.377966	
chunk0088_394_1	chr18	54409816	54410414	+	0	NA	Intergenic	Intergenic	49587	NM_001288982	162681	Hs.208701	NM_173529	ENSG00000166845	C18orf54	LAS2	chromosome 18 open reading frame 54	protein-coding	0.006689	0.358932	
chunk0075_370_1	chr16	56462213	56462799	+	0	NA	intron (NM_018233, intron 3 of 12)	intron (NM_018233, intron 3 of 12)	10994	NM_018233	55239	Hs.231883	NM_018233	ENSG00000087263	OGFOD1	TPA1	2-oxoglutarate and iron dependent oxygenase domain containing 1	protein-coding	0.005119	0.367973	
chunk0051_74_1	chr12	113259867	113260171	+	0	NA	intron (NM_001301214, intron 1 of 26)	L1MC4a|LINE|L1	15758	NM_001301214	53373	Hs.524763	NM_017901	ENSG00000186815	TPCN1	TPC1	two pore segment channel 1	protein-coding	0.009868	0.377049	
chunk0018_180_1	chr1	219177990	219178481	+	0	NA	intron (NM_001300772, intron 1 of 4)	intron (NM_001300772, intron 1 of 4)	3266	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.002037	0.367886	
chunk0033_269_1	chr11	19091924	19092638	+	0	NA	Intergenic	L1MD2|LINE|L1	-24864	NM_001001483	54503	Hs.188569	NM_019028	ENSG00000177054	ZDHHC13	HIP14L|HIP3RP	zinc finger DHHC-type containing 13	protein-coding	0.002801	0.318881	
chunk0199_339_1	chr9	11065119	11065318	+	0	NA	Intergenic	LTR9A1|LTR|ERV1	452012	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.010050	0.450000	
chunk0116_198_1	chr21	37253949	37254421	+	0	NA	intron (NM_006052, intron 1 of 7)	intron (NM_006052, intron 1 of 7)	13347	NM_006052	10311	Hs.369488	NM_006052	ENSG00000157538	VPS26C	DCRA|DSCR3|DSCRA	VPS26 endosomal protein sorting factor C	protein-coding	0.012712	0.454545	
chunk0098_103_1	chr2	68018542	68019164	+	0	NA	Intergenic	L1MEg|LINE|L1	44174	NM_006333	10438	Hs.602900	NM_006333	ENSG00000197223	C1D	LRP1|Rrp47|SUN-CoR|SUNCOR|hC1D	C1D nuclear receptor corepressor	protein-coding	0.011254	0.418941	
chunk0020_36_1	chr1	232164350	232164915	+	0	NA	Intergenic	Intergenic	238798	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.003540	0.339223	
chunk0059_302_1	chr14	36062295	36062591	+	0	NA	Intergenic	LTR33C|LTR|ERVL	-7984	NR_073454	101101773	Hs.640678	NR_073454	ENSG00000257585	LINC00609	-	long intergenic non-protein coding RNA 609	ncRNA	0.013514	0.447811	
chunk0061_105_1	chr14	57757250	57757616	+	0	NA	intron (NM_001306087, intron 1 of 7)	L1MEc|LINE|L1	108441	NM_001206920	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.002732	0.267030	
chunk0177_152_1	chr7	22937901	22938471	+	0	NA	Intergenic	Intergenic	75965	NM_032581	84668	Hs.85603	NM_032581	ENSG00000122591	FAM126A	DRCTNNB1A|HCC|HLD5|HYCC1	family with sequence similarity 126 member A	protein-coding	0.003509	0.380035	
chunk0202_381_1	chr9	80873922	80874286	+	0	NA	Intergenic	Intergenic	815431	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.005495	0.339726	
chunk0152_53_1	chr5	57482093	57482297	+	0	NA	exon (NM_001017992, exon 1 of 1)	exon (NM_001017992, exon 1 of 1)	614	NM_001017992	345651	Hs.482167	NM_001017992	ENSG00000169067	ACTBL2	ACT	actin beta like 2	protein-coding	0.024510	0.551220	
chunk0040_174_1	chr11	114013818	114014143	+	0	NA	Intergenic	AluJb|SINE|Alu	36480	NM_001161772	3359	Hs.413899	NM_000869	ENSG00000166736	HTR3A	5-HT-3|5-HT3A|5-HT3R|5HT3R|HTR3	5-hydroxytryptamine receptor 3A	protein-coding	0.015385	0.481595	
chunk0072_318_1	chr15	98907684	98908304	+	0	NA	intron (NM_001291858, intron 5 of 20)	MER5A|DNA|hAT-Charlie	97662	NM_001102612	145814	Hs.592021	NM_001102612	ENSG00000183571	PGPEP1L	-	pyroglutamyl-peptidase I like	protein-coding	0.012903	0.558776	
chunk0015_343_1	chr1	189921046	189921525	+	0	NA	Intergenic	L1PB4|LINE|L1	556344	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004175	0.485417	
chunk0041_335_1	chr11	130551607	130551858	+	0	NA	Intergenic	Intergenic	102758	NM_139055	170689	Hs.534221	NM_139055	ENSG00000166106	ADAMTS15	-	ADAM metallopeptidase with thrombospondin type 1 motif 15	protein-coding	0.007968	0.392857	128(GAGAACACTGTGTATC,-,0.00),129(AGAACACTGTGTATCT,+,0.00)
chunk0189_99_1	chr8	21844784	21844983	+	0	NA	Intergenic	Intergenic	-56049	NM_001495	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.025126	0.560000	
chunk0126_67_1	chr3	74456718	74456917	+	0	NA	intron (NM_020872, intron 3 of 21)	intron (NM_020872, intron 3 of 21)	64323	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.290000	
chunk0089_432_1	chr18	70020874	70021562	+	0	NA	intron (NM_173630, intron 44 of 48)	MIRc|SINE|MIR	-64042	NM_006566	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.002907	0.332366	
chunk0124_140_1	chr3	54546938	54547388	+	0	NA	intron (NM_018398, intron 5 of 37)	intron (NM_018398, intron 5 of 37)	92694	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.006667	0.416851	
chunk0172_202_1	chr6	136682176	136682557	+	0	NA	intron (NM_005923, intron 7 of 29)	intron (NM_005923, intron 7 of 29)	53252	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.005249	0.348168	
chunk0176_144_1	chr7	12896940	12897340	+	0	NA	Intergenic	Intergenic	209854	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.000000	0.319202	
chunk0170_348_1	chr6	116399470	116399960	+	0	NA	intron (NM_001080976, intron 2 of 5)	intron (NM_001080976, intron 2 of 5)	28768	NM_013352	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.010204	0.423625	
chunk0183_264_1	chr7	107315473	107315933	+	0	NA	intron (NM_006348, intron 11 of 21)	intron (NM_006348, intron 11 of 21)	146688	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.000000	0.312364	297(AGGGACTGTATGTGCT,-,0.00),298(GGGACTGTATGTGCTA,+,0.00)
chunk0156_368_1	chr5	112691743	112692056	+	0	NA	Intergenic	LTR41|LTR|ERVL	-9011	NR_104673	102467216	Hs.174158	NR_104673		LOC102467216	-	uncharacterized LOC102467216	ncRNA	0.009585	0.496815	
chunk0121_370_1	chr3	24998302	24998815	+	0	NA	Intergenic	Intergenic	-175774	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.001949	0.371595	
chunk0150_164_1	chr5	34010438	34010645	+	0	NA	intron (NR_037951, intron 6 of 8)	L1MA4A|LINE|L1	-2426	NM_014324	23600	Hs.508343	NM_014324	ENSG00000242110	AMACR	AMACRD|CBAS4|P504S|RACE|RM	alpha-methylacyl-CoA racemase	protein-coding	0.000000	0.355769	
chunk0099_297_1	chr2	98908811	98909254	+	0	NA	intron (NM_207362, intron 1 of 9)	intron (NM_207362, intron 1 of 9)	27189	NM_207362	343990	Hs.469398	NM_207362	ENSG00000196872	KIAA1211L	C2orf55	KIAA1211 like	protein-coding	0.009029	0.430180	
chunk0049_69_1	chr12	90284324	90284529	+	0	NA	Intergenic	L1M7|LINE|L1	575471	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.014634	0.330097	89(GGGAACATAATGTTTC,-,0.00),90(GGAACATAATGTTTCT,+,0.00)
chunk0064_38_1	chr14	89604233	89604464	+	0	NA	intron (NM_001085471, intron 1 of 6)	L1MEd|LINE|L1	14802	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.043290	0.405172	
chunk0140_444_1	chr4	76266911	76267210	+	0	NA	intron (NM_001242936, intron 3 of 7)	L2a|LINE|L2	15360	NM_001136570	100129583	Hs.720509	NM_001136570	ENSG00000189157	FAM47E	-	family with sequence similarity 47 member E	protein-coding	0.003344	0.366667	
chunk0026_155_1	chr10	62518485	62518687	+	0	NA	intron (NM_199451, intron 4 of 7)	intron (NM_199451, intron 4 of 7)	-1862	NM_199452	22891	Hs.22653	NM_014951	ENSG00000138311	ZNF365	Su48|UAN|ZNF365D	zinc finger protein 365	protein-coding	0.000000	0.339901	
chunk0205_150_1	chr9	108400776	108401092	+	0	NA	Intergenic	Tigger6b|DNA|TcMar-Tigger	455061	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.006329	0.350158	
chunk0163_244_1	chr6	12416075	12416501	+	0	NA	Intergenic	Intergenic	125992	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.004695	0.360656	
chunk0184_273_1	chr7	118582164	118582363	+	0	NA	Intergenic	Intergenic	357605	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.005025	0.390000	
chunk0062_348_1	chr14	73711878	73712350	+	0	NA	3' UTR (NM_006029, exon 1 of 1)	3' UTR (NM_006029, exon 1 of 1)	2311	NM_006029	9240	Hs.194709	NM_006029	ENSG00000176903	PNMA1	MA1	PNMA family member 1	protein-coding	0.019068	0.376321	
chunk0077_4_1	chr16	74499127	74499605	+	0	NA	intron (NR_027264, intron 4 of 26)	AluJo|SINE|Alu	-77896	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.000000	0.419624	280(TGGAACACTGTGTTTT,-,0.00),281(GGAACACTGTGTTTTT,+,0.00)
chunk0097_241_1	chr2	53606921	53607412	+	0	NA	Intergenic	Intergenic	-160626	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.002037	0.341463	
chunk0048_356_1	chr12	85363714	85364021	+	0	NA	Intergenic	Intergenic	83609	NM_006982	8092	Hs.41683	NM_006982	ENSG00000180318	ALX1	CART1|FND3|HEL23	ALX homeobox 1	protein-coding	0.006515	0.357143	
chunk0139_110_1	chr4	52234447	52234768	+	0	NA	Intergenic	Intergenic	183276	NM_001297608	132671	Hs.527090	NM_145263	ENSG00000163071	SPATA18	Mieap|SPETEX1	spermatogenesis associated 18	protein-coding	0.006231	0.366460	
chunk0060_202_1	chr14	48335120	48335431	+	0	NA	Intergenic	MER50|LTR|ERV1	-540261	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.009646	0.490385	
chunk0077_293_1	chr16	81383978	81384323	+	0	NA	promoter-TSS (NR_039871)	promoter-TSS (NR_039871)	-868	NR_039871	100616150		NR_039871	ENSG00000284473	MIR4720	-	microRNA 4720	ncRNA	0.000000	0.332370	228(CAACACATTCTGTTCT,-,0.00),229(AACACATTCTGTTCTT,+,0.00)
chunk0019_355_1	chr1	229579692	229580234	+	0	NA	Intergenic	Intergenic	-21268	NM_012089	23456	Hs.17614	NM_012089	ENSG00000135776	ABCB10	EST20237|M-ABC2|MTABC2	ATP binding cassette subfamily B member 10	protein-coding	0.007380	0.388582	259(CAGCACACTATGTTTC,-,0.00),260(AGCACACTATGTTTCT,+,0.00)
chunk0004_197_1	chr1	46515638	46516406	+	0	NA	Intergenic	Intergenic	9026	NM_147192	127343	Hs.375623	NM_147192	ENSG00000197587	DMBX1	MBX|OTX3|PAXB	diencephalon/mesencephalon homeobox 1	protein-coding	0.015625	0.556567	170(AAGCTCTGACTGTCCC,-,0.00),171(AGCTCTGACTGTCCCT,+,0.00),378(AAAGACACTGTGTACT,-,0.00),379(AAGACACTGTGTACTG,+,0.00)
chunk0200_458_1	chr9	31776398	31776864	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-607972	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.006438	0.417559	
chunk0042_414_1	chr12	11706888	11707183	+	0	NA	intron (NM_001987, intron 1 of 7)	intron (NM_001987, intron 1 of 7)	57181	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.006780	0.462838	
chunk0166_114_1	chr6	44360252	44360599	+	0	NA	intron (NM_145026, intron 3 of 8)	intron (NM_145026, intron 3 of 8)	17765	NM_145026	221409	Hs.135283	NM_145026	ENSG00000249481	SPATS1	DDIP|SPATA8|SRSP1	spermatogenesis associated serine rich 1	protein-coding	0.014409	0.431034	
chunk0101_381_1	chr2	138516698	138517144	+	0	NA	intron (NM_001001664, intron 1 of 10)	L2c|LINE|L2	15141	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.002242	0.342282	
chunk0186_301_1	chr7	142895079	142895753	+	0	NA	Intergenic	MIRc|SINE|MIR	-9671	NM_018646	55503	Hs.302740	NM_014274	ENSG00000165125	TRPV6	ABP/ZF|CAT1|CATL|ECAC2|HRPTTN|HSA277909|LP6728|ZFAB	transient receptor potential cation channel subfamily V member 6	protein-coding	0.005935	0.440000	
chunk0174_98_1	chr6	156822731	156823144	+	0	NA	intron (NM_017519, intron 1 of 18)	intron (NM_017519, intron 1 of 18)	-43206	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.026634	0.521739	
chunk0138_399_1	chr4	42881257	42881623	+	0	NA	Intergenic	Intergenic	-11826	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.002732	0.326975	
chunk0200_324_1	chr9	23659759	23660223	+	0	NA	intron (NR_121602, intron 4 of 27)	intron (NR_121602, intron 4 of 27)	12408	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.010776	0.445161	
chunk0117_71_1	chr22	17073522	17074123	+	0	NA	Intergenic	L1M3f|LINE|L1	-11137	NM_001289905	23765	Hs.48353	NM_014339	ENSG00000177663	IL17RA	CANDF5|CD217|CDw217|IL-17RA|IL17R|IMD51|hIL-17R	interleukin 17 receptor A	protein-coding	0.003328	0.345515	
chunk0137_318_1	chr4	24583482	24583736	+	0	NA	intron (NM_001358, intron 1 of 13)	intron (NM_001358, intron 1 of 13)	952	NM_001358	1665	Hs.696074	NM_001358	ENSG00000109606	DHX15	DBP1|DDX15|HRH2|PRP43|PRPF43|PrPp43p	DEAH-box helicase 15	protein-coding	0.035433	0.498039	
chunk0140_301_1	chr4	72959310	72959856	+	0	NA	Intergenic	L1PA15-16|LINE|L1	110176	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.005495	0.435101	
chunk0011_122_1	chr1	147076293	147076908	+	0	NA	Intergenic	Intergenic	8156	NR_121645	101447996		NR_121645	ENSG00000286172	RNVU1-8	RNU1-145|vU1.8	RNA, variant U1 small nuclear 8	snRNA	0.013008	0.418831	
chunk0201_253_1	chr9	38023113	38023438	+	0	NA	intron (NM_003028, intron 1 of 5)	MIRc|SINE|MIR	45938	NM_003028	6461	Hs.521482	NM_003028	ENSG00000107338	SHB	bA3J10.2	SH2 domain containing adaptor protein B	protein-coding	0.021538	0.518405	
chunk0150_414_1	chr5	40254051	40254455	+	0	NA	Intergenic	L2a|LINE|L2	201962	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.004950	0.385185	
chunk0052_444_1	chr12	132455614	132456021	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-34754	NM_001142641	57666	Hs.411138	NM_001142641	ENSG00000112787	FBRSL1	-	fibrosin like 1	protein-coding	0.034398	0.500000	
chunk0037_202_1	chr11	74398751	74399033	+	0	NA	promoter-TSS (NR_039710)	promoter-TSS (NR_039710)	-345	NR_039710	100616215		NR_039710	ENSG00000264402	MIR548AL	-	microRNA 548al	ncRNA	0.060284	0.551237	
chunk0079_132_1	chr17	12726172	12726673	+	0	NA	intron (NM_001146312, intron 5 of 13)	intron (NM_001146312, intron 5 of 13)	-20287	NR_104605	101928418	Hs.620346	NR_104605	ENSG00000227274	LOC101928418	-	uncharacterized LOC101928418	ncRNA	0.003992	0.426295	
chunk0033_370_1	chr11	23288593	23288896	+	0	NA	Intergenic	Intergenic	130446	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.006601	0.282895	
chunk0186_444_1	chr7	147946080	147946605	+	0	NA	intron (NM_014141, intron 14 of 23)	intron (NM_014141, intron 14 of 23)	-568221	NR_031645	100313895		NR_031645	ENSG00000221442	MIR548F4	MIR548F-4|MIRN548F4|hsa-mir-548f-4	microRNA 548f-4	ncRNA	0.003810	0.408745	
chunk0111_119_1	chr20	24034845	24035172	+	0	NA	Intergenic	Intergenic	-46229	NM_178311	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.006116	0.484756	
chunk0002_192_1	chr1	19433393	19434043	+	0	NA	intron (NM_001313932, intron 1 of 4)	intron (NM_001313932, intron 1 of 4)	50989	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.009231	0.436252	
chunk0185_340_1	chr7	132100342	132101024	+	0	NA	Intergenic	Intergenic	190463	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.005865	0.427526	
chunk0116_356_1	chr21	41580157	41580769	+	0	NA	Intergenic	Intergenic	-72305	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.013072	0.464927	
chunk0124_52_1	chr3	52770899	52771153	+	0	NA	promoter-TSS (NM_003157)	promoter-TSS (NM_003157)	-77	NM_001193533	6787	Hs.631921	NM_003157	ENSG00000114904	NEK4	NRK2|STK2|pp12301	NIMA related kinase 4	protein-coding	0.098425	0.658824	
chunk0103_386_1	chr2	168785114	168785825	+	0	NA	intron (NR_045786, intron 1 of 3)	intron (NR_045786, intron 1 of 3)	960	NR_045786	100861402	Hs.506829	NR_045786	ENSG00000227617	CERS6-AS1	-	CERS6 antisense RNA 1	ncRNA	0.005626	0.411517	
chunk0136_179_1	chr4	6695681	6696757	+	0	NA	intron (NM_005980, intron 1 of 1)	intron (NM_005980, intron 1 of 1)	2380	NM_005980	6286	Hs.2962	NM_005980	ENSG00000163993	S100P	MIG9	S100 calcium binding protein P	protein-coding	0.019517	0.523677	
chunk0096_381_1	chr2	36967444	36968252	+	0	NA	Intergenic	Intergenic	-1376	NM_003162	6801	Hs.127486	NM_003162	ENSG00000115808	STRN	PPP2R6A|SG2NA|STRN1	striatin	protein-coding	0.016089	0.407911	521(AAAGACATCCTGTCCC,-,0.00),522(AAGACATCCTGTCCCT,+,0.00)
chunk0132_293_1	chr3	160049001	160049626	+	0	NA	intron (NR_108088, intron 3 of 9)	intron (NR_108088, intron 3 of 9)	28664	NR_104132	730109	Hs.99333	NR_104132		LINC01100	-	long intergenic non-protein coding RNA 1100	ncRNA	0.006400	0.421725	
chunk0129_156_1	chr3	120591992	120592259	+	0	NA	Intergenic	Intergenic	-4156	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.000000	0.406716	
chunk0075_269_1	chr16	53768654	53769182	+	0	NA	intron (NM_001080432, intron 1 of 8)	UCON8|DNA|DNA	64955	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.005682	0.387524	
chunk0035_19_1	chr11	40296978	40297273	+	0	NA	intron (NM_001258419, intron 4 of 6)	intron (NM_001258419, intron 4 of 6)	-3995	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003390	0.314189	
chunk0087_1_1	chr18	30211150	30211611	+	0	NA	Intergenic	Intergenic	-87530	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.000000	0.329004	
chunk0166_464_1	chr6	53358492	53358929	+	0	NA	Intergenic	L2a|LINE|L2	-9531	NM_021814	60481	Hs.520189	NM_021814	ENSG00000012660	ELOVL5	HELO1|SCA38|dJ483K16.1	ELOVL fatty acid elongase 5	protein-coding	0.032037	0.486301	
chunk0042_164_1	chr12	4449807	4450190	+	0	NA	Intergenic	LTR88b|LTR|Gypsy?	-4384	NM_020996	2251	Hs.166015	NM_020996	ENSG00000111241	FGF6	HBGF-6|HST2	fibroblast growth factor 6	protein-coding	0.010444	0.489583	162(GGATCTCCCTGTTCTC,+,0.00)
chunk0014_270_1	chr1	180311711	180312227	+	0	NA	intron (NM_032360, intron 7 of 7)	L1ME3A|LINE|L1	-37288	NR_037642	100527964	Hs.496545	NR_037642	ENSG00000230124	LHX4-AS1	-	LHX4 antisense RNA 1	ncRNA	0.003876	0.350097	
chunk0013_61_1	chr1	167326419	167326630	+	0	NA	intron (NR_037163, intron 2 of 16)	intron (NR_037163, intron 2 of 16)	-2520	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.004739	0.471698	
chunk0039_151_1	chr11	98795034	98795515	+	0	NA	Intergenic	Intergenic	-225702	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004158	0.315353	
chunk0107_103_1	chr2	214003960	214005268	+	0	NA	intron (NR_047659, intron 14 of 17)	MER67B|LTR|ERV1	246547	NR_039640	100616375		NR_039640	ENSG00000265734	MIR4438	-	microRNA 4438	ncRNA	0.009939	0.406417	
chunk0117_335_1	chr22	25139807	25140006	+	0	NA	intron (NM_001145206, intron 4 of 10)	L2a|LINE|L2	-27214	NR_038941	100128531	Hs.662126	NR_038941	ENSG00000203280	LOC100128531	-	uncharacterized LOC100128531	ncRNA	0.010050	0.480000	65(AAGGACGGAGTGTGCT,-,0.00),66(AGGACGGAGTGTGCTG,+,0.00)
chunk0090_100_1	chr18	70872237	70872436	+	0	NA	Intergenic	L1MC4|LINE|L1	-221479	NM_001278515									0.005025	0.375000	
chunk0175_188_1	chr7	5469665	5470002	+	0	NA	Intergenic	Intergenic	26084	NR_030318	693174		NR_030318	ENSG00000207973	MIR589	MIRN589|hsa-mir-589|mir-589	microRNA 589	ncRNA	0.035608	0.559172	
chunk0149_248_1	chr5	23611790	23612354	+	0	NA	Intergenic	L1MA2|LINE|L1	104417	NM_001310214	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.003546	0.353982	
chunk0064_213_1	chr14	93065041	93065702	+	0	NA	intron (NM_001142594, intron 3 of 10)	intron (NM_001142594, intron 3 of 10)	-2081	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.003026	0.471299	
chunk0209_254_1	chrX	46103116	46103595	+	0	NA	Intergenic	L1PA10|LINE|L1	224319	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.000000	0.360417	
chunk0086_174_1	chr18	21842902	21843316	+	0	NA	intron (NM_020774, intron 13 of 20)	intron (NM_020774, intron 13 of 20)	-11703	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.007246	0.337349	
chunk0080_378_1	chr17	33618551	33618861	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-84946	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.006452	0.453376	
chunk0102_253_1	chr2	149232089	149232346	+	0	NA	Intergenic	L1PB1|LINE|L1	-97768	NM_001195685	130574	Hs.21929	NM_194317	ENSG00000187123	LYPD6	-	LY6/PLAUR domain containing 6	protein-coding	0.003891	0.337209	
chunk0212_119_1	chrX	130691649	130692119	+	0	NA	intron (NM_006375, intron 4 of 14)	intron (NM_006375, intron 4 of 14)	196943	NR_027141	55855	Hs.567120	NM_018472		DENND10P1	FAM45B|FAM45BP|HT011	DENND10 pseudogene 1	pseudo	0.006383	0.377919	
chunk0005_15_1	chr1	54265964	54266632	+	0	NA	intron (NM_018070, intron 5 of 16)	intron (NM_018070, intron 5 of 16)	29855	NR_103541	619518	Hs.591438	NM_001034847	ENSG00000198711	SSBP3-AS1	C1orf191|MST128|MSTP128	SSBP3 antisense RNA 1	ncRNA	0.013473	0.470852	
chunk0043_389_1	chr12	25251210	25251606	+	0	NA	promoter-TSS (NM_004985)	promoter-TSS (NM_004985)	-477	NM_004985	3845	Hs.505033	NM_004985	ENSG00000133703	KRAS	C-K-RAS|CFC2|K-RAS2A|K-RAS2B|K-RAS4A|K-RAS4B|K-Ras|KI-RAS|KRAS1|KRAS2|NS|NS3|RALD|RASK2|c-Ki-ras2	KRAS proto-oncogene, GTPase	protein-coding	0.101010	0.670025	
chunk0072_131_1	chr15	92618248	92618835	+	0	NA	3' UTR (NM_207446, exon 3 of 3)	3' UTR (NM_207446, exon 3 of 3)	37260	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.017036	0.489796	
chunk0152_174_1	chr5	59617284	59617920	+	0	NA	intron (NM_001165899, intron 3 of 16)	MLT1C|LTR|ERVL-MaLR	-31104	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.012579	0.411303	
chunk0187_452_1	chr7	159189712	159190002	+	0	NA	Intergenic	L1ME3|LINE|L1	-44900	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.003448	0.323024	
chunk0092_128_1	chr19	27901819	27902497	+	0	NA	Intergenic	L2b|LINE|L2	-108218	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.005900	0.480118	374(GGGGACAGTAAGTACC,-,0.00),375(GGGACAGTAAGTACCC,+,0.00)
chunk0007_147_1	chr1	79517263	79518051	+	0	NA	Intergenic	Intergenic	-510847	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.003807	0.325729	
chunk0103_20_1	chr2	159024850	159025115	+	0	NA	intron (NM_001145909, intron 2 of 26)	Tigger3c|DNA|TcMar-Tigger	56348	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.003774	0.409774	28(AGTAACATGCTGTTCT,-,0.00),29(GTAACATGCTGTTCTG,+,0.00),102(AAGTACACTCTGTTAC,-,0.00)
chunk0048_198_1	chr12	81209086	81209449	+	0	NA	intron (NM_024560, intron 9 of 15)	intron (NM_024560, intron 9 of 15)	50879	NR_039848	100616133		NR_039848	ENSG00000265227	MIR4699	-	microRNA 4699	ncRNA	0.000000	0.348901	
chunk0108_241_1	chr2	233754143	233754503	+	0	NA	TTS (NR_037695)	TTS (NR_037695)	1022	NR_037695	100286922	Hs.124112	NR_037694	ENSG00000178836	LOC100286922	-	DnaJ heat shock protein family (Hsp40) member B3 pseudogene	pseudo	0.011111	0.365651	134(ATGAACATTCTGTCCT,-,0.00),135(TGAACATTCTGTCCTA,+,0.00)
chunk0160_131_1	chr5	151282291	151282990	+	0	NA	intron (NM_181774, intron 8 of 9)	L1ME3G|LINE|L1	21133	NM_181774	285641	Hs.720893	NM_181774	ENSG00000186334	SLC36A3	PAT3|TRAMD2|tramdorin2	solute carrier family 36 member 3	protein-coding	0.017167	0.404286	
chunk0032_152_1	chr11	4841100	4841305	+	0	NA	Intergenic	L1MA1|LINE|L1	8006	NM_001004758	119692	Hs.553561	NM_001004758	ENSG00000176922	OR51S1	OR11-24	olfactory receptor family 51 subfamily S member 1	protein-coding	0.004878	0.320388	
chunk0041_71_1	chr11	123744340	123744618	+	0	NA	Intergenic	L1ME3G|LINE|L1	-2796	NM_001301780	7753	Hs.112556	NM_003455	ENSG00000166261	ZNF202	ZKSCAN10|ZSCAN42	zinc finger protein 202	protein-coding	0.007194	0.387097	
chunk0057_149_1	chr13	100269934	100270206	+	0	NA	intron (NM_001127692, intron 10 of 22)	MLT1G|LTR|ERVL-MaLR	181055	NM_000282	5095	Hs.80741	NM_000282	ENSG00000175198	PCCA	-	propionyl-CoA carboxylase subunit alpha	protein-coding	0.007353	0.490842	
chunk0188_183_1	chr8	11468926	11469276	+	0	NA	Intergenic	L1ME4a|LINE|L1	-2334	NM_053279	83648	Hs.124299	NM_053279	ENSG00000154319	FAM167A	C8orf13|D8S265|DIORA-1	family with sequence similarity 167 member A	protein-coding	0.008571	0.376068	
chunk0040_45_1	chr11	110774270	110774643	+	0	NA	Intergenic	Intergenic	-61267	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.005362	0.465241	182(TAGAACAAATTGTGCT,-,0.00),183(AGAACAAATTGTGCTG,+,0.00)
chunk0167_292_1	chr6	70816247	70816901	+	0	NA	intron (NM_001044305, intron 6 of 10)	intron (NM_001044305, intron 6 of 10)	140511	NM_080742	135152	Hs.713609	NM_080742	ENSG00000112309	B3GAT2	GLCATS	beta-1,3-glucuronyltransferase 2	protein-coding	0.003058	0.322137	414(CAAAACAAAATGTCCT,-,0.00),415(AAAACAAAATGTCCTG,+,0.00)
chunk0063_25_1	chr14	76651600	76652244	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-109970	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.003106	0.488372	
chunk0096_155_1	chr2	29276183	29276534	+	0	NA	intron (NM_004304, intron 9 of 28)	intron (NM_004304, intron 9 of 28)	160932	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.005698	0.460227	
chunk0204_89_1	chr9	94135110	94135807	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-40499	NR_029476	406881		NR_029476	ENSG00000199165	MIRLET7A1	LET7A1|MIRNLET7A1|let-7a-1	microRNA let-7a-1	ncRNA	0.004304	0.404011	335(AGGAACAGTCTGTTCT,-,0.00),336(GGAACAGTCTGTTCTT,+,0.00)
chunk0039_385_1	chr11	107102993	107103365	+	0	NA	Intergenic	L1PB3|LINE|L1	-84734	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.010753	0.506702	
chunk0054_138_1	chr13	43614773	43615204	+	0	NA	intron (NM_001127615, intron 1 of 16)	intron (NM_001127615, intron 1 of 16)	14489	NM_001127615	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.002320	0.375000	
chunk0109_240_1	chr20	5977188	5977710	+	0	NA	intron (NM_182802, intron 12 of 18)	intron (NM_182802, intron 12 of 18)	26797	NM_001281520	84515	Hs.597484	NM_032485	ENSG00000125885	MCM8	C20orf154|POF10|dJ967N21.5	minichromosome maintenance 8 homologous recombination repair factor	protein-coding	0.005747	0.405354	
chunk0153_416_1	chr5	75620510	75621007	+	0	NA	intron (NM_001276713, intron 3 of 13)	MamSINE1|SINE|tRNA-RTE	9282	NM_001276713	728780	Hs.370455	NM_001271529	ENSG00000189045	ANKDD1B	-	ankyrin repeat and death domain containing 1B	protein-coding	0.006036	0.431727	
chunk0151_161_1	chr5	49658851	49659118	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	782416	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.018727	0.417910	
chunk0138_338_1	chr4	41607105	41607352	+	0	NA	intron (NM_001112717, intron 6 of 25)	intron (NM_001112717, intron 6 of 25)	-5544	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.334677	86(AGAAACATTCAGTTCC,-,0.00),87(GAAACATTCAGTTCCT,+,0.00)
chunk0046_12_1	chr12	54136766	54137366	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	10995	NR_026656	400043	Hs.19193	NR_026656	ENSG00000250742	LINC02381	-	long intergenic non-protein coding RNA 2381	ncRNA	0.008333	0.415973	
chunk0090_425_1	chr18	79199686	79200316	+	0	NA	intron (NM_001306085, intron 9 of 28)	Tigger3b|DNA|TcMar-Tigger	130726	NM_001306085	374868	Hs.465475	NM_198531	ENSG00000166377	ATP9B	ATPASEP|ATPIIB|HUSSY-20|NEO1L|hMMR1	ATPase phospholipid transporting 9B (putative)	protein-coding	0.011111	0.415214	
chunk0058_258_1	chr14	25842333	25842828	+	0	NA	Intergenic	Intergenic	755174	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.002020	0.300403	
chunk0128_147_1	chr3	106957176	106957855	+	0	NA	Intergenic	Intergenic	283123	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.005891	0.336765	364(TGGAACATTTTGTTCC,-,0.00),365(GGAACATTTTGTTCCC,+,0.00)
chunk0015_329_1	chr1	189681698	189681923	+	0	NA	Intergenic	Intergenic	795819	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004444	0.336283	
chunk0194_140_1	chr8	84471443	84472172	+	0	NA	intron (NM_001100392, intron 2 of 9)	MIR|SINE|MIR	-234120	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.001372	0.336986	
chunk0141_441_1	chr4	89045250	89045851	+	0	NA	intron (NM_014883, intron 1 of 23)	L1M7|LINE|L1	11645	NM_014883	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.004992	0.368771	
chunk0076_15_1	chr16	58756241	58756454	+	0	NA	Intergenic	(TATGTG)n|Simple_repeat|Simple_repeat	-21990	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.018779	0.471963	
chunk0062_203_1	chr14	70047812	70048620	+	0	NA	intron (NR_104122, intron 5 of 5)	intron (NR_104122, intron 5 of 5)	32001	NM_182936	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.004950	0.391842	
chunk0146_266_1	chr4	162851756	162852331	+	0	NA	Intergenic	Intergenic	241585	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.005217	0.364583	
chunk0046_73_1	chr12	56041601	56042030	+	0	NA	promoter-TSS (NM_001029)	promoter-TSS (NM_001029)	-87	NM_001029	6231	Hs.447562	NM_001029	ENSG00000197728	RPS26	DBA10|S26|eS26	ribosomal protein S26	protein-coding	0.060606	0.548837	
chunk0009_319_1	chr1	108699766	108700540	+	0	NA	non-coding (NR_037185, exon 7 of 7)	non-coding (NR_037185, exon 7 of 7)	7840	NR_037185									0.015504	0.369032	460(ATGCACAGATTGTTCT,-,0.00),461(TGCACAGATTGTTCTT,+,0.00),501(ATGTACAGTCTGTACA,-,0.00),502(TGTACAGTCTGTACAT,+,0.00)
chunk0137_375_1	chr4	26207086	26207285	+	0	NA	Intergenic	Intergenic	-112525	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.010050	0.455000	
chunk0196_67_1	chr8	102367104	102367376	+	0	NA	intron (NM_015902, intron 1 of 58)	intron (NM_015902, intron 1 of 58)	45449	NM_015902	51366	Hs.492445	NM_015902	ENSG00000104517	UBR5	DD5|EDD|EDD1|HYD	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.014706	0.406593	
chunk0109_322_1	chr20	9168245	9168531	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	-49002	NM_182797	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.013986	0.439024	
chunk0029_297_1	chr10	103970901	103971148	+	0	NA	intron (NM_001304743, intron 1 of 17)	Tigger4a|DNA|TcMar-Tigger	3839	NM_014720	9748	Hs.591922	NM_014720	ENSG00000065613	SLK	LOSK|STK2|bA16H23.1|se20-9	STE20 like kinase	protein-coding	0.004049	0.358871	
chunk0165_10_1	chr6	28692600	28692902	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-105416	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.019868	0.432343	
chunk0106_188_1	chr2	201422047	201422335	+	0	NA	intron (NM_015049, intron 1 of 15)	L1ME4b|LINE|L1	29405	NM_015049	66008	Hs.152774	NM_015049	ENSG00000115993	TRAK2	ALS2CR3|CALS-C|GRIF-1|GRIF1|MILT2|OIP98	trafficking kinesin protein 2	protein-coding	0.006944	0.349481	
chunk0100_384_1	chr2	118208012	118208336	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	119700	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.015432	0.489231	
chunk0059_317_1	chr14	36443426	36443659	+	0	NA	Intergenic	Intergenic	70243	NM_001101341	253970	Hs.509165	NM_001101341	ENSG00000229415	SFTA3	NANCI|SFTPH|SP-H|SPH	surfactant associated 3	ncRNA	0.012876	0.461538	
chunk0191_370_1	chr8	56967155	56967765	+	0	NA	intron (NM_017813, intron 3 of 4)	intron (NM_017813, intron 3 of 4)	26411	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.004918	0.451718	
chunk0201_321_1	chr9	62871461	62871660	+	0	NA	intron (NR_122076, intron 1 of 5)	L1MD2|LINE|L1	-25816	NR_126047	728673	Hs.380240	NR_126047	ENSG00000170161	LOC728673	-	uncharacterized LOC728673	ncRNA	0.005025	0.290000	
chunk0056_276_1	chr13	90352817	90353300	+	0	NA	Intergenic	L1MC1|LINE|L1	121876	NR_030754	693207		NR_030754	ENSG00000283783	MIR622	MIRN622|hsa-mir-622	microRNA 622	ncRNA	0.002070	0.427686	
chunk0129_339_1	chr3	124772528	124772727	+	0	NA	intron (NM_002213, intron 11 of 14)	intron (NM_002213, intron 11 of 14)	40188	NR_036088	100422864		NR_036088	ENSG00000265981	MIR544B	-	microRNA 544b	ncRNA	0.015075	0.495000	
chunk0090_36_1	chr19	1400103	1400870	+	0	NA	intron (NM_000156, intron 1 of 5)	intron (NM_000156, intron 1 of 5)	1084	NM_138924	2593	Hs.81131	NM_000156	ENSG00000130005	GAMT	CCDS2|HEL-S-20|PIG2|TP53I2	guanidinoacetate N-methyltransferase	protein-coding	0.028683	0.654948	316(GGGAACAGCGTGGGCC,-,0.00),317(GGAACAGCGTGGGCCC,+,0.00)
chunk0199_398_1	chr9	13367019	13367456	+	0	NA	Intergenic	Intergenic	64092	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.002288	0.292237	
chunk0145_33_1	chr4	143781286	143782603	+	0	NA	Intergenic	Intergenic	-81269	NM_001168235	166752	Hs.252714	NM_001168235	ENSG00000183090	FREM3	-	FRAS1 related extracellular matrix 3	protein-coding	0.001519	0.343703	317(AGGGTCATCTTGTTCT,-,0.00),318(GGGTCATCTTGTTCTT,+,0.00)
chunk0118_315_1	chr22	35191301	35191880	+	0	NA	intron (NR_126356, intron 2 of 5)	MER68|LTR|ERVL	39466	NR_126356	104310353	Hs.581009	NR_126356	ENSG00000233080	LINC01399	-	long intergenic non-protein coding RNA 1399	ncRNA	0.008636	0.451724	
chunk0067_153_1	chr15	43793774	43794018	+	0	NA	promoter-TSS (NR_031695)	promoter-TSS (NR_031695)	-137	NR_031695	100302254		NR_031695	ENSG00000221792	MIR1282	MIRN1282|hsa-mir-1282	microRNA 1282	ncRNA	0.032787	0.616327	
chunk0038_150_1	chr11	84512218	84512433	+	0	NA	intron (NM_001142699, intron 7 of 27)	UCON46|Unknown|Unknown	-194986	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.384259	140(TAGAACTGACAGTACC,-,0.00),141(AGAACTGACAGTACCT,+,0.00)
chunk0182_267_1	chr7	97817724	97818044	+	0	NA	Intergenic	Intergenic	54281	NM_133436	440	Hs.489207	NM_001673	ENSG00000070669	ASNS	ASNSD|TS11	asparagine synthetase (glutamine-hydrolyzing)	protein-coding	0.012500	0.461059	148(GGGAACAGCTTGAACT,-,0.00),149(GGAACAGCTTGAACTC,+,0.00)
chunk0070_247_1	chr15	73504784	73505316	+	0	NA	intron (NM_001042367, intron 2 of 5)	intron (NM_001042367, intron 2 of 5)	61892	NM_001042367	283677	Hs.743574	NM_001042367	ENSG00000183324	REC114	C15orf60|CT147	REC114 meiotic recombination protein	protein-coding	0.000000	0.322702	
chunk0182_276_1	chr7	98137452	98137823	+	0	NA	intron (NM_014916, intron 2 of 13)	MER58A|DNA|hAT-Charlie	30752	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.005391	0.403226	
chunk0206_37_1	chr9	116525066	116525487	+	0	NA	intron (NR_033973, intron 1 of 11)	THE1D-int|LTR|ERVL-MaLR	20993	NR_033973	100128505	Hs.675821	NR_033973	ENSG00000229105	ASTN2-AS1	-	ASTN2 antisense RNA 1	ncRNA	0.007126	0.466825	254(GTGGACAGTATGTGCT,-,0.00),255(TGGACAGTATGTGCTG,+,0.00)
chunk0044_341_1	chr12	38570796	38571361	+	0	NA	Intergenic	L1MA1|LINE|L1	254323	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.005310	0.386926	
chunk0080_315_1	chr17	31880156	31880828	+	0	NA	intron (NM_018428, intron 11 of 18)	intron (NM_018428, intron 11 of 18)	-21185	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.019345	0.473997	
chunk0097_136_1	chr2	47233027	47233317	+	0	NA	intron (NR_110207, intron 1 of 2)	MIRb|SINE|MIR	-56236	NM_001305625	805	Hs.468442	NM_001743	ENSG00000143933	CALM2	CALM|CALML2|CAM1|CAM3|CAMC|CAMII|CAMIII|LQT15|PHKD|PHKD2|caM	calmodulin 2	protein-coding	0.017241	0.463918	
chunk0070_365_1	chr15	76233872	76234511	+	0	NA	intron (NM_000126, intron 9 of 11)	intron (NM_000126, intron 9 of 11)	25961	NR_028510	7302	Hs.684881	NR_002721		TYRO3P	-	TYRO3P protein tyrosine kinase pseudogene	pseudo	0.001565	0.365625	
chunk0182_345_1	chr7	99460402	99460814	+	0	NA	intron (NM_001003713, intron 1 of 3)	MIR|SINE|MIR	5593	NM_001003713	9551	Hs.521056	NM_004889	ENSG00000241468	ATP5MF	ATP5J2|ATP5JL	ATP synthase membrane subunit f	protein-coding	0.026699	0.496368	
chunk0111_391_1	chr20	34159121	34159746	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-47077	NM_003908	8894	Hs.429180	NM_003908	ENSG00000125977	EIF2S2	EIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta	eukaryotic translation initiation factor 2 subunit beta	protein-coding	0.014400	0.447284	
chunk0162_247_1	chr6	4982084	4982310	+	0	NA	Intergenic	MER34B|LTR|ERV1	-21619	NR_126017	100129461	Hs.131700	NR_126015	ENSG00000272142	LYRM4-AS1	-	LYRM4 antisense RNA 1	ncRNA	0.026549	0.528634	
chunk0056_345_1	chr13	91656620	91656961	+	0	NA	intron (NM_004466, intron 2 of 7)	intron (NM_004466, intron 2 of 7)	258171	NM_004466	2262	Hs.655675	NM_004466	ENSG00000179399	GPC5	-	glypican 5	protein-coding	0.008798	0.353801	
chunk0014_187_1	chr1	178745257	178745764	+	0	NA	intron (NM_001286247, intron 1 of 18)	L1MEc|LINE|L1	20363	NM_152663	55103	Hs.632485	NM_018037	ENSG00000116191	RALGPS2	dJ595C2.1	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.003945	0.328740	
chunk0041_171_1	chr11	126115952	126116290	+	0	NA	Intergenic	Intergenic	-52829	NM_016952	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.035503	0.566372	
chunk0013_330_1	chr1	171663260	171664054	+	0	NA	Intergenic	Intergenic	-11024	NM_000261	4653	Hs.436037	NM_000261	ENSG00000034971	MYOC	GLC1A|GPOA|JOAG|JOAG1|TIGR	myocilin	protein-coding	0.010076	0.401258	237(GAGAACAGTGTGTCCT,-,0.00),238(AGAACAGTGTGTCCTT,+,0.00),614(AAGAACATAATGTGAT,-,0.00)
chunk0024_291_1	chr10	42084909	42085117	+	0	NA	Intergenic	Intergenic	283032	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.048077	0.358852	
chunk0100_252_1	chr2	113117121	113117342	+	0	NA	promoter-TSS (NM_000577)	promoter-TSS (NM_000577)	-662	NM_000577	3557	Hs.81134	NM_000577	ENSG00000136689	IL1RN	DIRA|ICIL-1RA|IL-1RN|IL-1ra|IL-1ra3|IL1F3|IL1RA|IRAP|MVCD4	interleukin 1 receptor antagonist	protein-coding	0.018100	0.536036	
chunk0138_111_1	chr4	36214580	36214779	+	0	NA	intron (NM_015230, intron 2 of 32)	intron (NM_015230, intron 2 of 32)	-29437	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.000000	0.270000	159(AAGGACATTTTGTACA,-,0.00),160(AGGACATTTTGTACAA,+,0.00)
chunk0044_404_1	chr12	41044170	41044582	+	0	NA	intron (NM_175038, intron 21 of 21)	intron (NM_175038, intron 21 of 21)	136019	NM_175038	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.000000	0.285714	
chunk0063_83_1	chr14	77802991	77803190	+	0	NA	intron (NM_020421, intron 1 of 10)	intron (NM_020421, intron 1 of 10)	3007	NM_020421	57143	Hs.413208	NM_020421	ENSG00000063761	ADCK1	-	aarF domain containing kinase 1	protein-coding	0.000000	0.455000	
chunk0012_182_1	chr1	159380071	159380447	+	0	NA	Intergenic	L1MB2|LINE|L1	-59463	NM_012351	26476	Hs.532661	NM_012351	ENSG00000196184	OR10J1	HGMP07J|HSHGMP07J	olfactory receptor family 10 subfamily J member 1	protein-coding	0.000000	0.283820	
chunk0003_449_1	chr1	41458213	41458626	+	0	NA	Intergenic	Intergenic	26264	NM_001956	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.007264	0.415459	
chunk0164_242_1	chr6	23305540	23305893	+	0	NA	Intergenic	Intergenic	736267	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.002833	0.384181	
chunk0149_303_1	chr5	25734811	25735443	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-894544	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.004747	0.295419	
chunk0048_139_1	chr12	80031247	80032322	+	0	NA	Intergenic	Intergenic	-96329	NM_001244990	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.004651	0.420074	436(GAGAACAGAATGTACT,-,0.00),437(AGAACAGAATGTACTT,+,0.00)
chunk0022_128_1	chr10	11655873	11656215	+	0	NA	Intergenic	L1MC4|LINE|L1	-44255	NM_014688	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.000000	0.384840	98(ATGACACAGTGTACTT,+,0.00)
chunk0046_315_1	chr12	62506804	62507400	+	0	NA	intron (NM_001278469, intron 7 of 35)	intron (NM_001278469, intron 7 of 35)	40285	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.000000	0.324958	291(CAGCTCATCATGTTCT,-,0.00),292(AGCTCATCATGTTCTG,+,0.00)
chunk0037_217_1	chr11	74806137	74806834	+	0	NA	intron (NM_001098638, intron 2 of 5)	L1ME3A|LINE|L1	57617	NM_001098638	254225	Hs.370145	NM_001098638	ENSG00000166439	RNF169	-	ring finger protein 169	protein-coding	0.004304	0.339542	331(GAGAACAGTGTGTATA,-,0.00)
chunk0136_20_1	chr4	451008	451207	+	0	NA	intron (NM_133474, intron 2 of 2)	L1MB2|LINE|L1	23102	NR_002451	79963	Hs.677493	NM_024903	ENSG00000251595	ABCA11P	ABCA11|EST1133530	ATP binding cassette subfamily A member 11, pseudogene	pseudo	0.005025	0.275000	
chunk0134_296_1	chr3	180169147	180169474	+	0	NA	Intergenic	L1MA5A|LINE|L1	-132257	NM_001256750	51555	Hs.235331	NM_016559	ENSG00000114757	PEX5L	PEX5R|PEX5RP|PXR2|PXR2B|TRIP8b	peroxisomal biogenesis factor 5 like	protein-coding	0.006116	0.509146	114(GTGCACACTTTGTGCT,-,0.00),115(TGCACACTTTGTGCTC,+,0.00)
chunk0028_116_1	chr10	84511137	84511496	+	0	NA	intron (NM_001284243, intron 7 of 7)	intron (NM_001284243, intron 7 of 7)	86134	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.005571	0.325000	
chunk0053_447_1	chr13	39900057	39900860	+	0	NA	Intergenic	Intergenic	-236323	NR_036190	100422940		NR_036190	ENSG00000264171	MIR4305	-	microRNA 4305	ncRNA	0.004981	0.402985	
chunk0057_123_1	chr13	99382464	99382759	+	0	NA	intron (NM_001144072, intron 8 of 8)	intron (NM_001144072, intron 8 of 8)	26480	NR_030353	693208		NR_030353	ENSG00000207719	MIR623	MIRN623|hsa-mir-623	microRNA 623	ncRNA	0.016949	0.581081	
chunk0025_408_1	chr10	59648725	59649139	+	0	NA	Intergenic	Intergenic	60959	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.016908	0.426506	
chunk0055_93_1	chr13	55255942	55256367	+	0	NA	Intergenic	Intergenic	81700	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.004706	0.262911	
chunk0183_333_1	chr7	108286754	108287177	+	0	NA	intron (NM_001193582, intron 3 of 30)	intron (NM_001193582, intron 3 of 30)	-46795	NM_001037132	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.014184	0.332547	
chunk0174_212_1	chr6	160364894	160365098	+	0	NA	intron (NM_021977, intron 1 of 10)	intron (NM_021977, intron 1 of 10)	16623	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.000000	0.214634	
chunk0017_441_1	chr1	214216674	214217112	+	0	NA	Intergenic	Intergenic	-64329	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.002283	0.425968	
chunk0020_100_1	chr1	232938093	232938374	+	0	NA	Intergenic	Intergenic	-12391	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.014235	0.436170	
chunk0043_176_1	chr12	17257136	17257378	+	0	NA	Intergenic	Intergenic	268510	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.004132	0.366255	164(AAGAACACTATGAACC,-,0.00),165(AGAACACTATGAACCT,+,0.00)
chunk0074_308_1	chr16	30437373	30437888	+	0	NA	Intergenic	L2a|LINE|L2	-7578	NM_024096	79077	Hs.632191	NM_024096	ENSG00000179958	DCTPP1	CDA03|RS21C6|XTP3TPA	dCTP pyrophosphatase 1	protein-coding	0.005825	0.453488	
chunk0030_153_1	chr10	113914971	113915452	+	0	NA	Intergenic	Intergenic	60579	NM_198514	374354	Hs.369924	NM_198514	ENSG00000196865	NHLRC2	FINCA	NHL repeat containing 2	protein-coding	0.004158	0.419087	217(AAGGACATTTTGTTCT,-,0.00),218(AGGACATTTTGTTCTG,+,0.00)
chunk0125_56_1	chr3	64040909	64041278	+	0	NA	Intergenic	Intergenic	-17083	NM_001271780	9861	Hs.152536	NM_014814	ENSG00000163636	PSMD6	Rpn7|S10|SGA-113M|p42A|p44S10	proteasome 26S subunit, non-ATPase 6	protein-coding	0.002710	0.343243	
chunk0074_229_1	chr16	27173836	27174410	+	0	NA	Intergenic	Intergenic	-29363	NM_024773	79831	Hs.145717	NM_024773	ENSG00000155666	KDM8	JMJD5	lysine demethylase 8	protein-coding	0.017422	0.509565	
chunk0131_195_1	chr3	148608792	148609051	+	0	NA	Intergenic	L1PB1|LINE|L1	-88950	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.011583	0.357692	
chunk0113_396_1	chr20	60216287	60216801	+	0	NA	intron (NR_046099, intron 3 of 4)	L1ME4b|LINE|L1	78052	NR_046099	284757	Hs.542528	NM_001004305	ENSG00000228340	MIR646HG	-	MIR646 host gene	ncRNA	0.015564	0.431068	
chunk0159_346_1	chr5	144198204	144198744	+	0	NA	intron (NM_020768, intron 2 of 3)	intron (NM_020768, intron 2 of 3)	27601	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.007407	0.390018	
chunk0161_134_1	chr5	168362003	168362661	+	0	NA	intron (NM_001161661, intron 1 of 22)	MIR|SINE|MIR	70272	NM_001161661	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.007599	0.438543	
chunk0199_156_1	chr9	4276530	4277125	+	0	NA	intron (NM_001042413, intron 2 of 10)	intron (NM_001042413, intron 2 of 10)	23208	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.008403	0.375839	
chunk0151_411_1	chr5	55629816	55630044	+	0	NA	intron (NM_001282429, intron 13 of 14)	Charlie1a|DNA|hAT-Charlie	63123	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.008772	0.340611	
chunk0153_177_1	chr5	71561470	71561827	+	0	NA	intron (NM_018429, intron 37 of 38)	MER58A|DNA|hAT-Charlie	-25640	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.011204	0.424581	200(TAGAGCATACTGTGCT,-,0.00),201(AGAGCATACTGTGCTG,+,0.00)
chunk0019_181_1	chr1	226534529	226534728	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-14172	NM_001003665	375057	Hs.116827	NM_001003665	ENSG00000203685	STUM	C1orf95	stum, mechanosensory transduction mediator homolog	protein-coding	0.000000	0.440000	
chunk0153_166_1	chr5	71291077	71291524	+	0	NA	Intergenic	Intergenic	-32005	NR_033968	100049076	Hs.665231	NR_033968		GUSBP9	-	GUSB pseudogene 9	pseudo	0.006711	0.341518	
chunk0194_52_1	chr8	82057171	82058002	+	0	NA	Intergenic	Intergenic	-215300	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.002407	0.365385	
chunk0213_33_1	chrY	56846085	56846386	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-108020	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.006645	0.490066	
chunk0026_381_1	chr10	69425818	69426153	+	0	NA	Intergenic	Intergenic	-9067	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.011940	0.446429	
chunk0170_216_1	chr6	113129312	113130010	+	0	NA	Intergenic	L2c|LINE|L2	520414	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.008596	0.399142	
chunk0180_277_1	chr7	69830423	69830884	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	231734	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.008677	0.318182	
chunk0072_246_1	chr15	96051550	96051948	+	0	NA	Intergenic	Intergenic	-274179	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.007538	0.413534	206(CTGAACTTTCTGTACC,-,0.00),207(TGAACTTTCTGTACCC,+,0.00)
chunk0180_266_1	chr7	69647778	69648101	+	0	NA	intron (NM_015570, intron 1 of 18)	MLT1C|LTR|ERVL-MaLR	49020	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.006192	0.410494	
chunk0080_73_1	chr17	22125602	22125871	+	0	NA	Intergenic	Intergenic	-173028	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.000000	0.274074	
chunk0206_96_1	chr9	120707209	120707515	+	0	NA	intron (NM_001080497, intron 1 of 5)	MER46C|DNA|TcMar-Tigger	7125	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.006536	0.371336	
chunk0101_155_1	chr2	128231033	128231739	+	0	NA	Intergenic	L1ME1|LINE|L1	87211	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.009915	0.411598	
chunk0118_12_1	chr22	25628324	25629025	+	0	NA	intron (NM_005160, intron 2 of 20)	intron (NM_005160, intron 2 of 20)	63780	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.008559	0.423077	
chunk0103_179_1	chr2	163254849	163255487	+	0	NA	Intergenic	Intergenic	-416421	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.003135	0.350548	
chunk0152_45_1	chr5	57243950	57244611	+	0	NA	intron (NM_022913, intron 6 of 11)	intron (NM_022913, intron 6 of 11)	30206	NM_001127236	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.000000	0.351964	
chunk0061_420_1	chr14	65118128	65118878	+	0	NA	Intergenic	Intergenic	-15808	NR_073137	4149	Hs.285354	NM_002382	ENSG00000125952	MAX	bHLHd4	MYC associated factor X	protein-coding	0.009333	0.414115	406(AGGAACACAGTGTCCT,-,0.00),407(GGAACACAGTGTCCTT,+,0.00)
chunk0207_205_1	chr9	131347587	131347890	+	0	NA	Intergenic	Intergenic	58044	NM_032728	84814	Hs.134292	NM_032728	ENSG00000160539	PLPP7	C9orf67|NET39|PPAPDC3	phospholipid phosphatase 7 (inactive)	protein-coding	0.039604	0.588816	
chunk0130_292_1	chr3	136752391	136752648	+	0	NA	promoter-TSS (NM_005862)	promoter-TSS (NM_005862)	-116	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.128405	0.724806	
chunk0118_73_1	chr22	28813663	28814064	+	0	NA	Intergenic	Intergenic	-13291	NM_005080	7494	Hs.437638	NM_005080	ENSG00000100219	XBP1	TREB-5|TREB5|XBP-1|XBP2	X-box binding protein 1	protein-coding	0.007481	0.460199	
chunk0178_200_1	chr7	34504711	34505056	+	0	NA	intron (NR_033665, intron 2 of 3)	intron (NR_033665, intron 2 of 3)	-153356	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.011594	0.494220	
chunk0018_266_1	chr1	220458038	220458375	+	0	NA	Intergenic	MER61B|LTR|ERV1	-69977	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.008902	0.500000	
chunk0027_359_1	chr10	78973926	78974180	+	0	NA	intron (NR_015429, intron 3 of 7)	CpG	93395	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.106299	0.698039	
chunk0018_277_1	chr1	220588852	220589198	+	0	NA	intron (NM_001286128, intron 3 of 15)	intron (NM_001286128, intron 3 of 15)	60842	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.008671	0.461095	210(AGGAACAAGCTGAACC,-,0.00)
chunk0203_326_1	chr9	89664745	89665381	+	0	NA	non-coding (NR_024280, exon 2 of 6)	non-coding (NR_024280, exon 2 of 6)	25280	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.023585	0.562009	327(AGGAACAAAGTGTTCC,-,0.00),328(GGAACAAAGTGTTCCG,+,0.00)
chunk0006_370_1	chr1	73226123	73226369	+	0	NA	Intergenic	Intergenic	-79924	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.004065	0.311741	
chunk0080_12_1	chr17	20933401	20933934	+	0	NA	Intergenic	Intergenic	-4853	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.005629	0.426966	
chunk0072_375_1	chr15	100042932	100043247	+	0	NA	intron (NM_139057, intron 18 of 21)	intron (NM_139057, intron 18 of 21)	-236162	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.009524	0.373418	
chunk0169_133_1	chr6	101194732	101194953	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-204143	NM_001166247	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004525	0.324324	
chunk0081_51_1	chr17	38320562	38320959	+	0	NA	exon (NM_032351, exon 6 of 8).2	exon (NM_032351, exon 6 of 8).2	23050	NM_001004334	440435	Hs.462915	NM_001004334	ENSG00000277399	GPR179	CSNB1E|GPR158L|GPR158L1	G protein-coupled receptor 179	protein-coding	0.025189	0.500000	312(AGGTACACTGTGATCT,-,0.00),313(GGTACACTGTGATCTG,+,0.00)
chunk0053_22_1	chr13	26635565	26636055	+	0	NA	intron (NM_006646, intron 2 of 9)	L1PA6|LINE|L1	78107	NM_001291965	10810	Hs.618732	NM_006646	ENSG00000132970	WASF3	Brush-1|SCAR3|WAVE3	WASP family member 3	protein-coding	0.014286	0.488798	
chunk0068_309_1	chr15	57205232	57205914	+	0	NA	intron (NM_003205, intron 8 of 19)	intron (NM_003205, intron 8 of 19)	-13857	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.007331	0.366032	
chunk0160_246_1	chr5	156590251	156590685	+	0	NA	intron (NM_000337, intron 5 of 8)	intron (NM_000337, intron 5 of 8)	-260070	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.006912	0.434483	
chunk0108_136_1	chr2	230630539	230631166	+	0	NA	Intergenic	L1MC1|LINE|L1	69677	NR_040038	151475	Hs.528154	NR_040038	ENSG00000226125	LINC01907	-	long intergenic non-protein coding RNA 1907	ncRNA	0.007974	0.386943	
chunk0117_171_1	chr22	20450253	20450819	+	0	NA	intron (NR_033825, intron 4 of 5)	intron (NR_033825, intron 4 of 5)	-12677	NM_153334	91179	Hs.474251	NM_153334	ENSG00000244486	SCARF2	NSR1|SREC-II|SREC2|SRECRP-1|VDEGS	scavenger receptor class F member 2	protein-coding	0.003534	0.456790	
chunk0071_56_1	chr15	80198518	80198922	+	0	NA	non-coding (NR_120317, exon 3 of 3)	non-coding (NR_120317, exon 3 of 3)	45829	NM_000137	2184	Hs.73875	NM_000137	ENSG00000103876	FAH	-	fumarylacetoacetate hydrolase	protein-coding	0.007426	0.390123	
chunk0086_45_1	chr18	12675327	12675766	+	0	NA	intron (NM_024899, intron 10 of 11)	L2c|LINE|L2	16807	NM_147163	56984	Hs.464652	NM_020232	ENSG00000128789	PSMG2	CLAST3|HCCA3|HsT1707|MDS003|PAC2|TNFSF5IP1	proteasome assembly chaperone 2	protein-coding	0.013667	0.356818	
chunk0112_370_1	chr20	45779063	45779474	+	0	NA	intron (NM_080614, intron 4 of 6)	intron (NM_080614, intron 4 of 6)	12640	NM_080614	140686	Hs.419126	NM_080614	ENSG00000124116	WFDC3	WAP14|dJ447F3.3	WAP four-disulfide core domain 3	protein-coding	0.009732	0.451456	
chunk0088_279_1	chr18	49446257	49446826	+	0	NA	intron (NM_017653, intron 1 of 16)	intron (NM_017653, intron 1 of 16)	14168	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.005272	0.354386	
chunk0171_389_1	chr6	131122541	131123036	+	0	NA	Intergenic	Intergenic	-12898	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.004040	0.304435	
chunk0195_446_1	chr8	101326965	101327169	+	0	NA	Intergenic	Intergenic	-41826	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.024510	0.434146	72(TGGAACACAGAGTGCT,-,0.00),73(GGAACACAGAGTGCTG,+,0.00)
chunk0018_205_1	chr1	219371605	219371826	+	0	NA	Intergenic	MER57B2|LTR|ERV1	196746	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.009050	0.418919	
chunk0163_74_1	chr6	9345224	9345702	+	0	NA	Intergenic	Intergenic	693254	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.006276	0.365344	
chunk0207_277_1	chr9	132431137	132431336	+	0	NA	intron (NM_001282957, intron 1 of 5)	L1MEb|LINE|L1	21040	NM_207417	389799	Hs.201709	NM_207417	ENSG00000188523	CFAP77	C9orf171	cilia and flagella associated protein 77	protein-coding	0.005025	0.345000	
chunk0049_206_1	chr12	93156061	93156590	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-18041	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.015123	0.475472	
chunk0124_88_1	chr3	53484798	53485465	+	0	NA	Intergenic	Intergenic	-9918	NM_000720	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.002999	0.377246	207(TGGGACAAGATGTCCA,-,0.00),208(GGGACAAGATGTCCAA,+,0.00)
chunk0053_48_1	chr13	27572218	27572537	+	0	NA	intron (NM_153371, intron 2 of 9)	intron (NM_153371, intron 2 of 9)	48206	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.000000	0.428125	151(CAGAACAGCATGTGAC,-,0.00)
chunk0158_193_1	chr5	127958279	127958966	+	0	NA	Intergenic	Intergenic	124452	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.005822	0.395349	
chunk0117_214_1	chr22	22095351	22096099	+	0	NA	Intergenic	L1PA16|LINE|L1	-112882	NM_001282112	8940	Hs.436401	NM_003935	ENSG00000100038	TOP3B	TOP3B1	DNA topoisomerase III beta	protein-coding	0.008021	0.423231	
chunk0042_190_1	chr12	5250921	5251120	+	0	NA	Intergenic	Intergenic	-7869	NR_120477	101929584	Hs.436529	NR_120476	ENSG00000256115	LINC02443	-	long intergenic non-protein coding RNA 2443	ncRNA	0.000000	0.375000	
chunk0055_255_1	chr13	63345788	63346400	+	0	NA	Intergenic	L2b|LINE|L2	-18000	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.000000	0.332790	
chunk0135_335_1	chr3	190268601	190269392	+	0	NA	Intergenic	Intergenic	53450	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.005057	0.367424	
chunk0169_435_1	chr6	108710086	108710509	+	0	NA	Intergenic	Intergenic	-41357	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.004728	0.448113	
chunk0061_280_1	chr14	61542604	61543006	+	0	NA	intron (NM_006255, intron 12 of 13)	intron (NM_006255, intron 12 of 13)	27389	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.012438	0.429280	122(AGAACAGGATGGACTT,+,0.00),227(GGGAACAGAGTGTTTA,-,0.00),228(GGAACAGAGTGTTTAG,+,0.00)
chunk0098_120_1	chr2	68730912	68731131	+	0	NA	Intergenic	Intergenic	-3760	NM_001007231	9938	Hs.531807	NM_014882	ENSG00000163219	ARHGAP25	HEL-S-308|KAIA0053	Rho GTPase activating protein 25	protein-coding	0.013699	0.440909	
chunk0122_469_1	chr3	40020030	40020707	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	-79643	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.008863	0.387906	
chunk0165_394_1	chr6	38803058	38803681	+	0	NA	intron (NM_001206927, intron 22 of 92)	MER68|LTR|ERVL	88028	NM_001206927	1769	Hs.520106	NM_001371	ENSG00000124721	DNAH8	ATPase|hdhc9	dynein axonemal heavy chain 8	protein-coding	0.008026	0.358974	
chunk0083_236_1	chr17	67556914	67557214	+	0	NA	intron (NM_181671, intron 4 of 9)	MLT1A|LTR|ERVL-MaLR	-85479	NR_030385	693131		NR_030385	ENSG00000263690	MIR548D2	MIRN548D2	microRNA 548d-2	ncRNA	0.010000	0.514950	
chunk0030_64_1	chr10	111984886	111985201	+	0	NA	Intergenic	Intergenic	198736	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.006349	0.335443	
chunk0183_76_1	chr7	104595006	104595930	+	0	NA	intron (NM_199000, intron 1 of 2)	L1P2|LINE|L1	208624	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.016234	0.492973	
chunk0153_105_1	chr5	68534233	68534847	+	0	NA	Intergenic	Intergenic	241972	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.014658	0.549593	280(GGTACAGGCTCTTCTC,+,0.00)
chunk0132_61_1	chr3	155149271	155150077	+	0	NA	intron (NM_000902, intron 16 of 22)	intron (NM_000902, intron 16 of 22)	69384	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.004963	0.366791	270(TGGAACACGAAGTCCA,-,0.00),271(GGAACACGAAGTCCAG,+,0.00)
chunk0180_205_1	chr7	66429875	66430357	+	0	NA	Intergenic	Intergenic	-29708	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.006224	0.405797	
chunk0101_453_1	chr2	140127083	140127334	+	0	NA	Intergenic	L1MEd|LINE|L1	459477	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.007968	0.285714	
chunk0013_4_1	chr1	165685480	165685912	+	0	NA	intron (NM_000696, intron 2 of 10)	intron (NM_000696, intron 2 of 10)	12967	NM_000696	223	Hs.2533	NM_000696	ENSG00000143149	ALDH9A1	ALDH4|ALDH7|ALDH9|E3|TMABADH	aldehyde dehydrogenase 9 family member A1	protein-coding	0.006944	0.452656	
chunk0013_293_1	chr1	171141420	171141913	+	0	NA	intron (NR_002601, intron 1 of 6)	intron (NR_002601, intron 1 of 6)	3926	NR_002601	388714	Hs.448988	NR_002601	ENSG00000117507	FMO6P	FMO6	flavin containing dimethylaniline monoxygenase 6, pseudogene	pseudo	0.006085	0.439271	
chunk0059_243_1	chr14	34875020	34875324	+	0	NA	5' UTR (NM_013448, exon 1 of 27)	5' UTR (NM_013448, exon 1 of 27)	475	NM_182648	11177	Hs.509140	NM_013448	ENSG00000198604	BAZ1A	ACF1|WALp1|WCRF180|hACF1	bromodomain adjacent to zinc finger domain 1A	protein-coding	0.128289	0.740984	
chunk0198_434_1	chr8	143445986	143446351	+	0	NA	intron (NM_015117, intron 9 of 11)	L1M5|LINE|L1	-15736	NM_201589	389692		NM_201589	ENSG00000182759	MAFA	INSDM|RIPE3b1|hMafA	MAF bZIP transcription factor A	protein-coding	0.027397	0.459016	
chunk0156_81_1	chr5	104295060	104295862	+	0	NA	Intergenic	Intergenic	-732660	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.003741	0.346202	
chunk0208_441_1	chrX	30880220	30880419	+	0	NA	intron (NM_152787, intron 1 of 10)	L1ME3A|LINE|L1	9075	NM_152787	257397	Hs.188256	NM_152787	ENSG00000157625	TAB3	MAP3K7IP3|NAP1	TGF-beta activated kinase 1 (MAP3K7) binding protein 3	protein-coding	0.010050	0.375000	
chunk0211_370_1	chrX	126317549	126318150	+	0	NA	Intergenic	MER83|LTR|ERV1	-151752	NM_001013628	340578	Hs.181867	NM_001013628	ENSG00000198354	DCAF12L2	WDR40C	DDB1 and CUL4 associated factor 12 like 2	protein-coding	0.009983	0.403654	254(CAGGACACATAGTCCT,-,0.00),255(AGGACACATAGTCCTC,+,0.00)
chunk0194_109_1	chr8	83602126	83602807	+	0	NA	Intergenic	L1PA6|LINE|L1	198708	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.005874	0.492669	
chunk0036_125_1	chr11	61695279	61696124	+	0	NA	intron (NM_006133, intron 1 of 19)	intron (NM_006133, intron 1 of 19)	15268	NM_006133	747	Hs.241564	NM_006133	ENSG00000134780	DAGLA	C11orf11|DAGL(ALPHA)|DAGLALPHA|NSDDR	diacylglycerol lipase alpha	protein-coding	0.020118	0.609929	339(AGGGACAGAATGTCCT,-,0.00),340(GGGACAGAATGTCCTG,+,0.00)
chunk0180_84_1	chr7	55019202	55019721	+	0	NA	intron (NM_201283, intron 1 of 9)	CpG	429	NM_005228	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.138728	0.732692	
chunk0072_86_1	chr15	90860524	90861584	+	0	NA	Intergenic	MIRb|SINE|MIR	-7538	NM_002569	5045	Hs.513153	NM_002569	ENSG00000140564	FURIN	FUR|PACE|PCSK3|SPC1	furin, paired basic amino acid cleaving enzyme	protein-coding	0.016981	0.473139	156(GGAACTCTTAGTCCTT,+,0.00)
chunk0167_298_1	chr6	71253764	71254099	+	0	NA	Intergenic	MER39|LTR|ERV1	-34843	NM_024576	79627	Hs.648434	NM_024576	ENSG00000119900	OGFRL1	dJ331H24.1	opioid growth factor receptor like 1	protein-coding	0.002985	0.443452	141(GAAGACAGGATGTTCC,-,0.00),142(AAGACAGGATGTTCCT,+,0.00)
chunk0015_202_1	chr1	187396225	187396576	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-47228	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.443182	
chunk0070_313_1	chr15	75182756	75183011	+	0	NA	Intergenic	Intergenic	-18997	NM_015492	56905	Hs.17936	NM_015492	ENSG00000167173	C15orf39	-	chromosome 15 open reading frame 39	protein-coding	0.007843	0.593750	105(AGGCACAGGATGTCCA,-,0.00),106(GGCACAGGATGTCCAG,+,0.00)
chunk0192_391_1	chr8	68754139	68754724	+	0	NA	intron (NM_052958, intron 10 of 13)	intron (NM_052958, intron 10 of 13)	349759	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.006838	0.354949	
chunk0115_318_1	chr21	28744195	28744479	+	0	NA	Intergenic	Intergenic	141036	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.003521	0.312281	
chunk0080_363_1	chr17	33079066	33079596	+	0	NA	intron (NM_183377, intron 3 of 9)	L2c|LINE|L2	87467	NM_173847	124912	Hs.434112	NM_173847	ENSG00000141316	SPACA3	ALLP17|CT54|LYC3|LYZC|LYZL3|SLLP1	sperm acrosome associated 3	protein-coding	0.007547	0.448211	
chunk0131_2_1	chr3	141642304	141642592	+	0	NA	Intergenic	Intergenic	-95761	NM_014245	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.006944	0.397924	
chunk0203_40_1	chr9	83064203	83064630	+	0	NA	Intergenic	Intergenic	-1288	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.000000	0.296729	
chunk0148_321_1	chr5	13944639	13945961	+	0	NA	promoter-TSS (NM_001369)	promoter-TSS (NM_001369)	-820	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.010590	0.431595	
chunk0095_176_1	chr2	17729810	17730539	+	0	NA	intron (NM_024624, intron 6 of 26)	MIR1_Amn|SINE|MIR	23655	NM_024624	79677	Hs.526728	NM_024624	ENSG00000163029	SMC6	SMC-6|SMC6L1|hSMC6	structural maintenance of chromosomes 6	protein-coding	0.002743	0.358904	415(AGAACTACATGTACCC,+,0.00)
chunk0030_455_1	chr10	121137537	121138034	+	0	NA	Intergenic	Intergenic	-286606	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.002012	0.395582	
chunk0082_81_1	chr17	51850103	51850500	+	0	NA	intron (NM_001082534, intron 4 of 9)	intron (NM_001082534, intron 4 of 9)	308471	NM_020178	56934	Hs.463466	NM_020178	ENSG00000154975	CA10	CA-RPX|CARPX|HUCEP-15	carbonic anhydrase 10	protein-coding	0.007557	0.396985	190(AGGAACACGGAGATCC,-,0.00)
chunk0095_167_1	chr2	17336281	17337021	+	0	NA	Intergenic	Intergenic	181788	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.002703	0.376518	
chunk0178_351_1	chr7	38791451	38791833	+	0	NA	intron (NM_080631, intron 8 of 27)	intron (NM_080631, intron 8 of 27)	-104553	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.007853	0.467363	
chunk0018_84_1	chr1	217471286	217471876	+	0	NA	intron (NM_018040, intron 8 of 9)	intron (NM_018040, intron 8 of 9)	159521	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.003390	0.313029	
chunk0127_164_1	chr3	94813225	94813615	+	0	NA	Intergenic	Intergenic	-124843	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.283887	
chunk0113_152_1	chr20	52606188	52606820	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-14334	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.011076	0.409163	
chunk0017_19_1	chr1	204433072	204433420	+	0	NA	intron (NM_002646, intron 27 of 33)	intron (NM_002646, intron 27 of 33)	-21429	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.014368	0.507163	
chunk0004_353_1	chr1	51329159	51329684	+	0	NA	promoter-TSS (NR_123731)	promoter-TSS (NR_123731)	-233	NR_123731	102724097	Hs.568648	NR_123731	ENSG00000261664	TTC39A-AS1	-	TTC39A antisense RNA 1	ncRNA	0.009524	0.558935	181(AGGAACAGCCAGCCCC,-,0.00),306(CAGGCCAGGGTGTCCC,-,0.00),307(AGGCCAGGGTGTCCCC,+,0.00)
chunk0060_343_1	chr14	52005671	52006015	+	0	NA	exon (NM_007361, exon 21 of 22)	exon (NM_007361, exon 21 of 22)	16333	NM_016039	51637	Hs.534457	NM_016039	ENSG00000087302	RTRAF	C14orf166|CGI-99|CGI99|CLE|CLE7|LCRP369|RLLM1|hCLE|hCLE1	RNA transcription, translation and transport factor	protein-coding	0.005814	0.420290	
chunk0162_313_1	chr6	6688207	6688870	+	0	NA	Intergenic	(TTTCCC)n|Simple_repeat|Simple_repeat	-65712	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.001508	0.400602	
chunk0147_37_1	chr4	172024477	172025140	+	0	NA	intron (NM_001034845, intron 2 of 12)	(CTTC)n|Simple_repeat|Simple_repeat	211384	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.003017	0.337349	
chunk0109_454_1	chr2	241833242	241833625	+	0	NA	Intergenic	L1MC1|LINE|L1	22501	NM_080741	129807	Hs.551747	NM_080741	ENSG00000204099	NEU4	-	neuraminidase 4	protein-coding	0.026110	0.411458	
chunk0176_437_1	chr7	19964473	19964813	+	0	NA	intron (NR_110114, intron 4 of 5)	intron (NR_110114, intron 4 of 5)	175783	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.005882	0.404692	
chunk0160_86_1	chr5	150024427	150024626	+	0	NA	exon (NM_014983, exon 7 of 20)	exon (NM_014983, exon 7 of 20)	-23359	NM_030953	81789	Hs.169333	NM_030953	ENSG00000164296	TIGD6	-	tigger transposable element derived 6	protein-coding	0.025126	0.535000	
chunk0202_453_1	chr9	82556803	82557243	+	0	NA	Intergenic	Intergenic	506105	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.004545	0.396825	160(GAGCACAAAGTGTTCT,-,0.00),161(AGCACAAAGTGTTCTA,+,0.00)
chunk0109_209_1	chr20	5345005	5345204	+	0	NA	Intergenic	Intergenic	-30735	NM_144773	128674	Hs.375029	NM_144773	ENSG00000101292	PROKR2	GPR73L1|GPR73b|GPRg2|HH3|KAL3|PKR2|dJ680N4.3	prokineticin receptor 2	protein-coding	0.000000	0.485000	
chunk0011_96_1	chr1	145860665	145860937	+	0	NA	Intergenic	L2c|LINE|L2	-1720	NM_006099	10401	Hs.435761	NM_006099	ENSG00000131788	PIAS3	ZMIZ5	protein inhibitor of activated STAT 3	protein-coding	0.018382	0.435897	
chunk0178_249_1	chr7	36186698	36187331	+	0	NA	intron (NM_030636, intron 2 of 7)	intron (NM_030636, intron 2 of 7)	33787	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.007899	0.380126	
chunk0139_126_1	chr4	53187859	53188467	+	0	NA	intron (NM_152540, intron 4 of 8)	intron (NM_152540, intron 4 of 8)	177912	NM_152540	152579	Hs.302287	NM_152540	ENSG00000184178	SCFD2	STXBP1L1	sec1 family domain containing 2	protein-coding	0.001645	0.349754	
chunk0070_306_1	chr15	74937969	74938314	+	0	NA	promoter-TSS (NM_004255)	promoter-TSS (NM_004255)	13	NM_004255	9377	Hs.401903	NM_004255	ENSG00000178741	COX5A	COX|COX-VA|VA	cytochrome c oxidase subunit 5A	protein-coding	0.130435	0.716763	
chunk0110_360_1	chr20	19785370	19785766	+	0	NA	Intergenic	Intergenic	-100953	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.005051	0.420655	
chunk0128_18_1	chr3	104127977	104128277	+	0	NA	Intergenic	Intergenic	-604011	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.010000	0.388704	
chunk0134_55_1	chr3	175988651	175989128	+	0	NA	Intergenic	L1PA17|LINE|L1	-212556	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.479079	
chunk0029_121_1	chr10	98502342	98502973	+	0	NA	intron (NM_001166246, intron 9 of 12)	L1PB1|LINE|L1	-55694	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.007924	0.365506	
chunk0057_97_1	chr13	98910308	98910996	+	0	NA	intron (NM_001130049, intron 9 of 32)	intron (NM_001130049, intron 9 of 32)	67432	NM_001130050	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.004360	0.423803	86(AAATACAGTGTGTTCT,-,0.00),87(AATACAGTGTGTTCTC,+,0.00)
chunk0041_214_1	chr11	127106880	127107277	+	0	NA	Intergenic	Intergenic	40076	NR_120578	101929473	Hs.737523	NR_120578	ENSG00000255087	LOC101929473	-	uncharacterized LOC101929473	ncRNA	0.007557	0.510050	
chunk0037_343_1	chr11	77389253	77389452	+	0	NA	intron (NM_001128620, intron 2 of 15)	L1MB8|LINE|L1	84711	NM_001128620	5058	Hs.435714	NM_002576	ENSG00000149269	PAK1	IDDMSSD|PAKalpha	p21 (RAC1) activated kinase 1	protein-coding	0.000000	0.345000	
chunk0068_340_1	chr15	57706437	57706746	+	0	NA	promoter-TSS (NM_015532)	promoter-TSS (NM_015532)	70	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.080906	0.532258	
chunk0084_189_1	chr17	77951278	77951490	+	0	NA	Intergenic	Intergenic	-52853	NM_001142640	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.014151	0.483568	
chunk0023_2_1	chr10	20605101	20605632	+	0	NA	Intergenic	Intergenic	53396	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.009416	0.349624	
chunk0186_137_1	chr7	138514464	138514912	+	0	NA	intron (NM_015905, intron 2 of 18)	L2c|LINE|L2	54354	NM_015905	8805	Hs.490287	NM_003852	ENSG00000122779	TRIM24	PTC6|RNF82|TF1A|TIF1|TIF1A|TIF1ALPHA|hTIF1	tripartite motif containing 24	protein-coding	0.008929	0.398664	81(TTGTACATGCTGTTCT,-,0.00),82(TGTACATGCTGTTCTC,+,0.00)
chunk0209_75_1	chrX	38062527	38062942	+	0	NA	intron (NM_138780, intron 3 of 16)	MER90a|LTR|ERV1	29200	NM_001163334	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.007229	0.387019	
chunk0208_304_1	chrX	23511868	23512084	+	0	NA	Intergenic	Intergenic	-155552	NM_006406	10549	Hs.83383	NM_006406	ENSG00000123131	PRDX4	AOE37-2|AOE372|HEL-S-97n|PRX-4	peroxiredoxin 4	protein-coding	0.000000	0.428571	156(ATGAACAAGCTGTTTC,-,0.00)
chunk0002_139_1	chr1	17012071	17012270	+	0	NA	promoter-TSS (NM_001141974)	promoter-TSS (NM_001141974)	-198	NM_001141974	23400	Hs.128866	NM_022089	ENSG00000159363	ATP13A2	CLN12|HSA9947|KRPPD|PARK9|SPG78	ATPase cation transporting 13A2	protein-coding	0.045226	0.580000	
chunk0146_84_1	chr4	158090370	158090569	+	0	NA	Intergenic	Intergenic	82097	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.340000	
chunk0168_219_1	chr6	86233889	86234215	+	0	NA	Intergenic	L1MA2|LINE|L1	-555319	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.003067	0.553517	
chunk0162_306_1	chr6	6593713	6594285	+	0	NA	intron (NM_004271, intron 1 of 4)	L4_B_Mam|LINE|RTE-X	5298	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.010490	0.476440	
chunk0046_363_1	chr12	63079962	63080487	+	0	NA	Intergenic	Intergenic	72586	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.000000	0.444867	332(AAGAACTCTTTGTCCT,-,0.00),333(AGAACTCTTTGTCCTC,+,0.00)
chunk0028_405_1	chr10	93260976	93261556	+	0	NA	Intergenic	Intergenic	187376	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.003448	0.402754	
chunk0159_98_1	chr5	138287437	138288001	+	0	NA	intron (NM_001287582, intron 10 of 13)	intron (NM_001287582, intron 10 of 13)	-13155	NM_001496	2676	Hs.58042	NM_001496	ENSG00000146013	GFRA3	GDNFR3	GDNF family receptor alpha 3	protein-coding	0.001773	0.373451	
chunk0039_26_1	chr11	95664160	95664947	+	0	NA	Intergenic	L1MB1|LINE|L1	125237	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.000000	0.290609	
chunk0067_455_1	chr15	50299922	50300419	+	0	NA	intron (NM_002041, intron 6 of 7)	intron (NM_002041, intron 6 of 7)	-34205	NM_002112	3067	Hs.1481	NM_002112	ENSG00000140287	HDC	-	histidine decarboxylase	protein-coding	0.002012	0.421687	
chunk0088_360_1	chr18	52945959	52946363	+	0	NA	intron (NM_005215, intron 5 of 28)	L2c|LINE|L2	-290940	NR_130465	100616232		NR_130465	ENSG00000263872	MIR4528	-	microRNA 4528	ncRNA	0.002475	0.392593	
chunk0112_269_1	chr20	43183685	43183994	+	0	NA	intron (NM_133170, intron 1 of 31)	L1MB7|LINE|L1	6078	NM_133170	11122	Hs.526879	NM_007050	ENSG00000196090	PTPRT	RPTPrho	protein tyrosine phosphatase receptor type T	protein-coding	0.012945	0.435484	
chunk0078_310_1	chr17	8332674	8333057	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-7005	NM_153007	146852	Hs.186045	NM_153007	ENSG00000184650	ODF4	CT134|CT136|OPPO1	outer dense fiber of sperm tails 4	protein-coding	0.015666	0.505208	
chunk0091_182_1	chr19	8240391	8240638	+	0	NA	intron (NM_024552, intron 2 of 11)	intron (NM_024552, intron 2 of 11)	31181	NM_024552	79603	Hs.515111	NM_024552	ENSG00000090661	CERS4	LASS4|Trh1	ceramide synthase 4	protein-coding	0.028340	0.604839	
chunk0114_47_1	chr21	8442237	8442482	+	0	NA	non-coding (NR_003287, exon 1 of 1)	non-coding (NR_003287, exon 1 of 1)	1213	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.171429	0.804878	
chunk0137_307_1	chr4	24434833	24435089	+	0	NA	Intergenic	Intergenic	85329	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.019531	0.420233	
chunk0036_31_1	chr11	58632490	58632953	+	0	NA	Intergenic	Intergenic	10048	NM_000614	1270	Hs.524920	NM_000614	ENSG00000242689	CNTF	HCNTF	ciliary neurotrophic factor	protein-coding	0.002160	0.439655	
chunk0067_64_1	chr15	40966622	40966849	+	0	NA	Intergenic	Intergenic	13297	NM_001142776	79094	Hs.155569	NM_024111	ENSG00000128965	CHAC1	-	ChaC glutathione specific gamma-glutamylcyclotransferase 1	protein-coding	0.008811	0.302632	
chunk0136_94_1	chr4	2745512	2746020	+	0	NA	intron (NM_001161527, intron 2 of 5)	intron (NM_001161527, intron 2 of 5)	10259	NM_001161527	79155	Hs.368551	NM_024309	ENSG00000168884	TNIP2	ABIN2|FLIP1|KLIP	TNFAIP3 interacting protein 2	protein-coding	0.009843	0.538310	
chunk0203_63_1	chr9	83445463	83445871	+	0	NA	intron (NM_001244959, intron 1 of 14)	intron (NM_001244959, intron 1 of 14)	22075	NM_001244960	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.000000	0.366748	
chunk0070_28_1	chr15	69296046	69296592	+	0	NA	Intergenic	Intergenic	-2636	NM_017705	54852	Hs.591096	NM_017705	ENSG00000137819	PAQR5	MPRG	progestin and adipoQ receptor family member 5	protein-coding	0.003663	0.460695	
chunk0066_436_1	chr15	39748180	39748591	+	0	NA	intron (NM_152597, intron 5 of 11)	intron (NM_152597, intron 5 of 11)	34453	NM_152597	161835	Hs.129598	NM_152597	ENSG00000150667	FSIP1	HSD10	fibrous sheath interacting protein 1	protein-coding	0.007299	0.366505	
chunk0007_434_1	chr1	86764925	86765594	+	0	NA	Intergenic	Intergenic	60689	NM_016009	51100	Hs.136309	NM_016009	ENSG00000097033	SH3GLB1	Bif-1|CGI-61|PPP1R70|dJ612B15.2	SH3 domain containing GRB2 like, endophilin B1	protein-coding	0.002990	0.402985	324(GGGAACGCCCTGTCCT,-,0.00),325(GGAACGCCCTGTCCTA,+,0.00)
chunk0022_122_1	chr10	11544837	11545276	+	0	NA	intron (NM_014688, intron 2 of 14)	intron (NM_014688, intron 2 of 14)	-12776	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.002278	0.381818	226(AGTACATCCTGAACTT,+,0.00)
chunk0070_87_1	chr15	70173913	70174133	+	0	NA	Intergenic	Intergenic	-76106	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.004545	0.470588	
chunk0154_201_1	chr5	80252678	80253025	+	0	NA	intron (NM_178276, intron 1 of 12)	MIRb|SINE|MIR	3231	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.011527	0.393678	
chunk0049_213_1	chr12	93223354	93223716	+	0	NA	intron (NR_040096, intron 2 of 4)	intron (NR_040096, intron 2 of 4)	49169	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.005525	0.396694	
chunk0012_188_1	chr1	159641130	159641676	+	0	NA	Intergenic	L1ME4b|LINE|L1	53577	NM_001639	325	Hs.507080	NM_001639	ENSG00000132703	APCS	HEL-S-92n|PTX2|SAP	amyloid P component, serum	protein-coding	0.003663	0.369287	
chunk0100_258_1	chr2	113219748	113220284	+	0	NA	intron (NM_013992, intron 8 of 8)	intron (NM_013992, intron 8 of 8)	-15511	NR_047570	654433	Hs.656660	NR_015377	ENSG00000189223	PAX8-AS1	-	PAX8 antisense RNA 1	ncRNA	0.005597	0.567970	
chunk0164_248_1	chr6	23393042	23393545	+	0	NA	Intergenic	Intergenic	-732893	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.007952	0.327381	120(AAAACAAGGTGTACCT,+,0.00),274(AGGTACAGGCAGTTCT,-,0.00),275(GGTACAGGCAGTTCTC,+,0.00)
chunk0082_373_1	chr17	60442907	60443194	+	0	NA	TTS (NM_001282476)	TTS (NM_001282476)	20546	NM_181707	124773	Hs.129312	NM_181707	ENSG00000141371	C17orf64	-	chromosome 17 open reading frame 64	protein-coding	0.003484	0.357639	
chunk0014_14_1	chr1	174426615	174426983	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	-21275	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.005435	0.314363	
chunk0096_453_1	chr2	39762456	39762864	+	0	NA	intron (NR_028102, intron 5 of 10)	Tigger10|DNA|TcMar-Tigger	16616	NM_025264	80745	Hs.468254	NM_025264	ENSG00000138050	THUMPD2	C2orf8	THUMP domain containing 2	protein-coding	0.004902	0.330073	
chunk0183_290_1	chr7	107739529	107740106	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-3880	NM_001284291	79872	Hs.592271	NM_024814	ENSG00000105879	CBLL1	HAKAI|RNF188	Cbl proto-oncogene like 1	protein-coding	0.005199	0.387543	
chunk0090_285_1	chr18	74948697	74949406	+	0	NA	intron (NM_017757, intron 7 of 7)	intron (NM_017757, intron 7 of 7)	256462	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.005642	0.329577	
chunk0077_61_1	chr16	76780540	76781018	+	0	NA	Intergenic	Intergenic	-88157	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.000000	0.342380	
chunk0141_19_1	chr4	76716211	76716422	+	0	NA	intron (NM_020859, intron 3 of 10)	intron (NM_020859, intron 3 of 10)	140765	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.018957	0.495283	52(AGGCACATGTAGTACT,-,0.00),53(GGCACATGTAGTACTT,+,0.00)
chunk0003_400_1	chr1	40024721	40025077	+	0	NA	Intergenic	L1M5|LINE|L1	-15684	NM_006367	10487	Hs.370581	NM_006367	ENSG00000131236	CAP1	CAP|CAP1-PEN	cyclase associated actin cytoskeleton regulatory protein 1	protein-coding	0.005618	0.333333	
chunk0134_184_1	chr3	178170590	178171116	+	0	NA	Intergenic	Intergenic	-248348	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.007605	0.362429	259(TGGGACATTTTGTCCA,-,0.00),260(GGGACATTTTGTCCAT,+,0.00)
chunk0090_123_1	chr18	71778440	71778930	+	0	NA	intron (NR_126324, intron 1 of 4)	intron (NR_126324, intron 1 of 4)	3541	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.006122	0.336049	
chunk0184_268_1	chr7	118462521	118463017	+	0	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	238111	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.004032	0.404427	
chunk0085_327_1	chr18	8391413	8392105	+	0	NA	intron (NM_001105244, intron 31 of 32)	L1MC5a|LINE|L1	-24725	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.010116	0.363636	
chunk0098_54_1	chr2	66595540	66595947	+	0	NA	intron (NR_110156, intron 1 of 5)	L1MC4|LINE|L1	21713	NR_110156	100507073	Hs.667940	NR_110156	ENSG00000232046	LINC01798	-	long intergenic non-protein coding RNA 1798	ncRNA	0.004914	0.367647	107(TGGAACAAGCTGTTCC,-,0.00),108(GGAACAAGCTGTTCCT,+,0.00)
chunk0081_231_1	chr17	42833182	42833528	+	0	NA	non-coding (NR_049772, exon 1 of 10)	non-coding (NR_049772, exon 1 of 10)	213	NM_001267045	10197	Hs.152978	NM_005789	ENSG00000131467	PSME3	HEL-S-283|Ki|PA28-gamma|PA28G|PA28gamma|REG-GAMMA	proteasome activator subunit 3	protein-coding	0.098266	0.657061	
chunk0058_384_1	chr14	29500066	29500484	+	0	NA	Intergenic	Intergenic	427418	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.019139	0.379475	
chunk0074_302_1	chr16	30061031	30061445	+	0	NA	intron (NM_000034, intron 4 of 13)	intron (NM_000034, intron 4 of 13)	-3041	NM_184043	226	Hs.513490	NM_000034	ENSG00000149925	ALDOA	ALDA|GSD12|HEL-S-87p	aldolase, fructose-bisphosphate A	protein-coding	0.004831	0.520482	183(AAGGACACGCTGCTCC,-,0.00),184(AGGACACGCTGCTCCT,+,0.00)
chunk0025_402_1	chr10	59536472	59537376	+	0	NA	Intergenic	Intergenic	172967	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.004425	0.420994	344(AGGAACGCTGTGTGCC,-,0.00),345(GGAACGCTGTGTGCCC,+,0.00)
chunk0162_87_1	chr6	2057149	2057364	+	0	NA	intron (NM_001253846, intron 4 of 10)	L2a|LINE|L2	118735	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.000000	0.407407	
chunk0065_183_1	chr15	26615674	26616051	+	0	NA	non-coding (NR_103801, exon 6 of 7)	non-coding (NR_103801, exon 6 of 7)	13316	NM_001191321	2562	Hs.302352	NM_000814	ENSG00000166206	GABRB3	ECA5|EIEE43	gamma-aminobutyric acid type A receptor beta3 subunit	protein-coding	0.005305	0.494709	
chunk0011_37_1	chr1	143234920	143235149	+	0	NA	Intergenic	Intergenic	187558	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.048035	0.391304	
chunk0147_96_1	chr4	173369215	173369414	+	0	NA	Intergenic	Intergenic	-1628	NM_003864	8819	Hs.591715	NM_003864	ENSG00000164105	SAP30	-	Sin3A associated protein 30	protein-coding	0.015075	0.365000	102(AGGTACACAATGTACT,-,0.00),103(GGTACACAATGTACTT,+,0.00)
chunk0211_269_1	chrX	121477127	121478251	+	0	NA	Intergenic	MER47A|DNA|TcMar-Tigger	106717	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.003559	0.313778	150(GAAACATAATGTACCT,+,0.00)
chunk0150_190_1	chr5	34693665	34693896	+	0	NA	intron (NM_001145525, intron 4 of 19)	intron (NM_001145525, intron 4 of 19)	6221	NM_001145523	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.012987	0.443966	
chunk0019_228_1	chr1	227344144	227344787	+	0	NA	Intergenic	MIR3|SINE|MIR	-26340	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.003110	0.347826	336(GGGAACATCCAGTCCA,-,0.00),337(GGAACATCCAGTCCAA,+,0.00)
chunk0008_263_1	chr1	94590195	94590797	+	0	NA	Intergenic	Intergenic	-48639	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.006645	0.464345	
chunk0204_119_1	chr9	95115754	95116319	+	0	NA	intron (NM_001243744, intron 11 of 13)	intron (NM_001243744, intron 11 of 13)	-29942	NR_036109	100422842		NR_036109	ENSG00000207617	MIR3074	mir-3074	microRNA 3074	ncRNA	0.017699	0.420495	
chunk0069_277_1	chr15	64943739	64943938	+	0	NA	intron (NM_182703, intron 11 of 14)	L2c|LINE|L2	31936	NM_182703	348094	Hs.207157	NM_182703	ENSG00000166839	ANKDD1A	-	ankyrin repeat and death domain containing 1A	protein-coding	0.005025	0.545000	
chunk0069_266_1	chr15	64651549	64651921	+	0	NA	intron (NM_015042, intron 2 of 8)	intron (NM_015042, intron 2 of 8)	51546	NM_001301302	4947	Hs.744924	NM_002537	ENSG00000180304	OAZ2	AZ2	ornithine decarboxylase antizyme 2	protein-coding	0.005376	0.469169	
chunk0169_73_1	chr6	99132867	99133362	+	0	NA	Intergenic	Intergenic	8505	NR_039672	100616347		NR_039672	ENSG00000265226	MIR548AI	-	microRNA 548ai	ncRNA	0.012121	0.340726	
chunk0188_196_1	chr8	11808783	11809297	+	0	NA	promoter-TSS (NM_001287751)	promoter-TSS (NM_001287751)	-104	NM_001287751	2222	Hs.593928	NM_004462	ENSG00000079459	FDFT1	DGPT|ERG9|SQS|SQSD|SS	farnesyl-diphosphate farnesyltransferase 1	protein-coding	0.031128	0.504854	
chunk0148_58_1	chr5	1929890	1930323	+	0	NA	Intergenic	(GTGTCGT)n|Simple_repeat|Simple_repeat	42775	NR_109912	101929081	Hs.519180	NR_109912	ENSG00000249326	CTD-2194D22.4	-	uncharacterized LOC101929081	ncRNA	0.013857	0.488479	
chunk0029_282_1	chr10	103735076	103735275	+	0	NA	intron (NM_014631, intron 4 of 13)	intron (NM_014631, intron 4 of 13)	-11604	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.010050	0.515000	
chunk0174_261_1	chr6	161162570	161163207	+	0	NA	promoter-TSS (NR_024277)	promoter-TSS (NR_024277)	-906	NR_024277	79992	Hs.664873	NM_024929	ENSG00000279355	AGPAT4-IT1	C6orf59|NCRNA00241	AGPAT4 intronic transcript 1	ncRNA	0.021978	0.498433	
chunk0118_133_1	chr22	29813173	29813691	+	0	NA	exon (NM_032204, exon 8 of 20)	exon (NM_032204, exon 8 of 20)	24872	NM_001242906	84164	Hs.731754	NM_032204	ENSG00000100325	ASCC2	ASC1p100|p100	activating signal cointegrator 1 complex subunit 2	protein-coding	0.007722	0.450867	
chunk0089_375_1	chr18	67411063	67411587	+	0	NA	Intergenic	Intergenic	-105221	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.003817	0.325714	
chunk0127_334_1	chr3	100481945	100482169	+	0	NA	Intergenic	L2|LINE|L2	-10562	NM_018004	55076	Hs.658956	NM_018004	ENSG00000181458	TMEM45A	DERP7|DNAPTP4	transmembrane protein 45A	protein-coding	0.000000	0.351111	
chunk0193_41_1	chr8	71610316	71610761	+	0	NA	Intergenic	Intergenic	-232585	NR_033652	100132891	Hs.137674	NR_033651	ENSG00000235531	MSC-AS1	-	MSC antisense RNA 1	ncRNA	0.004494	0.356502	
chunk0078_430_1	chr16	89430975	89431547	+	0	NA	non-coding (NR_110932, exon 1 of 3)	non-coding (NR_110932, exon 1 of 3)	343	NR_110932	101927817	Hs.667942	NR_110931		LOC101927817	-	uncharacterized LOC101927817	ncRNA	0.026224	0.527051	
chunk0114_253_1	chr21	16086610	16087574	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	15978	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002075	0.316062	683(AGGAACATCATGTTAC,-,0.00)
chunk0163_445_1	chr6	17501797	17502030	+	0	NA	non-coding (NR_110855, exon 4 of 4)	non-coding (NR_110855, exon 4 of 4)	9352	NR_110855	101928491	Hs.622876	NR_110855		LOC101928491	-	uncharacterized LOC101928491	ncRNA	0.012876	0.435897	
chunk0184_211_1	chr7	117269071	117269677	+	0	NA	Intergenic	Intergenic	53915	NR_024047	7472	Hs.567356	NM_003391	ENSG00000105989	WNT2	INT1L1|IRP	Wnt family member 2	protein-coding	0.009901	0.367381	260(GAGTTCAGGCTGTGCC,-,0.00),261(AGTTCAGGCTGTGCCT,+,0.00)
chunk0095_337_1	chr2	20837774	20838232	+	0	NA	Intergenic	Intergenic	-14873	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.004367	0.344227	
chunk0068_181_1	chr15	54584573	54584789	+	0	NA	intron (NM_001080534, intron 28 of 30)	intron (NM_001080534, intron 28 of 30)	571777	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.004630	0.373272	
chunk0075_59_1	chr16	47664774	47665080	+	0	NA	exon (NM_000293, exon 25 of 31)	exon (NM_000293, exon 25 of 31)	-193654	NR_110650	101927132	Hs.589404	NR_110650	ENSG00000261231	LINC02133	-	long intergenic non-protein coding RNA 2133	ncRNA	0.009804	0.403909	
chunk0089_246_1	chr18	62169406	62169795	+	0	NA	intron (NM_176787, intron 1 of 30)	L1ME1|LINE|L1	17456	NM_012327	23556	Hs.157031	NM_012327	ENSG00000197563	PIGN	MCAHS|MCAHS1|MCD4|MDC4|PIG-N	phosphatidylinositol glycan anchor biosynthesis class N	protein-coding	0.015424	0.441026	
chunk0140_367_1	chr4	74487593	74488202	+	0	NA	Intergenic	Intergenic	42799	NM_001657	374	Hs.270833	NM_001657	ENSG00000109321	AREG	AR|AREGB|CRDGF|SDGF	amphiregulin	protein-coding	0.001642	0.336066	273(ATGAACACGCTGTTCT,-,0.00),274(TGAACACGCTGTTCTT,+,0.00)
chunk0187_385_1	chr7	157677595	157677899	+	0	NA	intron (NM_001308268, intron 13 of 22)	intron (NM_001308268, intron 13 of 22)	-103325	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.019737	0.485246	
chunk0140_376_1	chr4	74774176	74774508	+	0	NA	intron (NM_001729, intron 1 of 5)	HAL1|LINE|L1	20344	NM_001316963	685	Hs.591704	NM_001729	ENSG00000174808	BTC	-	betacellulin	protein-coding	0.006024	0.363363	
chunk0133_353_1	chr3	173371137	173371829	+	0	NA	Intergenic	L2|LINE|L2	-26965	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.002890	0.399711	
chunk0127_272_1	chr3	97698745	97698944	+	0	NA	intron (NM_001080448, intron 14 of 17)	L2c|LINE|L2	-65677	NR_103511	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.015075	0.360000	
chunk0010_196_1	chr1	116015462	116016125	+	0	NA	intron (NM_018420, intron 2 of 11)	intron (NM_018420, intron 2 of 11)	-38517	NR_125970	101928977	Hs.627914	NR_125970		LOC101928977	-	uncharacterized LOC101928977	ncRNA	0.004525	0.332831	
chunk0053_233_1	chr13	32468198	32468644	+	0	NA	intron (NM_001278432, intron 6 of 9)	L3b|LINE|CR1	30071	NR_051980	100462953	Hs.687692	NR_051980		MICOS10P1	CG012|MINOS1P1|N4BP2L2-IT|N4BP2L2-IT1|N4BP2L2IT1	MICOS10 pseudogene 1	pseudo	0.002242	0.340045	
chunk0169_12_1	chr6	96574102	96574444	+	0	NA	intron (NM_020482, intron 2 of 6)	intron (NM_020482, intron 2 of 6)	11725	NM_020482	9457	Hs.632608	NM_020482	ENSG00000112214	FHL5	1700027G07Rik|ACT|FHL-5|dJ393D12.2	four and a half LIM domains 5	protein-coding	0.002924	0.297376	107(GTGTACAGAAAGTTCT,-,0.00),108(TGTACAGAAAGTTCTT,+,0.00)
chunk0050_377_1	chr12	108639397	108639646	+	0	NA	Intergenic	L2a|LINE|L2	3711	NR_039717	100616240		NR_039717	ENSG00000284388	MIR4496	-	microRNA 4496	ncRNA	0.016064	0.520000	
chunk0050_366_1	chr12	107941418	107942069	+	0	NA	Intergenic	L1MA4|LINE|L1	-37972	NR_037629	728739	Hs.741995	NR_037629		LOC728739	-	programmed cell death 2 pseudogene	pseudo	0.001536	0.430982	283(CAGGACAGGCAGTACT,-,0.00),284(AGGACAGGCAGTACTC,+,0.00)
chunk0063_175_1	chr14	80419295	80419817	+	0	NA	intron (NR_038355, intron 8 of 8)	intron (NR_038355, intron 8 of 8)	-188502	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.007663	0.407266	
chunk0061_159_1	chr14	59766667	59766892	+	0	NA	intron (NM_021136, intron 1 of 8)	intron (NM_021136, intron 1 of 8)	104060	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.008889	0.336283	
chunk0096_27_1	chr2	26598985	26599363	+	0	NA	intron (NM_001029881, intron 3 of 6)	intron (NM_001029881, intron 3 of 6)	36561	NM_001105519	339778	Hs.407083	NM_001105519	ENSG00000173557	C2orf70	-	chromosome 2 open reading frame 70	protein-coding	0.010582	0.350923	
chunk0014_192_1	chr1	178904114	178904423	+	0	NA	intron (NM_001286247, intron 17 of 18)	L1PB1|LINE|L1	-33188	NM_004673	9068	Hs.591474	NM_004673	ENSG00000116194	ANGPTL1	ANG3|ANGPT3|ARP1|AngY|UNQ162|dJ595C2.2	angiopoietin like 1	protein-coding	0.009709	0.348387	
chunk0030_75_1	chr10	112227474	112227986	+	0	NA	Intergenic	Intergenic	-43951	NM_001244949	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.011719	0.520468	
chunk0195_299_1	chr8	98726400	98726817	+	0	NA	intron (NM_006281, intron 4 of 10)	intron (NM_006281, intron 4 of 10)	99063	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004796	0.416268	
chunk0103_393_1	chr2	168999230	168999548	+	0	NA	intron (NM_003742, intron 5 of 27)	L1MD1|LINE|L1	31934	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.000000	0.332288	
chunk0096_88_1	chr2	27998797	27999473	+	0	NA	intron (NM_199191, intron 4 of 11)	L2c|LINE|L2	2768	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.000000	0.358936	
chunk0057_72_1	chr13	98291820	98292252	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	83512	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.000000	0.411085	4(AAGAACAGTCTGTGTA,-,0.00)
chunk0144_372_1	chr4	139976025	139976304	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	177915	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.003584	0.378571	
chunk0200_26_1	chr9	14761644	14762145	+	0	NA	intron (NM_144966, intron 28 of 37)	MER44B|DNA|TcMar-Tigger	17639	NM_001177704	158326	Hs.50850	NM_144966	ENSG00000164946	FREM1	BNAR|C9orf143|C9orf145|C9orf154|MOTA|TILRR|TRIGNO2	FRAS1 related extracellular matrix 1	protein-coding	0.001996	0.404382	
chunk0125_238_1	chr3	68482648	68483884	+	0	NA	intron (NM_213609, intron 3 of 4)	MER58B|DNA|hAT-Charlie	449344	NM_001005527	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.004045	0.411479	
chunk0132_286_1	chr3	159962836	159963473	+	0	NA	intron (NR_108088, intron 9 of 9)	Tigger2b_Pri|DNA|TcMar-Tigger	-25682	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.004710	0.410658	
chunk0190_457_1	chr8	42151813	42152134	+	0	NA	promoter-TSS (NM_006803)	promoter-TSS (NM_006803)	-973	NM_006803	10947	Hs.654529	NM_006803	ENSG00000070718	AP3M2	AP47B|CLA20|P47B	adaptor related protein complex 3 subunit mu 2	protein-coding	0.018692	0.475155	
chunk0135_165_1	chr3	187947035	187947521	+	0	NA	Intergenic	Intergenic	-201553	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.016461	0.511294	
chunk0076_275_1	chr16	69565732	69566189	+	0	NA	promoter-TSS (NM_138714)	promoter-TSS (NM_138714)	-6	NM_138714	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.096280	0.724891	
chunk0036_43_1	chr11	59008951	59009305	+	0	NA	intron (NR_033853, intron 3 of 5)	intron (NR_033853, intron 3 of 5)	49324	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.002825	0.400000	
chunk0183_32_1	chr7	103660534	103660877	+	0	NA	intron (NM_005045, intron 12 of 64)	intron (NM_005045, intron 12 of 64)	-214528	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.002915	0.375000	
chunk0108_305_1	chr2	235166282	235166551	+	0	NA	Intergenic	Intergenic	214432	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.011152	0.500000	
chunk0148_154_1	chr5	6580510	6581064	+	0	NA	Intergenic	Intergenic	-1349	NR_024423	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.000000	0.329730	
chunk0144_234_1	chr4	134887616	134887816	+	0	NA	Intergenic	Intergenic	-685968	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.010000	0.288557	
chunk0140_80_1	chr4	67712031	67712746	+	0	NA	intron (NR_015439, intron 1 of 1)	intron (NR_015439, intron 1 of 1)	11110	NR_015439	550112	Hs.479879	NR_015439	ENSG00000248049	UBA6-AS1	-	UBA6 antisense RNA 1 (head to head)	ncRNA	0.004196	0.463687	
chunk0007_314_1	chr1	84410183	84410920	+	0	NA	intron (NM_021233, intron 3 of 5)	AmnSINE1|SINE|5S-Deu-L2	2200	NM_058248	58511	Hs.129142	NM_021233	ENSG00000137976	DNASE2B	DLAD	deoxyribonuclease 2 beta	protein-coding	0.004071	0.345528	
chunk0066_316_1	chr15	35991736	35991935	+	0	NA	Intergenic	Intergenic	64979	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.005025	0.450000	
chunk0186_80_1	chr7	137266780	137267303	+	0	NA	intron (NM_002825, intron 1 of 4)	Harlequin-int|LTR|ERV1	76759	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.007648	0.370229	
chunk0101_27_1	chr2	121755482	121755809	+	0	NA	promoter-TSS (NM_001261401)	promoter-TSS (NM_001261401)	100	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.125382	0.685976	
chunk0197_263_1	chr8	123580951	123581595	+	0	NA	Intergenic	Intergenic	-40020	NM_001242463	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.012422	0.485271	
chunk0179_345_1	chr7	50771191	50771920	+	0	NA	intron (NM_001001555, intron 1 of 16)	intron (NM_001001555, intron 1 of 16)	21907	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.012346	0.508219	
chunk0052_80_1	chr13	21729482	21729831	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	58580	NM_002010	2254	Hs.111	NM_002010	ENSG00000102678	FGF9	FGF-9|GAF|HBFG-9|HBGF-9|SYNS3	fibroblast growth factor 9	protein-coding	0.014327	0.442857	
chunk0205_443_1	chr9	115408603	115408842	+	0	NA	Intergenic	Intergenic	266904	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.000000	0.425000	
chunk0179_267_1	chr7	49257364	49257731	+	0	NA	Intergenic	Intergenic	332986	NR_003595									0.013624	0.331522	
chunk0179_276_1	chr7	49462871	49463546	+	0	NA	Intergenic	L1M1|LINE|L1	-310453	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.004444	0.399408	
chunk0001_127_1	chr1	4711075	4711393	+	0	NA	intron (NM_001042478, intron 1 of 5)	intron (NM_001042478, intron 1 of 5)	56189	NM_018836	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.050314	0.551724	
chunk0029_428_1	chr10	110002587	110003360	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-2995	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.002587	0.360465	
chunk0142_377_1	chr4	102098798	102099457	+	0	NA	Intergenic	L1ME1|LINE|L1	225185	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.003035	0.319697	
chunk0134_400_1	chr3	183094521	183095084	+	0	NA	intron (NM_001293273, intron 1 of 16)	intron (NM_001293273, intron 1 of 16)	4441	NR_120640	56922	Hs.47649	NM_020166	ENSG00000078070	MCCC1	MCC-B|MCCA	methylcrotonoyl-CoA carboxylase 1	protein-coding	0.005329	0.407801	
chunk0066_303_1	chr15	35646803	35647173	+	0	NA	intron (NR_038251, intron 1 of 2)	intron (NR_038251, intron 1 of 2)	-100785	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.002703	0.328841	
chunk0189_217_1	chr8	24349003	24349521	+	0	NA	intron (NR_130710, intron 18 of 22)	intron (NR_130710, intron 18 of 22)	-35023	NM_001145272	27299	Hs.521459	NM_014479	ENSG00000134028	ADAMDEC1	M12.219	ADAM like decysin 1	protein-coding	0.007722	0.350674	
chunk0016_154_1	chr1	197552155	197552455	+	0	NA	TTS (NM_144977)	TTS (NM_144977)	223188	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.006667	0.289037	
chunk0003_184_1	chr1	33697074	33697462	+	0	NA	intron (NM_052896, intron 24 of 69)	intron (NM_052896, intron 24 of 69)	-163207	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.010309	0.439589	
chunk0135_415_1	chr3	192928582	192929169	+	0	NA	Intergenic	L2c|LINE|L2	-10714	NM_178496	151963	Hs.151443	NM_178496	ENSG00000180611	MB21D2	C3orf59	Mab-21 domain containing 2	protein-coding	0.013629	0.375850	
chunk0169_315_1	chr6	106147634	106148055	+	0	NA	Intergenic	Intergenic	48982	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.004751	0.398104	
chunk0115_361_1	chr21	29730031	29730305	+	0	NA	intron (NM_175611, intron 1 of 15)	intron (NM_175611, intron 1 of 15)	-18007	NR_027021	642976	Hs.473554	NR_027021		GRIK1-AS1	C21orf9|GRIK1-AS|GRIK1AS|NCRNA00110	GRIK1 antisense RNA 1	ncRNA	0.010949	0.330909	
chunk0099_91_1	chr2	85516799	85516998	+	0	NA	Intergenic	Intergenic	21988	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.015075	0.405000	
chunk0199_34_1	chr9	818896	819314	+	0	NA	Intergenic	Intergenic	-22585	NM_021951	1761	Hs.98586	NM_021951	ENSG00000137090	DMRT1	CT154|DMT1	doublesex and mab-3 related transcription factor 1	protein-coding	0.007177	0.412888	
chunk0064_271_1	chr14	94867139	94867338	+	0	NA	Intergenic	Intergenic	-97076	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.015075	0.500000	
chunk0029_354_1	chr10	107527136	107527750	+	0	NA	Intergenic	L3|LINE|CR1	-362735	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.003257	0.385366	
chunk0012_197_1	chr1	159881971	159882240	+	0	NA	intron (NM_012337, intron 7 of 11)	intron (NM_012337, intron 7 of 11)	17974	NR_130464	100422852		NR_130464	ENSG00000266458	MIR4259	-	microRNA 4259	ncRNA	0.011152	0.533333	
chunk0052_367_1	chr12	128205654	128206236	+	0	NA	Intergenic	(CACATC)n|Simple_repeat|Simple_repeat	-38561	NR_039720									0.015464	0.481990	
chunk0202_88_1	chr9	72009705	72010052	+	0	NA	Intergenic	MER4A|LTR|ERV1	50727	NM_001128618	138240	Hs.371235	NM_001128618	ENSG00000204669	C9orf57	-	chromosome 9 open reading frame 57	protein-coding	0.008646	0.373563	
chunk0052_376_1	chr12	128943003	128943595	+	0	NA	intron (NR_133646, intron 7 of 10)	intron (NR_133646, intron 7 of 10)	89865	NM_144669	144423	Hs.655668	NM_144669	ENSG00000151948	GLT1D1	-	glycosyltransferase 1 domain containing 1	protein-coding	0.015203	0.379427	
chunk0209_64_1	chrX	37666374	37667055	+	0	NA	intron (NM_198511, intron 3 of 5)	intron (NM_198511, intron 3 of 5)	-19166	NM_021083	7504	Hs.78919	NM_021083	ENSG00000047597	XK	KX|NA|NAC|X1k|XKR1	X-linked Kx blood group	protein-coding	0.004405	0.334311	
chunk0003_55_1	chr1	30905787	30906193	+	0	NA	intron (NM_014654, intron 1 of 4)	intron (NM_014654, intron 1 of 4)	2643	NM_014654	9672	Hs.158287	NM_014654	ENSG00000162512	SDC3	SDCN|SYND3	syndecan 3	protein-coding	0.009852	0.567568	222(AGGGTCATCATGTCCC,-,0.00),223(GGGTCATCATGTCCCT,+,0.00)
chunk0077_30_1	chr16	75307937	75308681	+	0	NA	intron (NM_006324, intron 5 of 6)	LTR16E1|LTR|ERVL	-40256	NM_001170715	9564	Hs.479747	NM_014567	ENSG00000050820	BCAR1	CAS|CAS1|CASS1|CRKAS|P130Cas	BCAR1 scaffold protein, Cas family member	protein-coding	0.009409	0.446980	
chunk0176_317_1	chr7	17016353	17016897	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-134636	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.001838	0.390826	518(AAGCACTTGTTGTTCC,-,0.00),519(AGCACTTGTTGTTCCC,+,0.00)
chunk0046_133_1	chr12	57726972	57727720	+	0	NA	non-coding (NR_027032, exon 2 of 2)	non-coding (NR_027032, exon 2 of 2)	1106	NR_027032	100130776	Hs.656080	NR_027032	ENSG00000255737	AGAP2-AS1	PUNISHER	AGAP2 antisense RNA 1	ncRNA	0.086898	0.668892	
chunk0130_287_1	chr3	136566537	136567123	+	0	NA	intron (NM_005862, intron 5 of 33)	L1MC5a|LINE|L1	185573	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.005119	0.306644	
chunk0002_369_1	chr1	26234999	26235351	+	0	NA	intron (NM_022778, intron 1 of 13)	L2b|LINE|L2	1022	NM_001281517	64793	Hs.63795	NM_022778	ENSG00000130695	CEP85	CCDC21	centrosomal protein 85	protein-coding	0.028409	0.458924	
chunk0128_95_1	chr3	105835712	105836090	+	0	NA	intron (NM_170662, intron 3 of 18)	intron (NM_170662, intron 3 of 18)	33142	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.002646	0.350923	
chunk0138_412_1	chr4	44104179	44104448	+	0	NA	Intergenic	L1PA13|LINE|L1	87251	NR_131958	100506827	Hs.156197	NR_131958	ENSG00000251350	LINC02475	LVCAT1	long intergenic non-protein coding RNA 2475	ncRNA	0.003717	0.581481	
chunk0192_456_1	chr8	70238468	70238908	+	0	NA	intron (NM_006540, intron 2 of 22)	intron (NM_006540, intron 2 of 22)	165097	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.006818	0.414966	187(GTGGACTGTCTGTCCC,-,0.00),188(TGGACTGTCTGTCCCT,+,0.00)
chunk0031_300_1	chr10	128691269	128691717	+	0	NA	Intergenic	Intergenic	405543	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.013393	0.454343	
chunk0182_5_1	chr7	90932699	90932898	+	0	NA	intron (NM_001287136, intron 7 of 13)	MLT1F2|LTR|ERVL-MaLR	222982	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.005025	0.505000	
chunk0173_165_1	chr6	144330644	144330843	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	39006	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.020101	0.520000	
chunk0198_314_1	chr8	139655141	139655582	+	0	NA	intron (NM_001282534, intron 1 of 1)	intron (NM_001282534, intron 1 of 1)	47695	NM_001282534	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.018141	0.588235	
chunk0106_221_1	chr2	202560209	202560747	+	0	NA	3' UTR (NM_001204, exon 13 of 13)	3' UTR (NM_001204, exon 13 of 13)	-74700	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.001859	0.356215	
chunk0052_245_1	chr12	123379266	123379818	+	0	NA	Intergenic	LTR50|LTR|ERVL	-4615	NM_020382	387893	Hs.443735	NM_020382	ENSG00000183955	KMT5A	PR-Set7|PR/SET07|SET07|SET8|SETD8	lysine methyltransferase 5A	protein-coding	0.010870	0.493671	
chunk0115_438_1	chr21	32009348	32009547	+	0	NA	Intergenic	Intergenic	76848	NR_038033	100551499	Hs.224449	NR_038033		LINC00159	C21orf44|NCRNA00159	long intergenic non-protein coding RNA 159	ncRNA	0.015075	0.490000	
chunk0093_226_1	chr19	50178377	50178901	+	0	NA	Intergenic	L1ME3A|LINE|L1	-15358	NM_152358	126123	Hs.414175	NM_152358	ENSG00000161652	IZUMO2	C19orf41|PLAL6978|PRO21961|SCRL	IZUMO family member 2	protein-coding	0.001908	0.440000	231(GAGTACAGACTGTACT,-,0.00),232(AGTACAGACTGTACTG,+,0.00)
chunk0056_5_1	chr13	77013804	77014321	+	0	NA	intron (NM_012158, intron 4 of 4)	L2c|LINE|L2	13134	NM_012158	26224	Hs.508284	NM_012158	ENSG00000005812	FBXL3	FBL3|FBL3A|FBXL3A|IDDSFAS	F-box and leucine rich repeat protein 3	protein-coding	0.007737	0.405405	210(AAGTTCACAGTGTTCT,-,0.00),211(AGTTCACAGTGTTCTG,+,0.00)
chunk0070_433_1	chr15	78067417	78067782	+	0	NA	intron (NM_015079, intron 1 of 12)	intron (NM_015079, intron 1 of 12)	10053	NM_144572	23102	Hs.567426	NM_015079	ENSG00000167202	TBC1D2B	-	TBC1 domain family member 2B	protein-coding	0.002740	0.508197	38(AAGCACAGCCTCTCCT,-,0.00),39(AGCACAGCCTCTCCTG,+,0.00)
chunk0120_395_1	chr3	12484061	12484372	+	0	NA	promoter-TSS (NM_001145394)	promoter-TSS (NM_001145394)	-216	NM_001145393	80746	Hs.335550	NM_025265	ENSG00000154743	TSEN2	PCH2B|SEN2|SEN2L	tRNA splicing endonuclease subunit 2	protein-coding	0.061093	0.551282	
chunk0097_305_1	chr2	55907586	55908157	+	0	NA	intron (NM_001039349, intron 4 of 10)	intron (NM_001039349, intron 4 of 10)	16292	NM_001039349	2202	Hs.76224	NM_004105	ENSG00000115380	EFEMP1	DHRD|DRAD|FBLN3|FBNL|FIBL-3|MLVT|MTLV|S1-5	EGF containing fibulin extracellular matrix protein 1	protein-coding	0.007005	0.428322	
chunk0036_60_1	chr11	59551069	59551268	+	0	NA	Intergenic	Intergenic	36255	NM_001004711	390199	Hs.553757	NM_001004711	ENSG00000172742	OR4D9	OR11-253	olfactory receptor family 4 subfamily D member 9	protein-coding	0.020101	0.430000	
chunk0150_215_1	chr5	35214074	35214297	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	16404	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.000000	0.450893	
chunk0038_429_1	chr11	94592218	94592560	+	0	NA	intron (NM_152431, intron 8 of 19)	L2c|LINE|L2	25081	NM_152431	143689	Hs.660188	NM_152431	ENSG00000134627	PIWIL4	HIWI2|MIWI2	piwi like RNA-mediated gene silencing 4	protein-coding	0.011696	0.402332	
chunk0167_90_1	chr6	56897748	56897980	+	0	NA	intron (NM_001144769, intron 3 of 96)	LTR33|LTR|ERVL	-45948	NM_001144770	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.008621	0.532189	
chunk0110_130_1	chr20	13393384	13393631	+	0	NA	intron (NM_017714, intron 13 of 13)	intron (NM_017714, intron 13 of 13)	-153820	NR_040043	100505536	Hs.665253	NR_040043		ISM1-AS1	-	ISM1 antisense RNA 1	ncRNA	0.008097	0.512097	
chunk0065_78_1	chr15	23565394	23565730	+	0	NA	5' UTR (NM_005664, exon 1 of 1)	5' UTR (NM_005664, exon 1 of 1)	255	NM_005664	7681	Hs.72964	NM_005664	ENSG00000179455	MKRN3	CPPB2|D15S9|RNF63|ZFP127|ZNF127	makorin ring finger protein 3	protein-coding	0.044643	0.548961	
chunk0045_226_1	chr12	48171231	48171776	+	0	NA	Intergenic	L1MC5a|LINE|L1	-12080	NM_001013635	387856	Hs.251699	NM_001013635	ENSG00000177875	CCDC184	C12orf68	coiled-coil domain containing 184	protein-coding	0.007339	0.313187	
chunk0038_289_1	chr11	90185732	90186107	+	0	NA	intron (NM_001300930, intron 17 of 17)	intron (NM_001300930, intron 17 of 17)	37445	NM_001144073	26973	Hs.22857	NM_012124	ENSG00000110172	CHORDC1	CHP1	cysteine and histidine rich domain containing 1	protein-coding	0.000000	0.295213	
chunk0155_44_1	chr5	91139796	91140002	+	0	NA	intron (NR_003149, intron 87 of 89)	intron (NR_003149, intron 87 of 89)	174503	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.000000	0.429952	
chunk0001_291_1	chr1	8848763	8849023	+	0	NA	Intergenic	Intergenic	17697	NR_106786	102465436		NR_106786	ENSG00000274258	MIR6728	hsa-mir-6728	microRNA 6728	ncRNA	0.023077	0.597701	
chunk0144_378_1	chr4	140036268	140036470	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	117710	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.014851	0.492611	
chunk0125_232_1	chr3	68242025	68242651	+	0	NA	intron (NM_213609, intron 2 of 4)	intron (NM_213609, intron 2 of 4)	238122	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.003195	0.355662	
chunk0183_413_1	chr7	110754548	110755177	+	0	NA	intron (NM_032549, intron 5 of 5)	intron (NM_032549, intron 5 of 5)	-336144	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.007949	0.303175	290(AAGAACATTATGCTCT,-,0.00),291(AGAACATTATGCTCTT,+,0.00)
chunk0090_72_1	chr19	2490785	2490990	+	0	NA	Intergenic	Intergenic	14762	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.024390	0.538835	33(CTGCACTGCGTGTTCC,-,0.00),34(TGCACTGCGTGTTCCC,+,0.00)
chunk0014_198_1	chr1	179048546	179048887	+	0	NA	intron (NM_014864, intron 2 of 7)	intron (NM_014864, intron 2 of 7)	22777	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.000000	0.327485	
chunk0070_135_1	chr15	70920048	70920592	+	0	NA	intron (NM_017691, intron 7 of 15)	intron (NM_017691, intron 7 of 15)	27877	NM_001199017	54839	Hs.12692	NM_017691	ENSG00000137821	LRRC49	PGs4	leucine rich repeat containing 49	protein-coding	0.001838	0.365138	142(AAGAACTAAGTGTACT,-,0.00),143(AGAACTAAGTGTACTA,+,0.00)
chunk0103_230_1	chr2	164620926	164621145	+	0	NA	intron (NM_004490, intron 1 of 13)	intron (NM_004490, intron 1 of 13)	815	NM_004490	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.050228	0.622727	
chunk0097_366_1	chr2	60758554	60759076	+	0	NA	intron (NM_022894, intron 1 of 21)	intron (NM_022894, intron 1 of 21)	2585	NM_022894	64895	Hs.387471	NM_022894	ENSG00000115421	PAPOLG	-	poly(A) polymerase gamma	protein-coding	0.015326	0.399618	
chunk0184_53_1	chr7	112321768	112322141	+	0	NA	intron (NM_021994, intron 5 of 11)	L1M4|LINE|L1	-101190	NM_001197080	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.005362	0.363636	
chunk0177_383_1	chr7	26925629	26926149	+	0	NA	Intergenic	L1MB7|LINE|L1	-61146	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.005769	0.364683	
chunk0141_148_1	chr4	81378445	81378904	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	93254	NM_001300736	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.002179	0.352174	264(TGGTACAGTGTGTACT,-,0.00),265(GGTACAGTGTGTACTA,+,0.00)
chunk0130_427_1	chr3	140906253	140906760	+	0	NA	Intergenic	Intergenic	-35314	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.005917	0.417323	
chunk0208_142_1	chrX	15714491	15715018	+	0	NA	Intergenic	Intergenic	-23535	NM_007220	11238	Hs.653287	NM_007220	ENSG00000169239	CA5B	CA-VB|CAVB	carbonic anhydrase 5B	protein-coding	0.005693	0.464015	253(AAGATCAGCATGTCCC,-,0.00),254(AGATCAGCATGTCCCT,+,0.00)
chunk0125_374_1	chr3	71532695	71532972	+	0	NA	intron (NM_032682, intron 2 of 20)	intron (NM_032682, intron 2 of 20)	9256	NR_031697	100302112		NR_031697	ENSG00000221264	MIR1284	MIRN1284|hsa-mir-1284|mir-1284	microRNA 1284	ncRNA	0.014440	0.417266	84(GAGAACAGAAAGTGCC,-,0.00),85(AGAACAGAAAGTGCCG,+,0.00)
chunk0054_431_1	chr13	51227394	51227727	+	0	NA	intron (NM_145019, intron 1 of 4)	intron (NM_145019, intron 1 of 4)	5226	NM_001242312	220108	Hs.71913	NM_145019	ENSG00000150510	FAM124A	-	family with sequence similarity 124 member A	protein-coding	0.003003	0.383234	224(AAGGACAGCCAGTTCC,-,0.00),225(AGGACAGCCAGTTCCT,+,0.00)
chunk0042_263_1	chr12	6775784	6776250	+	0	NA	intron (NM_002286, intron 5 of 7)	intron (NM_002286, intron 5 of 7)	3513	NM_002286	3902	Hs.409523	NM_002286	ENSG00000089692	LAG3	CD223	lymphocyte activating 3	protein-coding	0.017167	0.434690	
chunk0158_260_1	chr5	131024063	131025017	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	140808	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.005241	0.349738	136(AGAACTTTCTGTCTTT,+,0.00)
chunk0199_387_1	chr9	13184917	13185224	+	0	NA	intron (NM_003829, intron 18 of 45)	intron (NM_003829, intron 18 of 45)	94494	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.009772	0.344156	
chunk0166_206_1	chr6	46661353	46661860	+	0	NA	intron (NM_001204051, intron 3 of 8)	MIR|SINE|MIR	8691	NM_004277	9481	Hs.40510	NM_004277	ENSG00000153291	SLC25A27	UCP4	solute carrier family 25 member 27	protein-coding	0.005917	0.364173	
chunk0107_204_1	chr2	216551507	216552012	+	0	NA	Intergenic	L2a|LINE|L2	52962	NM_000998	6168	Hs.433701	NM_000998	ENSG00000197756	RPL37A	L37A	ribosomal protein L37a	protein-coding	0.011881	0.466403	
chunk0164_29_1	chr6	18288871	18289142	+	0	NA	Intergenic	L2|LINE|L2	-24438	NM_001134709	7913	Hs.484813	NM_003472	ENSG00000124795	DEK	D6S231E	DEK proto-oncogene	protein-coding	0.014760	0.437500	
chunk0157_457_1	chr5	125011620	125011819	+	0	NA	Intergenic	Intergenic	-25112	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.010050	0.390000	
chunk0116_369_1	chr21	41932937	41933187	+	0	NA	intron (NM_015500, intron 2 of 13)	intron (NM_015500, intron 2 of 13)	-6372	NM_199050	25966	Hs.473894	NM_015500	ENSG00000157617	C2CD2	C21orf25|C21orf258|TMEM24L	C2 calcium dependent domain containing 2	protein-coding	0.024000	0.561753	
chunk0031_6_1	chr10	121453239	121453665	+	0	NA	Intergenic	Intergenic	140515	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.007042	0.496487	204(AAGAACAGAGAGTTCC,-,0.00),205(AGAACAGAGAGTTCCT,+,0.00)
chunk0136_157_1	chr4	5603408	5603922	+	0	NA	intron (NM_147127, intron 16 of 21)	intron (NM_147127, intron 16 of 21)	78509	NR_126518	10141	Hs.177972	NM_005750	ENSG00000082929	LINC01587	C4orf6|aC1	long intergenic non-protein coding RNA 1587	ncRNA	0.009728	0.407767	
chunk0129_169_1	chr3	120743312	120743933	+	0	NA	intron (NM_005513, intron 1 of 4)	L2c|LINE|L2	911	NM_005513	2960	Hs.445272	NM_005513	ENSG00000153767	GTF2E1	FE|TF2E1|TFIIE-A	general transcription factor IIE subunit 1	protein-coding	0.011272	0.463023	141(GGAACAAAACGTGCCT,+,0.00),418(AGGAACAGCATGTGCA,-,0.00),419(GGAACAGCATGTGCAA,+,0.00)
chunk0132_194_1	chr3	157166471	157167171	+	0	NA	Intergenic	Intergenic	-6061	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.004286	0.386591	377(CTGAACTGGTTGTTCT,-,0.00),378(TGAACTGGTTGTTCTC,+,0.00)
chunk0051_50_1	chr12	112356780	112357318	+	0	NA	intron (NM_001109662, intron 1 of 75)	intron (NM_001109662, intron 1 of 75)	25043	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.005576	0.358071	304(AGGAACTCAGTGTTTT,-,0.00),305(GGAACTCAGTGTTTTC,+,0.00)
chunk0008_215_1	chr1	93743613	93743921	+	0	NA	intron (NM_001261408, intron 2 of 13)	intron (NM_001261408, intron 2 of 13)	-61929	NM_003567	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.003247	0.365696	10(AAGCACATGGTGTTTT,-,0.00),11(AGCACATGGTGTTTTC,+,0.00)
chunk0046_435_1	chr12	64810956	64811298	+	0	NA	Intergenic	Intergenic	-13445	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.002924	0.338192	
chunk0090_13_1	chr19	571135	571334	+	0	NA	promoter-TSS (NM_198591)	promoter-TSS (NM_198591)	-43	NM_198590	682	Hs.501293	NM_001728	ENSG00000172270	BSG	5F7|CD147|EMMPRIN|EMPRIN|OK|SLC7A11|TCSF	basigin (Ok blood group)	protein-coding	0.050251	0.610000	
chunk0075_256_1	chr16	53449659	53449858	+	0	NA	intron (NM_005611, intron 4 of 21)	intron (NM_005611, intron 4 of 21)	15319	NM_005611	5934	Hs.513609	NM_005611	ENSG00000103479	RBL2	P130|Rb2	RB transcriptional corepressor like 2	protein-coding	0.000000	0.295000	
chunk0123_349_1	chr3	48013844	48014114	+	0	NA	intron (NM_030885, intron 1 of 3)	intron (NM_030885, intron 1 of 3)	75300	NM_002375	4134	Hs.517949	NM_002375	ENSG00000047849	MAP4	-	microtubule associated protein 4	protein-coding	0.003704	0.391144	51(GGGAACACACAGTTTT,-,0.00),52(GGAACACACAGTTTTC,+,0.00)
chunk0032_21_1	chr11	783517	783949	+	0	NA	non-coding (NR_126343, exon 2 of 2)	non-coding (NR_126343, exon 2 of 2)	6155	NR_126343	171391	Hs.117183	NR_046316	ENSG00000255284	LOC171391	NS3BP	uncharacterized LOC171391	ncRNA	0.050926	0.584296	202(CAGAACAGGCTGTGCT,-,0.00),203(AGAACAGGCTGTGCTG,+,0.00)
chunk0048_270_1	chr12	82266940	82267196	+	0	NA	Intergenic	Intergenic	91352	NM_014167	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.007812	0.389105	
chunk0181_8_1	chr7	77685152	77685754	+	0	NA	intron (NR_038361, intron 1 of 2)	intron (NR_038361, intron 1 of 2)	-10973	NM_198467	222194	Hs.72451	NM_198467	ENSG00000187257	RSBN1L	-	round spermatid basic protein 1 like	protein-coding	0.009967	0.402985	351(CGGCACTTCGTGTCCC,-,0.00),352(GGCACTTCGTGTCCCT,+,0.00)
chunk0156_199_1	chr5	107964069	107964860	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-293569	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.001264	0.345960	497(AGAACTGATAGTCCCC,+,0.00)
chunk0130_24_1	chr3	128707877	128708214	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-18091	NM_004637	7879	Hs.684374	NM_004637	ENSG00000075785	RAB7A	PRO2706|RAB7	RAB7A, member RAS oncogene family	protein-coding	0.008902	0.491124	
chunk0071_232_1	chr15	85067014	85067277	+	0	NA	exon (NM_173454, exon 3 of 21)	exon (NM_173454, exon 3 of 21)	85171	NM_173454	5151	Hs.9333	NM_002605	ENSG00000073417	PDE8A	HsT19550	phosphodiesterase 8A	protein-coding	0.007605	0.443182	91(AGGCTCAGGCTGTCCT,-,0.00),92(GGCTCAGGCTGTCCTT,+,0.00)
chunk0106_197_1	chr2	202040617	202041227	+	0	NA	Intergenic	Intergenic	6335	NM_003507	8324	Hs.173859	NM_003507	ENSG00000155760	FZD7	FzE3	frizzled class receptor 7	protein-coding	0.008197	0.378069	
chunk0064_114_1	chr14	91164701	91164900	+	0	NA	intron (NM_001102369, intron 5 of 14)	L1M1|LINE|L1	38374	NR_003709	100124539	Hs.693444	NR_003709	ENSG00000221102	SNORA11B	-	small nucleolar RNA, H/ACA box 11B	snoRNA	0.000000	0.555000	
chunk0082_199_1	chr17	56822896	56823221	+	0	NA	intron (NM_001085430, intron 4 of 7)	intron (NM_001085430, intron 4 of 7)	10837	NM_001085430	339210	Hs.658949	NM_001085430	ENSG00000214226	C17orf67	-	chromosome 17 open reading frame 67	protein-coding	0.012308	0.469325	
chunk0029_288_1	chr10	103794321	103794563	+	0	NA	intron (NM_014631, intron 2 of 13)	intron (NM_014631, intron 2 of 13)	47663	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.024793	0.526749	
chunk0055_17_1	chr13	51797957	51798538	+	0	NA	intron (NM_001270424, intron 2 of 9)	MER5B|DNA|hAT-Charlie	5915	NM_024705	79758	Hs.266728	NM_024705	ENSG00000102796	DHRS12	SDR40C1	dehydrogenase/reductase 12	protein-coding	0.012048	0.451890	
chunk0135_113_1	chr3	186942138	186942616	+	0	NA	intron (NM_173216, intron 1 of 7)	intron (NM_173216, intron 1 of 7)	11851	NM_173217	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.012552	0.440501	262(AAGAACTGCATGTCCC,-,0.00),263(AGAACTGCATGTCCCA,+,0.00)
chunk0047_456_1	chr12	76764667	76764867	+	0	NA	intron (NM_015336, intron 1 of 16)	intron (NM_015336, intron 1 of 16)	693	NM_015336	23390	Hs.4014	NM_015336	ENSG00000186908	ZDHHC17	DHHC-17|HIP14|HIP3|HSPC294|HYPH	zinc finger DHHC-type containing 17	protein-coding	0.035000	0.522388	
chunk0166_38_1	chr6	42147125	42147625	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4398	NM_001164446	647024	Hs.444277	NM_001164446	ENSG00000188112	C6orf132	bA7K24.2	chromosome 6 open reading frame 132	protein-coding	0.024000	0.467066	
chunk0105_308_1	chr2	190370122	190370596	+	0	NA	intron (NM_001128928, intron 6 of 6)	intron (NM_001128928, intron 6 of 6)	26889	NM_002194	3628	Hs.32309	NM_002194	ENSG00000151689	INPP1	-	inositol polyphosphate-1-phosphatase	protein-coding	0.002110	0.351579	
chunk0077_426_1	chr16	85484303	85484629	+	0	NA	Intergenic	Intergenic	-126957	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.024540	0.501529	
chunk0127_278_1	chr3	97775713	97776272	+	0	NA	intron (NR_103511, intron 3 of 9)	L1MA4|LINE|L1	11471	NM_032146	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.001789	0.308929	
chunk0005_212_1	chr1	59159587	59160121	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	-13047	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.003745	0.409346	
chunk0054_368_1	chr13	49858421	49859077	+	0	NA	Intergenic	Intergenic	-31660	NR_003268	220429	Hs.448219	NR_003268	ENSG00000181358	CTAGE10P	-	CTAGE family member 10, pseudogene	pseudo	0.003049	0.342466	310(GAGTACAGCCTGTTCA,-,0.00),311(AGTACAGCCTGTTCAG,+,0.00)
chunk0155_227_1	chr5	95508348	95509052	+	0	NA	intron (NM_014639, intron 29 of 42)	L2a|LINE|L2	46305	NM_014639	9652	Hs.482868	NM_014639	ENSG00000198677	TTC37	KIAA0372|Ski3|THES	tetratricopeptide repeat domain 37	protein-coding	0.002841	0.364539	
chunk0151_331_1	chr5	53798479	53798844	+	0	NA	Intergenic	Intergenic	152938	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.021918	0.527322	
chunk0188_284_1	chr8	15567236	15567550	+	0	NA	intron (NM_006765, intron 1 of 10)	intron (NM_006765, intron 1 of 10)	27306	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.003185	0.301587	
chunk0026_140_1	chr10	62183988	62184256	+	0	NA	Intergenic	Intergenic	84741	NM_001282941	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.011194	0.375465	
chunk0193_323_1	chr8	78708873	78709250	+	0	NA	intron (NM_016010, intron 7 of 8)	intron (NM_016010, intron 7 of 8)	15313	NR_077236	101241902	Hs.388511	NR_077236		LOC101241902	-	chromosome 4 open reading frame 46 pseudogene	pseudo	0.010610	0.351852	
chunk0105_229_1	chr2	188307597	188308104	+	0	NA	intron (NR_045563, intron 2 of 12)	intron (NR_045563, intron 2 of 12)	10358	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.001972	0.356299	
chunk0168_9_1	chr6	76853966	76854342	+	0	NA	Intergenic	Intergenic	609249	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.002660	0.275862	
chunk0074_144_1	chr16	23152936	23153308	+	0	NA	Intergenic	Intergenic	-3852	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.010753	0.420912	
chunk0053_390_1	chr13	36262022	36262321	+	0	NA	intron (NM_001144984, intron 2 of 5)	intron (NM_001144984, intron 2 of 5)	35684	NM_001144984	728591	Hs.656745	NM_001144981	ENSG00000242715	CCDC169	C13orf38	coiled-coil domain containing 169	protein-coding	0.000000	0.423333	163(CAGCACATAGTGTTCA,-,0.00),164(AGCACATAGTGTTCAG,+,0.00)
chunk0023_210_1	chr10	25396928	25397392	+	0	NA	intron (NM_020752, intron 3 of 10)	MLT1E1A|LTR|ERVL-MaLR	-220884	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.006466	0.412903	
chunk0069_84_1	chr15	61126772	61127000	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	102417	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.017544	0.432314	
chunk0108_377_1	chr2	236874928	236875169	+	0	NA	Intergenic	Intergenic	-210393	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.008299	0.462810	
chunk0009_439_1	chr1	111391543	111392317	+	0	NA	Intergenic	Intergenic	-2079	NR_029429	441897	Hs.568387	NR_029429	ENSG00000227179	PGCP1	-	progastricsin pseudogene 1	pseudo	0.002584	0.449032	617(GGAACAATTTGCTCTT,+,0.00)
chunk0076_207_1	chr16	68200046	68200867	+	0	NA	intron (NM_173165, intron 9 of 9)	L3|LINE|CR1	33043	NR_106831	102466194		NR_106831	ENSG00000284259	MIR6773	hsa-mir-6773	microRNA 6773	ncRNA	0.008526	0.375912	
chunk0091_197_1	chr19	8459944	8460510	+	0	NA	intron (NM_001297418, intron 3 of 13)	intron (NM_001297418, intron 3 of 13)	15308	NM_005968	4670	Hs.465808	NM_005968	ENSG00000099783	HNRNPM	CEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP M	heterogeneous nuclear ribonucleoprotein M	protein-coding	0.010601	0.417989	
chunk0031_349_1	chr10	129631160	129631620	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	164206	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.015217	0.373102	
chunk0169_363_1	chr6	106913778	106914135	+	0	NA	Intergenic	L2c|LINE|L2	60083	NM_001291739	100133941	Hs.644105	NM_013230	ENSG00000272398	CD24	CD24A	CD24 molecule	protein-coding	0.002801	0.458101	
chunk0187_26_1	chr8	700931	701560	+	0	NA	intron (NM_001303100, intron 2 of 5)	CpG	29994	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.060413	0.617460	529(GGGAGCATGCTGTACC,-,0.00),530(GGAGCATGCTGTACCC,+,0.00)
chunk0014_356_1	chr1	182384596	182385441	+	0	NA	intron (NM_001033056, intron 6 of 6)	intron (NM_001033056, intron 6 of 6)	6386	NM_001033056	2752	Hs.132016	NM_002065	ENSG00000135821	GLUL	GLNS|GS|PIG43|PIG59	glutamate-ammonia ligase	protein-coding	0.011834	0.407801	
chunk0158_379_1	chr5	134279718	134280101	+	0	NA	Intergenic	L1MEg|LINE|L1	-53650	NM_002715	5515	Hs.105818	NM_002715	ENSG00000113575	PPP2CA	NEDLBA|PP2Ac|PP2CA|PP2Calpha|RP-C	protein phosphatase 2 catalytic subunit alpha	protein-coding	0.015666	0.416667	
chunk0025_101_1	chr10	50585099	50585433	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	38711	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.002994	0.337313	
chunk0194_381_1	chr8	90626865	90627481	+	0	NA	intron (NM_001146273, intron 1 of 1)	intron (NM_001146273, intron 1 of 1)	18732	NM_001008495	169200	Hs.567759	NM_001008495	ENSG00000180694	TMEM64	-	transmembrane protein 64	protein-coding	0.009740	0.400324	
chunk0034_179_1	chr11	31478341	31478547	+	0	NA	intron (NM_144981, intron 1 of 6)	intron (NM_144981, intron 1 of 6)	31184	NM_001304274	196294	Hs.502223	NM_144981	ENSG00000148950	IMMP1L	IMMP1|IMP1|IMP1-LIKE	inner mitochondrial membrane peptidase subunit 1	protein-coding	0.004854	0.285024	
chunk0017_148_1	chr1	206730899	206731158	+	0	NA	intron (NM_032960, intron 6 of 9)	intron (NM_032960, intron 6 of 9)	41466	NM_000572	3586	Hs.193717	NM_000572	ENSG00000136634	IL10	CSIF|GVHDS|IL-10|IL10A|TGIF	interleukin 10	protein-coding	0.019305	0.523077	
chunk0167_24_1	chr6	53746536	53746873	+	0	NA	Intergenic	MIRb|SINE|MIR	-48276	NM_018214	55227	Hs.606493	NM_018214	ENSG00000137269	LRRC1	LANO|dJ523E19.1	leucine rich repeat containing 1	protein-coding	0.002967	0.393491	
chunk0079_81_1	chr17	11700138	11700425	+	0	NA	intron (NM_001372, intron 23 of 68)	intron (NM_001372, intron 23 of 68)	101850	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.010453	0.493056	
chunk0170_68_1	chr6	109741063	109741570	+	0	NA	intron (NM_014845, intron 7 of 22)	intron (NM_014845, intron 7 of 22)	11900	NR_106988									0.009862	0.411417	
chunk0015_99_1	chr1	185072901	185073210	+	0	NA	intron (NM_007212, intron 1 of 6)	L1ME3G|LINE|L1	27636	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.006472	0.303226	
chunk0123_251_1	chr3	45783314	45783513	+	0	NA	intron (NM_020208, intron 1 of 10)	intron (NM_020208, intron 1 of 10)	13130	NM_020208	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.005025	0.430000	
chunk0063_107_1	chr14	78951493	78951868	+	0	NA	intron (NM_004796, intron 7 of 16)	L2a|LINE|L2	-327659	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.005333	0.412234	
chunk0050_305_1	chr12	106825086	106825416	+	0	NA	intron (NM_018157, intron 3 of 8)	intron (NM_018157, intron 3 of 8)	-50420	NR_040246	100287944	Hs.742087	NR_040246	ENSG00000257545	LOC100287944	-	uncharacterized LOC100287944	ncRNA	0.003030	0.350453	
chunk0084_444_1	chr17	82882705	82883028	+	0	NA	intron (NM_005993, intron 14 of 38)	intron (NM_005993, intron 14 of 38)	-42811	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.065015	0.660494	
chunk0040_273_1	chr11	116740824	116741236	+	0	NA	Intergenic	Intergenic	31968	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.007282	0.506053	
chunk0033_256_1	chr11	18394077	18394319	+	0	NA	promoter-TSS (NM_001165416)	promoter-TSS (NM_001165416)	-191	NM_001135239	3939	Hs.2795	NM_005566	ENSG00000134333	LDHA	GSD11|HEL-S-133P|LDHM|PIG19	lactate dehydrogenase A	protein-coding	0.024793	0.477366	
chunk0213_16_1	chrY	21261996	21262276	+	0	NA	Intergenic	L1PA16|LINE|L1	124224	NM_001282471	100533178		NM_001282471		PRORY	CYorf17	proline rich Y-linked	protein-coding	0.003571	0.330961	
chunk0022_421_1	chr10	19111388	19111763	+	0	NA	intron (NM_001142308, intron 5 of 39)	L2|LINE|L2	62804	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.005333	0.390957	
chunk0131_210_1	chr3	148951555	148952145	+	0	NA	Intergenic	Intergenic	-39558	NM_001184721	2992	Hs.477892	NM_004130	ENSG00000163754	GYG1	GSD15|GYG	glycogenin 1	protein-coding	0.005085	0.336717	
chunk0087_126_1	chr18	33532892	33533098	+	0	NA	Intergenic	L1PA17|LINE|L1	-45582	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.000000	0.338164	
chunk0134_449_1	chr3	183845511	183845759	+	0	NA	intron (NM_018622, intron 4 of 9)	intron (NM_018622, intron 4 of 9)	-20030	NM_024871	79929	Hs.478465	NM_024871	ENSG00000180834	MAP6D1	MAPO6D1|SL21	MAP6 domain containing 1	protein-coding	0.008065	0.493976	
chunk0122_89_1	chr3	30046495	30046727	+	0	NA	Intergenic	Intergenic	-112455	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.008621	0.326180	
chunk0150_263_1	chr5	36535384	36535766	+	0	NA	Intergenic	Intergenic	-70780	NM_001166695	6507	Hs.481918	NM_004172	ENSG00000079215	SLC1A3	EA6|EAAT1|GLAST|GLAST1	solute carrier family 1 member 3	protein-coding	0.013089	0.480418	
chunk0161_364_1	chr5	175779001	175779415	+	0	NA	Intergenic	Intergenic	-17399	NM_006650	10814	Hs.193235	NM_006650	ENSG00000145920	CPLX2	921-L|CPX-2|CPX2|Hfb1	complexin 2	protein-coding	0.012077	0.556627	175(GAGAACATGCTGGGCT,-,0.00),176(AGAACATGCTGGGCTC,+,0.00)
chunk0167_427_1	chr6	75621906	75622376	+	0	NA	intron (NM_001304792, intron 2 of 14)	intron (NM_001304792, intron 2 of 14)	20632	NM_015571	26054	Hs.485784	NM_015571	ENSG00000112701	SENP6	SSP1|SUSP1	SUMO specific peptidase 6	protein-coding	0.004255	0.380042	
chunk0080_435_1	chr17	36020701	36021109	+	0	NA	Intergenic	L1P2|LINE|L1	-2937	NM_145898	6368	Hs.169191	NM_005064	ENSG00000274736	CCL23	CK-BETA-8|CKb8|Ckb-8|Ckb-8-1|MIP-3|MIP3|MPIF-1|SCYA23|hmrp-2a	C-C motif chemokine ligand 23	protein-coding	0.007353	0.386308	
chunk0196_291_1	chr8	109580010	109580497	+	0	NA	intron (NM_017786, intron 6 of 8)	intron (NM_017786, intron 6 of 8)	39627	NM_001278938	9166	Hs.409368	NM_004215	ENSG00000147654	EBAG9	EB9|PDAF	estrogen receptor binding site associated antigen 9	protein-coding	0.008214	0.395492	
chunk0171_101_1	chr6	122103732	122104721	+	0	NA	Intergenic	Intergenic	-295325	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.003033	0.311111	159(GAGCACATGGAGTTCC,-,0.00),160(AGCACATGGAGTTCCT,+,0.00)
chunk0173_113_1	chr6	143516185	143516384	+	0	NA	Intergenic	LTR81B|LTR|Gypsy	-4401	NM_032020	2519	Hs.17680	NM_032020	ENSG00000001036	FUCA2	dJ20N2.5	alpha-L-fucosidase 2	protein-coding	0.020101	0.505000	21(AGGGACGGCGTGTTCC,-,0.00),22(GGGACGGCGTGTTCCT,+,0.00)
chunk0003_296_1	chr1	37514674	37514992	+	0	NA	promoter-TSS (NM_001270876)	promoter-TSS (NM_001270876)	-14	NM_001270876	64769	Hs.17118	NM_022756	ENSG00000163875	MEAF6	C1orf149|CENP-28|EAF6|NY-SAR-91	MYST/Esa1 associated factor 6	protein-coding	0.138365	0.724138	
chunk0139_66_1	chr4	49100058	49100399	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	113586	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.026393	0.423977	
chunk0183_406_1	chr7	110407334	110407731	+	0	NA	Intergenic	Intergenic	-447319	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.005038	0.276382	
chunk0032_383_1	chr11	11465432	11465631	+	0	NA	intron (NM_198516, intron 1 of 10)	intron (NM_198516, intron 1 of 10)	-112174	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.030151	0.605000	
chunk0176_243_1	chr7	16097969	16098658	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-112173	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.001451	0.302899	302(AAGAACACAATGTACT,-,0.00),303(AGAACACAATGTACTC,+,0.00)
chunk0145_41_1	chr4	144433167	144433518	+	0	NA	Intergenic	Intergenic	-212654	NM_022475	64399	Hs.507991	NM_022475	ENSG00000164161	HHIP	HIP	hedgehog interacting protein	protein-coding	0.008547	0.332386	
chunk0069_205_1	chr15	63472929	63473355	+	0	NA	Intergenic	Intergenic	-31369	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.004695	0.416862	
chunk0181_344_1	chr7	88274804	88275094	+	0	NA	Intergenic	MER41B|LTR|ERV1	31964	NM_001205316	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.003448	0.415808	
chunk0158_79_1	chr5	126423262	126423588	+	0	NA	5' UTR (NM_001146320, exon 1 of 13)	5' UTR (NM_001146320, exon 1 of 13)	248	NM_001146320	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.092025	0.666667	
chunk0010_352_1	chr1	118660328	118661243	+	0	NA	Intergenic	Intergenic	328771	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.002186	0.378821	
chunk0184_174_1	chr7	116514898	116515298	+	0	NA	Intergenic	Intergenic	-9687	NM_001753	857	Hs.74034	NM_001753	ENSG00000105974	CAV1	BSCL3|CGL3|LCCNS|MSTP085|PPH3|VIP21	caveolin 1	protein-coding	0.000000	0.376559	170(AAGAACTGCCAGTTCC,-,0.00),171(AGAACTGCCAGTTCCC,+,0.00)
chunk0029_422_1	chr10	109985657	109986172	+	0	NA	intron (NR_038943, intron 2 of 4)	L1PB1|LINE|L1	-20054	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.005825	0.343023	
chunk0163_143_1	chr6	10778204	10778481	+	0	NA	intron (NM_001242385, intron 11 of 12)	L2b|LINE|L2	30583	NM_030969	81853	Hs.95600	NM_030969	ENSG00000137210	TMEM14B	-	transmembrane protein 14B	protein-coding	0.003610	0.377698	
chunk0048_369_1	chr12	86052851	86053197	+	0	NA	intron (NM_013244, intron 3 of 6)	intron (NM_013244, intron 3 of 6)	178729	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.017341	0.406340	
chunk0123_6_1	chr3	40119269	40119583	+	0	NA	intron (NM_001284426, intron 1 of 14)	L1ME4b|LINE|L1	19415	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.009554	0.358730	
chunk0149_436_1	chr5	29729279	29729823	+	0	NA	Intergenic	Intergenic	-333575	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.001838	0.359633	
chunk0118_435_1	chr22	38706843	38707051	+	0	NA	intron (NM_004286, intron 1 of 11)	intron (NM_004286, intron 1 of 11)	1145	NM_004286	9567	Hs.276925	NM_004286	ENSG00000100226	GTPBP1	GP-1|GP1|HSPC018	GTP binding protein 1	protein-coding	0.028846	0.473684	
chunk0200_385_1	chr9	26791445	26792014	+	0	NA	Intergenic	Intergenic	101099	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.003515	0.342105	
chunk0089_307_1	chr18	63809363	63809562	+	0	NA	Intergenic	L2c|LINE|L2	31685	NM_001261830	8710	Hs.138202	NM_003784	ENSG00000166396	SERPINB7	MEGSIN|PPKN|TP55	serpin family B member 7	protein-coding	0.010050	0.560000	
chunk0197_278_1	chr8	124057139	124057426	+	0	NA	intron (NM_001039112, intron 22 of 40)	L1MEg|LINE|L1	-16500	NR_040044	439941	Hs.683919	NM_001038706	ENSG00000181171	FER1L6-AS1	C8orf54	FER1L6 antisense RNA 1	ncRNA	0.003484	0.340278	
chunk0162_371_1	chr6	7258799	7259270	+	0	NA	Intergenic	Intergenic	54280	NM_003144	6745	Hs.114033	NM_003144	ENSG00000124783	SSR1	TRAPA	signal sequence receptor subunit 1	protein-coding	0.025478	0.502119	
chunk0150_272_1	chr5	36864591	36865265	+	0	NA	Intergenic	L1MB8|LINE|L1	11766	NR_046262	646719	Hs.355684	NR_046262	ENSG00000285967	NIPBL-DT	NIPBL-AS|NIPBL-AS1	NIPBL divergent transcript	ncRNA	0.000000	0.357037	
chunk0051_445_1	chr12	123231080	123231694	+	0	NA	intron (NM_022782, intron 1 of 23)	intron (NM_022782, intron 1 of 23)	1851	NR_103517	10198	Hs.577404	NM_022782	ENSG00000051825	MPHOSPH9	MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding	0.003257	0.401626	
chunk0004_188_1	chr1	46181916	46182125	+	0	NA	intron (NM_005727, intron 3 of 8)	L2b|LINE|L2	-5525	NM_001303427	110117499	Hs.655387	NM_001303427	ENSG00000278139	LOC110117498-PIK3R3	-	LOC110117498-PIK3R3 readthrough	protein-coding	0.014354	0.542857	
chunk0065_196_1	chr14	100039726	100040479	+	0	NA	Intergenic	Intergenic	-25312	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.014608	0.488064	
chunk0183_172_1	chr7	106165708	106166413	+	0	NA	Intergenic	Intergenic	-53413	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.007092	0.396601	
chunk0044_277_1	chr12	32533931	32534437	+	0	NA	promoter-TSS (NM_001304480)	promoter-TSS (NM_001304480)	-109	NM_001304480	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.007905	0.404339	
chunk0094_67_1	chr2	3440447	3440862	+	0	NA	intron (NM_016030, intron 5 of 11)	L1MC2|LINE|L1	60979	NM_016030	51112	Hs.252713	NM_016030	ENSG00000171853	TRAPPC12	CGI-87|PEBAS|TTC-15|TTC15	trafficking protein particle complex 12	protein-coding	0.002410	0.346154	
chunk0044_266_1	chr12	32375526	32375731	+	0	NA	intron (NM_001003398, intron 8 of 8)	intron (NM_001003398, intron 8 of 8)	-110344	NM_001304481	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.004878	0.315534	
chunk0093_210_1	chr19	49672274	49672473	+	0	NA	intron (NR_104201, intron 6 of 6)	L2c|LINE|L2	-4779	NR_033397	3276	Hs.20521	NM_001536	ENSG00000126457	PRMT1	ANM1|HCP1|HRMT1L2|IR1B4	protein arginine methyltransferase 1	protein-coding	0.040201	0.615000	
chunk0144_73_1	chr4	127820659	127821351	+	0	NA	intron (NM_014278, intron 14 of 18)	intron (NM_014278, intron 14 of 18)	38707	NM_014278	22824	Hs.135554	NM_014278	ENSG00000164070	HSPA4L	APG-1|HSPH3|Osp94	heat shock protein family A (Hsp70) member 4 like	protein-coding	0.001445	0.308802	
chunk0011_281_1	chr1	151391126	151391654	+	0	NA	Intergenic	Intergenic	-8175	NM_002796	5692	Hs.89545	NM_002796	ENSG00000159377	PSMB4	HN3|HsN3|PRAAS3|PROS-26|PROS26	proteasome subunit beta 4	protein-coding	0.007576	0.431002	
chunk0096_140_1	chr2	28796521	28797108	+	0	NA	intron (NM_206876, intron 8 of 8)	L1PA16|LINE|L1	-14020	NM_001142634	245711	Hs.511956	NM_182756	ENSG00000163806	SPDYA	RINGO3|RINGOA|SPDY1|SPY1	speedy/RINGO cell cycle regulator family member A	protein-coding	0.006814	0.369048	
chunk0191_256_1	chr8	53353842	53354539	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-102493	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.010043	0.444126	
chunk0201_47_1	chr9	33739882	33740238	+	0	NA	Intergenic	L1MEc|LINE|L1	-1644	NR_109755	101929688	Hs.372465	NR_109755	ENSG00000233776	LINC01251	-	long intergenic non-protein coding RNA 1251	ncRNA	0.002809	0.341737	
chunk0185_181_1	chr7	128077127	128077326	+	0	NA	intron (NM_014390, intron 17 of 23)	intron (NM_014390, intron 17 of 23)	-4635	NR_030324	693178		NR_030324	ENSG00000207588	MIR593	MIRN593|hsa-mir-593	microRNA 593	ncRNA	0.010050	0.570000	
chunk0144_12_1	chr4	124754061	124754276	+	0	NA	Intergenic	MIR|SINE|MIR	-41436	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.004651	0.513889	
chunk0030_409_1	chr10	120173083	120173327	+	0	NA	Intergenic	Intergenic	182018	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.004098	0.363265	
chunk0030_254_1	chr10	115653559	115653959	+	0	NA	intron (NM_207303, intron 26 of 28)	L2c|LINE|L2	560394	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.000000	0.374065	
chunk0101_52_1	chr2	123105045	123105248	+	0	NA	Intergenic	L1MCb|LINE|L1	-920141	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.009852	0.279412	
chunk0150_334_1	chr5	38542554	38542931	+	0	NA	intron (NM_002310, intron 1 of 19)	L2c|LINE|L2	13904	NM_001127671	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.010610	0.468254	279(CAGTGCACACTGTTCC,-,0.00),280(AGTGCACACTGTTCCA,+,0.00)
chunk0133_197_1	chr3	170804405	170804999	+	0	NA	Intergenic	L1PB1|LINE|L1	65554	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.005051	0.376471	
chunk0105_243_1	chr2	188573241	188573940	+	0	NA	intron (NR_045563, intron 10 of 12)	intron (NR_045563, intron 10 of 12)	216514	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.002861	0.335714	313(AGGAACACAAAGTACC,-,0.00),314(GGAACACAAAGTACCT,+,0.00)
chunk0137_438_1	chr4	28728625	28729180	+	0	NA	Intergenic	L1PA16|LINE|L1	-90680	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.001802	0.339928	
chunk0161_233_1	chr5	171236678	171237051	+	0	NA	intron (NM_022897, intron 22 of 27)	MIR|SINE|MIR	-72420	NM_021025	30012	Hs.249125	NM_021025	ENSG00000164438	TLX3	HOX11L2|RNX	T cell leukemia homeobox 3	protein-coding	0.002681	0.393048	
chunk0194_155_1	chr8	84756189	84756447	+	0	NA	intron (NM_001287244, intron 1 of 7)	intron (NM_001287244, intron 1 of 7)	50391	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.007752	0.366795	
chunk0082_138_1	chr17	55362679	55363143	+	0	NA	Intergenic	LTR33|LTR|ERVL	59069	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.000000	0.425806	
chunk0002_14_1	chr1	12231014	12231381	+	0	NA	intron (NM_018156, intron 1 of 68)	intron (NM_018156, intron 1 of 68)	1158	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.038147	0.622283	
chunk0100_11_1	chr2	105005550	105006001	+	0	NA	intron (NR_110603, intron 1 of 2)	MER58A|DNA|hAT-Charlie	-32250	NM_182640	64965	Hs.590900	NM_182640	ENSG00000135972	MRPS9	MRP-S9|RPMS9|S9mt	mitochondrial ribosomal protein S9	protein-coding	0.002217	0.393805	
chunk0041_165_1	chr11	126062894	126063380	+	0	NA	intron (NM_016952, intron 1 of 19)	intron (NM_016952, intron 1 of 19)	155	NM_001243597	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.086420	0.675565	
chunk0205_289_1	chr9	111920544	111920942	+	0	NA	intron (NM_003358, intron 2 of 8)	intron (NM_003358, intron 2 of 8)	-11357	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.022613	0.413534	
chunk0099_288_1	chr2	98714589	98714791	+	0	NA	intron (NM_012214, intron 2 of 15)	L1MC4a|LINE|L1	16436	NM_012214	11320	Hs.177576	NM_012214	ENSG00000071073	MGAT4A	GNT-IV|GNT-IVA|GnT-4a	alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A	protein-coding	0.004950	0.443350	
chunk0112_59_1	chr20	37496790	37497360	+	0	NA	Intergenic	(AAGCAA)n|Simple_repeat|Simple_repeat	-24130	NM_181689	4826	Hs.504703	NM_005386	ENSG00000053438	NNAT	Peg5	neuronatin	protein-coding	0.012281	0.392294	
chunk0169_372_1	chr6	107231141	107231594	+	0	NA	intron (NM_020381, intron 4 of 7)	intron (NM_020381, intron 4 of 7)	-116935	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.006623	0.361233	
chunk0129_387_1	chr3	126300404	126300603	+	0	NA	Intergenic	Intergenic	56890	NM_014079	28999	Hs.272215	NM_014079	ENSG00000163884	KLF15	KKLF	Kruppel like factor 15	protein-coding	0.035176	0.645000	
chunk0180_259_1	chr7	69549464	69549996	+	0	NA	Intergenic	Intergenic	47765	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.030075	0.521576	203(ATGGACAAGGTGTTCC,-,0.00),204(TGGACAAGGTGTTCCA,+,0.00)
chunk0038_145_1	chr11	84411881	84412149	+	0	NA	intron (NM_001142699, intron 7 of 27)	intron (NM_001142699, intron 7 of 27)	-94676	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003731	0.405204	
chunk0083_442_1	chr17	72676393	72676758	+	0	NA	intron (NM_001159770, intron 7 of 9)	MER68|LTR|ERVL	-36103	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.013699	0.409836	
chunk0103_157_1	chr2	162317050	162317461	+	0	NA	intron (NM_022168, intron 1 of 15)	MER58B|DNA|hAT-Charlie	1453	NM_022168	64135	Hs.163173	NM_022168	ENSG00000115267	IFIH1	AGS7|Hlcd|IDDM19|MDA-5|MDA5|RLR-2|SGMRT1	interferon induced with helicase C domain 1	protein-coding	0.004866	0.378641	
chunk0116_187_1	chr21	36932390	36932827	+	0	NA	intron (NM_001242785, intron 5 of 11)	intron (NM_001242785, intron 5 of 11)	34048	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.006865	0.404110	237(CAGAACACTGAGTACC,-,0.00),238(AGAACACTGAGTACCC,+,0.00)
chunk0154_345_1	chr5	86679522	86679896	+	0	NA	Intergenic	Intergenic	59212	NR_037402	109623460		NR_037402		SNORD138	MIR3607|mir-3607	small nucleolar RNA, C/D box 138	snoRNA	0.002674	0.389333	
chunk0180_404_1	chr7	75732631	75733073	+	0	NA	intron (NM_005338, intron 1 of 30)	MER5A1|DNA|hAT-Charlie	6120	NM_001243198	3092	Hs.329266	NM_005338	ENSG00000127946	HIP1	HIP-I|ILWEQ|SHON|SHONbeta|SHONgamma	huntingtin interacting protein 1	protein-coding	0.022624	0.519187	
chunk0199_169_1	chr9	4491634	4491983	+	0	NA	intron (NM_004170, intron 1 of 11)	intron (NM_004170, intron 1 of 11)	1381	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.020057	0.548571	186(GGGGACAGCTTGTTTC,-,0.00),187(GGGACAGCTTGTTTCC,+,0.00)
chunk0153_159_1	chr5	69521271	69521507	+	0	NA	intron (NM_002538, intron 4 of 8)	L1ME3G|LINE|L1	17212	NM_001205255	100506658	Hs.592605	NM_002538	ENSG00000197822	OCLN	BLCPMG|PPP1R115|PTORCH1	occludin	protein-coding	0.008475	0.362869	
chunk0020_72_1	chr1	232678287	232678486	+	0	NA	Intergenic	Intergenic	64329	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.020101	0.485000	
chunk0016_82_1	chr1	194230909	194231108	+	0	NA	Intergenic	MER52C|LTR|ERV1	926263	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.005025	0.545000	
chunk0056_350_1	chr13	91954913	91955414	+	0	NA	intron (NM_004466, intron 6 of 7)	L1ME3|LINE|L1	397044	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.005988	0.286853	
chunk0102_47_1	chr2	142535275	142535646	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-342166	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.002695	0.346774	181(AAGAACACTTTGTTAT,-,0.00)
chunk0055_209_1	chr13	62085912	62086322	+	0	NA	Intergenic	Intergenic	-56569	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004878	0.379562	
chunk0137_361_1	chr4	26022267	26022800	+	0	NA	Intergenic	Intergenic	108341	NM_001145432	389203	Hs.479386	NM_001145432	ENSG00000250317	SMIM20	C4orf52|MITRAC7|PNX	small integral membrane protein 20	protein-coding	0.009381	0.443820	
chunk0055_454_1	chr13	75813408	75813721	+	0	NA	intron (NM_001306080, intron 11 of 30)	intron (NM_001306080, intron 11 of 30)	52903	NM_015842	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.006390	0.550955	123(CTGTACAGTGTGTGCA,-,0.00),124(TGTACAGTGTGTGCAG,+,0.00)
chunk0117_415_1	chr21	45846910	45847198	+	0	NA	Intergenic	L1MC4|LINE|L1	-2907	NM_020528	54039	Hs.474049	NM_020528	ENSG00000183570	PCBP3	ALPHA-CP3|PCBP3-OT1|PCBP3OT	poly(rC) binding protein 3	protein-coding	0.000000	0.380623	
chunk0051_65_1	chr12	112932930	112933262	+	0	NA	Intergenic	Intergenic	-5337	NM_006187	4940	Hs.528634	NM_006187	ENSG00000111331	OAS3	p100|p100OAS	2'-5'-oligoadenylate synthetase 3	protein-coding	0.003012	0.423423	164(AAGAACACACTGTCTT,-,0.00),165(AGAACACACTGTCTTA,+,0.00)
chunk0005_207_1	chr1	59099131	59099476	+	0	NA	Intergenic	Intergenic	47504	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.008696	0.390173	
chunk0027_366_1	chr10	79097293	79097530	+	0	NA	intron (NM_020338, intron 1 of 24)	intron (NM_020338, intron 1 of 24)	28376	NM_020338	57178	Hs.193118	NM_020338	ENSG00000108175	ZMIZ1	MIZ|RAI17|TRAFIP10|ZIMP10	zinc finger MIZ-type containing 1	protein-coding	0.008439	0.563025	
chunk0154_276_1	chr5	82164573	82165412	+	0	NA	intron (NM_031482, intron 4 of 7)	intron (NM_031482, intron 4 of 7)	113424	NM_001025	6228	Hs.527193	NM_001025	ENSG00000186468	RPS23	BTDD|MABAS|MCINS|PAMAS|S23|uS12	ribosomal protein S23	protein-coding	0.004768	0.394048	
chunk0027_377_1	chr10	79399184	79399439	+	0	NA	intron (NM_153367, intron 2 of 3)	intron (NM_153367, intron 2 of 3)	46316	NM_153367	219654	Hs.523080	NM_153367	ENSG00000165424	ZCCHC24	C10orf56|Z3CXXC8	zinc finger CCHC-type containing 24	protein-coding	0.027451	0.562500	
chunk0018_259_1	chr1	220323832	220324067	+	0	NA	Intergenic	Intergenic	-51448	NM_012414	25782	Hs.654849	NM_012414	ENSG00000118873	RAB3GAP2	RAB3-GAP150|RAB3GAP150|SPG69|WARBM2|p150	RAB3 GTPase activating non-catalytic protein subunit 2	protein-coding	0.008511	0.423729	101(AGGTCAGACTGTACAT,+,0.00)
chunk0018_404_1	chr1	222632741	222633250	+	0	NA	intron (NM_198551, intron 5 of 27)	intron (NM_198551, intron 5 of 27)	-11308	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.013752	0.380392	
chunk0067_382_1	chr15	49071188	49071597	+	0	NA	Intergenic	L1PA7|LINE|L1	-24829	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.014670	0.395122	
chunk0055_328_1	chr13	68854192	68854631	+	0	NA	Intergenic	MER68|LTR|ERVL	30914	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.015945	0.393182	
chunk0160_361_1	chr5	160923897	160924273	+	0	NA	Intergenic	Intergenic	14541	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.002660	0.469496	
chunk0081_35_1	chr17	37501890	37502241	+	0	NA	intron (NM_007026, intron 1 of 2)	intron (NM_007026, intron 1 of 2)	12220	NM_007026	11072	Hs.91448	NM_007026	ENSG00000276023	DUSP14	MKP-L|MKP6	dual specificity phosphatase 14	protein-coding	0.005698	0.366477	
chunk0176_229_1	chr7	15643825	15644038	+	0	NA	intron (NM_005924, intron 1 of 2)	L1PA17|LINE|L1	42752	NM_005924	4223	Hs.170355	NM_005924	ENSG00000106511	MEOX2	GAX|MOX2	mesenchyme homeobox 2	protein-coding	0.004695	0.574766	
chunk0202_140_1	chr9	73404937	73405434	+	0	NA	Intergenic	Intergenic	253454	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.004024	0.345382	
chunk0065_358_1	chr14	103775565	103775778	+	0	NA	intron (NM_015316, intron 4 of 16)	intron (NM_015316, intron 4 of 16)	59927	NM_024071	79038	Hs.592322	NM_024071	ENSG00000100711	ZFYVE21	HCVP7TP1|ZF21	zinc finger FYVE-type containing 21	protein-coding	0.018779	0.434579	
chunk0199_419_1	chr9	13651965	13652583	+	0	NA	Intergenic	Intergenic	-220945	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.006472	0.408724	
chunk0061_62_1	chr14	56533396	56533999	+	0	NA	Intergenic	Intergenic	-46096	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.011609	0.402318	
chunk0152_262_1	chr5	61003104	61003303	+	0	NA	intron (NM_174889, intron 1 of 3)	intron (NM_174889, intron 1 of 3)	58074	NM_174889	91942	Hs.591757	NM_174889	ENSG00000164182	NDUFAF2	B17.2L|MC1DN10|MMTN|NDUFA12L|mimitin	NADH:ubiquinone oxidoreductase complex assembly factor 2	protein-coding	0.015075	0.380000	
chunk0073_142_1	chr16	6595062	6595319	+	0	NA	intron (NM_018723, intron 2 of 15)	L1MB7|LINE|L1	-178619	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.015564	0.453488	114(AAAGACACGTTGTCCC,-,0.00),115(AAGACACGTTGTCCCC,+,0.00)
chunk0008_278_1	chr1	94753263	94753493	+	0	NA	intron (NR_104131, intron 1 of 4)	intron (NR_104131, intron 1 of 4)	-7478	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.017391	0.441558	84(CAGGACACAGTGAACC,-,0.00),85(AGGACACAGTGAACCT,+,0.00)
chunk0065_424_1	chr14	106052383	106052835	+	0	NA	Intergenic	HUERS-P1-int|LTR|ERV1	-80340	NR_002224	8755	Hs.662288	NR_002224	ENSG00000271968	ADAM6	C14orf96|tMDCIV	ADAM metallopeptidase domain 6 (pseudogene)	pseudo	0.011062	0.377483	
chunk0170_104_1	chr6	110554969	110555365	+	0	NA	Intergenic	Intergenic	-78526	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.020202	0.445844	
chunk0099_422_1	chr2	102594702	102595252	+	0	NA	Intergenic	Intergenic	-24712	NM_003048	6549	Hs.250083	NM_003048	ENSG00000115616	SLC9A2	NHE2	solute carrier family 9 member A2	protein-coding	0.007273	0.335753	
chunk0193_6_1	chr8	70478412	70478942	+	0	NA	intron (NR_110653, intron 2 of 3)	MER58A|DNA|hAT-Charlie	7543	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.003774	0.425612	
chunk0178_85_1	chr7	30501702	30502167	+	0	NA	intron (NM_001199815, intron 1 of 3)	intron (NM_001199815, intron 1 of 3)	2907	NM_001199817	79017	Hs.530024	NM_024051	ENSG00000006625	GGCT	C7orf24|CRF21|GCTG|GGC	gamma-glutamylcyclotransferase	protein-coding	0.004301	0.399142	
chunk0076_212_1	chr16	68228757	68229407	+	0	NA	3' UTR (NM_004555, exon 11 of 11)	3' UTR (NM_004555, exon 11 of 11)	4417	NR_106831	102466194		NR_106831	ENSG00000284259	MIR6773	hsa-mir-6773	microRNA 6773	ncRNA	0.007692	0.443932	
chunk0018_341_1	chr1	221496310	221496785	+	0	NA	Intergenic	Intergenic	-160251	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.006316	0.386555	267(AAGGACTGGCTGTCCT,-,0.00),268(AGGACTGGCTGTCCTT,+,0.00)
chunk0148_82_1	chr5	2877431	2877897	+	0	NA	Intergenic	Intergenic	125533	NM_001306150	153571	Hs.148486	NM_178569	ENSG00000186493	C5orf38	CEI|IRX2NB	chromosome 5 open reading frame 38	protein-coding	0.015021	0.464668	
chunk0175_197_1	chr7	5667698	5668140	+	0	NA	intron (NR_046834, intron 1 of 2)	intron (NR_046834, intron 1 of 2)	12542	NR_046834	100874342	Hs.665728	NR_046834	ENSG00000237738	RNF216-IT1	-	RNF216 intronic transcript 1	ncRNA	0.011312	0.510158	
chunk0144_315_1	chr4	138822789	138822997	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-192866	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.009615	0.421053	
chunk0192_89_1	chr8	61023101	61023575	+	0	NA	Intergenic	Intergenic	-55590	NR_034003	100130298	Hs.636194	NR_034003		LOC100130298	-	hCG1816373-like	ncRNA	0.016878	0.383158	
chunk0007_235_1	chr1	82197947	82198386	+	0	NA	Intergenic	Intergenic	397769	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.011390	0.309091	
chunk0163_129_1	chr6	10510790	10511737	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-10072	NM_145649	2651	Hs.519884	NM_001491	ENSG00000111846	GCNT2	CCAT|CTRCT13|GCNT2C|GCNT5|IGNT|II|NACGT1|NAGCT1|ULG3|bA360O19.2|bA421M1.1	glucosaminyl (N-acetyl) transferase 2 (I blood group)	protein-coding	0.016895	0.414557	
chunk0180_341_1	chr7	73504773	73505054	+	0	NA	intron (NM_032408, intron 3 of 19)	intron (NM_032408, intron 3 of 19)	17372	NM_032408	9031	Hs.743372	NM_023005	ENSG00000009954	BAZ1B	WBSCR10|WBSCR9|WSTF	bromodomain adjacent to zinc finger domain 1B	protein-coding	0.000000	0.418440	
chunk0036_296_1	chr11	65791729	65791976	+	0	NA	promoter-TSS (NR_108085)	promoter-TSS (NR_108085)	-984	NR_108085	101927828	Hs.666246	NR_108085	ENSG00000255120	OVOL1-AS1	-	OVOL1 antisense RNA 1	ncRNA	0.036437	0.608871	
chunk0145_300_1	chr4	150052907	150053259	+	0	NA	Intergenic	Intergenic	-25191	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.002841	0.368272	
chunk0100_325_1	chr2	116537411	116537858	+	0	NA	Intergenic	L1ME1|LINE|L1	-1277045	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.002237	0.312500	
chunk0063_112_1	chr14	79089837	79090375	+	0	NA	intron (NR_073547, intron 14 of 20)	intron (NR_073547, intron 14 of 20)	-189233	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.000000	0.328386	258(GAGGACTGACTGTACT,-,0.00),259(AGGACTGACTGTACTG,+,0.00)
chunk0126_291_1	chr3	80328796	80329302	+	0	NA	Intergenic	L1MC4|LINE|L1	-561140	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.001976	0.307692	
chunk0005_98_1	chr1	56545467	56546038	+	0	NA	intron (NM_003713, intron 1 of 5)	intron (NM_003713, intron 1 of 5)	33832	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.017513	0.477273	
chunk0117_165_1	chr22	20230197	20230487	+	0	NA	Intergenic	Intergenic	18869	NR_031618	100302118		NR_031618	ENSG00000221039	MIR1286	MIRN1286|hsa-mir-1286|mir-1286	microRNA 1286	ncRNA	0.020690	0.611684	
chunk0143_238_1	chr4	114562340	114563090	+	0	NA	Intergenic	L2b|LINE|L2	-35740	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.001333	0.348868	
chunk0157_395_1	chr5	124136910	124137249	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	301441	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005900	0.338235	
chunk0160_438_1	chr5	164637960	164638365	+	0	NA	Intergenic	Intergenic	167883	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.009877	0.408867	
chunk0184_45_1	chr7	112262164	112262697	+	0	NA	intron (NM_021994, intron 1 of 11)	intron (NM_021994, intron 1 of 11)	55842	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.007505	0.301498	
chunk0127_215_1	chr3	96516456	96517110	+	0	NA	Intergenic	L1MA1|LINE|L1	156819	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.004587	0.314504	
chunk0165_130_1	chr6	33277041	33277320	+	0	NA	promoter-TSS (NM_003782)	promoter-TSS (NM_003782)	40	NM_003782	8705	Hs.534375	NM_003782	ENSG00000235863	B3GALT4	BETA3GALT4|GALT2|GALT4	beta-1,3-galactosyltransferase 4	protein-coding	0.157706	0.785714	
chunk0067_254_1	chr15	45732781	45733211	+	0	NA	Intergenic	Intergenic	98256	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.006977	0.519722	
chunk0006_256_1	chr1	69510001	69510302	+	0	NA	Intergenic	L2c|LINE|L2	-250024	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.000000	0.384106	
chunk0013_286_1	chr1	170941191	170941703	+	0	NA	intron (NM_025063, intron 1 of 14)	ERVL-B4-int|LTR|ERVL	5952	NM_025063	80133	Hs.591489	NM_025063	ENSG00000117501	MROH9	ARMC11|C1orf129	maestro heat like repeat family member 9	protein-coding	0.000000	0.407407	308(AGGAACACCATGATCA,-,0.00)
chunk0138_92_1	chr4	35712846	35713050	+	0	NA	Intergenic	L1MA4A|LINE|L1	-531168	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004902	0.541463	
chunk0193_251_1	chr8	76916288	76917001	+	0	NA	Intergenic	Intergenic	50206	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.014025	0.380952	
chunk0104_370_1	chr2	180150515	180150898	+	0	NA	Intergenic	Intergenic	-143653	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.002611	0.325521	
chunk0031_323_1	chr10	129236003	129236442	+	0	NA	Intergenic	Intergenic	-230962	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.015945	0.411364	
chunk0092_421_1	chr19	38058009	38058630	+	0	NA	intron (NM_015073, intron 2 of 21)	intron (NM_015073, intron 2 of 21)	151098	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.016103	0.585209	
chunk0034_386_1	chr11	36509728	36510464	+	0	NA	5' UTR (NM_004620, exon 1 of 7)	5' UTR (NM_004620, exon 1 of 7)	217	NM_004620	7189	Hs.444172	NM_004620	ENSG00000175104	TRAF6	MGC:3310|RNF85	TNF receptor associated factor 6	protein-coding	0.100543	0.712347	
chunk0042_272_1	chr12	6978599	6978799	+	0	NA	intron (NM_005768, intron 7 of 12)	intron (NM_005768, intron 7 of 12)	7918	NM_006331	10436	Hs.558447	NM_006331	ENSG00000126749	EMG1	C2F|Grcc2f|NEP1	EMG1 N1-specific pseudouridine methyltransferase	protein-coding	0.005000	0.487562	
chunk0089_312_1	chr18	63892470	63892672	+	0	NA	intron (NM_002575, intron 2 of 7)	intron (NM_002575, intron 2 of 7)	4866	NM_001143818	5055	Hs.594481	NM_002575	ENSG00000197632	SERPINB2	HsT1201|PAI|PAI-2|PAI2|PLANH2	serpin family B member 2	protein-coding	0.024752	0.443350	
chunk0079_362_1	chr17	17947958	17948433	+	0	NA	intron (NM_001033551, intron 1 of 13)	intron (NM_001033551, intron 1 of 13)	24275	NM_001033551	146691	Hs.462379	NM_144678	ENSG00000175662	TOM1L2	-	target of myb1 like 2 membrane trafficking protein	protein-coding	0.002105	0.401261	
chunk0100_46_1	chr2	105749515	105749745	+	0	NA	intron (NM_001004722, intron 1 of 3)	intron (NM_001004722, intron 1 of 3)	4567	NM_003581	8440	Hs.529244	NM_003581	ENSG00000071051	NCK2	GRB4|NCKbeta	NCK adaptor protein 2	protein-coding	0.021739	0.506494	107(CAGAACACAGTGTCCT,-,0.00),108(AGAACACAGTGTCCTT,+,0.00)
chunk0041_415_1	chr11	134022677	134023034	+	0	NA	Intergenic	LTR86B1|LTR|ERVL	-9417	NR_027276	100128239	Hs.423734	NR_027276	ENSG00000204241	LINC02731	-	long intergenic non-protein coding RNA 2731	ncRNA	0.022409	0.550279	
chunk0189_208_1	chr8	24220421	24220790	+	0	NA	Intergenic	Intergenic	-73435	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.002710	0.402703	
chunk0072_438_1	chr15	101382625	101382863	+	0	NA	intron (NM_002570, intron 10 of 21)	intron (NM_002570, intron 10 of 21)	48307	NR_132373	105371027		NR_132373	ENSG00000259764	PCSK6-AS1	-	PCSK6 antisense RNA 1	ncRNA	0.012605	0.430962	
chunk0021_197_1	chr10	5778944	5779298	+	0	NA	intron (NM_001494, intron 6 of 10)	L1M4a1|LINE|L1	34428	NM_001115156	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.016949	0.354930	
chunk0095_101_1	chr2	15284309	15285123	+	0	NA	intron (NR_052013, intron 42 of 50)	intron (NR_052013, intron 42 of 50)	276632	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.003686	0.346012	
chunk0096_52_1	chr2	27249673	27250277	+	0	NA	Intergenic	FLAM_A|SINE|Alu	13117	NM_003459	7781	Hs.467981	NM_003459	ENSG00000115194	SLC30A3	ZNT3	solute carrier family 30 member 3	protein-coding	0.014901	0.581818	
chunk0124_381_1	chr3	59573921	59574316	+	0	NA	Intergenic	MER44B|DNA|TcMar-Tigger	-524129	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.010127	0.404040	
chunk0189_329_1	chr8	26364156	26364819	+	0	NA	intron (NM_001177591, intron 8 of 9)	intron (NM_001177591, intron 8 of 9)	-18520	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.006033	0.396084	
chunk0171_337_1	chr6	129945328	129946047	+	0	NA	Intergenic	Intergenic	-72896	NM_032438	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.002782	0.261111	
chunk0175_221_1	chr7	6238234	6238906	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	34041	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.007440	0.353640	
chunk0055_240_1	chr13	62908500	62908866	+	0	NA	Intergenic	Intergenic	-101324	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.005464	0.367847	
chunk0041_113_1	chr11	124930304	124930842	+	0	NA	intron (NM_152722, intron 1 of 6)	L1ME3A|LINE|L1	5839	NM_152722	220296	Hs.745294	NM_152722	ENSG00000165478	HEPACAM	GlialCAM|HEPN1|MLC2A|MLC2B	hepatic and glial cell adhesion molecule	protein-coding	0.007435	0.382189	
chunk0043_101_1	chr12	14842184	14842721	+	0	NA	intron (NM_021071, intron 1 of 2)	intron (NM_021071, intron 1 of 2)	1027	NM_021071	420	Hs.591158	NM_021071	ENSG00000111339	ART4	ARTC4|CD297|DO|DO/ART4|DOK1	ADP-ribosyltransferase 4 (Dombrock blood group)	protein-coding	0.007449	0.308550	
chunk0050_7_1	chr12	99580294	99580667	+	0	NA	intron (NM_152788, intron 9 of 25)	L1MA4|LINE|L1	-67270	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.005362	0.328877	173(GAGAACATTATGTTAT,-,0.00)
chunk0130_170_1	chr3	133188925	133189749	+	0	NA	intron (NM_001282865, intron 1 of 3)	intron (NM_001282865, intron 1 of 3)	64516	NM_001282865	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.002427	0.393939	726(TGAGACACAGTGTTCT,-,0.00),727(GAGACACAGTGTTCTA,+,0.00)
chunk0083_448_1	chr17	72934937	72935231	+	0	NA	intron (NM_139177, intron 5 of 9)	L1ME1|LINE|L1	157630	NM_139177	201266	Hs.221127	NM_139177	ENSG00000133195	SLC39A11	C17orf26|ZIP-11|ZIP11	solute carrier family 39 member 11	protein-coding	0.023810	0.400000	
chunk0119_327_1	chr22	46842627	46842826	+	0	NA	intron (NM_014346, intron 4 of 12)	L1ME2z|LINE|L1	68799	NM_001284305	25771	Hs.435044	NM_014346	ENSG00000054611	TBC1D22A	C22orf4|HSC79E021	TBC1 domain family member 22A	protein-coding	0.040201	0.560000	
chunk0003_43_1	chr1	30715299	30715547	+	0	NA	intron (NM_002379, intron 5 of 7)	intron (NM_002379, intron 5 of 7)	-3349	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.000000	0.502008	
chunk0047_89_1	chr12	68498834	68499068	+	0	NA	Intergenic	Intergenic	-47467	NR_120458	100507195	Hs.450772	NR_120458	ENSG00000251301	LINC02384	-	long intergenic non-protein coding RNA 2384	ncRNA	0.008547	0.548936	
chunk0007_95_1	chr1	78687550	78687749	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	37857	NM_006417	10561	Hs.82316	NM_006417	ENSG00000137965	IFI44	MTAP44|TLDC5|p44	interferon induced protein 44	protein-coding	0.000000	0.305000	
chunk0126_127_1	chr3	75840204	75840613	+	0	NA	Intergenic	Intergenic	-54825	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.009780	0.336585	
chunk0169_378_1	chr6	107276438	107276788	+	0	NA	intron (NM_020381, intron 2 of 7)	MLT1H2-int|LTR|ERVL-MaLR	-162181	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.005714	0.455840	
chunk0105_317_1	chr2	190507148	190507570	+	0	NA	3' UTR (NM_001142645, exon 9 of 9)	3' UTR (NM_001142645, exon 9 of 9)	27383	NM_001142645	100131211	Hs.659824	NM_001142645	ENSG00000189362	NEMP2	TMEM194B	nuclear envelope integral membrane protein 2	protein-coding	0.009479	0.406619	
chunk0067_388_1	chr15	49094345	49095093	+	0	NA	Intergenic	Intergenic	-48156	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.010695	0.395194	
chunk0055_322_1	chr13	68743138	68743580	+	0	NA	Intergenic	Intergenic	141966	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.002262	0.349887	
chunk0112_256_1	chr20	42114982	42115272	+	0	NA	intron (NM_133170, intron 23 of 31)	L2b|LINE|L2	-496633	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.013793	0.501718	
chunk0163_50_1	chr6	8731773	8732391	+	0	NA	intron (NR_038980, intron 3 of 4)	intron (NR_038980, intron 3 of 4)	79873	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.004854	0.421648	
chunk0089_131_1	chr18	58788880	58789748	+	0	NA	Intergenic	Intergenic	-73515	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.010369	0.468354	
chunk0058_46_1	chr14	20299211	20299613	+	0	NA	exon (NM_138376, exon 4 of 10)	exon (NM_138376, exon 4 of 10)	6582	NM_138376	91875	Hs.98553	NM_138376	ENSG00000136319	TTC5	Strap	tetratricopeptide repeat domain 5	protein-coding	0.009950	0.446650	
chunk0026_27_1	chr10	60706615	60707058	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	26690	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.002257	0.288288	244(AAGCACAGTAAGTTCA,-,0.00),245(AGCACAGTAAGTTCAG,+,0.00)
chunk0026_88_1	chr10	61457960	61458465	+	0	NA	intron (NR_120643, intron 1 of 5)	HAL1ME|LINE|L1	-4762	NM_178505	219623	Hs.623955	NM_178505	ENSG00000196932	TMEM26	-	transmembrane protein 26	protein-coding	0.005941	0.428854	
chunk0010_78_1	chr1	113283961	113284326	+	0	NA	Intergenic	Intergenic	-77890	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.000000	0.409836	185(GAGCACAGCATGTCCT,-,0.00),186(AGCACAGCATGTCCTT,+,0.00)
chunk0155_319_1	chr5	96663319	96663946	+	0	NA	intron (NM_001042440, intron 1 of 29)	intron (NM_001042440, intron 1 of 29)	1475	NM_001042440	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.036683	0.496815	
chunk0125_299_1	chr3	70066616	70067099	+	0	NA	Intergenic	Intergenic	67113	NR_110000	101927152	Hs.382046	NR_110000	ENSG00000240405	SAMMSON	LINC01212	survival associated mitochondrial melanoma specific oncogenic non-coding RNA	ncRNA	0.006211	0.340909	
chunk0040_268_1	chr11	116397866	116398142	+	0	NA	Intergenic	Intergenic	374994	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.010870	0.411552	
chunk0132_410_1	chr3	164352685	164353348	+	0	NA	Intergenic	Intergenic	-181460	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.325301	
chunk0148_47_1	chr5	1363930	1364756	+	0	NA	non-coding (NR_125810, exon 2 of 2)	non-coding (NR_125810, exon 2 of 2)	15730	NR_125810	100506791	Hs.146092	NR_125810	ENSG00000250584	LINC01511	-	long intergenic non-protein coding RNA 1511	ncRNA	0.024213	0.466747	641(AAGGACACTTAGTCCC,-,0.00),642(AGGACACTTAGTCCCC,+,0.00)
chunk0209_397_1	chrX	55149306	55149505	+	0	NA	intron (NM_138362, intron 2 of 3)	MER4-int|LTR|ERV1	11697	NM_001166703	90736	Hs.415414	NM_138362	ENSG00000182518	FAM104B	CXorf44	family with sequence similarity 104 member B	protein-coding	0.010050	0.380000	169(AATACACTGTGTTCAT,+,0.00)
chunk0107_70_1	chr2	212264300	212264609	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	161906	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.003236	0.432258	
chunk0193_300_1	chr8	77969679	77970239	+	0	NA	Intergenic	Intergenic	519262	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.278075	296(AGGAACAGGAAGTTTT,-,0.00)
chunk0106_353_1	chr2	206822977	206823648	+	0	NA	Intergenic	L2c|LINE|L2	-40004	NR_036077	100422993		NR_036077	ENSG00000283469	MIR3130-1	MIR3130-3|mir-3130-1	microRNA 3130-1	ncRNA	0.013413	0.401786	411(GGGAACTGTAAGTGCT,-,0.00),412(GGAACTGTAAGTGCTT,+,0.00)
chunk0113_383_1	chr20	59957642	59958032	+	0	NA	promoter-TSS (NM_177980)	promoter-TSS (NM_177980)	-579	NM_177980	60437	Hs.729046	NM_021810	ENSG00000124215	CDH26	VR20	cadherin 26	protein-coding	0.002564	0.365729	
chunk0025_337_1	chr10	57997626	57998324	+	0	NA	Intergenic	Intergenic	269959	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.004298	0.323319	
chunk0030_440_1	chr10	120850915	120851689	+	0	NA	promoter-TSS (NR_033850)	promoter-TSS (NR_033850)	-123	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.052972	0.565161	
chunk0140_189_1	chr4	69984131	69984330	+	0	NA	Intergenic	(GCT)n|Simple_repeat|Simple_repeat	-11701	NM_003154	6779	Hs.654495	NM_003154	ENSG00000126549	STATH	STR	statherin	protein-coding	0.000000	0.480000	
chunk0004_182_1	chr1	46039477	46039746	+	0	NA	TTS (NM_001114172)	TTS (NM_001114172)	93097	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.011152	0.485185	
chunk0117_106_1	chr22	17891775	17891977	+	0	NA	intron (NM_015241, intron 11 of 31)	intron (NM_015241, intron 11 of 31)	15010	NM_001122731	57553	Hs.528024	NM_015241	ENSG00000243156	MICAL3	MICAL-3	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding	0.019802	0.527094	
chunk0197_272_1	chr8	123843585	123843918	+	0	NA	Intergenic	Intergenic	-8236	NM_001039112	654463	Hs.632058	NM_001039112	ENSG00000214814	FER1L6	C8ORFK23	fer-1 like family member 6	protein-coding	0.003003	0.305389	231(AAGCACAGTCTGTTTT,-,0.00),232(AGCACAGTCTGTTTTT,+,0.00)
chunk0131_226_1	chr3	149277134	149277752	+	0	NA	Intergenic	Intergenic	-55398	NM_000096	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.004854	0.399031	304(CAGTACTTCCTGTTCC,-,0.00),305(AGTACTTCCTGTTCCT,+,0.00)
chunk0134_283_1	chr3	179739828	179740259	+	0	NA	intron (NM_003940, intron 10 of 20)	intron (NM_003940, intron 10 of 20)	86898	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.013921	0.442130	
chunk0099_282_1	chr2	98588664	98588996	+	0	NA	3' UTR (NM_001134224, exon 26 of 26)	3' UTR (NM_001134224, exon 26 of 26)	19688	NM_001008215	493753	Hs.596537	NM_001008215	ENSG00000183513	COA5	6330578E17Rik|C2orf64|CEMCOX3|Pet191	cytochrome c oxidase assembly factor 5	protein-coding	0.003012	0.339339	
chunk0161_390_1	chr5	176964075	176964533	+	0	NA	intron (NM_016290, intron 6 of 14)	L1ME4a|LINE|L1	42138	NM_016290	51720	Hs.232721	NM_016290	ENSG00000087206	UIMC1	RAP80|X2HRIP110	ubiquitin interaction motif containing 1	protein-coding	0.002183	0.335512	
chunk0145_6_1	chr4	143015782	143016540	+	0	NA	Intergenic	L1MA5|LINE|L1	-168756	NM_001290326	84640	Hs.480848	NM_032557	ENSG00000170185	USP38	HP43.8KD	ubiquitin specific peptidase 38	protein-coding	0.007916	0.322793	424(GGGAACATGTTGTTCC,-,0.00),425(GGAACATGTTGTTCCA,+,0.00)
chunk0082_132_1	chr17	55294425	55295194	+	0	NA	intron (NM_002126, intron 2 of 3)	intron (NM_002126, intron 2 of 3)	29849	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.013004	0.422078	
chunk0031_16_1	chr10	121785319	121785615	+	0	NA	intron (NM_001001976, intron 11 of 11)	intron (NM_001001976, intron 11 of 11)	142596	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.006757	0.444444	
chunk0058_325_1	chr14	28278041	28278563	+	0	NA	Intergenic	Intergenic	487017	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.011494	0.332696	
chunk0137_432_1	chr4	28402574	28402773	+	0	NA	Intergenic	LTR1A2|LTR|ERV1	-416909	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.020101	0.460000	
chunk0197_334_1	chr8	125203972	125204600	+	0	NA	intron (NM_173685, intron 5 of 7)	intron (NM_173685, intron 5 of 7)	112445	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.007962	0.403816	
chunk0054_81_1	chr13	42415803	42416346	+	0	NA	Intergenic	Intergenic	143921	NM_016248	11215	Hs.105105	NM_016248	ENSG00000023516	AKAP11	AKAP-11|AKAP220|PPP1R44|PRKA11	A-kinase anchoring protein 11	protein-coding	0.011050	0.341912	
chunk0207_341_1	chr9	134534521	134535146	+	0	NA	Intergenic	Intergenic	-106972	NM_001278074	1289	Hs.210283	NM_000093	ENSG00000130635	COL5A1	EDSC|EDSCL1	collagen type V alpha 1 chain	protein-coding	0.030400	0.520767	
chunk0063_331_1	chr14	85285068	85285482	+	0	NA	Intergenic	Intergenic	-108604	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.002415	0.313253	
chunk0123_41_1	chr3	40886839	40887525	+	0	NA	Intergenic	Intergenic	-312269	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.008746	0.467249	
chunk0037_99_1	chr11	72066420	72066776	+	0	NA	intron (NM_001286561, intron 2 of 26)	L2c|LINE|L2	5704	NR_036123	100422953		NR_036123	ENSG00000263742	MIR3165	mir-3165	microRNA 3165	ncRNA	0.005618	0.445378	
chunk0077_410_1	chr16	85045147	85045445	+	0	NA	intron (NM_001286566, intron 1 of 11)	intron (NM_001286566, intron 1 of 11)	17545	NM_014732	9764	Hs.301658	NM_014732	ENSG00000135709	KIAA0513	-	KIAA0513	protein-coding	0.010067	0.481605	148(AAGCACTCACTGTTCT,-,0.00),149(AGCACTCACTGTTCTT,+,0.00)
chunk0187_151_1	chr7	150003217	150003713	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-129603	NR_027040	401431	Hs.556998	NM_001008745	ENSG00000204934	ATP6V0E2-AS1	-	ATP6V0E2 antisense RNA 1	ncRNA	0.006048	0.446680	
chunk0117_113_1	chr22	17954411	17954935	+	0	NA	intron (NM_015241, intron 1 of 31)	intron (NM_015241, intron 1 of 31)	26288	NR_030378	693233		NR_030378	ENSG00000207780	MIR648	MIRN648|hsa-mir-648	microRNA 648	ncRNA	0.020992	0.474286	
chunk0128_314_1	chr3	111763775	111764257	+	0	NA	intron (NM_001134437, intron 1 of 17)	MIRb|SINE|MIR	31536	NM_001134437	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.010373	0.422360	
chunk0139_1_1	chr4	47715984	47716536	+	0	NA	intron (NM_001278585, intron 4 of 19)	intron (NM_001278585, intron 4 of 19)	63591	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.001812	0.363472	
chunk0003_60_1	chr1	31129611	31130229	+	0	NA	Intergenic	Intergenic	-64203	NM_014676	9698	Hs.281707	NM_014676	ENSG00000134644	PUM1	HSPUM|PUMH|PUMH1|PUML1|SCA47	pumilio RNA binding family member 1	protein-coding	0.006472	0.402262	
chunk0198_95_1	chr8	130324062	130324274	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	-27635	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.004717	0.478873	
chunk0102_82_1	chr2	143333266	143333861	+	0	NA	intron (NM_018460, intron 6 of 13)	intron (NM_018460, intron 6 of 13)	204233	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.015126	0.374161	
chunk0133_221_1	chr3	171171468	171171706	+	0	NA	intron (NM_001161560, intron 9 of 31)	intron (NM_001161560, intron 9 of 31)	-64828	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.004202	0.460251	
chunk0068_355_1	chr15	57914539	57915164	+	0	NA	Intergenic	Intergenic	99246	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.012800	0.480831	380(GAAAACACCATGTGCT,-,0.00),381(AAAACACCATGTGCTA,+,0.00)
chunk0122_456_1	chr3	39858975	39859473	+	0	NA	intron (NM_015460, intron 1 of 16)	L1MA9|LINE|L1	49564	NR_104316	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.006024	0.324649	
chunk0190_395_1	chr8	40179912	40180387	+	0	NA	Intergenic	LTR78|LTR|ERV1	26681	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.000000	0.397059	
chunk0111_89_1	chr20	23397020	23397436	+	0	NA	intron (NM_001283018, intron 2 of 10)	intron (NM_001283018, intron 2 of 10)	24291	NM_001283026	63908	Hs.269471	NM_022080	ENSG00000125814	NAPB	SNAP-BETA|SNAPB	NSF attachment protein beta	protein-coding	0.007212	0.470024	
chunk0062_39_1	chr14	67240456	67240774	+	0	NA	promoter-TSS (NM_001256550)	promoter-TSS (NM_001256550)	-680	NM_022474	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.047170	0.564263	
chunk0060_99_1	chr14	43308264	43308661	+	0	NA	Intergenic	Tigger17b|DNA|TcMar-Tigger	1198834	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.005038	0.359296	
chunk0144_363_1	chr4	139865893	139866448	+	0	NA	intron (NM_018717, intron 3 of 5)	MER115|DNA|hAT-Tip100	200402	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.007207	0.501799	297(TAGGACATATTGTACT,-,0.00),298(AGGACATATTGTACTT,+,0.00)
chunk0083_380_1	chr17	71502497	71502884	+	0	NA	Intergenic	Intergenic	-300511	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.002584	0.371134	
chunk0084_137_1	chr17	76281982	76282654	+	0	NA	intron (NR_130649, intron 7 of 18)	intron (NR_130649, intron 7 of 18)	17113	NM_182565	283991	Hs.744981	NM_182565	ENSG00000185262	UBALD2	FAM100B	UBA like domain containing 2	protein-coding	0.026786	0.592868	
chunk0143_232_1	chr4	114326411	114326755	+	0	NA	Intergenic	MER90|LTR|ERV1	-271872	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.002907	0.368116	181(AAGAACAACATGGCCT,-,0.00)
chunk0044_84_1	chr12	28230878	28231789	+	0	NA	Intergenic	Intergenic	-25867	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.000000	0.331140	562(TAGTACAGCTTGTTCC,-,0.00),563(AGTACAGCTTGTTCCT,+,0.00)
chunk0207_404_1	chr9	136944522	136944848	+	0	NA	promoter-TSS (NM_000606)	promoter-TSS (NM_000606)	69	NM_018998	54461	Hs.522507	NM_018998	ENSG00000159069	FBXW5	Fbw5	F-box and WD repeat domain containing 5	protein-coding	0.153374	0.785933	
chunk0005_275_1	chr1	59941135	59941726	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-14679	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.000000	0.388514	
chunk0002_187_1	chr1	19420560	19421010	+	0	NA	intron (NM_001313932, intron 1 of 4)	intron (NM_001313932, intron 1 of 4)	63922	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.008889	0.481153	
chunk0101_109_1	chr2	125657003	125657253	+	0	NA	Intergenic	L1MA5A|LINE|L1	-998807	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.004000	0.326693	
chunk0110_257_1	chr20	16729823	16730119	+	0	NA	promoter-TSS (NM_003092)	promoter-TSS (NM_003092)	7	NM_198220	6629	Hs.280378	NM_003092	ENSG00000125870	SNRPB2	Msl1|U2B''	small nuclear ribonucleoprotein polypeptide B2	protein-coding	0.077703	0.599327	
chunk0114_321_1	chr21	17435509	17436153	+	0	NA	Intergenic	LTR54B|LTR|ERV1	-3059	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.006211	0.379845	
chunk0067_440_1	chr15	50112456	50113089	+	0	NA	intron (NR_073596, intron 1 of 27)	intron (NR_073596, intron 1 of 27)	544	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.007899	0.507886	
chunk0038_443_1	chr11	94736988	94737190	+	0	NA	Intergenic	Intergenic	-31253	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.000000	0.334975	
chunk0186_189_1	chr7	139703435	139703858	+	0	NA	intron (NM_001113239, intron 2 of 14)	intron (NM_001113239, intron 2 of 14)	74248	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.009456	0.500000	180(GAGAACACCATGCACC,-,0.00)
chunk0123_16_1	chr3	40265245	40265462	+	0	NA	intron (NR_033965, intron 2 of 2)	intron (NR_033965, intron 2 of 2)	-44329	NM_005875	10289	Hs.315230	NM_005875	ENSG00000114784	EIF1B	GC20	eukaryotic translation initiation factor 1B	protein-coding	0.000000	0.385321	
chunk0005_346_1	chr1	61241453	61241777	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	11903	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.009259	0.446154	
chunk0059_144_1	chr14	32076350	32076847	+	0	NA	promoter-TSS (NM_001030055)	promoter-TSS (NM_001030055)	101	NR_027263	84837	Hs.496755	NM_032751		ARHGAP5-AS1	C14orf128	ARHGAP5 antisense RNA 1 (head to head)	ncRNA	0.060362	0.584337	
chunk0061_336_1	chr14	63404319	63404596	+	0	NA	intron (NR_104104, intron 4 of 12)	intron (NR_104104, intron 4 of 12)	-85578	NM_145171	122876	Hs.375028	NM_145171	ENSG00000179600	GPHB5	B5|GPB5|ZLUT1	glycoprotein hormone subunit beta 5	protein-coding	0.007220	0.410072	
chunk0079_368_1	chr17	18000137	18000336	+	0	NA	intron (NM_031294, intron 9 of 13)	(TGTG)n|Simple_repeat|Simple_repeat	27423	NM_001130091	83450	Hs.579264	NM_031294	ENSG00000171962	DRC3	CFAP134|LRRC48	dynein regulatory complex subunit 3	protein-coding	0.025126	0.480000	
chunk0072_432_1	chr15	101217576	101217909	+	0	NA	intron (NM_014918, intron 2 of 2)	L1MC3|LINE|L1	34190	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.012012	0.440120	
chunk0036_55_1	chr11	59089015	59089498	+	0	NA	Intergenic	L1ME3G|LINE|L1	-17929	NM_198947	374393	Hs.186579	NM_198947	ENSG00000189057	FAM111B	CANP|POIKTMP	family with sequence similarity 111 member B	protein-coding	0.008282	0.388430	
chunk0189_202_1	chr8	23808822	23809571	+	0	NA	Intergenic	L1MC3|LINE|L1	45611	NM_003155	6781	Hs.25590	NM_003155	ENSG00000159167	STC1	STC	stanniocalcin 1	protein-coding	0.006676	0.356000	
chunk0151_107_1	chr5	43421917	43422561	+	0	NA	Intergenic	Intergenic	-9848	NM_148672	56477	Hs.656904	NM_019846	ENSG00000151882	CCL28	CCK1|MEC|SCYA28	C-C motif chemokine ligand 28	protein-coding	0.003106	0.350388	
chunk0052_189_1	chr13	24591517	24592020	+	0	NA	intron (NR_002815, intron 5 of 8)	LTR5_Hs|LTR|ERVK	11560	NR_002815	374491	Hs.406779	NR_002815		TPTE2P6	-	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 6	pseudo	0.015905	0.456349	
chunk0031_41_1	chr10	122190169	122190821	+	0	NA	intron (NM_001291878, intron 1 of 16)	intron (NM_001291878, intron 1 of 16)	27069	NM_001291878	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.026074	0.477795	324(CAGCACAGTCTGTCCC,-,0.00),325(AGCACAGTCTGTCCCC,+,0.00)
chunk0143_374_1	chr4	122568573	122568980	+	0	NA	Intergenic	L1MA3|LINE|L1	-50207	NR_104126	100996941	Hs.439487	NR_104126	ENSG00000227145	IL21-AS1	-	IL21 antisense RNA 1	ncRNA	0.000000	0.294118	
chunk0089_318_1	chr18	64804123	64804527	+	0	NA	Intergenic	L1MD2|LINE|L1	-544270	NR_033983	400654	Hs.434235	NR_033983	ENSG00000266952	LINC01538	-	long intergenic non-protein coding RNA 1538	ncRNA	0.002475	0.353086	
chunk0206_281_1	chr9	124364922	124365171	+	0	NA	intron (NM_002799, intron 6 of 7)	intron (NM_002799, intron 6 of 7)	11573	NR_027406	100129034	Hs.654980	NR_027406		LOC100129034	-	uncharacterized LOC100129034	ncRNA	0.020080	0.492000	101(AAGTACAGAGTGCTCT,-,0.00),102(AGTACAGAGTGCTCTT,+,0.00)
chunk0172_99_1	chr6	134806451	134806985	+	0	NA	Intergenic	Intergenic	143404	NM_170771	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.005618	0.377570	
chunk0201_82_1	chr9	34515409	34515713	+	0	NA	intron (NM_001281428, intron 18 of 19)	L1MB8|LINE|L1	7478	NM_198573	375704	Hs.522085	NM_198573	ENSG00000168913	ENHO	C9orf165|UNQ470	energy homeostasis associated	protein-coding	0.003289	0.396721	
chunk0099_428_1	chr2	102767428	102767627	+	0	NA	intron (NM_144632, intron 3 of 4)	intron (NM_144632, intron 3 of 4)	5496	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.010050	0.370000	
chunk0069_180_1	chr15	63065676	63066355	+	0	NA	TTS (NM_000366)	TTS (NM_000366)	17578	NM_001301289	7168	Hs.133892	NM_000366	ENSG00000140416	TPM1	C15orf13|CMD1Y|CMH3|HEL-S-265|HTM-alpha|LVNC9|TMSA	tropomyosin 1	protein-coding	0.010309	0.422059	348(AGGCACACACTGTGCT,-,0.00),349(GGCACACACTGTGCTT,+,0.00)
chunk0205_429_1	chr9	115107866	115108878	+	0	NA	intron (NM_002160, intron 1 of 27)	L2a|LINE|L2	9885	NM_002160	3371	Hs.143250	NM_002160	ENSG00000041982	TNC	150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C	tenascin C	protein-coding	0.003953	0.421520	
chunk0030_388_1	chr10	119593110	119593431	+	0	NA	intron (NM_003252, intron 1 of 11)	intron (NM_003252, intron 1 of 11)	3759	NM_003252	7073	Hs.501203	NM_003252	ENSG00000151923	TIAL1	TCBP|TIAR	TIA1 cytotoxic granule associated RNA binding protein like 1	protein-coding	0.000000	0.347826	
chunk0008_272_1	chr1	94707089	94707657	+	0	NA	intron (NR_104131, intron 2 of 4)	Charlie15b|DNA|hAT-Charlie	38527	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.017606	0.413005	
chunk0073_148_1	chr16	6616644	6617271	+	0	NA	intron (NM_018723, intron 2 of 15)	MER58A|DNA|hAT-Charlie	-156852	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.012759	0.433121	
chunk0036_184_1	chr11	62841277	62841667	+	0	NA	Intergenic	Intergenic	-1316	NM_018093	54663	Hs.654620	NM_018093	ENSG00000133316	WDR74	Nsa1	WD repeat domain 74	protein-coding	0.041026	0.439898	
chunk0099_354_1	chr2	100407144	100407676	+	0	NA	intron (NM_004854, intron 2 of 6)	intron (NM_004854, intron 2 of 6)	10258	NM_004854	9486	Hs.516370	NM_004854	ENSG00000115526	CHST10	HNK-1ST|HNK1ST	carbohydrate sulfotransferase 10	protein-coding	0.015038	0.517824	
chunk0006_59_1	chr1	64601382	64601735	+	0	NA	intron (NM_020925, intron 3 of 26)	intron (NM_020925, intron 3 of 26)	21711	NR_039957	100616338		NR_039957	ENSG00000264470	MIR4794	-	microRNA 4794	ncRNA	0.011331	0.426554	
chunk0129_34_1	chr3	117263050	117263745	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	341966	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.014388	0.346264	353(TTGTACAAGATGTTCT,-,0.00),354(TGTACAAGATGTTCTA,+,0.00)
chunk0098_70_1	chr2	67142385	67142818	+	0	NA	intron (NR_038844, intron 6 of 7)	intron (NR_038844, intron 6 of 7)	56155	NR_110564	102800447	Hs.144196	NR_110564		LINC01828	-	long intergenic non-protein coding RNA 1828	ncRNA	0.002309	0.322581	
chunk0053_364_1	chr13	35283895	35284243	+	0	NA	intron (NM_015678, intron 34 of 57)	MER58B|DNA|hAT-Charlie	192626	NM_005584	4081	Hs.584776	NM_005584	ENSG00000180660	MAB21L1	CAGR1|Nbla00126	mab-21 like 1	protein-coding	0.000000	0.378223	
chunk0152_268_1	chr5	61163018	61163616	+	0	NA	promoter-TSS (NM_001048249)	promoter-TSS (NM_001048249)	-842	NM_001048249	643155	Hs.508479	NM_001048249	ENSG00000188725	SMIM15	C5orf43	small integral membrane protein 15	protein-coding	0.015050	0.398998	
chunk0041_106_1	chr11	124841787	124842539	+	0	NA	Intergenic	L2c|LINE|L2	-23246	NM_022370	64221	Hs.435621	NM_022370	ENSG00000154134	ROBO3	HGPPS|HGPPS1|HGPS|RBIG1|RIG1	roundabout guidance receptor 3	protein-coding	0.007979	0.494024	
chunk0194_453_1	chr8	92678871	92679107	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-23495	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.000000	0.362869	
chunk0065_352_1	chr14	103708694	103709066	+	0	NA	intron (NM_005432, intron 4 of 9)	intron (NM_005432, intron 4 of 9)	6606	NM_005432	7517	Hs.592325	NM_005432	ENSG00000126215	XRCC3	CMM6	X-ray repair cross complementing 3	protein-coding	0.034946	0.595174	
chunk0039_452_1	chr11	108503140	108503448	+	0	NA	Intergenic	Intergenic	-4862	NM_153705	143888	Hs.83286	NM_153705	ENSG00000178202	POGLUT3	KDELC2	protein O-glucosyltransferase 3	protein-coding	0.000000	0.330097	
chunk0145_349_1	chr4	151038363	151038702	+	0	NA	Intergenic	Intergenic	-23035	NM_006726	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.011799	0.455882	
chunk0029_91_1	chr10	97318872	97319511	+	0	NA	promoter-TSS (NM_005479)	promoter-TSS (NM_005479)	-74	NM_005479	10023	Hs.126057	NM_005479	ENSG00000165879	FRAT1	-	FRAT regulator of WNT signaling pathway 1	protein-coding	0.095462	0.678125	
chunk0051_143_1	chr12	115750478	115750677	+	0	NA	Intergenic	L2|LINE|L2	398077	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.005025	0.450000	
chunk0045_210_1	chr12	47900071	47900791	+	0	NA	intron (NM_001017535, intron 1 of 10)	MIRb|SINE|MIR	4600	NM_000376	7421	Hs.524368	NM_000376	ENSG00000111424	VDR	NR1I1|PPP1R163	vitamin D receptor	protein-coding	0.005556	0.492372	
chunk0011_421_1	chr1	154463654	154463915	+	0	NA	intron (NM_000565, intron 9 of 9)	intron (NM_000565, intron 9 of 9)	38266	NM_001010846	126669	Hs.591481	NM_001010846	ENSG00000169291	SHE	-	Src homology 2 domain containing E	protein-coding	0.007663	0.507634	
chunk0063_118_1	chr14	79285078	79285784	+	0	NA	intron (NM_138970, intron 1 of 5)	MLT1B|LTR|ERVL-MaLR	6092	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004249	0.403112	
chunk0164_436_1	chr6	27568040	27568633	+	0	NA	Intergenic	MER4A|LTR|ERV1	-95218	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.013491	0.425926	
chunk0213_6_1	chrY	19644786	19645296	+	0	NA	Intergenic	L1PA6|LINE|L1	77683	NR_045129	246126	Hs.522863	NM_001005852	ENSG00000131002	TXLNGY	CYorf15A|CYorf15B|TXLNG2P	taxilin gamma pseudogene, Y-linked	pseudo	0.003922	0.465753	408(AGGGGCAGTCTGTCCA,-,0.00),409(GGGGCAGTCTGTCCAG,+,0.00)
chunk0079_431_1	chr17	19942109	19943109	+	0	NA	intron (NM_007202, intron 5 of 14)	L1ME3G|LINE|L1	35247	NM_007202	11216	Hs.642676	NM_007202	ENSG00000108599	AKAP10	AKAP-10|D-AKAP-2|D-AKAP2|PRKA10	A-kinase anchoring protein 10	protein-coding	0.005000	0.351648	
chunk0034_94_1	chr11	27506819	27507057	+	0	NA	promoter-TSS (NR_033313)	promoter-TSS (NR_033313)	86	NR_033313	497258	Hs.675323	NR_002832	ENSG00000245573	BDNF-AS	ANTI-BDNF|BDNF|BDNF-AS1|BDNFAS|BDNFOS|NCRNA00049	BDNF antisense RNA	ncRNA	0.075630	0.610879	
chunk0204_391_1	chr9	102250205	102250888	+	0	NA	Intergenic	Intergenic	-269091	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.004392	0.320175	
chunk0044_205_1	chr12	30820481	30820993	+	0	NA	Intergenic	MER61F|LTR|ERV1	25056	NR_040245	100287314	Hs.355210	NR_040245		LINC00941	lncRNA-MUF	long intergenic non-protein coding RNA 941	ncRNA	0.003906	0.419103	
chunk0058_11_1	chr14	18675128	18675591	+	0	NA	Intergenic	L1MEh|LINE|L1	-41725	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.010799	0.336207	
chunk0054_373_1	chr13	49976327	49976889	+	0	NA	Intergenic	L2b|LINE|L2	19893	NR_037407	100500908		NR_037407	ENSG00000264864	MIR3613	-	microRNA 3613	ncRNA	0.012456	0.481350	
chunk0167_170_1	chr6	63292519	63292759	+	0	NA	intron (NM_016571, intron 2 of 3)	MER77B|LTR|ERVL	27338	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.008333	0.477178	200(GTGAACATTCTGTGCT,-,0.00),201(TGAACATTCTGTGCTT,+,0.00)
chunk0138_173_1	chr4	37891264	37891575	+	0	NA	intron (NM_015173, intron 1 of 19)	CpG	335	NM_015173	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.109325	0.750000	
chunk0134_31_1	chr3	175591258	175591804	+	0	NA	intron (NM_207015, intron 10 of 13)	L2c|LINE|L2	184802	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.001832	0.283364	
chunk0072_1_1	chr16	45402	45819	+	0	NA	Intergenic	HERV3-int|LTR|ERV1	8022	NM_016310	51728	Hs.632223	NM_016310	ENSG00000161980	POLR3K	C11|C11-RNP3|My010|RPC10|RPC11|RPC12.5	RNA polymerase III subunit K	protein-coding	0.011990	0.454545	
chunk0108_354_1	chr2	236120052	236120251	+	0	NA	intron (NM_001037131, intron 16 of 17)	intron (NM_001037131, intron 16 of 17)	47858	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.045226	0.590000	
chunk0047_114_1	chr12	68924587	68924786	+	0	NA	intron (NM_001005502, intron 2 of 8)	intron (NM_001005502, intron 2 of 8)	8513	NM_198320	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.010050	0.345000	
chunk0102_416_1	chr2	156781637	156782175	+	0	NA	Intergenic	L1PB1|LINE|L1	345518	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.005576	0.358071	
chunk0036_301_1	chr11	65922818	65923027	+	0	NA	Intergenic	L1ME3|LINE|L1	3665	NM_006442	10589	Hs.356742	NM_006442	ENSG00000175550	DRAP1	NC2-alpha	DR1 associated protein 1	protein-coding	0.004785	0.457143	
chunk0112_290_1	chr20	43918739	43919118	+	0	NA	intron (NM_001098796, intron 1 of 8)	MIR|SINE|MIR	2786	NM_032883	84969	Hs.26608	NM_032883	ENSG00000124191	TOX2	C20orf100|GCX-1|GCX1|dJ1108D11.2|dJ495O3.1	TOX high mobility group box family member 2	protein-coding	0.010554	0.452632	
chunk0165_274_1	chr6	36027508	36027707	+	0	NA	promoter-TSS (NM_139012)	promoter-TSS (NM_139012)	-70	NM_139012	1432	Hs.485233	NM_001315	ENSG00000112062	MAPK14	CSBP|CSBP1|CSBP2|CSPB1|EXIP|Mxi2|PRKM14|PRKM15|RK|SAPK2A|p38|p38ALPHA	mitogen-activated protein kinase 14	protein-coding	0.085427	0.625000	
chunk0119_106_1	chr22	42229296	42229812	+	0	NA	intron (NM_005650, intron 1 of 5)	intron (NM_005650, intron 1 of 5)	-14213	NM_181492	6942	Hs.475018	NM_005650	ENSG00000100207	TCF20	AR1|DDVIBA|SPBP|TCF-20	transcription factor 20	protein-coding	0.013566	0.439072	
chunk0079_160_1	chr17	13482738	13483436	+	0	NA	Intergenic	Intergenic	60559	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.002865	0.311874	
chunk0175_49_1	chr7	1455205	1455559	+	0	NA	intron (NM_182924, intron 1 of 16)	intron (NM_182924, intron 1 of 16)	4091	NM_182924	79778	Hs.376617	NM_024723	ENSG00000164877	MICALL2	JRAB|MICAL-L2	MICAL like 2	protein-coding	0.036723	0.664789	
chunk0124_39_1	chr3	52332777	52333039	+	0	NA	intron (NM_015512, intron 8 of 77)	AluJo|SINE|Alu	16589	NM_015512	25981	Hs.655469	NM_015512	ENSG00000114841	DNAH1	CILD37|DNAHC1|HDHC7|HL-11|HL11|HSRF-1|SPGF18|XLHSRF-1	dynein axonemal heavy chain 1	protein-coding	0.000000	0.482890	30(AGGCTCATTGTGTACT,-,0.00),31(GGCTCATTGTGTACTT,+,0.00)
chunk0126_306_1	chr3	80985339	80985795	+	0	NA	Intergenic	MIRb|SINE|MIR	-8301	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.004386	0.297593	
chunk0179_451_1	chr7	52769623	52769859	+	0	NA	Intergenic	L1ME1|LINE|L1	-265915	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008475	0.345992	117(TTGTACAAAGTGTTCT,-,0.00),118(TGTACAAAGTGTTCTT,+,0.00)
chunk0014_364_1	chr1	182484664	182485069	+	0	NA	intron (NM_001137669, intron 6 of 21)	L1M2a|LINE|L1	34745	NM_001137669	353299	Hs.121200	NM_032267	ENSG00000121446	RGSL1	RGSL|RGSL2	regulator of G protein signaling like 1	protein-coding	0.002469	0.559113	
chunk0089_110_1	chr18	58549726	58550438	+	0	NA	intron (NM_052947, intron 4 of 12)	intron (NM_052947, intron 4 of 12)	-50538	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.008427	0.495091	
chunk0154_21_1	chr5	76771616	76771815	+	0	NA	Intergenic	Intergenic	-47293	NM_005242	2150	Hs.744181	NM_005242	ENSG00000164251	F2RL1	GPR11|PAR2	F2R like trypsin receptor 1	protein-coding	0.000000	0.385000	
chunk0149_421_1	chr5	29514462	29514919	+	0	NA	Intergenic	L1M5|LINE|L1	-118714	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.270742	216(TAAAACAGTCTGTCCT,-,0.00),217(AAAACAGTCTGTCCTC,+,0.00)
chunk0050_288_1	chr12	106644849	106645273	+	0	NA	intron (NM_001206691, intron 3 of 17)	intron (NM_001206691, intron 3 of 17)	-39638	NM_032491	5992	Hs.388827	NM_002920	ENSG00000111783	RFX4	NYD-SP10	regulatory factor X4	protein-coding	0.030660	0.543529	
chunk0160_1_1	chr5	148926384	148926751	+	0	NA	Intergenic	Intergenic	99974	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.010899	0.464674	
chunk0139_432_1	chr4	64504286	64504747	+	0	NA	Intergenic	L1MC1|LINE|L1	-95056	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.004338	0.320346	
chunk0165_332_1	chr6	37339731	37340154	+	0	NA	Intergenic	L1MEf|LINE|L1	-14030	NM_183078	9025	Hs.485278	NM_003958	ENSG00000112130	RNF8	hRNF8	ring finger protein 8	protein-coding	0.007092	0.405660	
chunk0013_373_1	chr1	172473920	172474248	+	0	NA	Intergenic	Intergenic	21191	NM_001300760	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.000000	0.334347	
chunk0083_188_1	chr17	66503011	66503210	+	0	NA	intron (NM_002737, intron 3 of 16)	intron (NM_002737, intron 3 of 16)	-86256	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.015075	0.410000	
chunk0101_342_1	chr2	137521671	137522003	+	0	NA	intron (NM_001316349, intron 15 of 27)	intron (NM_001316349, intron 15 of 27)	406095	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.003012	0.492492	175(CAGGGCAGACTGTGCT,-,0.00),176(AGGGCAGACTGTGCTG,+,0.00)
chunk0094_433_1	chr2	10859326	10859800	+	0	NA	Intergenic	L1ME3E|LINE|L1	-18704	NR_110575	101929733	Hs.736697	NR_110575	ENSG00000271952	LINC01954	-	long intergenic non-protein coding RNA 1954	ncRNA	0.014768	0.362105	
chunk0033_264_1	chr11	18802421	18803382	+	0	NA	Intergenic	Intergenic	-10180	NM_001278236	84867	Hs.79092	NM_006906	ENSG00000110786	PTPN5	PTPSTEP|STEP|STEP61	protein tyrosine phosphatase non-receptor type 5	protein-coding	0.012487	0.432432	
chunk0048_48_1	chr12	78095119	78095864	+	0	NA	intron (NM_014903, intron 12 of 38)	intron (NM_014903, intron 12 of 38)	264202	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.005369	0.372654	
chunk0039_99_1	chr11	97310364	97310570	+	0	NA	Intergenic	Intergenic	-803590	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.004854	0.309179	
chunk0110_399_1	chr20	20361219	20361682	+	0	NA	TTS (NM_015585)	TTS (NM_015585)	-6671	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.004320	0.398707	424(TGGTACACACTGTGTC,-,0.00)
chunk0199_334_1	chr9	10923936	10924407	+	0	NA	Intergenic	L1M5|LINE|L1	310965	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.006369	0.324153	
chunk0203_161_1	chr9	85895245	85895548	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	-45746	NM_024635	60560	Hs.436098	NM_021929	ENSG00000135040	NAA35	EGAP|MAK10|MAK10P|bA379P1.1	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding	0.000000	0.365132	
chunk0161_356_1	chr5	174709222	174709898	+	0	NA	Intergenic	Intergenic	-15012	NM_002449	4488	Hs.89404	NM_002449	ENSG00000120149	MSX2	CRS2|FPP|HOX8|MSH|PFM|PFM1	msh homeobox 2	protein-coding	0.008876	0.462334	248(CTGGACAGGTTGTCCT,-,0.00),249(TGGACAGGTTGTCCTG,+,0.00),341(CAGAACAAAATGATCC,-,0.00),342(AGAACAAAATGATCCC,+,0.00)
chunk0201_416_1	chr9	69594451	69594650	+	0	NA	intron (NM_001163, intron 1 of 12)	intron (NM_001163, intron 1 of 12)	77809	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.000000	0.340000	
chunk0145_102_1	chr4	146047297	146048053	+	0	NA	Intergenic	L1PA6|LINE|L1	74238	NR_038331	100505545	Hs.122199	NR_038331	ENSG00000248809	LINC01095	-	long intergenic non-protein coding RNA 1095	ncRNA	0.022487	0.507266	
chunk0126_87_1	chr3	74738614	74738916	+	0	NA	Intergenic	L1ME2|LINE|L1	-217625	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.003311	0.363036	
chunk0063_310_1	chr14	84959310	84959529	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	-434460	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.004566	0.450000	
chunk0110_77_1	chr20	11155255	11155655	+	0	NA	Intergenic	Intergenic	117928	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.002500	0.376559	
chunk0173_219_1	chr6	145849836	145850278	+	0	NA	intron (NR_038246, intron 2 of 2)	MLT2B1|LTR|ERVL	35181	NR_038245	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.006787	0.437923	
chunk0049_89_1	chr12	90808618	90808914	+	0	NA	Intergenic	Intergenic	-109257	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.006757	0.387205	
chunk0126_28_1	chr3	73673294	73673499	+	0	NA	Intergenic	L2c|LINE|L2	-48475	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.004878	0.344660	
chunk0176_149_1	chr7	12949472	12949681	+	0	NA	Intergenic	Intergenic	262290	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.009569	0.404762	
chunk0183_269_1	chr7	107494573	107494853	+	0	NA	intron (NM_006348, intron 6 of 21)	intron (NM_006348, intron 6 of 21)	24656	NM_005295	2845	Hs.657277	NM_005295	ENSG00000172209	GPR22	-	G protein-coupled receptor 22	protein-coding	0.007143	0.359431	
chunk0136_53_1	chr4	1541051	1541762	+	0	NA	Intergenic	Intergenic	-134964	NM_001290079	54729	Hs.526396	NM_001290079	ENSG00000235608	NKX1-1	HSPX153|NKX-1.1|SAX2	NK1 homeobox 1	protein-coding	0.028129	0.606742	
chunk0021_49_1	chr10	1003997	1004227	+	0	NA	intron (NM_012341, intron 8 of 16)	L1M2a|LINE|L1	15703	NM_012341	23560	Hs.215766	NM_012341	ENSG00000107937	GTPBP4	CRFG|NGB|NOG1	GTP binding protein 4	protein-coding	0.008696	0.601732	
chunk0009_95_1	chr1	101608861	101609118	+	0	NA	Intergenic	Intergenic	238091	NR_110212	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.007782	0.531008	
chunk0202_220_1	chr9	76292414	76292693	+	0	NA	intron (NM_001190482, intron 25 of 36)	intron (NM_001190482, intron 25 of 36)	101975	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.014337	0.478571	127(CAGATCTTGCTGTTCT,-,0.00),128(AGATCTTGCTGTTCTT,+,0.00)
chunk0100_167_1	chr2	109328245	109328738	+	0	NA	intron (NM_001099289, intron 1 of 9)	L1MC5a|LINE|L1	-14866	NR_036224	100423027		NR_036224	ENSG00000265965	MIR4266	-	microRNA 4266	ncRNA	0.006085	0.447368	
chunk0022_436_1	chr10	19422245	19422532	+	0	NA	intron (NM_001142308, intron 28 of 39)	intron (NM_001142308, intron 28 of 39)	306162	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.000000	0.291667	
chunk0138_394_1	chr4	42750534	42750810	+	0	NA	Intergenic	Intergenic	-93567	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.003623	0.328520	
chunk0142_422_1	chr4	103424954	103425198	+	0	NA	promoter-TSS (NR_125925)	promoter-TSS (NR_125925)	34	NR_125925	101929448	Hs.570839	NR_125925	ENSG00000248740	LINC02428	-	long intergenic non-protein coding RNA 2428	ncRNA	0.004098	0.404082	
chunk0066_122_1	chr15	31007956	31008264	+	0	NA	intron (NM_001252020, intron 26 of 26).2	L1MEf|LINE|L1	-16506	NM_017762	54893	Hs.30141	NM_017762	ENSG00000166912	MTMR10	-	myotubularin related protein 10	protein-coding	0.003247	0.297735	
chunk0168_335_1	chr6	92706415	92707086	+	0	NA	Intergenic	L1MB8|LINE|L1	712832	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.000000	0.300595	
chunk0073_340_1	chr16	14549756	14550205	+	0	NA	intron (NM_002582, intron 21 of 23)	MIRb|SINE|MIR	80291	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.013363	0.460000	
chunk0153_321_1	chr5	73795684	73796239	+	0	NA	intron (NM_001080479, intron 9 of 36)	intron (NM_001080479, intron 9 of 36)	-17557	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.001802	0.485612	
chunk0030_180_1	chr10	114195002	114195617	+	0	NA	intron (NM_198795, intron 3 of 25)	L1MD1|LINE|L1	16039	NM_198795	56165	Hs.333132	NM_198795	ENSG00000095627	TDRD1	CT41.1	tudor domain containing 1	protein-coding	0.003252	0.370130	
chunk0191_333_1	chr8	55988753	55989245	+	0	NA	intron (NM_001111097, intron 10 of 12)	intron (NM_001111097, intron 10 of 12)	84902	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.016260	0.472617	
chunk0140_449_1	chr4	76386875	76387317	+	0	NA	intron (NM_001042784, intron 3 of 23)	L1MA2|LINE|L1	20209	NM_001042784	339965	Hs.529680	NM_178555	ENSG00000163749	CCDC158	-	coiled-coil domain containing 158	protein-coding	0.011312	0.519187	
chunk0060_452_1	chr14	55051088	55051485	+	0	NA	promoter-TSS (NM_144578)	promoter-TSS (NM_144578)	-358	NM_144578	93487	Hs.594338	NM_144578	ENSG00000168175	MAPK1IP1L	C14orf32|MISS|c14_5346	mitogen-activated protein kinase 1 interacting protein 1 like	protein-coding	0.050378	0.502513	
chunk0132_431_1	chr3	164977710	164978346	+	0	NA	TTS (NM_001041)	TTS (NM_001041)	100467	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.003145	0.335950	
chunk0184_157_1	chr7	116231822	116232404	+	0	NA	intron (NM_152829, intron 1 of 6)	intron (NM_152829, intron 1 of 6)	9162	NM_152829	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.003436	0.384220	
chunk0043_252_1	chr12	20547091	20547685	+	0	NA	intron (NM_000921, intron 1 of 15)	L2a|LINE|L2	-24476	NM_001244683	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.005051	0.342857	
chunk0200_208_1	chr9	20551742	20552220	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	-49639	NR_039685	100616441		NR_039685	ENSG00000264941	MIR4474	-	microRNA 4474	ncRNA	0.010460	0.373695	
chunk0042_419_1	chr12	11780491	11780753	+	0	NA	intron (NM_001987, intron 2 of 7)	intron (NM_001987, intron 2 of 7)	130768	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.011450	0.501901	
chunk0188_237_1	chr8	13595558	13596051	+	0	NA	Intergenic	Intergenic	28961	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.004057	0.297571	
chunk0154_383_1	chr5	87865193	87865776	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	403395	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.000000	0.321918	
chunk0211_76_1	chrX	110057786	110058183	+	0	NA	intron (NM_032227, intron 2 of 6)	L1MA9|LINE|L1	2655	NR_030381	724022		NR_030381	ENSG00000208013	MIR652	MIRN652|hsa-mir-652	microRNA 652	ncRNA	0.005038	0.311558	
chunk0182_152_1	chr7	95318311	95318870	+	0	NA	intron (NM_000446, intron 1 of 8)	intron (NM_000446, intron 1 of 8)	5982	NM_000446	5444	Hs.370995	NM_000446	ENSG00000005421	PON1	ESA|MVCD5|PON	paraoxonase 1	protein-coding	0.012522	0.426786	
chunk0067_180_1	chr15	44385415	44385794	+	0	NA	intron (NM_177974, intron 8 of 8)	AluJo|SINE|Alu	-41777	NM_016396	51496	Hs.497967	NM_016396	ENSG00000137770	CTDSPL2	HSPC058|HSPC129	CTD small phosphatase like 2	protein-coding	0.000000	0.428947	
chunk0038_183_1	chr11	85832057	85832490	+	0	NA	Intergenic	MIRb|SINE|MIR	-21114	NM_001289608	54843	Hs.369520	NM_032379	ENSG00000137501	SYTL2	CHR11SYT|EXO4|PPP1R151|SGA72M|SLP2|SLP2A	synaptotagmin like 2	protein-coding	0.002309	0.347926	
chunk0204_347_1	chr9	101543323	101543774	+	0	NA	intron (NM_019592, intron 5 of 19)	intron (NM_019592, intron 5 of 19)	9699	NM_019592	56254	Hs.729085	NM_019592	ENSG00000155827	RNF20	BRE1|BRE1A|hBRE1	ring finger protein 20	protein-coding	0.022173	0.528761	
chunk0100_417_1	chr2	119828079	119828319	+	0	NA	intron (NM_002830, intron 2 of 26)	MLT1G3|LTR|ERVL-MaLR	68568	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.008333	0.481328	
chunk0111_114_1	chr20	23963810	23964078	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	22931	NM_178312	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.000000	0.323420	
chunk0201_166_1	chr9	36080835	36081559	+	0	NA	intron (NM_001316345, intron 9 of 22)	L2c|LINE|L2	44284	NM_001316346	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.006906	0.441379	404(AGGAACAAAGAGTTCT,-,0.00),405(GGAACAAAGAGTTCTT,+,0.00)
chunk0144_427_1	chr4	140720811	140721016	+	0	NA	intron (NM_015130, intron 1 of 20)	intron (NM_015130, intron 1 of 20)	35404	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.009756	0.524272	47(GGGAACAACATGACCC,-,0.00),48(GGAACAACATGACCCT,+,0.00)
chunk0163_351_1	chr6	15505074	15505284	+	0	NA	intron (NM_001267040, intron 9 of 17)	intron (NM_001267040, intron 9 of 17)	157879	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.057143	0.597156	
chunk0038_225_1	chr11	86961957	86962493	+	0	NA	intron (NR_038905, intron 2 of 2)	MLT2F|LTR|ERVL	6604	NR_038905	100506368	Hs.559920	NR_038905	ENSG00000246523	FZD4-DT	-	FZD4 divergent transcript	ncRNA	0.011194	0.459963	
chunk0150_419_1	chr5	40348378	40348618	+	0	NA	Intergenic	L1MA2|LINE|L1	296207	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.004167	0.522822	
chunk0203_411_1	chr9	90894751	90894950	+	0	NA	intron (NM_001135052, intron 12 of 12)	intron (NM_001135052, intron 12 of 12)	67430	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.005025	0.435000	
chunk0127_34_1	chr3	88645948	88646496	+	0	NA	Intergenic	Intergenic	-461302	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003650	0.316940	425(AAGCACAGTCAGTTCT,-,0.00),426(AGCACAGTCAGTTCTT,+,0.00)
chunk0027_91_1	chr10	73676897	73677132	+	0	NA	intron (NM_001144000, intron 6 of 7)	intron (NM_001144000, intron 6 of 7)	20782	NM_001144000	729092	Hs.651147	NM_001144000	ENSG00000172650	AGAP5	CTGLF2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 5	protein-coding	0.004255	0.389831	
chunk0052_449_1	chr12	132536389	132536676	+	0	NA	intron (NM_001142641, intron 4 of 16)	intron (NM_001142641, intron 4 of 16)	-45465	NR_106821	102465975		NR_106821	ENSG00000277052	MIR6763	hsa-mir-6763	microRNA 6763	ncRNA	0.013937	0.454861	
chunk0125_357_1	chr3	71351362	71352028	+	0	NA	intron (NM_032682, intron 4 of 20)	intron (NM_032682, intron 4 of 20)	-46935	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.004505	0.383808	306(AAGAACATTCTGAACT,-,0.00),307(AGAACATTCTGAACTT,+,0.00)
chunk0006_333_1	chr1	71947579	71948051	+	0	NA	intron (NM_173808, intron 1 of 6)	Charlie2a|DNA|hAT-Charlie	-110803	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.002119	0.340381	238(TAGAACTATCTGTTCC,-,0.00),239(AGAACTATCTGTTCCT,+,0.00)
chunk0042_169_1	chr12	4587639	4587951	+	0	NA	Intergenic	Intergenic	-2277	NM_003845	8798	Hs.439530	NM_003845	ENSG00000010219	DYRK4	-	dual specificity tyrosine phosphorylation regulated kinase 4	protein-coding	0.006410	0.469649	
chunk0136_174_1	chr4	6505949	6506173	+	0	NA	intron (NM_001206995, intron 2 of 9)	L1ME2|LINE|L1	-33462	NM_020416	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.000000	0.360000	
chunk0013_81_1	chr1	167645100	167645666	+	0	NA	intron (NM_052862, intron 1 of 6)	L2c|LINE|L2	15146	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.005300	0.396825	
chunk0108_282_1	chr2	234713427	234714014	+	0	NA	intron (NR_132376, intron 2 of 2)	intron (NR_132376, intron 2 of 2)	31052	NR_132376	106144537	Hs.580616	NR_132376	ENSG00000280744	LINC01173	-	long intergenic non-protein coding RNA 1173	ncRNA	0.010221	0.353741	
chunk0077_431_1	chr16	85558230	85558556	+	0	NA	Intergenic	Intergenic	-53030	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.018405	0.522936	
chunk0075_264_1	chr16	53703688	53704053	+	0	NA	promoter-TSS (NM_001308334)	promoter-TSS (NM_001308334)	64	NM_015272	23322	Hs.298382	NM_015272	ENSG00000103494	RPGRIP1L	CORS3|FTM|JBTS7|MKS5|NPHP8|PPP1R134	RPGRIP1 like	protein-coding	0.076712	0.655738	
chunk0169_170_1	chr6	102076762	102077422	+	0	NA	Intergenic	Intergenic	678107	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003030	0.341906	
chunk0151_326_1	chr5	53743770	53744260	+	0	NA	Intergenic	L1PB1|LINE|L1	183380	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.006122	0.360489	
chunk0204_265_1	chr9	98191899	98192116	+	0	NA	intron (NM_052820, intron 1 of 11)	CpG	667	NM_052820	7464	Hs.113094	NM_003389	ENSG00000106789	CORO2A	CLIPINB|IR10|WDR2	coronin 2A	protein-coding	0.055300	0.655963	
chunk0119_113_1	chr22	42262688	42262966	+	0	NA	intron (NM_005650, intron 1 of 5)	intron (NM_005650, intron 1 of 5)	-6926	NR_036498	388906	Hs.730075	NR_036498		OGFRP1	-	opioid growth factor receptor pseudogene 1	pseudo	0.007194	0.448029	
chunk0137_1_1	chr4	10492363	10492842	+	0	NA	intron (NM_052964, intron 18 of 18)	intron (NM_052964, intron 18 of 18)	-35194	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.025052	0.487500	
chunk0152_179_1	chr5	59715526	59715725	+	0	NA	intron (NM_001165899, intron 3 of 16)	HERVL18-int|LTR|ERVL	-11922	NR_030308	693167		NR_030308	ENSG00000202601	MIR582	MIRN582|hsa-mir-582	microRNA 582	ncRNA	0.005025	0.495000	
chunk0156_4_1	chr5	101929632	101929867	+	0	NA	Intergenic	Intergenic	366800	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.309322	
chunk0079_410_1	chr17	19629990	19630645	+	0	NA	Intergenic	L2a|LINE|L2	-18434	NM_001031806	224	Hs.499886	NM_000382	ENSG00000072210	ALDH3A2	ALDH10|FALDH|SLS	aldehyde dehydrogenase 3 family member A2	protein-coding	0.007634	0.445122	
chunk0035_222_1	chr11	45305843	45306442	+	0	NA	Intergenic	L1ME1|LINE|L1	-19809	NM_020826	57586	Hs.436643	NM_020826	ENSG00000019505	SYT13	-	synaptotagmin 13	protein-coding	0.006678	0.443333	
chunk0189_151_1	chr8	23021732	23021994	+	0	NA	non-coding (NR_027140, exon 9 of 9)	non-coding (NR_027140, exon 9 of 9)	22284	NM_015178	23221	Hs.372688	NM_015178	ENSG00000008853	RHOBTB2	DBC2|EIEE64	Rho related BTB domain containing 2	protein-coding	0.000000	0.391635	
chunk0126_313_1	chr3	81514029	81514365	+	0	NA	intron (NM_000158, intron 14 of 15)	intron (NM_000158, intron 14 of 15)	247602	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.002976	0.278932	
chunk0012_236_1	chr1	160638872	160639260	+	0	NA	intron (NR_104400, intron 1 of 4)	L2a|LINE|L2	8245	NR_104401	6504	Hs.523660	NM_003037	ENSG00000117090	SLAMF1	CD150|CDw150|SLAM	signaling lymphocytic activation molecule family member 1	protein-coding	0.005155	0.434447	67(AGTACTCGGAGTTCTC,+,0.00)
chunk0112_76_1	chr20	37852811	37853010	+	0	NA	intron (NM_030877, intron 13 of 15)	MIR3|SINE|MIR	-50187	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.010050	0.425000	
chunk0161_198_1	chr5	170375834	170376114	+	0	NA	intron (NM_001034838, intron 1 of 7)	MIR|SINE|MIR	-13519	NR_109899	101928033	Hs.709167	NR_109899	ENSG00000253647	CTD-2270F17.1	-	uncharacterized LOC101928033	ncRNA	0.010714	0.423488	
chunk0185_19_1	chr7	124034768	124035224	+	0	NA	Intergenic	Intergenic	-1527	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.004386	0.319475	
chunk0029_305_1	chr10	104260304	104260838	+	0	NA	intron (NM_001191002, intron 3 of 4)	intron (NM_001191002, intron 3 of 4)	5861	NM_004832	9446	Hs.190028	NM_004832	ENSG00000148834	GSTO1	GSTO 1-1|GSTTLp28|HEL-S-21|P28|SPG-R	glutathione S-transferase omega 1	protein-coding	0.003745	0.358879	259(AAGAACTGTTTGTACC,-,0.00),260(AGAACTGTTTGTACCT,+,0.00)
chunk0041_327_1	chr11	130241906	130242249	+	0	NA	intron (NM_014155, intron 2 of 5)	L1ME3B|LINE|L1	72635	NM_001301099	29068	Hs.721470	NM_014155	ENSG00000196323	ZBTB44	BTBD15|HSPC063|ZNF851	zinc finger and BTB domain containing 44	protein-coding	0.002915	0.316860	
chunk0045_231_1	chr12	48302319	48302882	+	0	NA	Intergenic	MER51B|LTR|ERV1	-26380	NM_181788	341567	Hs.155833	NM_181788	ENSG00000187166	H1FNT	H1.7|H1T2	H1 histone family member N, testis specific	protein-coding	0.000000	0.390071	337(TGTACAGGGTGTACAC,+,0.00)
chunk0168_71_1	chr6	79461163	79461574	+	0	NA	Intergenic	MER77B|LTR|ERVL	76062	NM_181714	167691	Hs.21945	NM_181714	ENSG00000135338	LCA5	C6orf152	lebercilin LCA5	protein-coding	0.007299	0.453883	153(AAGAACTGATTGTTCT,-,0.00),154(AGAACTGATTGTTCTC,+,0.00)
chunk0102_166_1	chr2	147477278	147477477	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-367140	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.345000	103(ATCACAGAGTGTACTT,+,0.00)
chunk0047_464_1	chr12	76885723	76886083	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-6863	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.011111	0.401662	
chunk0135_219_1	chr3	188528490	188528841	+	0	NA	intron (NM_001167671, intron 5 of 10)	MIRc|SINE|MIR	40001	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.008547	0.375000	
chunk0016_105_1	chr1	195710995	195711334	+	0	NA	Intergenic	MER45C|DNA|hAT-Tip100	871317	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.008850	0.491176	
chunk0102_177_1	chr2	147525561	147526259	+	0	NA	Intergenic	Intergenic	-318607	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.005731	0.403433	
chunk0082_4_1	chr17	49677805	49678074	+	0	NA	5' UTR (NM_003563, exon 1 of 11)	5' UTR (NM_003563, exon 1 of 11)	224	NM_001007228	8405	Hs.463382	NM_003563	ENSG00000121067	SPOP	BTBD32|TEF2	speckle type BTB/POZ protein	protein-coding	0.059480	0.644444	
chunk0209_259_1	chrX	46371746	46372272	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-44335	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.003802	0.316888	
chunk0190_261_1	chr8	37239722	37239966	+	0	NA	Intergenic	Intergenic	254069	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.004098	0.440816	
chunk0102_403_1	chr2	156021714	156022073	+	0	NA	non-coding (NR_110250, exon 4 of 4)	non-coding (NR_110250, exon 4 of 4)	233038	NR_110250	101929378	Hs.171192	NR_110249	ENSG00000226383	LINC01876	-	long intergenic non-protein coding RNA 1876	ncRNA	0.002786	0.363889	
chunk0193_108_1	chr8	73965437	73965726	+	0	NA	intron (NM_001204858, intron 1 of 4)	L1ME2z|LINE|L1	6327	NM_001204862	6921	Hs.533437	NM_005648	ENSG00000154582	ELOC	SIII|TCEB1	elongin C	protein-coding	0.003460	0.310345	
chunk0105_285_1	chr2	189813966	189814433	+	0	NA	intron (NR_110332, intron 5 of 12)	intron (NR_110332, intron 5 of 12)	-29828	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.002141	0.386752	225(GAGAACTATGTGTTCT,-,0.00),226(AGAACTATGTGTTCTC,+,0.00),249(TAGAACATGGTGTTCC,-,0.00),250(AGAACATGGTGTTCCA,+,0.00)
chunk0035_340_1	chr11	48007675	48007920	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	27239	NM_002843	5795	Hs.318547	NM_002843	ENSG00000149177	PTPRJ	CD148|DEP1|HPTPeta|R-PTP-ETA|SCC1	protein tyrosine phosphatase receptor type J	protein-coding	0.016327	0.520325	
chunk0057_144_1	chr13	100068767	100069100	+	0	NA	Intergenic	L1MC5a|LINE|L1	20010	NR_132422	105370333	Hs.186291	NR_132422	ENSG00000274605	LOC105370333	-	uncharacterized LOC105370333	ncRNA	0.003003	0.338323	
chunk0183_370_1	chr7	109409918	109410303	+	0	NA	Intergenic	Intergenic	-525523	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.007792	0.349741	
chunk0002_22_1	chr1	12368572	12369098	+	0	NA	intron (NM_018156, intron 52 of 68)	intron (NM_018156, intron 52 of 68)	-138411	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.003802	0.366224	
chunk0036_444_1	chr11	68536025	68536238	+	0	NA	intron (NM_018312, intron 3 of 22)	intron (NM_018312, intron 3 of 22)	75413	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.000000	0.341121	
chunk0121_264_1	chr3	23203181	23203608	+	0	NA	5' UTR (NM_152653, exon 1 of 6)	5' UTR (NM_152653, exon 1 of 6)	101	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.114754	0.738318	172(GGGGACATCCCGTCCC,-,0.00),173(GGGACATCCCGTCCCT,+,0.00)
chunk0187_202_1	chr7	151780582	151781196	+	0	NA	intron (NM_001040633, intron 3 of 15)	intron (NM_001040633, intron 3 of 15)	33982	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.013029	0.517073	
chunk0107_93_1	chr2	213148712	213149188	+	0	NA	intron (NM_016260, intron 1 of 7)	intron (NM_016260, intron 1 of 7)	1384	NM_016260	22807	Hs.604950	NM_016260	ENSG00000030419	IKZF2	ANF1A2|HELIOS|ZNF1A2|ZNFN1A2	IKAROS family zinc finger 2	protein-coding	0.002101	0.406709	
chunk0011_29_1	chr1	143221708	143221957	+	0	NA	Intergenic	Intergenic	200760	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.028112	0.344000	
chunk0077_368_1	chr16	84449738	84450582	+	0	NA	intron (NM_001291454, intron 14 of 23)	intron (NM_001291454, intron 14 of 23)	43572	NM_001291454	9914	Hs.6168	NM_014861	ENSG00000064270	ATP2C2	SPCA2	ATPase secretory pathway Ca2+ transporting 2	protein-coding	0.031991	0.579882	
chunk0087_318_1	chr18	39788284	39789129	+	0	NA	Intergenic	Intergenic	-36711	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.003550	0.349882	
chunk0054_426_1	chr13	51042338	51042756	+	0	NA	intron (NR_003923, intron 3 of 16)	MER58A|DNA|hAT-Charlie	23610	NR_003923	2974	Hs.411573	NM_004129	ENSG00000123201	GUCY1B2	GC-SB2	guanylate cyclase 1 soluble subunit beta 2 (pseudogene)	pseudo	0.011962	0.439141	
chunk0116_48_1	chr21	33679120	33679342	+	0	NA	intron (NM_001001132, intron 1 of 29)	intron (NM_001001132, intron 1 of 29)	36753	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.009009	0.336323	
chunk0103_45_1	chr2	159319373	159319596	+	0	NA	3' UTR (NM_013450, exon 37 of 37)	3' UTR (NM_013450, exon 37 of 37)	-32685	NM_001128212	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.008969	0.321429	
chunk0116_22_1	chr21	32969974	32970459	+	0	NA	Intergenic	Intergenic	-55692	NM_005806	10215	Hs.176977	NM_005806	ENSG00000205927	OLIG2	BHLHB1|OLIGO2|PRKCBP2|RACK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding	0.006186	0.382716	
chunk0054_286_1	chr13	47168590	47168789	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-271613	NM_001165947	3356	Hs.72630	NM_000621	ENSG00000102468	HTR2A	5-HT2A|HTR2	5-hydroxytryptamine receptor 2A	protein-coding	0.015075	0.380000	
chunk0211_333_1	chrX	124084838	124085575	+	0	NA	intron (NM_001042749, intron 29 of 34)	L1ME3C|LINE|L1	123500	NM_001042751	10735	Hs.496710	NM_006603	ENSG00000101972	STAG2	NEDXCF|SA-2|SA2|SCC3B|bA517O1.1	stromal antigen 2	protein-coding	0.010855	0.402439	
chunk0185_441_1	chr7	134959779	134960317	+	0	NA	exon (NM_033140, exon 9 of 12)	exon (NM_033140, exon 9 of 12)	-26460	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.011152	0.395176	233(GGATCTTCCTGTTCCT,+,0.00)
chunk0031_117_1	chr10	124677886	124678256	+	0	NA	intron (NM_014661, intron 4 of 4)	intron (NM_014661, intron 4 of 4)	-25957	NR_120630	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.016216	0.506739	
chunk0151_40_1	chr5	42057035	42057514	+	0	NA	Intergenic	L1MB1|LINE|L1	118071	NR_104635	101926960	Hs.365692	NR_104635		LOC101926960	-	uncharacterized LOC101926960	ncRNA	0.008351	0.389583	
chunk0073_228_1	chr16	11152887	11153314	+	0	NA	intron (NM_015226, intron 21 of 22)	intron (NM_015226, intron 21 of 22)	103082	NM_003745	8651	Hs.50640	NM_003745	ENSG00000185338	SOCS1	CIS1|CISH1|JAB|SOCS-1|SSI-1|SSI1|TIP-3|TIP3	suppressor of cytokine signaling 1	protein-coding	0.025761	0.483645	
chunk0145_108_1	chr4	146180744	146181047	+	0	NA	intron (NM_007080, intron 1 of 3)	intron (NM_007080, intron 1 of 3)	5212	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.003300	0.345395	
chunk0002_48_1	chr1	12722636	12722919	+	0	NA	intron (NR_111984, intron 2 of 2)	intron (NR_111984, intron 2 of 2)	6662	NR_111984	126767	Hs.464705	NM_001103169	ENSG00000188984	AADACL3	-	arylacetamide deacetylase like 3	protein-coding	0.003534	0.408451	208(TGGTACAGTCAGTCCT,-,0.00),209(GGTACAGTCAGTCCTC,+,0.00)
chunk0140_400_1	chr4	75505560	75505990	+	0	NA	intron (NM_001278539, intron 3 of 8)	L1MEg|LINE|L1	3521	NR_103725	25898	Hs.48297	NM_015436	ENSG00000163743	RCHY1	ARNIP|CHIMP|PIRH2|PRO1996|RNF199|ZCHY|ZNF363	ring finger and CHY zinc finger domain containing 1	protein-coding	0.002326	0.341067	
chunk0105_425_1	chr2	193272845	193273582	+	0	NA	Intergenic	Intergenic	523368	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.002714	0.310298	
chunk0163_200_1	chr6	11785286	11786165	+	0	NA	Intergenic	Intergenic	-6678	NM_001143948	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.011377	0.430682	
chunk0204_38_1	chr9	92666163	92666445	+	0	NA	intron (NM_022755, intron 1 of 12)	L3|LINE|CR1	3961	NM_022755	64768	Hs.459896	NM_022755	ENSG00000127080	IPPK	C9orf12|INSP5K2|IP5K|IPK1|bA476B13.1	inositol-pentakisphosphate 2-kinase	protein-coding	0.017730	0.551237	
chunk0093_231_1	chr19	50518245	50518458	+	0	NA	exon (NM_001080457, exon 3 of 3)	exon (NM_001080457, exon 3 of 3)	-3661	NM_001024656	554235	Hs.436338	NM_001024656	ENSG00000204653	ASPDH	-	aspartate dehydrogenase domain containing	protein-coding	0.103286	0.700935	
chunk0006_76_1	chr1	64944340	64944689	+	0	NA	intron (NM_002227, intron 1 of 24)	L1M4|LINE|L1	21990	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.005731	0.348571	
chunk0148_416_1	chr5	14989392	14989989	+	0	NA	Intergenic	Intergenic	-117912	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.003350	0.337793	227(GGAGCTGTATGTTCTC,+,0.00)
chunk0065_150_1	chr15	25426032	25426245	+	0	NA	intron (NM_130839, intron 1 of 12)	intron (NM_130839, intron 1 of 12)	12890	NM_130839	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.000000	0.275701	
chunk0167_234_1	chr6	67352133	67352509	+	0	NA	Intergenic	(GTTT)n|Simple_repeat|Simple_repeat	-703030	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.005319	0.286472	
chunk0106_236_1	chr2	202892270	202892823	+	0	NA	intron (NM_018256, intron 8 of 12)	intron (NM_018256, intron 8 of 12)	-19672	NM_001104586	79800	Hs.444982	NM_024744	ENSG00000138380	CARF	ALS2CR8|NYD-SP24	calcium responsive transcription factor	protein-coding	0.005425	0.337545	318(AAGTACAGTCAGTTCT,-,0.00),319(AGTACAGTCAGTTCTC,+,0.00)
chunk0202_348_1	chr9	79667976	79668560	+	0	NA	intron (NM_001282760, intron 9 of 20)	intron (NM_001282760, intron 9 of 20)	96495	NM_001282753	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.017123	0.435897	
chunk0139_361_1	chr4	60312792	60313338	+	0	NA	Intergenic	Intergenic	-609554	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.005495	0.292505	
chunk0165_461_1	chr6	41142700	41143210	+	0	NA	Intergenic	L1MB7|LINE|L1	11394	NM_001271807	340205	Hs.117331	NM_178174	ENSG00000161911	TREML1	GLTL1825|PRO3438|TLT-1|TLT1|dJ238O23.3	triggering receptor expressed on myeloid cells like 1	protein-coding	0.007843	0.352250	
chunk0119_415_1	chr22	49786232	49786431	+	0	NA	intron (NM_001304808, intron 8 of 12)	intron (NM_001304808, intron 8 of 12)	39569	NM_001304809	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.045226	0.585000	
chunk0212_271_1	chrX	139738396	139738905	+	0	NA	intron (NM_001010986, intron 27 of 28)	intron (NM_001010986, intron 27 of 28)	-30428	NM_001171876	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.000000	0.388235	349(AAGCACAGCCTGTTTC,-,0.00),350(AGCACAGCCTGTTTCC,+,0.00)
chunk0142_354_1	chr4	101865777	101866033	+	0	NA	intron (NM_017935, intron 4 of 16)	L1MCa|LINE|L1	52079	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.007812	0.346304	
chunk0016_403_1	chr1	203257128	203257340	+	0	NA	Intergenic	L1P2|LINE|L1	-27502	NM_001270509	1118	Hs.201688	NM_003465	ENSG00000133063	CHIT1	CHI3|CHIT|CHITD	chitinase 1	protein-coding	0.004717	0.525822	
chunk0016_166_1	chr1	197844252	197844506	+	0	NA	Intergenic	Intergenic	-58173	NM_001024594	388722	Hs.61329	NM_001024594	ENSG00000203724	C1orf53	-	chromosome 1 open reading frame 53	protein-coding	0.015748	0.419608	145(CAGTACATCATGTTCA,-,0.00),146(AGTACATCATGTTCAT,+,0.00)
chunk0191_290_1	chr8	54109070	54109980	+	0	NA	Intergenic	L1MA10|LINE|L1	-7508	NM_001279357	10434	Hs.744046	NM_006330	ENSG00000120992	LYPLA1	APT-1|APT1|LPL-I|LPL1|hAPT1	lysophospholipase 1	protein-coding	0.004396	0.340285	
chunk0055_54_1	chr13	52484659	52485185	+	0	NA	Intergenic	L1ME3A|LINE|L1	-4071	NR_002793	220115	Hs.528448	NR_002793		TPTE2P3	TPTEps1	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 3	pseudo	0.007605	0.404175	298(GAGTACATACTGTACT,-,0.00),299(AGTACATACTGTACTG,+,0.00)
chunk0102_105_1	chr2	144349757	144350350	+	0	NA	Intergenic	Intergenic	-17519	NM_001284235	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.011804	0.422559	
chunk0051_223_1	chr12	116738114	116738347	+	0	NA	promoter-TSS (NM_001109903)	promoter-TSS (NM_001109903)	-61	NM_001109903	84900	Hs.437195	NM_032814	ENSG00000135119	RNFT2	TMEM118	ring finger protein, transmembrane 2	protein-coding	0.090129	0.632479	
chunk0029_366_1	chr10	107668472	107668955	+	0	NA	Intergenic	MER70A|LTR|ERVL	400580	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.002070	0.425620	289(TAGAACAACTTGTTCT,-,0.00),290(AGAACAACTTGTTCTA,+,0.00)
chunk0066_128_1	chr15	31083432	31083733	+	0	NA	intron (NM_001252024, intron 1 of 27)	intron (NM_001252024, intron 1 of 27)	18144	NM_001252024	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.016611	0.622517	
chunk0142_428_1	chr4	104771164	104771546	+	0	NA	Intergenic	Intergenic	-276454	NM_025212	80319	Hs.12248	NM_025212	ENSG00000168772	CXXC4	IDAX	CXXC finger protein 4	protein-coding	0.005236	0.399478	145(AAGGACAGACTGTGCT,-,0.00),146(AGGACAGACTGTGCTT,+,0.00)
chunk0128_439_1	chr3	115011527	115012206	+	0	NA	intron (NM_015642, intron 1 of 9)	L1MA3|LINE|L1	59548	NM_001164343	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.004418	0.311765	
chunk0023_146_1	chr10	24153277	24153747	+	0	NA	intron (NM_001098500, intron 2 of 18)	intron (NM_001098500, intron 2 of 18)	-55279	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.006383	0.356688	
chunk0105_36_1	chr2	182784239	182784766	+	0	NA	Intergenic	Intergenic	68461	NR_073367	54431	Hs.516632	NM_018981	ENSG00000077232	DNAJC10	ERdj5|JPDI|MTHr|PDIA19	DnaJ heat shock protein family (Hsp40) member C10	protein-coding	0.005693	0.367424	252(AAGCACAGTGTGTATT,-,0.00),253(AGCACAGTGTGTATTT,+,0.00)
chunk0199_278_1	chr9	6448673	6449216	+	0	NA	intron (NM_152896, intron 3 of 15)	intron (NM_152896, intron 3 of 15)	35793	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.009208	0.378676	
chunk0026_216_1	chr10	64573474	64574119	+	0	NA	Intergenic	L1MB7|LINE|L1	-251732	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.003101	0.379257	
chunk0112_333_1	chr20	44999800	45000500	+	0	NA	intron (NM_006282, intron 7 of 10)	intron (NM_006282, intron 7 of 10)	33671	NM_006282	6789	Hs.472838	NM_006282	ENSG00000101109	STK4	KRS2|MST1|YSK3	serine/threonine kinase 4	protein-coding	0.011429	0.402282	
chunk0138_10_1	chr4	30361131	30361377	+	0	NA	Intergenic	L1PA15|LINE|L1	-359154	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.000000	0.493927	135(CAGATCAGACTGTCCC,-,0.00),136(AGATCAGACTGTCCCC,+,0.00)
chunk0058_417_1	chr13	112760214	112760905	+	0	NA	intron (NM_032189, intron 1 of 28)	intron (NM_032189, intron 1 of 28)	-5828	NR_046661	100874205	Hs.658692	NR_046661	ENSG00000232684	ATP11A-AS1	-	ATP11A antisense RNA 1	ncRNA	0.013025	0.408960	
chunk0108_422_1	chr2	237743907	237744243	+	0	NA	intron (NM_001137550, intron 11 of 23)	intron (NM_001137550, intron 11 of 23)	51911	NM_004735	9208	Hs.471779	NM_004735	ENSG00000124831	LRRFIP1	FLAP-1|FLAP1|FLIIAP1|GCF-2|GCF2|HUFI-1|TRIP	LRR binding FLII interacting protein 1	protein-coding	0.011905	0.418398	
chunk0056_396_1	chr13	93788470	93788871	+	0	NA	intron (NM_005708, intron 2 of 8)	intron (NM_005708, intron 2 of 8)	69803	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.004988	0.407960	
chunk0054_30_1	chr13	40975026	40975410	+	0	NA	intron (NM_001145353, intron 1 of 7)	intron (NM_001145353, intron 1 of 7)	7064	NM_001145353	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.005208	0.348052	
chunk0182_396_1	chr7	100550530	100550849	+	0	NA	intron (NM_006076, intron 3 of 11)	intron (NM_006076, intron 3 of 11)	11478	NM_006076	3268	Hs.521083	NM_006076	ENSG00000106351	AGFG2	HRBL|RABR	ArfGAP with FG repeats 2	protein-coding	0.012539	0.415625	141(AAGGACAACTTGTTCT,-,0.00),142(AGGACAACTTGTTCTC,+,0.00)
chunk0204_206_1	chr9	96695445	96695706	+	0	NA	Intergenic	L1MA5|LINE|L1	-30246	NR_026792	441455	Hs.229613	NR_026792		LOC441455	-	makorin ring finger protein 1 pseudogene	pseudo	0.011494	0.324427	
chunk0008_419_1	chr1	98675618	98676181	+	0	NA	intron (NR_033716, intron 2 of 8)	intron (NR_033716, intron 2 of 8)	14219	NM_015976	51375	Hs.197015	NM_015976	ENSG00000162627	SNX7	-	sorting nexin 7	protein-coding	0.010657	0.322695	311(TAGCACATCATGTACA,-,0.00),312(AGCACATCATGTACAA,+,0.00)
chunk0170_381_1	chr6	116963737	116964216	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	86763	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.002088	0.433333	
chunk0046_239_1	chr12	60265409	60266741	+	0	NA	Intergenic	Intergenic	576738	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.004505	0.337584	
chunk0085_171_1	chr18	4510746	4511038	+	0	NA	Intergenic	(GTG)n|Simple_repeat|Simple_repeat	-55626	NM_004746	9229	Hs.594640	NM_004746	ENSG00000170579	DLGAP1	DAP-1|DAP-1-ALPHA|DAP-1-BETA|DAP1|DLGAP1A|DLGAP1B|GKAP|SAPAP1	DLG associated protein 1	protein-coding	0.000000	0.610922	
chunk0111_271_1	chr20	31075454	31075943	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-181966	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.012270	0.410204	
chunk0116_447_1	chr21	43585908	43586391	+	0	NA	intron (NM_007031, intron 8 of 8)	intron (NM_007031, intron 8 of 8)	23840	NR_106718	102464825		NR_106718	ENSG00000278433	MIR6070	hsa-mir-6070	microRNA 6070	ncRNA	0.018634	0.431818	253(CAATACACTCTGTCCT,-,0.00),254(AATACACTCTGTCCTC,+,0.00)
chunk0139_438_1	chr4	64623210	64623656	+	0	NA	Intergenic	LTR22A|LTR|ERVK	-213973	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.002242	0.429530	
chunk0165_338_1	chr6	37568543	37568835	+	0	NA	Intergenic	Intergenic	-13267	NR_039669	100616413		NR_039669	ENSG00000263926	MIR4462	-	microRNA 4462	ncRNA	0.006849	0.433447	59(AAAAACACTCTGTCCC,-,0.00),60(AAAACACTCTGTCCCA,+,0.00)
chunk0181_33_1	chr7	78442993	78443225	+	0	NA	intron (NM_001301128, intron 6 of 20)	intron (NM_001301128, intron 6 of 20)	95867	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.008621	0.364807	
chunk0132_362_1	chr3	161606983	161607548	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	110457	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.001770	0.316254	
chunk0194_68_1	chr8	82504196	82504628	+	0	NA	Intergenic	Intergenic	-662126	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.006944	0.325635	
chunk0101_348_1	chr2	137747489	137748763	+	0	NA	Intergenic	Intergenic	179806	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.003925	0.365490	622(GAGAACACCGAGTACA,-,0.00)
chunk0083_182_1	chr17	66375955	66376246	+	0	NA	intron (NM_002737, intron 2 of 16)	MER5A|DNA|hAT-Charlie	40754	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.003436	0.479452	
chunk0078_83_1	chr17	1976721	1977250	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	48360	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.020794	0.462264	
chunk0050_282_1	chr12	106357530	106358104	+	0	NA	promoter-TSS (NM_001160708)	promoter-TSS (NM_001160708)	159	NM_018082	55703	Hs.62696	NM_018082	ENSG00000013503	POLR3B	C128|HLD8|INMAP|RPC2	RNA polymerase III subunit B	protein-coding	0.085366	0.610435	
chunk0104_178_1	chr2	174614214	174614586	+	0	NA	intron (NM_001077269, intron 1 of 7)	intron (NM_001077269, intron 1 of 7)	20179	NM_003387	7456	Hs.128067	NM_003387	ENSG00000115935	WIPF1	PRPL-2|WAS2|WASPIP|WIP	WAS/WASL interacting protein family member 1	protein-coding	0.016129	0.404826	
chunk0097_288_1	chr2	55163805	55164216	+	0	NA	Intergenic	L2c|LINE|L2	-67893	NM_001135592	6233	Hs.311640	NM_002954	ENSG00000143947	RPS27A	CEP80|HEL112|S27A|UBA80|UBC|UBCEP1|UBCEP80	ribosomal protein S27a	protein-coding	0.014599	0.500000	
chunk0201_105_1	chr9	34991813	34992177	+	0	NA	intron (NM_001135004, intron 2 of 4)	intron (NM_001135004, intron 2 of 4)	1725	NM_001135005	25822	Hs.237506	NM_012266	ENSG00000137094	DNAJB5	Hsc40	DnaJ heat shock protein family (Hsp40) member B5	protein-coding	0.008242	0.600000	132(AAGGACACCCTGTACA,-,0.00),133(AGGACACCCTGTACAC,+,0.00)
chunk0062_381_1	chr14	74437794	74437993	+	0	NA	Intergenic	Intergenic	-11791	NM_001105579	646658	Hs.12400	NM_001105579	ENSG00000183379	SYNDIG1L	CAPUCIN|DSPC1|IFITMD4|TMEM90A	synapse differentiation inducing 1 like	protein-coding	0.015075	0.505000	
chunk0204_213_1	chr9	96989672	96990436	+	0	NA	intron (NR_002894, intron 1 of 4)	L1MC3|LINE|L1	23526	NR_002894									0.002618	0.368627	
chunk0095_252_1	chr2	19370605	19371266	+	0	NA	Intergenic	Intergenic	-12324	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.007564	0.386707	365(AGGAACAGAGTGTTCC,-,0.00),366(GGAACAGAGTGTTCCT,+,0.00)
chunk0155_434_1	chr5	100677349	100677609	+	0	NA	Intergenic	Intergenic	139086	NR_031686	100302288		NR_031686	ENSG00000221263	MIR548P	MIRN548P|hsa-mir-548p	microRNA 548p	ncRNA	0.011538	0.402299	
chunk0131_146_1	chr3	146000448	146000892	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	160825	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.000000	0.305618	
chunk0129_215_1	chr3	121813892	121814645	+	0	NA	intron (NM_001023571, intron 5 of 11)	L1PA8|LINE|L1	20811	NM_001023570	9657	Hs.604110	NM_001023570	ENSG00000173226	IQCB1	NPHP5|PIQ|SLSN5	IQ motif containing B1	protein-coding	0.013280	0.379310	254(CGGCACAAGCTGCTCC,-,0.00),255(GGCACAAGCTGCTCCT,+,0.00),334(AAAGACACAATGTGCC,-,0.00),335(AAGACACAATGTGCCA,+,0.00)
chunk0159_395_1	chr5	147215648	147215847	+	0	NA	Intergenic	Intergenic	-19269	NM_001287740	202374	Hs.585069	NM_145001	ENSG00000169302	STK32A	YANK1	serine/threonine kinase 32A	protein-coding	0.000000	0.370000	
chunk0036_250_1	chr11	64505014	64505293	+	0	NA	Intergenic	MER70B|LTR|ERVL	-50448	NM_001307985	55867	Hs.220844	NM_018484	ENSG00000168065	SLC22A11	OAT4|hOAT4	solute carrier family 22 member 11	protein-coding	0.003584	0.510714	143(TAGAACAAGATGTCCT,-,0.00),144(AGAACAAGATGTCCTG,+,0.00)
chunk0008_169_1	chr1	92848834	92849355	+	0	NA	intron (NM_001252271, intron 3 of 4)	L1M|LINE|L1	8375	NR_002444	26782	Hs.180946	NR_002444	ENSG00000207523	SNORA66	RNU66|U66	small nucleolar RNA, H/ACA box 66	snoRNA	0.001919	0.310345	232(TAGTTCATCCTGTCCT,-,0.00),233(AGTTCATCCTGTCCTT,+,0.00)
chunk0156_330_1	chr5	111643260	111643661	+	0	NA	intron (NR_040093, intron 1 of 6)	intron (NR_040093, intron 1 of 6)	112791	NM_001142483	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.004988	0.338308	
chunk0069_409_1	chr15	67941870	67942148	+	0	NA	Intergenic	Charlie16a|DNA|hAT-Charlie	-101964	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.010791	0.401434	
chunk0035_309_1	chr11	47213002	47213213	+	0	NA	Intergenic	Intergenic	-1835	NM_001300734	1643	Hs.700338	NM_000107	ENSG00000134574	DDB2	DDBB|UV-DDB2|XPE	damage specific DNA binding protein 2	protein-coding	0.037915	0.561321	
chunk0069_254_1	chr15	64490700	64490988	+	0	NA	Intergenic	Intergenic	-8576	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.411765	
chunk0157_261_1	chr5	120007543	120008081	+	0	NA	Intergenic	L3b|LINE|CR1	378253	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.007435	0.356215	
chunk0024_371_1	chr10	44358150	44358537	+	0	NA	Intergenic	Intergenic	26754	NM_001178134	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.012920	0.528351	
chunk0161_192_1	chr5	170248412	170248849	+	0	NA	3' UTR (NM_005565, exon 21 of 21)	3' UTR (NM_005565, exon 21 of 21)	15623	NM_001305394	133874	Hs.519749	NM_001102609	ENSG00000234511	C5orf58	-	chromosome 5 open reading frame 58	protein-coding	0.011442	0.401826	
chunk0021_141_1	chr10	4129760	4130360	+	0	NA	Intergenic	Intergenic	78334	NR_120632	101927964	Hs.737041	NR_120632	ENSG00000236990	LOC101927964	-	uncharacterized LOC101927964	ncRNA	0.015000	0.434276	
chunk0118_239_1	chr22	32557219	32557834	+	0	NA	intron (NM_003490, intron 6 of 12)	MIR|SINE|MIR	82289	NM_001257990	25793	Hs.5912	NM_012179	ENSG00000100225	FBXO7	FBX|FBX07|FBX7|PARK15|PKPS	F-box protein 7	protein-coding	0.009756	0.472403	
chunk0134_367_1	chr3	182702291	182702610	+	0	NA	Intergenic	L1PB1|LINE|L1	-91053	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.003135	0.350000	
chunk0026_203_1	chr10	63713295	63713688	+	0	NA	Intergenic	Intergenic	192128	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.010178	0.449239	221(AAAACAGATTGTACTT,+,0.00)
chunk0114_159_1	chr21	10637693	10637892	+	0	NA	Intergenic	MER89-int|LTR|ERV1	116278	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.000000	0.360000	
chunk0058_176_1	chr14	23895020	23895500	+	0	NA	Intergenic	LTR43B|LTR|ERV1	-58475	NM_001282990	10901	Hs.528385	NM_021004	ENSG00000157326	DHRS4	CR|NRDR|PHCR|PSCD|SCAD-SRL|SDR-SRL|SDR25C1|SDR25C2	dehydrogenase/reductase 4	protein-coding	0.002083	0.415800	
chunk0058_167_1	chr14	23527352	23527595	+	0	NA	intron (NM_033400, intron 7 of 9)	intron (NM_033400, intron 7 of 9)	14663	NR_046052	79178	Hs.655179	NM_024328	ENSG00000259431	THTPA	THTP|THTPASE	thiamine triphosphatase	protein-coding	0.016461	0.561475	
chunk0035_228_1	chr11	45765848	45766235	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-5391	NR_027134	374387	Hs.632142	NM_199137	ENSG00000205106	LINC02716	DKFZp779M0652	long intergenic non-protein coding RNA 2716	ncRNA	0.007752	0.489691	190(AGGAACACCAAGTGCT,-,0.00),191(GGAACACCAAGTGCTT,+,0.00)
chunk0003_137_1	chr1	32767179	32767797	+	0	NA	intron (NM_001198972, intron 1 of 6)	intron (NM_001198972, intron 1 of 6)	1854	NM_001198972	57648	Hs.591502	NM_020888	ENSG00000162522	KIAA1522	-	KIAA1522	protein-coding	0.016181	0.495961	
chunk0126_42_1	chr3	73804076	73804781	+	0	NA	Intergenic	Intergenic	-179507	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.009929	0.453258	
chunk0210_261_1	chrX	84037707	84038281	+	0	NA	Intergenic	L1PB4|LINE|L1	149941	NM_014496	27330	Hs.234478	NM_014496	ENSG00000072133	RPS6KA6	PP90RSK4|RSK-4|RSK4|S6K-alpha-6|p90RSK6	ribosomal protein S6 kinase A6	protein-coding	0.001742	0.297391	
chunk0134_245_1	chr3	179322891	179323246	+	0	NA	promoter-TSS (NM_001303425)	promoter-TSS (NM_001303425)	77	NM_001303425	51193	Hs.632578	NM_016331	ENSG00000121864	ZNF639	ANC-2H01|ANC_2H01|ZASC1	zinc finger protein 639	protein-coding	0.146479	0.817416	
chunk0113_276_1	chr20	56668969	56669298	+	0	NA	Intergenic	L2a|LINE|L2	39831	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.003040	0.345455	118(GAGAACATGCTGCCCT,-,0.00),119(AGAACATGCTGCCCTT,+,0.00)
chunk0192_114_1	chr8	61724865	61725416	+	0	NA	Intergenic	Intergenic	10352	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.007260	0.454710	
chunk0053_139_1	chr13	29957230	29957539	+	0	NA	Intergenic	Intergenic	20853	NR_033889	440131	Hs.132371	NM_001010918		LINC00544	-	long intergenic non-protein coding RNA 544	ncRNA	0.025890	0.500000	
chunk0090_144_1	chr18	72239955	72240471	+	0	NA	Intergenic	L1MC|LINE|L1	304275	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.001938	0.352031	
chunk0187_329_1	chr7	156695126	156695656	+	0	NA	intron (NM_022458, intron 15 of 16)	MSTA|LTR|ERVL-MaLR	51590	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.009434	0.453861	
chunk0193_102_1	chr8	73736266	73736605	+	0	NA	intron (NM_001164380, intron 3 of 14)	L2c|LINE|L2	10492	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.000000	0.373529	
chunk0126_247_1	chr3	79366409	79366747	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-45149	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.017751	0.436578	
chunk0105_97_1	chr2	184444308	184444507	+	0	NA	Intergenic	Intergenic	65432	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.010050	0.380000	
chunk0197_419_1	chr8	127340692	127340894	+	0	NA	intron (NR_117099, intron 3 of 3)	L2a|LINE|L2	-59606	NR_109834	101805488	Hs.745578	NR_109834	ENSG00000280997	CCAT2	LINC00873|NCCP1	colon cancer associated transcript 2	ncRNA	0.000000	0.379310	
chunk0050_354_1	chr12	107765467	107765728	+	0	NA	Intergenic	L2a|LINE|L2	-4460	NM_012406	11108	Hs.506655	NM_012406	ENSG00000110851	PRDM4	PFM1	PR/SET domain 4	protein-coding	0.000000	0.343511	
chunk0048_22_1	chr12	77344685	77345315	+	0	NA	Intergenic	Intergenic	-279420	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.001587	0.385103	241(AATAACATACTGTTCC,-,0.00),242(ATAACATACTGTTCCA,+,0.00)
chunk0074_72_1	chr16	21300551	21300779	+	0	NA	promoter-TSS (NR_026675)	promoter-TSS (NR_026675)	-184	NR_026675	400508	Hs.578949	NM_001101368		CRYM-AS1	NCRNA00169	CRYM antisense RNA 1	ncRNA	0.026316	0.506550	140(GAGAACTCCTTGTCCT,-,0.00),141(AGAACTCCTTGTCCTG,+,0.00)
chunk0160_295_1	chr5	158331718	158331959	+	0	NA	intron (NR_109888, intron 5 of 6)	L1PA15|LINE|L1	77935	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.008299	0.376033	
chunk0092_29_1	chr19	19021210	19021409	+	0	NA	intron (NM_001017392, intron 3 of 10)	intron (NM_001017392, intron 3 of 10)	12262	NM_014884	10147	Hs.77876	NM_014884	ENSG00000064607	SUGP2	SFRS14|SRFS14	SURP and G-patch domain containing 2	protein-coding	0.015075	0.410000	
chunk0045_51_1	chr12	45226055	45226316	+	0	NA	intron (NM_001142679, intron 1 of 19)	intron (NM_001142679, intron 1 of 19)	-10179	NR_037144	51054	Hs.233495	NM_015899	ENSG00000134297	PLEKHA8P1	FAPP-2|FAPP2|PLEKHA8|PLEKHA9|hFAPP2	pleckstrin homology domain containing A8 pseudogene 1	pseudo	0.000000	0.358779	
chunk0050_428_1	chr12	110048378	110048852	+	0	NA	intron (NM_207435, intron 4 of 4)	CpG	19080	NM_207435	400073	Hs.44817	NM_207435	ENSG00000174456	C12orf76	-	chromosome 12 open reading frame 76	protein-coding	0.071730	0.576842	
chunk0098_255_1	chr2	75062760	75062993	+	0	NA	intron (NM_001058, intron 2 of 4)	L1ME4a|LINE|L1	-27936	NR_049796	100846995		NR_049796	ENSG00000263909	MIR5000	-	microRNA 5000	ncRNA	0.000000	0.350427	
chunk0182_158_1	chr7	95432797	95433046	+	0	NA	intron (NM_001018161, intron 1 of 8)	intron (NM_001018161, intron 1 of 8)	2151	NM_000305	5445	Hs.514420	NM_000305	ENSG00000105854	PON2	-	paraoxonase 2	protein-coding	0.008032	0.484000	
chunk0097_422_1	chr2	63183551	63184598	+	0	NA	intron (NR_122106, intron 8 of 11)	L1PB4|LINE|L1	-64532	NR_036635	100169989	Hs.606147	NR_036635	ENSG00000242412	DBIL5P2	ELP1P	diazepam binding inhibitor-like 5 pseudogene 2	pseudo	0.003820	0.331107	
chunk0149_281_1	chr5	25105917	25106307	+	0	NA	Intergenic	L1PA16|LINE|L1	-265529	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.005128	0.396419	
chunk0072_295_1	chr15	98682197	98682464	+	0	NA	intron (NM_001291858, intron 1 of 20)	intron (NM_001291858, intron 1 of 20)	-31109	NR_126453	104472848	Hs.349049	NR_126453		IRAIN	IGF1R-AS	IGF1R antisense imprinted non-protein coding RNA	ncRNA	0.014981	0.447761	
chunk0016_416_1	chr1	203396918	203397726	+	0	NA	Intergenic	Intergenic	-45893	NR_103757	2331	Hs.519168	NM_002023	ENSG00000122176	FMOD	FM|SLRR2E	fibromodulin	protein-coding	0.012376	0.407911	
chunk0006_290_1	chr1	70868287	70868632	+	0	NA	intron (NR_028294, intron 3 of 5)	intron (NR_028294, intron 3 of 5)	162006	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.002899	0.378613	
chunk0185_304_1	chr7	131246886	131247114	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	80779	NR_125364	100506881	Hs.660830	NR_125364	ENSG00000236753	MKLN1-AS	MKLN1-AS2	MKLN1 antisense RNA	ncRNA	0.000000	0.393013	
chunk0130_372_1	chr3	139344289	139344566	+	0	NA	intron (NM_020191, intron 1 of 7)	L2b|LINE|L2	408	NM_020191	56945	Hs.745001	NM_020191	ENSG00000175110	MRPS22	C3orf5|COXPD5|GIBT|GK002|MRP-S22|ODG7|RPMS22	mitochondrial ribosomal protein S22	protein-coding	0.025271	0.507194	
chunk0108_288_1	chr2	234867729	234868358	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-83941	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.004769	0.400000	
chunk0186_400_1	chr7	144632352	144633080	+	0	NA	intron (NM_001042482, intron 5 of 7)	intron (NM_001042482, intron 5 of 7)	203337	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.006868	0.390947	390(AGGAACATTTTGTTAT,-,0.00),458(AAGAACTGCCTGAGCC,-,0.00),459(AGAACTGCCTGAGCCT,+,0.00)
chunk0052_400_1	chr12	130885958	130886597	+	0	NA	Intergenic	L1MC|LINE|L1	14283	NM_001300796	5901	Hs.10842	NM_006325	ENSG00000132341	RAN	ARA24|Gsp1|TC4	RAN, member RAS oncogene family	protein-coding	0.015649	0.435937	
chunk0148_166_1	chr5	6926640	6926873	+	0	NA	Intergenic	Intergenic	-98835	NR_036242	100422999		NR_036242	ENSG00000283420	MIR4278	-	microRNA 4278	ncRNA	0.004292	0.487179	
chunk0191_76_1	chr8	47365768	47366370	+	0	NA	intron (NR_104581, intron 5 of 16)	intron (NR_104581, intron 5 of 16)	105191	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.006645	0.439469	83(CAGGACAGGAAGTGCA,-,0.00),84(AGGACAGGAAGTGCAG,+,0.00)
chunk0091_236_1	chr19	10625161	10625679	+	0	NA	promoter-TSS (NM_020428)	promoter-TSS (NM_020428)	-75	NM_020428	57153	Hs.534560	NM_020428	ENSG00000129353	SLC44A2	CTL2|PP1292	solute carrier family 44 member 2	protein-coding	0.083012	0.682081	
chunk0148_403_1	chr5	14864334	14864893	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	7165	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.003578	0.348214	190(GAGGTCACAGTGTCCT,-,0.00),191(AGGTCACAGTGTCCTT,+,0.00)
chunk0126_365_1	chr3	83405237	83405487	+	0	NA	Intergenic	LTR40b|LTR|ERVL	1464213	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.008000	0.366534	
chunk0078_25_1	chr17	837200	837727	+	0	NA	intron (NM_022463, intron 1 of 7)	MIRb|SINE|MIR	26648	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.015180	0.532197	
chunk0165_111_1	chr6	32722812	32723112	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-18424	NM_020056	3118	Hs.591798	NM_020056	ENSG00000237541	HLA-DQA2	DC-alpha|DX-ALPHA|HLA-DCA|HLA-DXA|HLADQA2	major histocompatibility complex, class II, DQ alpha 2	protein-coding	0.000000	0.305648	
chunk0119_165_1	chr22	43278255	43278577	+	0	NA	intron (NM_173050, intron 4 of 21)	intron (NM_173050, intron 4 of 21)	64972	NM_173050	80274	Hs.133995	NM_152514	ENSG00000159307	SCUBE1	-	signal peptide, CUB domain and EGF like domain containing 1	protein-coding	0.018634	0.603715	
chunk0117_219_1	chr22	22420407	22420835	+	0	NA	Intergenic	Intergenic	88566	NM_080764	140883	Hs.43834	NM_080764	ENSG00000275004	ZNF280B	5'OY11.1|D87009.C22.3|SUHW2|ZNF279|ZNF632	zinc finger protein 280B	protein-coding	0.014019	0.393939	
chunk0124_68_1	chr3	53085793	53086349	+	0	NA	Intergenic	Intergenic	-39998	NM_016329	51460	Hs.343679	NM_016329	ENSG00000163935	SFMBT1	RU1|SFMBT|hSFMBT	Scm like with four mbt domains 1	protein-coding	0.007194	0.362657	
chunk0055_405_1	chr13	74365917	74366211	+	0	NA	Intergenic	Intergenic	-53109	NR_047005	100874151	Hs.564552	NR_047005	ENSG00000226240	LINC00381	-	long intergenic non-protein coding RNA 381	ncRNA	0.006803	0.355932	25(AGGAACATACTGTCTT,-,0.00),26(GGAACATACTGTCTTG,+,0.00),83(AAGAACTAGCTGTTCT,-,0.00),84(AGAACTAGCTGTTCTT,+,0.00)
chunk0122_464_1	chr3	39981914	39982113	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	-117998	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.000000	0.325000	49(AAGAACTCAAAGTCCT,-,0.00)
chunk0012_49_1	chr1	155379816	155380072	+	0	NA	intron (NM_018489, intron 8 of 27)	intron (NM_018489, intron 8 of 27)	-33499	NR_030282	693140		NR_030282	ENSG00000283701	MIR555	MIRN555|hsa-mir-555	microRNA 555	ncRNA	0.000000	0.408560	
chunk0031_102_1	chr10	124106309	124106704	+	0	NA	Intergenic	Intergenic	-12899	NM_001270764	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.015190	0.464646	
chunk0027_288_1	chr10	77557059	77557747	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	80416	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.004360	0.433962	
chunk0088_274_1	chr18	49286153	49286452	+	0	NA	intron (NM_017653, intron 9 of 16)	intron (NM_017653, intron 9 of 16)	174407	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.000000	0.336667	17(TAGTACAGACTGACCC,-,0.00),18(AGTACAGACTGACCCA,+,0.00)
chunk0075_290_1	chr16	54000114	54000473	+	0	NA	intron (NM_001080432, intron 8 of 8)	intron (NM_001080432, intron 8 of 8)	-39100	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.005571	0.388889	
chunk0001_42_1	chr1	1758709	1759383	+	0	NA	promoter-TSS (NM_001198995)	promoter-TSS (NM_001198995)	-404	NM_001198995	65220	Hs.654792	NM_023018	ENSG00000008130	NADK	dJ283E3.1	NAD kinase	protein-coding	0.047478	0.668148	
chunk0171_384_1	chr6	131108669	131109302	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-26701	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.001580	0.378549	
chunk0115_1_1	chr21	20132332	20132663	+	0	NA	Intergenic	Intergenic	670611	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.003021	0.364458	
chunk0066_37_1	chr15	27691323	27691861	+	0	NA	Intergenic	Intergenic	407720	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.011152	0.456401	
chunk0207_153_1	chr9	129851537	129851737	+	0	NA	intron (NM_001008563, intron 2 of 25)	intron (NM_001008563, intron 2 of 25)	16220	NM_001110303	10868	Hs.5452	NM_006676	ENSG00000136878	USP20	LSFR3A|VDU2|hVDU2	ubiquitin specific peptidase 20	protein-coding	0.010000	0.388060	
chunk0054_410_1	chr13	50611372	50611915	+	0	NA	Intergenic	Intergenic	-84194	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.007366	0.417279	249(AGGAACTAGATGTTCC,-,0.00),250(GGAACTAGATGTTCCA,+,0.00)
chunk0155_18_1	chr5	90896697	90896980	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	338038	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.000000	0.390845	137(ATGAACTCCTTGTGCC,-,0.00)
chunk0130_363_1	chr3	139117002	139117586	+	0	NA	intron (NR_026783, intron 2 of 2)	Tigger3|DNA|TcMar-Tigger	13109	NR_026783	60467	Hs.512673	NM_021812	ENSG00000232416	BPESC1	NCRNA00187	blepharophimosis, epicanthus inversus and ptosis candidate 1	ncRNA	0.003425	0.347009	
chunk0186_283_1	chr7	142234652	142234851	+	0	NA	Intergenic	L1PA13|LINE|L1	12316	NR_024346	100289017	Hs.641504	NR_024346	ENSG00000240268	MOXD2P	MOXD2	monooxygenase DBH like 2, pseudogene	pseudo	0.025126	0.600000	
chunk0103_211_1	chr2	163889325	163889854	+	0	NA	Intergenic	Intergenic	-153586	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.005671	0.335849	
chunk0101_203_1	chr2	130106917	130107478	+	0	NA	intron (NM_001099771, intron 8 of 16)	Zaphod2|DNA|hAT-Tip100	22025	NM_001099771	728378	Hs.580547	NM_001099771	ENSG00000196604	POTEF	A26C1B|ACTB|POTE2alpha|POTEACTIN	POTE ankyrin domain family member F	protein-coding	0.005348	0.359431	294(CAGAGCATCTTGTTCT,-,0.00)
chunk0132_81_1	chr3	155316276	155316843	+	0	NA	Intergenic	Intergenic	-22859	NR_037902									0.001764	0.367958	
chunk0106_141_1	chr2	200077063	200077570	+	0	NA	Intergenic	Intergenic	-121580	NR_109906	129450	Hs.204619	NM_152382	ENSG00000162971	TYW5	C2orf60|hTYW5	tRNA-yW synthesizing protein 5	protein-coding	0.005917	0.340551	
chunk0052_125_1	chr13	23471267	23471638	+	0	NA	intron (NR_038995, intron 2 of 2)	intron (NR_038995, intron 2 of 2)	1940	NR_038995	100506697	Hs.50118	NR_038995	ENSG00000232977	LINC00327	NCRNA00327	long intergenic non-protein coding RNA 327	ncRNA	0.010782	0.330645	
chunk0129_278_1	chr3	123068548	123069493	+	0	NA	intron (NM_006810, intron 1 of 16)	intron (NM_006810, intron 1 of 16)	2011	NR_028444	10954	Hs.477352	NM_006810	ENSG00000065485	PDIA5	PDIR	protein disulfide isomerase family A member 5	protein-coding	0.014815	0.468288	274(CAGAACTGCAAGTGCT,-,0.00),275(AGAACTGCAAGTGCTG,+,0.00)
chunk0046_298_1	chr12	62234867	62235066	+	0	NA	Intergenic	Intergenic	-25374	NM_001252078	9958	Hs.434951	NM_006313	ENSG00000135655	USP15	UNPH-2|UNPH4	ubiquitin specific peptidase 15	protein-coding	0.025126	0.565000	
chunk0148_280_1	chr5	10779628	10779888	+	0	NA	Intergenic	L1M2b|LINE|L1	-18483	NM_004394	1611	Hs.75189	NM_004394	ENSG00000112977	DAP	-	death associated protein	protein-coding	0.000000	0.574713	
chunk0017_340_1	chr1	211643658	211644091	+	0	NA	intron (NR_131925, intron 2 of 2)	intron (NR_131925, intron 2 of 2)	4066	NR_131925	105748977	Hs.553186	NR_131925		LINC01693	-	long intergenic non-protein coding RNA 1693	ncRNA	0.016166	0.592166	
chunk0164_421_1	chr6	27236644	27237243	+	0	NA	Intergenic	L1MC5a|LINE|L1	-10780	NM_005865	10279	Hs.274407	NM_005865	ENSG00000112812	PRSS16	TSSP	serine protease 16	protein-coding	0.011686	0.365000	
chunk0143_357_1	chr4	122069398	122069991	+	0	NA	Intergenic	L1MC4|LINE|L1	-100909	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.003373	0.345118	297(TGGCACAAGATGTTCC,-,0.00),298(GGCACAAGATGTTCCA,+,0.00)
chunk0015_452_1	chr1	192418863	192419319	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	102099	NM_001039152	431704	Hs.558673	NM_001039152	ENSG00000253148	RGS21	-	regulator of G protein signaling 21	protein-coding	0.000000	0.367615	
chunk0142_91_1	chr4	94166302	94166550	+	0	NA	intron (NR_125922, intron 1 of 8)	intron (NR_125922, intron 1 of 8)	41130	NR_125922	101929210	Hs.518877	NR_125922	ENSG00000246541	LOC101929210	-	uncharacterized LOC101929210	ncRNA	0.008065	0.337349	
chunk0140_31_1	chr4	66035506	66036247	+	0	NA	Intergenic	Intergenic	-240948	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.006748	0.336927	
chunk0064_89_1	chr14	90733387	90733866	+	0	NA	intron (NM_001010854, intron 4 of 19)	intron (NM_001010854, intron 4 of 19)	82791	NM_001010854	145567	Hs.655697	NM_001010854	ENSG00000165914	TTC7B	TTC7L1|c14_5685	tetratricopeptide repeat domain 7B	protein-coding	0.020877	0.510417	
chunk0030_205_1	chr10	114507467	114507792	+	0	NA	intron (NM_001003407, intron 6 of 21)	intron (NM_001003407, intron 6 of 21)	19297	NM_006720	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.012308	0.555215	
chunk0203_25_1	chr9	82881719	82882302	+	0	NA	Intergenic	MamGypLTR2c|LTR|Gypsy	181118	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.001715	0.416096	196(AAAGACATCATGTTCC,-,0.00),197(AAGACATCATGTTCCA,+,0.00)
chunk0104_32_1	chr2	170928897	170929199	+	0	NA	5' UTR (NM_015530, exon 1 of 10)	5' UTR (NM_015530, exon 1 of 10)	522	NM_015530	26003	Hs.431317	NM_015530	ENSG00000115806	GORASP2	GOLPH6|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding	0.096026	0.673267	
chunk0053_356_1	chr13	35050766	35050968	+	0	NA	intron (NM_015678, intron 6 of 57)	intron (NM_015678, intron 6 of 57)	108580	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.000000	0.334975	
chunk0082_61_1	chr17	51354381	51354880	+	0	NA	Intergenic	Intergenic	17915	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.006012	0.438000	
chunk0198_439_1	chr8	143756045	143756437	+	0	NA	Intergenic	Intergenic	22101	NR_033849	100128338	Hs.493171	NR_033849	ENSG00000203499	FAM83H-AS1	onco-lncRNA-3	FAM83H antisense RNA 1 (head to head)	ncRNA	0.007653	0.483461	
chunk0099_377_1	chr2	101114430	101114633	+	0	NA	intron (NM_001102426, intron 1 of 19)	intron (NM_001102426, intron 1 of 19)	36853	NM_001102426	11138	Hs.442657	NM_007063	ENSG00000204634	TBC1D8	AD3|GRAMD8|HBLP1|TBC1D8A|VRP	TBC1 domain family member 8	protein-coding	0.009852	0.382353	
chunk0099_366_1	chr2	100947571	100948143	+	0	NA	intron (NM_002518, intron 5 of 20)	intron (NM_002518, intron 5 of 20)	29304	NR_110213	101927142	Hs.656556	NR_110213		LOC101927142	-	uncharacterized LOC101927142	ncRNA	0.012238	0.453752	
chunk0151_310_1	chr5	53338935	53339379	+	0	NA	Intergenic	Intergenic	-141277	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.006757	0.377528	
chunk0002_57_1	chr1	13699683	13699882	+	0	NA	promoter-TSS (NM_001135610)	promoter-TSS (NM_001135610)	-458	NM_001135610	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.045226	0.530000	
chunk0180_64_1	chr7	54832996	54833685	+	0	NA	Intergenic	CpG	74027	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.072569	0.626087	
chunk0072_66_1	chr15	90419704	90420106	+	0	NA	intron (NM_003870, intron 2 of 37)	intron (NM_003870, intron 2 of 37)	31664	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.009950	0.372208	154(TGGAACACAGTGTTCA,-,0.00),155(GGAACACAGTGTTCAG,+,0.00)
chunk0133_236_1	chr3	171356341	171356566	+	0	NA	intron (NR_027767, intron 2 of 2)	intron (NR_027767, intron 2 of 2)	103955	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.004444	0.345133	72(AAAAACACAGTGTCCC,-,0.00),73(AAAACACAGTGTCCCC,+,0.00)
chunk0121_290_1	chr3	23673794	23674018	+	0	NA	Intergenic	L1MC3|LINE|L1	-131987	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.017857	0.413333	
chunk0051_249_1	chr12	117176875	117177354	+	0	NA	intron (NM_033624, intron 4 of 11)	intron (NM_033624, intron 4 of 11)	13381	NM_015002	23014	Hs.740376	NM_015002	ENSG00000135108	FBXO21	FBX21	F-box protein 21	protein-coding	0.006263	0.337500	233(AAGAACATTCTGTCCT,-,0.00),234(AGAACATTCTGTCCTC,+,0.00)
chunk0077_373_1	chr16	84540160	84540637	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-35716	NM_020947	57707	Hs.288274	NM_020947	ENSG00000140950	MEAK7	KIAA1609|TLDC1|mEAK-7	MTOR associated protein, eak-7 homolog	protein-coding	0.014675	0.481172	294(GGGGACACACTGTCTC,-,0.00),295(GGGACACACTGTCTCT,+,0.00)
chunk0197_387_1	chr8	127022354	127022880	+	0	NA	Intergenic	L1M5|LINE|L1	9463	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.007605	0.297913	
chunk0202_203_1	chr9	75500918	75501417	+	0	NA	Intergenic	L1PA15|LINE|L1	-389477	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.008016	0.374000	
chunk0184_393_1	chr7	121623580	121624245	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-227544	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.003008	0.387387	
chunk0109_459_1	chr2	242075600	242076049	+	0	NA	intron (NR_110220, intron 3 of 3)	intron (NR_110220, intron 3 of 3)	-12809	NR_130700	728323	Hs.380737	NR_024437		LINC01881	-	long intergenic non-protein coding RNA 1881	ncRNA	0.013363	0.453333	
chunk0018_64_1	chr1	216902535	216903328	+	0	NA	intron (NM_001243507, intron 2 of 7)	intron (NM_001243507, intron 2 of 7)	36742	NM_001243513	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.006305	0.435768	254(TGGAACATGCTGATCT,-,0.00),255(GGAACATGCTGATCTA,+,0.00)
chunk0160_66_1	chr5	149791440	149792096	+	0	NA	intron (NM_001172699, intron 1 of 10)	intron (NM_001172699, intron 1 of 10)	19828	NM_001172699	133522	Hs.483816	NM_133263	ENSG00000155846	PPARGC1B	ERRL1|PERC|PGC-1(beta)|PGC1B	PPARG coactivator 1 beta	protein-coding	0.003049	0.480974	628(GAGAACAGAGTGGCCT,-,0.00),629(AGAACAGAGTGGCCTG,+,0.00)
chunk0029_7_1	chr10	95308742	95309139	+	0	NA	Intergenic	AluYb8|SINE|Alu	-17792	NM_020992	9124	Hs.368525	NM_020992	ENSG00000107438	PDLIM1	CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1	PDZ and LIM domain 1	protein-coding	0.007557	0.482412	
chunk0114_336_1	chr21	17590170	17590835	+	0	NA	intron (NM_001207066, intron 7 of 7)	intron (NM_001207066, intron 7 of 7)	22448	NM_006806	10950	Hs.473420	NM_006806	ENSG00000154640	BTG3	ANA|ANA/BTG3|APRO4|TOB5|TOB55|TOFA	BTG anti-proliferation factor 3	protein-coding	0.006015	0.342342	
chunk0061_321_1	chr14	62967738	62968085	+	0	NA	intron (NM_172375, intron 6 of 9)	intron (NM_172375, intron 6 of 9)	77327	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.000000	0.324713	
chunk0138_279_1	chr4	40548180	40548379	+	0	NA	intron (NM_001098634, intron 1 of 6)	intron (NM_001098634, intron 1 of 6)	-32306	NM_019027	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.030151	0.530000	68(CAGAACAGTCAGTTCC,-,0.00),69(AGAACAGTCAGTTCCT,+,0.00)
chunk0165_77_1	chr6	31216181	31216608	+	0	NA	Intergenic	LTR10B1|LTR|ERV1	18634	NR_026791	253018	Hs.659818	NR_026791	ENSG00000206344	HCG27	bCX101P6.9|bPG299F13.9|bQB115I13.2	HLA complex group 27	ncRNA	0.007026	0.429907	
chunk0044_388_1	chr12	40013853	40014278	+	0	NA	intron (NM_052885, intron 3 of 9)	intron (NM_052885, intron 3 of 9)	91794	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.004706	0.321596	
chunk0051_351_1	chr12	120480192	120480642	+	0	NA	intron (NM_001037494, intron 1 of 2)	intron (NM_001037494, intron 1 of 2)	10560	NM_001037494	8655	Hs.5120	NM_003746	ENSG00000088986	DYNLL1	DLC1|DLC8|DNCL1|DNCLC1|LC8|LC8a|PIN|hdlc1	dynein light chain LC8-type 1	protein-coding	0.002222	0.514412	
chunk0041_219_1	chr11	127628224	127628801	+	0	NA	Intergenic	Intergenic	357442	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.020797	0.472318	182(AGGCACAGGGTGTGCA,-,0.00),183(GGCACAGGGTGTGCAG,+,0.00),326(AGGAACTGCATGTTCT,-,0.00),327(GGAACTGCATGTTCTT,+,0.00)
chunk0084_184_1	chr17	77681867	77682300	+	0	NA	Intergenic	Intergenic	46476	NR_104134	100132174	Hs.640110	NR_104134	ENSG00000267790	LINC01987	-	long intergenic non-protein coding RNA 1987	ncRNA	0.020785	0.518433	
chunk0135_327_1	chr3	190124014	190124370	+	0	NA	intron (NR_126419, intron 1 of 3)	intron (NR_126419, intron 1 of 3)	-1755	NM_001134418	55214	Hs.374191	NM_018192	ENSG00000090530	P3H2	LEPREL1|MCVD|MLAT4	prolyl 3-hydroxylase 2	protein-coding	0.005618	0.428571	112(AGGACAAAAAGTTCAT,+,0.00),172(CAGGTCATGCTGTCCC,-,0.00),173(AGGTCATGCTGTCCCA,+,0.00)
chunk0178_244_1	chr7	36164174	36164804	+	0	NA	intron (NM_030636, intron 2 of 7)	Tigger13a|DNA|TcMar-Tigger	11262	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.001587	0.386688	208(AAGCACATGATGCCCT,-,0.00)
chunk0121_76_1	chr3	15904991	15905484	+	0	NA	Intergenic	MIR|SINE|MIR	31466	NR_030289	693148		NR_030289	ENSG00000207815	MIR563	MIRN563|hsa-mir-563	microRNA 563	ncRNA	0.002028	0.398785	
chunk0021_236_1	chr1	242403050	242403249	+	0	NA	intron (NM_152666, intron 2 of 10)	intron (NM_152666, intron 2 of 10)	46333	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.020101	0.515000	
chunk0141_222_1	chr4	84697601	84698020	+	0	NA	intron (NM_014991, intron 56 of 67)	intron (NM_014991, intron 56 of 67)	114906	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.007160	0.297619	
chunk0171_252_1	chr6	127204987	127205535	+	0	NA	Intergenic	Intergenic	-61421	NM_001242851	81847	Hs.267120	NM_030963	ENSG00000118518	RNF146	-	ring finger protein 146	protein-coding	0.003650	0.344262	
chunk0067_205_1	chr15	44987774	44988494	+	0	NA	Intergenic	Intergenic	31432	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.004167	0.425798	
chunk0052_31_1	chr13	20532579	20532843	+	0	NA	Intergenic	L1ME1|LINE|L1	-6838	NM_015974	51084	Hs.370703	NM_015974	ENSG00000165475	CRYL1	GDH|HEL30|gul3DH|lambda-CRY	crystallin lambda 1	protein-coding	0.007576	0.362264	
chunk0112_264_1	chr20	43050229	43050577	+	0	NA	intron (NM_133170, intron 1 of 31)	intron (NM_133170, intron 1 of 31)	139514	NM_133170	11122	Hs.526879	NM_007050	ENSG00000196090	PTPRT	RPTPrho	protein tyrosine phosphatase receptor type T	protein-coding	0.022989	0.567335	
chunk0013_368_1	chr1	172446952	172447529	+	0	NA	intron (NM_139240, intron 2 of 6)	intron (NM_139240, intron 2 of 6)	-3150	NM_002642	5279	Hs.188456	NM_002642	ENSG00000135845	PIGC	GPI2|GPIBD16|MRT62	phosphatidylinositol glycan anchor biosynthesis class C	protein-coding	0.008666	0.435986	
chunk0022_29_1	chr10	7926182	7926705	+	0	NA	intron (NM_031923, intron 2 of 6)	intron (NM_031923, intron 2 of 6)	107939	NM_031923	83860	Hs.527688	NM_031923	ENSG00000165632	TAF3	TAF140|TAFII-140|TAFII140	TATA-box binding protein associated factor 3	protein-coding	0.005736	0.290076	319(AAGAACAAAATGTTCT,-,0.00),320(AGAACAAAATGTTCTT,+,0.00)
chunk0144_170_1	chr4	132760273	132760728	+	0	NA	Intergenic	Intergenic	169411	NR_126401	104355285	Hs.123483	NR_126401	ENSG00000251398	LINC01256	TCONS_l2_00021715	long intergenic non-protein coding RNA 1256	ncRNA	0.000000	0.291667	
chunk0208_228_1	chrX	19217278	19217750	+	0	NA	Intergenic	HAL1|LINE|L1	-94877	NM_001184837	10149	Hs.146978	NM_005756	ENSG00000173698	ADGRG2	CBAVDX|EDDM6|GPR64|HE6|TM7LN2	adhesion G protein-coupled receptor G2	protein-coding	0.008475	0.384778	212(TGGAACATGATGTCCC,-,0.00),213(GGAACATGATGTCCCA,+,0.00)
chunk0193_117_1	chr8	74227769	74227968	+	0	NA	Intergenic	Intergenic	93459	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.000000	0.430000	
chunk0132_373_1	chr3	162938223	162938613	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	364883	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.002564	0.332481	148(GTGAACACACTGTTAT,-,0.00)
chunk0201_420_1	chr9	69645440	69645668	+	0	NA	intron (NM_001163, intron 1 of 12)	MLT1N2|LTR|ERVL-MaLR	26805	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.026316	0.537118	
chunk0063_326_1	chr14	85205792	85206638	+	0	NA	Intergenic	Intergenic	-187664	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005910	0.358914	
chunk0127_419_1	chr3	102593700	102594269	+	0	NA	Intergenic	Intergenic	158969	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.003515	0.324561	
chunk0146_64_1	chr4	155935872	155936185	+	0	NA	intron (NM_001334, intron 5 of 7)	intron (NM_001334, intron 5 of 7)	17868	NM_001334	1519	Hs.75262	NM_001334	ENSG00000256043	CTSO	CTSO1	cathepsin O	protein-coding	0.003195	0.356688	
chunk0196_247_1	chr8	108560977	108561605	+	0	NA	Intergenic	Intergenic	117667	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.001592	0.357711	
chunk0150_34_1	chr5	31220875	31221485	+	0	NA	intron (NM_004932, intron 1 of 11)	(ACTC)n|Simple_repeat|Simple_repeat	27525	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.006557	0.396072	140(GATACAGGCTGTTCAG,+,0.00)
chunk0152_94_1	chr5	58259797	58260517	+	0	NA	Intergenic	Intergenic	-137816	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.009722	0.406380	
chunk0176_36_1	chr7	9598330	9598994	+	0	NA	Intergenic	L1MC4|LINE|L1	-35608	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.004518	0.338346	
chunk0014_390_1	chr1	182759978	182760241	+	0	NA	Intergenic	MIRb|SINE|MIR	-29340	NM_001200056	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.007605	0.397727	
chunk0168_214_1	chr6	85912428	85913064	+	0	NA	Intergenic	Intergenic	-234013	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.006289	0.372057	
chunk0027_422_1	chr10	80827769	80828300	+	0	NA	Intergenic	Intergenic	287215	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.005650	0.530075	
chunk0087_307_1	chr18	39406758	39407364	+	0	NA	intron (NR_024391, intron 3 of 3)	L2b|LINE|L2	215114	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.009901	0.372323	348(ATGTACACCTTGTTCT,-,0.00),349(TGTACACCTTGTTCTC,+,0.00)
chunk0079_194_1	chr17	14305035	14305310	+	0	NA	non-coding (NR_026880, exon 1 of 1)	non-coding (NR_026880, exon 1 of 1)	1432	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.021818	0.518116	
chunk0141_340_1	chr4	87435182	87435692	+	0	NA	intron (NM_001248011, intron 2 of 6)	intron (NM_001248011, intron 2 of 6)	12840	NM_198038	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.003922	0.332681	
chunk0105_100_1	chr2	184532974	184533560	+	0	NA	Intergenic	Intergenic	-65099	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.005119	0.345826	
chunk0196_42_1	chr8	101765153	101765437	+	0	NA	intron (NM_001040630, intron 3 of 5)	intron (NM_001040630, intron 3 of 5)	25916	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.014085	0.466667	
chunk0067_84_1	chr15	41827651	41827895	+	0	NA	promoter-TSS (NM_001198588)	promoter-TSS (NM_001198588)	-312	NM_001114632	100137047	Hs.198161	NM_001114632	ENSG00000243789	JMJD7	-	jumonji domain containing 7	protein-coding	0.065574	0.559184	
chunk0080_298_1	chr17	31549906	31550355	+	0	NA	Intergenic	CpG	-9866	NR_029710	406968		NR_029710	ENSG00000207614	MIR193A	MIRN193|MIRN193A|mir-193a	microRNA 193a	ncRNA	0.106904	0.693333	
chunk0007_439_1	chr1	86865302	86865764	+	0	NA	intron (NM_203341, intron 3 of 3)	L1MB2|LINE|L1	48891	NM_004261	9403	Hs.362728	NM_004261	ENSG00000183291	SELENOF	SEP15	selenoprotein F	protein-coding	0.002165	0.336933	
chunk0154_451_1	chr5	90553380	90554000	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-5110	NR_003149	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.000000	0.407407	238(GGTACACTATGACCCT,+,0.00)
chunk0203_83_1	chr9	83962167	83962467	+	0	NA	Intergenic	LTR16D|LTR|ERVL	-5569	NM_032307	84267	Hs.208914	NM_032307	ENSG00000165118	C9orf64	-	chromosome 9 open reading frame 64	protein-coding	0.006667	0.471761	
chunk0100_408_1	chr2	119434040	119434239	+	0	NA	intron (NM_183240, intron 1 of 1)	intron (NM_183240, intron 1 of 1)	2269	NM_183240	140738	Hs.26216	NM_183240	ENSG00000171227	TMEM37	PR|PR1	transmembrane protein 37	protein-coding	0.020101	0.535000	108(AGGGACAGGACGTGCC,-,0.00),109(GGGACAGGACGTGCCT,+,0.00)
chunk0068_19_1	chr15	50767172	50767975	+	0	NA	Intergenic	L2c|LINE|L2	-1860	NM_032802	84888	Hs.401537	NM_032802	ENSG00000138600	SPPL2A	IMP3|PSL2	signal peptide peptidase like 2A	protein-coding	0.002491	0.435323	
chunk0189_26_1	chr8	19686494	19686886	+	0	NA	Intergenic	Intergenic	-3940	NR_024040	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.002551	0.488550	
chunk0138_360_1	chr4	42138857	42139060	+	0	NA	intron (NM_001159547, intron 3 of 5)	Kanga1a|DNA|TcMar-Tc2	13920	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.004926	0.318627	
chunk0167_363_1	chr6	73276865	73277266	+	0	NA	intron (NR_027005, intron 3 of 4)	intron (NR_027005, intron 3 of 4)	-13869	NM_030568	80759	Hs.433062	NM_030568	ENSG00000135314	KHDC1	C6orf147|C6orf148|Em:AC019205.8|KHDC1L|NDG1|bA257K9.4	KH domain containing 1	protein-coding	0.009975	0.355721	
chunk0020_144_1	chr1	233714832	233715099	+	0	NA	Intergenic	LTR82B|LTR|ERVL	90813	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.007491	0.414179	
chunk0190_15_1	chr8	28852286	28852815	+	0	NA	intron (NR_026826, intron 1 of 14)	intron (NR_026826, intron 1 of 14)	37365	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.003781	0.315094	
chunk0026_348_1	chr10	68683666	68684034	+	0	NA	intron (NM_030625, intron 10 of 11)	intron (NM_030625, intron 10 of 11)	-37294	NM_001282960	55749	Hs.49853	NM_018237	ENSG00000060339	CCAR1	-	cell division cycle and apoptosis regulator 1	protein-coding	0.013587	0.384824	
chunk0140_283_1	chr4	72298933	72299132	+	0	NA	intron (NM_014243, intron 17 of 21)	intron (NM_014243, intron 17 of 21)	259900	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.005025	0.345000	
chunk0070_67_1	chr15	69736226	69736444	+	0	NA	Intergenic	Intergenic	-98899	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.000000	0.506849	
chunk0104_115_1	chr2	172885788	172886586	+	0	NA	intron (NM_001282899, intron 1 of 27)	intron (NM_001282899, intron 1 of 27)	26149	NM_001282900	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.006266	0.440551	
chunk0057_437_1	chr13	110507172	110507661	+	0	NA	intron (NM_001846, intron 46 of 47)	L4_A_Mam|LINE|RTE-X	763	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.020450	0.542857	
chunk0122_114_1	chr3	31166706	31166924	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-5028	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.004587	0.401826	
chunk0013_431_1	chr1	173459314	173459554	+	0	NA	intron (NR_125960, intron 1 of 1)	L1M5|LINE|L1	1928	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.004167	0.307054	
chunk0187_343_1	chr7	156958877	156959087	+	0	NA	intron (NM_138400, intron 3 of 10)	intron (NM_138400, intron 3 of 10)	9259	NM_138400	64434	Hs.15825	NM_138400	ENSG00000146909	NOM1	C7orf3|PPP1R113|SGD1	nucleolar protein with MIF4G domain 1	protein-coding	0.019048	0.412322	
chunk0134_189_1	chr3	178289389	178289923	+	0	NA	Intergenic	Intergenic	-129545	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.005618	0.371963	
chunk0094_371_1	chr2	9808952	9809268	+	0	NA	Intergenic	Intergenic	-34332	NM_005680	9014	Hs.584833	NM_005680	ENSG00000115750	TAF1B	MGC:9349|RAF1B|RAFI63|SL1|TAFI63	TATA-box binding protein associated factor, RNA polymerase I subunit B	protein-coding	0.015823	0.580442	
chunk0077_81_1	chr16	77304750	77305340	+	0	NA	intron (NM_199355, intron 16 of 22)	intron (NM_199355, intron 16 of 22)	105593	NM_001129979	100130958	Hs.734779	NM_001129979	ENSG00000205078	SYCE1L	MRP2	synaptonemal complex central element protein 1 like	protein-coding	0.005085	0.328257	
chunk0025_252_1	chr10	54837840	54838065	+	0	NA	Intergenic	Intergenic	-36661	NM_001142773	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.008889	0.464602	
chunk0211_264_1	chrX	121128274	121128629	+	0	NA	Intergenic	L1M5|LINE|L1	80843	NM_012084	2747	Hs.368538	NM_012084	ENSG00000182890	GLUD2	GDH2|GLUDP1	glutamate dehydrogenase 2	protein-coding	0.002817	0.325843	
chunk0176_425_1	chr7	19681447	19682037	+	0	NA	Intergenic	Intergenic	23694	NR_036101	100422967		NR_036101	ENSG00000265932	MIR3146	mir-3146	microRNA 3146	ncRNA	0.011864	0.409475	
chunk0102_420_1	chr2	156887009	156887503	+	0	NA	Intergenic	Intergenic	-370572	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.000000	0.339394	
chunk0096_203_1	chr2	30274560	30275035	+	0	NA	Intergenic	Intergenic	43266	NM_030915	81606	Hs.567598	NM_030915	ENSG00000213626	LBH	-	LBH regulator of WNT signaling pathway	protein-coding	0.010526	0.483193	
chunk0084_55_1	chr17	74443222	74443547	+	0	NA	intron (NM_018653, intron 2 of 3)	intron (NM_018653, intron 2 of 3)	9687	NM_018653	55890	Hs.446438	NM_018653	ENSG00000170412	GPRC5C	RAIG-3|RAIG3	G protein-coupled receptor class C group 5 member C	protein-coding	0.030769	0.616564	
chunk0101_216_1	chr2	130728893	130729456	+	0	NA	exon (NM_207364, exon 1 of 1)	exon (NM_207364, exon 1 of 1)	104	NM_207364	344561	Hs.452574	NM_207364	ENSG00000173302	GPR148	BTR|PGR6	G protein-coupled receptor 148	protein-coding	0.012433	0.576241	
chunk0118_298_1	chr22	34887467	34887996	+	0	NA	Intergenic	Intergenic	-178405	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.000000	0.360377	264(ATGTACTTTCTGTCCT,-,0.00),265(TGTACTTTCTGTCCTC,+,0.00)
chunk0008_387_1	chr1	97171369	97172002	+	0	NA	intron (NM_000110, intron 20 of 22)	intron (NM_000110, intron 20 of 22)	75762	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.003160	0.370662	
chunk0044_440_1	chr12	42315246	42315674	+	0	NA	intron (NM_033114, intron 5 of 7)	intron (NM_033114, intron 5 of 7)	8399	NR_107005	102467003		NR_107005	ENSG00000278520	MIR7851	hsa-mir-7851	microRNA 7851	ncRNA	0.000000	0.333333	
chunk0003_250_1	chr1	36225560	36225886	+	0	NA	intron (NM_005119, intron 1 of 11)	intron (NM_005119, intron 1 of 11)	1307	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.030675	0.400612	216(GGGCTCAGTTTGTTCT,-,0.00),217(GGCTCAGTTTGTTCTT,+,0.00)
chunk0170_155_1	chr6	111478833	111479125	+	0	NA	intron (NM_001286431, intron 2 of 34)	Tigger19b|DNA|TcMar-Tigger	-4493	NR_034109	643749	Hs.486228	NR_034108	ENSG00000231889	TRAF3IP2-AS1	C6UAS|C6orf3|NCRNA00248|TRAF3IP2-AS2	TRAF3IP2 antisense RNA 1	ncRNA	0.003425	0.430034	
chunk0089_126_1	chr18	58739601	58740090	+	0	NA	intron (NM_006785, intron 13 of 16)	MLT2D|LTR|ERVL	-67972	NM_001289967	101927322	Hs.644875	NM_001289967		LOC101927322	-	uncharacterized LOC101927322	protein-coding	0.010225	0.428571	
chunk0016_280_1	chr1	200713293	200713762	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	-26031	NM_001297707	23271	Hs.23585	NM_203459	ENSG00000118200	CAMSAP2	CAMSAP1L1	calmodulin regulated spectrin associated protein family member 2	protein-coding	0.004264	0.380851	
chunk0068_441_1	chr15	59668624	59669226	+	0	NA	exon (NM_004330, exon 9 of 10)	exon (NM_004330, exon 9 of 10)	-11387	NM_004492	2958	Hs.512934	NM_004492	ENSG00000140307	GTF2A2	HsT18745|T18745|TF2A2|TFIIA|TFIIA-12|TFIIA-gamma|TFIIAS	general transcription factor IIA subunit 2	protein-coding	0.016611	0.321725	
chunk0016_420_1	chr1	203434494	203434969	+	0	NA	Intergenic	L2b|LINE|L2	-41024	NM_201348	5549	Hs.632481	NM_002725	ENSG00000188783	PRELP	MST161|MSTP161|SLRR2A	proline and arginine rich end leucine rich repeat protein	protein-coding	0.002105	0.418067	
chunk0176_123_1	chr7	12220604	12221103	+	0	NA	intron (NM_001134232, intron 3 of 7)	L1MC5a|LINE|L1	9631	NM_018374	54664	Hs.396358	NM_018374	ENSG00000106460	TMEM106B	HLD16	transmembrane protein 106B	protein-coding	0.002004	0.338000	
chunk0051_200_1	chr12	116375539	116375830	+	0	NA	Intergenic	Intergenic	52634	NR_039683	100616309		NR_039683	ENSG00000264037	MIR4472-2	-	microRNA 4472-2	ncRNA	0.010309	0.438356	
chunk0058_408_1	chr13	112397511	112398197	+	0	NA	intron (NM_145248, intron 2 of 6)	intron (NM_145248, intron 2 of 6)	21517	NM_145248	122258	Hs.97592	NM_145248	ENSG00000153498	SPACA7	C13orf28	sperm acrosome associated 7	protein-coding	0.027697	0.512373	430(AGGAACTGTGTGTACA,-,0.00),431(GGAACTGTGTGTACAT,+,0.00)
chunk0015_324_1	chr1	189515993	189516331	+	0	NA	Intergenic	L1PA10|LINE|L1	961467	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.306785	
chunk0028_93_1	chr10	84039081	84039492	+	0	NA	Intergenic	(TATT)n|Simple_repeat|Simple_repeat	-100143	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.402913	
chunk0102_280_1	chr2	150207931	150208526	+	0	NA	Intergenic	Intergenic	279467	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.005042	0.382550	284(GAGCACATACAGTGCT,-,0.00),285(AGCACATACAGTGCTG,+,0.00)
chunk0176_285_1	chr7	16712405	16713077	+	0	NA	Intergenic	Intergenic	-40985	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.004464	0.377415	
chunk0032_345_1	chr11	10309219	10309778	+	0	NA	intron (NR_103765, intron 1 of 3)	intron (NR_103765, intron 1 of 3)	1185	NR_103765	100130460	Hs.501890	NR_103765		CAND1.11	-	uncharacterized LOC100130460	ncRNA	0.017889	0.503571	435(AAGAACACATTGTTTA,-,0.00)
chunk0063_40_1	chr14	76831726	76832093	+	0	NA	intron (NM_194287, intron 3 of 13)	intron (NM_194287, intron 3 of 13)	5527	NM_194287	145497	Hs.147276	NM_194287	ENSG00000100565	LRRC74A	C14orf166B|LRRC74	leucine rich repeat containing 74A	protein-coding	0.002725	0.372283	
chunk0121_333_1	chr3	24428344	24428714	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-65558	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.008108	0.420485	
chunk0015_458_1	chr1	192582434	192582633	+	0	NA	Intergenic	Intergenic	6806	NM_002922	5996	Hs.75256	NM_002922	ENSG00000090104	RGS1	1R20|BL34|HEL-S-87|IER1|IR20	regulator of G protein signaling 1	protein-coding	0.005025	0.330000	
chunk0130_315_1	chr3	137328794	137329288	+	0	NA	Intergenic	Intergenic	371176	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.004049	0.351515	
chunk0059_72_1	chr14	30450570	30451182	+	0	NA	Intergenic	Intergenic	-108247	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.009804	0.450245	
chunk0110_461_1	chr20	21373405	21373671	+	0	NA	intron (NM_012255, intron 27 of 29)	L1ME3A|LINE|L1	23871	NM_033176	644524		NM_033176	ENSG00000125816	NKX2-4	NKX2.4|NKX2D	NK2 homeobox 4	protein-coding	0.003759	0.408240	
chunk0188_150_1	chr8	10351727	10351948	+	0	NA	intron (NM_001135671, intron 5 of 5)	MER5A1|DNA|hAT-Charlie	-122728	NR_120604	101929191	Hs.595262	NR_120604	ENSG00000253641	LINCR-0001	-	uncharacterized LINCR-0001	ncRNA	0.022624	0.477477	
chunk0078_411_1	chr16	89125790	89126041	+	0	NA	intron (NM_001127214, intron 6 of 9)	intron (NM_001127214, intron 6 of 9)	-10633	NR_045667	197322	Hs.461727	NM_174917	ENSG00000176715	ACSF3	-	acyl-CoA synthetase family member 3	protein-coding	0.051793	0.432540	81(GTGAACACAGTGTGTC,-,0.00),82(TGAACACAGTGTGTCT,+,0.00)
chunk0103_53_1	chr2	159536795	159537049	+	0	NA	intron (NM_001289975, intron 2 of 35)	Charlie21a|DNA|hAT-Charlie	-78372	NR_110588	643072	Hs.632541	NR_110587		LOC643072	-	uncharacterized LOC643072	ncRNA	0.015748	0.286275	
chunk0100_389_1	chr2	118347875	118348083	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	254987	NR_110272	101927709	Hs.274529	NR_110272		LOC101927709	-	uncharacterized LOC101927709	ncRNA	0.004808	0.363636	
chunk0032_267_1	chr11	9056981	9057521	+	0	NA	intron (NM_020974, intron 9 of 21)	intron (NM_020974, intron 9 of 21)	33128	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.003704	0.327172	
chunk0044_382_1	chr12	39905229	39905434	+	0	NA	intron (NM_052885, intron 4 of 9)	intron (NM_052885, intron 4 of 9)	200528	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.004878	0.490291	
chunk0163_223_1	chr6	12182739	12183556	+	0	NA	Intergenic	Intergenic	-107149	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.009792	0.371638	
chunk0140_423_1	chr4	76016470	76016705	+	0	NA	intron (NM_001130017, intron 1 of 9)	L1M1|LINE|L1	5407	NM_001130017	419	Hs.24976	NM_001179	ENSG00000156219	ART3	ARTC3	ADP-ribosyltransferase 3	protein-coding	0.004255	0.550847	
chunk0059_13_1	chr14	29757246	29757445	+	0	NA	intron (NM_002742, intron 1 of 17)	L2c|LINE|L2	170348	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.460000	
chunk0104_413_1	chr2	180763442	180763885	+	0	NA	intron (NR_104324, intron 3 of 4)	intron (NR_104324, intron 3 of 4)	71559	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.000000	0.369369	
chunk0122_271_1	chr3	35409258	35409975	+	0	NA	Intergenic	Intergenic	-15593	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.005579	0.334262	341(AAGGACACTGAGTACT,-,0.00),342(AGGACACTGAGTACTT,+,0.00)
chunk0091_49_1	chr19	4559337	4559569	+	0	NA	intron (NM_032108, intron 1 of 16)	intron (NM_032108, intron 1 of 16)	306	NM_032108	10501	Hs.465642	NM_020241	ENSG00000167680	SEMA6B	SEM-SEMA-Y|SEMA-VIB|SEMAN|semaZ	semaphorin 6B	protein-coding	0.021552	0.566524	
chunk0062_453_1	chr14	75644039	75644336	+	0	NA	intron (NM_017791, intron 9 of 9)	intron (NM_017791, intron 9 of 9)	17008	NM_007176	11161	Hs.15106	NM_007176	ENSG00000133935	ERG28	C14orf1|NET51	ergosterol biosynthesis 28 homolog	protein-coding	0.010101	0.342282	
chunk0009_314_1	chr1	108583692	108584035	+	0	NA	intron (NM_001010883, intron 1 of 10)	intron (NM_001010883, intron 1 of 10)	23514	NM_001010883	284611	Hs.200230	NM_001010883	ENSG00000162636	FAM102B	SYM-3B	family with sequence similarity 102 member B	protein-coding	0.014577	0.415698	238(GAGGACAGGGTGTTCA,-,0.00),239(AGGACAGGGTGTTCAG,+,0.00)
chunk0150_387_1	chr5	39633105	39633749	+	0	NA	Intergenic	Intergenic	112996	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.004658	0.373643	
chunk0163_185_1	chr6	11491157	11491710	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-46794	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.005425	0.429603	
chunk0196_28_1	chr8	101543282	101543827	+	0	NA	intron (NM_024915, intron 2 of 15)	intron (NM_024915, intron 2 of 15)	51114	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.003670	0.423077	
chunk0017_228_1	chr1	208047525	208047961	+	0	NA	intron (NM_025179, intron 17 of 31)	intron (NM_025179, intron 17 of 31)	-136405	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.011468	0.494279	129(AAGTACACACTGTCCT,-,0.00),130(AGTACACACTGTCCTG,+,0.00)
chunk0067_277_1	chr15	47176885	47177559	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-6984	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.007418	0.413333	
chunk0067_266_1	chr15	45958816	45959515	+	0	NA	Intergenic	Intergenic	324425	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.007153	0.331429	
chunk0006_264_1	chr1	70143179	70143447	+	0	NA	Intergenic	Intergenic	62365	NM_017768	55631	Hs.147836	NM_017768	ENSG00000066557	LRRC40	dJ677H15.1	leucine rich repeat containing 40	protein-coding	0.007463	0.330855	
chunk0023_51_1	chr10	21688308	21688995	+	0	NA	intron (NM_004641, intron 14 of 23)	intron (NM_004641, intron 14 of 23)	154006	NM_001195626	8028	Hs.30385	NM_004641	ENSG00000078403	MLLT10	AF10	MLLT10 histone lysine methyltransferase DOT1L cofactor	protein-coding	0.000000	0.353198	391(ATGAACTATATGTTCT,-,0.00),392(TGAACTATATGTTCTT,+,0.00)
chunk0167_73_1	chr6	56514261	56515698	+	0	NA	intron (NM_183380, intron 63 of 93)	intron (NM_183380, intron 63 of 93)	127917	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.004175	0.349096	398(GAGTACATTCTGTACA,-,0.00),399(AGTACATTCTGTACAG,+,0.00)
chunk0145_117_1	chr4	146319066	146319581	+	0	NA	intron (NM_001029998, intron 6 of 11)	L2a|LINE|L2	-89260	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.000000	0.383721	227(TGCACTTAGTGTTCCT,+,0.00)
chunk0114_62_1	chr21	9008773	9009032	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	21532	NR_037458									0.000000	0.565385	
chunk0075_333_1	chr16	54739062	54739955	+	0	NA	Intergenic	Intergenic	189270	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.005599	0.380313	
chunk0129_334_1	chr3	124607163	124607500	+	0	NA	intron (NM_007064, intron 1 of 26)	L1ME3G|LINE|L1	22672	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.002967	0.366864	
chunk0201_280_1	chr9	38714847	38715496	+	0	NA	Intergenic	Intergenic	94083	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.007704	0.395385	179(GGGAACACTCTGTACT,-,0.00),180(GGAACACTCTGTACTA,+,0.00),467(TGGAACAACATGTACT,-,0.00),468(GGAACAACATGTACTT,+,0.00)
chunk0024_433_1	chr10	46084516	46084821	+	0	NA	Intergenic	Intergenic	-24827	NR_126580	653268	Hs.447454	NM_001077685		AGAP7P	AGAP-7|AGAP7|CTGLF4|bA109G10.1	ArfGAP with GTPase domain, ankyrin repeat and PH domain 7, pseudogene	pseudo	0.013115	0.480392	
chunk0174_395_1	chr6	165436173	165436652	+	0	NA	intron (NM_006661, intron 6 of 22)	intron (NM_006661, intron 6 of 22)	26811	NR_106988									0.002088	0.304167	
chunk0116_134_1	chr21	36202481	36203218	+	0	NA	intron (NM_005128, intron 4 of 36)	intron (NM_005128, intron 4 of 36)	38308	NM_005128	9980	Hs.204575	NM_005128	ENSG00000142197	DOP1B	21orf5|C21orf5|DOPEY2	DOP1 leucine zipper like protein B	protein-coding	0.012212	0.426829	
chunk0046_292_1	chr12	62139897	62140263	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	52759	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.005464	0.354223	
chunk0008_34_1	chr1	88736913	88737161	+	0	NA	intron (NM_006256, intron 1 of 21)	L1M1|LINE|L1	-51833	NR_110682	101927891	Hs.637231	NR_110682	ENSG00000237505	PKN2-AS1	-	PKN2 antisense RNA 1	ncRNA	0.012097	0.554217	
chunk0169_287_1	chr6	105809345	105809943	+	0	NA	Intergenic	Intergenic	-276676	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.001672	0.419032	
chunk0001_313_1	chr1	9369829	9370122	+	0	NA	TTS (NM_025106)	TTS (NM_025106)	58941	NR_104623	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.020478	0.506803	
chunk0129_272_1	chr3	122752232	122753006	+	0	NA	exon (NM_024610, exon 6 of 8)	exon (NM_024610, exon 6 of 8)	41200	NM_024610	79663	Hs.29169	NM_024610	ENSG00000169087	HSPBAP1	PASS1	HSPB1 associated protein 1	protein-coding	0.012920	0.379355	
chunk0157_15_1	chr5	115403227	115403636	+	0	NA	Intergenic	Intergenic	-106670	NM_001040440	153733	Hs.436121	NM_152549	ENSG00000164221	CCDC112	MBC1	coiled-coil domain containing 112	protein-coding	0.002445	0.351220	
chunk0136_45_1	chr4	1203512	1203728	+	0	NA	intron (NR_024569, intron 2 of 3)	L1MB7|LINE|L1	5342	NM_001199021	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.032407	0.497696	
chunk0026_342_1	chr10	68556541	68557060	+	0	NA	Intergenic	L1ME3G|LINE|L1	-3560	NM_030625	80312	Hs.258855	NM_030625	ENSG00000138336	TET1	CXXC6|LCX|bA119F7.1	tet methylcytosine dioxygenase 1	protein-coding	0.003854	0.411538	
chunk0131_51_1	chr3	142697477	142698172	+	0	NA	intron (NM_002670, intron 11 of 15)	L1ME3G|LINE|L1	-26600	NM_001251845	7220	Hs.250687	NM_003304	ENSG00000144935	TRPC1	HTRP-1|TRP1	transient receptor potential cation channel subfamily C member 1	protein-coding	0.002878	0.343391	
chunk0166_391_1	chr6	51858117	51858638	+	0	NA	intron (NM_138694, intron 48 of 66)	intron (NM_138694, intron 48 of 66)	229248	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.005758	0.340996	
chunk0090_437_1	chr18	79569774	79570047	+	0	NA	Intergenic	Intergenic	-109891	NM_004715	9150	Hs.465490	NM_004715	ENSG00000060069	CTDP1	CCFDN|FCP1	CTD phosphatase subunit 1	protein-coding	0.054945	0.580292	
chunk0063_63_1	chr14	77184721	77185131	+	0	NA	intron (NM_020431, intron 1 of 23)	intron (NM_020431, intron 1 of 23)	3167	NM_020431	57156	Hs.22452	NM_020431	ENSG00000165548	TMEM63C	C14orf171|CSC1|hsCSC1	transmembrane protein 63C	protein-coding	0.014634	0.530414	210(CAGGACTCCATGTTCT,-,0.00),211(AGGACTCCATGTTCTG,+,0.00)
chunk0044_254_1	chr12	32093249	32093839	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-13707	NM_001003398	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.010169	0.409475	281(AACACAAAATGTTCTT,+,0.00)
chunk0206_436_1	chr9	127912821	127913097	+	0	NA	intron (NM_175040, intron 2 of 4)	MIR|SINE|MIR	4067	NM_175040	27090	Hs.3972	NM_014403	ENSG00000136840	ST6GALNAC4	IV|SIAT3-C|SIAT3C|SIAT7-D|SIAT7D|ST6GALNACIV|ST6GalNAc	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding	0.010870	0.472924	
chunk0130_12_1	chr3	128373271	128373841	+	0	NA	intron (NM_021937, intron 6 of 6)	intron (NM_021937, intron 6 of 6)	-90038	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.008772	0.556918	
chunk0048_134_1	chr12	79961270	79962141	+	0	NA	Intergenic	Intergenic	-26250	NM_001244990	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.002296	0.345183	
chunk0080_292_1	chr17	31479932	31480480	+	0	NA	intron (NM_032932, intron 3 of 14)	intron (NM_032932, intron 3 of 14)	-7795	NM_001303542	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.014599	0.502732	353(GAGAACATTGTGTGCC,-,0.00),354(AGAACATTGTGTGCCA,+,0.00)
chunk0210_15_1	chrX	66906452	66907580	+	0	NA	Intergenic	Intergenic	-267718	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.003546	0.372011	750(GGGAACAGAGTGTGAT,-,0.00),751(GGAACAGAGTGTGATT,+,0.00)
chunk0030_277_1	chr10	116583207	116583751	+	0	NA	Intergenic	Intergenic	-7480	NM_006229	5407	Hs.73923	NM_006229	ENSG00000187021	PNLIPRP1	PLRP1	pancreatic lipase related protein 1	protein-coding	0.014706	0.381651	
chunk0030_266_1	chr10	116327727	116328148	+	0	NA	intron (NM_198515, intron 3 of 8)	intron (NM_198515, intron 3 of 8)	3509	NM_198515	374355	Hs.233407	NM_198515	ENSG00000182645	CCDC172	C10orf96	coiled-coil domain containing 172	protein-coding	0.000000	0.284360	
chunk0086_386_1	chr18	26510387	26510586	+	0	NA	intron (NM_001258222, intron 1 of 4)	intron (NM_001258222, intron 1 of 4)	38050	NM_001142730	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.005025	0.400000	
chunk0001_306_1	chr1	9156888	9157369	+	0	NA	intron (NR_132742, intron 1 of 1)	intron (NR_132742, intron 1 of 1)	-5351	NR_029610	407040		NR_029610	ENSG00000284357	MIR34A	MIRN34A|miRNA34A|mir-34|mir-34a	microRNA 34a	ncRNA	0.033264	0.578838	
chunk0205_225_1	chr9	109887883	109888524	+	0	NA	intron (NM_053016, intron 3 of 6)	MIRb|SINE|MIR	107906	NM_053016	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.012480	0.501558	271(GGAAACAGTGTGTGCT,-,0.00),272(GAAACAGTGTGTGCTT,+,0.00)
chunk0026_220_1	chr10	64796076	64796313	+	0	NA	Intergenic	L2a|LINE|L2	-29334	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.016878	0.352941	
chunk0161_139_1	chr5	168486287	168486737	+	0	NA	promoter-TSS (NM_002887)	promoter-TSS (NM_002887)	54	NM_002887	5917	Hs.654907	NM_002887	ENSG00000113643	RARS	ArgRS|DALRD1|HLD9	arginyl-tRNA synthetase	protein-coding	0.077778	0.645233	
chunk0074_224_1	chr16	26642128	26642355	+	0	NA	Intergenic	Intergenic	-424657	NM_001145545	162083	Hs.120831	NM_182831		C16orf82	TNT	chromosome 16 open reading frame 82	protein-coding	0.008811	0.543860	
chunk0105_149_1	chr2	186521511	186521777	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	35486	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.011278	0.400749	
chunk0025_258_1	chr10	55221104	55221794	+	0	NA	Intergenic	MER63D|DNA|hAT-Blackjack	-377541	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.004348	0.342981	
chunk0120_261_1	chr3	9125929	9126128	+	0	NA	intron (NM_001033117, intron 1 of 21)	intron (NM_001033117, intron 1 of 21)	-66465	NR_121663	101927416	Hs.475364	NR_121663	ENSG00000228723	SRGAP3-AS2	-	SRGAP3 antisense RNA 2	ncRNA	0.010050	0.505000	
chunk0155_147_1	chr5	93718947	93719508	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	22376	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.003565	0.384342	
chunk0169_90_1	chr6	99802689	99803239	+	0	NA	Intergenic	Intergenic	-191074	NR_038384	728012	Hs.434366	NR_038384	ENSG00000229315	MCHR2-AS1	-	MCHR2 antisense RNA 1	ncRNA	0.005455	0.375681	189(TAGAACAATCTGTTCC,-,0.00),190(AGAACAATCTGTTCCC,+,0.00)
chunk0205_183_1	chr9	109036117	109036522	+	0	NA	exon (NM_032012, exon 16 of 18)	exon (NM_032012, exon 16 of 18)	9979	NR_029506	407036		NR_029506	ENSG00000207698	MIR32	MIRN32|hsa-mir-32|miR-32|miRNA32	microRNA 32	ncRNA	0.002469	0.386700	
chunk0164_281_1	chr6	24336339	24336718	+	0	NA	intron (NM_001195610, intron 3 of 10)	intron (NM_001195610, intron 3 of 10)	-20375	NM_181337	353219	Hs.697888	NM_181337	ENSG00000146049	KAAG1	RU2AS	kidney associated antigen 1	protein-coding	0.000000	0.315789	
chunk0052_423_1	chr12	131695545	131695958	+	0	NA	Intergenic	Intergenic	-15336	NM_004592	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.016949	0.516908	
chunk0081_195_1	chr17	42310648	42310972	+	0	NA	3' UTR (NM_003152, exon 20 of 20)	3' UTR (NM_003152, exon 20 of 20)	22754	NM_001288720	6776	Hs.437058	NM_003152	ENSG00000126561	STAT5A	MGF|STAT5	signal transducer and activator of transcription 5A	protein-coding	0.024691	0.532308	
chunk0012_141_1	chr1	157315494	157315745	+	0	NA	Intergenic	L1PA6|LINE|L1	-177028	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.003984	0.519841	
chunk0141_228_1	chr4	84772892	84773286	+	0	NA	intron (NM_014991, intron 29 of 67)	intron (NM_014991, intron 29 of 67)	190185	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.002538	0.331646	
chunk0103_174_1	chr2	163113384	163113586	+	0	NA	Intergenic	Intergenic	-274738	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.000000	0.290640	
chunk0195_357_1	chr8	99789300	99789519	+	0	NA	intron (NM_152564, intron 43 of 61)	intron (NM_152564, intron 43 of 61)	104605	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.004566	0.354545	
chunk0180_153_1	chr7	64498156	64498783	+	0	NA	Intergenic	Intergenic	64658	NM_001130022	340252	Hs.520886	NM_178558	ENSG00000173041	ZNF680	-	zinc finger protein 680	protein-coding	0.004785	0.364650	
chunk0034_262_1	chr11	34480396	34480832	+	0	NA	intron (NM_001243080, intron 4 of 4)	intron (NM_001243080, intron 4 of 4)	31185	NM_001243081	2001	Hs.11713	NM_001422	ENSG00000135374	ELF5	ESE2	E74 like ETS transcription factor 5	protein-coding	0.006881	0.411899	
chunk0153_253_1	chr5	72670860	72671213	+	0	NA	Intergenic	Intergenic	-10367	NR_105007	102477328	Hs.254516	NR_105007	ENSG00000248371	LINC02056	-	long intergenic non-protein coding RNA 2056	ncRNA	0.002833	0.322034	
chunk0177_345_1	chr7	26534983	26536335	+	0	NA	non-coding (NR_022006, exon 2 of 2)	non-coding (NR_022006, exon 2 of 2)	3166	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.010355	0.402069	
chunk0042_387_1	chr12	10718117	10718616	+	0	NA	intron (NM_003651, intron 2 of 9)	intron (NM_003651, intron 2 of 9)	4988	NM_003651	8531	Hs.221889	NM_003651	ENSG00000060138	YBX3	CSDA|CSDA1|DBPA|ZONAB	Y-box binding protein 3	protein-coding	0.006012	0.416000	
chunk0199_263_1	chr9	6239799	6240233	+	0	NA	intron (NM_001314045, intron 1 of 7)	L1MC5a|LINE|L1	2935	NM_001314045	90865	Hs.731660	NM_033439	ENSG00000137033	IL33	C9orf26|DVS27|IL1F11|NF-HEV|NFEHEV	interleukin 33	protein-coding	0.004608	0.395402	
chunk0045_146_1	chr12	46483680	46484195	+	0	NA	intron (NR_125380, intron 3 of 3)	intron (NR_125380, intron 3 of 3)	99830	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.003883	0.374031	
chunk0186_423_1	chr7	146606754	146607145	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	490588	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.002558	0.364796	208(CAGAACAGTTTGTCCC,-,0.00),209(AGAACAGTTTGTCCCA,+,0.00)
chunk0033_333_1	chr11	22674706	22675105	+	0	NA	exon (NM_005256, exon 1 of 7)	exon (NM_005256, exon 1 of 7)	132	NM_005256	2620	Hs.711297	NM_005256	ENSG00000148935	GAS2	GAS-2	growth arrest specific 2	protein-coding	0.007519	0.382500	
chunk0106_49_1	chr2	196267861	196268444	+	0	NA	intron (NM_020760, intron 17 of 28)	intron (NM_020760, intron 17 of 28)	8128	NR_110226	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.001715	0.352740	60(GGTACTGGGAGTCCTT,+,0.00),243(TAAAACAGAATGTTCT,-,0.00),244(AAAACAGAATGTTCTC,+,0.00)
chunk0104_163_1	chr2	174166368	174166690	+	0	NA	intron (NM_001011708, intron 3 of 9)	intron (NM_001011708, intron 3 of 9)	82108	NM_013341	29789	Hs.157351	NM_013341	ENSG00000138430	OLA1	DOC45|GBP45|GTBP9|GTPBP9|PTD004	Obg like ATPase 1	protein-coding	0.006211	0.368421	
chunk0069_75_1	chr15	60991027	60991396	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	238092	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.010840	0.370270	
chunk0177_276_1	chr7	25565999	25566237	+	0	NA	Intergenic	Intergenic	-337632	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.021008	0.384937	
chunk0187_217_1	chr7	152076604	152076835	+	0	NA	intron (NM_001304514, intron 1 of 10)	LTR16C|LTR|ERVL	51045	NM_022087	63917	Hs.647109	NM_022087	ENSG00000178234	GALNT11	GALNAC-T11|GALNACT11	polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0.012987	0.495690	
chunk0001_28_1	chr1	1340853	1341278	+	0	NA	intron (NM_004421, intron 5 of 14)	intron (NM_004421, intron 5 of 14)	-1357	NR_106866	102466740		NR_106866	ENSG00000284372	MIR6808	hsa-mir-6808	microRNA 6808	ncRNA	0.049412	0.603286	
chunk0086_20_1	chr18	12277443	12277863	+	0	NA	TTS (NR_036468)	TTS (NR_036468)	23292	NR_036468									0.011905	0.432304	
chunk0167_315_1	chr6	72077049	72077592	+	0	NA	intron (NM_014989, intron 2 of 33)	L2a|LINE|L2	-135491	NM_001168408	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.009208	0.443015	
chunk0001_87_1	chr1	2683955	2684280	+	0	NA	intron (NM_001242672, intron 4 of 6)	intron (NM_001242672, intron 4 of 6)	-51075	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.018462	0.616564	
chunk0014_233_1	chr1	179883139	179883466	+	0	NA	intron (NM_001267578, intron 1 of 9)	intron (NM_001267578, intron 1 of 9)	1260	NM_015602	26092	Hs.496459	NM_015602	ENSG00000143337	TOR1AIP1	LAP1|LAP1B|LGMD2Y	torsin 1A interacting protein 1	protein-coding	0.055046	0.576220	
chunk0013_362_1	chr1	172398069	172398512	+	0	NA	intron (NM_001136127, intron 19 of 19)	intron (NM_001136127, intron 19 of 19)	-22398	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.004515	0.380631	39(GAAACATTATGTACCT,+,0.00)
chunk0171_258_1	chr6	127347058	127347605	+	0	NA	Intergenic	Intergenic	-3722	NM_001002030	55862	Hs.486410	NM_018479	ENSG00000093144	ECHDC1	HEL-S-76|MMCD|dJ351K20.2	ethylmalonyl-CoA decarboxylase 1	protein-coding	0.003656	0.308394	
chunk0208_222_1	chrX	18955411	18955891	+	0	NA	intron (NM_000292, intron 1 of 32)	intron (NM_000292, intron 1 of 32)	28711	NM_000292	5256	Hs.54941	NM_000292	ENSG00000044446	PHKA2	GSD9A|PHK|PYK|PYKL|XLG|XLG2	phosphorylase kinase regulatory subunit alpha 2	protein-coding	0.000000	0.320166	
chunk0018_153_1	chr1	218708272	218708628	+	0	NA	intron (NR_031644, intron 4 of 6)	intron (NR_031644, intron 4 of 6)	265824	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.005618	0.439776	
chunk0072_126_1	chr15	92614394	92614903	+	0	NA	Intergenic	MIRb|SINE|MIR	41153	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.013752	0.500000	231(ATGATCAGTCTGTTCC,-,0.00),232(TGATCAGTCTGTTCCA,+,0.00)
chunk0210_207_1	chrX	80845116	80845468	+	0	NA	Intergenic	Intergenic	-35558	NM_153252	254065	Hs.147027	NM_153252	ENSG00000165288	BRWD3	BRODL|MRX93	bromodomain and WD repeat domain containing 3	protein-coding	0.000000	0.368272	
chunk0201_159_1	chr9	36021061	36021374	+	0	NA	Intergenic	Intergenic	-15696	NM_001316348	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.009585	0.477707	
chunk0047_38_1	chr12	66648372	66648586	+	0	NA	intron (NM_021150, intron 1 of 23)	L2b|LINE|L2	30666	NM_021150	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.014019	0.404651	
chunk0118_24_1	chr22	26436782	26437383	+	0	NA	intron (NM_020437, intron 2 of 3)	intron (NM_020437, intron 2 of 3)	7768	NM_020437	57168	Hs.567547	NM_020437	ENSG00000128203	ASPHD2	-	aspartate beta-hydroxylase domain containing 2	protein-coding	0.014975	0.506645	
chunk0169_298_1	chr6	106003233	106003681	+	0	NA	Intergenic	Intergenic	-82863	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.000000	0.380846	
chunk0006_172_1	chr1	66719562	66719957	+	0	NA	intron (NM_032291, intron 19 of 24)	MLT1L|LTR|ERVL-MaLR	-32698	NM_152665	200132	Hs.479226	NM_152665	ENSG00000152760	TCTEX1D1	-	Tctex1 domain containing 1	protein-coding	0.007595	0.328283	
chunk0088_168_1	chr18	46877183	46877668	+	0	NA	intron (NM_004671, intron 2 of 13)	LTR10B1|LTR|ERV1	40107	NM_173206	9063	Hs.57769	NM_004671	ENSG00000078043	PIAS2	ARIP3|DIP|MIZ1|PIASX|SIZ2|ZMIZ4	protein inhibitor of activated STAT 2	protein-coding	0.020619	0.427984	
chunk0181_251_1	chr7	85751990	85752890	+	0	NA	Intergenic	L1PA13|LINE|L1	-630509	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.356271	
chunk0060_26_1	chr14	39986360	39986577	+	0	NA	Intergenic	Intergenic	-553968	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.000000	0.321101	
chunk0192_265_1	chr8	66020732	66021159	+	0	NA	promoter-TSS (NM_033105)	promoter-TSS (NM_033105)	-611	NM_033105	85479	Hs.491885	NM_033105	ENSG00000147570	DNAJC5B	CSP-beta	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding	0.011710	0.474299	
chunk0078_118_1	chr17	2933650	2934287	+	0	NA	intron (NM_015085, intron 3 of 24)	intron (NM_015085, intron 3 of 24)	31927	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.026688	0.536050	
chunk0043_46_1	chr12	13453984	13454648	+	0	NA	Intergenic	Intergenic	-77571	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.007530	0.436090	150(AGAACTGTGAGTCCAT,+,0.00)
chunk0113_201_1	chr20	53661750	53662106	+	0	NA	Intergenic	Intergenic	-78831	NM_006526	7764	Hs.155040	NM_006526	ENSG00000171940	ZNF217	ZABC1	zinc finger protein 217	protein-coding	0.002809	0.397759	
chunk0136_273_1	chr3	194495046	194495342	+	0	NA	Intergenic	Intergenic	8054	NR_033929	401106	Hs.407087	NR_033929		LINC00884	-	long intergenic non-protein coding RNA 884	ncRNA	0.016892	0.481481	
chunk0109_54_1	chr20	1078508	1078707	+	0	NA	Intergenic	Intergenic	-34656	NM_178578	9491	Hs.471917	NM_006814	ENSG00000125818	PSMF1	PI31	proteasome inhibitor subunit 1	protein-coding	0.005025	0.470000	75(TAGGACTAGATGTTCT,-,0.00),76(AGGACTAGATGTTCTT,+,0.00)
chunk0090_317_1	chr18	75673387	75673668	+	0	NA	Intergenic	L1ME2|LINE|L1	-245824	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.000000	0.315603	
chunk0026_39_1	chr10	60768149	60768409	+	0	NA	Intergenic	L1ME4c|LINE|L1	-10052	NM_001170406	983	Hs.732435	NM_001786	ENSG00000170312	CDK1	CDC2|CDC28A|P34CDC2	cyclin dependent kinase 1	protein-coding	0.007692	0.291188	
chunk0116_364_1	chr21	41748413	41748888	+	0	NA	intron (NM_020639, intron 4 of 7)	L1MB2|LINE|L1	-1809	NR_106872	102465488		NR_106872	ENSG00000275166	MIR6814	hsa-mir-6814	microRNA 6814	ncRNA	0.014737	0.483193	
chunk0056_21_1	chr13	77171557	77171912	+	0	NA	intron (NM_015057, intron 37 of 82)	intron (NM_015057, intron 37 of 82)	96220	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.002817	0.311798	
chunk0110_168_1	chr20	14198027	14198606	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	139351	NM_198391	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.006908	0.377586	
chunk0019_19_1	chr1	223541288	223541539	+	0	NA	TTS (NM_001143962)	TTS (NM_001143962)	124321	NM_001143962	388743	Hs.291487	NM_001143962	ENSG00000203697	CAPN8	nCL-2	calpain 8	protein-coding	0.011952	0.503968	
chunk0075_406_1	chr16	57050623	57050822	+	0	NA	intron (NM_032206, intron 22 of 47)	intron (NM_032206, intron 22 of 47)	33648	NM_032206	84166	Hs.528836	NM_032206	ENSG00000140853	NLRC5	CLR16.1|NOD27|NOD4	NLR family CARD domain containing 5	protein-coding	0.010050	0.480000	
chunk0192_347_1	chr8	67737434	67737892	+	0	NA	intron (NM_020361, intron 1 of 10)	L2c|LINE|L2	8722	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.004367	0.437908	
chunk0132_199_1	chr3	157274699	157275190	+	0	NA	intron (NM_001167911, intron 11 of 12)	intron (NM_001167911, intron 11 of 12)	-114184	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.004073	0.410569	
chunk0160_126_1	chr5	151014756	151015421	+	0	NA	Intergenic	MER68|LTR|ERVL	-5350	NM_002084	2878	Hs.386793	NM_002084	ENSG00000211445	GPX3	GPx-P|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding	0.004511	0.436937	
chunk0058_101_1	chr14	21703328	21703776	+	0	NA	Intergenic	MIRc|SINE|MIR	38469	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.002232	0.349666	
chunk0125_379_1	chr3	71586435	71586634	+	0	NA	Intergenic	Intergenic	-2545	NM_032682	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.010050	0.360000	111(AAGAACTCGATGTCCA,-,0.00),112(AGAACTCGATGTCCAT,+,0.00)
chunk0172_26_1	chr6	133070412	133070777	+	0	NA	Intergenic	Intergenic	-17486	NR_026969	285735	Hs.407549	NM_001037231		LINC00326	NCRNA00326	long intergenic non-protein coding RNA 326	ncRNA	0.008219	0.387978	
chunk0080_24_1	chr17	21002869	21003272	+	0	NA	exon (NM_015276, exon 13 of 13)	exon (NM_015276, exon 13 of 13)	39969	NM_015276	23326	Hs.462492	NM_015276	ENSG00000124422	USP22	USP3L	ubiquitin specific peptidase 22	protein-coding	0.024814	0.581683	190(TAGAACAGCAAGTACC,-,0.00),191(AGAACAGCAAGTACCT,+,0.00)
chunk0068_148_1	chr15	53630541	53631215	+	0	NA	intron (NR_102334, intron 14 of 19)	L1M4|LINE|L1	-89775	NR_102335	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.007418	0.342222	
chunk0182_21_1	chr7	91314522	91314822	+	0	NA	Intergenic	L1ME4b|LINE|L1	50204	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.003333	0.312292	
chunk0107_209_1	chr2	216615489	216616142	+	0	NA	Intergenic	Intergenic	-8877	NR_110392	101928232	Hs.694592	NR_110392		LINC01280	-	long intergenic non-protein coding RNA 1280	ncRNA	0.009188	0.501529	
chunk0166_456_1	chr6	53281656	53282259	+	0	NA	intron (NM_001242830, intron 3 of 6)	intron (NM_001242830, intron 3 of 6)	4964	NR_049866	100847075		NR_049866	ENSG00000264056	MIR5685	-	microRNA 5685	ncRNA	0.003317	0.417219	291(AGAAACAGCCTGTCCT,-,0.00),292(GAAACAGCCTGTCCTC,+,0.00)
chunk0042_156_1	chr12	3931745	3932331	+	0	NA	Intergenic	Intergenic	-58590	NM_001286521	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.010239	0.463373	
chunk0107_454_1	chr2	225761523	225761767	+	0	NA	Intergenic	FAM|SINE|Alu	360759	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.008197	0.424490	
chunk0031_8_1	chr10	121470114	121470548	+	0	NA	Intergenic	Intergenic	123636	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.032258	0.531034	166(CTGAACTTGGTGTTCC,-,0.00),167(TGAACTTGGTGTTCCA,+,0.00)
chunk0082_194_1	chr17	56794099	56794523	+	0	NA	intron (NM_001085430, intron 7 of 7)	intron (NM_001085430, intron 7 of 7)	39584	NM_001085430	339210	Hs.658949	NM_001085430	ENSG00000214226	C17orf67	-	chromosome 17 open reading frame 67	protein-coding	0.002358	0.430588	
chunk0125_79_1	chr3	64560743	64561176	+	0	NA	promoter-TSS (NR_110151)	promoter-TSS (NR_110151)	-387	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.004619	0.380184	213(ATGGACACAATGTTTT,-,0.00)
chunk0043_325_1	chr12	22543331	22543746	+	0	NA	intron (NM_001286174, intron 1 of 25)	intron (NM_001286174, intron 1 of 25)	1008	NM_001286174	9847	Hs.271014	NM_014802	ENSG00000111731	C2CD5	CDP138|KIAA0528	C2 calcium dependent domain containing 5	protein-coding	0.014458	0.490385	
chunk0010_289_1	chr1	117571068	117571709	+	0	NA	Intergenic	MIR|SINE|MIR	34382	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.012480	0.457944	
chunk0106_442_1	chr2	208939782	208940028	+	0	NA	Intergenic	Intergenic	-484142	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.004065	0.344130	
chunk0181_6_1	chr7	77654364	77654662	+	0	NA	Intergenic	Intergenic	-41913	NM_198467	222194	Hs.72451	NM_198467	ENSG00000187257	RSBN1L	-	round spermatid basic protein 1 like	protein-coding	0.003356	0.344482	
chunk0102_159_1	chr2	147260589	147260788	+	0	NA	Intergenic	Intergenic	-583829	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.355000	
chunk0047_206_1	chr12	71572496	71572915	+	0	NA	intron (NM_003667, intron 12 of 17)	MARNA|DNA|TcMar-Mariner	-91192	NM_031435	83591	Hs.245798	NM_031435	ENSG00000173451	THAP2	-	THAP domain containing 2	protein-coding	0.007160	0.383333	
chunk0209_277_1	chrX	47151210	47151853	+	0	NA	intron (NM_152856, intron 2 of 22)	L1M5|LINE|L1	6313	NM_001204468	8241	Hs.401509	NM_005676	ENSG00000182872	RBM10	DXS8237E|GPATC9|GPATCH9|S1-1|TARPS|ZRANB5	RNA binding motif protein 10	protein-coding	0.001555	0.377329	
chunk0086_157_1	chr18	21534232	21534636	+	0	NA	intron (NM_052911, intron 10 of 11)	intron (NM_052911, intron 10 of 11)	66298	NM_052911	114799	Hs.464733	NM_052911	ENSG00000141446	ESCO1	A930014I12Rik|CTF|ECO1|EFO1|ESO1	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.004950	0.380247	
chunk0059_36_1	chr14	29905627	29906027	+	0	NA	intron (NM_002742, intron 1 of 17)	L4_A_Mam|LINE|RTE-X	21866	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.017500	0.403990	
chunk0020_302_1	chr1	237366314	237366970	+	0	NA	intron (NM_001035, intron 5 of 104)	intron (NM_001035, intron 5 of 104)	-104477	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.004573	0.395738	
chunk0152_157_1	chr5	59380542	59381264	+	0	NA	intron (NM_001165899, intron 3 of 16)	MER58A|DNA|hAT-Charlie	-24002	NM_001197219	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002770	0.360996	
chunk0041_9_1	chr12	309335	309696	+	0	NA	intron (NM_001042603, intron 22 of 27)	MER6|DNA|TcMar-Tigger	-46642	NM_016615	6540	Hs.504398	NM_016615	ENSG00000010379	SLC6A13	GAT-2|GAT2|GAT3	solute carrier family 6 member 13	protein-coding	0.002770	0.309392	175(GAGGACTTACTGTACT,-,0.00),176(AGGACTTACTGTACTC,+,0.00)
chunk0123_344_1	chr3	47781763	47781976	+	0	NA	promoter-TSS (NM_003074)	promoter-TSS (NM_003074)	46	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.154930	0.785047	
chunk0093_35_1	chr19	39411497	39411733	+	0	NA	Intergenic	L2a|LINE|L2	-1495	NM_022835	64857	Hs.631574	NM_022835	ENSG00000090924	PLEKHG2	ARHGEF42|CLG|CTB-60E11.4|LDAMD	pleckstrin homology and RhoGEF domain containing G2	protein-coding	0.012712	0.485232	
chunk0197_392_1	chr8	127052529	127052947	+	0	NA	Intergenic	Intergenic	-27136	NR_109833	101867536	Hs.652970	NR_109833	ENSG00000282961	PRNCR1	CARLo-3|PCAT8	prostate cancer associated non-coding RNA 1	ncRNA	0.009569	0.470167	
chunk0212_213_1	chrX	135907335	135907590	+	0	NA	intron (NM_018666, intron 9 of 19)	intron (NM_018666, intron 9 of 19)	13828	NM_018666	55511	Hs.195292	NM_018666	ENSG00000181433	SAGE1	CT14|SAGE	sarcoma antigen 1	protein-coding	0.011765	0.394531	
chunk0120_218_1	chr3	7687933	7688554	+	0	NA	intron (NM_181874, intron 10 of 10)	intron (NM_181874, intron 10 of 10)	-152959	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.006441	0.310289	
chunk0080_427_1	chr17	35821197	35821835	+	0	NA	intron (NM_139215, intron 5 of 15)	intron (NM_139215, intron 5 of 15)	12061	NM_139215	8148	Hs.402752	NM_003487	ENSG00000270647	TAF15	Npl3|RBP56|TAF2N|TAFII68	TATA-box binding protein associated factor 15	protein-coding	0.004702	0.325509	310(GGGAACATACTGATCT,-,0.00),311(GGAACATACTGATCTT,+,0.00)
chunk0156_194_1	chr5	107930936	107931208	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-260177	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.003676	0.388278	
chunk0164_122_1	chr6	20817406	20818167	+	0	NA	intron (NM_017774, intron 8 of 15)	intron (NM_017774, intron 8 of 15)	283329	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.003942	0.360892	466(AAGAACTGCCTGATCT,-,0.00),467(AGAACTGCCTGATCTC,+,0.00)
chunk0034_53_1	chr11	27013973	27014476	+	0	NA	Intergenic	Intergenic	20143	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.003976	0.380952	
chunk0105_224_1	chr2	188280764	188281426	+	0	NA	intron (NR_126396, intron 1 of 2)	intron (NR_126396, intron 1 of 2)	6596	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.004532	0.345400	
chunk0121_163_1	chr3	19569384	19569583	+	0	NA	Intergenic	Intergenic	-254552	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.000000	0.255000	
chunk0024_28_1	chr10	33193878	33194679	+	0	NA	intron (NM_001244972, intron 12 of 16)	intron (NM_001244972, intron 12 of 16)	140627	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.008739	0.376559	482(CAGCACACACAGTTCT,-,0.00),483(AGCACACACAGTTCTG,+,0.00)
chunk0118_427_1	chr22	38570800	38571465	+	0	NA	promoter-TSS (NM_007068)	promoter-TSS (NM_007068)	-936	NR_103474	11144	Hs.339396	NM_007068	ENSG00000100206	DMC1	DMC1H|LIM15|dJ199H16.1	DNA meiotic recombinase 1	protein-coding	0.021053	0.457958	
chunk0031_401_1	chr10	131643099	131643344	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	146978	NR_038365	399827	Hs.523353	NM_001001677	ENSG00000189275	LINC01164	-	long intergenic non-protein coding RNA 1164	ncRNA	0.012245	0.556911	
chunk0033_413_1	chr11	24769002	24769223	+	0	NA	intron (NM_001252010, intron 5 of 9)	L1MA6|LINE|L1	272142	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.324324	
chunk0092_303_1	chr19	34310331	34311039	+	0	NA	intron (NM_014686, intron 2 of 13)	intron (NM_014686, intron 2 of 13)	-54055	NM_001184722	2821	Hs.466471	NM_000175	ENSG00000105220	GPI	AMF|GNPI|NLK|PGI|PHI|SA-36|SA36	glucose-6-phosphate isomerase	protein-coding	0.012712	0.541608	116(GAGAACAGGCTGTCTT,-,0.00),117(AGAACAGGCTGTCTTG,+,0.00)
chunk0153_47_1	chr5	67267966	67268844	+	0	NA	Intergenic	Intergenic	-71616	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.013667	0.492605	
chunk0073_355_1	chr16	14974599	14975319	+	0	NA	promoter-TSS (NM_001285444).2	promoter-TSS (NM_001285444).2	-4	NM_001285445	23042	Hs.370781	NM_015027	ENSG00000179889	PDXDC1	LP8165	pyridoxal dependent decarboxylase domain containing 1	protein-coding	0.090278	0.665742	
chunk0071_379_1	chr15	89125419	89125836	+	0	NA	intron (NM_007011, intron 7 of 14)	MER81|DNA|hAT-Blackjack	37477	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.004796	0.435407	
chunk0012_380_1	chr1	163336171	163336507	+	0	NA	intron (NM_145697, intron 5 of 13)	L1MEc|LINE|L1	14406	NM_145697	83540	Hs.651950	NM_031423	ENSG00000143228	NUF2	CDCA1|CT106|NUF2R	NUF2 component of NDC80 kinetochore complex	protein-coding	0.000000	0.376855	
chunk0188_289_1	chr8	15625350	15625802	+	0	NA	intron (NM_006765, intron 2 of 10)	intron (NM_006765, intron 2 of 10)	85489	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.002212	0.335541	
chunk0057_243_1	chr13	104571493	104571821	+	0	NA	Intergenic	Intergenic	-894210	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.021341	0.468085	
chunk0165_173_1	chr6	34303457	34303656	+	0	NA	intron (NM_006703, intron 2 of 4)	L1M5|LINE|L1	-54448	NM_001287396	221491	Hs.381300	NM_178508	ENSG00000186577	SMIM29	C6orf1|LBH	small integral membrane protein 29	protein-coding	0.005025	0.310000	
chunk0111_38_1	chr20	22288261	22288559	+	0	NA	Intergenic	HAL1ME|LINE|L1	-5609	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.010067	0.535117	80(AAGTACACTGTGTTCC,-,0.00),81(AGTACACTGTGTTCCT,+,0.00)
chunk0212_206_1	chrX	135017896	135018329	+	0	NA	Intergenic	Intergenic	4424	NM_001078173	441518	Hs.378813	NM_001078173	ENSG00000212747	RTL8B	CXX1c|FAM127C|MAR8B|SIRH4	retrotransposon Gag like 8B	protein-coding	0.006928	0.465438	224(CTGGACAGTTTGTTCT,-,0.00),225(TGGACAGTTTGTTCTG,+,0.00)
chunk0070_127_1	chr15	70778814	70779091	+	0	NA	Intergenic	L2a|LINE|L2	-15441	NM_018003	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.007220	0.410072	
chunk0139_307_1	chr4	57688342	57688916	+	0	NA	Intergenic	Intergenic	262757	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003484	0.307826	
chunk0078_331_1	chr17	8614840	8615069	+	0	NA	intron (NM_001256095, intron 2 of 41)	L1ME3B|LINE|L1	15807	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.000000	0.321739	
chunk0069_64_1	chr15	60852194	60852852	+	0	NA	intron (NM_134261, intron 1 of 10)	MIRb|SINE|MIR	170954	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.012158	0.435508	
chunk0158_374_1	chr5	134053942	134054331	+	0	NA	Intergenic	Intergenic	-49003	NM_003374	7416	Hs.519320	NM_003374	ENSG00000213585	VDAC1	PORIN|VDAC-1	voltage dependent anion channel 1	protein-coding	0.010283	0.430769	
chunk0005_395_1	chr1	62306658	62307179	+	0	NA	intron (NM_181712, intron 1 of 9)	intron (NM_181712, intron 1 of 9)	12494	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.003839	0.367816	
chunk0103_262_1	chr2	165556841	165557653	+	0	NA	intron (NM_001172173, intron 3 of 6)	MER58B|DNA|hAT-Charlie	-15089	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.007389	0.366544	
chunk0091_442_1	chr19	17227785	17227993	+	0	NA	exon (NM_024578, exon 4 of 6)	exon (NM_024578, exon 4 of 6)	1685	NM_024578	79629	Hs.422676	NM_024578	ENSG00000099330	OCEL1	FWP009|S863-9	occludin/ELL domain containing 1	protein-coding	0.028846	0.598086	
chunk0062_27_1	chr14	66986287	66986717	+	0	NA	intron (NM_001024218, intron 8 of 21)	intron (NM_001024218, intron 8 of 21)	-202891	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.000000	0.296984	
chunk0190_275_1	chr8	37591374	37591746	+	0	NA	Intergenic	Intergenic	-70174	NR_121621	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.002688	0.506702	
chunk0033_406_1	chr11	24731386	24732058	+	0	NA	intron (NM_001009909, intron 2 of 11)	intron (NM_001009909, intron 2 of 11)	234752	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004464	0.353640	
chunk0112_178_1	chr20	39953682	39954170	+	0	NA	Intergenic	Intergenic	-50535	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.006148	0.378323	
chunk0182_383_1	chr7	100126790	100127017	+	0	NA	5' UTR (NM_203397, exon 1 of 2)	5' UTR (NM_203397, exon 1 of 2)	206	NM_203397	255374	Hs.632319	NM_203397	ENSG00000214309	MBLAC1	-	metallo-beta-lactamase domain containing 1	protein-coding	0.083700	0.618421	
chunk0092_316_1	chr19	34645031	34645556	+	0	NA	promoter-TSS (NR_045208)	promoter-TSS (NR_045208)	-580	NR_045208	100130342	Hs.679909	NR_045208		SCGB2B3P	C2B|SCGB4A3P	secretoglobin family 2B member 3, pseudogene	pseudo	0.019048	0.553232	
chunk0154_152_1	chr5	79478480	79478702	+	0	NA	intron (NM_001277077, intron 1 of 5)	intron (NM_001277077, intron 1 of 5)	35245	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.013514	0.372197	
chunk0033_163_1	chr11	15650178	15650377	+	0	NA	intron (NM_001293172, intron 1 of 2)	CpG	6392	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.095477	0.730000	
chunk0098_209_1	chr2	72975804	72976074	+	0	NA	intron (NM_144579, intron 10 of 13)	L1ME3Cz|LINE|L1	58464	NM_004097	2016	Hs.516090	NM_004097	ENSG00000135638	EMX1	-	empty spiracles homeobox 1	protein-coding	0.003704	0.365314	
chunk0046_427_1	chr12	64633869	64634375	+	0	NA	intron (NR_040718, intron 1 of 3)	AluJb|SINE|Alu	-11517	NR_037515	100500856		NR_037515	ENSG00000266016	MIR548Z	-	microRNA 548z	ncRNA	0.001976	0.435897	
chunk0128_44_1	chr3	104632608	104632906	+	0	NA	Intergenic	Intergenic	-733956	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006711	0.341137	113(GAAGACACGCTGTTCC,-,0.00),114(AAGACACGCTGTTCCA,+,0.00)
chunk0079_61_1	chr17	10999539	10999989	+	0	NA	Intergenic	L1ME3A|LINE|L1	-161663	NM_001101387	644139	Hs.553909	NM_001101387	ENSG00000233670	PIRT	-	phosphoinositide interacting regulator of transient receptor potential channels	protein-coding	0.006667	0.403548	
chunk0170_27_1	chr6	109257619	109257898	+	0	NA	exon (NM_001277339, exon 6 of 10)	exon (NM_001277339, exon 6 of 10)	21144	NM_001277339	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.007168	0.525000	
chunk0130_435_1	chr3	140943180	140943495	+	0	NA	intron (NM_018155, intron 1 of 6)	intron (NM_018155, intron 1 of 6)	1517	NM_018155	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.015873	0.379747	
chunk0123_401_1	chr3	48926796	48927340	+	0	NA	intron (NM_006321, intron 2 of 15)	intron (NM_006321, intron 2 of 15)	-7683	NM_001123040	646450	Hs.720727	NM_001123040	ENSG00000221883	ARIH2OS	C3orf71	ariadne RBR E3 ubiquitin protein ligase 2 opposite strand	ncRNA	0.003676	0.427523	
chunk0121_413_1	chr3	25735379	25735616	+	0	NA	intron (NM_001145293, intron 7 of 11)	L1MEg|LINE|L1	48001	NM_001145293	55768	Hs.368960	NM_018297	ENSG00000151092	NGLY1	CDDG|CDG1V|PNG1|PNGase	N-glycanase 1	protein-coding	0.008439	0.327731	
chunk0084_449_1	chr17	83020837	83021221	+	0	NA	intron (NM_001009905, intron 4 of 12)	intron (NM_001009905, intron 4 of 12)	30781	NM_001009905	146712	Hs.607824	NM_001009905	ENSG00000175711	B3GNTL1	3-Gn-T8|B3GNT8|BGnT-8|beta-1|beta3Gn-T8|beta3GnTL1	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1	protein-coding	0.015625	0.394805	
chunk0149_96_1	chr5	18638708	18638994	+	0	NA	Intergenic	Intergenic	1247421	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006993	0.271777	
chunk0151_3_1	chr5	40690279	40690575	+	0	NA	intron (NM_000958, intron 2 of 2)	L2c|LINE|L2	10497	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.010135	0.373737	
chunk0137_126_1	chr4	14910438	14911016	+	0	NA	non-coding (NR_038857, exon 8 of 8)	non-coding (NR_038857, exon 8 of 8)	-22558	NR_126435	201853	Hs.551051	NR_126435	ENSG00000248360	LINC00504	-	long intergenic non-protein coding RNA 504	ncRNA	0.012111	0.430052	
chunk0081_210_1	chr17	42474960	42475507	+	0	NA	intron (NM_001130021, intron 5 of 21)	intron (NM_001130021, intron 5 of 21)	16389	NM_001130021	535	Hs.463074	NM_005177	ENSG00000033627	ATP6V0A1	ATP6N1|ATP6N1A|Stv1|VPP1|Vph1|a1	ATPase H+ transporting V0 subunit a1	protein-coding	0.005484	0.385036	290(TTGAACTGGATGTGCT,-,0.00),291(TGAACTGGATGTGCTA,+,0.00)
chunk0046_24_1	chr12	54389589	54389805	+	0	NA	intron (NM_001130967, intron 1 of 7)	intron (NM_001130967, intron 1 of 7)	1608	NM_001130967	25946	Hs.505653	NM_015481	ENSG00000161642	ZNF385A	HZF|RZF|ZFP385|ZNF385	zinc finger protein 385A	protein-coding	0.009259	0.576037	
chunk0014_48_1	chr1	175206740	175207157	+	0	NA	Intergenic	Intergenic	-13855	NM_001162894	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.000000	0.392344	
chunk0156_426_1	chr5	114473470	114473999	+	0	NA	intron (NM_170775, intron 3 of 5)	MIR|SINE|MIR	40204	NM_170775	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.005671	0.360377	264(GAGCACTTTCTGTGCC,-,0.00),265(AGCACTTTCTGTGCCA,+,0.00)
chunk0008_392_1	chr1	97239799	97240093	+	0	NA	intron (NM_000110, intron 18 of 22)	intron (NM_000110, intron 18 of 22)	144023	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.010204	0.294915	
chunk0109_120_1	chr20	2780804	2781003	+	0	NA	Intergenic	Intergenic	19743	NM_019609	56265	Hs.659346	NM_019609	ENSG00000088882	CPXM1	CPX1|CPXM	carboxypeptidase X, M14 family member 1	protein-coding	0.020101	0.480000	
chunk0183_256_1	chr7	107233924	107234607	+	0	NA	intron (NM_006348, intron 18 of 21)	intron (NM_006348, intron 18 of 21)	65250	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.007321	0.400585	201(TGGGACACACTGTACA,-,0.00),202(GGGACACACTGTACAG,+,0.00)
chunk0210_98_1	chrX	71540028	71540588	+	0	NA	intron (NM_181673, intron 3 of 21)	intron (NM_181673, intron 3 of 21)	7246	NM_181672	8473	Hs.405410	NM_003605	ENSG00000147162	OGT	HINCUT-1|HRNT1|MRX106|O-GLCNAC|OGT1	O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding	0.003571	0.335116	332(TAGTACATTGTGTACC,-,0.00),333(AGTACATTGTGTACCT,+,0.00)
chunk0122_69_1	chr3	29209660	29210079	+	0	NA	Intergenic	Intergenic	71070	NR_109804	100873979	Hs.99391	NR_109804		RBMS3-AS3	-	RBMS3 antisense RNA 3	ncRNA	0.002387	0.330952	36(AAGCACACAGTGTTAT,-,0.00)
chunk0043_11_1	chr12	12872169	12872940	+	0	NA	Intergenic	Intergenic	-2923	NR_003932	387841	Hs.631728	NR_003932	ENSG00000234498	RPL13AP20	RPL13A_9_1211	ribosomal protein L13a pseudogene 20	pseudo	0.012970	0.483161	
chunk0071_260_1	chr15	85514251	85514696	+	0	NA	intron (NM_007200, intron 2 of 36)	L1MC4|LINE|L1	-105477	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.004494	0.376682	
chunk0111_206_1	chr20	26223583	26223891	+	0	NA	Intergenic	Intergenic	-14504	NR_040095	284801	Hs.370699	NR_040095	ENSG00000227195	MIR663AHG	-	MIR663A host gene	ncRNA	0.000000	0.330097	225(ATGAACACTGTGTACA,-,0.00),226(TGAACACTGTGTACAG,+,0.00)
chunk0117_9_1	chr22	11051805	11052026	+	0	NA	Intergenic	Intergenic	-90386	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.013575	0.518018	
chunk0134_444_1	chr3	183760010	183760371	+	0	NA	intron (NM_018023, intron 13 of 30)	intron (NM_018023, intron 13 of 30)	62372	NM_018023	55689	Hs.632575	NM_018023	ENSG00000163872	YEATS2	-	YEATS domain containing 2	protein-coding	0.011080	0.350829	
chunk0150_156_1	chr5	33985347	33985597	+	0	NA	promoter-TSS (NM_001297417)	promoter-TSS (NM_001297417)	-797	NM_001012509	51151	Hs.278962	NM_016180	ENSG00000164175	SLC45A2	1A1|AIM1|MATP|OCA4|SHEP5	solute carrier family 45 member 2	protein-coding	0.012000	0.414343	
chunk0059_97_1	chr14	30948689	30949186	+	0	NA	intron (NM_001083893, intron 4 of 17)	intron (NM_001083893, intron 4 of 17)	-59129	NR_038356	100506071	Hs.729195	NR_038356	ENSG00000258525	LOC100506071	-	uncharacterized LOC100506071	ncRNA	0.000000	0.389558	
chunk0139_86_1	chr4	49494877	49495209	+	0	NA	Intergenic	MER61C|LTR|ERV1	508401	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.018072	0.483483	
chunk0027_121_1	chr10	74176375	74176574	+	0	NA	promoter-TSS (NM_001202449)	promoter-TSS (NM_001202449)	-15	NM_001202449	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.060302	0.605000	
chunk0194_342_1	chr8	89090870	89091073	+	0	NA	Intergenic	Intergenic	666740	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.000000	0.318627	
chunk0001_433_1	chr1	11422078	11422518	+	0	NA	Intergenic	L2a|LINE|L2	-56940	NM_020780	57540	Hs.202355	NM_020780	ENSG00000204624	DISP3	PTCHD2	dispatched RND transporter family member 3	protein-coding	0.020455	0.473923	
chunk0178_50_1	chr7	29836143	29836546	+	0	NA	intron (NM_001080529, intron 2 of 8)	intron (NM_001080529, intron 2 of 8)	29790	NM_001080529	644150	Hs.380698	NM_001080529	ENSG00000122574	WIPF3	CR16	WAS/WASL interacting protein family member 3	protein-coding	0.002481	0.336634	
chunk0114_105_1	chr21	9539286	9539541	+	0	NA	Intergenic	MIR|SINE|MIR	281648	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.351562	
chunk0048_364_1	chr12	85860846	85861124	+	0	NA	Intergenic	L1PA8A|LINE|L1	-13310	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.010791	0.362007	
chunk0184_179_1	chr7	116571512	116571986	+	0	NA	intron (NR_120506, intron 3 of 4)	intron (NR_120506, intron 3 of 4)	43071	NR_120506	100996266	Hs.552122	NR_120506		LINC01510	-	long intergenic non-protein coding RNA 1510	ncRNA	0.004219	0.368421	
chunk0207_75_1	chrX	9267453	9267827	+	0	NA	Intergenic	Intergenic	-195655	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.013369	0.480000	
chunk0211_178_1	chrX	116924546	116924909	+	0	NA	Intergenic	MER51B|LTR|ERV1	-461694	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.002755	0.390110	
chunk0157_98_1	chr5	116736490	116737103	+	0	NA	Intergenic	L1ME4b|LINE|L1	25413	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.004894	0.377850	
chunk0077_199_1	chr16	79850391	79850772	+	0	NA	Intergenic	MIR|SINE|MIR	55332	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.007874	0.371728	
chunk0024_313_1	chr10	42718686	42719243	+	0	NA	Intergenic	Intergenic	-27205	NR_120658	101929397	Hs.729796	NR_120656		LINC01518	-	long intergenic non-protein coding RNA 1518	ncRNA	0.003591	0.326165	
chunk0085_463_1	chr18	11767268	11767655	+	0	NA	intron (NM_182978, intron 4 of 11)	intron (NM_182978, intron 4 of 11)	15989	NM_001142339	2774	Hs.136295	NM_002071	ENSG00000141404	GNAL	DYT25	G protein subunit alpha L	protein-coding	0.007752	0.512887	
chunk0054_293_1	chr13	48142371	48142854	+	0	NA	Intergenic	Intergenic	-47471	NM_001270629	29079	Hs.181112	NM_014166	ENSG00000136146	MED4	ARC36|DRIP36|HSPC126|TRAP36|VDRIP	mediator complex subunit 4	protein-coding	0.006211	0.433884	
chunk0037_26_1	chr11	69653954	69655073	+	0	NA	TTS (NM_053056)	TTS (NM_053056)	13408	NM_053056	595	Hs.523852	NM_053056	ENSG00000110092	CCND1	BCL1|D11S287E|PRAD1|U21B31	cyclin D1	protein-coding	0.048257	0.605357	125(AGGGTCATCCTGTGCT,-,0.00),126(GGGTCATCCTGTGCTC,+,0.00)
chunk0035_355_1	chr11	48993462	48993817	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-37961	NM_001206626	283116	Hs.448644	NM_001206626	ENSG00000182053	TRIM49B	-	tripartite motif containing 49B	protein-coding	0.002817	0.367978	56(CTGTACAGCATGTTCT,-,0.00),57(TGTACAGCATGTTCTG,+,0.00)
chunk0129_414_1	chr3	127051989	127052221	+	0	NA	Intergenic	Intergenic	63511	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.021552	0.570815	
chunk0181_349_1	chr7	88303419	88304028	+	0	NA	intron (NM_001205315, intron 1 of 5)	intron (NM_001205315, intron 1 of 5)	3190	NM_001205316	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.001642	0.355738	
chunk0075_413_1	chr16	57235207	57235550	+	0	NA	intron (NM_133368, intron 14 of 14)	intron (NM_133368, intron 14 of 14)	-9748	NM_012106	23568	Hs.632873	NM_012106	ENSG00000102931	ARL2BP	BART|BART1|RP66	ADP ribosylation factor like GTPase 2 binding protein	protein-coding	0.002915	0.369186	
chunk0012_448_1	chr1	165069611	165070288	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	286292	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.004431	0.367257	
chunk0120_212_1	chr3	7388431	7389000	+	0	NA	intron (NM_000844, intron 4 of 9)	L1PA17|LINE|L1	146569	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.003515	0.310526	
chunk0018_75_1	chr1	217163153	217163476	+	0	NA	Intergenic	Intergenic	-25559	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.354938	
chunk0150_392_1	chr5	39657572	39657918	+	0	NA	Intergenic	Intergenic	137314	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.000000	0.345821	
chunk0127_339_1	chr3	100562919	100563477	+	0	NA	intron (NM_018004, intron 4 of 5)	MLT1C|LTR|ERVL-MaLR	-46391	NM_032787	84873	Hs.334511	NM_032787	ENSG00000144820	ADGRG7	GPR128	adhesion G protein-coupled receptor G7	protein-coding	0.001792	0.416816	
chunk0114_403_1	chr20	63659380	63659579	+	0	NA	non-coding (NR_037882, exon 2 of 38)	non-coding (NR_037882, exon 2 of 38)	1669	NM_016434	51750	Hs.745057	NM_016434	ENSG00000258366	RTEL1	C20orf41|DKCA4|DKCB5|NHL|PFBMFT3|RTEL	regulator of telomere elongation helicase 1	protein-coding	0.020101	0.570000	174(CAGGACGGGGTGTGCT,-,0.00),175(AGGACGGGGTGTGCTT,+,0.00)
chunk0020_308_1	chr1	237472728	237472927	+	0	NA	intron (NM_001035, intron 17 of 104)	intron (NM_001035, intron 17 of 104)	1708	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.010050	0.385000	
chunk0162_291_1	chr6	6320850	6321424	+	0	NA	promoter-TSS (NM_000129)	promoter-TSS (NM_000129)	-446	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.006969	0.483478	273(GAGAGCAACGTGTCCC,-,0.00),274(AGAGCAACGTGTCCCT,+,0.00)
chunk0114_177_1	chr21	14877671	14878178	+	0	NA	Intergenic	Intergenic	186881	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.003945	0.375984	
chunk0114_166_1	chr21	14222605	14223119	+	0	NA	intron (NM_144770, intron 3 of 4)	MIR|SINE|MIR	6717	NM_144770	54033	Hs.283828	NM_144770	ENSG00000185272	RBM11	-	RNA binding motif protein 11	protein-coding	0.007782	0.361165	
chunk0204_114_1	chr9	94991942	94992274	+	0	NA	intron (NM_032823, intron 9 of 14)	intron (NM_032823, intron 9 of 14)	-73242	NR_106729	102466518		NR_106729	ENSG00000274115	MIR6081	hsa-mir-6081	microRNA 6081	ncRNA	0.006024	0.432432	
chunk0106_448_1	chr2	209297855	209298299	+	0	NA	Intergenic	Intergenic	-125970	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.004505	0.310112	
chunk0186_43_1	chr7	136153684	136154220	+	0	NA	Intergenic	Intergenic	-176496	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.005597	0.424581	275(GGGGACAGAATGTTCT,-,0.00),276(GGGACAGAATGTTCTA,+,0.00)
chunk0033_32_1	chr11	12991454	12991763	+	0	NA	Intergenic	Ricksha_b|DNA|MULE-MuDR	-2060	NR_038904	100506305	Hs.153408	NR_038904	ENSG00000251381	LINC00958	BLACAT2	long intergenic non-protein coding RNA 958	ncRNA	0.000000	0.293548	
chunk0008_156_1	chr1	92494599	92494798	+	0	NA	Intergenic	Intergenic	-7822	NM_005263	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.005025	0.460000	
chunk0075_115_1	chr16	49158037	49158334	+	0	NA	Intergenic	Intergenic	123646	NM_004352	869	Hs.458423	NM_004352	ENSG00000102924	CBLN1	-	cerebellin 1 precursor	protein-coding	0.006734	0.503356	
chunk0085_165_1	chr18	3740666	3740899	+	0	NA	intron (NM_001308390, intron 3 of 10)	(ACC)n|Simple_repeat|Simple_repeat	104576	NM_001242766	9229	Hs.594640	NM_004746	ENSG00000170579	DLGAP1	DAP-1|DAP-1-ALPHA|DAP-1-BETA|DAP1|DLGAP1A|DLGAP1B|GKAP|SAPAP1	DLG associated protein 1	protein-coding	0.021459	0.512821	
chunk0044_397_1	chr12	40646732	40647023	+	0	NA	Intergenic	Intergenic	-45565	NM_001843	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.006873	0.308219	
chunk0147_316_1	chr4	184951394	184951646	+	0	NA	Intergenic	L1MB7|LINE|L1	-13080	NR_039660	100616111		NR_039660	ENSG00000263458	MIR4455	-	microRNA 4455	ncRNA	0.051587	0.509881	
chunk0104_76_1	chr2	171850851	171851312	+	0	NA	intron (NR_047549, intron 3 of 16)	intron (NR_047549, intron 3 of 16)	43225	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.004338	0.383117	
chunk0004_236_1	chr1	47221452	47221947	+	0	NA	intron (NM_001290404, intron 5 of 5)	intron (NM_001290404, intron 5 of 5)	10016	NM_001287347	6886	Hs.705618	NM_003189	ENSG00000162367	TAL1	SCL|TCL5|bHLHa17|tal-1	TAL bHLH transcription factor 1, erythroid differentiation factor	protein-coding	0.006061	0.506048	164(AGGAACTGCCAGTCCT,-,0.00),165(GGAACTGCCAGTCCTA,+,0.00)
chunk0020_229_1	chr1	235549952	235550305	+	0	NA	3' UTR (NM_004485, exon 3 of 3)	3' UTR (NM_004485, exon 3 of 3)	37305	NR_039973									0.011331	0.432203	
chunk0111_265_1	chr20	31068101	31069215	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-189006	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.014363	0.401794	
chunk0070_291_1	chr15	74642809	74643755	+	0	NA	intron (NM_025083, intron 4 of 6)	intron (NM_025083, intron 4 of 6)	28288	NM_001130028	1198	Hs.511790	NM_001292	ENSG00000179335	CLK3	PHCLK3|PHCLK3/152	CDC like kinase 3	protein-coding	0.011628	0.469905	651(AAGTACACTCAGTACA,-,0.00)
chunk0090_243_1	chr18	73848735	73849263	+	0	NA	Intergenic	Intergenic	298765	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.001894	0.389414	
chunk0022_320_1	chr10	16303607	16304048	+	0	NA	Intergenic	Intergenic	-133116	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.002268	0.332579	
chunk0099_136_1	chr2	86480182	86480629	+	0	NA	intron (NM_018433, intron 16 of 25)	intron (NM_018433, intron 16 of 25)	38944	NM_001146688	55818	Hs.557425	NM_018433	ENSG00000115548	KDM3A	JHDM2A|JHMD2A|JMJD1|JMJD1A|TSGA	lysine demethylase 3A	protein-coding	0.013423	0.486607	
chunk0061_58_1	chr14	56522216	56522835	+	0	NA	Intergenic	L1PB3|LINE|L1	-57268	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.003231	0.374194	
chunk0078_112_1	chr17	2580410	2580686	+	0	NA	Intergenic	Intergenic	-13081	NM_000430	5048	Hs.77318	NM_000430	ENSG00000007168	PAFAH1B1	LIS1|LIS2|MDCR|MDS|NudF|PAFAH	platelet activating factor acetylhydrolase 1b regulatory subunit 1	protein-coding	0.007246	0.386282	
chunk0195_294_1	chr8	98598913	98599478	+	0	NA	intron (NM_001256313, intron 4 of 8)	intron (NM_001256313, intron 4 of 8)	172173	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.000000	0.333922	
chunk0205_78_1	chr9	106966360	106966846	+	0	NA	intron (NM_021224, intron 7 of 12)	L2c|LINE|L2	103506	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.008230	0.383984	319(CAGAACAGGGTCTCCT,-,0.00)
chunk0083_353_1	chr17	70387651	70388124	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	218352	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.006342	0.402954	
chunk0006_178_1	chr1	67132687	67133148	+	0	NA	intron (NM_001276351, intron 1 of 7)	intron (NM_001276351, intron 1 of 7)	2054	NM_001276351	400757	Hs.666621	NM_001013674	ENSG00000203963	C1orf141	-	chromosome 1 open reading frame 141	protein-coding	0.002169	0.290043	
chunk0169_292_1	chr6	105911408	105911674	+	0	NA	Intergenic	Intergenic	-174779	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.003759	0.505618	
chunk0011_303_1	chr1	151733281	151733586	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	11896	NM_001144956	284485	Hs.297967	NM_001144956	ENSG00000178796	RIIAD1	C1orf230|NCRNA00166	regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1	protein-coding	0.016393	0.522876	
chunk0088_162_1	chr18	46738841	46739159	+	0	NA	intron (NM_001307986, intron 1 of 7)	intron (NM_001307986, intron 1 of 7)	18169	NM_001307987	29906	Hs.465025	NM_013305	ENSG00000101638	ST8SIA5	SIAT8-E|SIAT8E|ST8SiaV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding	0.006289	0.514107	280(AAGAACACCGTGGGCT,-,0.00),281(AGAACACCGTGGGCTG,+,0.00)
chunk0061_154_1	chr14	59691177	59691419	+	0	NA	intron (NM_021136, intron 3 of 8)	L1PA15-16|LINE|L1	-44278	NR_049851	100847088		NR_049851	ENSG00000263629	MIR5586	-	microRNA 5586	ncRNA	0.000000	0.374486	
chunk0177_5_1	chr7	20305822	20306131	+	0	NA	non-coding (NR_110117, exon 4 of 5)	non-coding (NR_110117, exon 4 of 5)	9268	NR_110117	101927769	Hs.256080	NR_110117	ENSG00000226097	LOC101927769	-	uncharacterized LOC101927769	ncRNA	0.003236	0.367742	
chunk0096_68_1	chr2	27706199	27706649	+	0	NA	Intergenic	Intergenic	-42584	NM_001282731	9913	Hs.6232	NM_014860	ENSG00000119760	SUPT7L	SPT7L|STAF65|STAF65(gamma)|STAF65G|SUPT7H	SPT7 like, STAGA complex gamma subunit	protein-coding	0.002222	0.532151	
chunk0037_385_1	chr11	78648762	78649092	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-74063	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.003030	0.422961	
chunk0130_133_1	chr3	132179780	132180068	+	0	NA	Intergenic	Intergenic	-137443	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.000000	0.366782	189(CTGTACAGAATGTTCC,-,0.00),190(TGTACAGAATGTTCCT,+,0.00)
chunk0121_115_1	chr3	17372681	17373283	+	0	NA	intron (NM_014744, intron 12 of 21)	MER58B|DNA|hAT-Charlie	327038	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.004983	0.334992	
chunk0178_129_1	chr7	32169610	32169828	+	0	NA	intron (NM_001191058, intron 3 of 18)	intron (NM_001191058, intron 3 of 18)	-98283	NM_001191059	5137	Hs.143821	NM_005020	ENSG00000154678	PDE1C	DFNA74|Hcam3|cam-PDE 1C|hCam-3	phosphodiesterase 1C	protein-coding	0.000000	0.415525	
chunk0139_246_1	chr4	56078866	56079425	+	0	NA	Intergenic	Intergenic	-18284	NR_106988									0.007156	0.428571	246(GAGTCCAGCGTGTCCT,-,0.00),247(AGTCCAGCGTGTCCTG,+,0.00)
chunk0034_211_1	chr11	32567251	32567953	+	0	NA	Intergenic	L1MC1|LINE|L1	-16165	NM_006360	10480	Hs.502244	NM_006360	ENSG00000149100	EIF3M	B5|GA17|PCID1|TANGO7|hfl-B5	eukaryotic translation initiation factor 3 subunit M	protein-coding	0.005698	0.423898	48(TAAACACTCTGTGCTC,+,0.00)
chunk0128_191_1	chr3	107504519	107504943	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-18205	NM_001276286	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.002358	0.371765	
chunk0212_265_1	chrX	139657332	139657900	+	0	NA	intron (NM_001171876, intron 1 of 28)	MER103C|DNA|hAT-Charlie	-14775	NM_001171878	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.003521	0.351494	135(CAATACAGCATGTGCT,-,0.00),136(AATACAGCATGTGCTT,+,0.00)
chunk0144_239_1	chr4	135113955	135114697	+	0	NA	Intergenic	LTR84b|LTR|ERVL	773767	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.004043	0.339166	
chunk0007_319_1	chr1	84433272	84433691	+	0	NA	Intergenic	Intergenic	25130	NM_058248	58511	Hs.129142	NM_021233	ENSG00000137976	DNASE2B	DLAD	deoxyribonuclease 2 beta	protein-coding	0.016706	0.411905	218(AAGGACACCATGTCCC,-,0.00),219(AGGACACCATGTCCCC,+,0.00)
chunk0080_90_1	chr17	26619892	26620158	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	673971	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.011278	0.419476	
chunk0139_375_1	chr4	60872354	60872960	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-49962	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.003300	0.398682	
chunk0082_30_1	chr17	50749089	50749367	+	0	NA	intron (NM_016424, intron 9 of 9)	intron (NM_016424, intron 9 of 9)	18287	NR_073199									0.010791	0.451613	
chunk0163_85_1	chr6	9467819	9468220	+	0	NA	Intergenic	Intergenic	815810	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.007481	0.412935	
chunk0190_207_1	chr8	35611769	35612125	+	0	NA	intron (NM_080872, intron 4 of 16)	intron (NM_080872, intron 4 of 16)	98373	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.005618	0.327731	
chunk0124_216_1	chr3	56109566	56109974	+	0	NA	intron (NR_132749, intron 6 of 17)	intron (NR_132749, intron 6 of 17)	-257176	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.004902	0.369193	
chunk0140_60_1	chr4	67043430	67043898	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	378336	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.000000	0.383795	
chunk0038_196_1	chr11	86161113	86161315	+	0	NA	Intergenic	Intergenic	-83170	NM_001308007	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.000000	0.344828	
chunk0156_30_1	chr5	102461644	102462133	+	0	NA	intron (NM_001289004, intron 3 of 12)	L1PB1|LINE|L1	37128	NM_001289002	133482	Hs.388874	NM_173488	ENSG00000205359	SLCO6A1	CT48|GST|OATP-I|OATP6A1|OATPY	solute carrier organic anion transporter family member 6A1	protein-coding	0.002045	0.316327	210(AAGAACTTCTTGTCCT,-,0.00),211(AGAACTTCTTGTCCTA,+,0.00)
chunk0027_297_1	chr10	77634928	77635448	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	2631	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.007692	0.397313	
chunk0110_162_1	chr20	14053959	14054435	+	0	NA	intron (NM_080676, intron 2 of 16)	intron (NM_080676, intron 2 of 16)	58697	NM_080676	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.006303	0.387841	
chunk0017_181_1	chr1	207298822	207299044	+	0	NA	Intergenic	Intergenic	-22539	NM_001300902	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.004505	0.363229	
chunk0194_348_1	chr8	89253600	89253959	+	0	NA	Intergenic	L1PA16|LINE|L1	503932	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.002786	0.550000	182(GAGAGCATGGTGTACT,-,0.00),183(AGAGCATGGTGTACTC,+,0.00)
chunk0186_60_1	chr7	136682012	136682375	+	0	NA	Intergenic	L1MC1|LINE|L1	-186459	NM_001006627	1129	Hs.535891	NM_000739	ENSG00000181072	CHRM2	HM2	cholinergic receptor muscarinic 2	protein-coding	0.005510	0.370879	
chunk0197_156_1	chr8	120445142	120445395	+	0	NA	promoter-TSS (NM_022045)	promoter-TSS (NM_022045)	-130	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.059289	0.511811	
chunk0121_465_1	chr3	27281691	27282278	+	0	NA	intron (NM_199347, intron 23 of 24)	HAL1|LINE|L1	-65461	NM_001031741	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.005111	0.357143	
chunk0032_5_1	chr11	315395	315720	+	0	NA	TTS (NM_003641)	TTS (NM_003641)	1566	NM_003641	8519	Hs.458414	NM_003641	ENSG00000185885	IFITM1	9-27|CD225|DSPA2a|IFI17|LEU13	interferon induced transmembrane protein 1	protein-coding	0.009231	0.604294	92(AAGGACACACTGTCCA,-,0.00),93(AGGACACACTGTCCAG,+,0.00)
chunk0024_42_1	chr10	33631602	33632044	+	0	NA	Intergenic	Intergenic	140857	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.013575	0.505643	
chunk0036_245_1	chr11	64433880	64434488	+	0	NA	Intergenic	Intergenic	-14873	NR_073177	100996455	Hs.634142	NR_073177	ENSG00000181908	LINC02724	-	long intergenic non-protein coding RNA 2724	ncRNA	0.014803	0.543514	
chunk0047_347_1	chr12	74907420	74907630	+	0	NA	Intergenic	L2c|LINE|L2	302223	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.000000	0.388626	
chunk0106_380_1	chr2	207316709	207316943	+	0	NA	Intergenic	MER65A|LTR|ERV1	-47402	NR_031633	100302130		NR_031633	ENSG00000221628	MIR1302-4	MIRN1302-4|hsa-mir-1302-4	microRNA 1302-4	ncRNA	0.000000	0.323404	
chunk0153_82_1	chr5	68109512	68109966	+	0	NA	Intergenic	Intergenic	-80137	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.000000	0.283516	
chunk0191_178_1	chr8	51121118	51121317	+	0	NA	Intergenic	L1M6|LINE|L1	688228	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.005025	0.355000	
chunk0052_60_1	chr13	21164367	21165080	+	0	NA	intron (NM_145061, intron 4 of 8)	intron (NM_145061, intron 4 of 8)	-11510	NM_024026	78988	Hs.458367	NM_024026	ENSG00000173141	MRPL57	MRP63|bMRP63	mitochondrial ribosomal protein L57	protein-coding	0.009818	0.319328	
chunk0075_32_1	chr16	46954638	46955011	+	0	NA	TTS (NM_005880)	TTS (NM_005880)	18890	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.008043	0.393048	
chunk0008_398_1	chr1	97411636	97412235	+	0	NA	intron (NM_000110, intron 14 of 22)	intron (NM_000110, intron 14 of 22)	316012	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.005008	0.311667	
chunk0011_316_1	chr1	151932060	151932269	+	0	NA	Intergenic	HAL1M8|LINE|L1	-22279	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.004785	0.404762	
chunk0209_205_1	chrX	44149688	44150132	+	0	NA	intron (NM_025184, intron 14 of 14)	intron (NM_025184, intron 14 of 14)	-176235	NM_000266	4693	Hs.522615	NM_000266	ENSG00000124479	NDP	EVR2|FEVR|ND	norrin cystine knot growth factor NDP	protein-coding	0.013514	0.375281	
chunk0047_265_1	chr12	72920646	72921171	+	0	NA	Intergenic	Alu|SINE|Alu	-238282	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.003810	0.359316	
chunk0036_367_1	chr11	67177690	67178030	+	0	NA	intron (NR_027473, intron 2 of 20)	Tigger3b|DNA|TcMar-Tigger	58591	NM_012308	22992	Hs.124147	NM_012308	ENSG00000173120	KDM2A	CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA	lysine demethylase 2A	protein-coding	0.005882	0.331378	
chunk0012_442_1	chr1	165034187	165034572	+	0	NA	Intergenic	Intergenic	-259738	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.007792	0.406736	
chunk0110_412_1	chr20	20573775	20574106	+	0	NA	intron (NM_020343, intron 20 of 39)	L1ME1|LINE|L1	138683	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.006042	0.337349	
chunk0049_391_1	chr12	96428792	96429214	+	0	NA	Intergenic	Intergenic	-28415	NM_002595	5128	Hs.506415	NM_002595	ENSG00000059758	CDK17	PCTAIRE2|PCTK2	cyclin dependent kinase 17	protein-coding	0.007109	0.375887	
chunk0029_359_1	chr10	107612098	107612314	+	0	NA	Intergenic	L1PB4|LINE|L1	-447498	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.004630	0.354839	138(AAGCACAGGCTGAACT,-,0.00),139(AGCACAGGCTGAACTT,+,0.00)
chunk0211_172_1	chrX	115405788	115406318	+	0	NA	Intergenic	L2c|LINE|L2	116336	NM_016383	51213	Hs.242183	NM_016383	ENSG00000102021	LUZP4	CT-28|CT-8|CT28|HOM-TES-85	leucine zipper protein 4	protein-coding	0.005660	0.365348	164(TAGAGCACTCTGTTCA,-,0.00),165(AGAGCACTCTGTTCAT,+,0.00)
chunk0165_92_1	chr6	31919639	31920330	+	0	NA	intron (NM_001178063, intron 1 of 13)	intron (NM_001178063, intron 1 of 13)	-7493	NM_000063	717	Hs.408903	NM_000063	ENSG00000166278	C2	ARMD14|CO2	complement C2	protein-coding	0.008683	0.455202	
chunk0054_330_1	chr13	49308083	49308665	+	0	NA	TTS (NM_030925)	TTS (NM_030925)	60463	NR_036439	81602	Hs.388220	NM_030911	ENSG00000102543	CDADC1	NYD-SP15|bA103J18.1	cytidine and dCMP deaminase domain containing 1	protein-coding	0.012027	0.547170	286(AAGAACATTATGATCT,-,0.00),287(AGAACATTATGATCTC,+,0.00)
chunk0126_371_1	chr3	84024018	84024217	+	0	NA	Intergenic	L2|LINE|L2	845458	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.005025	0.340000	
chunk0138_130_1	chr4	36676575	36676989	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-250354	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.004831	0.378313	
chunk0060_385_1	chr14	52790511	52790863	+	0	NA	intron (NM_198066, intron 1 of 5)	intron (NM_198066, intron 1 of 5)	981	NM_198066	64841	Hs.478025	NM_198066	ENSG00000100522	GNPNAT1	GNA1|GNPNAT|Gpnat1	glucosamine-phosphate N-acetyltransferase 1	protein-coding	0.031250	0.422096	
chunk0192_38_1	chr8	58666119	58666494	+	0	NA	Intergenic	Intergenic	-6461	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.002667	0.380319	
chunk0190_98_1	chr8	30325334	30325563	+	0	NA	Intergenic	Intergenic	-59053	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.008734	0.395652	
chunk0119_171_1	chr22	43419656	43420241	+	0	NA	intron (NM_001044370, intron 1 of 6)	intron (NM_001044370, intron 1 of 6)	7934	NM_001044370	758	Hs.159538	NM_001044370	ENSG00000186732	MPPED1	239AB|C22orf1|FAM1A	metallophosphoesterase domain containing 1	protein-coding	0.013675	0.537543	
chunk0134_250_1	chr3	179361251	179361765	+	0	NA	intron (NM_033540, intron 4 of 17)	L1PA17|LINE|L1	13816	NM_033540	55669	Hs.478383	NM_017927	ENSG00000171109	MFN1	hfzo1|hfzo2	mitofusin 1	protein-coding	0.009728	0.450485	
chunk0209_84_1	chrX	38965803	38966223	+	0	NA	Intergenic	Intergenic	-162130	NR_046706	100874211	Hs.662789	NR_046706		MID1IP1-AS1	-	MID1IP1 antisense RNA 1	ncRNA	0.014286	0.460808	
chunk0091_448_1	chr19	17466662	17466873	+	0	NA	Intergenic	Intergenic	-3677	NM_198580	376497	Hs.363138	NM_198580	ENSG00000130304	SLC27A1	ACSVL5|FATP|FATP-1|FATP1	solute carrier family 27 member 1	protein-coding	0.023697	0.514151	22(TGGAACAGTTTGTGCC,-,0.00),23(GGAACAGTTTGTGCCC,+,0.00)
chunk0098_240_1	chr2	74761080	74761713	+	0	NA	Intergenic	Intergenic	-71259	NM_000189	3099	Hs.406266	NM_000189	ENSG00000159399	HK2	HKII|HXK2	hexokinase 2	protein-coding	0.007899	0.463722	
chunk0176_13_1	chr7	8239591	8240746	+	0	NA	intron (NM_001276478, intron 1 of 13)	L1PA6|LINE|L1	21884	NM_022307	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.015584	0.504325	64(ATGACAGACTGTACCT,+,0.00)
chunk0103_268_1	chr2	165620962	165621495	+	0	NA	intron (NM_001172173, intron 4 of 6)	intron (NM_001172173, intron 4 of 6)	48892	NM_024969	80034	Hs.470479	NM_024969	ENSG00000178662	CSRNP3	FAM130A2|PPP1R73|TAIP-2|TAIP2	cysteine and serine rich nuclear protein 3	protein-coding	0.007505	0.368914	
chunk0024_365_1	chr10	44195611	44196185	+	0	NA	Intergenic	Intergenic	-96852	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.008711	0.486957	
chunk0147_303_1	chr4	184792930	184793786	+	0	NA	intron (NM_001286712, intron 2 of 21)	intron (NM_001286712, intron 2 of 21)	5688	NR_003542	643036	Hs.689630	NR_003542	ENSG00000249138	SLED1	-	proteoglycan 3, pro eosinophil major basic protein 2 pseudogene	pseudo	0.017523	0.472579	
chunk0157_275_1	chr5	120433357	120433913	+	0	NA	Intergenic	L1MC1|LINE|L1	-30643	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.008993	0.326750	
chunk0183_59_1	chr7	104126284	104126908	+	0	NA	3' UTR (NM_002553, exon 14 of 14)	3' UTR (NM_002553, exon 14 of 14)	81451	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.008013	0.398400	303(TAGAACAGATTGTGCT,-,0.00),304(AGAACAGATTGTGCTC,+,0.00)
chunk0121_32_1	chr3	15212352	15212914	+	0	NA	intron (NM_014296, intron 2 of 20)	intron (NM_014296, intron 2 of 20)	6407	NM_014296	23473	Hs.595234	NM_014296	ENSG00000131375	CAPN7	CALPAIN7|PALBH	calpain 7	protein-coding	0.005338	0.337478	
chunk0039_217_1	chr11	101227362	101227694	+	0	NA	Intergenic	L1MEd|LINE|L1	-97715	NM_000926	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.006024	0.348348	
chunk0013_138_1	chr1	168297049	168297443	+	0	NA	intron (NM_005149, intron 3 of 7)	intron (NM_005149, intron 3 of 7)	16206	NM_005149	9095	Hs.716656	NM_005149	ENSG00000143178	TBX19	TBS19|TPIT|dJ747L4.1	T-box transcription factor 19	protein-coding	0.010152	0.397468	
chunk0019_441_1	chr1	231243051	231243373	+	0	NA	intron (NM_001316350, intron 1 of 14)	L2c|LINE|L2	-2025	NM_001300830	128061	Hs.743464	NM_152379	ENSG00000143633	C1orf131	-	chromosome 1 open reading frame 131	protein-coding	0.003106	0.396285	
chunk0098_322_1	chr2	76748158	76748811	+	0	NA	3' UTR (NM_001134745, exon 4 of 4)	3' UTR (NM_001134745, exon 4 of 4)	-237481	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.024502	0.437309	
chunk0059_123_1	chr14	31510371	31510684	+	0	NA	Intergenic	Intergenic	-22582	NR_036675	2856	Hs.727479	NM_001197184	ENSG00000214943	GPR33	-	G protein-coupled receptor 33 (gene/pseudogene)	protein-coding	0.000000	0.369427	161(AGGAACAAGGTGTTCT,-,0.00),162(GGAACAAGGTGTTCTA,+,0.00)
chunk0163_23_1	chr6	8057652	8058260	+	0	NA	intron (NM_001199322, intron 2 of 5)	L2c|LINE|L2	6458	NM_201280	63915	Hs.719272	NM_201280	ENSG00000188428	BLOC1S5	BLOS5|MU|MUTED	biogenesis of lysosomal organelles complex 1 subunit 5	protein-coding	0.006579	0.374384	
chunk0210_275_1	chrX	84644728	84645374	+	0	NA	Intergenic	Intergenic	-142572	NM_144657	139324	Hs.559546	NM_144657	ENSG00000165259	HDX	CXorf43|D030011N01Rik	highly divergent homeobox	protein-coding	0.000000	0.287481	
chunk0203_107_1	chr9	84600725	84601134	+	0	NA	Intergenic	Intergenic	-67529	NM_001291937	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.009780	0.465854	
chunk0192_206_1	chr8	64856810	64857572	+	0	NA	Intergenic	Intergenic	-58400	NM_004820	9420	Hs.657330	NM_004820	ENSG00000172817	CYP7B1	CBAS3|CP7B|SPG5A	cytochrome P450 family 7 subfamily B member 1	protein-coding	0.003937	0.419397	
chunk0158_238_1	chr5	129098581	129098792	+	0	NA	TTS (NR_039776)	TTS (NR_039776)	998	NR_039776	100616175		NR_039776	ENSG00000264563	MIR4633	-	microRNA 4633	ncRNA	0.004739	0.500000	
chunk0151_430_1	chr5	55853814	55854400	+	0	NA	intron (NM_001297572, intron 2 of 10)	MIRb|SINE|MIR	785	NM_001242636	133396	Hs.55378	NM_139017	ENSG00000164509	IL31RA	CRL|CRL3|GLM-R|GLMR|GPL|IL-31RA|PLCA2|PRO21384|hGLM-R	interleukin 31 receptor A	protein-coding	0.006826	0.371380	
chunk0112_172_1	chr20	39900744	39901207	+	0	NA	Intergenic	Intergenic	-103486	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.002160	0.284483	
chunk0157_346_1	chr5	122846085	122846383	+	0	NA	intron (NM_014035, intron 1 of 6)	intron (NM_014035, intron 1 of 6)	769	NM_014035	28966	Hs.483200	NM_014035	ENSG00000064652	SNX24	PRO1284|SBBI31	sorting nexin 24	protein-coding	0.010067	0.401338	
chunk0154_158_1	chr5	79504026	79504501	+	0	NA	intron (NM_001277077, intron 1 of 5)	intron (NM_001277077, intron 1 of 5)	9573	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.004211	0.331933	
chunk0018_440_1	chr1	222933069	222933630	+	0	NA	intron (NM_032890, intron 3 of 9)	intron (NM_032890, intron 3 of 9)	118260	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.005348	0.307829	365(AAGAACAGTATGTTCT,-,0.00),366(AGAACAGTATGTTCTC,+,0.00)
chunk0011_248_1	chr1	150613691	150613959	+	0	NA	Intergenic	Intergenic	15308	NM_207045	2029	Hs.632456	NM_004436	ENSG00000143420	ENSA	ARPP-19e	endosulfine alpha	protein-coding	0.018657	0.405204	
chunk0142_121_1	chr4	94611193	94611550	+	0	NA	intron (NM_001256426, intron 11 of 16)	intron (NM_001256426, intron 11 of 16)	146162	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.002801	0.385475	171(AAGCACAGTATGTCCT,-,0.00),172(AGCACAGTATGTCCTA,+,0.00)
chunk0066_421_1	chr15	39575126	39575847	+	0	NA	Intergenic	Intergenic	-5593	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.009709	0.483380	
chunk0187_99_1	chr8	4586694	4587086	+	0	NA	intron (NM_033225, intron 2 of 69)	intron (NM_033225, intron 2 of 69)	407916	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.007653	0.384224	70(TGGCACTTTCTGTGCT,-,0.00),71(GGCACTTTCTGTGCTC,+,0.00)
chunk0144_298_1	chr4	138367926	138368428	+	0	NA	intron (NR_051987, intron 2 of 2)	intron (NR_051987, intron 2 of 2)	58466	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.001992	0.377734	
chunk0135_9_1	chr3	184134253	184134549	+	0	NA	promoter-TSS (NM_003907)	promoter-TSS (NM_003907)	-621	NM_003907	8893	Hs.283551	NM_003907	ENSG00000145191	EIF2B5	CACH|CLE|EIF-2B|EIF2Bepsilon|LVWM	eukaryotic translation initiation factor 2B subunit epsilon	protein-coding	0.047297	0.565657	
chunk0084_125_1	chr17	76160959	76161677	+	0	NA	intron (NM_052916, intron 11 of 18)	intron (NM_052916, intron 11 of 18)	-20019	NM_001454	2302	Hs.651204	NM_001454	ENSG00000129654	FOXJ1	FKHL13|HFH-4|HFH4	forkhead box J1	protein-coding	0.013928	0.432545	356(CTGGACACCAAGTTCC,-,0.00),357(TGGACACCAAGTTCCC,+,0.00)
chunk0087_432_1	chr18	42392292	42392874	+	0	NA	intron (NR_046174, intron 4 of 9)	intron (NR_046174, intron 4 of 9)	205915	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.001718	0.387650	
chunk0074_97_1	chr16	22189726	22190414	+	0	NA	Intergenic	CpG	-16201	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.081395	0.616836	
chunk0198_191_1	chr8	133516705	133517265	+	0	NA	intron (NM_003033, intron 2 of 8)	intron (NM_003033, intron 2 of 8)	54955	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.005357	0.481283	
chunk0165_168_1	chr6	34180029	34180266	+	0	NA	Intergenic	Intergenic	-24525	NM_001256809	2914	Hs.429018	NM_000841	ENSG00000124493	GRM4	GPRC1D|MGLUR4|mGlu4	glutamate metabotropic receptor 4	protein-coding	0.012658	0.449580	
chunk0004_141_1	chr1	44985774	44986068	+	0	NA	intron (NM_001166588, intron 1 of 9)	intron (NM_001166588, intron 1 of 9)	801	NM_001166588	8891	Hs.533549	NM_020365	ENSG00000070785	EIF2B3	EIF-2B|EIF2Bgamma	eukaryotic translation initiation factor 2B subunit gamma	protein-coding	0.023810	0.501695	
chunk0181_16_1	chr7	77751491	77751906	+	0	NA	intron (NM_198467, intron 3 of 7)	MIRb|SINE|MIR	46732	NM_032936	85025	Hs.19025	NM_032936	ENSG00000135211	TMEM60	C7orf35|DC32	transmembrane protein 60	protein-coding	0.007229	0.358173	170(GAGTACTGACTGTGCC,-,0.00),171(AGTACTGACTGTGCCA,+,0.00),186(AAGGACTAGTTGTTCT,-,0.00),187(AGGACTAGTTGTTCTG,+,0.00)
chunk0143_260_1	chr4	115877017	115877294	+	0	NA	Intergenic	MER77|LTR|ERVL	-422570	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.007220	0.395683	
chunk0120_207_1	chr3	7372143	7372573	+	0	NA	intron (NM_000844, intron 4 of 9)	intron (NM_000844, intron 4 of 9)	162926	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.009302	0.408353	
chunk0084_283_1	chr17	79892644	79892879	+	0	NA	Intergenic	Intergenic	-26596	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.017021	0.576271	153(GAGACAGTGTGTGCAT,+,0.00)
chunk0171_11_1	chr6	119678583	119679286	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-187632	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.005690	0.367898	
chunk0115_126_1	chr21	23219123	23219599	+	0	NA	Intergenic	Intergenic	140077	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.006303	0.278826	
chunk0047_69_1	chr12	67696028	67696304	+	0	NA	Intergenic	Intergenic	33309	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.007246	0.371841	
chunk0097_297_1	chr2	55660701	55661032	+	0	NA	intron (NM_033109, intron 14 of 27)	intron (NM_033109, intron 14 of 27)	33044	NM_033109	87178	Hs.388733	NM_033109	ENSG00000138035	PNPT1	COXPD13|DFNB70|OLD35|PNPASE|old-35	polyribonucleotide nucleotidyltransferase 1	protein-coding	0.006042	0.457831	
chunk0099_241_1	chr2	96960252	96960558	+	0	NA	exon (NM_001122646, exon 6 of 17)	exon (NM_001122646, exon 6 of 17)	26159	NM_001122646	51252	Hs.107922	NM_016490	ENSG00000168754	FAM178B	-	family with sequence similarity 178 member B	protein-coding	0.022876	0.638436	159(AGGGACACTGAGTACT,-,0.00),160(GGGACACTGAGTACTT,+,0.00)
chunk0002_233_1	chr1	20321571	20321863	+	0	NA	intron (NM_001039500, intron 7 of 21)	L2c|LINE|L2	30798	NM_001039500	127731	Hs.205178	NM_144623	ENSG00000158816	VWA5B1	-	von Willebrand factor A domain containing 5B1	protein-coding	0.013699	0.484642	
chunk0081_226_1	chr17	42749205	42749783	+	0	NA	Intergenic	Intergenic	-4441	NM_001991	2145	Hs.194669	NM_001991	ENSG00000108799	EZH1	KMT6B	enhancer of zeste 1 polycomb repressive complex 2 subunit	protein-coding	0.013841	0.528497	
chunk0168_113_1	chr6	81491647	81491864	+	0	NA	Intergenic	Intergenic	260956	NM_017633	55603	Hs.10784	NM_017633	ENSG00000112773	TENT5A	C6orf37|FAM46A|OI18|XTP11	terminal nucleotidyltransferase 5A	protein-coding	0.000000	0.325688	
chunk0137_110_1	chr4	13851417	13851616	+	0	NA	intron (NR_121681, intron 3 of 3)	intron (NR_121681, intron 3 of 3)	196337	NR_121681	101929071	Hs.543714	NR_121681	ENSG00000250634	LINC01182	-	long intergenic non-protein coding RNA 1182	ncRNA	0.015075	0.430000	183(AAGCCCAGGCTGTTCT,-,0.00),184(AGCCCAGGCTGTTCTG,+,0.00)
chunk0079_4_1	chr17	9142824	9143077	+	0	NA	intron (NM_004822, intron 2 of 6)	L2a|LINE|L2	36168	NR_110828	101928266	Hs.639880	NR_110828	ENSG00000262966	LOC101928266	-	uncharacterized LOC101928266	ncRNA	0.011858	0.401575	
chunk0062_52_1	chr14	67385120	67385390	+	0	NA	3' UTR (NM_004094, exon 8 of 8)	3' UTR (NM_004094, exon 8 of 8)	24938	NM_004094	1965	Hs.151777	NM_004094	ENSG00000134001	EIF2S1	EIF-2|EIF-2A|EIF-2alpha|EIF2|EIF2A	eukaryotic translation initiation factor 2 subunit alpha	protein-coding	0.003704	0.424354	
chunk0145_401_1	chr4	152678957	152679228	+	0	NA	intron (NM_152680, intron 1 of 6)	intron (NM_152680, intron 1 of 6)	1073	NM_152680	201799	Hs.518900	NM_152680	ENSG00000170006	TMEM154	-	transmembrane protein 154	protein-coding	0.003690	0.393382	
chunk0021_380_1	chr1	246488791	246489089	+	0	NA	intron (NM_001167740, intron 1 of 11)	MER5A|DNA|hAT-Charlie	18402	NM_001167740	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.020134	0.478261	
chunk0079_293_1	chr17	16918441	16918728	+	0	NA	Intergenic	L2a|LINE|L2	53504	NM_012452	23495	Hs.158341	NM_012452	ENSG00000240505	TNFRSF13B	CD267|CVID|CVID2|IGAD2|RYZN|TACI|TNFRSF14B	TNF receptor superfamily member 13B	protein-coding	0.010453	0.524306	
chunk0017_355_1	chr1	211896918	211897490	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-66432	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.017483	0.418848	
chunk0155_314_1	chr5	96624614	96625026	+	0	NA	intron (NR_130776, intron 4 of 4)	intron (NR_130776, intron 4 of 4)	-37217	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.007282	0.384988	
chunk0015_26_1	chr1	184386969	184387183	+	0	NA	promoter-TSS (NM_030806)	promoter-TSS (NM_030806)	60	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.130841	0.725581	
chunk0180_440_1	chr7	77008000	77008357	+	0	NA	intron (NR_023383, intron 6 of 10)	intron (NR_023383, intron 6 of 10)	27356	NR_023383	441263	Hs.675888	NR_023383	ENSG00000265479	DTX2P1-UPK3BP1-PMS2P11	PMS2L11	DTX2P1-UPK3BP1-PMS2P11 readthrough, transcribed pseudogene	pseudo	0.028011	0.564246	
chunk0191_115_1	chr8	48269689	48270353	+	0	NA	Intergenic	Arthur1C|DNA|hAT-Tip100	261586	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.010542	0.467669	271(AGGTACAGAGTGTTCC,-,0.00),272(GGTACAGAGTGTTCCT,+,0.00),536(GGCCCATGCTGTCCTT,+,0.00)
chunk0033_178_1	chr11	15901709	15902043	+	0	NA	Intergenic	Intergenic	67745	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.014970	0.507463	
chunk0082_410_1	chr17	61014359	61014742	+	0	NA	intron (NM_017679, intron 15 of 23)	L1MC|LINE|L1	336739	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.000000	0.348958	
chunk0119_71_1	chr22	41239889	41240138	+	0	NA	intron (NM_138481, intron 1 of 5)	intron (NM_138481, intron 1 of 5)	918	NM_138481	150356	Hs.344488	NM_138481	ENSG00000100399	CHADL	SLRR4B	chondroadherin like	protein-coding	0.008032	0.532000	
chunk0207_382_1	chr9	136229389	136229971	+	0	NA	intron (NM_181701, intron 1 of 11)	intron (NM_181701, intron 1 of 11)	16161	NM_181701	169714	Hs.144073	NM_181701	ENSG00000165661	QSOX2	QSCN6L1|SOXN	quiescin sulfhydryl oxidase 2	protein-coding	0.022337	0.490566	
chunk0161_14_1	chr5	165629186	165629896	+	0	NA	Intergenic	Intergenic	1159262	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.004225	0.355837	
chunk0185_148_1	chr7	127666421	127667012	+	0	NA	intron (NM_014390, intron 1 of 23)	intron (NM_014390, intron 1 of 23)	14568	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.006768	0.400338	
chunk0105_13_1	chr2	181973255	181973454	+	0	NA	intron (NR_048567, intron 1 of 4)	intron (NR_048567, intron 1 of 4)	-12470	NM_001261425	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.010050	0.335000	
chunk0026_68_1	chr10	61179076	61180062	+	0	NA	Intergenic	UCON4|Unknown|Unknown	163294	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.005071	0.360689	
chunk0020_243_1	chr1	235948665	235949440	+	0	NA	Intergenic	Intergenic	-65344	NR_102436	1130	Hs.532411	NM_000081	ENSG00000143669	LYST	CHS|CHS1	lysosomal trafficking regulator	protein-coding	0.007742	0.439433	384(CAGAACATCAAGTTCC,-,0.00),385(AGAACATCAAGTTCCT,+,0.00)
chunk0210_218_1	chrX	82093471	82093856	+	0	NA	Intergenic	L1PB4|LINE|L1	-891721	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.002597	0.290155	
chunk0152_393_1	chr5	64737116	64737315	+	0	NA	intron (NM_173829, intron 3 of 4)	L1M3|LINE|L1	31454	NM_173829	285672	Hs.69504	NM_173829	ENSG00000153006	SREK1IP1	P18SRP|SFRS12IP1	SREK1 interacting protein 1	protein-coding	0.000000	0.330000	
chunk0205_196_1	chr9	109241060	109241795	+	0	NA	3' UTR (NM_018424, exon 16 of 16)	3' UTR (NM_018424, exon 16 of 16)	-74136	NM_014334	23732	Hs.347537	NM_014334	ENSG00000260230	FRRS1L	C9orf4|CG-6|CG6|EIEE37	ferric chelate reductase 1 like	protein-coding	0.009524	0.388587	
chunk0177_201_1	chr7	23844870	23845643	+	0	NA	Intergenic	L1PA6|LINE|L1	134930	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.014230	0.531008	
chunk0048_390_1	chr12	87319462	87319989	+	0	NA	Intergenic	MIR|SINE|MIR	464986	NR_033410	400058	Hs.572212	NR_033410		MKRN9P	MKRN5|MKRN9|MKRNP6|RNF65|ZNF127L3	makorin ring finger protein 9, pseudogene	pseudo	0.000000	0.297348	
chunk0016_336_1	chr1	201799127	201799378	+	0	NA	intron (NM_020443, intron 15 of 29)	L1MC4|LINE|L1	-9359	NR_031599	100302158		NR_031599	ENSG00000221028	MIR1231	MIRN1231|hsa-mir-1231	microRNA 1231	ncRNA	0.000000	0.353175	
chunk0139_131_1	chr4	53274852	53275051	+	0	NA	intron (NM_152540, intron 3 of 8)	intron (NM_152540, intron 3 of 8)	91124	NM_152540	152579	Hs.302287	NM_152540	ENSG00000184178	SCFD2	STXBP1L1	sec1 family domain containing 2	protein-coding	0.000000	0.340000	
chunk0086_393_1	chr18	26631201	26631616	+	0	NA	intron (NM_198991, intron 1 of 5)	Tigger3a|DNA|TcMar-Tigger	8936	NM_198991	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.004819	0.348558	
chunk0157_218_1	chr5	119334853	119335271	+	0	NA	intron (NM_001286814, intron 1 of 1)	intron (NM_001286814, intron 1 of 1)	1887	NM_001286814	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.021531	0.460621	
chunk0175_380_1	chr6	168196279	168196864	+	0	NA	Intergenic	Intergenic	-46367	NR_110870	101929420	Hs.571211	NR_110870	ENSG00000234647	LOC101929420	-	uncharacterized LOC101929420	ncRNA	0.025641	0.416382	
chunk0090_308_1	chr18	75395734	75396158	+	0	NA	Intergenic	Intergenic	31757	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.016509	0.428235	
chunk0092_242_1	chr19	32826682	32827111	+	0	NA	Intergenic	Intergenic	42881	NM_001243036	11136	Hs.743345	NM_014270	ENSG00000021488	SLC7A9	BAT1|CSNU3	solute carrier family 7 member 9	protein-coding	0.011655	0.425581	
chunk0061_47_1	chr14	56199201	56199617	+	0	NA	intron (NM_021255, intron 2 of 5)	intron (NM_021255, intron 2 of 5)	81034	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.009615	0.386091	
chunk0127_398_1	chr3	102350004	102350645	+	0	NA	Intergenic	Intergenic	-84691	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.004680	0.372274	
chunk0133_448_1	chr3	175121118	175121499	+	0	NA	intron (NM_207015, intron 2 of 13)	intron (NM_207015, intron 2 of 13)	-6066	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.005249	0.416230	
chunk0080_170_1	chr17	28525165	28525364	+	0	NA	intron (NM_003593, intron 2 of 7)	Tigger19b|DNA|TcMar-Tigger	1323	NM_003593	8456	Hs.58611	NM_003593	ENSG00000109101	FOXN1	FKHL20|RONU|WHN	forkhead box N1	protein-coding	0.000000	0.490000	
chunk0190_212_1	chr8	35714312	35714771	+	0	NA	intron (NM_080872, intron 8 of 16)	intron (NM_080872, intron 8 of 16)	-4221	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.006536	0.400000	
chunk0006_32_1	chr1	64161572	64162235	+	0	NA	intron (NM_005012, intron 8 of 8)	intron (NM_005012, intron 8 of 8)	-41904	NM_152489	148581	Hs.388746	NM_152489	ENSG00000177414	UBE2U	-	ubiquitin conjugating enzyme E2 U	protein-coding	0.003017	0.375000	
chunk0166_89_1	chr6	43706538	43707177	+	0	NA	Intergenic	Intergenic	-19045	NM_018135	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.015649	0.490625	
chunk0053_270_1	chr13	33172392	33172913	+	0	NA	intron (NM_001243476, intron 5 of 17)	intron (NM_001243476, intron 5 of 17)	13427	NM_178007	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.005758	0.379310	227(GGGAACAGTGTGTTCT,-,0.00),228(GGAACAGTGTGTTCTC,+,0.00)
chunk0090_229_1	chr18	73707025	73707373	+	0	NA	Intergenic	L1MC1|LINE|L1	382258	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.002874	0.372493	
chunk0054_61_1	chr13	41811899	41812204	+	0	NA	intron (NM_015058, intron 16 of 44)	MIRb|SINE|MIR	149034	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.009836	0.362745	
chunk0038_78_1	chr11	83139161	83139942	+	0	NA	Intergenic	MIRc|SINE|MIR	-17544	NM_015885	51585	Hs.128959	NM_015885	ENSG00000165494	PCF11	-	PCF11 cleavage and polyadenylation factor subunit	protein-coding	0.011524	0.419437	
chunk0211_406_1	chrX	128769803	128770044	+	0	NA	Intergenic	Intergenic	-717520	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.012448	0.417355	100(AAGCTCAATCTGTTCT,-,0.00),101(AGCTCAATCTGTTCTC,+,0.00)
chunk0179_152_1	chr7	46315588	46316223	+	0	NA	Intergenic	MIR|SINE|MIR	-394633	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.007874	0.421384	
chunk0065_289_1	chr14	102667539	102668182	+	0	NA	intron (NM_015156, intron 2 of 11)	intron (NM_015156, intron 2 of 11)	75201	NM_015156	23186	Hs.510521	NM_015156	ENSG00000089902	RCOR1	COREST|RCOR	REST corepressor 1	protein-coding	0.009331	0.408385	
chunk0129_190_1	chr3	121229871	121230818	+	0	NA	intron (NM_014980, intron 11 of 27)	MER101-int|LTR|ERV1	180704	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.004224	0.302743	
chunk0088_407_1	chr18	54636944	54637498	+	0	NA	Intergenic	Intergenic	46062	NM_173629	284254	Hs.376146	NM_173629	ENSG00000178690	DYNAP	C18orf26	dynactin associated protein	protein-coding	0.005415	0.360360	
chunk0102_62_1	chr2	142863522	142863812	+	0	NA	Intergenic	Intergenic	-13959	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.000000	0.347079	
chunk0088_173_1	chr18	47213763	47214214	+	0	NA	intron (NM_001278063, intron 6 of 6)	intron (NM_001278063, intron 6 of 6)	35195	NM_001278063	652991	Hs.585834	NM_001037802	ENSG00000215474	SKOR2	CH18515|CORL2|FUSSEL18	SKI family transcriptional corepressor 2	protein-coding	0.002217	0.418142	252(GGGCACAAGGAGTTCC,-,0.00),253(GGCACAAGGAGTTCCA,+,0.00)
chunk0025_46_1	chr10	49328425	49328798	+	0	NA	Intergenic	Intergenic	29469	NM_001135196	118461	Hs.585480	NM_199459	ENSG00000177354	C10orf71	CEFIP	chromosome 10 open reading frame 71	protein-coding	0.013405	0.526738	
chunk0084_31_1	chr17	73634515	73635055	+	0	NA	intron (NM_001144952, intron 1 of 44)	MIR|SINE|MIR	9303	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.011111	0.438078	291(CAGAACACTGTGTCCT,-,0.00),292(AGAACACTGTGTCCTA,+,0.00)
chunk0147_248_1	chr4	183130550	183131246	+	0	NA	intron (NM_024949, intron 1 of 22)	MLT2D|LTR|ERVL	31588	NM_024949	80014	Hs.333179	NM_024949	ENSG00000151718	WWC2	BOMB	WW and C2 domain containing 2	protein-coding	0.010057	0.375897	
chunk0184_94_1	chr7	113366579	113367509	+	0	NA	Intergenic	Intergenic	-248462	NR_015442									0.002151	0.349087	
chunk0003_80_1	chr1	31475140	31475572	+	0	NA	Intergenic	L1PBa|LINE|L1	-24729	NR_034112	149086	Hs.729905	NR_034112	ENSG00000260386	LDC1P	LINC01225	leucine decarboxylase 1, pseudogene	pseudo	0.000000	0.341801	
chunk0116_390_1	chr21	42342105	42342386	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	8854	NM_005423	7032	Hs.2979	NM_005423	ENSG00000160181	TFF2	SML1|SP	trefoil factor 2	protein-coding	0.014235	0.418440	
chunk0074_36_1	chr16	20647713	20648192	+	0	NA	intron (NM_052956, intron 6 of 12)	LTR14B|LTR|ERVK	43304	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.008351	0.458333	
chunk0032_201_1	chr11	7281739	7282313	+	0	NA	intron (NM_175733, intron 1 of 6)	intron (NM_175733, intron 1 of 6)	30076	NM_175733	143425	Hs.177193	NM_175733	ENSG00000170743	SYT9	-	synaptotagmin 9	protein-coding	0.001742	0.351304	
chunk0148_336_1	chr5	14272017	14272673	+	0	NA	intron (NM_007118, intron 2 of 56)	intron (NM_007118, intron 2 of 56)	128625	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.009146	0.343988	
chunk0126_135_1	chr3	76100014	76100441	+	0	NA	Intergenic	Intergenic	-314644	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.007026	0.357477	
chunk0108_297_1	chr2	235027785	235027984	+	0	NA	intron (NM_014521, intron 2 of 5)	intron (NM_014521, intron 2 of 5)	75900	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.040201	0.530000	
chunk0094_247_1	chr2	7158119	7158463	+	0	NA	Intergenic	Intergenic	-80411	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.000000	0.301449	
chunk0171_325_1	chr6	129801832	129802340	+	0	NA	Intergenic	Intergenic	59185	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.007874	0.471513	
chunk0007_191_1	chr1	80987895	80988401	+	0	NA	Intergenic	Intergenic	346861	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.001976	0.319527	
chunk0111_69_1	chr20	23040089	23040318	+	0	NA	Intergenic	L2a|LINE|L2	4783	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.013100	0.547826	44(GGGCACAAGGTGTTCC,-,0.00),45(GGCACAAGGTGTTCCT,+,0.00),77(GGGAACAGCATGTGCA,-,0.00),78(GGAACAGCATGTGCAA,+,0.00)
chunk0046_170_1	chr12	58526350	58526951	+	0	NA	Intergenic	Intergenic	-65052	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.001664	0.337209	
chunk0162_470_1	chr5	181263527	181264164	+	0	NA	non-coding (NR_102759, exon 2 of 2)	non-coding (NR_102759, exon 2 of 2)	2633	NR_102762	100507602	Hs.126768	NR_102759	ENSG00000248275	TRIM52-AS1	-	TRIM52 antisense RNA 1 (head to head)	ncRNA	0.007849	0.468652	
chunk0040_393_1	chr11	120316841	120317118	+	0	NA	intron (NM_014352, intron 11 of 12)	intron (NM_014352, intron 11 of 12)	-8150	NM_001198671	219902	Hs.643516	NM_174926	ENSG00000181264	TLCD5	TMEM136	TLC domain containing 5	protein-coding	0.007220	0.546763	
chunk0009_147_1	chr1	104911390	104911636	+	0	NA	Intergenic	LTR10A|LTR|ERV1	707422	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.000000	0.469636	
chunk0164_96_1	chr6	20288034	20288480	+	0	NA	Intergenic	L1MB7|LINE|L1	-75793	NR_073465	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.006726	0.402685	
chunk0063_3_1	chr14	75864380	75865072	+	0	NA	intron (NM_015072, intron 29 of 31)	intron (NM_015072, intron 29 of 31)	117296	NM_003239	7043	Hs.592317	NM_003239	ENSG00000119699	TGFB3	ARVD|ARVD1|LDS5|RNHF|TGF-beta3	transforming growth factor beta 3	protein-coding	0.005780	0.326118	
chunk0021_448_1	chr1	248692516	248692715	+	0	NA	Intergenic	Intergenic	-4447	NR_125950	101928226		NR_125950		LYPD9P	-	LY6/PLAUR domain containing 9, pseudogene	pseudo	0.025126	0.515000	
chunk0028_240_1	chr10	90024812	90025364	+	0	NA	Intergenic	Intergenic	-67715	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.001812	0.311031	
chunk0211_413_1	chrX	128882992	128883381	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	640319	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.010283	0.353846	
chunk0141_355_1	chr4	87866174	87866420	+	0	NA	Intergenic	MER4CL34|LTR|ERV1	31594	NM_001291183	56955	Hs.676357	NM_020203	ENSG00000152595	MEPE	OF45	matrix extracellular phosphoglycoprotein	protein-coding	0.000000	0.404858	
chunk0180_388_1	chr7	74535186	74535719	+	0	NA	intron (NM_001199207, intron 10 of 26)	MIR|SINE|MIR	81662	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.024390	0.591760	167(CTGGACAGAGAGTACT,-,0.00),168(TGGACAGAGAGTACTA,+,0.00)
chunk0136_268_1	chr3	194440663	194441196	+	0	NA	intron (NM_024524, intron 15 of 31)	intron (NM_024524, intron 15 of 31)	27310	NM_024524	79572	Hs.529609	NM_024524	ENSG00000133657	ATP13A3	AFURS1	ATPase 13A3	protein-coding	0.003752	0.389513	
chunk0110_173_1	chr20	14307775	14308325	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	29617	NM_198391	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.003636	0.353902	
chunk0075_178_1	chr16	52068168	52068781	+	0	NA	intron (NM_001242473, intron 1 of 5)	intron (NM_001242473, intron 1 of 5)	5461	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.006525	0.368078	178(GTGAACACCTTGTCCA,-,0.00)
chunk0059_149_1	chr14	32109704	32110410	+	0	NA	intron (NM_001173, intron 2 of 6)	L1M6|LINE|L1	32768	NM_001173	394	Hs.592313	NM_001173	ENSG00000100852	ARHGAP5	GFI2|RhoGAP5|p190-B|p190BRhoGAP	Rho GTPase activating protein 5	protein-coding	0.007082	0.369165	684(AAGCTCAAGCTGTCCT,-,0.00),685(AGCTCAAGCTGTCCTT,+,0.00)
chunk0191_32_1	chr8	43050666	43051207	+	0	NA	Intergenic	L1ME3B|LINE|L1	-5363	NM_002027	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.007394	0.398524	
chunk0062_140_1	chr14	68937868	68938302	+	0	NA	intron (NM_001130004, intron 1 of 21)	intron (NM_001130004, intron 1 of 21)	41281	NM_001130005	87	Hs.235750	NM_001102	ENSG00000072110	ACTN1	BDPLT15	actinin alpha 1	protein-coding	0.016129	0.572414	
chunk0205_358_1	chr9	113521773	113522348	+	0	NA	intron (NM_017790, intron 14 of 17)	intron (NM_017790, intron 14 of 17)	-14417	NM_001276260	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.005217	0.381944	
chunk0181_41_1	chr7	78713748	78713947	+	0	NA	intron (NM_001301128, intron 2 of 20)	intron (NM_001301128, intron 2 of 20)	-295141	NR_046689	100874021	Hs.128252	NR_046689	ENSG00000226978	MAGI2-AS2	-	MAGI2 antisense RNA 2	ncRNA	0.015075	0.340000	
chunk0139_318_1	chr4	58260399	58260922	+	0	NA	Intergenic	L1MC1|LINE|L1	834788	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003824	0.351145	
chunk0099_359_1	chr2	100755338	100755965	+	0	NA	Intergenic	L2c|LINE|L2	-64500	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.004785	0.410828	
chunk0165_418_1	chr6	39279580	39279842	+	0	NA	Intergenic	Intergenic	34749	NM_031460	89822	Hs.162282	NM_031460	ENSG00000124780	KCNK17	K2p17.1|TALK-2|TALK2|TASK-4|TASK4	potassium two pore domain channel subfamily K member 17	protein-coding	0.007634	0.585551	167(CAGAACAGTATGTCTT,-,0.00),168(AGAACAGTATGTCTTG,+,0.00)
chunk0171_46_1	chr6	120979473	120979989	+	0	NA	Intergenic	Intergenic	354769	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.000000	0.326886	230(AGGAACATTTTGTTCT,-,0.00),231(GGAACATTTTGTTCTT,+,0.00)
chunk0160_110_1	chr5	150777314	150777513	+	0	NA	promoter-TSS (NM_032947)	promoter-TSS (NM_032947)	-533	NM_032947	85027	Hs.29444	NM_032947	ENSG00000256235	SMIM3	C5orf62|MST150|NID67	small integral membrane protein 3	protein-coding	0.000000	0.475000	
chunk0039_202_1	chr11	100916308	100916777	+	0	NA	intron (NM_152432, intron 5 of 23)	intron (NM_152432, intron 5 of 23)	-75538	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.004264	0.321277	
chunk0122_38_1	chr3	28125569	28125776	+	0	NA	Intergenic	L1MC2|LINE|L1	-115961	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.000000	0.322115	
chunk0120_98_1	chr3	4413409	4413844	+	0	NA	intron (NM_182760, intron 6 of 8)	intron (NM_182760, intron 6 of 8)	53656	NM_182760	285362	Hs.350475	NM_182760	ENSG00000144455	SUMF1	AAPA3037|FGE|UNQ3037	sulfatase modifying factor 1	protein-coding	0.002299	0.378440	
chunk0052_55_1	chr13	21014482	21014976	+	0	NA	intron (NM_014572, intron 2 of 7)	intron (NM_014572, intron 2 of 7)	46854	NM_014572	26524	Hs.78960	NM_014572	ENSG00000150457	LATS2	KPM	large tumor suppressor kinase 2	protein-coding	0.008097	0.393939	
chunk0212_69_1	chrY	11333864	11334452	+	0	NA	Intergenic	LSAU|Satellite|Satellite	1087432	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.051020	0.607810	
chunk0074_425_1	chr16	46390286	46390885	+	0	NA	Intergenic	Intergenic	178512	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.055092	0.376667	
chunk0025_325_1	chr10	57848933	57849538	+	0	NA	Intergenic	Intergenic	418699	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.003306	0.298680	
chunk0206_320_1	chr9	125214351	125214625	+	0	NA	intron (NM_001174152, intron 5 of 8)	intron (NM_001174152, intron 5 of 8)	13905	NM_005833	10244	Hs.19012	NM_005833	ENSG00000136933	RABEPK	RAB9P40|bA65N13.1|p40	Rab9 effector protein with kelch motifs	protein-coding	0.014599	0.400000	
chunk0003_376_1	chr1	39653066	39653879	+	0	NA	Intergenic	Intergenic	-13796	NM_014571	26508	Hs.472566	NM_014571	ENSG00000163909	HEYL	HESR3|HEY3|HRT3|bHLHb33	hes related family bHLH transcription factor with YRPW motif like	protein-coding	0.019680	0.497543	
chunk0003_367_1	chr1	39459738	39460118	+	0	NA	intron (NM_012090, intron 86 of 92)	intron (NM_012090, intron 86 of 92)	-31718	NM_181809	353500	Hs.472497	NM_181809	ENSG00000183682	BMP8A	-	bone morphogenetic protein 8a	protein-coding	0.002632	0.372703	
chunk0188_443_1	chr8	19306636	19306976	+	0	NA	Intergenic	MIRc|SINE|MIR	-6764	NM_001174160	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.005882	0.454545	
chunk0036_189_1	chr11	62939054	62939555	+	0	NA	Intergenic	L1ME5|LINE|L1	-17764	NM_000738	1128	Hs.632119	NM_000738	ENSG00000168539	CHRM1	HM1|M1|M1R	cholinergic receptor muscarinic 1	protein-coding	0.013972	0.446215	
chunk0196_371_1	chr8	115263389	115263744	+	0	NA	Intergenic	Intergenic	404446	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.008451	0.306180	
chunk0182_451_1	chr7	101941607	101942381	+	0	NA	intron (NM_001202544, intron 2 of 21)	intron (NM_001202544, intron 2 of 21)	124392	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.015504	0.452903	398(CAGTACACACTGTTTC,-,0.00),399(AGTACACACTGTTTCC,+,0.00)
chunk0006_115_1	chr1	65565691	65566074	+	0	NA	intron (NM_001003680, intron 3 of 19)	(CA)n|Simple_repeat|Simple_repeat	40193	NM_001198687	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.005222	0.369792	247(CTGTACATGTTGTTCT,-,0.00),248(TGTACATGTTGTTCTG,+,0.00)
chunk0134_137_1	chr3	177590837	177591248	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	149121	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.004866	0.458738	
chunk0213_8_1	chrY	19978812	19979278	+	0	NA	Intergenic	Intergenic	-234106	NM_004653	8284	Hs.80358	NM_004653	ENSG00000012817	KDM5D	HY|HYA|JARID1D|SMCY	lysine demethylase 5D	protein-coding	0.004292	0.374732	
chunk0072_110_1	chr15	91379935	91380221	+	0	NA	Intergenic	L1MC1|LINE|L1	-83261	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.003497	0.344948	
chunk0058_337_1	chr14	28695141	28695792	+	0	NA	Intergenic	Intergenic	69853	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.003072	0.363497	
chunk0112_413_1	chr20	47294816	47295085	+	0	NA	intron (NM_001281771, intron 4 of 20)	intron (NM_001281771, intron 4 of 20)	-23552	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.007435	0.351852	109(TGGAACAAAATGTACC,-,0.00),110(GGAACAAAATGTACCA,+,0.00)
chunk0010_443_1	chr1	120176477	120176684	+	0	NA	promoter-TSS (NM_004892)	promoter-TSS (NM_004892)	-59	NM_004892	9554	Hs.632438	NM_004892	ENSG00000265808	SEC22B	ERS-24|SEC22L1	SEC22 homolog B, vesicle trafficking protein (gene/pseudogene)	protein-coding	0.053140	0.548077	
chunk0138_257_1	chr4	39898624	39898906	+	0	NA	intron (NM_001100400, intron 15 of 15)	intron (NM_001100400, intron 15 of 15)	79191	NM_001100399	23244	Hs.331431	NM_015200	ENSG00000121892	PDS5A	PIG54|SCC-112|SCC112	PDS5 cohesin associated factor A	protein-coding	0.003546	0.307420	
chunk0124_348_1	chr3	58452168	58452638	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-18551	NM_000925	5162	Hs.161357	NM_000925	ENSG00000168291	PDHB	PDHBD|PDHE1-B|PDHE1B|PHE1B	pyruvate dehydrogenase E1 beta subunit	protein-coding	0.002128	0.426752	
chunk0003_245_1	chr1	36163377	36163827	+	0	NA	intron (NM_001286365, intron 1 of 15)	intron (NM_001286365, intron 1 of 15)	-7549	NM_001270895	27095	Hs.523131	NM_014408	ENSG00000054116	TRAPPC3	BET3	trafficking protein particle complex 3	protein-coding	0.002222	0.339246	
chunk0127_156_1	chr3	94570580	94570918	+	0	NA	Intergenic	Intergenic	-367514	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.002959	0.292035	
chunk0050_121_1	chr12	102061018	102061749	+	0	NA	intron (NM_016053, intron 1 of 6)	intron (NM_016053, intron 1 of 6)	741	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.025992	0.454918	
chunk0168_106_1	chr6	80228942	80229298	+	0	NA	intron (NM_000056, intron 8 of 10)	L2a|LINE|L2	122493	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.002809	0.397759	
chunk0121_178_1	chr3	20055675	20056315	+	0	NA	intron (NM_003884, intron 1 of 17)	L1ME2|LINE|L1	15963	NM_003884	8850	Hs.533055	NM_003884	ENSG00000114166	KAT2B	CAF|P/CAF|PCAF	lysine acetyltransferase 2B	protein-coding	0.007812	0.385335	224(TAGTACATACTGTTCT,-,0.00),225(AGTACATACTGTTCTT,+,0.00)
chunk0083_221_1	chr17	67120674	67120901	+	0	NA	intron (NM_014877, intron 26 of 32)	intron (NM_014877, intron 26 of 32)	76251	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.000000	0.333333	
chunk0156_160_1	chr5	107440544	107440840	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	230203	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.006757	0.417508	
chunk0137_460_1	chr4	30077832	30078362	+	0	NA	Intergenic	L1PA13|LINE|L1	-642311	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.003774	0.359699	
chunk0203_112_1	chr9	84718629	84718976	+	0	NA	intron (NM_001007097, intron 6 of 12)	intron (NM_001007097, intron 6 of 12)	48425	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.008646	0.390805	210(AAGTACAGATTGTTTT,-,0.00),211(AGTACAGATTGTTTTT,+,0.00)
chunk0094_42_1	chr2	2102384	2102798	+	0	NA	intron (NM_015025, intron 3 of 24)	intron (NM_015025, intron 3 of 24)	-216641	NR_024468	730811	Hs.629472	NR_024468	ENSG00000225619	MYT1L-AS1	-	MYT1L antisense RNA 1	ncRNA	0.009662	0.392771	
chunk0037_151_1	chr11	73486988	73487213	+	0	NA	intron (NM_001286050, intron 1 of 8)	intron (NM_001286050, intron 1 of 8)	110432	NM_032871	84957	Hs.533720	NM_032871	ENSG00000054967	RELT	AI3C|TNFRSF19L|TRLT	RELT TNF receptor	protein-coding	0.004444	0.371681	
chunk0109_103_1	chr20	2337045	2337520	+	0	NA	intron (NM_003245, intron 11 of 12)	intron (NM_003245, intron 11 of 12)	41315	NM_003245	7053	Hs.2022	NM_003245	ENSG00000125780	TGM3	TGE|UHS2	transglutaminase 3	protein-coding	0.012632	0.502101	343(GAGAACATTCTGTACT,-,0.00),344(AGAACATTCTGTACTA,+,0.00)
chunk0202_104_1	chr9	72441033	72441295	+	0	NA	Intergenic	L2c|LINE|L2	-75917	NM_001102421	7763	Hs.406096	NM_006007	ENSG00000107372	ZFAND5	ZA20D2|ZFAND5A|ZNF216	zinc finger AN1-type containing 5	protein-coding	0.011450	0.463878	102(GGGCACAGACTGTGCA,-,0.00),103(GGCACAGACTGTGCAC,+,0.00)
chunk0008_339_1	chr1	95640625	95641409	+	0	NA	Intergenic	Intergenic	130901	NR_110621	100996635	Hs.639548	NR_110621	ENSG00000228971	LINC02607	-	long intergenic non-protein coding RNA 2607	ncRNA	0.008929	0.391083	
chunk0044_153_1	chr12	29743054	29743389	+	0	NA	intron (NM_001193451, intron 5 of 17)	MIR|SINE|MIR	40589	NM_001193451	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.011940	0.431548	
chunk0032_350_1	chr11	10432464	10432731	+	0	NA	Intergenic	L1MB7|LINE|L1	-17724	NM_001172431	272	Hs.501890	NM_000480	ENSG00000133805	AMPD3	-	adenosine monophosphate deaminase 3	protein-coding	0.000000	0.369403	
chunk0010_145_1	chr1	115075968	115076233	+	0	NA	intron (NM_001308315, intron 1 of 6)	intron (NM_001308315, intron 1 of 6)	13400	NM_001308316	10100	Hs.310458	NM_005725	ENSG00000134198	TSPAN2	NET3|TSN2|TSPAN-2	tetraspanin 2	protein-coding	0.011321	0.439850	
chunk0113_5_1	chr20	49278686	49278906	+	0	NA	promoter-TSS (NR_002433)	promoter-TSS (NR_002433)	-149	NR_002433	26765		NR_002433	ENSG00000209042	SNORD12C	E2|E2-1|E3|RNU106|SNORD106|U106	small nucleolar RNA, C/D box 12C	snoRNA	0.045455	0.538462	60(GAAACTCCATGTTCTT,+,0.00)
chunk0069_397_1	chr15	67785346	67785631	+	0	NA	intron (NM_001206804, intron 21 of 21)	intron (NM_001206804, intron 21 of 21)	-34216	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.017544	0.482517	
chunk0094_28_1	chr2	1631699	1632519	+	0	NA	3' UTR (NM_012293, exon 23 of 23)	3' UTR (NM_012293, exon 23 of 23)	112438	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.009756	0.408039	
chunk0191_163_1	chr8	49713018	49713282	+	0	NA	Intergenic	L1MDb|LINE|L1	-196639	NM_001287813	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.007576	0.471698	
chunk0048_233_1	chr12	81551598	81551837	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-39326	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.004184	0.295833	
chunk0107_17_1	chr2	210207926	210208370	+	0	NA	intron (NM_001608, intron 5 of 10)	intron (NM_001608, intron 5 of 10)	17343	NM_001608	33	Hs.471277	NM_001608	ENSG00000115361	ACADL	ACAD4|LCAD	acyl-CoA dehydrogenase long chain	protein-coding	0.002252	0.325843	
chunk0006_413_1	chr1	76012639	76012913	+	0	NA	intron (NR_125939, intron 1 of 2)	intron (NR_125939, intron 1 of 2)	1452	NR_125939	101927342	Hs.216363	NR_125939		LOC101927342	-	uncharacterized LOC101927342	ncRNA	0.000000	0.450909	
chunk0152_230_1	chr5	60463170	60463784	+	0	NA	intron (NM_001165899, intron 1 of 16)	MER5A|DNA|hAT-Charlie	-24236	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.006515	0.469919	
chunk0109_405_1	chr2	240447843	240448200	+	0	NA	intron (NM_002081, intron 1 of 8)	intron (NM_002081, intron 1 of 8)	-7980	NR_029702	406941		NR_029702	ENSG00000207611	MIR149	MIRN149|mir-149	microRNA 149	ncRNA	0.042017	0.639665	186(TGGAACACAGTGTCCC,-,0.00),187(GGAACACAGTGTCCCC,+,0.00)
chunk0087_361_1	chr18	41237739	41237974	+	0	NA	Intergenic	L1PA8A|LINE|L1	282741	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.004255	0.440678	112(AGGAACAGCATGTTCT,-,0.00),113(GGAACAGCATGTTCTC,+,0.00)
chunk0210_212_1	chrX	81286023	81286346	+	0	NA	intron (NM_003022, intron 3 of 3)	intron (NM_003022, intron 3 of 3)	-84242	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.006192	0.314815	
chunk0149_128_1	chr5	19667342	19667541	+	0	NA	intron (NM_001167667, intron 5 of 12)	intron (NM_001167667, intron 5 of 12)	218831	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.195000	
chunk0168_165_1	chr6	83829885	83830270	+	0	NA	Intergenic	Intergenic	-23189	NM_001009994	134701	Hs.149454	NM_001009994	ENSG00000203877	RIPPLY2	C6orf159|SCDO6|dJ237I15.1	ripply transcriptional repressor 2	protein-coding	0.002597	0.391192	183(GAGGACAGTTTGTTCT,-,0.00),184(AGGACAGTTTGTTCTC,+,0.00)
chunk0089_295_1	chr18	63262857	63263146	+	0	NA	intron (NM_000633, intron 2 of 2)	intron (NM_000633, intron 2 of 2)	56379	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.010381	0.441379	59(GGGAACAAAGTGATCC,-,0.00),60(GGAACAAAGTGATCCA,+,0.00)
chunk0022_303_1	chr10	15656740	15656980	+	0	NA	intron (NM_001291494, intron 9 of 28)	intron (NM_001291494, intron 9 of 28)	63475	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.012500	0.456432	
chunk0179_158_1	chr7	46476507	46476809	+	0	NA	Intergenic	Intergenic	-555386	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.009934	0.369637	157(AAGAACATTCTGTTTT,-,0.00),158(AGAACATTCTGTTTTC,+,0.00)
chunk0057_229_1	chr13	104324860	104325512	+	0	NA	Intergenic	L2a|LINE|L2	899986	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.007669	0.358346	
chunk0195_79_1	chr8	94081905	94082508	+	0	NA	Intergenic	Intergenic	126381	NM_004063	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.011609	0.480132	
chunk0074_285_1	chr16	29341959	29342215	+	0	NA	intron (NR_002939, intron 5 of 8)	intron (NR_002939, intron 5 of 8)	39800	NR_002939	440352	Hs.658149	NR_002939		SNX29P2	RUNDC2C	sorting nexin 29 pseudogene 2	pseudo	0.019531	0.412451	
chunk0108_121_1	chr2	229832076	229832416	+	0	NA	intron (NM_001284214, intron 6 of 41)	MER58A|DNA|hAT-Charlie	47882	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.005882	0.346041	
chunk0190_218_1	chr8	35727266	35727500	+	0	NA	intron (NM_080872, intron 10 of 16)	intron (NM_080872, intron 10 of 16)	-17063	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.008547	0.412766	
chunk0188_145_1	chr8	9674735	9674980	+	0	NA	intron (NM_003747, intron 3 of 26)	intron (NM_003747, intron 3 of 26)	-66815	NR_030327	693182		NR_030327	ENSG00000207701	MIR597	MIRN597|hsa-mir-597|mir-597	microRNA 597	ncRNA	0.000000	0.365854	
chunk0057_308_1	chr13	106552603	106553208	+	0	NA	intron (NM_018011, intron 3 of 3)	intron (NM_018011, intron 3 of 3)	15261	NM_018011	55082	Hs.508644	NM_018011	ENSG00000134884	ARGLU1	-	arginine and glutamate rich 1	protein-coding	0.006612	0.310231	
chunk0133_442_1	chr3	175101884	175102669	+	0	NA	intron (NM_207015, intron 2 of 13)	L1ME3G|LINE|L1	12966	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.002548	0.304071	
chunk0114_420_1	chr20	64149776	64150068	+	0	NA	Intergenic	Intergenic	-14552	NM_004535	4661	Hs.279562	NM_004535	ENSG00000196132	MYT1	C20orf36|MTF1|MYTI|NZF2|PLPB1|ZC2H2C1|ZC2HC4A	myelin transcription factor 1	protein-coding	0.054795	0.535836	
chunk0203_331_1	chr9	89755798	89756090	+	0	NA	Intergenic	L1ME2z|LINE|L1	116161	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.027397	0.470990	
chunk0127_392_1	chr3	102238016	102238771	+	0	NA	Intergenic	Intergenic	-196622	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.003974	0.394180	
chunk0023_35_1	chr10	21184207	21184686	+	0	NA	Intergenic	Intergenic	10144	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.004175	0.408333	242(CGGTACACAATGTGCT,-,0.00),243(GGTACACAATGTGCTC,+,0.00)
chunk0007_227_1	chr1	81775427	81775916	+	0	NA	intron (NM_001297704, intron 2 of 20)	intron (NM_001297704, intron 2 of 20)	-24726	NM_012302	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.000000	0.355102	
chunk0074_123_1	chr16	22664993	22665656	+	0	NA	Intergenic	Intergenic	119626	NR_003676	653786	Hs.564945	NR_003676	ENSG00000257838	OTOAP1	-	OTOA pseudogene 1	pseudo	0.018100	0.444277	
chunk0153_154_1	chr5	69492883	69493255	+	0	NA	intron (NM_001205254, intron 1 of 8)	CpG	306	NM_001205254	100506658	Hs.592605	NM_002538	ENSG00000197822	OCLN	BLCPMG|PPP1R115|PTORCH1	occludin	protein-coding	0.102151	0.672922	
chunk0211_115_1	chrX	112001635	112002171	+	0	NA	intron (NM_012471, intron 1 of 10)	L2|LINE|L2	80873	NM_012471	7224	Hs.657709	NM_012471	ENSG00000072315	TRPC5	PPP1R159|TRP5	transient receptor potential cation channel subfamily C member 5	protein-coding	0.007463	0.407821	
chunk0199_164_1	chr9	4407628	4407849	+	0	NA	Intergenic	L1MA2|LINE|L1	-82689	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.018100	0.369369	
chunk0122_347_1	chr3	37322088	37322287	+	0	NA	intron (NM_002078, intron 13 of 23)	intron (NM_002078, intron 13 of 23)	-64082	NM_178344	339883	Hs.475945	NM_178339	ENSG00000198590	C3orf35	APRG1	chromosome 3 open reading frame 35	protein-coding	0.005025	0.480000	
chunk0094_306_1	chr2	8738280	8738479	+	0	NA	intron (NM_020738, intron 26 of 29)	L1MC4a|LINE|L1	56396	NM_002166	3398	Hs.180919	NM_002166	ENSG00000115738	ID2	GIG8|ID2A|ID2H|bHLHb26	inhibitor of DNA binding 2	protein-coding	0.010050	0.395000	
chunk0020_317_1	chr1	237667061	237667413	+	0	NA	intron (NM_001035, intron 57 of 104)	intron (NM_001035, intron 57 of 104)	-194938	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.008523	0.305949	
chunk0125_186_1	chr3	66712142	66712699	+	0	NA	Intergenic	Intergenic	-211999	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.007181	0.388889	
chunk0050_297_1	chr12	106774207	106774415	+	0	NA	promoter-TSS (NM_018157)	promoter-TSS (NM_018157)	-310	NM_018157	55188	Hs.131306	NM_018157	ENSG00000111785	RIC8B	RIC8|hSyn	RIC8 guanine nucleotide exchange factor B	protein-coding	0.033654	0.511962	
chunk0144_292_1	chr4	138256606	138256992	+	0	NA	Intergenic	LTR86C|LTR|ERVL	-14450	NM_014331	23657	Hs.390594	NM_014331	ENSG00000151012	SLC7A11	CCBR1|xCT	solute carrier family 7 member 11	protein-coding	0.012953	0.467700	
chunk0007_44_1	chr1	77756805	77757534	+	0	NA	intron (NM_015017, intron 1 of 24)	L2c|LINE|L2	2710	NM_015017	23032	Hs.480597	NM_015017	ENSG00000077254	USP33	VDU1	ubiquitin specific peptidase 33	protein-coding	0.002743	0.350685	
chunk0087_438_1	chr18	42484708	42485000	+	0	NA	intron (NR_046174, intron 6 of 9)	intron (NR_046174, intron 6 of 9)	298186	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.000000	0.406143	
chunk0195_379_1	chr8	100073438	100073729	+	0	NA	intron (NM_001286692, intron 4 of 27)	MamRTE1|LINE|RTE-BovB	32043	NM_001286693	26166	Hs.120021	NM_015668	ENSG00000132554	RGS22	CT145|PRTD-NY2	regulator of G protein signaling 22	protein-coding	0.006873	0.390411	
chunk0035_181_1	chr11	44141659	44142097	+	0	NA	intron (NM_207122, intron 7 of 13)	intron (NM_207122, intron 7 of 13)	45681	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.006849	0.348519	345(GAGAACTCAGTGTTTT,-,0.00),346(AGAACTCAGTGTTTTC,+,0.00)
chunk0103_273_1	chr2	165808963	165809458	+	0	NA	Intergenic	Intergenic	-14917	NM_004482	2591	Hs.170986	NM_004482	ENSG00000115339	GALNT3	GalNAc-T3|HFTC|HFTC1|HHS	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.002020	0.344758	
chunk0180_409_1	chr7	75914577	75915280	+	0	NA	promoter-TSS (NM_000941)	promoter-TSS (NM_000941)	-174	NM_000941	5447	Hs.354056	NM_000941	ENSG00000127948	POR	CPR|CYPOR|P450R	cytochrome p450 oxidoreductase	protein-coding	0.099573	0.694602	
chunk0180_254_1	chr7	69361029	69361361	+	0	NA	Intergenic	Intergenic	236300	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.012048	0.408408	50(CTGAACATTTTGTCCC,-,0.00),51(TGAACATTTTGTCCCC,+,0.00)
chunk0011_242_1	chr1	150567825	150568679	+	0	NA	intron (NR_104133, intron 2 of 3)	intron (NR_104133, intron 2 of 3)	6300	NR_104133	574406	Hs.516243	NM_001025493	ENSG00000203804	ADAMTSL4-AS1	C1orf138	ADAMTSL4 antisense RNA 1	ncRNA	0.010539	0.473684	416(CAGCACACCTTGTCCC,-,0.00),417(AGCACACCTTGTCCCA,+,0.00)
chunk0005_457_1	chr1	63593603	63593802	+	0	NA	promoter-TSS (NM_001172819)	promoter-TSS (NM_001172819)	-107	NM_001172819	5236	Hs.1869	NM_002633	ENSG00000079739	PGM1	CDG1T|GSD14	phosphoglucomutase 1	protein-coding	0.130653	0.715000	
chunk0014_134_1	chr1	177689230	177689429	+	0	NA	Intergenic	Intergenic	-11195	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.000000	0.495000	
chunk0126_433_1	chr3	86993719	86993924	+	0	NA	Intergenic	Intergenic	-2714	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.024390	0.422330	
chunk0076_395_1	chr16	72552652	72553274	+	0	NA	intron (NR_126330, intron 3 of 13)	Cheshire|DNA|hAT-Charlie	112046	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.000000	0.325843	
chunk0033_172_1	chr11	15700121	15700589	+	0	NA	intron (NM_001293172, intron 1 of 2)	L2b|LINE|L2	56470	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.008547	0.371002	
chunk0018_254_1	chr1	220235364	220235843	+	0	NA	intron (NM_012414, intron 1 of 34)	L2a|LINE|L2	32112	NR_001587	6791	Hs.654849	NR_001587		AURKAP1	AURKAPS1|AurAps1|STK6P	aurora kinase A pseudogene 1	pseudo	0.002088	0.318750	
chunk0122_265_1	chr3	35158950	35159999	+	0	NA	intron (NR_110817, intron 2 of 3)	L1MCa|LINE|L1	234549	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.001907	0.318095	
chunk0169_239_1	chr6	105121823	105122428	+	0	NA	intron (NM_007073, intron 5 of 7)	intron (NM_007073, intron 5 of 7)	14221	NM_147147	11149	Hs.221660	NM_007073	ENSG00000112276	BVES	CARICK|HBVES|LGMD2X|LGMDR25|POP1|POPDC1	blood vessel epicardial substance	protein-coding	0.008264	0.417492	
chunk0055_459_1	chr13	76384218	76384566	+	0	NA	Intergenic	Intergenic	502013	NM_138444	115207	Hs.644125	NM_138444	ENSG00000178695	KCTD12	C13orf2|PFET1|PFETIN	potassium channel tetramerization domain containing 12	protein-coding	0.000000	0.418338	
chunk0011_320_1	chr1	151990060	151990470	+	0	NA	intron (NM_002966, intron 1 of 2)	intron (NM_002966, intron 1 of 2)	3973	NM_002966	6281	Hs.143873	NM_002966	ENSG00000197747	S100A10	42C|ANX2L|ANX2LG|CAL1L|CLP11|Ca[1]|GP11|P11|p10	S100 calcium binding protein A10	protein-coding	0.009756	0.450122	
chunk0055_204_1	chr13	61949741	61950508	+	0	NA	Intergenic	HAL1M8|LINE|L1	79424	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.003911	0.305990	
chunk0065_429_1	chr14	106258598	106259170	+	0	NA	Intergenic	Intergenic	-28790	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.003497	0.413613	259(GGGAACATGGTGTGAT,-,0.00),309(AAGAACAGCATGTTTC,-,0.00),310(AGAACAGCATGTTTCC,+,0.00)
chunk0170_109_1	chr6	110633206	110634075	+	0	NA	intron (NM_015076, intron 5 of 12)	intron (NM_015076, intron 5 of 12)	-156999	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.002301	0.337931	87(TAGTTCAGTGTGTGCT,-,0.00),88(AGTTCAGTGTGTGCTG,+,0.00)
chunk0061_82_1	chr14	56854198	56854901	+	0	NA	intron (NR_029385, intron 1 of 3)	intron (NR_029385, intron 1 of 3)	41366	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.002845	0.384943	
chunk0110_92_1	chr20	11353645	11353844	+	0	NA	Intergenic	LTR1B|LTR|ERV1	-80361	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.020101	0.540000	
chunk0112_32_1	chr20	36447207	36447436	+	0	NA	intron (NM_014902, intron 7 of 12)	intron (NM_014902, intron 7 of 12)	-14094	NM_001042486	22839	Hs.249600	NM_014902	ENSG00000080845	DLGAP4	DAP-4|DAP4|DLP4|SAPAP-4|SAPAP4	DLG associated protein 4	protein-coding	0.000000	0.504348	
chunk0209_180_1	chrX	43693937	43694233	+	0	NA	intron (NM_000240, intron 3 of 14)	intron (NM_000240, intron 3 of 14)	39178	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.000000	0.434343	
chunk0014_57_1	chr1	175725894	175726093	+	0	NA	intron (NM_003285, intron 1 of 22)	intron (NM_003285, intron 1 of 22)	17623	NM_003285	7143	Hs.659864	NM_003285	ENSG00000116147	TNR	TN-R	tenascin R	protein-coding	0.005025	0.395000	
chunk0015_385_1	chr1	190592280	190593111	+	0	NA	Intergenic	Intergenic	-32195	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.008424	0.469952	
chunk0178_65_1	chr7	30238888	30239158	+	0	NA	Intergenic	Intergenic	-45284	NM_147128	223082	Hs.263912	NM_147128	ENSG00000180233	ZNRF2	RNF202	zinc and ring finger 2	protein-coding	0.000000	0.416974	
chunk0039_208_1	chr11	101015491	101015881	+	0	NA	Intergenic	Intergenic	23606	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.005128	0.342711	208(GGGTACATTAAGTACC,-,0.00)
chunk0176_224_1	chr7	15167992	15168234	+	0	NA	Intergenic	Intergenic	-326663	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.004132	0.448560	
chunk0184_386_1	chr7	121544918	121545132	+	0	NA	Intergenic	MER92C|LTR|ERV1	-148657	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.004673	0.413953	83(TAGCACTCACTGTCCA,-,0.00),84(AGCACTCACTGTCCAT,+,0.00)
chunk0205_352_1	chr9	113470142	113470454	+	0	NA	intron (NM_017790, intron 1 of 17)	L1MEg|LINE|L1	6598	NM_001282923	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.003205	0.357827	
chunk0094_313_1	chr2	8890907	8891106	+	0	NA	intron (NM_138799, intron 4 of 12)	L2c|LINE|L2	-53381	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.000000	0.340000	
chunk0098_17_1	chr2	65386264	65386799	+	0	NA	intron (NM_181784, intron 1 of 5)	intron (NM_181784, intron 1 of 5)	-19734	NM_001128210	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.005607	0.391791	
chunk0139_312_1	chr4	58090909	58091109	+	0	NA	Intergenic	Intergenic	665137	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.000000	0.358209	124(AAGGACACACTGTCTT,-,0.00),125(AGGACACACTGTCTTT,+,0.00)
chunk0101_39_1	chr2	122509246	122509797	+	0	NA	Intergenic	Intergenic	753976	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.000000	0.375000	
chunk0165_412_1	chr6	39061240	39061723	+	0	NA	intron (NM_002062, intron 3 of 12)	intron (NM_002062, intron 3 of 12)	12700	NM_002062	2740	Hs.351883	NM_002062	ENSG00000112164	GLP1R	GLP-1|GLP-1-R|GLP-1R	glucagon like peptide 1 receptor	protein-coding	0.016563	0.504132	
chunk0206_248_1	chr9	123745558	123746437	+	0	NA	intron (NM_024820, intron 5 of 20)	L1ME3B|LINE|L1	184141	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.003413	0.318182	
chunk0102_336_1	chr2	152132497	152132852	+	0	NA	intron (NM_005843, intron 10 of 13)	intron (NM_005843, intron 10 of 13)	-33595	NM_001145798	785	Hs.120725	NM_000726	ENSG00000182389	CACNB4	CAB4|CACNLB4|EA5|EIG9|EJM|EJM4|EJM6	calcium voltage-gated channel auxiliary subunit beta 4	protein-coding	0.005634	0.269663	
chunk0181_323_1	chr7	87785373	87785665	+	0	NA	intron (NM_001134406, intron 8 of 9)	L1PA16|LINE|L1	-72196	NM_000927	5243	Hs.489033	NM_000927	ENSG00000085563	ABCB1	ABC20|CD243|CLCS|GP170|MDR1|P-GP|PGY1	ATP binding cassette subfamily B member 1	protein-coding	0.006849	0.590444	190(CAGTGCAGGCTGTGCT,-,0.00),191(AGTGCAGGCTGTGCTC,+,0.00)
chunk0192_69_1	chr8	60535201	60535471	+	0	NA	intron (NM_001242644, intron 1 of 6)	L1ME4b|LINE|L1	18426	NM_002865	5862	Hs.369017	NM_002865	ENSG00000104388	RAB2A	LHX|RAB2	RAB2A, member RAS oncogene family	protein-coding	0.003704	0.357934	
chunk0142_297_1	chr4	100257182	100257876	+	0	NA	Intergenic	L2b|LINE|L2	-67031	NM_145244	115265	Hs.480378	NM_145244	ENSG00000145358	DDIT4L	REDD2|Rtp801L	DNA damage inducible transcript 4 like	protein-coding	0.005764	0.410072	
chunk0121_172_1	chr3	19940484	19940988	+	0	NA	Intergenic	Intergenic	-6344	NM_001292048	5868	Hs.475663	NM_004162	ENSG00000144566	RAB5A	RAB5	RAB5A, member RAS oncogene family	protein-coding	0.003968	0.425743	
chunk0146_254_1	chr4	162679689	162679963	+	0	NA	Intergenic	L1P4d|LINE|L1	413802	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003650	0.327273	
chunk0062_109_1	chr14	68305969	68306641	+	0	NA	intron (NM_133509, intron 8 of 10)	intron (NM_133509, intron 8 of 10)	486526	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.005952	0.395245	
chunk0161_187_1	chr5	169939453	169939765	+	0	NA	intron (NM_001129891, intron 1 of 3)	Tigger3b|DNA|TcMar-Tigger	41131	NM_001129891	100131897	Hs.721917	NM_001129891	ENSG00000204767	INSYN2B	C5orf57|FAM196B	inhibitory synaptic factor family member 2B	protein-coding	0.016026	0.329073	
chunk0203_118_1	chr9	84851461	84851721	+	0	NA	intron (NM_001018064, intron 11 of 16)	intron (NM_001018064, intron 11 of 16)	181214	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.003846	0.402299	
chunk0148_62_1	chr5	2055657	2055995	+	0	NA	Intergenic	L1ME2|LINE|L1	168495	NR_109912	101929081	Hs.519180	NR_109912	ENSG00000249326	CTD-2194D22.4	-	uncharacterized LOC101929081	ncRNA	0.011834	0.418879	
chunk0124_342_1	chr3	58361315	58361860	+	0	NA	intron (NM_001289101, intron 1 of 14)	L1MD1|LINE|L1	28697	NM_001289101	54899	Hs.190544	NM_017771	ENSG00000168297	PXK	MONAKA|SLOB	PX domain containing serine/threonine kinase like	protein-coding	0.005505	0.342491	
chunk0078_175_1	chr17	4483527	4483833	+	0	NA	intron (NM_182538, intron 9 of 11)	intron (NM_182538, intron 9 of 11)	-15154	NM_001124758	124976	Hs.22824	NM_001124758	ENSG00000183018	SPNS2	DFNB115|SLC62A2	sphingolipid transporter 2	protein-coding	0.006536	0.566775	
chunk0088_92_1	chr18	44917954	44918398	+	0	NA	intron (NM_015559, intron 3 of 5)	intron (NM_015559, intron 3 of 5)	51990	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.015766	0.496629	230(CGGGACAGCCTGTTCC,-,0.00),231(GGGACAGCCTGTTCCT,+,0.00)
chunk0064_391_1	chr14	99171253	99171626	+	0	NA	3' UTR (NM_138576, exon 4 of 4)	3' UTR (NM_138576, exon 4 of 4)	100274	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.005362	0.312834	
chunk0163_124_1	chr6	10314425	10314806	+	0	NA	Intergenic	Intergenic	-97703	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.023622	0.437173	
chunk0097_121_1	chr2	46621328	46621986	+	0	NA	intron (NM_014171, intron 3 of 4)	L2a|LINE|L2	4485	NM_014171	9419	Hs.133998	NM_014171	ENSG00000119878	CRIPT	HSPC139|SSMDF	CXXC repeat containing interactor of PDZ3 domain	protein-coding	0.003040	0.353566	
chunk0028_209_1	chr10	89301862	89302359	+	0	NA	5' UTR (NM_001547, exon 1 of 2)	5' UTR (NM_001547, exon 1 of 2)	161	NM_001547	3433	Hs.437609	NM_001547	ENSG00000119922	IFIT2	G10P2|GARG-39|IFI-54|IFI-54K|IFI54|IFIT-2|ISG-54 K|ISG-54K|ISG54|P54|cig42	interferon induced protein with tetratricopeptide repeats 2	protein-coding	0.012072	0.421687	
chunk0120_346_1	chr3	11431303	11431566	+	0	NA	intron (NM_001136031, intron 17 of 17)	L1MB7|LINE|L1	137490	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.007605	0.469697	
chunk0177_350_1	chr7	26584343	26584842	+	0	NA	Intergenic	Intergenic	-45767	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.012024	0.386000	
chunk0198_44_1	chr8	128423622	128424065	+	0	NA	intron (NR_121672, intron 3 of 7)	MIRb|SINE|MIR	140836	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.002257	0.380631	
chunk0028_454_1	chr10	94778086	94778407	+	0	NA	intron (NM_000769, intron 3 of 8)	LTR22A|LTR|ERVK	15565	NM_000769	1557	Hs.282409	NM_000769	ENSG00000165841	CYP2C19	CPCJ|CYP2C|CYPIIC17|CYPIIC19|P450C2C|P450IIC19	cytochrome P450 family 2 subfamily C member 19	protein-coding	0.015576	0.468944	
chunk0052_296_1	chr12	124566311	124566566	+	0	NA	intron (NM_006312, intron 1 of 48)	CpG	1026	NM_006312	9612	Hs.137510	NM_006312	ENSG00000196498	NCOR2	CTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1	nuclear receptor corepressor 2	protein-coding	0.070588	0.648438	100(AGGTACAGCCTGTCTC,-,0.00),101(GGTACAGCCTGTCTCT,+,0.00)
chunk0022_316_1	chr10	16159532	16160158	+	0	NA	Intergenic	Intergenic	-277098	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.006390	0.377990	
chunk0028_328_1	chr10	91980231	91980509	+	0	NA	intron (NM_003972, intron 14 of 37)	intron (NM_003972, intron 14 of 37)	56391	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.003597	0.329749	
chunk0042_339_1	chr12	9883306	9883507	+	0	NA	intron (NM_001190765, intron 1 of 5)	L4_A_Mam|LINE|RTE-X	1917	NM_001190765	100431172	Hs.725113	NM_001190765	ENSG00000256797	KLRF2	NKp65	killer cell lectin like receptor F2	protein-coding	0.000000	0.381188	
chunk0059_100_1	chr14	30957793	30958476	+	0	NA	intron (NM_001083893, intron 1 of 17)	AluJo|SINE|Alu	56608	NR_030354	693209		NR_030354	ENSG00000207952	MIR624	MIRN624|hsa-mir-624|mir-624	microRNA 624	ncRNA	0.007321	0.366959	
chunk0073_181_1	chr16	8945387	8945588	+	0	NA	intron (NM_003470, intron 1 of 30)	intron (NM_003470, intron 1 of 30)	-8758	NM_001286457	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.000000	0.410891	
chunk0200_99_1	chr9	16648371	16648759	+	0	NA	intron (NM_017637, intron 3 of 6)	intron (NM_017637, intron 3 of 6)	222223	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.007732	0.403599	
chunk0004_49_1	chr1	42946485	42946901	+	0	NA	intron (NM_006516, intron 1 of 9)	L2b|LINE|L2	-12356	NR_033967	440584	Hs.260928	NR_033967	ENSG00000227533	SLC2A1-AS1	-	SLC2A1 antisense RNA 1	ncRNA	0.012019	0.534772	171(CAGAACAGTATGTGCA,-,0.00),172(AGAACAGTATGTGCAA,+,0.00)
chunk0132_311_1	chr3	160547385	160547637	+	0	NA	intron (NM_002268, intron 1 of 16)	L1MC1|LINE|L1	18077	NM_002268	3840	Hs.467866	NM_002268	ENSG00000186432	KPNA4	IPOA3|QIP1|SRP3	karyopherin subunit alpha 4	protein-coding	0.003968	0.407115	74(AAGTACAGACAGTTCC,-,0.00),75(AGTACAGACAGTTCCC,+,0.00)
chunk0067_259_1	chr15	45802189	45802631	+	0	NA	Intergenic	Intergenic	167670	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.006787	0.399549	
chunk0147_242_1	chr4	182993529	182993785	+	0	NA	Intergenic	L1M4c|LINE|L1	-44008	NR_003612	403315	Hs.652187	NR_003612	ENSG00000230219	FAM92A1P2	FAM92A3	family with sequence similarity 92, member A3	pseudo	0.003906	0.486381	
chunk0063_430_1	chr14	88590045	88590432	+	0	NA	intron (NM_207660, intron 9 of 13)	L2a|LINE|L2	-4148	NM_207662	79882	Hs.684046	NM_024824	ENSG00000100722	ZC3H14	MRT56|MSUT-2|NY-REN-37|SUT2|UKp68	zinc finger CCCH-type containing 14	protein-coding	0.012920	0.507732	
chunk0084_423_1	chr17	82507774	82507973	+	0	NA	Intergenic	LOR1a|LTR|ERV1	-11845	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.020101	0.500000	
chunk0040_230_1	chr11	114439277	114439894	+	0	NA	exon (NM_015523, exon 1 of 7)	exon (NM_015523, exon 1 of 7)	199	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.090762	0.676375	
chunk0207_440_1	chr9	137550054	137550310	+	0	NA	exon (NM_152286, exon 1 of 34)	exon (NM_152286, exon 1 of 34)	387	NM_152286	375775	Hs.294147	NM_152286	ENSG00000130653	PNPLA7	C9orf111|NTE-R1|NTEL1	patatin like phospholipase domain containing 7	protein-coding	0.027344	0.560311	
chunk0178_445_1	chr7	41955858	41956341	+	0	NA	Intergenic	Intergenic	-252991	NM_002192	3624	Hs.28792	NM_002192	ENSG00000122641	INHBA	EDF|FRP	inhibin subunit beta A	protein-coding	0.018634	0.570248	
chunk0136_262_1	chr3	194321831	194322398	+	0	NA	Intergenic	Intergenic	-9310	NR_024480	100131551	Hs.128066	NR_024480	ENSG00000214145	LINC00887	HEIRCC	long intergenic non-protein coding RNA 887	ncRNA	0.024691	0.589789	337(CTGAACACTCTGACCC,-,0.00),338(TGAACACTCTGACCCG,+,0.00)
chunk0201_336_1	chr9	63859543	63859915	+	0	NA	promoter-TSS (NR_033907)	promoter-TSS (NR_033907)	-95	NR_033907	642236	Hs.650100	NR_033907		FRG1JP	-	FSHD region gene 1 family member J, pseudogene	pseudo	0.077957	0.675603	
chunk0189_324_1	chr8	26307862	26308065	+	0	NA	intron (NM_001177591, intron 2 of 9)	Tigger1|DNA|TcMar-Tigger	14747	NM_001177591	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.004926	0.352941	
chunk0120_275_1	chr3	9388908	9389120	+	0	NA	non-coding (NR_132780, exon 4 of 4)	non-coding (NR_132780, exon 4 of 4)	7609	NR_132781	440944	Hs.598958	NM_001013713	ENSG00000206573	THUMPD3-AS1	SETD5-AS1	THUMPD3 antisense RNA 1	ncRNA	0.004717	0.389671	
chunk0066_281_1	chr15	35142754	35143094	+	0	NA	Intergenic	Intergenic	-94402	NR_003144	723972	Hs.631698	NR_003144	ENSG00000259516	ANP32AP1	-	acidic nuclear phosphoprotein 32 family member A pseudogene 1	pseudo	0.008824	0.483871	
chunk0131_35_1	chr3	142489396	142490108	+	0	NA	intron (NM_001184, intron 35 of 46)	L1ME2|LINE|L1	-41690	NM_001282859	54464	Hs.435103	NM_019001	ENSG00000114127	XRN1	SEP1	5'-3' exoribonuclease 1	protein-coding	0.007022	0.346424	
chunk0147_320_1	chr4	184988676	184989140	+	0	NA	Intergenic	Intergenic	-29933	NM_001300782	391723	Hs.531242	NM_001029887	ENSG00000187821	HELT	HCM1228|HESL|Mgn|bHLHb44	helt bHLH transcription factor	protein-coding	0.025862	0.522581	221(GGGAACTGGATGTGCT,-,0.00),222(GGAACTGGATGTGCTT,+,0.00)
chunk0189_458_1	chr8	28516576	28517021	+	0	NA	intron (NM_017412, intron 3 of 7)	L1ME1|LINE|L1	-11616	NR_036250	100422903		NR_036250	ENSG00000265251	MIR4288	-	microRNA 4288	ncRNA	0.002247	0.257848	
chunk0024_19_1	chr10	33009874	33010731	+	0	NA	Intergenic	Intergenic	-51937	NM_002211	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.016336	0.475524	
chunk0026_106_1	chr10	61828915	61829201	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-72196	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.006993	0.390244	
chunk0142_270_1	chr4	99408885	99409406	+	0	NA	Intergenic	Intergenic	25989	NM_001166504	131	Hs.389	NM_000673	ENSG00000196344	ADH7	ADH4	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding	0.011516	0.348659	
chunk0048_305_1	chr12	82841886	82842545	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	155060	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.006070	0.336364	
chunk0114_164_1	chr21	10814257	10814504	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	292866	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.012146	0.379032	
chunk0019_306_1	chr1	228978618	228979038	+	0	NA	Intergenic	Intergenic	195973	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.016667	0.551069	
chunk0179_360_1	chr7	50978623	50978979	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-185339	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.002809	0.417367	
chunk0208_291_1	chrX	21973971	21974241	+	0	NA	intron (NM_004595, intron 4 of 10)	intron (NM_004595, intron 4 of 10)	33533	NM_004595	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.003704	0.453875	
chunk0022_235_1	chr10	14163248	14163810	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	89245	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.021352	0.404973	
chunk0157_401_1	chr5	124263367	124263576	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	175049	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004785	0.319048	
chunk0135_52_1	chr3	185658489	185659062	+	0	NA	intron (NM_001007225, intron 9 of 14)	intron (NM_001007225, intron 9 of 14)	-54477	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.015707	0.491289	334(AAGAACAGAGTGTGCT,-,0.00),335(AGAACAGAGTGTGCTG,+,0.00)
chunk0004_234_1	chr1	47175199	47175398	+	0	NA	Intergenic	L2b|LINE|L2	-3952	NR_047498	100874253	Hs.435758	NR_047498	ENSG00000224805	LINC00853	PDZK1IP1-AS1|ncRNA-a4	long intergenic non-protein coding RNA 853	ncRNA	0.030151	0.500000	128(GGGGACATCCCGTCCT,-,0.00),129(GGGACATCCCGTCCTC,+,0.00)
chunk0069_269_1	chr15	64681387	64681896	+	0	NA	intron (NM_015042, intron 8 of 8)	intron (NM_015042, intron 8 of 8)	21640	NM_001301302	4947	Hs.744924	NM_002537	ENSG00000180304	OAZ2	AZ2	ornithine decarboxylase antizyme 2	protein-coding	0.015717	0.513725	179(TGGAACACAGTGTCCC,-,0.00),180(GGAACACAGTGTCCCC,+,0.00)
chunk0131_243_1	chr3	149401272	149402169	+	0	NA	Intergenic	Intergenic	-23939	NM_014220	4071	Hs.351316	NM_014220	ENSG00000169908	TM4SF1	H-L6|L6|M3S1|TAAL6	transmembrane 4 L six family member 1	protein-coding	0.005574	0.385301	
chunk0172_3_1	chr6	132337552	132337936	+	0	NA	intron (NM_015529, intron 4 of 11)	intron (NM_015529, intron 4 of 11)	63790	NM_015529	26002	Hs.6909	NM_015529	ENSG00000079931	MOXD1	MOX|PRO5780|dJ248E1.1	monooxygenase DBH like 1	protein-coding	0.002604	0.285714	
chunk0167_448_1	chr6	75941429	75941777	+	0	NA	intron (NM_001282368, intron 13 of 15)	intron (NM_001282368, intron 13 of 15)	131075	NM_001282368	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.002874	0.312321	
chunk0008_154_1	chr1	92443637	92444468	+	0	NA	Intergenic	Intergenic	39747	NM_001127215	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.013237	0.426683	148(ATAACAGAATGTACCT,+,0.00)
chunk0087_50_1	chr18	31473986	31474407	+	0	NA	exon (NM_001944, exon 15 of 16)	exon (NM_001944, exon 15 of 16)	-23868	NM_001943	1829	Hs.412597	NM_001943	ENSG00000046604	DSG2	CDHF5|HDGC	desmoglein 2	protein-coding	0.011876	0.454976	107(ATTACAGAATGTTCTC,+,0.00)
chunk0055_69_1	chr13	52759898	52760583	+	0	NA	Intergenic	L1M6B|LINE|L1	-20428	NM_001011705	11061	Hs.421391	NM_007015	ENSG00000136110	CNMD	BRICD3|CHM-I|CHM1|LECT1|MYETS1	chondromodulin	protein-coding	0.005839	0.467930	
chunk0099_134_1	chr2	86470610	86471257	+	0	NA	intron (NM_018433, intron 11 of 25)	L1MC5|LINE|L1	29472	NM_001146688	55818	Hs.557425	NM_018433	ENSG00000115548	KDM3A	JHDM2A|JHMD2A|JMJD1|JMJD1A|TSGA	lysine demethylase 3A	protein-coding	0.003091	0.344136	159(TGCACACCCTGTTTTG,+,0.00)
chunk0010_199_1	chr1	116068343	116068819	+	0	NA	3' UTR (NM_018420, exon 12 of 12)	3' UTR (NM_018420, exon 12 of 12)	-43174	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.004202	0.394130	
chunk0113_173_1	chr20	53119140	53119603	+	0	NA	intron (NM_173485, intron 1 of 2)	L2c|LINE|L2	-65912	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.012959	0.400862	
chunk0065_132_1	chr15	24942733	24942932	+	0	NA	intron (NM_022808, intron 3 of 11)	ERVL-B4-int|LTR|ERVL	-12091	NM_022804	8926	Hs.564847	NM_005678	ENSG00000273173	SNURF	-	SNRPN upstream reading frame	protein-coding	0.010050	0.495000	
chunk0183_388_1	chr7	110147292	110148158	+	0	NA	Intergenic	Intergenic	-187512	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.004619	0.334487	
chunk0001_142_1	chr1	5949086	5949285	+	0	NA	intron (NM_001291593, intron 6 of 26)	intron (NM_001291593, intron 6 of 26)	-43113	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.010050	0.340000	
chunk0113_407_1	chr20	61329233	61329491	+	0	NA	intron (NM_001794, intron 2 of 15)	intron (NM_001794, intron 2 of 15)	76936	NM_001794	1002	Hs.473231	NM_001794	ENSG00000179242	CDH4	CAD4|R-CAD|RCAD	cadherin 4	protein-coding	0.038760	0.590734	
chunk0156_284_1	chr5	109982849	109983278	+	0	NA	Intergenic	Intergenic	99881	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.000000	0.425581	
chunk0210_401_1	chrX	98778796	98779202	+	0	NA	Intergenic	Intergenic	1160844	NR_024608	442459	Hs.706599	NM_001127438		XRCC6P5	-	X-ray repair cross complementing 6 pseudogene 5	pseudo	0.002463	0.294840	
chunk0201_215_1	chr9	37229886	37230587	+	0	NA	intron (NM_032226, intron 2 of 8)	Tigger3b|DNA|TcMar-Tigger	109638	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.005706	0.337607	
chunk0004_372_1	chr1	51669047	51669550	+	0	NA	intron (NR_036662, intron 2 of 22)	intron (NR_036662, intron 2 of 22)	52424	NM_148909	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.007952	0.446429	
chunk0062_9_1	chr14	66133518	66133856	+	0	NA	Intergenic	Intergenic	-352684	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.000000	0.501475	277(GAGAACAGATAGTCCC,-,0.00),278(AGAACAGATAGTCCCA,+,0.00)
chunk0089_249_1	chr18	62201864	62202295	+	0	NA	intron (NM_020854, intron 1 of 28)	intron (NM_020854, intron 1 of 28)	14788	NM_020854	57614	Hs.465323	NM_020854	ENSG00000134444	RELCH	HsT3308|HsT885|KIAA1468	RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing	protein-coding	0.002320	0.291667	
chunk0177_418_1	chr7	27730080	27730482	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-9092	NM_001206901	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.012438	0.416873	
chunk0132_289_1	chr3	159995709	159995941	+	0	NA	3' UTR (NM_000882, exon 7 of 7)	3' UTR (NM_000882, exon 7 of 7)	6989	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.000000	0.261803	
chunk0076_349_1	chr16	71682403	71682902	+	0	NA	intron (NM_001289003, intron 5 of 17)	intron (NM_001289003, intron 5 of 17)	16049	NR_033337	100379141	Hs.725116	NR_033337	ENSG00000263666	SNORA70D	U70D	small nucleolar RNA, H/ACA box 70D	snoRNA	0.010020	0.364000	
chunk0019_28_1	chr1	223734407	223735071	+	0	NA	intron (NM_001748, intron 2 of 20)	intron (NM_001748, intron 2 of 20)	22322	NM_001748	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.016566	0.494737	286(TGGCACACCATGTACC,-,0.00),287(GGCACACCATGTACCA,+,0.00)
chunk0067_178_1	chr15	44315406	44316226	+	0	NA	intron (NM_177974, intron 1 of 8)	intron (NM_177974, intron 1 of 8)	27105	NM_138423	113201	Hs.512867	NM_138423	ENSG00000166734	CASC4	H63	cancer susceptibility 4	protein-coding	0.006098	0.355664	
chunk0195_296_1	chr8	98649483	98650335	+	0	NA	intron (NM_001256313, intron 4 of 8)	L1M5|LINE|L1	175762	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.002347	0.262603	
chunk0017_127_1	chr1	206511766	206512248	+	0	NA	intron (NM_182663, intron 1 of 5)	intron (NM_182663, intron 1 of 5)	4477	NM_182663	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.020747	0.492754	
chunk0123_98_1	chr3	42135134	42135333	+	0	NA	intron (NM_001042646, intron 2 of 15)	L2b|LINE|L2	-14002	NM_001265609	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.005025	0.500000	
chunk0163_110_1	chr6	10163345	10163872	+	0	NA	Intergenic	Intergenic	-248710	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.017078	0.473485	
chunk0045_302_1	chr12	50556177	50556632	+	0	NA	intron (NM_173602, intron 1 of 37)	intron (NM_173602, intron 1 of 37)	51419	NM_173602	57609	Hs.505516	NM_020849	ENSG00000066084	DIP2B	-	disco interacting protein 2 homolog B	protein-coding	0.024176	0.445175	
chunk0139_244_1	chr4	55920433	55920936	+	0	NA	Intergenic	Intergenic	-28124	NM_025009	9662	Hs.518767	NM_014645	ENSG00000174799	CEP135	CEP4|KIAA0635|MCPH8	centrosomal protein 135	protein-coding	0.013917	0.482143	247(CAGAGCACCGTGTACC,-,0.00)
chunk0061_156_1	chr14	59695121	59695673	+	0	NA	intron (NM_021136, intron 3 of 8)	MLT1I|LTR|ERVL-MaLR	-48377	NR_049851	100847088		NR_049851	ENSG00000263629	MIR5586	-	microRNA 5586	ncRNA	0.010870	0.477396	262(GGGAACACGATGTTCA,-,0.00),263(GGAACACGATGTTCAC,+,0.00),351(CAGGACAGCATGTCCT,-,0.00),352(AGGACAGCATGTCCTA,+,0.00)
chunk0019_87_1	chr1	224529909	224530364	+	0	NA	Intergenic	Intergenic	-86341	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.008791	0.462719	
chunk0050_369_1	chr12	108278407	108278749	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	42084	NM_001142345	1240	Hs.197143	NM_004072	ENSG00000174600	CMKLR1	CHEMERINR|ChemR23|DEZ|RVER1	chemerin chemokine-like receptor 1	protein-coding	0.005848	0.437318	
chunk0166_240_1	chr6	47236048	47236426	+	0	NA	intron (NM_014452, intron 4 of 5)	intron (NM_014452, intron 4 of 5)	73710	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.007937	0.464380	
chunk0157_8_1	chr5	115186188	115186462	+	0	NA	Intergenic	Intergenic	-5779	NM_018700	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.010949	0.447273	
chunk0118_221_1	chr22	32128246	32128587	+	0	NA	intron (NR_040114, intron 2 of 3)	MIRb|SINE|MIR	6439	NR_040114	23782	Hs.581098	NR_040114	ENSG00000234479	AP1B1P1	ADTB1L1|dJ127L4.2	AP1B1 pseudogene 1	pseudo	0.008798	0.479532	97(AGGAACACCCTGTCCT,-,0.00),98(GGAACACCCTGTCCTC,+,0.00)
chunk0066_319_1	chr15	36177921	36178365	+	0	NA	Intergenic	Intergenic	251287	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.000000	0.366292	
chunk0008_58_1	chr1	89458463	89458843	+	0	NA	Intergenic	L1MA10|LINE|L1	50974	NR_003133	400759	Hs.661968	NR_003133	ENSG00000225492	GBP1P1	-	guanylate binding protein 1 pseudogene 1	pseudo	0.007895	0.317585	
chunk0117_88_1	chr22	17298768	17299429	+	0	NA	Intergenic	L1PA6|LINE|L1	-32365	NR_038398	27442	Hs.517394	NR_038398	ENSG00000241832	CECR3	-	cat eye syndrome chromosome region, candidate 3	ncRNA	0.012103	0.530211	
chunk0148_263_1	chr5	10366607	10367192	+	0	NA	intron (NM_001270661, intron 1 of 22)	LTR3B_|LTR|ERVK	13260	NM_001270661	10299	Hs.432862	NM_005885	ENSG00000145495	MARCH6	DOA10|MARCH-VI|RNF176|TEB4	membrane associated ring-CH-type finger 6	protein-coding	0.013675	0.447099	
chunk0130_380_1	chr3	139930149	139930560	+	0	NA	Intergenic	Intergenic	-4831	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.000000	0.371359	
chunk0053_121_1	chr13	29616098	29616350	+	0	NA	Intergenic	L1PB1|LINE|L1	-20536	NM_003045	6541	Hs.14846	NM_003045	ENSG00000139514	SLC7A1	ATRC1|CAT-1|ERR|HCAT1|REC1L	solute carrier family 7 member 1	protein-coding	0.003968	0.367589	
chunk0038_194_1	chr11	86134971	86135300	+	0	NA	Intergenic	L2c|LINE|L2	-65254	NM_001206947	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.003040	0.442424	97(GAGAACTGTGTGTACA,-,0.00),98(AGAACTGTGTGTACAA,+,0.00)
chunk0124_214_1	chr3	56077761	56078132	+	0	NA	intron (NR_132749, intron 7 of 17)	MIRb|SINE|MIR	-225352	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.005391	0.357527	
chunk0117_27_1	chr22	11897035	11897290	+	0	NA	promoter-TSS (NR_110761)	promoter-TSS (NR_110761)	-244	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.015686	0.484375	
chunk0169_188_1	chr6	102484024	102484658	+	0	NA	Intergenic	L1MA6|LINE|L1	1085356	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003155	0.313386	
chunk0068_135_1	chr15	52705913	52706563	+	0	NA	Intergenic	L1MC4|LINE|L1	-27604	NR_104457	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.001538	0.337942	327(GTGAACGCAATGTTCT,-,0.00),328(TGAACGCAATGTTCTC,+,0.00)
chunk0210_8_1	chrX	66863539	66863738	+	0	NA	Intergenic	L2|LINE|L2	-224340	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.010050	0.435000	
chunk0102_215_1	chr2	148466003	148466493	+	0	NA	intron (NM_018328, intron 8 of 14)	intron (NM_018328, intron 8 of 14)	-178743	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.000000	0.291242	
chunk0059_2_1	chr14	29643471	29643711	+	0	NA	intron (NM_002742, intron 4 of 17)	intron (NM_002742, intron 4 of 17)	284102	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.369295	
chunk0028_89_1	chr10	83938422	83938775	+	0	NA	Intergenic	Intergenic	-200831	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.011331	0.449153	
chunk0077_289_1	chr16	81329573	81329879	+	0	NA	intron (NM_022041, intron 1 of 10)	L2|LINE|L2	14760	NM_022041	8139	Hs.112569	NM_022041	ENSG00000261609	GAN	GAN1|KLHL16	gigaxonin	protein-coding	0.003268	0.436482	
chunk0123_207_1	chr3	44870306	44870872	+	0	NA	Intergenic	Intergenic	-4017	NM_003241	7047	Hs.438265	NM_003241	ENSG00000163810	TGM4	TGP|hTGP	transglutaminase 4	protein-coding	0.012367	0.440917	
chunk0140_260_1	chr4	71525219	71526040	+	0	NA	intron (NM_001098484, intron 16 of 25)	intron (NM_001098484, intron 16 of 25)	186576	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.004872	0.329684	
chunk0156_352_1	chr5	112160528	112161049	+	0	NA	promoter-TSS (NR_002922)	promoter-TSS (NR_002922)	262	NR_015370	114915	Hs.12082	NM_053000		EPB41L4A-AS1	C5orf26|NCRNA00219|TIGA1	EPB41L4A antisense RNA 1	ncRNA	0.072937	0.637931	
chunk0063_151_1	chr14	79997845	79998117	+	0	NA	Intergenic	Intergenic	-213438	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.011029	0.369963	
chunk0036_232_1	chr11	64185080	64185710	+	0	NA	promoter-TSS (NM_001282653)	promoter-TSS (NM_001282653)	123	NM_001282652	10963	Hs.337295	NM_006819	ENSG00000168439	STIP1	HEL-S-94n|HOP|IEF-SSP-3521|P60|STI1|STI1L	stress induced phosphoprotein 1	protein-coding	0.088889	0.665610	434(AGGGACAGGCAGCTCC,-,0.00),435(GGGACAGGCAGCTCCC,+,0.00)
chunk0031_98_1	chr10	124075074	124075458	+	0	NA	intron (NM_001270764, intron 1 of 7)	intron (NM_001270764, intron 1 of 7)	17158	NM_015892	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.007812	0.472727	141(AAGAACAGGCTGTGCA,-,0.00),142(AGAACAGGCTGTGCAT,+,0.00)
chunk0054_225_1	chr13	45536163	45536616	+	0	NA	3' UTR (NM_031431, exon 23 of 23)	3' UTR (NM_031431, exon 23 of 23)	71494	NM_031431	83548	Hs.507948	NM_031431	ENSG00000136152	COG3	SEC34	component of oligomeric golgi complex 3	protein-coding	0.004415	0.255507	
chunk0197_154_1	chr8	120436300	120436845	+	0	NA	intron (NM_014078, intron 2 of 6)	L1MD|LINE|L1	-8826	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.001835	0.333333	
chunk0011_314_1	chr1	151925384	151925738	+	0	NA	Intergenic	Intergenic	-15676	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.000000	0.425352	
chunk0046_221_1	chr12	59629227	59629665	+	0	NA	intron (NM_001270622, intron 1 of 5)	intron (NM_001270622, intron 1 of 5)	33406	NM_001270623	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.002283	0.302961	
chunk0054_183_1	chr13	44759946	44760313	+	0	NA	Intergenic	Intergenic	49501	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.010899	0.486413	
chunk0173_52_1	chr6	142350147	142350861	+	0	NA	intron (NM_020455, intron 2 of 25)	intron (NM_020455, intron 2 of 25)	48585	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.002801	0.330070	
chunk0167_380_1	chr6	73883274	73883571	+	0	NA	Intergenic	L2a|LINE|L2	-186029	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.006734	0.328859	
chunk0051_126_1	chr12	115383697	115384161	+	0	NA	Intergenic	Intergenic	-699765	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.017241	0.479570	
chunk0143_55_1	chr4	107694659	107694877	+	0	NA	intron (NM_005443, intron 2 of 11)	intron (NM_005443, intron 2 of 11)	25495	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.004587	0.342466	
chunk0052_79_1	chr13	21712800	21713221	+	0	NA	Intergenic	L1MEc|LINE|L1	41934	NM_002010	2254	Hs.111	NM_002010	ENSG00000102678	FGF9	FGF-9|GAF|HBFG-9|HBGF-9|SYNS3	fibroblast growth factor 9	protein-coding	0.002375	0.305687	
chunk0183_440_1	chr7	111187390	111188002	+	0	NA	intron (NM_032549, intron 3 of 5)	MIR|SINE|MIR	96690	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.004902	0.353997	
chunk0030_178_1	chr10	114179482	114180136	+	0	NA	intron (NM_198795, intron 1 of 25)	intron (NM_198795, intron 1 of 25)	539	NM_198795	56165	Hs.333132	NM_198795	ENSG00000095627	TDRD1	CT41.1	tudor domain containing 1	protein-coding	0.029052	0.465649	
chunk0036_374_1	chr11	67452259	67452758	+	0	NA	promoter-TSS (NM_001300896)	promoter-TSS (NM_001300896)	93	NM_001300896	57010	Hs.143036	NM_145200	ENSG00000175544	CABP4	CRSD|CSNB2B	calcium binding protein 4	protein-coding	0.046092	0.666000	359(AGGAAGACCGTGTCCC,-,0.00)
chunk0016_263_1	chr1	200296387	200296626	+	0	NA	Intergenic	Intergenic	77286	NR_040064	554279	Hs.434694	NR_040064	ENSG00000203721	LINC00862	C1orf98|SMIM16	long intergenic non-protein coding RNA 862	ncRNA	0.004184	0.437500	
chunk0142_369_1	chr4	101970404	101970790	+	0	NA	intron (NM_017935, intron 7 of 16)	intron (NM_017935, intron 7 of 16)	156771	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.005181	0.413437	
chunk0025_157_1	chr10	52452694	52452901	+	0	NA	intron (NR_120641, intron 3 of 3)	intron (NR_120641, intron 3 of 3)	2475	NR_120642	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.004831	0.375000	
chunk0179_279_1	chr7	49488226	49488501	+	0	NA	Intergenic	Intergenic	-285298	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.300725	33(GTGAACAGGCTGTTAT,-,0.00)
chunk0106_133_1	chr2	199816501	199817145	+	0	NA	intron (NR_034096, intron 3 of 3)	L2a|LINE|L2	34350	NR_034096									0.006211	0.333333	
chunk0155_248_1	chr5	95727795	95728040	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-3229	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.000000	0.406504	
chunk0002_366_1	chr1	26097541	26098270	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-13260	NM_001243532	149420	Hs.468801	NM_152835	ENSG00000175087	PDIK1L	CLIK1L|STK35L2	PDLIM1 interacting kinase 1 like	protein-coding	0.004115	0.439726	
chunk0186_379_1	chr7	144255386	144255692	+	0	NA	intron (NR_126023, intron 3 of 4).2	intron (NR_126023, intron 3 of 4).2	-3936	NR_002158	401428	Hs.490448	NR_002158	ENSG00000170356	OR2A20P	OR2A20	olfactory receptor family 2 subfamily A member 20 pseudogene	pseudo	0.009804	0.446254	
chunk0099_57_1	chr2	84532233	84532661	+	0	NA	intron (NM_001370, intron 4 of 76)	intron (NM_001370, intron 4 of 76)	15992	NM_001370	1768	Hs.249972	NM_001370	ENSG00000115423	DNAH6	DNHL1|Dnahc6|HL-2|HL2	dynein axonemal heavy chain 6	protein-coding	0.002336	0.331002	
chunk0168_68_1	chr6	79408543	79409095	+	0	NA	Intergenic	Intergenic	-95435	NR_130915	80078		NR_130915	ENSG00000286042	LCAL1	onco-lncRNA-27	lung cancer associated lncRNA 1	ncRNA	0.010870	0.397830	
chunk0141_127_1	chr4	80161822	80162427	+	0	NA	Intergenic	Intergenic	-23146	NM_020226	56978	Hs.373642	NM_020226	ENSG00000152784	PRDM8	EPM10|KMT8D|PFM5	PR/SET domain 8	protein-coding	0.006612	0.371287	59(AGGTGCACTCTGTGCC,-,0.00),60(GGTGCACTCTGTGCCT,+,0.00)
chunk0085_39_1	chr18	649353	649702	+	0	NA	TTS (NM_001012716)	TTS (NM_001012716)	-8077	NM_001071	7298	Hs.369762	NM_001071	ENSG00000176890	TYMS	HST422|TMS|TS	thymidylate synthetase	protein-coding	0.014327	0.405714	
chunk0052_379_1	chr12	129064334	129064652	+	0	NA	Intergenic	Intergenic	-45197	NR_104173	283352	Hs.665667	NR_104172	ENSG00000249196	TMEM132D-AS1	-	TMEM132D antisense RNA 1	ncRNA	0.009434	0.579937	
chunk0143_184_1	chr4	112237905	112238348	+	0	NA	intron (NM_001128426, intron 1 of 8)	MER58A|DNA|hAT-Charlie	6387	NM_001128426	55435	Hs.435991	NM_018569	ENSG00000138660	AP1AR	2C18|C4orf16|GBAR|PRO0971|gamma-BAR	adaptor related protein complex 1 associated regulatory protein	protein-coding	0.002257	0.400901	
chunk0037_3_1	chr11	68847356	68848061	+	0	NA	Intergenic	Intergenic	-5777	NM_001031847	1374	Hs.503043	NM_001876	ENSG00000110090	CPT1A	CPT1|CPT1-L|L-CPT1	carnitine palmitoyltransferase 1A	protein-coding	0.012766	0.470255	292(CAGGACACCGTGTACT,-,0.00),293(AGGACACCGTGTACTG,+,0.00)
chunk0019_313_1	chr1	229069479	229069839	+	0	NA	Intergenic	L1MC|LINE|L1	105142	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.000000	0.373961	
chunk0089_351_1	chr18	66152539	66153088	+	0	NA	Intergenic	Intergenic	401892	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.003643	0.329091	
chunk0023_243_1	chr10	27033472	27034004	+	0	NA	intron (NM_014915, intron 24 of 33)	intron (NM_014915, intron 24 of 33)	66760	NM_014915	22852	Hs.361041	NM_014915	ENSG00000107890	ANKRD26	THC2|bA145E8.1	ankyrin repeat domain 26	protein-coding	0.007519	0.395872	
chunk0041_88_1	chr11	124492702	124492901	+	0	NA	Intergenic	Intergenic	50853	NM_001005195	219858	Hs.553634	NM_001005195	ENSG00000170953	OR8B12	OR11-317	olfactory receptor family 8 subfamily B member 12	protein-coding	0.005025	0.450000	
chunk0005_323_1	chr1	60940637	60941175	+	0	NA	intron (NR_110617, intron 6 of 6)	MER51B|LTR|ERV1	29870	NR_110618	100996570	Hs.46616	NR_110617	ENSG00000237928	NFIA-AS2	-	NFIA antisense RNA 2	ncRNA	0.005576	0.432282	
chunk0093_229_1	chr19	50492519	50492740	+	0	NA	Intergenic	Intergenic	-15883	NM_138411	112703	Hs.448941	NM_138411	ENSG00000142530	FAM71E1	-	family with sequence similarity 71 member E1	protein-coding	0.013575	0.567568	53(AGGAGCAGTGTGTGCA,-,0.00)
chunk0029_48_1	chr10	96381555	96382173	+	0	NA	intron (NM_012465, intron 16 of 20)	intron (NM_012465, intron 16 of 20)	-22499	NM_033207	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.006472	0.466882	
chunk0177_168_1	chr7	23299267	23299466	+	0	NA	promoter-TSS (NM_138446)	promoter-TSS (NM_138446)	45	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.130653	0.720000	
chunk0157_344_1	chr5	122750046	122750292	+	0	NA	Intergenic	MIR|SINE|MIR	-19609	NR_109881	101927379	Hs.536399	NR_109881	ENSG00000251538	LINC02201	-	long intergenic non-protein coding RNA 2201	ncRNA	0.004065	0.433198	
chunk0171_157_1	chr6	124038968	124039299	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	235287	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.000000	0.277108	
chunk0197_58_1	chr8	118609025	118609642	+	0	NA	intron (NR_109794, intron 1 of 4)	MER6|DNA|TcMar-Tigger	-11668	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.006483	0.386731	
chunk0076_6_1	chr16	58509580	58509798	+	0	NA	intron (NM_020465, intron 15 of 15)	intron (NM_020465, intron 15 of 15)	-5790	NM_024860	79918	Hs.731691	NM_024860	ENSG00000103037	SETD6	-	SET domain containing 6, protein lysine methyltransferase	protein-coding	0.018349	0.648402	
chunk0193_212_1	chr8	76314613	76315268	+	0	NA	Intergenic	L1M5|LINE|L1	-91714	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.004580	0.333841	
chunk0128_421_1	chr3	114880096	114880503	+	0	NA	intron (NM_001164343, intron 3 of 11)	intron (NM_001164343, intron 3 of 11)	7266	NR_126422	104413890	Hs.612732	NR_126422	ENSG00000239946	ZBTB20-AS3	-	ZBTB20 antisense RNA 3	ncRNA	0.009828	0.431373	
chunk0196_142_1	chr8	104423872	104424273	+	0	NA	intron (NM_001385, intron 7 of 9)	intron (NM_001385, intron 7 of 9)	42977	NM_001385	1807	Hs.443161	NM_001385	ENSG00000147647	DPYS	DHP|DHPase	dihydropyrimidinase	protein-coding	0.007481	0.373134	
chunk0041_27_1	chr12	737182	737519	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-15573	NM_001184985	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.011869	0.378698	126(AAGGACACCATGTCTT,-,0.00),127(AGGACACCATGTCTTA,+,0.00)
chunk0192_459_1	chr8	70271567	70271850	+	0	NA	intron (NM_006540, intron 2 of 22)	intron (NM_006540, intron 2 of 22)	132077	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.010601	0.436620	
chunk0135_140_1	chr3	187389756	187389955	+	0	NA	Intergenic	L1PB1|LINE|L1	21475	NM_022147	64108	Hs.43388	NM_022147	ENSG00000136514	RTP4	IFRG28|Z3CXXC4	receptor transporter protein 4	protein-coding	0.000000	0.350000	
chunk0192_204_1	chr8	64506027	64506340	+	0	NA	Intergenic	L1ME2|LINE|L1	71080	NR_015374	401463	Hs.651960	NR_015374	ENSG00000254102	LOC401463	-	uncharacterized LOC401463	ncRNA	0.003195	0.315287	
chunk0072_124_1	chr15	92600817	92601237	+	0	NA	Intergenic	Intergenic	-28764	NR_021493	100144604	Hs.245476	NR_021493	ENSG00000258647	LINC00930	-	long intergenic non-protein coding RNA 930	ncRNA	0.009524	0.446556	
chunk0190_8_1	chr8	28799776	28800550	+	0	NA	intron (NR_026826, intron 6 of 14)	L2b|LINE|L2	89752	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.009044	0.480000	
chunk0029_22_1	chr10	95561705	95561958	+	0	NA	promoter-TSS (NM_001290295)	promoter-TSS (NM_001290295)	-411	NM_001290295	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.039526	0.437008	
chunk0027_187_1	chr10	75518937	75519236	+	0	NA	intron (NM_001305581, intron 2 of 6)	L1PA6|LINE|L1	-33372	NR_030337	693191		NR_030337	ENSG00000207583	MIR606	MIRN606|hsa-mir-606	microRNA 606	ncRNA	0.000000	0.380000	
chunk0038_286_1	chr11	90104103	90104331	+	0	NA	Intergenic	Intergenic	18267	NM_001143975	642623	Hs.719885	NM_001143975	ENSG00000255009	UBTFL1	C11orf27|HMGPI	upstream binding transcription factor like 1	protein-coding	0.004386	0.292576	
chunk0173_109_1	chr6	143440162	143440391	+	0	NA	intron (NM_182503, intron 1 of 5)	intron (NM_182503, intron 1 of 5)	2401	NM_001286259	134637	Hs.709561	NM_182503	ENSG00000189007	ADAT2	DEADC1|TAD2|dJ20N2|dJ20N2.1	adenosine deaminase tRNA specific 2	protein-coding	0.000000	0.408696	
chunk0067_172_1	chr15	44189204	44189580	+	0	NA	intron (NM_001286490, intron 1 of 15)	intron (NM_001286490, intron 1 of 15)	5054	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.002660	0.408488	
chunk0204_405_1	chr9	102771588	102771974	+	0	NA	Intergenic	L1MA8|LINE|L1	-223530	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.002591	0.312661	
chunk0075_259_1	chr16	53471781	53472238	+	0	NA	intron (NM_005611, intron 17 of 21)	L1MB5|LINE|L1	31295	NM_001012398	64400	Hs.380897	NM_022476	ENSG00000166971	AKTIP	FT1|FTS	AKT interacting protein	protein-coding	0.004376	0.379913	
chunk0169_182_1	chr6	102420884	102421472	+	0	NA	Intergenic	L1PA15|LINE|L1	1022193	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003401	0.329372	
chunk0129_403_1	chr3	126768289	126768513	+	0	NA	intron (NM_032343, intron 4 of 7)	MSTA|LTR|ERVL-MaLR	64181	NM_032343	84303	Hs.518119	NM_032343	ENSG00000159685	CHCHD6	CHCM1|MICOS25|Mic25|PPP1R23	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.004464	0.448889	
chunk0160_124_1	chr5	150999631	151000356	+	0	NA	Intergenic	Intergenic	-20445	NM_002084	2878	Hs.386793	NM_002084	ENSG00000211445	GPX3	GPx-P|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding	0.008276	0.480716	
chunk0075_404_1	chr16	56967662	56968362	+	0	NA	intron (NM_001286085, intron 2 of 14)	intron (NM_001286085, intron 2 of 14)	6089	NM_000078	1071	Hs.89538	NM_000078	ENSG00000087237	CETP	BPIFF|HDLCQ10	cholesteryl ester transfer protein	protein-coding	0.014286	0.405136	
chunk0024_304_1	chr10	42619369	42619918	+	0	NA	intron (NR_130949, intron 3 of 5)	L1MB4|LINE|L1	19194	NM_001305038	7582	Hs.435774	NM_006955	ENSG00000196693	ZNF33B	KOX2|KOX31|ZNF11B	zinc finger protein 33B	protein-coding	0.000000	0.303636	
chunk0108_270_1	chr2	234368787	234369417	+	0	NA	Intergenic	Intergenic	127947	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.004762	0.458003	350(AGGAACAAACAGTGCT,-,0.00),351(GGAACAAACAGTGCTT,+,0.00)
chunk0116_377_1	chr21	42086150	42086665	+	0	NA	intron (NM_001004416, intron 4 of 22)	intron (NM_001004416, intron 4 of 22)	15090	NM_001004416	89766	Hs.242520	NM_173568	ENSG00000177398	UMODL1	-	uromodulin like 1	protein-coding	0.011650	0.550388	
chunk0195_184_1	chr8	96371677	96372158	+	0	NA	TTS (NR_125829)	TTS (NR_125829)	14731	NR_125829	102724804	Hs.571415	NR_125828	ENSG00000253105	LOC102724804	-	uncharacterized LOC102724804	ncRNA	0.008316	0.479253	
chunk0116_366_1	chr21	41767209	41767693	+	0	NA	promoter-TSS (NM_020639)	promoter-TSS (NM_020639)	-362	NM_020639	54101	Hs.517310	NM_020639	ENSG00000183421	RIPK4	ANKK2|ANKRD3|CHANDS|DIK|NKRD3|PKK|PPS2|RIP4	receptor interacting serine/threonine kinase 4	protein-coding	0.033058	0.437113	
chunk0076_300_1	chr16	70058239	70058554	+	0	NA	intron (NR_003610, intron 1 of 25)	intron (NR_003610, intron 1 of 25)	7552	NR_003610	283970	Hs.513695	NM_199134	ENSG00000196696	PDXDC2P-NPIPB14P	-	nuclear pore complex-interacting protein	pseudo	0.006349	0.405063	49(AAGAACATAATGTTCC,-,0.00),50(AGAACATAATGTTCCT,+,0.00)
chunk0166_209_1	chr6	46762775	46763220	+	0	NA	Intergenic	Intergenic	16080	NM_001162435	100287718	Hs.736491	NM_001162435	ENSG00000230062	ANKRD66	-	ankyrin repeat domain 66	protein-coding	0.000000	0.331839	
chunk0206_314_1	chr9	125147571	125147822	+	0	NA	3' UTR (NM_002721, exon 7 of 7)	3' UTR (NM_002721, exon 7 of 7)	-4137	NM_173690	286205	Hs.59504	NM_173690	ENSG00000173611	SCAI	C9orf126|NET40	suppressor of cancer cell invasion	protein-coding	0.007968	0.361111	
chunk0166_454_1	chr6	53279360	53279711	+	0	NA	intron (NM_001242830, intron 3 of 6)	L2b|LINE|L2	2542	NR_049866	100847075		NR_049866	ENSG00000264056	MIR5685	-	microRNA 5685	ncRNA	0.008547	0.431818	
chunk0042_154_1	chr12	3872275	3872908	+	0	NA	intron (NM_001286522, intron 1 of 7)	intron (NM_001286522, intron 1 of 7)	857	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.022117	0.454259	313(AAGAACATACAGTCCA,-,0.00),314(AGAACATACAGTCCAT,+,0.00)
chunk0026_415_1	chr10	70452950	70453295	+	0	NA	Intergenic	Intergenic	-11413	NM_018055	4838	Hs.370414	NM_018055	ENSG00000156574	NODAL	HTX5	nodal growth differentiation factor	protein-coding	0.002899	0.315029	104(AGGCACTGACTGTACC,-,0.00),105(GGCACTGACTGTACCA,+,0.00)
chunk0071_60_1	chr15	80419594	80420104	+	0	NA	intron (NM_014862, intron 1 of 18)	intron (NM_014862, intron 1 of 18)	15499	NM_014862	9915	Hs.459070	NM_014862	ENSG00000172379	ARNT2	WEDAS|bHLHe1	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.013725	0.522505	
chunk0165_350_1	chr6	38051982	38052475	+	0	NA	intron (NM_021943, intron 2 of 5)	intron (NM_021943, intron 2 of 5)	232697	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.002028	0.325911	
chunk0167_442_1	chr6	75874319	75874593	+	0	NA	intron (NM_001300899, intron 20 of 32)	L2b|LINE|L2	125264	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.007299	0.469091	71(CTGGTCAGCATGTTCT,-,0.00),72(TGGTCAGCATGTTCTG,+,0.00)
chunk0081_72_1	chr17	39110565	39110991	+	0	NA	intron (NM_020405, intron 2 of 13)	intron (NM_020405, intron 2 of 13)	40871	NM_020405	57125	Hs.125036	NM_020405	ENSG00000161381	PLXDC1	TEM3|TEM7	plexin domain containing 1	protein-coding	0.032864	0.625293	
chunk0102_263_1	chr2	149562541	149562829	+	0	NA	Intergenic	Intergenic	-24673	NR_110240	101929231	Hs.5324	NR_110240	ENSG00000231969	LOC101929231	-	uncharacterized LOC101929231	ncRNA	0.003472	0.335640	
chunk0209_264_1	chrX	46667063	46667279	+	0	NA	intron (NM_001257291, intron 5 of 16)	MIRb|SINE|MIR	92001	NM_032591	84679	Hs.91389	NM_032591	ENSG00000065923	SLC9A7	MRX108|NHE-7|NHE7|SLC9A6	solute carrier family 9 member A7	protein-coding	0.009259	0.460829	42(GGGTACACTCAGTGCC,-,0.00),43(GGTACACTCAGTGCCT,+,0.00),146(GGGGACAATGTGTGCC,-,0.00),147(GGGACAATGTGTGCCC,+,0.00)
chunk0047_204_1	chr12	71273736	71274063	+	0	NA	Intergenic	Intergenic	-115900	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.006116	0.362805	188(AAGAACATCGAGTTCT,-,0.00),189(AGAACATCGAGTTCTG,+,0.00)
chunk0070_181_1	chr15	71717408	71717757	+	0	NA	intron (NM_001286429, intron 2 of 11)	intron (NM_001286429, intron 2 of 11)	-26043	NR_120346	101929173	Hs.680593	NR_120346		THSD4-AS2	-	THSD4 antisense RNA 2	ncRNA	0.005731	0.411429	
chunk0203_99_1	chr9	84258418	84258777	+	0	NA	Intergenic	Intergenic	82182	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.019499	0.475000	103(GGGTACACTCTGTTCC,-,0.00),104(GGTACACTCTGTTCCT,+,0.00)
chunk0042_58_1	chr12	1936272	1937077	+	0	NA	promoter-TSS (NR_036546)	promoter-TSS (NR_036546)	-98	NR_036546	100271702	Hs.737031	NR_036546	ENSG00000235049	LINC00940	-	long intergenic non-protein coding RNA 940	ncRNA	0.032298	0.527295	
chunk0033_341_1	chr11	22798322	22798685	+	0	NA	intron (NM_177553, intron 7 of 7)	intron (NM_177553, intron 7 of 7)	31333	NM_148893	258010	Hs.349096	NM_148893	ENSG00000198168	SVIP	-	small VCP interacting protein	protein-coding	0.008264	0.315934	
chunk0115_23_1	chr21	20848163	20848627	+	0	NA	Intergenic	Intergenic	-45287	NR_109788	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.015086	0.361290	
chunk0195_55_1	chr8	93666239	93667456	+	0	NA	intron (NR_033858, intron 3 of 10)	SATR2|Satellite|Satellite	33586	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.015612	0.336617	
chunk0038_30_1	chr11	81166439	81166887	+	0	NA	Intergenic	Intergenic	-403860	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.004464	0.296214	
chunk0012_133_1	chr1	157221535	157222077	+	0	NA	Intergenic	L1MA8|LINE|L1	-83215	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.005535	0.364641	213(AATAACATAATGTTCT,-,0.00),214(ATAACATAATGTTCTC,+,0.00)
chunk0106_435_1	chr2	208489711	208490162	+	0	NA	intron (NM_001309516, intron 11 of 12)	L2a|LINE|L2	83106	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.004435	0.402655	
chunk0156_196_1	chr5	107945084	107945646	+	0	NA	intron (NM_001163315, intron 7 of 8)	L1ME3Cz|LINE|L1	-274470	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.005338	0.314387	
chunk0148_215_1	chr5	8675396	8675595	+	0	NA	Intergenic	Intergenic	-164237	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.005025	0.400000	
chunk0154_10_1	chr5	76570158	76570853	+	0	NA	intron (NM_006633, intron 3 of 35)	intron (NM_006633, intron 3 of 35)	23096	NM_001285460	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.012950	0.403736	
chunk0089_200_1	chr18	60024836	60025327	+	0	NA	Intergenic	L2a|LINE|L2	125121	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.002037	0.378049	208(TAGAACAGACTGTTCC,-,0.00),209(AGAACAGACTGTTCCA,+,0.00)
chunk0172_430_1	chr6	140749406	140750008	+	0	NA	Intergenic	L1M1|LINE|L1	65893	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.004983	0.344942	
chunk0119_216_1	chr22	45105099	45105725	+	0	NA	Intergenic	L1MC4|LINE|L1	47172	NR_038957	100506714	Hs.189902	NR_038956		NUP50-DT	NUP50-AS1	NUP50 divergent transcript	ncRNA	0.022364	0.473684	
chunk0123_346_1	chr3	47964709	47964919	+	0	NA	intron (NM_001134364, intron 3 of 17)	intron (NM_001134364, intron 3 of 17)	115259	NR_031595	100302232		NR_031595	ENSG00000221585	MIR1226	MIRN1226|hsa-mir-1226|mir-1226	microRNA 1226	ncRNA	0.014286	0.308057	
chunk0177_412_1	chr7	27548386	27548766	+	0	NA	intron (NM_152740, intron 4 of 7)	L2a|LINE|L2	-67398	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.002632	0.349081	
chunk0014_241_1	chr1	179954674	179954970	+	0	NA	promoter-TSS (NM_014810)	promoter-TSS (NM_014810)	49	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.084459	0.696970	
chunk0162_181_1	chr6	3741218	3741498	+	0	NA	intron (NM_183373, intron 1 of 4)	intron (NM_183373, intron 1 of 4)	10654	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.014286	0.430605	
chunk0105_226_1	chr2	188283502	188283892	+	0	NA	intron (NR_126396, intron 1 of 2)	L1PA16|LINE|L1	3994	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.002564	0.393862	136(GAATACAGCATGTTCT,-,0.00),137(AATACAGCATGTTCTC,+,0.00)
chunk0121_404_1	chr3	25595630	25595973	+	0	NA	intron (NM_001290216, intron 7 of 7)	intron (NM_001290216, intron 7 of 7)	68571	NM_001068	7155	Hs.475733	NM_001068	ENSG00000077097	TOP2B	TOPIIB|top2beta	DNA topoisomerase II beta	protein-coding	0.008746	0.377907	
chunk0004_378_1	chr1	51762585	51762909	+	0	NA	intron (NR_036662, intron 10 of 22)	L1ME3G|LINE|L1	32933	NM_148905	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.006173	0.360000	
chunk0125_60_1	chr3	64166917	64167309	+	0	NA	intron (NM_198859, intron 2 of 7)	intron (NM_198859, intron 2 of 7)	-20431	NR_046702	100874243	Hs.670840	NR_046702	ENSG00000226017	PRICKLE2-AS3	-	PRICKLE2 antisense RNA 3	ncRNA	0.002551	0.371501	
chunk0001_148_1	chr1	6052550	6053066	+	0	NA	intron (NM_001199862, intron 2 of 15)	MER53|DNA|hAT	6694	NM_001199863	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.027132	0.454545	
chunk0183_382_1	chr7	109812602	109812836	+	0	NA	Intergenic	L1MD2|LINE|L1	147494	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.004274	0.327660	
chunk0032_162_1	chr11	4956258	4956942	+	0	NA	promoter-TSS (NM_001004748)	promoter-TSS (NM_001004748)	-887	NM_001004748	401667	Hs.553805	NM_001004748	ENSG00000205496	OR51A2	-	olfactory receptor family 51 subfamily A member 2	protein-coding	0.004386	0.378102	382(TGGGACACAATGTGTT,-,0.00)
chunk0081_13_1	chr17	37270558	37270958	+	0	NA	exon (NM_198839, exon 14 of 60)	exon (NM_198839, exon 14 of 60)	25957	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.000000	0.341646	
chunk0043_230_1	chr12	19988132	19988840	+	0	NA	Intergenic	Intergenic	-26199	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.007062	0.400564	
chunk0194_71_1	chr8	82600270	82600469	+	0	NA	Intergenic	Intergenic	-758083	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.010050	0.310000	
chunk0029_447_1	chr10	110426283	110426482	+	0	NA	Intergenic	HAL1|LINE|L1	-71485	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.015075	0.440000	
chunk0091_435_1	chr19	17075301	17075779	+	0	NA	promoter-TSS (NM_001130065)	promoter-TSS (NM_001130065)	-7	NM_001011699	93323	Hs.404088	NM_033417	ENSG00000131351	HAUS8	DGT4|HICE1|NY-SAR-48	HAUS augmin like complex subunit 8	protein-coding	0.108787	0.701461	
chunk0119_203_1	chr22	44755699	44756318	+	0	NA	intron (NM_181335, intron 1 of 11)	intron (NM_181335, intron 1 of 11)	3450	NM_001017526	23779	Hs.102336	NM_181335	ENSG00000241484	ARHGAP8	BPGAP1|PP610	Rho GTPase activating protein 8	protein-coding	0.019386	0.525806	
chunk0061_392_1	chr14	64521495	64522177	+	0	NA	exon (NM_014950, exon 2 of 3)	exon (NM_014950, exon 2 of 3)	-16623	NM_001304508	7597	Hs.654571	NM_006977	ENSG00000089775	ZBTB25	C14orf51|KUP|ZNF46	zinc finger and BTB domain containing 25	protein-coding	0.008798	0.401171	
chunk0005_41_1	chr1	54882198	54883069	+	0	NA	intron (NM_014762, intron 2 of 8)	L1ME1|LINE|L1	4615	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.003444	0.376147	
chunk0212_204_1	chrX	134591297	134591813	+	0	NA	intron (NM_001316889, intron 1 of 1)	L1MDa|LINE|L1	41531	NR_038998	100506757	Hs.130961	NR_038998		LINC00629	LINC00629A|LINC00629B|LINC00629C|LINC00629D	long intergenic non-protein coding RNA 629	ncRNA	0.005814	0.384913	
chunk0121_341_1	chr3	24514161	24514668	+	0	NA	Intergenic	Intergenic	7021	NR_039955									0.007890	0.330709	
chunk0135_109_1	chr3	186860439	186860723	+	0	NA	Intergenic	Intergenic	-4458	NR_046662	100874095	Hs.638968	NR_046662	ENSG00000226482	ADIPOQ-AS1	-	ADIPOQ antisense RNA 1	ncRNA	0.000000	0.256140	
chunk0056_130_1	chr13	83166574	83167068	+	0	NA	Intergenic	MER54A|LTR|ERVL	715572	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002024	0.420202	
chunk0037_430_1	chr11	80196948	80197623	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	565518	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.005926	0.443787	
chunk0110_5_1	chr20	9581342	9581854	+	0	NA	intron (NM_020341, intron 4 of 10)	intron (NM_020341, intron 4 of 10)	-66600	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.007812	0.354776	
chunk0013_145_1	chr1	168491786	168492366	+	0	NA	intron (NR_125956, intron 2 of 4)	CR1_Mam|LINE|CR1	3568	NR_125956	101928565	Hs.563806	NR_125956	ENSG00000228697	LOC101928565	-	uncharacterized LOC101928565	ncRNA	0.001724	0.375215	
chunk0108_369_1	chr2	236679804	236680484	+	0	NA	Intergenic	L1M5|LINE|L1	110407	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.007353	0.381791	
chunk0009_436_1	chr1	111225589	111225818	+	0	NA	Intergenic	Intergenic	-1956	NM_001025197	1117	Hs.514840	NM_004000	ENSG00000064886	CHI3L2	CHIL2|YKL-39|YKL39	chitinase 3 like 2	protein-coding	0.017467	0.404348	
chunk0190_344_1	chr8	39237426	39237625	+	0	NA	intron (NM_001313994, intron 13 of 21)	L1PB1|LINE|L1	-77138	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.005025	0.595000	
chunk0196_148_1	chr8	104568722	104569088	+	0	NA	intron (NM_013437, intron 1 of 6)	L1MB7|LINE|L1	20119	NM_001135703	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.000000	0.354223	
chunk0020_35_1	chr1	232149980	232150179	+	0	NA	Intergenic	Intergenic	224245	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.010050	0.285000	
chunk0032_412_1	chr11	11993762	11994193	+	0	NA	intron (NM_001018057, intron 3 of 6)	intron (NM_001018057, intron 3 of 6)	14662	NM_001018057	27122	Hs.292156	NM_013253	ENSG00000050165	DKK3	REIC|RIG	dickkopf WNT signaling pathway inhibitor 3	protein-coding	0.018561	0.504630	266(AGGAACACAGAGCTCC,-,0.00),267(GGAACACAGAGCTCCT,+,0.00)
chunk0022_95_1	chr10	9605279	9605620	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-309856	NR_120635	101928272	Hs.650697	NR_120635		LOC101928272	-	uncharacterized LOC101928272	ncRNA	0.002933	0.447368	145(GAGAACAGCATGTTCC,-,0.00),146(AGAACAGCATGTTCCA,+,0.00)
chunk0200_331_1	chr9	23826185	23826601	+	0	NA	promoter-TSS (NM_004432)	promoter-TSS (NM_004432)	-328	NM_004432	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.062500	0.558753	
chunk0093_302_1	chr19	53103149	53103496	+	0	NA	5' UTR (NM_033288, exon 1 of 6)	5' UTR (NM_033288, exon 1 of 6)	112	NM_001102603	90338	Hs.655967	NM_033288	ENSG00000170949	ZNF160	F11|HKr18|HZF5|KR18	zinc finger protein 160	protein-coding	0.083573	0.629310	
chunk0033_404_1	chr11	24678969	24679464	+	0	NA	intron (NM_001252008, intron 1 of 11)	intron (NM_001252008, intron 1 of 11)	182246	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002020	0.290323	
chunk0088_5_1	chr18	43135634	43136188	+	0	NA	Intergenic	Intergenic	-20219	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.003610	0.396396	
chunk0071_43_1	chr15	79902067	79902569	+	0	NA	intron (NM_001100880, intron 2 of 2)	L2a|LINE|L2	-5033	NM_001199758	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.009960	0.429423	
chunk0130_442_1	chr3	141274891	141275458	+	0	NA	intron (NM_001282728, intron 3 of 6)	intron (NM_001282728, intron 3 of 6)	43349	NM_001037172	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.005291	0.512324	230(TAGTACAGGGTGATCT,-,0.00),231(AGTACAGGGTGATCTC,+,0.00)
chunk0208_127_1	chrX	15502419	15502975	+	0	NA	intron (NM_203281, intron 1 of 18)	intron (NM_203281, intron 1 of 18)	1920	NM_203281	660	Hs.495731	NM_001721	ENSG00000102010	BMX	ETK|PSCTK2|PSCTK3	BMX non-receptor tyrosine kinase	protein-coding	0.005396	0.403950	
chunk0193_218_1	chr8	76407009	76407555	+	0	NA	intron (NR_105006, intron 1 of 5)	intron (NR_105006, intron 1 of 5)	628	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.000000	0.285192	
chunk0031_275_1	chr10	128081233	128081727	+	0	NA	intron (NM_001316676, intron 21 of 21)	intron (NM_001316676, intron 21 of 21)	33931	NM_130435	5791	Hs.127022	NM_006504	ENSG00000132334	PTPRE	HPTPE|PTPE|R-PTP-EPSILON	protein tyrosine phosphatase receptor type E	protein-coding	0.010121	0.450505	
chunk0158_245_1	chr5	130391608	130391967	+	0	NA	Intergenic	L1PA7|LINE|L1	486957	NM_175856	337876	Hs.213137	NM_175856	ENSG00000198108	CHSY3	CHSY2|CSS3	chondroitin sulfate synthase 3	protein-coding	0.005571	0.333333	113(TGAACAACCTGCTCTT,+,0.00),196(AAAGACACAATGTACC,-,0.00)
chunk0104_180_1	chr2	174806519	174807276	+	0	NA	intron (NM_001822, intron 11 of 12)	intron (NM_001822, intron 11 of 12)	40721	NM_001206602	1123	Hs.380138	NM_001822	ENSG00000128656	CHN1	ARHGAP2|CHN|DURS2|NC|RHOGAP2	chimerin 1	protein-coding	0.014531	0.415567	
chunk0187_112_1	chr7	148437246	148437525	+	0	NA	Intergenic	LTR1A2|LTR|ERV1	-153180	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.017921	0.546429	
chunk0097_270_1	chr2	54866515	54866997	+	0	NA	intron (NM_001039753, intron 12 of 40)	intron (NM_001039753, intron 12 of 40)	141744	NM_001039753	400954	Hs.656692	NM_001039753	ENSG00000214595	EML6	-	EMAP like 6	protein-coding	0.012448	0.387164	
chunk0019_42_1	chr1	224040119	224040798	+	0	NA	Intergenic	Intergenic	-47814	NR_132119	441124	Hs.520589	NR_132119		GTF2IP20	-	general transcription factor IIi pseudogene 20	pseudo	0.008837	0.410294	
chunk0132_429_1	chr3	164938383	164938710	+	0	NA	Intergenic	HAL1|LINE|L1	-107066	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.000000	0.384146	
chunk0183_254_1	chr7	107224421	107224620	+	0	NA	intron (NM_006348, intron 19 of 21)	intron (NM_006348, intron 19 of 21)	55505	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.005025	0.535000	104(AGGGACAAGCTGTCCC,-,0.00),105(GGGACAAGCTGTCCCT,+,0.00)
chunk0082_358_1	chr17	60171062	60171636	+	0	NA	Intergenic	Intergenic	21408	NM_000717	762	Hs.89485	NM_000717	ENSG00000167434	CA4	CAIV|Car4|RP17	carbonic anhydrase 4	protein-coding	0.008711	0.509565	541(TGGAGCACTGTGTGCT,-,0.00),542(GGAGCACTGTGTGCTT,+,0.00)
chunk0075_341_1	chr16	55306121	55306409	+	0	NA	Intergenic	Intergenic	-18294	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.006944	0.397924	
chunk0183_409_1	chr7	110534665	110535196	+	0	NA	Intergenic	MIRb|SINE|MIR	-556076	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.005650	0.426692	
chunk0064_93_1	chr14	90815040	90815402	+	0	NA	intron (NM_001010854, intron 1 of 19)	intron (NM_001010854, intron 1 of 19)	1196	NM_001010854	145567	Hs.655697	NM_001010854	ENSG00000165914	TTC7B	TTC7L1|c14_5685	tetratricopeptide repeat domain 7B	protein-coding	0.016575	0.479339	
chunk0115_85_1	chr21	22225295	22225494	+	0	NA	Intergenic	MER57B1|LTR|ERV1	126777	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.000000	0.385000	
chunk0155_320_1	chr5	96677256	96677804	+	0	NA	intron (NM_001042440, intron 2 of 29)	intron (NM_001042440, intron 2 of 29)	15373	NM_001042440	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.005474	0.362477	113(ATGTACAGGATGTACA,-,0.00)
chunk0003_299_1	chr1	37537045	37537304	+	0	NA	3' UTR (NM_024700, exon 4 of 4)	3' UTR (NM_024700, exon 4 of 4)	17170	NM_024700	79753	Hs.47232	NM_024700	ENSG00000163877	SNIP1	PML1|PMRED	Smad nuclear interacting protein 1	protein-coding	0.003861	0.419231	
chunk0095_393_1	chr2	24015523	24015912	+	0	NA	intron (NM_001080473, intron 2 of 12)	intron (NM_001080473, intron 2 of 12)	5634	NM_001080473	388931	Hs.407482	NM_001080473	ENSG00000205639	MFSD2B	-	major facilitator superfamily domain containing 2B	protein-coding	0.005141	0.430769	199(GAAACACAGTGTCCAC,+,0.00),317(GAAACACAGTGTCCAC,+,0.00)
chunk0137_124_1	chr4	14866583	14866887	+	0	NA	intron (NR_126435, intron 1 of 6)	intron (NR_126435, intron 1 of 6)	21434	NR_126435	201853	Hs.551051	NR_126435	ENSG00000248360	LINC00504	-	long intergenic non-protein coding RNA 504	ncRNA	0.003289	0.380328	
chunk0024_441_1	chr10	46523999	46524375	+	0	NA	Intergenic	LTR8|LTR|ERV1	31884	NM_014696	9721	Hs.523375	NM_014696	ENSG00000204175	GPRIN2	GRIN2|KIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding	0.018617	0.456233	
chunk0036_238_1	chr11	64285497	64286059	+	0	NA	promoter-TSS (NM_001170880)	promoter-TSS (NM_001170880)	-332	NM_001170880	56834	Hs.523763	NM_020155	ENSG00000173264	GPR137	C11orf4|GPR137A|TM7SF1L1	G protein-coupled receptor 137	protein-coding	0.115658	0.721137	
chunk0019_247_1	chr1	227579366	227579872	+	0	NA	intron (NR_033184, intron 1 of 3)	L1PA13|LINE|L1	16100	NM_178549	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.005929	0.571992	
chunk0158_80_1	chr5	126503598	126504285	+	0	NA	Intergenic	Intergenic	38846	NM_001146322	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.010189	0.425872	
chunk0023_317_1	chr10	29104781	29105335	+	0	NA	Intergenic	Intergenic	-184003	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.010830	0.425225	
chunk0156_358_1	chr5	112364387	112364614	+	0	NA	intron (NM_022140, intron 1 of 22)	intron (NM_022140, intron 1 of 22)	54813	NM_022140	64097	Hs.584954	NM_022140	ENSG00000129595	EPB41L4A	EPB41L4|NBL4	erythrocyte membrane protein band 4.1 like 4A	protein-coding	0.004405	0.350877	
chunk0150_154_1	chr5	33888633	33888945	+	0	NA	intron (NM_030955, intron 1 of 23)	intron (NM_030955, intron 1 of 23)	3230	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.009615	0.415335	
chunk0019_365_1	chr1	229822025	229822798	+	0	NA	Intergenic	L1ME4a|LINE|L1	196195	NM_014777	9816	Hs.533628	NM_014777	ENSG00000135763	URB2	KIAA0133|NET10|NPA2	URB2 ribosome biogenesis homolog	protein-coding	0.006468	0.390181	
chunk0155_242_1	chr5	95677039	95677342	+	0	NA	intron (NR_125327, intron 2 of 8)	L2a|LINE|L2	5820	NR_125328	83890	Hs.50499	NM_031952	ENSG00000145757	SPATA9	NYD-SP16	spermatogenesis associated 9	protein-coding	0.006601	0.355263	
chunk0125_43_1	chr3	63821737	63821936	+	0	NA	intron (NR_026866, intron 1 of 6)	L1MD1|LINE|L1	2471	NR_026866									0.020101	0.410000	
chunk0039_411_1	chr11	107507942	107508365	+	0	NA	intron (NM_138775, intron 11 of 11)	intron (NM_138775, intron 11 of 11)	-50307	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.007092	0.405660	
chunk0065_311_1	chr14	103031295	103031549	+	0	NA	intron (NM_006035, intron 1 of 36)	intron (NM_006035, intron 1 of 36)	25983	NM_006035	9578	Hs.654634	NM_006035	ENSG00000198752	CDC42BPB	MRCKB	CDC42 binding protein kinase beta	protein-coding	0.007874	0.356863	
chunk0149_439_1	chr5	29780481	29780882	+	0	NA	Intergenic	Intergenic	-384705	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004988	0.365672	
chunk0048_377_1	chr12	86356991	86357490	+	0	NA	intron (NM_013244, intron 2 of 6)	L1PA5|LINE|L1	481664	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.008016	0.484000	
chunk0026_165_1	chr10	63202474	63203145	+	0	NA	intron (NM_001282948, intron 9 of 24)	intron (NM_001282948, intron 9 of 24)	66414	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.005961	0.333333	
chunk0205_160_1	chr9	108590215	108590616	+	0	NA	Intergenic	Intergenic	265580	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.009975	0.407960	189(AGGCACTCTTTGTTCT,-,0.00),190(GGCACTCTTTGTTCTC,+,0.00)
chunk0017_291_1	chr1	210377608	210378074	+	0	NA	intron (NM_001170580, intron 3 of 11)	intron (NM_001170580, intron 3 of 11)	48545	NM_001170580	55733	Hs.58650	NM_018194	ENSG00000054392	HHAT	MART2|SKI1|Skn	hedgehog acyltransferase	protein-coding	0.004292	0.413276	222(CAGGGCAGCCTGTGCC,-,0.00),223(AGGGCAGCCTGTGCCT,+,0.00)
chunk0129_416_1	chr3	127074027	127074719	+	0	NA	Intergenic	Intergenic	85779	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.008671	0.502165	
chunk0030_172_1	chr10	114162447	114163031	+	0	NA	exon (NM_018017, exon 2 of 16)	exon (NM_018017, exon 2 of 16)	11440	NR_031747	100302224		NR_031747	ENSG00000284442	MIR2110	hsa-mir-2110|mir-2110	microRNA 2110	ncRNA	0.008562	0.331624	279(TGGTACTCGATGTTCT,-,0.00),280(GGTACTCGATGTTCTG,+,0.00)
chunk0085_104_1	chr18	2755839	2756079	+	0	NA	intron (NM_015295, intron 34 of 47)	L1ME3B|LINE|L1	-91071	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.016667	0.352697	
chunk0122_70_1	chr3	29488927	29489197	+	0	NA	intron (NM_001003793, intron 3 of 14)	intron (NM_001003793, intron 3 of 14)	207750	NM_014483	27303	Hs.221436	NM_014483	ENSG00000144642	RBMS3	-	RNA binding motif single stranded interacting protein 3	protein-coding	0.000000	0.357934	
chunk0015_3_1	chr1	184074938	184075500	+	0	NA	Intergenic	Intergenic	23568	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.005338	0.373002	
chunk0067_413_1	chr15	49620594	49621252	+	0	NA	promoter-TSS (NM_020234)	promoter-TSS (NM_020234)	-2	NM_152647	196951	Hs.712959	NM_152647	ENSG00000166262	FAM227B	C15orf33	family with sequence similarity 227 member B	protein-coding	0.083587	0.610015	
chunk0038_410_1	chr11	94116452	94116689	+	0	NA	Intergenic	Intergenic	-12358	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.000000	0.411765	
chunk0191_259_1	chr8	53386848	53387131	+	0	NA	Intergenic	Intergenic	-135292	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.007067	0.436620	
chunk0193_275_1	chr8	77303757	77304032	+	0	NA	Intergenic	Intergenic	-146803	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.007273	0.344203	109(CTGCACTCCGTGTTCT,-,0.00),110(TGCACTCCGTGTTCTG,+,0.00)
chunk0031_218_1	chr10	126032375	126032838	+	0	NA	intron (NM_001288973, intron 21 of 22)	intron (NM_001288973, intron 21 of 22)	-59333	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.004320	0.398707	
chunk0191_404_1	chr8	57571496	57571791	+	0	NA	Intergenic	L2c|LINE|L2	227856	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.003390	0.422297	
chunk0044_269_1	chr12	32399002	32399924	+	0	NA	Intergenic	CpG	-86509	NM_001304481	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.106291	0.703142	361(GGGCACAGCAAGTTCT,-,0.00),362(GGCACAGCAAGTTCTT,+,0.00)
chunk0131_302_1	chr3	150696828	150697429	+	0	NA	intron (NM_152394, intron 3 of 13)	L1ME3G|LINE|L1	-6436	NR_121675	101928085	Hs.561114	NR_121674	ENSG00000240137	ERICH6-AS1	-	ERICH6 antisense RNA 1	ncRNA	0.008319	0.338870	
chunk0100_262_1	chr2	113253425	113253791	+	0	NA	intron (NR_015377, intron 2 of 5)	L2c|LINE|L2	17339	NR_015377	654433	Hs.656660	NR_015377	ENSG00000189223	PAX8-AS1	-	PAX8 antisense RNA 1	ncRNA	0.010929	0.495913	126(AGTAACAGTGTGTCCC,-,0.00),127(GTAACAGTGTGTCCCC,+,0.00),156(TTGCACATGCTGTTCC,-,0.00),157(TGCACATGCTGTTCCC,+,0.00)
chunk0204_54_1	chr9	93223317	93223882	+	0	NA	intron (NM_001282394, intron 1 of 29)	intron (NM_001282394, intron 1 of 29)	38669	NM_001282394	65268	Hs.654856	NM_006648	ENSG00000165238	WNK2	NY-CO-43|P/OKcl.13|PRKWNK2|SDCCAG43	WNK lysine deficient protein kinase 2	protein-coding	0.015929	0.584806	
chunk0065_199_1	chr14	100059191	100059827	+	0	NA	Intergenic	Intergenic	-5905	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.006289	0.474097	
chunk0073_127_1	chr16	4888840	4889121	+	0	NA	exon (NM_002705, exon 19 of 22)	exon (NM_002705, exon 19 of 22)	40600	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.021352	0.507092	
chunk0202_165_1	chr9	73806707	73807260	+	0	NA	Intergenic	Intergenic	-564548	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.003617	0.361011	
chunk0145_207_1	chr4	147940151	147940656	+	0	NA	intron (NM_024605, intron 14 of 22)	intron (NM_024605, intron 14 of 22)	157808	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.007921	0.448617	245(GATAACACAGTGTTCT,-,0.00),246(ATAACACAGTGTTCTT,+,0.00)
chunk0195_60_1	chr8	93726909	93727291	+	0	NA	intron (NR_104268, intron 8 of 8)	MER58A|DNA|hAT-Charlie	-13011	NR_027259	55472	Hs.192788	NM_018608	ENSG00000279331	RBM12B-AS1	C8orf39|PRO1905	RBM12B antisense RNA 1	ncRNA	0.002618	0.352480	
chunk0010_132_1	chr1	114715656	114715855	+	0	NA	intron (NM_002524, intron 2 of 6)	intron (NM_002524, intron 2 of 6)	1139	NM_002524	4893	Hs.486502	NM_002524	ENSG00000213281	NRAS	ALPS4|CMNS|N-ras|NCMS|NRAS1|NS6	NRAS proto-oncogene, GTPase	protein-coding	0.005025	0.345000	
chunk0077_443_1	chr16	85720218	85720563	+	0	NA	intron (NM_206967, intron 2 of 3)	intron (NM_206967, intron 2 of 3)	21310	NR_031731	100302261		NR_031731	ENSG00000283416	MIR1910	MIRN1910|hsa-mir-1910|mir-1910	microRNA 1910	ncRNA	0.014493	0.595376	
chunk0205_286_1	chr9	111887213	111887489	+	0	NA	Intergenic	Intergenic	-9415	NM_003358	7357	Hs.304249	NM_003358	ENSG00000148154	UGCG	GCS|GLCT1	UDP-glucose ceramide glucosyltransferase	protein-coding	0.047101	0.498195	
chunk0184_252_1	chr7	117959653	117960047	+	0	NA	Intergenic	Intergenic	-86343	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.002538	0.389873	
chunk0043_157_1	chr12	16473611	16474407	+	0	NA	Intergenic	Intergenic	120592	NM_145764	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.006281	0.382685	440(GTGAACAATTTGTTCT,-,0.00),441(TGAACAATTTGTTCTG,+,0.00)
chunk0117_140_1	chr22	19479192	19479524	+	0	NA	promoter-TSS (NM_001178011)	promoter-TSS (NM_001178011)	-143	NM_001035247	7353	Hs.474213	NM_005659	ENSG00000070010	UFD1	UFD1L	ubiquitin recognition factor in ER associated degradation 1	protein-coding	0.054217	0.504505	
chunk0120_401_1	chr3	12598831	12599473	+	0	NA	intron (NM_002880, intron 10 of 16)	intron (NM_002880, intron 10 of 16)	42138	NM_001271707	23609	Hs.591666	NM_014160	ENSG00000075975	MKRN2	HSPC070|RNF62	makorin ring finger protein 2	protein-coding	0.000000	0.385692	
chunk0133_435_1	chr3	174949645	174949848	+	0	NA	intron (NM_207015, intron 1 of 13)	intron (NM_207015, intron 1 of 13)	90425	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.004926	0.367647	
chunk0086_325_1	chr18	24421331	24422140	+	0	NA	Intergenic	MER57E1|LTR|ERV1	-4910	NM_018439	55364	Hs.515317	NM_018439	ENSG00000154059	IMPACT	RWDD5	impact RWD domain protein	protein-coding	0.002472	0.349383	294(AAGATCATTGTGTACT,-,0.00),295(AGATCATTGTGTACTA,+,0.00),759(TAGAGCAGTTTGTTCT,-,0.00),760(AGAGCAGTTTGTTCTA,+,0.00)
chunk0173_27_1	chr6	141980283	141980534	+	0	NA	Intergenic	Intergenic	108391	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.003984	0.317460	
chunk0188_132_1	chr8	9354149	9354569	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	29308	NR_040039	157273	Hs.650222	NR_040039	ENSG00000248538	LOC157273	-	uncharacterized LOC157273	ncRNA	0.007143	0.358670	
chunk0173_88_1	chr6	142845708	142846296	+	0	NA	intron (NM_006734, intron 1 of 9)	intron (NM_006734, intron 1 of 9)	99199	NM_006734	3097	Hs.510172	NM_006734	ENSG00000010818	HIVEP2	HIV-EP2|MBP-2|MIBP1|MRD43|SHN2|ZAS2|ZNF40B	human immunodeficiency virus type I enhancer binding protein 2	protein-coding	0.030612	0.560272	362(GAGGACAGCCTGCACC,-,0.00),363(AGGACAGCCTGCACCA,+,0.00)
chunk0006_341_1	chr1	72441766	72441965	+	0	NA	Intergenic	Intergenic	-159271	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.005025	0.295000	
chunk0193_346_1	chr8	79618340	79618556	+	0	NA	intron (NM_001199214, intron 1 of 5)	intron (NM_001199214, intron 1 of 5)	7634	NM_001199214	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.004630	0.322581	
chunk0055_38_1	chr13	52117752	52118444	+	0	NA	intron (NM_199289, intron 4 of 21)	intron (NM_199289, intron 4 of 21)	-10797	NR_110306	101929657	Hs.637461	NR_110306	ENSG00000273523	LOC101929657	-	uncharacterized LOC101929657	ncRNA	0.002890	0.399711	377(AGGAACACAGTGCTCT,-,0.00),378(GGAACACAGTGCTCTG,+,0.00)
chunk0030_406_1	chr10	120100901	120101509	+	0	NA	Intergenic	FLAM_C|SINE|Alu	142692	NR_039830	100616322		NR_039830	ENSG00000265370	MIR4682	-	microRNA 4682	ncRNA	0.008224	0.430213	
chunk0016_278_1	chr1	200707517	200707919	+	0	NA	Intergenic	L2a|LINE|L2	-31840	NM_001297707	23271	Hs.23585	NM_203459	ENSG00000118200	CAMSAP2	CAMSAP1L1	calmodulin regulated spectrin associated protein family member 2	protein-coding	0.000000	0.436725	200(AGGAACAGAATGGTCC,-,0.00),201(GGAACAGAATGGTCCA,+,0.00)
chunk0011_235_1	chr1	150529024	150529382	+	0	NA	Intergenic	L2|LINE|L2	13446	NR_051960	100874054	Hs.576460	NR_051960	ENSG00000228126	FALEC	FAL1|LINC00568|ncRNA-a1	focally amplified long non-coding RNA in epithelial cancer	ncRNA	0.011173	0.445682	
chunk0094_304_1	chr2	8605624	8606143	+	0	NA	Intergenic	Intergenic	-22091	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.013487	0.396154	
chunk0079_183_1	chr17	14098390	14099068	+	0	NA	intron (NM_001303, intron 3 of 6)	MamRTE1|LINE|RTE-BovB	-29271	NR_049718	100874058	Hs.720411	NR_049718	ENSG00000236088	COX10-AS1	COX10-AS|COX10AS	COX10 antisense RNA 1	ncRNA	0.008850	0.422680	538(CAGAACAGGCTGTACC,-,0.00),539(AGAACAGGCTGTACCC,+,0.00)
chunk0082_78_1	chr17	51640240	51640568	+	0	NA	intron (NM_001082534, intron 7 of 9)	intron (NM_001082534, intron 7 of 9)	303689	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.009146	0.465046	
chunk0125_184_1	chr3	66693343	66693926	+	0	NA	Intergenic	Intergenic	-193213	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.013722	0.462329	
chunk0199_403_1	chr9	13459310	13459555	+	0	NA	Intergenic	Intergenic	-28103	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.008163	0.451220	
chunk0004_12_1	chr1	42081569	42081868	+	0	NA	Intergenic	L1MA4A|LINE|L1	-45793	NR_038261	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.006689	0.586667	
chunk0041_52_1	chr11	123221425	123222152	+	0	NA	Intergenic	Intergenic	-26483	NM_024769	79827	Hs.591949	NM_024769	ENSG00000166250	CLMP	ACAM|ASAM|CSBM|CSBS	CXADR like membrane protein	protein-coding	0.004127	0.357143	
chunk0199_166_1	chr9	4425437	4425948	+	0	NA	Intergenic	Intergenic	-64735	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.003914	0.505859	
chunk0199_177_1	chr9	4591021	4591367	+	0	NA	Intergenic	Intergenic	-71100	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.005780	0.446686	
chunk0034_402_1	chr11	37365070	37365269	+	0	NA	Intergenic	L1PB3|LINE|L1	-766890	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.005025	0.485000	
chunk0101_165_1	chr2	128595180	128595429	+	0	NA	Intergenic	L2a|LINE|L2	-269296	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.020080	0.536000	
chunk0096_415_1	chr2	38156623	38156977	+	0	NA	intron (NR_027252, intron 2 of 2)	intron (NR_027252, intron 2 of 2)	25695	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.008475	0.400000	
chunk0206_95_1	chr9	120663963	120664413	+	0	NA	intron (NM_001080497, intron 1 of 5)	intron (NM_001080497, intron 1 of 5)	50299	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.000000	0.356984	
chunk0180_256_1	chr7	69398714	69398967	+	0	NA	Intergenic	Intergenic	198655	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.007905	0.472441	
chunk0156_78_1	chr5	104005129	104005479	+	0	NA	Intergenic	Intergenic	-442503	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.008571	0.310541	108(CAGTACTTTATGTTCT,-,0.00),109(AGTACTTTATGTTCTA,+,0.00)
chunk0198_281_1	chr8	135536177	135536423	+	0	NA	intron (NM_006558, intron 2 of 8)	intron (NM_006558, intron 2 of 8)	78835	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.004065	0.360324	
chunk0120_8_1	chr3	900512	900818	+	0	NA	Intergenic	L1MA6|LINE|L1	-191993	NM_001289080	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.009804	0.527687	
chunk0018_256_1	chr1	220240837	220241490	+	0	NA	intron (NM_012414, intron 1 of 34)	intron (NM_012414, intron 1 of 34)	26552	NR_001587	6791	Hs.654849	NR_001587		AURKAP1	AURKAPS1|AurAps1|STK6P	aurora kinase A pseudogene 1	pseudo	0.001531	0.290520	349(CTGAACAGTCTGTCCT,-,0.00),350(TGAACAGTCTGTCCTC,+,0.00)
chunk0154_279_1	chr5	82473813	82474203	+	0	NA	Intergenic	L1ME4c|LINE|L1	194546	NM_001017971	92270	Hs.676227	NM_001017971	ENSG00000205464	ATP6AP1L	-	ATPase H+ transporting accessory protein 1 like	protein-coding	0.005128	0.363171	
chunk0027_369_1	chr10	79246014	79246643	+	0	NA	intron (NM_020338, intron 7 of 24)	intron (NM_020338, intron 7 of 24)	-101136	NM_005729	10105	Hs.381072	NM_005729	ENSG00000108179	PPIF	CYP3|CyP-M|Cyp-D|CypD	peptidylprolyl isomerase F	protein-coding	0.030207	0.598413	357(AGGAACAGAGAGTTCT,-,0.00),358(GGAACAGAGAGTTCTG,+,0.00),587(GGTACAGAGTGCACCT,+,0.00)
chunk0097_187_1	chr2	50407770	50408467	+	0	NA	intron (NM_001135659, intron 18 of 23)	L2c|LINE|L2	-60362	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.002869	0.359599	
chunk0071_55_1	chr15	80197293	80197770	+	0	NA	non-coding (NR_120317, exon 3 of 3)	non-coding (NR_120317, exon 3 of 3)	44640	NM_000137	2184	Hs.73875	NM_000137	ENSG00000103876	FAH	-	fumarylacetoacetate hydrolase	protein-coding	0.002096	0.504184	
chunk0086_46_1	chr18	12738466	12738687	+	0	NA	TTS (NR_110763)	TTS (NR_110763)	10846	NR_110763	100996324	Hs.333275	NR_110763		LINC01882	-	long intergenic non-protein coding RNA 1882	ncRNA	0.009050	0.549550	
chunk0084_193_1	chr17	78029088	78029557	+	0	NA	intron (NM_018996, intron 2 of 20)	Tigger3|DNA|TcMar-Tigger	25085	NM_018996	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.012793	0.414894	
chunk0177_407_1	chr7	27459653	27460033	+	0	NA	Intergenic	Intergenic	-156131	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.007895	0.364829	
chunk0177_173_1	chr7	23332098	23332773	+	0	NA	intron (NM_006547, intron 10 of 14)	intron (NM_006547, intron 10 of 14)	33114	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.000000	0.362426	
chunk0076_41_1	chr16	59880579	59881162	+	0	NA	intron (NR_110917, intron 1 of 3)	intron (NR_110917, intron 1 of 3)	25517	NR_110917	101927580	Hs.552235	NR_110917	ENSG00000261807	LINC02141	-	long intergenic non-protein coding RNA 2141	ncRNA	0.003431	0.386986	
chunk0004_73_1	chr1	43541449	43542412	+	0	NA	intron (NM_130440, intron 2 of 32)	intron (NM_130440, intron 2 of 32)	11054	NM_002840	5792	Hs.272062	NM_002840	ENSG00000142949	PTPRF	BNAH2|LAR	protein tyrosine phosphatase receptor type F	protein-coding	0.016615	0.511411	
chunk0104_266_1	chr2	177882376	177882938	+	0	NA	intron (NM_001077197, intron 5 of 20)	intron (NM_001077197, intron 5 of 20)	6082	NM_001077196	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.001779	0.300178	
chunk0110_201_1	chr20	14879008	14879347	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	50341	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.005900	0.320588	
chunk0040_46_1	chr11	110775215	110775830	+	0	NA	Intergenic	MIRc|SINE|MIR	-62333	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.006504	0.443182	
chunk0101_415_1	chr2	139189360	139189959	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	292335	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005008	0.335000	
chunk0096_165_1	chr2	29450781	29451309	+	0	NA	intron (NM_004304, intron 4 of 28)	intron (NM_004304, intron 4 of 28)	335619	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.009470	0.431002	
chunk0102_272_1	chr2	150120215	150120621	+	0	NA	Intergenic	Intergenic	367277	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.022167	0.393120	
chunk0195_43_1	chr8	93360337	93360612	+	0	NA	intron (NR_033858, intron 10 of 10)	intron (NR_033858, intron 10 of 10)	-193624	NM_001242668									0.003636	0.391304	28(TGGCACAAACTGTGCA,-,0.00),29(GGCACAAACTGTGCAG,+,0.00)
chunk0184_384_1	chr7	121475736	121476234	+	0	NA	Intergenic	Intergenic	-79617	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.004016	0.402806	
chunk0192_70_1	chr8	60593209	60593587	+	0	NA	intron (NM_001242644, intron 5 of 6)	L1MD1|LINE|L1	76488	NM_002865	5862	Hs.369017	NM_002865	ENSG00000104388	RAB2A	LHX|RAB2	RAB2A, member RAS oncogene family	protein-coding	0.010582	0.459103	
chunk0058_268_1	chr14	26087532	26087888	+	0	NA	Intergenic	Intergenic	510044	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.005618	0.400560	174(GGGAACACTTTGTACA,-,0.00),175(GGAACACTTTGTACAT,+,0.00)
chunk0035_127_1	chr11	42724431	42724813	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-470932	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.005236	0.357702	
chunk0199_416_1	chr9	13615741	13616113	+	0	NA	Intergenic	L3|LINE|CR1	-184598	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.000000	0.364611	
chunk0151_151_1	chr5	49599436	49600910	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	841227	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.007463	0.455593	
chunk0176_226_1	chr7	15295663	15296036	+	0	NA	intron (NM_001004320, intron 12 of 12)	intron (NM_001004320, intron 12 of 12)	266166	NM_001004320	392636	Hs.670634	NM_001004320	ENSG00000187546	AGMO	TMEM195	alkylglycerol monooxygenase	protein-coding	0.005362	0.278075	
chunk0135_27_1	chr3	184718511	184718807	+	0	NA	Intergenic	L2c|LINE|L2	-6611	NM_022149	64110	Hs.306123	NM_022149	ENSG00000177383	MAGEF1	MAGE-F1	MAGE family member F1	protein-coding	0.010135	0.498316	
chunk0187_107_1	chr8	5675989	5676310	+	0	NA	Intergenic	Intergenic	-681343	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.003115	0.354037	
chunk0094_441_1	chr2	11387858	11388365	+	0	NA	Intergenic	MER57E1|LTR|ERV1	-5870	NR_047499	100874055	Hs.102428	NR_047499	ENSG00000224177	LINC00570	ncRNA-a5	long intergenic non-protein coding RNA 570	ncRNA	0.015779	0.411417	
chunk0055_213_1	chr13	62203953	62204336	+	0	NA	Intergenic	Intergenic	-8138	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.007833	0.299479	
chunk0086_11_1	chr18	12103201	12103714	+	0	NA	intron (NM_001277333, intron 7 of 13)	intron (NM_001277333, intron 7 of 13)	9608	NM_001277333	342850	Hs.448906	NM_001277333	ENSG00000181626	ANKRD62	DKFZp779B1634	ankyrin repeat domain 62	protein-coding	0.000000	0.280156	
chunk0179_394_1	chr7	51440609	51440878	+	0	NA	Intergenic	L1MB8|LINE|L1	-123925	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.003717	0.292593	
chunk0114_190_1	chr21	15054573	15055124	+	0	NA	intron (NM_003489, intron 1 of 3)	intron (NM_003489, intron 1 of 3)	9957	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.007260	0.403986	
chunk0102_334_1	chr2	151959234	151959589	+	0	NA	intron (NM_001005746, intron 2 of 13)	intron (NM_001005746, intron 2 of 13)	14560	NM_001005747	785	Hs.120725	NM_000726	ENSG00000182389	CACNB4	CAB4|CACNLB4|EA5|EIG9|EJM|EJM4|EJM6	calcium voltage-gated channel auxiliary subunit beta 4	protein-coding	0.002817	0.390449	150(CAGAACAAGGTGTCCC,-,0.00),151(AGAACAAGGTGTCCCA,+,0.00)
chunk0003_238_1	chr1	35929677	35930076	+	0	NA	TTS (NM_012199)	TTS (NM_012199)	-1206	NM_024852	192669	Hs.657659	NM_024852	ENSG00000126070	AGO3	EIF2C3	argonaute RISC catalytic component 3	protein-coding	0.002506	0.335000	190(AGGTACATGCTGTTCT,-,0.00),191(GGTACATGCTGTTCTC,+,0.00)
chunk0124_335_1	chr3	58260828	58261038	+	0	NA	intron (NM_020676, intron 2 of 8)	intron (NM_020676, intron 2 of 8)	23401	NM_020676	57406	Hs.476454	NM_020676	ENSG00000163686	ABHD6	-	abhydrolase domain containing 6	protein-coding	0.009524	0.559242	
chunk0036_299_1	chr11	65873437	65873774	+	0	NA	promoter-TSS (NR_037718)	promoter-TSS (NR_037718)	-671	NM_016938	30008	Hs.731454	NM_016938	ENSG00000172638	EFEMP2	ARCL1B|FBLN4|MBP1|UPH1	EGF containing fibulin extracellular matrix protein 2	protein-coding	0.077151	0.677515	
chunk0088_201_1	chr18	47873351	47873688	+	0	NA	intron (NM_001003652, intron 2 of 10)	L1M5|LINE|L1	57080	NM_005901	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.000000	0.295858	
chunk0152_11_1	chr5	56300982	56301222	+	0	NA	Intergenic	Intergenic	-67743	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.000000	0.510373	7(CTGCACATTCTGTGCC,-,0.00),8(TGCACATTCTGTGCCC,+,0.00)
chunk0093_317_1	chr19	53775401	53775890	+	0	NA	Intergenic	Intergenic	-12030	NR_029864	442916		NR_029864	ENSG00000199031	MIR371A	MIR371|MIRN371|hsa-mir-371|hsa-mir-371a	microRNA 371a	ncRNA	0.044990	0.508163	
chunk0119_348_1	chr22	47144405	47144703	+	0	NA	intron (NM_014346, intron 12 of 12)	intron (NM_014346, intron 12 of 12)	-228512	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.043624	0.628763	
chunk0004_315_1	chr1	49464909	49465127	+	0	NA	intron (NR_046839, intron 2 of 3)	intron (NR_046839, intron 2 of 3)	7067	NR_046839	100874313	Hs.551277	NR_046839	ENSG00000225623	AGBL4-IT1	-	AGBL4 intronic transcript 1	ncRNA	0.000000	0.424658	
chunk0052_294_1	chr12	124520126	124520694	+	0	NA	intron (NM_006312, intron 2 of 48)	intron (NM_006312, intron 2 of 48)	47054	NM_006312	9612	Hs.137510	NM_006312	ENSG00000196498	NCOR2	CTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1	nuclear receptor corepressor 2	protein-coding	0.029930	0.562390	
chunk0147_235_1	chr4	182568871	182569239	+	0	NA	intron (NM_001080477, intron 3 of 27)	L1ME2|LINE|L1	325624	NM_001080477	55714	Hs.130438	NM_001080477	ENSG00000218336	TENM3	MCOPCB9|ODZ3|TNM3|Ten-m3|ten-3	teneurin transmembrane protein 3	protein-coding	0.008152	0.398374	167(GAAGACAGTGTGTGCT,-,0.00),168(AAGACAGTGTGTGCTA,+,0.00)
chunk0083_427_1	chr17	72468239	72468687	+	0	NA	intron (NR_036488, intron 1 of 3)	intron (NR_036488, intron 1 of 3)	124341	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.022321	0.518931	192(CTGAACTGTGTGTGCT,-,0.00),193(TGAACTGTGTGTGCTT,+,0.00)
chunk0123_218_1	chr3	45202452	45202687	+	0	NA	Intergenic	L1ME3A|LINE|L1	23753	NM_015444	25907	Hs.740403	NM_015444	ENSG00000249992	TMEM158	BBP|RIS1|p40BBP	transmembrane protein 158 (gene/pseudogene)	protein-coding	0.008511	0.415254	
chunk0090_35_1	chr19	1383600	1383891	+	0	NA	promoter-TSS (NM_024407)	promoter-TSS (NM_024407)	-139	NM_024407	374291	Hs.211914	NM_024407	ENSG00000115286	NDUFS7	CI-20|CI-20KD|MC1DN3|MY017|PSST	NADH:ubiquinone oxidoreductase core subunit S7	protein-coding	0.113402	0.650685	
chunk0126_148_1	chr3	76565646	76566381	+	0	NA	Intergenic	Intergenic	-474130	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.006803	0.427989	
chunk0008_82_1	chr1	89992013	89992335	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	2792	NR_002830	492303	Hs.550796	NR_002830		GEMIN8P4	-	gem nuclear organelle associated protein 8 pseudogene 4	pseudo	0.006211	0.405573	
chunk0092_95_1	chr19	23107545	23108071	+	0	NA	Intergenic	Intergenic	-9167	NM_001277403	100129543	Hs.427120	NM_001277403	ENSG00000183850	ZNF730	-	zinc finger protein 730	protein-coding	0.005703	0.375712	
chunk0120_344_1	chr3	11366902	11367716	+	0	NA	intron (NM_001136031, intron 16 of 17)	intron (NM_001136031, intron 16 of 17)	94985	NM_001144912	10533	Hs.38032	NM_006395	ENSG00000197548	ATG7	APG7-LIKE|APG7L|GSA7	autophagy related 7	protein-coding	0.003686	0.431902	
chunk0202_415_1	chr9	81619034	81619371	+	0	NA	intron (NM_005077, intron 9 of 19)	intron (NM_005077, intron 9 of 19)	70333	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002967	0.402367	
chunk0109_271_1	chr20	8066661	8067424	+	0	NA	Intergenic	Intergenic	-47213	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.007864	0.342932	
chunk0028_456_1	chr10	94784199	94784537	+	0	NA	intron (NM_000769, intron 5 of 8)	L1MB5|LINE|L1	21687	NM_000769	1557	Hs.282409	NM_000769	ENSG00000165841	CYP2C19	CPCJ|CYP2C|CYPIIC17|CYPIIC19|P450C2C|P450IIC19	cytochrome P450 family 2 subfamily C member 19	protein-coding	0.000000	0.318584	
chunk0056_257_1	chr13	89799505	89799704	+	0	NA	Intergenic	L1PA16|LINE|L1	-235191	NR_046991	100874139	Hs.742173	NR_046991		LINC00353	-	long intergenic non-protein coding RNA 353	ncRNA	0.000000	0.295000	
chunk0027_270_1	chr10	77381712	77382340	+	0	NA	intron (NM_001271518, intron 1 of 27)	intron (NM_001271518, intron 1 of 27)	31154	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.007962	0.475358	
chunk0006_404_1	chr1	75590897	75591201	+	0	NA	intron (NM_001130058, intron 1 of 23)	L1MA1|LINE|L1	20065	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.003289	0.501639	
chunk0154_360_1	chr5	87540987	87541469	+	0	NA	Intergenic	Intergenic	-128195	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.002075	0.383023	
chunk0145_98_1	chr4	146020636	146020864	+	0	NA	Intergenic	L1MA3|LINE|L1	-81790	NM_001306215	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.000000	0.279476	
chunk0038_160_1	chr11	84858425	84859145	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	64636	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.005556	0.323162	
chunk0013_289_1	chr1	171061922	171062121	+	0	NA	intron (NM_001163629, intron 20 of 21)	intron (NM_001163629, intron 20 of 21)	-28856	NM_001002294	2328	Hs.445350	NM_006894	ENSG00000007933	FMO3	FMOII|TMAU|dJ127D3.1	flavin containing dimethylaniline monoxygenase 3	protein-coding	0.000000	0.270000	
chunk0006_259_1	chr1	69573727	69574021	+	0	NA	Intergenic	Intergenic	-186301	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.006803	0.298305	
chunk0005_300_1	chr1	60374499	60375302	+	0	NA	Intergenic	Intergenic	-301130	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.003736	0.415423	
chunk0138_451_1	chr4	47435868	47436467	+	0	NA	Intergenic	Intergenic	27492	NM_017845	54951	Hs.23956	NM_017845	ENSG00000169019	COMMD8	-	COMM domain containing 8	protein-coding	0.011686	0.398333	274(CAGAACATCCAGTACT,-,0.00),275(AGAACATCCAGTACTC,+,0.00)
chunk0040_325_1	chr11	118157043	118157244	+	0	NA	Intergenic	Intergenic	-4228	NM_174934	6330	Hs.65239	NM_174934	ENSG00000177098	SCN4B	ATFB17|LQT10|Navbeta4	sodium voltage-gated channel beta subunit 4	protein-coding	0.039801	0.549505	3(CAGGACAGCATGTACC,-,0.00),4(AGGACAGCATGTACCA,+,0.00)
chunk0186_294_1	chr7	142612322	142612906	+	0	NA	Intergenic	MER70B|LTR|ERVL	-53685	NM_001190487	100463482		NM_001190487	ENSG00000270672	MTRNR2L6	HN6	MT-RNR2 like 6	protein-coding	0.000000	0.437607	303(AAGTGCACTCTGTCCT,-,0.00),304(AGTGCACTCTGTCCTG,+,0.00),362(TGGGACATCCTGTTCC,-,0.00),363(GGGACATCCTGTTCCA,+,0.00)
chunk0108_187_1	chr2	232254347	232254950	+	0	NA	intron (NR_046476, intron 12 of 20)	intron (NR_046476, intron 12 of 20)	81995	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.008292	0.408940	
chunk0132_443_1	chr3	165137431	165137928	+	0	NA	Intergenic	L1PA5|LINE|L1	59002	NM_014926	22865	Hs.101745	NM_014926	ENSG00000121871	SLITRK3	-	SLIT and NTRK like family member 3	protein-coding	0.000000	0.363454	
chunk0070_355_1	chr15	76105737	76106204	+	0	NA	intron (NM_152335, intron 1 of 10)	intron (NM_152335, intron 1 of 10)	46012	NM_152335	123591	Hs.661411	NM_152335	ENSG00000169758	TMEM266	C15orf27|HVRP1|HsHVRP1|hTMEM266	transmembrane protein 266	protein-coding	0.008565	0.497863	
chunk0021_435_1	chr1	247712173	247712372	+	0	NA	exon (NM_001005286, exon 1 of 1)	exon (NM_001005286, exon 1 of 1)	483	NM_001005286	343169	Hs.591529	NM_001005286	ENSG00000169214	OR6F1	OR1-34|OR1-38|OST731	olfactory receptor family 6 subfamily F member 1	protein-coding	0.020101	0.600000	
chunk0150_47_1	chr5	31683195	31683846	+	0	NA	Intergenic	Intergenic	-115404	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.009217	0.322086	372(AAGCACAAGAAGTTCT,-,0.00),373(AGCACAAGAAGTTCTG,+,0.00)
chunk0171_393_1	chr6	131150583	131150949	+	0	NA	intron (NM_016377, intron 2 of 7)	intron (NM_016377, intron 2 of 7)	15080	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.005464	0.305177	138(GAGGACAGTTAGTTCA,-,0.00),139(AGGACAGTTAGTTCAG,+,0.00)
chunk0030_413_1	chr10	120205624	120205823	+	0	NA	Intergenic	Intergenic	149500	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.000000	0.455000	
chunk0129_280_1	chr3	123089868	123090245	+	0	NA	intron (NM_006810, intron 2 of 16)	intron (NM_006810, intron 2 of 16)	23047	NR_028444	10954	Hs.477352	NM_006810	ENSG00000065485	PDIA5	PDIR	protein disulfide isomerase family A member 5	protein-coding	0.021220	0.571429	
chunk0178_432_1	chr7	41189830	41190340	+	0	NA	Intergenic	Intergenic	88481	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.005882	0.428571	
chunk0087_143_1	chr18	33926857	33927718	+	0	NA	intron (NM_001198548, intron 7 of 8)	intron (NM_001198548, intron 7 of 8)	121325	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.003484	0.353828	619(AAGTACAGCCTGTCCT,-,0.00),620(AGTACAGCCTGTCCTG,+,0.00)
chunk0158_189_1	chr5	127918096	127918551	+	0	NA	Intergenic	Intergenic	164751	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.002198	0.366228	
chunk0148_278_1	chr5	10762672	10762919	+	0	NA	Intergenic	L2a|LINE|L2	-1520	NM_004394	1611	Hs.75189	NM_004394	ENSG00000112977	DAP	-	death associated protein	protein-coding	0.012146	0.508065	
chunk0078_99_1	chr17	2101600	2101935	+	0	NA	intron (NM_001256827, intron 6 of 11)	MIR|SINE|MIR	-13006	NM_001282326	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.032836	0.511905	
chunk0034_389_1	chr11	36630370	36631044	+	0	NA	intron (NM_001276725, intron 2 of 3)	intron (NM_001276725, intron 2 of 3)	-32428	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.004451	0.370370	
chunk0134_56_1	chr3	176008955	176009426	+	0	NA	Intergenic	Intergenic	-232857	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.006369	0.296610	
chunk0021_133_1	chr10	3829307	3829824	+	0	NA	Intergenic	Intergenic	-44284	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.005803	0.482625	
chunk0030_115_1	chr10	112811734	112812321	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-11469	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.017036	0.459184	
chunk0110_350_1	chr20	19665547	19665883	+	0	NA	intron (NM_020689, intron 7 of 16)	intron (NM_020689, intron 7 of 16)	-220806	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.005952	0.459941	
chunk0150_82_1	chr5	32225547	32225788	+	0	NA	Intergenic	Intergenic	-51348	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.008299	0.429752	74(CTGGACATAGTGTGCT,-,0.00),75(TGGACATAGTGTGCTG,+,0.00)
chunk0007_421_1	chr1	86281564	86281882	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	75964	NR_107010	102465842		NR_107010	ENSG00000278281	MIR7856	hsa-mir-7856	microRNA 7856	ncRNA	0.006289	0.463950	
chunk0129_420_1	chr3	127141864	127142617	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	-50891	NM_001007534	285311	Hs.591284	NM_001007534	ENSG00000214324	C3orf56	-	chromosome 3 open reading frame 56	protein-coding	0.025232	0.543767	
chunk0115_124_1	chr21	23193634	23194403	+	0	NA	Intergenic	HAL1ME|LINE|L1	114734	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.001300	0.276623	
chunk0087_445_1	chr18	42632973	42633185	+	0	NA	intron (NR_046174, intron 7 of 9)	intron (NR_046174, intron 7 of 9)	446411	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.000000	0.417840	
chunk0194_214_1	chr8	86108626	86109388	+	0	NA	intron (NM_152565, intron 1 of 7)	intron (NM_152565, intron 1 of 7)	10097	NM_152565	245972	Hs.436360	NM_152565	ENSG00000147614	ATP6V0D2	ATP6D2|VMA6	ATPase H+ transporting V0 subunit d2	protein-coding	0.005249	0.376147	
chunk0034_408_1	chr11	38041747	38042280	+	0	NA	Intergenic	L1M5|LINE|L1	604343	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.001876	0.264045	
chunk0076_323_1	chr16	70697050	70697357	+	0	NA	exon (NM_018052, exon 16 of 19)	exon (NM_018052, exon 16 of 19)	-11152	NM_138383	92154	Hs.432387	NM_138383	ENSG00000132613	MTSS2	ABBA|ABBA-1|ABBA1|MTSS1L	MTSS I-BAR domain containing 2	protein-coding	0.032573	0.629870	
chunk0137_85_1	chr4	13181384	13182124	+	0	NA	Intergenic	Intergenic	302611	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.013514	0.406208	351(CAGTACACTCTGTTTT,-,0.00),352(AGTACACTCTGTTTTC,+,0.00)
chunk0050_187_1	chr12	103929530	103929799	+	0	NA	promoter-TSS (NM_003299)	promoter-TSS (NM_003299)	547	NR_027249	253724	Hs.506549	NR_027249	ENSG00000214198	TTC41P	GNN|GNNP	tetratricopeptide repeat domain 41, pseudogene	pseudo	0.044610	0.544444	
chunk0109_114_1	chr20	2652282	2652681	+	0	NA	promoter-TSS (NM_006392)	promoter-TSS (NM_006392)	-51	NM_006392	10528	Hs.376064	NM_006392	ENSG00000101361	NOP56	NOL5A|SCA36	NOP56 ribonucleoprotein	protein-coding	0.122807	0.717500	
chunk0193_98_1	chr8	73665501	73665744	+	0	NA	intron (NM_001164383, intron 1 of 9)	intron (NM_001164383, intron 1 of 9)	81305	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.008230	0.393443	
chunk0202_113_1	chr9	72583510	72583809	+	0	NA	intron (NM_138691, intron 2 of 23)	L4_B_Mam|LINE|RTE-X	61858	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.000000	0.373333	
chunk0063_385_1	chr14	86748093	86748647	+	0	NA	Intergenic	L1PA6|LINE|L1	-157408	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.001805	0.372973	209(AGGAACAGATTGTTCA,-,0.00),210(GGAACAGATTGTTCAG,+,0.00)
chunk0081_224_1	chr17	42736807	42737166	+	0	NA	intron (NM_001991, intron 1 of 20)	intron (NM_001991, intron 1 of 20)	8067	NM_001991	2145	Hs.194669	NM_001991	ENSG00000108799	EZH1	KMT6B	enhancer of zeste 1 polycomb repressive complex 2 subunit	protein-coding	0.027855	0.444444	156(AGGAACTCCCTGTACT,-,0.00),157(GGAACTCCCTGTACTA,+,0.00)
chunk0113_412_1	chr20	61621010	61621519	+	0	NA	intron (NM_001252339, intron 1 of 14)	intron (NM_001252339, intron 1 of 14)	21503	NM_001252339	1002	Hs.473231	NM_001794	ENSG00000179242	CDH4	CAD4|R-CAD|RCAD	cadherin 4	protein-coding	0.025540	0.421569	
chunk0035_291_1	chr11	46899386	46899588	+	0	NA	exon (NM_002334, exon 5 of 38)	exon (NM_002334, exon 5 of 38)	19135	NM_002334	4038	Hs.4930	NM_002334	ENSG00000134569	LRP4	CLSS|CMS17|LRP-4|LRP10|MEGF7|SOST2	LDL receptor related protein 4	protein-coding	0.049505	0.596059	
chunk0112_259_1	chr20	42496983	42497262	+	0	NA	intron (NM_133170, intron 7 of 31)	Tigger2|DNA|TcMar-Tigger	-188361	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.003584	0.425000	
chunk0083_287_1	chr17	68723848	68724348	+	0	NA	Intergenic	Intergenic	95944	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.002000	0.339321	213(AAGTACATGCAGTACT,-,0.00),214(AGTACATGCAGTACTC,+,0.00)
chunk0144_182_1	chr4	133433630	133433900	+	0	NA	Intergenic	Intergenic	284475	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.003704	0.350554	
chunk0205_194_1	chr9	109100506	109101108	+	0	NA	intron (NM_032012, intron 3 of 17)	MIRb|SINE|MIR	19138	NM_032012	23731	Hs.308074	NM_032012	ENSG00000106771	TMEM245	C9orf5|CG-2|CG2	transmembrane protein 245	protein-coding	0.004983	0.416252	
chunk0068_371_1	chr15	58159757	58160223	+	0	NA	intron (NM_020980, intron 1 of 5)	L1MA4|LINE|L1	21781	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.008584	0.359743	
chunk0131_229_1	chr3	149278869	149279347	+	0	NA	Intergenic	Intergenic	54364	NM_001184723	116441	Hs.22026	NM_138786	ENSG00000163762	TM4SF18	L6D	transmembrane 4 L six family member 18	protein-coding	0.004184	0.417537	
chunk0074_195_1	chr16	24954151	24954649	+	0	NA	intron (NM_018054, intron 10 of 18)	MER112|DNA|hAT-Charlie	60978	NM_018054	55114	Hs.373793	NM_018054	ENSG00000140750	ARHGAP17	MST066|MST110|MSTP038|MSTP066|MSTP110|NADRIN|PP367|PP4534|RICH-1|RICH1|WBP15	Rho GTPase activating protein 17	protein-coding	0.010040	0.434870	182(GAGGTCAGGGTGTACC,-,0.00),183(AGGTCAGGGTGTACCA,+,0.00)
chunk0045_317_1	chr12	50725284	50725495	+	0	NA	intron (NM_173602, intron 28 of 37)	intron (NM_173602, intron 28 of 37)	-38617	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.009479	0.353774	
chunk0015_430_1	chr1	191607832	191608065	+	0	NA	Intergenic	MER50B|LTR|ERV1	-550514	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.004292	0.474359	
chunk0029_134_1	chr10	99042511	99042710	+	0	NA	intron (NM_001166246, intron 3 of 12)	L1PA16|LINE|L1	-118042	NR_106762	102465253		NR_106762	ENSG00000274056	MIR6507	hsa-mir-6507	microRNA 6507	ncRNA	0.020101	0.590000	
chunk0177_92_1	chr7	21782909	21783108	+	0	NA	intron (NM_001277115, intron 57 of 81)	intron (NM_001277115, intron 57 of 81)	162916	NM_018719	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.000000	0.260000	
chunk0140_186_1	chr4	69885542	69885770	+	0	NA	Intergenic	Intergenic	-25504	NM_005420	6783	Hs.479898	NM_005420	ENSG00000109193	SULT1E1	EST|EST-1|ST1E1|STE	sulfotransferase family 1E member 1	protein-coding	0.004386	0.344978	
chunk0131_308_1	chr3	150748175	150748490	+	0	NA	intron (NM_005067, intron 1 of 1)	intron (NM_005067, intron 1 of 1)	-9347	NR_121657	101928105		NR_121657		LOC101928105	-	uncharacterized LOC101928105	ncRNA	0.000000	0.370253	
chunk0189_40_1	chr8	19887759	19888242	+	0	NA	Intergenic	L2c|LINE|L2	-51071	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.010352	0.400826	
chunk0009_29_1	chr1	100249271	100249506	+	0	NA	intron (NM_001918, intron 1 of 10)	L2c|LINE|L2	465	NM_001918	1629	Hs.709187	NM_001918	ENSG00000137992	DBT	BCATE2|BCKAD-E2|BCKADE2|BCOADC-E2|E2|E2B	dihydrolipoamide branched chain transacylase E2	protein-coding	0.038298	0.487288	
chunk0016_272_1	chr1	200551014	200551213	+	0	NA	TTS (NM_014875)	TTS (NM_014875)	67725	NM_001305792	9928	Hs.3104	NM_014875	ENSG00000118193	KIF14	MCPH20|MKS12	kinesin family member 14	protein-coding	0.000000	0.400000	
chunk0089_223_1	chr18	61504571	61505156	+	0	NA	intron (NM_031891, intron 4 of 10)	intron (NM_031891, intron 4 of 10)	14321	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.008547	0.412969	
chunk0094_19_1	chr2	1123496	1123995	+	0	NA	intron (NM_018968, intron 4 of 16)	L1MA7|LINE|L1	172877	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.008016	0.388000	
chunk0096_106_1	chr2	28319160	28319772	+	0	NA	intron (NM_199192, intron 12 of 12)	intron (NM_199192, intron 12 of 12)	-9007	NR_038319	100505716	Hs.679092	NR_038319	ENSG00000223522	LOC100505716	-	uncharacterized LOC100505716	ncRNA	0.013072	0.553018	
chunk0087_65_1	chr18	31738616	31739204	+	0	NA	Intergenic	LTR10A|LTR|ERV1	21970	NM_001034172	147407	Hs.567708	NM_001034172	ENSG00000141437	SLC25A52	MCART2	solute carrier family 25 member 52	protein-coding	0.013605	0.460102	245(GTGAACTCCATGTTCC,-,0.00),246(TGAACTCCATGTTCCT,+,0.00)
chunk0101_113_1	chr2	125926315	125927103	+	0	NA	Intergenic	Intergenic	-729226	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.006345	0.363752	
chunk0103_101_1	chr2	161279920	161280400	+	0	NA	Intergenic	Intergenic	-25517	NR_110593	101929512	Hs.666488	NR_110593		LOC101929512	-	uncharacterized LOC101929512	ncRNA	0.027083	0.419958	
chunk0147_95_1	chr4	173331358	173331688	+	0	NA	3' UTR (NM_002129, exon 5 of 5)	3' UTR (NM_002129, exon 5 of 5)	2246	NM_001130689	3148	Hs.434953	NM_002129	ENSG00000164104	HMGB2	HMG2	high mobility group box 2	protein-coding	0.009091	0.271903	
chunk0089_185_1	chr18	59882057	59882350	+	0	NA	Intergenic	Intergenic	-17757	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.010239	0.472789	
chunk0211_259_1	chrX	120746046	120746661	+	0	NA	Intergenic	Intergenic	-116203	NM_152692	29071	Hs.643920	NM_152692	ENSG00000171155	C1GALT1C1	C1GALT2|C38H2-L1|COSMC|HSPC067|MST143|TNPS	C1GALT1 specific chaperone 1	protein-coding	0.006504	0.402597	
chunk0211_404_1	chrX	128739551	128740107	+	0	NA	Intergenic	Intergenic	-687426	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.001799	0.389587	
chunk0188_138_1	chr8	9512934	9513435	+	0	NA	Intergenic	Intergenic	-42751	NM_003747	8658	Hs.370267	NM_003747	ENSG00000173273	TNKS	ARTD5|PARP-5a|PARP5A|PARPL|TIN1|TINF1|TNKS1|pART5	tankyrase	protein-coding	0.011976	0.380478	
chunk0108_14_1	chr2	226168671	226169355	+	0	NA	intron (NR_046102, intron 4 of 6)	intron (NR_046102, intron 4 of 6)	26219	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.004386	0.338686	
chunk0160_23_1	chr5	149134365	149134685	+	0	NA	Intergenic	Intergenic	-6958	NM_014945	22885	Hs.49688	NM_014945	ENSG00000173210	ABLIM3	HMFN1661	actin binding LIM protein family member 3	protein-coding	0.012500	0.570093	196(CTGGACACGTTGTCCT,-,0.00),197(TGGACACGTTGTCCTC,+,0.00)
chunk0092_235_1	chr19	32669966	32670393	+	0	NA	intron (NM_032139, intron 1 of 28)	intron (NM_032139, intron 1 of 28)	5017	NM_032139	84079	Hs.59236	NM_032139	ENSG00000105186	ANKRD27	PP12899|VARP	ankyrin repeat domain 27	protein-coding	0.014052	0.469626	
chunk0143_43_1	chr4	107557755	107557976	+	0	NA	Intergenic	Intergenic	162398	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.000000	0.301802	
chunk0023_229_1	chr10	26766218	26766555	+	0	NA	intron (NM_001178116, intron 7 of 11)	intron (NM_001178116, intron 7 of 11)	68720	NM_014317	23590	Hs.558468	NM_014317	ENSG00000148459	PDSS1	COQ1|COQ10D2|COQ1A|DPS|SPS|TPRT|TPT|TPT 1|hDPS1	decaprenyl diphosphate synthase subunit 1	protein-coding	0.002967	0.349112	
chunk0148_334_1	chr5	14261138	14261448	+	0	NA	intron (NM_007118, intron 1 of 56)	intron (NM_007118, intron 1 of 56)	117573	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.016129	0.472669	
chunk0099_48_1	chr2	84242676	84242876	+	0	NA	Intergenic	Intergenic	-47906	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.000000	0.383085	
chunk0032_92_1	chr11	3099274	3099514	+	0	NA	intron (NM_020896, intron 14 of 21)	L1MC2|LINE|L1	-41943	NM_139273	833	Hs.274873	NM_001751	ENSG00000110619	CARS	CARS1|CYSRS|MGC:11246	cysteinyl-tRNA synthetase	protein-coding	0.004167	0.410788	206(AGGAACTCTCTGTACT,-,0.00),207(GGAACTCTCTGTACTT,+,0.00)
chunk0002_7_1	chr1	12049630	12050225	+	0	NA	Intergenic	Intergenic	-13450	NM_001281430	943	Hs.1314	NM_001243	ENSG00000120949	TNFRSF8	CD30|D1S166E|Ki-1	TNF receptor superfamily member 8	protein-coding	0.010084	0.493289	
chunk0179_10_1	chr7	42472798	42473090	+	0	NA	Intergenic	Intergenic	233503	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.017123	0.453925	
chunk0104_205_1	chr2	175835000	175835441	+	0	NA	Intergenic	Intergenic	167125	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.002268	0.303167	
chunk0185_433_1	chr7	134852630	134853108	+	0	NA	intron (NM_033157, intron 2 of 14)	intron (NM_033157, intron 2 of 14)	-38531	NM_033139	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.006276	0.413361	186(GAGAACATCTTGTTTT,-,0.00),187(AGAACATCTTGTTTTC,+,0.00)
chunk0122_204_1	chr3	33165389	33165770	+	0	NA	intron (NM_015551, intron 4 of 4)	L1M7|LINE|L1	51621	NM_006371	10491	Hs.517888	NM_006371	ENSG00000170275	CRTAP	CASP|LEPREL3|OI7|P3H5	cartilage associated protein	protein-coding	0.002625	0.353403	157(GTGGACACCATGTACC,-,0.00),158(TGGACACCATGTACCA,+,0.00)
chunk0023_308_1	chr10	28900527	28900783	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	54247	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.015625	0.494163	
chunk0211_341_1	chrX	124389926	124390309	+	0	NA	intron (NM_001163278, intron 28 of 31)	intron (NM_001163278, intron 28 of 31)	43835	NM_002351	4068	Hs.349094	NM_002351	ENSG00000183918	SH2D1A	DSHP|EBVS|IMD5|LYP|MTCP1|SAP|SAP/SH2D1A|XLP|XLPD|XLPD1	SH2 domain containing 1A	protein-coding	0.010444	0.369792	
chunk0066_191_1	chr15	33173816	33174531	+	0	NA	intron (NM_001277313, intron 3 of 20)	intron (NM_001277313, intron 3 of 20)	20560	NM_001277314	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.008392	0.370112	
chunk0057_35_1	chr13	95886690	95887431	+	0	NA	intron (NM_020121, intron 26 of 38)	AluJb|SINE|Alu	166422	NM_020121	55757	Hs.193226	NM_020121	ENSG00000102595	UGGT2	HUGT2|UGCGL2|UGT2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding	0.005398	0.388140	
chunk0119_342_1	chr22	47049078	47049277	+	0	NA	intron (NM_014346, intron 11 of 12)	intron (NM_014346, intron 11 of 12)	-133135	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.045226	0.570000	65(GGGTACACGTTGTGCT,-,0.00),66(GGTACACGTTGTGCTC,+,0.00)
chunk0055_265_1	chr13	63622285	63622484	+	0	NA	Intergenic	Intergenic	-115051	NR_002171	283491	Hs.363054	NR_002171		OR7E156P	-	olfactory receptor family 7 subfamily E member 156 pseudogene	pseudo	0.000000	0.270000	
chunk0198_421_1	chr8	142981887	142982141	+	0	NA	TTS (NR_026913).2	TTS (NR_026913).2	-13814	NR_102426	100128627		NR_102426		CDC42P3	-	cell division cycle 42 pseudogene 3	pseudo	0.000000	0.372549	
chunk0123_212_1	chr3	45056845	45057463	+	0	NA	Intergenic	Intergenic	27024	NM_001308394	7123	Hs.476092	NM_003278	ENSG00000163815	CLEC3B	TN|TNA	C-type lectin domain family 3 member B	protein-coding	0.006472	0.492730	358(AAGAACATCCAGTGCA,-,0.00),359(AGAACATCCAGTGCAC,+,0.00)
chunk0052_186_1	chr13	24512150	24512678	+	0	NA	intron (NM_006437, intron 1 of 33)	CpG	396	NM_006437	143	Hs.744855	NM_006437	ENSG00000102699	PARP4	ADPRTL1|ARTD4|PARP-4|PARPL|PH5P|VAULT3|VPARP|VWA5C|p193	poly(ADP-ribose) polymerase family member 4	protein-coding	0.070076	0.574669	
chunk0029_57_1	chr10	96521718	96522163	+	0	NA	3' UTR (NM_020123, exon 15 of 15)	3' UTR (NM_020123, exon 15 of 15)	-8014	NM_012465	7093	Hs.154296	NM_012465	ENSG00000095587	TLL2	-	tolloid like 2	protein-coding	0.006742	0.352018	
chunk0055_347_1	chr13	70246093	70246555	+	0	NA	Intergenic	Intergenic	-137831	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.004329	0.358531	
chunk0111_70_1	chr20	23073050	23073333	+	0	NA	Intergenic	L1ME1|LINE|L1	13149	NM_012072	22918	Hs.97199	NM_012072	ENSG00000125810	CD93	C1QR1|C1qR(P)|C1qRP|CDw93|ECSM3|MXRA4|dJ737E23.1	CD93 molecule	protein-coding	0.014134	0.373239	
chunk0171_230_1	chr6	126396244	126396457	+	0	NA	intron (NR_104462, intron 2 of 3)	L1MA2|LINE|L1	56561	NM_001286524	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.009390	0.551402	
chunk0165_5_1	chr6	28661342	28661613	+	0	NA	Intergenic	Intergenic	-74142	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.000000	0.356618	
chunk0039_83_1	chr11	97114649	97115109	+	0	NA	Intergenic	Intergenic	-608002	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.004348	0.316703	
chunk0093_243_1	chr19	50850548	50851235	+	0	NA	intron (NR_131203, intron 2 of 2)	LTR40a|LTR|ERVL	-4024	NM_001030047	354	Hs.171995	NM_001648	ENSG00000142515	KLK3	APS|KLK2A1|PSA|hK3	kallikrein related peptidase 3	protein-coding	0.010189	0.456395	
chunk0073_291_1	chr16	14020004	14020850	+	0	NA	non-coding (NR_110915, exon 2 of 3)	non-coding (NR_110915, exon 2 of 3)	650	NR_110915	101927348	Hs.569621	NR_110915	ENSG00000261856	LINC02186	-	long intergenic non-protein coding RNA 2186	ncRNA	0.004728	0.455726	
chunk0197_47_1	chr8	118410249	118410467	+	0	NA	intron (NR_109794, intron 3 of 4)	intron (NR_109794, intron 3 of 4)	-210643	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.004587	0.383562	
chunk0186_186_1	chr7	139675163	139675391	+	0	NA	intron (NM_001113239, intron 2 of 14)	L2c|LINE|L2	102617	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.008772	0.419214	
chunk0119_220_1	chr22	45161991	45162193	+	0	NA	intron (NR_038956, intron 1 of 2)	MER41C|LTR|ERV1	1689	NR_038956	100506714	Hs.189902	NR_038956		NUP50-DT	NUP50-AS1	NUP50 divergent transcript	ncRNA	0.024752	0.413793	
chunk0146_59_1	chr4	155717407	155717624	+	0	NA	intron (NM_000856, intron 9 of 10)	LTR67B|LTR|ERVL	-41458	NM_000857	2983	Hs.77890	NM_000857	ENSG00000061918	GUCY1B1	GC-S-beta-1|GC-SB3|GUC1B3|GUCB3|GUCSB3|GUCY1B3	guanylate cyclase 1 soluble subunit beta 1	protein-coding	0.000000	0.321101	19(GAGAACACAATCTTCT,-,0.00),20(AGAACACAATCTTCTC,+,0.00)
chunk0096_113_1	chr2	28508256	28508509	+	0	NA	intron (NM_001170585, intron 1 of 56)	intron (NM_001170585, intron 1 of 56)	12311	NM_153021	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.011858	0.507874	
chunk0101_106_1	chr2	125216391	125216636	+	0	NA	Intergenic	L1MA5A|LINE|L1	1191226	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.304878	
chunk0189_63_1	chr8	20219439	20219638	+	0	NA	intron (NM_001693, intron 13 of 13)	L1ME3A|LINE|L1	22345	NM_001693	526	Hs.295917	NM_001693	ENSG00000147416	ATP6V1B2	ATP6B1B2|ATP6B2|DOOD|HO57|VATB|VPP3|Vma2|ZLS2	ATPase H+ transporting V1 subunit B2	protein-coding	0.005025	0.360000	
chunk0133_133_1	chr3	169151034	169151483	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-3524	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.004454	0.395556	
chunk0142_187_1	chr4	96332367	96332675	+	0	NA	Intergenic	AluSx4|SINE|Alu	492433	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.016234	0.469256	
chunk0077_145_1	chr16	78886079	78886598	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	714387	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.009634	0.351923	245(GAGTACATTTTGTGCA,-,0.00),246(AGTACATTTTGTGCAT,+,0.00)
chunk0058_262_1	chr14	25965069	25965943	+	0	NA	Intergenic	Intergenic	632248	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.002288	0.362286	
chunk0010_311_1	chr1	118052657	118053083	+	0	NA	intron (NM_206996, intron 20 of 48)	intron (NM_206996, intron 20 of 48)	123121	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.000000	0.288056	
chunk0181_395_1	chr7	89733107	89733394	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-386150	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.006969	0.420139	
chunk0049_93_1	chr12	90832648	90832863	+	0	NA	Intergenic	L2|LINE|L2	-85268	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.009302	0.430556	
chunk0205_426_1	chr9	115070901	115071198	+	0	NA	intron (NM_002160, intron 10 of 27)	L2c|LINE|L2	47208	NM_002160	3371	Hs.143250	NM_002160	ENSG00000041982	TNC	150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C	tenascin C	protein-coding	0.016835	0.422819	
chunk0072_85_1	chr15	90790143	90790356	+	0	NA	intron (NM_001287246, intron 15 of 22)	intron (NM_001287246, intron 15 of 22)	72922	NM_001287246	641	Hs.725208	NM_000057	ENSG00000197299	BLM	BS|MGRISCE1|RECQ2|RECQL2|RECQL3	BLM RecQ like helicase	protein-coding	0.014085	0.514019	28(AAGAACGTATTGTTCC,-,0.00),29(AGAACGTATTGTTCCT,+,0.00)
chunk0112_341_1	chr20	45104414	45104885	+	0	NA	Intergenic	MIRb|SINE|MIR	-3537	NM_002251	3787	Hs.117780	NM_002251	ENSG00000124134	KCNS1	Kv9.1	potassium voltage-gated channel modifier subfamily S member 1	protein-coding	0.014862	0.453390	353(CAGCACATGCTGTTCC,-,0.00),354(AGCACATGCTGTTCCC,+,0.00)
chunk0042_82_1	chr12	2291252	2291525	+	0	NA	intron (NM_001129846, intron 3 of 45)	intron (NM_001129846, intron 3 of 45)	21612	NR_046769	100874370	Hs.653548	NR_046769		CACNA1C-IT3	-	CACNA1C intronic transcript 3	ncRNA	0.018315	0.459854	
chunk0113_162_1	chr20	52833838	52834546	+	0	NA	Intergenic	L2|LINE|L2	-138215	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.005650	0.420310	
chunk0188_311_1	chr8	17085465	17086070	+	0	NA	intron (NM_181723, intron 6 of 14)	intron (NM_181723, intron 6 of 14)	58529	NM_181723	286097	Hs.403594	NM_181723	ENSG00000155970	MICU3	EFHA2	mitochondrial calcium uptake family member 3	protein-coding	0.001653	0.359736	
chunk0118_353_1	chr22	36157235	36157459	+	0	NA	intron (NM_030644, intron 1 of 4)	intron (NM_030644, intron 1 of 4)	3582	NM_030644	80833	Hs.474737	NM_014349	ENSG00000128284	APOL3	APOLIII|CG121|CG12_1|apoL-III	apolipoprotein L3	protein-coding	0.008929	0.417778	
chunk0206_235_1	chr9	123594584	123595129	+	0	NA	intron (NM_024820, intron 11 of 20)	intron (NM_024820, intron 11 of 20)	-109234	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.005505	0.437729	197(ATGCACAAAATGTGCC,-,0.00),198(TGCACAAAATGTGCCC,+,0.00)
chunk0025_230_1	chr10	54055076	54055835	+	0	NA	intron (NM_001142769, intron 20 of 35)	intron (NM_001142769, intron 20 of 35)	552502	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.000000	0.342105	
chunk0097_14_1	chr2	41670453	41670706	+	0	NA	Intergenic	Intergenic	-206976	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.003953	0.330709	
chunk0209_290_1	chrX	48287875	48288457	+	0	NA	Intergenic	AluSc8|SINE|Alu	18013	NR_073393	280660	Hs.553667	NM_174962	ENSG00000204648	SSX9P	SSX9	SSX family member 9, pseudogene	pseudo	0.015464	0.454545	
chunk0193_207_1	chr8	76116708	76117135	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-289733	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.000000	0.359813	
chunk0178_361_1	chr7	39072693	39073375	+	0	NA	intron (NM_007252, intron 2 of 10)	L2a|LINE|L2	95025	NM_001166018	11281	Hs.137106	NM_007252	ENSG00000106536	POU6F2	RPF-1|WT5|WTSL	POU class 6 homeobox 2	protein-coding	0.010264	0.382138	
chunk0003_232_1	chr1	35719007	35719444	+	0	NA	promoter-TSS (NM_152374)	promoter-TSS (NM_152374)	-36	NM_152374	127703	Hs.112023	NM_152374	ENSG00000142686	C1orf216	-	chromosome 1 open reading frame 216	protein-coding	0.059497	0.550228	268(TGGCACGCACTGTTCC,-,0.00),269(GGCACGCACTGTTCCC,+,0.00)
chunk0083_90_1	chr17	64315236	64315863	+	0	NA	Intergenic	Intergenic	-52226	NM_018469	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.006380	0.425159	
chunk0155_303_1	chr5	96338482	96339094	+	0	NA	intron (NR_130776, intron 3 of 4)	intron (NR_130776, intron 3 of 4)	93371	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.004902	0.445351	272(CAGAACATCCTGTTCC,-,0.00),273(AGAACATCCTGTTCCT,+,0.00)
chunk0109_464_1	chr2	242134555	242134758	+	0	NA	intron (NR_130702, intron 4 of 6)	L2a|LINE|L2	46023	NR_130699	728323	Hs.380737	NR_024437		LINC01881	-	long intergenic non-protein coding RNA 1881	ncRNA	0.000000	0.303922	
chunk0104_84_1	chr2	171994225	171994436	+	0	NA	Intergenic	Intergenic	-5567	NM_199227	254042	Hs.298250	NM_199227	ENSG00000172878	METAP1D	MAP 1D|MAP1D|MetAP 1D|Metap1l	methionyl aminopeptidase type 1D, mitochondrial	protein-coding	0.000000	0.405660	
chunk0145_275_1	chr4	149604769	149605125	+	0	NA	Intergenic	Intergenic	450652	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.000000	0.397759	130(AGGCACAGTCTGTTCA,-,0.00),131(GGCACAGTCTGTTCAT,+,0.00)
chunk0202_106_1	chr9	72484021	72484254	+	0	NA	Intergenic	Intergenic	-37664	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.012876	0.448718	
chunk0168_104_1	chr6	80188145	80188422	+	0	NA	intron (NM_000056, intron 6 of 10)	L1PA15|LINE|L1	81656	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.003610	0.420863	
chunk0087_74_1	chr18	31987481	31987698	+	0	NA	Intergenic	Intergenic	-30893	NM_017831	54941	Hs.633703	NM_017831	ENSG00000101695	RNF125	TNORS|TRAC-1|TRAC1	ring finger protein 125	protein-coding	0.000000	0.344037	
chunk0030_290_1	chr10	117229615	117229985	+	0	NA	Intergenic	L1MC5|LINE|L1	-11273	NM_003054	6571	Hs.596992	NM_003054	ENSG00000165646	SLC18A2	PKDYS2|SVAT|SVMT|VAT2|VMAT2	solute carrier family 18 member A2	protein-coding	0.002703	0.439353	
chunk0078_202_1	chr17	5306127	5306326	+	0	NA	intron (NM_001291581, intron 1 of 16)	Tigger5b|DNA|TcMar-Tigger	23963	NM_001291582	9135	Hs.584784	NM_004703	ENSG00000029725	RABEP1	RAB5EP|RABPT5	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.010050	0.380000	
chunk0054_284_1	chr13	47002604	47002855	+	0	NA	Intergenic	Intergenic	-105653	NM_001165947	3356	Hs.72630	NM_000621	ENSG00000102468	HTR2A	5-HT2A|HTR2	5-hydroxytryptamine receptor 2A	protein-coding	0.003984	0.373016	
chunk0199_62_1	chr9	2188664	2189114	+	0	NA	intron (NM_003070, intron 32 of 33)	MLT1E2|LTR|ERVL-MaLR	30433	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.006667	0.452328	
chunk0149_227_1	chr5	22953240	22953439	+	0	NA	Intergenic	Intergenic	-99717	NM_004061	1010	Hs.113684	NM_004061	ENSG00000154162	CDH12	CDHB	cadherin 12	protein-coding	0.005025	0.270000	
chunk0121_205_1	chr3	21514332	21514753	+	0	NA	intron (NM_024697, intron 3 of 7)	MER57B2|LTR|ERV1	-28247	NR_046731	100874216	Hs.661720	NR_046731	ENSG00000225542	ZNF385D-AS1	-	ZNF385D antisense RNA 1	ncRNA	0.014252	0.364929	
chunk0065_81_1	chr15	23598892	23599643	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	33960	NM_005664	7681	Hs.72964	NM_005664	ENSG00000179455	MKRN3	CPPB2|D15S9|RNF63|ZFP127|ZNF127	makorin ring finger protein 3	protein-coding	0.002663	0.393617	
chunk0197_253_1	chr8	123416476	123416922	+	0	NA	promoter-TSS (NM_001283027)	promoter-TSS (NM_001283027)	-26	NM_001283027	55093	Hs.18029	NM_018024	ENSG00000156795	WDYHV1	C8orf32	WDYHV motif containing 1	protein-coding	0.107623	0.740492	
chunk0211_180_1	chrX	117034118	117034507	+	0	NA	Intergenic	L1ME4b|LINE|L1	-571279	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.007712	0.310256	
chunk0025_179_1	chr10	52999654	53000082	+	0	NA	Intergenic	Intergenic	-228168	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.007009	0.370629	
chunk0158_301_1	chr5	132327576	132328360	+	0	NA	intron (NM_003059, intron 5 of 9)	L2a|LINE|L2	33516	NM_003059	6583	Hs.310591	NM_003059	ENSG00000197208	SLC22A4	DFNB60|OCTN1	solute carrier family 22 member 4	protein-coding	0.002551	0.435669	548(AGAGACACTGTGTGCC,-,0.00),549(GAGACACTGTGTGCCA,+,0.00)
chunk0179_257_1	chr7	48798428	48798899	+	0	NA	Intergenic	L1MB1|LINE|L1	-125898	NR_003595									0.002123	0.305085	239(AGAAACACAGTGTACC,-,0.00),240(GAAACACAGTGTACCA,+,0.00)
chunk0034_101_1	chr11	27649290	27649520	+	0	NA	intron (NR_002832, intron 4 of 7)	intron (NR_002832, intron 4 of 7)	10244	NM_170735	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.000000	0.402597	
chunk0167_236_1	chr6	67472024	67472358	+	0	NA	Intergenic	Intergenic	-583160	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.005988	0.340299	
chunk0106_234_1	chr2	202870128	202870800	+	0	NA	intron (NM_001288622, intron 1 of 12)	intron (NM_001288622, intron 1 of 12)	1008	NM_001288623	130026	Hs.516629	NM_138468	ENSG00000163596	ICA1L	ALS2CR14|ALS2CR15	islet cell autoantigen 1 like	protein-coding	0.010417	0.319465	
chunk0067_76_1	chr15	41404783	41405374	+	0	NA	Intergenic	Intergenic	-2618	NR_045620	51103	Hs.106529	NM_016013	ENSG00000137806	NDUFAF1	CGI-65|CGI65|CIA30|MC1DN11	NADH:ubiquinone oxidoreductase complex assembly factor 1	protein-coding	0.010152	0.488176	
chunk0148_414_1	chr5	14983527	14984238	+	0	NA	Intergenic	Intergenic	-112104	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.005626	0.425562	
chunk0119_39_1	chr22	40535674	40535927	+	0	NA	intron (NM_001282661, intron 3 of 13)	intron (NM_001282661, intron 3 of 13)	14000	NR_109965	101927257	Hs.662725	NR_109965	ENSG00000232564	MRTFA-AS1	-	MRTFA antisense RNA 1	ncRNA	0.007905	0.401575	
chunk0153_34_1	chr5	67149031	67149471	+	0	NA	intron (NM_001290227, intron 21 of 25)	intron (NM_001290227, intron 21 of 25)	47538	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.015909	0.444444	
chunk0175_363_1	chr6	167839695	167840266	+	0	NA	intron (NM_001291964, intron 1 of 32)	L2b|LINE|L2	12345	NM_001291964	4301	Hs.614974	NM_005936	ENSG00000130396	AFDN	AF6|MLL-AF6|MLLT4|l-afadin	afadin, adherens junction formation factor	protein-coding	0.012259	0.458042	254(GTGTACACACTGTACT,-,0.00),255(TGTACACACTGTACTA,+,0.00)
chunk0007_128_1	chr1	79149248	79149909	+	0	NA	Intergenic	Intergenic	-142768	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.009077	0.362538	280(CAGGACAATTTGTACT,-,0.00),281(AGGACAATTTGTACTG,+,0.00)
chunk0060_326_1	chr14	51431846	51432412	+	0	NA	Intergenic	Intergenic	-56992	NM_001042481	122786	Hs.434914	NM_152330	ENSG00000139926	FRMD6	C14orf31|EX1|Willin|c14_5320	FERM domain containing 6	protein-coding	0.003534	0.359788	
chunk0092_147_1	chr19	28754632	28754872	+	0	NA	Intergenic	L1PA13|LINE|L1	-27058	NR_110759	100420587	Hs.569956	NR_110759	ENSG00000283403	LOC100420587	-	SHC binding and spindle associated 1 pseudogene	pseudo	0.000000	0.560166	
chunk0032_399_1	chr11	11661905	11662352	+	0	NA	Intergenic	LTR85a|LTR|Gypsy?	-5406	NR_036184	100423026		NR_036184	ENSG00000266645	MIR4299	-	microRNA 4299	ncRNA	0.008949	0.412946	
chunk0029_364_1	chr10	107652794	107653321	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	416236	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.003795	0.458333	312(TGGAACAGTGTGTGCC,-,0.00),313(GGAACAGTGTGTGCCT,+,0.00)
chunk0190_117_1	chr8	30504177	30504619	+	0	NA	exon (NM_001008710, exon 5 of 9)	exon (NM_001008710, exon 5 of 9)	-118997	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.020362	0.433409	
chunk0124_106_1	chr3	53835043	53835448	+	0	NA	intron (NM_018397, intron 2 of 8)	L1MC5a|LINE|L1	11148	NM_018397	55349	Hs.126688	NM_018397	ENSG00000016391	CHDH	-	choline dehydrogenase	protein-coding	0.000000	0.463054	
chunk0075_84_1	chr16	48268236	48268751	+	0	NA	intron (NM_031490, intron 6 of 14)	L1MC|LINE|L1	24326	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.001942	0.315891	
chunk0053_91_1	chr13	28489966	28490165	+	0	NA	intron (NM_001159920, intron 1 of 12)	MIR3|SINE|MIR	5063	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.015075	0.445000	
chunk0095_386_1	chr2	23901922	23902702	+	0	NA	intron (NR_125717, intron 1 of 28)	intron (NR_125717, intron 1 of 28)	24802	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.005128	0.352113	
chunk0010_368_1	chr1	119045474	119045735	+	0	NA	exon (NM_201263, exon 3 of 6)	exon (NM_201263, exon 3 of 6)	-1801	NR_126447	104472716	Hs.689536	NR_126447		WARS2-IT1	-	WARS2 intronic transcript 1	ncRNA	0.003831	0.389313	
chunk0003_56_1	chr1	30923055	30923651	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	12423	NR_033295	692235		NR_033295		SNORD103B	U103B	small nucleolar RNA, C/D box 103B	snoRNA	0.006711	0.363484	272(AAGAACATGTTGTCCT,-,0.00),273(AGAACATGTTGTCCTT,+,0.00)
chunk0132_237_1	chr3	158652495	158652942	+	0	NA	intron (NM_001308164, intron 7 of 18)	intron (NM_001308164, intron 7 of 18)	8190	NM_001308166	85476	Hs.518355	NM_024996	ENSG00000168827	GFM1	COXPD1|EFG|EFG1|EFGM|EGF1|GFM|hEFG1|mtEF-G1	G elongation factor mitochondrial 1	protein-coding	0.006711	0.408482	
chunk0056_394_1	chr13	93756621	93756984	+	0	NA	intron (NM_005708, intron 2 of 8)	intron (NM_005708, intron 2 of 8)	101671	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.005510	0.384615	
chunk0050_198_1	chr12	104090576	104091191	+	0	NA	intron (NM_013320, intron 9 of 14)	HAL1|LINE|L1	26425	NM_013320	29915	Hs.506558	NM_013320	ENSG00000111727	HCFC2	HCF-2|HCF2	host cell factor C2	protein-coding	0.006504	0.371753	
chunk0052_357_1	chr12	127204107	127204319	+	0	NA	Intergenic	Intergenic	135859	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.014151	0.464789	
chunk0084_260_1	chr17	79116027	79116235	+	0	NA	intron (NM_001082575, intron 4 of 14)	L1MD1|LINE|L1	41194	NM_001042573	64772	Hs.29288	NM_022759	ENSG00000167280	ENGASE	-	endo-beta-N-acetylglucosaminidase	protein-coding	0.009615	0.425837	
chunk0159_16_1	chr5	136249800	136250207	+	0	NA	intron (NM_001167576, intron 4 of 9)	intron (NM_001167576, intron 4 of 9)	51853	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.012285	0.450980	122(GGGCACAGCGTGAACC,-,0.00),123(GGCACAGCGTGAACCG,+,0.00)
chunk0143_283_1	chr4	117224581	117224876	+	0	NA	Intergenic	Intergenic	-139148	NM_152402	133022	Hs.570737	NM_152402	ENSG00000174599	TRAM1L1	-	translocation associated membrane protein 1 like 1	protein-coding	0.013559	0.320946	
chunk0097_192_1	chr2	50554523	50555132	+	0	NA	intron (NM_001135659, intron 9 of 23)	intron (NM_001135659, intron 9 of 23)	141435	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.003284	0.283607	
chunk0023_144_1	chr10	24047891	24048194	+	0	NA	intron (NM_001098500, intron 2 of 18)	MamSINE1|SINE|tRNA-RTE	-160749	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.000000	0.378289	
chunk0103_408_1	chr2	169340997	169341325	+	0	NA	intron (NM_004525, intron 1 of 78)	L2a|LINE|L2	21451	NM_004525	4036	Hs.657729	NM_004525	ENSG00000081479	LRP2	DBS|GP330|LRP-2	LDL receptor related protein 2	protein-coding	0.009146	0.404255	
chunk0186_357_1	chr7	143849886	143850085	+	0	NA	Intergenic	L1MA6|LINE|L1	-13268	NR_015421	154761	Hs.716689	NR_015421	ENSG00000253882	LOC154761	-	family with sequence similarity 115, member C pseudogene	pseudo	0.000000	0.330000	
chunk0200_83_1	chr9	16446549	16446857	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-170390	NR_073471									0.006494	0.326861	122(GTTACAGAATGTTCTT,+,0.00)
chunk0083_298_1	chr17	69326452	69326654	+	0	NA	intron (NM_172232, intron 1 of 38)	intron (NM_172232, intron 1 of 38)	629	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.044554	0.448276	
chunk0182_394_1	chr7	100436342	100436635	+	0	NA	promoter-TSS (NM_145030)	promoter-TSS (NM_145030)	-17	NM_145030	221908	Hs.413359	NM_145030	ENSG00000160813	PPP1R35	C7orf47	protein phosphatase 1 regulatory subunit 35	protein-coding	0.071672	0.656463	
chunk0164_319_1	chr6	25122699	25123068	+	0	NA	intron (NR_027626, intron 2 of 6)	intron (NR_027626, intron 2 of 6)	14940	NR_002174	8418	Hs.484918	NR_002174	ENSG00000168405	CMAHP	CMAH|CSAH	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	pseudo	0.005420	0.405405	
chunk0075_205_1	chr16	52545099	52545885	+	0	NA	intron (NM_001146188, intron 1 of 7)	intron (NM_001146188, intron 1 of 7)	1402	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.045802	0.512071	
chunk0143_125_1	chr4	109496654	109496997	+	0	NA	intron (NM_001300813, intron 7 of 24)	intron (NM_001300813, intron 7 of 24)	8127	NR_030302	693161		NR_030302	ENSG00000207988	MIR576	MIRN576|hsa-mir-576	microRNA 576	ncRNA	0.000000	0.325581	
chunk0209_32_1	chrX	36072141	36072684	+	0	NA	intron (NM_001304548, intron 28 of 63)	intron (NM_001304548, intron 28 of 63)	152678	NM_152632	286464	Hs.376425	NM_152632	ENSG00000165164	CFAP47	CHDC2|CXorf22|CXorf30|CXorf59	cilia and flagella associated protein 47	protein-coding	0.003683	0.321691	222(AAGCACTCTCTGTGCA,-,0.00),223(AGCACTCTCTGTGCAC,+,0.00)
chunk0128_96_1	chr3	105845459	105845820	+	0	NA	intron (NM_170662, intron 3 of 18)	intron (NM_170662, intron 3 of 18)	23404	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.002770	0.337017	
chunk0192_103_1	chr8	61657193	61657733	+	0	NA	intron (NM_001164750, intron 3 of 24)	Tigger3a|DNA|TcMar-Tigger	32386	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.011111	0.432532	264(CAGCACGTACTGTACC,-,0.00),265(AGCACGTACTGTACCG,+,0.00)
chunk0121_84_1	chr3	16104872	16105102	+	0	NA	Intergenic	L1ME3A|LINE|L1	-69690	NM_054110	117248	Hs.411308	NM_054110	ENSG00000131386	GALNT15	GALNACT15|GALNT13|GALNT7|GALNTL2|PIH5|pp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.026087	0.398268	
chunk0125_449_1	chr3	72938458	72938786	+	0	NA	intron (NM_001080393, intron 3 of 6)	intron (NM_001080393, intron 3 of 6)	50388	NM_001080393	727936	Hs.710275	NM_001080393	ENSG00000172986	GXYLT2	GLT8D4	glucoside xylosyltransferase 2	protein-coding	0.012195	0.455927	
chunk0149_44_1	chr5	16573239	16573803	+	0	NA	intron (NM_001034850, intron 1 of 8)	intron (NM_001034850, intron 1 of 8)	-42405	NR_109946	101929524	Hs.734029	NR_109946	ENSG00000246214	LOC101929524	-	uncharacterized LOC101929524	ncRNA	0.008865	0.400000	
chunk0058_53_1	chr14	20565333	20565539	+	0	NA	Intergenic	L1MA4|LINE|L1	-4505	NM_001110361	390443	Hs.533972	NM_001001673	ENSG00000188655	RNASE9	HEL128|RAK1|h461	ribonuclease A family member 9 (inactive)	protein-coding	0.000000	0.362319	
chunk0059_226_1	chr14	34222891	34223156	+	0	NA	Intergenic	Intergenic	239239	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.015094	0.413534	
chunk0077_237_1	chr16	80671574	80671773	+	0	NA	intron (NM_152342, intron 2 of 6)	intron (NM_152342, intron 2 of 6)	-98865	NR_104666	101928276	Hs.149769	NR_104665	ENSG00000260737	LINC01227	-	long intergenic non-protein coding RNA 1227	ncRNA	0.015075	0.420000	
chunk0177_77_1	chr7	21476395	21476822	+	0	NA	intron (NM_003112, intron 3 of 5)	intron (NM_003112, intron 3 of 5)	5550	NR_031594	100302122		NR_031594	ENSG00000221783	MIR1183	MIRN1183|hsa-mir-1183	microRNA 1183	ncRNA	0.004684	0.292056	
chunk0105_195_1	chr2	187639474	187639793	+	0	NA	Intergenic	L1MEg|LINE|L1	-85141	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.003135	0.271875	
chunk0084_79_1	chr17	75105564	75105882	+	0	NA	intron (NM_004695, intron 6 of 6)	intron (NM_004695, intron 6 of 6)	-4229	NM_001304271	79637	Hs.413047	NM_024585	ENSG00000125449	ARMC7	-	armadillo repeat containing 7	protein-coding	0.009434	0.479624	
chunk0008_253_1	chr1	94487047	94487544	+	0	NA	intron (NM_002858, intron 10 of 22)	intron (NM_002858, intron 10 of 22)	54562	NM_001993	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.010060	0.359438	
chunk0134_374_1	chr3	182794292	182794551	+	0	NA	intron (NM_014616, intron 1 of 29)	CpG	918	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.069498	0.523077	
chunk0114_263_1	chr21	16176775	16177477	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	-17253	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.001425	0.301565	
chunk0058_174_1	chr14	23869617	23869915	+	0	NA	Intergenic	Intergenic	-83969	NM_001282990	10901	Hs.528385	NM_021004	ENSG00000157326	DHRS4	CR|NRDR|PHCR|PSCD|SCAD-SRL|SDR-SRL|SDR25C1|SDR25C2	dehydrogenase/reductase 4	protein-coding	0.006711	0.408027	155(TGGCACAGACTGTCCT,-,0.00),156(GGCACAGACTGTCCTT,+,0.00)
chunk0178_131_1	chr7	32463197	32463821	+	0	NA	Intergenic	Intergenic	-5015	NR_038454	100130673	Hs.609282	NR_038454		LOC100130673	-	phosphoribosyl pyrophosphate synthetase 2 pseudogene	pseudo	0.006410	0.433600	
chunk0113_332_1	chr20	58645582	58645857	+	0	NA	Intergenic	Intergenic	-5534	NM_001001433	8675	Hs.307913	NM_003763	ENSG00000124222	STX16	SYN16	syntaxin 16	protein-coding	0.010909	0.427536	
chunk0011_18_1	chr1	143194438	143194740	+	0	NA	Intergenic	Intergenic	228003	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.066225	0.379538	
chunk0065_373_1	chr14	104037880	104038191	+	0	NA	intron (NM_153046, intron 32 of 35)	intron (NM_153046, intron 32 of 35)	-47651	NM_001080464	374569	Hs.146239	NM_001080464	ENSG00000166183	ASPG	C14orf76|GPA/WT|LYSOLP	asparaginase	protein-coding	0.009646	0.528846	
chunk0174_251_1	chr6	161035738	161036284	+	0	NA	intron (NM_006724, intron 2 of 25)	intron (NM_006724, intron 2 of 25)	44284	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.010989	0.376600	
chunk0170_327_1	chr6	116192834	116193544	+	0	NA	intron (NM_152729, intron 6 of 11)	intron (NM_152729, intron 6 of 11)	60909	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.005634	0.360056	
chunk0159_41_1	chr5	137080097	137080601	+	0	NA	intron (NM_004598, intron 5 of 10)	intron (NM_004598, intron 5 of 10)	418980	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.005952	0.429703	
chunk0144_221_1	chr4	134499267	134499610	+	0	NA	Intergenic	Intergenic	-297690	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005831	0.290698	
chunk0051_1_1	chr12	111117546	111117762	+	0	NA	intron (NM_015267, intron 1 of 21)	MIR|SINE|MIR	83630	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.000000	0.396313	
chunk0140_357_1	chr4	74156415	74156769	+	0	NA	Intergenic	L1MC3|LINE|L1	-1520	NM_001144978	441024	Hs.721011	NM_001004346	ENSG00000163738	MTHFD2L	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like	protein-coding	0.008475	0.346479	
chunk0156_183_1	chr5	107782733	107783287	+	0	NA	Intergenic	Intergenic	-112115	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.005415	0.333333	
chunk0185_28_1	chr7	124288375	124288872	+	0	NA	Intergenic	Intergenic	63473	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.004024	0.353414	284(AGGAACTTCATGTTCT,-,0.00),285(GGAACTTCATGTTCTA,+,0.00)
chunk0161_288_1	chr5	172983513	172983868	+	0	NA	promoter-TSS (NM_003945)	promoter-TSS (NM_003945)	-70	NM_003945	8992	Hs.484188	NM_003945	ENSG00000113732	ATP6V0E1	ATP6H|ATP6V0E|M9.2|Vma21|Vma21p	ATPase H+ transporting V0 subunit e1	protein-coding	0.070423	0.615169	
chunk0206_147_1	chr9	121366414	121366701	+	0	NA	intron (NR_073037, intron 1 of 7)	intron (NR_073037, intron 1 of 7)	3747	NM_001270526	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.000000	0.295139	
chunk0082_225_1	chr17	57253155	57253717	+	0	NA	Intergenic	(TCAT)n|Simple_repeat|Simple_repeat	-3134	NM_138962	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.014235	0.412078	
chunk0142_198_1	chr4	97114280	97114559	+	0	NA	Intergenic	Intergenic	-252507	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.010753	0.250000	
chunk0134_232_1	chr3	178900157	178900722	+	0	NA	Intergenic	Intergenic	-40034	NR_126561	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.000000	0.371025	
chunk0062_327_1	chr14	73368698	73369064	+	0	NA	intron (NM_001005743, intron 2 of 12)	intron (NM_001005743, intron 2 of 12)	89699	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.000000	0.316076	
chunk0002_241_1	chr1	20618789	20619181	+	0	NA	TTS (NM_001785)	TTS (NM_001785)	-14470	NM_032409	65018	Hs.389171	NM_032409	ENSG00000158828	PINK1	BRPK|PARK6	PTEN induced kinase 1	protein-coding	0.012755	0.493639	
chunk0156_225_1	chr5	108263279	108263667	+	0	NA	intron (NM_001163315, intron 4 of 8)	Charlie4a|DNA|hAT-Charlie	118625	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.002577	0.272494	
chunk0033_84_1	chr11	13972011	13972384	+	0	NA	intron (NM_006108, intron 1 of 15)	L3|LINE|CR1	9560	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.002681	0.449198	
chunk0113_274_1	chr20	56629161	56629526	+	0	NA	promoter-TSS (NM_003222)	promoter-TSS (NM_003222)	41	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.120548	0.702186	
chunk0079_78_1	chr17	11614967	11615401	+	0	NA	intron (NM_001372, intron 4 of 68)	MER63B|DNA|hAT-Blackjack	16753	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.013825	0.471264	
chunk0100_211_1	chr2	111908639	111909058	+	0	NA	intron (NM_006343, intron 1 of 18)	MLT1J|LTR|ERVL-MaLR	10234	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.002387	0.380952	136(TAGAACACATTGTTCC,-,0.00),137(AGAACACATTGTTCCT,+,0.00)
chunk0133_363_1	chr3	173563216	173563423	+	0	NA	intron (NM_014932, intron 2 of 6)	intron (NM_014932, intron 2 of 6)	164871	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.014493	0.336538	14(GAGAACACAGTGTGCT,-,0.00),15(AGAACACAGTGTGCTT,+,0.00)
chunk0185_87_1	chr7	125408015	125408419	+	0	NA	Intergenic	Intergenic	-143926	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.002475	0.271605	
chunk0192_116_1	chr8	61734487	61734714	+	0	NA	Intergenic	Intergenic	19812	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.008811	0.337719	
chunk0082_183_1	chr17	56263136	56263335	+	0	NA	intron (NM_153228, intron 2 of 16)	intron (NM_153228, intron 2 of 16)	109760	NM_153228	162282	Hs.673040	NM_153228	ENSG00000153930	ANKFN1	-	ankyrin repeat and fibronectin type III domain containing 1	protein-coding	0.010050	0.405000	
chunk0111_405_1	chr20	34412330	34412909	+	0	NA	exon (NM_031483, exon 5 of 25)	exon (NM_031483, exon 5 of 25)	49384	NM_001257137	83737	Hs.632272	NM_031483	ENSG00000078747	ITCH	ADMFD|AIF4|AIP4|NAPP1	itchy E3 ubiquitin protein ligase	protein-coding	0.005181	0.286207	
chunk0094_142_1	chr2	5044594	5044911	+	0	NA	Intergenic	L2c|LINE|L2	-388530	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009464	0.386792	
chunk0130_236_1	chr3	134699024	134699777	+	0	NA	Intergenic	Intergenic	-48378	NM_178554	339855	Hs.146730	NM_178554	ENSG00000174611	KY	MFM7	kyphoscoliosis peptidase	protein-coding	0.010624	0.506631	178(AACACATTATGTGCTT,+,0.00),500(CAGGACAGACTGTCTC,-,0.00),501(AGGACAGACTGTCTCT,+,0.00)
chunk0035_67_1	chr11	41713975	41714174	+	0	NA	promoter-TSS (NR_120584)	promoter-TSS (NR_120584)	-494	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.005025	0.410000	159(TAGAACTTAATGTTCC,-,0.00),160(AGAACTTAATGTTCCA,+,0.00)
chunk0127_321_1	chr3	100023216	100023441	+	0	NA	intron (NM_001042459, intron 1 of 4)	intron (NM_001042459, intron 1 of 4)	-58930	NR_037486	100500859		NR_037486	ENSG00000264897	MIR3921	-	microRNA 3921	ncRNA	0.013333	0.420354	
chunk0200_25_1	chr9	14756185	14756422	+	0	NA	intron (NM_144966, intron 30 of 37)	intron (NM_144966, intron 30 of 37)	23230	NM_001177704	158326	Hs.50850	NM_144966	ENSG00000164946	FREM1	BNAR|C9orf143|C9orf145|C9orf154|MOTA|TILRR|TRIGNO2	FRAS1 related extracellular matrix 1	protein-coding	0.004219	0.365546	
chunk0033_205_1	chr11	16925783	16926027	+	0	NA	intron (NM_175058, intron 3 of 22)	G-rich|Low_complexity|Low_complexity	88511	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.073770	0.665306	
chunk0009_320_1	chr1	108704546	108705197	+	0	NA	Intergenic	Intergenic	-8063	NM_001144937	163479	Hs.258253	NM_173532	ENSG00000143107	FNDC7	-	fibronectin type III domain containing 7	protein-coding	0.010753	0.423313	
chunk0143_31_1	chr4	106361053	106361385	+	0	NA	intron (NM_001195138, intron 1 of 1)	L2a|LINE|L2	6216	NM_001195138	100507096	Hs.722750	NM_001195138	ENSG00000250298	GIMD1	-	GIMAP family P-loop NTPase domain containing 1	protein-coding	0.000000	0.372372	
chunk0037_326_1	chr11	77020003	77020614	+	0	NA	exon (NM_001300953, exon 10 of 10)	exon (NM_001300953, exon 10 of 10)	-14033	NM_138706	192134	Hs.352622	NM_138706	ENSG00000198488	B3GNT6	B3Gn-T6|BGnT-6|beta-1,3-Gn-T6|beta3Gn-T6	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6	protein-coding	0.003273	0.398693	
chunk0043_94_1	chr12	14781435	14782005	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	7384	NM_177925	55766	Hs.524280	NM_018267	ENSG00000246705	H2AFJ	H2AJ	H2A histone family member J	protein-coding	0.005263	0.418564	294(ATATACAGAGTGTTCT,-,0.00)
chunk0108_192_1	chr2	232300141	232300742	+	0	NA	intron (NR_046476, intron 14 of 20)	intron (NR_046476, intron 14 of 20)	-78093	NM_001632	250	Hs.284255	NM_001632	ENSG00000163283	ALPP	ALP|ALPI|IAP|PALP|PLAP|PLAP-1	alkaline phosphatase, placental	protein-coding	0.003328	0.441860	
chunk0115_249_1	chr21	27557512	27558218	+	0	NA	Intergenic	Intergenic	-164514	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.002833	0.350778	
chunk0015_310_1	chr1	189132678	189132989	+	0	NA	Intergenic	Intergenic	1344796	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.006431	0.503205	
chunk0038_4_1	chr11	80757926	80758453	+	0	NA	intron (NR_120570, intron 2 of 2)	intron (NR_120570, intron 2 of 2)	4614	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.001898	0.303030	
chunk0045_437_1	chr12	53561616	53561992	+	0	NA	intron (NM_006856, intron 2 of 11)	intron (NM_006856, intron 2 of 11)	47820	NR_046221	100652999	Hs.633602	NR_046221	ENSG00000257550	LOC100652999	-	uncharacterized LOC100652999	ncRNA	0.005319	0.363395	
chunk0067_290_1	chr15	47441286	47441701	+	0	NA	intron (NM_001198999, intron 2 of 19)	intron (NM_001198999, intron 2 of 19)	257287	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.000000	0.338942	111(AGGAACAAGGTGTATT,-,0.00)
chunk0124_113_1	chr3	53952482	53953131	+	0	NA	Intergenic	Intergenic	-60844	NM_021237	58515	Hs.58471	NM_021237	ENSG00000113811	SELENOK	HSPC030|HSPC297|SELK	selenoprotein K	protein-coding	0.001541	0.318462	
chunk0209_115_1	chrX	40518093	40518586	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	-62625	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.014199	0.463563	
chunk0016_414_1	chr1	203379621	203379999	+	0	NA	Intergenic	Intergenic	-28381	NR_103757	2331	Hs.519168	NM_002023	ENSG00000122176	FMOD	FM|SLRR2E	fibromodulin	protein-coding	0.010582	0.469657	
chunk0128_37_1	chr3	104566208	104566539	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-800340	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.003021	0.343373	
chunk0135_155_1	chr3	187745439	187745898	+	0	NA	promoter-TSS (NM_001706)	promoter-TSS (NM_001706)	57	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.050109	0.543478	
chunk0009_242_1	chr1	106986430	106986931	+	0	NA	Intergenic	LTR53|LTR|ERVL	-69965	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.003992	0.464143	
chunk0177_399_1	chr7	27175063	27175579	+	0	NA	promoter-TSS (NM_018951)	promoter-TSS (NM_018951)	-985	NM_018951	3206	Hs.110637	NM_018951	ENSG00000253293	HOXA10	HOX1|HOX1.8|HOX1H|PL	homeobox A10	protein-coding	0.017442	0.578337	
chunk0212_405_1	chrX	151754739	151755091	+	0	NA	Intergenic	Intergenic	20169	NM_005140	1260	Hs.447360	NM_005140	ENSG00000183862	CNGA2	CNCA|CNCA1|CNG2|OCNC1|OCNCALPHA|OCNCa	cyclic nucleotide gated channel alpha 2	protein-coding	0.022727	0.507082	
chunk0091_234_1	chr19	10567239	10567438	+	0	NA	exon (NM_079421, exon 3 of 3)	exon (NM_079421, exon 3 of 3)	-1312	NM_023008	65095	Hs.709967	NM_023008	ENSG00000129347	KRI1	-	KRI1 homolog	protein-coding	0.040201	0.615000	
chunk0148_164_1	chr5	6766584	6766818	+	0	NA	Intergenic	(CTCC)n|Simple_repeat|Simple_repeat	20713	NM_001171806	11044	Hs.481542	NM_006999	ENSG00000112941	TENT4A	LAK-1|LAK1|PAPD7|POLK|POLS|TRF4|TRF4-1|TRF41|TUTASE5	terminal nucleotidyltransferase 4A	protein-coding	0.025641	0.642553	
chunk0014_305_1	chr1	181051530	181052163	+	0	NA	intron (NM_001195035, intron 4 of 4)	intron (NM_001195035, intron 4 of 4)	18421	NM_001310213	3140	Hs.13500	NM_001531	ENSG00000153029	MR1	HLALS	major histocompatibility complex, class I-related	protein-coding	0.012638	0.422713	307(GAGAACAAGGAGTTCT,-,0.00),308(AGAACAAGGAGTTCTA,+,0.00)
chunk0084_379_1	chr17	81867805	81868317	+	0	NA	non-coding (NR_125441, exon 5 of 5)	non-coding (NR_125441, exon 5 of 5)	2913	NM_001301241	396	Hs.159161	NM_004309	ENSG00000141522	ARHGDIA	GDIA1|HEL-S-47e|NPHS8|RHOGDI|RHOGDI-1	Rho GDP dissociation inhibitor alpha	protein-coding	0.033203	0.658869	
chunk0083_292_1	chr17	69239761	69240394	+	0	NA	intron (NM_080282, intron 1 of 39)	ERV3-16A3_I-int|LTR|ERVL	4738	NM_080282	10349	Hs.25377	NM_080282	ENSG00000154263	ABCA10	EST698739	ATP binding cassette subfamily A member 10	protein-coding	0.009479	0.429022	251(TTAACAGTGTGTTCTT,+,0.00)
chunk0209_413_1	chrX	56803983	56804383	+	0	NA	intron (NR_015367, intron 2 of 2)	intron (NR_015367, intron 2 of 2)	-66599	NR_002308	442454	Hs.663220	NR_002308		UQCRBP1	-	ubiquinol-cytochrome c reductase binding protein pseudogene 1	pseudo	0.010000	0.543641	209(GGGAACACACTGTTTC,-,0.00),210(GGAACACACTGTTTCT,+,0.00)
chunk0185_365_1	chr7	132830488	132831092	+	0	NA	intron (NM_017812, intron 6 of 7)	intron (NM_017812, intron 6 of 7)	181996	NR_046323	286023	Hs.671875	NM_173682	ENSG00000183470	FLJ40288	-	uncharacterized FLJ40288	ncRNA	0.006623	0.363636	
chunk0124_415_1	chr3	60921271	60921664	+	0	NA	intron (NM_001166243, intron 3 of 9)	intron (NM_001166243, intron 3 of 9)	-303597	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.002545	0.319797	
chunk0102_414_1	chr2	156566275	156566655	+	0	NA	intron (NM_001083112, intron 9 of 16)	L1MB3|LINE|L1	130077	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.007895	0.377953	
chunk0169_353_1	chr6	106650951	106651343	+	0	NA	intron (NM_018292, intron 5 of 10)	L1MB2|LINE|L1	21581	NM_018292	55278	Hs.406917	NM_018292	ENSG00000130348	QRSL1	GatA	glutaminyl-tRNA amidotransferase subunit QRSL1	protein-coding	0.007653	0.343511	
chunk0133_12_1	chr3	165583030	165583462	+	0	NA	Intergenic	L1ME3A|LINE|L1	254219	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.002315	0.281755	189(CAGTACATGCAGTACT,-,0.00),190(AGTACATGCAGTACTG,+,0.00)
chunk0064_209_1	chr14	93026562	93027200	+	0	NA	intron (NM_001142594, intron 3 of 10)	L1ME4b|LINE|L1	-40571	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.012539	0.428795	214(AGAACGGGGAGTGCTT,+,0.00)
chunk0103_402_1	chr2	169065465	169065881	+	0	NA	Intergenic	L1M5|LINE|L1	-1362	NM_001289763	10170	Hs.179608	NM_005771	ENSG00000073737	DHRS9	3-alpha-HSD|3ALPHA-HSD|RDH-E2|RDH-TBE|RDH15|RDHL|RDHTBE|RETSDR8|SDR9C4	dehydrogenase/reductase 9	protein-coding	0.002404	0.354916	
chunk0108_356_1	chr2	236417124	236417418	+	0	NA	intron (NM_001270584, intron 7 of 17)	intron (NM_001270584, intron 7 of 17)	86426	NM_001270585	79781	Hs.591594	NM_024726	ENSG00000132321	IQCA1	4930465P12Rik|DRC11|IQCA	IQ motif containing with AAA domain 1	protein-coding	0.020408	0.518644	
chunk0060_63_1	chr14	41824687	41824886	+	0	NA	intron (NM_152447, intron 2 of 5)	intron (NM_152447, intron 2 of 5)	217225	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.000000	0.525000	
chunk0126_304_1	chr3	80900672	80901032	+	0	NA	Intergenic	Intergenic	-93016	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.002778	0.332410	
chunk0174_300_1	chr6	162662310	162662512	+	0	NA	intron (NM_013988, intron 1 of 8)	L1PB4|LINE|L1	-64721	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.000000	0.310345	
chunk0014_366_1	chr1	182578208	182578433	+	0	NA	intron (NM_021133, intron 5 of 6)	L1PB4|LINE|L1	10939	NM_021133	6041	Hs.518545	NM_021133	ENSG00000135828	RNASEL	PRCA1|RNS4	ribonuclease L	protein-coding	0.004444	0.287611	
chunk0014_377_1	chr1	182680777	182681350	+	0	NA	Intergenic	MIRb|SINE|MIR	-8131	NM_033345	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.005236	0.500000	
chunk0165_267_1	chr6	35831582	35832154	+	0	NA	Intergenic	Intergenic	26574	NM_182548	222662	Hs.367947	NM_182548	ENSG00000197753	LHFPL5	DFNB67|TMHS|dJ510O8.8	LHFPL tetraspan subfamily member 5	protein-coding	0.006993	0.371728	234(GAAAACACTGTGTTCT,-,0.00),235(AAAACACTGTGTTCTA,+,0.00)
chunk0125_400_1	chr3	71991604	71992298	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	108504	NR_104116	285286	Hs.559386	NR_104116	ENSG00000241163	LINC00877	-	long intergenic non-protein coding RNA 877	ncRNA	0.002882	0.433094	270(AAGGACTGAGTGTCCT,-,0.00),271(AGGACTGAGTGTCCTT,+,0.00)
chunk0027_139_1	chr10	74548557	74549103	+	0	NA	intron (NM_001123, intron 7 of 10)	intron (NM_001123, intron 7 of 10)	-19506	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.005495	0.347349	
chunk0212_103_1	chrY	15285819	15286154	+	0	NA	Intergenic	Intergenic	-481953	NR_046504	100874056	Hs.743197	NR_046504	ENSG00000228787	NLGN4Y-AS1	NLGN4Y-AS|NLGN4YAS	NLGN4Y antisense RNA 1	ncRNA	0.002985	0.383929	
chunk0050_192_1	chr12	103965627	103965960	+	0	NA	promoter-TSS (NM_003211)	promoter-TSS (NM_003211)	-22	NM_003211	6996	Hs.584809	NM_003211	ENSG00000139372	TDG	hTDG	thymine DNA glycosylase	protein-coding	0.072072	0.634731	
chunk0064_328_1	chr14	96362064	96362362	+	0	NA	intron (NM_018036, intron 1 of 41)	intron (NM_018036, intron 1 of 41)	1128	NM_018036	55102	Hs.168241	NM_018036	ENSG00000066739	ATG2B	C14orf103	autophagy related 2B	protein-coding	0.023490	0.444816	
chunk0089_85_1	chr18	58299896	58300419	+	0	NA	intron (NM_001144970, intron 4 of 28)	MIR|SINE|MIR	78635	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.003824	0.398855	
chunk0195_31_1	chr8	93204777	93205354	+	0	NA	Intergenic	L1PA6|LINE|L1	-38215	NM_001242668									0.006932	0.474048	
chunk0123_261_1	chr3	45984292	45984871	+	0	NA	intron (NM_024513, intron 2 of 17)	intron (NM_024513, intron 2 of 17)	11243	NM_024513	79443	Hs.200227	NM_024513	ENSG00000163820	FYCO1	CATC2|CTRCT18|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding	0.008636	0.477586	
chunk0165_345_1	chr6	37958524	37959071	+	0	NA	intron (NM_021943, intron 2 of 5)	intron (NM_021943, intron 2 of 5)	139266	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.009141	0.381387	
chunk0109_69_1	chr20	1486947	1487751	+	0	NA	intron (NM_001134836, intron 1 of 4)	L1ME1|LINE|L1	4238	NM_001134836	284759	Hs.721685	NM_001122962	ENSG00000196209	SIRPB2	PTPN1L|PTPNS1L3|dJ776F14.2	signal regulatory protein beta 2	protein-coding	0.003731	0.311801	374(AGGTACACACTGTTCA,-,0.00),375(GGTACACACTGTTCAT,+,0.00)
chunk0185_247_1	chr7	130095810	130096116	+	0	NA	intron (NM_014997, intron 1 of 9)	L2b|LINE|L2	25454	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.003268	0.384365	
chunk0199_336_1	chr9	10969227	10969833	+	0	NA	Intergenic	Intergenic	356324	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.000000	0.329489	
chunk0122_120_1	chr3	31254809	31255583	+	0	NA	Intergenic	Intergenic	-93409	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.002584	0.419355	
chunk0133_73_1	chr3	166992388	166992829	+	0	NA	Intergenic	LTR40b|LTR|ERVL	387675	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.002268	0.380090	
chunk0206_18_1	chr9	115808072	115808322	+	0	NA	Intergenic	Intergenic	-63958	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.004000	0.358566	
chunk0033_277_1	chr11	19331069	19331807	+	0	NA	Intergenic	Intergenic	-19286	NM_001111018	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.008130	0.431664	
chunk0078_329_1	chr17	8611077	8611723	+	0	NA	intron (NM_001256095, intron 2 of 41)	intron (NM_001256095, intron 2 of 41)	19361	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.006192	0.394127	
chunk0021_315_1	chr1	245179735	245180079	+	0	NA	intron (NM_018012, intron 2 of 14)	L2b|LINE|L2	24922	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.023256	0.591304	111(GTGGACAGGATGTTCT,-,0.00),112(TGGACAGGATGTTCTG,+,0.00)
chunk0161_354_1	chr5	174693857	174694339	+	0	NA	Intergenic	L2a|LINE|L2	-30474	NM_002449	4488	Hs.89404	NM_002449	ENSG00000120149	MSX2	CRS2|FPP|HOX8|MSH|PFM|PFM1	msh homeobox 2	protein-coding	0.020747	0.501035	
chunk0201_414_1	chr9	69593693	69594038	+	0	NA	intron (NM_001163, intron 1 of 12)	intron (NM_001163, intron 1 of 12)	78494	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.011594	0.326590	
chunk0137_185_1	chr4	17577099	17577332	+	0	NA	promoter-TSS (NM_015907)	promoter-TSS (NM_015907)	-89	NM_015907	51056	Hs.570791	NM_015907	ENSG00000002549	LAP3	HEL-S-106|LAP|LAPEP|PEPS	leucine aminopeptidase 3	protein-coding	0.137339	0.696581	
chunk0150_253_1	chr5	36301999	36302564	+	0	NA	promoter-TSS (NM_001161429)	promoter-TSS (NM_001161429)	-372	NM_001161429	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.005310	0.392226	
chunk0078_208_1	chr17	5436073	5436721	+	0	NA	intron (NM_001212, intron 2 of 5)	L1MB7|LINE|L1	2754	NM_001212	708	Hs.555866	NM_001212	ENSG00000108561	C1QBP	COXPD33|GC1QBP|HABP1|SF2AP32|SF2p32|gC1Q-R|gC1qR|p32	complement C1q binding protein	protein-coding	0.007716	0.389831	
chunk0205_61_1	chr9	106601056	106601255	+	0	NA	TTS (NR_107048)	TTS (NR_107048)	227	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.005025	0.490000	
chunk0139_65_1	chr4	49092480	49092694	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	105945	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.023364	0.409302	
chunk0111_103_1	chr20	23622939	23623394	+	0	NA	Intergenic	Intergenic	14882	NM_001288614	1471	Hs.304682	NM_000099	ENSG00000101439	CST3	ARMD11|HEL-S-2	cystatin C	protein-coding	0.010989	0.438596	181(TTGGACATTCTGTTCC,-,0.00),182(TGGACATTCTGTTCCC,+,0.00)
chunk0113_111_1	chr20	51350579	51351313	+	0	NA	Intergenic	L1M5|LINE|L1	102031	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.006812	0.391837	501(CAGGACACTCAGTTTT,-,0.00),502(AGGACACTCAGTTTTC,+,0.00)
chunk0106_378_1	chr2	207269724	207270158	+	0	NA	promoter-TSS (NR_031633)	promoter-TSS (NR_031633)	-517	NR_031633	100302130		NR_031633	ENSG00000221628	MIR1302-4	MIRN1302-4|hsa-mir-1302-4	microRNA 1302-4	ncRNA	0.009217	0.393103	
chunk0100_174_1	chr2	109720475	109720809	+	0	NA	Intergenic	Intergenic	-72116	NM_001123363	729540	Hs.535589	NM_001037866	ENSG00000183054	RGPD6	RGP6|RGPD7|RanBP2L1|RanBP2L2	RANBP2 like and GRIP domain containing 6	protein-coding	0.000000	0.444776	131(AAGAACTTGGTGTGCC,-,0.00),132(AGAACTTGGTGTGCCA,+,0.00)
chunk0116_241_1	chr21	38488173	38488631	+	0	NA	intron (NR_111949, intron 3 of 4)	(TTTATTG)n|Simple_repeat|Simple_repeat	10102	NM_001136155	2078	Hs.473819	NM_004449	ENSG00000157554	ERG	erg-3|p55	ETS transcription factor ERG	protein-coding	0.010917	0.429194	
chunk0191_180_1	chr8	51226149	51226597	+	0	NA	Intergenic	L1M4b|LINE|L1	583072	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.006696	0.349666	
chunk0137_223_1	chr4	20009511	20010181	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-242059	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.007463	0.345753	
chunk0161_428_1	chr5	178426477	178426991	+	0	NA	intron (NM_173465, intron 2 of 28)	L1MC1|LINE|L1	163821	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.038911	0.526214	
chunk0185_42_1	chr7	124502401	124502600	+	0	NA	Intergenic	MIR|SINE|MIR	-150404	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.005025	0.310000	
chunk0010_362_1	chr1	118826696	118827016	+	0	NA	Intergenic	Intergenic	162700	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.009375	0.433022	
chunk0138_396_1	chr4	42852751	42853309	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-40236	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.001792	0.357782	
chunk0157_117_1	chr5	116896138	116896692	+	0	NA	Intergenic	L1MC1|LINE|L1	-134206	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.007220	0.371171	
chunk0105_2_1	chr2	181575899	181576490	+	0	NA	intron (NR_027690, intron 2 of 11)	L1MC4|LINE|L1	80913	NM_001030313	375298	Hs.732358	NM_201548	ENSG00000188452	CERKL	RP26	ceramide kinase like	protein-coding	0.001692	0.329392	249(GGGAACATTCTGTTCT,-,0.00),250(GGAACATTCTGTTCTA,+,0.00)
chunk0022_434_1	chr10	19390738	19391121	+	0	NA	intron (NM_001142308, intron 28 of 39)	intron (NM_001142308, intron 28 of 39)	337621	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.002611	0.317708	
chunk0136_417_1	chr3	197427280	197427572	+	0	NA	Intergenic	Intergenic	-128154	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.013699	0.412969	
chunk0004_435_1	chr1	52941838	52942240	+	0	NA	intron (NM_001193599, intron 2 of 14)	intron (NM_001193599, intron 2 of 14)	1725	NR_039972									0.002488	0.401985	
chunk0054_196_1	chr13	44921656	44922978	+	0	NA	Intergenic	Intergenic	67161	NM_012345	26747	Hs.525006	NM_012345	ENSG00000083635	NUFIP1	NUFIP|bA540M5.1	nuclear FMR1 interacting protein 1	protein-coding	0.004539	0.432351	349(AGGAACAAAATGTTCC,-,0.00),350(GGAACAAAATGTTCCT,+,0.00)
chunk0039_175_1	chr11	100103006	100103309	+	0	NA	intron (NM_014361, intron 13 of 24)	intron (NM_014361, intron 13 of 24)	547012	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.009901	0.328947	245(GAGAACAGTCTGTTAA,-,0.00)
chunk0182_10_1	chr7	91054431	91054768	+	0	NA	intron (NM_001287136, intron 10 of 13)	intron (NM_001287136, intron 10 of 13)	-209869	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.005935	0.414201	
chunk0107_119_1	chr2	214473610	214473968	+	0	NA	intron (NM_001080500, intron 3 of 3)	intron (NM_001080500, intron 3 of 3)	-36393	NR_047698	100885780	Hs.665982	NR_047698	ENSG00000224257	VWC2L-IT1	-	VWC2L intronic transcript 1	ncRNA	0.005587	0.362117	
chunk0048_359_1	chr12	85688778	85689299	+	0	NA	Intergenic	Intergenic	147502	NM_005447	9182	Hs.527881	NM_005447	ENSG00000198774	RASSF9	P-CIP1|PAMCI|PCIP1	Ras association domain family member 9	protein-coding	0.001919	0.406130	
chunk0168_342_1	chr6	92976967	92977627	+	0	NA	Intergenic	Intergenic	442285	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.003030	0.341906	318(TAGAACTAAGTGTTCC,-,0.00),319(AGAACTAAGTGTTCCA,+,0.00)
chunk0058_211_1	chr14	24954015	24954850	+	0	NA	intron (NM_014178, intron 2 of 5)	intron (NM_014178, intron 2 of 5)	94568	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004790	0.476077	409(GGGAACAGAGAGTGCT,-,0.00),410(GGAACAGAGAGTGCTG,+,0.00)
chunk0091_378_1	chr19	15837811	15838365	+	0	NA	Intergenic	LTR10C|LTR|ERV1	9141	NR_015379	652995	Hs.644234	NR_015379	ENSG00000214049	UCA1	CUDR|LINC00178|NCRNA00178|UCAT1|onco-lncRNA-36	urothelial cancer associated 1	ncRNA	0.010830	0.322523	207(ATGTACTTTATGTTCC,-,0.00),208(TGTACTTTATGTTCCT,+,0.00)
chunk0111_116_1	chr20	23983385	23983643	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	3361	NM_178312	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.011628	0.509653	
chunk0175_12_1	chr7	214380	214874	+	0	NA	intron (NM_020223, intron 3 of 9)	MIR3|SINE|MIR	21658	NM_020223	56975	Hs.134742	NM_020223	ENSG00000177706	FAM20C	DMP-4|DMP4|G-CK|GEF-CK|RNS	FAM20C golgi associated secretory pathway kinase	protein-coding	0.048583	0.547475	
chunk0173_453_1	chr6	151801117	151801452	+	0	NA	intron (NM_001122742, intron 2 of 9)	intron (NM_001122742, intron 2 of 9)	-4389	NM_001122741	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.000000	0.300595	
chunk0147_147_1	chr4	175267029	175267558	+	0	NA	Intergenic	Intergenic	348935	NM_001130704	11086	Hs.126838	NM_014269	ENSG00000168594	ADAM29	CT73|svph1	ADAM metallopeptidase domain 29	protein-coding	0.009452	0.309434	263(GAGTACACATTGTCCA,-,0.00),264(AGTACACATTGTCCAT,+,0.00)
chunk0072_185_1	chr15	94228367	94228674	+	0	NA	Intergenic	Intergenic	-69681	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.013029	0.334416	
chunk0101_71_1	chr2	123719160	123719851	+	0	NA	Intergenic	Intergenic	-305782	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.005789	0.359827	
chunk0094_148_1	chr2	5125605	5125812	+	0	NA	Intergenic	Penelope1_Vert|LINE|Penelope	-469486	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.004831	0.408654	
chunk0117_381_1	chr21	45182146	45183108	+	0	NA	non-coding (NR_073200, exon 6 of 13)	non-coding (NR_073200, exon 6 of 13)	105269	NM_133635	23275	Hs.592164	NM_015227	ENSG00000186866	POFUT2	C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding	0.006237	0.364486	628(AGGACAGGAAGCTCTT,+,0.00)
chunk0201_164_1	chr9	36075066	36075464	+	0	NA	intron (NM_001316345, intron 8 of 22)	intron (NM_001316345, intron 8 of 22)	38352	NM_001316346	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.005025	0.428571	
chunk0048_241_1	chr12	81572039	81572959	+	0	NA	intron (NM_001220474, intron 2 of 30)	L2a|LINE|L2	25872	NM_001220478	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.002174	0.386536	
chunk0069_59_1	chr15	60800241	60800440	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	118771	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.015075	0.395000	18(AATGACACGCTGTTCC,-,0.00),19(ATGACACGCTGTTCCA,+,0.00)
chunk0210_467_1	chrX	107548391	107548625	+	0	NA	intron (NM_032428, intron 6 of 15)	L2b|LINE|L2	-2687	NR_046750	100874122	Hs.600967	NR_046750	ENSG00000227610	FRMPD3-AS1	-	FRMPD3 antisense RNA 1	ncRNA	0.004274	0.421277	
chunk0092_18_1	chr19	18713193	18713392	+	0	NA	intron (NM_001098482, intron 1 of 14)	L1MB5|LINE|L1	29677	NM_001098482	23373	Hs.371096	NM_015321	ENSG00000105662	CRTC1	MAML2|MECT1|Mam-2|TORC-1|TORC1|WAMTP1	CREB regulated transcription coactivator 1	protein-coding	0.000000	0.480000	70(GAGCACATTCTGTTCA,-,0.00),71(AGCACATTCTGTTCAG,+,0.00)
chunk0160_185_1	chr5	154215924	154216419	+	0	NA	intron (NM_198321, intron 1 of 11)	intron (NM_198321, intron 1 of 11)	25436	NM_198321	55568	Hs.631797	NM_017540	ENSG00000164574	GALNT10	GALNACT10|PPGALNACT10|PPGANTASE10	polypeptide N-acetylgalactosaminyltransferase 10	protein-coding	0.002020	0.362903	
chunk0158_250_1	chr5	130908112	130908763	+	0	NA	Intergenic	Intergenic	256911	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.009217	0.340491	
chunk0153_387_1	chr5	75082358	75083000	+	0	NA	intron (NM_001164443, intron 23 of 24)	intron (NM_001164443, intron 23 of 24)	-30036	NR_126375	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.001558	0.335925	
chunk0042_253_1	chr12	6532651	6532912	+	0	NA	TTS (NM_014865)	TTS (NM_014865)	-1624	NM_001289745	2597	Hs.544577	NM_002046	ENSG00000111640	GAPDH	G3PD|GAPD|HEL-S-162eP	glyceraldehyde-3-phosphate dehydrogenase	protein-coding	0.026820	0.545802	
chunk0019_371_1	chr1	229888929	229889279	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-168685	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.000000	0.447293	
chunk0195_125_1	chr8	94951335	94951534	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-2047	NM_001135733	94241	Hs.492261	NM_033285	ENSG00000164938	TP53INP1	SIP|TP53DINP1|TP53INP1A|TP53INP1B|Teap|p53DINP1	tumor protein p53 inducible nuclear protein 1	protein-coding	0.015075	0.395000	
chunk0089_23_1	chr18	57757220	57757424	+	0	NA	intron (NM_005603, intron 1 of 27)	L1MC4|LINE|L1	45773	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.000000	0.468293	
chunk0009_248_1	chr1	107057274	107057527	+	0	NA	exon (NM_018137, exon 1 of 1)	exon (NM_018137, exon 1 of 1)	755	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.075099	0.657480	
chunk0172_40_1	chr6	134003584	134004015	+	0	NA	intron (NM_145176, intron 3 of 4)	L3|LINE|CR1	48852	NM_145176	154091	Hs.486508	NM_145176	ENSG00000146411	SLC2A12	GLUT12|GLUT8	solute carrier family 2 member 12	protein-coding	0.011601	0.416667	
chunk0203_343_1	chr9	89798165	89798440	+	0	NA	Intergenic	Intergenic	158519	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.021818	0.485507	
chunk0038_330_1	chr11	92666712	92667040	+	0	NA	intron (NM_001008781, intron 2 of 24)	MLT1J1|LTR|ERVL-MaLR	-302747	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.012195	0.510638	
chunk0075_277_1	chr16	53836275	53836670	+	0	NA	intron (NM_001080432, intron 3 of 8)	L2c|LINE|L2	132509	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.005063	0.371212	
chunk0149_191_1	chr5	21411931	21412209	+	0	NA	Intergenic	Intergenic	-47410	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.000000	0.229391	
chunk0175_73_1	chr7	2193221	2193869	+	0	NA	intron (NM_003550, intron 10 of 18)	intron (NM_003550, intron 10 of 18)	39403	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.041667	0.560863	
chunk0075_266_1	chr16	53714506	53714979	+	0	NA	intron (NM_001080432, intron 1 of 8)	intron (NM_001080432, intron 1 of 8)	10779	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.010571	0.409283	
chunk0115_200_1	chr21	26225520	26226113	+	0	NA	Intergenic	Intergenic	-54688	NM_001136131	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.001686	0.294613	182(AGGCACTGAGTGTACT,-,0.00),183(GGCACTGAGTGTACTT,+,0.00)
chunk0136_167_1	chr4	6186343	6186761	+	0	NA	intron (NM_001099433, intron 1 of 20)	L1M4b|LINE|L1	8067	NM_001306133	152789	Hs.479066	NM_144720	ENSG00000152969	JAKMIP1	Gababrbp|JAMIP1|MARLIN1	janus kinase and microtubule interacting protein 1	protein-coding	0.002392	0.434368	
chunk0145_15_1	chr4	143389507	143389963	+	0	NA	intron (NM_002039, intron 1 of 9)	L2a|LINE|L2	46275	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.000000	0.378556	
chunk0136_176_1	chr4	6556428	6556728	+	0	NA	promoter-TSS (NM_001206995)	promoter-TSS (NM_001206995)	-900	NM_001206995	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.016667	0.531561	0(AGAACAACTAGTTCTC,+,0.00)
chunk0103_389_1	chr2	168828406	168828605	+	0	NA	intron (NM_001171631, intron 9 of 20)	intron (NM_001171631, intron 9 of 20)	25908	NM_052946	115677	Hs.189780	NM_052946	ENSG00000163072	NOSTRIN	DaIP2	nitric oxide synthase trafficking	protein-coding	0.005025	0.360000	
chunk0116_359_1	chr21	41583133	41583790	+	0	NA	Intergenic	Intergenic	-75303	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.018265	0.510638	
chunk0195_283_1	chr8	98402429	98403004	+	0	NA	Intergenic	Intergenic	-24306	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.010435	0.588542	293(GGGAACAGTCTGTGCT,-,0.00),294(GGAACAGTCTGTGCTT,+,0.00)
chunk0085_216_1	chr18	6745794	6746586	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-88243	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.008838	0.418663	309(GGGATCATTTTGTTCT,-,0.00),310(GGATCATTTTGTTCTA,+,0.00),424(GAGAACGGAATGTTCT,-,0.00),425(AGAACGGAATGTTCTT,+,0.00)
chunk0012_234_1	chr1	160588678	160589216	+	0	NA	Intergenic	Intergenic	-9431	NM_001184881	8832	Hs.398093	NM_003874	ENSG00000066294	CD84	LY9B|SLAMF5|hCD84|mCD84	CD84 molecule	protein-coding	0.005576	0.358071	287(AAGAACAGCAAGTCCC,-,0.00),288(AGAACAGCAAGTCCCC,+,0.00)
chunk0043_386_1	chr12	25115691	25115975	+	0	NA	intron (NM_001082972, intron 12 of 15)	L1M4|LINE|L1	63586	NM_001204127	4033	Hs.124922	NM_006152	ENSG00000118308	LRMP	JAW1	lymphoid restricted membrane protein	protein-coding	0.007042	0.400000	121(AGGTACATACTGAACT,-,0.00)
chunk0212_116_1	chrX	130555891	130556534	+	0	NA	Intergenic	Intergenic	61271	NR_027141	55855	Hs.567120	NM_018472		DENND10P1	FAM45B|FAM45BP|HT011	DENND10 pseudogene 1	pseudo	0.006221	0.374224	
chunk0021_12_1	chr10	366371	366643	+	0	NA	intron (NM_014974, intron 18 of 36)	intron (NM_014974, intron 18 of 36)	-84421	NR_106988									0.018382	0.465201	
chunk0209_406_1	chrX	56000678	56001336	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-231382	NM_007250	11279	Hs.646614	NM_007250	ENSG00000102349	KLF8	BKLF3|ZNF741	Kruppel like factor 8	protein-coding	0.003040	0.359636	513(CTGTACAATGTGTACT,-,0.00),514(TGTACAATGTGTACTT,+,0.00)
chunk0020_51_1	chr1	232378304	232378643	+	0	NA	Intergenic	Intergenic	137135	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.017699	0.567647	
chunk0102_164_1	chr2	147306046	147306344	+	0	NA	Intergenic	Intergenic	-538322	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.003356	0.428094	114(CAGCACACAAAGTCCC,-,0.00),115(AGCACACAAAGTCCCT,+,0.00)
chunk0076_33_1	chr16	59486705	59487093	+	0	NA	Intergenic	L1PA16|LINE|L1	268292	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.002577	0.359897	
chunk0209_163_1	chrX	43264771	43265053	+	0	NA	Intergenic	L1MA2|LINE|L1	87918	NR_110387	101927501	Hs.495998	NR_110387	ENSG00000224294	PINCR	-	p53-induced noncoding RNA	ncRNA	0.003546	0.310954	
chunk0124_165_1	chr3	55217018	55217327	+	0	NA	Intergenic	L1MA7|LINE|L1	-250084	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.003236	0.361290	
chunk0047_103_1	chr12	68847948	68848310	+	0	NA	Intergenic	AluJr4|SINE|Alu	39112	NM_001145337	4193	Hs.484551	NM_002392	ENSG00000135679	MDM2	ACTFS|HDMX|hdm2	MDM2 proto-oncogene	protein-coding	0.008287	0.454545	194(ATAACAGTATGTTCAT,+,0.00)
chunk0202_71_1	chr9	71742148	71742671	+	0	NA	intron (NM_001135820, intron 4 of 22)	intron (NM_001135820, intron 4 of 22)	26475	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.013384	0.375954	
chunk0122_54_1	chr3	28727179	28727820	+	0	NA	intron (NR_038840, intron 2 of 4)	intron (NR_038840, intron 2 of 4)	152221	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.001560	0.341121	
chunk0057_146_1	chr13	100197471	100198402	+	0	NA	intron (NM_001127692, intron 5 of 22)	intron (NM_001127692, intron 5 of 22)	108921	NM_000282	5095	Hs.80741	NM_000282	ENSG00000175198	PCCA	-	propionyl-CoA carboxylase subunit alpha	protein-coding	0.006445	0.443133	279(AAGTACACTGAGTTCA,-,0.00),280(AGTACACTGAGTTCAG,+,0.00)
chunk0138_158_1	chr4	37648121	37648524	+	0	NA	intron (NM_001085399, intron 2 of 6)	intron (NM_001085399, intron 2 of 6)	38055	NM_001085400	768211	Hs.283378	NM_001085399	ENSG00000181826	RELL1	-	RELT like 1	protein-coding	0.007444	0.527228	
chunk0098_119_1	chr2	68575076	68575341	+	0	NA	intron (NM_173545, intron 9 of 9)	L2a|LINE|L2	-70614	NM_138964	10887	Hs.683430	NM_138964	ENSG00000169618	PROKR1	GPR73|GPR73a|PK-R1|PKR1|ZAQ	prokineticin receptor 1	protein-coding	0.003774	0.421053	
chunk0054_358_1	chr13	49619065	49619383	+	0	NA	Intergenic	Intergenic	-9075	NM_138450	115761	Hs.558599	NM_138450	ENSG00000152213	ARL11	ARLTS1	ADP ribosylation factor like GTPase 11	protein-coding	0.012579	0.473354	
chunk0099_390_1	chr2	101815827	101816588	+	0	NA	intron (NM_145686, intron 3 of 30)	L1MEc|LINE|L1	118131	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.014455	0.475066	
chunk0126_441_1	chr3	87137442	87138189	+	0	NA	intron (NR_104153, intron 1 of 2)	intron (NR_104153, intron 1 of 2)	48535	NR_047469	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.001339	0.318182	
chunk0021_73_1	chr10	1494315	1494762	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	-32092	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.002237	0.350446	
chunk0121_266_1	chr3	23259946	23260358	+	0	NA	intron (NM_152653, intron 3 of 5)	intron (NM_152653, intron 3 of 5)	56859	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.000000	0.261501	
chunk0121_277_1	chr3	23468294	23468665	+	0	NA	intron (NM_152653, intron 3 of 5)	intron (NM_152653, intron 3 of 5)	265186	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.002695	0.322581	
chunk0096_335_1	chr2	35345980	35346511	+	0	NA	Intergenic	L1M4b|LINE|L1	-125160	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.000000	0.313910	
chunk0037_63_1	chr11	71103261	71103699	+	0	NA	intron (NM_012309, intron 5 of 24)	intron (NM_012309, intron 5 of 24)	121316	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.018265	0.537585	
chunk0161_282_1	chr5	172847100	172847305	+	0	NA	intron (NM_001031711, intron 1 of 9)	MLT1J2|LTR|ERVL-MaLR	12982	NM_001031711	57222	Hs.509163	NM_020462	ENSG00000113719	ERGIC1	AMCN|ERGIC-32|ERGIC32|NET24	endoplasmic reticulum-golgi intermediate compartment 1	protein-coding	0.009756	0.592233	
chunk0166_93_1	chr6	43733191	43733770	+	0	NA	Intergenic	Intergenic	-36729	NM_001025367	7422	Hs.73793	NM_003376	ENSG00000112715	VEGFA	MVCD1|VEGF|VPF	vascular endothelial growth factor A	protein-coding	0.001727	0.437931	148(AGGGACTCATTGTACC,-,0.00),149(GGGACTCATTGTACCT,+,0.00)
chunk0015_326_1	chr1	189604904	189605228	+	0	NA	Intergenic	MIR|SINE|MIR	872563	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.338462	
chunk0071_31_1	chr15	79582555	79582833	+	0	NA	Intergenic	L1MB2|LINE|L1	150178	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.007194	0.326165	
chunk0114_278_1	chr21	16342055	16342430	+	0	NA	intron (NR_027790, intron 4 of 7)	L1M5|LINE|L1	147863	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002667	0.255319	
chunk0104_341_1	chr2	179741343	179741808	+	0	NA	intron (NM_152520, intron 3 of 9)	intron (NM_152520, intron 3 of 9)	4467	NM_001113397	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.000000	0.341202	205(TAGAACATTCTGTTCT,-,0.00),206(AGAACATTCTGTTCTG,+,0.00)
chunk0065_368_1	chr14	103995784	103995983	+	0	NA	intron (NM_153046, intron 12 of 35)	intron (NM_153046, intron 12 of 35)	-53575	NM_001257268	647286	Hs.632325	NM_001257268	ENSG00000227729	RD3L	TDRD9-AS1|TDRD9AS1	retinal degeneration 3 like	protein-coding	0.015075	0.425000	
chunk0081_36_1	chr17	37510089	37510462	+	0	NA	intron (NM_007026, intron 1 of 2)	intron (NM_007026, intron 1 of 2)	20430	NM_007026	11072	Hs.91448	NM_007026	ENSG00000276023	DUSP14	MKP-L|MKP6	dual specificity phosphatase 14	protein-coding	0.042895	0.582888	98(TGGTGCACACTGTCCT,-,0.00),99(GGTGCACACTGTCCTC,+,0.00)
chunk0164_227_1	chr6	22966890	22967139	+	0	NA	Intergenic	Intergenic	397565	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.004016	0.376000	
chunk0171_94_1	chr6	121946171	121946653	+	0	NA	Intergenic	L1PB1|LINE|L1	-453139	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.004149	0.354037	
chunk0153_419_1	chr5	75668777	75668992	+	0	NA	intron (NM_001276713, intron 12 of 13)	MER5A1|DNA|hAT-Charlie	43571	NM_152408	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.004651	0.453704	
chunk0160_351_1	chr5	160240089	160240805	+	0	NA	Intergenic	Intergenic	11017	NM_001445	2172	Hs.519719	NM_001445	ENSG00000170231	FABP6	I-15P|I-BABP|I-BALB|I-BAP|ILBP|ILBP3|ILLBP	fatty acid binding protein 6	protein-coding	0.008380	0.447699	
chunk0032_332_1	chr11	10195127	10195397	+	0	NA	intron (NM_030962, intron 1 of 39)	MER20|DNA|hAT-Charlie	98945	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.007407	0.424354	
chunk0178_86_1	chr7	30519071	30519502	+	0	NA	Intergenic	Intergenic	-14445	NM_001199816	79017	Hs.530024	NM_024051	ENSG00000006625	GGCT	C7orf24|CRF21|GCTG|GGC	gamma-glutamylcyclotransferase	protein-coding	0.006961	0.361111	
chunk0017_67_1	chr1	205552467	205552982	+	0	NA	Intergenic	HAL1|LINE|L1	3911	NR_027086	284578	Hs.537020	NR_027086		MFSD4A-AS1	-	MFSD4A antisense RNA 1	ncRNA	0.009709	0.393411	
chunk0103_417_1	chr2	169665627	169665860	+	0	NA	intron (NM_001085447, intron 4 of 8)	MER83|LTR|ERV1	28678	NM_001085447	129881	Hs.370111	NM_001085447	ENSG00000154479	CCDC173	C2orf77	coiled-coil domain containing 173	protein-coding	0.000000	0.444444	
chunk0184_325_1	chr7	120442520	120443237	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	169210	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.002789	0.362117	
chunk0078_343_1	chr16	86100264	86100654	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-95722	NR_103859	100506542	Hs.111902	NR_103859	ENSG00000269186	LINC01082	TCONS_00024492	long intergenic non-protein coding RNA 1082	ncRNA	0.005128	0.450128	
chunk0042_321_1	chr12	9066086	9066285	+	0	NA	non-coding (NR_026971, exon 3 of 3)	non-coding (NR_026971, exon 3 of 3)	1008	NR_026971	144571	Hs.592432	NR_026971	ENSG00000245105	A2M-AS1	-	A2M antisense RNA 1	ncRNA	0.005025	0.540000	
chunk0139_50_1	chr4	48689013	48689367	+	0	NA	intron (NM_015030, intron 2 of 63)	intron (NM_015030, intron 2 of 63)	91109	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.000000	0.295775	
chunk0209_172_1	chrX	43626267	43626527	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-28510	NM_001270458	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.007692	0.279693	
chunk0072_351_1	chr15	99620367	99620664	+	0	NA	intron (NM_005587, intron 2 of 10)	L1PA16|LINE|L1	-12463	NM_001130928	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.016835	0.385906	
chunk0005_33_1	chr1	54834071	54834595	+	0	NA	intron (NM_001110533, intron 9 of 9)	L2a|LINE|L2	28270	NM_152607	163747	Hs.376018	NM_152607	ENSG00000162398	LEXM	C1orf177|LEM	lymphocyte expansion molecule	protein-coding	0.001908	0.382857	
chunk0085_348_1	chr18	8963228	8963460	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-139286	NM_021074	4729	Hs.464572	NM_021074	ENSG00000178127	NDUFV2	CI-24k|MC1DN7	NADH:ubiquinone oxidoreductase core subunit V2	protein-coding	0.021552	0.515021	
chunk0012_363_1	chr1	162888682	162888909	+	0	NA	Intergenic	Intergenic	-19980	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.004405	0.539474	
chunk0133_378_1	chr3	173889455	173890020	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	31059	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.010619	0.351590	
chunk0119_68_1	chr22	41190471	41190925	+	0	NA	intron (NR_110514, intron 2 of 2)	L1ME2|LINE|L1	6803	NR_110514	101927279	Hs.517517	NR_110514		EP300-AS1	-	EP300 antisense RNA 1	ncRNA	0.008811	0.327473	
chunk0010_81_1	chr1	113391195	113392012	+	0	NA	intron (NM_152900, intron 1 of 20)	intron (NM_152900, intron 1 of 20)	750	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.042840	0.558680	
chunk0009_316_1	chr1	108692741	108692940	+	0	NA	exon (NM_018061, exon 1 of 6)	exon (NM_018061, exon 1 of 6)	527	NR_037185									0.055276	0.540000	
chunk0146_269_1	chr4	163107222	163107657	+	0	NA	Intergenic	Intergenic	-13811	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.013793	0.461009	147(GAGAGCAGCCTGTGCT,-,0.00),148(AGAGCAGCCTGTGCTC,+,0.00),207(AGGTACACTGTGCTCT,-,0.00),208(GGTACACTGTGCTCTC,+,0.00)
chunk0055_114_1	chr13	57107313	57107979	+	0	NA	Intergenic	Intergenic	-33272	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.001502	0.296852	
chunk0117_155_1	chr22	19932070	19932591	+	0	NA	intron (NM_006440, intron 1 of 17)	intron (NM_006440, intron 1 of 17)	-9410	NM_000754	1312	Hs.370408	NM_000754	ENSG00000093010	COMT	HEL-S-98n	catechol-O-methyltransferase	protein-coding	0.019194	0.570881	
chunk0037_310_1	chr11	76773835	76774473	+	0	NA	Intergenic	Intergenic	-8159	NM_001258210	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.003135	0.530516	
chunk0064_17_1	chr14	89326622	89326990	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	90304	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.013587	0.365854	
chunk0182_279_1	chr7	98164035	98164364	+	0	NA	intron (NM_014916, intron 6 of 13)	intron (NM_014916, intron 6 of 13)	-48055	NM_177455	168620	Hs.511979	NM_177455	ENSG00000180535	BHLHA15	BHLHB8|MIST1	basic helix-loop-helix family member a15	protein-coding	0.021277	0.421212	
chunk0178_307_1	chr7	37974860	37975099	+	0	NA	Intergenic	Intergenic	53660	NM_001242948	54749	Hs.563491	NM_017549	ENSG00000086289	EPDR1	EPDR|MERP-1|MERP1|UCC1	ependymin related 1	protein-coding	0.008368	0.412500	144(GAGAGCAGACAGTTCC,-,0.00),145(AGAGCAGACAGTTCCT,+,0.00)
chunk0106_73_1	chr2	196987256	196987946	+	0	NA	3' UTR (NM_001195144, exon 28 of 28)	3' UTR (NM_001195144, exon 28 of 28)	-60871	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.001449	0.296671	
chunk0067_264_1	chr15	45855641	45855842	+	0	NA	Intergenic	Intergenic	221001	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.004975	0.544554	
chunk0006_266_1	chr1	70252658	70253200	+	0	NA	TTS (NM_004768)	TTS (NM_004768)	47247	NM_004768	9295	Hs.479693	NM_004768	ENSG00000116754	SRSF11	NET2|SFRS11|dJ677H15.2|p54	serine and arginine rich splicing factor 11	protein-coding	0.003690	0.333333	
chunk0174_41_1	chr6	154569581	154570058	+	0	NA	Intergenic	MIRc|SINE|MIR	-59200	NM_173515	154043	Hs.16064	NM_173515	ENSG00000153721	CNKSR3	CNK3|CNK3/IPCEF1|MAGI1	CNKSR family member 3	protein-coding	0.006289	0.391213	
chunk0149_319_1	chr5	26400163	26400394	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	638304	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.000000	0.469828	
chunk0025_94_1	chr10	50561116	50561670	+	0	NA	intron (NM_147156, intron 2 of 10)	MIR|SINE|MIR	62584	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.012635	0.403604	
chunk0039_331_1	chr11	104351909	104352485	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	99606	NR_106987									0.006944	0.310225	221(CAGAACATGGTGTACA,-,0.00),222(AGAACATGGTGTACAG,+,0.00)
chunk0125_31_1	chr3	62319754	62320241	+	0	NA	intron (NM_020685, intron 2 of 5)	intron (NM_020685, intron 2 of 5)	954	NM_020685	57415	Hs.47166	NM_020685	ENSG00000114405	C3orf14	HT021	chromosome 3 open reading frame 14	protein-coding	0.010267	0.418033	
chunk0065_431_1	chr14	106308984	106309183	+	0	NA	Intergenic	Intergenic	21409	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.045226	0.650000	
chunk0001_441_1	chr1	11606270	11606528	+	0	NA	Intergenic	L2b|LINE|L2	-3132	NR_104624	101929181	Hs.568616	NR_104624	ENSG00000235643	LINC01647	-	long intergenic non-protein coding RNA 1647	ncRNA	0.023256	0.490347	
chunk0155_29_1	chr5	91049060	91049465	+	0	NA	intron (NR_003149, intron 85 of 89)	intron (NR_003149, intron 85 of 89)	265140	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.000000	0.312808	
chunk0210_102_1	chrX	71623413	71623785	+	0	NA	Intergenic	Intergenic	-5082	NM_001504	2833	Hs.198252	NM_001504	ENSG00000186810	CXCR3	CD182|CD183|CKR-L2|CMKAR3|GPR9|IP10-R|Mig-R|MigR	C-X-C motif chemokine receptor 3	protein-coding	0.021505	0.538874	
chunk0116_136_1	chr21	36232721	36232969	+	0	NA	exon (NM_005128, exon 15 of 37)	exon (NM_005128, exon 15 of 37)	68304	NM_005128	9980	Hs.204575	NM_005128	ENSG00000142197	DOP1B	21orf5|C21orf5|DOPEY2	DOP1 leucine zipper like protein B	protein-coding	0.024194	0.510040	
chunk0148_190_1	chr5	8144146	8144515	+	0	NA	Intergenic	Intergenic	275226	NM_002454	4552	Hs.481551	NM_002454	ENSG00000124275	MTRR	MSR|cblE	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding	0.008130	0.362162	
chunk0049_322_1	chr12	94662692	94663396	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-12482	NM_020698	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.007102	0.388652	287(AGGCACGAAATGTTCC,-,0.00)
chunk0014_7_1	chr1	174217975	174218619	+	0	NA	intron (NM_014857, intron 1 of 20)	L2a|LINE|L2	58883	NM_014857	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.006211	0.382946	
chunk0192_120_1	chr8	61750286	61750555	+	0	NA	Intergenic	MER21C|LTR|ERVL	35632	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.003717	0.396296	
chunk0129_336_1	chr3	124728976	124729715	+	0	NA	Intergenic	L1MA5|LINE|L1	-1021	NR_033434	7372	Hs.2057	NM_000373	ENSG00000114491	UMPS	OPRT	uridine monophosphate synthetase	protein-coding	0.004060	0.340541	
chunk0046_188_1	chr12	58801640	58802128	+	0	NA	intron (NR_126341, intron 1 of 1)	intron (NR_126341, intron 1 of 1)	-20168	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.002049	0.388548	
chunk0056_279_1	chr13	90385853	90386772	+	0	NA	Intergenic	Intergenic	-106976	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.003264	0.351087	
chunk0100_45_1	chr2	105730185	105730500	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-14721	NM_001004722	8440	Hs.529244	NM_003581	ENSG00000071051	NCK2	GRB4|NCKbeta	NCK adaptor protein 2	protein-coding	0.003175	0.436709	180(GGGCACACAGTGTGTT,-,0.00),181(GGCACACAGTGTGTTT,+,0.00)
chunk0164_44_1	chr6	18457058	18457352	+	0	NA	exon (NM_182757, exon 5 of 8)	exon (NM_182757, exon 5 of 8)	69855	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.013605	0.474576	175(CAGGACAGCCTGTGCT,-,0.00),176(AGGACAGCCTGTGCTG,+,0.00)
chunk0079_352_1	chr17	17811577	17812148	+	0	NA	TTS (NM_030665)	TTS (NM_030665)	1683	NR_106835	102465466		NR_106835	ENSG00000274111	MIR6777	hsa-mir-6777	microRNA 6777	ncRNA	0.014011	0.554196	
chunk0087_244_1	chr18	36732340	36732561	+	0	NA	intron (NM_001281739, intron 16 of 23)	intron (NM_001281739, intron 16 of 23)	-69032	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.000000	0.472973	
chunk0194_415_1	chr8	91773333	91773638	+	0	NA	Intergenic	L2|LINE|L2	244195	NM_175636	862	Hs.368431	NM_004349	ENSG00000079102	RUNX1T1	AML1-MTG8|AML1T1|CBFA2T1|CDR|ETO|MTG8|ZMYND2	RUNX1 partner transcriptional co-repressor 1	protein-coding	0.022951	0.401961	
chunk0211_84_1	chrX	110119936	110120906	+	0	NA	intron (NM_032227, intron 4 of 6)	MER5B|DNA|hAT-Charlie	38303	NR_039774	100616491		NR_039774	ENSG00000265584	MIR3978	-	microRNA 3978	ncRNA	0.004124	0.416066	
chunk0195_400_1	chr8	100400893	100401294	+	0	NA	Intergenic	L1MC5a|LINE|L1	18330	NR_039681	100616451		NR_039681	ENSG00000265599	MIR4471	-	microRNA 4471	ncRNA	0.000000	0.343284	
chunk0180_370_1	chr7	74022996	74023434	+	0	NA	Intergenic	Intergenic	-4574	NM_000501	2006	Hs.647061	NM_000501	ENSG00000049540	ELN	ADCL1|SVAS|WBS|WS	elastin	protein-coding	0.031963	0.574032	164(CGGCTCACGATGTTCC,-,0.00),165(GGCTCACGATGTTCCC,+,0.00)
chunk0136_402_1	chr3	197206036	197206385	+	0	NA	intron (NM_004087, intron 4 of 25)	intron (NM_004087, intron 4 of 25)	-22079	NM_001204388	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.014327	0.394286	
chunk0097_139_1	chr2	47429646	47430020	+	0	NA	exon (NM_000251, exon 7 of 16)	exon (NM_000251, exon 7 of 16)	26766	NM_000251	4436	Hs.597656	NM_000251	ENSG00000095002	MSH2	COCA1|FCC1|HNPCC|HNPCC1|LCFS2|hMSH2	mutS homolog 2	protein-coding	0.013369	0.320000	
chunk0196_304_1	chr8	109643902	109644228	+	0	NA	promoter-TSS (NM_001099756)	promoter-TSS (NM_001099756)	757	NM_001099754	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.039877	0.553517	
chunk0075_180_1	chr16	52097205	52097466	+	0	NA	intron (NR_104655, intron 2 of 2)	L1ME2|LINE|L1	12054	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.000000	0.370229	
chunk0190_108_1	chr8	30391209	30391672	+	0	NA	intron (NM_006867, intron 1 of 9)	intron (NM_006867, intron 1 of 9)	-6039	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.002160	0.465517	
chunk0049_240_1	chr12	93552380	93552921	+	0	NA	Intergenic	Intergenic	-17172	NM_003877	8835	Hs.485572	NM_003877	ENSG00000120833	SOCS2	CIS2|Cish2|SOCS-2|SSI-2|SSI2|STATI2	suppressor of cytokine signaling 2	protein-coding	0.009242	0.442804	
chunk0107_391_1	chr2	223782375	223782929	+	0	NA	intron (NR_110905, intron 1 of 5)	intron (NR_110905, intron 1 of 5)	54950	NR_110905	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.010830	0.389189	
chunk0081_97_1	chr17	39773769	39774015	+	0	NA	intron (NM_001257413, intron 3 of 3)	intron (NM_001257413, intron 3 of 3)	4333	NM_001284516	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.004065	0.327935	71(AAGGACAGTATGTGCA,-,0.00),72(AGGACAGTATGTGCAA,+,0.00)
chunk0071_125_1	chr15	81499218	81499498	+	0	NA	Intergenic	Intergenic	-125281	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.003571	0.548043	
chunk0134_299_1	chr3	180601859	180602194	+	0	NA	promoter-TSS (NM_133462)	promoter-TSS (NM_133462)	-104	NM_133462	151613	Hs.43213	NM_133462	ENSG00000163728	TTC14	DRDL5813|PRO19630	tetratricopeptide repeat domain 14	protein-coding	0.068657	0.523810	
chunk0141_67_1	chr4	77871652	77872076	+	0	NA	intron (NM_020236, intron 2 of 8)	intron (NM_020236, intron 2 of 8)	9213	NM_020236	65008	Hs.532019	NM_020236	ENSG00000169288	MRPL1	BM022|L1MT|MRP-L1	mitochondrial ribosomal protein L1	protein-coding	0.007075	0.280000	
chunk0191_277_1	chr8	53748636	53749264	+	0	NA	intron (NM_015941, intron 12 of 13)	intron (NM_015941, intron 12 of 13)	94092	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.000000	0.316375	
chunk0174_16_1	chr6	152673405	152673959	+	0	NA	Intergenic	Intergenic	-24213	NM_025107	80177	Hs.18160	NM_025107	ENSG00000120279	MYCT1	MTLC	MYC target 1	protein-coding	0.009025	0.318919	
chunk0191_266_1	chr8	53564273	53564736	+	0	NA	Intergenic	MSTA|LTR|ERVL-MaLR	278538	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.006479	0.413793	
chunk0128_122_1	chr3	106417343	106417730	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-548493	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.015504	0.376289	
chunk0026_335_1	chr10	68422452	68422758	+	0	NA	intron (NM_001080449, intron 15 of 20)	intron (NM_001080449, intron 15 of 20)	-15311	NM_001278225	55680	Hs.653144	NM_017987	ENSG00000204130	RUFY2	RABIP4R|ZFYVE13	RUN and FYVE domain containing 2	protein-coding	0.006536	0.397394	
chunk0118_188_1	chr22	31260079	31260730	+	0	NA	intron (NM_005569, intron 5 of 15)	L2a|LINE|L2	12042	NM_016733	3985	Hs.474596	NM_005569	ENSG00000182541	LIMK2	-	LIM domain kinase 2	protein-coding	0.007680	0.441718	156(TGGCACTTACTGTTCT,-,0.00),157(GGCACTTACTGTTCTC,+,0.00)
chunk0044_256_1	chr12	32135930	32136227	+	0	NA	intron (NM_001003398, intron 1 of 8)	intron (NM_001003398, intron 1 of 8)	28827	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.006734	0.385906	
chunk0184_11_1	chr7	111750109	111751283	+	0	NA	intron (NM_014705, intron 41 of 51)	LTR80A|LTR|ERVL	-57809	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.008518	0.392340	316(ATTACAGAATGTCCCT,+,0.00)
chunk0003_446_1	chr1	41360281	41360620	+	0	NA	Intergenic	L2a|LINE|L2	-1481	NM_001291281	100132074	Hs.559677	NM_001291281		FOXO6	-	forkhead box O6	protein-coding	0.017699	0.517647	
chunk0176_2_1	chr7	8090549	8090853	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-121949	NR_110018	100505921	Hs.634989	NR_110018		LOC100505921	-	uncharacterized LOC100505921	ncRNA	0.006579	0.439344	
chunk0059_210_1	chr14	33759101	33759590	+	0	NA	intron (NM_022123, intron 6 of 10)	intron (NM_022123, intron 6 of 10)	50408	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.002045	0.414286	
chunk0071_283_1	chr15	85805521	85805920	+	0	NA	Intergenic	L1MD1|LINE|L1	-10762	NM_022480	64410	Hs.498371	NM_022480	ENSG00000183655	KLHL25	ENC-2|ENC2	kelch like family member 25	protein-coding	0.007519	0.342500	
chunk0159_349_1	chr5	144370289	144370714	+	0	NA	intron (NM_020768, intron 3 of 3)	MIR3|SINE|MIR	199628	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.004706	0.363850	
chunk0175_378_1	chr6	168139546	168139880	+	0	NA	Intergenic	L2a|LINE|L2	-58156	NR_110312	79981	Hs.266746	NM_024919	ENSG00000153303	FRMD1	bA164L23.1	FERM domain containing 1	protein-coding	0.008982	0.388060	
chunk0074_226_1	chr16	27005524	27005813	+	0	NA	Intergenic	L1MD1|LINE|L1	-61230	NM_001145545	162083	Hs.120831	NM_182831		C16orf82	TNT	chromosome 16 open reading frame 82	protein-coding	0.000000	0.306897	
chunk0091_12_1	chr19	2923689	2923888	+	0	NA	Intergenic	MER68|LTR|ERVL	21183	NM_021217	58492	Hs.38004	NM_021217	ENSG00000175691	ZNF77	pT1	zinc finger protein 77	protein-coding	0.015075	0.470000	
chunk0068_28_1	chr15	50865474	50865830	+	0	NA	Intergenic	Intergenic	-43020	NM_007347	23431	Hs.413366	NM_007347	ENSG00000081014	AP4E1	CPSQ4|SPG51|STUT1	adaptor related protein complex 4 subunit epsilon 1	protein-coding	0.005618	0.372549	165(AGGTACACCATGTTCT,-,0.00),166(GGTACACCATGTTCTT,+,0.00),191(AGGACTGAATGCTCTT,+,0.00)
chunk0086_384_1	chr18	26507559	26508069	+	0	NA	intron (NM_001258222, intron 1 of 4)	L1ME3|LINE|L1	40722	NM_001142730	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.007843	0.389432	
chunk0030_264_1	chr10	116212757	116213451	+	0	NA	intron (NM_005264, intron 4 of 10)	L1M5|LINE|L1	59203	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.007205	0.374101	
chunk0010_373_1	chr1	119140669	119140923	+	0	NA	promoter-TSS (NM_201263)	promoter-TSS (NM_201263)	-124	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.051181	0.576471	
chunk0001_304_1	chr1	9128672	9128898	+	0	NA	exon (NM_024980, exon 1 of 4)	exon (NM_024980, exon 1 of 4)	385	NM_024980	80045	Hs.632367	NM_024980	ENSG00000180758	GPR157	-	G protein-coupled receptor 157	protein-coding	0.119469	0.678414	
chunk0163_1_1	chr6	7594706	7595322	+	0	NA	intron (NM_152551, intron 3 of 8)	intron (NM_152551, intron 3 of 8)	4815	NM_152551	154007	Hs.13366	NM_152551	ENSG00000168566	SNRNP48	C6orf151|dJ336K20B.1|dJ512B11.2	small nuclear ribonucleoprotein U11/U12 subunit 48	protein-coding	0.006494	0.353323	
chunk0043_179_1	chr12	17600757	17601292	+	0	NA	Intergenic	L1M4b|LINE|L1	-72275	NR_039770	100616279		NR_039770	ENSG00000283665	MIR3974	-	microRNA 3974	ncRNA	0.009346	0.348881	
chunk0192_54_1	chr8	59620223	59620479	+	0	NA	Intergenic	Intergenic	-501143	NM_014729	9760	Hs.491805	NM_014729	ENSG00000198846	TOX	TOX1	thymocyte selection associated high mobility group box	protein-coding	0.007812	0.404669	
chunk0152_384_1	chr5	64591715	64591958	+	0	NA	intron (NM_001029875, intron 3 of 5)	intron (NM_001029875, intron 3 of 5)	16186	NR_073511	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.000000	0.307377	
chunk0053_288_1	chr13	33479364	33479761	+	0	NA	intron (NM_001243476, intron 4 of 17)	L1MC5|LINE|L1	-193798	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.010076	0.396985	
chunk0068_87_1	chr15	52021322	52022050	+	0	NA	intron (NM_002748, intron 1 of 5)	intron (NM_002748, intron 1 of 5)	2472	NM_002748	5597	Hs.411847	NM_002748	ENSG00000069956	MAPK6	ERK3|HsT17250|PRKM6|p97MAPK	mitogen-activated protein kinase 6	protein-coding	0.005495	0.314129	338(AAGGACAGATAGTACT,-,0.00),339(AGGACAGATAGTACTT,+,0.00)
chunk0140_193_1	chr4	70217205	70217592	+	0	NA	Intergenic	Intergenic	-8673	NM_152997	260436	Hs.733448	NM_152997	ENSG00000181617	FDCSP	C4orf7|FDC-SP	follicular dendritic cell secreted protein	protein-coding	0.000000	0.350515	
chunk0131_437_1	chr3	153753258	153753737	+	0	NA	Intergenic	Intergenic	269002	NM_001101337									0.000000	0.314583	
chunk0194_165_1	chr8	84848471	84848972	+	0	NA	intron (NM_001100393, intron 4 of 8)	L1MB2|LINE|L1	142794	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005988	0.314741	
chunk0169_221_1	chr6	104229008	104229361	+	0	NA	Intergenic	Intergenic	630735	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.008499	0.406780	
chunk0103_167_1	chr2	162607949	162608431	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-160746	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.010373	0.380952	
chunk0103_176_1	chr2	163158894	163159099	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-320249	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.000000	0.300971	
chunk0096_171_1	chr2	29611108	29612205	+	0	NA	intron (NM_004304, intron 3 of 28)	MSTA|LTR|ERVL-MaLR	309955	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.008204	0.467213	
chunk0072_249_1	chr15	96149544	96149973	+	0	NA	intron (NR_125738, intron 3 of 4)	intron (NR_125738, intron 3 of 4)	-176170	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.013986	0.341860	
chunk0170_219_1	chr6	113161849	113162140	+	0	NA	Intergenic	MIR|SINE|MIR	488081	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.003436	0.349315	
chunk0113_77_1	chr20	50588041	50588349	+	0	NA	intron (NM_080829, intron 20 of 21)	intron (NM_080829, intron 20 of 21)	2409	NR_030375	693230		NR_030375	ENSG00000208018	MIR645	MIRN645|hsa-mir-645	microRNA 645	ncRNA	0.032468	0.611650	191(CAGGACAGCCTGTGCC,-,0.00),192(AGGACAGCCTGTGCCA,+,0.00)
chunk0045_144_1	chr12	46477634	46478251	+	0	NA	intron (NR_125380, intron 3 of 3)	L2b|LINE|L2	93835	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.003241	0.435275	
chunk0079_284_1	chr17	16486490	16487070	+	0	NA	intron (NM_207387, intron 1 of 2)	intron (NM_207387, intron 1 of 2)	5411	NM_001113567	388341	Hs.25425	NM_207387	ENSG00000181350	LRRC75A	C17orf76|FAM211A	leucine rich repeat containing 75A	protein-coding	0.034483	0.550775	
chunk0060_310_1	chr14	50975405	50975885	+	0	NA	3' UTR (NM_015163, exon 10 of 10)	3' UTR (NM_015163, exon 10 of 10)	-31115	NM_001163940	5836	Hs.282417	NM_002863	ENSG00000100504	PYGL	GSD6	glycogen phosphorylase L	protein-coding	0.004167	0.324324	
chunk0125_283_1	chr3	69723375	69723671	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-15912	NM_198159	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.013514	0.471380	
chunk0153_169_1	chr5	71481439	71481656	+	0	NA	intron (NM_018429, intron 7 of 38)	AluJo|SINE|Alu	25932	NM_018429	55814	Hs.258272	NM_018429	ENSG00000145734	BDP1	DFNB112|HSA238520|TAF3B1|TFC5|TFIIIB''|TFIIIB150|TFIIIB90|TFNR	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.000000	0.422018	
chunk0162_340_1	chr6	6915631	6916313	+	0	NA	Intergenic	Intergenic	-191625	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.014663	0.428990	249(AAGAACACCCCGTACT,-,0.00),250(AGAACACCCCGTACTG,+,0.00)
chunk0200_161_1	chr9	18684599	18685018	+	0	NA	3' UTR (NM_052866, exon 13 of 13)	3' UTR (NM_052866, exon 13 of 13)	111502	NR_036107	100422869		NR_036107	ENSG00000264638	MIR3152	-	microRNA 3152	ncRNA	0.009547	0.378571	213(AAGCACAGACTGTTCT,-,0.00),214(AGCACAGACTGTTCTA,+,0.00)
chunk0039_118_1	chr11	97871844	97872414	+	0	NA	Intergenic	L1MA2|LINE|L1	-1148847	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003509	0.523643	329(CAGAGCACTTTGTCCT,-,0.00),330(AGAGCACTTTGTCCTG,+,0.00)
chunk0055_464_1	chr13	76833392	76833801	+	0	NA	Intergenic	Intergenic	52809	NM_138444	115207	Hs.644125	NM_138444	ENSG00000178695	KCTD12	C13orf2|PFET1|PFETIN	potassium channel tetramerization domain containing 12	protein-coding	0.012225	0.397561	
chunk0137_351_1	chr4	25445588	25446309	+	0	NA	Intergenic	L2a|LINE|L2	68722	NM_001286756	29945	Hs.152173	NM_013367	ENSG00000053900	ANAPC4	APC4	anaphase promoting complex subunit 4	protein-coding	0.012483	0.506925	
chunk0189_3_1	chr8	19421506	19421913	+	0	NA	intron (NM_001130518, intron 6 of 9)	intron (NM_001130518, intron 6 of 9)	107733	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.012285	0.443627	
chunk0108_139_1	chr2	230719785	230720360	+	0	NA	intron (NM_001130849, intron 1 of 8)	intron (NM_001130849, intron 1 of 8)	6524	NM_001130849	51719	Hs.603930	NM_016289	ENSG00000135932	CAB39	CGI-66|MO25	calcium binding protein 39	protein-coding	0.005217	0.385417	
chunk0203_208_1	chr9	86592073	86592536	+	0	NA	Intergenic	L1MA7|LINE|L1	-237817	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.004320	0.288793	
chunk0084_294_1	chr17	79960182	79960577	+	0	NA	intron (NM_019020, intron 3 of 11)	L1ME1|LINE|L1	-9522	NM_001271845	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.010127	0.393939	232(AGGAACATGATGTGAT,-,0.00)
chunk0160_249_1	chr5	156647482	156647683	+	0	NA	intron (NM_000337, intron 7 of 8)	intron (NM_000337, intron 7 of 8)	-202956	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.004975	0.391089	
chunk0021_378_1	chr1	246468905	246469250	+	0	NA	intron (NM_001167740, intron 1 of 11)	LTR81A|LTR|Gypsy	38265	NM_001167740	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.002899	0.508671	
chunk0040_252_1	chr11	115478458	115478702	+	0	NA	intron (NM_001301043, intron 1 of 11)	L1ME3G|LINE|L1	25943	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.004098	0.322449	
chunk0143_449_1	chr4	124230141	124230828	+	0	NA	Intergenic	Intergenic	327950	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.004367	0.347384	
chunk0104_404_1	chr2	180696042	180696449	+	0	NA	intron (NR_104320, intron 1 of 3)	Tigger3a|DNA|TcMar-Tigger	4141	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.004914	0.333333	137(ATCACAGAGTGTACTT,+,0.00)
chunk0167_49_1	chr6	55519229	55519919	+	0	NA	intron (NM_019036, intron 4 of 9)	intron (NM_019036, intron 4 of 9)	59640	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.002899	0.303907	
chunk0057_231_1	chr13	104374259	104374962	+	0	NA	Intergenic	Intergenic	949410	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.007112	0.421875	
chunk0104_259_1	chr2	177660472	177660997	+	0	NA	intron (NM_001077197, intron 20 of 20)	intron (NM_001077197, intron 20 of 20)	-41768	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.011429	0.418251	
chunk0177_274_1	chr7	25484993	25485440	+	0	NA	Intergenic	Intergenic	-256730	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.002237	0.343750	
chunk0122_405_1	chr3	38135310	38135603	+	0	NA	intron (NR_024024, intron 2 of 9)	LTR5B|LTR|ERVK	1786	NM_001130410	30	Hs.643487	NM_001607	ENSG00000060971	ACAA1	ACAA|PTHIO|THIO	acetyl-CoA acyltransferase 1	protein-coding	0.000000	0.438776	
chunk0024_148_1	chr10	35250506	35250715	+	0	NA	5' UTR (NM_181698, exon 3 of 12)	5' UTR (NM_181698, exon 3 of 12)	3629	NM_181698	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.009569	0.452381	
chunk0203_329_1	chr9	89686284	89686483	+	0	NA	intron (NR_024280, intron 3 of 5)	intron (NR_024280, intron 3 of 5)	46600	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.015075	0.580000	
chunk0154_257_1	chr5	81589135	81589376	+	0	NA	intron (NM_001256733, intron 4 of 15)	CR1_Mam|LINE|CR1	161998	NM_012446	23635	Hs.102735	NM_012446	ENSG00000145687	SSBP2	HSPC116|SOSS-B2	single stranded DNA binding protein 2	protein-coding	0.004149	0.297521	
chunk0150_321_1	chr5	38129703	38129902	+	0	NA	Intergenic	Intergenic	-128607	NM_001205301	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.015075	0.425000	
chunk0033_180_1	chr11	15955315	15955773	+	0	NA	Intergenic	L2a|LINE|L2	14077	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.002183	0.363834	
chunk0027_356_1	chr10	78933042	78933404	+	0	NA	Intergenic	Intergenic	134225	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.030387	0.559229	
chunk0018_269_1	chr1	220492719	220493450	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-35099	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.002736	0.430328	
chunk0070_340_1	chr15	75776786	75777178	+	0	NA	Intergenic	Intergenic	-14667	NR_036198	100423035		NR_036198	ENSG00000284385	MIR4313	-	microRNA 4313	ncRNA	0.000000	0.407125	
chunk0034_337_1	chr11	35666013	35666434	+	0	NA	intron (NM_017583, intron 1 of 4)	L1ME3B|LINE|L1	3471	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.002375	0.360190	258(GTGAACAGCATGTTTT,-,0.00),259(TGAACAGCATGTTTTC,+,0.00)
chunk0172_310_1	chr6	138222747	138223226	+	0	NA	intron (NM_020340, intron 4 of 33)	intron (NM_020340, intron 4 of 33)	-4496	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.006263	0.429167	
chunk0162_222_1	chr6	4403753	4404229	+	0	NA	Intergenic	Intergenic	-24011	NR_106988									0.008403	0.438155	220(AAGCACAATGTGTCCC,-,0.00),221(AGCACAATGTGTCCCA,+,0.00)
chunk0106_315_1	chr2	205187100	205187425	+	0	NA	intron (NM_205863, intron 14 of 21)	L2c|LINE|L2	-495238	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.009231	0.447853	
chunk0051_66_1	chr12	113017841	113018391	+	0	NA	Intergenic	AluJo|SINE|Alu	39647	NM_016817	4939	Hs.414332	NM_002535	ENSG00000111335	OAS2	-	2'-5'-oligoadenylate synthetase 2	protein-coding	0.016364	0.499093	
chunk0158_137_1	chr5	127313384	127313935	+	0	NA	intron (NM_001308119, intron 2 of 14)	intron (NM_001308119, intron 2 of 14)	22895	NM_001308121	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.005445	0.326087	
chunk0049_328_1	chr12	94743735	94744214	+	0	NA	Intergenic	Intergenic	-90424	NR_030171	574449		NR_030171	ENSG00000283998	MIR492	MIRN492|hsa-mir-492	microRNA 492	ncRNA	0.004175	0.387500	
chunk0087_450_1	chr18	42670985	42671377	+	0	NA	intron (NR_046174, intron 7 of 9)	intron (NR_046174, intron 7 of 9)	444511	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.012755	0.320611	
chunk0122_103_1	chr3	30482546	30482993	+	0	NA	Intergenic	Intergenic	-123733	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.000000	0.270089	153(AGGAACACAGAGTTCT,-,0.00),154(GGAACACAGAGTTCTT,+,0.00)
chunk0068_365_1	chr15	58038478	58039202	+	0	NA	intron (NM_003888, intron 1 of 12)	intron (NM_003888, intron 1 of 12)	-24743	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.004144	0.398621	
chunk0210_108_1	chrX	72216857	72217484	+	0	NA	intron (NM_017669, intron 1 of 1)	L4_C_Mam|LINE|RTE-X	21838	NM_017669	54821	Hs.47558	NM_017669	ENSG00000186871	ERCC6L	PICH|RAD26L	ERCC excision repair 6 like, spindle assembly checkpoint helicase	protein-coding	0.004785	0.399682	
chunk0047_54_1	chr12	67391850	67392052	+	0	NA	Intergenic	Intergenic	122670	NM_018448	55832	Hs.546407	NM_018448	ENSG00000111530	CAND1	TIP120|TIP120A	cullin associated and neddylation dissociated 1	protein-coding	0.004950	0.477833	
chunk0187_161_1	chr7	150428799	150429002	+	0	NA	Intergenic	Intergenic	-4754	NR_034033	285972	Hs.647110	NR_034033	ENSG00000242258	LINC00996	-	long intergenic non-protein coding RNA 996	ncRNA	0.014778	0.539216	
chunk0007_37_1	chr1	77683256	77683592	+	0	NA	promoter-TSS (NM_001308237)	promoter-TSS (NM_001308237)	3	NM_001308237	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.136905	0.750742	
chunk0091_363_1	chr19	15479665	15480129	+	0	NA	promoter-TSS (NM_052890)	promoter-TSS (NM_052890)	-393	NM_052890	114770	Hs.282244	NM_052890	ENSG00000161031	PGLYRP2	HMFT0141|PGLYRPL|PGRP-L|PGRPL|TAGL-like|tagL|tagL-alpha|tagl-beta	peptidoglycan recognition protein 2	protein-coding	0.017241	0.582796	
chunk0078_217_1	chr17	6233414	6233688	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	162937	NM_015253	23302	Hs.370166	NM_015253	ENSG00000179314	WSCD1	-	WSC domain containing 1	protein-coding	0.003650	0.432727	
chunk0207_269_1	chr9	132367608	132367953	+	0	NA	Intergenic	Intergenic	-12795	NM_015046	23064	Hs.460317	NM_015046	ENSG00000107290	SETX	ALS4|AOA2|SCAN2|SCAR1|Sen1|bA479K20.2	senataxin	protein-coding	0.011594	0.465318	203(GAGTACAGGGTGTTCC,-,0.00),204(AGTACAGGGTGTTCCG,+,0.00)
chunk0012_315_1	chr1	162302813	162303530	+	0	NA	intron (NM_001164757, intron 4 of 9)	L1ME1|LINE|L1	-39375	NR_030283	693141		NR_030283	ENSG00000207729	MIR556	MIRN556|hsa-mir-556|mir-556	microRNA 556	ncRNA	0.008368	0.363510	
chunk0025_20_1	chr10	48213028	48213337	+	0	NA	intron (NM_001018071, intron 12 of 28)	intron (NM_001018071, intron 12 of 28)	-38039	NM_001042512	143162	Hs.664786	NM_152428	ENSG00000170324	FRMPD2	PDZD5C|PDZK4|PDZK5C	FERM and PDZ domain containing 2	protein-coding	0.000000	0.519355	95(AAGAGCACAGTGTCCA,-,0.00),96(AGAGCACAGTGTCCAC,+,0.00)
chunk0191_84_1	chr8	47612548	47612976	+	0	NA	intron (NM_001080394, intron 10 of 19)	intron (NM_001080394, intron 10 of 19)	125402	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.011682	0.428904	212(CTGGACAGAGTGTGCT,-,0.00),213(TGGACAGAGTGTGCTC,+,0.00)
chunk0132_150_1	chr3	156555142	156555368	+	0	NA	promoter-TSS (NM_007107)	promoter-TSS (NM_007107)	-55	NM_001308197	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.101770	0.651982	
chunk0144_353_1	chr4	139681625	139682124	+	0	NA	intron (NM_001204368, intron 2 of 3)	L2a|LINE|L2	16106	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.004008	0.390000	
chunk0171_386_1	chr6	131112350	131112549	+	0	NA	Intergenic	L1MB7|LINE|L1	-23237	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.000000	0.415000	
chunk0088_276_1	chr18	49369126	49369325	+	0	NA	intron (NM_017653, intron 5 of 16)	intron (NM_017653, intron 5 of 16)	91484	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.005025	0.510000	
chunk0190_102_1	chr8	30358522	30359048	+	0	NA	Intergenic	Intergenic	-25716	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.007605	0.428843	
chunk0167_141_1	chr6	62373965	62374173	+	0	NA	Intergenic	Intergenic	-87874	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.004808	0.392344	
chunk0093_144_1	chr19	46669297	46669628	+	0	NA	intron (NR_040042, intron 2 of 2)	intron (NR_040042, intron 2 of 2)	7984	NR_040041	100506068	Hs.434327	NR_040041	ENSG00000245598	DACT3-AS1	-	DACT3 antisense RNA 1	ncRNA	0.015106	0.433735	
chunk0174_323_1	chr6	163494093	163494721	+	0	NA	intron (NM_206853, intron 3 of 6)	intron (NM_206853, intron 3 of 6)	79764	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.014331	0.348172	
chunk0015_63_1	chr1	184639501	184639797	+	0	NA	Intergenic	Intergenic	115258	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.010135	0.427609	
chunk0088_345_1	chr18	51569220	51569507	+	0	NA	Intergenic	Intergenic	177321	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.006969	0.465278	
chunk0079_424_1	chr17	19808647	19809225	+	0	NA	intron (NM_001142610, intron 14 of 27)	L1MB2|LINE|L1	58990	NM_001142610	9706	Hs.168762	NM_014683	ENSG00000083290	ULK2	ATG1B|Unc51.2	unc-51 like autophagy activating kinase 2	protein-coding	0.000000	0.347150	
chunk0110_276_1	chr20	17405907	17406389	+	0	NA	intron (NM_002594, intron 5 of 11)	intron (NM_002594, intron 5 of 11)	125221	NM_001195	631	Hs.129702	NM_001195	ENSG00000125864	BFSP1	CP115|CP94|CTRCT33|LIFL-H	beaded filament structural protein 1	protein-coding	0.010373	0.362319	
chunk0212_120_1	chrX	130769583	130770161	+	0	NA	intron (NM_182314, intron 3 of 15)	intron (NM_182314, intron 3 of 15)	133445	NM_001281736	10495	Hs.171458	NM_006375	ENSG00000165675	ENOX2	APK1|COVA1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.012111	0.373057	
chunk0110_267_1	chr20	16939621	16939820	+	0	NA	Intergenic	MER50|LTR|ERV1	191367	NM_020157	56914	Hs.41119	NM_020157	ENSG00000125879	OTOR	FDP|MIAL1	otoraplin	protein-coding	0.005025	0.475000	
chunk0136_408_1	chr3	197329719	197330171	+	0	NA	Intergenic	L1ME4a|LINE|L1	-30673	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.006637	0.324503	
chunk0068_247_1	chr15	55964881	55965417	+	0	NA	intron (NM_006154, intron 2 of 28)	MSTA1|LTR|ERVL-MaLR	28597	NM_006154	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.011194	0.459963	
chunk0201_190_1	chr9	36419742	36420325	+	0	NA	Intergenic	Intergenic	-18835	NM_194330	152006	Hs.333503	NM_022781	ENSG00000137075	RNF38	-	ring finger protein 38	protein-coding	0.020583	0.489726	
chunk0083_239_1	chr17	67605351	67605786	+	0	NA	intron (NM_181671, intron 5 of 9)	intron (NM_181671, intron 5 of 9)	-112265	NM_001303272	25926	Hs.463936	NM_015462	ENSG00000130935	NOL11	-	nucleolar protein 11	protein-coding	0.036782	0.477064	262(GAGTACAGTAAGTCCT,-,0.00),263(AGTACAGTAAGTCCTT,+,0.00)
chunk0036_56_1	chr11	59154679	59154979	+	0	NA	3' UTR (NM_001142519, exon 5 of 5)	3' UTR (NM_001142519, exon 5 of 5)	10050	NM_001312911	63901	Hs.150651	NM_022074	ENSG00000166801	FAM111A	GCLEB|KCS2	family with sequence similarity 111 member A	protein-coding	0.016667	0.438538	
chunk0079_358_1	chr17	17888560	17889172	+	0	NA	intron (NM_001033551, intron 3 of 13)	intron (NM_001033551, intron 3 of 13)	-51855	NM_001005291	6720	Hs.592123	NM_004176	ENSG00000072310	SREBF1	SREBP1|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.013072	0.533442	
chunk0135_381_1	chr3	191025730	191025976	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	147923	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.004065	0.421053	
chunk0086_258_1	chr18	23431095	23431593	+	0	NA	intron (NM_032933, intron 1 of 14)	intron (NM_032933, intron 1 of 14)	6617	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.002008	0.390782	
chunk0053_428_1	chr13	38335383	38335991	+	0	NA	Intergenic	Intergenic	-14084	NM_016617	51569	Hs.643655	NM_016617	ENSG00000120686	UFM1	BM-002|C13orf20|HLD14	ubiquitin fold modifier 1	protein-coding	0.004934	0.307061	
chunk0183_397_1	chr7	110272817	110273222	+	0	NA	Intergenic	Intergenic	-312806	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.354680	203(ATAACAATGTGTTCCT,+,0.00)
chunk0065_362_1	chr14	103878573	103878777	+	0	NA	Intergenic	MER41D|LTR|ERV1	30954	NR_038436	145216	Hs.578091	NR_038436	ENSG00000258735	LINC00637	-	long intergenic non-protein coding RNA 637	ncRNA	0.004902	0.375610	
chunk0196_19_1	chr8	101504606	101505255	+	0	NA	intron (NM_024915, intron 1 of 15)	intron (NM_024915, intron 1 of 15)	12490	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.012327	0.406154	290(GGGAACAAAAAGTACC,-,0.00),291(GGAACAAAAAGTACCT,+,0.00)
chunk0120_117_1	chr3	4698443	4698662	+	0	NA	intron (NM_002222, intron 33 of 57)	MER58A|DNA|hAT-Charlie	53038	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.009132	0.395455	
chunk0194_106_1	chr8	83566620	83566904	+	0	NA	Intergenic	Intergenic	163004	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.014085	0.308772	
chunk0163_295_1	chr6	14117029	14117278	+	0	NA	promoter-TSS (NM_001251901)	promoter-TSS (NM_001251901)	-103	NM_001251901	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.020080	0.380000	
chunk0133_234_1	chr3	171295757	171296328	+	0	NA	intron (NM_001161560, intron 2 of 31)	intron (NM_001161560, intron 2 of 31)	164366	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.007005	0.437063	302(TAGAACAGTATGTGTC,-,0.00),303(AGAACAGTATGTGTCA,+,0.00)
chunk0025_386_1	chr10	59300200	59300918	+	0	NA	intron (NM_001001971, intron 5 of 11)	intron (NM_001001971, intron 5 of 11)	62035	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.006964	0.356050	
chunk0068_42_1	chr15	51336580	51337159	+	0	NA	intron (NM_031226, intron 1 of 10)	intron (NM_031226, intron 1 of 10)	1729	NM_031226	1588	Hs.260074	NM_000103	ENSG00000137869	CYP19A1	ARO|ARO1|CPV1|CYAR|CYP19|CYPXIX|P-450AROM	cytochrome P450 family 19 subfamily A member 1	protein-coding	0.005181	0.384483	214(TAGCACACAATGTTCT,-,0.00),215(AGCACACAATGTTCTT,+,0.00)
chunk0053_354_1	chr13	34964072	34964406	+	0	NA	intron (NM_015678, intron 1 of 57)	intron (NM_015678, intron 1 of 57)	21952	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.005988	0.373134	
chunk0152_258_1	chr5	60944852	60945151	+	0	NA	promoter-TSS (NM_000082)	promoter-TSS (NM_000082)	77	NM_001007234	1161	Hs.435237	NM_000082	ENSG00000049167	ERCC8	CKN1|CSA|UVSS2	ERCC excision repair 8, CSA ubiquitin ligase complex subunit	protein-coding	0.050167	0.550000	
chunk0022_147_1	chr10	12350367	12350669	+	0	NA	intron (NM_020397, intron 1 of 9)	CpG	975	NM_153498	57118	Hs.600547	NM_020397	ENSG00000183049	CAMK1D	CKLiK|CaM-K1|CaMKID	calcium/calmodulin dependent protein kinase ID	protein-coding	0.089404	0.623762	
chunk0099_364_1	chr2	100835106	100835362	+	0	NA	intron (NM_002518, intron 1 of 20)	MIR|SINE|MIR	15083	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.019531	0.408560	
chunk0085_220_1	chr18	6775194	6776057	+	0	NA	Intergenic	Intergenic	-58808	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.010429	0.358796	
chunk0114_272_1	chr21	16281351	16281814	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	87203	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.004320	0.286638	
chunk0109_206_1	chr20	5233968	5234626	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	80072	NM_144773	128674	Hs.375029	NM_144773	ENSG00000101292	PROKR2	GPR73L1|GPR73b|GPRg2|HH3|KAL3|PKR2|dJ680N4.3	prokineticin receptor 2	protein-coding	0.003040	0.329287	
chunk0111_120_1	chr20	24106532	24106867	+	0	NA	Intergenic	L1ME1|LINE|L1	-93068	NR_040102	400839	Hs.651965	NR_040102	ENSG00000230133	LINC01721	-	long intergenic non-protein coding RNA 1721	ncRNA	0.005970	0.351190	
chunk0168_203_1	chr6	85621335	85622086	+	0	NA	intron (NM_001159674, intron 8 of 11)	intron (NM_001159674, intron 8 of 11)	19741	NM_001159675	10492	Hs.571177	NM_006372	ENSG00000135316	SYNCRIP	GRY-RBP|GRYRBP|HNRNPQ|HNRPQ1|NSAP1|PP68|hnRNP-Q	synaptotagmin binding cytoplasmic RNA interacting protein	protein-coding	0.007989	0.405585	
chunk0137_200_1	chr4	17972113	17972610	+	0	NA	intron (NM_001166139, intron 2 of 6)	intron (NM_001166139, intron 2 of 6)	49499	NM_153686	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.004024	0.265060	
chunk0179_130_1	chr7	45909643	45909842	+	0	NA	Intergenic	Intergenic	11530	NM_000598	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.000000	0.445000	
chunk0127_253_1	chr3	97188692	97188928	+	0	NA	intron (NM_001080448, intron 3 of 17)	L1ME3G|LINE|L1	-250783	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.265823	
chunk0129_62_1	chr3	117591638	117592113	+	0	NA	Intergenic	L1MC3|LINE|L1	670444	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.008421	0.346639	
chunk0085_342_1	chr18	8703920	8704591	+	0	NA	intron (NR_120598, intron 1 of 1)	intron (NR_120598, intron 1 of 1)	3366	NR_120598	100287082	Hs.439434	NR_120598	ENSG00000265962	GACAT2	MTCL1-AS1|MTCL1AS1	gastric cancer associated transcript 2	ncRNA	0.032787	0.571429	259(GAGGACAGGCTGGCCC,-,0.00),260(AGGACAGGCTGGCCCC,+,0.00),356(TGCACGGTGTGTTCTG,+,0.00)
chunk0176_195_1	chr7	14050750	14051268	+	0	NA	Intergenic	L1PA11|LINE|L1	-59584	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.005792	0.393064	
chunk0114_334_1	chr21	17577861	17578076	+	0	NA	intron (NM_001207066, intron 7 of 7)	L1MB1|LINE|L1	34982	NM_006806	10950	Hs.473420	NM_006806	ENSG00000154640	BTG3	ANA|ANA/BTG3|APRO4|TOB5|TOB55|TOFA	BTG anti-proliferation factor 3	protein-coding	0.000000	0.328704	
chunk0102_190_1	chr2	147681397	147681852	+	0	NA	Intergenic	L2a|LINE|L2	-162893	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002198	0.346491	247(AGGCACTCAGTGTGCT,-,0.00),248(GGCACTCAGTGTGCTA,+,0.00)
chunk0115_223_1	chr21	27105250	27105691	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-138350	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.009070	0.382353	
chunk0198_37_1	chr8	128275737	128276370	+	0	NA	Intergenic	Intergenic	125937	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.004739	0.354890	
chunk0194_113_1	chr8	83842710	83843160	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-340283	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002222	0.390244	
chunk0001_19_1	chr1	1166114	1166403	+	0	NA	promoter-TSS (NR_029639)	promoter-TSS (NR_029639)	-846	NR_029639	406984		NR_029639	ENSG00000207730	MIR200B	MIRN200B|mir-200b	microRNA 200b	ncRNA	0.031142	0.662069	89(AAGGACGGCGTGTCCA,-,0.00),90(AGGACGGCGTGTCCAG,+,0.00)
chunk0039_112_1	chr11	97719915	97720489	+	0	NA	Intergenic	L1MB7|LINE|L1	-1213325	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.000000	0.286957	
chunk0111_54_1	chr20	22630830	22631176	+	0	NA	Intergenic	Intergenic	-23486	NR_109883	101929685	Hs.563018	NR_109883	ENSG00000237396	LNCNEF	LINC01384|lncRNA-NEF	lncRNA neighboring enhancer of FOXA2	ncRNA	0.008671	0.461095	
chunk0070_228_1	chr15	72879616	72879933	+	0	NA	Intergenic	L1ME1|LINE|L1	-95989	NR_023319									0.000000	0.317610	
chunk0021_234_1	chr10	6938642	6938898	+	0	NA	Intergenic	MER63B|DNA|hAT-Blackjack	159172	NR_038291	100507127	Hs.498571	NR_038291	ENSG00000238266	LINC00707	-	long intergenic non-protein coding RNA 707	ncRNA	0.007812	0.431907	
chunk0007_96_1	chr1	78719409	78719999	+	0	NA	Intergenic	Intergenic	69912	NM_006417	10561	Hs.82316	NM_006417	ENSG00000137965	IFI44	MTAP44|TLDC5|p44	interferon induced protein 44	protein-coding	0.001695	0.292724	
chunk0115_185_1	chr21	26008392	26008724	+	0	NA	intron (NM_001136016, intron 6 of 16)	MER63D|DNA|hAT-Blackjack	131832	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.003012	0.399399	
chunk0070_309_1	chr15	75142782	75143039	+	0	NA	Intergenic	MER52-int|LTR|ERV1	-58970	NM_015492	56905	Hs.17936	NM_015492	ENSG00000167173	C15orf39	-	chromosome 15 open reading frame 39	protein-coding	0.007782	0.476744	
chunk0139_129_1	chr4	53222403	53222811	+	0	NA	intron (NM_152540, intron 4 of 8)	intron (NM_152540, intron 4 of 8)	143468	NM_152540	152579	Hs.302287	NM_152540	ENSG00000184178	SCFD2	STXBP1L1	sec1 family domain containing 2	protein-coding	0.002451	0.303178	
chunk0178_246_1	chr7	36176577	36177008	+	0	NA	intron (NM_030636, intron 2 of 7)	intron (NM_030636, intron 2 of 7)	23565	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.006961	0.324074	
chunk0058_45_1	chr14	20240775	20241143	+	0	NA	Intergenic	Intergenic	-1833	NM_001004479	390442	Hs.553767	NM_001004479	ENSG00000176198	OR11H4	OR14-36	olfactory receptor family 11 subfamily H member 4	protein-coding	0.008152	0.344173	
chunk0207_370_1	chr9	135980754	135981453	+	0	NA	Intergenic	Intergenic	-19723	NM_016172	10422	Hs.9194	NM_016172	ENSG00000130560	UBAC1	GBDR1|KPC2|UBADC1	UBA domain containing 1	protein-coding	0.027182	0.657143	338(GGGAACACAGCGTTCT,-,0.00),339(GGAACACAGCGTTCTC,+,0.00)
chunk0162_228_1	chr6	4577411	4577920	+	0	NA	Intergenic	Intergenic	-32900	NR_122107	497048	Hs.591355	NM_001011540	ENSG00000205444	KU-MEL-3	-	uncharacterized LOC497048	ncRNA	0.005894	0.407843	
chunk0063_324_1	chr14	85187574	85187773	+	0	NA	Intergenic	Intergenic	-206206	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005025	0.350000	
chunk0024_142_1	chr10	35149233	35149555	+	0	NA	intron (NR_051975, intron 2 of 3)	L2c|LINE|L2	11612	NM_183011	1390	Hs.200250	NM_001881	ENSG00000095794	CREM	CREM-2|ICER|hCREM-2	cAMP responsive element modulator	protein-coding	0.012422	0.461300	
chunk0112_266_1	chr20	43135320	43135943	+	0	NA	intron (NM_133170, intron 1 of 31)	intron (NM_133170, intron 1 of 31)	54286	NM_133170	11122	Hs.526879	NM_007050	ENSG00000196090	PTPRT	RPTPrho	protein tyrosine phosphatase receptor type T	protein-coding	0.008026	0.389423	
chunk0072_200_1	chr15	94780022	94780553	+	0	NA	Intergenic	Intergenic	-75076	NR_077061	440311	Hs.745156	NR_077061	ENSG00000277654	LOC440311	-	NOP53 ribosome biogenesis factor pseudogene	pseudo	0.015066	0.426692	
chunk0012_73_1	chr1	155744236	155744435	+	0	NA	Intergenic	AluJb|SINE|Alu	-1433	NR_024117	100129405	Hs.656361	NR_024117		MSTO2P	MSTO2	misato family member 2, pseudogene	pseudo	0.020101	0.440000	
chunk0189_430_1	chr8	28028598	28029369	+	0	NA	intron (NM_001010906, intron 17 of 18)	MIR|SINE|MIR	-36131	NM_173833	286133	Hs.591833	NM_173833	ENSG00000168079	SCARA5	NET33|Tesr	scavenger receptor class A member 5	protein-coding	0.011673	0.492228	
chunk0006_205_1	chr1	67715644	67716029	+	0	NA	intron (NM_018841, intron 2 of 3)	intron (NM_018841, intron 2 of 3)	30659	NM_001924	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.005195	0.437824	
chunk0112_277_1	chr20	43466479	43466960	+	0	NA	Intergenic	L1MC5|LINE|L1	8855	NM_006275	6431	Hs.684950	NM_006275	ENSG00000124193	SRSF6	B52|HEL-S-91|SFRS6|SRP55	serine and arginine rich splicing factor 6	protein-coding	0.008316	0.396266	
chunk0081_285_1	chr17	44438738	44438966	+	0	NA	intron (NM_001304942, intron 2 of 6)	intron (NM_001304942, intron 2 of 6)	-2001	NM_001304943	23131	Hs.463129	NM_001002909	ENSG00000186566	GPATCH8	GPATC8|KIAA0553	G-patch domain containing 8	protein-coding	0.004386	0.493450	111(AAGGACATTTTGTGCT,-,0.00),112(AGGACATTTTGTGCTA,+,0.00)
chunk0164_191_1	chr6	22244718	22245206	+	0	NA	Intergenic	MIR|SINE|MIR	52539	NM_000948	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.002049	0.390593	
chunk0178_375_1	chr7	40134479	40134806	+	0	NA	promoter-TSS (NM_001193313)	promoter-TSS (NM_001193313)	10	NM_138701	136647	Hs.654989	NM_138701	ENSG00000168303	MPLKIP	ABHS|C7orf11|ORF20|TTD4	M-phase specific PLK1 interacting protein	protein-coding	0.064220	0.570122	159(GAGAACTGCTAGTCCT,-,0.00),160(AGAACTGCTAGTCCTT,+,0.00)
chunk0040_258_1	chr11	115964032	115964454	+	0	NA	Intergenic	Intergenic	-204043	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.007109	0.432624	
chunk0021_372_1	chr1	246400614	246400938	+	0	NA	intron (NM_001167740, intron 1 of 11)	intron (NM_001167740, intron 1 of 11)	16636	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003086	0.313846	
chunk0202_214_1	chr9	76181056	76181271	+	0	NA	intron (NM_001190482, intron 15 of 36)	intron (NM_001190482, intron 15 of 36)	213365	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.000000	0.430556	
chunk0061_387_1	chr14	64467536	64468250	+	0	NA	intron (NM_004857, intron 1 of 1)	intron (NM_004857, intron 1 of 1)	2394	NM_004857	9495	Hs.656683	NM_004857	ENSG00000179841	AKAP5	AKAP75|AKAP79|H21	A-kinase anchoring protein 5	protein-coding	0.000000	0.338462	
chunk0079_196_1	chr17	14336222	14336421	+	0	NA	intron (NR_130138, intron 1 of 2)	intron (NR_130138, intron 1 of 2)	32581	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.010050	0.400000	
chunk0162_309_1	chr6	6668452	6669160	+	0	NA	Intergenic	L1P2|LINE|L1	-45980	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.012712	0.528914	
chunk0081_123_1	chr17	40284122	40284471	+	0	NA	Intergenic	Intergenic	-3598	NM_001254	990	Hs.405958	NM_001254	ENSG00000094804	CDC6	CDC18L|HsCDC18|HsCDC6|MGORS5	cell division cycle 6	protein-coding	0.005731	0.420000	
chunk0168_216_1	chr6	85976289	85976600	+	0	NA	Intergenic	Intergenic	-297711	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.000000	0.419872	
chunk0002_136_1	chr1	16905177	16905624	+	0	NA	Intergenic	Intergenic	9420	NR_004400	26863		NR_004400	ENSG00000206737	RNVU1-18	RNU1-25|RNU1-25P|RNU1-5|RNU1P1|RNU1P9|U1.15|U1P101|U1P15|vU1.18	RNA, variant U1 small nuclear 18	snRNA	0.011186	0.404018	
chunk0090_231_1	chr18	73714942	73715559	+	0	NA	Intergenic	Intergenic	390309	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.030794	0.432039	
chunk0118_182_1	chr22	31177035	31177235	+	0	NA	intron (NR_024212, intron 1 of 5)	intron (NR_024212, intron 1 of 5)	16983	NR_024210	91445	Hs.517553	NM_152267	ENSG00000138942	RNF185	-	ring finger protein 185	protein-coding	0.000000	0.482587	
chunk0106_363_1	chr2	207088851	207089320	+	0	NA	intron (NR_073108, intron 3 of 4)	intron (NR_073108, intron 3 of 4)	20988	NR_036227	100423036		NR_036227	ENSG00000253008	MIR2355	mir-2355	microRNA 2355	ncRNA	0.006397	0.397872	
chunk0173_381_1	chr6	149860738	149861152	+	0	NA	intron (NM_032832, intron 1 of 6)	MIR|SINE|MIR	-2553	NR_045126	100652739	Hs.642734	NR_045126	ENSG00000223701	RAET1E-AS1	RAET1G-AS1	RAET1E antisense RNA 1	ncRNA	0.012077	0.510843	
chunk0159_300_1	chr5	142937323	142937961	+	0	NA	intron (NM_015071, intron 11 of 22)	L1MD2|LINE|L1	-68732	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.009404	0.378717	
chunk0130_141_1	chr3	132237445	132238311	+	0	NA	Intergenic	Intergenic	-79489	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.002309	0.372549	586(GAGATCAGTGTGTCCC,-,0.00),587(AGATCAGTGTGTCCCT,+,0.00)
chunk0142_139_1	chr4	94833216	94833777	+	0	NA	intron (NM_001203, intron 1 of 12)	intron (NM_001203, intron 1 of 12)	75519	NM_001203	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.000000	0.359431	292(AGATCTCAGTGTTCTC,+,0.00)
chunk0066_439_1	chr15	39784254	39784976	+	0	NA	Intergenic	MER99|DNA|hAT?	-1777	NM_152597	161835	Hs.129598	NM_152597	ENSG00000150667	FSIP1	HSD10	fibrous sheath interacting protein 1	protein-coding	0.005540	0.395574	
chunk0205_293_1	chr9	111949270	111949469	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	17269	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.010050	0.465000	
chunk0122_116_1	chr3	31227252	31227513	+	0	NA	Intergenic	Intergenic	-65595	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.000000	0.374046	
chunk0077_150_1	chr16	78915691	78916368	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	684696	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.020679	0.412979	
chunk0055_271_1	chr13	64151659	64152414	+	0	NA	Intergenic	L1MA7|LINE|L1	-307911	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.002649	0.313492	
chunk0187_411_1	chr7	158148954	158149176	+	0	NA	intron (NM_001308268, intron 6 of 22)	intron (NM_001308268, intron 6 of 22)	294480	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.040541	0.569507	
chunk0205_4_1	chr9	104810545	104811302	+	0	NA	exon (NM_005502, exon 29 of 50)	exon (NM_005502, exon 29 of 50)	47182	NR_130760	55335	Hs.429294	NM_018376	ENSG00000165028	NIPSNAP3B	FP944|NIPSNAP3|SNAP1	nipsnap homolog 3B	protein-coding	0.015852	0.515831	
chunk0211_277_1	chrX	122087250	122087905	+	0	NA	Intergenic	Intergenic	716605	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.003053	0.365854	291(AAGAACAATGTGTACT,-,0.00),292(AGAACAATGTGTACTT,+,0.00)
chunk0031_15_1	chr10	121738470	121738704	+	0	NA	Intergenic	Intergenic	-140129	NM_000141	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.008547	0.387234	
chunk0047_120_1	chr12	68999933	69000304	+	0	NA	Intergenic	Intergenic	-36878	NM_001874	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.008086	0.392473	
chunk0057_51_1	chr13	97133913	97134205	+	0	NA	Intergenic	Intergenic	45563	NR_125725	103625683	Hs.679591	NR_125725	ENSG00000233124	LINC00456	-	long intergenic non-protein coding RNA 456	ncRNA	0.010274	0.440273	
chunk0053_282_1	chr13	33322098	33322587	+	0	NA	intron (NM_001243476, intron 5 of 17)	intron (NM_001243476, intron 5 of 17)	-36578	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.016360	0.346939	
chunk0080_182_1	chr17	28854643	28854900	+	0	NA	promoter-TSS (NM_005702)	promoter-TSS (NM_005702)	-254	NM_005702	26284	Hs.3426	NM_005702	ENSG00000132591	ERAL1	CEGA|ERA|ERA-W|ERAL1A|ERAL1B|H-ERA|HERA-A|HERA-B|PRLTS6	Era like 12S mitochondrial rRNA chaperone 1	protein-coding	0.027237	0.492248	
chunk0208_67_1	chrX	11792308	11792787	+	0	NA	Intergenic	Intergenic	32931	NM_006800	10943	Hs.655288	NM_006800	ENSG00000005302	MSL3	MSL3L1	MSL complex subunit 3	protein-coding	0.004175	0.329167	
chunk0089_124_1	chr18	58716060	58716479	+	0	NA	intron (NM_006785, intron 9 of 16)	intron (NM_006785, intron 9 of 16)	-44396	NM_001289967	101927322	Hs.644875	NM_001289967		LOC101927322	-	uncharacterized LOC101927322	protein-coding	0.009547	0.364286	
chunk0175_372_1	chr6	167952555	167952843	+	0	NA	intron (NM_001040000, intron 29 of 29)	MER58A|DNA|hAT-Charlie	24240	NM_001129895	100128124	Hs.448059	NM_001129895		HGC6.3	-	uncharacterized LOC100128124	protein-coding	0.003472	0.425606	
chunk0101_214_1	chr2	130360410	130360849	+	0	NA	intron (NM_014369, intron 5 of 14)	MER58A|DNA|hAT-Charlie	4622	NM_001142370	26469	Hs.516390	NM_014369	ENSG00000072135	PTPN18	BDP1|PTP-HSCF	protein tyrosine phosphatase non-receptor type 18	protein-coding	0.002278	0.350000	
chunk0121_314_1	chr3	24213216	24213586	+	0	NA	intron (NM_000461, intron 3 of 9)	L4_C_Mam|LINE|RTE-X	62077	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.002703	0.425876	
chunk0160_393_1	chr5	163427073	163427272	+	0	NA	Intergenic	L1PB1|LINE|L1	-10399	NM_199246	900	Hs.79101	NM_004060	ENSG00000113328	CCNG1	CCNG	cyclin G1	protein-coding	0.005025	0.355000	
chunk0151_294_1	chr5	52894986	52895544	+	0	NA	intron (NM_181501, intron 9 of 28)	intron (NM_181501, intron 9 of 28)	-94061	NR_073104	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.003584	0.370304	
chunk0055_380_1	chr13	73248708	73249172	+	0	NA	Intergenic	Intergenic	190148	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.006466	0.436559	266(AGGCACAGTTTGTTTC,-,0.00),267(GGCACAGTTTGTTTCC,+,0.00)
chunk0189_449_1	chr8	28322722	28322928	+	0	NA	intron (NM_006228, intron 1 of 3)	MIRb|SINE|MIR	5693	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.004854	0.381643	
chunk0087_268_1	chr18	37300502	37300810	+	0	NA	intron (NM_001025089, intron 3 of 11)	L2a|LINE|L2	165848	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.009740	0.508091	136(AGGAACAAAGAGTCCC,-,0.00),137(GGAACAAAGAGTCCCT,+,0.00)
chunk0143_3_1	chr4	105670734	105670933	+	0	NA	intron (NM_001242729, intron 13 of 13)	intron (NM_001242729, intron 13 of 13)	37891	NM_001142471	57117	Hs.480454	NM_020395	ENSG00000138785	INTS12	INT12|PHF22|SBBI22	integrator complex subunit 12	protein-coding	0.000000	0.430000	
chunk0037_184_1	chr11	74103065	74103376	+	0	NA	exon (NM_015531, exon 14 of 31)	exon (NM_015531, exon 14 of 31)	67799	NM_015531	26005	Hs.557938	NM_015531	ENSG00000168014	C2CD3	OFD14	C2 domain containing 3 centriole elongation regulator	protein-coding	0.012862	0.413462	
chunk0177_302_1	chr7	25945291	25945537	+	0	NA	Intergenic	Intergenic	4572	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.016260	0.493927	80(AAGAACAGACTGCCCT,-,0.00),81(AGAACAGACTGCCCTG,+,0.00)
chunk0063_379_1	chr14	86298516	86298879	+	0	NA	Intergenic	Intergenic	364019	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.005510	0.425824	
chunk0061_355_1	chr14	63695695	63696076	+	0	NA	intron (NM_030791, intron 2 of 2)	AluJr4|SINE|Alu	32210	NM_030791	81537	Hs.24678	NM_030791	ENSG00000126821	SGPP1	SPP-1|SPPase1	sphingosine-1-phosphate phosphatase 1	protein-coding	0.005249	0.452880	
chunk0013_207_1	chr1	169451413	169451931	+	0	NA	intron (NM_001300968, intron 2 of 6)	intron (NM_001300968, intron 2 of 6)	8997	NM_001300968	57821	Hs.567557	NM_021179	ENSG00000117477	CCDC181	C1orf114	coiled-coil domain containing 181	protein-coding	0.007722	0.379576	194(CAGAACAAATAGTTCT,-,0.00),195(AGAACAAATAGTTCTG,+,0.00)
chunk0174_61_1	chr6	155275788	155276394	+	0	NA	exon (NM_001001346, exon 2 of 2)	exon (NM_001001346, exon 2 of 2)	12078	NM_001001346	49861	Hs.567491	NM_001001346	ENSG00000171217	CLDN20	-	claudin 20	protein-coding	0.016502	0.481054	
chunk0007_59_1	chr1	77997888	77998656	+	0	NA	Intergenic	Intergenic	-6680	NM_007034	11080	Hs.13852	NM_007034	ENSG00000162616	DNAJB4	DNAJW|DjB4|HLJ1	DnaJ heat shock protein family (Hsp40) member B4	protein-coding	0.015625	0.407022	
chunk0173_270_1	chr6	147328148	147328358	+	0	NA	intron (NM_001127715, intron 18 of 27)	Charlie17a|DNA|hAT-Charlie	-123639	NR_034115	729178	Hs.557608	NR_034115		STXBP5-AS1	-	STXBP5 antisense RNA 1	ncRNA	0.000000	0.440758	
chunk0081_257_1	chr17	43357034	43357340	+	0	NA	Intergenic	PRIMA41-int|LTR|ERV1	31711	NR_027413	100130581	Hs.546897	NR_027412	ENSG00000188825	LINC00910	-	long intergenic non-protein coding RNA 910	ncRNA	0.013072	0.491857	
chunk0118_89_1	chr22	29089870	29090382	+	0	NA	intron (NM_001039570, intron 1 of 8)	L2a|LINE|L2	17048	NM_032045	83999	Hs.229335	NM_032045	ENSG00000183762	KREMEN1	ECTD13|KREMEN|KRM1	kringle containing transmembrane protein 1	protein-coding	0.009766	0.409357	
chunk0059_152_1	chr14	32134375	32135189	+	0	NA	intron (NM_001173, intron 3 of 6)	intron (NM_001173, intron 3 of 6)	57493	NM_001173	394	Hs.592313	NM_001173	ENSG00000100852	ARHGAP5	GFI2|RhoGAP5|p190-B|p190BRhoGAP	Rho GTPase activating protein 5	protein-coding	0.004914	0.348466	
chunk0117_14_1	chr22	11211754	11211999	+	0	NA	Intergenic	SAR|Satellite|Satellite	-250347	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.004082	0.182927	
chunk0093_162_1	chr19	47648031	47648677	+	0	NA	intron (NM_015711, intron 1 of 14)	intron (NM_015711, intron 1 of 14)	40158	NM_015711	29998	Hs.97244	NM_015711	ENSG00000063169	BICRA	GLTSCR1	BRD4 interacting chromatin remodeling complex associated protein	protein-coding	0.030960	0.568779	
chunk0009_333_1	chr1	109100061	109100285	+	0	NA	promoter-TSS (NR_003023)	promoter-TSS (NR_003023)	-20	NR_003023	677766	Hs.550815	NR_003023	ENSG00000278249	SCARNA2	HBII-382|mgU2-25/61	small Cajal body-specific RNA 2	ncRNA	0.089286	0.653333	
chunk0092_341_1	chr19	35248314	35249108	+	0	NA	promoter-TSS (NM_001260490)	promoter-TSS (NM_001260490)	55	NM_001260490	51599	Hs.466507	NM_015925	ENSG00000105699	LSR	ILDR3|LISCH7	lipolysis stimulated lipoprotein receptor	protein-coding	0.084383	0.674214	
chunk0067_248_1	chr15	45634561	45635151	+	0	NA	5' UTR (NM_021199, exon 1 of 10)	5' UTR (NM_021199, exon 1 of 10)	116	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.079661	0.676819	93(GGAACAGCCAGAGCCT,+,0.00)
chunk0031_443_1	chr10	132575297	132575799	+	0	NA	intron (NM_005539, intron 1 of 15)	intron (NM_005539, intron 1 of 15)	37699	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.027888	0.550696	
chunk0203_238_1	chr9	87239178	87239757	+	0	NA	Intergenic	Intergenic	90823	NM_001001709									0.008636	0.456897	
chunk0068_336_1	chr15	57662051	57662534	+	0	NA	intron (NR_104369, intron 11 of 12)	intron (NR_104369, intron 11 of 12)	-44229	NM_015532	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.002070	0.402893	
chunk0135_369_1	chr3	190760776	190761541	+	0	NA	Intergenic	L1MA9|LINE|L1	101518	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.011765	0.348564	
chunk0057_201_1	chr13	103510083	103510282	+	0	NA	Intergenic	Intergenic	84982	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.035176	0.480000	47(CAGAGCATTTTGTTCT,-,0.00),48(AGAGCATTTTGTTCTT,+,0.00)
chunk0072_393_1	chr15	100601832	100602031	+	0	NA	promoter-TSS (NM_024708)	promoter-TSS (NM_024708)	309	NM_001040616	55180	Hs.105633	NM_018148	ENSG00000140471	LINS1	LINS|MRT27|WINS1	lines homolog 1	protein-coding	0.070352	0.615000	
chunk0122_435_1	chr3	39275323	39275801	+	0	NA	intron (NM_001171174, intron 1 of 1)	MER67C|LTR|ERV1	4474	NM_001337	1524	Hs.78913	NM_001337	ENSG00000168329	CX3CR1	CCRL1|CMKBRL1|CMKDR1|GPR13|GPRV28|V28	C-X3-C motif chemokine receptor 1	protein-coding	0.004184	0.386221	
chunk0164_64_1	chr6	19382602	19383153	+	0	NA	Intergenic	Intergenic	-202397	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.012704	0.438406	
chunk0139_174_1	chr4	54052129	54052621	+	0	NA	intron (NM_012110, intron 1 of 5)	intron (NM_012110, intron 1 of 5)	12273	NM_012110	26511	Hs.335393	NM_012110	ENSG00000109220	CHIC2	BTL	cysteine rich hydrophobic domain 2	protein-coding	0.002033	0.310345	
chunk0100_65_1	chr2	106559628	106560261	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-91599	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.011058	0.416404	249(ATGTACTTTATGTTCT,-,0.00),250(TGTACTTTATGTTCTT,+,0.00)
chunk0034_307_1	chr11	35061356	35062208	+	0	NA	Intergenic	L1ME3|LINE|L1	76250	NR_120528	100507144	Hs.673491	NR_120528	ENSG00000255521	LOC100507144	-	uncharacterized LOC100507144	ncRNA	0.007042	0.356389	361(GGGCACAGGGAGTGCT,-,0.00),362(GGCACAGGGAGTGCTC,+,0.00),633(GTGAACTTGTTGTTCT,-,0.00),634(TGAACTTGTTGTTCTC,+,0.00)
chunk0126_263_1	chr3	79868040	79868265	+	0	NA	Intergenic	L2c|LINE|L2	-100243	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004444	0.393805	
chunk0166_170_1	chr6	45924895	45925318	+	0	NA	intron (NR_045673, intron 1 of 4)	MLT1J|LTR|ERVL-MaLR	12491	NR_045674	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.011820	0.408019	
chunk0076_410_1	chr16	72773984	72774484	+	0	NA	Intergenic	L1MEg|LINE|L1	-109225	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.008000	0.457086	
chunk0159_4_1	chr5	136027886	136028447	+	0	NA	promoter-TSS (NM_000358)	promoter-TSS (NM_000358)	-729	NM_000358	7045	Hs.369397	NM_000358	ENSG00000120708	TGFBI	BIGH3|CDB1|CDG2|CDGG1|CSD|CSD1|CSD2|CSD3|EBMD|LCD1	transforming growth factor beta induced	protein-coding	0.008913	0.483986	
chunk0002_415_1	chr1	27601932	27602131	+	0	NA	intron (NM_001029882, intron 1 of 6)	intron (NM_001029882, intron 1 of 6)	1463	NM_001029882	27245	Hs.469280	NM_001029882	ENSG00000126705	AHDC1	MRD25	AT-hook DNA binding motif containing 1	protein-coding	0.030151	0.685000	
chunk0186_151_1	chr7	139099168	139099594	+	0	NA	intron (NM_020119, intron 1 of 12)	intron (NM_020119, intron 1 of 12)	10338	NM_020119	56829	Hs.133512	NM_020119	ENSG00000105939	ZC3HAV1	ARTD13|FLB6421|PARP13|ZAP|ZC3H2|ZC3HDC2	zinc finger CCCH-type containing, antiviral 1	protein-coding	0.007042	0.400468	
chunk0099_220_1	chr2	96094651	96094903	+	0	NA	Intergenic	L1MB5|LINE|L1	21468	NM_000682	151	Hs.247686	NM_000682	ENSG00000274286	ADRA2B	ADRA2L1|ADRA2RL1|ADRARL1|ALPHA2BAR|FAME2|alpha-2BAR	adrenoceptor alpha 2B	protein-coding	0.007937	0.351779	
chunk0116_113_1	chr21	35637342	35638000	+	0	NA	Intergenic	Intergenic	-56907	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.007599	0.438543	369(AAGGACACTCTGTCAT,-,0.00),370(AGGACACTCTGTCATC,+,0.00)
chunk0017_47_1	chr1	205275060	205275580	+	0	NA	Intergenic	Intergenic	19119	NM_001297613	9911	Hs.6360	NM_014858	ENSG00000133069	TMCC2	HUCEP11	transmembrane and coiled-coil domain family 2	protein-coding	0.007692	0.585413	
chunk0024_414_1	chr10	45445502	45446031	+	0	NA	3' UTR (NM_001256154, exon 13 of 13)	3' UTR (NM_001256154, exon 13 of 13)	7355	NR_120674	102724323	Hs.559151	NR_120674	ENSG00000231964	LOC102724323	-	uncharacterized LOC102724323	ncRNA	0.020794	0.515094	
chunk0208_82_1	chrX	13064462	13065250	+	0	NA	Intergenic	Intergenic	-20058	NM_174901	171484	Hs.667546	NM_174901	ENSG00000187268	FAM9C	TEX39C	family with sequence similarity 9 member C	protein-coding	0.003807	0.430925	411(CAGAACATTCTGGACT,-,0.00),412(AGAACATTCTGGACTC,+,0.00)
chunk0164_455_1	chr6	28402121	28402673	+	0	NA	Intergenic	Intergenic	-2630	NM_001163391	9753	Hs.134816	NM_014724	ENSG00000158691	ZSCAN12	ZFP96|ZNF29K1|ZNF305|ZNF96|dJ29K1.2	zinc finger and SCAN domain containing 12	protein-coding	0.005435	0.381555	
chunk0113_243_1	chr20	54207717	54208243	+	0	NA	promoter-TSS (NM_002623)	promoter-TSS (NM_002623)	17	NM_002623	5203	Hs.91161	NM_002623	ENSG00000101132	PFDN4	C1|PFD4	prefoldin subunit 4	protein-coding	0.093156	0.662239	
chunk0159_293_1	chr5	142796725	142796924	+	0	NA	intron (NM_015071, intron 1 of 22)	intron (NM_015071, intron 1 of 22)	26097	NM_015071	23092	Hs.654668	NM_015071	ENSG00000145819	ARHGAP26	GRAF|GRAF1|OPHN1L|OPHN1L1	Rho GTPase activating protein 26	protein-coding	0.000000	0.470000	
chunk0100_445_1	chr2	120817378	120818008	+	0	NA	intron (NM_005270, intron 1 of 12)	intron (NM_005270, intron 1 of 12)	20402	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.026984	0.606973	
chunk0204_315_1	chr9	100351463	100351772	+	0	NA	intron (NM_017746, intron 1 of 14)	intron (NM_017746, intron 1 of 14)	954	NM_001161584	54881	Hs.494648	NM_017746	ENSG00000136891	TEX10	Ipi1|bA208F1.2	testis expressed 10	protein-coding	0.006472	0.348387	
chunk0152_460_1	chr5	66616648	66616961	+	0	NA	intron (NM_198828, intron 1 of 5)	intron (NM_198828, intron 1 of 5)	20456	NM_001290228	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.006390	0.426752	
chunk0048_106_1	chr12	79415709	79416077	+	0	NA	intron (NM_001291901, intron 8 of 9)	intron (NM_001291901, intron 8 of 9)	-3364	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.005435	0.371274	
chunk0180_421_1	chr7	76108364	76109156	+	0	NA	Intergenic	Intergenic	60741	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.012626	0.433796	
chunk0048_463_1	chr12	89119995	89120307	+	0	NA	Intergenic	L2c|LINE|L2	-100459	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.000000	0.412141	154(TTGCACATGCTGTTCC,-,0.00),155(TGCACATGCTGTTCCT,+,0.00)
chunk0205_300_1	chr9	112066404	112066795	+	0	NA	intron (NM_022486, intron 12 of 16)	intron (NM_022486, intron 12 of 16)	108698	NM_001282643	64420	Hs.494827	NM_022486	ENSG00000106868	SUSD1	-	sushi domain containing 1	protein-coding	0.020460	0.487245	210(TGGGACACCTTGTGCC,-,0.00),211(GGGACACCTTGTGCCT,+,0.00)
chunk0026_305_1	chr10	67976762	67976961	+	0	NA	intron (NM_022079, intron 15 of 25)	L1MA2|LINE|L1	34022	NR_131184	100009667		NR_131184		POU5F1P5	Oct4-pg5	POU class 5 homeobox 1 pseudogene 5	pseudo	0.000000	0.500000	
chunk0206_259_1	chr9	123822890	123823142	+	0	NA	intron (NM_024820, intron 2 of 20)	MIRb|SINE|MIR	107122	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.015873	0.383399	
chunk0089_179_1	chr18	59695324	59695661	+	0	NA	intron (NM_133459, intron 2 of 10)	intron (NM_133459, intron 2 of 10)	1920	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.020772	0.470414	
chunk0206_404_1	chr9	127285808	127286211	+	0	NA	intron (NR_104591, intron 1 of 26)	intron (NR_104591, intron 1 of 26)	21532	NR_104591	84253	Hs.29304	NM_032293	ENSG00000136895	GARNL3	bA356B19.1	GTPase activating Rap/RanGAP domain like 3	protein-coding	0.002481	0.353960	
chunk0019_105_1	chr1	225017529	225017728	+	0	NA	intron (NM_001145154, intron 10 of 10)	L1PA16|LINE|L1	87967	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.010050	0.600000	
chunk0018_421_1	chr1	222737047	222737369	+	0	NA	promoter-TSS (NM_207468)	promoter-TSS (NM_207468)	-8	NM_207468	400823	Hs.697608	NM_207468	ENSG00000197520	FAM177B	-	family with sequence similarity 177 member B	protein-coding	0.003106	0.408669	
chunk0142_140_1	chr4	94851730	94852069	+	0	NA	intron (NM_001203, intron 1 of 12)	L2b|LINE|L2	93922	NM_001203	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.008850	0.355882	
chunk0066_440_1	chr15	39794988	39795273	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-12292	NM_152597	161835	Hs.129598	NM_152597	ENSG00000150667	FSIP1	HSD10	fibrous sheath interacting protein 1	protein-coding	0.003509	0.405594	
chunk0058_143_1	chr14	22994983	22995225	+	0	NA	intron (NM_001130706, intron 4 of 7)	intron (NM_001130706, intron 4 of 7)	5933	NM_001282969	60686	Hs.255874	NM_021944	ENSG00000100802	C14orf93	RTFC	chromosome 14 open reading frame 93	protein-coding	0.004132	0.530864	
chunk0187_189_1	chr7	151537810	151538252	+	0	NA	Intergenic	Intergenic	-18107	NM_005614	6009	Hs.283521	NM_005614	ENSG00000106615	RHEB	RHEB2	Ras homolog, mTORC1 binding	protein-coding	0.009050	0.415350	
chunk0154_97_1	chr5	78095009	78095684	+	0	NA	intron (NM_003664, intron 21 of 26)	intron (NM_003664, intron 21 of 26)	137099	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.004444	0.380178	
chunk0039_444_1	chr11	108316293	108316540	+	0	NA	intron (NM_000051, intron 42 of 62)	MIRb|SINE|MIR	93584	NM_000051	472	Hs.367437	NM_000051	ENSG00000149311	ATM	AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1	ATM serine/threonine kinase	protein-coding	0.004049	0.379032	
chunk0040_110_1	chr11	111981990	111982213	+	0	NA	intron (NM_001037954, intron 6 of 19)	intron (NM_001037954, intron 6 of 19)	4792	NM_033425	85458	Hs.655626	NM_033425	ENSG00000150764	DIXDC1	CCD1	DIX domain containing 1	protein-coding	0.008969	0.486607	
chunk0001_334_1	chr1	9589965	9590295	+	0	NA	intron (NM_001010866, intron 1 of 5)	intron (NM_001010866, intron 1 of 5)	1256	NM_001130924	199953	Hs.632365	NM_001010866	ENSG00000188807	TMEM201	Ima1|NET5|SAMP1	transmembrane protein 201	protein-coding	0.018182	0.561934	
chunk0131_173_1	chr3	147386176	147386737	+	0	NA	non-coding (NR_033119, exon 3 of 3)	non-coding (NR_033119, exon 3 of 3)	5974	NR_040762	84107	Hs.415766	NM_032153	ENSG00000174963	ZIC4	-	Zic family member 4	protein-coding	0.001783	0.346975	
chunk0131_407_1	chr3	152941769	152942347	+	0	NA	Intergenic	Intergenic	107365	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.005190	0.395509	
chunk0063_79_1	chr14	77699046	77699272	+	0	NA	intron (NM_006020, intron 2 of 5)	MER58A|DNA|hAT-Charlie	8854	NM_006020	8846	Hs.94542	NM_006020	ENSG00000100601	ALKBH1	ABH|ABH1|ALKBH|alkB|hABH	alkB homolog 1, histone H2A dioxygenase	protein-coding	0.017699	0.400881	
chunk0051_11_1	chr12	111557799	111558254	+	0	NA	intron (NM_001310121, intron 1 of 25)	intron (NM_001310121, intron 1 of 25)	41647	NM_001310123	6311	Hs.76253	NM_002973	ENSG00000204842	ATXN2	ATX2|SCA2|TNRC13	ataxin 2	protein-coding	0.010989	0.361842	
chunk0055_448_1	chr13	75719813	75720012	+	0	NA	intron (NM_001306080, intron 2 of 30)	L1MC1|LINE|L1	-40749	NM_015842	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.015075	0.350000	
chunk0178_337_1	chr7	38448093	38448886	+	0	NA	intron (NM_001635, intron 11 of 20)	MER44A|DNA|TcMar-Tigger	106912	NR_040085	100506776	Hs.173034	NR_040085	ENSG00000281103	TRG-AS1	TCRGV	T cell receptor gamma locus antisense RNA 1	ncRNA	0.006305	0.356423	310(GGTACAGATAGTACTG,+,0.00)
chunk0044_37_1	chr12	27451561	27451774	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-5033	NR_109975	101928646	Hs.434269	NR_109975	ENSG00000245311	ARNTL2-AS1	-	ARNTL2 antisense RNA 1	ncRNA	0.014085	0.453271	
chunk0106_70_1	chr2	196977487	196978033	+	0	NA	Intergenic	L1MB7|LINE|L1	-51030	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.005495	0.334552	
chunk0152_110_1	chr5	58504550	58505876	+	0	NA	Intergenic	Intergenic	13778	NM_152687	202309	Hs.547697	NM_152687	ENSG00000175857	GAPT	C5orf29	GRB2 binding adaptor protein, transmembrane	protein-coding	0.006033	0.369254	438(GTGTACAATATGTCCT,-,0.00),439(TGTACAATATGTCCTC,+,0.00)
chunk0112_235_1	chr20	41192064	41192436	+	0	NA	intron (NM_015035, intron 3 of 3)	L1MA4A|LINE|L1	23227	NR_106931	102466912		NR_106931	ENSG00000276169	MIR6871	hsa-mir-6871	microRNA 6871	ncRNA	0.005376	0.571046	
chunk0170_121_1	chr6	110680196	110680472	+	0	NA	intron (NM_015076, intron 2 of 12)	intron (NM_015076, intron 2 of 12)	-134287	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.003623	0.407942	127(GAGCACAATAAGTGCT,-,0.00)
chunk0107_353_1	chr2	222287909	222288310	+	0	NA	intron (NM_181457, intron 4 of 7)	intron (NM_181457, intron 4 of 7)	-10038	NM_153038	151278	Hs.350729	NM_153038	ENSG00000163081	CCDC140	-	coiled-coil domain containing 140	ncRNA	0.007481	0.348259	
chunk0065_401_1	chr14	105221788	105222079	+	0	NA	intron (NM_001242787, intron 10 of 17)	intron (NM_001242787, intron 10 of 17)	25952	NM_145685	2972	Hs.424484	NM_001519	ENSG00000185024	BRF1	BRF|BRF-1|CFDS|GTF3B|HEL-S-76p|TAF3B2|TAF3C|TAFIII90|TF3B90|TFIIIB90|hBRF	BRF1 RNA polymerase III transcription initiation factor subunit	protein-coding	0.051546	0.606164	
chunk0050_140_1	chr12	102502951	102504321	+	0	NA	Intergenic	Intergenic	-22991	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.002920	0.392414	
chunk0024_164_1	chr10	35612744	35613270	+	0	NA	Intergenic	Intergenic	7597	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.005703	0.457306	348(AGGGACTACATGTTCT,-,0.00),349(GGGACTACATGTTCTG,+,0.00)
chunk0083_240_1	chr17	67637937	67638264	+	0	NA	intron (NM_181671, intron 6 of 9)	intron (NM_181671, intron 6 of 9)	-79733	NM_001303272	25926	Hs.463936	NM_015462	ENSG00000130935	NOL11	-	nucleolar protein 11	protein-coding	0.018349	0.515244	
chunk0176_451_1	chr7	20107756	20108695	+	0	NA	intron (NR_110114, intron 1 of 5)	intron (NR_110114, intron 1 of 5)	32201	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.004260	0.353191	
chunk0086_110_1	chr18	14432230	14432577	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	66303	NR_024076	440224	Hs.721675	NR_024076	ENSG00000265766	CXADRP3	-	CXADR pseudogene 3	pseudo	0.017291	0.408046	
chunk0060_55_1	chr14	41521860	41522258	+	0	NA	Intergenic	LTR47A2|LTR|ERVL	-85502	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.007538	0.398496	
chunk0135_270_1	chr3	189263096	189263577	+	0	NA	intron (NM_198485, intron 4 of 5)	L2b|LINE|L2	-22742	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.002079	0.441909	252(AAGAACAGAGAGAGCT,-,0.00),253(AGAACAGAGAGAGCTT,+,0.00)
chunk0129_306_1	chr3	123732486	123732685	+	0	NA	intron (NM_053026, intron 10 of 32)	intron (NM_053026, intron 10 of 32)	42941	NR_046629	100873940	Hs.667316	NR_046629	ENSG00000250174	MYLK-AS2	-	MYLK antisense RNA 2	ncRNA	0.010050	0.415000	86(ATGAACACTCAGTTCT,-,0.00),87(TGAACACTCAGTTCTC,+,0.00)
chunk0173_369_1	chr6	149454652	149454866	+	0	NA	intron (NM_207360, intron 4 of 5)	intron (NM_207360, intron 4 of 5)	30253	NM_207360	340152	Hs.632618	NM_207360	ENSG00000178199	ZC3H12D	C6orf95|MCPIP4|TFL|dJ281H8.1|p34	zinc finger CCCH-type containing 12D	protein-coding	0.028037	0.586047	
chunk0062_121_1	chr14	68458933	68459563	+	0	NA	intron (NM_133509, intron 9 of 10)	intron (NM_133509, intron 9 of 10)	334666	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.007937	0.475436	
chunk0146_421_1	chr4	169168018	169168567	+	0	NA	intron (NM_020870, intron 2 of 11)	intron (NM_020870, intron 2 of 11)	102806	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.000000	0.381818	284(TTGTACATAATGTACT,-,0.00),285(TGTACATAATGTACTG,+,0.00)
chunk0183_319_1	chr7	108043741	108044277	+	0	NA	intron (NM_007356, intron 28 of 33)	intron (NM_007356, intron 28 of 33)	-40650	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.007463	0.301676	
chunk0064_298_1	chr14	95381102	95381434	+	0	NA	Intergenic	Intergenic	28822	NR_026779									0.009036	0.438438	
chunk0154_425_1	chr5	89230904	89231501	+	0	NA	Intergenic	L1MCb|LINE|L1	-327097	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.005025	0.369565	
chunk0195_430_1	chr8	100906829	100907195	+	0	NA	Intergenic	Intergenic	43559	NM_001135702	7534	Hs.492407	NM_003406	ENSG00000164924	YWHAZ	14-3-3-zeta|HEL-S-3|HEL-S-93|HEL4|KCIP-1|POPCHAS|YWHAD	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	protein-coding	0.013661	0.465940	
chunk0157_132_1	chr5	117355134	117355699	+	0	NA	Intergenic	Intergenic	-60096	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.005310	0.349823	
chunk0120_199_1	chr3	7144017	7144572	+	0	NA	intron (NM_000844, intron 1 of 9)	MIRb|SINE|MIR	-250277	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.010811	0.345324	
chunk0045_168_1	chr12	46839938	46840568	+	0	NA	Intergenic	Intergenic	-14256	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.004762	0.372425	
chunk0083_322_1	chr17	69560805	69561502	+	0	NA	Intergenic	Intergenic	-32834	NR_109971	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.004304	0.434097	370(GTGACATCGTGTGCTT,+,0.00)
chunk0140_151_1	chr4	69388949	69389607	+	0	NA	Intergenic	Intergenic	106630	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.007599	0.347496	
chunk0172_55_1	chr6	134162857	134163177	+	0	NA	Intergenic	Intergenic	11879	NM_005627	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.009375	0.442368	130(GTGAACAGTCTGTACT,-,0.00),131(TGAACAGTCTGTACTT,+,0.00)
chunk0196_334_1	chr8	113049593	113049792	+	0	NA	intron (NM_198123, intron 5 of 70)	intron (NM_198123, intron 5 of 70)	327461	NM_198124	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.005025	0.285000	
chunk0190_138_1	chr8	30722824	30723375	+	0	NA	intron (NM_000637, intron 1 of 12)	intron (NM_000637, intron 1 of 12)	4870	NM_001195103	2936	Hs.271510	NM_000637	ENSG00000104687	GSR	GR|HEL-75|HEL-S-122m	glutathione-disulfide reductase	protein-coding	0.010889	0.461957	
chunk0063_260_1	chr14	83419359	83419594	+	0	NA	Intergenic	Intergenic	-1796415	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.008511	0.402542	
chunk0036_99_1	chr11	61034060	61034346	+	0	NA	Intergenic	LTR84b|LTR|ERVL	62562	NM_006725	923	Hs.744366	NM_006725	ENSG00000013725	CD6	TP120	CD6 molecule	protein-coding	0.013986	0.463415	
chunk0092_404_1	chr19	37467446	37467674	+	0	NA	promoter-TSS (NM_152484)	promoter-TSS (NM_152484)	-123	NM_152484	148266	Hs.511848	NM_152484	ENSG00000196437	ZNF569	ZAP1|ZNF	zinc finger protein 569	protein-coding	0.048246	0.589520	
chunk0132_218_1	chr3	157701908	157702108	+	0	NA	Intergenic	Intergenic	158664	NR_024016	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.015000	0.393035	
chunk0033_314_1	chr11	20599806	20600005	+	0	NA	intron (NM_004211, intron 1 of 15)	intron (NM_004211, intron 1 of 15)	505	NM_004211	9152	Hs.136557	NM_004211	ENSG00000165970	SLC6A5	GLYT-2|GLYT2|HKPX3|NET1	solute carrier family 6 member 5	protein-coding	0.040201	0.555000	
chunk0141_47_1	chr4	77360550	77360935	+	0	NA	Intergenic	Intergenic	-151011	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.012987	0.417098	
chunk0030_248_1	chr10	115441941	115442666	+	0	NA	intron (NM_207303, intron 21 of 28)	(CT)n|Simple_repeat|Simple_repeat	348938	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.004138	0.385675	
chunk0172_184_1	chr6	136557662	136557917	+	0	NA	exon (NM_005923, exon 30 of 30)	exon (NM_005923, exon 30 of 30)	-6970	NM_001198616	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.019608	0.414062	
chunk0093_412_1	chr19	57302572	57303078	+	0	NA	Intergenic	L1M2a|LINE|L1	-17672	NM_213598	125919	Hs.202544	NM_213598	ENSG00000178229	ZNF543	-	zinc finger protein 543	protein-coding	0.005929	0.552268	
chunk0032_302_1	chr11	9740176	9740375	+	0	NA	exon (NM_001297714, exon 8 of 11)	exon (NM_001297714, exon 8 of 11)	-18018	NR_036485	283104	Hs.632156	NR_036485	ENSG00000246273	SBF2-AS1	-	SBF2 antisense RNA 1	ncRNA	0.020101	0.500000	
chunk0211_235_1	chrX	119001651	119001993	+	0	NA	intron (NM_001031855, intron 5 of 10)	intron (NM_001031855, intron 5 of 10)	25490	NM_001289109	79836	Hs.144266	NM_024778	ENSG00000175556	LONRF3	RNF127	LON peptidase N-terminal domain and ring finger 3	protein-coding	0.002924	0.329446	
chunk0013_98_1	chr1	167737367	167737591	+	0	NA	intron (NM_024569, intron 1 of 4)	MamRep605|LTR?|LTR?	15529	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.017857	0.475556	
chunk0138_226_1	chr4	39110005	39110437	+	0	NA	intron (NM_001007075, intron 9 of 11)	Charlie15b|DNA|hAT-Charlie	47989	NM_199039	51088	Hs.272251	NM_015990	ENSG00000109790	KLHL5	-	kelch like family member 5	protein-coding	0.000000	0.290993	
chunk0145_289_1	chr4	149901115	149901493	+	0	NA	Intergenic	Intergenic	-176970	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.010582	0.350923	
chunk0139_53_1	chr4	48754677	48755329	+	0	NA	intron (NM_015030, intron 1 of 63)	L3|LINE|CR1	25296	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.012270	0.444104	
chunk0155_178_1	chr5	94403383	94403994	+	0	NA	exon (NM_001145678, exon 16 of 21)	exon (NM_001145678, exon 16 of 21)	214916	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.009820	0.349673	
chunk0069_122_1	chr15	61772196	61772448	+	0	NA	Intergenic	L1MEc|LINE|L1	288143	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.003968	0.296443	161(CAGAACAAAGTGGCCC,-,0.00)
chunk0123_443_1	chr3	50583920	50584409	+	0	NA	3' UTR (NM_016173, exon 11 of 11)	3' UTR (NM_016173, exon 11 of 11)	-13137	NM_001171741	51161	Hs.517860	NM_016210	ENSG00000088543	C3orf18	G20	chromosome 3 open reading frame 18	protein-coding	0.012270	0.536735	230(GAGAACAGGCTGTCCT,-,0.00),231(AGAACAGGCTGTCCTT,+,0.00)
chunk0066_388_1	chr15	38903631	38904036	+	0	NA	Intergenic	Intergenic	207235	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.004938	0.344828	191(ATGAACAAACTGTCCT,-,0.00),192(TGAACAAACTGTCCTT,+,0.00)
chunk0005_30_1	chr1	54601077	54601276	+	0	NA	intron (NM_147161, intron 8 of 15)	(GT)n|Simple_repeat|Simple_repeat	22351	NM_176782	338094	Hs.234786	NM_176782	ENSG00000162391	FAM151A	C1orf179	family with sequence similarity 151 member A	protein-coding	0.010050	0.540000	
chunk0060_184_1	chr14	46900545	46901050	+	0	NA	intron (NM_182830, intron 10 of 16)	L1MD2|LINE|L1	-248972	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.003960	0.333992	
chunk0154_36_1	chr5	77074342	77074541	+	0	NA	Intergenic	Intergenic	6130	NR_003014	677828	Hs.693249	NR_003014	ENSG00000238961	SNORA47	HBI-115	small nucleolar RNA, H/ACA box 47	snoRNA	0.010050	0.480000	
chunk0137_393_1	chr4	27046690	27047286	+	0	NA	Intergenic	Intergenic	-170491	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.008389	0.400335	
chunk0014_214_1	chr1	179329984	179330233	+	0	NA	intron (NM_001252512, intron 2 of 14)	LTR8B|LTR|ERV1	-35612	NM_144696	126859	Hs.658505	NM_144696	ENSG00000162779	AXDND1	C1orf125	axonemal dynein light chain domain containing 1	protein-coding	0.004016	0.472000	
chunk0078_299_1	chr17	8154154	8154856	+	0	NA	Intergenic	Intergenic	-2070	NM_002616	5187	Hs.445534	NM_002616	ENSG00000179094	PER1	PER|RIGUI|hPER	period circadian regulator 1	protein-coding	0.041311	0.620199	305(GGGAACATCATGTTCT,-,0.00),306(GGAACATCATGTTCTC,+,0.00)
chunk0204_73_1	chr9	93705296	93705608	+	0	NA	Intergenic	L1M4|LINE|L1	110611	NR_049853	100847045		NR_049853	ENSG00000283146	MIR548AU	-	microRNA 548au	ncRNA	0.000000	0.341853	
chunk0027_88_1	chr10	73586648	73587132	+	0	NA	Intergenic	Intergenic	-11215	NM_152586	159195	Hs.657355	NM_152586	ENSG00000166348	USP54	C10orf29|bA137L10.3|bA137L10.4	ubiquitin specific peptidase 54	protein-coding	0.004132	0.325773	
chunk0090_350_1	chr18	76580368	76580737	+	0	NA	Intergenic	Intergenic	-39225	NR_120419	400660	Hs.131718	NR_120419	ENSG00000266256	LINC00683	-	long intergenic non-protein coding RNA 683	ncRNA	0.016260	0.610811	
chunk0051_325_1	chr12	120079663	120080032	+	0	NA	intron (NM_207311, intron 6 of 8)	intron (NM_207311, intron 6 of 8)	36992	NM_001167606	11021	Hs.524788	NM_006861	ENSG00000111737	RAB35	H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding	0.013550	0.497297	
chunk0156_395_1	chr5	113426022	113426247	+	0	NA	intron (NM_001085377, intron 1 of 18)	intron (NM_001085377, intron 1 of 18)	8897	NM_032028	83942	Hs.519507	NM_032028	ENSG00000212122	TSSK1B	FKSG81|SPOGA4|STK22D|TSK1|TSSK1	testis specific serine kinase 1B	protein-coding	0.004444	0.575221	
chunk0062_297_1	chr14	72763299	72763515	+	0	NA	intron (NM_001280542, intron 2 of 10)	L1ME1|LINE|L1	129242	NM_001280544	8110	Hs.162868	NM_012074	ENSG00000205683	DPF3	BAF45C|CERD4	double PHD fingers 3	protein-coding	0.004630	0.317972	
chunk0126_215_1	chr3	78798246	78799025	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	220824	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.001284	0.332051	
chunk0088_35_1	chr18	43862933	43863499	+	0	NA	Intergenic	Intergenic	-585566	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.003534	0.363316	340(TGGGACAAATTGTTCC,-,0.00),341(GGGACAAATTGTTCCT,+,0.00)
chunk0066_254_1	chr15	34716119	34716571	+	0	NA	Intergenic	Intergenic	38236	NM_020660	57369	Hs.283816	NM_020660	ENSG00000159248	GJD2	CX36|GJA9	gap junction protein delta 2	protein-coding	0.019912	0.494481	200(AAGTACATGGTGTTTT,-,0.00),201(AGTACATGGTGTTTTC,+,0.00)
chunk0007_256_1	chr1	82850335	82850591	+	0	NA	Intergenic	LTR33|LTR|ERVL	134459	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.011719	0.466926	
chunk0123_145_1	chr3	42841302	42842153	+	0	NA	intron (NM_001296, intron 2 of 2)	L2c|LINE|L2	32255	NM_001296	1238	Hs.146346	NM_001296	ENSG00000144648	ACKR2	CCBP2|CCR10|CCR9|CMKBR9|D6|hD6	atypical chemokine receptor 2	protein-coding	0.007051	0.460094	304(AAGATCACAGTGTTCA,-,0.00),305(AGATCACAGTGTTCAG,+,0.00)
chunk0159_330_1	chr5	143673863	143674246	+	0	NA	Intergenic	L2a|LINE|L2	-5806	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.007833	0.401042	
chunk0041_187_1	chr11	126365514	126365713	+	0	NA	intron (NM_006278, intron 1 of 10)	intron (NM_006278, intron 1 of 10)	9719	NM_006278	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.005025	0.575000	
chunk0068_62_1	chr15	51799484	51800108	+	0	NA	intron (NM_014548, intron 8 of 9)	intron (NM_014548, intron 8 of 9)	-29832	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.008013	0.419200	
chunk0066_409_1	chr15	39399331	39399815	+	0	NA	Intergenic	Intergenic	148904	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.000000	0.358763	
chunk0142_109_1	chr4	94472168	94472367	+	0	NA	intron (NM_001256428, intron 2 of 11)	intron (NM_001256428, intron 2 of 11)	20410	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.010050	0.410000	
chunk0020_5_1	chr1	231626392	231626662	+	0	NA	promoter-TSS (NM_001164537)	promoter-TSS (NM_001164537)	-288	NM_001164550	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.029630	0.564576	
chunk0124_359_1	chr3	58723130	58723720	+	0	NA	Intergenic	Intergenic	-56591	NM_138805	131177	Hs.61265	NM_138805	ENSG00000198643	FAM3D	EF7|OIT1	family with sequence similarity 3 member D	protein-coding	0.005085	0.362098	
chunk0001_278_1	chr1	8702128	8702733	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	115210	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.019835	0.386139	
chunk0011_341_1	chr1	152198946	152199378	+	0	NA	Intergenic	Intergenic	25034	NM_001009931	388697	Hs.490162	NM_001009931	ENSG00000197915	HRNR	FLG3|S100A16|S100a18	hornerin	protein-coding	0.000000	0.399538	
chunk0175_204_1	chr7	6009239	6009438	+	0	NA	promoter-TSS (NM_000535)	promoter-TSS (NM_000535)	87	NM_006303	7965	Hs.301613	NM_006303	ENSG00000106305	AIMP2	HLD17|JTV-1|JTV1|P38	aminoacyl tRNA synthetase complex interacting multifunctional protein 2	protein-coding	0.085427	0.625000	
chunk0171_85_1	chr6	121838815	121839395	+	0	NA	Intergenic	Intergenic	403528	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.008621	0.461274	
chunk0043_124_1	chr12	15669899	15670136	+	0	NA	intron (NM_004447, intron 4 of 20)	intron (NM_004447, intron 4 of 20)	119559	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.008439	0.298319	
chunk0029_203_1	chr10	101694217	101694500	+	0	NA	intron (NM_022039, intron 1 of 8)	CpG	628	NM_022039	6468	Hs.500822	NM_022039	ENSG00000107829	FBXW4	DAC|FBW4|FBWD4|SHFM3|SHSF3	F-box and WD repeat domain containing 4	protein-coding	0.130742	0.742958	
chunk0082_395_1	chr17	60764500	60764740	+	0	NA	intron (NM_017679, intron 6 of 23)	L1PA6|LINE|L1	86809	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.004167	0.402490	
chunk0145_429_1	chr4	153058592	153059038	+	0	NA	Intergenic	Intergenic	-94303	NM_001130067	23321	Hs.435711	NM_015271	ENSG00000109654	TRIM2	CMT2R|RNF86	tripartite motif containing 2	protein-coding	0.004484	0.409396	
chunk0073_154_1	chr16	7290761	7291221	+	0	NA	intron (NM_018723, intron 4 of 15)	intron (NM_018723, intron 4 of 15)	-41759	NM_145893	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.006522	0.394794	
chunk0141_82_1	chr4	78602377	78602908	+	0	NA	intron (NM_005139, intron 11 of 12)	L2c|LINE|L2	-43352	NR_038303	100505702	Hs.235795	NR_038303		LINC01094	-	long intergenic non-protein coding RNA 1094	ncRNA	0.009416	0.475564	
chunk0170_297_1	chr6	115533664	115534068	+	0	NA	Intergenic	L1MC1|LINE|L1	-504865	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.004950	0.330864	
chunk0129_42_1	chr3	117404983	117405613	+	0	NA	Intergenic	Intergenic	483867	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.003175	0.396197	242(CAGCACACTCTGCACT,-,0.00),243(AGCACACTCTGCACTT,+,0.00)
chunk0099_348_1	chr2	100183977	100184473	+	0	NA	Intergenic	Intergenic	-24029	NR_103730	150577	Hs.434127	NM_001102655	ENSG00000232084	LINC01104	-	long intergenic non-protein coding RNA 1104	ncRNA	0.008065	0.440644	
chunk0045_412_1	chr12	53061409	53061853	+	0	NA	intron (NM_198316, intron 21 of 28)	intron (NM_198316, intron 21 of 28)	4687	NR_106815	102466193		NR_106815	ENSG00000278108	MIR6757	hsa-mir-6757	microRNA 6757	ncRNA	0.009009	0.584270	
chunk0113_317_1	chr20	58140580	58140867	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-10204	NM_178456	128602	Hs.43977	NM_178456	ENSG00000124237	C20orf85	LLC1|bA196N14.1	chromosome 20 open reading frame 85	protein-coding	0.013937	0.500000	
chunk0177_229_1	chr7	24485746	24485999	+	0	NA	Intergenic	HAL1|LINE|L1	-87474	NM_016447	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.019763	0.389764	
chunk0059_158_1	chr14	32256277	32256968	+	0	NA	Intergenic	Intergenic	-53353	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.001447	0.330925	
chunk0093_168_1	chr19	48367814	48368226	+	0	NA	intron (NM_012451, intron 2 of 4)	intron (NM_012451, intron 2 of 4)	3626	NM_012451	23546	Hs.408333	NM_012451	ENSG00000105467	SYNGR4	-	synaptogyrin 4	protein-coding	0.012136	0.539952	
chunk0129_247_1	chr3	122094764	122094966	+	0	NA	intron (NM_001206924, intron 2 of 5)	intron (NM_001206924, intron 2 of 5)	17016	NM_176892	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.009901	0.472906	
chunk0108_140_1	chr2	230739008	230739282	+	0	NA	intron (NM_001130849, intron 1 of 8)	intron (NM_001130849, intron 1 of 8)	25597	NM_001130849	51719	Hs.603930	NM_016289	ENSG00000135932	CAB39	CGI-66|MO25	calcium binding protein 39	protein-coding	0.003650	0.330909	
chunk0101_7_1	chr2	121282444	121283268	+	0	NA	intron (NM_014553, intron 1 of 14)	intron (NM_014553, intron 1 of 14)	2346	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.015777	0.469091	334(TGGTACAATCTGTTCC,-,0.00),335(GGTACAATCTGTTCCT,+,0.00)
chunk0131_92_1	chr3	143587164	143587451	+	0	NA	intron (NM_173653, intron 6 of 15)	L2a|LINE|L2	245061	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.000000	0.364583	
chunk0025_85_1	chr10	50395320	50395695	+	0	NA	intron (NM_147156, intron 6 of 10)	Tigger13a|DNA|TcMar-Tigger	-146897	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.002667	0.367021	
chunk0087_262_1	chr18	37152316	37152674	+	0	NA	intron (NM_020776, intron 7 of 9)	MER34B|LTR|ERV1	314009	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.013966	0.456825	
chunk0094_190_1	chr2	6188296	6188663	+	0	NA	Intergenic	Intergenic	186943	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.005450	0.396739	
chunk0005_426_1	chr1	62783880	62784176	+	0	NA	promoter-TSS (NM_178221)	promoter-TSS (NM_178221)	-78	NM_032852	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.067568	0.545455	
chunk0177_308_1	chr7	26022437	26023046	+	0	NA	Intergenic	Intergenic	-72755	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.006568	0.413115	
chunk0073_58_1	chr16	3455985	3456320	+	0	NA	intron (NM_001083601, intron 2 of 7)	intron (NM_001083601, intron 2 of 7)	-1840	NM_001083600	79903	Hs.513296	NM_024845	ENSG00000122390	NAA60	HAT4|NAT15|NatF|hNaa60	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding	0.023881	0.467262	45(ATGTACATGCTGTTCT,-,0.00),46(TGTACATGCTGTTCTG,+,0.00)
chunk0154_123_1	chr5	78855303	78855709	+	0	NA	intron (NM_198709, intron 6 of 7)	L1MA5|LINE|L1	130437	NM_198709	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.004926	0.545455	
chunk0070_339_1	chr15	75709519	75709781	+	0	NA	intron (NM_001897, intron 1 of 9)	intron (NM_001897, intron 1 of 9)	3198	NM_001897	1464	Hs.513044	NM_001897	ENSG00000173546	CSPG4	HMW-MAA|MCSP|MCSPG|MEL-CSPG|MSK16|NG2	chondroitin sulfate proteoglycan 4	protein-coding	0.041985	0.615970	
chunk0203_374_1	chr9	90162769	90163073	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-121422	NR_038882	286370	Hs.407589	NR_038882	ENSG00000227555	MIR4290HG	-	MIR4290 host gene	ncRNA	0.003289	0.501639	
chunk0210_311_1	chrX	90459052	90459251	+	0	NA	Intergenic	LTR35B|LTR|ERV1	537210	NM_138960	90316	Hs.592220	NM_138960	ENSG00000153779	TGIF2LX	TGIFLX	TGFB induced factor homeobox 2 like X-linked	protein-coding	0.015075	0.480000	
chunk0151_186_1	chr5	50441123	50441548	+	0	NA	promoter-TSS (NM_198449)	promoter-TSS (NM_198449)	65	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.089412	0.692488	
chunk0019_416_1	chr1	230744221	230744440	+	0	NA	Intergenic	Intergenic	-3054	NM_006615	10753	Hs.498021	NM_006615	ENSG00000135773	CAPN9	GC36|nCL-4	calpain 9	protein-coding	0.013699	0.477273	
chunk0072_230_1	chr15	95799741	95800146	+	0	NA	Intergenic	Intergenic	366850	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.004938	0.389163	
chunk0028_197_1	chr10	88858767	88859010	+	0	NA	Intergenic	Intergenic	-6913	NM_144590	118932	Hs.217484	NM_144590	ENSG00000152766	ANKRD22	-	ankyrin repeat domain 22	protein-coding	0.004115	0.356557	
chunk0189_400_1	chr8	27543986	27544209	+	0	NA	intron (NM_001256483, intron 16 of 17)	intron (NM_001256483, intron 16 of 17)	52929	NM_001256484	2053	Hs.212088	NM_001979	ENSG00000120915	EPHX2	ABHD20|CEH|SEH	epoxide hydrolase 2	protein-coding	0.013453	0.526786	
chunk0006_235_1	chr1	68851611	68852408	+	0	NA	Intergenic	L1PB3|LINE|L1	-354788	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.001255	0.363409	
chunk0037_296_1	chr11	76235775	76235974	+	0	NA	Intergenic	CpG	-29344	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.075377	0.530000	
chunk0015_43_1	chr1	184503831	184504439	+	0	NA	intron (NM_030806, intron 2 of 5)	intron (NM_030806, intron 2 of 5)	117119	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.016447	0.436782	107(AGAAACAGACTGTACC,-,0.00),108(GAAACAGACTGTACCC,+,0.00)
chunk0129_365_1	chr3	125359536	125360314	+	0	NA	intron (NM_021964, intron 1 of 8)	intron (NM_021964, intron 1 of 8)	15429	NM_021964	7707	Hs.592591	NM_021964	ENSG00000163848	ZNF148	BERF-1|BFCOL1|GDACCF|HT-BETA|ZBP-89|ZFP148|pHZ-52	zinc finger protein 148	protein-coding	0.012853	0.445443	
chunk0002_106_1	chr1	15626072	15626520	+	0	NA	intron (NM_032341, intron 1 of 9)	L2a|LINE|L2	8838	NM_032341	84301	Hs.718857	NM_032341	ENSG00000197312	DDI2	-	DNA damage inducible 1 homolog 2	protein-coding	0.008929	0.367483	
chunk0116_165_1	chr21	36691208	36691407	+	0	NA	Intergenic	Intergenic	-7826	NM_005069	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.020101	0.390000	
chunk0127_291_1	chr3	97940233	97940566	+	0	NA	intron (NM_153605, intron 19 of 21)	MIRb|SINE|MIR	32052	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.006006	0.371257	
chunk0090_201_1	chr18	73189651	73190247	+	0	NA	intron (NR_034133, intron 3 of 5)	MER110A|LTR|ERV1	74549	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.006711	0.381910	
chunk0157_311_1	chr5	121736800	121737518	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-114796	NM_177478	94033	Hs.105324	NM_177478	ENSG00000181867	FTMT	MTF	ferritin mitochondrial	protein-coding	0.006964	0.369958	
chunk0203_232_1	chr9	87062872	87063161	+	0	NA	Intergenic	Intergenic	-20890	NR_027471	440173	Hs.127361	NR_027471	ENSG00000269994	LOC440173	-	uncharacterized LOC440173	ncRNA	0.000000	0.351724	212(AAGTACAGTCTGTTCT,-,0.00),213(AGTACAGTCTGTTCTC,+,0.00)
chunk0032_229_1	chr11	7597648	7597977	+	0	NA	intron (NM_003621, intron 5 of 23)	intron (NM_003621, intron 5 of 23)	626	NM_001256568	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.024316	0.584848	
chunk0155_172_1	chr5	94376754	94377482	+	0	NA	intron (NM_001145678, intron 20 of 20)	intron (NM_001145678, intron 20 of 20)	241486	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.005495	0.401920	
chunk0117_187_1	chr22	21457212	21457411	+	0	NA	Intergenic	Intergenic	-9859	NM_001207052	645426	Hs.376511	NM_001207052	ENSG00000206140	TMEM191C	-	transmembrane protein 191C	protein-coding	0.010050	0.475000	
chunk0058_445_1	chr13	113733502	113734027	+	0	NA	intron (NM_002929, intron 6 of 6)	intron (NM_002929, intron 6 of 6)	17325	NR_028064	100130386	Hs.704121	NM_001137672	ENSG00000279770	LINC00552	-	long intergenic non-protein coding RNA 552	ncRNA	0.072381	0.528517	
chunk0133_459_1	chr3	175248726	175249388	+	0	NA	intron (NR_046713, intron 1 of 2)	intron (NR_046713, intron 1 of 2)	22039	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.003021	0.262443	
chunk0093_418_1	chr19	57492210	57492451	+	0	NA	intron (NM_001291745, intron 3 of 3)	intron (NM_001291745, intron 3 of 3)	4619	NM_001098494	79744	Hs.744339	NM_024691	ENSG00000105136	ZNF419	ZAPHIR|ZNF419A	zinc finger protein 419	protein-coding	0.004149	0.471074	
chunk0030_242_1	chr10	115095811	115096597	+	0	NA	intron (NM_207303, intron 1 of 28)	intron (NM_207303, intron 1 of 28)	2839	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.003817	0.332910	388(TAGGACTCATTGTACT,-,0.00),389(AGGACTCATTGTACTC,+,0.00)
chunk0194_136_1	chr8	84335776	84336279	+	0	NA	intron (NM_001100391, intron 1 of 8)	intron (NM_001100391, intron 1 of 8)	151162	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005964	0.378968	
chunk0171_23_1	chr6	120221389	120222036	+	0	NA	Intergenic	Intergenic	206533	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.004637	0.322531	
chunk0032_308_1	chr11	9874848	9875402	+	0	NA	intron (NM_030962, intron 17 of 39)	intron (NM_030962, intron 17 of 39)	35983	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.001805	0.351351	
chunk0133_204_1	chr3	170867347	170868054	+	0	NA	intron (NM_001099645, intron 3 of 3)	intron (NM_001099645, intron 3 of 3)	2556	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.001414	0.357345	
chunk0147_341_1	chr4	185541081	185541677	+	0	NA	Intergenic	(GCCA)n|Simple_repeat|Simple_repeat	-5821	NM_001114107	27295	Hs.701364	NM_014476	ENSG00000154553	PDLIM3	ALP	PDZ and LIM domain 3	protein-coding	0.018456	0.484087	
chunk0132_212_1	chr3	157540448	157541198	+	0	NA	Intergenic	Intergenic	-2521	NM_001099777	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.005333	0.410120	
chunk0096_7_1	chr2	25842176	25842492	+	0	NA	intron (NM_018263, intron 2 of 11)	intron (NM_018263, intron 2 of 11)	36109	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.003165	0.347003	
chunk0018_281_1	chr1	220619690	220620066	+	0	NA	intron (NM_001286128, intron 8 of 15)	intron (NM_001286128, intron 8 of 15)	-70408	NM_024709	79762	Hs.519839	NM_024709	ENSG00000162817	C1orf115	-	chromosome 1 open reading frame 115	protein-coding	0.000000	0.342175	
chunk0108_52_1	chr2	227036577	227036904	+	0	NA	intron (NM_000092, intron 37 of 47)	intron (NM_000092, intron 37 of 47)	127819	NM_000092	1286	Hs.591645	NM_000092	ENSG00000081052	COL4A4	ATS2|BFH|CA44	collagen type IV alpha 4 chain	protein-coding	0.009174	0.429878	
chunk0149_397_1	chr5	28862706	28863201	+	0	NA	Intergenic	Intergenic	-63917	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.014141	0.372984	
chunk0100_143_1	chr2	108892157	108892548	+	0	NA	Intergenic	L1MA4A|LINE|L1	97020	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.000000	0.548469	
chunk0208_47_1	chrX	11447469	11447989	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-19944	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.003846	0.349328	
chunk0002_113_1	chr1	16013682	16014069	+	0	NA	TTS (NM_014424)	TTS (NM_014424)	4915	NM_014424	27129	Hs.502612	NM_014424	ENSG00000173641	HSPB7	cvHSP	heat shock protein family B (small) member 7	protein-coding	0.023256	0.536082	
chunk0137_230_1	chr4	20168411	20168735	+	0	NA	Intergenic	Intergenic	-83332	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.000000	0.301538	
chunk0168_233_1	chr6	87558560	87559009	+	0	NA	intron (NM_020320, intron 4 of 19)	Tigger3b|DNA|TcMar-Tigger	31233	NM_020320	57038	Hs.485910	NM_020320	ENSG00000146282	RARS2	ArgRS|DALRD2|PCH6|PRO1992|RARSL	arginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.000000	0.368889	
chunk0035_154_1	chr11	43358691	43359052	+	0	NA	promoter-TSS (NM_001307943)	promoter-TSS (NM_001307943)	-14	NM_001307943	55761	Hs.191186	NM_018259	ENSG00000052841	TTC17	-	tetratricopeptide repeat domain 17	protein-coding	0.085873	0.646409	
chunk0136_361_1	chr3	196012529	196012758	+	0	NA	Intergenic	L1MEf|LINE|L1	-22364	NR_003264	255812	Hs.566872	NR_003264	ENSG00000185485	SDHAP1	SDHAL1|SDHALP1	succinate dehydrogenase complex flavoprotein subunit A pseudogene 1	pseudo	0.017467	0.386957	
chunk0172_296_1	chr6	137942544	137943087	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-74582	NR_049793	100130476	Hs.598050	NR_049793	ENSG00000237499	WAKMAR2	lnc-TNFAIP3	wound and keratinocyte migration associated lncRNA 2	ncRNA	0.001842	0.415441	
chunk0153_181_1	chr5	71588393	71588687	+	0	NA	intron (NM_022132, intron 1 of 16)	intron (NM_022132, intron 1 of 16)	1252	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.010204	0.379661	
chunk0030_320_1	chr10	118063768	118064300	+	0	NA	intron (NR_026940, intron 3 of 3)	intron (NR_026940, intron 3 of 3)	17213	NR_026941	255082	Hs.89387	NM_178816	ENSG00000177640	CASC2	C10orf5	cancer susceptibility 2	ncRNA	0.003759	0.311445	
chunk0179_100_1	chr7	44776317	44776703	+	0	NA	Intergenic	Intergenic	-20126	NM_021130	5478	Hs.356331	NM_021130	ENSG00000196262	PPIA	CYPA|CYPH|HEL-S-69p	peptidylprolyl isomerase A	protein-coding	0.010363	0.459948	
chunk0019_166_1	chr1	226083525	226083865	+	0	NA	Intergenic	CpG	20968	NR_002315	440926	Hs.533624	NR_002315		H3F3AP4	p13	H3 histone, family 3A, pseudogene 4	pseudo	0.102941	0.765396	
chunk0105_21_1	chr2	182049987	182050238	+	0	NA	intron (NM_001080545, intron 2 of 4)	intron (NM_001080545, intron 2 of 4)	64288	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.003984	0.341270	
chunk0200_189_1	chr9	19598730	19599140	+	0	NA	intron (NM_020344, intron 3 of 9)	intron (NM_020344, intron 3 of 9)	188084	NM_020344	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.004878	0.362530	
chunk0026_377_1	chr10	69385830	69386495	+	0	NA	intron (NM_033497, intron 15 of 20)	intron (NM_033497, intron 15 of 20)	30756	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.013534	0.427928	
chunk0114_304_1	chr21	17053300	17053761	+	0	NA	Intergenic	Intergenic	-385360	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.015184	0.370130	191(ATGACAGGATGTTCCG,+,0.00)
chunk0066_382_1	chr15	38885397	38885862	+	0	NA	Intergenic	Intergenic	189031	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.008602	0.384120	
chunk0048_165_1	chr12	80793328	80793887	+	0	NA	Intergenic	L2b|LINE|L2	30453	NR_120470	101928420	Hs.739989	NR_120468	ENSG00000257741	LINC01490	-	long intergenic non-protein coding RNA 1490	ncRNA	0.001789	0.337500	
chunk0196_278_1	chr8	109276950	109277304	+	0	NA	intron (NM_001128211, intron 6 of 9)	MIR|SINE|MIR	52806	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.002825	0.332394	
chunk0122_133_1	chr3	31693431	31693700	+	0	NA	intron (NM_017784, intron 7 of 11)	intron (NM_017784, intron 7 of 11)	-10648	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.011152	0.388889	
chunk0185_159_1	chr7	127741252	127741665	+	0	NA	intron (NM_014390, intron 10 of 23)	MER5B|DNA|hAT-Charlie	89310	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.007264	0.403382	
chunk0013_346_1	chr1	172164094	172164318	+	0	NA	intron (NM_001136127, intron 14 of 19)	(TTTTCT)n|Simple_repeat|Simple_repeat	-19371	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.004464	0.320000	
chunk0059_396_1	chr14	37546830	37547431	+	0	NA	3' UTR (NM_138731, exon 14 of 14)	3' UTR (NM_138731, exon 14 of 14)	47990	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.006656	0.368771	
chunk0029_216_1	chr10	102247500	102248161	+	0	NA	intron (NM_001199378, intron 1 of 39)	intron (NM_001199378, intron 1 of 39)	2332	NM_001199379	8729	Hs.290243	NM_004193	ENSG00000107862	GBF1	ARF1GEF	golgi brefeldin A resistant guanine nucleotide exchange factor 1	protein-coding	0.001513	0.410876	
chunk0031_145_1	chr10	125029599	125030255	+	0	NA	intron (NM_001290215, intron 3 of 10)	intron (NM_001290215, intron 3 of 10)	-2043	NM_022802	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.010671	0.461187	
chunk0005_194_1	chr1	58976293	58976723	+	0	NA	Intergenic	Intergenic	-43968	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.002326	0.399072	183(AGGTACACCATGTACA,-,0.00),184(GGTACACCATGTACAG,+,0.00)
chunk0158_175_1	chr5	127731149	127731348	+	0	NA	Intergenic	L1PA10|LINE|L1	78233	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.005025	0.375000	
chunk0035_58_1	chr11	41418261	41418685	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	41163	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.011792	0.390588	208(AGGGTCACTATGTTCT,-,0.00),209(GGGTCACTATGTTCTG,+,0.00)
chunk0049_239_1	chr12	93524502	93524798	+	0	NA	Intergenic	L2b|LINE|L2	-45172	NM_003877	8835	Hs.485572	NM_003877	ENSG00000120833	SOCS2	CIS2|Cish2|SOCS-2|SSI-2|SSI2|STATI2	suppressor of cytokine signaling 2	protein-coding	0.013514	0.437710	
chunk0139_211_1	chr4	54967271	54967569	+	0	NA	Intergenic	Intergenic	158175	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.006711	0.421405	191(TTGAACATTTTGTTCC,-,0.00),192(TGAACATTTTGTTCCT,+,0.00)
chunk0025_23_1	chr10	48287679	48288059	+	0	NA	Intergenic	Intergenic	-12971	NM_001018071	143162	Hs.664786	NM_152428	ENSG00000170324	FRMPD2	PDZD5C|PDZK4|PDZK5C	FERM and PDZ domain containing 2	protein-coding	0.007895	0.556430	251(AAGGACAGGGAGTCCA,-,0.00),252(AGGACAGGGAGTCCAG,+,0.00)
chunk0097_140_1	chr2	47445153	47445699	+	0	NA	intron (NM_001258281, intron 8 of 16)	intron (NM_001258281, intron 8 of 16)	42359	NM_000251	4436	Hs.597656	NM_000251	ENSG00000095002	MSH2	COCA1|FCC1|HNPCC|HNPCC1|LCFS2|hMSH2	mutS homolog 2	protein-coding	0.005495	0.297989	
chunk0055_442_1	chr13	75640537	75641340	+	0	NA	intron (NM_001306080, intron 1 of 30)	intron (NM_001306080, intron 1 of 30)	4650	NM_001306080	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.011208	0.439055	
chunk0205_251_1	chr9	110631504	110631711	+	0	NA	Intergenic	L1M5|LINE|L1	-37164	NM_001166280	4593	Hs.521653	NM_005592	ENSG00000030304	MUSK	CMS9|FADS|FADS1	muscle associated receptor tyrosine kinase	protein-coding	0.000000	0.298077	
chunk0190_132_1	chr8	30675582	30676151	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	-17645	NM_002095	2961	Hs.77100	NM_002095	ENSG00000197265	GTF2E2	FE|TF2E2|TFIIE-B|TTD6	general transcription factor IIE subunit 2	protein-coding	0.003515	0.405263	
chunk0050_109_1	chr12	101995621	101996132	+	0	NA	Intergenic	L2c|LINE|L2	66248	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.007828	0.384766	
chunk0015_60_1	chr1	184622100	184622849	+	0	NA	3' UTR (NM_030806, exon 6 of 6)	3' UTR (NM_030806, exon 6 of 6)	132433	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.013351	0.496000	
chunk0045_162_1	chr12	46784793	46785217	+	0	NA	intron (NM_018018, intron 6 of 16)	intron (NM_018018, intron 6 of 16)	40992	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.002358	0.352941	
chunk0119_447_1	chr22	50213204	50213748	+	0	NA	intron (NM_031454, intron 5 of 8)	L1MB3|LINE|L1	12497	NM_031454	83642	Hs.365405	NM_031454	ENSG00000073169	SELENOO	SELO	selenoprotein O	protein-coding	0.022059	0.511927	
chunk0083_328_1	chr17	69960788	69960995	+	0	NA	promoter-TSS (NR_110875)	promoter-TSS (NR_110875)	-816	NR_110874	102723487	Hs.451409	NR_110874	ENSG00000237560	LINC01497	-	long intergenic non-protein coding RNA 1497	ncRNA	0.000000	0.519231	
chunk0182_224_1	chr7	96439797	96440295	+	0	NA	Intergenic	L2c|LINE|L2	63477	NM_001201451	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.004016	0.384770	
chunk0136_438_1	chr3	197823604	197824164	+	0	NA	intron (NM_032773, intron 4 of 18)	HAL1|LINE|L1	32658	NM_032773	84859	Hs.518414	NM_032773	ENSG00000186001	LRCH3	-	leucine rich repeats and calponin homology domain containing 3	protein-coding	0.005357	0.438503	
chunk0056_224_1	chr13	88548542	88548741	+	0	NA	Intergenic	Intergenic	7812	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.000000	0.250000	
chunk0064_292_1	chr14	95304417	95304905	+	0	NA	intron (NM_024734, intron 1 of 12)	HAL1|LINE|L1	15247	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.008197	0.501022	
chunk0124_241_1	chr3	56764944	56765349	+	0	NA	intron (NM_001128615, intron 5 of 12)	intron (NM_001128615, intron 5 of 12)	10571	NM_001128616	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.014815	0.455665	
chunk0011_404_1	chr1	154199448	154199913	+	0	NA	intron (NM_001010979, intron 3 of 3)	intron (NM_001010979, intron 3 of 3)	-5937	NR_030600	100126346		NR_030600	ENSG00000215938	MIR190B	MIRN190B|mir-190b	microRNA 190b	ncRNA	0.010753	0.459227	
chunk0083_209_1	chr17	66952198	66952397	+	0	NA	Intergenic	Intergenic	-12567	NM_014405	27092	Hs.514423	NM_014405	ENSG00000075461	CACNG4	-	calcium voltage-gated channel auxiliary subunit gamma 4	protein-coding	0.035176	0.550000	
chunk0083_454_1	chr17	73203443	73203912	+	0	NA	exon (NM_018714, exon 9 of 14)	exon (NM_018714, exon 9 of 14)	10643	NM_018714	9382	Hs.103555	NM_018714	ENSG00000166685	COG1	CDG2G|LDLB	component of oligomeric golgi complex 1	protein-coding	0.008529	0.431915	
chunk0013_275_1	chr1	170231655	170232291	+	0	NA	Intergenic	Intergenic	52235	NR_026957	284688	Hs.135668	NR_026957	ENSG00000224286	LINC01142	-	long intergenic non-protein coding RNA 1142	ncRNA	0.003145	0.392465	
chunk0011_259_1	chr1	150922426	150922701	+	0	NA	Intergenic	L1ME3G|LINE|L1	-3776	NM_001243491	9869	Hs.643565	NM_012432	ENSG00000143379	SETDB1	ESET|H3-K9-HMTase4|KG1T|KMT1E|TDRD21	SET domain bifurcated histone lysine methyltransferase 1	protein-coding	0.007273	0.438406	
chunk0101_377_1	chr2	138491213	138491412	+	0	NA	Intergenic	Intergenic	-10468	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.000000	0.355000	
chunk0166_427_1	chr6	52660885	52661452	+	0	NA	Intergenic	Intergenic	-3233	NR_024405	730101	Hs.7921	NR_024403	ENSG00000216775	LOC730101	-	uncharacterized LOC730101	ncRNA	0.000000	0.350352	
chunk0042_127_1	chr12	3484390	3484667	+	0	NA	non-coding (NR_126055, exon 2 of 2)	non-coding (NR_126055, exon 2 of 2)	-6670	NM_019854	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.010830	0.460432	
chunk0073_47_1	chr16	2973219	2973526	+	0	NA	3' UTR (NM_152341, exon 3 of 3)	3' UTR (NM_152341, exon 3 of 3)	4030	NM_001284513	124222	Hs.351474	NM_152341	ENSG00000162073	PAQR4	-	progestin and adipoQ receptor family member 4	protein-coding	0.013029	0.535714	
chunk0033_235_1	chr11	17813726	17814014	+	0	NA	intron (NM_012139, intron 10 of 10)	intron (NM_012139, intron 10 of 10)	77922	NM_004976	3746	Hs.552896	NM_004976	ENSG00000129159	KCNC1	EPM7|KV3.1|KV4|NGK2	potassium voltage-gated channel subfamily C member 1	protein-coding	0.006944	0.456747	
chunk0020_201_1	chr1	234961728	234962225	+	0	NA	intron (NR_125945, intron 1 of 3)	intron (NR_125945, intron 1 of 3)	2023	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.012072	0.495984	
chunk0199_365_1	chr9	12793955	12794638	+	0	NA	intron (NR_125775, intron 1 of 3)	intron (NR_125775, intron 1 of 3)	19283	NM_203403	286343	Hs.445356	NM_203403	ENSG00000153714	LURAP1L	C9orf150|HYST0841|LRAP35b|bA3L8.2	leucine rich adaptor protein 1 like	protein-coding	0.004392	0.331871	
chunk0160_157_1	chr5	151759686	151759885	+	0	NA	Intergenic	Intergenic	-1136	NM_004045	475	Hs.125213	NM_004045	ENSG00000177556	ATOX1	ATX1|HAH1	antioxidant 1 copper chaperone	protein-coding	0.015075	0.560000	
chunk0069_96_1	chr15	61353217	61353735	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-124173	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.009653	0.450867	
chunk0211_314_1	chrX	123672537	123673165	+	0	NA	intron (NM_001081550, intron 8 of 38)	intron (NM_001081550, intron 8 of 38)	60203	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.006369	0.359300	310(CAATACACTATGTTCT,-,0.00),311(AATACACTATGTTCTT,+,0.00)
chunk0177_243_1	chr7	24953623	24953933	+	0	NA	intron (NM_015550, intron 1 of 22)	intron (NM_015550, intron 1 of 22)	26434	NM_015550	26031	Hs.520259	NM_015550	ENSG00000070882	OSBPL3	ORP-3|ORP3|OSBP3	oxysterol binding protein like 3	protein-coding	0.006452	0.398714	
chunk0104_147_1	chr2	173760776	173761034	+	0	NA	Intergenic	Intergenic	203314	NM_001017371	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.000000	0.277992	
chunk0151_379_1	chr5	55211214	55211476	+	0	NA	Intergenic	Intergenic	15970	NM_001190787	345643	Hs.394578	NM_001190787	ENSG00000234602	MCIDAS	IDAS|MCI|MCIN	multiciliate differentiation and DNA synthesis associated cell cycle protein	protein-coding	0.000000	0.296578	
chunk0045_173_1	chr12	46892781	46893265	+	0	NA	Intergenic	Intergenic	-67026	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.008264	0.352577	
chunk0045_407_1	chr12	52915610	52916161	+	0	NA	intron (NM_001256293, intron 1 of 8)	intron (NM_001256293, intron 1 of 8)	10584	NM_001256282	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.012704	0.447464	
chunk0185_336_1	chr7	132007496	132007791	+	0	NA	Intergenic	L1ME2|LINE|L1	97423	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.006780	0.368243	49(CAGCACAATTTGTTCA,-,0.00),50(AGCACAATTTGTTCAA,+,0.00),143(TTGAACTTTCTGTTCT,-,0.00),144(TGAACTTTCTGTTCTA,+,0.00)
chunk0023_168_1	chr10	24408406	24408918	+	0	NA	intron (NM_019590, intron 3 of 20)	L2a|LINE|L2	-40771	NM_001282769	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.005859	0.438596	253(TGTACTTTCTGTTCTT,+,0.00)
chunk0199_247_1	chr9	5627211	5627415	+	0	NA	Intergenic	Intergenic	-1806	NM_001206557	57589	Hs.211520	NM_020829	ENSG00000107036	RIC1	CIP150|KIAA1432|bA207C16.1	RIC1 homolog, RAB6A GEF complex partner 1	protein-coding	0.000000	0.400000	
chunk0149_64_1	chr5	17060686	17060956	+	0	NA	Intergenic	Intergenic	-124545	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.014815	0.394834	
chunk0072_157_1	chr15	92882655	92882854	+	0	NA	promoter-TSS (NR_037600)	promoter-TSS (NR_037600)	-89	NR_037600	100507217	Hs.622504	NR_037600		LINC01578	-	long intergenic non-protein coding RNA 1578	ncRNA	0.090452	0.715000	
chunk0179_36_1	chr7	43209895	43210340	+	0	NA	intron (NM_015052, intron 2 of 29)	intron (NM_015052, intron 2 of 29)	59222	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.011236	0.500000	
chunk0089_94_1	chr18	58360218	58360738	+	0	NA	intron (NM_001144970, intron 17 of 28)	L1MEd|LINE|L1	-90596	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.005769	0.310940	
chunk0212_435_1	chrX	154046587	154047434	+	0	NA	intron (NM_001110792, intron 1 of 2)	HAL1b|LINE|L1	-27021	NR_031757	100313781		NR_031757	ENSG00000284286	MIR718	hsa-mir-718	microRNA 718	ncRNA	0.010626	0.412736	707(GAATACACCATGTTCC,-,0.00),708(AATACACCATGTTCCC,+,0.00)
chunk0189_31_1	chr8	19726572	19727112	+	0	NA	Intergenic	Intergenic	-44092	NR_024040	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.003704	0.390018	
chunk0091_204_1	chr19	9270082	9270352	+	0	NA	Intergenic	Intergenic	19173	NM_001079935	26648	Hs.129832	NM_001079935	ENSG00000237521	OR7E24	HSHT2|OR19-8|OR7E24P|OR7E24Q	olfactory receptor family 7 subfamily E member 24	protein-coding	0.014815	0.446494	
chunk0070_398_1	chr15	77107840	77108573	+	0	NA	TTS (NM_024776)	TTS (NM_024776)	-36978	NM_005724	10099	Hs.744863	NM_005724	ENSG00000140391	TSPAN3	TM4-A|TM4SF8|TSPAN-3	tetraspanin 3	protein-coding	0.005457	0.446866	
chunk0014_335_1	chr1	182173718	182174570	+	0	NA	Intergenic	Intergenic	-112432	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.007042	0.436108	363(AGGAACAGTCTGTTCA,-,0.00),364(GGAACAGTCTGTTCAT,+,0.00)
chunk0024_190_1	chr10	36165926	36166375	+	0	NA	Intergenic	Kanga1a|DNA|TcMar-Tc2	387848	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.000000	0.326667	
chunk0091_459_1	chr19	18031270	18031893	+	0	NA	Intergenic	Intergenic	23413	NM_015683	27106	Hs.515249	NM_015683	ENSG00000105643	ARRDC2	CLONE24945|PP2703	arrestin domain containing 2	protein-coding	0.009631	0.498397	371(CAGGACGGGCTGTTCC,-,0.00),372(AGGACGGGCTGTTCCA,+,0.00)
chunk0167_213_1	chr6	66189916	66190264	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	402211	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.008621	0.358166	
chunk0138_210_1	chr4	38828001	38828527	+	0	NA	exon (NM_006068, exon 2 of 2)	exon (NM_006068, exon 2 of 2)	-23473	NM_003263	7096	Hs.621817	NM_003263	ENSG00000174125	TLR1	CD281|TIL|TIL. LPRS5|rsc786	toll like receptor 1	protein-coding	0.011407	0.360531	
chunk0168_364_1	chr6	93418883	93419578	+	0	NA	intron (NM_004440, intron 1 of 16)	CpG	352	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.074820	0.581897	
chunk0176_21_1	chr7	8365409	8365936	+	0	NA	Intergenic	Intergenic	-68283	NM_152745	30010	Hs.487564	NM_152745	ENSG00000122584	NXPH1	NPH1|Nbla00697	neurexophilin 1	protein-coding	0.003795	0.420455	
chunk0004_103_1	chr1	44118162	44118494	+	0	NA	promoter-TSS (NM_173484)	promoter-TSS (NM_173484)	-522	NM_173484	128209	Hs.567674	NM_173484	ENSG00000171872	KLF17	ZNF393|Zfp393	Kruppel like factor 17	protein-coding	0.018072	0.465465	
chunk0117_270_1	chr22	24042957	24043292	+	0	NA	intron (NM_012295, intron 6 of 36)	intron (NM_012295, intron 6 of 36)	31754	NM_001199281	23523	Hs.517478	NM_012295	ENSG00000099991	CABIN1	CAIN|KB-318B8.7|PPP3IN	calcineurin binding protein 1	protein-coding	0.008955	0.464286	
chunk0199_42_1	chr9	1232283	1232744	+	0	NA	Intergenic	Intergenic	181893	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.017354	0.448052	
chunk0155_406_1	chr5	99145055	99145583	+	0	NA	Intergenic	L1MC3|LINE|L1	216185	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.000000	0.351607	
chunk0202_366_1	chr9	80391963	80392314	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	417115	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.002849	0.357955	
chunk0186_26_1	chr7	135931112	135931454	+	0	NA	intron (NM_001128619, intron 3 of 3)	L2c|LINE|L2	46173	NM_145808	136319	Hs.602015	NM_145808	ENSG00000105887	MTPN	GCDP|V-1	myotrophin	protein-coding	0.008772	0.443149	
chunk0130_38_1	chr3	129161073	129161440	+	0	NA	promoter-TSS (NM_020701)	promoter-TSS (NM_020701)	-26	NM_001199469	57461	Hs.512661	NM_020701	ENSG00000240682	ISY1	FSAP33	ISY1 splicing factor homolog	protein-coding	0.065395	0.529891	
chunk0155_163_1	chr5	94240752	94241322	+	0	NA	intron (NM_001145678, intron 20 of 20)	intron (NM_001145678, intron 20 of 20)	-129338	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.007018	0.385289	
chunk0052_26_1	chr13	20497439	20497638	+	0	NA	intron (NM_015974, intron 2 of 7)	(CA)n|Simple_repeat|Simple_repeat	28335	NM_015974	51084	Hs.370703	NM_015974	ENSG00000165475	CRYL1	GDH|HEL30|gul3DH|lambda-CRY	crystallin lambda 1	protein-coding	0.005025	0.450000	
chunk0149_455_1	chr5	30001818	30002325	+	0	NA	Intergenic	L1MCa|LINE|L1	-606095	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.003945	0.307087	
chunk0029_348_1	chr10	106917726	106917953	+	0	NA	intron (NM_052918, intron 2 of 25)	intron (NM_052918, intron 2 of 25)	246869	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.004405	0.403509	
chunk0027_52_1	chr10	72816527	72817159	+	0	NA	intron (NR_073062, intron 3 of 9)	intron (NR_073062, intron 3 of 9)	-76713	NR_130125	170392	Hs.8366	NM_152635	ENSG00000138315	OIT3	LZP	oncoprotein induced transcript 3	protein-coding	0.003165	0.385466	
chunk0010_344_1	chr1	118588727	118589070	+	0	NA	Intergenic	L1MA7|LINE|L1	400658	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.000000	0.345930	
chunk0039_137_1	chr11	98509342	98509641	+	0	NA	Intergenic	Intergenic	-511485	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.006689	0.333333	
chunk0016_148_1	chr1	197463283	197463515	+	0	NA	intron (NR_047564, intron 11 of 11)	intron (NR_047564, intron 11 of 11)	195195	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.000000	0.364807	
chunk0181_352_1	chr7	88334196	88334493	+	0	NA	Intergenic	Intergenic	-27431	NM_024636	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.010101	0.352349	
chunk0193_145_1	chr8	74547870	74548454	+	0	NA	promoter-TSS (NR_049860)	promoter-TSS (NR_049860)	-381	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.005137	0.439316	
chunk0166_24_1	chr6	41859222	41859858	+	0	NA	intron (NM_001286554, intron 1 of 5)	L2c|LINE|L2	12097	NM_001286554	25862	Hs.593575	NM_018561	ENSG00000164663	USP49	-	ubiquitin specific peptidase 49	protein-coding	0.011006	0.395604	
chunk0205_323_1	chr9	112814638	112815012	+	0	NA	intron (NM_001012994, intron 2 of 8)	L1ME3Cz|LINE|L1	63971	NM_001012994	401548	Hs.522350	NM_001012994	ENSG00000148158	SNX30	ATG24A	sorting nexin family member 30	protein-coding	0.008021	0.304000	
chunk0090_5_1	chr19	434219	434520	+	0	NA	intron (NM_012435, intron 8 of 12)	intron (NM_012435, intron 8 of 12)	-25199	NM_001136263	126567	Hs.223770	NM_001136263	ENSG00000183186	C2CD4C	FAM148C|KIAA1957|NLF3	C2 calcium dependent domain containing 4C	protein-coding	0.016611	0.456954	
chunk0179_425_1	chr7	51915763	51916428	+	0	NA	Intergenic	Intergenic	-599277	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.004511	0.367868	
chunk0196_215_1	chr8	106980590	106980949	+	0	NA	Intergenic	Intergenic	-210525	NM_139166	137735	Hs.374668	NM_139166	ENSG00000174429	ABRA	STARS	actin binding Rho activating protein	protein-coding	0.002786	0.338889	
chunk0163_11_1	chr6	7780905	7781530	+	0	NA	intron (NM_001718, intron 1 of 6)	MIRc|SINE|MIR	54439	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.011200	0.445687	
chunk0151_79_1	chr5	42763030	42763472	+	0	NA	intron (NM_001134848, intron 3 of 8)	L1MC3|LINE|L1	6433	NM_001134848	100129792	Hs.745017	NM_001134848	ENSG00000198865	CCDC152	CH5400	coiled-coil domain containing 152	protein-coding	0.011312	0.374718	
chunk0188_344_1	chr8	17801471	17801693	+	0	NA	promoter-TSS (NM_001001925)	promoter-TSS (NM_001001925)	-665	NM_001001924	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.166667	0.775785	
chunk0034_318_1	chr11	35179504	35179866	+	0	NA	intron (NM_001001392, intron 2 of 3)	intron (NM_001001392, intron 2 of 3)	40815	NM_001202557	960	Hs.502328	NM_000610	ENSG00000026508	CD44	CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1	CD44 molecule (Indian blood group)	protein-coding	0.002762	0.468320	
chunk0194_359_1	chr8	89666848	89667047	+	0	NA	Intergenic	MIR3|SINE|MIR	90764	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.000000	0.395000	
chunk0132_207_1	chr3	157369931	157370358	+	0	NA	intron (NM_001167911, intron 7 of 12)	intron (NM_001167911, intron 7 of 12)	-66647	NM_002852	5806	Hs.591286	NM_002852	ENSG00000163661	PTX3	TNFAIP5|TSG-14	pentraxin 3	protein-coding	0.007026	0.429907	
chunk0031_289_1	chr10	128422303	128422651	+	0	NA	Intergenic	Intergenic	136527	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.031609	0.478510	
chunk0014_71_1	chr1	176089287	176089668	+	0	NA	intron (NM_001001740, intron 8 of 18)	intron (NM_001001740, intron 8 of 18)	117767	NM_001286644	64326	Hs.523744	NM_022457	ENSG00000143207	COP1	RFWD2|RNF200	COP1 E3 ubiquitin ligase	protein-coding	0.000000	0.316754	
chunk0120_132_1	chr3	4978587	4978873	+	0	NA	promoter-TSS (NM_003670)	promoter-TSS (NM_003670)	-682	NM_003670	8553	Hs.744856	NM_003670	ENSG00000134107	BHLHE40	BHLHB2|Clast5|DEC1|HLHB2|SHARP-2|SHARP2|STRA13|Stra14	basic helix-loop-helix family member e40	protein-coding	0.101399	0.745645	
chunk0157_199_1	chr5	119009134	119009531	+	0	NA	Intergenic	MER92B|LTR|ERV1	-20727	NM_173666	285605	Hs.655891	NM_173666	ENSG00000169570	DTWD2	-	DTW domain containing 2	protein-coding	0.002519	0.419598	
chunk0188_401_1	chr8	18723019	18723355	+	0	NA	intron (NM_015310, intron 9 of 15)	intron (NM_015310, intron 9 of 15)	85708	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.014881	0.418398	
chunk0040_126_1	chr11	112318573	112318772	+	0	NA	intron (NR_126004, intron 2 of 3)	MER89|LTR|ERV1	47923	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.005025	0.475000	
chunk0107_197_1	chr2	216256943	216257437	+	0	NA	TTS (NM_020814)	TTS (NM_020814)	40301	NR_037701	150967	Hs.56876	NM_001199924	ENSG00000260804	LINC01963	PKI55	long intergenic non-protein coding RNA 1963	ncRNA	0.006073	0.428283	
chunk0183_44_1	chr7	103929568	103930281	+	0	NA	intron (NM_005045, intron 1 of 64)	Tigger17a|DNA|TcMar-Tigger	59592	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.005610	0.411765	
chunk0004_116_1	chr1	44606712	44606938	+	0	NA	intron (NM_018150, intron 2 of 14)	L2b|LINE|L2	61332	NR_049849	100847089		NR_049849	ENSG00000263381	MIR5584	-	microRNA 5584	ncRNA	0.008850	0.427313	
chunk0125_3_1	chr3	61650176	61650884	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	88961	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.014124	0.387870	78(GGGGCACCATGTACCT,+,0.00)
chunk0103_438_1	chr2	170003152	170003754	+	0	NA	intron (NM_172070, intron 27 of 38)	intron (NM_172070, intron 27 of 38)	-174692	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.016611	0.396352	
chunk0200_80_1	chr9	16419172	16419586	+	0	NA	exon (NM_017637, exon 7 of 7)	exon (NM_017637, exon 7 of 7)	-143066	NR_073471									0.038647	0.580723	
chunk0174_4_1	chr6	152220178	152220377	+	0	NA	intron (NM_033071, intron 118 of 145)	intron (NM_033071, intron 118 of 145)	-160253	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.005025	0.310000	
chunk0204_234_1	chr9	97757059	97757291	+	0	NA	Intergenic	LTR33|LTR|ERVL	-59766	NM_000380	7507	Hs.654364	NM_000380	ENSG00000136936	XPA	XP1|XPAC	XPA, DNA damage recognition and repair factor	protein-coding	0.000000	0.532189	
chunk0075_235_1	chr16	53022558	53023008	+	0	NA	Intergenic	AluSq|SINE|Alu	-32250	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.022222	0.487805	
chunk0194_241_1	chr8	86370013	86370764	+	0	NA	intron (NM_007013, intron 2 of 24)	intron (NM_007013, intron 2 of 24)	27623	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.001332	0.328457	
chunk0069_37_1	chr15	60508245	60508594	+	0	NA	intron (NM_134260, intron 6 of 11)	MIR3|SINE|MIR	29241	NR_120340	101928784	Hs.655155	NR_120339	ENSG00000245534	RORA-AS1	-	RORA antisense RNA 1	ncRNA	0.008596	0.394286	
chunk0162_156_1	chr6	3438237	3438599	+	0	NA	intron (NM_021945, intron 1 of 10)	intron (NM_021945, intron 1 of 10)	6595	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.033149	0.550964	
chunk0046_456_1	chr12	64942586	64943092	+	0	NA	intron (NR_033988, intron 2 of 2)	intron (NR_033988, intron 2 of 2)	59065	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.005929	0.309665	
chunk0035_47_1	chr11	41160761	41161227	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	298642	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.004292	0.319058	
chunk0189_283_1	chr8	25424006	25424355	+	0	NA	5' UTR (NM_000825, exon 1 of 3)	5' UTR (NM_000825, exon 1 of 3)	860	NM_000825	2796	Hs.82963	NM_000825	ENSG00000147437	GNRH1	GNRH|GRH|LHRH|LNRH	gonadotropin releasing hormone 1	protein-coding	0.008596	0.425714	
chunk0099_216_1	chr2	95552101	95552438	+	0	NA	Intergenic	Intergenic	-39749	NM_138800	129868	Hs.232026	NM_138800	ENSG00000144015	TRIM43	TRIM43A	tripartite motif containing 43	protein-coding	0.002967	0.319527	
chunk0151_260_1	chr5	52448825	52449255	+	0	NA	Intergenic	Intergenic	-338900	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.002326	0.338747	
chunk0126_278_1	chr3	80079758	80080335	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-312137	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.001733	0.387543	
chunk0109_141_1	chr20	3393353	3393940	+	0	NA	intron (NM_001009984, intron 1 of 36)	L1ME3G|LINE|L1	14016	NM_001009984	25943	Hs.516853	NM_001009984	ENSG00000088854	C20orf194	-	chromosome 20 open reading frame 194	protein-coding	0.006814	0.386054	
chunk0015_55_1	chr1	184597684	184598070	+	0	NA	intron (NM_030806, intron 4 of 5)	intron (NM_030806, intron 4 of 5)	157030	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.010363	0.426357	
chunk0192_133_1	chr8	61909762	61909965	+	0	NA	Intergenic	Intergenic	195075	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.000000	0.333333	
chunk0179_97_1	chr7	44680606	44681394	+	0	NA	intron (NM_001165036, intron 9 of 22)	L1MC4|LINE|L1	-67566	NM_001300959	83637	Hs.77978	NM_031449	ENSG00000122515	ZMIZ2	NET27|TRAFIP20|ZIMP7|hZIMP7	zinc finger MIZ-type containing 2	protein-coding	0.006345	0.471483	284(GGAACAGTGTGAGCAT,+,0.00)
chunk0189_125_1	chr8	22311412	22312060	+	0	NA	intron (NM_018068, intron 16 of 22)	intron (NM_018068, intron 16 of 22)	36169	NM_001135721	55124	Hs.614809	NM_018068	ENSG00000197181	PIWIL2	CT80|HILI|PIWIL1L|mili	piwi like RNA-mediated gene silencing 2	protein-coding	0.015432	0.436055	163(TAGAACATGTTGTGCT,-,0.00),164(AGAACATGTTGTGCTC,+,0.00)
chunk0038_6_1	chr11	80772398	80772657	+	0	NA	Intergenic	Intergenic	-9724	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.353846	
chunk0049_298_1	chr12	94257923	94258484	+	0	NA	intron (NM_005761, intron 17 of 30)	intron (NM_005761, intron 17 of 30)	-4318	NR_037687	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.028520	0.414591	
chunk0163_46_1	chr6	8628078	8628456	+	0	NA	intron (NR_038980, intron 3 of 4)	MLT1A|LTR|ERVL-MaLR	-23942	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.000000	0.385224	
chunk0001_215_1	chr1	8017646	8017957	+	0	NA	intron (NM_018948, intron 1 of 3)	intron (NM_018948, intron 1 of 3)	8532	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.009646	0.365385	
chunk0204_372_1	chr9	101980845	101981044	+	0	NA	Intergenic	Intergenic	-242364	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.010050	0.365000	
chunk0074_152_1	chr16	23258278	23258795	+	0	NA	Intergenic	L2c|LINE|L2	-43734	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.017408	0.486486	
chunk0135_14_1	chr3	184248759	184249015	+	0	NA	promoter-TSS (NM_032331)	promoter-TSS (NM_032331)	84	NR_024533	10195	Hs.478481	NM_005787	ENSG00000214160	ALG3	CDG1D|CDGS4|CDGS6|D16Ertd36e|NOT56L|Not56|not	ALG3 alpha-1,3- mannosyltransferase	protein-coding	0.101562	0.692607	
chunk0041_270_1	chr11	129191730	129192059	+	0	NA	intron (NM_001142685, intron 1 of 21)	intron (NM_001142685, intron 1 of 21)	304	NM_001142685	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.009119	0.412121	
chunk0159_61_1	chr5	137283841	137284181	+	0	NA	intron (NM_004598, intron 2 of 10)	MIRb|SINE|MIR	215318	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.002941	0.457478	
chunk0050_88_1	chr12	101768195	101768540	+	0	NA	intron (NM_024312, intron 10 of 20)	intron (NM_024312, intron 10 of 20)	-28895	NM_153694	50511	Hs.506504	NM_153694	ENSG00000139351	SYCP3	COR1|RPRGL4|SCP3|SPGF4	synaptonemal complex protein 3	protein-coding	0.011594	0.381503	
chunk0200_376_1	chr9	26408415	26408816	+	0	NA	Intergenic	L2c|LINE|L2	341940	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.000000	0.442786	
chunk0200_367_1	chr9	25751210	25751686	+	0	NA	Intergenic	Intergenic	-28608	NR_121604	101929582	Hs.140547	NR_121604	ENSG00000236306	LINC01241	-	long intergenic non-protein coding RNA 1241	ncRNA	0.006303	0.364780	
chunk0083_17_1	chr17	63005041	63005515	+	0	NA	Intergenic	L1ME2z|LINE|L1	-4259	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.002110	0.305263	227(CTGGACTGTCTGTTCT,-,0.00),228(TGGACTGTCTGTTCTA,+,0.00)
chunk0078_232_1	chr17	6603445	6604150	+	0	NA	intron (NM_014804, intron 12 of 18)	L1MDa|LINE|L1	-37105	NM_032731	84817	Hs.408236	NM_032731	ENSG00000129235	TXNDC17	TRP14|TXNL5	thioredoxin domain containing 17	protein-coding	0.007092	0.437677	208(CAGAGCAGTGAGTTCT,-,0.00),209(AGAGCAGTGAGTTCTT,+,0.00),594(GGGAACAGACAGAGCC,-,0.00)
chunk0096_377_1	chr2	36891470	36891879	+	0	NA	intron (NM_003162, intron 7 of 17)	intron (NM_003162, intron 7 of 17)	74798	NM_003162	6801	Hs.127486	NM_003162	ENSG00000115808	STRN	PPP2R6A|SG2NA|STRN1	striatin	protein-coding	0.002445	0.343902	
chunk0096_366_1	chr2	36505734	36506139	+	0	NA	intron (NM_016441, intron 8 of 16)	MER6|DNA|TcMar-Tigger	92253	NM_005102	9637	Hs.258563	NM_005102	ENSG00000171055	FEZ2	HUM3CL	fasciculation and elongation protein zeta 2	protein-coding	0.009877	0.423645	
chunk0050_27_1	chr12	99957565	99958290	+	0	NA	intron (NM_152788, intron 1 of 25)	L2c|LINE|L2	26727	NM_152788	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.005517	0.411846	
chunk0176_383_1	chr7	18667363	18667955	+	0	NA	3' UTR (NM_014707, exon 12 of 12)	3' UTR (NM_014707, exon 12 of 12)	158382	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.005068	0.338954	
chunk0150_127_1	chr5	33236217	33236837	+	0	NA	Intergenic	Intergenic	-204169	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.001613	0.312399	
chunk0144_119_1	chr4	128835582	128835828	+	0	NA	intron (NM_024900, intron 2 of 8)	intron (NM_024900, intron 2 of 8)	23861	NM_001287443	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.012195	0.570850	127(GTGCACACCATGTCCA,-,0.00)
chunk0093_92_1	chr19	42208513	42209001	+	0	NA	intron (NR_073046, intron 3 of 4)	intron (NR_073046, intron 3 of 4)	9035	NR_073052	162989	Hs.515432	NM_133328	ENSG00000160570	DEDD2	FLAME-3|FLAME3	death effector domain containing 2	protein-coding	0.024590	0.543967	
chunk0038_251_1	chr11	87628316	87628541	+	0	NA	Intergenic	Intergenic	547039	NM_022337	23682	Hs.591975	NM_022337	ENSG00000123892	RAB38	NY-MEL-1|rrGTPbp	RAB38, member RAS oncogene family	protein-coding	0.013333	0.477876	55(AAGTACATGCTGTGCC,-,0.00),56(AGTACATGCTGTGCCT,+,0.00)
chunk0163_325_1	chr6	14927365	14927743	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-318421	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.013228	0.469657	237(AAGGACAAAGAGTGCC,-,0.00),238(AGGACAAAGAGTGCCA,+,0.00)
chunk0106_459_1	chr2	209416873	209417316	+	0	NA	Intergenic	L1MC2|LINE|L1	-6953	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.000000	0.340090	
chunk0181_284_1	chr7	86867020	86867667	+	0	NA	Intergenic	L1MA7|LINE|L1	98632	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.006182	0.427469	
chunk0102_142_1	chr2	146247112	146247764	+	0	NA	Intergenic	HAL1|LINE|L1	-339619	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.001534	0.332312	
chunk0078_374_1	chr16	87549875	87550366	+	0	NA	Intergenic	Intergenic	-51715	NR_073379	57338	Hs.592068	NM_020655	ENSG00000154118	JPH3	CAGL237|HDL2|JP-3|JP3|TNRC22	junctophilin 3	protein-coding	0.050916	0.542683	
chunk0085_390_1	chr18	9952603	9953203	+	0	NA	intron (NM_194434, intron 5 of 5)	intron (NM_194434, intron 5 of 5)	38945	NM_003574	9218	Hs.165195	NM_003574	ENSG00000101558	VAPA	VAP-33|VAP-A|VAP33|hVAP-33	VAMP associated protein A	protein-coding	0.000000	0.382696	
chunk0158_331_1	chr5	132962482	132962712	+	0	NA	intron (NM_014423, intron 1 of 20)	intron (NM_014423, intron 1 of 20)	1065	NM_014423	27125	Hs.519313	NM_014423	ENSG00000072364	AFF4	AF5Q31|CHOPS|MCEF	AF4/FMR2 family member 4	protein-coding	0.021739	0.437229	
chunk0208_58_1	chrX	11540439	11541272	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-113070	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.004802	0.462830	266(AAGAACATAGTGTACT,-,0.00),267(AGAACATAGTGTACTT,+,0.00),291(AAGAACATGGTGAACC,-,0.00),292(AGAACATGGTGAACCT,+,0.00)
chunk0106_204_1	chr2	202265650	202265856	+	0	NA	promoter-TSS (NM_015934)	promoter-TSS (NM_015934)	-39	NM_015934	51602	Hs.471104	NM_015934	ENSG00000055044	NOP58	HSPC120|NOP5|NOP5/NOP58	NOP58 ribonucleoprotein	protein-coding	0.092233	0.584541	
chunk0117_369_1	chr21	45054951	45055214	+	0	NA	Intergenic	Intergenic	18129	NR_027292	728039	Hs.309203	NM_032653	ENSG00000235374	SSR4P1	C21orf122|PRED57|PRED90	signal sequence receptor subunit 4 pseudogene 1	pseudo	0.057034	0.655303	
chunk0010_8_1	chr1	111884922	111885373	+	0	NA	intron (NM_172198, intron 2 of 6)	L3|LINE|CR1	-24510	NR_046619	100873995	Hs.535274	NR_046619	ENSG00000237556	KCND3-AS1	-	KCND3 antisense RNA 1	ncRNA	0.013304	0.446903	300(CAGGACACTGTGTACC,-,0.00),301(AGGACACTGTGTACCC,+,0.00)
chunk0128_256_1	chr3	109099286	109099776	+	0	NA	intron (NM_014429, intron 5 of 27)	intron (NM_014429, intron 5 of 27)	18615	NM_014429	27136	Hs.591296	NM_014429	ENSG00000114487	MORC1	CT33|MORC|ZCW6	MORC family CW-type zinc finger 1	protein-coding	0.010204	0.405295	195(AAGAACATCATGTTTT,-,0.00),196(AGAACATCATGTTTTA,+,0.00),264(GTAACAGGATGTTCTT,+,0.00)
chunk0137_157_1	chr4	15851954	15852535	+	0	NA	non-coding (NR_132660, exon 7 of 7)	non-coding (NR_132660, exon 7 of 7)	73979	NM_001775	952	Hs.479214	NM_001775	ENSG00000004468	CD38	ADPRC 1|ADPRC1	CD38 molecule	protein-coding	0.010327	0.383162	
chunk0026_7_1	chr10	60387315	60388109	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	2164	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.003778	0.373585	
chunk0124_136_1	chr3	54393622	54393913	+	0	NA	intron (NM_018398, intron 4 of 37)	L1MA6|LINE|L1	246090	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.017182	0.558219	
chunk0023_418_1	chr10	31301624	31302361	+	0	NA	Intergenic	L1MA8|LINE|L1	17103	NR_024284	220930	Hs.372654	NR_024284	ENSG00000237036	ZEB1-AS1	-	ZEB1 antisense RNA 1	ncRNA	0.005427	0.349593	
chunk0047_435_1	chr12	76386919	76387356	+	0	NA	intron (NM_001003712, intron 11 of 22)	Charlie6|DNA|hAT-Charlie	-38695	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.004577	0.385845	
chunk0183_227_1	chr7	106891188	106891881	+	0	NA	intron (NM_002649, intron 10 of 10)	intron (NM_002649, intron 10 of 10)	26055	NM_002649	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.008658	0.404899	377(AGGAACAACTCGTTCT,-,0.00),378(GGAACAACTCGTTCTT,+,0.00)
chunk0044_122_1	chr12	29165410	29165997	+	0	NA	intron (NM_001271783, intron 1 of 11)	intron (NM_001271783, intron 1 of 11)	16700	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.003407	0.312925	277(AAGAACAGAGTGTCTT,-,0.00),278(AGAACAGAGTGTCTTT,+,0.00)
chunk0165_35_1	chr6	29951825	29952132	+	0	NA	Intergenic	Charlie9|DNA|hAT-Charlie	9508	NM_001242758	3105	Hs.181244	NM_002116	ENSG00000206503	HLA-A	HLAA	major histocompatibility complex, class I, A	protein-coding	0.003257	0.405844	
chunk0113_308_1	chr20	57983233	57983527	+	0	NA	Intergenic	Intergenic	87986	NR_039757									0.037415	0.586441	
chunk0016_142_1	chr1	197267686	197268389	+	0	NA	promoter-TSS (NM_001257966)	promoter-TSS (NM_001257966)	-167	NM_201253	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.009957	0.407670	
chunk0181_358_1	chr7	88392408	88393164	+	0	NA	Intergenic	Intergenic	-85873	NM_024636	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.002646	0.365918	
chunk0012_459_1	chr1	165281320	165281991	+	0	NA	intron (NM_177398, intron 3 of 8)	MamRTE1|LINE|RTE-BovB	74586	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.004471	0.438988	
chunk0013_212_1	chr1	169479049	169479377	+	0	NA	intron (NM_006996, intron 1 of 5)	intron (NM_006996, intron 1 of 5)	6757	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.003049	0.334347	
chunk0169_391_1	chr6	107979194	107979605	+	0	NA	Intergenic	Intergenic	-21121	NM_007214	11231	Hs.26904	NM_007214	ENSG00000025796	SEC63	DNAJC23|ERdj2|PCLD2|PRO2507|SEC63L	SEC63 homolog, protein translocation regulator	protein-coding	0.002433	0.327670	
chunk0108_88_1	chr2	227818032	227818625	+	0	NA	TTS (NM_004591)	TTS (NM_004591)	4486	NM_001130046	6364	Hs.75498	NM_004591	ENSG00000115009	CCL20	CKb4|Exodus|LARC|MIP-3-alpha|MIP-3a|MIP3A|SCYA20|ST38	C-C motif chemokine ligand 20	protein-coding	0.011804	0.456229	367(AGGTTCAGTATGTGCT,-,0.00),368(GGTTCAGTATGTGCTG,+,0.00)
chunk0029_342_1	chr10	106428762	106429335	+	0	NA	Intergenic	Intergenic	-608715	NR_120625	101927549	Hs.556885	NR_120625		LINC02627	-	long intergenic non-protein coding RNA 2627	ncRNA	0.003490	0.317073	
chunk0017_58_1	chr1	205384472	205384862	+	0	NA	intron (NR_037583, intron 2 of 3)	HAL1b|LINE|L1	11415	NR_038425	284576	Hs.585440	NR_038425	ENSG00000226235	LEMD1-AS1	-	LEMD1 antisense RNA 1	ncRNA	0.007692	0.347826	
chunk0209_436_1	chrX	63350968	63351229	+	0	NA	5' UTR (NM_001012968, exon 1 of 1)	5' UTR (NM_001012968, exon 1 of 1)	241	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.091954	0.625954	40(TGGGACAGCGTGTGCC,-,0.00),41(GGGACAGCGTGTGCCT,+,0.00)
chunk0074_396_1	chr16	35382352	35382713	+	0	NA	non-coding (NR_027079, exon 6 of 9)	non-coding (NR_027079, exon 6 of 9)	19001	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.008310	0.303867	
chunk0076_30_1	chr16	59337312	59337888	+	0	NA	Intergenic	L2a|LINE|L2	417591	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.003472	0.388215	
chunk0177_317_1	chr7	26112625	26113320	+	0	NA	Intergenic	L1ME4b|LINE|L1	-39255	NM_004289	9603	Hs.404741	NM_004289	ENSG00000050344	NFE2L3	NRF3	nuclear factor, erythroid 2 like 3	protein-coding	0.007194	0.372126	
chunk0113_229_1	chr20	53959691	53959899	+	0	NA	intron (NM_003657, intron 9 of 11)	intron (NM_003657, intron 9 of 11)	-84086	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.009615	0.416268	94(AAGATCAGACTGTCCT,-,0.00),95(AGATCAGACTGTCCTC,+,0.00)
chunk0181_424_1	chr7	90387480	90388323	+	0	NA	3' UTR (NM_001042717, exon 8 of 8)	3' UTR (NM_001042717, exon 8 of 8)	-8391	NR_102424	101409256		NR_102424		LOC101409256	-	cell division cycle 42 pseudogene	pseudo	0.002372	0.336493	
chunk0108_27_1	chr2	226553050	226553264	+	0	NA	Intergenic	Intergenic	105636	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.004673	0.390698	
chunk0187_367_1	chr7	157459321	157459611	+	0	NA	Intergenic	Intergenic	-6765	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.027586	0.457045	
chunk0140_385_1	chr4	74966792	74967574	+	0	NA	non-coding (NR_121617, exon 3 of 4)	non-coding (NR_121617, exon 3 of 4)	3179	NR_121617	100507388	Hs.570765	NR_121617	ENSG00000249717	LOC100507388	-	uncharacterized LOC100507388	ncRNA	0.007673	0.407407	
chunk0008_127_1	chr1	91790870	91791463	+	0	NA	intron (NR_036634, intron 4 of 17)	intron (NR_036634, intron 4 of 17)	95113	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.008432	0.415825	
chunk0034_312_1	chr11	35099345	35099950	+	0	NA	Intergenic	Intergenic	38385	NR_120528	100507144	Hs.673491	NR_120528	ENSG00000255521	LOC100507144	-	uncharacterized LOC100507144	ncRNA	0.009917	0.414191	
chunk0158_112_1	chr5	126881976	126882535	+	0	NA	intron (NM_178450, intron 3 of 4)	intron (NM_178450, intron 3 of 4)	105102	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.008945	0.401786	
chunk0089_386_1	chr18	67651308	67652021	+	0	NA	intron (NR_033921, intron 1 of 4)	intron (NR_033921, intron 1 of 4)	-134934	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.007013	0.439776	
chunk0134_208_1	chr3	178511520	178511755	+	0	NA	Intergenic	Intergenic	-24661	NM_181361	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.021277	0.436441	
chunk0094_414_1	chr2	10473678	10473877	+	0	NA	Intergenic	Intergenic	24049	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.010050	0.370000	
chunk0075_95_1	chr16	48413302	48413731	+	0	NA	Intergenic	Intergenic	-28198	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.006993	0.441860	
chunk0029_220_1	chr10	102268362	102268846	+	0	NA	intron (NM_001199378, intron 3 of 39)	intron (NM_001199378, intron 3 of 39)	23106	NM_001199379	8729	Hs.290243	NM_004193	ENSG00000107862	GBF1	ARF1GEF	golgi brefeldin A resistant guanine nucleotide exchange factor 1	protein-coding	0.000000	0.410309	
chunk0057_5_1	chr13	95494171	95494827	+	0	NA	intron (NR_046533, intron 3 of 3)	intron (NR_046533, intron 3 of 3)	39411	NR_046533	100874194	Hs.569229	NR_046533	ENSG00000223392	CLDN10-AS1	-	CLDN10 antisense RNA 1	ncRNA	0.013720	0.354642	
chunk0167_347_1	chr6	72820722	72821110	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	146837	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.007732	0.398458	
chunk0058_129_1	chr14	22410152	22410386	+	0	NA	Intergenic	Intergenic	178968	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.004274	0.442553	
chunk0037_60_1	chr11	70854887	70855225	+	0	NA	intron (NM_012309, intron 10 of 24)	intron (NM_012309, intron 10 of 24)	-7734	NR_073536	220070	Hs.326766	NM_145308	ENSG00000171671	SHANK2-AS3	C11orf76	SHANK2 antisense RNA 3	ncRNA	0.020710	0.510324	
chunk0096_305_1	chr2	32970099	32970521	+	0	NA	intron (NM_206943, intron 2 of 33)	L1PA15|LINE|L1	23008	NM_206943	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.002370	0.340426	
chunk0084_458_1	chr17	83174289	83174800	+	0	NA	Intergenic	Intergenic	-52353	NR_029406	388574	Hs.546918	NR_029406	ENSG00000232938	RPL23AP87	-	ribosomal protein L23a pseudogene 87	pseudo	0.019569	0.583984	
chunk0150_291_1	chr5	37318210	37318544	+	0	NA	intron (NM_001278312, intron 20 of 33)	GA-rich|Low_complexity|Low_complexity	52749	NM_004298	9631	Hs.547696	NM_004298	ENSG00000113569	NUP155	ATFB15|N155	nucleoporin 155	protein-coding	0.005988	0.340299	
chunk0043_23_1	chr12	13102014	13102508	+	0	NA	intron (NM_001080554, intron 1 of 6)	intron (NM_001080554, intron 1 of 6)	1435	NM_001080554	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.012146	0.456566	
chunk0192_435_1	chr8	69711980	69712269	+	0	NA	intron (NM_001146009, intron 3 of 7)	intron (NM_001146009, intron 3 of 7)	119224	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.000000	0.327586	
chunk0203_299_1	chr9	89253921	89254536	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-56967	NM_001827	1164	Hs.83758	NM_001827	ENSG00000123975	CKS2	CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding	0.014634	0.485390	
chunk0060_43_1	chr14	41030497	41030696	+	0	NA	intron (NR_109758, intron 3 of 3)	intron (NR_109758, intron 3 of 3)	75885	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.000000	0.355000	
chunk0022_341_1	chr10	16802876	16803456	+	0	NA	intron (NM_152724, intron 1 of 7)	L1MC2|LINE|L1	14288	NM_152724	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.005172	0.327022	
chunk0187_80_1	chr8	2980476	2980747	+	0	NA	intron (NM_033225, intron 54 of 69)	intron (NM_033225, intron 54 of 69)	-252160	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.011070	0.459559	
chunk0162_392_1	chr5	179605134	179605537	+	0	NA	intron (NM_001040451, intron 14 of 16)	intron (NM_001040451, intron 14 of 16)	-1594	NR_110560	101928445	Hs.663255	NR_110560	ENSG00000244945	LOC101928445	-	uncharacterized LOC101928445	ncRNA	0.009926	0.482673	160(AGGATCAGACTGTTTC,-,0.00)
chunk0084_324_1	chr17	80734157	80734376	+	0	NA	intron (NM_020761, intron 5 of 33)	intron (NM_020761, intron 5 of 33)	71366	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.041096	0.545455	
chunk0030_316_1	chr10	117946586	117946825	+	0	NA	Intergenic	Intergenic	99898	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.020921	0.433333	
chunk0196_263_1	chr8	108805062	108805679	+	0	NA	Intergenic	LTR54|LTR|ERV1	-17829	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.008104	0.393204	
chunk0135_187_1	chr3	188176492	188176830	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	-1882	NR_024413	401105	Hs.679026	NM_207488	ENSG00000279891	FLJ42393	AVPC1948	uncharacterized LOC401105	ncRNA	0.000000	0.398230	
chunk0183_191_1	chr7	106284036	106284290	+	0	NA	intron (NM_005746, intron 1 of 10)	intron (NM_005746, intron 1 of 10)	1029	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.055118	0.545098	
chunk0132_346_1	chr3	161390225	161390683	+	0	NA	Intergenic	Intergenic	-18371	NM_001040100	165679	Hs.369104	NM_145035	ENSG00000196542	SPTSSB	ADMP|C3orf57|SSSPTB	serine palmitoyltransferase small subunit B	protein-coding	0.004367	0.370370	117(AACACAACCTGTCCTT,+,0.00)
chunk0070_392_1	chr15	76963119	76963483	+	0	NA	Intergenic	MIR|SINE|MIR	31680	NM_002902	5955	Hs.79088	NM_002902	ENSG00000117906	RCN2	E6BP|ERC-55|ERC55|TCBP49	reticulocalbin 2	protein-coding	0.005495	0.378082	197(TGGCACACAAAGTCCT,-,0.00),198(GGCACACAAAGTCCTC,+,0.00)
chunk0005_160_1	chr1	58304323	58304653	+	0	NA	Intergenic	Intergenic	-53949	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.009091	0.350453	
chunk0131_412_1	chr3	152953605	152954178	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	119198	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.005236	0.371080	
chunk0109_49_1	chr20	885137	885339	+	0	NA	exon (NM_015985, exon 4 of 9)	exon (NM_015985, exon 4 of 9)	31079	NM_015985	51378	Hs.278973	NM_015985	ENSG00000101280	ANGPT4	ANG3|ANG4	angiopoietin 4	protein-coding	0.079208	0.679803	90(CGGCTCAGCGTGTTCA,-,0.00),91(GGCTCAGCGTGTTCAG,+,0.00)
chunk0191_314_1	chr8	55568847	55569260	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-113732	NR_027765	100133234	Hs.729852	NR_027765	ENSG00000248522	SBF1P1	-	SET binding factor 1 pseudogene 1	pseudo	0.014528	0.490338	
chunk0089_20_1	chr18	57744328	57744762	+	0	NA	intron (NM_005603, intron 1 of 27)	intron (NM_005603, intron 1 of 27)	58550	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.006912	0.377011	
chunk0132_275_1	chr3	159669958	159670301	+	0	NA	intron (NM_001197108, intron 1 of 6)	intron (NM_001197108, intron 1 of 6)	98483	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.005831	0.369186	159(AGGGACTTTATGTTCT,-,0.00),160(GGGACTTTATGTTCTG,+,0.00)
chunk0172_43_1	chr6	134015633	134016047	+	0	NA	intron (NM_145176, intron 2 of 4)	intron (NM_145176, intron 2 of 4)	36811	NM_145176	154091	Hs.486508	NM_145176	ENSG00000146411	SLC2A12	GLUT12|GLUT8	solute carrier family 2 member 12	protein-coding	0.004831	0.385542	
chunk0067_303_1	chr15	47774257	47774887	+	0	NA	TTS (NM_001198999)	TTS (NM_001198999)	56083	NM_024966	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.009524	0.393027	
chunk0038_300_1	chr11	90758122	90758470	+	0	NA	intron (NR_104190, intron 3 of 6)	L1ME1|LINE|L1	110906	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.008621	0.329513	
chunk0155_115_1	chr5	92946107	92946667	+	0	NA	Intergenic	Intergenic	624956	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.008929	0.356506	
chunk0175_70_1	chr7	2157663	2158128	+	0	NA	intron (NM_003550, intron 10 of 18)	intron (NM_003550, intron 10 of 18)	75053	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.025806	0.493562	
chunk0028_353_1	chr10	92431969	92432998	+	0	NA	Intergenic	Intergenic	13822	NR_038243	100507674	Hs.568772	NR_038243		MARK2P9	-	microtubule affinity regulating kinase 2 pseudogene 9	pseudo	0.007775	0.416505	
chunk0115_230_1	chr21	27272616	27272822	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-305599	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.004854	0.347826	
chunk0100_50_1	chr2	106138660	106139317	+	0	NA	promoter-TSS (NM_001253876)	promoter-TSS (NM_001253876)	-107	NM_001253876	80146	Hs.469561	NM_025076	ENSG00000115652	UXS1	SDR6E1|UGD	UDP-glucuronate decarboxylase 1	protein-coding	0.016743	0.486322	
chunk0179_123_1	chr7	45670609	45670948	+	0	NA	intron (NM_021116, intron 8 of 19)	intron (NM_021116, intron 8 of 19)	96252	NM_021116	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.008850	0.564706	
chunk0182_72_1	chr7	92279634	92280185	+	0	NA	intron (NM_019004, intron 1 of 19)	MER68-int|LTR|ERVL	33675	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.001815	0.396739	
chunk0097_27_1	chr2	42368897	42369220	+	0	NA	Intergenic	Intergenic	-7842	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.018576	0.524691	
chunk0019_420_1	chr1	230824975	230825358	+	0	NA	Intergenic	Intergenic	30870	NM_001136495	84886	Hs.520494	NM_032800	ENSG00000119280	C1orf198	-	chromosome 1 open reading frame 198	protein-coding	0.013055	0.427083	
chunk0141_58_1	chr4	77636201	77636782	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	124738	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.017212	0.558419	
chunk0071_430_1	chr15	89856789	89857239	+	0	NA	intron (NM_001199058, intron 8 of 9)	intron (NM_001199058, intron 8 of 9)	-6293	NR_049817	100847059		NR_049817	ENSG00000264966	MIR5094	-	microRNA 5094	ncRNA	0.011111	0.416851	
chunk0078_238_1	chr17	6686049	6686547	+	0	NA	exon (NM_001143838, exon 11 of 11)	exon (NM_001143838, exon 11 of 11)	27123	NM_001284509	284111	Hs.399496	NM_177550	ENSG00000141485	SLC13A5	EIEE25|INDY|NACT|mIndy	solute carrier family 13 member 5	protein-coding	0.014056	0.541082	84(CTGTACAAGGTGTGCC,-,0.00)
chunk0111_133_1	chr20	24657103	24657673	+	0	NA	intron (NM_024893, intron 3 of 3)	intron (NM_024893, intron 3 of 3)	188189	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.017544	0.483363	
chunk0145_145_1	chr4	147029135	147029734	+	0	NA	Intergenic	Intergenic	-83552	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.001669	0.395000	311(AAGGACACTTTGTACA,-,0.00),312(AGGACACTTTGTACAC,+,0.00)
chunk0097_88_1	chr2	45443626	45443952	+	0	NA	intron (NM_018079, intron 16 of 20)	intron (NM_018079, intron 16 of 20)	167505	NM_018079	55133	Hs.14229	NM_018079	ENSG00000068784	SRBD1	-	S1 RNA binding domain 1	protein-coding	0.006135	0.348624	
chunk0056_72_1	chr13	79484983	79485631	+	0	NA	intron (NM_019080, intron 1 of 7)	intron (NM_019080, intron 1 of 7)	-4076	NR_046685	100874208	Hs.602801	NR_046685	ENSG00000232132	NDFIP2-AS1	-	NDFIP2 antisense RNA 1	ncRNA	0.006173	0.406780	
chunk0074_158_1	chr16	23351331	23351695	+	0	NA	intron (NM_000336, intron 2 of 12)	intron (NM_000336, intron 2 of 12)	49243	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.008242	0.509589	
chunk0033_95_1	chr11	14148626	14149039	+	0	NA	intron (NM_006108, intron 6 of 15)	intron (NM_006108, intron 6 of 15)	186195	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.004843	0.403382	
chunk0023_412_1	chr10	31202457	31202883	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	116425	NR_024284	220930	Hs.372654	NR_024284	ENSG00000237036	ZEB1-AS1	-	ZEB1 antisense RNA 1	ncRNA	0.009390	0.367681	
chunk0202_305_1	chr9	77965822	77966260	+	0	NA	intron (NM_002072, intron 1 of 6)	L1ME1|LINE|L1	65408	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.011416	0.375854	
chunk0061_181_1	chr14	59997392	59997785	+	0	NA	intron (NR_075071, intron 17 of 32)	intron (NR_075071, intron 17 of 32)	77875	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.002545	0.340102	
chunk0199_87_1	chr9	2632861	2633254	+	0	NA	intron (NM_003383, intron 1 of 18)	(GT)n|Simple_repeat|Simple_repeat	-10684	NR_015375	401491	Hs.416043	NR_015375	ENSG00000236404	VLDLR-AS1	linc-VLDLR|lincRNA-VLDLR	VLDLR antisense RNA 1	ncRNA	0.007634	0.421320	
chunk0044_128_1	chr12	29304102	29304681	+	0	NA	intron (NM_001271784, intron 3 of 10)	L2b|LINE|L2	13457	NR_103860	100506606	Hs.298851	NR_103860	ENSG00000257176	LOC100506606	-	uncharacterized LOC100506606	ncRNA	0.001727	0.389655	394(AAGACAGTGTGTCCAC,+,0.00)
chunk0077_275_1	chr16	81035613	81035850	+	0	NA	promoter-TSS (NM_015251)	promoter-TSS (NM_015251)	-122	NM_015251	23300	Hs.16349	NM_015251	ENSG00000166454	ATMIN	ASCIZ|ZNF822	ATM interactor	protein-coding	0.097046	0.676471	
chunk0042_291_1	chr12	7566479	7566734	+	0	NA	Intergenic	Intergenic	-62788	NM_203416	9332	Hs.504641	NM_004244	ENSG00000177575	CD163	M130|MM130|SCARI1	CD163 molecule	protein-coding	0.003922	0.480469	
chunk0022_404_1	chr10	18263881	18264247	+	0	NA	intron (NM_000724, intron 1 of 12)	intron (NM_000724, intron 1 of 12)	3409	NM_000724	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.005464	0.326975	
chunk0037_43_1	chr11	70366115	70366685	+	0	NA	intron (NM_003626, intron 21 of 27)	intron (NM_003626, intron 21 of 27)	-32106	NM_005231	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.012281	0.374781	534(GTGGACAGGCAGTTCT,-,0.00),535(TGGACAGGCAGTTCTA,+,0.00)
chunk0085_233_1	chr18	6965667	6966097	+	0	NA	intron (NM_005559, intron 49 of 62)	intron (NM_005559, intron 49 of 62)	11205	NR_126040	101927188	Hs.680444	NR_126040	ENSG00000265069	LOC101927188	-	uncharacterized LOC101927188	ncRNA	0.009302	0.317865	
chunk0022_259_1	chr10	14821720	14821980	+	0	NA	intron (NM_001029954, intron 3 of 3)	intron (NM_001029954, intron 3 of 3)	16134	NM_001029954	441549	Hs.559067	NM_001029954	ENSG00000185267	CDNF	ARMETL1	cerebral dopamine neurotrophic factor	protein-coding	0.011538	0.375479	
chunk0004_405_1	chr1	52259821	52260020	+	0	NA	intron (NM_007324, intron 4 of 17)	L1ME3G|LINE|L1	106285	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.010050	0.330000	
chunk0056_13_1	chr13	77113496	77113793	+	0	NA	intron (NM_015057, intron 55 of 82)	intron (NM_015057, intron 55 of 82)	38130	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.000000	0.395973	
chunk0182_13_1	chr7	91103299	91103786	+	0	NA	intron (NM_001287136, intron 11 of 13)	intron (NM_001287136, intron 11 of 13)	-160926	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.002053	0.424180	210(AGGCACTGTTTGTTCC,-,0.00),211(GGCACTGTTTGTTCCT,+,0.00)
chunk0197_127_1	chr8	120009964	120010163	+	0	NA	intron (NM_022783, intron 8 of 8)	MIRb|SINE|MIR	-115045	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.020101	0.400000	
chunk0131_162_1	chr3	146477583	146477880	+	0	NA	intron (NM_020359, intron 1 of 8)	L1PA6|LINE|L1	-8430	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.003367	0.530201	
chunk0102_148_1	chr2	146939499	146939781	+	0	NA	Intergenic	Intergenic	352583	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.003546	0.342756	
chunk0015_296_1	chr1	188821987	188822387	+	0	NA	Intergenic	Intergenic	1378559	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007500	0.374065	
chunk0164_397_1	chr6	26295815	26296493	+	0	NA	Intergenic	LTR3|LTR|ERVK	-10655	NM_003543	8365	Hs.591790	NM_003543	ENSG00000158406	HIST1H4H	H4/h|H4FH	histone cluster 1 H4 family member h	protein-coding	0.011799	0.456554	
chunk0199_28_1	chr9	732461	732755	+	0	NA	exon (NM_001256877, exon 7 of 13)	exon (NM_001256877, exon 7 of 13)	25802	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.003401	0.450847	
chunk0123_429_1	chr3	50164062	50164454	+	0	NA	intron (NM_004186, intron 2 of 18)	intron (NM_004186, intron 2 of 18)	8843	NM_004186	6405	Hs.32981	NM_004186	ENSG00000001617	SEMA3F	SEMA-IV|SEMA4|SEMAK	semaphorin 3F	protein-coding	0.015306	0.575064	
chunk0006_314_1	chr1	71461367	71461895	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	375381	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.003788	0.359168	
chunk0148_142_1	chr5	6063074	6063332	+	0	NA	Intergenic	Intergenic	274089	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.003876	0.301158	
chunk0064_239_1	chr14	94356510	94357030	+	0	NA	Intergenic	L2a|LINE|L2	9932	NM_006220	390502	Hs.525557	NM_006220	ENSG00000258597	SERPINA2	ARGS|ATR|PIL|SERPINA2P|psiATR	serpin family A member 2 (gene/pseudogene)	protein-coding	0.005769	0.456814	341(CTGCACAGCCAGTGCT,-,0.00),342(TGCACAGCCAGTGCTT,+,0.00)
chunk0043_85_1	chr12	14651265	14652002	+	0	NA	intron (NM_004963, intron 14 of 26)	intron (NM_004963, intron 14 of 26)	44952	NM_004963	2984	Hs.524278	NM_004963	ENSG00000070019	GUCY2C	DIAR6|GC-C|GUC2C|MECIL|MUCIL|STAR	guanylate cyclase 2C	protein-coding	0.009498	0.364499	
chunk0120_138_1	chr3	5122221	5122420	+	0	NA	promoter-TSS (NM_018184)	promoter-TSS (NM_018184)	75	NM_018184	55207	Hs.250009	NM_018184	ENSG00000134108	ARL8B	ARL10C|Gie1	ADP ribosylation factor like GTPase 8B	protein-coding	0.150754	0.750000	
chunk0205_16_1	chr9	105065129	105065792	+	0	NA	Intergenic	Intergenic	-137214	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.007541	0.432229	
chunk0060_60_1	chr14	41636791	41637112	+	0	NA	intron (NM_152447, intron 1 of 5)	MER70A|LTR|ERVL	29390	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.003115	0.453416	
chunk0126_334_1	chr3	82056124	82056812	+	0	NA	Intergenic	L2b|LINE|L2	-294669	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004360	0.297533	344(GAGCACAGTATGTGCT,-,0.00),345(AGCACAGTATGTGCTG,+,0.00)
chunk0174_330_1	chr6	163565925	163566519	+	0	NA	3' UTR (NM_206855, exon 6 of 6)	3' UTR (NM_206855, exon 6 of 6)	151579	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.006734	0.344538	
chunk0173_187_1	chr6	145111199	145111654	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-623443	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.002198	0.359649	336(ATGTACTTTATGTTCT,-,0.00),337(TGTACTTTATGTTCTT,+,0.00),414(TAGGTCATCCTGTTCC,-,0.00),415(AGGTCATCCTGTTCCT,+,0.00)
chunk0125_430_1	chr3	72557997	72558312	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-111531	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.012698	0.414557	219(CAGAACTTATTGTACT,-,0.00),220(AGAACTTATTGTACTT,+,0.00)
chunk0119_134_1	chr22	42933673	42934516	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	12947	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.013049	0.443128	352(AAGAACAGCCAGTTCT,-,0.00),353(AGAACAGCCAGTTCTT,+,0.00)
chunk0190_199_1	chr8	34229072	34229317	+	0	NA	Intergenic	Intergenic	-554727	NR_125746	103689844	Hs.590682	NR_125746	ENSG00000254344	LINC01288	TCONS_00014671	long intergenic non-protein coding RNA 1288	ncRNA	0.000000	0.313008	
chunk0027_109_1	chr10	74051594	74051793	+	0	NA	intron (NM_003373, intron 2 of 20)	MIR|SINE|MIR	53579	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.000000	0.335000	
chunk0212_133_1	chrX	131630793	131631262	+	0	NA	Intergenic	Intergenic	86953	NM_001004486	347468	Hs.553711	NM_001004486	ENSG00000171054	OR13H1	ORX1	olfactory receptor family 13 subfamily H member 1	protein-coding	0.010661	0.372340	
chunk0204_378_1	chr9	102097281	102097494	+	0	NA	Intergenic	Intergenic	-358807	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.018779	0.415888	
chunk0128_59_1	chr3	104947107	104947319	+	0	NA	Intergenic	L1PA13|LINE|L1	-419500	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.009434	0.399061	
chunk0101_305_1	chr2	135091651	135092331	+	0	NA	intron (NM_001172435, intron 4 of 24)	intron (NM_001172435, intron 4 of 24)	39726	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.005882	0.336270	
chunk0186_385_1	chr7	144414920	144415153	+	0	NA	Intergenic	L1MEc|LINE|L1	-4809	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.004292	0.388889	
chunk0130_265_1	chr3	136182327	136182526	+	0	NA	intron (NM_018133, intron 1 of 1)	L1MEc|LINE|L1	12042	NM_001145417	55167	Hs.18631	NM_018133	ENSG00000174579	MSL2	MSL-2|MSL2L1|RNF184	MSL complex subunit 2	protein-coding	0.010050	0.390000	
chunk0049_292_1	chr12	94073009	94073733	+	0	NA	Intergenic	Intergenic	-75352	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.008287	0.440000	153(TGGCACATTGTGTTCC,-,0.00),154(GGCACATTGTGTTCCA,+,0.00),320(CAGAACACCCAGTCTT,-,0.00),490(GGGGACAGCCTGTTCT,-,0.00),491(GGGACAGCCTGTTCTG,+,0.00)
chunk0073_82_1	chr16	3874844	3875538	+	0	NA	intron (NM_001079846, intron 1 of 29)	intron (NM_001079846, intron 1 of 29)	4929	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.017291	0.443165	
chunk0141_154_1	chr4	81655081	81655449	+	0	NA	Intergenic	L1MA1|LINE|L1	-183337	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.005435	0.336043	
chunk0126_272_1	chr3	79983983	79984210	+	0	NA	Intergenic	Intergenic	-216187	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.236842	
chunk0166_287_1	chr6	48499734	48499937	+	0	NA	Intergenic	Intergenic	-431146	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.004926	0.357843	
chunk0199_306_1	chr9	7052697	7052896	+	0	NA	intron (NM_015061, intron 17 of 21)	intron (NM_015061, intron 17 of 21)	295155	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.005025	0.520000	
chunk0201_148_1	chr9	35869895	35870162	+	0	NA	exon (NM_001004487, exon 1 of 1)	exon (NM_001004487, exon 1 of 1)	373	NM_001004487	392309	Hs.527480	NM_001004487	ENSG00000168828	OR13J1	OR9-2	olfactory receptor family 13 subfamily J member 1	protein-coding	0.033708	0.608209	
chunk0172_60_1	chr6	134199889	134200279	+	0	NA	intron (NM_001143676, intron 3 of 13)	intron (NM_001143676, intron 3 of 13)	-22212	NM_001143677	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.005128	0.368286	
chunk0133_70_1	chr3	166980768	166981138	+	0	NA	Intergenic	L1MB8|LINE|L1	399330	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.002703	0.304582	
chunk0171_249_1	chr6	127176191	127176621	+	0	NA	intron (NM_032784, intron 4 of 4)	intron (NM_032784, intron 4 of 4)	57503	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.004651	0.343387	
chunk0147_205_1	chr4	178808426	178808625	+	0	NA	Intergenic	Intergenic	-900589	NR_108093	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.005025	0.335000	
chunk0136_307_1	chr3	195182289	195182755	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	34651	NR_102710	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.012876	0.415418	242(GAGCACAGTGTGTTAC,-,0.00),243(AGCACAGTGTGTTACT,+,0.00)
chunk0024_263_1	chr10	41848406	41848629	+	0	NA	Intergenic	Intergenic	519528	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.058296	0.375000	
chunk0037_31_1	chr11	70116674	70116955	+	0	NA	intron (NM_018043, intron 8 of 25)	intron (NM_018043, intron 8 of 25)	31404	NR_030691	55107	Hs.503074	NM_018043	ENSG00000131620	ANO1	DOG1|ORAOV2|TAOS2|TMEM16A	anoctamin 1	protein-coding	0.014235	0.549645	
chunk0064_170_1	chr14	92315320	92315703	+	0	NA	Intergenic	Intergenic	-7070	NM_153648	123041	Hs.385530	NM_153646	ENSG00000140090	SLC24A4	AI2A5|NCKX4|SHEP6|SLC24A2	solute carrier family 24 member 4	protein-coding	0.023499	0.518229	217(AAGGACACCGAGTTCT,-,0.00),218(AGGACACCGAGTTCTC,+,0.00)
chunk0137_94_1	chr4	13395112	13395595	+	0	NA	intron (NM_001017979, intron 4 of 6)	intron (NM_001017979, intron 4 of 6)	89012	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.004141	0.270661	
chunk0143_326_1	chr4	119791703	119791970	+	0	NA	Intergenic	L1ME1|LINE|L1	12679	NR_110660	101927007	Hs.143958	NR_110660	ENSG00000250772	LINC01365	-	long intergenic non-protein coding RNA 1365	ncRNA	0.014981	0.391791	
chunk0023_332_1	chr10	29304335	29305105	+	0	NA	intron (NM_032517, intron 3 of 4)	intron (NM_032517, intron 3 of 4)	15659	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.007792	0.428016	292(CAGGACAGACTGTCTA,-,0.00),293(AGGACAGACTGTCTAT,+,0.00),667(TAGTACAAAATGTGCT,-,0.00),668(AGTACAAAATGTGCTC,+,0.00)
chunk0048_214_1	chr12	81407674	81408031	+	0	NA	intron (NM_001220478, intron 3 of 28)	intron (NM_001220478, intron 3 of 28)	-38438	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.332402	
chunk0067_436_1	chr15	49987085	49987559	+	0	NA	intron (NR_073596, intron 11 of 27)	intron (NR_073596, intron 11 of 27)	125994	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.006329	0.437895	
chunk0006_434_1	chr1	76515732	76516124	+	0	NA	intron (NM_152996, intron 3 of 4)	L1MA6|LINE|L1	-351573	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.005102	0.346056	
chunk0005_330_1	chr1	61089503	61089702	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	7294	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.015075	0.370000	
chunk0061_340_1	chr14	63459125	63459849	+	0	NA	intron (NM_001282180, intron 2 of 13)	intron (NM_001282180, intron 2 of 13)	48751	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.006906	0.331034	
chunk0201_304_1	chr9	42261539	42261785	+	0	NA	Intergenic	Intergenic	62800	NR_126166	100996582		NR_126166		FAM74A7	-	family with sequence similarity 74 member A7	ncRNA	0.004065	0.307692	
chunk0097_453_1	chr2	64634996	64635232	+	0	NA	3' UTR (NM_014755, exon 2 of 2)	3' UTR (NM_014755, exon 2 of 2)	18798	NM_014755	9792	Hs.591569	NM_014755	ENSG00000179833	SERTAD2	Sei-2|TRIP-Br2|TRIPBR2	SERTA domain containing 2	protein-coding	0.004237	0.455696	
chunk0210_373_1	chrX	97260627	97261528	+	0	NA	intron (NM_006729, intron 23 of 26)	intron (NM_006729, intron 23 of 26)	303458	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.009989	0.332594	
chunk0021_405_1	chr1	246689664	246689894	+	0	NA	Intergenic	LTR41|LTR|ERVL	-34297	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.039130	0.627706	
chunk0122_378_1	chr3	37751709	37752272	+	0	NA	intron (NM_002207, intron 23 of 27)	intron (NM_002207, intron 23 of 27)	109790	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.014210	0.498227	
chunk0023_274_1	chr10	28219405	28220100	+	0	NA	intron (NM_173496, intron 4 of 18)	intron (NM_173496, intron 4 of 18)	62386	NM_173496	143098	Hs.499159	NM_173496	ENSG00000150054	MPP7	-	membrane palmitoylated protein 7	protein-coding	0.010072	0.331897	
chunk0049_427_1	chr12	97907216	97907648	+	0	NA	Intergenic	Intergenic	31689	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.002315	0.323326	
chunk0081_360_1	chr17	47850505	47850954	+	0	NA	intron (NM_199262, intron 1 of 1)	intron (NM_199262, intron 1 of 1)	421	NM_001258248	80320	Hs.253603	NM_199262	ENSG00000189120	SP6	EPFN|EPIPROFIN|KLF14	Sp6 transcription factor	protein-coding	0.069042	0.617778	162(AGTACTCCCAGTTCTC,+,0.00)
chunk0178_402_1	chr7	40910285	40910848	+	0	NA	Intergenic	Intergenic	69373	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.003552	0.397163	
chunk0173_356_1	chr6	149151666	149151866	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-66158	NM_001292035	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.010000	0.472637	
chunk0152_66_1	chr5	57862652	57862919	+	0	NA	Intergenic	Intergenic	36377	NR_109900	101928539	Hs.639385	NR_109900	ENSG00000249584	LINC02225	-	long intergenic non-protein coding RNA 2225	ncRNA	0.003745	0.395522	
chunk0098_182_1	chr2	71350770	71351345	+	0	NA	intron (NM_014497, intron 2 of 27)	intron (NM_014497, intron 2 of 27)	19302	NM_001252612	27332	Hs.434401	NM_014497	ENSG00000075292	ZNF638	NP220|ZFML|Zfp638	zinc finger protein 638	protein-coding	0.008696	0.321181	217(TAGAACATACTGTTCA,-,0.00),218(AGAACATACTGTTCAG,+,0.00)
chunk0071_310_1	chr15	86180376	86181091	+	0	NA	intron (NM_152336, intron 4 of 23)	L1ME1|LINE|L1	38722	NM_152336	123624	Hs.31795	NM_152336	ENSG00000273540	AGBL1	CCP4|FECD8	ATP/GTP binding protein like 1	protein-coding	0.001399	0.307263	
chunk0061_222_1	chr14	60616552	60617163	+	0	NA	Intergenic	Intergenic	-22359	NR_126480	104548971		NR_126480		SALRNA1	SAL-RNA1|XLOC_023166	senescence associated long non-coding RNA 1	ncRNA	0.016367	0.423203	
chunk0110_231_1	chr20	16098633	16098937	+	0	NA	Intergenic	L1ME2z|LINE|L1	-112903	NR_130924	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.003289	0.272131	
chunk0159_426_1	chr5	148107636	148107882	+	0	NA	intron (NM_006846, intron 17 of 32)	MamTip3|DNA|hAT-Tip100	43787	NM_001127699	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.004065	0.384615	
chunk0075_18_1	chr16	46864464	46864692	+	0	NA	Intergenic	LTR24C|LTR|ERV1	-19802	NM_133443	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.004386	0.401747	80(AGGAACATCCTGTCTC,-,0.00),81(GGAACATCCTGTCTCA,+,0.00)
chunk0025_249_1	chr10	54603153	54603389	+	0	NA	intron (NM_001142769, intron 2 of 35)	L1M4|LINE|L1	4686	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.000000	0.295359	
chunk0195_40_1	chr8	93291815	93292252	+	0	NA	Intergenic	Intergenic	-125183	NM_001242668									0.002288	0.367580	131(ATGTACATAGTGTGCT,-,0.00),132(TGTACATAGTGTGCTA,+,0.00)
chunk0106_120_1	chr2	197878808	197879523	+	0	NA	intron (NM_006226, intron 1 of 5)	intron (NM_006226, intron 1 of 5)	74463	NM_006226	5334	Hs.153322	NM_006226	ENSG00000115896	PLCL1	PLCE|PLCL|PLDL1|PPP1R127|PRIP	phospholipase C like 1 (inactive)	protein-coding	0.001399	0.403631	
chunk0136_86_1	chr4	2489864	2490539	+	0	NA	intron (NM_001185009, intron 2 of 8)	intron (NM_001185009, intron 2 of 8)	20748	NM_001185009	6047	Hs.66394	NM_002938	ENSG00000063978	RNF4	RES4-26|SLX5|SNURF	ring finger protein 4	protein-coding	0.011852	0.440828	
chunk0056_97_1	chr13	82354007	82354391	+	0	NA	Intergenic	L1MA6|LINE|L1	-1127216	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.007812	0.355844	263(TAGGAGAGTCTGTTCT,-,0.00),264(AGGAGAGTCTGTTCTT,+,0.00)
chunk0092_266_1	chr19	33187038	33187396	+	0	NA	Intergenic	Intergenic	-7476	NM_002333	4037	Hs.515340	NM_002333	ENSG00000130881	LRP3	-	LDL receptor related protein 3	protein-coding	0.019553	0.490251	
chunk0192_73_1	chr8	60697727	60698253	+	0	NA	intron (NM_017780, intron 1 of 37)	MamRTE1|LINE|RTE-BovB	19225	NM_017780	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.003802	0.388994	
chunk0092_277_1	chr19	33433021	33433549	+	0	NA	intron (NM_001166056, intron 7 of 12)	intron (NM_001166056, intron 7 of 12)	58761	NM_001252296	1054	Hs.429666	NM_001806	ENSG00000153879	CEBPG	GPE1BP|IG/EBP-1	CCAAT enhancer binding protein gamma	protein-coding	0.003788	0.459357	
chunk0105_158_1	chr2	186701569	186702019	+	0	NA	intron (NM_177454, intron 1 of 7)	intron (NM_177454, intron 1 of 7)	7732	NM_177454	165215	Hs.28872	NM_177454	ENSG00000144369	FAM171B	KIAA1946	family with sequence similarity 171 member B	protein-coding	0.000000	0.328160	
chunk0017_321_1	chr1	211391887	211392371	+	0	NA	intron (NR_026761, intron 3 of 5)	L2c|LINE|L2	9374	NR_026761	84791	Hs.523932	NM_032705		LINC00467	C1orf97	long intergenic non-protein coding RNA 467	ncRNA	0.004132	0.331959	
chunk0164_440_1	chr6	27791348	27791547	+	0	NA	Intergenic	Intergenic	16484	NM_003519	8340	Hs.137594	NM_003519	ENSG00000185130	HIST1H2BL	H2B/c|H2BFC|dJ97D16.4	histone cluster 1 H2B family member l	protein-coding	0.025126	0.505000	
chunk0036_343_1	chr11	66782720	66782936	+	0	NA	intron (NM_001302084, intron 2 of 14)	intron (NM_001302084, intron 2 of 14)	38092	NM_024650	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.004630	0.368664	
chunk0172_283_1	chr6	137748693	137749188	+	0	NA	Intergenic	Intergenic	-9903	NR_121618	100507406	Hs.556703	NR_121618	ENSG00000234956	LINC02539	-	long intergenic non-protein coding RNA 2539	ncRNA	0.000000	0.433468	
chunk0187_137_1	chr7	149490303	149490502	+	0	NA	intron (NM_152557, intron 4 of 6)	L2a|LINE|L2	7405	NM_001163474	155061	Hs.24643	NM_152557	ENSG00000181220	ZNF746	PARIS	zinc finger protein 746	protein-coding	0.030151	0.555000	
chunk0060_125_1	chr14	44009717	44009916	+	0	NA	Intergenic	Intergenic	497480	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.005025	0.305000	
chunk0147_84_1	chr4	173170661	173170971	+	0	NA	intron (NM_017423, intron 1 of 11)	intron (NM_017423, intron 1 of 11)	2063	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.012903	0.363344	136(AGGTTCAGAATGTCCC,-,0.00),137(GGTTCAGAATGTCCCG,+,0.00)
chunk0003_208_1	chr1	35182179	35182693	+	0	NA	Intergenic	Intergenic	10706	NM_005066	6421	Hs.355934	NM_005066	ENSG00000116560	SFPQ	POMP100|PPP1R140|PSF	splicing factor proline and glutamine rich	protein-coding	0.003891	0.372816	277(TAGCACACCATGTACC,-,0.00),278(AGCACACCATGTACCT,+,0.00)
chunk0148_19_1	chr5	401572	401859	+	0	NA	intron (NM_020731, intron 4 of 11)	intron (NM_020731, intron 4 of 11)	41445	NR_126522	116349	Hs.446702	NM_138464	ENSG00000221990	EXOC3-AS1	C5orf55	EXOC3 antisense RNA 1	ncRNA	0.038328	0.576389	106(GGGCACAGAGTGTGAT,-,0.00)
chunk0209_303_1	chrX	49002349	49002669	+	0	NA	promoter-TSS (NM_020137)	promoter-TSS (NM_020137)	-245	NM_020137	56850	Hs.109929	NM_020137	ENSG00000068400	GRIPAP1	GRASP-1	GRIP1 associated protein 1	protein-coding	0.053125	0.489097	
chunk0155_290_1	chr5	96212381	96212654	+	0	NA	intron (NR_130776, intron 1 of 4)	L1MD|LINE|L1	133379	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.000000	0.343066	
chunk0142_155_1	chr4	95045352	95045906	+	0	NA	intron (NM_001256792, intron 1 of 10)	L2c|LINE|L2	-6050	NM_001256793	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.007220	0.409009	188(CTGTACTGCCTGTTCT,-,0.00),189(TGTACTGCCTGTTCTC,+,0.00)
chunk0125_310_1	chr3	70745877	70746209	+	0	NA	Intergenic	L1ME3A|LINE|L1	318880	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.000000	0.378378	
chunk0184_460_1	chr7	123598749	123598951	+	0	NA	intron (NR_111926, intron 1 of 7)	intron (NR_111926, intron 1 of 7)	2801	NR_111926	4698	Hs.651219	NM_005000	ENSG00000128609	NDUFA5	B13|CI-13KD-B|CI-13kB|NUFM|UQOR13	NADH:ubiquinone oxidoreductase subunit A5	protein-coding	0.009901	0.403941	
chunk0060_283_1	chr14	50452245	50452675	+	0	NA	intron (NM_006575, intron 14 of 31)	MER110-int|LTR|ERV1	-55056	NM_001282236	8814	Hs.280881	NM_004196	ENSG00000100490	CDKL1	KKIALRE|P42	cyclin dependent kinase like 1	protein-coding	0.002326	0.368910	
chunk0084_151_1	chr17	76645546	76645831	+	0	NA	Intergenic	Intergenic	-1850	NR_110309	55808	Hs.105352	NM_018414	ENSG00000070526	ST6GALNAC1	HSY11339|SIAT7A|ST6GalNAcI|STYI	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	protein-coding	0.014035	0.524476	153(GTGGACAATCTGTCCC,-,0.00),154(TGGACAATCTGTCCCT,+,0.00)
chunk0032_437_1	chr10	132765665	132766175	+	0	NA	intron (NM_005539, intron 12 of 15)	intron (NM_005539, intron 12 of 15)	20113	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.033333	0.522505	
chunk0126_414_1	chr3	85758283	85758884	+	0	NA	intron (NM_153184, intron 1 of 9)	intron (NM_153184, intron 1 of 9)	32101	NM_153184	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.323920	
chunk0014_113_1	chr1	176911520	176911933	+	0	NA	intron (NM_004319, intron 16 of 22)	Tigger3b|DNA|TcMar-Tigger	117719	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.012107	0.350242	
chunk0157_81_1	chr5	116532803	116533427	+	0	NA	intron (NM_001300780, intron 1 of 19)	intron (NM_001300780, intron 1 of 19)	41811	NM_020796	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.003205	0.393600	
chunk0134_99_1	chr3	176868505	176868761	+	0	NA	Intergenic	L1M1|LINE|L1	-51632	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.011719	0.529183	
chunk0083_255_1	chr17	68235613	68235812	+	0	NA	Intergenic	Intergenic	-12292	NM_001289054	51321	Hs.293560	NM_016627	ENSG00000196704	AMZ2	-	archaelysin family metallopeptidase 2	protein-coding	0.025126	0.610000	97(AGGAGCAGCGTGTGCC,-,0.00),98(GGAGCAGCGTGTGCCA,+,0.00),143(GGTACGTGCTGTGCCC,+,0.00)
chunk0199_433_1	chr9	13838735	13838991	+	0	NA	Intergenic	L1ME1|LINE|L1	-89108	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.000000	0.295720	
chunk0056_425_1	chr13	94641839	94642514	+	0	NA	Intergenic	Intergenic	40326	NM_180989	160897	Hs.439363	NM_180989	ENSG00000152749	GPR180	ITR	G protein-coupled receptor 180	protein-coding	0.007407	0.363905	
chunk0102_441_1	chr2	157867240	157867641	+	0	NA	intron (NM_001111067, intron 1 of 10)	intron (NM_001111067, intron 1 of 10)	7671	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.004988	0.480100	
chunk0034_432_1	chr11	38835936	38836289	+	0	NA	Intergenic	Intergenic	187254	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.008499	0.432203	178(TTGCACAGCTTGTGCT,-,0.00),179(TGCACAGCTTGTGCTT,+,0.00)
chunk0037_125_1	chr11	72935666	72936024	+	0	NA	intron (NM_014824, intron 8 of 19)	intron (NM_014824, intron 8 of 19)	55925	NR_039664									0.000000	0.314763	
chunk0009_172_1	chr1	105467144	105467536	+	0	NA	Intergenic	Intergenic	151595	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002551	0.376590	
chunk0151_193_1	chr5	50581953	50582414	+	0	NA	Intergenic	L1PA10|LINE|L1	-83716	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.002169	0.357143	
chunk0182_425_1	chr7	101252203	101252432	+	0	NA	Intergenic	CpG	-7227	NM_016068	51024	Hs.423968	NM_016068	ENSG00000214253	FIS1	CGI-135|TTC11	fission, mitochondrial 1	protein-coding	0.074236	0.595652	
chunk0050_155_1	chr12	103161632	103162133	+	0	NA	intron (NR_126333, intron 3 of 6)	intron (NR_126333, intron 3 of 6)	10040	NR_126333	101929058	Hs.171310	NR_126333	ENSG00000257860	LOC101929058	-	uncharacterized LOC101929058	ncRNA	0.003992	0.392430	202(AAGAACTTTATGTACT,-,0.00),203(AGAACTTTATGTACTT,+,0.00)
chunk0091_120_1	chr19	6250157	6250716	+	0	NA	intron (NM_005934, intron 3 of 11)	MER2B|DNA|TcMar-Tigger	29512	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.007156	0.407143	
chunk0037_283_1	chr11	75903627	75904039	+	0	NA	intron (NM_003369, intron 5 of 14)	intron (NM_003369, intron 5 of 14)	88666	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.007282	0.353511	
chunk0068_280_1	chr15	56887075	56888051	+	0	NA	non-coding (NR_015419, exon 4 of 4)	non-coding (NR_015419, exon 4 of 4)	30936	NR_015419	145783	Hs.620525	NR_015419	ENSG00000285331	LOC145783	-	uncharacterized LOC145783	ncRNA	0.074795	0.619243	258(AAGGACAAATAGTTCC,-,0.00),259(AGGACAAATAGTTCCG,+,0.00)
chunk0085_48_1	chr18	781314	781557	+	0	NA	intron (NM_005433, intron 1 of 11)	L2b|LINE|L2	30891	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.012346	0.418033	
chunk0044_421_1	chr12	41956358	41956683	+	0	NA	Intergenic	L1MC4|LINE|L1	188351	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.006154	0.374233	
chunk0184_110_1	chr7	113678229	113678428	+	0	NA	Intergenic	(AAAC)n|Simple_repeat|Simple_repeat	240699	NM_002711	5506	Hs.458309	NM_002711	ENSG00000154415	PPP1R3A	GM|PP1G|PPP1R3	protein phosphatase 1 regulatory subunit 3A	protein-coding	0.000000	0.390000	
chunk0059_21_1	chr14	29806438	29806664	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	121142	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.008850	0.356828	
chunk0119_364_1	chr22	47474820	47475417	+	0	NA	intron (NR_109967, intron 1 of 2)	L1MC3|LINE|L1	11993	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.006700	0.409699	321(GAGAACAGATCGTTCT,-,0.00),322(AGAACAGATCGTTCTG,+,0.00)
chunk0094_272_1	chr2	8070432	8070792	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	-93798	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.002778	0.337950	
chunk0106_54_1	chr2	196285025	196285756	+	0	NA	intron (NM_020760, intron 14 of 28)	intron (NM_020760, intron 14 of 28)	25366	NR_110226	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.005472	0.331967	
chunk0139_273_1	chr4	56728447	56729033	+	0	NA	Intergenic	Intergenic	-47034	NM_001145460	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.017065	0.466780	290(GAGAACGAAGTGTTCC,-,0.00),291(AGAACGAAGTGTTCCC,+,0.00)
chunk0029_39_1	chr10	96271408	96271896	+	0	NA	promoter-TSS (NM_013314)	promoter-TSS (NM_013314)	-76	NM_013314	29760	Hs.665244	NM_013314	ENSG00000095585	BLNK	AGM4|BASH|BLNK-S|LY57|SLP-65|SLP65|bca	B cell linker	protein-coding	0.008197	0.456033	
chunk0025_351_1	chr10	58300803	58301002	+	0	NA	Intergenic	Intergenic	31800	NM_018464	55847	Hs.370102	NM_018464	ENSG00000122873	CISD1	C10orf70|MDS029|ZCD1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding	0.000000	0.380000	
chunk0174_160_1	chr6	158335545	158335885	+	0	NA	intron (NM_001007466, intron 1 of 12)	L1MC4|LINE|L1	23055	NM_001007466	56995	Hs.486993	NM_020245	ENSG00000130338	TULP4	TUSP	TUB like protein 4	protein-coding	0.008824	0.354839	232(CAGCACATGGTGTGCC,-,0.00),233(AGCACATGGTGTGCCA,+,0.00)
chunk0016_19_1	chr1	192854359	192854928	+	0	NA	Intergenic	Intergenic	45604	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.001757	0.375439	
chunk0014_106_1	chr1	176761089	176761663	+	0	NA	intron (NM_020318, intron 14 of 22)	intron (NM_020318, intron 14 of 22)	268069	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.008711	0.424348	
chunk0107_182_1	chr2	215835382	215836083	+	0	NA	intron (NR_037195, intron 1 of 9)	intron (NR_037195, intron 1 of 9)	7804	NR_037195	646324	Hs.655713	NR_037195	ENSG00000235770	LINC00607	-	long intergenic non-protein coding RNA 607	ncRNA	0.002853	0.324786	
chunk0108_453_1	chr2	238299579	238300283	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-11365	NM_022817	8864	Hs.58756	NM_003894	ENSG00000132326	PER2	FASPS|FASPS1	period circadian regulator 2	protein-coding	0.015625	0.478014	192(GAGAACAGGTTGTTCT,-,0.00),193(AGAACAGGTTGTTCTT,+,0.00)
chunk0055_236_1	chr13	62821938	62822438	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-14829	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.004000	0.301397	
chunk0155_76_1	chr5	91813832	91814151	+	0	NA	Intergenic	Intergenic	-430659	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003135	0.306250	
chunk0135_356_1	chr3	190590871	190591070	+	0	NA	intron (NM_134470, intron 3 of 8)	intron (NM_134470, intron 3 of 8)	76919	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.005025	0.330000	
chunk0185_105_1	chr7	125648607	125648950	+	0	NA	Intergenic	L1MCb|LINE|L1	-384487	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.002915	0.325581	
chunk0177_437_1	chr7	27990838	27991618	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	-189229	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.001282	0.335467	422(GGGACTGTGTGTTTTC,+,0.00)
chunk0004_70_1	chr1	43395517	43396893	+	0	NA	intron (NM_015284, intron 1 of 70)	L3|LINE|CR1	6320	NM_015284	23334	Hs.643560	NM_015284	ENSG00000198198	SZT2	C1orf84|EIEE18|KIAA0467|SZT2A|SZT2B	SZT2 subunit of KICSTOR complex	protein-coding	0.005814	0.392157	
chunk0115_179_1	chr21	25865260	25866151	+	0	NA	Intergenic	Intergenic	-130051	NM_001685	522	Hs.246310	NM_001685	ENSG00000154723	ATP5PF	ATP5|ATP5A|ATP5J|ATPM|CF6|F6	ATP synthase peripheral stalk subunit F6	protein-coding	0.004489	0.386771	
chunk0170_91_1	chr6	110389732	110390281	+	0	NA	Intergenic	Intergenic	25544	NM_004032	8528	Hs.591348	NM_003649	ENSG00000203797	DDO	DASOX|DDO-1|DDO-2	D-aspartate oxidase	protein-coding	0.005464	0.463636	
chunk0172_31_1	chr6	133548703	133549021	+	0	NA	intron (NR_109982, intron 5 of 8)	L2a|LINE|L2	-272285	NR_027030	154089	Hs.126165	NR_027030		LINC01312	-	long intergenic non-protein coding RNA 1312	ncRNA	0.006289	0.398119	
chunk0051_252_1	chr12	117393770	117394143	+	0	NA	Intergenic	L2b|LINE|L2	-32154	NM_000620	4842	Hs.654410	NM_000620	ENSG00000089250	NOS1	IHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS	nitric oxide synthase 1	protein-coding	0.016086	0.516043	
chunk0089_157_1	chr18	59084950	59085277	+	0	NA	Intergenic	Intergenic	49434	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.009174	0.530488	
chunk0206_277_1	chr9	124259522	124259782	+	0	NA	intron (NM_001166168, intron 1 of 9)	intron (NM_001166168, intron 1 of 9)	1401	NM_001166168	10783	Hs.197071	NM_014397	ENSG00000119408	NEK6	SID6-1512	NIMA related kinase 6	protein-coding	0.015385	0.505747	
chunk0033_18_1	chr11	12504501	12504746	+	0	NA	intron (NM_018222, intron 6 of 12)	intron (NM_018222, intron 6 of 12)	127144	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.008163	0.455285	121(GGAAGAGCGTGTGCTT,+,0.00)
chunk0072_94_1	chr15	91007246	91007707	+	0	NA	exon (NM_018668, exon 8 of 23)	exon (NM_018668, exon 8 of 23)	-12825	NM_003981	9055	Hs.366401	NM_003981	ENSG00000198901	PRC1	ASE1	protein regulator of cytokinesis 1	protein-coding	0.006508	0.500000	
chunk0180_96_1	chr7	55177508	55178189	+	0	NA	intron (NM_005228, intron 19 of 27)	intron (NM_005228, intron 19 of 27)	11101	NR_047551	100507500	Hs.720489	NR_047551	ENSG00000224057	EGFR-AS1	-	EGFR antisense RNA 1	ncRNA	0.027900	0.536657	
chunk0182_36_1	chr7	91596448	91596698	+	0	NA	Intergenic	Intergenic	284147	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.004000	0.398406	
chunk0206_266_1	chr9	124008855	124009249	+	0	NA	Intergenic	CpG	-2558	NM_004789	9355	Hs.696425	NM_004789	ENSG00000106689	LHX2	LH2|hLhx2	LIM homeobox 2	protein-coding	0.078680	0.630380	
chunk0070_34_1	chr15	69387877	69388264	+	0	NA	intron (NM_001104554, intron 5 of 8)	intron (NM_001104554, intron 5 of 8)	-26176	NM_001281301	9493	Hs.270845	NM_004856	ENSG00000137807	KIF23	CHO1|KNSL5|MKLP-1|MKLP1	kinesin family member 23	protein-coding	0.010336	0.567010	186(AGGAACATCTAGTCCA,-,0.00)
chunk0109_442_1	chr2	241506870	241507266	+	0	NA	intron (NM_001282305, intron 1 of 10)	intron (NM_001282305, intron 1 of 10)	1292	NM_001271978	10494	Hs.516807	NM_006374	ENSG00000115694	STK25	SOK1|YSK1	serine/threonine kinase 25	protein-coding	0.027778	0.554156	81(CTGCACATGGTGTTCC,-,0.00),82(TGCACATGGTGTTCCG,+,0.00)
chunk0040_66_1	chr11	111253143	111253543	+	0	NA	Intergenic	Charlie17a|DNA|hAT-Charlie	-2639	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.002500	0.421446	
chunk0056_36_1	chr13	77323547	77323890	+	0	NA	intron (NM_015057, intron 1 of 82)	L2a|LINE|L2	3324	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.008746	0.392442	
chunk0002_171_1	chr1	18903232	18903768	+	0	NA	promoter-TSS (NM_170726)	promoter-TSS (NM_170726)	-701	NM_003748	8659	Hs.77448	NM_003748	ENSG00000159423	ALDH4A1	ALDH4|P5CD|P5CDh	aldehyde dehydrogenase 4 family member A1	protein-coding	0.018657	0.417132	
chunk0116_214_1	chr21	37599223	37599729	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	179176	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.013834	0.426036	
chunk0113_144_1	chr20	52186179	52186572	+	0	NA	intron (NM_018197, intron 2 of 5)	intron (NM_018197, intron 2 of 5)	5610	NM_022088	55734	Hs.473082	NM_018197	ENSG00000020256	ZFP64	ZNF338	ZFP64 zinc finger protein	protein-coding	0.002545	0.362944	
chunk0141_321_1	chr4	87251110	87251497	+	0	NA	Intergenic	Intergenic	-30695	NM_001292007	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.015504	0.422680	
chunk0159_194_1	chr5	140323066	140323771	+	0	NA	Intergenic	Intergenic	-20314	NM_002622	5201	Hs.483564	NM_002622	ENSG00000113068	PFDN1	PDF|PFD1	prefoldin subunit 1	protein-coding	0.011348	0.577904	
chunk0010_102_1	chr1	114053990	114054214	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	74711	NM_001286352	56944	Hs.9315	NM_020190	ENSG00000116774	OLFML3	HNOEL-iso|OLF44	olfactomedin like 3	protein-coding	0.004464	0.426667	16(AGGTCTCTGTGTTCTT,+,0.00)
chunk0138_2_1	chr4	30191751	30192374	+	0	NA	Intergenic	Intergenic	-528346	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.001605	0.339744	
chunk0164_388_1	chr6	26158784	26159147	+	0	NA	TTS (NM_021063)	TTS (NM_021063)	844	NM_138720	3017	Hs.591797	NM_021063	ENSG00000158373	HIST1H2BD	H2B.1B|H2B/a|H2B/b|H2B/g|H2B/h|H2B/k|H2B/l|H2BFA|H2BFB|H2BFG|H2BFH|H2BFK|H2BFL|HIRIP2|HIST1H2BC|HIST1H2BE|HIST1H2BF|HIST1H2BG|HIST1H2BI|dJ221C16.6	histone cluster 1 H2B family member d	protein-coding	0.033058	0.445055	
chunk0105_396_1	chr2	192536207	192536839	+	0	NA	Intergenic	Intergenic	-213322	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.003165	0.285940	
chunk0015_449_1	chr1	192262712	192263065	+	0	NA	Intergenic	Intergenic	-54104	NM_001039152	431704	Hs.558673	NM_001039152	ENSG00000253148	RGS21	-	regulator of G protein signaling 21	protein-coding	0.000000	0.288136	
chunk0104_95_1	chr2	172282025	172282320	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-145182	NM_001316306	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.003390	0.368243	
chunk0011_84_1	chr1	145256031	145256496	+	0	NA	Intergenic	L1ME4a|LINE|L1	-14064	NM_001164262	728945		NM_001164262	ENSG00000279782	PPIAL4F	-	peptidylprolyl isomerase A like 4F	protein-coding	0.002151	0.268240	
chunk0090_345_1	chr18	76428365	76428699	+	0	NA	intron (NM_014643, intron 3 of 6)	intron (NM_014643, intron 3 of 6)	66658	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.014970	0.417910	
chunk0160_94_1	chr5	150263302	150263613	+	0	NA	intron (NM_171825, intron 3 of 17)	(AC)n|Simple_repeat|Simple_repeat	26383	NM_015981	815	Hs.743976	NM_015981	ENSG00000070808	CAMK2A	CAMKA|CaMKIINalpha|MRD53|MRT63	calcium/calmodulin dependent protein kinase II alpha	protein-coding	0.012862	0.451923	
chunk0171_351_1	chr6	130232516	130232738	+	0	NA	intron (NM_001258275, intron 2 of 13)	MIRc|SINE|MIR	-9673	NM_001017373	154075	Hs.440508	NM_152552	ENSG00000164483	SAMD3	-	sterile alpha motif domain containing 3	protein-coding	0.009009	0.349776	27(TGAAACACTATGTTCT,-,0.00),28(GAAACACTATGTTCTG,+,0.00)
chunk0144_89_1	chr4	128349731	128350131	+	0	NA	Intergenic	Intergenic	-61102	NM_006320	10424	Hs.507910	NM_006320	ENSG00000164040	PGRMC2	DG6|PMBP	progesterone receptor membrane component 2	protein-coding	0.010000	0.331671	
chunk0062_91_1	chr14	68108211	68108837	+	0	NA	intron (NM_133509, intron 7 of 10)	L1MB7|LINE|L1	288745	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.009585	0.328549	
chunk0131_274_1	chr3	150193843	150194649	+	0	NA	Intergenic	Intergenic	-44273	NR_110168	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.001241	0.334572	
chunk0018_96_1	chr1	217724801	217725008	+	0	NA	intron (NM_138796, intron 5 of 10)	L1M5|LINE|L1	60216	NR_125784	103752555	Hs.602803	NR_125784	ENSG00000234070	SPATA17-AS1	-	SPATA17 antisense RNA 1	ncRNA	0.000000	0.307692	
chunk0030_436_1	chr10	120729364	120729918	+	0	NA	Intergenic	Intergenic	-121534	NM_018117	55717	Hs.144447	NM_018117	ENSG00000120008	WDR11	BRWD2|DR11|HH14|SRI1|WDR15	WD repeat domain 11	protein-coding	0.007220	0.356757	
chunk0133_103_1	chr3	167977952	167978741	+	0	NA	Intergenic	Intergenic	82398	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.007605	0.443038	
chunk0041_139_1	chr11	125300782	125301384	+	0	NA	intron (NM_022062, intron 2 of 12)	intron (NM_022062, intron 2 of 12)	136420	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.008306	0.514096	
chunk0201_19_1	chr9	33082966	33083356	+	0	NA	Intergenic	Intergenic	-6445	NM_018225	55234	Hs.655351	NM_018225	ENSG00000122692	SMU1	BWD|SMU-1|fSAP57	SMU1 DNA replication regulator and spliceosomal factor	protein-coding	0.007692	0.544757	
chunk0198_269_1	chr8	134990918	134991236	+	0	NA	Intergenic	L1MC4|LINE|L1	141142	NR_125427	101927845	Hs.559609	NR_125427	ENSG00000251218	LOC101927845	-	uncharacterized LOC101927845	ncRNA	0.018868	0.401254	
chunk0105_152_1	chr2	186543994	186544914	+	0	NA	Intergenic	Intergenic	-45609	NM_001145000	3685	Hs.436873	NM_002210	ENSG00000138448	ITGAV	CD51|MSK8|VNRA|VTNR	integrin subunit alpha V	protein-coding	0.004348	0.355049	
chunk0027_381_1	chr10	79560430	79560631	+	0	NA	promoter-TSS (NM_001098668)	promoter-TSS (NM_001098668)	-123	NM_001098668	729238	Hs.523084	NM_001098668	ENSG00000185303	SFTPA2	COLEC5|PSAP|PSP-A|PSPA|SFTP1|SFTPA2B|SP-2A|SP-A|SPA2|SPAII	surfactant protein A2	protein-coding	0.000000	0.475248	
chunk0039_245_1	chr11	102118882	102119150	+	0	NA	intron (NM_001282098, intron 2 of 6)	intron (NM_001282098, intron 2 of 6)	6576	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.011194	0.405204	
chunk0109_380_1	chr2	239815829	239816035	+	0	NA	Intergenic	Intergenic	53072	NR_037808	150935	Hs.555582	NR_037808		LOC150935	-	uncharacterized LOC150935	ncRNA	0.043689	0.541063	
chunk0212_12_1	chrY	7794474	7794673	+	0	NA	Intergenic	Intergenic	-10351	NR_001551	83867	Hs.667616	NR_001551	ENSG00000237048	TTTY12	NCRNA00135|TTY11|TTY12	testis-specific transcript, Y-linked 12	ncRNA	0.005025	0.425000	
chunk0023_461_1	chr10	32360985	32361263	+	0	NA	intron (NR_104163, intron 1 of 1)	LTR56|LTR|ERV1	13760	NR_104163	102031319	Hs.128132	NR_104163	ENSG00000229327	LOC102031319	-	uncharacterized LOC102031319	ncRNA	0.000000	0.401434	
chunk0137_386_1	chr4	26787656	26787956	+	0	NA	Intergenic	Intergenic	-72885	NM_020860	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.010000	0.504983	207(GTGGACTTCCTGTGCC,-,0.00),208(TGGACTTCCTGTGCCC,+,0.00)
chunk0019_159_1	chr1	225958402	225958618	+	0	NA	Intergenic	Intergenic	-17127	NM_003240	7044	Hs.520187	NM_003240	ENSG00000143768	LEFTY2	EBAF|LEFTA|LEFTYA|TGFB4	left-right determination factor 2	protein-coding	0.023148	0.548387	
chunk0025_200_1	chr10	53473641	53474051	+	0	NA	Intergenic	L1ME2z|LINE|L1	-702146	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.004878	0.326034	
chunk0039_367_1	chr11	106127667	106128043	+	0	NA	Intergenic	Intergenic	-50117	NM_152433	143879	Hs.101949	NM_152433	ENSG00000182359	KBTBD3	BKLHD3	kelch repeat and BTB domain containing 3	protein-coding	0.010638	0.331565	
chunk0026_359_1	chr10	69114345	69114801	+	0	NA	Intergenic	HSMAR1|DNA|TcMar-Mariner	-9579	NM_004896	9559	Hs.499925	NM_004896	ENSG00000122958	VPS26A	HB58|Hbeta58|PEP8A|VPS26	VPS26, retromer complex component A	protein-coding	0.013158	0.352298	
chunk0007_370_1	chr1	85214550	85215252	+	0	NA	Intergenic	Intergenic	-13856	NM_032184	84144	Hs.533853	NM_032184	ENSG00000097096	SYDE2	-	synapse defective Rho GTPase homolog 2	protein-coding	0.014245	0.351351	
chunk0093_77_1	chr19	40720612	40720914	+	0	NA	intron (NM_025194, intron 1 of 6)	L2c|LINE|L2	3660	NM_025194	80271	Hs.515415	NM_025194	ENSG00000086544	ITPKC	IP3-3KC|IP3KC	inositol-trisphosphate 3-kinase C	protein-coding	0.026490	0.554455	126(GAGTACACACTGTTCC,-,0.00),127(AGTACACACTGTTCCT,+,0.00)
chunk0046_391_1	chr12	63862372	63862731	+	0	NA	intron (NM_020762, intron 1 of 21)	intron (NM_020762, intron 1 of 21)	17790	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.005571	0.405556	
chunk0129_371_1	chr3	125512395	125512603	+	0	NA	intron (NM_003794, intron 1 of 13)	intron (NM_003794, intron 1 of 13)	7715	NR_073435	8723	Hs.507243	NM_003794	ENSG00000114520	SNX4	ATG24B	sorting nexin 4	protein-coding	0.000000	0.325359	
chunk0164_254_1	chr6	23486630	23486922	+	0	NA	Intergenic	L1MB3|LINE|L1	-639410	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.006849	0.361775	
chunk0083_93_1	chr17	64360301	64360784	+	0	NA	intron (NM_000442, intron 6 of 15)	intron (NM_000442, intron 6 of 15)	30336	NM_000442	5175	Hs.376675	NM_000442	ENSG00000261371	PECAM1	CD31|CD31/EndoCAM|GPIIA'|PECA1|PECAM-1|endoCAM	platelet and endothelial cell adhesion molecule 1	protein-coding	0.010352	0.423554	
chunk0100_244_1	chr2	112939397	112939952	+	0	NA	Intergenic	Intergenic	24481	NM_173205	27178	Hs.166371	NM_014439	ENSG00000125571	IL37	FIL1|FIL1(ZETA)|FIL1Z|IL-1F7|IL-1H|IL-1H4|IL-1RP1|IL-37|IL1F7|IL1H4|IL1RP1	interleukin 37	protein-coding	0.009009	0.462230	247(TGGGACTACCTGTGCC,-,0.00),248(GGGACTACCTGTGCCT,+,0.00),336(TGGAGCAGGCTGTCCT,-,0.00),337(GGAGCAGGCTGTCCTT,+,0.00)
chunk0202_136_1	chr9	73335262	73335768	+	0	NA	Intergenic	L1MC4|LINE|L1	183784	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.003953	0.323471	
chunk0002_214_1	chr1	19629263	19629635	+	0	NA	non-coding (NR_033758, exon 5 of 5)	non-coding (NR_033758, exon 5 of 5)	-13780	NM_001278164	4681	Hs.654502	NM_005380	ENSG00000158747	NBL1	D1S1733E|DAN|DAND1|NB|NO3	NBL1, DAN family BMP antagonist	protein-coding	0.008065	0.453083	
chunk0103_318_1	chr2	167508543	167509198	+	0	NA	Intergenic	Intergenic	-309802	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.001527	0.312500	
chunk0116_171_1	chr21	36788034	36788751	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	89259	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.016736	0.473538	
chunk0168_134_1	chr6	82877097	82877743	+	0	NA	Intergenic	Intergenic	188421	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.003096	0.426584	
chunk0035_253_1	chr11	46289955	46290259	+	0	NA	intron (NM_052854, intron 1 of 11)	intron (NM_052854, intron 1 of 11)	12469	NM_052854	90993	Hs.405961	NM_052854	ENSG00000157613	CREB3L1	OASIS|OI16	cAMP responsive element binding protein 3 like 1	protein-coding	0.006579	0.609836	230(AGGGACAGGCTGTTCC,-,0.00),231(GGGACAGGCTGTTCCT,+,0.00)
chunk0024_215_1	chr10	37159919	37160130	+	0	NA	intron (NM_052997, intron 15 of 35)	intron (NM_052997, intron 15 of 35)	34167	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.037915	0.462264	112(CTGTACATATTGTCCT,-,0.00),113(TGTACATATTGTCCTG,+,0.00)
chunk0014_165_1	chr1	178304497	178304784	+	0	NA	intron (NM_170692, intron 3 of 17)	L2|LINE|L2	-36831	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.010453	0.371528	
chunk0148_304_1	chr5	12688533	12688829	+	0	NA	intron (NR_033383, intron 2 of 3)	L2a|LINE|L2	20822	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.030405	0.451178	
chunk0158_411_1	chr5	134904669	134905516	+	0	NA	promoter-TSS (NM_032151)	promoter-TSS (NM_032151)	-28	NM_032151	84105	Hs.710014	NM_032151	ENSG00000132570	PCBD2	DCOH2|DCOHM|PHS2	pterin-4 alpha-carbinolamine dehydratase 2	protein-coding	0.128689	0.742925	
chunk0149_75_1	chr5	17216007	17216342	+	0	NA	promoter-TSS (NM_001271606)	promoter-TSS (NM_001271606)	-649	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.038806	0.473214	152(AGGGCCACCCTGTCCC,-,0.00),153(GGGCCACCCTGTCCCT,+,0.00)
chunk0110_51_1	chr20	10754749	10755158	+	0	NA	TTS (NR_110611)	TTS (NR_110611)	1863	NR_110611	101929395	Hs.244862	NR_110611		LINC01752	-	long intergenic non-protein coding RNA 1752	ncRNA	0.004890	0.382927	
chunk0012_54_1	chr1	155478004	155478381	+	0	NA	exon (NM_018489, exon 3 of 28)	exon (NM_018489, exon 3 of 28)	45012	NR_034180	645682	Hs.632482	NR_034180	ENSG00000237872	POU5F1P4	OCT3|OCT4|OTF-3|OTF3|Oct-3|Oct-4|Oct4-pg4|POU5F1|POU5FLC1	POU class 5 homeobox 1 pseudogene 4	pseudo	0.013263	0.468254	
chunk0179_13_1	chr7	42485195	42485613	+	0	NA	Intergenic	L1ME4a|LINE|L1	221043	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.004785	0.322196	
chunk0190_373_1	chr8	39947302	39947564	+	0	NA	intron (NM_194294, intron 1 of 10)	LTR10C|LTR|ERV1	12478	NM_194294	169355	Hs.676257	NM_194294	ENSG00000188676	IDO2	INDOL1	indoleamine 2,3-dioxygenase 2	protein-coding	0.003817	0.365019	74(ATGTACTTTATGTTCT,-,0.00),75(TGTACTTTATGTTCTT,+,0.00)
chunk0047_315_1	chr12	74093518	74094261	+	0	NA	Intergenic	L1MB1|LINE|L1	198742	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.002692	0.306452	
chunk0036_217_1	chr11	63634453	63635001	+	0	NA	intron (NM_015459, intron 10 of 12)	intron (NM_015459, intron 10 of 12)	-20258	NM_001128203	11145	Hs.502775	NM_007069	ENSG00000176485	PLAAT3	AdPLA|H-REV107|H-REV107-1|HRASLS3|HREV107|HREV107-1|HREV107-3|HRSL3|PLA2G16|PLAAT-3	phospholipase A and acyltransferase 3	protein-coding	0.012774	0.422587	
chunk0185_177_1	chr7	128012107	128012589	+	0	NA	intron (NM_014390, intron 16 of 23)	intron (NM_014390, intron 16 of 23)	14839	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.008299	0.480331	257(CAGCACTGCATGTCCC,-,0.00),258(AGCACTGCATGTCCCA,+,0.00)
chunk0005_4_1	chr1	53956570	53957111	+	0	NA	intron (NM_052940, intron 2 of 7)	intron (NM_052940, intron 2 of 7)	10514	NM_001256409	115353	Hs.40094	NM_052940	ENSG00000116212	LRRC42	dJ167A19.4	leucine rich repeat containing 42	protein-coding	0.005545	0.400369	
chunk0185_166_1	chr7	127840905	127841231	+	0	NA	intron (NM_014390, intron 11 of 23)	intron (NM_014390, intron 11 of 23)	-156441	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.000000	0.418960	
chunk0175_116_1	chr7	3275903	3276104	+	0	NA	Intergenic	Intergenic	-25445	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.004975	0.405941	129(CAGAACATGATGTTCT,-,0.00),130(AGAACATGATGTTCTG,+,0.00)
chunk0111_12_1	chr20	21872891	21873135	+	0	NA	Intergenic	L1MC2|LINE|L1	167354	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.000000	0.371429	
chunk0108_155_1	chr2	231058629	231058990	+	0	NA	intron (NR_034059, intron 1 of 23)	L2a|LINE|L2	1945	NM_002807	5707	Hs.3887	NM_002807	ENSG00000173692	PSMD1	P112|Rpn2|S1	proteasome 26S subunit, non-ATPase 1	protein-coding	0.008310	0.433702	103(TGGACTTTTTGTTCCT,+,0.00),153(TGGCACATTCTGTTCC,-,0.00),154(GGCACATTCTGTTCCT,+,0.00)
chunk0070_387_1	chr15	76768850	76769083	+	0	NA	intron (NM_020843, intron 9 of 30)	L1ME1|LINE|L1	92978	NM_001145923	49855	Hs.458986	NM_020843	ENSG00000140386	SCAPER	IDDRP|MSTP063|ZNF291|Zfp291	S-phase cyclin A associated protein in the ER	protein-coding	0.008584	0.307692	
chunk0093_399_1	chr19	56930691	56931530	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	90208	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.005959	0.321429	
chunk0033_147_1	chr11	15493770	15494395	+	0	NA	Intergenic	MER54B|LTR|ERVL	-149803	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.001600	0.452077	
chunk0005_293_1	chr1	60149279	60149716	+	0	NA	Intergenic	Intergenic	-75727	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.006865	0.463470	
chunk0056_123_1	chr13	83065083	83065674	+	0	NA	Intergenic	Intergenic	817015	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.005076	0.429054	296(AGGCACATTCTGTTCC,-,0.00),297(GGCACATTCTGTTCCC,+,0.00)
chunk0044_281_1	chr12	32660120	32660319	+	0	NA	Intergenic	Intergenic	-18981	NM_012063	10059	Hs.556296	NM_005690	ENSG00000087470	DNM1L	DLP1|DRP1|DVLP|DYMPLE|EMPF|EMPF1|HDYNIV|OPA5	dynamin 1 like	protein-coding	0.015075	0.450000	
chunk0061_228_1	chr14	60622561	60622926	+	0	NA	Intergenic	Intergenic	-16473	NR_126480	104548971		NR_126480		SALRNA1	SAL-RNA1|XLOC_023166	senescence associated long non-coding RNA 1	ncRNA	0.005479	0.382514	
chunk0098_188_1	chr2	71772689	71773134	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	306209	NM_001130983	8291	Hs.252180	NM_003494	ENSG00000135636	DYSF	FER1L1|LGMD2B|LGMDR2|MMD1	dysferlin	protein-coding	0.008989	0.354260	
chunk0037_423_1	chr11	80067169	80067368	+	0	NA	Intergenic	Intergenic	-626617	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.010050	0.380000	152(CTGAACAGTATGTTCT,-,0.00),153(TGAACAGTATGTTCTG,+,0.00)
chunk0016_441_1	chr1	204074265	204074727	+	0	NA	intron (NM_005686, intron 1 of 13)	CpG	1378	NM_005686	9580	Hs.201671	NM_005686	ENSG00000143842	SOX13	ICA12|Sox-13	SRY-box transcription factor 13	protein-coding	0.088745	0.654428	
chunk0135_192_1	chr3	188220949	188221401	+	0	NA	intron (NM_005578, intron 1 of 10)	L2c|LINE|L2	-4230	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.017699	0.467991	216(GAGAACACCCTGAACT,-,0.00),217(AGAACACCCTGAACTC,+,0.00),249(TTGCACATTGTGTTCC,-,0.00),250(TGCACATTGTGTTCCC,+,0.00)
chunk0011_277_1	chr1	151328025	151328359	+	0	NA	promoter-TSS (NM_001198775)	promoter-TSS (NM_001198775)	-477	NM_001198774	5298	Hs.632465	NM_002651	ENSG00000143393	PI4KB	NPIK|PI4K-BETA|PI4K92|PI4KBETA|PI4KIIIBETA|PIK4CB	phosphatidylinositol 4-kinase beta	protein-coding	0.065868	0.594030	
chunk0196_190_1	chr8	106168562	106169198	+	0	NA	Intergenic	Intergenic	-101298	NM_001198533	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.006289	0.381476	282(CAGCACATCATGTTTC,-,0.00),283(AGCACATCATGTTTCT,+,0.00)
chunk0178_408_1	chr7	40976926	40977201	+	0	NA	intron (NR_110831, intron 1 of 2)	intron (NR_110831, intron 1 of 2)	2876	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.010909	0.442029	
chunk0011_266_1	chr1	151064374	151064862	+	0	NA	intron (NM_006818, intron 1 of 1)	intron (NM_006818, intron 1 of 1)	4943	NM_006818	10962	Hs.75823	NM_006818	ENSG00000213190	MLLT11	AF1Q	MLLT11 transcription factor 7 cofactor	protein-coding	0.006148	0.456033	
chunk0050_453_1	chr12	110790158	110790803	+	0	NA	Intergenic	L1ME3E|LINE|L1	-47502	NM_002710	5501	Hs.79081	NM_002710	ENSG00000186298	PPP1CC	PP-1G|PP1C|PPP1G	protein phosphatase 1 catalytic subunit gamma	protein-coding	0.003101	0.382353	
chunk0061_309_1	chr14	61911625	61911982	+	0	NA	Intergenic	Intergenic	-84020	NM_031914	83851	Hs.404139	NM_031914	ENSG00000139973	SYT16	CHR14SYT|SYT14L|Strep14|syt14r	synaptotagmin 16	protein-coding	0.011204	0.385475	147(AAGAACTCAATGTTCC,-,0.00),148(AGAACTCAATGTTCCA,+,0.00)
chunk0162_387_1	chr5	179459820	179460199	+	0	NA	Intergenic	Intergenic	-90552	NM_025158	80230	Hs.306769	NM_025158	ENSG00000176783	RUFY1	RABIP4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding	0.026385	0.555263	142(CAGAACACCTTGTCCT,-,0.00),143(AGAACACCTTGTCCTT,+,0.00)
chunk0088_51_1	chr18	44066464	44067660	+	0	NA	Intergenic	Intergenic	464635	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.004181	0.365079	
chunk0056_285_1	chr13	90432597	90432841	+	0	NA	Intergenic	PRIMA4-int|LTR|ERV1	-60569	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.012295	0.412245	
chunk0179_72_1	chr7	44073539	44073961	+	0	NA	promoter-TSS (NR_106897)	promoter-TSS (NR_106897)	-317	NR_106897	102465504		NR_106897	ENSG00000283969	MIR6838	hsa-mir-6838	microRNA 6838	ncRNA	0.035545	0.621749	
chunk0165_146_1	chr6	33713762	33714238	+	0	NA	Intergenic	Intergenic	-2249	NM_032340	84300	Hs.732448	NM_032340	ENSG00000137288	UQCC2	C6orf125|C6orf126|Cbp6|M19|MC3DN7|MNF1|bA6B20.2	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding	0.006303	0.438155	
chunk0078_56_1	chr17	1452069	1452451	+	0	NA	intron (NM_005206, intron 1 of 2)	MIR|SINE|MIR	4007	NM_005206	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.005236	0.362924	234(AGGTACATAAAGTACT,-,0.00),235(GGTACATAAAGTACTC,+,0.00)
chunk0101_136_1	chr2	127431645	127432466	+	0	NA	Intergenic	Intergenic	-8437	NR_039944	100616187		NR_039944	ENSG00000264075	MIR4783	-	microRNA 4783	ncRNA	0.023143	0.461071	
chunk0182_123_1	chr7	94253132	94253331	+	0	NA	Intergenic	Intergenic	-141330	NM_000089	1278	Hs.489142	NM_000089	ENSG00000164692	COL1A2	EDSARTH2|EDSCV|OI4	collagen type I alpha 2 chain	protein-coding	0.000000	0.415000	
chunk0057_276_1	chr13	105949670	105949869	+	0	NA	Intergenic	Intergenic	242939	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.005025	0.345000	
chunk0185_416_1	chr7	134300122	134300321	+	0	NA	exon (NM_032826, exon 7 of 10)	exon (NM_032826, exon 7 of 10)	16854	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.010050	0.405000	
chunk0124_366_1	chr3	59193832	59194378	+	0	NA	Intergenic	L1M5|LINE|L1	-144116	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.010989	0.365631	
chunk0164_382_1	chr6	26025441	26025671	+	0	NA	Intergenic	Intergenic	1696	NM_003544	8366	Hs.143080	NM_003544	ENSG00000278705	HIST1H4B	H4/I|H4FI	histone cluster 1 H4 family member b	protein-coding	0.013043	0.471861	
chunk0010_108_1	chr1	114188450	114188884	+	0	NA	Intergenic	AluSx3|SINE|Alu	-34817	NM_001270805	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.013825	0.501149	
chunk0117_139_1	chr22	19440925	19441160	+	0	NA	3' UTR (NM_001166242, exon 3 of 3)	3' UTR (NM_001166242, exon 3 of 3)	7190	NM_001166242	128977	Hs.659565	NM_173793	ENSG00000242259	C22orf39	-	chromosome 22 open reading frame 39	protein-coding	0.004255	0.470339	
chunk0029_104_1	chr10	97596554	97597072	+	0	NA	intron (NM_001134670, intron 1 of 2)	intron (NM_001134670, intron 1 of 2)	7120	NM_001009997	414157	Hs.662302	NM_001009997	ENSG00000203942	C10orf62	bA548K23.1	chromosome 10 open reading frame 62	protein-coding	0.009653	0.462428	282(ATCACACAGTGTCCCC,+,0.00)
chunk0158_161_1	chr5	127649324	127650030	+	0	NA	intron (NM_001048252, intron 1 of 2)	intron (NM_001048252, intron 1 of 2)	656	NM_001048252	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.014164	0.381895	
chunk0131_338_1	chr3	151277600	151277967	+	0	NA	intron (NM_014879, intron 1 of 2)	intron (NM_014879, intron 1 of 2)	659	NM_014879	9934	Hs.2465	NM_014879	ENSG00000174944	P2RY14	BPR105|GPR105|P2Y14	purinergic receptor P2Y14	protein-coding	0.005450	0.279891	
chunk0014_415_1	chr1	183088821	183089589	+	0	NA	intron (NM_002293, intron 1 of 27)	intron (NM_002293, intron 1 of 27)	65745	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.003906	0.387516	
chunk0212_315_1	chrX	143659035	143659558	+	0	NA	Intergenic	Intergenic	-23189	NM_001184749	139065	Hs.272284	NM_173078	ENSG00000179542	SLITRK4	-	SLIT and NTRK like family member 4	protein-coding	0.005736	0.314885	
chunk0142_453_1	chr4	105560381	105560773	+	0	NA	intron (NM_017700, intron 1 of 3)	intron (NM_017700, intron 1 of 3)	-1014	NR_046840	100874374	Hs.668908	NR_046840	ENSG00000249885	ARHGEF38-IT1	-	ARHGEF38 intronic transcript 1	ncRNA	0.002551	0.333333	200(AGGAACACAGAGTGCT,-,0.00),201(GGAACACAGAGTGCTA,+,0.00)
chunk0066_153_1	chr15	31811605	31812044	+	0	NA	intron (NR_038253, intron 2 of 7)	intron (NR_038253, intron 2 of 7)	-156485	NM_130901	161725	Hs.355236	NM_130901	ENSG00000169918	OTUD7A	C15orf16|C16ORF15|CEZANNE2|OTUD7	OTU deubiquitinase 7A	protein-coding	0.027335	0.611364	203(CAGAACACCATGTTCC,-,0.00),204(AGAACACCATGTTCCC,+,0.00)
chunk0007_269_1	chr1	83407259	83407619	+	0	NA	Intergenic	Intergenic	-421231	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.011111	0.365651	
chunk0121_147_1	chr3	18987989	18988406	+	0	NA	Intergenic	Intergenic	-160328	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.016787	0.406699	
chunk0051_258_1	chr12	117527330	117528261	+	0	NA	intron (NM_173598, intron 12 of 19)	intron (NM_173598, intron 12 of 19)	-165993	NM_000620	4842	Hs.654410	NM_000620	ENSG00000089250	NOS1	IHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS	nitric oxide synthase 1	protein-coding	0.009667	0.431330	246(AGGATCTCAGTGTTCT,-,0.00),247(GGATCTCAGTGTTCTT,+,0.00)
chunk0043_185_1	chr12	18712486	18712862	+	0	NA	intron (NR_073075, intron 6 of 14)	intron (NR_073075, intron 6 of 14)	25385	NM_033123	89869	Hs.97542	NM_033123	ENSG00000139151	PLCZ1	NYD-SP27|PLC-zeta-1|PLCzeta|SPGF17	phospholipase C zeta 1	protein-coding	0.002660	0.310345	147(GAAACACTATGTACCT,+,0.00)
chunk0012_120_1	chr1	156970356	156970793	+	0	NA	intron (NM_014784, intron 7 of 39)	MIRc|SINE|MIR	-34330	NR_030527	768220		NR_030527	ENSG00000211581	MIR765	MIRN765|hsa-mir-765|mir-765	microRNA 765	ncRNA	0.006865	0.442922	
chunk0148_441_1	chr4	189505135	189505427	+	0	NA	Intergenic	Intergenic	-154325	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.010274	0.525597	
chunk0194_7_1	chr8	81399896	81400390	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	47341	NM_002677	5375	Hs.571512	NM_002677	ENSG00000147588	PMP2	CMT1G|FABP8|M-FABP|MP2|P2	peripheral myelin protein 2	protein-coding	0.006073	0.389899	
chunk0103_131_1	chr2	162049308	162049994	+	0	NA	intron (NM_001935, intron 2 of 25)	L1PA11|LINE|L1	24891	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.002915	0.362445	
chunk0200_137_1	chr9	17737970	17738180	+	0	NA	intron (NM_003026, intron 1 of 8)	L2c|LINE|L2	159121	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.000000	0.369668	
chunk0057_345_1	chr13	107875502	107875728	+	0	NA	Intergenic	L1PA15|LINE|L1	-8503	NM_001080396	728215	Hs.535394	NM_001080396	ENSG00000204442	FAM155A	-	family with sequence similarity 155 member A	protein-coding	0.017699	0.599119	
chunk0188_108_1	chr8	8990792	8991042	+	0	NA	Intergenic	Intergenic	-11887	NM_153332	90459	Hs.20000	NM_153332	ENSG00000104626	ERI1	3'HEXO|HEXO|THEX1	exoribonuclease 1	protein-coding	0.012000	0.422311	
chunk0001_190_1	chr1	7418529	7418734	+	0	NA	intron (NM_015215, intron 5 of 22)	L2|LINE|L2	-352638	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.009756	0.567961	
chunk0092_205_1	chr19	31203296	31203574	+	0	NA	Intergenic	L2a|LINE|L2	145849	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.000000	0.483871	
chunk0143_40_1	chr4	107392697	107393493	+	0	NA	Intergenic	Intergenic	327168	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.005025	0.419072	501(TGGGACACCCTGTCAT,-,0.00)
chunk0208_321_1	chrX	24166395	24166748	+	0	NA	intron (NM_001178085, intron 4 of 10)	intron (NM_001178085, intron 4 of 10)	16834	NM_003410	7543	Hs.336681	NM_003410	ENSG00000005889	ZFX	ZNF926	zinc finger protein X-linked	protein-coding	0.005666	0.282486	
chunk0198_370_1	chr8	141055972	141056205	+	0	NA	Intergenic	MIRb|SINE|MIR	-54775	NM_001316342	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.021459	0.555556	
chunk0013_261_1	chr1	170088601	170088841	+	0	NA	Intergenic	HAL1M8|LINE|L1	-13983	NM_014970	22920	Hs.433442	NM_014970	ENSG00000075945	KIFAP3	FLA3|KAP-1|KAP-3|KAP3|SMAP|Smg-GDS|dJ190I16.1	kinesin associated protein 3	protein-coding	0.020833	0.373444	
chunk0159_286_1	chr5	142711108	142711791	+	0	NA	Intergenic	LTR66|LTR|ERVL	-13379	NM_001144935	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.013177	0.459064	
chunk0023_111_1	chr10	22998286	22998907	+	0	NA	intron (NM_173081, intron 11 of 18)	L1ME3E|LINE|L1	70572	NM_001282746	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.022544	0.385852	
chunk0021_103_1	chr10	3051793	3052388	+	0	NA	Intergenic	MER51B|LTR|ERV1	-15430	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.018487	0.468121	
chunk0097_155_1	chr2	48344217	48344416	+	0	NA	intron (NM_002158, intron 2 of 6)	intron (NM_002158, intron 2 of 6)	29660	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.010050	0.345000	
chunk0166_292_1	chr6	48892668	48894089	+	0	NA	Intergenic	Intergenic	569950	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.001407	0.321378	
chunk0009_178_1	chr1	105621443	105621827	+	0	NA	Intergenic	L1M3c|LINE|L1	-2700	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002604	0.311688	
chunk0026_241_1	chr10	66140268	66140911	+	0	NA	intron (NM_001127384, intron 13 of 17)	intron (NM_001127384, intron 13 of 17)	569164	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.006221	0.329193	383(AGGAACATTCTGTCCT,-,0.00),384(GGAACATTCTGTCCTA,+,0.00)
chunk0099_68_1	chr2	84958366	84959154	+	0	NA	Intergenic	L2a|LINE|L2	-12348	NM_020122	56888	Hs.654968	NM_020122	ENSG00000176407	KCMF1	DEBT91|FIGC|PCMF|ZZZ1	potassium channel modulatory factor 1	protein-coding	0.015228	0.446134	
chunk0190_81_1	chr8	30019900	30020739	+	0	NA	Intergenic	Intergenic	62889	NM_016127	51669	Hs.521487	NM_016127	ENSG00000133872	SARAF	FOAP-7|HSPC035|TMEM66|XTP3	store-operated calcium entry associated regulatory factor	protein-coding	0.004768	0.375000	
chunk0111_315_1	chr20	32285669	32286048	+	0	NA	intron (NM_004798, intron 1 of 8)	intron (NM_004798, intron 1 of 8)	8207	NM_004798	9371	Hs.369670	NM_004798	ENSG00000101350	KIF3B	FLA8|HH0048|KLP-11	kinesin family member 3B	protein-coding	0.007916	0.418421	
chunk0049_287_1	chr12	94012212	94012486	+	0	NA	Intergenic	Intergenic	-136374	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.007299	0.400000	152(TGGGACATTGAGTGCC,-,0.00),153(GGGACATTGAGTGCCG,+,0.00)
chunk0075_147_1	chr16	50552922	50553150	+	0	NA	intron (NM_033119, intron 3 of 9)	L1MEh|LINE|L1	4706	NM_033119	85407	Hs.187578	NM_033119	ENSG00000140807	NKD1	Naked1	NKD inhibitor of WNT signaling pathway 1	protein-coding	0.021930	0.432314	
chunk0192_363_1	chr8	68188924	68189461	+	0	NA	intron (NM_024870, intron 35 of 39)	intron (NM_024870, intron 35 of 39)	-141530	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.003724	0.395911	278(AAGGACACACAGACCT,-,0.00),279(AGGACACACAGACCTT,+,0.00)
chunk0034_438_1	chr11	39381249	39381448	+	0	NA	Intergenic	LTR1D|LTR|ERV1	732490	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.005025	0.570000	
chunk0133_116_1	chr3	168139961	168140380	+	0	NA	Intergenic	Intergenic	-44245	NM_001308155	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.004773	0.380952	
chunk0047_12_1	chr12	65157126	65157325	+	0	NA	Intergenic	Intergenic	-12346	NM_014319	23592	Hs.744150	NM_014319	ENSG00000174106	LEMD3	MAN1	LEM domain containing 3	protein-coding	0.010050	0.455000	139(CAGAACAGGCTGTGCT,-,0.00),140(AGAACAGGCTGTGCTG,+,0.00)
chunk0092_84_1	chr19	21435145	21435441	+	0	NA	Intergenic	HERV3-int|LTR|ERV1	38174	NM_145326	284443	Hs.656558	NM_145326	ENSG00000196268	ZNF493	-	zinc finger protein 493	protein-coding	0.010135	0.363636	
chunk0031_150_1	chr10	125123829	125124210	+	0	NA	intron (NM_001083914, intron 1 of 10)	intron (NM_001083914, intron 1 of 10)	34796	NM_001290215	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.018373	0.609948	
chunk0173_192_1	chr6	145189959	145190173	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-544803	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.362791	
chunk0118_391_1	chr22	37664402	37664750	+	0	NA	intron (NM_020315, intron 1 of 1)	MIRb|SINE|MIR	-3450	NR_039973									0.008621	0.461318	51(GGAAACAATCTGTACT,-,0.00),52(GAAACAATCTGTACTC,+,0.00)
chunk0047_73_1	chr12	67709279	67709562	+	0	NA	non-coding (NR_110063, exon 5 of 5)	non-coding (NR_110063, exon 5 of 5)	20055	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.000000	0.373239	
chunk0147_266_1	chr4	183671557	183672097	+	0	NA	intron (NM_199053, intron 5 of 30)	intron (NM_199053, intron 5 of 30)	12560	NM_021942	60684	Hs.443240	NM_021942	ENSG00000168538	TRAPPC11	C4orf41|FOIGR|GRY|LGMD2S|LGMDR18	trafficking protein particle complex 11	protein-coding	0.014815	0.362292	
chunk0197_67_1	chr8	118862237	118862487	+	0	NA	Intergenic	MER110A|LTR|ERV1	89782	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.000000	0.266932	
chunk0136_375_1	chr3	196361574	196361945	+	0	NA	intron (NM_015562, intron 10 of 10)	Tigger1|DNA|TcMar-Tigger	-23339	NM_001204897	116211	Hs.733264	NM_138461	ENSG00000145107	TM4SF19	OCTM4	transmembrane 4 L six family member 19	protein-coding	0.008086	0.387097	
chunk0065_117_1	chr15	24753061	24753260	+	0	NA	Intergenic	Intergenic	-70487	NM_022808	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.000000	0.340000	
chunk0107_188_1	chr2	216130180	216130826	+	0	NA	intron (NM_021141, intron 8 of 20)	intron (NM_021141, intron 8 of 20)	21206	NM_021141	7520	Hs.388739	NM_021141	ENSG00000079246	XRCC5	KARP-1|KARP1|KU80|KUB2|Ku86|NFIV	X-ray repair cross complementing 5	protein-coding	0.007740	0.332303	254(GAGAACATTTTGTTCT,-,0.00),255(AGAACATTTTGTTCTG,+,0.00)
chunk0160_386_1	chr5	161812275	161812813	+	0	NA	Intergenic	Intergenic	-34647	NM_000806	2554	Hs.175934	NM_000806	ENSG00000022355	GABRA1	ECA4|EIEE19|EJM|EJM5	gamma-aminobutyric acid type A receptor alpha1 subunit	protein-coding	0.013011	0.374768	194(CAGAACAGGGTGATCC,-,0.00),195(AGAACAGGGTGATCCG,+,0.00)
chunk0094_278_1	chr2	8225317	8226088	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	102717	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.014267	0.496114	
chunk0112_434_1	chr20	47599044	47599486	+	0	NA	intron (NM_001174087, intron 2 of 22)	L1MB8|LINE|L1	97408	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.009050	0.390519	53(AGGGACACTCTGTGAT,-,0.00)
chunk0195_326_1	chr8	99013188	99013583	+	0	NA	intron (NR_047582, intron 1 of 8)	CpG	119	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.075949	0.651515	34(AGGGACAGTTTGTTTT,-,0.00),35(GGGACAGTTTGTTTTG,+,0.00)
chunk0048_171_1	chr12	80849287	80850025	+	0	NA	intron (NM_004664, intron 2 of 5)	intron (NM_004664, intron 2 of 5)	-17027	NR_030348	693202		NR_030348	ENSG00000207763	MIR617	MIRN617|hsa-mir-617	microRNA 617	ncRNA	0.002710	0.401894	
chunk0208_253_1	chrX	20322561	20323037	+	0	NA	Intergenic	Intergenic	-56167	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.014706	0.425577	
chunk0116_335_1	chr21	41395150	41395658	+	0	NA	intron (NM_002463, intron 6 of 13)	intron (NM_002463, intron 6 of 13)	-25154	NM_001144925	4599	Hs.517307	NM_002462	ENSG00000157601	MX1	IFI-78K|IFI78|MX|MxA	MX dynamin like GTPase 1	protein-coding	0.009843	0.500982	
chunk0174_194_1	chr6	160007076	160008100	+	0	NA	promoter-TSS (NR_047514)	promoter-TSS (NR_047514)	76	NR_047511	100271873	Hs.742166	NR_047511	ENSG00000268257	AIRN	AIR|IGF2R-AS|IGF2R-AS1|IGF2RAS|NCRNA00088	antisense of IGF2R non-protein coding RNA	ncRNA	0.002930	0.352195	213(TAGGACATAATGTCCT,-,0.00),214(AGGACATAATGTCCTG,+,0.00)
chunk0129_135_1	chr3	120147371	120147868	+	0	NA	Intergenic	Intergenic	-53202	NM_001146156	2932	Hs.445733	NM_002093	ENSG00000082701	GSK3B	-	glycogen synthase kinase 3 beta	protein-coding	0.008048	0.425703	
chunk0087_174_1	chr18	35194585	35194879	+	0	NA	Intergenic	Intergenic	-46298	NM_032347	84307	Hs.591061	NM_032347	ENSG00000186812	ZNF397	ZNF47|ZSCAN15	zinc finger protein 397	protein-coding	0.006803	0.369492	
chunk0119_390_1	chr22	48618122	48618645	+	0	NA	intron (NM_015381, intron 1 of 3)	intron (NM_015381, intron 1 of 3)	42077	NM_015381	25817	Hs.436854	NM_015381	ENSG00000219438	TAFA5	FAM19A5|QLLK5208|TAFA-5|UNQ5208	TAFA chemokine like family member 5	protein-coding	0.038241	0.562977	
chunk0073_321_1	chr16	14382606	14383049	+	0	NA	Intergenic	L1MB5|LINE|L1	-12561	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.009029	0.382883	
chunk0153_340_1	chr5	74165921	74166410	+	0	NA	Intergenic	Intergenic	142160	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.004090	0.371429	
chunk0028_188_1	chr10	88507611	88507899	+	0	NA	intron (NM_001031709, intron 4 of 6)	intron (NM_001031709, intron 4 of 6)	75570	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.000000	0.297578	
chunk0049_170_1	chr12	92266154	92266511	+	0	NA	Intergenic	Intergenic	-120435	NM_001731	694	Hs.255935	NM_001731	ENSG00000133639	BTG1	APRO2	BTG anti-proliferation factor 1	protein-coding	0.005602	0.432961	
chunk0186_452_1	chr7	148276516	148276746	+	0	NA	intron (NM_014141, intron 21 of 23)	LTR16C|LTR|ERVL	-313934	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.026087	0.445887	
chunk0070_169_1	chr15	71455813	71456572	+	0	NA	intron (NM_024817, intron 6 of 16)	intron (NM_024817, intron 6 of 16)	-91010	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.006588	0.415789	
chunk0182_149_1	chr7	95295347	95295755	+	0	NA	3' UTR (NM_017650, exon 16 of 16)	3' UTR (NM_017650, exon 16 of 16)	29021	NM_000446	5444	Hs.370995	NM_000446	ENSG00000005421	PON1	ESA|MVCD5|PON	paraoxonase 1	protein-coding	0.000000	0.354523	107(TTGCACTGTGTGTTCT,-,0.00),108(TGCACTGTGTGTTCTT,+,0.00)
chunk0147_180_1	chr4	176883206	176883604	+	0	NA	Intergenic	Intergenic	-90660	NM_005429	7424	Hs.435215	NM_005429	ENSG00000150630	VEGFC	Flt4-L|LMPH1D|LMPHM4|VRP	vascular endothelial growth factor C	protein-coding	0.012563	0.388471	
chunk0006_147_1	chr1	66282880	66283198	+	0	NA	intron (NM_001037340, intron 5 of 14)	L2c|LINE|L2	-49069	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.000000	0.385580	
chunk0003_217_1	chr1	35363893	35364235	+	0	NA	intron (NM_005095, intron 5 of 29)	intron (NM_005095, intron 5 of 29)	95097	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.000000	0.349854	
chunk0153_222_1	chr5	72076629	72077090	+	0	NA	Intergenic	Intergenic	-30432	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.006508	0.458874	
chunk0080_119_1	chr17	27241734	27241985	+	0	NA	Intergenic	Intergenic	52137	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.007968	0.480159	
chunk0180_122_1	chr7	55569492	55569735	+	0	NA	intron (NM_030796, intron 1 of 4)	MIR|SINE|MIR	2894	NM_030796	81552	Hs.488307	NM_030796	ENSG00000154978	VOPP1	ECOP|GASP|WBP1L2	VOPP1 WW domain binding protein	protein-coding	0.008230	0.401639	
chunk0023_399_1	chr10	30980834	30981512	+	0	NA	intron (NM_001143767, intron 1 of 5)	intron (NM_001143767, intron 1 of 5)	18344	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.007375	0.430044	
chunk0139_268_1	chr4	56681311	56682182	+	0	NA	promoter-TSS (NM_139212)	promoter-TSS (NM_139212)	-40	NM_001145460	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.026406	0.466743	478(GGGCACAGAATGTACA,-,0.00),479(GGCACAGAATGTACAC,+,0.00)
chunk0189_184_1	chr8	23593690	23594201	+	0	NA	Intergenic	Intergenic	65095	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.003914	0.404297	
chunk0030_29_1	chr10	111265276	111265714	+	0	NA	Intergenic	L1MC5a|LINE|L1	188463	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.002283	0.396355	
chunk0037_449_1	chr11	80635221	80635436	+	0	NA	Intergenic	Intergenic	127475	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.004651	0.421296	
chunk0202_241_1	chr9	76646300	76646736	+	0	NA	intron (NM_001308051, intron 3 of 8)	intron (NM_001308051, intron 3 of 8)	45897	NM_001308051	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.009174	0.466819	
chunk0120_373_1	chr3	11868152	11868351	+	0	NA	Intergenic	AluJr|SINE|Alu	-21332	NM_138807	132001	Hs.475472	NM_138807	ENSG00000144559	TAMM41	C3orf31|RAM41|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding	0.010050	0.405000	
chunk0052_452_1	chr12	132679453	132679850	+	0	NA	exon (NM_006231, exon 6 of 49)	exon (NM_006231, exon 6 of 49)	7873	NM_006231	5426	Hs.524871	NM_006231	ENSG00000177084	POLE	CRCS12|FILS|IMAGEI|POLE1	DNA polymerase epsilon, catalytic subunit	protein-coding	0.035264	0.487437	
chunk0192_234_1	chr8	65485376	65485860	+	0	NA	Intergenic	Intergenic	77048	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.006198	0.435052	
chunk0093_338_1	chr19	54793367	54793782	+	0	NA	intron (NR_110737, intron 3 of 3).12	L1MEg|LINE|L1	-10038	NM_001080770	3805	Hs.661219	NM_002255	ENSG00000189013	KIR2DL4	CD158D|G9P|KIR-103AS|KIR-2DL4|KIR103|KIR103AS	killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4	protein-coding	0.004819	0.317308	
chunk0096_359_1	chr2	36375468	36376457	+	0	NA	intron (NM_016441, intron 1 of 16)	intron (NM_016441, intron 1 of 16)	19735	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.003033	0.347475	
chunk0136_318_1	chr3	195371841	195372448	+	0	NA	intron (NM_012287, intron 4 of 22)	Charlie17|DNA|hAT-Charlie	70944	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.014827	0.401316	
chunk0184_126_1	chr7	114759547	114760100	+	0	NA	Intergenic	L2a|LINE|L2	106478	NR_037439	100500896		NR_037439	ENSG00000272230	MIR3666	-	microRNA 3666	ncRNA	0.001808	0.445848	
chunk0130_114_1	chr3	131394393	131394770	+	0	NA	Intergenic	MIRb|SINE|MIR	12800	NR_033268	131870	Hs.282050	NM_152395	ENSG00000198585	NUDT16	-	nudix hydrolase 16	protein-coding	0.000000	0.380952	
chunk0149_440_1	chr5	29790950	29791220	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-395109	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.011111	0.424354	
chunk0023_77_1	chr10	22230770	22231130	+	0	NA	Intergenic	Intergenic	-20967	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.008333	0.360111	
chunk0123_237_1	chr3	45593829	45594268	+	0	NA	promoter-TSS (NM_014240)	promoter-TSS (NM_014240)	-783	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.127563	0.775000	
chunk0036_202_1	chr11	63301685	63302140	+	0	NA	intron (NM_001039752, intron 6 of 9)	intron (NM_001039752, intron 6 of 9)	11954	NM_001039752	387775	Hs.188982	NM_001039752	ENSG00000184999	SLC22A10	OAT5|hOAT5	solute carrier family 22 member 10	protein-coding	0.002198	0.436404	156(CAGAACACTGTGCTCC,-,0.00),157(AGAACACTGTGCTCCC,+,0.00)
chunk0189_55_1	chr8	20059336	20059662	+	0	NA	Intergenic	Intergenic	120428	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.009202	0.507645	
chunk0032_144_1	chr11	4713258	4713557	+	0	NA	Intergenic	Intergenic	-15561	NM_030774	81285	Hs.501758	NM_030774	ENSG00000167332	OR51E2	HPRAJ|OR51E3P|OR52A2|PSGR	olfactory receptor family 51 subfamily E member 2	protein-coding	0.003344	0.423333	
chunk0170_288_1	chr6	115125640	115126006	+	0	NA	Intergenic	Intergenic	-912908	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.002732	0.280654	
chunk0187_444_1	chr7	159019105	159019444	+	0	NA	intron (NR_024394, intron 2 of 4)	intron (NR_024394, intron 2 of 4)	10920	NR_024394	154822	Hs.544783	NM_198345	ENSG00000231419	LINC00689	-	long intergenic non-protein coding RNA 689	ncRNA	0.008850	0.476471	199(GAGAACACAATGATCT,-,0.00),200(AGAACACAATGATCTG,+,0.00)
chunk0199_371_1	chr9	12877033	12877593	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-62924	NR_125775	101929467	Hs.586443	NR_125775	ENSG00000235448	LURAP1L-AS1	-	LURAP1L antisense RNA 1	ncRNA	0.003571	0.370766	
chunk0039_189_1	chr11	100789443	100789851	+	0	NA	intron (NM_152432, intron 2 of 23)	LTR18A|LTR|ERVL	-101692	NR_133571	100128386	Hs.635125	NR_133571	ENSG00000248027	LOC100128386	-	uncharacterized LOC100128386	ncRNA	0.014706	0.459658	
chunk0112_18_1	chr20	36085570	36085831	+	0	NA	Intergenic	Intergenic	-5804	NM_001258331	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.000000	0.469466	
chunk0209_320_1	chrX	50363726	50364282	+	0	NA	Intergenic	L1PB4|LINE|L1	79464	NM_033031	85417	Hs.130310	NM_033031	ENSG00000147082	CCNB3	-	cyclin B3	protein-coding	0.003597	0.333932	
chunk0128_269_1	chr3	110562055	110562356	+	0	NA	Intergenic	L1MA3|LINE|L1	507754	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.000000	0.466887	
chunk0062_288_1	chr14	72404185	72404618	+	0	NA	intron (NM_001204418, intron 3 of 16)	intron (NM_001204418, intron 3 of 16)	-112419	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.006928	0.497696	
chunk0163_384_1	chr6	16357691	16358117	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	119324	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.014085	0.451991	
chunk0009_115_1	chr1	102757477	102757718	+	0	NA	Intergenic	Intergenic	350899	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.008299	0.380165	
chunk0114_148_1	chr21	10359750	10359999	+	0	NA	Intergenic	L1MA8|LINE|L1	-53646	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.004016	0.368000	
chunk0097_381_1	chr2	61421122	61421512	+	0	NA	intron (NM_014709, intron 1 of 79)	LTR50|LTR|ERVL	-3940	NR_003707	100124537	Hs.675825	NR_003707	ENSG00000206937	SNORA70B	-	small nucleolar RNA, H/ACA box 70B	snoRNA	0.005128	0.416880	272(GAGAACATTCAGTTCT,-,0.00),273(AGAACATTCAGTTCTC,+,0.00)
chunk0152_1_1	chr5	56097165	56097413	+	0	NA	Intergenic	Intergenic	102122	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.004032	0.389558	
chunk0041_198_1	chr11	126544133	126545145	+	0	NA	intron (NM_032531, intron 2 of 16)	intron (NM_032531, intron 2 of 16)	-108139	NR_120532	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.014822	0.475814	
chunk0181_225_1	chr7	85182820	85183347	+	0	NA	Intergenic	Intergenic	-61152	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.005693	0.354167	
chunk0055_49_1	chr13	52374269	52374881	+	0	NA	Intergenic	Intergenic	31919	NM_018676	55901	Hs.325667	NM_018676	ENSG00000136114	THSD1	TMTSP|UNQ3010	thrombospondin type 1 domain containing 1	protein-coding	0.009804	0.376835	
chunk0101_241_1	chr2	131524028	131524424	+	0	NA	Intergenic	Intergenic	-3608	NM_001258305	90557	Hs.351461	NM_138770	ENSG00000163040	CCDC74A	-	coiled-coil domain containing 74A	protein-coding	0.007576	0.433249	
chunk0165_231_1	chr6	35486267	35486478	+	0	NA	intron (NM_003214, intron 2 of 12)	CpG	10712	NM_003214	7005	Hs.485205	NM_003214	ENSG00000007866	TEAD3	DTEF-1|ETFR-1|TEAD-3|TEAD5|TEF-5|TEF5	TEA domain transcription factor 3	protein-coding	0.104265	0.707547	
chunk0084_26_1	chr17	73552649	73552903	+	0	NA	intron (NM_001144952, intron 1 of 44)	intron (NM_001144952, intron 1 of 44)	91312	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.035433	0.556863	
chunk0086_1_1	chr18	11908269	11908582	+	0	NA	non-coding (NR_040243, exon 1 of 12)	non-coding (NR_040243, exon 1 of 12)	372	NM_001242904	65258	Hs.712666	NM_023075	ENSG00000154889	MPPE1	PGAP5	metallophosphoesterase 1	protein-coding	0.127796	0.732484	
chunk0012_405_1	chr1	164015814	164016697	+	0	NA	Intergenic	L1MC3|LINE|L1	-543105	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.001133	0.298643	
chunk0106_466_1	chr2	209485473	209485848	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	61613	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.005333	0.382979	
chunk0048_71_1	chr12	78805959	78806185	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	-57921	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.004425	0.259912	
chunk0209_242_1	chrX	45502446	45502875	+	0	NA	Intergenic	Intergenic	-2728	NR_104645	101927528	Hs.550772	NR_104644	ENSG00000229563	LINC01204	-	long intergenic non-protein coding RNA 1204	ncRNA	0.004662	0.420930	
chunk0106_103_1	chr2	197433508	197434137	+	0	NA	intron (NM_001308824, intron 1 of 3)	L2b|LINE|L2	1271	NM_001308824	23451	Hs.632554	NM_012433	ENSG00000115524	SF3B1	Hsh155|MDS|PRP10|PRPF10|SAP155|SF3b155	splicing factor 3b subunit 1	protein-coding	0.009539	0.384127	
chunk0035_321_1	chr11	47478534	47479059	+	0	NA	intron (NM_198700, intron 8 of 13)	intron (NM_198700, intron 8 of 13)	10228	NM_001025596	10658	Hs.595333	NM_006560	ENSG00000149187	CELF1	BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50	CUGBP Elav-like family member 1	protein-coding	0.005714	0.461977	
chunk0031_237_1	chr10	126749035	126749471	+	0	NA	Intergenic	Intergenic	-156156	NM_001290223	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.011468	0.505721	
chunk0069_421_1	chr15	68080935	68081284	+	0	NA	intron (NM_016166, intron 1 of 13)	intron (NM_016166, intron 1 of 13)	26875	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.005731	0.380000	
chunk0063_193_1	chr14	80907914	80908223	+	0	NA	intron (NM_152446, intron 3 of 23)	L1MEg|LINE|L1	31472	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.009709	0.306452	
chunk0160_179_1	chr5	154084300	154084654	+	0	NA	Intergenic	Intergenic	45518	NM_001135037	4238	Hs.432818	NM_005927	ENSG00000037749	MFAP3	-	microfibril associated protein 3	protein-coding	0.005650	0.445070	
chunk0040_1_1	chr11	108572040	108572563	+	0	NA	intron (NM_001308019, intron 2 of 6)	intron (NM_001308019, intron 2 of 6)	-20096	NM_001144763	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.007648	0.412214	
chunk0045_332_1	chr12	51024790	51025359	+	0	NA	intron (NM_001174125, intron 1 of 15)	intron (NM_001174125, intron 1 of 15)	1067	NM_001174129	4891	Hs.505545	NM_000617	ENSG00000110911	SLC11A2	AHMIO1|DCT1|DMT1|NRAMP2	solute carrier family 11 member 2	protein-coding	0.012302	0.385965	
chunk0125_326_1	chr3	71007450	71007915	+	0	NA	intron (NM_032682, intron 12 of 20)	intron (NM_032682, intron 12 of 20)	57241	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.010753	0.375536	
chunk0101_359_1	chr2	137954842	137955201	+	0	NA	Intergenic	Intergenic	-9217	NM_001024074	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.000000	0.358333	
chunk0168_48_1	chr6	78608012	78608550	+	0	NA	Intergenic	Intergenic	-259263	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.005576	0.324675	
chunk0174_426_1	chr6	165937398	165937672	+	0	NA	intron (NR_026861, intron 1 of 1)	intron (NR_026861, intron 1 of 1)	-50016	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.003650	0.280000	
chunk0081_394_1	chr17	48232379	48232692	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-61812	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.006390	0.359873	
chunk0058_74_1	chr14	21103633	21104170	+	0	NA	TTS (NM_001146683)	TTS (NM_001146683)	803	NM_001102454	51222	Hs.250493	NM_016423	ENSG00000165804	ZNF219	ZFP219	zinc finger protein 219	protein-coding	0.078212	0.667286	
chunk0027_155_1	chr10	74821535	74822134	+	0	NA	Intergenic	Intergenic	-4579	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.008347	0.453333	288(GAGGACAGGGTGTGCT,-,0.00),289(AGGACAGGGTGTGCTG,+,0.00)
chunk0076_4_1	chr16	58477439	58478079	+	0	NA	intron (NM_022910, intron 1 of 15)	L1MC4a|LINE|L1	12937	NM_022910	65009	Hs.322430	NM_020465	ENSG00000103034	NDRG4	BDM1|SMAP-8|SMAP8	NDRG family member 4	protein-coding	0.004687	0.383775	
chunk0103_246_1	chr2	164910160	164910654	+	0	NA	intron (NM_173512, intron 8 of 9)	intron (NM_173512, intron 8 of 9)	45118	NM_173512	151258	Hs.658702	NM_173512	ENSG00000169507	SLC38A11	AVT2	solute carrier family 38 member 11	protein-coding	0.010121	0.416162	
chunk0144_456_1	chr4	142226119	142226518	+	0	NA	intron (NM_001101669, intron 12 of 25)	intron (NM_001101669, intron 12 of 25)	589722	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.000000	0.357500	
chunk0072_179_1	chr15	94084737	94085127	+	0	NA	intron (NR_120320, intron 1 of 8)	intron (NR_120320, intron 1 of 8)	23006	NR_120320	101927112	Hs.134687	NR_120320	ENSG00000259724	LINC01581	-	long intergenic non-protein coding RNA 1581	ncRNA	0.002564	0.419437	260(ATGAACTCTCTGTCCA,-,0.00),261(TGAACTCTCTGTCCAC,+,0.00)
chunk0011_180_1	chr1	148366311	148366834	+	0	NA	Intergenic	Intergenic	-4039	NR_104082	101954273		NR_104082	ENSG00000207340	RNVU1-1	RNU1-10P|RNU1-53|RNU1P10|RNVU1-10|U1.4|U1P14|vU1.1|vU1.10	RNA, variant U1 small nuclear 1	snRNA	0.009560	0.444656	346(TAGCACAGGATGTACC,-,0.00),347(AGCACAGGATGTACCA,+,0.00)
chunk0091_103_1	chr19	5828418	5828617	+	0	NA	TTS (NM_004558)	TTS (NM_004558)	4710	NM_004558	4902	Hs.234775	NM_004558	ENSG00000171119	NRTN	NTN	neurturin	protein-coding	0.045226	0.595000	
chunk0091_466_1	chr19	18376945	18377430	+	0	NA	Intergenic	L1MB8|LINE|L1	-8971	NM_004864	9518	Hs.616962	NM_004864	ENSG00000130513	GDF15	GDF-15|MIC-1|MIC1|NAG-1|PDF|PLAB|PTGFB	growth differentiation factor 15	protein-coding	0.012371	0.407407	
chunk0167_114_1	chr6	57378437	57378960	+	0	NA	intron (NM_000947, intron 5 of 13)	intron (NM_000947, intron 5 of 13)	-11434	NR_036097	100422884		NR_036097	ENSG00000212017	MIR548U	-	microRNA 548u	ncRNA	0.009560	0.343511	
chunk0106_116_1	chr2	197674521	197674890	+	0	NA	intron (NM_144629, intron 1 of 8)	intron (NM_144629, intron 1 of 8)	1155	NM_144629	130132	Hs.591615	NM_144629	ENSG00000162944	RFTN2	C2orf11|Raftlin-2	raftlin family member 2	protein-coding	0.005420	0.354054	205(GGAACAGAGAGTTTCT,+,0.00)
chunk0009_465_1	chr1	111704415	111704795	+	0	NA	intron (NM_001010935, intron 7 of 8)	intron (NM_001010935, intron 7 of 8)	34819	NM_019099	55924	Hs.193406	NM_019099	ENSG00000197852	INKA2	C1orf183|FAM212B	inka box actin regulator 2	protein-coding	0.002632	0.328084	
chunk0210_368_1	chrX	96715577	96715832	+	0	NA	intron (NM_006729, intron 1 of 26)	intron (NM_006729, intron 1 of 26)	31041	NM_007309	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.003922	0.363281	
chunk0187_301_1	chr7	156202980	156203616	+	0	NA	Intergenic	Intergenic	240666	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.025157	0.458399	
chunk0022_84_1	chr10	8973741	8973948	+	0	NA	Intergenic	Intergenic	75855	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.000000	0.293269	
chunk0207_128_1	chr9	129052613	129052930	+	0	NA	intron (NM_032809, intron 6 of 15)	intron (NM_032809, intron 6 of 15)	15797	NM_032809	84895	Hs.632693	NM_032809	ENSG00000148343	MIGA2	C9orf54|FAM73B	mitoguardin 2	protein-coding	0.022082	0.578616	
chunk0120_81_1	chr3	3685793	3686167	+	0	NA	Intergenic	MIR3|SINE|MIR	-113457	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.021390	0.424000	
chunk0068_105_1	chr15	52295949	52296148	+	0	NA	promoter-TSS (NM_018728)	promoter-TSS (NM_018728)	-250	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.030151	0.420000	
chunk0122_363_1	chr3	37608297	37609125	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	156389	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.004831	0.393245	
chunk0116_71_1	chr21	34598365	34598564	+	0	NA	intron (NM_004414, intron 1 of 3)	intron (NM_004414, intron 1 of 3)	15379	NM_001285389	1827	Hs.282326	NM_004414	ENSG00000159200	RCAN1	ADAPT78|CSP1|DSC1|DSCR1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.005025	0.360000	
chunk0048_335_1	chr12	84116775	84117454	+	0	NA	Intergenic	(CT)n|Simple_repeat|Simple_repeat	795715	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.005891	0.348529	
chunk0022_205_1	chr10	13717575	13718494	+	0	NA	intron (NM_018027, intron 12 of 24)	intron (NM_018027, intron 12 of 24)	131095	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.032644	0.532609	491(GGAACACCTCGTGCTT,+,0.00)
chunk0157_431_1	chr5	124764983	124765693	+	0	NA	Intergenic	MIRb|SINE|MIR	-20226	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.004225	0.340366	
chunk0089_393_1	chr18	68053209	68053566	+	0	NA	Intergenic	L1ME3|LINE|L1	-536657	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.005602	0.279330	
chunk0140_452_1	chr4	76434681	76435266	+	0	NA	promoter-TSS (NM_020859)	promoter-TSS (NM_020859)	-127	NM_020859	57619	Hs.683808	NM_020859	ENSG00000138771	SHROOM3	APXL3|MSTP013|SHRM|ShrmL	shroom family member 3	protein-coding	0.010256	0.395904	
chunk0136_131_1	chr4	3798828	3799027	+	0	NA	Intergenic	Intergenic	32358	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.015075	0.510000	
chunk0060_449_1	chr14	54831170	54831639	+	0	NA	Intergenic	L1PA16|LINE|L1	46789	NR_036194	100422984		NR_036194	ENSG00000265432	MIR4308	-	microRNA 4308	ncRNA	0.002132	0.317021	
chunk0046_119_1	chr12	57309397	57309806	+	0	NA	intron (NM_014925, intron 1 of 21)	intron (NM_014925, intron 1 of 21)	862	NM_014925	22864	Hs.443673	NM_014925	ENSG00000179912	R3HDM2	CAG6|PR01365	R3H domain containing 2	protein-coding	0.004890	0.368293	
chunk0041_356_1	chr11	130850283	130850880	+	0	NA	intron (NR_125383, intron 3 of 5)	intron (NR_125383, intron 3 of 5)	11529	NR_125383	100507431	Hs.375101	NR_125383		LINC02551	-	long intergenic non-protein coding RNA 2551	ncRNA	0.010050	0.416388	
chunk0194_366_1	chr8	89892392	89892697	+	0	NA	Intergenic	L1MA3|LINE|L1	-9324	NM_004337	734	Hs.436445	NM_004337	ENSG00000164823	OSGIN2	C8orf1|hT41	oxidative stress induced growth inhibitor family member 2	protein-coding	0.016393	0.568627	
chunk0143_310_1	chr4	119013202	119013714	+	0	NA	intron (NM_133477, intron 1 of 4)	Charlie1a|DNA|hAT-Charlie	-122326	NM_016599	51778	Hs.732122	NM_016599	ENSG00000172399	MYOZ2	C4orf5|CMH16|CS-1|FATZ-2	myozenin 2	protein-coding	0.001953	0.331384	
chunk0170_422_1	chr6	118408461	118408724	+	0	NA	Intergenic	L1PA13|LINE|L1	-92781	NR_002730	23629	Hs.648050	NR_002730		BRD7P3	BP75	bromodomain containing 7 pseudogene 3	pseudo	0.003802	0.556818	
chunk0113_437_1	chr20	62427436	62427839	+	0	NA	promoter-TSS (NM_080833)	promoter-TSS (NM_080833)	-64	NM_080833	140893	Hs.180374	NM_080833	ENSG00000130701	RBBP8NL	C20orf151	RBBP8 N-terminal like	protein-coding	0.039702	0.613861	
chunk0191_147_1	chr8	48858258	48858654	+	0	NA	Intergenic	Intergenic	62984	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.007576	0.506297	238(AGGCACACCATGTTCC,-,0.00),239(GGCACACCATGTTCCA,+,0.00)
chunk0131_399_1	chr3	152827932	152828737	+	0	NA	Intergenic	Intergenic	-6359	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.006211	0.394541	
chunk0169_89_1	chr6	99793258	99793793	+	0	NA	Intergenic	L2a|LINE|L2	186751	NM_021620	59336	Hs.287386	NM_021620	ENSG00000112238	PRDM13	MU-MB-20.220|PFM10	PR/SET domain 13	protein-coding	0.003738	0.416045	280(AAGTACAAGTTGTTCT,-,0.00),281(AGTACAAGTTGTTCTA,+,0.00)
chunk0070_419_1	chr15	77784401	77784688	+	0	NA	intron (NM_001301186, intron 2 of 5)	intron (NM_001301186, intron 2 of 5)	2470	NM_001301195	84894	Hs.656765	NM_032808	ENSG00000169783	LINGO1	LERN1|LRRN6A|MRT64|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding	0.013937	0.465278	
chunk0176_152_1	chr7	13100596	13100921	+	0	NA	Intergenic	Intergenic	413472	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.003077	0.334356	
chunk0206_180_1	chr9	122698987	122699469	+	0	NA	Intergenic	AluSz|SINE|Alu	24098	NM_001005234	26735	Hs.626839	NM_001005234	ENSG00000171481	OR1L3	OR9-28|OR9-D	olfactory receptor family 1 subfamily L member 3	protein-coding	0.016598	0.393375	
chunk0111_234_1	chr20	29396127	29396357	+	0	NA	Intergenic	Intergenic	20719	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.008696	0.393939	
chunk0064_90_1	chr14	90739809	90740336	+	0	NA	intron (NM_001010854, intron 4 of 19)	intron (NM_001010854, intron 4 of 19)	76345	NM_001010854	145567	Hs.655697	NM_001010854	ENSG00000165914	TTC7B	TTC7L1|c14_5685	tetratricopeptide repeat domain 7B	protein-coding	0.013283	0.441288	
chunk0168_447_1	chr6	95841443	95841980	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-174258	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.379182	
chunk0036_208_1	chr11	63531584	63531909	+	0	NA	Intergenic	MER66C|LTR|ERV1	-5055	NM_004585	5920	Hs.17466	NM_004585	ENSG00000133321	PLAAT4	HRASLS4|HRSL4|PLA1/2-3|PLAAT-4|RARRES3|RIG1|TIG3	phospholipase A and acyltransferase 4	protein-coding	0.006154	0.441718	
chunk0001_164_1	chr1	6398907	6399106	+	0	NA	Intergenic	L2a|LINE|L2	-5240	NM_007274	11332	Hs.126137	NM_007274	ENSG00000097021	ACOT7	ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH	acyl-CoA thioesterase 7	protein-coding	0.010050	0.545000	
chunk0196_414_1	chr8	116045457	116045668	+	0	NA	intron (NR_046215, intron 7 of 13)	L1PA16|LINE|L1	279497	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.000000	0.400943	126(GAGAACAAACTGTGTT,-,0.00),127(AGAACAAACTGTGTTT,+,0.00)
chunk0021_54_1	chr10	1115368	1115718	+	0	NA	intron (NM_014023, intron 11 of 13)	intron (NM_014023, intron 11 of 13)	-44225	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.014286	0.447293	
chunk0136_312_1	chr3	195258596	195258990	+	0	NA	intron (NM_152531, intron 1 of 3)	intron (NM_152531, intron 1 of 3)	-10873	NM_001308069	152002	Hs.478741	NM_152531	ENSG00000173950	XXYLT1	C3orf21	xyloside xylosyltransferase 1	protein-coding	0.017766	0.516456	
chunk0195_310_1	chr8	98831642	98831898	+	0	NA	intron (NM_001256312, intron 3 of 12)	intron (NM_001256312, intron 3 of 12)	-6089	NM_006281	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.000000	0.307393	
chunk0003_343_1	chr1	39016282	39016924	+	0	NA	Intergenic	Intergenic	-9692	NM_001184979	4725	Hs.632385	NM_004552	ENSG00000168653	NDUFS5	CI-15k|CI15K	NADH:ubiquinone oxidoreductase subunit S5	protein-coding	0.012461	0.477449	
chunk0111_372_1	chr20	33820446	33820802	+	0	NA	intron (NM_176812, intron 1 of 4)	L2c|LINE|L2	9320	NM_176812	128866	Hs.472471	NM_176812	ENSG00000101421	CHMP4B	C20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4	charged multivesicular body protein 4B	protein-coding	0.002809	0.378151	
chunk0125_40_1	chr3	62824941	62825343	+	0	NA	intron (NM_003716, intron 1 of 29)	intron (NM_003716, intron 1 of 29)	50247	NM_183394	8618	Hs.654933	NM_003716	ENSG00000163618	CADPS	CADPS1|CAPS|CAPS1|UNC-31	calcium dependent secretion activator	protein-coding	0.007463	0.399504	341(AGGCACTTAATGTCCT,-,0.00),342(GGCACTTAATGTCCTT,+,0.00)
chunk0174_30_1	chr6	154167588	154168028	+	0	NA	intron (NM_001130699, intron 12 of 12)	intron (NM_001130699, intron 12 of 12)	78046	NM_001285528	4988	Hs.2353	NM_000914	ENSG00000112038	OPRM1	LMOR|M-OR-1|MOP|MOR|MOR1|OPRM	opioid receptor mu 1	protein-coding	0.018182	0.385488	
chunk0149_409_1	chr5	29400787	29401121	+	0	NA	Intergenic	L1MB7|LINE|L1	-4978	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.253731	
chunk0103_86_1	chr2	160634375	160634834	+	0	NA	Intergenic	Intergenic	-140797	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.004357	0.402174	
chunk0132_261_1	chr3	159139251	159139634	+	0	NA	intron (NM_001042706, intron 1 of 3)	intron (NM_001042706, intron 1 of 3)	70190	NM_001197114	100505385	Hs.134665	NM_001197113	ENSG00000283154	IQCJ-SCHIP1	-	IQCJ-SCHIP1 readthrough	protein-coding	0.005222	0.432292	
chunk0041_192_1	chr11	126450701	126451088	+	0	NA	intron (NM_032531, intron 7 of 16)	intron (NM_032531, intron 7 of 16)	44712	NM_001254759	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.025840	0.518041	
chunk0133_120_1	chr3	168197107	168197587	+	0	NA	Intergenic	Intergenic	-52175	NR_021485	93556	Hs.478158	NR_021485		EGFEM1P	C3orf50|NCRNA00259	EGF like and EMI domain containing 1, pseudogene	pseudo	0.006250	0.351351	
chunk0050_381_1	chr12	108731254	108731719	+	0	NA	promoter-TSS (NM_001276471)	promoter-TSS (NM_001276471)	64	NM_014325	23603	Hs.330384	NM_014325	ENSG00000110880	CORO1C	HCRNN4	coronin 1C	protein-coding	0.131183	0.776824	
chunk0062_282_1	chr14	72129174	72129648	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	196342	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.008439	0.433684	
chunk0187_250_1	chr7	153731526	153731918	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-155375	NM_001039350	1804	Hs.490684	NM_001936	ENSG00000130226	DPP6	DPL1|DPPX|MRD33|VF2	dipeptidyl peptidase like 6	protein-coding	0.017857	0.524173	143(GGTACTTGGAGTTCTT,+,0.00),208(CAATACAGGATGTGCT,-,0.00),209(AATACAGGATGTGCTG,+,0.00)
chunk0085_134_1	chr18	3162191	3162733	+	0	NA	intron (NM_019856, intron 10 of 36)	MER74B|LTR|ERVL	57646	NM_003803	8736	Hs.464469	NM_003803	ENSG00000101605	MYOM1	SKELEMIN	myomesin 1	protein-coding	0.007380	0.467772	
chunk0022_277_1	chr10	15158375	15159031	+	0	NA	intron (NM_001308295, intron 1 of 12)	MLT1A|LTR|ERVL-MaLR	-3356	NR_036506	100192204	Hs.714691	NR_036506	ENSG00000206448	PPIAP30	-	peptidylprolyl isomerase A pseudogene 30	pseudo	0.006098	0.414003	
chunk0114_142_1	chr21	10270183	10270425	+	0	NA	Intergenic	HSATI|Satellite|Satellite	-143216	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.008264	0.341564	
chunk0122_73_1	chr3	29551812	29552024	+	0	NA	intron (NM_001003793, intron 3 of 14)	intron (NM_001003793, intron 3 of 14)	270606	NM_014483	27303	Hs.221436	NM_014483	ENSG00000144642	RBMS3	-	RNA binding motif single stranded interacting protein 3	protein-coding	0.004717	0.375587	100(TGCACACGCAGTACCT,+,0.00)
chunk0012_116_1	chr1	156894746	156894968	+	0	NA	intron (NM_001080471, intron 1 of 22)	intron (NM_001080471, intron 1 of 22)	1126	NM_001080471	375033	Hs.142003	NM_207369	ENSG00000187800	PEAR1	JEDI|MEGF12	platelet endothelial aggregation receptor 1	protein-coding	0.022523	0.632287	35(AGGAACAGCTTGTGCT,-,0.00),36(GGAACAGCTTGTGCTG,+,0.00)
chunk0091_405_1	chr19	16488799	16489258	+	0	NA	intron (NM_145046, intron 3 of 8)	MER58B|DNA|hAT-Charlie	7164	NM_145046	125972	Hs.304020	NM_145046	ENSG00000269058	CALR3	CMH19|CRT2|CT93	calreticulin 3	protein-coding	0.010893	0.397826	
chunk0167_271_1	chr6	70280431	70280733	+	0	NA	intron (NM_001851, intron 10 of 37)	intron (NM_001851, intron 10 of 37)	2626	NM_078485	1297	Hs.590892	NM_001851	ENSG00000112280	COL9A1	DJ149L1.1.2|EDM6|MED|STL4	collagen type IX alpha 1 chain	protein-coding	0.033113	0.557756	
chunk0192_378_1	chr8	68502639	68503007	+	0	NA	intron (NM_052958, intron 5 of 13)	L1MC5|LINE|L1	-171332	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.008152	0.346883	184(TGGGACATTATGTGCC,-,0.00),185(GGGACATTATGTGCCT,+,0.00)
chunk0027_453_1	chr10	81314463	81315009	+	0	NA	Intergenic	L2|LINE|L2	-560578	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.005495	0.382084	
chunk0119_233_1	chr22	45335284	45335578	+	0	NA	intron (NM_001104595, intron 8 of 9)	intron (NM_001104595, intron 8 of 9)	25527	NM_017911	55007	Hs.265018	NM_017911	ENSG00000100376	FAM118A	C22orf8	family with sequence similarity 118 member A	protein-coding	0.020408	0.447458	
chunk0110_146_1	chr20	13656922	13657191	+	0	NA	Intergenic	Intergenic	-18120	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.011152	0.377778	
chunk0182_100_1	chr7	93226027	93226612	+	0	NA	intron (NM_001288804, intron 1 of 10)	intron (NM_001288804, intron 1 of 10)	200	NM_001288804	253012	Hs.443169	NM_198151	ENSG00000188175	HEPACAM2	MIKI	HEPACAM family member 2	protein-coding	0.003419	0.363481	
chunk0212_234_1	chrX	136477016	136477215	+	0	NA	Intergenic	Intergenic	-10851	NM_001727	680	Hs.121484	NM_001727	ENSG00000102239	BRS3	BB3|BB3R|BBR3	bombesin receptor subtype 3	protein-coding	0.010050	0.485000	
chunk0068_177_1	chr15	54215939	54216138	+	0	NA	intron (NM_001080534, intron 3 of 30)	intron (NM_001080534, intron 3 of 30)	203134	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.000000	0.380000	
chunk0068_166_1	chr15	54096819	54097603	+	0	NA	intron (NM_001080534, intron 1 of 30)	intron (NM_001080534, intron 1 of 30)	84307	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.002551	0.328662	359(GGAACACCCAGTCTTT,+,0.00)
chunk0175_54_1	chr7	1653760	1654068	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	39444	NR_001288	260341	Hs.534596	NR_001288		TFAMP1	MTTF1|TCF6L1	transcription factor A, mitochondrial pseudogene 1	pseudo	0.012987	0.482201	212(AGGTACATACTGTGCA,-,0.00),213(GGTACATACTGTGCAC,+,0.00)
chunk0002_71_1	chr1	14081501	14081951	+	0	NA	Intergenic	Intergenic	332345	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.006667	0.399113	
chunk0189_296_1	chr8	25976760	25977170	+	0	NA	intron (NM_022659, intron 6 of 15)	intron (NM_022659, intron 6 of 15)	68159	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.009756	0.430657	151(AGGAACGCTCTGTGCA,-,0.00),152(GGAACGCTCTGTGCAC,+,0.00)
chunk0056_100_1	chr13	82467733	82468063	+	0	NA	Intergenic	L1MA2|LINE|L1	-1240915	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.003030	0.362538	
chunk0028_182_1	chr10	88439794	88440332	+	0	NA	intron (NM_001031709, intron 4 of 6)	L2c|LINE|L2	143262	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.000000	0.384045	
chunk0037_400_1	chr11	79353558	79354255	+	0	NA	intron (NM_001098816, intron 1 of 33)	MER58A|DNA|hAT-Charlie	48203	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.008608	0.378223	
chunk0068_403_1	chr15	58905967	58906769	+	0	NA	intron (NM_001013843, intron 5 of 20)	intron (NM_001013843, intron 5 of 20)	27285	NM_024755	79811	Hs.512932	NM_017968	ENSG00000137776	SLTM	Met	SAFB like transcription modulator	protein-coding	0.002494	0.331258	
chunk0164_75_1	chr6	19779221	19779789	+	0	NA	Intergenic	Intergenic	-57865	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.010563	0.369069	
chunk0018_128_1	chr1	218537796	218538726	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	95635	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.004301	0.353383	
chunk0009_163_1	chr1	105286055	105286489	+	0	NA	Intergenic	Intergenic	332663	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002304	0.271264	
chunk0100_74_1	chr2	106751283	106751927	+	0	NA	Intergenic	L1MC3|LINE|L1	134549	NM_001142351	84620	Hs.98265	NM_032528	ENSG00000144057	ST6GAL2	SIAT2|ST6GalII	ST6 beta-galactoside alpha-2,6-sialyltransferase 2	protein-coding	0.001553	0.359690	
chunk0171_223_1	chr6	126280830	126281220	+	0	NA	Intergenic	Intergenic	-58764	NR_104462	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.000000	0.281330	
chunk0009_406_1	chr1	110407469	110408005	+	0	NA	promoter-TSS (NR_102697)	promoter-TSS (NR_102697)	-72	NR_102697	101410535	Hs.559121	NR_102697		LAMTOR5-AS1	-	LAMTOR5 antisense RNA 1	ncRNA	0.100746	0.629423	
chunk0045_111_1	chr12	46224447	46224884	+	0	NA	intron (NM_001077484, intron 5 of 16)	intron (NM_001077484, intron 5 of 16)	41830	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.004577	0.442922	
chunk0141_253_1	chr4	85595099	85595551	+	0	NA	intron (NM_001025616, intron 2 of 9)	intron (NM_001025616, intron 2 of 9)	120194	NM_001025616	83478	Hs.444229	NM_031305	ENSG00000138639	ARHGAP24	FILGAP|RC-GAP72|RCGAP72|p73|p73RhoGAP	Rho GTPase activating protein 24	protein-coding	0.011062	0.379691	
chunk0153_309_1	chr5	73552696	73553322	+	0	NA	intron (NM_023039, intron 8 of 8)	intron (NM_023039, intron 8 of 8)	12677	NM_023039	57763	Hs.239154	NM_023039	ENSG00000164331	ANKRA2	ANKRA	ankyrin repeat family A member 2	protein-coding	0.001597	0.315789	
chunk0093_332_1	chr19	54431621	54431937	+	0	NA	intron (NM_001005367, intron 10 of 12).3	intron (NM_001005367, intron 10 of 12).3	16348	NM_020659	57348	Hs.268728	NM_020659	ENSG00000167614	TTYH1	-	tweety family member 1	protein-coding	0.022152	0.526814	
chunk0052_458_1	chr12	132827935	132828944	+	0	NA	5' UTR (NM_005895, exon 1 of 24)	5' UTR (NM_005895, exon 1 of 24)	263	NM_005895	2802	Hs.507333	NM_005895	ENSG00000090615	GOLGA3	GCP170|MEA-2	golgin A3	protein-coding	0.087215	0.662376	
chunk0168_22_1	chr6	77012169	77012567	+	0	NA	Intergenic	MER52A|LTR|ERV1	451035	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.012563	0.538847	
chunk0174_286_1	chr6	162058390	162058589	+	0	NA	intron (NM_004562, intron 4 of 11)	intron (NM_004562, intron 4 of 11)	-668643	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.020101	0.500000	17(AGGGACAAGGTGATCT,-,0.00),18(GGGACAAGGTGATCTC,+,0.00)
chunk0033_434_1	chr11	25297988	25298833	+	0	NA	Intergenic	L1ME2z|LINE|L1	801440	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002367	0.283688	
chunk0094_263_1	chr2	7773326	7773569	+	0	NA	Intergenic	Intergenic	126208	NR_110256	101929551	Hs.116006	NR_110256	ENSG00000226506	LOC101929551	-	uncharacterized LOC101929551	ncRNA	0.024691	0.500000	
chunk0180_128_1	chr7	55944759	55945146	+	0	NA	Intergenic	Intergenic	-6966	NM_015969	51373	Hs.44298	NM_015969	ENSG00000239789	MRPS17	HSPC011|MRP-S17|RPMS17|S17mt	mitochondrial ribosomal protein S17	protein-coding	0.018088	0.417526	
chunk0212_372_1	chrX	150058283	150058496	+	0	NA	Intergenic	Intergenic	119841	NR_027456	100272228	Hs.496916	NR_027456	ENSG00000235703	LINC00894	-	long intergenic non-protein coding RNA 894	ncRNA	0.004695	0.401869	
chunk0040_295_1	chr11	117139502	117139955	+	0	NA	Intergenic	Intergenic	-4556	NM_002572	5049	Hs.728488	NM_002572	ENSG00000168092	PAFAH1B2	HEL-S-303	platelet activating factor acetylhydrolase 1b catalytic subunit 2	protein-coding	0.011038	0.418502	
chunk0139_262_1	chr4	56622121	56622810	+	0	NA	Intergenic	Intergenic	34057	NM_139211	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.002903	0.371014	
chunk0165_51_1	chr6	30556521	30556726	+	0	NA	promoter-TSS (NM_025263)	promoter-TSS (NM_025263)	-86	NM_001077497	80742	Hs.118354	NM_025263	ENSG00000204576	PRR3	CAT56	proline rich 3	protein-coding	0.087805	0.660194	
chunk0186_458_1	chr7	148345696	148346053	+	0	NA	intron (NM_014141, intron 21 of 23)	intron (NM_014141, intron 21 of 23)	-244691	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.002801	0.405028	
chunk0103_307_1	chr2	167013947	167014514	+	0	NA	intron (NM_001079810, intron 2 of 9)	HAL1|LINE|L1	125743	NM_001079810	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.001764	0.311620	
chunk0069_281_1	chr15	65021405	65021912	+	0	NA	intron (NM_139242, intron 3 of 8)	intron (NM_139242, intron 3 of 8)	7981	NM_139242	123263	Hs.531615	NM_139242	ENSG00000103707	MTFMT	COXPD15|FMT1|MC1DN27	mitochondrial methionyl-tRNA formyltransferase	protein-coding	0.001972	0.389764	
chunk0122_315_1	chr3	37029048	37029481	+	0	NA	intron (NM_001167618, intron 13 of 18)	intron (NM_001167618, intron 13 of 18)	35487	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.002309	0.366359	
chunk0066_397_1	chr15	39183453	39183772	+	0	NA	Intergenic	Intergenic	-67057	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.003135	0.396875	182(CAGAACAATCAGTCCT,-,0.00),183(AGAACAATCAGTCCTG,+,0.00)
chunk0190_431_1	chr8	41590457	41590801	+	0	NA	intron (NM_178819, intron 1 of 12)	MIRb|SINE|MIR	-12261	NR_125824	102723729	Hs.586384	NR_125824		LOC102723729	-	uncharacterized LOC102723729	ncRNA	0.014535	0.469565	
chunk0211_147_1	chrX	113603654	113603907	+	0	NA	Intergenic	MER70C|LTR|ERVL	334438	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.000000	0.456693	
chunk0104_314_1	chr2	179226445	179226930	+	0	NA	intron (NM_178123, intron 1 of 17)	intron (NM_178123, intron 1 of 17)	37936	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.006186	0.349794	
chunk0145_150_1	chr4	147053991	147054799	+	0	NA	Intergenic	Intergenic	-108513	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.003713	0.389370	
chunk0200_444_1	chr9	30553596	30554198	+	0	NA	Intergenic	L1M5|LINE|L1	-145443	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.004983	0.276949	
chunk0045_461_1	chr12	53804304	53804925	+	0	NA	Intergenic	Intergenic	-47580	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.006441	0.487138	
chunk0140_458_1	chr4	76526342	76527038	+	0	NA	intron (NM_020859, intron 1 of 10)	intron (NM_020859, intron 1 of 10)	-46878	NR_039654	100616299		NR_039654	ENSG00000263445	MIR4450	mir-4450	microRNA 4450	ncRNA	0.008621	0.426112	
chunk0062_354_1	chr14	73764952	73765161	+	0	NA	intron (NM_001043318, intron 1 of 11)	intron (NM_001043318, intron 1 of 11)	-4758	NM_194278	91748	Hs.594157	NM_194278	ENSG00000156030	ELMSAN1	C14orf117|C14orf43|LSR68|MIDEAS|c14_5541	ELM2 and Myb/SANT domain containing 1	protein-coding	0.014354	0.580952	
chunk0009_413_1	chr1	110612162	110612520	+	0	NA	intron (NM_001204269, intron 1 of 4)	Tigger3c|DNA|TcMar-Tigger	-5988	NM_004974	3737	Hs.248139	NM_004974	ENSG00000177301	KCNA2	EIEE32|HBK5|HK4|HUKIV|KV1.2|MK2|NGK1|RBK2	potassium voltage-gated channel subfamily A member 2	protein-coding	0.019553	0.487465	
chunk0020_345_1	chr1	239212655	239212980	+	0	NA	Intergenic	Intergenic	-416256	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.009231	0.358896	241(CATAACAGGCTGTTCT,-,0.00),242(ATAACAGGCTGTTCTG,+,0.00)
chunk0038_33_1	chr11	81192272	81193047	+	0	NA	Intergenic	Intergenic	-429856	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.001290	0.351804	
chunk0012_103_1	chr1	156510595	156511283	+	0	NA	Intergenic	Intergenic	-10097	NM_005920	4209	Hs.314327	NM_005920	ENSG00000116604	MEF2D	-	myocyte enhancer factor 2D	protein-coding	0.023256	0.523948	350(GGGAACAGGGTGTGCT,-,0.00),351(GGAACAGGGTGTGCTT,+,0.00)
chunk0106_405_1	chr2	207882115	207882365	+	0	NA	intron (NM_001080475, intron 6 of 7)	intron (NM_001080475, intron 6 of 7)	-112821	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.012000	0.430279	
chunk0154_13_1	chr5	76617987	76618186	+	0	NA	exon (NM_001256566, exon 2 of 2)	exon (NM_001256566, exon 2 of 2)	5327	NM_001256566	2151	Hs.42502	NM_004101	ENSG00000164220	F2RL2	PAR-3|PAR3	coagulation factor II thrombin receptor like 2	protein-coding	0.015075	0.490000	
chunk0172_400_1	chr6	139961296	139961595	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-14874	NR_121623	100507477	Hs.179213	NR_121622	ENSG00000236013	LOC100507477	-	uncharacterized LOC100507477	ncRNA	0.000000	0.346667	
chunk0086_295_1	chr18	23834434	23834641	+	0	NA	intron (NM_001127717, intron 24 of 73)	intron (NM_001127717, intron 24 of 73)	-38483	NM_001127718	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.000000	0.336538	
chunk0146_128_1	chr4	159153656	159153991	+	0	NA	Intergenic	Intergenic	-24929	NR_037459	100500881		NR_037459	ENSG00000264105	MIR3688-1	MIR3688|mir-3688-1	microRNA 3688-1	ncRNA	0.008955	0.369048	168(AAGTACAGGATGTTTT,-,0.00),169(AGTACAGGATGTTTTA,+,0.00)
chunk0062_428_1	chr14	75278415	75278872	+	0	NA	promoter-TSS (NM_005252)	promoter-TSS (NM_005252)	-135	NM_005252	2353	Hs.25647	NM_005252	ENSG00000170345	FOS	AP-1|C-FOS|p55	Fos proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.083151	0.650655	
chunk0092_180_1	chr19	30028511	30028763	+	0	NA	Intergenic	L1MB7|LINE|L1	86398	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.003968	0.347826	
chunk0140_324_1	chr4	73631794	73632106	+	0	NA	Intergenic	L1PB3|LINE|L1	-11319	NM_001270392	166824	Hs.529677	NM_177532	ENSG00000169435	RASSF6	-	Ras association domain family member 6	protein-coding	0.003205	0.511182	
chunk0176_158_1	chr7	13339496	13339933	+	0	NA	Intergenic	Intergenic	646800	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.004577	0.381279	
chunk0170_354_1	chr6	116436461	116436660	+	0	NA	exon (NM_013352, exon 6 of 6)	exon (NM_013352, exon 6 of 6)	-24810	NM_001010919	441168	Hs.381220	NM_001010919	ENSG00000188820	CALHM6	C6orf187|FAM26F|INAM|dJ93H18.5	calcium homeostasis modulator family member 6	protein-coding	0.020101	0.500000	
chunk0078_446_1	chr16	89705225	89705463	+	0	NA	Intergenic	Intergenic	-3631	NM_152339	124044	Hs.374556	NM_152339	ENSG00000158792	SPATA2L	C16orf76|tamo	spermatogenesis associated 2 like	protein-coding	0.025210	0.497908	
chunk0047_372_1	chr12	75147757	75148085	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	61827	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.003049	0.310030	
chunk0121_434_1	chr3	25998584	25998953	+	0	NA	Intergenic	L1PA6|LINE|L1	-125073	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.000000	0.491892	
chunk0065_108_1	chr15	24268376	24268665	+	0	NA	Intergenic	Intergenic	-98614	NR_026647	791115	Hs.560378	NR_026647	ENSG00000260551	PWRN2	NCRNA00199	Prader-Willi region non-protein coding RNA 2	ncRNA	0.013841	0.424138	
chunk0006_18_1	chr1	63947912	63948406	+	0	NA	intron (NM_001083592, intron 1 of 6)	MIR|SINE|MIR	164046	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.006073	0.311111	223(CAGTCCACACTGTTCT,-,0.00),224(AGTCCACACTGTTCTA,+,0.00)
chunk0013_15_1	chr1	165837892	165838245	+	0	NA	intron (NM_012474, intron 1 of 6)	intron (NM_012474, intron 1 of 6)	10573	NM_012474	7371	Hs.458360	NM_012474	ENSG00000143179	UCK2	TSA903|UK|UMPK	uridine-cytidine kinase 2	protein-coding	0.008499	0.449153	
chunk0081_10_1	chr17	37188144	37188343	+	0	NA	intron (NM_198836, intron 39 of 55).2	intron (NM_198836, intron 39 of 55).2	-56558	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.010050	0.425000	
chunk0043_200_1	chr12	19299742	19300079	+	0	NA	intron (NM_001143821, intron 14 of 27)	intron (NM_001143821, intron 14 of 27)	94585	NM_001256787	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.008902	0.426036	
chunk0020_267_1	chr1	236333211	236333614	+	0	NA	Intergenic	Intergenic	-51373	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.009926	0.428218	
chunk0020_276_1	chr1	236483274	236483473	+	0	NA	3' UTR (NM_145861, exon 6 of 6)	3' UTR (NM_145861, exon 6 of 6)	-34841	NM_201545	3964	Hs.4082	NM_006499	ENSG00000116977	LGALS8	Gal-8|PCTA-1|PCTA1|Po66-CBP	galectin 8	protein-coding	0.010050	0.425000	
chunk0175_120_1	chr7	3338151	3338686	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	36970	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005607	0.419776	
chunk0001_414_1	chr1	11071759	11072359	+	0	NA	intron (NM_001001998, intron 20 of 24)	intron (NM_001001998, intron 20 of 24)	-12025	NM_003132	6723	Hs.76244	NM_003132	ENSG00000116649	SRM	PAPT|SPDSY|SPS1|SRML1	spermidine synthase	protein-coding	0.016667	0.477537	
chunk0115_386_1	chr21	30372329	30372731	+	0	NA	promoter-TSS (NM_181621)	promoter-TSS (NM_181621)	-291	NM_181621	337959	Hs.58152	NM_181621	ENSG00000182816	KRTAP13-2	KAP13-2	keratin associated protein 13-2	protein-coding	0.004975	0.344913	215(GAGTACAGTGAGTCCT,-,0.00),216(AGTACAGTGAGTCCTT,+,0.00)
chunk0045_338_1	chr12	51146510	51147119	+	0	NA	intron (NM_001173453, intron 1 of 13)	L2c|LINE|L2	26329	NM_005653	7024	Hs.48849	NM_005653	ENSG00000135457	TFCP2	LBP1C|LSF|LSF1D|SEF|TFCP2C	transcription factor CP2	protein-coding	0.004926	0.391803	
chunk0112_147_1	chr20	38826264	38826512	+	0	NA	intron (NM_015568, intron 1 of 10)	intron (NM_015568, intron 1 of 10)	20695	NM_001172735	26051	Hs.45719	NM_015568	ENSG00000101445	PPP1R16B	ANKRD4|TIMAP	protein phosphatase 1 regulatory subunit 16B	protein-coding	0.016129	0.502008	
chunk0099_39_1	chr2	83831850	83832517	+	0	NA	Intergenic	L1MA8|LINE|L1	-458499	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.005997	0.306886	
chunk0084_385_1	chr17	81976715	81976914	+	0	NA	promoter-TSS (NM_001251888)	promoter-TSS (NM_001251888)	-736	NM_001251888	79058	Hs.298351	NM_024083	ENSG00000169696	ASPSCR1	ASPCR1|ASPL|ASPS|RCC17|TUG|UBXD9|UBXN9	ASPSCR1 tether for SLC2A4, UBX domain containing	protein-coding	0.050251	0.660000	
chunk0085_57_1	chr18	1074518	1074878	+	0	NA	Intergenic	Intergenic	169502	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.008333	0.343490	
chunk0005_61_1	chr1	55474735	55475366	+	0	NA	Intergenic	Intergenic	249409	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.003170	0.393987	
chunk0133_54_1	chr3	166574298	166574626	+	0	NA	Intergenic	MIR3|SINE|MIR	-736997	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.012195	0.352584	105(AAGCACATAATGTTCT,-,0.00),106(AGCACATAATGTTCTA,+,0.00)
chunk0173_139_1	chr6	143880484	143881168	+	0	NA	intron (NM_001013623, intron 1 of 7)	L1MC4a|LINE|L1	16390	NM_001013623	153918	Hs.121188	NM_001013623	ENSG00000118491	ZC2HC1B	C6orf94|FAM164B|dJ468K18.5	zinc finger C2HC-type containing 1B	protein-coding	0.005848	0.347445	
chunk0204_435_1	chr9	103883499	103883798	+	0	NA	Intergenic	L1ME2|LINE|L1	-116061	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.003344	0.303333	
chunk0079_395_1	chr17	19268820	19269581	+	0	NA	intron (NM_001102664, intron 1 of 7)	intron (NM_001102664, intron 1 of 7)	-2193	NR_046824	100874309	Hs.733657	NR_046824		EPN2-IT1	-	EPN2 intronic transcript 1	ncRNA	0.002628	0.417323	
chunk0017_253_1	chr1	209155926	209156557	+	0	NA	Intergenic	L3|LINE|CR1	-272582	NM_001104548									0.009509	0.354430	
chunk0129_433_1	chr3	127613471	127613741	+	0	NA	intron (NM_004526, intron 8 of 15)	intron (NM_004526, intron 8 of 15)	15249	NR_073375	4171	Hs.477481	NM_004526	ENSG00000073111	MCM2	BM28|CCNL1|CDCL1|D3S3194|DFNA70|MITOTIN|cdc19	minichromosome maintenance complex component 2	protein-coding	0.000000	0.416974	
chunk0087_211_1	chr18	36035305	36035520	+	0	NA	intron (NM_018170, intron 1 of 6)	MIR|SINE|MIR	32182	NM_001303411	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.000000	0.379630	
chunk0075_434_1	chr16	57786916	57787357	+	0	NA	intron (NM_001130099, intron 2 of 18)	intron (NM_001130099, intron 2 of 18)	10881	NM_001130099	3801	Hs.23131	NM_005550	ENSG00000140859	KIFC3	-	kinesin family member C3	protein-coding	0.029478	0.619910	276(GGGAACACACTGGACT,-,0.00),277(GGAACACACTGGACTC,+,0.00)
chunk0210_362_1	chrX	96542581	96542976	+	0	NA	Intergenic	Intergenic	-141885	NM_006729	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.015190	0.378788	
chunk0077_261_1	chr16	80946463	80946918	+	0	NA	Intergenic	Intergenic	-54094	NR_131947	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.010989	0.366228	213(AAGAACATGTTGTCCA,-,0.00),214(AGAACATGTTGTCCAA,+,0.00)
chunk0019_62_1	chr1	224211109	224211757	+	0	NA	intron (NR_110669, intron 1 of 1)	intron (NR_110669, intron 1 of 1)	1846	NR_110669	101927143	Hs.638720	NR_110669	ENSG00000232628	LOC101927143	-	uncharacterized LOC101927143	ncRNA	0.007716	0.420647	
chunk0021_120_1	chr10	3648619	3648974	+	0	NA	intron (NR_131187, intron 1 of 1)	(CA)n|Simple_repeat|Simple_repeat	136485	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.016901	0.516854	
chunk0188_117_1	chr8	9088664	9088882	+	0	NA	Intergenic	Intergenic	40328	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.004587	0.488584	
chunk0178_167_1	chr7	34036861	34037513	+	0	NA	intron (NM_133468, intron 7 of 15)	AluJr4|SINE|Alu	132276	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.009202	0.413476	
chunk0178_176_1	chr7	34148187	34148574	+	0	NA	intron (NM_133468, intron 15 of 15)	L2c|LINE|L2	243469	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.000000	0.384021	
chunk0071_63_1	chr15	80500071	80500312	+	0	NA	intron (NM_014862, intron 5 of 18)	intron (NM_014862, intron 5 of 18)	62753	NR_120363	101929586	Hs.569426	NR_120363	ENSG00000259175	LOC101929586	-	uncharacterized LOC101929586	ncRNA	0.000000	0.512397	165(AAGAACACACTGTCAC,-,0.00),166(AGAACACACTGTCACT,+,0.00)
chunk0159_352_1	chr5	144470505	144470708	+	0	NA	intron (NM_020768, intron 3 of 3)	intron (NM_020768, intron 3 of 3)	299733	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.000000	0.323529	
chunk0198_153_1	chr8	133001351	133001712	+	0	NA	intron (NM_003235, intron 35 of 47)	intron (NM_003235, intron 35 of 47)	45050	NR_107002	102466865		NR_107002	ENSG00000276961	MIR7848	hsa-mir-7848	microRNA 7848	ncRNA	0.011080	0.447514	234(AGGCCACTATGTCCTG,+,0.00)
chunk0148_28_1	chr5	652907	653320	+	0	NA	exon (NM_018140, exon 12 of 12)	exon (NM_018140, exon 12 of 12)	40282	NM_007030	11076	Hs.481466	NM_007030	ENSG00000171368	TPPP	TPPP/p25|TPPP1|p24|p25|p25alpha	tubulin polymerization promoting protein	protein-coding	0.019370	0.555556	
chunk0193_362_1	chr8	79937762	79938161	+	0	NA	intron (NM_014018, intron 2 of 2)	intron (NM_014018, intron 2 of 2)	-66224	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.002506	0.362500	
chunk0174_78_1	chr6	156240923	156241859	+	0	NA	Intergenic	L3|LINE|CR1	294594	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.005342	0.403415	
chunk0194_233_1	chr8	86300725	86301538	+	0	NA	Intergenic	Intergenic	-41634	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.003690	0.361179	
chunk0117_91_1	chr22	17349104	17349644	+	0	NA	Intergenic	L2c|LINE|L2	-10575	NM_001290046	27443	Hs.231895	NM_031413	ENSG00000099954	CECR2	-	CECR2 histone acetyl-lysine reader	protein-coding	0.020370	0.438078	
chunk0039_232_1	chr11	101932606	101933293	+	0	NA	intron (NM_020802, intron 2 of 10)	intron (NM_020802, intron 2 of 10)	-16427	NM_178127	253935	Hs.318370	NM_178127	ENSG00000187151	ANGPTL5	-	angiopoietin like 5	protein-coding	0.002911	0.344477	
chunk0137_384_1	chr4	26583884	26584083	+	0	NA	promoter-TSS (NM_001292054)	promoter-TSS (NM_001292054)	59	NM_001292054	55296	Hs.479403	NM_018317	ENSG00000109680	TBC1D19	-	TBC1 domain family member 19	protein-coding	0.065327	0.605000	
chunk0043_1_1	chr12	12741629	12741963	+	0	NA	intron (NM_001130415, intron 1 of 1)	MIRb|SINE|MIR	15879	NM_001130415	81575	Hs.23388	NM_030817	ENSG00000178878	APOLD1	VERGE	apolipoprotein L domain containing 1	protein-coding	0.002994	0.411940	
chunk0163_179_1	chr6	11310152	11310615	+	0	NA	intron (NM_001142393, intron 1 of 7)	L2|LINE|L2	71965	NM_001142393	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.008639	0.540948	
chunk0161_155_1	chr5	169022754	169023072	+	0	NA	intron (NR_109897, intron 1 of 4)	intron (NR_109897, intron 1 of 4)	9686	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.012579	0.451411	
chunk0060_193_1	chr14	47776318	47776617	+	0	NA	intron (NR_039996, intron 2 of 2)	MER34A|LTR|ERV1	-15363	NR_037503	100500919		NR_037503	ENSG00000263945	MIR548Y	-	microRNA 548y	ncRNA	0.006689	0.353333	
chunk0021_114_1	chr10	3451636	3451884	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	133065	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.008065	0.457831	
chunk0148_87_1	chr5	3212313	3212512	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	34577	NR_104617	102467074	Hs.575250	NR_104617	ENSG00000249808	LINC01377	-	long intergenic non-protein coding RNA 1377	ncRNA	0.020101	0.520000	
chunk0054_41_1	chr13	41065232	41065587	+	0	NA	intron (NM_007187, intron 4 of 9)	intron (NM_007187, intron 4 of 9)	3848	NM_007187	11193	Hs.411300	NM_007187	ENSG00000120688	WBP4	FBP21	WW domain binding protein 4	protein-coding	0.000000	0.356742	
chunk0134_107_1	chr3	176994968	176995410	+	0	NA	Intergenic	Intergenic	-178188	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.002262	0.338600	
chunk0123_81_1	chr3	41819735	41820330	+	0	NA	intron (NM_017886, intron 18 of 36)	intron (NM_017886, intron 18 of 36)	142136	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.003361	0.305369	
chunk0058_307_1	chr14	27099274	27100159	+	0	NA	Intergenic	Intergenic	191074	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.005650	0.472912	
chunk0066_370_1	chr15	38467621	38468089	+	0	NA	intron (NM_173611, intron 3 of 7)	L1ME4b|LINE|L1	13728	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.002137	0.345416	
chunk0008_228_1	chr1	94022453	94022874	+	0	NA	intron (NM_000350, intron 32 of 49)	L2|LINE|L2	98486	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.009501	0.540284	
chunk0001_420_1	chr1	11158928	11159450	+	0	NA	intron (NM_004958, intron 29 of 57)	intron (NM_004958, intron 29 of 57)	15291	NR_046600	100873935	Hs.679133	NR_046600	ENSG00000225602	MTOR-AS1	-	MTOR antisense RNA 1	ncRNA	0.011494	0.456979	269(GAGAACATCTTGATCT,-,0.00),270(AGAACATCTTGATCTA,+,0.00),290(GAGTACATGAAGTGCC,-,0.00),291(AGTACATGAAGTGCCC,+,0.00)
chunk0075_29_1	chr16	46920498	46921101	+	0	NA	intron (NM_001142466, intron 8 of 11)	intron (NM_001142466, intron 8 of 11)	35685	NM_001142466	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.014925	0.481788	
chunk0039_374_1	chr11	106425827	106426516	+	0	NA	Intergenic	Intergenic	174764	NR_120551	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.005806	0.357971	
chunk0035_169_1	chr11	43868530	43869127	+	0	NA	Intergenic	Intergenic	-11979	NM_139178	221120	Hs.720708	NM_139178	ENSG00000166199	ALKBH3	ABH3|DEPC-1|DEPC1|PCA1|hABH3	alkB homolog 3, alpha-ketoglutaratedependent dioxygenase	protein-coding	0.011725	0.382943	
chunk0189_79_1	chr8	21036476	21036837	+	0	NA	Intergenic	Intergenic	62670	NR_033894	286114	Hs.651884	NR_033894	ENSG00000253199	LINC02153	-	long intergenic non-protein coding RNA 2153	ncRNA	0.024931	0.533149	
chunk0168_136_1	chr6	82902040	82902682	+	0	NA	intron (NM_198920, intron 9 of 9)	L1MD2|LINE|L1	163480	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.004673	0.385692	
chunk0002_216_1	chr1	19648501	19648805	+	0	NA	intron (NM_001278166, intron 1 of 3)	intron (NM_001278166, intron 1 of 3)	1043	NM_001278166	4681	Hs.654502	NM_005380	ENSG00000158747	NBL1	D1S1733E|DAN|DAND1|NB|NO3	NBL1, DAN family BMP antagonist	protein-coding	0.023026	0.603279	206(CAGCTCAGAATGTACC,-,0.00)
chunk0061_67_1	chr14	56606860	56607258	+	0	NA	intron (NM_017799, intron 5 of 15)	L4_C_Mam|LINE|RTE-X	27266	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.015075	0.365915	
chunk0015_357_1	chr1	190327708	190327907	+	0	NA	intron (NM_199051, intron 2 of 7)	L1PA16|LINE|L1	149822	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.005025	0.365000	
chunk0090_111_1	chr18	71208738	71209266	+	0	NA	Intergenic	(ATTTTA)n|Simple_repeat|Simple_repeat	369954	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.005682	0.275992	
chunk0176_279_1	chr7	16628709	16629530	+	0	NA	intron (NM_020319, intron 2 of 9)	intron (NM_020319, intron 2 of 9)	16698	NM_020319	57037	Hs.157378	NM_020319	ENSG00000106524	ANKMY2	ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding	0.010962	0.439173	
chunk0192_141_1	chr8	61988656	61989312	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-259958	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.009146	0.372907	306(GAGTACACGGTGTTCT,-,0.00),307(AGTACACGGTGTTCTT,+,0.00)
chunk0164_256_1	chr6	23499454	23499987	+	0	NA	Intergenic	Intergenic	-626466	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.003752	0.308989	
chunk0109_133_1	chr20	3263861	3264060	+	0	NA	intron (NM_001009984, intron 31 of 36)	intron (NM_001009984, intron 31 of 36)	-24719	NM_001174089	83959	Hs.105607	NM_032034	ENSG00000088836	SLC4A11	BTR1|CDPD1|CHED|CHED2|NABC1|dJ794I6.2	solute carrier family 4 member 11	protein-coding	0.005025	0.485000	91(AGCACACTCTCTCCTT,+,0.00)
chunk0202_134_1	chr9	73263509	73263872	+	0	NA	Intergenic	Intergenic	111959	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.002755	0.260989	
chunk0008_309_1	chr1	95130427	95130998	+	0	NA	intron (NM_001199691, intron 1 of 7)	intron (NM_001199691, intron 1 of 7)	12789	NM_001199691	100527978	Hs.483512	NM_001199691	ENSG00000271092	TLCD4-RWDD3	TMEM56-RWDD3	TLCD4-RWDD3 readthrough	protein-coding	0.005254	0.351399	
chunk0189_379_1	chr8	27366764	27367293	+	0	NA	intron (NM_004103, intron 2 of 31)	MamRep4096|DNA|hAT-Tip100	41464	NM_173175	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.003781	0.513208	
chunk0119_305_1	chr22	46596889	46597205	+	0	NA	Intergenic	Intergenic	-29714	NM_015124	23151	Hs.475150	NM_015124	ENSG00000075240	GRAMD4	DIP	GRAM domain containing 4	protein-coding	0.022152	0.599369	
chunk0096_57_1	chr2	27398154	27398540	+	0	NA	intron (NM_177983, intron 1 of 9)	L1MB7|LINE|L1	-4771	NR_002201	2498	Hs.658438	NR_002201		FTH1P3	FTHL3|FTHL3P	ferritin heavy chain 1 pseudogene 3	pseudo	0.005181	0.341085	
chunk0063_449_1	chr14	89040621	89041348	+	0	NA	Intergenic	Intergenic	216831	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.030261	0.559066	
chunk0003_83_1	chr1	31627394	31627866	+	0	NA	TTS (NM_001525)	TTS (NM_001525)	9930	NM_001525	3061	Hs.388226	NM_001525	ENSG00000121764	HCRTR1	OX1R	hypocretin receptor 1	protein-coding	0.023305	0.579281	210(TGGCACTGAATGTTCC,-,0.00),211(GGCACTGAATGTTCCC,+,0.00)
chunk0207_439_1	chr9	137534961	137535334	+	0	NA	intron (NM_001098537, intron 8 of 34)	L1ME3|LINE|L1	15422	NM_152286	375775	Hs.294147	NM_152286	ENSG00000130653	PNPLA7	C9orf111|NTE-R1|NTEL1	patatin like phospholipase domain containing 7	protein-coding	0.008043	0.457219	206(TACACAGTGTGTGCTT,+,0.00)
chunk0160_252_1	chr5	156728827	156729083	+	0	NA	intron (NM_000337, intron 7 of 8)	intron (NM_000337, intron 7 of 8)	-121583	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.007812	0.319066	
chunk0148_306_1	chr5	12758125	12758649	+	0	NA	intron (NR_033383, intron 3 of 3)	MER58A|DNA|hAT-Charlie	90528	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.013359	0.377143	
chunk0032_231_1	chr11	7622703	7623331	+	0	NA	intron (NM_003621, intron 7 of 23)	MIRb|SINE|MIR	17283	NM_001256569	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.006369	0.465819	
chunk0040_249_1	chr11	115420529	115420869	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	83824	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.014706	0.434018	
chunk0104_242_1	chr2	177030399	177030598	+	0	NA	Intergenic	Intergenic	-182196	NM_194247	220988	Hs.516539	NM_194247	ENSG00000170144	HNRNPA3	2610510D13Rik|D10S102|FBRNP|HNRPA3	heterogeneous nuclear ribonucleoprotein A3	protein-coding	0.020101	0.490000	
chunk0098_292_1	chr2	75997406	75998095	+	0	NA	Intergenic	Intergenic	-286765	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.004354	0.315942	
chunk0200_56_1	chr9	15658998	15659208	+	0	NA	intron (NM_173550, intron 8 of 25)	intron (NM_173550, intron 8 of 25)	106004	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.000000	0.407583	
chunk0029_113_1	chr10	97989248	97989483	+	0	NA	intron (NM_018058, intron 2 of 14)	Tigger3a|DNA|TcMar-Tigger	41463	NM_018058	55118	Hs.500736	NM_018058	ENSG00000095713	CRTAC1	ASPIC|ASPIC1|CEP-68|CEP68|LOTUS	cartilage acidic protein 1	protein-coding	0.008511	0.415254	
chunk0086_351_1	chr18	25366341	25366841	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-14341	NM_015461	25925	Hs.116935	NM_015461	ENSG00000198795	ZNF521	EHZF|Evi3	zinc finger protein 521	protein-coding	0.006000	0.449102	
chunk0185_164_1	chr7	127790640	127791010	+	0	NA	intron (NM_014390, intron 10 of 23)	intron (NM_014390, intron 10 of 23)	138677	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.010811	0.390836	
chunk0031_373_1	chr10	130491711	130492114	+	0	NA	Intergenic	Intergenic	355537	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.017370	0.467822	
chunk0121_29_1	chr3	15154570	15154891	+	0	NA	Intergenic	Intergenic	51229	NR_027927	344875	Hs.722756	NR_027927	ENSG00000230524	COL6A4P1	COL6A4|COL6A4P|DIVA|DVWA|VWA6	collagen type VI alpha 4 pseudogene 1	pseudo	0.006231	0.335404	
chunk0011_264_1	chr1	151056447	151056998	+	0	NA	5' UTR (NM_001038707, exon 2 of 6)	5' UTR (NM_001038707, exon 2 of 6)	2927	NM_001038707	56882	Hs.22065	NM_020239	ENSG00000197622	CDC42SE1	SCIP1|SPEC1	CDC42 small effector 1	protein-coding	0.007260	0.500000	
chunk0026_48_1	chr10	60934446	60934896	+	0	NA	intron (NM_014836, intron 2 of 10)	intron (NM_014836, intron 2 of 10)	9604	NM_014836	9886	Hs.737374	NM_014836	ENSG00000072422	RHOBTB1	-	Rho related BTB domain containing 1	protein-coding	0.006667	0.383592	
chunk0051_94_1	chr12	114655894	114656704	+	0	NA	Intergenic	Intergenic	27865	NM_005996	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.014815	0.480888	268(TGGAACATGGAGTTCT,-,0.00),269(GGAACATGGAGTTCTC,+,0.00)
chunk0104_320_1	chr2	179279201	179279400	+	0	NA	Intergenic	L1MA2|LINE|L1	-14677	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.000000	0.340000	
chunk0165_144_1	chr6	33621496	33622201	+	0	NA	intron (NM_002224, intron 1 of 57)	CpG	469	NM_002224	3710	Hs.65758	NM_002224	ENSG00000096433	ITPR3	IP3R|IP3R3	inositol 1,4,5-trisphosphate receptor type 3	protein-coding	0.073759	0.667139	
chunk0110_437_1	chr20	20847607	20847877	+	0	NA	Intergenic	Intergenic	-135119	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.007407	0.405904	
chunk0079_6_1	chr17	9184014	9184349	+	0	NA	intron (NM_004822, intron 5 of 6)	intron (NM_004822, intron 5 of 6)	-5063	NR_110828	101928266	Hs.639880	NR_110828	ENSG00000262966	LOC101928266	-	uncharacterized LOC101928266	ncRNA	0.017910	0.529762	
chunk0208_387_1	chrX	28757129	28757641	+	0	NA	intron (NM_014271, intron 1 of 10)	intron (NM_014271, intron 1 of 10)	169821	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.003906	0.413255	
chunk0101_134_1	chr2	127411294	127411577	+	0	NA	Intergenic	Intergenic	-6985	NM_000312	5624	Hs.224698	NM_000312	ENSG00000115718	PROC	APC|PC|PROC1|THPH3|THPH4	protein C, inactivator of coagulation factors Va and VIIIa	protein-coding	0.010601	0.362676	
chunk0058_86_1	chr14	21449235	21449450	+	0	NA	Intergenic	MIRb|SINE|MIR	-12044	NM_020920	57680	Hs.530698	NM_020920	ENSG00000100888	CHD8	AUTS18|HELSNF1	chromodomain helicase DNA binding protein 8	protein-coding	0.000000	0.342593	
chunk0138_97_1	chr4	35890834	35891299	+	0	NA	Intergenic	Intergenic	-353050	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.006452	0.401288	
chunk0140_310_1	chr4	73087883	73088132	+	0	NA	intron (NM_032217, intron 29 of 33)	GA-rich|Low_complexity|Low_complexity	-18248	NM_001297733	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.000000	0.388000	
chunk0034_143_1	chr11	29469539	29469843	+	0	NA	Intergenic	L1MA7|LINE|L1	512702	NR_132652	106456574	Hs.128812	NR_132652	ENSG00000261340	LINC01616	n341006	long intergenic non-protein coding RNA 1616	ncRNA	0.006579	0.386885	
chunk0199_142_1	chr9	4094515	4094714	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	57569	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.005025	0.340000	
chunk0141_34_1	chr4	76955224	76955531	+	0	NA	intron (NM_018243, intron 1 of 9)	L2c|LINE|L2	5663	NM_018243	55752	Hs.128199	NM_018243	ENSG00000138758	SEPTIN11	SEPT11	septin 11	protein-coding	0.003257	0.480519	160(GGAAACAGCATGTGCC,-,0.00),161(GAAACAGCATGTGCCA,+,0.00)
chunk0212_49_1	chrY	11311589	11311802	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1109895	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.004695	0.462617	
chunk0029_106_1	chr10	97823654	97824110	+	0	NA	Intergenic	Intergenic	25916	NR_108035	100505561	Hs.351904	NR_108035	ENSG00000227356	LINC00866	-	long intergenic non-protein coding RNA 866	ncRNA	0.028509	0.597374	259(GAGGACACTGTGTCCT,-,0.00),260(AGGACACTGTGTCCTG,+,0.00)
chunk0124_364_1	chr3	59112209	59112521	+	0	NA	Intergenic	L1MC5|LINE|L1	-62376	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.000000	0.364217	194(TGGAACATCTTGTCCT,-,0.00),195(GGAACATCTTGTCCTA,+,0.00)
chunk0185_414_1	chr7	134293095	134293381	+	0	NA	3' UTR (NM_032826, exon 10 of 10)	3' UTR (NM_032826, exon 10 of 10)	23837	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.017483	0.459930	
chunk0057_274_1	chr13	105904449	105904683	+	0	NA	Intergenic	Intergenic	197736	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.008547	0.382979	124(CAGACCAGTCTGTTCA,-,0.00),125(AGACCAGTCTGTTCAC,+,0.00)
chunk0177_231_1	chr7	24542742	24543089	+	0	NA	Intergenic	L1MB8|LINE|L1	-30431	NM_016447	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.005764	0.304598	
chunk0102_365_1	chr2	152718017	152718639	+	0	NA	promoter-TSS (NM_017892)	promoter-TSS (NM_017892)	435	NR_024526	151188	Hs.643580	NM_152522	ENSG00000177917	ARL6IP6	AIP-6|AIP6|PFAAP1	ADP ribosylation factor like GTPase 6 interacting protein 6	protein-coding	0.091640	0.646870	
chunk0176_360_1	chr7	18309377	18309871	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-182315	NR_031635	100302140		NR_031635	ENSG00000221393	MIR1302-6	MIRN1302-6|hsa-mir-1302-6	microRNA 1302-6	ncRNA	0.006073	0.325253	
chunk0014_39_1	chr1	174963469	174963964	+	0	NA	intron (NM_001243765, intron 3 of 8)	MER58A|DNA|hAT-Charlie	-1052	NM_001243764	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.004040	0.342742	
chunk0016_306_1	chr1	201340169	201340545	+	0	NA	Intergenic	L1MEf|LINE|L1	37343	NM_001276347	7139	Hs.533613	NM_000364	ENSG00000118194	TNNT2	CMD1D|CMH2|CMPD2|LVNC6|RCM3|TnTC|cTnT	troponin T2, cardiac type	protein-coding	0.000000	0.312997	
chunk0150_340_1	chr5	38565810	38566191	+	0	NA	intron (NR_103553, intron 1 of 2)	intron (NR_103553, intron 1 of 2)	-8439	NR_037423	100500824		NR_037423	ENSG00000265304	MIR3650	-	microRNA 3650	ncRNA	0.007874	0.363874	221(ATGGTCAGAATGTCCT,-,0.00),222(TGGTCAGAATGTCCTT,+,0.00)
chunk0066_269_1	chr15	34955812	34956292	+	0	NA	intron (NM_014691, intron 3 of 34)	L1ME3A|LINE|L1	13742	NM_014691	9716	Hs.510958	NM_014691	ENSG00000021776	AQR	IBP160|fSAP164	aquarius intron-binding spliceosomal factor	protein-coding	0.014583	0.351351	
chunk0007_153_1	chr1	79716530	79716915	+	0	NA	Intergenic	Intergenic	-709912	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.002597	0.352332	
chunk0070_321_1	chr15	75432966	75433574	+	0	NA	intron (NM_001145357, intron 1 of 20)	intron (NM_001145357, intron 1 of 20)	18315	NM_015477	25942	Hs.513039	NM_015477	ENSG00000169375	SIN3A	WITKOS	SIN3 transcription regulator family member A	protein-coding	0.011513	0.379310	
chunk0074_257_1	chr16	27960831	27961328	+	0	NA	intron (NM_001109763, intron 2 of 6)	intron (NM_001109763, intron 2 of 6)	-72922	NM_144675	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.020121	0.512048	
chunk0078_137_1	chr17	3742991	3743411	+	0	NA	intron (NM_002208, intron 19 of 30)	intron (NM_002208, intron 19 of 30)	19298	NM_031965	83903	Hs.534059	NM_031965	ENSG00000177602	HASPIN	GSG2	histone H3 associated protein kinase	protein-coding	0.016667	0.548694	
chunk0144_17_1	chr4	124844996	124845472	+	0	NA	Intergenic	Intergenic	-132502	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.000000	0.276730	
chunk0171_66_1	chr6	121449481	121449680	+	0	NA	3' UTR (NM_000165, exon 2 of 2)	3' UTR (NM_000165, exon 2 of 2)	14003	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.005025	0.350000	
chunk0201_42_1	chr9	33690390	33690669	+	0	NA	Intergenic	Intergenic	-13109	NR_023917	11191	Hs.493716	NR_023917	ENSG00000237984	PTENP1	PTEN-rs|PTEN2|PTENpg1|PTH2|psiPTEN	phosphatase and tensin homolog pseudogene 1	pseudo	0.003584	0.375000	
chunk0148_313_1	chr5	13428370	13428587	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	516002	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.013825	0.440367	
chunk0052_310_1	chr12	124939371	124939991	+	0	NA	Intergenic	tRNA-Asp-GAY|tRNA|tRNA	24134	NR_049820	100847004		NR_049820	ENSG00000265345	MIR5188	mir-5188	microRNA 5188	ncRNA	0.045161	0.516908	
chunk0090_338_1	chr18	76348336	76348812	+	0	NA	Intergenic	Intergenic	146616	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.029412	0.605870	
chunk0096_134_1	chr2	28736781	28737023	+	0	NA	Intergenic	L1ME3|LINE|L1	-14846	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.012397	0.403292	
chunk0123_373_1	chr3	48577154	48577514	+	0	NA	intron (NM_000094, intron 64 of 117)	intron (NM_000094, intron 64 of 117)	1643	NR_031756	100313843		NR_031756	ENSG00000284251	MIR711	hsa-mir-711	microRNA 711	ncRNA	0.005556	0.512465	
chunk0033_29_1	chr11	12853333	12854294	+	0	NA	intron (NM_021961, intron 3 of 12)	intron (NM_021961, intron 3 of 12)	135735	NR_038904	100506305	Hs.153408	NR_038904	ENSG00000251381	LINC00958	BLACAT2	long intergenic non-protein coding RNA 958	ncRNA	0.008325	0.425156	424(GAGAACACAGTGTTCT,-,0.00),425(AGAACACAGTGTTCTA,+,0.00)
chunk0020_399_1	chr1	240736328	240736774	+	0	NA	Intergenic	Intergenic	-124389	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.015695	0.489933	
chunk0057_332_1	chr13	107026064	107026331	+	0	NA	Intergenic	Intergenic	372317	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.003745	0.466418	
chunk0050_219_1	chr12	104624880	104625477	+	0	NA	intron (NM_001173982, intron 2 of 2)	intron (NM_001173982, intron 2 of 2)	33545	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.015075	0.473244	
chunk0197_309_1	chr8	124671403	124671852	+	0	NA	intron (NM_001282974, intron 3 of 13)	intron (NM_001282974, intron 3 of 13)	56880	NM_014751	9788	Hs.336994	NM_014751	ENSG00000170873	MTSS1	MIM|MIMA|MIMB	MTSS I-BAR domain containing 1	protein-coding	0.011136	0.451111	173(GGAGACAGAGTGTTCC,-,0.00),174(GAGACAGAGTGTTCCA,+,0.00)
chunk0044_227_1	chr12	31421721	31422092	+	0	NA	intron (NM_001308339, intron 13 of 22)	intron (NM_001308339, intron 13 of 22)	-95681	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.005391	0.395161	
chunk0040_351_1	chr11	118646281	118646711	+	0	NA	intron (NM_015157, intron 18 of 23)	Tigger20a|DNA|TcMar-Tigger	2496	NR_106773	102466719		NR_106773	ENSG00000284246	MIR6716	hsa-mir-6716	microRNA 6716	ncRNA	0.004651	0.466357	
chunk0083_119_1	chr17	65017059	65017708	+	0	NA	intron (NM_001282425, intron 3 of 3)	intron (NM_001282425, intron 3 of 3)	38391	NM_001282425	10672	Hs.515018	NM_006572	ENSG00000120063	GNA13	G13	G protein subunit alpha 13	protein-coding	0.020031	0.427692	
chunk0150_222_1	chr5	35441929	35442416	+	0	NA	Intergenic	L1MC3|LINE|L1	-175715	NM_144722	79925	Hs.298863	NM_024867	ENSG00000152582	SPEF2	CT122|KPL2	sperm flagellar 2	protein-coding	0.002053	0.356557	
chunk0159_284_1	chr5	142608154	142608429	+	0	NA	intron (NM_000800, intron 2 of 3)	intron (NM_000800, intron 2 of 3)	5870	NM_033137	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.018182	0.471014	
chunk0197_228_1	chr8	123022206	123022510	+	0	NA	intron (NM_001134671, intron 5 of 7)	intron (NM_001134671, intron 5 of 7)	20065	NM_001134671	79139	Hs.241576	NM_024295	ENSG00000136986	DERL1	DER-1|DER1|derlin-1	derlin 1	protein-coding	0.009868	0.409836	
chunk0162_321_1	chr6	6748684	6749398	+	0	NA	Intergenic	Intergenic	-126215	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.018207	0.433566	
chunk0003_25_1	chr1	29355077	29355751	+	0	NA	Intergenic	Intergenic	-5300	NR_110758	101928460	Hs.434659	NR_110758	ENSG00000230523	LINC01756	-	long intergenic non-protein coding RNA 1756	ncRNA	0.008902	0.487407	
chunk0154_226_1	chr5	80763178	80764497	+	0	NA	intron (NM_002439, intron 13 of 23)	intron (NM_002439, intron 13 of 23)	-108856	NM_001290357	1719	Hs.592364	NM_000791	ENSG00000228716	DHFR	DHFRP1|DYR	dihydrofolate reductase	protein-coding	0.005307	0.387879	1008(GGGTACAGATTGTGCC,-,0.00),1009(GGTACAGATTGTGCCA,+,0.00)
chunk0055_378_1	chr13	73210109	73210551	+	0	NA	Intergenic	Intergenic	151538	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.004525	0.422122	
chunk0201_365_1	chr9	68564937	68565136	+	0	NA	Intergenic	L2b|LINE|L2	-18434	NR_109769	101927015	Hs.406454	NR_109769	ENSG00000234506	LINC01506	-	long intergenic non-protein coding RNA 1506	ncRNA	0.005025	0.460000	
chunk0044_44_1	chr12	27643963	27644320	+	0	NA	intron (NM_003622, intron 4 of 29)	AluJo|SINE|Alu	-52354	NM_001029874	387849	Hs.269836	NM_001029874	ENSG00000174236	REP15	RAB15EP	RAB15 effector protein	protein-coding	0.005602	0.446927	
chunk0079_349_1	chr17	17810020	17810426	+	0	NA	3' UTR (NM_030665, exon 6 of 6)	3' UTR (NM_030665, exon 6 of 6)	3322	NR_106835	102465466		NR_106835	ENSG00000274111	MIR6777	hsa-mir-6777	microRNA 6777	ncRNA	0.096059	0.712531	191(CGGCACAGGGCGTTCT,-,0.00),192(GGCACAGGGCGTTCTT,+,0.00)
chunk0111_49_1	chr20	22403952	22404257	+	0	NA	intron (NR_027090, intron 1 of 2)	intron (NR_027090, intron 1 of 2)	16539	NR_027090	284788	Hs.651993	NR_027089	ENSG00000204684	LOC284788	-	uncharacterized LOC284788	ncRNA	0.019672	0.437908	
chunk0087_402_1	chr18	41949089	41949777	+	0	NA	Intergenic	Intergenic	-5765	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.004360	0.380261	
chunk0072_384_1	chr15	100463604	100463847	+	0	NA	intron (NM_001290341, intron 12 of 13)	intron (NM_001290341, intron 12 of 13)	80561	NM_001290342	204219	Hs.662371	NM_178842	ENSG00000154227	CERS3	ARCI9|LASS3	ceramide synthase 3	protein-coding	0.012346	0.500000	
chunk0173_288_1	chr6	148257790	148258358	+	0	NA	Intergenic	Intergenic	-84519	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.014085	0.421793	
chunk0102_42_1	chr2	142220990	142221191	+	0	NA	Intergenic	Intergenic	-89389	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.009950	0.495050	81(GAGCACACACAGTTCT,-,0.00),82(AGCACACACAGTTCTC,+,0.00)
chunk0016_87_1	chr1	194437078	194437297	+	0	NA	Intergenic	L1PA13|LINE|L1	1132442	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.004566	0.540909	
chunk0031_81_1	chr10	123180446	123181014	+	0	NA	Intergenic	L1MB3|LINE|L1	26486	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.007042	0.390158	
chunk0090_461_1	chr18	80201400	80201921	+	0	NA	intron (NM_032510, intron 2 of 2)	intron (NM_032510, intron 2 of 2)	45854	NM_032510	84552	Hs.654920	NM_032510	ENSG00000178184	PARD6G	PAR-6G|PAR6gamma	par-6 family cell polarity regulator gamma	protein-coding	0.028791	0.580460	
chunk0069_319_1	chr15	65870410	65870799	+	0	NA	intron (NM_001206836, intron 1 of 4)	intron (NM_001206836, intron 1 of 4)	1145	NM_001206836	8766	Hs.321541	NM_004663	ENSG00000103769	RAB11A	YL8	RAB11A, member RAS oncogene family	protein-coding	0.025707	0.502564	
chunk0145_431_1	chr4	153204868	153205442	+	0	NA	intron (NM_001302693, intron 1 of 2)	intron (NM_001302693, intron 1 of 2)	741	NM_015271	23321	Hs.435711	NM_015271	ENSG00000109654	TRIM2	CMT2R|RNF86	tripartite motif containing 2	protein-coding	0.027875	0.516522	
chunk0190_150_1	chr8	31138350	31138931	+	0	NA	intron (NM_000553, intron 24 of 34)	intron (NM_000553, intron 24 of 34)	-104925	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.001721	0.328179	
chunk0201_247_1	chr9	37872135	37872476	+	0	NA	Intergenic	Intergenic	32048	NR_024872	92014	Hs.634120	NM_033412	ENSG00000122696	SLC25A51	CG7943|MCART1	solute carrier family 25 member 51	protein-coding	0.005865	0.426901	220(AAGAACAATGTGTCCC,-,0.00),221(AGAACAATGTGTCCCT,+,0.00)
chunk0138_36_1	chr4	31222972	31223652	+	0	NA	Intergenic	LTR86A2|LTR|ERVL	52168	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.005882	0.339207	
chunk0068_190_1	chr15	54812685	54813188	+	0	NA	Intergenic	Intergenic	384097	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.000000	0.337302	
chunk0037_193_1	chr11	74283833	74284281	+	0	NA	intron (NM_001288748, intron 7 of 12)	L2a|LINE|L2	-27305	NR_120556	101928580	Hs.569025	NR_120556	ENSG00000246211	P4HA3-AS1	-	P4HA3 antisense RNA 1	ncRNA	0.002232	0.425390	
chunk0189_260_1	chr8	25243642	25244281	+	0	NA	intron (NM_024940, intron 2 of 51)	intron (NM_024940, intron 2 of 51)	59189	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.010955	0.462500	484(CAGCACTAAATGTTCC,-,0.00),485(AGCACTAAATGTTCCC,+,0.00)
chunk0054_16_1	chr13	40571769	40572367	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	-91062	NR_024506	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.010033	0.323873	
chunk0195_324_1	chr8	98989581	98990041	+	0	NA	Intergenic	Intergenic	-23455	NM_181661	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.015217	0.433839	
chunk0151_283_1	chr5	52800475	52800922	+	0	NA	exon (NM_015946, exon 2 of 3)	exon (NM_015946, exon 2 of 3)	12396	NM_181501	3672	Hs.644352	NM_181501	ENSG00000213949	ITGA1	CD49a|VLA1	integrin subunit alpha 1	protein-coding	0.046980	0.600446	
chunk0135_422_1	chr3	193673794	193674230	+	0	NA	intron (NM_130831, intron 26 of 27)	intron (NM_130831, intron 26 of 27)	-46680	NR_046634	100873941	Hs.679364	NR_046634	ENSG00000224855	OPA1-AS1	-	OPA1 antisense RNA 1	ncRNA	0.016055	0.427918	
chunk0169_322_1	chr6	106286900	106287562	+	0	NA	intron (NR_104402, intron 3 of 5)	intron (NR_104402, intron 3 of 5)	29035	NR_104403	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.001511	0.402715	
chunk0056_2_1	chr13	76925595	76926236	+	0	NA	Intergenic	Intergenic	-2536	NR_026983	690	Hs.567241	NR_026983		BTF3P11	BTF3L1|HUMBTFB|OCIF|OPG|TNFRSF11B	basic transcription factor 3 pseudogene 11	pseudo	0.006240	0.384735	
chunk0160_384_1	chr5	161337397	161338007	+	0	NA	intron (NM_021911, intron 6 of 10)	intron (NM_021911, intron 6 of 10)	210422	NM_000813	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.000000	0.360065	
chunk0166_188_1	chr6	46199452	46199768	+	0	NA	Intergenic	Intergenic	-28600	NM_001290073	59084	Hs.35198	NM_021572	ENSG00000112796	ENPP5	NPP-5|NPP5	ectonucleotide pyrophosphatase/phosphodiesterase family member 5	protein-coding	0.012658	0.444795	
chunk0105_10_1	chr2	181892137	181892628	+	0	NA	intron (NM_001130445, intron 1 of 17)	CpG	666	NM_001287505	6744	Hs.196983	NM_006751	ENSG00000138434	ITPRID2	CS-1|CS1|KRAP|SPAG13|SSFA2	ITPR interacting domain containing 2	protein-coding	0.085540	0.668699	
chunk0143_324_1	chr4	119736962	119737271	+	0	NA	Intergenic	Intergenic	67399	NR_110660	101927007	Hs.143958	NR_110660	ENSG00000250772	LINC01365	-	long intergenic non-protein coding RNA 1365	ncRNA	0.000000	0.293548	
chunk0042_228_1	chr12	6237599	6238236	+	0	NA	3' UTR (NM_001769, exon 8 of 8)	3' UTR (NM_001769, exon 8 of 8)	37601	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.007849	0.371473	
chunk0007_64_1	chr1	78223401	78223753	+	0	NA	Intergenic	L2b|LINE|L2	-6022	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.008523	0.447592	210(TGGGGCACAGTGTGCC,-,0.00),211(GGGGCACAGTGTGCCA,+,0.00)
chunk0111_141_1	chr20	24990788	24991004	+	0	NA	intron (NM_020531, intron 1 of 8)	intron (NM_020531, intron 1 of 8)	1893	NM_020531	57136	Hs.472330	NM_020531	ENSG00000101474	APMAP	BSCv|C20orf3	adipocyte plasma membrane associated protein	protein-coding	0.004630	0.373272	
chunk0024_159_1	chr10	35492284	35492661	+	0	NA	intron (NM_145012, intron 2 of 9)	MER104|DNA|TcMar-Tc2	-112938	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.007958	0.436508	
chunk0098_298_1	chr2	76182850	76183280	+	0	NA	Intergenic	Intergenic	-472080	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.002326	0.329466	
chunk0116_203_1	chr21	37430626	37430825	+	0	NA	intron (NM_130436, intron 1 of 10)	intron (NM_130436, intron 1 of 10)	10425	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.015075	0.515000	
chunk0160_258_1	chr5	156924694	156925228	+	0	NA	intron (NM_001146726, intron 5 of 7)	intron (NM_001146726, intron 5 of 7)	38294	NM_001146726	91937	Hs.334907	NM_138379	ENSG00000145850	TIMD4	SMUCKLER|TIM4	T cell immunoglobulin and mucin domain containing 4	protein-coding	0.003745	0.392523	246(TAGAACTCCCTGTACT,-,0.00),247(AGAACTCCCTGTACTC,+,0.00)
chunk0023_345_1	chr10	29630103	29630354	+	0	NA	intron (NM_003174, intron 3 of 35)	intron (NM_003174, intron 3 of 35)	4744	NM_021738	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.011952	0.452381	
chunk0042_309_1	chr12	7989953	7990542	+	0	NA	Intergenic	Intergenic	-42516	NM_018416	55810	Hs.120844	NM_018416	ENSG00000065970	FOXJ2	FHX	forkhead box J2	protein-coding	0.011885	0.461017	
chunk0141_387_1	chr4	88318855	88319485	+	0	NA	Intergenic	Intergenic	-34339	NM_152542	152926	Hs.43744	NM_152542	ENSG00000163644	PPM1K	BDP|MSUDMV|PP2Ckappa|PP2Cm|PTMP|UG0882E07	protein phosphatase, Mg2+/Mn2+ dependent 1K	protein-coding	0.004762	0.383518	
chunk0019_215_1	chr1	227146177	227146530	+	0	NA	intron (NM_014826, intron 7 of 34)	intron (NM_014826, intron 7 of 34)	171772	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.000000	0.296610	
chunk0104_248_1	chr2	177263406	177263705	+	0	NA	5' UTR (NM_001145412, exon 1 of 5)	5' UTR (NM_001145412, exon 1 of 5)	576	NM_001313900	4780	Hs.744006	NM_006164	ENSG00000116044	NFE2L2	HEBP1|IMDDHH|NRF2	nuclear factor, erythroid 2 like 2	protein-coding	0.083612	0.590000	
chunk0059_130_1	chr14	31811617	31812377	+	0	NA	intron (NM_001201573, intron 5 of 8)	L1PA6|LINE|L1	97428	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.010526	0.490145	
chunk0184_23_1	chr7	111942269	111942515	+	0	NA	intron (NM_014705, intron 10 of 51)	intron (NM_014705, intron 10 of 51)	133887	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.008130	0.400810	
chunk0065_261_1	chr14	101792314	101792966	+	0	NA	intron (NM_001161726, intron 3 of 14)	L1MC5a|LINE|L1	-17163	NM_178587	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.006135	0.375191	
chunk0114_371_1	chr20	62916261	62917111	+	0	NA	intron (NM_022105, intron 1 of 5)	Charlie1a|DNA|hAT-Charlie	9865	NM_001193370	11083	Hs.517172	NM_022105	ENSG00000101191	DIDO1	BYE1|C20orf158|DATF-1|DATF1|DIDO2|DIDO3|DIO-1|DIO1|dJ885L7.8	death inducer-obliterator 1	protein-coding	0.009412	0.396005	12(TAAAACAGAATGTACC,-,0.00),13(AAAACAGAATGTACCA,+,0.00)
chunk0056_195_1	chr13	85709763	85710098	+	0	NA	Intergenic	Intergenic	89418	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.002985	0.309524	
chunk0048_216_1	chr12	81409632	81410008	+	0	NA	intron (NM_001220478, intron 3 of 28)	intron (NM_001220478, intron 3 of 28)	-40406	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.002660	0.342175	
chunk0188_15_1	chr8	6433988	6434754	+	0	NA	intron (NM_001172575, intron 4 of 6)	intron (NM_001172575, intron 4 of 6)	27779	NM_001172574	79648	Hs.593807	NM_024596	ENSG00000147316	MCPH1	BRIT1|MCT	microcephalin 1	protein-coding	0.010444	0.443286	393(CAGCACAATCTGTCCC,-,0.00),394(AGCACAATCTGTCCCC,+,0.00)
chunk0193_431_1	chr8	80940590	80941576	+	0	NA	Intergenic	Intergenic	-66302	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.001014	0.382979	
chunk0005_225_1	chr1	59393420	59393968	+	0	NA	intron (NM_001244714, intron 3 of 13)	intron (NM_001244714, intron 3 of 13)	83616	NM_001244714	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.007299	0.420765	488(AAGTACACATTGTTCA,-,0.00),489(AGTACACATTGTTCAT,+,0.00)
chunk0063_400_1	chr14	88010533	88011422	+	0	NA	exon (NM_003608, exon 2 of 2)	exon (NM_003608, exon 2 of 2)	5853	NM_003608	8477	Hs.443243	NM_003608	ENSG00000140030	GPR65	TDAG8|hTDAG8	G protein-coupled receptor 65	protein-coding	0.008999	0.374157	334(AAGAACAGCATGACCT,-,0.00),335(AGAACAGCATGACCTG,+,0.00)
chunk0199_148_1	chr9	4174884	4175111	+	0	NA	intron (NM_001042413, intron 2 of 10)	intron (NM_001042413, intron 2 of 10)	-22814	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.017621	0.469298	104(GGGATCAGAGTGTACT,-,0.00),105(GGATCAGAGTGTACTT,+,0.00)
chunk0201_306_1	chr9	42387881	42388374	+	0	NA	Intergenic	Intergenic	181222	NR_126050	103908605	Hs.721139	NR_126050		LOC103908605	-	uncharacterized LOC103908605	ncRNA	0.010142	0.427126	477(GAGAACACTGTGCTCA,-,0.00),478(AGAACACTGTGCTCAG,+,0.00)
chunk0010_15_1	chr1	112063719	112064151	+	0	NA	Intergenic	Intergenic	73367	NM_001270945									0.013889	0.561201	273(GAGGACACGGTGAGCC,-,0.00),274(AGGACACGGTGAGCCC,+,0.00)
chunk0173_428_1	chr6	151065458	151065784	+	0	NA	intron (NM_001242767, intron 26 of 27)	intron (NM_001242767, intron 26 of 27)	162836	NR_125868	102723831	Hs.684425	NR_125868		LOC102723831	-	uncharacterized LOC102723831	ncRNA	0.003067	0.544343	
chunk0133_271_1	chr3	171953404	171953674	+	0	NA	Intergenic	Intergenic	-52799	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.003704	0.372694	
chunk0102_87_1	chr2	143515896	143516399	+	0	NA	intron (NM_018460, intron 9 of 13)	L2c|LINE|L2	386817	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.005964	0.394841	
chunk0085_241_1	chr18	7104480	7105106	+	0	NA	intron (NM_005559, intron 1 of 62)	intron (NM_005559, intron 1 of 62)	13021	NM_005559	284217	Hs.270364	NM_005559	ENSG00000101680	LAMA1	LAMA|PTBHS|S-LAM-alpha	laminin subunit alpha 1	protein-coding	0.012780	0.500797	
chunk0173_354_1	chr6	149111693	149112151	+	0	NA	Intergenic	Intergenic	-106002	NM_001292035	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.004367	0.344227	
chunk0072_258_1	chr15	96251024	96251322	+	0	NA	intron (NR_125738, intron 2 of 4)	L2b|LINE|L2	-74755	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.006711	0.478261	
chunk0054_323_1	chr13	49094103	49094533	+	0	NA	intron (NM_001278438, intron 3 of 25)	intron (NM_001278438, intron 3 of 25)	-15985	NM_014923	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.002326	0.313225	169(AAGCACAGAGTGTCCT,-,0.00),170(AGCACAGAGTGTCCTT,+,0.00)
chunk0170_139_1	chr6	111105609	111105808	+	0	NA	intron (NM_018593, intron 1 of 5)	intron (NM_018593, intron 1 of 5)	18130	NM_018593	117247	Hs.591327	NM_018593	ENSG00000112394	SLC16A10	MCT10|PRO0813|TAT1	solute carrier family 16 member 10	protein-coding	0.020101	0.495000	
chunk0130_54_1	chr3	129576691	129577101	+	0	NA	intron (NM_015103, intron 9 of 35)	intron (NM_015103, intron 9 of 35)	28511	NM_001308262	132243	Hs.97358	NM_153833	ENSG00000178804	H1FOO	H1.8|H1oo|osH1	H1 histone family member O oocyte specific	protein-coding	0.017073	0.527981	
chunk0138_123_1	chr4	36427579	36427778	+	0	NA	Intergenic	L1PA14|LINE|L1	-1250	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.010050	0.585000	
chunk0212_141_1	chrX	131795431	131795834	+	0	NA	intron (NR_026975, intron 4 of 12)	intron (NR_026975, intron 4 of 12)	35011	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.037221	0.631188	
chunk0032_51_1	chr11	1691270	1691501	+	0	NA	Intergenic	Intergenic	-5756	NR_026642	100132464	Hs.117797	NR_026642	ENSG00000205865	FAM99B	-	family with sequence similarity 99 member B	ncRNA	0.008658	0.482759	
chunk0194_390_1	chr8	90950916	90951371	+	0	NA	exon (NM_022351, exon 12 of 13)	exon (NM_022351, exon 12 of 13)	34114	NM_001190972	100127983	Hs.733266	NM_001190972	ENSG00000253250	C8orf88	-	chromosome 8 open reading frame 88	protein-coding	0.002198	0.320175	
chunk0008_340_1	chr1	95766181	95766509	+	0	NA	Intergenic	Intergenic	-225723	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.003049	0.322188	
chunk0138_285_1	chr4	40629768	40630095	+	0	NA	promoter-TSS (NM_001098634)	promoter-TSS (NM_001098634)	-65	NM_001098634	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.085627	0.634146	
chunk0016_247_1	chr1	200051611	200052160	+	0	NA	intron (NM_205860, intron 5 of 7)	MER112|DNA|hAT-Charlie	9060	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.010929	0.376364	276(CAGGACATAGTGTACC,-,0.00),277(AGGACATAGTGTACCA,+,0.00)
chunk0013_117_1	chr1	167932790	167933113	+	0	NA	intron (NR_026550, intron 1 of 4)	L4_A_Mam|LINE|RTE-X	3250	NR_026550	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.003096	0.391975	
chunk0092_264_1	chr19	33176942	33177265	+	0	NA	Intergenic	CpG	-17590	NM_002333	4037	Hs.515340	NM_002333	ENSG00000130881	LRP3	-	LDL receptor related protein 3	protein-coding	0.074303	0.564815	
chunk0102_306_1	chr2	150936959	150937593	+	0	NA	Intergenic	Intergenic	308379	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.004732	0.387402	
chunk0057_111_1	chr13	99098120	99098508	+	0	NA	Intergenic	L1MB7|LINE|L1	11591	NR_047482	100861541	Hs.344872	NR_047482		DOCK9-DT	DOCK9-AS2	DOCK9 divergent transcript	ncRNA	0.012887	0.359897	
chunk0146_439_1	chr4	169767535	169767864	+	0	NA	Intergenic	L1M5|LINE|L1	-9757	NM_017867	54969	Hs.406756	NM_017867	ENSG00000056050	HPF1	C4orf27	histone PARylation factor 1	protein-coding	0.003040	0.287879	
chunk0062_139_1	chr14	68908229	68908662	+	0	NA	intron (NM_001130004, intron 6 of 21)	intron (NM_001130004, intron 6 of 21)	70921	NM_001130005	87	Hs.235750	NM_001102	ENSG00000072110	ACTN1	BDPLT15	actinin alpha 1	protein-coding	0.013857	0.562212	179(CTGAACACTGTGTTCT,-,0.00),180(TGAACACTGTGTTCTC,+,0.00)
chunk0108_219_1	chr2	233460835	233461480	+	0	NA	intron (NM_003648, intron 23 of 28)	CpG	73003	NM_003648	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.049612	0.597523	
chunk0008_222_1	chr1	93915753	93916195	+	0	NA	Intergenic	L1PA6|LINE|L1	-6376	NM_001308253	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.011312	0.496614	
chunk0201_87_1	chr9	34637185	34637384	+	0	NA	exon (NM_005866, exon 2 of 4)	exon (NM_005866, exon 2 of 4)	542	NM_001282205	10280	Hs.522087	NM_005866	ENSG00000147955	SIGMAR1	ALS16|DSMA2|OPRS1|SIG-1R|SR-BP|SR-BP1|SRBP|hSigmaR1|sigma1R	sigma non-opioid intracellular receptor 1	protein-coding	0.090452	0.695000	
chunk0047_141_1	chr12	69589695	69589956	+	0	NA	intron (NM_006431, intron 7 of 15)	intron (NM_006431, intron 7 of 15)	4143	NM_001198842	10576	Hs.189772	NM_006431	ENSG00000166226	CCT2	99D8.1|CCT-beta|CCTB|HEL-S-100n|PRO1633|TCP-1-beta	chaperonin containing TCP1 subunit 2	protein-coding	0.007663	0.370229	
chunk0187_56_1	chr8	1867875	1868081	+	0	NA	intron (NM_001308152, intron 6 of 27).2	intron (NM_001308152, intron 6 of 27).2	44002	NM_001308153	9639	Hs.98594	NM_014629	ENSG00000104728	ARHGEF10	GEF10|SNCV	Rho guanine nucleotide exchange factor 10	protein-coding	0.019417	0.314010	
chunk0173_282_1	chr6	147909209	147909987	+	0	NA	Intergenic	(TCTT)n|Simple_repeat|Simple_repeat	400906	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.010283	0.390244	
chunk0034_445_1	chr11	39489984	39490205	+	0	NA	Intergenic	Intergenic	803036	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.351351	
chunk0198_64_1	chr8	129549934	129550296	+	0	NA	intron (NR_130917, intron 1 of 3)	Charlie17a|DNA|hAT-Charlie	24903	NR_130918	137196	Hs.679457	NR_130917	ENSG00000229140	CCDC26	RAM	CCDC26 long non-coding RNA	ncRNA	0.002762	0.451791	
chunk0148_247_1	chr5	10140340	10141013	+	0	NA	Intergenic	L2c|LINE|L2	109233	NM_199133	134145	Hs.481569	NM_199133	ENSG00000150756	ATPSCKMT	FAM173B|JS-2|hFAM173B	ATP synthase c subunit lysine N-methyltransferase	protein-coding	0.004458	0.599407	
chunk0026_22_1	chr10	60648852	60649401	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	-76170	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005464	0.429091	183(AGGGACATAATGTCCT,-,0.00),184(GGGACATAATGTCCTT,+,0.00)
chunk0017_387_1	chr1	212238656	212239233	+	0	NA	non-coding (NR_125984, exon 2 of 4)	non-coding (NR_125984, exon 2 of 4)	-4208	NR_125983	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.010399	0.460208	
chunk0180_439_1	chr7	76863744	76864158	+	0	NA	Intergenic	Intergenic	-116871	NR_023383	441263	Hs.675888	NR_023383	ENSG00000265479	DTX2P1-UPK3BP1-PMS2P11	PMS2L11	DTX2P1-UPK3BP1-PMS2P11 readthrough, transcribed pseudogene	pseudo	0.007246	0.363855	
chunk0107_298_1	chr2	218975490	218975998	+	0	NA	promoter-TSS (NR_024385)	promoter-TSS (NR_024385)	-540	NR_024385	151300	Hs.420716	NR_015390		LINC00608	-	long intergenic non-protein coding RNA 608	ncRNA	0.005906	0.469548	205(AGGGACAAAATGTACT,-,0.00),206(GGGACAAAATGTACTT,+,0.00)
chunk0210_150_1	chrX	76438855	76439346	+	0	NA	Intergenic	L1MA4A|LINE|L1	11447	NM_020932	57692	Hs.8453	NM_020932	ENSG00000198934	MAGEE1	DAMAGE|HCA1	MAGE family member E1	protein-coding	0.000000	0.345528	194(AAAACAAGATGTCCTT,+,0.00)
chunk0055_372_1	chr13	73060985	73061611	+	0	NA	intron (NM_001730, intron 1 of 3)	intron (NM_001730, intron 1 of 3)	2506	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.006390	0.352472	
chunk0135_428_1	chr3	193802190	193802389	+	0	NA	Intergenic	L1M5|LINE|L1	-174957	NR_046634	100873941	Hs.679364	NR_046634	ENSG00000224855	OPA1-AS1	-	OPA1 antisense RNA 1	ncRNA	0.000000	0.300000	
chunk0126_177_1	chr3	78087047	78087662	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	932105	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004878	0.347403	
chunk0126_166_1	chr3	77703397	77703596	+	0	NA	Intergenic	MER39|LTR|ERV1	605484	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.005025	0.400000	
chunk0148_365_1	chr5	14615299	14615909	+	0	NA	3' UTR (NM_019018, exon 8 of 8)	3' UTR (NM_019018, exon 8 of 8)	33822	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.011475	0.430442	
chunk0166_182_1	chr6	46135968	46136279	+	0	NA	intron (NM_014936, intron 1 of 3)	intron (NM_014936, intron 1 of 3)	6159	NM_014936	22875	Hs.643497	NM_014936	ENSG00000001561	ENPP4	NPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4	protein-coding	0.003215	0.298077	
chunk0119_377_1	chr22	47828027	47828459	+	0	NA	intron (NR_122046, intron 8 of 8)	intron (NR_122046, intron 8 of 8)	196569	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.002315	0.404157	
chunk0130_120_1	chr3	131476066	131476495	+	0	NA	intron (NM_007208, intron 6 of 9)	intron (NM_007208, intron 6 of 9)	2953	NR_002985	677836	Hs.735762	NR_002985		SNORA58	ACA58|SNORA58B	small nucleolar RNA, H/ACA box 58	snoRNA	0.000000	0.316279	236(GAGAACAGAGTGTACC,-,0.00),237(AGAACAGAGTGTACCT,+,0.00)
chunk0079_300_1	chr17	17025652	17025879	+	0	NA	Intergenic	Intergenic	-16995	NM_201274	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.008811	0.574561	
chunk0053_381_1	chr13	36029094	36029734	+	0	NA	intron (NM_004734, intron 3 of 17)	L2c|LINE|L2	101963	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.014063	0.404056	
chunk0167_54_1	chr6	55544270	55544871	+	0	NA	intron (NM_001042406, intron 1 of 8)	intron (NM_001042406, intron 1 of 8)	34644	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.004992	0.372093	288(GTCACACTCTGTCCTT,+,0.00)
chunk0135_354_1	chr3	190540857	190541131	+	0	NA	intron (NM_001167930, intron 1 of 7)	MER67C|LTR|ERV1	26943	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.003650	0.407273	
chunk0169_454_1	chr6	108916697	108917287	+	0	NA	intron (NM_001286609, intron 9 of 16)	intron (NM_001286609, intron 9 of 16)	7111	NR_104137	101929716		NR_104137		ARMC2-AS1	-	ARMC2 antisense RNA 1	ncRNA	0.006780	0.428088	244(GAGAACATCATGTACA,-,0.00),245(AGAACATCATGTACAA,+,0.00)
chunk0209_314_1	chrX	50081668	50081981	+	0	NA	exon (NM_000084, exon 6 of 12)	exon (NM_000084, exon 6 of 12)	12323	NM_001282163	1184	Hs.166486	NM_000084	ENSG00000171365	CLCN5	CLC5|CLCK2|ClC-5|DENTS|NPHL1|NPHL2|XLRH|XRN|hCIC-K2	chloride voltage-gated channel 5	protein-coding	0.006390	0.458599	120(GGGAACATCCTGTGCC,-,0.00),121(GGAACATCCTGTGCCA,+,0.00)
chunk0169_209_1	chr6	102937267	102937547	+	0	NA	Intergenic	L1MCa|LINE|L1	1538422	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003571	0.295374	
chunk0036_161_1	chr11	62508173	62508955	+	0	NA	intron (NM_024060, intron 4 of 5)	intron (NM_024060, intron 4 of 5)	38296	NM_024060	79026	Hs.502756	NM_001620	ENSG00000124942	AHNAK	AHNAKRS|PM227	AHNAK nucleoprotein	protein-coding	0.025575	0.499361	300(TAGAACGCCCTGTCCA,-,0.00)
chunk0064_353_1	chr14	96836841	96837367	+	0	NA	intron (NM_003384, intron 2 of 12)	L2a|LINE|L2	39757	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.001901	0.373814	
chunk0136_450_1	chr3	198000692	198000994	+	0	NA	intron (NR_026787, intron 11 of 15)	MER112|DNA|hAT-Charlie	38624	NR_046669	100873947	Hs.637166	NR_046669	ENSG00000232832	LMLN-AS1	-	LMLN antisense RNA 1	ncRNA	0.016556	0.359736	
chunk0029_415_1	chr10	109961697	109962056	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-38323	NR_030724									0.011142	0.444444	
chunk0055_234_1	chr13	62780946	62781597	+	0	NA	intron (NR_047029, intron 2 of 7)	intron (NR_047029, intron 2 of 7)	15421	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.004608	0.296012	
chunk0197_340_1	chr8	125273289	125273496	+	0	NA	intron (NM_173685, intron 5 of 7)	intron (NM_173685, intron 5 of 7)	-156929	NM_025195	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.004831	0.331731	
chunk0206_264_1	chr9	123941438	123942091	+	0	NA	Intergenic	Intergenic	-11626	NM_024820	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.010720	0.444954	403(AGGGACAAGCCGTTCC,-,0.00),404(GGGACAAGCCGTTCCT,+,0.00)
chunk0048_203_1	chr12	81380359	81380728	+	0	NA	intron (NM_001220474, intron 7 of 30)	intron (NM_001220474, intron 7 of 30)	-11129	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.010840	0.313514	
chunk0191_436_1	chr8	57888132	57888640	+	0	NA	Intergenic	L1ME3D|LINE|L1	-89972	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.001969	0.373281	
chunk0086_200_1	chr18	22275508	22275964	+	0	NA	Intergenic	Intergenic	106299	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.010965	0.459519	123(TGGAACACCGTGTGCT,-,0.00),124(GGAACACCGTGTGCTG,+,0.00)
chunk0109_435_1	chr2	241352134	241352657	+	0	NA	3' UTR (NM_006155, exon 13 of 13)	3' UTR (NM_006155, exon 13 of 13)	-3854	NM_001282984	9855	Hs.726316	NM_014808	ENSG00000006607	FARP2	FIR|FRG|PLEKHC3	FERM, ARH/RhoGEF and pleckstrin domain protein 2	protein-coding	0.005736	0.347328	
chunk0113_146_1	chr20	52411781	52412041	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-208927	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.003846	0.375479	
chunk0131_345_1	chr3	151519934	151520525	+	0	NA	Intergenic	Intergenic	45766	NR_049818	100847036		NR_049818	ENSG00000264330	MIR5186	-	microRNA 5186	ncRNA	0.001692	0.320946	
chunk0105_394_1	chr2	192468338	192468575	+	0	NA	Intergenic	Intergenic	-273523	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.004219	0.273109	
chunk0090_274_1	chr18	74672221	74672777	+	0	NA	intron (NM_001146189, intron 2 of 6)	intron (NM_001146189, intron 2 of 6)	41536	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.014388	0.409336	154(GAGCACTGTTTGTTCA,-,0.00),155(AGCACTGTTTGTTCAT,+,0.00),234(GAGCACTGTTTGTTCA,-,0.00),235(AGCACTGTTTGTTCAT,+,0.00),318(GAGCACTGTTTGTTCA,-,0.00),319(AGCACTGTTTGTTCAT,+,0.00),337(GAGCACTGTTTGTTCA,-,0.00),338(AGCACTGTTTGTTCAT,+,0.00)
chunk0116_216_1	chr21	37646268	37646765	+	0	NA	intron (NM_002240, intron 3 of 3)	intron (NM_002240, intron 3 of 3)	226216	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.028169	0.485944	
chunk0085_359_1	chr18	9289685	9290113	+	0	NA	Intergenic	Intergenic	-44868	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.002336	0.363636	
chunk0131_276_1	chr3	150238503	150238873	+	0	NA	promoter-TSS (NR_110167)	promoter-TSS (NR_110167)	-12	NR_110167	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.013514	0.433962	
chunk0131_267_1	chr3	150082496	150082799	+	0	NA	Intergenic	L2c|LINE|L2	-99281	NM_001079809	653659	Hs.652908	NM_001079809		TMEM183B	C1ORF37DUP|C1orf37-DUP	transmembrane protein 183B	protein-coding	0.016502	0.447368	
chunk0208_34_1	chrX	11326380	11326781	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-7894	NR_049865	100847063		NR_049865	ENSG00000263652	MIR548AX	-	microRNA 548ax	ncRNA	0.017456	0.383085	
chunk0100_307_1	chr2	115537163	115537436	+	0	NA	intron (NM_001178037, intron 5 of 25)	intron (NM_001178037, intron 5 of 25)	375192	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.000000	0.350365	
chunk0095_1_1	chr2	11655629	11656131	+	0	NA	Intergenic	L1ME4c|LINE|L1	14323	NM_012344	23620	Hs.131138	NM_012344	ENSG00000169006	NTSR2	NTR2	neurotensin receptor 2	protein-coding	0.005976	0.381710	
chunk0150_228_1	chr5	35761657	35761978	+	0	NA	intron (NM_024867, intron 25 of 36)	intron (NM_024867, intron 25 of 36)	-95058	NR_120485	3575	Hs.591742	NM_002185	ENSG00000168685	IL7R	CD127|CDW127|IL-7R-alpha|IL7RA|ILRA	interleukin 7 receptor	protein-coding	0.009346	0.378882	104(CAGTACATTCTGTTCT,-,0.00),105(AGTACATTCTGTTCTC,+,0.00),189(AAGAACATCCAGTTCT,-,0.00),190(AGAACATCCAGTTCTT,+,0.00)
chunk0198_455_1	chr8	144357504	144357978	+	0	NA	promoter-TSS (NM_024531)	promoter-TSS (NM_024531)	782	NM_012162	26233	Hs.12271	NM_012162	ENSG00000182325	FBXL6	FBL6|FBL6A|PP14630	F-box and leucine rich repeat protein 6	protein-coding	0.086498	0.692632	214(AGGGTCACGGTGTGCC,-,0.00),215(GGGTCACGGTGTGCCA,+,0.00)
chunk0034_65_1	chr11	27158011	27158468	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	60529	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.004376	0.360262	
chunk0043_295_1	chr12	21813622	21814757	+	0	NA	intron (NM_020297, intron 33 of 37)	intron (NM_020297, intron 33 of 37)	-39368	NM_004982	3764	Hs.102308	NM_004982	ENSG00000121361	KCNJ8	KIR6.1|uKATP-1	potassium voltage-gated channel subfamily J member 8	protein-coding	0.005286	0.343310	294(AAGCACTCCTTGTACT,-,0.00),295(AGCACTCCTTGTACTG,+,0.00)
chunk0192_49_1	chr8	58889027	58889519	+	0	NA	intron (NM_014729, intron 3 of 8)	L1ME4b|LINE|L1	-229428	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.002033	0.352941	
chunk0057_338_1	chr13	107266659	107267383	+	0	NA	intron (NM_001080396, intron 1 of 2)	intron (NM_001080396, intron 1 of 2)	264227	NR_031671	100302286		NR_031671	ENSG00000221650	MIR1267	MIRN1267|hsa-mir-1267	microRNA 1267	ncRNA	0.002762	0.415172	
chunk0145_362_1	chr4	151305540	151306149	+	0	NA	Intergenic	L1ME1|LINE|L1	28671	NM_183375	345062	Hs.651266	NM_183375	ENSG00000189099	PRSS48	ESSPL	serine protease 48	protein-coding	0.003284	0.327869	
chunk0183_128_1	chr7	105653389	105653993	+	0	NA	intron (NM_138495, intron 2 of 9)	intron (NM_138495, intron 2 of 9)	25471	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.013245	0.530579	
chunk0021_271_1	chr1	243901875	243902634	+	0	NA	Intergenic	Intergenic	-15148	NR_033883	339529	Hs.209374	NR_033883	ENSG00000226828	LINC02774	-	long intergenic non-protein coding RNA 2774	ncRNA	0.002635	0.364474	
chunk0148_42_1	chr5	1246953	1247211	+	0	NA	TTS (NM_182632)	TTS (NM_182632)	21727	NM_182632	348932	Hs.213284	NM_182632	ENSG00000164363	SLC6A18	Xtrp2	solute carrier family 6 member 18	protein-coding	0.058140	0.613900	
chunk0090_332_1	chr18	76167318	76167687	+	0	NA	Intergenic	Intergenic	44504	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.018970	0.518919	
chunk0150_309_1	chr5	37741361	37741584	+	0	NA	intron (NM_018034, intron 17 of 17)	MER1B|DNA|hAT-Charlie	93350	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.008969	0.446429	
chunk0161_453_1	chr5	178940312	178940627	+	0	NA	promoter-TSS (NM_182594)	promoter-TSS (NM_182594)	-724	NM_001178089	285676	Hs.259441	NM_182594	ENSG00000178187	ZNF454	-	zinc finger protein 454	protein-coding	0.025397	0.512658	219(AAGCACGAAGTGTTCT,-,0.00),220(AGCACGAAGTGTTCTG,+,0.00)
chunk0064_221_1	chr14	93759527	93760061	+	0	NA	intron (NM_178013, intron 3 of 4)	intron (NM_178013, intron 3 of 4)	28626	NM_178013	145270	Hs.432401	NM_178004	ENSG00000175785	PRIMA1	PRIMA	proline rich membrane anchor 1	protein-coding	0.024345	0.601869	307(AAGGACGTGGTGTTCA,-,0.00)
chunk0004_347_1	chr1	50970381	50970580	+	0	NA	exon (NM_001262, exon 2 of 3)	exon (NM_001262, exon 2 of 3)	510	NM_078626	1031	Hs.525324	NM_001262	ENSG00000123080	CDKN2C	INK4C|p18|p18-INK4C	cyclin dependent kinase inhibitor 2C	protein-coding	0.035176	0.465000	
chunk0202_447_1	chr9	82308184	82308414	+	0	NA	Intergenic	Intergenic	319527	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.004348	0.337662	
chunk0111_236_1	chr20	29411189	29411756	+	0	NA	Intergenic	CpG	5489	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.081129	0.651408	
chunk0142_327_1	chr4	101061267	101061542	+	0	NA	intron (NM_001130692, intron 8 of 11)	intron (NM_001130692, intron 8 of 11)	179468	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.000000	0.304348	
chunk0198_397_1	chr8	141538337	141538559	+	0	NA	Intergenic	Intergenic	-31218	NM_207414	389690	Hs.689547	NM_207414	ENSG00000226807	MROH5	-	maestro heat like repeat family member 5 (gene/pseudogene)	protein-coding	0.031532	0.591928	
chunk0138_149_1	chr4	37279220	37279419	+	0	NA	intron (NM_001144990, intron 1 of 6)	intron (NM_001144990, intron 1 of 6)	34251	NM_001144990	57495	Hs.4280	NM_001144990	ENSG00000174145	NWD2	KIAA1239	NACHT and WD repeat domain containing 2	protein-coding	0.005025	0.335000	
chunk0080_255_1	chr17	30468393	30468869	+	0	NA	3' UTR (NM_001199775, exon 21 of 21)	3' UTR (NM_001199775, exon 21 of 21)	-8777	NM_001007024	9527	Hs.462680	NM_004871	ENSG00000108587	GOSR1	GOLIM2|GOS-28|GOS28|GOS28/P28|GS28|P28	golgi SNAP receptor complex member 1	protein-coding	0.004202	0.329140	
chunk0179_226_1	chr7	47846019	47846546	+	0	NA	intron (NM_138295, intron 32 of 56)	intron (NM_138295, intron 32 of 56)	50991	NM_001302627	80099	Hs.287647	NM_025031		C7orf69	-	chromosome 7 open reading frame 69	ncRNA	0.005693	0.395833	
chunk0001_403_1	chr1	10860817	10861126	+	0	NA	Intergenic	Intergenic	-64295	NM_017766	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.025890	0.577419	
chunk0178_53_1	chr7	29964784	29965579	+	0	NA	intron (NM_001145515, intron 1 of 6)	intron (NM_001145515, intron 1 of 6)	24628	NM_001145515	9805	Hs.520740	NM_014766	ENSG00000136193	SCRN1	SES1	secernin 1	protein-coding	0.017610	0.456030	284(GGGAACTCTCTGTGCC,-,0.00),285(GGAACTCTCTGTGCCT,+,0.00)
chunk0003_411_1	chr1	40281660	40282453	+	0	NA	intron (NM_005857, intron 7 of 9)	L2c|LINE|L2	24006	NM_005857	10269	Hs.132642	NM_005857	ENSG00000084073	ZMPSTE24	FACE-1|FACE1|HGPS|PRO1|STE24|Ste24p	zinc metallopeptidase STE24	protein-coding	0.003783	0.328715	
chunk0001_177_1	chr1	6928375	6929129	+	0	NA	intron (NM_015215, intron 3 of 22)	L2b|LINE|L2	143428	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.011936	0.499338	
chunk0196_416_1	chr8	116085922	116086475	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	238861	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.005425	0.388087	
chunk0054_349_1	chr13	49569718	49570367	+	0	NA	intron (NM_018191, intron 2 of 12)	intron (NM_018191, intron 2 of 12)	15541	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.007704	0.390769	215(AGGAACAAGATGCCCC,-,0.00),216(GGAACAAGATGCCCCT,+,0.00)
chunk0170_198_1	chr6	112395731	112396032	+	0	NA	Intergenic	L1MA5A|LINE|L1	48551	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.006645	0.337748	
chunk0153_67_1	chr5	67878966	67879208	+	0	NA	Intergenic	Intergenic	85874	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.000000	0.382716	
chunk0117_422_1	chr21	46058655	46058900	+	0	NA	Intergenic	Intergenic	-39342	NM_058174	1292	Hs.420269	NM_001849	ENSG00000142173	COL6A2	BTHLM1|PP3610|UCMD1	collagen type VI alpha 2 chain	protein-coding	0.028571	0.577236	
chunk0114_135_1	chr21	10012215	10012507	+	0	NA	Intergenic	(TGTT)n|Simple_repeat|Simple_repeat	-191300	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.324232	126(CAGCACAATGTGTTTT,-,0.00),127(AGCACAATGTGTTTTT,+,0.00)
chunk0176_394_1	chr7	18849795	18850089	+	0	NA	intron (NM_178425, intron 20 of 24)	intron (NM_178425, intron 20 of 24)	267730	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.003401	0.342373	
chunk0154_210_1	chr5	80410179	80410857	+	0	NA	intron (NM_001284237, intron 1 of 3)	intron (NM_001284237, intron 1 of 3)	2505	NM_001284236	9765	Hs.482660	NM_014733	ENSG00000039319	ZFYVE16	PPP1R69	zinc finger FYVE-type containing 16	protein-coding	0.020649	0.403535	
chunk0089_11_1	chr18	57565566	57565782	+	0	NA	intron (NM_001012515, intron 5 of 10)	intron (NM_001012515, intron 5 of 10)	21063	NM_000140	2235	Hs.365365	NM_000140	ENSG00000066926	FECH	EPP|EPP1|FCE	ferrochelatase	protein-coding	0.000000	0.308756	
chunk0149_256_1	chr5	23877572	23878111	+	0	NA	Intergenic	Intergenic	-73507	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.005566	0.305556	
chunk0206_333_1	chr9	125392297	125392719	+	0	NA	Intergenic	MIR|SINE|MIR	93618	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.007109	0.437352	
chunk0079_16_1	chr17	9669480	9670068	+	0	NA	intron (NM_153210, intron 3 of 14)	L2b|LINE|L2	24237	NM_153210	124739	Hs.709621	NM_153210	ENSG00000154914	USP43	-	ubiquitin specific peptidase 43	protein-coding	0.013605	0.494058	
chunk0172_357_1	chr6	139124946	139125202	+	0	NA	Intergenic	Intergenic	-10038	NM_016217	51696	Hs.197644	NM_016217	ENSG00000112406	HECA	HDC|HDCL|HHDC|dJ225E12.1	hdc homolog, cell cycle regulator	protein-coding	0.007812	0.459144	148(TGGTACAAACTGTCCC,-,0.00),149(GGTACAAACTGTCCCT,+,0.00)
chunk0004_265_1	chr1	48250963	48251594	+	0	NA	Intergenic	Intergenic	28593	NM_001135181	200010	Hs.37890	NM_001011547	ENSG00000117834	SLC5A9	SGLT4	solute carrier family 5 member 9	protein-coding	0.003170	0.424051	
chunk0112_29_1	chr20	36298109	36298418	+	0	NA	Intergenic	Intergenic	-8060	NM_014902	22839	Hs.249600	NM_014902	ENSG00000080845	DLGAP4	DAP-4|DAP4|DLP4|SAPAP-4|SAPAP4	DLG associated protein 4	protein-coding	0.009709	0.519355	
chunk0039_299_1	chr11	102987993	102988401	+	0	NA	Intergenic	L1MB5|LINE|L1	-32463	NM_002427	4322	Hs.2936	NM_002427	ENSG00000137745	MMP13	CLG3|MANDP1|MDST|MMP-13	matrix metallopeptidase 13	protein-coding	0.000000	0.337408	178(ATGTACAGACTGTCTT,-,0.00),179(TGTACAGACTGTCTTT,+,0.00)
chunk0123_368_1	chr3	48345919	48346288	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	-17762	NM_001080525	646424	Hs.257687	NM_001080525	ENSG00000229453	SPINK8	-	serine peptidase inhibitor, Kazal type 8 (putative)	protein-coding	0.002710	0.391892	
chunk0022_264_1	chr10	14909108	14909595	+	0	NA	intron (NM_022487, intron 12 of 12)	intron (NM_022487, intron 12 of 12)	30451	NM_024670	79723	Hs.554883	NM_024670	ENSG00000152455	SUV39H2	KMT1B	suppressor of variegation 3-9 homolog 2	protein-coding	0.006160	0.397541	
chunk0145_373_1	chr4	151535472	151536017	+	0	NA	intron (NM_001109977, intron 3 of 13)	L2a|LINE|L2	126498	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.001835	0.318681	
chunk0155_205_1	chr5	94944750	94945142	+	0	NA	intron (NM_024717, intron 3 of 22)	MIRb|SINE|MIR	136920	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.002551	0.358779	
chunk0013_102_1	chr1	167764090	167764769	+	0	NA	intron (NM_024569, intron 1 of 4)	intron (NM_024569, intron 1 of 4)	42479	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.004418	0.314706	
chunk0101_447_1	chr2	139692467	139692981	+	0	NA	Intergenic	L2b|LINE|L2	795400	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.007782	0.326214	
chunk0212_236_1	chrX	136622822	136623021	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-16622	NR_038462	100128420	Hs.152595	NR_038461	ENSG00000233093	LINC00892	-	long intergenic non-protein coding RNA 892	ncRNA	0.005025	0.360000	
chunk0110_144_1	chr20	13653957	13654434	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-15259	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.004193	0.443515	
chunk0106_271_1	chr2	203900256	203900568	+	0	NA	Intergenic	Intergenic	32624	NM_005214	1493	Hs.247824	NM_005214	ENSG00000163599	CTLA4	ALPS5|CD|CD152|CELIAC3|CTLA-4|GRD4|GSE|IDDM12	cytotoxic T-lymphocyte associated protein 4	protein-coding	0.006410	0.380192	
chunk0012_114_1	chr1	156784606	156784828	+	0	NA	intron (NM_005973, intron 2 of 6)	intron (NM_005973, intron 2 of 6)	17235	NM_005973	5546	Hs.516948	NM_005973	ENSG00000143294	PRCC	RCCP1|TPRC	proline rich mitotic checkpoint control factor	protein-coding	0.004505	0.461883	
chunk0059_257_1	chr14	35174092	35174839	+	0	NA	intron (NM_014672, intron 4 of 7)	L2a|LINE|L2	51913	NM_001256680	9692	Hs.458487	NM_014672	ENSG00000100890	PRORP	KIAA0391|MRPP3	protein only RNase P catalytic subunit	protein-coding	0.004016	0.374332	
chunk0093_267_1	chr19	51221508	51221780	+	0	NA	Intergenic	L1ME1|LINE|L1	-3435	NM_001082618	945	Hs.83731	NM_001772	ENSG00000105383	CD33	SIGLEC-3|SIGLEC3|p67	CD33 molecule	protein-coding	0.000000	0.355311	
chunk0078_301_1	chr17	8173296	8173495	+	0	NA	TTS (NR_033294)	TTS (NR_033294)	193	NR_033294	727676		NR_033294	ENSG00000200463	SNORD118	LCC|U8	small nucleolar RNA, C/D box 118	snoRNA	0.010050	0.390000	
chunk0043_66_1	chr12	14255529	14255928	+	0	NA	Intergenic	L2b|LINE|L2	-109904	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.007519	0.362500	
chunk0093_276_1	chr19	51751764	51752418	+	0	NA	promoter-TSS (NM_002029)	promoter-TSS (NM_002029)	-194	NM_001193306	2357	Hs.753	NM_002029	ENSG00000171051	FPR1	FMLP|FPR	formyl peptide receptor 1	protein-coding	0.004587	0.487023	555(CAGGACAGCGCGTCCA,-,0.00),556(AGGACAGCGCGTCCAC,+,0.00)
chunk0009_259_1	chr1	107414593	107414905	+	0	NA	intron (NM_014917, intron 5 of 5)	MIR|SINE|MIR	266680	NM_001113226	22854	Hs.133046	NM_014917	ENSG00000162631	NTNG1	Lmnt1	netrin G1	protein-coding	0.009615	0.361022	
chunk0183_96_1	chr7	105112299	105112715	+	0	NA	exon (NM_182931, exon 27 of 27)	exon (NM_182931, exon 27 of 27)	98317	NM_018682	55904	Hs.592262	NM_018682	ENSG00000005483	KMT2E	HDCMC04P|MLL5|NKp44L	lysine methyltransferase 2E	protein-coding	0.014423	0.496403	
chunk0055_363_1	chr13	71675712	71676252	+	0	NA	intron (NM_080760, intron 2 of 7)	intron (NM_080760, intron 2 of 7)	191210	NM_080759	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.005556	0.293900	
chunk0030_18_1	chr10	110950407	110950920	+	0	NA	intron (NM_007373, intron 1 of 8)	L1MA9|LINE|L1	-13408	NR_026715	644511	Hs.632083	NR_026715	ENSG00000234118	RPL13AP6	RPL13A_7_1096|bA348N5.5	ribosomal protein L13a pseudogene 6	pseudo	0.005848	0.317121	
chunk0189_294_1	chr8	25973118	25973317	+	0	NA	intron (NM_022659, intron 6 of 15)	intron (NM_022659, intron 6 of 15)	71907	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.000000	0.360000	
chunk0173_91_1	chr6	143013167	143013795	+	0	NA	intron (NR_038987, intron 2 of 2)	intron (NR_038987, intron 2 of 2)	24101	NR_038987	100507489	Hs.486645	NR_038987		LINC01277	-	long intergenic non-protein coding RNA 1277	ncRNA	0.006369	0.314785	
chunk0155_84_1	chr5	92084275	92084662	+	0	NA	Intergenic	Intergenic	-701136	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.298969	
chunk0104_303_1	chr2	178824608	178825015	+	0	NA	Intergenic	Intergenic	-17388	NM_001256850	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.004914	0.330882	
chunk0134_118_1	chr3	177212087	177212434	+	0	NA	Intergenic	Intergenic	-15000	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.005764	0.462644	
chunk0202_22_1	chr9	70474764	70475561	+	0	NA	Intergenic	Intergenic	-60505	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.002509	0.407268	
chunk0186_326_1	chr7	143131521	143132153	+	0	NA	promoter-TSS (NM_002652)	promoter-TSS (NM_002652)	-244	NM_002652	5304	Hs.99949	NM_002652	ENSG00000159763	PIP	GCDFP-15|GCDFP15|GPIP4	prolactin induced protein	protein-coding	0.006329	0.456556	
chunk0058_318_1	chr14	27573000	27573385	+	0	NA	Intergenic	L1PA15|LINE|L1	-39396	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.005195	0.523316	
chunk0098_239_1	chr2	74614328	74614581	+	0	NA	intron (NM_138804, intron 3 of 10)	intron (NM_138804, intron 3 of 10)	33583	NM_138804	130951	Hs.348645	NM_138804	ENSG00000159374	M1AP	C2orf65|D6Mm5e|SPATA37	meiosis 1 associated protein	protein-coding	0.011858	0.405512	
chunk0158_202_1	chr5	128053668	128054006	+	0	NA	intron (NR_015360, intron 2 of 2)	intron (NR_015360, intron 2 of 2)	29237	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.002959	0.294985	
chunk0174_284_1	chr6	161908987	161909248	+	0	NA	intron (NM_013988, intron 3 of 8)	intron (NM_013988, intron 3 of 8)	-635042	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.022989	0.427481	89(TGGTACTTCCTGTTCT,-,0.00),90(GGTACTTCCTGTTCTT,+,0.00)
chunk0130_405_1	chr3	140417875	140418074	+	0	NA	intron (NM_022131, intron 4 of 16)	intron (NM_022131, intron 4 of 16)	90815	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.000000	0.370000	
chunk0088_144_1	chr18	46104537	46105114	+	0	NA	promoter-TSS (NM_001001937)	promoter-TSS (NM_001001937)	493	NM_138443	115106	Hs.436617	NM_138443	ENSG00000152240	HAUS1	CCDC5|HEI-C|HEIC|HsT1461	HAUS augmin like complex subunit 1	protein-coding	0.046794	0.500000	424(AAGAACGGATTGTTCT,-,0.00),425(AGAACGGATTGTTCTC,+,0.00)
chunk0163_94_1	chr6	9583662	9583907	+	0	NA	Intergenic	Intergenic	-828534	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.004082	0.313008	
chunk0211_29_1	chrX	108098155	108098413	+	0	NA	intron (NM_052936, intron 1 of 12)	intron (NM_052936, intron 1 of 12)	6615	NM_178270	115201	Hs.8763	NM_052936	ENSG00000101844	ATG4A	APG4A|AUTL2	autophagy related 4A cysteine peptidase	protein-coding	0.011628	0.332046	
chunk0115_252_1	chr21	27644490	27644882	+	0	NA	Intergenic	Intergenic	-77693	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.002551	0.343511	161(GAGGACAACATGTTCA,-,0.00),162(AGGACAACATGTTCAT,+,0.00)
chunk0052_326_1	chr12	125832933	125833426	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	150195	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.002028	0.412955	
chunk0048_348_1	chr12	84726064	84726295	+	0	NA	Intergenic	Intergenic	186650	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.000000	0.314655	
chunk0117_288_1	chr22	24304744	24305538	+	0	NA	intron (NM_001145468, intron 2 of 15)	intron (NM_001145468, intron 2 of 15)	34324	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.008816	0.372327	
chunk0169_17_1	chr6	96756964	96757373	+	0	NA	Intergenic	L1MA8|LINE|L1	80309	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.000000	0.441463	
chunk0062_356_1	chr14	73852614	73852845	+	0	NA	intron (NM_152444, intron 1 of 9)	intron (NM_152444, intron 1 of 9)	811	NM_152444	145482	Hs.632344	NM_152444	ENSG00000140043	PTGR2	HEL-S-298|PGR2|ZADH1	prostaglandin reductase 2	protein-coding	0.017316	0.465517	
chunk0127_222_1	chr3	96676827	96677164	+	0	NA	Intergenic	Intergenic	-137586	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002967	0.402367	
chunk0007_397_1	chr1	85496190	85496792	+	0	NA	intron (NM_001134445, intron 1 of 6)	intron (NM_001134445, intron 1 of 6)	-31285	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.001661	0.333333	
chunk0147_76_1	chr4	173006355	173006554	+	0	NA	intron (NM_001034845, intron 10 of 12)	intron (NM_001034845, intron 10 of 12)	-162299	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.010050	0.395000	
chunk0200_446_1	chr9	31003668	31004581	+	0	NA	Intergenic	L1MD1|LINE|L1	-595670	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.002191	0.355580	580(TAGAACATGCTGTTAC,-,0.00)
chunk0047_236_1	chr12	71954837	71955291	+	0	NA	intron (NM_173353, intron 5 of 10)	intron (NM_173353, intron 5 of 10)	16218	NM_173353	121278	Hs.736576	NM_173353	ENSG00000139287	TPH2	ADHD7|NTPH	tryptophan hydroxylase 2	protein-coding	0.004405	0.347253	
chunk0025_1_1	chr10	46640003	46640208	+	0	NA	intron (NR_027632, intron 2 of 6)	L1MC4a|LINE|L1	11871	NR_027632	414241	Hs.594331	NM_001098846	ENSG00000165874	SHLD2P1	FAM35B|FAM35BP|FAM35EP|bA38L15.1	shieldin complex subunit 2 pseudogene 1	pseudo	0.000000	0.368932	94(CATAACAGTATGTCCT,-,0.00),95(ATAACAGTATGTCCTG,+,0.00),167(TAGTACATAGTGTTCC,-,0.00),168(AGTACATAGTGTTCCA,+,0.00)
chunk0104_316_1	chr2	179232990	179233493	+	0	NA	intron (NM_178123, intron 1 of 17)	L1MC4a|LINE|L1	31382	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.009940	0.331349	
chunk0020_332_1	chr1	238524125	238524501	+	0	NA	Intergenic	L2|LINE|L2	-38296	NR_015407	339535	Hs.532047	NR_015407	ENSG00000215808	LINC01139	LINK-A|LINKA	long intergenic non-protein coding RNA 1139	ncRNA	0.010638	0.411141	
chunk0014_68_1	chr1	176051382	176051674	+	0	NA	intron (NM_001001740, intron 10 of 18)	Tigger3b|DNA|TcMar-Tigger	-82988	NR_002998	677679		NR_002998	ENSG00000252906	SCARNA3	HBI-100	small Cajal body-specific RNA 3	ncRNA	0.006849	0.358362	
chunk0140_326_1	chr4	73653633	73654214	+	0	NA	Intergenic	Intergenic	-33292	NM_001270392	166824	Hs.529677	NM_177532	ENSG00000169435	RASSF6	-	Ras association domain family member 6	protein-coding	0.012048	0.365979	
chunk0096_447_1	chr2	39393133	39393514	+	0	NA	intron (NM_003618, intron 1 of 33)	intron (NM_003618, intron 1 of 33)	43989	NM_003618	8491	Hs.655750	NM_003618	ENSG00000011566	MAP4K3	GLK|MAPKKKK3|MEKKK 3|MEKKK3|RAB8IPL1	mitogen-activated protein kinase kinase kinase kinase 3	protein-coding	0.005249	0.303665	
chunk0027_219_1	chr10	76201999	76202375	+	0	NA	intron (NR_131178, intron 6 of 7)	MLT1H2|LTR|ERVL-MaLR	419426	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.010638	0.445623	
chunk0122_49_1	chr3	28544312	28544766	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-30739	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.004405	0.424176	
chunk0012_464_1	chr1	165598408	165598735	+	0	NA	Intergenic	Intergenic	-16416	NR_026744	400794	Hs.374847	NR_026744	ENSG00000237463	LRRC52-AS1	-	LRRC52 antisense RNA 1	ncRNA	0.033639	0.524390	
chunk0091_271_1	chr19	11555366	11555848	+	0	NA	intron (NM_032377, intron 1 of 3)	intron (NM_032377, intron 1 of 3)	3629	NM_032377	84337	Hs.631633	NM_032377	ENSG00000130165	ELOF1	ELF1	elongation factor 1 homolog	protein-coding	0.012448	0.554865	
chunk0071_452_1	chr15	90183977	90184228	+	0	NA	promoter-TSS (NM_020210)	promoter-TSS (NM_020210)	-818	NM_020210	10509	Hs.474935	NM_020210	ENSG00000185033	SEMA4B	SEMAC|SemC	semaphorin 4B	protein-coding	0.031873	0.563492	
chunk0167_405_1	chr6	75262909	75263108	+	0	NA	intron (NM_018247, intron 3 of 6)	L2c|LINE|L2	-19080	NR_029466	1347	Hs.70312	NM_001865	ENSG00000112695	COX7A2	COX7AL|COX7AL1|COXVIIAL|COXVIIa-L|VIIAL	cytochrome c oxidase subunit 7A2	protein-coding	0.000000	0.350000	
chunk0041_422_1	chr11	134264908	134265327	+	0	NA	3' UTR (NM_014384, exon 11 of 11)	3' UTR (NM_014384, exon 11 of 11)	-11264	NM_001080407	112937	Hs.721382	NM_138416	ENSG00000166105	GLB1L3	-	galactosidase beta 1 like 3	protein-coding	0.011933	0.504762	
chunk0089_325_1	chr18	65215853	65216511	+	0	NA	Intergenic	Intergenic	-534070	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.016717	0.400607	
chunk0127_340_1	chr3	100591364	100591650	+	0	NA	Intergenic	Intergenic	-18082	NM_032787	84873	Hs.334511	NM_032787	ENSG00000144820	ADGRG7	GPR128	adhesion G protein-coupled receptor G7	protein-coding	0.003497	0.362369	
chunk0020_274_1	chr1	236399398	236399988	+	0	NA	intron (NM_080738, intron 1 of 5)	intron (NM_080738, intron 1 of 5)	4277	NM_080738	128178	Hs.352224	NM_080738	ENSG00000186197	EDARADD	ECTD11A|ECTD11B|ED3|EDA3	EDAR associated death domain	protein-coding	0.011864	0.502538	
chunk0069_227_1	chr15	63825349	63825715	+	0	NA	intron (NM_003922, intron 1 of 77)	intron (NM_003922, intron 1 of 77)	8416	NM_003922	8925	Hs.210385	NM_003922	ENSG00000103657	HERC1	MDFPMR|p532|p619	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding	0.000000	0.305177	
chunk0009_341_1	chr1	109280666	109281042	+	0	NA	exon (NM_032636, exon 6 of 8)	exon (NM_032636, exon 6 of 8)	2314	NM_001005290	84722	Hs.405925	NM_032636	ENSG00000134222	PSRC1	DDA3|FP3214	proline and serine rich coiled-coil 1	protein-coding	0.031915	0.588859	
chunk0136_74_1	chr4	2185782	2186047	+	0	NA	intron (NM_181808, intron 7 of 25)	intron (NM_181808, intron 7 of 25)	56250	NM_001303143	79441	Hs.665869	NM_024511	ENSG00000214367	HAUS3	C4orf15|IT1|dgt3	HAUS augmin like complex subunit 3	protein-coding	0.007547	0.364662	
chunk0067_18_1	chr15	40103136	40103424	+	0	NA	intron (NM_001003943, intron 3 of 3)	intron (NM_001003943, intron 3 of 3)	2806	NM_001003942	90427	Hs.591104	NM_033503	ENSG00000104081	BMF	-	Bcl2 modifying factor	protein-coding	0.020833	0.570934	123(AAGTACAGAATGTGTT,-,0.00),124(AGTACAGAATGTGTTC,+,0.00)
chunk0141_419_1	chr4	88630774	88631265	+	0	NA	intron (NM_014606, intron 3 of 25)	intron (NM_014606, intron 3 of 25)	38596	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.006110	0.398374	
chunk0076_183_1	chr16	67632824	67633028	+	0	NA	intron (NM_001191022, intron 8 of 9)	intron (NM_001191022, intron 8 of 9)	-12201	NM_001317026	146206	Hs.611432	NM_001013838	ENSG00000159753	CARMIL2	CARMIL2b|IMD58|LRRC16C|RLTPR	capping protein regulator and myosin 1 linker 2	protein-coding	0.014706	0.478049	112(GTGTACATTTTGTGCC,-,0.00),113(TGTACATTTTGTGCCG,+,0.00)
chunk0171_1_1	chr6	119459651	119460085	+	0	NA	intron (NR_046100, intron 3 of 5)	L3|LINE|CR1	31434	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.004608	0.340230	
chunk0196_166_1	chr8	105537993	105538356	+	0	NA	intron (NM_012082, intron 3 of 7)	intron (NM_012082, intron 3 of 7)	219255	NM_012082	23414	Hs.431009	NM_012082	ENSG00000169946	ZFPM2	DIH3|FOG2|SRXY9|ZC2HC11B|ZNF89B|hFOG-2	zinc finger protein, FOG family member 2	protein-coding	0.005510	0.329670	
chunk0011_290_1	chr1	151492251	151492520	+	0	NA	Intergenic	Intergenic	-19001	NM_020770	57530	Hs.591464	NM_020770	ENSG00000143375	CGN	-	cingulin	protein-coding	0.000000	0.462963	
chunk0001_416_1	chr1	11151007	11151364	+	0	NA	intron (NM_004958, intron 30 of 57)	intron (NM_004958, intron 30 of 57)	7287	NR_046600	100873935	Hs.679133	NR_046600	ENSG00000225602	MTOR-AS1	-	MTOR antisense RNA 1	ncRNA	0.011204	0.505587	
chunk0183_37_1	chr7	103771850	103772283	+	0	NA	intron (NM_005045, intron 4 of 64)	intron (NM_005045, intron 4 of 64)	217450	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.006928	0.421659	
chunk0076_225_1	chr16	68704486	68704725	+	0	NA	Intergenic	(AGGG)n|Simple_repeat|Simple_repeat	-32687	NM_004360	999	Hs.461086	NM_004360	ENSG00000039068	CDH1	Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO	cadherin 1	protein-coding	0.025105	0.587500	
chunk0135_91_1	chr3	186413485	186414103	+	0	NA	Intergenic	Intergenic	-51560	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.025890	0.513732	279(CAGGACAAGTTGTACT,-,0.00),280(AGGACAAGTTGTACTT,+,0.00)
chunk0035_34_1	chr11	40743905	40744325	+	0	NA	intron (NM_020929, intron 1 of 4)	L2a|LINE|L2	-450985	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.007143	0.351544	
chunk0174_352_1	chr6	164361912	164362269	+	0	NA	Intergenic	Intergenic	459973	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.000000	0.318436	
chunk0057_77_1	chr13	98416239	98416999	+	0	NA	intron (NM_001286839, intron 16 of 27)	intron (NM_001286839, intron 16 of 27)	105506	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.014474	0.484888	
chunk0157_237_1	chr5	119537481	119538114	+	0	NA	intron (NM_000414, intron 23 of 23)	MER58A|DNA|hAT-Charlie	85300	NM_001292028	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.003160	0.397476	
chunk0024_336_1	chr10	43194421	43195328	+	0	NA	3' UTR (NM_145313, exon 13 of 13)	3' UTR (NM_145313, exon 13 of 13)	34865	NM_001282862	221002	Hs.125293	NM_145313	ENSG00000198915	RASGEF1A	CG4853	RasGEF domain family member 1A	protein-coding	0.016538	0.505507	
chunk0119_7_1	chr22	40040867	40041541	+	0	NA	Intergenic	Intergenic	-3613	NM_001024843	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.010386	0.496296	348(AAGAACATAGTGCACT,-,0.00),349(AGAACATAGTGCACTT,+,0.00)
chunk0144_322_1	chr4	138934488	138934770	+	0	NA	Intergenic	Intergenic	-81130	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.007092	0.314488	
chunk0063_283_1	chr14	84279888	84280376	+	0	NA	Intergenic	Intergenic	-1113747	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.008197	0.314928	
chunk0017_169_1	chr1	207027881	207028417	+	0	NA	intron (NM_023938, intron 1 of 3)	intron (NM_023938, intron 1 of 3)	4607	NM_001083924	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.003731	0.366853	
chunk0075_436_1	chr16	57818632	57818981	+	0	NA	Intergenic	Intergenic	8169	NM_001278081	388282	Hs.434720	NM_001278081		LOC388282	-	uncharacterized LOC388282	protein-coding	0.011461	0.491429	
chunk0046_255_1	chr12	60565001	60565279	+	0	NA	Intergenic	L1PA15|LINE|L1	875803	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.010791	0.577061	
chunk0037_357_1	chr11	77890574	77890900	+	0	NA	intron (NR_133637, intron 4 of 4)	intron (NR_133637, intron 4 of 4)	69623	NM_001316957	28971	Hs.745040	NM_024684	ENSG00000087884	AAMDC	C11orf67|CK067|PTD015	adipogenesis associated Mth938 domain containing	protein-coding	0.006135	0.406728	
chunk0031_368_1	chr10	130360997	130361249	+	0	NA	Intergenic	Intergenic	224748	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.035714	0.565217	
chunk0002_342_1	chr1	25032060	25032823	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	8938	NR_039623	100616365		NR_039623	ENSG00000264371	MIR4425	-	microRNA 4425	ncRNA	0.026212	0.472513	
chunk0089_46_1	chr18	58077244	58077781	+	0	NA	intron (NM_001144964, intron 1 of 30)	L1ME2z|LINE|L1	30286	NM_001144964	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.016760	0.455390	
chunk0079_41_1	chr17	10310509	10311210	+	0	NA	intron (NM_003802, intron 33 of 40)	intron (NM_003802, intron 33 of 40)	62146	NM_003802	8735	Hs.711142	NM_003802	ENSG00000006788	MYH13	MyHC-IIL|MyHC-eo	myosin heavy chain 13	protein-coding	0.014265	0.440171	
chunk0128_64_1	chr3	105095204	105095437	+	0	NA	Intergenic	MIR|SINE|MIR	-271393	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.341880	
chunk0107_239_1	chr2	217195872	217196405	+	0	NA	Intergenic	Intergenic	-86595	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.005629	0.440075	
chunk0063_125_1	chr14	79338055	79338631	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	59004	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.012153	0.431542	
chunk0087_176_1	chr18	35426982	35427228	+	0	NA	Intergenic	Intergenic	-49768	NM_145756	252884	Hs.351005	NM_145756	ENSG00000186496	ZNF396	ZSCAN14	zinc finger protein 396	protein-coding	0.008130	0.421053	
chunk0176_10_1	chr7	8212735	8212934	+	0	NA	intron (NM_001136020, intron 6 of 13)	intron (NM_001136020, intron 6 of 13)	49218	NM_022307	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.005025	0.440000	
chunk0174_196_1	chr6	160085046	160085700	+	0	NA	intron (NM_000876, intron 41 of 47)	intron (NM_000876, intron 41 of 47)	-7709	NR_003288	729603	Hs.674810	NR_003288	ENSG00000213073	LOC729603	-	calcineurin like EF-hand protein 1 pseudogene	pseudo	0.013761	0.453435	
chunk0191_29_1	chr8	42999168	42999542	+	0	NA	intron (NM_032410, intron 16 of 21)	intron (NM_032410, intron 16 of 21)	-56944	NM_002027	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.005348	0.344000	
chunk0147_333_1	chr4	185269358	185269784	+	0	NA	intron (NM_031953, intron 5 of 18)	MamGypsy2-I|LTR|Gypsy	59441	NM_031953	83891	Hs.369091	NM_031953	ENSG00000109762	SNX25	MSTP043|SBBI31	sorting nexin 25	protein-coding	0.004695	0.381733	
chunk0004_213_1	chr1	46689327	46689596	+	0	NA	intron (NM_014774, intron 6 of 10)	intron (NM_014774, intron 6 of 10)	15425	NR_038827	100130197	Hs.568643	NR_038827	ENSG00000228237	EFCAB14-AS1	KIAA0494-AS1	EFCAB14 antisense RNA 1	ncRNA	0.003717	0.455556	
chunk0188_261_1	chr8	14770555	14770904	+	0	NA	intron (NM_139167, intron 1 of 7)	L2c|LINE|L2	82781	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.000000	0.311429	
chunk0063_423_1	chr14	88503967	88504407	+	0	NA	intron (NM_007039, intron 6 of 18)	intron (NM_007039, intron 6 of 18)	50592	NM_007039	11099	Hs.437040	NM_007039	ENSG00000070778	PTPN21	PTPD1|PTPRL10	protein tyrosine phosphatase non-receptor type 21	protein-coding	0.002273	0.356009	
chunk0129_142_1	chr3	120444746	120445014	+	0	NA	intron (NM_007085, intron 2 of 10)	intron (NM_007085, intron 2 of 10)	6191	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.014925	0.334572	
chunk0013_108_1	chr1	167829265	167829671	+	0	NA	intron (NM_001167749, intron 22 of 29)	intron (NM_001167749, intron 22 of 29)	84758	NM_001167749	55811	Hs.320892	NM_018417	ENSG00000143199	ADCY10	HCA2|HEL-S-7a|SAC|SACI|Sacy|hsAC	adenylate cyclase 10	protein-coding	0.004926	0.393120	226(AGGTACATGGTGTCCT,-,0.00),227(GGTACATGGTGTCCTC,+,0.00)
chunk0081_158_1	chr17	40910044	40910413	+	0	NA	Intergenic	Intergenic	-24985	NM_019010	54474	Hs.84905	NM_019010	ENSG00000171431	KRT20	CD20|CK-20|CK20|K20|KRT21	keratin 20	protein-coding	0.021680	0.421622	
chunk0116_342_1	chr21	41501007	41501332	+	0	NA	intron (NM_005656, intron 1 of 13)	intron (NM_005656, intron 1 of 13)	6896	NM_001135099	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.015385	0.472393	
chunk0010_261_1	chr1	116674709	116675214	+	0	NA	Intergenic	L2a|LINE|L2	3212	NR_031564	100302117		NR_031564	ENSG00000211543	MIR320B1	MIR320B-1|MIRN320B1|hsa-mir-320b-1|mir-320b-1	microRNA 320b-1	ncRNA	0.005941	0.387352	
chunk0158_329_1	chr5	132905873	132906537	+	0	NA	intron (NM_014423, intron 5 of 20)	L1MB7|LINE|L1	32539	NM_052971	116842	Hs.337588	NM_052971	ENSG00000164406	LEAP2	LEAP-2	liver enriched antimicrobial peptide 2	protein-coding	0.003012	0.342857	
chunk0026_57_1	chr10	61075637	61076160	+	0	NA	Intergenic	Intergenic	59623	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.003824	0.421756	
chunk0140_40_1	chr4	66590154	66590680	+	0	NA	Intergenic	L1MA5|LINE|L1	313593	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.005703	0.356736	
chunk0115_258_1	chr21	27739270	27739469	+	0	NA	intron (NR_024357, intron 1 of 3)	MLT1C|LTR|ERVL-MaLR	16990	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.000000	0.465000	
chunk0196_105_1	chr8	103071856	103072294	+	0	NA	3' UTR (NM_001695, exon 13 of 13)	3' UTR (NM_001695, exon 13 of 13)	51055	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.006849	0.391800	
chunk0163_20_1	chr6	7981606	7982282	+	0	NA	intron (NR_037616, intron 4 of 12)	L1ME3A|LINE|L1	-4158	NR_027712	206426	Hs.676966	NR_027712		PIP5K1P1	-	phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1	pseudo	0.002959	0.290990	
chunk0067_147_1	chr15	43248434	43248886	+	0	NA	intron (NM_201631, intron 6 of 12)	intron (NM_201631, intron 6 of 12)	18197	NM_201631	9333	Hs.129719	NM_004245	ENSG00000104055	TGM5	PSS2|TGASE5|TGASEX|TGM6|TGMX|TGX	transglutaminase 5	protein-coding	0.008850	0.399558	195(GGGAACATTCCGTACT,-,0.00),196(GGAACATTCCGTACTA,+,0.00)
chunk0203_137_1	chr9	85480523	85480810	+	0	NA	Intergenic	L2a|LINE|L2	261363	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.020906	0.524306	
chunk0036_83_1	chr11	60728973	60729572	+	0	NA	intron (NM_001310141, intron 1 of 5)	intron (NM_001310141, intron 1 of 5)	5263	NM_001310141	728588	Hs.739039	NM_001310141	ENSG00000214782	MS4A18	-	membrane spanning 4-domains A18	protein-coding	0.010017	0.446667	167(GAAAACAGTGTGTTCT,-,0.00),168(AAAACAGTGTGTTCTT,+,0.00)
chunk0100_131_1	chr2	108678106	108678694	+	0	NA	intron (NM_001193482, intron 8 of 9)	intron (NM_001193482, intron 8 of 9)	23588	NM_001193485	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.010204	0.404075	
chunk0092_76_1	chr19	20676113	20676312	+	0	NA	Intergenic	Intergenic	-14616	NM_145297	199777	Hs.657001	NM_145297	ENSG00000188171	ZNF626	-	zinc finger protein 626	protein-coding	0.005025	0.325000	
chunk0158_208_1	chr5	128199127	128199545	+	0	NA	Intergenic	MER54A|LTR|ERVL	115545	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.009569	0.489260	
chunk0151_400_1	chr5	55526870	55527347	+	0	NA	intron (NR_103485, intron 1 of 6)	intron (NR_103485, intron 1 of 6)	7434	NR_001575	379013	Hs.745164	NR_001575		RNF138P1	-	ring finger protein 138 pseudogene 1	pseudo	0.012579	0.397490	
chunk0108_327_1	chr2	235663948	235664319	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	158382	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.026954	0.500000	
chunk0028_292_1	chr10	91467214	91467947	+	0	NA	intron (NM_001284274, intron 5 of 21)	L1PA13|LINE|L1	57295	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.010914	0.580381	
chunk0116_220_1	chr21	37716250	37716494	+	0	NA	intron (NM_002240, intron 2 of 3)	intron (NM_002240, intron 2 of 3)	200066	NM_002240	3763	Hs.626242	NM_002240	ENSG00000157542	KCNJ6	BIR1|GIRK-2|GIRK2|KATP-2|KATP2|KCNJ7|KIR3.2|KPLBS|hiGIRK2	potassium voltage-gated channel subfamily J member 6	protein-coding	0.004098	0.387755	
chunk0189_186_1	chr8	23614163	23615010	+	0	NA	Intergenic	Intergenic	68303	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.004723	0.353774	
chunk0168_241_1	chr6	87865412	87865723	+	0	NA	intron (NR_110869, intron 2 of 4)	intron (NR_110869, intron 2 of 4)	80707	NR_110869	101928911	Hs.571178	NR_110869		LOC101928911	-	uncharacterized LOC101928911	ncRNA	0.003215	0.384615	
chunk0186_63_1	chr7	136987478	136987730	+	0	NA	intron (NM_001006626, intron 3 of 4)	intron (NM_001006626, intron 3 of 4)	84437	NR_030165	574443		NR_030165	ENSG00000207597	MIR490	MIRN490|hsa-mir-490|miR-490	microRNA 490	ncRNA	0.019841	0.466403	
chunk0032_146_1	chr11	4727075	4727763	+	0	NA	Intergenic	Intergenic	-29573	NM_030774	81285	Hs.501758	NM_030774	ENSG00000167332	OR51E2	HPRAJ|OR51E3P|OR52A2|PSGR	olfactory receptor family 51 subfamily E member 2	protein-coding	0.013081	0.361393	
chunk0083_391_1	chr17	71638498	71639319	+	0	NA	Intergenic	Intergenic	387071	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.007308	0.364964	
chunk0184_124_1	chr7	114394191	114394579	+	0	NA	intron (NR_033766, intron 2 of 19)	intron (NR_033766, intron 2 of 19)	-20612	NM_001172766	93986	Hs.282787	NM_014491	ENSG00000128573	FOXP2	CAGH44|SPCH1|TNRC10	forkhead box P2	protein-coding	0.005155	0.329049	
chunk0035_387_1	chr11	56180591	56180817	+	0	NA	Intergenic	L1MDa|LINE|L1	4086	NM_001005492	282775	Hs.537145	NM_001005492	ENSG00000174957	OR5J2	OR11-266	olfactory receptor family 5 subfamily J member 2	protein-coding	0.004425	0.480176	
chunk0193_81_1	chr8	73360204	73360473	+	0	NA	Intergenic	L1MC5a|LINE|L1	-3877	NR_125388	101926926	Hs.640090	NR_125388	ENSG00000250295	RDH10-AS1	-	RDH10 antisense RNA 1	ncRNA	0.003717	0.344444	
chunk0020_111_1	chr1	233161280	233161595	+	0	NA	intron (NM_014801, intron 17 of 33)	intron (NM_014801, intron 17 of 33)	134276	NM_014801	80003	Hs.370605	NM_014801	ENSG00000135749	PCNX2	PCNXL2	pecanex 2	protein-coding	0.019048	0.490506	
chunk0046_93_1	chr12	56677647	56677951	+	0	NA	intron (NM_001282601, intron 1 of 6)	MER119|DNA|hAT-Charlie	10198	NR_104219	10728	Hs.50425	NM_006601	ENSG00000110958	PTGES3	P23|TEBP|cPGES	prostaglandin E synthase 3	protein-coding	0.000000	0.383607	
chunk0041_282_1	chr11	129364093	129364650	+	0	NA	Intergenic	CpG	-11615	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.034111	0.510753	
chunk0209_235_1	chrX	45295796	45296562	+	0	NA	Intergenic	L1ME4a|LINE|L1	-95278	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.006527	0.332464	
chunk0124_233_1	chr3	56626042	56626487	+	0	NA	intron (NM_001112736, intron 21 of 23)	intron (NM_001112736, intron 21 of 23)	37782	NM_015224	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.002247	0.338565	384(TGGCACATACAGTTCA,-,0.00),385(GGCACATACAGTTCAG,+,0.00)
chunk0117_354_1	chr21	44509528	44509944	+	0	NA	intron (NR_103707, intron 5 of 6)	intron (NR_103707, intron 5 of 6)	3692	NR_103707	54082	Hs.570444	NR_103707	ENSG00000235890	TSPEAR-AS1	C21orf31	TSPEAR antisense RNA 1	ncRNA	0.031250	0.625899	
chunk0128_153_1	chr3	107026099	107026298	+	0	NA	Intergenic	Intergenic	214440	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.010050	0.380000	
chunk0206_290_1	chr9	124409376	124409831	+	0	NA	intron (NM_002799, intron 4 of 7)	intron (NM_002799, intron 4 of 7)	5870	NM_002799	5695	Hs.213470	NM_002799	ENSG00000136930	PSMB7	Z	proteasome subunit beta 7	protein-coding	0.006593	0.385965	229(AAGAACACCTTGTACT,-,0.00),230(AGAACACCTTGTACTC,+,0.00)
chunk0091_114_1	chr19	6079049	6079467	+	0	NA	intron (NM_000635, intron 1 of 17)	intron (NM_000635, intron 1 of 17)	31395	NM_134433	5990	Hs.465709	NM_000635	ENSG00000087903	RFX2	-	regulatory factor X2	protein-coding	0.021531	0.405728	
chunk0054_300_1	chr13	48383593	48383925	+	0	NA	intron (NM_000321, intron 17 of 26)	A-rich|Low_complexity|Low_complexity	29758	NM_001162498	10161	Hs.123464	NM_005767	ENSG00000139679	LPAR6	ARWH1|HYPT8|LAH3|P2RY5|P2Y5	lysophosphatidic acid receptor 6	protein-coding	0.000000	0.288288	207(AAGCACATAGAGTACT,-,0.00),208(AGCACATAGAGTACTT,+,0.00)
chunk0167_103_1	chr6	57156312	57156752	+	0	NA	intron (NM_001031623, intron 13 of 14)	intron (NM_001031623, intron 13 of 14)	15681	NR_110742	101927211	Hs.705718	NR_110742		ZNF451-AS1	-	ZNF451 regulatory antisense RNA 1	ncRNA	0.002273	0.342404	179(TAAACATGGTGTTCCT,+,0.00)
chunk0170_192_1	chr6	112097269	112098064	+	0	NA	intron (NM_001033564, intron 2 of 3)	intron (NM_001033564, intron 2 of 3)	-10118	NM_016262	51175	Hs.34851	NM_016262	ENSG00000074935	TUBE1	TUBE|dJ142L7.2	tubulin epsilon 1	protein-coding	0.002516	0.327889	271(GAAAACATTGTGTACT,-,0.00),272(AAAACATTGTGTACTA,+,0.00),294(GAAAACATTGTGTACT,-,0.00),295(AAAACATTGTGTACTA,+,0.00),317(GAAAACATTGTGTACT,-,0.00),318(AAAACATTGTGTACTA,+,0.00),340(GAAAACATTGTGTACT,-,0.00),341(AAAACATTGTGTACTA,+,0.00),386(GAAAACAGTGTGTACT,-,0.00),387(AAAACAGTGTGTACTA,+,0.00),409(GAAAACATTGTGTACT,-,0.00),410(AAAACATTGTGTACTA,+,0.00),455(GAAAACATTGTGTACT,-,0.00),456(AAAACATTGTGTACTA,+,0.00)
chunk0120_150_1	chr3	5309472	5309924	+	0	NA	Intergenic	Intergenic	-59443	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.008850	0.375276	
chunk0177_146_1	chr7	22718140	22718885	+	0	NA	Intergenic	Intergenic	-8635	NM_000600	3569	Hs.654458	NM_000600	ENSG00000136244	IL6	BSF-2|BSF2|CDF|HGF|HSF|IFN-beta-2|IFNB2|IL-6	interleukin 6	protein-coding	0.009396	0.443700	
chunk0045_345_1	chr12	51430394	51430731	+	0	NA	intron (NM_001258403, intron 1 of 16)	intron (NM_001258403, intron 1 of 16)	5445	NM_001258403	9498	Hs.4749	NM_004858	ENSG00000050438	SLC4A8	NBC3|NDCBE	solute carrier family 4 member 8	protein-coding	0.005935	0.434911	
chunk0011_333_1	chr1	152168404	152169107	+	0	NA	Intergenic	MIRb|SINE|MIR	-9527	NM_001122965	126638	Hs.376144	NM_152364	ENSG00000215853	RPTN	-	repetin	protein-coding	0.001422	0.431818	232(CAGGACTCTATGTTCT,-,0.00),233(AGGACTCTATGTTCTA,+,0.00)
chunk0004_38_1	chr1	42761290	42761584	+	0	NA	intron (NM_001243246, intron 2 of 13)	L1ME4a|LINE|L1	5647	NM_001146289	64175	Hs.720014	NM_022356	ENSG00000117385	P3H1	GROS1|LEPRE1|OI8	prolyl 3-hydroxylase 1	protein-coding	0.000000	0.291525	
chunk0174_424_1	chr6	165919379	165920065	+	0	NA	Intergenic	Intergenic	-67829	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.005831	0.407569	
chunk0126_420_1	chr3	86048526	86048974	+	0	NA	intron (NM_153184, intron 8 of 9)	intron (NM_153184, intron 8 of 9)	-220700	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.002232	0.280624	
chunk0081_396_1	chr17	48240545	48240969	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-53590	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.004717	0.432941	
chunk0079_323_1	chr17	17354776	17355289	+	0	NA	Intergenic	Intergenic	51666	NM_020201	56953	Hs.513977	NM_020201	ENSG00000205309	NT5M	dNT-2|dNT2|mdN	5',3'-nucleotidase, mitochondrial	protein-coding	0.021442	0.577821	269(AGGAACTTGGAGTCCT,-,0.00),270(GGAACTTGGAGTCCTT,+,0.00)
chunk0130_103_1	chr3	131086463	131086681	+	0	NA	intron (NM_145910, intron 4 of 14)	L1MC4a|LINE|L1	-59718	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.004587	0.374429	
chunk0202_48_1	chr9	71269803	71270182	+	0	NA	Intergenic	Intergenic	-148394	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.007916	0.381579	
chunk0064_197_1	chr14	92794049	92794286	+	0	NA	promoter-TSS (NM_005113)	promoter-TSS (NM_005113)	-64	NM_005113	9950	Hs.104320	NM_005113	ENSG00000066455	GOLGA5	GOLIM5|RFG5|ret-II	golgin A5	protein-coding	0.135021	0.726891	
chunk0049_353_1	chr12	95383808	95384222	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	74092	NR_037456	100500802		NR_037456	ENSG00000265917	MIR3685	-	microRNA 3685	ncRNA	0.016908	0.438554	
chunk0167_116_1	chr6	57549191	57549408	+	0	NA	intron (NM_000947, intron 10 of 13)	MIRb|SINE|MIR	159167	NR_036097	100422884		NR_036097	ENSG00000212017	MIR548U	-	microRNA 548u	ncRNA	0.009217	0.403670	
chunk0012_271_1	chr1	161788037	161788493	+	0	NA	intron (NM_007348, intron 4 of 15)	L1M5|LINE|L1	22021	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.002193	0.352298	211(GGCACAATGTGTTTTT,+,0.00)
chunk0100_318_1	chr2	116425157	116425512	+	0	NA	Intergenic	Intergenic	1263227	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.016901	0.410112	
chunk0103_244_1	chr2	164850077	164850687	+	0	NA	TTS (NR_110574)	TTS (NR_110574)	-8214	NM_001278460	22837	Hs.470457	NM_014900	ENSG00000082438	COBLL1	COBLR1	cordon-bleu WH2 repeat protein like 1	protein-coding	0.006557	0.322422	276(CAGAACAAGCTGAGCT,-,0.00),277(AGAACAAGCTGAGCTG,+,0.00)
chunk0144_209_1	chr4	134248139	134248454	+	0	NA	Intergenic	L1MD2|LINE|L1	-46548	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.003175	0.351266	
chunk0080_93_1	chr17	26797775	26797985	+	0	NA	Intergenic	Intergenic	496116	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.033333	0.369668	
chunk0144_454_1	chr4	142130619	142130979	+	0	NA	intron (NM_001101669, intron 18 of 25)	intron (NM_001101669, intron 18 of 25)	494203	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.002778	0.401662	256(GAGAACACAGTGTCAT,-,0.00)
chunk0090_77_1	chr18	70361226	70361652	+	0	NA	Intergenic	Intergenic	23152	NR_110764	101060542	Hs.586967	NR_110764	ENSG00000266278	LINC01910	-	long intergenic non-protein coding RNA 1910	ncRNA	0.011737	0.388759	
chunk0140_63_1	chr4	67084791	67085175	+	0	NA	Intergenic	Intergenic	337017	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.005208	0.392208	
chunk0190_237_1	chr8	36645753	36646012	+	0	NA	Intergenic	Intergenic	-138442	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.007722	0.403846	
chunk0161_381_1	chr5	176811220	176811433	+	0	NA	intron (NM_133369, intron 1 of 14)	intron (NM_133369, intron 1 of 14)	767	NM_133369	90249	Hs.33191	NM_133369	ENSG00000113763	UNC5A	UNC5H1	unc-5 netrin receptor A	protein-coding	0.056338	0.612150	87(CAGAACACAGTGTCCT,-,0.00),88(AGAACACAGTGTCCTC,+,0.00)
chunk0045_267_1	chr12	49629496	49629915	+	0	NA	intron (NM_012272, intron 1 of 24)	L2a|LINE|L2	6085	NM_012272	25766	Hs.706827	NM_012272	ENSG00000110844	PRPF40B	HYPC	pre-mRNA processing factor 40 homolog B	protein-coding	0.004773	0.395238	
chunk0095_66_1	chr2	14481010	14481596	+	0	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	-80345	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.003413	0.410562	
chunk0030_147_1	chr10	113762127	113762508	+	0	NA	intron (NM_001193435, intron 2 of 10)	L1ME1|LINE|L1	-2502	NM_182601	79949	Hs.228320	NM_024889	ENSG00000148735	PLEKHS1	C10orf81|HEL185	pleckstrin homology domain containing S1	protein-coding	0.002625	0.321990	
chunk0090_399_1	chr18	78313386	78313585	+	0	NA	Intergenic	CpG	-319758	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.070352	0.580000	
chunk0019_334_1	chr1	229229617	229230379	+	0	NA	Intergenic	Intergenic	-41064	NR_073545	5867	Hs.296169	NM_004578	ENSG00000168118	RAB4A	HRES-1|HRES-1/RAB4|HRES1|RAB4	RAB4A, member RAS oncogene family	protein-coding	0.013123	0.525557	
chunk0073_387_1	chr16	16011196	16011510	+	0	NA	intron (NM_004996, intron 3 of 30)	intron (NM_004996, intron 3 of 30)	61776	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.012739	0.460317	97(GTGAACAGTGTGTCCA,-,0.00),98(TGAACAGTGTGTCCAG,+,0.00)
chunk0071_458_1	chr15	90315686	90315915	+	0	NA	Intergenic	Intergenic	33647	NR_028287	23766	Hs.592014	NR_028287		GABARAPL3	ATG8D	GABA type A receptor associated protein like 3 pseudogene	pseudo	0.004367	0.521739	
chunk0026_134_1	chr10	62111428	62111889	+	0	NA	Intergenic	MIR|SINE|MIR	62447	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.006508	0.346320	
chunk0020_338_1	chr1	239040968	239041448	+	0	NA	Intergenic	Intergenic	-555191	NR_015407	339535	Hs.532047	NR_015407	ENSG00000215808	LINC01139	LINK-A|LINKA	long intergenic non-protein coding RNA 1139	ncRNA	0.000000	0.307692	
chunk0052_40_1	chr13	20831155	20831705	+	0	NA	intron (NM_022459, intron 6 of 22)	intron (NM_022459, intron 6 of 22)	-57512	NM_174928	221143	Hs.26674	NM_174928	ENSG00000150456	EEF1AKMT1	ESP13|N6AMT2	EEF1A lysine methyltransferase 1	protein-coding	0.003636	0.270417	
chunk0132_117_1	chr3	155956870	155958019	+	0	NA	Intergenic	L1MC3|LINE|L1	86908	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.006092	0.402609	329(AGACCAGTATGTACTC,+,0.00)
chunk0105_279_1	chr2	189641130	189641372	+	0	NA	Intergenic	L2b|LINE|L2	-20148	NM_019048	54529	Hs.101364	NM_019048	ENSG00000138381	ASNSD1	NBLA00058|NS3TP1	asparagine synthetase domain containing 1	protein-coding	0.004132	0.395062	
chunk0127_228_1	chr3	96750478	96750853	+	0	NA	Intergenic	MER52C|LTR|ERV1	-63916	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002667	0.579787	
chunk0186_40_1	chr7	136076966	136077248	+	0	NA	Intergenic	Intergenic	-99651	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.000000	0.487633	
chunk0087_417_1	chr18	42231621	42231996	+	0	NA	intron (NR_046454, intron 3 of 6)	L1ME3G|LINE|L1	45140	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.002667	0.356383	
chunk0155_266_1	chr5	95878852	95879770	+	0	NA	Intergenic	Intergenic	27079	NR_026936	202299	Hs.8373	NM_175616	ENSG00000236882	LINC01554	C5orf27|FIS	long intergenic non-protein coding RNA 1554	ncRNA	0.005447	0.438520	
chunk0055_73_1	chr13	52949869	52950094	+	0	NA	Intergenic	Intergenic	-78760	NM_006418	10562	Hs.508113	NM_006418	ENSG00000102837	OLFM4	GC1|GW112|OLM4|OlfD|UNQ362|bA209J19.1|hGC-1|hOLfD	olfactomedin 4	protein-coding	0.004444	0.570796	99(AAGGACACAGTGTTCT,-,0.00),100(AGGACACAGTGTTCTG,+,0.00)
chunk0155_277_1	chr5	96006959	96007580	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	-45198	NM_012081	22936	Hs.192221	NM_012081	ENSG00000118985	ELL2	MRCCAT1	elongation factor for RNA polymerase II 2	protein-coding	0.001610	0.358521	300(TGGTACAGAGTGTTCT,-,0.00),301(GGTACAGAGTGTTCTT,+,0.00)
chunk0048_342_1	chr12	84308902	84309523	+	0	NA	Intergenic	Intergenic	603617	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.000000	0.286174	142(ATCACAGTCTGTTCCA,+,0.00)
chunk0168_359_1	chr6	93342250	93342938	+	0	NA	intron (NM_004440, intron 5 of 16)	intron (NM_004440, intron 5 of 16)	76988	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.002907	0.319303	
chunk0117_282_1	chr22	24275038	24275431	+	0	NA	intron (NM_001145468, intron 1 of 15)	intron (NM_001145468, intron 1 of 15)	4417	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.012723	0.489848	110(TGGCACACTATGTCTC,-,0.00),111(GGCACACTATGTCTCG,+,0.00)
chunk0006_29_1	chr1	64052040	64052650	+	0	NA	intron (NM_001083592, intron 4 of 6)	intron (NM_001083592, intron 4 of 6)	59860	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.003279	0.346972	
chunk0055_12_1	chr13	51727720	51727949	+	0	NA	intron (NM_052950, intron 6 of 11)	intron (NM_052950, intron 6 of 11)	76328	NM_024705	79758	Hs.266728	NM_024705	ENSG00000102796	DHRS12	SDR40C1	dehydrogenase/reductase 12	protein-coding	0.008734	0.413043	
chunk0019_272_1	chr1	228458434	228458635	+	0	NA	promoter-TSS (NM_033445)	promoter-TSS (NM_033445)	427	NM_175055	128312	Hs.376691	NM_175055	ENSG00000196890	HIST3H2BB	H2Bb	histone cluster 3 H2B family member b	protein-coding	0.064677	0.584158	
chunk0194_364_1	chr8	89770414	89770671	+	0	NA	intron (NM_003821, intron 4 of 10)	intron (NM_003821, intron 4 of 10)	12795	NM_003821	8767	Hs.103755	NM_003821	ENSG00000104312	RIPK2	CARD3|CARDIAK|CCK|GIG30|RICK|RIP2	receptor interacting serine/threonine kinase 2	protein-coding	0.000000	0.302326	
chunk0086_223_1	chr18	22609821	22610094	+	0	NA	Intergenic	Intergenic	176880	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.018315	0.485401	
chunk0041_354_1	chr11	130769660	130770328	+	0	NA	Intergenic	MIR|SINE|MIR	92116	NR_125383	100507431	Hs.375101	NR_125383		LINC02551	-	long intergenic non-protein coding RNA 2551	ncRNA	0.014970	0.464873	
chunk0001_105_1	chr1	3454983	3455278	+	0	NA	intron (NM_014448, intron 1 of 14)	intron (NM_014448, intron 1 of 14)	547	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.071186	0.662162	
chunk0092_290_1	chr19	34027835	34028177	+	0	NA	Intergenic	LTR54B|LTR|ERV1	-144441	NM_015578	26065	Hs.744009	NM_015578	ENSG00000257103	LSM14A	C19orf13|FAM61A|RAP55|RAP55A	LSM14A mRNA processing body assembly factor	protein-coding	0.014620	0.475219	
chunk0066_256_1	chr15	34804906	34805365	+	0	NA	intron (NR_120329, intron 2 of 2)	intron (NR_120329, intron 2 of 2)	-9409	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.010893	0.402174	
chunk0105_130_1	chr2	185620593	185621050	+	0	NA	Intergenic	L2a|LINE|L2	-117807	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.006565	0.384279	
chunk0074_279_1	chr16	28743305	28743627	+	0	NA	Intergenic	Intergenic	-8969	NM_001287251	100507607	Hs.710214	NM_001287250	ENSG00000196993	NPIPB9	-	nuclear pore complex interacting protein family member B9	protein-coding	0.018634	0.470588	
chunk0007_409_1	chr1	85808144	85808567	+	0	NA	intron (NM_152890, intron 47 of 59)	ERVL-E-int|LTR|ERVL	-99922	NM_017953	54680	Hs.5111	NM_017953	ENSG00000117174	ZNHIT6	BCD1|C1orf181|NY-BR-75	zinc finger HIT-type containing 6	protein-coding	0.002364	0.384434	
chunk0082_41_1	chr17	50935361	50936111	+	0	NA	Intergenic	Intergenic	-67758	NM_001243877	10140	Hs.703321	NM_005749	ENSG00000141232	TOB1	APRO5|APRO6|PIG49|TOB|TROB|TROB1	transducer of ERBB2, 1	protein-coding	0.022667	0.474035	
chunk0168_7_1	chr6	76819200	76819761	+	0	NA	Intergenic	L1ME3B|LINE|L1	643923	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.005348	0.300712	
chunk0187_299_1	chr7	156118099	156118494	+	0	NA	Intergenic	Intergenic	155664	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.012658	0.398990	245(CGGAACGTTCTGTTCA,-,0.00),246(GGAACGTTCTGTTCAT,+,0.00)
chunk0100_438_1	chr2	120687356	120687809	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-109709	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.004415	0.449339	
chunk0072_46_1	chr16	1199898	1200153	+	0	NA	intron (NM_021098, intron 6 of 34)	intron (NM_021098, intron 6 of 34)	25229	NM_012467	25823	Hs.592076	NM_012467	ENSG00000116176	TPSG1	PRSS31|TMT|trpA	tryptase gamma 1	protein-coding	0.007843	0.539062	
chunk0180_44_1	chr7	54615107	54615583	+	0	NA	Intergenic	Intergenic	58375	NR_038994	285878	Hs.335933	NR_038994	ENSG00000224223	VSTM2A-OT1	GS1-18A18.1	VSTM2A overlapping transcript 1	ncRNA	0.000000	0.303983	223(ATGAACTTTCTGTCCT,-,0.00),224(TGAACTTTCTGTCCTT,+,0.00)
chunk0043_126_1	chr12	15729550	15730137	+	0	NA	intron (NM_004447, intron 1 of 20)	L1MD|LINE|L1	59733	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.006814	0.341837	
chunk0123_132_1	chr3	42602024	42602590	+	0	NA	intron (NM_005385, intron 2 of 16)	Tigger3a|DNA|TcMar-Tigger	-1227	NM_001201572	9117	Hs.445892	NM_004206	ENSG00000093183	SEC22C	SEC22L3	SEC22 homolog C, vesicle trafficking protein	protein-coding	0.014134	0.405644	
chunk0151_55_1	chr5	42461359	42462181	+	0	NA	intron (NM_001242401, intron 1 of 10)	intron (NM_001242401, intron 1 of 10)	36778	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.003650	0.443499	374(CAGCACAGAATGTCTC,-,0.00),375(AGCACAGAATGTCTCT,+,0.00)
chunk0021_38_1	chr10	870813	871165	+	0	NA	intron (NM_015155, intron 3 of 17)	intron (NM_015155, intron 3 of 17)	60716	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.008523	0.376771	
chunk0036_107_1	chr11	61319682	61320175	+	0	NA	intron (NM_001923, intron 10 of 26)	L1MC4a|LINE|L1	-13254	NM_015533	26007	Hs.6278	NM_015533	ENSG00000149476	TKFC	DAK|NET45	triokinase and FMN cyclase	protein-coding	0.006085	0.350202	
chunk0057_173_1	chr13	102325548	102326091	+	0	NA	intron (NR_036486, intron 3 of 3)	L2a|LINE|L2	-41711	NR_125912	100874081	Hs.569296	NR_125912	ENSG00000234445	FGF14-AS1	-	FGF14 antisense RNA 1	ncRNA	0.007366	0.360294	
chunk0164_370_1	chr6	25804666	25805299	+	0	NA	intron (NM_005074, intron 10 of 12)	L1PB3|LINE|L1	27077	NM_005074	6568	Hs.205816	NM_005074	ENSG00000124568	SLC17A1	NAPI-1|NPT-1|NPT1	solute carrier family 17 member 1	protein-coding	0.003160	0.323344	
chunk0057_407_1	chr13	109777241	109778151	+	0	NA	intron (NM_003749, intron 1 of 1)	intron (NM_003749, intron 1 of 1)	8871	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.006593	0.338090	
chunk0011_413_1	chr1	154380581	154380792	+	0	NA	Intergenic	L1ME3|LINE|L1	-24507	NM_001206866	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.000000	0.292453	
chunk0171_110_1	chr6	122166097	122166656	+	0	NA	Intergenic	HAL1b|LINE|L1	-233175	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.001789	0.307143	
chunk0198_382_1	chr8	141239146	141239712	+	0	NA	intron (NM_001286646, intron 1 of 7)	intron (NM_001286646, intron 1 of 7)	-10855	NM_001080431	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.014134	0.463845	
chunk0160_46_1	chr5	149583457	149583815	+	0	NA	intron (NM_001001669, intron 1 of 12)	intron (NM_001001669, intron 1 of 12)	2064	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.000000	0.431755	
chunk0081_451_1	chr17	49338658	49338918	+	0	NA	intron (NM_014897, intron 1 of 5)	L2|LINE|L2	-22377	NR_110884	102724596	Hs.559253	NR_110882	ENSG00000248714	LOC102724596	-	uncharacterized LOC102724596	ncRNA	0.000000	0.402299	
chunk0035_398_1	chr11	56691099	56691620	+	0	NA	Intergenic	Intergenic	-9029	NM_001005213	390174	Hs.553752	NM_001005213	ENSG00000174914	OR9G1	OR9G5	olfactory receptor family 9 subfamily G member 1	protein-coding	0.005758	0.344828	
chunk0209_147_1	chrX	42274497	42275203	+	0	NA	Intergenic	Intergenic	-351816	NM_001126055	8573	Hs.495984	NM_003688	ENSG00000147044	CASK	CAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK	calcium/calmodulin dependent serine protein kinase	protein-coding	0.001416	0.421499	
chunk0073_156_1	chr16	7456180	7456849	+	0	NA	intron (NM_145892, intron 1 of 12)	intron (NM_145892, intron 1 of 12)	123764	NM_145892	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.013453	0.476119	
chunk0096_233_1	chr2	30804001	30804379	+	0	NA	intron (NM_144575, intron 1 of 22)	MER103C|DNA|hAT-Charlie	3255	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.005291	0.480211	
chunk0022_178_1	chr10	13137945	13138937	+	0	NA	TTS (NM_021980)	TTS (NM_021980)	-23113	NM_182751	55388	Hs.198363	NM_018518	ENSG00000065328	MCM10	CNA43|DNA43|PRO2249	minichromosome maintenance 10 replication initiation factor	protein-coding	0.003024	0.315206	170(AGCCCAGTATGTGCTG,+,0.00)
chunk0018_44_1	chr1	215794089	215794469	+	0	NA	intron (NM_206933, intron 50 of 71)	intron (NM_206933, intron 50 of 71)	226887	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.021053	0.427822	
chunk0076_78_1	chr16	63629139	63629675	+	0	NA	Intergenic	Intergenic	1492730	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.000000	0.474860	
chunk0136_143_1	chr4	4526161	4526973	+	0	NA	intron (NM_016930, intron 1 of 10)	intron (NM_016930, intron 1 of 10)	15481	NM_016930	53407	Hs.584913	NM_016930	ENSG00000168818	STX18	Ufe1	syntaxin 18	protein-coding	0.011084	0.413284	199(GGAACACAGTGTCTAT,+,0.00)
chunk0001_62_1	chr1	2248319	2249035	+	0	NA	intron (NM_003036, intron 1 of 6)	intron (NM_003036, intron 1 of 6)	19982	NM_003036	6497	Hs.656507	NM_003036	ENSG00000157933	SKI	SGS|SKV	SKI proto-oncogene	protein-coding	0.030726	0.563459	321(AGGCACTGGCTGTACC,-,0.00),322(GGCACTGGCTGTACCT,+,0.00)
chunk0117_121_1	chr22	18892373	18892629	+	0	NA	Intergenic	AluSc8|SINE|Alu	-13722	NM_005675	8214	Hs.474185	NM_005675	ENSG00000183628	DGCR6	-	DiGeorge syndrome critical region gene 6	protein-coding	0.011719	0.517510	
chunk0027_9_1	chr10	72030851	72031050	+	0	NA	Intergenic	MER67A|LTR|ERV1	57823	NM_001244950	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.030151	0.620000	32(TGGAACAAACAGTTCT,-,0.00),33(GGAACAAACAGTTCTG,+,0.00)
chunk0053_27_1	chr13	26849293	26849626	+	0	NA	Intergenic	Intergenic	-88674	NM_005288	2835	Hs.123034	NM_005288	ENSG00000132975	GPR12	GPCR12|GPCR21|PPP1R84	G protein-coupled receptor 12	protein-coding	0.009009	0.389222	
chunk0131_201_1	chr3	148689077	148689632	+	0	NA	Intergenic	Intergenic	-8517	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.003604	0.339928	283(AGTAACAATCTGTTCC,-,0.00),284(GTAACAATCTGTTCCC,+,0.00)
chunk0018_227_1	chr1	219714901	219715207	+	0	NA	Intergenic	Intergenic	213597	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.009804	0.472313	
chunk0203_367_1	chr9	89982028	89982526	+	0	NA	intron (NR_109791, intron 2 of 2)	L2|LINE|L2	12861	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.008032	0.515030	232(GGGAACATTCTGTCAC,-,0.00),233(GGAACATTCTGTCACT,+,0.00)
chunk0072_325_1	chr15	99135120	99135580	+	0	NA	TTS (NM_001288616)	TTS (NM_001288616)	30270	NM_145728	23336	Hs.207106	NM_015286	ENSG00000182253	SYNM	DMN|SYN	synemin	protein-coding	0.008696	0.366594	
chunk0053_88_1	chr13	28480741	28481145	+	0	NA	intron (NM_001159920, intron 1 of 12)	intron (NM_001159920, intron 1 of 12)	14185	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.019802	0.446914	108(AGGTCACGTTGTGCTT,+,0.00),211(CAGGACTTCATGTTCT,-,0.00),212(AGGACTTCATGTTCTT,+,0.00)
chunk0006_320_1	chr1	71621918	71622237	+	0	NA	intron (NM_173808, intron 4 of 6)	intron (NM_173808, intron 4 of 6)	214935	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.006270	0.381250	
chunk0203_376_1	chr9	90272020	90272580	+	0	NA	Intergenic	L2a|LINE|L2	161189	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.010714	0.467023	425(GAGAACATACTGTACC,-,0.00),426(AGAACATACTGTACCA,+,0.00)
chunk0021_206_1	chr10	5897479	5898119	+	0	NA	intron (NM_032807, intron 2 of 21)	intron (NM_032807, intron 2 of 21)	3413	NM_032807	84893	Hs.498543	NM_032807	ENSG00000134452	FBH1	FBXO18|Fbx18|hFBH1	F-box DNA helicase 1	protein-coding	0.015625	0.441498	288(CAGAACACAGTGTTCC,-,0.00),289(AGAACACAGTGTTCCA,+,0.00)
chunk0068_278_1	chr15	56732910	56733126	+	0	NA	intron (NM_001002843, intron 1 of 20)	intron (NM_001002843, intron 1 of 20)	1068	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.032407	0.543779	171(CGGCACAAAATGTACC,-,0.00),172(GGCACAAAATGTACCA,+,0.00)
chunk0175_38_1	chr7	907490	907752	+	0	NA	intron (NM_001284308, intron 4 of 10)	intron (NM_001284308, intron 4 of 10)	13268	NM_001284311	11033	Hs.602573	NM_006869	ENSG00000105963	ADAP1	CENTA1|GCS1L|p42IP4	ArfGAP with dual PH domains 1	protein-coding	0.049618	0.627376	152(TGGAACTCTGTGTCCT,-,0.00),153(GGAACTCTGTGTCCTG,+,0.00)
chunk0005_424_1	chr1	62749637	62750046	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-34265	NM_032852	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.002445	0.470732	
chunk0067_235_1	chr15	45467597	45468176	+	0	NA	Intergenic	Intergenic	34836	NR_030599	100126311		NR_030599	ENSG00000284386	MIR147B	MIRN147B|mir-147b	microRNA 147b	ncRNA	0.006908	0.384483	
chunk0180_227_1	chr7	67198553	67198906	+	0	NA	intron (NM_018264, intron 15 of 15)	MER58C|DNA|hAT-Charlie	-84332	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.000000	0.336158	
chunk0203_245_1	chr9	87386471	87386941	+	0	NA	Intergenic	Intergenic	-110522	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.004255	0.418259	
chunk0037_294_1	chr11	76140331	76141113	+	0	NA	exon (NM_003369, exon 15 of 15)	exon (NM_003369, exon 15 of 15)	65808	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.011509	0.469987	
chunk0103_129_1	chr2	162025433	162025948	+	0	NA	intron (NM_001935, intron 10 of 25)	intron (NM_001935, intron 10 of 25)	48852	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.005825	0.420543	
chunk0042_355_1	chr12	10220294	10220910	+	0	NA	intron (NM_031412, intron 3 of 3)	intron (NM_031412, intron 3 of 3)	7712	NM_031412	23710	Hs.524250	NM_031412	ENSG00000139112	GABARAPL1	APG8-LIKE|APG8L|ATG8|ATG8B|ATG8L|GEC1	GABA type A receptor associated protein like 1	protein-coding	0.011364	0.426256	
chunk0122_448_1	chr3	39460658	39460966	+	0	NA	Intergenic	Intergenic	-6761	NR_103505	4336	Hs.121333	NM_182935	ENSG00000168314	MOBP	-	myelin associated oligodendrocyte basic protein	protein-coding	0.006494	0.443366	127(GGGAACACTATGTACA,-,0.00),128(GGAACACTATGTACAT,+,0.00)
chunk0013_8_1	chr1	165738412	165738613	+	0	NA	intron (NM_019026, intron 6 of 6)	intron (NM_019026, intron 6 of 6)	30410	NM_001256165	54499	Hs.31498	NM_019026	ENSG00000143183	TMCO1	HP10122|PCIA3|PNAS-136|TMCC4	transmembrane and coiled-coil domains 1	protein-coding	0.004975	0.316832	
chunk0025_110_1	chr10	51092425	51092688	+	0	NA	intron (NM_006258, intron 1 of 17)	intron (NM_006258, intron 1 of 17)	18082	NM_006258	5592	Hs.407535	NM_006258	ENSG00000185532	PRKG1	AAT8|PKG|PKG1|PRKG1B|PRKGR1B|cGK|cGK 1|cGK1|cGKI|cGKI-BETA|cGKI-alpha	protein kinase cGMP-dependent 1	protein-coding	0.003802	0.488636	
chunk0206_115_1	chr9	120889903	120890171	+	0	NA	intron (NM_001286840, intron 1 of 14)	L2b|LINE|L2	4859	NM_001286840	26147	Hs.460124	NM_015651	ENSG00000119403	PHF19	MTF2L1|PCL3|TDRD19B	PHD finger protein 19	protein-coding	0.000000	0.438662	
chunk0048_39_1	chr12	77998359	77998906	+	0	NA	intron (NM_014903, intron 7 of 38)	intron (NM_014903, intron 7 of 38)	167343	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.003656	0.343066	
chunk0208_339_1	chrX	24988358	24988708	+	0	NA	intron (NM_016937, intron 36 of 36)	intron (NM_016937, intron 36 of 36)	27415	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.008571	0.424501	
chunk0194_57_1	chr8	82200322	82200763	+	0	NA	Intergenic	Intergenic	-358256	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.294118	
chunk0002_104_1	chr1	15538692	15539164	+	0	NA	intron (NR_109898, intron 4 of 14)	intron (NR_109898, intron 4 of 14)	12115	NM_015291	23341	Hs.655410	NM_015291	ENSG00000116138	DNAJC16	-	DnaJ heat shock protein family (Hsp40) member C16	protein-coding	0.014831	0.393235	
chunk0006_242_1	chr1	69088325	69089019	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-591451	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.004323	0.384173	
chunk0024_105_1	chr10	34633246	34633774	+	0	NA	intron (NM_019619, intron 2 of 24)	L1MA7|LINE|L1	181815	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.022727	0.427221	
chunk0160_325_1	chr5	159511411	159512014	+	0	NA	Intergenic	Intergenic	-45436	NR_027110	285627	Hs.552766	NR_027110	ENSG00000253298	LINC01845	-	long intergenic non-protein coding RNA 1845	ncRNA	0.004975	0.432119	
chunk0003_112_1	chr1	32309998	32310485	+	0	NA	intron (NM_004964, intron 2 of 13)	intron (NM_004964, intron 2 of 13)	18134	NM_004964	3065	Hs.88556	NM_004964	ENSG00000116478	HDAC1	GON-10|HD1|KDAC1|RPD3|RPD3L1	histone deacetylase 1	protein-coding	0.004107	0.395492	
chunk0090_92_1	chr18	70683335	70683893	+	0	NA	Intergenic	Intergenic	-32757	NM_001278515									0.008961	0.341682	
chunk0087_337_1	chr18	40156102	40156335	+	0	NA	Intergenic	L1ME2|LINE|L1	89932	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.235043	
chunk0092_32_1	chr19	19059815	19060565	+	0	NA	Intergenic	L2c|LINE|L2	-3804	NM_178526	284439	Hs.303669	NM_178526	ENSG00000181035	SLC25A42	MECREN	solute carrier family 25 member 42	protein-coding	0.013333	0.585885	
chunk0191_320_1	chr8	55774359	55774937	+	0	NA	intron (NM_024831, intron 1 of 12)	L2c|LINE|L2	-1241	NM_001286661	137695	Hs.420076	NM_152417	ENSG00000167904	TMEM68	-	transmembrane protein 68	protein-coding	0.008651	0.347150	296(CAAGACATTCTGTCCT,-,0.00),297(AAGACATTCTGTCCTT,+,0.00)
chunk0150_355_1	chr5	38731406	38731849	+	0	NA	intron (NR_109951, intron 3 of 3)	intron (NR_109951, intron 3 of 3)	-11354	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.009029	0.540541	
chunk0163_157_1	chr6	11054885	11055547	+	0	NA	intron (NR_038964, intron 3 of 4)	intron (NR_038964, intron 3 of 4)	10525	NR_038962	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.006042	0.325792	
chunk0201_371_1	chr9	68710746	68710945	+	0	NA	intron (NM_001278253, intron 1 of 13)	intron (NM_001278253, intron 1 of 13)	5431	NM_001278253	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.000000	0.325000	97(ATGCACAGTAAGTTCT,-,0.00),98(TGCACAGTAAGTTCTT,+,0.00)
chunk0023_201_1	chr10	25209626	25210052	+	0	NA	intron (NM_020752, intron 1 of 10)	intron (NM_020752, intron 1 of 10)	-33563	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.007042	0.377049	
chunk0021_213_1	chr10	5977605	5978007	+	0	NA	promoter-TSS (NM_002189)	promoter-TSS (NM_002189)	-195	NM_001256765	3601	Hs.445124	NM_002189	ENSG00000134470	IL15RA	CD215	interleukin 15 receptor subunit alpha	protein-coding	0.097015	0.702233	
chunk0109_372_1	chr2	239359760	239360166	+	0	NA	intron (NM_006037, intron 1 of 26)	intron (NM_006037, intron 1 of 26)	-8159	NR_039948	100616360		NR_039948	ENSG00000264292	MIR2467	mir-2467	microRNA 2467	ncRNA	0.022167	0.508600	146(GAGAACACAGAGTACT,-,0.00),147(AGAACACAGAGTACTT,+,0.00)
chunk0211_248_1	chrX	120523376	120523824	+	0	NA	TTS (NM_001079872)	TTS (NM_001079872)	37362	NM_001079872	8450	Hs.102914	NM_003588	ENSG00000158290	CUL4B	CUL-4B|MRXHF2|MRXS15|MRXSC|SFM2	cullin 4B	protein-coding	0.002232	0.302895	
chunk0070_47_1	chr15	69484803	69485168	+	0	NA	Intergenic	Intergenic	32165	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.013699	0.549180	
chunk0198_254_1	chr8	134690785	134691287	+	0	NA	intron (NM_001289394, intron 1 of 16)	intron (NM_001289394, intron 1 of 16)	5522	NM_001029939	57623	Hs.446172	NM_020863	ENSG00000066827	ZFAT	AITD3|ZFAT1|ZNF406	zinc finger and AT-hook domain containing	protein-coding	0.001992	0.465209	250(AAGGACAGAGTGTCCA,-,0.00),251(AGGACAGAGTGTCCAA,+,0.00)
chunk0196_62_1	chr8	102260027	102260656	+	0	NA	intron (NM_015902, intron 56 of 58)	MER68B|LTR|ERVL	20890	NR_125415	101927221	Hs.492445	NR_125415	ENSG00000246263	UBR5-AS1	-	UBR5 antisense RNA 1	ncRNA	0.001590	0.398413	
chunk0137_325_1	chr4	24795614	24795834	+	0	NA	intron (NM_003102, intron 1 of 1)	intron (NM_003102, intron 1 of 1)	261	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.013636	0.511312	
chunk0198_409_1	chr8	142383394	142383685	+	0	NA	intron (NM_145003, intron 1 of 13)	intron (NM_145003, intron 1 of 13)	19710	NM_001291931	203062	Hs.370931	NM_145003	ENSG00000171045	TSNARE1	-	t-SNARE domain containing 1	protein-coding	0.017182	0.616438	
chunk0158_99_1	chr5	126680346	126680574	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	48738	NM_207408	389320	Hs.177983	NM_207408	ENSG00000196900	TEX43	C5orf48|Tseg7	testis expressed 43	protein-coding	0.013158	0.537118	
chunk0194_134_1	chr8	84333217	84333459	+	0	NA	intron (NM_001100391, intron 1 of 8)	intron (NM_001100391, intron 1 of 8)	148473	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004132	0.329218	89(ATGCACTAGGTGTTCT,-,0.00),90(TGCACTAGGTGTTCTT,+,0.00)
chunk0204_141_1	chr9	95494429	95494671	+	0	NA	intron (NM_001083606, intron 2 of 23)	intron (NM_001083606, intron 2 of 23)	12649	NM_001083607	5727	Hs.494538	NM_000264	ENSG00000185920	PTCH1	BCNS|NBCCS|PTC|PTC1|PTCH	patched 1	protein-coding	0.061983	0.621399	
chunk0078_189_1	chr17	4898455	4898778	+	0	NA	TTS (NM_153827)	TTS (NM_153827)	-1037	NM_001145536	100130311	Hs.579243	NM_001145536	ENSG00000205710	C17orf107	-	chromosome 17 open reading frame 107	protein-coding	0.034056	0.549383	
chunk0035_156_1	chr11	43370437	43370737	+	0	NA	intron (NM_018259, intron 1 of 23)	intron (NM_018259, intron 1 of 23)	11702	NM_018259	55761	Hs.191186	NM_018259	ENSG00000052841	TTC17	-	tetratricopeptide repeat domain 17	protein-coding	0.010000	0.289037	
chunk0085_305_1	chr18	8140023	8140553	+	0	NA	intron (NM_001105244, intron 13 of 32)	intron (NM_001105244, intron 13 of 32)	226746	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.013208	0.448211	280(GAGTACATCGTGTTCT,-,0.00),281(AGTACATCGTGTTCTC,+,0.00)
chunk0046_17_1	chr12	54230446	54230994	+	0	NA	TTS (NR_039851)	TTS (NR_039851)	756	NR_039851	100616400		NR_039851	ENSG00000283803	MIR3198-2	mir-3198-2	microRNA 3198-2	ncRNA	0.003650	0.398907	259(AGGTACACACTGAACC,-,0.00)
chunk0191_242_1	chr8	53038937	53039482	+	0	NA	Intergenic	L1PREC2|LINE|L1	99301	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.003670	0.342491	
chunk0176_257_1	chr7	16293395	16293832	+	0	NA	intron (NM_001101417, intron 4 of 8)	intron (NM_001101417, intron 4 of 8)	83127	NR_038947	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.004577	0.360731	
chunk0109_234_1	chr20	5956033	5956232	+	0	NA	intron (NM_182802, intron 5 of 18)	intron (NM_182802, intron 5 of 18)	5480	NM_001281520	84515	Hs.597484	NM_032485	ENSG00000125885	MCM8	C20orf154|POF10|dJ967N21.5	minichromosome maintenance 8 homologous recombination repair factor	protein-coding	0.005025	0.465000	
chunk0202_233_1	chr9	76516957	76517511	+	0	NA	Intergenic	MIR|SINE|MIR	16601	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.005415	0.390991	
chunk0003_462_1	chr1	41789717	41790737	+	0	NA	intron (NM_024503, intron 1 of 8)	MSTB1|LTR|ERVL-MaLR	128480	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.006863	0.467189	
chunk0020_168_1	chr1	234437761	234438104	+	0	NA	intron (NM_005646, intron 12 of 29)	L1MEf|LINE|L1	41171	NM_005646	6894	Hs.498115	NM_005646	ENSG00000059588	TARBP1	TRM3|TRMT3|TRP-185|TRP185	TAR (HIV-1) RNA binding protein 1	protein-coding	0.011662	0.534884	
chunk0026_364_1	chr10	69250703	69251149	+	0	NA	intron (NM_025130, intron 12 of 17)	intron (NM_025130, intron 12 of 17)	-18436	NR_120648	101928994	Hs.562925	NR_120648	ENSG00000229261	LOC101928994	-	uncharacterized LOC101928994	ncRNA	0.008969	0.380313	
chunk0116_39_1	chr21	33474803	33475025	+	0	NA	intron (NR_040016, intron 1 of 8)	L1ME3D|LINE|L1	5095	NM_006134	757	Hs.433668	NM_006134	ENSG00000142188	TMEM50B	C21orf4|HCVP7TP3	transmembrane protein 50B	protein-coding	0.009009	0.399103	
chunk0074_360_1	chr16	34571454	34573239	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	-412310	NR_038368									0.037616	0.361481	
chunk0125_151_1	chr3	66418451	66418855	+	0	NA	intron (NM_015541, intron 3 of 18)	intron (NM_015541, intron 3 of 18)	81768	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.029703	0.508642	
chunk0065_207_1	chr14	100132289	100132797	+	0	NA	intron (NM_016337, intron 7 of 13)	intron (NM_016337, intron 7 of 13)	22888	NR_029888	442909		NR_029888	ENSG00000199082	MIR342	MIRN342|hsa-mir-342	microRNA 342	ncRNA	0.029528	0.587426	104(GGGGACAGAGCGTGCC,-,0.00),105(GGGACAGAGCGTGCCC,+,0.00)
chunk0019_164_1	chr1	226001853	226002342	+	0	NA	Intergenic	Intergenic	-2732	NM_152608	163859	Hs.520192	NM_152608	ENSG00000143751	SDE2	C1orf55|dJ671D7.1	SDE2 telomere maintenance homolog	protein-coding	0.006135	0.416327	
chunk0084_310_1	chr17	80258767	80259078	+	0	NA	Intergenic	Intergenic	-1939	NM_020954	57674	Hs.195642	NM_020914	ENSG00000173821	RNF213	ALO17|C17orf27|KIAA1618|MYMY2|MYSTR|NET57	ring finger protein 213	protein-coding	0.022508	0.461538	
chunk0129_19_1	chr3	117064238	117064765	+	0	NA	Intergenic	L2|LINE|L2	143070	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.007590	0.393939	
chunk0041_121_1	chr11	125019501	125019882	+	0	NA	intron (NM_025004, intron 13 of 15)	L2c|LINE|L2	-43426	NM_001145290	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.005249	0.379581	187(GGGTACATGTTGTACT,-,0.00),188(GGTACATGTTGTACTA,+,0.00)
chunk0175_213_1	chr7	6055472	6055696	+	0	NA	intron (NM_001134335, intron 1 of 14)	intron (NM_001134335, intron 1 of 14)	3645	NM_014413	27102	Hs.520205	NM_014413	ENSG00000086232	EIF2AK1	HCR|HRI	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.013393	0.404444	
chunk0013_344_1	chr1	172125452	172125819	+	0	NA	intron (NM_001136127, intron 13 of 19)	intron (NM_001136127, intron 13 of 19)	-13173	NR_036066	100422882		NR_036066	ENSG00000283152	MIR3120	mir-3120	microRNA 3120	ncRNA	0.002725	0.369565	
chunk0005_196_1	chr1	58982541	58983045	+	0	NA	Intergenic	Intergenic	-37683	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.007937	0.499010	
chunk0169_255_1	chr6	105302035	105302837	+	0	NA	intron (NM_002726, intron 10 of 14)	intron (NM_002726, intron 10 of 14)	100688	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.033666	0.489415	
chunk0010_218_1	chr1	116207004	116207744	+	0	NA	Intergenic	L1ME3|LINE|L1	95619	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.005405	0.380567	
chunk0185_263_1	chr7	130423470	130424075	+	0	NA	intron (NM_001257160, intron 2 of 2)	L1MB7|LINE|L1	17438	NM_001257158	95681	Hs.368315	NM_018718	ENSG00000106477	CEP41	JBTS15|TSGA14	centrosomal protein 41	protein-coding	0.004959	0.361386	
chunk0102_371_1	chr2	153378061	153378510	+	0	NA	Intergenic	(ATAG)n|Simple_repeat|Simple_repeat	100523	NM_019845	56475	Hs.100890	NM_019845	ENSG00000177519	RPRM	REPRIMO	reprimo, TP53 dependent G2 arrest mediator homolog	protein-coding	0.000000	0.275556	
chunk0170_14_1	chr6	109095774	109095973	+	0	NA	intron (NM_001271852, intron 1 of 10)	intron (NM_001271852, intron 1 of 10)	720	NM_001083535	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.045226	0.525000	
chunk0082_16_1	chr17	50318846	50319269	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-26975	NM_022167	64132	Hs.463416	NM_022167	ENSG00000015532	XYLT2	PXYLT2|SOS|XT-II|XT2|xylT-II	xylosyltransferase 2	protein-coding	0.016548	0.516509	
chunk0015_79_1	chr1	184818669	184818914	+	0	NA	exon (NM_052966, exon 9 of 14)	exon (NM_052966, exon 9 of 14)	-63884	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.024490	0.536585	
chunk0120_289_1	chr3	9792689	9793144	+	0	NA	promoter-TSS (NM_001198780)	promoter-TSS (NM_001198780)	95	NM_133480	10474	Hs.386390	NM_006354	ENSG00000171148	TADA3	ADA3|NGG1|STAF54|TADA3L|hADA3	transcriptional adaptor 3	protein-coding	0.074725	0.600877	
chunk0072_11_1	chr16	388322	388858	+	0	NA	intron (NR_024453, intron 2 of 2)	LTR5B|LTR|ERVK	6349	NR_024453	100134368	Hs.621241	NR_024453	ENSG00000236829	LOC100134368	-	uncharacterized LOC100134368	ncRNA	0.018657	0.474860	199(CAGTGCACTGTGTCCC,-,0.00),200(AGTGCACTGTGTCCCT,+,0.00)
chunk0206_32_1	chr9	116435139	116435677	+	0	NA	intron (NM_198186, intron 7 of 7)	intron (NM_198186, intron 7 of 7)	-34802	NR_103711	493913	Hs.728832	NR_103711	ENSG00000256040	PAPPA-AS1	DIPAS|NCRNA00156|PAPPA-AS|PAPPAAS|PAPPAS|TAF2C2|TAF4B|TAFII105	PAPPA antisense RNA 1	ncRNA	0.001859	0.419295	
chunk0182_226_1	chr7	96447075	96447692	+	0	NA	Intergenic	Intergenic	56140	NM_001201451	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.009724	0.320388	
chunk0034_244_1	chr11	34168706	34169265	+	0	NA	intron (NM_145804, intron 5 of 16)	intron (NM_145804, intron 5 of 16)	63421	NM_001144030	55226	Hs.577281	NM_024662	ENSG00000135372	NAT10	ALP|Kre33|NET43	N-acetyltransferase 10	protein-coding	0.017889	0.480357	
chunk0122_380_1	chr3	37753266	37753983	+	0	NA	TTS (NR_110531)	TTS (NR_110531)	108156	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.005579	0.452646	34(CAGAACTCACTGTCTT,-,0.00),35(AGAACTCACTGTCTTG,+,0.00)
chunk0161_52_1	chr5	166074998	166075404	+	0	NA	Intergenic	LTR85c|LTR|Gypsy?	851169	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.002463	0.452088	
chunk0092_115_1	chr19	24191261	24191752	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-28059	NR_003603	100101266	Hs.149312	NR_003603	ENSG00000268442	HAVCR1P1	-	hepatitis A virus cellular receptor 1 pseudogene 1	pseudo	0.008147	0.406504	
chunk0088_302_1	chr18	50174891	50175135	+	0	NA	intron (NM_001080467, intron 1 of 39)	intron (NM_001080467, intron 1 of 39)	20068	NM_001080467	4645	Hs.720076	NM_001080467	ENSG00000167306	MYO5B	-	myosin VB	protein-coding	0.004098	0.506122	
chunk0011_163_1	chr1	147637826	147638376	+	0	NA	Intergenic	L2a|LINE|L2	32411	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.003636	0.370236	
chunk0028_427_1	chr10	93710189	93710693	+	0	NA	Intergenic	Intergenic	-7869	NM_145246	118924	Hs.586650	NM_145246	ENSG00000148690	FRA10AC1	C10orf4|F26C11.1-like|FRA10A	FRA10A associated CGG repeat 1	protein-coding	0.007937	0.469307	186(AAGGACTGAAAGTTCC,-,0.00),187(AGGACTGAAAGTTCCC,+,0.00)
chunk0114_28_1	chr21	7924911	7925245	+	0	NA	Intergenic	(ATTCCATTCC)n|Simple_repeat|Simple_repeat	-154530	NM_001282537	101928147	Hs.303798	NM_001282537	ENSG00000222018	FAM243A	C21orf140	family with sequence similarity 243 member A	protein-coding	0.020958	0.385075	76(GAGTACGTTCTGTTCC,-,0.00),77(AGTACGTTCTGTTCCA,+,0.00)
chunk0056_226_1	chr13	88586811	88587138	+	0	NA	Intergenic	Intergenic	46145	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.006116	0.286585	
chunk0093_5_1	chr2	33662	34353	+	0	NA	Intergenic	Intergenic	12581	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.015919	0.452312	
chunk0071_151_1	chr15	82890935	82891473	+	0	NA	intron (NM_199330, intron 2 of 8)	intron (NM_199330, intron 2 of 8)	61520	NM_004839	9455	Hs.578443	NM_004839	ENSG00000103942	HOMER2	ACPD|CPD|DFNA68|HOMER-2|VESL-2	homer scaffold protein 2	protein-coding	0.013011	0.523191	
chunk0062_14_1	chr14	66269818	66270382	+	0	NA	Intergenic	Intergenic	-216271	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.005319	0.472566	203(AGGATCACAGTGTCCA,-,0.00),204(GGATCACAGTGTCCAT,+,0.00)
chunk0146_44_1	chr4	155508079	155508356	+	0	NA	Intergenic	Intergenic	-131247	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.003610	0.323741	
chunk0181_410_1	chr7	90157411	90157861	+	0	NA	intron (NM_012449, intron 1 of 4)	MLT1K|LTR|ERVL-MaLR	3261	NM_012449	26872	Hs.61635	NM_012449	ENSG00000164647	STEAP1	PRSS24|STEAP	STEAP family member 1	protein-coding	0.006667	0.365854	
chunk0190_145_1	chr8	30902045	30902449	+	0	NA	Intergenic	Intergenic	-53230	NM_031271									0.007426	0.400000	
chunk0037_186_1	chr11	74138303	74138938	+	0	NA	intron (NM_001286577, intron 5 of 32)	intron (NM_001286577, intron 5 of 32)	32399	NM_015531	26005	Hs.557938	NM_015531	ENSG00000168014	C2CD3	OFD14	C2 domain containing 3 centriole elongation regulator	protein-coding	0.007874	0.391509	
chunk0023_350_1	chr10	29688407	29688675	+	0	NA	intron (NM_003174, intron 1 of 35)	intron (NM_003174, intron 1 of 35)	47260	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.007463	0.431227	
chunk0068_272_1	chr15	56677180	56677667	+	0	NA	intron (NM_001002843, intron 11 of 20)	intron (NM_001002843, intron 11 of 20)	56663	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.002053	0.354508	152(TAGCACAGTAAGTCCA,-,0.00),153(AGCACAGTAAGTCCAT,+,0.00)
chunk0114_42_1	chr21	8420102	8420562	+	0	NA	Intergenic	(TCTC)n|Simple_repeat|Simple_repeat	-12198	NR_128716	103504739		NR_128716	ENSG00000277379	MIR6724-3	hsa-mir-6724-3	microRNA 6724-3	ncRNA	0.002174	0.496746	
chunk0121_316_1	chr3	24237627	24238268	+	0	NA	intron (NM_000461, intron 2 of 9)	intron (NM_000461, intron 2 of 9)	86623	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.009360	0.440810	
chunk0009_180_1	chr1	105669356	105669875	+	0	NA	Intergenic	L2c|LINE|L2	-50680	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001927	0.328846	
chunk0045_5_1	chr12	42915322	42915923	+	0	NA	Intergenic	Intergenic	-269124	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.006656	0.390365	
chunk0151_296_1	chr5	52922324	52922550	+	0	NA	intron (NM_181501, intron 17 of 28)	intron (NM_181501, intron 17 of 28)	-66889	NR_073104	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.004425	0.392070	
chunk0127_181_1	chr3	95460301	95460805	+	0	NA	Intergenic	Intergenic	222640	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.003968	0.392079	286(AAGCACAATTTGTGCT,-,0.00),287(AGCACAATTTGTGCTT,+,0.00)
chunk0005_352_1	chr1	61322435	61323400	+	0	NA	intron (NM_001145511, intron 3 of 10)	L2a|LINE|L2	-69399	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.005181	0.381988	
chunk0066_59_1	chr15	28800310	28800699	+	0	NA	intron (NR_037599, intron 3 of 13)	intron (NR_037599, intron 3 of 13)	10670	NR_037599	646278	Hs.590143	NR_037599		PDCD6IPP2	-	PDCD6IP pseudogene 2	pseudo	0.000000	0.374359	
chunk0031_311_1	chr10	128871005	128871507	+	0	NA	Intergenic	Intergenic	585306	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.015936	0.538767	115(AGGTACACACCGTTCT,-,0.00),116(GGTACACACCGTTCTT,+,0.00)
chunk0120_429_1	chr3	13314483	13314715	+	0	NA	Intergenic	Intergenic	105720	NM_024923	23225	Hs.475525	NM_024923	ENSG00000132182	NUP210	GP210|POM210	nucleoporin 210	protein-coding	0.012931	0.626609	209(CAGGACACCCTGTCCC,-,0.00),210(AGGACACCCTGTCCCA,+,0.00)
chunk0154_195_1	chr5	80230554	80230753	+	0	NA	intron (NM_178276, intron 1 of 12)	MIRb|SINE|MIR	25429	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.010050	0.450000	
chunk0016_371_1	chr1	202528196	202528618	+	0	NA	intron (NM_002481, intron 18 of 23)	intron (NM_002481, intron 18 of 23)	-11707	NM_001197131	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.004739	0.397163	
chunk0068_334_1	chr15	57635452	57636019	+	0	NA	intron (NR_104371, intron 8 of 16)	intron (NR_104371, intron 8 of 16)	43831	NM_001285900	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.007055	0.433099	291(GTGAACGGCATGTCCT,-,0.00)
chunk0038_395_1	chr11	93645584	93646157	+	0	NA	Intergenic	Intergenic	-15780	NM_033395	85459	Hs.458418	NM_033395	ENSG00000166004	CEP295	KIAA1731	centrosomal protein 295	protein-coding	0.008726	0.388502	
chunk0029_171_1	chr10	100341540	100342412	+	0	NA	Intergenic	Intergenic	-5039	NM_005063	6319	Hs.558396	NM_005063	ENSG00000099194	SCD	FADS5|MSTP008|SCD1|SCDOS|hSCD1	stearoyl-CoA desaturase	protein-coding	0.012615	0.523482	754(GGGACTGTCAGTACCC,+,0.00)
chunk0086_23_1	chr18	12408020	12408240	+	0	NA	intron (NM_001142405, intron 1 of 6)	CpG	234	NM_006553	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.150000	0.773756	
chunk0006_248_1	chr1	69272598	69273211	+	0	NA	Intergenic	L2c|LINE|L2	-487271	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.009788	0.348534	583(AAGAACAAAGTGTGCA,-,0.00),584(AGAACAAAGTGTGCAA,+,0.00)
chunk0055_133_1	chr13	59363303	59363540	+	0	NA	Intergenic	Intergenic	-649297	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.008439	0.432773	
chunk0126_159_1	chr3	77688836	77689311	+	0	NA	Intergenic	MER34B|LTR|ERV1	591061	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.006316	0.415966	
chunk0122_442_1	chr3	39348988	39349439	+	0	NA	Intergenic	HERV15-int|LTR|ERV1	19507	NM_005201	1237	Hs.113222	NM_005201	ENSG00000179934	CCR8	CC-CKR-8|CCR-8|CDw198|CKRL1|CMKBR8|CMKBRL2|CY6|GPRCY6|TER1	C-C motif chemokine receptor 8	protein-coding	0.006652	0.442478	
chunk0146_191_1	chr4	161200881	161201141	+	0	NA	Intergenic	Intergenic	-821722	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.291188	
chunk0094_280_1	chr2	8230745	8231328	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	97383	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.003431	0.390411	
chunk0032_35_1	chr11	1051076	1051275	+	0	NA	Intergenic	Intergenic	-14469	NM_005961	4588	Hs.528432	NM_005961	ENSG00000184956	MUC6	MUC-6	mucin 6, oligomeric mucus/gel-forming	protein-coding	0.040201	0.690000	
chunk0139_176_1	chr4	54064583	54065068	+	0	NA	promoter-TSS (NM_012110)	promoter-TSS (NM_012110)	-177	NM_012110	26511	Hs.335393	NM_012110	ENSG00000109220	CHIC2	BTL	cysteine rich hydrophobic domain 2	protein-coding	0.113402	0.660494	347(TGGGACATGCAGTTCC,-,0.00),348(GGGACATGCAGTTCCC,+,0.00)
chunk0011_32_1	chr1	143223459	143223668	+	0	NA	Intergenic	Intergenic	199029	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.047847	0.385714	
chunk0008_355_1	chr1	96387743	96387972	+	0	NA	Intergenic	Intergenic	-13732	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.008734	0.395652	
chunk0075_316_1	chr16	54489832	54490060	+	0	NA	Intergenic	Intergenic	-203480	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.008772	0.366812	
chunk0133_347_1	chr3	173075993	173076207	+	0	NA	intron (NM_031955, intron 2 of 10)	intron (NM_031955, intron 2 of 10)	65168	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.014019	0.306977	
chunk0193_199_1	chr8	75844872	75845140	+	0	NA	Intergenic	Intergenic	305038	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.000000	0.319703	
chunk0085_366_1	chr18	9428208	9428656	+	0	NA	Intergenic	Intergenic	-47100	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.024554	0.536748	
chunk0024_416_1	chr10	45502369	45502797	+	0	NA	intron (NM_001002266, intron 2 of 6)	L1MEf|LINE|L1	32811	NM_001282866	220972	Hs.499489	NM_145021	ENSG00000165406	MARCH8	CMIR|MARCH-VIII|MIR|RNF178|c-MIR	membrane associated ring-CH-type finger 8	protein-coding	0.004673	0.344988	
chunk0090_407_1	chr18	78809632	78810053	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-170433	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.023753	0.488152	
chunk0085_377_1	chr18	9653463	9653669	+	0	NA	Intergenic	Intergenic	38302	NR_110774	101927323	Hs.151204	NR_110773	ENSG00000263627	PPP4R1-AS1	-	PPP4R1 antisense RNA 1	ncRNA	0.014563	0.560386	
chunk0063_60_1	chr14	77099465	77099876	+	0	NA	intron (NM_033426, intron 1 of 3)	intron (NM_033426, intron 1 of 3)	1435	NM_033426	85457	Hs.709066	NM_033426	ENSG00000198894	CIPC	KIAA1737	CLOCK interacting pacemaker	protein-coding	0.009732	0.378641	
chunk0206_163_1	chr9	121738889	121739190	+	0	NA	intron (NM_032552, intron 3 of 16)	L2a|LINE|L2	-3746	NM_138709	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.000000	0.456954	
chunk0100_432_1	chr2	120422275	120422777	+	0	NA	Intergenic	Intergenic	43823	NR_027181	84931	Hs.334519	NM_032845	ENSG00000280409	LINC01101	-	long intergenic non-protein coding RNA 1101	ncRNA	0.011952	0.457256	
chunk0040_85_1	chr11	111446516	111446822	+	0	NA	Intergenic	Intergenic	-28483	NR_046085	100132078	Hs.672662	NR_046085	ENSG00000255428	LOC100132078	-	uncharacterized LOC100132078	ncRNA	0.006536	0.472313	
chunk0206_406_1	chr9	127303874	127304156	+	0	NA	intron (NR_104591, intron 2 of 26)	intron (NR_104591, intron 2 of 26)	39538	NR_104591	84253	Hs.29304	NM_032293	ENSG00000136895	GARNL3	bA356B19.1	GTPase activating Rap/RanGAP domain like 3	protein-coding	0.000000	0.409894	
chunk0204_49_1	chr9	93136189	93136388	+	0	NA	Intergenic	Intergenic	-2000	NM_004148	4814	Hs.494457	NM_004148	ENSG00000131669	NINJ1	NIN1|NINJURIN	ninjurin 1	protein-coding	0.025126	0.555000	
chunk0065_275_1	chr14	102057396	102057618	+	0	NA	Intergenic	L2a|LINE|L2	29668	NM_005348	3320	Hs.525600	NM_005348	ENSG00000080824	HSP90AA1	EL52|HEL-S-65p|HSP86|HSP89A|HSP90A|HSP90N|HSPC1|HSPCA|HSPCAL1|HSPCAL4|HSPN|Hsp103|Hsp89|Hsp90|LAP-2|LAP2	heat shock protein 90 alpha family class A member 1	protein-coding	0.027027	0.520179	
chunk0079_33_1	chr17	10126411	10126610	+	0	NA	intron (NM_201433, intron 1 of 13)	(CA)n|Simple_repeat|Simple_repeat	72041	NM_201433	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.075377	0.535000	
chunk0134_411_1	chr3	183210783	183210982	+	0	NA	intron (NM_015078, intron 22 of 29)	intron (NM_015078, intron 22 of 29)	-42362	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.000000	0.500000	
chunk0048_104_1	chr12	79403965	79404301	+	0	NA	intron (NM_001291901, intron 8 of 9)	intron (NM_001291901, intron 8 of 9)	-15124	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.002976	0.344214	
chunk0114_365_1	chr21	19864272	19864984	+	0	NA	Intergenic	Intergenic	938480	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005618	0.374474	
chunk0039_446_1	chr11	108340955	108341224	+	0	NA	intron (NM_000051, intron 56 of 62)	L2a|LINE|L2	118257	NM_000051	472	Hs.367437	NM_000051	ENSG00000149311	ATM	AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1	ATM serine/threonine kinase	protein-coding	0.000000	0.451852	
chunk0091_69_1	chr19	4976333	4976955	+	0	NA	intron (NM_015015, intron 1 of 22)	intron (NM_015015, intron 1 of 22)	7531	NM_015015	23030	Hs.654816	NM_015015	ENSG00000127663	KDM4B	JMJD2B|TDRD14B	lysine demethylase 4B	protein-coding	0.040193	0.531300	
chunk0041_297_1	chr11	129642058	129642631	+	0	NA	Intergenic	Intergenic	-25075	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.001745	0.381533	
chunk0065_346_1	chr14	103576685	103576982	+	0	NA	intron (NR_126431, intron 4 of 5)	intron (NR_126431, intron 4 of 5)	13876	NM_001302653	84334	Hs.598441	NM_001302652	ENSG00000256053	COA8	APOP|APOP1|APOPT1|C14orf153	cytochrome c oxidase assembly factor 8	protein-coding	0.016835	0.580537	
chunk0130_70_1	chr3	129913563	129913938	+	0	NA	Intergenic	Intergenic	19879	NR_037893	100507032	Hs.529562	NR_037893	ENSG00000271270	TMCC1-AS1	-	TMCC1 antisense RNA 1 (head to head)	ncRNA	0.005333	0.515957	
chunk0007_440_1	chr1	86869065	86869287	+	0	NA	intron (NM_004261, intron 3 of 4)	L1M5|LINE|L1	45248	NM_004261	9403	Hs.362728	NM_004261	ENSG00000183291	SELENOF	SEP15	selenoprotein F	protein-coding	0.009009	0.367713	
chunk0062_187_1	chr14	69755558	69756296	+	0	NA	Intergenic	Intergenic	-11185	NM_001039465	6430	Hs.632326	NM_006925	ENSG00000100650	SRSF5	HRS|SFRS5|SRP40	serine and arginine rich splicing factor 5	protein-coding	0.002710	0.431664	
chunk0161_109_1	chr5	167513310	167513782	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	228708	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.016949	0.399577	
chunk0114_247_1	chr21	16024521	16025570	+	0	NA	Intergenic	Intergenic	-45477	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002860	0.295238	
chunk0070_82_1	chr15	70098624	70099084	+	0	NA	promoter-TSS (NM_001282980)	promoter-TSS (NM_001282980)	-937	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.093478	0.707158	253(GGGAACTCCGAGTTCC,-,0.00),254(GGAACTCCGAGTTCCC,+,0.00)
chunk0133_265_1	chr3	171788646	171789299	+	0	NA	intron (NM_001130081, intron 1 of 25)	L2b|LINE|L2	21522	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.009188	0.425076	
chunk0129_441_1	chr3	128065221	128065765	+	0	NA	intron (NM_013336, intron 8 of 11)	intron (NM_013336, intron 8 of 11)	-10317	NR_046645	100874089	Hs.581603	NR_046645	ENSG00000239608	RUVBL1-AS1	-	RUVBL1 antisense RNA 1	ncRNA	0.012868	0.352294	
chunk0096_390_1	chr2	37617484	37617894	+	0	NA	Intergenic	Intergenic	54510	NM_001270438	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.017073	0.403893	
chunk0099_335_1	chr2	100056436	100056828	+	0	NA	intron (NM_001025108, intron 2 of 23)	L3|LINE|CR1	48951	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.005102	0.353690	
chunk0169_93_1	chr6	99990236	99990527	+	0	NA	intron (NM_032503, intron 1 of 5)	intron (NM_032503, intron 1 of 5)	-3657	NR_038384	728012	Hs.434366	NR_038384	ENSG00000229315	MCHR2-AS1	-	MCHR2 antisense RNA 1	ncRNA	0.000000	0.328767	
chunk0156_323_1	chr5	111498240	111498517	+	0	NA	non-coding (NR_131754, exon 5 of 5)	non-coding (NR_131754, exon 5 of 5)	-13848	NR_040093	100505678	Hs.745061	NR_040093	ENSG00000246859	STARD4-AS1	-	STARD4 antisense RNA 1	ncRNA	0.007220	0.356115	112(AGGGACATCCAGTTCA,-,0.00),113(GGGACATCCAGTTCAG,+,0.00)
chunk0198_388_1	chr8	141290291	141290777	+	0	NA	Intergenic	Intergenic	-35905	NM_001286646	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.034979	0.552361	
chunk0166_353_1	chr6	51203865	51204430	+	0	NA	Intergenic	Intergenic	385421	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.003540	0.326855	
chunk0143_385_1	chr4	122700025	122700677	+	0	NA	Intergenic	MER70A|LTR|ERVL	32107	NR_024041	729338	Hs.647968	NR_024041		CETN4P	-	centrin 4, pseudogene	pseudo	0.012270	0.488515	297(CGGAACAGCCTGGGCT,-,0.00),298(GGAACAGCCTGGGCTC,+,0.00),335(CAGCACAGGATGTCCT,-,0.00),336(AGCACAGGATGTCCTC,+,0.00)
chunk0206_413_1	chr9	127453620	127454010	+	0	NA	intron (NM_001005374, intron 1 of 24)	L2b|LINE|L2	1560	NM_001005374	90678	Hs.495188	NM_138361	ENSG00000148356	LRSAM1	CMT2P|RIFLE|TAL	leucine rich repeat and sterile alpha motif containing 1	protein-coding	0.012821	0.519182	158(AAGAACAAGGAGTACT,-,0.00),159(AGAACAAGGAGTACTG,+,0.00)
chunk0110_229_1	chr20	15954637	15954990	+	0	NA	intron (NM_001033087, intron 8 of 13)	MIR|SINE|MIR	31069	NR_130924	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.000000	0.341808	
chunk0134_161_1	chr3	177852380	177852612	+	0	NA	intron (NR_110826, intron 1 of 2)	intron (NR_110826, intron 1 of 2)	35631	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.008621	0.300429	
chunk0210_145_1	chrX	75351703	75352163	+	0	NA	Intergenic	L1PA7|LINE|L1	77874	NR_030774	139596	Hs.91612	NM_145052	ENSG00000094841	UPRT	FUR1|UPP	uracil phosphoribosyltransferase homolog	protein-coding	0.006522	0.392625	
chunk0128_75_1	chr3	105356874	105357277	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	-9638	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.002481	0.413366	
chunk0129_304_1	chr3	123660992	123661231	+	0	NA	intron (NM_053025, intron 23 of 33)	intron (NM_053025, intron 23 of 33)	-28533	NR_046629	100873940	Hs.667316	NR_046629	ENSG00000250174	MYLK-AS2	-	MYLK antisense RNA 2	ncRNA	0.037657	0.575000	
chunk0024_166_1	chr10	35633504	35633735	+	0	NA	Intergenic	Intergenic	7633	NR_039831	100616500		NR_039831	ENSG00000284265	MIR4683	-	microRNA 4683	ncRNA	0.012987	0.495690	
chunk0112_242_1	chr20	41399445	41399895	+	0	NA	Intergenic	Intergenic	-32812	NM_052846	90187	Hs.726525	NM_052846	ENSG00000183798	EMILIN3	C20orf130|EMILIN5|dJ620E11.4	elastin microfibril interfacer 3	protein-coding	0.006667	0.472284	
chunk0024_403_1	chr10	45178757	45179352	+	0	NA	intron (NR_033891, intron 6 of 7)	intron (NR_033891, intron 6 of 7)	15040	NR_036112	100422988		NR_036112	ENSG00000263476	MIR3156-1	mir-3156-1	microRNA 3156-1	ncRNA	0.001681	0.365772	
chunk0064_182_1	chr14	92694111	92694327	+	0	NA	Intergenic	LTR40a|LTR|ERVL	54483	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.023148	0.552995	
chunk0116_104_1	chr21	35367630	35368083	+	0	NA	Intergenic	Intergenic	212908	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.011038	0.405286	
chunk0005_284_1	chr1	60094445	60095154	+	0	NA	Intergenic	L1ME3A|LINE|L1	-21029	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.004231	0.343662	
chunk0101_390_1	chr2	138683677	138684278	+	0	NA	intron (NM_007226, intron 1 of 1)	intron (NM_007226, intron 1 of 1)	96264	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.000000	0.303987	
chunk0086_85_1	chr18	13542122	13542589	+	0	NA	intron (NM_181481, intron 3 of 5)	intron (NM_181481, intron 3 of 5)	-68759	NR_039752	100616130		NR_039752	ENSG00000263527	MIR4526	mir-4526	microRNA 4526	ncRNA	0.023555	0.532051	
chunk0098_170_1	chr2	70708037	70708367	+	0	NA	intron (NM_001185055, intron 1 of 11)	intron (NM_001185055, intron 1 of 11)	59513	NM_001185054	119	Hs.66187	NM_001617	ENSG00000075340	ADD2	ADDB	adducin 2	protein-coding	0.006061	0.510574	
chunk0136_445_1	chr3	197949837	197950067	+	0	NA	promoter-TSS (NM_001134435)	promoter-TSS (NM_001134435)	-27	NM_001134435	84223	Hs.591675	NM_032263	ENSG00000114473	IQCG	CFAP122|DRC9	IQ motif containing G	protein-coding	0.034783	0.467532	
chunk0178_262_1	chr7	36348366	36348565	+	0	NA	intron (NM_001300956, intron 1 of 5)	MER102b|DNA|hAT-Charlie	18708	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.000000	0.375000	
chunk0124_22_1	chr3	51942226	51942528	+	0	NA	promoter-TSS (NM_004704)	promoter-TSS (NM_004704)	72	NM_001003931	10039	Hs.271742	NM_005485	ENSG00000041880	PARP3	ADPRT3|ADPRTL2|ADPRTL3|ARTD3|IRT1|PADPRT-3	poly(ADP-ribose) polymerase family member 3	protein-coding	0.096026	0.693069	
chunk0157_145_1	chr5	117561768	117562264	+	0	NA	intron (NR_046089, intron 5 of 5)	L1ME3A|LINE|L1	146504	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.006048	0.289738	
chunk0088_308_1	chr18	50472094	50472338	+	0	NA	Intergenic	Intergenic	-87898	NM_002747	5596	Hs.433728	NM_002747	ENSG00000141639	MAPK4	ERK-4|ERK4|PRKM4|p63-MAPK|p63MAPK	mitogen-activated protein kinase 4	protein-coding	0.008197	0.420408	190(TAGAACAAGGTGTGCC,-,0.00),191(AGAACAAGGTGTGCCA,+,0.00)
chunk0207_227_1	chr9	131754945	131755247	+	0	NA	Intergenic	Intergenic	-15152	NM_001304275	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.013245	0.498350	
chunk0196_336_1	chr8	113871778	113872093	+	0	NA	Intergenic	L1PA10|LINE|L1	-434922	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.000000	0.325949	
chunk0003_331_1	chr1	38826168	38826695	+	0	NA	Intergenic	Intergenic	33392	NM_001271851	64121	Hs.532461	NM_022157	ENSG00000116954	RRAGC	GTR2|RAGC|TIB929	Ras related GTP binding C	protein-coding	0.005693	0.323864	248(AGGTACAGTAAGTGCC,-,0.00),249(GGTACAGTAAGTGCCT,+,0.00)
chunk0106_69_1	chr2	196885785	196886236	+	0	NA	intron (NM_024989, intron 10 of 26)	intron (NM_024989, intron 10 of 26)	40720	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.008869	0.358407	
chunk0152_85_1	chr5	58127383	58128444	+	0	NA	Intergenic	Intergenic	-5572	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.011310	0.404896	573(CAGCACAGCCTCTTCT,-,0.00),574(AGCACAGCCTCTTCTT,+,0.00)
chunk0209_18_1	chrX	35449301	35449881	+	0	NA	Intergenic	Intergenic	-348751	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.001724	0.340792	
chunk0112_320_1	chr20	44708362	44708844	+	0	NA	Intergenic	L1M5|LINE|L1	-6641	NM_003881	8839	Hs.592145	NM_003881	ENSG00000064205	CCN5	CT58|CTGF-L|WISP2	cellular communication network factor 5	protein-coding	0.002075	0.308489	
chunk0172_186_1	chr6	136563320	136563855	+	0	NA	intron (NM_005923, intron 26 of 29)	intron (NM_005923, intron 26 of 29)	-12768	NM_001198616	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.009346	0.345149	241(TGGTACATTCAGTTCC,-,0.00),242(GGTACATTCAGTTCCT,+,0.00)
chunk0180_191_1	chr7	66125323	66125769	+	0	NA	intron (NM_001040648, intron 1 of 2)	intron (NM_001040648, intron 1 of 2)	10728	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.008969	0.357942	305(AGGCAGAGGGTGTTCT,-,0.00),306(GGCAGAGGGTGTTCTT,+,0.00)
chunk0124_447_1	chr3	61547730	61548032	+	0	NA	Intergenic	L1ME1|LINE|L1	-13688	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.006623	0.356436	
chunk0131_350_1	chr3	151637052	151637487	+	0	NA	Intergenic	Intergenic	-71274	NR_049818	100847036		NR_049818	ENSG00000264330	MIR5186	-	microRNA 5186	ncRNA	0.004598	0.412844	
chunk0099_71_1	chr2	85175322	85175865	+	0	NA	intron (NM_031283, intron 3 of 11)	intron (NM_031283, intron 3 of 11)	42133	NM_031283	83439	Hs.516297	NM_031283	ENSG00000152284	TCF7L1	TCF-3|TCF3	transcription factor 7 like 1	protein-coding	0.014733	0.470588	241(AGGTACACCCTGTTCT,-,0.00),242(GGTACACCCTGTTCTT,+,0.00)
chunk0051_230_1	chr12	116919353	116920519	+	0	NA	intron (NM_153348, intron 1 of 10)	intron (NM_153348, intron 1 of 10)	8980	NM_153348	26259	Hs.624537	NM_012174	ENSG00000174989	FBXW8	FBW6|FBW8|FBX29|FBXO29|FBXW6	F-box and WD repeat domain containing 8	protein-coding	0.008576	0.407883	
chunk0058_438_1	chr13	113383259	113383778	+	0	NA	Intergenic	L1PB1|LINE|L1	-19370	NM_024719	79774	Hs.745043	NM_024719	ENSG00000139835	GRTP1	TBC1D6	growth hormone regulated TBC protein 1	protein-coding	0.013487	0.388462	
chunk0092_406_1	chr19	37507014	37507232	+	0	NA	promoter-TSS (NR_110723)	promoter-TSS (NR_110723)	-36	NR_110723	101927720	Hs.18070	NR_110723	ENSG00000266916	ZNF793-AS1	-	ZNF793 antisense RNA 1 (head to head)	ncRNA	0.059633	0.584475	
chunk0011_115_1	chr1	146376964	146377175	+	0	NA	TTS (NR_004400).6	TTS (NR_004400).6	262	NR_004408	26869		NR_004408	ENSG00000207513	RNU1-3	HSD4|RNU1G3	RNA, U1 small nuclear 3	snRNA	0.056872	0.457547	
chunk0033_316_1	chr11	20728022	20728247	+	0	NA	intron (NM_006157, intron 2 of 19)	L1P4|LINE|L1	58583	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.013333	0.336283	
chunk0028_90_1	chr10	83944925	83945487	+	0	NA	Intergenic	Intergenic	-194223	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.007117	0.419183	
chunk0109_378_1	chr2	239494493	239494853	+	0	NA	Intergenic	L1MC2|LINE|L1	-93724	NM_006037	9759	Hs.20516	NM_006037	ENSG00000068024	HDAC4	AHO3|BDMR|HA6116|HD4|HDAC-4|HDAC-A|HDACA	histone deacetylase 4	protein-coding	0.008333	0.418283	110(AAGTACAGAGAGTCCT,-,0.00),111(AGTACAGAGAGTCCTT,+,0.00)
chunk0211_242_1	chrX	119756144	119756412	+	0	NA	Intergenic	Intergenic	-2335	NM_001105576	347454	Hs.355223	NM_001105576	ENSG00000187808	SOWAHD	ANKRD58	sosondowah ankyrin repeat domain family member D	protein-coding	0.014925	0.423792	
chunk0136_65_1	chr4	1880465	1880772	+	0	NA	intron (NM_001042424, intron 1 of 21)	L1MC5|LINE|L1	9222	NM_001042424	7468	Hs.113876	NM_007331	ENSG00000109685	NSD2	KMT3F|KMT3G|MMSET|REIIBP|TRX5|WHS|WHSC1	nuclear receptor binding SET domain protein 2	protein-coding	0.003257	0.412338	
chunk0195_26_1	chr8	93160217	93160760	+	0	NA	intron (NM_001242668, intron 1 of 2)	intron (NM_001242668, intron 1 of 2)	6362	NM_001242668									0.003683	0.386029	
chunk0138_224_1	chr4	39097200	39097621	+	0	NA	intron (NM_001007075, intron 7 of 11)	L1MC4|LINE|L1	35178	NM_199039	51088	Hs.272251	NM_015990	ENSG00000109790	KLHL5	-	kelch like family member 5	protein-coding	0.014252	0.388626	
chunk0121_303_1	chr3	24042680	24042939	+	0	NA	Intergenic	Intergenic	60438	NR_026834	152024	Hs.385606	NR_026834	ENSG00000224074	LINC00691	-	long intergenic non-protein coding RNA 691	ncRNA	0.007722	0.376923	
chunk0123_311_1	chr3	47075745	47076277	+	0	NA	intron (NM_014159, intron 12 of 20)	L2b|LINE|L2	64469	NR_024046	100129354	Hs.201522	NR_024046		NRADDP	-	neurotrophin receptor associated death domain, pseudogene	pseudo	0.003759	0.367730	
chunk0040_23_1	chr11	110085049	110085753	+	0	NA	Intergenic	Intergenic	-7960	NM_033390	85463	Hs.376289	NM_033390	ENSG00000149289	ZC3H12C	MCPIP3	zinc finger CCCH-type containing 12C	protein-coding	0.004261	0.347518	353(CAGAACAGTGTCTTCT,-,0.00),354(AGAACAGTGTCTTCTC,+,0.00)
chunk0207_44_1	chrX	6982131	6982358	+	0	NA	Intergenic	LTR8A|LTR|ERV1	-165616	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.013216	0.425439	
chunk0103_50_1	chr2	159441247	159441623	+	0	NA	intron (NM_001289975, intron 6 of 35)	intron (NM_001289975, intron 6 of 35)	-154636	NM_001128212	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.002660	0.363395	
chunk0117_297_1	chr22	24514158	24514729	+	0	NA	intron (NM_016327, intron 5 of 9)	intron (NM_016327, intron 5 of 9)	19160	NM_016327	51733	Hs.731656	NM_016327	ENSG00000100024	UPB1	BUP1	beta-ureidopropionase 1	protein-coding	0.014011	0.564685	
chunk0014_216_1	chr1	179365863	179366185	+	0	NA	promoter-TSS (NR_073544)	promoter-TSS (NR_073544)	52	NR_073544	126859	Hs.658505	NM_144696	ENSG00000162779	AXDND1	C1orf125	axonemal dynein light chain domain containing 1	protein-coding	0.077640	0.631579	
chunk0095_126_1	chr2	16049378	16049629	+	0	NA	promoter-TSS (NR_126559)	promoter-TSS (NR_126559)	-924	NR_126559	104797537	Hs.435748	NR_126559	ENSG00000236289	GACAT3	LINC01458|lncRNA-AC130710	gastric cancer associated transcript 3	ncRNA	0.011952	0.488095	
chunk0139_417_1	chr4	64109241	64109802	+	0	NA	Intergenic	Intergenic	299939	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.001783	0.327402	
chunk0184_200_1	chr7	117035941	117036556	+	0	NA	intron (NM_021908, intron 1 of 15)	intron (NM_021908, intron 1 of 15)	16037	NR_106748	102466616		NR_106748	ENSG00000283923	MIR6132	hsa-mir-6132	microRNA 6132	ncRNA	0.008130	0.384740	253(TGGAACTCTTTGTTCC,-,0.00),254(GGAACTCTTTGTTCCT,+,0.00)
chunk0202_390_1	chr9	81146313	81146616	+	0	NA	Intergenic	Intergenic	543071	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.006601	0.411184	
chunk0007_388_1	chr1	85359877	85360368	+	0	NA	intron (NM_001134445, intron 2 of 6)	intron (NM_001134445, intron 2 of 6)	-83218	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.002037	0.333333	
chunk0198_440_1	chr8	143833198	143833554	+	0	NA	TTS (NM_178564)	TTS (NM_178564)	-3990	NM_001271099	22827	Hs.521924	NM_014281	ENSG00000179950	PUF60	FIR|RoBPI|SIAHBP1|VRJS	poly(U) binding splicing factor 60	protein-coding	0.016854	0.431373	141(TAGAACACCGTGTTCT,-,0.00),142(AGAACACCGTGTTCTC,+,0.00)
chunk0191_248_1	chr8	53206576	53206929	+	0	NA	Intergenic	Intergenic	44882	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.008499	0.381356	322(ATGGACAGAGTGCTCT,-,0.00),323(TGGACAGAGTGCTCTT,+,0.00)
chunk0073_392_1	chr16	16036293	16036767	+	0	NA	exon (NM_004996, exon 7 of 31)	exon (NM_004996, exon 7 of 31)	86953	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.018987	0.562105	
chunk0177_35_1	chr7	20892842	20893112	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	57546	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.003704	0.321033	
chunk0149_370_1	chr5	28117785	28118142	+	0	NA	Intergenic	Intergenic	645671	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.002801	0.354749	
chunk0085_7_1	chr18	189021	189609	+	0	NA	intron (NM_001037334, intron 4 of 14)	L1M5|LINE|L1	30832	NM_001037334	9097	Hs.464416	NM_005151	ENSG00000101557	USP14	TGT	ubiquitin specific peptidase 14	protein-coding	0.003401	0.327674	
chunk0063_55_1	chr14	77040033	77040913	+	0	NA	promoter-TSS (NR_110554)	promoter-TSS (NR_110554)	-576	NR_110554	283575	Hs.651736	NR_110554	ENSG00000246548	LINC02288	-	long intergenic non-protein coding RNA 2288	ncRNA	0.035227	0.545970	
chunk0182_210_1	chr7	96308773	96309056	+	0	NA	intron (NR_027662, intron 1 of 16)	L1M5|LINE|L1	13233	NM_014251	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.003534	0.383803	
chunk0018_319_1	chr1	221282756	221283369	+	0	NA	Intergenic	L2c|LINE|L2	53234	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.001631	0.353420	368(CAGCACATCATGTGTT,-,0.00)
chunk0172_260_1	chr6	137417093	137417794	+	0	NA	Intergenic	MIRb|SINE|MIR	76951	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.005706	0.435897	
chunk0080_240_1	chr17	30149216	30149690	+	0	NA	intron (NM_032141, intron 2 of 6)	intron (NM_032141, intron 2 of 6)	-32293	NR_036149	100423003		NR_036149	ENSG00000284399	MIR3184	-	microRNA 3184	ncRNA	0.006329	0.393684	
chunk0012_206_1	chr1	160055411	160056077	+	0	NA	intron (NM_002241, intron 1 of 1)	intron (NM_002241, intron 1 of 1)	14517	NM_002241	3766	Hs.408960	NM_002241	ENSG00000177807	KCNJ10	BIRK-10|KCNJ13-PEN|KIR1.2|KIR4.1|SESAME	potassium voltage-gated channel subfamily J member 10	protein-coding	0.013514	0.455772	
chunk0021_69_1	chr10	1375638	1375905	+	0	NA	intron (NM_018702, intron 2 of 9)	(CA)n|Simple_repeat|Simple_repeat	-150859	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.033708	0.555970	
chunk0106_265_1	chr2	203730289	203730713	+	0	NA	intron (NM_001243077, intron 3 of 3)	intron (NM_001243077, intron 3 of 3)	24026	NM_001243078	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.007075	0.345882	
chunk0115_46_1	chr21	21266944	21267599	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	268956	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.001527	0.312500	341(TAGTACACAATGTTCT,-,0.00),342(AGTACACAATGTTCTT,+,0.00)
chunk0187_374_1	chr7	157521840	157522191	+	0	NA	Intergenic	Intergenic	52407	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.042735	0.500000	
chunk0053_140_1	chr13	30026812	30027082	+	0	NA	Intergenic	MER34B|LTR|ERV1	81928	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.000000	0.413284	
chunk0173_121_1	chr6	143639003	143639870	+	0	NA	intron (NM_001100166, intron 1 of 11)	MARNA|DNA|TcMar-Mariner	31256	NM_014721	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.003460	0.337558	225(AAGTACAGTCTGTCTT,-,0.00),226(AGTACAGTCTGTCTTT,+,0.00)
chunk0062_369_1	chr14	74062783	74063104	+	0	NA	intron (NM_001278593, intron 11 of 11)	L2b|LINE|L2	21550	NM_001278593	4329	Hs.293970	NM_005589	ENSG00000119711	ALDH6A1	MMSADHA|MMSDH	aldehyde dehydrogenase 6 family member A1	protein-coding	0.000000	0.419255	
chunk0019_190_1	chr1	226702792	226703306	+	0	NA	intron (NM_002221, intron 2 of 7)	intron (NM_002221, intron 2 of 7)	-27981	NR_103784	100506443	Hs.664293	NR_103784		ITPKB-IT1	-	ITPKB intronic transcript 1	ncRNA	0.013619	0.440777	
chunk0074_394_1	chr16	35377147	35377609	+	0	NA	intron (NR_027080, intron 2 of 6)	intron (NR_027080, intron 2 of 6)	13847	NR_027079	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.004329	0.401728	
chunk0056_210_1	chr13	86383470	86383703	+	0	NA	Intergenic	Intergenic	-528334	NR_132371	106144533	Hs.525107	NR_132371		LINC00430	-	long intergenic non-protein coding RNA 430	ncRNA	0.004292	0.303419	
chunk0181_426_1	chr7	90411442	90412158	+	0	NA	intron (NM_001185073, intron 2 of 2)	intron (NM_001185073, intron 2 of 2)	8466	NM_001185072	9069	Hs.731917	NM_012129	ENSG00000157224	CLDN12	-	claudin 12	protein-coding	0.005587	0.372385	
chunk0102_433_1	chr2	157764462	157764671	+	0	NA	intron (NM_001111067, intron 8 of 10)	intron (NM_001111067, intron 8 of 10)	110545	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.043062	0.557143	
chunk0199_441_1	chr9	14015792	14016125	+	0	NA	Intergenic	L2a|LINE|L2	87987	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.015015	0.416168	
chunk0026_390_1	chr10	69662127	69662713	+	0	NA	Intergenic	MIRb|SINE|MIR	32173	NM_145306	219738	Hs.522992	NM_145306	ENSG00000171224	FAM241B	C10orf35	family with sequence similarity 241 member B	protein-coding	0.017065	0.485520	
chunk0205_395_1	chr9	114544453	114544796	+	0	NA	Intergenic	Intergenic	-39168	NM_001173425	25861	Hs.93836	NM_015404	ENSG00000095397	WHRN	CIP98|DFNB31|PDZD7B|USH2D|WI	whirlin	protein-coding	0.014577	0.421512	180(CAGGGCAGTCTGTCCC,-,0.00),181(AGGGCAGTCTGTCCCC,+,0.00)
chunk0020_173_1	chr1	234478544	234478782	+	0	NA	exon (NM_005646, exon 1 of 30)	exon (NM_005646, exon 1 of 30)	440	NM_005646	6894	Hs.498115	NM_005646	ENSG00000059588	TARBP1	TRM3|TRMT3|TRP-185|TRP185	TAR (HIV-1) RNA binding protein 1	protein-coding	0.159664	0.794979	
chunk0156_349_1	chr5	111984731	111985450	+	0	NA	intron (NR_046678, intron 3 of 3)	intron (NR_046678, intron 3 of 3)	-8159	NM_001142475	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.004172	0.361111	539(TGGAACAGAGTGTCCA,-,0.00),540(GGAACAGAGTGTCCAA,+,0.00)
chunk0060_260_1	chr14	50165023	50165680	+	0	NA	intron (NM_006939, intron 8 of 22)	L1MC4|LINE|L1	-48772	NM_024558	79609	Hs.558541	NM_024558	ENSG00000100483	VCPKMT	C14orf138|METTL21D|VCP-KMT	valosin containing protein lysine methyltransferase	protein-coding	0.010654	0.340426	
chunk0043_460_1	chr12	26763948	26764177	+	0	NA	intron (NM_002223, intron 2 of 56)	L1MC|LINE|L1	69136	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.000000	0.334783	
chunk0020_407_1	chr1	241306445	241306709	+	0	NA	intron (NM_001282775, intron 2 of 17)	(CA)n|Simple_repeat|Simple_repeat	50653	NM_001282775	6000	Hs.655739	NM_002924	ENSG00000182901	RGS7	-	regulator of G protein signaling 7	protein-coding	0.022727	0.475472	
chunk0080_322_1	chr17	32240825	32241024	+	0	NA	Intergenic	Intergenic	-25252	NM_138328	162494	Hs.655027	NM_138328	ENSG00000141314	RHBDL3	RHBDL4|VRHO	rhomboid like 3	protein-coding	0.015075	0.565000	
chunk0089_384_1	chr18	67549853	67550063	+	0	NA	intron (NR_033921, intron 1 of 4)	intron (NR_033921, intron 1 of 4)	-33228	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.004762	0.312796	
chunk0123_199_1	chr3	44559665	44560235	+	0	NA	intron (NM_025169, intron 2 of 5)	intron (NM_025169, intron 2 of 5)	4775	NM_025169	55888	Hs.529512	NM_018651	ENSG00000196345	ZKSCAN7	ZFP|ZNF167|ZNF448|ZNF64|ZSCAN39	zinc finger with KRAB and SCAN domains 7	protein-coding	0.003509	0.425569	
chunk0107_90_1	chr2	213082090	213082685	+	0	NA	intron (NM_016260, intron 3 of 7)	intron (NM_016260, intron 3 of 7)	67947	NM_016260	22807	Hs.604950	NM_016260	ENSG00000030419	IKZF2	ANF1A2|HELIOS|ZNF1A2|ZNFN1A2	IKAROS family zinc finger 2	protein-coding	0.003361	0.290268	
chunk0077_8_1	chr16	74575301	74576083	+	0	NA	intron (NR_027264, intron 1 of 26)	AluSx3|SINE|Alu	31452	NR_027264	2734	Hs.109731	NM_012201	ENSG00000090863	GLG1	CFR-1|ESL-1|MG-160|MG160	golgi glycoprotein 1	protein-coding	0.012788	0.408685	568(AAGCACAGTGTGCTCT,-,0.00),569(AGCACAGTGTGCTCTC,+,0.00)
chunk0166_221_1	chr6	46944309	46944808	+	0	NA	intron (NM_015234, intron 1 of 20)	MER5A|DNA|hAT-Charlie	10380	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.002004	0.414000	299(TTGCACAAACTGTGCT,-,0.00),300(TGCACAAACTGTGCTT,+,0.00)
chunk0170_369_1	chr6	116902523	116902962	+	0	NA	intron (NM_173560, intron 6 of 18)	intron (NM_173560, intron 6 of 18)	25529	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.002278	0.356818	
chunk0082_349_1	chr17	59964761	59964969	+	0	NA	promoter-TSS (NR_110816)	promoter-TSS (NR_110816)	-109	NM_016125	51136	Hs.531701	NM_016125	ENSG00000189050	RNFT1	PTD016	ring finger protein, transmembrane 1	protein-coding	0.110577	0.636364	
chunk0111_448_1	chr20	35373618	35374125	+	0	NA	intron (NM_018244, intron 5 of 9)	intron (NM_018244, intron 5 of 9)	38271	NM_018244	55245	Hs.726290	NM_018244	ENSG00000101019	UQCC1	BFZB|C20orf44|CBP3|UQCC	ubiquinol-cytochrome c reductase complex assembly factor 1	protein-coding	0.005917	0.375984	
chunk0106_347_1	chr2	206751271	206751490	+	0	NA	intron (NM_001039845, intron 5 of 11)	intron (NM_001039845, intron 5 of 11)	-14008	NM_014929	22868	Hs.5930	NM_014929	ENSG00000118246	FASTKD2	KIAA0971	FAST kinase domains 2	protein-coding	0.000000	0.359091	
chunk0139_389_1	chr4	61921811	61922416	+	0	NA	intron (NM_015236, intron 10 of 22)	intron (NM_015236, intron 10 of 22)	239652	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.004959	0.331683	
chunk0099_171_1	chr2	88698873	88699486	+	0	NA	intron (NM_144563, intron 2 of 8)	intron (NM_144563, intron 2 of 8)	7521	NM_144563	22934	Hs.469264	NM_144563	ENSG00000153574	RPIA	RPI|RPIAD	ribose 5-phosphate isomerase A	protein-coding	0.001631	0.431596	288(AGGAACACTTTGTTAT,-,0.00)
chunk0175_69_1	chr7	2149132	2149378	+	0	NA	intron (NM_003550, intron 10 of 18)	intron (NM_003550, intron 10 of 18)	83693	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.020325	0.550607	121(AGGCACACTCAGTTCC,-,0.00),122(GGCACACTCAGTTCCA,+,0.00)
chunk0161_88_1	chr5	167229508	167229890	+	0	NA	Intergenic	L1MA4A|LINE|L1	-55139	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.005236	0.561358	
chunk0012_38_1	chr1	155131144	155131784	+	0	NA	exon (NM_004428, exon 2 of 5)	exon (NM_004428, exon 2 of 5)	3591	NM_182685	1942	Hs.516664	NM_004428	ENSG00000169242	EFNA1	B61|ECKLG|EFL1|EPLG1|LERK-1|LERK1|TNFAIP4	ephrin A1	protein-coding	0.015625	0.507020	298(CAGTACATACTGTACC,-,0.00),299(AGTACATACTGTACCT,+,0.00)
chunk0010_98_1	chr1	113912881	113913396	+	0	NA	3' UTR (NM_022836, exon 4 of 4)	3' UTR (NM_022836, exon 4 of 4)	7845	NM_022836	64858	Hs.591412	NM_022836	ENSG00000118655	DCLRE1B	APOLLO|SNM1B|SNMIB	DNA cross-link repair 1B	protein-coding	0.007767	0.501938	
chunk0190_429_1	chr8	41577844	41578218	+	0	NA	promoter-TSS (NM_178819)	promoter-TSS (NM_178819)	-157	NM_178819	137964	Hs.355753	NM_178819	ENSG00000158669	GPAT4	1-AGPAT 6|AGPAT6|LPAAT-zeta|LPAATZ|TSARG7	glycerol-3-phosphate acyltransferase 4	protein-coding	0.133690	0.754667	
chunk0115_325_1	chr21	28794304	28794784	+	0	NA	Intergenic	Intergenic	90829	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.002083	0.345114	
chunk0024_280_1	chr10	41883770	41884318	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	484001	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.016423	0.409836	
chunk0201_433_1	chr9	70038110	70038611	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	-5221	NM_153267	256691	Hs.547172	NM_153267	ENSG00000165072	MAMDC2	-	MAM domain containing 2	protein-coding	0.007984	0.392430	
chunk0090_412_1	chr18	78975341	78976003	+	0	NA	Intergenic	Intergenic	-4603	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.019637	0.431373	
chunk0033_248_1	chr11	18195553	18196357	+	0	NA	Intergenic	L2b|LINE|L2	-13183	NR_026541	494141	Hs.446327	NR_026541	ENSG00000189332	SLC25A51P4	-	SLC25A51 pseudogene 4	pseudo	0.008706	0.431056	412(GAGAACACAGTGTGCT,-,0.00),413(AGAACACAGTGTGCTG,+,0.00)
chunk0076_284_1	chr16	69654424	69654623	+	0	NA	intron (NM_006599, intron 4 of 13)	intron (NM_006599, intron 4 of 13)	72107	NM_001025434	1728	Hs.406515	NM_000903	ENSG00000181019	NQO1	DHQU|DIA4|DTD|NMOR1|NMORI|QR1	NAD(P)H quinone dehydrogenase 1	protein-coding	0.005025	0.370000	
chunk0030_314_1	chr10	117817002	117817201	+	0	NA	Intergenic	MIRb|SINE|MIR	229502	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.000000	0.445000	
chunk0084_326_1	chr17	80760538	80761186	+	0	NA	intron (NM_020761, intron 6 of 33)	intron (NM_020761, intron 6 of 33)	44770	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.020062	0.434515	
chunk0036_118_1	chr11	61609268	61609663	+	0	NA	Intergenic	Intergenic	-5571	NR_002775	113157	Hs.502733	NR_002775	ENSG00000243742	RPLP0P2	RPLP0L2|RPLP0_3_1146	ribosomal protein lateral stalk subunit P0 pseudogene 2	pseudo	0.032911	0.578283	
chunk0196_159_1	chr8	104785498	104785697	+	0	NA	Intergenic	Intergenic	-196573	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.005025	0.435000	
chunk0192_442_1	chr8	69791879	69792115	+	0	NA	intron (NM_030958, intron 2 of 9)	intron (NM_030958, intron 2 of 9)	41172	NM_001146009	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.000000	0.299578	
chunk0161_27_1	chr5	165783027	165783416	+	0	NA	Intergenic	Intergenic	1143149	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.010283	0.387179	
chunk0057_418_1	chr13	109984747	109985288	+	0	NA	Intergenic	Intergenic	-68268	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.003697	0.343173	
chunk0178_273_1	chr7	36963625	36964059	+	0	NA	intron (NM_001206482, intron 16 of 21)	intron (NM_001206482, intron 16 of 21)	21270	NM_001039459	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.002304	0.367816	
chunk0081_383_1	chr17	48085230	48085748	+	0	NA	intron (NM_001127228, intron 1 of 4)	intron (NM_001127228, intron 1 of 4)	15709	NM_006807	10951	Hs.77254	NM_006807	ENSG00000108468	CBX1	CBX|HP1-BETA|HP1Hs-beta|HP1Hsbeta|M31|MOD1|p25beta	chromobox 1	protein-coding	0.001931	0.373796	
chunk0006_303_1	chr1	71321105	71321647	+	0	NA	Intergenic	L1PA7|LINE|L1	240052	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.005535	0.322284	
chunk0007_75_1	chr1	78373595	78374029	+	0	NA	Intergenic	Intergenic	-117231	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.002304	0.347126	
chunk0093_350_1	chr19	55065577	55065779	+	0	NA	intron (NM_138412, intron 1 of 7).8	MER58A|DNA|hAT-Charlie	-2461	NM_001145971	112724	Hs.327631	NM_138412	ENSG00000160439	RDH13	SDR7C3	retinol dehydrogenase 13	protein-coding	0.019802	0.492611	
chunk0059_360_1	chr14	37288924	37289277	+	0	NA	intron (NM_001195296, intron 9 of 14)	intron (NM_001195296, intron 9 of 14)	91187	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.002833	0.333333	
chunk0022_413_1	chr10	18505394	18505684	+	0	NA	intron (NM_001167945, intron 5 of 13)	intron (NM_001167945, intron 5 of 13)	104955	NM_201570	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.006897	0.319588	
chunk0141_398_1	chr4	88456750	88457055	+	0	NA	promoter-TSS (NM_016323)	promoter-TSS (NM_016323)	-215	NM_016323	51191	Hs.26663	NM_016323	ENSG00000138646	HERC5	CEB1|CEBP1	HECT and RLD domain containing E3 ubiquitin protein ligase 5	protein-coding	0.068852	0.555556	
chunk0188_98_1	chr8	8836688	8837133	+	0	NA	intron (NM_004225, intron 1 of 2)	intron (NM_004225, intron 1 of 2)	56711	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.008989	0.369955	
chunk0077_401_1	chr16	84944710	84945598	+	0	NA	Intergenic	L1MC4|LINE|L1	66381	NM_001145548	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.010135	0.474691	
chunk0017_156_1	chr1	206924060	206924561	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-2277	NM_001142473	9214	Hs.58831	NM_005449	ENSG00000162894	FCMR	FAIM3|TOSO	Fc fragment of IgM receptor	protein-coding	0.003992	0.498008	
chunk0063_184_1	chr14	80606271	80607100	+	0	NA	intron (NM_152446, intron 18 of 23)	intron (NM_152446, intron 18 of 23)	332855	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.003619	0.330120	383(GGAAACAGAATGTACT,-,0.00),384(GAAACAGAATGTACTG,+,0.00)
chunk0052_3_1	chr13	18294735	18294946	+	0	NA	Intergenic	Intergenic	99543	NR_027278	26080	Hs.448583	NR_027278	ENSG00000279516	FAM230C	LINC00281|NCRNA00281	family with sequence similarity 230 member C	ncRNA	0.009479	0.400943	
chunk0050_9_1	chr12	99649145	99649353	+	0	NA	intron (NM_153364, intron 1 of 1)	intron (NM_153364, intron 1 of 1)	1499	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.000000	0.387560	
chunk0037_379_1	chr11	78508671	78508915	+	0	NA	intron (NM_024678, intron 6 of 13)	L1M4c|LINE|L1	-24383	NR_120566	101928896	Hs.659055	NR_120566	ENSG00000255084	LOC101928896	-	uncharacterized LOC101928896	ncRNA	0.004098	0.420408	
chunk0197_181_1	chr8	121318917	121319364	+	0	NA	Intergenic	MER63D|DNA|hAT-Blackjack	-320206	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.004474	0.314732	219(CAATACATAGTGTTCT,-,0.00),220(AATACATAGTGTTCTG,+,0.00)
chunk0120_443_1	chr3	14117632	14118535	+	0	NA	intron (NM_001098502, intron 1 of 2)	intron (NM_001098502, intron 1 of 2)	6788	NM_144636	131474	Hs.517815	NM_144636	ENSG00000163528	CHCHD4	MIA40|TIMM40	coiled-coil-helix-coiled-coil-helix domain containing 4	protein-coding	0.014396	0.503319	39(GAGAACAGACAGAGCC,-,0.00),182(CAGGACAGGATGCTCT,-,0.00),183(AGGACAGGATGCTCTG,+,0.00)
chunk0109_315_1	chr20	9075487	9076191	+	0	NA	intron (NM_001172646, intron 1 of 37)	MER102b|DNA|hAT-Charlie	6785	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.007102	0.439716	445(GGAAACACCGTGTACT,-,0.00),446(GAAACACCGTGTACTA,+,0.00)
chunk0014_348_1	chr1	182278246	182278512	+	0	NA	intron (NR_104175, intron 2 of 2)	L2a|LINE|L2	35682	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.007519	0.404494	
chunk0090_162_1	chr18	72490454	72491069	+	0	NA	Intergenic	Intergenic	53727	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.004878	0.360390	
chunk0034_74_1	chr11	27190936	27191640	+	0	NA	intron (NR_125766, intron 2 of 4)	L2|LINE|L2	27480	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.005682	0.418440	
chunk0181_194_1	chr7	83476522	83477082	+	0	NA	intron (NM_001178129, intron 2 of 16)	intron (NM_001178129, intron 2 of 16)	164629	NM_001178129	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.007143	0.324421	
chunk0145_132_1	chr4	146381890	146382483	+	0	NA	intron (NM_001029998, intron 5 of 11)	intron (NM_001029998, intron 5 of 11)	-26397	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.005059	0.345118	
chunk0057_168_1	chr13	101709953	101710208	+	0	NA	intron (NM_001271754, intron 8 of 10)	intron (NM_001271754, intron 8 of 10)	206565	NM_004115	2259	Hs.508616	NM_004115	ENSG00000102466	FGF14	FGF-14|FHF-4|FHF4|SCA27	fibroblast growth factor 14	protein-coding	0.003922	0.343750	
chunk0082_6_1	chr17	49723014	49723339	+	0	NA	intron (NM_030802, intron 2 of 7)	intron (NM_030802, intron 2 of 7)	-15225	NM_001278784	10237	Hs.154073	NM_005827	ENSG00000121073	SLC35B1	UGTREL1	solute carrier family 35 member B1	protein-coding	0.006154	0.481595	
chunk0025_126_1	chr10	51720352	51720864	+	0	NA	intron (NM_006258, intron 3 of 17)	intron (NM_006258, intron 3 of 17)	-21013	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.007812	0.384016	279(TGGAACAACATGTGCA,-,0.00),280(GGAACAACATGTGCAA,+,0.00)
chunk0010_207_1	chr1	116139215	116139468	+	0	NA	Intergenic	Intergenic	27586	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.023715	0.519685	
chunk0121_248_1	chr3	22886467	22886976	+	0	NA	Intergenic	Intergenic	-316572	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.007859	0.492157	
chunk0051_157_1	chr12	115857826	115858430	+	0	NA	Intergenic	L2a|LINE|L2	290526	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.009934	0.489256	316(TAGGACATTTTGTTCC,-,0.00),317(AGGACATTTTGTTCCC,+,0.00)
chunk0140_3_1	chr4	65241736	65242311	+	0	NA	Intergenic	MER52A|LTR|ERV1	-237523	NR_033976	401134	Hs.165899	NR_033976	ENSG00000250125	LINC02232	-	long intergenic non-protein coding RNA 2232	ncRNA	0.027826	0.560764	502(TGCCCAGGCTGTTCTT,+,0.00)
chunk0077_344_1	chr16	83300162	83300853	+	0	NA	intron (NM_001220488, intron 6 of 14)	intron (NM_001220488, intron 6 of 14)	-207839	NR_036147	100422853		NR_036147	ENSG00000263785	MIR3182	mir-3182	microRNA 3182	ncRNA	0.004342	0.346821	187(GTGTACTTACTGTTCT,-,0.00),188(TGTACTTACTGTTCTT,+,0.00)
chunk0135_121_1	chr3	187032078	187032403	+	0	NA	intron (NM_003032, intron 1 of 6)	intron (NM_003032, intron 1 of 6)	10363	NM_003032	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.000000	0.414110	
chunk0089_252_1	chr18	62400038	62400306	+	0	NA	Intergenic	Intergenic	74885	NM_001270951	8792	Hs.204044	NM_003839	ENSG00000141655	TNFRSF11A	CD265|FEO|LOH18CR1|ODFR|OFE|OPTB7|OSTS|PDB2|RANK|TRANCER	TNF receptor superfamily member 11a	protein-coding	0.011194	0.535316	
chunk0136_50_1	chr4	1458158	1458661	+	0	NA	Intergenic	Intergenic	-51967	NM_001290079	54729	Hs.526396	NM_001290079	ENSG00000235608	NKX1-1	HSPX153|NKX-1.1|SAX2	NK1 homeobox 1	protein-coding	0.009940	0.511905	294(TTGCACTCTCTGTTCT,-,0.00),295(TGCACTCTCTGTTCTG,+,0.00)
chunk0062_270_1	chr14	71958938	71959538	+	0	NA	intron (NM_001204418, intron 1 of 16)	intron (NM_001204418, intron 1 of 16)	26169	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.010000	0.387687	
chunk0022_406_1	chr10	18326028	18326712	+	0	NA	intron (NM_000724, intron 1 of 12)	intron (NM_000724, intron 1 of 12)	-14315	NM_201590	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.005848	0.351825	
chunk0022_163_1	chr10	12611853	12612703	+	0	NA	intron (NM_020397, intron 2 of 9)	intron (NM_020397, intron 2 of 9)	33525	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.012941	0.473561	
chunk0168_305_1	chr6	91694199	91694673	+	0	NA	Intergenic	Intergenic	-4008	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.008439	0.355789	
chunk0103_65_1	chr2	159907769	159908401	+	0	NA	Intergenic	L2c|LINE|L2	-3329	NM_001198760	100526664	Hs.153563	NM_001198759	ENSG00000248672	LY75-CD302	CD205|CLEC13B|DEC-205|LY75|Ly-75|gp200-MR6	LY75-CD302 readthrough	protein-coding	0.003165	0.399684	300(TAGATCATTCTGTGCT,-,0.00),301(AGATCATTCTGTGCTT,+,0.00),544(TTGAACTGGATGTCCT,-,0.00),545(TGAACTGGATGTCCTT,+,0.00)
chunk0116_68_1	chr21	34178573	34179082	+	0	NA	Intergenic	Intergenic	-1850	NR_027267	114036	Hs.720230	NM_153751	ENSG00000227456	LINC00310	C21orf82|NCRNA00310	long intergenic non-protein coding RNA 310	ncRNA	0.009823	0.454902	267(GGGTACAGGATGTACA,-,0.00),268(GGTACAGGATGTACAT,+,0.00)
chunk0029_71_1	chr10	96616393	96616629	+	0	NA	intron (NM_152309, intron 13 of 16)	L2c|LINE|L2	-29459	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.008475	0.464135	
chunk0193_311_1	chr8	78222872	78223430	+	0	NA	Intergenic	Intergenic	-292950	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.001792	0.350626	
chunk0006_316_1	chr1	71470587	71470961	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	366238	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005348	0.384000	
chunk0132_401_1	chr3	164119090	164119487	+	0	NA	Intergenic	Intergenic	52268	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.266332	
chunk0149_269_1	chr5	24128934	24129388	+	0	NA	intron (NR_131245, intron 4 of 4)	L1ME1|LINE|L1	177813	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.002203	0.327473	
chunk0200_238_1	chr9	20830960	20831440	+	0	NA	intron (NM_017794, intron 17 of 45)	intron (NM_017794, intron 17 of 45)	115095	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.006250	0.365904	
chunk0083_89_1	chr17	64299942	64300440	+	0	NA	Intergenic	L1M5|LINE|L1	-36868	NM_018469	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.016064	0.432866	
chunk0127_355_1	chr3	101310504	101311178	+	0	NA	intron (NM_016247, intron 2 of 18)	MamTip2|DNA|hAT-Tip100	9734	NM_016247	50939	Hs.209249	NM_016247	ENSG00000081148	IMPG2	IPM200|RP56|SPACRCAN|VMD5	interphotoreceptor matrix proteoglycan 2	protein-coding	0.002967	0.365926	344(AGCACAAGCTGTCTCC,+,0.00)
chunk0188_207_1	chr8	12705003	12705202	+	0	NA	Intergenic	SATR2|Satellite|Satellite	-14025	NR_049875	100847066		NR_049875	ENSG00000266318	MIR5692A1	-	microRNA 5692a-1	ncRNA	0.015075	0.370000	
chunk0015_294_1	chr1	188779278	188779896	+	0	NA	Intergenic	Intergenic	1335959	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003236	0.260097	
chunk0156_251_1	chr5	108932602	108932996	+	0	NA	intron (NM_001308031, intron 1 of 10)	L1PA7|LINE|L1	8193	NM_001308031	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.002538	0.359494	
chunk0009_277_1	chr1	107502451	107503161	+	0	NA	Intergenic	Intergenic	185698	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002817	0.385373	
chunk0115_11_1	chr21	20367619	20367983	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	435307	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005495	0.336986	130(TAGTACAATATGTACT,-,0.00),131(AGTACAATATGTACTA,+,0.00)
chunk0194_22_1	chr8	81619708	81619941	+	0	NA	Intergenic	Intergenic	66530	NM_005536	3612	Hs.656694	NM_005536	ENSG00000133731	IMPA1	IMP|IMPA|MRT59	inositol monophosphatase 1	protein-coding	0.008584	0.367521	
chunk0210_289_1	chrX	85844126	85844460	+	0	NA	Intergenic	L1M2|LINE|L1	8513	NR_031710	100302171		NR_031710	ENSG00000283435	MIR1321	MIRN1321|hsa-mir-1321	microRNA 1321	ncRNA	0.008982	0.367164	
chunk0171_126_1	chr6	122712677	122713246	+	0	NA	intron (NM_001270394, intron 6 of 7)	intron (NM_001270394, intron 6 of 7)	60232	NM_001270395	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.008787	0.368421	
chunk0189_193_1	chr8	23643476	23644160	+	0	NA	Intergenic	Intergenic	39071	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.007310	0.448175	
chunk0036_331_1	chr11	66616130	66616408	+	0	NA	promoter-TSS (NM_001198846)	promoter-TSS (NM_001198846)	-313	NM_006328	10432	Hs.533712	NM_006328	ENSG00000239306	RBM14	COAA|PSP2|SIP|SYTIP1|TMEM137	RNA binding motif protein 14	protein-coding	0.086331	0.673835	
chunk0183_421_1	chr7	110909003	110909530	+	0	NA	intron (NM_032549, intron 4 of 5)	intron (NM_032549, intron 4 of 5)	-181740	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.009488	0.410985	
chunk0172_79_1	chr6	134453710	134454025	+	0	NA	intron (NR_038219, intron 2 of 4)	intron (NR_038219, intron 2 of 4)	15477	NR_038219	154092	Hs.223718	NR_038216		LINC01010	-	long intergenic non-protein coding RNA 1010	ncRNA	0.003175	0.424051	
chunk0103_445_1	chr2	170119698	170120411	+	0	NA	Intergenic	U6|snRNA|snRNA	-58091	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.014025	0.413165	
chunk0144_255_1	chr4	136567165	136567689	+	0	NA	Intergenic	L1MA8|LINE|L1	-653747	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.001908	0.361905	348(TGCACTATCTGTCCCT,+,0.00)
chunk0110_243_1	chr20	16459351	16459704	+	0	NA	intron (NM_001199865, intron 12 of 24)	intron (NM_001199865, intron 12 of 24)	113907	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.002833	0.446328	
chunk0049_188_1	chr12	92827962	92828161	+	0	NA	exon (NM_003566, exon 12 of 29)	exon (NM_003566, exon 12 of 29)	91572	NM_001004330	440107	Hs.591013	NM_001004330	ENSG00000187510	PLEKHG7	-	pleckstrin homology and RhoGEF domain containing G7	protein-coding	0.005025	0.370000	
chunk0126_336_1	chr3	82095462	82096065	+	0	NA	Intergenic	Intergenic	-333964	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.003317	0.302980	257(AAAACATGCTGTTCAT,+,0.00),290(AAGAACAATTTGTTTC,-,0.00)
chunk0012_213_1	chr1	160131841	160132584	+	0	NA	intron (NM_000702, intron 13 of 22)	L2|LINE|L2	16482	NM_000702	477	Hs.34114	NM_000702	ENSG00000018625	ATP1A2	FHM2|MHP2	ATPase Na+/K+ transporting subunit alpha 2	protein-coding	0.009421	0.500000	329(GGGAACAGTGTGTACC,-,0.00),330(GGAACAGTGTGTACCC,+,0.00)
chunk0075_248_1	chr16	53183223	53183567	+	0	NA	intron (NM_001308319, intron 1 of 37)	L1ME3Cz|LINE|L1	27469	NM_001308319	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.005814	0.295652	
chunk0091_265_1	chr19	11298031	11298230	+	0	NA	intron (NM_012466, intron 1 of 6)	intron (NM_012466, intron 1 of 6)	1991	NM_001282509	26526	Hs.579784	NM_012466	ENSG00000130167	TSPAN16	TM-8|TM4-B|TM4SF16	tetraspanin 16	protein-coding	0.020101	0.500000	
chunk0148_135_1	chr5	5814823	5815168	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	392322	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.011594	0.326590	
chunk0082_251_1	chr17	57530513	57530996	+	0	NA	intron (NM_138962, intron 7 of 13)	intron (NM_138962, intron 7 of 13)	-7157	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.008282	0.514463	
chunk0060_79_1	chr14	42114934	42115461	+	0	NA	Intergenic	Intergenic	507636	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.001898	0.346591	
chunk0157_289_1	chr5	120863995	120864596	+	0	NA	Intergenic	Intergenic	332831	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.004992	0.373754	
chunk0088_243_1	chr18	48615956	48616446	+	0	NA	intron (NM_001142397, intron 2 of 12)	intron (NM_001142397, intron 2 of 12)	-54399	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.034694	0.586558	
chunk0147_178_1	chr4	176800847	176801402	+	0	NA	Intergenic	Intergenic	-8379	NM_005429	7424	Hs.435215	NM_005429	ENSG00000150630	VEGFC	Flt4-L|LMPH1D|LMPHM4|VRP	vascular endothelial growth factor C	protein-coding	0.003604	0.352518	
chunk0091_347_1	chr19	14610269	14610573	+	0	NA	non-coding (NR_109785, exon 13 of 13)	non-coding (NR_109785, exon 13 of 13)	-11792	NR_132784	106635534		NR_132784		SNORA104	-	small nucleolar RNA, H/ACA box 104	snoRNA	0.009868	0.544262	
chunk0017_398_1	chr1	212525401	212525989	+	0	NA	Intergenic	Intergenic	-19999	NR_125985	101929565		NR_125985	ENSG00000228067	LINC01740	-	long intergenic non-protein coding RNA 1740	ncRNA	0.013605	0.519525	305(TTGAACATGATGTACT,-,0.00),306(TGAACATGATGTACTT,+,0.00)
chunk0165_302_1	chr6	36829802	36830294	+	0	NA	intron (NM_001314017, intron 1 of 6)	MIR|SINE|MIR	9396	NM_020939	57699	Hs.372129	NM_020939	ENSG00000124772	CPNE5	COPN5|CPN5	copine 5	protein-coding	0.010163	0.464503	
chunk0094_166_1	chr2	5444696	5445119	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	246211	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.016548	0.422170	
chunk0043_110_1	chr12	15243863	15244763	+	0	NA	Intergenic	Intergenic	-22836	NM_001190726	85004	Hs.199487	NM_032918	ENSG00000134533	RERG	-	RAS like estrogen regulated growth inhibitor	protein-coding	0.005556	0.399556	
chunk0071_26_1	chr15	79204941	79205357	+	0	NA	intron (NR_038997, intron 1 of 1)	intron (NR_038997, intron 1 of 1)	-4639	NR_029705	406960		NR_029705	ENSG00000207695	MIR184	EDICT|MIRN184|miR-184	microRNA 184	ncRNA	0.021635	0.549161	
chunk0109_12_1	chr20	289520	289915	+	0	NA	intron (NM_153269, intron 2 of 10)	MIR|SINE|MIR	1061	NM_080571	140680	Hs.348112	NM_080571	ENSG00000196476	C20orf96	dJ1103G7.2	chromosome 20 open reading frame 96	protein-coding	0.005063	0.446970	
chunk0212_380_1	chrX	150203082	150203669	+	0	NA	Intergenic	Intergenic	-24629	NR_031748	100313839		NR_031748	ENSG00000252454	MIR2114	-	microRNA 2114	ncRNA	0.005111	0.435374	
chunk0198_75_1	chr8	130021590	130022102	+	0	NA	Intergenic	Intergenic	-5195	NR_046361									0.015625	0.497076	
chunk0065_218_1	chr14	100302653	100302992	+	0	NA	intron (NM_001039355, intron 1 of 3)	L1MEj|LINE|L1	3725	NM_001039355	123096	Hs.578109	NM_152333	ENSG00000197119	SLC25A29	C14orf69|CACL|ORNT3	solute carrier family 25 member 29	protein-coding	0.002950	0.417647	
chunk0053_52_1	chr13	27603622	27603879	+	0	NA	intron (NM_153371, intron 1 of 9)	intron (NM_153371, intron 1 of 9)	16833	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.000000	0.372093	
chunk0174_183_1	chr6	159752095	159752645	+	0	NA	intron (NM_001270531, intron 6 of 7)	intron (NM_001270531, intron 6 of 7)	-9587	NM_005891	39	Hs.571037	NM_005891	ENSG00000120437	ACAT2	-	acetyl-CoA acetyltransferase 2	protein-coding	0.003636	0.323049	
chunk0199_304_1	chr9	7008405	7008698	+	0	NA	intron (NR_130707, intron 13 of 14)	L1M3e|LINE|L1	250910	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.003413	0.571429	
chunk0107_287_1	chr2	218356841	218357153	+	0	NA	intron (NM_198559, intron 1 of 9)	intron (NM_198559, intron 1 of 9)	141	NM_198559	375307	Hs.645453	NM_198559	ENSG00000158428	CATIP	C2orf62	ciliogenesis associated TTC17 interacting protein	protein-coding	0.016026	0.613419	
chunk0046_240_1	chr12	60380699	60381019	+	0	NA	Intergenic	L1PA10|LINE|L1	691522	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.000000	0.283489	198(ATGAACAGACTCTTCT,-,0.00),199(TGAACAGACTCTTCTT,+,0.00)
chunk0192_448_1	chr8	70128000	70128428	+	0	NA	intron (NM_006540, intron 18 of 22)	Tigger17a|DNA|TcMar-Tigger	-56887	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.007009	0.410256	
chunk0107_427_1	chr2	224792596	224792934	+	0	NA	intron (NM_014689, intron 47 of 55)	intron (NM_014689, intron 47 of 55)	154300	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.000000	0.315634	150(GAGAACATACAGTTCT,-,0.00),151(AGAACATACAGTTCTA,+,0.00)
chunk0095_110_1	chr2	15561319	15561540	+	0	NA	promoter-TSS (NM_015909)	promoter-TSS (NM_015909)	-81	NM_015909	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.040724	0.490991	
chunk0057_412_1	chr13	109812578	109812864	+	0	NA	Intergenic	Intergenic	-26154	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.010490	0.463415	
chunk0014_220_1	chr1	179585900	179586543	+	0	NA	Intergenic	Intergenic	-5392	NM_001199091	163589	Hs.197354	NM_173533	ENSG00000162782	TDRD5	TUDOR3	tudor domain containing 5	protein-coding	0.059098	0.541925	253(TGGAACATTTTGTTCC,-,0.00),254(GGAACATTTTGTTCCC,+,0.00)
chunk0185_272_1	chr7	130853612	130853855	+	0	NA	Intergenic	Intergenic	23077	NR_029503	407021		NR_029503	ENSG00000284032	MIR29A	MIRN29|MIRN29A|hsa-mir-29|hsa-mir-29a|miRNA29A|mir-29a	microRNA 29a	ncRNA	0.004115	0.389344	
chunk0134_83_1	chr3	176565680	176566448	+	0	NA	Intergenic	Intergenic	50961	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.003906	0.330299	
chunk0090_418_1	chr18	79062841	79063208	+	0	NA	Intergenic	MER74A|LTR|ERVL	-6251	NM_198531	374868	Hs.465475	NM_198531	ENSG00000166377	ATP9B	ATPASEP|ATPIIB|HUSSY-20|NEO1L|hMMR1	ATPase phospholipid transporting 9B (putative)	protein-coding	0.021798	0.551630	81(GAGAACAGGCTGGGCA,-,0.00)
chunk0130_459_1	chr3	141487088	141487408	+	0	NA	intron (NM_006506, intron 1 of 23)	CpG	201	NM_001303245	5922	Hs.98445	NM_006506	ENSG00000155903	RASA2	GAP1M	RAS p21 protein activator 2	protein-coding	0.140625	0.775701	
chunk0211_316_1	chrX	123745547	123745975	+	0	NA	Intergenic	Intergenic	-12707	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.004673	0.398601	
chunk0022_32_1	chr10	7950960	7951529	+	0	NA	intron (NM_031923, intron 2 of 6)	MLT1H2|LTR|ERVL-MaLR	101247	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.010545	0.456140	
chunk0208_398_1	chrX	29044334	29044817	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	457011	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.012422	0.365702	
chunk0094_105_1	chr2	4234398	4235200	+	0	NA	Intergenic	Intergenic	-260767	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.003741	0.351183	
chunk0063_296_1	chr14	84520641	84520851	+	0	NA	Intergenic	L1MA3|LINE|L1	-873133	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.502370	
chunk0136_129_1	chr4	3763201	3763410	+	0	NA	Intergenic	Intergenic	-3264	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.052632	0.614286	86(GGGTACGTGCTGTTCT,-,0.00),87(GGTACGTGCTGTTCTG,+,0.00)
chunk0014_342_1	chr1	182228248	182228525	+	0	NA	intron (NR_104175, intron 2 of 2)	L3|LINE|CR1	85675	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.007220	0.374101	
chunk0203_189_1	chr9	86404130	86404644	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-49900	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.005837	0.444660	308(AAGAACATTATGTTAT,-,0.00)
chunk0212_442_1	chrX	155068684	155068894	+	0	NA	intron (NM_001018025, intron 1 of 4)	intron (NM_001018025, intron 1 of 4)	2483	NM_001018024	100272147	Hs.6917	NM_001018024	ENSG00000182712	CMC4	C6.1B|MTCP1|MTCP1B|MTCP1NB|p8|p8MTCP1	C-X9-C motif containing 4	protein-coding	0.009524	0.312796	
chunk0097_9_1	chr2	41448394	41449146	+	0	NA	Intergenic	Intergenic	-428785	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.007979	0.361222	388(AGGACTCAGTGATCCT,+,0.00)
chunk0033_320_1	chr11	20840341	20840785	+	0	NA	intron (NM_001288714, intron 3 of 18)	MLT1G|LTR|ERVL-MaLR	171012	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.002252	0.449438	
chunk0052_430_1	chr12	131865920	131866144	+	0	NA	Intergenic	L1ME3F|LINE|L1	-28702	NM_003565	8408	Hs.47061	NM_003565	ENSG00000177169	ULK1	ATG1|ATG1A|UNC51|Unc51.1|hATG1	unc-51 like autophagy activating kinase 1	protein-coding	0.013393	0.364444	
chunk0076_196_1	chr16	67926218	67926749	+	0	NA	intron (NM_006742, intron 2 of 2)	intron (NM_006742, intron 2 of 2)	5392	NM_001907	1506	Hs.654546	NM_001907	ENSG00000141086	CTRL	CTRL1	chymotrypsin like	protein-coding	0.022599	0.569549	412(GGGGACAGAATGTACT,-,0.00),413(GGGACAGAATGTACTA,+,0.00)
chunk0183_281_1	chr7	107597739	107598310	+	0	NA	intron (NM_001008405, intron 4 of 7)	intron (NM_001008405, intron 4 of 7)	17265	NM_001008405	55973	Hs.303787	NM_018844	ENSG00000075790	BCAP29	BAP29	B cell receptor associated protein 29	protein-coding	0.010508	0.346154	
chunk0148_433_1	chr4	189121364	189121834	+	0	NA	Intergenic	L1PB1|LINE|L1	-538007	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.008511	0.371550	
chunk0103_143_1	chr2	162125307	162125832	+	0	NA	intron (NR_110255, intron 1 of 3)	L2c|LINE|L2	11128	NR_110255	101929532	Hs.639883	NR_110255	ENSG00000236841	LOC101929532	-	uncharacterized LOC101929532	ncRNA	0.009524	0.437262	
chunk0210_429_1	chrX	103236313	103236694	+	0	NA	Intergenic	L1MD2|LINE|L1	18690	NM_153333	90843	Hs.389734	NM_153333	ENSG00000180964	TCEAL8	WEX3	transcription elongation factor A like 8	protein-coding	0.002625	0.348168	
chunk0135_297_1	chr3	189674373	189674573	+	0	NA	intron (NM_001114978, intron 1 of 12)	LTR16E1|LTR|ERVL	43046	NM_001114978	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.015000	0.407960	
chunk0011_172_1	chr1	147716792	147717282	+	0	NA	Intergenic	Intergenic	43569	NM_181703	2702	Hs.447968	NM_005266	ENSG00000265107	GJA5	ATFB11|CX40	gap junction protein alpha 5	protein-coding	0.006122	0.407332	
chunk0155_404_1	chr5	99089860	99090122	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	160857	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.003817	0.429658	
chunk0109_363_1	chr2	239299121	239299617	+	0	NA	intron (NM_006037, intron 2 of 26)	intron (NM_006037, intron 2 of 26)	-6093	NR_036229	100423043		NR_036229	ENSG00000265215	MIR4269	-	microRNA 4269	ncRNA	0.022177	0.466801	
chunk0118_328_1	chr22	35430882	35431254	+	0	NA	Intergenic	Intergenic	30945	NM_006739	4174	Hs.517582	NM_006739	ENSG00000100297	MCM5	CDC46|MGORS8|P1-CDC46	minichromosome maintenance complex component 5	protein-coding	0.026882	0.584450	
chunk0002_68_1	chr1	13957787	13958304	+	0	NA	Intergenic	Intergenic	208664	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.009671	0.405405	
chunk0155_259_1	chr5	95784515	95785127	+	0	NA	intron (NM_014899, intron 10 of 11)	intron (NM_014899, intron 10 of 11)	38052	NM_001243658	2745	Hs.28988	NM_002064	ENSG00000173221	GLRX	GRX|GRX1	glutaredoxin	protein-coding	0.009804	0.417618	
chunk0202_364_1	chr9	80387897	80388500	+	0	NA	Intergenic	Intergenic	413175	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.004975	0.400662	
chunk0156_300_1	chr5	110178252	110178611	+	0	NA	Intergenic	Intergenic	295249	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.002786	0.313889	
chunk0168_366_1	chr6	93472072	93472271	+	0	NA	Intergenic	Intergenic	-52589	NM_001288629	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.005025	0.360000	
chunk0168_377_1	chr6	93940159	93940917	+	0	NA	Intergenic	Intergenic	233455	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.002639	0.361001	
chunk0009_84_1	chr1	101156176	101156375	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	80253	NR_104626	101928370	Hs.534209	NR_104626		LOC101928370	-	uncharacterized LOC101928370	ncRNA	0.005025	0.395000	
chunk0004_464_1	chr1	53898907	53899481	+	0	NA	intron (NM_001039715, intron 1 of 2)	intron (NM_001039715, intron 1 of 2)	5006	NM_001039716	1733	Hs.251415	NM_000792	ENSG00000211452	DIO1	5DI|TXDI1	iodothyronine deiodinase 1	protein-coding	0.013937	0.469565	
chunk0128_382_1	chr3	113536690	113537014	+	0	NA	intron (NM_001308350, intron 1 of 25)	intron (NM_001308350, intron 1 of 25)	4481	NM_017699	54847	Hs.591291	NM_017699	ENSG00000072858	SIDT1	SID-1|SID1	SID1 transmembrane family member 1	protein-coding	0.000000	0.415385	
chunk0022_465_1	chr10	20457326	20457755	+	0	NA	Intergenic	Intergenic	-94430	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.002331	0.300000	
chunk0118_454_1	chr22	39773799	39774315	+	0	NA	intron (NM_152512, intron 5 of 6)	L2c|LINE|L2	119733	NM_152512	150350	Hs.474869	NM_152512	ENSG00000176177	ENTHD1	CACNA1I|dJ370M22.3	ENTH domain containing 1	protein-coding	0.007752	0.419729	161(CTGTACACAATGTGCT,-,0.00),162(TGTACACAATGTGCTG,+,0.00),452(GTAAACAGTCTGTCCT,-,0.00),453(TAAACAGTCTGTCCTT,+,0.00)
chunk0071_385_1	chr15	89136636	89137213	+	0	NA	intron (NM_007011, intron 7 of 14)	intron (NM_007011, intron 7 of 14)	48774	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.013865	0.484429	
chunk0112_316_1	chr20	44548186	44548851	+	0	NA	intron (NM_007066, intron 1 of 3)	intron (NM_007066, intron 1 of 3)	16737	NM_007066	11142	Hs.472831	NM_007066	ENSG00000168734	PKIG	PKI-gamma	cAMP-dependent protein kinase inhibitor gamma	protein-coding	0.006015	0.345345	
chunk0111_442_1	chr20	35308221	35308512	+	0	NA	intron (NM_199487, intron 7 of 8)	intron (NM_199487, intron 7 of 8)	-15944	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.020619	0.558219	
chunk0003_107_1	chr1	32179144	32179791	+	0	NA	promoter-TSS (NM_175852)	promoter-TSS (NM_175852)	-277	NM_175852	200081	Hs.17987	NM_175852	ENSG00000084652	TXLNA	IL14|TXLN	taxilin alpha	protein-coding	0.064915	0.591049	98(GAGAACAGAACGTCCA,-,0.00),99(AGAACAGAACGTCCAG,+,0.00)
chunk0188_346_1	chr8	17836214	17837074	+	0	NA	Intergenic	Intergenic	-35727	NM_001001924	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.004651	0.370499	
chunk0080_209_1	chr17	29412972	29413369	+	0	NA	intron (NM_025142, intron 1 of 17)	Tigger15a|DNA|TcMar-Tigger	22245	NM_020791	57551	Hs.597434	NM_020791	ENSG00000160551	TAOK1	KFC-B|MAP3K16|MARKK|PSK-2|PSK2|TAO1|hKFC-B|hTAOK1	TAO kinase 1	protein-coding	0.007557	0.371859	
chunk0152_124_1	chr5	58809986	58810683	+	0	NA	intron (NM_138453, intron 3 of 4)	intron (NM_138453, intron 3 of 4)	189598	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002869	0.455587	365(AAGTACTCTGTGTGCT,-,0.00),366(AGTACTCTGTGTGCTC,+,0.00)
chunk0080_328_1	chr17	32422879	32423369	+	0	NA	Intergenic	Intergenic	-21339	NM_002815	5717	Hs.443379	NM_002815	ENSG00000108671	PSMD11	Rpn6|S9|p44.5	proteasome 26S subunit, non-ATPase 11	protein-coding	0.000000	0.393075	
chunk0086_124_1	chr18	20970114	20970313	+	0	NA	intron (NM_005406, intron 23 of 32)	intron (NM_005406, intron 23 of 32)	141638	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.000000	0.285000	
chunk0053_109_1	chr13	28952640	28952950	+	0	NA	Intergenic	L1MC4a|LINE|L1	-71816	NM_001033602	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.006452	0.295820	
chunk0193_132_1	chr8	74406027	74406653	+	0	NA	Intergenic	Intergenic	55957	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.003195	0.363636	
chunk0084_63_1	chr17	74707129	74707366	+	0	NA	intron (NM_001289082, intron 1 of 6)	L1M3|LINE|L1	5753	NM_001289084	146722	Hs.567706	NM_139018	ENSG00000186074	CD300LF	CD300f|CLM-1|CLM1|IREM-1|IREM1|IgSF13|LMIR3|NKIR	CD300 molecule like family member f	protein-coding	0.004219	0.361345	
chunk0049_182_1	chr12	92564077	92564501	+	0	NA	Intergenic	Intergenic	-136141	NM_001025232	574016	Hs.551199	NM_001025232	ENSG00000205057	CLLU1OS	-	chronic lymphocytic leukemia up-regulated 1 opposite strand	protein-coding	0.000000	0.327059	177(CAGAACACTGTGAGCT,-,0.00),178(AGAACACTGTGAGCTT,+,0.00)
chunk0134_25_1	chr3	175537555	175538003	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	168239	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.002232	0.318486	
chunk0040_124_1	chr11	112307673	112308066	+	0	NA	intron (NR_126004, intron 2 of 3)	MIRb|SINE|MIR	37120	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.000000	0.416244	
chunk0192_380_1	chr8	68596644	68597014	+	0	NA	intron (NM_052958, intron 7 of 13)	LTR40a|LTR|ERVL	-265338	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.002703	0.382749	
chunk0046_328_1	chr12	62724971	62725281	+	0	NA	intron (NM_020700, intron 5 of 9)	Kanga1b|DNA|TcMar-Tc2	121440	NR_029661	406891		NR_029661	ENSG00000199179	MIRLET7I	LET7I|MIRNLET7I|hsa-let-7i|let-7i	microRNA let-7i	ncRNA	0.009677	0.472669	
chunk0112_303_1	chr20	44344865	44345471	+	0	NA	intron (NM_178491, intron 3 of 4)	intron (NM_178491, intron 3 of 4)	8010	NM_178491	140902	Hs.580807	NM_178491	ENSG00000101074	R3HDML	dJ881L22.3	R3H domain containing like	protein-coding	0.014851	0.462932	
chunk0138_13_1	chr4	30393248	30393461	+	0	NA	Intergenic	Intergenic	-327054	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.004695	0.373832	
chunk0054_33_1	chr13	41017122	41017537	+	0	NA	intron (NM_172373, intron 1 of 8)	MIR3|SINE|MIR	2043	NM_172373	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.004819	0.362981	183(TGGCACAAGCAGTTCC,-,0.00),184(GGCACAAGCAGTTCCA,+,0.00)
chunk0023_5_1	chr10	20648751	20648950	+	0	NA	Intergenic	MER51E|LTR|ERV1	96880	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.000000	0.520000	
chunk0204_236_1	chr9	97871411	97871650	+	0	NA	Intergenic	L1PB|LINE|L1	18275	NM_004473	2304		NM_004473	ENSG00000178919	FOXE1	FKHL15|FOXE2|HFKH4|HFKL5|NMTC4|TITF2|TTF-2|TTF2	forkhead box E1	protein-coding	0.000000	0.341667	
chunk0098_427_1	chr2	81559342	81559787	+	0	NA	Intergenic	L1MC1|LINE|L1	-92618	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.004494	0.304933	
chunk0046_209_1	chr12	59263534	59264176	+	0	NA	Intergenic	L2a|LINE|L2	-332185	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.007788	0.359253	
chunk0046_454_1	chr12	64919117	64919435	+	0	NA	intron (NR_033988, intron 2 of 2)	intron (NR_033988, intron 2 of 2)	35502	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.006289	0.485893	
chunk0166_197_1	chr6	46506299	46506503	+	0	NA	intron (NR_125837, intron 1 of 2)	intron (NR_125837, intron 1 of 2)	-14334	NM_001251973	10231	Hs.440168	NM_005822	ENSG00000172348	RCAN2	CSP2|DSCR1L1|MCIP2|RCN2|ZAKI-4|ZAKI4	regulator of calcineurin 2	protein-coding	0.009804	0.448780	
chunk0022_115_1	chr10	10879045	10879337	+	0	NA	Intergenic	Intergenic	72972	NR_024411	254312	Hs.498620	NR_015413	ENSG00000229240	LINC00710	-	long intergenic non-protein coding RNA 710	ncRNA	0.013699	0.447099	
chunk0045_350_1	chr12	51546197	51546670	+	0	NA	Intergenic	L1ME2|LINE|L1	-44803	NM_001177984	6334	Hs.436550	NM_014191	ENSG00000196876	SCN8A	BFIS5|CERIII|CIAT|EIEE13|MED|MYOCL2|NaCh6|Nav1.6|PN4	sodium voltage-gated channel alpha subunit 8	protein-coding	0.004228	0.356540	
chunk0004_114_1	chr1	44532485	44532961	+	0	NA	intron (NM_018150, intron 2 of 14)	MIRb|SINE|MIR	-12770	NR_049849	100847089		NR_049849	ENSG00000263381	MIR5584	-	microRNA 5584	ncRNA	0.008403	0.452830	
chunk0075_320_1	chr16	54540665	54541217	+	0	NA	Intergenic	Intergenic	-254475	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.021739	0.470163	249(TGGGACAGCTTGTGCT,-,0.00),250(GGGACAGCTTGTGCTG,+,0.00)
chunk0065_212_1	chr14	100209900	100210267	+	0	NA	Intergenic	FLAM_C|SINE|Alu	-28682	NM_003403	7528	Hs.388927	NM_003403	ENSG00000100811	YY1	DELTA|GADEVS|INO80S|NF-E1|UCRBP|YIN-YANG-1	YY1 transcription factor	protein-coding	0.019074	0.467391	
chunk0076_424_1	chr16	72989534	72990694	+	0	NA	intron (NM_006885, intron 1 of 9)	intron (NM_006885, intron 1 of 9)	58261	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.018966	0.484065	184(CAGCACACAGAGTTCT,-,0.00),185(AGCACACAGAGTTCTA,+,0.00),790(GAGAACACAGAGTTTC,-,0.00)
chunk0017_392_1	chr1	212414262	212414739	+	0	NA	intron (NM_001198862, intron 1 of 8)	CpG	401	NM_001198862	55248	Hs.445386	NM_018252	ENSG00000065600	PACC1	C1orf75|PAC|TMEM206	proton activated chloride channel 1	protein-coding	0.098532	0.702929	
chunk0106_38_1	chr2	196145786	196146043	+	0	NA	exon (NM_004226, exon 4 of 8)	exon (NM_004226, exon 4 of 8)	25698	NM_004226	9262	Hs.88297	NM_004226	ENSG00000081320	STK17B	DRAK2	serine/threonine kinase 17b	protein-coding	0.007782	0.360465	
chunk0181_30_1	chr7	78350765	78351301	+	0	NA	intron (NR_003680, intron 3 of 5)	intron (NR_003680, intron 3 of 5)	3791	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.005597	0.446927	
chunk0024_420_1	chr10	45697854	45698096	+	0	NA	Intergenic	Intergenic	-25162	NR_104256	93550	Hs.89029	NM_174890	ENSG00000172671	ZFAND4	ANUBL1	zinc finger AN1-type containing 4	protein-coding	0.016529	0.374486	
chunk0078_80_1	chr17	1787418	1787865	+	0	NA	intron (NM_052928, intron 5 of 10)	intron (NM_052928, intron 5 of 10)	25676	NM_002615	5176	Hs.532768	NM_002615	ENSG00000132386	SERPINF1	EPC-1|OI12|OI6|PEDF|PIG35	serpin family F member 1	protein-coding	0.029083	0.544643	
chunk0076_358_1	chr16	71771578	71771782	+	0	NA	intron (NM_001128, intron 4 of 22)	intron (NM_001128, intron 4 of 22)	-13193	NR_003059	692111		NR_003059	ENSG00000223224	SNORD71	HBII-239|MIRN768|hsa-mir-768	small nucleolar RNA, C/D box 71	snoRNA	0.000000	0.273171	
chunk0108_9_1	chr2	226002402	226002775	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-140206	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.008043	0.449198	330(TAGGACTTCCTGTACT,-,0.00),331(AGGACTTCCTGTACTT,+,0.00)
chunk0138_72_1	chr4	34280862	34281232	+	0	NA	Intergenic	L1PBb|LINE|L1	-241154	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.002703	0.466307	
chunk0039_56_1	chr11	96212665	96212864	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-128674	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.010050	0.365000	
chunk0201_135_1	chr9	35696730	35697264	+	0	NA	TTS (NM_006289)	TTS (NM_006289)	-6941	NM_001301226	7169	Hs.300772	NM_003289	ENSG00000198467	TPM2	AMCD1|DA1|DA2B|DA2B4|HEL-S-273|NEM4|TMSB	tropomyosin 2	protein-coding	0.009363	0.497196	296(AAGAACAGAATGTCCT,-,0.00),297(AGAACAGAATGTCCTG,+,0.00)
chunk0165_229_1	chr6	35401592	35401941	+	0	NA	intron (NM_001171818, intron 3 of 8)	intron (NM_001171818, intron 3 of 8)	-50595	NM_021922	2178	Hs.302003	NM_021922	ENSG00000112039	FANCE	FACE|FAE	FA complementation group E	protein-coding	0.014327	0.554286	
chunk0206_178_1	chr9	122524320	122524745	+	0	NA	Intergenic	Intergenic	2761	NM_012363	138883	Hs.553604	NM_012363	ENSG00000171505	OR1N1	OR1-26|OR1N3|OR9-22	olfactory receptor family 1 subfamily N member 1	protein-coding	0.011765	0.401408	
chunk0211_303_1	chrX	123309264	123310000	+	0	NA	intron (NM_007325, intron 3 of 15)	intron (NM_007325, intron 3 of 15)	125389	NM_007325	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.004076	0.421981	
chunk0200_374_1	chr9	26331242	26331701	+	0	NA	Intergenic	Intergenic	264796	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.006536	0.389130	
chunk0073_339_1	chr16	14528402	14528646	+	0	NA	intron (NM_002582, intron 21 of 23)	intron (NM_002582, intron 21 of 23)	101747	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.008197	0.428571	75(AGGGACATGCTGTCAT,-,0.00),76(GGGACATGCTGTCATT,+,0.00)
chunk0070_58_1	chr15	69594116	69595020	+	0	NA	intron (NR_126438, intron 1 of 3)	intron (NR_126438, intron 1 of 3)	2368	NR_126437	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.025442	0.554696	624(ATCACAGGCTGTTCTA,+,0.00)
chunk0121_242_1	chr3	22682691	22683258	+	0	NA	Intergenic	MIRb|SINE|MIR	-520319	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005291	0.339789	
chunk0005_78_1	chr1	55988656	55989197	+	0	NA	Intergenic	Intergenic	590658	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.007394	0.372694	
chunk0184_185_1	chr7	116738262	116738924	+	0	NA	intron (NM_000245, intron 3 of 20)	intron (NM_000245, intron 3 of 20)	66188	NM_000245	4233	Hs.132966	NM_000245	ENSG00000105976	MET	AUTS9|DFNB97|HGFR|RCCP2|c-Met	MET proto-oncogene, receptor tyrosine kinase	protein-coding	0.004532	0.369532	
chunk0012_347_1	chr1	162660540	162661079	+	0	NA	intron (NM_006182, intron 2 of 17)	MER58A|DNA|hAT-Charlie	28371	NM_006182	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.005566	0.416667	
chunk0078_245_1	chr17	7088149	7088836	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-8211	NM_182906	10462	Hs.54403	NM_006344	ENSG00000132514	CLEC10A	CD301|CLECSF13|CLECSF14|HML|HML2|MGL	C-type lectin domain containing 10A	protein-coding	0.007278	0.453488	461(AGGGACACAGTGCACT,-,0.00),462(GGGACACAGTGCACTG,+,0.00)
chunk0096_364_1	chr2	36479559	36479916	+	0	NA	intron (NM_016441, intron 7 of 16)	intron (NM_016441, intron 7 of 16)	118452	NM_005102	9637	Hs.258563	NM_005102	ENSG00000171055	FEZ2	HUM3CL	fasciculation and elongation protein zeta 2	protein-coding	0.039216	0.480447	
chunk0184_223_1	chr7	117471755	117472214	+	0	NA	Intergenic	Intergenic	-7979	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.004357	0.347826	
chunk0140_430_1	chr4	76148315	76148719	+	0	NA	promoter-TSS (NM_001278603)	promoter-TSS (NM_001278603)	-2	NM_017426	53371	Hs.430435	NM_017426	ENSG00000138750	NUP54	-	nucleoporin 54	protein-coding	0.071782	0.609877	143(CAGATCACCGAGTTCC,-,0.00)
chunk0015_186_1	chr1	187236089	187236379	+	0	NA	intron (NR_126347, intron 1 of 3)	intron (NR_126347, intron 1 of 3)	143392	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.006897	0.353952	
chunk0090_168_1	chr18	72645665	72646034	+	0	NA	Intergenic	Intergenic	-101361	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.008130	0.470270	
chunk0163_230_1	chr6	12293823	12294199	+	0	NA	exon (NM_001168319, exon 3 of 5)	exon (NM_001168319, exon 3 of 5)	3715	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.007979	0.427056	
chunk0110_317_1	chr20	18686569	18687255	+	0	NA	intron (NR_109955, intron 2 of 3)	L2a|LINE|L2	11796	NR_109955	101929526	Hs.639402	NR_109955	ENSG00000233993	LOC101929526	-	uncharacterized LOC101929526	ncRNA	0.001458	0.451237	
chunk0078_376_1	chr16	87616702	87617039	+	0	NA	intron (NM_020655, intron 1 of 4)	L1MD1|LINE|L1	13983	NM_001271605	57338	Hs.592068	NM_020655	ENSG00000154118	JPH3	CAGL237|HDL2|JP-3|JP3|TNRC22	junctophilin 3	protein-coding	0.044510	0.553254	
chunk0181_286_1	chr7	86876184	86876437	+	0	NA	TTS (NM_152748)	TTS (NM_152748)	89665	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.000000	0.370079	
chunk0093_201_1	chr19	49412911	49413322	+	0	NA	intron (NM_144688, intron 16 of 19)	intron (NM_144688, intron 16 of 19)	10325	NM_178449	113091	Hs.339845	NM_178449	ENSG00000142538	PTH2	TIP39	parathyroid hormone 2	protein-coding	0.014599	0.563107	178(GAGGACTGGATGTGCC,-,0.00),179(AGGACTGGATGTGCCC,+,0.00)
chunk0047_442_1	chr12	76439748	76440181	+	0	NA	intron (NM_001003712, intron 3 of 22)	L1ME3D|LINE|L1	-91522	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.002309	0.315668	
chunk0091_213_1	chr19	9768697	9768896	+	0	NA	promoter-TSS (NM_001077624)	promoter-TSS (NM_001077624)	-62	NM_001077624	162993	Hs.665717	NM_001077624	ENSG00000196605	ZNF846	-	zinc finger protein 846	protein-coding	0.075377	0.575000	
chunk0078_367_1	chr16	87379197	87379731	+	0	NA	intron (NM_001282683, intron 2 of 9)	LTR22A|LTR|ERVK	4329	NM_024735	79791	Hs.567582	NM_024735	ENSG00000103264	FBXO31	FBX14|FBXO14|Fbx31|MRT45|pp2386	F-box protein 31	protein-coding	0.005618	0.497196	261(CAGCACATGATGTTCC,-,0.00),262(AGCACATGATGTTCCC,+,0.00)
chunk0200_232_1	chr9	20725617	20726196	+	0	NA	intron (NM_017794, intron 6 of 45)	intron (NM_017794, intron 6 of 45)	9801	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.008636	0.363793	183(GGGTCTGGCTGTGCTT,+,0.00)
chunk0207_319_1	chr9	134065871	134066517	+	0	NA	intron (NM_007371, intron 1 of 11)	intron (NM_007371, intron 1 of 11)	1825	NM_007371	8019	Hs.522472	NM_007371	ENSG00000169925	BRD3	ORFX|RING3L	bromodomain containing 3	protein-coding	0.032508	0.542504	
chunk0167_204_1	chr6	64932580	64932838	+	0	NA	intron (NM_001142800, intron 15 of 42)	L1MB7|LINE|L1	-368709	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.000000	0.374517	
chunk0106_206_1	chr2	202339549	202339989	+	0	NA	Intergenic	Intergenic	-36558	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.004545	0.394558	
chunk0104_29_1	chr2	170739159	170739996	+	0	NA	intron (NR_110185, intron 1 of 5)	MER113|DNA|hAT-Charlie	24230	NM_001003845	389058	Hs.368802	NM_001003845	ENSG00000204335	SP5	-	Sp5 transcription factor	protein-coding	0.004779	0.386635	
chunk0012_265_1	chr1	161736512	161736778	+	0	NA	Intergenic	LTR78|LTR|ERV1	-13123	NM_007240	11266	Hs.416216	NM_007240	ENSG00000081721	DUSP12	DUSP1|YVH1	dual specificity phosphatase 12	protein-coding	0.000000	0.400749	
chunk0121_320_1	chr3	24287686	24288693	+	0	NA	intron (NM_000461, intron 2 of 9)	intron (NM_000461, intron 2 of 9)	136865	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.005958	0.405754	
chunk0088_317_1	chr18	50813224	50813423	+	0	NA	intron (NM_001127174, intron 1 of 5)	intron (NM_001127174, intron 1 of 5)	6741	NM_001127175	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.000000	0.455000	
chunk0124_134_1	chr3	54370418	54370986	+	0	NA	intron (NM_018398, intron 3 of 37)	L1MB8|LINE|L1	248036	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.005282	0.355009	203(AAGGACTTATTGTACC,-,0.00),204(AGGACTTATTGTACCC,+,0.00)
chunk0176_130_1	chr7	12618539	12618842	+	0	NA	intron (NM_033128, intron 2 of 13)	intron (NM_033128, intron 2 of 13)	29167	NM_033128	85477	Hs.633359	NM_033128	ENSG00000006747	SCIN	-	scinderin	protein-coding	0.003300	0.348684	
chunk0068_215_1	chr15	55228795	55229195	+	0	NA	intron (NM_183236, intron 4 of 6)	intron (NM_183236, intron 4 of 6)	-31962	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.002500	0.356608	
chunk0102_135_1	chr2	145799404	145799784	+	0	NA	Intergenic	Intergenic	-787463	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.007895	0.393701	
chunk0128_254_1	chr3	108981103	108981534	+	0	NA	intron (NM_014429, intron 23 of 27)	intron (NM_014429, intron 23 of 27)	-27488	NM_005459	9626	Hs.233363	NM_005459	ENSG00000138472	GUCA1C	GCAP3	guanylate cyclase activator 1C	protein-coding	0.004640	0.324074	
chunk0098_24_1	chr2	65432552	65432775	+	0	NA	promoter-TSS (NM_181784)	promoter-TSS (NM_181784)	-141	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.080717	0.593750	
chunk0126_62_1	chr3	74393402	74393748	+	0	NA	intron (NM_020872, intron 4 of 21)	L2b|LINE|L2	127565	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.008671	0.438040	
chunk0128_409_1	chr3	114566818	114567151	+	0	NA	intron (NR_121662, intron 3 of 6)	intron (NR_121662, intron 3 of 6)	57222	NM_001164347	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.000000	0.431138	
chunk0087_288_1	chr18	38883327	38884113	+	0	NA	Intergenic	Intergenic	738455	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.006361	0.378653	
chunk0104_300_1	chr2	178802506	178803412	+	0	NA	intron (NM_133378, intron 2 of 311)	intron (NM_133378, intron 2 of 311)	4464	NM_133437	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.002208	0.392503	330(AGGGACACTGTCTTCT,-,0.00),331(GGGACACTGTCTTCTT,+,0.00),510(AAGAACTACATGTCCA,-,0.00),511(AGAACTACATGTCCAT,+,0.00)
chunk0056_464_1	chr13	95288820	95289283	+	0	NA	intron (NM_001105515, intron 1 of 20)	intron (NM_001105515, intron 1 of 20)	12395	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.008639	0.362069	
chunk0044_98_1	chr12	28464268	28464556	+	0	NA	intron (NM_018318, intron 10 of 11)	L1MA2|LINE|L1	207212	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.006944	0.529412	
chunk0191_33_1	chr8	43056119	43056318	+	0	NA	promoter-TSS (NM_002027)	promoter-TSS (NM_002027)	-81	NM_002027	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.085427	0.695000	
chunk0172_414_1	chr6	140125510	140126088	+	0	NA	Intergenic	MIRb|SINE|MIR	-79453	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.000000	0.307427	456(TAGTACAGACAGTTCC,-,0.00),457(AGTACAGACAGTTCCC,+,0.00)
chunk0093_182_1	chr19	48684471	48684697	+	0	NA	Intergenic	Intergenic	-11387	NM_000511	2524	Hs.579928	NM_000511	ENSG00000176920	FUT2	B12QTL1|SE|SEC2|Se2|sej	fucosyltransferase 2	protein-coding	0.004425	0.475771	
chunk0184_68_1	chr7	112531860	112532421	+	0	NA	Intergenic	Intergenic	51129	NM_182597	286006	Hs.396189	NM_182597	ENSG00000181016	LSMEM1	C7orf53	leucine rich single-pass membrane protein 1	protein-coding	0.001783	0.336299	
chunk0070_444_1	chr15	78348170	78348464	+	0	NA	TTS (NM_004378)	TTS (NM_004378)	7993	NM_004378	1381	Hs.346950	NM_004378	ENSG00000166426	CRABP1	CRABP|CRABP-I|CRABPI|RBP5	cellular retinoic acid binding protein 1	protein-coding	0.027211	0.501695	
chunk0147_4_1	chr4	170512192	170512568	+	0	NA	Intergenic	Intergenic	285789	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.005319	0.350133	143(CTGAACAAAATGTTCT,-,0.00),144(TGAACAAAATGTTCTT,+,0.00)
chunk0105_315_1	chr2	190499165	190499846	+	0	NA	intron (NM_017694, intron 7 of 7)	intron (NM_017694, intron 7 of 7)	35237	NM_001142645	100131211	Hs.659824	NM_001142645	ENSG00000189362	NEMP2	TMEM194B	nuclear envelope integral membrane protein 2	protein-coding	0.005874	0.365103	
chunk0173_402_1	chr6	150659814	150660106	+	0	NA	intron (NM_001029884, intron 2 of 16)	intron (NM_001029884, intron 2 of 16)	60097	NM_001029884	57480	Hs.189781	NM_001029884	ENSG00000120278	PLEKHG1	ARHGEF41	pleckstrin homology and RhoGEF domain containing G1	protein-coding	0.006849	0.361775	
chunk0178_356_1	chr7	38858499	38858874	+	0	NA	intron (NM_014396, intron 4 of 28)	Tigger3b|DNA|TcMar-Tigger	50514	NM_080631	27072	Hs.592184	NM_014396	ENSG00000006715	VPS41	HVPS41|HVSP41|hVps41p	VPS41 subunit of HOPS complex	protein-coding	0.005333	0.345745	
chunk0135_389_1	chr3	191282812	191283429	+	0	NA	intron (NM_198152, intron 4 of 8)	intron (NM_198152, intron 4 of 8)	-45965	NM_174908	152137	Hs.478682	NM_174908	ENSG00000152492	CCDC50	C3orf6|DFNA44|YMER	coiled-coil domain containing 50	protein-coding	0.003241	0.339806	
chunk0095_171_1	chr2	17593693	17594195	+	0	NA	intron (NM_003385, intron 2 of 3)	intron (NM_003385, intron 2 of 3)	53404	NM_003385	7447	Hs.444212	NM_003385	ENSG00000163032	VSNL1	HLP3|HPCAL3|HUVISL1|VILIP|VILIP-1	visinin like 1	protein-coding	0.005976	0.385686	300(GAGAGCACCGTGTGCC,-,0.00),301(AGAGCACCGTGTGCCA,+,0.00)
chunk0179_69_1	chr7	43952055	43952625	+	0	NA	intron (NM_015983, intron 6 of 6)	intron (NM_015983, intron 6 of 6)	25904	NM_015983	51619	Hs.19196	NM_015983	ENSG00000078967	UBE2D4	HBUCE1	ubiquitin conjugating enzyme E2 D4 (putative)	protein-coding	0.007018	0.497373	242(AGTACAAACTGACCTT,+,0.00)
chunk0126_125_1	chr3	75782474	75782818	+	0	NA	intron (NM_001290209, intron 2 of 4)	intron (NM_001290209, intron 2 of 4)	2458	NM_001128223	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.026163	0.495652	
chunk0028_332_1	chr10	92052158	92052552	+	0	NA	exon (NM_014912, exon 10 of 10)	exon (NM_014912, exon 10 of 10)	128376	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.045685	0.521519	
chunk0126_283_1	chr3	80141957	80142459	+	0	NA	Intergenic	L1MEg|LINE|L1	-374299	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003984	0.345924	
chunk0021_2_1	chr10	135911	136167	+	0	NA	intron (NM_001202464, intron 1 of 13)	CpG	555	NM_001202464	10771	Hs.292265	NM_006624	ENSG00000015171	ZMYND11	BRAM1|BS69|MRD30	zinc finger MYND-type containing 11	protein-coding	0.148438	0.778210	114(CGGCACGTCGTGTGCT,-,0.00)
chunk0042_202_1	chr12	5878405	5879183	+	0	NA	intron (NM_001278596, intron 3 of 25)	intron (NM_001278596, intron 3 of 25)	66465	NM_001278596	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.007712	0.432606	420(AGAAACACACTGTCCA,-,0.00),421(GAAACACACTGTCCAG,+,0.00)
chunk0162_444_1	chr5	180605833	180606305	+	0	NA	intron (NM_182925, intron 29 of 29)	LTR16D|LTR|ERVL	-14582	NM_052863	92304	Hs.62492	NM_052863	ENSG00000161055	SCGB3A1	HIN-1|HIN1|LU105|PnSP-2|UGRP2	secretoglobin family 3A member 1	protein-coding	0.021186	0.532770	
chunk0046_144_1	chr12	58120015	58120660	+	0	NA	Intergenic	L1MC5|LINE|L1	178675	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.001550	0.376161	
chunk0142_318_1	chr4	100829092	100829531	+	0	NA	Intergenic	MER68|LTR|ERVL	-154198	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.002278	0.406818	
chunk0043_214_1	chr12	19620246	19620445	+	0	NA	Intergenic	Intergenic	179764	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.025126	0.460000	
chunk0208_446_1	chrX	31376374	31376936	+	0	NA	intron (NM_004021, intron 17 of 34)	intron (NM_004021, intron 17 of 34)	-109748	NM_004015	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.003559	0.458259	
chunk0189_278_1	chr8	25383180	25383469	+	0	NA	intron (NM_024940, intron 40 of 51)	intron (NM_024940, intron 40 of 51)	37922	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.010381	0.303448	
chunk0008_208_1	chr1	93584717	93585665	+	0	NA	promoter-TSS (NM_001308251)	promoter-TSS (NM_001308251)	-29	NM_001308251	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.014768	0.482613	
chunk0022_61_1	chr10	8407446	8408181	+	0	NA	Intergenic	Intergenic	-139508	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.000000	0.421196	
chunk0001_400_1	chr1	10788693	10788968	+	0	NA	intron (NM_001079843, intron 1 of 20)	intron (NM_001079843, intron 1 of 20)	7846	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.032727	0.670290	
chunk0170_174_1	chr6	111707908	111708209	+	0	NA	intron (NM_153048, intron 3 of 10)	intron (NM_153048, intron 3 of 10)	12004	NM_153047	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.009967	0.443709	
chunk0050_131_1	chr12	102234482	102234706	+	0	NA	Intergenic	Intergenic	-36749	NM_002674	5367	Hs.707990	NM_002674	ENSG00000183395	PMCH	MCH|ppMCH	pro-melanin concentrating hormone	protein-coding	0.000000	0.377778	
chunk0134_127_1	chr3	177371282	177371599	+	0	NA	Intergenic	Arthur1A|DNA|hAT-Tip100	-70481	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.000000	0.349057	
chunk0108_312_1	chr2	235344329	235344589	+	0	NA	Intergenic	(CACACA)n|Simple_repeat|Simple_repeat	-149630	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.007692	0.547893	
chunk0058_327_1	chr14	28403862	28404194	+	0	NA	Intergenic	Intergenic	361291	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.006024	0.312312	
chunk0181_290_1	chr7	86942227	86942481	+	0	NA	intron (NM_001291990, intron 4 of 21)	intron (NM_001291990, intron 4 of 21)	23621	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.003937	0.403922	
chunk0085_384_1	chr18	9854917	9855724	+	0	NA	intron (NM_006868, intron 6 of 6)	intron (NM_006868, intron 6 of 6)	-30406	NM_001098529	84203	Hs.98712	NM_032243	ENSG00000168454	TXNDC2	SPTRX|SPTRX1	thioredoxin domain containing 2	protein-coding	0.017348	0.424505	426(AAGGACAACTTGTTCT,-,0.00),427(AGGACAACTTGTTCTG,+,0.00)
chunk0120_64_1	chr3	3216245	3216444	+	0	NA	Intergenic	Intergenic	-36627	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.000000	0.415000	
chunk0094_43_1	chr2	2238327	2238779	+	0	NA	intron (NM_015025, intron 2 of 24)	intron (NM_015025, intron 2 of 24)	-80679	NR_024468	730811	Hs.629472	NR_024468	ENSG00000225619	MYT1L-AS1	-	MYT1L antisense RNA 1	ncRNA	0.019912	0.452539	
chunk0013_37_1	chr1	166852802	166853105	+	0	NA	3' UTR (NM_017542, exon 6 of 6)	3' UTR (NM_017542, exon 6 of 6)	13549	NM_001314014	57645	Hs.432752	NM_017542	ENSG00000143157	POGK	BASS2|KRBOX2|LST003	pogo transposable element derived with KRAB domain	protein-coding	0.003300	0.398026	
chunk0008_329_1	chr1	95384693	95384987	+	0	NA	Intergenic	Intergenic	-89897	NR_033966	440594	Hs.514123	NR_033966	ENSG00000233907	LINC01761	-	long intergenic non-protein coding RNA 1761	ncRNA	0.003401	0.508475	
chunk0083_231_1	chr17	67422056	67422266	+	0	NA	intron (NM_181671, intron 1 of 9)	intron (NM_181671, intron 1 of 9)	44880	NM_181671	26207	Hs.591185	NM_012417	ENSG00000154217	PITPNC1	M-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1	phosphatidylinositol transfer protein cytoplasmic 1	protein-coding	0.004762	0.445498	129(CAAAACAGCATGTTCC,-,0.00),130(AAAACAGCATGTTCCC,+,0.00)
chunk0089_7_1	chr18	57381864	57382489	+	0	NA	Intergenic	L1ME1|LINE|L1	29686	NM_015879	51046	Hs.23172	NM_015879	ENSG00000177511	ST8SIA3	SIAT8C|ST8SiaIII	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.011200	0.373802	
chunk0145_370_1	chr4	151459407	151459959	+	0	NA	intron (NM_001109977, intron 2 of 13)	intron (NM_001109977, intron 2 of 13)	50437	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.007246	0.363472	
chunk0201_63_1	chr9	33916466	33916982	+	0	NA	intron (NM_017811, intron 4 of 4)	intron (NM_017811, intron 4 of 4)	17640	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.013566	0.415861	
chunk0187_169_1	chr7	150735878	150736498	+	0	NA	intron (NM_001199577, intron 3 of 5)	MER67C|LTR|ERV1	-1160	NM_018384	55340	Hs.647079	NM_018384	ENSG00000196329	GIMAP5	HIMAP3|IAN-5|IAN4|IAN4L1|IAN5|IMAP3|IROD	GTPase, IMAP family member 5	protein-coding	0.004839	0.412238	
chunk0025_335_1	chr10	57987008	57987207	+	0	NA	Intergenic	Intergenic	280827	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.005025	0.325000	
chunk0049_201_1	chr12	93094782	93095448	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-79251	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.003003	0.427286	243(GGGAACACCTTGTCCC,-,0.00),244(GGAACACCTTGTCCCT,+,0.00)
chunk0154_213_1	chr5	80474912	80475546	+	0	NA	intron (NM_001105251, intron 18 of 18)	intron (NM_001105251, intron 18 of 18)	-12752	NM_205548	167555	Hs.338182	NM_205548	ENSG00000152380	FAM151B	UNQ9217	family with sequence similarity 151 member B	protein-coding	0.007886	0.387402	
chunk0205_434_1	chr9	115212278	115212717	+	0	NA	intron (NM_017418, intron 1 of 7)	MIR|SINE|MIR	70679	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.004556	0.370455	240(GAGGACTAAATGTACC,-,0.00)
chunk0175_2_1	chr7	82040	82239	+	0	NA	Intergenic	(CACACC)n|Simple_repeat|Simple_repeat	-67579	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.035176	0.625000	
chunk0209_395_1	chrX	55106535	55106734	+	0	NA	Intergenic	L1MA4|LINE|L1	17582	NM_207339	203569	Hs.662489	NM_207339	ENSG00000234068	PAGE2	CT16.4|GAGEC2|GAGEE2|PAGE-2	PAGE family member 2	protein-coding	0.005025	0.290000	
chunk0034_27_1	chr11	26270679	26270950	+	0	NA	intron (NM_001313726, intron 1 of 27)	L2c|LINE|L2	17193	NR_132968	105376599	Hs.125537	NR_132968	ENSG00000254819	ANO3-AS1	-	ANO3 antisense RNA 1	ncRNA	0.003690	0.378676	
chunk0077_122_1	chr16	78364577	78364794	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	265272	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.004608	0.376147	
chunk0074_435_1	chr16	46401195	46401726	+	0	NA	Intergenic	Intergenic	167637	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.037665	0.362782	
chunk0062_53_1	chr14	67393666	67394180	+	0	NA	intron (NM_016445, intron 3 of 8)	LTR47A2|LTR|ERVL	18188	NM_016445	26499	Hs.170473	NM_016445	ENSG00000100558	PLEK2	-	pleckstrin 2	protein-coding	0.013619	0.464078	420(CAGAACAGGGTGTTCA,-,0.00),421(AGAACAGGGTGTTCAG,+,0.00)
chunk0151_105_1	chr5	43374078	43374295	+	0	NA	Intergenic	L2a|LINE|L2	23078	NM_001301875	56477	Hs.656904	NM_019846	ENSG00000151882	CCL28	CCK1|MEC|SCYA28	C-C motif chemokine ligand 28	protein-coding	0.000000	0.362385	
chunk0212_152_1	chrX	132060031	132060585	+	0	NA	intron (NM_001042452, intron 2 of 9)	L2b|LINE|L2	36700	NM_001042452	51765	Hs.444247	NM_016542	ENSG00000134602	STK26	MASK|MST4	serine/threonine kinase 26	protein-coding	0.003610	0.363964	
chunk0002_223_1	chr1	19947012	19947255	+	0	NA	Intergenic	Intergenic	-23516	NM_014589	30814	Hs.272372	NM_014589	ENSG00000188784	PLA2G2E	GIIE sPLA2|sPLA2-IIE	phospholipase A2 group IIE	protein-coding	0.004115	0.368852	110(TGGAACGAACTGTGCT,-,0.00),111(GGAACGAACTGTGCTG,+,0.00)
chunk0135_402_1	chr3	192597612	192597940	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	129823	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.006098	0.434650	
chunk0011_293_1	chr1	151514335	151514906	+	0	NA	intron (NM_020770, intron 1 of 20)	L2a|LINE|L2	3234	NM_020770	57530	Hs.591464	NM_020770	ENSG00000143375	CGN	-	cingulin	protein-coding	0.007005	0.456294	
chunk0169_302_1	chr6	106055453	106055821	+	0	NA	Intergenic	Intergenic	-30683	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.008152	0.373984	
chunk0105_12_1	chr2	181929872	181930225	+	0	NA	non-coding (NR_109843, exon 18 of 18)	non-coding (NR_109843, exon 18 of 18)	-24193	NR_048567	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.000000	0.313559	
chunk0178_198_1	chr7	34472576	34473232	+	0	NA	intron (NR_033665, intron 2 of 3)	L1MC3|LINE|L1	-185335	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.001524	0.360731	
chunk0196_400_1	chr8	115900868	115901339	+	0	NA	Intergenic	Intergenic	-232075	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004246	0.347458	
chunk0011_4_1	chr1	125168553	125168953	+	0	NA	Intergenic	Intergenic	3649641	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.030000	0.344140	
chunk0024_184_1	chr10	36097828	36098324	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	319774	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.004032	0.338028	412(CGGAACATTCTGTTCT,-,0.00),413(GGAACATTCTGTTCTT,+,0.00)
chunk0076_180_1	chr16	67481163	67481497	+	0	NA	promoter-TSS (NM_004691)	promoter-TSS (NM_004691)	-144	NM_004691	9114	Hs.106876	NM_004691	ENSG00000159720	ATP6V0D1	ATP6D|ATP6DV|P39|VATX|VMA6|VPATPD	ATPase H+ transporting V0 subunit d1	protein-coding	0.086826	0.662687	
chunk0110_255_1	chr20	16655508	16655966	+	0	NA	Intergenic	Intergenic	-74227	NM_003092	6629	Hs.280378	NM_003092	ENSG00000125870	SNRPB2	Msl1|U2B''	small nuclear ribonucleoprotein polypeptide B2	protein-coding	0.013100	0.511983	
chunk0002_185_1	chr1	19179084	19179387	+	0	NA	intron (NM_020765, intron 17 of 105)	intron (NM_020765, intron 17 of 105)	31017	NM_020765	23352	Hs.148078	NM_020765	ENSG00000127481	UBR4	RBAF600|ZUBR1|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding	0.009901	0.417763	
chunk0144_243_1	chr4	135306721	135306997	+	0	NA	Intergenic	Intergenic	581234	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.003623	0.321300	
chunk0195_304_1	chr8	98767944	98768311	+	0	NA	intron (NM_006281, intron 2 of 10)	MIRb|SINE|MIR	57544	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.008174	0.358696	
chunk0026_94_1	chr10	61610678	61611158	+	0	NA	Intergenic	Intergenic	-52043	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.008333	0.432432	
chunk0005_277_1	chr1	59949112	59949795	+	0	NA	Intergenic	Intergenic	-22702	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.002928	0.358187	
chunk0032_119_1	chr11	3987409	3988001	+	0	NA	intron (NM_001277961, intron 2 of 11)	intron (NM_001277961, intron 2 of 11)	-106989	NM_001033	6240	Hs.445705	NM_001033	ENSG00000167325	RRM1	R1|RIR1|RR1	ribonucleotide reductase catalytic subunit M1	protein-coding	0.003378	0.423272	
chunk0051_48_1	chr12	112335682	112335935	+	0	NA	intron (NM_001109662, intron 1 of 75)	L1PB1|LINE|L1	46284	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.007905	0.350394	105(AAGCACAACCTGTTCC,-,0.00),106(AGCACAACCTGTTCCC,+,0.00)
chunk0105_73_1	chr2	183763161	183764072	+	0	NA	Intergenic	Intergenic	-615359	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.003293	0.384868	124(GGAACAGAAAGATCCT,+,0.00)
chunk0084_135_1	chr17	76279269	76279490	+	0	NA	exon (NM_032134, exon 13 of 19)	exon (NM_032134, exon 13 of 19)	14174	NM_182565	283991	Hs.744981	NM_182565	ENSG00000185262	UBALD2	FAM100B	UBA like domain containing 2	protein-coding	0.040724	0.617117	84(GGGCACTCACTGTCCA,-,0.00),85(GGCACTCACTGTCCAG,+,0.00)
chunk0119_11_1	chr22	40053435	40053869	+	0	NA	intron (NM_001024843, intron 1 of 23)	L2c|LINE|L2	8835	NM_001024843	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.004608	0.335632	234(AGGCACATACTGTACT,-,0.00),235(GGCACATACTGTACTG,+,0.00)
chunk0156_29_1	chr5	102379306	102379563	+	0	NA	intron (NM_001289004, intron 11 of 12)	L1ME3A|LINE|L1	-82885	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.007782	0.348837	
chunk0185_193_1	chr7	128386214	128386715	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	19506	NM_001142574	3614	Hs.654401	NM_000883	ENSG00000106348	IMPDH1	IMPD|IMPD1|IMPDH-I|LCA11|RP10|sWSS2608	inosine monophosphate dehydrogenase 1	protein-coding	0.001996	0.432271	
chunk0170_53_1	chr6	109470751	109471451	+	0	NA	intron (NM_014797, intron 5 of 6)	L1ME4b|LINE|L1	-5133	NM_001286613	64780	Hs.33476	NM_022765	ENSG00000135596	MICAL1	MICAL|MICAL-1|NICAL	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding	0.008571	0.429387	
chunk0173_389_1	chr6	150147397	150147868	+	0	NA	intron (NM_030949, intron 1 of 3)	intron (NM_030949, intron 1 of 3)	4580	NM_030949	81706	Hs.486798	NM_030949	ENSG00000198729	PPP1R14C	CPI17-like|KEPI|NY-BR-81	protein phosphatase 1 regulatory inhibitor subunit 14C	protein-coding	0.010616	0.423729	
chunk0142_131_1	chr4	94685806	94686638	+	0	NA	Intergenic	Intergenic	71311	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.013221	0.403361	
chunk0088_255_1	chr18	48946437	48946845	+	0	NA	intron (NM_001190822, intron 2 of 3)	intron (NM_001190822, intron 2 of 3)	2692	NM_001190822	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.012255	0.444988	
chunk0066_431_1	chr15	39641445	39641745	+	0	NA	intron (NM_152597, intron 10 of 11)	intron (NM_152597, intron 10 of 11)	60516	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.010000	0.342193	
chunk0190_397_1	chr8	40186969	40187380	+	0	NA	Intergenic	Intergenic	33706	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.007299	0.347087	
chunk0126_31_1	chr3	73709788	73710528	+	0	NA	Intergenic	L2c|LINE|L2	-85237	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.002703	0.329285	
chunk0063_280_1	chr14	84254080	84254758	+	0	NA	Intergenic	Intergenic	-1139460	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.010324	0.402062	
chunk0115_136_1	chr21	23406823	23407304	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-22228	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.008316	0.410788	
chunk0082_29_1	chr17	50719411	50719625	+	0	NA	promoter-TSS (NM_006107)	promoter-TSS (NM_006107)	-47	NM_016424	51747	Hs.130293	NM_006107	ENSG00000108848	LUC7L3	CRA|CREAP-1|CROP|LUC7A|OA48-18|hLuc7A	LUC7 like 3 pre-mRNA splicing factor	protein-coding	0.140187	0.762791	
chunk0079_248_1	chr17	16108235	16109018	+	0	NA	intron (NM_001190438, intron 16 of 18)	L2a|LINE|L2	86013	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.010217	0.321429	401(AAAAACATTATGTTCA,-,0.00)
chunk0187_419_1	chr7	158431244	158431840	+	0	NA	intron (NM_130842, intron 1 of 21)	intron (NM_130842, intron 1 of 21)	101271	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.011745	0.601340	
chunk0111_152_1	chr20	25058988	25059294	+	0	NA	promoter-TSS (NM_001252675)	promoter-TSS (NM_001252675)	-959	NM_032501	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.029412	0.478827	
chunk0086_348_1	chr18	25230941	25231140	+	0	NA	intron (NM_001308225, intron 2 of 6)	intron (NM_001308225, intron 2 of 6)	121210	NM_001308225	25925	Hs.116935	NM_015461	ENSG00000198795	ZNF521	EHZF|Evi3	zinc finger protein 521	protein-coding	0.015075	0.475000	
chunk0080_144_1	chr17	27747923	27748122	+	0	NA	Intergenic	Intergenic	52507	NM_000625	4843	Hs.709191	NM_000625	ENSG00000007171	NOS2	HEP-NOS|INOS|NOS|NOS2A	nitric oxide synthase 2	protein-coding	0.020101	0.460000	
chunk0172_164_1	chr6	135946512	135947293	+	0	NA	intron (NM_018945, intron 1 of 12)	intron (NM_018945, intron 1 of 12)	95206	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.008963	0.346547	
chunk0138_405_1	chr4	43017968	43018305	+	0	NA	intron (NM_001080476, intron 2 of 3)	intron (NM_001080476, intron 2 of 3)	124870	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.002967	0.514793	
chunk0183_102_1	chr7	105238229	105238479	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	30723	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.020000	0.513944	134(AGGTACAGTCTGTCCT,-,0.00),135(GGTACAGTCTGTCCTT,+,0.00)
chunk0044_207_1	chr12	30851397	30852201	+	0	NA	Intergenic	LTR13_|LTR|ERVK	56118	NR_040245	100287314	Hs.355210	NR_040245		LINC00941	lncRNA-MUF	long intergenic non-protein coding RNA 941	ncRNA	0.024876	0.489441	
chunk0164_199_1	chr6	22471026	22471506	+	0	NA	Intergenic	Intergenic	-98183	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.006250	0.432432	
chunk0182_114_1	chr7	93810541	93811137	+	0	NA	Intergenic	Intergenic	80152	NM_001271004	7980	Hs.438231	NM_006528	ENSG00000105825	TFPI2	PP5|REF1|TFPI-2	tissue factor pathway inhibitor 2	protein-coding	0.000000	0.306533	
chunk0025_71_1	chr10	50007725	50008202	+	0	NA	intron (NM_001077665, intron 6 of 7)	intron (NM_001077665, intron 6 of 7)	19645	NM_001077665	414189	Hs.536158	NM_001077665	ENSG00000204149	AGAP6	AGAP-6|CTGLF3	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	protein-coding	0.008386	0.359833	
chunk0013_96_1	chr1	167714578	167714800	+	0	NA	Intergenic	Intergenic	-7261	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.081081	0.623318	
chunk0050_318_1	chr12	107104828	107105459	+	0	NA	Intergenic	Intergenic	-11286	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.011094	0.379747	
chunk0145_269_1	chr4	149140769	149141410	+	0	NA	Intergenic	L2b|LINE|L2	-13206	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.003120	0.336449	
chunk0020_298_1	chr1	237234790	237235491	+	0	NA	intron (NM_001035, intron 1 of 104)	MamRep1527|LTR|LTR	192738	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.004280	0.411681	
chunk0162_301_1	chr6	6530185	6530881	+	0	NA	intron (NR_026970, intron 3 of 7)	intron (NR_026970, intron 3 of 7)	-58168	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.001437	0.388809	
chunk0037_414_1	chr11	79866525	79866905	+	0	NA	Intergenic	L1PA7|LINE|L1	-426064	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.002632	0.356955	
chunk0150_202_1	chr5	35044572	35044771	+	0	NA	intron (NM_001306173, intron 1 of 12)	(CTTC)n|Simple_repeat|Simple_repeat	3464	NM_001306173	64902	Hs.34494	NM_031900	ENSG00000113492	AGXT2	AGT2|BAIBA|DAIBAT	alanine--glyoxylate aminotransferase 2	protein-coding	0.015075	0.550000	
chunk0019_294_1	chr1	228853689	228854384	+	0	NA	Intergenic	LTR88b|LTR|Gypsy?	118959	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.007194	0.400862	190(TAGCACATACTGTACA,-,0.00),191(AGCACATACTGTACAT,+,0.00),390(GAGGACAATATGTTCT,-,0.00),391(AGGACAATATGTTCTT,+,0.00)
chunk0114_3_1	chr21	5357874	5358155	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-203284	NM_005049	5822	Hs.449076	NM_005049	ENSG00000241945	PWP2	EHOC-17|PWP2H|UTP1	PWP2 small subunit processome component	protein-coding	0.000000	0.386525	
chunk0152_348_1	chr5	62642743	62643857	+	0	NA	Intergenic	Intergenic	64565	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.008977	0.439462	635(AAGCTCTCTCTGTTCT,-,0.00)
chunk0053_244_1	chr13	32698255	32698514	+	0	NA	intron (NM_015032, intron 15 of 34)	Charlie14a|DNA|hAT-Charlie	111957	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.003861	0.350000	
chunk0024_55_1	chr10	33799342	33799924	+	0	NA	Intergenic	Intergenic	-26953	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.006873	0.413379	497(GGGCACATTCTGACCT,-,0.00),498(GGCACATTCTGACCTT,+,0.00)
chunk0016_326_1	chr1	201721152	201721351	+	0	NA	intron (NM_020443, intron 3 of 29)	intron (NM_020443, intron 3 of 29)	1743	NR_049823	100847050		NR_049823	ENSG00000264802	MIR5191	-	microRNA 5191	ncRNA	0.005025	0.420000	
chunk0149_132_1	chr5	19854933	19855210	+	0	NA	intron (NM_001167667, intron 2 of 12)	L1MA3|LINE|L1	31201	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.010830	0.374101	
chunk0066_368_1	chr15	38440399	38440615	+	0	NA	Intergenic	L1PB4|LINE|L1	-13620	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.009259	0.497696	171(CTGAACTTCCTGTTCT,-,0.00),172(TGAACTTCCTGTTCTG,+,0.00)
chunk0029_126_1	chr10	98558166	98558494	+	0	NA	intron (NM_001166246, intron 9 of 12)	L1ME3A|LINE|L1	-111367	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.006098	0.349544	
chunk0092_330_1	chr19	35040826	35041360	+	0	NA	TTS (NM_001037)	TTS (NM_001037)	587	NM_182983	3249	Hs.182385	NM_002151	ENSG00000105707	HPN	TMPRSS1	hepsin	protein-coding	0.058052	0.676636	227(CGGGACAGTGTGTTAT,-,0.00),228(GGGACAGTGTGTTATC,+,0.00)
chunk0118_144_1	chr22	29934648	29935589	+	0	NA	intron (NM_021090, intron 1 of 19)	intron (NM_021090, intron 1 of 19)	51949	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.007439	0.339703	
chunk0127_343_1	chr3	100635033	100635782	+	0	NA	promoter-TSS (NM_001308362)	promoter-TSS (NM_001308362)	-131	NM_001308362	84873	Hs.334511	NM_032787	ENSG00000144820	ADGRG7	GPR128	adhesion G protein-coupled receptor G7	protein-coding	0.013351	0.404000	521(GTGGACATGGTGTTCA,-,0.00),522(TGGACATGGTGTTCAG,+,0.00)
chunk0201_40_1	chr9	33629188	33629534	+	0	NA	Intergenic	Intergenic	5136	NR_003573	304	Hs.534301	NR_003573		ANXA2P2	ANX2L2|ANX2P2|LPC2B	annexin A2 pseudogene 2	pseudo	0.005780	0.432277	
chunk0085_252_1	chr18	7576641	7577020	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	9514	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.000000	0.360526	
chunk0070_301_1	chr15	74815109	74815512	+	0	NA	intron (NM_021819, intron 1 of 13)	intron (NM_021819, intron 1 of 13)	2457	NM_021819	79748	Hs.620644	NM_021819	ENSG00000140506	LMAN1L	ERGIC-53L|ERGL	lectin, mannose binding 1 like	protein-coding	0.012407	0.603960	
chunk0139_121_1	chr4	53010225	53010838	+	0	NA	intron (NM_152540, intron 5 of 8)	intron (NM_152540, intron 5 of 8)	148203	NM_023940	65997	Hs.8035	NM_023940	ENSG00000128045	RASL11B	-	RAS like family 11 member B	protein-coding	0.017945	0.403909	
chunk0041_176_1	chr11	126217307	126217679	+	0	NA	intron (NM_024556, intron 1 of 8)	intron (NM_024556, intron 1 of 8)	5769	NM_024556	79607	Hs.276315	NM_024556	ENSG00000197798	FAM118B	-	family with sequence similarity 118 member B	protein-coding	0.000000	0.412869	158(ATTACAGTGTGTTCCT,+,0.00)
chunk0198_237_1	chr8	134157700	134158242	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	271475	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.009225	0.368324	
chunk0102_326_1	chr2	151774408	151775144	+	0	NA	Intergenic	Intergenic	-40289	NM_001271208	4703	Hs.588655	NM_004543	ENSG00000183091	NEB	NEB177D|NEM2	nebulin	protein-coding	0.005435	0.371777	690(GGGAACTCTCTGTGCA,-,0.00),691(GGAACTCTCTGTGCAG,+,0.00)
chunk0181_333_1	chr7	88045443	88045738	+	0	NA	intron (NM_021721, intron 3 of 27)	L1MA8|LINE|L1	111339	NM_021721	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.006780	0.361486	
chunk0194_157_1	chr8	84763804	84764575	+	0	NA	intron (NM_001287244, intron 1 of 7)	intron (NM_001287244, intron 1 of 7)	58262	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.014267	0.353627	
chunk0163_134_1	chr6	10612844	10613493	+	0	NA	intron (NM_145655, intron 1 of 2)	intron (NM_145655, intron 1 of 2)	27408	NM_145655	2651	Hs.519884	NM_001491	ENSG00000111846	GCNT2	CCAT|CTRCT13|GCNT2C|GCNT5|IGNT|II|NACGT1|NAGCT1|ULG3|bA360O19.2|bA421M1.1	glucosaminyl (N-acetyl) transferase 2 (I blood group)	protein-coding	0.006163	0.340000	
chunk0111_396_1	chr20	34252483	34253185	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-7531	NM_001672	434	Hs.659995	NM_001672	ENSG00000101440	ASIP	AGSW|AGTI|AGTIL|ASP|SHEP9	agouti signaling protein	protein-coding	0.012821	0.459459	343(CAGTGCATTGTGTCCC,-,0.00),344(AGTGCATTGTGTCCCT,+,0.00)
chunk0133_195_1	chr3	170765594	170765966	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	104476	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.005376	0.426273	
chunk0097_131_1	chr2	46987449	46988024	+	0	NA	intron (NM_001288953, intron 6 of 20)	intron (NM_001288953, intron 6 of 20)	-45881	NM_001171511	90411	Hs.662152	NM_139279	ENSG00000180398	MCFD2	F5F8D|F5F8D2|LMAN1IP|SDNSF	multiple coagulation factor deficiency 2	protein-coding	0.013913	0.517361	
chunk0176_372_1	chr7	18522790	18523161	+	0	NA	intron (NM_001204147, intron 1 of 9)	L2c|LINE|L2	13698	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.000000	0.389785	
chunk0105_363_1	chr2	191898887	191899383	+	0	NA	Intergenic	Intergenic	-51855	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.002016	0.305835	
chunk0193_269_1	chr8	77181562	77182183	+	0	NA	Intergenic	Intergenic	-180828	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.000000	0.331190	
chunk0065_439_1	chr14	106529321	106530103	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	47273	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.001279	0.259259	
chunk0005_84_1	chr1	56102358	56102924	+	0	NA	Intergenic	L1MA5A|LINE|L1	476943	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.001767	0.343915	
chunk0044_275_1	chr12	32515161	32515759	+	0	NA	intron (NM_001304483, intron 1 of 16)	intron (NM_001304483, intron 1 of 16)	13417	NM_001304484	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.001672	0.409015	507(TTGCACATGCTGTGCC,-,0.00),508(TGCACATGCTGTGCCA,+,0.00)
chunk0061_83_1	chr14	56900764	56901061	+	0	NA	intron (NR_029385, intron 3 of 3)	intron (NR_029385, intron 3 of 3)	87729	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.016835	0.392617	
chunk0001_449_1	chr1	11812692	11813284	+	0	NA	intron (NM_001256959, intron 2 of 21)	LTR48B|LTR|ERV1	-6885	NM_005957	4524	Hs.214142	NM_005957	ENSG00000177000	MTHFR	-	methylenetetrahydrofolate reductase	protein-coding	0.008446	0.448567	270(CTGGACAAACTGTCCC,-,0.00),271(TGGACAAACTGTCCCA,+,0.00)
chunk0138_103_1	chr4	36088511	36089055	+	0	NA	intron (NM_015230, intron 28 of 32)	intron (NM_015230, intron 28 of 32)	-155333	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.001838	0.400000	234(AAGCACACGGAGTGCT,-,0.00),235(AGCACACGGAGTGCTG,+,0.00)
chunk0110_93_1	chr20	11368480	11369151	+	0	NA	Intergenic	Intergenic	-95432	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.014903	0.415179	211(AGGAACAGCCTGTCCT,-,0.00),212(GGAACAGCCTGTCCTG,+,0.00)
chunk0112_33_1	chr20	36624101	36624826	+	0	NA	intron (NM_032214, intron 5 of 7)	L2a|LINE|L2	18729	NM_199483	55969	Hs.584985	NM_018840	ENSG00000101084	RAB5IF	C20orf24|PNAS-11|RIP5	RAB5 interacting factor	protein-coding	0.019310	0.502755	296(TGGCACTCTGTGTCCT,-,0.00),297(GGCACTCTGTGTCCTC,+,0.00)
chunk0124_230_1	chr3	56621497	56622241	+	0	NA	TTS (NM_001141947)	TTS (NM_001141947)	42177	NM_015224	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.005376	0.320805	
chunk0206_4_1	chr9	115642280	115642638	+	0	NA	Intergenic	Intergenic	101780	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.002793	0.339833	
chunk0109_257_1	chr20	7667233	7667585	+	0	NA	Intergenic	Intergenic	273037	NM_017545	54363	Hs.193640	NM_017545	ENSG00000101323	HAO1	GOX|GOX1|HAOX1	hydroxyacid oxidase 1	protein-coding	0.011364	0.339943	
chunk0176_234_1	chr7	15837285	15837538	+	0	NA	Intergenic	Intergenic	149033	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.003953	0.374016	114(AAACACAGCCTGTCCT,-,0.00),115(AACACAGCCTGTCCTT,+,0.00)
chunk0072_359_1	chr15	99762302	99762742	+	0	NA	Intergenic	Intergenic	-29078	NM_001284421	145748	Hs.562568	NM_152449	ENSG00000183060	LYSMD4	-	LysM domain containing 4	protein-coding	0.002273	0.342404	
chunk0201_326_1	chr9	63807558	63808179	+	0	NA	Intergenic	Intergenic	-11706	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.006441	0.446945	
chunk0173_408_1	chr6	150876609	150876920	+	0	NA	intron (NM_001242767, intron 2 of 27)	intron (NM_001242767, intron 2 of 27)	10431	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.012862	0.512821	
chunk0154_265_1	chr5	81996874	81997277	+	0	NA	intron (NM_031482, intron 2 of 7)	L1PA14|LINE|L1	25050	NM_001131028	83734	Hs.713698	NM_031482	ENSG00000152348	ATG10	APG10|APG10L|pp12616	autophagy related 10	protein-coding	0.009926	0.497525	
chunk0093_188_1	chr19	49116424	49117042	+	0	NA	intron (NM_022165, intron 4 of 5)	L2b|LINE|L2	2372	NM_022165	64130	Hs.221737	NM_022165	ENSG00000104863	LIN7B	LIN-7B|MALS-2|MALS2|VELI2	lin-7 homolog B, crumbs cell polarity complex component	protein-coding	0.011327	0.515347	410(AGGTACAGGGTGTTCC,-,0.00),411(GGTACAGGGTGTTCCT,+,0.00)
chunk0084_433_1	chr17	82660149	82660548	+	0	NA	intron (NM_006822, intron 3 of 5)	intron (NM_006822, intron 3 of 5)	7959	NR_039751	100616196		NR_039751	ENSG00000266107	MIR4525	-	microRNA 4525	ncRNA	0.032581	0.510000	
chunk0117_417_1	chr21	45885443	45886099	+	0	NA	intron (NM_001130141, intron 1 of 12)	L1MDa|LINE|L1	35810	NM_001130141	54039	Hs.474049	NM_020528	ENSG00000183570	PCBP3	ALPHA-CP3|PCBP3-OT1|PCBP3OT	poly(rC) binding protein 3	protein-coding	0.010671	0.458143	
chunk0146_261_1	chr4	162783232	162783668	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	310178	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.006881	0.432494	253(TGGAACAACATGTCCA,-,0.00),254(GGAACAACATGTCCAA,+,0.00)
chunk0073_56_1	chr16	3342884	3343088	+	0	NA	Intergenic	L1MD2|LINE|L1	-12903	NM_012368	4993	Hs.258574	NM_012368	ENSG00000168158	OR2C1	OLFmf3|OR2C2P	olfactory receptor family 2 subfamily C member 1	protein-coding	0.009804	0.321951	
chunk0003_67_1	chr1	31258381	31259112	+	0	NA	TTS (NM_004814)	TTS (NM_004814)	-18859	NM_024522	79570	Hs.470259	NM_024522	ENSG00000084628	NKAIN1	FAM77C	sodium/potassium transporting ATPase interacting 1	protein-coding	0.005472	0.413934	
chunk0016_40_1	chr1	193121672	193122296	+	0	NA	promoter-TSS (NM_024529)	promoter-TSS (NM_024529)	26	NM_024529	79577	Hs.378996	NM_024529	ENSG00000134371	CDC73	C1orf28|FIHP|HPTJT|HRPT1|HRPT2|HYX	cell division cycle 73	protein-coding	0.116987	0.684800	
chunk0087_282_1	chr18	38720250	38720634	+	0	NA	Intergenic	LTR10C|LTR|ERV1	901733	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.005208	0.363636	218(CAGAACATGAAGTCCC,-,0.00),219(AGAACATGAAGTCCCG,+,0.00)
chunk0141_446_1	chr4	89175537	89175952	+	0	NA	Intergenic	Intergenic	62927	NM_145715	166815	Hs.58924	NM_145715	ENSG00000180346	TIGD2	HEL106	tigger transposable element derived 2	protein-coding	0.000000	0.444712	
chunk0212_396_1	chrX	150873710	150874011	+	0	NA	intron (NM_001242614, intron 1 of 11)	intron (NM_001242614, intron 1 of 11)	24956	NM_031462	83692	Hs.522805	NM_031462	ENSG00000102181	CD99L2	CD99B|MIC2L1	CD99 molecule like 2	protein-coding	0.000000	0.473510	139(TGAAACAGGATGTACC,-,0.00),140(GAAACAGGATGTACCT,+,0.00)
chunk0051_22_1	chr12	111816880	111817385	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	17298	NR_106819	102465456		NR_106819	ENSG00000274697	MIR6761	hsa-mir-6761	microRNA 6761	ncRNA	0.009901	0.409091	
chunk0083_51_1	chr17	63659791	63660253	+	0	NA	intron (NM_203351, intron 6 of 16)	MER5C|DNA|hAT-Charlie	37581	NM_002401	4215	Hs.29282	NM_002401	ENSG00000198909	MAP3K3	MAPKKK3|MEKK3	mitogen-activated protein kinase kinase kinase 3	protein-coding	0.010823	0.410367	
chunk0162_250_1	chr6	5068182	5068604	+	0	NA	intron (NR_126015, intron 2 of 3)	intron (NR_126015, intron 2 of 3)	-17093	NM_001145115	648791	Hs.653089	NM_001145115	ENSG00000219607	PPP1R3G	-	protein phosphatase 1 regulatory subunit 3G	protein-coding	0.026066	0.513002	
chunk0142_312_1	chr4	100630025	100630810	+	0	NA	Intergenic	L1M5|LINE|L1	44696	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.003822	0.326972	330(AAGTACAATGTGTCCT,-,0.00),331(AGTACAATGTGTCCTC,+,0.00)
chunk0211_33_1	chrX	108331234	108331592	+	0	NA	intron (NM_001287760, intron 2 of 42)	Tigger3a|DNA|TcMar-Tigger	107017	NM_001287760	1288	Hs.145586	NM_001847	ENSG00000197565	COL4A6	CXDELq22.3|DELXq22.3|DFNX6	collagen type IV alpha 6 chain	protein-coding	0.011173	0.348189	
chunk0099_110_1	chr2	85756777	85757339	+	0	NA	intron (NM_032827, intron 1 of 2)	intron (NM_032827, intron 1 of 2)	3272	NM_032827	84913	Hs.135569	NM_032827	ENSG00000168874	ATOH8	HATH6|bHLHa21	atonal bHLH transcription factor 8	protein-coding	0.010676	0.538188	
chunk0042_208_1	chr12	6020697	6021406	+	0	NA	intron (NM_000552, intron 27 of 51)	intron (NM_000552, intron 27 of 51)	-74819	NM_001278597	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.016925	0.530986	
chunk0143_304_1	chr4	118762314	118762904	+	0	NA	intron (NM_014822, intron 10 of 22)	intron (NM_014822, intron 10 of 22)	73562	NM_014822	9871	Hs.189641	NM_014822	ENSG00000150961	SEC24D	CLCRP2	SEC24 homolog D, COPII coat complex component	protein-coding	0.008475	0.335025	
chunk0104_349_1	chr2	179900723	179901088	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-39400	NM_152520	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.010959	0.344262	
chunk0151_177_1	chr5	50343620	50344209	+	0	NA	Intergenic	MER70A|LTR|ERVL	97486	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.005093	0.415254	270(AAGAACGTAATGTTCT,-,0.00),271(AGAACGTAATGTTCTC,+,0.00)
chunk0153_411_1	chr5	75496094	75496447	+	0	NA	intron (NM_031361, intron 2 of 16)	L1ME1|LINE|L1	15359	NM_031361	10087	Hs.270437	NM_005713	ENSG00000113163	CERT1	CERT|CERTL|COL4A3BP|GPBP|MRD34|STARD11	ceramide transporter 1	protein-coding	0.005666	0.316384	
chunk0160_359_1	chr5	160870108	160870709	+	0	NA	Intergenic	L1MC1|LINE|L1	-18196	NM_025153	23120	Hs.109358	NM_025153	ENSG00000118322	ATP10B	ATPVB	ATPase phospholipid transporting 10B (putative)	protein-coding	0.006656	0.363787	222(TGGTACATCATGTTCA,-,0.00),223(GGTACATCATGTTCAG,+,0.00)
chunk0040_342_1	chr11	118516499	118517002	+	0	NA	intron (NR_120574, intron 2 of 2)	L2c|LINE|L2	-10745	NM_001080441	143941	Hs.653449	NM_001080441	ENSG00000172425	TTC36	HBP21	tetratricopeptide repeat domain 36	protein-coding	0.003976	0.392857	238(CAGAACAGATTGTTCC,-,0.00),239(AGAACAGATTGTTCCT,+,0.00)
chunk0154_347_1	chr5	86902496	86902817	+	0	NA	Intergenic	L2|LINE|L2	155838	NR_105017	100505878	Hs.246405	NR_105017		LINC02059	-	long intergenic non-protein coding RNA 2059	ncRNA	0.006231	0.385093	
chunk0101_179_1	chr2	129334547	129335309	+	0	NA	Intergenic	MIRb|SINE|MIR	-61037	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.019685	0.462647	445(AGGTACAGACTGTTCC,-,0.00),446(GGTACAGACTGTTCCC,+,0.00)
chunk0064_5_1	chr14	89207469	89207984	+	0	NA	intron (NM_001085471, intron 4 of 6)	intron (NM_001085471, intron 4 of 6)	209384	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.005825	0.405039	
chunk0070_250_1	chr15	73575634	73575877	+	0	NA	intron (NM_012428, intron 4 of 8)	intron (NM_012428, intron 4 of 8)	-6212	NR_103844	101241892	Hs.656678	NR_103844	ENSG00000281183	NPTN-IT1	lncRNA-LET	NPTN intronic transcript 1	ncRNA	0.000000	0.491803	112(GTCACAGAATGTGCTT,+,0.00)
chunk0038_147_1	chr11	84419274	84419622	+	0	NA	intron (NM_001142699, intron 7 of 27)	intron (NM_001142699, intron 7 of 27)	-102109	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.011494	0.326648	203(CTGAACATACTGTCTC,-,0.00)
chunk0042_329_1	chr12	9721250	9721696	+	0	NA	intron (NM_001253750, intron 2 of 3)	intron (NM_001253750, intron 2 of 3)	11826	NM_001253750	160365	Hs.560087	NM_172004	ENSG00000184293	CLECL1	DCAL-1|DCAL1	C-type lectin like 1	protein-coding	0.008969	0.326622	
chunk0028_338_1	chr10	92122007	92122488	+	0	NA	intron (NM_001178137, intron 6 of 9)	L2c|LINE|L2	121032	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.006237	0.450207	
chunk0137_359_1	chr4	25928375	25928632	+	0	NA	intron (NM_001145432, intron 2 of 2)	intron (NM_001145432, intron 2 of 2)	14311	NM_001145432	389203	Hs.479386	NM_001145432	ENSG00000250317	SMIM20	C4orf52|MITRAC7|PNX	small integral membrane protein 20	protein-coding	0.015564	0.368217	
chunk0097_318_1	chr2	56799464	56799757	+	0	NA	Intergenic	Intergenic	-613840	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.003413	0.292517	
chunk0150_208_1	chr5	35163202	35163565	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	-45261	NM_001204318	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.019284	0.445055	
chunk0117_167_1	chr22	20255167	20255590	+	0	NA	intron (NM_023004, intron 1 of 1)	intron (NM_023004, intron 1 of 1)	-6167	NR_031618	100302118		NR_031618	ENSG00000221039	MIR1286	MIRN1286|hsa-mir-1286|mir-1286	microRNA 1286	ncRNA	0.009456	0.502358	324(CAGGACACTATGGGCT,-,0.00)
chunk0108_131_1	chr2	230222879	230223078	+	0	NA	intron (NM_001185015, intron 1 of 15)	intron (NM_001185015, intron 1 of 15)	2751	NM_001185015	3431	Hs.145150	NM_004509	ENSG00000135899	SP110	IFI41|IFI75|IPR1|VODI	SP110 nuclear body protein	protein-coding	0.005025	0.390000	
chunk0062_211_1	chr14	70836981	70837218	+	0	NA	Intergenic	L1ME1|LINE|L1	-27928	NM_001284230	4293	Hs.445496	NM_033141	ENSG00000006432	MAP3K9	MEKK9|MLK1|PRKE1	mitogen-activated protein kinase kinase kinase 9	protein-coding	0.000000	0.352941	
chunk0160_241_1	chr5	156176455	156176654	+	0	NA	Intergenic	Intergenic	-150203	NM_172244	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.000000	0.305000	
chunk0197_202_1	chr8	122499741	122499951	+	0	NA	intron (NR_131202, intron 2 of 3)	(CA)n|Simple_repeat|Simple_repeat	68798	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.009524	0.398104	
chunk0143_441_1	chr4	124060233	124060965	+	0	NA	Intergenic	Intergenic	286335	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.004098	0.380628	149(GGGTACAATATGTACC,-,0.00),150(GGTACAATATGTACCA,+,0.00)
chunk0100_327_1	chr2	116644770	116645072	+	0	NA	Intergenic	Tigger4|DNA|TcMar-Tigger	-1169758	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.000000	0.389439	
chunk0148_40_1	chr5	1227728	1228173	+	0	NA	intron (NM_182632, intron 1 of 11)	intron (NM_182632, intron 1 of 11)	2595	NM_182632	348932	Hs.213284	NM_182632	ENSG00000164363	SLC6A18	Xtrp2	solute carrier family 6 member 18	protein-coding	0.033708	0.470852	
chunk0193_370_1	chr8	80077995	80078770	+	0	NA	intron (NM_001025253, intron 1 of 7)	Charlie23a|DNA|hAT-Charlie	2449	NM_001025252	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.006452	0.371134	190(AGGAACATCCTGCCCA,-,0.00),191(GGAACATCCTGCCCAT,+,0.00)
chunk0007_237_1	chr1	82322750	82323221	+	0	NA	Intergenic	Intergenic	522588	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.004246	0.351695	
chunk0074_133_1	chr16	22727318	22728239	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-86761	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.010858	0.377440	753(AGGAACAGCAAGTTCA,-,0.00),754(GGAACAGCAAGTTCAA,+,0.00),777(GAGGCCAGAATGTGCT,-,0.00)
chunk0018_261_1	chr1	220372769	220373105	+	0	NA	Intergenic	Intergenic	-100436	NM_012414	25782	Hs.654849	NM_012414	ENSG00000118873	RAB3GAP2	RAB3-GAP150|RAB3GAP150|SPG69|WARBM2|p150	RAB3 GTPase activating non-catalytic protein subunit 2	protein-coding	0.008929	0.486647	
chunk0111_158_1	chr20	25115980	25116376	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	31815	NR_027093	284798	Hs.334934	NR_027091	ENSG00000230725	LOC284798	-	uncharacterized LOC284798	ncRNA	0.012626	0.556675	
chunk0086_342_1	chr18	24868817	24869200	+	0	NA	Intergenic	Mam_R4|LINE|Dong-R4	240826	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.007833	0.361979	
chunk0175_195_1	chr7	5586175	5586715	+	0	NA	Intergenic	Intergenic	-6360	NM_003088	6624	Hs.118400	NM_003088	ENSG00000075618	FSCN1	FAN1|HSN|SNL|p55	fascin actin-bundling protein 1	protein-coding	0.025926	0.585952	
chunk0078_253_1	chr17	7242285	7243100	+	0	NA	promoter-TSS (NM_007278)	promoter-TSS (NM_007278)	-258	NM_007278	11337	Hs.647421	NM_007278	ENSG00000170296	GABARAP	ATG8A|GABARAP-a|MM46	GABA type A receptor-associated protein	protein-coding	0.077301	0.556373	
chunk0048_223_1	chr12	81486935	81487225	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	25311	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.006897	0.378007	
chunk0092_4_1	chr19	18460354	18460870	+	0	NA	intron (NM_006532, intron 5 of 11)	intron (NM_006532, intron 5 of 11)	-22311	NR_045573	51477	Hs.405873	NM_016368	ENSG00000105655	ISYNA1	INO1|INOS|IPS|IPS 1|IPS-1	inositol-3-phosphate synthase 1	protein-coding	0.023256	0.588008	
chunk0180_261_1	chr7	69561267	69561771	+	0	NA	Intergenic	Intergenic	35976	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.011905	0.431683	
chunk0072_241_1	chr15	95976464	95977033	+	0	NA	Intergenic	Intergenic	-349180	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.003515	0.326316	230(AGGAACAGATTGTACT,-,0.00),231(GGAACAGATTGTACTA,+,0.00)
chunk0061_25_1	chr14	55795787	55796041	+	0	NA	intron (NR_026796, intron 1 of 3)	L2a|LINE|L2	760	NR_026797	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.003937	0.380392	
chunk0152_220_1	chr5	60353207	60353466	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-134377	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.003861	0.515385	
chunk0092_293_1	chr19	34216533	34217035	+	0	NA	intron (NM_015578, intron 6 of 9).2	intron (NM_015578, intron 6 of 9).2	-37767	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.027888	0.455268	
chunk0170_211_1	chr6	113036065	113037147	+	0	NA	Intergenic	Intergenic	613469	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.005545	0.342567	
chunk0026_386_1	chr10	69458187	69458933	+	0	NA	intron (NM_012339, intron 1 of 7)	intron (NM_012339, intron 1 of 7)	7090	NM_012339	23555	Hs.499941	NM_012339	ENSG00000099282	TSPAN15	2700063A19Rik|NET-7|NET7|TM4SF15	tetraspanin 15	protein-coding	0.014745	0.456493	
chunk0066_362_1	chr15	38368806	38369506	+	0	NA	Intergenic	L1MEc|LINE|L1	-84971	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.002857	0.278174	
chunk0019_186_1	chr1	226632260	226632942	+	0	NA	3' UTR (NM_002221, exon 8 of 8)	3' UTR (NM_002221, exon 8 of 8)	42467	NR_103784	100506443	Hs.664293	NR_103784		ITPKB-IT1	-	ITPKB intronic transcript 1	ncRNA	0.007331	0.456808	454(TGGAACATTTTGTTCT,-,0.00),455(GGAACATTTTGTTCTC,+,0.00)
chunk0153_161_1	chr5	70401388	70401601	+	0	NA	intron (NR_027386, intron 3 of 5).3	LTR12E|LTR|ERV1	-13876	NR_033417	653238	Hs.607501	NM_001098729		GTF2H2B	-	general transcription factor IIH subunit 2B (pseudogene)	pseudo	0.107981	0.752336	
chunk0200_169_1	chr9	19102880	19103187	+	0	NA	promoter-TSS (NM_017645)	promoter-TSS (NM_017645)	-91	NM_001270890	54801	Hs.533468	NM_017645	ENSG00000147874	HAUS6	Dgt6|FAM29A	HAUS augmin like complex subunit 6	protein-coding	0.071661	0.577922	
chunk0199_151_1	chr9	4244113	4244645	+	0	NA	intron (NM_001042413, intron 2 of 10)	Tigger13a|DNA|TcMar-Tigger	55656	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.007519	0.371482	
chunk0130_100_1	chr3	130906742	130907130	+	0	NA	intron (NM_001001485, intron 2 of 27)	L1ME1|LINE|L1	12346	NM_001001486	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.007732	0.341902	
chunk0079_320_1	chr17	17275875	17276328	+	0	NA	exon (NM_003653, exon 2 of 12)	exon (NM_003653, exon 2 of 12)	4597	NM_001199125	8533	Hs.6076	NM_003653	ENSG00000141030	COPS3	CSN3|SGN3	COP9 signalosome subunit 3	protein-coding	0.011038	0.438326	103(AAGTGCACAGTGTTCC,-,0.00),104(AGTGCACAGTGTTCCA,+,0.00)
chunk0069_212_1	chr15	63504606	63504853	+	0	NA	non-coding (NR_046341, exon 1 of 16)	non-coding (NR_046341, exon 1 of 16)	218	NR_046341	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.101215	0.709677	
chunk0135_408_1	chr3	192706362	192706742	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	21047	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.034211	0.456693	
chunk0169_308_1	chr6	106097485	106098233	+	0	NA	intron (NM_001198, intron 3 of 6)	intron (NM_001198, intron 3 of 6)	-1003	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.024064	0.411215	
chunk0178_192_1	chr7	34366353	34366609	+	0	NA	intron (NR_033664, intron 4 of 4)	intron (NR_033664, intron 4 of 4)	-291758	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.007812	0.365759	
chunk0126_423_1	chr3	86345700	86345899	+	0	NA	Intergenic	L1MA2|LINE|L1	-517749	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.005025	0.455000	
chunk0095_214_1	chr2	18709578	18709975	+	0	NA	Intergenic	L1MDa|LINE|L1	-120196	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.002519	0.331658	218(GAGAACAATGTGTACT,-,0.00),219(AGAACAATGTGTACTC,+,0.00)
chunk0011_330_1	chr1	152109304	152109617	+	0	NA	exon (NM_007113, exon 3 of 3)	exon (NM_007113, exon 3 of 3)	5994	NM_007113	7062	Hs.432416	NM_007113	ENSG00000159450	TCHH	THH|THL|TRHY|UHS3	trichohyalin	protein-coding	0.044728	0.535032	
chunk0043_171_1	chr12	17097627	17097830	+	0	NA	Intergenic	Intergenic	108981	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.024631	0.504902	
chunk0017_446_1	chr1	214251316	214251544	+	0	NA	Intergenic	Intergenic	-29792	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.004386	0.331878	
chunk0169_229_1	chr6	104711082	104711595	+	0	NA	Intergenic	Intergenic	148581	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.009747	0.404669	
chunk0120_153_1	chr3	5350630	5351275	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-100697	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.004651	0.379257	371(AGCTCACTATGTACTT,+,0.00)
chunk0104_6_1	chr2	170321573	170321947	+	0	NA	intron (NR_045684, intron 7 of 34)	intron (NR_045684, intron 7 of 34)	29183	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.013369	0.448000	232(TGGCACTGTGTGTTCC,-,0.00),233(GGCACTGTGTGTTCCT,+,0.00)
chunk0045_182_1	chr12	47082477	47082768	+	0	NA	intron (NM_001281429, intron 1 of 2)	MIRb|SINE|MIR	-2671	NM_181847	347902	Hs.121520	NM_181847	ENSG00000139211	AMIGO2	ALI1|AMIGO-2|DEGA	adhesion molecule with Ig like domain 2	protein-coding	0.006873	0.342466	
chunk0132_128_1	chr3	156134389	156135075	+	0	NA	intron (NM_001308217, intron 1 of 12)	intron (NM_001308217, intron 1 of 12)	-8230	NM_003471	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.002915	0.337700	
chunk0107_399_1	chr2	223950617	223951348	+	0	NA	Intergenic	L2a|LINE|L2	-5595	NM_020830	57590	Hs.368359	NM_020830	ENSG00000085449	WDFY1	FENS-1|FENS1|WDF1|ZFYVE17	WD repeat and FYVE domain containing 1	protein-coding	0.002736	0.397541	
chunk0134_291_1	chr3	179927413	179927753	+	0	NA	intron (NM_001256750, intron 1 of 14)	MER5C|DNA|hAT-Charlie	28046	NR_110061	101928790	Hs.667247	NR_110059	ENSG00000244302	PEX5L-AS2	-	PEX5L antisense RNA 2	ncRNA	0.002941	0.357771	
chunk0087_354_1	chr18	40975725	40976036	+	0	NA	Intergenic	L1MA4A|LINE|L1	544717	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.000000	0.525641	
chunk0054_316_1	chr13	48914854	48915165	+	0	NA	Intergenic	Intergenic	-60903	NM_001079673	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.012862	0.448718	
chunk0127_217_1	chr3	96576623	96577172	+	0	NA	Intergenic	MIR|SINE|MIR	216933	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.012750	0.365455	
chunk0026_20_1	chr10	60630780	60630979	+	0	NA	intron (NM_001204403, intron 1 of 43)	L2a|LINE|L2	-57923	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.015075	0.455000	
chunk0024_296_1	chr10	42104556	42104974	+	0	NA	Intergenic	Intergenic	263280	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.047847	0.365155	
chunk0049_350_1	chr12	95305116	95305590	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-3067	NR_029895	442903		NR_029895	ENSG00000199172	MIR331	MIRN331|hsa-mir-331|mir-331	microRNA 331	ncRNA	0.010549	0.336842	
chunk0157_397_1	chr5	124176762	124177070	+	0	NA	intron (NR_125774, intron 4 of 5)	LTR16A1|LTR|ERVL	261604	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.000000	0.491909	
chunk0077_37_1	chr16	75462450	75462806	+	0	NA	intron (NM_001304998, intron 1 of 2)	L1MC4|LINE|L1	1788	NM_001304997	124491	Hs.487510	NM_145254	ENSG00000166822	TMEM170A	TMEM170	transmembrane protein 170A	protein-coding	0.011236	0.380952	
chunk0008_217_1	chr1	93804432	93805009	+	0	NA	intron (NM_001261408, intron 2 of 13)	MER44B|DNA|TcMar-Tigger	-42112	NR_030621	100126348		NR_030621	ENSG00000211575	MIR760	MIRN760|hsa-mir-760|mir-760	microRNA 760	ncRNA	0.006932	0.370242	
chunk0046_437_1	chr12	64820515	64821315	+	0	NA	Intergenic	Intergenic	-3657	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.005000	0.365793	
chunk0162_137_1	chr6	3139030	3139504	+	0	NA	intron (NR_026649, intron 6 of 7)	intron (NR_026649, intron 6 of 7)	18282	NM_001310315	7280	Hs.654543	NM_001069	ENSG00000137267	TUBB2A	CDCBM5|TUBB|TUBB2	tubulin beta 2A class IIa	protein-coding	0.018987	0.452632	
chunk0016_310_1	chr1	201461034	201461524	+	0	NA	Intergenic	L2c|LINE|L2	7892	NM_012396	23612	Hs.153944	NM_012396	ENSG00000174307	PHLDA3	TIH1	pleckstrin homology like domain family A member 3	protein-coding	0.008163	0.480652	
chunk0184_39_1	chr7	112168255	112168530	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	38015	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.007273	0.445652	
chunk0186_306_1	chr7	142901875	142902145	+	0	NA	Intergenic	L2|LINE|L2	-16265	NM_018646	55503	Hs.302740	NM_014274	ENSG00000165125	TRPV6	ABP/ZF|CAT1|CATL|ECAC2|HRPTTN|HSA277909|LP6728|ZFAB	transient receptor potential cation channel subfamily V member 6	protein-coding	0.022222	0.479705	
chunk0136_155_1	chr4	4801631	4802082	+	0	NA	Intergenic	Intergenic	40096	NR_125892	101928279	Hs.586152	NR_125892		LOC101928279	-	uncharacterized LOC101928279	ncRNA	0.013304	0.515487	
chunk0101_386_1	chr2	138564756	138565358	+	0	NA	intron (NM_001001664, intron 10 of 10)	intron (NM_001001664, intron 10 of 10)	63277	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.004983	0.384743	
chunk0015_414_1	chr1	191358332	191358901	+	0	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	733726	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.005272	0.354386	
chunk0029_110_1	chr10	97903062	97903853	+	0	NA	intron (NM_018058, intron 7 of 14)	intron (NM_018058, intron 7 of 14)	53219	NM_001010917	401647	Hs.567524	NM_001010917	ENSG00000155265	GOLGA7B	C10orf132|C10orf133|bA451M19.3|bA459F3.4	golgin A7 family member B	protein-coding	0.010114	0.537879	364(CAGGACGAGCTGTCCT,-,0.00),365(AGGACGAGCTGTCCTG,+,0.00)
chunk0157_455_1	chr5	125004374	125004619	+	0	NA	Intergenic	Intergenic	-32335	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.004082	0.296748	
chunk0107_111_1	chr2	214375502	214375886	+	0	NA	intron (NR_047659, intron 17 of 17)	intron (NR_047659, intron 17 of 17)	-36043	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.007812	0.374026	
chunk0011_61_1	chr1	143271449	143271724	+	0	NA	Intergenic	Intergenic	151006	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.061818	0.384058	
chunk0199_385_1	chr9	13149308	13149987	+	0	NA	intron (NM_003829, intron 25 of 45)	L2b|LINE|L2	129917	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.002946	0.361765	
chunk0069_98_1	chr15	61389452	61390151	+	0	NA	Intergenic	MIRc|SINE|MIR	-160498	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.002861	0.401429	
chunk0048_351_1	chr12	85041344	85041920	+	0	NA	intron (NM_001079910, intron 3 of 26)	L2a|LINE|L2	5311	NM_001079910	84125	Hs.402200	NM_032165	ENSG00000133640	LRRIQ1	-	leucine rich repeats and IQ motif containing 1	protein-coding	0.001736	0.346620	
chunk0097_246_1	chr2	53631038	53631705	+	0	NA	Intergenic	Intergenic	-136421	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.002999	0.381737	
chunk0058_219_1	chr14	25035266	25035478	+	0	NA	intron (NM_001304476, intron 1 of 6)	intron (NM_001304476, intron 1 of 6)	13628	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.014151	0.403756	
chunk0028_399_1	chr10	93244049	93244274	+	0	NA	Intergenic	Intergenic	170271	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.017778	0.442478	
chunk0023_188_1	chr10	25016581	25016780	+	0	NA	promoter-TSS (NM_145010)	promoter-TSS (NM_145010)	101	NM_024838	79896	Hs.645274	NM_024838	ENSG00000185875	THNSL1	TSH1	threonine synthase like 1	protein-coding	0.095477	0.690000	
chunk0203_253_1	chr9	87501661	87502321	+	0	NA	intron (NM_001288730, intron 2 of 25)	intron (NM_001288730, intron 2 of 25)	3456	NM_001288729	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.004545	0.425113	
chunk0013_122_1	chr1	167959205	167959654	+	0	NA	intron (NM_001198957, intron 2 of 20)	L1MC1|LINE|L1	-22360	NM_015415	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.011136	0.384444	
chunk0140_313_1	chr4	73264381	73264951	+	0	NA	Intergenic	L1ME4a|LINE|L1	-5881	NM_198889	26057	Hs.601206	NM_015574	ENSG00000132466	ANKRD17	GTAR|MASK2|NY-BR-16	ankyrin repeat domain 17	protein-coding	0.003509	0.339755	
chunk0210_455_1	chrX	106613005	106613417	+	0	NA	intron (NM_001184782, intron 1 of 12)	intron (NM_001184782, intron 1 of 12)	1281	NM_001184782	55086	Hs.274267	NM_018015	ENSG00000147231	RADX	CXorf57	RPA1 related single stranded DNA binding protein, X-linked	protein-coding	0.021845	0.358354	
chunk0167_97_1	chr6	57120480	57121153	+	0	NA	intron (NR_110742, intron 2 of 3)	L1MC1|LINE|L1	30786	NM_015555	26036	Hs.485628	NM_015555	ENSG00000112200	ZNF451	COASTER|dJ417I1.1	zinc finger protein 451	protein-coding	0.005944	0.347181	
chunk0070_137_1	chr15	70995278	70995995	+	0	NA	intron (NM_017691, intron 11 of 15)	intron (NM_017691, intron 11 of 15)	103193	NM_001199017	54839	Hs.12692	NM_017691	ENSG00000137821	LRRC49	PGs4	leucine rich repeat containing 49	protein-coding	0.006974	0.362117	
chunk0009_358_1	chr1	109724174	109724655	+	0	NA	Intergenic	MER4A1|LTR|ERV1	12172	NM_000851	2949	Hs.75652	NM_000851	ENSG00000134201	GSTM5	GSTM5-5|GTM5	glutathione S-transferase mu 5	protein-coding	0.008316	0.381743	
chunk0097_375_1	chr2	61213879	61214078	+	0	NA	intron (NM_014709, intron 68 of 79)	intron (NM_014709, intron 68 of 79)	36558	NM_152392	130872	Hs.655602	NM_152392	ENSG00000173209	AHSA2P	AHA1|AHSA2|Hch1	activator of HSP90 ATPase homolog 2, pseudogene	pseudo	0.000000	0.330000	
chunk0113_119_1	chr20	51491550	51491790	+	0	NA	intron (NM_001136021, intron 3 of 10)	MER63B|DNA|hAT-Blackjack	-38693	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.029167	0.502075	
chunk0104_323_1	chr2	179379324	179379625	+	0	NA	Intergenic	L2a|LINE|L2	-114851	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.006645	0.321192	
chunk0116_249_1	chr21	38787547	38787992	+	0	NA	Intergenic	Intergenic	-14292	NR_027065	400866	Hs.278704	NM_001001789	ENSG00000223806	LINC00114	C21orf24|NCRNA00114	long intergenic non-protein coding RNA 114	ncRNA	0.022472	0.526906	
chunk0009_424_1	chr1	111045109	111045779	+	0	NA	Intergenic	Intergenic	-81500	NM_001006945	55791	Hs.25245	NM_018372	ENSG00000121931	LRIF1	C1orf103|HBiX1|RIF1	ligand dependent nuclear receptor interacting factor 1	protein-coding	0.002985	0.399404	
chunk0179_38_1	chr7	43240427	43240777	+	0	NA	intron (NM_015052, intron 2 of 29)	intron (NM_015052, intron 2 of 29)	89707	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.014286	0.427350	
chunk0101_20_1	chr2	121588200	121588798	+	0	NA	intron (NM_015282, intron 2 of 38)	intron (NM_015282, intron 2 of 38)	57619	NR_023343	100151683	Hs.689638	NR_023343	ENSG00000264229	RNU4ATAC	MOPD1|RFMN|RNU4ATAC1|TALS|U4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	snRNA	0.001672	0.382304	
chunk0060_190_1	chr14	47562118	47562541	+	0	NA	intron (NM_001113498, intron 1 of 16)	L1PA15|LINE|L1	112625	NM_001113498	161357	Hs.436380	NM_182830	ENSG00000139915	MDGA2	MAMDC1|c14_5286	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.000000	0.405660	
chunk0052_87_1	chr13	22107318	22107996	+	0	NA	Intergenic	Intergenic	-102628	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.008850	0.446244	
chunk0202_386_1	chr9	81029853	81030566	+	0	NA	Intergenic	Intergenic	659326	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.000000	0.305322	
chunk0130_36_1	chr3	129067470	129067964	+	0	NA	Intergenic	LTR12C|LTR|ERV1	6950	NM_000174	2815	Hs.1144	NM_000174	ENSG00000169704	GP9	CD42a|GPIX	glycoprotein IX platelet	protein-coding	0.024291	0.484848	
chunk0186_28_1	chr7	135962659	135963223	+	0	NA	intron (NM_001128619, intron 1 of 3)	intron (NM_001128619, intron 1 of 3)	14515	NM_145808	136319	Hs.602015	NM_145808	ENSG00000105887	MTPN	GCDP|V-1	myotrophin	protein-coding	0.007092	0.353982	307(AGGTACATACTGTACT,-,0.00),308(GGTACATACTGTACTG,+,0.00)
chunk0117_402_1	chr21	45525351	45525713	+	0	NA	intron (NM_194255, intron 5 of 5)	intron (NM_194255, intron 5 of 5)	9096	NM_001205207	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.041436	0.652893	152(AAGGACACCAAGTTCC,-,0.00),153(AGGACACCAAGTTCCG,+,0.00)
chunk0123_269_1	chr3	46108317	46108789	+	0	NA	Intergenic	MER67C|LTR|ERV1	-81066	NM_005283	2829	Hs.128375	NM_005283	ENSG00000173578	XCR1	CCXCR1|GPR5	X-C motif chemokine receptor 1	protein-coding	0.014831	0.403805	
chunk0168_384_1	chr6	93999721	94000302	+	0	NA	Intergenic	Intergenic	292928	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.001721	0.293814	
chunk0081_49_1	chr17	37802872	37803524	+	0	NA	Intergenic	MLT1K-int|LTR|ERVL-MaLR	-58120	NM_001165923	6928	Hs.191144	NM_000458	ENSG00000275410	HNF1B	FJHN|HNF-1-beta|HNF-1B|HNF1beta|HNF2|HPC11|LF-B3|LFB3|MODY5|TCF-2|TCF2|VHNF1	HNF1 homeobox B	protein-coding	0.003067	0.485452	
chunk0205_147_1	chr9	108290734	108291011	+	0	NA	Intergenic	Intergenic	565123	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.003610	0.388489	
chunk0155_225_1	chr5	95410205	95410406	+	0	NA	intron (NM_152548, intron 3 of 9)	MLT1J|LTR|ERVL-MaLR	18961	NM_152548	153643	Hs.276287	NM_152548	ENSG00000153347	FAM81B	-	family with sequence similarity 81 member B	protein-coding	0.004975	0.475248	
chunk0210_64_1	chrX	69685205	69685737	+	0	NA	intron (NM_001005613, intron 2 of 2)	intron (NM_001005613, intron 2 of 2)	69404	NM_001399	1896	Hs.105407	NM_001399	ENSG00000158813	EDA	ECTD1|ED1|ED1-A1|ED1-A2|EDA-A1|EDA-A2|EDA1|EDA2|HED|HED1|ODT1|STHAGX1|TNLG7C|XHED|XLHED	ectodysplasin A	protein-coding	0.000000	0.268293	
chunk0198_150_1	chr8	132930844	132931146	+	0	NA	intron (NM_003235, intron 23 of 47)	MLT1B|LTR|ERVL-MaLR	64035	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.006623	0.488449	
chunk0012_2_1	chr1	154663423	154663771	+	0	NA	Intergenic	Intergenic	-35617	NM_001025107	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.002874	0.372493	
chunk0109_130_1	chr20	3022807	3023442	+	0	NA	intron (NM_080840, intron 15 of 22)	LTR5B|LTR|ERVK	-20498	NM_001501	2797	Hs.129715	NM_001501	ENSG00000125787	GNRH2	GnRH-II|LH-RHII	gonadotropin releasing hormone 2	protein-coding	0.015748	0.473270	410(AGGGACACAATGCACT,-,0.00),411(GGGACACAATGCACTG,+,0.00)
chunk0124_157_1	chr3	54940954	54941303	+	0	NA	intron (NM_001304389, intron 1 of 2)	intron (NM_001304389, intron 1 of 2)	-13054	NM_020678	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.005731	0.348571	213(CAAAACATGTTGTCCT,-,0.00),214(AAAACATGTTGTCCTC,+,0.00)
chunk0156_436_1	chr5	114669711	114670018	+	0	NA	intron (NR_130785, intron 1 of 12)	LTR82A|LTR|ERVL	103549	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.370130	
chunk0106_195_1	chr2	201758719	201759197	+	0	NA	TTS (NM_001135745)	TTS (NM_001135745)	22214	NM_001135745	57679	Hs.471096	NM_020919	ENSG00000003393	ALS2	ALS2CR6|ALSJ|IAHSP|PLSJ	alsin Rho guanine nucleotide exchange factor ALS2	protein-coding	0.010460	0.348643	
chunk0179_206_1	chr7	47497511	47498018	+	0	NA	intron (NM_022748, intron 3 of 30)	intron (NM_022748, intron 3 of 30)	84380	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.017751	0.501969	
chunk0001_423_1	chr1	11179067	11179379	+	0	NA	intron (NM_004958, intron 28 of 57)	MER104|DNA|TcMar-Tc2	-10066	NM_021146	10218	Hs.146559	NM_021146	ENSG00000171819	ANGPTL7	AngX|CDT6|dJ647M16.1	angiopoietin like 7	protein-coding	0.000000	0.440895	
chunk0157_64_1	chr5	116222334	116222758	+	0	NA	intron (NM_001308080, intron 5 of 6)	intron (NM_001308080, intron 5 of 6)	137084	NM_001308080	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.000000	0.312941	
chunk0041_389_1	chr11	132739126	132739454	+	0	NA	intron (NM_001012393, intron 2 of 7)	MER34A1|LTR|ERV1	203852	NM_002545	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.006098	0.392097	
chunk0207_15_1	chrM	12376	13187	+	0	NA	NA	Intergenic	NA	NA									0.020962	0.450739	
chunk0142_307_1	chr4	100585704	100586162	+	0	NA	Intergenic	Charlie23a|DNA|hAT-Charlie	-67840	NM_016242	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.008734	0.291939	
chunk0066_373_1	chr15	38540963	38541286	+	0	NA	intron (NM_001306086, intron 2 of 14)	MIRc|SINE|MIR	23682	NM_001306086	10125	Hs.591127	NM_005739	ENSG00000172575	RASGRP1	CALDAG-GEFI|CALDAG-GEFII|RASGRP	RAS guanyl releasing protein 1	protein-coding	0.012384	0.484568	
chunk0027_131_1	chr10	74310202	74310401	+	0	NA	intron (NM_001123, intron 3 of 10)	intron (NM_001123, intron 3 of 10)	133812	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.005025	0.315000	126(CAGCACAATCAGTTCC,-,0.00),127(AGCACAATCAGTTCCC,+,0.00)
chunk0098_111_1	chr2	68407009	68407409	+	0	NA	Intergenic	L1PA7|LINE|L1	42019	NM_002664	5341	Hs.468840	NM_002664	ENSG00000115956	PLEK	P47	pleckstrin	protein-coding	0.005000	0.374065	
chunk0169_243_1	chr6	105147212	105147435	+	0	NA	non-coding (NR_037157, exon 2 of 4)	non-coding (NR_037157, exon 2 of 4)	9636	NR_037157	154442	Hs.586271	NR_037157	ENSG00000203808	BVES-AS1	C6orf112|bA99L11.2	BVES antisense RNA 1	ncRNA	0.004484	0.375000	
chunk0187_34_1	chr8	1157610	1158179	+	0	NA	Intergenic	Intergenic	144713	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.017575	0.454386	
chunk0077_96_1	chr16	77677106	77677722	+	0	NA	Intergenic	Intergenic	-45078	NM_001243660	283927	Hs.282665	NM_001105663	ENSG00000140876	NUDT7	-	nudix hydrolase 7	protein-coding	0.014610	0.437601	332(AGGAACACAGTGTGAC,-,0.00)
chunk0107_338_1	chr2	221308132	221308757	+	0	NA	Intergenic	Intergenic	263914	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.001600	0.405751	
chunk0108_246_1	chr2	233889273	233889695	+	0	NA	Intergenic	Intergenic	-21075	NR_024322	151507	Hs.355809	NM_001166217	ENSG00000224287	MSL3P1	MSL3L2	MSL complex subunit 3 pseudogene 1	pseudo	0.002370	0.326241	
chunk0087_91_1	chr18	32371958	32373325	+	0	NA	intron (NM_001242409, intron 2 of 5)	intron (NM_001242409, intron 2 of 5)	97843	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.003658	0.383041	
chunk0031_269_1	chr10	127834031	127834236	+	0	NA	Intergenic	MER53|DNA|hAT	58814	NM_152311	119467	Hs.242014	NM_152311	ENSG00000180745	CLRN3	TMEM12|USH3AL1	clarin 3	protein-coding	0.000000	0.402913	
chunk0050_307_1	chr12	106869870	106870123	+	0	NA	intron (NM_018157, intron 8 of 8)	intron (NM_018157, intron 8 of 8)	-85770	NM_152261	90488	Hs.257664	NM_152261	ENSG00000151135	TMEM263	C12orf23	transmembrane protein 263	protein-coding	0.019763	0.385827	88(AAAAACAGTATGTACT,-,0.00),89(AAAACAGTATGTACTT,+,0.00)
chunk0197_217_1	chr8	122745458	122746216	+	0	NA	Intergenic	Intergenic	-35825	NM_014943	22882	Hs.377090	NM_014943	ENSG00000178764	ZHX2	AFR1|RAF	zinc fingers and homeoboxes 2	protein-coding	0.002639	0.454545	
chunk0147_61_1	chr4	172661295	172661942	+	0	NA	intron (NR_125894, intron 2 of 2)	intron (NR_125894, intron 2 of 2)	27299	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.001546	0.390432	
chunk0096_20_1	chr2	26302892	26303341	+	0	NA	Intergenic	HERV15-int|LTR|ERV1	15933	NM_001145168	165082	Hs.631878	NM_153835	ENSG00000173567	ADGRF3	GPR113|PGR23	adhesion G protein-coupled receptor F3	protein-coding	0.020045	0.488889	
chunk0094_296_1	chr2	8493191	8493917	+	0	NA	Intergenic	Intergenic	90238	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.013774	0.478680	
chunk0063_105_1	chr14	78851158	78851717	+	0	NA	intron (NM_004796, intron 7 of 16)	LTR79|LTR|ERVL	-427902	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.008945	0.425000	
chunk0179_213_1	chr7	47683783	47684176	+	0	NA	Intergenic	Intergenic	28735	NM_001123065	401335	Hs.520816	NM_001123065		C7orf65	-	chromosome 7 open reading frame 65	protein-coding	0.010178	0.500000	
chunk0055_394_1	chr13	73717900	73718117	+	0	NA	intron (NM_007249, intron 6 of 7)	intron (NM_007249, intron 6 of 7)	153764	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.000000	0.261468	168(AAGAACACTTTGTTTT,-,0.00),169(AGAACACTTTGTTTTG,+,0.00)
chunk0025_214_1	chr10	53843921	53844201	+	0	NA	intron (NM_001142769, intron 30 of 35)	L2a|LINE|L2	763896	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.003571	0.352313	120(GGGAACAATGTGTGCT,-,0.00),121(GGAACAATGTGTGCTG,+,0.00)
chunk0196_423_1	chr8	116222801	116223056	+	0	NA	intron (NR_046215, intron 4 of 13)	intron (NR_046215, intron 4 of 13)	102131	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.003922	0.429688	
chunk0059_435_1	chr14	38431258	38431547	+	0	NA	Intergenic	Intergenic	-175032	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.006920	0.431034	141(GAACACAGCCTGTTCA,-,0.00),142(AACACAGCCTGTTCAA,+,0.00)
chunk0072_136_1	chr15	92653993	92654664	+	0	NA	intron (NM_207446, intron 1 of 2)	intron (NM_207446, intron 1 of 2)	1473	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.010432	0.504464	
chunk0037_190_1	chr11	74184522	74184918	+	0	NA	intron (NM_001271593, intron 1 of 13)	intron (NM_001271593, intron 1 of 13)	13657	NM_016147	51400	Hs.503251	NM_016147	ENSG00000214517	PPME1	ABDH19|PME-1	protein phosphatase methylesterase 1	protein-coding	0.005051	0.375315	
chunk0068_193_1	chr15	54839100	54839789	+	0	NA	Intergenic	MIR|SINE|MIR	357589	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.007257	0.379710	
chunk0163_48_1	chr6	8664692	8665530	+	0	NA	intron (NR_038980, intron 3 of 4)	intron (NR_038980, intron 3 of 4)	12902	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.004773	0.327771	695(TAGAACATTGTGTTCT,-,0.00),696(AGAACATTGTGTTCTT,+,0.00)
chunk0140_28_1	chr4	65826486	65826884	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-156190	NM_004439	2044	Hs.654492	NM_004439	ENSG00000145242	EPHA5	CEK7|EHK-1|EHK1|EK7|HEK7|TYRO4	EPH receptor A5	protein-coding	0.005025	0.355890	267(GAGGACAATCTGTACA,-,0.00),268(AGGACAATCTGTACAT,+,0.00)
chunk0053_74_1	chr13	28392513	28392715	+	0	NA	intron (NM_001159920, intron 12 of 12)	intron (NM_001159920, intron 12 of 12)	102514	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.004950	0.399015	
chunk0019_79_1	chr1	224326544	224327051	+	0	NA	intron (NM_002533, intron 1 of 22)	MER119|DNA|hAT-Charlie	3392	NM_001243147	4931	Hs.497867	NM_002533	ENSG00000143748	NVL	NVL2	nuclear VCP like	protein-coding	0.001972	0.360236	
chunk0076_205_1	chr16	68116874	68117114	+	0	NA	intron (NM_173163, intron 1 of 10)	Tigger15a|DNA|TcMar-Tigger	31628	NM_004555	4775	Hs.436585	NM_004555	ENSG00000072736	NFATC3	NF-AT4c|NFAT4|NFATX	nuclear factor of activated T cells 3	protein-coding	0.004167	0.352697	51(AAGAACAAGTTGTTCT,-,0.00),52(AGAACAAGTTGTTCTG,+,0.00)
chunk0091_195_1	chr19	8449897	8450156	+	0	NA	intron (NM_005968, intron 1 of 15)	intron (NM_005968, intron 1 of 15)	5107	NM_005968	4670	Hs.465808	NM_005968	ENSG00000099783	HNRNPM	CEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP M	heterogeneous nuclear ribonucleoprotein M	protein-coding	0.015444	0.500000	
chunk0108_375_1	chr2	236824712	236825435	+	0	NA	Intergenic	Intergenic	255336	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.004149	0.383978	
chunk0039_156_1	chr11	98861834	98862315	+	0	NA	Intergenic	Intergenic	-158902	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004158	0.350622	
chunk0132_37_1	chr3	154784347	154784998	+	0	NA	Intergenic	L1M5|LINE|L1	-294975	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.000000	0.296012	
chunk0089_305_1	chr18	63705415	63705768	+	0	NA	intron (NM_001291279, intron 1 of 6)	L1ME5|LINE|L1	2632	NM_001291278	89778	Hs.350958	NM_080475	ENSG00000206072	SERPINB11	EPIPIN|SERPIN11	serpin family B member 11 (gene/pseudogene)	protein-coding	0.002833	0.370056	
chunk0130_97_1	chr3	130850863	130851343	+	0	NA	intron (NM_001199181, intron 1 of 26)	intron (NM_001199181, intron 1 of 26)	578	NM_001199181	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.014583	0.355509	248(GGAACATTCAGATCCT,+,0.00)
chunk0050_86_1	chr12	101714065	101714343	+	0	NA	exon (NM_020244, exon 2 of 9)	exon (NM_020244, exon 2 of 9)	16565	NM_020244	56994	Hs.293077	NM_020244	ENSG00000111666	CHPT1	CPT|CPT1	choline phosphotransferase 1	protein-coding	0.000000	0.354839	
chunk0022_293_1	chr10	15515171	15515968	+	0	NA	3' UTR (NM_003638, exon 30 of 30)	3' UTR (NM_003638, exon 30 of 30)	-144510	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.010038	0.353383	396(TGGGTCAGCTTGTTCT,-,0.00),397(GGGTCAGCTTGTTCTA,+,0.00)
chunk0200_387_1	chr9	26801727	26802169	+	0	NA	Intergenic	Intergenic	90880	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.009050	0.458239	
chunk0052_313_1	chr12	125041501	125041893	+	0	NA	Intergenic	L1ME4b|LINE|L1	-14274	NR_110375	102659353	Hs.596464	NR_110375	ENSG00000280634	THRIL	BRI3BP-AS1|BRI3BPAS1|Linc1992|TCONS_00020260	TNF and HNRNPL related immunoregulatory long non-coding RNA	ncRNA	0.007653	0.463104	
chunk0107_461_1	chr2	225841213	225841812	+	0	NA	Intergenic	MER54A|LTR|ERVL	-301282	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003339	0.420000	
chunk0019_379_1	chr1	229988596	229988890	+	0	NA	Intergenic	Intergenic	-69046	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.017007	0.416949	
chunk0118_437_1	chr22	38896771	38896970	+	0	NA	Intergenic	L1MC5a|LINE|L1	-24536	NM_001303494	23466	Hs.592201	NM_014292	ENSG00000183741	CBX6	-	chromobox 6	protein-coding	0.000000	0.335000	
chunk0105_234_1	chr2	188348277	188348656	+	0	NA	intron (NR_045563, intron 2 of 12)	Charlie14a|DNA|hAT-Charlie	50974	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.005277	0.352632	
chunk0034_52_1	chr11	26958447	26958803	+	0	NA	Intergenic	Intergenic	-35456	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.002809	0.336134	
chunk0007_150_1	chr1	79637488	79637919	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-630893	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.002320	0.310185	
chunk0022_4_1	chr10	7090372	7090838	+	0	NA	Intergenic	Intergenic	96179	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.012876	0.370450	224(GAAACTCAATGTTCCT,+,0.00)
chunk0041_402_1	chr11	133582649	133582940	+	0	NA	Intergenic	Intergenic	-50286	NM_001012393	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.020619	0.496575	
chunk0161_244_1	chr5	171622034	171622404	+	0	NA	Intergenic	Intergenic	-163653	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.005405	0.541779	
chunk0026_179_1	chr10	63446490	63447154	+	0	NA	intron (NM_032776, intron 1 of 25)	L2-3_Crp|LINE|L2	-18407	NR_027182	84989	Hs.659950	NM_032903	ENSG00000272767	JMJD1C-AS1	-	JMJD1C antisense RNA 1	ncRNA	0.006024	0.353383	
chunk0149_199_1	chr5	21641446	21641907	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	182196	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.008677	0.413420	
chunk0176_363_1	chr7	18389831	18390769	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-105446	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.007463	0.412141	
chunk0129_151_1	chr3	120555846	120556653	+	0	NA	Intergenic	Intergenic	-40032	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.007435	0.509901	
chunk0029_460_1	chr10	110604176	110604809	+	0	NA	3' UTR (NM_005445, exon 29 of 29)	3' UTR (NM_005445, exon 29 of 29)	36801	NM_005445	9126	Hs.24485	NM_005445	ENSG00000108055	SMC3	BAM|BMH|CDLS3|CSPG6|HCAP|SMC3L1	structural maintenance of chromosomes 3	protein-coding	0.001580	0.304416	
chunk0015_164_1	chr1	186568208	186568738	+	0	NA	Intergenic	L2a|LINE|L2	-107365	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.005660	0.329567	
chunk0186_313_1	chr7	143002770	143003526	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	23984	NM_001001658	135924	Hs.553594	NM_001001658	ENSG00000179468	OR9A2	-	olfactory receptor family 9 subfamily A member 2	protein-coding	0.010582	0.468956	
chunk0096_386_1	chr2	37143156	37143667	+	0	NA	intron (NM_001135651, intron 4 of 16)	L1M7|LINE|L1	4411	NM_001135652	5610	Hs.131431	NM_002759	ENSG00000055332	EIF2AK2	EIF2AK1|PKR|PPP1R83|PRKR	eukaryotic translation initiation factor 2 alpha kinase 2	protein-coding	0.009785	0.388672	
chunk0116_351_1	chr21	41530265	41530960	+	0	NA	Intergenic	Intergenic	-22454	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.008633	0.410920	527(AGGGACAGAATGCTCA,-,0.00)
chunk0103_381_1	chr2	168672366	168672576	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	89528	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.009524	0.369668	
chunk0181_264_1	chr7	86074149	86074635	+	0	NA	Intergenic	Intergenic	-569522	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.004115	0.285421	234(AGTAACAATCTGTTCT,-,0.00),235(GTAACAATCTGTTCTT,+,0.00)
chunk0127_202_1	chr3	96220110	96220501	+	0	NA	Intergenic	Intergenic	-139659	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.002558	0.270408	
chunk0131_188_1	chr3	148335629	148335964	+	0	NA	Intergenic	L1ME3F|LINE|L1	-362075	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.005970	0.345238	
chunk0208_56_1	chrX	11477955	11478473	+	0	NA	intron (NR_109776, intron 1 of 14)	L1ME2|LINE|L1	-50429	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.001931	0.325626	
chunk0090_292_1	chr18	75012034	75012554	+	0	NA	intron (NM_017757, intron 7 of 7)	intron (NM_017757, intron 7 of 7)	193219	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.007692	0.364683	
chunk0057_298_1	chr13	106348992	106349300	+	0	NA	Intergenic	Intergenic	-27417	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.032468	0.488673	
chunk0043_335_1	chr12	22756200	22756565	+	0	NA	Intergenic	L1MC|LINE|L1	131240	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.000000	0.248634	
chunk0171_214_1	chr6	126041985	126042253	+	0	NA	Intergenic	Intergenic	55689	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.000000	0.364312	136(GAGAACATAGTGTCTA,-,0.00)
chunk0080_437_1	chr17	36074173	36074734	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	10181	NM_002988	6362	Hs.143961	NM_002988	ENSG00000275385	CCL18	AMAC-1|AMAC1|CKb7|DC-CK1|DCCK1|MIP-4|PARC|SCYA18	C-C motif chemokine ligand 18	protein-coding	0.005348	0.387900	
chunk0167_425_1	chr6	75602251	75602545	+	0	NA	5' UTR (NM_001100409, exon 1 of 23)	5' UTR (NM_001100409, exon 1 of 23)	889	NM_015571	26054	Hs.485784	NM_015571	ENSG00000112701	SENP6	SSP1|SUSP1	SUMO specific peptidase 6	protein-coding	0.139456	0.745763	
chunk0117_389_1	chr21	45401240	45401439	+	0	NA	Intergenic	L1MEc|LINE|L1	-3798	NM_130445	80781	Hs.517356	NM_030582	ENSG00000182871	COL18A1	KNO|KNO1|KS	collagen type XVIII alpha 1 chain	protein-coding	0.010050	0.400000	
chunk0154_69_1	chr5	77426171	77426704	+	0	NA	intron (NM_001029854, intron 20 of 20)	intron (NM_001029854, intron 20 of 20)	66070	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.011257	0.434457	
chunk0048_249_1	chr12	81611904	81612339	+	0	NA	intron (NM_001220474, intron 2 of 30)	L1PA16|LINE|L1	-13750	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.004598	0.467890	
chunk0168_252_1	chr6	88920784	88921297	+	0	NA	intron (NM_003800, intron 4 of 15)	intron (NM_003800, intron 4 of 15)	42589	NM_003800	8732	Hs.567378	NM_003800	ENSG00000111880	RNGTT	CAP1A|HCE|HCE1|hCAP	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0.001949	0.326848	183(GAGCACAGGATGTATT,-,0.00),184(AGCACAGGATGTATTG,+,0.00)
chunk0066_81_1	chr15	29489704	29489921	+	0	NA	intron (NM_015307, intron 1 of 10)	intron (NM_015307, intron 1 of 10)	80911	NM_015307	23359	Hs.383564	NM_015307	ENSG00000104059	FAM189A1	TMEM228	family with sequence similarity 189 member A1	protein-coding	0.032258	0.518349	
chunk0108_86_1	chr2	227667317	227667649	+	0	NA	Intergenic	Intergenic	-34163	NM_001162483	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.021084	0.486486	
chunk0171_171_1	chr6	124999985	125000227	+	0	NA	intron (NR_104440, intron 2 of 6)	intron (NR_104440, intron 2 of 6)	16742	NR_104440	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.004132	0.308642	
chunk0051_134_1	chr12	115496784	115497496	+	0	NA	Intergenic	Intergenic	651514	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.001404	0.429173	
chunk0069_346_1	chr15	66590672	66591172	+	0	NA	intron (NR_110372, intron 1 of 4)	MLT1E2|LTR|ERVL-MaLR	8732	NR_110372	102723165	Hs.636703	NR_110372	ENSG00000259471	LINC01169	-	long intergenic non-protein coding RNA 1169	ncRNA	0.010000	0.441118	
chunk0173_417_1	chr6	151027087	151027750	+	0	NA	intron (NM_001242767, intron 24 of 27)	intron (NM_001242767, intron 24 of 27)	161085	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.004525	0.397590	237(TGGTACACAAAGTCCC,-,0.00),238(GGTACACAAAGTCCCT,+,0.00)
chunk0017_56_1	chr1	205369665	205370055	+	0	NA	Intergenic	Intergenic	-3392	NR_038425	284576	Hs.585440	NR_038425	ENSG00000226235	LEMD1-AS1	-	LEMD1 antisense RNA 1	ncRNA	0.007692	0.460358	
chunk0167_285_1	chr6	70576016	70576353	+	0	NA	intron (NM_145267, intron 1 of 2)	intron (NM_145267, intron 1 of 2)	9262	NM_145267	135154	Hs.418495	NM_145267	ENSG00000154079	SDHAF4	C6orf57|Sdh8	succinate dehydrogenase complex assembly factor 4	protein-coding	0.011869	0.464497	171(AGGAGCACAGTGTCCC,-,0.00),172(GGAGCACAGTGTCCCA,+,0.00)
chunk0008_343_1	chr1	95926989	95927301	+	0	NA	Intergenic	Intergenic	-64923	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.006410	0.392971	
chunk0117_408_1	chr21	45662061	45662885	+	0	NA	Intergenic	L1PB4|LINE|L1	-120002	NM_001205206	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.009709	0.425455	467(GGGCACGAGCTGTTCC,-,0.00)
chunk0187_387_1	chr7	157678560	157678896	+	0	NA	intron (NM_001308268, intron 13 of 22)	intron (NM_001308268, intron 13 of 22)	-104306	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.023810	0.507418	
chunk0140_365_1	chr4	74445297	74445640	+	0	NA	intron (NM_001657, intron 1 of 5)	intron (NM_001657, intron 1 of 5)	370	NM_001657	374	Hs.270833	NM_001657	ENSG00000109321	AREG	AR|AREGB|CRDGF|SDGF	amphiregulin	protein-coding	0.061224	0.578488	289(CAGGACAAGGTGTCCC,-,0.00),290(AGGACAAGGTGTCCCA,+,0.00)
chunk0001_31_1	chr1	1375012	1375528	+	0	NA	promoter-TSS (NM_001127230)	promoter-TSS (NM_001127230)	-70	NM_001127229	54998	Hs.632515	NM_017900	ENSG00000175756	AURKAIP1	AIP|AKIP|MRP-S38	aurora kinase A interacting protein 1	protein-coding	0.120155	0.705996	
chunk0125_441_1	chr3	72763342	72764010	+	0	NA	intron (NM_018130, intron 10 of 10)	MLT1C|LTR|ERVL-MaLR	84771	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.004491	0.430493	
chunk0165_93_1	chr6	31971958	31972163	+	0	NA	exon (NM_004197, exon 1 of 8)	exon (NM_004197, exon 1 of 8)	191	NM_032454	8859	Hs.654371	NM_004197	ENSG00000204344	STK19	D6S60|D6S60E|G11|HLA-RP1|RP1	serine/threonine kinase 19	protein-coding	0.087805	0.635922	
chunk0095_335_1	chr2	20832978	20833610	+	0	NA	Intergenic	Intergenic	-10164	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.004747	0.363349	262(GAGTACAGTATGTTCC,-,0.00),263(AGTACAGTATGTTCCC,+,0.00)
chunk0054_320_1	chr13	48983481	48983832	+	0	NA	intron (NM_001278438, intron 1 of 25)	L2c|LINE|L2	7047	NM_001278438	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.005698	0.343750	
chunk0101_94_1	chr2	124566389	124567017	+	0	NA	intron (NM_130773, intron 11 of 23)	intron (NM_130773, intron 11 of 23)	541416	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.003185	0.416534	
chunk0167_123_1	chr6	61628497	61628696	+	0	NA	Intergenic	Intergenic	54493	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.000000	0.415000	
chunk0138_120_1	chr4	36363236	36363702	+	0	NA	Intergenic	L1MC3|LINE|L1	62959	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.000000	0.282655	287(AGGAACTCTCTGTACT,-,0.00),288(GGAACTCTCTGTACTA,+,0.00)
chunk0010_439_1	chr1	119974643	119975000	+	0	NA	intron (NM_024408, intron 5 of 33)	L2b|LINE|L2	-78297	NM_021794	11085	Hs.283011	NM_021794	ENSG00000134249	ADAM30	svph4	ADAM metallopeptidase domain 30	protein-coding	0.008403	0.452514	
chunk0079_316_1	chr17	17252052	17252339	+	0	NA	intron (NM_001316356, intron 8 of 10)	L1ME3A|LINE|L1	-15007	NM_144997	201163	Hs.31652	NM_144606	ENSG00000154803	FLCN	BHD|DENND8B|FLCL	folliculin	protein-coding	0.010453	0.420139	
chunk0190_64_1	chr8	29756778	29757192	+	0	NA	intron (NR_125814, intron 1 of 3)	intron (NR_125814, intron 1 of 3)	8676	NR_125815	101929450	Hs.512440	NR_125814	ENSG00000253490	LINC02099	-	long intergenic non-protein coding RNA 2099	ncRNA	0.007246	0.409639	
chunk0163_447_1	chr6	17502249	17502805	+	0	NA	intron (NR_110855, intron 3 of 3)	intron (NR_110855, intron 3 of 3)	8738	NR_110855	101928491	Hs.622876	NR_110855		LOC101928491	-	uncharacterized LOC101928491	ncRNA	0.001799	0.364452	
chunk0042_217_1	chr12	6149929	6150242	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-25415	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.019169	0.522293	
chunk0092_61_1	chr19	20181755	20182287	+	0	NA	intron (NM_052852, intron 1 of 3)	intron (NM_052852, intron 1 of 3)	14807	NM_052852	90649	Hs.590991	NM_052852	ENSG00000256229	ZNF486	KRBO2	zinc finger protein 486	protein-coding	0.005639	0.373358	
chunk0089_377_1	chr18	67422488	67422752	+	0	NA	Intergenic	L1MC1|LINE|L1	-93926	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.022727	0.400000	2(AAGTACAAAGAGTTCC,-,0.00),3(AGTACAAAGAGTTCCC,+,0.00)
chunk0188_439_1	chr8	19273618	19274266	+	0	NA	Intergenic	Intergenic	-28420	NR_038919	100128993	Hs.697742	NR_038919		LOC100128993	-	uncharacterized LOC100128993	ncRNA	0.021605	0.482280	
chunk0002_351_1	chr1	25587578	25588189	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-29585	NM_001289010	57134	Hs.197043	NM_020379	ENSG00000117643	MAN1C1	HMIC|MAN1A3|MAN1C|pp6318	mannosidase alpha class 1C member 1	protein-coding	0.018003	0.485294	
chunk0075_33_1	chr16	46967855	46968299	+	0	NA	intron (NM_005880, intron 4 of 8)	intron (NM_005880, intron 4 of 8)	5637	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.022523	0.404494	
chunk0069_275_1	chr15	64866990	64867490	+	0	NA	3' UTR (NM_001195059, exon 5 of 5)	3' UTR (NM_001195059, exon 5 of 5)	25357	NM_025201	80301	Hs.709337	NM_025201	ENSG00000241839	PLEKHO2	PLEKHQ1|PP1628|pp9099	pleckstrin homology domain containing O2	protein-coding	0.016000	0.588822	
chunk0164_311_1	chr6	25006307	25006941	+	0	NA	intron (NM_001286446, intron 1 of 13)	intron (NM_001286446, intron 1 of 13)	35544	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.003155	0.436220	259(TGGAACTCTCTGTTCT,-,0.00),260(GGAACTCTCTGTTCTT,+,0.00),345(GAGTACGGACTGTACC,-,0.00)
chunk0204_451_1	chr9	104327720	104328384	+	0	NA	Intergenic	Intergenic	-176211	NM_001004485	138805	Hs.553602	NM_001004485	ENSG00000186881	OR13F1	OR9-6	olfactory receptor family 13 subfamily F member 1	protein-coding	0.004518	0.406015	344(AGGCACAAATTGTTCA,-,0.00),345(GGCACAAATTGTTCAA,+,0.00)
chunk0153_83_1	chr5	68134238	68135000	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-55257	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.013123	0.422018	
chunk0038_434_1	chr11	94658370	94658860	+	0	NA	Intergenic	Intergenic	91307	NM_152431	143689	Hs.660188	NM_152431	ENSG00000134627	PIWIL4	HIWI2|MIWI2	piwi like RNA-mediated gene silencing 4	protein-coding	0.010204	0.401222	
chunk0122_396_1	chr3	37963090	37963470	+	0	NA	intron (NM_001008392, intron 3 of 7)	intron (NM_001008392, intron 3 of 7)	-6124	NR_029499	407015		NR_029499	ENSG00000199075	MIR26A1	MIR26A|MIRN26A1|mir-26a-1	microRNA 26a-1	ncRNA	0.010526	0.417323	
chunk0152_216_1	chr5	60308839	60309347	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-178620	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.003937	0.383104	
chunk0158_309_1	chr5	132414721	132415054	+	0	NA	intron (NR_045116, intron 1 of 3)	intron (NR_045116, intron 1 of 3)	4114	NR_045116									0.006006	0.356287	
chunk0050_246_1	chr12	105367096	105367520	+	0	NA	intron (NM_001145199, intron 4 of 5)	intron (NM_001145199, intron 4 of 5)	36672	NM_001145199	387882	Hs.368938	NM_207376	ENSG00000235162	C12orf75	AGD3|OCC-1|OCC1	chromosome 12 open reading frame 75	protein-coding	0.002358	0.291765	
chunk0098_332_1	chr2	76944310	76944560	+	0	NA	intron (NM_001282924, intron 3 of 3)	L2c|LINE|L2	-41530	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.000000	0.342629	
chunk0140_42_1	chr4	66607007	66607305	+	0	NA	Intergenic	Intergenic	330332	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.000000	0.387960	
chunk0059_133_1	chr14	31845594	31846122	+	0	NA	intron (NM_001201573, intron 6 of 8)	intron (NM_001201573, intron 6 of 8)	131289	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.017045	0.408318	
chunk0034_109_1	chr11	27873498	27873890	+	0	NA	Intergenic	Intergenic	-151636	NM_170731	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.012755	0.427481	
chunk0196_125_1	chr8	103872997	103873498	+	0	NA	intron (NM_001282881, intron 1 of 20)	intron (NM_001282881, intron 1 of 20)	54059	NM_014677	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.001996	0.378486	
chunk0108_307_1	chr2	235182256	235182843	+	0	NA	Intergenic	L1MC2|LINE|L1	230565	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.010221	0.442177	
chunk0116_200_1	chr21	37368380	37368579	+	0	NA	intron (NM_101395, intron 1 of 12)	intron (NM_101395, intron 1 of 12)	922	NM_101395	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.025126	0.460000	
chunk0176_73_1	chr7	11261361	11261920	+	0	NA	Intergenic	LTR57|LTR|ERVL	287768	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.000000	0.403571	
chunk0104_41_1	chr2	171141303	171141767	+	0	NA	intron (NM_001136554, intron 1 of 20)	L1MEg|LINE|L1	19365	NM_012290	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.002155	0.376344	
chunk0032_391_1	chr11	11596562	11596782	+	0	NA	intron (NM_198516, intron 1 of 10)	L1PA8A|LINE|L1	25342	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.004545	0.294118	
chunk0076_277_1	chr16	69583300	69583957	+	0	NA	intron (NM_138713, intron 2 of 14)	intron (NM_138713, intron 2 of 14)	17662	NM_006599	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.001522	0.379939	
chunk0086_216_1	chr18	22499562	22499785	+	0	NA	Intergenic	L1MD1|LINE|L1	-81758	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.000000	0.348214	
chunk0196_283_1	chr8	109355019	109355629	+	0	NA	Intergenic	Alu|SINE|Alu	-7153	NM_177531	93035	Hs.170128	NM_177531	ENSG00000205038	PKHD1L1	PKHDL1	PKHD1 like 1	protein-coding	0.008197	0.379705	
chunk0091_2_1	chr19	2528616	2529199	+	0	NA	intron (NM_052847, intron 3 of 4)	intron (NM_052847, intron 3 of 4)	52782	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.018868	0.570205	321(TGGAACATCCTGCACC,-,0.00),322(GGAACATCCTGCACCC,+,0.00)
chunk0071_441_1	chr15	90035525	90035771	+	0	NA	intron (NM_198526, intron 1 of 4)	intron (NM_198526, intron 1 of 4)	28893	NR_036135	100422841		NR_036135	ENSG00000265871	MIR3174	-	microRNA 3174	ncRNA	0.032520	0.542510	
chunk0062_45_1	chr14	67276146	67276550	+	0	NA	intron (NM_001256550, intron 2 of 14)	L2c|LINE|L2	35053	NM_001256550	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.000000	0.353086	116(ATGTACAGCATGTTCC,-,0.00),117(TGTACAGCATGTTCCC,+,0.00)
chunk0146_15_1	chr4	155041847	155042740	+	0	NA	Intergenic	L1M5|LINE|L1	-166336	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.002240	0.354586	
chunk0135_167_1	chr3	187959301	187959665	+	0	NA	Intergenic	Charlie17a|DNA|hAT-Charlie	-194390	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.002747	0.408219	
chunk0049_5_1	chr12	89192343	89192833	+	0	NA	Intergenic	Intergenic	160271	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.010204	0.380855	
chunk0170_45_1	chr6	109428751	109429239	+	0	NA	intron (NM_001111298, intron 3 of 8)	intron (NM_001111298, intron 3 of 8)	-11733	NM_003080	6610	Hs.55235	NM_003080	ENSG00000135587	SMPD2	ISC1|NSMASE|NSMASE1	sphingomyelin phosphodiesterase 2	protein-coding	0.010246	0.380368	
chunk0013_128_1	chr1	168116125	168116861	+	0	NA	intron (NM_001267610, intron 1 of 6)	intron (NM_001267610, intron 1 of 6)	19943	NM_001267612	23432	Hs.271809	NM_007369	ENSG00000143147	GPR161	RE2	G protein-coupled receptor 161	protein-coding	0.009511	0.514247	
chunk0009_352_1	chr1	109563313	109563733	+	0	NA	intron (NM_006496, intron 1 of 8)	intron (NM_006496, intron 1 of 8)	14959	NM_006496	2773	Hs.73799	NM_006496	ENSG00000065135	GNAI3	87U6|ARCND1	G protein subunit alpha i3	protein-coding	0.004762	0.408551	
chunk0063_177_1	chr14	80468591	80468970	+	0	NA	Intergenic	HERVK22-int|LTR|ERVK	-237726	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.007916	0.415789	
chunk0023_182_1	chr10	24643087	24643321	+	0	NA	intron (NM_020824, intron 4 of 25)	L2a|LINE|L2	80464	NM_020824	57584	Hs.524195	NM_020824	ENSG00000107863	ARHGAP21	ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.004274	0.348936	
chunk0050_375_1	chr12	108625281	108625980	+	0	NA	intron (NM_003006, intron 1 of 1)	intron (NM_003006, intron 1 of 1)	6448	NM_001206609	6404	Hs.591014	NM_003006	ENSG00000110876	SELPLG	CD162|CLA|PSGL-1|PSGL1	selectin P ligand	protein-coding	0.007153	0.464286	
chunk0012_195_1	chr1	159863859	159864094	+	0	NA	Intergenic	Intergenic	-1319	NM_001013661	391123	Hs.647718	NM_001013661	ENSG00000243284	VSIG8	-	V-set and immunoglobulin domain containing 8	protein-coding	0.017021	0.457627	
chunk0141_56_1	chr4	77605032	77605623	+	0	NA	intron (NM_006419, intron 1 of 4)	intron (NM_006419, intron 1 of 4)	93574	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.013536	0.452703	
chunk0022_330_1	chr10	16559099	16559331	+	0	NA	Intergenic	L1PA15|LINE|L1	-37210	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.000000	0.489270	
chunk0055_10_1	chr13	51674200	51674723	+	0	NA	intron (NM_052950, intron 2 of 11)	intron (NM_052950, intron 2 of 11)	90113	NM_052950	115825	Hs.46506	NM_052950	ENSG00000139668	WDFY2	PROF|WDF2|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.011472	0.437023	
chunk0135_417_1	chr3	193262927	193263584	+	0	NA	intron (NM_020386, intron 3 of 3)	intron (NM_020386, intron 3 of 3)	21476	NR_026877	84789	Hs.676481	NM_032703		MGC2889	-	uncharacterized protein MGC2889	ncRNA	0.010654	0.384498	
chunk0086_203_1	chr18	22298979	22299249	+	0	NA	Intergenic	Intergenic	118801	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.014815	0.531365	
chunk0169_317_1	chr6	106180376	106180801	+	0	NA	Intergenic	L2c|LINE|L2	81726	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.009412	0.377934	
chunk0094_55_1	chr2	3224922	3225181	+	0	NA	intron (NM_003310, intron 4 of 8)	intron (NM_003310, intron 4 of 8)	-99025	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.015444	0.450000	
chunk0209_457_1	chrX	66712582	66712914	+	0	NA	Intergenic	L2c|LINE|L2	-73450	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.000000	0.348348	
chunk0106_2_1	chr2	195319551	195320043	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-337011	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.002033	0.330629	
chunk0073_446_1	chr16	19389248	19389450	+	0	NA	Intergenic	Intergenic	-21190	NM_001308161	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.019802	0.532020	
chunk0041_408_1	chr11	133901840	133902075	+	0	NA	promoter-TSS (NR_024344)	promoter-TSS (NR_024344)	-217	NR_024344	283174	Hs.504370	NM_001001873	ENSG00000280237	MIR4697HG	LINC00947	MIR4697 host gene	ncRNA	0.017021	0.504237	
chunk0097_86_1	chr2	45330856	45331319	+	0	NA	Intergenic	Intergenic	-76146	NR_033831	400952	Hs.468368	NR_033831	ENSG00000205054	LINC01121	UNQ6975	long intergenic non-protein coding RNA 1121	ncRNA	0.010799	0.467672	
chunk0048_200_1	chr12	81245406	81245964	+	0	NA	intron (NM_024560, intron 13 of 15)	L1ME1|LINE|L1	-33504	NR_120491	102724663	Hs.667264	NR_120491	ENSG00000257467	PPFIA2-AS1	-	PPFIA2 antisense RNA 1	ncRNA	0.007168	0.407871	202(AGGAACACAGTGTTTT,-,0.00),203(GGAACACAGTGTTTTG,+,0.00)
chunk0177_391_1	chr7	27031627	27031898	+	0	NA	Intergenic	MIR|SINE|MIR	64244	NM_005522	3198	Hs.67397	NM_005522	ENSG00000105991	HOXA1	BSAS|HOX1|HOX1F	homeobox A1	protein-coding	0.003690	0.363971	
chunk0142_375_1	chr4	102097206	102097712	+	0	NA	Intergenic	L1M4|LINE|L1	226853	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.000000	0.254438	
chunk0018_15_1	chr1	215181751	215181950	+	0	NA	intron (NM_001017424, intron 5 of 6)	L1PA11|LINE|L1	98633	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.010050	0.505000	
chunk0001_125_1	chr1	4648810	4649903	+	0	NA	Intergenic	Intergenic	-5689	NM_001042478	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.002745	0.484461	
chunk0197_343_1	chr8	125345238	125345936	+	0	NA	intron (NM_173685, intron 5 of 7)	L2c|LINE|L2	-84734	NM_025195	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.004298	0.420601	
chunk0084_371_1	chr17	81636931	81637208	+	0	NA	promoter-TSS (NM_017921)	promoter-TSS (NM_017921)	84	NM_017921	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.155235	0.805755	
chunk0179_265_1	chr7	49241208	49241592	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	316839	NR_003595									0.007812	0.329870	
chunk0201_310_1	chr9	43058345	43058559	+	0	NA	Intergenic	Intergenic	270052	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.004673	0.334884	
chunk0142_246_1	chr4	98908641	98909792	+	0	NA	intron (NM_001968, intron 1 of 6)	intron (NM_001968, intron 1 of 6)	19876	NM_001130678	1977	Hs.13211	NM_001968	ENSG00000151247	EIF4E	AUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding	0.004344	0.359375	872(AAAAACACCCTGTACA,-,0.00),873(AAAACACCCTGTACAT,+,0.00),920(CAGTACTAAATGTTCT,-,0.00),921(AGTACTAAATGTTCTT,+,0.00)
chunk0052_42_1	chr13	20832919	20833303	+	0	NA	intron (NM_022459, intron 6 of 22)	intron (NM_022459, intron 6 of 22)	-59193	NM_174928	221143	Hs.26674	NM_174928	ENSG00000150456	EEF1AKMT1	ESP13|N6AMT2	EEF1A lysine methyltransferase 1	protein-coding	0.015625	0.348052	
chunk0095_71_1	chr2	14548714	14549379	+	0	NA	Intergenic	Intergenic	-83640	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.004511	0.342342	
chunk0168_258_1	chr6	89117328	89117546	+	0	NA	intron (NM_080743, intron 1 of 4)	CpG	644	NM_080743	135295	Hs.254414	NM_080743	ENSG00000154548	SRSF12	SFRS13B|SFRS19|SRrp35	serine and arginine rich splicing factor 12	protein-coding	0.100917	0.630137	
chunk0179_347_1	chr7	50784240	50784478	+	0	NA	intron (NM_001001555, intron 1 of 16)	intron (NM_001001555, intron 1 of 16)	9103	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.012605	0.514644	
chunk0061_161_1	chr14	59788206	59788566	+	0	NA	intron (NM_021136, intron 1 of 8)	L1ME4b|LINE|L1	82453	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.005556	0.362881	
chunk0180_15_1	chr7	53306997	53307196	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	271440	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.010050	0.510000	
chunk0024_60_1	chr10	33934684	33935050	+	0	NA	Intergenic	Intergenic	-162187	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.008197	0.346049	
chunk0040_216_1	chr11	114197877	114198566	+	0	NA	intron (NM_006006, intron 4 of 6)	intron (NM_006006, intron 4 of 6)	-97592	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.013062	0.485507	428(TGTACAGTCAGTGCCC,+,0.00)
chunk0164_138_1	chr6	21184935	21185643	+	0	NA	intron (NM_017774, intron 13 of 15)	intron (NM_017774, intron 13 of 15)	326603	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.005650	0.359661	
chunk0063_416_1	chr14	88417506	88418169	+	0	NA	intron (NM_001040428, intron 4 of 10)	L1MCb|LINE|L1	32193	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.001508	0.329819	
chunk0127_329_1	chr3	100401431	100401630	+	0	NA	promoter-TSS (NM_014820)	promoter-TSS (NM_014820)	-132	NM_014820	9868	Hs.227253	NM_014820	ENSG00000154174	TOMM70	TOMM70A|Tom70	translocase of outer mitochondrial membrane 70	protein-coding	0.065327	0.560000	
chunk0199_26_1	chr9	694060	694259	+	0	NA	intron (NM_015158, intron 2 of 11)	intron (NM_015158, intron 2 of 11)	-12647	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.000000	0.355000	
chunk0206_61_1	chr9	119556585	119556858	+	0	NA	Intergenic	Intergenic	-187260	NM_014618	1620	Hs.532316	NM_014618	ENSG00000078725	BRINP1	DBC1|DBCCR1|FAM5A	BMP/retinoic acid inducible neural specific 1	protein-coding	0.029304	0.492701	39(ATGCACAGGATGTCCC,-,0.00),40(TGCACAGGATGTCCCC,+,0.00)
chunk0004_226_1	chr1	46931075	46931274	+	0	NA	intron (NM_000778, intron 11 of 11)	intron (NM_000778, intron 11 of 11)	10310	NM_000778	1579	Hs.1645	NM_000778	ENSG00000187048	CYP4A11	CP4Y|CYP4A2|CYP4AII|CYPIVA11	cytochrome P450 family 4 subfamily A member 11	protein-coding	0.005025	0.595000	97(TGGCTCAGAATGTCCT,-,0.00),98(GGCTCAGAATGTCCTC,+,0.00)
chunk0127_208_1	chr3	96416293	96416666	+	0	NA	Intergenic	L1PA14|LINE|L1	56515	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.545455	
chunk0186_42_1	chr7	136121714	136122346	+	0	NA	Intergenic	Intergenic	-144574	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.001582	0.372828	
chunk0090_298_1	chr18	75172699	75172898	+	0	NA	Intergenic	Intergenic	32715	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.010050	0.515000	51(GGCACACAGTGATCAT,+,0.00)
chunk0115_241_1	chr21	27464042	27464525	+	0	NA	Intergenic	Intergenic	-258096	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.002070	0.285124	
chunk0144_229_1	chr4	134687928	134688211	+	0	NA	Intergenic	L1PA13|LINE|L1	-486321	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.007067	0.580986	99(CAGCACAGGCTGCTCT,-,0.00),100(AGCACAGGCTGCTCTG,+,0.00)
chunk0009_284_1	chr1	107626252	107626585	+	0	NA	intron (NM_006113, intron 20 of 26)	intron (NM_006113, intron 20 of 26)	62086	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.003003	0.404192	
chunk0097_307_1	chr2	55995108	55995760	+	0	NA	intron (NR_126406, intron 2 of 2)	intron (NR_126406, intron 2 of 2)	5361	NR_030623	100126319		NR_030623	ENSG00000211520	MIR216B	MIRN216B|mir-216b	microRNA 216b	ncRNA	0.003067	0.362940	294(AAGCACATTGTGTGCT,-,0.00),295(AGCACATTGTGTGCTT,+,0.00),359(AGTACATGGTGATCTT,+,0.00)
chunk0150_217_1	chr5	35247708	35248166	+	0	NA	Intergenic	Intergenic	-17348	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.013100	0.418301	
chunk0120_397_1	chr3	12556750	12557038	+	0	NA	promoter-TSS (NM_014160)	promoter-TSS (NM_014160)	-120	NM_014160	23609	Hs.591666	NM_014160	ENSG00000075975	MKRN2	HSPC070|RNF62	makorin ring finger protein 2	protein-coding	0.086806	0.643599	
chunk0196_31_1	chr8	101579130	101579567	+	0	NA	intron (NM_024915, intron 7 of 15)	intron (NM_024915, intron 7 of 15)	86908	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.000000	0.358447	
chunk0210_153_1	chrX	77504963	77505477	+	0	NA	3' UTR (NM_000489, exon 35 of 35)	3' UTR (NM_000489, exon 35 of 35)	57545	NM_003868	8823	Hs.666364	NM_003868	ENSG00000196468	FGF16	FGF-16|MF4	fibroblast growth factor 16	protein-coding	0.003891	0.380583	
chunk0096_94_1	chr2	28089241	28089879	+	0	NA	intron (NM_199191, intron 6 of 11)	MIRb|SINE|MIR	93193	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.004702	0.338028	
chunk0122_158_1	chr3	32192872	32193255	+	0	NA	Intergenic	Intergenic	-45616	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.002611	0.361979	
chunk0173_167_1	chr6	144386318	144387254	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	-18869	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.011752	0.354322	
chunk0186_247_1	chr7	140973025	140973507	+	0	NA	Intergenic	Intergenic	41413	NM_016071	51650	Hs.416207	NM_016071	ENSG00000090263	MRPS33	CGI-139|MRP-S33|PTD003|S33mt	mitochondrial ribosomal protein S33	protein-coding	0.010373	0.432712	203(AGGGCCATGGTGTCCC,-,0.00),204(GGGCCATGGTGTCCCT,+,0.00)
chunk0002_249_1	chr1	21050203	21050482	+	0	NA	intron (NM_001198801, intron 4 of 34)	intron (NM_001198801, intron 4 of 34)	61041	NM_003760	8672	Hs.467084	NM_003760	ENSG00000075151	EIF4G3	eIF-4G 3|eIF4G 3|eIF4GII	eukaryotic translation initiation factor 4 gamma 3	protein-coding	0.010753	0.375000	
chunk0144_308_1	chr4	138571489	138571869	+	0	NA	Intergenic	Intergenic	261968	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.002632	0.299213	
chunk0205_18_1	chr9	105131895	105132322	+	0	NA	Intergenic	Intergenic	-112505	NM_080546	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.007026	0.471963	203(TGGAACAGAGTGACCC,-,0.00),204(GGAACAGAGTGACCCA,+,0.00)
chunk0100_219_1	chr2	111946593	111946991	+	0	NA	intron (NM_006343, intron 3 of 18)	intron (NM_006343, intron 3 of 18)	48178	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.005025	0.416040	
chunk0107_332_1	chr2	220959588	220959787	+	0	NA	Intergenic	L1MEg1|LINE|L1	612671	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.000000	0.415000	
chunk0183_117_1	chr7	105366777	105367253	+	0	NA	intron (NM_182692, intron 2 of 15)	Tigger2|DNA|TcMar-Tigger	21915	NM_182692	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.006303	0.383648	
chunk0157_153_1	chr5	117800288	117800839	+	0	NA	intron (NR_104997, intron 1 of 2)	L1PA16|LINE|L1	70202	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.000000	0.364130	218(CAGTACTAAATGTTCT,-,0.00),219(AGTACTAAATGTTCTA,+,0.00)
chunk0186_365_1	chr7	143936443	143936780	+	0	NA	TTS (NM_001004685)	TTS (NM_001004685)	1378	NM_001004685	135948	Hs.553596	NM_001004685	ENSG00000221910	OR2F2	OR7-1	olfactory receptor family 2 subfamily F member 2	protein-coding	0.008902	0.319527	
chunk0102_310_1	chr2	151112916	151113570	+	0	NA	Intergenic	L3|LINE|CR1	148632	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.006116	0.383206	
chunk0176_315_1	chr7	16989906	16990469	+	0	NA	Intergenic	Intergenic	-108198	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.012433	0.450355	299(GAGCACACAAAGTCCC,-,0.00),300(AGCACACAAAGTCCCA,+,0.00)
chunk0094_184_1	chr2	6100911	6101377	+	0	NA	Intergenic	L1PB1|LINE|L1	119166	NR_026833	400940	Hs.378814	NM_207479		LOC400940	-	uncharacterized LOC400940	ncRNA	0.008584	0.319058	
chunk0079_303_1	chr17	17078405	17078710	+	0	NA	intron (NM_015134, intron 3 of 22)	intron (NM_015134, intron 3 of 22)	35797	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.016393	0.558824	
chunk0125_304_1	chr3	70606504	70606794	+	0	NA	Intergenic	Intergenic	458274	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.000000	0.281787	
chunk0174_404_1	chr6	165573795	165573994	+	0	NA	intron (NM_001130690, intron 1 of 21)	intron (NM_001130690, intron 1 of 21)	88206	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.020101	0.505000	
chunk0052_365_1	chr12	127780141	127780574	+	0	NA	Intergenic	L1MC2|LINE|L1	-101260	NR_033987	400087	Hs.524846	NR_033987	ENSG00000256597	LINC02393	-	long intergenic non-protein coding RNA 2393	ncRNA	0.011547	0.389401	127(AAGTACAGAGAGTTCC,-,0.00),128(AGTACAGAGAGTTCCC,+,0.00)
chunk0174_259_1	chr6	161140098	161140524	+	0	NA	intron (NM_020133, intron 7 of 8)	intron (NM_020133, intron 7 of 8)	21671	NR_024277	79992	Hs.664873	NM_024929	ENSG00000279355	AGPAT4-IT1	C6orf59|NCRNA00241	AGPAT4 intronic transcript 1	ncRNA	0.028169	0.578454	167(CAGGACTGGGTGTCCA,-,0.00),168(AGGACTGGGTGTCCAG,+,0.00)
chunk0166_276_1	chr6	48253362	48253895	+	0	NA	Intergenic	L1MEd|LINE|L1	-184939	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.003752	0.355805	
chunk0107_274_1	chr2	217953145	217953487	+	0	NA	Intergenic	Intergenic	-9243	NM_022648	7145	Hs.471381	NM_022648	ENSG00000079308	TNS1	MST091|MST122|MST127|MSTP091|MSTP122|MSTP127|MXRA6|PPP1R155|TNS	tensin 1	protein-coding	0.011696	0.530612	193(TGGAACATTGTGTTCA,-,0.00),194(GGAACATTGTGTTCAG,+,0.00)
chunk0126_400_1	chr3	84988184	84988575	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	29397	NM_001167675	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.364796	
chunk0063_336_1	chr14	85350559	85351271	+	0	NA	Intergenic	Intergenic	-42964	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.008427	0.354839	
chunk0011_194_1	chr1	149932370	149932682	+	0	NA	intron (NM_001145862, intron 10 of 16)	L1MB7|LINE|L1	3847	NM_181873	10903	Hs.425144	NM_006697	ENSG00000014914	MTMR11	CRA	myotubularin related protein 11	protein-coding	0.009615	0.402556	
chunk0207_346_1	chr9	134896301	134896890	+	0	NA	Intergenic	Intergenic	15783	NM_004108	2220	Hs.54517	NM_004108	ENSG00000160339	FCN2	EBP-37|FCNL|P35|ficolin-2	ficolin 2	protein-coding	0.020374	0.503390	
chunk0121_16_1	chr3	14676878	14677437	+	0	NA	intron (NM_001184957, intron 1 of 16)	intron (NM_001184957, intron 1 of 16)	2058	NM_001184957	84077	Hs.661452	NM_032137	ENSG00000131379	C3orf20	-	chromosome 3 open reading frame 20	protein-coding	0.010733	0.448214	292(GAGAACACCGTGACCA,-,0.00),293(AGAACACCGTGACCAG,+,0.00)
chunk0112_6_1	chr20	35751474	35752005	+	0	NA	Intergenic	L1MB5|LINE|L1	-9403	NR_040722	9584	Hs.282901	NM_004902	ENSG00000131051	RBM39	CAPER|CAPERalpha|FSAP59|HCC1|RNPC2	RNA binding motif protein 39	protein-coding	0.009416	0.439850	
chunk0024_283_1	chr10	41914909	41915141	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	453020	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.025862	0.416309	
chunk0180_207_1	chr7	66442622	66443304	+	0	NA	Intergenic	L1MEc|LINE|L1	-42555	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.007331	0.389458	
chunk0103_109_1	chr2	161406257	161406635	+	0	NA	intron (NM_005805, intron 10 of 11)	intron (NM_005805, intron 10 of 11)	-9663	NM_006593	10716	Hs.210862	NM_006593	ENSG00000136535	TBR1	IDDAS|TBR-1|TES-56	T-box brain transcription factor 1	protein-coding	0.015873	0.403694	
chunk0208_238_1	chrX	19893638	19894056	+	0	NA	Intergenic	Intergenic	-6221	NM_031892	30011	Hs.726365	NM_031892	ENSG00000147010	SH3KBP1	AGMX2|CD2BP3|CIN85|GIG10|HSB-1|HSB1|IMD61|MIG18	SH3 domain containing kinase binding protein 1	protein-coding	0.014354	0.412888	
chunk0160_305_1	chr5	159089360	159089726	+	0	NA	intron (NM_001290360, intron 4 of 15)	intron (NM_001290360, intron 4 of 15)	10237	NM_182708	1879	Hs.573143	NM_024007	ENSG00000164330	EBF1	COE1|EBF|O/E-1|OLF1	EBF transcription factor 1	protein-coding	0.010929	0.332425	
chunk0092_30_1	chr19	19026768	19026982	+	0	NA	intron (NM_001017392, intron 2 of 10)	MLT1M|LTR|ERVL-MaLR	6696	NM_014884	10147	Hs.77876	NM_014884	ENSG00000064607	SUGP2	SFRS14|SRFS14	SURP and G-patch domain containing 2	protein-coding	0.014019	0.530233	
chunk0141_374_1	chr4	88080622	88081020	+	0	NA	Intergenic	Intergenic	73174	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.002513	0.325815	
chunk0033_41_1	chr11	13182968	13183755	+	0	NA	Intergenic	Intergenic	-94366	NM_001297719	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.007624	0.361675	
chunk0127_99_1	chr3	89993242	89993764	+	0	NA	Intergenic	L1MA3|LINE|L1	885979	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.001916	0.355641	
chunk0002_124_1	chr1	16349763	16350278	+	0	NA	intron (NM_018994, intron 1 of 9)	intron (NM_018994, intron 1 of 9)	2471	NM_018994	54455	Hs.522384	NM_018994	ENSG00000037637	FBXO42	Fbx42|JFK	F-box protein 42	protein-coding	0.009709	0.387597	
chunk0057_24_1	chr13	95614576	95615207	+	0	NA	intron (NM_198968, intron 10 of 22)	intron (NM_198968, intron 10 of 22)	29815	NM_014934	22873	Hs.656580	NM_014934	ENSG00000134874	DZIP1	DZIP|DZIPt1	DAZ interacting zinc finger protein 1	protein-coding	0.007924	0.441456	
chunk0024_125_1	chr10	34919146	34919871	+	0	NA	Intergenic	Intergenic	103740	NR_108043	100505601	Hs.549790	NR_108043	ENSG00000226386	PARD3-AS1	-	PARD3 antisense RNA 1	ncRNA	0.009655	0.447658	
chunk0119_252_1	chr22	45806682	45807098	+	0	NA	intron (NM_001167621, intron 8 of 10)	intron (NM_001167621, intron 8 of 10)	46366	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.004808	0.357314	
chunk0027_432_1	chr10	80996666	80997028	+	0	NA	Intergenic	L1PB1|LINE|L1	456028	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.019337	0.570248	
chunk0148_3_1	chr5	81648	81883	+	0	NA	Intergenic	Intergenic	-58493	NM_052909	153478	Hs.535800	NM_052909	ENSG00000153404	PLEKHG4B	-	pleckstrin homology and RhoGEF domain containing G4B	protein-coding	0.025532	0.588983	
chunk0135_337_1	chr3	190297040	190297239	+	0	NA	Intergenic	Intergenic	25307	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.000000	0.285000	
chunk0120_440_1	chr3	13648424	13648749	+	0	NA	Intergenic	Intergenic	-2135	NR_027103	285375	Hs.319969	NR_027103	ENSG00000224514	LINC00620	-	long intergenic non-protein coding RNA 620	ncRNA	0.012308	0.616564	
chunk0169_437_1	chr6	108739488	108739827	+	0	NA	Intergenic	Intergenic	-11997	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.014749	0.508824	
chunk0177_456_1	chr7	28469421	28469990	+	0	NA	intron (NM_004904, intron 1 of 10)	MIR|SINE|MIR	34090	NM_004904	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.000000	0.298246	
chunk0055_257_1	chr13	63385285	63385683	+	0	NA	Intergenic	Intergenic	-57390	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.000000	0.260652	
chunk0001_60_1	chr1	2238685	2238918	+	0	NA	intron (NM_003036, intron 1 of 6)	intron (NM_003036, intron 1 of 6)	10106	NM_003036	6497	Hs.656507	NM_003036	ENSG00000157933	SKI	SGS|SKV	SKI proto-oncogene	protein-coding	0.038627	0.628205	
chunk0086_68_1	chr18	13126938	13127706	+	0	NA	Intergenic	Intergenic	-91408	NM_181482	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.027344	0.570871	
chunk0005_259_1	chr1	59757392	59757631	+	0	NA	intron (NM_001244714, intron 12 of 13)	intron (NM_001244714, intron 12 of 13)	-15284	NR_110627	101926944	Hs.720353	NR_110627		LOC101926944	-	uncharacterized LOC101926944	ncRNA	0.016736	0.454167	
chunk0212_21_1	chrY	9186457	9186851	+	0	NA	Intergenic	Intergenic	136220	NR_001547	286557	Hs.567833	NR_001547		RBMY1A3P	-	RNA binding motif protein, Y-linked, family 1, member A3 pseudogene	pseudo	0.000000	0.278481	
chunk0093_353_1	chr19	55338660	55339102	+	0	NA	promoter-TSS (NM_032701)	promoter-TSS (NM_032701)	-972	NM_032701	84787	Hs.590982	NM_032701	ENSG00000133247	KMT5C	SUV420H2|Suv4-20h2	lysine methyltransferase 5C	protein-coding	0.036199	0.541761	
chunk0021_226_1	chr10	6297654	6298363	+	0	NA	Intergenic	Intergenic	-28536	NR_040079	399715		NR_040079	ENSG00000215244	LINC02649	-	long intergenic non-protein coding RNA 2649	ncRNA	0.005642	0.454930	
chunk0152_68_1	chr5	58038761	58039189	+	0	NA	Intergenic	L1MC3|LINE|L1	83366	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.004673	0.393939	33(TAGCACACCCAGTGCC,-,0.00),34(AGCACACCCAGTGCCA,+,0.00)
chunk0146_98_1	chr4	158380772	158381011	+	0	NA	Intergenic	L2a|LINE|L2	-140823	NM_001253727	59350	Hs.591686	NM_021634	ENSG00000171509	RXFP1	LGR7|RXFPR1	relaxin family peptide receptor 1	protein-coding	0.000000	0.379167	
chunk0141_232_1	chr4	84821049	84821738	+	0	NA	exon (NM_014991, exon 11 of 68)	exon (NM_014991, exon 11 of 68)	144998	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.002903	0.330435	
chunk0005_404_1	chr1	62511778	62512704	+	0	NA	intron (NM_001272001, intron 32 of 47)	intron (NM_001272001, intron 32 of 47)	75529	NM_003368	7398	Hs.35086	NM_003368	ENSG00000162607	USP1	UBP	ubiquitin specific peptidase 1	protein-coding	0.003240	0.318231	
chunk0059_363_1	chr14	37306496	37306695	+	0	NA	intron (NM_001195296, intron 9 of 14)	intron (NM_001195296, intron 9 of 14)	108682	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.005025	0.280000	
chunk0207_275_1	chr9	132408553	132408886	+	0	NA	Intergenic	LTR46|LTR|ERV1	-1477	NM_001282957	389799	Hs.201709	NM_207417	ENSG00000188523	CFAP77	C9orf171	cilia and flagella associated protein 77	protein-coding	0.018018	0.523952	121(AGGAACATCACGTTCC,-,0.00),122(GGAACATCACGTTCCA,+,0.00)
chunk0098_162_1	chr2	70514619	70515129	+	0	NA	exon (NM_003236, exon 2 of 6)	exon (NM_003236, exon 2 of 6)	-33234	NR_046798	100874273	Hs.682157	NR_046798	ENSG00000224606	TGFA-IT1	-	TGFA intronic transcript 1	ncRNA	0.029412	0.587084	248(GGGGACGTGCTGTTCT,-,0.00),249(GGGACGTGCTGTTCTC,+,0.00)
chunk0081_380_1	chr17	48053390	48053820	+	0	NA	intron (NM_003204, intron 2 of 5)	intron (NM_003204, intron 2 of 5)	5281	NM_003204	4779	Hs.514284	NM_003204	ENSG00000082641	NFE2L1	LCR-F1|NRF1|TCF11	nuclear factor, erythroid 2 like 1	protein-coding	0.006977	0.531323	256(GAGAACATACTGTCTC,-,0.00),257(AGAACATACTGTCTCT,+,0.00)
chunk0178_270_1	chr7	36945907	36946638	+	0	NA	intron (NM_001206482, intron 16 of 21)	intron (NM_001206482, intron 16 of 21)	-26840	NR_031604	100302113		NR_031604	ENSG00000221325	MIR1200	MIRN1200|hsa-mir-1200	microRNA 1200	ncRNA	0.008208	0.474044	
chunk0185_294_1	chr7	131111243	131112338	+	0	NA	intron (NM_001145354, intron 1 of 18)	(ATAA)n|Simple_repeat|Simple_repeat	1694	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.011872	0.364964	662(GAGAACACAGTGTGAC,-,0.00),663(AGAACACAGTGTGACT,+,0.00)
chunk0113_89_1	chr20	50848834	50849475	+	0	NA	intron (NM_198799, intron 4 of 4)	intron (NM_198799, intron 4 of 4)	54260	NM_001010974	55653	Hs.381178	NM_017843	ENSG00000124243	BCAS4	CNOL	breast carcinoma amplified sequence 4	protein-coding	0.024961	0.601246	
chunk0006_300_1	chr1	71303489	71304148	+	0	NA	Intergenic	Intergenic	222494	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.006070	0.404545	
chunk0211_6_1	chrX	107675798	107676081	+	0	NA	Intergenic	L1MB7|LINE|L1	40542	NM_001015881	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.017668	0.482394	
chunk0085_11_1	chr18	215682	215932	+	0	NA	intron (NM_005131, intron 19 of 20)	intron (NM_005131, intron 19 of 20)	52252	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.004000	0.410359	
chunk0056_213_1	chr13	86732086	86732676	+	0	NA	Intergenic	L1MA4A|LINE|L1	-179539	NR_132371	106144533	Hs.525107	NR_132371		LINC00430	-	long intergenic non-protein coding RNA 430	ncRNA	0.001695	0.370558	
chunk0026_393_1	chr10	69703702	69704111	+	0	NA	Intergenic	L1ME2|LINE|L1	73659	NM_145306	219738	Hs.522992	NM_145306	ENSG00000171224	FAM241B	C10orf35	family with sequence similarity 241 member B	protein-coding	0.014670	0.397561	
chunk0176_435_1	chr7	19927836	19928131	+	0	NA	intron (NR_110114, intron 5 of 5)	intron (NR_110114, intron 5 of 5)	-155202	NM_152774	256130	Hs.487670	NM_152774	ENSG00000173452	TMEM196	-	transmembrane protein 196	protein-coding	0.000000	0.293919	
chunk0102_430_1	chr2	157732385	157732859	+	0	NA	Intergenic	Intergenic	-103735	NM_001111032	130399	Hs.562901	NM_145259	ENSG00000123612	ACVR1C	ACVRLK7|ALK7	activin A receptor type 1C	protein-coding	0.008439	0.366316	
chunk0061_118_1	chr14	58465632	58466117	+	0	NA	exon (NM_001244190, exon 16 of 32)	exon (NM_001244190, exon 16 of 32)	26193	NM_001244193	9786	Hs.232532	NM_014749	ENSG00000100578	KIAA0586	JBTS23|SRTD14|Talpid3	KIAA0586	protein-coding	0.006186	0.345679	275(TGAAACATTCTGTTCC,-,0.00),276(GAAACATTCTGTTCCT,+,0.00)
chunk0136_27_1	chr4	694387	695320	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-5412	NM_001294341	84179	Hs.567612	NM_032219	ENSG00000169026	SLC49A3	LP2561|MFSD7	solute carrier family 49 member 3	protein-coding	0.019293	0.431478	138(GGTCACAGTCTGTTCC,-,0.00),139(GTCACAGTCTGTTCCT,+,0.00)
chunk0013_421_1	chr1	173339751	173340222	+	0	NA	intron (NR_037845, intron 2 of 2)	MLT2B4|LTR|ERVL	121376	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.004246	0.381356	
chunk0019_193_1	chr1	226711306	226711589	+	0	NA	intron (NM_002221, intron 2 of 7)	(TG)n|Simple_repeat|Simple_repeat	27728	NM_002221	3707	Hs.528087	NM_002221	ENSG00000143772	ITPKB	IP3-3KB|IP3K|IP3K-B|IP3KB|PIG37	inositol-trisphosphate 3-kinase B	protein-coding	0.014134	0.485915	
chunk0190_75_1	chr8	29923430	29924224	+	0	NA	intron (NR_024473, intron 2 of 2)	L1ME4b|LINE|L1	2314	NR_024473	286135	Hs.376840	NR_024473	ENSG00000253279	LINC02209	FAM183CP	long intergenic non-protein coding RNA 2209	ncRNA	0.002519	0.345912	350(AGGAACAGCCTGTACA,-,0.00),351(GGAACAGCCTGTACAC,+,0.00)
chunk0075_16_1	chr16	46848423	46848810	+	0	NA	Intergenic	Intergenic	-17454	NM_001001436	388272	Hs.406551	NM_001001436	ENSG00000155330	C16orf87	-	chromosome 16 open reading frame 87	protein-coding	0.010336	0.376289	
chunk0172_263_1	chr6	137484035	137484479	+	0	NA	Intergenic	Intergenic	10137	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.002252	0.361798	
chunk0089_136_1	chr18	58880690	58881045	+	0	NA	intron (NM_018181, intron 3 of 10)	intron (NM_018181, intron 3 of 10)	18038	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.025352	0.379213	
chunk0035_299_1	chr11	47004775	47005089	+	0	NA	intron (NR_103472, intron 2 of 7)	intron (NR_103472, intron 2 of 7)	68243	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.000000	0.460317	
chunk0136_88_1	chr4	2583528	2583843	+	0	NA	Intergenic	Intergenic	-41747	NM_003704	8603	Hs.652364	NM_003704	ENSG00000125386	FAM193A	C4orf8|RES4-22	family with sequence similarity 193 member A	protein-coding	0.012698	0.458861	
chunk0149_373_1	chr5	28193376	28193946	+	0	NA	Intergenic	Intergenic	721369	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.005263	0.355517	281(AAACACACGATGTGCT,-,0.00),282(AACACACGATGTGCTG,+,0.00)
chunk0112_251_1	chr20	41717466	41717712	+	0	NA	Intergenic	Intergenic	-99095	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.012195	0.562753	184(TTGCACAAGCTGTTCT,-,0.00),185(TGCACAAGCTGTTCTC,+,0.00)
chunk0182_213_1	chr7	96327385	96327775	+	0	NA	Intergenic	Intergenic	-5433	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.005128	0.450128	
chunk0092_286_1	chr19	33895055	33895312	+	0	NA	Intergenic	Intergenic	98337	NM_024076	79047	Hs.221873	NM_024076	ENSG00000153885	KCTD15	-	potassium channel tetramerization domain containing 15	protein-coding	0.019455	0.569767	
chunk0030_457_1	chr10	121260415	121260672	+	0	NA	Intergenic	Intergenic	333424	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.003891	0.375969	
chunk0118_243_1	chr22	32684939	32685155	+	0	NA	intron (NM_003490, intron 5 of 12)	MER58A|DNA|hAT-Charlie	-115769	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.009259	0.423963	
chunk0071_148_1	chr15	82889058	82889411	+	0	NA	intron (NM_199330, intron 2 of 8)	intron (NM_199330, intron 2 of 8)	63490	NM_004839	9455	Hs.578443	NM_004839	ENSG00000103942	HOMER2	ACPD|CPD|DFNA68|HOMER-2|VESL-2	homer scaffold protein 2	protein-coding	0.008499	0.548023	
chunk0007_429_1	chr1	86704709	86705397	+	0	NA	intron (NM_001206653, intron 1 of 7)	CpG	483	NM_016009	51100	Hs.136309	NM_016009	ENSG00000097033	SH3GLB1	Bif-1|CGI-61|PPP1R70|dJ612B15.2	SH3 domain containing GRB2 like, endophilin B1	protein-coding	0.097384	0.708273	
chunk0203_82_1	chr9	83957105	83957487	+	0	NA	promoter-TSS (NM_032307)	promoter-TSS (NM_032307)	-548	NM_032307	84267	Hs.208914	NM_032307	ENSG00000165118	C9orf64	-	chromosome 9 open reading frame 64	protein-coding	0.023560	0.443864	
chunk0036_127_1	chr11	61806779	61807162	+	0	NA	intron (NM_013402, intron 5 of 11)	intron (NM_013402, intron 5 of 11)	8270	NR_031729	100302263		NR_031729	ENSG00000284416	MIR1908	MIRN1908|hsa-mir-1908|mir-1908	microRNA 1908	ncRNA	0.010444	0.528646	
chunk0057_427_1	chr13	110089745	110090208	+	0	NA	Intergenic	Intergenic	36691	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.008639	0.398707	
chunk0051_364_1	chr12	121299844	121300653	+	0	NA	Intergenic	Intergenic	-1940	NM_172216	10645	Hs.297343	NM_006549	ENSG00000110931	CAMKK2	CAMKK|CAMKKB	calcium/calmodulin dependent protein kinase kinase 2	protein-coding	0.007417	0.404938	
chunk0043_106_1	chr12	15002038	15002498	+	0	NA	intron (NR_120466, intron 1 of 3)	intron (NR_120466, intron 1 of 3)	435	NR_120466	101928340	Hs.401232	NR_120466	ENSG00000255727	LINC01489	-	long intergenic non-protein coding RNA 1489	ncRNA	0.010870	0.498915	56(AAGAAGACAGTGTGCT,-,0.00)
chunk0175_226_1	chr7	6269368	6269899	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	2978	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.007533	0.404135	310(AGGAACAATGTGTTCT,-,0.00),311(GGAACAATGTGTTCTT,+,0.00)
chunk0074_378_1	chr16	34595987	34596202	+	0	NA	Intergenic	Intergenic	-436058	NR_038368									0.032558	0.370370	
chunk0147_194_1	chr4	177625733	177626125	+	0	NA	Intergenic	Intergenic	-102828	NR_028342	285501	Hs.722466	NM_001085490	ENSG00000231171	LINC01098	-	long intergenic non-protein coding RNA 1098	ncRNA	0.007653	0.356234	
chunk0052_135_1	chr13	23722348	23723185	+	0	NA	Intergenic	Intergenic	143406	NM_018647	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.011947	0.441527	459(GGAAACATACTGTGCT,-,0.00),460(GAAACATACTGTGCTG,+,0.00)
chunk0188_319_1	chr8	17350863	17351677	+	0	NA	intron (NM_004686, intron 4 of 13)	intron (NM_004686, intron 4 of 13)	62261	NM_004686	9108	Hs.625674	NM_004686	ENSG00000003987	MTMR7	-	myotubularin related protein 7	protein-coding	0.003686	0.458896	
chunk0161_50_1	chr5	166062582	166063374	+	0	NA	Intergenic	Intergenic	863392	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005051	0.353090	
chunk0110_240_1	chr20	16351334	16351857	+	0	NA	intron (NM_001199865, intron 22 of 24)	intron (NM_001199865, intron 22 of 24)	221839	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.021033	0.494275	264(TAGAACGTGCTGTTCT,-,0.00),265(AGAACGTGCTGTTCTC,+,0.00)
chunk0206_30_1	chr9	116323465	116323975	+	0	NA	intron (NM_002581, intron 10 of 21)	intron (NM_002581, intron 10 of 21)	76886	NR_103711	493913	Hs.728832	NR_103711	ENSG00000256040	PAPPA-AS1	DIPAS|NCRNA00156|PAPPA-AS|PAPPAAS|PAPPAS|TAF2C2|TAF4B|TAFII105	PAPPA antisense RNA 1	ncRNA	0.000000	0.412916	
chunk0182_206_1	chr7	96275994	96276343	+	0	NA	intron (NM_014251, intron 3 of 17)	intron (NM_014251, intron 3 of 17)	45979	NM_014251	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.002865	0.400000	
chunk0067_457_1	chr15	50344162	50344361	+	0	NA	intron (NM_002041, intron 1 of 7)	intron (NM_002041, intron 1 of 7)	-9913	NR_024490	100129387	Hs.659360	NR_024490		GABPB1-AS1	-	GABPB1 antisense RNA 1	ncRNA	0.000000	0.325000	
chunk0079_436_1	chr17	20024232	20024707	+	0	NA	intron (NM_001243439, intron 1 of 14)	intron (NM_001243439, intron 1 of 14)	15133	NM_001243439	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.006316	0.392857	
chunk0056_206_1	chr13	85900553	85901102	+	0	NA	Intergenic	MIRb|SINE|MIR	-101479	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.003643	0.323636	170(TGGTACATTTTGTACT,-,0.00),171(GGTACATTTTGTACTA,+,0.00)
chunk0189_190_1	chr8	23626215	23626717	+	0	NA	Intergenic	Intergenic	56423	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.007968	0.367793	
chunk0085_46_1	chr18	776922	777454	+	0	NA	intron (NM_005433, intron 1 of 11)	L2c|LINE|L2	35138	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.003759	0.339587	
chunk0024_31_1	chr10	33240588	33241008	+	0	NA	intron (NM_001244972, intron 6 of 16)	intron (NM_001244972, intron 6 of 16)	94107	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.007143	0.427553	
chunk0017_374_1	chr1	212090498	212090879	+	0	NA	intron (NM_016448, intron 13 of 14)	intron (NM_016448, intron 13 of 14)	13075	NR_036068	100422947		NR_036068	ENSG00000264358	MIR3122	mir-3122	microRNA 3122	ncRNA	0.002625	0.363874	
chunk0028_173_1	chr10	87817213	87817439	+	0	NA	promoter-TSS (NR_028492)	promoter-TSS (NR_028492)	834	NM_032810	84896	Hs.435948	NM_032810	ENSG00000138138	ATAD1	AFDC1|FNP001|HKPX4|THORASE	ATPase family AAA domain containing 1	protein-coding	0.017699	0.356828	
chunk0075_41_1	chr16	47175744	47176161	+	0	NA	intron (NM_030790, intron 14 of 17)	intron (NM_030790, intron 14 of 17)	31884	NR_110904	101927102	Hs.634652	NR_110903		ITFG1-AS1	-	ITFG1 antisense RNA 1	ncRNA	0.004796	0.471292	182(AGTCCAGGGTGTGCTT,+,0.00)
chunk0124_94_1	chr3	53535271	53535745	+	0	NA	intron (NM_000720, intron 3 of 48)	intron (NM_000720, intron 3 of 48)	40459	NM_001128840	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.008439	0.448421	328(TAGAACATGTTGTTTC,-,0.00),329(AGAACATGTTGTTTCT,+,0.00)
chunk0186_135_1	chr7	138491219	138491793	+	0	NA	intron (NM_015905, intron 1 of 18)	L1MB4|LINE|L1	31172	NM_015905	8805	Hs.490287	NM_003852	ENSG00000122779	TRIM24	PTC6|RNF82|TF1A|TIF1|TIF1A|TIF1ALPHA|hTIF1	tripartite motif containing 24	protein-coding	0.006969	0.382609	
chunk0126_184_1	chr3	78208167	78208827	+	0	NA	Intergenic	Intergenic	810962	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003030	0.366112	
chunk0046_243_1	chr12	60423756	60424088	+	0	NA	Intergenic	LTR59|LTR|ERV1	734585	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.003012	0.360360	
chunk0107_162_1	chr2	215361836	215362127	+	0	NA	exon (NM_212482, exon 45 of 46)	exon (NM_212482, exon 45 of 46)	50025	NM_004044	471	Hs.90280	NM_004044	ENSG00000138363	ATIC	AICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding	0.010309	0.431507	
chunk0119_384_1	chr22	48256396	48256953	+	0	NA	Intergenic	Intergenic	-17690	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.021544	0.564516	
chunk0193_59_1	chr8	72778784	72779282	+	0	NA	intron (NM_004770, intron 2 of 2)	intron (NM_004770, intron 2 of 2)	46988	NR_110656	101926908	Hs.680588	NR_110656	ENSG00000253726	LOC101926908	-	uncharacterized LOC101926908	ncRNA	0.016064	0.464930	
chunk0041_101_1	chr11	124705430	124705629	+	0	NA	Intergenic	Intergenic	-29226	NM_001199922	54414	Hs.10056	NM_018978	ENSG00000110013	SIAE	AIS6|CSE-C|CSEC|LSE|YSG2	sialic acid acetylesterase	protein-coding	0.000000	0.390000	
chunk0173_337_1	chr6	148915842	148916464	+	0	NA	intron (NM_005715, intron 2 of 7)	MIR|SINE|MIR	48531	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.011254	0.418941	
chunk0094_400_1	chr2	10389587	10390217	+	0	NA	intron (NM_001258359, intron 1 of 4)	L1ME3A|LINE|L1	21138	NM_001258359	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.011111	0.492868	234(GGGACAAATTGTGCAG,+,0.00),248(AGCTCTGAGTGTTCCT,+,0.00)
chunk0110_322_1	chr20	18989788	18990012	+	0	NA	Intergenic	Intergenic	-159697	NM_001302818									0.013393	0.453333	141(AGACACACCATGTTCC,-,0.00),142(GACACACCATGTTCCT,+,0.00)
chunk0095_415_1	chr2	24571795	24572306	+	0	NA	Intergenic	MIRb|SINE|MIR	-12427	NM_003743	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.003914	0.341797	
chunk0139_91_1	chr4	49575630	49575843	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	589094	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.004695	0.523364	
chunk0039_34_1	chr11	95849082	95849355	+	0	NA	intron (NM_201278, intron 11 of 16)	intron (NM_201278, intron 11 of 16)	58757	NM_014679	9702	Hs.101014	NM_014679	ENSG00000166037	CEP57	MVA2|PIG8|TSP57	centrosomal protein 57	protein-coding	0.010989	0.430657	
chunk0112_349_1	chr20	45219161	45219551	+	0	NA	Intergenic	Intergenic	-2013	NM_003008	6407	Hs.537218	NM_003008	ENSG00000124157	SEMG2	SGII	semenogelin 2	protein-coding	0.005128	0.322251	
chunk0081_448_1	chr17	49315636	49315835	+	0	NA	intron (NM_001145365, intron 2 of 5)	intron (NM_001145365, intron 2 of 5)	-27281	NR_106745	102465137		NR_106745	ENSG00000273500	MIR6129	hsa-mir-6129	microRNA 6129	ncRNA	0.015075	0.470000	
chunk0088_240_1	chr18	48573256	48573455	+	0	NA	intron (NM_001142397, intron 2 of 12)	intron (NM_001142397, intron 2 of 12)	34299	NM_014772	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.010050	0.525000	
chunk0033_16_1	chr11	12497439	12497837	+	0	NA	intron (NM_018222, intron 5 of 12)	intron (NM_018222, intron 5 of 12)	120159	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.017588	0.511278	201(GGGCACAGGGCGTTCT,-,0.00),202(GGCACAGGGCGTTCTT,+,0.00)
chunk0182_38_1	chr7	91611840	91612478	+	0	NA	Intergenic	(GCTGT)n|Simple_repeat|Simple_repeat	268561	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.001567	0.447574	219(CAGAACAGCTTGTATC,-,0.00),220(AGAACAGCTTGTATCT,+,0.00)
chunk0163_390_1	chr6	16446510	16447002	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	208176	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.002033	0.332657	
chunk0128_443_1	chr3	115072585	115073003	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	-1380	NM_001164343	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.007177	0.379475	
chunk0058_9_1	chr14	18673493	18673967	+	0	NA	Intergenic	Intergenic	-40096	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.010549	0.410526	
chunk0085_325_1	chr18	8382209	8382743	+	0	NA	intron (NM_001105244, intron 29 of 32)	intron (NM_001105244, intron 29 of 32)	-15442	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.007491	0.388785	
chunk0065_227_1	chr14	100888478	100888677	+	0	NA	Intergenic	Intergenic	-3730	NM_001134888	388015	Hs.298602	NM_001134888	ENSG00000254656	RTL1	HUR1|MART1|Mar1|PEG11|SIRH2	retrotransposon Gag like 1	protein-coding	0.000000	0.250000	
chunk0061_331_1	chr14	63286000	63286648	+	0	NA	intron (NM_020663, intron 4 of 4)	L2c|LINE|L2	32555	NM_145171	122876	Hs.375028	NM_145171	ENSG00000179600	GPHB5	B5|GPB5|ZLUT1	glycoprotein hormone subunit beta 5	protein-coding	0.004630	0.440678	
chunk0005_341_1	chr1	61182048	61182480	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	71254	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.004630	0.360277	
chunk0164_368_1	chr6	25659583	25660365	+	0	NA	intron (NM_006998, intron 2 of 10)	intron (NM_006998, intron 2 of 10)	7773	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.006394	0.426564	
chunk0073_299_1	chr16	14088383	14088964	+	0	NA	intron (NM_001308142, intron 2 of 16)	intron (NM_001308142, intron 2 of 16)	17359	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.012048	0.393471	
chunk0090_287_1	chr18	74951182	74951616	+	0	NA	intron (NM_017757, intron 7 of 7)	intron (NM_017757, intron 7 of 7)	254114	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.009217	0.429885	
chunk0040_68_1	chr11	111279255	111279454	+	0	NA	intron (NM_198498, intron 1 of 3)	MLT1C|LTR|ERVL-MaLR	-19192	NM_001271458	120376	Hs.31409	NM_001136105	ENSG00000214290	COLCA2	C11orf93|CASC13|LOH11CR1G	colorectal cancer associated 2	protein-coding	0.005025	0.450000	
chunk0126_55_1	chr3	74329316	74329644	+	0	NA	intron (NM_020872, intron 12 of 21)	intron (NM_020872, intron 12 of 21)	191660	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.003049	0.355623	
chunk0056_38_1	chr13	77344999	77345304	+	0	NA	Intergenic	Intergenic	-18109	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.000000	0.405229	
chunk0023_221_1	chr10	26486900	26487221	+	0	NA	intron (NM_019043, intron 2 of 14)	intron (NM_019043, intron 2 of 14)	48723	NM_019043	54518	Hs.310421	NM_019043	ENSG00000077420	APBB1IP	INAG1|PREL1|RARP1|RIAM	amyloid beta precursor protein binding family B member 1 interacting protein	protein-coding	0.006231	0.400621	
chunk0181_178_1	chr7	83051180	83051379	+	0	NA	intron (NM_014510, intron 3 of 19)	L1MC|LINE|L1	111602	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.005025	0.320000	
chunk0098_412_1	chr2	79984666	79985447	+	0	NA	intron (NM_004389, intron 7 of 17)	MER58A|DNA|hAT-Charlie	-118473	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.002561	0.482097	
chunk0032_456_1	chr10	133520504	133520942	+	0	NA	Intergenic	Intergenic	-6640	NM_000773	1571	Hs.12907	NM_000773	ENSG00000130649	CYP2E1	CPE1|CYP2E|P450-J|P450C2E	cytochrome P450 family 2 subfamily E member 1	protein-coding	0.022831	0.471526	
chunk0016_3_1	chr1	192679969	192680346	+	0	NA	Intergenic	Intergenic	-36171	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.002653	0.378307	
chunk0165_17_1	chr6	28978203	28978472	+	0	NA	Intergenic	MER31A|LTR|ERV1	26923	NM_001010877	282890	Hs.148218	NM_001010877	ENSG00000197935	ZNF311	zf31	zinc finger protein 311	protein-coding	0.003717	0.474074	156(CAGGACACACTGCTCC,-,0.00),157(AGGACACACTGCTCCT,+,0.00)
chunk0191_300_1	chr8	54635961	54636160	+	0	NA	Intergenic	MER54A|LTR|ERVL	19993	NM_006269	6101	Hs.732820	NM_006269	ENSG00000104237	RP1	DCDC4A|ORP1	RP1 axonemal microtubule associated	protein-coding	0.010050	0.465000	
chunk0154_114_1	chr5	78720619	78720937	+	0	NA	Intergenic	Intergenic	-71953	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.012579	0.479624	
chunk0029_1_1	chr10	95273402	95274172	+	0	NA	intron (NM_020992, intron 1 of 6)	L4_C_Mam|LINE|RTE-X	17361	NM_020992	9124	Hs.368525	NM_020992	ENSG00000107438	PDLIM1	CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1	PDZ and LIM domain 1	protein-coding	0.016883	0.476005	
chunk0018_98_1	chr1	217887786	217887991	+	0	NA	Intergenic	Intergenic	-5012	NR_048550	100885798	Hs.434632	NR_048550	ENSG00000231814	LINC00210	NCRNA00210	long intergenic non-protein coding RNA 210	ncRNA	0.019512	0.514563	
chunk0066_199_1	chr15	33501514	33501952	+	0	NA	intron (NM_001036, intron 2 of 103)	intron (NM_001036, intron 2 of 103)	190771	NM_001036	6263	Hs.709373	NM_001036	ENSG00000198838	RYR3	RYR-3	ryanodine receptor 3	protein-coding	0.002283	0.371298	
chunk0211_349_1	chrX	125308918	125309506	+	0	NA	Intergenic	Intergenic	-10908	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.008503	0.336163	
chunk0104_33_1	chr2	170938205	170938404	+	0	NA	intron (NM_015530, intron 1 of 9)	intron (NM_015530, intron 1 of 9)	9778	NM_015530	26003	Hs.431317	NM_015530	ENSG00000115806	GORASP2	GOLPH6|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding	0.010050	0.320000	
chunk0062_273_1	chr14	72002969	72003314	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	70072	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.008696	0.361272	
chunk0187_156_1	chr7	150202411	150202890	+	0	NA	Intergenic	Intergenic	100330	NM_001164459	653857	Hs.664579	NM_001164458	ENSG00000106526	ACTR3C	ARP11	actin related protein 3C	protein-coding	0.000000	0.320833	
chunk0198_429_1	chr8	143208442	143208690	+	0	NA	Intergenic	Intergenic	-4627	NM_178172	338328	Hs.426410	NM_178172	ENSG00000277494	GPIHBP1	GPI-HBP1|HYPL1D	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	protein-coding	0.032258	0.518072	130(TGGGACACTCAGTCCT,-,0.00),131(GGGACACTCAGTCCTC,+,0.00)
chunk0200_392_1	chr9	26958337	26958815	+	0	NA	intron (NM_001099224, intron 1 of 13)	intron (NM_001099224, intron 1 of 13)	2203	NM_001099224	80173	Hs.145402	NM_025103	ENSG00000096872	IFT74	BBS20|CCDC2|CMG-1|CMG1	intraflagellar transport 74	protein-coding	0.002092	0.388309	
chunk0022_160_1	chr10	12586601	12587068	+	0	NA	intron (NM_020397, intron 2 of 9)	intron (NM_020397, intron 2 of 9)	8081	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.012848	0.452991	
chunk0205_235_1	chr9	110040768	110041214	+	0	NA	intron (NM_147150, intron 7 of 9)	intron (NM_147150, intron 7 of 9)	-7607	NM_001004065	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.002242	0.407159	
chunk0161_129_1	chr5	168282994	168283570	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-8778	NM_001161662	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.013889	0.445407	
chunk0154_271_1	chr5	82108926	82109441	+	0	NA	intron (NM_031482, intron 3 of 7)	intron (NM_031482, intron 3 of 7)	137158	NM_001131028	83734	Hs.713698	NM_031482	ENSG00000152348	ATG10	APG10|APG10L|pp12616	autophagy related 10	protein-coding	0.007767	0.412791	
chunk0074_234_1	chr16	27242915	27243567	+	0	NA	intron (NM_145080, intron 2 of 7)	intron (NM_145080, intron 2 of 7)	-24964	NR_037184	400512	Hs.434412	NR_037184	ENSG00000245888	NSMCE1-DT	-	NSMCE1 divergent transcript	ncRNA	0.018405	0.503828	393(GAGGTCACTCTGTTCC,-,0.00),394(AGGTCACTCTGTTCCC,+,0.00)
chunk0100_9_1	chr2	104755408	104755894	+	0	NA	intron (NR_038231, intron 1 of 3)	intron (NR_038231, intron 1 of 3)	2068	NR_038231	284998	Hs.410180	NR_038231	ENSG00000234177	LINC01114	PANCAT	long intergenic non-protein coding RNA 1114	ncRNA	0.043210	0.579055	
chunk0130_72_1	chr3	130222796	130223247	+	0	NA	intron (NR_027898, intron 6 of 22)	MIR1_Amn|SINE|MIR	10201	NR_027898	646300	Hs.170475	NR_027898		COL6A4P2	COL6A4	collagen type VI alpha 4 pseudogene 2	pseudo	0.006652	0.477876	
chunk0082_303_1	chr17	58734067	58734563	+	0	NA	TTS (NM_058216)	TTS (NM_058216)	-21554	NR_048561	22843	Hs.245044	NM_014906	ENSG00000175175	PPM1E	CaMKP-N|POPX1|PP2CH|caMKN	protein phosphatase, Mg2+/Mn2+ dependent 1E	protein-coding	0.006048	0.338028	
chunk0078_154_1	chr17	4145227	4145825	+	0	NA	intron (NM_144611, intron 1 of 3)	intron (NM_144611, intron 1 of 3)	1905	NM_001254755	124936	Hs.513871	NM_144611	ENSG00000167740	CYB5D2	-	cytochrome b5 domain containing 2	protein-coding	0.021739	0.455760	
chunk0137_377_1	chr4	26239277	26239742	+	0	NA	Intergenic	Intergenic	-80201	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.004301	0.412017	
chunk0146_275_1	chr4	163411042	163411249	+	0	NA	Intergenic	Intergenic	62750	NM_032136	84076	Hs.303923	NM_032136	ENSG00000151005	TKTL2	-	transketolase like 2	protein-coding	0.014493	0.389423	
chunk0109_360_1	chr2	239208675	239208874	+	0	NA	intron (NM_006037, intron 3 of 26)	L1ME3Cz|LINE|L1	-13317	NR_026664	85009	Hs.744565	NM_032923		MGC16025	-	uncharacterized LOC85009	ncRNA	0.010050	0.305000	
chunk0157_75_1	chr5	116424862	116425276	+	0	NA	Intergenic	L2b|LINE|L2	-22429	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.002415	0.450602	
chunk0128_145_1	chr3	106945662	106946347	+	0	NA	Intergenic	L1MEi|LINE|L1	294634	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.007299	0.397959	
chunk0090_427_1	chr18	79346089	79346359	+	0	NA	intron (NM_001306085, intron 23 of 28)	intron (NM_001306085, intron 23 of 28)	-49548	NM_006162	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.062963	0.583026	
chunk0146_346_1	chr4	166264638	166265291	+	0	NA	Intergenic	MIRb|SINE|MIR	391706	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.003063	0.295107	
chunk0063_62_1	chr14	77123523	77124029	+	0	NA	Intergenic	Intergenic	18015	NM_174976	283576	Hs.525485	NM_174976	ENSG00000177108	ZDHHC22	C14orf59	zinc finger DHHC-type containing 22	protein-coding	0.005929	0.573964	301(CTGCACAATCTGTCCT,-,0.00),302(TGCACAATCTGTCCTC,+,0.00)
chunk0200_156_1	chr9	18382717	18383208	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-91119	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.008147	0.384146	
chunk0083_35_1	chr17	63331563	63332088	+	0	NA	intron (NM_025185, intron 9 of 24)	intron (NM_025185, intron 9 of 24)	109021	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.011429	0.349810	
chunk0039_387_1	chr11	107139431	107139807	+	0	NA	Intergenic	Intergenic	-121174	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.010638	0.474801	173(AAGCACAACCTGTTCT,-,0.00),174(AGCACAACCTGTTCTG,+,0.00)
chunk0048_124_1	chr12	79864252	79864622	+	0	NA	intron (NM_001244990, intron 3 of 24)	L1PA7|LINE|L1	49474	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.005405	0.345013	
chunk0191_6_1	chr8	42449295	42449966	+	0	NA	intron (NM_006749, intron 5 of 10)	intron (NM_006749, intron 5 of 10)	51830	NM_001257180	6575	Hs.653173	NM_006749	ENSG00000168575	SLC20A2	GLVR-2|GLVR2|IBGC1|IBGC3|MLVAR|PIT-2|PIT2|RAM1|Ram-1	solute carrier family 20 member 2	protein-coding	0.013413	0.351190	
chunk0096_157_1	chr2	29404233	29404732	+	0	NA	intron (NM_004304, intron 4 of 28)	intron (NM_004304, intron 4 of 28)	289056	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.010020	0.394000	
chunk0130_13_1	chr3	128380523	128380802	+	0	NA	intron (NM_021937, intron 6 of 6)	intron (NM_021937, intron 6 of 6)	-82932	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.025090	0.467857	139(TGGAACTTGCTGTTCT,-,0.00),140(GGAACTTGCTGTTCTG,+,0.00)
chunk0071_142_1	chr15	82487124	82487350	+	0	NA	intron (NR_026811, intron 1 of 7)	LTR10B1|LTR|ERV1	26758	NR_102748	727751	Hs.546614	NR_102747		LOC727751	-	golgin A2 pseudogene	pseudo	0.022124	0.458150	
chunk0060_215_1	chr14	48872998	48873246	+	0	NA	Intergenic	Intergenic	713294	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.321285	
chunk0192_21_1	chr8	58458129	58458503	+	0	NA	Intergenic	Intergenic	41845	NM_000780	1581	Hs.1644	NM_000780	ENSG00000167910	CYP7A1	CP7A|CYP7|CYPVII	cytochrome P450 family 7 subfamily A member 1	protein-coding	0.000000	0.378667	125(TGGAACATTGAGTTCT,-,0.00),126(GGAACATTGAGTTCTC,+,0.00)
chunk0057_90_1	chr13	98760405	98760625	+	0	NA	Intergenic	LTR61|LTR|ERV1	-7840	NM_005073	6564	Hs.436893	NM_005073	ENSG00000088386	SLC15A1	HPECT1|HPEPT1|PEPT1	solute carrier family 15 member 1	protein-coding	0.000000	0.361991	
chunk0201_3_1	chr9	32003470	32003998	+	0	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	-380869	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.005682	0.323251	229(AAGAACATGAAGTTCT,-,0.00),230(AGAACATGAAGTTCTT,+,0.00)
chunk0043_415_1	chr12	25852685	25853255	+	0	NA	Intergenic	L2b|LINE|L2	21109	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.000000	0.350263	
chunk0119_258_1	chr22	45823683	45824186	+	0	NA	intron (NM_001167621, intron 9 of 10)	intron (NM_001167621, intron 9 of 10)	63410	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.013917	0.496032	130(AGAGACACTGTGTGCT,-,0.00),131(GAGACACTGTGTGCTC,+,0.00)
chunk0166_5_1	chr6	41435167	41435558	+	0	NA	Intergenic	L1MC3|LINE|L1	-67082	NR_120347	103106903	Hs.563396	NR_120347	ENSG00000226917	LINC01276	-	long intergenic non-protein coding RNA 1276	ncRNA	0.017903	0.420918	176(GAGGACAAAGTGTCTC,-,0.00),177(AGGACAAAGTGTCTCC,+,0.00)
chunk0014_185_1	chr1	178739288	178740054	+	0	NA	intron (NM_001286247, intron 1 of 18)	intron (NM_001286247, intron 1 of 18)	14524	NM_152663	55103	Hs.632485	NM_018037	ENSG00000116191	RALGPS2	dJ595C2.1	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.005222	0.389831	508(GGGAACAGGCAGTACT,-,0.00),509(GGAACAGGCAGTACTA,+,0.00)
chunk0056_347_1	chr13	91701866	91702521	+	0	NA	intron (NM_004466, intron 3 of 7)	L1MA9|LINE|L1	303574	NM_004466	2262	Hs.655675	NM_004466	ENSG00000179399	GPC5	-	glypican 5	protein-coding	0.000000	0.344512	
chunk0090_24_1	chr19	1057154	1057353	+	0	NA	intron (NM_019112, intron 34 of 46)	intron (NM_019112, intron 34 of 46)	-8670	NM_001258328	23526	Hs.465521	NM_012292	ENSG00000180448	ARHGAP45	HA-1|HLA-HA1|HMHA1	Rho GTPase activating protein 45	protein-coding	0.005025	0.530000	
chunk0120_254_1	chr3	8937028	8937562	+	0	NA	intron (NM_020165, intron 6 of 12)	intron (NM_020165, intron 6 of 12)	26180	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.003745	0.357009	
chunk0162_245_1	chr6	4937872	4938344	+	0	NA	intron (NR_026590, intron 6 of 8)	intron (NR_026590, intron 6 of 8)	48116	NM_001143971	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.008475	0.376321	
chunk0006_349_1	chr1	72589276	72589735	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-306911	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.004357	0.323913	152(CATAACACTGTGTTCT,-,0.00),153(ATAACACTGTGTTCTA,+,0.00)
chunk0182_347_1	chr7	99466000	99466310	+	0	NA	promoter-TSS (NM_004889)	promoter-TSS (NM_004889)	46	NM_001003713	9551	Hs.521056	NM_004889	ENSG00000241468	ATP5MF	ATP5J2|ATP5JL	ATP synthase membrane subunit f	protein-coding	0.051613	0.630225	
chunk0070_376_1	chr15	76387803	76388264	+	0	NA	intron (NM_020843, intron 26 of 30)	L3|LINE|CR1	51309	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.008677	0.398268	
chunk0080_317_1	chr17	32007763	32008288	+	0	NA	Intergenic	CpG	-13111	NM_052888	114659	Hs.514071	NM_052888	ENSG00000185158	LRRC37B	LRRC37	leucine rich repeat containing 37B	protein-coding	0.076190	0.655894	
chunk0145_59_1	chr4	145333089	145333650	+	0	NA	Intergenic	Intergenic	-148430	NM_005900	4086	Hs.604588	NM_005900	ENSG00000170365	SMAD1	BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1	SMAD family member 1	protein-coding	0.005348	0.345196	
chunk0191_251_1	chr8	53224309	53224693	+	0	NA	Intergenic	Intergenic	27133	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.007812	0.342857	
chunk0070_245_1	chr15	73501972	73502503	+	0	NA	intron (NM_001042367, intron 2 of 5)	intron (NM_001042367, intron 2 of 5)	59079	NM_001042367	283677	Hs.743574	NM_001042367	ENSG00000183324	REC114	C15orf60|CT147	REC114 meiotic recombination protein	protein-coding	0.009416	0.389098	
chunk0052_433_1	chr12	131929072	131929271	+	0	NA	promoter-TSS (NM_025215)	promoter-TSS (NM_025215)	-29	NM_001002020	80324	Hs.592004	NM_025215	ENSG00000177192	PUS1	MLASA1	pseudouridine synthase 1	protein-coding	0.090452	0.695000	
chunk0172_215_1	chr6	136792420	136792887	+	0	NA	promoter-TSS (NM_005923)	promoter-TSS (NM_005923)	-135	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.122056	0.720085	
chunk0114_40_1	chr21	8401974	8402185	+	0	NA	TTS (NR_003287)	TTS (NR_003287)	6472	NR_003285	100008587	Hs.426704	NR_003285		RNA5-8SN5	RN5-8S1|RNA5-8S5	RNA, 5.8S ribosomal N5	rRNA	0.199052	0.811321	
chunk0098_168_1	chr2	70692921	70693402	+	0	NA	intron (NM_001185055, intron 5 of 11)	MER90|LTR|ERV1	74554	NM_001185054	119	Hs.66187	NM_001617	ENSG00000075340	ADD2	ADDB	adducin 2	protein-coding	0.014553	0.485477	229(ATCACAGAATGTCCTG,+,0.00)
chunk0148_430_1	chr4	188953376	188953730	+	0	NA	Intergenic	Intergenic	497975	NR_033869	401164	Hs.435756	NR_033869	ENSG00000249378	LINC01060	-	long intergenic non-protein coding RNA 1060	ncRNA	0.011299	0.326761	
chunk0141_238_1	chr4	84955218	84955465	+	0	NA	intron (NM_014991, intron 1 of 67)	intron (NM_014991, intron 1 of 67)	11050	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.012146	0.403226	
chunk0078_58_1	chr17	1455890	1456089	+	0	NA	exon (NM_016823, exon 1 of 3)	exon (NM_016823, exon 1 of 3)	278	NM_005206	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.100503	0.700000	121(AGGAACACCCCGTGCC,-,0.00),122(GGAACACCCCGTGCCG,+,0.00)
chunk0186_433_1	chr7	146715239	146715655	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	382162	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.009615	0.424460	
chunk0125_142_1	chr3	66065188	66065387	+	0	NA	Intergenic	MIRb|SINE|MIR	-26453	NM_001033057	9223	Hs.476636	NM_004742	ENSG00000151276	MAGI1	AIP-3|AIP3|BAIAP1|BAP-1|BAP1|MAGI-1|MAGI-1b|Magi1d|TNRC19|WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.005025	0.460000	172(TAGATCACTCTGTGCC,-,0.00),173(AGATCACTCTGTGCCA,+,0.00)
chunk0069_15_1	chr15	60335387	60335658	+	0	NA	Intergenic	L1PA3|LINE|L1	62464	NM_001136015	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.007380	0.444853	
chunk0056_265_1	chr13	90036864	90037419	+	0	NA	Intergenic	Intergenic	82576	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.009009	0.312950	
chunk0184_220_1	chr7	117459536	117459735	+	0	NA	Intergenic	Intergenic	-20328	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.000000	0.275000	
chunk0059_12_1	chr14	29749334	29749907	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	178073	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005236	0.397213	
chunk0103_52_1	chr2	159516605	159517176	+	0	NA	intron (NM_001289975, intron 2 of 35)	intron (NM_001289975, intron 2 of 35)	-98404	NR_110588	643072	Hs.632541	NR_110587		LOC643072	-	uncharacterized LOC643072	ncRNA	0.005254	0.328671	
chunk0057_287_1	chr13	106177698	106178203	+	0	NA	Intergenic	HAL1ME|LINE|L1	-198613	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.007921	0.284585	
chunk0164_362_1	chr6	25578382	25578626	+	0	NA	intron (NM_017640, intron 29 of 36)	intron (NM_017640, intron 29 of 36)	-73697	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.000000	0.281633	
chunk0203_47_1	chr9	83082635	83082861	+	0	NA	Intergenic	Intergenic	-19620	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.004425	0.317181	
chunk0007_289_1	chr1	83970085	83970702	+	0	NA	intron (NM_024686, intron 1 of 20)	intron (NM_024686, intron 1 of 20)	28757	NM_024686	79739	Hs.445826	NM_024686	ENSG00000137941	TTLL7	-	tubulin tyrosine ligase like 7	protein-coding	0.001621	0.318770	318(AGGAACATACAGTACA,-,0.00),319(GGAACATACAGTACAC,+,0.00)
chunk0043_165_1	chr12	16939882	16940320	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-48646	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.013699	0.503417	
chunk0158_181_1	chr5	127833215	127833664	+	0	NA	Intergenic	Intergenic	180424	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.000000	0.304444	261(AAGGACATTATGTTCC,-,0.00),262(AGGACATTATGTTCCA,+,0.00)
chunk0211_300_1	chrX	123046288	123047005	+	0	NA	Intergenic	Intergenic	-137597	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.002789	0.330084	302(ATGCACACTGAGTGCT,-,0.00)
chunk0194_179_1	chr8	85127762	85128061	+	0	NA	intron (NM_033402, intron 9 of 18)	L1M6|LINE|L1	20823	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.003344	0.386667	132(GGGAACAGGATGTCTC,-,0.00),133(GGAACAGGATGTCTCA,+,0.00)
chunk0034_381_1	chr11	36464713	36465183	+	0	NA	3' UTR (NM_024841, exon 10 of 10)	3' UTR (NM_024841, exon 10 of 10)	45365	NM_004620	7189	Hs.444172	NM_004620	ENSG00000175104	TRAF6	MGC:3310|RNF85	TNF receptor associated factor 6	protein-coding	0.006383	0.354565	
chunk0184_342_1	chr7	120719165	120719814	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	138634	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.004622	0.304615	360(AAGCACACATTGTACA,-,0.00),361(AGCACACATTGTACAT,+,0.00)
chunk0092_426_1	chr19	38079923	38080425	+	0	NA	intron (NM_015073, intron 2 of 21)	intron (NM_015073, intron 2 of 21)	144076	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.001992	0.485089	
chunk0053_445_1	chr13	39816287	39816733	+	0	NA	Intergenic	L3|LINE|CR1	-152375	NR_036190	100422940		NR_036190	ENSG00000264171	MIR4305	-	microRNA 4305	ncRNA	0.000000	0.384787	256(TAGAACAGTCTGTTCT,-,0.00),257(AGAACAGTCTGTTCTC,+,0.00)
chunk0206_194_1	chr9	122976418	122976693	+	0	NA	intron (NM_012197, intron 2 of 25)	intron (NM_012197, intron 2 of 25)	35546	NM_012197	23637	Hs.271341	NM_012197	ENSG00000011454	RABGAP1	GAPCENA|TBC1D11	RAB GTPase activating protein 1	protein-coding	0.000000	0.304348	
chunk0028_92_1	chr10	83994065	83994272	+	0	NA	Intergenic	Intergenic	-145261	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.437500	
chunk0202_157_1	chr9	73692199	73692825	+	0	NA	Intergenic	Intergenic	540781	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.006390	0.342903	
chunk0016_430_1	chr1	203772104	203772421	+	0	NA	intron (NM_001282878, intron 4 of 4)	intron (NM_001282878, intron 4 of 4)	2624	NM_001282878	54900	Hs.272794	NM_017773	ENSG00000122188	LAX1	LAX	lymphocyte transmembrane adaptor 1	protein-coding	0.009464	0.446541	
chunk0109_279_1	chr20	8117966	8118329	+	0	NA	Intergenic	Intergenic	-14118	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.005510	0.412088	
chunk0176_133_1	chr7	12675163	12675378	+	0	NA	Intergenic	Intergenic	-11557	NM_212460	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.004651	0.467593	
chunk0121_323_1	chr3	24351949	24352335	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-141945	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.002591	0.361757	
chunk0193_256_1	chr8	76962715	76962917	+	0	NA	Intergenic	Intergenic	4034	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004950	0.315271	
chunk0159_277_1	chr5	142451171	142451692	+	0	NA	intron (NR_120664, intron 3 of 3)	MER58A|DNA|hAT-Charlie	126138	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.003839	0.450192	
chunk0006_251_1	chr1	69404076	69404363	+	0	NA	Intergenic	Intergenic	-355956	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.000000	0.312500	
chunk0159_266_1	chr5	142248620	142249262	+	0	NA	Intergenic	Intergenic	69381	NR_131221	100642175	Hs.684549	NR_131221		SPRY4-IT1	SPRIGHTLY	SPRY4 intronic transcript 1	ncRNA	0.020249	0.440124	
chunk0059_73_1	chr14	30494701	30495038	+	0	NA	Intergenic	L2b|LINE|L2	-64254	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.002967	0.417160	149(GAGTACATACTGTTCC,-,0.00),150(AGTACATACTGTTCCC,+,0.00)
chunk0013_281_1	chr1	170894770	170895122	+	0	NA	Intergenic	MIRb|SINE|MIR	-40525	NM_001163629	80133	Hs.591489	NM_025063	ENSG00000117501	MROH9	ARMC11|C1orf129	maestro heat like repeat family member 9	protein-coding	0.000000	0.337110	
chunk0138_459_1	chr4	47678016	47678347	+	0	NA	intron (NM_001278585, intron 6 of 19)	intron (NM_001278585, intron 6 of 19)	25512	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.003021	0.352410	134(AGAAACAAGGTGTTCT,-,0.00),135(GAAACAAGGTGTTCTG,+,0.00)
chunk0098_418_1	chr2	80342079	80342841	+	0	NA	intron (NM_001282599, intron 1 of 11)	intron (NM_001282599, intron 1 of 11)	29081	NM_001282599	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.002625	0.331586	
chunk0138_204_1	chr4	38663897	38664123	+	0	NA	promoter-TSS (NM_016531)	promoter-TSS (NM_016531)	-159	NM_016531	51274	Hs.298658	NM_016531	ENSG00000109787	KLF3	BKLF	Kruppel like factor 3	protein-coding	0.137168	0.792952	
chunk0094_449_1	chr2	11513977	11514598	+	0	NA	Intergenic	MIRb|SINE|MIR	-19829	NM_014668	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.004831	0.434084	
chunk0045_353_1	chr12	51632560	51633052	+	0	NA	intron (NM_014191, intron 1 of 26)	intron (NM_014191, intron 1 of 26)	41570	NM_014191	6334	Hs.436550	NM_014191	ENSG00000196876	SCN8A	BFIS5|CERIII|CIAT|EIEE13|MED|MYOCL2|NaCh6|Nav1.6|PN4	sodium voltage-gated channel alpha subunit 8	protein-coding	0.006098	0.385396	
chunk0072_377_1	chr15	100083608	100083855	+	0	NA	intron (NM_139057, intron 15 of 21)	intron (NM_139057, intron 15 of 21)	258247	NM_139057	170691	Hs.513200	NM_139057	ENSG00000140470	ADAMTS17	WMS4	ADAM metallopeptidase with thrombospondin type 1 motif 17	protein-coding	0.000000	0.495968	
chunk0036_291_1	chr11	65507565	65507840	+	0	NA	Intergenic	Intergenic	9940	NR_002819	378938	Hs.621695	NR_002819	ENSG00000251562	MALAT1	HCN|LINC00047|NCRNA00047|NEAT2|PRO2853	metastasis associated lung adenocarcinoma transcript 1	ncRNA	0.010909	0.485507	
chunk0167_13_1	chr6	53524444	53524715	+	0	NA	intron (NM_001197115, intron 1 of 14)	intron (NM_001197115, intron 1 of 14)	20550	NM_001498	2729	Hs.654465	NM_001498	ENSG00000001084	GCLC	GCL|GCS|GLCL|GLCLC	glutamate-cysteine ligase catalytic subunit	protein-coding	0.003690	0.433824	
chunk0088_209_1	chr18	48133747	48134140	+	0	NA	intron (NM_001039360, intron 1 of 2)	intron (NM_001039360, intron 1 of 2)	3366	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.007634	0.434010	
chunk0112_300_1	chr20	44302093	44302727	+	0	NA	Intergenic	Intergenic	8839	NM_001080472	128486	Hs.632269	NM_001080472	ENSG00000197296	FITM2	C20orf142|Fit2|dJ881L22.2	fat storage inducing transmembrane protein 2	protein-coding	0.011041	0.474016	
chunk0072_366_1	chr15	99878805	99879273	+	0	NA	Intergenic	Intergenic	-72112	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.006410	0.368870	
chunk0018_275_1	chr1	220582222	220582925	+	0	NA	3' UTR (NM_001286129, exon 3 of 3)	3' UTR (NM_001286129, exon 3 of 3)	54390	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.004267	0.373580	280(TTGTACACAGTGTCCC,-,0.00),281(TGTACACAGTGTCCCT,+,0.00)
chunk0088_454_1	chr18	57242559	57242787	+	0	NA	Intergenic	Intergenic	95611	NM_001257964	284257	Hs.127882	NM_001257964	ENSG00000228075	BOD1L2	BOD1P|FAM44C	biorientation of chromosomes in cell division 1 like 2	protein-coding	0.004386	0.436681	
chunk0049_267_1	chr12	93768562	93769046	+	0	NA	intron (NM_003805, intron 2 of 2)	L1ME3A|LINE|L1	-30981	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.004132	0.319588	
chunk0207_207_1	chr9	131367508	131368008	+	0	NA	Intergenic	Intergenic	-62332	NM_013318	84726	Hs.743955	NM_013318	ENSG00000130723	PRRC2B	BAT2L|BAT2L1|KIAA0515|LQFBS-1	proline rich coiled-coil 2B	protein-coding	0.002000	0.395210	
chunk0053_65_1	chr13	28145020	28145546	+	0	NA	intron (NM_175854, intron 1 of 18)	intron (NM_175854, intron 1 of 18)	-6109	NR_029383	100288730	Hs.123191	NR_029383		PAN3-AS1	-	PAN3 antisense RNA 1	ncRNA	0.015209	0.394687	
chunk0018_346_1	chr1	221561193	221561598	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	175505	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.007407	0.332512	
chunk0110_209_1	chr20	15296983	15297465	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	100366	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.006224	0.430642	
chunk0101_157_1	chr2	128248915	128249843	+	0	NA	Intergenic	L1M5|LINE|L1	69218	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.006466	0.416577	
chunk0180_275_1	chr7	69742934	69743625	+	0	NA	intron (NM_015570, intron 1 of 18)	MIR|SINE|MIR	144360	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.005789	0.395954	
chunk0129_458_1	chr3	128285611	128286337	+	0	NA	intron (NM_021937, intron 4 of 6)	MER113A|DNA|hAT-Charlie	132517	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.013774	0.466300	
chunk0017_238_1	chr1	208203590	208203901	+	0	NA	intron (NM_025179, intron 3 of 31)	MIRc|SINE|MIR	40575	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.016077	0.461538	
chunk0024_423_1	chr10	45962747	45963250	+	0	NA	intron (NR_029388, intron 1 of 12)	intron (NR_029388, intron 1 of 12)	9430	NR_029388	728407	Hs.499594	NR_029388		PARGP1	-	poly(ADP-ribose) glycohydrolase pseudogene 1	pseudo	0.009940	0.373016	
chunk0110_328_1	chr20	19114212	19114711	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-98185	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.006012	0.412000	
chunk0116_124_1	chr21	36135076	36135364	+	0	NA	exon (NM_001236, exon 1 of 3)	exon (NM_001236, exon 1 of 3)	255	NM_001236	874	Hs.154510	NM_001236	ENSG00000159231	CBR3	HEL-S-25|SDR21C2|hCBR3	carbonyl reductase 3	protein-coding	0.118056	0.733564	
chunk0153_175_1	chr5	71532231	71532827	+	0	NA	intron (NM_018429, intron 26 of 38)	intron (NM_018429, intron 26 of 38)	-54759	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.005034	0.304858	
chunk0114_63_1	chr21	9018816	9019128	+	0	NA	Intergenic	Intergenic	31602	NR_037458									0.009615	0.600639	
chunk0107_168_1	chr2	215498224	215498838	+	0	NA	Intergenic	Intergenic	44824	NR_110607	102724849	Hs.116161	NR_110607	ENSG00000225166	LOC102724849	-	uncharacterized LOC102724849	ncRNA	0.016287	0.429268	
chunk0160_377_1	chr5	161231328	161231837	+	0	NA	Intergenic	Intergenic	-292956	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.005894	0.364706	
chunk0160_366_1	chr5	161148230	161148735	+	0	NA	Intergenic	Intergenic	-209856	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.001980	0.337945	
chunk0129_324_1	chr3	124465115	124465314	+	0	NA	intron (NM_003947, intron 25 of 33)	intron (NM_003947, intron 25 of 33)	90882	NR_106731	102464832		NR_106731	ENSG00000276656	MIR6083	hsa-mir-6083	microRNA 6083	ncRNA	0.000000	0.355000	
chunk0037_278_1	chr11	75768354	75768602	+	0	NA	promoter-TSS (NM_001253891)	promoter-TSS (NM_001253891)	169	NR_046090	283214	Hs.591972	NR_046090	ENSG00000247867	LOC283214	-	uncharacterized LOC283214	ncRNA	0.088710	0.666667	
chunk0061_107_1	chr14	57818383	57819071	+	0	NA	intron (NM_001306087, intron 1 of 7)	ERV3-16A3_I-int|LTR|ERVL	47147	NM_001206920	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.004360	0.381713	
chunk0162_189_1	chr6	3841473	3842026	+	0	NA	Intergenic	Intergenic	-7649	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.005425	0.474729	
chunk0028_168_1	chr10	87594778	87595154	+	0	NA	Intergenic	Intergenic	-64753	NM_001015880	9060	Hs.524491	NM_004670	ENSG00000198682	PAPSS2	ATPSK2|BCYM4|SK2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding	0.002660	0.387268	235(AGGAACAGTCTCTGCC,-,0.00),236(GGAACAGTCTCTGCCC,+,0.00)
chunk0121_251_1	chr3	22959394	22959835	+	0	NA	Intergenic	L2a|LINE|L2	-243679	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.002268	0.416290	
chunk0006_323_1	chr1	71648219	71648644	+	0	NA	intron (NM_173808, intron 4 of 6)	MIR3|SINE|MIR	188581	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.004706	0.375587	
chunk0141_299_1	chr4	87006754	87007263	+	0	NA	promoter-TSS (NM_005935)	promoter-TSS (NM_005935)	7	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.102161	0.684314	
chunk0151_336_1	chr5	54012008	54012493	+	0	NA	intron (NM_019087, intron 4 of 4)	intron (NM_019087, intron 4 of 4)	-60651	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.002062	0.323045	
chunk0169_144_1	chr6	101501513	101501746	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	102644	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.376068	
chunk0075_6_1	chr16	46757356	46757593	+	0	NA	intron (NM_001308301, intron 1 of 11)	intron (NM_001308301, intron 1 of 11)	5772	NM_001308301	91807	Hs.130465	NM_182493	ENSG00000140795	MYLK3	MLCK|MLCK2|caMLCK	myosin light chain kinase 3	protein-coding	0.046414	0.596639	
chunk0134_67_1	chr3	176233924	176234472	+	0	NA	Intergenic	L1ME2z|LINE|L1	-280905	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.001825	0.304189	
chunk0136_140_1	chr4	4487577	4488250	+	0	NA	intron (NM_016930, intron 1 of 10)	intron (NM_016930, intron 1 of 10)	-6213	NR_126434	104472519	Hs.691848	NR_126434	ENSG00000248221	STX18-IT1	-	STX18 intronic transcript 1	ncRNA	0.011887	0.359050	
chunk0077_421_1	chr16	85321800	85322441	+	0	NA	Intergenic	Intergenic	-15795	NR_049816	100847022		NR_049816	ENSG00000266307	MIR5093	-	microRNA 5093	ncRNA	0.026521	0.570093	
chunk0031_256_1	chr10	127206512	127206742	+	0	NA	intron (NM_001290223, intron 27 of 51)	intron (NM_001290223, intron 27 of 51)	-10469	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.013043	0.415584	
chunk0157_440_1	chr5	124855807	124856511	+	0	NA	Intergenic	L2b|LINE|L2	-111047	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.005682	0.445390	321(TAGGACTTCTTGTTCT,-,0.00),322(AGGACTTCTTGTTCTC,+,0.00),543(TAGACCAGGATGTCCC,-,0.00),544(AGACCAGGATGTCCCT,+,0.00)
chunk0185_379_1	chr7	133178799	133179217	+	0	NA	Intergenic	HAL1|LINE|L1	-74059	NM_021807	60412	Hs.321273	NM_021807	ENSG00000131558	EXOC4	SEC8|SEC8L1|Sec8p	exocyst complex component 4	protein-coding	0.004785	0.336516	
chunk0047_451_1	chr12	76621634	76621950	+	0	NA	Intergenic	Intergenic	-61983	NM_020841	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.000000	0.400631	10(AGGTCAGACAGTTCCC,+,0.00)
chunk0190_409_1	chr8	40485452	40485651	+	0	NA	Intergenic	Intergenic	332083	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.010050	0.380000	
chunk0050_432_1	chr12	110250636	110250913	+	0	NA	Intergenic	Intergenic	-30453	NM_170665	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.007220	0.482014	
chunk0115_305_1	chr21	28517186	28517519	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	-21966	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.012012	0.467066	213(AGGAACTTCCAGTGCT,-,0.00),214(GGAACTTCCAGTGCTC,+,0.00)
chunk0070_189_1	chr15	71962453	71962933	+	0	NA	intron (NM_006901, intron 13 of 41)	MIRb|SINE|MIR	-151565	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.004167	0.347193	
chunk0122_21_1	chr3	27686649	27686989	+	0	NA	Intergenic	Intergenic	35896	NM_001278183	8320	Hs.591663	NM_005442	ENSG00000163508	EOMES	TBR2	eomesodermin	protein-coding	0.002941	0.363636	87(AGCACAGTATGTTTAT,+,0.00)
chunk0093_197_1	chr19	49301777	49302168	+	0	NA	intron (NM_014037, intron 7 of 11)	intron (NM_014037, intron 7 of 11)	6896	NR_036209	100422979		NR_036209	ENSG00000265407	MIR4324	mir-4324	microRNA 4324	ncRNA	0.015345	0.604592	
chunk0147_160_1	chr4	175873821	175874020	+	0	NA	intron (NR_048571, intron 1 of 5)	intron (NR_048571, intron 1 of 5)	-60806	NM_201591	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.000000	0.285000	
chunk0152_39_1	chr5	57033796	57034178	+	0	NA	Intergenic	L1ME4a|LINE|L1	-81857	NM_001297599	166968	Hs.657594	NM_152622	ENSG00000155545	MIER3	-	MIER family member 3	protein-coding	0.000000	0.253264	
chunk0097_438_1	chr2	64083213	64083448	+	0	NA	Intergenic	L2c|LINE|L2	61141	NM_020651	57162	Hs.7886	NM_020651	ENSG00000197329	PELI1	-	pellino E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.330508	
chunk0179_114_1	chr7	45242895	45243110	+	0	NA	Intergenic	Intergenic	85234	NM_005856	10268	Hs.25691	NM_005856	ENSG00000122679	RAMP3	-	receptor activity modifying protein 3	protein-coding	0.004651	0.564815	133(TTGGACAGGCTGTTCT,-,0.00),134(TGGACAGGCTGTTCTT,+,0.00)
chunk0034_155_1	chr11	30281970	30282191	+	0	NA	Intergenic	L1PA16|LINE|L1	-41019	NM_152316	120534	Hs.502208	NM_152316	ENSG00000152219	ARL14EP	ARF7EP|C11orf46|dJ299F11.1	ADP ribosylation factor like GTPase 14 effector protein	protein-coding	0.013575	0.612613	
chunk0086_39_1	chr18	12640266	12640912	+	0	NA	intron (NM_001128626, intron 1 of 16)	L2b|LINE|L2	16143	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.007740	0.420402	451(AAGAAGAATCTGTTCC,-,0.00)
chunk0084_306_1	chr17	80102916	80103185	+	0	NA	intron (NM_000152, intron 1 of 19)	intron (NM_000152, intron 1 of 19)	1494	NM_001079803	2548	Hs.1437	NM_000152	ENSG00000171298	GAA	LYAG	glucosidase alpha, acid	protein-coding	0.026022	0.525926	
chunk0158_355_1	chr5	133751133	133751591	+	0	NA	Intergenic	Intergenic	-138830	NM_015082	23105	Hs.483390	NM_015082	ENSG00000053108	FSTL4	-	follistatin like 4	protein-coding	0.006550	0.444444	
chunk0078_47_1	chr17	1188919	1189170	+	0	NA	Intergenic	Intergenic	-1722	NM_001159746	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.035857	0.531746	
chunk0144_437_1	chr4	141023519	141023934	+	0	NA	intron (NM_020724, intron 1 of 6)	MER33|DNA|hAT-Charlie	109736	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.009639	0.334135	
chunk0189_164_1	chr8	23246742	23246984	+	0	NA	exon (NM_152272, exon 2 of 11)	exon (NM_152272, exon 2 of 11)	3226	NM_152272	91782	Hs.5019	NM_152272	ENSG00000147457	CHMP7	-	charged multivesicular body protein 7	protein-coding	0.082645	0.687243	
chunk0080_302_1	chr17	31630068	31630437	+	0	NA	Intergenic	Intergenic	54841	NR_029856	100126356		NR_029856	ENSG00000283978	MIR365B	MIR365-2|MIRN365-2|hsa-mir-365b|mir-365b	microRNA 365b	ncRNA	0.008130	0.513514	
chunk0183_344_1	chr7	108517226	108517640	+	0	NA	intron (NM_001256008, intron 1 of 9)	L1MC1|LINE|L1	8885	NM_001256009	50640	Hs.617340	NM_015723	ENSG00000135241	PNPLA8	IPLA2-2|IPLA2G|MMLA|PNPLA-gamma|iPLA2gamma	patatin like phospholipase domain containing 8	protein-coding	0.012077	0.368675	
chunk0164_373_1	chr6	25868475	25868901	+	0	NA	intron (NM_001098486, intron 1 of 12)	MIRb|SINE|MIR	5555	NM_001098486	10786	Hs.327179	NM_006632	ENSG00000124564	SLC17A3	GOUT4|NPT4|UAQTL4	solute carrier family 17 member 3	protein-coding	0.002347	0.412178	
chunk0170_268_1	chr6	114045829	114046412	+	0	NA	intron (NR_125845, intron 4 of 9)	OldhAT1|DNA|hAT-Ac	16757	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.006861	0.440068	
chunk0082_248_1	chr17	57459458	57459657	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	64040	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.005025	0.475000	
chunk0180_218_1	chr7	67067213	67067987	+	0	NA	intron (NM_018264, intron 10 of 15)	L1M4|LINE|L1	46797	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.009044	0.361290	
chunk0015_263_1	chr1	188203281	188203587	+	0	NA	Intergenic	Intergenic	759806	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006536	0.426710	
chunk0079_29_1	chr17	9936955	9937644	+	0	NA	intron (NM_001130831, intron 8 of 13)	intron (NM_001130831, intron 8 of 13)	22150	NM_003644	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.021771	0.552174	373(CAGGACACAGTGTCCT,-,0.00),374(AGGACACAGTGTCCTT,+,0.00)
chunk0035_374_1	chr11	49432439	49432923	+	0	NA	Intergenic	Intergenic	-125847	NR_027044	440040	Hs.655746	NR_027044	ENSG00000205035	LOC440040	-	glutamate metabotropic receptor 5 pseudogene	pseudo	0.002066	0.342268	217(CAGGACACCAAGTGCT,-,0.00),218(AGGACACCAAGTGCTT,+,0.00)
chunk0020_427_1	chr1	241679897	241680354	+	0	NA	intron (NM_144625, intron 5 of 26)	intron (NM_144625, intron 5 of 26)	27847	NM_144625	128025	Hs.97527	NM_144625	ENSG00000162843	WDR64	-	WD repeat domain 64	protein-coding	0.008753	0.373362	
chunk0166_201_1	chr6	46624108	46624474	+	0	NA	intron (NM_016593, intron 7 of 11)	intron (NM_016593, intron 7 of 11)	28539	NM_001278739	51302	Hs.387367	NM_016593	ENSG00000146233	CYP39A1	-	cytochrome P450 family 39 subfamily A member 1	protein-coding	0.002732	0.408719	
chunk0022_194_1	chr10	13491529	13492241	+	0	NA	intron (NM_001100912, intron 4 of 7)	intron (NM_001100912, intron 4 of 7)	11091	NM_001100912	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.014045	0.356241	
chunk0112_16_1	chr20	35991070	35991436	+	0	NA	intron (NM_080834, intron 7 of 11)	MER63D|DNA|hAT-Blackjack	22672	NM_001207076	140894	Hs.732697	NM_080834	ENSG00000149646	CNBD2	C20orf152|CNMPD1	cyclic nucleotide binding domain containing 2	protein-coding	0.005464	0.378747	
chunk0019_357_1	chr1	229601389	229601913	+	0	NA	3' UTR (NM_001025247, exon 4 of 4)	3' UTR (NM_001025247, exon 4 of 4)	24396	NM_014409	27097	Hs.270621	NM_014409	ENSG00000135801	TAF5L	PAF65B	TATA-box binding protein associated factor 5 like	protein-coding	0.011450	0.453333	
chunk0004_195_1	chr1	46399317	46399535	+	0	NA	intron (NM_001441, intron 1 of 14)	intron (NM_001441, intron 1 of 14)	5159	NM_001441	2166	Hs.720143	NM_001441	ENSG00000117480	FAAH	FAAH-1|PSAB	fatty acid amide hydrolase	protein-coding	0.013761	0.442922	
chunk0105_133_1	chr2	185813685	185814176	+	0	NA	exon (NM_173651, exon 18 of 23)	exon (NM_173651, exon 18 of 23)	-73453	NR_110217	101927196	Hs.244783	NR_110214	ENSG00000226747	FSIP2-AS2	-	FSIP2 antisense RNA 2	ncRNA	0.006110	0.392276	
chunk0121_6_1	chr3	14420359	14420599	+	0	NA	intron (NM_001134367, intron 2 of 14)	intron (NM_001134367, intron 2 of 14)	17903	NM_003043	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.004167	0.423237	
chunk0107_92_1	chr2	213130603	213131206	+	0	NA	intron (NM_016260, intron 3 of 7)	intron (NM_016260, intron 3 of 7)	19430	NM_016260	22807	Hs.604950	NM_016260	ENSG00000030419	IKZF2	ANF1A2|HELIOS|ZNF1A2|ZNFN1A2	IKAROS family zinc finger 2	protein-coding	0.003317	0.296358	
chunk0155_352_1	chr5	97104116	97104526	+	0	NA	intron (NM_153234, intron 4 of 5)	intron (NM_153234, intron 4 of 5)	38495	NM_153234	167410	Hs.656702	NM_153234	ENSG00000145721	LIX1	C5orf11|Lft	limb and CNS expressed 1	protein-coding	0.004878	0.391727	
chunk0099_295_1	chr2	98868713	98868919	+	0	NA	intron (NM_207362, intron 1 of 9)	intron (NM_207362, intron 1 of 9)	67405	NM_207362	343990	Hs.469398	NM_207362	ENSG00000196872	KIAA1211L	C2orf55	KIAA1211 like	protein-coding	0.009709	0.415459	62(GGCACACTCTGCTCAC,+,0.00)
chunk0178_14_1	chr7	29163917	29164168	+	0	NA	intron (NM_001293069, intron 2 of 13)	L1ME1|LINE|L1	17495	NM_001293069	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.007968	0.380952	
chunk0096_230_1	chr2	30648728	30649303	+	0	NA	Intergenic	Intergenic	158430	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.003478	0.463542	244(GAGGGCATCCTGTGCC,-,0.00),245(AGGGCATCCTGTGCCA,+,0.00)
chunk0128_289_1	chr3	110939994	110940193	+	0	NA	Intergenic	Intergenic	129866	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.000000	0.440000	
chunk0177_89_1	chr7	21738003	21738391	+	0	NA	intron (NM_001277115, intron 46 of 81)	intron (NM_001277115, intron 46 of 81)	194982	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.015464	0.439589	223(CTACACACACTGTTCT,-,0.00),224(TACACACACTGTTCTT,+,0.00)
chunk0097_361_1	chr2	60539983	60540480	+	0	NA	intron (NM_138559, intron 2 of 4)	intron (NM_138559, intron 2 of 4)	13267	NM_138559	53335	Hs.370549	NM_018014	ENSG00000119866	BCL11A	BCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856	BAF chromatin remodeling complex subunit BCL11A	protein-coding	0.004024	0.339357	
chunk0035_232_1	chr11	45848463	45848928	+	0	NA	intron (NM_021117, intron 1 of 11)	intron (NM_021117, intron 1 of 11)	1289	NM_021117	1408	Hs.532491	NM_021117	ENSG00000121671	CRY2	HCRY2|PHLL2	cryptochrome circadian regulator 2	protein-coding	0.017204	0.487124	
chunk0118_302_1	chr22	34979655	34980060	+	0	NA	Intergenic	Intergenic	-86279	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.002469	0.450739	177(AGGAACACTGTGTCCT,-,0.00),178(GGAACACTGTGTCCTG,+,0.00)
chunk0181_406_1	chr7	90066988	90067629	+	0	NA	intron (NR_110029, intron 2 of 2)	intron (NR_110029, intron 2 of 2)	-52092	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.009360	0.366044	
chunk0041_337_1	chr11	130571055	130571446	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-95485	NR_107019	102466873		NR_107019	ENSG00000274999	MIR8052	hsa-mir-8052	microRNA 8052	ncRNA	0.005115	0.426020	265(ATGAGCACAGTGTTCC,-,0.00)
chunk0045_221_1	chr12	48050135	48050413	+	0	NA	intron (NR_051991, intron 14 of 18)	intron (NR_051991, intron 14 of 18)	-45772	NM_001844	1280	Hs.408182	NM_001844	ENSG00000139219	COL2A1	ANFH|AOM|COL11A3|SEDC|STL1	collagen type II alpha 1 chain	protein-coding	0.017986	0.487455	
chunk0173_101_1	chr6	143162798	143163025	+	0	NA	intron (NM_001286587, intron 3 of 6)	MER115|DNA|hAT-Tip100	102069	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.013216	0.535088	
chunk0171_113_1	chr6	122431734	122432063	+	0	NA	intron (NM_004506, intron 12 of 12)	intron (NM_004506, intron 12 of 12)	32347	NM_001135564	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.009119	0.369697	
chunk0159_180_1	chr5	140141392	140141896	+	0	NA	Intergenic	Intergenic	-15675	NR_130738	101929719	Hs.150064	NR_130738	ENSG00000254363	LOC101929719	-	uncharacterized LOC101929719	ncRNA	0.003968	0.514851	
chunk0084_28_1	chr17	73564827	73565203	+	0	NA	intron (NM_001144952, intron 1 of 44)	L1MEb|LINE|L1	79073	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.005319	0.453581	
chunk0174_205_1	chr6	160249595	160249890	+	0	NA	intron (NM_003058, intron 3 of 10)	intron (NM_003058, intron 3 of 10)	9189	NM_003058	6582	Hs.436385	NM_003058	ENSG00000112499	SLC22A2	OCT2	solute carrier family 22 member 2	protein-coding	0.003390	0.351351	
chunk0112_41_1	chr20	36813659	36814259	+	0	NA	intron (NM_080627, intron 5 of 14)	L2b|LINE|L2	-40132	NM_001145318	79980	Hs.632268	NM_024918	ENSG00000149636	DSN1	C20orf172|KNL3|MIS13|dJ469A13.2|hKNL-3	DSN1 component of MIS12 kinetochore complex	protein-coding	0.018333	0.470882	325(GAAAACACTGTGTTCC,-,0.00),326(AAAACACTGTGTTCCC,+,0.00)
chunk0065_319_1	chr14	103142249	103142818	+	0	NA	Intergenic	MER83|LTR|ERV1	16206	NM_006291	7127	Hs.525607	NM_006291	ENSG00000185215	TNFAIP2	B94|EXOC3L3	TNF alpha induced protein 2	protein-coding	0.014060	0.473684	
chunk0039_419_1	chr11	107708812	107709388	+	0	NA	intron (NM_003063, intron 1 of 1)	intron (NM_003063, intron 1 of 1)	2961	NM_003063	6588	Hs.334629	NM_003063	ENSG00000170290	SLN	-	sarcolipin	protein-coding	0.006944	0.396880	325(ATGTACAGATTGTCCA,-,0.00),326(TGTACAGATTGTCCAT,+,0.00)
chunk0199_458_1	chr9	14199115	14199403	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	-18457	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.017361	0.501730	
chunk0149_431_1	chr5	29696879	29697443	+	0	NA	Intergenic	L1MC3|LINE|L1	-301185	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.003546	0.345133	
chunk0017_299_1	chr1	210775255	210775506	+	0	NA	exon (NM_172362, exon 10 of 11)	exon (NM_172362, exon 10 of 11)	358735	NM_172362	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.015936	0.476190	
chunk0010_44_1	chr1	112841208	112841566	+	0	NA	intron (NR_103746, intron 2 of 6)	L2a|LINE|L2	9256	NR_103746	100996702	Hs.632431	NR_103746	ENSG00000215866	LINC01356	-	long intergenic non-protein coding RNA 1356	ncRNA	0.005587	0.395543	
chunk0168_46_1	chr6	78535303	78535545	+	0	NA	Intergenic	L2c|LINE|L2	-332120	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.004132	0.386831	
chunk0190_382_1	chr8	40054690	40055236	+	0	NA	Intergenic	Intergenic	-98505	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.016484	0.484461	
chunk0053_50_1	chr13	27601696	27602431	+	0	NA	intron (NM_153371, intron 1 of 9)	L1ME2z|LINE|L1	18520	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.008163	0.383152	
chunk0199_324_1	chr9	7704718	7705172	+	0	NA	Intergenic	Intergenic	94854	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.002203	0.329670	247(TTGGACAAGTTGTTCC,-,0.00),248(TGGACAAGTTGTTCCT,+,0.00)
chunk0157_388_1	chr5	124044024	124044357	+	0	NA	Intergenic	Intergenic	394330	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.003003	0.323353	
chunk0165_322_1	chr6	37161229	37161614	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	-8725	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.007792	0.352332	254(GGAACACTCTGTGTAT,+,0.00)
chunk0033_6_1	chr11	12326415	12326751	+	0	NA	intron (NM_032867, intron 5 of 8)	intron (NM_032867, intron 5 of 8)	39683	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.008929	0.436202	
chunk0109_10_1	chr20	257315	257950	+	0	NA	promoter-TSS (NM_207469)	promoter-TSS (NM_207469)	-104	NM_207469	400830	Hs.516819	NM_207469	ENSG00000186458	DEFB132	BD-32|DEFB-32|DEFB32|HEL-75|KFLL827|UNQ827	defensin beta 132	protein-coding	0.012598	0.476415	
chunk0072_7_1	chr16	325600	325824	+	0	NA	intron (NM_003502, intron 2 of 10)	intron (NM_003502, intron 2 of 10)	26964	NM_181050	8312	Hs.592082	NM_003502	ENSG00000103126	AXIN1	AXIN|PPP1R49	axin 1	protein-coding	0.049107	0.595556	
chunk0094_423_1	chr2	10600076	10600554	+	0	NA	intron (NR_048552, intron 16 of 19)	intron (NR_048552, intron 16 of 19)	89672	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.006276	0.344468	278(AAGAACACCAAGTCCA,-,0.00),279(AGAACACCAAGTCCAA,+,0.00)
chunk0183_401_1	chr7	110282960	110283442	+	0	NA	Intergenic	Intergenic	-322988	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.004149	0.385093	
chunk0075_349_1	chr16	55559170	55559759	+	0	NA	intron (NM_017839, intron 11 of 13)	intron (NM_017839, intron 11 of 13)	-7208	NM_032330	84290	Hs.660027	NM_032330	ENSG00000256812	CAPNS2	CSS2	calpain small subunit 2	protein-coding	0.001698	0.345763	
chunk0059_378_1	chr14	37406169	37406754	+	0	NA	intron (NM_001195296, intron 12 of 14)	intron (NM_001195296, intron 12 of 14)	188659	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.005128	0.341297	
chunk0194_20_1	chr8	81596868	81597292	+	0	NA	Intergenic	Intergenic	-65765	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.000000	0.355294	
chunk0011_160_1	chr1	147626659	147627304	+	0	NA	TTS (NM_004326)	TTS (NM_004326)	43531	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.012403	0.458204	
chunk0171_106_1	chr6	122126528	122127126	+	0	NA	Intergenic	L1M5|LINE|L1	-272724	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.005017	0.327212	
chunk0143_148_1	chr4	109993971	109994630	+	0	NA	intron (NM_001963, intron 19 of 23)	intron (NM_001963, intron 19 of 23)	81416	NM_001178130	1950	Hs.419815	NM_001963	ENSG00000138798	EGF	HOMG4|URG	epidermal growth factor	protein-coding	0.007587	0.380303	505(TAGGACTGGGTGTTCT,-,0.00),506(AGGACTGGGTGTTCTT,+,0.00)
chunk0029_66_1	chr10	96576862	96577131	+	0	NA	intron (NM_020123, intron 1 of 14)	intron (NM_020123, intron 1 of 14)	10056	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.000000	0.303704	
chunk0122_383_1	chr3	37802973	37803410	+	0	NA	intron (NR_110532, intron 4 of 5)	intron (NR_110532, intron 4 of 5)	58589	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.013730	0.413242	239(AAGAACATAGTGTGTC,-,0.00),240(AGAACATAGTGTGTCC,+,0.00)
chunk0203_154_1	chr9	85691554	85691980	+	0	NA	intron (NM_001286715, intron 2 of 24)	L1ME4a|LINE|L1	50262	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.011737	0.306792	
chunk0210_388_1	chrX	97854477	97854888	+	0	NA	Intergenic	Intergenic	-290147	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.002433	0.381068	
chunk0165_240_1	chr6	35610757	35611453	+	0	NA	intron (NM_001145777, intron 5 of 6)	HAL1ME|LINE|L1	53684	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.008621	0.416069	313(AAGAACAGTGTGTACC,-,0.00),314(AGAACAGTGTGTACCT,+,0.00)
chunk0056_69_1	chr13	79357076	79357275	+	0	NA	intron (NM_022118, intron 11 of 20)	intron (NM_022118, intron 11 of 20)	49046	NM_022118	64062	Hs.558528	NM_018605	ENSG00000139746	RBM26	ARRS2|C13orf10|PPP1R132|PRO1777|SE70-2|ZC3H17	RNA binding motif protein 26	protein-coding	0.005025	0.320000	
chunk0207_212_1	chr9	131402914	131403113	+	0	NA	Intergenic	Intergenic	-27077	NM_013318	84726	Hs.743955	NM_013318	ENSG00000130723	PRRC2B	BAT2L|BAT2L1|KIAA0515|LQFBS-1	proline rich coiled-coil 2B	protein-coding	0.035176	0.505000	
chunk0203_58_1	chr9	83384019	83384500	+	0	NA	intron (NM_001244959, intron 2 of 14)	intron (NM_001244959, intron 2 of 14)	-52298	NM_001244961	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.008316	0.460581	
chunk0200_339_1	chr9	24297346	24297802	+	0	NA	Intergenic	Intergenic	248102	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.002193	0.378556	
chunk0042_99_1	chr12	2812616	2813057	+	0	NA	exon (NM_018463, exon 1 of 12)	exon (NM_018463, exon 1 of 12)	214	NR_130744	55846	Hs.239	NM_018463	ENSG00000111203	ITFG2	FGGAP1|MDS028	integrin alpha FG-GAP repeat containing 2	protein-coding	0.068027	0.567873	
chunk0164_81_1	chr6	19908333	19908817	+	0	NA	Intergenic	Intergenic	71205	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.016529	0.414433	189(CAGAACGCTATGTTCT,-,0.00),190(AGAACGCTATGTTCTG,+,0.00)
chunk0211_41_1	chrX	108516106	108516738	+	0	NA	intron (NM_033380, intron 1 of 50)	intron (NM_033380, intron 1 of 50)	76578	NM_000495	1287	Hs.369089	NM_000495	ENSG00000188153	COL4A5	ASLN|ATS|ATS1|CA54	collagen type IV alpha 5 chain	protein-coding	0.003165	0.358610	
chunk0149_368_1	chr5	28102887	28103299	+	0	NA	Intergenic	Intergenic	630801	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.009709	0.292978	190(TGTACACGTTGTACTG,+,0.00)
chunk0098_92_1	chr2	67702853	67703355	+	0	NA	Intergenic	Intergenic	122458	NR_110271	101927701	Hs.348697	NR_110271	ENSG00000237013	LINC01812	-	long intergenic non-protein coding RNA 1812	ncRNA	0.003984	0.351889	
chunk0066_132_1	chr15	31125107	31125486	+	0	NA	intron (NM_001252020, intron 1 of 26).2	L1MC2|LINE|L1	-23570	NM_001252030	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.021108	0.426316	
chunk0033_251_1	chr11	18254016	18254272	+	0	NA	Intergenic	Intergenic	-5470	NM_001127380	6289	Hs.731376	NM_030754	ENSG00000134339	SAA2	SAA|SAA1	serum amyloid A2	protein-coding	0.019531	0.536965	
chunk0168_325_1	chr6	92449159	92449606	+	0	NA	Intergenic	L1M2|LINE|L1	-758954	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.004474	0.491071	
chunk0021_210_1	chr10	5950117	5950809	+	0	NA	Intergenic	Intergenic	27148	NM_172200	3601	Hs.445124	NM_002189	ENSG00000134470	IL15RA	CD215	interleukin 15 receptor subunit alpha	protein-coding	0.015896	0.477633	
chunk0155_284_1	chr5	96124650	96125119	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	45746	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.004264	0.323404	
chunk0007_145_1	chr1	79373740	79373941	+	0	NA	Intergenic	Intergenic	-367030	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.004975	0.435644	
chunk0182_69_1	chr7	92252545	92253297	+	0	NA	intron (NM_019004, intron 1 of 19)	L1MC4|LINE|L1	6687	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.003989	0.381142	249(CAGAACAAGCTGTTCC,-,0.00),250(AGAACAAGCTGTTCCT,+,0.00)
chunk0194_386_1	chr8	90873398	90874092	+	0	NA	intron (NM_022351, intron 4 of 12)	intron (NM_022351, intron 4 of 12)	82052	NM_022351	64168	Hs.719466	NM_022351	ENSG00000123119	NECAB1	EFCBP1|STIP-1	N-terminal EF-hand calcium binding protein 1	protein-coding	0.001441	0.356835	
chunk0088_17_1	chr18	43392215	43392657	+	0	NA	Intergenic	Intergenic	-114786	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.006787	0.349887	
chunk0025_106_1	chr10	50844237	50844436	+	0	NA	intron (NM_014576, intron 3 of 12)	intron (NM_014576, intron 3 of 12)	41339	NM_138933	29974	Hs.282795	NM_014576	ENSG00000148584	A1CF	ACF|ACF64|ACF65|APOBEC1CF|ASP	APOBEC1 complementation factor	protein-coding	0.000000	0.305000	
chunk0014_351_1	chr1	182291763	182292165	+	0	NA	intron (NR_104175, intron 2 of 2)	intron (NR_104175, intron 2 of 2)	22097	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.004975	0.449132	
chunk0189_414_1	chr8	27748516	27748734	+	0	NA	intron (NM_018246, intron 5 of 8)	intron (NM_018246, intron 5 of 8)	24028	NR_130761	55246	Hs.445512	NM_018246	ENSG00000147419	CCDC25	-	coiled-coil domain containing 25	protein-coding	0.022936	0.488584	
chunk0060_278_1	chr14	50399839	50400588	+	0	NA	Intergenic	Intergenic	-2809	NM_001282236	8814	Hs.280881	NM_004196	ENSG00000100490	CDKL1	KKIALRE|P42	cyclin dependent kinase like 1	protein-coding	0.006676	0.396000	
chunk0074_363_1	chr16	34581197	34581868	+	0	NA	Intergenic	Intergenic	-421496	NR_038368									0.031297	0.358631	
chunk0121_349_1	chr3	24657747	24658552	+	0	NA	Intergenic	L1MA5A|LINE|L1	-136714	NR_039955									0.001242	0.346154	
chunk0135_101_1	chr3	186612666	186613178	+	0	NA	promoter-TSS (NM_001622)	promoter-TSS (NM_001622)	-139	NM_001622	197	Hs.324746	NM_001622	ENSG00000145192	AHSG	A2HS|AHS|APMR1|FETUA|HSGA	alpha 2-HS glycoprotein	protein-coding	0.009766	0.512671	
chunk0124_179_1	chr3	55423899	55424215	+	0	NA	Intergenic	L2c|LINE|L2	57341	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.012658	0.511041	128(CAACACACCATGTGCC,-,0.00)
chunk0202_230_1	chr9	76423717	76424246	+	0	NA	Intergenic	Intergenic	-17685	NM_001097634	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.000000	0.330189	
chunk0147_410_1	chr4	186949856	186950434	+	0	NA	Intergenic	MIRc|SINE|MIR	-226312	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.015571	0.367876	
chunk0108_361_1	chr2	236569333	236569956	+	0	NA	promoter-TSS (NM_020311)	promoter-TSS (NM_020311)	-93	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.017657	0.504808	
chunk0117_337_1	chr21	43956767	43956966	+	0	NA	intron (NM_001037553, intron 1 of 8)	MLT1F1|LTR|ERVL-MaLR	31468	NM_001037553	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.020101	0.540000	
chunk0066_311_1	chr15	35757834	35758320	+	0	NA	intron (NR_038251, intron 2 of 2)	(AC)n|Simple_repeat|Simple_repeat	-168779	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.004115	0.377823	
chunk0152_104_1	chr5	58428953	58429232	+	0	NA	Intergenic	LTR33A|LTR|ERVL	31047	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.010753	0.475000	
chunk0003_127_1	chr1	32574606	32574945	+	0	NA	intron (NR_111980, intron 2 of 3)	AluJr|SINE|Alu	35630	NM_001291496	653121	Hs.546479	NM_144621	ENSG00000160062	ZBTB8A	BOZF1|ZBTB8|ZNF916A	zinc finger and BTB domain containing 8A	protein-coding	0.002950	0.379412	
chunk0206_160_1	chr9	121662591	121662958	+	0	NA	intron (NM_032552, intron 1 of 16)	intron (NM_032552, intron 1 of 16)	-80011	NM_138709	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.008174	0.464674	
chunk0080_229_1	chr17	29826853	29827182	+	0	NA	intron (NM_033389, intron 1 of 14)	intron (NM_033389, intron 1 of 14)	-65585	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.006079	0.384848	
chunk0090_170_1	chr18	72687821	72688122	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-143483	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.009967	0.360927	
chunk0180_212_1	chr7	66716583	66716872	+	0	NA	intron (NM_001287060, intron 2 of 9)	L1MD2|LINE|L1	-23929	NM_001287062	27342	Hs.530053	NM_014504	ENSG00000154710	RABGEF1	RABEX5|RAP1|rabex-5	RAB guanine nucleotide exchange factor 1	protein-coding	0.006920	0.365517	
chunk0187_339_1	chr7	156852669	156852914	+	0	NA	intron (NM_022458, intron 1 of 16)	MER20|DNA|hAT-Charlie	40417	NM_022458	64327	Hs.209989	NM_022458	ENSG00000105983	LMBR1	ACHP|C7orf2|DIF14|LSS|PPD2|THYP|TPT|ZRS	limb development membrane protein 1	protein-coding	0.012245	0.418699	135(AAGAACAATCTGTCCA,-,0.00),136(AGAACAATCTGTCCAG,+,0.00)
chunk0170_262_1	chr6	113858634	113859070	+	0	NA	intron (NM_002356, intron 1 of 1)	CpG	1517	NM_002356	4082	Hs.519909	NM_002356	ENSG00000277443	MARCKS	80K-L|MACS|PKCSL|PRKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.080275	0.643021	
chunk0082_242_1	chr17	57410059	57410596	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	113270	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.013035	0.462825	
chunk0156_320_1	chr5	111246583	111246782	+	0	NA	intron (NM_001744, intron 1 of 10)	intron (NM_001744, intron 1 of 10)	22433	NM_001744	814	Hs.438801	NM_001744	ENSG00000152495	CAMK4	CaMK IV|CaMK-GR|CaMKIV|caMK	calcium/calmodulin dependent protein kinase IV	protein-coding	0.000000	0.475000	
chunk0116_85_1	chr21	34734689	34735092	+	0	NA	intron (NR_024351, intron 1 of 5)	MamRTE1|LINE|RTE-BovB	2292	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.017370	0.470297	202(GGGCCAAGCTGTTCTT,+,0.00)
chunk0076_341_1	chr16	71505391	71505746	+	0	NA	Intergenic	L1MB5|LINE|L1	-16217	NM_006961	7567	Hs.660076	NM_006961	ENSG00000157429	ZNF19	KOX12	zinc finger protein 19	protein-coding	0.008451	0.370787	
chunk0132_281_1	chr3	159829800	159830040	+	0	NA	intron (NM_014575, intron 2 of 7)	Charlie15b|DNA|hAT-Charlie	-9941	NM_001197109	29970	Hs.134665	NM_014575	ENSG00000151967	SCHIP1	SCHIP-1	schwannomin interacting protein 1	protein-coding	0.004167	0.327801	
chunk0118_308_1	chr22	35065567	35066092	+	0	NA	promoter-TSS (NM_001303508)	promoter-TSS (NM_001303508)	-307	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.001905	0.551331	
chunk0007_443_1	chr1	86913784	86914209	+	0	NA	promoter-TSS (NM_001134492)	promoter-TSS (NM_001134492)	428	NM_004261	9403	Hs.362728	NM_004261	ENSG00000183291	SELENOF	SEP15	selenoprotein F	protein-coding	0.054118	0.546948	
chunk0151_62_1	chr5	42496611	42496856	+	0	NA	intron (NM_001242401, intron 2 of 10)	intron (NM_001242401, intron 2 of 10)	-51310	NM_001242402	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.004082	0.373984	18(AAGGACAGATTGTCTT,-,0.00),19(AGGACAGATTGTCTTC,+,0.00)
chunk0022_286_1	chr10	15444098	15444499	+	0	NA	Intergenic	MIR|SINE|MIR	-73239	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.007481	0.375622	
chunk0035_238_1	chr11	46031028	46031543	+	0	NA	intron (NM_016621, intron 5 of 17)	intron (NM_016621, intron 5 of 17)	90149	NM_001101802	51317	Hs.502458	NM_016621	ENSG00000135365	PHF21A	BHC80|BM-006	PHD finger protein 21A	protein-coding	0.005825	0.424419	
chunk0050_361_1	chr12	107892145	107892502	+	0	NA	Intergenic	MIRb|SINE|MIR	11448	NR_037629	728739	Hs.741995	NR_037629		LOC728739	-	programmed cell death 2 pseudogene	pseudo	0.005602	0.399441	
chunk0118_229_1	chr22	32237294	32237589	+	0	NA	intron (NM_014227, intron 6 of 14)	intron (NM_014227, intron 6 of 14)	17890	NM_014227	6527	Hs.130101	NM_014227	ENSG00000100191	SLC5A4	DJ90G24.4|SAAT1|SGLT3	solute carrier family 5 member 4	protein-coding	0.003390	0.456081	
chunk0171_165_1	chr6	124742894	124743509	+	0	NA	intron (NM_001300740, intron 3 of 5)	MIR|SINE|MIR	-219344	NM_001286398	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.004878	0.357143	328(AGGAACACATAGTTCC,-,0.00),329(GGAACACATAGTTCCT,+,0.00)
chunk0092_410_1	chr19	37655857	37656241	+	0	NA	promoter-TSS (NM_014898)	promoter-TSS (NM_014898)	-637	NM_014898	22835	Hs.668737	NM_014898	ENSG00000120784	ZFP30	ZNF745	ZFP30 zinc finger protein	protein-coding	0.093750	0.675325	
chunk0195_148_1	chr8	95262780	95263077	+	0	NA	intron (NM_177965, intron 2 of 5)	L1ME3Cz|LINE|L1	-5908	NR_038206	100616530	Hs.554328	NR_038201	ENSG00000253773	C8orf37-AS1	-	C8orf37 antisense RNA 1	ncRNA	0.006734	0.338926	
chunk0010_191_1	chr1	115954398	115955040	+	0	NA	intron (NR_125970, intron 2 of 4)	L2b|LINE|L2	-21779	NM_018420	55356	Hs.125482	NM_018420	ENSG00000163393	SLC22A15	FLIPT1|PRO34686	solute carrier family 22 member 15	protein-coding	0.004673	0.421462	
chunk0009_225_1	chr1	106644078	106644765	+	0	NA	Intergenic	MIR|SINE|MIR	-412224	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.010189	0.350291	
chunk0033_300_1	chr11	20063079	20063479	+	0	NA	intron (NM_001244963, intron 22 of 39)	intron (NM_001244963, intron 22 of 39)	-13976	NR_046672	100874014	Hs.557916	NR_046672	ENSG00000254453	NAV2-AS2	-	NAV2 antisense RNA 2	ncRNA	0.012500	0.366584	
chunk0190_440_1	chr8	41617579	41618018	+	0	NA	intron (NM_178819, intron 10 of 12)	intron (NM_178819, intron 10 of 12)	29561	NM_152568	157848		NM_152568	ENSG00000165066	NKX6-3	NKX6.3	NK6 homeobox 3	protein-coding	0.006834	0.506818	
chunk0181_115_1	chr7	80659045	80659291	+	0	NA	intron (NM_001289908, intron 2 of 9)	intron (NM_001289908, intron 2 of 9)	12515	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.000000	0.352227	
chunk0140_371_1	chr4	74740021	74740397	+	0	NA	Intergenic	Intergenic	54477	NM_001316963	685	Hs.591704	NM_001729	ENSG00000174808	BTC	-	betacellulin	protein-coding	0.002660	0.307692	192(TGTACTCAATGTTCTT,+,0.00)
chunk0009_183_1	chr1	105716779	105717067	+	0	NA	Intergenic	Intergenic	-97988	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.006944	0.287197	
chunk0210_254_1	chrX	83115971	83116527	+	0	NA	Intergenic	L1MC3|LINE|L1	-392012	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.001799	0.335727	
chunk0089_241_1	chr18	62023706	62023957	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-130760	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.000000	0.396825	
chunk0074_12_1	chr16	19753891	19754570	+	0	NA	intron (NR_130967, intron 5 of 7)	L2b|LINE|L2	-36060	NM_001012991	400506	Hs.585209	NM_001012991	ENSG00000103550	KNOP1	101F10.1|C16orf88|FAM191A|TSG118	lysine rich nucleolar protein 1	protein-coding	0.010309	0.441176	
chunk0068_186_1	chr15	54792568	54792777	+	0	NA	Intergenic	Intergenic	404361	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004785	0.480952	
chunk0091_226_1	chr19	10315395	10315594	+	0	NA	TTS (NM_133452)	TTS (NM_133452)	521	NM_001031734	112812	Hs.654865	NM_080665	ENSG00000267673	FDX2	FDX1L|MEOAL	ferredoxin 2	protein-coding	0.055276	0.595000	
chunk0023_353_1	chr10	29791626	29791955	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-55989	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.009119	0.442424	
chunk0028_162_1	chr10	87053010	87053593	+	0	NA	intron (NM_005271, intron 12 of 12)	intron (NM_005271, intron 12 of 12)	33012	NM_001146157	643161	Hs.729945	NM_001146157	ENSG00000188100	FAM25A	bA96C23.5	family with sequence similarity 25 member A	protein-coding	0.006861	0.400685	
chunk0001_55_1	chr1	2001846	2002205	+	0	NA	intron (NM_001304360, intron 1 of 38)	L1MC4|LINE|L1	1812	NM_001304360	85452	Hs.232092	NM_001003808	ENSG00000142609	CFAP74	C1orf222|KIAA1751	cilia and flagella associated protein 74	protein-coding	0.019499	0.513889	
chunk0139_282_1	chr4	57119410	57119609	+	0	NA	intron (NR_034081, intron 1 of 4)	intron (NR_034081, intron 1 of 4)	-9124	NM_001553	3490	Hs.479808	NM_001553	ENSG00000163453	IGFBP7	AGM|FSTL2|IBP-7|IGFBP-7|IGFBP-7v|IGFBPRP1|MAC25|PSF|RAMSVPS|TAF	insulin like growth factor binding protein 7	protein-coding	0.010050	0.520000	
chunk0044_15_1	chr12	27087141	27088020	+	0	NA	Intergenic	Ricksha_c|DNA|MULE-MuDR	-5058	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.005688	0.407955	
chunk0087_297_1	chr18	39004824	39005108	+	0	NA	Intergenic	L1MC4a|LINE|L1	617209	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.000000	0.294737	158(AAGAACACAATGTTAT,-,0.00),159(AGAACACAATGTTATT,+,0.00)
chunk0107_407_1	chr2	224180611	224180912	+	0	NA	Intergenic	Intergenic	-141442	NM_006216	5270	Hs.38449	NM_006216	ENSG00000135919	SERPINE2	GDN|GDNPF|PI-7|PI7|PN-1|PN1|PNI	serpin family E member 2	protein-coding	0.013289	0.506623	122(AGGAACAATGTGTACA,-,0.00),123(GGAACAATGTGTACAC,+,0.00)
chunk0006_41_1	chr1	64370056	64370505	+	0	NA	Intergenic	L2a|LINE|L2	-100513	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.002227	0.424444	230(GGGAACAGCTAGTGCA,-,0.00),231(GGAACAGCTAGTGCAT,+,0.00)
chunk0174_277_1	chr6	161644403	161644984	+	0	NA	intron (NM_013988, intron 4 of 8)	MLT1K|LTR|ERVL-MaLR	-370618	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.017212	0.475945	279(GGGAACTACCTGTGCT,-,0.00),280(GGAACTACCTGTGCTC,+,0.00)
chunk0014_200_1	chr1	179063615	179064119	+	0	NA	intron (NM_014864, intron 4 of 7)	intron (NM_014864, intron 4 of 7)	-18110	NM_022371	64222	Hs.584957	NM_022371	ENSG00000186283	TOR3A	ADIR|ADIR2	torsin family 3 member A	protein-coding	0.009921	0.409901	
chunk0174_266_1	chr6	161331290	161331949	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-57544	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.004552	0.368182	551(ATGTACTTTATGTTCT,-,0.00),552(TGTACTTTATGTTCTT,+,0.00)
chunk0208_299_1	chrX	22808393	22808977	+	0	NA	intron (NR_073010, intron 3 of 5)	L1MA8|LINE|L1	-191276	NM_182699	168400	Hs.434416	NM_182699	ENSG00000184735	DDX53	CAGE|CT26	DEAD-box helicase 53	protein-coding	0.001712	0.326496	150(TAGTACTGGATGTCCT,-,0.00),151(AGTACTGGATGTCCTA,+,0.00)
chunk0191_16_1	chr8	42642411	42642816	+	0	NA	Intergenic	Intergenic	-54806	NM_000749	1142	Hs.654576	NM_000749	ENSG00000147432	CHRNB3	-	cholinergic receptor nicotinic beta 3 subunit	protein-coding	0.004938	0.490148	
chunk0157_409_1	chr5	124465392	124465955	+	0	NA	Intergenic	(TGAA)n|Simple_repeat|Simple_repeat	-27153	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005329	0.370567	
chunk0069_261_1	chr15	64589011	64589268	+	0	NA	intron (NM_015042, intron 1 of 8)	intron (NM_015042, intron 1 of 8)	89719	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.426357	
chunk0157_254_1	chr5	119879405	119880199	+	0	NA	Intergenic	Intergenic	250243	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.003778	0.329560	
chunk0094_125_1	chr2	4594610	4594861	+	0	NA	Intergenic	Intergenic	61487	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.000000	0.345238	192(CAGTACAGTCAGTACA,-,0.00),193(AGTACAGTCAGTACAT,+,0.00)
chunk0055_130_1	chr13	58185914	58186240	+	0	NA	intron (NR_120416, intron 1 of 2)	MIRc|SINE|MIR	20250	NR_120416	101926897	Hs.640215	NR_120416	ENSG00000277448	LINC02338	-	long intergenic non-protein coding RNA 2338	ncRNA	0.003067	0.342508	
chunk0188_191_1	chr8	11748264	11748557	+	0	NA	intron (NM_002052, intron 2 of 6)	intron (NM_002052, intron 2 of 6)	-12846	NR_103552									0.003413	0.377551	
chunk0136_109_1	chr4	3320389	3320991	+	0	NA	intron (NM_198229, intron 2 of 17)	intron (NM_198229, intron 2 of 17)	6543	NM_002926	6002	Hs.527061	NM_002926	ENSG00000159788	RGS12	-	regulator of G protein signaling 12	protein-coding	0.029900	0.557214	
chunk0020_90_1	chr1	232816405	232816809	+	0	NA	Intergenic	Intergenic	11715	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.004950	0.358025	
chunk0022_30_1	chr10	7942229	7942469	+	0	NA	intron (NM_031923, intron 2 of 6)	intron (NM_031923, intron 2 of 6)	110142	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.012500	0.273859	
chunk0037_334_1	chr11	77252821	77253327	+	0	NA	intron (NM_182833, intron 10 of 15)	L1M2a|LINE|L1	34344	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.003953	0.500986	
chunk0067_395_1	chr15	49157709	49157968	+	0	NA	non-coding (NR_036507, exon 1 of 1)	non-coding (NR_036507, exon 1 of 1)	1540	NR_036507	100306975	Hs.692164	NR_036507		NDUFAF4P1	-	NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 1	pseudo	0.003861	0.369231	
chunk0050_438_1	chr12	110339196	110339932	+	0	NA	exon (NM_001681, exon 13 of 21)	exon (NM_001681, exon 13 of 21)	58337	NM_001681	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.010870	0.407056	
chunk0197_99_1	chr8	119672246	119672893	+	0	NA	Intergenic	Intergenic	-33703	NM_001040092	5168	Hs.190977	NM_006209	ENSG00000136960	ENPP2	ATX|ATX-X|AUTOTAXIN|LysoPLD|NPP2|PD-IALPHA|PDNP2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.034003	0.509259	420(AGAAACTGGCTGTGCC,-,0.00)
chunk0084_42_1	chr17	73956101	73956687	+	0	NA	Intergenic	Intergenic	-127857	NR_027146	283982	Hs.464079	NM_182564		LINC00469	C17orf54	long intergenic non-protein coding RNA 469	ncRNA	0.008532	0.478705	
chunk0099_1_1	chr2	82521394	82521593	+	0	NA	Intergenic	Intergenic	-335310	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.000000	0.305000	
chunk0028_412_1	chr10	93421533	93422130	+	0	NA	intron (NM_013451, intron 5 of 53)	MSTB1|LTR|ERVL-MaLR	60486	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.011725	0.441472	
chunk0093_221_1	chr19	50010044	50010684	+	0	NA	intron (NM_001308420, intron 3 of 12)	L1MEd|LINE|L1	15022	NM_001308420	51231	Hs.443330	NM_016440	ENSG00000105053	VRK3	-	VRK serine/threonine kinase 3	protein-coding	0.006250	0.379095	
chunk0106_226_1	chr2	202589311	202589620	+	0	NA	Intergenic	L1PA17|LINE|L1	-45713	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.006472	0.564516	
chunk0167_224_1	chr6	66848228	66848834	+	0	NA	Intergenic	Intergenic	1060652	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.004950	0.304778	
chunk0030_395_1	chr10	119894041	119894390	+	0	NA	intron (NR_037771, intron 1 of 17)	intron (NR_037771, intron 1 of 17)	1642	NM_007190	11196	Hs.435004	NM_007190	ENSG00000107651	SEC23IP	MSTP053|P125|P125A	SEC23 interacting protein	protein-coding	0.008596	0.397143	
chunk0051_233_1	chr12	116980075	116980417	+	0	NA	intron (NR_103809, intron 3 of 3)	MLT1O|LTR|ERVL-MaLR	7091	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.002924	0.451895	
chunk0126_60_1	chr3	74348908	74349565	+	0	NA	intron (NM_020872, intron 10 of 21)	L2c|LINE|L2	171904	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.001522	0.369301	
chunk0142_438_1	chr4	105203264	105203827	+	0	NA	intron (NM_017628, intron 2 of 2)	intron (NM_017628, intron 2 of 2)	56860	NM_001127208	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.005329	0.340426	
chunk0207_218_1	chr9	131636021	131636308	+	0	NA	intron (NM_198679, intron 5 of 23)	L2c|LINE|L2	73678	NM_198679	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.010453	0.489583	
chunk0192_451_1	chr8	70163662	70163861	+	0	NA	intron (NM_006540, intron 7 of 22)	intron (NM_006540, intron 7 of 22)	-92434	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.025126	0.455000	22(GAAACACTATGTACCT,+,0.00)
chunk0198_443_1	chr8	143894955	143895444	+	0	NA	Intergenic	L1MC5|LINE|L1	-16735	NM_031308	83481	Hs.200412	NM_031308	ENSG00000261150	EPPK1	EPIPL|EPIPL1	epiplakin 1	protein-coding	0.030675	0.465306	
chunk0186_371_1	chr7	143972653	143973282	+	0	NA	Intergenic	Intergenic	13040	NM_012369	26211	Hs.553595	NM_012369	ENSG00000213215	OR2F1	7M1-2|OLF3|OR14-60|OR2F3|OR2F3P|OR2F4|OR2F5|OR7-139|OR7-140	olfactory receptor family 2 subfamily F member 1 (gene/pseudogene)	protein-coding	0.001590	0.298413	
chunk0211_323_1	chrX	123881315	123881703	+	0	NA	intron (NR_037916, intron 1 of 5)	intron (NR_037916, intron 1 of 5)	21342	NR_037916	331	Hs.356076	NM_001167	ENSG00000101966	XIAP	API3|BIRC4|IAP-3|ILP1|MIHA|XLP2|hIAP-3|hIAP3	X-linked inhibitor of apoptosis	protein-coding	0.000000	0.357326	
chunk0202_393_1	chr9	81224474	81224788	+	0	NA	Intergenic	Intergenic	464904	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.009554	0.463492	
chunk0020_287_1	chr1	237029381	237029690	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-12867	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.006472	0.400000	
chunk0155_196_1	chr5	94709280	94709684	+	0	NA	intron (NM_024717, intron 21 of 22)	intron (NM_024717, intron 21 of 22)	90796	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.002475	0.395062	
chunk0109_394_1	chr2	240237117	240237316	+	0	NA	Intergenic	Intergenic	-96560	NM_148961	150677	Hs.148586	NM_148961	ENSG00000178602	OTOS	OTOSP	otospiralin	protein-coding	0.000000	0.405000	
chunk0161_445_1	chr5	178676318	178676875	+	0	NA	Intergenic	L1MD2|LINE|L1	-49543	NM_020666	57396	Hs.406557	NM_020666	ENSG00000113240	CLK4	-	CDC like kinase 4	protein-coding	0.010772	0.372760	
chunk0172_334_1	chr6	138492764	138493609	+	0	NA	intron (NM_020464, intron 2 of 6)	intron (NM_020464, intron 2 of 6)	6256	NM_001144060	57224	Hs.652741	NM_020464	ENSG00000135540	NHSL1	C6orf63	NHS like 1	protein-coding	0.007101	0.322695	
chunk0073_238_1	chr16	11506379	11506707	+	0	NA	Intergenic	Intergenic	41283	NR_110907	101927131	Hs.569654	NR_110907	ENSG00000262999	LOC101927131	-	uncharacterized LOC101927131	ncRNA	0.021341	0.562310	
chunk0052_371_1	chr12	128717191	128717390	+	0	NA	Intergenic	Intergenic	106706	NM_145648	121260	Hs.507260	NM_145648	ENSG00000139370	SLC15A4	FP12591|PHT1|PTR4	solute carrier family 15 member 4	protein-coding	0.010050	0.505000	
chunk0191_41_1	chr8	43140986	43141185	+	0	NA	intron (NM_152419, intron 1 of 17)	CpG	636	NM_152419	138050	Hs.600384	NM_152419	ENSG00000165102	HGSNAT	HGNAT|MPS3C|RP73|TMEM76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding	0.105528	0.725000	
chunk0157_382_1	chr5	124000267	124000848	+	0	NA	Intergenic	Intergenic	437963	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.006885	0.360825	
chunk0123_59_1	chr3	41199232	41199777	+	0	NA	promoter-TSS (NM_001904)	promoter-TSS (NM_001904)	53	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.122936	0.732601	
chunk0165_328_1	chr6	37259739	37260011	+	0	NA	intron (NR_130108, intron 1 of 12)	MIRb|SINE|MIR	-1720	NR_104442	221468	Hs.520101	NM_145316	ENSG00000172738	TMEM217	C6orf128|dJ355M6.2	transmembrane protein 217	protein-coding	0.003676	0.347985	
chunk0181_32_1	chr7	78412567	78412962	+	0	NA	intron (NM_001301128, intron 6 of 20)	MamRep434|DNA|TcMar-Tigger	65522	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.005063	0.373737	177(GAGAACAGTTTGTTAC,-,0.00)
chunk0064_267_1	chr14	94822883	94823143	+	0	NA	Intergenic	Intergenic	-52851	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.003846	0.490421	
chunk0064_276_1	chr14	95141668	95142110	+	0	NA	intron (NM_030621, intron 1 of 28)	intron (NM_030621, intron 1 of 28)	-3903	NR_036131	100422981		NR_036131	ENSG00000264607	MIR3173	mir-3173	microRNA 3173	ncRNA	0.002262	0.316027	
chunk0076_259_1	chr16	69298770	69299147	+	0	NA	intron (NM_006750, intron 5 of 6)	L2b|LINE|L2	-12426	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.013263	0.468254	
chunk0024_400_1	chr10	45122601	45123306	+	0	NA	intron (NR_024472, intron 5 of 8)	intron (NR_024472, intron 5 of 8)	31643	NR_024472	100133308	Hs.434365	NR_024472		RSU1P2	-	Ras suppressor protein 1 pseudogene 2	pseudo	0.008511	0.324363	
chunk0161_65_1	chr5	166535809	166536394	+	0	NA	Intergenic	Intergenic	390269	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.001709	0.313993	
chunk0139_354_1	chr4	60140682	60141017	+	0	NA	Intergenic	LTR108a_Mam|LTR|ERVL	-781770	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.002985	0.333333	
chunk0074_315_1	chr16	30556095	30556478	+	0	NA	intron (NM_033410, intron 2 of 2)	intron (NM_033410, intron 2 of 2)	2035	NM_001172679	92595	Hs.132227	NM_033410	ENSG00000169951	ZNF764	-	zinc finger protein 764	protein-coding	0.026110	0.593750	
chunk0165_454_1	chr6	40918089	40918665	+	0	NA	intron (NR_110873, intron 1 of 5)	L2b|LINE|L2	104903	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.008681	0.514731	
chunk0142_361_1	chr4	101921220	101921848	+	0	NA	intron (NM_017935, intron 7 of 16)	intron (NM_017935, intron 7 of 16)	107708	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.007962	0.311606	
chunk0205_314_1	chr9	112688211	112688484	+	0	NA	intron (NM_021218, intron 4 of 4)	intron (NM_021218, intron 4 of 4)	29760	NM_021218	58493	Hs.658575	NM_021218	ENSG00000148153	INIP	C9orf80|HSPC043|MISE|SOSSC|SSBIP1|hSSBIP1	INTS3 and NABP interacting protein	protein-coding	0.003663	0.408759	
chunk0165_209_1	chr6	34953643	34953946	+	0	NA	intron (NM_015245, intron 1 of 23)	intron (NM_015245, intron 1 of 23)	64533	NM_015245	23294	Hs.656492	NM_015245	ENSG00000064999	ANKS1A	ANKS1	ankyrin repeat and sterile alpha motif domain containing 1A	protein-coding	0.003300	0.434211	
chunk0078_82_1	chr17	1966623	1966827	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	58620	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.014706	0.546341	81(AGGACACAGAGATCCT,+,0.00)
chunk0179_271_1	chr7	49346262	49346721	+	0	NA	Intergenic	L2|LINE|L2	421930	NR_003595									0.002179	0.380435	
chunk0199_452_1	chr9	14106449	14107303	+	0	NA	intron (NM_001282787, intron 9 of 10)	intron (NM_001282787, intron 9 of 10)	73926	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.003513	0.353216	
chunk0045_197_1	chr12	47561606	47561895	+	0	NA	Intergenic	Intergenic	144311	NM_001146076	79657	Hs.437855	NM_024604	ENSG00000005175	RPAP3	Tah1|hSpagh	RNA polymerase II associated protein 3	protein-coding	0.006920	0.427586	
chunk0206_410_1	chr9	127433408	127433655	+	0	NA	intron (NM_001286698, intron 2 of 2)	intron (NM_001286698, intron 2 of 2)	9157	NM_001286696	7633	Hs.522399	NM_007135	ENSG00000196152	ZNF79	pT7	zinc finger protein 79	protein-coding	0.012146	0.483871	
chunk0084_365_1	chr17	81576445	81577205	+	0	NA	intron (NM_017921, intron 12 of 16)	intron (NM_017921, intron 12 of 16)	608	NR_130139	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.018421	0.484888	484(AGGACACACAGACCCT,+,0.00)
chunk0210_382_1	chrX	97531837	97532486	+	0	NA	intron (NR_125391, intron 2 of 2)	intron (NR_125391, intron 2 of 2)	32374	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.007704	0.338462	
chunk0112_323_1	chr20	44780106	44780551	+	0	NA	intron (NM_001205317, intron 1 of 5)	intron (NM_001205317, intron 1 of 5)	30010	NM_182970	140730	Hs.517065	NM_182970	ENSG00000101098	RIMS4	C20orf190|RIM 4|RIM-4|RIM4|RIM4-gamma|RIM4gamma	regulating synaptic membrane exocytosis 4	protein-coding	0.013483	0.443946	
chunk0077_281_1	chr16	81165588	81165915	+	0	NA	intron (NR_126532, intron 19 of 42)	intron (NR_126532, intron 19 of 42)	15611	NM_001278423	114780	Hs.413525	NM_052892	ENSG00000166473	PKD1L2	PC1L2	polycystin 1 like 2 (gene/pseudogene)	protein-coding	0.009174	0.576220	
chunk0048_85_1	chr12	79111879	79112115	+	0	NA	intron (NM_001135805, intron 4 of 11)	intron (NM_001135805, intron 4 of 11)	66344	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.008475	0.312236	
chunk0146_212_1	chr4	161554450	161554723	+	0	NA	intron (NM_001128427, intron 8 of 15)	intron (NM_001128427, intron 8 of 15)	-468147	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.007326	0.364964	
chunk0143_142_1	chr4	109914402	109914920	+	0	NA	intron (NM_001963, intron 1 of 23)	L2b|LINE|L2	1777	NM_001178130	1950	Hs.419815	NM_001963	ENSG00000138798	EGF	HOMG4|URG	epidermal growth factor	protein-coding	0.005792	0.441233	
chunk0084_247_1	chr17	78934297	78934519	+	0	NA	Intergenic	Intergenic	-9018	NM_003255	7077	Hs.633514	NM_003255	ENSG00000035862	TIMP2	CSC-21K|DDC8	TIMP metallopeptidase inhibitor 2	protein-coding	0.027027	0.565022	
chunk0063_159_1	chr14	80152978	80153392	+	0	NA	Intergenic	Intergenic	-58234	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.004831	0.286747	
chunk0040_104_1	chr11	111840157	111840468	+	0	NA	intron (NM_024740, intron 10 of 14)	intron (NM_024740, intron 10 of 14)	30969	NM_001077692	79796	Hs.745155	NM_024740	ENSG00000086848	ALG9	CDG1L|DIBD1|GIKANIS|LOH11CR1J	ALG9 alpha-1,2-mannosyltransferase	protein-coding	0.003215	0.429487	
chunk0008_99_1	chr1	91016076	91016684	+	0	NA	intron (NM_032186, intron 1 of 3)	Tigger3a|DNA|TcMar-Tigger	5128	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.001645	0.353038	
chunk0046_308_1	chr12	62325304	62325858	+	0	NA	intron (NM_006313, intron 5 of 20)	L2a|LINE|L2	65222	NR_106740	102465133		NR_106740	ENSG00000284360	MIR6125	hsa-mir-6125|mir-6125	microRNA 6125	ncRNA	0.005415	0.295495	
chunk0178_187_1	chr7	34298699	34299010	+	0	NA	Intergenic	Intergenic	-359385	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.009646	0.426282	
chunk0194_94_1	chr8	83129981	83130428	+	0	NA	Intergenic	Intergenic	-273554	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.002237	0.345982	
chunk0064_345_1	chr14	96690750	96691052	+	0	NA	Intergenic	L2b|LINE|L2	-106446	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.013245	0.521452	
chunk0101_393_1	chr2	138724861	138725347	+	0	NA	intron (NM_007226, intron 1 of 1)	intron (NM_007226, intron 1 of 1)	55137	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.004115	0.338809	
chunk0098_407_1	chr2	79892091	79892603	+	0	NA	intron (NM_004389, intron 6 of 17)	intron (NM_004389, intron 6 of 17)	-25764	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.003906	0.292398	248(TGAAACATTGTGTCCC,-,0.00),249(GAAACATTGTGTCCCT,+,0.00)
chunk0059_372_1	chr14	37363403	37363932	+	0	NA	intron (NM_001195296, intron 11 of 14)	L1PA6|LINE|L1	165754	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.017013	0.530189	
chunk0098_173_1	chr2	71129444	71130136	+	0	NA	promoter-TSS (NM_005791)	promoter-TSS (NM_005791)	474	NM_032601	84693	Hs.94949	NM_032601	ENSG00000124370	MCEE	GLOD2	methylmalonyl-CoA epimerase	protein-coding	0.043353	0.484848	
chunk0184_71_1	chr7	112572391	112573284	+	0	NA	Intergenic	Intergenic	-45228	NR_110159	100996249	Hs.561749	NR_110159		LOC100996249	-	uncharacterized LOC100996249	ncRNA	0.001120	0.383669	
chunk0176_448_1	chr7	20077371	20077656	+	0	NA	intron (NR_110114, intron 1 of 5)	Tigger3a|DNA|TcMar-Tigger	62913	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.007018	0.328671	
chunk0005_115_1	chr1	56733578	56733840	+	0	NA	intron (NM_001004303, intron 15 of 19)	L1P1|LINE|L1	85987	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.003817	0.365019	
chunk0018_401_1	chr1	222622741	222623327	+	0	NA	intron (NM_198551, intron 2 of 27)	intron (NM_198551, intron 2 of 27)	4932	NM_198551	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.010239	0.402044	
chunk0148_26_1	chr5	614719	615021	+	0	NA	intron (NM_018140, intron 1 of 11)	L1MDa|LINE|L1	2580	NM_018140	55722	Hs.591741	NM_018140	ENSG00000112877	CEP72	-	centrosomal protein 72	protein-coding	0.000000	0.353135	
chunk0074_236_1	chr16	27334381	27334593	+	0	NA	intron (NM_000418, intron 2 of 10)	intron (NM_000418, intron 2 of 10)	20578	NM_001257406	3566	Hs.513457	NM_000418	ENSG00000077238	IL4R	CD124|IL-4RA|IL4RA	interleukin 4 receptor	protein-coding	0.028302	0.507042	
chunk0174_76_1	chr6	156098655	156099096	+	0	NA	Intergenic	Intergenic	152078	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.006803	0.346154	
chunk0091_13_1	chr19	2933703	2934283	+	0	NA	exon (NM_021217, exon 4 of 4)	exon (NM_021217, exon 4 of 4)	10978	NM_021217	58492	Hs.38004	NM_021217	ENSG00000175691	ZNF77	pT1	zinc finger protein 77	protein-coding	0.037931	0.490534	
chunk0013_44_1	chr1	166989458	166989657	+	0	NA	intron (NM_001286377, intron 1 of 10)	intron (NM_001286377, intron 1 of 10)	468	NM_001286377	84944	Hs.651245	NM_032858	ENSG00000143194	MAEL	CT128|SPATA35	maelstrom spermatogenic transposon silencer	protein-coding	0.040201	0.655000	
chunk0059_49_1	chr14	29991930	29992388	+	0	NA	Intergenic	L1ME3A|LINE|L1	-64466	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.002183	0.305011	
chunk0197_462_1	chr8	127923633	127924056	+	0	NA	intron (NR_003367, intron 2 of 8)	intron (NR_003367, intron 2 of 8)	24879	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.021277	0.523585	
chunk0131_427_1	chr3	153596951	153597662	+	0	NA	Intergenic	Intergenic	112811	NM_001101337									0.002813	0.262640	
chunk0155_160_1	chr5	94182633	94183134	+	0	NA	intron (NM_001145678, intron 20 of 20)	L2b|LINE|L2	-71184	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.000000	0.346614	
chunk0205_242_1	chr9	110151530	110152065	+	0	NA	intron (NM_001004065, intron 2 of 3)	L5|LINE|RTE-X	26296	NM_001136562	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.016822	0.444030	361(TGGCACTGTGTGTTCA,-,0.00),362(GGCACTGTGTGTTCAT,+,0.00)
chunk0117_273_1	chr22	24123474	24123981	+	0	NA	intron (NM_012295, intron 28 of 36)	intron (NM_012295, intron 28 of 36)	-57749	NM_019601	56241	Hs.131819	NM_019601	ENSG00000099994	SUSD2	BK65A6.2|W5C5	sushi domain containing 2	protein-coding	0.003945	0.517717	
chunk0004_100_1	chr1	43913207	43913559	+	0	NA	intron (NM_174966, intron 9 of 9)	MIRb|SINE|MIR	-19937	NM_057091	9048	Hs.632404	NM_003976	ENSG00000117407	ARTN	ART|ENOVIN|EVN|NBN	artemin	protein-coding	0.011364	0.458924	202(GAGGACACAATGTGCC,-,0.00),203(AGGACACAATGTGCCC,+,0.00)
chunk0071_135_1	chr15	82041020	82041261	+	0	NA	TTS (NM_032246)	TTS (NM_032246)	5003	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.012448	0.495868	
chunk0166_418_1	chr6	52552302	52552518	+	0	NA	intron (NM_012288, intron 1 of 10)	intron (NM_012288, intron 1 of 10)	24654	NM_012288	9697	Hs.520182	NM_012288	ENSG00000065308	TRAM2	-	translocation associated membrane protein 2	protein-coding	0.013889	0.511521	
chunk0019_283_1	chr1	228728043	228728911	+	0	NA	intron (NR_037962, intron 1 of 2)	intron (NR_037962, intron 1 of 2)	-6600	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.002304	0.361335	433(CAGTACTTCATGTTCC,-,0.00),434(AGTACTTCATGTTCCT,+,0.00)
chunk0211_457_1	chrX	130197412	130198030	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	25922	NM_004794	9363	Hs.654356	NM_004794	ENSG00000134594	RAB33A	RabS10	RAB33A, member RAS oncogene family	protein-coding	0.009709	0.434572	276(AAAAACACATTGTACT,-,0.00)
chunk0145_440_1	chr4	153398767	153399140	+	0	NA	intron (NR_045605, intron 8 of 9)	intron (NR_045605, intron 8 of 9)	54304	NM_032117	84057	Hs.294088	NM_032117	ENSG00000121211	MND1	GAJ	meiotic nuclear divisions 1	protein-coding	0.008043	0.393048	173(TAGAACATTGTGTACC,-,0.00),174(AGAACATTGTGTACCT,+,0.00)
chunk0200_154_1	chr9	18349773	18350373	+	0	NA	Intergenic	Intergenic	-124008	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.005000	0.462562	
chunk0099_200_1	chr2	94583385	94583595	+	0	NA	intron (NR_024443, intron 2 of 3)	intron (NR_024443, intron 2 of 3)	3693	NR_024443	100133920	Hs.645503	NR_024443	ENSG00000261522	LOC100133920	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like pseudogene	pseudo	0.004762	0.407583	
chunk0208_80_1	chrX	13002335	13002604	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	27362	NM_021109	7114	Hs.437277	NM_021109	ENSG00000205542	TMSB4X	FX|PTMB4|TB4X|TMSB4	thymosin beta 4 X-linked	protein-coding	0.007435	0.407407	
chunk0163_7_1	chr6	7687713	7688465	+	0	NA	Intergenic	L1ME1|LINE|L1	-38689	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.007979	0.371846	
chunk0146_344_1	chr4	166128424	166128892	+	0	NA	Intergenic	Intergenic	255400	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.004274	0.368870	
chunk0092_196_1	chr19	30630286	30630680	+	0	NA	Intergenic	Intergenic	258090	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.020305	0.521519	
chunk0206_424_1	chr9	127578661	127579223	+	0	NA	promoter-TSS (NM_001035534)	promoter-TSS (NM_001035534)	65	NM_001035534	64855	Hs.522401	NM_022833	ENSG00000136830	NIBAN2	C9orf88|FAM129B|MEG-3|MINERVA|OC58|bA356B19.6	niban apoptosis regulator 2	protein-coding	0.017794	0.545293	
chunk0195_371_1	chr8	99965749	99966372	+	0	NA	intron (NM_001286692, intron 23 of 27)	intron (NM_001286692, intron 23 of 27)	58024	NR_031675									0.003210	0.315705	
chunk0048_126_1	chr12	79869464	79869819	+	0	NA	intron (NM_001244990, intron 3 of 24)	intron (NM_001244990, intron 3 of 24)	44270	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.002817	0.370787	
chunk0026_325_1	chr10	68221387	68221693	+	0	NA	Intergenic	Intergenic	10573	NM_145178	220202	Hs.175396	NM_145178	ENSG00000179774	ATOH7	Math5|NCRNA|PHPVAR|RNANC|bHLHa13	atonal bHLH transcription factor 7	protein-coding	0.000000	0.280130	
chunk0205_320_1	chr9	112772474	112772791	+	0	NA	intron (NM_001012994, intron 1 of 8)	intron (NM_001012994, intron 1 of 8)	21778	NM_001012994	401548	Hs.522350	NM_001012994	ENSG00000148158	SNX30	ATG24A	sorting nexin family member 30	protein-coding	0.015773	0.405660	
chunk0107_5_1	chr2	209771181	209771584	+	0	NA	promoter-TSS (NM_182587)	promoter-TSS (NM_182587)	-611	NM_032504	285175	Hs.396201	NM_032504	ENSG00000144406	UNC80	C2orf21|UNC-80	unc-80 homolog, NALCN channel complex subunit	protein-coding	0.014888	0.435644	
chunk0057_221_1	chr13	104130561	104131199	+	0	NA	Intergenic	Intergenic	705680	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.007837	0.312989	260(ATTACAGTGTGTTCTT,+,0.00)
chunk0018_8_1	chr1	215109402	215109986	+	0	NA	intron (NM_001017424, intron 2 of 6)	L1MA4A|LINE|L1	26477	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.008562	0.341880	288(CAGTACAATATGTCCC,-,0.00),289(AGTACAATATGTCCCT,+,0.00)
chunk0120_256_1	chr3	8965126	8965503	+	0	NA	Intergenic	Intergenic	-1839	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.010610	0.428571	204(AAAAACAAAATGTTCC,-,0.00),205(AAAACAAAATGTTCCA,+,0.00)
chunk0177_240_1	chr7	24830662	24830982	+	0	NA	exon (NM_145320, exon 14 of 21)	exon (NM_145320, exon 14 of 21)	61799	NM_145321	26031	Hs.520259	NM_015550	ENSG00000070882	OSBPL3	ORP-3|ORP3|OSBP3	oxysterol binding protein like 3	protein-coding	0.015625	0.411215	
chunk0208_245_1	chrX	20101940	20102623	+	0	NA	intron (NM_152780, intron 1 of 15)	intron (NM_152780, intron 1 of 15)	14357	NM_001168467	256714	Hs.127951	NM_152780	ENSG00000184368	MAP7D2	-	MAP7 domain containing 2	protein-coding	0.002928	0.409357	461(GAGAACAGCATGTACA,-,0.00),462(AGAACAGCATGTACAC,+,0.00)
chunk0108_129_1	chr2	229944275	229944594	+	0	NA	intron (NM_174899, intron 1 of 3)	intron (NM_174899, intron 1 of 3)	21943	NM_174899	130888	Hs.140666	NM_174899	ENSG00000153832	FBXO36	Fbx36	F-box protein 36	protein-coding	0.006270	0.293750	
chunk0008_112_1	chr1	91537773	91537972	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	36764	NM_001134420	8317	Hs.533573	NM_003503	ENSG00000097046	CDC7	CDC7L1|HsCDC7|Hsk1|huCDC7	cell division cycle 7	protein-coding	0.000000	0.420000	140(AAGAACACTGTGTTCC,-,0.00),141(AGAACACTGTGTTCCT,+,0.00)
chunk0185_184_1	chr7	128200077	128200551	+	0	NA	Intergenic	L2c|LINE|L2	-7558	NR_029596	406917		NR_029596	ENSG00000207705	MIR129-1	MIR-129b|MIRN129-1|mir-129-1	microRNA 129-1	ncRNA	0.012658	0.486316	
chunk0158_127_1	chr5	127112743	127113235	+	0	NA	Intergenic	L1PA16|LINE|L1	-39497	NM_001164479	401207	Hs.49573	NM_001164478	ENSG00000164241	C5orf63	YDR286C	chromosome 5 open reading frame 63	protein-coding	0.004065	0.395538	62(AAAGACATAATGTACT,-,0.00),63(AAGACATAATGTACTC,+,0.00)
chunk0022_78_1	chr10	8850866	8851334	+	0	NA	Intergenic	L1MA7|LINE|L1	-46889	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.000000	0.368870	214(AAGGACATTATGTTCC,-,0.00),215(AGGACATTATGTTCCA,+,0.00)
chunk0200_58_1	chr9	15684354	15684942	+	0	NA	intron (NM_173550, intron 10 of 25)	intron (NM_173550, intron 10 of 25)	131549	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.005102	0.307301	
chunk0150_331_1	chr5	38469128	38469337	+	0	NA	Intergenic	Intergenic	23756	NM_182801	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.014354	0.485714	68(GAGAACATTATGTCTC,-,0.00),69(AGAACATTATGTCTCA,+,0.00)
chunk0070_374_1	chr15	76367942	76368325	+	0	NA	intron (NM_020843, intron 28 of 30)	intron (NM_020843, intron 28 of 30)	31409	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.007833	0.434896	177(GAGAACAGAAAGTCCT,-,0.00),178(AGAACAGAAAGTCCTT,+,0.00)
chunk0076_178_1	chr16	67461582	67462350	+	0	NA	intron (NM_004691, intron 1 of 7)	intron (NM_004691, intron 1 of 7)	19220	NM_004691	9114	Hs.106876	NM_004691	ENSG00000159720	ATP6V0D1	ATP6D|ATP6DV|P39|VATX|VMA6|VPATPD	ATPase H+ transporting V0 subunit d1	protein-coding	0.011719	0.565670	54(AAAGACAGTAAGTTCT,-,0.00),55(AAGACAGTAAGTTCTC,+,0.00),356(AGGAACACCTTGTCCC,-,0.00),357(GGAACACCTTGTCCCT,+,0.00)
chunk0058_27_1	chr14	19918785	19919096	+	0	NA	Intergenic	Intergenic	-1667	NM_001005483	79317	Hs.554585	NM_001005483	ENSG00000176281	OR4K5	OR14-16	olfactory receptor family 4 subfamily K member 5	protein-coding	0.006431	0.294872	
chunk0026_46_1	chr10	60931923	60932399	+	0	NA	intron (NM_014836, intron 2 of 10)	intron (NM_014836, intron 2 of 10)	12114	NM_014836	9886	Hs.737374	NM_014836	ENSG00000072422	RHOBTB1	-	Rho related BTB domain containing 1	protein-coding	0.002101	0.366876	228(ATGTACACTCAGTGCC,-,0.00),229(TGTACACTCAGTGCCC,+,0.00)
chunk0138_213_1	chr4	38867155	38867408	+	0	NA	promoter-TSS (NM_138389)	promoter-TSS (NM_138389)	-452	NM_138389	92689	Hs.476517	NM_138389	ENSG00000197712	FAM114A1	Noxp20	family with sequence similarity 114 member A1	protein-coding	0.015810	0.425197	
chunk0167_210_1	chr6	65448368	65448971	+	0	NA	intron (NM_198283, intron 4 of 9)	intron (NM_198283, intron 4 of 9)	131135	NM_198283	346007	Hs.25067	NM_198283	ENSG00000188107	EYS	C6orf178|C6orf179|C6orf180|EGFL10|EGFL11|RP25|SPAM|bA166P24.2|bA307F22.3|bA74E24.1|dJ1018A4.2|dJ22I17.2|dJ303F19.1	eyes shut homolog	protein-coding	0.000000	0.298013	
chunk0024_193_1	chr10	36177969	36178579	+	0	NA	Intergenic	L2c|LINE|L2	399972	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.003279	0.369885	
chunk0112_457_1	chr20	48945726	48946216	+	0	NA	intron (NM_006420, intron 3 of 38)	intron (NM_006420, intron 3 of 38)	24233	NM_006420	10564	Hs.62578	NM_006420	ENSG00000124198	ARFGEF2	BIG2|PVNH2|dJ1164I10.1	ADP ribosylation factor guanine nucleotide exchange factor 2	protein-coding	0.008163	0.470468	
chunk0125_135_1	chr3	65953430	65953739	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	59768	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.012945	0.535484	
chunk0011_284_1	chr1	151435250	151435544	+	0	NA	intron (NM_001194938, intron 2 of 17)	intron (NM_001194938, intron 2 of 17)	6808	NM_207171	23126	Hs.489873	NM_015100	ENSG00000143442	POGZ	MRD37|WHSUS|ZNF280E|ZNF635|ZNF635m	pogo transposable element derived with ZNF domain	protein-coding	0.000000	0.294915	
chunk0115_390_1	chr21	30472132	30472331	+	0	NA	Intergenic	Intergenic	8086	NM_181607	337882	Hs.61552	NM_181607	ENSG00000184351	KRTAP19-1	KAP19.1	keratin associated protein 19-1	protein-coding	0.010050	0.390000	
chunk0063_278_1	chr14	84230177	84230497	+	0	NA	Intergenic	Intergenic	-1163542	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.006250	0.367601	
chunk0087_369_1	chr18	41490977	41491243	+	0	NA	intron (NR_002838, intron 3 of 5)	L2a|LINE|L2	29487	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.000000	0.367041	
chunk0013_227_1	chr1	169548432	169548631	+	0	NA	intron (NM_000130, intron 10 of 24)	intron (NM_000130, intron 10 of 24)	38000	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.005025	0.400000	
chunk0045_170_1	chr12	46872202	46872456	+	0	NA	Intergenic	L2b|LINE|L2	-46332	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.011811	0.443137	
chunk0070_232_1	chr15	72975195	72975501	+	0	NA	Intergenic	Intergenic	-77136	NM_001172624	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.003268	0.540717	
chunk0208_367_1	chrX	26286526	26286835	+	0	NA	Intergenic	L1PA6|LINE|L1	70511	NM_001271752	347541	Hs.224079	NM_001271752	ENSG00000188408	MAGEB5	CT3.3|MAGE-B5	MAGE family member B5	protein-coding	0.016181	0.525806	
chunk0208_376_1	chrX	27967167	27967878	+	0	NA	Intergenic	Intergenic	13927	NM_001017930	139425	Hs.447365	NM_001017930	ENSG00000226372	DCAF8L1	WDR42B	DDB1 and CUL4 associated factor 8 like 1	protein-coding	0.004219	0.358146	
chunk0146_8_1	chr4	154959096	154959340	+	0	NA	Intergenic	L1ME1|LINE|L1	177713	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.008197	0.469388	
chunk0124_384_1	chr3	59605724	59606605	+	0	NA	Intergenic	Intergenic	-556175	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.009081	0.421769	394(TTGGACAGGTTGTACC,-,0.00),395(TGGACAGGTTGTACCC,+,0.00)
chunk0095_104_1	chr2	15413306	15413505	+	0	NA	intron (NR_052013, intron 25 of 50)	L2c|LINE|L2	147943	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.000000	0.380000	
chunk0102_385_1	chr2	154587746	154588511	+	0	NA	Intergenic	MIR|SINE|MIR	-110453	NM_002239	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.003922	0.395561	518(ATGAACTGAATGTTCC,-,0.00),519(TGAACTGAATGTTCCC,+,0.00)
chunk0032_240_1	chr11	7908227	7908579	+	0	NA	Intergenic	LTR23|LTR|ERV1	-2448	NR_036678	283299	Hs.501825	NM_001190788	ENSG00000254951	LOC283299	-	uncharacterized LOC283299	ncRNA	0.000000	0.388102	162(AAAGACATTTTGTTCC,-,0.00),163(AAGACATTTTGTTCCT,+,0.00)
chunk0176_380_1	chr7	18602705	18602989	+	0	NA	intron (NM_001204147, intron 5 of 9)	L1MC2|LINE|L1	93570	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.003521	0.322807	119(TACACATTCTGTTCCT,+,0.00)
chunk0130_210_1	chr3	133963622	133964090	+	0	NA	intron (NM_005630, intron 3 of 13)	intron (NM_005630, intron 3 of 13)	-34044	NM_025041	80111	Hs.287691	NM_025041	ENSG00000174640	C3orf36	-	chromosome 3 open reading frame 36	ncRNA	0.004274	0.445629	272(TGGAACAGACTGTCCC,-,0.00),273(GGAACAGACTGTCCCA,+,0.00)
chunk0069_102_1	chr15	61421706	61422335	+	0	NA	Intergenic	L2b|LINE|L2	-192717	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.003180	0.420635	280(AAGAACATTCTGCTCC,-,0.00),281(AGAACATTCTGCTCCT,+,0.00)
chunk0078_398_1	chr16	88686689	88686895	+	0	NA	promoter-TSS (NM_178310)	promoter-TSS (NM_178310)	-318	NM_178310	333929	Hs.673548	NM_178310	ENSG00000185669	SNAI3	SMUC|SNAIL3|ZNF293|Zfp293	snail family transcriptional repressor 3	protein-coding	0.082524	0.623188	
chunk0005_32_1	chr1	54724997	54725196	+	0	NA	intron (NR_037639, intron 28 of 32)	L1M4|LINE|L1	9274	NM_001291333	7268	Hs.412482	NM_004623	ENSG00000243725	TTC4	CNS1	tetratricopeptide repeat domain 4	protein-coding	0.005025	0.510000	
chunk0171_68_1	chr6	121455278	121455790	+	0	NA	Intergenic	Intergenic	19957	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.023438	0.419103	
chunk0051_305_1	chr12	119053932	119054364	+	0	NA	intron (NM_194286, intron 1 of 12)	L1MA2|LINE|L1	72653	NM_194286	84530	Hs.744964	NM_194286	ENSG00000139767	SRRM4	KIAA1853|MU-MB-2.76|nSR100	serine/arginine repetitive matrix 4	protein-coding	0.009259	0.374134	369(GAGCACTCACTGTGCC,-,0.00),370(AGCACTCACTGTGCCA,+,0.00)
chunk0164_237_1	chr6	23269203	23269909	+	0	NA	Intergenic	Intergenic	700107	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007082	0.387553	
chunk0064_77_1	chr14	90396933	90397160	+	0	NA	promoter-TSS (NM_006888)	promoter-TSS (NM_006888)	63	NM_006888	801	Hs.282410	NM_006888	ENSG00000198668	CALM1	CALML2|CAM2|CAM3|CAMB|CAMC|CAMI|CAMIII|CPVT4|DD132|LQT14|PHKD|caM	calmodulin 1	protein-coding	0.158590	0.723684	
chunk0092_424_1	chr19	38070391	38071109	+	0	NA	intron (NM_015073, intron 2 of 21)	intron (NM_015073, intron 2 of 21)	153500	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.011142	0.485396	74(GGGCACAGTCTGTCCT,-,0.00),75(GGCACAGTCTGTCCTG,+,0.00)
chunk0168_157_1	chr6	83290256	83290532	+	0	NA	intron (NM_002395, intron 6 of 13)	L1PA7|LINE|L1	-96458	NM_001199917	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.007246	0.382671	61(GGTACATTGTGTCTTT,+,0.00)
chunk0085_393_1	chr18	9959157	9959356	+	0	NA	3' UTR (NM_003574, exon 7 of 7)	3' UTR (NM_003574, exon 7 of 7)	45298	NM_003574	9218	Hs.165195	NM_003574	ENSG00000101558	VAPA	VAP-33|VAP-A|VAP33|hVAP-33	VAMP associated protein A	protein-coding	0.000000	0.370000	
chunk0153_99_1	chr5	68406709	68406933	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	114253	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.013393	0.520000	
chunk0026_11_1	chr10	60490181	60490519	+	0	NA	intron (NM_001204403, intron 2 of 43)	MER5A|DNA|hAT-Charlie	82606	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005917	0.442478	
chunk0090_197_1	chr18	73168420	73168816	+	0	NA	intron (NR_034133, intron 3 of 5)	intron (NR_034133, intron 3 of 5)	95880	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.005051	0.345088	
chunk0073_189_1	chr16	9003367	9003832	+	0	NA	Intergenic	Intergenic	-40115	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.006452	0.429185	
chunk0023_24_1	chr10	21042765	21043358	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	103498	NM_001010896	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.005059	0.368687	
chunk0132_319_1	chr3	160804894	160805138	+	0	NA	intron (NM_139245, intron 1 of 3)	intron (NM_139245, intron 1 of 3)	48808	NM_139245	151742	Hs.389027	NM_139245	ENSG00000163590	PPM1L	PP2C-epsilon|PP2CE|PPM1-LIKE	protein phosphatase, Mg2+/Mn2+ dependent 1L	protein-coding	0.004098	0.542857	
chunk0193_409_1	chr8	80640044	80640685	+	0	NA	3' UTR (NM_001033723, exon 9 of 9)	3' UTR (NM_001033723, exon 9 of 9)	154151	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.007800	0.429907	
chunk0067_251_1	chr15	45706949	45707148	+	0	NA	Intergenic	AluSz|SINE|Alu	72308	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.010050	0.445000	165(TAGTACAGGCTGTTTC,-,0.00),166(AGTACAGGCTGTTTCT,+,0.00)
chunk0155_410_1	chr5	99331148	99331347	+	0	NA	Intergenic	Intergenic	-202743	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.000000	0.375000	
chunk0197_112_1	chr8	119883854	119884053	+	0	NA	intron (NM_001283012, intron 1 of 6)	intron (NM_001283012, intron 1 of 6)	10298	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.010050	0.440000	
chunk0087_270_1	chr18	37442457	37442931	+	0	NA	intron (NM_001025088, intron 2 of 12)	intron (NM_001025088, intron 2 of 12)	23810	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.023207	0.545263	207(GGAAACAGATTGTGCT,-,0.00),208(GAAACAGATTGTGCTG,+,0.00)
chunk0122_257_1	chr3	35033447	35033687	+	0	NA	intron (NR_110817, intron 2 of 3)	intron (NR_110817, intron 2 of 3)	360456	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.000000	0.311203	
chunk0052_148_1	chr13	23793351	23793893	+	0	NA	intron (NM_005932, intron 16 of 18)	L2a|LINE|L2	-95267	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.001845	0.425414	
chunk0014_1_1	chr1	174044485	174044803	+	0	NA	Intergenic	Intergenic	-51572	NM_172071	149041	Hs.30258	NM_172071	ENSG00000135870	RC3H1	RNF198|ROQUIN	ring finger and CCCH-type domains 1	protein-coding	0.003145	0.338558	
chunk0016_26_1	chr1	192907582	192907945	+	0	NA	Intergenic	Intergenic	40494	NR_126003	102724954	Hs.243488	NR_126003		LINC01032	-	long intergenic non-protein coding RNA 1032	ncRNA	0.002755	0.370879	
chunk0174_290_1	chr6	162250098	162250601	+	0	NA	intron (NM_013987, intron 3 of 10)	intron (NM_013987, intron 3 of 10)	-476783	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.005964	0.408730	
chunk0156_314_1	chr5	111011413	111011612	+	0	NA	Intergenic	Intergenic	-58568	NR_045089	85480	Hs.389874	NM_033035	ENSG00000145777	TSLP	-	thymic stromal lymphopoietin	protein-coding	0.005025	0.490000	
chunk0150_118_1	chr5	32935026	32935861	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	-12000	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.005988	0.345694	
chunk0201_385_1	chr9	68981872	68982122	+	0	NA	intron (NM_001278253, intron 13 of 13)	intron (NM_001278253, intron 13 of 13)	-6156	NR_110647	101927069	Hs.663405	NR_110647		LOC101927069	-	uncharacterized LOC101927069	ncRNA	0.016000	0.474104	
chunk0126_294_1	chr3	80564266	80564813	+	0	NA	Intergenic	Intergenic	-429329	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.003656	0.301095	277(CAGGACATTCTGCACC,-,0.00)
chunk0049_274_1	chr12	93813835	93814678	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-76433	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.015421	0.464455	
chunk0023_427_1	chr10	31669422	31669957	+	0	NA	Intergenic	LTR16A|LTR|ERVL	239237	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.001869	0.466418	
chunk0098_5_1	chr2	65017411	65018251	+	0	NA	intron (NM_003038, intron 5 of 7)	intron (NM_003038, intron 5 of 7)	28470	NM_003038	6509	Hs.654352	NM_003038	ENSG00000115902	SLC1A4	ASCT1|SATT|SPATCCM	solute carrier family 1 member 4	protein-coding	0.021429	0.444709	
chunk0082_314_1	chr17	59209867	59210089	+	0	NA	promoter-TSS (NM_018149)	promoter-TSS (NM_018149)	-32	NM_018149	55181	Hs.7296	NM_018149	ENSG00000167447	SMG8	C17orf71	SMG8 nonsense mediated mRNA decay factor	protein-coding	0.049550	0.479821	
chunk0183_218_1	chr7	106660996	106661347	+	0	NA	promoter-TSS (NM_175884)	promoter-TSS (NM_175884)	17	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.071225	0.642045	
chunk0154_405_1	chr5	88664497	88665035	+	0	NA	non-coding (NR_024384, exon 3 of 3)	non-coding (NR_024384, exon 3 of 3)	2173	NR_030741	407047		NR_030741	ENSG00000284447	MIR9-2	MIRN9-2|hsa-mir-9-2|miRNA9-2|mir-9-2	microRNA 9-2	ncRNA	0.003717	0.333952	
chunk0173_268_1	chr6	147231580	147232209	+	0	NA	intron (NM_001127715, intron 2 of 27)	intron (NM_001127715, intron 2 of 27)	-27280	NR_034115	729178	Hs.557608	NR_034115		STXBP5-AS1	-	STXBP5 antisense RNA 1	ncRNA	0.001590	0.296825	392(GGGAACATTTAGTTCT,-,0.00),393(GGAACATTTAGTTCTA,+,0.00)
chunk0025_68_1	chr10	49844857	49845389	+	0	NA	intron (NR_130169, intron 11 of 16)	L1MC4|LINE|L1	-82744	NM_001143997	55753	Hs.17860	NM_018245	ENSG00000197444	OGDHL	-	oxoglutarate dehydrogenase like	protein-coding	0.009398	0.341463	
chunk0106_13_1	chr2	195391328	195391741	+	0	NA	Intergenic	Intergenic	-265274	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.004843	0.321256	
chunk0186_148_1	chr7	139041434	139041689	+	0	NA	Intergenic	MIR|SINE|MIR	-5532	NM_080660	92092	Hs.512833	NM_080660	ENSG00000146858	ZC3HAV1L	C7orf39	zinc finger CCCH-type containing, antiviral 1 like	protein-coding	0.007843	0.480469	60(AGGTAGAGACTGTTCC,-,0.00),61(GGTAGAGACTGTTCCT,+,0.00)
chunk0011_352_1	chr1	152507215	152507488	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-3493	NM_178438	254910	Hs.516410	NM_178438	ENSG00000186207	LCE5A	LEP18|SPRL5A	late cornified envelope 5A	protein-coding	0.000000	0.478102	
chunk0083_302_1	chr17	69343296	69343582	+	0	NA	Intergenic	Intergenic	-16257	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.010490	0.421603	
chunk0097_129_1	chr2	46866630	46867331	+	0	NA	Intergenic	Intergenic	39116	NR_024452	100134259	Hs.114449	NR_024452	ENSG00000239332	LINC01119	-	long intergenic non-protein coding RNA 1119	ncRNA	0.017118	0.558405	402(GGGAACACCGCGTTCT,-,0.00),403(GGAACACCGCGTTCTC,+,0.00)
chunk0088_456_1	chr18	57272944	57273619	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-79209	NM_015879	51046	Hs.23172	NM_015879	ENSG00000177511	ST8SIA3	SIAT8C|ST8SiaIII	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.004444	0.465976	
chunk0039_321_1	chr11	103609389	103609800	+	0	NA	Intergenic	LTR50|LTR|ERVL	-240312	NR_039842	100616457		NR_039842	ENSG00000264200	MIR4693	-	microRNA 4693	ncRNA	0.000000	0.458738	
chunk0065_421_1	chr14	105944767	105945164	+	0	NA	Intergenic	Intergenic	26986	NR_026800	9834	Hs.649259	NM_014151	ENSG00000226777	FAM30A	C14orf110|HSPC053|KIAA0125	family with sequence similarity 30 member A	ncRNA	0.047859	0.557789	
chunk0142_50_1	chr4	91551368	91551906	+	0	NA	intron (NM_001145065, intron 10 of 10)	intron (NM_001145065, intron 10 of 10)	725665	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.005576	0.358071	
chunk0027_143_1	chr10	74600078	74600506	+	0	NA	intron (NM_001123, intron 8 of 10)	intron (NM_001123, intron 8 of 10)	-70968	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.004673	0.319347	
chunk0018_344_1	chr1	221553979	221554289	+	0	NA	Intergenic	Intergenic	182766	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.012903	0.491961	
chunk0136_9_1	chr4	47818	48767	+	0	NA	Intergenic	Intergenic	-4993	NM_001286054	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.004215	0.374737	
chunk0192_130_1	chr8	61810872	61811397	+	0	NA	Intergenic	Intergenic	96346	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.001905	0.321293	
chunk0166_168_1	chr6	45922676	45923020	+	0	NA	intron (NR_045673, intron 1 of 4)	(AG)n|Simple_repeat|Simple_repeat	14749	NR_045674	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.011628	0.455072	
chunk0042_468_1	chr12	12716959	12717343	+	0	NA	promoter-TSS (NM_004064)	promoter-TSS (NM_004064)	-119	NM_004064	1027	Hs.238990	NM_004064	ENSG00000111276	CDKN1B	CDKN4|KIP1|MEN1B|MEN4|P27KIP1	cyclin dependent kinase inhibitor 1B	protein-coding	0.117188	0.693506	
chunk0081_435_1	chr17	48881024	48881749	+	0	NA	Intergenic	Intergenic	-11400	NM_001002027	516	Hs.80986	NM_005175	ENSG00000159199	ATP5MC1	ATP5A|ATP5G|ATP5G1	ATP synthase membrane subunit c locus 1	protein-coding	0.013793	0.544077	
chunk0138_38_1	chr4	31239787	31240264	+	0	NA	Intergenic	Intergenic	68881	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.000000	0.338912	219(AGGAACATTCTGTGCA,-,0.00),220(GGAACATTCTGTGCAA,+,0.00)
chunk0189_280_1	chr8	25407878	25408717	+	0	NA	intron (NM_024940, intron 49 of 51)	intron (NM_024940, intron 49 of 51)	16743	NM_000825	2796	Hs.82963	NM_000825	ENSG00000147437	GNRH1	GNRH|GRH|LHRH|LNRH	gonadotropin releasing hormone 1	protein-coding	0.011919	0.436905	
chunk0116_126_1	chr21	36155500	36155883	+	0	NA	intron (NR_038892, intron 1 of 3)	intron (NR_038892, intron 1 of 3)	617	NR_038892	100506428	Hs.651214	NR_038892	ENSG00000236830	CBR3-AS1	PlncRNA-1|PlncRNA1	CBR3 antisense RNA 1	ncRNA	0.041775	0.588542	
chunk0054_18_1	chr13	40596549	40596748	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	69949	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.015075	0.450000	159(AAGCACGCTCTGTTCT,-,0.00),160(AGCACGCTCTGTTCTC,+,0.00)
chunk0012_72_1	chr1	155695169	155695527	+	0	NA	intron (NM_033657, intron 1 of 12)	HERVKC4-int|LTR|ERVK	6254	NM_004632	7818	Hs.516746	NM_004632	ENSG00000132676	DAP3	DAP-3|MRP-S29|MRPS29|S29mt|bMRP-10	death associated protein 3	protein-coding	0.011173	0.428969	
chunk0144_146_1	chr4	130107986	130108279	+	0	NA	Intergenic	Intergenic	-336654	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.003413	0.302721	
chunk0207_344_1	chr9	134768861	134769118	+	0	NA	intron (NM_000093, intron 25 of 65)	intron (NM_000093, intron 25 of 65)	80380	NR_039691	100616333		NR_039691	ENSG00000264744	MIR3689C	-	microRNA 3689c	ncRNA	0.042802	0.511628	
chunk0011_196_1	chr1	149988413	149988939	+	0	NA	intron (NM_020205, intron 1 of 11)	intron (NM_020205, intron 1 of 11)	22061	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.000000	0.333966	
chunk0008_118_1	chr1	91673643	91673999	+	0	NA	Intergenic	Intergenic	172713	NM_001134420	8317	Hs.533573	NM_003503	ENSG00000097046	CDC7	CDC7L1|HsCDC7|Hsk1|huCDC7	cell division cycle 7	protein-coding	0.002809	0.394958	116(AAGTACACTGTGTTCT,-,0.00),117(AGTACACTGTGTTCTT,+,0.00)
chunk0063_334_1	chr14	85332815	85333015	+	0	NA	Intergenic	Intergenic	-60964	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.020000	0.358209	
chunk0162_238_1	chr6	4806514	4807067	+	0	NA	intron (NM_004824, intron 1 of 6)	L1MC4a|LINE|L1	-29308	NM_001143970	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.023508	0.478339	
chunk0197_331_1	chr8	125145002	125145606	+	0	NA	intron (NM_173685, intron 3 of 7)	intron (NM_173685, intron 3 of 7)	53463	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.008278	0.400000	
chunk0033_395_1	chr11	24491886	24492455	+	0	NA	Intergenic	Intergenic	-4800	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.005272	0.312281	
chunk0081_133_1	chr17	40549216	40549734	+	0	NA	Intergenic	Intergenic	10919	NM_001301718	1236	Hs.370036	NM_001838	ENSG00000126353	CCR7	BLR2|CC-CKR-7|CCR-7|CD197|CDw197|CMKBR7|EBI1	C-C motif chemokine receptor 7	protein-coding	0.009653	0.460501	
chunk0147_424_1	chr4	187364744	187365211	+	0	NA	intron (NR_038931, intron 1 of 4)	MER21C|LTR|ERVL	140636	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.017131	0.429487	
chunk0002_126_1	chr1	16559710	16559909	+	0	NA	Intergenic	AluSq2|SINE|Alu	10895	NR_037446	100500876		NR_037446	ENSG00000263811	MIR3675	-	microRNA 3675	ncRNA	0.015075	0.460000	
chunk0169_51_1	chr6	97962930	97963725	+	0	NA	Intergenic	L1M5|LINE|L1	-61204	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.007547	0.350503	
chunk0094_357_1	chr2	9586581	9587264	+	0	NA	intron (NM_006826, intron 5 of 5)	intron (NM_006826, intron 5 of 5)	-31134	NM_003183	6868	Hs.404914	NM_003183	ENSG00000151694	ADAM17	ADAM18|CD156B|CSVP|NISBD|NISBD1|TACE	ADAM metallopeptidase domain 17	protein-coding	0.004392	0.347953	
chunk0001_79_1	chr1	2617636	2618216	+	0	NA	intron (NM_033467, intron 2 of 23)	intron (NM_033467, intron 2 of 23)	15116	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.003448	0.402754	
chunk0131_90_1	chr3	143503342	143503608	+	0	NA	intron (NM_173653, intron 9 of 15)	intron (NM_173653, intron 9 of 15)	161229	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.007519	0.501873	
chunk0014_295_1	chr1	180806458	180806942	+	0	NA	intron (NM_001135669, intron 6 of 13)	intron (NM_001135669, intron 6 of 13)	-106477	NM_020950	57710	Hs.734816	NM_020950	ENSG00000135835	KIAA1614	-	KIAA1614	protein-coding	0.004132	0.307216	
chunk0070_238_1	chr15	73002405	73002917	+	0	NA	Intergenic	Intergenic	-49823	NM_001172624	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.015625	0.497076	
chunk0028_350_1	chr10	92292333	92292772	+	0	NA	intron (NM_017824, intron 1 of 5)	intron (NM_017824, intron 1 of 5)	1389	NM_017824	54708	Hs.573490	NM_017824	ENSG00000198060	MARCH5	MARCH-V|MITOL|RNF153	membrane associated ring-CH-type finger 5	protein-coding	0.002278	0.402273	
chunk0063_272_1	chr14	84085474	84085838	+	0	NA	Intergenic	Intergenic	-1308223	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.312329	178(AAGATCAGCATGTCCT,-,0.00),179(AGATCAGCATGTCCTT,+,0.00)
chunk0141_245_1	chr4	85018665	85019134	+	0	NA	Intergenic	L2a|LINE|L2	52081	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.008529	0.351064	
chunk0177_454_1	chr7	28359172	28359654	+	0	NA	intron (NM_182899, intron 1 of 9)	L1MA7|LINE|L1	-53112	NM_182898	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.012448	0.347826	298(AAGGACAGTCTGTTCA,-,0.00),299(AGGACAGTCTGTTCAA,+,0.00)
chunk0179_54_1	chr7	43588922	43589400	+	0	NA	intron (NM_004760, intron 1 of 6)	intron (NM_004760, intron 1 of 6)	6068	NM_004760	9263	Hs.709489	NM_004760	ENSG00000164543	STK17A	DRAK1	serine/threonine kinase 17a	protein-coding	0.000000	0.354906	
chunk0185_296_1	chr7	131138650	131138937	+	0	NA	intron (NM_001145354, intron 1 of 18)	intron (NM_001145354, intron 1 of 18)	28697	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.010453	0.357639	
chunk0154_103_1	chr5	78358545	78358863	+	0	NA	TTS (NR_105014)	TTS (NR_105014)	-1799	NR_110885	9522	Hs.482587	NM_004866	ENSG00000085365	SCAMP1	SCAMP|SCAMP37	secretory carrier membrane protein 1	protein-coding	0.012579	0.432602	179(AAGAACATACTGAGCC,-,0.00),180(AGAACATACTGAGCCT,+,0.00)
chunk0012_13_1	chr1	154835804	154836464	+	0	NA	intron (NM_001204087, intron 1 of 8)	intron (NM_001204087, intron 1 of 8)	23728	NM_170782	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.013636	0.518911	
chunk0038_303_1	chr11	90792222	90792864	+	0	NA	intron (NR_104190, intron 3 of 6)	intron (NR_104190, intron 3 of 6)	76659	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.004673	0.334370	255(AGGCACTTCATGTGCT,-,0.00),256(GGCACTTCATGTGCTT,+,0.00)
chunk0067_300_1	chr15	47764027	47764715	+	0	NA	intron (NM_020858, intron 11 of 16)	intron (NM_020858, intron 11 of 16)	45882	NM_024966	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.018895	0.478955	
chunk0005_163_1	chr1	58483403	58483602	+	0	NA	intron (NM_145243, intron 8 of 8)	intron (NM_145243, intron 8 of 8)	63297	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.005025	0.390000	
chunk0021_224_1	chr10	6287316	6287843	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-38965	NR_040079	399715		NR_040079	ENSG00000215244	LINC02649	-	long intergenic non-protein coding RNA 2649	ncRNA	0.007590	0.373106	269(AAGTACACTCTGTGAT,-,0.00),371(GAGTACTCCCAGTTCC,-,0.00),372(AGTACTCCCAGTTCCT,+,0.00)
chunk0005_406_1	chr1	62557920	62558490	+	0	NA	intron (NM_001272001, intron 20 of 47)	L2c|LINE|L2	-39282	NM_014495	27329	Hs.209153	NM_014495	ENSG00000132855	ANGPTL3	ANG-5|ANGPT5|ANL3|FHBL2	angiopoietin like 3	protein-coding	0.001754	0.348511	
chunk0129_40_1	chr3	117399457	117399656	+	0	NA	Intergenic	Intergenic	478125	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.505000	
chunk0145_409_1	chr4	152822211	152822899	+	0	NA	intron (NM_001287433, intron 2 of 8)	L1PB3|LINE|L1	42618	NM_001025595	27236	Hs.416089	NM_014447	ENSG00000164144	ARFIP1	HSU52521	ADP ribosylation factor interacting protein 1	protein-coding	0.002907	0.336720	575(ATGAACAATCTGCTCT,-,0.00),576(TGAACAATCTGCTCTT,+,0.00)
chunk0047_130_1	chr12	69429482	69429735	+	0	NA	Intergenic	Intergenic	-40741	NM_001278354	10818	Hs.593446	NM_006654	ENSG00000166225	FRS2	FRS1A|FRS2A|FRS2alpha|SNT|SNT-1|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.003953	0.346457	
chunk0145_254_1	chr4	148918419	148918841	+	0	NA	Intergenic	Intergenic	-235665	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.014218	0.397163	
chunk0141_80_1	chr4	78561592	78562030	+	0	NA	intron (NM_005139, intron 2 of 12)	intron (NM_005139, intron 2 of 12)	10223	NM_005139	306	Hs.480042	NM_005139	ENSG00000138772	ANXA3	ANX3	annexin A3	protein-coding	0.000000	0.416856	
chunk0193_388_1	chr8	80366743	80367105	+	0	NA	Intergenic	Intergenic	-118695	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.008287	0.402204	
chunk0092_284_1	chr19	33806030	33806670	+	0	NA	intron (NM_024076, intron 4 of 6)	intron (NM_024076, intron 4 of 6)	9504	NM_024076	79047	Hs.221873	NM_024076	ENSG00000153885	KCTD15	-	potassium channel tetramerization domain containing 15	protein-coding	0.014063	0.553822	
chunk0097_50_1	chr2	43410406	43410938	+	0	NA	intron (NR_073394, intron 26 of 35)	L1ME1|LINE|L1	183461	NR_027251	100129726	Hs.194480	NM_178529	ENSG00000279873	LINC01126	-	long intergenic non-protein coding RNA 1126	ncRNA	0.009398	0.335835	
chunk0127_175_1	chr3	95263939	95264380	+	0	NA	Intergenic	Intergenic	325896	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.004535	0.384615	
chunk0089_134_1	chr18	58862509	58862837	+	0	NA	promoter-TSS (NM_018181)	promoter-TSS (NM_018181)	-156	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.030488	0.419453	189(ATGTACAATATGTGCT,-,0.00),190(TGTACAATATGTGCTT,+,0.00)
chunk0068_60_1	chr15	51796748	51796982	+	0	NA	intron (NM_014548, intron 7 of 9)	MER44D|DNA|TcMar-Tigger	-32763	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.017094	0.489362	
chunk0142_129_1	chr4	94670190	94670729	+	0	NA	Intergenic	Intergenic	87074	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.005566	0.322222	
chunk0128_138_1	chr3	106726106	106726694	+	0	NA	Intergenic	Intergenic	514238	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.005102	0.349745	314(CAGTACTTTCTGTACT,-,0.00),315(AGTACTTTCTGTACTC,+,0.00)
chunk0016_385_1	chr1	202860836	202861039	+	0	NA	promoter-TSS (NR_002929)	promoter-TSS (NR_002929)	-817	NR_002929	148709	Hs.162880	NR_002929	ENSG00000234996	LOC148709	-	actin gamma 1 pseudogene	pseudo	0.054187	0.598039	
chunk0001_379_1	chr1	10475449	10475649	+	0	NA	intron (NM_004565, intron 1 of 8)	intron (NM_004565, intron 1 of 8)	603	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.045000	0.527363	
chunk0198_199_1	chr8	133595153	133595484	+	0	NA	Intergenic	LTR16D|LTR|ERVL	-23378	NM_173344	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.009063	0.548193	64(GTGCACTGAGTGTTCT,-,0.00),65(TGCACTGAGTGTTCTA,+,0.00)
chunk0201_26_1	chr9	33234660	33234896	+	0	NA	Intergenic	L2a|LINE|L2	-5420	NM_014471	27290	Hs.555934	NM_014471	ENSG00000122711	SPINK4	HEL136|PEC-60|PEC60	serine peptidase inhibitor, Kazal type 4	protein-coding	0.008475	0.514768	
chunk0175_224_1	chr7	6264639	6264999	+	0	NA	intron (NM_004227, intron 1 of 12)	L2a|LINE|L2	7792	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.005556	0.360111	
chunk0051_377_1	chr12	121712645	121712844	+	0	NA	promoter-TSS (NM_001080825)	promoter-TSS (NM_001080825)	-8	NM_001080825	144404	Hs.644504	NM_001080825	ENSG00000188735	TMEM120B	-	transmembrane protein 120B	protein-coding	0.180905	0.825000	
chunk0051_366_1	chr12	121316781	121317318	+	0	NA	intron (NM_001137559, intron 15 of 16)	L1MB5|LINE|L1	-18741	NM_172216	10645	Hs.297343	NM_006549	ENSG00000110931	CAMKK2	CAMKK|CAMKKB	calcium/calmodulin dependent protein kinase kinase 2	protein-coding	0.011173	0.386617	
chunk0043_104_1	chr12	14919587	14920075	+	0	NA	intron (NM_152321, intron 4 of 6)	intron (NM_152321, intron 4 of 6)	9294	NM_001300784	121506	Hs.162143	NM_152321	ENSG00000139055	ERP27	C12orf46|PDIA8	endoplasmic reticulum protein 27	protein-coding	0.000000	0.368098	
chunk0140_142_1	chr4	69238838	69239789	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-24582	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.010515	0.366597	475(AAGAACATAAAGTACA,-,0.00),476(AGAACATAAAGTACAT,+,0.00)
chunk0060_159_1	chr14	45251043	45251435	+	0	NA	intron (NM_018353, intron 1 of 16)	Tigger3a|DNA|TcMar-Tigger	2163	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.002551	0.318066	
chunk0042_112_1	chr12	3205933	3206267	+	0	NA	intron (NM_001168320, intron 2 of 7)	intron (NM_001168320, intron 2 of 7)	128745	NM_001168320	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.011976	0.555224	
chunk0027_65_1	chr10	73117799	73118406	+	0	NA	intron (NR_104264, intron 2 of 8)	intron (NR_104264, intron 2 of 8)	7727	NM_015901	25961	Hs.533657	NM_015901	ENSG00000166321	NUDT13	-	nudix hydrolase 13	protein-coding	0.004942	0.351974	264(AAGTACAGGTTGTACC,-,0.00),265(AGTACAGGTTGTACCA,+,0.00)
chunk0199_310_1	chr9	7121557	7122013	+	0	NA	intron (NM_015061, intron 18 of 21)	intron (NM_015061, intron 18 of 21)	364144	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.006579	0.358862	
chunk0206_352_1	chr9	125633098	125633666	+	0	NA	intron (NM_001006618, intron 4 of 7)	intron (NM_001006618, intron 4 of 7)	73852	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.005282	0.416520	
chunk0186_142_1	chr7	138752644	138753011	+	0	NA	exon (NM_130841, exon 10 of 21)	exon (NM_130841, exon 10 of 21)	21210	NM_130841	50617	Hs.98967	NM_020632	ENSG00000105929	ATP6V0A4	A4|ATP6N1B|ATP6N2|RDRTA2|RTA1C|RTADR|STV1|VPH1|VPP2	ATPase H+ transporting V0 subunit a4	protein-coding	0.027248	0.532609	
chunk0075_395_1	chr16	56815857	56816355	+	0	NA	intron (NM_014669, intron 5 of 21)	MIR|SINE|MIR	32605	NM_001242796	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.004016	0.454910	
chunk0125_433_1	chr3	72658013	72658504	+	0	NA	Intergenic	MIRb|SINE|MIR	190189	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.012220	0.420732	
chunk0011_358_1	chr1	152981704	152981903	+	0	NA	Intergenic	(CAGT)n|Simple_repeat|Simple_repeat	-2285	NM_001199828	6698	Hs.46320	NM_005987	ENSG00000169474	SPRR1A	SPRK	small proline rich protein 1A	protein-coding	0.020101	0.530000	14(AGGTACACTGTGTACC,-,0.00),15(GGTACACTGTGTACCG,+,0.00)
chunk0173_262_1	chr6	147156920	147157284	+	0	NA	intron (NR_034115, intron 3 of 10)	intron (NR_034115, intron 3 of 10)	-1823	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.008242	0.427397	186(AAGAACGTCCTGTTCC,-,0.00),187(AGAACGTCCTGTTCCC,+,0.00)
chunk0079_434_1	chr17	20010709	20011416	+	0	NA	intron (NM_001243439, intron 1 of 14)	L1MB2|LINE|L1	1726	NM_001243439	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.004243	0.344633	419(AGGATCAGGCTGTCCT,-,0.00),420(GGATCAGGCTGTCCTC,+,0.00)
chunk0212_130_1	chrX	131149690	131150158	+	0	NA	Intergenic	L1MC3|LINE|L1	91682	NM_001282607	158763	Hs.22905	NM_144967	ENSG00000147256	ARHGAP36	-	Rho GTPase activating protein 36	protein-coding	0.006410	0.343284	
chunk0182_204_1	chr7	96244649	96245055	+	0	NA	intron (NM_014251, intron 3 of 17)	intron (NM_014251, intron 3 of 17)	-25096	NR_030322	693176		NR_030322	ENSG00000208025	MIR591	MIRN591|hsa-mir-591	microRNA 591	ncRNA	0.009852	0.429975	
chunk0147_196_1	chr4	177771664	177772116	+	0	NA	intron (NR_028342, intron 2 of 5)	intron (NR_028342, intron 2 of 5)	43133	NR_028342	285501	Hs.722466	NM_001085490	ENSG00000231171	LINC01098	-	long intergenic non-protein coding RNA 1098	ncRNA	0.002212	0.328918	
chunk0044_117_1	chr12	29101271	29101990	+	0	NA	Intergenic	L1MC2|LINE|L1	-47373	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.002782	0.344444	
chunk0050_129_1	chr12	102200184	102200875	+	0	NA	Intergenic	L1ME3G|LINE|L1	-2684	NM_002674	5367	Hs.707990	NM_002674	ENSG00000183395	PMCH	MCH|ppMCH	pro-melanin concentrating hormone	protein-coding	0.002894	0.299133	266(AAGTACAGGATGTTCT,-,0.00),267(AGTACAGGATGTTCTC,+,0.00)
chunk0015_62_1	chr1	184632648	184633365	+	0	NA	Intergenic	Intergenic	121901	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.009763	0.498607	361(GAGAACAACTTGTCCA,-,0.00),362(AGAACAACTTGTCCAC,+,0.00)
chunk0150_112_1	chr5	32867622	32867848	+	0	NA	Intergenic	Intergenic	-79708	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.000000	0.361233	
chunk0011_424_1	chr1	154485669	154486220	+	0	NA	exon (NM_001010846, exon 5 of 6)	exon (NM_001010846, exon 5 of 6)	16106	NM_001010846	126669	Hs.591481	NM_001010846	ENSG00000169291	SHE	-	Src homology 2 domain containing E	protein-coding	0.009074	0.436594	220(GTCACACAGTGTTCCT,+,0.00)
chunk0083_229_1	chr17	67390587	67391580	+	0	NA	intron (NM_181671, intron 1 of 9)	(GT)n|Simple_repeat|Simple_repeat	13802	NM_181671	26207	Hs.591185	NM_012417	ENSG00000154217	PITPNC1	M-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1	phosphatidylinositol transfer protein cytoplasmic 1	protein-coding	0.010070	0.417505	161(GAGGACACACTGTCTT,-,0.00),162(AGGACACACTGTCTTG,+,0.00)
chunk0056_204_1	chr13	85799336	85799951	+	0	NA	promoter-TSS (NM_032229)	promoter-TSS (NM_032229)	-295	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.008130	0.349026	
chunk0037_159_1	chr11	73647680	73648189	+	0	NA	promoter-TSS (NM_001130036)	promoter-TSS (NM_001130036)	385	NM_001130035	58473	Hs.445489	NM_021200	ENSG00000021300	PLEKHB1	KPL1|PHR1|PHRET1	pleckstrin homology domain containing B1	protein-coding	0.023576	0.554902	
chunk0008_331_1	chr1	95413780	95413992	+	0	NA	Intergenic	Intergenic	-60851	NR_033966	440594	Hs.514123	NR_033966	ENSG00000233907	LINC01761	-	long intergenic non-protein coding RNA 1761	ncRNA	0.004717	0.309859	
chunk0017_367_1	chr1	212004823	212005361	+	0	NA	intron (NR_037667, intron 8 of 20)	L1ME3B|LINE|L1	-30461	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.013011	0.363636	
chunk0056_459_1	chr13	95271324	95271994	+	0	NA	intron (NM_001105515, intron 1 of 20)	intron (NM_001105515, intron 1 of 20)	29787	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.016418	0.436662	
chunk0052_142_1	chr13	23754695	23754972	+	0	NA	intron (NM_005932, intron 18 of 18)	intron (NM_005932, intron 18 of 18)	-134056	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.018051	0.521583	
chunk0053_361_1	chr13	35231298	35231754	+	0	NA	intron (NM_015678, intron 33 of 57)	intron (NM_015678, intron 33 of 57)	245169	NM_005584	4081	Hs.584776	NM_005584	ENSG00000180660	MAB21L1	CAGR1|Nbla00126	mab-21 like 1	protein-coding	0.002193	0.323851	
chunk0119_386_1	chr22	48370014	48370220	+	0	NA	Intergenic	Intergenic	95753	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.009709	0.487923	
chunk0207_8_1	chrM	9802	10900	+	0	NA	NA	Intergenic	NA	NA									0.022769	0.389445	
chunk0017_245_1	chr1	208496526	208497143	+	0	NA	Intergenic	L1PA16|LINE|L1	-252514	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.009724	0.569579	
chunk0049_338_1	chr12	94980041	94980517	+	0	NA	intron (NM_001258338, intron 2 of 2)	L2b|LINE|L2	23434	NM_001258338	55967	Hs.506374	NM_018838	ENSG00000184752	NDUFA12	B17.2|DAP13|MC1DN23	NADH:ubiquinone oxidoreductase subunit A12	protein-coding	0.012605	0.436059	
chunk0126_186_1	chr3	78228943	78229142	+	0	NA	Intergenic	Intergenic	790417	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.285000	16(AAGAACAAAATGTACT,-,0.00),17(AGAACAAAATGTACTT,+,0.00)
chunk0166_162_1	chr6	45645138	45645466	+	0	NA	Intergenic	Intergenic	222725	NM_001278478	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.006098	0.443769	280(CAGCTCAGAATGTTCT,-,0.00),281(AGCTCAGAATGTTCTA,+,0.00)
chunk0095_39_1	chr2	13502225	13502808	+	0	NA	Intergenic	Intergenic	-495503	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.008576	0.323630	
chunk0123_75_1	chr3	41562027	41562274	+	0	NA	intron (NM_017886, intron 32 of 36)	L1PA4|LINE|L1	362699	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.012146	0.391129	106(AGGAGCAGCTTGTTCT,-,0.00),107(GGAGCAGCTTGTTCTG,+,0.00)
chunk0009_61_1	chr1	100769601	100770043	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	50182	NM_001199834	7412	Hs.109225	NM_001078	ENSG00000162692	VCAM1	CD106|INCAM-100	vascular cell adhesion molecule 1	protein-coding	0.009050	0.361174	
chunk0036_181_1	chr11	62761614	62761932	+	0	NA	intron (NM_002696, intron 1 of 7)	CpG	234	NM_002696	5436	Hs.14839	NM_002696	ENSG00000168002	POLR2G	RPB19|RPB7|hRPB19|hsRPB7	RNA polymerase II subunit G	protein-coding	0.056604	0.623824	
chunk0071_433_1	chr15	89864033	89864466	+	0	NA	intron (NM_001199058, intron 8 of 9)	intron (NM_001199058, intron 8 of 9)	-13528	NR_049817	100847059		NR_049817	ENSG00000264966	MIR5094	-	microRNA 5094	ncRNA	0.000000	0.306452	
chunk0143_371_1	chr4	122331207	122331552	+	0	NA	exon (NM_015312, exon 65 of 84)	exon (NM_015312, exon 65 of 84)	-47587	NM_139243	132612	Hs.518957	NM_139243	ENSG00000164113	ADAD1	Tenr	adenosine deaminase domain containing 1	protein-coding	0.011594	0.346821	
chunk0111_130_1	chr20	24649999	24650416	+	0	NA	intron (NM_024893, intron 3 of 3)	intron (NM_024893, intron 3 of 3)	181008	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.016787	0.502392	
chunk0193_440_1	chr8	81088097	81088385	+	0	NA	intron (NM_018440, intron 1 of 8)	intron (NM_018440, intron 1 of 8)	23827	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.003472	0.342561	118(TGGAACACTGTGTTTC,-,0.00),119(GGAACACTGTGTTTCA,+,0.00)
chunk0078_392_1	chr16	88077185	88077959	+	0	NA	TTS (NM_001173542)	TTS (NM_001173542)	23413	NR_120310	400553	Hs.592071	NR_120310	ENSG00000205037	LOC400553	-	uncharacterized LOC400553	ncRNA	0.034884	0.554839	262(CGGGACAGTCAGTTCT,-,0.00),263(GGGACAGTCAGTTCTG,+,0.00),330(TGGAACTTCTTGTTCT,-,0.00),331(GGAACTTCTTGTTCTC,+,0.00)
chunk0013_191_1	chr1	169161093	169161699	+	0	NA	intron (NR_104229, intron 12 of 12)	MamRep564|Unknown|Unknown	54687	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.004950	0.400329	193(TGTACAAGTTGTTCCC,+,0.00)
chunk0179_120_1	chr7	45584816	45585212	+	0	NA	intron (NM_021116, intron 1 of 19)	intron (NM_021116, intron 1 of 19)	10488	NM_021116	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.015152	0.518892	125(CAGGGCAGCCTGTTCT,-,0.00),126(AGGGCAGCCTGTTCTG,+,0.00),140(TGGAACATTCTGTTCC,-,0.00),141(GGAACATTCTGTTCCC,+,0.00)
chunk0059_141_1	chr14	32053883	32054091	+	0	NA	Intergenic	Intergenic	22712	NR_027263	84837	Hs.496755	NM_032751		ARHGAP5-AS1	C14orf128	ARHGAP5 antisense RNA 1 (head to head)	ncRNA	0.004808	0.330144	
chunk0019_423_1	chr1	230849623	230849895	+	0	NA	intron (NM_001136495, intron 2 of 3)	intron (NM_001136495, intron 2 of 3)	6277	NM_001136495	84886	Hs.520494	NM_032800	ENSG00000119280	C1orf198	-	chromosome 1 open reading frame 198	protein-coding	0.011029	0.421245	
chunk0001_260_1	chr1	8467331	8467690	+	0	NA	intron (NM_001042681, intron 10 of 22)	L2b|LINE|L2	27403	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.005571	0.400000	
chunk0092_352_1	chr19	35430229	35430907	+	0	NA	Intergenic	MER87|LTR|ERV1	-19147	NM_005306	2867	Hs.248056	NM_005306	ENSG00000126262	FFAR2	FFA2R|GPR43	free fatty acid receptor 2	protein-coding	0.008850	0.435935	401(AGGAACATTGTGACCT,-,0.00),402(GGAACATTGTGACCTC,+,0.00)
chunk0053_438_1	chr13	39242443	39242974	+	0	NA	Intergenic	Intergenic	204397	NM_001012754	387921	Hs.507783	NM_001012754	ENSG00000188811	NHLRC3	-	NHL repeat containing 3	protein-coding	0.005650	0.327068	
chunk0149_150_1	chr5	20215290	20215489	+	0	NA	intron (NM_001291956, intron 2 of 14)	L1MC3|LINE|L1	-227145	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.005025	0.265000	
chunk0038_316_1	chr11	91556329	91556726	+	0	NA	Intergenic	Intergenic	-687325	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.000000	0.334171	144(AAGCACAGGGTGTTCA,-,0.00),145(AGCACAGGGTGTTCAT,+,0.00)
chunk0023_90_1	chr10	22466709	22467297	+	0	NA	Intergenic	L2b|LINE|L2	-29074	NR_036533	100499489	Hs.7444	NR_036533		LOC100499489	-	uncharacterized LOC100499489	ncRNA	0.006803	0.378608	
chunk0131_287_1	chr3	150459418	150460027	+	0	NA	non-coding (NR_130136, exon 5 of 5)	non-coding (NR_130136, exon 5 of 5)	51387	NM_014779	9819	Hs.722470	NM_014779	ENSG00000196428	TSC22D2	TILZ4a|TILZ4b|TILZ4c	TSC22 domain family member 2	protein-coding	0.011494	0.296721	
chunk0032_209_1	chr11	7494538	7495007	+	0	NA	intron (NM_198474, intron 2 of 2)	intron (NM_198474, intron 2 of 2)	9403	NM_198474	283298	Hs.503500	NM_198474	ENSG00000183801	OLFML1	MVAL564|UNQ564	olfactomedin like 1	protein-coding	0.004264	0.504255	
chunk0032_454_1	chr10	133313411	133314179	+	0	NA	TTS (NM_145806)	TTS (NM_145806)	-1458	NR_046330	10844	Hs.523370	NM_006659	ENSG00000130640	TUBGCP2	ALP4|GCP-2|GCP2|Grip103|SPBC97|SPC97|Spc97p|h103p|hGCP2|hSpc97	tubulin gamma complex associated protein 2	protein-coding	0.023438	0.517555	180(GGGGGCAGTGTGTCCT,-,0.00),181(GGGGCAGTGTGTCCTG,+,0.00),326(GGGCACGAGCTGTTCC,-,0.00)
chunk0068_43_1	chr15	51424733	51425358	+	0	NA	Intergenic	MER4-int|LTR|ERV1	83529	NM_181789	342035	Hs.526441	NM_181789	ENSG00000186417	GLDN	CLOM|COLM|CRG-L2|CRGL2|LCCS11|UNC-112	gliomedin	protein-coding	0.001600	0.365815	300(CAGGACTTGATGTCCT,-,0.00),301(AGGACTTGATGTCCTT,+,0.00)
chunk0158_291_1	chr5	132180340	132180608	+	0	NA	Intergenic	Intergenic	-4402	NR_047470	100861518	Hs.519568	NR_047470	ENSG00000237714	P4HA2-AS1	-	P4HA2 antisense RNA 1	ncRNA	0.007463	0.438662	
chunk0085_230_1	chr18	6943074	6943588	+	0	NA	exon (NM_005559, exon 62 of 63)	exon (NM_005559, exon 62 of 63)	-11346	NR_126040	101927188	Hs.680444	NR_126040	ENSG00000265069	LOC101927188	-	uncharacterized LOC101927188	ncRNA	0.011673	0.442718	
chunk0187_154_1	chr7	150186610	150187013	+	0	NA	Intergenic	Intergenic	116169	NM_001164459	653857	Hs.664579	NM_001164458	ENSG00000106526	ACTR3C	ARP11	actin related protein 3C	protein-coding	0.007444	0.353960	
chunk0145_382_1	chr4	151639481	151639680	+	0	NA	intron (NM_001109977, intron 9 of 13)	intron (NM_001109977, intron 9 of 13)	121443	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.010050	0.450000	
chunk0007_199_1	chr1	81234145	81234783	+	0	NA	Intergenic	Intergenic	323238	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.009404	0.348983	
chunk0133_224_1	chr3	171228014	171228681	+	0	NA	intron (NM_001161560, intron 2 of 31)	intron (NM_001161560, intron 2 of 31)	-121588	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.008996	0.374251	
chunk0032_328_1	chr11	10105391	10105790	+	0	NA	intron (NM_030962, intron 2 of 39)	intron (NM_030962, intron 2 of 39)	188617	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.007519	0.340000	
chunk0148_151_1	chr5	6519590	6520024	+	0	NA	Intergenic	Intergenic	-62329	NR_024423	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.011521	0.577011	9(CAGGGCATCCTGTACC,-,0.00),10(AGGGCATCCTGTACCC,+,0.00),76(CGGAGCATCGTGTACC,-,0.00),77(GGAGCATCGTGTACCC,+,0.00),110(CGGGGCATCCTGTACC,-,0.00),111(GGGGCATCCTGTACCC,+,0.00),127(TGGAGCATCCTGTACC,-,0.00),128(GGAGCATCCTGTACCC,+,0.00),160(CAGAACATCCTGTACC,-,0.00),161(AGAACATCCTGTACCC,+,0.00),210(CAGAACATCCTGTACC,-,0.00),211(AGAACATCCTGTACCC,+,0.00),243(CAGAGCATCCTGTACC,-,0.00),244(AGAGCATCCTGTACCC,+,0.00),277(TGGAACATCCTGTACC,-,0.00),278(GGAACATCCTGTACCC,+,0.00)
chunk0082_235_1	chr17	57337537	57337741	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	80626	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.039216	0.565854	
chunk0128_199_1	chr3	107712553	107712752	+	0	NA	intron (NM_001276286, intron 4 of 16)	L2|LINE|L2	165416	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.005025	0.475000	
chunk0194_258_1	chr8	86763959	86764274	+	0	NA	Intergenic	Intergenic	-20441	NM_019098	54714	Hs.154433	NM_019098	ENSG00000170289	CNGB3	ACHM1	cyclic nucleotide gated channel beta 3	protein-coding	0.000000	0.376582	
chunk0034_219_1	chr11	32913458	32914014	+	0	NA	intron (NM_001076786, intron 1 of 12)	MIR|SINE|MIR	20558	NM_001076786	79832	Hs.369368	NM_024774	ENSG00000060749	QSER1	-	glutamine and serine rich 1	protein-coding	0.014388	0.385996	
chunk0007_311_1	chr1	84332351	84332764	+	0	NA	intron (NM_001010971, intron 3 of 3)	L1PA15|LINE|L1	29906	NM_001134664	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.007264	0.316425	
chunk0205_303_1	chr9	112376965	112377730	+	0	NA	Intergenic	AluJr4|SINE|Alu	-2562	NR_036651	84263	Hs.59486	NM_032303	ENSG00000119471	HSDL2	C9orf99|SDR13C1	hydroxysteroid dehydrogenase like 2	protein-coding	0.003922	0.425587	
chunk0198_138_1	chr8	132763912	132764172	+	0	NA	Intergenic	L2c|LINE|L2	-3374	NM_001145153	137835	Hs.293842	NM_144649	ENSG00000165071	TMEM71	-	transmembrane protein 71	protein-coding	0.011538	0.413793	107(TGGAACACTGTGTCCC,-,0.00),108(GGAACACTGTGTCCCA,+,0.00)
chunk0086_106_1	chr18	14120768	14121396	+	0	NA	intron (NM_145287, intron 2 of 2)	L1MA9|LINE|L1	11408	NM_145287	162655	Hs.352635	NM_145287	ENSG00000175322	ZNF519	HsT2362	zinc finger protein 519	protein-coding	0.001592	0.330684	
chunk0084_19_1	chr17	73427071	73427826	+	0	NA	intron (NM_001144952, intron 12 of 44)	MER58A|DNA|hAT-Charlie	-115444	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.002649	0.361111	
chunk0047_257_1	chr12	72557844	72558487	+	0	NA	intron (NM_013381, intron 7 of 18)	L2c|LINE|L2	-284656	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.001555	0.366460	
chunk0113_240_1	chr20	54109898	54110493	+	0	NA	Intergenic	Intergenic	-39430	NM_003657	8537	Hs.400556	NM_003657	ENSG00000064787	BCAS1	AIBC1|NABC1	breast carcinoma amplified sequence 1	protein-coding	0.001681	0.348993	
chunk0129_310_1	chr3	123831231	123831839	+	0	NA	intron (NM_053025, intron 3 of 33)	intron (NM_053025, intron 3 of 33)	52767	NM_053028	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.016447	0.540230	
chunk0062_337_1	chr14	73439020	73439837	+	0	NA	intron (NM_001005743, intron 1 of 12)	intron (NM_001005743, intron 1 of 12)	19152	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.001224	0.306846	
chunk0134_222_1	chr3	178802905	178803230	+	0	NA	intron (NR_126561, intron 2 of 5)	MIRb|SINE|MIR	57338	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.009231	0.331288	
chunk0076_413_1	chr16	72836161	72836805	+	0	NA	intron (NM_006885, intron 4 of 9)	intron (NM_006885, intron 4 of 9)	-171474	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.015528	0.455814	
chunk0156_235_1	chr5	108338296	108338495	+	0	NA	intron (NM_001163315, intron 4 of 8)	intron (NM_001163315, intron 4 of 8)	43703	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.005025	0.280000	
chunk0116_110_1	chr21	35575804	35576145	+	0	NA	intron (NR_073512, intron 1 of 2)	intron (NR_073512, intron 1 of 2)	4790	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.011730	0.426901	
chunk0131_170_1	chr3	146870946	146871208	+	0	NA	Intergenic	L1PA16|LINE|L1	-264861	NM_001085420	389158	Hs.254692	NM_001085420	ENSG00000231213	PLSCR5	-	phospholipid scramblase family member 5	protein-coding	0.003817	0.330798	
chunk0155_426_1	chr5	100494919	100495251	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-40220	NM_198507	345757	Hs.356108	NM_198507	ENSG00000174132	FAM174A	HGS_RE408|NS5ATP6|TMEM157|UNQ1912	family with sequence similarity 174 member A	protein-coding	0.003012	0.354354	
chunk0029_249_1	chr10	102782850	102783294	+	0	NA	intron (NM_017787, intron 1 of 3)	intron (NM_017787, intron 1 of 3)	6941	NM_017787	54838	Hs.500897	NM_017787	ENSG00000166272	WBP1L	C10orf26|OPA1L|OPAL1	WW domain binding protein 1 like	protein-coding	0.027027	0.512360	
chunk0068_55_1	chr15	51692349	51692795	+	0	NA	intron (NM_001165257, intron 6 of 10)	intron (NM_001165257, intron 6 of 10)	11219	NM_013243	29106	Hs.232618	NM_013243	ENSG00000104112	SCG3	SGIII	secretogranin III	protein-coding	0.004484	0.362416	
chunk0004_123_1	chr1	44667744	44668176	+	0	NA	intron (NM_001300748, intron 1 of 2)	intron (NM_001300748, intron 1 of 2)	6648	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.004630	0.406467	339(CAGTACAATATGTACT,-,0.00),340(AGTACAATATGTACTT,+,0.00)
chunk0077_227_1	chr16	80421204	80421522	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-119371	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.006289	0.366771	158(AGGAACAGGATGAACC,-,0.00),159(GGAACAGGATGAACCT,+,0.00)
chunk0027_50_1	chr10	72807316	72807543	+	0	NA	intron (NR_073062, intron 3 of 9)	intron (NR_073062, intron 3 of 9)	-86127	NR_130125	170392	Hs.8366	NM_152635	ENSG00000138315	OIT3	LZP	oncoprotein induced transcript 3	protein-coding	0.000000	0.315789	
chunk0170_337_1	chr6	116280349	116281025	+	0	NA	promoter-TSS (NM_003309)	promoter-TSS (NM_003309)	567	NM_001080976	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.011834	0.392910	
chunk0190_59_1	chr8	29715326	29715839	+	0	NA	Intergenic	L1ME1|LINE|L1	32527	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.009747	0.315175	
chunk0142_143_1	chr4	94893881	94894185	+	0	NA	intron (NM_001203, intron 2 of 12)	intron (NM_001203, intron 2 of 12)	-102199	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.009868	0.370492	
chunk0123_388_1	chr3	48774532	48774870	+	0	NA	intron (NM_004157, intron 5 of 10)	L1MA4A|LINE|L1	-57423	NM_001146179	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.002959	0.380531	
chunk0058_140_1	chr14	22903259	22903609	+	0	NA	intron (NM_001077352, intron 8 of 11)	intron (NM_001077352, intron 8 of 11)	15753	NM_001308044	55147	Hs.4997	NM_018107	ENSG00000100461	RBM23	CAPERbeta|PP239|RNPC4	RNA binding motif protein 23	protein-coding	0.002857	0.464387	235(TGGTACTGACAGTTCC,-,0.00),236(GGTACTGACAGTTCCT,+,0.00)
chunk0022_284_1	chr10	15310324	15310523	+	0	NA	intron (NM_001010924, intron 1 of 7)	MIRc|SINE|MIR	60636	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.005025	0.490000	
chunk0051_7_1	chr12	111237868	111238551	+	0	NA	intron (NM_015267, intron 3 of 21)	L2b|LINE|L2	-65933	NR_106818	102465455		NR_106818	ENSG00000273700	MIR6760	hsa-mir-6760	microRNA 6760	ncRNA	0.010249	0.466374	
chunk0098_350_1	chr2	77349047	77349345	+	0	NA	intron (NM_001282924, intron 3 of 3)	L1ME4c|LINE|L1	173172	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.000000	0.290970	
chunk0043_68_1	chr12	14257616	14258004	+	0	NA	Intergenic	Intergenic	-107822	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.025773	0.511568	
chunk0093_287_1	chr19	52026740	52026973	+	0	NA	intron (NM_025040, intron 1 of 4)	LTR5B|LTR|ERVK	1571	NM_025040	80110	Hs.292336	NM_025040	ENSG00000142556	ZNF614	-	zinc finger protein 614	protein-coding	0.017167	0.461538	
chunk0045_427_1	chr12	53390774	53390973	+	0	NA	intron (NM_138473, intron 3 of 5)	intron (NM_138473, intron 3 of 5)	10229	NM_003109	6667	Hs.620754	NM_003109	ENSG00000185591	SP1	-	Sp1 transcription factor	protein-coding	0.020101	0.355000	
chunk0091_224_1	chr19	10194849	10195405	+	0	NA	promoter-TSS (NM_001130823)	promoter-TSS (NM_001130823)	-48	NM_001379	1786	Hs.202672	NM_001379	ENSG00000130816	DNMT1	ADCADN|AIM|CXXC9|DNMT|HSN1E|MCMT|m.HsaI	DNA methyltransferase 1	protein-coding	0.075540	0.621185	
chunk0068_184_1	chr15	54724690	54725027	+	0	NA	Intergenic	L1MA2|LINE|L1	472175	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.000000	0.325444	
chunk0139_198_1	chr4	54774571	54775070	+	0	NA	Intergenic	Intergenic	116892	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.008016	0.398000	354(GAGCACAGCCTGTTCA,-,0.00),355(AGCACAGCCTGTTCAG,+,0.00)
chunk0160_390_1	chr5	162676195	162676595	+	0	NA	Intergenic	Intergenic	608753	NM_198904	2566	Hs.7195	NM_000816	ENSG00000113327	GABRG2	CAE2|ECA2|EIEE74|FEB8|GEFSP3	gamma-aminobutyric acid type A receptor gamma2 subunit	protein-coding	0.000000	0.304239	
chunk0030_16_1	chr10	110926119	110926561	+	0	NA	intron (NM_007373, intron 1 of 8)	intron (NM_007373, intron 1 of 8)	6797	NM_007373	8036	Hs.104315	NM_007373	ENSG00000108061	SHOC2	SIAA0862|SOC2|SUR8	SHOC2 leucine rich repeat scaffold protein	protein-coding	0.002262	0.336343	
chunk0203_392_1	chr9	90555252	90556077	+	0	NA	intron (NR_034157, intron 1 of 5)	L1ME4b|LINE|L1	27082	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.009697	0.395884	
chunk0126_260_1	chr3	79622247	79622587	+	0	NA	intron (NM_002941, intron 1 of 30)	L1PA8A|LINE|L1	114530	NR_037488	100500877		NR_037488	ENSG00000265193	MIR3923	-	microRNA 3923	ncRNA	0.005882	0.560117	
chunk0151_278_1	chr5	52725039	52726150	+	0	NA	Intergenic	Intergenic	-62346	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.008101	0.417266	
chunk0174_264_1	chr6	161228760	161229262	+	0	NA	intron (NM_020133, intron 2 of 8)	intron (NM_020133, intron 2 of 8)	45064	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.015936	0.429423	
chunk0127_331_1	chr3	100437926	100438160	+	0	NA	intron (NM_001085451, intron 2 of 3)	MIRb|SINE|MIR	-36645	NM_014820	9868	Hs.227253	NM_014820	ENSG00000154174	TOMM70	TOMM70A|Tom70	translocase of outer mitochondrial membrane 70	protein-coding	0.000000	0.429787	132(AGGTACATACTGTGCA,-,0.00),133(GGTACATACTGTGCAC,+,0.00)
chunk0067_41_1	chr15	40554819	40555444	+	0	NA	intron (NM_001080791, intron 3 of 3)	intron (NM_001080791, intron 3 of 3)	9926	NM_001289132	90416	Hs.654661	NM_052849	ENSG00000128891	CCDC32	C15orf57	coiled-coil domain containing 32	protein-coding	0.008000	0.380192	532(AGGAACATGCTGATCT,-,0.00),533(GGAACATGCTGATCTG,+,0.00)
chunk0130_226_1	chr3	134302738	134303090	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	-52170	NM_001005861	6259	Hs.654562	NM_002958	ENSG00000163785	RYK	D3S3195|JTK5|JTK5A|RYK1	receptor like tyrosine kinase	protein-coding	0.002841	0.413598	
chunk0097_445_1	chr2	64369283	64369901	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	-28744	NR_106995	102465833		NR_106995	ENSG00000264297	MIR4433B	hsa-mir-4433b	microRNA 4433b	ncRNA	0.003236	0.468498	
chunk0075_457_1	chr16	58413133	58413667	+	0	NA	Intergenic	Intergenic	21006	NM_001126130	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.007491	0.429907	240(AAGAACAATGTGTCAC,-,0.00),281(AAGAACAAAGTGTTCA,-,0.00),282(AGAACAAAGTGTTCAG,+,0.00)
chunk0037_336_1	chr11	77309732	77309931	+	0	NA	Intergenic	Intergenic	-22413	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.010050	0.430000	86(AGGAACACTCTGTCTC,-,0.00),87(GGAACACTCTGTCTCA,+,0.00)
chunk0006_395_1	chr1	75368276	75368607	+	0	NA	intron (NM_001130058, intron 3 of 23)	MER8|DNA|TcMar-Tigger	233559	NM_001256114	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.009063	0.367470	
chunk0009_330_1	chr1	109076096	109076457	+	0	NA	promoter-TSS (NM_005645)	promoter-TSS (NM_005645)	-274	NM_005645	6884	Hs.632426	NM_005645	ENSG00000197780	TAF13	MRT60|TAF(II)18|TAF2K|TAFII-18|TAFII18	TATA-box binding protein associated factor 13	protein-coding	0.036011	0.433702	
chunk0038_248_1	chr11	87301015	87301258	+	0	NA	intron (NM_022918, intron 7 of 14)	intron (NM_022918, intron 7 of 14)	263292	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.004115	0.372951	
chunk0157_256_1	chr5	119914017	119914468	+	0	NA	Intergenic	L1PB1|LINE|L1	284683	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.006652	0.378319	
chunk0108_65_1	chr2	227349892	227350715	+	0	NA	intron (NM_001277067, intron 6 of 7)	intron (NM_001277067, intron 6 of 7)	21625	NM_001277068	56947	Hs.471528	NM_020194	ENSG00000168958	MFF	C2orf33|EMPF2|GL004	mitochondrial fission factor	protein-coding	0.009721	0.325243	
chunk0019_449_1	chr1	231337342	231338081	+	0	NA	promoter-TSS (NM_001261462)	promoter-TSS (NM_001261462)	161	NM_175876	149371	Hs.356198	NM_175876	ENSG00000116903	EXOC8	EXO84|Exo84p|SEC84	exocyst complex component 8	protein-coding	0.096076	0.640541	
chunk0147_78_1	chr4	173036625	173037684	+	0	NA	intron (NM_001034845, intron 12 of 12)	intron (NM_001034845, intron 12 of 12)	-131599	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.005666	0.427358	
chunk0167_226_1	chr6	67131812	67132378	+	0	NA	Intergenic	Intergenic	-923256	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.003534	0.405644	
chunk0106_224_1	chr2	202568793	202569118	+	0	NA	Intergenic	Intergenic	-66223	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.006154	0.383436	
chunk0150_107_1	chr5	32810926	32811422	+	0	NA	Intergenic	Intergenic	99842	NM_001204375	4883	Hs.13528	NM_000908	ENSG00000113389	NPR3	ANP-C|ANPR-C|ANPRC|C5orf23|GUCY2B|NPR-C|NPRC	natriuretic peptide receptor 3	protein-coding	0.012097	0.448692	
chunk0022_352_1	chr10	17135151	17135446	+	0	NA	Intergenic	Intergenic	-5481	NM_001081	8029	Hs.166206	NM_001081	ENSG00000107611	CUBN	IFCR|MGA1|gp280	cubilin	protein-coding	0.006780	0.425676	
chunk0030_41_1	chr10	111581326	111581898	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	504580	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.005245	0.445026	
chunk0093_90_1	chr19	42131357	42131845	+	0	NA	intron (NM_001207025, intron 1 of 13)	MIRb|SINE|MIR	872	NM_001207025	5452	Hs.147381	NM_002698	ENSG00000028277	POU2F2	OCT2|OTF2|Oct-2	POU class 2 homeobox 2	protein-coding	0.010246	0.476483	
chunk0171_39_1	chr6	120589236	120589620	+	0	NA	Intergenic	Intergenic	574249	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.007812	0.374026	
chunk0111_257_1	chr20	30824866	30825142	+	0	NA	Intergenic	Intergenic	-421542	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.018116	0.509025	
chunk0088_89_1	chr18	44916418	44916744	+	0	NA	intron (NM_015559, intron 3 of 5)	intron (NM_015559, intron 3 of 5)	53585	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.006135	0.373089	
chunk0044_102_1	chr12	28536444	28536830	+	0	NA	intron (NM_018318, intron 11 of 11)	MIR|SINE|MIR	279437	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.000000	0.284238	138(GGGCCAGTTTGTTCTT,+,0.00)
chunk0014_66_1	chr1	176032111	176032638	+	0	NA	intron (NM_001001740, intron 13 of 18)	intron (NM_001001740, intron 13 of 18)	-63834	NR_002998	677679		NR_002998	ENSG00000252906	SCARNA3	HBI-100	small Cajal body-specific RNA 3	ncRNA	0.003795	0.376894	
chunk0060_336_1	chr14	51616934	51617151	+	0	NA	intron (NM_001042481, intron 2 of 14)	intron (NM_001042481, intron 2 of 14)	-17090	NR_051990	100874185	Hs.578226	NR_047477	ENSG00000258537	FRMD6-AS2	-	FRMD6 antisense RNA 2	ncRNA	0.013825	0.417431	165(AGGGACAGGCAGTGTT,-,0.00)
chunk0191_395_1	chr8	57424049	57424445	+	0	NA	Intergenic	Intergenic	80460	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.007576	0.375315	
chunk0110_89_1	chr20	11289425	11289943	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-16301	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.001931	0.412331	233(GGGCACTGACTGTCCT,-,0.00),234(GGCACTGACTGTCCTT,+,0.00)
chunk0008_175_1	chr1	92915468	92916003	+	0	NA	intron (NM_001252273, intron 1 of 4)	L1MB7|LINE|L1	-38585	NM_001252271	388650	Hs.180946	NM_001006605	ENSG00000154511	DIPK1A	FAM69A	divergent protein kinase domain 1A	protein-coding	0.001869	0.324627	
chunk0161_432_1	chr5	178473986	178474229	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	116448	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.024691	0.495902	
chunk0085_157_1	chr18	3596854	3597279	+	0	NA	non-coding (NR_024101, exon 3 of 3)	non-coding (NR_024101, exon 3 of 3)	2952	NR_024101	649446	Hs.19872	NM_001039796		DLGAP1-AS1	HsT914	DLGAP1 antisense RNA 1	ncRNA	0.018824	0.483568	
chunk0105_442_1	chr2	194697160	194697869	+	0	NA	Intergenic	Intergenic	-33081	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.001410	0.305634	222(GAGAACACAGAGTCCT,-,0.00),223(AGAACACAGAGTCCTT,+,0.00)
chunk0067_16_1	chr15	40069214	40069637	+	0	NA	Intergenic	Intergenic	30114	NR_040059	100131089	Hs.386000	NR_040059	ENSG00000248508	SRP14-AS1	-	SRP14 antisense RNA1 (head to head)	ncRNA	0.042553	0.658019	
chunk0172_336_1	chr6	138498578	138498814	+	0	NA	intron (NM_020464, intron 1 of 6)	intron (NM_020464, intron 1 of 6)	746	NM_001144060	57224	Hs.652741	NM_020464	ENSG00000135540	NHSL1	C6orf63	NHS like 1	protein-coding	0.004237	0.362869	
chunk0168_393_1	chr6	94514277	94514492	+	0	NA	Intergenic	L1PA8A|LINE|L1	807301	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.000000	0.365741	
chunk0137_390_1	chr4	27006020	27006520	+	0	NA	intron (NM_020860, intron 7 of 11)	intron (NM_020860, intron 7 of 11)	145579	NM_001169117	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.018000	0.389222	
chunk0149_237_1	chr5	23424111	23424464	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	-83322	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.008499	0.474576	
chunk0199_63_1	chr9	2292390	2292589	+	0	NA	Intergenic	Intergenic	134033	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.010050	0.400000	
chunk0155_194_1	chr5	94704130	94704460	+	0	NA	Intergenic	Intergenic	85609	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.012121	0.326284	
chunk0049_77_1	chr12	90449540	90449995	+	0	NA	Intergenic	L1MD1|LINE|L1	-468256	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.002198	0.375000	
chunk0086_113_1	chr18	14917523	14918104	+	0	NA	Intergenic	Intergenic	-28454	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.008606	0.491409	
chunk0196_186_1	chr8	106085264	106085840	+	0	NA	Intergenic	L2a|LINE|L2	-25049	NR_125797	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.001736	0.317158	
chunk0187_47_1	chr8	1662789	1663004	+	0	NA	intron (NM_001277161, intron 5 of 10)	(GT)n|Simple_repeat|Simple_repeat	-41232	NR_103863	100507435	Hs.667133	NR_103863	ENSG00000253267	DLGAP2-AS1	-	DLGAP2 antisense RNA 1	ncRNA	0.023256	0.537037	
chunk0055_21_1	chr13	51892944	51893464	+	0	NA	Intergenic	Intergenic	31223	NM_031290	83446	Hs.120573	NM_031290	ENSG00000123171	CCDC70	-	coiled-coil domain containing 70	protein-coding	0.003846	0.426104	
chunk0025_39_1	chr10	49021753	49022120	+	0	NA	intron (NM_001031746, intron 7 of 7)	intron (NM_001031746, intron 7 of 7)	-36349	NR_036182	100422895		NR_036182	ENSG00000264800	MIR4294	-	microRNA 4294	ncRNA	0.016349	0.377717	
chunk0209_33_1	chrX	36076435	36076876	+	0	NA	intron (NM_001304548, intron 29 of 63)	L1MA8|LINE|L1	156921	NM_152632	286464	Hs.376425	NM_152632	ENSG00000165164	CFAP47	CHDC2|CXorf22|CXorf30|CXorf59	cilia and flagella associated protein 47	protein-coding	0.000000	0.350679	
chunk0049_399_1	chr12	96809962	96810527	+	0	NA	intron (NM_001306084, intron 63 of 67)	HAL1|LINE|L1	-96979	NM_001135177	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.008850	0.436396	
chunk0076_406_1	chr16	72677669	72678412	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-13031	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.002692	0.372312	
chunk0074_49_1	chr16	20805438	20805912	+	0	NA	promoter-TSS (NM_030941)	promoter-TSS (NM_030941)	-770	NM_030941	81691	Hs.177926	NM_030941	ENSG00000005189	REXO5	NEF-sp	RNA exonuclease 5	protein-coding	0.014768	0.391579	155(ATGTACTTTATGTTCT,-,0.00),156(TGTACTTTATGTTCTT,+,0.00)
chunk0083_243_1	chr17	67717256	67718203	+	0	NA	promoter-TSS (NM_001303272)	promoter-TSS (NM_001303272)	-104	NM_001303272	25926	Hs.463936	NM_015462	ENSG00000130935	NOL11	-	nucleolar protein 11	protein-coding	0.050686	0.532700	
chunk0064_274_1	chr14	95121626	95122461	+	0	NA	intron (NM_001195573, intron 7 of 24)	intron (NM_001195573, intron 7 of 24)	11460	NM_001195573	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.005988	0.361244	
chunk0076_163_1	chr16	67363210	67363871	+	0	NA	intron (NM_018296, intron 5 of 13)	intron (NM_018296, intron 5 of 13)	16185	NM_001161575	55282	Hs.125139	NM_018296	ENSG00000159708	LRRC36	RORBP70|XLHSRF2	leucine rich repeat containing 36	protein-coding	0.006051	0.395770	
chunk0029_351_1	chr10	107076553	107077023	+	0	NA	intron (NM_052918, intron 1 of 25)	Helitron1Nb_Mam|RC|Helitron	87920	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.006383	0.373673	
chunk0050_143_1	chr12	102534019	102534370	+	0	NA	Intergenic	Intergenic	-53549	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.008547	0.502841	96(AAGGACACTGTGTGTT,-,0.00),97(AGGACACTGTGTGTTT,+,0.00),158(AAGGAGAGGATGTTCT,-,0.00),159(AGGAGAGGATGTTCTG,+,0.00),209(CAGTGCAGACTGTGCT,-,0.00),210(AGTGCAGACTGTGCTT,+,0.00)
chunk0126_379_1	chr3	84144626	84145151	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	724687	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.003810	0.326996	
chunk0058_52_1	chr14	20496031	20496310	+	0	NA	Intergenic	Intergenic	-14302	NM_001012975	338879	Hs.451057	NM_001012975	ENSG00000182545	RNASE10	RAH1|RNASE9	ribonuclease A family member 10 (inactive)	protein-coding	0.010753	0.471429	
chunk0010_421_1	chr1	119686603	119686877	+	0	NA	Intergenic	Intergenic	-25056	NM_006623	26227	Hs.487296	NM_006623	ENSG00000092621	PHGDH	3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA	phosphoglycerate dehydrogenase	protein-coding	0.010949	0.436364	
chunk0159_76_1	chr5	137515177	137515778	+	0	NA	Intergenic	Intergenic	-16148	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.009983	0.426910	
chunk0165_456_1	chr6	40928529	40929228	+	0	NA	intron (NR_110873, intron 1 of 5)	intron (NR_110873, intron 1 of 5)	94402	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.005722	0.427143	
chunk0212_257_1	chrX	139543778	139544526	+	0	NA	intron (NM_000133, intron 4 of 7)	intron (NM_000133, intron 4 of 7)	13416	NM_000133	2158	Hs.522798	NM_000133	ENSG00000101981	F9	F9 p22|FIX|HEMB|P19|PTC|THPH8	coagulation factor IX	protein-coding	0.008021	0.415220	
chunk0139_356_1	chr4	60233395	60233889	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-688977	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.010121	0.501010	
chunk0048_110_1	chr12	79523130	79523484	+	0	NA	Intergenic	Intergenic	104050	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.005650	0.374648	
chunk0032_17_1	chr11	689469	690045	+	0	NA	intron (NM_021008, intron 2 of 11)	intron (NM_021008, intron 2 of 11)	-5834	NM_001276274	283232	Hs.448664	NM_174940	ENSG00000177042	TMEM80	-	transmembrane protein 80	protein-coding	0.017361	0.538995	
chunk0205_316_1	chr9	112714672	112715167	+	0	NA	intron (NM_021218, intron 2 of 4)	Tigger3|DNA|TcMar-Tigger	3188	NM_021218	58493	Hs.658575	NM_021218	ENSG00000148153	INIP	C9orf80|HSPC043|MISE|SOSSC|SSBIP1|hSSBIP1	INTS3 and NABP interacting protein	protein-coding	0.004040	0.330645	
chunk0119_179_1	chr22	43745766	43746290	+	0	NA	intron (NM_198856, intron 4 of 29)	intron (NM_198856, intron 4 of 29)	66309	NM_022785	64800	Hs.658996	NM_022785	ENSG00000186976	EFCAB6	DJBP|HSCBCIP1|dJ185D5.1	EF-hand calcium binding domain 6	protein-coding	0.022901	0.424762	
chunk0152_113_1	chr5	58582405	58582731	+	0	NA	promoter-TSS (NM_138453)	promoter-TSS (NM_138453)	-544	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.058282	0.501529	
chunk0063_263_1	chr14	83740520	83740920	+	0	NA	Intergenic	Intergenic	-1653159	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.010000	0.356608	
chunk0188_421_1	chr8	18980161	18980490	+	0	NA	intron (NM_015310, intron 1 of 15)	intron (NM_015310, intron 1 of 15)	33361	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.009119	0.500000	
chunk0040_106_1	chr11	111879014	111879529	+	0	NA	promoter-TSS (NM_022761)	promoter-TSS (NM_022761)	47	NM_022761	64776	Hs.17546	NM_022761	ENSG00000137720	C11orf1	-	chromosome 11 open reading frame 1	protein-coding	0.073786	0.602713	
chunk0138_69_1	chr4	33481781	33482142	+	0	NA	Intergenic	Intergenic	557932	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.005540	0.328729	
chunk0195_433_1	chr8	101028473	101028705	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-23465	NR_033962	441374	Hs.652045	NR_033962	ENSG00000248599	FLJ42969	-	uncharacterized LOC441374	ncRNA	0.012931	0.540773	
chunk0132_227_1	chr3	158110106	158110596	+	0	NA	intron (NM_001271838, intron 1 of 9)	CpG	299	NM_001271834	51319	Hs.591283	NM_016625	ENSG00000174891	RSRC1	BM-011|MRT70|SFRS21|SRrp53	arginine and serine rich coiled-coil 1	protein-coding	0.077551	0.647658	
chunk0064_332_1	chr14	96473666	96474357	+	0	NA	intron (NM_152327, intron 14 of 17)	LTR4|LTR|ERV1	28315	NR_122121	730202	Hs.647565	NR_122121		LOC730202	-	uncharacterized LOC730202	ncRNA	0.010130	0.430636	
chunk0127_118_1	chr3	91891113	91891353	+	0	NA	Intergenic	ACRO1|Satellite|acro	2082848	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.020833	0.493776	
chunk0005_172_1	chr1	58597852	58598086	+	0	NA	Intergenic	Intergenic	-20475	NM_002353	4070	Hs.23582	NM_002353	ENSG00000184292	TACSTD2	EGP-1|EGP1|GA733-1|GA7331|GP50|M1S1|TROP2	tumor associated calcium signal transducer 2	protein-coding	0.012821	0.472340	97(TAGAACAGAGTGTTCC,-,0.00),98(AGAACAGAGTGTTCCA,+,0.00)
chunk0031_388_1	chr10	131047856	131048180	+	0	NA	Intergenic	Intergenic	-47200	NR_120623	101927489	Hs.659317	NR_120623	ENSG00000230098	TCERG1L-AS1	-	TCERG1L antisense RNA 1	ncRNA	0.021605	0.461538	
chunk0033_457_1	chr11	25697797	25698019	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-491215	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.000000	0.300448	
chunk0208_189_1	chrX	17182294	17182966	+	0	NA	Intergenic	Intergenic	-192790	NM_198270	4810	Hs.201623	NM_198270	ENSG00000188158	NHS	CTRCT40|CXN|SCML1	NHS actin remodeling regulator	protein-coding	0.008929	0.424963	
chunk0154_120_1	chr5	78773701	78774212	+	0	NA	Intergenic	Intergenic	-125131	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.015656	0.488281	
chunk0195_135_1	chr8	95070233	95070605	+	0	NA	intron (NR_132986, intron 1 of 1)	intron (NR_132986, intron 1 of 1)	-2495	NR_036105	100422964		NR_036105	ENSG00000283522	MIR3150A	MIR3150|mir-3150a	microRNA 3150a	ncRNA	0.002688	0.308311	
chunk0074_141_1	chr16	23114638	23114875	+	0	NA	intron (NM_020718, intron 1 of 15)	intron (NM_020718, intron 1 of 15)	34514	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.012658	0.428571	
chunk0038_320_1	chr11	91608578	91609164	+	0	NA	Intergenic	Intergenic	-739669	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.010239	0.396934	
chunk0067_323_1	chr15	48017625	48018218	+	0	NA	Intergenic	Intergenic	-103051	NM_205850	283652	Hs.710240	NM_205850	ENSG00000188467	SLC24A5	JSX|NCKX5|OCA6|SHEP4	solute carrier family 24 member 5	protein-coding	0.010118	0.468013	312(GAGGACACGCTGTGCC,-,0.00),313(AGGACACGCTGTGCCC,+,0.00)
chunk0101_11_1	chr2	121355510	121355869	+	0	NA	intron (NM_015282, intron 36 of 38)	intron (NM_015282, intron 36 of 38)	-70487	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.002786	0.450000	
chunk0040_165_1	chr11	113875717	113876027	+	0	NA	promoter-TSS (NM_001301029)	promoter-TSS (NM_001301029)	-302	NM_020886	57646	Hs.503891	NM_020886	ENSG00000048028	USP28	-	ubiquitin specific peptidase 28	protein-coding	0.077419	0.604502	
chunk0139_192_1	chr4	54554478	54554945	+	0	NA	Intergenic	MIRc|SINE|MIR	-103217	NM_000222	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.012848	0.493590	207(GGGAACACAAAGTGCT,-,0.00),208(GGAACACAAAGTGCTC,+,0.00)
chunk0200_47_1	chr9	15444136	15444586	+	0	NA	intron (NM_001039697, intron 3 of 8)	MIRb|SINE|MIR	21577	NM_001039697	6619	Hs.546299	NM_003084	ENSG00000164975	SNAPC3	PTFbeta|SNAP50	small nuclear RNA activating complex polypeptide 3	protein-coding	0.006667	0.374723	
chunk0108_143_1	chr2	230800624	230800873	+	0	NA	intron (NM_016289, intron 5 of 8)	L3|LINE|CR1	-63850	NM_001287241	81618	Hs.111577	NM_030926	ENSG00000135916	ITM2C	BRI3|BRICD2C|E25|E25C|ITM3	integral membrane protein 2C	protein-coding	0.008032	0.532000	
chunk0031_409_1	chr10	131997484	131998257	+	0	NA	Intergenic	Intergenic	-15857	NM_004052	664	Hs.144873	NM_004052	ENSG00000176171	BNIP3	NIP3	BCL2 interacting protein 3	protein-coding	0.021992	0.480620	
chunk0031_254_1	chr10	127157858	127158454	+	0	NA	intron (NM_001039762, intron 4 of 5)	intron (NM_001039762, intron 4 of 5)	38002	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.001678	0.370184	307(GGGAACACAGAGTGCT,-,0.00),308(GGAACACAGAGTGCTG,+,0.00)
chunk0151_334_1	chr5	53974083	53974282	+	0	NA	intron (NM_019087, intron 4 of 4)	intron (NM_019087, intron 4 of 4)	-22583	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.000000	0.465000	156(GAGCACAGGCAGTGCC,-,0.00),157(AGCACAGGCAGTGCCT,+,0.00)
chunk0175_72_1	chr7	2172882	2173234	+	0	NA	intron (NM_003550, intron 10 of 18)	HAL1|LINE|L1	59890	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.028409	0.504249	
chunk0004_97_1	chr1	43847457	43848016	+	0	NA	intron (NM_001270466, intron 4 of 4)	L1MB2|LINE|L1	9114	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.007156	0.339286	
chunk0160_233_1	chr5	155625874	155626743	+	0	NA	Intergenic	MER102c|DNA|hAT-Charlie	612608	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.006904	0.388506	
chunk0187_82_1	chr8	3073077	3073469	+	0	NA	intron (NM_033225, intron 49 of 69)	L1M2|LINE|L1	-344822	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.000000	0.315522	176(AAGAACAGCATGTCCA,-,0.00),177(AGAACAGCATGTCCAG,+,0.00)
chunk0064_111_1	chr14	91158046	91158581	+	0	NA	intron (NM_001102369, intron 4 of 14)	intron (NM_001102369, intron 4 of 14)	31887	NR_003709	100124539	Hs.693444	NR_003709	ENSG00000221102	SNORA11B	-	small nucleolar RNA, H/ACA box 11B	snoRNA	0.003738	0.490672	293(GGGGACTAAGTGTTCT,-,0.00),294(GGGACTAAGTGTTCTC,+,0.00)
chunk0038_242_1	chr11	87150654	87150911	+	0	NA	intron (NM_001168724, intron 4 of 13)	HAL1|LINE|L1	112938	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.011673	0.344961	
chunk0010_281_1	chr1	117478535	117479019	+	0	NA	intron (NM_006699, intron 8 of 12)	L1ME1|LINE|L1	111314	NM_006699	10905	Hs.435938	NM_006699	ENSG00000198162	MAN1A2	MAN1B	mannosidase alpha class 1A member 2	protein-coding	0.004132	0.315464	243(CAACACAGTGTGTACC,-,0.00),244(AACACAGTGTGTACCA,+,0.00)
chunk0086_415_1	chr18	26941566	26942026	+	0	NA	intron (NM_001256316, intron 4 of 4)	intron (NM_001256316, intron 4 of 4)	-76044	NM_001650	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.013043	0.429501	
chunk0175_13_1	chr7	220246	220646	+	0	NA	intron (NM_020223, intron 3 of 9)	intron (NM_020223, intron 3 of 9)	27477	NM_020223	56975	Hs.134742	NM_020223	ENSG00000177706	FAM20C	DMP-4|DMP4|G-CK|GEF-CK|RNS	FAM20C golgi associated secretory pathway kinase	protein-coding	0.042500	0.593516	
chunk0190_256_1	chr8	37074902	37075208	+	0	NA	Intergenic	Intergenic	290731	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.000000	0.364821	
chunk0152_415_1	chr5	65624880	65625122	+	0	NA	promoter-TSS (NM_001656)	promoter-TSS (NM_001656)	270	NM_001093756	80006	Hs.591760	NM_024941	ENSG00000113597	TRAPPC13	C5orf44|SHLD3	trafficking protein particle complex 13	protein-coding	0.037190	0.489712	
chunk0068_296_1	chr15	57053372	57054001	+	0	NA	intron (NM_003205, intron 3 of 19)	MER58A|DNA|hAT-Charlie	135051	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.006359	0.382540	
chunk0189_166_1	chr8	23392240	23392509	+	0	NA	intron (NM_002318, intron 1 of 13)	MamGypsy2-I|LTR|Gypsy	11835	NM_002318	4017	Hs.626637	NM_002318	ENSG00000134013	LOXL2	LOR|LOR2|WS9-14	lysyl oxidase like 2	protein-coding	0.007435	0.514815	
chunk0189_177_1	chr8	23552268	23552508	+	0	NA	intron (NM_016612, intron 1 of 3)	MIRb|SINE|MIR	23538	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.020833	0.443983	
chunk0009_4_1	chr1	99821659	99822020	+	0	NA	Intergenic	L2c|LINE|L2	-28245	NM_000642	178	Hs.904	NM_000028	ENSG00000162688	AGL	GDE	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	protein-coding	0.000000	0.342541	
chunk0151_272_1	chr5	52646387	52646689	+	0	NA	Intergenic	Intergenic	-141402	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.003311	0.353135	148(AATACATAATGTTCTG,+,0.00)
chunk0179_116_1	chr7	45543496	45543780	+	0	NA	Intergenic	Intergenic	-30502	NM_001281768	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.010563	0.361404	
chunk0092_78_1	chr19	20769307	20769692	+	0	NA	Intergenic	LTR10B1|LTR|ERV1	-107903	NM_145297	199777	Hs.657001	NM_145297	ENSG00000188171	ZNF626	-	zinc finger protein 626	protein-coding	0.012987	0.458549	
chunk0202_11_1	chr9	70384624	70384850	+	0	NA	3' UTR (NM_001206, exon 2 of 2)	3' UTR (NM_001206, exon 2 of 2)	29920	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.008850	0.308370	
chunk0015_159_1	chr1	186535694	186535893	+	0	NA	Intergenic	Intergenic	-74685	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.005025	0.325000	
chunk0035_367_1	chr11	49195595	49195835	+	0	NA	intron (NM_001193473, intron 2 of 16)	L1M5|LINE|L1	12955	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.008333	0.282158	
chunk0210_59_1	chrX	69314459	69315060	+	0	NA	Intergenic	L2b|LINE|L2	135202	NR_103715	100996279		NR_103715	ENSG00000215162	LINC00269	CXorf62|NCRNA00269	long intergenic non-protein coding RNA 269	ncRNA	0.019967	0.569767	
chunk0046_35_1	chr12	54689169	54689386	+	0	NA	Intergenic	Intergenic	-40784	NM_053283	117159	Hs.350570	NM_053283	ENSG00000161634	DCD	AIDD|DCD-1|DSEP|HCAP|PIF	dermcidin	protein-coding	0.027650	0.481651	
chunk0035_376_1	chr11	49670313	49670826	+	0	NA	intron (NR_027044, intron 2 of 6)	intron (NR_027044, intron 2 of 6)	112041	NR_027044	440040	Hs.655746	NR_027044	ENSG00000205035	LOC440040	-	glutamate metabotropic receptor 5 pseudogene	pseudo	0.003899	0.317121	
chunk0029_200_1	chr10	101629954	101630178	+	0	NA	intron (NM_022039, intron 5 of 8)	intron (NM_022039, intron 5 of 8)	-28569	NR_036115	100423033		NR_036115	ENSG00000283558	MIR3158-2	mir-3158-2	microRNA 3158-2	ncRNA	0.008929	0.515556	
chunk0008_107_1	chr1	91429580	91430154	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-24998	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.003484	0.391304	
chunk0021_72_1	chr10	1437713	1437912	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	-88818	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.025126	0.480000	
chunk0058_109_1	chr14	21915564	21916247	+	0	NA	Intergenic	Intergenic	250822	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.002928	0.413743	420(GAGAACGGAGAGTTCC,-,0.00)
chunk0125_371_1	chr3	71498017	71498661	+	0	NA	intron (NM_032682, intron 2 of 20)	intron (NM_032682, intron 2 of 20)	43750	NR_031697	100302112		NR_031697	ENSG00000221264	MIR1284	MIRN1284|hsa-mir-1284|mir-1284	microRNA 1284	ncRNA	0.009317	0.446512	
chunk0041_262_1	chr11	129048812	129049099	+	0	NA	intron (NM_001142685, intron 9 of 21)	intron (NM_001142685, intron 9 of 21)	-24762	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.006969	0.375000	141(CAGAACATCCAGTTTC,-,0.00),142(AGAACATCCAGTTTCT,+,0.00)
chunk0096_325_1	chr2	33589575	33589925	+	0	NA	intron (NM_015475, intron 3 of 7)	MER58A|DNA|hAT-Charlie	9612	NM_001304538	25940	Hs.468140	NM_015475	ENSG00000119812	FAM98A	-	family with sequence similarity 98 member A	protein-coding	0.002857	0.361823	
chunk0166_92_1	chr6	43726677	43727074	+	0	NA	Intergenic	MIR|SINE|MIR	-39063	NM_018135	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.010076	0.472362	
chunk0198_132_1	chr8	132440232	132440520	+	0	NA	intron (NM_004519, intron 1 of 14)	L2a|LINE|L2	6886	NM_001204824	3786	Hs.374023	NM_004519	ENSG00000184156	KCNQ3	BFNC2|EBN2|KV7.3	potassium voltage-gated channel subfamily Q member 3	protein-coding	0.017361	0.550173	
chunk0054_434_1	chr13	51295367	51296052	+	0	NA	Intergenic	Intergenic	-45323	NM_001101320	647174	Hs.685891	NM_001101320	ENSG00000253309	SERPINE3	-	serpin family E member 3	protein-coding	0.007299	0.367347	365(AAGAACTCAGTGTGCC,-,0.00),366(AGAACTCAGTGTGCCA,+,0.00)
chunk0194_252_1	chr8	86508324	86508800	+	0	NA	exon (NM_016033, exon 1 of 10)	exon (NM_016033, exon 1 of 10)	218	NM_016033	51115	Hs.145386	NM_016033	ENSG00000176623	RMDN1	CGI-90|FAM82B|RMD-1|RMD1	regulator of microtubule dynamics 1	protein-coding	0.084034	0.660377	
chunk0163_366_1	chr6	15776397	15776646	+	0	NA	Intergenic	Intergenic	-113463	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.000000	0.356000	83(AGCTCATTGTGTGCTC,+,0.00)
chunk0201_151_1	chr9	35957526	35957942	+	0	NA	exon (NM_019897, exon 1 of 1)	exon (NM_019897, exon 1 of 1)	420	NM_019897	56656	Hs.553540	NM_019897	ENSG00000278889	OR2S2	OR37A|OST715	olfactory receptor family 2 subfamily S member 2 (gene/pseudogene)	protein-coding	0.012019	0.544365	
chunk0185_60_1	chr7	124814847	124815341	+	0	NA	Intergenic	Intergenic	-24284	NM_001024603	154872	Hs.444163	NM_001024603	ENSG00000275356	C7orf77	-	chromosome 7 open reading frame 77	protein-coding	0.002024	0.303030	
chunk0163_377_1	chr6	16179164	16179440	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	37746	NR_039782	100616269		NR_039782	ENSG00000263712	MIR4639	-	microRNA 4639	ncRNA	0.007246	0.447653	
chunk0021_13_1	chr10	408374	408573	+	0	NA	intron (NM_014974, intron 9 of 36)	intron (NM_014974, intron 9 of 36)	-126387	NR_106988									0.010050	0.400000	
chunk0123_382_1	chr3	48715365	48715564	+	0	NA	5' UTR (NM_001190317, exon 2 of 3)	5' UTR (NM_001190317, exon 2 of 3)	1814	NM_001005910	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.000000	0.465000	
chunk0089_447_1	chr18	70281710	70282162	+	0	NA	Intergenic	Intergenic	-6965	NM_004232	9306	Hs.44439	NM_004232	ENSG00000170677	SOCS6	CIS-4|CIS4|HSPC060|SOCS-4|SOCS-6|SOCS4|SSI4|STAI4|STATI4	suppressor of cytokine signaling 6	protein-coding	0.011062	0.412804	
chunk0113_328_1	chr20	58565888	58566087	+	0	NA	intron (NR_034147, intron 6 of 6)	intron (NR_034147, intron 6 of 6)	50608	NR_034147	149773	Hs.685214	NR_034147	ENSG00000231290	APCDD1L-DT	APCDD1L-AS1	APCDD1L divergent transcript	ncRNA	0.020101	0.585000	
chunk0012_224_1	chr1	160251901	160252376	+	0	NA	intron (NR_028104, intron 1 of 12)	intron (NR_028104, intron 1 of 12)	10349	NR_028106	50717	Hs.632447	NM_015726	ENSG00000132716	DCAF8	GAN2|H326|WDR42A	DDB1 and CUL4 associated factor 8	protein-coding	0.002105	0.386555	
chunk0109_152_1	chr20	3811770	3812166	+	0	NA	intron (NR_109859, intron 3 of 3)	intron (NR_109859, intron 3 of 3)	3474	NR_109859	101929125	Hs.744106	NR_109859	ENSG00000275491	LINC01730	-	long intergenic non-protein coding RNA 1730	ncRNA	0.025253	0.649874	
chunk0105_380_1	chr2	192207300	192207776	+	0	NA	Intergenic	Charlie4z|DNA|hAT-Charlie	-12605	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.002101	0.287212	
chunk0035_245_1	chr11	46170765	46171480	+	0	NA	promoter-TSS (NR_120565)	promoter-TSS (NR_120565)	-833	NR_120565	101928894	Hs.552679	NR_120565	ENSG00000255314	LOC101928894	-	uncharacterized LOC101928894	ncRNA	0.002797	0.374302	
chunk0001_294_1	chr1	8986192	8986432	+	0	NA	Intergenic	Intergenic	40033	NM_207420	155184	Hs.531239	NM_207420	ENSG00000197241	SLC2A7	GLUT-7|GLUT7	solute carrier family 2 member 7	protein-coding	0.016667	0.539419	
chunk0181_259_1	chr7	85838907	85839320	+	0	NA	Intergenic	L3|LINE|CR1	-717182	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.243961	
chunk0076_32_1	chr16	59467116	59467489	+	0	NA	Intergenic	Intergenic	287889	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.008043	0.355615	
chunk0181_404_1	chr7	90060999	90061557	+	0	NA	intron (NR_110029, intron 2 of 2)	intron (NR_110029, intron 2 of 2)	-58122	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.005376	0.411449	
chunk0113_209_1	chr20	53785187	53785559	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	90336	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.013441	0.423592	
chunk0101_325_1	chr2	135965782	135966436	+	0	NA	intron (NM_001293312, intron 2 of 14)	intron (NM_001293312, intron 2 of 14)	-19067	NR_110199	101928243	Hs.602178	NR_110199	ENSG00000231890	DARS-AS1	-	DARS antisense RNA 1	ncRNA	0.003058	0.343511	294(AGGAGCAGTGTGTACA,-,0.00)
chunk0184_171_1	chr7	116421315	116421750	+	0	NA	Intergenic	Intergenic	-78069	NM_001233	858	Hs.212332	NM_001233	ENSG00000105971	CAV2	CAV	caveolin 2	protein-coding	0.002299	0.325688	
chunk0077_191_1	chr16	79758808	79759497	+	0	NA	intron (NR_104663, intron 2 of 5)	intron (NR_104663, intron 2 of 5)	-11319	NR_104660	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.015965	0.397101	
chunk0172_62_1	chr6	134272808	134273271	+	0	NA	intron (NM_001143676, intron 1 of 13)	intron (NM_001143676, intron 1 of 13)	45019	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.004320	0.403017	
chunk0112_395_1	chr20	46808483	46809113	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-85826	NM_005244	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.001587	0.331220	
chunk0181_341_1	chr7	88243419	88243622	+	0	NA	Intergenic	Intergenic	-16527	NM_001256892	6717	Hs.489040	NM_003130	ENSG00000075142	SRI	CP-22|CP22|SCN|V19	sorcin	protein-coding	0.004926	0.406863	
chunk0122_130_1	chr3	31562112	31562311	+	0	NA	intron (NM_178862, intron 1 of 15)	L1MA4A|LINE|L1	29710	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.010050	0.605000	
chunk0199_326_1	chr9	8329808	8330116	+	0	NA	intron (NM_001040712, intron 28 of 29)	L1PA7|LINE|L1	403984	NM_130393	5789	Hs.446083	NM_002839	ENSG00000153707	PTPRD	HPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA	protein tyrosine phosphatase receptor type D	protein-coding	0.025974	0.553398	260(GGGCCAGAGTGTACTG,+,0.00)
chunk0031_382_1	chr10	130925553	130925803	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	36990	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.012000	0.501992	
chunk0171_104_1	chr6	122117162	122117520	+	0	NA	Intergenic	MIR3|SINE|MIR	-282210	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.002793	0.337047	
chunk0196_294_1	chr8	109593192	109593724	+	0	NA	intron (NM_017786, intron 5 of 8)	intron (NM_017786, intron 5 of 8)	49732	NM_001099756	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.007519	0.439024	
chunk0192_257_1	chr8	65836014	65836656	+	0	NA	intron (NM_001242318, intron 1 of 12)	intron (NM_001242318, intron 1 of 12)	5399	NM_001242318	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.003115	0.340591	
chunk0142_65_1	chr4	92483300	92483682	+	0	NA	intron (NM_001286838, intron 1 of 14)	intron (NM_001286838, intron 1 of 14)	179092	NM_001510	2895	Hs.162727	NM_001510	ENSG00000152208	GRID2	GluD2|SCAR18	glutamate ionotropic receptor delta type subunit 2	protein-coding	0.005236	0.370757	
chunk0127_112_1	chr3	90180722	90181270	+	0	NA	Intergenic	Intergenic	1073472	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005474	0.351548	
chunk0080_35_1	chr17	21174225	21174548	+	0	NA	intron (NM_015510, intron 2 of 6)	intron (NM_015510, intron 2 of 6)	40209	NM_003876	8834	Hs.592945	NM_003876	ENSG00000178307	TMEM11	C17orf35|PM1|PMI	transmembrane protein 11	protein-coding	0.021672	0.469136	127(AGGAACAGAACGTTCT,-,0.00),128(GGAACAGAACGTTCTG,+,0.00)
chunk0082_95_1	chr17	53931833	53932184	+	0	NA	Intergenic	L1MA2|LINE|L1	109130	NM_032559	84643	Hs.226805	NM_032559	ENSG00000141200	KIF2B	-	kinesin family member 2B	protein-coding	0.008547	0.505682	
chunk0161_361_1	chr5	175506379	175506690	+	0	NA	intron (NM_022754, intron 2 of 10)	L1ME4a|LINE|L1	28023	NM_022754	94081	Hs.369440	NM_022754	ENSG00000164466	SFXN1	SLC56A1|TCC	sideroflexin 1	protein-coding	0.000000	0.291667	
chunk0203_156_1	chr9	85808165	85808866	+	0	NA	intron (NR_029410, intron 1 of 8)	intron (NR_029410, intron 1 of 8)	2513	NR_029410	389765	Hs.715986	NR_029410		LOC389765	-	kinesin family member 27 pseudogene	pseudo	0.009986	0.383191	
chunk0095_68_1	chr2	14514352	14514551	+	0	NA	Intergenic	Intergenic	-113493	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.000000	0.415000	
chunk0064_338_1	chr14	96571826	96572329	+	0	NA	Intergenic	Intergenic	69212	NM_001293628	10914	Hs.253726	NM_032632	ENSG00000090060	PAPOLA	PAP|PAP-alpha	poly(A) polymerase alpha	protein-coding	0.011928	0.414683	
chunk0028_5_1	chr10	82037206	82037545	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	159688	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.000000	0.497059	
chunk0060_62_1	chr14	41652633	41653260	+	0	NA	intron (NM_152447, intron 1 of 5)	L1P3|LINE|L1	45385	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.001595	0.345541	332(GAGAACTGTCTGTTCA,-,0.00),333(AGAACTGTCTGTTCAT,+,0.00)
chunk0093_427_1	chr19	57824324	57824572	+	0	NA	TTS (NR_024162)	TTS (NR_024162)	3014	NR_024162	2282	Hs.720356	NR_024162		FKBP1AP1	FKBP12|FKBP1P1	FKBP prolyl isomerase 1A pseudogene 1	pseudo	0.016129	0.497992	
chunk0022_424_1	chr10	19178711	19178970	+	0	NA	intron (NM_001142308, intron 14 of 39)	intron (NM_001142308, intron 14 of 39)	130069	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.015444	0.411538	
chunk0083_317_1	chr17	69501044	69501440	+	0	NA	intron (NM_002758, intron 1 of 11)	intron (NM_002758, intron 1 of 11)	86545	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.020202	0.455919	
chunk0004_425_1	chr1	52662633	52663169	+	0	NA	Intergenic	Intergenic	29507	NM_001042693	348378	Hs.424589	NM_001042693	ENSG00000182183	SHISAL2A	FAM159A|PRO7171|WWLS2783	shisa like 2A	protein-coding	0.016791	0.517691	
chunk0007_132_1	chr1	79190707	79191008	+	0	NA	Intergenic	LTR1F|LTR|ERV1	-184047	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.013289	0.523179	
chunk0073_376_1	chr16	15812130	15812357	+	0	NA	intron (NM_001040113, intron 3 of 42)	MIRb|SINE|MIR	44787	NM_022844	4629	Hs.460109	NM_002474	ENSG00000133392	MYH11	AAT4|FAA4|SMHC|SMMHC	myosin heavy chain 11	protein-coding	0.022026	0.504386	
chunk0098_201_1	chr2	72551791	72552459	+	0	NA	intron (NM_015189, intron 8 of 21)	L2a|LINE|L2	273923	NM_015189	23233	Hs.303454	NM_015189	ENSG00000144036	EXOC6B	SEC15B|SEC15L2|SEMDJL3	exocyst complex component 6B	protein-coding	0.005988	0.298954	
chunk0044_108_1	chr12	28871162	28871401	+	0	NA	Intergenic	Intergenic	-277722	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.000000	0.408333	
chunk0123_254_1	chr3	45843029	45843525	+	0	NA	intron (NM_001276378, intron 3 of 11)	intron (NM_001276378, intron 3 of 11)	-1119	NR_075080	54585	Hs.30824	NM_020347	ENSG00000163818	LZTFL1	BBS17	leucine zipper transcription factor like 1	protein-coding	0.012097	0.446680	
chunk0093_24_1	chr2	311035	311710	+	0	NA	Intergenic	Intergenic	-23064	NM_001002919	285016	Hs.355207	NM_001002919	ENSG00000189292	ALKAL2	AUGA|FAM150B|PRO1097|RGPG542	ALK and LTK ligand 2	protein-coding	0.022222	0.449704	
chunk0142_445_1	chr4	105436679	105436878	+	0	NA	intron (NM_176866, intron 2 of 7)	L1PA15-16|LINE|L1	37292	NM_176866	27068	Hs.654957	NM_006903	ENSG00000138777	PPA2	HSPC124|SCFAI|SCFI|SID6-306	pyrophosphatase (inorganic) 2	protein-coding	0.000000	0.340000	
chunk0117_262_1	chr22	23567480	23567776	+	0	NA	Intergenic	(AG)n|Simple_repeat|Simple_repeat	12680	NM_152855	3543	Hs.348935	NM_020070	ENSG00000128322	IGLL1	14.1|AGM2|CD179b|IGL1|IGL5|IGLJ14.1|IGLL|IGO|IGVPB|VPREB2	immunoglobulin lambda like polypeptide 1	protein-coding	0.006757	0.602694	210(ATGGACACGGTGTCCT,-,0.00),211(TGGACACGGTGTCCTG,+,0.00)
chunk0084_441_1	chr17	82864207	82864661	+	0	NA	intron (NM_005993, intron 13 of 38)	intron (NM_005993, intron 13 of 38)	-24379	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.026432	0.564835	190(AGGGACGTTCTGTGCT,-,0.00),191(GGGACGTTCTGTGCTC,+,0.00)
chunk0101_46_1	chr2	122933062	122933675	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-1091919	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.006525	0.395765	
chunk0096_11_1	chr2	26011005	26011599	+	0	NA	Intergenic	L1ME3A|LINE|L1	-22558	NM_016131	10890	Hs.467960	NM_016131	ENSG00000084733	RAB10	-	RAB10, member RAS oncogene family	protein-coding	0.005051	0.401681	
chunk0020_197_1	chr1	234943910	234944142	+	0	NA	Intergenic	Intergenic	19973	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.017241	0.515021	
chunk0189_416_1	chr8	27792468	27792759	+	0	NA	intron (NM_001017420, intron 8 of 10)	intron (NM_001017420, intron 8 of 10)	18072	NM_001017420	157570	Hs.99480	NM_001017420	ENSG00000171320	ESCO2	2410004I17Rik|EFO2|EFO2p|RBS|hEFO2	establishment of sister chromatid cohesion N-acetyltransferase 2	protein-coding	0.000000	0.284247	
chunk0152_165_1	chr5	59521710	59521969	+	0	NA	intron (NM_001165899, intron 3 of 16)	L2a|LINE|L2	64659	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.007722	0.365385	
chunk0179_103_1	chr7	44848336	44848538	+	0	NA	promoter-TSS (NM_012412)	promoter-TSS (NM_012412)	-311	NM_012412	94239	Hs.488189	NM_012412	ENSG00000105968	H2AFV	H2A.Z-2|H2AV	H2A histone family member V	protein-coding	0.064356	0.536946	
chunk0030_323_1	chr10	118126042	118126446	+	0	NA	intron (NR_026940, intron 3 of 3)	L1PB4|LINE|L1	79423	NR_026941	255082	Hs.89387	NM_178816	ENSG00000177640	CASC2	C10orf5	cancer susceptibility 2	ncRNA	0.002475	0.400000	
chunk0078_339_1	chr17	8985327	8985894	+	0	NA	Intergenic	L1M4|LINE|L1	-19898	NM_001142633	23533	Hs.278901	NM_014308	ENSG00000141506	PIK3R5	F730038I15Rik|FOAP-2|P101-PI3K|p101	phosphoinositide-3-kinase regulatory subunit 5	protein-coding	0.007055	0.434859	
chunk0019_400_1	chr1	230498649	230499027	+	0	NA	Intergenic	Intergenic	-72910	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.015873	0.448549	
chunk0161_438_1	chr5	178552934	178553543	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	37317	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.022989	0.465574	259(CAAGACAGCGTGTGCC,-,0.00),260(AAGACAGCGTGTGCCC,+,0.00)
chunk0164_150_1	chr6	21462109	21462932	+	0	NA	Intergenic	Intergenic	49372	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.002430	0.398058	
chunk0073_245_1	chr16	11700289	11701014	+	0	NA	intron (NM_015914, intron 5 of 11)	intron (NM_015914, intron 5 of 11)	32218	NM_003498	8303	Hs.618526	NM_003498	ENSG00000184602	SNN	-	stannin	protein-coding	0.012414	0.446281	577(AGGCACATGCTGTTCT,-,0.00),578(GGCACATGCTGTTCTC,+,0.00)
chunk0100_140_1	chr2	108825291	108825924	+	0	NA	intron (NR_130121, intron 10 of 13)	L1MB8|LINE|L1	38857	NM_001303106	165055	Hs.362702	NM_144978	ENSG00000163006	CCDC138	-	coiled-coil domain containing 138	protein-coding	0.007899	0.339117	183(CAGCACTTCCAGTCCT,-,0.00)
chunk0086_165_1	chr18	21678735	21679408	+	0	NA	intron (NM_138340, intron 4 of 8)	intron (NM_138340, intron 4 of 8)	-4439	NR_031565	100302135		NR_031565	ENSG00000221493	MIR320C1	MIR320C-1|MIRN320C1|hsa-mir-320c-1|mir-320c-1	microRNA 320c-1	ncRNA	0.004458	0.367953	
chunk0057_353_1	chr13	108554970	108555177	+	0	NA	Intergenic	Intergenic	-41079	NM_015011	23026	Hs.656587	NM_015011	ENSG00000041515	MYO16	MYAP3|MYR8|Myo16b|NYAP3|PPP1R107	myosin XVI	protein-coding	0.004831	0.288462	
chunk0102_324_1	chr2	151720304	151720550	+	0	NA	intron (NM_001164507, intron 9 of 181)	intron (NM_001164507, intron 9 of 181)	14060	NM_001164507	4703	Hs.588655	NM_004543	ENSG00000183091	NEB	NEB177D|NEM2	nebulin	protein-coding	0.000000	0.368421	
chunk0003_228_1	chr1	35678882	35679206	+	0	NA	Intergenic	Intergenic	-37200	NM_002794	5690	Hs.471441	NM_002794	ENSG00000126067	PSMB2	HC7-I	proteasome subunit beta 2	protein-coding	0.009259	0.480000	
chunk0072_48_1	chr16	1264749	1265111	+	0	NA	Intergenic	Intergenic	8658	NM_012217	23430	Hs.677789	NM_012217	ENSG00000095917	TPSD1	MCP7-LIKE|MCP7L1|MMCP-7L	tryptase delta 1	protein-coding	0.024862	0.465565	
chunk0124_325_1	chr3	58144610	58145261	+	0	NA	intron (NM_001164317, intron 33 of 46)	L1ME4b|LINE|L1	66068	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.006144	0.380368	
chunk0209_323_1	chrX	50403853	50404531	+	0	NA	intron (NM_001013742, intron 4 of 27)	intron (NM_001013742, intron 4 of 27)	66546	NM_001013742	139189	Hs.38132	NM_001013742	ENSG00000274588	DGKK	-	diacylglycerol kinase kappa	protein-coding	0.013274	0.438881	
chunk0060_105_1	chr14	43399162	43399709	+	0	NA	Intergenic	Intergenic	1107861	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.001828	0.330292	
chunk0053_307_1	chr13	33882623	33883304	+	0	NA	intron (NM_181558, intron 8 of 8)	L1MD2|LINE|L1	64894	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.001468	0.362170	
chunk0128_81_1	chr3	105425132	105425426	+	0	NA	intron (NM_001627, intron 1 of 15)	intron (NM_001627, intron 1 of 15)	58566	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006803	0.379661	
chunk0026_252_1	chr10	66513459	66513658	+	0	NA	intron (NM_001127384, intron 11 of 17)	L1MA5A|LINE|L1	-412476	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.010050	0.555000	
chunk0102_458_1	chr2	158602000	158602367	+	0	NA	intron (NM_001005476, intron 3 of 20)	intron (NM_001005476, intron 3 of 20)	145303	NM_001005476	8502	Hs.407580	NM_003628	ENSG00000144283	PKP4	p0071	plakophilin 4	protein-coding	0.005450	0.358696	
chunk0044_344_1	chr12	38602000	38602285	+	0	NA	Intergenic	Intergenic	285387	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.000000	0.377622	
chunk0095_203_1	chr2	18406209	18406600	+	0	NA	Intergenic	Intergenic	154289	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.005115	0.426020	
chunk0064_418_1	chr14	99604078	99604352	+	0	NA	5' UTR (NM_001144995, exon 1 of 6)	5' UTR (NM_001144995, exon 1 of 6)	175	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.164234	0.843636	
chunk0015_280_1	chr1	188554661	188555075	+	0	NA	Intergenic	Intergenic	1111240	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.009662	0.334940	
chunk0149_443_1	chr5	29817312	29817806	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-421583	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.006073	0.331313	
chunk0181_180_1	chr7	83065038	83065394	+	0	NA	intron (NM_014510, intron 3 of 19)	intron (NM_014510, intron 3 of 19)	97665	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.002809	0.319328	169(CAGCTCAGTATGTTCT,-,0.00),170(AGCTCAGTATGTTCTT,+,0.00)
chunk0195_42_1	chr8	93318166	93318378	+	0	NA	Intergenic	Intergenic	-151422	NM_001242668									0.009434	0.375587	
chunk0152_71_1	chr5	58042165	58042364	+	0	NA	Intergenic	Intergenic	80077	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.000000	0.365000	
chunk0106_100_1	chr2	197287245	197287475	+	0	NA	intron (NR_046837, intron 5 of 5)	intron (NR_046837, intron 5 of 5)	15159	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.008696	0.346320	
chunk0172_105_1	chr6	134903530	134903936	+	0	NA	Intergenic	Intergenic	46389	NM_170771	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.024631	0.466830	271(GGGTACAGGCTGTTCC,-,0.00),272(GGTACAGGCTGTTCCG,+,0.00)
chunk0159_406_1	chr5	147708794	147709129	+	0	NA	intron (NM_001270941, intron 1 of 21)	Tigger12c|DNA|TcMar-Tigger	73887	NM_014790	9832	Hs.740461	NM_014790	ENSG00000176049	JAKMIP2	JAMIP2|NECC1	janus kinase and microtubule interacting protein 2	protein-coding	0.005970	0.392857	
chunk0050_74_1	chr12	101608185	101609084	+	0	NA	intron (NM_001254722, intron 1 of 27)	intron (NM_001254722, intron 1 of 27)	13703	NM_001254719	4604	Hs.654589	NM_002465	ENSG00000196091	MYBPC1	LCCS4|MYBPCC|MYBPCS	myosin binding protein C, slow type	protein-coding	0.012236	0.435556	713(AAAGACATAGTGTTCC,-,0.00),714(AAGACATAGTGTTCCT,+,0.00)
chunk0198_362_1	chr8	140922340	140922885	+	0	NA	intron (NM_001316342, intron 1 of 32)	intron (NM_001316342, intron 1 of 32)	78701	NM_005607	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.009174	0.406593	252(AAGCACACTGAGTCCA,-,0.00),253(AGCACACTGAGTCCAT,+,0.00)
chunk0159_163_1	chr5	139562179	139562378	+	0	NA	5' UTR (NM_181838, exon 2 of 8)	5' UTR (NM_181838, exon 2 of 8)	1112	NM_181838	7322	Hs.108332	NM_003339	ENSG00000131508	UBE2D2	E2(17)KB2|PUBC1|UBC4|UBC4/5|UBCH4|UBCH5B	ubiquitin conjugating enzyme E2 D2	protein-coding	0.040201	0.560000	
chunk0143_28_1	chr4	106165317	106165759	+	0	NA	intron (NM_001163435, intron 23 of 25)	intron (NM_001163435, intron 23 of 25)	-143060	NR_125928	101929577	Hs.631131	NR_125928	ENSG00000249635	LOC101929577	-	uncharacterized LOC101929577	ncRNA	0.002262	0.311512	233(TAGAACATCATGTCCT,-,0.00),234(AGAACATCATGTCCTT,+,0.00)
chunk0160_48_1	chr5	149594551	149594893	+	0	NA	intron (NM_001001669, intron 1 of 12)	intron (NM_001001669, intron 1 of 12)	13150	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.005848	0.358601	
chunk0017_301_1	chr1	211145988	211146198	+	0	NA	Intergenic	L2|LINE|L2	-11978	NM_002238	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.009524	0.440758	
chunk0025_348_1	chr10	58151909	58152209	+	0	NA	Intergenic	Intergenic	115875	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.000000	0.421927	
chunk0076_76_1	chr16	63505991	63506311	+	0	NA	Intergenic	L1MA10|LINE|L1	-1469316	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.006250	0.501558	
chunk0048_1_1	chr12	76915616	76916210	+	0	NA	Intergenic	Intergenic	-36873	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.008418	0.341176	
chunk0168_179_1	chr6	84467282	84467481	+	0	NA	intron (NR_132100, intron 2 of 4)	intron (NR_132100, intron 2 of 4)	7548	NR_132100	105377880	Hs.171384	NR_132100	ENSG00000231776	LINC01611	TCONS_l2_00025430	long intergenic non-protein coding RNA 1611	ncRNA	0.000000	0.295000	
chunk0035_137_1	chr11	42830936	42831402	+	0	NA	Intergenic	Intergenic	438200	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.000000	0.423983	
chunk0021_425_1	chr1	247104232	247104481	+	0	NA	promoter-TSS (NM_024804)	promoter-TSS (NM_024804)	16	NM_001142572	79862	Hs.163754	NM_024804	ENSG00000188295	ZNF669	-	zinc finger protein 669	protein-coding	0.060241	0.660000	
chunk0049_173_1	chr12	92336479	92336890	+	0	NA	Intergenic	Intergenic	-84847	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.004866	0.330097	
chunk0201_324_1	chr9	63608964	63609172	+	0	NA	Intergenic	Intergenic	-210506	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.009615	0.334928	
chunk0145_64_1	chr4	145513020	145513702	+	0	NA	intron (NM_001003688, intron 1 of 6)	L1MEg|LINE|L1	3833	NR_126371	104326058	Hs.714527	NR_126371	ENSG00000250902	SMAD1-AS1	-	SMAD1 antisense RNA 1	ncRNA	0.005865	0.393851	457(GGTACAGTATGTGTCC,+,0.00)
chunk0195_247_1	chr8	97733441	97734125	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-41798	NM_018407	55353	Hs.492314	NM_018407	ENSG00000104341	LAPTM4B	LAPTM4beta|LC27	lysosomal protein transmembrane 4 beta	protein-coding	0.008772	0.367883	
chunk0212_394_1	chrX	150806769	150807233	+	0	NA	intron (NM_134446, intron 2 of 8)	intron (NM_134446, intron 2 of 8)	91815	NM_031462	83692	Hs.522805	NM_031462	ENSG00000102181	CD99L2	CD99B|MIC2L1	CD99 molecule like 2	protein-coding	0.004310	0.421505	
chunk0122_279_1	chr3	35652902	35653370	+	0	NA	intron (NM_016300, intron 1 of 19)	intron (NM_016300, intron 1 of 19)	10779	NM_016300	10777	Hs.475902	NM_016300	ENSG00000172995	ARPP21	ARPP-21|R3HDM3|RCS|TARPP	cAMP regulated phosphoprotein 21	protein-coding	0.004274	0.328358	258(AGGGACTTTGTGTGCC,-,0.00),259(GGGACTTTGTGTGCCT,+,0.00)
chunk0175_36_1	chr7	873291	873685	+	0	NA	3' UTR (NM_025154, exon 18 of 18)	3' UTR (NM_025154, exon 18 of 18)	-3066	NM_015949	51608	Hs.107387	NM_015949	ENSG00000239857	GET4	C7orf20|CEE|CGI-20|TRC35	guided entry of tail-anchored proteins factor 4	protein-coding	0.038071	0.508861	
chunk0085_94_1	chr18	2658194	2658533	+	0	NA	intron (NM_015295, intron 1 of 47)	intron (NM_015295, intron 1 of 47)	2476	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.008850	0.338235	
chunk0153_343_1	chr5	74207062	74207271	+	0	NA	Intergenic	Intergenic	101159	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.009569	0.495238	
chunk0061_202_1	chr14	60284716	60285381	+	0	NA	intron (NM_021003, intron 2 of 5)	intron (NM_021003, intron 2 of 5)	35800	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.003008	0.273273	
chunk0177_255_1	chr7	25249666	25250315	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-21504	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.009245	0.493846	
chunk0119_393_1	chr22	48878465	48879088	+	0	NA	intron (NR_038944, intron 1 of 6)	L1ME1|LINE|L1	12006	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.008026	0.362179	277(TGAACTCTTTGTTCTC,+,0.00)
chunk0185_31_1	chr7	124318664	124319454	+	0	NA	Intergenic	L1MA4|LINE|L1	33037	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.006329	0.318584	
chunk0161_318_1	chr5	173565777	173565988	+	0	NA	Intergenic	Intergenic	-13752	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.009479	0.415094	
chunk0203_387_1	chr9	90457647	90457846	+	0	NA	Intergenic	L2b|LINE|L2	-24257	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.025126	0.550000	
chunk0126_193_1	chr3	78496234	78496728	+	0	NA	Intergenic	Intergenic	522978	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.010121	0.367677	
chunk0133_97_1	chr3	167899256	167899621	+	0	NA	intron (NR_033843, intron 1 of 7)	intron (NR_033843, intron 1 of 7)	3490	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.010959	0.385246	
chunk0053_86_1	chr13	28455831	28456210	+	0	NA	intron (NM_001159920, intron 3 of 12)	L1MC3|LINE|L1	39108	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.007916	0.407895	
chunk0068_449_1	chr15	59783716	59784488	+	0	NA	Intergenic	L1PB|LINE|L1	-94659	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.010363	0.514877	
chunk0008_83_1	chr1	90008078	90008703	+	0	NA	intron (NM_182976, intron 5 of 11)	intron (NM_182976, intron 5 of 11)	13271	NM_182976	284695	Hs.306221	NM_181781	ENSG00000162664	ZNF326	ZAN75|ZIRD|Zfp326|dJ871E2.1	zinc finger protein 326	protein-coding	0.003200	0.313099	
chunk0143_306_1	chr4	118835133	118835372	+	0	NA	intron (NM_014822, intron 1 of 22)	intron (NM_014822, intron 1 of 22)	919	NM_014822	9871	Hs.189641	NM_014822	ENSG00000150961	SEC24D	CLCRP2	SEC24 homolog D, COPII coat complex component	protein-coding	0.029289	0.516667	
chunk0151_164_1	chr5	49660890	49661244	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	780333	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.025424	0.419718	
chunk0087_198_1	chr18	35785251	35785617	+	0	NA	Intergenic	L2a|LINE|L2	119492	NR_029616	406963		NR_029616	ENSG00000207797	MIR187	MIRN187|miR-187|miRNA187	microRNA 187	ncRNA	0.010929	0.408719	39(TTGCACTGACTGTTCC,-,0.00),40(TGCACTGACTGTTCCC,+,0.00),208(TAGAACATCGTGTGCC,-,0.00),209(AGAACATCGTGTGCCT,+,0.00)
chunk0040_335_1	chr11	118366207	118366805	+	0	NA	intron (NM_001204077, intron 2 of 19)	intron (NM_001204077, intron 2 of 19)	6925	NM_004788	9354	Hs.75275	NM_004788	ENSG00000110344	UBE4A	E4|UBOX2|UFD2	ubiquitination factor E4A	protein-coding	0.006689	0.405676	
chunk0093_292_1	chr19	52342941	52343346	+	0	NA	intron (NM_001161427, intron 1 of 4)	L2a|LINE|L2	-2286	NM_173530	162963	Hs.147025	NM_173530	ENSG00000167554	ZNF610	-	zinc finger protein 610	protein-coding	0.009877	0.450739	213(AGGGACACCCTGTACT,-,0.00),214(GGGACACCCTGTACTT,+,0.00)
chunk0065_96_1	chr15	23925577	23926216	+	0	NA	Intergenic	Intergenic	-49251	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.009390	0.415625	
chunk0027_244_1	chr10	77069016	77069546	+	0	NA	intron (NM_001014797, intron 14 of 28)	CR1_Mam|LINE|CR1	-71550	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.003774	0.416196	216(ATGAACAGCATGTTCC,-,0.00),217(TGAACAGCATGTTCCA,+,0.00)
chunk0195_365_1	chr8	99928020	99928410	+	0	NA	Intergenic	Intergenic	-34201	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.005128	0.368286	
chunk0147_183_1	chr4	177304113	177304611	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-5475	NM_018248	55247	Hs.405467	NM_018248	ENSG00000109674	NEIL3	FGP2|FPG2|NEI3|ZGRF3|hFPG2|hNEI3	nei like DNA glycosylase 3	protein-coding	0.008032	0.330661	
chunk0133_425_1	chr3	174826013	174826608	+	0	NA	Intergenic	MIR|SINE|MIR	-33011	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.003361	0.352349	
chunk0089_390_1	chr18	67875992	67876420	+	0	NA	intron (NR_033921, intron 4 of 4)	L1ME1|LINE|L1	-359476	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.004673	0.368298	
chunk0117_174_1	chr22	20701007	20701234	+	0	NA	promoter-TSS (NR_026815)	promoter-TSS (NR_026815)	6	NR_026815	84222	Hs.546454	NM_032262	ENSG00000226287	TMEM191A	TMEM191AP	transmembrane protein 191A (pseudogene)	pseudo	0.017621	0.434211	
chunk0078_169_1	chr17	4316106	4316460	+	0	NA	intron (NM_003342, intron 1 of 5)	intron (NM_003342, intron 1 of 5)	-44389	NR_110982	103021295	Hs.741319	NR_110982		LOC103021295	-	uncharacterized LOC103021295	ncRNA	0.005650	0.366197	
chunk0088_119_1	chr18	45713180	45713693	+	0	NA	Intergenic	Intergenic	-10687	NM_001308279	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.003899	0.406615	
chunk0152_335_1	chr5	62425611	62426205	+	0	NA	intron (NM_001134779, intron 1 of 29)	intron (NM_001134779, intron 1 of 29)	7024	NM_001134779	51194	Hs.482269	NM_016338	ENSG00000086200	IPO11	RanBP11	importin 11	protein-coding	0.011785	0.369748	313(AAGAACATTAAGTACC,-,0.00),314(AGAACATTAAGTACCT,+,0.00)
chunk0021_97_1	chr10	2986043	2986837	+	0	NA	Intergenic	Intergenic	-81080	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.023929	0.485535	415(CAGAACAGATTGTGTC,-,0.00),416(AGAACAGATTGTGTCT,+,0.00)
chunk0047_394_1	chr12	75651337	75651536	+	0	NA	Intergenic	Intergenic	-139798	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.005025	0.395000	175(AAGAACATCTTGCCCT,-,0.00)
chunk0166_77_1	chr6	43335413	43335671	+	0	NA	TTS (NM_014345)	TTS (NM_014345)	-26750	NM_206922	401262	Hs.653165	NM_206922	ENSG00000146215	CRIP3	CRP-3|TLP|TLP-A|h6LIMo	cysteine rich protein 3	protein-coding	0.007752	0.397683	
chunk0066_237_1	chr15	34265762	34266386	+	0	NA	intron (NM_001042497, intron 1 of 23)	intron (NM_001042497, intron 1 of 23)	41077	NM_016454	51234	Hs.250905	NM_016454	ENSG00000128463	EMC4	PIG17|TMEM85	ER membrane protein complex subunit 4	protein-coding	0.001603	0.315200	
chunk0139_14_1	chr4	48038707	48038947	+	0	NA	Intergenic	Intergenic	22053	NM_207330	152519	Hs.134190	NM_207330	ENSG00000163293	NIPAL1	NPAL1	NIPA like domain containing 1	protein-coding	0.008333	0.431535	158(AGGCTCATTGTGTACC,-,0.00)
chunk0164_289_1	chr6	24613498	24613846	+	0	NA	intron (NM_001168374, intron 1 of 21)	intron (NM_001168374, intron 1 of 21)	-30445	NM_001252328	9856	Hs.26441	NM_014809	ENSG00000137261	KIAA0319	AAVR|DYLX2|DYX2|NMIG	KIAA0319	protein-coding	0.002874	0.355301	
chunk0012_149_1	chr1	157736062	157736669	+	0	NA	Intergenic	L1PA7|LINE|L1	-35508	NM_052939	115352	Hs.292449	NM_052939	ENSG00000160856	FCRL3	CD307c|FCRH3|IFGP3|IRTA3|SPAP2	Fc receptor like 3	protein-coding	0.006590	0.379934	291(GAGAACTGTCTGTTCA,-,0.00),292(AGAACTGTCTGTTCAT,+,0.00)
chunk0155_61_1	chr5	91528742	91529322	+	0	NA	Intergenic	L2c|LINE|L2	-145700	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003448	0.368330	
chunk0110_119_1	chr20	12910631	12911086	+	0	NA	intron (NR_109868, intron 6 of 11)	intron (NR_109868, intron 6 of 11)	26105	NR_109872	102606466	Hs.602196	NR_109872		LOC102606466	-	uncharacterized LOC102606466	ncRNA	0.008791	0.412281	
chunk0073_137_1	chr16	6482121	6482403	+	0	NA	intron (NM_018723, intron 2 of 15)	intron (NM_018723, intron 2 of 15)	-291547	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.000000	0.346290	
chunk0143_313_1	chr4	119080901	119081501	+	0	NA	Intergenic	L2c|LINE|L2	-54583	NM_016599	51778	Hs.732122	NM_016599	ENSG00000172399	MYOZ2	C4orf5|CMH16|CS-1|FATZ-2	myozenin 2	protein-coding	0.003333	0.417637	
chunk0141_301_1	chr4	87029211	87029916	+	0	NA	intron (NM_001313960, intron 1 of 17)	intron (NM_001313960, intron 1 of 17)	22562	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.007092	0.433428	281(AGGAACATTAAGTTCT,-,0.00),282(GGAACATTAAGTTCTG,+,0.00),384(ATGGACTCCCTGTGCC,-,0.00),385(TGGACTCCCTGTGCCT,+,0.00)
chunk0010_122_1	chr1	114505111	114505634	+	0	NA	intron (NM_033020, intron 1 of 18)	intron (NM_033020, intron 1 of 18)	5788	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.009560	0.423664	
chunk0200_253_1	chr9	21344927	21345179	+	0	NA	Intergenic	L1PA10|LINE|L1	5834	NM_021002	3443	Hs.533470	NM_021002	ENSG00000120235	IFNA6	IFN-alphaK	interferon alpha 6	protein-coding	0.007937	0.391304	
chunk0020_188_1	chr1	234861691	234862384	+	0	NA	Intergenic	L1ME4b|LINE|L1	101962	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.010101	0.345821	
chunk0044_8_1	chr12	26987537	26988015	+	0	NA	intron (NM_016551, intron 6 of 11)	L1MC4|LINE|L1	26630	NM_016551	51768	Hs.438641	NM_016551	ENSG00000064115	TM7SF3	-	transmembrane 7 superfamily member 3	protein-coding	0.002092	0.363257	
chunk0026_384_1	chr10	69446583	69446937	+	0	NA	Intergenic	L2b|LINE|L2	-4710	NM_012339	23555	Hs.499941	NM_012339	ENSG00000099282	TSPAN15	2700063A19Rik|NET-7|NET7|TM4SF15	tetraspanin 15	protein-coding	0.008475	0.470423	
chunk0137_48_1	chr4	11521962	11522390	+	0	NA	Intergenic	Intergenic	-93263	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.011682	0.491841	
chunk0156_18_1	chr5	102149798	102150097	+	0	NA	Intergenic	Intergenic	146602	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.353333	
chunk0161_131_1	chr5	168348019	168348257	+	0	NA	intron (NM_001161661, intron 1 of 22)	MIRb|SINE|MIR	56078	NM_001161661	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.016807	0.531381	
chunk0105_141_1	chr2	186299610	186300197	+	0	NA	Intergenic	L2c|LINE|L2	-186255	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.001704	0.367347	
chunk0019_55_1	chr1	224173499	224173971	+	0	NA	Intergenic	Intergenic	-9473	NM_003676	8560	Hs.299878	NM_003676	ENSG00000143753	DEGS1	DEGS|DEGS-1|DES1|Des-1|FADS7|HLD18|MIG15|MLD	delta 4-desaturase, sphingolipid 1	protein-coding	0.014831	0.412262	
chunk0099_23_1	chr2	83116528	83116766	+	0	NA	Intergenic	Intergenic	259844	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.004202	0.343096	
chunk0185_125_1	chr7	126440420	126440909	+	0	NA	intron (NR_028041, intron 10 of 10)	Tigger3b|DNA|TcMar-Tigger	617520	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.004090	0.338776	
chunk0017_444_1	chr1	214234551	214234837	+	0	NA	Intergenic	Intergenic	-46528	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.003497	0.376307	
chunk0045_298_1	chr12	50401789	50402051	+	0	NA	intron (NM_199188, intron 1 of 15)	intron (NM_199188, intron 1 of 15)	1111	NM_001170804	113251	Hs.26613	NM_052879	ENSG00000161813	LARP4	PP13296	La ribonucleoprotein domain family member 4	protein-coding	0.019084	0.387833	172(CAGATCATATTGTTCT,-,0.00),173(AGATCATATTGTTCTT,+,0.00)
chunk0004_72_1	chr1	43537592	43537968	+	0	NA	intron (NM_130440, intron 1 of 32)	L2b|LINE|L2	6904	NM_002840	5792	Hs.272062	NM_002840	ENSG00000142949	PTPRF	BNAH2|LAR	protein tyrosine phosphatase receptor type F	protein-coding	0.010638	0.575597	
chunk0034_9_1	chr11	25989917	25990717	+	0	NA	Intergenic	Intergenic	-198806	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.005000	0.335830	
chunk0120_269_1	chr3	9309979	9310577	+	0	NA	Intergenic	Intergenic	-52755	NM_015453	25917	Hs.443081	NM_015453	ENSG00000134077	THUMPD3	-	THUMP domain containing 3	protein-coding	0.006689	0.460768	
chunk0082_18_1	chr17	50440234	50440562	+	0	NA	intron (NM_001288968, intron 2 of 16)	intron (NM_001288968, intron 2 of 16)	14240	NM_025149	80221	Hs.288959	NM_025149	ENSG00000167107	ACSF2	ACSMW|AVYV493	acyl-CoA synthetase family member 2	protein-coding	0.003049	0.580547	
chunk0063_190_1	chr14	80777990	80778495	+	0	NA	intron (NM_152446, intron 14 of 23)	L2b|LINE|L2	161298	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.009901	0.361660	
chunk0004_13_1	chr1	42119616	42120166	+	0	NA	Intergenic	Intergenic	-33530	NM_007102	2981	Hs.32966	NM_007102	ENSG00000044012	GUCA2B	GCAP-II|UGN	guanylate cyclase activator 2B	protein-coding	0.007273	0.401089	
chunk0041_53_1	chr11	123243741	123244207	+	0	NA	Intergenic	Intergenic	-48669	NM_024769	79827	Hs.591949	NM_024769	ENSG00000166250	CLMP	ACAM|ASAM|CSBM|CSBS	CXADR like membrane protein	protein-coding	0.017167	0.402570	
chunk0122_360_1	chr3	37542947	37543338	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	90820	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.007673	0.474490	
chunk0087_356_1	chr18	40978677	40979184	+	0	NA	Intergenic	Intergenic	541667	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.001972	0.360236	
chunk0037_105_1	chr11	72183257	72183905	+	0	NA	Intergenic	Intergenic	-5977	NM_016725	2348	Hs.73769	NM_000802	ENSG00000110195	FOLR1	FBP|FOLR|FRalpha	folate receptor alpha	protein-coding	0.012346	0.462250	423(GGGGACAGACAGTCCC,-,0.00),424(GGGACAGACAGTCCCT,+,0.00)
chunk0008_25_1	chr1	87866384	87866836	+	0	NA	Intergenic	L1MEc|LINE|L1	-494955	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.006637	0.335541	
chunk0166_399_1	chr6	51960382	51961044	+	0	NA	intron (NM_138694, intron 35 of 66)	intron (NM_138694, intron 35 of 66)	126912	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.006042	0.404223	
chunk0002_295_1	chr1	23083615	23084096	+	0	NA	TTS (NM_015013)	TTS (NM_015013)	-25921	NR_039614									0.004158	0.410788	
chunk0197_83_1	chr8	119137287	119137951	+	0	NA	Intergenic	L1ME2|LINE|L1	70434	NM_006438	10584	Hs.176615	NM_006438	ENSG00000184374	COLEC10	3MC3|CL-34|CLL1	collectin subfamily member 10	protein-coding	0.007530	0.351880	
chunk0076_290_1	chr16	69851787	69852308	+	0	NA	intron (NM_007014, intron 7 of 24)	L1MC1|LINE|L1	13310	NM_001270453	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.013436	0.427203	
chunk0114_26_1	chr21	7917796	7918047	+	0	NA	Intergenic	(ATTCCATTCC)n|Simple_repeat|Simple_repeat	-147373	NM_001282537	101928147	Hs.303798	NM_001282537	ENSG00000222018	FAM243A	C21orf140	family with sequence similarity 243 member A	protein-coding	0.027888	0.412698	
chunk0054_314_1	chr13	48783406	48783666	+	0	NA	Intergenic	L1PBb|LINE|L1	129825	NM_001308467	57105	Hs.253706	NM_020377	ENSG00000152207	CYSLTR2	CYSLT2|CYSLT2R|GPCR21|HG57|HPN321|KPG_011|PSEC0146|hGPCR21	cysteinyl leukotriene receptor 2	protein-coding	0.015385	0.498084	
chunk0024_294_1	chr10	42093349	42093733	+	0	NA	Intergenic	Intergenic	274504	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.049479	0.353247	
chunk0044_401_1	chr12	40988770	40989242	+	0	NA	intron (NM_175038, intron 14 of 21)	intron (NM_175038, intron 14 of 21)	80649	NM_175038	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.004237	0.393235	
chunk0159_413_1	chr5	147905032	147905366	+	0	NA	intron (NM_206966, intron 1 of 3)	intron (NM_206966, intron 1 of 3)	1339	NM_206966	389336	Hs.660038	NM_206966	ENSG00000178776	C5orf46	SSSP1	chromosome 5 open reading frame 46	protein-coding	0.008982	0.265672	
chunk0081_378_1	chr17	48008440	48008879	+	0	NA	Intergenic	L1MC4|LINE|L1	28588	NR_029687	406943		NR_029687	ENSG00000207947	MIR152	MIRN152|mir-152	microRNA 152	ncRNA	0.004556	0.334091	217(GGAGACATCCTGTCCC,-,0.00),218(GAGACATCCTGTCCCT,+,0.00)
chunk0065_37_1	chr15	21250047	21250741	+	0	NA	Intergenic	Intergenic	47435	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.002882	0.294964	287(CTAAACACAGTGTTCC,-,0.00),288(TAAACACAGTGTTCCA,+,0.00)
chunk0116_1_1	chr21	32655145	32655528	+	0	NA	intron (NM_001160302, intron 21 of 31)	CR1_Mam|LINE|CR1	-42728	NM_021254	56683	Hs.5811	NM_017835	ENSG00000159079	CFAP298	C21orf48|C21orf59|CILD26|FBB18|Kur	cilia and flagella associated protein 298	protein-coding	0.000000	0.369792	
chunk0079_235_1	chr17	15892630	15893220	+	0	NA	Intergenic	Intergenic	-51992	NM_000676	136	Hs.167046	NM_000676	ENSG00000170425	ADORA2B	ADORA2	adenosine A2b receptor	protein-coding	0.013559	0.401015	
chunk0009_160_1	chr1	105138051	105138356	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	480732	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.016393	0.555556	127(GTGCACATCTTGTGCC,-,0.00),128(TGCACATCTTGTGCCT,+,0.00)
chunk0051_241_1	chr12	117059938	117060506	+	0	NA	intron (NM_017899, intron 2 of 7)	L1ME3A|LINE|L1	39224	NM_001168325	54997	Hs.525709	NM_017899	ENSG00000088992	TESC	CHP3|TSC	tescalcin	protein-coding	0.019366	0.469244	
chunk0161_312_1	chr5	173486194	173486860	+	0	NA	Intergenic	Intergenic	-93107	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.004505	0.460270	281(GGGAACATTCTGTCCT,-,0.00),282(GGAACATTCTGTCCTG,+,0.00)
chunk0105_49_1	chr2	183013767	183014319	+	0	NA	intron (NM_205842, intron 3 of 31)	L2a|LINE|L2	24815	NM_205842	10787	Hs.603732	NM_013436	ENSG00000061676	NCKAP1	HEM2|NAP1|NAP125|p125Nap1	NCK associated protein 1	protein-coding	0.005435	0.412297	15(TGGCACTTCATGTCCT,-,0.00),16(GGCACTTCATGTCCTA,+,0.00),132(CAGCACAGAATGCTCC,-,0.00),133(AGCACAGAATGCTCCT,+,0.00)
chunk0037_166_1	chr11	73820349	73820991	+	0	NA	intron (NM_016055, intron 3 of 7)	L2b|LINE|L2	32798	NM_016055	51642	Hs.503239	NM_016055	ENSG00000175581	MRPL48	CGI-118|HSPC290|L48MT|MRP-L48	mitochondrial ribosomal protein L48	protein-coding	0.003115	0.424572	188(AGGTGCATTCTGTCCC,-,0.00),189(GGTGCATTCTGTCCCT,+,0.00)
chunk0037_177_1	chr11	74050587	74050979	+	0	NA	intron (NM_001286577, intron 26 of 32)	intron (NM_001286577, intron 26 of 32)	-41546	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.005102	0.407125	
chunk0109_451_1	chr2	241640781	241641033	+	0	NA	intron (NM_178326, intron 1 of 12)	L2a|LINE|L2	3295	NM_013325	23192	Hs.283610	NM_013325	ENSG00000168397	ATG4B	APG4B|AUTL1	autophagy related 4B cysteine peptidase	protein-coding	0.015873	0.505929	
chunk0061_208_1	chr14	60351724	60352028	+	0	NA	Intergenic	Intergenic	102628	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.006579	0.344262	
chunk0068_400_1	chr15	58701396	58702101	+	0	NA	intron (NM_001110, intron 2 of 15)	L1MA4A|LINE|L1	-8141	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.022695	0.419263	
chunk0037_403_1	chr11	79489745	79490360	+	0	NA	Intergenic	Intergenic	-49401	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.001626	0.365260	
chunk0028_267_1	chr10	90890375	90890748	+	0	NA	intron (NM_006413, intron 6 of 10)	intron (NM_006413, intron 6 of 10)	18609	NM_006413	10556	Hs.139120	NM_006413	ENSG00000148688	RPP30	TSG15	ribonuclease P/MRP subunit p30	protein-coding	0.005362	0.350267	
chunk0119_230_1	chr22	45313888	45314249	+	0	NA	intron (NM_001104595, intron 2 of 9)	MIRb|SINE|MIR	4164	NM_017911	55007	Hs.265018	NM_017911	ENSG00000100376	FAM118A	C22orf8	family with sequence similarity 118 member A	protein-coding	0.005540	0.472376	
chunk0002_1_1	chr1	11890749	11890970	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-17295	NR_002754	26829		NR_002754	ENSG00000199347	RNU5E-1	RNU5E|U5E	RNA, U5E small nuclear 1	snRNA	0.004525	0.441441	
chunk0070_446_1	chr15	78397080	78397406	+	0	NA	Intergenic	Intergenic	-40933	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.015337	0.577982	
chunk0138_271_1	chr4	40445738	40446132	+	0	NA	intron (NM_019027, intron 2 of 4)	intron (NM_019027, intron 2 of 4)	56184	NR_039966	100616274		NR_039966	ENSG00000263642	MIR4802	-	microRNA 4802	ncRNA	0.002538	0.369620	
chunk0172_416_1	chr6	140166153	140166468	+	0	NA	Intergenic	L1MB4|LINE|L1	-38942	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.003175	0.376582	
chunk0127_161_1	chr3	94794432	94794915	+	0	NA	Intergenic	Intergenic	-143590	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.303719	
chunk0093_298_1	chr19	52685760	52686285	+	0	NA	intron (NM_001277947, intron 1 of 5)	intron (NM_001277947, intron 1 of 5)	4559	NM_001277947	55769	Hs.467210	NM_018300	ENSG00000167766	ZNF83	HPF1|ZNF816B	zinc finger protein 83	protein-coding	0.005714	0.376426	
chunk0032_93_1	chr11	3124346	3124681	+	0	NA	intron (NM_020896, intron 3 of 21)	L2b|LINE|L2	40839	NM_020896	114879	Hs.436166	NM_020896	ENSG00000021762	OSBPL5	OBPH1|ORP5	oxysterol binding protein like 5	protein-coding	0.005970	0.577381	162(TGGCACATGGTGTTCC,-,0.00),163(GGCACATGGTGTTCCC,+,0.00)
chunk0148_324_1	chr5	13969348	13969560	+	0	NA	Intergenic	L1PB1|LINE|L1	-24974	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.004717	0.366197	
chunk0023_239_1	chr10	26987817	26988432	+	0	NA	Intergenic	PRIMA4-int|LTR|ERV1	-46123	NR_026795	387644	Hs.529965	NR_026795	ENSG00000283709	FAM238C	C10orf51|LINC00202|LINC00202-1|NCRNA00202|bB27G4.1	family with sequence similarity 238 member C	ncRNA	0.003252	0.426948	290(GGGATCAGACTGTTCA,-,0.00),291(GGATCAGACTGTTCAT,+,0.00),530(GGGACACTTTGTCTCT,+,0.00)
chunk0060_416_1	chr14	53304891	53305553	+	0	NA	Intergenic	LTR88c|LTR|Gypsy?	151868	NR_110062	101927620		NR_110062	ENSG00000258731	LOC101927620	-	uncharacterized LOC101927620	ncRNA	0.004532	0.460030	271(GGGGTCATTCTGTCCC,-,0.00),272(GGGTCATTCTGTCCCA,+,0.00)
chunk0094_260_1	chr2	7697794	7698052	+	0	NA	Intergenic	Intergenic	201732	NR_110256	101929551	Hs.116006	NR_110256	ENSG00000226506	LOC101929551	-	uncharacterized LOC101929551	ncRNA	0.019380	0.444015	176(AGAACAAAGTGAACCT,+,0.00)
chunk0043_216_1	chr12	19701255	19701604	+	0	NA	Intergenic	L1PA15|LINE|L1	260848	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.005731	0.574286	
chunk0111_10_1	chr20	21818223	21818577	+	0	NA	Intergenic	L1ME1|LINE|L1	112741	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.002825	0.332394	
chunk0198_431_1	chr8	143310242	143310441	+	0	NA	intron (NM_001258446, intron 13 of 14)	intron (NM_001258446, intron 13 of 14)	18952	NM_030895	79943	Hs.512740	NM_030895	ENSG00000185730	ZNF696	-	zinc finger protein 696	protein-coding	0.035176	0.630000	
chunk0087_192_1	chr18	35620878	35621109	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	29256	NR_039771	100616257		NR_039771	ENSG00000283514	MIR3975	-	microRNA 3975	ncRNA	0.008658	0.379310	
chunk0183_15_1	chr7	103009592	103009797	+	0	NA	intron (NM_145032, intron 6 of 19)	L1PA15|LINE|L1	36257	NM_001085386	58160	Hs.621233	NM_001085386	ENSG00000230257	NFE4	NF-E4	nuclear factor, erythroid 4	protein-coding	0.000000	0.577670	
chunk0028_345_1	chr10	92230095	92230784	+	0	NA	intron (NM_001178137, intron 2 of 9)	intron (NM_001178137, intron 2 of 9)	12840	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.000000	0.346377	253(CAGTACACAATGTTTC,-,0.00),254(AGTACACAATGTTTCC,+,0.00)
chunk0141_250_1	chr4	85045998	85046749	+	0	NA	Intergenic	L1PA7|LINE|L1	79555	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.002663	0.353723	421(CTGAACAACCTGTTCC,-,0.00),422(TGAACAACCTGTTCCT,+,0.00)
chunk0185_423_1	chr7	134553827	134554365	+	0	NA	intron (NM_001080538, intron 1 of 11)	HERVS71-int|LTR|ERV1	4999	NM_001080538	441282	Hs.729418	NM_001080538	ENSG00000227471	AKR1B15	AKR1B10L|AKR1B10L, AK1R1B7|AKR1R1B7	aldo-keto reductase family 1 member B15	protein-coding	0.011152	0.502783	
chunk0046_146_1	chr12	58133822	58134440	+	0	NA	Intergenic	L2c|LINE|L2	192469	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.004854	0.434572	27(AAGAAGACAATGTTCC,-,0.00),324(TTGCACATGCAGTTCC,-,0.00),325(TGCACATGCAGTTCCC,+,0.00)
chunk0174_172_1	chr6	158786909	158787157	+	0	NA	intron (NM_003379, intron 3 of 12)	intron (NM_003379, intron 3 of 12)	-22280	NR_037482	100500851		NR_037482	ENSG00000265558	MIR3918	mir-3918	microRNA 3918	ncRNA	0.008065	0.397590	
chunk0103_219_1	chr2	164092015	164092556	+	0	NA	Intergenic	Intergenic	-356282	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.003697	0.304428	
chunk0042_83_1	chr12	2342720	2343400	+	0	NA	intron (NM_001129846, intron 3 of 45)	MIRb|SINE|MIR	73284	NR_046769	100874370	Hs.653548	NR_046769		CACNA1C-IT3	-	CACNA1C intronic transcript 3	ncRNA	0.004412	0.414097	386(CAGGACTGGGTGTCCT,-,0.00),387(AGGACTGGGTGTCCTG,+,0.00)
chunk0102_452_1	chr2	158314902	158315492	+	0	NA	intron (NM_001301684, intron 5 of 11)	intron (NM_001301684, intron 5 of 11)	141556	NM_138803	130940	Hs.668597	NM_138803	ENSG00000153237	CCDC148	-	coiled-coil domain containing 148	protein-coding	0.001695	0.338409	
chunk0079_95_1	chr17	12050812	12051107	+	0	NA	intron (NM_001281435, intron 2 of 11)	intron (NM_001281435, intron 2 of 11)	30141	NM_001281435	6416	Hs.514681	NM_003010	ENSG00000065559	MAP2K4	JNKK|JNKK1|MAPKK4|MEK4|MKK4|PRKMK4|SAPKK-1|SAPKK1|SEK1|SERK1|SKK1	mitogen-activated protein kinase kinase 4	protein-coding	0.003390	0.439189	143(GAAGACACTGTGTGCC,-,0.00),144(AAGACACTGTGTGCCG,+,0.00)
chunk0025_220_1	chr10	53886105	53886335	+	0	NA	intron (NM_001142769, intron 28 of 35)	MIRb|SINE|MIR	721737	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.008696	0.385281	
chunk0170_176_1	chr6	111730824	111731243	+	0	NA	intron (NM_002037, intron 3 of 13)	intron (NM_002037, intron 3 of 13)	-10971	NM_153047	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.026253	0.500000	
chunk0082_147_1	chr17	55484580	55484866	+	0	NA	Intergenic	L1MC5a|LINE|L1	-62743	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.006993	0.404181	
chunk0114_385_1	chr20	63166717	63167167	+	0	NA	Intergenic	Intergenic	-11558	NR_029670	406909		NR_029670	ENSG00000207598	MIR124-3	MIRN124-3|MIRN124A3|mir-124-3	microRNA 124-3	ncRNA	0.046667	0.614191	
chunk0115_57_1	chr21	21376380	21376970	+	0	NA	intron (NM_004540, intron 9 of 17)	intron (NM_004540, intron 9 of 17)	360644	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.005085	0.285956	
chunk0137_447_1	chr4	29151128	29151584	+	0	NA	Intergenic	Intergenic	331774	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.000000	0.260394	
chunk0206_183_1	chr9	122819227	122819594	+	0	NA	3' UTR (NM_005388, exon 4 of 4)	3' UTR (NM_005388, exon 4 of 4)	9246	NM_005388	5082	Hs.271749	NM_005388	ENSG00000136940	PDCL	PhLP	phosducin like	protein-coding	0.002725	0.385870	
chunk0003_222_1	chr1	35505760	35506203	+	0	NA	intron (NM_024874, intron 3 of 20)	intron (NM_024874, intron 3 of 20)	51455	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.002257	0.409910	
chunk0123_397_1	chr3	48897392	48897913	+	0	NA	intron (NM_000387, intron 1 of 8)	intron (NM_000387, intron 1 of 8)	1341	NM_000387	788	Hs.13845	NM_000387	ENSG00000178537	SLC25A20	CAC|CACT	solute carrier family 25 member 20	protein-coding	0.013436	0.484674	
chunk0153_217_1	chr5	72016216	72016427	+	0	NA	Intergenic	L2a|LINE|L2	-90970	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.000000	0.391509	
chunk0062_176_1	chr14	69643238	69643805	+	0	NA	intron (NM_014734, intron 1 of 5)	intron (NM_014734, intron 1 of 5)	31928	NM_014734	9766	Hs.440025	NM_014734	ENSG00000100647	SUSD6	DRAGO|KIAA0247	sushi domain containing 6	protein-coding	0.003527	0.417254	
chunk0117_211_1	chr22	22061513	22061943	+	0	NA	Intergenic	Intergenic	-78885	NM_001282112	8940	Hs.436401	NM_003935	ENSG00000100038	TOP3B	TOP3B1	DNA topoisomerase III beta	protein-coding	0.009302	0.436195	
chunk0187_253_1	chr7	153938972	153939610	+	0	NA	intron (NM_001039350, intron 1 of 25)	intron (NM_001039350, intron 1 of 25)	52194	NM_001039350	1804	Hs.490684	NM_001936	ENSG00000130226	DPP6	DPL1|DPPX|MRD33|VF2	dipeptidyl peptidase like 6	protein-coding	0.009404	0.377152	
chunk0189_62_1	chr8	20159748	20160423	+	0	NA	intron (NM_001142324, intron 10 of 15)	intron (NM_001142324, intron 10 of 15)	23121	NM_001142324	6570	Hs.158322	NM_003053	ENSG00000036565	SLC18A1	CGAT|VAT1|VMAT1	solute carrier family 18 member A1	protein-coding	0.010370	0.387574	
chunk0165_391_1	chr6	38721932	38722555	+	0	NA	intron (NM_001206927, intron 1 of 92)	intron (NM_001206927, intron 1 of 92)	6902	NM_001206927	1769	Hs.520106	NM_001371	ENSG00000124721	DNAH8	ATPase|hdhc9	dynein axonemal heavy chain 8	protein-coding	0.004815	0.405449	433(TGCACAGTGAGTACCT,+,0.00)
chunk0133_123_1	chr3	168566088	168566473	+	0	NA	intron (NR_021485, intron 4 of 15)	MER57A-int|LTR|ERV1	14426	NR_030294	693136		NR_030294	ENSG00000207717	MIR551B	MIRN551B|mir-551b	microRNA 551b	ncRNA	0.002597	0.378238	
chunk0049_92_1	chr12	90828514	90828826	+	0	NA	Intergenic	MIRb|SINE|MIR	-89353	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.003205	0.392971	
chunk0018_117_1	chr1	218339759	218340133	+	0	NA	Intergenic	Intergenic	-5388	NM_003238	7042	Hs.133379	NM_003238	ENSG00000092969	TGFB2	G-TSF|LDS4|TGF-beta2	transforming growth factor beta 2	protein-coding	0.005348	0.357333	
chunk0205_436_1	chr9	115257077	115257299	+	0	NA	intron (NM_017418, intron 2 of 7)	(ACAGAC)n|Simple_repeat|Simple_repeat	115370	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.000000	0.448430	
chunk0198_368_1	chr8	141018461	141019295	+	0	NA	Intergenic	Intergenic	-17565	NM_001316342	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.011990	0.486228	429(CAGAACACTGTGTACT,-,0.00),430(AGAACACTGTGTACTC,+,0.00)
chunk0003_340_1	chr1	38997869	38998113	+	0	NA	intron (NM_001136275, intron 1 of 3)	intron (NM_001136275, intron 1 of 3)	6747	NM_001136275	79647	Hs.293563	NM_024595	ENSG00000174574	AKIRIN1	C1orf108|STRF2	akirin 1	protein-coding	0.012295	0.420408	90(AAGAACATACTGTCTT,-,0.00),91(AGAACATACTGTCTTT,+,0.00)
chunk0212_10_1	chrY	7449795	7450367	+	0	NA	Intergenic	Intergenic	176109	NR_028062	5616	Hs.584730	NM_002760	ENSG00000099725	PRKY	PRKXP3|PRKYP	protein kinase Y-linked (pseudogene)	pseudo	0.003497	0.387435	
chunk0097_74_1	chr2	44434129	44434390	+	0	NA	intron (NM_024766, intron 3 of 10)	intron (NM_024766, intron 3 of 10)	72355	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.011494	0.370229	175(AAGCACAGGAAGTGCA,-,0.00),176(AGCACAGGAAGTGCAT,+,0.00)
chunk0133_285_1	chr3	172125721	172126529	+	0	NA	intron (NM_022763, intron 2 of 25)	intron (NM_022763, intron 2 of 25)	85571	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.016089	0.407911	
chunk0013_439_1	chr1	173527107	173527662	+	0	NA	intron (NM_178527, intron 18 of 27)	intron (NM_178527, intron 18 of 27)	50037	NM_004905	9588	Hs.120	NM_004905	ENSG00000117592	PRDX6	1-Cys|AOP2|HEL-S-128m|NSGPx|PRX|aiPLA2|p29	peroxiredoxin 6	protein-coding	0.005405	0.428058	227(AAGATCAGTATGTACT,-,0.00),228(AGATCAGTATGTACTC,+,0.00)
chunk0058_381_1	chr14	29436735	29436934	+	0	NA	Intergenic	Intergenic	490859	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.465000	
chunk0134_181_1	chr3	178131949	178132415	+	0	NA	Intergenic	(ATTTT)n|Simple_repeat|Simple_repeat	-287019	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.004292	0.299786	
chunk0045_292_1	chr12	50257809	50258392	+	0	NA	intron (NM_001113546, intron 1 of 10)	L1MC4a|LINE|L1	-23888	NR_031625	100302220		NR_031625	ENSG00000221604	MIR1293	MIRN1293|hsa-mir-1293|mir-1293	microRNA 1293	ncRNA	0.006861	0.438356	
chunk0024_186_1	chr10	36118150	36118562	+	0	NA	Intergenic	Intergenic	340054	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.009709	0.423729	
chunk0072_447_1	chr15	101641069	101641314	+	0	NA	TTS (NM_025141)	TTS (NM_025141)	11200	NM_025141	80213	Hs.288912	NM_025141	ENSG00000184277	TM2D3	BLP2	TM2 domain containing 3	protein-coding	0.016327	0.382114	
chunk0064_162_1	chr14	92088380	92089021	+	0	NA	intron (NR_028457, intron 5 of 11)	intron (NR_028457, intron 5 of 11)	17921	NR_028453	4287	Hs.532632	NM_004993	ENSG00000066427	ATXN3	AT3|ATX3|JOS|MJD|MJD1|SCA3	ataxin 3	protein-coding	0.009360	0.358255	
chunk0159_32_1	chr5	136908988	136909496	+	0	NA	Intergenic	Intergenic	-543766	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.003937	0.357564	
chunk0170_417_1	chr6	118307543	118308099	+	0	NA	intron (NM_001029858, intron 7 of 7)	intron (NM_001029858, intron 7 of 7)	-193552	NR_002730	23629	Hs.648050	NR_002730		BRD7P3	BP75	bromodomain containing 7 pseudogene 3	pseudo	0.019784	0.456014	
chunk0178_282_1	chr7	37254427	37254777	+	0	NA	intron (NM_001206482, intron 6 of 21)	Tigger3c|DNA|TcMar-Tigger	99066	NM_001206482	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.011429	0.387464	
chunk0154_204_1	chr5	80375397	80375757	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-23611	NR_003665	441089	Hs.568291	NR_003665		CRSP8P	-	mediator complex subunit 27 pseudogene	pseudo	0.002778	0.340720	
chunk0007_431_1	chr1	86714860	86715195	+	0	NA	intron (NM_001206653, intron 1 of 7)	intron (NM_001206653, intron 1 of 7)	10457	NM_016009	51100	Hs.136309	NM_016009	ENSG00000097033	SH3GLB1	Bif-1|CGI-61|PPP1R70|dJ612B15.2	SH3 domain containing GRB2 like, endophilin B1	protein-coding	0.002985	0.294643	
chunk0021_123_1	chr10	3747751	3748459	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	37176	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.018362	0.397743	
chunk0209_16_1	chrX	35379790	35380330	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-418282	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.003704	0.349353	
chunk0146_117_1	chr4	158860902	158861668	+	0	NA	intron (NM_020840, intron 10 of 16)	intron (NM_020840, intron 10 of 16)	92255	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.010444	0.419817	
chunk0062_417_1	chr14	75171715	75171914	+	0	NA	intron (NM_006827, intron 1 of 4)	MLT1D|LTR|ERVL-MaLR	4832	NM_006827	10972	Hs.74137	NM_006827	ENSG00000170348	TMED10	P24(DELTA)|S31I125|S31III125|TMP21|Tmp-21-I|p23|p24d1	transmembrane p24 trafficking protein 10	protein-coding	0.010050	0.405000	151(AAGTACTGTGTGTTCC,-,0.00),152(AGTACTGTGTGTTCCT,+,0.00)
chunk0129_430_1	chr3	127560068	127560366	+	0	NA	Intergenic	Intergenic	15114	NR_106883	102466199		NR_106883	ENSG00000275067	MIR6825	hsa-mir-6825	microRNA 6825	ncRNA	0.003356	0.454849	97(TAGCACTTACTGTTCC,-,0.00),98(AGCACTTACTGTTCCA,+,0.00),181(CTGTACTTCCTGTTCC,-,0.00),182(TGTACTTCCTGTTCCC,+,0.00)
chunk0160_447_1	chr5	164987322	164987530	+	0	NA	Intergenic	LTR1F2|LTR|ERV1	517147	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.019231	0.531100	
chunk0017_250_1	chr1	208607076	208607451	+	0	NA	Intergenic	Intergenic	-362943	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.005333	0.436170	
chunk0193_64_1	chr8	72945116	72945433	+	0	NA	Intergenic	Intergenic	-63588	NM_017489	7013	Hs.442707	NM_003218	ENSG00000147601	TERF1	PIN2|TRBF1|TRF|TRF1|hTRF1-AS|t-TRF1	telomeric repeat binding factor 1	protein-coding	0.003155	0.320755	
chunk0021_285_1	chr1	244409665	244410013	+	0	NA	intron (NM_001126, intron 12 of 12)	intron (NM_001126, intron 12 of 12)	42295	NM_001126	159	Hs.498313	NM_001126	ENSG00000035687	ADSS	ADEH|ADSS 2|ADSS2	adenylosuccinate synthase	protein-coding	0.005747	0.381089	
chunk0042_25_1	chr12	1396617	1396822	+	0	NA	intron (NM_178040, intron 16 of 18)	L1MEd|LINE|L1	-103772	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.004878	0.470874	
chunk0195_87_1	chr8	94223941	94224149	+	0	NA	Intergenic	MIRb|SINE|MIR	-6742	NM_001144663	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.009615	0.368421	
chunk0092_183_1	chr19	30144123	30144488	+	0	NA	Intergenic	Intergenic	202066	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.030137	0.524590	
chunk0182_116_1	chr7	93862665	93863149	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	28084	NM_001271004	7980	Hs.438231	NM_006528	ENSG00000105825	TFPI2	PP5|REF1|TFPI-2	tissue factor pathway inhibitor 2	protein-coding	0.004132	0.402062	
chunk0172_166_1	chr6	135976556	135976965	+	0	NA	intron (NM_018945, intron 2 of 12)	intron (NM_018945, intron 2 of 12)	125064	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.000000	0.387805	
chunk0012_100_1	chr1	156476800	156477010	+	0	NA	intron (NM_005920, intron 7 of 11)	intron (NM_005920, intron 7 of 11)	13694	NM_001271629	4209	Hs.314327	NM_005920	ENSG00000116604	MEF2D	-	myocyte enhancer factor 2D	protein-coding	0.000000	0.497630	
chunk0067_33_1	chr15	40420132	40420418	+	0	NA	3' UTR (NM_001159508, exon 11 of 11)	3' UTR (NM_001159508, exon 11 of 11)	14790	NM_001159508	3712	Hs.513646	NM_002225	ENSG00000128928	IVD	ACAD2	isovaleryl-CoA dehydrogenase	protein-coding	0.027972	0.602787	
chunk0089_233_1	chr18	61831521	61831866	+	0	NA	intron (NM_173557, intron 1 of 1)	(CAAA)n|Simple_repeat|Simple_repeat	61378	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.002899	0.289017	113(AGAACACAATGCTCAC,+,0.00)
chunk0160_22_1	chr5	149118616	149119129	+	0	NA	Intergenic	MER102a|DNA|hAT-Charlie	-22611	NM_014945	22885	Hs.49688	NM_014945	ENSG00000173210	ABLIM3	HMFN1661	actin binding LIM protein family member 3	protein-coding	0.001949	0.422179	
chunk0092_225_1	chr19	32269788	32270359	+	0	NA	Intergenic	Intergenic	-75535	NM_014910	22847	Hs.205392	NM_014910	ENSG00000168813	ZNF507	-	zinc finger protein 507	protein-coding	0.012259	0.438811	
chunk0208_301_1	chrX	23218080	23218479	+	0	NA	intron (NR_073010, intron 2 of 5)	intron (NR_073010, intron 2 of 5)	74867	NR_073010	100873065	Hs.628459	NR_046436		PTCHD1-AS	DDX53-AS1|PTCHD1AS1|PTCHD1AS2	PTCHD1 antisense RNA (head to head)	ncRNA	0.005013	0.415000	241(TAGCACACTGTGTTTC,-,0.00),242(AGCACACTGTGTTTCA,+,0.00)
chunk0053_246_1	chr13	32839010	32839304	+	0	NA	intron (NR_047020, intron 4 of 4)	intron (NR_047020, intron 4 of 4)	72495	NR_047020	100874167	Hs.406290	NR_047020		LINC00423	-	long intergenic non-protein coding RNA 423	ncRNA	0.010204	0.447458	
chunk0009_410_1	chr1	110464239	110464699	+	0	NA	Intergenic	Intergenic	13303	NM_032414	84432	Hs.514793	NM_032414	ENSG00000143125	PROK1	EGVEGF|PK1|PRK1	prokineticin 1	protein-coding	0.006522	0.396963	
chunk0056_116_1	chr13	82950003	82950465	+	0	NA	Intergenic	Intergenic	932159	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002165	0.291577	
chunk0048_295_1	chr12	82755871	82756516	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	69038	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.003101	0.329721	
chunk0195_28_1	chr8	93184675	93185227	+	0	NA	Intergenic	L1MC5a|LINE|L1	-18101	NM_001242668									0.007246	0.358047	
chunk0145_153_1	chr4	147085014	147085463	+	0	NA	Intergenic	Intergenic	-139356	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.004454	0.420000	
chunk0051_359_1	chr12	121210103	121210414	+	0	NA	exon (NM_001256796, exon 1 of 13)	exon (NM_001256796, exon 1 of 13)	397	NR_046373	5025	Hs.321709	NM_002560	ENSG00000135124	P2RX4	P2X4|P2X4R	purinergic receptor P2X 4	protein-coding	0.147910	0.750000	
chunk0043_203_1	chr12	19403096	19403436	+	0	NA	Intergenic	L1PBb|LINE|L1	-36408	NM_001114176	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.008824	0.533724	
chunk0020_182_1	chr1	234616562	234617044	+	0	NA	Intergenic	Intergenic	-7278	NM_001077397	359948	Hs.350268	NM_182972	ENSG00000168264	IRF2BP2	CVID14	interferon regulatory factor 2 binding protein 2	protein-coding	0.004149	0.434783	
chunk0015_420_1	chr1	191520443	191520814	+	0	NA	Intergenic	LTR40A1|LTR|ERVL	-637834	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.008086	0.381720	
chunk0108_74_1	chr2	227518055	227518478	+	0	NA	intron (NM_001135189, intron 2 of 11)	L1ME2|LINE|L1	46094	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.007092	0.341981	
chunk0016_324_1	chr1	201610514	201610741	+	0	NA	Intergenic	Intergenic	-37695	NM_020443	89796	Hs.585374	NM_020443	ENSG00000134369	NAV1	POMFIL3|STEERIN1|UNC53H1	neuron navigator 1	protein-coding	0.008811	0.561404	
chunk0149_145_1	chr5	20062339	20062538	+	0	NA	intron (NM_001291956, intron 2 of 14)	intron (NM_001291956, intron 2 of 14)	-74194	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.010050	0.450000	
chunk0001_357_1	chr1	9910575	9911580	+	0	NA	promoter-TSS (NM_020248)	promoter-TSS (NM_020248)	-819	NM_020248	56998	Hs.463759	NM_020248	ENSG00000178585	CTNNBIP1	ICAT	catenin beta interacting protein 1	protein-coding	0.041791	0.521869	174(AGGAGCACAGTGTTCC,-,0.00),175(GGAGCACAGTGTTCCG,+,0.00)
chunk0072_22_1	chr16	509100	509632	+	0	NA	intron (NM_014700, intron 8 of 13)	HAL1|LINE|L1	18041	NR_024121	64493	Hs.721553	NR_024121		LINC00235	C16orf10|LA16c-356B8.1|NCRNA00235	long intergenic non-protein coding RNA 235	ncRNA	0.028195	0.577861	
chunk0036_340_1	chr11	66748923	66749468	+	0	NA	intron (NM_024650, intron 2 of 16)	intron (NM_024650, intron 2 of 16)	4459	NM_024650	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.003670	0.415751	
chunk0106_285_1	chr2	204183741	204183971	+	0	NA	Intergenic	Intergenic	247108	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.008696	0.441558	
chunk0111_279_1	chr20	31572811	31573346	+	0	NA	intron (NR_046853, intron 1 of 2)	CpG	185	NR_046853	100874042	Hs.373741	NR_046853	ENSG00000230613	HM13-AS1	-	HM13 antisense RNA 1	ncRNA	0.089720	0.729478	
chunk0164_443_1	chr6	27836756	27837505	+	0	NA	TTS (NM_003510)	TTS (NM_003510)	1209	NM_003510	8330	Hs.734717	NM_003510	ENSG00000275221	HIST1H2AK	H2A/d|H2AFD	histone cluster 1 H2A family member k	protein-coding	0.028037	0.468000	
chunk0113_255_1	chr20	55721709	55722037	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	283599	NM_080617	140689	Hs.126141	NM_080617	ENSG00000054803	CBLN4	CBLNL1	cerebellin 4 precursor	protein-coding	0.000000	0.446809	105(ATAAACACTATGTCCC,-,0.00)
chunk0049_418_1	chr12	97462665	97462910	+	0	NA	Intergenic	Intergenic	-2234	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.012245	0.487805	
chunk0069_344_1	chr15	66554434	66554768	+	0	NA	intron (NM_001278562, intron 7 of 11)	L1ME4b|LINE|L1	10896	NM_207338	197021	Hs.680983	NM_207338	ENSG00000188501	LCTL	KLG|KLPH	lactase like	protein-coding	0.000000	0.373134	
chunk0051_136_1	chr12	115660340	115661399	+	0	NA	Intergenic	Intergenic	487785	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.013220	0.400000	
chunk0158_67_1	chr5	126212831	126213137	+	0	NA	Intergenic	Intergenic	33407	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.003268	0.358306	
chunk0027_74_1	chr10	73185314	73185739	+	0	NA	intron (NM_173348, intron 3 of 13)	AluJb|SINE|Alu	17407	NM_173348	317662	Hs.408577	NM_173348	ENSG00000138286	FAM149B1	KIAA0974	family with sequence similarity 149 member B1	protein-coding	0.007059	0.417840	
chunk0012_425_1	chr1	164644736	164645205	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	85610	NM_001204963	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.010661	0.442553	
chunk0128_368_1	chr3	113262023	113262334	+	0	NA	intron (NM_001301861, intron 4 of 19)	intron (NM_001301861, intron 4 of 19)	49681	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.006431	0.445513	
chunk0062_389_1	chr14	74732450	74733175	+	0	NA	exon (NM_015962, exon 6 of 8)	exon (NM_015962, exon 6 of 8)	19665	NM_015962	51077	Hs.579828	NM_015962	ENSG00000119616	FCF1	Bka|C14orf111|CGI-35|UTP24	FCF1 rRNA-processing protein	protein-coding	0.004138	0.348485	
chunk0174_413_1	chr6	165675210	165675580	+	0	NA	Intergenic	Intergenic	-13295	NM_001130690	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.005405	0.293801	
chunk0089_364_1	chr18	66997571	66997975	+	0	NA	Intergenic	L1PA15|LINE|L1	-83811	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.000000	0.335802	
chunk0054_235_1	chr13	45781786	45782090	+	0	NA	3' UTR (NM_198849, exon 2 of 2)	3' UTR (NM_198849, exon 2 of 2)	69773	NM_198849	283514	Hs.368483	NM_198849	ENSG00000215475	SIAH3	-	siah E3 ubiquitin protein ligase family member 3	protein-coding	0.009868	0.531148	
chunk0186_19_1	chr7	135773384	135773869	+	0	NA	Intergenic	Intergenic	-24780	NM_205855	389558	Hs.55200	NM_205855	ENSG00000189320	FAM180A	UNQ1940	family with sequence similarity 180 member A	protein-coding	0.010309	0.454733	
chunk0134_355_1	chr3	182626404	182627192	+	0	NA	Intergenic	Intergenic	-140436	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.005076	0.382763	
chunk0184_106_1	chr7	113452204	113452695	+	0	NA	Intergenic	Intergenic	-333867	NR_015442									0.008147	0.365854	
chunk0079_314_1	chr17	17237004	17237538	+	0	NA	promoter-TSS (NM_144606)	promoter-TSS (NM_144606)	-83	NM_144997	201163	Hs.31652	NM_144606	ENSG00000154803	FLCN	BHD|DENND8B|FLCL	folliculin	protein-coding	0.071161	0.628037	
chunk0060_280_1	chr14	50441823	50442619	+	0	NA	intron (NM_006575, intron 21 of 31)	L1MC4|LINE|L1	-44817	NM_001282236	8814	Hs.280881	NM_004196	ENSG00000100490	CDKL1	KKIALRE|P42	cyclin dependent kinase like 1	protein-coding	0.005025	0.314931	
chunk0184_463_1	chr7	123648059	123648611	+	0	NA	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	-7472	NM_207163	442721	Hs.592260	NM_207163	ENSG00000170807	LMOD2	C-LMOD|CLMOD	leiomodin 2	protein-coding	0.001812	0.374322	
chunk0125_313_1	chr3	70797021	70797243	+	0	NA	Intergenic	L1MDa|LINE|L1	267791	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.004505	0.497758	
chunk0193_397_1	chr8	80534457	80534706	+	0	NA	Intergenic	Intergenic	48368	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.004016	0.448000	
chunk0170_389_1	chr6	117147703	117148136	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-117639	NM_182645	245806	Hs.99324	NM_153453	ENSG00000170162	VGLL2	VGL2|VITO1	vestigial like family member 2	protein-coding	0.002309	0.322581	
chunk0052_19_1	chr13	20171075	20172037	+	0	NA	Intergenic	Intergenic	-10512	NM_021954	2700	Hs.130313	NM_021954	ENSG00000121743	GJA3	CTRCT14|CX46|CZP3	gap junction protein alpha 3	protein-coding	0.006237	0.411215	223(AGGAACTCAGTGTCCC,-,0.00),224(GGAACTCAGTGTCCCC,+,0.00)
chunk0085_179_1	chr18	5631096	5631530	+	0	NA	Intergenic	Intergenic	-2322	NM_001281535	23136	Hs.213394	NM_012307	ENSG00000082397	EPB41L3	4.1B|DAL-1|DAL1	erythrocyte membrane protein band 4.1 like 3	protein-coding	0.023041	0.524138	344(CTGCACAGTCTGTCCC,-,0.00),345(TGCACAGTCTGTCCCT,+,0.00)
chunk0136_219_1	chr4	7923821	7924204	+	0	NA	intron (NM_198595, intron 1 of 16)	intron (NM_198595, intron 1 of 16)	-14989	NM_203423	389199	Hs.375210	NM_203423		LOC389199	-	uncharacterized LOC389199	protein-coding	0.005222	0.395833	
chunk0096_258_1	chr2	31414739	31415088	+	0	NA	promoter-TSS (NM_000379)	promoter-TSS (NM_000379)	-168	NM_000379	7498	Hs.250	NM_000379	ENSG00000158125	XDH	XAN1|XO|XOR	xanthine dehydrogenase	protein-coding	0.011461	0.474286	
chunk0050_244_1	chr12	105352931	105353341	+	0	NA	intron (NM_001145199, intron 2 of 5)	MLT1K|LTR|ERVL-MaLR	22500	NM_001145199	387882	Hs.368938	NM_207376	ENSG00000235162	C12orf75	AGD3|OCC-1|OCC1	chromosome 12 open reading frame 75	protein-coding	0.009756	0.418491	
chunk0005_333_1	chr1	61122105	61122304	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	39896	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.010050	0.315000	81(GGGAACATACTGTATC,-,0.00),82(GGAACATACTGTATCA,+,0.00)
chunk0093_239_1	chr19	50841982	50842729	+	0	NA	intron (NR_131203, intron 2 of 2)	LTR40a|LTR|ERVL	-10832	NR_102274	55554	Hs.567535	NM_017509	ENSG00000174562	KLK15	ACO|HSRNASPH	kallikrein related peptidase 15	protein-coding	0.010710	0.429144	
chunk0126_357_1	chr3	83004209	83004616	+	0	NA	Intergenic	Intergenic	-1242613	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.017199	0.384804	
chunk0153_202_1	chr5	71767931	71768395	+	0	NA	Intergenic	Intergenic	49000	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.010776	0.397849	
chunk0061_343_1	chr14	63490433	63490632	+	0	NA	intron (NM_001282180, intron 2 of 13)	L1PA17|LINE|L1	17706	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.005025	0.370000	
chunk0122_394_1	chr3	37931883	37932331	+	0	NA	intron (NM_001008392, intron 1 of 7)	intron (NM_001008392, intron 1 of 7)	-37297	NR_029499	407015		NR_029499	ENSG00000199075	MIR26A1	MIR26A|MIRN26A1|mir-26a-1	microRNA 26a-1	ncRNA	0.002232	0.309577	
chunk0212_279_1	chrX	140432571	140432961	+	0	NA	Intergenic	Intergenic	72294	NM_005634	6658	Hs.157429	NM_005634	ENSG00000134595	SOX3	GHDX|MRGH|PHP|PHPX|SOXB	SRY-box transcription factor 3	protein-coding	0.005128	0.544757	
chunk0104_395_1	chr2	180558557	180558886	+	0	NA	Intergenic	L1PA10|LINE|L1	-133383	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.003040	0.442424	
chunk0161_86_1	chr5	167183132	167183686	+	0	NA	Intergenic	Intergenic	-101429	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.003610	0.360360	
chunk0119_157_1	chr22	43143357	43143556	+	0	NA	promoter-TSS (NR_046423)	promoter-TSS (NR_046423)	-59	NM_173467	27349	Hs.349111	NM_014507	ENSG00000100294	MCAT	FASN2C|MCT|MCT1|MT|NET62|fabD	malonyl-CoA-acyl carrier protein transacylase	protein-coding	0.130653	0.700000	
chunk0053_318_1	chr13	34169550	34170120	+	0	NA	Intergenic	Intergenic	351766	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.005263	0.336252	
chunk0010_96_1	chr1	113904232	113904431	+	0	NA	promoter-TSS (NM_022836)	promoter-TSS (NM_022836)	592	NM_001253852	10717	Hs.515048	NM_006594	ENSG00000134262	AP4B1	BETA-4|CPSQ5|SPG47	adaptor related protein complex 4 subunit beta 1	protein-coding	0.035176	0.455000	
chunk0012_36_1	chr1	155125634	155126240	+	0	NA	Intergenic	Intergenic	-1936	NM_004428	1942	Hs.516664	NM_004428	ENSG00000169242	EFNA1	B61|ECKLG|EFL1|EPLG1|LERK-1|LERK1|TNFAIP4	ephrin A1	protein-coding	0.051155	0.586491	
chunk0168_94_1	chr6	80015686	80016409	+	0	NA	intron (NM_001166691, intron 10 of 21)	L1ME3|LINE|L1	11442	NM_001166691	7272	Hs.169840	NM_003318	ENSG00000112742	TTK	CT96|ESK|MPH1|MPS1|MPS1L1|PYT	TTK protein kinase	protein-coding	0.001383	0.328729	
chunk0086_214_1	chr18	22493328	22493765	+	0	NA	Intergenic	Intergenic	-75631	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.000000	0.410959	
chunk0098_345_1	chr2	77308846	77309360	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	213265	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.007782	0.355340	
chunk0135_174_1	chr3	188053014	188053351	+	0	NA	Intergenic	MIRc|SINE|MIR	-100691	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.002967	0.411243	
chunk0180_102_1	chr7	55265808	55266467	+	0	NA	Intergenic	L1M3e|LINE|L1	-10502	NR_110426	102725541	Hs.590524	NR_110426		ELDR	Fabl|LINC01156	EGFR long non-coding downstream RNA	ncRNA	0.007587	0.359091	
chunk0024_260_1	chr10	38919695	38920235	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	223369	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.003704	0.475046	
chunk0064_407_1	chr14	99526526	99526832	+	0	NA	intron (NM_001144995, intron 2 of 5)	intron (NM_001144995, intron 2 of 5)	45277	NM_001099402	8812	Hs.510409	NM_003858	ENSG00000090061	CCNK	CPR4|IDDHDF	cyclin K	protein-coding	0.029412	0.644951	99(GGGAACACCCCGTCCC,-,0.00),100(GGAACACCCCGTCCCC,+,0.00)
chunk0064_173_1	chr14	92408216	92408558	+	0	NA	intron (NM_153646, intron 2 of 16)	intron (NM_153646, intron 2 of 16)	84579	NM_153646	123041	Hs.385530	NM_153646	ENSG00000140090	SLC24A4	AI2A5|NCKX4|SHEP6|SLC24A2	solute carrier family 24 member 4	protein-coding	0.002924	0.437318	
chunk0076_264_1	chr16	69400639	69401180	+	0	NA	Intergenic	Intergenic	-14921	NM_005652	7014	Hs.63335	NM_005652	ENSG00000132604	TERF2	TRBF2|TRF2	telomeric repeat binding factor 2	protein-coding	0.011091	0.407749	
chunk0185_449_1	chr7	135012281	135012776	+	0	NA	intron (NM_178563, intron 4 of 16)	intron (NM_178563, intron 4 of 16)	26020	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.002020	0.352823	
chunk0073_301_1	chr16	14092564	14093021	+	0	NA	intron (NM_001308142, intron 2 of 16)	intron (NM_001308142, intron 2 of 16)	21478	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.000000	0.310044	
chunk0071_313_1	chr15	86316707	86316978	+	0	NA	non-coding (NR_046012, exon 1 of 4)	non-coding (NR_046012, exon 1 of 4)	126	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.007380	0.500000	
chunk0141_137_1	chr4	81119089	81119645	+	0	NA	intron (NM_001282483, intron 9 of 13)	L1MC1|LINE|L1	34790	NM_001282481	5593	Hs.232044	NM_006259	ENSG00000138669	PRKG2	PKG2|PRKGR2|cGK2|cGKII	protein kinase cGMP-dependent 2	protein-coding	0.003597	0.344704	
chunk0130_2_1	chr3	128323519	128323996	+	0	NA	intron (NM_021937, intron 4 of 6)	intron (NM_021937, intron 4 of 6)	-139837	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.016771	0.548117	
chunk0018_102_1	chr1	218138438	218138678	+	0	NA	Intergenic	MER66B|LTR|ERV1	95053	NR_110794	101929631	Hs.407614	NR_110794	ENSG00000232100	LINC01653	-	long intergenic non-protein coding RNA 1653	ncRNA	0.020833	0.518672	59(AGGAACAGTAAGTCCT,-,0.00),60(GGAACAGTAAGTCCTG,+,0.00)
chunk0081_363_1	chr17	47883061	47883824	+	0	NA	Intergenic	L2a|LINE|L2	-12708	NM_003110	6668	Hs.514276	NM_003110	ENSG00000167182	SP2	-	Sp2 transcription factor	protein-coding	0.013106	0.573298	341(GTGAACAAACTGTTCT,-,0.00),342(TGAACAAACTGTTCTT,+,0.00),364(GGGGACACCCTGCTCC,-,0.00),365(GGGACACCCTGCTCCC,+,0.00)
chunk0063_164_1	chr14	80264693	80265117	+	0	NA	intron (NR_038355, intron 2 of 8)	intron (NR_038355, intron 2 of 8)	-33851	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.007075	0.397647	
chunk0197_161_1	chr8	120508122	120508321	+	0	NA	intron (NM_022045, intron 16 of 21)	intron (NM_022045, intron 16 of 21)	-62814	NM_014078	28998	Hs.333823	NM_014078	ENSG00000172172	MRPL13	L13|L13A|L13mt|RPL13|RPML13	mitochondrial ribosomal protein L13	protein-coding	0.000000	0.295000	
chunk0210_370_1	chrX	97057352	97057883	+	0	NA	intron (NM_006729, intron 17 of 26)	intron (NM_006729, intron 17 of 26)	173709	NM_013347	29935	Hs.659349	NM_013347	ENSG00000204086	RPA4	HSU24186	replication protein A4	protein-coding	0.007533	0.392857	
chunk0097_450_1	chr2	64448876	64449383	+	0	NA	Intergenic	Intergenic	-5064	NM_014181	29094	Hs.372208	NM_014181	ENSG00000119862	LGALSL	GRP|HSPC159	galectin like	protein-coding	0.001972	0.397638	180(GAGCACATTATGTCCA,-,0.00),181(AGCACATTATGTCCAC,+,0.00)
chunk0078_34_1	chr17	915479	915745	+	0	NA	intron (NM_022463, intron 1 of 7)	intron (NM_022463, intron 1 of 7)	-51501	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.007519	0.456929	
chunk0188_96_1	chr8	8806034	8806638	+	0	NA	intron (NM_004225, intron 1 of 2)	intron (NM_004225, intron 1 of 2)	87285	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.009934	0.438017	
chunk0047_279_1	chr12	73098373	73098773	+	0	NA	Intergenic	Intergenic	-60617	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.391521	
chunk0065_122_1	chr15	24824178	24824984	+	0	NA	intron (NM_022808, intron 1 of 11)	intron (NM_022808, intron 1 of 11)	934	NM_022806	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.008685	0.348203	
chunk0170_402_1	chr6	117602326	117602671	+	0	NA	promoter-TSS (NM_001017408)	promoter-TSS (NM_001017408)	44	NM_020399	57120	Hs.191539	NM_020399	ENSG00000047932	GOPC	CAL|FIG|GOPC1|PIST|dJ94G16.2	golgi associated PDZ and coiled-coil motif containing	protein-coding	0.098551	0.653179	
chunk0073_444_1	chr16	19331057	19331447	+	0	NA	Intergenic	Intergenic	45469	NM_001256720	728276	Hs.632180	NM_001256720	ENSG00000261210	CLEC19A	-	C-type lectin domain containing 19A	protein-coding	0.002564	0.468031	
chunk0167_2_1	chr6	53394122	53394707	+	0	NA	Intergenic	L1ME4a|LINE|L1	-45235	NM_021814	60481	Hs.520189	NM_021814	ENSG00000012660	ELOVL5	HELO1|SCA38|dJ483K16.1	ELOVL fatty acid elongase 5	protein-coding	0.005128	0.447099	
chunk0009_30_1	chr1	100249744	100250070	+	0	NA	promoter-TSS (NM_001918)	promoter-TSS (NM_001918)	-54	NM_001918	1629	Hs.709187	NM_001918	ENSG00000137992	DBT	BCATE2|BCKAD-E2|BCKADE2|BCOADC-E2|E2|E2B	dihydrolipoamide branched chain transacylase E2	protein-coding	0.049080	0.602446	
chunk0090_182_1	chr18	72899194	72899636	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-31840	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.006787	0.413093	
chunk0131_298_1	chr3	150603560	150604178	+	0	NA	intron (NM_016275, intron 1 of 5)	CpG	590	NM_016275	51714	Hs.369052	NM_016275	ENSG00000198843	SELENOT	SELT	selenoprotein T	protein-coding	0.072816	0.588045	567(AGGAGCACGTTGTTCT,-,0.00),568(GGAGCACGTTGTTCTT,+,0.00)
chunk0099_124_1	chr2	86072294	86072826	+	0	NA	intron (NM_015425, intron 12 of 33)	intron (NM_015425, intron 12 of 33)	33595	NM_015425	25885	Hs.531818	NM_015425	ENSG00000068654	POLR1A	A190|AFDCIN|RPA1|RPA194|RPO1-4|RPO14	RNA polymerase I subunit A	protein-coding	0.013158	0.545966	
chunk0165_119_1	chr6	32920683	32921333	+	0	NA	Intergenic	L1MEh|LINE|L1	20062	NM_002118	3109	Hs.351279	NM_002118	ENSG00000242574	HLA-DMB	D6S221E|RING7	major histocompatibility complex, class II, DM beta	protein-coding	0.003077	0.281106	
chunk0116_66_1	chr21	34151512	34151788	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-29027	NR_027267	114036	Hs.720230	NM_153751	ENSG00000227456	LINC00310	C21orf82|NCRNA00310	long intergenic non-protein coding RNA 310	ncRNA	0.010870	0.411552	
chunk0202_258_1	chr9	76863590	76863789	+	0	NA	intron (NM_015225, intron 1 of 18)	intron (NM_015225, intron 1 of 18)	42398	NR_131751	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.000000	0.400000	59(CAGCACACTCTGTACA,-,0.00),60(AGCACACTCTGTACAA,+,0.00)
chunk0197_411_1	chr8	127268876	127269185	+	0	NA	intron (NR_117099, intron 1 of 3)	intron (NR_117099, intron 1 of 3)	24393	NR_117099	103021164	Hs.571531	NR_117099		CASC21	CARLO2|CARLo-2|LINC01244	cancer susceptibility 21	ncRNA	0.006472	0.390323	
chunk0069_8_1	chr15	60070799	60071279	+	0	NA	Intergenic	Intergenic	66817	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.006250	0.411642	
chunk0040_214_1	chr11	114179025	114179850	+	0	NA	intron (NM_006006, intron 3 of 6)	intron (NM_006006, intron 3 of 6)	-116376	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.007273	0.450363	317(AAGAACACACAGTGCC,-,0.00),318(AGAACACACAGTGCCG,+,0.00),478(TGGTACACTCTGTACT,-,0.00),479(GGTACACTCTGTACTT,+,0.00)
chunk0043_348_1	chr12	23042936	23043498	+	0	NA	Intergenic	Intergenic	-132419	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.001779	0.333925	
chunk0142_244_1	chr4	98903142	98903469	+	0	NA	intron (NM_001968, intron 1 of 6)	intron (NM_001968, intron 1 of 6)	25787	NM_001130678	1977	Hs.13211	NM_001968	ENSG00000151247	EIF4E	AUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding	0.003058	0.359756	
chunk0123_455_1	chr3	51284741	51284940	+	0	NA	intron (NM_004947, intron 27 of 52)	L1M3de|LINE|L1	-100397	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.005025	0.455000	
chunk0022_183_1	chr10	13220336	13220688	+	0	NA	Intergenic	Intergenic	3243	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.008523	0.456091	231(GACACATGTTGTTCTC,+,0.00)
chunk0146_102_1	chr4	158672087	158672286	+	0	NA	promoter-TSS (NM_001281737)	promoter-TSS (NM_001281737)	69	NR_077235	201725	Hs.380920	NM_001008393	ENSG00000205208	C4orf46	RCDG1	chromosome 4 open reading frame 46	protein-coding	0.100503	0.650000	98(GGGACTTGGAGTCCCT,+,0.00)
chunk0125_28_1	chr3	62211580	62212217	+	0	NA	intron (NM_002841, intron 12 of 29)	intron (NM_002841, intron 12 of 29)	107049	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.015699	0.427900	
chunk0071_306_1	chr15	86115725	86116672	+	0	NA	intron (NR_120368, intron 1 of 5)	intron (NR_120368, intron 1 of 5)	519	NR_120368	101929701	Hs.132570	NR_120368	ENSG00000260477	LINC01584	-	long intergenic non-protein coding RNA 1584	ncRNA	0.002112	0.398734	
chunk0111_360_1	chr20	33622658	33623090	+	0	NA	intron (NM_001032999, intron 4 of 10)	L2c|LINE|L2	-39412	NM_080825	128864	Hs.324104	NM_080825	ENSG00000149609	C20orf144	dJ63M2.6	chromosome 20 open reading frame 144	protein-coding	0.002315	0.406467	
chunk0022_225_1	chr10	14012126	14012583	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-61930	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.006565	0.491266	
chunk0135_53_1	chr3	185664038	185664281	+	0	NA	intron (NM_001007225, intron 9 of 14)	intron (NM_001007225, intron 9 of 14)	-49093	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.008230	0.512295	93(GGAGCTGCCTGTCCTG,+,0.00)
chunk0159_178_1	chr5	140126550	140127168	+	0	NA	5' UTR (NM_001007189, exon 1 of 1)	5' UTR (NM_001007189, exon 1 of 1)	923	NM_001007189	492311	Hs.696360	NM_001007189	ENSG00000182700	IGIP	C5orf53	IgA inducing protein	protein-coding	0.006472	0.447496	
chunk0149_289_1	chr5	25412925	25413278	+	0	NA	Intergenic	Intergenic	-572518	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.002833	0.279661	
chunk0091_123_1	chr19	6273772	6274160	+	0	NA	intron (NM_005934, intron 1 of 11)	intron (NM_005934, intron 1 of 11)	5982	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.051546	0.596401	
chunk0037_280_1	chr11	75823495	75823924	+	0	NA	intron (NM_003369, intron 1 of 14)	intron (NM_003369, intron 1 of 14)	8542	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.009324	0.425581	
chunk0068_283_1	chr15	56943015	56943350	+	0	NA	intron (NM_003205, intron 3 of 19)	intron (NM_003205, intron 3 of 19)	24547	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.002985	0.348214	147(GGGAACAAATAGTTCT,-,0.00),148(GGAACAAATAGTTCTG,+,0.00)
chunk0107_345_1	chr2	221610501	221611170	+	0	NA	Intergenic	Intergenic	-36633	NM_001304536	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.017937	0.468657	310(TGGTACTGCATGTTCC,-,0.00),311(GGTACTGCATGTTCCA,+,0.00),333(AAGCACAACACGTTCT,-,0.00),334(AGCACAACACGTTCTT,+,0.00)
chunk0080_231_1	chr17	29910321	29910717	+	0	NA	intron (NM_001282129, intron 1 of 15)	UCON40|Unknown|Unknown	-19337	NM_001145053	374786	Hs.662411	NM_198529	ENSG00000176927	EFCAB5	-	EF-hand calcium binding domain 5	protein-coding	0.000000	0.319899	
chunk0009_286_1	chr1	107663978	107664528	+	0	NA	intron (NM_006113, intron 19 of 26)	L1PA11|LINE|L1	24251	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.007273	0.366606	
chunk0010_37_1	chr1	112643100	112643507	+	0	NA	intron (NM_006135, intron 1 of 9)	intron (NM_006135, intron 1 of 9)	23850	NM_006135	829	Hs.744974	NM_006135	ENSG00000116489	CAPZA1	CAPPA1|CAPZ|CAZ1	capping actin protein of muscle Z-line subunit alpha 1	protein-coding	0.004914	0.330882	
chunk0012_97_1	chr1	156437448	156437660	+	0	NA	Intergenic	Intergenic	-8162	NM_006365	10485	Hs.380027	NM_006365	ENSG00000125462	C1orf61	CROC4	chromosome 1 open reading frame 61	protein-coding	0.023585	0.539906	
chunk0210_269_1	chrX	84234804	84235299	+	0	NA	Intergenic	Intergenic	-9223	NR_031690	100302191		NR_031690	ENSG00000221494	MIR548I4	MIR548I-4|MIRN548I4|hsa-mir-548i-4	microRNA 548i-4	ncRNA	0.002020	0.415323	306(AATCACACTGTGTTCT,-,0.00),307(ATCACACTGTGTTCTC,+,0.00)
chunk0049_168_1	chr12	92243874	92244518	+	0	NA	Intergenic	L2a|LINE|L2	-98299	NM_001731	694	Hs.255935	NM_001731	ENSG00000133639	BTG1	APRO2	BTG anti-proliferation factor 1	protein-coding	0.004658	0.381395	335(CTGAACATTATGTTCT,-,0.00),336(TGAACATTATGTTCTC,+,0.00)
chunk0207_108_1	chr9	128802393	128803005	+	0	NA	intron (NM_001286772, intron 7 of 9)	L1MC5a|LINE|L1	15492	NM_001286772	54662	Hs.3376	NM_018201	ENSG00000107021	TBC1D13	-	TBC1 domain family member 13	protein-coding	0.013072	0.456770	314(AAGAACACATTGTCCT,-,0.00),315(AGAACACATTGTCCTC,+,0.00)
chunk0199_430_1	chr9	13775009	13775630	+	0	NA	Intergenic	Intergenic	-152652	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.009662	0.405145	
chunk0091_285_1	chr19	11924698	11925437	+	0	NA	promoter-TSS (NM_144566)	promoter-TSS (NM_144566)	-1	NM_001271848	90592	Hs.528486	NM_144566	ENSG00000196757	ZNF700	-	zinc finger protein 700	protein-coding	0.054127	0.616216	
chunk0068_125_1	chr15	52624195	52624711	+	0	NA	intron (NM_019600, intron 2 of 12)	MamSINE1|SINE|tRNA-RTE	27597	NM_001286495	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.003876	0.382979	296(ATGGACAGACTGTACT,-,0.00),297(TGGACAGACTGTACTG,+,0.00)
chunk0166_332_1	chr6	50093811	50094334	+	0	NA	Intergenic	Intergenic	-45421	NM_001037498	245915	Hs.571092	NM_001037498	ENSG00000180872	DEFB112	DEFB-12	defensin beta 112	protein-coding	0.001912	0.314885	
chunk0173_174_1	chr6	144556644	144556871	+	0	NA	intron (NM_007124, intron 48 of 73)	intron (NM_007124, intron 48 of 73)	151102	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.017621	0.447368	
chunk0140_19_1	chr4	65590706	65591384	+	0	NA	intron (NM_001281765, intron 3 of 17)	intron (NM_001281765, intron 3 of 17)	-78916	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.002950	0.300442	
chunk0071_87_1	chr15	80816627	80817270	+	0	NA	intron (NM_018689, intron 1 of 28)	intron (NM_018689, intron 1 of 28)	25125	NR_030393	693132		NR_030393	ENSG00000208003	MIR549A	MIR549|MIRN549|hsa-mir-549|hsa-mir-549a|mir-549a	microRNA 549a	ncRNA	0.017107	0.444099	140(GAGGACATTGTGTCCT,-,0.00),141(AGGACATTGTGTCCTT,+,0.00),558(TGGGACAGGCTGCCCT,-,0.00),559(GGGACAGGCTGCCCTG,+,0.00)
chunk0017_137_1	chr1	206612170	206612625	+	0	NA	5' UTR (NM_001201478, exon 1 of 13)	5' UTR (NM_001201478, exon 1 of 13)	154	NM_006893	1939	Hs.497581	NM_006893	ENSG00000143486	EIF2D	HCA56|LGTN	eukaryotic translation initiation factor 2D	protein-coding	0.061538	0.686404	
chunk0008_161_1	chr1	92759886	92760096	+	0	NA	intron (NM_001308248, intron 1 of 18)	intron (NM_001308248, intron 1 of 18)	32413	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.000000	0.322275	
chunk0108_450_1	chr2	238285694	238286055	+	0	NA	intron (NM_022817, intron 1 of 22)	intron (NM_022817, intron 1 of 22)	2692	NM_022817	8864	Hs.58756	NM_003894	ENSG00000132326	PER2	FASPS|FASPS1	period circadian regulator 2	protein-coding	0.019391	0.522099	
chunk0157_269_1	chr5	120105155	120105462	+	0	NA	Intergenic	MIR|SINE|MIR	-358970	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.000000	0.308442	
chunk0174_406_1	chr6	165599071	165599520	+	0	NA	intron (NM_006661, intron 1 of 22)	intron (NM_006661, intron 1 of 22)	62805	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.008909	0.400000	
chunk0176_49_1	chr7	11029522	11030144	+	0	NA	intron (NR_033435, intron 6 of 15)	intron (NR_033435, intron 6 of 15)	55961	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.001608	0.284109	
chunk0021_149_1	chr10	4354050	4354536	+	0	NA	Intergenic	Intergenic	-29953	NR_108055	100507059	Hs.158438	NR_108054	ENSG00000224382	LINC00703	-	long intergenic non-protein coding RNA 703	ncRNA	0.006173	0.379877	
chunk0107_267_1	chr2	217672469	217672857	+	0	NA	intron (NR_026597, intron 1 of 12)	intron (NR_026597, intron 1 of 12)	83930	NR_026597	729582	Hs.572788	NR_026597		DIRC3	-	disrupted in renal carcinoma 3	ncRNA	0.007732	0.501285	
chunk0166_274_1	chr6	48172764	48172963	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-104174	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.010050	0.370000	
chunk0107_276_1	chr2	218017668	218018088	+	0	NA	Intergenic	Intergenic	-17056	NR_034176	285180	Hs.570069	NM_198483	ENSG00000188282	RUFY4	ZFYVE31	RUN and FYVE domain containing 4	protein-coding	0.014286	0.515439	247(TGGAACACACAGTTCA,-,0.00),248(GGAACACACAGTTCAC,+,0.00)
chunk0118_231_1	chr22	32408784	32408983	+	0	NA	intron (NM_014306, intron 1 of 11)	intron (NM_014306, intron 1 of 11)	3404	NM_014306	51493	Hs.474643	NM_014306	ENSG00000100220	RTCB	C22orf28|DJ149A16.6|FAAP|HSPC117	RNA 2',3'-cyclic phosphate and 5'-OH ligase	protein-coding	0.015075	0.400000	
chunk0188_37_1	chr8	6624355	6625052	+	0	NA	intron (NM_024596, intron 13 of 13)	intron (NM_024596, intron 13 of 13)	-2483	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.018651	0.446991	432(CAGAACACACAGTCCA,-,0.00),433(AGAACACACAGTCCAG,+,0.00)
chunk0071_28_1	chr15	79382965	79383167	+	0	NA	3' UTR (NM_001301203, exon 3 of 3)	3' UTR (NM_001301203, exon 3 of 3)	-49450	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.014851	0.541872	
chunk0184_113_1	chr7	113714274	113714865	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	204458	NM_002711	5506	Hs.458309	NM_002711	ENSG00000154415	PPP1R3A	GM|PP1G|PPP1R3	protein phosphatase 1 regulatory subunit 3A	protein-coding	0.005076	0.380068	
chunk0114_151_1	chr21	10425752	10426108	+	0	NA	intron (NM_001187, intron 3 of 4)	L1MC5|LINE|L1	12398	NM_182484	85316	Hs.545789	NM_182484		BAGE5	CT2.5	BAGE family member 5	protein-coding	0.008427	0.358543	
chunk0139_270_1	chr4	56704565	56704842	+	0	NA	Intergenic	Intergenic	-22997	NM_001145460	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.000000	0.492806	
chunk0005_290_1	chr1	60108182	60108675	+	0	NA	Intergenic	Intergenic	-34658	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.006085	0.408907	
chunk0015_416_1	chr1	191424108	191424315	+	0	NA	Intergenic	L1MEg|LINE|L1	-734251	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.000000	0.365385	87(GAGGACAGTAAGTCCC,-,0.00),88(AGGACAGTAAGTCCCT,+,0.00)
chunk0208_137_1	chrX	15623116	15623356	+	0	NA	Intergenic	Intergenic	20355	NR_126564	104798195	Hs.131674	NR_126564	ENSG00000225833	GS1-594A7.3	-	uncharacterized LOC104798195	ncRNA	0.000000	0.390041	
chunk0185_400_1	chr7	133871842	133872069	+	0	NA	intron (NM_021807, intron 11 of 17)	intron (NM_021807, intron 11 of 17)	-47067	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.000000	0.355263	
chunk0190_370_1	chr8	39915075	39915425	+	0	NA	intron (NM_002164, intron 1 of 9)	intron (NM_002164, intron 1 of 9)	1441	NM_002164	3620	Hs.840	NM_002164	ENSG00000131203	IDO1	IDO|IDO-1|INDO	indoleamine 2,3-dioxygenase 1	protein-coding	0.002857	0.364672	
chunk0200_321_1	chr9	23598948	23599470	+	0	NA	intron (NR_121602, intron 11 of 27)	MER103C|DNA|hAT-Charlie	73190	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.005747	0.384321	
chunk0204_257_1	chr9	98146517	98146805	+	0	NA	intron (NM_003389, intron 2 of 11)	intron (NM_003389, intron 2 of 11)	26231	NM_003389	7464	Hs.113094	NM_003389	ENSG00000106789	CORO2A	CLIPINB|IR10|WDR2	coronin 2A	protein-coding	0.013889	0.508651	
chunk0168_20_1	chr6	76980319	76981298	+	0	NA	Intergenic	L1PA7|LINE|L1	482595	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.010215	0.353061	
chunk0087_139_1	chr18	33810178	33810377	+	0	NA	Intergenic	AluJr|SINE|Alu	231700	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.015075	0.535000	
chunk0184_415_1	chr7	122630383	122630824	+	0	NA	intron (NM_017954, intron 3 of 29)	L2|LINE|L2	68551	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.002268	0.380090	
chunk0127_25_1	chr3	88528382	88528709	+	0	NA	Intergenic	L1PA8A|LINE|L1	-378679	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.009174	0.539634	
chunk0023_292_1	chr10	28685204	28685477	+	0	NA	Intergenic	Intergenic	7845	NM_012342	25805	Hs.533336	NM_012342	ENSG00000095739	BAMBI	NMA	BMP and activin membrane bound inhibitor	protein-coding	0.007326	0.430657	
chunk0132_439_1	chr3	165106261	165106784	+	0	NA	Intergenic	Intergenic	-28027	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.005736	0.299618	
chunk0053_312_1	chr13	34124741	34125360	+	0	NA	Intergenic	Intergenic	306981	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.004847	0.380645	
chunk0153_208_1	chr5	71924943	71925333	+	0	NA	Intergenic	L3|LINE|CR1	-182153	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.007692	0.404092	
chunk0052_304_1	chr12	124825581	124826106	+	0	NA	intron (NM_001082959, intron 1 of 11)	L1MA9|LINE|L1	38130	NM_005505	949	Hs.731377	NM_005505	ENSG00000073060	SCARB1	CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1	scavenger receptor class B member 1	protein-coding	0.024762	0.520913	
chunk0203_169_1	chr9	86046663	86047261	+	0	NA	intron (NM_177937, intron 4 of 9)	intron (NM_177937, intron 4 of 9)	52633	NM_016548	51280	Hs.494337	NM_016548	ENSG00000135052	GOLM1	C9orf155|GOLPH2|GP73|HEL46|PSEC0257|bA379P1.3	golgi membrane protein 1	protein-coding	0.015050	0.520868	358(TGGACACCCTGCCCTC,+,0.00)
chunk0055_158_1	chr13	60175435	60175939	+	0	NA	Intergenic	Intergenic	-11702	NM_001258369	81624	Hs.283127	NM_030932	ENSG00000139734	DIAPH3	AN|AUNA1|DIA2|DRF3|NSDAN|diap3|mDia2	diaphanous related formin 3	protein-coding	0.009921	0.390099	12(GAAAACAGACTGTGCC,-,0.00),13(AAAACAGACTGTGCCT,+,0.00)
chunk0182_120_1	chr7	94129573	94130017	+	0	NA	Intergenic	Intergenic	-125417	NM_005868	10282	Hs.489132	NM_005868	ENSG00000105829	BET1	HBET1	Bet1 golgi vesicular membrane trafficking protein	protein-coding	0.002252	0.370787	216(AGGAACACAGAGTGCT,-,0.00),217(GGAACACAGAGTGCTG,+,0.00)
chunk0125_247_1	chr3	68936615	68937471	+	0	NA	Intergenic	UCON6|Unknown|Unknown	-4433	NM_182522	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.012850	0.417736	441(AAGAACATCACGTCCC,-,0.00),442(AGAACATCACGTCCCT,+,0.00)
chunk0150_161_1	chr5	33999259	33999855	+	0	NA	intron (NM_203382, intron 2 of 3)	intron (NM_203382, intron 2 of 3)	8558	NM_203382	23600	Hs.508343	NM_014324	ENSG00000242110	AMACR	AMACRD|CBAS4|P504S|RACE|RM	alpha-methylacyl-CoA racemase	protein-coding	0.005034	0.388610	325(AAGAAGATGATGTTCT,-,0.00)
chunk0050_450_1	chr12	110582403	110582936	+	0	NA	intron (NM_139283, intron 1 of 5)	CpG	590	NM_139283	160760	Hs.13854	NM_139283	ENSG00000196850	PPTC7	TA-PP2C|TAPP2C	PTC7 protein phosphatase homolog	protein-coding	0.106942	0.672285	
chunk0194_46_1	chr8	81991065	81991264	+	0	NA	Intergenic	L1PA6|LINE|L1	-148878	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.030151	0.525000	
chunk0018_108_1	chr1	218273938	218274467	+	0	NA	Intergenic	Intergenic	-11085	NM_016052	51018	Hs.660109	NM_016052	ENSG00000067533	RRP15	CGI-115|KIAA0507	ribosomal RNA processing 15 homolog	protein-coding	0.003781	0.392453	
chunk0029_85_1	chr10	96933933	96934541	+	0	NA	intron (NM_032440, intron 4 of 7)	intron (NM_032440, intron 4 of 7)	-47047	NM_015652	84458	Hs.427927	NM_015652	ENSG00000196233	LCOR	C10orf12|MLR2	ligand dependent nuclear receptor corepressor	protein-coding	0.001645	0.346470	
chunk0171_203_1	chr6	125752649	125753373	+	0	NA	intron (NM_012259, intron 3 of 4)	intron (NM_012259, intron 3 of 4)	3425	NM_012259	23493	Hs.144287	NM_012259	ENSG00000135547	HEY2	CHF1|GRIDLOCK|GRL|HERP1|HESR2|HRT2|bHLHb32	hes related family bHLH transcription factor with YRPW motif 2	protein-coding	0.004144	0.313103	
chunk0173_211_1	chr6	145513826	145514034	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-220939	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.430622	
chunk0046_51_1	chr12	54949267	54949822	+	0	NA	3' UTR (NM_001261844, exon 10 of 10)	3' UTR (NM_001261844, exon 10 of 10)	24188	NM_014796	9840	Hs.33187	NM_014796	ENSG00000135426	TESPA1	HSPC257|ITPRID3|KIAA0748	thymocyte expressed, positive selection associated 1	protein-coding	0.001802	0.350719	271(GAGCACTGCATGTGCT,-,0.00),272(AGCACTGCATGTGCTC,+,0.00)
chunk0196_193_1	chr8	106187165	106187455	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-82868	NM_001198533	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.003448	0.326460	
chunk0192_279_1	chr8	66177341	66177758	+	0	NA	intron (NM_000756, intron 1 of 1)	CpG	1062	NM_000756	1392	Hs.75294	NM_000756	ENSG00000147571	CRH	CRF|CRH1	corticotropin releasing hormone	protein-coding	0.074341	0.660287	
chunk0176_141_1	chr7	12787976	12788616	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	101010	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.006250	0.365055	410(TTGGACAGTATGTTCT,-,0.00),411(TGGACAGTATGTTCTA,+,0.00)
chunk0183_261_1	chr7	107304652	107305388	+	0	NA	intron (NM_006348, intron 11 of 21)	L2a|LINE|L2	136005	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.005435	0.421981	
chunk0056_120_1	chr13	83062825	83063074	+	0	NA	Intergenic	Intergenic	819444	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.304000	
chunk0037_420_1	chr11	79940029	79940443	+	0	NA	Intergenic	Intergenic	-499585	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.007246	0.438554	
chunk0168_386_1	chr6	94025842	94026302	+	0	NA	Intergenic	Intergenic	318989	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.013043	0.370933	
chunk0174_32_1	chr6	154298242	154298654	+	0	NA	intron (NM_001130700, intron 1 of 11)	intron (NM_001130700, intron 1 of 11)	31633	NM_001130699	26034	Hs.146100	NM_015553	ENSG00000074706	IPCEF1	PIP3-E	interaction protein for cytohesin exchange factors 1	protein-coding	0.007282	0.348668	281(AGAAACAGACTGTGCC,-,0.00),282(GAAACAGACTGTGCCC,+,0.00)
chunk0149_429_1	chr5	29686741	29687066	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-290927	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.361963	
chunk0128_362_1	chr3	113103511	113104116	+	0	NA	Intergenic	Intergenic	63918	NR_110823	101929717	Hs.638426	NR_110823	ENSG00000243795	LINC02044	-	long intergenic non-protein coding RNA 2044	ncRNA	0.006612	0.391089	120(GAAGACAGTTTGTTCT,-,0.00),121(AAGACAGTTTGTTCTC,+,0.00)
chunk0072_57_1	chr16	1630601	1631422	+	0	NA	intron (NM_020825, intron 2 of 19)	L1MC4|LINE|L1	16371	NM_020825	57585	Hs.603676	NM_020825	ENSG00000007545	CRAMP1	CRAMP1L|HN1L|TCE4	cramped chromatin regulator homolog 1	protein-coding	0.031669	0.523114	
chunk0109_383_1	chr2	239942403	239942787	+	0	NA	TTS (NR_039949)	TTS (NR_039949)	499	NR_039949	100616417		NR_039949	ENSG00000264279	MIR4786	mir-4786	microRNA 4786	ncRNA	0.028646	0.436364	
chunk0202_384_1	chr9	80932692	80933385	+	0	NA	Intergenic	Intergenic	756497	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.008658	0.406340	407(AGGAACATCTTGTTCT,-,0.00),408(GGAACATCTTGTTCTG,+,0.00)
chunk0061_217_1	chr14	60558994	60559679	+	0	NA	Intergenic	Intergenic	50116	NM_007374	4990	Hs.194756	NM_007374	ENSG00000184302	SIX6	MCOPCT2|ODRMD|OPTX2|Six9	SIX homeobox 6	protein-coding	0.005839	0.361516	
chunk0125_42_1	chr3	63815443	63815671	+	0	NA	Intergenic	L2b|LINE|L2	-3808	NR_026866									0.008772	0.436681	
chunk0081_315_1	chr17	46003795	46004289	+	0	NA	intron (NM_001203251, intron 7 of 9).3	intron (NM_001203251, intron 7 of 9).3	4792	NM_001007532	246744	Hs.661831	NM_001007532	ENSG00000256762	STH	MAPTIT	saitohin	protein-coding	0.008097	0.527273	
chunk0110_391_1	chr20	20217550	20217773	+	0	NA	intron (NM_015585, intron 17 of 26)	intron (NM_015585, intron 17 of 26)	-150460	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.008969	0.459821	
chunk0095_348_1	chr2	21263710	21263909	+	0	NA	Intergenic	Intergenic	139823	NM_001306137	100129278	Hs.651096	NM_001306137	ENSG00000218819	TDRD15	-	tudor domain containing 15	protein-coding	0.010050	0.465000	91(GGGATCACCGTGTTCC,-,0.00),92(GGATCACCGTGTTCCC,+,0.00)
chunk0049_412_1	chr12	97368284	97368591	+	0	NA	Intergenic	Intergenic	-96584	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.006515	0.405844	
chunk0122_10_1	chr3	27354231	27355151	+	0	NA	intron (NM_199347, intron 2 of 24)	intron (NM_199347, intron 2 of 24)	14769	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.007609	0.403909	140(GAGATCAGCATGTACT,-,0.00),141(AGATCAGCATGTACTC,+,0.00),765(GAGGACACACAGTCCC,-,0.00),766(AGGACACACAGTCCCA,+,0.00)
chunk0167_195_1	chr6	64488429	64488880	+	0	NA	intron (NM_001142800, intron 26 of 42)	intron (NM_001142800, intron 26 of 42)	-812764	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.004435	0.300885	
chunk0198_81_1	chr8	130122241	130122535	+	0	NA	intron (NM_001247996, intron 19 of 30)	L2|LINE|L2	-37620	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.003401	0.383051	
chunk0156_434_1	chr5	114617831	114618110	+	0	NA	intron (NR_130785, intron 3 of 12)	L1MC1|LINE|L1	155443	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.253571	
chunk0096_252_1	chr2	31295091	31295290	+	0	NA	Intergenic	Intergenic	61176	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.005025	0.415000	
chunk0036_309_1	chr11	66084111	66084417	+	0	NA	intron (NM_018026, intron 1 of 23)	L2a|LINE|L2	13911	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.013072	0.495114	161(GGGAACAAGAAGTACT,-,0.00),162(GGAACAAGAAGTACTG,+,0.00)
chunk0064_92_1	chr14	90781908	90782271	+	0	NA	intron (NM_001010854, intron 2 of 19)	intron (NM_001010854, intron 2 of 19)	34328	NM_001010854	145567	Hs.655697	NM_001010854	ENSG00000165914	TTC7B	TTC7L1|c14_5685	tetratricopeptide repeat domain 7B	protein-coding	0.016529	0.505495	177(AGGTACAGCGTGTTAC,-,0.00)
chunk0071_247_1	chr15	85400438	85400872	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	20039	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.002304	0.314943	
chunk0194_325_1	chr8	88681070	88681275	+	0	NA	Intergenic	Intergenic	-353684	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.000000	0.383495	
chunk0091_36_1	chr19	3626809	3627064	+	0	NA	promoter-TSS (NM_021231)	promoter-TSS (NM_021231)	-121	NM_001080543	58509	Hs.128425	NM_021231	ENSG00000105298	CACTIN	C19orf29|NY-REN-24|fSAPc	cactin, spliceosome C complex subunit	protein-coding	0.066667	0.660156	
chunk0036_228_1	chr11	63978938	63979187	+	0	NA	Intergenic	Intergenic	4455	NM_004074	1351	Hs.743989	NM_004074	ENSG00000176340	COX8A	COX|COX8|COX8-2|COX8L|VIII|VIII-L	cytochrome c oxidase subunit 8A	protein-coding	0.016064	0.568000	
chunk0082_434_1	chr17	61542290	61542936	+	0	NA	Intergenic	L1MC1|LINE|L1	48589	NM_199290	342538	Hs.591178	NM_199290	ENSG00000253506	NACA2	ANAC|NACAL	nascent polypeptide associated complex subunit alpha 2	protein-coding	0.004644	0.353941	
chunk0179_204_1	chr7	47470463	47471082	+	0	NA	intron (NM_022748, intron 4 of 30)	intron (NM_022748, intron 4 of 30)	111372	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.019386	0.522581	
chunk0179_459_1	chr7	52816411	52816853	+	0	NA	Intergenic	L1MA9|LINE|L1	-219024	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.009050	0.530474	
chunk0144_35_1	chr4	125096615	125097071	+	0	NA	Intergenic	Intergenic	-219569	NM_024582	79633	Hs.563205	NM_024582	ENSG00000196159	FAT4	CDHF14|CDHR11|FAT-J|FATJ|HKLLS2|NBLA00548|VMLDS2	FAT atypical cadherin 4	protein-coding	0.006579	0.382932	
chunk0025_203_1	chr10	53556307	53556550	+	0	NA	Intergenic	L1MCc|LINE|L1	-784728	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.340164	
chunk0108_244_1	chr2	233868366	233868565	+	0	NA	promoter-TSS (NR_024322)	promoter-TSS (NR_024322)	-56	NR_024322	151507	Hs.355809	NM_001166217	ENSG00000224287	MSL3P1	MSL3L2	MSL complex subunit 3 pseudogene 1	pseudo	0.110553	0.535000	
chunk0019_60_1	chr1	224203607	224204023	+	0	NA	Intergenic	Intergenic	9464	NR_110669	101927143	Hs.638720	NR_110669	ENSG00000232628	LOC101927143	-	uncharacterized LOC101927143	ncRNA	0.014423	0.534772	
chunk0137_57_1	chr4	11727472	11728025	+	0	NA	Intergenic	L1ME2|LINE|L1	-298835	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.003617	0.281588	
chunk0049_162_1	chr12	92070508	92071001	+	0	NA	intron (NR_132341, intron 1 of 4)	intron (NR_132341, intron 1 of 4)	70959	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.006085	0.364372	268(GGGAACTCTGTGTTCT,-,0.00),269(GGAACTCTGTGTTCTC,+,0.00)
chunk0054_95_1	chr13	42689305	42689867	+	0	NA	Intergenic	LTR52|LTR|ERVL	-91964	NM_182508	144809	Hs.16970	NM_182508	ENSG00000179813	FAM216B	C13orf30	family with sequence similarity 216 member B	protein-coding	0.007117	0.403197	
chunk0021_100_1	chr10	3009209	3009833	+	0	NA	Intergenic	Intergenic	-57999	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.014423	0.481600	
chunk0127_83_1	chr3	89655544	89655953	+	0	NA	Intergenic	L1PREC2|LINE|L1	548224	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.329268	
chunk0199_3_1	chr9	335977	336746	+	0	NA	intron (NM_001190458, intron 10 of 45)	intron (NM_001190458, intron 10 of 45)	63313	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.005202	0.468831	298(CAGGAGACCCTGTTCT,-,0.00),299(AGGAGACCCTGTTCTG,+,0.00)
chunk0106_36_1	chr2	196122044	196122500	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	49340	NM_004226	9262	Hs.88297	NM_004226	ENSG00000081320	STK17B	DRAK2	serine/threonine kinase 17b	protein-coding	0.006579	0.374179	
chunk0152_171_1	chr5	59587563	59587816	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-1191	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.023715	0.562992	
chunk0189_159_1	chr8	23202431	23202944	+	0	NA	exon (NM_003844, exon 3 of 10)	exon (NM_003844, exon 3 of 10)	22480	NM_003844	8797	Hs.213467	NM_003844	ENSG00000104689	TNFRSF10A	APO2|CD261|DR4|TRAILR-1|TRAILR1	TNF receptor superfamily member 10a	protein-coding	0.009747	0.480545	
chunk0055_396_1	chr13	73911930	73912331	+	0	NA	intron (NM_007249, intron 3 of 7)	intron (NM_007249, intron 3 of 7)	221799	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.000000	0.375622	
chunk0009_194_1	chr1	105941430	105941926	+	0	NA	Intergenic	L1PB1|LINE|L1	-322743	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002016	0.342052	
chunk0025_216_1	chr10	53867338	53867938	+	0	NA	intron (NM_001142769, intron 28 of 35)	intron (NM_001142769, intron 28 of 35)	740319	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.008333	0.297837	
chunk0113_93_1	chr20	50895040	50895752	+	0	NA	intron (NM_015339, intron 4 of 4)	Tigger3|DNA|TcMar-Tigger	14395	NM_001282532	23394	Hs.293736	NM_015339	ENSG00000101126	ADNP	ADNP1|HVDAS|MRD28	activity dependent neuroprotector homeobox	protein-coding	0.005618	0.405330	
chunk0205_29_1	chr9	105569180	105569601	+	0	NA	intron (NM_006731, intron 1 of 9)	intron (NM_006731, intron 1 of 9)	11260	NM_001198963	2218	Hs.55777	NM_006731	ENSG00000106692	FKTN	CMD1X|FCMD|LGMD2M|LGMDR13|MDDGA4|MDDGB4|MDDGC4	fukutin	protein-coding	0.000000	0.360190	
chunk0117_45_1	chr22	12388966	12389274	+	0	NA	Intergenic	L1PA3|LINE|L1	491714	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.022727	0.501618	
chunk0209_251_1	chrX	46044255	46044866	+	0	NA	Intergenic	Intergenic	-193070	NR_125365	401585	Hs.633348	NR_125365	ENSG00000231566	LINC02595	-	long intergenic non-protein coding RNA 2595	ncRNA	0.000000	0.354575	
chunk0142_450_1	chr4	105505151	105505676	+	0	NA	Intergenic	Intergenic	-31343	NM_176867	27068	Hs.654957	NM_006903	ENSG00000138777	PPA2	HSPC124|SCFAI|SCFI|SID6-306	pyrophosphatase (inorganic) 2	protein-coding	0.005714	0.433460	
chunk0080_51_1	chr17	21660487	21661029	+	0	NA	Intergenic	L1ME1|LINE|L1	-31765	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.005535	0.294659	
chunk0161_246_1	chr5	171661380	171661913	+	0	NA	Intergenic	L1MC1|LINE|L1	-124226	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.015009	0.361423	243(TAGTACAGAGAGTTCT,-,0.00),244(AGTACAGAGAGTTCTT,+,0.00)
chunk0145_397_1	chr4	152565257	152565787	+	0	NA	Intergenic	L1M5|LINE|L1	29094	NR_039658	100616193		NR_039658	ENSG00000283792	MIR4453	-	microRNA 4453	ncRNA	0.011321	0.369115	255(AAGTACATGCAGTTCC,-,0.00),256(AGTACATGCAGTTCCA,+,0.00)
chunk0058_453_1	chr13	113881889	113882318	+	0	NA	Intergenic	Intergenic	-13000	NM_001278674	643365	Hs.127655	NM_001039767		LINC00452	LINC00453	long intergenic non-protein coding RNA 452	protein-coding	0.020979	0.530233	216(AAGTGCACTGTGTGCT,-,0.00),217(AGTGCACTGTGTGCTT,+,0.00),413(CAGGACTCTGTGTTCC,-,0.00),414(AGGACTCTGTGTTCCT,+,0.00)
chunk0154_70_1	chr5	77449216	77449881	+	0	NA	intron (NM_018268, intron 8 of 12)	intron (NM_018268, intron 8 of 12)	42959	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.006015	0.403904	298(GAGATCATTATGTTCT,-,0.00),299(AGATCATTATGTTCTC,+,0.00)
chunk0174_115_1	chr6	157089327	157089862	+	0	NA	intron (NM_017519, intron 5 of 18)	intron (NM_017519, intron 5 of 18)	234665	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.003738	0.401119	
chunk0166_461_1	chr6	53356641	53357020	+	0	NA	Intergenic	L2c|LINE|L2	-7651	NM_021814	60481	Hs.520189	NM_021814	ENSG00000012660	ELOVL5	HELO1|SCA38|dJ483K16.1	ELOVL fatty acid elongase 5	protein-coding	0.000000	0.371053	130(TAGAACAATATGTTCC,-,0.00),131(AGAACAATATGTTCCT,+,0.00)
chunk0042_161_1	chr12	4071083	4071502	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	-197844	NM_001286521	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.014320	0.419048	
chunk0043_220_1	chr12	19867562	19868326	+	0	NA	Intergenic	Intergenic	-146741	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.005236	0.346405	
chunk0015_177_1	chr1	186997287	186998222	+	0	NA	Intergenic	MIR3|SINE|MIR	-95088	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.002139	0.322650	
chunk0060_420_1	chr14	53705646	53706291	+	0	NA	Intergenic	L1PA11|LINE|L1	242516	NR_049843	100847076		NR_049843	ENSG00000266431	MIR5580	-	microRNA 5580	ncRNA	0.009302	0.359133	
chunk0175_100_1	chr7	2838033	2838328	+	0	NA	intron (NM_001293092, intron 1 of 2)	intron (NM_001293092, intron 1 of 2)	6145	NM_001293092	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.006780	0.375000	
chunk0015_166_1	chr1	186577711	186578606	+	0	NA	Intergenic	Intergenic	102269	NM_000963	5743	Hs.196384	NM_000963	ENSG00000073756	PTGS2	COX-2|COX2|GRIPGHS|PGG/HS|PGHS-2|PHS-2|hCox-2	prostaglandin-endoperoxide synthase 2	protein-coding	0.006704	0.486607	689(AGGAGCAGGATGTCCA,-,0.00)
chunk0077_439_1	chr16	85658980	85659289	+	0	NA	intron (NM_014615, intron 8 of 15)	intron (NM_014615, intron 8 of 15)	29848	NM_016095	51659	Hs.433180	NM_016095	ENSG00000131153	GINS2	HSPC037|PSF2|Pfs2	GINS complex subunit 2	protein-coding	0.019417	0.538710	
chunk0109_21_1	chr20	409941	410261	+	0	NA	intron (NM_031229, intron 2 of 11)	MIR|SINE|MIR	2036	NM_006462	10616	Hs.29546	NM_006462	ENSG00000125826	RBCK1	C20orf18|HOIL-1|HOIL1|PBMEI|PGBM1|RBCK2|RNF54|UBCE7IP3|XAP3|XAP4|ZRANB4	RANBP2-type and C3HC4-type zinc finger containing 1	protein-coding	0.012500	0.504673	
chunk0131_292_1	chr3	150538741	150539382	+	0	NA	Intergenic	Intergenic	7580	NM_014445	27230	Hs.518326	NM_014445	ENSG00000120742	SERP1	RAMP4	stress associated endoplasmic reticulum protein 1	protein-coding	0.009360	0.451713	
chunk0015_403_1	chr1	191055049	191055469	+	0	NA	Intergenic	Intergenic	430369	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.002381	0.287411	
chunk0065_128_1	chr15	24879478	24880198	+	0	NA	intron (NM_022805, intron 1 of 11)	MER58A|DNA|hAT-Charlie	23287	NM_022805	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.008333	0.399445	
chunk0170_408_1	chr6	117935848	117936123	+	0	NA	intron (NM_001029858, intron 1 of 7)	HAL1ME|LINE|L1	28459	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.003636	0.373188	
chunk0057_182_1	chr13	102664154	102664552	+	0	NA	intron (NM_003291, intron 25 of 28)	intron (NM_003291, intron 25 of 28)	30168	NM_001010977	196541	Hs.508623	NM_001010977	ENSG00000139780	METTL21C	C13orf39	methyltransferase like 21C	protein-coding	0.000000	0.330827	
chunk0081_12_1	chr17	37264020	37264376	+	0	NA	intron (NM_198836, intron 10 of 55).2	intron (NM_198836, intron 10 of 55).2	19397	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.002809	0.322129	215(ATGTACAACTTGTTCC,-,0.00)
chunk0162_56_1	chr6	1347171	1347442	+	0	NA	Intergenic	Intergenic	34866	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.007380	0.488971	
chunk0186_441_1	chr7	147578953	147579643	+	0	NA	intron (NM_014141, intron 12 of 23)	intron (NM_014141, intron 12 of 23)	-201177	NR_031645	100313895		NR_031645	ENSG00000221442	MIR548F4	MIR548F-4|MIRN548F4|hsa-mir-548f-4	microRNA 548f-4	ncRNA	0.002899	0.303907	
chunk0001_193_1	chr1	7572905	7573392	+	0	NA	intron (NM_015215, intron 6 of 22)	intron (NM_015215, intron 6 of 22)	-198121	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.008214	0.530738	
chunk0194_11_1	chr8	81508593	81508810	+	0	NA	Intergenic	L1MC1|LINE|L1	22614	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.000000	0.371560	
chunk0198_373_1	chr8	141146692	141147053	+	0	NA	intron (NM_014957, intron 5 of 22)	intron (NM_014957, intron 5 of 22)	18251	NM_014957	22898	Hs.18166	NM_014957	ENSG00000105339	DENND3	-	DENN domain containing 3	protein-coding	0.041551	0.519337	
chunk0181_277_1	chr7	86600691	86600915	+	0	NA	Intergenic	L1PA13|LINE|L1	-43111	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.013393	0.568889	
chunk0164_145_1	chr6	21360601	21361041	+	0	NA	Intergenic	HERVL32-int|LTR|ERVL	151071	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.006818	0.496599	
chunk0078_387_1	chr16	87866140	87866465	+	0	NA	intron (NM_003486, intron 1 of 9)	intron (NM_003486, intron 1 of 9)	3192	NM_003486	8140	Hs.513797	NM_003486	ENSG00000103257	SLC7A5	4F2LC|CD98|D16S469E|E16|LAT1|MPE16	solute carrier family 7 member 5	protein-coding	0.024615	0.503067	89(GAGAACAAGTTGTACA,-,0.00),90(AGAACAAGTTGTACAT,+,0.00)
chunk0100_155_1	chr2	109177371	109177675	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	-35935	NR_036223	100422863		NR_036223	ENSG00000264934	MIR4265	-	microRNA 4265	ncRNA	0.003289	0.508197	
chunk0073_250_1	chr16	11754332	11754568	+	0	NA	intron (NM_014153, intron 21 of 22)	intron (NM_014153, intron 21 of 22)	-11572	NM_001303447	51061	Hs.313847	NM_015914	ENSG00000153066	TXNDC11	EFP1	thioredoxin domain containing 11	protein-coding	0.008475	0.417722	
chunk0118_51_1	chr22	27913084	27913283	+	0	NA	intron (NM_001284277, intron 2 of 10)	L3|LINE|CR1	6031	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.000000	0.370000	
chunk0091_97_1	chr19	5773536	5774040	+	0	NA	intron (NM_152784, intron 20 of 21)	AluJo|SINE|Alu	10977	NM_001134316	163154	Hs.631838	NM_153359	ENSG00000212123	PRR22	-	proline rich 22	protein-coding	0.013889	0.479208	348(CGGGACACAATGTTTT,-,0.00),349(GGGACACAATGTTTTG,+,0.00)
chunk0161_375_1	chr5	176490736	176490935	+	0	NA	intron (NM_014613, intron 4 of 10)	intron (NM_014613, intron 4 of 10)	42480	NM_014613	23197	Hs.484242	NM_014613	ENSG00000113194	FAF2	ETEA|UBXD8|UBXN3B	Fas associated factor family member 2	protein-coding	0.005025	0.265000	
chunk0043_342_1	chr12	22878455	22878725	+	0	NA	Intergenic	Intergenic	253448	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.011111	0.313653	
chunk0146_108_1	chr4	158820012	158820220	+	0	NA	intron (NM_020840, intron 1 of 16)	(GTTTTT)n|Simple_repeat|Simple_repeat	51086	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.000000	0.315789	
chunk0140_304_1	chr4	73015618	73016125	+	0	NA	Intergenic	Intergenic	53888	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.003945	0.338583	
chunk0007_81_1	chr1	78455783	78455982	+	0	NA	Intergenic	Intergenic	-35161	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.000000	0.375000	
chunk0202_252_1	chr9	76818391	76818647	+	0	NA	intron (NM_015225, intron 6 of 18)	intron (NM_015225, intron 6 of 18)	54083	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.007812	0.509728	
chunk0052_441_1	chr12	132343413	132343967	+	0	NA	Intergenic	Intergenic	13840	NR_120467	101928416		NR_120467	ENSG00000255916	LOC101928416	-	uncharacterized LOC101928416	ncRNA	0.037906	0.562162	310(TGGAACAGCTTGCTCC,-,0.00),311(GGAACAGCTTGCTCCT,+,0.00)
chunk0172_420_1	chr6	140353435	140354039	+	0	NA	Intergenic	Intergenic	148485	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.003311	0.355372	300(GTGAACATTCTGTACT,-,0.00),301(TGAACATTCTGTACTT,+,0.00)
chunk0058_14_1	chr14	19167915	19168114	+	0	NA	Intergenic	Intergenic	-74677	NR_073459	414763	Hs.617315	NR_073459		BMS1P18	C14orf17|LINC00516	BMS1 pseudogene 18	pseudo	0.025126	0.590000	
chunk0080_201_1	chr17	29251265	29251464	+	0	NA	intron (NM_005208, intron 3 of 5)	MER30|DNA|hAT-Charlie	4507	NM_005208	1411	Hs.46275	NM_005208	ENSG00000108255	CRYBA1	CRYB1|CTRCT10	crystallin beta A1	protein-coding	0.010050	0.420000	
chunk0075_352_1	chr16	55911262	55911571	+	0	NA	intron (NM_001190158, intron 2 of 13)	MLT1J|LTR|ERVL-MaLR	-36046	NM_145024	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.009709	0.403226	
chunk0134_34_1	chr3	175610140	175610561	+	0	NA	intron (NM_207015, intron 10 of 13)	intron (NM_207015, intron 10 of 13)	165983	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.308057	
chunk0057_89_1	chr13	98658794	98659235	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-81863	NM_001032296	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.020408	0.493213	
chunk0199_400_1	chr9	13410528	13410835	+	0	NA	intron (NR_033863, intron 2 of 2)	intron (NR_033863, intron 2 of 2)	20648	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.000000	0.376623	
chunk0040_7_1	chr11	108619470	108619669	+	0	NA	Intergenic	Intergenic	-25831	NM_001308019	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.010050	0.415000	
chunk0166_302_1	chr6	49522981	49523557	+	0	NA	intron (NM_001010904, intron 5 of 5)	MER68|LTR|ERVL	23311	NM_001010904	389396	Hs.585172	NM_001010904	ENSG00000203972	GLYATL3	C6orf140|bA28H17.2	glycine-N-acyltransferase like 3	protein-coding	0.012153	0.450607	
chunk0014_384_1	chr1	182732083	182732605	+	0	NA	Intergenic	Intergenic	-57105	NM_001200056	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.005747	0.391969	
chunk0079_180_1	chr17	14052814	14053655	+	0	NA	intron (NR_049718, intron 1 of 2)	intron (NR_049718, intron 1 of 2)	-16168	NM_001303	1352	Hs.462278	NM_001303	ENSG00000006695	COX10	-	cytochrome c oxidase assembly factor heme A:farnesyltransferase COX10	protein-coding	0.007134	0.400238	559(GGGCACACGCTGTACT,-,0.00),560(GGCACACGCTGTACTT,+,0.00)
chunk0053_101_1	chr13	28658784	28659191	+	0	NA	promoter-TSS (NM_015932)	promoter-TSS (NM_015932)	-17	NM_015932	51371	Hs.268742	NM_015932	ENSG00000132963	POMP	C13orf12|HSPC014|PNAS-110|PRAAS2|UMP1	proteasome maturation protein	protein-coding	0.076167	0.598039	
chunk0051_113_1	chr12	115104069	115104398	+	0	NA	Intergenic	Intergenic	-420069	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.021277	0.515152	
chunk0045_240_1	chr12	48869058	48869625	+	0	NA	Intergenic	MamRep1879|DNA|hAT-Tip100?	-3471	NM_014470	27289	Hs.124940	NM_014470	ENSG00000172602	RND1	ARHS|RHO6|RHOS	Rho family GTPase 1	protein-coding	0.010582	0.494718	
chunk0131_17_1	chr3	142079322	142079754	+	0	NA	intron (NM_001178138, intron 3 of 13)	L1MA3|LINE|L1	-50873	NM_006286	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.004630	0.367206	
chunk0050_268_1	chr12	106084615	106085172	+	0	NA	intron (NM_014840, intron 3 of 6)	intron (NM_014840, intron 3 of 6)	55140	NM_014840	9891	Hs.524692	NM_014840	ENSG00000074590	NUAK1	ARK5	NUAK family kinase 1	protein-coding	0.010772	0.422939	
chunk0116_11_1	chr21	32739114	32739703	+	0	NA	intron (NR_038879, intron 3 of 3)	MIR|SINE|MIR	11294	NR_038880	100506215	Hs.657123	NR_038879	ENSG00000238197	PAXBP1-AS1	GCFC1-AS1	PAXBP1 antisense RNA 1	ncRNA	0.015280	0.428814	275(AAAAACAGCGTGTACC,-,0.00),276(AAAACAGCGTGTACCT,+,0.00)
chunk0145_319_1	chr4	150644328	150644911	+	0	NA	intron (NM_001199282, intron 37 of 56)	Cheshire|DNA|hAT-Charlie	62694	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.005146	0.308219	
chunk0017_107_1	chr1	205945057	205945468	+	0	NA	intron (NR_110983, intron 2 of 3)	intron (NR_110983, intron 2 of 3)	-1802	NM_052934	115019	Hs.164073	NM_052934	ENSG00000174502	SLC26A9	-	solute carrier family 26 member 9	protein-coding	0.009732	0.466019	
chunk0029_94_1	chr10	97326199	97326634	+	0	NA	Intergenic	Intergenic	7151	NM_005479	10023	Hs.126057	NM_005479	ENSG00000165879	FRAT1	-	FRAT regulator of WNT signaling pathway 1	protein-coding	0.013793	0.461009	
chunk0035_331_1	chr11	47677625	47678079	+	0	NA	intron (NM_024783, intron 13 of 18)	L2c|LINE|L2	-35198	NM_014342	23788	Hs.269944	NM_014342	ENSG00000109919	MTCH2	HSPC032|MIMP|SLC25A50	mitochondrial carrier 2	protein-coding	0.011013	0.441758	
chunk0129_31_1	chr3	117255766	117256081	+	0	NA	Intergenic	Intergenic	334492	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.313291	
chunk0208_175_1	chrX	16966875	16967384	+	0	NA	intron (NM_004726, intron 1 of 17)	MER58B|DNA|hAT-Charlie	20438	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.003929	0.356863	
chunk0031_227_1	chr10	126372355	126372719	+	0	NA	intron (NM_001288973, intron 1 of 22)	intron (NM_001288973, intron 1 of 22)	16021	NM_001288975	8038	Hs.594351	NM_003474	ENSG00000148848	ADAM12	ADAM12-OT1|CAR10|MCMP|MCMPMltna|MLTN|MLTNA	ADAM metallopeptidase domain 12	protein-coding	0.002747	0.427397	
chunk0097_262_1	chr2	54518417	54518923	+	0	NA	intron (NM_003128, intron 1 of 35)	intron (NM_003128, intron 1 of 35)	-10552	NR_002229	56969	Hs.657366	NM_020217		RPL23AP32	RPL23A_9_220	ribosomal protein L23a pseudogene 32	pseudo	0.003953	0.345168	
chunk0159_29_1	chr5	136818752	136819282	+	0	NA	Intergenic	Intergenic	-453541	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.003774	0.406780	
chunk0084_190_1	chr17	77958315	77958597	+	0	NA	Intergenic	CpG	-45781	NM_001142640	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.117021	0.710247	
chunk0113_24_1	chr20	49656160	49656780	+	0	NA	intron (NM_004776, intron 2 of 8)	intron (NM_004776, intron 2 of 8)	57414	NM_004776	9334	Hs.370487	NM_004776	ENSG00000158470	B4GALT5	B4Gal-T5|BETA4-GALT-IV|beta4Gal-T5|beta4GalT-V|gt-V	beta-1,4-galactosyltransferase 5	protein-coding	0.012903	0.428341	
chunk0174_436_1	chr6	166078412	166079249	+	0	NA	Intergenic	Intergenic	89839	NM_001270484	6862	Hs.389457	NM_003181	ENSG00000164458	TBXT	SAVA|T|TFT	T-box transcription factor T	protein-coding	0.010753	0.441527	
chunk0073_118_1	chr16	4828999	4829213	+	0	NA	intron (NM_001308096, intron 5 of 15)	intron (NM_001308096, intron 5 of 15)	18196	NM_032569	84656	Hs.387255	NM_032569	ENSG00000140632	GLYR1	BM045|HIBDL|N-PAC|NP60	glyoxylate reductase 1 homolog	protein-coding	0.004673	0.497674	
chunk0083_168_1	chr17	66143883	66144082	+	0	NA	intron (NM_001302891, intron 4 of 24)	MLT1F2-int|LTR|ERVL-MaLR	47887	NM_001302891	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.005025	0.455000	
chunk0076_248_1	chr16	69244244	69244808	+	0	NA	intron (NM_006750, intron 1 of 6)	intron (NM_006750, intron 1 of 6)	57379	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.005319	0.346903	
chunk0132_388_1	chr3	163476179	163476678	+	0	NA	Intergenic	Intergenic	-173127	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.004008	0.328000	
chunk0125_336_1	chr3	71060497	71061004	+	0	NA	intron (NM_032682, intron 7 of 20)	intron (NM_032682, intron 7 of 20)	4173	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.009862	0.352362	
chunk0031_44_1	chr10	122390696	122391023	+	0	NA	intron (NM_001195608, intron 1 of 13)	L1MB5|LINE|L1	-1444	NM_021622	59338	Hs.643512	NM_021622	ENSG00000107679	PLEKHA1	TAPP1	pleckstrin homology domain containing A1	protein-coding	0.006116	0.405488	
chunk0170_432_1	chr6	118784156	118784355	+	0	NA	TTS (NR_037662)	TTS (NR_037662)	1547	NR_037662	100287632	Hs.334026	NR_037662		SELENOKP3	-	selenoprotein K pseudogene 3	pseudo	0.005025	0.310000	
chunk0113_427_1	chr20	62215032	62215877	+	0	NA	3' UTR (NM_007232, exon 3 of 3)	3' UTR (NM_007232, exon 3 of 3)	4813	NM_007232	11255	Hs.251399	NM_007232	ENSG00000101180	HRH3	GPCR97|HH3R	histamine receptor H3	protein-coding	0.028402	0.631206	334(AGGAACATCAAGTTCA,-,0.00),335(GGAACATCAAGTTCAC,+,0.00)
chunk0009_33_1	chr1	100266134	100266424	+	0	NA	promoter-TSS (NR_110434)	promoter-TSS (NR_110434)	-105	NR_110434	100506007	Hs.192268	NR_110434		RTCA-AS1	-	RTCA antisense RNA 1	ncRNA	0.089655	0.652921	
chunk0203_181_1	chr9	86304369	86304939	+	0	NA	intron (NM_024617, intron 24 of 26)	intron (NM_024617, intron 24 of 26)	-22079	NM_030940	81689	Hs.449291	NM_030940	ENSG00000135070	ISCA1	HBLD2|ISA1|MMDS5|hIscA	iron-sulfur cluster assembly 1	protein-coding	0.005263	0.378284	
chunk0072_39_1	chr16	959589	960137	+	0	NA	intron (NR_033645, intron 1 of 11)	L1MC3|LINE|L1	11121	NR_033646	64788	Hs.71912	NM_022773	ENSG00000103227	LMF1	C16orf26|HMFN1876|JFP11|TMEM112|TMEM112A	lipase maturation factor 1	protein-coding	0.029197	0.561020	248(GAATACACCGTGTGCC,-,0.00),278(GAATACACCATGTTCC,-,0.00),279(AATACACCATGTTCCA,+,0.00),308(GAATACACCGTGTGCC,-,0.00)
chunk0087_52_1	chr18	31531444	31531948	+	0	NA	intron (NM_001943, intron 9 of 14)	intron (NM_001943, intron 9 of 14)	25215	NR_045216	100652770	Hs.562766	NR_045216	ENSG00000264859	DSG2-AS1	-	DSG2 antisense RNA 1	ncRNA	0.007937	0.366337	
chunk0121_352_1	chr3	24704473	24704701	+	0	NA	Intergenic	Intergenic	-183152	NR_039955									0.004386	0.296943	
chunk0140_278_1	chr4	72240283	72240645	+	0	NA	Intergenic	Intergenic	201332	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.002762	0.380165	109(AAATACACTATGTGCC,-,0.00),110(AATACACTATGTGCCT,+,0.00),196(CTGGACAGACTGTACT,-,0.00),197(TGGACAGACTGTACTG,+,0.00)
chunk0115_68_1	chr21	21709008	21709227	+	0	NA	Intergenic	L1PA4|LINE|L1	28202	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.004566	0.372727	
chunk0150_189_1	chr5	34624507	34624725	+	0	NA	Intergenic	Intergenic	-31712	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.004587	0.465753	
chunk0124_1_1	chr3	51411601	51411882	+	0	NA	intron (NM_014703, intron 23 of 25)	intron (NM_014703, intron 23 of 25)	20473	NM_013286	29890	Hs.118738	NM_013286	ENSG00000259956	RBM15B	HUMAGCGB|HsOTT3|OTT3	RNA binding motif protein 15B	protein-coding	0.017794	0.390071	
chunk0183_289_1	chr7	107718013	107718272	+	0	NA	TTS (NM_000441)	TTS (NM_000441)	-25555	NM_001284291	79872	Hs.592271	NM_024814	ENSG00000105879	CBLL1	HAKAI|RNF188	Cbl proto-oncogene like 1	protein-coding	0.000000	0.307692	
chunk0100_187_1	chr2	110948225	110948629	+	0	NA	intron (NM_001142807, intron 12 of 17)	intron (NM_001142807, intron 12 of 17)	167161	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.017327	0.479012	
chunk0016_294_1	chr1	201154586	201154865	+	0	NA	promoter-TSS (NM_001288568)	promoter-TSS (NM_001288568)	-170	NM_001288570	252839	Hs.181444	NM_016456	ENSG00000116857	TMEM9	DERM4|TMEM9A	transmembrane protein 9	protein-coding	0.035842	0.460714	
chunk0210_421_1	chrX	101366569	101366923	+	0	NA	intron (NM_001287345, intron 6 of 16)	intron (NM_001287345, intron 6 of 16)	-17777	NM_004085	1678	Hs.447877	NM_004085	ENSG00000126953	TIMM8A	DDP|DDP1|DFN1|MTS|TIM8	translocase of inner mitochondrial membrane 8A	protein-coding	0.002825	0.428169	
chunk0067_410_1	chr15	49494554	49495168	+	0	NA	intron (NM_152647, intron 11 of 15)	intron (NM_152647, intron 11 of 15)	71683	NM_002009	2252	Hs.567268	NM_002009	ENSG00000140285	FGF7	HBGF-7|KGF	fibroblast growth factor 7	protein-coding	0.001629	0.347967	
chunk0038_413_1	chr11	94145950	94146276	+	0	NA	intron (NM_015368, intron 1 of 4)	L1MC4|LINE|L1	17185	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.012270	0.415902	158(CAGAACATTTTGTACC,-,0.00),159(AGAACATTTTGTACCA,+,0.00)
chunk0126_26_1	chr3	73607067	73607593	+	0	NA	intron (NM_015009, intron 2 of 9)	intron (NM_015009, intron 2 of 9)	-16238	NR_046681	101927249	Hs.733334	NR_046681		PDZRN3-AS1	-	PDZRN3 antisense RNA 1	ncRNA	0.017110	0.464896	
chunk0158_47_1	chr5	125949167	125949466	+	0	NA	Intergenic	Intergenic	-230261	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.000000	0.303333	
chunk0019_326_1	chr1	229208018	229208354	+	0	NA	Intergenic	Intergenic	-33385	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.005952	0.427300	
chunk0160_39_1	chr5	149489385	149490286	+	0	NA	Intergenic	Intergenic	59189	NR_029686	406937		NR_029686	ENSG00000276365	MIR145	MIRN145|miR-145|miRNA145	microRNA 145	ncRNA	0.008879	0.337029	582(TAAGACATTCTGTTCC,-,0.00),583(AAGACATTCTGTTCCA,+,0.00),637(AAGAACACCCTGTCAA,-,0.00)
chunk0044_81_1	chr12	28216577	28217221	+	0	NA	Intergenic	Intergenic	-40301	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.007764	0.330233	
chunk0162_99_1	chr6	2464380	2464712	+	0	NA	Intergenic	Intergenic	170057	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.015060	0.501502	
chunk0092_395_1	chr19	37179379	37179629	+	0	NA	Intergenic	Intergenic	-6763	NM_152655	199704	Hs.659236	NM_152655	ENSG00000196967	ZNF585A	-	zinc finger protein 585A	protein-coding	0.016000	0.458167	
chunk0026_126_1	chr10	62018437	62018988	+	0	NA	intron (NM_032199, intron 4 of 9)	intron (NM_032199, intron 4 of 9)	-30499	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.010889	0.400362	376(AAGAACAATCTGTGAC,-,0.00)
chunk0048_325_1	chr12	83667504	83667834	+	0	NA	Intergenic	Intergenic	980514	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.000000	0.305136	
chunk0130_451_1	chr3	141382101	141382554	+	0	NA	intron (NM_001080412, intron 4 of 7)	intron (NM_001080412, intron 4 of 7)	58114	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.013245	0.378855	
chunk0146_132_1	chr4	159182004	159182205	+	0	NA	Intergenic	Intergenic	-53210	NR_037459	100500881		NR_037459	ENSG00000264105	MIR3688-1	MIR3688|mir-3688-1	microRNA 3688-1	ncRNA	0.004975	0.331683	
chunk0071_336_1	chr15	87949195	87949846	+	0	NA	intron (NM_002530, intron 14 of 18)	intron (NM_002530, intron 14 of 18)	-303210	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.015361	0.516871	254(CGAGACACTGTGTTCC,-,0.00),255(GAGACACTGTGTTCCC,+,0.00),337(GAGGACTGTCTGTTCT,-,0.00),338(AGGACTGTCTGTTCTG,+,0.00)
chunk0077_440_1	chr16	85674072	85674515	+	0	NA	3' UTR (NM_001278184, exon 15 of 15)	3' UTR (NM_001278184, exon 15 of 15)	14689	NM_016095	51659	Hs.433180	NM_016095	ENSG00000131153	GINS2	HSPC037|PSF2|Pfs2	GINS complex subunit 2	protein-coding	0.024831	0.578829	374(GAGGTCAGCATGTTCC,-,0.00),375(AGGTCAGCATGTTCCA,+,0.00)
chunk0135_50_1	chr3	185645994	185646196	+	0	NA	intron (NM_001291873, intron 14 of 14)	intron (NM_001291873, intron 14 of 14)	59852	NM_021627	59343	Hs.401388	NM_021627	ENSG00000163904	SENP2	AXAM2|SMT3IP2	SUMO specific peptidase 2	protein-coding	0.000000	0.605911	148(AGGAACAGGCTGTTCA,-,0.00),149(GGAACAGGCTGTTCAG,+,0.00)
chunk0136_121_1	chr4	3637586	3638148	+	0	NA	Intergenic	L1MEc|LINE|L1	39988	NR_034136	100133461	Hs.554274	NR_034136	ENSG00000250632	LINC02171	-	long intergenic non-protein coding RNA 2171	ncRNA	0.019573	0.426288	
chunk0098_35_1	chr2	66024038	66024430	+	0	NA	Intergenic	Intergenic	334094	NR_039938	100616464		NR_039938	ENSG00000264525	MIR4778	-	microRNA 4778	ncRNA	0.002551	0.391858	
chunk0167_451_1	chr6	76276134	76276336	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-203557	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.004950	0.482759	
chunk0005_303_1	chr1	60428023	60428736	+	0	NA	Intergenic	Intergenic	-354609	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.007013	0.364146	397(AAGGACAGACTGTCCT,-,0.00),398(AGGACAGACTGTCCTG,+,0.00)
chunk0054_84_1	chr13	42503862	42504305	+	0	NA	Intergenic	Intergenic	-58653	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.002257	0.396396	
chunk0093_209_1	chr19	49631082	49631398	+	0	NA	Intergenic	Intergenic	8903	NM_006270	6237	Hs.515536	NM_006270	ENSG00000126458	RRAS	R-Ras	RAS related	protein-coding	0.009494	0.570978	
chunk0185_3_1	chr7	123748847	123749054	+	0	NA	5' UTR (NM_003941, exon 1 of 11)	5' UTR (NM_003941, exon 1 of 11)	121	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.130435	0.725962	
chunk0207_311_1	chr9	133881245	133881679	+	0	NA	intron (NM_001134398, intron 2 of 29)	intron (NM_001134398, intron 2 of 29)	110862	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.034562	0.622989	
chunk0137_39_1	chr4	11423515	11424019	+	0	NA	intron (NM_005114, intron 1 of 1)	intron (NM_005114, intron 1 of 1)	5146	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.013889	0.431683	261(GAGCACTGTCTGTGCT,-,0.00),262(AGCACTGTCTGTGCTC,+,0.00)
chunk0211_78_1	chrX	110081761	110082646	+	0	NA	promoter-TSS (NR_039774)	promoter-TSS (NR_039774)	85	NR_039774	100616491		NR_039774	ENSG00000265584	MIR3978	-	microRNA 3978	ncRNA	0.007910	0.475169	75(GGGGCCAGCATGTTCT,-,0.00),76(GGGCCAGCATGTTCTT,+,0.00)
chunk0038_406_1	chr11	93844698	93844938	+	0	NA	intron (NM_001144871, intron 1 of 3)	intron (NM_001144871, intron 1 of 3)	5684	NM_001144871	387804	Hs.512252	NM_001144871	ENSG00000214376	VSTM5	C11orf90	V-set and transmembrane domain containing 5	protein-coding	0.020833	0.535270	171(AGGCACAGTGCGTGCT,-,0.00),172(GGCACAGTGCGTGCTC,+,0.00)
chunk0027_273_1	chr10	77413642	77414101	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	62999	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.010893	0.513043	190(AGGGACACACTGTCCA,-,0.00),191(GGGACACACTGTCCAC,+,0.00)
chunk0038_163_1	chr11	84870519	84870769	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	52777	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004000	0.342629	
chunk0067_160_1	chr15	44009793	44010379	+	0	NA	intron (NM_001286491, intron 1 of 14)	intron (NM_001286491, intron 1 of 14)	-131915	NR_003571	728758	Hs.658099	NR_003571		PIN4P1	-	peptidylprolyl cis/trans isomerase, NIMA-interacting 4 pseudogene 1	pseudo	0.000000	0.405451	
chunk0180_132_1	chr7	56033870	56034088	+	0	NA	5' UTR (NM_004577, exon 2 of 8)	5' UTR (NM_004577, exon 2 of 8)	17596	NM_004577	5723	Hs.512656	NM_004577	ENSG00000146733	PSPH	PSP|PSPHD	phosphoserine phosphatase	protein-coding	0.059633	0.643836	
chunk0148_294_1	chr5	11992393	11993062	+	0	NA	Intergenic	Intergenic	-88684	NM_001288717	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.002990	0.350746	
chunk0128_401_1	chr3	114142976	114143464	+	0	NA	intron (NM_001282563, intron 5 of 7)	intron (NM_001282563, intron 5 of 7)	35556	NM_001290809	1814	Hs.121478	NM_000796	ENSG00000151577	DRD3	D3DR|ETM1|FET1	dopamine receptor D3	protein-coding	0.004098	0.431493	
chunk0014_252_1	chr1	180099445	180099879	+	0	NA	intron (NM_014810, intron 37 of 37)	intron (NM_014810, intron 37 of 37)	-55171	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.004608	0.312644	
chunk0204_123_1	chr9	95129807	95130365	+	0	NA	intron (NM_001243744, intron 8 of 13)	intron (NM_001243744, intron 8 of 13)	-43992	NR_036109	100422842		NR_036109	ENSG00000207617	MIR3074	mir-3074	microRNA 3074	ncRNA	0.005376	0.463327	
chunk0087_140_1	chr18	33816766	33817063	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	231698	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.003367	0.432886	
chunk0153_374_1	chr5	74841344	74842113	+	0	NA	intron (NM_015566, intron 1 of 12)	intron (NM_015566, intron 1 of 12)	24659	NR_046462	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.006502	0.307792	
chunk0073_331_1	chr16	14486804	14487198	+	0	NA	intron (NM_002582, intron 21 of 23)	intron (NM_002582, intron 21 of 23)	-116735	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.035533	0.526582	
chunk0042_189_1	chr12	5173609	5174048	+	0	NA	Intergenic	L2c|LINE|L2	69323	NR_120476	101929584	Hs.436529	NR_120476	ENSG00000256115	LINC02443	-	long intergenic non-protein coding RNA 2443	ncRNA	0.020501	0.554545	
chunk0141_107_1	chr4	79598774	79599145	+	0	NA	Intergenic	LFSINE_Vert|SINE|tRNA	106366	NR_038826	100506035	Hs.507664	NR_038826	ENSG00000250334	LINC00989	-	long intergenic non-protein coding RNA 989	ncRNA	0.010782	0.451613	204(GAGGACAGCTTGTACT,-,0.00),205(AGGACAGCTTGTACTT,+,0.00)
chunk0116_325_1	chr21	41172262	41172471	+	0	NA	intron (NM_138991, intron 1 of 7)	intron (NM_138991, intron 1 of 7)	4565	NM_138992	25825	Hs.43047	NM_012105	ENSG00000182240	BACE2	AEPLC|ALP56|ASP1|ASP21|BAE2|CDA13|CEAP1|DRAP	beta-secretase 2	protein-coding	0.014354	0.452381	
chunk0018_132_1	chr1	218571335	218571992	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	129037	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.012177	0.382979	
chunk0061_299_1	chr14	61766081	61766619	+	0	NA	intron (NM_003082, intron 1 of 9)	LTR10C|LTR|ERV1	3993	NM_003082	6617	Hs.179312	NM_003082	ENSG00000023608	SNAPC1	PTFgamma|SNAP43	small nuclear RNA activating complex polypeptide 1	protein-coding	0.009294	0.346939	
chunk0075_284_1	chr16	53899045	53899386	+	0	NA	intron (NM_001080432, intron 7 of 8)	intron (NM_001080432, intron 7 of 8)	-140178	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.002933	0.315789	
chunk0204_285_1	chr9	99105715	99106004	+	0	NA	intron (NM_001306210, intron 1 of 8)	CpG	770	NM_004612	7046	Hs.494622	NM_004612	ENSG00000106799	TGFBR1	AAT5|ACVRLK4|ALK-5|ALK5|ESS1|LDS1|LDS1A|LDS2A|MSSE|SKR4|TBR-i|TBRI|TGFR-1|tbetaR-I	transforming growth factor beta receptor 1	protein-coding	0.083045	0.696552	
chunk0108_262_1	chr2	234203331	234203678	+	0	NA	Intergenic	Intergenic	152802	NM_006944	6694	Hs.444488	NM_006944	ENSG00000072080	SPP2	SPP-24|SPP24	secreted phosphoprotein 2	protein-coding	0.014409	0.399425	318(GGGTGCAGTGTGTGCC,-,0.00),319(GGTGCAGTGTGTGCCT,+,0.00)
chunk0195_159_1	chr8	95612762	95613356	+	0	NA	intron (NR_038205, intron 2 of 2)	intron (NR_038205, intron 2 of 2)	335289	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.006734	0.341176	265(GGAGACAGAGTGTACT,-,0.00),266(GAGACAGAGTGTACTT,+,0.00)
chunk0035_118_1	chr11	42569837	42570219	+	0	NA	Intergenic	MIRb|SINE|MIR	-316338	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002618	0.342037	
chunk0112_78_1	chr20	37951301	37951519	+	0	NA	Intergenic	Intergenic	48313	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.000000	0.278539	
chunk0155_349_1	chr5	97081798	97082213	+	0	NA	Intergenic	Intergenic	60811	NM_153234	167410	Hs.656702	NM_153234	ENSG00000145721	LIX1	C5orf11|Lft	limb and CNS expressed 1	protein-coding	0.007229	0.338942	
chunk0181_235_1	chr7	85243062	85243442	+	0	NA	Intergenic	L1MC1|LINE|L1	-121321	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.005263	0.430446	
chunk0051_106_1	chr12	114914034	114914848	+	0	NA	Intergenic	Intergenic	-230277	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.013514	0.465031	
chunk0102_186_1	chr2	147566908	147567576	+	0	NA	Intergenic	Intergenic	-277275	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.007485	0.378176	
chunk0128_8_1	chr3	103680564	103680763	+	0	NA	Intergenic	Intergenic	-156547	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.360000	
chunk0010_256_1	chr1	116622577	116622895	+	0	NA	intron (NM_001007237, intron 2 of 10)	MIRb|SINE|MIR	44220	NM_001542	3321	Hs.171057	NM_001542	ENSG00000143061	IGSF3	EWI-3|LCDD|V8	immunoglobulin superfamily member 3	protein-coding	0.003145	0.357367	
chunk0190_281_1	chr8	37754484	37754714	+	0	NA	3' UTR (NM_007175, exon 12 of 12)	3' UTR (NM_007175, exon 12 of 12)	-6553	NR_003671	728024	Hs.647135	NR_003671		LOC728024	-	chromosome X open reading frame 56 pseudogene	pseudo	0.000000	0.467532	
chunk0023_17_1	chr10	20950115	20950516	+	0	NA	intron (NM_213569, intron 4 of 6)	intron (NM_213569, intron 4 of 6)	-52713	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.019950	0.427861	
chunk0105_347_1	chr2	191382575	191383206	+	0	NA	intron (NM_001130158, intron 14 of 30)	intron (NM_001130158, intron 14 of 30)	137362	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.003170	0.363924	
chunk0165_221_1	chr6	35259291	35259821	+	0	NA	promoter-TSS (NM_001292032)	promoter-TSS (NM_001292032)	-158	NM_001292032	7629	Hs.388024	NM_003427	ENSG00000065029	ZNF76	D6S229E|ZNF523|Zfp523	zinc finger protein 76	protein-coding	0.116981	0.704331	
chunk0161_337_1	chr5	173941873	173942343	+	0	NA	intron (NM_001308192, intron 3 of 8)	L2c|LINE|L2	-47051	NM_001144954	133491	Hs.131469	NM_001144954	ENSG00000185056	C5orf47	-	chromosome 5 open reading frame 47	protein-coding	0.008511	0.452229	
chunk0188_256_1	chr8	14597732	14598027	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	255631	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.003390	0.358108	
chunk0086_7_1	chr18	11990194	11990393	+	0	NA	intron (NM_014214, intron 1 of 7)	L2c|LINE|L2	8865	NM_014214	3613	Hs.743311	NM_014214	ENSG00000141401	IMPA2	-	inositol monophosphatase 2	protein-coding	0.010050	0.575000	
chunk0044_373_1	chr12	39806833	39807034	+	0	NA	intron (NM_052885, intron 7 of 9)	L1MD2|LINE|L1	180763	NM_001031748	283461	Hs.648205	NM_001031748	ENSG00000180116	C12orf40	HEL-206|HEL-S-94	chromosome 12 open reading frame 40	protein-coding	0.014925	0.336634	
chunk0032_170_1	chr11	5471670	5472195	+	0	NA	intron (NR_038321, intron 1 of 4)	intron (NR_038321, intron 1 of 4)	-16753	NM_001005163	390066	Hs.553734	NM_001005163	ENSG00000181609	OR52D1	OR11-43	olfactory receptor family 52 subfamily D member 1	protein-coding	0.011429	0.395437	223(CGGCACAAGATGTACT,-,0.00),224(GGCACAAGATGTACTG,+,0.00)
chunk0083_418_1	chr17	72338458	72338728	+	0	NA	Intergenic	Intergenic	217573	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.007407	0.505535	
chunk0184_136_1	chr7	115634592	115634943	+	0	NA	Intergenic	Intergenic	333546	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.011396	0.411932	
chunk0107_35_1	chr2	211035564	211036033	+	0	NA	Intergenic	L2b|LINE|L2	418227	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.006397	0.400000	350(AAGTACATTTTGTGCC,-,0.00),351(AGTACATTTTGTGCCA,+,0.00)
chunk0173_50_1	chr6	142322678	142323028	+	0	NA	intron (NM_020455, intron 2 of 25)	intron (NM_020455, intron 2 of 25)	20934	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.000000	0.358974	
chunk0209_330_1	chrX	51316180	51316767	+	0	NA	Intergenic	L1MC4|LINE|L1	-15758	NM_153183	170685	Hs.375178	NM_153183	ENSG00000122824	NUDT10	APS2|DIPP3-alpha|DIPP3a	nudix hydrolase 10	protein-coding	0.001704	0.335034	
chunk0116_46_1	chr21	33656964	33657456	+	0	NA	intron (NM_001001132, intron 1 of 29)	L1PA17|LINE|L1	14732	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.008130	0.423935	
chunk0206_395_1	chr9	127076122	127076386	+	0	NA	intron (NM_001190729, intron 8 of 17)	intron (NM_001190729, intron 8 of 17)	46511	NM_012098	23452	Hs.653262	NM_012098	ENSG00000136859	ANGPTL2	ARP2|HARP	angiopoietin like 2	protein-coding	0.003788	0.335849	
chunk0025_390_1	chr10	59337265	59337693	+	0	NA	intron (NM_001001971, intron 3 of 11)	intron (NM_001001971, intron 3 of 11)	25115	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.000000	0.412587	
chunk0152_7_1	chr5	56245469	56246097	+	0	NA	Intergenic	Intergenic	-12424	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.006369	0.349762	
chunk0077_388_1	chr16	84732913	84733844	+	0	NA	intron (NM_001272075, intron 2 of 14)	intron (NM_001272075, intron 2 of 14)	33429	NR_073577	9100	Hs.136778	NM_005153	ENSG00000103194	USP10	UBPO	ubiquitin specific peptidase 10	protein-coding	0.006445	0.332618	
chunk0121_424_1	chr3	25854069	25854917	+	0	NA	Intergenic	Intergenic	19202	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.003538	0.399293	
chunk0154_73_1	chr5	77459914	77460210	+	0	NA	intron (NM_018268, intron 4 of 12)	MER47B|DNA|TcMar-Tigger	32445	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.000000	0.410774	
chunk0127_367_1	chr3	101792469	101793140	+	0	NA	intron (NM_145037, intron 4 of 7)	L1PA14|LINE|L1	13362	NM_001134456	91775	Hs.595933	NM_145037	ENSG00000144815	NXPE3	FAM55C|MST115|MSTP115	neurexophilin and PC-esterase domain family member 3	protein-coding	0.001490	0.354167	
chunk0054_277_1	chr13	46655856	46656101	+	0	NA	intron (NM_001164213, intron 2 of 18)	intron (NM_001164213, intron 2 of 18)	102817	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.012245	0.463415	
chunk0127_376_1	chr3	101987938	101988640	+	0	NA	intron (NR_026934, intron 2 of 3)	intron (NR_026934, intron 2 of 3)	47430	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.002849	0.351351	
chunk0175_130_1	chr7	3423674	3423978	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	122378	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.003289	0.318033	
chunk0077_409_1	chr16	85016079	85016681	+	0	NA	Intergenic	Intergenic	-4845	NM_017740	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.008306	0.409619	
chunk0204_36_1	chr9	92654754	92655200	+	0	NA	intron (NM_022755, intron 3 of 12)	intron (NM_022755, intron 3 of 12)	15288	NM_022755	64768	Hs.459896	NM_022755	ENSG00000127080	IPPK	C9orf12|INSP5K2|IP5K|IPK1|bA476B13.1	inositol-pentakisphosphate 2-kinase	protein-coding	0.024664	0.590604	
chunk0121_358_1	chr3	24825000	24825245	+	0	NA	Intergenic	Intergenic	-303687	NR_039955									0.008163	0.418699	144(CAGCACAGGATGTACT,-,0.00),145(AGCACAGGATGTACTG,+,0.00)
chunk0170_438_1	chr6	118894450	118894749	+	0	NA	intron (NM_014034, intron 1 of 3)	CpG	522	NM_014034	25842	Hs.292316	NM_014034	ENSG00000111875	ASF1A	CGI-98|CIA|HSPC146	anti-silencing function 1A histone chaperone	protein-coding	0.120401	0.663333	
chunk0139_381_1	chr4	61277609	61278037	+	0	NA	Intergenic	Intergenic	-219298	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.002336	0.351981	
chunk0099_179_1	chr2	89833487	89833971	+	0	NA	Intergenic	(ATTCC)n|Simple_repeat|Simple_repeat	1021359	NR_039635	100616399		NR_039635	ENSG00000265510	MIR4436A	mir-4436a	microRNA 4436a	ncRNA	0.012397	0.379381	
chunk0051_165_1	chr12	115996445	115996898	+	0	NA	exon (NM_015335, exon 16 of 31)	exon (NM_015335, exon 16 of 31)	151983	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.006623	0.405286	
chunk0205_178_1	chr9	108956479	108957108	+	0	NA	intron (NM_003798, intron 11 of 18)	MER33|DNA|hAT-Charlie	22400	NM_017832	54942	Hs.29276	NM_017832	ENSG00000119328	ABITRAM	C9orf6|CG-8|FAM206A|Simiate	actin binding transcription modulator	protein-coding	0.000000	0.282540	
chunk0190_421_1	chr8	41301567	41302271	+	0	NA	intron (NM_003012, intron 2 of 2)	intron (NM_003012, intron 2 of 2)	7552	NM_003012	6422	Hs.213424	NM_003012	ENSG00000104332	SFRP1	FRP|FRP-1|FRP1|FrzA|SARP2	secreted frizzled related protein 1	protein-coding	0.012784	0.466667	
chunk0047_224_1	chr12	71771158	71771584	+	0	NA	intron (NM_014999, intron 3 of 6)	intron (NM_014999, intron 3 of 6)	16493	NM_014999	23011	Hs.524590	NM_014999	ENSG00000080371	RAB21	-	RAB21, member RAS oncogene family	protein-coding	0.004695	0.318501	
chunk0069_362_1	chr15	67146947	67147471	+	0	NA	intron (NM_001145103, intron 1 of 8)	intron (NM_001145103, intron 1 of 8)	9188	NM_001145103	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.020992	0.537143	
chunk0101_110_1	chr2	125708347	125708694	+	0	NA	Intergenic	Intergenic	-947415	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.002882	0.347701	
chunk0146_138_1	chr4	159398117	159398662	+	0	NA	Intergenic	Intergenic	130543	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.016514	0.439560	
chunk0029_386_1	chr10	109545660	109546618	+	0	NA	Intergenic	L1P2|LINE|L1	377414	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.007307	0.530761	868(ATGACAGACTGTACTG,+,0.00)
chunk0140_334_1	chr4	73779951	73780432	+	0	NA	Intergenic	Intergenic	39685	NM_000584	3576	Hs.624	NM_000584	ENSG00000169429	CXCL8	GCP-1|GCP1|IL8|LECT|LUCT|LYNAP|MDNCF|MONAP|NAF|NAP-1|NAP1	C-X-C motif chemokine ligand 8	protein-coding	0.004158	0.321577	
chunk0154_12_1	chr5	76584493	76584786	+	0	NA	intron (NM_006633, intron 5 of 35)	intron (NM_006633, intron 5 of 35)	-24456	NM_001285462	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.020478	0.506803	167(AGGAACAGAGAGTCCC,-,0.00),168(GGAACAGAGAGTCCCC,+,0.00)
chunk0016_186_1	chr1	198213357	198213664	+	0	NA	intron (NM_133494, intron 1 of 9)	L1PB3|LINE|L1	56532	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.006515	0.525974	
chunk0089_220_1	chr18	61350575	61350840	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	-139835	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.007547	0.439850	
chunk0127_245_1	chr3	97011268	97011609	+	0	NA	intron (NM_001080448, intron 3 of 17)	LTR38|LTR|ERV1	196857	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.394737	
chunk0095_364_1	chr2	23162666	23163283	+	0	NA	Intergenic	Intergenic	-222453	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.011345	0.401294	55(ATGACATCCTGTGCTG,+,0.00)
chunk0024_324_1	chr10	43093840	43094135	+	0	NA	intron (NM_020975, intron 1 of 19)	intron (NM_020975, intron 1 of 19)	16918	NM_020630	5979	Hs.350321	NM_000323	ENSG00000165731	RET	CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1	ret proto-oncogene	protein-coding	0.023729	0.543919	
chunk0076_320_1	chr16	70594532	70594961	+	0	NA	intron (NM_001172771, intron 1 of 6)	intron (NM_001172771, intron 1 of 6)	14851	NM_001172771	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.000000	0.479070	178(CAGAACACACTGGTCC,-,0.00),179(AGAACACACTGGTCCT,+,0.00)
chunk0204_425_1	chr9	103137934	103138546	+	0	NA	Intergenic	Intergenic	142929	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.000000	0.264274	
chunk0141_175_1	chr4	82614798	82615398	+	0	NA	intron (NR_024087, intron 1 of 3)	intron (NR_024087, intron 1 of 3)	6339	NR_024087	439934	Hs.457189	NM_001033661	ENSG00000231782	LINC00575	C4orf11	long intergenic non-protein coding RNA 575	ncRNA	0.008333	0.400998	
chunk0143_159_1	chr4	110248421	110249266	+	0	NA	Intergenic	LTR62|LTR|ERVL	-50179	NM_024090	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.013018	0.439716	191(AGTACTTCCTGTTCAC,+,0.00)
chunk0105_38_1	chr2	182884696	182885085	+	0	NA	Intergenic	L1MB7|LINE|L1	-18120	NM_001463	2487	Hs.128453	NM_001463	ENSG00000162998	FRZB	FRE|FRITZ|FRP-3|FRZB-1|FRZB-PEN|FRZB1|FZRB|OS1|SFRP3|SRFP3|hFIZ	frizzled related protein	protein-coding	0.007712	0.394872	
chunk0160_104_1	chr5	150510669	150511004	+	0	NA	intron (NM_001543, intron 1 of 14)	intron (NM_001543, intron 1 of 14)	2724	NM_001543	3340	Hs.222055	NM_001543	ENSG00000070614	NDST1	HSST|MRT46|NST1	N-deacetylase and N-sulfotransferase 1	protein-coding	0.005970	0.461310	
chunk0123_191_1	chr3	44353204	44353644	+	0	NA	intron (NM_001282914, intron 1 of 10)	L1MC1|LINE|L1	14972	NM_173826	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.009091	0.394558	
chunk0071_62_1	chr15	80476118	80476532	+	0	NA	intron (NM_014862, intron 5 of 18)	Tigger9b|DNA|TcMar-Tigger	71975	NM_014862	9915	Hs.459070	NM_014862	ENSG00000172379	ARNT2	WEDAS|bHLHe1	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.014493	0.385542	
chunk0166_229_1	chr6	46995715	46996292	+	0	NA	Intergenic	HAL1|LINE|L1	-41065	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.005199	0.375433	
chunk0021_130_1	chr10	3786024	3786339	+	0	NA	promoter-TSS (NM_001160125)	promoter-TSS (NM_001160125)	-900	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.034921	0.484177	
chunk0033_196_1	chr11	16394977	16395518	+	0	NA	intron (NM_033326, intron 1 of 15)	L2b|LINE|L2	7620	NM_017508	55553	Hs.368226	NM_017508	ENSG00000110693	SOX6	HSSOX6|SOXD	SRY-box transcription factor 6	protein-coding	0.007394	0.383764	
chunk0127_80_1	chr3	89529749	89530417	+	0	NA	Intergenic	Intergenic	422559	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.008982	0.328849	248(AAGAACACAGTGTACA,-,0.00),249(AGAACACAGTGTACAT,+,0.00)
chunk0170_361_1	chr6	116780047	116780345	+	0	NA	Intergenic	Intergenic	-14473	NM_001085480	221303	Hs.126712	NM_001085480	ENSG00000183807	FAM162B	C6orf189|bA86F4.2	family with sequence similarity 162 member B	protein-coding	0.006711	0.324415	156(TAGGACATCCAGTTCA,-,0.00),157(AGGACATCCAGTTCAC,+,0.00)
chunk0011_395_1	chr1	154019310	154019654	+	0	NA	intron (NM_207308, intron 32 of 39)	intron (NM_207308, intron 32 of 39)	28719	NM_001030	6232	Hs.546291	NM_001030	ENSG00000177954	RPS27	DBA17|MPS-1|MPS1|S27	ribosomal protein S27	protein-coding	0.005814	0.382609	
chunk0075_358_1	chr16	56031723	56032239	+	0	NA	Intergenic	L1MD1|LINE|L1	-75950	NM_001190158	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.005814	0.344294	
chunk0088_353_1	chr18	52288491	52289086	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-51384	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.011765	0.427852	
chunk0045_328_1	chr12	51005787	51005986	+	0	NA	intron (NM_001174125, intron 3 of 15)	MER4D1|LTR|ERV1	3384	NM_001174130	4891	Hs.505545	NM_000617	ENSG00000110911	SLC11A2	AHMIO1|DCT1|DMT1|NRAMP2	solute carrier family 11 member 2	protein-coding	0.010050	0.455000	
chunk0072_104_1	chr15	91217167	91217465	+	0	NA	intron (NM_014848, intron 2 of 13)	L2c|LINE|L2	117007	NM_014848	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.006711	0.381271	
chunk0132_382_1	chr3	163206496	163207023	+	0	NA	intron (NR_033945, intron 2 of 6)	intron (NR_033945, intron 2 of 6)	96542	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.001898	0.285985	
chunk0144_276_1	chr4	137659295	137659501	+	0	NA	Intergenic	Intergenic	-126900	NM_001300828	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.357488	24(ATCACACACTGTGCCT,+,0.00)
chunk0194_66_1	chr8	82440966	82441165	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-598779	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.020101	0.425000	
chunk0018_311_1	chr1	221143206	221143932	+	0	NA	Intergenic	L1MEh|LINE|L1	192727	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.002755	0.325997	264(AAGAACATCAAGTACA,-,0.00)
chunk0097_268_1	chr2	54840556	54840780	+	0	NA	intron (NM_001039753, intron 6 of 40)	intron (NM_001039753, intron 6 of 40)	115656	NM_001039753	400954	Hs.656692	NM_001039753	ENSG00000214595	EML6	-	EMAP like 6	protein-coding	0.004464	0.328889	
chunk0045_454_1	chr12	53658866	53659359	+	0	NA	Intergenic	Intergenic	17213	NM_005176	517	Hs.524464	NM_005176	ENSG00000135390	ATP5MC2	ATP5A|ATP5G2	ATP synthase membrane subunit c locus 2	protein-coding	0.008114	0.487854	
chunk0045_209_1	chr12	47878263	47878731	+	0	NA	intron (NM_001017536, intron 3 of 9)	intron (NM_001017536, intron 3 of 9)	26534	NM_000376	7421	Hs.524368	NM_000376	ENSG00000111424	VDR	NR1I1|PPP1R163	vitamin D receptor	protein-coding	0.010684	0.513859	201(CAGGACAAACAGTCCT,-,0.00),202(AGGACAAACAGTCCTT,+,0.00)
chunk0181_95_1	chr7	80462914	80463447	+	0	NA	intron (NM_001102386, intron 5 of 7)	L2c|LINE|L2	48746	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.005629	0.335206	
chunk0173_129_1	chr6	143721644	143722271	+	0	NA	intron (NM_001100166, intron 2 of 11)	L3|LINE|CR1	43992	NM_001100165	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.000000	0.377389	
chunk0046_350_1	chr12	62967700	62967999	+	0	NA	Intergenic	L2c|LINE|L2	-32964	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.003344	0.410000	
chunk0029_20_1	chr10	95549945	95550462	+	0	NA	intron (NM_001290294, intron 1 of 31)	intron (NM_001290294, intron 1 of 31)	11217	NM_001290294	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.011605	0.465251	
chunk0202_110_1	chr9	72564450	72564782	+	0	NA	intron (NM_138691, intron 1 of 23)	intron (NM_138691, intron 1 of 23)	42815	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.000000	0.411411	
chunk0199_449_1	chr9	14098029	14098556	+	0	NA	intron (NM_001190738, intron 8 of 8)	intron (NM_001190738, intron 8 of 8)	82510	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.009488	0.356061	
chunk0008_189_1	chr1	93238343	93238786	+	0	NA	intron (NM_206886, intron 19 of 27)	intron (NM_206886, intron 19 of 27)	57848	NM_001306076	343099	Hs.482873	NM_206886	ENSG00000122483	CCDC18	NY-SAR-41	coiled-coil domain containing 18	protein-coding	0.002257	0.324324	
chunk0204_97_1	chr9	94520449	94520719	+	0	NA	Intergenic	L1MDa|LINE|L1	-34461	NR_121566	101928099	Hs.674409	NR_121566		PCAT7	PCAN-R2	prostate cancer associated transcript 7	ncRNA	0.007407	0.298893	
chunk0117_445_1	chr21	46496840	46497216	+	0	NA	exon (NM_001146115, exon 4 of 20)	exon (NM_001146115, exon 4 of 20)	34557	NR_046400	100862692	Hs.737163	NR_046400	ENSG00000223692	DIP2A-IT1	-	DIP2A intronic transcript 1	ncRNA	0.013298	0.408488	
chunk0058_187_1	chr14	24141127	24141337	+	0	NA	exon (NM_016049, exon 2 of 6)	exon (NM_016049, exon 2 of 6)	356	NM_016049	51016	Hs.271614	NM_016049	ENSG00000100908	EMC9	C14orf122|CGI-112|FAM158A	ER membrane protein complex subunit 9	protein-coding	0.071429	0.658768	
chunk0122_72_1	chr3	29521685	29522212	+	0	NA	intron (NM_001003793, intron 3 of 14)	intron (NM_001003793, intron 3 of 14)	240636	NM_014483	27303	Hs.221436	NM_014483	ENSG00000144642	RBMS3	-	RNA binding motif single stranded interacting protein 3	protein-coding	0.003795	0.365530	
chunk0133_130_1	chr3	168958081	168958629	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	56410	NR_109989	100507661	Hs.65918	NR_109989	ENSG00000242268	LINC02082	-	long intergenic non-protein coding RNA 2082	ncRNA	0.003650	0.320583	258(AAGAACAGGATGTTCT,-,0.00),259(AGAACAGGATGTTCTT,+,0.00)
chunk0156_259_1	chr5	109215142	109215360	+	0	NA	Intergenic	Intergenic	194723	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.009174	0.493151	
chunk0137_104_1	chr4	13670713	13671185	+	0	NA	intron (NR_121681, intron 2 of 3)	MLT1B|LTR|ERVL-MaLR	15770	NR_121681	101929071	Hs.543714	NR_121681	ENSG00000250634	LINC01182	-	long intergenic non-protein coding RNA 1182	ncRNA	0.004237	0.395349	
chunk0122_13_1	chr3	27363422	27363638	+	0	NA	intron (NM_199347, intron 2 of 24)	intron (NM_199347, intron 2 of 24)	5930	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.004630	0.359447	
chunk0156_404_1	chr5	113998852	113999111	+	0	NA	Intergenic	L2a|LINE|L2	-363338	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.007722	0.403846	
chunk0183_429_1	chr7	111076250	111076453	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	-14655	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.000000	0.387255	
chunk0111_224_1	chr20	28956112	28956330	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-124169	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.000000	0.333333	
chunk0155_300_1	chr5	96332710	96333554	+	0	NA	intron (NR_130776, intron 3 of 4)	intron (NR_130776, intron 3 of 4)	99027	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.016588	0.511243	537(CTGTACAGTGTGTTCC,-,0.00),538(TGTACAGTGTGTTCCT,+,0.00)
chunk0038_115_1	chr11	83908508	83908794	+	0	NA	intron (NM_001142700, intron 7 of 19)	intron (NM_001142700, intron 7 of 19)	-226226	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.006993	0.390244	
chunk0083_412_1	chr17	72151453	72152170	+	0	NA	Intergenic	Intergenic	30791	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.018131	0.486072	
chunk0003_398_1	chr1	39944620	39945098	+	0	NA	Intergenic	MER21-int|LTR|ERVL	-10253	NM_001287809	84879	Hs.655177	NM_032793	ENSG00000168389	MFSD2A	MCPH15|MFSD2|NLS1	major facilitator superfamily domain containing 2A	protein-coding	0.008368	0.390397	166(CGGTACAGTGTGTTCT,-,0.00),167(GGTACAGTGTGTTCTT,+,0.00),311(TAGAACAAGGAGTTCC,-,0.00),312(AGAACAAGGAGTTCCA,+,0.00)
chunk0102_294_1	chr2	150612840	150613498	+	0	NA	Intergenic	Intergenic	-15728	NR_110247	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.010638	0.441578	303(TAGTACAGGGTGCTCC,-,0.00),304(AGTACAGGGTGCTCCT,+,0.00)
chunk0154_315_1	chr5	83790761	83791025	+	0	NA	Intergenic	Intergenic	-69816	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.003788	0.384906	
chunk0106_257_1	chr2	203631061	203631710	+	0	NA	Intergenic	Intergenic	-75090	NM_001243077	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.012327	0.369231	462(GTGCACATGCAGTTCT,-,0.00),463(TGCACATGCAGTTCTC,+,0.00)
chunk0113_287_1	chr20	57143661	57144410	+	0	NA	Intergenic	L1MB8|LINE|L1	-69661	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.009346	0.432000	273(CAGAAGAGTGTGTGCC,-,0.00),274(AGAAGAGTGTGTGCCT,+,0.00)
chunk0209_4_1	chrX	34924159	34924647	+	0	NA	Intergenic	Intergenic	-18393	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.002049	0.337423	
chunk0179_234_1	chr7	47976740	47977419	+	0	NA	intron (NM_004507, intron 3 of 7)	intron (NM_004507, intron 3 of 7)	2546	NR_037917	3364	Hs.152983	NM_004507	ENSG00000136273	HUS1	hHUS1	HUS1 checkpoint clamp component	protein-coding	0.011782	0.425000	
chunk0082_259_1	chr17	57583009	57583426	+	0	NA	intron (NM_138962, intron 7 of 13)	Charlie7|DNA|hAT-Charlie	25195	NR_110807	101927539	Hs.680439	NR_110807	ENSG00000263499	LOC101927539	-	uncharacterized LOC101927539	ncRNA	0.002398	0.421053	
chunk0118_350_1	chr22	36143188	36143387	+	0	NA	intron (NM_145639, intron 3 of 3)	MER77B|LTR|ERVL	17642	NM_030644	80833	Hs.474737	NM_014349	ENSG00000128284	APOL3	APOLIII|CG121|CG12_1|apoL-III	apolipoprotein L3	protein-coding	0.015075	0.475000	62(GAGAACACAGCGTCCT,-,0.00),63(AGAACACAGCGTCCTG,+,0.00)
chunk0180_138_1	chr7	56295710	56296319	+	0	NA	Intergenic	Intergenic	152361	NR_029420	650226	Hs.448401	NR_029420		LOC650226	-	ankyrin repeat domain 26 pseudogene	pseudo	0.008210	0.426230	
chunk0164_15_1	chr6	17851295	17851743	+	0	NA	intron (NM_022113, intron 7 of 38)	intron (NM_022113, intron 7 of 38)	136104	NM_022113	63971	Hs.94499	NM_022113	ENSG00000137177	KIF13A	RBKIN|bA500C11.2	kinesin family member 13A	protein-coding	0.002232	0.418708	
chunk0185_430_1	chr7	134799236	134799853	+	0	NA	intron (NM_033157, intron 1 of 14)	intron (NM_033157, intron 1 of 14)	20131	NM_004342	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.008104	0.385113	355(AAGAACATGTTGTACC,-,0.00),356(AGAACATGTTGTACCA,+,0.00)
chunk0017_175_1	chr1	207038052	207038584	+	0	NA	Intergenic	L2a|LINE|L2	-5562	NM_023938	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.003759	0.339587	
chunk0168_23_1	chr6	77072744	77073318	+	0	NA	Intergenic	Intergenic	390372	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.006969	0.424348	
chunk0193_319_1	chr8	78600759	78601055	+	0	NA	intron (NM_181839, intron 2 of 2)	intron (NM_181839, intron 2 of 2)	-42404	NR_125389	101927003	Hs.614849	NR_125389	ENSG00000254266	PKIA-AS1	-	PKIA antisense RNA 1	ncRNA	0.003378	0.360269	
chunk0019_40_1	chr1	224014766	224015011	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	-22244	NR_132119	441124	Hs.520589	NR_132119		GTF2IP20	-	general transcription factor IIi pseudogene 20	pseudo	0.036735	0.451220	
chunk0132_254_1	chr3	158801953	158802190	+	0	NA	exon (NM_022736, exon 1 of 16)	exon (NM_022736, exon 1 of 16)	145	NR_110328	64747	Hs.58663	NM_022736	ENSG00000118855	MFSD1	SMAP4	major facilitator superfamily domain containing 1	protein-coding	0.097046	0.680672	
chunk0132_409_1	chr3	164351098	164351413	+	0	NA	Intergenic	Intergenic	-179699	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.344937	
chunk0147_395_1	chr4	186697780	186698402	+	0	NA	intron (NM_005245, intron 2 of 26)	intron (NM_005245, intron 2 of 26)	25742	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.022508	0.479936	
chunk0172_371_1	chr6	139275342	139275932	+	0	NA	intron (NM_153235, intron 3 of 9)	intron (NM_153235, intron 3 of 9)	16434	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.006780	0.370558	
chunk0136_297_1	chr3	195057024	195057560	+	0	NA	Intergenic	Intergenic	-37296	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.013060	0.474860	
chunk0052_334_1	chr12	126114319	126114878	+	0	NA	Intergenic	Intergenic	18606	NR_110053	101927464	Hs.443932	NR_110053	ENSG00000284848	LINC02359	-	long intergenic non-protein coding RNA 2359	ncRNA	0.008945	0.398214	418(TGGGCACACTGTGCTT,+,0.00)
chunk0153_238_1	chr5	72273570	72274006	+	0	NA	intron (NM_001286748, intron 4 of 11)	Tigger3b|DNA|TcMar-Tigger	46469	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.011468	0.315789	
chunk0096_110_1	chr2	28356075	28356362	+	0	NA	Intergenic	Intergenic	-36694	NM_005253	2355	Hs.220971	NM_005253	ENSG00000075426	FOSL2	FRA2	FOS like 2, AP-1 transcription factor subunit	protein-coding	0.031359	0.631944	
chunk0212_224_1	chrX	136202824	136203312	+	0	NA	intron (NM_001159699, intron 1 of 5)	intron (NM_001159699, intron 1 of 5)	6172	NM_001159699	2273	Hs.435369	NM_001449	ENSG00000022267	FHL1	FCMSU|FHL-1|FHL1A|FHL1B|FLH1A|KYOT|RBMX1A|RBMX1B|SLIM|SLIM-1|SLIM1|SLIMMER|XMPMA	four and a half LIM domains 1	protein-coding	0.010246	0.351738	
chunk0035_112_1	chr11	42507149	42507603	+	0	NA	Intergenic	L2a|LINE|L2	-253686	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002203	0.305495	
chunk0001_151_1	chr1	6157690	6158487	+	0	NA	intron (NM_015557, intron 3 of 41)	intron (NM_015557, intron 3 of 41)	22046	NM_015557	26038	Hs.522898	NM_015557	ENSG00000116254	CHD5	CHD-5	chromodomain helicase DNA binding protein 5	protein-coding	0.022585	0.535088	395(GGGAGCACAGTGTTCC,-,0.00),396(GGAGCACAGTGTTCCT,+,0.00)
chunk0093_240_1	chr19	50844341	50844725	+	0	NA	intron (NR_131203, intron 2 of 2)	L1PBa|LINE|L1	-10382	NM_001030047	354	Hs.171995	NM_001648	ENSG00000142515	KLK3	APS|KLK2A1|PSA|hK3	kallikrein related peptidase 3	protein-coding	0.013021	0.555844	
chunk0060_371_1	chr14	52480166	52480417	+	0	NA	intron (NM_001160047, intron 14 of 20)	L1PB1|LINE|L1	72292	NM_001160047	57544	Hs.532609	NM_020784	ENSG00000087301	TXNDC16	ERp90|KIAA1344	thioredoxin domain containing 16	protein-coding	0.003984	0.345238	
chunk0051_415_1	chr12	122319394	122319616	+	0	NA	intron (NM_001247997, intron 17 of 25)	intron (NM_001247997, intron 17 of 25)	-52984	NM_022916	65082	Hs.487883	NM_022916	ENSG00000139719	VPS33A	MPSPS	VPS33A core subunit of CORVET and HOPS complexes	protein-coding	0.013514	0.470852	
chunk0171_233_1	chr6	126447452	126447971	+	0	NA	intron (NR_104462, intron 3 of 3)	intron (NR_104462, intron 3 of 3)	-36920	NR_030316	693173		NR_030316	ENSG00000207632	MIR588	MIRN588|hsa-mir-588	microRNA 588	ncRNA	0.005780	0.411538	
chunk0119_185_1	chr22	44036124	44036542	+	0	NA	intron (NM_001243386, intron 1 of 11)	Tigger2b_Pri|DNA|TcMar-Tigger	10029	NM_001243386	29780	Hs.475074	NM_013327	ENSG00000188677	PARVB	CGI-56	parvin beta	protein-coding	0.004785	0.343675	
chunk0135_129_1	chr3	187263077	187263649	+	0	NA	intron (NR_033519, intron 1 of 9)	L2a|LINE|L2	28659	NM_001879	5648	Hs.89983	NM_001879	ENSG00000127241	MASP1	3MC1|CRARF|CRARF1|MAP1|MASP|MASP3|MAp44|PRSS5|RaRF	mannan binding lectin serine peptidase 1	protein-coding	0.001748	0.394415	
chunk0188_59_1	chr8	7032532	7032763	+	0	NA	Intergenic	L1MB8|LINE|L1	-3158	NR_073421	724068	Hs.690600	NR_073421	ENSG00000234178	DEFA11P	DEFAP3	defensin alpha 11, pseudogene	pseudo	0.004329	0.422414	
chunk0148_186_1	chr5	7878156	7878476	+	0	NA	exon (NM_024010, exon 5 of 15)	exon (NM_024010, exon 5 of 15)	9212	NM_002454	4552	Hs.481551	NM_002454	ENSG00000124275	MTRR	MSR|cblE	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	protein-coding	0.006250	0.398754	
chunk0014_258_1	chr1	180129670	180129974	+	0	NA	Intergenic	Intergenic	-25011	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.009868	0.449180	
chunk0191_78_1	chr8	47476580	47476779	+	0	NA	intron (NR_104581, intron 6 of 16)	intron (NR_104581, intron 6 of 16)	215801	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.010050	0.415000	
chunk0201_294_1	chr9	41087430	41087680	+	0	NA	Intergenic	Intergenic	-12930	NR_002836	595135	Hs.571593	NR_002836	ENSG00000277778	PGM5P2	-	phosphoglucomutase 5 pseudogene 2	pseudo	0.012000	0.490040	
chunk0126_385_1	chr3	84222240	84222791	+	0	NA	Intergenic	MER50-int|LTR|ERV1	647060	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.000000	0.307971	
chunk0052_272_1	chr12	124142813	124143148	+	0	NA	intron (NM_001204299, intron 2 of 4)	MER61E|LTR|ERV1	-146184	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.020896	0.455357	
chunk0205_32_1	chr9	105586971	105587252	+	0	NA	intron (NM_006731, intron 2 of 9)	intron (NM_006731, intron 2 of 9)	28981	NM_001198963	2218	Hs.55777	NM_006731	ENSG00000106692	FKTN	CMD1X|FCMD|LGMD2M|LGMDR13|MDDGA4|MDDGB4|MDDGC4	fukutin	protein-coding	0.007117	0.379433	
chunk0021_257_1	chr1	243421807	243422211	+	0	NA	intron (NM_006642, intron 15 of 17)	intron (NM_006642, intron 15 of 17)	75833	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.014851	0.456790	
chunk0163_113_1	chr6	10180133	10180562	+	0	NA	Intergenic	Intergenic	-231971	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.020979	0.481395	
chunk0161_101_1	chr5	167378891	167379454	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	94334	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.008881	0.365248	
chunk0208_462_1	chrX	34716758	34717334	+	0	NA	Intergenic	Intergenic	-59758	NM_031442	83604	Hs.8769	NM_031442	ENSG00000147027	TMEM47	BCMP1|TM4SF10|VAB-9	transmembrane protein 47	protein-coding	0.003472	0.331023	
chunk0181_314_1	chr7	87423834	87424433	+	0	NA	intron (NM_018849, intron 16 of 27)	L2c|LINE|L2	51570	NM_018849	5244	Hs.654403	NM_000443	ENSG00000005471	ABCB4	ABC21|GBD1|ICP3|MDR2|MDR2/3|MDR3|PFIC-3|PGY3	ATP binding cassette subfamily B member 4	protein-coding	0.013356	0.458333	128(TGGCACATACTGTTCC,-,0.00),129(GGCACATACTGTTCCC,+,0.00)
chunk0177_427_1	chr7	27915724	27915954	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	175744	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.000000	0.285714	
chunk0129_449_1	chr3	128227041	128227251	+	0	NA	intron (NM_021937, intron 1 of 6)	X2_LINE|LINE|CR1	73689	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.000000	0.478673	49(CAGTGCAGTGTGTTCC,-,0.00),50(AGTGCAGTGTGTTCCT,+,0.00)
chunk0154_378_1	chr5	87756943	87757314	+	0	NA	Intergenic	L1MA7|LINE|L1	-344095	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.002695	0.376344	
chunk0145_44_1	chr4	144647165	144647826	+	0	NA	intron (NM_022475, intron 1 of 12)	intron (NM_022475, intron 1 of 12)	-1476	NR_037595	646576	Hs.632595	NR_037595	ENSG00000248890	HHIP-AS1	-	HHIP antisense RNA 1	ncRNA	0.030257	0.422961	86(ATGAACAGTGTGTTTT,-,0.00),87(TGAACAGTGTGTTTTG,+,0.00)
chunk0027_268_1	chr10	77371638	77372397	+	0	NA	intron (NR_126365, intron 3 of 5)	intron (NR_126365, intron 3 of 5)	21145	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.003953	0.459211	
chunk0055_226_1	chr13	62629554	62629862	+	0	NA	Intergenic	LTR47A|LTR|ERVL	166984	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.012987	0.401294	
chunk0112_352_1	chr20	45257858	45258216	+	0	NA	Intergenic	MIRb|SINE|MIR	-3473	NM_003064	6590	Hs.517070	NM_003064	ENSG00000124107	SLPI	ALK1|ALP|BLPI|HUSI|HUSI-I|MPI|WAP4|WFDC4	secretory leukocyte peptidase inhibitor	protein-coding	0.011173	0.440111	
chunk0171_364_1	chr6	130794791	130795392	+	0	NA	Intergenic	Intergenic	-32314	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.006656	0.393688	
chunk0199_423_1	chr9	13685628	13685870	+	0	NA	Intergenic	Intergenic	-242222	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.008264	0.465021	
chunk0056_435_1	chr13	95100529	95100775	+	0	NA	intron (NM_001105515, intron 20 of 20)	intron (NM_001105515, intron 20 of 20)	140611	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.008130	0.396761	
chunk0004_10_1	chr1	42052204	42052604	+	0	NA	Intergenic	UCON99|DNA|DNA	-16479	NR_038261	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.012500	0.428928	
chunk0006_196_1	chr1	67578665	67578980	+	0	NA	Intergenic	Intergenic	-106355	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.009524	0.452532	
chunk0193_191_1	chr8	75557580	75557779	+	0	NA	intron (NM_004133, intron 6 of 9)	L1MA9|LINE|L1	17711	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.005025	0.385000	
chunk0041_50_1	chr11	123211427	123211639	+	0	NA	Intergenic	Intergenic	-16228	NM_024769	79827	Hs.591949	NM_024769	ENSG00000166250	CLMP	ACAM|ASAM|CSBM|CSBS	CXADR like membrane protein	protein-coding	0.014151	0.502347	
chunk0176_213_1	chr7	14769225	14769873	+	0	NA	intron (NM_145695, intron 1 of 23)	intron (NM_145695, intron 1 of 23)	71901	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.004630	0.363636	
chunk0037_135_1	chr11	73094618	73094964	+	0	NA	intron (NM_014824, intron 2 of 19)	intron (NM_014824, intron 2 of 19)	47307	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.008671	0.296830	
chunk0173_143_1	chr6	143953469	143953668	+	0	NA	intron (NM_001289047, intron 2 of 3)	intron (NM_001289047, intron 2 of 3)	54836	NM_001080956	5325	Hs.743225	NM_002656	ENSG00000118495	PLAGL1	LOT1|ZAC|ZAC1	PLAG1 like zinc finger 1	protein-coding	0.000000	0.375000	64(AGGGACAGGGTGTGTT,-,0.00),65(GGGACAGGGTGTGTTC,+,0.00)
chunk0130_383_1	chr3	139941678	139941888	+	0	NA	intron (NM_022131, intron 1 of 16)	intron (NM_022131, intron 1 of 16)	6598	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.009524	0.436019	
chunk0186_263_1	chr7	141541579	141541818	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-9580	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.000000	0.508333	
chunk0147_457_1	chr4	188473501	188474050	+	0	NA	intron (NR_033869, intron 2 of 4)	intron (NR_033869, intron 2 of 4)	18197	NR_033869	401164	Hs.435756	NR_033869	ENSG00000249378	LINC01060	-	long intergenic non-protein coding RNA 1060	ncRNA	0.003643	0.356364	
chunk0148_260_1	chr5	10331372	10331729	+	0	NA	Intergenic	Intergenic	-22089	NM_001270660	10299	Hs.432862	NM_005885	ENSG00000145495	MARCH6	DOA10|MARCH-VI|RNF176|TEB4	membrane associated ring-CH-type finger 6	protein-coding	0.019608	0.555866	
chunk0016_79_1	chr1	193927467	193927709	+	0	NA	Intergenic	LTR2752|LTR|ERV1	622843	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.016529	0.547325	
chunk0091_130_1	chr19	6516364	6516613	+	0	NA	Intergenic	CpG	-13640	NM_001289127	10382	Hs.110837	NM_006087	ENSG00000104833	TUBB4A	DYT4|TUBB4|beta-5	tubulin beta 4A class IVa	protein-coding	0.056225	0.616000	
chunk0020_89_1	chr1	232802547	232802981	+	0	NA	Intergenic	MIR|SINE|MIR	-2128	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.004608	0.319540	
chunk0044_431_1	chr12	42145064	42145263	+	0	NA	promoter-TSS (NM_173601)	promoter-TSS (NM_173601)	-292	NM_001099650	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.025126	0.480000	
chunk0134_419_1	chr3	183295262	183295716	+	0	NA	intron (NM_015078, intron 12 of 29)	intron (NM_015078, intron 12 of 29)	42245	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.008811	0.498901	
chunk0094_458_1	chr2	11599870	11600225	+	0	NA	intron (NM_014668, intron 15 of 32)	intron (NM_014668, intron 15 of 32)	57322	NM_033090	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.022535	0.491573	
chunk0182_435_1	chr7	101488648	101489118	+	0	NA	intron (NM_001278563, intron 3 of 12)	LTR37A|LTR|ERV1	80123	NR_103748	100506527	Hs.535863	NR_103747	ENSG00000233123	LINC01007	-	long intergenic non-protein coding RNA 1007	ncRNA	0.034043	0.433121	
chunk0138_448_1	chr4	46695616	46695834	+	0	NA	Intergenic	MER1A|DNA|hAT-Charlie	213510	NM_130902	170712	Hs.479656	NM_130902	ENSG00000170516	COX7B2	-	cytochrome c oxidase subunit 7B2	protein-coding	0.000000	0.502283	123(AGGGACTACATGTACT,-,0.00)
chunk0131_240_1	chr3	149388897	149389205	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-11270	NM_014220	4071	Hs.351316	NM_014220	ENSG00000169908	TM4SF1	H-L6|L6|M3S1|TAAL6	transmembrane 4 L six family member 1	protein-coding	0.003247	0.430421	
chunk0120_421_1	chr3	13021580	13021841	+	0	NA	intron (NM_001134382, intron 1 of 13)	MIRb|SINE|MIR	51407	NM_001134382	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.045977	0.595420	
chunk0045_17_1	chr12	43350224	43350675	+	0	NA	Intergenic	Intergenic	201472	NM_025003	80070	Hs.287554	NM_025003	ENSG00000173157	ADAMTS20	ADAM-TS20|ADAMTS-20|GON-1	ADAM metallopeptidase with thrombospondin type 1 motif 20	protein-coding	0.002217	0.298673	
chunk0086_305_1	chr18	24033512	24033711	+	0	NA	intron (NM_001135993, intron 1 of 13)	Tigger6a|DNA|TcMar-Tigger	-18151	NR_110796	102724246	Hs.569872	NR_110796	ENSG00000264745	TTC39C-AS1	-	TTC39C antisense RNA 1	ncRNA	0.000000	0.405000	
chunk0036_156_1	chr11	62353972	62354171	+	0	NA	intron (NM_001083926, intron 2 of 6)	MIR|SINE|MIR	16769	NM_025080	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.000000	0.375000	
chunk0029_179_1	chr10	100780303	100780815	+	0	NA	intron (NM_003987, intron 4 of 10)	intron (NM_003987, intron 4 of 10)	34848	NM_003990	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.005859	0.504873	248(GGGCCAGGCTGTACCT,+,0.00)
chunk0175_257_1	chr7	7120548	7120869	+	0	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	-23922	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.012461	0.388199	
chunk0179_363_1	chr7	51075526	51075780	+	0	NA	intron (NM_001287438, intron 7 of 7)	intron (NM_001287438, intron 7 of 7)	241165	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.003937	0.301961	
chunk0033_78_1	chr11	13881641	13881961	+	0	NA	Intergenic	Intergenic	-80836	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.012500	0.473520	
chunk0084_414_1	chr17	82319512	82319713	+	0	NA	Intergenic	CpG	-2008	NM_006137	924	Hs.36972	NM_006137	ENSG00000173762	CD7	GP40|LEU-9|TP41|Tp40	CD7 molecule	protein-coding	0.074627	0.594059	
chunk0197_245_1	chr8	123377619	123377818	+	0	NA	intron (NM_014109, intron 2 of 27)	Charlie29a|DNA|hAT-Charlie	18747	NM_014109	29028	Hs.370834	NM_014109	ENSG00000156802	ATAD2	ANCCA|CT137|PRO2000	ATPase family AAA domain containing 2	protein-coding	0.010050	0.380000	
chunk0152_305_1	chr5	61767611	61768058	+	0	NA	Intergenic	Intergenic	-32136	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.011186	0.448661	102(AGGAACATTTTGACCT,-,0.00),103(GGAACATTTTGACCTT,+,0.00)
chunk0058_270_1	chr14	26101518	26101931	+	0	NA	Intergenic	Intergenic	496030	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.009685	0.318841	
chunk0066_207_1	chr15	33761001	33761200	+	0	NA	intron (NM_001036, intron 60 of 103)	L1PA7|LINE|L1	-207788	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.000000	0.355000	57(AAAGACACAATGTACC,-,0.00)
chunk0099_386_1	chr2	101518795	101519454	+	0	NA	Intergenic	Intergenic	-44421	NM_001145664	731220	Hs.662488	NM_207403	ENSG00000196460	RFX8	-	RFX family member 8, lacking RFX DNA binding domain	protein-coding	0.015175	0.451515	
chunk0197_367_1	chr8	126379259	126379845	+	0	NA	Intergenic	Intergenic	54057	NR_125421	101927657	Hs.552133	NR_125421	ENSG00000244791	LOC101927657	-	uncharacterized LOC101927657	ncRNA	0.011945	0.437819	431(AAGTACAGAATGTTTC,-,0.00),432(AGTACAGAATGTTTCT,+,0.00)
chunk0131_322_1	chr3	151041266	151041553	+	0	NA	intron (NR_024066, intron 1 of 5)	L1MC5|LINE|L1	-45389	NM_053002	116931	Hs.744234	NM_053002	ENSG00000144893	MED12L	NOPAR|TNRC11L|TRALP|TRALPUSH	mediator complex subunit 12L	protein-coding	0.000000	0.274306	
chunk0043_390_1	chr12	25286803	25287397	+	0	NA	Intergenic	L2c|LINE|L2	-36169	NM_004985	3845	Hs.505033	NM_004985	ENSG00000133703	KRAS	C-K-RAS|CFC2|K-RAS2A|K-RAS2B|K-RAS4A|K-RAS4B|K-Ras|KI-RAS|KRAS1|KRAS2|NS|NS3|RALD|RASK2|c-Ki-ras2	KRAS proto-oncogene, GTPase	protein-coding	0.000000	0.400000	260(AGGTACATCCAGTTCT,-,0.00),261(GGTACATCCAGTTCTG,+,0.00)
chunk0017_118_1	chr1	206113098	206113530	+	0	NA	intron (NM_000707, intron 1 of 1)	intron (NM_000707, intron 1 of 1)	3734	NM_000707	553	Hs.1372	NM_000707	ENSG00000198049	AVPR1B	AVPR3|V1bR	arginine vasopressin receptor 1B	protein-coding	0.011574	0.558891	286(GGGAACTGTGTGTACT,-,0.00),287(GGAACTGTGTGTACTG,+,0.00)
chunk0191_424_1	chr8	57804135	57804886	+	0	NA	Intergenic	Intergenic	-173848	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.017310	0.376330	
chunk0073_107_1	chr16	4575366	4575565	+	0	NA	exon (NM_001145011, exon 5 of 16)	exon (NM_001145011, exon 5 of 16)	18975	NM_001145011	342346	Hs.684212	NM_001145011	ENSG00000205832	C16orf96	-	chromosome 16 open reading frame 96	protein-coding	0.015075	0.660000	
chunk0141_331_1	chr4	87365383	87365709	+	0	NA	intron (NM_016245, intron 4 of 6)	PABL_A-int|LTR|ERV1	25757	NM_016245	51170	Hs.594923	NM_016245	ENSG00000198189	HSD17B11	17-BETA-HSD11|17-BETA-HSDXI|17BHSD11|DHRS8|PAN1B|RETSDR2|SDR16C2	hydroxysteroid 17-beta dehydrogenase 11	protein-coding	0.003067	0.351682	66(AAGGACAAACTGTTTC,-,0.00),67(AGGACAAACTGTTTCT,+,0.00)
chunk0195_62_1	chr8	93796936	93797228	+	0	NA	intron (NM_153704, intron 18 of 27)	intron (NM_153704, intron 18 of 27)	42238	NM_001142301	91147	Hs.116240	NM_153704	ENSG00000164953	TMEM67	JBTS6|MECKELIN|MKS3|NPHP11|TNEM67	transmembrane protein 67	protein-coding	0.006849	0.320819	
chunk0145_227_1	chr4	148360067	148360533	+	0	NA	intron (NM_000901, intron 2 of 8)	intron (NM_000901, intron 2 of 8)	82220	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.002146	0.327623	239(ATGACACTATGTGCTT,+,0.00)
chunk0113_170_1	chr20	53055677	53056164	+	0	NA	intron (NM_173485, intron 1 of 2)	MER58A|DNA|hAT-Charlie	83513	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.002053	0.383197	
chunk0127_189_1	chr3	95967915	95968622	+	0	NA	Intergenic	Intergenic	-285075	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.000000	0.292373	
chunk0044_368_1	chr12	39372353	39372726	+	0	NA	intron (NM_017641, intron 1 of 36)	MIR3|SINE|MIR	70851	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.002681	0.368984	
chunk0160_68_1	chr5	149829312	149829849	+	0	NA	intron (NM_001172699, intron 3 of 10)	intron (NM_001172699, intron 3 of 10)	57640	NM_001172699	133522	Hs.483816	NM_133263	ENSG00000155846	PPARGC1B	ERRL1|PERC|PGC-1(beta)|PGC1B	PPARG coactivator 1 beta	protein-coding	0.014898	0.492565	316(AGGTACACTCTGTACC,-,0.00),317(GGTACACTCTGTACCT,+,0.00)
chunk0177_24_1	chr7	20607039	20607926	+	0	NA	Intergenic	Intergenic	-8140	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.004510	0.367117	657(AGGCTCACACAGTTCT,-,0.00),658(GGCTCACACAGTTCTT,+,0.00)
chunk0191_358_1	chr8	56656575	56656977	+	0	NA	Intergenic	Intergenic	-96953	NR_038236	100507632	Hs.583755	NR_038236	ENSG00000246430	LINC00968	-	long intergenic non-protein coding RNA 968	ncRNA	0.000000	0.389578	
chunk0031_319_1	chr10	129163293	129163970	+	0	NA	Intergenic	Intergenic	-303553	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.014771	0.415929	
chunk0084_164_1	chr17	77116417	77116899	+	0	NA	intron (NM_001204410, intron 2 of 17)	intron (NM_001204410, intron 2 of 17)	-24265	NM_001143999	6397	Hs.464184	NM_003003	ENSG00000129657	SEC14L1	PRELID4A|SEC14L	SEC14 like lipid binding 1	protein-coding	0.004149	0.476190	
chunk0034_288_1	chr11	34676648	34677159	+	0	NA	Intergenic	L2a|LINE|L2	44439	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.007828	0.376953	
chunk0148_379_1	chr5	14711363	14711674	+	0	NA	intron (NM_054027, intron 11 of 11)	intron (NM_054027, intron 11 of 11)	-1176	NR_046285	100130744	Hs.660550	NR_046285		LOC100130744	-	uncharacterized LOC100130744	ncRNA	0.025723	0.586538	101(TAGCTCAGTGTGTTCC,-,0.00),102(AGCTCAGTGTGTTCCT,+,0.00),178(GAGGACACCATGTCCC,-,0.00),179(AGGACACCATGTCCCA,+,0.00)
chunk0205_115_1	chr9	107794197	107794494	+	0	NA	Intergenic	Intergenic	-304625	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.003367	0.352349	
chunk0026_110_1	chr10	61900257	61901099	+	0	NA	promoter-TSS (NM_032199)	promoter-TSS (NM_032199)	-576	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.036817	0.438909	
chunk0189_306_1	chr8	26038729	26038929	+	0	NA	intron (NM_022659, intron 5 of 15)	intron (NM_022659, intron 5 of 15)	6295	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.005000	0.472637	
chunk0139_155_1	chr4	53702666	53703152	+	0	NA	intron (NR_125918, intron 1 of 2)	intron (NR_125918, intron 1 of 2)	7008	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.030864	0.568789	
chunk0074_114_1	chr16	22369323	22369585	+	0	NA	intron (NM_001802, intron 1 of 4)	intron (NM_001802, intron 1 of 4)	5163	NM_001802	1039	Hs.513430	NM_001802	ENSG00000140743	CDR2	CDR62|Yo	cerebellar degeneration related protein 2	protein-coding	0.003817	0.425856	61(TGGAACTACCTGTGCT,-,0.00),62(GGAACTACCTGTGCTA,+,0.00)
chunk0018_199_1	chr1	219337333	219337608	+	0	NA	Intergenic	Intergenic	162501	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.000000	0.336957	
chunk0196_385_1	chr8	115668693	115668906	+	0	NA	promoter-TSS (NM_001282902)	promoter-TSS (NM_001282902)	229	NM_014112	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.032864	0.476636	
chunk0137_68_1	chr4	12443553	12444057	+	0	NA	Intergenic	Intergenic	220354	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.001984	0.398020	
chunk0061_232_1	chr14	60665072	60665748	+	0	NA	Intergenic	Intergenic	-15973	NM_005982	6495	Hs.633506	NM_005982	ENSG00000126778	SIX1	BOS3|DFNA23|TIP39	SIX homeobox 1	protein-coding	0.007396	0.381093	
chunk0066_98_1	chr15	29813997	29814560	+	0	NA	intron (NM_001301025, intron 2 of 28).2	intron (NM_001301025, intron 2 of 28).2	7270	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.007105	0.319149	
chunk0008_80_1	chr1	89931878	89932452	+	0	NA	intron (NM_001134479, intron 2 of 2)	intron (NM_001134479, intron 2 of 2)	62801	NR_002830	492303	Hs.550796	NR_002830		GEMIN8P4	-	gem nuclear organelle associated protein 8 pseudogene 4	pseudo	0.008711	0.386087	
chunk0143_336_1	chr4	120869507	120870004	+	0	NA	intron (NM_001300824, intron 2 of 13)	intron (NM_001300824, intron 2 of 13)	53111	NM_001300824	11107	Hs.666782	NM_018699	ENSG00000138738	PRDM5	BCS2|PFM2	PR/SET domain 5	protein-coding	0.000000	0.363454	
chunk0180_199_1	chr7	66261997	66262345	+	0	NA	intron (NM_003596, intron 2 of 5)	intron (NM_003596, intron 2 of 5)	56899	NM_003596	8460	Hs.421194	NM_003596	ENSG00000169902	TPST1	TANGO13A	tyrosylprotein sulfotransferase 1	protein-coding	0.000000	0.504298	
chunk0117_50_1	chr22	12691682	12692074	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	794472	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.011662	0.488372	
chunk0135_143_1	chr3	187621468	187622196	+	0	NA	Intergenic	Intergenic	48581	NM_001048	6750	Hs.12409	NM_001048	ENSG00000157005	SST	SMST	somatostatin	protein-coding	0.006868	0.433471	
chunk0103_297_1	chr2	166334997	166335196	+	0	NA	intron (NM_002977, intron 1 of 26)	intron (NM_002977, intron 1 of 26)	40891	NM_002977	6335	Hs.439145	NM_002977	ENSG00000169432	SCN9A	ETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP	sodium voltage-gated channel alpha subunit 9	protein-coding	0.000000	0.285000	
chunk0023_322_1	chr10	29158427	29159080	+	0	NA	Intergenic	Intergenic	-130308	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.004594	0.412844	
chunk0039_67_1	chr11	96329303	96329766	+	0	NA	intron (NM_032427, intron 1 of 4)	MIR1_Amn|SINE|MIR	-11904	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.004320	0.400862	
chunk0112_284_1	chr20	43728026	43728397	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-1209	NM_001008901	149699	Hs.447626	NM_176791	ENSG00000124196	GTSF1L	C20orf65|FAM112A|dJ1028D15.4	gametocyte specific factor 1 like	protein-coding	0.000000	0.408602	
chunk0083_407_1	chr17	72079630	72080297	+	0	NA	TTS (NR_103737)	TTS (NR_103737)	7630	NR_110827	101928205	Hs.620808	NR_110827	ENSG00000226101	LINC02097	-	long intergenic non-protein coding RNA 2097	ncRNA	0.007496	0.374251	
chunk0064_144_1	chr14	91609061	91609781	+	0	NA	intron (NM_024764, intron 21 of 26)	Tigger2b_Pri|DNA|TcMar-Tigger	-98941	NM_001284281	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.004167	0.332871	418(TAGTACAGTGTGTACT,-,0.00),419(AGTACAGTGTGTACTA,+,0.00)
chunk0083_173_1	chr17	66298346	66299168	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4051	NM_002737	5578	Hs.531704	NM_002737	ENSG00000154229	PRKCA	AAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACA	protein kinase C alpha	protein-coding	0.007299	0.341434	223(TGAAACAGTGTGTTCC,-,0.00),224(GAAACAGTGTGTTCCT,+,0.00),366(GAGAACTATCTGTTCA,-,0.00),367(AGAACTATCTGTTCAC,+,0.00)
chunk0178_9_1	chr7	29066744	29066943	+	0	NA	intron (NM_019029, intron 9 of 12)	L2a|LINE|L2	-58190	NR_120523	101928168	Hs.666750	NR_120523	ENSG00000285412	LOC101928168	-	uncharacterized LOC101928168	ncRNA	0.005025	0.510000	
chunk0005_320_1	chr1	60896305	60896686	+	0	NA	Intergenic	Intergenic	-70911	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.002625	0.335079	
chunk0040_305_1	chr11	117232648	117232866	+	0	NA	promoter-TSS (NM_001278249)	promoter-TSS (NM_001278249)	21	NM_001077239	257160	Hs.591934	NM_207343	ENSG00000167257	RNF214	-	ring finger protein 214	protein-coding	0.133028	0.803653	
chunk0130_21_1	chr3	128671350	128671722	+	0	NA	Intergenic	L1MC1|LINE|L1	-20660	NM_002950	6184	Hs.518244	NM_002950	ENSG00000163902	RPN1	OST1|RBPH1	ribophorin I	protein-coding	0.010753	0.447721	163(AGGTACAGAGAGTTCT,-,0.00),164(GGTACAGAGAGTTCTC,+,0.00)
chunk0123_319_1	chr3	47394246	47394848	+	0	NA	intron (NM_015466, intron 1 of 24)	AluJr|SINE|Alu	13565	NM_001304482	25930	Hs.25524	NM_015466	ENSG00000076201	PTPN23	HD-PTP|HDPTP|PTP-TD14	protein tyrosine phosphatase non-receptor type 23	protein-coding	0.011628	0.470978	393(AGGAACAGGTTGTGCA,-,0.00),394(GGAACAGGTTGTGCAG,+,0.00)
chunk0006_424_1	chr1	76366363	76366928	+	0	NA	intron (NM_152996, intron 2 of 4)	intron (NM_152996, intron 2 of 4)	291941	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.007080	0.321555	
chunk0176_38_1	chr7	9889706	9889938	+	0	NA	Intergenic	L1MA2|LINE|L1	255552	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.004310	0.510730	
chunk0032_24_1	chr11	825930	826184	+	0	NA	TTS (NM_020376)	TTS (NM_020376)	-2203	NM_001286606	283229	Hs.660936	NM_173584	ENSG00000177685	CRACR2B	EFCAB4A	calcium release activated channel regulator 2B	protein-coding	0.023622	0.647059	
chunk0119_249_1	chr22	45785402	45785807	+	0	NA	intron (NM_001167621, intron 8 of 10)	MIRb|SINE|MIR	25080	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.017284	0.435961	
chunk0008_245_1	chr1	94334533	94334948	+	0	NA	Intergenic	Intergenic	-83637	NM_002858	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.009639	0.473558	
chunk0192_13_1	chr8	58385779	58386136	+	0	NA	Intergenic	L1MC2|LINE|L1	-25307	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.002801	0.324022	
chunk0187_127_1	chr7	149195482	149195708	+	0	NA	exon (NM_001303481, exon 1 of 9)	exon (NM_001303481, exon 1 of 9)	133	NM_003575	8427	Hs.729056	NM_003575	ENSG00000170265	ZNF282	HUB1	zinc finger protein 282	protein-coding	0.053097	0.678414	
chunk0053_337_1	chr13	34467122	34467432	+	0	NA	intron (NR_047036, intron 2 of 2)	intron (NR_047036, intron 2 of 2)	173408	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.009677	0.350482	
chunk0036_398_1	chr11	68065896	68066343	+	0	NA	intron (NM_001277, intron 8 of 11)	intron (NM_001277, intron 8 of 11)	21325	NR_106811	102465451		NR_106811	ENSG00000275022	MIR6753	hsa-mir-6753	microRNA 6753	ncRNA	0.015660	0.497768	226(CAGAACATTGTGTCTC,-,0.00),227(AGAACATTGTGTCTCC,+,0.00)
chunk0032_427_1	chr11	12234342	12234573	+	0	NA	intron (NM_001282663, intron 15 of 27)	intron (NM_001282663, intron 15 of 27)	-52443	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.004329	0.448276	16(TAGGACATTCTGTACT,-,0.00),17(AGGACATTCTGTACTT,+,0.00)
chunk0095_233_1	chr2	19009215	19009937	+	0	NA	Intergenic	Intergenic	-338853	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.005540	0.384509	
chunk0003_339_1	chr1	38991093	38991402	+	0	NA	promoter-TSS (NM_024595)	promoter-TSS (NM_024595)	3	NM_001136275	79647	Hs.293563	NM_024595	ENSG00000174574	AKIRIN1	C1orf108|STRF2	akirin 1	protein-coding	0.110032	0.735484	
chunk0194_295_1	chr8	87877256	87877456	+	0	NA	Intergenic	L1MC1|LINE|L1	-3288	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.005000	0.348259	
chunk0208_112_1	chrX	13845655	13846257	+	0	NA	intron (NM_001001994, intron 1 of 6)	intron (NM_001001994, intron 1 of 6)	-28761	NM_001001996	2824	Hs.495710	NM_005278	ENSG00000046653	GPM6B	M6B	glycoprotein M6B	protein-coding	0.011628	0.447761	153(AGTACACGCTGAACTT,+,0.00),312(AGGGACACTGTGTCCA,-,0.00),313(GGGACACTGTGTCCAA,+,0.00)
chunk0211_284_1	chrX	122281373	122281937	+	0	NA	Intergenic	L1M1|LINE|L1	-902588	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.005319	0.318584	
chunk0106_130_1	chr2	199692758	199693362	+	0	NA	Intergenic	Intergenic	84992	NR_110270	101927641	Hs.549598	NR_110270	ENSG00000238217	LINC01877	-	long intergenic non-protein coding RNA 1877	ncRNA	0.003311	0.338843	358(CAGTACATTCTGTTTT,-,0.00),359(AGTACATTCTGTTTTC,+,0.00)
chunk0114_357_1	chr21	19525961	19526160	+	0	NA	Intergenic	LTR84b|LTR|ERVL	-766248	NR_109925	101927797	Hs.551743	NR_109925		MIR548XHG	-	MIR548X host gene	ncRNA	0.000000	0.380000	141(GAAACTTTGTGTTCCT,+,0.00)
chunk0110_221_1	chr20	15488148	15488347	+	0	NA	intron (NM_001033087, intron 3 of 13)	intron (NM_001033087, intron 3 of 13)	291389	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.010050	0.515000	
chunk0058_369_1	chr14	29169408	29170034	+	0	NA	Intergenic	MER52A|LTR|ERV1	397017	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.009585	0.475279	
chunk0016_260_1	chr1	200172722	200172963	+	0	NA	intron (NM_205860, intron 7 of 7)	intron (NM_205860, intron 7 of 7)	130017	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.008299	0.351240	
chunk0174_29_1	chr6	153832611	153832941	+	0	NA	Intergenic	(ACACAT)n|Simple_repeat|Simple_repeat	-177720	NM_001145280	4988	Hs.2353	NM_000914	ENSG00000112038	OPRM1	LMOR|M-OR-1|MOP|MOR|MOR1|OPRM	opioid receptor mu 1	protein-coding	0.027273	0.459215	
chunk0148_79_1	chr5	2695608	2695902	+	0	NA	Intergenic	Intergenic	55900	NM_033267	153572	Hs.282089	NM_033267	ENSG00000170561	IRX2	IRXA2	iroquois homeobox 2	protein-coding	0.010204	0.457627	
chunk0069_373_1	chr15	67320074	67320277	+	0	NA	intron (NM_001031715, intron 4 of 20)	intron (NM_001031715, intron 4 of 20)	-64977	NM_001271885	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.000000	0.426471	
chunk0192_72_1	chr8	60658577	60658857	+	0	NA	Intergenic	Intergenic	-20048	NM_017780	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.000000	0.530249	
chunk0087_27_1	chr18	31143095	31143383	+	0	NA	intron (NM_024421, intron 8 of 15)	intron (NM_024421, intron 8 of 15)	19617	NM_024421	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.006944	0.356401	
chunk0035_107_1	chr11	42361703	42361907	+	0	NA	Intergenic	Intergenic	-108115	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.439024	
chunk0096_126_1	chr2	28635125	28635616	+	0	NA	intron (NM_001170585, intron 55 of 56)	MIR3|SINE|MIR	-116378	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.006110	0.426829	245(CAGAACATTCTGTAAC,-,0.00),296(AACACAGACTGTTCAT,+,0.00)
chunk0184_359_1	chr7	120951064	120951308	+	0	NA	exon (NM_198267, exon 2 of 5)	exon (NM_198267, exon 2 of 5)	423	NM_198267	54556	Hs.489811	NM_019071	ENSG00000071243	ING3	Eaf4|ING2|MEAF4|p47ING3	inhibitor of growth family member 3	protein-coding	0.102459	0.624490	
chunk0103_121_1	chr2	161761062	161761631	+	0	NA	intron (NM_001178016, intron 2 of 26)	intron (NM_001178016, intron 2 of 26)	137011	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.007030	0.394737	
chunk0012_130_1	chr1	157132550	157133097	+	0	NA	TTS (NM_005240)	TTS (NM_005240)	4461	NR_001560	360155	Hs.491808	NR_001560	ENSG00000235700	CYCSP52	HC6|HCP2	CYCS pseudogene 52	pseudo	0.003656	0.392336	
chunk0109_2_1	chr20	61557	61983	+	0	NA	Intergenic	(ATTCC)n|Simple_repeat|Simple_repeat	-25902	NM_153325	245938	Hs.380220	NM_153325	ENSG00000178591	DEFB125	DEFB-25	defensin beta 125	protein-coding	0.011737	0.475410	
chunk0067_30_1	chr15	40389727	40390624	+	0	NA	intron (NM_001142762, intron 6 of 7)	intron (NM_001142762, intron 6 of 7)	7454	NM_001142761	90417	Hs.525796	NM_033286	ENSG00000128944	KNSTRN	C15orf23|HSD11|SKAP|TRAF4AF1	kinetochore localized astrin (SPAG5) binding protein	protein-coding	0.002230	0.432071	484(AGAAACACTTTGTTCC,-,0.00),485(GAAACACTTTGTTCCT,+,0.00)
chunk0004_394_1	chr1	52071281	52071790	+	0	NA	intron (NM_001243767, intron 3 of 4)	L2a|LINE|L2	15350	NM_001136497	91408	Hs.429839	NM_152265	ENSG00000134717	BTF3L4	-	basic transcription factor 3 like 4	protein-coding	0.009823	0.384314	
chunk0172_433_1	chr6	140775211	140775691	+	0	NA	Intergenic	Intergenic	91637	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.006250	0.330561	
chunk0022_395_1	chr10	17882483	17882762	+	0	NA	intron (NM_002438, intron 21 of 29)	intron (NM_002438, intron 21 of 29)	37515	NR_030167	574445		NR_030167	ENSG00000207938	MIR511	MIR511-1|MIR511-2|MIRN511-1|MIRN511-2|hsa-mir-511|hsa-mir-511-2|mir-511	microRNA 511	ncRNA	0.003584	0.353571	183(GAGAACACATTGTACA,-,0.00),184(AGAACACATTGTACAA,+,0.00)
chunk0166_317_1	chr6	49753445	49754012	+	0	NA	Intergenic	L1PREC2|LINE|L1	-9273	NM_006061	10321	Hs.404466	NM_006061	ENSG00000096006	CRISP3	Aeg2|CRISP-3|CRS3|SGP28|dJ442L6.3	cysteine rich secretory protein 3	protein-coding	0.001764	0.362676	
chunk0090_456_1	chr18	80128127	80128348	+	0	NA	intron (NM_014913, intron 2 of 3)	intron (NM_014913, intron 2 of 3)	19206	NM_014913	22850	Hs.131915	NM_014913	ENSG00000101544	ADNP2	ZNF508	ADNP homeobox 2	protein-coding	0.000000	0.337838	
chunk0208_331_1	chrX	24661167	24661750	+	0	NA	intron (NM_001163264, intron 1 of 7)	L1MC5|LINE|L1	11385	NR_046638	100874088		NR_046638	ENSG00000236836	PCYT1B-AS1	-	PCYT1B antisense RNA 1	ncRNA	0.000000	0.357877	
chunk0158_58_1	chr5	126009643	126009990	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-169761	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.014409	0.445402	
chunk0186_215_1	chr7	140025179	140025729	+	0	NA	intron (NR_130117, intron 10 of 10)	intron (NR_130117, intron 10 of 10)	38267	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.010909	0.421053	
chunk0028_35_1	chr10	82888116	82888453	+	0	NA	intron (NM_001010848, intron 4 of 8)	intron (NM_001010848, intron 4 of 8)	-655364	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.005935	0.352071	
chunk0198_344_1	chr8	140250959	140251283	+	0	NA	intron (NM_001160372, intron 16 of 22)	intron (NM_001160372, intron 16 of 22)	206641	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.009259	0.516923	
chunk0200_127_1	chr9	17423429	17423860	+	0	NA	intron (NM_017738, intron 18 of 25)	L1M1|LINE|L1	-155310	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.011601	0.493056	
chunk0138_442_1	chr4	45869266	45869641	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	254612	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.008000	0.337766	
chunk0211_424_1	chrX	129192508	129193016	+	0	NA	Intergenic	Intergenic	330743	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.001969	0.392927	
chunk0060_433_1	chr14	54343575	54343807	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-53264	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.017241	0.442060	
chunk0117_129_1	chr22	19178746	19179142	+	0	NA	promoter-TSS (NM_001256534)	promoter-TSS (NM_001256534)	-81	NM_005984	6576	Hs.111024	NM_005984	ENSG00000100075	SLC25A1	CMS23|CTP|D2L2AD|SEA|SLC20A3	solute carrier family 25 member 1	protein-coding	0.128788	0.775819	269(AGGTGCACTGTGTGCC,-,0.00)
chunk0177_90_1	chr7	21749547	21749840	+	0	NA	exon (NM_001277115, exon 53 of 82)	exon (NM_001277115, exon 53 of 82)	196231	NM_018719	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.017065	0.472789	
chunk0007_8_1	chr1	77196516	77197063	+	0	NA	intron (NM_005482, intron 3 of 10)	L1PA16|LINE|L1	22658	NM_005482	10026	Hs.178305	NM_005482	ENSG00000142892	PIGK	GPI8	phosphatidylinositol glycan anchor biosynthesis class K	protein-coding	0.003656	0.326642	
chunk0131_454_1	chr3	154106618	154107176	+	0	NA	intron (NR_037901, intron 2 of 3)	intron (NR_037901, intron 2 of 3)	-14106	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.010753	0.406082	
chunk0176_347_1	chr7	17777334	17777533	+	0	NA	Intergenic	L1ME2|LINE|L1	163075	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.000000	0.335000	
chunk0032_287_1	chr11	9460960	9461247	+	0	NA	promoter-TSS (NR_036539)	promoter-TSS (NR_036539)	138	NM_003442	7702	Hs.523471	NM_003442	ENSG00000166478	ZNF143	SBF|STAF|pHZ-1	zinc finger protein 143	protein-coding	0.101045	0.656250	
chunk0044_362_1	chr12	39238409	39238934	+	0	NA	Intergenic	Intergenic	204719	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.009524	0.372624	
chunk0163_165_1	chr6	11120681	11120996	+	0	NA	intron (NM_001135575, intron 1 of 1)	MIRc|SINE|MIR	-9000	NM_207582	405754	Hs.631996	NM_207582	ENSG00000244476	ERVFRD-1	ERVFRDE1|GLLL6191|HERV-FRD|HERV-W/FRD|UNQ6191|envFRD	endogenous retrovirus group FRD member 1, envelope	protein-coding	0.006349	0.386076	
chunk0135_65_1	chr3	185853699	185854065	+	0	NA	Intergenic	AluSz|SINE|Alu	-28843	NM_001007225	10644	Hs.35354	NM_006548	ENSG00000073792	IGF2BP2	IMP-2|IMP2|VICKZ2	insulin like growth factor 2 mRNA binding protein 2	protein-coding	0.010929	0.495913	
chunk0131_328_1	chr3	151121161	151121397	+	0	NA	intron (NM_053002, intron 2 of 42)	intron (NM_053002, intron 2 of 42)	34481	NM_053002	116931	Hs.744234	NM_053002	ENSG00000144893	MED12L	NOPAR|TNRC11L|TRALP|TRALPUSH	mediator complex subunit 12L	protein-coding	0.008475	0.316456	
chunk0017_112_1	chr1	205962579	205962895	+	0	NA	intron (NR_110983, intron 2 of 3)	intron (NR_110983, intron 2 of 3)	4812	NR_110982	103021295	Hs.741319	NR_110982		LOC103021295	-	uncharacterized LOC103021295	ncRNA	0.003165	0.539432	
chunk0013_409_1	chr1	173079280	173079587	+	0	NA	Intergenic	L1PA15|LINE|L1	-28470	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.006515	0.538961	
chunk0081_204_1	chr17	42413675	42413925	+	0	NA	intron (NM_012232, intron 1 of 1)	intron (NM_012232, intron 1 of 1)	9520	NM_012232	284119	Hs.437191	NM_012232	ENSG00000177469	CAVIN1	CAVIN|CGL4|FKSG13|PTRF|cavin-1	caveolae associated protein 1	protein-coding	0.004000	0.458167	
chunk0027_262_1	chr10	77287539	77288226	+	0	NA	intron (NM_001271518, intron 1 of 27)	intron (NM_001271518, intron 1 of 27)	-62990	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.002911	0.446221	195(AAGCACACCAAGTGCT,-,0.00),196(AGCACACCAAGTGCTC,+,0.00)
chunk0085_85_1	chr18	2385677	2385937	+	0	NA	Intergenic	L1ME1|LINE|L1	185696	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.003846	0.402299	
chunk0154_372_1	chr5	87686026	87686739	+	0	NA	Intergenic	Intergenic	-273349	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.000000	0.284314	
chunk0038_172_1	chr11	85137527	85137929	+	0	NA	intron (NM_001142699, intron 5 of 27)	intron (NM_001142699, intron 5 of 27)	-214307	NM_001300983	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.431762	
chunk0081_459_1	chr17	49373618	49374322	+	0	NA	intron (NR_110883, intron 3 of 4)	Tigger14a|DNA|TcMar-Tigger	-11497	NM_014897	22834	Hs.463375	NM_014897	ENSG00000198740	ZNF652	-	zinc finger protein 652	protein-coding	0.004261	0.414184	
chunk0013_254_1	chr1	169872509	169872708	+	0	NA	intron (NM_020423, intron 5 of 12)	THE1B-int|LTR|ERVL-MaLR	21351	NM_181093	57147	Hs.435560	NM_020423	ENSG00000000457	SCYL3	PACE-1|PACE1	SCY1 like pseudokinase 3	protein-coding	0.005025	0.560000	
chunk0006_284_1	chr1	70610888	70611252	+	0	NA	Intergenic	Intergenic	-95383	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.005495	0.350685	
chunk0067_286_1	chr15	47428014	47428491	+	0	NA	intron (NM_001198999, intron 2 of 19)	intron (NM_001198999, intron 2 of 19)	244046	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.006289	0.332636	
chunk0110_197_1	chr20	14820884	14821811	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	108171	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.009709	0.392241	
chunk0135_445_1	chr3	194094976	194095328	+	0	NA	Intergenic	L1ME4b|LINE|L1	-40990	NM_005524	3280	Hs.250666	NM_005524	ENSG00000114315	HES1	HES-1|HHL|HRY|bHLHb39	hes family bHLH transcription factor 1	protein-coding	0.017045	0.424929	
chunk0169_345_1	chr6	106517660	106518008	+	0	NA	intron (NM_001624, intron 1 of 19)	MIR3|SINE|MIR	5979	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.005747	0.401146	181(GAGCACATTTTGTTTC,-,0.00),182(AGCACATTTTGTTTCT,+,0.00)
chunk0105_69_1	chr2	183677742	183678127	+	0	NA	Intergenic	Intergenic	553579	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.002597	0.305699	175(TAGCTCACAGTGTTCT,-,0.00),176(AGCTCACAGTGTTCTG,+,0.00)
chunk0201_260_1	chr9	38362399	38363049	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-29940	NM_000692	219	Hs.436219	NM_000692	ENSG00000137124	ALDH1B1	ALDH5|ALDHX	aldehyde dehydrogenase 1 family member B1	protein-coding	0.024615	0.420891	
chunk0189_247_1	chr8	25010329	25010745	+	0	NA	Intergenic	Intergenic	-53668	NM_006158	4747	Hs.521461	NM_006158	ENSG00000277586	NEFL	CMT1F|CMT2E|CMTDIG|NF-L|NF68|NFL|PPP1R110	neurofilament light	protein-coding	0.014423	0.383693	148(AAGCACAGTTTGTTCC,-,0.00),149(AGCACAGTTTGTTCCT,+,0.00)
chunk0040_366_1	chr11	118907026	118907389	+	0	NA	intron (NM_182557, intron 3 of 7)	intron (NM_182557, intron 3 of 7)	-3501	NR_039713	100616376		NR_039713	ENSG00000264211	MIR4492	mir-4492	microRNA 4492	ncRNA	0.016529	0.593407	
chunk0040_377_1	chr11	119230481	119231173	+	0	NA	intron (NM_005188, intron 1 of 15)	L1MEd|LINE|L1	24551	NM_005188	867	Hs.504096	NM_005188	ENSG00000110395	CBL	C-CBL|CBL2|FRA11B|NSLL|RNF55	Cbl proto-oncogene	protein-coding	0.004335	0.357864	292(CTGGACTTTCTGTTCC,-,0.00),293(TGGACTTTCTGTTCCA,+,0.00)
chunk0189_365_1	chr8	27146337	27146667	+	0	NA	Intergenic	Intergenic	-97539	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.009091	0.323263	
chunk0150_80_1	chr5	32193406	32194106	+	0	NA	Intergenic	Intergenic	-19437	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.017143	0.449358	505(CGGCTCACTCTGTGCC,-,0.00),506(GGCTCACTCTGTGCCT,+,0.00)
chunk0205_413_1	chr9	114969096	114969636	+	0	NA	Intergenic	L2b|LINE|L2	-38771	NM_001252290	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.003704	0.390018	
chunk0094_452_1	chr2	11539299	11539997	+	0	NA	promoter-TSS (NM_148903)	promoter-TSS (NM_148903)	-306	NM_148903	9687	Hs.467733	NM_014668	ENSG00000196208	GREB1	-	growth regulating estrogen receptor binding 1	protein-coding	0.021490	0.526466	
chunk0154_234_1	chr5	80912513	80912714	+	0	NA	Intergenic	L1ME1|LINE|L1	-48076	NM_006909	5924	Hs.162129	NM_006909	ENSG00000113319	RASGRF2	GRF2|RAS-GRF2	Ras protein specific guanine nucleotide releasing factor 2	protein-coding	0.000000	0.381188	
chunk0074_271_1	chr16	28191332	28191852	+	0	NA	intron (NM_015171, intron 1 of 23)	MIR3|SINE|MIR	20326	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.005769	0.449136	218(GAGCACAGCAAGTCCA,-,0.00)
chunk0007_401_1	chr1	85530004	85530420	+	0	NA	intron (NM_001134445, intron 1 of 6)	MIR|SINE|MIR	48151	NM_001134445	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.007212	0.405276	
chunk0158_154_1	chr5	127549434	127550015	+	0	NA	intron (NM_001286808, intron 8 of 9)	MER58A|DNA|hAT-Charlie	32115	NM_130809	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.005164	0.350515	
chunk0179_315_1	chr7	50489748	50490023	+	0	NA	intron (NM_001082971, intron 9 of 14)	MER4B-int|LTR|ERV1	-39495	NM_001287494	63979	Hs.137516	NM_022116	ENSG00000132436	FIGNL1	-	fidgetin like 1	protein-coding	0.000000	0.271739	
chunk0034_354_1	chr11	35949935	35950533	+	0	NA	intron (NM_001304263, intron 1 of 4)	intron (NM_001304263, intron 1 of 4)	6253	NM_001304264	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.011706	0.427379	
chunk0047_13_1	chr12	65281425	65281624	+	0	NA	intron (NM_001193461, intron 1 of 6)	intron (NM_001193461, intron 1 of 6)	2537	NM_001193461	253827	Hs.339024	NM_198080	ENSG00000174099	MSRB3	DFNB74	methionine sulfoxide reductase B3	protein-coding	0.010050	0.440000	
chunk0207_199_1	chr9	131145249	131145827	+	0	NA	intron (NM_005085, intron 12 of 35)	L1ME3G|LINE|L1	19977	NM_005085	8021	Hs.654530	NM_005085	ENSG00000126883	NUP214	CAIN|CAN	nucleoporin 214	protein-coding	0.006920	0.421416	
chunk0129_400_1	chr3	126652664	126652993	+	0	NA	intron (NM_001173513, intron 1 of 14)	MER6|DNA|TcMar-Tigger	2296	NM_001173513	114112	Hs.477475	NM_052883	ENSG00000197763	TXNRD3	TGR|TR2|TR2IT1|TRXR3|TXNRD3IT1|TXNRD3NB|TXNRD3NT1	thioredoxin reductase 3	protein-coding	0.012158	0.442424	
chunk0115_104_1	chr21	22675643	22676500	+	0	NA	Intergenic	Intergenic	-403213	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.005834	0.341492	
chunk0169_276_1	chr6	105602573	105603183	+	0	NA	Intergenic	Intergenic	-199754	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.008197	0.335516	
chunk0088_197_1	chr18	47771729	47772056	+	0	NA	Intergenic	X7A_LINE|LINE|CR1	158707	NM_005901	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.006116	0.536585	
chunk0034_428_1	chr11	38585733	38586052	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	60464	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.012539	0.456250	152(GGTACTCAGTGTGCAT,+,0.00)
chunk0208_118_1	chrX	14398796	14399106	+	0	NA	Intergenic	Intergenic	-130347	NM_001171942	2742	Hs.2700	NM_002063	ENSG00000101958	GLRA2	GLR	glycine receptor alpha 2	protein-coding	0.006452	0.382637	
chunk0193_227_1	chr8	76616969	76617476	+	0	NA	intron (NR_024360, intron 2 of 3)	intron (NR_024360, intron 2 of 3)	-64058	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.003945	0.409449	103(TGGAACACATTGTTCT,-,0.00),104(GGAACACATTGTTCTC,+,0.00)
chunk0143_62_1	chr4	107929934	107930643	+	0	NA	intron (NR_125929, intron 1 of 6)	intron (NR_125929, intron 1 of 6)	-1273	NM_183075	113612	Hs.109087	NM_183075	ENSG00000155016	CYP2U1	P450TEC|SPG49|SPG56	cytochrome P450 family 2 subfamily U member 1	protein-coding	0.005642	0.321127	374(GAGAACAGAGTGGACT,-,0.00),375(AGAACAGAGTGGACTT,+,0.00)
chunk0066_346_1	chr15	37926097	37926296	+	0	NA	Intergenic	L1M3b|LINE|L1	-8411	NM_152453	145942	Hs.179646	NM_152453	ENSG00000166069	TMCO5A	TMCO5	transmembrane and coiled-coil domains 5A	protein-coding	0.000000	0.325000	
chunk0211_196_1	chrX	117644386	117644843	+	0	NA	Intergenic	Intergenic	329124	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.000000	0.393013	
chunk0212_72_1	chrY	11525185	11525424	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	896286	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.033473	0.408333	
chunk0191_284_1	chr8	53910367	53910825	+	0	NA	intron (NR_104579, intron 1 of 3)	L1ME1|LINE|L1	29724	NR_104578	8601	Hs.368733	NM_003702	ENSG00000147509	RGS20	RGSZ1|ZGAP1|g(z)GAP|gz-GAP	regulator of G protein signaling 20	protein-coding	0.010917	0.381264	
chunk0168_124_1	chr6	82082582	82082781	+	0	NA	Intergenic	Intergenic	165073	NM_001300906	25998	Hs.306425	NM_015525	ENSG00000005700	IBTK	BTBD26|BTKI	inhibitor of Bruton tyrosine kinase	protein-coding	0.005025	0.305000	22(AGTGCAATGTGTTCTT,+,0.00)
chunk0095_390_1	chr2	23927024	23927272	+	0	NA	promoter-TSS (NM_001242338)	promoter-TSS (NM_001242338)	-34	NM_001242338	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.137097	0.742972	
chunk0092_457_1	chr19	39149783	39150227	+	0	NA	intron (NM_001014834, intron 1 of 7)	L1MB4|LINE|L1	24225	NM_001014834	10298	Hs.20447	NM_005884	ENSG00000130669	PAK4	-	p21 (RAC1) activated kinase 4	protein-coding	0.006757	0.379775	
chunk0083_92_1	chr17	64342770	64343003	+	0	NA	intron (NM_000442, intron 13 of 15)	intron (NM_000442, intron 13 of 15)	47992	NM_000442	5175	Hs.376675	NM_000442	ENSG00000261371	PECAM1	CD31|CD31/EndoCAM|GPIIA'|PECA1|PECAM-1|endoCAM	platelet and endothelial cell adhesion molecule 1	protein-coding	0.004292	0.448718	
chunk0155_323_1	chr5	96756941	96757140	+	0	NA	intron (NM_173060, intron 19 of 28)	intron (NM_173060, intron 19 of 28)	13500	NR_104285	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.005025	0.480000	
chunk0073_175_1	chr16	8783427	8784344	+	0	NA	3' UTR (NM_000663, exon 16 of 16)	3' UTR (NM_000663, exon 16 of 16)	13763	NM_015421	25880	Hs.513330	NM_015421	ENSG00000184857	TMEM186	C16orf51	transmembrane protein 186	protein-coding	0.008724	0.425926	
chunk0041_129_1	chr11	125069075	125069341	+	0	NA	intron (NM_198277, intron 1 of 18)	MIRb|SINE|MIR	6091	NM_198277	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.007519	0.408240	
chunk0076_316_1	chr16	70561666	70561896	+	0	NA	exon (NM_012426, exon 17 of 26)	exon (NM_012426, exon 17 of 26)	-18114	NM_152456	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.030435	0.545455	
chunk0086_366_1	chr18	26034927	26035535	+	0	NA	intron (NM_005637, intron 7 of 9)	intron (NM_005637, intron 7 of 9)	55416	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.008224	0.379310	
chunk0102_379_1	chr2	154349545	154350102	+	0	NA	intron (NM_052917, intron 9 of 12)	intron (NM_052917, intron 9 of 12)	107615	NM_001256368									0.001795	0.403226	
chunk0066_275_1	chr15	35103541	35103972	+	0	NA	Intergenic	Intergenic	-115460	NM_014106	54989	Hs.744990	NM_014106	ENSG00000198146	ZNF770	PRO1914	zinc finger protein 770	protein-coding	0.002320	0.354167	
chunk0093_17_1	chr2	252886	253085	+	0	NA	intron (NR_104223, intron 4 of 11)	intron (NR_104223, intron 4 of 11)	3355	NM_001282687	26751	Hs.515951	NM_015677	ENSG00000035115	SH3YL1	RAY	SH3 and SYLF domain containing 1	protein-coding	0.005025	0.385000	
chunk0205_406_1	chr9	114779283	114779482	+	0	NA	Intergenic	Intergenic	13148	NM_001204344	9966	Hs.23349	NM_005118	ENSG00000181634	TNFSF15	TL1|TL1A|TNLG1B|VEGI|VEGI192A	TNF superfamily member 15	protein-coding	0.010050	0.450000	
chunk0152_366_1	chr5	64319487	64320428	+	0	NA	intron (NM_001113561, intron 5 of 7)	intron (NM_001113561, intron 5 of 7)	154113	NM_178532	285671	Hs.657843	NM_178532	ENSG00000164197	RNF180	RINES	ring finger protein 180	protein-coding	0.001063	0.388535	166(AAGTACATCATGTACC,-,0.00),167(AGTACATCATGTACCC,+,0.00)
chunk0152_377_1	chr5	64496772	64497140	+	0	NA	Intergenic	Intergenic	-8991	NM_001029875	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.002717	0.355014	
chunk0205_163_1	chr9	108625955	108626448	+	0	NA	Intergenic	Intergenic	229794	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.002028	0.453441	
chunk0173_65_1	chr6	142513733	142513932	+	0	NA	Intergenic	L1PB1|LINE|L1	124004	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.005025	0.365000	
chunk0212_13_1	chrY	8102863	8103372	+	0	NA	Intergenic	L1M2|LINE|L1	298193	NR_001551	83867	Hs.667616	NR_001551	ENSG00000237048	TTTY12	NCRNA00135|TTY11|TTY12	testis-specific transcript, Y-linked 12	ncRNA	0.001965	0.280392	
chunk0141_112_1	chr4	79652178	79653004	+	0	NA	Intergenic	Intergenic	159998	NR_038826	100506035	Hs.507664	NR_038826	ENSG00000250334	LINC00989	-	long intergenic non-protein coding RNA 989	ncRNA	0.004843	0.357920	
chunk0120_281_1	chr3	9615222	9615674	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-33985	NM_022485	64419	Hs.475382	NM_022485	ENSG00000163719	MTMR14	C3orf29	myotubularin related protein 14	protein-coding	0.013274	0.419426	
chunk0173_445_1	chr6	151658583	151658875	+	0	NA	Intergenic	MIRb|SINE|MIR	-31767	NM_001122742	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.000000	0.296928	
chunk0111_72_1	chr20	23090506	23091118	+	0	NA	Intergenic	Intergenic	-4472	NM_012072	22918	Hs.97199	NM_012072	ENSG00000125810	CD93	C1QR1|C1qR(P)|C1qRP|CDw93|ECSM3|MXRA4|dJ737E23.1	CD93 molecule	protein-coding	0.014706	0.406199	
chunk0056_133_1	chr13	83223969	83224250	+	0	NA	Intergenic	L1MC1|LINE|L1	658284	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.007117	0.382979	
chunk0164_261_1	chr6	23565997	23566765	+	0	NA	Intergenic	MIR3|SINE|MIR	-559805	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.011719	0.430429	328(GAGAACATCTAGTTCC,-,0.00),329(AGAACATCTAGTTCCA,+,0.00)
chunk0199_125_1	chr9	3702446	3702745	+	0	NA	Intergenic	Intergenic	34509	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.003344	0.410000	
chunk0085_23_1	chr18	387046	387373	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	113520	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.015291	0.411585	
chunk0061_238_1	chr14	60760618	60760997	+	0	NA	intron (NM_002431, intron 1 of 7)	intron (NM_002431, intron 1 of 7)	26066	NM_002431	4331	Hs.509523	NM_002431	ENSG00000020426	MNAT1	CAP35|MAT1|RNF66|TFB3	MNAT1 component of CDK activating kinase	protein-coding	0.002639	0.371053	168(AAGTACATTGTGCCCT,-,0.00),169(AGTACATTGTGCCCTC,+,0.00)
chunk0179_73_1	chr7	44195367	44195606	+	0	NA	Intergenic	AluSz6|SINE|Alu	-5493	NM_006555	10652	Hs.520794	NM_006555	ENSG00000106636	YKT6	-	YKT6 v-SNARE homolog	protein-coding	0.012552	0.475000	
chunk0079_266_1	chr17	16204589	16204883	+	0	NA	intron (NM_006311, intron 1 of 45)	MIR|SINE|MIR	-10097	NM_001190440	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.003401	0.338983	
chunk0079_277_1	chr17	16429390	16429614	+	0	NA	intron (NM_016113, intron 10 of 14)	L2a|LINE|L2	-9485	NR_027162	125144	Hs.368934	NM_152350	ENSG00000175061	SNHG29	C17orf45|C17orf76-AS1|FAM211A-AS1|LRRC75A-AS1|NCRNA00188|TSAP19	small nucleolar RNA host gene 29	ncRNA	0.000000	0.435556	
chunk0145_191_1	chr4	147824772	147824987	+	0	NA	intron (NM_024605, intron 3 of 22)	MIR|SINE|MIR	42284	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.009302	0.453704	
chunk0101_126_1	chr2	127128658	127128942	+	0	NA	Intergenic	Intergenic	-21473	NM_139351	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.017606	0.491228	
chunk0125_159_1	chr3	66491270	66491867	+	0	NA	intron (NM_015541, intron 1 of 18)	intron (NM_015541, intron 1 of 18)	8853	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.001675	0.317726	
chunk0182_133_1	chr7	94543033	94543252	+	0	NA	intron (NM_022900, intron 10 of 17)	intron (NM_022900, intron 10 of 17)	33284	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.009132	0.359091	
chunk0042_367_1	chr12	10409275	10409854	+	0	NA	exon (NM_013431, exon 1 of 4)	exon (NM_013431, exon 1 of 4)	193	NM_013431	8302	Hs.721094	NM_013431	ENSG00000183542	KLRC4	NKG2-F|NKG2F	killer cell lectin like receptor C4	protein-coding	0.001727	0.363793	
chunk0199_283_1	chr9	6516626	6517385	+	0	NA	Intergenic	L1MD2|LINE|L1	103854	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.005270	0.381579	
chunk0089_216_1	chr18	61204107	61204567	+	0	NA	Intergenic	HAL1|LINE|L1	-286205	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.002174	0.301518	
chunk0163_415_1	chr6	17045700	17046139	+	0	NA	Intergenic	Intergenic	-56339	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.006834	0.443182	
chunk0097_273_1	chr2	54946557	54946974	+	0	NA	intron (NM_001039753, intron 27 of 40)	intron (NM_001039753, intron 27 of 40)	63569	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.021583	0.399522	159(GTGAACATCCAGTACT,-,0.00)
chunk0140_215_1	chr4	70805049	70805287	+	0	NA	intron (NM_001037442, intron 17 of 17)	MIR|SINE|MIR	34335	NM_001098477	2926	Hs.309763	NM_002092	ENSG00000132463	GRSF1	-	G-rich RNA sequence binding factor 1	protein-coding	0.012605	0.422594	
chunk0032_90_1	chr11	3000274	3000795	+	0	NA	TTS (NM_001751)	TTS (NM_001751)	-8157	NM_005969	4676	Hs.731784	NM_005969	ENSG00000205531	NAP1L4	NAP1L4b|NAP2|NAP2L|hNAP2	nucleosome assembly protein 1 like 4	protein-coding	0.023033	0.574713	
chunk0184_241_1	chr7	117672329	117673111	+	0	NA	Intergenic	Intergenic	192757	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.006394	0.376756	
chunk0203_355_1	chr9	89874470	89874746	+	0	NA	Intergenic	Intergenic	-94808	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.018116	0.588448	
chunk0201_379_1	chr9	68846349	68846777	+	0	NA	intron (NM_003558, intron 4 of 15)	intron (NM_003558, intron 4 of 15)	66515	NM_138333	116224	Hs.655572	NM_138333	ENSG00000187866	FAM122A	C9orf42	family with sequence similarity 122A	protein-coding	0.004673	0.370629	
chunk0017_462_1	chr1	214549021	214549325	+	0	NA	intron (NM_005401, intron 1 of 18)	intron (NM_005401, intron 1 of 18)	2508	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.003289	0.472131	
chunk0023_209_1	chr10	25367689	25368009	+	0	NA	intron (NM_020752, intron 2 of 10)	L1ME3|LINE|L1	-191573	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.000000	0.380062	
chunk0046_5_1	chr12	54003005	54003501	+	0	NA	TTS (NM_006897)	TTS (NM_006897)	3160	NM_006897	3225	Hs.658823	NM_006897	ENSG00000180806	HOXC9	HOX3|HOX3B	homeobox C9	protein-coding	0.036290	0.527163	213(CTGTACATAGTGTTCC,-,0.00),214(TGTACATAGTGTTCCC,+,0.00)
chunk0042_245_1	chr12	6375880	6376682	+	0	NA	promoter-TSS (NM_001038)	promoter-TSS (NM_001038)	-542	NM_001038	6337	Hs.591047	NM_001038	ENSG00000111319	SCNN1A	BESC2|ENaCa|ENaCalpha|LIDLS3|SCNEA|SCNN1	sodium channel epithelial 1 alpha subunit	protein-coding	0.018703	0.592777	437(TAGGACATTCTGTTCT,-,0.00),438(AGGACATTCTGTTCTT,+,0.00)
chunk0177_287_1	chr7	25718516	25718988	+	0	NA	Intergenic	Intergenic	231234	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.008475	0.424947	
chunk0193_44_1	chr8	71658666	71658907	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-184337	NR_033652	100132891	Hs.137674	NR_033651	ENSG00000235531	MSC-AS1	-	MSC antisense RNA 1	ncRNA	0.020747	0.466942	
chunk0013_382_1	chr1	172547040	172547283	+	0	NA	intron (NM_014283, intron 1 of 23)	L1ME2|LINE|L1	14043	NM_001282751	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.000000	0.352459	
chunk0006_352_1	chr1	72734097	72734512	+	0	NA	Intergenic	Intergenic	-451710	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.002410	0.367788	
chunk0111_13_1	chr20	21886998	21887559	+	0	NA	Intergenic	Intergenic	-166812	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.001783	0.402135	
chunk0198_401_1	chr8	141796809	141797087	+	0	NA	Intergenic	Intergenic	-10635	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.014388	0.537634	
chunk0204_149_1	chr9	95721082	95721834	+	0	NA	Intergenic	Intergenic	-154160	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.007979	0.378486	
chunk0065_59_1	chr15	22931000	22931445	+	0	NA	intron (NM_001287810, intron 12 of 31)	intron (NM_001287810, intron 12 of 31)	-13909	NM_001033028	23191	Hs.26704	NM_014608	ENSG00000273749	CYFIP1	P140SRA-1|SHYC|SRA-1|SRA1	cytoplasmic FMR1 interacting protein 1	protein-coding	0.011236	0.556054	107(GGGGACAGGGTGCTCA,-,0.00),108(GGGACAGGGTGCTCAT,+,0.00)
chunk0078_181_1	chr17	4679659	4679944	+	0	NA	intron (NM_014389, intron 5 of 16)	intron (NM_014389, intron 5 of 16)	-24429	NR_103482	101559451	Hs.634966	NR_103482	ENSG00000244184	LOC101559451	-	uncharacterized LOC101559451	ncRNA	0.014035	0.416084	
chunk0174_248_1	chr6	161004699	161004967	+	0	NA	intron (NM_006724, intron 1 of 25)	MER92-int|LTR|ERV1	13106	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.011194	0.312268	
chunk0192_123_1	chr8	61782668	61783385	+	0	NA	Intergenic	Intergenic	68238	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.006974	0.363510	
chunk0045_255_1	chr12	49370418	49370846	+	0	NA	intron (NM_001293286, intron 1 of 12)	intron (NM_001293286, intron 1 of 12)	3727	NR_120663	65244	Hs.654826	NM_023071	ENSG00000123352	SPATS2	Nbla00526|P59SCR|SCR59|SPATA10	spermatogenesis associated serine rich 2	protein-coding	0.009346	0.440559	
chunk0052_190_1	chr13	24670918	24671187	+	0	NA	Intergenic	Intergenic	-9359	NM_001185085	479	Hs.147111	NM_001676	ENSG00000075673	ATP12A	ATP1AL1|HK	ATPase H+/K+ transporting non-gastric alpha2 subunit	protein-coding	0.014870	0.492593	
chunk0209_30_1	chrX	36040420	36040850	+	0	NA	intron (NM_001304548, intron 25 of 63)	L1M5|LINE|L1	120901	NM_152632	286464	Hs.376425	NM_152632	ENSG00000165164	CFAP47	CHDC2|CXorf22|CXorf30|CXorf59	cilia and flagella associated protein 47	protein-coding	0.004651	0.250580	
chunk0047_36_1	chr12	66631146	66631717	+	0	NA	intron (NM_021150, intron 1 of 23)	intron (NM_021150, intron 1 of 23)	47714	NM_021150	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.010508	0.381119	
chunk0076_436_1	chr16	73328790	73329079	+	0	NA	Intergenic	Intergenic	-57871	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.006920	0.427586	234(AGGTACATTCAGTTCA,-,0.00),235(GGTACATTCAGTTCAG,+,0.00)
chunk0098_51_1	chr2	66538161	66538556	+	0	NA	intron (NM_002398, intron 8 of 12)	MIR|SINE|MIR	-35672	NR_110156	100507073	Hs.667940	NR_110156	ENSG00000232046	LINC01798	-	long intergenic non-protein coding RNA 1798	ncRNA	0.005063	0.345960	
chunk0043_48_1	chr12	13464539	13465212	+	0	NA	Intergenic	Intergenic	-88130	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.005944	0.354599	
chunk0192_285_1	chr8	66406001	66406501	+	0	NA	Intergenic	Intergenic	22726	NR_040434	100505676	Hs.121613	NM_001242759	ENSG00000246145	RRS1-AS1	-	RRS1 antisense RNA 1 (head to head)	ncRNA	0.004000	0.427146	
chunk0059_206_1	chr14	33490427	33491010	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-218219	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.012007	0.470890	
chunk0186_190_1	chr7	139724126	139724378	+	0	NA	intron (NM_001113239, intron 1 of 14)	intron (NM_001113239, intron 1 of 14)	53642	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.000000	0.320158	
chunk0014_11_1	chr1	174365555	174365754	+	0	NA	intron (NM_014857, intron 11 of 20)	L1M1|LINE|L1	-82420	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.010050	0.535000	
chunk0018_373_1	chr1	222010248	222010673	+	0	NA	Intergenic	Intergenic	-169794	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.002353	0.424883	
chunk0027_174_1	chr10	75021748	75022617	+	0	NA	exon (NM_012330, exon 16 of 18)	exon (NM_012330, exon 16 of 18)	36332	NM_001003892	338599	Hs.535090	NM_001003892	ENSG00000188716	DUPD1	DUSP27|FMDSP	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.016110	0.470115	
chunk0095_22_1	chr2	12683430	12683928	+	0	NA	Intergenic	Intergenic	-33193	NM_021643	28951	Hs.467751	NM_021643	ENSG00000071575	TRIB2	C5FW|GS3955|TRB2	tribbles pseudokinase 2	protein-coding	0.008032	0.350701	
chunk0088_188_1	chr18	47519203	47519945	+	0	NA	Intergenic	L2c|LINE|L2	139078	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.006739	0.441454	
chunk0038_264_1	chr11	89555615	89556119	+	0	NA	intron (NM_001143837, intron 1 of 20)	intron (NM_001143837, intron 1 of 20)	33744	NM_001143837	50507	Hs.371036	NM_016931	ENSG00000086991	NOX4	KOX|KOX-1|RENOX	NADPH oxidase 4	protein-coding	0.003968	0.366337	
chunk0049_243_1	chr12	93570784	93571236	+	0	NA	promoter-TSS (NM_001270469)	promoter-TSS (NM_001270469)	29	NM_001270468	8835	Hs.485572	NM_003877	ENSG00000120833	SOCS2	CIS2|Cish2|SOCS-2|SSI-2|SSI2|STATI2	suppressor of cytokine signaling 2	protein-coding	0.117257	0.710817	
chunk0120_122_1	chr3	4772258	4772556	+	0	NA	intron (NM_002222, intron 42 of 57)	intron (NM_002222, intron 42 of 57)	-20817	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.006711	0.481605	
chunk0172_87_1	chr6	134599229	134599459	+	0	NA	Intergenic	Intergenic	-59339	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.008696	0.463203	
chunk0083_399_1	chr17	71926234	71926495	+	0	NA	Intergenic	Intergenic	99615	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.000000	0.366412	
chunk0040_136_1	chr11	112564254	112564904	+	0	NA	Intergenic	Intergenic	-8777	NR_104155	387810	Hs.512255	NR_104155	ENSG00000255484	LINC02764	-	long intergenic non-protein coding RNA 2764	ncRNA	0.004615	0.491551	
chunk0180_373_1	chr7	74098316	74098609	+	0	NA	intron (NM_002314, intron 4 of 15)	intron (NM_002314, intron 4 of 15)	5306	NM_001204426	3984	Hs.647035	NM_002314	ENSG00000106683	LIMK1	LIMK|LIMK-1	LIM domain kinase 1	protein-coding	0.020478	0.517007	194(GGCACGCACAGTTCCT,+,0.00)
chunk0002_258_1	chr1	21319571	21319899	+	0	NA	intron (NM_001113348, intron 1 of 18)	intron (NM_001113348, intron 1 of 18)	25806	NM_001113348	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.018293	0.610942	
chunk0195_177_1	chr8	96235313	96235617	+	0	NA	intron (NM_001199975, intron 1 of 4)	intron (NM_001199975, intron 1 of 4)	169	NM_006294	7381	Hs.131255	NM_006294	ENSG00000156467	UQCRB	MC3DN3|QCR7|QP-C|QPC|UQBC|UQBP|UQCR6|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding	0.059211	0.547541	
chunk0103_354_1	chr2	168142624	168143230	+	0	NA	intron (NM_013233, intron 5 of 17)	intron (NM_013233, intron 5 of 17)	104668	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.003300	0.357496	277(AAGTACATAGTGTGCT,-,0.00),278(AGTACATAGTGTGCTT,+,0.00)
chunk0064_302_1	chr14	95511778	95511977	+	0	NA	Intergenic	Intergenic	21752	NR_003002	677768	Hs.448753	NR_003002	ENSG00000252481	SCARNA13	U93	small Cajal body-specific RNA 13	ncRNA	0.025126	0.535000	
chunk0116_384_1	chr21	42259056	42259336	+	0	NA	intron (NM_207627, intron 3 of 15)	intron (NM_207627, intron 3 of 15)	39298	NM_207174	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.014286	0.537367	
chunk0110_188_1	chr20	14710038	14710437	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	155853	NR_104193	140848	Hs.570367	NR_104193	ENSG00000227927	MACROD2-IT1	C20orf68|NCRNA00227|bA467D7.4	MACROD2 intronic transcript 1	ncRNA	0.005013	0.372500	211(AAACACAGGATGTACT,-,0.00),212(AACACAGGATGTACTT,+,0.00)
chunk0195_166_1	chr8	95843522	95843970	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	104602	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.008929	0.380846	
chunk0067_61_1	chr15	40957793	40958511	+	0	NA	Intergenic	L2b|LINE|L2	4714	NM_001142776	79094	Hs.155569	NM_024111	ENSG00000128965	CHAC1	-	ChaC glutathione specific gamma-glutamylcyclotransferase 1	protein-coding	0.015320	0.588317	438(GGAACAACACGTGCCT,+,0.00),478(TGGAACAGAGTGGCCC,-,0.00),479(GGAACAGAGTGGCCCG,+,0.00)
chunk0126_452_1	chr3	87240723	87241050	+	0	NA	intron (NM_014043, intron 2 of 5)	intron (NM_014043, intron 2 of 5)	13623	NM_014043	25978	Hs.476930	NM_014043	ENSG00000083937	CHMP2B	ALS17|CHMP2.5|DMT1|VPS2-2|VPS2B	charged multivesicular body protein 2B	protein-coding	0.009174	0.335366	
chunk0136_91_1	chr4	2614898	2615505	+	0	NA	Intergenic	HY3|scRNA|scRNA	-10231	NM_003704	8603	Hs.652364	NM_003704	ENSG00000125386	FAM193A	C4orf8|RES4-22	family with sequence similarity 193 member A	protein-coding	0.000000	0.310855	
chunk0122_149_1	chr3	32095503	32095864	+	0	NA	Intergenic	L1MC4|LINE|L1	-10828	NM_015141	23171	Hs.82432	NM_015141	ENSG00000152642	GPD1L	GPD1-L	glycerol-3-phosphate dehydrogenase 1 like	protein-coding	0.008310	0.342541	
chunk0075_225_1	chr16	52862841	52863548	+	0	NA	Intergenic	Intergenic	-191839	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.009901	0.439266	296(GAGAACAAGTTGTTCT,-,0.00),297(AGAACAAGTTGTTCTG,+,0.00)
chunk0020_119_1	chr1	233373149	233373836	+	0	NA	intron (NM_032435, intron 6 of 9)	intron (NM_032435, intron 6 of 9)	45724	NM_032435	84451	Hs.547779	NM_032435	ENSG00000143674	MAP3K21	MLK4|dJ862P8.3	mitogen-activated protein kinase kinase kinase 21	protein-coding	0.013100	0.501453	
chunk0172_28_1	chr6	133083633	133084050	+	0	NA	Intergenic	Intergenic	-4239	NR_026969	285735	Hs.407549	NM_001037231		LINC00326	NCRNA00326	long intergenic non-protein coding RNA 326	ncRNA	0.002398	0.375598	
chunk0158_321_1	chr5	132830686	132830898	+	0	NA	5' UTR (NM_001172700, exon 1 of 10)	5' UTR (NM_001172700, exon 1 of 10)	106	NM_001172700	134549	Hs.519574	NM_133456	ENSG00000164403	SHROOM1	APXL2	shroom family member 1	protein-coding	0.136792	0.769953	99(GTGGACAGTGCGTTCC,-,0.00),100(TGGACAGTGCGTTCCC,+,0.00)
chunk0034_121_1	chr11	28238945	28239224	+	0	NA	intron (NM_001113528, intron 4 of 6)	L2a|LINE|L2	130833	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.000000	0.367857	
chunk0210_37_1	chrX	67949168	67949804	+	0	NA	Intergenic	AluJo|SINE|Alu	380645	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.006289	0.357928	
chunk0212_97_1	chrY	13243173	13243461	+	0	NA	Intergenic	L1MA4A|LINE|L1	237353	NR_047606	7404	Hs.115277	NM_007125	ENSG00000183878	UTY	KDM6AL|KDM6C|UTY1	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	protein-coding	0.006944	0.328720	
chunk0209_286_1	chrX	47619757	47620081	+	0	NA	promoter-TSS (NM_133499)	promoter-TSS (NM_133499)	-62	NM_006950	6853	Hs.225936	NM_006950	ENSG00000008056	SYN1	SYN1a|SYN1b|SYNI	synapsin I	protein-coding	0.148148	0.763077	
chunk0097_45_1	chr2	43269728	43270116	+	0	NA	intron (NR_073394, intron 34 of 35)	intron (NR_073394, intron 34 of 35)	42711	NR_027251	100129726	Hs.194480	NM_178529	ENSG00000279873	LINC01126	-	long intergenic non-protein coding RNA 1126	ncRNA	0.007732	0.542416	211(CAGAACACTTAGTTCT,-,0.00),212(AGAACACTTAGTTCTT,+,0.00)
chunk0150_137_1	chr5	33487045	33487787	+	0	NA	Intergenic	LTR24C|LTR|ERV1	46640	NR_047676	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.005391	0.382234	348(GAAAACAGGCTGTACA,-,0.00),349(AAAACAGGCTGTACAG,+,0.00)
chunk0032_298_1	chr11	9646160	9646892	+	0	NA	Intergenic	Intergenic	-17551	NM_001297714	23075	Hs.153026	NM_015055	ENSG00000133789	SWAP70	HSPC321|SWAP-70	switching B cell complex subunit SWAP70	protein-coding	0.006831	0.455662	
chunk0093_93_1	chr19	42302317	42302762	+	0	NA	5' UTR (NM_001145939, exon 1 of 6)	5' UTR (NM_001145939, exon 1 of 6)	105	NM_002573	5050	Hs.466831	NM_002573	ENSG00000079462	PAFAH1B3	PAFAHG	platelet activating factor acetylhydrolase 1b catalytic subunit 3	protein-coding	0.094382	0.672646	
chunk0100_139_1	chr2	108813956	108814321	+	0	NA	intron (NR_130121, intron 9 of 13)	L1ME2z|LINE|L1	27388	NM_001303106	165055	Hs.362702	NM_144978	ENSG00000163006	CCDC138	-	coiled-coil domain containing 138	protein-coding	0.005479	0.357923	
chunk0124_126_1	chr3	54322121	54322927	+	0	NA	intron (NM_018398, intron 3 of 37)	MIR|SINE|MIR	199858	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.012407	0.442379	
chunk0044_132_1	chr12	29367758	29368108	+	0	NA	intron (NM_016570, intron 4 of 13)	intron (NM_016570, intron 4 of 13)	13277	NM_016570	51290	Hs.339453	NM_016570	ENSG00000087502	ERGIC2	CDA14|Erv41|PTX1|cd002	ERGIC and golgi 2	protein-coding	0.005714	0.307692	
chunk0059_38_1	chr14	29906670	29907226	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	20745	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005396	0.378815	
chunk0129_55_1	chr3	117482907	117483298	+	0	NA	Intergenic	Intergenic	561671	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002558	0.262755	
chunk0135_74_1	chr3	185921992	185922470	+	0	NA	intron (NM_001243879, intron 3 of 7)	intron (NM_001243879, intron 3 of 7)	15905	NM_001243879	6434	Hs.533122	NM_004593	ENSG00000136527	TRA2B	Htra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B	transformer 2 beta homolog	protein-coding	0.008368	0.369520	
chunk0060_306_1	chr14	50939262	50939603	+	0	NA	intron (NM_002863, intron 1 of 19)	intron (NM_002863, intron 1 of 19)	5098	NM_002863	5836	Hs.282417	NM_002863	ENSG00000100504	PYGL	GSD6	glycogen phosphorylase L	protein-coding	0.008798	0.380117	
chunk0146_81_1	chr4	158020249	158020536	+	0	NA	Intergenic	Intergenic	152174	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.378472	
chunk0048_252_1	chr12	81645938	81646137	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-47666	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.005025	0.490000	
chunk0019_3_1	chr1	223182137	223182958	+	0	NA	Intergenic	L1MD1|LINE|L1	-39265	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.008526	0.374696	
chunk0037_313_1	chr11	76793425	76793939	+	0	NA	intron (NM_015516, intron 1 of 1)	intron (NM_015516, intron 1 of 1)	10441	NM_015516	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.007782	0.522330	288(TGGAACACTCTGTCCT,-,0.00),289(GGAACACTCTGTCCTG,+,0.00)
chunk0114_294_1	chr21	16741545	16742541	+	0	NA	Intergenic	Intergenic	151806	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.004016	0.415246	310(GGAACAGGCAGACCCT,+,0.00)
chunk0078_222_1	chr17	6445627	6445948	+	0	NA	intron (NM_019013, intron 2 of 5)	L2c|LINE|L2	1372	NM_001195228	54478	Hs.592116	NM_019013	ENSG00000129195	PIMREG	CATS|FAM64A|RCS1	PICALM interacting mitotic regulator	protein-coding	0.006231	0.493789	
chunk0024_26_1	chr10	33155965	33156545	+	0	NA	Intergenic	Intergenic	178650	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.015517	0.411360	
chunk0157_37_1	chr5	115784961	115785529	+	0	NA	Intergenic	Intergenic	31463	NM_001801	1036	Hs.442378	NM_001801	ENSG00000129596	CDO1	CDO-I	cysteine dioxygenase type 1	protein-coding	0.005282	0.321617	
chunk0161_402_1	chr5	177301686	177302106	+	0	NA	intron (NM_001031677, intron 7 of 7)	intron (NM_001031677, intron 7 of 7)	1848	NR_109789	53917	Hs.16258	NM_130781	ENSG00000169228	RAB24	-	RAB24, member RAS oncogene family	protein-coding	0.011905	0.553444	
chunk0026_1_1	chr10	60331167	60331366	+	0	NA	intron (NM_001204403, intron 2 of 43)	L1PA7|LINE|L1	58610	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005025	0.295000	
chunk0121_183_1	chr3	20091235	20091671	+	0	NA	intron (NM_003884, intron 2 of 17)	L1MA5|LINE|L1	-46112	NR_036086	100422901		NR_036086	ENSG00000266745	MIR3135A	MIR3135|hsa-mir-3135a	microRNA 3135a	ncRNA	0.002294	0.286041	
chunk0041_244_1	chr11	128607758	128608382	+	0	NA	Intergenic	Intergenic	-20512	NM_001143820	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.009615	0.454400	
chunk0188_269_1	chr8	14962618	14963087	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	-109342	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.006397	0.353191	242(GAGAACAGTTTGTTCT,-,0.00),243(AGAACAGTTTGTTCTT,+,0.00)
chunk0095_447_1	chr2	25607578	25608096	+	0	NA	intron (NM_001256303, intron 4 of 19)	intron (NM_001256303, intron 4 of 19)	42385	NM_001256308	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.007722	0.373796	
chunk0172_306_1	chr6	138157010	138157346	+	0	NA	Intergenic	Intergenic	-4738	NM_020340	57221	Hs.194408	NM_020340	ENSG00000112379	ARFGEF3	A7322|BIG3|C6orf92|KIAA1244|PPP1R33|dJ171N11.1	ARFGEF family member 3	protein-coding	0.000000	0.433234	144(TAGAACACAATGTGCC,-,0.00),145(AGAACACAATGTGCCT,+,0.00)
chunk0199_60_1	chr9	2178091	2178909	+	0	NA	intron (NM_003070, intron 29 of 33)	intron (NM_003070, intron 29 of 33)	20044	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.013447	0.426129	
chunk0149_207_1	chr5	21688584	21688895	+	0	NA	Intergenic	THE1A|LTR|ERVL-MaLR	-195715	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.009646	0.419872	
chunk0121_225_1	chr3	21843740	21844130	+	0	NA	Intergenic	Intergenic	-92611	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.005128	0.347826	
chunk0084_278_1	chr17	79829347	79829936	+	0	NA	Intergenic	Intergenic	9773	NM_003655	8535	Hs.405046	NM_003655	ENSG00000141582	CBX4	NBP16|PC2	chromobox 4	protein-coding	0.006791	0.498305	
chunk0162_343_1	chr6	6966066	6966504	+	0	NA	Intergenic	Intergenic	-141312	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.004566	0.371298	109(CTGAACATACTGTTCT,-,0.00),110(TGAACATACTGTTCTC,+,0.00)
chunk0051_214_1	chr12	116592323	116592811	+	0	NA	Intergenic	Intergenic	33186	NM_001085481	643246	Hs.356061	NM_001085481	ENSG00000258102	MAP1LC3B2	ATG8G	microtubule associated protein 1 light chain 3 beta 2	protein-coding	0.020492	0.525562	
chunk0177_298_1	chr7	25913936	25914213	+	0	NA	Intergenic	Intergenic	35912	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.007220	0.374101	178(CAGCTCAGCATGTTCT,-,0.00),179(AGCTCAGCATGTTCTC,+,0.00)
chunk0062_86_1	chr14	67940772	67941220	+	0	NA	intron (NM_133509, intron 7 of 10)	UCON97|DNA|DNA	121217	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.008929	0.369710	
chunk0125_280_1	chr3	69531401	69531784	+	0	NA	Intergenic	Intergenic	-145288	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.005222	0.354167	
chunk0047_97_1	chr12	68686826	68687237	+	0	NA	promoter-TSS (NM_020401)	promoter-TSS (NM_020401)	80	NM_020401	57122	Hs.524574	NM_020401	ENSG00000111581	NUP107	NPHS11|NUP84|ODG6|ODG6; GAMOS7	nucleoporin 107	protein-coding	0.051095	0.555825	
chunk0060_313_1	chr14	51182476	51182675	+	0	NA	Intergenic	Intergenic	-57593	NM_030755	81542	Hs.125221	NM_030755	ENSG00000139921	TMX1	PDIA11|TMX|TXNDC|TXNDC1	thioredoxin related transmembrane protein 1	protein-coding	0.015075	0.380000	
chunk0187_67_1	chr8	2029432	2029790	+	0	NA	Intergenic	(TGTA)n|Simple_repeat|Simple_repeat	-15432	NM_003970	9172	Hs.443683	NM_003970	ENSG00000036448	MYOM2	TTNAP	myomesin 2	protein-coding	0.013966	0.415042	
chunk0103_282_1	chr2	165952709	165953209	+	0	NA	intron (NM_024753, intron 1 of 28)	intron (NM_024753, intron 1 of 28)	879	NM_024753	79809	Hs.310672	NM_024753	ENSG00000123607	TTC21B	ATD4|IFT139|IFT139B|JBTS11|NPHP12|Nbla10696|SRTD4|THM1	tetratricopeptide repeat domain 21B	protein-coding	0.008000	0.371257	
chunk0116_252_1	chr21	38805782	38805981	+	0	NA	promoter-TSS (NM_005239)	promoter-TSS (NM_005239)	50	NM_005239	2114	Hs.644231	NM_005239	ENSG00000157557	ETS2	ETS2IT1	ETS proto-oncogene 2, transcription factor	protein-coding	0.065327	0.665000	
chunk0018_81_1	chr1	217334298	217334509	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	-196648	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.004739	0.438679	157(GGGGCCACTGTGTTCC,-,0.00),158(GGGCCACTGTGTTCCC,+,0.00)
chunk0212_425_1	chrX	153209286	153209821	+	0	NA	Intergenic	Intergenic	30269	NM_004988	4100	Hs.72879	NM_004988	ENSG00000198681	MAGEA1	CT1.1|MAGE1	MAGE family member A1	protein-coding	0.005607	0.330224	245(TAGGACACAGTGTACT,-,0.00),246(AGGACACAGTGTACTT,+,0.00)
chunk0042_137_1	chr12	3802662	3803117	+	0	NA	Intergenic	MIRb|SINE|MIR	-49689	NM_001144958	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.010989	0.449561	
chunk0115_348_1	chr21	29222714	29222956	+	0	NA	intron (NR_027072, intron 1 of 1)	intron (NR_027072, intron 1 of 1)	29341	NR_027072	193629	Hs.720711	NM_138968	ENSG00000215533	LINC00189	C21orf109|NCRNA00189	long intergenic non-protein coding RNA 189	ncRNA	0.020661	0.526749	
chunk0127_301_1	chr3	98275173	98275494	+	0	NA	Intergenic	LTR28C|LTR|ERV1	-7555	NM_001005482	79310	Hs.554711	NM_001005482	ENSG00000197938	OR5H2	OR3-10	olfactory receptor family 5 subfamily H member 2	protein-coding	0.006231	0.565217	
chunk0170_86_1	chr6	110089363	110089604	+	0	NA	Intergenic	L1MEg|LINE|L1	90521	NM_001024935	8936	Hs.75850	NM_003931	ENSG00000112290	WASF1	SCAR1|WAVE|WAVE1	WASP family member 1	protein-coding	0.000000	0.318182	
chunk0089_68_1	chr18	58201399	58202060	+	0	NA	intron (NM_001144970, intron 1 of 28)	L1MC5a|LINE|L1	6339	NM_001144970	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.010590	0.371601	393(TGGTACATACTGTTCT,-,0.00),394(GGTACATACTGTTCTG,+,0.00)
chunk0070_343_1	chr15	75862940	75863171	+	0	NA	intron (NM_001145335, intron 3 of 12)	HAL1|LINE|L1	19011	NM_001145335	92912	Hs.23033	NM_173469	ENSG00000140367	UBE2Q2	-	ubiquitin conjugating enzyme E2 Q2	protein-coding	0.000000	0.431034	119(GAGAACAGTGTGTTTC,-,0.00),120(AGAACAGTGTGTTTCA,+,0.00)
chunk0182_363_1	chr7	99919273	99919479	+	0	NA	exon (NM_033017, exon 1 of 7)	exon (NM_033017, exon 1 of 7)	224	NM_033091	89122	Hs.50749	NM_033017	ENSG00000146833	TRIM4	RNF87	tripartite motif containing 4	protein-coding	0.092233	0.685990	
chunk0033_183_1	chr11	15970388	15971175	+	0	NA	3' UTR (NM_017508, exon 15 of 15)	3' UTR (NM_017508, exon 15 of 15)	-1160	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.003812	0.413706	
chunk0105_271_1	chr2	189483923	189484410	+	0	NA	Intergenic	Intergenic	42733	NM_001303096	84128	Hs.399984	NM_032168	ENSG00000115368	WDR75	NET16|UTP17	WD repeat domain 75	protein-coding	0.012320	0.532787	209(AGGACAAGGAGTCCAT,+,0.00)
chunk0138_49_1	chr4	31517408	31517989	+	0	NA	Intergenic	MIRc|SINE|MIR	346554	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.000000	0.283505	
chunk0056_363_1	chr13	92428397	92428707	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	-61611	NR_049840	100847092		NR_049840	ENSG00000263741	MIR548AS	-	microRNA 548as	ncRNA	0.009677	0.382637	
chunk0156_84_1	chr5	104312374	104312884	+	0	NA	Intergenic	Intergenic	-749828	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.001961	0.262231	
chunk0168_351_1	chr6	93165899	93166486	+	0	NA	Intergenic	Intergenic	253390	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.005111	0.365646	
chunk0208_411_1	chrX	29520420	29520953	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-53592	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.005629	0.318352	
chunk0210_96_1	chrX	71367303	71367798	+	0	NA	exon (NM_001286074, exon 2 of 38)	exon (NM_001286074, exon 2 of 38)	1311	NR_104389	6872	Hs.158560	NM_004606	ENSG00000147133	TAF1	BA2R|CCG1|CCGS|DYT3|DYT3/TAF1|KAT4|MRXS33|N-TAF1|NSCL2|OF|P250|TAF(II)250|TAF2A|TAFII-250|TAFII250|XDP	TATA-box binding protein associated factor 1	protein-coding	0.036364	0.506048	
chunk0179_435_1	chr7	52197138	52197753	+	0	NA	Intergenic	L1MB3|LINE|L1	-838211	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.001626	0.331169	
chunk0212_36_1	chrY	11281458	11281742	+	0	NA	Intergenic	MER21C|LTR|ERVL	1139990	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.003521	0.463158	
chunk0082_205_1	chr17	56868058	56868267	+	0	NA	3' UTR (NM_003647, exon 12 of 12)	3' UTR (NM_003647, exon 12 of 12)	16751	NR_027025	246754	Hs.720736	NR_027025		MTVR2	-	mouse mammary tumor virus receptor homolog 2	pseudo	0.004785	0.423810	
chunk0139_27_1	chr4	48375940	48376249	+	0	NA	intron (NM_020846, intron 2 of 7)	L2c|LINE|L2	34498	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.009709	0.435484	
chunk0012_279_1	chr1	161885175	161885462	+	0	NA	intron (NM_007348, intron 14 of 15)	intron (NM_007348, intron 14 of 15)	119074	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.003484	0.364583	
chunk0175_394_1	chr6	168414614	168415340	+	0	NA	Intergenic	L2c|LINE|L2	-26174	NM_022138	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.019284	0.423659	
chunk0188_370_1	chr8	18186437	18186636	+	0	NA	intron (NM_001160179, intron 2 of 4)	L1MEg|LINE|L1	16074	NM_001291962	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.010050	0.270000	
chunk0071_280_1	chr15	85735782	85736294	+	0	NA	intron (NM_007200, intron 32 of 36)	intron (NM_007200, intron 32 of 36)	22687	NR_120366	101929679	Hs.513112	NR_120366		LOC101929679	-	uncharacterized LOC101929679	ncRNA	0.001953	0.366472	355(AAGGACATTATGAACT,-,0.00)
chunk0059_213_1	chr14	33837898	33838524	+	0	NA	Intergenic	Intergenic	112615	NM_001308103	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.006390	0.373206	
chunk0144_201_1	chr4	133855683	133856317	+	0	NA	Intergenic	Intergenic	345748	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.001577	0.296063	
chunk0016_193_1	chr1	198510315	198510627	+	0	NA	Intergenic	L1M1|LINE|L1	30474	NM_133326	127124	Hs.127743	NM_133262	ENSG00000151418	ATP6V1G3	ATP6G3|Vma10	ATPase H+ transporting V1 subunit G3	protein-coding	0.000000	0.520767	
chunk0205_333_1	chr9	113122616	113122897	+	0	NA	Intergenic	MER41D|LTR|ERV1	9860	NR_024366	286333	Hs.99052	NR_024366	ENSG00000231528	FAM225A	C9orf109|LINC00256A|NCRNA00256A	family with sequence similarity 225 member A	ncRNA	0.000000	0.382979	
chunk0198_108_1	chr8	130823281	130823744	+	0	NA	intron (NM_001115, intron 12 of 17)	intron (NM_001115, intron 12 of 17)	217077	NM_001115	114	Hs.591859	NM_001115	ENSG00000155897	ADCY8	AC8|ADCY3|HBAC1	adenylate cyclase 8	protein-coding	0.000000	0.308190	
chunk0086_136_1	chr18	21150534	21150857	+	0	NA	Intergenic	L1MD3|LINE|L1	-38844	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.000000	0.293210	
chunk0111_425_1	chr20	34938523	34938832	+	0	NA	intron (NM_000178, intron 6 of 12)	intron (NM_000178, intron 6 of 12)	17121	NM_000178	2937	Hs.82327	NM_000178	ENSG00000100983	GSS	GSHS|HEL-S-64p|HEL-S-88n	glutathione synthetase	protein-coding	0.016181	0.548387	
chunk0108_45_1	chr2	226738454	226739394	+	0	NA	intron (NM_005544, intron 1 of 1)	intron (NM_005544, intron 1 of 1)	59866	NM_005544	3667	Hs.471508	NM_005544	ENSG00000169047	IRS1	HIRS-1	insulin receptor substrate 1	protein-coding	0.008511	0.426142	490(AGGAACACACTGTACC,-,0.00),491(GGAACACACTGTACCC,+,0.00)
chunk0030_61_1	chr10	111962920	111963657	+	0	NA	Intergenic	Intergenic	220491	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.009498	0.363144	
chunk0156_205_1	chr5	107984990	107985722	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-314461	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.000000	0.371078	456(GAGAACATTCTGTCTT,-,0.00),457(AGAACATTCTGTCTTT,+,0.00)
chunk0184_7_1	chr7	111650724	111650979	+	0	NA	Intergenic	Intergenic	-88334	NM_001244606	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.011765	0.414062	
chunk0146_373_1	chr4	168355495	168355936	+	0	NA	Intergenic	L1MCa|LINE|L1	-36908	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.004535	0.418552	239(AAGAACAGAGTGCTCT,-,0.00),240(AGAACAGAGTGCTCTG,+,0.00)
chunk0140_190_1	chr4	70056327	70057065	+	0	NA	intron (NM_002159, intron 5 of 5)	L1PA8A|LINE|L1	6281	NM_002159	3346	Hs.250959	NM_002159	ENSG00000126550	HTN1	HIS1	histatin 1	protein-coding	0.006775	0.368065	403(ATGAACAGATAGTTCT,-,0.00),404(TGAACAGATAGTTCTC,+,0.00)
chunk0037_87_1	chr11	71580043	71580371	+	0	NA	Intergenic	HAL1M8|LINE|L1	2668	NM_001005405	440051	Hs.679617	NM_001005405	ENSG00000204571	KRTAP5-11	KRTAP5-5|KRTAP5-6|KRTAP5.11	keratin associated protein 5-11	protein-coding	0.018293	0.498480	
chunk0199_43_1	chr9	1383985	1384221	+	0	NA	Intergenic	Intergenic	333483	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.004237	0.417722	
chunk0163_71_1	chr6	9208256	9208670	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	556254	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.004831	0.433735	
chunk0170_307_1	chr6	115919885	115920084	+	0	NA	Intergenic	Intergenic	-118747	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.005025	0.435000	
chunk0010_370_1	chr1	119052538	119053209	+	0	NA	intron (NR_126447, intron 1 of 1)	MLT1I|LTR|ERVL-MaLR	5468	NR_126447	104472716	Hs.689536	NR_126447		WARS2-IT1	-	WARS2 intronic transcript 1	ncRNA	0.001490	0.404762	336(CTGAACATTCTGTTCT,-,0.00),337(TGAACATTCTGTTCTC,+,0.00),416(CTGAACATGGTGTACA,-,0.00),417(TGAACATGGTGTACAT,+,0.00)
chunk0037_28_1	chr11	69808494	69808872	+	0	NA	Intergenic	MIR|SINE|MIR	10741	NM_005247	2248	Hs.37092	NM_005247	ENSG00000186895	FGF3	HBGF-3|INT2	fibroblast growth factor 3	protein-coding	0.021164	0.554090	
chunk0037_42_1	chr11	70354603	70354996	+	0	NA	intron (NM_003626, intron 17 of 27)	intron (NM_003626, intron 17 of 27)	-43707	NM_005231	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.005089	0.413706	205(AGGACAACCCGTGCCT,+,0.00)
chunk0085_223_1	chr18	6795262	6795525	+	0	NA	Intergenic	Intergenic	-39040	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.011407	0.515152	47(GGGCACAGCCTGTGTT,-,0.00),48(GGCACAGCCTGTGTTG,+,0.00),108(GGGAACAGTGTGTTCC,-,0.00),109(GGAACAGTGTGTTCCC,+,0.00)
chunk0041_450_1	chr11	134980093	134980293	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	543711	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.020000	0.412935	
chunk0056_12_1	chr13	77112713	77113034	+	0	NA	intron (NM_015057, intron 55 of 82)	L2c|LINE|L2	37359	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.006231	0.357143	
chunk0114_186_1	chr21	15030796	15031082	+	0	NA	intron (NM_003489, intron 2 of 3)	intron (NM_003489, intron 2 of 3)	33866	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.017483	0.473868	
chunk0141_161_1	chr4	82248411	82248921	+	0	NA	Intergenic	Intergenic	125330	NM_002138	3184	Hs.480073	NM_002138	ENSG00000138668	HNRNPD	AUF1|AUF1A|HNRPD|P37|hnRNPD0	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.013725	0.426614	258(GAGCACAGGATGTTCC,-,0.00),259(AGCACAGGATGTTCCT,+,0.00)
chunk0081_54_1	chr17	38454485	38454937	+	0	NA	intron (NM_001199417, intron 1 of 23)	intron (NM_001199417, intron 1 of 23)	26235	NM_001199417	57636	Hs.374446	NM_020876	ENSG00000275832	ARHGAP23	-	Rho GTPase activating protein 23	protein-coding	0.030973	0.622517	259(CTGAACACTGTGCTCC,-,0.00),260(TGAACACTGTGCTCCC,+,0.00)
chunk0143_416_1	chr4	123555650	123555859	+	0	NA	Intergenic	Intergenic	-97031	NR_027105	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.009569	0.476190	
chunk0044_138_1	chr12	29498662	29498919	+	0	NA	Intergenic	Intergenic	-1104	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.003891	0.410853	166(CAGAACATTCTGTCAT,-,0.00),167(AGAACATTCTGTCATC,+,0.00)
chunk0160_216_1	chr5	154899124	154899493	+	0	NA	exon (NM_015465, exon 22 of 28)	exon (NM_015465, exon 22 of 28)	38908	NM_001252156	25929	Hs.483921	NM_015465	ENSG00000082516	GEMIN5	GEMIN-5	gem nuclear organelle associated protein 5	protein-coding	0.016260	0.489189	261(CAGGACAAACTGTCCC,-,0.00),262(AGGACAAACTGTCCCT,+,0.00)
chunk0123_439_1	chr3	50445823	50446418	+	0	NA	intron (NM_001005505, intron 2 of 37)	intron (NM_001005505, intron 2 of 37)	57477	NM_001005505	9254	Hs.476273	NM_006030	ENSG00000007402	CACNA2D2	CACNA2D	calcium voltage-gated channel auxiliary subunit alpha2delta 2	protein-coding	0.011765	0.528523	328(AGGCACATGCTGTGCC,-,0.00),329(GGCACATGCTGTGCCT,+,0.00)
chunk0050_45_1	chr12	100631775	100632024	+	0	NA	Intergenic	Intergenic	38281	NM_001303131	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.016064	0.408000	
chunk0170_375_1	chr6	116931393	116931640	+	0	NA	3' UTR (NM_173560, exon 19 of 19)	3' UTR (NM_173560, exon 19 of 19)	54303	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.000000	0.411290	
chunk0182_12_1	chr7	91093834	91094121	+	0	NA	intron (NM_001287136, intron 11 of 13)	L1PA16|LINE|L1	-170491	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.006969	0.430556	
chunk0072_216_1	chr15	95614807	95615473	+	0	NA	Intergenic	Intergenic	182047	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.009009	0.376312	
chunk0209_194_1	chrX	43908992	43909812	+	0	NA	Intergenic	Intergenic	-26927	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.002439	0.349574	
chunk0102_193_1	chr2	147812203	147812832	+	0	NA	Intergenic	Intergenic	-32000	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.004769	0.355556	
chunk0061_56_1	chr14	56512369	56512970	+	0	NA	Intergenic	Intergenic	-67124	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.006656	0.411960	
chunk0111_285_1	chr20	31663931	31664586	+	0	NA	TTS (NM_138578)	TTS (NM_138578)	26370	NM_032609	84701	Hs.277101	NM_032609	ENSG00000131055	COX4I2	COX4|COX4-2|COX4B|COX4L2|COXIV-2|dJ857M17.2	cytochrome c oxidase subunit 4I2	protein-coding	0.007634	0.525915	
chunk0049_317_1	chr12	94607654	94608461	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	8094	NM_001301036	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.003717	0.363861	
chunk0082_266_1	chr17	57901050	57901810	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	1959	NM_001292025	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.007895	0.490145	
chunk0025_134_1	chr10	52110730	52111770	+	0	NA	intron (NM_006258, intron 7 of 17)	intron (NM_006258, intron 7 of 17)	202878	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.005769	0.356388	102(CAGAACTGCATGTTCC,-,0.00),103(AGAACTGCATGTTCCA,+,0.00)
chunk0127_250_1	chr3	97123889	97124226	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	309476	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.349112	
chunk0019_430_1	chr1	230934440	230934865	+	0	NA	intron (NM_024525, intron 8 of 22)	intron (NM_024525, intron 8 of 22)	44220	NM_024525	79573	Hs.424788	NM_024525	ENSG00000143643	TTC13	-	tetratricopeptide repeat domain 13	protein-coding	0.007059	0.354460	
chunk0082_277_1	chr17	58007303	58007502	+	0	NA	promoter-TSS (NR_034041)	promoter-TSS (NR_034041)	-56	NM_001078166	6426	Hs.68714	NM_006924	ENSG00000136450	SRSF1	ASF|SF2|SF2p33|SFRS1|SRp30a	serine and arginine rich splicing factor 1	protein-coding	0.125628	0.595000	
chunk0156_277_1	chr5	109831011	109831305	+	0	NA	intron (NM_002372, intron 16 of 21)	MIR|SINE|MIR	-52024	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.003401	0.444068	
chunk0137_203_1	chr4	18033340	18033767	+	0	NA	Intergenic	Intergenic	-11693	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.002342	0.315421	240(ATGTACATTGTGTACT,-,0.00),241(TGTACATTGTGTACTA,+,0.00)
chunk0168_200_1	chr6	85579671	85580068	+	0	NA	intron (NM_001304479, intron 1 of 28)	L1M1|LINE|L1	14287	NM_153816	57231	Hs.485871	NM_020468	ENSG00000135317	SNX14	RGS-PX2|SCAR20	sorting nexin 14	protein-coding	0.005038	0.489950	
chunk0161_408_1	chr5	177455231	177455456	+	0	NA	exon (NM_001174101, exon 2 of 3)	exon (NM_001174101, exon 2 of 3)	7018	NM_001174102	80758	Hs.534492	NM_030567	ENSG00000131188	PRR7	-	proline rich 7, synaptic	protein-coding	0.146667	0.769912	
chunk0156_266_1	chr5	109387624	109388183	+	0	NA	intron (NM_014819, intron 1 of 9)	intron (NM_014819, intron 1 of 9)	22071	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.003578	0.358929	
chunk0185_40_1	chr7	124488321	124488713	+	0	NA	Intergenic	L1MC4a|LINE|L1	-136421	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.002551	0.312977	
chunk0062_375_1	chr14	74293454	74294012	+	0	NA	intron (NM_005050, intron 7 of 18)	L2b|LINE|L2	9331	NR_003256	5826	Hs.94395	NM_005050	ENSG00000119688	ABCD4	ABC41|EST352188|MAHCJ|P70R|P79R|PMP69|PXMP1L	ATP binding cassette subfamily D member 4	protein-coding	0.005376	0.443649	353(GAGTACTAAGTGTGCC,-,0.00),354(AGTACTAAGTGTGCCC,+,0.00)
chunk0192_97_1	chr8	61441781	61442545	+	0	NA	intron (NM_173519, intron 3 of 5)	L1MD1|LINE|L1	154197	NM_173519	157807	Hs.591874	NM_173519	ENSG00000177182	CLVS1	C6orf212L|CRALBPL|RLBP1L1	clavesin 1	protein-coding	0.005236	0.363399	
chunk0005_29_1	chr1	54567938	54568365	+	0	NA	intron (NM_147161, intron 1 of 15)	intron (NM_147161, intron 1 of 15)	20017	NM_015547	26027	Hs.745173	NM_015547	ENSG00000162390	ACOT11	BFIT|STARD14|THEA|THEM1	acyl-CoA thioesterase 11	protein-coding	0.011710	0.476636	167(TTGCACTGTCTGTTCT,-,0.00),168(TGCACTGTCTGTTCTC,+,0.00)
chunk0111_123_1	chr20	24207062	24207347	+	0	NA	intron (NR_040102, intron 1 of 3)	intron (NR_040102, intron 1 of 3)	7437	NR_040102	400839	Hs.651965	NR_040102	ENSG00000230133	LINC01721	-	long intergenic non-protein coding RNA 1721	ncRNA	0.017544	0.472028	173(AATAACATGCTGTTCC,-,0.00),174(ATAACATGCTGTTCCA,+,0.00)
chunk0144_350_1	chr4	139557062	139557640	+	0	NA	promoter-TSS (NM_001306199)	promoter-TSS (NM_001306199)	-582	NM_001306199	80854	Hs.480792	NM_030648	ENSG00000145391	SETD7	KMT7|SET7|SET7/9|SET9	SET domain containing 7, histone lysine methyltransferase	protein-coding	0.048443	0.523316	365(ATGTACACAATGTACC,-,0.00),366(TGTACACAATGTACCG,+,0.00)
chunk0129_296_1	chr3	123611972	123612336	+	0	NA	TTS (NM_053032)	TTS (NM_053032)	8529	NM_053032	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.005495	0.394521	
chunk0132_153_1	chr3	156584923	156585316	+	0	NA	Intergenic	L1ME3|LINE|L1	-29919	NM_001308197	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.007634	0.380711	
chunk0105_114_1	chr2	185062082	185062356	+	0	NA	Intergenic	MIRb|SINE|MIR	463853	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.000000	0.338182	
chunk0088_182_1	chr18	47390434	47390912	+	0	NA	Intergenic	Intergenic	10177	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.004184	0.490605	
chunk0200_67_1	chr9	15845759	15846392	+	0	NA	intron (NM_173550, intron 21 of 25)	intron (NM_173550, intron 21 of 25)	292976	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.004739	0.307571	
chunk0155_33_1	chr5	91060983	91061436	+	0	NA	intron (NR_003149, intron 85 of 89)	Tigger10|DNA|TcMar-Tigger	253193	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.004415	0.411894	372(GGGAACAGGCTGCTCA,-,0.00),373(GGAACAGGCTGCTCAG,+,0.00)
chunk0087_453_1	chr18	42698833	42699111	+	0	NA	Intergenic	Intergenic	416720	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.003597	0.401434	170(CAGAACAAAAAGTTCA,-,0.00),171(AGAACAAAAAGTTCAG,+,0.00)
chunk0096_66_1	chr2	27691008	27691583	+	0	NA	intron (NM_018158, intron 12 of 13)	L1PBa|LINE|L1	-27455	NM_001282731	9913	Hs.6232	NM_014860	ENSG00000119760	SUPT7L	SPT7L|STAF65|STAF65(gamma)|STAF65G|SUPT7H	SPT7 like, STAGA complex gamma subunit	protein-coding	0.001739	0.338542	
chunk0046_267_1	chr12	61246583	61247179	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	945958	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.001678	0.294807	260(TAGTACATACTGTACT,-,0.00),261(AGTACATACTGTACTA,+,0.00)
chunk0017_411_1	chr1	212924798	212925018	+	0	NA	Intergenic	Intergenic	-25612	NM_001136475	79805	Hs.96885	NM_024749	ENSG00000143494	VASH2	-	vasohibin 2	protein-coding	0.004545	0.447964	
chunk0174_242_1	chr6	160967372	160967708	+	0	NA	Intergenic	MIRb|SINE|MIR	-24187	NM_006724	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.011905	0.400593	
chunk0046_276_1	chr12	61429730	61430201	+	0	NA	Intergenic	Intergenic	762874	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.008493	0.355932	217(TTGTACTCACTGTTCT,-,0.00),218(TGTACTCACTGTTCTT,+,0.00)
chunk0133_10_1	chr3	165544976	165545515	+	0	NA	Intergenic	MER110|LTR|ERV1	292220	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.007421	0.322222	
chunk0009_6_1	chr1	99849407	99849683	+	0	NA	promoter-TSS (NM_000644)	promoter-TSS (NM_000644)	-539	NM_000642	178	Hs.904	NM_000028	ENSG00000162688	AGL	GDE	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	protein-coding	0.021739	0.465704	
chunk0064_229_1	chr14	94070692	94071193	+	0	NA	intron (NM_020414, intron 2 of 8)	L1PB1|LINE|L1	10270	NM_020414	57062	Hs.510328	NM_020414	ENSG00000089737	DDX24	-	DEAD-box helicase 24	protein-coding	0.001996	0.366534	
chunk0053_417_1	chr13	37127630	37127966	+	0	NA	Intergenic	Intergenic	-22134	NM_145203	122011	Hs.512897	NM_145203	ENSG00000180138	CSNK1A1L	CK1	casein kinase 1 alpha 1 like	protein-coding	0.008929	0.424332	
chunk0103_422_1	chr2	169716403	169717075	+	0	NA	intron (NM_001199290, intron 3 of 5)	HERVL18-int|LTR|ERVL	-17107	NM_144711	151230	Hs.655150	NM_144711	ENSG00000213160	KLHL23	DITHP	kelch like family member 23	protein-coding	0.019345	0.567608	
chunk0051_171_1	chr12	116064456	116064962	+	0	NA	intron (NM_015335, intron 4 of 30)	intron (NM_015335, intron 4 of 30)	83945	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.009881	0.420118	
chunk0126_458_1	chr3	87359150	87359349	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-82662	NM_001122757	5449	Hs.591654	NM_000306	ENSG00000064835	POU1F1	CPHD1|GHF-1|PIT1|POU1F1a|Pit-1	POU class 1 homeobox 1	protein-coding	0.005025	0.390000	
chunk0046_345_1	chr12	62934328	62934527	+	0	NA	intron (NM_020700, intron 1 of 9)	CpG	458	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.080402	0.680000	
chunk0201_193_1	chr9	36526727	36527283	+	0	NA	Intergenic	L1M4|LINE|L1	-45857	NM_001256690	9833	Hs.184339	NM_014791	ENSG00000165304	MELK	HPK38	maternal embryonic leucine zipper kinase	protein-coding	0.008993	0.382406	
chunk0125_420_1	chr3	72336884	72337542	+	0	NA	Intergenic	Intergenic	109410	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.036474	0.596358	307(TGGAACAGGATGTTCC,-,0.00),308(GGAACAGGATGTTCCA,+,0.00)
chunk0212_123_1	chrX	130896047	130896488	+	0	NA	intron (NM_006375, intron 2 of 14)	intron (NM_006375, intron 2 of 14)	7050	NM_001281736	10495	Hs.171458	NM_006375	ENSG00000165675	ENOX2	APK1|COVA1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.004535	0.393665	
chunk0002_252_1	chr1	21163190	21163550	+	0	NA	intron (NM_001198803, intron 3 of 14)	intron (NM_001198803, intron 3 of 14)	11388	NM_001198803	8672	Hs.467084	NM_003760	ENSG00000075151	EIF4G3	eIF-4G 3|eIF4G 3|eIF4GII	eukaryotic translation initiation factor 4 gamma 3	protein-coding	0.000000	0.340720	
chunk0064_308_1	chr14	95649293	95649651	+	0	NA	Intergenic	L2c|LINE|L2	-1706	NR_028288	27004	Hs.510368	NM_012468		TCL6	TNG1|TNG2	T cell leukemia/lymphoma 6	ncRNA	0.016760	0.473538	
chunk0138_141_1	chr4	36981186	36981573	+	0	NA	Intergenic	Intergenic	260612	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.000000	0.311856	
chunk0003_419_1	chr1	40773466	40773838	+	0	NA	Intergenic	Intergenic	-10360	NM_004700	9132	Hs.473058	NM_004700	ENSG00000117013	KCNQ4	DFNA2|DFNA2A|KV7.4	potassium voltage-gated channel subfamily Q member 4	protein-coding	0.005376	0.482574	
chunk0174_320_1	chr6	163264387	163264590	+	0	NA	intron (NM_001080378, intron 5 of 5)	intron (NM_001080378, intron 5 of 5)	59985	NR_028390	285796	Hs.668693	NR_028390	ENSG00000281692	PACRG-AS1	-	PACRG antisense RNA 1	ncRNA	0.024631	0.573529	81(GGGGACACTGTGTGCA,-,0.00),82(GGGACACTGTGTGCAC,+,0.00)
chunk0004_257_1	chr1	47837901	47838385	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	158747	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.006198	0.505155	
chunk0077_153_1	chr16	78962495	78962762	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	638097	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.003745	0.380597	
chunk0043_447_1	chr12	26654603	26654802	+	0	NA	intron (NM_002223, intron 20 of 56)	MLT1F1|LTR|ERVL-MaLR	178496	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.000000	0.495000	
chunk0117_450_1	chr21	46569223	46569722	+	0	NA	3' UTR (NM_001146116, exon 38 of 38)	3' UTR (NM_001146116, exon 38 of 38)	35650	NM_006272	6285	Hs.422181	NM_006272	ENSG00000160307	S100B	NEF|S100|S100-B|S100beta	S100 calcium binding protein B	protein-coding	0.000000	0.336000	
chunk0060_247_1	chr14	49941077	49941325	+	0	NA	Intergenic	Intergenic	-25198	NR_106724	102464828		NR_106724	ENSG00000278038	MIR6076	hsa-mir-6076	microRNA 6076	ncRNA	0.000000	0.337349	
chunk0008_137_1	chr1	92005985	92006312	+	0	NA	intron (NM_001726, intron 18 of 18)	L1MEc|LINE|L1	-23828	NM_173567	253152	Hs.201555	NM_173567	ENSG00000172031	EPHX4	ABHD7|EH4|EPHXRP	epoxide hydrolase 4	protein-coding	0.003058	0.304878	
chunk0101_66_1	chr2	123513844	123514141	+	0	NA	Intergenic	Intergenic	-511295	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.352349	240(AGAAACAGATTGTACT,-,0.00),241(GAAACAGATTGTACTC,+,0.00)
chunk0205_290_1	chr9	111922412	111922923	+	0	NA	intron (NM_003358, intron 2 of 8)	intron (NM_003358, intron 2 of 8)	-9433	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.000000	0.363281	
chunk0026_295_1	chr10	67810395	67810735	+	0	NA	TTS (NM_201262)	TTS (NM_201262)	27614	NM_021800	56521	Hs.260720	NM_021800	ENSG00000108176	DNAJC12	HPANBH4|JDP1	DnaJ heat shock protein family (Hsp40) member C12	protein-coding	0.014706	0.422287	
chunk0017_161_1	chr1	207004681	207005341	+	0	NA	Intergenic	Intergenic	27745	NM_001083924	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.010606	0.485628	249(AGGAACAGGCCGTACA,-,0.00)
chunk0056_315_1	chr13	91044829	91045216	+	0	NA	Intergenic	Intergenic	44595	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.005168	0.298969	
chunk0171_57_1	chr6	121306055	121306714	+	0	NA	intron (NM_152730, intron 5 of 31)	L2a|LINE|L2	28116	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.010622	0.342424	
chunk0058_139_1	chr14	22870910	22871732	+	0	NA	promoter-TSS (NM_014045)	promoter-TSS (NM_014045)	-430	NM_014045	26020	Hs.525232	NM_014045	ENSG00000197324	LRP10	LRP-10|LRP9|MST087|MSTP087	LDL receptor related protein 10	protein-coding	0.026764	0.453220	
chunk0182_315_1	chr7	98921031	98921517	+	0	NA	intron (NM_003496, intron 20 of 70)	intron (NM_003496, intron 20 of 70)	39577	NR_132754	106633801		NR_132754		SCARNA28	ZL1	small Cajal body-specific RNA 28	ncRNA	0.016461	0.462012	
chunk0149_275_1	chr5	24547140	24547485	+	0	NA	intron (NM_006727, intron 2 of 11)	L1MEg|LINE|L1	97664	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.005797	0.398844	
chunk0159_303_1	chr5	142975647	142976101	+	0	NA	intron (NM_015071, intron 11 of 22)	MamRep137|DNA|TcMar-Tigger	-106964	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.013216	0.382418	
chunk0134_339_1	chr3	182271521	182272257	+	0	NA	Intergenic	Intergenic	214473	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.013587	0.446404	
chunk0198_102_1	chr8	130720871	130721378	+	0	NA	Intergenic	Kanga11a|DNA|TcMar-Tc2	-277464	NM_001247996	50807	Hs.655552	NM_018482	ENSG00000153317	ASAP1	AMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14P	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	protein-coding	0.007890	0.366142	
chunk0118_267_1	chr22	33411334	33411550	+	0	NA	intron (NM_133642, intron 7 of 14)	intron (NM_133642, intron 7 of 14)	25227	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.004630	0.354839	
chunk0044_311_1	chr12	33558838	33559096	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-119148	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.000000	0.362934	
chunk0118_276_1	chr22	33672810	33673056	+	0	NA	intron (NM_133642, intron 2 of 14)	intron (NM_133642, intron 2 of 14)	-52053	NR_038949	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.012195	0.461538	138(AAGTACAGGGTGCTCT,-,0.00),139(AGTACAGGGTGCTCTG,+,0.00)
chunk0054_259_1	chr13	46318019	46318462	+	0	NA	Intergenic	L1MA5A|LINE|L1	-20396	NR_047493	100861554	Hs.90866	NR_047493	ENSG00000261097	LINC00563	-	long intergenic non-protein coding RNA 563	ncRNA	0.002257	0.349099	
chunk0080_345_1	chr17	32824707	32825115	+	0	NA	intron (NM_015194, intron 1 of 21)	intron (NM_015194, intron 1 of 21)	52262	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.004902	0.344743	
chunk0172_365_1	chr6	139240553	139241061	+	0	NA	3' UTR (NM_153235, exon 10 of 10)	3' UTR (NM_153235, exon 10 of 10)	51264	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.001969	0.383104	270(AAGCACTTTGTGTGCC,-,0.00),271(AGCACTTTGTGTGCCT,+,0.00)
chunk0054_404_1	chr13	50513216	50513566	+	0	NA	intron (NR_109974, intron 5 of 6)	intron (NR_109974, intron 5 of 6)	14058	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.005714	0.407407	
chunk0106_360_1	chr2	207044502	207045011	+	0	NA	Intergenic	Intergenic	65317	NR_036227	100423036		NR_036227	ENSG00000253008	MIR2355	mir-2355	microRNA 2355	ncRNA	0.015717	0.449020	169(ATGCACAGAGAGTGCC,-,0.00),170(TGCACAGAGAGTGCCG,+,0.00)
chunk0149_346_1	chr5	27247311	27247579	+	0	NA	Intergenic	Intergenic	-208863	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.007463	0.330855	
chunk0185_63_1	chr7	124835088	124835618	+	0	NA	exon (NM_015450, exon 15 of 19)	exon (NM_015450, exon 15 of 19)	-44543	NM_001024603	154872	Hs.444163	NM_001024603	ENSG00000275356	C7orf77	-	chromosome 7 open reading frame 77	protein-coding	0.011321	0.357815	
chunk0070_217_1	chr15	72626084	72626395	+	0	NA	Intergenic	L1MD2|LINE|L1	-28458	NM_018652	55889	Hs.546408	NM_018652	ENSG00000215186	GOLGA6B	GOLGA|GOLGA6D	golgin A6 family member B	protein-coding	0.006431	0.413462	
chunk0021_10_1	chr10	336255	336789	+	0	NA	intron (NM_014974, intron 29 of 36)	L1PREC2|LINE|L1	-54436	NR_106988									0.013109	0.418692	
chunk0080_276_1	chr17	31126836	31127225	+	0	NA	intron (NM_001042492, intron 1 of 57)	L1ME3D|LINE|L1	32103	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.002571	0.330769	
chunk0172_247_1	chr6	137222392	137222821	+	0	NA	Intergenic	Intergenic	-3176	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.006993	0.397674	198(TGGAACAAACTGTGCA,-,0.00),199(GGAACAAACTGTGCAT,+,0.00)
chunk0047_285_1	chr12	73383496	73384283	+	0	NA	Intergenic	Intergenic	224699	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.332487	
chunk0080_267_1	chr17	31054700	31055247	+	0	NA	Intergenic	Intergenic	39452	NR_039886	100616266		NR_039886	ENSG00000265444	MIR4733	-	microRNA 4733	ncRNA	0.007313	0.468978	
chunk0036_387_1	chr11	67657816	67658089	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-7293	NM_080658	91703	Hs.126265	NM_080658	ENSG00000132744	ACY3	ACY-3|HCBP1	aminoacylase 3	protein-coding	0.003663	0.372263	
chunk0060_365_1	chr14	52363371	52363642	+	0	NA	Intergenic	MIR|SINE|MIR	49208	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.003690	0.389706	
chunk0099_157_1	chr2	88124226	88124443	+	0	NA	intron (NM_001443, intron 3 of 3)	intron (NM_001443, intron 3 of 3)	3797	NM_001443	2168	Hs.380135	NM_001443	ENSG00000163586	FABP1	FABPL|L-FABP	fatty acid binding protein 1	protein-coding	0.009217	0.550459	
chunk0192_36_1	chr8	58662434	58663160	+	0	NA	Intergenic	Intergenic	-2952	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.005510	0.403026	
chunk0053_176_1	chr13	30925801	30926288	+	0	NA	TTS (NM_032849)	TTS (NM_032849)	6564	NR_038288	100507064	Hs.654878	NR_038287	ENSG00000224743	TEX26-AS1	LINC00447	TEX26 antisense RNA 1	ncRNA	0.008214	0.338115	
chunk0053_167_1	chr13	30796536	30797137	+	0	NA	Intergenic	Intergenic	-6370	NR_047012	100874158	Hs.577982	NR_047012	ENSG00000237879	LINC00398	-	long intergenic non-protein coding RNA 398	ncRNA	0.023295	0.486711	
chunk0045_93_1	chr12	46020687	46021349	+	0	NA	Intergenic	L1PB2|LINE|L1	-30400	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.001511	0.330317	
chunk0047_123_1	chr12	69186231	69186597	+	0	NA	Intergenic	MER4A1|LTR|ERV1	-53123	NM_007007	11052	Hs.369606	NM_007007	ENSG00000111605	CPSF6	CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding	0.005464	0.441417	
chunk0181_434_1	chr7	90488992	90489397	+	0	NA	Intergenic	HAL1ME|LINE|L1	85860	NM_001185072	9069	Hs.731917	NM_012129	ENSG00000157224	CLDN12	-	claudin 12	protein-coding	0.002469	0.300493	
chunk0103_288_1	chr2	166031466	166031755	+	0	NA	intron (NR_110598, intron 3 of 3)	L3|LINE|CR1	42029	NM_001165963	6323	Hs.22654	NM_006920	ENSG00000144285	SCN1A	EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI	sodium voltage-gated channel alpha subunit 1	protein-coding	0.000000	0.286207	
chunk0025_57_1	chr10	49520986	49521605	+	0	NA	intron (NM_170753, intron 1 of 1)	intron (NM_170753, intron 1 of 1)	2986	NM_170753	267004	Hs.49063	NM_170753	ENSG00000225830	PGBD3	-	piggyBac transposable element derived 3	protein-coding	0.009693	0.445161	341(CTGCACAGCCTGTACT,-,0.00),342(TGCACAGCCTGTACTA,+,0.00)
chunk0013_397_1	chr1	172905395	172905704	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	145414	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.003236	0.406452	
chunk0059_347_1	chr14	37060424	37060902	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	-108272	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.004184	0.379958	
chunk0073_25_1	chr16	2339638	2340040	+	0	NA	intron (NM_001089, intron 1 of 32)	CpG	907	NM_001089	21	Hs.26630	NM_001089	ENSG00000167972	ABCA3	ABC-C|ABC3|EST111653|LBM180|SMDP3	ATP binding cassette subfamily A member 3	protein-coding	0.087065	0.642680	
chunk0177_292_1	chr7	25773978	25774387	+	0	NA	Intergenic	Intergenic	175804	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.004890	0.434146	
chunk0031_439_1	chr10	132535080	132535279	+	0	NA	Intergenic	(TGTGCA)n|Simple_repeat|Simple_repeat	-2670	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.050251	0.570000	
chunk0035_83_1	chr11	41989851	41990595	+	0	NA	Intergenic	Intergenic	263467	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.001344	0.324832	
chunk0151_304_1	chr5	53115051	53115289	+	0	NA	TTS (NR_034107)	TTS (NR_034107)	5328	NR_104654	257396	Hs.12326	NR_034107	ENSG00000247796	LOC257396	-	uncharacterized LOC257396	ncRNA	0.000000	0.292887	
chunk0194_110_1	chr8	83698113	83698669	+	0	NA	Intergenic	L1ME3A|LINE|L1	294633	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003597	0.341113	
chunk0143_166_1	chr4	110798874	110799218	+	0	NA	Intergenic	Intergenic	61601	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.017442	0.388406	
chunk0084_272_1	chr17	79665122	79665471	+	0	NA	Intergenic	Intergenic	41953	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.034384	0.522857	
chunk0143_177_1	chr4	111883517	111884199	+	0	NA	Intergenic	Intergenic	-261539	NM_152400	132720	Hs.23439	NM_152400	ENSG00000174749	FAM241A	C4orf32	family with sequence similarity 241 member A	protein-coding	0.001466	0.357247	
chunk0115_220_1	chr21	27047334	27047737	+	0	NA	Intergenic	Intergenic	-80415	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.004963	0.398515	
chunk0143_403_1	chr4	123308759	123309080	+	0	NA	intron (NM_145207, intron 15 of 15)	intron (NM_145207, intron 15 of 15)	-87876	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.003115	0.409938	
chunk0141_411_1	chr4	88593833	88594377	+	0	NA	intron (NM_001271602, intron 1 of 24)	intron (NM_001271602, intron 1 of 24)	1682	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.011029	0.363303	
chunk0160_203_1	chr5	154727033	154727544	+	0	NA	intron (NM_015315, intron 1 of 18)	L1MEg|LINE|L1	14386	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.005871	0.359375	
chunk0137_216_1	chr4	19739492	19739699	+	0	NA	Intergenic	Intergenic	-512310	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.004831	0.389423	
chunk0081_120_1	chr17	40100316	40100689	+	0	NA	5' UTR (NM_021724, exon 1 of 8)	5' UTR (NM_021724, exon 1 of 8)	223	NM_021724	9572	Hs.724	NM_021724	ENSG00000126368	NR1D1	EAR1|REVERBA|REVERBalpha|THRA1|THRAL|ear-1|hRev	nuclear receptor subfamily 1 group D member 1	protein-coding	0.061662	0.622995	
chunk0095_48_1	chr2	13587947	13588375	+	0	NA	Intergenic	L2b|LINE|L2	-581148	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.000000	0.333333	
chunk0109_210_1	chr20	5365665	5365864	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-51395	NM_144773	128674	Hs.375029	NM_144773	ENSG00000101292	PROKR2	GPR73L1|GPR73b|GPRg2|HH3|KAL3|PKR2|dJ680N4.3	prokineticin receptor 2	protein-coding	0.005025	0.325000	
chunk0153_446_1	chr5	76379656	76380020	+	0	NA	Intergenic	MIRc|SINE|MIR	-23417	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.008242	0.364384	
chunk0043_22_1	chr12	13097777	13098333	+	0	NA	intron (NM_001080554, intron 1 of 6)	intron (NM_001080554, intron 1 of 6)	-2249	NM_001206845	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.030576	0.443447	
chunk0192_425_1	chr8	69588417	69588831	+	0	NA	intron (NM_015170, intron 7 of 22)	intron (NM_015170, intron 7 of 22)	-4276	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.024155	0.371084	
chunk0060_42_1	chr14	40983458	40983944	+	0	NA	intron (NR_109758, intron 3 of 3)	L1MA2|LINE|L1	28990	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.008230	0.371663	
chunk0175_10_1	chr7	165181	165456	+	0	NA	Intergenic	Intergenic	15600	NR_108065	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.007273	0.405797	
chunk0189_433_1	chr8	28117544	28117773	+	0	NA	intron (NM_018091, intron 7 of 14)	intron (NM_018091, intron 7 of 14)	24591	NM_001284224	55140	Hs.491336	NM_018091	ENSG00000134014	ELP3	KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.004367	0.334783	
chunk0027_211_1	chr10	76051314	76051856	+	0	NA	intron (NR_131178, intron 5 of 7)	intron (NR_131178, intron 5 of 7)	268824	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.009225	0.440147	
chunk0084_334_1	chr17	81043897	81044098	+	0	NA	intron (NM_006340, intron 1 of 14)	intron (NM_006340, intron 1 of 14)	8850	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.029851	0.529703	37(TGGCACAGAGAGTACT,-,0.00),38(GGCACAGAGAGTACTG,+,0.00),83(TGGGACAGAAAGTTCT,-,0.00),84(GGGACAGAAAGTTCTT,+,0.00)
chunk0066_15_1	chr15	27208071	27208393	+	0	NA	intron (NM_033223, intron 3 of 9)	intron (NM_033223, intron 3 of 9)	-46913	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.003106	0.517028	
chunk0036_419_1	chr11	68213510	68214007	+	0	NA	promoter-TSS (NM_016028)	promoter-TSS (NM_016028)	14	NM_001300908	51111	Hs.632120	NM_016028	ENSG00000110066	KMT5B	CGI-85|CGI85|MRD51|SUV420H1	lysine methyltransferase 5B	protein-coding	0.164990	0.769076	
chunk0041_74_1	chr11	124035749	124036181	+	0	NA	Intergenic	Intergenic	3036	NM_001004463	390265	Hs.553761	NM_001004463	ENSG00000182634	OR10G7	OR11-283	olfactory receptor family 10 subfamily G member 7	protein-coding	0.004630	0.318707	
chunk0098_146_1	chr2	69682235	69682719	+	0	NA	Intergenic	Intergenic	-38632	NM_014911	22848	Hs.468878	NM_014911	ENSG00000115977	AAK1	-	AP2 associated kinase 1	protein-coding	0.006198	0.274227	
chunk0108_211_1	chr2	233271725	233272186	+	0	NA	intron (NM_017974, intron 6 of 16)	intron (NM_017974, intron 6 of 16)	-3771	NR_003008	677775	Hs.663619	NR_003008	ENSG00000252010	SCARNA5	U87	small Cajal body-specific RNA 5	ncRNA	0.004338	0.363636	
chunk0196_324_1	chr8	111793810	111794205	+	0	NA	Intergenic	Intergenic	-557804	NR_125418	101927487	Hs.630004	NR_125418	ENSG00000253103	LINC01609	-	long intergenic non-protein coding RNA 1609	ncRNA	0.002532	0.323232	
chunk0143_280_1	chr4	117153221	117153523	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-67792	NM_152402	133022	Hs.570737	NM_152402	ENSG00000174599	TRAM1L1	-	translocation associated membrane protein 1 like 1	protein-coding	0.009934	0.524752	
chunk0084_263_1	chr17	79361645	79361907	+	0	NA	intron (NM_001082575, intron 2 of 14)	intron (NM_001082575, intron 2 of 14)	154372	NM_001082575	146713	Hs.135229	NM_001025448	ENSG00000167281	RBFOX3	FOX-3|FOX3|HRNBP3|NEUN	RNA binding fox-1 homolog 3	protein-coding	0.007634	0.422053	
chunk0190_128_1	chr8	30615450	30616232	+	0	NA	intron (NM_002095, intron 3 of 7)	L1MC1|LINE|L1	-22759	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.010230	0.378033	
chunk0157_122_1	chr5	117096265	117096787	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-318986	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.013410	0.405354	
chunk0055_2_1	chr13	51551498	51551822	+	0	NA	promoter-TSS (NR_039852)	promoter-TSS (NR_039852)	-929	NR_039852	100616423		NR_039852	ENSG00000266611	MIR4703	-	microRNA 4703	ncRNA	0.003086	0.347692	
chunk0083_332_1	chr17	70107517	70107736	+	0	NA	intron (NM_001291623, intron 1 of 2)	intron (NM_001291623, intron 1 of 2)	2781	NM_170742	3773	Hs.463985	NM_018658	ENSG00000153822	KCNJ16	BIR9|KIR5.1	potassium voltage-gated channel subfamily J member 16	protein-coding	0.000000	0.354545	96(AGGCACAGACAGTACC,-,0.00),97(GGCACAGACAGTACCA,+,0.00)
chunk0136_422_1	chr3	197487999	197488198	+	0	NA	Intergenic	Intergenic	67889	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.010050	0.570000	99(AGGGACATTGTGTCAT,-,0.00)
chunk0181_18_1	chr7	77753147	77753704	+	0	NA	intron (NM_198467, intron 3 of 7)	L1ME3A|LINE|L1	45005	NM_032936	85025	Hs.19025	NM_032936	ENSG00000135211	TMEM60	C7orf35|DC32	transmembrane protein 60	protein-coding	0.001795	0.322581	
chunk0007_117_1	chr1	78997786	78998343	+	0	NA	intron (NM_022159, intron 2 of 14)	intron (NM_022159, intron 2 of 14)	8746	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.007181	0.406810	
chunk0074_213_1	chr16	25496888	25497332	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	-194916	NM_006040	9951	Hs.655275	NM_006040	ENSG00000182601	HS3ST4	3-OST-4|30ST4|3OST4|h3-OST-4	heparan sulfate-glucosamine 3-sulfotransferase 4	protein-coding	0.000000	0.359551	182(TGGCACACTGTGTCCT,-,0.00),183(GGCACACTGTGTCCTC,+,0.00)
chunk0170_131_1	chr6	110936549	110936975	+	0	NA	Intergenic	Intergenic	-21798	NM_138408	112495	Hs.418520	NM_138408	ENSG00000155115	GTF3C6	C6orf51|TFIIIC35|bA397G5.3	general transcription factor IIIC subunit 6	protein-coding	0.023474	0.435597	
chunk0021_360_1	chr1	246315363	246316173	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	101644	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.008642	0.348952	
chunk0142_53_1	chr4	91840226	91840946	+	0	NA	Intergenic	Intergenic	436716	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.004167	0.335645	285(GGGAACAGCCTGGACT,-,0.00),286(GGAACAGCCTGGACTC,+,0.00)
chunk0212_149_1	chrX	131920950	131921369	+	0	NA	Intergenic	L1MA3|LINE|L1	-90516	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.004773	0.326190	
chunk0199_296_1	chr9	6855906	6856185	+	0	NA	intron (NR_130707, intron 5 of 14)	intron (NR_130707, intron 5 of 14)	98404	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.007168	0.453571	
chunk0112_225_1	chr20	40903519	40903783	+	0	NA	Intergenic	L2a|LINE|L2	-125171	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.003788	0.411321	
chunk0049_302_1	chr12	94438319	94438984	+	0	NA	intron (NM_016122, intron 1 of 16)	L1PB1|LINE|L1	21337	NM_016122	51134	Hs.279209	NM_016122	ENSG00000173588	CEP83	CCDC41|NPHP18|NY-REN-58	centrosomal protein 83	protein-coding	0.006015	0.322823	
chunk0026_66_1	chr10	61164447	61164646	+	0	NA	Intergenic	Intergenic	148271	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.000000	0.410000	
chunk0135_244_1	chr3	188786596	188786952	+	0	NA	intron (NM_001167671, intron 8 of 10)	L1MD2|LINE|L1	97993	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.005618	0.378151	
chunk0015_87_1	chr1	184905201	184906155	+	0	NA	intron (NM_052966, intron 1 of 13)	intron (NM_052966, intron 1 of 13)	68908	NM_052966	116496	Hs.518662	NM_052966	ENSG00000135842	NIBAN1	C1orf24|FAM129A|GIG39|NIBAN	niban apoptosis regulator 1	protein-coding	0.004193	0.443979	
chunk0081_405_1	chr17	48341479	48341815	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	47300	NR_131240	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.000000	0.305638	
chunk0210_122_1	chrX	72994779	72994978	+	0	NA	Intergenic	L1MA1|LINE|L1	7978	NR_110398	101928345	Hs.584657	NR_110398	ENSG00000226725	PABPC1L2B-AS1	-	PABPC1L2B antisense RNA 1 (head to head)	ncRNA	0.010050	0.350000	
chunk0112_183_1	chr20	40055607	40055885	+	0	NA	Intergenic	Intergenic	51285	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.007194	0.379928	
chunk0149_218_1	chr5	22065567	22066227	+	0	NA	intron (NM_004061, intron 5 of 14)	ERVL-B4-int|LTR|ERVL	-76455	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.003030	0.399395	332(GGGGTCATCCTGTTCC,-,0.00),333(GGGTCATCCTGTTCCT,+,0.00),444(AAAAACAGAGAGTCCT,-,0.00),445(AAAACAGAGAGTCCTT,+,0.00)
chunk0083_274_1	chr17	68453948	68454558	+	0	NA	intron (NM_017983, intron 1 of 12)	intron (NM_017983, intron 1 of 12)	3259	NM_017983	55062	Hs.463964	NM_017983	ENSG00000070540	WIPI1	ATG18|ATG18A|WIPI49	WD repeat domain, phosphoinositide interacting 1	protein-coding	0.008197	0.417349	
chunk0059_69_1	chr14	30332393	30332894	+	0	NA	Intergenic	Intergenic	-226480	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.000000	0.328685	
chunk0013_64_1	chr1	167363639	167364004	+	0	NA	intron (NR_037163, intron 3 of 16)	intron (NR_037163, intron 3 of 16)	34777	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.005479	0.330601	
chunk0069_132_1	chr15	62109125	62109522	+	0	NA	Intergenic	Charlie15b|DNA|hAT-Charlie	42346	NM_207322	145741	Hs.202656	NM_207322	ENSG00000198535	C2CD4A	FAM148A|NLF1	C2 calcium dependent domain containing 4A	protein-coding	0.000000	0.271357	
chunk0140_164_1	chr4	69601278	69601531	+	0	NA	intron (NM_001301239, intron 1 of 4)	L1PBa|LINE|L1	38238	NM_001105677	574537	Hs.225950	NM_001105677	ENSG00000271271	UGT2A2	-	UDP glucuronosyltransferase family 2 member A2	protein-coding	0.011858	0.527559	
chunk0146_368_1	chr4	168304995	168305328	+	0	NA	intron (NM_017631, intron 5 of 37)	Tigger3b|DNA|TcMar-Tigger	13646	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.006006	0.335329	
chunk0131_255_1	chr3	149643049	149643475	+	0	NA	intron (NM_015472, intron 2 of 6)	intron (NM_015472, intron 2 of 6)	14763	NM_001168280	25937	Hs.477921	NM_015472	ENSG00000018408	WWTR1	TAZ	WW domain containing transcription regulator 1	protein-coding	0.007042	0.337237	
chunk0030_4_1	chr10	110818891	110819098	+	0	NA	intron (NM_001134363, intron 9 of 13)	intron (NM_001134363, intron 9 of 13)	51910	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.000000	0.456731	
chunk0204_72_1	chr9	93620679	93621252	+	0	NA	intron (NM_005392, intron 1 of 21)	intron (NM_005392, intron 1 of 21)	26124	NR_049853	100847045		NR_049853	ENSG00000283146	MIR548AU	-	microRNA 548au	ncRNA	0.012216	0.517422	232(GAGAACAGGATGGCCC,-,0.00),233(AGAACAGGATGGCCCC,+,0.00)
chunk0198_467_1	chr8	144684208	144684693	+	0	NA	intron (NM_001308208, intron 1 of 10)	CpG	1362	NM_001308208	80728	Hs.148988	NM_025251	ENSG00000147799	ARHGAP39	CrGAP|Vilse	Rho GTPase activating protein 39	protein-coding	0.063918	0.590535	
chunk0120_37_1	chr3	2597502	2598335	+	0	NA	intron (NM_001206955, intron 3 of 23)	intron (NM_001206955, intron 3 of 23)	-294297	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.009604	0.422062	
chunk0030_293_1	chr10	117241367	117242106	+	0	NA	exon (NM_003054, exon 2 of 16)	exon (NM_003054, exon 2 of 16)	663	NM_003054	6571	Hs.596992	NM_003054	ENSG00000165646	SLC18A2	PKDYS2|SVAT|SVMT|VAT2|VMAT2	solute carrier family 18 member A2	protein-coding	0.094723	0.683784	384(AAGCTCATCCTGTTCA,-,0.00),385(AGCTCATCCTGTTCAT,+,0.00)
chunk0028_231_1	chr10	89891216	89891923	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	62076	NR_038382	643529	Hs.618956	NR_038382	ENSG00000232229	LINC00865	-	long intergenic non-protein coding RNA 865	ncRNA	0.002829	0.402542	
chunk0208_25_1	chrX	11073363	11074165	+	0	NA	Intergenic	L1MC3|LINE|L1	-37522	NM_001171991	3052	Hs.211571	NM_005333	ENSG00000004961	HCCS	CCHL|LSDMCA1|MCOPS7|MLS	holocytochrome c synthase	protein-coding	0.006234	0.364882	
chunk0211_225_1	chrX	118772486	118772954	+	0	NA	intron (NM_001560, intron 8 of 10)	intron (NM_001560, intron 8 of 10)	45124	NM_001560	3597	Hs.496646	NM_001560	ENSG00000131724	IL13RA1	CD213A1|CT19|IL-13Ra|NR4	interleukin 13 receptor subunit alpha 1	protein-coding	0.006410	0.298507	
chunk0175_360_1	chr6	167809035	167809348	+	0	NA	Intergenic	L1ME3B|LINE|L1	-12332	NR_026773	26238	Hs.520583	NM_014356	ENSG00000146521	LINC01558	C6orf123|HGC6.2|LINC01557|dJ431P23.4	long intergenic non-protein coding RNA 1558	ncRNA	0.000000	0.350318	
chunk0015_306_1	chr1	189020444	189020665	+	0	NA	Intergenic	L1MC3|LINE|L1	1457075	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004525	0.288288	41(AAGTTCAGGATGTCCT,-,0.00),42(AGTTCAGGATGTCCTT,+,0.00)
chunk0100_192_1	chr2	111055620	111055963	+	0	NA	intron (NM_001142807, intron 16 of 17)	intron (NM_001142807, intron 16 of 17)	59797	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.002915	0.491279	
chunk0204_13_1	chr9	91714116	91714735	+	0	NA	Intergenic	CpG	-78080	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.058158	0.493548	257(CAGAACAGTTTGTGCT,-,0.00),258(AGAACAGTTTGTGCTC,+,0.00)
chunk0186_414_1	chr7	146216131	146216770	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	100089	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.009390	0.442188	340(CAGCACACCCTGTTCC,-,0.00),341(AGCACACCCTGTTCCT,+,0.00)
chunk0044_199_1	chr12	30764315	30764545	+	0	NA	Intergenic	Intergenic	-9916	NM_001002259	65981	Hs.234355	NM_023925	ENSG00000110888	CAPRIN2	C1QDC1|EEG-1|EEG1|RNG140	caprin family member 2	protein-coding	0.008696	0.463203	
chunk0052_414_1	chr12	131456801	131457117	+	0	NA	Intergenic	Intergenic	109489	NR_103736	338797	Hs.592007	NM_001025466		LINC02370	-	long intergenic non-protein coding RNA 2370	ncRNA	0.060127	0.618297	
chunk0042_301_1	chr12	7896795	7897156	+	0	NA	Intergenic	Intergenic	-5779	NM_001286237	144195	Hs.655169	NM_153449	ENSG00000173262	SLC2A14	GLUT14|SLC2A3P3	solute carrier family 2 member 14	protein-coding	0.011080	0.453039	60(CAGGTCTGAGTGTTCC,-,0.00),90(CAGGACTGGATGTTCT,-,0.00),91(AGGACTGGATGTTCTG,+,0.00)
chunk0065_269_1	chr14	101869386	101869599	+	0	NA	intron (NM_178586, intron 2 of 12)	L1MD3|LINE|L1	59689	NM_002719	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.028169	0.425234	
chunk0137_348_1	chr4	25368248	25368678	+	0	NA	intron (NM_024936, intron 12 of 12)	intron (NM_024936, intron 12 of 12)	-8763	NM_013367	29945	Hs.152173	NM_013367	ENSG00000053900	ANAPC4	APC4	anaphase promoting complex subunit 4	protein-coding	0.013953	0.443155	
chunk0114_379_1	chr20	63061210	63061748	+	0	NA	intron (NR_033370, intron 1 of 4)	(TCCGTG)n|Simple_repeat|Simple_repeat	23468	NR_033369	100144597	Hs.636485	NR_033369	ENSG00000237119	LINC01056	-	long intergenic non-protein coding RNA 1056	ncRNA	0.042751	0.552876	
chunk0193_439_1	chr8	81085218	81085694	+	0	NA	intron (NM_018440, intron 1 of 8)	intron (NM_018440, intron 1 of 8)	26612	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.004202	0.383648	228(AGGTGCATTGTGTTCT,-,0.00),229(GGTGCATTGTGTTCTG,+,0.00)
chunk0202_295_1	chr9	77793924	77794169	+	0	NA	intron (NM_002072, intron 5 of 6)	intron (NM_002072, intron 5 of 6)	-145730	NM_004297	9630	Hs.657795	NM_004297	ENSG00000156049	GNA14	-	G protein subunit alpha 14	protein-coding	0.008163	0.394309	
chunk0184_305_1	chr7	120069395	120069693	+	0	NA	Intergenic	L1MA5|LINE|L1	-162169	NR_131963	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.006711	0.488294	
chunk0134_156_1	chr3	177787757	177788377	+	0	NA	Intergenic	MIRc|SINE|MIR	-28798	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.008065	0.391304	
chunk0150_444_1	chr5	40554842	40555041	+	0	NA	Intergenic	Intergenic	-124989	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.005025	0.420000	40(AGTACTTTCTGTTCAC,+,0.00)
chunk0104_424_1	chr2	180934610	180935370	+	0	NA	Intergenic	L3|LINE|CR1	-45395	NM_182678	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.005263	0.373193	
chunk0122_425_1	chr3	39130422	39130992	+	0	NA	exon (NM_145755, exon 18 of 29)	exon (NM_145755, exon 18 of 29)	-7499	NR_106880	102466743		NR_106880	ENSG00000284158	MIR6822	hsa-mir-6822	microRNA 6822	ncRNA	0.005263	0.506130	318(CAGGACTTTCTGTGCT,-,0.00),319(AGGACTTTCTGTGCTG,+,0.00)
chunk0009_323_1	chr1	108736744	108736963	+	0	NA	intron (NM_001144937, intron 10 of 12)	intron (NM_001144937, intron 10 of 12)	-9810	NM_007269	6814	Hs.530436	NM_007269	ENSG00000116266	STXBP3	MUNC18-3|MUNC18C|PSP|UNC-18C	syntaxin binding protein 3	protein-coding	0.004566	0.377273	
chunk0018_368_1	chr1	221929130	221929346	+	0	NA	Intergenic	L1MA3|LINE|L1	-88572	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.013889	0.539171	
chunk0025_48_1	chr10	49374656	49375360	+	0	NA	intron (NM_001276451, intron 6 of 6)	intron (NM_001276451, intron 6 of 6)	21008	NM_001276451	644168	Hs.534530	NM_001080520	ENSG00000165606	DRGX	DRG11|PRRXL1	dorsal root ganglia homeobox	protein-coding	0.008523	0.375887	478(CTGGACACACTGTCTT,-,0.00),479(TGGACACACTGTCTTC,+,0.00)
chunk0198_117_1	chr8	131842885	131843604	+	0	NA	Intergenic	L2c|LINE|L2	-60865	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.006954	0.381944	270(AAGGACAGCATGCCCC,-,0.00),271(AGGACAGCATGCCCCA,+,0.00)
chunk0104_358_1	chr2	179953835	179954538	+	0	NA	intron (NM_020943, intron 16 of 19)	intron (NM_020943, intron 16 of 19)	52867	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.008535	0.321023	
chunk0160_348_1	chr5	160119016	160119303	+	0	NA	exon (NM_001267035, exon 1 of 3)	exon (NM_001267035, exon 1 of 3)	286	NM_001130864	114825	Hs.744960	NM_052927	ENSG00000170234	PWWP2A	MST101	PWWP domain containing 2A	protein-coding	0.118467	0.743056	
chunk0023_255_1	chr10	27532539	27532774	+	0	NA	intron (NR_046172, intron 3 of 5)	intron (NR_046172, intron 3 of 5)	28482	NM_001256411	22931	Hs.406799	NM_021252	ENSG00000099246	RAB18	RAB18LI1|WARBM3	RAB18, member RAS oncogene family	protein-coding	0.004255	0.275424	
chunk0042_444_1	chr12	12403862	12404229	+	0	NA	intron (NM_058169, intron 2 of 3)	intron (NM_058169, intron 2 of 3)	46966	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.010899	0.383152	
chunk0140_414_1	chr4	75765754	75766088	+	0	NA	intron (NM_001290049, intron 5 of 25)	intron (NM_001290049, intron 5 of 25)	41399	NM_001290049	8615	Hs.744877	NM_003715	ENSG00000138768	USO1	P115|TAP|VDP	USO1 vesicle transport factor	protein-coding	0.002994	0.367164	
chunk0163_214_1	chr6	12044549	12045240	+	0	NA	intron (NM_002114, intron 2 of 8)	intron (NM_002114, intron 2 of 8)	32403	NM_002114	3096	Hs.567284	NM_002114	ENSG00000095951	HIVEP1	CIRIP|CRYBP1|GAAP|MBP-1|PRDII-BF1|Schnurri-1|ZAS1|ZNF40|ZNF40A	human immunodeficiency virus type I enhancer binding protein 1	protein-coding	0.007236	0.511561	190(GAGGACTTGCTGTCCC,-,0.00),191(AGGACTTGCTGTCCCC,+,0.00),572(AGCACAGTCAGCTCTG,+,0.00)
chunk0203_309_1	chr9	89437286	89437502	+	0	NA	intron (NM_006378, intron 2 of 17)	intron (NM_006378, intron 2 of 17)	42302	NM_006378	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.023148	0.599078	
chunk0150_301_1	chr5	37649187	37649552	+	0	NA	intron (NM_018034, intron 10 of 17)	(TTTA)n|Simple_repeat|Simple_repeat	185453	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.002740	0.382514	
chunk0097_211_1	chr2	51295777	51295976	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-263340	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.395000	
chunk0139_140_1	chr4	53522327	53522806	+	0	NA	intron (NM_001126328, intron 2 of 10)	intron (NM_001126328, intron 2 of 10)	22489	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.000000	0.379167	
chunk0052_164_1	chr13	24069152	24069479	+	0	NA	intron (NM_001286792, intron 3 of 14)	L1PA13|LINE|L1	89689	NM_001286792	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.003058	0.347561	
chunk0125_105_1	chr3	65568492	65568898	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-325121	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.007389	0.407862	
chunk0164_98_1	chr6	20368044	20368438	+	0	NA	Intergenic	Intergenic	-33665	NM_001949	1871	Hs.269408	NM_001949	ENSG00000112242	E2F3	E2F-3	E2F transcription factor 3	protein-coding	0.002538	0.407595	
chunk0095_57_1	chr2	14084743	14085153	+	0	NA	Intergenic	L1PA7|LINE|L1	316010	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.002439	0.338200	224(CTGAACAACCTGTTCC,-,0.00),225(TGAACAACCTGTTCCT,+,0.00)
chunk0124_110_1	chr3	53859074	53859533	+	0	NA	intron (NM_018725, intron 9 of 10)	intron (NM_018725, intron 9 of 10)	12753	NM_018725	55540	Hs.654970	NM_018725	ENSG00000056736	IL17RB	CRL4|EVI27|IL17BR|IL17RH1	interleukin 17 receptor B	protein-coding	0.010893	0.456522	205(GAGAACAGCATGTTCT,-,0.00),206(AGAACAGCATGTTCTG,+,0.00)
chunk0038_290_1	chr11	90222498	90222863	+	0	NA	intron (NM_012124, intron 1 of 10)	CpG	684	NM_001144073	26973	Hs.22857	NM_012124	ENSG00000110172	CHORDC1	CHP1	cysteine and histidine rich domain containing 1	protein-coding	0.084932	0.655738	
chunk0067_293_1	chr15	47466168	47466752	+	0	NA	intron (NM_001198999, intron 2 of 19)	L1MA9|LINE|L1	-252029	NM_153618	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.001712	0.340171	
chunk0089_39_1	chr18	57980818	57981355	+	0	NA	Intergenic	Intergenic	-63292	NM_001243960	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.005587	0.353160	205(AAGAACTCTGTGTACT,-,0.00),206(AGAACTCTGTGTACTT,+,0.00)
chunk0176_114_1	chr7	11988178	11988577	+	0	NA	Intergenic	Intergenic	-156179	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.002506	0.300000	228(TAGAACAGTCTGTGAC,-,0.00),229(AGAACAGTCTGTGACT,+,0.00)
chunk0170_318_1	chr6	116111403	116112109	+	0	NA	intron (NM_152729, intron 4 of 11)	(TGTT)n|Simple_repeat|Simple_repeat	10920	NM_152729	221294	Hs.520341	NM_152729	ENSG00000178425	NT5DC1	C6orf200|LP2642|NT5C2L1	5'-nucleotidase domain containing 1	protein-coding	0.004249	0.342291	
chunk0173_244_1	chr6	146866540	146867103	+	0	NA	intron (NR_034115, intron 7 of 10)	MamGypLTR3a|LTR|Gypsy	-62997	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.012433	0.420213	280(AAGAACACTATGGACT,-,0.00),281(AGAACACTATGGACTT,+,0.00)
chunk0067_4_1	chr15	39900688	39901323	+	0	NA	intron (NM_001271854, intron 1 of 3)	intron (NM_001271854, intron 1 of 3)	19887	NM_001271854	11245	Hs.37196	NM_007223	ENSG00000166073	GPR176	HB-954	G protein-coupled receptor 176	protein-coding	0.001575	0.382075	
chunk0136_288_1	chr3	194870844	194871736	+	0	NA	Intergenic	Intergenic	162869	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.015695	0.494961	537(GGGGACACTCTGTTCT,-,0.00),538(GGGACACTCTGTTCTC,+,0.00)
chunk0015_313_1	chr1	189172088	189172574	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	1305298	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.006173	0.449692	
chunk0085_351_1	chr18	9067745	9068134	+	0	NA	Intergenic	MER110|LTR|ERV1	-34691	NM_021074	4729	Hs.464572	NM_021074	ENSG00000178127	NDUFV2	CI-24k|MC1DN7	NADH:ubiquinone oxidoreductase core subunit V2	protein-coding	0.010283	0.433333	
chunk0065_370_1	chr14	104008770	104009263	+	0	NA	intron (NM_153046, intron 20 of 35)	Tigger3b|DNA|TcMar-Tigger	-66708	NM_001257268	647286	Hs.632325	NM_001257268	ENSG00000227729	RD3L	TDRD9-AS1|TDRD9AS1	retinal degeneration 3 like	protein-coding	0.012170	0.419028	
chunk0001_324_1	chr1	9453494	9454021	+	0	NA	Intergenic	Intergenic	-24761	NR_104622	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.026565	0.500000	
chunk0142_174_1	chr4	95591224	95591849	+	0	NA	Intergenic	L2a|LINE|L2	-42326	NM_003728	8633	Hs.388565	NM_003728	ENSG00000182168	UNC5C	UNC5H3	unc-5 netrin receptor C	protein-coding	0.011200	0.346645	
chunk0018_431_1	chr1	222829806	222830182	+	0	NA	intron (NM_032890, intron 1 of 9)	intron (NM_032890, intron 1 of 9)	14905	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.000000	0.323607	
chunk0053_389_1	chr13	36195257	36195456	+	0	NA	intron (NM_017826, intron 2 of 10)	L2b|LINE|L2	19259	NM_017826	54937	Hs.124519	NM_017826	ENSG00000120669	SOHLH2	SOSF2|SPATA28|TEB1|bHLHe81	spermatogenesis and oogenesis specific basic helix-loop-helix 2	protein-coding	0.010050	0.535000	124(AGGTACAAGATGTCCA,-,0.00),125(GGTACAAGATGTCCAG,+,0.00)
chunk0050_53_1	chr12	101047560	101047974	+	0	NA	intron (NM_001286616, intron 12 of 26)	intron (NM_001286616, intron 12 of 26)	146121	NM_001286616	121601	Hs.58785	NM_178826	ENSG00000151572	ANO4	TMEM16D	anoctamin 4	protein-coding	0.000000	0.342169	
chunk0114_260_1	chr21	16169640	16170251	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	-24434	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.001637	0.339869	
chunk0091_10_1	chr19	2895712	2896068	+	0	NA	Intergenic	Intergenic	-5008	NM_173480	126295	Hs.591378	NM_173480	ENSG00000171970	ZNF57	ZNF424	zinc finger protein 57	protein-coding	0.014045	0.422969	
chunk0008_250_1	chr1	94422927	94423167	+	0	NA	intron (NM_001122674, intron 1 of 8)	L2b|LINE|L2	4670	NM_001122674	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.004167	0.406639	104(GGGTACTCTCTGTTCC,-,0.00),105(GGTACTCTCTGTTCCA,+,0.00)
chunk0036_169_1	chr11	62548632	62549303	+	0	NA	Intergenic	Intergenic	-2107	NM_001620	79026	Hs.502756	NM_001620	ENSG00000124942	AHNAK	AHNAKRS|PM227	AHNAK nucleoprotein	protein-coding	0.020864	0.501488	
chunk0120_96_1	chr3	4322500	4323138	+	0	NA	Intergenic	L1MB7|LINE|L1	19206	NR_024022	6419	Hs.475300	NM_006515	ENSG00000170364	SETMAR	METNASE|Mar1	SET domain and mariner transposase fusion gene	protein-coding	0.003135	0.389671	
chunk0122_36_1	chr3	27972449	27972922	+	0	NA	Intergenic	Intergenic	-138549	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.006342	0.375527	252(TAGAACTTTATGTACT,-,0.00),253(AGAACTTTATGTACTT,+,0.00)
chunk0029_157_1	chr10	99647446	99647804	+	0	NA	Intergenic	L1PB4|LINE|L1	-11881	NM_020354	57089	Hs.28326	NM_020354	ENSG00000198018	ENTPD7	LALP1	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding	0.000000	0.331476	
chunk0159_248_1	chr5	141921093	141921315	+	0	NA	Intergenic	Intergenic	-2616	NM_014773	9812	Hs.210532	NM_014773	ENSG00000081791	DELE1	DELE|KIAA0141	DAP3 binding cell death enhancer 1	protein-coding	0.000000	0.421525	158(TAGTACAAGATGTTCT,-,0.00),159(AGTACAAGATGTTCTG,+,0.00)
chunk0012_394_1	chr1	163616767	163617558	+	0	NA	Intergenic	L2a|LINE|L2	-193971	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.005057	0.343434	
chunk0004_130_1	chr1	44730648	44731422	+	0	NA	TTS (NR_002755)	TTS (NR_002755)	133	NR_002755	26830		NR_002755	ENSG00000200169	RNU5D-1	RNU5D|U5DL|U5DS	RNA, U5D small nuclear 1	snRNA	0.023256	0.419355	
chunk0071_105_1	chr15	81064558	81064757	+	0	NA	Intergenic	Intergenic	63703	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.005025	0.405000	
chunk0051_71_1	chr12	113185375	113185829	+	0	NA	promoter-TSS (NM_024072)	promoter-TSS (NM_024072)	76	NM_001286215	84934	Hs.524762	NM_032848	ENSG00000139405	RITA1	C12orf52|RITA	RBPJ interacting and tubulin associated 1	protein-coding	0.092511	0.696703	
chunk0133_360_1	chr3	173513061	173513399	+	0	NA	intron (NM_014932, intron 2 of 6)	L1MCa|LINE|L1	114782	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.005917	0.404130	101(GTTACAGAATGTTCTG,+,0.00)
chunk0208_83_1	chrX	13094142	13094501	+	0	NA	Intergenic	L1ME3|LINE|L1	-49523	NM_174901	171484	Hs.667546	NM_174901	ENSG00000187268	FAM9C	TEX39C	family with sequence similarity 9 member C	protein-coding	0.000000	0.347222	207(TTGTACAGAATGTACT,-,0.00),208(TGTACAGAATGTACTC,+,0.00)
chunk0058_198_1	chr14	24541622	24541986	+	0	NA	Intergenic	L1PA15|LINE|L1	-33539	NM_001836	1215	Hs.135626	NM_001836	ENSG00000092009	CMA1	CYH|MCT1|chymase	chymase 1	protein-coding	0.000000	0.375342	
chunk0180_431_1	chr7	76379857	76380060	+	0	NA	Intergenic	CpG	-17566	NM_007155	7784	Hs.656137	NM_007155	ENSG00000188372	ZP3	OOMD3|ZP3A|ZP3B|ZPC|Zp-3	zona pellucida glycoprotein 3	protein-coding	0.064039	0.700980	
chunk0128_102_1	chr3	106025255	106026339	+	0	NA	Intergenic	L1MEi|LINE|L1	-156754	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.007380	0.356682	
chunk0096_1_1	chr2	25786998	25787473	+	0	NA	intron (NM_018263, intron 4 of 11)	LTR40c|LTR|ERVL	91208	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.006316	0.392857	
chunk0137_220_1	chr4	19983716	19984149	+	0	NA	Intergenic	L1MD1|LINE|L1	-267973	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.009238	0.364055	
chunk0191_183_1	chr8	51340389	51340879	+	0	NA	intron (NM_144651, intron 20 of 22)	intron (NM_144651, intron 20 of 22)	468811	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.002041	0.309572	
chunk0081_116_1	chr17	40054179	40054605	+	0	NA	non-coding (NR_052017, exon 1 of 25)	non-coding (NR_052017, exon 1 of 25)	244	NM_014815	9862	Hs.462983	NM_014815	ENSG00000008838	MED24	ARC100|CRSP100|CRSP4|DRIP100|MED5|THRAP4|TRAP100	mediator complex subunit 24	protein-coding	0.032864	0.508197	
chunk0141_25_1	chr4	76857034	76857315	+	0	NA	Intergenic	Intergenic	40675	NM_001029870	345079	Hs.257292	NM_001029870	ENSG00000186212	SOWAHB	ANKRD56	sosondowah ankyrin repeat domain family member B	protein-coding	0.010676	0.365248	127(AAGAACAAGTTGTACC,-,0.00),128(AGAACAAGTTGTACCA,+,0.00)
chunk0109_226_1	chr20	5835403	5835804	+	0	NA	intron (NM_001303478, intron 3 of 3)	intron (NM_001303478, intron 3 of 3)	-75725	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.004988	0.495025	
chunk0183_150_1	chr7	105839825	105840114	+	0	NA	intron (NM_020725, intron 2 of 11)	L2c|LINE|L2	36616	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.003460	0.489655	
chunk0073_411_1	chr16	17759361	17759647	+	0	NA	Intergenic	Intergenic	-288623	NM_022166	64131	Hs.22907	NM_022166	ENSG00000103489	XYLT1	DBQD2|PXYLT1|XT-I|XT1|XTI|XYLTI|xylT-I	xylosyltransferase 1	protein-coding	0.003497	0.376307	
chunk0108_53_1	chr2	227038587	227039053	+	0	NA	intron (NM_000092, intron 37 of 47)	intron (NM_000092, intron 37 of 47)	125739	NM_000092	1286	Hs.591645	NM_000092	ENSG00000081052	COL4A4	ATS2|BFH|CA44	collagen type IV alpha 4 chain	protein-coding	0.000000	0.359743	
chunk0071_403_1	chr15	89576134	89576690	+	0	NA	intron (NM_001308025, intron 1 of 21)	intron (NM_001308025, intron 1 of 21)	825	NM_152259	90381	Hs.441708	NM_152259	ENSG00000140534	TICRR	C15orf42|SLD3|Treslin	TOPBP1 interacting checkpoint and replication regulator	protein-coding	0.021583	0.470377	
chunk0071_177_1	chr15	83339161	83339675	+	0	NA	Intergenic	Tigger5b|DNA|TcMar-Tigger	-54702	NM_001717	646	Hs.459153	NM_001717	ENSG00000169594	BNC1	BNC|BSN1|HsT19447	basonuclin 1	protein-coding	0.007782	0.415534	
chunk0071_166_1	chr15	83053064	83053622	+	0	NA	intron (NM_025238, intron 2 of 7)	intron (NM_025238, intron 2 of 7)	-13992	NR_039740	100616404		NR_039740	ENSG00000263643	MIR4515	mir-4515	microRNA 4515	ncRNA	0.003584	0.364937	
chunk0069_138_1	chr15	62125531	62125916	+	0	NA	Intergenic	L1MEi|LINE|L1	39560	NM_001007595	388125	Hs.144372	NM_001007595	ENSG00000205502	C2CD4B	FAM148B|NLF2	C2 calcium dependent domain containing 4B	protein-coding	0.005195	0.383420	
chunk0129_60_1	chr3	117575494	117576115	+	0	NA	Intergenic	L1MA4A|LINE|L1	654373	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001610	0.327974	
chunk0146_362_1	chr4	168221208	168221569	+	0	NA	intron (NM_017631, intron 36 of 37)	intron (NM_017631, intron 36 of 37)	97419	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.005540	0.350829	
chunk0191_225_1	chr8	52743426	52743722	+	0	NA	Intergenic	L1ME1|LINE|L1	-29108	NM_001083617	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.000000	0.383838	124(AGTACAGACAGATCTT,+,0.00)
chunk0074_347_1	chr16	33337718	33337917	+	0	NA	Intergenic	(TGGCTTGGC)n|Simple_repeat|Simple_repeat	-23060	NM_016212	24150	Hs.592038	NM_015369	ENSG00000183632	TP53TG3	P53TG3|TP53TG3A|TP53TG3E|TP53TG3F	TP53 target 3	protein-coding	0.005025	0.665000	
chunk0087_381_1	chr18	41666534	41666763	+	0	NA	Intergenic	Intergenic	-146051	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.004367	0.360870	
chunk0074_265_1	chr16	28160344	28160834	+	0	NA	intron (NM_001270940, intron 7 of 24)	HAL1b|LINE|L1	51329	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.010204	0.364562	
chunk0053_408_1	chr13	36890381	36890605	+	0	NA	intron (NM_001127217, intron 1 of 6)	intron (NM_001127217, intron 1 of 6)	29779	NM_005905	4093	Hs.123119	NM_005905	ENSG00000120693	SMAD9	MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B	SMAD family member 9	protein-coding	0.004464	0.328889	
chunk0137_342_1	chr4	25086297	25086496	+	0	NA	Intergenic	MIRc|SINE|MIR	-55604	NM_018176	55203	Hs.12488	NM_018176	ENSG00000153012	LGI2	LGIL2	leucine rich repeat LGI family member 2	protein-coding	0.005025	0.400000	
chunk0189_371_1	chr8	27297118	27297537	+	0	NA	intron (NM_001304495, intron 1 of 3)	intron (NM_001304495, intron 1 of 3)	13992	NM_171982	23087	Hs.104223	NM_171982	ENSG00000104228	TRIM35	HLS5|MAIR	tripartite motif containing 35	protein-coding	0.004773	0.497619	
chunk0142_211_1	chr4	97624110	97624849	+	0	NA	intron (NM_174952, intron 10 of 10)	L1PA10|LINE|L1	257553	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.006766	0.347297	
chunk0023_93_1	chr10	22501094	22501430	+	0	NA	Intergenic	Intergenic	-63333	NR_036533	100499489	Hs.7444	NR_036533		LOC100499489	-	uncharacterized LOC100499489	ncRNA	0.005952	0.403561	
chunk0152_359_1	chr5	63757816	63758410	+	0	NA	Intergenic	LTR10C|LTR|ERV1	204179	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.003367	0.260504	
chunk0205_264_1	chr9	111348725	111349287	+	0	NA	Intergenic	LTR44|LTR|ERV1	-20573	NM_205859	26248	Hs.381312	NM_205859	ENSG00000171133	OR2K2	HSHTPCRH06|HTPCRH06|OR2AN1P|OR2AR1P	olfactory receptor family 2 subfamily K member 2	protein-coding	0.007117	0.383659	
chunk0040_241_1	chr11	114682124	114682336	+	0	NA	intron (NM_182495, intron 2 of 5)	MER4-int|LTR|ERV1	3752	NM_182495	120406	Hs.446760	NM_182495	ENSG00000204361	NXPE2	FAM55B	neurexophilin and PC-esterase domain family member 2	protein-coding	0.004717	0.300469	
chunk0032_239_1	chr11	7752609	7752982	+	0	NA	Intergenic	L2a|LINE|L2	44147	NM_153444	120065	Hs.351824	NM_153444	ENSG00000183303	OR5P2	JCG3|JCG4	olfactory receptor family 5 subfamily P member 2	protein-coding	0.002681	0.377005	
chunk0207_431_1	chr9	137328165	137328533	+	0	NA	intron (NM_017820, intron 17 of 21)	intron (NM_017820, intron 17 of 21)	-26098	NM_001004354	441478	Hs.535075	NM_001004354	ENSG00000198435	NRARP	-	NOTCH regulated ankyrin repeat protein	protein-coding	0.008152	0.271003	
chunk0119_23_1	chr22	40204096	40204300	+	0	NA	intron (NM_015088, intron 1 of 20)	intron (NM_015088, intron 1 of 20)	26273	NM_015088	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.004902	0.341463	
chunk0027_45_1	chr10	72742134	72742366	+	0	NA	intron (NR_073062, intron 3 of 9)	Tigger3a|DNA|TcMar-Tigger	21221	NR_039823	100616286		NR_039823	ENSG00000266719	MIR4676	-	microRNA 4676	ncRNA	0.008621	0.403433	51(AGGAACATGTTGTACA,-,0.00),52(GGAACATGTTGTACAG,+,0.00)
chunk0084_215_1	chr17	78211106	78211575	+	0	NA	Intergenic	Intergenic	-2856	NM_001168	332	Hs.744872	NM_001168	ENSG00000089685	BIRC5	API4|EPR-1	baculoviral IAP repeat containing 5	protein-coding	0.025586	0.551064	
chunk0197_444_1	chr8	127763364	127764039	+	0	NA	Intergenic	Intergenic	27632	NM_002467	4609	Hs.202453	NM_002467	ENSG00000136997	MYC	MRTL|MYCC|bHLHe39|c-Myc	MYC proto-oncogene, bHLH transcription factor	protein-coding	0.011852	0.442308	
chunk0068_40_1	chr15	51307814	51308105	+	0	NA	intron (NM_000103, intron 1 of 9)	MIRb|SINE|MIR	-6075	NR_107012	102466250		NR_107012	ENSG00000278098	MIR7973-1	hsa-mir-7973-1	microRNA 7973-1	ncRNA	0.006873	0.462329	139(ATGAACACAAAGTTCT,-,0.00),140(TGAACACAAAGTTCTT,+,0.00)
chunk0106_394_1	chr2	207734332	207734648	+	0	NA	intron (NM_152523, intron 5 of 10)	intron (NM_152523, intron 5 of 10)	-20317	NR_039934	100616361		NR_039934	ENSG00000284079	MIR4775	-	microRNA 4775	ncRNA	0.009494	0.403785	109(AGGAACAGCTTGTCCT,-,0.00),110(GGAACAGCTTGTCCTC,+,0.00)
chunk0199_55_1	chr9	1953943	1954363	+	0	NA	Intergenic	Intergenic	-61066	NM_001289397	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.002381	0.353919	
chunk0167_396_1	chr6	74930282	74930813	+	0	NA	Intergenic	Intergenic	275360	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.003766	0.310150	
chunk0064_317_1	chr14	95887166	95887926	+	0	NA	intron (NR_038861, intron 1 of 1)	intron (NR_038861, intron 1 of 1)	10774	NR_038861	100507043	Hs.455955	NR_038861	ENSG00000250366	TUNAR	HI-LNC78|LINC00617|TUNA	TCL1 upstream neural differentiation-associated RNA	ncRNA	0.009211	0.441524	
chunk0085_200_1	chr18	6568798	6569112	+	0	NA	intron (NR_120518, intron 2 of 5)	intron (NR_120518, intron 2 of 5)	57539	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.006369	0.368254	
chunk0194_126_1	chr8	84103558	84104119	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-79380	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.008913	0.320285	
chunk0171_22_1	chr6	120098032	120098241	+	0	NA	Intergenic	L1MB5|LINE|L1	82957	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.004785	0.342857	
chunk0009_16_1	chr1	100006423	100006622	+	0	NA	intron (NM_001271684, intron 3 of 5)	L1M2|LINE|L1	-31711	NM_033055	64645	Hs.124156	NM_033055	ENSG00000156875	MFSD14A	HIAT1	major facilitator superfamily domain containing 14A	protein-coding	0.015075	0.560000	
chunk0102_357_1	chr2	152617104	152617887	+	0	NA	intron (NM_052905, intron 13 of 25)	intron (NM_052905, intron 13 of 25)	99966	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.008940	0.415816	
chunk0125_403_1	chr3	72152796	72153197	+	0	NA	intron (NR_038221, intron 1 of 2)	intron (NR_038221, intron 1 of 2)	1739	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.034913	0.507463	
chunk0157_128_1	chr5	117256381	117256583	+	0	NA	Intergenic	Intergenic	-159030	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.000000	0.344828	
chunk0165_182_1	chr6	34392499	34393033	+	0	NA	promoter-TSS (NM_006703)	promoter-TSS (NM_006703)	-86	NM_006703	11165	Hs.188882	NM_006703	ENSG00000272325	NUDT3	DIPP|DIPP-1|DIPP1	nudix hydrolase 3	protein-coding	0.153558	0.742056	
chunk0079_259_1	chr17	16162727	16163086	+	0	NA	intron (NM_006311, intron 5 of 45)	L1ME3D|LINE|L1	31733	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.005571	0.325000	
chunk0003_34_1	chr1	30110632	30111152	+	0	NA	Intergenic	L1ME1|LINE|L1	-73280	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.017308	0.441459	
chunk0212_100_1	chrY	13576312	13576774	+	0	NA	Intergenic	L1PA8|LINE|L1	-95873	NR_047617	7404	Hs.115277	NM_007125	ENSG00000183878	UTY	KDM6AL|KDM6C|UTY1	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	protein-coding	0.006494	0.393089	
chunk0182_234_1	chr7	96688943	96689642	+	0	NA	intron (NM_006304, intron 2 of 2)	intron (NM_006304, intron 2 of 2)	20599	NM_006304	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.000000	0.281429	
chunk0083_338_1	chr17	70196445	70196864	+	0	NA	Intergenic	Intergenic	27119	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.004773	0.404762	
chunk0136_428_1	chr3	197609340	197609693	+	0	NA	Intergenic	L1MA3|LINE|L1	18365	NR_003266	220729	Hs.478854	NR_003266	ENSG00000214135	LOC220729	-	succinate dehydrogenase complex flavoprotein subunit A pseudogene	pseudo	0.002833	0.338983	
chunk0174_303_1	chr6	162695717	162696281	+	0	NA	intron (NM_013988, intron 1 of 8)	MIRb|SINE|MIR	-31133	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.010638	0.336283	
chunk0035_161_1	chr11	43489730	43490514	+	0	NA	intron (NM_018259, intron 21 of 23)	MIRb|SINE|MIR	-69534	NR_031577	100313777		NR_031577	ENSG00000211568	MIR670	hsa-mir-670	microRNA 670	ncRNA	0.008929	0.445860	366(TGGAACAGAAAGTGCT,-,0.00),367(GGAACAGAAAGTGCTG,+,0.00)
chunk0056_234_1	chr13	88948410	88949107	+	0	NA	Intergenic	Intergenic	-286533	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.005739	0.343840	297(GAGGACAACTTGTTCT,-,0.00),298(AGGACAACTTGTTCTC,+,0.00)
chunk0196_452_1	chr8	116657912	116658610	+	0	NA	intron (NM_003756, intron 3 of 7)	intron (NM_003756, intron 3 of 7)	97562	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.012894	0.396280	
chunk0192_149_1	chr8	62043879	62044451	+	0	NA	Intergenic	L1MC4a|LINE|L1	-204777	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.013986	0.389180	
chunk0176_271_1	chr7	16493844	16494076	+	0	NA	Intergenic	MER130|DNA|DNA	-28111	NM_015464	25928	Hs.648106	NM_015464	ENSG00000171243	SOSTDC1	CDA019|DAND7|ECTODIN|USAG1	sclerostin domain containing 1	protein-coding	0.008621	0.386266	
chunk0209_410_1	chrX	56308590	56309195	+	0	NA	Intergenic	L1PA15|LINE|L1	76455	NM_001159296	11279	Hs.646614	NM_007250	ENSG00000102349	KLF8	BKLF3|ZNF741	Kruppel like factor 8	protein-coding	0.001653	0.376238	301(GGTAACAGTCTGTCCC,-,0.00),302(GTAACAGTCTGTCCCT,+,0.00)
chunk0169_350_1	chr6	106608159	106608628	+	0	NA	intron (NM_032730, intron 4 of 8)	L1MA5|LINE|L1	21105	NM_032730	84816	Hs.155839	NM_032730	ENSG00000130347	RTN4IP1	NIMP|OPA10	reticulon 4 interacting protein 1	protein-coding	0.004264	0.359574	
chunk0008_301_1	chr1	95022615	95022981	+	0	NA	intron (NR_131032, intron 2 of 2)	intron (NR_131032, intron 2 of 2)	-38798	NR_132786	101928098	Hs.730090	NR_132786	ENSG00000230427	LOC101928098	-	uncharacterized LOC101928098	ncRNA	0.000000	0.346049	
chunk0135_450_1	chr3	194271214	194271769	+	0	NA	Intergenic	Intergenic	-21338	NR_125403	100505920	Hs.436654	NR_125403	ENSG00000225742	LINC02036	-	long intergenic non-protein coding RNA 2036	ncRNA	0.025225	0.625899	177(GAAGACAGCCAGTCCT,-,0.00),178(AAGACAGCCAGTCCTC,+,0.00),280(GGGCACACCCCGTCCC,-,0.00),281(GGCACACCCCGTCCCT,+,0.00)
chunk0210_128_1	chrX	74181200	74181706	+	0	NA	intron (NR_028379, intron 5 of 6)	HERVK3-int|LTR|ERVK	37008	NR_030398	693122		NR_030398	ENSG00000202566	MIR421	MIRN421|hsa-mir-421	microRNA 421	ncRNA	0.007905	0.390533	
chunk0028_51_1	chr10	83207071	83207349	+	0	NA	Intergenic	L1PREC2|LINE|L1	-932219	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.003597	0.358423	
chunk0182_372_1	chr7	100017321	100017752	+	0	NA	intron (NM_001287055, intron 1 of 3)	intron (NM_001287055, intron 1 of 3)	1964	NM_001287055	7586	Hs.615360	NM_003439	ENSG00000106261	ZKSCAN1	KOX18|PHZ-37|ZNF139|ZNF36|ZSCAN33	zinc finger with KRAB and SCAN domains 1	protein-coding	0.023202	0.476852	
chunk0207_368_1	chr9	135971879	135972201	+	0	NA	Intergenic	Intergenic	-10660	NM_016172	10422	Hs.9194	NM_016172	ENSG00000130560	UBAC1	GBDR1|KPC2|UBADC1	UBA domain containing 1	protein-coding	0.027950	0.640867	
chunk0122_123_1	chr3	31285680	31286265	+	0	NA	Intergenic	Intergenic	-124185	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.006838	0.395904	
chunk0097_174_1	chr2	49805206	49805584	+	0	NA	Intergenic	Intergenic	542361	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.015873	0.395778	
chunk0161_417_1	chr5	178204487	178204687	+	0	NA	promoter-TSS (NM_031266)	promoter-TSS (NM_031266)	80	NM_031266	3182	Hs.591731	NM_004499	ENSG00000197451	HNRNPAB	ABBP1|HNRPAB	heterogeneous nuclear ribonucleoprotein A/B	protein-coding	0.115000	0.706468	
chunk0025_22_1	chr10	48251685	48252051	+	0	NA	intron (NM_001018071, intron 1 of 28)	L2b|LINE|L2	23030	NM_001018071	143162	Hs.664786	NM_152428	ENSG00000170324	FRMPD2	PDZD5C|PDZK4|PDZK5C	FERM and PDZ domain containing 2	protein-coding	0.016393	0.498638	
chunk0201_357_1	chr9	68492781	68493431	+	0	NA	intron (NM_021965, intron 9 of 10)	intron (NM_021965, intron 9 of 10)	47761	NM_153237	169693	Hs.663056	NM_153237	ENSG00000181778	TMEM252	C9orf71	transmembrane protein 252	protein-coding	0.010769	0.402458	
chunk0122_285_1	chr3	36142653	36143044	+	0	NA	Intergenic	L1PA17|LINE|L1	-237639	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.000000	0.288265	
chunk0049_229_1	chr12	93445089	93445288	+	0	NA	Intergenic	Intergenic	-2938	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.020101	0.390000	118(AAGAACAGGTTGTCAC,-,0.00)
chunk0113_292_1	chr20	57530291	57530724	+	0	NA	Intergenic	Intergenic	-4855	NM_001269040	140690	Hs.131543	NM_080618	ENSG00000124092	CTCFL	BORIS|CT27|CTCF-T|HMGB1L1|dJ579F20.2	CCCTC-binding factor like	protein-coding	0.004619	0.394009	
chunk0035_411_1	chr11	56967615	56968193	+	0	NA	Intergenic	L1PA11|LINE|L1	-21010	NM_001005323	390181	Hs.554520	NM_001005323	ENSG00000181273	OR5AK2	-	olfactory receptor family 5 subfamily AK member 2	protein-coding	0.001730	0.379965	
chunk0069_311_1	chr15	65610874	65611365	+	0	NA	promoter-TSS (NR_045106)	promoter-TSS (NR_045106)	29	NR_045106	81556	Hs.6686	NM_030800	ENSG00000138614	INTS14	C15orf44|VWA9	integrator complex subunit 14	protein-coding	0.103870	0.678862	
chunk0015_365_1	chr1	190411148	190411855	+	0	NA	intron (NM_199051, intron 2 of 7)	intron (NM_199051, intron 2 of 7)	66128	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.002829	0.303672	
chunk0164_275_1	chr6	23960625	23960824	+	0	NA	Intergenic	Intergenic	-165462	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.005025	0.420000	114(TAGCACACACTGTCCA,-,0.00),115(AGCACACACTGTCCAA,+,0.00)
chunk0181_147_1	chr7	81781308	81781690	+	0	NA	Intergenic	Intergenic	-11363	NM_001010934	3082	Hs.396530	NM_000601	ENSG00000019991	HGF	DFNB39|F-TCF|HGFB|HPTA|SF	hepatocyte growth factor	protein-coding	0.002618	0.373368	
chunk0145_439_1	chr4	153394999	153395488	+	0	NA	intron (NM_001253861, intron 5 of 6)	intron (NM_001253861, intron 5 of 6)	50594	NM_032117	84057	Hs.294088	NM_032117	ENSG00000121211	MND1	GAJ	meiotic nuclear divisions 1	protein-coding	0.006135	0.377551	
chunk0047_100_1	chr12	68755231	68755844	+	0	NA	intron (NM_018656, intron 3 of 4)	MSTB|LTR|ERVL-MaLR	9381	NM_018656	55508	Hs.506011	NM_018656	ENSG00000175782	SLC35E3	BLOV1	solute carrier family 35 member E3	protein-coding	0.003263	0.415309	
chunk0209_160_1	chrX	42925706	42926327	+	0	NA	Intergenic	L1MA3|LINE|L1	-147781	NR_002191									0.003221	0.324759	
chunk0125_416_1	chr3	72317384	72317708	+	0	NA	Intergenic	Intergenic	129077	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.018519	0.538462	
chunk0184_366_1	chr7	121069398	121069752	+	0	NA	intron (NM_001105533, intron 4 of 17)	intron (NM_001105533, intron 4 of 17)	80184	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.008475	0.402817	143(TAACACAGTCTGTTCC,-,0.00),144(AACACAGTCTGTTCCA,+,0.00)
chunk0184_377_1	chr7	121384408	121384608	+	0	NA	intron (NM_001040020, intron 1 of 9)	intron (NM_001040020, intron 1 of 9)	11860	NM_001040020	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.005000	0.412935	142(AGGTACTTGATGTTCT,-,0.00),143(GGTACTTGATGTTCTA,+,0.00)
chunk0077_397_1	chr16	84913164	84913788	+	0	NA	Intergenic	L1MC4|LINE|L1	93495	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.019231	0.507200	295(GGAGACACTGTGTCCT,-,0.00),296(GAGACACTGTGTCCTT,+,0.00)
chunk0097_53_1	chr2	43452344	43452768	+	0	NA	intron (NM_001083953, intron 26 of 37)	intron (NM_001083953, intron 26 of 37)	143418	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.002358	0.428235	212(GAGGACACACTGTGAC,-,0.00)
chunk0089_104_1	chr18	58438330	58438655	+	0	NA	Intergenic	Intergenic	-12582	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.006154	0.500000	
chunk0174_316_1	chr6	163108642	163109156	+	0	NA	intron (NM_001080378, intron 5 of 5)	intron (NM_001080378, intron 5 of 5)	-54738	NR_110871	101929239	Hs.571035	NR_110871	ENSG00000225437	PACRG-AS2	-	PACRG antisense RNA 2	ncRNA	0.007782	0.394175	
chunk0119_85_1	chr22	41448247	41448493	+	0	NA	Intergenic	Intergenic	-1347	NM_016272	10766	Hs.474978	NM_016272	ENSG00000183864	TOB2	APRO5|TOB4|TOBL|TROB2	transducer of ERBB2, 2	protein-coding	0.056911	0.651822	
chunk0128_108_1	chr3	106202709	106203242	+	0	NA	Intergenic	Intergenic	-333932	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.265918	359(AAGTACAACTTGTTCA,-,0.00)
chunk0058_192_1	chr14	24290740	24291381	+	0	NA	intron (NM_001136050, intron 8 of 8)	intron (NM_001136050, intron 8 of 8)	8400	NM_138452	115817	Hs.348350	NM_138452	ENSG00000157379	DHRS1	SDR19C1	dehydrogenase/reductase 1	protein-coding	0.020281	0.560748	
chunk0134_392_1	chr3	182962016	182962530	+	0	NA	intron (NM_001308101, intron 3 of 6)	LTR50|LTR|ERVL	18328	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.001946	0.405825	226(AAGGACATAGTGTCCA,-,0.00),227(AGGACATAGTGTCCAG,+,0.00)
chunk0043_134_1	chr12	15911326	15911525	+	0	NA	intron (NM_015954, intron 1 of 8)	CpG	253	NM_001300779	51071	Hs.39429	NM_015954	ENSG00000023697	DERA	CGI-26|DEOC	deoxyribose-phosphate aldolase	protein-coding	0.130653	0.770000	
chunk0167_158_1	chr6	62663494	62663927	+	0	NA	Intergenic	Tigger14a|DNA|TcMar-Tigger	-377515	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.000000	0.313364	
chunk0164_346_1	chr6	25426552	25427023	+	0	NA	intron (NM_017640, intron 4 of 36)	intron (NM_017640, intron 4 of 36)	147359	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.004246	0.338983	
chunk0008_444_1	chr1	99645841	99646061	+	0	NA	promoter-TSS (NM_017734)	promoter-TSS (NM_017734)	76	NM_017734	54873	Hs.483993	NM_017734	ENSG00000099260	PALMD	C1orf11|PALML	palmdelphin	protein-coding	0.013636	0.470588	
chunk0072_220_1	chr15	95679783	95680427	+	0	NA	Intergenic	L1MC2|LINE|L1	247012	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.007764	0.401550	367(GGGAACTCTCTGTACT,-,0.00),368(GGAACTCTCTGTACTT,+,0.00)
chunk0006_225_1	chr1	68525927	68526195	+	0	NA	intron (NR_110671, intron 1 of 2)	intron (NR_110671, intron 1 of 2)	-28840	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.003731	0.453532	
chunk0020_391_1	chr1	240507973	240508764	+	0	NA	intron (NM_022469, intron 1 of 1)	intron (NM_022469, intron 1 of 1)	103794	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.007585	0.352273	
chunk0050_211_1	chr12	104334609	104335191	+	0	NA	intron (NM_003330, intron 13 of 14)	intron (NM_003330, intron 13 of 14)	31168	NM_001008394	493861	Hs.659857	NM_001008394	ENSG00000255150	EID3	NS4EB|NSE4B|NSMCE4B	EP300 interacting inhibitor of differentiation 3	protein-coding	0.013746	0.425386	
chunk0160_342_1	chr5	160048889	160049470	+	0	NA	intron (NM_003314, intron 5 of 7)	MER58B|DNA|hAT-Charlie	40079	NM_001282500	7265	Hs.519718	NM_003314	ENSG00000113312	TTC1	TPR1	tetratricopeptide repeat domain 1	protein-coding	0.010327	0.400344	
chunk0018_362_1	chr1	221742282	221742528	+	0	NA	promoter-TSS (NM_007207)	promoter-TSS (NM_007207)	-229	NM_007207	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.065041	0.570850	
chunk0083_111_1	chr17	64720353	64720793	+	0	NA	Intergenic	L1ME3C|LINE|L1	-58305	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.018182	0.417234	
chunk0173_450_1	chr6	151757687	151758143	+	0	NA	intron (NM_001122742, intron 2 of 9)	intron (NM_001122742, intron 2 of 9)	-47758	NM_001122741	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.008772	0.411379	
chunk0203_222_1	chr9	86943429	86943943	+	0	NA	TTS (NM_002048)	TTS (NM_002048)	3503	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.015564	0.392233	
chunk0013_153_1	chr1	168631589	168632164	+	0	NA	Intergenic	Intergenic	55403	NM_002995	6375	Hs.546295	NM_002995	ENSG00000143184	XCL1	ATAC|LPTN|LTN|SCM-1|SCM-1a|SCM1|SCM1A|SCYC1	X-C motif chemokine ligand 1	protein-coding	0.010435	0.453125	236(CAGCACACGCTGTTCT,-,0.00),237(AGCACACGCTGTTCTT,+,0.00)
chunk0006_183_1	chr1	67382306	67382804	+	0	NA	intron (NM_001258216, intron 13 of 13)	L2c|LINE|L2	47885	NM_001018067	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.002008	0.464930	290(AAGTACTGGCTGTTCC,-,0.00),291(AGTACTGGCTGTTCCC,+,0.00)
chunk0086_241_1	chr18	22913819	22914289	+	0	NA	Intergenic	Intergenic	-19278	NM_002894	5932	Hs.546282	NM_002894	ENSG00000101773	RBBP8	COM1|CTIP|JWDS|RIM|SAE2|SCKL2	RB binding protein 8, endonuclease	protein-coding	0.006383	0.454352	
chunk0130_396_1	chr3	140223806	140224005	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	284884	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.010050	0.445000	
chunk0108_174_1	chr2	231811417	231811637	+	0	NA	Intergenic	Intergenic	25144	NM_001282950	64708	Hs.335061	NM_022730	ENSG00000144524	COPS7B	CSN7B|SGN7b	COP9 signalosome subunit 7B	protein-coding	0.004545	0.420814	
chunk0131_93_1	chr3	143594275	143594528	+	0	NA	intron (NM_173653, intron 6 of 15)	MIRb|SINE|MIR	252155	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.011858	0.374016	
chunk0072_342_1	chr15	99490843	99491289	+	0	NA	Intergenic	L1MEg|LINE|L1	-74862	NM_001130927	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.020179	0.451902	
chunk0115_203_1	chr21	26505466	26505714	+	0	NA	intron (NM_052954, intron 2 of 3)	MIRb|SINE|MIR	67672	NM_052954	116159	Hs.37445	NM_052954	ENSG00000166265	CYYR1	C21orf95	cysteine and tyrosine rich 1	protein-coding	0.000000	0.329317	
chunk0009_41_1	chr1	100449541	100449855	+	0	NA	intron (NM_003672, intron 7 of 15)	L2c|LINE|L2	-88474	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.003185	0.393651	
chunk0177_239_1	chr7	24769732	24770114	+	0	NA	Intergenic	MER21C|LTR|ERVL	-11903	NM_001127454	1687	Hs.520708	NM_004403	ENSG00000105928	GSDME	DFNA5|ICERE-1	gasdermin E	protein-coding	0.005236	0.399478	
chunk0143_420_1	chr4	123609667	123610316	+	0	NA	Intergenic	Intergenic	-42794	NR_027105	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.007704	0.386154	
chunk0139_109_1	chr4	52035214	52035531	+	0	NA	intron (NM_000232, intron 1 of 5)	intron (NM_000232, intron 1 of 5)	2947	NM_000232	6443	Hs.438953	NM_000232	ENSG00000163069	SGCB	A3b|LGMD2E|LGMDR4|SGC	sarcoglycan beta	protein-coding	0.000000	0.402516	
chunk0012_10_1	chr1	154815457	154815973	+	0	NA	intron (NM_170782, intron 2 of 7)	intron (NM_170782, intron 2 of 7)	44147	NM_170782	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.013566	0.471954	
chunk0067_330_1	chr15	48285853	48286309	+	0	NA	intron (NM_001184832, intron 21 of 26)	intron (NM_001184832, intron 21 of 26)	-45343	NM_001025248	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.021930	0.442013	
chunk0038_333_1	chr11	92734124	92735066	+	0	NA	intron (NM_001008781, intron 3 of 24)	intron (NM_001008781, intron 3 of 24)	-235028	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.006369	0.384942	
chunk0203_340_1	chr9	89790656	89790866	+	0	NA	Intergenic	Intergenic	150978	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.004762	0.511848	
chunk0061_446_1	chr14	65810061	65810283	+	0	NA	Intergenic	Intergenic	339070	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.000000	0.390135	
chunk0055_195_1	chr13	61813154	61813381	+	0	NA	Intergenic	Intergenic	216281	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.013216	0.364035	
chunk0160_214_1	chr5	154868804	154869094	+	0	NA	intron (NM_001301077, intron 3 of 6)	intron (NM_001301077, intron 3 of 6)	10430	NM_001301080	9337	Hs.26703	NM_004779	ENSG00000155508	CNOT8	CAF1|CALIF|Caf1b|POP2|hCAF1	CCR4-NOT transcription complex subunit 8	protein-coding	0.010345	0.563574	
chunk0121_293_1	chr3	23735571	23735852	+	0	NA	Intergenic	Intergenic	-70182	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.010676	0.429078	
chunk0200_309_1	chr9	23141070	23141269	+	0	NA	Intergenic	Intergenic	494969	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.005025	0.275000	
chunk0149_8_1	chr5	15797965	15798386	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-137007	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.007126	0.443128	
chunk0062_244_1	chr14	71443296	71443590	+	0	NA	Intergenic	Intergenic	-44418	NR_027046	145474	Hs.658241	NR_027046		LOC145474	-	uncharacterized LOC145474	ncRNA	0.003401	0.294915	
chunk0163_348_1	chr6	15456683	15456890	+	0	NA	intron (NM_001267040, intron 4 of 17)	intron (NM_001267040, intron 4 of 17)	206272	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.000000	0.298077	
chunk0020_255_1	chr1	236149755	236150035	+	0	NA	intron (NM_003272, intron 1 of 6)	(GTGTGT)n|Simple_repeat|Simple_repeat	7363	NM_003272	7107	Hs.498160	NM_003272	ENSG00000077585	GPR137B	TM7SF1	G protein-coupled receptor 137B	protein-coding	0.025000	0.580071	
chunk0114_184_1	chr21	15022545	15023012	+	0	NA	intron (NM_003489, intron 2 of 3)	L1MB8|LINE|L1	42027	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.008565	0.341880	196(GGGAACAGACAGTTCC,-,0.00),197(GGAACAGACAGTTCCT,+,0.00)
chunk0142_402_1	chr4	102775911	102776134	+	0	NA	Intergenic	L1MC3|LINE|L1	-1015	NR_125932	102723704	Hs.638374	NR_125932		LOC102723704	-	uncharacterized LOC102723704	ncRNA	0.004484	0.366071	
chunk0121_4_1	chr3	14403136	14403354	+	0	NA	intron (NM_001134367, intron 1 of 14)	intron (NM_001134367, intron 1 of 14)	669	NM_003043	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.032110	0.543379	
chunk0200_228_1	chr9	20685167	20685703	+	0	NA	promoter-TSS (NR_121601)	promoter-TSS (NR_121601)	-685	NR_121601	101929548	Hs.668302	NR_121601	ENSG00000227071	FOCAD-AS1	-	FOCAD antisense RNA 1	ncRNA	0.005597	0.338920	
chunk0158_34_1	chr5	125601955	125602693	+	0	NA	TTS (NR_109887)	TTS (NR_109887)	109063	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.008130	0.388363	
chunk0175_152_1	chr7	3710564	3711779	+	0	NA	intron (NM_152744, intron 4 of 44)	intron (NM_152744, intron 4 of 44)	409723	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005761	0.384868	
chunk0034_14_1	chr11	26032214	26032475	+	0	NA	Intergenic	L1MD1|LINE|L1	-156779	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.003831	0.301527	
chunk0069_289_1	chr15	65286051	65286450	+	0	NA	intron (NM_017851, intron 1 of 5)	intron (NM_017851, intron 1 of 5)	593	NM_001316944	54956	Hs.30634	NM_017851	ENSG00000138617	PARP16	ARTD15|C15orf30|pART15	poly(ADP-ribose) polymerase family member 16	protein-coding	0.072682	0.637500	
chunk0145_122_1	chr4	146365353	146365962	+	0	NA	intron (NM_001029998, intron 5 of 11)	intron (NM_001029998, intron 5 of 11)	-42926	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.004926	0.380328	
chunk0073_202_1	chr16	9472649	9473020	+	0	NA	Intergenic	L1ME2|LINE|L1	-17329	NR_126349	104266959	Hs.578888	NR_126349	ENSG00000261075	LINC01195	-	long intergenic non-protein coding RNA 1195	ncRNA	0.008086	0.341398	
chunk0032_188_1	chr11	6433905	6434554	+	0	NA	intron (NM_000613, intron 7 of 9)	intron (NM_000613, intron 7 of 9)	6795	NM_000613	3263	Hs.426485	NM_000613	ENSG00000110169	HPX	HX	hemopexin	protein-coding	0.007704	0.438462	
chunk0047_2_1	chr12	65010312	65011037	+	0	NA	Intergenic	Intergenic	110892	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.004138	0.371901	
chunk0025_136_1	chr10	52117159	52117484	+	0	NA	intron (NM_006258, intron 7 of 17)	intron (NM_006258, intron 7 of 17)	196807	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.000000	0.401840	
chunk0183_368_1	chr7	109253089	109253503	+	0	NA	Intergenic	Intergenic	-368709	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.000000	0.269880	
chunk0082_264_1	chr17	57853676	57854152	+	0	NA	Intergenic	Intergenic	-3842	NM_016070	51649	Hs.5836	NM_016070	ENSG00000181610	MRPS23	CGI-138|HSPC329|MRP-S23	mitochondrial ribosomal protein S23	protein-coding	0.021008	0.536688	228(TGGAACATAAAGTTCT,-,0.00),229(GGAACATAAAGTTCTA,+,0.00)
chunk0209_196_1	chrX	43918249	43918763	+	0	NA	Intergenic	L1ME4a|LINE|L1	-36031	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.001946	0.283495	
chunk0072_214_1	chr15	95574437	95575034	+	0	NA	Intergenic	Intergenic	141642	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.006700	0.351171	
chunk0029_11_1	chr10	95405667	95406001	+	0	NA	intron (NM_001290298, intron 7 of 25)	L2a|LINE|L2	35346	NM_001290296	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.000000	0.501493	175(CAGAACATCCTGTTCT,-,0.00),176(AGAACATCCTGTTCTT,+,0.00)
chunk0116_94_1	chr21	34965784	34965983	+	0	NA	intron (NM_001754, intron 2 of 8)	intron (NM_001754, intron 2 of 8)	73543	NR_026812	80215	Hs.672131	NM_025143		RUNX1-IT1	C21orf96	RUNX1 intronic transcript 1	ncRNA	0.005025	0.535000	
chunk0202_200_1	chr9	75432761	75433402	+	0	NA	Intergenic	Intergenic	344599	NM_012383	26578	Hs.494192	NM_012383	ENSG00000134996	OSTF1	OSF|SH3P2|bA235O14.1	osteoclast stimulating factor 1	protein-coding	0.000000	0.370717	288(AAGTACAAATTGTTCA,-,0.00),289(AGTACAAATTGTTCAG,+,0.00),307(AGGAACATTGTGTTCT,-,0.00),308(GGAACATTGTGTTCTG,+,0.00)
chunk0156_264_1	chr5	109370331	109370634	+	0	NA	intron (NM_014819, intron 4 of 9)	intron (NM_014819, intron 4 of 9)	39492	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.006601	0.361842	
chunk0016_31_1	chr1	193054629	193055143	+	0	NA	intron (NR_037607, intron 1 of 10)	intron (NR_037607, intron 1 of 10)	4507	NM_001199261	51377	Hs.145469	NM_015984	ENSG00000116750	UCHL5	CGI-70|INO80R|UCH-L5|UCH37	ubiquitin C-terminal hydrolase L5	protein-coding	0.007782	0.411650	
chunk0077_370_1	chr16	84505090	84505289	+	0	NA	promoter-TSS (NM_020947)	promoter-TSS (NM_020947)	-507	NM_020947	57707	Hs.288274	NM_020947	ENSG00000140950	MEAK7	KIAA1609|TLDC1|mEAK-7	MTOR associated protein, eak-7 homolog	protein-coding	0.045226	0.705000	
chunk0045_119_1	chr12	46258951	46259574	+	0	NA	intron (NM_001278387, intron 1 of 17)	Charlie19a|DNA|hAT-Charlie	7233	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.008026	0.336538	
chunk0110_298_1	chr20	17928418	17929033	+	0	NA	Intergenic	Intergenic	34221	NR_003045	692086	Hs.680747	NR_003045	ENSG00000212232	SNORD17	HBI-43	small nucleolar RNA, C/D box 17	snoRNA	0.027642	0.595779	
chunk0095_241_1	chr2	19172085	19172657	+	0	NA	Intergenic	Intergenic	-176058	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.001748	0.324607	251(ATGACATAATGTTCTT,+,0.00)
chunk0075_4_1	chr16	46630088	46630505	+	0	NA	Intergenic	Intergenic	-8897	NM_024745	79801	Hs.123253	NM_024745	ENSG00000171241	SHCBP1	PAL	SHC binding and spindle associated 1	protein-coding	0.011990	0.452153	
chunk0054_413_1	chr13	50660297	50660513	+	0	NA	Intergenic	L1ME1|LINE|L1	-132956	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.004630	0.359447	
chunk0207_150_1	chr9	129712294	129712606	+	0	NA	TTS (NR_132102)	TTS (NR_132102)	6256	NR_132102	101929437	Hs.112596	NR_132102	ENSG00000236024	PRRX2-AS1	-	PRRX2 antisense RNA 1	ncRNA	0.019231	0.421725	
chunk0105_116_1	chr2	185097910	185098348	+	0	NA	Intergenic	L1ME3G|LINE|L1	499763	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.000000	0.298405	
chunk0149_401_1	chr5	28939955	28940349	+	0	NA	Intergenic	L1MA3|LINE|L1	13282	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.000000	0.349367	
chunk0129_294_1	chr3	123597517	123597962	+	0	NA	intron (NR_038266, intron 1 of 2)	LTR40A1|LTR|ERVL	12226	NR_121654	100506826	Hs.556600	NR_038266	ENSG00000239523	MYLK-AS1	-	MYLK antisense RNA 1	ncRNA	0.008989	0.439462	
chunk0178_155_1	chr7	33527868	33528119	+	0	NA	intron (NM_014451, intron 18 of 20)	intron (NM_014451, intron 18 of 20)	-376918	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.003984	0.261905	
chunk0132_269_1	chr3	159619225	159619972	+	0	NA	intron (NM_001197108, intron 1 of 6)	intron (NM_001197108, intron 1 of 6)	149014	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.004016	0.401070	
chunk0159_314_1	chr5	143181157	143181740	+	0	NA	intron (NM_015071, intron 20 of 22)	intron (NM_015071, intron 20 of 22)	-11052	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.010292	0.455479	223(GGGAACACTGTGTTCT,-,0.00),224(GGAACACTGTGTTCTT,+,0.00)
chunk0019_26_1	chr1	223706455	223706767	+	0	NA	intron (NM_001146068, intron 1 of 20)	intron (NM_001146068, intron 1 of 20)	5018	NM_001146068	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.009615	0.479233	
chunk0075_293_1	chr16	54172293	54173067	+	0	NA	Intergenic	Intergenic	98199	NR_126340	100996338	Hs.232014	NR_126340		LINC02169	-	long intergenic non-protein coding RNA 2169	ncRNA	0.016796	0.401290	
chunk0050_389_1	chr12	109089806	109090130	+	0	NA	intron (NM_001205180, intron 2 of 2)	intron (NM_001205180, intron 2 of 2)	3520	NM_001205179	121642	Hs.374458	NM_001001655	ENSG00000189046	ALKBH2	ABH2	alkB homolog 2, alpha-ketoglutarate dependent dioxygenase	protein-coding	0.021605	0.498462	
chunk0021_152_1	chr10	4639988	4640503	+	0	NA	Intergenic	Intergenic	-15911	NR_015425	338588	Hs.121365	NR_015425		LINC00705	-	long intergenic non-protein coding RNA 705	ncRNA	0.003883	0.434109	
chunk0109_13_1	chr20	345454	345826	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-1086	NM_024958	80023	Hs.416024	NM_024958	ENSG00000125841	NRSN2	C20orf98|dJ1103G7.6	neurensin 2	protein-coding	0.005376	0.455764	
chunk0189_148_1	chr8	23019946	23020492	+	0	NA	TTS (NM_003842)	TTS (NM_003842)	20640	NM_015178	23221	Hs.372688	NM_015178	ENSG00000008853	RHOBTB2	DBC2|EIEE64	Rho related BTB domain containing 2	protein-coding	0.012821	0.469835	244(TTGTACACAATGTGCT,-,0.00),245(TGTACACAATGTGCTT,+,0.00)
chunk0148_283_1	chr5	11561169	11561787	+	0	NA	intron (NR_109988, intron 3 of 21)	intron (NR_109988, intron 3 of 21)	27439	NM_001288716	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.001618	0.376414	365(GAGAACACAATGTTCC,-,0.00),366(AGAACACAATGTTCCC,+,0.00)
chunk0198_15_1	chr9	308074	308536	+	0	NA	intron (NM_001190458, intron 4 of 45)	L1MA5|LINE|L1	35257	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.004329	0.315335	
chunk0036_321_1	chr11	66189095	66189915	+	0	NA	intron (NM_018026, intron 1 of 23)	intron (NM_018026, intron 1 of 23)	-67789	NM_001134775	64837	Hs.280792	NM_022822	ENSG00000174996	KLC2	-	kinesin light chain 2	protein-coding	0.012195	0.400731	
chunk0052_280_1	chr12	124238973	124239172	+	0	NA	intron (NM_001204299, intron 3 of 4)	intron (NM_001204299, intron 3 of 4)	-50092	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.015075	0.490000	
chunk0017_343_1	chr1	211734777	211735202	+	0	NA	Intergenic	L2a|LINE|L2	-59359	NM_001204182	4751	Hs.153704	NM_002497	ENSG00000117650	NEK2	HsPK21|NEK2A|NLK1|PPP1R111|RP67	NIMA related kinase 2	protein-coding	0.011765	0.455399	
chunk0109_72_1	chr20	1756763	1757393	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	22668	NR_037142	100289473	Hs.641525	NR_037142	ENSG00000232528	LOC100289473	-	cytoskeleton associated protein 2-like pseudogene	pseudo	0.006349	0.389857	
chunk0117_86_1	chr22	17242717	17243258	+	0	NA	Intergenic	MIRb|SINE|MIR	-21133	NM_001282227	51816	Hs.170310	NM_017424	ENSG00000093072	ADA2	ADGF|CECR1|IDGFL|PAN|SNEDS|VAIHS	adenosine deaminase 2	protein-coding	0.003697	0.433579	
chunk0194_23_1	chr8	81622541	81622740	+	0	NA	Intergenic	L1ME4b|LINE|L1	63714	NM_005536	3612	Hs.656694	NM_005536	ENSG00000133731	IMPA1	IMP|IMPA|MRT59	inositol monophosphatase 1	protein-coding	0.010050	0.395000	51(CAGAACAGTGTGTATT,-,0.00),52(AGAACAGTGTGTATTG,+,0.00)
chunk0171_136_1	chr6	123453008	123453420	+	0	NA	intron (NR_110844, intron 1 of 2)	L1PB1|LINE|L1	13610	NR_110844	101927990	Hs.660877	NR_110844		TRDN-AS1	HRAT13	TRDN antisense RNA 1	ncRNA	0.000000	0.355932	
chunk0114_55_1	chr21	8849873	8850072	+	0	NA	Intergenic	Intergenic	-137027	NR_128711	103504731		NR_128711	ENSG00000264462	MIR3648-2	hsa-mir-3648-2	microRNA 3648-2	ncRNA	0.015075	0.495000	
chunk0088_298_1	chr18	49943368	49943721	+	0	NA	intron (NM_001080467, intron 14 of 39)	intron (NM_001080467, intron 14 of 39)	129521	NR_003003	677769		NR_003003	ENSG00000267322	SCARNA17	U91	small Cajal body-specific RNA 17	ncRNA	0.005666	0.355932	
chunk0046_332_1	chr12	62800054	62800378	+	0	NA	intron (NM_020700, intron 3 of 9)	intron (NM_020700, intron 3 of 9)	134669	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.018519	0.381538	
chunk0119_126_1	chr22	42804721	42806085	+	0	NA	intron (NM_001142293, intron 13 of 14)	intron (NM_001142293, intron 13 of 14)	51999	NM_014570	26286	Hs.685225	NM_014570	ENSG00000242247	ARFGAP3	ARFGAP1	ADP ribosylation factor GTPase activating protein 3	protein-coding	0.013930	0.516484	974(AGGCACAGGGTGTGCT,-,0.00),975(GGCACAGGGTGTGCTC,+,0.00)
chunk0186_280_1	chr7	142166203	142166996	+	0	NA	intron (NM_001293626, intron 25 of 47)	MIR3|SINE|MIR	54850	NM_001293626	93432	Hs.647098	NM_001008748	ENSG00000257743	MGAM2	-	maltase-glucoamylase 2 (putative)	protein-coding	0.003783	0.420655	366(AAGGTCAGGCTGTTCC,-,0.00),367(AGGTCAGGCTGTTCCT,+,0.00)
chunk0130_360_1	chr3	139064535	139065150	+	0	NA	Intergenic	L1MC1|LINE|L1	-19950	NM_001134657	389152	Hs.531377	NM_001004315	ENSG00000233701	PRR23C	-	proline rich 23C	protein-coding	0.001626	0.337662	
chunk0192_195_1	chr8	64266643	64267238	+	0	NA	intron (NR_125826, intron 1 of 4)	intron (NR_125826, intron 1 of 4)	101618	NR_125826	102724623	Hs.586375	NR_125826	ENSG00000253554	LINC01414	-	long intergenic non-protein coding RNA 1414	ncRNA	0.003361	0.449664	
chunk0101_200_1	chr2	129968659	129968969	+	0	NA	intron (NR_036537, intron 4 of 5)	MIRb|SINE|MIR	-10848	NM_032144	84084	Hs.591552	NM_032144	ENSG00000222014	RAB6C	WTH3	RAB6C, member RAS oncogene family	protein-coding	0.012903	0.408360	
chunk0060_19_1	chr14	39605874	39606206	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-173540	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.003012	0.402402	
chunk0080_332_1	chr17	32591144	32591454	+	0	NA	intron (NM_015194, intron 21 of 21)	intron (NM_015194, intron 21 of 21)	104212	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.009677	0.450161	
chunk0031_96_1	chr10	123963231	123963436	+	0	NA	Intergenic	Intergenic	-71349	NM_198148	119587	Hs.656887	NM_198148	ENSG00000121898	CPXM2	CPX2|UNQ676	carboxypeptidase X, M14 family member 2	protein-coding	0.009756	0.466019	
chunk0179_448_1	chr7	52725405	52725802	+	0	NA	Intergenic	Intergenic	-310053	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.000000	0.346734	
chunk0002_20_1	chr1	12356059	12356334	+	0	NA	intron (NM_018156, intron 47 of 68)	intron (NM_018156, intron 47 of 68)	126157	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.007273	0.387681	
chunk0182_49_1	chr7	91880731	91880984	+	0	NA	promoter-TSS (NM_001301135)	promoter-TSS (NM_001301135)	-137	NM_001301135	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.075099	0.637795	
chunk0193_128_1	chr8	74350464	74350729	+	0	NA	intron (NM_018972, intron 1 of 5)	CpG	213	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.067925	0.650376	70(AAGCTCATTCTGTACC,-,0.00)
chunk0208_217_1	chrX	18630962	18631236	+	0	NA	intron (NM_001037343, intron 19 of 21)	intron (NM_001037343, intron 19 of 21)	41004	NM_000330	6247	Hs.715725	NM_000330	ENSG00000102104	RS1	RS|XLRS1	retinoschisin 1	protein-coding	0.025547	0.450909	
chunk0166_231_1	chr6	47045075	47045301	+	0	NA	Intergenic	Intergenic	-2825	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.004425	0.392070	
chunk0054_163_1	chr13	44218661	44219377	+	0	NA	Intergenic	Intergenic	-22819	NR_107046	102465876		NR_107046	ENSG00000276319	MIR8079	hsa-mir-8079	microRNA 8079	ncRNA	0.013966	0.513250	
chunk0037_19_1	chr11	69223048	69223332	+	0	NA	Intergenic	L1MD1|LINE|L1	-51628	NR_104161	338694	Hs.564235	NR_104161	ENSG00000261070	LOC338694	-	uncharacterized LOC338694	ncRNA	0.003521	0.357895	
chunk0133_152_1	chr3	169453602	169453838	+	0	NA	intron (NM_004991, intron 1 of 16)	intron (NM_004991, intron 1 of 16)	210055	NM_004991	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.008475	0.400844	
chunk0167_360_1	chr6	73129468	73129975	+	0	NA	intron (NM_001160134, intron 9 of 11)	intron (NM_001160134, intron 9 of 11)	13793	NR_046621	100873997	Hs.741819	NR_046621	ENSG00000229154	KCNQ5-AS1	-	KCNQ5 antisense RNA 1	ncRNA	0.009862	0.383858	
chunk0056_49_1	chr13	77604398	77604597	+	0	NA	intron (NM_003843, intron 18 of 31)	intron (NM_003843, intron 18 of 31)	2054	NR_126412	104355296	Hs.667682	NR_126412	ENSG00000224347	SCEL-AS1	-	SCEL antisense RNA 1	ncRNA	0.010050	0.365000	
chunk0054_406_1	chr13	50519725	50520379	+	0	NA	TTS (NR_125753)	TTS (NR_125753)	7397	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.003058	0.406107	297(AGGCACACACTGTCCA,-,0.00),298(GGCACACACTGTCCAT,+,0.00),319(CTGAACAATCAGTGCT,-,0.00),320(TGAACAATCAGTGCTG,+,0.00)
chunk0211_61_1	chrX	109760150	109760551	+	0	NA	Intergenic	Intergenic	-26958	NM_004458	2182	Hs.268785	NM_004458	ENSG00000068366	ACSL4	ACS4|FACL4|LACS4|MRX63|MRX68	acyl-CoA synthetase long chain family member 4	protein-coding	0.004988	0.353234	
chunk0085_1_1	chr18	150675	151361	+	0	NA	Intergenic	Intergenic	-7465	NM_005151	9097	Hs.464416	NM_005151	ENSG00000101557	USP14	TGT	ubiquitin specific peptidase 14	protein-coding	0.008746	0.388646	
chunk0209_358_1	chrX	53522596	53522912	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	33587	NR_029513	407054		NR_029513	ENSG00000271886	MIR98	MIRLET7L|MIRN98|hsa-mir-98|miR-98	microRNA 98	ncRNA	0.003165	0.353312	134(TAGTACATGCTGTACT,-,0.00),135(AGTACATGCTGTACTA,+,0.00)
chunk0044_443_1	chr12	42344029	42344495	+	0	NA	intron (NM_201440, intron 3 of 9)	intron (NM_201440, intron 3 of 9)	18117	NM_201440	51535	Hs.444157	NM_016488	ENSG00000134283	PPHLN1	CR|HSPC206|HSPC232	periphilin 1	protein-coding	0.006438	0.342612	
chunk0080_274_1	chr17	31118392	31118591	+	0	NA	intron (NM_001042492, intron 1 of 57)	L1PA7|LINE|L1	23564	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.015075	0.460000	
chunk0095_359_1	chr2	22939259	22939987	+	0	NA	Intergenic	L1ME1|LINE|L1	403144	NR_110577	102723362	Hs.502887	NR_110577	ENSG00000233587	LINC01884	-	long intergenic non-protein coding RNA 1884	ncRNA	0.000000	0.322359	
chunk0169_418_1	chr6	108592847	108593469	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	32292	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.009646	0.370787	252(AAGAACTAGTTGTTCT,-,0.00),253(AGAACTAGTTGTTCTT,+,0.00),335(GTAACAAGATGTTCTT,+,0.00)
chunk0111_2_1	chr20	21741502	21741927	+	0	NA	Intergenic	L1MEf|LINE|L1	36055	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.002353	0.342723	
chunk0071_190_1	chr15	83705422	83705747	+	0	NA	intron (NM_207517, intron 3 of 29)	intron (NM_207517, intron 3 of 29)	51498	NM_001301110	57188	Hs.459162	NM_207517	ENSG00000156218	ADAMTSL3	ADAMTSL-3	ADAMTS like 3	protein-coding	0.003077	0.524540	
chunk0118_332_1	chr22	35478062	35478350	+	0	NA	Intergenic	Intergenic	-63099	NM_014310	23551	Hs.474711	NM_014310	ENSG00000100302	RASD2	Rhes|TEM2	RASD family member 2	protein-coding	0.020833	0.560554	
chunk0209_424_1	chrX	57551295	57551974	+	0	NA	Intergenic	L1PBa|LINE|L1	-40202	NM_007157	158586	Hs.156257	NM_007157	ENSG00000198455	ZXDB	ZNF905|dJ83L6.1	zinc finger X-linked duplicated B	protein-coding	0.007364	0.326471	
chunk0181_436_1	chr7	90540503	90540712	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-55755	NM_001287135	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.004785	0.480952	
chunk0187_340_1	chr7	156903332	156904068	+	0	NA	Intergenic	Intergenic	-10492	NM_022458	64327	Hs.209989	NM_022458	ENSG00000105983	LMBR1	ACHP|C7orf2|DIF14|LSS|PPD2|THYP|TPT|ZRS	limb development membrane protein 1	protein-coding	0.016304	0.472185	350(AGGAACAACCTGGGCC,-,0.00)
chunk0029_325_1	chr10	104477104	104477887	+	0	NA	intron (NR_120624, intron 1 of 2)	intron (NR_120624, intron 1 of 2)	2780	NR_120624	101927523	Hs.407539	NR_120624	ENSG00000225768	LINC02620	-	long intergenic non-protein coding RNA 2620	ncRNA	0.003831	0.405612	
chunk0142_389_1	chr4	102542288	102542624	+	0	NA	intron (NM_003998, intron 5 of 23)	L1ME3Cz|LINE|L1	41127	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.000000	0.338279	
chunk0053_174_1	chr13	30918647	30918996	+	0	NA	intron (NM_032849, intron 2 of 4)	intron (NM_032849, intron 2 of 4)	12646	NM_032849	84935	Hs.147880	NM_032849	ENSG00000102802	MEDAG	AWMS3|C13orf33|MEDA-4|MEDA4|hAWMS3	mesenteric estrogen dependent adipogenesis	protein-coding	0.008596	0.377143	177(AGGAACAGAATGCCCA,-,0.00)
chunk0033_293_1	chr11	19790444	19791093	+	0	NA	intron (NM_001244963, intron 1 of 39)	intron (NM_001244963, intron 1 of 39)	-30685	NR_039843	100616426		NR_039843	ENSG00000264309	MIR4694	-	microRNA 4694	ncRNA	0.003082	0.398462	
chunk0123_37_1	chr3	40773541	40773740	+	0	NA	Intergenic	L1MB8|LINE|L1	248762	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.000000	0.235000	
chunk0168_66_1	chr6	79372889	79373251	+	0	NA	Intergenic	Intergenic	-59686	NR_130915	80078		NR_130915	ENSG00000286042	LCAL1	onco-lncRNA-27	lung cancer associated lncRNA 1	ncRNA	0.005525	0.388430	
chunk0185_452_1	chr7	135095219	135095690	+	0	NA	intron (NM_001305630, intron 2 of 2)	L1MCb|LINE|L1	-52560	NM_018295	55281	Hs.521213	NM_018295	ENSG00000146859	TMEM140	-	transmembrane protein 140	protein-coding	0.002123	0.364407	
chunk0151_306_1	chr5	53253759	53254347	+	0	NA	Intergenic	Intergenic	144211	NR_104654	257396	Hs.12326	NR_034107	ENSG00000247796	LOC257396	-	uncharacterized LOC257396	ncRNA	0.005102	0.336163	
chunk0143_164_1	chr4	110767168	110767367	+	0	NA	Intergenic	MER45C|DNA|hAT-Tip100	93380	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.015075	0.515000	
chunk0010_64_1	chr1	113050118	113050799	+	0	NA	intron (NR_103777, intron 1 of 2)	L1ME1|LINE|L1	22644	NR_103777	100996251	Hs.382067	NR_103777	ENSG00000238198	LRIG2-DT	-	LRIG2 divergent transcript	ncRNA	0.004405	0.388563	462(GAGTACATGCTGTACT,-,0.00),463(AGTACATGCTGTACTA,+,0.00)
chunk0055_149_1	chr13	59916031	59916387	+	0	NA	exon (NM_001258370, exon 13 of 16)	exon (NM_001258370, exon 13 of 16)	-96509	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.005618	0.313725	
chunk0153_444_1	chr5	76368832	76369359	+	0	NA	Intergenic	L2b|LINE|L2	-34160	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.003795	0.412879	
chunk0050_402_1	chr12	109386137	109386354	+	0	NA	Intergenic	L1ME2|LINE|L1	-2474	NM_001101421	283446	Hs.512008	NM_173597	ENSG00000174527	MYO1H	-	myosin IH	protein-coding	0.013825	0.412844	
chunk0177_188_1	chr7	23628641	23628883	+	0	NA	intron (NM_138771, intron 3 of 3)	L1MDa|LINE|L1	31383	NM_138771	90693	Hs.232296	NM_138771	ENSG00000169193	CCDC126	-	coiled-coil domain containing 126	protein-coding	0.004132	0.555556	
chunk0141_343_1	chr4	87492981	87493556	+	0	NA	intron (NM_004684, intron 4 of 10)	intron (NM_004684, intron 4 of 10)	36235	NM_001128310	8404	Hs.62886	NM_004684	ENSG00000152583	SPARCL1	MAST 9|MAST9|PIG33|SC1	SPARC like 1	protein-coding	0.006957	0.397569	
chunk0115_335_1	chr21	29102965	29103277	+	0	NA	intron (NM_020152, intron 7 of 9)	MER58A|DNA|hAT-Charlie	10867	NM_001286619	56911	Hs.222802	NM_020152	ENSG00000156265	MAP3K7CL	C21orf7|HC21ORF7|TAK1L|TAKL|TAKL-1|TAKL-2|TAKL-4	MAP3K7 C-terminal like	protein-coding	0.006410	0.437700	
chunk0137_214_1	chr4	19482720	19482935	+	0	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	-769078	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.000000	0.250000	
chunk0188_64_1	chr8	8270259	8270787	+	0	NA	Intergenic	Intergenic	41953	NR_024363	286042	Hs.656318	NR_024361	ENSG00000173295	FAM86B3P	-	family with sequence similarity 86, member A pseudogene	pseudo	0.015152	0.489603	
chunk0212_2_1	chrY	3669025	3669289	+	0	NA	Intergenic	L1M4|LINE|L1	90072	NM_139214	90655	Hs.112148	NM_139214	ENSG00000176679	TGIF2LY	TGIFLY	TGFB induced factor homeobox 2 like Y-linked	protein-coding	0.011364	0.294340	197(ATGCACATATTGTTCT,-,0.00),198(TGCACATATTGTTCTG,+,0.00)
chunk0041_86_1	chr11	124428030	124428253	+	0	NA	Intergenic	Intergenic	-3270	NM_001005196	283162	Hs.553671	NM_001005196	ENSG00000280090	OR8B4	OR11-315|OR8B4P	olfactory receptor family 8 subfamily B member 4 (gene/pseudogene)	protein-coding	0.000000	0.437500	
chunk0048_94_1	chr12	79294676	79294934	+	0	NA	intron (NM_001291901, intron 5 of 9)	intron (NM_001291901, intron 5 of 9)	-124452	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.007752	0.316602	
chunk0103_192_1	chr2	163578372	163578926	+	0	NA	Intergenic	Intergenic	157354	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.005415	0.327928	
chunk0144_407_1	chr4	140333409	140333986	+	0	NA	intron (NR_033939, intron 2 of 4)	intron (NR_033939, intron 2 of 4)	-9746	NM_001153635	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.001733	0.333910	
chunk0197_56_1	chr8	118607536	118608195	+	0	NA	intron (NR_109794, intron 1 of 4)	intron (NR_109794, intron 1 of 4)	-13136	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.001517	0.351515	
chunk0038_205_1	chr11	86274809	86275343	+	0	NA	intron (NM_001308007, intron 10 of 12)	L1MD1|LINE|L1	-3257	NR_106813	102465452		NR_106813	ENSG00000283744	MIR6755	hsa-mir-6755	microRNA 6755	ncRNA	0.009363	0.411215	
chunk0148_31_1	chr5	663764	664432	+	0	NA	3' UTR (NM_007030, exon 4 of 4)	3' UTR (NM_007030, exon 4 of 4)	29297	NM_007030	11076	Hs.481466	NM_007030	ENSG00000171368	TPPP	TPPP/p25|TPPP1|p24|p25|p25alpha	tubulin polymerization promoting protein	protein-coding	0.043413	0.638266	
chunk0201_423_1	chr9	69678859	69679497	+	0	NA	Intergenic	Intergenic	-6819	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.006270	0.363067	269(GGGGACTGTCTGTACT,-,0.00),270(GGGACTGTCTGTACTT,+,0.00)
chunk0132_370_1	chr3	162711741	162711973	+	0	NA	Intergenic	Intergenic	591444	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.000000	0.347639	
chunk0201_283_1	chr9	38839197	38839449	+	0	NA	Intergenic	L2b|LINE|L2	218235	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.003968	0.335968	
chunk0009_457_1	chr1	111620018	111620340	+	0	NA	promoter-TSS (NM_001291896)	promoter-TSS (NM_001291896)	32	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.099379	0.718266	213(GAGGACATTGTGTCCC,-,0.00),214(AGGACATTGTGTCCCC,+,0.00)
chunk0137_171_1	chr4	16662234	16662476	+	0	NA	intron (NM_001290, intron 2 of 7)	intron (NM_001290, intron 2 of 7)	236454	NM_001290	9079	Hs.714330	NM_001290	ENSG00000169744	LDB2	CLIM1|LDB-2|LDB1	LIM domain binding 2	protein-coding	0.000000	0.358025	
chunk0189_142_1	chr8	22909741	22909940	+	0	NA	intron (NM_144962, intron 3 of 6)	MIRb|SINE|MIR	18068	NM_144962	157310	Hs.491242	NM_144962	ENSG00000134020	PEBP4	CORK-1|CORK1|GWTM1933|HEL-S-300|PEBP-4|PRO4408|hPEBP4	phosphatidylethanolamine binding protein 4	protein-coding	0.005025	0.520000	
chunk0075_330_1	chr16	54685055	54685634	+	0	NA	Intergenic	Intergenic	243434	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.010363	0.375862	
chunk0151_247_1	chr5	51810618	51811030	+	0	NA	Intergenic	Intergenic	-427492	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.007282	0.433414	
chunk0021_158_1	chr10	4902273	4902868	+	0	NA	intron (NR_026743, intron 2 of 10)	intron (NR_026743, intron 2 of 10)	13703	NR_026743	389932	Hs.631812	NR_026743		AKR1C6P	TAKR	aldo-keto reductase family 1 member C6, pseudogene	pseudo	0.006723	0.337248	323(ATGAACAACATGTACT,-,0.00),324(TGAACAACATGTACTT,+,0.00)
chunk0212_195_1	chrX	134167615	134168289	+	0	NA	Intergenic	Intergenic	1500	NR_029852	574031		NR_029852	ENSG00000284499	MIR363	MIR-363|MIRN363|hsa-mir-363	microRNA 363	ncRNA	0.007418	0.389630	325(GAGAACTAAATGTTCA,-,0.00),326(AGAACTAAATGTTCAT,+,0.00)
chunk0027_167_1	chr10	74947303	74948445	+	0	NA	intron (NM_001256468, intron 3 of 17)	intron (NM_001256468, intron 3 of 17)	110640	NM_001003892	338599	Hs.535090	NM_001003892	ENSG00000188716	DUPD1	DUSP27|FMDSP	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.002627	0.380577	
chunk0138_73_1	chr4	34366735	34367380	+	0	NA	Intergenic	Intergenic	-327164	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.006202	0.286378	
chunk0038_266_1	chr11	89557256	89557867	+	0	NA	intron (NM_001143837, intron 1 of 20)	intron (NM_001143837, intron 1 of 20)	32050	NM_001143837	50507	Hs.371036	NM_016931	ENSG00000086991	NOX4	KOX|KOX-1|RENOX	NADPH oxidase 4	protein-coding	0.004910	0.377451	
chunk0038_277_1	chr11	89672437	89672845	+	0	NA	intron (NM_153696, intron 5 of 13)	intron (NM_153696, intron 5 of 13)	13344	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.004902	0.322738	
chunk0110_292_1	chr20	17869612	17869926	+	0	NA	Intergenic	Intergenic	93177	NR_003045	692086	Hs.680747	NR_003045	ENSG00000212232	SNORD17	HBI-43	small nucleolar RNA, C/D box 17	snoRNA	0.022293	0.603175	
chunk0059_204_1	chr14	33488556	33488868	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-220225	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.009615	0.434505	88(CAGGACTGTCTGTCCT,-,0.00),89(AGGACTGTCTGTCCTA,+,0.00)
chunk0096_351_1	chr2	35942171	35942813	+	0	NA	Intergenic	L1MC4|LINE|L1	413078	NR_037631	100288911	Hs.432924	NR_037631		CRIM1-DT	-	CRIM1 divergent transcript	ncRNA	0.009346	0.371695	
chunk0195_164_1	chr8	95819635	95820021	+	0	NA	Intergenic	L1MEg2|LINE|L1	128520	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.005181	0.302326	
chunk0054_32_1	chr13	40996055	40996626	+	0	NA	intron (NM_172373, intron 1 of 8)	L1MC1|LINE|L1	-14058	NM_001145353	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.001751	0.379371	
chunk0116_386_1	chr21	42300034	42300280	+	0	NA	Intergenic	Intergenic	15439	NM_003226	7033	Hs.82961	NM_003226	ENSG00000160180	TFF3	ITF|P1B|TFI	trefoil factor 3	protein-coding	0.016260	0.534413	
chunk0103_356_1	chr2	168212132	168212537	+	0	NA	intron (NM_013233, intron 1 of 17)	intron (NM_013233, intron 1 of 17)	35261	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.012346	0.448276	152(GAAACTTACTGTTCTT,+,0.00)
chunk0169_162_1	chr6	102008047	102008468	+	0	NA	intron (NM_001166247, intron 13 of 16)	intron (NM_001166247, intron 13 of 16)	609272	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.002375	0.362559	
chunk0152_57_1	chr5	57682977	57683350	+	0	NA	Intergenic	Intergenic	32503	NR_104668	101928505	Hs.119998	NR_104668		LOC101928505	-	uncharacterized LOC101928505	ncRNA	0.005362	0.366310	
chunk0001_310_1	chr1	9303240	9303439	+	0	NA	intron (NM_025106, intron 1 of 2)	ERVL-int|LTR|ERVL	10457	NM_025106	80176	Hs.8261	NM_025106	ENSG00000171621	SPSB1	SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding	0.010050	0.475000	
chunk0046_338_1	chr12	62899477	62899676	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	35309	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.010050	0.405000	
chunk0086_57_1	chr18	13008996	13009447	+	0	NA	intron (NM_032142, intron 4 of 44)	intron (NM_032142, intron 4 of 44)	17859	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.011086	0.378319	
chunk0199_379_1	chr9	13033822	13034584	+	0	NA	Intergenic	Intergenic	-61570	NR_132976	106635615		NR_132976		SNORD137	-	small nucleolar RNA, C/D box 137	snoRNA	0.024934	0.431193	
chunk0098_437_1	chr2	81895861	81896206	+	0	NA	Intergenic	PABL_B|LTR|ERV1	-429087	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.011594	0.404624	
chunk0182_141_1	chr7	94764564	94765048	+	0	NA	Intergenic	Intergenic	108481	NM_001172438	23089	Hs.147492	NM_015068	ENSG00000242265	PEG10	EDR|HB-1|MEF3L|Mar2|Mart2|RGAG3|RTL2|SIRH1	paternally expressed 10	protein-coding	0.016529	0.406186	197(CAGGACAGCCAGTTCC,-,0.00),198(AGGACAGCCAGTTCCT,+,0.00)
chunk0042_56_1	chr12	1873604	1874127	+	0	NA	intron (NM_172364, intron 18 of 37)	UCON105|Unknown|Unknown	44839	NM_172364	93589	Hs.13768	NM_172364	ENSG00000151062	CACNA2D4	RCD4	calcium voltage-gated channel auxiliary subunit alpha2delta 4	protein-coding	0.001912	0.494275	
chunk0010_153_1	chr1	115356143	115356347	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-18009	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.004902	0.556098	
chunk0044_145_1	chr12	29610878	29611192	+	0	NA	intron (NM_001193451, intron 6 of 17)	intron (NM_001193451, intron 6 of 17)	-113349	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.006369	0.355556	
chunk0199_79_1	chr9	2477550	2478270	+	0	NA	Intergenic	Intergenic	-143883	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.005556	0.363384	
chunk0200_222_1	chr9	20619032	20619696	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	2623	NM_001286691	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.013554	0.360902	
chunk0209_284_1	chrX	47561274	47561601	+	0	NA	intron (NM_001256196, intron 1 of 15)	CpG	337	NM_001256197	369	Hs.446641	NM_001654	ENSG00000078061	ARAF	A-RAF|ARAF1|PKS2|RAFA1	A-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.091743	0.673780	
chunk0170_450_1	chr6	119260358	119260557	+	0	NA	intron (NM_005907, intron 5 of 12)	L1ME3G|LINE|L1	89309	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.000000	0.325000	
chunk0163_342_1	chr6	15432608	15432858	+	0	NA	intron (NM_001267040, intron 3 of 17)	MER51A|LTR|ERV1	183878	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.004000	0.410359	
chunk0043_359_1	chr12	23375525	23375869	+	0	NA	Intergenic	L1PA17|LINE|L1	200061	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.008721	0.553623	
chunk0041_375_1	chr11	131680310	131680509	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	-16853	NR_126159	101929637	Hs.730330	NM_207432	ENSG00000224795	NTM-AS1	C11orf39	NTM antisense RNA 1	ncRNA	0.010050	0.480000	
chunk0023_391_1	chr10	30849401	30849918	+	0	NA	exon (NM_001143770, exon 8 of 9)	exon (NM_001143770, exon 8 of 9)	149858	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.003868	0.476834	209(AAGATCAACTTGTTCT,-,0.00),210(AGATCAACTTGTTCTT,+,0.00)
chunk0066_108_1	chr15	29886812	29887180	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1M5|LINE|L1	-64493	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.005435	0.406504	
chunk0142_408_1	chr4	103020345	103020711	+	0	NA	promoter-TSS (NM_139173)	promoter-TSS (NM_139173)	-789	NR_047515	150159	Hs.666728	NM_139173	ENSG00000164037	SLC9B1	NHA1|NHEDC1	solute carrier family 9 member B1	protein-coding	0.024590	0.395095	
chunk0016_423_1	chr1	203465225	203465565	+	0	NA	Intergenic	Intergenic	-10360	NM_201348	5549	Hs.632481	NM_002725	ENSG00000188783	PRELP	MST161|MSTP161|SLRR2A	proline and arginine rich end leucine rich repeat protein	protein-coding	0.026471	0.489736	
chunk0037_441_1	chr11	80379845	80380276	+	0	NA	Intergenic	MIRb|SINE|MIR	382743	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.002320	0.375000	
chunk0124_124_1	chr3	54247553	54247752	+	0	NA	intron (NM_018398, intron 2 of 37)	HAL1M8|LINE|L1	124986	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.005025	0.330000	
chunk0056_141_1	chr13	83508780	83509177	+	0	NA	Intergenic	Intergenic	373415	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002519	0.359296	
chunk0146_150_1	chr4	159669636	159670111	+	0	NA	Intergenic	L1M7|LINE|L1	402027	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.002105	0.344538	
chunk0151_42_1	chr5	42108428	42108916	+	0	NA	Intergenic	Intergenic	66673	NR_104635	101926960	Hs.365692	NR_104635		LOC101926960	-	uncharacterized LOC101926960	ncRNA	0.000000	0.286299	
chunk0041_246_1	chr11	128665825	128666027	+	0	NA	Intergenic	Intergenic	-20609	NM_001271012	2313	Hs.504281	NM_002017	ENSG00000151702	FLI1	BDPLT21|EWSR2|SIC-1	Fli-1 proto-oncogene, ETS transcription factor	protein-coding	0.004950	0.443350	
chunk0065_397_1	chr14	105006052	105006264	+	0	NA	Intergenic	Intergenic	14930	NM_017955	55038	Hs.34045	NM_017955	ENSG00000170779	CDCA4	HEPP|SEI-3/HEPP	cell division cycle associated 4	protein-coding	0.018868	0.657277	3(TGGTACAGCCAGTCCC,-,0.00),4(GGTACAGCCAGTCCCC,+,0.00)
chunk0200_340_1	chr9	24349006	24349380	+	0	NA	Intergenic	Intergenic	196483	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.008021	0.314667	
chunk0116_20_1	chr21	32917566	32918028	+	0	NA	Intergenic	Intergenic	-104054	NM_019596	56245	Hs.517235	NM_019596	ENSG00000205929	C21orf62	B37|C21orf120|PRED81	chromosome 21 open reading frame 62	protein-coding	0.012987	0.520518	325(AGGAACATCCAGTCCT,-,0.00),326(GGAACATCCAGTCCTC,+,0.00)
chunk0104_410_1	chr2	180723275	180723482	+	0	NA	intron (NR_104320, intron 1 of 3)	intron (NR_104320, intron 1 of 3)	31274	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.000000	0.346154	
chunk0073_329_1	chr16	14449389	14449763	+	0	NA	intron (NM_002582, intron 22 of 23)	L1MC4a|LINE|L1	-79310	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.010695	0.341333	
chunk0162_161_1	chr6	3500810	3501030	+	0	NA	Intergenic	Intergenic	-44361	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.009091	0.352941	
chunk0017_217_1	chr1	207950580	207951316	+	0	NA	Intergenic	Intergenic	-39610	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.002717	0.449118	366(AAGAGCAGTGTGTGCT,-,0.00),367(AGAGCAGTGTGTGCTG,+,0.00)
chunk0140_420_1	chr4	75947775	75948333	+	0	NA	Intergenic	L1MC5a|LINE|L1	-7041	NM_001042402	27163	Hs.437365	NM_014435	ENSG00000138744	NAAA	ASAHL|PLT	N-acylethanolamine acid amidase	protein-coding	0.003584	0.393560	121(AAGAACAAGGTGATCT,-,0.00),122(AGAACAAGGTGATCTG,+,0.00),159(AGGAACAGCCTGTTTT,-,0.00),160(GGAACAGCCTGTTTTG,+,0.00)
chunk0184_233_1	chr7	117572887	117573475	+	0	NA	intron (NM_000492, intron 11 of 26)	intron (NM_000492, intron 11 of 26)	93218	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.000000	0.329372	
chunk0163_220_1	chr6	12137535	12138702	+	0	NA	intron (NM_002114, intron 7 of 8)	intron (NM_002114, intron 7 of 8)	125627	NM_002114	3096	Hs.567284	NM_002114	ENSG00000095951	HIVEP1	CIRIP|CRYBP1|GAAP|MBP-1|PRDII-BF1|Schnurri-1|ZAS1|ZNF40|ZNF40A	human immunodeficiency virus type I enhancer binding protein 1	protein-coding	0.004284	0.377568	
chunk0173_312_1	chr6	148530337	148530760	+	0	NA	intron (NM_015278, intron 12 of 19)	intron (NM_015278, intron 12 of 19)	187955	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.018913	0.400943	
chunk0172_304_1	chr6	138149710	138150483	+	0	NA	Intergenic	Intergenic	-11820	NM_020340	57221	Hs.194408	NM_020340	ENSG00000112379	ARFGEF3	A7322|BIG3|C6orf92|KIAA1244|PPP1R33|dJ171N11.1	ARFGEF family member 3	protein-coding	0.007762	0.372093	
chunk0073_208_1	chr16	10051118	10051347	+	0	NA	intron (NM_001134407, intron 2 of 12)	intron (NM_001134407, intron 2 of 12)	130835	NM_001134408	2903	Hs.411472	NM_000833	ENSG00000183454	GRIN2A	EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A	glutamate ionotropic receptor NMDA type subunit 2A	protein-coding	0.000000	0.439130	34(AGAAACACTGTGTGCA,-,0.00)
chunk0145_128_1	chr4	146377417	146377968	+	0	NA	intron (NM_001029998, intron 5 of 11)	MER21B|LTR|ERVL	-30891	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.001815	0.414855	
chunk0188_153_1	chr8	10466201	10466678	+	0	NA	Intergenic	L1ME3B|LINE|L1	-8126	NR_120604	101929191	Hs.595262	NR_120604	ENSG00000253641	LINCR-0001	-	uncharacterized LINCR-0001	ncRNA	0.008386	0.389121	
chunk0183_362_1	chr7	108815941	108816260	+	0	NA	Intergenic	Intergenic	68487	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.006270	0.450000	
chunk0032_182_1	chr11	6234861	6235239	+	0	NA	promoter-TSS (NM_032127)	promoter-TSS (NM_032127)	-339	NM_032127	84067	Hs.501793	NM_032127	ENSG00000051009	FAM160A2	C11orf56|FHIP	family with sequence similarity 160 member A2	protein-coding	0.055556	0.612137	
chunk0085_295_1	chr18	7974486	7974906	+	0	NA	intron (NM_001105244, intron 7 of 32)	intron (NM_001105244, intron 7 of 32)	392338	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.016667	0.399050	
chunk0079_172_1	chr17	13931974	13932384	+	0	NA	Intergenic	Intergenic	-92319	NR_003261	94158	Hs.633073	NR_003261		CDRT15P1	CDRT15P	CMT1A duplicated region transcript 15 pseudogene 1	pseudo	0.007317	0.403893	
chunk0021_396_1	chr1	246617361	246618269	+	0	NA	intron (NM_152609, intron 2 of 10)	intron (NM_152609, intron 2 of 10)	51478	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.004405	0.377338	571(AAGAACAACCTGCTCT,-,0.00),572(AGAACAACCTGCTCTT,+,0.00),618(AAGGACATTCAGTTTT,-,0.00)
chunk0208_343_1	chrX	25168940	25169531	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-153287	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.003384	0.412162	
chunk0033_330_1	chr11	22457076	22457277	+	0	NA	intron (NR_120583, intron 3 of 3)	LTR8|LTR|ERV1	34843	NR_120583	102723378	Hs.374255	NR_120583	ENSG00000255323	LINC01495	-	long intergenic non-protein coding RNA 1495	ncRNA	0.000000	0.450495	
chunk0153_250_1	chr5	72596985	72597276	+	0	NA	intron (NR_105007, intron 1 of 2)	intron (NR_105007, intron 1 of 2)	40053	NR_105008	102503427	Hs.429280	NR_105008		LOC102503427	-	uncharacterized LOC102503427	ncRNA	0.003436	0.441781	
chunk0158_387_1	chr5	134487772	134488360	+	0	NA	Intergenic	L1ME1|LINE|L1	-18486	NR_105045	101927934	Hs.535775	NR_105045	ENSG00000251169	LINC01843	-	long intergenic non-protein coding RNA 1843	ncRNA	0.011905	0.375212	227(ATGAACATTGTGTACA,-,0.00)
chunk0185_324_1	chr7	131555669	131556048	+	0	NA	intron (NM_005397, intron 1 of 7)	CpG	759	NM_001018111	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.060686	0.584211	
chunk0210_439_1	chrX	103769981	103770524	+	0	NA	Intergenic	MER90a|LTR|ERV1	-6254	NM_001128834	5354	Hs.1787	NM_000533	ENSG00000123560	PLP1	GPM6C|HLD1|MMPL|PLP|PLP/DM20|PMD|SPG2	proteolipid protein 1	protein-coding	0.012891	0.426471	297(TAGAACAGTAAGTCCC,-,0.00),298(AGAACAGTAAGTCCCA,+,0.00)
chunk0131_391_1	chr3	152505592	152505806	+	0	NA	Intergenic	L1M1|LINE|L1	-164709	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.014019	0.502326	
chunk0108_389_1	chr2	237069030	237069625	+	0	NA	Intergenic	Intergenic	-16114	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.003361	0.354027	
chunk0180_150_1	chr7	62349980	62350427	+	0	NA	Intergenic	Intergenic	953853	NR_003952	643955	Hs.583308	NR_003952	ENSG00000185037	ZNF733P	ZNF733	zinc finger protein 733, pseudogene	pseudo	0.040268	0.370536	
chunk0161_45_1	chr5	166025324	166025629	+	0	NA	Intergenic	Intergenic	900894	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.009836	0.356209	
chunk0185_458_1	chr7	135407970	135408176	+	0	NA	intron (NM_001008225, intron 7 of 10)	intron (NM_001008225, intron 7 of 10)	102054	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.000000	0.314010	
chunk0148_423_1	chr5	15103861	15104259	+	0	NA	Intergenic	MIRb|SINE|MIR	162500	NR_109944	101929454	Hs.453273	NR_109944		LINC02149	-	long intergenic non-protein coding RNA 2149	ncRNA	0.007538	0.363409	
chunk0178_453_1	chr7	42069696	42070600	+	0	NA	intron (NM_000168, intron 4 of 14)	intron (NM_000168, intron 4 of 14)	166871	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.006637	0.416575	
chunk0134_82_1	chr3	176554659	176554874	+	0	NA	Intergenic	MIRb|SINE|MIR	39663	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.018605	0.453704	
chunk0018_150_1	chr1	218702728	218703373	+	0	NA	intron (NR_031644, intron 4 of 6)	intron (NR_031644, intron 4 of 6)	260424	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.003101	0.331269	217(CAGGACACTAAGTGCT,-,0.00),218(AGGACACTAAGTGCTT,+,0.00)
chunk0107_437_1	chr2	224901224	224901667	+	0	NA	intron (NM_014689, intron 3 of 55)	intron (NM_014689, intron 3 of 55)	45620	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.009029	0.436937	
chunk0048_20_1	chr12	77186764	77187166	+	0	NA	Intergenic	Intergenic	-121385	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.007463	0.334988	
chunk0014_230_1	chr1	179882014	179882280	+	0	NA	5' UTR (NM_015602, exon 1 of 10)	5' UTR (NM_015602, exon 1 of 10)	105	NM_015602	26092	Hs.496459	NM_015602	ENSG00000143337	TOR1AIP1	LAP1|LAP1B|LGMD2Y	torsin 1A interacting protein 1	protein-coding	0.048872	0.595506	
chunk0074_70_1	chr16	21275400	21276016	+	0	NA	intron (NM_001888, intron 4 of 9)	MIRb|SINE|MIR	-25141	NR_026675	400508	Hs.578949	NM_001101368		CRYM-AS1	NCRNA00169	CRYM antisense RNA 1	ncRNA	0.006494	0.435981	476(AGCACATGGTGAGCCC,+,0.00)
chunk0004_451_1	chr1	53439148	53439347	+	0	NA	intron (NR_002314, intron 1 of 1)	CpG	773	NR_002314	163742	Hs.99394	NR_002314	ENSG00000236253	SLC25A3P1	-	solute carrier family 25 member 3 pseudogene 1	pseudo	0.085427	0.705000	
chunk0055_100_1	chr13	56163269	56163606	+	0	NA	Intergenic	Intergenic	-977481	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.000000	0.242604	
chunk0097_402_1	chr2	62423482	62423718	+	0	NA	Intergenic	Intergenic	82869	NM_198276	200728	Hs.308028	NM_198276	ENSG00000186889	TMEM17	-	transmembrane protein 17	protein-coding	0.016949	0.459916	
chunk0043_241_1	chr12	20268349	20268749	+	0	NA	Intergenic	Intergenic	-100696	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.012500	0.401496	
chunk0176_54_1	chr7	11142206	11142405	+	0	NA	intron (NR_033436, intron 16 of 16)	intron (NR_033436, intron 16 of 16)	168433	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.005025	0.290000	
chunk0060_441_1	chr14	54529095	54529406	+	0	NA	intron (NM_006568, intron 2 of 5)	intron (NM_006568, intron 2 of 5)	19381	NM_006568	10668	Hs.59106	NM_006568	ENSG00000100532	CGRRF1	CGR19|RNF197	cell growth regulator with ring finger domain 1	protein-coding	0.006431	0.394231	
chunk0136_139_1	chr4	4477808	4478176	+	0	NA	non-coding (NR_126434, exon 3 of 4)	non-coding (NR_126434, exon 3 of 4)	3708	NR_126434	104472519	Hs.691848	NR_126434	ENSG00000248221	STX18-IT1	-	STX18 intronic transcript 1	ncRNA	0.027174	0.417344	
chunk0162_411_1	chr5	179906463	179907344	+	0	NA	intron (NM_015043, intron 1 of 20)	intron (NM_015043, intron 1 of 20)	953	NM_015043	23061	Hs.155829	NM_015043	ENSG00000197226	TBC1D9B	GRAMD9B	TBC1 domain family member 9B	protein-coding	0.041998	0.603175	247(CAGAACAGTCTCTTCC,-,0.00),248(AGAACAGTCTCTTCCA,+,0.00),634(AGGAACACCCTGTGCC,-,0.00),635(GGAACACCCTGTGCCG,+,0.00)
chunk0046_111_1	chr12	57266599	57266798	+	0	NA	intron (NM_014925, intron 17 of 21)	intron (NM_014925, intron 17 of 21)	-15505	NR_104422	246329	Hs.417595	NM_145064	ENSG00000185482	STAC3	MYPBB|NAM	SH3 and cysteine rich domain 3	protein-coding	0.000000	0.530000	
chunk0020_93_1	chr1	232820322	232820810	+	0	NA	Intergenic	LTR33|LTR|ERVL	15674	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.002049	0.449898	
chunk0037_304_1	chr11	76462318	76462630	+	0	NA	intron (NM_020193, intron 6 of 20)	L2c|LINE|L2	17449	NM_001300942	56946	Hs.352588	NM_020193	ENSG00000158636	EMSY	C11orf30|GL002	EMSY transcriptional repressor, BRCA2 interacting	protein-coding	0.000000	0.396166	
chunk0050_408_1	chr12	109624889	109625108	+	0	NA	Intergenic	Intergenic	51303	NM_001114185	4598	Hs.130607	NM_000431	ENSG00000110921	MVK	LRBP|MK|MVLK|POROK3	mevalonate kinase	protein-coding	0.013699	0.545455	
chunk0177_182_1	chr7	23376796	23377138	+	0	NA	intron (NM_006547, intron 3 of 14)	L1M5|LINE|L1	77646	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.008772	0.335277	
chunk0202_351_1	chr9	79782353	79782552	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-42078	NR_121213	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.025126	0.505000	
chunk0104_160_1	chr2	174152595	174153048	+	0	NA	intron (NM_001011708, intron 3 of 9)	intron (NM_001011708, intron 3 of 9)	95816	NM_013341	29789	Hs.157351	NM_013341	ENSG00000138430	OLA1	DOC45|GBP45|GTBP9|GTPBP9|PTD004	Obg like ATPase 1	protein-coding	0.002208	0.314978	
chunk0126_40_1	chr3	73753898	73754457	+	0	NA	Intergenic	Intergenic	-129256	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.010733	0.433929	
chunk0187_228_1	chr7	152361585	152362284	+	0	NA	intron (NM_170606, intron 1 of 58)	intron (NM_170606, intron 1 of 58)	74071	NM_170606	58508	Hs.647120	NM_021230	ENSG00000055609	KMT2C	HALR|KLEFS2|MLL3	lysine methyltransferase 2C	protein-coding	0.001431	0.291429	
chunk0152_134_1	chr5	59063136	59063348	+	0	NA	intron (NM_006203, intron 5 of 14)	intron (NM_006203, intron 5 of 14)	-23730	NM_001197222	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004717	0.403756	
chunk0096_249_1	chr2	31227491	31228083	+	0	NA	Intergenic	Intergenic	-6227	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.021959	0.483980	
chunk0072_171_1	chr15	93424252	93424451	+	0	NA	Intergenic	Intergenic	-335137	NM_020211	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.025126	0.600000	
chunk0047_195_1	chr12	71137813	71138226	+	0	NA	exon (NM_004616, exon 6 of 9)	exon (NM_004616, exon 6 of 9)	19980	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.009685	0.352657	
chunk0040_57_1	chr11	111185537	111185766	+	0	NA	Intergenic	Intergenic	-70331	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.000000	0.439130	
chunk0027_417_1	chr10	80647089	80647833	+	0	NA	TTS (NM_001145719)	TTS (NM_001145719)	106642	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.010753	0.385235	
chunk0093_119_1	chr19	44694593	44695194	+	0	NA	Intergenic	L2a|LINE|L2	-4258	NM_001039213	388551	Hs.456381	NM_001039213	ENSG00000213892	CEACAM16	CEAL2|DFNA4B|DFNB113	carcinoembryonic antigen related cell adhesion molecule 16	protein-coding	0.011647	0.483389	
chunk0133_158_1	chr3	169754519	169754754	+	0	NA	Intergenic	Intergenic	10424	NR_001566	7012	Hs.436182	NR_001566	ENSG00000277925	TERC	DKCA1|PFBMFT2|SCARNA19|TR|TRC3|hTR	telomerase RNA component	ncRNA	0.000000	0.419492	
chunk0144_92_1	chr4	128386930	128387500	+	0	NA	Intergenic	Intergenic	-40801	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.022807	0.553415	
chunk0175_396_1	chr6	168526892	168527494	+	0	NA	intron (NM_022138, intron 3 of 12)	intron (NM_022138, intron 3 of 12)	86042	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.016611	0.515755	296(AAGGACAGGCTGTTCT,-,0.00),297(AGGACAGGCTGTTCTG,+,0.00)
chunk0102_31_1	chr2	141701622	141702104	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	429838	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.006224	0.335404	
chunk0187_309_1	chr7	156438187	156438430	+	0	NA	non-coding (NR_038232, exon 3 of 3)	non-coding (NR_038232, exon 3 of 3)	7280	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.008230	0.360656	
chunk0100_91_1	chr2	107789219	107789482	+	0	NA	intron (NR_126370, intron 2 of 4)	L1MB2|LINE|L1	35238	NR_126369	104326057	Hs.585967	NR_126369	ENSG00000232991	GACAT1	LINC00876	gastric cancer associated transcript 1	ncRNA	0.000000	0.321970	222(AAGAACAGAGTGCACA,-,0.00),223(AGAACAGAGTGCACAT,+,0.00)
chunk0084_62_1	chr17	74706770	74706978	+	0	NA	intron (NM_001289082, intron 1 of 6)	L1M3|LINE|L1	6126	NM_001289084	146722	Hs.567706	NM_139018	ENSG00000186074	CD300LF	CD300f|CLM-1|CLM1|IREM-1|IREM1|IgSF13|LMIR3|NKIR	CD300 molecule like family member f	protein-coding	0.033654	0.535885	
chunk0086_134_1	chr18	21104598	21105091	+	0	NA	intron (NM_005406, intron 1 of 32)	intron (NM_005406, intron 1 of 32)	7007	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.012170	0.334008	
chunk0179_442_1	chr7	52442223	52442697	+	0	NA	Intergenic	L1MC2|LINE|L1	-593196	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.006329	0.332632	
chunk0064_35_1	chr14	89572424	89573725	+	0	NA	intron (NM_001085471, intron 1 of 6)	intron (NM_001085471, intron 1 of 6)	-3142	NR_024620	29018	Hs.673124	NM_014099	ENSG00000259073	FOXN3-AS2	PRO1768	FOXN3 antisense RNA 2	ncRNA	0.011530	0.446237	
chunk0069_429_1	chr15	68309180	68309383	+	0	NA	intron (NM_001004439, intron 26 of 29)	HSMAR2|DNA|TcMar-Mariner	31478	NM_015322	10116	Hs.362733	NM_015322	ENSG00000169018	FEM1B	F1A-ALPHA|F1AA|FEM1-beta	fem-1 homolog B	protein-coding	0.004926	0.411765	
chunk0048_386_1	chr12	87082778	87083127	+	0	NA	Intergenic	MIR|SINE|MIR	-244048	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.005731	0.322857	
chunk0035_329_1	chr11	47572400	47572702	+	0	NA	non-coding (NR_024222, exon 4 of 4)	non-coding (NR_024222, exon 4 of 4)	6418	NM_016506	55709	Hs.718483	NM_016506	ENSG00000123444	KBTBD4	BKLHD4|HSPC252	kelch repeat and BTB domain containing 4	protein-coding	0.000000	0.422442	230(GAGGAGAGGCTGTGCC,-,0.00),231(AGGAGAGGCTGTGCCT,+,0.00)
chunk0026_185_1	chr10	63520800	63521186	+	0	NA	promoter-TSS (NM_001001330)	promoter-TSS (NM_001001330)	-370	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.046632	0.560724	217(TTGGACACCGAGTTCC,-,0.00),218(TGGACACCGAGTTCCT,+,0.00)
chunk0117_246_1	chr22	23192222	23192627	+	0	NA	intron (NM_021574, intron 1 of 21)	intron (NM_021574, intron 1 of 21)	12059	NM_004327	613	Hs.517461	NM_004327	ENSG00000186716	BCR	ALL|BCR1|CML|D22S11|D22S662|PHL	BCR activator of RhoGEF and GTPase	protein-coding	0.009877	0.524631	
chunk0160_171_1	chr5	153504896	153505225	+	0	NA	intron (NM_001258019, intron 2 of 14)	intron (NM_001258019, intron 2 of 14)	12888	NM_001258021	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.003040	0.463636	
chunk0191_61_1	chr8	46903946	46904320	+	0	NA	Intergenic	Intergenic	63247	NR_027012	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.008021	0.442667	
chunk0195_414_1	chr8	100662805	100663286	+	0	NA	Intergenic	L1PA17|LINE|L1	-13380	NM_152628	169166	Hs.567758	NM_152628	ENSG00000174226	SNX31	-	sorting nexin 31	protein-coding	0.022869	0.406639	
chunk0101_351_1	chr2	137873949	137874515	+	0	NA	Intergenic	L1M6B|LINE|L1	53700	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.001767	0.370370	
chunk0035_208_1	chr11	44804431	44804655	+	0	NA	intron (NM_130783, intron 1 of 8)	(GGAG)n|Simple_repeat|Simple_repeat	40117	NM_130783	90139	Hs.385634	NM_130783	ENSG00000157570	TSPAN18	TSPAN	tetraspanin 18	protein-coding	0.013393	0.506667	
chunk0196_310_1	chr8	110403213	110403625	+	0	NA	Intergenic	Intergenic	-428689	NM_014379	27012	Hs.13285	NM_014379	ENSG00000164794	KCNV1	HNKA|KCNB3|KV2.3|KV8.1	potassium voltage-gated channel modifier subfamily V member 1	protein-coding	0.002427	0.302663	
chunk0135_312_1	chr3	189992645	189993268	+	0	NA	intron (NM_001134418, intron 3 of 14)	intron (NM_001134418, intron 3 of 14)	-128008	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.016051	0.366987	
chunk0054_178_1	chr13	44500876	44501281	+	0	NA	intron (NM_183422, intron 1 of 2)	intron (NM_183422, intron 1 of 2)	-26777	NM_001243798	8848	Hs.436383	NM_006022	ENSG00000102804	TSC22D1	Ptg-2|TGFB1I4|TSC22	TSC22 domain family member 1	protein-coding	0.009877	0.445813	
chunk0109_224_1	chr20	5779324	5779954	+	0	NA	intron (NM_152504, intron 2 of 2)	intron (NM_152504, intron 2 of 2)	29252	NM_152504	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.004762	0.458003	
chunk0202_223_1	chr9	76302389	76302588	+	0	NA	intron (NM_001190482, intron 27 of 36)	intron (NM_001190482, intron 27 of 36)	92040	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.020101	0.475000	
chunk0100_282_1	chr2	113966588	113967249	+	0	NA	Intergenic	Intergenic	-12651	NR_034128	440900	Hs.662205	NR_034128	ENSG00000234199	LINC01191	VIN|lnc-ACTR3	long intergenic non-protein coding RNA 1191	ncRNA	0.010590	0.394260	414(CAGGACAGTGTGTGTT,-,0.00),415(AGGACAGTGTGTGTTT,+,0.00)
chunk0071_164_1	chr15	83011011	83011306	+	0	NA	intron (NM_144597, intron 1 of 3)	L2c|LINE|L2	483	NR_027650	123207	Hs.352541	NM_144597	ENSG00000169609	C15orf40	-	chromosome 15 open reading frame 40	protein-coding	0.044068	0.594595	
chunk0138_378_1	chr4	42558040	42558605	+	0	NA	intron (NM_001105529, intron 14 of 35)	intron (NM_001105529, intron 14 of 35)	98783	NM_001105529	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.001770	0.319788	
chunk0012_152_1	chr1	157910709	157910978	+	0	NA	Intergenic	MSTB2-int|LTR|ERVL-MaLR	-68999	NM_005894	922	Hs.134035	NM_005894	ENSG00000073754	CD5L	AIM|API6|CT-2|PRO229|SP-ALPHA|Spalpha|hAIM	CD5 molecule like	protein-coding	0.003717	0.588889	
chunk0081_114_1	chr17	40032473	40032865	+	0	NA	exon (NM_001079518, exon 8 of 25)	exon (NM_001079518, exon 8 of 25)	-5024	NR_102369	101340251		NR_102369	ENSG00000238793	SNORD124	-	small nucleolar RNA, C/D box 124	snoRNA	0.015306	0.559796	
chunk0063_313_1	chr14	85081773	85082165	+	0	NA	Intergenic	MIR|SINE|MIR	-311910	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005102	0.356234	
chunk0211_4_1	chrX	107670145	107670594	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	41945	NM_002764	5631	Hs.56	NM_002764	ENSG00000147224	PRPS1	ARTS|CMTX5|DFN2|DFNX1|PPRibP|PRS-I|PRSI	phosphoribosyl pyrophosphate synthetase 1	protein-coding	0.002227	0.442222	
chunk0164_8_1	chr6	17706452	17706805	+	0	NA	5' UTR (NM_001278209, exon 1 of 23)	5' UTR (NM_001278209, exon 1 of 23)	206	NM_001278209	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.101983	0.697740	
chunk0051_348_1	chr12	120439018	120439332	+	0	NA	intron (NM_004373, intron 2 of 2)	intron (NM_004373, intron 2 of 2)	1085	NM_004373	1337	Hs.369624	NM_004373	ENSG00000111775	COX6A1	CMTRID|COX6A|COX6AL	cytochrome c oxidase subunit 6A1	protein-coding	0.022293	0.453968	
chunk0211_293_1	chrX	122711245	122711546	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-472848	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.006645	0.427152	
chunk0129_79_1	chr3	117875494	117875851	+	0	NA	Intergenic	LTR24C|LTR|ERV1	954241	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002801	0.382682	191(AGGAACAGACTGTAAC,-,0.00)
chunk0197_446_1	chr8	127796435	127796786	+	0	NA	TTS (NR_031609)	TTS (NR_031609)	648	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.014245	0.511364	180(TAAGACACCCTGTTCT,-,0.00),181(AAGACACCCTGTTCTT,+,0.00)
chunk0030_225_1	chr10	114779800	114780300	+	0	NA	TTS (NR_120628)	TTS (NR_120628)	15262	NR_120628	101927692	Hs.576909	NR_120628	ENSG00000228484	LOC101927692	-	uncharacterized LOC101927692	ncRNA	0.002000	0.401198	
chunk0158_419_1	chr5	135115927	135116502	+	0	NA	intron (NM_001277348, intron 2 of 5)	intron (NM_001277348, intron 2 of 5)	-76167	NR_105050	101927953	Hs.436898	NR_105049	ENSG00000249082	C5orf66-AS1	Epist	C5orf66 antisense RNA 1	ncRNA	0.012174	0.531250	361(GGGCACTCGCAGTTCT,-,0.00),362(GGCACTCGCAGTTCTT,+,0.00)
chunk0205_266_1	chr9	111349801	111350197	+	0	NA	Intergenic	L1ME1|LINE|L1	-21566	NM_205859	26248	Hs.381312	NM_205859	ENSG00000171133	OR2K2	HSHTPCRH06|HTPCRH06|OR2AN1P|OR2AR1P	olfactory receptor family 2 subfamily K member 2	protein-coding	0.012626	0.340050	
chunk0205_277_1	chr9	111586016	111586260	+	0	NA	exon (NM_012212, exon 5 of 10)	exon (NM_012212, exon 5 of 10)	13293	NM_012212	22949	Hs.584864	NM_012212	ENSG00000106853	PTGR1	LTB4DH|PGR1|ZADH3	prostaglandin reductase 1	protein-coding	0.004098	0.457143	
chunk0030_183_1	chr10	114206796	114207383	+	0	NA	intron (NM_198795, intron 11 of 25)	intron (NM_198795, intron 11 of 25)	27819	NM_198795	56165	Hs.333132	NM_198795	ENSG00000095627	TDRD1	CT41.1	tudor domain containing 1	protein-coding	0.008518	0.420068	
chunk0057_255_1	chr13	105363996	105364264	+	0	NA	Intergenic	Intergenic	-101737	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.011194	0.390335	
chunk0194_124_1	chr8	84062537	84062751	+	0	NA	Intergenic	L1MA2|LINE|L1	-120574	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.009346	0.530233	
chunk0073_343_1	chr16	14559628	14560212	+	0	NA	intron (NM_002582, intron 18 of 23)	intron (NM_002582, intron 18 of 23)	70351	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.013699	0.422222	
chunk0055_36_1	chr13	52034712	52035420	+	0	NA	Intergenic	Intergenic	10375	NM_021645	9724	Hs.512963	NM_021645	ENSG00000253797	UTP14C	2700066J21Rik|KIAA0266|UTP14B	UTP14C small subunit processome component	protein-coding	0.007062	0.383639	510(AAGAACAGTCTGTCAA,-,0.00)
chunk0106_396_1	chr2	207768519	207768733	+	0	NA	exon (NM_003468, exon 2 of 2)	exon (NM_003468, exon 2 of 2)	793	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.102804	0.697674	
chunk0058_422_1	chr13	112905950	112906706	+	0	NA	Intergenic	Intergenic	62310	NR_034002	100289410	Hs.667436	NR_034002		MCF2L-AS1	-	MCF2L antisense RNA 1	ncRNA	0.027778	0.548217	719(GGGAACATGTTGTTCA,-,0.00),720(GGAACATGTTGTTCAG,+,0.00)
chunk0146_237_1	chr4	162241742	162242272	+	0	NA	Intergenic	MIRb|SINE|MIR	-77973	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.001887	0.276836	223(TAGGACAAACTGTACA,-,0.00),224(AGGACAAACTGTACAC,+,0.00)
chunk0046_77_1	chr12	56122705	56123036	+	0	NA	TTS (NM_032786)	TTS (NM_032786)	4310	NM_001303125	84872	Hs.632706	NM_032786	ENSG00000135482	ZC3H10	ZC3HDC10	zinc finger CCCH-type containing 10	protein-coding	0.006042	0.490964	
chunk0093_391_1	chr19	56638137	56638337	+	0	NA	Intergenic	CpG	-4922	NM_001193628	147670	Hs.336588	NM_001193628	ENSG00000268182	SMIM17	-	small integral membrane protein 17	protein-coding	0.050000	0.646766	
chunk0052_105_1	chr13	22596113	22596499	+	0	NA	Intergenic	Intergenic	301875	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.002591	0.395349	
chunk0034_270_1	chr11	34595471	34595816	+	0	NA	Intergenic	Intergenic	-25398	NM_012153	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.005797	0.421965	
chunk0019_151_1	chr1	225820743	225821238	+	0	NA	intron (NM_001291163, intron 1 of 8)	intron (NM_001291163, intron 1 of 8)	-4311	NM_000120	2052	Hs.89649	NM_000120	ENSG00000143819	EPHX1	EPHX|EPOX|HYL1|MEH	epoxide hydrolase 1	protein-coding	0.004040	0.356855	
chunk0072_71_1	chr15	90465153	90465523	+	0	NA	intron (NM_003870, intron 15 of 37)	intron (NM_003870, intron 15 of 37)	-64548	NM_022769	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.002703	0.393531	
chunk0161_53_1	chr5	166081262	166081768	+	0	NA	Intergenic	L2a|LINE|L2	844855	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.001976	0.309665	
chunk0015_19_1	chr1	184294924	184295537	+	0	NA	Intergenic	Intergenic	-91786	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.384365	
chunk0079_163_1	chr17	13557024	13557223	+	0	NA	intron (NM_006042, intron 1 of 1)	intron (NM_006042, intron 1 of 1)	-13477	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.025126	0.435000	
chunk0206_33_1	chr9	116450917	116451132	+	0	NA	intron (NM_198186, intron 5 of 7)	intron (NM_198186, intron 5 of 7)	-50418	NR_103711	493913	Hs.728832	NR_103711	ENSG00000256040	PAPPA-AS1	DIPAS|NCRNA00156|PAPPA-AS|PAPPAAS|PAPPAS|TAF2C2|TAF4B|TAFII105	PAPPA antisense RNA 1	ncRNA	0.000000	0.504630	
chunk0182_236_1	chr7	96747301	96747715	+	0	NA	Intergenic	Intergenic	-37617	NM_006304	7979	Hs.489201	NM_006304	ENSG00000127922	SEM1	C7orf76|DSS1|ECD|SHFD1|SHFM1|SHSF1|Shfdg1	SEM1 26S proteasome complex subunit	protein-coding	0.004831	0.407229	
chunk0082_76_1	chr17	51608231	51608979	+	0	NA	Intergenic	Intergenic	271890	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.012032	0.423231	
chunk0079_406_1	chr17	19519512	19520103	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-14047	NM_018242	55244	Hs.232054	NM_018242	ENSG00000142494	SLC47A1	MATE1	solute carrier family 47 member 1	protein-coding	0.010152	0.488176	
chunk0046_399_1	chr12	64028607	64028806	+	0	NA	intron (NM_020762, intron 4 of 21)	MLT1A0|LTR|ERVL-MaLR	183945	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.010050	0.480000	
chunk0156_76_1	chr5	103986187	103986807	+	0	NA	Intergenic	Intergenic	-423696	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.003226	0.331723	
chunk0164_401_1	chr6	26507461	26508104	+	0	NA	intron (NM_001732, intron 4 of 6)	intron (NM_001732, intron 4 of 6)	6515	NM_001732	696	Hs.153058	NM_001732	ENSG00000124557	BTN1A1	BT|BTN|BTN1	butyrophilin subfamily 1 member A1	protein-coding	0.013997	0.434783	
chunk0112_293_1	chr20	44087414	44087724	+	0	NA	Intergenic	Intergenic	100009	NM_175913	57158	Hs.441737	NM_020433	ENSG00000149596	JPH2	CMH17|JP-2|JP2	junctophilin 2	protein-coding	0.012903	0.504823	
chunk0101_185_1	chr2	129382511	129382797	+	0	NA	Intergenic	L1MD2|LINE|L1	-108763	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.003497	0.376307	91(CTGGACTTTCTGTTCT,-,0.00),92(TGGACTTTCTGTTCTG,+,0.00)
chunk0154_448_1	chr5	90473958	90474364	+	0	NA	promoter-TSS (NM_006467)	promoter-TSS (NM_006467)	607	NM_203406	153364	Hs.64004	NM_203406	ENSG00000176055	MBLAC2	-	metallo-beta-lactamase domain containing 2	protein-coding	0.098522	0.668305	
chunk0186_105_1	chr7	137919987	137920247	+	0	NA	intron (NM_194071, intron 2 of 11)	intron (NM_194071, intron 2 of 11)	-33231	NM_001243523									0.000000	0.482759	
chunk0136_356_1	chr3	195906044	195907373	+	0	NA	intron (NM_005781, intron 1 of 14)	L1ME1|LINE|L1	2301	NM_005781	10188	Hs.518513	NM_005781	ENSG00000061938	TNK2	ACK|ACK-1|ACK1|p21cdc42Hs	tyrosine kinase non receptor 2	protein-coding	0.023326	0.468421	808(GGGAACAGTCTGACCC,-,0.00),809(GGAACAGTCTGACCCT,+,0.00),1109(AAAACAGACCGTTCTC,+,0.00)
chunk0145_37_1	chr4	144106142	144106386	+	0	NA	Intergenic	LTR78|LTR|ERV1	34522	NM_001308187	2993	Hs.434973	NM_002099	ENSG00000170180	GYPA	CD235a|GPA|GPErik|GPSAT|HGpMiV|HGpMiXI|HGpSta(C)|MN|MNS|PAS-2	glycophorin A (MNS blood group)	protein-coding	0.000000	0.367347	
chunk0112_4_1	chr20	35742199	35742657	+	0	NA	promoter-TSS (NM_001242600)	promoter-TSS (NM_001242600)	-92	NR_040722	9584	Hs.282901	NM_004902	ENSG00000131051	RBM39	CAPER|CAPERalpha|FSAP59|HCC1|RNPC2	RNA binding motif protein 39	protein-coding	0.072052	0.601307	
chunk0041_131_1	chr11	125168594	125169008	+	0	NA	intron (NM_022062, intron 1 of 12)	intron (NM_022062, intron 1 of 12)	4138	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.014493	0.373494	
chunk0173_307_1	chr6	148516459	148516808	+	0	NA	intron (NM_015278, intron 9 of 19)	MIR|SINE|MIR	174040	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.020057	0.500000	146(GGGCACACCGTGTGCC,-,0.00),147(GGCACACCGTGTGCCA,+,0.00)
chunk0198_261_1	chr8	134794021	134794839	+	0	NA	Intergenic	Intergenic	6177	NR_029666	407030		NR_029666	ENSG00000207582	MIR30B	MIRN30B|mir-30b	microRNA 30b	ncRNA	0.008557	0.343101	
chunk0094_430_1	chr2	10757416	10757685	+	0	NA	intron (NM_001039362, intron 4 of 13)	intron (NM_001039362, intron 4 of 13)	35901	NM_001039362	245973	Hs.580464	NM_144583	ENSG00000143882	ATP6V1C2	ATP6C2|VMA5	ATPase H+ transporting V1 subunit C2	protein-coding	0.022305	0.466667	
chunk0055_425_1	chr13	75369985	75370321	+	0	NA	intron (NM_001286659, intron 1 of 18)	L2a|LINE|L2	112015	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.008929	0.442136	149(CAGAACATCAAGTACT,-,0.00),150(AGAACATCAAGTACTA,+,0.00)
chunk0144_168_1	chr4	132001735	132002125	+	0	NA	Intergenic	Intergenic	237092	NR_125883	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.000000	0.304348	
chunk0165_298_1	chr6	36642956	36643338	+	0	NA	Intergenic	Intergenic	-20635	NR_037491	100500885		NR_037491	ENSG00000263894	MIR3925	-	microRNA 3925	ncRNA	0.000000	0.519582	
chunk0017_202_1	chr1	207649345	207649544	+	0	NA	intron (NM_175710, intron 1 of 11)	intron (NM_175710, intron 1 of 11)	4331	NM_175710	1379	Hs.628568	NM_175710	ENSG00000197721	CR1L	-	complement C3b/C4b receptor 1 like	protein-coding	0.015075	0.420000	
chunk0031_122_1	chr10	124739204	124739611	+	0	NA	intron (NM_014661, intron 1 of 4)	intron (NM_014661, intron 1 of 4)	4954	NM_014661	9679	Hs.129195	NM_014661	ENSG00000189319	FAM53B	KIAA0140|bA12J10.2|smp	family with sequence similarity 53 member B	protein-coding	0.009828	0.487745	
chunk0097_167_1	chr2	49449431	49450077	+	0	NA	Intergenic	Intergenic	-295227	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.006192	0.323029	
chunk0097_176_1	chr2	49885102	49885596	+	0	NA	Intergenic	L1PA7|LINE|L1	462407	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.004049	0.337374	
chunk0117_318_1	chr22	24841258	24841755	+	0	NA	intron (NM_001039948, intron 2 of 25)	L1MB2|LINE|L1	35285	NM_001098498	129049	Hs.474397	NM_133454	ENSG00000167037	SGSM1	RUTBC2	small G protein signaling modulator 1	protein-coding	0.004024	0.399598	
chunk0001_40_1	chr1	1678676	1679505	+	0	NA	intron (NM_001110781, intron 1 of 8)	intron (NM_001110781, intron 1 of 8)	13714	NM_001110781	728661	Hs.655255	NM_001110781	ENSG00000189339	SLC35E2B	SLC35E2	solute carrier family 35 member E2B	protein-coding	0.026538	0.579518	625(CAGAACAGTCTGTCCA,-,0.00),626(AGAACAGTCTGTCCAC,+,0.00)
chunk0143_190_1	chr4	112283406	112283607	+	0	NA	intron (NM_052864, intron 1 of 1)	intron (NM_052864, intron 1 of 1)	2397	NM_052864	92610	Hs.310640	NM_052864	ENSG00000145365	TIFA	T2BP|T6BP|TIFAA	TRAF interacting protein with forkhead associated domain	protein-coding	0.004975	0.381188	
chunk0137_71_1	chr4	12576031	12576483	+	0	NA	Intergenic	Intergenic	352806	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.000000	0.331126	272(CAGCACATACAGTACT,-,0.00),273(AGCACATACAGTACTT,+,0.00)
chunk0176_405_1	chr7	19302772	19303429	+	0	NA	Intergenic	Intergenic	-157679	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.004566	0.355623	
chunk0082_290_1	chr17	58377282	58377505	+	0	NA	intron (NM_001305544, intron 2 of 9)	intron (NM_001305544, intron 2 of 9)	-25155	NM_003168	6827	Hs.439481	NM_003168	ENSG00000213246	SUPT4H1	SPT4|SPT4H|SUPT4H|Supt4a	SPT4 homolog, DSIF elongation factor subunit	protein-coding	0.008969	0.504464	
chunk0118_399_1	chr22	37887565	37888100	+	0	NA	intron (NM_016091, intron 12 of 12)	intron (NM_016091, intron 12 of 12)	-18316	NM_033386	85377	Hs.517610	NM_033386	ENSG00000100139	MICALL1	MICAL-L1|MIRAB13	MICAL like 1	protein-coding	0.003738	0.522388	
chunk0063_28_1	chr14	76653827	76654235	+	0	NA	Intergenic	L2a|LINE|L2	-107861	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.007353	0.440098	
chunk0096_185_1	chr2	29874897	29875117	+	0	NA	intron (NM_004304, intron 1 of 28)	L1MB4|LINE|L1	46604	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.004545	0.375566	
chunk0063_87_1	chr14	77981585	77982037	+	0	NA	Intergenic	Intergenic	181728	NM_020421	57143	Hs.413208	NM_020421	ENSG00000063761	ADCK1	-	aarF domain containing kinase 1	protein-coding	0.015487	0.408389	
chunk0126_310_1	chr3	81185996	81186529	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	192394	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.007505	0.391386	
chunk0174_314_1	chr6	162916568	162916849	+	0	NA	intron (NM_152410, intron 3 of 6)	L1ME2|LINE|L1	137453	NR_110872	101929239	Hs.571035	NR_110871	ENSG00000225437	PACRG-AS2	-	PACRG antisense RNA 2	ncRNA	0.003559	0.365248	
chunk0065_455_1	chr14	106680746	106680945	+	0	NA	Intergenic	Intergenic	44134	NR_106988									0.010050	0.560000	
chunk0089_106_1	chr18	58476306	58476641	+	0	NA	Intergenic	Intergenic	-25321	NR_039899	100616357		NR_039899	ENSG00000207778	MIR3591	-	microRNA 3591	ncRNA	0.011940	0.392857	
chunk0156_290_1	chr5	110017893	110018461	+	0	NA	Intergenic	L1M3|LINE|L1	134995	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.005282	0.405975	
chunk0168_1_1	chr6	76499275	76499510	+	0	NA	Intergenic	Intergenic	-426714	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.004255	0.377119	
chunk0119_110_1	chr22	42260025	42260412	+	0	NA	intron (NM_005650, intron 1 of 5)	L2a|LINE|L2	-9535	NR_036498	388906	Hs.730075	NR_036498		OGFRP1	-	opioid growth factor receptor pseudogene 1	pseudo	0.000000	0.425258	
chunk0048_179_1	chr12	80925155	80926430	+	0	NA	intron (NM_004664, intron 1 of 5)	intron (NM_004664, intron 1 of 5)	10041	NR_030349	693203		NR_030349	ENSG00000208022	MIR618	MIRN618|hsa-mir-618|mir-618	microRNA 618	ncRNA	0.003137	0.346395	
chunk0058_288_1	chr14	26808255	26808823	+	0	NA	promoter-TSS (NR_110556)	promoter-TSS (NR_110556)	-809	NR_110557	102724890	Hs.569381	NR_110556	ENSG00000257185	LINC02293	-	long intergenic non-protein coding RNA 2293	ncRNA	0.001761	0.356766	
chunk0079_413_1	chr17	19642614	19642839	+	0	NA	Intergenic	Intergenic	-6025	NM_001031806	224	Hs.499886	NM_000382	ENSG00000072210	ALDH3A2	ALDH10|FALDH|SLS	aldehyde dehydrogenase 3 family member A2	protein-coding	0.008889	0.384956	
chunk0100_428_1	chr2	120223150	120223447	+	0	NA	5' UTR (NM_024121, exon 1 of 1)	5' UTR (NM_024121, exon 1 of 1)	110	NM_024121	79134	Hs.376722	NM_024121	ENSG00000226479	TMEM185B	FAM11B	transmembrane protein 185B	protein-coding	0.144781	0.751678	
chunk0076_18_1	chr16	58773758	58774332	+	0	NA	Intergenic	L2c|LINE|L2	-39688	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.001742	0.363478	
chunk0023_119_1	chr10	23399841	23400199	+	0	NA	Intergenic	Intergenic	6615	NR_039606									0.016760	0.417827	
chunk0105_120_1	chr2	185318441	185318750	+	0	NA	Intergenic	MER67C|LTR|ERV1	-420033	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.003236	0.400000	
chunk0196_40_1	chr8	101741078	101741544	+	0	NA	intron (NM_001040630, intron 3 of 5)	intron (NM_001040630, intron 3 of 5)	49900	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.006438	0.411135	
chunk0097_417_1	chr2	62820432	62820706	+	0	NA	intron (NM_001142614, intron 4 of 22)	L1MB4|LINE|L1	113672	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.007299	0.349091	
chunk0026_249_1	chr10	66440675	66440997	+	0	NA	intron (NM_001127384, intron 11 of 17)	MIR|SINE|MIR	-485198	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.003106	0.328173	
chunk0113_188_1	chr20	53327504	53327721	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	142329	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.009217	0.417431	
chunk0008_446_1	chr1	99662573	99663185	+	0	NA	intron (NM_017734, intron 2 of 7)	intron (NM_017734, intron 2 of 7)	17004	NM_017734	54873	Hs.483993	NM_017734	ENSG00000099260	PALMD	C1orf11|PALML	palmdelphin	protein-coding	0.004902	0.389886	
chunk0055_97_1	chr13	56079109	56079467	+	0	NA	Intergenic	Intergenic	904834	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.002793	0.367688	202(AAAACATCGTGTTCAT,+,0.00)
chunk0164_344_1	chr6	25416170	25416681	+	0	NA	intron (NM_017640, intron 2 of 36)	MIR|SINE|MIR	136997	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.001957	0.380859	
chunk0135_86_1	chr3	186372337	186372672	+	0	NA	Intergenic	Intergenic	-10270	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.014925	0.377976	
chunk0043_136_1	chr12	15984109	15984855	+	0	NA	intron (NM_015954, intron 6 of 8)	intron (NM_015954, intron 6 of 8)	73310	NM_001300779	51071	Hs.39429	NM_015954	ENSG00000023697	DERA	CGI-26|DEOC	deoxyribose-phosphate aldolase	protein-coding	0.008043	0.394913	515(TGAACACTCTGGTCTT,+,0.00)
chunk0080_399_1	chr17	35196565	35196799	+	0	NA	Intergenic	L1M2|LINE|L1	-2289	NM_152462	146861	Hs.514814	NM_152462	ENSG00000164729	SLC35G3	AMAC1|TMEM21A	solute carrier family 35 member G3	protein-coding	0.000000	0.314894	
chunk0123_122_1	chr3	42544393	42545296	+	0	NA	Intergenic	Intergenic	-12238	NR_046654	100874007	Hs.600642	NR_046654		VIPR1-AS1	-	VIPR1 antisense RNA 1	ncRNA	0.013289	0.551991	230(AAAACATCCAGTTCCC,+,0.00),548(TGGCACAGGCTGTTTC,-,0.00),549(GGCACAGGCTGTTTCC,+,0.00),678(GGGGACAGCATGTTCC,-,0.00),679(GGGACAGCATGTTCCA,+,0.00)
chunk0069_443_1	chr15	68537514	68537798	+	0	NA	Intergenic	L1PA10|LINE|L1	-41313	NM_006091	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.024648	0.505263	
chunk0085_66_1	chr18	1270085	1270284	+	0	NA	intron (NR_023925, intron 6 of 6)	L2c|LINE|L2	89445	NR_023927	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.005025	0.335000	
chunk0080_77_1	chr17	22140190	22140752	+	0	NA	Intergenic	L2a|LINE|L2	-158293	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.005338	0.335702	
chunk0075_61_1	chr16	47848224	47848655	+	0	NA	TTS (NR_110649)	TTS (NR_110649)	-10142	NR_110650	101927132	Hs.589404	NR_110650	ENSG00000261231	LINC02133	-	long intergenic non-protein coding RNA 2133	ncRNA	0.006961	0.421296	232(GGTCCAGCGTGTTCCC,+,0.00)
chunk0103_139_1	chr2	162103467	162103666	+	0	NA	Intergenic	Intergenic	-10875	NR_110255	101929532	Hs.639883	NR_110255	ENSG00000236841	LOC101929532	-	uncharacterized LOC101929532	ncRNA	0.010050	0.440000	
chunk0160_335_1	chr5	159907989	159908216	+	0	NA	Intergenic	Intergenic	-8631	NM_000679	147	Hs.368632	NM_000679	ENSG00000170214	ADRA1B	ADRA1|ALPHA1BAR	adrenoceptor alpha 1B	protein-coding	0.000000	0.469298	
chunk0090_93_1	chr18	70730465	70730674	+	0	NA	Intergenic	MIR|SINE|MIR	-79712	NM_001278515									0.009569	0.390476	
chunk0087_327_1	chr18	39985199	39985667	+	0	NA	Intergenic	L1ME2z|LINE|L1	-80853	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.266525	
chunk0213_37_1	chrY	56870740	56871079	+	0	NA	Intergenic	Intergenic	-83346	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.011799	0.529412	
chunk0154_380_1	chr5	87762450	87763101	+	0	NA	Intergenic	Intergenic	-349742	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.007680	0.404908	
chunk0145_96_1	chr4	145974169	145974535	+	0	NA	Intergenic	L1MD1|LINE|L1	-35392	NM_001306215	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.002732	0.253406	
chunk0067_183_1	chr15	44536511	44536710	+	0	NA	promoter-TSS (NM_003758)	promoter-TSS (NM_003758)	290	NR_034171	645212	Hs.594287	NR_034170		EIF3J-DT	EIF3J-AS1	EIF3J divergent transcript	ncRNA	0.100503	0.710000	
chunk0027_402_1	chr10	80415977	80416875	+	0	NA	intron (NM_001243782, intron 1 of 5)	intron (NM_001243782, intron 1 of 5)	2607	NM_001243778	84293	Hs.500333	NM_032333	ENSG00000122378	PRXL2A	Adrx|C10orf58|FAM213A|PAMM	peroxiredoxin like 2A	protein-coding	0.008909	0.454950	
chunk0081_464_1	chr17	49440177	49440727	+	0	NA	Intergenic	Intergenic	21297	NR_110805	101927207	Hs.638402	NR_110805	ENSG00000249497	LINC02075	-	long intergenic non-protein coding RNA 2075	ncRNA	0.010909	0.557169	
chunk0169_173_1	chr6	102214979	102215762	+	0	NA	Intergenic	Intergenic	816385	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.005109	0.332908	
chunk0169_407_1	chr6	108432814	108433013	+	0	NA	intron (NM_145315, intron 7 of 12)	intron (NM_145315, intron 7 of 12)	-126910	NM_201559	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.005025	0.495000	
chunk0129_260_1	chr3	122416316	122416624	+	0	NA	promoter-TSS (NM_019069)	promoter-TSS (NM_019069)	264	NR_125405	102723582	Hs.675056	NR_125405	ENSG00000272758	LOC102723582	-	uncharacterized LOC102723582	ncRNA	0.042208	0.508091	
chunk0108_167_1	chr2	231456146	231456345	+	0	NA	promoter-TSS (NR_002921)	promoter-TSS (NR_002921)	278	NR_002908	6082		NR_002908	ENSG00000207280	SNORD20	RNU20|U20	small nucleolar RNA, C/D box 20	snoRNA	0.005025	0.340000	
chunk0001_63_1	chr1	2255377	2255576	+	0	NA	intron (NM_003036, intron 1 of 6)	intron (NM_003036, intron 1 of 6)	26781	NM_003036	6497	Hs.656507	NM_003036	ENSG00000157933	SKI	SGS|SKV	SKI proto-oncogene	protein-coding	0.005025	0.510000	31(TGGAACACTGTGTCCT,-,0.00),32(GGAACACTGTGTCCTG,+,0.00),63(TGGAGCACACTGTCCT,-,0.00),64(GGAGCACACTGTCCTG,+,0.00),95(TGGAACACACTGTGTC,-,0.00),96(GGAACACACTGTGTCC,+,0.00),97(GAACACACTGTGTCCT,-,0.00),98(AACACACTGTGTCCTG,+,0.00)
chunk0117_131_1	chr22	19237377	19237894	+	0	NA	intron (NM_001835, intron 5 of 31)	L1ME4b|LINE|L1	54081	NM_001835	8218	Hs.368266	NM_001835	ENSG00000070371	CLTCL1	CHC22|CLH22|CLTCL|CLTD	clathrin heavy chain like 1	protein-coding	0.003868	0.401544	214(TGGAGCACAATGTTCC,-,0.00),215(GGAGCACAATGTTCCT,+,0.00),342(TGGAACAGAATGATCT,-,0.00),343(GGAACAGAATGATCTA,+,0.00)
chunk0091_396_1	chr19	16362996	16363604	+	0	NA	intron (NR_047665, intron 21 of 22)	intron (NR_047665, intron 21 of 22)	38460	NM_016270	10365	Hs.685136	NM_016270	ENSG00000127528	KLF2	LKLF	Kruppel like factor 2	protein-coding	0.024671	0.587849	312(AGGAACTGCCTGTCCC,-,0.00),313(GGAACTGCCTGTCCCT,+,0.00)
chunk0158_169_1	chr5	127682524	127683004	+	0	NA	Intergenic	L1MC5|LINE|L1	29749	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.002083	0.295218	
chunk0014_157_1	chr1	178224222	178224756	+	0	NA	intron (NM_170692, intron 1 of 17)	intron (NM_170692, intron 1 of 17)	-116982	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.007491	0.293458	
chunk0141_202_1	chr4	84318017	84318419	+	0	NA	Intergenic	Intergenic	-19049	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.004975	0.327543	
chunk0005_434_1	chr1	63245122	63245870	+	0	NA	intron (NR_038252, intron 4 of 11)	MLT1A1|LTR|ERVL-MaLR	71761	NR_038252	199899	Hs.116210	NR_038252	ENSG00000224209	LINC00466	-	long intergenic non-protein coding RNA 466	ncRNA	0.004011	0.364486	250(GTGAACACTGTGTCCT,-,0.00),251(TGAACACTGTGTCCTC,+,0.00)
chunk0034_369_1	chr11	36164724	36165125	+	0	NA	intron (NM_174902, intron 4 of 5)	intron (NM_174902, intron 4 of 5)	124525	NM_001307937	29099	Hs.99443	NM_014186	ENSG00000110442	COMMD9	C11orf55|HSPC166|LINC00610	COMM domain containing 9	protein-coding	0.007481	0.358209	
chunk0118_77_1	chr22	28896563	28896819	+	0	NA	intron (NM_001206998, intron 1 of 8)	intron (NM_001206998, intron 1 of 8)	12924	NM_001206998	84133	Hs.604200	NM_032173	ENSG00000183579	ZNRF3	BK747E2.3|RNF203	zinc and ring finger 3	protein-coding	0.003906	0.381323	
chunk0006_330_1	chr1	71885956	71886623	+	0	NA	intron (NM_173808, intron 2 of 6)	intron (NM_173808, intron 2 of 6)	-49277	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.004498	0.330838	473(ATGACCAGTGTGTTCT,-,0.00),474(TGACCAGTGTGTTCTT,+,0.00)
chunk0041_318_1	chr11	130102790	130103496	+	0	NA	intron (NM_001243299, intron 1 of 16)	intron (NM_001243299, intron 1 of 16)	32575	NM_001243299	334	Hs.370247	NM_001642	ENSG00000084234	APLP2	APLP-2|APPH|APPL2|CDEBP	amyloid beta precursor like protein 2	protein-coding	0.001416	0.379066	337(AGGCACAGTCTGTGCT,-,0.00),338(GGCACAGTCTGTGCTT,+,0.00)
chunk0124_23_1	chr3	51995779	51996061	+	0	NA	promoter-TSS (NM_000992)	promoter-TSS (NM_000992)	22	NM_000992	6159	Hs.425125	NM_000992	ENSG00000162244	RPL29	HIP|HUMRPL29|L29|RPL29P10|RPL29_3_370	ribosomal protein L29	protein-coding	0.106383	0.646643	
chunk0154_442_1	chr5	90298509	90299141	+	0	NA	Intergenic	Intergenic	-8754	NR_120601	101929495	Hs.346679	NR_120601		LINC01339	-	long intergenic non-protein coding RNA 1339	ncRNA	0.009494	0.350711	
chunk0134_58_1	chr3	176137148	176137443	+	0	NA	Intergenic	L1PA15|LINE|L1	-360962	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.331081	
chunk0135_375_1	chr3	190899470	190899933	+	0	NA	Intergenic	L1PB1|LINE|L1	21771	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.004320	0.336207	
chunk0088_239_1	chr18	48546111	48546500	+	0	NA	intron (NM_001142397, intron 2 of 12)	L2a|LINE|L2	7249	NM_014772	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.010283	0.435897	
chunk0167_10_1	chr6	53469046	53469698	+	0	NA	Intergenic	L1MA3|LINE|L1	75757	NM_001498	2729	Hs.654465	NM_001498	ENSG00000001084	GCLC	GCL|GCS|GLCL|GLCLC	glutamate-cysteine ligase catalytic subunit	protein-coding	0.001534	0.344564	
chunk0104_194_1	chr2	175233103	175233695	+	0	NA	Intergenic	Intergenic	-51637	NM_001190329	518	Hs.429	NM_001689	ENSG00000154518	ATP5MC3	ATP5G3|P3	ATP synthase membrane subunit c locus 3	protein-coding	0.006757	0.325464	
chunk0112_330_1	chr20	44969838	44970473	+	0	NA	intron (NM_006282, intron 1 of 10)	L1PA3|LINE|L1	3676	NM_006282	6789	Hs.472838	NM_006282	ENSG00000101109	STK4	KRS2|MST1|YSK3	serine/threonine kinase 4	protein-coding	0.009449	0.330189	
chunk0066_117_1	chr15	30740685	30741154	+	0	NA	intron (NR_038255, intron 2 of 3).2	L1PB1|LINE|L1	-77117	NR_072991	390561	Hs.721293	NR_072991		HERC2P10	-	hect domain and RLD 2 pseudogene 10	pseudo	0.002132	0.370213	
chunk0122_195_1	chr3	32872700	32873506	+	0	NA	intron (NM_001039111, intron 1 of 3)	intron (NM_001039111, intron 1 of 3)	55085	NM_001039111	131405	Hs.113170	NM_001039111	ENSG00000206557	TRIM71	LIN-41|LIN41	tripartite motif containing 71	protein-coding	0.003722	0.491945	
chunk0207_237_1	chr9	131951957	131952173	+	0	NA	intron (NM_001253881, intron 3 of 6)	LTR33|LTR|ERVL	127822	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.009259	0.497696	1(GTGGACAGACTGTTCA,-,0.00),2(TGGACAGACTGTTCAT,+,0.00)
chunk0003_321_1	chr1	38272510	38272782	+	0	NA	Intergenic	Intergenic	-57879	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.011029	0.490842	
chunk0199_294_1	chr9	6758619	6758888	+	0	NA	intron (NR_130707, intron 1 of 14)	CpG	1112	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.070632	0.618519	
chunk0031_128_1	chr10	124830852	124831145	+	0	NA	intron (NM_032182, intron 7 of 8)	intron (NM_032182, intron 7 of 8)	29213	NM_032182	23172	Hs.280695	NM_032182	ENSG00000165660	ABRAXAS2	ABRO1|FAM175B|KIAA0157	abraxas 2, BRISC complex subunit	protein-coding	0.000000	0.275510	
chunk0117_312_1	chr22	24630488	24630694	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-2324	NR_024494	644165	Hs.531306	NR_024494		BCRP3	BCR3|BCRL3|BCRL6	BCR pseudogene 3	pseudo	0.009709	0.487923	
chunk0209_78_1	chrX	38112760	38113221	+	0	NA	intron (NM_138780, intron 13 of 16)	intron (NM_138780, intron 13 of 16)	79456	NM_001163334	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.008677	0.409091	
chunk0025_241_1	chr10	54326464	54326663	+	0	NA	intron (NM_001142767, intron 6 of 30)	MIR|SINE|MIR	281394	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.000000	0.300000	
chunk0050_176_1	chr12	103851042	103851744	+	0	NA	intron (NR_027249, intron 14 of 15)	intron (NR_027249, intron 14 of 15)	-10196	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.001425	0.357041	
chunk0159_95_1	chr5	138154416	138154633	+	0	NA	intron (NM_139199, intron 20 of 26)	intron (NM_139199, intron 20 of 26)	-15081	NM_003551	8382	Hs.730856	NM_003551	ENSG00000112981	NME5	NM23-H5|NM23H5|RSPH23	NME/NM23 family member 5	protein-coding	0.000000	0.380734	
chunk0165_292_1	chr6	36443281	36443480	+	0	NA	promoter-TSS (NM_152990)	promoter-TSS (NM_152990)	-491	NM_152990	222659	Hs.520097	NM_152990	ENSG00000179165	PXT1	STEPP	peroxisomal testis enriched protein 1	protein-coding	0.055276	0.620000	
chunk0017_208_1	chr1	207826378	207826764	+	0	NA	Intergenic	Intergenic	8192	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.010363	0.472868	
chunk0144_162_1	chr4	131270633	131270858	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-494093	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.000000	0.292035	
chunk0076_147_1	chr16	67147584	67147972	+	0	NA	TTS (NM_033309)	TTS (NM_033309)	3221	NM_033309	84752	Hs.744158	NM_033309	ENSG00000237172	B3GNT9	-	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9	protein-coding	0.007732	0.539846	
chunk0083_276_1	chr17	68511992	68512406	+	0	NA	promoter-TSS (NM_002734)	promoter-TSS (NM_002734)	-180	NM_001276289	5573	Hs.280342	NM_002734	ENSG00000108946	PRKAR1A	ACRDYS1|ADOHR|CAR|CNC|CNC1|PKR1|PPNAD1|PRKAR1|TSE1	protein kinase cAMP-dependent type I regulatory subunit alpha	protein-coding	0.070048	0.612048	
chunk0017_329_1	chr1	211521418	211521791	+	0	NA	Intergenic	Intergenic	-28687	NM_183059	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.002681	0.470588	
chunk0114_60_1	chr21	8988050	8988255	+	0	NA	TTS (NR_037421).2	TTS (NR_037421).2	782	NR_037458									0.136585	0.679612	
chunk0073_217_1	chr16	10628118	10628489	+	0	NA	intron (NM_144674, intron 6 of 6)	L2a|LINE|L2	-47587	NM_001424	2013	Hs.531561	NM_001424	ENSG00000213853	EMP2	XMP	epithelial membrane protein 2	protein-coding	0.021563	0.475806	
chunk0135_246_1	chr3	188863441	188863672	+	0	NA	intron (NM_001167671, intron 8 of 10)	intron (NM_001167671, intron 8 of 10)	84083	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.012987	0.512931	
chunk0163_203_1	chr6	11856370	11856595	+	0	NA	Intergenic	HAL1ME|LINE|L1	-77435	NM_001143948	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.000000	0.340708	
chunk0140_403_1	chr4	75532576	75532835	+	0	NA	Intergenic	THE1B-int|LTR|ERVL-MaLR	18261	NM_144721	152815	Hs.479971	NM_144721	ENSG00000174796	THAP6	-	THAP domain containing 6	protein-coding	0.007722	0.534615	
chunk0140_177_1	chr4	69823413	69823829	+	0	NA	Intergenic	HERV3-int|LTR|ERV1	36531	NM_005420	6783	Hs.479898	NM_005420	ENSG00000109193	SULT1E1	EST|EST-1|ST1E1|STE	sulfotransferase family 1E member 1	protein-coding	0.007212	0.462830	
chunk0095_136_1	chr2	16727271	16727770	+	0	NA	Intergenic	Intergenic	-61654	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.008016	0.420000	
chunk0070_25_1	chr15	69222174	69222394	+	0	NA	intron (NM_015554, intron 2 of 4)	L1P4e|LINE|L1	61650	NM_015554	26035	Hs.183006	NM_015554	ENSG00000138604	GLCE	HSEPI	glucuronic acid epimerase	protein-coding	0.009091	0.619910	
chunk0010_397_1	chr1	119482055	119482553	+	0	NA	Intergenic	Intergenic	-24899	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.000000	0.432866	219(GTCACACACTGTCCCT,+,0.00)
chunk0069_145_1	chr15	62440738	62441022	+	0	NA	Intergenic	Intergenic	97851	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.007042	0.421053	
chunk0054_172_1	chr13	44350752	44351126	+	0	NA	Intergenic	Intergenic	-22903	NM_001010897	387923	Hs.377972	NM_001010897	ENSG00000151778	SERP2	C13orf21|bA269C23.1	stress associated endoplasmic reticulum protein family member 2	protein-coding	0.010695	0.408000	
chunk0099_11_1	chr2	82795927	82796211	+	0	NA	Intergenic	Intergenic	-60734	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.000000	0.301754	
chunk0012_158_1	chr1	158196286	158196890	+	0	NA	Intergenic	(ATTTT)n|Simple_repeat|Simple_repeat	16641	NM_001766	912	Hs.1799	NM_001766	ENSG00000158473	CD1D	CD1A|R3|R3G1	CD1d molecule	protein-coding	0.000000	0.323967	
chunk0138_372_1	chr4	42358495	42358695	+	0	NA	Intergenic	Intergenic	-39244	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.000000	0.388060	
chunk0090_255_1	chr18	74260730	74261065	+	0	NA	intron (NM_001914, intron 3 of 5)	intron (NM_001914, intron 3 of 5)	31119	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.008955	0.345238	
chunk0058_428_1	chr13	113013148	113013347	+	0	NA	intron (NM_024979, intron 1 of 29)	intron (NM_024979, intron 1 of 29)	11533	NM_024979	23263	Hs.170422	NM_024979	ENSG00000126217	MCF2L	ARHGEF14|DBS|OST	MCF.2 cell line derived transforming sequence like	protein-coding	0.025126	0.540000	
chunk0015_304_1	chr1	188953543	188953742	+	0	NA	Intergenic	L1PA16|LINE|L1	1510014	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.550000	
chunk0171_241_1	chr6	127026535	127026860	+	0	NA	Intergenic	Intergenic	-92206	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.000000	0.276074	
chunk0186_416_1	chr7	146419849	146420048	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	303587	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.000000	0.330000	
chunk0004_21_1	chr1	42258986	42259392	+	0	NA	intron (NM_014947, intron 4 of 12)	L1ME1|LINE|L1	75776	NM_001198851	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.007389	0.346437	
chunk0147_33_1	chr4	171769666	171769865	+	0	NA	Intergenic	(TGTGTT)n|Simple_repeat|Simple_repeat	-43659	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.000000	0.320000	
chunk0016_400_1	chr1	203172741	203173037	+	0	NA	intron (NM_004997, intron 3 of 10)	intron (NM_004997, intron 3 of 10)	2925	NM_004997	4608	Hs.927	NM_004997	ENSG00000133055	MYBPH	-	myosin binding protein H	protein-coding	0.006757	0.602694	149(AGGAACACGGTGTCTC,-,0.00),150(GGAACACGGTGTCTCT,+,0.00)
chunk0191_293_1	chr8	54211996	54212475	+	0	NA	Intergenic	Intergenic	77014	NM_014175	29088	Hs.18349	NM_014175	ENSG00000137547	MRPL15	HSPC145|L15mt|MRP-L15|MRP-L7|RPML7	mitochondrial ribosomal protein L15	protein-coding	0.010438	0.422917	85(AAGAACAAAATGAGCT,-,0.00)
chunk0063_42_1	chr14	76888105	76888378	+	0	NA	Intergenic	Intergenic	61859	NM_194287	145497	Hs.147276	NM_194287	ENSG00000100565	LRRC74A	C14orf166B|LRRC74	leucine rich repeat containing 74A	protein-coding	0.021978	0.594891	232(GGGAACATCTAGTACC,-,0.00),233(GGAACATCTAGTACCT,+,0.00)
chunk0040_22_1	chr11	109738833	109739032	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	316812	NM_207645	399947	Hs.172982	NM_207645	ENSG00000185742	C11orf87	LOH11CR1A|NEURIM1	chromosome 11 open reading frame 87	protein-coding	0.005025	0.415000	
chunk0058_354_1	chr14	28949484	28949954	+	0	NA	Intergenic	L1PA10|LINE|L1	177015	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.010638	0.365180	
chunk0134_154_1	chr3	177723960	177724351	+	0	NA	intron (NR_047568, intron 3 of 3)	intron (NR_047568, intron 3 of 3)	-92710	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.012788	0.436224	
chunk0079_115_1	chr17	12404430	12404773	+	0	NA	Intergenic	MIR3|SINE|MIR	-145367	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.005831	0.444767	
chunk0059_70_1	chr14	30429946	30430244	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-129028	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.010067	0.434783	126(AAGAGCACAGTGTTCC,-,0.00),127(AGAGCACAGTGTTCCA,+,0.00)
chunk0138_234_1	chr4	39343287	39343911	+	0	NA	intron (NM_002913, intron 3 of 24)	intron (NM_002913, intron 3 of 24)	22782	NM_001204747	5981	Hs.507475	NM_002913	ENSG00000035928	RFC1	A1|CANVAS|MHCBFB|PO-GA|RECC1|RFC|RFC140	replication factor C subunit 1	protein-coding	0.011218	0.414400	
chunk0015_441_1	chr1	191928064	191928593	+	0	NA	Intergenic	L1MA1|LINE|L1	-230134	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.007561	0.471698	
chunk0057_93_1	chr13	98822233	98822740	+	0	NA	intron (NM_001130048, intron 46 of 55)	intron (NM_001130048, intron 46 of 55)	-9598	NR_046663	100874096	Hs.578066	NR_046663	ENSG00000229918	DOCK9-AS1	-	DOCK9 antisense RNA 1	ncRNA	0.005917	0.419291	
chunk0086_22_1	chr18	12336797	12337438	+	0	NA	intron (NM_006796, intron 16 of 16)	intron (NM_006796, intron 16 of 16)	29058	NM_001303526	84617	Hs.193491	NM_032525	ENSG00000176014	TUBB6	FPVEPD|HsT1601|TUBB-5	tubulin beta 6 class V	protein-coding	0.014041	0.419003	
chunk0027_408_1	chr10	80467723	80468464	+	0	NA	intron (NM_030927, intron 1 of 8)	intron (NM_030927, intron 1 of 8)	13811	NM_001128309	81619	Hs.308615	NM_030927	ENSG00000108219	TSPAN14	DC-TM4F2|TM4SF14|tspan-14	tetraspanin 14	protein-coding	0.012146	0.478437	363(GGAGACAAAATGTTCT,-,0.00),364(GAGACAAAATGTTCTT,+,0.00)
chunk0171_359_1	chr6	130630242	130630823	+	0	NA	Intergenic	Intergenic	193415	NM_052913	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.005164	0.309278	325(AAGAACACATTGTTCT,-,0.00),326(AGAACACATTGTTCTA,+,0.00)
chunk0055_123_1	chr13	57457563	57457820	+	0	NA	Intergenic	L1MEg2|LINE|L1	-173964	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.003891	0.391473	
chunk0120_439_1	chr3	13632874	13633393	+	0	NA	intron (NM_001165035, intron 16 of 17)	intron (NM_001165035, intron 16 of 17)	14752	NR_132775	106635526		NR_132775		SNORA93	-	small nucleolar RNA, H/ACA box 93	snoRNA	0.021195	0.575000	202(GAGGACAGACTCTCCC,-,0.00),203(AGGACAGACTCTCCCT,+,0.00)
chunk0195_190_1	chr8	96656591	96656790	+	0	NA	intron (NM_016134, intron 1 of 7)	L1M3b|LINE|L1	11463	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.020101	0.510000	
chunk0053_45_1	chr13	27495553	27495971	+	0	NA	Intergenic	L1ME2|LINE|L1	-45160	NM_152912	219402	Hs.534582	NM_152912	ENSG00000122033	MTIF3	IF3mt	mitochondrial translational initiation factor 3	protein-coding	0.007177	0.393795	
chunk0124_85_1	chr3	53347347	53347926	+	0	NA	promoter-TSS (NM_018403)	promoter-TSS (NM_018403)	-9	NM_018403	55802	Hs.476353	NM_018403	ENSG00000272886	DCP1A	HSA275986|Nbla00360|SMAD4IP1|SMIF	decapping mRNA 1A	protein-coding	0.084629	0.662069	
chunk0127_56_1	chr3	89184265	89184595	+	0	NA	intron (NM_005233, intron 2 of 16)	intron (NM_005233, intron 2 of 16)	76906	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.006061	0.365559	
chunk0163_216_1	chr6	12102725	12103157	+	0	NA	intron (NM_002114, intron 3 of 8)	intron (NM_002114, intron 3 of 8)	90450	NM_002114	3096	Hs.567284	NM_002114	ENSG00000095951	HIVEP1	CIRIP|CRYBP1|GAAP|MBP-1|PRDII-BF1|Schnurri-1|ZAS1|ZNF40|ZNF40A	human immunodeficiency virus type I enhancer binding protein 1	protein-coding	0.004630	0.272517	
chunk0208_202_1	chrX	17735193	17735724	+	0	NA	3' UTR (NM_198270, exon 8 of 8)	3' UTR (NM_198270, exon 8 of 8)	-1991	NM_006746	6322	Hs.109655	NM_006746	ENSG00000047634	SCML1	-	Scm polycomb group protein like 1	protein-coding	0.015066	0.370301	
chunk0061_250_1	chr14	61252486	61252737	+	0	NA	Intergenic	L1P3|LINE|L1	29201	NM_001017970	161291	Hs.146180	NM_001017970	ENSG00000182107	TMEM30B	CDC50B	transmembrane protein 30B	protein-coding	0.003984	0.424603	
chunk0152_22_1	chr5	56489322	56489531	+	0	NA	Intergenic	MIRb|SINE|MIR	-7657	NR_104664	102467147	Hs.650177	NR_104664	ENSG00000248727	LINC01948	-	long intergenic non-protein coding RNA 1948	ncRNA	0.014354	0.400000	
chunk0166_146_1	chr6	45038509	45038732	+	0	NA	intron (NM_181356, intron 5 of 12)	intron (NM_181356, intron 5 of 12)	159150	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.004484	0.294643	
chunk0041_312_1	chr11	130025298	130025913	+	0	NA	Intergenic	Intergenic	-22770	NM_020228	56980	Hs.275086	NM_020228	ENSG00000170325	PRDM10	PFM7|TRIS	PR/SET domain 10	protein-coding	0.003252	0.402597	385(GAGAACTGAGTGTCTT,-,0.00),386(AGAACTGAGTGTCTTC,+,0.00)
chunk0193_37_1	chr8	71355386	71355742	+	0	NA	intron (NM_001288574, intron 2 of 17)	intron (NM_001288574, intron 2 of 17)	947	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.005618	0.386555	
chunk0052_403_1	chr12	130898443	130898642	+	0	NA	Intergenic	L1ME4b|LINE|L1	26548	NM_001300796	5901	Hs.10842	NM_006325	ENSG00000132341	RAN	ARA24|Gsp1|TC4	RAN, member RAS oncogene family	protein-coding	0.020101	0.460000	
chunk0052_177_1	chr13	24202111	24202749	+	0	NA	intron (NM_153023, intron 1 of 11)	intron (NM_153023, intron 1 of 11)	40014	NR_031753	100313842		NR_031753	ENSG00000252695	MIR2276	-	microRNA 2276	ncRNA	0.015674	0.395931	
chunk0114_43_1	chr21	8434058	8434308	+	0	NA	non-coding (NR_046235, exon 1 of 1)	non-coding (NR_046235, exon 1 of 1)	961	NR_046235	100861532		NR_046235		RNA45SN5	RNA45S5	RNA, 45S pre-ribosomal N5	rRNA	0.152000	0.745020	
chunk0089_415_1	chr18	68775232	68775516	+	0	NA	intron (NM_001093729, intron 3 of 9)	intron (NM_001093729, intron 3 of 9)	-22706	NM_024781	79839	Hs.280781	NM_024781	ENSG00000150636	CCDC102B	ACY1L|AN|C18orf14|HsT1731	coiled-coil domain containing 102B	protein-coding	0.000000	0.245614	
chunk0052_166_1	chr13	24076179	24076602	+	0	NA	intron (NM_001286792, intron 3 of 14)	intron (NM_001286792, intron 3 of 14)	-84326	NM_001166271	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.014184	0.443396	
chunk0186_166_1	chr7	139308278	139308493	+	0	NA	TTS (NM_173569)	TTS (NM_173569)	-31974	NM_001244585	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.000000	0.416667	
chunk0006_4_1	chr1	63787861	63788463	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	14143	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.004983	0.417910	
chunk0186_177_1	chr7	139434614	139434815	+	0	NA	Intergenic	Intergenic	-7188	NR_033999	100129148	Hs.744449	NR_033999		LOC100129148	-	uncharacterized LOC100129148	ncRNA	0.049751	0.485149	64(CAGCACGCTGTGTTCT,-,0.00),65(AGCACGCTGTGTTCTT,+,0.00)
chunk0186_403_1	chr7	144775084	144775337	+	0	NA	intron (NM_001042482, intron 2 of 7)	intron (NM_001042482, intron 2 of 7)	60843	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.015810	0.452756	
chunk0035_217_1	chr11	44979950	44980188	+	0	NA	Intergenic	MIRb|SINE|MIR	6167	NR_026681	221122	Hs.551656	NR_026681	ENSG00000254654	LINC02685	-	long intergenic non-protein coding RNA 2685	ncRNA	0.025210	0.556485	
chunk0002_179_1	chr1	19066155	19066802	+	0	NA	Intergenic	MER53|DNA|hAT	-110146	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.021638	0.555556	
chunk0006_293_1	chr1	71060939	71061381	+	0	NA	intron (NR_038420, intron 2 of 2)	intron (NR_038420, intron 2 of 2)	6556	NR_029707	406962		NR_029707	ENSG00000207721	MIR186	MIRN186|miR-186	microRNA 186	ncRNA	0.004525	0.340858	
chunk0176_116_1	chr7	12000874	12001502	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	-168990	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.001592	0.305246	
chunk0142_167_1	chr4	95319074	95319328	+	0	NA	intron (NM_003728, intron 2 of 15)	MER5B|DNA|hAT-Charlie	227710	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.000000	0.439216	
chunk0142_176_1	chr4	95628233	95628802	+	0	NA	Intergenic	Intergenic	-79307	NM_003728	8633	Hs.388565	NM_003728	ENSG00000182168	UNC5C	UNC5H3	unc-5 netrin receptor C	protein-coding	0.001757	0.429825	
chunk0058_282_1	chr14	26444839	26445038	+	0	NA	TTS (NM_006489)	TTS (NM_006489)	152816	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.005025	0.360000	146(CAGCACACTGTGTCTC,-,0.00),147(AGCACACTGTGTCTCA,+,0.00)
chunk0001_326_1	chr1	9482655	9483529	+	0	NA	Intergenic	Intergenic	-54096	NR_104622	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.025172	0.573714	
chunk0169_92_1	chr6	99979813	99980381	+	0	NA	intron (NM_032503, intron 1 of 5)	intron (NM_032503, intron 1 of 5)	-13941	NR_038384	728012	Hs.434366	NR_038384	ENSG00000229315	MCHR2-AS1	-	MCHR2 antisense RNA 1	ncRNA	0.003521	0.365554	
chunk0012_396_1	chr1	163648278	163648787	+	0	NA	Intergenic	L2a|LINE|L2	-225341	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.007859	0.403922	
chunk0203_67_1	chr9	83555543	83555756	+	0	NA	Intergenic	L1PA14|LINE|L1	-17216	NM_174938	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.000000	0.518692	
chunk0204_210_1	chr9	96874982	96875744	+	0	NA	Intergenic	MIRb|SINE|MIR	6463	NR_038890	100132781	Hs.710921	NR_038890		LOC100132781	-	cyclin Y like 1 pseudogene	pseudo	0.041995	0.513761	292(AAGAACAAAGTGTCTT,-,0.00),293(AGAACAAAGTGTCTTC,+,0.00)
chunk0115_171_1	chr21	25406737	25406937	+	0	NA	intron (NR_024027, intron 4 of 4)	L1M1|LINE|L1	24864	NR_024027	54072	Hs.234016	NM_058184	ENSG00000185433	LINC00158	C21orf42|NCRNA00158	long intergenic non-protein coding RNA 158	ncRNA	0.005000	0.542289	
chunk0036_253_1	chr11	64779122	64779344	+	0	NA	promoter-TSS (NM_004630)	promoter-TSS (NM_004630)	-389	NM_201995	7536	Hs.502829	NM_004630	ENSG00000168066	SF1	BBP|D11S636|MBBP|ZCCHC25|ZFM1|ZNF162	splicing factor 1	protein-coding	0.054054	0.443946	
chunk0123_128_1	chr3	42571650	42571855	+	0	NA	intron (NM_001201572, intron 1 of 6)	L1MD2|LINE|L1	10276	NM_004206	9117	Hs.445892	NM_004206	ENSG00000093183	SEC22C	SEC22L3	SEC22 homolog C, vesicle trafficking protein	protein-coding	0.004878	0.368932	33(TGAGACAGCCTGTACT,-,0.00),34(GAGACAGCCTGTACTC,+,0.00)
chunk0081_271_1	chr17	43771986	43773205	+	0	NA	intron (NM_004090, intron 2 of 2)	intron (NM_004090, intron 2 of 2)	6405	NM_004090	1845	Hs.181046	NM_004090	ENSG00000108861	DUSP3	VHR	dual specificity phosphatase 3	protein-coding	0.008203	0.492623	
chunk0011_33_1	chr1	143225352	143225663	+	0	NA	Intergenic	Intergenic	197085	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.032154	0.355769	
chunk0102_449_1	chr2	158231411	158232057	+	0	NA	intron (NM_001301684, intron 8 of 11)	intron (NM_001301684, intron 8 of 11)	65084	NR_038850	554201	Hs.570262	NR_038850	ENSG00000227480	CCDC148-AS1	-	CCDC148 antisense RNA 1	ncRNA	0.001548	0.389490	
chunk0162_83_1	chr6	1894866	1895252	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	280932	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.012953	0.423773	177(CAGCACACTCTGAACC,-,0.00),178(AGCACACTCTGAACCT,+,0.00)
chunk0086_447_1	chr18	29707494	29707954	+	0	NA	Intergenic	L1PB3|LINE|L1	-591186	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.002174	0.342733	
chunk0152_447_1	chr5	66363101	66363684	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	148212	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.008576	0.375000	
chunk0004_383_1	chr1	51839386	51839921	+	0	NA	intron (NM_002525, intron 2 of 32)	intron (NM_002525, intron 2 of 32)	-3251	NR_031580	100313892		NR_031580	ENSG00000283899	MIR761	hsa-mir-761	microRNA 761	ncRNA	0.005607	0.361940	
chunk0050_417_1	chr12	109864229	109864845	+	0	NA	intron (NM_016433, intron 1 of 4)	intron (NM_016433, intron 1 of 4)	15951	NM_016433	51228	Hs.381256	NM_016433	ENSG00000139433	GLTP	-	glycolipid transfer protein	protein-coding	0.006494	0.476499	
chunk0079_32_1	chr17	10119714	10120032	+	0	NA	intron (NM_201433, intron 1 of 13)	intron (NM_201433, intron 1 of 13)	78678	NM_201433	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.015723	0.551724	
chunk0127_374_1	chr3	101925402	101926016	+	0	NA	Intergenic	HAL1|LINE|L1	-15150	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003257	0.373984	
chunk0210_44_1	chrX	68363969	68364316	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	69315	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.005764	0.379310	169(AAGAACAGCCTGTCTT,-,0.00),170(AGAACAGCCTGTCTTG,+,0.00)
chunk0141_99_1	chr4	79173227	79173686	+	0	NA	intron (NR_038342, intron 3 of 5)	L2a|LINE|L2	152561	NM_032693	84779	Hs.676048	NM_032693	ENSG00000156269	NAA11	ARD1B|ARD2|hARD2	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding	0.006536	0.358696	
chunk0118_173_1	chr22	30767245	30767536	+	0	NA	intron (NM_001282740, intron 1 of 12)	L1MC5|LINE|L1	3137	NM_001282740	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.006873	0.438356	
chunk0054_264_1	chr13	46555479	46556115	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	2636	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.006289	0.348509	
chunk0114_31_1	chr21	8208950	8209149	+	0	NA	promoter-TSS (NR_003286).7	promoter-TSS (NR_003286).7	205	NR_128714									0.180905	0.870000	
chunk0071_278_1	chr15	85727137	85727598	+	0	NA	intron (NM_007200, intron 28 of 36)	intron (NM_007200, intron 28 of 36)	31358	NR_120366	101929679	Hs.513112	NR_120366		LOC101929679	-	uncharacterized LOC101929679	ncRNA	0.008677	0.469697	
chunk0105_204_1	chr2	187847261	187847488	+	0	NA	Intergenic	L2|LINE|L2	-292882	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.385965	134(AGGTACTGAATGTTCT,-,0.00),135(GGTACTGAATGTTCTT,+,0.00)
chunk0041_432_1	chr11	134406727	134407142	+	0	NA	intron (NM_054025, intron 1 of 5)	intron (NM_054025, intron 1 of 5)	4984	NM_054025	27087	Hs.381050	NM_018644	ENSG00000109956	B3GAT1	CD57|GLCATP|GLCUATP|HNK1|LEU7|NK-1|NK1	beta-1,3-glucuronyltransferase 1	protein-coding	0.019277	0.545673	
chunk0101_85_1	chr2	124083761	124084136	+	0	NA	intron (NM_130773, intron 1 of 23)	L1MD1|LINE|L1	58661	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.002667	0.284574	
chunk0014_94_1	chr1	176652668	176652867	+	0	NA	intron (NM_020318, intron 3 of 22)	L1M3f|LINE|L1	189596	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.480000	51(ATGGACAGTTAGTTCT,-,0.00),52(TGGACAGTTAGTTCTC,+,0.00)
chunk0105_459_1	chr2	195276575	195277082	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-379980	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.005917	0.342520	
chunk0025_7_1	chr10	47190311	47190695	+	0	NA	Intergenic	L1ME4c|LINE|L1	-109721	NM_004962	2662	Hs.2171	NM_004962	ENSG00000266524	GDF10	BIP|BMP-3b|BMP3B	growth differentiation factor 10	protein-coding	0.013021	0.368831	
chunk0147_16_1	chr4	170721169	170721611	+	0	NA	Intergenic	L1PA15|LINE|L1	-319212	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.006787	0.325056	
chunk0152_390_1	chr5	64665285	64665691	+	0	NA	Intergenic	Intergenic	-24820	NM_001164442	100132916	Hs.591776	NM_001164442	ENSG00000145642	SHISAL2B	FAM159B	shisa like 2B	protein-coding	0.007389	0.324324	
chunk0122_210_1	chr3	33236091	33236555	+	0	NA	Intergenic	Intergenic	-17108	NM_015551	26032	Hs.196647	NM_015551	ENSG00000173705	SUSD5	-	sushi domain containing 5	protein-coding	0.002155	0.361290	
chunk0048_393_1	chr12	87712720	87713179	+	0	NA	Intergenic	L1MC3|LINE|L1	71762	NR_033410	400058	Hs.572212	NR_033410		MKRN9P	MKRN5|MKRN9|MKRNP6|RNF65|ZNF127L3	makorin ring finger protein 9, pseudogene	pseudo	0.004357	0.321739	
chunk0081_69_1	chr17	39036058	39036299	+	0	NA	intron (NR_033753, intron 2 of 4)	intron (NR_033753, intron 2 of 4)	6272	NR_033753	342666	Hs.129645	NM_198502	ENSG00000214553	LRRC37A11P	LRRC37F	leucine rich repeat containing 37 member A11, pseudogene	pseudo	0.004149	0.454545	
chunk0069_237_1	chr15	64050497	64050966	+	0	NA	Intergenic	Intergenic	-4409	NM_014326	23604	Hs.237886	NM_014326	ENSG00000035664	DAPK2	DRP-1|DRP1	death associated protein kinase 2	protein-coding	0.006397	0.546809	
chunk0020_240_1	chr1	235826034	235826548	+	0	NA	TTS (NR_102436)	TTS (NR_102436)	26769	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.000000	0.328155	
chunk0092_323_1	chr19	34678301	34678825	+	0	NA	intron (NM_018675, intron 1 of 4)	intron (NM_018675, intron 1 of 4)	924	NM_001289188	55900	Hs.436350	NM_018443	ENSG00000089335	ZNF302	HSD16|MST154|MSTP154|ZNF135L|ZNF140L|ZNF327	zinc finger protein 302	protein-coding	0.034351	0.468571	292(AGAAACACCCTGTTCC,-,0.00),293(GAAACACCCTGTTCCT,+,0.00)
chunk0150_299_1	chr5	37549323	37549809	+	0	NA	intron (NM_018034, intron 9 of 17)	L1MA2|LINE|L1	170256	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.000000	0.316222	
chunk0211_160_1	chrX	114563995	114564284	+	0	NA	Intergenic	L1PA13|LINE|L1	-19939	NM_001256760	3358	Hs.149037	NM_000868	ENSG00000147246	HTR2C	5-HT1C|5-HT2C|5-HTR2C|5HTR2C|HTR1C	5-hydroxytryptamine receptor 2C	protein-coding	0.003460	0.396552	
chunk0019_452_1	chr1	231349805	231350259	+	0	NA	intron (NM_001010984, intron 3 of 3)	intron (NM_001010984, intron 3 of 3)	12096	NM_001010984	83932	Hs.554892	NM_032018	ENSG00000010072	SPRTN	C1orf124|DVC1|PRO4323|spartan	SprT-like N-terminal domain	protein-coding	0.019824	0.426374	
chunk0127_232_1	chr3	96794969	96795260	+	0	NA	Intergenic	L1MA4A|LINE|L1	-19467	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.010309	0.534247	
chunk0157_44_1	chr5	115947391	115947776	+	0	NA	Intergenic	Intergenic	-14871	NM_173800	206338	Hs.98288	NM_173800	ENSG00000172901	LVRN	APQ|AQPEP|TAQPEP	laeverin	protein-coding	0.005195	0.321244	
chunk0047_226_1	chr12	71786593	71787455	+	0	NA	3' UTR (NM_014999, exon 7 of 7)	3' UTR (NM_014999, exon 7 of 7)	32146	NM_014999	23011	Hs.524590	NM_014999	ENSG00000080371	RAB21	-	RAB21, member RAS oncogene family	protein-coding	0.004640	0.332561	515(GAACACAGAATGTTCT,-,0.00),516(AACACAGAATGTTCTG,+,0.00)
chunk0136_14_1	chr4	68128	68416	+	0	NA	intron (NM_182524, intron 3 of 3)	intron (NM_182524, intron 3 of 3)	14987	NM_001286053	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.027778	0.498270	
chunk0067_78_1	chr15	41476417	41476834	+	0	NA	intron (NM_015138, intron 12 of 17)	intron (NM_015138, intron 12 of 17)	-17233	NM_002220	3706	Hs.2722	NM_002220	ENSG00000137825	ITPKA	IP3-3KA|IP3KA	inositol-trisphosphate 3-kinase A	protein-coding	0.011990	0.440191	229(CAACACAGTGTGTTCT,-,0.00),230(AACACAGTGTGTTCTT,+,0.00)
chunk0120_319_1	chr3	10320175	10320411	+	0	NA	intron (NM_001136026, intron 1 of 9)	intron (NM_001136026, intron 1 of 9)	748	NM_001136232	6396	Hs.166924	NM_030673	ENSG00000157020	SEC13	D3S1231E|SEC13L1|SEC13R|npp-20	SEC13 homolog, nuclear pore and COPII coat complex component	protein-coding	0.000000	0.451477	59(AAGAACACAGTGTTCT,-,0.00),60(AGAACACAGTGTTCTG,+,0.00)
chunk0203_291_1	chr9	88968129	88968360	+	0	NA	Intergenic	Intergenic	-22619	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.008658	0.435345	
chunk0133_21_1	chr3	165723571	165723980	+	0	NA	Intergenic	Intergenic	113690	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.004890	0.334146	
chunk0043_305_1	chr12	22161021	22161447	+	0	NA	Intergenic	Charlie8|DNA|hAT-Charlie	115058	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.004695	0.351288	
chunk0095_366_1	chr2	23376119	23376353	+	0	NA	Intergenic	L2c|LINE|L2	-9191	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.012821	0.446809	
chunk0016_184_1	chr1	198208057	198208500	+	0	NA	intron (NM_133494, intron 1 of 9)	L1MEg|LINE|L1	51300	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.004515	0.382883	
chunk0164_102_1	chr6	20487702	20488465	+	0	NA	intron (NM_001243076, intron 5 of 6)	intron (NM_001243076, intron 5 of 6)	-46374	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.010485	0.397906	
chunk0003_154_1	chr1	33153281	33153525	+	0	NA	intron (NM_018207, intron 4 of 4)	MER20|DNA|hAT-Charlie	28667	NM_018207	55223	Hs.656006	NM_018207	ENSG00000116525	TRIM62	DEAR1	tripartite motif containing 62	protein-coding	0.000000	0.546939	55(GAGCACAGTCTGTTCC,-,0.00),56(AGCACAGTCTGTTCCT,+,0.00)
chunk0100_297_1	chr2	115084387	115084996	+	0	NA	intron (NM_001178037, intron 1 of 25)	intron (NM_001178037, intron 1 of 25)	20021	NM_001178037	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.009852	0.442623	
chunk0020_322_1	chr1	237756553	237757063	+	0	NA	intron (NM_001035, intron 81 of 104)	MER58B|DNA|hAT-Charlie	-105367	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.005882	0.336595	
chunk0183_199_1	chr7	106346448	106346767	+	0	NA	Intergenic	Charlie6|DNA|hAT-Charlie	-61415	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.003135	0.356250	
chunk0029_384_1	chr10	109539753	109540147	+	0	NA	Intergenic	L1PA7|LINE|L1	383603	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.002538	0.356962	
chunk0202_85_1	chr9	71929150	71929528	+	0	NA	intron (NM_182505, intron 1 of 3)	intron (NM_182505, intron 1 of 3)	17832	NM_182505	138241	Hs.534190	NM_182505	ENSG00000155621	C9orf85	-	chromosome 9 open reading frame 85	protein-coding	0.007937	0.345646	
chunk0160_106_1	chr5	150670544	150670858	+	0	NA	intron (NM_133371, intron 3 of 6)	MIR1_Amn|SINE|MIR	9860	NM_001122853	91977	Hs.91626	NM_133371	ENSG00000164591	MYOZ3	CS-3|CS3|FATZ-3|FRP3	myozenin 3	protein-coding	0.022293	0.504762	
chunk0016_55_1	chr1	193292654	193293038	+	0	NA	Intergenic	L2c|LINE|L2	-11899	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.002604	0.358442	
chunk0157_227_1	chr5	119441703	119442179	+	0	NA	Intergenic	L1PA6|LINE|L1	-10502	NM_001292027	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.002101	0.364780	197(CTGAACAACTTGTTCC,-,0.00),198(TGAACAACTTGTTCCT,+,0.00),281(AAAGACACAATGTACC,-,0.00)
chunk0024_326_1	chr10	43169980	43170301	+	0	NA	intron (NM_018590, intron 6 of 7)	intron (NM_018590, intron 6 of 7)	31695	NM_018590	55454	Hs.657569	NM_018590	ENSG00000169826	CSGALNACT2	CHGN2|ChGn-2|GALNACT-2|GALNACT2|PRO0082|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 2	protein-coding	0.006231	0.350932	
chunk0003_58_1	chr1	30970021	30970288	+	0	NA	intron (NM_001020658, intron 10 of 21)	intron (NM_001020658, intron 10 of 21)	-1917	NR_003066	692200		NR_003066		SNORD103C	HBII-251|SNORD85	small nucleolar RNA, C/D box 103C	snoRNA	0.000000	0.320896	
chunk0125_278_1	chr3	69434019	69434218	+	0	NA	Intergenic	Intergenic	-47814	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.020101	0.435000	
chunk0144_332_1	chr4	139098991	139099723	+	0	NA	intron (NM_201999, intron 3 of 8)	L2b|LINE|L2	-14943	NM_001276459	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.006831	0.386085	
chunk0050_337_1	chr12	107486146	107486467	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	-94551	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.000000	0.403727	
chunk0107_229_1	chr2	217047092	217047535	+	0	NA	Intergenic	L2a|LINE|L2	176541	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.009029	0.425676	
chunk0096_23_1	chr2	26350805	26351134	+	0	NA	intron (NM_033505, intron 1 of 9)	MER47B|DNA|TcMar-Tigger	-4152	NM_153835	165082	Hs.631878	NM_153835	ENSG00000173567	ADGRF3	GPR113|PGR23	adhesion G protein-coupled receptor F3	protein-coding	0.012158	0.372727	
chunk0063_135_1	chr14	79426197	79426914	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	147216	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.006974	0.413649	
chunk0207_145_1	chr9	129485796	129486164	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-2680	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.008152	0.474255	
chunk0058_121_1	chr14	22280041	22280455	+	0	NA	Intergenic	Intergenic	308989	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.000000	0.354217	263(CAACACAGAATGTTCC,-,0.00),264(AACACAGAATGTTCCC,+,0.00)
chunk0171_7_1	chr6	119584237	119584541	+	0	NA	Intergenic	Intergenic	-93087	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.000000	0.298361	
chunk0178_140_1	chr7	32881387	32881973	+	0	NA	intron (NM_015483, intron 1 of 3)	intron (NM_015483, intron 1 of 3)	10176	NM_015483	25948	Hs.372541	NM_015483	ENSG00000170852	KBTBD2	BKLHD1	kelch repeat and BTB domain containing 2	protein-coding	0.001706	0.361158	278(CAGAACAGCATGTCAC,-,0.00)
chunk0134_321_1	chr3	181823801	181824009	+	0	NA	Intergenic	Intergenic	111981	NM_003106	6657	Hs.518438	NM_003106	ENSG00000181449	SOX2	ANOP3|MCOPS3	SRY-box transcription factor 2	protein-coding	0.004808	0.430622	
chunk0130_257_1	chr3	135930956	135931485	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-34453	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.013233	0.364151	
chunk0082_413_1	chr17	61106240	61106720	+	0	NA	intron (NM_017679, intron 22 of 23)	Tigger3a|DNA|TcMar-Tigger	293126	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.010417	0.380457	
chunk0012_451_1	chr1	165106425	165106649	+	0	NA	Intergenic	L1PA6|LINE|L1	249704	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.008929	0.351111	
chunk0128_98_1	chr3	105930792	105931082	+	0	NA	Intergenic	Intergenic	-61894	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.010345	0.415808	
chunk0059_405_1	chr14	37658224	37658739	+	0	NA	intron (NM_001310135, intron 3 of 32)	intron (NM_001310135, intron 3 of 32)	63282	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.000000	0.406977	
chunk0210_227_1	chrX	82385168	82385863	+	0	NA	Intergenic	Intergenic	-1122746	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.001439	0.323276	
chunk0072_106_1	chr15	91261252	91261730	+	0	NA	intron (NM_001167580, intron 5 of 11)	L1ME4c|LINE|L1	161182	NM_014848	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.000000	0.334029	
chunk0180_443_1	chr7	77327033	77327302	+	0	NA	intron (NM_017439, intron 22 of 30)	intron (NM_017439, intron 22 of 30)	-88031	NR_110073	101927243	Hs.547753	NR_110073		LOC101927243	-	uncharacterized LOC101927243	ncRNA	0.022305	0.459259	
chunk0144_274_1	chr4	137601824	137602264	+	0	NA	Intergenic	Intergenic	-69546	NM_001300828	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.004545	0.349206	
chunk0021_383_1	chr1	246503258	246503793	+	0	NA	intron (NM_001167740, intron 1 of 11)	intron (NM_001167740, intron 1 of 11)	3817	NM_001167740	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.013084	0.432836	
chunk0126_3_1	chr3	73298528	73299013	+	0	NA	Intergenic	Intergenic	135226	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.012371	0.388889	
chunk0113_221_1	chr20	53866197	53866672	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	9275	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.008421	0.401261	
chunk0137_113_1	chr4	13964985	13965240	+	0	NA	Intergenic	Intergenic	-146856	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.007843	0.453125	
chunk0168_110_1	chr6	80531582	80531951	+	0	NA	Intergenic	Intergenic	425139	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.005420	0.305405	
chunk0002_230_1	chr1	20140286	20140617	+	0	NA	intron (NM_022819, intron 2 of 4)	intron (NM_022819, intron 2 of 4)	1121	NM_022819	64600	Hs.302034	NM_022819	ENSG00000158786	PLA2G2F	GIIFsPLA2|sPLA2-IIF	phospholipase A2 group IIF	protein-coding	0.006042	0.518072	
chunk0119_1_1	chr22	39941777	39941976	+	0	NA	intron (NM_001291828, intron 1 of 4)	intron (NM_001291828, intron 1 of 4)	-4941	NM_001291825	9402	Hs.517499	NM_004810	ENSG00000100351	GRAP2	GADS|GRAP-2|GRB2L|GRBLG|GRID|GRPL|GrbX|Grf40|Mona|P38	GRB2 related adaptor protein 2	protein-coding	0.000000	0.435000	
chunk0045_456_1	chr12	53775426	53775907	+	0	NA	Intergenic	Intergenic	-18632	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.010395	0.427386	212(GAGCACTTTGTGTCCA,-,0.00),213(AGCACTTTGTGTCCAC,+,0.00),392(ATGAACACAATGACCT,-,0.00),393(TGAACACAATGACCTT,+,0.00)
chunk0076_235_1	chr16	68940933	68941476	+	0	NA	intron (NM_024562, intron 14 of 17)	MER101-int|LTR|ERV1	97598	NM_024562	79613	Hs.13526	NM_024562	ENSG00000103047	TANGO6	TMCO7	transport and golgi organization 6 homolog	protein-coding	0.001842	0.284926	
chunk0057_17_1	chr13	95559892	95560736	+	0	NA	intron (NM_006984, intron 2 of 4)	intron (NM_006984, intron 2 of 4)	7621	NM_006984	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.013033	0.381065	
chunk0181_248_1	chr7	85426510	85426772	+	0	NA	Intergenic	L1MA2|LINE|L1	-304710	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.003817	0.456274	
chunk0101_23_1	chr2	121626818	121627785	+	0	NA	intron (NM_015282, intron 1 of 38)	intron (NM_015282, intron 1 of 38)	22175	NM_001142274	23332	Hs.469840	NM_015282	ENSG00000074054	CLASP1	MAST1	cytoplasmic linker associated protein 1	protein-coding	0.007239	0.400826	410(AAGAACTCCCTGTACA,-,0.00),411(AGAACTCCCTGTACAT,+,0.00),551(GAGTACTTAATGTACC,-,0.00)
chunk0017_99_1	chr1	205827664	205827994	+	0	NA	TTS (NM_152491)	TTS (NM_152491)	-14633	NM_173854	254428	Hs.20274	NM_173854	ENSG00000133065	SLC41A1	MgtE	solute carrier family 41 member 1	protein-coding	0.003030	0.598187	
chunk0206_323_1	chr9	125296870	125297415	+	0	NA	intron (NM_001282679, intron 3 of 27)	intron (NM_001282679, intron 3 of 27)	-1748	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.005505	0.410256	
chunk0165_24_1	chr6	29602590	29602900	+	0	NA	3' UTR (NM_021903, exon 18 of 18)	3' UTR (NM_021903, exon 18 of 18)	14839	NM_007160	7932	Hs.529493	NM_007160	ENSG00000204657	OR2H2	FAT11|OLFR2|OLFR42B|OR2H3|dJ271M21.2|hs6M1-12	olfactory receptor family 2 subfamily H member 2	protein-coding	0.019355	0.469453	
chunk0117_432_1	chr21	46188470	46189276	+	0	NA	TTS (NM_001145437)	TTS (NM_001145437)	-4414	NM_032261	84221	Hs.381214	NM_032261	ENSG00000160284	SPATC1L	C21orf56	spermatogenesis and centriole associated 1 like	protein-coding	0.018610	0.464684	
chunk0114_125_1	chr21	9735481	9735680	+	0	NA	Intergenic	LTR12C|LTR|ERV1	85481	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.030151	0.675000	
chunk0029_252_1	chr10	102821644	102821867	+	0	NA	Intergenic	Intergenic	15778	NM_000102	1586	Hs.438016	NM_000102	ENSG00000148795	CYP17A1	CPT7|CYP17|P450C17|S17AH	cytochrome P450 family 17 subfamily A member 1	protein-coding	0.013453	0.455357	
chunk0195_215_1	chr8	97025756	97026393	+	0	NA	intron (NM_016134, intron 5 of 7)	intron (NM_016134, intron 5 of 7)	251874	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.003140	0.358934	
chunk0148_55_1	chr5	1772535	1772967	+	0	NA	Intergenic	Intergenic	27091	NM_032479	64979	Hs.719465	NM_032479	ENSG00000171421	MRPL36	BRIP1|L36mt|MRP-L36|PRPL36|RPMJ	mitochondrial ribosomal protein L36	protein-coding	0.011574	0.473441	
chunk0194_200_1	chr8	85562647	85562891	+	0	NA	Intergenic	Intergenic	92907	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.016393	0.493878	
chunk0011_16_1	chr1	143186886	143187131	+	0	NA	Intergenic	Intergenic	235584	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.061224	0.382114	
chunk0121_194_1	chr3	20751253	20751839	+	0	NA	Intergenic	Intergenic	409078	NR_110814	101927829	Hs.639381	NR_110814	ENSG00000231304	LOC101927829	-	uncharacterized LOC101927829	ncRNA	0.006826	0.356048	
chunk0160_113_1	chr5	150826772	150827071	+	0	NA	Intergenic	L1MA8|LINE|L1	-19602	NM_001145805	345611	Hs.519680	NM_001145805	ENSG00000237693	IRGM	IFI1|IRGM1|LRG-47|LRG47	immunity related GTPase M	protein-coding	0.006689	0.346667	
chunk0146_443_1	chr4	169823746	169823967	+	0	NA	Intergenic	Intergenic	-65914	NM_017867	54969	Hs.406756	NM_017867	ENSG00000056050	HPF1	C4orf27	histone PARylation factor 1	protein-coding	0.018100	0.486486	
chunk0062_143_1	chr14	69053291	69053621	+	0	NA	3' UTR (NM_001284207, exon 9 of 9)	3' UTR (NM_001284207, exon 9 of 9)	73774	NR_073422	161159	Hs.603341	NR_073422	ENSG00000259062	ACTN1-AS1	C14orf84	ACTN1 antisense RNA 1	ncRNA	0.030303	0.468278	
chunk0085_126_1	chr18	3057090	3057622	+	0	NA	Intergenic	Intergenic	-45409	NM_014646	9663	Hs.132342	NM_014646	ENSG00000101577	LPIN2	-	lipin 2	protein-coding	0.011278	0.487805	
chunk0109_100_1	chr20	2300416	2300691	+	0	NA	intron (NM_003245, intron 1 of 12)	intron (NM_003245, intron 1 of 12)	4586	NM_003245	7053	Hs.2022	NM_003245	ENSG00000125780	TGM3	TGE|UHS2	transglutaminase 3	protein-coding	0.003636	0.518116	
chunk0068_151_1	chr15	53730276	53730636	+	0	NA	intron (NR_102334, intron 2 of 19)	intron (NR_102334, intron 2 of 19)	29206	NM_182758	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.011111	0.393352	141(TAGAACAAAAAGTACC,-,0.00),142(AGAACAAAAAGTACCT,+,0.00)
chunk0175_21_1	chr7	468089	468332	+	0	NA	Intergenic	Intergenic	51634	NM_002607	5154	Hs.535898	NM_002607	ENSG00000197461	PDGFA	PDGF-A|PDGF1	platelet derived growth factor subunit A	protein-coding	0.004115	0.504098	
chunk0111_226_1	chr20	29080029	29080591	+	0	NA	promoter-TSS (NR_132316)	promoter-TSS (NR_132316)	-80	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.062278	0.616341	
chunk0156_163_1	chr5	107517500	107517699	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	153296	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.010050	0.325000	
chunk0137_106_1	chr4	13723317	13723736	+	0	NA	intron (NR_121681, intron 2 of 3)	L1MD1|LINE|L1	68347	NR_121681	101929071	Hs.543714	NR_121681	ENSG00000250634	LINC01182	-	long intergenic non-protein coding RNA 1182	ncRNA	0.004773	0.359524	
chunk0185_26_1	chr7	124131489	124131764	+	0	NA	Intergenic	Intergenic	-98157	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.007273	0.434783	
chunk0064_231_1	chr14	94120852	94121563	+	0	NA	Intergenic	MER54A|LTR|ERVL	8413	NM_032036	83982	Hs.94695	NM_032036	ENSG00000119632	IFI27L2	FAM14A|ISG12B|TLH29	interferon alpha inducible protein 27 like 2	protein-coding	0.009845	0.480337	
chunk0156_406_1	chr5	114129049	114129297	+	0	NA	Intergenic	Intergenic	-233146	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.000000	0.433735	
chunk0128_207_1	chr3	107939627	107940226	+	0	NA	Intergenic	Intergenic	56721	NR_015394	285205	Hs.134882	NR_015394	ENSG00000240423	LINC00636	-	long intergenic non-protein coding RNA 636	ncRNA	0.010017	0.438333	
chunk0079_76_1	chr17	11608336	11608916	+	0	NA	intron (NM_001372, intron 2 of 68)	intron (NM_001372, intron 2 of 68)	10195	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.010345	0.487091	
chunk0179_236_1	chr7	48028454	48029074	+	0	NA	intron (NM_152782, intron 2 of 10)	(GTAACAGA)n|Simple_repeat|Simple_repeat	355	NM_152782	256979	Hs.406741	NM_152782	ENSG00000164744	SUN3	SUNC1	Sad1 and UNC84 domain containing 3	protein-coding	0.016129	0.386473	
chunk0082_406_1	chr17	60888797	60889503	+	0	NA	intron (NM_017679, intron 9 of 23)	intron (NM_017679, intron 9 of 23)	211339	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.005666	0.367751	
chunk0133_383_1	chr3	173959102	173959301	+	0	NA	intron (NM_014932, intron 4 of 6)	MER52A|LTR|ERV1	-38405	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.005025	0.625000	
chunk0170_143_1	chr6	111239387	111239941	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-19615	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.009025	0.338739	
chunk0082_163_1	chr17	55739389	55739931	+	0	NA	Intergenic	Intergenic	-7539	NM_001099640	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.003690	0.399632	
chunk0072_113_1	chr15	91532527	91532872	+	0	NA	Intergenic	Intergenic	69360	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.005797	0.456647	
chunk0190_191_1	chr8	33513381	33513637	+	0	NA	promoter-TSS (NM_001265581)	promoter-TSS (NM_001265581)	34	NR_003041	692084		NR_003041	ENSG00000239039	SNORD13	RNU13|SNORD13A|U13	small nucleolar RNA, C/D box 13	snoRNA	0.035156	0.424125	
chunk0112_410_1	chr20	47181343	47181542	+	0	NA	intron (NM_005244, intron 14 of 15)	MLT1J2|LTR|ERVL-MaLR	14475	NR_037410	100500814		NR_037410	ENSG00000264901	MIR3616	mir-3616	microRNA 3616	ncRNA	0.005025	0.460000	
chunk0089_71_1	chr18	58202741	58202955	+	0	NA	intron (NM_001144970, intron 1 of 28)	intron (NM_001144970, intron 1 of 28)	7458	NM_001144970	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.004673	0.367442	
chunk0098_229_1	chr2	73877515	73877951	+	0	NA	Intergenic	Intergenic	-15233	NM_001199893	72	Hs.516105	NM_001615	ENSG00000163017	ACTG2	ACT|ACTA3|ACTE|ACTL3|ACTSG|VSCM	actin gamma 2, smooth muscle	protein-coding	0.018349	0.391304	
chunk0046_407_1	chr12	64318604	64319061	+	0	NA	exon (NM_001170633, exon 4 of 13)	exon (NM_001170633, exon 4 of 13)	71733	NM_001099676	115749	Hs.535190	NM_001099676	ENSG00000185306	C12orf56	-	chromosome 12 open reading frame 56	protein-coding	0.008753	0.447598	
chunk0046_173_1	chr12	58561083	58561303	+	0	NA	Intergenic	L1MB1|LINE|L1	-30509	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.004545	0.316742	
chunk0147_41_1	chr4	172139877	172140161	+	0	NA	intron (NM_001034845, intron 2 of 12)	intron (NM_001034845, intron 2 of 12)	326595	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.000000	0.291228	
chunk0030_78_1	chr10	112287018	112287505	+	0	NA	intron (NM_058222, intron 4 of 9)	intron (NM_058222, intron 4 of 9)	3605	NM_058222	6975	Hs.345485	NM_058222	ENSG00000119913	TECTB	-	tectorin beta	protein-coding	0.002053	0.442623	
chunk0033_426_1	chr11	25008157	25008535	+	0	NA	intron (NM_001009909, intron 9 of 11)	LTR27E|LTR|ERV1	511376	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.013228	0.540897	49(AGGGACTCTGTGTTCA,-,0.00),50(GGGACTCTGTGTTCAG,+,0.00)
chunk0186_336_1	chr7	143301144	143301917	+	0	NA	intron (NM_001224, intron 9 of 11)	intron (NM_001224, intron 9 of 11)	11942	NM_001224	835	Hs.368982	NM_001224	ENSG00000106144	CASP2	CASP-2|ICH1|NEDD-2|NEDD2|PPP1R57	caspase 2	protein-coding	0.009056	0.388889	376(AGGTACAAACTGTACT,-,0.00),377(GGTACAAACTGTACTT,+,0.00)
chunk0022_251_1	chr10	14585547	14585922	+	0	NA	intron (NM_001282695, intron 2 of 5)	intron (NM_001282695, intron 2 of 5)	-13361	NM_001282700	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.018667	0.457447	
chunk0116_393_1	chr21	42376609	42376867	+	0	NA	intron (NR_046020, intron 10 of 12)	intron (NR_046020, intron 10 of 12)	-10203	NM_003225	7031	Hs.162807	NM_003225	ENSG00000160182	TFF1	BCEI|D21S21|HP1.A|HPS2|pNR-2|pS2	trefoil factor 1	protein-coding	0.054264	0.606178	
chunk0052_336_1	chr12	126163980	126164337	+	0	NA	Intergenic	LTR18B|LTR|ERVL	68166	NR_110053	101927464	Hs.443932	NR_110053	ENSG00000284848	LINC02359	-	long intergenic non-protein coding RNA 2359	ncRNA	0.019608	0.533520	
chunk0132_256_1	chr3	158911604	158911847	+	0	NA	Intergenic	LTR18C|LTR|ERVL	109799	NR_110328	64747	Hs.58663	NM_022736	ENSG00000118855	MFSD1	SMAP4	major facilitator superfamily domain containing 1	protein-coding	0.012346	0.459016	
chunk0129_193_1	chr3	121284336	121284581	+	0	NA	intron (NM_014980, intron 20 of 27)	intron (NM_014980, intron 20 of 27)	234818	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.000000	0.369919	
chunk0198_212_1	chr8	133851249	133852240	+	0	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	-34752	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.010091	0.380040	
chunk0096_85_1	chr2	27975953	27976152	+	0	NA	intron (NM_199191, intron 3 of 11)	L1ME1|LINE|L1	-20315	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.010050	0.325000	
chunk0088_170_1	chr18	46886831	46887422	+	0	NA	intron (NM_004671, intron 2 of 13)	L1M5|LINE|L1	30406	NM_173206	9063	Hs.57769	NM_004671	ENSG00000078043	PIAS2	ARIP3|DIP|MIZ1|PIASX|SIZ2|ZMIZ4	protein inhibitor of activated STAT 2	protein-coding	0.006768	0.324324	
chunk0075_194_1	chr16	52473032	52473291	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	73733	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.023166	0.403846	
chunk0123_421_1	chr3	49671802	49672364	+	0	NA	TTS (NM_003458)	TTS (NM_003458)	-1919	NM_001640	327	Hs.517969	NM_001640	ENSG00000164062	APEH	AARE|ACPH|APH|D3F15S2|D3S48E|DNF15S2|OPH	acylaminoacyl-peptide hydrolase	protein-coding	0.010676	0.452931	
chunk0163_68_1	chr6	9141072	9141305	+	0	NA	Intergenic	Intergenic	488979	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.012876	0.376068	
chunk0051_39_1	chr12	112239758	112240072	+	0	NA	exon (NM_001109662, exon 33 of 76)	exon (NM_001109662, exon 33 of 76)	-76594	NR_106921	102465519		NR_106921	ENSG00000283793	MIR6861	hsa-mir-6861	microRNA 6861	ncRNA	0.022293	0.419048	
chunk0070_107_1	chr15	70421164	70421364	+	0	NA	Intergenic	L2a|LINE|L2	-194283	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.010000	0.447761	
chunk0212_226_1	chrX	136217311	136217696	+	0	NA	3' UTR (NM_024597, exon 19 of 19)	3' UTR (NM_024597, exon 19 of 19)	20607	NM_001159699	2273	Hs.435369	NM_001449	ENSG00000022267	FHL1	FCMSU|FHL-1|FHL1A|FHL1B|FLH1A|KYOT|RBMX1A|RBMX1B|SLIM|SLIM-1|SLIM1|SLIMMER|XMPMA	four and a half LIM domains 1	protein-coding	0.010390	0.380829	
chunk0021_21_1	chr10	496469	496675	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	145206	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.019417	0.468599	
chunk0165_427_1	chr6	39617104	39617447	+	0	NA	intron (NM_145027, intron 5 of 22)	intron (NM_145027, intron 5 of 22)	108130	NM_145027	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.000000	0.383721	
chunk0211_410_1	chrX	128862588	128862838	+	0	NA	Intergenic	Intergenic	660792	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.004000	0.386454	
chunk0028_243_1	chr10	90233872	90234132	+	0	NA	Intergenic	L1PB1|LINE|L1	-276629	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.003846	0.337165	
chunk0201_296_1	chr9	41201816	41202288	+	0	NA	Intergenic	Intergenic	-12651	NM_001286836	220869	Hs.355950	NM_001024916	ENSG00000147996	CBWD5	CBWD3|DC36	COBW domain containing 5	protein-coding	0.002119	0.340381	
chunk0040_390_1	chr11	119960496	119960718	+	0	NA	Intergenic	L1MEh|LINE|L1	177548	NM_012101	23650	Hs.504115	NM_012101	ENSG00000137699	TRIM29	ATDC	tripartite motif containing 29	protein-coding	0.000000	0.376682	
chunk0077_59_1	chr16	76705376	76705787	+	0	NA	Intergenic	Intergenic	70583	NR_110934	101928203	Hs.737035	NR_110934	ENSG00000250514	LINC02125	-	long intergenic non-protein coding RNA 2125	ncRNA	0.012165	0.332524	160(GAGAACATGGAGTTCC,-,0.00),161(AGAACATGGAGTTCCC,+,0.00)
chunk0104_61_1	chr2	171564405	171564861	+	0	NA	Intergenic	Intergenic	42277	NM_001127383	79901	Hs.221941	NM_024843	ENSG00000071967	CYBRD1	CYB561A2|DCYTB|FRRS3	cytochrome b reductase 1	protein-coding	0.015351	0.371991	
chunk0097_337_1	chr2	57976473	57977041	+	0	NA	intron (NM_001288837, intron 1 of 15)	L1PA15|LINE|L1	69106	NM_001288837	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.003521	0.328647	
chunk0080_92_1	chr17	26796941	26797171	+	0	NA	Intergenic	Intergenic	496940	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.026087	0.359307	
chunk0082_32_1	chr17	50763890	50764587	+	0	NA	intron (NR_073199, intron 2 of 3)	intron (NR_073199, intron 2 of 3)	3277	NR_073199									0.004304	0.441261	
chunk0070_175_1	chr15	71626570	71627213	+	0	NA	intron (NM_001286429, intron 1 of 11)	L1M5|LINE|L1	64648	NR_120346	101929173	Hs.680593	NR_120346		THSD4-AS2	-	THSD4 antisense RNA 2	ncRNA	0.006221	0.354037	
chunk0062_65_1	chr14	67529828	67530584	+	0	NA	Intergenic	MIRb|SINE|MIR	-3085	NM_020715	57475	Hs.594236	NM_020715	ENSG00000054690	PLEKHH1	-	pleckstrin homology, MyTH4 and FERM domain containing H1	protein-coding	0.003968	0.429326	
chunk0185_385_1	chr7	133363310	133363588	+	0	NA	intron (NM_001037126, intron 6 of 9)	intron (NM_001037126, intron 6 of 9)	72568	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.000000	0.318996	
chunk0165_287_1	chr6	36343089	36343604	+	0	NA	Intergenic	L2b|LINE|L2	-6461	NM_001010903	389384	Hs.162104	NM_001010903	ENSG00000189325	BNIP5	C6orf222	BCL2 interacting protein 5	protein-coding	0.009709	0.476744	289(CAGAACAGCTTGTCCT,-,0.00),290(AGAACAGCTTGTCCTT,+,0.00)
chunk0041_361_1	chr11	130916333	130916616	+	0	NA	promoter-TSS (NM_014758)	promoter-TSS (NM_014758)	13	NM_014758	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.141343	0.746479	
chunk0144_338_1	chr4	139172024	139172325	+	0	NA	Intergenic	L1ME1|LINE|L1	-32698	NM_201999	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.009967	0.357616	
chunk0007_218_1	chr1	81660118	81660587	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-39418	NM_001297704	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.000000	0.389362	
chunk0190_227_1	chr8	35818583	35819400	+	0	NA	Intergenic	L1PA8|LINE|L1	-108671	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.007344	0.344743	
chunk0156_32_1	chr5	102514918	102515206	+	0	NA	Intergenic	Intergenic	-16046	NM_001289004	133482	Hs.388874	NM_173488	ENSG00000205359	SLCO6A1	CT48|GST|OATP-I|OATP6A1|OATPY	solute carrier organic anion transporter family member 6A1	protein-coding	0.010417	0.321799	77(GGAACATGCTGTCTAT,+,0.00)
chunk0014_386_1	chr1	182743761	182744136	+	0	NA	Intergenic	L2a|LINE|L2	-45501	NM_001200056	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.002667	0.359043	
chunk0107_302_1	chr2	219093329	219093944	+	0	NA	intron (NM_024782, intron 5 of 7)	intron (NM_024782, intron 5 of 7)	-33120	NM_002181	3549	Hs.654504	NM_002181	ENSG00000163501	IHH	BDA1|HHG2	Indian hedgehog signaling molecule	protein-coding	0.003252	0.396104	251(GGGAACAGAATGACCT,-,0.00),252(GGAACAGAATGACCTT,+,0.00)
chunk0170_65_1	chr6	109609478	109610165	+	0	NA	intron (NM_001145128, intron 17 of 40)	intron (NM_001145128, intron 17 of 40)	81391	NM_001145128	221264	Hs.205144	NM_145025	ENSG00000155085	AK9	AK 9|AKD1|AKD2|C6orf199|C6orf224|dJ70A9.1	adenylate kinase 9	protein-coding	0.004367	0.350291	
chunk0090_17_1	chr19	715340	715625	+	0	NA	intron (NM_001040134, intron 1 of 7)	intron (NM_001040134, intron 1 of 7)	6529	NM_002579	5064	Hs.631841	NM_002579	ENSG00000099864	PALM	PALM1	paralemmin	protein-coding	0.007018	0.489510	
chunk0162_175_1	chr6	3675416	3675627	+	0	NA	Intergenic	L1PA6|LINE|L1	76491	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.004739	0.377358	
chunk0118_92_1	chr22	29113270	29113720	+	0	NA	intron (NM_001039570, intron 3 of 8)	intron (NM_001039570, intron 3 of 8)	40417	NM_032045	83999	Hs.229335	NM_032045	ENSG00000183762	KREMEN1	ECTD13|KREMEN|KRM1	kringle containing transmembrane protein 1	protein-coding	0.008889	0.390244	
chunk0079_333_1	chr17	17538563	17539008	+	0	NA	intron (NM_148172, intron 2 of 6)	intron (NM_148172, intron 2 of 6)	38680	NM_148173	10400	Hs.714193	NM_007169	ENSG00000133027	PEMT	PEAMT|PEMPT|PEMT2|PLMT|PNMT	phosphatidylethanolamine N-methyltransferase	protein-coding	0.020225	0.417040	
chunk0149_117_1	chr5	19370672	19370967	+	0	NA	Intergenic	Intergenic	515453	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003390	0.327703	
chunk0206_16_1	chr9	115690982	115691245	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	53126	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.000000	0.390152	
chunk0126_430_1	chr3	86916727	86917478	+	0	NA	Intergenic	Intergenic	74005	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.003995	0.329787	
chunk0002_393_1	chr1	27008048	27008561	+	0	NA	intron (NM_052943, intron 1 of 1)	intron (NM_052943, intron 1 of 1)	4538	NM_052943	115572	Hs.632378	NM_052943	ENSG00000158246	TENT5B	FAM46B	terminal nucleotidyltransferase 5B	protein-coding	0.013645	0.548638	257(CAGACCAGGCTGTTCT,-,0.00),258(AGACCAGGCTGTTCTC,+,0.00)
chunk0128_275_1	chr3	110711155	110711539	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	358612	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.002604	0.384416	
chunk0055_13_1	chr13	51739295	51739957	+	0	NA	intron (NM_052950, intron 7 of 11)	intron (NM_052950, intron 7 of 11)	64536	NM_024705	79758	Hs.266728	NM_024705	ENSG00000102796	DHRS12	SDR40C1	dehydrogenase/reductase 12	protein-coding	0.007553	0.401207	303(CAGTACATTTTGTACT,-,0.00),304(AGTACATTTTGTACTT,+,0.00)
chunk0086_233_1	chr18	22788943	22789436	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-2352	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.004057	0.323887	
chunk0006_410_1	chr1	75877536	75878096	+	0	NA	intron (NM_002440, intron 10 of 19)	L2b|LINE|L2	54615	NR_026546	127247	Hs.125423	NM_080868	ENSG00000154007	ASB17	Asb-17	ankyrin repeat and SOCS box containing 17	protein-coding	0.003571	0.326203	
chunk0016_296_1	chr1	201177098	201177339	+	0	NA	Intergenic	Intergenic	-5636	NM_001288564	252839	Hs.181444	NM_016456	ENSG00000116857	TMEM9	DERM4|TMEM9A	transmembrane protein 9	protein-coding	0.004149	0.528926	194(AAGGAGACACTGTCCT,-,0.00),195(AGGAGACACTGTCCTC,+,0.00)
chunk0191_160_1	chr8	49156298	49156703	+	0	NA	Intergenic	L2a|LINE|L2	84159	NM_001256597	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.012346	0.435961	
chunk0032_353_1	chr11	10522336	10522840	+	0	NA	intron (NM_016422, intron 4 of 5)	Plat_L3|LINE|CR1	-13412	NM_001190702	100463486		NM_001190702	ENSG00000255823	MTRNR2L8	HN8	MT-RNR2 like 8	protein-coding	0.001984	0.378218	
chunk0188_382_1	chr8	18409254	18409520	+	0	NA	Intergenic	LTR19B|LTR|ERV1	18142	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.011278	0.434457	
chunk0091_451_1	chr19	17565666	17565924	+	0	NA	intron (NM_024656, intron 3 of 11)	L1MB5|LINE|L1	10093	NM_024656	79709	Hs.418795	NM_024656	ENSG00000130309	COLGALT1	BSVD3|ColGalT 1|GLT25D1	collagen beta(1-O)galactosyltransferase 1	protein-coding	0.003876	0.428571	
chunk0208_99_1	chrX	13731461	13731962	+	0	NA	intron (NM_014563, intron 1 of 4)	L3|LINE|CR1	2924	NM_001011658	6399	Hs.592238	NM_014563	ENSG00000196459	TRAPPC2	MIP2A|SEDL|SEDT|TRAPPC2P1|TRS20|ZNF547L|hYP38334	trafficking protein particle complex 2	protein-coding	0.011976	0.406375	
chunk0026_124_1	chr10	62016782	62017398	+	0	NA	intron (NM_032199, intron 4 of 9)	intron (NM_032199, intron 4 of 9)	-32121	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.008117	0.408428	312(ATAAACAGTATGTGCC,-,0.00),313(TAAACAGTATGTGCCT,+,0.00)
chunk0114_423_1	chr20	64215083	64215495	+	0	NA	intron (NM_004535, intron 10 of 22)	MIRb|SINE|MIR	-40406	NM_001104925	55251	Hs.744845	NM_018257	ENSG00000203880	PCMTD2	C20orf36	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding	0.024272	0.493947	
chunk0038_341_1	chr11	92861571	92862028	+	0	NA	intron (NM_001008781, intron 20 of 24)	intron (NM_001008781, intron 20 of 24)	-107824	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.006565	0.390830	210(AGGTACAGTATGTGCC,-,0.00),211(GGTACAGTATGTGCCT,+,0.00)
chunk0074_120_1	chr16	22646801	22647087	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	101246	NR_003676	653786	Hs.564945	NR_003676	ENSG00000257838	OTOAP1	-	OTOA pseudogene 1	pseudo	0.003497	0.491289	
chunk0019_324_1	chr1	229181935	229182454	+	0	NA	Intergenic	Intergenic	-7393	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003854	0.351923	
chunk0024_63_1	chr10	34075216	34075785	+	0	NA	Intergenic	Intergenic	-302820	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.014060	0.533333	
chunk0164_108_1	chr6	20589141	20589717	+	0	NA	intron (NM_017774, intron 4 of 15)	intron (NM_017774, intron 4 of 15)	54972	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.008681	0.306759	
chunk0010_382_1	chr1	119279127	119279496	+	0	NA	Intergenic	L2c|LINE|L2	-89465	NM_001005783	51179	Hs.659767	NM_016527	ENSG00000116882	HAO2	GIG16|HAOX2	hydroxyacid oxidase 2	protein-coding	0.010840	0.381081	
chunk0062_445_1	chr14	75469789	75470151	+	0	NA	3' UTR (NM_130469, exon 4 of 4)	3' UTR (NM_130469, exon 4 of 4)	37836	NM_001135049	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.049724	0.647383	
chunk0020_209_1	chr1	235128719	235129177	+	0	NA	promoter-TSS (NM_014765)	promoter-TSS (NM_014765)	-7	NM_014765	9804	Hs.533192	NM_014765	ENSG00000173726	TOMM20	MAS20|MOM19|TOM20	translocase of outer mitochondrial membrane 20	protein-coding	0.096070	0.627451	
chunk0200_355_1	chr9	25472429	25472678	+	0	NA	Intergenic	L1PA11|LINE|L1	206305	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.004016	0.552000	
chunk0019_458_1	chr1	231417648	231418301	+	0	NA	intron (NM_022051, intron 1 of 4)	MIRc|SINE|MIR	7070	NM_022051	54583	Hs.444450	NM_022051	ENSG00000135766	EGLN1	C1orf12|ECYT3|HALAH|HIF-PH2|HIFPH2|HPH-2|HPH2|PHD2|SM20|ZMYND6	egl-9 family hypoxia inducible factor 1	protein-coding	0.003063	0.350153	
chunk0127_238_1	chr3	96860361	96860890	+	0	NA	intron (NM_001080448, intron 1 of 17)	intron (NM_001080448, intron 1 of 17)	46044	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.005671	0.320755	
chunk0143_215_1	chr4	113645785	113646250	+	0	NA	intron (NM_172114, intron 3 of 17)	intron (NM_172114, intron 3 of 17)	115910	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.002151	0.407725	
chunk0055_72_1	chr13	52903479	52903711	+	0	NA	Intergenic	L2c|LINE|L2	-54955	NM_002590	5100	Hs.19492	NM_002590	ENSG00000136099	PCDH8	ARCADLIN|PAPC	protocadherin 8	protein-coding	0.017241	0.420601	
chunk0151_371_1	chr5	54990249	54990453	+	0	NA	Intergenic	Intergenic	-4765	NM_001135604	11082	Hs.129944	NM_007036	ENSG00000164283	ESM1	endocan	endothelial cell specific molecule 1	protein-coding	0.004902	0.468293	
chunk0160_415_1	chr5	164083065	164083281	+	0	NA	Intergenic	Intergenic	384229	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.009259	0.317972	
chunk0038_404_1	chr11	93768218	93768608	+	0	NA	Intergenic	L2c|LINE|L2	-15826	NM_004268	9440	Hs.444931	NM_004268	ENSG00000042429	MED17	CRSP6|CRSP77|DRIP80|SRB4|TRAP80	mediator complex subunit 17	protein-coding	0.005128	0.391304	183(TGGTACATATTGTACT,-,0.00),184(GGTACATATTGTACTG,+,0.00),198(TGGTACATACTGTGCC,-,0.00),199(GGTACATACTGTGCCA,+,0.00)
chunk0144_111_1	chr4	128649613	128650047	+	0	NA	Intergenic	Intergenic	-159793	NM_024900	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.002304	0.445977	
chunk0083_5_1	chr17	62702883	62703268	+	0	NA	intron (NM_001100875, intron 10 of 10)	intron (NM_001100875, intron 10 of 10)	75674	NM_006039	9902	Hs.7835	NM_006039	ENSG00000011028	MRC2	CD280|CLEC13E|ENDO180|UPARAP	mannose receptor C type 2	protein-coding	0.010390	0.593264	
chunk0006_160_1	chr1	66388989	66389226	+	0	NA	Intergenic	Intergenic	34729	NM_001297442	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.004219	0.462185	
chunk0191_410_1	chr8	57654166	57654561	+	0	NA	Intergenic	Intergenic	310576	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.002532	0.388889	
chunk0180_145_1	chr7	57342843	57343302	+	0	NA	Intergenic	L2a|LINE|L2	-61695	NR_120505	100653233	Hs.127379	NR_120505	ENSG00000260653	LOC100653233	-	uncharacterized LOC100653233	ncRNA	0.013072	0.543478	
chunk0203_127_1	chr9	85146934	85147671	+	0	NA	Intergenic	L2a|LINE|L2	476925	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.006784	0.426829	
chunk0082_115_1	chr17	54969715	54970268	+	0	NA	intron (NM_178509, intron 1 of 17)	L2a|LINE|L2	1226	NM_178509	252983	Hs.35199	NM_178509	ENSG00000166263	STXBP4	Synip	syntaxin binding protein 4	protein-coding	0.012658	0.411552	400(AAGGCCACTGTGTTCC,-,0.00),401(AGGCCACTGTGTTCCC,+,0.00)
chunk0098_302_1	chr2	76256573	76257224	+	0	NA	Intergenic	MER70B|LTR|ERVL	-545913	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.003072	0.423313	
chunk0059_103_1	chr14	31031637	31031836	+	0	NA	intron (NM_001254728, intron 1 of 5)	intron (NM_001254728, intron 1 of 5)	5093	NM_001254728	11154	Hs.293411	NM_007077	ENSG00000100478	AP4S1	AP47B|CLA20|CLAPS4|CPSQ6|SPG52	adaptor related protein complex 4 subunit sigma 1	protein-coding	0.010050	0.440000	
chunk0034_139_1	chr11	29069564	29070154	+	0	NA	Intergenic	Intergenic	-592311	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.005085	0.333333	
chunk0074_54_1	chr16	20896552	20897349	+	0	NA	intron (NM_173475, intron 1 of 2)	intron (NM_173475, intron 1 of 2)	-2918	NM_020424	57149	Hs.745012	NM_020424	ENSG00000102897	LYRM1	A211C6.1	LYR motif containing 1	protein-coding	0.006274	0.397243	
chunk0108_337_1	chr2	235729782	235730079	+	0	NA	intron (NM_001037131, intron 3 of 17)	intron (NM_001037131, intron 3 of 17)	224179	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.016835	0.409396	
chunk0176_70_1	chr7	11252822	11253228	+	0	NA	Intergenic	LTR40b|LTR|ERVL	279153	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.007389	0.437346	
chunk0148_296_1	chr5	12110079	12110520	+	0	NA	Intergenic	Intergenic	-206256	NM_001288717	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.004535	0.350679	
chunk0156_115_1	chr5	105883068	105883318	+	0	NA	Intergenic	Intergenic	783719	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.008000	0.418327	
chunk0177_353_1	chr7	26629569	26630157	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-8008	NM_001145531									0.006803	0.400679	
chunk0119_295_1	chr22	46301111	46301331	+	0	NA	intron (NM_016426, intron 2 of 11)	L1ME4b|LINE|L1	4480	NM_016426	51512	Hs.386189	NM_016426	ENSG00000075218	GTSE1	B99	G2 and S-phase expressed 1	protein-coding	0.013636	0.452489	
chunk0100_121_1	chr2	108556268	108556658	+	0	NA	intron (NM_001193483, intron 1 of 9)	L1MB4|LINE|L1	22108	NM_001193483	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.002564	0.363171	
chunk0153_245_1	chr5	72434759	72435282	+	0	NA	Intergenic	Intergenic	72402	NM_152625	167465	Hs.224794	NM_152625	ENSG00000178175	ZNF366	DC-SCRIPT|DCSCRIPT	zinc finger protein 366	protein-coding	0.005736	0.387405	164(AAGAACAGTGTGTTCC,-,0.00),165(AGAACAGTGTGTTCCT,+,0.00)
chunk0192_226_1	chr8	65337221	65337742	+	0	NA	Intergenic	Intergenic	-157141	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.009597	0.392720	
chunk0147_323_1	chr4	185086283	185087042	+	0	NA	Intergenic	Intergenic	-56601	NM_001151	291	Hs.246506	NM_001151	ENSG00000151729	SLC25A4	AAC1|ANT|ANT 1|ANT1|MTDPS12|MTDPS12A|PEO2|PEO3|PEOA2|T1	solute carrier family 25 member 4	protein-coding	0.023715	0.475000	
chunk0092_16_1	chr19	18697688	18699323	+	0	NA	intron (NM_001098482, intron 1 of 14)	intron (NM_001098482, intron 1 of 14)	14890	NM_001098482	23373	Hs.371096	NM_015321	ENSG00000105662	CRTC1	MAML2|MECT1|Mam-2|TORC-1|TORC1|WAMTP1	CREB regulated transcription coactivator 1	protein-coding	0.017737	0.551956	355(GTGCACGGTGTGTTCT,-,0.00),356(TGCACGGTGTGTTCTG,+,0.00),530(GTGCACAGTGTGTACT,-,0.00),531(TGCACAGTGTGTACTC,+,0.00),561(AGGCACAGTGTGTACT,-,0.00),562(GGCACAGTGTGTACTC,+,0.00),594(GTGCACAGTGTGTACT,-,0.00),595(TGCACAGTGTGTACTC,+,0.00),625(AGGCACAGTGTGTACT,-,0.00),626(GGCACAGTGTGTACTC,+,0.00),658(GTGCACAGTGTGTACT,-,0.00),659(TGCACAGTGTGTACTC,+,0.00),762(GTGCACAGTGTGTACT,-,0.00),763(TGCACAGTGTGTACTC,+,0.00),793(AGGCACAGTGTGTACT,-,0.00),794(GGCACAGTGTGTACTC,+,0.00),835(AGGCACAGTGTGTACT,-,0.00),836(GGCACAGTGTGTACTC,+,0.00),868(GTGCACAGTGTGTACT,-,0.00),869(TGCACAGTGTGTACTC,+,0.00),921(AGGCGCAGTGTGTGCT,-,0.00),922(GGCGCAGTGTGTGCTC,+,0.00),987(ATGCACAGTGTGTACT,-,0.00),988(TGCACAGTGTGTACTA,+,0.00),1018(AAGTGCAGTGTGTACT,-,0.00),1019(AGTGCAGTGTGTACTT,+,0.00),1173(GTGCACACTGTGTACT,-,0.00),1174(TGCACACTGTGTACTC,+,0.00),1193(AGGCGCAGTGTGTGCT,-,0.00),1194(GGCGCAGTGTGTGCTC,+,0.00),1389(AGGCACAGTGTGAACT,-,0.00),1390(GGCACAGTGTGAACTC,+,0.00)
chunk0199_357_1	chr9	12515921	12516479	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	-177186	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.005376	0.397138	
chunk0160_165_1	chr5	152225639	152226112	+	0	NA	intron (NR_109876, intron 1 of 2)	intron (NR_109876, intron 1 of 2)	179404	NM_020167	56923	Hs.731911	NM_020167	ENSG00000132911	NMUR2	FM-4|FM4|NMU-R2|NMU2R|TGR-1|TGR1	neuromedin U receptor 2	protein-coding	0.004228	0.369198	
chunk0064_51_1	chr14	89857008	89857434	+	0	NA	intron (NM_145231, intron 5 of 5)	intron (NM_145231, intron 5 of 5)	97336	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.011737	0.419204	
chunk0153_376_1	chr5	74868709	74869121	+	0	NA	Intergenic	MIR|SINE|MIR	-2077	NM_015566	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.000000	0.377724	
chunk0136_187_1	chr4	6746862	6747633	+	0	NA	Intergenic	Intergenic	31132	NM_018366	55330	Hs.7570	NM_018366	ENSG00000186222	BLOC1S4	BCAS4L|BLOS4|CNO	biogenesis of lysosomal organelles complex 1 subunit 4	protein-coding	0.023346	0.606218	
chunk0207_443_1	chr9	137612055	137612801	+	0	NA	intron (NM_152285, intron 1 of 7)	intron (NM_152285, intron 1 of 7)	6101	NR_122036	85026	Hs.522520	NM_032937	ENSG00000203993	ARRDC1-AS1	C9orf37	ARRDC1 antisense RNA 1	ncRNA	0.020107	0.597055	
chunk0084_420_1	chr17	82426054	82426642	+	0	NA	intron (NM_173620, intron 3 of 11)	LTR46|LTR|ERV1	-7711	NM_024648	79701	Hs.187505	NM_024648	ENSG00000181396	OGFOD3	C17orf101	2-oxoglutarate and iron dependent oxygenase domain containing 3	protein-coding	0.020408	0.531409	230(ATGATCAGGATGTTCC,-,0.00),231(TGATCAGGATGTTCCT,+,0.00),342(TGGGCAGGATGTTCCT,+,0.00)
chunk0121_30_1	chr3	15206862	15207359	+	0	NA	intron (NM_014296, intron 1 of 20)	Tigger3b|DNA|TcMar-Tigger	884	NM_014296	23473	Hs.595234	NM_014296	ENSG00000131375	CAPN7	CALPAIN7|PALBH	calpain 7	protein-coding	0.018109	0.425703	269(TGGTACAGCCTGTTCC,-,0.00),270(GGTACAGCCTGTTCCA,+,0.00)
chunk0043_377_1	chr12	24551465	24551759	+	0	NA	intron (NM_152989, intron 1 of 17)	L2a|LINE|L2	10837	NM_152989	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.020408	0.376271	
chunk0132_59_1	chr3	155134903	155135186	+	0	NA	intron (NM_000902, intron 8 of 22)	L1PA16|LINE|L1	54754	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.003534	0.338028	
chunk0094_310_1	chr2	8820205	8820406	+	0	NA	intron (NM_020738, intron 2 of 29)	L2a|LINE|L2	17320	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.009950	0.391089	
chunk0043_366_1	chr12	23533392	23533728	+	0	NA	3' UTR (NM_001261415, exon 15 of 15)	3' UTR (NM_001261415, exon 15 of 15)	51052	NM_178010	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.000000	0.347181	
chunk0210_191_1	chrX	80059907	80060174	+	0	NA	Intergenic	L1P4|LINE|L1	36980	NM_001303475	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.003745	0.309701	
chunk0076_95_1	chr16	65082319	65082544	+	0	NA	intron (NM_001797, intron 1 of 12)	intron (NM_001797, intron 1 of 12)	39706	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.008889	0.526549	
chunk0124_223_1	chr3	56296943	56297351	+	0	NA	intron (NR_132749, intron 2 of 17)	intron (NR_132749, intron 2 of 17)	171216	NR_132749	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.002451	0.369193	
chunk0029_258_1	chr10	102991780	102992275	+	0	NA	intron (NM_199076, intron 1 of 6)	(ATTTAC)n|Simple_repeat|Simple_repeat	73709	NM_017649	54805	Hs.643509	NM_017649	ENSG00000148842	CNNM2	ACDP2|HOMG6|HOMGSMR	cyclin and CBS domain divalent metal cation transport mediator 2	protein-coding	0.000000	0.330645	
chunk0010_254_1	chr1	116619130	116619416	+	0	NA	intron (NM_001007237, intron 2 of 10)	intron (NM_001007237, intron 2 of 10)	47683	NM_001542	3321	Hs.171057	NM_001542	ENSG00000143061	IGSF3	EWI-3|LCDD|V8	immunoglobulin superfamily member 3	protein-coding	0.013986	0.463415	
chunk0165_90_1	chr6	31877473	31878073	+	0	NA	promoter-TSS (NM_001178045).6	promoter-TSS (NM_001178045).6	-102	NM_001178045	80736	Hs.335355	NM_025257	ENSG00000204385	SLC44A4	C6orf29|CTL4|DFNA72|NG22|TPPT|hTPPT1	solute carrier family 44 member 4	protein-coding	0.015000	0.618968	
chunk0181_242_1	chr7	85290281	85290706	+	0	NA	Intergenic	Intergenic	-168562	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.004706	0.370892	
chunk0209_183_1	chrX	43707669	43708425	+	0	NA	intron (NM_000240, intron 3 of 14)	intron (NM_000240, intron 3 of 14)	53140	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.003968	0.377807	442(AGGGACATTGCGTTCT,-,0.00),443(GGGACATTGCGTTCTG,+,0.00)
chunk0124_185_1	chr3	55470288	55470562	+	0	NA	exon (NM_001256105, exon 5 of 5)	exon (NM_001256105, exon 5 of 5)	10973	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.054745	0.607273	
chunk0184_134_1	chr7	115491736	115491948	+	0	NA	Intergenic	Intergenic	-260487	NR_126407	104355291		NR_126407	ENSG00000233607	LINC01392	-	long intergenic non-protein coding RNA 1392	ncRNA	0.014151	0.314554	
chunk0206_41_1	chr9	116890868	116891444	+	0	NA	intron (NM_014010, intron 9 of 21)	intron (NM_014010, intron 9 of 21)	203854	NM_001099679	22954	Hs.591910	NM_012210	ENSG00000119401	TRIM32	BBS11|HT2A|LGMD2H|LGMDR8|TATIP	tripartite motif containing 32	protein-coding	0.005208	0.376083	
chunk0015_142_1	chr1	186037045	186037394	+	0	NA	intron (NM_031935, intron 36 of 106)	intron (NM_031935, intron 36 of 106)	-259054	NM_005807	10216	Hs.647723	NM_005807	ENSG00000116690	PRG4	CACP|HAPO|JCAP|MSF|SZP	proteoglycan 4	protein-coding	0.008596	0.322857	
chunk0188_254_1	chr8	14478017	14478483	+	0	NA	intron (NM_139167, intron 2 of 7)	L1MC1|LINE|L1	375260	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.006438	0.361884	
chunk0052_62_1	chr13	21176794	21177150	+	0	NA	promoter-TSS (NM_001166017)	promoter-TSS (NM_001166017)	-370	NM_001166017	221150	Hs.88523	NM_145061	ENSG00000165480	SKA3	C13orf3|RAMA1	spindle and kinetochore associated complex subunit 3	protein-coding	0.123596	0.700280	
chunk0046_92_1	chr12	56636950	56637195	+	0	NA	promoter-TSS (NM_013449)	promoter-TSS (NM_013449)	-693	NM_013449	11176	Hs.314263	NM_013449	ENSG00000076108	BAZ2A	TIP5|WALp3	bromodomain adjacent to zinc finger domain 2A	protein-coding	0.012245	0.540650	49(GAGCTCAGCTTGTCCC,-,0.00),50(AGCTCAGCTTGTCCCC,+,0.00)
chunk0161_262_1	chr5	172143870	172144141	+	0	NA	intron (NM_005990, intron 2 of 18)	intron (NM_005990, intron 2 of 18)	44337	NM_005990	6793	Hs.744005	NM_005990	ENSG00000072786	STK10	LOK|PRO2729	serine/threonine kinase 10	protein-coding	0.014760	0.455882	
chunk0181_320_1	chr7	87677327	87677552	+	0	NA	intron (NM_001134406, intron 2 of 9)	L1MA9|LINE|L1	35884	NM_000927	5243	Hs.489033	NM_000927	ENSG00000085563	ABCB1	ABC20|CD243|CLCS|GP170|MDR1|P-GP|PGY1	ATP binding cassette subfamily B member 1	protein-coding	0.008889	0.353982	
chunk0058_297_1	chr14	26943194	26943393	+	0	NA	Intergenic	Intergenic	34651	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.005025	0.410000	
chunk0024_40_1	chr10	33540405	33540761	+	0	NA	Intergenic	L1MEf|LINE|L1	-205678	NM_001024628	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.002809	0.294118	
chunk0028_317_1	chr10	91804030	91804652	+	0	NA	intron (NM_025235, intron 1 of 26)	intron (NM_025235, intron 1 of 26)	5947	NM_025235	80351	Hs.329327	NM_025235	ENSG00000107854	TNKS2	ARTD6|PARP-5b|PARP-5c|PARP5B|PARP5C|TANK2|TNKL|pART6	tankyrase 2	protein-coding	0.000000	0.373997	
chunk0194_249_1	chr8	86416788	86417501	+	0	NA	intron (NM_007013, intron 9 of 24)	intron (NM_007013, intron 9 of 24)	74379	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.008415	0.481793	373(AGGAACTCTGTGTTCT,-,0.00),374(GGAACTCTGTGTTCTG,+,0.00)
chunk0004_396_1	chr1	52098148	52098584	+	0	NA	Intergenic	MER1A|DNA|hAT-Charlie	42181	NM_001136497	91408	Hs.429839	NM_152265	ENSG00000134717	BTF3L4	-	basic transcription factor 3 like 4	protein-coding	0.013761	0.462243	
chunk0006_30_1	chr1	64137602	64137894	+	0	NA	intron (NM_001083592, intron 5 of 6)	L2b|LINE|L2	-23957	NR_110665	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.010274	0.395904	
chunk0057_322_1	chr13	106805037	106805578	+	0	NA	Intergenic	Intergenic	151427	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.007394	0.389299	
chunk0138_435_1	chr4	45558310	45558998	+	0	NA	Intergenic	Intergenic	565411	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.002907	0.265602	
chunk0144_77_1	chr4	127965085	127965348	+	0	NA	promoter-TSS (NM_001039717)	promoter-TSS (NM_001039717)	-90	NM_001039717	80167	Hs.143995	NM_025097	ENSG00000164074	ABHD18	C4orf29	abhydrolase domain containing 18	protein-coding	0.098859	0.640152	
chunk0081_38_1	chr17	37545512	37546250	+	0	NA	intron (NM_007247, intron 14 of 21)	intron (NM_007247, intron 14 of 21)	56036	NM_007026	11072	Hs.91448	NM_007026	ENSG00000276023	DUSP14	MKP-L|MKP6	dual specificity phosphatase 14	protein-coding	0.008130	0.305819	401(CAGAACACCGTGCCCC,-,0.00),402(AGAACACCGTGCCCCT,+,0.00),447(CAGGGCAGTATGTTCT,-,0.00),448(AGGGCAGTATGTTCTG,+,0.00)
chunk0107_317_1	chr2	219781104	219781654	+	0	NA	Intergenic	Intergenic	125186	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.007273	0.390200	
chunk0094_63_1	chr2	3404443	3405834	+	0	NA	intron (NM_016030, intron 3 of 11)	intron (NM_016030, intron 3 of 11)	25463	NM_016030	51112	Hs.252713	NM_016030	ENSG00000171853	TRAPPC12	CGI-87|PEBAS|TTC-15|TTC15	trafficking protein particle complex 12	protein-coding	0.015097	0.420259	
chunk0178_27_1	chr7	29370107	29370310	+	0	NA	intron (NM_001293069, intron 4 of 13)	intron (NM_001293069, intron 4 of 13)	-109504	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.014778	0.485294	
chunk0044_237_1	chr12	31651021	31651255	+	0	NA	intron (NM_001135864, intron 1 of 3)	LTR47A|LTR|ERVL	3978	NM_001135864	254013	Hs.740628	NM_173802	ENSG00000139160	ETFBKMT	C12orf72|ETFB-KMT|METTL20	electron transfer flavoprotein subunit beta lysine methyltransferase	protein-coding	0.017094	0.463830	
chunk0096_124_1	chr2	28633196	28633550	+	0	NA	intron (NM_001170585, intron 55 of 56)	MIRb|SINE|MIR	-118375	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.014124	0.439437	
chunk0212_210_1	chrX	135473282	135473522	+	0	NA	Intergenic	L1MA9|LINE|L1	-47228	NM_182540	203522	Hs.496829	NM_182540	ENSG00000165359	INTS6L	DDX26B	integrator complex subunit 6 like	protein-coding	0.000000	0.369295	
chunk0048_157_1	chr12	80627609	80628201	+	0	NA	intron (NM_001145026, intron 33 of 44)	intron (NM_001145026, intron 33 of 44)	-79724	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.003378	0.308600	284(GGGAACATTTTGTCCT,-,0.00),285(GGAACATTTTGTCCTC,+,0.00)
chunk0197_238_1	chr8	123173084	123173296	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-5857	NM_032899	84985	Hs.379821	NM_032899	ENSG00000147689	FAM83A	BJ-TSA-9	family with sequence similarity 83 member A	protein-coding	0.009434	0.328638	
chunk0162_331_1	chr6	6802769	6803543	+	0	NA	Intergenic	Intergenic	-180330	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.024548	0.540645	
chunk0211_426_1	chrX	129196166	129196365	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	327240	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.005025	0.465000	
chunk0022_41_1	chr10	8066579	8067214	+	0	NA	intron (NM_001002295, intron 4 of 5)	intron (NM_001002295, intron 4 of 5)	12192	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.004724	0.388365	
chunk0178_88_1	chr7	30520904	30521162	+	0	NA	Intergenic	Intergenic	-16192	NM_001199816	79017	Hs.530024	NM_024051	ENSG00000006625	GGCT	C7orf24|CRF21|GCTG|GGC	gamma-glutamylcyclotransferase	protein-coding	0.000000	0.389961	
chunk0120_44_1	chr3	2847480	2847866	+	0	NA	intron (NM_001206955, intron 6 of 23)	intron (NM_001206955, intron 6 of 23)	-44542	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.007772	0.490956	
chunk0090_454_1	chr18	79964343	79964665	+	0	NA	promoter-TSS (NM_001136180)	promoter-TSS (NM_001136180)	-78	NM_001136180	440498	Hs.191582	NM_001136180	ENSG00000226742	HSBP1L1	-	heat shock factor binding protein 1 like 1	protein-coding	0.124224	0.743034	
chunk0150_232_1	chr5	35853448	35853886	+	0	NA	Intergenic	Intergenic	-3208	NR_120485	3575	Hs.591742	NM_002185	ENSG00000168685	IL7R	CD127|CDW127|IL-7R-alpha|IL7RA|ILRA	interleukin 7 receptor	protein-coding	0.011416	0.412301	239(AAGGTCAGTGTGTTCT,-,0.00),240(AGGTCAGTGTGTTCTG,+,0.00)
chunk0157_319_1	chr5	121981721	121982527	+	0	NA	intron (NM_152546, intron 3 of 7)	intron (NM_152546, intron 3 of 7)	20163	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.004963	0.343247	
chunk0198_346_1	chr8	140285118	140285606	+	0	NA	intron (NM_001160372, intron 13 of 22)	intron (NM_001160372, intron 13 of 22)	172400	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.018443	0.537832	
chunk0147_251_1	chr4	183260372	183260988	+	0	NA	intron (NM_024949, intron 10 of 22)	Tigger3a|DNA|TcMar-Tigger	-20046	NR_126473	101928734	Hs.570713	NR_126473	ENSG00000251128	WWC2-AS1	-	WWC2 antisense RNA 1	ncRNA	0.014610	0.448947	301(AAGTACACTCTGTGAT,-,0.00)
chunk0057_240_1	chr13	104553620	104554164	+	0	NA	Intergenic	Intergenic	-911975	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.003676	0.400000	
chunk0012_383_1	chr1	163381770	163382176	+	0	NA	Intergenic	L2c|LINE|L2	41218	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.000000	0.329238	125(TAGAGCATCCTGTGCT,-,0.00),126(AGAGCATCCTGTGCTT,+,0.00)
chunk0066_8_1	chr15	26907560	26908170	+	0	NA	intron (NM_001165037, intron 6 of 10)	intron (NM_001165037, intron 6 of 10)	40739	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.009836	0.386252	
chunk0177_221_1	chr7	24179386	24179794	+	0	NA	Intergenic	L1ME4c|LINE|L1	-104598	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.002451	0.310513	
chunk0119_66_1	chr22	41066783	41067057	+	0	NA	Intergenic	Intergenic	6801	NR_132979	106635682		NR_132979		SNORD140	-	small nucleolar RNA, C/D box 140	snoRNA	0.010949	0.520000	9(GAGAACAATGTGCCCC,-,0.00)
chunk0033_410_1	chr11	24758457	24758947	+	0	NA	intron (NM_001009909, intron 4 of 11)	intron (NM_001009909, intron 4 of 11)	261732	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.262729	
chunk0078_127_1	chr17	3135950	3136646	+	0	NA	Intergenic	Intergenic	-8747	NM_003555	8390	Hs.248183	NM_003555	ENSG00000183024	OR1G1	OR17-130|OR17-209|OR1G2	olfactory receptor family 1 subfamily G member 1	protein-coding	0.004310	0.375897	
chunk0045_89_1	chr12	45990101	45990332	+	0	NA	intron (NM_004719, intron 1 of 14)	CpG	402	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.112554	0.711207	
chunk0021_451_1	chr1	248872918	248873341	+	0	NA	Intergenic	Intergenic	-14013	NM_017865	55657	Hs.377705	NM_017865	ENSG00000171163	ZNF692	AREBP|Zfp692	zinc finger protein 692	protein-coding	0.035461	0.518868	
chunk0156_178_1	chr5	107672282	107672650	+	0	NA	Intergenic	CpG-22318	-1571	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.100543	0.653117	
chunk0121_160_1	chr3	19389854	19390391	+	0	NA	intron (NM_144633, intron 5 of 15)	MIRb|SINE|MIR	-75191	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.009311	0.381041	339(TGGAACATTATGTGCT,-,0.00),340(GGAACATTATGTGCTC,+,0.00)
chunk0150_374_1	chr5	39178266	39178467	+	0	NA	intron (NM_001465, intron 2 of 18)	MIR|SINE|MIR	41212	NM_001465	2533	Hs.370503	NM_001465	ENSG00000082074	FYB1	ADAP|FYB|PRO0823|SLAP-130|SLAP130|THC3	FYN binding protein 1	protein-coding	0.009950	0.381188	
chunk0146_289_1	chr4	164434180	164434438	+	0	NA	Intergenic	Intergenic	-51054	NM_001166373	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.000000	0.343629	137(AAGCACAGTCTGTACC,-,0.00),138(AGCACAGTCTGTACCA,+,0.00)
chunk0070_331_1	chr15	75562101	75562527	+	0	NA	intron (NM_002833, intron 1 of 12)	intron (NM_002833, intron 1 of 12)	16977	NM_002833	5780	Hs.445775	NM_002833	ENSG00000169410	PTPN9	MEG2|PTPMEG2	protein tyrosine phosphatase non-receptor type 9	protein-coding	0.009390	0.444965	
chunk0161_273_1	chr5	172565615	172565880	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-75519	NM_001308177	54492	Hs.91521	NM_001142651	ENSG00000214357	NEURL1B	NEURL3|RNF67B|hNeur2|neur2	neuralized E3 ubiquitin protein ligase 1B	protein-coding	0.018868	0.530075	134(AGGCACTTGGTGTTCC,-,0.00),135(GGCACTTGGTGTTCCT,+,0.00)
chunk0210_319_1	chrX	92248998	92249530	+	0	NA	intron (NM_032969, intron 3 of 5)	intron (NM_032969, intron 3 of 5)	413803	NM_001168360	27328	Hs.655673	NM_014522	ENSG00000102290	PCDH11X	PCDH-X|PCDH-Y|PCDH11|PCDH11Y|PCDH22|PCDHX|PPP1R119	protocadherin 11 X-linked	protein-coding	0.005639	0.290807	
chunk0184_48_1	chr7	112268146	112268889	+	0	NA	intron (NM_021994, intron 1 of 11)	intron (NM_021994, intron 1 of 11)	61929	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.001346	0.318548	
chunk0118_418_1	chr22	38375813	38376111	+	0	NA	intron (NR_002821, intron 3 of 4)	Tigger1|DNA|TcMar-Tigger	22560	NM_001289912	102800317	Hs.720223	NM_001289912	ENSG00000283900	TPTEP2-CSNK1E	LOC400927-CSNK1E	TPTEP2-CSNK1E readthrough	protein-coding	0.006711	0.408027	
chunk0111_210_1	chr20	28557754	28557953	+	0	NA	Intergenic	Intergenic	44812	NR_132315	100289097	Hs.529357	NR_132315	ENSG00000282826	FRG1CP	-	FSHD region gene 1 family member C, pseudogene	pseudo	0.000000	0.270000	
chunk0151_135_1	chr5	44696498	44696697	+	0	NA	Intergenic	Intergenic	112196	NR_109864	100506674	Hs.575213	NR_109862		MRPS30-DT	BRCAT54	MRPS30 divergent transcript	ncRNA	0.015075	0.330000	
chunk0193_281_1	chr8	77400681	77401012	+	0	NA	Intergenic	Intergenic	-49851	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.301205	
chunk0081_206_1	chr17	42428559	42429000	+	0	NA	Intergenic	Intergenic	-5459	NM_012232	284119	Hs.437191	NM_012232	ENSG00000177469	CAVIN1	CAVIN|CGL4|FKSG13|PTRF|cavin-1	caveolae associated protein 1	protein-coding	0.006803	0.447964	
chunk0006_286_1	chr1	70688472	70689122	+	0	NA	Intergenic	Intergenic	-17656	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.001538	0.356375	
chunk0147_6_1	chr4	170524225	170524915	+	0	NA	Intergenic	Intergenic	297979	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.011594	0.280753	
chunk0135_432_1	chr3	193837261	193837585	+	0	NA	Intergenic	Intergenic	156815	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.015432	0.480000	142(CGGCACTCAGTGTGCC,-,0.00),143(GGCACTCAGTGTGCCC,+,0.00)
chunk0162_468_1	chr5	181207475	181207741	+	0	NA	Intergenic	Intergenic	-2315	NM_033342	81786	Hs.487412	NM_033342	ENSG00000146054	TRIM7	GNIP|RNF90	tripartite motif containing 7	protein-coding	0.052632	0.505618	
chunk0046_168_1	chr12	58521030	58521848	+	0	NA	Intergenic	Intergenic	-70263	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.003667	0.374847	
chunk0087_9_1	chr18	30746171	30746653	+	0	NA	Intergenic	Intergenic	296403	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.002075	0.312629	
chunk0040_364_1	chr11	118870220	118870848	+	0	NA	Intergenic	Intergenic	-13232	NM_001716	643	Hs.113916	NM_001716	ENSG00000160683	CXCR5	BLR1|CD185|MDR15	C-X-C motif chemokine receptor 5	protein-coding	0.017516	0.577107	295(CAGAACAGCGAGTTCC,-,0.00),296(AGAACAGCGAGTTCCA,+,0.00)
chunk0205_341_1	chr9	113287823	113288204	+	0	NA	intron (NM_001244926, intron 9 of 13)	intron (NM_001244926, intron 9 of 13)	11027	NM_145051	138065	Hs.729641	NM_145051	ENSG00000165188	RNF183	-	ring finger protein 183	protein-coding	0.002625	0.369110	
chunk0112_426_1	chr20	47411139	47411536	+	0	NA	Intergenic	Intergenic	-54448	NM_001281780	23613	Hs.446240	NM_012408	ENSG00000101040	ZMYND8	PRKCBP1|PRO2893|RACK7	zinc finger MYND-type containing 8	protein-coding	0.012594	0.437186	240(CTGGACAGGATGTTCC,-,0.00),241(TGGACAGGATGTTCCT,+,0.00)
chunk0195_334_1	chr8	99206220	99206763	+	0	NA	intron (NM_152564, intron 17 of 61)	intron (NM_152564, intron 17 of 61)	193225	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.007366	0.336397	
chunk0034_356_1	chr11	35953077	35953449	+	0	NA	intron (NM_001304263, intron 1 of 4)	intron (NM_001304263, intron 1 of 4)	9282	NM_001304264	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.021505	0.474531	
chunk0084_105_1	chr17	75693563	75694064	+	0	NA	intron (NM_001301855, intron 5 of 11)	intron (NM_001301855, intron 5 of 11)	-26624	NM_004259	9400	Hs.632229	NM_004259	ENSG00000108469	RECQL5	RECQ5	RecQ like helicase 5	protein-coding	0.013972	0.553785	392(AGGGACACTATGTTTC,-,0.00),393(GGGACACTATGTTTCT,+,0.00)
chunk0054_76_1	chr13	42164559	42165116	+	0	NA	intron (NR_123714, intron 5 of 27)	intron (NR_123714, intron 5 of 27)	26795	NR_123714	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.005386	0.358423	
chunk0027_337_1	chr10	78521049	78521258	+	0	NA	Intergenic	Intergenic	253825	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.004785	0.457143	
chunk0170_50_1	chr6	109466283	109466586	+	0	NA	promoter-TSS (NM_001286613)	promoter-TSS (NM_001286613)	-466	NM_001286613	64780	Hs.33476	NM_022765	ENSG00000135596	MICAL1	MICAL|MICAL-1|NICAL	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding	0.006601	0.450658	
chunk0142_101_1	chr4	94338620	94339267	+	0	NA	intron (NM_014485, intron 1 of 5)	L1M5|LINE|L1	3933	NM_014485	27306	Hs.128433	NM_014485	ENSG00000163106	HPGDS	GSTS|GSTS1|GSTS1-1|PGD2|PGDS	hematopoietic prostaglandin D synthase	protein-coding	0.006182	0.356481	
chunk0066_401_1	chr15	39260025	39260624	+	0	NA	Intergenic	L2a|LINE|L2	9655	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.001669	0.406667	206(AGGGACATGTTGTCTT,-,0.00)
chunk0124_351_1	chr3	58577236	58577866	+	0	NA	5' UTR (NM_007177, exon 1 of 5)	5' UTR (NM_007177, exon 1 of 5)	213	NM_001076778	11170	Hs.506357	NM_007177	ENSG00000168309	FAM107A	DRR1|TU3A	family with sequence similarity 107 member A	protein-coding	0.025397	0.508716	323(CGGAACATCATGTCCA,-,0.00),324(GGAACATCATGTCCAA,+,0.00)
chunk0120_227_1	chr3	8201980	8202511	+	0	NA	Intergenic	L2a|LINE|L2	-185938	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.011299	0.400376	
chunk0169_274_1	chr6	105593819	105594364	+	0	NA	Intergenic	Intergenic	-190967	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.005505	0.419414	
chunk0115_106_1	chr21	22769054	22769617	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-309949	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.001776	0.267730	
chunk0144_399_1	chr4	140237645	140238138	+	0	NA	Intergenic	Intergenic	-19395	NM_032547	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.024341	0.562753	
chunk0080_418_1	chr17	35783121	35783786	+	0	NA	intron (NR_111988, intron 1 of 8)	intron (NR_111988, intron 1 of 8)	12254	NM_024302	79148	Hs.380710	NM_024302	ENSG00000271447	MMP28	EPILYSIN|MM28|MMP-25|MMP-28|MMP25	matrix metallopeptidase 28	protein-coding	0.009023	0.478979	
chunk0182_448_1	chr7	101881120	101881689	+	0	NA	intron (NM_181552, intron 1 of 23)	intron (NM_181552, intron 1 of 23)	63802	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.019332	0.422807	
chunk0011_349_1	chr1	152386835	152387231	+	0	NA	Intergenic	Intergenic	-27027	NM_001014342	388698	Hs.156124	NM_001014342	ENSG00000143520	FLG2	IFPS|PSS6	filaggrin family member 2	protein-coding	0.005051	0.435768	
chunk0102_43_1	chr2	142291003	142291255	+	0	NA	Intergenic	Intergenic	-159428	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.007937	0.474308	
chunk0136_270_1	chr3	194446636	194447288	+	0	NA	exon (NM_024524, exon 13 of 32)	exon (NM_024524, exon 13 of 32)	21277	NM_024524	79572	Hs.529609	NM_024524	ENSG00000133657	ATP13A3	AFURS1	ATPase 13A3	protein-coding	0.007669	0.313936	
chunk0085_110_1	chr18	2804619	2804887	+	0	NA	3' UTR (NM_015295, exon 48 of 48)	3' UTR (NM_015295, exon 48 of 48)	-42277	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.003731	0.271375	
chunk0195_272_1	chr8	98111704	98112410	+	0	NA	intron (NM_005836, intron 1 of 5)	L1ME4b|LINE|L1	5133	NM_005836	10247	Hs.18426	NM_005836	ENSG00000132541	RIDA	HRSP12|P14.5|PSP|UK114|hp14.5	reactive intermediate imine deaminase A homolog	protein-coding	0.001416	0.333805	
chunk0008_238_1	chr1	94224903	94225155	+	0	NA	intron (NM_004815, intron 2 of 22)	intron (NM_004815, intron 2 of 22)	12722	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.003968	0.339921	
chunk0162_118_1	chr6	2838766	2839399	+	0	NA	intron (NR_073112, intron 2 of 6)	intron (NR_073112, intron 2 of 6)	2967	NR_073112	1992	Hs.381167	NM_030666	ENSG00000021355	SERPINB1	EI|ELANH2|HEL-S-27|HEL57|LEI|M/NEI|MNEI|PI-2|PI2	serpin family B member 1	protein-coding	0.004739	0.318612	
chunk0088_24_1	chr18	43634925	43635261	+	0	NA	Intergenic	Intergenic	-357443	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.002976	0.350148	
chunk0039_340_1	chr11	104994254	104994453	+	0	NA	intron (NR_024239, intron 7 of 7)	intron (NR_024239, intron 7 of 7)	-25755	NM_001225	837	Hs.138378	NM_001225	ENSG00000196954	CASP4	ICE(rel)II|ICEREL-II|ICH-2|Mih1|Mih1/TX|TX	caspase 4	protein-coding	0.000000	0.435000	
chunk0050_101_1	chr12	101919494	101919841	+	0	NA	intron (NM_018370, intron 5 of 6)	intron (NM_018370, intron 5 of 6)	42340	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.008646	0.410920	
chunk0109_285_1	chr20	8202521	8202948	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	70469	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.009368	0.413551	139(GAGTACAGTGTGTGCC,-,0.00),140(AGTACAGTGTGTGCCA,+,0.00)
chunk0004_158_1	chr1	45446455	45446900	+	0	NA	intron (NM_007170, intron 2 of 10)	L1M5|LINE|L1	44491	NM_007170	10420	Hs.591499	NM_007170	ENSG00000070759	TESK2	-	testis associated actin remodelling kinase 2	protein-coding	0.004494	0.316143	
chunk0066_344_1	chr15	37834697	37835094	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-99712	NM_152453	145942	Hs.179646	NM_152453	ENSG00000166069	TMCO5A	TMCO5	transmembrane and coiled-coil domains 5A	protein-coding	0.007557	0.374372	
chunk0043_7_1	chr12	12820071	12820422	+	0	NA	intron (NM_201224, intron 2 of 10)	intron (NM_201224, intron 2 of 10)	6900	NM_016355	51202	Hs.719938	NM_016355	ENSG00000213782	DDX47	E4-DBP|HQ0256|MSTP162|RRP3	DEAD-box helicase 47	protein-coding	0.002849	0.411932	
chunk0007_346_1	chr1	84839566	84840061	+	0	NA	intron (NM_012152, intron 2 of 2)	MIR|SINE|MIR	53400	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.004040	0.419355	
chunk0060_148_1	chr14	45069435	45069976	+	0	NA	intron (NR_131765, intron 18 of 19)	L1MD|LINE|L1	-14394	NM_017922	55015	Hs.274337	NM_017922	ENSG00000185246	PRPF39	-	pre-mRNA processing factor 39	protein-coding	0.011091	0.357934	
chunk0094_40_1	chr2	2046514	2046930	+	0	NA	intron (NM_015025, intron 4 of 24)	L1ME4b|LINE|L1	-272510	NR_024468	730811	Hs.629472	NR_024468	ENSG00000225619	MYT1L-AS1	-	MYT1L antisense RNA 1	ncRNA	0.004808	0.407674	
chunk0109_123_1	chr20	2846392	2846805	+	0	NA	intron (NM_080413, intron 1 of 19)	intron (NM_080413, intron 1 of 19)	-5355	NM_001271168	64773	Hs.29341	NM_022760	ENSG00000132635	PCED1A	C20orf81|FAM113A|bA12M19.1	PC-esterase domain containing 1A	protein-coding	0.004843	0.439614	
chunk0071_263_1	chr15	85528294	85528792	+	0	NA	intron (NM_007200, intron 3 of 36)	MIRb|SINE|MIR	-91407	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.002008	0.382766	
chunk0098_317_1	chr2	76656481	76656743	+	0	NA	Intergenic	L1MC1|LINE|L1	-329353	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.003817	0.319392	
chunk0124_249_1	chr3	56840243	56840449	+	0	NA	intron (NM_001128615, intron 4 of 12)	intron (NM_001128615, intron 4 of 12)	-38379	NM_019555	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.000000	0.425121	
chunk0011_251_1	chr1	150667031	150667620	+	0	NA	intron (NM_018178, intron 2 of 4)	intron (NM_018178, intron 2 of 4)	29871	NM_018178	55204	Hs.203699	NM_018178	ENSG00000143457	GOLPH3L	GPP34R	golgi phosphoprotein 3 like	protein-coding	0.005093	0.391525	
chunk0030_284_1	chr10	116867641	116868163	+	0	NA	intron (NM_001242699, intron 7 of 13)	intron (NM_001242699, intron 7 of 13)	18390	NM_001242699	387712	Hs.693248	NM_001242699	ENSG00000188316	ENO4	C10orf134	enolase 4	protein-coding	0.003831	0.405354	
chunk0194_223_1	chr8	86183791	86184176	+	0	NA	Intergenic	Intergenic	46392	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.000000	0.354922	
chunk0080_168_1	chr17	28497905	28498300	+	0	NA	TTS (NM_001145975)	TTS (NM_001145975)	24456	NM_003984	9058	Hs.102307	NM_003984	ENSG00000007216	SLC13A2	NADC1|NaCT|NaDC-1|SDCT1	solute carrier family 13 member 2	protein-coding	0.020253	0.606061	
chunk0172_148_1	chr6	135603256	135603689	+	0	NA	intron (NR_026805, intron 1 of 3)	MER52A|LTR|ERV1	105671	NR_026805	100131814	Hs.734007	NR_026805	ENSG00000231028	LINC00271	C6orf217|NCRNA00271	long intergenic non-protein coding RNA 271	ncRNA	0.009238	0.585253	
chunk0075_410_1	chr16	57194722	57195109	+	0	NA	intron (NM_001305163, intron 1 of 14)	intron (NM_001305163, intron 1 of 14)	8631	NM_001305164	89970	Hs.460885	NM_133368	ENSG00000159579	RSPRY1	SEMDFA	ring finger and SPRY domain containing 1	protein-coding	0.002584	0.345361	
chunk0039_222_1	chr11	101496891	101497536	+	0	NA	intron (NM_004621, intron 2 of 12)	intron (NM_004621, intron 2 of 12)	22692	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.013953	0.390093	
chunk0024_310_1	chr10	42689666	42690463	+	0	NA	intron (NR_120658, intron 1 of 3)	intron (NR_120658, intron 1 of 3)	1695	NR_120657	101929397	Hs.729796	NR_120656		LINC01518	-	long intergenic non-protein coding RNA 1518	ncRNA	0.012547	0.432331	
chunk0076_314_1	chr16	70427947	70428380	+	0	NA	intron (NM_006927, intron 1 of 6)	intron (NM_006927, intron 1 of 6)	10925	NM_006927	6483	Hs.368611	NM_006927	ENSG00000157350	ST3GAL2	Gal-NAc6S|SIAT4B|ST3GALII|ST3GalA.2	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	protein-coding	0.011547	0.573733	
chunk0054_290_1	chr13	47996762	47997157	+	0	NA	exon (NM_003850, exon 2 of 11)	exon (NM_003850, exon 2 of 11)	4367	NM_003850	8803	Hs.743361	NM_003850	ENSG00000136143	SUCLA2	A-BETA|A-SCS|MTDPS5|SCS-betaA	succinate-CoA ligase ADP-forming beta subunit	protein-coding	0.002532	0.363636	
chunk0110_24_1	chr20	10453014	10453489	+	0	NA	intron (NM_001009608, intron 1 of 7)	HAL1|LINE|L1	17948	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.012632	0.424370	
chunk0025_305_1	chr10	57539943	57540147	+	0	NA	Intergenic	Intergenic	-235486	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.000000	0.253659	
chunk0194_185_1	chr8	85197067	85197685	+	0	NA	intron (NM_001083589, intron 1 of 7)	intron (NM_001083589, intron 1 of 7)	9701	NM_001083589	1875	Hs.445758	NM_001951	ENSG00000133740	E2F5	E2F-5	E2F transcription factor 5	protein-coding	0.004854	0.355412	
chunk0049_231_1	chr12	93451689	93452224	+	0	NA	Intergenic	L2c|LINE|L2	-9706	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.003738	0.391791	
chunk0205_404_1	chr9	114746841	114747139	+	0	NA	Intergenic	Intergenic	45540	NM_001204344	9966	Hs.23349	NM_005118	ENSG00000181634	TNFSF15	TL1|TL1A|TNLG1B|VEGI|VEGI192A	TNF superfamily member 15	protein-coding	0.000000	0.391304	
chunk0007_275_1	chr1	83706556	83706955	+	0	NA	intron (NR_119375, intron 2 of 2)	intron (NR_119375, intron 2 of 2)	153791	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.002506	0.362500	
chunk0012_21_1	chr1	154936469	154937467	+	0	NA	promoter-TSS (NM_006556)	promoter-TSS (NM_006556)	40	NM_006556	10654	Hs.30954	NM_006556	ENSG00000163344	PMVK	HUMPMKI|PMK|PMKA|PMKASE|POROK1	phosphomevalonate kinase	protein-coding	0.079158	0.595596	
chunk0205_259_1	chr9	110936755	110937494	+	0	NA	intron (NM_057159, intron 4 of 4)	intron (NM_057159, intron 4 of 4)	100961	NM_057159	1902	Hs.126667	NM_001401	ENSG00000198121	LPAR1	EDG2|GPR26|Gpcr26|LPA1|Mrec1.3|VZG1|edg-2|rec.1.3|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.004060	0.421622	553(AAATACAGCATGTGCT,-,0.00),554(AATACAGCATGTGCTG,+,0.00)
chunk0074_405_1	chr16	35464789	35465522	+	0	NA	Intergenic	Intergenic	15441	NR_026980	146481	Hs.316564	NR_026980		FRG2DP	-	FSHD region gene 2 family member D, pseudogene	pseudo	0.004093	0.414169	
chunk0053_268_1	chr13	33119850	33120365	+	0	NA	intron (NM_001243476, intron 11 of 17)	intron (NM_001243476, intron 11 of 17)	65972	NM_178007	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.015534	0.408915	
chunk0129_357_1	chr3	125063009	125063388	+	0	NA	Intergenic	Intergenic	-7240	NM_020733	57493	Hs.477420	NM_020733	ENSG00000173706	HEG1	HEG|MST112|MSTP112	heart development protein with EGF like domains 1	protein-coding	0.007916	0.510526	
chunk0104_330_1	chr2	179538801	179539230	+	0	NA	intron (NR_104234, intron 4 of 12)	intron (NR_104234, intron 4 of 12)	23573	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.002331	0.427907	185(ATGTACACAATGTGCA,-,0.00)
chunk0112_194_1	chr20	40319720	40320281	+	0	NA	Intergenic	Intergenic	315539	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.014260	0.427046	445(AGGACAGTGAGACCCT,+,0.00)
chunk0047_210_1	chr12	71586031	71586276	+	0	NA	non-coding (NR_110596, exon 20 of 20)	non-coding (NR_110596, exon 20 of 20)	-77744	NM_031435	83591	Hs.245798	NM_031435	ENSG00000173451	THAP2	-	THAP domain containing 2	protein-coding	0.000000	0.239837	
chunk0103_187_1	chr2	163401063	163401362	+	0	NA	Intergenic	Intergenic	334791	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.003344	0.370000	
chunk0116_157_1	chr21	36522145	36522702	+	0	NA	intron (NM_001146077, intron 1 of 2)	intron (NM_001146077, intron 1 of 2)	20396	NM_001146078	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.028725	0.508961	
chunk0180_289_1	chr7	70081799	70082329	+	0	NA	intron (NM_015570, intron 2 of 18)	intron (NM_015570, intron 2 of 18)	483145	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.015094	0.350282	
chunk0136_369_1	chr3	196120581	196121192	+	0	NA	Intergenic	Intergenic	-21750	NR_034088	401109	Hs.280133	NM_001001699	ENSG00000224652	LINC00885	-	long intergenic non-protein coding RNA 885	ncRNA	0.013093	0.452614	
chunk0153_189_1	chr5	71663044	71663343	+	0	NA	Intergenic	Intergenic	-55970	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.006689	0.506667	
chunk0143_278_1	chr4	116935031	116935541	+	0	NA	Intergenic	L1MC2|LINE|L1	150294	NM_152402	133022	Hs.570737	NM_152402	ENSG00000174599	TRAM1L1	-	translocation associated membrane protein 1 like 1	protein-coding	0.001961	0.307241	185(TAGAACTGAAAGTTCT,-,0.00),186(AGAACTGAAAGTTCTC,+,0.00)
chunk0042_374_1	chr12	10615629	10616539	+	0	NA	Intergenic	Intergenic	-2475	NM_018048	55110	Hs.104650	NM_018048	ENSG00000111196	MAGOHB	MGN2|mago|magoh	mago homolog B, exon junction complex subunit	protein-coding	0.006593	0.362239	
chunk0089_214_1	chr18	61088771	61088986	+	0	NA	Intergenic	Intergenic	-401664	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.004651	0.453704	
chunk0191_30_1	chr8	43027117	43027593	+	0	NA	3' UTR (NM_032410, exon 22 of 22)	3' UTR (NM_032410, exon 22 of 22)	-28944	NM_002027	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.012605	0.394130	281(GAGAACATTCTGTCAT,-,0.00),282(AGAACATTCTGTCATT,+,0.00)
chunk0200_181_1	chr9	19380030	19380254	+	0	NA	promoter-TSS (NM_001010)	promoter-TSS (NM_001010)	95	NM_001010	6194	Hs.408073	NM_001010	ENSG00000137154	RPS6	S6	ribosomal protein S6	protein-coding	0.049107	0.564444	
chunk0073_99_1	chr16	4476180	4476584	+	0	NA	promoter-TSS (NM_002134).2	promoter-TSS (NM_002134).2	42	NM_001286268	3163	Hs.284279	NM_002134	ENSG00000103415	HMOX2	HO-2	heme oxygenase 2	protein-coding	0.101485	0.698765	
chunk0110_427_1	chr20	20752711	20753127	+	0	NA	Intergenic	Intergenic	-40296	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.012019	0.393285	
chunk0173_432_1	chr6	151299236	151299547	+	0	NA	intron (NM_005100, intron 2 of 4)	intron (NM_005100, intron 2 of 4)	-26140	NM_144497	9590	Hs.371240	NM_005100	ENSG00000131016	AKAP12	AKAP250|SSeCKS	A-kinase anchoring protein 12	protein-coding	0.003215	0.371795	234(TGGTACATATTGTTCC,-,0.00),235(GGTACATATTGTTCCA,+,0.00)
chunk0101_124_1	chr2	127100527	127100890	+	0	NA	intron (NM_004305, intron 1 of 14)	intron (NM_004305, intron 1 of 14)	6619	NM_139349	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.013774	0.560440	
chunk0125_263_1	chr3	69203522	69203953	+	0	NA	intron (NM_015123, intron 11 of 22)	MIRb|SINE|MIR	-81142	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.004640	0.439815	281(AAGAACTCTCAGTTCA,-,0.00),282(AGAACTCTCAGTTCAC,+,0.00)
chunk0003_82_1	chr1	31605287	31605596	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-12259	NM_001525	3061	Hs.388226	NM_001525	ENSG00000121764	HCRTR1	OX1R	hypocretin receptor 1	protein-coding	0.009709	0.354839	84(ATCACAGAGTGTACTT,+,0.00)
chunk0032_221_1	chr11	7542554	7543148	+	0	NA	intron (NM_003621, intron 1 of 23)	intron (NM_003621, intron 1 of 23)	29086	NM_003621	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.003367	0.376471	
chunk0207_429_1	chr9	137300607	137301292	+	0	NA	3' UTR (NM_001004354, exon 1 of 1)	3' UTR (NM_001004354, exon 1 of 1)	1302	NM_001004354	441478	Hs.535075	NM_001004354	ENSG00000198435	NRARP	-	NOTCH regulated ankyrin repeat protein	protein-coding	0.074453	0.602041	
chunk0023_456_1	chr10	32273814	32274377	+	0	NA	intron (NM_025209, intron 10 of 14)	intron (NM_025209, intron 10 of 14)	72953	NM_001272019	80314	Hs.167805	NM_025209	ENSG00000120616	EPC1	Epl1	enhancer of polycomb homolog 1	protein-coding	0.003552	0.310284	
chunk0028_302_1	chr10	91608458	91609239	+	0	NA	intron (NR_024467, intron 1 of 4)	intron (NR_024467, intron 1 of 4)	2612	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.014085	0.484655	
chunk0158_398_1	chr5	134648466	134648691	+	0	NA	promoter-TSS (NM_021982)	promoter-TSS (NM_021982)	-207	NM_021982	10802	Hs.595540	NM_021982	ENSG00000113615	SEC24A	-	SEC24 homolog A, COPII coat complex component	protein-coding	0.111111	0.676991	
chunk0034_198_1	chr11	32247231	32247457	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-103432	NR_132770	106635521		NR_132770		SNORA88	-	small nucleolar RNA, H/ACA box 88	snoRNA	0.000000	0.475771	
chunk0128_218_1	chr3	108080287	108080581	+	0	NA	intron (NM_198793, intron 1 of 8)	intron (NM_198793, intron 1 of 8)	10654	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.003401	0.288136	
chunk0133_451_1	chr3	175154237	175154822	+	0	NA	intron (NM_207015, intron 2 of 13)	MIR|SINE|MIR	-39287	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.003419	0.290102	342(AAGAACACTGTGTGTA,-,0.00),343(AGAACACTGTGTGTAT,+,0.00)
chunk0051_68_1	chr12	113098537	113098808	+	0	NA	TTS (NM_001193521)	TTS (NM_001193521)	36927	NM_001301202	8437	Hs.528693	NM_004658	ENSG00000111344	RASAL1	RASAL	RAS protein activator like 1	protein-coding	0.025830	0.525735	
chunk0122_226_1	chr3	33656724	33657282	+	0	NA	intron (NM_015097, intron 7 of 38)	L1ME3G|LINE|L1	2438	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.016129	0.314848	
chunk0163_39_1	chr6	8462045	8462985	+	0	NA	intron (NR_038979, intron 2 of 3)	L1PA16|LINE|L1	26892	NR_038979	100506207	Hs.311049	NR_038979	ENSG00000285219	LOC100506207	-	uncharacterized LOC100506207	ncRNA	0.007447	0.471838	292(AGAGACACTGTGTACT,-,0.00),293(GAGACACTGTGTACTG,+,0.00)
chunk0171_305_1	chr6	129207700	129208353	+	0	NA	intron (NM_001079823, intron 12 of 63)	MER110|LTR|ERV1	324885	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.003063	0.350153	
chunk0147_349_1	chr4	185651263	185651679	+	0	NA	intron (NM_001145670, intron 9 of 20)	intron (NM_001145670, intron 9 of 20)	5498	NM_001145674	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.004808	0.383693	232(GTTACAGTGTGTCCTT,+,0.00)
chunk0182_380_1	chr7	100100191	100101022	+	0	NA	promoter-TSS (NM_004722)	promoter-TSS (NM_004722)	174	NM_182776	4176	Hs.438720	NM_005916	ENSG00000166508	MCM7	CDC47|MCM2|P1.1-MCM3|P1CDC47|P85MCM|PNAS146|PPP1R104	minichromosome maintenance complex component 7	protein-coding	0.081829	0.647837	
chunk0018_289_1	chr1	220747816	220748456	+	0	NA	promoter-TSS (NM_017898)	promoter-TSS (NM_017898)	-198	NM_017898	54996	Hs.369042	NM_017898	ENSG00000117791	MARC2	MOSC2	mitochondrial amidoxime reducing component 2	protein-coding	0.064062	0.577223	
chunk0016_60_1	chr1	193341345	193341694	+	0	NA	intron (NR_125789, intron 1 of 3)	intron (NR_125789, intron 1 of 3)	36774	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.005731	0.334286	
chunk0130_130_1	chr3	131803525	131803956	+	0	NA	intron (NM_130808, intron 2 of 15)	L1ME4c|LINE|L1	182191	NR_049890	100847040		NR_049890	ENSG00000265859	MIR5704	-	microRNA 5704	ncRNA	0.006961	0.370370	176(GAGAACATGCTGTGCT,-,0.00),177(AGAACATGCTGTGCTC,+,0.00)
chunk0187_181_1	chr7	150976677	150977107	+	0	NA	intron (NM_172056, intron 1 of 8)	intron (NM_172056, intron 1 of 8)	1422	NM_172056	3757	Hs.647099	NM_000238	ENSG00000055118	KCNH2	ERG-1|ERG1|H-ERG|HERG|HERG1|Kv11.1|LQT2|SQT1	potassium voltage-gated channel subfamily H member 2	protein-coding	0.016279	0.596288	166(AGGATCATCTTGTTCC,-,0.00),167(GGATCATCTTGTTCCT,+,0.00),240(AAGCACGCGTTGTCCT,-,0.00)
chunk0068_385_1	chr15	58425300	58425670	+	0	NA	Intergenic	Intergenic	-6491	NM_000236	3990	Hs.654472	NM_000236	ENSG00000166035	LIPC	HDLCQ12|HL|HTGL|LIPH	lipase C, hepatic type	protein-coding	0.008108	0.444744	
chunk0162_462_1	chr5	180954182	180954617	+	0	NA	Intergenic	Intergenic	-34446	NM_197975	10917	Hs.225949	NM_006707	ENSG00000168903	BTNL3	BTN9.1|BTNLR	butyrophilin like 3	protein-coding	0.009195	0.433486	
chunk0046_162_1	chr12	58408405	58408946	+	0	NA	Intergenic	Intergenic	-183027	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.001848	0.411439	362(TGGCACAGTCTGTCCA,-,0.00),363(GGCACAGTCTGTCCAT,+,0.00)
chunk0171_366_1	chr6	130796447	130796646	+	0	NA	Intergenic	Intergenic	-30859	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.000000	0.440000	
chunk0088_287_1	chr18	49664105	49664666	+	0	NA	Intergenic	Intergenic	102354	NM_006033	9388	Hs.465102	NM_006033	ENSG00000101670	LIPG	EDL|EL|PRO719	lipase G, endothelial type	protein-coding	0.012478	0.542705	
chunk0011_300_1	chr1	151596157	151597005	+	0	NA	Intergenic	L2c|LINE|L2	-15605	NM_030918	81609	Hs.192326	NM_030918	ENSG00000143376	SNX27	MRT1|MY014	sorting nexin 27	protein-coding	0.005896	0.474676	291(AGACACACCATGTCCT,-,0.00),292(GACACACCATGTCCTT,+,0.00)
chunk0055_224_1	chr13	62513563	62514331	+	0	NA	Intergenic	L1MA7|LINE|L1	282745	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.002604	0.278283	
chunk0171_377_1	chr6	130964403	130964689	+	0	NA	intron (NM_001431, intron 1 of 19)	MIRb|SINE|MIR	36221	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.003497	0.299652	
chunk0118_412_1	chr22	38177968	38178479	+	0	NA	intron (NM_001199562, intron 1 of 15)	L2a|LINE|L2	3531	NM_003560	8398	Hs.170479	NM_003560	ENSG00000184381	PLA2G6	CaI-PLA2|GVI|INAD1|IPLA2-VIA|NBIA2|NBIA2A|NBIA2B|PARK14|PLA2|PNPLA9|iPLA2|iPLA2beta	phospholipase A2 group VI	protein-coding	0.017613	0.488281	213(CGGTACAGTGTGGCCC,-,0.00)
chunk0094_326_1	chr2	9010573	9011199	+	0	NA	Intergenic	Intergenic	-7139	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.006390	0.339713	
chunk0002_157_1	chr1	18166411	18166616	+	0	NA	intron (NM_032880, intron 1 of 9)	MIRb|SINE|MIR	58767	NM_032880	84966	Hs.212511	NM_032880	ENSG00000117154	IGSF21	-	immunoglobin superfamily member 21	protein-coding	0.053659	0.519417	
chunk0109_36_1	chr20	602092	602291	+	0	NA	Intergenic	Intergenic	8075	NM_004609	6939	Hs.437	NM_004609	ENSG00000125878	TCF15	EC2|PARAXIS|bHLHa40	transcription factor 15	protein-coding	0.000000	0.405000	
chunk0067_196_1	chr15	44853299	44853576	+	0	NA	Intergenic	Intergenic	-103265	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.014440	0.507194	
chunk0006_194_1	chr1	67572468	67573177	+	0	NA	Intergenic	Intergenic	-112355	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.021157	0.560563	345(CAGGACTCCCAGTCCT,-,0.00),346(AGGACTCCCAGTCCTC,+,0.00)
chunk0080_412_1	chr17	35700872	35701188	+	0	NA	intron (NM_001030006, intron 18 of 21)	intron (NM_001030006, intron 18 of 21)	-30630	NM_033315	91608	Hs.744994	NM_033315	ENSG00000270885	RASL10B	RRP17|VTS58635	RAS like family 10 member B	protein-coding	0.000000	0.365931	
chunk0164_117_1	chr6	20751425	20752094	+	0	NA	intron (NM_017774, intron 6 of 15)	intron (NM_017774, intron 6 of 15)	217302	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.004484	0.335821	
chunk0036_58_1	chr11	59156047	59156506	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	11497	NM_001312911	63901	Hs.150651	NM_022074	ENSG00000166801	FAM111A	GCLEB|KCS2	family with sequence similarity 111 member A	protein-coding	0.004357	0.317391	
chunk0180_429_1	chr7	76310682	76310898	+	0	NA	Intergenic	Intergenic	8232	NM_001540	3315	Hs.520973	NM_001540	ENSG00000106211	HSPB1	CMT2F|HEL-S-102|HMN2B|HS.76067|HSP27|HSP28|Hsp25|SRP27	heat shock protein family B (small) member 1	protein-coding	0.013889	0.594470	
chunk0206_251_1	chr9	123771532	123772239	+	0	NA	intron (NM_024820, intron 3 of 20)	intron (NM_024820, intron 3 of 20)	158253	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.002829	0.367232	
chunk0089_171_1	chr18	59547677	59548040	+	0	NA	intron (NM_133459, intron 2 of 10)	intron (NM_133459, intron 2 of 10)	149554	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.019284	0.469780	195(GAGATCATCCTGTTCT,-,0.00),196(AGATCATCCTGTTCTC,+,0.00)
chunk0037_142_1	chr11	73233630	73234286	+	0	NA	intron (NM_176071, intron 2 of 2)	MER58A|DNA|hAT-Charlie	15501	NM_176071	5029	Hs.339	NM_002564	ENSG00000175591	P2RY2	HP2U|P2RU1|P2U|P2U1|P2UR|P2Y2|P2Y2R	purinergic receptor P2Y2	protein-coding	0.016768	0.505327	
chunk0056_442_1	chr13	95150168	95150626	+	0	NA	intron (NM_001105515, intron 19 of 20)	intron (NM_001105515, intron 19 of 20)	151049	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.010917	0.424837	112(GGAACACTGTCTGCCT,+,0.00)
chunk0052_159_1	chr13	23966448	23967151	+	0	NA	Intergenic	Intergenic	-12827	NR_104595	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.008535	0.393466	
chunk0150_238_1	chr5	36033330	36033943	+	0	NA	Intergenic	Intergenic	-32608	NM_001171873	133688	Hs.254699	NM_152404	ENSG00000145626	UGT3A1	-	UDP glycosyltransferase family 3 member A1	protein-coding	0.001631	0.470684	268(CAGTACACAGTGAGCC,-,0.00),269(AGTACACAGTGAGCCT,+,0.00)
chunk0092_349_1	chr19	35357330	35357592	+	0	NA	Intergenic	L1MB7|LINE|L1	-1125	NM_005304	2865	Hs.248055	NM_005304	ENSG00000185897	FFAR3	FFA3R|GPR41|GPR42	free fatty acid receptor 3	protein-coding	0.007634	0.399240	
chunk0032_197_1	chr11	6675753	6676782	+	0	NA	Intergenic	L1MA9|LINE|L1	7134	NM_022061	63875	Hs.523456	NM_022061	ENSG00000158042	MRPL17	L17mt|LIP2|MRP-L17|MRP-L26|RPL17L|RPML26	mitochondrial ribosomal protein L17	protein-coding	0.005831	0.378641	77(CAAAACATTATGTACC,-,0.00)
chunk0108_101_1	chr2	229407251	229407500	+	0	NA	intron (NM_139072, intron 9 of 12)	intron (NM_139072, intron 9 of 12)	-136034	NM_001100818	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.040161	0.536000	
chunk0135_361_1	chr3	190641580	190642013	+	0	NA	intron (NM_002182, intron 9 of 11)	intron (NM_002182, intron 9 of 11)	127745	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.006928	0.391705	
chunk0197_232_1	chr8	123038587	123038953	+	0	NA	intron (NM_001134671, intron 1 of 7)	intron (NM_001134671, intron 1 of 7)	3653	NM_001134671	79139	Hs.241576	NM_024295	ENSG00000136986	DERL1	DER-1|DER1|derlin-1	derlin 1	protein-coding	0.008197	0.425068	
chunk0030_358_1	chr10	118706281	118706480	+	0	NA	intron (NM_153810, intron 4 of 8)	intron (NM_153810, intron 4 of 8)	48866	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.015075	0.400000	
chunk0190_319_1	chr8	38787533	38787824	+	0	NA	exon (NM_006283, exon 1 of 13)	exon (NM_006283, exon 1 of 13)	474	NM_001122824	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.099656	0.678082	213(AAGTACACGGCGTCCC,-,0.00),214(AGTACACGGCGTCCCC,+,0.00)
chunk0057_209_1	chr13	103868122	103868546	+	0	NA	Intergenic	L1MA4|LINE|L1	443134	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.007075	0.362353	214(AGATACAGAGTGTTCC,-,0.00),215(GATACAGAGTGTTCCG,+,0.00)
chunk0114_400_1	chr20	63628218	63628458	+	0	NA	non-coding (NR_132418, exon 2 of 2)	non-coding (NR_132418, exon 2 of 2)	1103	NR_132417	100505771	Hs.448392	NR_132417	ENSG00000232442	MHENCR	-	melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489	ncRNA	0.045833	0.593361	
chunk0106_21_1	chr2	195737485	195738139	+	0	NA	TTS (NM_001127257)	TTS (NM_001127257)	80684	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.006116	0.346565	
chunk0090_322_1	chr18	75754212	75754484	+	0	NA	Intergenic	MER52A|LTR|ERV1	-326645	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.003676	0.622711	
chunk0007_207_1	chr1	81484277	81484683	+	0	NA	Intergenic	Intergenic	73222	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.004926	0.402948	
chunk0074_103_1	chr16	22211825	22212416	+	0	NA	intron (NM_013302, intron 1 of 17)	intron (NM_013302, intron 1 of 17)	5849	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.016920	0.454392	383(GAAAACACAGTGTACT,-,0.00),384(AAAACACAGTGTACTG,+,0.00)
chunk0013_59_1	chr1	167211368	167211756	+	0	NA	Intergenic	L1MC4a|LINE|L1	-9267	NM_001198786	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.012887	0.393316	
chunk0065_382_1	chr14	104405571	104406273	+	0	NA	Intergenic	L1ME3A|LINE|L1	-173762	NM_001008404	400258	Hs.153827	NM_001008404	ENSG00000184601	C14orf180	C14orf77|NRAC	chromosome 14 open reading frame 180	protein-coding	0.009972	0.448080	409(CAGGACATCATGTGTT,-,0.00),410(AGGACATCATGTGTTC,+,0.00)
chunk0057_328_1	chr13	106927397	106927881	+	0	NA	Intergenic	L2c|LINE|L2	273759	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.004132	0.362887	
chunk0183_138_1	chr7	105718808	105719228	+	0	NA	intron (NM_020725, intron 3 of 11)	intron (NM_020725, intron 3 of 11)	-39856	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.007143	0.496437	2(TAGAACAGGAAGTTCA,-,0.00),3(AGAACAGGAAGTTCAG,+,0.00)
chunk0025_366_1	chr10	58629978	58630305	+	0	NA	intron (NM_001080512, intron 2 of 20)	MLT1M|LTR|ERVL-MaLR	-84874	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.006116	0.512195	
chunk0030_424_1	chr10	120337437	120338153	+	0	NA	Intergenic	Intergenic	17428	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.006983	0.365411	
chunk0156_172_1	chr5	107630204	107630695	+	0	NA	intron (NM_001962, intron 1 of 4)	Tigger3b|DNA|TcMar-Tigger	40446	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004073	0.343496	
chunk0191_426_1	chr8	57823703	57824215	+	0	NA	Intergenic	Intergenic	-154399	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.009766	0.378168	
chunk0206_6_1	chr9	115647642	115647939	+	0	NA	Intergenic	Intergenic	96449	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.003367	0.399329	130(AGGAACGGGATGTCCT,-,0.00),131(GGAACGGGATGTCCTT,+,0.00)
chunk0063_371_1	chr14	85909502	85910042	+	0	NA	Intergenic	Intergenic	-24906	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.000000	0.334566	
chunk0090_240_1	chr18	73799522	73800012	+	0	NA	Intergenic	Intergenic	347997	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.004082	0.405295	270(ATTACAGCATGTTCTC,+,0.00)
chunk0149_108_1	chr5	19133735	19134290	+	0	NA	Intergenic	L2a|LINE|L2	752260	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.001802	0.318345	
chunk0022_323_1	chr10	16409504	16409999	+	0	NA	Intergenic	Intergenic	-27192	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.008081	0.441532	
chunk0095_7_1	chr2	11776354	11776726	+	0	NA	intron (NM_001261428, intron 7 of 21)	intron (NM_001261428, intron 7 of 21)	9096	NR_036071	100422862		NR_036071	ENSG00000265056	MIR548S	-	microRNA 548s	ncRNA	0.005376	0.300268	
chunk0082_172_1	chr17	55862745	55863056	+	0	NA	Intergenic	Intergenic	111795	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.006431	0.375000	
chunk0192_210_1	chr8	65052228	65052494	+	0	NA	Intergenic	Intergenic	127979	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.000000	0.299625	
chunk0074_116_1	chr16	22388049	22388550	+	0	NA	Intergenic	MIRb|SINE|MIR	-13682	NM_001802	1039	Hs.513430	NM_001802	ENSG00000140743	CDR2	CDR62|Yo	cerebellar degeneration related protein 2	protein-coding	0.005988	0.400398	
chunk0173_438_1	chr6	151390303	151390855	+	0	NA	intron (NM_020861, intron 1 of 2)	CpG	1121	NM_020861	57621	Hs.520073	NM_020861	ENSG00000181472	ZBTB2	ZNF437	zinc finger and BTB domain containing 2	protein-coding	0.137681	0.770344	
chunk0104_4_1	chr2	170308017	170308556	+	0	NA	intron (NR_045684, intron 7 of 34)	intron (NR_045684, intron 7 of 34)	42657	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.007421	0.414815	158(CAGAACATGCTGTGAT,-,0.00)
chunk0143_272_1	chr4	116632163	116632753	+	0	NA	Intergenic	Intergenic	332733	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.000000	0.335025	255(AGAGCAGAATGTGCAT,+,0.00)
chunk0084_177_1	chr17	77530772	77531404	+	0	NA	Intergenic	Intergenic	-15853	NR_040050	100507351	Hs.514518	NR_040050		LOC100507351	-	uncharacterized LOC100507351	ncRNA	0.022152	0.442338	
chunk0084_166_1	chr17	77365732	77366245	+	0	NA	intron (NM_006640, intron 1 of 10)	intron (NM_006640, intron 1 of 10)	-7202	NM_001113493	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.017544	0.579767	299(AGGGACAGCCTGTTTC,-,0.00),300(GGGACAGCCTGTTTCT,+,0.00)
chunk0084_403_1	chr17	82204875	82205204	+	0	NA	intron (NM_198082, intron 1 of 16)	intron (NM_198082, intron 1 of 16)	7774	NM_198082	284001	Hs.631724	NM_152675	ENSG00000176155	CCDC57	-	coiled-coil domain containing 57	protein-coding	0.018237	0.527273	
chunk0078_291_1	chr17	8066727	8067016	+	0	NA	Intergenic	Intergenic	20832	NM_001139	242	Hs.136574	NM_001139	ENSG00000179477	ALOX12B	12R-LOX|ARCI2	arachidonate 12-lipoxygenase, 12R type	protein-coding	0.027682	0.496552	
chunk0081_347_1	chr17	47245418	47246300	+	0	NA	Intergenic	L1MEf|LINE|L1	-7983	NM_000212	3690	Hs.218040	NM_000212	ENSG00000259207	ITGB3	BDPLT16|BDPLT2|CD61|GP3A|GPIIIa|GT	integrin subunit beta 3	protein-coding	0.003401	0.446206	
chunk0147_300_1	chr4	184536825	184537567	+	0	NA	Intergenic	L1M6|LINE|L1	-62624	NM_002199	3660	Hs.654566	NM_002199	ENSG00000168310	IRF2	IRF-2	interferon regulatory factor 2	protein-coding	0.020216	0.479139	
chunk0016_43_1	chr1	193156720	193157022	+	0	NA	intron (NM_024529, intron 10 of 16)	L2b|LINE|L2	20368	NR_031691	100302163		NR_031691	ENSG00000221680	MIR1278	MIRN1278|hsa-mir-1278|mir-1278	microRNA 1278	ncRNA	0.009934	0.412541	
chunk0115_165_1	chr21	24941536	24942142	+	0	NA	intron (NR_046198, intron 2 of 3)	MER74A|LTR|ERVL	101289	NR_046198	339622	Hs.616316	NR_046198	ENSG00000226983	LINC01692	-	long intergenic non-protein coding RNA 1692	ncRNA	0.004950	0.406919	
chunk0007_98_1	chr1	78737151	78737810	+	0	NA	Intergenic	Intergenic	87688	NM_006417	10561	Hs.82316	NM_006417	ENSG00000137965	IFI44	MTAP44|TLDC5|p44	interferon induced protein 44	protein-coding	0.003035	0.336364	
chunk0112_286_1	chr20	43779369	43779639	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-52502	NM_001008901	149699	Hs.447626	NM_176791	ENSG00000124196	GTSF1L	C20orf65|FAM112A|dJ1028D15.4	gametocyte specific factor 1 like	protein-coding	0.003704	0.464945	67(GAAACAATTTGTTCTT,+,0.00)
chunk0109_97_1	chr20	2256191	2256589	+	0	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-39577	NM_003245	7053	Hs.2022	NM_003245	ENSG00000125780	TGM3	TGE|UHS2	transglutaminase 3	protein-coding	0.020101	0.551378	
chunk0081_265_1	chr17	43531550	43531749	+	0	NA	intron (NM_001079675, intron 8 of 12)	AluSx1|SINE|Alu	-1214	NM_001261439	2118	Hs.434059	NM_001986	ENSG00000175832	ETV4	E1A-F|E1AF|PEA3|PEAS3	ETS variant 4	protein-coding	0.015075	0.480000	
chunk0211_30_1	chrX	108168163	108168388	+	0	NA	intron (NM_001287760, intron 36 of 42)	intron (NM_001287760, intron 36 of 42)	76606	NM_178270	115201	Hs.8763	NM_052936	ENSG00000101844	ATG4A	APG4A|AUTL2	autophagy related 4A cysteine peptidase	protein-coding	0.004444	0.424779	176(AAGAACAGTTTGGTCC,-,0.00)
chunk0092_251_1	chr19	32997899	32998150	+	0	NA	intron (NM_033103, intron 10 of 14)	L2a|LINE|L2	25807	NM_152266	91442	Hs.579899	NM_152266	ENSG00000131944	FAAP24	C19orf40	FA core complex associated protein 24	protein-coding	0.035857	0.615079	
chunk0064_146_1	chr14	91621723	91622242	+	0	NA	intron (NM_024764, intron 18 of 26)	intron (NM_024764, intron 18 of 26)	110104	NM_024764	79820	Hs.131755	NM_024764	ENSG00000133962	CATSPERB	C14orf161|CatSper(beta)	cation channel sperm associated auxiliary subunit beta	protein-coding	0.005780	0.338462	
chunk0143_334_1	chr4	120281601	120281872	+	0	NA	Intergenic	L1ME3|LINE|L1	-214878	NM_002358	4085	Hs.591697	NM_002358	ENSG00000164109	MAD2L1	HSMAD2|MAD2	mitotic arrest deficient 2 like 1	protein-coding	0.000000	0.308824	
chunk0042_238_1	chr12	6312449	6313112	+	0	NA	5' UTR (NM_001144857, exon 1 of 15)	5' UTR (NM_001144857, exon 1 of 15)	129	NM_001144857	55200	Hs.631660	NM_018173	ENSG00000008323	PLEKHG6	MyoGEF	pleckstrin homology and RhoGEF domain containing G6	protein-coding	0.010558	0.590361	307(AGGTTCAGGGTGTCCC,-,0.00),308(GGTTCAGGGTGTCCCT,+,0.00)
chunk0071_215_1	chr15	84747355	84748011	+	0	NA	promoter-TSS (NM_014630)	promoter-TSS (NM_014630)	-904	NM_014630	9640	Hs.79347	NM_014630	ENSG00000166716	ZNF592	CAMOS|SCAR5	zinc finger protein 592	protein-coding	0.033537	0.547945	
chunk0151_433_1	chr5	55921424	55922230	+	0	NA	intron (NM_001242638, intron 17 of 17)	intron (NM_001242638, intron 17 of 17)	68505	NM_001242636	133396	Hs.55378	NM_139017	ENSG00000164509	IL31RA	CRL|CRL3|GLM-R|GLMR|GPL|IL-31RA|PLCA2|PRO21384|hGLM-R	interleukin 31 receptor A	protein-coding	0.013648	0.428748	356(ATTACAGAATGTTCTC,+,0.00)
chunk0199_193_1	chr9	4794689	4795158	+	0	NA	intron (NM_001286699, intron 1 of 6)	intron (NM_001286699, intron 1 of 6)	2089	NM_001286700	10171	Hs.194121	NM_005772	ENSG00000120158	RCL1	RNAC|RPCL1	RNA terminal phosphate cyclase like 1	protein-coding	0.014925	0.444681	
chunk0158_392_1	chr5	134612774	134612981	+	0	NA	intron (NM_001033503, intron 4 of 7)	LTR10C|LTR|ERV1	19966	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.014493	0.312500	180(ATGTACTTTATGTTCT,-,0.00),181(TGTACTTTATGTTCTT,+,0.00)
chunk0010_75_1	chr1	113242478	113242777	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-36374	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.013378	0.503333	
chunk0006_426_1	chr1	76390602	76390856	+	0	NA	intron (NM_152996, intron 2 of 4)	intron (NM_152996, intron 2 of 4)	316025	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.000000	0.435294	
chunk0193_421_1	chr8	80753178	80753646	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	121369	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.006410	0.460554	
chunk0034_192_1	chr11	31811920	31812233	+	0	NA	promoter-TSS (NM_001604)	promoter-TSS (NM_001604)	107	NM_001258463	5080	Hs.270303	NM_000280	ENSG00000007372	PAX6	AN|AN2|ASGD5|D11S812E|FVH1|MGDA|WAGR	paired box 6	protein-coding	0.047923	0.585987	
chunk0026_85_1	chr10	61417154	61417454	+	0	NA	intron (NM_178505, intron 4 of 5)	intron (NM_178505, intron 4 of 5)	-35335	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.000000	0.322259	
chunk0145_281_1	chr4	149716867	149717360	+	0	NA	Intergenic	MER21B|LTR|ERVL	-361161	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.004057	0.439271	85(AAGCACACTATGTGCC,-,0.00),86(AGCACACTATGTGCCA,+,0.00)
chunk0061_376_1	chr14	64137516	64138107	+	0	NA	exon (NM_015180, exon 79 of 115)	exon (NM_015180, exon 79 of 115)	-42686	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.010152	0.415541	
chunk0028_308_1	chr10	91689990	91690881	+	0	NA	Intergenic	Intergenic	-57334	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.006734	0.449552	
chunk0179_141_1	chr7	46091741	46091950	+	0	NA	Intergenic	L1PA15|LINE|L1	-170573	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.004785	0.404762	
chunk0184_22_1	chr7	111894451	111894656	+	0	NA	intron (NM_014705, intron 16 of 51)	L2c|LINE|L2	86048	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.000000	0.563107	
chunk0093_89_1	chr19	41934040	41934444	+	0	NA	Intergenic	Intergenic	25134	NM_006423	10567	Hs.11417	NM_006423	ENSG00000105404	RABAC1	PRA1|PRAF1|YIP3	Rab acceptor 1	protein-coding	0.009901	0.550617	
chunk0062_129_1	chr14	68550230	68550918	+	0	NA	intron (NM_133509, intron 10 of 10)	MamRep434|DNA|TcMar-Tigger	243340	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.007267	0.416546	371(GGAGACAGTTTGTTCT,-,0.00),372(GAGACAGTTTGTTCTT,+,0.00)
chunk0198_207_1	chr8	133806608	133807138	+	0	NA	Intergenic	Intergenic	-29521	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.003774	0.461394	349(TGGGTCAGAATGTCCC,-,0.00),350(GGGTCAGAATGTCCCT,+,0.00)
chunk0148_60_1	chr5	1966970	1967499	+	0	NA	Intergenic	Charlie5|DNA|hAT-Charlie	79903	NR_109912	101929081	Hs.519180	NR_109912	ENSG00000249326	CTD-2194D22.4	-	uncharacterized LOC101929081	ncRNA	0.011342	0.430189	
chunk0173_361_1	chr6	149371967	149372304	+	0	NA	intron (NM_001292034, intron 2 of 6)	intron (NM_001292034, intron 2 of 6)	-28224	NM_001002255	387082	Hs.657168	NM_001002255	ENSG00000177688	SUMO4	IDDM5|SMT3H4|SUMO-4|dJ281H8.4	small ubiquitin like modifier 4	protein-coding	0.005935	0.304734	
chunk0183_311_1	chr7	107958840	107959283	+	0	NA	intron (NM_002291, intron 20 of 33)	L2a|LINE|L2	44298	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.015801	0.441441	
chunk0106_383_1	chr2	207473209	207473408	+	0	NA	Intergenic	Intergenic	-56584	NM_004379	1385	Hs.516646	NM_004379	ENSG00000118260	CREB1	CREB|CREB-1	cAMP responsive element binding protein 1	protein-coding	0.025126	0.450000	
chunk0001_3_1	chr1	629818	630076	+	0	NA	promoter-TSS (NR_125957)	promoter-TSS (NR_125957)	-938	NR_125957	101928626	Hs.637667	NR_125957	ENSG00000230021	LOC101928626	-	uncharacterized LOC101928626	ncRNA	0.015504	0.428571	
chunk0113_353_1	chr20	58956353	58956552	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-24756	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.000000	0.385000	
chunk0004_152_1	chr1	45335986	45336264	+	0	NA	intron (NM_001128425, intron 1 of 15)	LTR29|LTR|ERV1	-3545	NM_025077	114034	Hs.525091	NM_025077	ENSG00000132773	TOE1	PCH7|hCaf1z	target of EGR1, exonuclease	protein-coding	0.003597	0.426523	
chunk0163_104_1	chr6	9932613	9932906	+	0	NA	Intergenic	Intergenic	-479559	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.017065	0.500000	
chunk0140_159_1	chr4	69435151	69435556	+	0	NA	Intergenic	L1M4b|LINE|L1	60555	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.002469	0.261084	
chunk0060_142_1	chr14	44995835	44996114	+	0	NA	intron (NR_131765, intron 2 of 19)	intron (NR_131765, intron 2 of 19)	33784	NM_001308120	23116	Hs.371078	NM_015091	ENSG00000198718	TOGARAM1	FAM179B|KIAA0423	TOG array regulator of axonemal microtubules 1	protein-coding	0.007168	0.335714	
chunk0184_447_1	chr7	123320047	123320259	+	0	NA	Intergenic	MER54B|LTR|ERVL	-120182	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.004717	0.497653	
chunk0097_101_1	chr2	46013555	46013911	+	0	NA	intron (NM_005400, intron 10 of 14)	intron (NM_005400, intron 10 of 14)	-283669	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.008427	0.358543	
chunk0162_112_1	chr6	2743699	2744571	+	0	NA	intron (NM_001012418, intron 2 of 12)	intron (NM_001012418, intron 2 of 12)	6785	NM_001012418	340156	Hs.127830	NM_001012418	ENSG00000145949	MYLK4	SgK085	myosin light chain kinase family member 4	protein-coding	0.021789	0.493700	
chunk0125_215_1	chr3	67563356	67563688	+	0	NA	intron (NM_001177599, intron 2 of 10)	L1ME3G|LINE|L1	91092	NM_001177599	8801	Hs.644919	NM_003848	ENSG00000172340	SUCLG2	G-SCS|GBETA|GTPSCS	succinate-CoA ligase GDP-forming beta subunit	protein-coding	0.015060	0.393393	211(CAGAACACAATGTACA,-,0.00),212(AGAACACAATGTACAA,+,0.00)
chunk0099_252_1	chr2	97890683	97891146	+	0	NA	intron (NM_015348, intron 3 of 40)	intron (NM_015348, intron 3 of 40)	104977	NM_015348	23505	Hs.469376	NM_015348	ENSG00000075568	TMEM131	CC28|PRO1048|RW1|YR-23	transmembrane protein 131	protein-coding	0.006479	0.346983	
chunk0159_434_1	chr5	148268434	148268723	+	0	NA	promoter-TSS (NM_001040129)	promoter-TSS (NM_001040129)	-282	NM_001040129	153218	Hs.483771	NM_001040129	ENSG00000214510	SPINK13	HBVDNAPTP1|HESPINTOR|LiESP6|SPINK5L3	serine peptidase inhibitor, Kazal type 13 (putative)	protein-coding	0.006920	0.458621	118(CAGTACTTCTTGTTCT,-,0.00),119(AGTACTTCTTGTTCTC,+,0.00)
chunk0065_409_1	chr14	105616187	105616503	+	0	NA	Intergenic	Intergenic	-4771	NR_107059	102466889		NR_107059	ENSG00000277030	MIR8071-2	hsa-mir-8071-2	microRNA 8071-2	ncRNA	0.044304	0.630915	
chunk0211_286_1	chrX	122382954	122383411	+	0	NA	Intergenic	Intergenic	-801061	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.006565	0.342795	
chunk0039_309_1	chr11	103175418	103176201	+	0	NA	intron (NM_001377, intron 36 of 88)	MIRc|SINE|MIR	66378	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.002554	0.302296	
chunk0170_129_1	chr6	110930706	110931404	+	0	NA	Intergenic	Intergenic	-27505	NM_138408	112495	Hs.418520	NM_138408	ENSG00000155115	GTF3C6	C6orf51|TFIIIC35|bA397G5.3	general transcription factor IIIC subunit 6	protein-coding	0.010029	0.414878	
chunk0061_80_1	chr14	56754931	56755152	+	0	NA	Intergenic	Intergenic	50622	NR_073036	5015	Hs.288655	NM_021728	ENSG00000165588	OTX2	CPHD6|MCOPS5	orthodenticle homeobox 2	protein-coding	0.013575	0.481982	
chunk0138_133_1	chr4	36730378	36731016	+	0	NA	Intergenic	Intergenic	-304269	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.003135	0.389671	
chunk0065_254_1	chr14	101505422	101506073	+	0	NA	Intergenic	Intergenic	49929	NR_002770	64150	Hs.525597	NR_002770	ENSG00000258498	DIO3OS	C14orf134|DIO3-AS1|DIO3-OS|NCRNA00041	DIO3 opposite strand upstream RNA	ncRNA	0.029186	0.565951	
chunk0112_30_1	chr20	36441191	36441865	+	0	NA	intron (NM_014902, intron 5 of 12)	L2a|LINE|L2	-19887	NM_001042486	22839	Hs.249600	NM_014902	ENSG00000080845	DLGAP4	DAP-4|DAP4|DLP4|SAPAP-4|SAPAP4	DLG associated protein 4	protein-coding	0.017804	0.536296	
chunk0092_6_1	chr19	18487486	18488117	+	0	NA	intron (NM_006532, intron 1 of 11)	intron (NM_006532, intron 1 of 11)	34326	NM_006532	8178	Hs.515260	NM_006532	ENSG00000105656	ELL	C19orf17|ELL1|MEN|PPP1R68	elongation factor for RNA polymerase II	protein-coding	0.014263	0.563291	354(CGGTACAATCTGTACT,-,0.00),355(GGTACAATCTGTACTT,+,0.00)
chunk0070_112_1	chr15	70507999	70508198	+	0	NA	Intergenic	MIRb|SINE|MIR	-107449	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.005025	0.445000	
chunk0124_200_1	chr3	55761020	55761644	+	0	NA	intron (NR_132749, intron 13 of 17)	MER53|DNA|hAT	91262	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.008013	0.366400	
chunk0172_142_1	chr6	135429172	135429568	+	0	NA	intron (NM_017651, intron 17 of 27)	intron (NM_017651, intron 17 of 27)	68395	NM_001134831	54806	Hs.386684	NM_017651	ENSG00000135541	AHI1	AHI-1|JBTS3|ORF1|dJ71N10.1	Abelson helper integration site 1	protein-coding	0.005051	0.307305	
chunk0176_459_1	chr7	20152783	20153202	+	0	NA	intron (NR_046756, intron 3 of 3)	intron (NR_046756, intron 3 of 3)	11076	NR_046756	100874041	Hs.145104	NR_046756	ENSG00000228598	MACC1-AS1	-	MACC1 antisense RNA 1	ncRNA	0.004773	0.388095	
chunk0008_374_1	chr1	96831929	96832201	+	0	NA	Intergenic	Intergenic	109427	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.311355	
chunk0039_228_1	chr11	101730304	101730597	+	0	NA	Intergenic	L1MB8|LINE|L1	-146522	NM_004621	7225	Hs.159003	NM_004621	ENSG00000137672	TRPC6	FSGS2|TRP6	transient receptor potential cation channel subfamily C member 6	protein-coding	0.006826	0.319728	
chunk0061_174_1	chr14	59936215	59936462	+	0	NA	intron (NR_075071, intron 6 of 32)	intron (NR_075071, intron 6 of 32)	16625	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.004049	0.314516	
chunk0040_105_1	chr11	111846351	111846701	+	0	NA	intron (NM_024740, intron 8 of 14)	intron (NM_024740, intron 8 of 14)	24755	NM_001077692	79796	Hs.745155	NM_024740	ENSG00000086848	ALG9	CDG1L|DIBD1|GIKANIS|LOH11CR1J	ALG9 alpha-1,2-mannosyltransferase	protein-coding	0.000000	0.350427	
chunk0005_120_1	chr1	56781045	56781465	+	0	NA	intron (NM_001004303, intron 4 of 19)	intron (NM_001004303, intron 4 of 19)	38441	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.007143	0.389549	
chunk0123_119_1	chr3	42490337	42490714	+	0	NA	intron (NM_001251882, intron 1 of 13)	intron (NM_001251882, intron 1 of 13)	1226	NM_001251882	7433	Hs.348500	NM_004624	ENSG00000114812	VIPR1	HVR1|II|PACAP-R-2|PACAP-R2|RDC1|V1RG|VAPC1|VIP-R-1|VIPR|VIRG|VPAC1|VPAC1R|VPCAP1R	vasoactive intestinal peptide receptor 1	protein-coding	0.005305	0.526455	
chunk0202_63_1	chr9	71709832	71710241	+	0	NA	intron (NM_001135820, intron 15 of 22)	intron (NM_001135820, intron 15 of 22)	58848	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.002445	0.321951	
chunk0023_122_1	chr10	23556909	23557314	+	0	NA	Intergenic	LTR88c|LTR|Gypsy?	117842	NM_001145373	220213	Hs.499042	NM_001145373	ENSG00000165312	OTUD1	DUBA7|OTDC1	OTU deubiquitinase 1	protein-coding	0.009877	0.453202	
chunk0143_136_1	chr4	109733844	109734518	+	0	NA	Intergenic	L2|LINE|L2	-4095	NM_030821	81579	Hs.389452	NM_030821	ENSG00000123739	PLA2G12A	GXII|PLA2G12|ROSSY	phospholipase A2 group XIIA	protein-coding	0.010386	0.442963	
chunk0180_399_1	chr7	75605079	75605278	+	0	NA	intron (NM_005338, intron 1 of 30)	MIR3|SINE|MIR	-77055	NR_028059	5387	Hs.659871	NM_005395	ENSG00000127957	PMS2P3	PMS2L3|PMS2L9|PMS5|PMSR3	PMS1 homolog 2, mismatch repair system component pseudogene 3	pseudo	0.010050	0.560000	
chunk0155_97_1	chr5	92369961	92370796	+	0	NA	Intergenic	Intergenic	-987046	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003593	0.344498	
chunk0064_344_1	chr14	96685979	96686717	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-110999	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.005420	0.468200	
chunk0083_373_1	chr17	71116242	71116747	+	0	NA	intron (NR_104152, intron 3 of 3)	intron (NR_104152, intron 3 of 3)	85685	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.009901	0.373518	
chunk0140_48_1	chr4	66639406	66639807	+	0	NA	Intergenic	Intergenic	362782	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.002494	0.360697	
chunk0163_28_1	chr6	8083617	8083890	+	0	NA	intron (NM_004280, intron 3 of 3)	intron (NM_004280, intron 3 of 3)	2780	NR_003703	100124533		NR_003703		SCARNA27	-	small Cajal body-specific RNA 27	ncRNA	0.018315	0.383212	
chunk0196_185_1	chr8	106046011	106046897	+	0	NA	intron (NR_125797, intron 1 of 4)	intron (NR_125797, intron 1 of 4)	14049	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.003386	0.344983	
chunk0204_300_1	chr9	100057064	100057662	+	0	NA	intron (NM_015051, intron 3 of 11)	L2c|LINE|L2	41689	NM_015051	23071	Hs.154023	NM_015051	ENSG00000023318	ERP44	PDIA10|TXNDC4	endoplasmic reticulum protein 44	protein-coding	0.003344	0.368948	
chunk0182_290_1	chr7	98276153	98276684	+	0	NA	Intergenic	L2a|LINE|L2	-5249	NM_001159491	25798	Hs.567438	NM_015379	ENSG00000164713	BRI3	I3	brain protein I3	protein-coding	0.007533	0.368421	
chunk0076_405_1	chr16	72666834	72667197	+	0	NA	Intergenic	Intergenic	-2006	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.000000	0.340659	
chunk0002_400_1	chr1	27327824	27328063	+	0	NA	intron (NR_037576, intron 1 of 6)	L2a|LINE|L2	4069	NR_033926	644961	Hs.660887	NR_033926		ACTG1P20	-	actin gamma 1 pseudogene 20	pseudo	0.008368	0.429167	
chunk0021_61_1	chr10	1212161	1212532	+	0	NA	intron (NM_018702, intron 7 of 9)	intron (NM_018702, intron 7 of 9)	52578	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.018868	0.467742	222(AGGTACATCCTGGTCT,-,0.00)
chunk0037_71_1	chr11	71192881	71193111	+	0	NA	intron (NM_012309, intron 1 of 24)	intron (NM_012309, intron 1 of 24)	31800	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.004348	0.398268	
chunk0148_179_1	chr5	7763865	7764220	+	0	NA	intron (NM_020546, intron 16 of 24)	intron (NM_020546, intron 16 of 24)	87448	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.014085	0.426966	164(GGGAACAGTGTGTTCA,-,0.00),165(GGAACAGTGTGTTCAG,+,0.00)
chunk0158_288_1	chr5	131865831	131866336	+	0	NA	intron (NM_001303622, intron 9 of 12)	L1M2|LINE|L1	-69020	NM_001008738	96459	Hs.591273	NM_133372	ENSG00000217128	FNIP1	-	folliculin interacting protein 1	protein-coding	0.001980	0.539526	
chunk0179_413_1	chr7	51690762	51691058	+	0	NA	Intergenic	L1PB4|LINE|L1	-374092	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.006757	0.306397	
chunk0059_235_1	chr14	34328710	34329738	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	133038	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.006809	0.318756	
chunk0068_1_1	chr15	50493669	50494046	+	0	NA	intron (NM_001283049, intron 12 of 16)	intron (NM_001283049, intron 12 of 16)	52848	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.007958	0.436508	
chunk0196_223_1	chr8	107436172	107436527	+	0	NA	intron (NM_001146, intron 1 of 8)	intron (NM_001146, intron 1 of 8)	61706	NM_001199859	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.005634	0.415730	
chunk0074_314_1	chr16	30551860	30552170	+	0	NA	Intergenic	Intergenic	6306	NM_001172679	92595	Hs.132227	NM_033410	ENSG00000169951	ZNF764	-	zinc finger protein 764	protein-coding	0.009677	0.488746	
chunk0189_106_1	chr8	21960092	21960801	+	0	NA	intron (NM_015024, intron 1 of 27)	intron (NM_015024, intron 1 of 27)	40777	NM_015024	23039	Hs.172685	NM_015024	ENSG00000130227	XPO7	EXP7|RANBP16	exportin 7	protein-coding	0.009873	0.412676	
chunk0139_355_1	chr4	60222832	60223359	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-699524	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.003795	0.367424	
chunk0191_396_1	chr8	57441740	57442008	+	0	NA	Intergenic	Intergenic	98087	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.000000	0.353160	
chunk0165_64_1	chr6	30946188	30946478	+	0	NA	intron (NM_080870, intron 1 of 2)	MIRb|SINE|MIR	5333	NM_080870	135656	Hs.631993	NM_080870	ENSG00000168631	MUCL3	C6orf37|DPCR1|PBLT	mucin like 3	protein-coding	0.013793	0.443299	
chunk0008_167_1	chr1	92817205	92817745	+	0	NA	Intergenic	Intergenic	-14562	NM_000969	6125	Hs.532359	NM_000969	ENSG00000122406	RPL5	L5|MSTP030|PPP1R135|uL18	ribosomal protein L5	protein-coding	0.003704	0.378928	
chunk0069_407_1	chr15	67922947	67923748	+	0	NA	Intergenic	L2a|LINE|L2	-83302	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.011236	0.411471	106(ATAACAATATGTTCCT,+,0.00)
chunk0029_260_1	chr10	103013174	103013561	+	0	NA	intron (NM_199076, intron 1 of 6)	intron (NM_199076, intron 1 of 6)	95049	NM_017649	54805	Hs.643509	NM_017649	ENSG00000148842	CNNM2	ACDP2|HOMG6|HOMGSMR	cyclin and CBS domain divalent metal cation transport mediator 2	protein-coding	0.010336	0.404639	
chunk0069_173_1	chr15	62853466	62854252	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	29902	NR_029709	406965		NR_029709	ENSG00000211137	MIR190A	MIR190|MIRN190|hsa-mir-190a|miR-190|mir-190a	microRNA 190a	ncRNA	0.012723	0.454892	215(ATGGACACACTGACCC,-,0.00)
chunk0105_434_1	chr2	193699748	193699947	+	0	NA	Intergenic	MER54A|LTR|ERVL	-644422	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.000000	0.445000	
chunk0058_169_1	chr14	23579396	23580132	+	0	NA	promoter-TSS (NM_001146028)	promoter-TSS (NM_001146028)	-964	NM_032452	84502	Hs.597841	NM_032452	ENSG00000092051	JPH4	JP4|JPHL1	junctophilin 4	protein-coding	0.000000	0.497965	312(CAGCACATCCTGACCT,-,0.00),313(AGCACATCCTGACCTT,+,0.00),348(AGGCACACACTGTCTT,-,0.00),349(GGCACACACTGTCTTC,+,0.00),432(GAGGACACTGTGTCCA,-,0.00),433(AGGACACTGTGTCCAA,+,0.00)
chunk0114_157_1	chr21	10548504	10548824	+	0	NA	intron (NM_199261, intron 7 of 23)	L1M2c|LINE|L1	27150	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.000000	0.548287	
chunk0109_395_1	chr2	240274432	240274812	+	0	NA	Intergenic	Intergenic	-133966	NM_148961	150677	Hs.148586	NM_148961	ENSG00000178602	OTOS	OTOSP	otospiralin	protein-coding	0.007895	0.349081	
chunk0175_61_1	chr7	1887820	1888326	+	0	NA	intron (NM_003550, intron 18 of 18)	(TGTG)n|Simple_repeat|Simple_repeat	-43820	NR_039799	100616160		NR_039799	ENSG00000265089	MIR4655	-	microRNA 4655	ncRNA	0.021739	0.548323	
chunk0003_139_1	chr1	32857598	32857914	+	0	NA	3' UTR (NM_001256121, exon 7 of 7)	3' UTR (NM_001256121, exon 7 of 7)	13057	NM_001171940	252995	Hs.524234	NM_153756	ENSG00000160097	FNDC5	FRCP2|irisin	fibronectin type III domain containing 5	protein-coding	0.012658	0.388013	
chunk0167_225_1	chr6	67082207	67082701	+	0	NA	Intergenic	MIR|SINE|MIR	-972897	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.004049	0.305051	
chunk0080_237_1	chr17	30115223	30115639	+	0	NA	Intergenic	L1MEc|LINE|L1	-1376	NM_032141	84081	Hs.462663	NM_032141	ENSG00000126653	NSRP1	CCDC55|HSPC095|NSrp70	nuclear speckle splicing regulatory protein 1	protein-coding	0.007212	0.352518	
chunk0208_312_1	chrX	23888911	23889597	+	0	NA	intron (NR_026545, intron 1 of 7)	L4_A_Mam|LINE|RTE-X	18686	NM_024122	79135	Hs.495851	NM_024122	ENSG00000184831	APOO	FAM121B|MIC26|MICOS26|Mic23|My025	apolipoprotein O	protein-coding	0.004373	0.393013	
chunk0163_306_1	chr6	14540293	14540575	+	0	NA	Intergenic	Intergenic	-254980	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.014184	0.561837	
chunk0168_452_1	chr6	95896285	95896557	+	0	NA	Intergenic	L1MC3|LINE|L1	-119548	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.007353	0.293040	
chunk0048_449_1	chr12	88706875	88707417	+	0	NA	Intergenic	L1PB4|LINE|L1	-126673	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.003690	0.344383	
chunk0138_180_1	chr4	37951477	37951950	+	0	NA	intron (NM_015173, intron 2 of 19)	LTR107_Mam|LTR|LTR	-8722	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.008457	0.421941	
chunk0167_183_1	chr6	63816489	63816858	+	0	NA	intron (NM_001142800, intron 36 of 42)	intron (NM_001142800, intron 36 of 42)	170147	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.013550	0.437838	
chunk0127_402_1	chr3	102424409	102425015	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-10303	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.006601	0.362438	
chunk0113_269_1	chr20	56555014	56555238	+	0	NA	Intergenic	Intergenic	21880	NM_001013646	388799	Hs.287759	NM_001013646	ENSG00000213714	FAM209B	C20orf107|dJ1153D9.4	family with sequence similarity 209 member B	protein-coding	0.008929	0.444444	
chunk0045_96_1	chr12	46083461	46083751	+	0	NA	Intergenic	LTR29|LTR|ERV1	-92988	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.003448	0.367698	
chunk0054_380_1	chr13	50149034	50149534	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	-22734	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.012000	0.391218	
chunk0030_394_1	chr10	119746155	119746497	+	0	NA	intron (NM_014937, intron 1 of 19)	intron (NM_014937, intron 1 of 19)	20279	NM_001243195	22876	Hs.369755	NM_014937	ENSG00000198825	INPP5F	MSTP007|MSTPO47|SAC2|hSAC2	inositol polyphosphate-5-phosphatase F	protein-coding	0.005848	0.443149	
chunk0036_198_1	chr11	63245839	63246657	+	0	NA	Intergenic	Intergenic	-16596	NM_199352	387601	Hs.332119	NM_199352	ENSG00000196600	SLC22A25	HIMTP|UST6	solute carrier family 22 member 25	protein-coding	0.004890	0.376068	366(AGAGACAGAGTGTTCT,-,0.00),367(GAGACAGAGTGTTCTT,+,0.00)
chunk0060_335_1	chr14	51565057	51565346	+	0	NA	intron (NR_047477, intron 2 of 3)	intron (NR_047477, intron 2 of 3)	34751	NR_047477	100874185	Hs.578226	NR_047477	ENSG00000258537	FRMD6-AS2	-	FRMD6 antisense RNA 2	ncRNA	0.010381	0.455172	
chunk0171_414_1	chr6	131388333	131388532	+	0	NA	Intergenic	Intergenic	138273	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.000000	0.485000	
chunk0190_93_1	chr8	30130006	30130568	+	0	NA	intron (NM_001128208, intron 3 of 3)	MER113A|DNA|hAT-Charlie	14397	NM_001100916	619373	Hs.627194	NM_001100916	ENSG00000177669	MBOAT4	FKSG89|GOAT|OACT4	membrane bound O-acyltransferase domain containing 4	protein-coding	0.003559	0.362345	
chunk0187_327_1	chr7	156674362	156674561	+	0	NA	intron (NR_131778, intron 7 of 8)	intron (NR_131778, intron 7 of 8)	30660	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.010050	0.515000	
chunk0091_330_1	chr19	13987465	13987707	+	0	NA	intron (NM_002918, intron 2 of 20)	intron (NM_002918, intron 2 of 20)	18736	NM_002918	5989	Hs.655215	NM_002918	ENSG00000132005	RFX1	EFC|RFX	regulatory factor X1	protein-coding	0.024793	0.617284	
chunk0058_419_1	chr13	112771906	112772105	+	0	NA	intron (NM_032189, intron 1 of 28)	LTR62|LTR|ERVL	-17274	NR_046661	100874205	Hs.658692	NR_046661	ENSG00000232684	ATP11A-AS1	-	ATP11A antisense RNA 1	ncRNA	0.040201	0.575000	
chunk0130_225_1	chr3	134238506	134238780	+	0	NA	intron (NM_002958, intron 1 of 14)	intron (NM_002958, intron 1 of 14)	12101	NM_002958	6259	Hs.654562	NM_002958	ENSG00000163785	RYK	D3S3195|JTK5|JTK5A|RYK1	receptor like tyrosine kinase	protein-coding	0.003650	0.403636	
chunk0029_79_1	chr10	96842984	96843349	+	0	NA	intron (NM_032440, intron 2 of 7)	AluJr4|SINE|Alu	10211	NM_032440	84458	Hs.427927	NM_015652	ENSG00000196233	LCOR	C10orf12|MLR2	ligand dependent nuclear receptor corepressor	protein-coding	0.005479	0.423497	
chunk0046_237_1	chr12	60256725	60257314	+	0	NA	Intergenic	Intergenic	567682	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001698	0.330508	
chunk0096_63_1	chr2	27613944	27614477	+	0	NA	intron (NM_001271318, intron 11 of 14)	intron (NM_001271318, intron 11 of 14)	-14438	NM_001145049	11321	Hs.18259	NM_007266	ENSG00000198522	GPN1	ATPBD1A|MBDIN|NTPBP|RPAP4|XAB1	GPN-loop GTPase 1	protein-coding	0.005629	0.350187	308(AAGAACTGTCTGTGCA,-,0.00),309(AGAACTGTCTGTGCAG,+,0.00)
chunk0008_417_1	chr1	98427849	98428048	+	0	NA	Intergenic	MLT1I-int|LTR|ERVL-MaLR	217237	NR_046088	729987	Hs.683961	NR_046088	ENSG00000226053	LINC01776	-	long intergenic non-protein coding RNA 1776	ncRNA	0.005025	0.395000	
chunk0006_396_1	chr1	75386502	75386701	+	0	NA	intron (NM_001130058, intron 3 of 23)	L1PA2|LINE|L1	224513	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.015075	0.400000	
chunk0004_30_1	chr1	42455847	42456100	+	0	NA	promoter-TSS (NM_001287506)	promoter-TSS (NM_001287506)	294	NM_001146192	84217	Hs.294009	NM_032257	ENSG00000066185	ZMYND12	-	zinc finger MYND-type containing 12	protein-coding	0.067194	0.614173	
chunk0067_394_1	chr15	49155670	49155905	+	0	NA	promoter-TSS (NM_004236)	promoter-TSS (NM_004236)	28	NM_001001556	2585	Hs.122006	NM_002044	ENSG00000156958	GALK2	GK2	galactokinase 2	protein-coding	0.059574	0.559322	
chunk0073_86_1	chr16	4053310	4053714	+	0	NA	intron (NM_001116, intron 2 of 10)	intron (NM_001116, intron 2 of 10)	62673	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.032178	0.469136	
chunk0083_81_1	chr17	64222447	64223598	+	0	NA	intron (NM_018469, intron 1 of 11)	intron (NM_018469, intron 1 of 11)	7734	NM_001288733	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.006950	0.381944	
chunk0130_183_1	chr3	133499092	133499585	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-74252	NM_017548	55573	Hs.518265	NM_017548	ENSG00000091527	CDV3	H41	CDV3 homolog	protein-coding	0.012170	0.388664	
chunk0094_124_1	chr2	4594091	4594297	+	0	NA	Intergenic	Intergenic	62028	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009709	0.362319	
chunk0015_214_1	chr1	187566721	187567355	+	0	NA	Intergenic	LOR1a|LTR|ERV1	123410	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007886	0.381102	
chunk0173_343_1	chr6	149054627	149055036	+	0	NA	intron (NM_005715, intron 7 of 7)	AluJb|SINE|Alu	-90147	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.009780	0.434146	
chunk0181_114_1	chr7	80647569	80647867	+	0	NA	intron (NM_001289908, intron 1 of 9)	intron (NM_001289908, intron 1 of 9)	1065	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.006711	0.394649	
chunk0171_164_1	chr6	124469345	124469749	+	0	NA	intron (NM_001300738, intron 4 of 7)	intron (NM_001300738, intron 4 of 7)	186542	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.000000	0.306173	
chunk0038_378_1	chr11	93480696	93481395	+	0	NA	intron (NM_020179, intron 2 of 2)	intron (NM_020179, intron 2 of 2)	62335	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.012876	0.447143	547(GAGAACAGCTTGTCTT,-,0.00),548(AGAACAGCTTGTCTTA,+,0.00)
chunk0116_449_1	chr21	43640324	43640693	+	0	NA	intron (NM_007031, intron 4 of 8)	L1MD2|LINE|L1	18985	NM_007031	11077	Hs.406157	NM_007031	ENSG00000160207	HSF2BP	-	heat shock transcription factor 2 binding protein	protein-coding	0.010840	0.397297	
chunk0154_178_1	chr5	80031645	80032001	+	0	NA	intron (NM_001306213, intron 2 of 22)	MLT1H|LTR|ERVL-MaLR	-3476	NM_003248	7060	Hs.211426	NM_003248	ENSG00000113296	THBS4	TSP-4|TSP4	thrombospondin 4	protein-coding	0.002809	0.394958	
chunk0205_12_1	chr9	104976123	104976596	+	0	NA	Intergenic	Intergenic	-48113	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.016913	0.424051	113(AAGTACAGTGAGTTCC,-,0.00),114(AGTACAGTGAGTTCCA,+,0.00)
chunk0161_301_1	chr5	173315088	173315757	+	0	NA	3' UTR (NM_003714, exon 4 of 4)	3' UTR (NM_003714, exon 4 of 4)	14081	NM_003714	8614	Hs.233160	NM_003714	ENSG00000113739	STC2	STC-2|STCRP	stanniocalcin 2	protein-coding	0.017937	0.405970	
chunk0210_255_1	chrX	83314324	83314586	+	0	NA	Intergenic	L1MA2|LINE|L1	-193806	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.000000	0.334601	
chunk0155_425_1	chr5	100294578	100294908	+	0	NA	Intergenic	L1M5|LINE|L1	93511	NR_027503	100133050	Hs.534796	NR_027503		LOC100133050	-	glucuronidase beta pseudogene	pseudo	0.003030	0.311178	
chunk0044_168_1	chr12	29929097	29930001	+	0	NA	Intergenic	Intergenic	-144790	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.005531	0.375691	
chunk0060_71_1	chr14	41934483	41934684	+	0	NA	Intergenic	L1MEd|LINE|L1	327022	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.014925	0.361386	
chunk0127_389_1	chr3	102180509	102181172	+	0	NA	Intergenic	Intergenic	239981	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003017	0.356928	
chunk0113_370_1	chr20	59299810	59300377	+	0	NA	promoter-TSS (NM_207034)	promoter-TSS (NM_207034)	-334	NM_207034	1908	Hs.1408	NM_000114	ENSG00000124205	EDN3	ET-3|ET3|HSCR4|PPET3|WS4B	endothelin 3	protein-coding	0.042328	0.596831	290(AAGTACACCGAGTTCC,-,0.00),291(AGTACACCGAGTTCCT,+,0.00)
chunk0141_131_1	chr4	80968207	80968570	+	0	NA	Intergenic	Intergenic	-62577	NM_001201	651	Hs.387411	NM_001201	ENSG00000152785	BMP3	BMP-3A	bone morphogenetic protein 3	protein-coding	0.008264	0.381868	
chunk0052_48_1	chr13	20924505	20924817	+	0	NA	Intergenic	Intergenic	-21887	NM_022459	64328	Hs.507452	NM_022459	ENSG00000132953	XPO4	exp4	exportin 4	protein-coding	0.006410	0.357827	
chunk0162_74_1	chr6	1817344	1817890	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	207171	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.009158	0.378428	
chunk0017_318_1	chr1	211382379	211382578	+	0	NA	promoter-TSS (NR_026761)	promoter-TSS (NR_026761)	-277	NR_026761	84791	Hs.523932	NM_032705		LINC00467	C1orf97	long intergenic non-protein coding RNA 467	ncRNA	0.030151	0.400000	
chunk0043_190_1	chr12	18998274	18998518	+	0	NA	Intergenic	L1MEf|LINE|L1	-131296	NM_001190860	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.008197	0.400000	
chunk0131_122_1	chr3	144111463	144111674	+	0	NA	Intergenic	L1ME4b|LINE|L1	138243	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.004739	0.353774	
chunk0197_176_1	chr8	121105290	121105776	+	0	NA	Intergenic	Intergenic	-293464	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.004115	0.488706	
chunk0186_48_1	chr7	136202382	136202801	+	0	NA	Intergenic	L1M5|LINE|L1	-225135	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.000000	0.254762	
chunk0004_286_1	chr1	48796328	48796542	+	0	NA	intron (NM_032785, intron 6 of 13)	intron (NM_032785, intron 6 of 13)	-19466	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.000000	0.381395	
chunk0117_202_1	chr22	21842579	21842924	+	0	NA	intron (NM_138957, intron 1 of 7)	L1ME4a|LINE|L1	24929	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.000000	0.323699	
chunk0081_29_1	chr17	37407156	37407355	+	0	NA	promoter-TSS (NM_001488)	promoter-TSS (NM_001488)	30	NM_133439	6871	Hs.500066	NM_001488	ENSG00000276234	TADA2A	ADA2|ADA2A|KL04P|TADA2L|hADA2	transcriptional adaptor 2A	protein-coding	0.060302	0.660000	
chunk0182_76_1	chr7	92336890	92337361	+	0	NA	intron (NM_019004, intron 5 of 19)	intron (NM_019004, intron 5 of 19)	90891	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.004246	0.334746	
chunk0211_152_1	chrX	113818146	113818720	+	0	NA	intron (NR_131204, intron 1 of 2)	intron (NR_131204, intron 1 of 2)	119785	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.005226	0.361739	
chunk0179_406_1	chr7	51613692	51614364	+	0	NA	Intergenic	Intergenic	-297210	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.010417	0.466568	331(GAAGACAGATTGTTCC,-,0.00),332(AAGACAGATTGTTCCT,+,0.00)
chunk0019_460_1	chr1	231425467	231425821	+	0	NA	promoter-TSS (NM_022051)	promoter-TSS (NM_022051)	-600	NM_022051	54583	Hs.444450	NM_022051	ENSG00000135766	EGLN1	C1orf12|ECYT3|HALAH|HIF-PH2|HIFPH2|HPH-2|HPH2|PHD2|SM20|ZMYND6	egl-9 family hypoxia inducible factor 1	protein-coding	0.005650	0.383099	
chunk0025_164_1	chr10	52631097	52631873	+	0	NA	Intergenic	L2a|LINE|L2	140215	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.003866	0.395109	
chunk0115_19_1	chr21	20569297	20569919	+	0	NA	Intergenic	L1MB8|LINE|L1	233500	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.003215	0.356340	
chunk0126_351_1	chr3	82874760	82875134	+	0	NA	Intergenic	L2|LINE|L2	-1113148	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.378667	
chunk0189_113_1	chr8	22137299	22137874	+	0	NA	TTS (NM_001316964)	TTS (NM_001316964)	4365	NM_001316964	80346	Hs.289063	NM_025232	ENSG00000168476	REEP4	C8orf20|PP432|Yip2c	receptor accessory protein 4	protein-coding	0.020870	0.612847	300(CAGAACTTAATGTCCC,-,0.00),301(AGAACTTAATGTCCCC,+,0.00)
chunk0099_186_1	chr2	90384374	90384656	+	0	NA	Intergenic	Intergenic	1275434	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.028369	0.346290	
chunk0061_53_1	chr14	56349799	56350511	+	0	NA	Intergenic	Intergenic	-229638	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.002809	0.441795	
chunk0134_270_1	chr3	179546757	179547143	+	0	NA	Intergenic	L1M1|LINE|L1	-15930	NM_004301	86	Hs.435326	NM_004301	ENSG00000136518	ACTL6A	ACTL6|ARPN-BETA|Arp4|BAF53A|INO80K	actin like 6A	protein-coding	0.005181	0.571059	
chunk0152_105_1	chr5	58452851	58453050	+	0	NA	Intergenic	Intergenic	7189	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.000000	0.390000	
chunk0119_151_1	chr22	43041998	43042707	+	0	NA	intron (NR_125362, intron 2 of 2)	intron (NR_125362, intron 2 of 2)	3767	NR_125362	100506679	Hs.706553	NR_125362	ENSG00000230319	LOC100506679	-	uncharacterized LOC100506679	ncRNA	0.032440	0.571831	
chunk0005_54_1	chr1	55211563	55211792	+	0	NA	intron (NM_015306, intron 1 of 67)	intron (NM_015306, intron 1 of 67)	3689	NM_015306	23358	Hs.477009	NM_015306	ENSG00000162402	USP24	-	ubiquitin specific peptidase 24	protein-coding	0.004367	0.395652	
chunk0036_356_1	chr11	66931379	66931833	+	0	NA	intron (NM_000920, intron 2 of 21)	intron (NM_000920, intron 2 of 21)	2900	NR_036121	100423029		NR_036121	ENSG00000266423	MIR3163	-	microRNA 3163	ncRNA	0.013216	0.408791	228(TGGCACACAGAGTACT,-,0.00),229(GGCACACAGAGTACTG,+,0.00)
chunk0086_105_1	chr18	14095588	14095950	+	0	NA	intron (NR_033354, intron 1 of 5)	L1M3e|LINE|L1	36721	NM_145287	162655	Hs.352635	NM_145287	ENSG00000175322	ZNF519	HsT2362	zinc finger protein 519	protein-coding	0.005525	0.559229	
chunk0012_4_1	chr1	154717413	154717839	+	0	NA	intron (NM_170782, intron 5 of 7)	intron (NM_170782, intron 5 of 7)	-89646	NM_001025107	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.018779	0.447307	183(CAGAACACGGAGTCCA,-,0.00),184(AGAACACGGAGTCCAG,+,0.00)
chunk0045_37_1	chr12	44484784	44485354	+	0	NA	Intergenic	L2a|LINE|L2	390592	NM_001145109	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.001754	0.343257	
chunk0016_179_1	chr1	198087691	198088140	+	0	NA	Intergenic	L2c|LINE|L2	-69063	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.002227	0.417778	
chunk0001_185_1	chr1	7270542	7270896	+	0	NA	intron (NM_015215, intron 5 of 22)	FLAM_A|SINE|Alu	485395	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.002825	0.388732	
chunk0014_43_1	chr1	175138597	175138906	+	0	NA	intron (NM_022093, intron 17 of 18)	Tigger3b|DNA|TcMar-Tigger	54062	NM_001162895	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.006472	0.419355	99(GAAGACAGGCTGTGCT,-,0.00),100(AAGACAGGCTGTGCTA,+,0.00)
chunk0189_415_1	chr8	27750497	27750702	+	0	NA	intron (NM_018246, intron 5 of 8)	intron (NM_018246, intron 5 of 8)	22054	NR_130761	55246	Hs.445512	NM_018246	ENSG00000147419	CCDC25	-	coiled-coil domain containing 25	protein-coding	0.014634	0.456311	
chunk0152_166_1	chr5	59523360	59523904	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	62866	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.003676	0.370642	139(AGCACACCTTGTTTTG,+,0.00)
chunk0041_208_1	chr11	126824141	126824495	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	-116428	NR_046986	100874251	Hs.319053	NR_046986	ENSG00000254960	KIRREL3-AS2	-	KIRREL3 antisense RNA 2	ncRNA	0.011299	0.478873	
chunk0093_37_1	chr19	39430588	39431144	+	0	NA	Intergenic	MER6B|DNA|TcMar-Tigger	5112	NM_001020	6217	Hs.397609	NM_001020	ENSG00000105193	RPS16	S16	ribosomal protein S16	protein-coding	0.028777	0.482944	
chunk0152_403_1	chr5	64917525	64917827	+	0	NA	intron (NM_001297644, intron 11 of 12)	MLT2B4|LTR|ERVL	148758	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.000000	0.448845	
chunk0141_312_1	chr4	87131289	87132079	+	0	NA	intron (NM_001313959, intron 16 of 19)	intron (NM_001313959, intron 16 of 19)	88584	NM_001292003	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.006329	0.364096	
chunk0210_93_1	chrX	71212554	71212814	+	0	NA	Intergenic	Intergenic	-2528	NM_001097642	2705	Hs.333303	NM_000166	ENSG00000169562	GJB1	CMTX|CMTX1|CX32	gap junction protein beta 1	protein-coding	0.011538	0.421456	
chunk0212_33_1	chrY	11099544	11099905	+	0	NA	Intergenic	GSATII|Satellite|centr	1188926	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.047091	0.621547	
chunk0076_116_1	chr16	66544364	66544660	+	0	NA	intron (NM_001272050, intron 2 of 9)	L2a|LINE|L2	5313	NM_001272050	7084	Hs.512619	NM_004614	ENSG00000166548	TK2	MTDPS2|MTTK|PEOB3|SCA31	thymidine kinase 2	protein-coding	0.016892	0.454545	
chunk0106_293_1	chr2	204424376	204424995	+	0	NA	Intergenic	L1PA15|LINE|L1	-121108	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.006462	0.346774	312(TAAACAACCTGTTCCT,+,0.00)
chunk0041_329_1	chr11	130242820	130243438	+	0	NA	intron (NM_014155, intron 2 of 5)	L1ME3B|LINE|L1	71583	NM_001301099	29068	Hs.721470	NM_014155	ENSG00000196323	ZBTB44	BTBD15|HSPC063|ZNF851	zinc finger and BTB domain containing 44	protein-coding	0.006472	0.363489	
chunk0086_403_1	chr18	26747026	26747251	+	0	NA	Intergenic	Intergenic	-43500	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.004444	0.323009	
chunk0135_217_1	chr3	188516687	188516932	+	0	NA	intron (NM_001167671, intron 4 of 10)	MER5A|DNA|hAT-Charlie	51857	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.008163	0.447154	
chunk0086_166_1	chr18	21704531	21704730	+	0	NA	exon (NM_138340, exon 1 of 9)	exon (NM_138340, exon 1 of 9)	175	NM_001308256	171586	Hs.397978	NM_138340	ENSG00000158201	ABHD3	LABH3	abhydrolase domain containing 3	protein-coding	0.100503	0.700000	
chunk0106_4_1	chr2	195341569	195342254	+	0	NA	Intergenic	Intergenic	-314897	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.004380	0.360058	
chunk0073_246_1	chr16	11704042	11704510	+	0	NA	intron (NM_001303447, intron 5 of 12)	L1MC4a|LINE|L1	35843	NM_003498	8303	Hs.618526	NM_003498	ENSG00000184602	SNN	-	stannin	protein-coding	0.002137	0.368870	227(GAGAACAGTCAGCTCT,-,0.00),228(AGAACAGTCAGCTCTT,+,0.00)
chunk0036_192_1	chr11	63144425	63144851	+	0	NA	promoter-TSS (NM_001136506)	promoter-TSS (NM_001136506)	-417	NM_173586	283238	Hs.375139	NM_173586	ENSG00000197658	SLC22A24	NET46	solute carrier family 22 member 24	protein-coding	0.002347	0.332553	241(AGATACACAGTGTGCT,-,0.00)
chunk0024_85_1	chr10	34415307	34415849	+	0	NA	intron (NM_001184790, intron 4 of 22)	intron (NM_001184790, intron 4 of 22)	399747	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.005535	0.377532	
chunk0199_46_1	chr9	1411898	1412168	+	0	NA	Intergenic	Intergenic	361413	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.003704	0.435424	
chunk0020_439_1	chr1	242007404	242008035	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-8636	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.007924	0.469937	409(AAGCACTGGATGTGCT,-,0.00),410(AGCACTGGATGTGCTG,+,0.00)
chunk0095_190_1	chr2	18005485	18005812	+	0	NA	Intergenic	Intergenic	126991	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.003058	0.320122	
chunk0153_45_1	chr5	67257477	67257972	+	0	NA	Intergenic	Intergenic	-60935	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.006061	0.364919	183(AGGTACAGAAAGTTCC,-,0.00),184(GGTACAGAAAGTTCCT,+,0.00)
chunk0168_324_1	chr6	92431830	92432157	+	0	NA	Intergenic	Intergenic	-741565	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.003058	0.307927	
chunk0186_22_1	chr7	135800894	135801436	+	0	NA	Intergenic	Intergenic	-52319	NM_205855	389558	Hs.55200	NM_205855	ENSG00000189320	FAM180A	UNQ1940	family with sequence similarity 180 member A	protein-coding	0.018450	0.406998	
chunk0202_326_1	chr9	78371467	78372261	+	0	NA	Intergenic	Intergenic	74789	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.006297	0.382390	
chunk0127_408_1	chr3	102480187	102480603	+	0	NA	TTS (NM_175056)	TTS (NM_175056)	45380	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.004808	0.431655	152(AGGATCTGGCTGTCCT,-,0.00),153(GGATCTGGCTGTCCTC,+,0.00)
chunk0071_359_1	chr15	88804546	88805093	+	0	NA	intron (NM_013227, intron 1 of 17)	intron (NM_013227, intron 1 of 17)	1376	NM_001135	176	Hs.2159	NM_001135	ENSG00000157766	ACAN	AGC1|AGCAN|CSPG1|CSPGCP|MSK16|SEDK|SSOAOD	aggrecan	protein-coding	0.012797	0.521898	
chunk0073_375_1	chr16	15672666	15673090	+	0	NA	intron (NM_017668, intron 3 of 8)	intron (NM_017668, intron 3 of 8)	22652	NM_017668	54820	Hs.655378	NM_017668	ENSG00000072864	NDE1	HOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1	nudE neurodevelopment protein 1	protein-coding	0.037736	0.538824	
chunk0157_93_1	chr5	116675835	116676071	+	0	NA	Intergenic	Intergenic	86256	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.004237	0.362869	
chunk0211_396_1	chrX	128504821	128505431	+	0	NA	Intergenic	MER70A|LTR|ERVL	-452723	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.001639	0.418985	330(CAGGACATTCTGTCCT,-,0.00),331(AGGACATTCTGTCCTA,+,0.00)
chunk0007_144_1	chr1	79363519	79363948	+	0	NA	Intergenic	Intergenic	-356923	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.004662	0.353488	235(GGGAACTTGCTGTACC,-,0.00),236(GGAACTTGCTGTACCT,+,0.00)
chunk0168_458_1	chr6	96040945	96041758	+	0	NA	intron (NM_006581, intron 1 of 2)	intron (NM_006581, intron 1 of 2)	25382	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.003690	0.374693	
chunk0161_250_1	chr5	171783042	171783320	+	0	NA	Intergenic	L1MD2|LINE|L1	-2691	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.003597	0.326165	
chunk0052_22_1	chr13	20195009	20195256	+	0	NA	Intergenic	Intergenic	-2157	NM_004004	2706	Hs.524894	NM_004004	ENSG00000165474	GJB2	CX26|DFNA3|DFNA3A|DFNB1|DFNB1A|HID|KID|NSRD1|PPK	gap junction protein beta 2	protein-coding	0.008097	0.439516	121(ATGTACATAGTGTCCT,-,0.00),122(TGTACATAGTGTCCTC,+,0.00)
chunk0063_216_1	chr14	81437409	81437723	+	0	NA	Intergenic	Intergenic	-10162	NM_001256430	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.003185	0.412698	
chunk0040_416_1	chr11	121131926	121132679	+	0	NA	intron (NM_005422, intron 9 of 22)	L1MC4|LINE|L1	29636	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.014608	0.385942	
chunk0186_447_1	chr7	148153481	148153961	+	0	NA	intron (NM_014141, intron 17 of 23)	intron (NM_014141, intron 17 of 23)	-436844	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.012500	0.559252	
chunk0062_83_1	chr14	67853827	67854207	+	0	NA	intron (NM_133509, intron 4 of 10)	intron (NM_133509, intron 4 of 10)	34238	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.005263	0.367454	
chunk0013_182_1	chr1	168991638	168991921	+	0	NA	intron (NR_104091, intron 3 of 4)	intron (NR_104091, intron 3 of 4)	95226	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.007067	0.419014	
chunk0100_419_1	chr2	119877169	119877398	+	0	NA	intron (NM_002830, intron 3 of 26)	intron (NM_002830, intron 3 of 26)	117652	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.000000	0.326087	
chunk0078_381_1	chr16	87762432	87763068	+	0	NA	intron (NM_017566, intron 1 of 11)	intron (NM_017566, intron 1 of 11)	3242	NM_017566	54758	Hs.123450	NM_017566	ENSG00000104731	KLHDC4	-	kelch domain containing 4	protein-coding	0.018868	0.532182	
chunk0181_271_1	chr7	86201819	86202156	+	0	NA	Intergenic	MER52A|LTR|ERV1	-441927	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.011869	0.585799	
chunk0044_412_1	chr12	41163730	41164114	+	0	NA	Intergenic	Intergenic	-24526	NM_001164595	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.013021	0.332468	
chunk0203_155_1	chr9	85795329	85795688	+	0	NA	Intergenic	L2b|LINE|L2	-10494	NR_029410	389765	Hs.715986	NR_029410		LOC389765	-	kinesin family member 27 pseudogene	pseudo	0.005571	0.388889	
chunk0030_10_1	chr10	110846289	110846509	+	0	NA	Intergenic	Intergenic	24505	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.004545	0.520362	198(GAGCACAGCCTCTCCC,-,0.00)
chunk0144_429_1	chr4	140739716	140740188	+	0	NA	intron (NM_015130, intron 1 of 20)	intron (NM_015130, intron 1 of 20)	16365	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.004237	0.410148	
chunk0104_383_1	chr2	180353936	180354426	+	0	NA	Intergenic	L1PBb|LINE|L1	-337923	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.008163	0.344196	
chunk0182_333_1	chr7	99134102	99134533	+	0	NA	intron (NM_020429, intron 1 of 18)	intron (NM_020429, intron 1 of 18)	9803	NM_020429	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.013921	0.368056	
chunk0101_326_1	chr2	135985062	135985299	+	0	NA	promoter-TSS (NR_110200)	promoter-TSS (NR_110200)	4	NR_110200	101928243	Hs.602178	NR_110199	ENSG00000231890	DARS-AS1	-	DARS antisense RNA 1	ncRNA	0.080169	0.668067	
chunk0145_391_1	chr4	152288858	152289233	+	0	NA	Intergenic	MIR|SINE|MIR	-48610	NR_104273	102191832	Hs.712524	NR_104273	ENSG00000270751	FBXW7-AS1	DEAR|DEspR	FBXW7 antisense RNA 1	ncRNA	0.008000	0.375000	
chunk0174_204_1	chr6	160218886	160219144	+	0	NA	intron (NM_003058, intron 10 of 10)	intron (NM_003058, intron 10 of 10)	39916	NM_003058	6582	Hs.436385	NM_003058	ENSG00000112499	SLC22A2	OCT2	solute carrier family 22 member 2	protein-coding	0.007752	0.467181	
chunk0158_282_1	chr5	131683815	131684109	+	0	NA	intron (NM_001008738, intron 10 of 16)	Tigger17a|DNA|TcMar-Tigger	-48726	NM_001164389	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.000000	0.362712	
chunk0170_83_1	chr6	109922008	109922595	+	0	NA	Intergenic	Intergenic	-55955	NM_001286099	2830	Hs.46332	NM_005284	ENSG00000146360	GPR6	-	G protein-coupled receptor 6	protein-coding	0.008518	0.430272	155(GAGGACATACTGTACA,-,0.00),156(AGGACATACTGTACAG,+,0.00)
chunk0042_167_1	chr12	4506314	4507154	+	0	NA	intron (NM_001304811, intron 9 of 13)	intron (NM_001304811, intron 9 of 13)	31774	NM_001304811	57102	Hs.302977	NM_020374	ENSG00000047621	C12orf4	-	chromosome 12 open reading frame 4	protein-coding	0.007143	0.315101	
chunk0126_200_1	chr3	78610628	78610829	+	0	NA	intron (NM_133631, intron 26 of 28)	intron (NM_133631, intron 26 of 28)	408731	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.306931	
chunk0149_35_1	chr5	16385701	16386061	+	0	NA	intron (NR_104625, intron 7 of 8)	intron (NR_104625, intron 7 of 8)	55221	NR_104625	101929505	Hs.639360	NR_104625	ENSG00000248150	LINC02150	-	long intergenic non-protein coding RNA 2150	ncRNA	0.005556	0.382271	
chunk0136_253_1	chr4	10256231	10256561	+	0	NA	Intergenic	Intergenic	-139447	NM_017491	9948	Hs.128548	NM_005112	ENSG00000071127	WDR1	AIP1|HEL-S-52|NORI-1	WD repeat domain 1	protein-coding	0.009091	0.459215	
chunk0015_171_1	chr1	186736047	186736659	+	0	NA	Intergenic	L2c|LINE|L2	55699	NR_125801	103752588	Hs.441636	NR_125801	ENSG00000273129	PACERR	PACER|PTGS2-AS1|PTGS2AS1	PTGS2 antisense NFKB1 complex-mediated expression regulator RNA	ncRNA	0.000000	0.321370	
chunk0199_325_1	chr9	8007669	8007868	+	0	NA	Intergenic	L1PA3|LINE|L1	-207969	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.000000	0.520000	
chunk0069_92_1	chr15	61273373	61273602	+	0	NA	Intergenic	Intergenic	-44184	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.017467	0.343478	80(TAGCACAGTGCGTTCC,-,0.00),81(AGCACAGTGCGTTCCA,+,0.00)
chunk0065_292_1	chr14	102691313	102692132	+	0	NA	intron (NM_015156, intron 3 of 11)	intron (NM_015156, intron 3 of 11)	-85757	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.008547	0.365854	
chunk0117_208_1	chr22	21867590	21867789	+	0	NA	promoter-TSS (NM_002745)	promoter-TSS (NM_002745)	-9	NM_138957	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.135678	0.765000	
chunk0163_365_1	chr6	15770145	15770962	+	0	NA	Intergenic	Intergenic	-107495	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.002448	0.469438	
chunk0150_167_1	chr5	34043332	34043744	+	0	NA	promoter-TSS (NM_030945)	promoter-TSS (NM_030945)	-272	NM_030945	114899	Hs.171929	NM_030945	ENSG00000082196	C1QTNF3	C1ATNF3|CORCS|CORS|CORS-26|CORS26|CTRP3	C1q and TNF related 3	protein-coding	0.012136	0.452785	
chunk0150_176_1	chr5	34468468	34468750	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-187719	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.000000	0.346290	
chunk0059_95_1	chr14	30947947	30948383	+	0	NA	intron (NM_001083893, intron 4 of 17)	intron (NM_001083893, intron 4 of 17)	-58357	NR_038356	100506071	Hs.729195	NR_038356	ENSG00000258525	LOC100506071	-	uncharacterized LOC100506071	ncRNA	0.000000	0.331808	
chunk0017_312_1	chr1	211236596	211236859	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-22639	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.007605	0.390152	
chunk0099_294_1	chr2	98800523	98801081	+	0	NA	intron (NM_207362, intron 7 of 9)	intron (NM_207362, intron 7 of 9)	-28904	NR_126337	101927070	Hs.469395	NR_126337		LINC02611	-	long intergenic non-protein coding RNA 2611	ncRNA	0.010753	0.502683	
chunk0010_239_1	chr1	116451907	116452570	+	0	NA	TTS (NR_125973)	TTS (NR_125973)	26588	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.003017	0.456325	
chunk0191_152_1	chr8	48945751	48946437	+	0	NA	Intergenic	L1P2|LINE|L1	-24654	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.002915	0.494905	
chunk0014_60_1	chr1	175790987	175791616	+	0	NA	Intergenic	Intergenic	-47685	NM_003285	7143	Hs.659864	NM_003285	ENSG00000116147	TNR	TN-R	tenascin R	protein-coding	0.003180	0.468254	268(CAGTACACTAAGTTCC,-,0.00),269(AGTACACTAAGTTCCA,+,0.00)
chunk0173_217_1	chr6	145744605	145744815	+	0	NA	intron (NR_038246, intron 1 of 2)	intron (NR_038246, intron 1 of 2)	-8855	NM_001018041	7957	Hs.486696	NM_005670	ENSG00000112425	EPM2A	EPM2|MELF	EPM2A glucan phosphatase, laforin	protein-coding	0.000000	0.322275	
chunk0183_267_1	chr7	107436594	107437152	+	0	NA	intron (NM_006348, intron 6 of 21)	intron (NM_006348, intron 6 of 21)	-33184	NM_005295	2845	Hs.657277	NM_005295	ENSG00000172209	GPR22	-	G protein-coupled receptor 22	protein-coding	0.005376	0.286225	
chunk0044_162_1	chr12	29864642	29864851	+	0	NA	Intergenic	Intergenic	-79987	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.004785	0.447619	
chunk0176_147_1	chr7	12942600	12943021	+	0	NA	Intergenic	Intergenic	255524	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.007126	0.407583	
chunk0198_144_1	chr8	132898662	132899595	+	0	NA	intron (NM_003235, intron 14 of 47)	MIRc|SINE|MIR	32168	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.011790	0.453961	
chunk0034_58_1	chr11	27108737	27109259	+	0	NA	intron (NM_003986, intron 5 of 8)	intron (NM_003986, intron 5 of 8)	68036	NM_003986	8424	Hs.591996	NM_003986	ENSG00000129151	BBOX1	BBH|BBOX|G-BBH|gamma-BBH	gamma-butyrobetaine hydroxylase 1	protein-coding	0.007663	0.353728	
chunk0208_131_1	chrX	15589565	15589909	+	0	NA	intron (NM_021804, intron 5 of 18)	MIRb|SINE|MIR	12332	NM_021804	59272	Hs.178098	NM_021804	ENSG00000130234	ACE2	ACEH	angiotensin I converting enzyme 2	protein-coding	0.000000	0.292754	
chunk0035_375_1	chr11	49477624	49478010	+	0	NA	Intergenic	Intergenic	-80711	NR_027044	440040	Hs.655746	NR_027044	ENSG00000205035	LOC440040	-	glutamate metabotropic receptor 5 pseudogene	pseudo	0.002591	0.359173	
chunk0024_23_1	chr10	33092337	33093133	+	0	NA	Intergenic	Intergenic	-134370	NM_002211	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.010050	0.429109	128(GAGCACAGTTAGTCCC,-,0.00),129(AGCACAGTTAGTCCCT,+,0.00),456(AGGGACTAAATGTGCT,-,0.00),457(GGGACTAAATGTGCTC,+,0.00)
chunk0204_251_1	chr9	98099819	98100164	+	0	NA	exon (NM_033219, exon 3 of 7)	exon (NM_033219, exon 3 of 7)	19362	NM_033219	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.011594	0.479769	
chunk0183_345_1	chr7	108524675	108525200	+	0	NA	intron (NM_001256011, intron 1 of 10)	intron (NM_001256011, intron 1 of 10)	1381	NM_001256009	50640	Hs.617340	NM_015723	ENSG00000135241	PNPLA8	IPLA2-2|IPLA2G|MMLA|PNPLA-gamma|iPLA2gamma	patatin like phospholipase domain containing 8	protein-coding	0.019048	0.389734	272(AAGTACAGGCTGTTCT,-,0.00),273(AGTACAGGCTGTTCTT,+,0.00)
chunk0103_321_1	chr2	167610416	167610617	+	0	NA	Intergenic	Intergenic	-208156	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.004975	0.341584	
chunk0207_77_1	chrX	9302429	9302788	+	0	NA	Intergenic	Intergenic	-160687	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.011142	0.438889	203(AGGAACACACAGTTCT,-,0.00),204(GGAACACACAGTTCTT,+,0.00)
chunk0163_247_1	chr6	12484704	12485128	+	0	NA	Intergenic	Intergenic	194620	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.007075	0.362353	
chunk0096_326_1	chr2	33599309	33599603	+	0	NA	promoter-TSS (NM_015475)	promoter-TSS (NM_015475)	-94	NM_015475	25940	Hs.468140	NM_015475	ENSG00000119812	FAM98A	-	family with sequence similarity 98 member A	protein-coding	0.088435	0.637288	
chunk0140_447_1	chr4	76373806	76374598	+	0	NA	intron (NM_001042784, intron 8 of 23)	intron (NM_001042784, intron 8 of 23)	33103	NM_001042784	339965	Hs.529680	NM_178555	ENSG00000163749	CCDC158	-	coiled-coil domain containing 158	protein-coding	0.008838	0.385876	362(AAGTACTTCTTGTGCT,-,0.00)
chunk0166_117_1	chr6	44557796	44558070	+	0	NA	Intergenic	Intergenic	122292	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.014599	0.494545	139(GGAAACAGCCTGTACT,-,0.00),140(GAAACAGCCTGTACTA,+,0.00)
chunk0188_239_1	chr8	13620773	13621383	+	0	NA	Intergenic	Intergenic	54235	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.006557	0.340426	
chunk0067_10_1	chr15	39979664	39980392	+	0	NA	intron (NM_001013703, intron 13 of 38)	intron (NM_001013703, intron 13 of 38)	45904	NM_001013703	440275	Hs.656673	NM_001013703	ENSG00000128829	EIF2AK4	GCN2|PVOD2	eukaryotic translation initiation factor 2 alpha kinase 4	protein-coding	0.010989	0.334705	
chunk0004_194_1	chr1	46395925	46397020	+	0	NA	intron (NM_001441, intron 1 of 14)	LTR5B|LTR|ERVK	2205	NM_001441	2166	Hs.720143	NM_001441	ENSG00000117480	FAAH	FAAH-1|PSAB	fatty acid amide hydrolase	protein-coding	0.014612	0.462591	
chunk0012_330_1	chr1	162526167	162526642	+	0	NA	3' UTR (NM_001184763, exon 8 of 8)	3' UTR (NM_001184763, exon 8 of 8)	28599	NM_175866	127933	Hs.127310	NM_144624	ENSG00000152332	UHMK1	KIS|KIST|P-CIP2	U2AF homology motif kinase 1	protein-coding	0.002105	0.348739	
chunk0207_399_1	chr9	136789550	136789749	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-1676	NM_032928	85014	Hs.356744	NM_032928	ENSG00000244187	TMEM141	-	transmembrane protein 141	protein-coding	0.005025	0.415000	
chunk0104_21_1	chr2	170647885	170648396	+	0	NA	intron (NR_045684, intron 32 of 34)	intron (NR_045684, intron 32 of 34)	66427	NR_027433	440925	Hs.668461	NM_001013712	ENSG00000222033	LINC01124	-	long intergenic non-protein coding RNA 1124	ncRNA	0.009785	0.447266	
chunk0047_33_1	chr12	66315879	66316328	+	0	NA	intron (NM_033647, intron 6 of 13)	Tigger3a|DNA|TcMar-Tigger	13548	NM_033647	92797	Hs.505941	NM_033647	ENSG00000127311	HELB	DHB|hDHB	DNA helicase B	protein-coding	0.008909	0.360000	
chunk0091_4_1	chr19	2543698	2544490	+	0	NA	intron (NM_052847, intron 3 of 4)	intron (NM_052847, intron 3 of 4)	67969	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.037879	0.578815	439(GAGAACACAGTGTTCA,-,0.00),440(AGAACACAGTGTTCAG,+,0.00)
chunk0086_416_1	chr18	26983008	26983224	+	0	NA	intron (NM_031422, intron 4 of 5)	intron (NM_031422, intron 4 of 5)	-117364	NM_001650	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.009259	0.451613	
chunk0088_397_1	chr18	54425859	54426578	+	0	NA	Intergenic	Intergenic	65690	NM_001288982	162681	Hs.208701	NM_173529	ENSG00000166845	C18orf54	LAS2	chromosome 18 open reading frame 54	protein-coding	0.002782	0.373611	372(CAGGACAACCTGTCCC,-,0.00),373(AGGACAACCTGTCCCT,+,0.00)
chunk0151_220_1	chr5	50895774	50896121	+	0	NA	Intergenic	Intergenic	74240	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.000000	0.330460	
chunk0190_255_1	chr8	37003415	37004338	+	0	NA	Intergenic	L2a|LINE|L2	219552	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.004334	0.418831	
chunk0062_25_1	chr14	66926220	66926471	+	0	NA	intron (NM_020806, intron 8 of 22)	L1MA3|LINE|L1	-263048	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.003984	0.329365	
chunk0115_304_1	chr21	28439720	28440423	+	0	NA	Intergenic	Intergenic	-99247	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.008535	0.345170	372(GAGTACAGCATGTGCT,-,0.00),373(AGTACAGCATGTGCTG,+,0.00)
chunk0038_234_1	chr11	87036866	87037369	+	0	NA	promoter-TSS (NR_033149)	promoter-TSS (NR_033149)	-727	NM_022918	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.017893	0.428571	
chunk0165_153_1	chr6	33730540	33731163	+	0	NA	intron (NM_054111, intron 2 of 5)	intron (NM_054111, intron 2 of 5)	16134	NM_001142883	117283	Hs.17253	NM_054111	ENSG00000161896	IP6K3	IHPK3|INSP6K3	inositol hexakisphosphate kinase 3	protein-coding	0.024077	0.564103	266(AAGGACAGGCTGTTCC,-,0.00),267(AGGACAGGCTGTTCCA,+,0.00),361(CTGGTCATTCTGTTCC,-,0.00)
chunk0152_416_1	chr5	65651090	65651669	+	0	NA	intron (NM_024941, intron 6 of 12)	AluJr|SINE|Alu	26648	NM_001093756	80006	Hs.591760	NM_024941	ENSG00000113597	TRAPPC13	C5orf44|SHLD3	trafficking protein particle complex 13	protein-coding	0.008636	0.412069	
chunk0189_165_1	chr8	23284364	23284699	+	0	NA	Intergenic	Intergenic	-3561	NR_125897	203069	Hs.458644	NM_001136108	ENSG00000104679	R3HCC1	-	R3H domain and coiled-coil containing 1	protein-coding	0.002985	0.377976	
chunk0034_154_1	chr11	30230046	30230502	+	0	NA	promoter-TSS (NM_001018080)	promoter-TSS (NM_001018080)	-742	NM_001018080	2488	Hs.36975	NM_000510	ENSG00000131808	FSHB	HH24	follicle stimulating hormone subunit beta	protein-coding	0.000000	0.391685	
chunk0050_446_1	chr12	110533521	110534018	+	0	NA	TTS (NM_139283)	TTS (NM_139283)	31426	NM_001286534	144715	Hs.97794	NM_152442	ENSG00000151164	RAD9B	-	RAD9 checkpoint clamp component B	protein-coding	0.012072	0.389558	
chunk0179_115_1	chr7	45366501	45366854	+	0	NA	Intergenic	(TGTGCA)n|Simple_repeat|Simple_repeat	-207463	NM_001281768	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.008499	0.491525	
chunk0159_70_1	chr5	137393605	137394060	+	0	NA	intron (NM_004598, intron 2 of 10)	L2a|LINE|L2	105497	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.000000	0.348684	
chunk0163_42_1	chr6	8520026	8520225	+	0	NA	intron (NR_038979, intron 2 of 3)	L1ME1|LINE|L1	84502	NR_038979	100506207	Hs.311049	NR_038979	ENSG00000285219	LOC100506207	-	uncharacterized LOC100506207	ncRNA	0.005025	0.345000	
chunk0140_22_1	chr4	65631590	65632240	+	0	NA	intron (NM_001281765, intron 2 of 17)	intron (NM_001281765, intron 2 of 17)	-38046	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.000000	0.311828	
chunk0158_354_1	chr5	133640287	133640658	+	0	NA	Intergenic	Intergenic	-27940	NM_015082	23105	Hs.483390	NM_015082	ENSG00000053108	FSTL4	-	follistatin like 4	protein-coding	0.005391	0.465054	161(TGGGACACCGTGTACC,-,0.00),162(GGGACACCGTGTACCT,+,0.00)
chunk0040_166_1	chr11	113895277	113895855	+	0	NA	Intergenic	Intergenic	-9230	NM_006028	9177	Hs.241377	NM_006028	ENSG00000149305	HTR3B	5-HT3B	5-hydroxytryptamine receptor 3B	protein-coding	0.013841	0.419689	319(CAGGACACTGTGTTAC,-,0.00),320(AGGACACTGTGTTACT,+,0.00)
chunk0063_203_1	chr14	81344258	81344988	+	0	NA	intron (NM_033104, intron 4 of 5)	intron (NM_033104, intron 4 of 5)	82589	NM_033104	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.004110	0.339261	
chunk0061_211_1	chr14	60382023	60382580	+	0	NA	Intergenic	L1PA6|LINE|L1	103745	NM_174978	317761	Hs.335754	NM_174978	ENSG00000179008	C14orf39	Six6os1	chromosome 14 open reading frame 39	protein-coding	0.017953	0.541219	
chunk0151_342_1	chr5	54279461	54280041	+	0	NA	intron (NM_019087, intron 1 of 4)	intron (NM_019087, intron 1 of 4)	30822	NM_019087	54622	Hs.659125	NM_019087	ENSG00000185305	ARL15	ARFRP2	ADP ribosylation factor like GTPase 15	protein-coding	0.012069	0.476764	
chunk0112_158_1	chr20	39258698	39259464	+	0	NA	Intergenic	Intergenic	-34333	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.009138	0.458931	535(AAAGACATTATGTGCT,-,0.00),536(AAGACATTATGTGCTT,+,0.00)
chunk0038_372_1	chr11	93386729	93387188	+	0	NA	intron (NM_181645, intron 8 of 13)	intron (NM_181645, intron 8 of 13)	56241	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.000000	0.341304	
chunk0199_11_1	chr9	494590	495396	+	0	NA	intron (NM_001256876, intron 3 of 15)	intron (NM_001256876, intron 3 of 15)	-9702	NM_015158	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.008685	0.408922	
chunk0169_145_1	chr6	101515712	101516110	+	0	NA	intron (NM_001166247, intron 1 of 16)	L1PB1|LINE|L1	116926	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.002513	0.345865	
chunk0196_200_1	chr8	106411188	106411549	+	0	NA	intron (NM_001198533, intron 2 of 16)	intron (NM_001198533, intron 2 of 16)	-36556	NM_001198532	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.005540	0.433702	203(TGGCACATAATGTGCA,-,0.00),204(GGCACATAATGTGCAC,+,0.00)
chunk0171_190_1	chr6	125254634	125254965	+	0	NA	intron (NM_001003396, intron 5 of 5)	(ATCTGATTAA)n|Simple_repeat|Simple_repeat	47337	NM_016063	51020	Hs.32826	NM_016063	ENSG00000111906	HDDC2	C6orf74|CGI-130|NS5ATP2|dJ167O5.2	HD domain containing 2	protein-coding	0.006042	0.322289	
chunk0049_344_1	chr12	95102943	95103513	+	0	NA	intron (NM_018351, intron 14 of 20)	MIR|SINE|MIR	-29600	NM_001032287	7181	Hs.108301	NM_003297	ENSG00000120798	NR2C1	TR2	nuclear receptor subfamily 2 group C member 1	protein-coding	0.010526	0.402802	
chunk0116_283_1	chr21	39807308	39808175	+	0	NA	Intergenic	Intergenic	-59680	NM_006198	5121	Hs.80296	NM_006198	ENSG00000183036	PCP4	PEP-19	Purkinje cell protein 4	protein-coding	0.011534	0.448157	
chunk0195_359_1	chr8	99847682	99848354	+	0	NA	intron (NM_152564, intron 54 of 61)	intron (NM_152564, intron 54 of 61)	45996	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.004464	0.404160	353(GTGAACATGATGTTCT,-,0.00),354(TGAACATGATGTTCTT,+,0.00)
chunk0011_2_1	chr1	125166534	125166768	+	0	NA	Intergenic	(GATTC)n|Simple_repeat|Simple_repeat	3647539	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.055556	0.361702	
chunk0103_253_1	chr2	165314454	165314840	+	0	NA	intron (NM_021007, intron 10 of 26)	intron (NM_021007, intron 10 of 26)	18874	NM_001040143	6326	Hs.93485	NM_021007	ENSG00000136531	SCN2A	BFIC3|BFIS3|BFNIS|EIEE11|HBA|HBSCI|HBSCII|NAC2|Na(v)1.2|Nav1.2|SCN2A1|SCN2A2	sodium voltage-gated channel alpha subunit 2	protein-coding	0.002591	0.333333	
chunk0110_455_1	chr20	21278673	21279369	+	0	NA	Intergenic	L1MC4|LINE|L1	-24283	NM_012255	22803	Hs.255932	NM_012255	ENSG00000088930	XRN2	-	5'-3' exoribonuclease 2	protein-coding	0.004310	0.385940	
chunk0141_307_1	chr4	87073672	87074042	+	0	NA	intron (NM_001313959, intron 3 of 19)	intron (NM_001313959, intron 3 of 19)	66856	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.016216	0.417790	
chunk0042_389_1	chr12	10780629	10781054	+	0	NA	Intergenic	Intergenic	21786	NM_023919	50837	Hs.533754	NM_023919	ENSG00000121377	TAS2R7	T2R7|TRB4	taste 2 receptor member 7	protein-coding	0.000000	0.380282	
chunk0073_131_1	chr16	4935196	4935652	+	0	NA	intron (NM_002705, intron 1 of 21)	intron (NM_002705, intron 1 of 21)	1711	NM_002705	5493	Hs.192233	NM_002705	ENSG00000118898	PPL	-	periplakin	protein-coding	0.026316	0.606127	
chunk0087_340_1	chr18	40236031	40236369	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	169914	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.011834	0.410029	
chunk0204_323_1	chr9	100621722	100622345	+	0	NA	Intergenic	Intergenic	43954	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.004815	0.304487	
chunk0129_325_1	chr3	124516503	124516771	+	0	NA	intron (NM_001024660, intron 33 of 59)	(A)n|Simple_repeat|Simple_repeat	-68022	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.003731	0.330855	
chunk0002_423_1	chr1	27858114	27858439	+	0	NA	Intergenic	Intergenic	-14267	NM_004848	9473	Hs.10649	NM_004848	ENSG00000130775	THEMIS2	C1orf38|ICB-1|ICB1	thymocyte selection associated family member 2	protein-coding	0.006154	0.552147	
chunk0116_125_1	chr21	36141653	36141924	+	0	NA	non-coding (NR_038894, exon 3 of 3)	non-coding (NR_038894, exon 3 of 3)	6823	NM_001236	874	Hs.154510	NM_001236	ENSG00000159231	CBR3	HEL-S-25|SDR21C2|hCBR3	carbonyl reductase 3	protein-coding	0.018450	0.536765	
chunk0093_128_1	chr19	45729561	45729869	+	0	NA	intron (NM_001080469, intron 1 of 1)	MIR|SINE|MIR	1178	NM_001080469	23403	Hs.128702	NM_001080469	ENSG00000177051	FBXO46	20D7-FC4|FBXO34L|Fbx46	F-box protein 46	protein-coding	0.006494	0.449838	
chunk0040_280_1	chr11	116836142	116836341	+	0	NA	exon (NM_000039, exon 4 of 4)	exon (NM_000039, exon 4 of 4)	124	NR_126362	104326055	Hs.627813	NR_126362	ENSG00000235910	APOA1-AS	-	APOA1 antisense RNA	ncRNA	0.040201	0.610000	
chunk0082_49_1	chr17	51015191	51015647	+	0	NA	intron (NM_001130528, intron 8 of 29)	intron (NM_001130528, intron 8 of 29)	31549	NM_001251971	9043	Hs.463439	NM_003971	ENSG00000008294	SPAG9	CT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6	sperm associated antigen 9	protein-coding	0.002193	0.435449	191(CAGAACAGTGAGACCT,-,0.00),192(AGAACAGTGAGACCTC,+,0.00)
chunk0079_448_1	chr17	20260298	20260641	+	0	NA	intron (NM_001033553, intron 12 of 14)	MER91A|DNA|hAT-Tip100	-60705	NR_023380	348254	Hs.462475	NR_023380		CCDC144CP	CCDC144C	coiled-coil domain containing 144C, pseudogene	pseudo	0.014577	0.508721	
chunk0201_386_1	chr9	69004548	69004960	+	0	NA	intron (NM_003558, intron 15 of 15)	intron (NM_003558, intron 15 of 15)	9369	NM_002732	5568	Hs.158029	NM_002732	ENSG00000165059	PRKACG	BDPLT19|KAPG|PKACg	protein kinase cAMP-activated catalytic subunit gamma	protein-coding	0.009709	0.430993	337(AAGAAGACGCTGTGCT,-,0.00),338(AGAAGACGCTGTGCTT,+,0.00)
chunk0131_96_1	chr3	143608931	143609467	+	0	NA	intron (NM_173653, intron 6 of 15)	MamRTE1|LINE|RTE-BovB	239332	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.009328	0.372439	288(CTGGACACAGTGTTCC,-,0.00),289(TGGACACAGTGTTCCA,+,0.00)
chunk0051_87_1	chr12	114371724	114372183	+	0	NA	intron (NM_080717, intron 6 of 7)	intron (NM_080717, intron 6 of 7)	34210	NM_181486	6910	Hs.381715	NM_000192	ENSG00000089225	TBX5	HOS	T-box transcription factor 5	protein-coding	0.017429	0.439130	279(GGGGACACAATGTTCT,-,0.00),280(GGGACACAATGTTCTC,+,0.00)
chunk0051_28_1	chr12	111924353	111924872	+	0	NA	Intergenic	L1MC2|LINE|L1	25549	NR_036636	8759	Hs.661708	NR_036636		ADAM1A	ADAM1|ADAM1P|FTNAP|Ftna|PH-30a	ADAM metallopeptidase domain 1A (pseudogene)	pseudo	0.001927	0.346154	
chunk0207_111_1	chr9	128840618	128841186	+	0	NA	intron (NR_109829, intron 3 of 12)	L1ME4b|LINE|L1	-11081	NM_016390	51490	Hs.224137	NM_016390	ENSG00000198917	SPOUT1	C9orf114|CENP-32|CENP32|HSPC109	SPOUT domain containing methyltransferase 1	protein-coding	0.014085	0.418278	214(AGGCACACACTGTTTC,-,0.00),215(GGCACACACTGTTTCT,+,0.00)
chunk0185_1_1	chr7	123707014	123707424	+	0	NA	intron (NM_003941, intron 2 of 10)	intron (NM_003941, intron 2 of 10)	41852	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.002439	0.316302	
chunk0005_103_1	chr1	56567626	56568018	+	0	NA	intron (NM_003713, intron 1 of 5)	L1MB8|LINE|L1	11762	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.017857	0.404580	
chunk0087_222_1	chr18	36120371	36120570	+	0	NA	intron (NM_001099406, intron 4 of 7)	intron (NM_001099406, intron 4 of 7)	8924	NM_012319	25800	Hs.79136	NM_012319	ENSG00000141424	SLC39A6	LIV-1|ZIP6	solute carrier family 39 member 6	protein-coding	0.005025	0.345000	
chunk0067_360_1	chr15	48610348	48610631	+	0	NA	intron (NM_000138, intron 4 of 65)	intron (NM_000138, intron 4 of 65)	35299	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.003534	0.369718	
chunk0038_363_1	chr11	93317326	93317561	+	0	NA	Intergenic	Intergenic	-13274	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.000000	0.326271	
chunk0154_406_1	chr5	88708018	88708217	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-23314	NR_015436	645323	Hs.12827	NR_015436	ENSG00000245526	LINC00461	ECONEXIN|EyeLinc1|VISC	long intergenic non-protein coding RNA 461	ncRNA	0.000000	0.410000	
chunk0066_231_1	chr15	34189388	34189922	+	0	NA	intron (NM_024713, intron 1 of 9)	LOR1-int|LTR|ERV1	20441	NM_024713	79768	Hs.633566	NM_024713	ENSG00000134152	KATNBL1	C15orf29	katanin regulatory subunit B1 like 1	protein-coding	0.003745	0.304673	
chunk0018_274_1	chr1	220565745	220565946	+	0	NA	intron (NM_001286128, intron 1 of 15)	LTR79|LTR|ERVL	37662	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.000000	0.435644	
chunk0154_163_1	chr5	79535668	79535931	+	0	NA	Intergenic	Intergenic	-21963	NM_004272	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.007605	0.382576	
chunk0137_19_1	chr4	10880564	10881162	+	0	NA	Intergenic	Intergenic	-196101	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.005017	0.382304	
chunk0209_130_1	chrX	40965093	40965667	+	0	NA	Intergenic	Intergenic	-120255	NM_001039590	8239	Hs.77578	NM_004652	ENSG00000124486	USP9X	DFFRX|FAF|FAM|MRX99|MRXS99F	ubiquitin specific peptidase 9 X-linked	protein-coding	0.003484	0.337391	
chunk0141_86_1	chr4	78645860	78646242	+	0	NA	promoter-TSS (NR_038308)	promoter-TSS (NR_038308)	57	NR_038305	100505702	Hs.235795	NR_038303		LINC01094	-	long intergenic non-protein coding RNA 1094	ncRNA	0.010471	0.472585	
chunk0114_393_1	chr20	63274388	63274679	+	0	NA	intron (NM_018209, intron 1 of 12)	intron (NM_018209, intron 1 of 12)	1748	NM_001281483	55738	Hs.25584	NM_018209	ENSG00000101199	ARFGAP1	ARF1GAP|HRIHFB2281	ADP ribosylation factor GTPase activating protein 1	protein-coding	0.013746	0.503425	146(GAGTTCAGCGTGTTCT,-,0.00),147(AGTTCAGCGTGTTCTC,+,0.00)
chunk0037_214_1	chr11	74681619	74682072	+	0	NA	Intergenic	Intergenic	29522	NM_001304417	25884	Hs.432379	NM_015424	ENSG00000054938	CHRDL2	BNF1|CHL2	chordin like 2	protein-coding	0.013245	0.572687	275(AGGTGCAGTCTGTGCC,-,0.00),276(GGTGCAGTCTGTGCCA,+,0.00)
chunk0088_64_1	chr18	44342958	44343410	+	0	NA	intron (NR_110792, intron 2 of 4)	Tigger3c|DNA|TcMar-Tigger	188513	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.004425	0.328918	
chunk0041_343_1	chr11	130653685	130654719	+	0	NA	Intergenic	Intergenic	-12533	NR_107019	102466873		NR_107019	ENSG00000274999	MIR8052	hsa-mir-8052	microRNA 8052	ncRNA	0.006770	0.449275	404(CGGCACACAGAGTGCA,-,0.00),405(GGCACACAGAGTGCAG,+,0.00)
chunk0015_335_1	chr1	189804987	189805520	+	0	NA	Intergenic	MLT1E2-int|LTR|ERVL-MaLR	672376	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003752	0.355805	257(AGTAACATTGTGTTCT,-,0.00),258(GTAACATTGTGTTCTC,+,0.00)
chunk0206_195_1	chr9	122996701	122996937	+	0	NA	intron (NM_012197, intron 8 of 25)	MIRc|SINE|MIR	-36824	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.004237	0.312236	
chunk0025_190_1	chr10	53272055	53272385	+	0	NA	Intergenic	L1PB2|LINE|L1	-500520	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.510574	
chunk0044_173_1	chr12	30048577	30049100	+	0	NA	Intergenic	Intergenic	-264079	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.003824	0.368321	
chunk0097_56_1	chr2	43524130	43524567	+	0	NA	intron (NR_073394, intron 22 of 35)	intron (NR_073394, intron 22 of 35)	71626	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.002288	0.328767	
chunk0138_205_1	chr4	38673599	38674047	+	0	NA	intron (NM_016531, intron 1 of 5)	intron (NM_016531, intron 1 of 5)	-9195	NR_026804	79667	Hs.29725	NM_024614	ENSG00000231160	KLF3-AS1	-	KLF3 antisense RNA 1	ncRNA	0.004464	0.452116	
chunk0003_192_1	chr1	34052516	34052957	+	0	NA	intron (NM_052896, intron 2 of 69)	L2a|LINE|L2	112538	NM_001281956	114784	Hs.656915	NM_052896	ENSG00000121904	CSMD2	dJ1007G16.1|dJ1007G16.2|dJ947L8.1	CUB and Sushi multiple domains 2	protein-coding	0.013605	0.443439	
chunk0107_15_1	chr2	210179607	210179950	+	0	NA	Intergenic	Intergenic	-8408	NM_152519	151050	Hs.282260	NM_152519	ENSG00000144445	KANSL1L	C2orf67|MSL1v2	KAT8 regulatory NSL complex subunit 1 like	protein-coding	0.000000	0.316860	213(GGTCCAGCCTGTTCTT,+,0.00)
chunk0184_336_1	chr7	120631406	120631913	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	226464	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.005917	0.301181	
chunk0148_94_1	chr5	3659952	3660227	+	0	NA	Intergenic	Intergenic	64035	NM_024337	79192	Hs.424156	NM_024337	ENSG00000170549	IRX1	IRX-5|IRXA1	iroquois homeobox 1	protein-coding	0.014545	0.496377	
chunk0201_20_1	chr9	33131415	33131966	+	0	NA	intron (NM_001497, intron 2 of 5)	intron (NM_001497, intron 2 of 5)	-35258	NR_108109	101929639	Hs.545818	NR_108108	ENSG00000233554	B4GALT1-AS1	-	B4GALT1 antisense RNA 1	ncRNA	0.001815	0.402174	375(AACACAGGCAGTTCCT,+,0.00)
chunk0030_279_1	chr10	116675870	116676256	+	0	NA	intron (NM_025015, intron 11 of 11)	intron (NM_025015, intron 11 of 11)	-6093	NM_144661	143379	Hs.121347	NM_144661	ENSG00000165863	C10orf82	-	chromosome 10 open reading frame 82	protein-coding	0.005181	0.462532	
chunk0133_4_1	chr3	165210115	165210371	+	0	NA	intron (NR_125764, intron 1 of 5)	intron (NR_125764, intron 1 of 5)	3283	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.000000	0.435798	
chunk0161_137_1	chr5	168464032	168464534	+	0	NA	intron (NM_015238, intron 20 of 22)	intron (NM_015238, intron 20 of 22)	-22175	NM_002887	5917	Hs.654907	NM_002887	ENSG00000113643	RARS	ArgRS|DALRD1|HLD9	arginyl-tRNA synthetase	protein-coding	0.009960	0.499006	
chunk0068_66_1	chr15	51855769	51855968	+	0	NA	intron (NM_014547, intron 1 of 9)	intron (NM_014547, intron 1 of 9)	26240	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.000000	0.415000	
chunk0085_452_1	chr18	11493868	11494272	+	0	NA	intron (NR_110778, intron 1 of 2)	MIR3|SINE|MIR	4022	NR_110778	101927433	Hs.331210	NR_110778	ENSG00000267252	LINC01255	-	long intergenic non-protein coding RNA 1255	ncRNA	0.000000	0.353086	
chunk0105_147_1	chr2	186486117	186486481	+	0	NA	5' UTR (NM_018471, exon 1 of 10)	5' UTR (NM_018471, exon 1 of 10)	141	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.093407	0.646575	
chunk0133_293_1	chr3	172170100	172170299	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	129645	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.000000	0.345000	
chunk0023_37_1	chr10	21195312	21195566	+	0	NA	Intergenic	Intergenic	21137	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.003937	0.384314	
chunk0012_61_1	chr1	155560368	155560791	+	0	NA	intron (NM_018489, intron 1 of 27)	intron (NM_018489, intron 1 of 27)	-1402	NR_027023	645676	Hs.568693	NR_027023	ENSG00000235919	ASH1L-AS1	-	ASH1L antisense RNA 1	ncRNA	0.007092	0.422170	
chunk0051_306_1	chr12	119319622	119320073	+	0	NA	Intergenic	LTR33|LTR|ERVL	-14865	NM_178499	160777	Hs.98188	NM_178499	ENSG00000183273	CCDC60	-	coiled-coil domain containing 60	protein-coding	0.004435	0.460177	
chunk0073_318_1	chr16	14219085	14219474	+	0	NA	intron (NM_001308142, intron 8 of 16)	L2b|LINE|L2	-83009	NR_132983	100129781	Hs.190748	NR_132983		MIR193BHG	-	MIR193B host gene	ncRNA	0.000000	0.317949	
chunk0172_214_1	chr6	136761249	136761530	+	0	NA	intron (NM_005923, intron 1 of 29)	intron (NM_005923, intron 1 of 29)	31129	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.014235	0.500000	
chunk0125_136_1	chr3	65998854	65999346	+	0	NA	intron (NM_015520, intron 1 of 24)	L1PA10|LINE|L1	39734	NM_015520	9223	Hs.476636	NM_004742	ENSG00000151276	MAGI1	AIP-3|AIP3|BAIAP1|BAP-1|BAP1|MAGI-1|MAGI-1b|Magi1d|TNRC19|WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.008130	0.377282	
chunk0147_2_1	chr4	170282445	170282726	+	0	NA	intron (NR_125889, intron 2 of 2)	intron (NR_125889, intron 2 of 2)	55994	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.010676	0.372340	
chunk0182_264_1	chr7	97752116	97752662	+	0	NA	Intergenic	L2c|LINE|L2	20430	NM_013998	6863	Hs.2563	NM_003182	ENSG00000006128	TAC1	Hs.2563|NK2|NKNA|NPK|TAC2	tachykinin precursor 1	protein-coding	0.009158	0.391225	
chunk0070_244_1	chr15	73380257	73380555	+	0	NA	Intergenic	MER67A|LTR|ERV1	-11142	NM_005477	10021	Hs.86941	NM_005477	ENSG00000138622	HCN4	SSS2	hyperpolarization activated cyclic nucleotide gated potassium channel 4	protein-coding	0.006711	0.418060	
chunk0045_122_1	chr12	46281147	46281374	+	0	NA	Intergenic	L1MA4|LINE|L1	-11835	NM_001278387	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.004405	0.574561	
chunk0067_279_1	chr15	47203730	47204087	+	0	NA	intron (NM_001198999, intron 1 of 19)	intron (NM_001198999, intron 1 of 19)	19702	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.002801	0.329609	
chunk0173_202_1	chr6	145347404	145347643	+	0	NA	Intergenic	Intergenic	-387346	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.004184	0.470833	
chunk0177_370_1	chr7	26751727	26753006	+	0	NA	intron (NM_001303468, intron 4 of 12)	L4_A_Mam|LINE|RTE-X	105357	NM_001303468	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.001564	0.360156	
chunk0017_307_1	chr1	211200182	211200777	+	0	NA	Intergenic	Intergenic	-58887	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.008403	0.390940	
chunk0056_264_1	chr13	90033261	90033837	+	0	NA	Intergenic	L1MB1|LINE|L1	86168	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.010417	0.417678	
chunk0116_31_1	chr21	33304432	33305219	+	0	NA	Intergenic	Intergenic	-20084	NM_000629	3454	Hs.529400	NM_000629	ENSG00000142166	IFNAR1	AVP|IFN-alpha-REC|IFNAR|IFNBR|IFRC	interferon alpha and beta receptor subunit 1	protein-coding	0.010165	0.442893	
chunk0084_390_1	chr17	82106291	82106898	+	0	NA	intron (NM_198082, intron 16 of 16)	intron (NM_198082, intron 16 of 16)	-8364	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.026359	0.615132	
chunk0208_375_1	chrX	27835844	27836071	+	0	NA	Intergenic	Intergenic	27967	NM_182506	139422	Hs.447363	NM_182506	ENSG00000177689	MAGEB10	-	MAGE family member B10	protein-coding	0.008811	0.394737	
chunk0035_131_1	chr11	42766853	42767397	+	0	NA	Intergenic	MIR3|SINE|MIR	502244	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.007353	0.376147	
chunk0166_102_1	chr6	43846520	43847298	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-44119	NR_024478	100132354	Hs.376232	NR_024478		LINC01512	HI-LNC77	long intergenic non-protein coding RNA 1512	ncRNA	0.014139	0.381258	
chunk0207_338_1	chr9	134387269	134387557	+	0	NA	intron (NM_001291920, intron 1 of 9)	intron (NM_001291920, intron 1 of 9)	8002	NR_039816	100616236		NR_039816	ENSG00000263897	MIR4669	-	microRNA 4669	ncRNA	0.041667	0.567474	
chunk0063_348_1	chr14	85471495	85472190	+	0	NA	Intergenic	Intergenic	-58302	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.008633	0.410920	
chunk0060_214_1	chr14	48865795	48866435	+	0	NA	Intergenic	Intergenic	720301	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.375975	
chunk0208_246_1	chrX	20103662	20104079	+	0	NA	intron (NM_152780, intron 1 of 15)	intron (NM_152780, intron 1 of 15)	12768	NM_001168467	256714	Hs.127951	NM_152780	ENSG00000184368	MAP7D2	-	MAP7 domain containing 2	protein-coding	0.000000	0.358852	
chunk0049_8_1	chr12	89262226	89262465	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	90514	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.000000	0.395833	
chunk0043_414_1	chr12	25839544	25839859	+	0	NA	Intergenic	Intergenic	34378	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.006349	0.373418	
chunk0051_313_1	chr12	119645715	119645914	+	0	NA	Intergenic	Intergenic	-22142	NM_006253	5564	Hs.741184	NM_006253	ENSG00000111725	PRKAB1	AMPK|HAMPKb	protein kinase AMP-activated non-catalytic subunit beta 1	protein-coding	0.020101	0.510000	
chunk0079_380_1	chr17	18303065	18303937	+	0	NA	intron (NM_004618, intron 5 of 18)	LTR5B|LTR|ERVK	11506	NM_004618	7156	Hs.592115	NM_004618	ENSG00000177302	TOP3A	MGRISCE2|PEOB5|TOP3|ZGRF7	DNA topoisomerase III alpha	protein-coding	0.020642	0.484536	
chunk0169_289_1	chr6	105872788	105873131	+	0	NA	Intergenic	Intergenic	-213361	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.008746	0.308140	174(GGGAACAAAGAGTACC,-,0.00),175(GGAACAAAGAGTACCT,+,0.00)
chunk0075_152_1	chr16	51225999	51226198	+	0	NA	intron (NR_039672, intron 5 of 6)	intron (NR_039672, intron 5 of 6)	-74826	NM_002968	6299	Hs.135787	NM_002968	ENSG00000103449	SALL1	HEL-S-89|HSAL1|Sal-1|TBS|ZNF794	spalt like transcription factor 1	protein-coding	0.015075	0.325000	
chunk0134_14_1	chr3	175428434	175428654	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	59004	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.000000	0.438914	
chunk0058_34_1	chr14	20080948	20081553	+	0	NA	Intergenic	L1PA16|LINE|L1	21205	NM_001004717	122742	Hs.553574	NM_001004717	ENSG00000176246	OR4L1	OR14-28|OR4L2P	olfactory receptor family 4 subfamily L member 1	protein-coding	0.004959	0.333333	
chunk0158_91_1	chr5	126600880	126601097	+	0	NA	promoter-TSS (NM_032177)	promoter-TSS (NM_032177)	73	NM_032177	51808	Hs.555731	NM_032177	ENSG00000164902	PHAX	RNUXA	phosphorylated adaptor for RNA export	protein-coding	0.110599	0.674312	
chunk0017_86_1	chr1	205712902	205713293	+	0	NA	3' UTR (NM_022731, exon 7 of 7)	3' UTR (NM_022731, exon 7 of 7)	-32595	NM_033102	85414	Hs.278695	NM_033102	ENSG00000158715	SLC45A3	IPCA-2|IPCA-6|IPCA-8|IPCA6|PCANAP2|PCANAP6|PCANAP8|PRST	solute carrier family 45 member 3	protein-coding	0.002558	0.336735	
chunk0178_67_1	chr7	30254905	30255664	+	0	NA	Intergenic	MIRb|SINE|MIR	-29023	NM_147128	223082	Hs.263912	NM_147128	ENSG00000180233	ZNRF2	RNF202	zinc and ring finger 2	protein-coding	0.005270	0.400000	318(GGGTACACTGCGTGCT,-,0.00)
chunk0071_136_1	chr15	82195903	82196178	+	0	NA	intron (NM_001040610, intron 13 of 17)	L2a|LINE|L2	66723	NM_001040610	79631	Hs.459114	NM_024580	ENSG00000140598	EFL1	EFTUD1|FAM42A|HsT19294|RIA1|SDS2	elongation factor like GTPase 1	protein-coding	0.021818	0.467391	145(AGAGACAGCGTGTACC,-,0.00),146(GAGACAGCGTGTACCG,+,0.00)
chunk0039_9_1	chr11	95087051	95087766	+	0	NA	Intergenic	Intergenic	-2402	NM_015036	23052	Hs.167115	NM_015036	ENSG00000149218	ENDOD1	-	endonuclease domain containing 1	protein-coding	0.002797	0.364525	
chunk0009_72_1	chr1	100916460	100917233	+	0	NA	intron (NM_001144884, intron 6 of 11)	L1MA1|LINE|L1	20768	NM_133496	148867	Hs.533903	NM_133496	ENSG00000162695	SLC30A7	ZNT7|ZnT-7|ZnTL2	solute carrier family 30 member 7	protein-coding	0.001294	0.347545	
chunk0108_56_1	chr2	227085227	227085507	+	0	NA	intron (NM_000092, intron 22 of 47)	intron (NM_000092, intron 22 of 47)	79192	NM_000092	1286	Hs.591645	NM_000092	ENSG00000081052	COL4A4	ATS2|BFH|CA44	collagen type IV alpha 4 chain	protein-coding	0.017857	0.462633	
chunk0098_15_1	chr2	65373258	65373846	+	0	NA	intron (NM_181784, intron 1 of 5)	intron (NM_181784, intron 1 of 5)	-6755	NM_001128210	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.003401	0.414261	
chunk0083_431_1	chr17	72534756	72535151	+	0	NA	intron (NR_036488, intron 1 of 3)	L2b|LINE|L2	57851	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.007595	0.398990	
chunk0136_321_1	chr3	195388263	195388744	+	0	NA	intron (NM_012287, intron 2 of 22)	intron (NM_012287, intron 2 of 22)	54585	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.002079	0.406639	
chunk0128_144_1	chr3	106839883	106840145	+	0	NA	Intergenic	Intergenic	400624	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.000000	0.384030	141(CAGAGCAGGCTGTTCT,-,0.00),142(AGAGCAGGCTGTTCTT,+,0.00)
chunk0205_372_1	chr9	113973916	113974115	+	0	NA	intron (NM_133374, intron 2 of 13)	L2a|LINE|L2	97733	NM_133374	114991	Hs.349208	NM_133374	ENSG00000157657	ZNF618	FP13169|NEDD10	zinc finger protein 618	protein-coding	0.000000	0.465000	
chunk0152_280_1	chr5	61439388	61440042	+	0	NA	intron (NM_020928, intron 1 of 13)	L1M5|LINE|L1	107442	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.006116	0.320611	
chunk0048_283_1	chr12	82683006	82683205	+	0	NA	Intergenic	Intergenic	-4050	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.010050	0.415000	
chunk0092_195_1	chr19	30593847	30594593	+	0	NA	Intergenic	Intergenic	221827	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.009383	0.512718	
chunk0001_200_1	chr1	7746030	7746261	+	0	NA	intron (NM_015215, intron 18 of 22)	intron (NM_015215, intron 18 of 22)	-25124	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.012987	0.353448	
chunk0008_408_1	chr1	98087798	98088936	+	0	NA	Intergenic	Intergenic	-38674	NR_046105	400765	Hs.451802	NM_001001688	ENSG00000225206	MIR137HG	-	MIR137 host gene	ncRNA	0.005272	0.265145	
chunk0160_19_1	chr5	149048415	149048913	+	0	NA	intron (NM_024577, intron 2 of 16)	L2a|LINE|L2	13745	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.006024	0.364729	238(CAAAACAGGCAGTCCC,-,0.00),239(AAAACAGGCAGTCCCT,+,0.00)
chunk0030_360_1	chr10	118711473	118711984	+	0	NA	intron (NM_153810, intron 3 of 8)	intron (NM_153810, intron 3 of 8)	43518	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.007828	0.296875	269(AAGTACTTTCTGTACT,-,0.00),270(AGTACTTTCTGTACTG,+,0.00)
chunk0019_126_1	chr1	225517385	225517638	+	0	NA	intron (NM_001008493, intron 5 of 14)	intron (NM_001008493, intron 5 of 14)	-88656	NM_194442	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.027668	0.574803	
chunk0146_332_1	chr4	165747363	165747718	+	0	NA	intron (NR_121676, intron 4 of 5)	intron (NR_121676, intron 4 of 5)	-4469	NR_121677	101928131	Hs.406479	NR_121677		LOC101928131	-	uncharacterized LOC101928131	ncRNA	0.002817	0.401685	
chunk0014_55_1	chr1	175590810	175591189	+	0	NA	intron (NM_003285, intron 1 of 22)	intron (NM_003285, intron 1 of 22)	152617	NM_003285	7143	Hs.659864	NM_003285	ENSG00000116147	TNR	TN-R	tenascin R	protein-coding	0.007916	0.473684	210(AGGCACAGTCAGATCT,-,0.00),211(GGCACAGTCAGATCTC,+,0.00)
chunk0026_326_1	chr10	68223549	68223974	+	0	NA	Intergenic	MER74B|LTR|ERVL	8352	NM_145178	220202	Hs.175396	NM_145178	ENSG00000179774	ATOH7	Math5|NCRNA|PHPVAR|RNANC|bHLHa13	atonal bHLH transcription factor 7	protein-coding	0.007059	0.438967	
chunk0069_168_1	chr15	62740473	62741049	+	0	NA	exon (NM_015059, exon 29 of 56)	exon (NM_015059, exon 29 of 56)	-83196	NR_029709	406965		NR_029709	ENSG00000211137	MIR190A	MIR190|MIRN190|hsa-mir-190a|miR-190|mir-190a	microRNA 190a	ncRNA	0.013889	0.462738	304(TGGGACACAATGTGCT,-,0.00),305(GGGACACAATGTGCTT,+,0.00)
chunk0188_298_1	chr8	15842215	15842637	+	0	NA	Intergenic	Intergenic	302339	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.011848	0.406619	
chunk0059_314_1	chr14	36419171	36419831	+	0	NA	Intergenic	Intergenic	94284	NM_001101341	253970	Hs.509165	NM_001101341	ENSG00000229415	SFTA3	NANCI|SFTPH|SP-H|SPH	surfactant associated 3	ncRNA	0.003030	0.394856	
chunk0175_293_1	chr7	7799068	7799642	+	0	NA	intron (NM_001302350, intron 3 of 4)	intron (NM_001302350, intron 3 of 4)	-80748	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.013937	0.323478	
chunk0005_116_1	chr1	56765058	56765318	+	0	NA	intron (NM_001004303, intron 5 of 19)	L1MDa|LINE|L1	54508	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.000000	0.475096	
chunk0078_155_1	chr17	4161123	4161797	+	0	NA	intron (NR_039973, intron 1 of 1).2	intron (NR_039973, intron 1 of 1).2	17839	NM_001254755	124936	Hs.513871	NM_144611	ENSG00000167740	CYB5D2	-	cytochrome b5 domain containing 2	protein-coding	0.010386	0.499259	
chunk0029_294_1	chr10	103935382	103935789	+	0	NA	Intergenic	L1PA13|LINE|L1	-17298	NM_024928	79991	Hs.62314	NM_024928	ENSG00000107960	STN1	AAF-44|AAF44|OBFC1|RPA-32|bA541N10.2	STN1 subunit of CST complex	protein-coding	0.007371	0.362745	
chunk0032_269_1	chr11	9059705	9059917	+	0	NA	intron (NM_020974, intron 8 of 21)	intron (NM_020974, intron 8 of 21)	30568	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.004717	0.323944	
chunk0207_461_1	chr9	137982563	137983098	+	0	NA	intron (NM_001243812, intron 12 of 45)	L3|LINE|CR1	-35770	NR_132978	105376331		NR_132977		LOC105376331	-	uncharacterized LOC105376331	ncRNA	0.011215	0.432836	
chunk0175_4_1	chr7	121865	122353	+	0	NA	Intergenic	Intergenic	-27609	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.016393	0.433538	
chunk0205_234_1	chr9	109975835	109976246	+	0	NA	intron (NM_147150, intron 6 of 9)	intron (NM_147150, intron 6 of 9)	-72558	NM_001004065	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.007299	0.429612	
chunk0154_413_1	chr5	88926672	88927105	+	0	NA	intron (NR_109941, intron 3 of 3)	Tigger3b|DNA|TcMar-Tigger	-22783	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.020785	0.380184	
chunk0010_298_1	chr1	117692346	117692678	+	0	NA	Intergenic	Intergenic	86530	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.012048	0.462462	
chunk0074_235_1	chr16	27258226	27258660	+	0	NA	intron (NM_145080, intron 1 of 7)	intron (NM_145080, intron 1 of 7)	-9762	NR_037184	400512	Hs.434412	NR_037184	ENSG00000245888	NSMCE1-DT	-	NSMCE1 divergent transcript	ncRNA	0.006912	0.429885	
chunk0034_47_1	chr11	26910412	26911166	+	0	NA	Intergenic	Intergenic	-83292	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.002653	0.352318	400(ATGTACAGCTTGTACT,-,0.00),401(TGTACAGCTTGTACTG,+,0.00)
chunk0195_241_1	chr8	97568046	97568436	+	0	NA	Intergenic	MER87B|LTR|ERV1	-75938	NM_178812	92140	Hs.377155	NM_178812	ENSG00000147649	MTDH	3D3|AEG-1|AEG1|LYRIC|LYRIC/3D3	metadherin	protein-coding	0.012821	0.411765	
chunk0153_53_1	chr5	67548994	67549399	+	0	NA	Intergenic	Intergenic	-244017	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.004938	0.416256	205(GAGTACACTGTGTTCT,-,0.00),206(AGTACACTGTGTTCTC,+,0.00)
chunk0146_274_1	chr4	163384965	163385302	+	0	NA	Intergenic	Intergenic	41194	NM_006174	4889	Hs.519058	NM_006174	ENSG00000164129	NPY5R	NPY5-R|NPYR5|NPYY5-R	neuropeptide Y receptor Y5	protein-coding	0.000000	0.322485	
chunk0121_152_1	chr3	19154842	19155254	+	0	NA	intron (NM_144633, intron 1 of 15)	intron (NM_144633, intron 1 of 15)	6523	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.004854	0.360775	
chunk0154_115_1	chr5	78727905	78728292	+	0	NA	Intergenic	Intergenic	-79273	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.007752	0.469072	
chunk0003_198_1	chr1	34737828	34738454	+	0	NA	Intergenic	MIR|SINE|MIR	-16906	NM_005268	2709	Hs.198249	NM_005268	ENSG00000189280	GJB5	CX31.1	gap junction protein beta 5	protein-coding	0.004792	0.377990	
chunk0050_56_1	chr12	101083114	101083574	+	0	NA	intron (NM_001286616, intron 14 of 26)	intron (NM_001286616, intron 14 of 26)	126894	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.000000	0.321041	242(CAGGACAGCTTGTCCC,-,0.00),243(AGGACAGCTTGTCCCT,+,0.00)
chunk0038_315_1	chr11	91396658	91397434	+	0	NA	Intergenic	L2a|LINE|L2	-527844	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.007732	0.398970	
chunk0118_150_1	chr22	29995161	29996074	+	0	NA	intron (NM_021090, intron 7 of 19)	intron (NM_021090, intron 7 of 19)	-11432	NR_106876	102466742		NR_106876	ENSG00000275818	MIR6818	hsa-mir-6818	microRNA 6818	ncRNA	0.003286	0.376368	
chunk0150_408_1	chr5	39995276	39995476	+	0	NA	Intergenic	Intergenic	-56915	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.005000	0.353234	
chunk0077_182_1	chr16	79677770	79678514	+	0	NA	Intergenic	L1ME2z|LINE|L1	-77417	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.009409	0.359732	
chunk0004_160_1	chr1	45502110	45502498	+	0	NA	intron (NM_015506, intron 1 of 3)	AluJr|SINE|Alu	2120	NM_015506	25974	Hs.13024	NM_015506	ENSG00000132763	MMACHC	cblC	metabolism of cobalamin associated C	protein-coding	0.007732	0.478149	
chunk0062_411_1	chr14	75100534	75101254	+	0	NA	intron (NM_033116, intron 16 of 21)	intron (NM_033116, intron 16 of 21)	26181	NM_033116	91754	Hs.7200	NM_033116	ENSG00000119638	NEK9	APUG|LCCS10|NC|NERCC|NERCC1	NIMA related kinase 9	protein-coding	0.011111	0.417476	
chunk0146_111_1	chr4	158826709	158827239	+	0	NA	intron (NM_020840, intron 2 of 16)	intron (NM_020840, intron 2 of 16)	57944	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.001887	0.399247	
chunk0120_93_1	chr3	4286555	4286938	+	0	NA	Intergenic	Intergenic	-16558	NM_006515	6419	Hs.475300	NM_006515	ENSG00000170364	SETMAR	METNASE|Mar1	SET domain and mariner transposase fusion gene	protein-coding	0.007833	0.304688	
chunk0137_304_1	chr4	24138070	24138724	+	0	NA	Intergenic	Intergenic	-248320	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.001529	0.462595	606(GAGAACTGTCTGTCTC,-,0.00),607(AGAACTGTCTGTCTCT,+,0.00)
chunk0197_402_1	chr8	127146125	127146602	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	51264	NR_120364	103021165	Hs.573407	NR_120364		CASC19	CARLO6|CARLo-6|LINC01245	cancer susceptibility 19	ncRNA	0.002096	0.317992	
chunk0143_241_1	chr4	114593929	114594352	+	0	NA	Intergenic	HERV1_I-int|LTR|ERV1	-4315	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.002364	0.462264	
chunk0155_100_1	chr5	92492107	92492787	+	0	NA	Intergenic	Intergenic	1078896	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.001471	0.345081	
chunk0076_54_1	chr16	61211978	61212832	+	0	NA	Intergenic	Intergenic	-156639	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.005855	0.339181	
chunk0160_441_1	chr5	164750555	164750754	+	0	NA	Intergenic	Intergenic	280375	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.005025	0.330000	
chunk0057_439_1	chr13	110541114	110541867	+	0	NA	intron (NM_017817, intron 1 of 1)	intron (NM_017817, intron 1 of 1)	20247	NM_017817	55647	Hs.743563	NM_017817	ENSG00000139832	RAB20	-	RAB20, member RAS oncogene family	protein-coding	0.013280	0.482759	506(GGGAACTGCCTGCCCT,-,0.00)
chunk0058_387_1	chr14	29576795	29577003	+	0	NA	3' UTR (NM_002742, exon 18 of 18)	3' UTR (NM_002742, exon 18 of 18)	350794	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.004808	0.358852	
chunk0099_260_1	chr2	98051919	98052140	+	0	NA	Intergenic	MER41-int|LTR|ERV1	-35103	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.009050	0.391892	114(TGGAACAGCATGTTTT,-,0.00),115(GGAACAGCATGTTTTC,+,0.00)
chunk0208_86_1	chrX	13123913	13124335	+	0	NA	Intergenic	Intergenic	-79326	NM_174901	171484	Hs.667546	NM_174901	ENSG00000187268	FAM9C	TEX39C	family with sequence similarity 9 member C	protein-coding	0.009479	0.356974	
chunk0085_324_1	chr18	8374798	8375034	+	0	NA	intron (NM_001105244, intron 24 of 32)	intron (NM_001105244, intron 24 of 32)	-7882	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.008475	0.337553	
chunk0053_250_1	chr13	32880995	32881357	+	0	NA	intron (NR_047020, intron 3 of 4)	intron (NR_047020, intron 3 of 4)	30476	NR_047020	100874167	Hs.406290	NR_047020		LINC00423	-	long intergenic non-protein coding RNA 423	ncRNA	0.011050	0.473829	173(CTGCACAGGCTGTGCT,-,0.00),174(TGCACAGGCTGTGCTG,+,0.00)
chunk0134_187_1	chr3	178248467	178248961	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-170487	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.006073	0.349495	
chunk0121_396_1	chr3	25397153	25397511	+	0	NA	intron (NM_001290300, intron 1 of 7)	L1PB1|LINE|L1	-30931	NM_001290266	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.005587	0.476323	
chunk0179_172_1	chr7	46900060	46900763	+	0	NA	Intergenic	Intergenic	681733	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.007112	0.457386	
chunk0151_216_1	chr5	50879426	50879663	+	0	NA	Intergenic	MER50|LTR|ERV1	90643	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.021097	0.504202	
chunk0092_2_1	chr19	18399010	18399389	+	0	NA	Intergenic	Intergenic	-1594	NM_145256	126364	Hs.332156	NM_145256	ENSG00000175489	LRRC25	MAPA	leucine rich repeat containing 25	protein-coding	0.015831	0.481579	
chunk0048_423_1	chr12	88362457	88362874	+	0	NA	Intergenic	Intergenic	217808	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.004796	0.344498	
chunk0152_420_1	chr5	65748315	65748657	+	0	NA	intron (NM_020726, intron 1 of 12)	AluJo|SINE|Alu	26290	NM_020726	57486	Hs.247460	NM_020726	ENSG00000123213	NLN	AGTBP|EP24.16|MEP|MOP	neurolysin	protein-coding	0.000000	0.446064	
chunk0072_441_1	chr15	101528536	101528735	+	0	NA	Intergenic	Intergenic	-38651	NM_001291309	5046	Hs.498494	NM_002570	ENSG00000140479	PCSK6	PACE4|SPC4	proprotein convertase subtilisin/kexin type 6	protein-coding	0.030151	0.625000	38(AGGCTCACGGTGTCCC,-,0.00),39(GGCTCACGGTGTCCCC,+,0.00)
chunk0066_51_1	chr15	28207806	28208225	+	0	NA	intron (NM_004667, intron 44 of 92)	intron (NM_004667, intron 44 of 92)	-108703	NM_001300984	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.007160	0.423810	
chunk0080_150_1	chr17	27873888	27874087	+	0	NA	Intergenic	Intergenic	19396	NM_001076680	201229	Hs.687951	NM_001076680	ENSG00000232859	LYRM9	C17orf108|HSD24	LYR motif containing 9	protein-coding	0.000000	0.405000	
chunk0201_94_1	chr9	34736462	34736905	+	0	NA	Intergenic	L1MCc|LINE|L1	-7145	NM_001141917	259308	Hs.522093	NM_001141917	ENSG00000205108	FAM205A	C9orf144B	family with sequence similarity 205 member A	protein-coding	0.004515	0.382883	
chunk0041_217_1	chr11	127412376	127412651	+	0	NA	Intergenic	MER52D|LTR|ERV1	141443	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.014545	0.652174	
chunk0119_385_1	chr22	48297864	48298162	+	0	NA	Intergenic	Intergenic	23649	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.006711	0.371237	
chunk0091_61_1	chr19	4872678	4872877	+	0	NA	Intergenic	Intergenic	-5009	NM_001164194	10226	Hs.140452	NM_005817	ENSG00000105355	PLIN3	M6PRBP1|PP17|TIP47	perilipin 3	protein-coding	0.035176	0.605000	
chunk0060_171_1	chr14	45492129	45492329	+	0	NA	Intergenic	L1M1|LINE|L1	-238827	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.010000	0.557214	
chunk0018_338_1	chr1	221470599	221470848	+	0	NA	Intergenic	Intergenic	-134427	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.004016	0.376000	
chunk0126_185_1	chr3	78217521	78217888	+	0	NA	Intergenic	LTR33C|LTR|ERVL	801755	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002725	0.426630	
chunk0017_246_1	chr1	208499535	208499860	+	0	NA	Intergenic	MER97b|DNA|hAT-Tip100	-255377	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.006154	0.340491	
chunk0135_329_1	chr3	190155805	190156071	+	0	NA	Intergenic	Intergenic	-33501	NM_001134418	55214	Hs.374191	NM_018192	ENSG00000090530	P3H2	LEPREL1|MCVD|MLAT4	prolyl 3-hydroxylase 2	protein-coding	0.007519	0.486891	43(ATCACAGTATGTGCTC,+,0.00)
chunk0148_386_1	chr5	14743633	14744016	+	0	NA	intron (NM_054027, intron 7 of 11)	intron (NM_054027, intron 7 of 11)	31130	NR_046285	100130744	Hs.660550	NR_046285		LOC100130744	-	uncharacterized LOC100130744	ncRNA	0.013055	0.398438	
chunk0035_312_1	chr11	47243476	47243768	+	0	NA	intron (NM_001302489, intron 7 of 10)	intron (NM_001302489, intron 7 of 10)	-4678	NM_001251934	10062	Hs.438863	NM_005693	ENSG00000025434	NR1H3	LXR-a|LXRA|RLD-1	nuclear receptor subfamily 1 group H member 3	protein-coding	0.010274	0.440273	
chunk0069_412_1	chr15	68019282	68019786	+	0	NA	Intergenic	L2b|LINE|L2	-34700	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.003968	0.512871	208(TGGGACAACATGTTCC,-,0.00),209(GGGACAACATGTTCCA,+,0.00),230(GGGAACAGACTGTGCA,-,0.00),231(GGAACAGACTGTGCAC,+,0.00)
chunk0096_310_1	chr2	33052137	33052493	+	0	NA	intron (NM_206943, intron 3 of 33)	intron (NM_206943, intron 3 of 33)	-82282	NM_001166265	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.016854	0.369748	
chunk0001_351_1	chr1	9842806	9843957	+	0	NA	Intergenic	Intergenic	-18855	NM_001009566	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.023458	0.644965	183(TGGCACAGGCTGGGCT,-,0.00),184(GGCACAGGCTGGGCTG,+,0.00)
chunk0135_208_1	chr3	188319462	188319836	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	94244	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.000000	0.349333	216(CAGTACAAAGAGTTCC,-,0.00),217(AGTACAAAGAGTTCCT,+,0.00)
chunk0126_223_1	chr3	78906158	78906677	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	113042	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003854	0.394231	
chunk0074_95_1	chr16	22092361	22092560	+	0	NA	promoter-TSS (NM_173615)	promoter-TSS (NM_173615)	-78	NM_173615	146177	Hs.10697	NM_173615	ENSG00000175267	VWA3A	-	von Willebrand factor A domain containing 3A	protein-coding	0.015075	0.540000	
chunk0075_396_1	chr16	56896241	56896519	+	0	NA	intron (NM_001126107, intron 22 of 25)	MER113|DNA|hAT-Charlie	-7884	NR_106923	102466752		NR_106923	ENSG00000283471	MIR6863	hsa-mir-6863	microRNA 6863	ncRNA	0.010791	0.534050	
chunk0044_92_1	chr12	28320723	28321250	+	0	NA	intron (NM_018318, intron 5 of 11)	intron (NM_018318, intron 5 of 11)	63786	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.001898	0.354167	
chunk0172_171_1	chr6	136338462	136338888	+	0	NA	Intergenic	Intergenic	-48824	NM_001077440	9774	Hs.486542	NM_014739	ENSG00000029363	BCLAF1	BTF|bK211L9.1	BCL2 associated transcription factor 1	protein-coding	0.009390	0.454333	172(GGAACGAGATGTGCTT,+,0.00)
chunk0127_417_1	chr3	102577175	102577906	+	0	NA	Intergenic	Intergenic	142525	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.001368	0.334699	
chunk0140_57_1	chr4	66901275	66901561	+	0	NA	Intergenic	Intergenic	520582	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.000000	0.337979	
chunk0026_40_1	chr10	60781626	60782037	+	0	NA	intron (NM_001786, intron 2 of 7)	L2a|LINE|L2	3377	NM_001170407	983	Hs.732435	NM_001786	ENSG00000170312	CDK1	CDC2|CDC28A|P34CDC2	cyclin dependent kinase 1	protein-coding	0.000000	0.398058	
chunk0087_228_1	chr18	36340215	36340592	+	0	NA	intron (NM_001281739, intron 1 of 23)	intron (NM_001281739, intron 1 of 23)	42707	NM_001281739	80206	Hs.436636	NM_025135	ENSG00000134775	FHOD3	FHOS2|Formactin2	formin homology 2 domain containing 3	protein-coding	0.010610	0.399471	
chunk0208_307_1	chrX	23743335	23743534	+	0	NA	promoter-TSS (NM_001033583)	promoter-TSS (NM_001033583)	-144	NM_001037171	23597	Hs.298885	NM_001033583	ENSG00000123130	ACOT9	ACATE2|CGI-16|MT-ACT48|MTACT48	acyl-CoA thioesterase 9	protein-coding	0.080402	0.605000	
chunk0164_35_1	chr6	18405626	18405829	+	0	NA	intron (NM_182757, intron 2 of 7)	intron (NM_182757, intron 2 of 7)	18377	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.009852	0.436275	
chunk0204_41_1	chr9	92734063	92734284	+	0	NA	intron (NM_001003800, intron 1 of 6)	L1ME3|LINE|L1	30628	NM_001003800	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.004525	0.378378	
chunk0100_34_1	chr2	105389003	105389372	+	0	NA	intron (NM_201557, intron 1 of 5)	intron (NM_201557, intron 1 of 5)	9931	NM_001039492	2274	Hs.443687	NM_001450	ENSG00000115641	FHL2	AAG11|DRAL|FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.018970	0.391892	
chunk0186_134_1	chr7	138477250	138477761	+	0	NA	intron (NM_015905, intron 1 of 18)	L1MC5a|LINE|L1	17171	NM_015905	8805	Hs.490287	NM_003852	ENSG00000122779	TRIM24	PTC6|RNF82|TF1A|TIF1|TIF1A|TIF1ALPHA|hTIF1	tripartite motif containing 24	protein-coding	0.005871	0.355469	
chunk0017_375_1	chr1	212124852	212125054	+	0	NA	Intergenic	Intergenic	47340	NR_036068	100422947		NR_036068	ENSG00000264358	MIR3122	mir-3122	microRNA 3122	ncRNA	0.019802	0.507389	
chunk0140_134_1	chr4	69194223	69194636	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	20302	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.004843	0.454106	
chunk0029_186_1	chr10	100962511	100963050	+	0	NA	3' UTR (NM_018121, exon 20 of 20)	3' UTR (NM_018121, exon 20 of 20)	-9749	NM_001203244	57715	Hs.591923	NM_017893	ENSG00000095539	SEMA4G	-	semaphorin 4G	protein-coding	0.005566	0.379630	
chunk0101_310_1	chr2	135163186	135163850	+	0	NA	intron (NM_001172435, intron 22 of 24)	intron (NM_001172435, intron 22 of 24)	111253	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.004518	0.381955	
chunk0146_338_1	chr4	165905278	165906016	+	0	NA	intron (NM_012464, intron 1 of 20)	intron (NM_012464, intron 1 of 20)	32389	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.009485	0.365359	
chunk0069_162_1	chr15	62557755	62558342	+	0	NA	Intergenic	Charlie15a|DNA|hAT-Charlie	87133	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.010221	0.409864	
chunk0095_164_1	chr2	17266008	17266628	+	0	NA	Intergenic	L1MC3|LINE|L1	252121	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.000000	0.344605	
chunk0008_402_1	chr1	97797765	97798278	+	0	NA	TTS (NR_046591)	TTS (NR_046591)	1100	NR_046591	100873933	Hs.568669	NR_046591	ENSG00000235777	DPYD-AS2	-	DPYD antisense RNA 2	ncRNA	0.001949	0.305447	229(GGGAACATAACGTTCT,-,0.00),230(GGAACATAACGTTCTG,+,0.00)
chunk0016_386_1	chr1	202871435	202871653	+	0	NA	intron (NR_002929, intron 1 of 2)	intron (NR_002929, intron 1 of 2)	9790	NR_002929	148709	Hs.162880	NR_002929	ENSG00000234996	LOC148709	-	actin gamma 1 pseudogene	pseudo	0.004587	0.424658	
chunk0003_356_1	chr1	39158214	39158788	+	0	NA	intron (NM_012090, intron 1 of 92)	intron (NM_012090, intron 1 of 92)	74334	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.008711	0.485217	
chunk0198_437_1	chr8	143598075	143598274	+	0	NA	promoter-TSS (NM_001289950)	promoter-TSS (NM_001289950)	270	NM_032862	84948	Hs.71574	NM_032862	ENSG00000179886	TIGD5	-	tigger transposable element derived 5	protein-coding	0.105528	0.685000	48(CAGGCCAGTGTGTGCC,-,0.00),49(AGGCCAGTGTGTGCCG,+,0.00)
chunk0139_181_1	chr4	54146137	54146509	+	0	NA	Intergenic	Intergenic	46242	NM_133267	170825	Hs.371899	NM_133267	ENSG00000180613	GSX2	GSH2	GS homeobox 2	protein-coding	0.008065	0.436997	
chunk0106_61_1	chr2	196799563	196799762	+	0	NA	5' UTR (NM_012086, exon 1 of 18)	5' UTR (NM_012086, exon 1 of 18)	106	NM_001206774	9330	Hs.470996	NM_012086	ENSG00000119041	GTF3C3	TFIIIC102|TFIIICgamma|TFiiiC2-102	general transcription factor IIIC subunit 3	protein-coding	0.065327	0.595000	
chunk0204_16_1	chr9	91784777	91785138	+	0	NA	intron (NM_004560, intron 1 of 8)	L2a|LINE|L2	-148612	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.005540	0.475138	
chunk0051_247_1	chr12	117165447	117165646	+	0	NA	exon (NM_015002, exon 9 of 12)	exon (NM_015002, exon 9 of 12)	24949	NM_015002	23014	Hs.740376	NM_015002	ENSG00000135108	FBXO21	FBX21	F-box protein 21	protein-coding	0.015075	0.490000	
chunk0037_171_1	chr11	73916318	73916740	+	0	NA	intron (NM_001267803, intron 9 of 12)	intron (NM_001267803, intron 9 of 12)	-33790	NM_153614	374407	Hs.567888	NM_153614	ENSG00000187726	DNAJB13	CILD34|RSPH16A|TSARG5|TSARG6	DnaJ heat shock protein family (Hsp40) member B13	protein-coding	0.002370	0.382979	
chunk0124_430_1	chr3	61200351	61200824	+	0	NA	intron (NM_001166243, intron 2 of 9)	intron (NM_001166243, intron 2 of 9)	50872	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.002114	0.383966	
chunk0028_261_1	chr10	90847046	90847463	+	0	NA	intron (NM_019859, intron 1 of 3)	MIRc|SINE|MIR	10660	NM_019859	3363	Hs.73739	NM_000872	ENSG00000148680	HTR7	5-HT7	5-hydroxytryptamine receptor 7	protein-coding	0.000000	0.373206	
chunk0109_457_1	chr2	241978942	241979172	+	0	NA	intron (NR_110220, intron 3 of 3)	L1MC3|LINE|L1	8374	NR_110592	102723927	Hs.733585	NR_110592	ENSG00000237940	LINC01238	-	long intergenic non-protein coding RNA 1238	ncRNA	0.000000	0.419913	
chunk0010_292_1	chr1	117591342	117591551	+	0	NA	Intergenic	Intergenic	14324	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.009569	0.509524	148(CAAAACAGGTTGTACT,-,0.00),149(AAAACAGGTTGTACTG,+,0.00)
chunk0159_459_1	chr5	148906780	148907188	+	0	NA	Intergenic	L2a|LINE|L2	80391	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.004902	0.452323	
chunk0038_73_1	chr11	83092937	83093271	+	0	NA	Intergenic	Intergenic	21038	NR_038903	100506233	Hs.503429	NR_038903	ENSG00000246067	RAB30-DT	RAB30-AS1	RAB30 divergent transcript	ncRNA	0.002994	0.450746	157(GGGAACAGGATGGTCT,-,0.00),158(GGAACAGGATGGTCTC,+,0.00)
chunk0138_277_1	chr4	40485008	40485229	+	0	NA	intron (NM_001098634, intron 2 of 6)	intron (NM_001098634, intron 2 of 6)	17001	NR_039966	100616274		NR_039966	ENSG00000263642	MIR4802	-	microRNA 4802	ncRNA	0.000000	0.355856	
chunk0065_239_1	chr14	101196328	101196656	+	0	NA	Intergenic	Intergenic	126581	NR_047664	100507257	Hs.301755	NR_047664	ENSG00000223403	MEG9	LINC00584	maternally expressed 9	ncRNA	0.009146	0.458967	
chunk0001_249_1	chr1	8391261	8391478	+	0	NA	intron (NM_001042682, intron 2 of 12)	intron (NM_001042682, intron 2 of 12)	32318	NM_001042682	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.004608	0.495413	
chunk0127_167_1	chr3	94982409	94982803	+	0	NA	intron (NR_015400, intron 4 of 7)	L1MC3|LINE|L1	44343	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.000000	0.334177	
chunk0062_161_1	chr14	69342762	69344054	+	0	NA	intron (NM_001168368, intron 12 of 14)	MARNA|DNA|TcMar-Mariner	54896	NM_004450	2079	Hs.509791	NM_004450	ENSG00000100632	ERH	DROER	ERH mRNA splicing and mitosis factor	protein-coding	0.013158	0.478732	
chunk0117_217_1	chr22	22349229	22349726	+	0	NA	Intergenic	Intergenic	51379	NR_027293	96610	Hs.449601	NM_080926		BMS1P20	IGL|IGLV|IGLV1	BMS1 pseudogene 20	pseudo	0.010060	0.508032	289(AGGGACGGGATGTTCA,-,0.00),290(GGGACGGGATGTTCAG,+,0.00)
chunk0014_296_1	chr1	180815146	180815607	+	0	NA	intron (NM_001135669, intron 7 of 13)	intron (NM_001135669, intron 7 of 13)	-97801	NM_020950	57710	Hs.734816	NM_020950	ENSG00000135835	KIAA1614	-	KIAA1614	protein-coding	0.008677	0.316017	
chunk0202_310_1	chr9	78044139	78044853	+	0	NA	Intergenic	Intergenic	-13047	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.011204	0.482517	
chunk0162_450_1	chr5	180668648	180669027	+	0	NA	Intergenic	Intergenic	-19213	NM_182925	2324	Hs.646917	NM_002020	ENSG00000037280	FLT4	FLT-4|FLT41|LMPH1A|LMPHM1|PCL|VEGFR-3|VEGFR3	fms related tyrosine kinase 4	protein-coding	0.023747	0.534211	221(AGGGACTCTGTGTCCC,-,0.00),222(GGGACTCTGTGTCCCC,+,0.00)
chunk0046_150_1	chr12	58199603	58199906	+	0	NA	Intergenic	Intergenic	258092	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.006601	0.391447	
chunk0051_42_1	chr12	112252106	112252653	+	0	NA	intron (NM_001109662, intron 23 of 75)	intron (NM_001109662, intron 23 of 75)	-89058	NR_106921	102465519		NR_106921	ENSG00000283793	MIR6861	hsa-mir-6861	microRNA 6861	ncRNA	0.007313	0.406934	279(TAGTACATTTTGTCCA,-,0.00),280(AGTACATTTTGTCCAC,+,0.00)
chunk0083_362_1	chr17	70855309	70855753	+	0	NA	Intergenic	Intergenic	346648	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.013514	0.424719	
chunk0018_111_1	chr1	218301014	218301332	+	0	NA	intron (NM_016052, intron 1 of 4)	intron (NM_016052, intron 1 of 4)	15886	NM_016052	51018	Hs.660109	NM_016052	ENSG00000067533	RRP15	CGI-115|KIAA0507	ribosomal RNA processing 15 homolog	protein-coding	0.000000	0.319749	
chunk0132_182_1	chr3	157058435	157058779	+	0	NA	Intergenic	Intergenic	-31274	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.002907	0.417391	
chunk0173_208_1	chr6	145453208	145453737	+	0	NA	Intergenic	Intergenic	-281397	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.330189	
chunk0072_304_1	chr15	98760161	98760691	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-24000	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.016981	0.450094	
chunk0088_153_1	chr18	46431909	46432240	+	0	NA	intron (NM_001256758, intron 1 of 5)	HAL1|LINE|L1	87012	NM_001145473	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.003021	0.406627	
chunk0084_233_1	chr17	78723185	78723530	+	0	NA	5' UTR (NM_001292018, exon 1 of 13)	5' UTR (NM_001292018, exon 1 of 13)	393	NM_001292018	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.046377	0.647399	
chunk0040_420_1	chr11	121257971	121258475	+	0	NA	Intergenic	L2c|LINE|L2	-34456	NM_006918	6309	Hs.287749	NM_006918	ENSG00000109929	SC5D	ERG3|S5DES|SC5DL	sterol-C5-desaturase	protein-coding	0.003968	0.334653	
chunk0073_312_1	chr16	14180641	14181262	+	0	NA	intron (NM_001308142, intron 3 of 16)	intron (NM_001308142, intron 3 of 16)	109637	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.006441	0.405145	408(AAGTACTGTATGTTCA,-,0.00),409(AGTACTGTATGTTCAG,+,0.00)
chunk0005_405_1	chr1	62547430	62547981	+	0	NA	intron (NM_001271999, intron 22 of 48)	intron (NM_001271999, intron 22 of 48)	-49782	NM_014495	27329	Hs.209153	NM_014495	ENSG00000132855	ANGPTL3	ANG-5|ANGPT5|ANL3|FHBL2	angiopoietin like 3	protein-coding	0.003630	0.318841	
chunk0063_220_1	chr14	81536243	81536820	+	0	NA	Intergenic	Intergenic	-2670	NM_001244984	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.003466	0.399654	
chunk0070_450_1	chr15	78449244	78449732	+	0	NA	intron (NM_004136, intron 2 of 21)	MER102a|DNA|hAT-Charlie	11312	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.006148	0.390593	
chunk0027_446_1	chr10	81193460	81193804	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	652813	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.002907	0.249275	
chunk0110_153_1	chr20	13809431	13809690	+	0	NA	intron (NM_001039375, intron 7 of 9)	L2b|LINE|L2	24534	NM_024120	79133	Hs.472165	NM_024120	ENSG00000101247	NDUFAF5	C20orf7|MC1DN16|bA526K24.2|dJ842G6.1	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.003861	0.438462	
chunk0099_79_1	chr2	85353902	85354101	+	0	NA	promoter-TSS (NM_001135023)	promoter-TSS (NM_001135023)	697	NM_017750	54884	Hs.440401	NM_017750	ENSG00000042445	RETSAT	-	retinol saturase	protein-coding	0.045226	0.545000	
chunk0144_145_1	chr4	130053730	130053929	+	0	NA	Intergenic	Intergenic	-282351	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.005025	0.420000	
chunk0002_283_1	chr1	22486000	22486387	+	0	NA	intron (NM_001083621, intron 2 of 18)	L1MC1|LINE|L1	34342	NM_001083621	9923	Hs.418966	NM_014870	ENSG00000184677	ZBTB40	ZNF923	zinc finger and BTB domain containing 40	protein-coding	0.002584	0.435567	140(GTGGACATGATGTACT,-,0.00),141(TGGACATGATGTACTG,+,0.00)
chunk0011_195_1	chr1	149972396	149972868	+	0	NA	intron (NM_020205, intron 2 of 11)	L2a|LINE|L2	-35734	NM_001145862	10903	Hs.425144	NM_006697	ENSG00000014914	MTMR11	CRA	myotubularin related protein 11	protein-coding	0.004237	0.380550	
chunk0116_423_1	chr21	42769303	42769713	+	0	NA	intron (NM_001315533, intron 17 of 19)	intron (NM_001315533, intron 17 of 19)	109767	NM_001260477	10785	Hs.248815	NM_018669	ENSG00000160193	WDR4	GAMOS6|MIGSB|TRM82|TRMT82	WD repeat domain 4	protein-coding	0.009756	0.525547	
chunk0024_124_1	chr10	34906158	34906357	+	0	NA	Intergenic	Intergenic	90489	NR_108043	100505601	Hs.549790	NR_108043	ENSG00000226386	PARD3-AS1	-	PARD3 antisense RNA 1	ncRNA	0.020101	0.535000	
chunk0123_391_1	chr3	48827354	48827759	+	0	NA	intron (NM_004157, intron 1 of 10)	Tigger3b|DNA|TcMar-Tigger	20281	NM_004157	5576	Hs.631923	NM_004157	ENSG00000114302	PRKAR2A	PKR2|PRKAR2	protein kinase cAMP-dependent type II regulatory subunit alpha	protein-coding	0.007407	0.342365	
chunk0160_304_1	chr5	158996035	158996470	+	0	NA	intron (NM_182708, intron 5 of 14)	intron (NM_182708, intron 5 of 14)	103528	NM_182708	1879	Hs.573143	NM_024007	ENSG00000164330	EBF1	COE1|EBF|O/E-1|OLF1	EBF transcription factor 1	protein-coding	0.002299	0.339450	
chunk0026_63_1	chr10	61130477	61131125	+	0	NA	Intergenic	Intergenic	114526	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.001543	0.380586	297(AGGTACACTGAGTACT,-,0.00),298(GGTACACTGAGTACTG,+,0.00)
chunk0166_108_1	chr6	43957330	43957529	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-43171	NM_001171992	221416	Hs.531926	NM_153246	ENSG00000181577	C6orf223	-	chromosome 6 open reading frame 223	ncRNA	0.005025	0.250000	
chunk0063_342_1	chr14	85372145	85372511	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-21551	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005464	0.408719	
chunk0141_375_1	chr4	88112063	88112539	+	0	NA	intron (NM_004827, intron 9 of 15)	intron (NM_004827, intron 9 of 15)	46558	NM_004827	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.000000	0.381551	
chunk0151_203_1	chr5	50725560	50726090	+	0	NA	intron (NM_024615, intron 2 of 25)	MamRTE1|LINE|RTE-BovB	58887	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.005660	0.344633	
chunk0153_211_1	chr5	71957036	71957579	+	0	NA	Intergenic	Intergenic	-149984	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.003683	0.387868	
chunk0168_26_1	chr6	77376577	77376944	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	86643	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.002725	0.404891	
chunk0154_290_1	chr5	82860263	82860787	+	0	NA	promoter-TSS (NR_105016)	promoter-TSS (NR_105016)	-689	NR_105016	102546175		NR_105016	ENSG00000281327	LINC01338	-	long intergenic non-protein coding RNA 1338	ncRNA	0.003817	0.340952	
chunk0085_151_1	chr18	3459383	3459740	+	0	NA	Intergenic	Intergenic	5787	NM_173211	7050	Hs.373550	NM_003244	ENSG00000177426	TGIF1	HPE4|TGIF	TGFB induced factor homeobox 1	protein-coding	0.011204	0.407821	
chunk0175_410_1	chr6	168782832	168783435	+	0	NA	Intergenic	Intergenic	341982	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.009950	0.425497	166(GAGAACACACTGAGCT,-,0.00),167(AGAACACACTGAGCTT,+,0.00)
chunk0139_222_1	chr4	55093423	55093814	+	0	NA	intron (NM_002253, intron 21 of 29)	intron (NM_002253, intron 21 of 29)	31977	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.005115	0.448980	
chunk0186_364_1	chr7	143926246	143926784	+	0	NA	Intergenic	Intergenic	-8718	NM_001004685	135948	Hs.553596	NM_001004685	ENSG00000221910	OR2F2	OR7-1	olfactory receptor family 2 subfamily F member 2	protein-coding	0.001859	0.296846	
chunk0130_284_1	chr3	136498576	136499041	+	0	NA	intron (NM_005862, intron 9 of 33)	Tigger13a|DNA|TcMar-Tigger	248483	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.004301	0.330472	
chunk0094_223_1	chr2	6759983	6760295	+	0	NA	intron (NR_038369, intron 1 of 5)	(TG)n|Simple_repeat|Simple_repeat	10172	NR_038369	400941	Hs.446195	NM_001001695	ENSG00000205837	LINC00487	-	long intergenic non-protein coding RNA 487	ncRNA	0.009615	0.488818	
chunk0180_168_1	chr7	65284288	65284845	+	0	NA	Intergenic	L1PA11|LINE|L1	-89233	NM_001287534	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.007181	0.388889	
chunk0015_113_1	chr1	185268416	185268900	+	0	NA	intron (NM_017673, intron 16 of 18)	intron (NM_017673, intron 16 of 18)	48671	NM_006469	10625	Hs.497183	NM_006469	ENSG00000116679	IVNS1ABP	ARA3|FLARA3|HSPC068|KLHL39|ND1|NS-1|NS1-BP|NS1BP	influenza virus NS1A binding protein	protein-coding	0.010331	0.362887	309(TAGAACATCTTGTTTT,-,0.00)
chunk0072_148_1	chr15	92770571	92771111	+	0	NA	Intergenic	MER87|LTR|ERV1	-24643	NR_033769	728619	Hs.684129	NR_033769		ASB9P1	-	ankyrin repeat and SOCS box containing 9 pseudogene 1	pseudo	0.011111	0.471349	218(CAGAACTTCTTGTTCA,-,0.00),219(AGAACTTCTTGTTCAC,+,0.00)
chunk0153_268_1	chr5	72878892	72879263	+	0	NA	TTS (NR_039968)	TTS (NR_039968)	486	NR_039968	100616152		NR_039968	ENSG00000263593	MIR4804	-	microRNA 4804	ncRNA	0.008086	0.459677	
chunk0199_258_1	chr9	6055369	6055568	+	0	NA	Intergenic	Intergenic	-39828	NM_001243202	26953	Hs.167496	NM_012416	ENSG00000137040	RANBP6	-	RAN binding protein 6	protein-coding	0.005025	0.400000	
chunk0039_219_1	chr11	101452010	101452454	+	0	NA	3' UTR (NM_004621, exon 13 of 13)	3' UTR (NM_004621, exon 13 of 13)	67673	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.004505	0.343820	
chunk0107_275_1	chr2	217988085	217988398	+	0	NA	Intergenic	Intergenic	-44168	NM_022648	7145	Hs.471381	NM_022648	ENSG00000079308	TNS1	MST091|MST122|MST127|MSTP091|MSTP122|MSTP127|MXRA6|PPP1R155|TNS	tensin 1	protein-coding	0.006390	0.611465	
chunk0149_231_1	chr5	23283306	23283853	+	0	NA	Intergenic	Intergenic	-224030	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.009141	0.348540	
chunk0125_305_1	chr3	70631598	70631817	+	0	NA	Intergenic	Intergenic	433216	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.009132	0.345455	
chunk0010_24_1	chr1	112443687	112443968	+	0	NA	intron (NM_018704, intron 3 of 5)	intron (NM_018704, intron 3 of 5)	18006	NR_036210	100422976		NR_036210	ENSG00000283296	MIR4256	-	microRNA 4256	ncRNA	0.000000	0.280142	
chunk0166_344_1	chr6	51063996	51064844	+	0	NA	Intergenic	Intergenic	245694	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.003538	0.409894	
chunk0104_158_1	chr2	174116724	174117168	+	0	NA	intron (NM_001011708, intron 6 of 9)	intron (NM_001011708, intron 6 of 9)	131691	NM_013341	29789	Hs.157351	NM_013341	ENSG00000138430	OLA1	DOC45|GBP45|GTBP9|GTPBP9|PTD004	Obg like ATPase 1	protein-coding	0.000000	0.328090	
chunk0139_340_1	chr4	59570757	59571198	+	0	NA	Intergenic	Intergenic	-1351642	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.004535	0.303167	
chunk0165_440_1	chr6	40396461	40397243	+	0	NA	intron (NM_020737, intron 2 of 2)	intron (NM_020737, intron 2 of 2)	18428	NR_024015									0.014066	0.492976	
chunk0212_6_1	chrY	6213332	6213684	+	0	NA	Intergenic	Intergenic	30102	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.000000	0.351275	176(CAGTACAATCTGTACC,-,0.00),177(AGTACAATCTGTACCT,+,0.00)
chunk0150_101_1	chr5	32574518	32575035	+	0	NA	Intergenic	Intergenic	-10723	NM_006713	10923	Hs.229641	NM_006713	ENSG00000113387	SUB1	P15|PC4|p14	SUB1 regulator of transcription	protein-coding	0.003868	0.455598	
chunk0146_418_1	chr4	169119589	169119788	+	0	NA	intron (NM_020870, intron 8 of 11)	intron (NM_020870, intron 8 of 11)	-109371	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.000000	0.335000	
chunk0188_24_1	chr8	6555719	6556008	+	0	NA	intron (NM_001147, intron 1 of 8)	intron (NM_001147, intron 1 of 8)	7400	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.017301	0.424138	
chunk0111_251_1	chr20	30424546	30424756	+	0	NA	Intergenic	Intergenic	-21189	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.019048	0.355450	
chunk0171_263_1	chr6	127457469	127457669	+	0	NA	intron (NM_001012279, intron 7 of 11)	intron (NM_001012279, intron 7 of 11)	1821	NM_014702	9729	Hs.319247	NM_014702	ENSG00000189367	KIAA0408	-	KIAA0408	protein-coding	0.000000	0.378109	61(GAGGACAGAGTGAGCT,-,0.00),62(AGGACAGAGTGAGCTG,+,0.00)
chunk0024_249_1	chr10	38902327	38902595	+	0	NA	Intergenic	(GAATGGAATG)n|Simple_repeat|Simple_repeat	205865	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.014925	0.371747	
chunk0194_40_1	chr8	81856994	81857718	+	0	NA	Intergenic	L1MA9|LINE|L1	-15070	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.001381	0.333793	
chunk0009_123_1	chr1	103295609	103295808	+	0	NA	Intergenic	Intergenic	-187212	NM_080629	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.000000	0.355000	
chunk0134_198_1	chr3	178421075	178421542	+	0	NA	intron (NR_046786, intron 1 of 2)	intron (NR_046786, intron 1 of 2)	2107	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.004283	0.356838	
chunk0021_410_1	chr1	246775259	246776112	+	0	NA	Intergenic	L1ME3B|LINE|L1	-13932	NR_015422	149134	Hs.720494	NM_207326		LINC01341	-	long intergenic non-protein coding RNA 1341	ncRNA	0.021102	0.420375	
chunk0028_218_1	chr10	89553269	89553468	+	0	NA	Intergenic	Intergenic	-17812	NM_213606	387700	Hs.530338	NM_213606	ENSG00000152779	SLC16A12	CJMG|CRT2|CTRCT47|MCT12	solute carrier family 16 member 12	protein-coding	0.000000	0.345000	
chunk0058_398_1	chr13	111464720	111464938	+	0	NA	Intergenic	L1PA16|LINE|L1	144185	NM_152324	121793	Hs.210677	NM_152324	ENSG00000153495	TEX29	C13orf16|bA474D23.1	testis expressed 29	protein-coding	0.013761	0.401826	
chunk0123_456_1	chr3	51353819	51354310	+	0	NA	intron (NM_004947, intron 40 of 52)	intron (NM_004947, intron 40 of 52)	-31173	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.000000	0.451220	
chunk0103_82_1	chr2	160610086	160610494	+	0	NA	Intergenic	Intergenic	-116483	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.004902	0.371638	
chunk0132_221_1	chr3	157823002	157823653	+	0	NA	Intergenic	Intergenic	279983	NR_024016	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.006144	0.328221	
chunk0133_160_1	chr3	169773010	169773686	+	0	NA	promoter-TSS (NM_001185119)	promoter-TSS (NM_001185119)	283	NM_001185118	55892	Hs.507025	NM_018657	ENSG00000085274	MYNN	OSZF|SBBIZ1|ZBTB31|ZNF902	myoneurin	protein-coding	0.069527	0.669129	259(TGGTACATCCTGTACC,-,0.00),260(GGTACATCCTGTACCG,+,0.00)
chunk0118_289_1	chr22	33939267	33939881	+	0	NA	Intergenic	Intergenic	-19146	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.001629	0.338211	
chunk0167_352_1	chr6	72929273	72929908	+	0	NA	intron (NM_019842, intron 1 of 13)	(TACATAAAG)n|Simple_repeat|Simple_repeat	38163	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.003150	0.327044	374(GAGTACATAAAGTACT,-,0.00),375(AGTACATAAAGTACTC,+,0.00)
chunk0063_39_1	chr14	76812873	76813251	+	0	NA	promoter-TSS (NM_015305)	promoter-TSS (NM_015305)	-122	NM_015305	23357	Hs.497448	NM_015305	ENSG00000013523	ANGEL1	Ccr4e|KIAA0759	angel homolog 1	protein-coding	0.055556	0.593668	
chunk0022_226_1	chr10	14025311	14025510	+	0	NA	intron (NM_018027, intron 2 of 24)	L1MB2|LINE|L1	-48874	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.005025	0.335000	
chunk0211_21_1	chrX	107857928	107858264	+	0	NA	intron (NM_052817, intron 3 of 9)	intron (NM_052817, intron 3 of 9)	32242	NM_052817	11043	Hs.12256	NM_012216	ENSG00000080561	MID2	FXY2|MRX101|RNF60|TRIM1	midline 2	protein-coding	0.002976	0.403561	
chunk0033_451_1	chr11	25553849	25554373	+	0	NA	Intergenic	Intergenic	-635012	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.005725	0.310476	
chunk0142_232_1	chr4	98517395	98517861	+	0	NA	intron (NM_005723, intron 1 of 7)	intron (NM_005723, intron 1 of 7)	141033	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.002146	0.468951	
chunk0036_369_1	chr11	67257697	67258053	+	0	NA	non-coding (NR_027473, exon 21 of 21)	non-coding (NR_027473, exon 21 of 21)	-8559	NM_001619	156	Hs.83636	NM_001619	ENSG00000173020	GRK2	ADRBK1|BARK1|BETA-ARK1	G protein-coupled receptor kinase 2	protein-coding	0.005618	0.319328	
chunk0111_6_1	chr20	21759115	21759358	+	0	NA	Intergenic	MIRb|SINE|MIR	53577	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.008230	0.393443	
chunk0004_330_1	chr1	50209817	50210128	+	0	NA	Intergenic	L2a|LINE|L2	100356	NM_001294348	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.003215	0.535256	54(AAGTACAGGCTGTTCT,-,0.00),55(AGTACAGGCTGTTCTG,+,0.00),154(GAGGACAGTGTGTCCC,-,0.00),155(AGGACAGTGTGTCCCA,+,0.00)
chunk0012_194_1	chr1	159853006	159853550	+	0	NA	intron (NM_001134233, intron 2 of 5)	intron (NM_001134233, intron 2 of 5)	2069	NM_001134233	284677	Hs.647718	NM_001134233	ENSG00000256029	SNHG28	C1orf204|VSIG8-OT1	small nucleolar RNA host gene 28	ncRNA	0.005515	0.381651	
chunk0147_210_1	chr4	180473079	180473467	+	0	NA	Intergenic	Intergenic	685876	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.002577	0.293059	
chunk0029_357_1	chr10	107573561	107573999	+	0	NA	Intergenic	L1MC2|LINE|L1	-409072	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.002283	0.353075	255(AGGTACACTCTGTATT,-,0.00)
chunk0073_432_1	chr16	19164263	19164744	+	0	NA	Intergenic	Intergenic	-3710	NM_016524	51760	Hs.258326	NM_016524	ENSG00000103528	SYT17	sytXVII	synaptotagmin 17	protein-coding	0.012474	0.491701	
chunk0010_427_1	chr1	119768793	119769317	+	0	NA	promoter-TSS (NM_005518)	promoter-TSS (NM_005518)	-123	NM_005518	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.015267	0.508571	
chunk0179_264_1	chr7	49179235	49179741	+	0	NA	Intergenic	Intergenic	254927	NR_003595									0.000000	0.370809	
chunk0091_30_1	chr19	3500560	3501116	+	0	NA	promoter-TSS (NM_031304)	promoter-TSS (NM_031304)	102	NM_001145165	83475	Hs.515064	NM_031304	ENSG00000129932	DOHH	HLRC1|hDOHH	deoxyhypusine hydroxylase	protein-coding	0.066547	0.585278	
chunk0189_214_1	chr8	24337155	24337808	+	0	NA	intron (NR_130710, intron 14 of 22)	L2b|LINE|L2	43441	NM_021777	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.009188	0.368502	
chunk0212_251_1	chrX	138886615	138887276	+	0	NA	intron (NM_001139500, intron 2 of 6)	intron (NM_001139500, intron 2 of 6)	-19390	NM_001139502	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.004539	0.388218	
chunk0173_99_1	chr6	143155846	143156062	+	0	NA	intron (NM_001286587, intron 3 of 6)	L2c|LINE|L2	95112	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.000000	0.506912	
chunk0053_189_1	chr13	31310963	31311192	+	0	NA	intron (NM_194318, intron 12 of 14)	LTR27E|LTR|ERV1	111102	NM_194318	145173	Hs.13205	NM_194318	ENSG00000187676	B3GLCT	B3GALTL|B3GTL|B3Glc-T|Gal-T|beta3Glc-T	beta 3-glucosyltransferase	protein-coding	0.008734	0.504348	
chunk0142_374_1	chr4	102071173	102071552	+	0	NA	intron (NM_017935, intron 14 of 16)	intron (NM_017935, intron 14 of 16)	252950	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.010554	0.315789	
chunk0098_275_1	chr2	75493230	75493641	+	0	NA	exon (NM_001135032, exon 4 of 4)	exon (NM_001135032, exon 4 of 4)	-30633	NR_110281	101927884	Hs.671110	NR_110281	ENSG00000231172	LOC101927884	-	uncharacterized LOC101927884	ncRNA	0.060827	0.592233	
chunk0207_162_1	chr9	130173325	130173531	+	0	NA	intron (NM_014286, intron 1 of 7)	intron (NM_014286, intron 1 of 7)	850	NM_014286	23413	Hs.642946	NM_014286	ENSG00000107130	NCS1	FLUP|FREQ	neuronal calcium sensor 1	protein-coding	0.038835	0.594203	
chunk0133_410_1	chr3	174436336	174436823	+	0	NA	Intergenic	MER101B|LTR|ERV1	-422742	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.004107	0.432377	174(ATGTACTCTGTGTTCT,-,0.00),175(TGTACTCTGTGTTCTC,+,0.00)
chunk0049_102_1	chr12	90916574	90916883	+	0	NA	Intergenic	Intergenic	-1295	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.000000	0.306452	
chunk0019_66_1	chr1	224262028	224262890	+	0	NA	intron (NM_206840, intron 17 of 21)	HAL1|LINE|L1	-5318	NR_031574	100313769		NR_031574	ENSG00000221406	MIR320B2	MIR320B-2|MIRN320B2|mir-320b-2	microRNA 320b-2	ncRNA	0.002320	0.345307	
chunk0182_178_1	chr7	95609620	95609932	+	0	NA	Intergenic	Intergenic	-13163	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.006410	0.386581	
chunk0157_240_1	chr5	119564177	119564689	+	0	NA	Intergenic	Intergenic	-65126	NM_001163991	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.005859	0.405458	
chunk0210_322_1	chrX	92759632	92760013	+	0	NA	Intergenic	L1MC5a|LINE|L1	65081	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.000000	0.348168	8(AGGAACAATTTGTACA,-,0.00)
chunk0112_383_1	chr20	46364638	46364918	+	0	NA	promoter-TSS (NM_001281460)	promoter-TSS (NM_001281460)	-320	NM_001281459	51006	Hs.593344	NM_015945	ENSG00000080189	SLC35C2	BA394O2.1|C20orf5|CGI-15|OVCOV1	solute carrier family 35 member C2	protein-coding	0.021429	0.434164	
chunk0031_456_1	chr10	132705168	132705758	+	0	NA	intron (NM_005539, intron 6 of 15)	intron (NM_005539, intron 6 of 15)	80570	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.028814	0.585448	
chunk0077_221_1	chr16	80198318	80198878	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-342136	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.007143	0.365419	
chunk0166_8_1	chr6	41532049	41532256	+	0	NA	intron (NR_126415, intron 1 of 1)	intron (NR_126415, intron 1 of 1)	14091	NR_126417	101060264	Hs.571099	NR_126415	ENSG00000234753	FOXP4-AS1	-	FOXP4 antisense RNA 1	ncRNA	0.033816	0.610577	
chunk0014_449_1	chr1	183887363	183887701	+	0	NA	intron (NM_001297672, intron 7 of 16)	intron (NM_001297672, intron 7 of 16)	82451	NM_001297671	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.014793	0.442478	
chunk0105_95_1	chr2	184391713	184392311	+	0	NA	Intergenic	Charlie20a|DNA|hAT-Charlie	13037	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.003344	0.280467	
chunk0021_160_1	chr10	5043627	5044004	+	0	NA	Intergenic	HERVK13-int|LTR|ERVK	-4951	NM_001253908	8644	Hs.78183	NM_003739	ENSG00000196139	AKR1C3	DD3|DDX|HA1753|HAKRB|HAKRe|HSD17B5|PGFS|hluPGFS	aldo-keto reductase family 1 member C3	protein-coding	0.002653	0.417989	
chunk0170_331_1	chr6	116244244	116244876	+	0	NA	3' UTR (NM_152729, exon 12 of 12)	3' UTR (NM_152729, exon 12 of 12)	9538	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.006329	0.379147	412(AAGAACATTGAGTCCA,-,0.00),413(AGAACATTGAGTCCAG,+,0.00)
chunk0145_89_1	chr4	145937425	145937624	+	0	NA	intron (NM_178835, intron 1 of 14)	CpG	1436	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.170854	0.840000	
chunk0121_451_1	chr3	26756734	26757398	+	0	NA	Intergenic	Intergenic	134257	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.004518	0.383459	289(AAGGACAGGGTGTACA,-,0.00),290(AGGACAGGGTGTACAT,+,0.00)
chunk0212_349_1	chrX	148066154	148066498	+	0	NA	Intergenic	L1MA4|LINE|L1	84997	NM_152578	158521	Hs.128580	NM_152578	ENSG00000176988	FMR1NB	CT37|NY-SAR-35|NYSAR35	FMR1 neighbor	protein-coding	0.000000	0.304348	
chunk0178_127_1	chr7	32077233	32077539	+	0	NA	intron (NM_001191058, intron 3 of 18)	intron (NM_001191058, intron 3 of 18)	-5950	NM_001191059	5137	Hs.143821	NM_005020	ENSG00000154678	PDE1C	DFNA74|Hcam3|cam-PDE 1C|hCam-3	phosphodiesterase 1C	protein-coding	0.006536	0.361564	
chunk0190_328_1	chr8	38936592	38937069	+	0	NA	intron (NM_021623, intron 3 of 11)	intron (NM_021623, intron 3 of 11)	35595	NM_021623	59339	Hs.369123	NM_021623	ENSG00000169499	PLEKHA2	TAPP2	pleckstrin homology domain containing A2	protein-coding	0.023061	0.604603	
chunk0044_77_1	chr12	28098453	28098653	+	0	NA	Intergenic	MIRb|SINE|MIR	-126570	NM_002820	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.010000	0.318408	
chunk0144_237_1	chr4	134959300	134959721	+	0	NA	Intergenic	Intergenic	-757762	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.007126	0.308057	
chunk0083_132_1	chr17	65463340	65463539	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	5898	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.015075	0.515000	10(GGGTACAGGCTGTACT,-,0.00),11(GGTACAGGCTGTACTC,+,0.00)
chunk0078_27_1	chr17	841361	841605	+	0	NA	intron (NM_022463, intron 1 of 7)	CpG	22628	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.102459	0.714286	
chunk0210_240_1	chrX	82718084	82718452	+	0	NA	Intergenic	Intergenic	-789993	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.000000	0.414634	311(AAGATCAAGGTGTTCC,-,0.00),312(AGATCAAGGTGTTCCC,+,0.00)
chunk0106_30_1	chr2	195968192	195968508	+	0	NA	intron (NM_018897, intron 17 of 64)	L1MA3|LINE|L1	100462	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.009494	0.523659	
chunk0104_396_1	chr2	180600973	180601262	+	0	NA	Intergenic	Intergenic	-90987	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.003460	0.268966	
chunk0190_209_1	chr8	35655746	35656445	+	0	NA	intron (NM_080872, intron 4 of 16)	intron (NM_080872, intron 4 of 16)	54225	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.002861	0.401429	561(TAGGACACACTGTATT,-,0.00),562(AGGACACACTGTATTT,+,0.00)
chunk0047_251_1	chr12	72376446	72377140	+	0	NA	intron (NM_013381, intron 2 of 18)	intron (NM_013381, intron 2 of 18)	-103284	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.001441	0.310791	
chunk0078_88_1	chr17	1999975	2000489	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	25113	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.019455	0.601942	340(AGGGACACAAAGTCCT,-,0.00),341(GGGACACAAAGTCCTA,+,0.00)
chunk0020_44_1	chr1	232285703	232286133	+	0	NA	Intergenic	Intergenic	229690	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.004651	0.470998	249(GGGCACTTTGTGTGCC,-,0.00),250(GGCACTTTGTGTGCCC,+,0.00)
chunk0027_299_1	chr10	77720941	77721296	+	0	NA	Intergenic	MER4A1|LTR|ERV1	-83299	NM_001161353	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.000000	0.382022	
chunk0190_454_1	chr8	42104651	42105070	+	0	NA	Intergenic	L1MEc|LINE|L1	-48086	NM_006803	10947	Hs.654529	NM_006803	ENSG00000070718	AP3M2	AP47B|CLA20|P47B	adaptor related protein complex 3 subunit mu 2	protein-coding	0.014320	0.390476	
chunk0062_331_1	chr14	73411403	73411791	+	0	NA	intron (NM_001005743, intron 1 of 12)	L2b|LINE|L2	46983	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.007732	0.293059	
chunk0122_41_1	chr3	28186727	28187132	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-54704	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.000000	0.293103	229(TAGTACATATTGTACT,-,0.00),230(AGTACATATTGTACTA,+,0.00)
chunk0042_101_1	chr12	2908034	2908553	+	0	NA	intron (NM_003324, intron 1 of 10)	intron (NM_003324, intron 1 of 10)	17426	NM_001160408	7289	Hs.655333	NM_003324	ENSG00000078246	TULP3	TUBL3	TUB like protein 3	protein-coding	0.013487	0.388462	
chunk0127_337_1	chr3	100522177	100522500	+	0	NA	intron (NM_018004, intron 1 of 5)	intron (NM_018004, intron 1 of 5)	29719	NM_018004	55076	Hs.658956	NM_018004	ENSG00000181458	TMEM45A	DERP7|DNAPTP4	transmembrane protein 45A	protein-coding	0.009288	0.490741	
chunk0211_383_1	chrX	127297489	127298045	+	0	NA	Intergenic	Intergenic	478003	NM_001122716	100130613	Hs.130370	NM_001122716	ENSG00000183631	PRR32	CXorf64	proline rich 32	protein-coding	0.003597	0.294434	288(AGGAACAGGATCTTCT,-,0.00)
chunk0054_236_1	chr13	45787852	45788185	+	0	NA	intron (NM_198849, intron 1 of 1)	intron (NM_198849, intron 1 of 1)	63693	NM_198849	283514	Hs.368483	NM_198849	ENSG00000215475	SIAH3	-	siah E3 ubiquitin protein ligase family member 3	protein-coding	0.006006	0.455090	
chunk0156_448_1	chr5	114867695	114868312	+	0	NA	Intergenic	L1PA11|LINE|L1	-94590	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.003241	0.373786	
chunk0114_179_1	chr21	14879013	14879410	+	0	NA	Intergenic	Intergenic	185594	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.015113	0.336683	
chunk0005_70_1	chr1	55823815	55824014	+	0	NA	Intergenic	L2c|LINE|L2	598273	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.015075	0.465000	
chunk0058_156_1	chr14	23237945	23238157	+	0	NA	5' UTR (NM_001282322, exon 1 of 15)	5' UTR (NM_001282322, exon 1 of 15)	133	NM_001282322	100507650		NM_001282322	ENSG00000215277	RNF212B	C14orf164	ring finger protein 212B	protein-coding	0.037736	0.549296	
chunk0185_110_1	chr7	125675740	125676514	+	0	NA	Intergenic	Intergenic	-411836	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.007752	0.325161	
chunk0075_451_1	chr16	58176788	58176993	+	0	NA	intron (NM_001896, intron 4 of 11)	intron (NM_001896, intron 4 of 11)	20988	NM_001896	1459	Hs.82201	NM_001896	ENSG00000070770	CSNK2A2	CK2A2|CK2alpha'|CSNK2A1	casein kinase 2 alpha 2	protein-coding	0.009756	0.504854	13(AAGAACACAATGTCCC,-,0.00),14(AGAACACAATGTCCCC,+,0.00)
chunk0111_349_1	chr20	33386554	33387084	+	0	NA	intron (NM_001278169, intron 6 of 13)	MER58A|DNA|hAT-Charlie	14750	NM_001278168	51654	Hs.435952	NM_016082	ENSG00000101391	CDK5RAP1	C20orf34|C42|CGI-05|HSPC167	CDK5 regulatory subunit associated protein 1	protein-coding	0.009434	0.370998	
chunk0002_43_1	chr1	12528227	12528803	+	0	NA	Intergenic	Intergenic	21269	NR_003025	677885	Hs.658450	NR_003025	ENSG00000239149	SNORA59A	ACA59	small nucleolar RNA, H/ACA box 59A	snoRNA	0.022569	0.542461	
chunk0036_270_1	chr11	65134463	65135465	+	0	NA	promoter-TSS (NM_172230)	promoter-TSS (NM_172230)	-432	NM_032431	84447	Hs.75859	NM_032431	ENSG00000162298	SYVN1	DER3|HRD1	synoviolin 1	protein-coding	0.055888	0.582253	
chunk0044_399_1	chr12	40895209	40895794	+	0	NA	intron (NM_001256064, intron 1 of 15)	MSTC|LTR|ERVL-MaLR	-12856	NM_175038	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.008547	0.411263	299(AGGGACTGCGTGTGCT,-,0.00),300(GGGACTGCGTGTGCTC,+,0.00)
chunk0079_49_1	chr17	10640423	10641032	+	0	NA	intron (NM_002470, intron 19 of 40)	MIR3|SINE|MIR	16582	NM_002470	4621	Hs.440895	NM_002470	ENSG00000109063	MYH3	CPSKF1A|CPSKF1B|DA2A|DA2B|DA2B3|DA8|HEMHC|MYHC-EMB|MYHSE1|SMHCE	myosin heavy chain 3	protein-coding	0.009852	0.439344	318(GAGAACATGTAGTTCA,-,0.00),319(AGAACATGTAGTTCAG,+,0.00)
chunk0204_33_1	chr9	92501465	92501815	+	0	NA	intron (NM_001197296, intron 8 of 9)	intron (NM_001197296, intron 8 of 9)	-19078	NM_017680	54829	Hs.435655	NM_017680	ENSG00000106819	ASPN	OS3|PLAP-1|PLAP1|SLRR1C	asporin	protein-coding	0.014286	0.512821	
chunk0024_351_1	chr10	43563262	43563817	+	0	NA	intron (NM_001099283, intron 1 of 1)	intron (NM_001099283, intron 1 of 1)	4920	NM_005674	8187	Hs.25040	NM_005674	ENSG00000196793	ZNF239	HOK-2|MOK2	zinc finger protein 239	protein-coding	0.005405	0.345324	
chunk0100_392_1	chr2	118571842	118572041	+	0	NA	Intergenic	Intergenic	31025	NR_110272	101927709	Hs.274529	NR_110272		LOC101927709	-	uncharacterized LOC101927709	ncRNA	0.015075	0.545000	85(AAGAACAACACGTTCC,-,0.00),86(AGAACAACACGTTCCC,+,0.00)
chunk0069_274_1	chr15	64844913	64845530	+	0	NA	intron (NM_001195059, intron 1 of 4)	(T)n|Simple_repeat|Simple_repeat	3338	NM_025201	80301	Hs.709337	NM_025201	ENSG00000241839	PLEKHO2	PLEKHQ1|PP1628|pp9099	pleckstrin homology domain containing O2	protein-coding	0.009724	0.553398	
chunk0015_106_1	chr1	185157960	185158564	+	0	NA	intron (NM_017673, intron 1 of 18)	intron (NM_017673, intron 1 of 18)	1103	NM_017673	54823	Hs.134183	NM_017673	ENSG00000116668	SWT1	C1orf26|HsSwt1	SWT1 RNA endoribonuclease homolog	protein-coding	0.019868	0.400000	
chunk0113_256_1	chr20	55750596	55751005	+	0	NA	Intergenic	Intergenic	254672	NM_080617	140689	Hs.126141	NM_080617	ENSG00000054803	CBLN4	CBLNL1	cerebellin 4 precursor	protein-coding	0.002445	0.356098	162(GGGAACACCATGACCC,-,0.00),163(GGAACACCATGACCCA,+,0.00)
chunk0093_281_1	chr19	51919592	51920016	+	0	NA	Intergenic	LTR3A|LTR|ERVK	-7631	NM_024840	79898	Hs.183390	NM_024840	ENSG00000176024	ZNF613	-	zinc finger protein 613	protein-coding	0.007075	0.498824	
chunk0181_206_1	chr7	84529123	84530022	+	0	NA	Intergenic	Intergenic	-2904	NR_110080	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.002225	0.354444	
chunk0018_418_1	chr1	222694347	222695010	+	0	NA	intron (NM_022831, intron 2 of 9)	intron (NM_022831, intron 2 of 9)	17844	NM_022831	64853	Hs.156625	NM_022831	ENSG00000186063	AIDA	C1orf80	axin interactor, dorsalization associated	protein-coding	0.003017	0.334337	
chunk0011_210_1	chr1	150079581	150079840	+	0	NA	intron (NM_007259, intron 7 of 14)	AluSz6|SINE|Alu	12042	NM_001279355	11311	Hs.443750	NM_007259	ENSG00000136631	VPS45	H1|H1VPS45|SCN5|VPS45A|VPS45B|VPS54A|VSP45|VSP45A	vacuolar protein sorting 45 homolog	protein-coding	0.023166	0.442308	
chunk0120_17_1	chr3	1506091	1506537	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	413656	NM_014461	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.002242	0.384787	
chunk0084_48_1	chr17	74203508	74203749	+	0	NA	promoter-TSS (NM_000999)	promoter-TSS (NM_000999)	-28	NM_001035258	6169	Hs.380953	NM_000999	ENSG00000172809	RPL38	L38	ribosomal protein L38	protein-coding	0.049793	0.537190	
chunk0095_334_1	chr2	20805260	20805459	+	0	NA	intron (NM_001282723, intron 1 of 5)	intron (NM_001282723, intron 1 of 5)	17771	NM_001282724	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.020101	0.385000	
chunk0135_99_1	chr3	186595891	186596100	+	0	NA	Intergenic	AluJo|SINE|Alu	-17066	NM_001622	197	Hs.324746	NM_001622	ENSG00000145192	AHSG	A2HS|AHS|APMR1|FETUA|HSGA	alpha 2-HS glycoprotein	protein-coding	0.023923	0.428571	
chunk0187_9_1	chr8	491587	491855	+	0	NA	3' UTR (NM_175075, exon 4 of 4)	3' UTR (NM_175075, exon 4 of 4)	53124	NM_001256113	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.003731	0.304833	
chunk0140_364_1	chr4	74397859	74398111	+	0	NA	Intergenic	MIR|SINE|MIR	32842	NM_001432	2069	Hs.115263	NM_001432	ENSG00000124882	EREG	EPR|ER|Ep	epiregulin	protein-coding	0.003968	0.399209	
chunk0096_430_1	chr2	38427960	38428311	+	0	NA	Intergenic	Intergenic	-50845	NR_024191									0.017094	0.497159	191(AGGTACAGTCTGTGCC,-,0.00),192(GGTACAGTCTGTGCCG,+,0.00)
chunk0035_432_1	chr11	57325448	57326096	+	0	NA	promoter-TSS (NM_033396)	promoter-TSS (NM_033396)	-833	NM_033396	85456	Hs.530730	NM_033396	ENSG00000149115	TNKS1BP1	TAB182	tankyrase 1 binding protein 1	protein-coding	0.021605	0.516179	406(CAGAACAGGATGTACC,-,0.00),407(AGAACAGGATGTACCT,+,0.00)
chunk0069_332_1	chr15	66389082	66389579	+	0	NA	intron (NM_002755, intron 1 of 10)	intron (NM_002755, intron 1 of 10)	2457	NM_002755	5604	Hs.145442	NM_002755	ENSG00000169032	MAP2K1	CFC3|MAPKK1|MEK1|MKK1|PRKMK1	mitogen-activated protein kinase kinase 1	protein-coding	0.010060	0.435743	
chunk0051_433_1	chr12	122961880	122962156	+	0	NA	intron (NM_019624, intron 1 of 10)	intron (NM_019624, intron 1 of 10)	4491	NM_001243014	23457	Hs.511951	NM_019624	ENSG00000150967	ABCB9	EST122234|TAPL	ATP binding cassette subfamily B member 9	protein-coding	0.007246	0.487365	
chunk0142_238_1	chr4	98661537	98662172	+	0	NA	Intergenic	L2c|LINE|L2	-3193	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.004724	0.382075	121(TGGACCACAATGTTCC,-,0.00),122(GGACCACAATGTTCCT,+,0.00)
chunk0043_334_1	chr12	22747815	22748418	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	122974	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.001658	0.311258	
chunk0171_215_1	chr6	126054266	126054734	+	0	NA	Intergenic	Intergenic	68070	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.008547	0.452026	
chunk0207_418_1	chr9	137125982	137126373	+	0	NA	Intergenic	L1MB4|LINE|L1	-11434	NM_013379	29952	Hs.37916	NM_013379	ENSG00000176978	DPP7	DPP2|DPPII|QPP	dipeptidyl peptidase 7	protein-coding	0.007673	0.329082	132(AAAAACTGTGTGTTCT,-,0.00),133(AAAACTGTGTGTTCTG,+,0.00)
chunk0167_358_1	chr6	73027672	73028169	+	0	NA	intron (NM_019842, intron 2 of 13)	intron (NM_019842, intron 2 of 13)	-60167	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.000000	0.341365	
chunk0012_286_1	chr1	162037072	162037744	+	0	NA	Intergenic	Intergenic	-12943	NM_001297713	25903	Hs.507515	NM_015441	ENSG00000162745	OLFML2B	-	olfactomedin like 2B	protein-coding	0.013393	0.465082	
chunk0009_97_1	chr1	102190514	102190988	+	0	NA	Intergenic	Intergenic	-193517	NM_001288823	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.002110	0.328421	
chunk0045_281_1	chr12	49947675	49947927	+	0	NA	Intergenic	Intergenic	-2940	NM_000486	359	Hs.130730	NM_000486	ENSG00000167580	AQP2	AQP-CD|WCH-CD	aquaporin 2	protein-coding	0.015873	0.537549	
chunk0161_376_1	chr5	176533812	176534146	+	0	NA	intron (NM_014901, intron 1 of 10)	intron (NM_014901, intron 1 of 10)	3441	NM_014901	22838	Hs.434888	NM_014901	ENSG00000146083	RNF44	-	ring finger protein 44	protein-coding	0.017964	0.567164	
chunk0128_308_1	chr3	111598269	111598947	+	0	NA	intron (NM_005816, intron 6 of 13)	intron (NM_005816, intron 6 of 13)	-3273	NM_024508	79413	Hs.136912	NM_024508	ENSG00000177494	ZBED2	-	zinc finger BED-type containing 2	protein-coding	0.002950	0.356406	
chunk0079_141_1	chr17	13018020	13018261	+	0	NA	promoter-TSS (NM_018127)	promoter-TSS (NM_018127)	-76	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.082988	0.586777	
chunk0084_22_1	chr17	73506483	73506747	+	0	NA	intron (NM_001144952, intron 2 of 44)	intron (NM_001144952, intron 2 of 44)	137473	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.011364	0.528302	
chunk0159_120_1	chr5	138752989	138753263	+	0	NA	promoter-TSS (NM_001903)	promoter-TSS (NM_001903)	-270	NM_001290309	1495	Hs.445981	NM_001903	ENSG00000044115	CTNNA1	CAP102|MDPT2	catenin alpha 1	protein-coding	0.087591	0.720000	
chunk0161_367_1	chr5	176117865	176118066	+	0	NA	Intergenic	Intergenic	-1584	NR_038402	100507387	Hs.368516	NR_038402	ENSG00000251623	LOC100507387	-	uncharacterized LOC100507387	ncRNA	0.014925	0.504950	
chunk0093_421_1	chr19	57642402	57642937	+	0	NA	non-coding (NR_049754, exon 5 of 5)	non-coding (NR_049754, exon 5 of 5)	9502	NR_049753	10520	Hs.590977	NM_006385	ENSG00000121417	ZNF211	C2H2-25|CH2H2-25|ZNF-25	zinc finger protein 211	protein-coding	0.005607	0.436567	
chunk0134_192_1	chr3	178314202	178314485	+	0	NA	Intergenic	L2c|LINE|L2	-104858	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.007067	0.404930	
chunk0126_85_1	chr3	74727052	74727416	+	0	NA	Intergenic	Intergenic	-206094	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.005495	0.287671	
chunk0028_212_1	chr10	89413984	89414560	+	0	NA	promoter-TSS (NM_012420)	promoter-TSS (NM_012420)	-296	NM_012420	24138	Hs.252839	NM_012420	ENSG00000152778	IFIT5	ISG58|P58|RI58	interferon induced protein with tetratricopeptide repeats 5	protein-coding	0.032986	0.447140	
chunk0149_51_1	chr5	16736159	16736589	+	0	NA	intron (NM_012334, intron 19 of 40)	intron (NM_012334, intron 19 of 40)	-119316	NM_001034850	54463	Hs.481704	NM_019000	ENSG00000154153	RETREG1	FAM134B|JK-1|JK1	reticulophagy regulator 1	protein-coding	0.018605	0.487239	
chunk0058_392_1	chr13	111237538	111238025	+	0	NA	intron (NM_001113513, intron 5 of 19)	intron (NM_001113513, intron 5 of 19)	50955	NM_001113513	8874	Hs.508738	NM_003899	ENSG00000102606	ARHGEF7	BETA-PIX|COOL-1|COOL1|Nbla10314|P50|P50BP|P85|P85COOL1|P85SPR|PAK3|PIXB	Rho guanine nucleotide exchange factor 7	protein-coding	0.006160	0.383197	
chunk0110_75_1	chr20	11001841	11002305	+	0	NA	Intergenic	Intergenic	-92801	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.010776	0.458065	
chunk0167_424_1	chr6	75524361	75525024	+	0	NA	Intergenic	Intergenic	-30863	NR_110608	27145	Hs.201488	NM_015687	ENSG00000118407	FILIP1	FILIP	filamin A interacting protein 1	protein-coding	0.013575	0.376506	
chunk0106_426_1	chr2	208257208	208257888	+	0	NA	Intergenic	LTR5B|LTR|ERVK	2315	NR_046452	100507475	Hs.668038	NR_046452	ENSG00000231908	IDH1-AS1	-	IDH1 antisense RNA 1	ncRNA	0.007353	0.440529	244(CAGTGCATTGTGTCCC,-,0.00),245(AGTGCATTGTGTCCCT,+,0.00)
chunk0105_235_1	chr2	188363848	188364413	+	0	NA	intron (NR_045563, intron 2 of 12)	Helitron3Na_Mam|RC|Helitron	66638	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.005310	0.381625	
chunk0184_403_1	chr7	122144151	122144817	+	0	NA	promoter-TSS (NM_005763)	promoter-TSS (NM_005763)	-194	NM_005763	10157	Hs.156738	NM_005763	ENSG00000008311	AASS	LKR/SDH|LKRSDH|LORSDH	aminoadipate-semialdehyde synthase	protein-coding	0.054054	0.536732	
chunk0004_4_1	chr1	41875580	41875972	+	0	NA	intron (NR_038260, intron 1 of 2)	L2b|LINE|L2	42931	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.012755	0.526718	158(TGGTACAGGCTGTCCC,-,0.00),159(GGTACAGGCTGTCCCC,+,0.00)
chunk0184_177_1	chr7	116557038	116557473	+	0	NA	intron (NM_001172895, intron 2 of 2)	intron (NM_001172895, intron 2 of 2)	30897	NM_001172897	857	Hs.74034	NM_001753	ENSG00000105974	CAV1	BSCL3|CGL3|LCCNS|MSTP085|PPH3|VIP21	caveolin 1	protein-coding	0.006897	0.385321	199(AGAAACAGAATGTTCT,-,0.00),200(GAAACAGAATGTTCTA,+,0.00)
chunk0174_116_1	chr6	157117655	157117923	+	0	NA	intron (NM_017519, intron 6 of 18)	intron (NM_017519, intron 6 of 18)	206470	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.003731	0.412639	
chunk0202_3_1	chr9	70205660	70206079	+	0	NA	intron (NM_153267, intron 11 of 13)	intron (NM_153267, intron 11 of 13)	-29981	NR_040076	100507244	Hs.556816	NR_040076	ENSG00000204706	MAMDC2-AS1	-	MAMDC2 antisense RNA 1	ncRNA	0.004773	0.414286	178(GAGACAGACAGTGCTT,+,0.00)
chunk0089_304_1	chr18	63697354	63697715	+	0	NA	Intergenic	L1ME2|LINE|L1	-4770	NM_080475	89778	Hs.350958	NM_080475	ENSG00000206072	SERPINB11	EPIPIN|SERPIN11	serpin family B member 11 (gene/pseudogene)	protein-coding	0.002770	0.323204	
chunk0200_9_1	chr9	14585857	14586056	+	0	NA	Intergenic	Intergenic	107526	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.025126	0.510000	
chunk0191_21_1	chr8	42843199	42843464	+	0	NA	promoter-TSS (NM_018105)	promoter-TSS (NM_018105)	0	NM_018105	55145	Hs.7432	NM_018105	ENSG00000131931	THAP1	DYT6	THAP domain containing 1	protein-coding	0.052830	0.586466	
chunk0073_438_1	chr16	19197051	19197518	+	0	NA	intron (NM_001308157, intron 5 of 7)	intron (NM_001308157, intron 5 of 7)	24927	NM_001308157	51760	Hs.258326	NM_016524	ENSG00000103528	SYT17	sytXVII	synaptotagmin 17	protein-coding	0.010707	0.408120	
chunk0077_197_1	chr16	79808962	79809832	+	0	NA	Intergenic	L3|LINE|CR1	14148	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.002299	0.381171	335(GAGAACAAAATGATCT,-,0.00),336(AGAACAAAATGATCTC,+,0.00)
chunk0198_243_1	chr8	134520983	134521499	+	0	NA	intron (NM_020863, intron 12 of 15)	intron (NM_020863, intron 12 of 15)	-76830	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.005814	0.355899	
chunk0107_98_1	chr2	213498166	213498477	+	0	NA	intron (NR_047659, intron 12 of 17)	intron (NR_047659, intron 12 of 17)	213942	NM_024532	79582	Hs.743365	NM_024532	ENSG00000144451	SPAG16	PF20|WDR29	sperm associated antigen 16	protein-coding	0.003215	0.333333	
chunk0069_111_1	chr15	61671752	61672268	+	0	NA	Intergenic	Intergenic	388455	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.013566	0.423598	310(CAGAACACTCTGACCT,-,0.00),311(AGAACACTCTGACCTG,+,0.00)
chunk0047_300_1	chr12	73711355	73711933	+	0	NA	Intergenic	L1MC3|LINE|L1	552454	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.001730	0.343696	
chunk0116_43_1	chr21	33588779	33589008	+	0	NA	promoter-TSS (NM_017613)	promoter-TSS (NM_017613)	-185	NM_017613	29980	Hs.436341	NM_017613	ENSG00000159147	DONSON	B17|C21orf60|MIMIS|MISSLA	downstream neighbor of SON	protein-coding	0.087336	0.652174	
chunk0178_291_1	chr7	37526871	37527461	+	0	NA	Intergenic	MIRc|SINE|MIR	-77840	NM_001206480	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.008475	0.424704	
chunk0161_80_1	chr5	166974961	166975420	+	0	NA	Intergenic	Intergenic	-48820	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.006536	0.402174	
chunk0038_133_1	chr11	84120054	84120413	+	0	NA	intron (NM_001142699, intron 9 of 27)	intron (NM_001142699, intron 9 of 27)	153047	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.002786	0.363889	
chunk0165_254_1	chr6	35722263	35722982	+	0	NA	intron (NM_001145775, intron 1 of 11)	L2c|LINE|L2	5961	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.022253	0.541667	418(TATACACACTGTTCCT,+,0.00)
chunk0010_90_1	chr1	113532237	113532577	+	0	NA	intron (NM_152900, intron 1 of 20)	intron (NM_152900, intron 1 of 20)	141554	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.000000	0.269795	
chunk0012_30_1	chr1	155038465	155039170	+	0	NA	intron (NM_152494, intron 4 of 16)	L2c|LINE|L2	5011	NM_152494	149095	Hs.567717	NM_152494	ENSG00000163357	DCST1	-	DC-STAMP domain containing 1	protein-coding	0.014184	0.491501	484(AGGGACTGCGAGTGCT,-,0.00),485(GGGACTGCGAGTGCTG,+,0.00)
chunk0165_409_1	chr6	38975872	38976083	+	0	NA	intron (NM_001206927, intron 85 of 92)	intron (NM_001206927, intron 85 of 92)	-22870	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.009479	0.466981	
chunk0154_333_1	chr5	85527476	85527900	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-754756	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.002358	0.355294	
chunk0070_129_1	chr15	70874724	70875107	+	0	NA	intron (NM_001284357, intron 2 of 16)	L2a|LINE|L2	17518	NM_020147	56906	Hs.591123	NM_020147	ENSG00000129028	THAP10	-	THAP domain containing 10	protein-coding	0.002611	0.390625	
chunk0034_253_1	chr11	34318591	34318933	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	39246	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.002924	0.413994	154(CAGAACTCAATGTTCT,-,0.00),155(AGAACTCAATGTTCTG,+,0.00)
chunk0055_395_1	chr13	73728958	73729536	+	0	NA	intron (NM_007249, intron 6 of 7)	intron (NM_007249, intron 6 of 7)	165003	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.001730	0.385147	
chunk0025_215_1	chr10	53865492	53865737	+	0	NA	intron (NM_001142769, intron 29 of 35)	intron (NM_001142769, intron 29 of 35)	742343	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.004082	0.341463	
chunk0059_434_1	chr14	38329399	38329822	+	0	NA	Intergenic	L1ME3|LINE|L1	-73240	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.002364	0.384434	
chunk0139_228_1	chr4	55278345	55278823	+	0	NA	Intergenic	L1MA9|LINE|L1	-67637	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.006276	0.373695	
chunk0091_194_1	chr19	8447940	8448240	+	0	NA	intron (NM_005968, intron 1 of 15)	intron (NM_005968, intron 1 of 15)	3171	NM_005968	4670	Hs.465808	NM_005968	ENSG00000099783	HNRNPM	CEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP M	heterogeneous nuclear ribonucleoprotein M	protein-coding	0.013333	0.475083	
chunk0108_374_1	chr2	236814639	236814984	+	0	NA	Intergenic	Intergenic	245074	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.011594	0.387283	
chunk0192_6_1	chr8	58236901	58237127	+	0	NA	Intergenic	Intergenic	35087	NR_105005	101929528	Hs.563551	NR_105005	ENSG00000253281	LOC101929528	-	uncharacterized LOC101929528	ncRNA	0.004425	0.334802	
chunk0013_353_1	chr1	172257187	172257497	+	0	NA	intron (NM_001136127, intron 15 of 19)	intron (NM_001136127, intron 15 of 19)	-112507	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.006452	0.337621	
chunk0101_3_1	chr2	121225618	121226311	+	0	NA	intron (NM_014553, intron 13 of 14)	CpG	59238	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.051948	0.538905	
chunk0018_162_1	chr1	218864770	218865298	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	308754	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.001894	0.344045	
chunk0083_311_1	chr17	69480037	69480655	+	0	NA	intron (NM_002758, intron 1 of 11)	intron (NM_002758, intron 1 of 11)	65649	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.012945	0.416801	281(CAGGACATTCCGTTCT,-,0.00),282(AGGACATTCCGTTCTT,+,0.00)
chunk0081_303_1	chr17	45388519	45388790	+	0	NA	Intergenic	L2c|LINE|L2	36992	NM_199282	201176	Hs.205326	NM_174919	ENSG00000159314	ARHGAP27	CAMGAP1|PP905|SH3D20|SH3P20	Rho GTPase activating protein 27	protein-coding	0.007380	0.555147	
chunk0162_129_1	chr6	2962827	2963174	+	0	NA	promoter-TSS (NM_001271825)	promoter-TSS (NM_001271825)	-830	NM_001271825	5269	Hs.519523	NM_004568	ENSG00000124570	SERPINB6	CAP|DFNB91|MSTP057|PI-6|PI6|PTI|SPI3	serpin family B member 6	protein-coding	0.002882	0.387931	
chunk0130_196_1	chr3	133642249	133643209	+	0	NA	intron (NM_007027, intron 12 of 27)	L1MC5|LINE|L1	19164	NM_007027	11073	Hs.593379	NM_007027	ENSG00000163781	TOPBP1	Dpb11|TOP2BP1	DNA topoisomerase II binding protein 1	protein-coding	0.004167	0.351717	385(AGGCACATCATGTCTT,-,0.00)
chunk0046_429_1	chr12	64650924	64651127	+	0	NA	intron (NR_040718, intron 1 of 3)	intron (NR_040718, intron 1 of 3)	-28420	NR_037515	100500856		NR_037515	ENSG00000266016	MIR548Z	-	microRNA 548z	ncRNA	0.009852	0.406863	
chunk0073_361_1	chr16	15036916	15037401	+	0	NA	TTS (NM_173474)	TTS (NM_173474)	18921	NM_001270766	123803	Hs.592045	NM_173474	ENSG00000157045	NTAN1	PNAA|PNAD	N-terminal asparagine amidase	protein-coding	0.022680	0.475309	80(AAGTACAGACTGTGCT,-,0.00),81(AGTACAGACTGTGCTC,+,0.00),335(GGCACTGCCCGTTCCT,+,0.00)
chunk0193_89_1	chr8	73606871	73607366	+	0	NA	intron (NM_001164384, intron 7 of 10)	L1ME1|LINE|L1	139809	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.006061	0.348790	
chunk0108_232_1	chr2	233649289	233649889	+	0	NA	intron (NM_019075, intron 1 of 4)	L1ME4a|LINE|L1	13112	NM_019075	54575	Hs.554822	NM_019075	ENSG00000242515	UGT1A10	GNT1|UDPGT|UGT-1A|UGT-1J|UGT1|UGT1-01|UGT1-10|UGT1.1|UGT1.10|UGT1A|UGT1A1|UGT1J|hUG-BR1	UDP glucuronosyltransferase family 1 member A10	protein-coding	0.001667	0.346090	266(CTGGACATGTTGTTCT,-,0.00),267(TGGACATGTTGTTCTT,+,0.00)
chunk0146_412_1	chr4	169070742	169071310	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-60709	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.012324	0.416520	
chunk0062_112_1	chr14	68323185	68323749	+	0	NA	intron (NM_133509, intron 8 of 10)	intron (NM_133509, intron 8 of 10)	470447	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.007092	0.504425	
chunk0104_152_1	chr2	173997777	173998185	+	0	NA	Intergenic	Intergenic	-32279	NM_003111	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.004902	0.381418	
chunk0020_191_1	chr1	234891025	234891309	+	0	NA	Intergenic	Intergenic	72832	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.007042	0.610526	
chunk0180_412_1	chr7	76000912	76001185	+	0	NA	intron (NM_016086, intron 7 of 8)	intron (NM_016086, intron 7 of 8)	-6374	NM_031925	83862	Hs.488835	NM_031925	ENSG00000189077	TMEM120A	NET29|TMPIT	transmembrane protein 120A	protein-coding	0.018315	0.554745	
chunk0064_117_1	chr14	91276353	91276660	+	0	NA	intron (NM_001080414, intron 29 of 29)	intron (NM_001080414, intron 29 of 29)	-22626	NM_003485	8111	Hs.8882	NM_003485	ENSG00000119714	GPR68	AI2A6|GPR12A|OGR1	G protein-coupled receptor 68	protein-coding	0.003257	0.457792	
chunk0106_194_1	chr2	201751589	201751866	+	0	NA	intron (NM_020919, intron 7 of 33)	intron (NM_020919, intron 7 of 33)	29445	NM_001135745	57679	Hs.471096	NM_020919	ENSG00000003393	ALS2	ALS2CR6|ALSJ|IAHSP|PLSJ	alsin Rho guanine nucleotide exchange factor ALS2	protein-coding	0.014440	0.309353	
chunk0095_278_1	chr2	19894436	19894990	+	0	NA	Intergenic	Intergenic	7270	NM_001008237	130502	Hs.591547	NM_001008237	ENSG00000183891	TTC32	-	tetratricopeptide repeat domain 32	protein-coding	0.007220	0.338739	
chunk0010_287_1	chr1	117562422	117563394	+	0	NA	Intergenic	Intergenic	42862	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.008230	0.535457	
chunk0194_326_1	chr8	88713267	88713664	+	0	NA	Intergenic	MER34-int|LTR|ERV1	-385977	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.007557	0.381910	
chunk0209_279_1	chrX	47190577	47190954	+	0	NA	promoter-TSS (NM_153280)	promoter-TSS (NM_153280)	-35	NM_153280	7317	Hs.533273	NM_003334	ENSG00000130985	UBA1	A1S9|A1S9T|A1ST|AMCX1|CFAP124|GXP1|POC20|SMAX2|UBA1A|UBE1|UBE1X	ubiquitin like modifier activating enzyme 1	protein-coding	0.066313	0.621693	
chunk0156_442_1	chr5	114753304	114753867	+	0	NA	intron (NR_130785, intron 1 of 12)	L1MEc|LINE|L1	19828	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.001776	0.290780	
chunk0152_159_1	chr5	59401674	59402016	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-44944	NM_001197219	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005848	0.440233	
chunk0126_23_1	chr3	73575536	73575905	+	0	NA	intron (NM_015009, intron 3 of 9)	MIR3|SINE|MIR	-6205	NM_001303139	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.005420	0.362162	
chunk0189_171_1	chr8	23508291	23508946	+	0	NA	Intergenic	Intergenic	-20232	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.019847	0.464939	
chunk0137_142_1	chr4	15587666	15588045	+	0	NA	exon (NM_001080522, exon 33 of 38)	exon (NM_001080522, exon 33 of 38)	67557	NM_001193535	26234	Hs.643433	NM_012161	ENSG00000118564	FBXL5	FBL4|FBL5|FLR1	F-box and leucine rich repeat protein 5	protein-coding	0.007916	0.386842	181(AAGAACATGCAGTACT,-,0.00),182(AGAACATGCAGTACTA,+,0.00)
chunk0136_58_1	chr4	1615014	1615277	+	0	NA	Intergenic	Intergenic	68846	NM_001013622	152877	Hs.143314	NM_001013622	ENSG00000174137	FAM53A	DNTNP	family with sequence similarity 53 member A	protein-coding	0.045627	0.640152	
chunk0074_147_1	chr16	23202363	23203483	+	0	NA	intron (NM_001039, intron 6 of 12)	L2c|LINE|L2	20204	NM_001039	6340	Hs.371727	NM_001039	ENSG00000166828	SCNN1G	BESC3|ENaCg|ENaCgamma|LDLS2|PHA1|SCNEG	sodium channel epithelial 1 gamma subunit	protein-coding	0.008036	0.443354	
chunk0098_98_1	chr2	67954180	67954807	+	0	NA	Intergenic	Intergenic	108534	NM_006333	10438	Hs.602900	NM_006333	ENSG00000197223	C1D	LRP1|Rrp47|SUN-CoR|SUNCOR|hC1D	C1D nuclear receptor corepressor	protein-coding	0.007974	0.472930	
chunk0007_243_1	chr1	82521177	82521518	+	0	NA	Intergenic	Intergenic	463575	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.005865	0.342105	
chunk0146_162_1	chr4	160009501	160010262	+	0	NA	Intergenic	Intergenic	742035	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.002628	0.413386	330(AGGAACATTGTGTTCC,-,0.00),331(GGAACATTGTGTTCCT,+,0.00),378(CAGAACACTGTGCACC,-,0.00),379(AGAACACTGTGCACCA,+,0.00)
chunk0035_438_1	chr11	57477805	57478324	+	0	NA	TTS (NM_178570)	TTS (NM_178570)	17527	NM_178570	349667	Hs.502618	NM_178570	ENSG00000186907	RTN4RL2	NGRH1|NgR2	reticulon 4 receptor like 2	protein-coding	0.011561	0.536538	
chunk0069_338_1	chr15	66410654	66410933	+	0	NA	intron (NM_002755, intron 1 of 10)	intron (NM_002755, intron 1 of 10)	23920	NM_002755	5604	Hs.145442	NM_002755	ENSG00000169032	MAP2K1	CFC3|MAPKK1|MEK1|MKK1|PRKMK1	mitogen-activated protein kinase kinase 1	protein-coding	0.014337	0.471429	
chunk0087_181_1	chr18	35481641	35482174	+	0	NA	intron (NM_194281, intron 1 of 4)	L1ME2|LINE|L1	15742	NM_001308064	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.022514	0.460674	
chunk0116_60_1	chr21	34023859	34024485	+	0	NA	Intergenic	L2c|LINE|L2	-49351	NM_006933	6526	Hs.302742	NM_006933	ENSG00000198743	SLC5A3	BCW2|SMIT|SMIT1|SMIT2	solute carrier family 5 member 3	protein-coding	0.011182	0.397129	
chunk0118_429_1	chr22	38611636	38611903	+	0	NA	intron (NM_001013647, intron 11 of 16)	L2b|LINE|L2	-41573	NR_103474	11144	Hs.339396	NM_007068	ENSG00000100206	DMC1	DMC1H|LIM15|dJ199H16.1	DNA meiotic recombinase 1	protein-coding	0.007491	0.455224	
chunk0030_130_1	chr10	113425444	113426087	+	0	NA	Intergenic	Intergenic	-125066	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.015552	0.454969	
chunk0018_412_1	chr1	222664396	222664985	+	0	NA	intron (NM_198551, intron 27 of 27)	intron (NM_198551, intron 27 of 27)	20387	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.003396	0.388136	
chunk0191_383_1	chr8	57029376	57029983	+	0	NA	Intergenic	L2a|LINE|L2	-35808	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.009885	0.439145	
chunk0096_3_1	chr2	25821858	25822084	+	0	NA	intron (NM_018263, intron 2 of 11)	intron (NM_018263, intron 2 of 11)	56472	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.013274	0.392070	46(GGCACAAACTGATCTA,+,0.00)
chunk0188_287_1	chr8	15618486	15618900	+	0	NA	intron (NM_006765, intron 1 of 10)	Tigger3b|DNA|TcMar-Tigger	78606	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.014493	0.404819	
chunk0071_366_1	chr15	89090592	89090845	+	0	NA	intron (NM_007011, intron 2 of 14)	intron (NM_007011, intron 2 of 14)	2568	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.015810	0.413386	
chunk0071_377_1	chr15	89121299	89121843	+	0	NA	intron (NM_007011, intron 7 of 14)	L1ME3|LINE|L1	33421	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.005515	0.444037	
chunk0155_224_1	chr5	95403271	95403590	+	0	NA	intron (NM_152548, intron 3 of 9)	intron (NM_152548, intron 3 of 9)	12086	NM_152548	153643	Hs.276287	NM_152548	ENSG00000153347	FAM81B	-	family with sequence similarity 81 member B	protein-coding	0.000000	0.284375	
chunk0183_350_1	chr7	108611059	108611653	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	-41588	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.008418	0.408403	
chunk0201_157_1	chr9	35980546	35981054	+	0	NA	Intergenic	L3|LINE|CR1	-22646	NM_019897	56656	Hs.553540	NM_019897	ENSG00000278889	OR2S2	OR37A|OST715	olfactory receptor family 2 subfamily S member 2 (gene/pseudogene)	protein-coding	0.003937	0.447937	
chunk0210_209_1	chrX	81206720	81207650	+	0	NA	intron (NM_003022, intron 1 of 3)	intron (NM_003022, intron 1 of 3)	-5243	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.002151	0.332975	
chunk0210_454_1	chrX	106394626	106395348	+	0	NA	Intergenic	Intergenic	-216943	NM_018015	55086	Hs.274267	NM_018015	ENSG00000147231	RADX	CXorf57	RPA1 related single stranded DNA binding protein, X-linked	protein-coding	0.008310	0.495159	
chunk0091_426_1	chr19	16957117	16957840	+	0	NA	intron (NM_015692, intron 19 of 41)	intron (NM_015692, intron 19 of 41)	68463	NM_003950	9002	Hs.137574	NM_003950	ENSG00000127533	F2RL3	PAR4	F2R like thrombin or trypsin receptor 3	protein-coding	0.019364	0.506906	
chunk0092_210_1	chr19	31448360	31448559	+	0	NA	Intergenic	Intergenic	-99175	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.010050	0.620000	
chunk0009_425_1	chr1	111056286	111056826	+	0	NA	Intergenic	L1PBa|LINE|L1	-83071	NM_001007794	10390	Hs.363572	NM_006090	ENSG00000134255	CEPT1	-	choline/ethanolamine phosphotransferase 1	protein-coding	0.003704	0.308688	
chunk0195_7_1	chr8	92927673	92927975	+	0	NA	intron (NM_001171798, intron 1 of 4)	L2|LINE|L2	37765	NM_001191036	286144	Hs.440643	NM_001171795	ENSG00000205133	TRIQK	C8orf83|PRO0845|UPF0599	triple QxxK/R motif containing	protein-coding	0.000000	0.379538	
chunk0210_328_1	chrX	94600068	94600694	+	0	NA	Intergenic	LTR66|LTR|ERVL	462845	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.012780	0.417863	71(AGGTACAGCCTGGGCT,-,0.00)
chunk0049_108_1	chr12	91152149	91152754	+	0	NA	intron (NM_001920, intron 6 of 7)	intron (NM_001920, intron 6 of 7)	26195	NM_133507	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.001653	0.303630	294(AAGAACATAGTGTTCC,-,0.00),295(AGAACATAGTGTTCCT,+,0.00)
chunk0130_358_1	chr3	138979626	138980077	+	0	NA	Intergenic	Intergenic	26417	NM_001134659	729627	Hs.121314	NM_001134659	ENSG00000206260	PRR23A	-	proline rich 23A	protein-coding	0.004435	0.535398	
chunk0157_209_1	chr5	119270624	119271922	+	0	NA	intron (NM_001077654, intron 1 of 1)	intron (NM_001077654, intron 1 of 1)	2581	NM_001286817	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.006163	0.416474	451(GAGGACAGGCTGTCCT,-,0.00),452(AGGACAGGCTGTCCTG,+,0.00)
chunk0136_154_1	chr4	4794296	4794517	+	0	NA	Intergenic	L2|LINE|L2	32646	NR_125892	101928279	Hs.586152	NR_125892		LOC101928279	-	uncharacterized LOC101928279	ncRNA	0.004525	0.391892	
chunk0015_415_1	chr1	191365098	191365297	+	0	NA	Intergenic	MER70C|LTR|ERVL	740307	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.010050	0.440000	
chunk0035_361_1	chr11	49165140	49165605	+	0	NA	intron (NM_001014986, intron 12 of 17)	L2a|LINE|L2	43298	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.002151	0.437768	
chunk0097_232_1	chr2	53174486	53175003	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-472129	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.001934	0.337838	
chunk0008_101_1	chr1	91129472	91129881	+	0	NA	Intergenic	Intergenic	-107421	NM_032186	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.007335	0.436585	
chunk0050_238_1	chr12	105215217	105215766	+	0	NA	intron (NM_018171, intron 4 of 20)	L2a|LINE|L2	17914	NM_001251905	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.009107	0.389091	
chunk0192_349_1	chr8	67810440	67811275	+	0	NA	Intergenic	Intergenic	-64472	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.008383	0.356459	
chunk0083_138_1	chr17	65634213	65634531	+	0	NA	Intergenic	Intergenic	-72750	NM_004655	8313	Hs.156527	NM_004655	ENSG00000168646	AXIN2	AXIL|ODCRCS	axin 2	protein-coding	0.000000	0.341693	
chunk0212_300_1	chrX	141199257	141199485	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-22157	NM_012317	23641	Hs.45231	NM_012317	ENSG00000182195	LDOC1	BCUR1|Mar7|Mart7|RTL7|SIRH7	LDOC1 regulator of NFKB signaling	protein-coding	0.004386	0.445415	
chunk0130_424_1	chr3	140830591	140830790	+	0	NA	Intergenic	Intergenic	-111130	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.005025	0.450000	
chunk0184_416_1	chr7	122648710	122648909	+	0	NA	intron (NM_017954, intron 3 of 29)	intron (NM_017954, intron 3 of 29)	50345	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.010050	0.470000	
chunk0003_14_1	chr1	28780214	28780717	+	0	NA	Intergenic	L2-3_Crp|LINE|L2	-31677	NM_000911	4985	Hs.372	NM_000911	ENSG00000116329	OPRD1	DOP|DOR|DOR1|OPRD	opioid receptor delta 1	protein-coding	0.005964	0.482143	
chunk0165_382_1	chr6	38376493	38377169	+	0	NA	intron (NM_001099272, intron 6 of 10)	intron (NM_001099272, intron 6 of 10)	219236	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.002959	0.338257	279(AAGAACTCTGTGTGCT,-,0.00),280(AGAACTCTGTGTGCTT,+,0.00)
chunk0157_328_1	chr5	122125598	122126253	+	0	NA	Intergenic	Intergenic	-3588	NM_207317	133923	Hs.729673	NM_207317	ENSG00000164185	ZNF474	-	zinc finger protein 474	protein-coding	0.006107	0.411585	
chunk0174_103_1	chr6	156883473	156883905	+	0	NA	intron (NM_020732, intron 3 of 19)	intron (NM_020732, intron 3 of 19)	-103958	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.020833	0.533487	
chunk0014_400_1	chr1	182962550	182962793	+	0	NA	Intergenic	Intergenic	-9253	NM_030933	81626	Hs.497034	NM_030933	ENSG00000157060	SHCBP1L	C1orf14|GE36	SHC binding and spindle associated 1 like	protein-coding	0.008230	0.450820	
chunk0048_43_1	chr12	78067150	78067349	+	0	NA	intron (NM_014903, intron 12 of 38)	intron (NM_014903, intron 12 of 38)	235960	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.000000	0.310000	
chunk0006_21_1	chr1	63983689	63984218	+	0	NA	intron (NM_001083592, intron 1 of 6)	MIRb|SINE|MIR	128252	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.007561	0.400000	
chunk0054_49_1	chr13	41671111	41671444	+	0	NA	intron (NM_015058, intron 36 of 44)	intron (NM_015058, intron 36 of 44)	-102882	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.015015	0.380240	
chunk0061_268_1	chr14	61438760	61439301	+	0	NA	intron (NM_006255, intron 2 of 13)	intron (NM_006255, intron 2 of 13)	117587	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.009242	0.437269	
chunk0056_406_1	chr13	94123572	94124210	+	0	NA	intron (NM_005708, intron 4 of 8)	intron (NM_005708, intron 4 of 8)	64100	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.003135	0.330203	326(AATCACAGAATGTTCT,-,0.00),327(ATCACAGAATGTTCTT,+,0.00)
chunk0028_207_1	chr10	89141087	89141738	+	0	NA	Intergenic	Intergenic	65902	NM_003956	9023	Hs.47357	NM_003956	ENSG00000138135	CH25H	C25H	cholesterol 25-hydroxylase	protein-coding	0.001536	0.323620	
chunk0037_106_1	chr11	72208238	72208924	+	0	NA	Intergenic	L1MB2|LINE|L1	-8194	NM_000803	2350	Hs.433159	NM_000803	ENSG00000165457	FOLR2	BETA-HFR|FBP|FBP/PL-1|FR-BETA|FR-P3|FRbeta	folate receptor beta	protein-coding	0.008746	0.455604	91(GTGCACAAACAGTTCC,-,0.00),144(GGGAACATCTAGTTCC,-,0.00),145(GGAACATCTAGTTCCC,+,0.00)
chunk0164_231_1	chr6	23106155	23106354	+	0	NA	Intergenic	L1PA16|LINE|L1	536805	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.000000	0.280000	
chunk0075_21_1	chr16	46876352	46877076	+	0	NA	Intergenic	Intergenic	-7666	NM_133443	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.012431	0.400000	
chunk0011_226_1	chr1	150281678	150282252	+	0	NA	promoter-TSS (NM_001300839)	promoter-TSS (NM_001300839)	-568	NM_001300840	148523	Hs.54680	NM_144697	ENSG00000159208	CIART	C1orf51|CHRONO|GM129	circadian associated repressor of transcription	protein-coding	0.062718	0.573913	175(AAGGACGCGGTGTTCT,-,0.00),176(AGGACGCGGTGTTCTC,+,0.00)
chunk0009_100_1	chr1	102235322	102235787	+	0	NA	Intergenic	Intergenic	-238320	NM_001288823	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.002151	0.328326	
chunk0168_151_1	chr6	83188311	83189348	+	0	NA	intron (NM_001199918, intron 1 of 11)	intron (NM_001199918, intron 1 of 11)	4464	NM_015599	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.006750	0.400771	
chunk0012_410_1	chr1	164128318	164128797	+	0	NA	Intergenic	L1M7|LINE|L1	-430803	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.002088	0.283333	
chunk0127_101_1	chr3	90007719	90008199	+	0	NA	Intergenic	Intergenic	900435	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.006250	0.426195	
chunk0189_71_1	chr8	20819216	20819631	+	0	NA	Intergenic	Intergenic	-134210	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.004819	0.432692	
chunk0002_296_1	chr1	23084705	23085247	+	0	NA	3' UTR (NM_001142546, exon 4 of 4)	3' UTR (NM_001142546, exon 4 of 4)	-27042	NR_039614									0.018450	0.491713	
chunk0172_113_1	chr6	135054848	135055134	+	0	NA	promoter-TSS (NM_001145207)	promoter-TSS (NM_001145207)	-93	NM_001145207	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.062937	0.581882	
chunk0115_148_1	chr21	23532381	23532808	+	0	NA	Intergenic	Intergenic	-147759	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.004684	0.341121	
chunk0090_191_1	chr18	73042903	73043512	+	0	NA	Intergenic	L2a|LINE|L2	-175632	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.006568	0.339344	
chunk0042_337_1	chr12	9868904	9869643	+	0	NA	5' UTR (NM_005127, exon 1 of 5)	5' UTR (NM_005127, exon 1 of 5)	586	NM_005127	9976	Hs.85201	NM_005127	ENSG00000110852	CLEC2B	AICL|CLECSF2|HP10085|IFNRG1	C-type lectin domain family 2 member B	protein-coding	0.009472	0.314865	
chunk0033_383_1	chr11	23822310	23822809	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-403369	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.008016	0.400000	253(GAGGACACAGTGTTCC,-,0.00),254(AGGACACAGTGTTCCC,+,0.00)
chunk0182_163_1	chr7	95544864	95545422	+	0	NA	Intergenic	Intergenic	51470	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.007168	0.415027	240(TGAAACAAACTGTCCC,-,0.00),241(GAAACAAACTGTCCCA,+,0.00)
chunk0179_76_1	chr7	44261627	44261826	+	0	NA	intron (NM_172084, intron 3 of 15)	MER113A|DNA|hAT-Charlie	60747	NM_006555	10652	Hs.520794	NM_006555	ENSG00000106636	YKT6	-	YKT6 v-SNARE homolog	protein-coding	0.010050	0.305000	
chunk0078_52_1	chr17	1376764	1377413	+	0	NA	intron (NR_024058, intron 1 of 6)	AluSx1|SINE|Alu	23174	NR_024058	7531	Hs.513851	NM_006761	ENSG00000108953	YWHAE	14-3-3E|HEL2|KCIP-1|MDCR|MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	protein-coding	0.010786	0.455385	
chunk0067_257_1	chr15	45755734	45756016	+	0	NA	Intergenic	L1PA6|LINE|L1	121135	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.003546	0.363958	44(AAGAGCAGGTTGTTCA,-,0.00)
chunk0182_406_1	chr7	100865800	100866396	+	0	NA	TTS (NM_001267814)	TTS (NM_001267814)	-1230	NM_003302	7205	Hs.534360	NM_003302	ENSG00000087077	TRIP6	OIP-1|OIP1|TRIP-6|TRIP6i2|ZRP-1	thyroid hormone receptor interactor 6	protein-coding	0.058725	0.703518	44(CTGAGCACCCTGTTCC,-,0.00),45(TGAGCACCCTGTTCCC,+,0.00)
chunk0110_440_1	chr20	20991277	20991573	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-134558	NM_001276389	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.006757	0.525253	242(AAGAACATGCTGTACT,-,0.00),243(AGAACATGCTGTACTT,+,0.00)
chunk0017_432_1	chr1	213518398	213518801	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-406150	NR_046189	100861504	Hs.742586	NR_046189		LINC00538	PROX1UT|Yiya	long intergenic non-protein coding RNA 538	ncRNA	0.007444	0.423267	
chunk0014_125_1	chr1	177589106	177589842	+	0	NA	Intergenic	Intergenic	-111050	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.004076	0.445047	577(AAGGACAGGATGTACC,-,0.00),578(AGGACAGGATGTACCA,+,0.00)
chunk0129_252_1	chr3	122266239	122266754	+	0	NA	intron (NM_000388, intron 4 of 6)	AluSx3|SINE|Alu	-58668	NM_005213	1475	Hs.518198	NM_005213	ENSG00000121552	CSTA	AREI|PSS4|STF1|STFA	cystatin A	protein-coding	0.007767	0.379845	451(AGGAACTGTCAGTTCC,-,0.00),452(GGAACTGTCAGTTCCT,+,0.00)
chunk0095_215_1	chr2	18745638	18746229	+	0	NA	Intergenic	L1ME1|LINE|L1	-156353	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.006768	0.349662	
chunk0088_440_1	chr18	55941322	55941738	+	0	NA	Intergenic	Intergenic	-21331	NR_110755	101927273	Hs.434335	NR_110755	ENSG00000260930	LINC01416	-	long intergenic non-protein coding RNA 1416	ncRNA	0.004808	0.388489	
chunk0081_248_1	chr17	43169728	43170277	+	0	NA	promoter-TSS (NM_031862)	promoter-TSS (NM_031862)	401	NR_110868	101929767	Hs.640892	NR_110868		LOC101929767	-	uncharacterized LOC101929767	ncRNA	0.051002	0.569091	
chunk0117_99_1	chr22	17637707	17638361	+	0	NA	promoter-TSS (NM_015367)	promoter-TSS (NM_015367)	-550	NM_015367	23786	Hs.631672	NM_015367	ENSG00000099968	BCL2L13	BCL-RAMBO|Bcl2-L-13|MIL1	BCL2 like 13	protein-coding	0.016820	0.451908	
chunk0014_283_1	chr1	180560282	180561060	+	0	NA	intron (NR_125716, intron 1 of 2)	MamGypsy2-I|LTR|Gypsy	1697	NR_125716	148756		NR_125716	ENSG00000236719	OVAAL	LINC01131|OVAL	ovarian adenocarcinoma amplified long non-coding RNA	ncRNA	0.007712	0.379974	
chunk0162_143_1	chr6	3244055	3244666	+	0	NA	Intergenic	Intergenic	-14568	NM_001128592	389362	Hs.207069	NM_001128591	ENSG00000180822	PSMG4	C6orf86|PAC4|bA506K6.2	proteasome assembly chaperone 4	protein-coding	0.008183	0.460784	
chunk0021_194_1	chr10	5772065	5772369	+	0	NA	intron (NM_001494, intron 7 of 10)	Tigger3b|DNA|TcMar-Tigger	41332	NM_001115156	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.003289	0.380328	
chunk0060_113_1	chr14	43608539	43608793	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	898630	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.003937	0.384314	
chunk0094_200_1	chr2	6384442	6384822	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-9210	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.013158	0.409449	
chunk0111_16_1	chr20	21957815	21958223	+	0	NA	Intergenic	Intergenic	-96071	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.012255	0.330073	
chunk0010_170_1	chr1	115693884	115694464	+	0	NA	3' UTR (NM_001172411, exon 8 of 8)	3' UTR (NM_001172411, exon 8 of 8)	51545	NM_001172412	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.003448	0.358003	
chunk0039_327_1	chr11	104322206	104322486	+	0	NA	Intergenic	Intergenic	69755	NR_106987									0.003571	0.409253	
chunk0170_107_1	chr6	110623136	110623586	+	0	NA	exon (NM_001300963, exon 10 of 14)	exon (NM_001300963, exon 10 of 14)	-146720	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.004444	0.379157	
chunk0121_21_1	chr3	14921105	14921304	+	0	NA	intron (NM_152536, intron 13 of 19)	intron (NM_152536, intron 13 of 19)	26301	NR_046254	100505641	Hs.517821	NR_046251	ENSG00000225733	FGD5-AS1	-	FGD5 antisense RNA 1	ncRNA	0.020101	0.595000	89(AGGGACATGGTGTCTT,-,0.00),90(GGGACATGGTGTCTTG,+,0.00)
chunk0065_427_1	chr14	106134983	106135452	+	0	NA	Intergenic	LTR19C|LTR|ERV1	-152457	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.008529	0.453191	
chunk0151_39_1	chr5	42014878	42015242	+	0	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	89806	NM_033484	26272	Hs.165575	NM_012176	ENSG00000151876	FBXO4	FBX4	F-box protein 4	protein-coding	0.000000	0.317808	
chunk0063_68_1	chr14	77457279	77457619	+	0	NA	promoter-TSS (NM_012111)	promoter-TSS (NM_012111)	191	NM_001193315	63894	Hs.16157	NM_022067	ENSG00000151445	VIPAS39	C14orf133|SPE-39|SPE39|VIPAR|VPS16B|hSPE-39	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog	protein-coding	0.052941	0.598240	
chunk0140_390_1	chr4	75158955	75159452	+	0	NA	Intergenic	MIR3|SINE|MIR	-188841	NR_121617	100507388	Hs.570765	NR_121617	ENSG00000249717	LOC100507388	-	uncharacterized LOC100507388	ncRNA	0.008048	0.397590	
chunk0048_184_1	chr12	81023762	81023961	+	0	NA	Intergenic	MIR|SINE|MIR	-54169	NM_024560	79611	Hs.259559	NM_024560	ENSG00000111058	ACSS3	-	acyl-CoA synthetase short chain family member 3	protein-coding	0.000000	0.290000	
chunk0122_251_1	chr3	34742480	34742893	+	0	NA	Intergenic	Intergenic	651337	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.002421	0.437198	183(AGGAACAAAATGCCCC,-,0.00),235(TAACACATCCTGTTCC,-,0.00),236(AACACATCCTGTTCCT,+,0.00)
chunk0142_299_1	chr4	100482899	100483419	+	0	NA	intron (NM_016242, intron 1 of 11)	MIR|SINE|MIR	34934	NM_001159694	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.000000	0.376200	217(AAGTACTGAGTGTGCC,-,0.00),218(AGTACTGAGTGTGCCA,+,0.00)
chunk0086_336_1	chr18	24661516	24662218	+	0	NA	non-coding (NR_040033, exon 3 of 3)	non-coding (NR_040033, exon 3 of 3)	33685	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.004274	0.307255	
chunk0047_41_1	chr12	66738836	66739298	+	0	NA	Intergenic	Intergenic	-59922	NM_001178074	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.006494	0.377970	
chunk0146_173_1	chr4	160459160	160459442	+	0	NA	Intergenic	L2a|LINE|L2	1191455	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.000000	0.332155	
chunk0062_107_1	chr14	68269626	68269942	+	0	NA	intron (NM_133509, intron 7 of 10)	L2a|LINE|L2	450005	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.009494	0.473186	
chunk0196_85_1	chr8	102835273	102835522	+	0	NA	intron (NM_001301668, intron 6 of 11)	intron (NM_001301668, intron 6 of 11)	28803	NM_148174	51582	Hs.459106	NM_015878	ENSG00000155096	AZIN1	AZI|AZI1|AZIA1|OAZI|OAZIN|ODC1L	antizyme inhibitor 1	protein-coding	0.008032	0.340000	148(AGGCACAGCATGATCC,-,0.00),149(GGCACAGCATGATCCC,+,0.00)
chunk0098_212_1	chr2	73069346	73070004	+	0	NA	intron (NM_144579, intron 1 of 13)	intron (NM_144579, intron 1 of 13)	2161	NM_144579	94097	Hs.368171	NM_144579	ENSG00000144040	SFXN5	BBG-TCC|SLC56A5	sideroflexin 5	protein-coding	0.010638	0.468892	
chunk0188_170_1	chr8	10821317	10821702	+	0	NA	intron (NM_017884, intron 5 of 6)	intron (NM_017884, intron 5 of 6)	3934	NR_031711	100302166		NR_031711	ENSG00000283210	MIR1322	MIRN1322|hsa-mir-1322	microRNA 1322	ncRNA	0.015584	0.471503	
chunk0023_421_1	chr10	31509997	31510222	+	0	NA	intron (NM_030751, intron 4 of 8)	MLT1J1|LTR|ERVL-MaLR	188974	NM_001174094	6935	Hs.124503	NM_030751	ENSG00000148516	ZEB1	AREB6|BZP|DELTAEF1|FECD6|NIL2A|PPCD3|TCF8|ZFHEP|ZFHX1A	zinc finger E-box binding homeobox 1	protein-coding	0.000000	0.433628	
chunk0032_256_1	chr11	8724371	8725005	+	0	NA	intron (NM_139157, intron 3 of 18)	LTR40a|LTR|ERVL	39249	NR_002977	677826	Hs.745552	NR_002977	ENSG00000212607	SNORA3B	ACA3-2|SNORA45|SNORA45B	small nucleolar RNA, H/ACA box 3B	snoRNA	0.009464	0.488189	339(AGGAACTGACAGTTCC,-,0.00),340(GGAACTGACAGTTCCA,+,0.00)
chunk0212_16_1	chrY	8611724	8612307	+	0	NA	Intergenic	SST1|Satellite|centr	71863	NR_001550	252950	Hs.522852	NR_001550		TTTY18	NCRNA00143	testis-specific transcript, Y-linked 18	ncRNA	0.008576	0.453767	
chunk0198_308_1	chr8	138953207	138953442	+	0	NA	Intergenic	Intergenic	-39318	NM_152888	169044	Hs.117169	NM_152888	ENSG00000169436	COL22A1	-	collagen type XXII alpha 1 chain	protein-coding	0.000000	0.508475	
chunk0207_92_1	chrX	9629127	9629400	+	0	NA	intron (NM_001139468, intron 3 of 17)	MER58A|DNA|hAT-Charlie	136702	NM_000273	4935	Hs.74124	NM_000273	ENSG00000101850	GPR143	NYS6|OA1	G protein-coupled receptor 143	protein-coding	0.007326	0.430657	
chunk0016_393_1	chr1	203069455	203069749	+	0	NA	intron (NM_001304331, intron 27 of 29)	CR1_Mam|LINE|CR1	16436	NM_002479	4656	Hs.2830	NM_002479	ENSG00000122180	MYOG	MYF4|bHLHc3|myf-4	myogenin	protein-coding	0.013605	0.515254	267(AGGGCCATTGTGTCCT,-,0.00),268(GGGCCATTGTGTCCTG,+,0.00)
chunk0143_305_1	chr4	118771707	118772181	+	0	NA	intron (NM_014822, intron 8 of 22)	intron (NM_014822, intron 8 of 22)	64227	NM_014822	9871	Hs.189641	NM_014822	ENSG00000150961	SEC24D	CLCRP2	SEC24 homolog D, COPII coat complex component	protein-coding	0.006329	0.343158	
chunk0153_273_1	chr5	72914126	72914465	+	0	NA	TTS (NM_002270)	TTS (NM_002270)	35704	NR_039968	100616152		NR_039968	ENSG00000263593	MIR4804	-	microRNA 4804	ncRNA	0.002950	0.300000	
chunk0122_349_1	chr3	37339165	37339744	+	0	NA	intron (NM_002078, intron 19 of 23)	L1MB5|LINE|L1	-46815	NM_178344	339883	Hs.475945	NM_178339	ENSG00000198590	C3orf35	APRG1	chromosome 3 open reading frame 35	protein-coding	0.006908	0.343103	
chunk0033_21_1	chr11	12585986	12586185	+	0	NA	Intergenic	MER63B|DNA|hAT-Blackjack	-88337	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.010050	0.440000	
chunk0147_226_1	chr4	181955691	181956304	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	188518	NR_027107	90768	Hs.175465	NR_027107		TENM3-AS1	-	TENM3 antisense RNA 1	ncRNA	0.004894	0.425081	
chunk0167_78_1	chr6	56532739	56533674	+	0	NA	intron (NM_183380, intron 54 of 93)	intron (NM_183380, intron 54 of 93)	109690	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.005348	0.360043	
chunk0020_319_1	chr1	237700116	237700437	+	0	NA	exon (NM_001035, exon 65 of 105)	exon (NM_001035, exon 65 of 105)	-161899	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.009346	0.434783	
chunk0050_299_1	chr12	106782391	106783646	+	0	NA	intron (NM_018157, intron 1 of 8)	MIR1_Amn|SINE|MIR	-8187	NR_040246	100287944	Hs.742087	NR_040246	ENSG00000257545	LOC100287944	-	uncharacterized LOC100287944	ncRNA	0.005578	0.395701	46(CAGGGCATTATGTCCT,-,0.00),47(AGGGCATTATGTCCTT,+,0.00),426(TAGTACTCAGTGTACT,-,0.00),427(AGTACTCAGTGTACTT,+,0.00),906(AGGTACACCCTGTTTT,-,0.00),907(GGTACACCCTGTTTTC,+,0.00)
chunk0027_232_1	chr10	76394156	76394785	+	0	NA	intron (NR_131178, intron 7 of 7)	intron (NR_131178, intron 7 of 7)	-493574	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.003180	0.380952	
chunk0119_452_1	chr22	50389121	50389357	+	0	NA	intron (NM_001242900, intron 2 of 22)	intron (NM_001242900, intron 2 of 22)	45922	NM_001242899	9701	Hs.449098	NM_014678	ENSG00000100239	PPP6R2	KIAA0685|PP6R2|SAP190|SAPS2	protein phosphatase 6 regulatory subunit 2	protein-coding	0.004237	0.493671	
chunk0057_44_1	chr13	96355521	96355720	+	0	NA	intron (NM_153456, intron 1 of 1)	Tigger1|DNA|TcMar-Tigger	-71609	NR_039723	100616137		NR_039723	ENSG00000283487	MIR4501	-	microRNA 4501	ncRNA	0.000000	0.320000	
chunk0083_199_1	chr17	66662525	66662922	+	0	NA	intron (NM_002737, intron 5 of 16)	intron (NM_002737, intron 5 of 16)	-124349	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.010076	0.399497	
chunk0129_384_1	chr3	126266122	126266712	+	0	NA	Intergenic	Intergenic	-85231	NM_001270364	10840	Hs.434435	NM_012190	ENSG00000144908	ALDH1L1	10-FTHFDH|10-fTHF|FDH|FTHFD	aldehyde dehydrogenase 1 family member L1	protein-coding	0.023729	0.539763	291(GAGAACACTGTGTCCA,-,0.00),292(AGAACACTGTGTCCAG,+,0.00)
chunk0110_388_1	chr20	20150672	20150871	+	0	NA	intron (NM_015585, intron 9 of 26)	L1PB1|LINE|L1	94125	NM_001167816	26074	Hs.729168	NM_015585	ENSG00000089101	CFAP61	C20orf26|CaM-IP3|dJ1002M8.3|dJ1178H5.4	cilia and flagella associated protein 61	protein-coding	0.000000	0.500000	
chunk0180_407_1	chr7	75910734	75911081	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4195	NM_000941	5447	Hs.354056	NM_000941	ENSG00000127948	POR	CPR|CYPOR|P450R	cytochrome p450 oxidoreductase	protein-coding	0.005764	0.419540	
chunk0116_184_1	chr21	36910606	36910805	+	0	NA	intron (NM_001242785, intron 6 of 11)	intron (NM_001242785, intron 6 of 11)	55951	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.025126	0.575000	
chunk0103_154_1	chr2	162290458	162290790	+	0	NA	intron (NM_022168, intron 4 of 15)	L2c|LINE|L2	28084	NM_022168	64135	Hs.163173	NM_022168	ENSG00000115267	IFIH1	AGS7|Hlcd|IDDM19|MDA-5|MDA5|RLR-2|SGMRT1	interferon induced with helicase C domain 1	protein-coding	0.003012	0.351351	
chunk0201_230_1	chr9	37540685	37540990	+	0	NA	intron (NM_012166, intron 2 of 10)	intron (NM_012166, intron 2 of 10)	35416	NM_012166	26267	Hs.709527	NM_012166	ENSG00000147912	FBXO10	FBX10|PRMT11	F-box protein 10	protein-coding	0.006557	0.509804	
chunk0208_438_1	chrX	30465304	30466031	+	0	NA	Intergenic	Intergenic	112249	NM_025159	80231	Hs.665009	NM_025159	ENSG00000120280	CXorf21	-	chromosome X open reading frame 21	protein-coding	0.005502	0.344780	
chunk0180_173_1	chr7	65397418	65397989	+	0	NA	intron (NM_001287533, intron 4 of 4)	intron (NM_001287533, intron 4 of 4)	23904	NM_152626	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.008757	0.354895	
chunk0021_426_1	chr1	247506085	247506458	+	0	NA	promoter-TSS (NM_001281853)	promoter-TSS (NM_001281853)	-787	NM_001281836	148823	Hs.732113	NM_145278	ENSG00000169224	GCSAML	C1orf150	germinal center associated signaling and motility like	protein-coding	0.008043	0.385027	
chunk0005_459_1	chr1	63701324	63701613	+	0	NA	Intergenic	MIR3|SINE|MIR	-72551	NM_005012	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.017301	0.489655	
chunk0141_432_1	chr4	88855238	88855882	+	0	NA	intron (NM_014883, intron 6 of 23)	intron (NM_014883, intron 6 of 23)	-32199	NM_001015045	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.001553	0.282171	
chunk0001_85_1	chr1	2653886	2654468	+	0	NA	intron (NM_001242672, intron 4 of 6)	intron (NM_001242672, intron 4 of 6)	-21135	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.020619	0.619211	
chunk0171_278_1	chr6	127956150	127956349	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-37618	NM_001164687	387357	Hs.661756	NM_001010923	ENSG00000172673	THEMIS	C6orf190|C6orf207|GASP|SPOT|TSEPA	thymocyte selection associated	protein-coding	0.005025	0.375000	
chunk0018_407_1	chr1	222643888	222644398	+	0	NA	promoter-TSS (NM_001300867)	promoter-TSS (NM_001300867)	-160	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.066667	0.610568	
chunk0088_388_1	chr18	54315991	54316762	+	0	NA	Intergenic	Intergenic	38197	NM_139171	147323	Hs.438779	NM_139171	ENSG00000174448	STARD6	-	StAR related lipid transfer domain containing 6	protein-coding	0.000000	0.366580	281(GGGACATTTTGATCCT,+,0.00)
chunk0027_374_1	chr10	79342092	79343271	+	0	NA	Intergenic	Intergenic	-4783	NM_005729	10105	Hs.381072	NM_005729	ENSG00000108179	PPIF	CYP3|CyP-M|Cyp-D|CypD	peptidylprolyl isomerase F	protein-coding	0.009330	0.536441	1108(CAGGACTGGCTGTGCA,-,0.00),1109(AGGACTGGCTGTGCAT,+,0.00)
chunk0189_335_1	chr8	26445335	26446010	+	0	NA	Intergenic	Intergenic	62665	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.017778	0.544379	272(AGGCTCACTCTGTTCT,-,0.00),273(GGCTCACTCTGTTCTG,+,0.00)
chunk0041_99_1	chr11	124690684	124691107	+	0	NA	intron (NM_017425, intron 3 of 4)	intron (NM_017425, intron 3 of 4)	-14592	NM_001199922	54414	Hs.10056	NM_018978	ENSG00000110013	SIAE	AIS6|CSE-C|CSEC|LSE|YSG2	sialic acid acetylesterase	protein-coding	0.004728	0.323113	
chunk0018_173_1	chr1	219125931	219126797	+	0	NA	intron (NR_038845, intron 3 of 4)	intron (NR_038845, intron 3 of 4)	47424	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.005774	0.425606	
chunk0154_264_1	chr5	81971945	81972316	+	0	NA	5' UTR (NM_001131028, exon 1 of 9)	5' UTR (NM_001131028, exon 1 of 9)	105	NM_001131028	83734	Hs.713698	NM_031482	ENSG00000152348	ATG10	APG10|APG10L|pp12616	autophagy related 10	protein-coding	0.115903	0.744624	
chunk0014_31_1	chr1	174717266	174717590	+	0	NA	intron (NM_014857, intron 17 of 20)	intron (NM_014857, intron 17 of 20)	-82469	NM_001243765	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.015432	0.412308	
chunk0069_77_1	chr15	61032815	61033326	+	0	NA	intron (NM_134261, intron 1 of 10)	MIRb|SINE|MIR	196233	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.009785	0.414062	
chunk0120_240_1	chr3	8529684	8529908	+	0	NA	intron (NM_001278233, intron 1 of 4)	intron (NM_001278233, intron 1 of 4)	27989	NM_001278234	29995	Hs.475353	NM_014583	ENSG00000071282	LMCD1	-	LIM and cysteine rich domains 1	protein-coding	0.004464	0.355556	
chunk0169_237_1	chr6	105091472	105091711	+	0	NA	Intergenic	MIRc|SINE|MIR	44755	NM_147147	11149	Hs.221660	NM_007073	ENSG00000112276	BVES	CARICK|HBVES|LGMD2X|LGMDR25|POP1|POPDC1	blood vessel epicardial substance	protein-coding	0.020921	0.516667	
chunk0131_421_1	chr3	153232602	153232801	+	0	NA	Intergenic	Intergenic	70489	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.000000	0.290000	
chunk0022_210_1	chr10	13839740	13840305	+	0	NA	intron (NM_018027, intron 3 of 24)	intron (NM_018027, intron 3 of 24)	-234262	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.010619	0.519435	215(CAGCACAGTGTGTCCC,-,0.00),216(AGCACAGTGTGTCCCT,+,0.00)
chunk0148_393_1	chr5	14807473	14807842	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	18355	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.005420	0.413514	
chunk0047_16_1	chr12	65323140	65323446	+	0	NA	intron (NM_001031679, intron 2 of 6)	intron (NM_001031679, intron 2 of 6)	44306	NM_001193461	253827	Hs.339024	NM_198080	ENSG00000174099	MSRB3	DFNB74	methionine sulfoxide reductase B3	protein-coding	0.016340	0.407166	
chunk0052_390_1	chr12	130137108	130137471	+	0	NA	Intergenic	Intergenic	24389	NR_033834	440119	Hs.288262	NR_033834	ENSG00000250208	FZD10-AS1	FZD10-DT	FZD10 antisense divergent transcript	ncRNA	0.033058	0.508242	
chunk0080_443_1	chr17	36721689	36722355	+	0	NA	Intergenic	Intergenic	120426	NM_024864	79922	Hs.194864	NM_024864	ENSG00000278619	MRM1	-	mitochondrial rRNA methyltransferase 1	protein-coding	0.025526	0.446777	
chunk0031_89_1	chr10	123315251	123315766	+	0	NA	Intergenic	Intergenic	161264	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.003883	0.414729	246(AGGAACAGCCTGATCC,-,0.00),247(GGAACAGCCTGATCCC,+,0.00)
chunk0112_451_1	chr20	48803706	48804023	+	0	NA	intron (NM_020820, intron 1 of 39)	MLT1K|LTR|ERVL-MaLR	24019	NM_020820	57580	Hs.153310	NM_020820	ENSG00000124126	PREX1	P-REX1	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	protein-coding	0.009464	0.515723	
chunk0159_405_1	chr5	147589706	147590145	+	0	NA	3' UTR (NM_001270934, exon 21 of 21)	3' UTR (NM_001270934, exon 21 of 21)	29931	NR_038902	153469	Hs.184323	NR_038902	ENSG00000280780	JAKMIP2-AS1	-	JAKMIP2 antisense RNA 1	ncRNA	0.000000	0.345455	
chunk0182_413_1	chr7	100983588	100983787	+	0	NA	intron (NM_001164462, intron 1 of 11)	L2b|LINE|L2	14064	NM_001164462	10071	Hs.489355	NM_001164462	ENSG00000205277	MUC12	MUC-11|MUC-12|MUC11	mucin 12, cell surface associated	protein-coding	0.020101	0.465000	
chunk0157_17_1	chr5	115429346	115429897	+	0	NA	Intergenic	Intergenic	115273	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.000000	0.414855	
chunk0056_413_1	chr13	94274145	94274650	+	0	NA	intron (NM_005708, intron 4 of 8)	intron (NM_005708, intron 4 of 8)	-86406	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.003960	0.341897	
chunk0068_110_1	chr15	52361085	52361318	+	0	NA	intron (NM_001142495, intron 24 of 39)	intron (NM_001142495, intron 24 of 39)	-65403	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.004292	0.457265	
chunk0037_113_1	chr11	72381318	72381615	+	0	NA	intron (NM_001258393, intron 2 of 14)	L1M3e|LINE|L1	53218	NM_001258394	81570	Hs.523877	NM_030813	ENSG00000162129	CLPB	ANKCLB|HSP78|MEGCANN|MGCA7|SKD3	ClpB homolog, mitochondrial AAA ATPase chaperonin	protein-coding	0.013468	0.630872	
chunk0019_1_1	chr1	223133851	223134165	+	0	NA	intron (NM_003268, intron 4 of 5)	intron (NM_003268, intron 4 of 5)	9274	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.057325	0.568254	
chunk0176_235_1	chr7	15873432	15873988	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	185332	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.007194	0.333932	
chunk0013_221_1	chr1	169514840	169515454	+	0	NA	intron (NM_000130, intron 24 of 24)	intron (NM_000130, intron 24 of 24)	-29177	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.003257	0.369106	
chunk0179_290_1	chr7	49687504	49687912	+	0	NA	Intergenic	Intergenic	-85953	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.004902	0.364303	
chunk0208_361_1	chrX	25941527	25941999	+	0	NA	Intergenic	Intergenic	-196580	NM_173699	286514	Hs.350683	NM_173699	ENSG00000176774	MAGEB18	-	MAGE family member B18	protein-coding	0.006356	0.350951	
chunk0025_278_1	chr10	56346092	56346516	+	0	NA	Intergenic	Intergenic	14969	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.268235	
chunk0044_332_1	chr12	38216822	38217548	+	0	NA	Intergenic	Intergenic	-99570	NM_001013620	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.006887	0.374140	
chunk0100_339_1	chr2	116926073	116926421	+	0	NA	Intergenic	Intergenic	-888432	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.000000	0.358166	
chunk0175_426_1	chr6	168953794	168954372	+	0	NA	Intergenic	L1ME1|LINE|L1	208218	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.008651	0.291883	
chunk0060_106_1	chr14	43410808	43411398	+	0	NA	Intergenic	Intergenic	1096193	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.005085	0.341794	
chunk0007_308_1	chr1	84272436	84272845	+	0	NA	Intergenic	Intergenic	-25726	NM_001010971	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.002445	0.414634	
chunk0060_463_1	chr14	55242540	55242878	+	0	NA	Intergenic	MIRc|SINE|MIR	-28594	NM_017943	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.005917	0.294985	
chunk0184_280_1	chr7	118645782	118646009	+	0	NA	Intergenic	L1MB5|LINE|L1	421237	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.000000	0.315789	
chunk0059_18_1	chr14	29802110	29802629	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	125324	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.325000	
chunk0043_263_1	chr12	20734290	20734987	+	0	NA	intron (NM_017435, intron 10 of 14)	intron (NM_017435, intron 10 of 14)	39173	NM_017435	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.004304	0.345272	
chunk0030_257_1	chr10	115708351	115708622	+	0	NA	intron (NM_207303, intron 26 of 28)	intron (NM_207303, intron 26 of 28)	563821	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.003690	0.308824	
chunk0210_17_1	chrX	66918417	66918804	+	0	NA	Intergenic	Intergenic	-279312	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.005168	0.471649	
chunk0034_321_1	chr11	35275618	35275846	+	0	NA	intron (NM_001195728, intron 10 of 11)	intron (NM_001195728, intron 10 of 11)	136862	NM_001202557	960	Hs.502328	NM_000610	ENSG00000026508	CD44	CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1	CD44 molecule (Indian blood group)	protein-coding	0.000000	0.427948	
chunk0118_443_1	chr22	39135098	39135382	+	0	NA	intron (NM_175709, intron 4 of 5)	intron (NM_175709, intron 4 of 5)	17293	NM_175709	23492	Hs.356416	NM_175709	ENSG00000100307	CBX7	-	chromobox 7	protein-coding	0.021127	0.624561	
chunk0071_7_1	chr15	78864320	78864861	+	0	NA	Intergenic	L1MC5a|LINE|L1	-8191	NM_001265603	10933	Hs.374503	NM_006791	ENSG00000185787	MORF4L1	Eaf3|FWP006|HsT17725|MEAF3|MORFRG15|MRG15|S863-6	mortality factor 4 like 1	protein-coding	0.001848	0.363469	
chunk0078_140_1	chr17	3795906	3796136	+	0	NA	intron (NM_002208, intron 1 of 30)	intron (NM_002208, intron 1 of 30)	5222	NM_002208	3682	Hs.513867	NM_002208	ENSG00000083457	ITGAE	CD103|HUMINAE	integrin subunit alpha E	protein-coding	0.056522	0.558442	
chunk0196_23_1	chr8	101521416	101522043	+	0	NA	intron (NM_024915, intron 1 of 15)	intron (NM_024915, intron 1 of 15)	29289	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.011164	0.409236	
chunk0163_135_1	chr6	10671026	10671379	+	0	NA	TTS (NM_001145020)	TTS (NM_001145020)	23404	NR_026737	347744	Hs.61389	NM_001145020	ENSG00000137434	C6orf52	-	chromosome 6 open reading frame 52	protein-coding	0.005666	0.403955	181(TGGCACAGCTTGTTCT,-,0.00),182(GGCACAGCTTGTTCTA,+,0.00)
chunk0133_194_1	chr3	170752114	170752592	+	0	NA	Intergenic	Intergenic	117903	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.002092	0.415449	
chunk0007_229_1	chr1	81789589	81789890	+	0	NA	intron (NM_001297704, intron 2 of 20)	intron (NM_001297704, intron 2 of 20)	-10658	NM_012302	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.013289	0.380795	
chunk0053_367_1	chr13	35618231	35618757	+	0	NA	intron (NM_001204197, intron 8 of 17)	intron (NM_001204197, intron 8 of 17)	-79030	NR_132116	100507114	Hs.236298	NR_132115	ENSG00000236036	LINC00445	-	long intergenic non-protein coding RNA 445	ncRNA	0.005703	0.314991	
chunk0164_51_1	chr6	19086656	19086879	+	0	NA	intron (NR_110860, intron 9 of 10)	intron (NR_110860, intron 9 of 10)	93713	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.013453	0.428571	
chunk0203_88_1	chr9	83999135	83999417	+	0	NA	intron (NM_024945, intron 1 of 2)	MIR|SINE|MIR	18554	NM_024945	80010	Hs.726327	NM_024945	ENSG00000178966	RMI1	BLAP75|C9orf76|FAAP75	RecQ mediated genome instability 1	protein-coding	0.003546	0.286219	
chunk0053_376_1	chr13	35858734	35859123	+	0	NA	intron (NM_004734, intron 5 of 17)	intron (NM_004734, intron 5 of 17)	-3067	NM_001195430	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.002571	0.366667	109(GGGAACAGCATGTACT,-,0.00),110(GGAACAGCATGTACTC,+,0.00)
chunk0099_357_1	chr2	100754717	100754929	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-65328	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.004717	0.370892	
chunk0060_165_1	chr14	45411892	45412270	+	0	NA	Intergenic	L1PA6|LINE|L1	-158679	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.015873	0.514512	
chunk0002_55_1	chr1	13663066	13663700	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-36857	NM_001135610	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.007886	0.448819	
chunk0163_433_1	chr6	17281804	17282142	+	0	NA	promoter-TSS (NM_153020)	promoter-TSS (NM_153020)	-91	NM_001143941	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.085799	0.646018	
chunk0149_146_1	chr5	20168602	20168932	+	0	NA	intron (NM_001291956, intron 2 of 14)	L1MA1|LINE|L1	-180523	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006061	0.341390	
chunk0003_369_1	chr1	39523031	39523230	+	0	NA	intron (NM_181809, intron 6 of 6)	intron (NM_181809, intron 6 of 6)	8264	NR_132962	192217	Hs.472491	NR_132962	ENSG00000237624	OXCT2P1	OXCT2P	3-oxoacid CoA-transferase 2 pseudogene 1	pseudo	0.030151	0.665000	
chunk0118_145_1	chr22	29941265	29941751	+	0	NA	intron (NM_021090, intron 1 of 19)	L1ME2|LINE|L1	58339	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.006173	0.355236	
chunk0036_187_1	chr11	62883209	62883504	+	0	NA	intron (NM_001013251, intron 3 of 8)	intron (NM_001013251, intron 3 of 8)	1657	NR_037193	6520	Hs.502769	NM_002394	ENSG00000168003	SLC3A2	4F2|4F2HC|4T2HC|CD98|CD98HC|MDU1|NACAE	solute carrier family 3 member 2	protein-coding	0.000000	0.418919	
chunk0198_302_1	chr8	138219350	138219755	+	0	NA	intron (NM_015912, intron 7 of 19)	intron (NM_015912, intron 7 of 19)	277270	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.009877	0.431034	
chunk0134_139_1	chr3	177596912	177597351	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	155210	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.004556	0.436364	
chunk0193_456_1	chr8	81304965	81305460	+	0	NA	Intergenic	Intergenic	24729	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.010101	0.370968	
chunk0174_54_1	chr6	154910326	154910765	+	0	NA	Intergenic	Intergenic	57185	NR_036100	100422821		NR_036100	ENSG00000264814	MIR1273C	-	microRNA 1273c	ncRNA	0.009112	0.338636	
chunk0006_451_1	chr1	76981374	76981960	+	0	NA	intron (NM_030965, intron 2 of 4)	L1PA6|LINE|L1	-78476	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.005119	0.521295	
chunk0058_339_1	chr14	28751123	28751426	+	0	NA	intron (NR_125758, intron 2 of 6)	intron (NR_125758, intron 2 of 6)	14045	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.009901	0.312500	
chunk0165_75_1	chr6	31203434	31203770	+	0	NA	non-coding (NR_026791, exon 2 of 2)	non-coding (NR_026791, exon 2 of 2)	5842	NR_026791	253018	Hs.659818	NR_026791	ENSG00000206344	HCG27	bCX101P6.9|bPG299F13.9|bQB115I13.2	HLA complex group 27	ncRNA	0.014881	0.442136	
chunk0106_160_1	chr2	200678079	200678805	+	0	NA	Intergenic	Intergenic	-17281	NR_001557									0.004132	0.334250	
chunk0091_410_1	chr19	16659342	16659608	+	0	NA	intron (NM_024104, intron 2 of 4)	intron (NM_024104, intron 2 of 4)	682	NM_001300925	79086	Hs.356467	NM_024104	ENSG00000214046	SMIM7	C19orf42	small integral membrane protein 7	protein-coding	0.011278	0.546816	139(TGGGACATAGAGTCCT,-,0.00),140(GGGACATAGAGTCCTC,+,0.00)
chunk0080_145_1	chr17	27793782	27794297	+	0	NA	intron (NM_000625, intron 2 of 26)	MIRc|SINE|MIR	6490	NM_000625	4843	Hs.709191	NM_000625	ENSG00000007171	NOS2	HEP-NOS|INOS|NOS|NOS2A	nitric oxide synthase 2	protein-coding	0.054369	0.562016	
chunk0098_218_1	chr2	73572490	73572847	+	0	NA	exon (NM_015120, exon 16 of 23)	exon (NM_015120, exon 16 of 23)	69742	NM_003960	9027	Hs.14637	NM_003960	ENSG00000144035	NAT8	ATase2|CCNAT|CML1|GLA|Hcml1|TSC501|TSC510	N-acetyltransferase 8 (putative)	protein-coding	0.011204	0.427374	
chunk0138_259_1	chr4	39991372	39991591	+	0	NA	Intergenic	Intergenic	-13525	NM_001100400	23244	Hs.331431	NM_015200	ENSG00000121892	PDS5A	PIG54|SCC-112|SCC112	PDS5 cohesin associated factor A	protein-coding	0.004566	0.363636	
chunk0138_404_1	chr4	42923121	42923662	+	0	NA	intron (NM_001080476, intron 1 of 3)	intron (NM_001080476, intron 1 of 3)	30125	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.001848	0.402214	
chunk0044_111_1	chr12	28963023	28963623	+	0	NA	Intergenic	Intergenic	-185680	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.003333	0.392679	
chunk0136_82_1	chr4	2430499	2430786	+	0	NA	intron (NM_001193282, intron 2 of 15)	MLT1C|LTR|ERVL-MaLR	11697	NM_001193282	402160	Hs.443116	NM_001193282	ENSG00000206113	CFAP99	-	cilia and flagella associated protein 99	protein-coding	0.038328	0.482639	
chunk0019_295_1	chr1	228860855	228861333	+	0	NA	Intergenic	Intergenic	126017	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.023013	0.498956	
chunk0053_245_1	chr13	32773531	32773730	+	0	NA	intron (NM_015032, intron 34 of 34)	intron (NM_015032, intron 34 of 34)	138022	NR_047020	100874167	Hs.406290	NR_047020		LINC00423	-	long intergenic non-protein coding RNA 423	ncRNA	0.005025	0.315000	
chunk0016_230_1	chr1	199691609	199691988	+	0	NA	Intergenic	Intergenic	-335804	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005277	0.421053	
chunk0056_115_1	chr13	82942955	82943636	+	0	NA	Intergenic	Intergenic	939098	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.325513	
chunk0048_296_1	chr12	82757063	82757616	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	70184	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.001808	0.332130	
chunk0037_415_1	chr11	79898190	79898412	+	0	NA	Intergenic	Intergenic	-457650	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.004505	0.376682	57(AAGAACTCTATGTACT,-,0.00),58(AGAACTCTATGTACTA,+,0.00)
chunk0008_337_1	chr1	95608489	95608783	+	0	NA	Intergenic	Intergenic	98520	NR_110621	100996635	Hs.639548	NR_110621	ENSG00000228971	LINC02607	-	long intergenic non-protein coding RNA 2607	ncRNA	0.003401	0.338983	200(GAGAACAGAATGTTCT,-,0.00),201(AGAACAGAATGTTCTT,+,0.00)
chunk0088_409_1	chr18	54765170	54765646	+	0	NA	Intergenic	Intergenic	-63069	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.002101	0.412998	
chunk0057_191_1	chr13	102945353	102945858	+	0	NA	Intergenic	Intergenic	65506	NR_026965	121952	Hs.660773	NR_026965	ENSG00000250878	METTL21EP	METTL21CP1	methyltransferase like 21E, pseudogene	pseudo	0.011881	0.337945	
chunk0088_254_1	chr18	48933390	48933667	+	0	NA	intron (NM_001190822, intron 3 of 3)	intron (NM_001190822, intron 3 of 3)	9279	NM_001190823	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.018051	0.550360	
chunk0207_407_1	chr9	136959169	136959560	+	0	NA	Intergenic	Intergenic	7048	NM_178536	286256	Hs.440519	NM_178536	ENSG00000184925	LCN12	-	lipocalin 12	protein-coding	0.017903	0.665816	184(GGGAACAGCCTGTGCC,-,0.00),185(GGAACAGCCTGTGCCT,+,0.00)
chunk0084_134_1	chr17	76225538	76225851	+	0	NA	intron (NM_052916, intron 1 of 18)	intron (NM_052916, intron 1 of 18)	14615	NM_052916	114804	Hs.500643	NM_052916	ENSG00000141576	RNF157	-	ring finger protein 157	protein-coding	0.006390	0.410828	
chunk0115_142_1	chr21	23470562	23470776	+	0	NA	Intergenic	Intergenic	-85834	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.009346	0.362791	
chunk0128_317_1	chr3	111828753	111829171	+	0	NA	intron (NM_001134437, intron 1 of 17)	intron (NM_001134437, intron 1 of 17)	-30218	NM_145753	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.004785	0.367542	
chunk0053_80_1	chr13	28401869	28402828	+	0	NA	intron (NM_001160031, intron 11 of 11)	intron (NM_001160031, intron 11 of 11)	92780	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.011470	0.331250	
chunk0094_249_1	chr2	7204923	7205518	+	0	NA	Intergenic	Intergenic	-127340	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.008403	0.419463	361(CAGCTCACAGTGTGCC,-,0.00),362(AGCTCACAGTGTGCCT,+,0.00)
chunk0081_320_1	chr17	46057128	46057900	+	0	NA	intron (NM_001193465, intron 7 of 15)	L1MC5|LINE|L1	58264	NM_001007532	246744	Hs.661831	NM_001007532	ENSG00000256762	STH	MAPTIT	saitohin	protein-coding	0.007772	0.338939	251(CTGTACAAACTGTACC,-,0.00),252(TGTACAAACTGTACCT,+,0.00)
chunk0158_297_1	chr5	132254670	132255236	+	0	NA	Intergenic	Intergenic	-2705	NM_001131027	8572	Hs.424312	NM_003687	ENSG00000131435	PDLIM4	RIL	PDZ and LIM domain 4	protein-coding	0.010601	0.506173	
chunk0124_40_1	chr3	52333907	52334281	+	0	NA	intron (NM_015512, intron 8 of 77)	Tigger3|DNA|TcMar-Tigger	17775	NM_015512	25981	Hs.655469	NM_015512	ENSG00000114841	DNAH1	CILD37|DNAHC1|HDHC7|HL-11|HL11|HSRF-1|SPGF18|XLHSRF-1	dynein axonemal heavy chain 1	protein-coding	0.002674	0.392000	
chunk0175_30_1	chr7	749072	749417	+	0	NA	intron (NM_017802, intron 4 of 12)	intron (NM_017802, intron 4 of 12)	-21568	NM_001164758	5575	Hs.520851	NM_002735	ENSG00000188191	PRKAR1B	PRKAR1	protein kinase cAMP-dependent type I regulatory subunit beta	protein-coding	0.037681	0.528902	99(CTGAACAGAGTGCCCT,-,0.00),100(TGAACAGAGTGCCCTT,+,0.00)
chunk0061_262_1	chr14	61421131	61421648	+	0	NA	intron (NM_006255, intron 2 of 13)	intron (NM_006255, intron 2 of 13)	99946	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.001934	0.384170	239(ATGTACAAATTGTTCT,-,0.00),240(TGTACAAATTGTTCTT,+,0.00)
chunk0152_62_1	chr5	57759155	57759505	+	0	NA	Intergenic	Intergenic	108670	NR_104668	101928505	Hs.119998	NR_104668		LOC101928505	-	uncharacterized LOC101928505	ncRNA	0.002857	0.293447	
chunk0009_149_1	chr1	104933136	104933498	+	0	NA	Intergenic	LTR2752|LTR|ERV1	685618	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.024862	0.526171	
chunk0176_95_1	chr7	11622969	11623517	+	0	NA	intron (NM_015204, intron 2 of 26)	intron (NM_015204, intron 2 of 26)	208955	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005474	0.393443	
chunk0024_223_1	chr10	37860713	37861138	+	0	NA	Intergenic	MER57C2|LTR|ERV1	-2841	NM_001267597	57209	Hs.528423	NM_021045	ENSG00000198105	ZNF248	bA162G10.3	zinc finger protein 248	protein-coding	0.002353	0.417840	
chunk0032_59_1	chr11	2092941	2093417	+	0	NA	Intergenic	Intergenic	41030	NR_030158	619552		NR_030158	ENSG00000207805	MIR483	MIRN483|hsa-mir-483|mir-483	microRNA 483	ncRNA	0.021008	0.660377	231(GAGGCCAGAGTGTGCC,-,0.00),232(AGGCCAGAGTGTGCCT,+,0.00)
chunk0194_310_1	chr8	88207301	88207504	+	0	NA	intron (NM_005941, intron 1 of 9)	Tigger2|DNA|TcMar-Tigger	120086	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.009852	0.377451	
chunk0143_366_1	chr4	122246135	122246728	+	0	NA	intron (NM_015312, intron 31 of 83)	intron (NM_015312, intron 31 of 83)	75828	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.005059	0.299663	253(TAGAACAGTGTGTAAT,-,0.00)
chunk0151_104_1	chr5	43348297	43348521	+	0	NA	Intergenic	Intergenic	-34897	NM_002130	3157	Hs.397729	NM_002130	ENSG00000112972	HMGCS1	HMGCS	3-hydroxy-3-methylglutaryl-CoA synthase 1	protein-coding	0.008929	0.502222	
chunk0110_409_1	chr20	20548712	20549058	+	0	NA	intron (NM_020343, intron 23 of 39)	intron (NM_020343, intron 23 of 39)	163738	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.008671	0.417867	108(AGGTACTCATTGTGCT,-,0.00),109(GGTACTCATTGTGCTG,+,0.00)
chunk0024_185_1	chr10	36115230	36115857	+	0	NA	Intergenic	Intergenic	337241	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.001595	0.340764	
chunk0110_254_1	chr20	16654870	16655380	+	0	NA	Intergenic	Intergenic	-74839	NM_003092	6629	Hs.280378	NM_003092	ENSG00000125870	SNRPB2	Msl1|U2B''	small nuclear ribonucleoprotein polypeptide B2	protein-coding	0.005882	0.377691	
chunk0065_90_1	chr15	23773940	23774147	+	0	NA	Intergenic	L1PA16|LINE|L1	-86740	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.004831	0.375000	
chunk0195_305_1	chr8	98771082	98771595	+	0	NA	intron (NM_006281, intron 2 of 10)	L1MB5|LINE|L1	54333	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.003899	0.299611	
chunk0002_184_1	chr1	19097380	19097693	+	0	NA	intron (NM_020765, intron 90 of 105)	intron (NM_020765, intron 90 of 105)	112716	NM_020765	23352	Hs.148078	NM_020765	ENSG00000127481	UBR4	RBAF600|ZUBR1|p600	ubiquitin protein ligase E3 component n-recognin 4	protein-coding	0.003195	0.343949	
chunk0081_242_1	chr17	42982232	42982517	+	0	NA	intron (NM_173079, intron 1 of 4)	intron (NM_173079, intron 1 of 4)	1809	NM_173079	146923	Hs.632255	NM_173079	ENSG00000198863	RUNDC1	-	RUN domain containing 1	protein-coding	0.000000	0.433566	
chunk0013_197_1	chr1	169238485	169238711	+	0	NA	intron (NR_104229, intron 7 of 12)	Charlie29a|DNA|hAT-Charlie	-129358	NM_003666	8548	Hs.130746	NM_003666	ENSG00000117475	BLZF1	GOLGIN-45|JEM-1|JEM-1s|JEM1	basic leucine zipper nuclear factor 1	protein-coding	0.008850	0.414097	
chunk0017_438_1	chr1	214051112	214051394	+	0	NA	Intergenic	Intergenic	62752	NM_002763	5629	Hs.741808	NM_002763	ENSG00000117707	PROX1	-	prospero homeobox 1	protein-coding	0.003546	0.399293	
chunk0129_258_1	chr3	122398775	122399443	+	0	NA	intron (NM_014367, intron 1 of 4)	L1PREC2|LINE|L1	14933	NM_014367	26355	Hs.584881	NM_014367	ENSG00000114023	FAM162A	C3orf28|E2IG5|HGTD-P	family with sequence similarity 162 member A	protein-coding	0.007485	0.376682	
chunk0111_323_1	chr20	32345159	32345588	+	0	NA	Intergenic	Intergenic	-12971	NM_001164603	171023	Hs.374043	NM_015338	ENSG00000171456	ASXL1	BOPS|MDS	ASXL transcriptional regulator 1	protein-coding	0.011655	0.423256	
chunk0023_281_1	chr10	28399997	28400380	+	0	NA	Intergenic	Intergenic	-110838	NR_107053	102465880		NR_107053	ENSG00000275036	MIR8086	hsa-mir-8086	microRNA 8086	ncRNA	0.020888	0.440104	211(TGGGACAGTTTGTTCT,-,0.00),212(GGGACAGTTTGTTCTT,+,0.00),280(CTGTACAACTTGTTCT,-,0.00),281(TGTACAACTTGTTCTG,+,0.00)
chunk0205_435_1	chr9	115213712	115213985	+	0	NA	intron (NM_017418, intron 1 of 7)	intron (NM_017418, intron 1 of 7)	72030	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.007326	0.419708	
chunk0026_430_1	chr10	70940317	70940667	+	0	NA	Intergenic	Intergenic	-51706	NM_000281	5092	Hs.3192	NM_000281	ENSG00000166228	PCBD1	DCOH|PCBD|PCD|PHS	pterin-4 alpha-carbinolamine dehydratase 1	protein-coding	0.014286	0.569801	158(GGGCCATTCTGTCCCC,+,0.00)
chunk0209_394_1	chrX	55022580	55022847	+	0	NA	intron (NM_001037968, intron 4 of 10)	L1ME3G|LINE|L1	8351	NM_000032	212	Hs.522666	NM_000032	ENSG00000158578	ALAS2	ALAS-E|ALASE|ANH1|ASB|SIDBA1|XLDPP|XLEPP|XLSA	5'-aminolevulinate synthase 2	protein-coding	0.000000	0.339552	
chunk0074_434_1	chr16	46400417	46401160	+	0	NA	Intergenic	Intergenic	168309	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.044415	0.361559	
chunk0025_334_1	chr10	57962710	57963314	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	304922	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.004967	0.366942	
chunk0179_333_1	chr7	50657409	50657615	+	0	NA	intron (NM_001001549, intron 4 of 14)	intron (NM_001001549, intron 4 of 14)	47789	NM_001001550	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.024272	0.444444	88(CGGTACATGGTGTTCC,-,0.00),89(GGTACATGGTGTTCCC,+,0.00)
chunk0018_92_1	chr1	217574645	217574870	+	0	NA	intron (NM_018040, intron 5 of 9)	MIRb|SINE|MIR	56345	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.008889	0.362832	
chunk0049_117_1	chr12	91388618	91389253	+	0	NA	Intergenic	Intergenic	-205811	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.001575	0.341195	
chunk0084_57_1	chr17	74465762	74465961	+	0	NA	promoter-TSS (NM_007261)	promoter-TSS (NM_007261)	-522	NM_007261	11314	Hs.9688	NM_007261	ENSG00000167851	CD300A	CLM-8|CMRF-35-H9|CMRF-35H|CMRF35-H|CMRF35-H9|CMRF35H|CMRF35H9|IGSF12|IRC1|IRC1/IRC2|IRC2|IRp60	CD300a molecule	protein-coding	0.000000	0.460000	
chunk0162_65_1	chr6	1667877	1668122	+	0	NA	intron (NM_001253846, intron 9 of 10)	intron (NM_001253846, intron 9 of 10)	57553	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.016327	0.378049	
chunk0177_59_1	chr7	21121646	21122065	+	0	NA	Intergenic	MIRb|SINE|MIR	286424	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.007160	0.397619	
chunk0197_337_1	chr8	125244615	125245160	+	0	NA	intron (NM_173685, intron 5 of 7)	intron (NM_173685, intron 5 of 7)	153046	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.011009	0.371795	
chunk0003_270_1	chr1	36359438	36359710	+	0	NA	intron (NM_001282546, intron 2 of 10)	intron (NM_001282546, intron 2 of 10)	26353	NM_001282546	83931	Hs.471768	NM_032017	ENSG00000196182	STK40	SHIK|SgK495	serine/threonine kinase 40	protein-coding	0.018382	0.516484	106(GGGGACTTTCTGTACT,-,0.00),107(GGGACTTTCTGTACTT,+,0.00)
chunk0182_32_1	chr7	91565371	91566138	+	0	NA	Intergenic	Intergenic	301286	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.011734	0.492188	
chunk0114_386_1	chr20	63198276	63198992	+	0	NA	intron (NM_017798, intron 4 of 4)	intron (NM_017798, intron 4 of 4)	17552	NM_017798	54915	Hs.744852	NM_017798	ENSG00000149658	YTHDF1	C20orf21	YTH N6-methyladenosine RNA binding protein 1	protein-coding	0.015363	0.442120	378(AAGCACAGCTCGTTCT,-,0.00),379(AGCACAGCTCGTTCTT,+,0.00)
chunk0007_302_1	chr1	84187784	84188177	+	0	NA	intron (NM_001300917, intron 5 of 8)	MER101-int|LTR|ERV1	6348	NM_001242862	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.005089	0.319797	
chunk0090_227_1	chr18	73661532	73661880	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	336765	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.005747	0.335244	
chunk0044_338_1	chr12	38555502	38556184	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	239088	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.002933	0.374817	
chunk0107_218_1	chr2	216856869	216857521	+	0	NA	Intergenic	Intergenic	2864	NM_003284	7141	Hs.3017	NM_003284	ENSG00000118245	TNP1	TP1	transition protein 1	protein-coding	0.004601	0.476263	
chunk0065_287_1	chr14	102531137	102531462	+	0	NA	Intergenic	MER51B|LTR|ERV1	-8345	NR_036192	100422954		NR_036192	ENSG00000266015	MIR4309	-	microRNA 4309	ncRNA	0.024615	0.475460	
chunk0141_361_1	chr4	87960941	87961176	+	0	NA	Intergenic	Intergenic	-14592	NM_001251829	6696	Hs.313	NM_000582	ENSG00000118785	SPP1	BNSP|BSPI|ETA-1|OPN	secreted phosphoprotein 1	protein-coding	0.004255	0.305085	
chunk0124_63_1	chr3	52935198	52935536	+	0	NA	intron (NM_016329, intron 4 of 20)	MER58A|DNA|hAT-Charlie	-37786	NM_001198974	100526772		NM_001198974	ENSG00000248592	STIMATE-MUSTN1	TMEM110-MUSTN1	STIMATE-MUSTN1 readthrough	protein-coding	0.005917	0.398230	
chunk0212_323_1	chrX	143963535	143963821	+	0	NA	Intergenic	L1PA13|LINE|L1	79607	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.003497	0.327526	
chunk0119_324_1	chr22	46801083	46801767	+	0	NA	intron (NM_014346, intron 4 of 12)	intron (NM_014346, intron 4 of 12)	27498	NM_001284305	25771	Hs.435044	NM_014346	ENSG00000054611	TBC1D22A	C22orf4|HSC79E021	TBC1 domain family member 22A	protein-coding	0.024854	0.423358	543(AGAACACGCAGTTTCC,+,0.00)
chunk0126_124_1	chr3	75772165	75772571	+	0	NA	intron (NM_001290209, intron 2 of 4)	MER52A|LTR|ERV1	12736	NM_001128223	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.009852	0.545455	
chunk0014_423_1	chr1	183425797	183426201	+	0	NA	Intergenic	Intergenic	-7500	NM_015039	23057	Hs.497123	NM_015039	ENSG00000157064	NMNAT2	C1orf15|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.004950	0.397531	
chunk0120_328_1	chr3	10779418	10779814	+	0	NA	Intergenic	Intergenic	-15424	NR_027102	285370	Hs.157613	NR_027102	ENSG00000226567	LINC00606	-	long intergenic non-protein coding RNA 606	ncRNA	0.020202	0.591940	
chunk0043_215_1	chr12	19700732	19700952	+	0	NA	Intergenic	L1PA15|LINE|L1	260261	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.018182	0.610860	
chunk0192_41_1	chr8	58805366	58805670	+	0	NA	TTS (NM_014729)	TTS (NM_014729)	-145673	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.016447	0.363934	
chunk0155_72_1	chr5	91689594	91690135	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-306532	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.404059	195(TTGAACAGTGAGTCCT,-,0.00),196(TGAACAGTGAGTCCTT,+,0.00)
chunk0051_371_1	chr12	121467374	121467623	+	0	NA	intron (NM_001005366, intron 12 of 22)	CpG	-23146	NR_106957	102465665		NR_106957	ENSG00000284402	MIR7107	hsa-mir-7107	microRNA 7107	ncRNA	0.140562	0.836000	
chunk0171_334_1	chr6	129937681	129938661	+	0	NA	Intergenic	L1MC3|LINE|L1	-76900	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.010204	0.373089	
chunk0133_30_1	chr3	165883512	165884225	+	0	NA	Intergenic	Intergenic	-46403	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.009818	0.319328	479(GGTGACAGAGTGTTCT,-,0.00),480(GTGACAGAGTGTTCTA,+,0.00)
chunk0027_238_1	chr10	76763266	76763952	+	0	NA	Intergenic	MER110|LTR|ERV1	-124435	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.008746	0.366812	
chunk0097_299_1	chr2	55810359	55811060	+	0	NA	Intergenic	Intergenic	113454	NM_001039349	2202	Hs.76224	NM_004105	ENSG00000115380	EFEMP1	DHRD|DRAD|FBLN3|FBNL|FIBL-3|MLVT|MTLV|S1-5	EGF containing fibulin extracellular matrix protein 1	protein-coding	0.005706	0.363248	
chunk0162_445_1	chr5	180646905	180647514	+	0	NA	intron (NM_182925, intron 1 of 29)	MamRTE1|LINE|RTE-BovB	2415	NM_002020	2324	Hs.646917	NM_002020	ENSG00000037280	FLT4	FLT-4|FLT41|LMPH1A|LMPHM1|PCL|VEGFR-3|VEGFR3	fms related tyrosine kinase 4	protein-coding	0.006568	0.578689	
chunk0120_454_1	chr3	14295649	14296331	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	56578	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.010264	0.389458	
chunk0155_13_1	chr5	90872882	90873476	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	314379	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.003367	0.411765	231(GGAAGAAACTGTTCTT,+,0.00)
chunk0186_233_1	chr7	140656773	140656972	+	0	NA	Intergenic	HERV3-int|LTR|ERV1	-16281	NM_052853	90956	Hs.744886	NM_052853	ENSG00000133597	ADCK2	AARF	aarF domain containing kinase 2	protein-coding	0.000000	0.545000	
chunk0122_300_1	chr3	36422546	36423224	+	0	NA	intron (NM_003149, intron 1 of 10)	intron (NM_003149, intron 1 of 10)	42398	NM_001292049	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.004425	0.326951	313(AGGTACAAAATGTTCA,-,0.00),314(GGTACAAAATGTTCAT,+,0.00)
chunk0037_165_1	chr11	73792417	73792709	+	0	NA	intron (NM_016055, intron 1 of 7)	intron (NM_016055, intron 1 of 7)	4691	NM_016055	51642	Hs.503239	NM_016055	ENSG00000175581	MRPL48	CGI-118|HSPC290|L48MT|MRP-L48	mitochondrial ribosomal protein L48	protein-coding	0.000000	0.399317	123(ATGAACAAAATGTCCT,-,0.00),124(TGAACAAAATGTCCTC,+,0.00)
chunk0056_465_1	chr13	95360199	95360682	+	0	NA	Intergenic	MER41C|LTR|ERV1	-58994	NM_001105515	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.006211	0.404959	
chunk0028_275_1	chr10	90971780	90972087	+	0	NA	intron (NR_131214, intron 3 of 5)	intron (NR_131214, intron 3 of 5)	24633	NR_131214	105378427		NR_131214		XLOC_008559	-	uncharacterized LOC105378427	ncRNA	0.006515	0.412338	
chunk0070_445_1	chr15	78387728	78387928	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	47504	NM_004378	1381	Hs.346950	NM_004378	ENSG00000166426	CRABP1	CRABP|CRABP-I|CRABPI|RBP5	cellular retinoic acid binding protein 1	protein-coding	0.000000	0.427861	
chunk0088_382_1	chr18	54260930	54261171	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-8429	NM_007195	11201	Hs.438533	NM_007195	ENSG00000101751	POLI	RAD30B|RAD3OB|eta2	DNA polymerase iota	protein-coding	0.016598	0.400826	
chunk0171_272_1	chr6	127693907	127694516	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	117037	NM_001010905	352999	Hs.226268	NM_001010905	ENSG00000184530	C6orf58	LEG1	chromosome 6 open reading frame 58	protein-coding	0.004926	0.334426	
chunk0144_150_1	chr4	130368860	130369059	+	0	NA	Intergenic	Intergenic	-597481	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.000000	0.305000	
chunk0052_233_1	chr13	25727186	25727719	+	0	NA	intron (NM_001313741, intron 25 of 35)	intron (NM_001313741, intron 25 of 35)	258678	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.013133	0.378277	
chunk0106_410_1	chr2	207935188	207935403	+	0	NA	intron (NM_001080475, intron 4 of 7)	MER103C|DNA|hAT-Charlie	90265	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.013953	0.476852	
chunk0148_230_1	chr5	9421758	9422378	+	0	NA	intron (NM_003966, intron 2 of 22)	intron (NM_003966, intron 2 of 22)	-89265	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.006452	0.360709	
chunk0116_296_1	chr21	40372043	40372655	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	-10734	NR_038896	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.003268	0.404568	
chunk0114_20_1	chr21	7289985	7290184	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	430913	NR_128718	103504736		NR_128718	ENSG00000278618	MIR8069-2	hsa-mir-8069-2	microRNA 8069-2	ncRNA	0.005025	0.375000	
chunk0172_415_1	chr6	140128435	140128706	+	0	NA	Intergenic	Intergenic	-76682	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.003690	0.562500	
chunk0091_160_1	chr19	7450334	7451077	+	0	NA	intron (NM_001130955, intron 5 of 19)	intron (NM_001130955, intron 5 of 19)	11017	NM_001130955	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.060565	0.451613	
chunk0164_144_1	chr6	21350648	21350953	+	0	NA	Intergenic	LTR82B|LTR|ERVL	161092	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.000000	0.428105	
chunk0100_154_1	chr2	109175278	109175642	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	-33872	NR_036223	100422863		NR_036223	ENSG00000264934	MIR4265	-	microRNA 4265	ncRNA	0.010989	0.438356	
chunk0012_284_1	chr1	162019309	162019889	+	0	NA	intron (NM_001297713, intron 2 of 7)	intron (NM_001297713, intron 2 of 7)	4866	NM_015441	25903	Hs.507515	NM_015441	ENSG00000162745	OLFML2B	-	olfactomedin like 2B	protein-coding	0.008621	0.526678	322(AAGAACGCTGAGTTCT,-,0.00),323(AGAACGCTGAGTTCTT,+,0.00)
chunk0113_388_1	chr20	59998764	59999244	+	0	NA	intron (NM_177980, intron 13 of 17)	intron (NM_177980, intron 13 of 17)	2642	NM_021810	60437	Hs.729046	NM_021810	ENSG00000124215	CDH26	VR20	cadherin 26	protein-coding	0.004167	0.413721	216(AGGAACATTCTGTGCT,-,0.00),217(GGAACATTCTGTGCTC,+,0.00)
chunk0106_358_1	chr2	206983484	206983950	+	0	NA	Intergenic	Intergenic	44163	NM_173077	130749	Hs.684103	NM_173077	ENSG00000144410	CPO	-	carboxypeptidase O	protein-coding	0.004292	0.436831	
chunk0035_143_1	chr11	42892001	42892557	+	0	NA	Intergenic	L1MEd|LINE|L1	377090	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.003597	0.314183	
chunk0003_297_1	chr1	37534343	37534749	+	0	NA	TTS (NM_024700)	TTS (NM_024700)	-19727	NM_001270876	64769	Hs.17118	NM_022756	ENSG00000163875	MEAF6	C1orf149|CENP-28|EAF6|NY-SAR-91	MYST/Esa1 associated factor 6	protein-coding	0.007389	0.356265	176(AGGAACACTGTGGGCT,-,0.00),177(GGAACACTGTGGGCTC,+,0.00)
chunk0043_336_1	chr12	22760115	22760702	+	0	NA	Intergenic	Intergenic	135266	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.005111	0.408163	352(TAGGCCACAGTGTTCT,-,0.00),353(AGGCCACAGTGTTCTC,+,0.00)
chunk0080_199_1	chr17	29176611	29177067	+	0	NA	intron (NM_203318, intron 1 of 40)	CpG	3550	NM_078471	399687	Hs.462590	NM_078471	ENSG00000196535	MYO18A	MAJN|MYSPDZ|SP-R210|SPR210	myosin XVIIIA	protein-coding	0.100877	0.719912	
chunk0019_249_1	chr1	227605418	227605640	+	0	NA	intron (NM_178549, intron 2 of 3)	L1MB7|LINE|L1	42010	NM_178549	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.009009	0.295964	
chunk0023_319_1	chr10	29150032	29150497	+	0	NA	Intergenic	Intergenic	-138797	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.010753	0.484979	
chunk0106_424_1	chr2	208187070	208187407	+	0	NA	intron (NM_001099334, intron 1 of 8)	intron (NM_001099334, intron 1 of 8)	2811	NM_001099334	389073	Hs.198416	NM_001099334	ENSG00000188674	C2orf80	GONDA1	chromosome 2 open reading frame 80	protein-coding	0.005935	0.414201	
chunk0167_426_1	chr6	75619233	75619851	+	0	NA	intron (NM_001304792, intron 1 of 14)	L1MC3|LINE|L1	18033	NM_015571	26054	Hs.485784	NM_015571	ENSG00000112701	SENP6	SSP1|SUSP1	SUMO specific peptidase 6	protein-coding	0.006472	0.374798	
chunk0076_38_1	chr16	59786295	59786890	+	0	NA	Intergenic	L1MC3|LINE|L1	-31401	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.003361	0.298658	
chunk0132_24_1	chr3	154584813	154585116	+	0	NA	Intergenic	L1MD2|LINE|L1	-155249	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.003300	0.305921	
chunk0030_21_1	chr10	111019327	111019727	+	0	NA	Intergenic	Intergenic	30601	NR_031614	100313921		NR_031614	ENSG00000221214	MIR548E	MIRN548E|hsa-mir-548e	microRNA 548e	ncRNA	0.002500	0.321696	
chunk0161_374_1	chr5	176388886	176389272	+	0	NA	promoter-TSS (NM_001291307)	promoter-TSS (NM_001291307)	296	NM_138820	192286	Hs.534575	NM_138820	ENSG00000146066	HIGD2A	RCF1b	HIG1 hypoxia inducible domain family member 2A	protein-coding	0.062176	0.594315	
chunk0150_273_1	chr5	36876515	36877017	+	0	NA	promoter-TSS (NM_133433)	promoter-TSS (NM_133433)	7	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.093625	0.675944	
chunk0105_320_1	chr2	190834827	190835213	+	0	NA	Intergenic	Intergenic	-45801	NM_001256310	2744	Hs.116448	NM_014905	ENSG00000115419	GLS	AAD20|CASGID|EIEE71|GAC|GAM|GDPAG|GLS1|KGA	glutaminase	protein-coding	0.002591	0.361757	
chunk0140_305_1	chr4	73034942	73035399	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	34589	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.004376	0.393013	
chunk0039_155_1	chr11	98855544	98856059	+	0	NA	Intergenic	L1MC1|LINE|L1	-165175	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.007767	0.354651	
chunk0089_306_1	chr18	63774522	63774741	+	0	NA	promoter-TSS (NM_001261831)	promoter-TSS (NM_001261831)	-744	NM_003784	8710	Hs.138202	NM_003784	ENSG00000166396	SERPINB7	MEGSIN|PPKN|TP55	serpin family B member 7	protein-coding	0.004566	0.504545	
chunk0048_379_1	chr12	86379378	86379908	+	0	NA	intron (NM_013244, intron 2 of 6)	intron (NM_013244, intron 2 of 6)	459261	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.003774	0.290019	
chunk0119_310_1	chr22	46649462	46649933	+	0	NA	intron (NM_015124, intron 2 of 17)	intron (NM_015124, intron 2 of 17)	22936	NM_015124	23151	Hs.475150	NM_015124	ENSG00000075240	GRAMD4	DIP	GRAM domain containing 4	protein-coding	0.019108	0.472458	
chunk0184_164_1	chr7	116273166	116273733	+	0	NA	Intergenic	Intergenic	13215	NR_130923	102724434	Hs.667624	NR_130921	ENSG00000237870	LOC102724434	-	uncharacterized LOC102724434	ncRNA	0.007055	0.378521	
chunk0134_288_1	chr3	179838179	179838651	+	0	NA	intron (NM_001256750, intron 8 of 14)	intron (NM_001256750, intron 8 of 14)	-59779	NR_110059	101928790	Hs.667247	NR_110059	ENSG00000244302	PEX5L-AS2	-	PEX5L antisense RNA 2	ncRNA	0.002119	0.308668	
chunk0037_68_1	chr11	71163727	71164555	+	0	NA	intron (NM_012309, intron 1 of 24)	intron (NM_012309, intron 1 of 24)	60655	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.008454	0.481303	225(TAGTACAGAGAGTTCC,-,0.00),226(AGTACAGAGAGTTCCC,+,0.00)
chunk0096_385_1	chr2	36981693	36982175	+	0	NA	intron (NM_019024, intron 35 of 35)	intron (NM_019024, intron 35 of 35)	-15462	NM_003162	6801	Hs.127486	NM_003162	ENSG00000115808	STRN	PPP2R6A|SG2NA|STRN1	striatin	protein-coding	0.004149	0.310559	
chunk0166_98_1	chr6	43753455	43754151	+	0	NA	Intergenic	HAL1|LINE|L1	-16406	NM_001025367	7422	Hs.73793	NM_003376	ENSG00000112715	VEGFA	MVCD1|VEGF|VPF	vascular endothelial growth factor A	protein-coding	0.004310	0.361549	
chunk0105_242_1	chr2	188551987	188552353	+	0	NA	intron (NR_045563, intron 8 of 12)	L1MA4A|LINE|L1	237934	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.002732	0.288828	
chunk0034_169_1	chr11	30990291	30991175	+	0	NA	intron (NM_020869, intron 1 of 19)	intron (NM_020869, intron 1 of 19)	1953	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.011312	0.425989	
chunk0010_221_1	chr1	116289281	116289545	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-83760	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.007576	0.430189	
chunk0014_357_1	chr1	182389532	182390019	+	0	NA	intron (NM_001033044, intron 1 of 6)	intron (NM_001033044, intron 1 of 6)	1629	NM_001033056	2752	Hs.132016	NM_002065	ENSG00000135821	GLUL	GLNS|GS|PIG43|PIG59	glutamate-ammonia ligase	protein-coding	0.022587	0.483607	212(GGGAACACATTGTTCT,-,0.00),213(GGAACACATTGTTCTC,+,0.00)
chunk0059_436_1	chr14	38432130	38432783	+	0	NA	Intergenic	Intergenic	-176086	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.004594	0.298165	
chunk0041_118_1	chr11	124984028	124984361	+	0	NA	intron (NM_025004, intron 6 of 15)	L1PA15|LINE|L1	30073	NM_025004	80071	Hs.287555	NM_025004	ENSG00000149548	CCDC15	-	coiled-coil domain containing 15	protein-coding	0.012012	0.574850	
chunk0165_256_1	chr6	35725596	35726064	+	0	NA	TTS (NR_027117)	TTS (NR_027117)	2753	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.017094	0.541578	
chunk0055_41_1	chr13	52167041	52167974	+	0	NA	TTS (NR_002816)	TTS (NR_002816)	-7646	NM_002498	4752	Hs.409989	NM_002498	ENSG00000136098	NEK3	HSPK36	NIMA related kinase 3	protein-coding	0.006431	0.376874	
chunk0135_107_1	chr3	186800763	186800962	+	0	NA	intron (NM_181573, intron 3 of 10)	intron (NM_181573, intron 3 of 10)	5639	NM_002916	5984	Hs.732098	NM_002916	ENSG00000163918	RFC4	A1|RFC37	replication factor C subunit 4	protein-coding	0.000000	0.280000	
chunk0169_373_1	chr6	107247063	107247742	+	0	NA	intron (NM_020381, intron 3 of 7)	intron (NM_020381, intron 3 of 7)	-132970	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.011782	0.395588	328(AAGAACATTTTGTTCT,-,0.00),329(AGAACATTTTGTTCTC,+,0.00)
chunk0076_206_1	chr16	68131885	68132084	+	0	NA	intron (NM_173163, intron 3 of 10)	intron (NM_173163, intron 3 of 10)	46618	NM_004555	4775	Hs.436585	NM_004555	ENSG00000072736	NFATC3	NF-AT4c|NFAT4|NFATX	nuclear factor of activated T cells 3	protein-coding	0.010050	0.385000	
chunk0074_29_1	chr16	20587659	20588264	+	0	NA	Intergenic	Intergenic	-11588	NM_001105069	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.004959	0.473597	98(GGGATCAGGCTGTTCT,-,0.00),99(GGATCAGGCTGTTCTT,+,0.00),120(AGGAACAAAATGTGCT,-,0.00),121(GGAACAAAATGTGCTT,+,0.00)
chunk0116_260_1	chr21	38950459	38951187	+	0	NA	Intergenic	Intergenic	-12394	NR_120405	400867	Hs.689509	NR_120405		LOC400867	-	uncharacterized LOC400867	ncRNA	0.005495	0.355281	
chunk0048_79_1	chr12	78993108	78993613	+	0	NA	intron (NM_001291901, intron 2 of 9)	intron (NM_001291901, intron 2 of 9)	-52293	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.000000	0.347826	
chunk0117_331_1	chr22	25131413	25131871	+	0	NA	intron (NM_001145206, intron 4 of 10)	intron (NM_001145206, intron 4 of 10)	-18950	NR_038941	100128531	Hs.662126	NR_038941	ENSG00000203280	LOC100128531	-	uncharacterized LOC100128531	ncRNA	0.010917	0.596950	
chunk0083_443_1	chr17	72683911	72684477	+	0	NA	intron (NM_001159770, intron 7 of 9)	intron (NM_001159770, intron 7 of 9)	-43722	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.012367	0.518519	
chunk0153_337_1	chr5	74112719	74113063	+	0	NA	Intergenic	Intergenic	195434	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.005814	0.423188	
chunk0207_5_1	chrM	6279	6533	+	0	NA	NA	Intergenic	NA	NA									0.015748	0.486275	
chunk0136_398_1	chr3	197161321	197161520	+	0	NA	intron (NM_001204386, intron 5 of 24)	intron (NM_001204386, intron 5 of 24)	22711	NM_001204387	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.000000	0.295000	99(AAGTTCATTGTGTCCC,-,0.00)
chunk0130_194_1	chr3	133626937	133627151	+	0	NA	intron (NM_007027, intron 16 of 27)	intron (NM_007027, intron 16 of 27)	34849	NM_007027	11073	Hs.593379	NM_007027	ENSG00000163781	TOPBP1	Dpb11|TOP2BP1	DNA topoisomerase II binding protein 1	protein-coding	0.004673	0.353488	47(TGGGACAGTCTGGTCC,-,0.00),48(GGGACAGTCTGGTCCT,+,0.00)
chunk0092_13_1	chr19	18571687	18571994	+	0	NA	promoter-TSS (NM_003333)	promoter-TSS (NM_003333)	36	NM_001033930	7311	Hs.5308	NM_003333	ENSG00000221983	UBA52	CEP52|HUBCEP52|L40|RPL40	ubiquitin A-52 residue ribosomal protein fusion product 1	protein-coding	0.133550	0.704545	
chunk0087_127_1	chr18	33696712	33696911	+	0	NA	intron (NM_030632, intron 8 of 11)	intron (NM_030632, intron 8 of 11)	118234	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.005025	0.430000	
chunk0160_135_1	chr5	151354189	151354771	+	0	NA	Intergenic	Intergenic	-6890	NM_181776	153201	Hs.483877	NM_181776	ENSG00000186335	SLC36A2	PAT2|TRAMD1	solute carrier family 36 member 2	protein-coding	0.006873	0.449400	
chunk0108_245_1	chr2	233886698	233886918	+	0	NA	Intergenic	Intergenic	-18399	NR_024322	151507	Hs.355809	NM_001166217	ENSG00000224287	MSL3P1	MSL3L2	MSL complex subunit 3 pseudogene 1	pseudo	0.000000	0.420814	
chunk0067_383_1	chr15	49075594	49076260	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-29364	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.000000	0.389805	279(AGGTACAGATTGTTCC,-,0.00),280(GGTACAGATTGTTCCT,+,0.00)
chunk0038_380_1	chr11	93491222	93491614	+	0	NA	intron (NM_020179, intron 2 of 2)	MIR|SINE|MIR	51962	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.005102	0.458015	
chunk0089_28_1	chr18	57803080	57803371	+	0	NA	promoter-TSS (NM_005603)	promoter-TSS (NM_005603)	-130	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.120275	0.763699	
chunk0213_17_1	chrY	21334309	21334819	+	0	NA	Intergenic	Intergenic	51796	NM_001282471	100533178		NM_001282471		PRORY	CYorf17	proline rich Y-linked	protein-coding	0.001961	0.346380	269(AAGACCATTGTGTACT,-,0.00),270(AGACCATTGTGTACTC,+,0.00)
chunk0033_257_1	chr11	18457072	18457271	+	0	NA	intron (NM_001144071, intron 2 of 7)	intron (NM_001144071, intron 2 of 7)	1344	NM_001144071	160287	Hs.668877	NM_144972	ENSG00000166800	LDHAL6A	LDH6A	lactate dehydrogenase A like 6A	protein-coding	0.015075	0.365000	
chunk0208_129_1	chrX	15568133	15568609	+	0	NA	intron (NM_021804, intron 15 of 18)	intron (NM_021804, intron 15 of 18)	33698	NM_021804	59272	Hs.178098	NM_021804	ENSG00000130234	ACE2	ACEH	angiotensin I converting enzyme 2	protein-coding	0.008403	0.322851	
chunk0040_263_1	chr11	116061307	116061890	+	0	NA	Intergenic	Intergenic	-301398	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.008576	0.517123	
chunk0089_87_1	chr18	58309488	58310079	+	0	NA	intron (NM_001144970, intron 4 of 28)	intron (NM_001144970, intron 4 of 28)	88261	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.013536	0.523649	287(GAGAACTGAGTGTTCT,-,0.00),288(AGAACTGAGTGTTCTT,+,0.00)
chunk0175_78_1	chr7	2232812	2233040	+	0	NA	promoter-TSS (NM_001013836)	promoter-TSS (NM_001013836)	22	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.153509	0.733624	
chunk0188_221_1	chr8	12795139	12795869	+	0	NA	intron (NR_102423, intron 1 of 1)	intron (NR_102423, intron 1 of 1)	1261	NR_102423	101409254	Hs.571476	NR_102423	ENSG00000255494	LINC00681	-	long intergenic non-protein coding RNA 681	ncRNA	0.009589	0.373461	
chunk0195_233_1	chr8	97460690	97460941	+	0	NA	Intergenic	Intergenic	-14318	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.007968	0.496032	
chunk0103_339_1	chr2	168009820	168010378	+	0	NA	intron (NM_013233, intron 16 of 17)	intron (NM_013233, intron 16 of 17)	-68955	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.001792	0.347048	297(AAGAACAATCTGATCC,-,0.00),298(AGAACAATCTGATCCT,+,0.00)
chunk0132_427_1	chr3	164681260	164681601	+	0	NA	Intergenic	Intergenic	150050	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.000000	0.318713	
chunk0047_457_1	chr12	76785387	76785862	+	0	NA	intron (NM_015336, intron 1 of 16)	L2c|LINE|L2	21550	NM_015336	23390	Hs.4014	NM_015336	ENSG00000186908	ZDHHC17	DHHC-17|HIP14|HIP3|HSPC294|HYPH	zinc finger DHHC-type containing 17	protein-coding	0.008421	0.371849	
chunk0055_16_1	chr13	51769789	51770177	+	0	NA	TTS (NM_001031719)	TTS (NM_001031719)	34179	NM_024705	79758	Hs.266728	NM_024705	ENSG00000102796	DHRS12	SDR40C1	dehydrogenase/reductase 12	protein-coding	0.020619	0.498715	185(GGGAACACAGTGTCTC,-,0.00),186(GGAACACAGTGTCTCC,+,0.00)
chunk0194_324_1	chr8	88547516	88547992	+	0	NA	Intergenic	Intergenic	-220266	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.002101	0.314465	211(ATCACATACTGTTCCT,+,0.00)
chunk0086_263_1	chr18	23494893	23495482	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-8283	NM_013326	29919	Hs.464779	NM_013326	ENSG00000141452	RMC1	C18orf8|HsT2591|MIC1|Mic-1|WDR98	regulator of MON1-CCZ1	protein-coding	0.001698	0.422034	
chunk0030_383_1	chr10	119494739	119495125	+	0	NA	Intergenic	Intergenic	41601	NM_002925	6001	Hs.501200	NM_002925	ENSG00000148908	RGS10	-	regulator of G protein signaling 10	protein-coding	0.007772	0.457364	
chunk0076_213_1	chr16	68234107	68234672	+	0	NA	promoter-TSS (NR_106831)	promoter-TSS (NR_106831)	-890	NR_106831	102466194		NR_106831	ENSG00000284259	MIR6773	hsa-mir-6773	microRNA 6773	ncRNA	0.012389	0.586572	
chunk0137_135_1	chr4	15169356	15170033	+	0	NA	intron (NR_125911, intron 2 of 5)	intron (NR_125911, intron 2 of 5)	167020	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.017725	0.507375	309(GGGAACAGGGAGTCCT,-,0.00),310(GGAACAGGGAGTCCTT,+,0.00)
chunk0134_422_1	chr3	183370685	183371236	+	0	NA	intron (NM_015078, intron 3 of 29)	intron (NM_015078, intron 3 of 29)	57309	NM_015078	23101	Hs.208267	NM_015078	ENSG00000053524	MCF2L2	ARHGEF22	MCF.2 cell line derived transforming sequence-like 2	protein-coding	0.007260	0.438406	281(AAGTACACTCTGTACT,-,0.00),282(AGTACACTCTGTACTC,+,0.00)
chunk0099_423_1	chr2	102618794	102619373	+	0	NA	promoter-TSS (NM_003048)	promoter-TSS (NM_003048)	-606	NM_003048	6549	Hs.250083	NM_003048	ENSG00000115616	SLC9A2	NHE2	solute carrier family 9 member A2	protein-coding	0.081174	0.624138	141(GGGAACACTGAGTTCC,-,0.00),142(GGAACACTGAGTTCCG,+,0.00)
chunk0156_435_1	chr5	114628994	114629277	+	0	NA	intron (NR_130785, intron 3 of 12)	L1MA6|LINE|L1	144278	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.348592	
chunk0167_194_1	chr6	64465257	64465844	+	0	NA	intron (NM_001142800, intron 26 of 42)	L1MA8|LINE|L1	819024	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.001704	0.329932	174(CAGAACAGAGAGTCCA,-,0.00),175(AGAACAGAGAGTCCAG,+,0.00)
chunk0104_10_1	chr2	170399944	170400449	+	0	NA	non-coding (NR_045683, exon 17 of 36)	non-coding (NR_045683, exon 17 of 36)	-49253	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.011881	0.413043	
chunk0106_196_1	chr2	201962921	201963120	+	0	NA	Intergenic	Intergenic	-71567	NM_003507	8324	Hs.173859	NM_003507	ENSG00000155760	FZD7	FzE3	frizzled class receptor 7	protein-coding	0.020101	0.535000	
chunk0082_435_1	chr17	61556387	61556937	+	0	NA	Intergenic	Intergenic	34540	NM_199290	342538	Hs.591178	NM_199290	ENSG00000253506	NACA2	ANAC|NACAL	nascent polypeptide associated complex subunit alpha 2	protein-coding	0.012727	0.401089	
chunk0194_458_1	chr8	92744693	92745368	+	0	NA	intron (NR_046114, intron 1 of 2)	intron (NR_046114, intron 1 of 2)	41030	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.004444	0.357988	
chunk0152_263_1	chr5	61028852	61029168	+	0	NA	intron (NM_174889, intron 1 of 3)	intron (NM_174889, intron 1 of 3)	83881	NM_174889	91942	Hs.591757	NM_174889	ENSG00000164182	NDUFAF2	B17.2L|MC1DN10|MMTN|NDUFA12L|mimitin	NADH:ubiquinone oxidoreductase complex assembly factor 2	protein-coding	0.006329	0.378549	142(GGAACTCTGTGCCCTT,+,0.00)
chunk0120_89_1	chr3	3992248	3993009	+	0	NA	Intergenic	L3|LINE|CR1	193191	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.010512	0.416010	
chunk0144_431_1	chr4	140800035	140800294	+	0	NA	Intergenic	Intergenic	-43847	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.000000	0.357692	
chunk0097_80_1	chr2	44740735	44741218	+	0	NA	intron (NM_024766, intron 7 of 10)	L2a|LINE|L2	200531	NR_103785	100506108	Hs.503113	NR_103785	ENSG00000236502	SIX3-AS1	SIX3OS	SIX3 antisense RNA 1	ncRNA	0.002070	0.398760	
chunk0048_260_1	chr12	81999150	81999994	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	45853	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.004739	0.435503	
chunk0191_130_1	chr8	48578611	48578888	+	0	NA	intron (NR_105002, intron 2 of 3)	intron (NR_105002, intron 2 of 3)	27182	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.003610	0.406475	
chunk0024_66_1	chr10	34138011	34138434	+	0	NA	intron (NM_019619, intron 22 of 24)	intron (NM_019619, intron 22 of 24)	-365542	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.009456	0.417453	
chunk0121_257_1	chr3	23113356	23113882	+	0	NA	Intergenic	Intergenic	-89674	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.013308	0.449715	
chunk0066_243_1	chr15	34461536	34462213	+	0	NA	Intergenic	L1MC3|LINE|L1	-24408	NR_027409	23015	Hs.182982	NM_181077	ENSG00000175265	GOLGA8A	GM88|GOLGA8B	golgin A8 family member A	protein-coding	0.008863	0.353982	
chunk0051_148_1	chr12	115794512	115794711	+	0	NA	Intergenic	L2a|LINE|L2	354043	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.010050	0.510000	
chunk0155_226_1	chr5	95473659	95473916	+	0	NA	intron (NM_014639, intron 40 of 42)	L1PA16|LINE|L1	81218	NM_014639	9652	Hs.482868	NM_014639	ENSG00000198677	TTC37	KIAA0372|Ski3|THES	tetratricopeptide repeat domain 37	protein-coding	0.003891	0.333333	
chunk0012_352_1	chr1	162710392	162710791	+	0	NA	intron (NM_001014796, intron 3 of 18)	intron (NM_001014796, intron 3 of 18)	78153	NM_006182	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.000000	0.402500	
chunk0138_178_1	chr4	37918176	37918470	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	27239	NM_015173	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.010204	0.308475	
chunk0071_364_1	chr15	89083768	89084328	+	0	NA	Intergenic	Intergenic	-4102	NM_152924	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.010714	0.390374	146(CAGGACATTCTGAACC,-,0.00),147(AGGACATTCTGAACCT,+,0.00),490(AGGAACTGTCTGTACT,-,0.00),491(GGAACTGTCTGTACTT,+,0.00)
chunk0054_378_1	chr13	50115211	50115859	+	0	NA	intron (NR_109974, intron 2 of 6)	LTR50|LTR|ERVL	10006	NR_002612	8847	Hs.547964	NR_002612	ENSG00000231607	DLEU2	ALT1|BCMSUN|DLB2|LEU2|LINC00022|MIR15AHG|NCRNA00022|RFP2|RFP2OS|TRIM13OS	deleted in lymphocytic leukemia 2	ncRNA	0.003086	0.469954	
chunk0127_268_1	chr3	97668038	97668444	+	0	NA	intron (NM_001080448, intron 14 of 17)	LTR82A|LTR|ERVL	-96280	NR_103511	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.007389	0.348894	
chunk0029_449_1	chr10	110447151	110447691	+	0	NA	Intergenic	Intergenic	-50446	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.005556	0.504621	
chunk0081_314_1	chr17	45940793	45941157	+	0	NA	intron (NM_001123067, intron 1 of 10).3	intron (NM_001123067, intron 1 of 10).3	45192	NR_024560	100130148	Hs.669307	NR_024560	ENSG00000279685	MAPT-IT1	-	MAPT intronic transcript 1	ncRNA	0.005495	0.493151	
chunk0077_427_1	chr16	85491910	85492300	+	0	NA	Intergenic	Intergenic	-119318	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.038462	0.634271	
chunk0091_424_1	chr19	16938470	16938669	+	0	NA	intron (NM_015692, intron 22 of 41)	intron (NM_015692, intron 22 of 41)	49554	NM_003950	9002	Hs.137574	NM_003950	ENSG00000127533	F2RL3	PAR4	F2R like thrombin or trypsin receptor 3	protein-coding	0.025126	0.585000	
chunk0117_118_1	chr22	18147013	18147416	+	0	NA	Intergenic	L1MC4|LINE|L1	-2777	NM_017414	11274	Hs.38260	NM_017414	ENSG00000184979	USP18	ISG43|PTORCH2|UBP43	ubiquitin specific peptidase 18	protein-coding	0.007444	0.450495	199(CAGAACAAGATGTCCT,-,0.00),200(AGAACAAGATGTCCTA,+,0.00)
chunk0097_376_1	chr2	61255472	61255829	+	0	NA	intron (NM_014709, intron 48 of 79)	intron (NM_014709, intron 48 of 79)	78230	NM_152392	130872	Hs.655602	NM_152392	ENSG00000173209	AHSA2P	AHA1|AHSA2|Hch1	activator of HSP90 ATPase homolog 2, pseudogene	pseudo	0.000000	0.365922	164(AGTACAAAAAGTCCCT,+,0.00)
chunk0031_322_1	chr10	129211331	129211966	+	0	NA	Intergenic	Intergenic	-255536	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.007874	0.389937	300(GATACAGCCTGTACCT,+,0.00)
chunk0210_456_1	chrX	106731151	106731381	+	0	NA	intron (NM_194463, intron 1 of 6)	intron (NM_194463, intron 1 of 6)	4602	NM_194463	79589	Hs.496542	NM_024539	ENSG00000133135	RNF128	GRAIL	ring finger protein 128	protein-coding	0.008696	0.367965	
chunk0097_367_1	chr2	60852229	60852861	+	0	NA	intron (NR_033980, intron 2 of 2)	intron (NR_033980, intron 2 of 2)	28769	NR_033980	400957	Hs.170358	NR_033980	ENSG00000228414	LINC01185	-	long intergenic non-protein coding RNA 1185	ncRNA	0.012658	0.417062	
chunk0091_358_1	chr19	15323690	15324247	+	0	NA	Intergenic	MIR3|SINE|MIR	-43517	NM_058243	23476	Hs.187763	NM_014299	ENSG00000141867	BRD4	CAP|HUNK1|HUNKI|MCAP	bromodomain containing 4	protein-coding	0.005386	0.528674	
chunk0169_81_1	chr6	99468382	99468871	+	0	NA	intron (NM_001080481, intron 9 of 17)	intron (NM_001080481, intron 9 of 17)	-43295	NM_032870	25957	Hs.520287	NM_015491	ENSG00000132424	PNISR	C6orf111|HSPC306|SFRS18|SRrp130|bA98I9.2	PNN interacting serine and arginine rich protein	protein-coding	0.004090	0.306122	
chunk0060_68_1	chr14	41917950	41918213	+	0	NA	Intergenic	L1MB4|LINE|L1	310520	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.000000	0.276515	
chunk0077_24_1	chr16	75054777	75055022	+	0	NA	intron (NM_032268, intron 1 of 4)	intron (NM_032268, intron 1 of 4)	55882	NM_032268	84937	Hs.427284	NM_032268	ENSG00000186187	ZNRF1	NIN283	zinc and ring finger 1	protein-coding	0.004082	0.471545	192(AGGAGCAGGGTGTCCT,-,0.00),193(GGAGCAGGGTGTCCTA,+,0.00)
chunk0027_189_1	chr10	75588707	75589418	+	0	NA	intron (NM_001305581, intron 2 of 6)	L1ME4b|LINE|L1	36604	NR_030337	693191		NR_030337	ENSG00000207583	MIR606	MIRN606|hsa-mir-606	microRNA 606	ncRNA	0.001406	0.311798	
chunk0095_62_1	chr2	14258349	14259100	+	0	NA	intron (NR_103814, intron 2 of 3)	L2c|LINE|L2	142234	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.001332	0.328457	
chunk0013_170_1	chr1	168824341	168824556	+	0	NA	Intergenic	Intergenic	37507	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.004651	0.444444	
chunk0129_179_1	chr3	120908294	120908639	+	0	NA	intron (NM_014980, intron 1 of 27)	CpG	263	NM_001308330	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.089855	0.658960	
chunk0145_17_1	chr4	143396898	143397151	+	0	NA	intron (NM_002039, intron 1 of 9)	intron (NM_002039, intron 1 of 9)	53564	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.003953	0.440945	
chunk0136_156_1	chr4	5503268	5503888	+	0	NA	Intergenic	Intergenic	-20991	NR_126519	10141	Hs.177972	NM_005750	ENSG00000082929	LINC01587	C4orf6|aC1	long intergenic non-protein coding RNA 1587	ncRNA	0.011290	0.504026	360(CAGCACAGTCTCTTCC,-,0.00)
chunk0186_305_1	chr7	142896408	142896728	+	0	NA	Intergenic	Intergenic	-10823	NM_018646	55503	Hs.302740	NM_014274	ENSG00000165125	TRPV6	ABP/ZF|CAT1|CATL|ECAC2|HRPTTN|HSA277909|LP6728|ZFAB	transient receptor potential cation channel subfamily V member 6	protein-coding	0.012500	0.473520	
chunk0038_448_1	chr11	94794112	94794729	+	0	NA	intron (NM_001301007, intron 1 of 11)	intron (NM_001301007, intron 1 of 11)	26078	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.006483	0.446602	
chunk0157_456_1	chr5	125005558	125006101	+	0	NA	Intergenic	Intergenic	-31002	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.001842	0.318015	
chunk0020_421_1	chr1	241603485	241604074	+	0	NA	intron (NM_014322, intron 2 of 3)	intron (NM_014322, intron 2 of 3)	32151	NM_001821	1122	Hs.654545	NM_001821	ENSG00000203668	CHML	REP2	CHM like Rab escort protein	protein-coding	0.006791	0.389831	
chunk0101_385_1	chr2	138564118	138564415	+	0	NA	intron (NM_001001664, intron 8 of 10)	intron (NM_001001664, intron 8 of 10)	62486	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.006734	0.332215	
chunk0116_379_1	chr21	42167473	42167757	+	0	NA	Intergenic	L1ME2z|LINE|L1	-32074	NM_207627	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.000000	0.466667	101(TTGCACAGTCTGTACT,-,0.00),102(TGCACAGTCTGTACTC,+,0.00)
chunk0126_460_1	chr3	87554180	87554496	+	0	NA	Intergenic	Intergenic	-277751	NM_001122757	5449	Hs.591654	NM_000306	ENSG00000064835	POU1F1	CPHD1|GHF-1|PIT1|POU1F1a|Pit-1	POU class 1 homeobox 1	protein-coding	0.006329	0.365931	
chunk0199_386_1	chr9	13181584	13181910	+	0	NA	intron (NM_003829, intron 19 of 45)	intron (NM_003829, intron 19 of 45)	97817	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.009202	0.397554	
chunk0166_207_1	chr6	46735541	46735948	+	0	NA	promoter-TSS (NM_005084)	promoter-TSS (NM_005084)	-51	NM_001168357	7941	Hs.584823	NM_005084	ENSG00000146070	PLA2G7	LDL-PLA2|LP-PLA2|PAFAD|PAFAH	phospholipase A2 group VII	protein-coding	0.044226	0.531863	
chunk0089_313_1	chr18	63987407	63987767	+	0	NA	TTS (NM_001031848)	TTS (NM_001031848)	17558	NM_198833	5271	Hs.368077	NM_002640	ENSG00000166401	SERPINB8	C18orf53|CAP2|PI-8|PI8|PSS5	serpin family B member 8	protein-coding	0.008333	0.534626	
chunk0067_21_1	chr15	40323450	40323707	+	0	NA	promoter-TSS (NM_001301268)	promoter-TSS (NM_001301268)	-478	NM_001301268	100505573	Hs.530791	NM_001301268	ENSG00000259330	INAFM2	LINC00984|OGU1	InaF motif containing 2	protein-coding	0.140078	0.759690	
chunk0019_351_1	chr1	229538288	229538487	+	0	NA	intron (NM_012089, intron 6 of 12)	intron (NM_012089, intron 6 of 12)	20308	NM_012089	23456	Hs.17614	NM_012089	ENSG00000135776	ABCB10	EST20237|M-ABC2|MTABC2	ATP binding cassette subfamily B member 10	protein-coding	0.005025	0.545000	
chunk0179_84_1	chr7	44468733	44469122	+	0	NA	intron (NM_015332, intron 2 of 5)	L1MC4|LINE|L1	21859	NM_015332	23386	Hs.488171	NM_015332	ENSG00000015676	NUDCD3	NudCL	NudC domain containing 3	protein-coding	0.002571	0.387179	
chunk0133_78_1	chr3	167115603	167115836	+	0	NA	Intergenic	MER52D|LTR|ERV1	264564	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.012876	0.615385	
chunk0130_426_1	chr3	140902710	140903206	+	0	NA	Intergenic	Intergenic	-38862	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.002016	0.309859	
chunk0206_13_1	chr9	115683675	115684244	+	0	NA	Intergenic	L1MEc|LINE|L1	60280	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.001757	0.271930	
chunk0015_39_1	chr1	184483544	184483872	+	0	NA	intron (NM_030806, intron 2 of 5)	(TTGT)n|Simple_repeat|Simple_repeat	96692	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.404255	
chunk0002_379_1	chr1	26692912	26693173	+	0	NA	Intergenic	Intergenic	-2989	NM_006015	8289	Hs.468972	NM_006015	ENSG00000117713	ARID1A	B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1	AT-rich interaction domain 1A	protein-coding	0.053640	0.572519	
chunk0186_377_1	chr7	144254707	144255137	+	0	NA	intron (NR_126023, intron 3 of 4).2	intron (NR_126023, intron 3 of 4).2	-3319	NR_002158	401428	Hs.490448	NR_002158	ENSG00000170356	OR2A20P	OR2A20	olfactory receptor family 2 subfamily A member 20 pseudogene	pseudo	0.002326	0.301624	
chunk0202_26_1	chr9	70574605	70574808	+	0	NA	intron (NM_024971, intron 22 of 25)	L2b|LINE|L2	-160049	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.004926	0.460784	
chunk0130_286_1	chr3	136534106	136534686	+	0	NA	intron (NM_005862, intron 6 of 33)	L1MA4A|LINE|L1	218007	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.005172	0.325301	
chunk0186_366_1	chr7	143964541	143964924	+	0	NA	Intergenic	Intergenic	4805	NM_012369	26211	Hs.553595	NM_012369	ENSG00000213215	OR2F1	7M1-2|OLF3|OR14-60|OR2F3|OR2F3P|OR2F4|OR2F5|OR7-139|OR7-140	olfactory receptor family 2 subfamily F member 1 (gene/pseudogene)	protein-coding	0.000000	0.346354	191(AGAAACACAATGTTCC,-,0.00),192(GAAACACAATGTTCCT,+,0.00)
chunk0176_316_1	chr7	17010807	17011062	+	0	NA	Intergenic	Intergenic	-128945	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.000000	0.468750	
chunk0141_129_1	chr4	80396210	80396533	+	0	NA	intron (NM_001206997, intron 2 of 6)	intron (NM_001206997, intron 2 of 6)	60651	NM_152770	255119	Hs.527104	NM_152770	ENSG00000197826	CFAP299	C4orf22	cilia and flagella associated protein 299	protein-coding	0.006192	0.333333	
chunk0020_281_1	chr1	236540936	236541424	+	0	NA	intron (NM_006499, intron 6 of 11)	Tigger3a|DNA|TcMar-Tigger	-16672	NR_034040	100287902	Hs.677376	NR_034040	ENSG00000223776	LGALS8-AS1	-	LGALS8 antisense RNA 1	ncRNA	0.008197	0.413088	
chunk0032_75_1	chr11	2623849	2624048	+	0	NA	non-coding (NR_002728, exon 1 of 1)	non-coding (NR_002728, exon 1 of 1)	76050	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.010050	0.405000	
chunk0098_8_1	chr2	65103219	65103852	+	0	NA	intron (NM_004161, intron 2 of 5)	Charlie1a|DNA|hAT-Charlie	26766	NM_004161	5861	Hs.310645	NM_004161	ENSG00000138069	RAB1A	RAB1|YPT1	RAB1A, member RAS oncogene family	protein-coding	0.006319	0.389590	10(GAGAACAGCTTGAGCC,-,0.00),11(AGAACAGCTTGAGCCT,+,0.00)
chunk0073_65_1	chr16	3553006	3553661	+	0	NA	intron (NM_178844, intron 9 of 19)	MER67C|LTR|ERV1	24071	NM_178844	197358	Hs.592091	NM_178844	ENSG00000167984	NLRC3	CLR16.2|NOD3	NLR family CARD domain containing 3	protein-coding	0.012214	0.446646	334(AGGAACAAAGAGTCCC,-,0.00),335(GGAACAAAGAGTCCCT,+,0.00)
chunk0052_366_1	chr12	128056905	128057188	+	0	NA	Intergenic	Intergenic	-29880	NR_131985	105370070		NR_131985	ENSG00000256643	LINC02441	CRAT8	long intergenic non-protein coding RNA 2441	ncRNA	0.007067	0.514085	
chunk0142_80_1	chr4	93894956	93895467	+	0	NA	Intergenic	L2a|LINE|L2	66284	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.005871	0.353516	
chunk0093_227_1	chr19	50242644	50242936	+	0	NA	intron (NM_001077186, intron 10 of 41)	Tigger17a|DNA|TcMar-Tigger	39162	NM_001145809	79784	Hs.467142	NM_024729	ENSG00000105357	MYH14	DFNA4|DFNA4A|FP17425|MHC16|MYH17|NMHC II-C|NMHC-II-C|PNMHH|myosin	myosin heavy chain 14	protein-coding	0.020548	0.453925	
chunk0043_62_1	chr12	14107141	14107458	+	0	NA	Intergenic	L1PB1|LINE|L1	-127211	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.000000	0.345912	
chunk0166_346_1	chr6	51083239	51083717	+	0	NA	Intergenic	L1P3|LINE|L1	264752	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.008368	0.373695	
chunk0183_92_1	chr7	105013369	105013781	+	0	NA	promoter-TSS (NM_182931)	promoter-TSS (NM_182931)	566	NR_024586	100216545	Hs.631150	NR_024586		KMT2E-AS1	-	KMT2E antisense RNA 1	ncRNA	0.070388	0.636804	
chunk0173_175_1	chr6	144606036	144606533	+	0	NA	intron (NM_007124, intron 50 of 73)	intron (NM_007124, intron 50 of 73)	200629	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.004024	0.325301	
chunk0171_159_1	chr6	124116327	124116526	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	-166579	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.010050	0.315000	
chunk0136_392_1	chr3	196942212	196942593	+	0	NA	promoter-TSS (NM_001308036)	promoter-TSS (NM_001308036)	38	NM_001308036	22916	Hs.591671	NM_007362	ENSG00000114503	NCBP2	CBC2|CBP20|NIP1|PIG55	nuclear cap binding protein subunit 2	protein-coding	0.089239	0.643979	
chunk0091_284_1	chr19	11853995	11854435	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-11814	NM_152262	90594	Hs.528731	NM_152262	ENSG00000171291	ZNF439	-	zinc finger protein 439	protein-coding	0.009091	0.419501	
chunk0195_390_1	chr8	100256862	100257411	+	0	NA	TTS (NM_015435)	TTS (NM_015435)	46123	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003643	0.338182	
chunk0077_287_1	chr16	81241611	81242153	+	0	NA	intron (NM_017429, intron 1 of 10)	MIR|SINE|MIR	3191	NM_017429	53630	Hs.212172	NM_017429	ENSG00000135697	BCO1	BCDO|BCDO1|BCMO|BCMO1|BCO	beta-carotene oxygenase 1	protein-coding	0.012915	0.515654	
chunk0093_44_1	chr19	39828361	39828663	+	0	NA	exon (NM_006483, exon 6 of 11)	exon (NM_006483, exon 6 of 11)	1290	NR_106777	102465974		NR_106777	ENSG00000277759	MIR6719	hsa-mir-6719	microRNA 6719	ncRNA	0.056291	0.600660	195(CGGAACATGAAGTGCC,-,0.00),196(GGAACATGAAGTGCCG,+,0.00)
chunk0004_183_1	chr1	46048081	46048454	+	0	NA	intron (NM_001303429, intron 6 of 8)	intron (NM_001303429, intron 6 of 8)	84441	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.000000	0.331551	
chunk0123_454_1	chr3	51158734	51159211	+	0	NA	intron (NM_004947, intron 10 of 52)	intron (NM_004947, intron 10 of 52)	-226265	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.004193	0.301255	
chunk0123_209_1	chr3	44921075	44921512	+	0	NA	3' UTR (NM_001135179, exon 7 of 7)	3' UTR (NM_001135179, exon 7 of 7)	46687	NM_003241	7047	Hs.438265	NM_003241	ENSG00000163810	TGM4	TGP|hTGP	transglutaminase 4	protein-coding	0.009153	0.472603	201(GAGAACAGGCTGTTCC,-,0.00),202(AGAACAGGCTGTTCCC,+,0.00)
chunk0132_90_1	chr3	155572918	155573514	+	0	NA	intron (NM_001130960, intron 5 of 22)	HAL1|LINE|L1	103100	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.003356	0.400335	
chunk0130_30_1	chr3	128879432	128879647	+	0	NA	promoter-TSS (NM_014049)	promoter-TSS (NM_014049)	49	NR_033426	28976	Hs.567482	NM_014049	ENSG00000177646	ACAD9	MC1DN20|NPD002	acyl-CoA dehydrogenase family member 9	protein-coding	0.106977	0.689815	
chunk0084_241_1	chr17	78764419	78764695	+	0	NA	intron (NM_004762, intron 1 of 12)	intron (NM_004762, intron 1 of 12)	17785	NM_004762	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.014493	0.404332	
chunk0197_273_1	chr8	123894918	123895222	+	0	NA	intron (NM_001039112, intron 1 of 40)	L1MC4|LINE|L1	43083	NM_001039112	654463	Hs.632058	NM_001039112	ENSG00000214814	FER1L6	C8ORFK23	fer-1 like family member 6	protein-coding	0.003289	0.347541	
chunk0101_26_1	chr2	121645263	121645828	+	0	NA	intron (NM_015282, intron 1 of 38)	intron (NM_015282, intron 1 of 38)	3931	NM_001142274	23332	Hs.469840	NM_015282	ENSG00000074054	CLASP1	MAST1	cytoplasmic linker associated protein 1	protein-coding	0.001770	0.409894	
chunk0165_59_1	chr6	30782128	30782835	+	0	NA	Intergenic	Intergenic	-37931	NM_003897	8870	Hs.76095	NM_003897	ENSG00000137331	IER3	DIF-2|DIF2|GLY96|IEX-1|IEX-1L|IEX1|PRG1	immediate early response 3	protein-coding	0.001414	0.406780	
chunk0178_181_1	chr7	34221838	34222099	+	0	NA	Intergenic	Intergenic	317057	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.000000	0.419847	
chunk0004_225_1	chr1	46907901	46908557	+	0	NA	Intergenic	L1MC1|LINE|L1	-7754	NR_002788	163720	Hs.591431	NR_002788	ENSG00000154198	CYP4Z2P	-	cytochrome P450 family 4 subfamily Z member 2, pseudogene	pseudo	0.006098	0.406393	
chunk0098_401_1	chr2	79796957	79797188	+	0	NA	intron (NM_004389, intron 3 of 17)	intron (NM_004389, intron 3 of 17)	69511	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.000000	0.353448	
chunk0113_382_1	chr20	59942711	59942924	+	0	NA	intron (NM_001190827, intron 3 of 3)	intron (NM_001190827, intron 3 of 3)	2428	NM_001190827	63939	Hs.54973	NM_022106	ENSG00000196227	FAM217B	C20orf177|dJ551D2.5	family with sequence similarity 217 member B	protein-coding	0.004695	0.280374	116(AGGAACAAAATGTTTT,-,0.00),195(GAGCACACGTTGTACT,-,0.00),196(AGCACACGTTGTACTA,+,0.00)
chunk0106_352_1	chr2	206805818	206806597	+	0	NA	Intergenic	Intergenic	-22899	NR_036077	100422993		NR_036077	ENSG00000283469	MIR3130-1	MIR3130-3|mir-3130-1	microRNA 3130-1	ncRNA	0.007702	0.424359	
chunk0161_238_1	chr5	171475542	171476126	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	56171	NM_003862	8817	Hs.87191	NM_003862	ENSG00000156427	FGF18	FGF-18|ZFGF5	fibroblast growth factor 18	protein-coding	0.000000	0.391453	
chunk0012_196_1	chr1	159867987	159868233	+	0	NA	Intergenic	Intergenic	-5453	NM_001013661	391123	Hs.647718	NM_001013661	ENSG00000243284	VSIG8	-	V-set and immunoglobulin domain containing 8	protein-coding	0.004065	0.526316	
chunk0105_248_1	chr2	188695985	188696409	+	0	NA	Intergenic	Intergenic	93907	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.007075	0.348235	
chunk0073_445_1	chr16	19382632	19382858	+	0	NA	Intergenic	Intergenic	-27794	NM_001308161	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.008850	0.475771	175(CAGTACTCTCTGTACT,-,0.00),176(AGTACTCTCTGTACTT,+,0.00)
chunk0002_79_1	chr1	14271872	14272116	+	0	NA	Intergenic	MIRb|SINE|MIR	-326723	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.012295	0.391837	
chunk0099_283_1	chr2	98598815	98599150	+	0	NA	TTS (NM_001008215)	TTS (NM_001008215)	9536	NM_001008215	493753	Hs.596537	NM_001008215	ENSG00000183513	COA5	6330578E17Rik|C2orf64|CEMCOX3|Pet191	cytochrome c oxidase assembly factor 5	protein-coding	0.000000	0.354167	
chunk0049_15_1	chr12	89352625	89353016	+	0	NA	promoter-TSS (NM_001946)	promoter-TSS (NM_001946)	39	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.056266	0.525510	
chunk0142_367_1	chr4	101952908	101953786	+	0	NA	intron (NM_017935, intron 7 of 16)	intron (NM_017935, intron 7 of 16)	139521	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.009112	0.361775	524(GAGAACAGACTGTCTT,-,0.00),525(AGAACAGACTGTCTTG,+,0.00)
chunk0001_126_1	chr1	4674231	4674430	+	0	NA	intron (NM_001042478, intron 1 of 5)	intron (NM_001042478, intron 1 of 5)	19285	NM_018836	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.005025	0.460000	
chunk0025_159_1	chr10	52541107	52541644	+	0	NA	Intergenic	Intergenic	-70842	NR_120641	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.003724	0.405204	260(CAAAACATTCTGTTCA,-,0.00),261(AAAACATTCTGTTCAG,+,0.00)
chunk0082_133_1	chr17	55295548	55295931	+	0	NA	intron (NM_002126, intron 2 of 3)	intron (NM_002126, intron 2 of 3)	30779	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.013055	0.468750	
chunk0179_266_1	chr7	49251032	49251491	+	0	NA	Intergenic	Intergenic	326700	NR_003595									0.004357	0.319565	
chunk0019_200_1	chr1	226875840	226876139	+	0	NA	intron (NM_012486, intron 3 of 12)	intron (NM_012486, intron 3 of 12)	5417	NM_000447	5664	Hs.25363	NM_000447	ENSG00000143801	PSEN2	AD3L|AD4|CMD1V|PS2|STM2	presenilin 2	protein-coding	0.023411	0.533333	
chunk0179_277_1	chr7	49470859	49471117	+	0	NA	Intergenic	Intergenic	-302673	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.011628	0.335907	
chunk0045_191_1	chr12	47340466	47340733	+	0	NA	Intergenic	Intergenic	23670	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.014981	0.436567	
chunk0031_209_1	chr10	125895352	125895736	+	0	NA	promoter-TSS (NM_145235)	promoter-TSS (NM_145235)	-995	NM_145235	92565	Hs.352591	NM_145235	ENSG00000203780	FANK1	HSD13	fibronectin type III and ankyrin repeat domains 1	protein-coding	0.020833	0.428571	
chunk0132_287_1	chr3	159990403	159990659	+	0	NA	intron (NM_000882, intron 2 of 6)	intron (NM_000882, intron 2 of 6)	1695	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.000000	0.420233	
chunk0076_347_1	chr16	71618152	71618368	+	0	NA	Intergenic	L1ME4b|LINE|L1	-7893	NM_001271329	91862	Hs.513706	NM_052858	ENSG00000140832	MARVELD3	MARVD3|MRVLDC3	MARVEL domain containing 3	protein-coding	0.009259	0.336406	
chunk0018_5_1	chr1	215001544	215001747	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-3897	NM_001017424	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.009852	0.455882	
chunk0091_352_1	chr19	15215336	15215807	+	0	NA	Intergenic	L2b|LINE|L2	-14590	NM_000435	4854	Hs.8546	NM_000435	ENSG00000074181	NOTCH3	CADASIL|CADASIL1|CASIL|IMF2|LMNS	notch receptor 3	protein-coding	0.008493	0.504237	
chunk0017_129_1	chr1	206526143	206526391	+	0	NA	intron (NM_182663, intron 1 of 5)	intron (NM_182663, intron 1 of 5)	18737	NM_182663	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.008065	0.578313	
chunk0143_233_1	chr4	114424624	114424857	+	0	NA	Intergenic	L1PA10|LINE|L1	-173715	NM_001128174	7368	Hs.144197	NM_003360	ENSG00000174607	UGT8	CGT|UGT4	UDP glycosyltransferase 8	protein-coding	0.000000	0.354701	
chunk0094_1_1	chr2	589465	589970	+	0	NA	Intergenic	Intergenic	87722	NM_152834	129787	Hs.6729	NM_152834	ENSG00000151353	TMEM18	lncND	transmembrane protein 18	protein-coding	0.013861	0.462451	239(AAGGACAAGATGTCCT,-,0.00),240(AGGACAAGATGTCCTT,+,0.00)
chunk0096_26_1	chr2	26539774	26539973	+	0	NA	intron (NM_194248, intron 1 of 46)	intron (NM_194248, intron 1 of 46)	18825	NM_001287489	9381	Hs.91608	NM_004802	ENSG00000115155	OTOF	AUNB1|DFNB6|DFNB9|FER1L2|NSRD9	otoferlin	protein-coding	0.000000	0.385000	
chunk0063_165_1	chr14	80276817	80277603	+	0	NA	intron (NR_038355, intron 2 of 8)	MIRb|SINE|MIR	-46156	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.002545	0.385006	
chunk0035_65_1	chr11	41708226	41708950	+	0	NA	Intergenic	MIRb|SINE|MIR	-5980	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.005525	0.384828	
chunk0050_367_1	chr12	108164747	108165095	+	0	NA	intron (NM_001304447, intron 1 of 9)	intron (NM_001304447, intron 1 of 9)	33190	NM_001304447	9671	Hs.143591	NM_014653	ENSG00000075035	WSCD2	-	WSC domain containing 2	protein-coding	0.002874	0.472779	
chunk0072_433_1	chr15	101244456	101244912	+	0	NA	intron (NM_014918, intron 1 of 2)	L1ME4a|LINE|L1	7248	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.002193	0.350109	
chunk0122_395_1	chr3	37934939	37935262	+	0	NA	intron (NM_001008392, intron 1 of 7)	L1ME4b|LINE|L1	-34304	NR_029499	407015		NR_029499	ENSG00000199075	MIR26A1	MIR26A|MIRN26A1|mir-26a-1	microRNA 26a-1	ncRNA	0.009288	0.441358	
chunk0066_317_1	chr15	35998060	35998613	+	0	NA	Intergenic	Intergenic	71480	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.005425	0.330325	
chunk0189_203_1	chr8	23951182	23951381	+	0	NA	Intergenic	Intergenic	-96474	NM_003155	6781	Hs.25590	NM_003155	ENSG00000159167	STC1	STC	stanniocalcin 1	protein-coding	0.015075	0.550000	
chunk0112_130_1	chr20	38548112	38549064	+	0	NA	intron (NM_020336, intron 19 of 29)	MER113A|DNA|hAT-Charlie	32025	NR_039605	100616190		NR_039605	ENSG00000275453	MIR548O2	-	microRNA 548o-2	ncRNA	0.004202	0.387198	
chunk0009_2_1	chr1	99806734	99807427	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	-41287	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.004329	0.402017	
chunk0104_394_1	chr2	180521250	180521517	+	0	NA	Intergenic	Intergenic	-170721	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.007491	0.373134	
chunk0003_121_1	chr1	32474783	32475557	+	0	NA	intron (NM_001145720, intron 2 of 3)	intron (NM_001145720, intron 2 of 3)	10113	NM_001145720	728116	Hs.647658	NM_001145720	ENSG00000273274	ZBTB8B	ZNF916B	zinc finger and BTB domain containing 8B	protein-coding	0.015504	0.458065	
chunk0196_126_1	chr8	103916760	103917266	+	0	NA	intron (NM_001282881, intron 6 of 20)	intron (NM_001282881, intron 6 of 20)	97825	NM_014677	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.000000	0.299803	
chunk0084_359_1	chr17	81397653	81398146	+	0	NA	Intergenic	CpG	-1822	NM_001291324	57597	Hs.514580	NM_024696	ENSG00000266074	BAHCC1	BAHD2	BAH domain and coiled-coil containing 1	protein-coding	0.042596	0.453441	
chunk0083_145_1	chr17	65774542	65774948	+	0	NA	intron (NM_001302891, intron 19 of 24)	intron (NM_001302891, intron 19 of 24)	51798	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.017241	0.515971	
chunk0002_260_1	chr1	21331954	21332634	+	0	NA	intron (NM_001113348, intron 1 of 18)	intron (NM_001113348, intron 1 of 18)	13247	NM_001113348	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.008824	0.531571	407(AGGCACTTAGTGTACT,-,0.00),408(GGCACTTAGTGTACTG,+,0.00)
chunk0038_442_1	chr11	94728857	94729414	+	0	NA	Intergenic	Intergenic	-39207	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.008977	0.444444	
chunk0076_265_1	chr16	69417666	69418472	+	0	NA	Intergenic	Intergenic	-6526	NM_030579	80777	Hs.461131	NM_030579	ENSG00000103018	CYB5B	CYB5-M|CYPB5M|OMB5	cytochrome b5 type B	protein-coding	0.006203	0.439901	
chunk0058_58_1	chr14	20613626	20613907	+	0	NA	Intergenic	Intergenic	-22943	NM_001024822	493901	Hs.729466	NM_001024822	ENSG00000258436	RNASE12	HEL-S-85p|RAI1	ribonuclease A family member 12 (inactive)	protein-coding	0.056940	0.549645	
chunk0128_35_1	chr3	104439640	104439958	+	0	NA	Intergenic	Intergenic	-915683	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.003145	0.373041	
chunk0098_344_1	chr2	77288256	77288749	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	233866	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.006085	0.271255	
chunk0190_456_1	chr8	42140060	42140259	+	0	NA	Intergenic	CpG	-12787	NM_006803	10947	Hs.654529	NM_006803	ENSG00000070718	AP3M2	AP47B|CLA20|P47B	adaptor related protein complex 3 subunit mu 2	protein-coding	0.150754	0.760000	
chunk0058_154_1	chr14	23235253	23235895	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-2344	NM_001282322	100507650		NM_001282322	ENSG00000215277	RNF212B	C14orf164	ring finger protein 212B	protein-coding	0.004673	0.342146	
chunk0087_291_1	chr18	38902740	38903129	+	0	NA	Intergenic	Intergenic	719241	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.002571	0.407692	
chunk0039_453_1	chr11	108524504	108524950	+	0	NA	intron (NM_001144765, intron 1 of 2)	MamRTE1|LINE|RTE-BovB	13480	NM_001144764	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.002242	0.413870	
chunk0065_353_1	chr14	103729685	103730154	+	0	NA	intron (NM_001198953, intron 6 of 7)	intron (NM_001198953, intron 6 of 7)	14175	NM_024071	79038	Hs.592322	NM_024071	ENSG00000100711	ZFYVE21	HCVP7TP1|ZF21	zinc finger FYVE-type containing 21	protein-coding	0.034115	0.557447	
chunk0089_365_1	chr18	67020985	67021566	+	0	NA	Intergenic	Intergenic	-60309	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.005164	0.333333	
chunk0050_80_1	chr12	101636162	101636767	+	0	NA	intron (NM_001254721, intron 7 of 28)	intron (NM_001254721, intron 7 of 28)	41533	NM_001254719	4604	Hs.654589	NM_002465	ENSG00000196091	MYBPC1	LCCS4|MYBPCC|MYBPCS	myosin binding protein C, slow type	protein-coding	0.008264	0.376238	
chunk0194_452_1	chr8	92643098	92643297	+	0	NA	intron (NR_125827, intron 2 of 4)	intron (NR_125827, intron 2 of 4)	12297	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.015075	0.345000	
chunk0054_234_1	chr13	45717936	45718289	+	0	NA	Intergenic	Intergenic	15643	NM_001286342	220082	Hs.186363	NM_152719	ENSG00000174015	SPERT	CBY2|NURIT	spermatid associated	protein-coding	0.005666	0.454802	
chunk0174_271_1	chr6	161418172	161418448	+	0	NA	intron (NM_013988, intron 6 of 8)	intron (NM_013988, intron 6 of 8)	-144235	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.014493	0.418773	
chunk0015_104_1	chr1	185139051	185139635	+	0	NA	intron (NM_030934, intron 9 of 14)	intron (NM_030934, intron 9 of 14)	17641	NM_030934	81627	Hs.107149	NM_030934	ENSG00000121486	TRMT1L	C1orf25|MST070|MSTP070|TRM1L|bG120K12.3	tRNA methyltransferase 1 like	protein-coding	0.008562	0.312821	
chunk0177_75_1	chr7	21444286	21444920	+	0	NA	intron (NM_003112, intron 3 of 5)	intron (NM_003112, intron 3 of 5)	16532	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.004732	0.343307	
chunk0069_276_1	chr15	64938108	64938601	+	0	NA	intron (NM_182703, intron 9 of 14)	L1MC3|LINE|L1	26452	NM_182703	348094	Hs.207157	NM_182703	ENSG00000166839	ANKDD1A	-	ankyrin repeat and death domain containing 1A	protein-coding	0.008114	0.408907	128(AAGTACAGGCTGTGCA,-,0.00),129(AGTACAGGCTGTGCAT,+,0.00)
chunk0188_197_1	chr8	11814252	11814511	+	0	NA	intron (NM_001287747, intron 3 of 7)	intron (NM_001287747, intron 3 of 7)	5237	NM_001287751	2222	Hs.593928	NM_004462	ENSG00000079459	FDFT1	DGPT|ERG9|SQS|SQSD|SS	farnesyl-diphosphate farnesyltransferase 1	protein-coding	0.007722	0.350000	
chunk0147_13_1	chr4	170672790	170673415	+	0	NA	Intergenic	Intergenic	-367500	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.004800	0.333866	
chunk0035_445_1	chr11	57615194	57615775	+	0	NA	TTS (NM_001032295)	TTS (NM_001032295)	17252	NM_001032295	710	Hs.384598	NM_000062	ENSG00000149131	SERPING1	C1IN|C1INH|C1NH|HAE1|HAE2	serpin family G member 1	protein-coding	0.006885	0.438144	
chunk0069_345_1	chr15	66582084	66582830	+	0	NA	intron (NR_110372, intron 1 of 4)	intron (NR_110372, intron 1 of 4)	267	NR_110372	102723165	Hs.636703	NR_110372	ENSG00000259471	LINC01169	-	long intergenic non-protein coding RNA 1169	ncRNA	0.012064	0.447122	
chunk0199_94_1	chr9	2678345	2679033	+	0	NA	Intergenic	Intergenic	-38837	NM_133497	169522	Hs.622675	NM_133497	ENSG00000168263	KCNV2	KV11.1|Kv8.2|RCD3B	potassium voltage-gated channel modifier subfamily V member 2	protein-coding	0.005814	0.404935	352(CAGCACATTATGTTCT,-,0.00),353(AGCACATTATGTTCTA,+,0.00)
chunk0208_50_1	chrX	11458980	11459288	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-31349	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.009740	0.343042	
chunk0012_358_1	chr1	162852337	162852941	+	0	NA	Intergenic	Intergenic	16176	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.016556	0.413223	21(TAGAGCACCGTGTGCC,-,0.00),22(AGAGCACCGTGTGCCA,+,0.00),261(TAAAACAGGATGTACT,-,0.00),262(AAAACAGGATGTACTA,+,0.00)
chunk0113_254_1	chr20	55051926	55052326	+	0	NA	Intergenic	Intergenic	-370917	NR_110629	102723578	Hs.446269	NR_110629	ENSG00000235166	LINC01440	-	long intergenic non-protein coding RNA 1440	ncRNA	0.005000	0.389027	
chunk0106_284_1	chr2	204109646	204109974	+	0	NA	Intergenic	Intergenic	173062	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.027439	0.510638	
chunk0181_204_1	chr7	84484674	84485306	+	0	NA	Intergenic	Intergenic	-47486	NR_110080	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.003165	0.289100	
chunk0099_31_1	chr2	83607189	83607772	+	0	NA	Intergenic	L1PB4|LINE|L1	-683202	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.000000	0.311644	
chunk0113_409_1	chr20	61579911	61580188	+	0	NA	intron (NM_001252338, intron 1 of 14)	intron (NM_001252338, intron 1 of 14)	-19712	NM_001252339	1002	Hs.473231	NM_001794	ENSG00000179242	CDH4	CAD4|R-CAD|RCAD	cadherin 4	protein-coding	0.018051	0.431655	
chunk0127_262_1	chr3	97327227	97327426	+	0	NA	intron (NM_001080448, intron 5 of 17)	L1MD2|LINE|L1	-112267	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.000000	0.305000	
chunk0054_372_1	chr13	49930412	49931098	+	0	NA	intron (NM_001127482, intron 1 of 3)	MIRc|SINE|MIR	5746	NR_023351	57213	Hs.44235	NM_020456	ENSG00000123178	SPRYD7	C13orf1|CLLD6	SPRY domain containing 7	protein-coding	0.010204	0.381368	
chunk0140_366_1	chr4	74480331	74480595	+	0	NA	Intergenic	Intergenic	35365	NM_001657	374	Hs.270833	NM_001657	ENSG00000109321	AREG	AR|AREGB|CRDGF|SDGF	amphiregulin	protein-coding	0.003788	0.445283	
chunk0051_142_1	chr12	115732889	115733228	+	0	NA	Intergenic	Intergenic	415596	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.002950	0.408824	
chunk0012_424_1	chr1	164630694	164630977	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	71475	NM_001204963	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.003534	0.426056	
chunk0005_69_1	chr1	55780876	55781368	+	0	NA	Intergenic	ERVL-int|LTR|ERVL	555481	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.010163	0.450304	
chunk0161_299_1	chr5	173093918	173094312	+	0	NA	intron (NM_153607, intron 4 of 8)	L1MA9|LINE|L1	37763	NM_001168393	153222	Hs.484195	NM_153607	ENSG00000164463	CREBRF	C5orf41|LRF	CREB3 regulatory factor	protein-coding	0.005076	0.384810	
chunk0016_325_1	chr1	201696482	201696729	+	0	NA	intron (NR_046696, intron 2 of 2)	intron (NR_046696, intron 2 of 2)	-22903	NR_049823	100847050		NR_049823	ENSG00000264802	MIR5191	-	microRNA 5191	ncRNA	0.016194	0.552419	
chunk0053_374_1	chr13	35852596	35853243	+	0	NA	intron (NM_001195430, intron 2 of 2)	intron (NM_001195430, intron 2 of 2)	2942	NM_001195416	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.009274	0.405864	375(AGAGACAGAATGTTCT,-,0.00),376(GAGACAGAATGTTCTC,+,0.00)
chunk0152_278_1	chr5	61397127	61397441	+	0	NA	intron (NM_020928, intron 1 of 13)	intron (NM_020928, intron 1 of 13)	65011	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.003185	0.333333	57(AGTTCAGGCTGTACCT,+,0.00)
chunk0173_331_1	chr6	148851952	148852730	+	0	NA	intron (NM_005715, intron 1 of 7)	intron (NM_005715, intron 1 of 7)	105206	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.010283	0.414634	241(GGGAACATTTTGTGTT,-,0.00),242(GGAACATTTTGTGTTT,+,0.00)
chunk0142_189_1	chr4	96429657	96430206	+	0	NA	Intergenic	MER21C|LTR|ERVL	589843	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.001821	0.354545	
chunk0076_69_1	chr16	63315111	63315571	+	0	NA	Intergenic	Intergenic	-1278506	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.002174	0.396963	229(GAGAACAGGCTGTTCA,-,0.00),230(AGAACAGGCTGTTCAC,+,0.00)
chunk0041_107_1	chr11	124876429	124876653	+	0	NA	intron (NM_022370, intron 17 of 27)	CpG-5001	11132	NM_022370	64221	Hs.435621	NM_022370	ENSG00000154134	ROBO3	HGPPS|HGPPS1|HGPS|RBIG1|RIG1	roundabout guidance receptor 3	protein-coding	0.080357	0.693333	
chunk0029_125_1	chr10	98536537	98536940	+	0	NA	intron (NM_001166246, intron 9 of 12)	L2a|LINE|L2	-89775	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.007444	0.455446	
chunk0187_140_1	chr7	149586672	149586985	+	0	NA	intron (NR_027788, intron 3 of 7)	ERVL-E-int|LTR|ERVL	37962	NR_027789	79970	Hs.520785	NM_024910	ENSG00000133624	ZNF767P	ZNF767	zinc finger family member 767, pseudogene	pseudo	0.006390	0.385350	
chunk0032_440_1	chr10	132927852	132928200	+	0	NA	intron (NM_001200049, intron 9 of 57)	intron (NM_001200049, intron 9 of 57)	14559	NM_001200049	54777	Hs.298038	NM_017609	ENSG00000171811	CFAP46	C10orf123|C10orf124|C10orf92|C10orf93|TTC40|bA288G11.4|bA288G11.5|bB137A17.2|bB137A17.3	cilia and flagella associated protein 46	protein-coding	0.028736	0.604585	172(AGGAACATGCTGTGCA,-,0.00),173(GGAACATGCTGTGCAG,+,0.00)
chunk0008_262_1	chr1	94550923	94551178	+	0	NA	Intergenic	Intergenic	-9193	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.007843	0.414062	
chunk0209_158_1	chrX	42833044	42833813	+	0	NA	Intergenic	Intergenic	-55193	NR_002191									0.003901	0.384416	641(ATGTACTTCATGTTCT,-,0.00),642(TGTACTTCATGTTCTT,+,0.00)
chunk0149_144_1	chr5	20056869	20057401	+	0	NA	intron (NM_001291956, intron 2 of 14)	L2a|LINE|L2	-68891	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.016917	0.348968	
chunk0175_284_1	chr7	7686678	7687489	+	0	NA	intron (NM_002947, intron 3 of 7)	MLT1J|LTR|ERVL-MaLR	31524	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.003699	0.396552	
chunk0071_390_1	chr15	89263810	89264407	+	0	NA	intron (NM_018193, intron 8 of 36)	intron (NM_018193, intron 8 of 36)	20145	NM_018193	55215	Hs.513126	NM_018193	ENSG00000140525	FANCI	KIAA1794	FA complementation group I	protein-coding	0.006700	0.381271	
chunk0138_163_1	chr4	37780686	37781242	+	0	NA	Intergenic	Intergenic	-45696	NM_018290	55276	Hs.23363	NM_018290	ENSG00000169299	PGM2	MSTP006	phosphoglucomutase 2	protein-coding	0.005396	0.384201	
chunk0167_160_1	chr6	62713411	62713705	+	0	NA	Intergenic	Intergenic	-427363	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.000000	0.308475	
chunk0037_39_1	chr11	70300847	70301307	+	0	NA	intron (NM_003626, intron 2 of 27)	MIRb|SINE|MIR	17122	NR_031624	100313770		NR_031624	ENSG00000221333	MIR548K	MIRN548K	microRNA 548k	ncRNA	0.006522	0.418655	
chunk0133_352_1	chr3	173338713	173339082	+	0	NA	Intergenic	Intergenic	-59551	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.010840	0.283784	
chunk0138_406_1	chr4	43135203	43135538	+	0	NA	Intergenic	Intergenic	242104	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.002985	0.383929	
chunk0085_3_1	chr18	165279	165597	+	0	NA	intron (NM_001037334, intron 2 of 14)	intron (NM_001037334, intron 2 of 14)	6955	NM_001037334	9097	Hs.464416	NM_005151	ENSG00000101557	USP14	TGT	ubiquitin specific peptidase 14	protein-coding	0.012579	0.354232	127(GGTACAGTATGAACCT,+,0.00)
chunk0193_454_1	chr8	81298151	81298603	+	0	NA	Intergenic	Intergenic	17894	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.008850	0.344371	188(CAAAACAATCTGTGCT,-,0.00),189(AAAACAATCTGTGCTC,+,0.00)
chunk0023_44_1	chr10	21292969	21293821	+	0	NA	Intergenic	Intergenic	119093	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.016432	0.384525	
chunk0105_303_1	chr2	190235203	190236057	+	0	NA	intron (NM_198047, intron 11 of 12)	L2c|LINE|L2	54675	NM_032321	84281	Hs.389311	NM_032321	ENSG00000187699	C2orf88	smAKAP	chromosome 2 open reading frame 88	protein-coding	0.005855	0.388304	
chunk0193_209_1	chr8	76255073	76255470	+	0	NA	Intergenic	L1MA4A|LINE|L1	-151383	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.000000	0.560302	
chunk0154_84_1	chr5	77803363	77803562	+	0	NA	Intergenic	L1MEd|LINE|L1	-27101	NM_001297738	6902	Hs.291212	NM_004607	ENSG00000171530	TBCA	-	tubulin folding cofactor A	protein-coding	0.000000	0.350000	
chunk0080_132_1	chr17	27404533	27404993	+	0	NA	Intergenic	Intergenic	-13242	NR_033892	440419	Hs.385755	NR_033892	ENSG00000266433	TBC1D3P5	-	TBC1 domain family member 3 pseudogene 5	pseudo	0.002174	0.433839	221(AGGAACAAGCAGTCCC,-,0.00),222(GGAACAAGCAGTCCCT,+,0.00)
chunk0164_437_1	chr6	27632965	27633460	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-60823	NR_038294	100507173	Hs.635987	NR_038292	ENSG00000281706	LINC01012	-	long intergenic non-protein coding RNA 1012	ncRNA	0.010101	0.461694	
chunk0092_224_1	chr19	32156476	32156852	+	0	NA	Intergenic	L1ME3G|LINE|L1	-50748	NR_110694	101927411	Hs.515337	NR_110694	ENSG00000267204	LINC01782	-	long intergenic non-protein coding RNA 1782	ncRNA	0.005319	0.262599	
chunk0005_265_1	chr1	59788837	59789469	+	0	NA	TTS (NR_110627)	TTS (NR_110627)	16358	NR_110627	101926944	Hs.720353	NR_110627		LOC101926944	-	uncharacterized LOC101926944	ncRNA	0.001582	0.334913	
chunk0103_392_1	chr2	168983467	168983699	+	0	NA	intron (NM_003742, intron 10 of 27)	intron (NM_003742, intron 10 of 27)	47740	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.004310	0.309013	
chunk0023_227_1	chr10	26754280	26754714	+	0	NA	intron (NM_001178125, intron 5 of 6)	intron (NM_001178125, intron 5 of 6)	56831	NM_014317	23590	Hs.558468	NM_014317	ENSG00000148459	PDSS1	COQ1|COQ10D2|COQ1A|DPS|SPS|TPRT|TPT|TPT 1|hDPS1	decaprenyl diphosphate synthase subunit 1	protein-coding	0.006912	0.402299	
chunk0183_418_1	chr7	110768730	110768929	+	0	NA	intron (NM_032549, intron 5 of 5)	L2c|LINE|L2	-322177	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.015075	0.390000	
chunk0144_373_1	chr4	139986208	139986415	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	167768	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.009662	0.408654	
chunk0154_205_1	chr5	80385547	80386199	+	0	NA	Intergenic	L2a|LINE|L2	-22140	NM_001284237	9765	Hs.482660	NM_014733	ENSG00000039319	ZFYVE16	PPP1R69	zinc finger FYVE-type containing 16	protein-coding	0.007669	0.390505	
chunk0132_170_1	chr3	156795935	156796275	+	0	NA	intron (NR_038387, intron 1 of 2)	Tigger6a|DNA|TcMar-Tigger	15916	NR_003284	647033	Hs.745109	NR_003284		PA2G4P4	PA2G4L1	proliferation-associated 2G4 pseudogene 4	pseudo	0.000000	0.348974	
chunk0088_256_1	chr18	48981207	48981406	+	0	NA	Intergenic	L1MB8|LINE|L1	-30595	NM_001190821	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.020101	0.425000	
chunk0122_457_1	chr3	39860887	39861208	+	0	NA	intron (NM_015460, intron 1 of 16)	L1PA15|LINE|L1	51387	NR_104316	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.009346	0.562112	
chunk0115_135_1	chr21	23353232	23353505	+	0	NA	Intergenic	Intergenic	31467	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.010989	0.357664	
chunk0155_210_1	chr5	95063855	95064125	+	0	NA	intron (NM_024717, intron 1 of 22)	Charlie20a|DNA|hAT-Charlie	17876	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.007407	0.387454	125(AGGAACACTGTGTGAT,-,0.00)
chunk0141_143_1	chr4	81352485	81353044	+	0	NA	Intergenic	Intergenic	119164	NM_001300736	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.005367	0.416071	
chunk0177_388_1	chr7	27023423	27023804	+	0	NA	Intergenic	Intergenic	72393	NM_005522	3198	Hs.67397	NM_005522	ENSG00000105991	HOXA1	BSAS|HOX1|HOX1F	homeobox A1	protein-coding	0.005249	0.395288	
chunk0125_390_1	chr3	71723792	71725003	+	0	NA	intron (NM_173359, intron 2 of 7)	L2a|LINE|L2	978	NM_001134651	317649	Hs.581355	NM_173359	ENSG00000163412	EIF4E3	eIF-4E3|eIF4E-3	eukaryotic translation initiation factor 4E family member 3	protein-coding	0.032205	0.490924	
chunk0052_7_1	chr13	19016499	19016972	+	0	NA	Intergenic	MER4A|LTR|ERV1	8476	NR_026852	348021	Hs.314114	NR_026852	ENSG00000232685	LINC00442	-	long intergenic non-protein coding RNA 442	ncRNA	0.002114	0.398734	
chunk0021_284_1	chr1	244369452	244369959	+	0	NA	intron (NM_001012970, intron 2 of 4)	LTR9A1|LTR|ERV1	17070	NM_001276348	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.027613	0.490157	315(TAGGACTAGGTGTGCT,-,0.00),316(AGGACTAGGTGTGCTG,+,0.00)
chunk0016_46_1	chr1	193206662	193206925	+	0	NA	intron (NM_024529, intron 11 of 16)	intron (NM_024529, intron 11 of 16)	-20180	NM_003783	8707	Hs.518834	NM_003783	ENSG00000162630	B3GALT2	BETA3GALT2|GLCT2|beta3Gal-T2	beta-1,3-galactosyltransferase 2	protein-coding	0.000000	0.321970	
chunk0014_193_1	chr1	178951678	178951926	+	0	NA	Intergenic	L1MC4a|LINE|L1	-74137	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.008065	0.449799	43(TAGCTCAGCCTGTTCC,-,0.00),44(AGCTCAGCCTGTTCCA,+,0.00)
chunk0073_50_1	chr16	3031572	3032061	+	0	NA	promoter-TSS (NR_047572)	promoter-TSS (NR_047572)	-665	NR_047572	100128770	Hs.666223	NR_047572	ENSG00000205890	LOC100128770	-	uncharacterized LOC100128770	ncRNA	0.022495	0.516327	
chunk0151_106_1	chr5	43418570	43418900	+	0	NA	Intergenic	L2b|LINE|L2	-6344	NM_148672	56477	Hs.656904	NM_019846	ENSG00000151882	CCL28	CCK1|MEC|SCYA28	C-C motif chemokine ligand 28	protein-coding	0.003030	0.413897	
chunk0042_268_1	chr12	6888532	6888873	+	0	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	4020	NR_033796	171220	Hs.661103	NR_033796	ENSG00000248593	DSTNP2	-	DSTN pseudogene 2	pseudo	0.011730	0.438596	
chunk0081_235_1	chr17	42906934	42907341	+	0	NA	intron (NM_001270397, intron 2 of 4)	L2a|LINE|L2	6340	NM_000151	2538	Hs.212293	NM_000151	ENSG00000131482	G6PC	G6PC1|G6PT|G6Pase|GSD1|GSD1a	glucose-6-phosphatase catalytic subunit	protein-coding	0.007371	0.450980	189(CAGAACAGAGTGTGCA,-,0.00),190(AGAACAGAGTGTGCAA,+,0.00)
chunk0079_378_1	chr17	18184493	18184803	+	0	NA	exon (NM_017758, exon 1 of 4)	exon (NM_017758, exon 1 of 4)	1095	NM_017758	54890	Hs.744130	NM_017758	ENSG00000091542	ALKBH5	ABH5|OFOXD|OFOXD1	alkB homolog 5, RNA demethylase	protein-coding	0.103226	0.659164	
chunk0055_349_1	chr13	70249278	70249643	+	0	NA	Intergenic	MER70B|LTR|ERVL	-140967	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.000000	0.439891	
chunk0065_221_1	chr14	100440987	100441219	+	0	NA	intron (NM_024515, intron 2 of 6)	intron (NM_024515, intron 2 of 6)	64607	NM_024515	79446	Hs.497599	NM_024515	ENSG00000176473	WDR25	C14orf67	WD repeat domain 25	protein-coding	0.004310	0.450644	
chunk0061_337_1	chr14	63437973	63438329	+	0	NA	intron (NR_104104, intron 2 of 12)	intron (NR_104104, intron 2 of 12)	70087	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.000000	0.436975	
chunk0123_17_1	chr3	40355506	40355965	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-31421	NM_001291961	956	Hs.441145	NM_001248	ENSG00000168032	ENTPD3	CD39L3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding	0.004357	0.404348	
chunk0005_347_1	chr1	61268735	61269192	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	-15445	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.017505	0.436681	
chunk0090_281_1	chr18	74909225	74909533	+	0	NA	intron (NM_001146189, intron 6 of 6)	intron (NM_001146189, intron 6 of 6)	278416	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.012987	0.307443	185(AGGTACATGTTGTTCT,-,0.00),186(GGTACATGTTGTTCTA,+,0.00)
chunk0002_186_1	chr1	19243227	19243427	+	0	NA	intron (NM_015047, intron 4 of 22)	intron (NM_015047, intron 4 of 22)	8232	NM_001271428	23065	Hs.439200	NM_015047	ENSG00000127463	EMC1	CAVIPMR|KIAA0090	ER membrane protein complex subunit 1	protein-coding	0.010000	0.318408	57(TAGGTCAGGCTGTTCT,-,0.00),58(AGGTCAGGCTGTTCTT,+,0.00)
chunk0110_256_1	chr20	16708754	16708968	+	0	NA	Intergenic	Intergenic	-21103	NM_003092	6629	Hs.280378	NM_003092	ENSG00000125870	SNRPB2	Msl1|U2B''	small nuclear ribonucleoprotein polypeptide B2	protein-coding	0.000000	0.413953	
chunk0028_8_1	chr10	82242699	82243297	+	0	NA	intron (NM_001165973, intron 2 of 10)	intron (NM_001165973, intron 2 of 10)	-10078	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.003344	0.382304	171(ATGCACAGTCTGTTTC,-,0.00),172(TGCACAGTCTGTTTCT,+,0.00)
chunk0184_190_1	chr7	116810745	116811094	+	0	NA	Intergenic	Intergenic	-51590	NM_006136	830	Hs.446123	NM_006136	ENSG00000198898	CAPZA2	CAPPA2|CAPZ	capping actin protein of muscle Z-line subunit alpha 2	protein-coding	0.005731	0.374286	
chunk0059_29_1	chr14	29890293	29890605	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	37244	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.009615	0.345048	
chunk0210_89_1	chrX	71093489	71093789	+	0	NA	Intergenic	L2c|LINE|L2	-2510	NM_001170931	4303	Hs.584654	NM_005938	ENSG00000184481	FOXO4	AFX|AFX1|MLLT7	forkhead box O4	protein-coding	0.003333	0.392027	
chunk0013_24_1	chr1	166235309	166235529	+	0	NA	Intergenic	L1PA14|LINE|L1	-68698	NM_001017961	149297	Hs.22930	NM_001017961	ENSG00000188859	FAM78B	-	family with sequence similarity 78 member B	protein-coding	0.000000	0.570136	
chunk0135_331_1	chr3	190173289	190173805	+	0	NA	Intergenic	Intergenic	-51110	NM_001134418	55214	Hs.374191	NM_018192	ENSG00000090530	P3H2	LEPREL1|MCVD|MLAT4	prolyl 3-hydroxylase 2	protein-coding	0.001938	0.319149	
chunk0197_262_1	chr8	123563614	123564036	+	0	NA	Intergenic	Intergenic	-22572	NM_001242463	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.011848	0.404255	176(CAGAACACAGTGCCCT,-,0.00),177(AGAACACAGTGCCCTT,+,0.00)
chunk0169_431_1	chr6	108683774	108683979	+	0	NA	3' UTR (NM_001455, exon 3 of 3)	3' UTR (NM_001455, exon 3 of 3)	-67778	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.014634	0.388350	
chunk0117_107_1	chr22	17924929	17925329	+	0	NA	intron (NM_015241, intron 1 of 31)	intron (NM_015241, intron 1 of 31)	-18243	NM_001136004	57553	Hs.528024	NM_015241	ENSG00000243156	MICAL3	MICAL-3	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding	0.010000	0.513716	370(AAAAACATACTGTTCT,-,0.00),371(AAAACATACTGTTCTC,+,0.00)
chunk0045_319_1	chr12	50746001	50746569	+	0	NA	3' UTR (NM_173602, exon 38 of 38)	3' UTR (NM_173602, exon 38 of 38)	-17721	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.008803	0.370826	
chunk0129_94_1	chr3	119463548	119463924	+	0	NA	promoter-TSS (NR_073506)	promoter-TSS (NR_073506)	-54	NM_018266	55254	Hs.594171	NM_018266	ENSG00000176142	TMEM39A	-	transmembrane protein 39A	protein-coding	0.074468	0.594164	
chunk0055_251_1	chr13	63221574	63221955	+	0	NA	intron (NR_126409, intron 5 of 6)	intron (NR_126409, intron 5 of 6)	106330	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.002625	0.329843	
chunk0150_268_1	chr5	36777102	36777354	+	0	NA	Intergenic	L1MEc|LINE|L1	99466	NR_046262	646719	Hs.355684	NR_046262	ENSG00000285967	NIPBL-DT	NIPBL-AS|NIPBL-AS1	NIPBL divergent transcript	ncRNA	0.015873	0.438735	
chunk0205_442_1	chr9	115359487	115359686	+	0	NA	intron (NM_017418, intron 4 of 7)	L2b|LINE|L2	217768	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.000000	0.440000	
chunk0183_168_1	chr7	106113448	106113656	+	0	NA	promoter-TSS (NM_006754)	promoter-TSS (NM_006754)	-905	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.038462	0.497608	65(CAGCACAGTCAGTGCT,-,0.00),66(AGCACAGTCAGTGCTC,+,0.00)
chunk0176_248_1	chr7	16167605	16168425	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-42471	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.006098	0.323995	307(CAGAACACTTTGTCTT,-,0.00)
chunk0145_322_1	chr4	150664910	150666022	+	0	NA	intron (NM_001199282, intron 37 of 56)	MER68|LTR|ERVL	83541	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.007194	0.371069	
chunk0018_201_1	chr1	219354455	219354754	+	0	NA	Intergenic	L1MC3|LINE|L1	179635	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.010033	0.310000	
chunk0074_436_1	chr16	46409190	46409470	+	0	NA	Intergenic	Intergenic	159767	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.025000	0.359431	
chunk0148_46_1	chr5	1344171	1344503	+	0	NA	intron (NM_030782, intron 2 of 16)	intron (NM_030782, intron 2 of 16)	550	NM_030782	81037	Hs.444673	NM_030782	ENSG00000049656	CLPTM1L	CRR9	CLPTM1 like	protein-coding	0.033133	0.477477	
chunk0209_396_1	chrX	55146004	55146293	+	0	NA	exon (NM_001166703, exon 3 of 3)	exon (NM_001166703, exon 3 of 3)	14954	NM_001166703	90736	Hs.415414	NM_138362	ENSG00000182518	FAM104B	CXorf44	family with sequence similarity 104 member B	protein-coding	0.010381	0.448276	
chunk0157_89_1	chr5	116599069	116599421	+	0	NA	Intergenic	Intergenic	-24319	NM_001300780	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.002841	0.339943	
chunk0208_65_1	chrX	11755689	11756104	+	0	NA	Intergenic	L2c|LINE|L2	-2263	NM_078629	10943	Hs.655288	NM_006800	ENSG00000005302	MSL3	MSL3L1	MSL complex subunit 3	protein-coding	0.004819	0.425481	
chunk0180_201_1	chr7	66326825	66327211	+	0	NA	intron (NM_003596, intron 3 of 5)	intron (NM_003596, intron 3 of 5)	73390	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.000000	0.315245	
chunk0034_34_1	chr11	26473161	26473558	+	0	NA	promoter-TSS (NM_001313727)	promoter-TSS (NM_001313727)	-543	NM_001313727	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.000000	0.339196	
chunk0175_352_1	chr6	167651797	167652023	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	27313	NR_117091	401286	Hs.487182	NR_117091	ENSG00000272549	LINC02538	-	long intergenic non-protein coding RNA 2538	ncRNA	0.017699	0.493392	
chunk0158_14_1	chr5	125243928	125244471	+	0	NA	intron (NR_109882, intron 4 of 5)	L1PA15|LINE|L1	207368	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.003683	0.375000	
chunk0031_17_1	chr10	121821925	121822124	+	0	NA	intron (NM_001001976, intron 10 of 11)	L1ME3A|LINE|L1	106039	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.020101	0.390000	
chunk0211_257_1	chrX	120738721	120739374	+	0	NA	Intergenic	Intergenic	-108897	NM_152692	29071	Hs.643920	NM_152692	ENSG00000171155	C1GALT1C1	C1GALT2|C38H2-L1|COSMC|HSPC067|MST143|TNPS	C1GALT1 specific chaperone 1	protein-coding	0.003063	0.403670	
chunk0166_218_1	chr6	46914533	46914745	+	0	NA	intron (NM_015234, intron 1 of 20)	intron (NM_015234, intron 1 of 20)	7338	NM_001098518	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.014151	0.399061	153(AAAACATTGAGTTCCT,+,0.00)
chunk0179_180_1	chr7	46986924	46987377	+	0	NA	Intergenic	MLT1E1-int|LTR|ERVL-MaLR	594994	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.004415	0.374449	
chunk0153_101_1	chr5	68418210	68418784	+	0	NA	Intergenic	Intergenic	125929	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.008711	0.384348	
chunk0145_240_1	chr4	148684587	148685271	+	0	NA	Intergenic	MIRb|SINE|MIR	-242409	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.004386	0.400000	247(CAGAACAAAGTGTTCT,-,0.00),248(AGAACAAAGTGTTCTG,+,0.00)
chunk0151_113_1	chr5	43524851	43525189	+	0	NA	Intergenic	Intergenic	-9849	NM_198566	375444	Hs.661641	NM_198566	ENSG00000172244	C5orf34	-	chromosome 5 open reading frame 34	protein-coding	0.008876	0.404130	121(AGGTACAGTGTGTTCC,-,0.00),122(GGTACAGTGTGTTCCT,+,0.00)
chunk0114_384_1	chr20	63140590	63140826	+	0	NA	Intergenic	Intergenic	-37792	NR_029670	406909		NR_029670	ENSG00000207598	MIR124-3	MIRN124-3|MIRN124A3|mir-124-3	microRNA 124-3	ncRNA	0.012712	0.472574	96(TAGCACTCCTTGTTCC,-,0.00),97(AGCACTCCTTGTTCCA,+,0.00)
chunk0163_148_1	chr6	10933048	10933669	+	0	NA	intron (NR_125851, intron 2 of 2)	MER58A|DNA|hAT-Charlie	20731	NR_125851	101928191	Hs.638939	NR_125851		LOC101928191	-	uncharacterized LOC101928191	ncRNA	0.011272	0.408360	
chunk0099_400_1	chr2	101895645	101896368	+	0	NA	Intergenic	Intergenic	-87459	NR_103791	100506328	Hs.516245	NR_103791		LINC01127	-	long intergenic non-protein coding RNA 1127	ncRNA	0.005533	0.440608	346(AAGCACTCAGAGTCCC,-,0.00),347(AGCACTCAGAGTCCCT,+,0.00)
chunk0140_7_1	chr4	65323240	65323743	+	0	NA	3' UTR (NM_182472, exon 17 of 17)	3' UTR (NM_182472, exon 17 of 17)	-318991	NR_033976	401134	Hs.165899	NR_033976	ENSG00000250125	LINC02232	-	long intergenic non-protein coding RNA 2232	ncRNA	0.001988	0.299603	
chunk0148_325_1	chr5	14008705	14009920	+	0	NA	Intergenic	Intergenic	-64832	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.009053	0.416941	256(CAGGACAAACTGATCC,-,0.00),257(AGGACAAACTGATCCA,+,0.00)
chunk0162_432_1	chr5	180320840	180321641	+	0	NA	intron (NM_005110, intron 9 of 18)	intron (NM_005110, intron 9 of 18)	-29169	NM_002752	5601	Hs.484371	NM_002752	ENSG00000050748	MAPK9	JNK-55|JNK2|JNK2A|JNK2ALPHA|JNK2B|JNK2BETA|PRKM9|SAPK|SAPK1a|p54a|p54aSAPK	mitogen-activated protein kinase 9	protein-coding	0.018727	0.389027	
chunk0046_132_1	chr12	57693748	57694130	+	0	NA	promoter-TSS (NM_001017957)	promoter-TSS (NM_001017957)	-16	NM_001261420	10956	Hs.527861	NM_006812	ENSG00000135506	OS9	ERLEC2|OS-9	OS9 endoplasmic reticulum lectin	protein-coding	0.065445	0.535248	
chunk0030_451_1	chr10	121054883	121055389	+	0	NA	Intergenic	Intergenic	-203957	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.009881	0.339250	
chunk0169_368_1	chr6	107140751	107140950	+	0	NA	Intergenic	Intergenic	-26418	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.005025	0.340000	
chunk0126_126_1	chr3	75785440	75785795	+	0	NA	promoter-TSS (NM_001128223)	promoter-TSS (NM_001128223)	-34	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.056338	0.620787	
chunk0144_81_1	chr4	128159960	128160295	+	0	NA	intron (NM_018078, intron 11 of 19)	MER58A|DNA|hAT-Charlie	98861	NM_001278604	55132	Hs.654971	NM_018078	ENSG00000138709	LARP1B	LARP2	La ribonucleoprotein domain family member 1B	protein-coding	0.005970	0.383929	
chunk0060_39_1	chr14	40955153	40955478	+	0	NA	intron (NR_109757, intron 1 of 3)	L1PA15|LINE|L1	604	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.006154	0.334356	
chunk0062_99_1	chr14	68174732	68175236	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	355205	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.003968	0.344554	258(AGGAACAGAATGTTCT,-,0.00),259(GGAACAGAATGTTCTC,+,0.00)
chunk0192_395_1	chr8	68854135	68854945	+	0	NA	Intergenic	Intergenic	249650	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.008642	0.356350	125(ATGGACTTTGTGTACT,-,0.00),467(TAGTACAGTCTGTACC,-,0.00),468(AGTACAGTCTGTACCT,+,0.00)
chunk0119_326_1	chr22	46816116	46816758	+	0	NA	intron (NM_014346, intron 4 of 12)	intron (NM_014346, intron 4 of 12)	42510	NM_001284305	25771	Hs.435044	NM_014346	ENSG00000054611	TBC1D22A	C22orf4|HSC79E021	TBC1 domain family member 22A	protein-coding	0.014019	0.499222	
chunk0130_160_1	chr3	132655347	132655705	+	0	NA	intron (NM_198329, intron 1 of 11)	L2a|LINE|L2	1080	NM_198329	79876	Hs.170737	NM_024818	ENSG00000081307	UBA5	EIEE44|SCAR24|THIFP1|UBE1DC1	ubiquitin like modifier activating enzyme 5	protein-coding	0.005587	0.456825	
chunk0017_143_1	chr1	206646543	206647141	+	0	NA	intron (NM_001004023, intron 3 of 3)	MIRc|SINE|MIR	11306	NM_001004023	8444	Hs.164267	NM_003582	ENSG00000143479	DYRK3	DYRK5|RED|REDK|hYAK3-2	dual specificity tyrosine phosphorylation regulated kinase 3	protein-coding	0.003344	0.409015	
chunk0035_50_1	chr11	41244052	41244622	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	215299	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005263	0.343257	
chunk0028_344_1	chr10	92207836	92208157	+	0	NA	intron (NM_001178137, intron 2 of 9)	intron (NM_001178137, intron 2 of 9)	35283	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.006231	0.366460	
chunk0036_121_1	chr11	61680363	61680579	+	0	NA	promoter-TSS (NM_006133)	promoter-TSS (NM_006133)	38	NM_006133	747	Hs.241564	NM_006133	ENSG00000134780	DAGLA	C11orf11|DAGL(ALPHA)|DAGLALPHA|NSDDR	diacylglycerol lipase alpha	protein-coding	0.171296	0.824885	
chunk0100_82_1	chr2	107692808	107693241	+	0	NA	Intergenic	Intergenic	-61088	NR_126370	104326057	Hs.585967	NR_126369	ENSG00000232991	GACAT1	LINC00876	gastric cancer associated transcript 1	ncRNA	0.002309	0.377880	
chunk0057_421_1	chr13	109999726	110000011	+	0	NA	Intergenic	Intergenic	-53417	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.017544	0.531469	
chunk0040_278_1	chr11	116813729	116814350	+	0	NA	Intergenic	Intergenic	9256	NM_000482	337	Hs.1247	NM_000482	ENSG00000110244	APOA4	-	apolipoprotein A4	protein-coding	0.009662	0.545016	232(GAGGACACGGCGTCCC,-,0.00),233(AGGACACGGCGTCCCC,+,0.00)
chunk0021_352_1	chr1	246212713	246213038	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	204537	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003077	0.371166	
chunk0170_99_1	chr6	110528077	110528942	+	0	NA	Intergenic	Intergenic	-51868	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.005780	0.372979	245(GGATACACTGTGTTCC,-,0.00),246(GATACACTGTGTTCCA,+,0.00)
chunk0187_52_1	chr8	1772924	1773173	+	0	NA	intron (NM_018941, intron 2 of 2).2	L2b|LINE|L2	9344	NM_018941	2055	Hs.127675	NM_018941	ENSG00000182372	CLN8	C8orf61|EPMR|TLCD6	CLN8 transmembrane ER and ERGIC protein	protein-coding	0.016064	0.524000	107(CAGTACAGACTGTTCA,-,0.00),108(AGTACAGACTGTTCAT,+,0.00)
chunk0109_33_1	chr20	543778	544196	+	0	NA	promoter-TSS (NM_001895)	promoter-TSS (NM_001895)	-149	NM_001895	1457	Hs.644056	NM_001895	ENSG00000101266	CSNK2A1	CK2A1|CKII|Cka1|Cka2|OCNDS	casein kinase 2 alpha 1	protein-coding	0.035885	0.529833	
chunk0131_44_1	chr3	142596005	142596472	+	0	NA	promoter-TSS (NM_001145319)	promoter-TSS (NM_001145319)	-149	NM_001145319	5357	Hs.203637	NM_002670	ENSG00000120756	PLS1	-	plastin 1	protein-coding	0.066381	0.581197	
chunk0070_432_1	chr15	78059909	78060383	+	0	NA	intron (NM_015079, intron 1 of 12)	intron (NM_015079, intron 1 of 12)	17506	NM_144572	23102	Hs.567426	NM_015079	ENSG00000167202	TBC1D2B	-	TBC1 domain family member 2B	protein-coding	0.006329	0.385263	
chunk0207_350_1	chr9	134961984	134962964	+	0	NA	Intergenic	Intergenic	-44514	NM_002003	2219	Hs.440898	NM_002003	ENSG00000085265	FCN1	FCNM	ficolin 1	protein-coding	0.017347	0.516820	829(TGGCCAGGCTGTTCTC,+,0.00)
chunk0026_26_1	chr10	60663864	60664139	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	69525	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.021818	0.442029	
chunk0116_294_1	chr21	40350940	40351504	+	0	NA	intron (NR_073202, intron 5 of 32)	intron (NR_073202, intron 5 of 32)	-31861	NR_038896	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.005319	0.444248	
chunk0138_413_1	chr4	44588784	44588983	+	0	NA	Intergenic	L1PB4|LINE|L1	62758	NM_182592	285525	Hs.596000	NM_182592	ENSG00000177752	YIPF7	FinGER9	Yip1 domain family member 7	protein-coding	0.015075	0.335000	
chunk0167_410_1	chr6	75351434	75352009	+	0	NA	intron (NM_001289987, intron 5 of 6)	Tigger3a|DNA|TcMar-Tigger	-31465	NR_125859	101928540	Hs.526972	NR_125859		LOC101928540	-	uncharacterized LOC101928540	ncRNA	0.005217	0.371528	221(AGTAACAGGCTGTGCC,-,0.00),222(GTAACAGGCTGTGCCA,+,0.00)
chunk0112_257_1	chr20	42367875	42368108	+	0	NA	intron (NM_133170, intron 9 of 31)	intron (NM_133170, intron 9 of 31)	-317492	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.004292	0.564103	
chunk0159_114_1	chr5	138641739	138642072	+	0	NA	Intergenic	Intergenic	-66276	NM_004134	3313	Hs.184233	NM_004134	ENSG00000113013	HSPA9	CRP40|CSA|EVPLS|GRP-75|GRP75|HEL-S-124m|HSPA9B|MOT|MOT2|MTHSP75|PBP74|SAAN|SIDBA4	heat shock protein family A (Hsp70) member 9	protein-coding	0.024024	0.577844	
chunk0024_1_1	chr10	32489466	32489816	+	0	NA	intron (NR_109826, intron 9 of 16)	intron (NR_109826, intron 9 of 16)	43559	NR_109826	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.002857	0.549858	
chunk0178_355_1	chr7	38840636	38841175	+	0	NA	intron (NM_014396, intron 4 of 28)	intron (NM_014396, intron 4 of 28)	68295	NM_080631	27072	Hs.592184	NM_014396	ENSG00000006715	VPS41	HVPS41|HVSP41|hVps41p	VPS41 subunit of HOPS complex	protein-coding	0.003711	0.350000	
chunk0083_429_1	chr17	72502010	72502361	+	0	NA	intron (NR_036488, intron 1 of 3)	intron (NR_036488, intron 1 of 3)	90619	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.037037	0.514205	
chunk0011_224_1	chr1	150253206	150253465	+	0	NA	Intergenic	L1M5|LINE|L1	-4408	NM_012113	23632	Hs.528988	NM_012113	ENSG00000118298	CA14	CAXiV	carbonic anhydrase 14	protein-coding	0.023166	0.430769	
chunk0202_151_1	chr9	73579703	73580638	+	0	NA	Intergenic	Intergenic	428439	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.008556	0.330128	
chunk0177_382_1	chr7	26901833	26902149	+	0	NA	Intergenic	Intergenic	-37248	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.018987	0.381703	
chunk0056_259_1	chr13	89823311	89823735	+	0	NA	Intergenic	Intergenic	-259110	NR_046991	100874139	Hs.742173	NR_046991		LINC00353	-	long intergenic non-protein coding RNA 353	ncRNA	0.004717	0.256471	178(AAGATCAATATGTTCT,-,0.00),179(AGATCAATATGTTCTC,+,0.00)
chunk0022_13_1	chr10	7398344	7398718	+	0	NA	intron (NM_001029880, intron 1 of 20)	intron (NM_001029880, intron 1 of 20)	10810	NM_001018039	57713	Hs.407983	NM_001018039	ENSG00000198879	SFMBT2	-	Scm like with four mbt domains 2	protein-coding	0.002674	0.370667	
chunk0125_233_1	chr3	68248418	68248762	+	0	NA	intron (NM_213609, intron 2 of 4)	LTR32|LTR|ERVL	244374	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.014535	0.449275	
chunk0182_259_1	chr7	97360173	97360372	+	0	NA	Intergenic	Intergenic	243679	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.015075	0.380000	
chunk0018_350_1	chr1	221594898	221595408	+	0	NA	Intergenic	Intergenic	141747	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.001961	0.334638	
chunk0013_287_1	chr1	170969884	170970105	+	0	NA	intron (NM_025063, intron 7 of 14)	intron (NM_025063, intron 7 of 14)	34499	NM_025063	80133	Hs.591489	NM_025063	ENSG00000117501	MROH9	ARMC11|C1orf129	maestro heat like repeat family member 9	protein-coding	0.018100	0.500000	
chunk0159_271_1	chr5	142357731	142357976	+	0	NA	intron (NR_120664, intron 3 of 3)	intron (NR_120664, intron 3 of 3)	32560	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.016327	0.495935	198(CTGTACAGAGTGTTCT,-,0.00),199(TGTACAGAGTGTTCTT,+,0.00)
chunk0103_398_1	chr2	169025919	169026492	+	0	NA	intron (NM_003742, intron 1 of 27)	MER90a|LTR|ERV1	5118	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.001745	0.385017	299(TGGAACAGGGTGTTCT,-,0.00),300(GGAACAGGGTGTTCTT,+,0.00)
chunk0054_315_1	chr13	48892532	48892943	+	0	NA	Intergenic	Intergenic	-83175	NM_001079673	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.009732	0.376214	54(GAGCACAATCAGTTCT,-,0.00),55(AGCACAATCAGTTCTC,+,0.00)
chunk0024_295_1	chr10	42099000	42099219	+	0	NA	Intergenic	Intergenic	268936	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.050228	0.377273	
chunk0138_115_1	chr4	36243343	36244051	+	0	NA	promoter-TSS (NR_122079)	promoter-TSS (NR_122079)	-419	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.024011	0.427362	
chunk0183_412_1	chr7	110677317	110677754	+	0	NA	intron (NM_032549, intron 5 of 5)	intron (NM_032549, intron 5 of 5)	-413471	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.011442	0.349315	
chunk0180_350_1	chr7	73612642	73613237	+	0	NA	intron (NM_032951, intron 2 of 16)	L2c|LINE|L2	11601	NM_032953	51085	Hs.647055	NM_032951	ENSG00000009950	MLXIPL	CHREBP|MIO|MLX|MONDOB|WBSCR14|WS-bHLH|bHLHd14	MLX interacting protein like	protein-coding	0.016807	0.528523	
chunk0131_191_1	chr3	148494496	148494779	+	0	NA	Intergenic	Intergenic	-203234	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.003534	0.359155	127(CAGAGCATGTTGTTCT,-,0.00),128(AGAGCATGTTGTTCTC,+,0.00)
chunk0201_11_1	chr9	32573055	32573396	+	0	NA	promoter-TSS (NM_002493)	promoter-TSS (NM_002493)	-41	NM_001199987	4712	Hs.493668	NM_002493	ENSG00000165264	NDUFB6	B17|CI	NADH:ubiquinone oxidoreductase subunit B6	protein-coding	0.087977	0.576023	266(GGGGACAAGGAGTACT,-,0.00),267(GGGACAAGGAGTACTC,+,0.00)
chunk0033_130_1	chr11	14753891	14754090	+	0	NA	intron (NM_000922, intron 1 of 15)	intron (NM_000922, intron 1 of 15)	110267	NM_000922	5140	Hs.445711	NM_000922	ENSG00000152270	PDE3B	HcGIP1|cGIPDE1	phosphodiesterase 3B	protein-coding	0.000000	0.250000	94(AAGAACTTCTTGTCCT,-,0.00),95(AGAACTTCTTGTCCTG,+,0.00)
chunk0100_47_1	chr2	106009956	106010699	+	0	NA	Intergenic	L1MB8|LINE|L1	-55330	NM_032411	84417	Hs.43125	NM_032411	ENSG00000119147	ECRG4	C2orf40	ECRG4 augurin precursor	protein-coding	0.009421	0.452957	
chunk0200_52_1	chr9	15543363	15543645	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-9595	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.007092	0.406360	
chunk0079_372_1	chr17	18064973	18065528	+	0	NA	3' UTR (NM_024052, exon 6 of 6)	3' UTR (NM_024052, exon 6 of 6)	-22617	NM_001388	1819	Hs.78582	NM_001388	ENSG00000108591	DRG2	-	developmentally regulated GTP binding protein 2	protein-coding	0.016216	0.455036	
chunk0185_124_1	chr7	126360428	126360664	+	0	NA	Intergenic	Intergenic	697638	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.004237	0.329114	
chunk0022_72_1	chr10	8795499	8795861	+	0	NA	Intergenic	Intergenic	-102309	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.005525	0.369146	
chunk0017_65_1	chr1	205525693	205525985	+	0	NA	intron (NM_002596, intron 5 of 15)	L2c|LINE|L2	21283	NM_212503	5129	Hs.445402	NM_002596	ENSG00000117266	CDK18	PCTAIRE|PCTAIRE3|PCTK3	cyclin dependent kinase 18	protein-coding	0.027397	0.546075	44(GGAACACACAGCCCTT,+,0.00)
chunk0101_151_1	chr2	127967708	127967907	+	0	NA	intron (NM_024545, intron 14 of 19)	L1M4|LINE|L1	59488	NM_001145928	79595	Hs.32995	NM_024545	ENSG00000136715	SAP130	-	Sin3A associated protein 130	protein-coding	0.005025	0.400000	
chunk0193_240_1	chr8	76736785	76737034	+	0	NA	intron (NM_024721, intron 3 of 10)	intron (NM_024721, intron 3 of 10)	-53634	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.004016	0.376000	
chunk0135_112_1	chr3	186941161	186941829	+	0	NA	intron (NM_173216, intron 1 of 7)	L3|LINE|CR1	10969	NM_173217	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.016467	0.485800	502(TGGAACAAGCTGTGTT,-,0.00)
chunk0086_272_1	chr18	23629250	23630005	+	0	NA	intron (NM_001308238, intron 6 of 8)	intron (NM_001308238, intron 6 of 8)	33258	NM_173505	147463	Hs.355689	NM_173505	ENSG00000154065	ANKRD29	-	ankyrin repeat domain 29	protein-coding	0.006623	0.461640	
chunk0209_152_1	chrX	42696567	42697169	+	0	NA	Intergenic	Intergenic	81367	NR_002191									0.004983	0.381426	
chunk0196_110_1	chr8	103252917	103253181	+	0	NA	Intergenic	Intergenic	-45384	NM_001164615	8323	Hs.591863	NM_003506	ENSG00000164930	FZD6	FZ-6|FZ6|HFZ6|NDNC10	frizzled class receptor 6	protein-coding	0.011364	0.392453	
chunk0019_223_1	chr1	227306109	227306355	+	0	NA	intron (NM_014826, intron 1 of 34)	intron (NM_014826, intron 1 of 34)	11893	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.004065	0.331984	
chunk0205_380_1	chr9	114082553	114082800	+	0	NA	Intergenic	Intergenic	-4204	NM_001633	259	Hs.436911	NM_001633	ENSG00000106927	AMBP	A1M|EDC1|HCP|HI30|IATIL|ITI|ITIL|ITILC|UTI	alpha-1-microglobulin/bikunin precursor	protein-coding	0.028340	0.540323	
chunk0152_272_1	chr5	61298096	61298761	+	0	NA	Intergenic	MIR|SINE|MIR	-33845	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.007519	0.423423	
chunk0088_59_1	chr18	44197653	44198022	+	0	NA	Intergenic	Intergenic	333860	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.002710	0.400000	
chunk0035_129_1	chr11	42756426	42757213	+	0	NA	Intergenic	Intergenic	-503129	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.379442	
chunk0048_186_1	chr12	81034901	81035492	+	0	NA	Intergenic	Intergenic	-42834	NM_024560	79611	Hs.259559	NM_024560	ENSG00000111058	ACSS3	-	acyl-CoA synthetase short chain family member 3	protein-coding	0.003384	0.405405	265(AGGCACACAATGTTTT,-,0.00),266(GGCACACAATGTTTTA,+,0.00)
chunk0114_258_1	chr21	16144252	16144480	+	0	NA	intron (NR_027790, intron 2 of 7)	L1PA13|LINE|L1	-50013	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.000000	0.344978	
chunk0071_233_1	chr15	85107535	85107824	+	0	NA	intron (NM_001243137, intron 11 of 21)	intron (NM_001243137, intron 11 of 21)	97608	NR_049748									0.000000	0.448276	101(TGGTACATGCTGTTCA,-,0.00),102(GGTACATGCTGTTCAG,+,0.00)
chunk0019_185_1	chr1	226575881	226576141	+	0	NA	intron (NM_001003665, intron 1 of 3)	intron (NM_001003665, intron 1 of 3)	27211	NM_001003665	375057	Hs.116827	NM_001003665	ENSG00000203685	STUM	C1orf95	stum, mechanosensory transduction mediator homolog	protein-coding	0.019231	0.532567	
chunk0118_138_1	chr22	29888332	29888646	+	0	NA	intron (NM_021090, intron 1 of 19)	intron (NM_021090, intron 1 of 19)	5320	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.009554	0.358730	
chunk0151_415_1	chr5	55635987	55636576	+	0	NA	intron (NR_047649, intron 10 of 13)	intron (NR_047649, intron 10 of 13)	56772	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.005093	0.333898	
chunk0193_322_1	chr8	78705222	78705506	+	0	NA	intron (NM_016010, intron 7 of 8)	L1PA13|LINE|L1	19010	NR_077236	101241902	Hs.388511	NR_077236		LOC101241902	-	chromosome 4 open reading frame 46 pseudogene	pseudo	0.000000	0.477193	
chunk0187_109_1	chr8	5783783	5784176	+	0	NA	Intergenic	Intergenic	622569	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.002545	0.309645	182(ATGAACTTTCTGTTCC,-,0.00),183(TGAACTTTCTGTTCCC,+,0.00)
chunk0117_175_1	chr22	20776715	20777070	+	0	NA	intron (NM_000185, intron 1 of 4)	intron (NM_000185, intron 1 of 4)	2797	NM_000185	3053	Hs.474270	NM_000185	ENSG00000099937	SERPIND1	D22S673|HC2|HCF2|HCII|HLS2|LS2|THPH10	serpin family D member 1	protein-coding	0.011268	0.393258	
chunk0110_59_1	chr20	10842293	10842542	+	0	NA	Intergenic	Intergenic	66855	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.012048	0.408000	
chunk0064_15_1	chr14	89319587	89320131	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	97251	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.011029	0.401835	
chunk0133_424_1	chr3	174786943	174787280	+	0	NA	Intergenic	Intergenic	-72210	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.002967	0.227811	
chunk0086_334_1	chr18	24659962	24660286	+	0	NA	intron (NR_040033, intron 2 of 2)	intron (NR_040033, intron 2 of 2)	31942	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.021605	0.507692	
chunk0036_297_1	chr11	65823016	65823531	+	0	NA	Intergenic	Intergenic	-10666	NM_152760	254122	Hs.591950	NM_152760	ENSG00000172803	SNX32	SNX6B	sorting nexin 32	protein-coding	0.017476	0.492248	
chunk0047_395_1	chr12	75661708	75662458	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-150445	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.004000	0.322237	268(TGGAACATTGTGTGCA,-,0.00),269(GGAACATTGTGTGCAG,+,0.00)
chunk0152_334_1	chr5	62412878	62413077	+	0	NA	intron (NM_016338, intron 1 of 29)	CpG	231	NM_016338	51194	Hs.482269	NM_016338	ENSG00000086200	IPO11	RanBP11	importin 11	protein-coding	0.085427	0.680000	
chunk0053_238_1	chr13	32633555	32634142	+	0	NA	intron (NM_015032, intron 1 of 34)	intron (NM_015032, intron 1 of 34)	47421	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.000000	0.333333	
chunk0032_409_1	chr11	11937772	11938469	+	0	NA	intron (NM_017944, intron 16 of 26)	intron (NM_017944, intron 16 of 26)	70519	NM_001018057	27122	Hs.292156	NM_013253	ENSG00000050165	DKK3	REIC|RIG	dickkopf WNT signaling pathway inhibitor 3	protein-coding	0.001435	0.319484	
chunk0049_261_1	chr12	93734815	93735052	+	0	NA	intron (NR_110093, intron 2 of 2)	L2c|LINE|L2	2890	NR_110092	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.004219	0.495798	
chunk0119_40_1	chr22	40542537	40543128	+	0	NA	intron (NM_001282661, intron 3 of 13)	L1ME4a|LINE|L1	21032	NR_109965	101927257	Hs.662725	NR_109965	ENSG00000232564	MRTFA-AS1	-	MRTFA antisense RNA 1	ncRNA	0.000000	0.300676	197(CAGAACAGAATGTTAT,-,0.00),198(AGAACAGAATGTTATG,+,0.00)
chunk0093_319_1	chr19	53864437	53864755	+	0	NA	promoter-TSS (NM_001290193)	promoter-TSS (NM_001290193)	-988	NM_001290193	91663	Hs.380906	NM_138373	ENSG00000179820	MYADM	SB135	myeloid associated differentiation marker	protein-coding	0.009434	0.504702	
chunk0005_213_1	chr1	59172616	59172854	+	0	NA	Intergenic	Intergenic	-25928	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.004202	0.376569	176(GAGAACAGCCTGTTTC,-,0.00),177(AGAACAGCCTGTTTCT,+,0.00)
chunk0113_75_1	chr20	50583627	50583847	+	0	NA	3' UTR (NM_002827, exon 10 of 10)	3' UTR (NM_002827, exon 10 of 10)	-2049	NR_030375	693230		NR_030375	ENSG00000208018	MIR645	MIRN645|hsa-mir-645	microRNA 645	ncRNA	0.009091	0.506787	113(AGGCCCAGCCTGTCCT,-,0.00),114(GGCCCAGCCTGTCCTG,+,0.00)
chunk0147_224_1	chr4	181859783	181860193	+	0	NA	Intergenic	Intergenic	284527	NR_027107	90768	Hs.175465	NR_027107		TENM3-AS1	-	TENM3 antisense RNA 1	ncRNA	0.002439	0.367397	
chunk0181_70_1	chr7	80258349	80258795	+	0	NA	Intergenic	Intergenic	115867	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.002242	0.297539	
chunk0090_421_1	chr18	79169441	79169640	+	0	NA	intron (NM_001306085, intron 7 of 28)	intron (NM_001306085, intron 7 of 28)	100265	NM_001306085	374868	Hs.465475	NM_198531	ENSG00000166377	ATP9B	ATPASEP|ATPIIB|HUSSY-20|NEO1L|hMMR1	ATPase phospholipid transporting 9B (putative)	protein-coding	0.015075	0.385000	
chunk0151_165_1	chr5	49661379	49661826	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	779798	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.029083	0.421875	
chunk0039_381_1	chr11	107005894	107006516	+	0	NA	intron (NM_001256424, intron 1 of 8)	intron (NM_001256424, intron 1 of 8)	12240	NM_000855	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.003215	0.362761	194(CAGAACAAACTGATCC,-,0.00),195(AGAACAAACTGATCCT,+,0.00)
chunk0103_156_1	chr2	162291634	162292251	+	0	NA	intron (NM_022168, intron 4 of 15)	intron (NM_022168, intron 4 of 15)	26766	NM_022168	64135	Hs.163173	NM_022168	ENSG00000115267	IFIH1	AGS7|Hlcd|IDDM19|MDA-5|MDA5|RLR-2|SGMRT1	interferon induced with helicase C domain 1	protein-coding	0.004862	0.331715	
chunk0189_220_1	chr8	24366863	24367484	+	0	NA	intron (NR_125808, intron 3 of 5)	intron (NR_125808, intron 3 of 5)	-17112	NM_001145272	27299	Hs.521459	NM_014479	ENSG00000134028	ADAMDEC1	M12.219	ADAM like decysin 1	protein-coding	0.004831	0.364952	
chunk0116_186_1	chr21	36927318	36927888	+	0	NA	intron (NM_001242785, intron 6 of 11)	intron (NM_001242785, intron 6 of 11)	39053	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.021053	0.413310	
chunk0054_12_1	chr13	40476428	40477055	+	0	NA	intron (NR_024507, intron 1 of 6)	L2b|LINE|L2	4265	NR_024507	646982	Hs.287664	NR_024505	ENSG00000215483	LINC00598	lncFOXO1	long intergenic non-protein coding RNA 598	ncRNA	0.006380	0.433121	
chunk0195_364_1	chr8	99876960	99877434	+	0	NA	TTS (NM_004374)	TTS (NM_004374)	16817	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.004219	0.383158	
chunk0138_32_1	chr4	31188029	31188412	+	0	NA	intron (NR_125935, intron 2 of 4)	intron (NR_125935, intron 2 of 4)	17076	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.015666	0.393229	
chunk0096_151_1	chr2	29183495	29183942	+	0	NA	TTS (NM_024692)	TTS (NM_024692)	68292	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.002237	0.319196	
chunk0001_110_1	chr1	3624535	3625109	+	0	NA	promoter-TSS (NM_182752)	promoter-TSS (NM_182752)	-170	NM_182752	127262	Hs.20529	NM_182752	ENSG00000158109	TPRG1L	FAM79A|h-mover|mover	tumor protein p63 regulated 1 like	protein-coding	0.128920	0.739130	
chunk0162_438_1	chr5	180542564	180542853	+	0	NA	intron (NM_001303241, intron 4 of 13)	intron (NM_001303241, intron 4 of 13)	48309	NM_001303241	57472	Hs.608380	NM_015455	ENSG00000113300	CNOT6	CCR4|Ccr4a	CCR4-NOT transcription complex subunit 6	protein-coding	0.006920	0.341379	
chunk0129_386_1	chr3	126270205	126270661	+	0	NA	Intergenic	Intergenic	86960	NM_014079	28999	Hs.272215	NM_014079	ENSG00000163884	KLF15	KKLF	Kruppel like factor 15	protein-coding	0.017544	0.514223	
chunk0169_362_1	chr6	106912920	106913410	+	0	NA	Intergenic	Intergenic	60874	NM_001291739	100133941	Hs.644105	NM_013230	ENSG00000272398	CD24	CD24A	CD24 molecule	protein-coding	0.002041	0.419552	
chunk0201_325_1	chr9	63661007	63661414	+	0	NA	Intergenic	Intergenic	-158364	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.007371	0.367647	
chunk0054_73_1	chr13	42153399	42153709	+	0	NA	intron (NR_123715, intron 2 of 31)	intron (NR_123715, intron 2 of 31)	15512	NR_123714	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.000000	0.360129	
chunk0027_367_1	chr10	79104484	79104861	+	0	NA	intron (NM_020338, intron 1 of 24)	intron (NM_020338, intron 1 of 24)	35637	NM_020338	57178	Hs.193118	NM_020338	ENSG00000108175	ZMIZ1	MIZ|RAI17|TRAFIP10|ZIMP10	zinc finger MIZ-type containing 1	protein-coding	0.015915	0.542328	
chunk0154_266_1	chr5	82010516	82011294	+	0	NA	intron (NM_031482, intron 2 of 7)	MIRc|SINE|MIR	38880	NM_001131028	83734	Hs.713698	NM_031482	ENSG00000152348	ATG10	APG10|APG10L|pp12616	autophagy related 10	protein-coding	0.006427	0.331194	295(CAGAACAAGTTGTGCA,-,0.00),296(AGAACAAGTTGTGCAC,+,0.00),356(ATGCACACAGTGTTCC,-,0.00),357(TGCACACAGTGTTCCT,+,0.00)
chunk0154_277_1	chr5	82262267	82262576	+	0	NA	Intergenic	L1MC5a|LINE|L1	15995	NM_001025	6228	Hs.527193	NM_001025	ENSG00000186468	RPS23	BTDD|MABAS|MCINS|PAMAS|S23|uS12	ribosomal protein S23	protein-coding	0.000000	0.306452	
chunk0027_376_1	chr10	79380287	79380593	+	0	NA	Intergenic	Intergenic	32976	NM_005729	10105	Hs.381072	NM_005729	ENSG00000108179	PPIF	CYP3|CyP-M|Cyp-D|CypD	peptidylprolyl isomerase F	protein-coding	0.013072	0.524430	
chunk0021_424_1	chr1	247097762	247098211	+	0	NA	Intergenic	Intergenic	6386	NM_001142572	79862	Hs.163754	NM_024804	ENSG00000188295	ZNF669	-	zinc finger protein 669	protein-coding	0.011136	0.340000	
chunk0005_206_1	chr1	59098077	59098763	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	48387	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.007289	0.387191	302(AAGAACTAAGAGTTCT,-,0.00)
chunk0097_189_1	chr2	50483791	50484244	+	0	NA	intron (NM_001135659, intron 16 of 23)	intron (NM_001135659, intron 16 of 23)	-136261	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.008830	0.334802	
chunk0137_371_1	chr4	26150905	26151767	+	0	NA	Intergenic	Intergenic	-168374	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.010441	0.415991	
chunk0070_438_1	chr15	78209871	78210399	+	0	NA	intron (NM_001199377, intron 1 of 13)	intron (NM_001199377, intron 1 of 13)	24572	NM_015162	23205	Hs.655760	NM_015162	ENSG00000103740	ACSBG1	BG|BG1|BGM|GR-LACS|LPD	acyl-CoA synthetase bubblegum family member 1	protein-coding	0.011364	0.461248	
chunk0025_62_1	chr10	49561766	49561989	+	0	NA	Intergenic	LTR41|LTR|ERVL	-22339	NM_001277059	2074	Hs.49063	NM_000124	ENSG00000225830	ERCC6	ARMD5|CKN2|COFS|COFS1|CSB|CSB-PGBD3|POF11|RAD26|UVSS1	ERCC excision repair 6, chromatin remodeling factor	protein-coding	0.017937	0.424107	95(AAGTACAGGCTGTTCC,-,0.00),96(AGTACAGGCTGTTCCT,+,0.00)
chunk0102_46_1	chr2	142531610	142531812	+	0	NA	Intergenic	MER21C|LTR|ERVL	-345915	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.014851	0.487685	
chunk0141_445_1	chr4	89119193	89119463	+	0	NA	Intergenic	L1MC3|LINE|L1	6511	NM_145715	166815	Hs.58924	NM_145715	ENSG00000180346	TIGD2	HEL106	tigger transposable element derived 2	protein-coding	0.003704	0.339483	
chunk0040_272_1	chr11	116723134	116723551	+	0	NA	Intergenic	L2c|LINE|L2	49656	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.011990	0.440191	
chunk0115_433_1	chr21	31875473	31876042	+	0	NA	intron (NM_014586, intron 1 of 10)	intron (NM_014586, intron 1 of 10)	2442	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.038664	0.505263	
chunk0104_279_1	chr2	178252061	178252695	+	0	NA	intron (NM_001201482, intron 1 of 23)	MER58A|DNA|hAT-Charlie	57897	NM_001201482	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.004732	0.346457	
chunk0075_130_1	chr16	50161786	50162245	+	0	NA	intron (NM_001040284, intron 2 of 12)	L1MD2|LINE|L1	9097	NM_001040284	64282	Hs.514342	NM_022447	ENSG00000121274	TENT4B	PAPD5|TRF4-2|TUT3	terminal nucleotidyltransferase 4B	protein-coding	0.006536	0.365217	
chunk0141_65_1	chr4	77835243	77835442	+	0	NA	Intergenic	Intergenic	-15952	NM_144571	246175	Hs.592519	NM_144571	ENSG00000138767	CNOT6L	CCR4b	CCR4-NOT transcription complex subunit 6 like	protein-coding	0.005025	0.385000	
chunk0173_112_1	chr6	143490909	143491165	+	0	NA	TTS (NM_003630)	TTS (NM_003630)	20846	NM_032020	2519	Hs.17680	NM_032020	ENSG00000001036	FUCA2	dJ20N2.5	alpha-L-fucosidase 2	protein-coding	0.015625	0.505837	
chunk0032_382_1	chr11	11444362	11444561	+	0	NA	intron (NM_198516, intron 2 of 10)	L2b|LINE|L2	-91104	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.040201	0.520000	
chunk0044_267_1	chr12	32384052	32384358	+	0	NA	Intergenic	Intergenic	-101767	NM_001304481	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.013072	0.384365	127(TAGAACATGGTGTTCT,-,0.00),128(AGAACATGGTGTTCTA,+,0.00)
chunk0183_162_1	chr7	105975991	105976468	+	0	NA	intron (NM_152750, intron 2 of 18)	MIR|SINE|MIR	13018	NM_152750	222256	Hs.150120	NM_152750	ENSG00000128536	CDHR3	CDH28	cadherin related family member 3	protein-coding	0.012579	0.464435	
chunk0188_353_1	chr8	17923409	17923834	+	0	NA	intron (NM_001315508, intron 1 of 35)	CpG	764	NM_001315508	5108	Hs.491148	NM_006197	ENSG00000078674	PCM1	PTC4|RET/PCM-1	pericentriolar material 1	protein-coding	0.058824	0.603286	
chunk0205_448_1	chr9	115484878	115485234	+	0	NA	Intergenic	L1ME4b|LINE|L1	259183	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.008427	0.383754	
chunk0150_262_1	chr5	36522529	36522839	+	0	NA	Intergenic	Intergenic	-83671	NM_001166695	6507	Hs.481918	NM_004172	ENSG00000079215	SLC1A3	EA6|EAAT1|GLAST|GLAST1	solute carrier family 1 member 3	protein-coding	0.003226	0.469453	141(GAGAACATAGTGTCAT,-,0.00),142(AGAACATAGTGTCATT,+,0.00)
chunk0129_20_1	chr3	117076328	117076668	+	0	NA	Intergenic	Intergenic	155067	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.005882	0.372434	
chunk0162_361_1	chr6	7190135	7190652	+	0	NA	intron (NM_001003698, intron 6 of 11)	MIR|SINE|MIR	82540	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.009671	0.351351	
chunk0073_129_1	chr16	4912321	4912884	+	0	NA	intron (NM_002705, intron 1 of 21)	intron (NM_002705, intron 1 of 21)	24533	NM_002705	5493	Hs.192233	NM_002705	ENSG00000118898	PPL	-	periplakin	protein-coding	0.028419	0.455674	
chunk0197_268_1	chr8	123749533	123749747	+	0	NA	Intergenic	Intergenic	-12233	NM_004306	312	Hs.181107	NM_004306	ENSG00000104537	ANXA13	ANX13|ISA	annexin A13	protein-coding	0.014019	0.418605	
chunk0145_454_1	chr4	153838549	153839029	+	0	NA	Intergenic	MIR|SINE|MIR	-49713	NM_003013	6423	Hs.481022	NM_003013	ENSG00000145423	SFRP2	FRP-2|SARP1|SDF-5	secreted frizzled related protein 2	protein-coding	0.006250	0.417879	
chunk0023_191_1	chr10	25100108	25100543	+	0	NA	Intergenic	MER97b|DNA|hAT-Tip100	-12733	NR_120649	101929025	Hs.553324	NR_120649	ENSG00000231422	LINC01516	-	long intergenic non-protein coding RNA 1516	ncRNA	0.011494	0.350917	
chunk0043_159_1	chr12	16524472	16524693	+	0	NA	Intergenic	Intergenic	80797	NM_001243611	55885	Hs.504908	NM_018640	ENSG00000048540	LMO3	RBTN3|RBTNL2|RHOM3|Rhom-3	LIM domain only 3	protein-coding	0.000000	0.391892	
chunk0041_175_1	chr11	126214537	126215237	+	0	NA	intron (NM_024556, intron 1 of 8)	intron (NM_024556, intron 1 of 8)	3163	NM_024556	79607	Hs.276315	NM_024556	ENSG00000197798	FAM118B	-	family with sequence similarity 118 member B	protein-coding	0.011429	0.372325	
chunk0029_423_1	chr10	109988832	109989325	+	0	NA	intron (NR_038943, intron 2 of 4)	L1ME3A|LINE|L1	-16890	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.012170	0.417004	
chunk0163_142_1	chr6	10747328	10747535	+	0	NA	promoter-TSS (NM_001286489)	promoter-TSS (NM_001286489)	-328	NM_001286489	81853	Hs.95600	NM_030969	ENSG00000137210	TMEM14B	-	transmembrane protein 14B	protein-coding	0.033816	0.576923	
chunk0056_341_1	chr13	91361783	91362386	+	0	NA	Intergenic	Intergenic	10770	NR_029508	407048	Hs.24115	NR_029508	ENSG00000283705	MIR92A1	C13orf25|MIR17HG|MIR92-1|MIRH1|MIRHG1|MIRN92-1|MIRN92A-1|MIRN92A1|miRNA92-1|mir-92a-1	microRNA 92a-1	ncRNA	0.001658	0.331126	
chunk0068_85_1	chr15	52011427	52012241	+	0	NA	Intergenic	UCON40|Unknown|Unknown	-7380	NM_002748	5597	Hs.411847	NM_002748	ENSG00000069956	MAPK6	ERK3|HsT17250|PRKM6|p97MAPK	mitogen-activated protein kinase 6	protein-coding	0.004914	0.404908	
chunk0190_89_1	chr8	30108987	30109584	+	0	NA	intron (NM_001128208, intron 3 of 3)	intron (NM_001128208, intron 3 of 3)	13879	NM_015344	23484	Hs.146585	NM_015344	ENSG00000104660	LEPROTL1	HSPC112|Vps55|my047	leptin receptor overlapping transcript like 1	protein-coding	0.011725	0.364548	
chunk0111_395_1	chr20	34190701	34191265	+	0	NA	Intergenic	Intergenic	-69382	NM_001672	434	Hs.659995	NM_001672	ENSG00000101440	ASIP	AGSW|AGTI|AGTIL|ASP|SHEP9	agouti signaling protein	protein-coding	0.005319	0.483186	
chunk0175_358_1	chr6	167750895	167751440	+	0	NA	Intergenic	Intergenic	45692	NR_026773	26238	Hs.520583	NM_014356	ENSG00000146521	LINC01558	C6orf123|HGC6.2|LINC01557|dJ431P23.4	long intergenic non-protein coding RNA 1558	ncRNA	0.012844	0.525641	
chunk0066_229_1	chr15	34101776	34101975	+	0	NA	promoter-TSS (NM_020154)	promoter-TSS (NM_020154)	-23	NM_020154	56851	Hs.160565	NM_020154	ENSG00000134153	EMC7	C11orf3|C15orf24|HT022|ORF1-FL1	ER membrane protein complex subunit 7	protein-coding	0.075377	0.660000	
chunk0121_130_1	chr3	18111426	18111655	+	0	NA	intron (NM_001257177, intron 4 of 4)	intron (NM_001257177, intron 4 of 4)	148968	NM_001257177									0.008734	0.304348	
chunk0133_196_1	chr3	170781148	170781347	+	0	NA	Intergenic	Intergenic	89009	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.000000	0.415000	
chunk0027_80_1	chr10	73425970	73426326	+	0	NA	exon (NM_001024593, exon 5 of 7)	exon (NM_001024593, exon 5 of 7)	7413	NM_001024593	118490	Hs.631823	NM_001024593	ENSG00000166343	MSS51	ZMYND17	MSS51 mitochondrial translational activator	protein-coding	0.016854	0.543417	
chunk0182_341_1	chr7	99325769	99325972	+	0	NA	promoter-TSS (NM_001190996)	promoter-TSS (NM_001190996)	-3	NM_006409	10552	Hs.124126	NM_006409	ENSG00000241685	ARPC1A	Arc40|HEL-68|HEL-S-307|SOP2Hs|SOP2L	actin related protein 2/3 complex subunit 1A	protein-coding	0.152709	0.725490	
chunk0080_311_1	chr17	31843079	31843402	+	0	NA	Intergenic	Intergenic	16067	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.015480	0.530864	
chunk0044_345_1	chr12	38610613	38611379	+	0	NA	Intergenic	Intergenic	294241	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.002611	0.308996	
chunk0010_353_1	chr1	118699819	118700166	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	289564	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.008646	0.387931	
chunk0025_105_1	chr10	50621837	50622348	+	0	NA	intron (NM_147156, intron 1 of 10)	(TGCT)n|Simple_repeat|Simple_repeat	1885	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.031311	0.564453	
chunk0170_202_1	chr6	112441509	112442180	+	0	NA	Intergenic	Intergenic	94514	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.001490	0.346726	311(AAGTACAGAATGTACT,-,0.00),312(AGTACAGAATGTACTG,+,0.00)
chunk0172_348_1	chr6	138972343	138972542	+	0	NA	intron (NM_001128617, intron 1 of 18)	intron (NM_001128617, intron 1 of 18)	15819	NM_001128617	85021	Hs.334603	NM_031922	ENSG00000135597	REPS1	NBIA7|RALBP1	RALBP1 associated Eps domain containing 1	protein-coding	0.005025	0.385000	9(AGGAACACACAGTCCC,-,0.00),10(GGAACACACAGTCCCT,+,0.00)
chunk0080_368_1	chr17	33093249	33093753	+	0	NA	intron (NM_183377, intron 2 of 9)	intron (NM_183377, intron 2 of 9)	101637	NM_173847	124912	Hs.434112	NM_173847	ENSG00000141316	SPACA3	ALLP17|CT54|LYC3|LYZC|LYZL3|SLLP1	sperm acrosome associated 3	protein-coding	0.005952	0.463366	
chunk0036_288_1	chr11	65468918	65469174	+	0	NA	Intergenic	Intergenic	24588	NR_030343	693197		NR_030343	ENSG00000283791	MIR612	MIRN612|hsa-mir-612	microRNA 612	ncRNA	0.011719	0.568093	
chunk0115_313_1	chr21	28633568	28634098	+	0	NA	Intergenic	Intergenic	94515	NR_026553	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.020755	0.423729	
chunk0189_39_1	chr8	19802314	19802744	+	0	NA	Intergenic	LTR28B|LTR|ERV1	-14878	NM_018142	55174	Hs.512627	NM_018142	ENSG00000104613	INTS10	C8orf35|INT10	integrator complex subunit 10	protein-coding	0.013953	0.552204	
chunk0076_114_1	chr16	66516613	66517352	+	0	NA	intron (NM_001271935, intron 6 of 7)	intron (NM_001271935, intron 6 of 7)	32843	NM_001272050	7084	Hs.512619	NM_004614	ENSG00000166548	TK2	MTDPS2|MTTK|PEOB3|SCA31	thymidine kinase 2	protein-coding	0.018945	0.563514	
chunk0024_110_1	chr10	34698898	34699384	+	0	NA	intron (NM_019619, intron 1 of 24)	Tigger20a|DNA|TcMar-Tigger	116184	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.006173	0.398357	
chunk0167_293_1	chr6	70950448	70950941	+	0	NA	intron (NM_080742, intron 1 of 3)	intron (NM_080742, intron 1 of 3)	6391	NM_080742	135152	Hs.713609	NM_080742	ENSG00000112309	B3GAT2	GLCATS	beta-1,3-glucuronyltransferase 2	protein-coding	0.010142	0.348178	
chunk0138_290_1	chr4	40849347	40849808	+	0	NA	intron (NM_001166051, intron 1 of 6)	intron (NM_001166051, intron 1 of 6)	7578	NM_001166051	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.004338	0.396104	
chunk0098_117_1	chr2	68548292	68548957	+	0	NA	intron (NM_173545, intron 8 of 9)	intron (NM_173545, intron 8 of 9)	81065	NM_173545	200558	Hs.720369	NM_173545	ENSG00000169621	APLF	APFL|C2orf13|PALF|Xip1|ZCCHH1	aprataxin and PNKP like factor	protein-coding	0.003008	0.315315	
chunk0202_324_1	chr9	78358413	78358729	+	0	NA	Intergenic	MER52A|LTR|ERV1	61496	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.031646	0.586751	
chunk0109_323_1	chr20	9174538	9175111	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	-42566	NM_182797	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.003490	0.339721	
chunk0022_425_1	chr10	19184051	19184309	+	0	NA	intron (NM_001142308, intron 14 of 39)	LTR86A1|LTR|ERVL	135409	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.003876	0.413127	
chunk0168_326_1	chr6	92558933	92559328	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	860452	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.005063	0.353535	184(CAGTACATACTGTACT,-,0.00),185(AGTACATACTGTACTA,+,0.00)
chunk0039_140_1	chr11	98598728	98599238	+	0	NA	Intergenic	L1M1|LINE|L1	-421993	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.309198	207(AAGTACAATGTGTCTT,-,0.00)
chunk0040_414_1	chr11	121118643	121119026	+	0	NA	intron (NM_005422, intron 6 of 22)	intron (NM_005422, intron 6 of 22)	16168	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.005222	0.455729	
chunk0063_214_1	chr14	81418344	81418900	+	0	NA	intron (NM_033104, intron 1 of 5)	intron (NM_033104, intron 1 of 5)	8590	NM_033104	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.007194	0.391382	
chunk0060_348_1	chr14	52073391	52073641	+	0	NA	Intergenic	Intergenic	-4288	NM_007361	22795	Hs.369840	NM_007361	ENSG00000087303	NID2	NID-2	nidogen 2	protein-coding	0.004000	0.394422	
chunk0123_255_1	chr3	45847445	45847706	+	0	NA	intron (NM_001276378, intron 3 of 11)	Tigger2|DNA|TcMar-Tigger	-5417	NR_075080	54585	Hs.30824	NM_020347	ENSG00000163818	LZTFL1	BBS17	leucine zipper transcription factor like 1	protein-coding	0.003831	0.423664	
chunk0121_279_1	chr3	23517472	23518213	+	0	NA	intron (NM_152653, intron 4 of 5)	intron (NM_152653, intron 4 of 5)	-288051	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.004049	0.328841	
chunk0007_146_1	chr1	79474087	79474407	+	0	NA	Intergenic	Intergenic	-467437	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.006250	0.314642	
chunk0066_144_1	chr15	31397892	31398479	+	0	NA	intron (NM_001302461, intron 1 of 1).2	intron (NM_001302461, intron 1 of 1).2	71330	NM_001302461	51621	Hs.376443	NM_015995	ENSG00000169926	KLF13	BTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel like factor 13	protein-coding	0.025554	0.569728	263(AAGCACAGGATGCTCC,-,0.00),264(AGCACAGGATGCTCCT,+,0.00)
chunk0142_444_1	chr4	105361114	105361313	+	0	NA	Intergenic	Intergenic	-8332	NR_126420	104384744	Hs.624109	NR_126420		TET2-AS1	-	TET2 antisense RNA 1	ncRNA	0.000000	0.480000	124(TGGACAGAATGCTCCT,+,0.00)
chunk0211_394_1	chrX	128494492	128495225	+	0	NA	Intergenic	Intergenic	-442455	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.004093	0.351499	
chunk0062_202_1	chr14	69998035	69998553	+	0	NA	intron (NM_022137, intron 7 of 11)	intron (NM_022137, intron 7 of 11)	81923	NM_182936	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.005792	0.396917	314(GAGAACAGCATCTTCC,-,0.00),315(AGAACAGCATCTTCCC,+,0.00)
chunk0199_230_1	chr9	5366875	5367210	+	0	NA	intron (NM_018465, intron 3 of 5)	(AC)n|Simple_repeat|Simple_repeat	-27169	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.002985	0.357143	
chunk0196_295_1	chr8	109603271	109603766	+	0	NA	intron (NM_017786, intron 5 of 8)	intron (NM_017786, intron 5 of 8)	39672	NM_001099756	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.002020	0.419355	266(GTGTACTCAGTGTTCT,-,0.00),267(TGTACTCAGTGTTCTC,+,0.00),307(CAGCCCACAATGTTCT,-,0.00),308(AGCCCACAATGTTCTG,+,0.00)
chunk0067_152_1	chr15	43792144	43792422	+	0	NA	promoter-TSS (NM_001199878)	promoter-TSS (NM_001199878)	-94	NM_001199878	10169	Hs.424126	NM_005770	ENSG00000140264	SERF2	4F5REL|FAM2C|H4F5REL|HsT17089	small EDRK-rich factor 2	protein-coding	0.100719	0.666667	
chunk0028_102_1	chr10	84317693	84318193	+	0	NA	Intergenic	L1M5|LINE|L1	-10646	NM_001284240	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.000000	0.299401	
chunk0034_398_1	chr11	37208101	37208601	+	0	NA	Intergenic	L1PA7|LINE|L1	-610072	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.004000	0.373253	166(GGTACATTGTGTCTTT,+,0.00)
chunk0210_469_1	chrX	107574302	107574631	+	0	NA	intron (NM_032428, intron 13 of 15)	MER58A|DNA|hAT-Charlie	-28645	NR_046750	100874122	Hs.600967	NR_046750	ENSG00000227610	FRMPD3-AS1	-	FRMPD3 antisense RNA 1	ncRNA	0.003040	0.412121	
chunk0158_198_1	chr5	127997471	127997993	+	0	NA	Intergenic	Intergenic	85342	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.007663	0.466539	
chunk0200_381_1	chr9	26721876	26722165	+	0	NA	Intergenic	Intergenic	170808	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.003460	0.362069	
chunk0176_29_1	chr7	9324686	9325037	+	0	NA	Intergenic	Intergenic	-309409	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.002849	0.394886	
chunk0014_260_1	chr1	180137821	180138289	+	0	NA	Intergenic	L1MEf|LINE|L1	-16778	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.004274	0.400853	
chunk0174_206_1	chr6	160278799	160279269	+	0	NA	Intergenic	L2a|LINE|L2	-20103	NM_003058	6582	Hs.436385	NM_003058	ENSG00000112499	SLC22A2	OCT2	solute carrier family 22 member 2	protein-coding	0.023404	0.524416	179(CAGCACACCCTGCTCC,-,0.00),180(AGCACACCCTGCTCCA,+,0.00),225(CAGAACACTTTGTTCC,-,0.00),226(AGAACACTTTGTTCCC,+,0.00)
chunk0191_10_1	chr8	42471155	42471446	+	0	NA	intron (NM_006749, intron 2 of 10)	intron (NM_006749, intron 2 of 10)	30160	NM_001257180	6575	Hs.653173	NM_006749	ENSG00000168575	SLC20A2	GLVR-2|GLVR2|IBGC1|IBGC3|MLVAR|PIT-2|PIT2|RAM1|Ram-1	solute carrier family 20 member 2	protein-coding	0.030928	0.503425	
chunk0042_174_1	chr12	4707262	4707816	+	0	NA	intron (NR_110112, intron 1 of 3)	L1MCa|LINE|L1	12563	NR_110112	101929549	Hs.663336	NR_110112	ENSG00000255474	GAU1	GALNT8-DT	GALNT8 antisense upstream 1	ncRNA	0.003610	0.284685	
chunk0153_389_1	chr5	75236239	75236739	+	0	NA	intron (NM_001164443, intron 1 of 24)	intron (NM_001164443, intron 1 of 24)	389	NM_001164443	256006	Hs.482533	NM_001164443	ENSG00000145700	ANKRD31	-	ankyrin repeat domain 31	protein-coding	0.018000	0.508982	159(GGGAACAGACTGTGTT,-,0.00),160(GGAACAGACTGTGTTT,+,0.00)
chunk0071_48_1	chr15	79993825	79994030	+	0	NA	Intergenic	L2b|LINE|L2	-22626	NM_001114735	597	Hs.227817	NM_004049	ENSG00000140379	BCL2A1	ACC-1|ACC-2|ACC1|ACC2|BCL2L5|BFL1|GRS|HBPA1	BCL2 related protein A1	protein-coding	0.004878	0.475728	
chunk0165_370_1	chr6	38262155	38262385	+	0	NA	intron (NM_001099272, intron 8 of 10)	intron (NM_001099272, intron 8 of 10)	333797	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.004348	0.432900	
chunk0013_298_1	chr1	171210233	171210764	+	0	NA	3' UTR (NM_001460, exon 9 of 9)	3' UTR (NM_001460, exon 9 of 9)	25290	NM_001460	2327	Hs.144912	NM_001460	ENSG00000094963	FMO2	FMO1B1	flavin containing dimethylaniline monoxygenase 2	protein-coding	0.001883	0.362782	
chunk0104_130_1	chr2	173210251	173210863	+	0	NA	intron (NR_033882, intron 5 of 7)	intron (NR_033882, intron 5 of 7)	71479	NR_033882	339751	Hs.570083	NR_033882	ENSG00000238133	MAP3K20-AS1	MLK7-AS1	MAP3K20 antisense RNA 1	ncRNA	0.013072	0.407830	
chunk0075_279_1	chr16	53875338	53875826	+	0	NA	intron (NM_001080432, intron 5 of 8)	intron (NM_001080432, intron 5 of 8)	-163811	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.004098	0.329243	
chunk0020_96_1	chr1	232868768	232869312	+	0	NA	Intergenic	Intergenic	64148	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.011029	0.449541	
chunk0101_458_1	chr2	140230080	140230292	+	0	NA	Intergenic	Intergenic	356499	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.009434	0.399061	119(GGGGACAGAAAGTGCC,-,0.00),120(GGGACAGAAAGTGCCT,+,0.00)
chunk0136_169_1	chr4	6362961	6363171	+	0	NA	intron (NM_001206995, intron 6 of 9)	intron (NM_001206995, intron 6 of 9)	18804	NM_181876	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.038095	0.549763	62(CAGAACACCGTGTGAC,-,0.00)
chunk0012_225_1	chr1	160260968	160262559	+	0	NA	intron (NM_015726, intron 1 of 13)	intron (NM_015726, intron 1 of 13)	724	NR_028106	50717	Hs.632447	NM_015726	ENSG00000132716	DCAF8	GAN2|H326|WDR42A	DDB1 and CUL4 associated factor 8	protein-coding	0.038341	0.498744	
chunk0078_327_1	chr17	8602810	8603118	+	0	NA	intron (NM_001256095, intron 3 of 41)	intron (NM_001256095, intron 3 of 41)	27797	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.000000	0.346278	
chunk0150_174_1	chr5	34450421	34450733	+	0	NA	Intergenic	MER70C|LTR|ERVL	-205751	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.006410	0.482428	
chunk0121_360_1	chr3	24838270	24839007	+	0	NA	Intergenic	Intergenic	-317203	NR_039955									0.000000	0.346883	
chunk0156_378_1	chr5	112827104	112827537	+	0	NA	intron (NM_001127511, intron 10 of 13)	intron (NM_001127511, intron 10 of 13)	-33868	NM_001204196	6728	Hs.637001	NM_003135	ENSG00000153037	SRP19	-	signal recognition particle 19	protein-coding	0.004619	0.338710	
chunk0042_53_1	chr12	1795207	1795580	+	0	NA	intron (NM_172364, intron 36 of 37)	intron (NM_172364, intron 36 of 37)	-24874	NM_001163925	654429	Hs.585579	NM_001039029	ENSG00000166159	LRTM2	-	leucine rich repeats and transmembrane domains 2	protein-coding	0.037534	0.590909	
chunk0164_243_1	chr6	23308265	23308520	+	0	NA	Intergenic	Intergenic	738943	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007843	0.390625	
chunk0183_274_1	chr7	107563569	107564025	+	0	NA	promoter-TSS (NM_001270419)	promoter-TSS (NM_001270419)	-160	NR_073003	11062	Hs.97627	NM_181581	ENSG00000105865	DUS4L	DUS4|PP35	dihydrouridine synthase 4 like	protein-coding	0.061404	0.636761	
chunk0115_87_1	chr21	22258874	22259368	+	0	NA	Intergenic	Intergenic	160504	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.002024	0.303030	
chunk0100_253_1	chr2	113134109	113134398	+	0	NA	TTS (NM_000577)	TTS (NM_000577)	6692	NM_173842	3557	Hs.81134	NM_000577	ENSG00000136689	IL1RN	DIRA|ICIL-1RA|IL-1RN|IL-1ra|IL-1ra3|IL1F3|IL1RA|IRAP|MVCD4	interleukin 1 receptor antagonist	protein-coding	0.003460	0.451724	
chunk0012_183_1	chr1	159421888	159422276	+	0	NA	Intergenic	L1MA4A|LINE|L1	-17640	NM_012351	26476	Hs.532661	NM_012351	ENSG00000196184	OR10J1	HGMP07J|HSHGMP07J	olfactory receptor family 10 subfamily J member 1	protein-coding	0.015464	0.573265	
chunk0049_218_1	chr12	93390079	93390404	+	0	NA	intron (NM_001301023, intron 1 of 4)	intron (NM_001301023, intron 1 of 4)	11691	NM_001301022	11163	Hs.506325	NM_019094	ENSG00000173598	NUDT4	DIPP-2B|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P|NUDT4B	nudix hydrolase 4	protein-coding	0.015385	0.374233	
chunk0092_100_1	chr19	23254432	23254967	+	0	NA	TTS (NR_103742)	TTS (NR_103742)	-4329	NR_045525									0.005607	0.416045	
chunk0035_244_1	chr11	46140684	46141070	+	0	NA	Intergenic	L1ME4a|LINE|L1	-19443	NM_016621	51317	Hs.502458	NM_016621	ENSG00000135365	PHF21A	BHC80|BM-006	PHD finger protein 21A	protein-coding	0.010363	0.315245	
chunk0001_295_1	chr1	9001694	9002742	+	0	NA	Intergenic	LTR5B|LTR|ERVK	24127	NM_207420	155184	Hs.531239	NM_207420	ENSG00000197241	SLC2A7	GLUT-7|GLUT7	solute carrier family 2 member 7	protein-coding	0.020992	0.499523	402(AGGGACACAATGCACT,-,0.00),403(GGGACACAATGCACTG,+,0.00)
chunk0008_211_1	chr1	93629010	93629470	+	0	NA	intron (NM_003567, intron 3 of 11)	intron (NM_003567, intron 3 of 11)	-15095	NM_001261410	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.015217	0.431670	230(GGGCACACGCTGTCTC,-,0.00),231(GGCACACGCTGTCTCC,+,0.00)
chunk0162_131_1	chr6	2989531	2989730	+	0	NA	non-coding (NR_026855, exon 2 of 2)	non-coding (NR_026855, exon 2 of 2)	1663	NR_026855	401232	Hs.720158	NM_207495		LINC01011	-	long intergenic non-protein coding RNA 1011	ncRNA	0.025126	0.450000	
chunk0014_79_1	chr1	176499658	176500245	+	0	NA	intron (NM_020318, intron 1 of 22)	intron (NM_020318, intron 1 of 22)	36780	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.001704	0.362245	283(GAGGTCATCATGTTCT,-,0.00),284(AGGTCATCATGTTCTT,+,0.00),312(GAGAACAGCCTGCTCT,-,0.00),313(AGAACAGCCTGCTCTT,+,0.00)
chunk0141_74_1	chr4	78105079	78105713	+	0	NA	intron (NM_025074, intron 2 of 73)	intron (NM_025074, intron 2 of 73)	47826	NM_025074	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.006309	0.403150	
chunk0157_119_1	chr5	116969793	116970087	+	0	NA	Intergenic	Intergenic	-207731	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.006803	0.345763	
chunk0198_146_1	chr8	132919542	132919809	+	0	NA	intron (NM_003235, intron 21 of 47)	MER20|DNA|hAT-Charlie	52715	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.000000	0.455224	
chunk0096_458_1	chr2	40113779	40114486	+	0	NA	3' UTR (NM_001112801, exon 8 of 8)	3' UTR (NM_001112801, exon 8 of 8)	196498	NR_038441	100128590	Hs.744988	NR_038441	ENSG00000227028	SLC8A1-AS1	-	SLC8A1 antisense RNA 1	ncRNA	0.008487	0.412429	318(GAGAACAGTATGTACT,-,0.00),319(AGAACAGTATGTACTA,+,0.00)
chunk0155_2_1	chr5	90697747	90698162	+	0	NA	intron (NR_003149, intron 34 of 89)	MIR1_Amn|SINE|MIR	139154	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.007229	0.314904	
chunk0036_422_1	chr11	68374308	68374685	+	0	NA	intron (NM_001291902, intron 5 of 22)	intron (NM_001291902, intron 5 of 22)	61887	NM_002335	4041	Hs.6347	NM_002335	ENSG00000162337	LRP5	BMND1|EVR1|EVR4|HBM|LR3|LRP-5|LRP-7|LRP7|OPPG|OPS|OPTA1|PCLD4|VBCH2	LDL receptor related protein 5	protein-coding	0.029178	0.462963	
chunk0174_213_1	chr6	160374990	160375754	+	0	NA	intron (NM_021977, intron 1 of 10)	intron (NM_021977, intron 1 of 10)	26999	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.002618	0.411765	
chunk0057_122_1	chr13	99365053	99365271	+	0	NA	intron (NM_001144072, intron 7 of 8)	L1ME3Cz|LINE|L1	9031	NR_030353	693208		NR_030353	ENSG00000207719	MIR623	MIRN623|hsa-mir-623	microRNA 623	ncRNA	0.000000	0.296804	
chunk0095_420_1	chr2	24754332	24755050	+	0	NA	intron (NM_147223, intron 18 of 21)	L2a|LINE|L2	-38615	NM_001199803	79172	Hs.731569	NM_024322	ENSG00000138092	CENPO	CENP-O|ICEN-36|MCM21R	centromere protein O	protein-coding	0.006964	0.379694	
chunk0054_435_1	chr13	51324069	51324923	+	0	NA	Intergenic	(AAAG)n|Simple_repeat|Simple_repeat	-16536	NM_001101320	647174	Hs.685891	NM_001101320	ENSG00000253309	SERPINE3	-	serpin family E member 3	protein-coding	0.010539	0.479532	
chunk0004_196_1	chr1	46406203	46406476	+	0	NA	exon (NM_001441, exon 7 of 15)	exon (NM_001441, exon 7 of 15)	12072	NM_001441	2166	Hs.720143	NM_001441	ENSG00000117480	FAAH	FAAH-1|PSAB	fatty acid amide hydrolase	protein-coding	0.029304	0.653285	
chunk0065_188_1	chr14	99980342	99981178	+	0	NA	Intergenic	Intergenic	-84654	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.013158	0.427718	
chunk0048_357_1	chr12	85497569	85497873	+	0	NA	Intergenic	Intergenic	217463	NM_006982	8092	Hs.41683	NM_006982	ENSG00000180318	ALX1	CART1|FND3|HEL23	ALX homeobox 1	protein-coding	0.016447	0.354098	
chunk0043_280_1	chr12	21116522	21116862	+	0	NA	Intergenic	L1M1|LINE|L1	-14502	NM_006446	10599	Hs.449738	NM_006446	ENSG00000134538	SLCO1B1	HBLRR|LST-1|LST1|OATP-C|OATP1B1|OATP2|OATPC|SLC21A6	solute carrier organic anion transporter family member 1B1	protein-coding	0.000000	0.269795	101(TGGCACATGTTGTCCC,-,0.00),102(GGCACATGTTGTCCCT,+,0.00)
chunk0184_263_1	chr7	118253192	118253853	+	0	NA	Intergenic	Intergenic	28864	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.003026	0.330816	
chunk0090_128_1	chr18	71830889	71831551	+	0	NA	Intergenic	Intergenic	-48994	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.001511	0.361991	280(GACACAACCTGTGCCT,+,0.00)
chunk0144_199_1	chr4	133836230	133836880	+	0	NA	Intergenic	L1MA4|LINE|L1	365193	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.006154	0.333333	
chunk0115_306_1	chr21	28537261	28537666	+	0	NA	Intergenic	Intergenic	-1855	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.002469	0.334975	91(GAGGACTCAATGTCCA,-,0.00)
chunk0075_360_1	chr16	56200969	56201322	+	0	NA	intron (NM_020988, intron 2 of 8)	L2c|LINE|L2	-6620	NR_026889	26077	Hs.721567	NR_026889	ENSG00000261439	DKFZP434H168	-	uncharacterized LOC26077	ncRNA	0.002833	0.474576	
chunk0124_151_1	chr3	54772341	54772742	+	0	NA	intron (NM_018398, intron 13 of 37)	intron (NM_018398, intron 13 of 37)	128714	NR_046666	100874237	Hs.570583	NR_046666	ENSG00000243715	CACNA2D3-AS1	-	CACNA2D3 antisense RNA 1	ncRNA	0.004988	0.353234	
chunk0085_310_1	chr18	8229109	8229310	+	0	NA	intron (NM_001105244, intron 14 of 32)	L2a|LINE|L2	137825	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.009950	0.420792	
chunk0011_149_1	chr1	147496493	147496736	+	0	NA	intron (NR_038423, intron 3 of 3)	intron (NR_038423, intron 3 of 3)	21261	NR_038423	100289211	Hs.323484	NR_038423	ENSG00000278811	LINC00624	-	long intergenic non-protein coding RNA 624	ncRNA	0.000000	0.413934	
chunk0050_444_1	chr12	110488640	110489241	+	0	NA	intron (NM_013300, intron 6 of 6)	intron (NM_013300, intron 6 of 6)	13200	NM_001282151	51699	Hs.600114	NM_016226	ENSG00000111237	VPS29	DC15|DC7|PEP11	VPS29 retromer complex component	protein-coding	0.003328	0.360465	
chunk0084_305_1	chr17	80068372	80069210	+	0	NA	intron (NM_017950, intron 10 of 19)	MamRep605|LTR?|LTR?	-30037	NR_039607	100616121		NR_039607	ENSG00000265561	MIR1268B	-	microRNA 1268b	ncRNA	0.022673	0.501788	
chunk0034_156_1	chr11	30322822	30323021	+	0	NA	promoter-TSS (NM_152316)	promoter-TSS (NM_152316)	-178	NM_152316	120534	Hs.502208	NM_152316	ENSG00000152219	ARL14EP	ARF7EP|C11orf46|dJ299F11.1	ADP ribosylation factor like GTPase 14 effector protein	protein-coding	0.045226	0.550000	
chunk0014_379_1	chr1	182703561	182704098	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-30897	NM_033345	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.007449	0.347584	
chunk0138_76_1	chr4	34921181	34921483	+	0	NA	Intergenic	Intergenic	-881439	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.003311	0.333333	
chunk0142_301_1	chr4	100495036	100495815	+	0	NA	intron (NM_016242, intron 1 of 11)	intron (NM_016242, intron 1 of 11)	22668	NM_001159694	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.003851	0.300000	
chunk0038_236_1	chr11	87120994	87121493	+	0	NA	intron (NM_001168724, intron 4 of 13)	intron (NM_001168724, intron 4 of 13)	83399	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.002004	0.364000	200(GTGCACAGGGAGTCCT,-,0.00),201(TGCACAGGGAGTCCTG,+,0.00)
chunk0039_52_1	chr11	96193277	96194223	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-147688	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.009514	0.379092	
chunk0165_269_1	chr6	35918657	35919243	+	0	NA	intron (NR_034069, intron 2 of 15)	intron (NR_034069, intron 2 of 15)	2230	NM_003137	6732	Hs.443861	NM_003137	ENSG00000096063	SRPK1	SFRSK1	SRSF protein kinase 1	protein-coding	0.006826	0.320273	
chunk0152_414_1	chr5	65497427	65497836	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-15754	NM_197941	11174	Hs.482291	NM_197941	ENSG00000049192	ADAMTS6	ADAM-TS 6|ADAM-TS6|ADAMTS-6	ADAM metallopeptidase with thrombospondin type 1 motif 6	protein-coding	0.007335	0.424390	
chunk0027_137_1	chr10	74433108	74433379	+	0	NA	intron (NM_001202450, intron 6 of 9)	intron (NM_001202450, intron 6 of 9)	96081	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.000000	0.316176	
chunk0040_164_1	chr11	113860276	113860505	+	0	NA	intron (NM_020886, intron 1 of 24)	intron (NM_020886, intron 1 of 24)	15180	NM_001301029	57646	Hs.503891	NM_020886	ENSG00000048028	USP28	-	ubiquitin specific peptidase 28	protein-coding	0.004367	0.282609	
chunk0046_368_1	chr12	63294271	63294635	+	0	NA	Intergenic	Intergenic	-141643	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.002747	0.372603	
chunk0169_132_1	chr6	101144709	101144908	+	0	NA	Intergenic	LTR33|LTR|ERVL	-254177	NM_001166247	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.505000	
chunk0159_69_1	chr5	137326756	137327085	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	172409	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.006079	0.342424	
chunk0097_250_1	chr2	53778076	53778472	+	0	NA	intron (NM_001164165, intron 1 of 9)	MER57D|LTR|ERV1	8574	NM_001201965	51130	Hs.40763	NM_016115	ENSG00000115239	ASB3	ASB-3	ankyrin repeat and SOCS box containing 3	protein-coding	0.005051	0.329975	
chunk0113_64_1	chr20	50443008	50443258	+	0	NA	Intergenic	L1ME4b|LINE|L1	-67188	NM_002827	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.024000	0.454183	
chunk0205_141_1	chr9	108194060	108194592	+	0	NA	Intergenic	L2a|LINE|L2	661669	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.000000	0.410882	
chunk0022_97_1	chr10	9606472	9606980	+	0	NA	Intergenic	L1MC|LINE|L1	-311133	NR_120635	101928272	Hs.650697	NR_120635		LOC101928272	-	uncharacterized LOC101928272	ncRNA	0.005906	0.330059	
chunk0130_293_1	chr3	136783848	136784121	+	0	NA	Intergenic	Intergenic	-31581	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.007326	0.434307	
chunk0033_279_1	chr11	19365448	19366253	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	15126	NM_001111018	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.002484	0.428040	
chunk0031_255_1	chr10	127190899	127191181	+	0	NA	intron (NM_001039762, intron 2 of 5)	intron (NM_001039762, intron 2 of 5)	5118	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.007092	0.487633	
chunk0034_392_1	chr11	36682665	36683418	+	0	NA	Intergenic	Intergenic	-84762	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.002656	0.347480	
chunk0199_393_1	chr9	13251606	13251937	+	0	NA	intron (NM_003829, intron 1 of 45)	intron (NM_003829, intron 1 of 45)	27793	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.006042	0.367470	
chunk0019_85_1	chr1	224503893	224504110	+	0	NA	Intergenic	Intergenic	-69702	NM_001115113	80232	Hs.497873	NM_025160	ENSG00000162923	WDR26	CDW2|GID7|MIP2|SKDEAS	WD repeat domain 26	protein-coding	0.009217	0.481651	
chunk0059_320_1	chr14	36482531	36482970	+	0	NA	intron (NM_001101341, intron 2 of 3)	LTR88b|LTR|Gypsy?	31035	NM_001101341	253970	Hs.509165	NM_001101341	ENSG00000229415	SFTA3	NANCI|SFTPH|SP-H|SPH	surfactant associated 3	ncRNA	0.002278	0.450000	
chunk0168_63_1	chr6	79272679	79273123	+	0	NA	Intergenic	Intergenic	-38163	NM_001201363	9324	Hs.77558	NM_004242	ENSG00000118418	HMGN3	PNAS-24|PNAS-25|TRIP7	high mobility group nucleosomal binding domain 3	protein-coding	0.002252	0.330337	
chunk0028_108_1	chr10	84362148	84362733	+	0	NA	intron (NM_001284240, intron 1 of 9)	intron (NM_001284240, intron 1 of 9)	33851	NM_018999	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.001709	0.360068	
chunk0211_10_1	chrX	107684837	107685228	+	0	NA	Intergenic	Intergenic	31449	NM_001015881	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.007673	0.525510	198(CAGGACTCCCAGTGCT,-,0.00),199(AGGACTCCCAGTGCTC,+,0.00)
chunk0108_444_1	chr2	238170133	238170903	+	0	NA	3' UTR (NM_030768, exon 12 of 12)	3' UTR (NM_030768, exon 12 of 12)	11510	NM_001291832	151176	Hs.24951	NM_152521	ENSG00000178752	ERFE	C1QTNF15|CTRP15|FAM132B	erythroferrone	protein-coding	0.024675	0.512322	
chunk0067_158_1	chr15	43975884	43976282	+	0	NA	intron (NM_001286491, intron 1 of 14)	L1M4|LINE|L1	-97912	NR_003571	728758	Hs.658099	NR_003571		PIN4P1	-	peptidylprolyl cis/trans isomerase, NIMA-interacting 4 pseudogene 1	pseudo	0.002513	0.308271	
chunk0115_247_1	chr21	27550189	27550851	+	0	NA	Intergenic	Intergenic	-171859	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.001511	0.307692	613(AAAACACAATGTTCAT,+,0.00)
chunk0143_134_1	chr4	109727963	109728611	+	0	NA	intron (NM_030821, intron 1 of 3)	L2a|LINE|L2	1799	NM_030821	81579	Hs.389452	NM_030821	ENSG00000123739	PLA2G12A	GXII|PLA2G12|ROSSY	phospholipase A2 group XIIA	protein-coding	0.012346	0.403698	
chunk0041_83_1	chr11	124256749	124257309	+	0	NA	Intergenic	Intergenic	7353	NR_045681	26494	Hs.448172	NM_001002905	ENSG00000197849	OR8G1	HSTPCR25|OR8G1P|TPCR25	olfactory receptor family 8 subfamily G member 1 (gene/pseudogene)	protein-coding	0.001786	0.326203	
chunk0205_49_1	chr9	106091253	106091460	+	0	NA	Intergenic	L1ME5|LINE|L1	396831	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.004831	0.346154	
chunk0045_439_1	chr12	53569199	53569691	+	0	NA	intron (NM_006856, intron 2 of 11)	L2c|LINE|L2	55461	NR_046221	100652999	Hs.633602	NR_046221	ENSG00000257550	LOC100652999	-	uncharacterized LOC100652999	ncRNA	0.000000	0.354970	
chunk0117_25_1	chr22	11471545	11471804	+	0	NA	Intergenic	L1MCa|LINE|L1	-425732	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.011583	0.438462	
chunk0169_311_1	chr6	106110085	106110560	+	0	NA	TTS (NM_001198)	TTS (NM_001198)	11460	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.014737	0.449580	
chunk0115_365_1	chr21	29875621	29876190	+	0	NA	intron (NM_175611, intron 1 of 15)	intron (NM_175611, intron 1 of 15)	64059	NM_175611	2897	Hs.664641	NM_000830	ENSG00000171189	GRIK1	EAA3|EEA3|GLR5|GLUR5|GluK1|gluR-5	glutamate ionotropic receptor kainate type subunit 1	protein-coding	0.003515	0.392982	
chunk0059_242_1	chr14	34700284	34700486	+	0	NA	Intergenic	Intergenic	13432	NM_021914	1073	Hs.180141	NM_021914	ENSG00000165410	CFL2	NEM7	cofilin 2	protein-coding	0.004950	0.369458	
chunk0209_451_1	chrX	65907179	65907556	+	0	NA	Intergenic	L1ME4c|LINE|L1	-111503	NR_029637	407008		NR_029637	ENSG00000284567	MIR223	MIRN223|miRNA223|mir-223	microRNA 223	ncRNA	0.000000	0.357143	
chunk0074_316_1	chr16	30570266	30570706	+	0	NA	intron (NM_001024683, intron 2 of 2)	intron (NM_001024683, intron 2 of 2)	1921	NM_145271	146542	Hs.301463	NM_145271	ENSG00000229809	ZNF688	-	zinc finger protein 688	protein-coding	0.015909	0.478458	
chunk0025_416_1	chr10	59704518	59705179	+	0	NA	intron (NM_194298, intron 1 of 5)	intron (NM_194298, intron 1 of 5)	5043	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.006051	0.379154	
chunk0084_366_1	chr17	81583956	81584434	+	0	NA	intron (NM_017921, intron 12 of 16)	intron (NM_017921, intron 12 of 16)	-6762	NR_130139	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.006276	0.384134	
chunk0060_220_1	chr14	49003886	49004149	+	0	NA	Intergenic	Intergenic	582399	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.268939	
chunk0043_420_1	chr12	25861280	25861479	+	0	NA	Intergenic	Intergenic	12700	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.005025	0.430000	
chunk0015_203_1	chr1	187454207	187454496	+	0	NA	intron (NR_132374, intron 1 of 2)	intron (NR_132374, intron 1 of 2)	10723	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006920	0.293103	
chunk0077_239_1	chr16	80703941	80704231	+	0	NA	intron (NM_152342, intron 1 of 6)	intron (NM_152342, intron 1 of 6)	100192	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.006897	0.463918	
chunk0191_394_1	chr8	57390466	57390831	+	0	NA	Intergenic	Intergenic	46861	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.013699	0.387978	
chunk0095_280_1	chr2	20094385	20094843	+	0	NA	Intergenic	Intergenic	-42586	NM_014713	9741	Hs.467807	NM_014713	ENSG00000068697	LAPTM4A	HUMORF13|LAPTM4|MBNT|Mtrp	lysosomal protein transmembrane 4 alpha	protein-coding	0.004367	0.481481	
chunk0008_174_1	chr1	92876322	92876727	+	0	NA	intron (NM_001252273, intron 1 of 4)	intron (NM_001252273, intron 1 of 4)	626	NM_001252271	388650	Hs.180946	NM_001006605	ENSG00000154511	DIPK1A	FAM69A	divergent protein kinase domain 1A	protein-coding	0.009877	0.384236	237(AGAACAAAGTGCACTT,+,0.00)
chunk0172_342_1	chr6	138834536	138835103	+	0	NA	intron (NM_001195037, intron 3 of 20)	intron (NM_001195037, intron 3 of 20)	38708	NM_001195037	345930	Hs.660603	NM_001077706	ENSG00000203734	ECT2L	ARHGEF32|C6orf91|FBXO49|LFDH|dJ509I19.2|dJ509I19.3|dJ509I19.5	epithelial cell transforming 2 like	protein-coding	0.010582	0.408451	
chunk0031_93_1	chr10	123561666	123562164	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-104440	NM_153442	2849	Hs.12751	NM_153442	ENSG00000154478	GPR26	-	G protein-coupled receptor 26	protein-coding	0.004016	0.400802	197(TGGATCACAGTGTGCC,-,0.00),198(GGATCACAGTGTGCCC,+,0.00),302(TAGAACAAAGAGTTCA,-,0.00)
chunk0036_282_1	chr11	65417762	65418158	+	0	NA	Intergenic	Intergenic	-4838	NR_028272	283131	Hs.523789	NR_002802	ENSG00000245532	NEAT1	LINC00084|NCRNA00084|TncRNA|VINC	nuclear paraspeckle assembly transcript 1	ncRNA	0.025253	0.629723	183(GAGGACAGGGTGTTCT,-,0.00),184(AGGACAGGGTGTTCTA,+,0.00)
chunk0155_195_1	chr5	94705617	94705928	+	0	NA	3' UTR (NM_001297777, exon 20 of 20)	3' UTR (NM_001297777, exon 20 of 20)	87086	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.000000	0.320513	199(TGGAACATTATGTTTT,-,0.00),200(GGAACATTATGTTTTT,+,0.00)
chunk0142_250_1	chr4	98918593	98919114	+	0	NA	intron (NM_001968, intron 1 of 6)	L1ME4b|LINE|L1	10239	NM_001130678	1977	Hs.13211	NM_001968	ENSG00000151247	EIF4E	AUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E	eukaryotic translation initiation factor 4E	protein-coding	0.000000	0.350575	189(AAAAACACAATGTGCC,-,0.00),190(AAAACACAATGTGCCA,+,0.00)
chunk0105_436_1	chr2	193733596	193734311	+	0	NA	Intergenic	Intergenic	-610316	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.000000	0.315642	354(AAGAACTTCATGTGCC,-,0.00),355(AGAACTTCATGTGCCT,+,0.00)
chunk0058_253_1	chr14	25681360	25681994	+	0	NA	Intergenic	MIR|SINE|MIR	-631380	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.006309	0.377953	401(AAGAACTGGTTGTTCA,-,0.00),402(AGAACTGGTTGTTCAT,+,0.00)
chunk0161_446_1	chr5	178710240	178710601	+	0	NA	Intergenic	LTR57|LTR|ERVL	20282	NM_005649	6940	Hs.484324	NM_005649	ENSG00000169131	ZNF354A	EZNF|HEL104|HKL1|KID-1|KID1|TCF17	zinc finger protein 354A	protein-coding	0.008310	0.491713	
chunk0167_330_1	chr6	72398289	72398516	+	0	NA	intron (NM_014989, intron 32 of 33)	intron (NM_014989, intron 32 of 33)	31672	NM_001168411	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.008811	0.359649	
chunk0166_261_1	chr6	47670131	47670767	+	0	NA	intron (NM_153839, intron 2 of 10)	intron (NM_153839, intron 2 of 10)	13859	NM_153839	222611	Hs.724860	NM_153839	ENSG00000164393	ADGRF2	GPR111|PGR20|hGPCR35	adhesion G protein-coupled receptor F2	protein-coding	0.009434	0.423862	
chunk0170_329_1	chr6	116211062	116211365	+	0	NA	intron (NM_152729, intron 6 of 11)	MLT1G|LTR|ERVL-MaLR	42885	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.009901	0.480263	
chunk0097_301_1	chr2	55857671	55858333	+	0	NA	Intergenic	Intergenic	66161	NM_001039349	2202	Hs.76224	NM_004105	ENSG00000115380	EFEMP1	DHRD|DRAD|FBLN3|FBNL|FIBL-3|MLVT|MTLV|S1-5	EGF containing fibulin extracellular matrix protein 1	protein-coding	0.003021	0.348416	
chunk0140_359_1	chr4	74158403	74159100	+	0	NA	intron (NM_001144978, intron 1 of 7)	intron (NM_001144978, intron 1 of 7)	639	NM_001144978	441024	Hs.721011	NM_001004346	ENSG00000163738	MTHFD2L	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like	protein-coding	0.030129	0.431232	
chunk0203_219_1	chr9	86787188	86787431	+	0	NA	Intergenic	Tigger20a|DNA|TcMar-Tigger	159880	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.008230	0.307377	
chunk0004_352_1	chr1	51283354	51283720	+	0	NA	Intergenic	MIR|SINE|MIR	14424	NM_001297667	22996	Hs.112949	NM_001080494	ENSG00000085831	TTC39A	C1orf34|DEME-6	tetratricopeptide repeat domain 39A	protein-coding	0.005464	0.359673	
chunk0163_304_1	chr6	14458852	14459641	+	0	NA	Intergenic	L1ME3A|LINE|L1	-173792	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.006337	0.367089	
chunk0120_391_1	chr3	12392057	12392644	+	0	NA	intron (NM_138711, intron 4 of 7)	intron (NM_138711, intron 4 of 7)	40848	NM_015869	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.010221	0.394558	386(GAGAACATTTAGTTCC,-,0.00),387(AGAACATTTAGTTCCA,+,0.00)
chunk0062_208_1	chr14	70359609	70359839	+	0	NA	promoter-TSS (NM_001204090)	promoter-TSS (NM_001204090)	7	NM_016468	51241	Hs.709581	NM_016468	ENSG00000133983	COX16	C14orf112|HSPC203|hCOX16	cytochrome c oxidase assembly factor COX16	protein-coding	0.073913	0.523810	
chunk0206_149_1	chr9	121372470	121372756	+	0	NA	Intergenic	Intergenic	-2309	NM_004099	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.006993	0.445993	
chunk0202_452_1	chr9	82454778	82455352	+	0	NA	Intergenic	Intergenic	466293	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.006969	0.393043	292(AAGCACTGCCTGTCCT,-,0.00),293(AGCACTGCCTGTCCTT,+,0.00)
chunk0172_220_1	chr6	136896924	136897536	+	0	NA	intron (NM_000288, intron 8 of 9)	intron (NM_000288, intron 8 of 9)	-25011	NM_001008783	340146	Hs.369703	NM_001008783	ENSG00000182747	SLC35D3	FRCL1	solute carrier family 35 member D3	protein-coding	0.001634	0.344209	
chunk0052_241_1	chr13	25978102	25978694	+	0	NA	intron (NM_001313741, intron 34 of 35)	intron (NM_001313741, intron 34 of 35)	72662	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.020270	0.433390	
chunk0106_225_1	chr2	202588721	202588943	+	0	NA	Intergenic	L1PA17|LINE|L1	-46346	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.031532	0.533632	
chunk0173_161_1	chr6	144297728	144298282	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	6268	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.007220	0.333333	
chunk0062_329_1	chr14	73401075	73401594	+	0	NA	intron (NM_001005743, intron 2 of 12)	L1MC1|LINE|L1	57246	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.005780	0.359615	
chunk0115_42_1	chr21	21238827	21239451	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	240824	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.009615	0.396800	
chunk0171_416_1	chr6	131458735	131459484	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-114095	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.004005	0.409333	
chunk0181_103_1	chr7	80512954	80513483	+	0	NA	Intergenic	Intergenic	-1292	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.005671	0.390566	
chunk0118_362_1	chr22	36386097	36386587	+	0	NA	intron (NM_002473, intron 1 of 40)	intron (NM_002473, intron 1 of 40)	1725	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.016327	0.517312	
chunk0044_5_1	chr12	26870732	26871168	+	0	NA	Intergenic	Intergenic	-37752	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.009174	0.480549	
chunk0073_450_1	chr16	19429127	19429668	+	0	NA	intron (NM_001261841, intron 1 of 21)	intron (NM_001261841, intron 1 of 21)	11701	NM_001261841	79838	Hs.115838	NM_024780	ENSG00000103534	TMC5	-	transmembrane channel like 5	protein-coding	0.007394	0.424354	
chunk0019_23_1	chr1	223700537	223700969	+	0	NA	promoter-TSS (NM_001146068)	promoter-TSS (NM_001146068)	-840	NM_001146068	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.013889	0.454965	187(GGGAACGCTTTGTGCC,-,0.00),188(GGAACGCTTTGTGCCT,+,0.00)
chunk0127_45_1	chr3	88958123	88958569	+	0	NA	Intergenic	Intergenic	-149178	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.002242	0.366890	
chunk0184_215_1	chr7	117364239	117364944	+	0	NA	intron (NM_130768, intron 12 of 12)	intron (NM_130768, intron 12 of 12)	-41302	NM_003391	7472	Hs.567356	NM_003391	ENSG00000105989	WNT2	INT1L1|IRP	Wnt family member 2	protein-coding	0.000000	0.396601	359(AGAAACATCCTGTGCT,-,0.00),360(GAAACATCCTGTGCTG,+,0.00)
chunk0163_441_1	chr6	17478455	17478948	+	0	NA	intron (NM_006366, intron 4 of 12)	intron (NM_006366, intron 4 of 12)	32564	NR_110855	101928491	Hs.622876	NR_110855		LOC101928491	-	uncharacterized LOC101928491	ncRNA	0.002028	0.388664	252(AGGAACACTCTGTCCT,-,0.00),253(GGAACACTCTGTCCTC,+,0.00)
chunk0140_241_1	chr4	71296969	71297409	+	0	NA	intron (NM_001098484, intron 3 of 25)	intron (NM_001098484, intron 3 of 25)	-41864	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.004545	0.467120	
chunk0132_239_1	chr3	158660517	158661140	+	0	NA	intron (NM_001308164, intron 10 of 18)	intron (NM_001308164, intron 10 of 18)	11865	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.009631	0.347756	
chunk0042_211_1	chr12	6058914	6059402	+	0	NA	intron (NM_000552, intron 13 of 51)	intron (NM_000552, intron 13 of 51)	65512	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.010246	0.456033	324(TGGCACATCCTGCCCC,-,0.00),325(GGCACATCCTGCCCCT,+,0.00)
chunk0052_359_1	chr12	127303066	127303651	+	0	NA	Intergenic	L1MA8|LINE|L1	36714	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.010256	0.390785	115(AGGAACTGTGCGTGCT,-,0.00)
chunk0153_408_1	chr5	75456984	75457352	+	0	NA	intron (NM_031361, intron 3 of 16)	intron (NM_031361, intron 3 of 16)	54461	NM_031361	10087	Hs.270437	NM_005713	ENSG00000113163	CERT1	CERT|CERTL|COL4A3BP|GPBP|MRD34|STARD11	ceramide transporter 1	protein-coding	0.005435	0.341463	133(TGAAACAGGCTGTTCT,-,0.00),134(GAAACAGGCTGTTCTC,+,0.00)
chunk0109_16_1	chr20	366450	366763	+	0	NA	Intergenic	L1ME4b|LINE|L1	-14023	NM_021158	57761	Hs.516826	NM_021158	ENSG00000101255	TRIB3	C20orf97|NIPK|SINK|SKIP3|TRB3	tribbles pseudokinase 3	protein-coding	0.006390	0.398089	
chunk0186_359_1	chr7	143887539	143888241	+	0	NA	intron (NM_001206938, intron 1 of 8)	L1ME3A|LINE|L1	-2517	NM_001206941	9747	Hs.735149	NM_014719	ENSG00000198420	TCAF1	FAM115A	TRPM8 channel associated factor 1	protein-coding	0.002849	0.332859	
chunk0015_216_1	chr1	187579254	187579526	+	0	NA	Intergenic	Intergenic	135762	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.011029	0.380952	
chunk0071_22_1	chr15	79059713	79059957	+	0	NA	intron (NM_001145648, intron 2 of 26)	intron (NM_001145648, intron 2 of 26)	31038	NM_001145648	5923	Hs.459035	NM_002891	ENSG00000058335	RASGRF1	CDC25|CDC25L|GNRP|GRF1|GRF55|H-GRF55|PP13187|ras-GRF1	Ras protein specific guanine nucleotide releasing factor 1	protein-coding	0.012295	0.355102	87(GAGAACATTGTGTCTC,-,0.00),88(AGAACATTGTGTCTCT,+,0.00)
chunk0164_317_1	chr6	25075698	25075989	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-33675	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.003436	0.332192	
chunk0053_56_1	chr13	27678089	27678464	+	0	NA	Intergenic	L1M5|LINE|L1	56497	NM_152705	51082	Hs.507584	NM_015972	ENSG00000186184	POLR1D	AC19|POLR1C|RPA16|RPA9|RPAC2|RPC16|RPO1-3|TCS2	RNA polymerase I and III subunit D	protein-coding	0.013333	0.468085	178(TTGTACAAAGTGTTCC,-,0.00),179(TGTACAAAGTGTTCCT,+,0.00)
chunk0185_200_1	chr7	128449986	128450350	+	0	NA	Intergenic	L1MEd|LINE|L1	-5662	NM_001098786	29923	Hs.706124	NM_013332	ENSG00000135245	HILPDA	C7orf68|HIG-2|HIG2	hypoxia inducible lipid droplet associated	protein-coding	0.005495	0.326027	
chunk0168_40_1	chr6	78391180	78391662	+	0	NA	Intergenic	Intergenic	-476123	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.006224	0.287785	
chunk0006_394_1	chr1	75319130	75319332	+	0	NA	intron (NM_001130058, intron 4 of 23)	intron (NM_001130058, intron 4 of 23)	184349	NM_001256114	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.004950	0.339901	
chunk0067_396_1	chr15	49172066	49172322	+	0	NA	intron (NM_002044, intron 1 of 9)	intron (NM_002044, intron 1 of 9)	2178	NM_002044	2585	Hs.122006	NM_002044	ENSG00000156958	GALK2	GK2	galactokinase 2	protein-coding	0.003906	0.280156	
chunk0099_55_1	chr2	84527576	84527892	+	0	NA	intron (NM_001370, intron 3 of 76)	intron (NM_001370, intron 3 of 76)	11279	NM_001370	1768	Hs.249972	NM_001370	ENSG00000115423	DNAH6	DNHL1|Dnahc6|HL-2|HL2	dynein axonemal heavy chain 6	protein-coding	0.003165	0.406940	
chunk0194_26_1	chr8	81653957	81654297	+	0	NA	Intergenic	L1M5|LINE|L1	32227	NM_005536	3612	Hs.656694	NM_005536	ENSG00000133731	IMPA1	IMP|IMPA|MRT59	inositol monophosphatase 1	protein-coding	0.005882	0.369501	273(CTGGACGCTCTGTCCC,-,0.00)
chunk0011_100_1	chr1	145917664	145918118	+	0	NA	intron (NR_073491, intron 1 of 3)	intron (NR_073491, intron 1 of 3)	567	NR_073493	8799	Hs.714608	NM_003846	ENSG00000131779	PEX11B	PEX11-BETA|PEX14B	peroxisomal biogenesis factor 11 beta	protein-coding	0.015419	0.518681	
chunk0083_150_1	chr17	65814536	65814931	+	0	NA	intron (NR_126542, intron 1 of 5)	intron (NR_126542, intron 1 of 5)	11810	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.340909	107(TAGCACAGGATGTGTC,-,0.00),108(AGCACAGGATGTGTCC,+,0.00)
chunk0173_411_1	chr6	150972804	150973602	+	0	NA	intron (NM_001242767, intron 20 of 27)	intron (NM_001242767, intron 20 of 27)	106870	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.007519	0.438048	393(AGAAGAGAGTGTGCTG,+,0.00)
chunk0171_403_1	chr6	131255270	131255708	+	0	NA	intron (NM_138633, intron 2 of 2)	intron (NM_138633, intron 2 of 2)	5330	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.004566	0.451025	
chunk0008_53_1	chr1	89308183	89308789	+	0	NA	Intergenic	L1ME3A|LINE|L1	-18124	NR_077244	729930	Hs.745054	NR_077244		LOC729930	-	chromosome 11 open reading frame 74 pseudogene	pseudo	0.001650	0.357496	
chunk0041_25_1	chr12	619271	619770	+	0	NA	intron (NM_016533, intron 1 of 3)	intron (NM_016533, intron 1 of 3)	-9107	NM_001294345	4815	Hs.655804	NM_016533	ENSG00000171840	NINJ2	-	ninjurin 2	protein-coding	0.008016	0.484000	276(AAGAACGCTGTGTCCT,-,0.00),277(AGAACGCTGTGTCCTC,+,0.00)
chunk0196_1_1	chr8	101393498	101393812	+	0	NA	Intergenic	MIR3|SINE|MIR	24762	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.015924	0.463492	
chunk0037_220_1	chr11	74853038	74853310	+	0	NA	intron (NM_001270381, intron 9 of 15)	L2a|LINE|L2	96013	NM_001270381	143570	Hs.370145	NM_182969	ENSG00000166435	XRRA1	-	X-ray radiation resistance associated 1	protein-coding	0.007353	0.457875	
chunk0181_116_1	chr7	80705197	80705473	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	58682	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.003623	0.447653	
chunk0091_183_1	chr19	8251120	8251514	+	0	NA	intron (NM_024552, intron 3 of 11)	intron (NM_024552, intron 3 of 11)	41984	NM_024552	79603	Hs.515111	NM_024552	ENSG00000090661	CERS4	LASS4|Trh1	ceramide synthase 4	protein-coding	0.032995	0.602532	
chunk0125_447_1	chr3	72887569	72887908	+	0	NA	promoter-TSS (NM_001080393)	promoter-TSS (NM_001080393)	-496	NM_001080393	727936	Hs.710275	NM_001080393	ENSG00000172986	GXYLT2	GLT8D4	glucoside xylosyltransferase 2	protein-coding	0.020649	0.450000	
chunk0050_250_1	chr12	105497668	105497991	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	167193	NM_001145199	387882	Hs.368938	NM_207376	ENSG00000235162	C12orf75	AGD3|OCC-1|OCC1	chromosome 12 open reading frame 75	protein-coding	0.006192	0.330247	
chunk0091_225_1	chr19	10252087	10252341	+	0	NA	5' UTR (NM_015956, exon 1 of 9)	5' UTR (NM_015956, exon 1 of 9)	250	NM_146388	51073	Hs.279652	NM_015956	ENSG00000105364	MRPL4	CGI-28|L4mt	mitochondrial ribosomal protein L4	protein-coding	0.137795	0.737255	
chunk0068_185_1	chr15	54760898	54761138	+	0	NA	Intergenic	L1MA1|LINE|L1	436015	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004167	0.468880	
chunk0174_347_1	chr6	164253433	164253671	+	0	NA	Intergenic	LTR86A2|LTR|ERVL	568511	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.004202	0.502092	
chunk0029_60_1	chr10	96561431	96561728	+	0	NA	intron (NM_020123, intron 4 of 14)	intron (NM_020123, intron 4 of 14)	25473	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.000000	0.372483	
chunk0149_308_1	chr5	25997235	25997602	+	0	NA	Intergenic	Intergenic	1041164	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.000000	0.269022	
chunk0082_372_1	chr17	60421035	60421349	+	0	NA	Intergenic	Intergenic	-1312	NM_181707	124773	Hs.129312	NM_181707	ENSG00000141371	C17orf64	-	chromosome 17 open reading frame 64	protein-coding	0.015924	0.396825	
chunk0049_212_1	chr12	93221312	93221580	+	0	NA	intron (NR_040096, intron 2 of 4)	intron (NR_040096, intron 2 of 4)	47080	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.000000	0.334572	
chunk0004_284_1	chr1	48661982	48662425	+	0	NA	intron (NM_032785, intron 7 of 13)	intron (NM_032785, intron 7 of 13)	114766	NM_001302082	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.013544	0.468468	257(CAGGACTGGGTGTGCT,-,0.00),258(AGGACTGGGTGTGCTG,+,0.00)
chunk0149_229_1	chr5	23195444	23196084	+	0	NA	Intergenic	Intergenic	-311845	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.004687	0.315133	
chunk0156_372_1	chr5	112802570	112803014	+	0	NA	intron (NM_001127511, intron 6 of 13)	intron (NM_001127511, intron 6 of 13)	-58396	NM_001204196	6728	Hs.637001	NM_003135	ENSG00000153037	SRP19	-	signal recognition particle 19	protein-coding	0.011261	0.274157	
chunk0022_285_1	chr10	15381660	15381867	+	0	NA	Intergenic	Intergenic	-10704	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.014493	0.447115	
chunk0063_171_1	chr14	80324877	80325451	+	0	NA	intron (NR_038355, intron 2 of 8)	L2a|LINE|L2	-94110	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.010453	0.434783	556(GAGAACAGCCTGGGCA,-,0.00)
chunk0197_174_1	chr8	121097455	121097762	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-285539	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.006515	0.474026	
chunk0099_184_1	chr2	90383742	90383969	+	0	NA	Intergenic	Intergenic	1276094	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.022026	0.368421	
chunk0090_122_1	chr18	71775570	71775852	+	0	NA	intron (NR_126324, intron 1 of 4)	MIR|SINE|MIR	6515	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.003546	0.318021	
chunk0003_91_1	chr1	31842789	31843341	+	0	NA	Intergenic	L2a|LINE|L2	-27014	NM_001281987	90853	Hs.62604	NM_144569	ENSG00000134668	SPOCD1	PPP1R146	SPOC domain containing 1	protein-coding	0.009058	0.502712	278(CAGGGCAGGCTGTTCC,-,0.00),279(AGGGCAGGCTGTTCCT,+,0.00)
chunk0025_166_1	chr10	52653404	52653917	+	0	NA	Intergenic	Intergenic	118040	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.009747	0.414397	
chunk0025_177_1	chr10	52938765	52938983	+	0	NA	Intergenic	L1ME2|LINE|L1	-167174	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.004587	0.301370	
chunk0036_428_1	chr11	68405663	68405987	+	0	NA	intron (NM_001291902, intron 8 of 22)	intron (NM_001291902, intron 8 of 22)	-54893	NM_001164164	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.018519	0.498462	
chunk0183_338_1	chr7	108328254	108328640	+	0	NA	intron (NM_001193582, intron 2 of 30)	intron (NM_001193582, intron 2 of 30)	-88277	NM_001037132	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.005181	0.428941	
chunk0179_259_1	chr7	49036329	49036528	+	0	NA	Intergenic	Intergenic	111867	NR_003595									0.000000	0.415000	
chunk0096_452_1	chr2	39751969	39752414	+	0	NA	intron (NR_028102, intron 9 of 10)	MIR|SINE|MIR	27085	NM_025264	80745	Hs.468254	NM_025264	ENSG00000138050	THUMPD2	C2orf8	THUMP domain containing 2	protein-coding	0.006742	0.336323	
chunk0076_271_1	chr16	69545649	69546176	+	0	NA	Intergenic	Intergenic	19956	NR_031719	100302119		NR_031719	ENSG00000223109	MIR1538	MIRN1538|hsa-mir-1538	microRNA 1538	ncRNA	0.007590	0.367424	
chunk0092_149_1	chr19	28844103	28844334	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	-116524	NR_110759	100420587	Hs.569956	NR_110759	ENSG00000283403	LOC100420587	-	SHC binding and spindle associated 1 pseudogene	pseudo	0.008658	0.327586	
chunk0030_158_1	chr10	113958881	113959687	+	0	NA	Intergenic	Intergenic	-84763	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.013648	0.473358	386(GGAACAGGATGTGATT,+,0.00)
chunk0135_161_1	chr3	187808911	187809330	+	0	NA	Intergenic	Intergenic	-63395	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.019093	0.461905	179(CAGTGCAGGATGTCCC,-,0.00)
chunk0082_363_1	chr17	60253141	60253351	+	0	NA	intron (NM_032582, intron 10 of 33)	intron (NM_032582, intron 10 of 33)	-21601	NR_002999	677681		NR_002999	ENSG00000252577	SCARNA20	ACA66	small Cajal body-specific RNA 20	ncRNA	0.004762	0.345972	
chunk0133_183_1	chr3	170221983	170222542	+	0	NA	promoter-TSS (NM_002740)	promoter-TSS (NM_002740)	-170	NM_002740	5584	Hs.478199	NM_002740	ENSG00000163558	PRKCI	DXS1179E|PKCI|nPKC-iota	protein kinase C iota	protein-coding	0.078712	0.623214	
chunk0189_68_1	chr8	20789153	20789392	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-164361	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.000000	0.454167	
chunk0032_455_1	chr10	133328131	133328336	+	0	NA	intron (NM_015722, intron 2 of 5)	intron (NM_015722, intron 2 of 5)	8738	NM_015722	50632	Hs.148680	NM_015722	ENSG00000130643	CALY	DRD1IP|NSG3	calcyon neuron specific vesicular protein	protein-coding	0.009756	0.635922	
chunk0080_81_1	chr17	22419640	22419839	+	0	NA	Intergenic	Intergenic	13720	NR_027084	284124	Hs.310247	NR_027084	ENSG00000276399	FLJ36000	-	uncharacterized FLJ36000	ncRNA	0.015075	0.345000	
chunk0182_84_1	chr7	92645966	92646442	+	0	NA	intron (NM_001145306, intron 5 of 7)	intron (NM_001145306, intron 5 of 7)	-55810	NR_109929	257415	Hs.18564	NM_152789	ENSG00000234545	FAM133B	-	family with sequence similarity 133 member B	protein-coding	0.004202	0.379455	
chunk0027_301_1	chr10	77857456	77857661	+	0	NA	intron (NM_004747, intron 2 of 31)	intron (NM_004747, intron 2 of 31)	69032	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.014634	0.597087	138(TAGGACTGAGTGTCCT,-,0.00),139(AGGACTGAGTGTCCTA,+,0.00)
chunk0070_86_1	chr15	70170427	70170678	+	0	NA	Intergenic	Intergenic	-72635	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.015936	0.571429	123(GGAGACAGTGTGTTCC,-,0.00),124(GAGACAGTGTGTTCCT,+,0.00)
chunk0190_391_1	chr8	40155084	40155379	+	0	NA	TTS (NM_020130)	TTS (NM_020130)	1763	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.006780	0.307432	
chunk0015_348_1	chr1	190098758	190098957	+	0	NA	exon (NM_199051, exon 8 of 8)	exon (NM_199051, exon 8 of 8)	378772	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.055276	0.525000	
chunk0187_155_1	chr7	150189957	150190207	+	0	NA	Intergenic	L1MC4|LINE|L1	112898	NM_001164459	653857	Hs.664579	NM_001164458	ENSG00000106526	ACTR3C	ARP11	actin related protein 3C	protein-coding	0.004000	0.350598	
chunk0137_306_1	chr4	24236433	24237033	+	0	NA	Intergenic	Intergenic	283557	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.010000	0.415973	269(AAACACACAGTGTTCT,-,0.00),270(AACACACAGTGTTCTT,+,0.00)
chunk0206_285_1	chr9	124390493	124391487	+	0	NA	intron (NM_002799, intron 5 of 7)	intron (NM_002799, intron 5 of 7)	24483	NM_002799	5695	Hs.213470	NM_002799	ENSG00000136930	PSMB7	Z	proteasome subunit beta 7	protein-coding	0.009054	0.390955	
chunk0147_97_1	chr4	173371643	173372354	+	0	NA	intron (NM_003864, intron 1 of 3)	CpG-21635	1056	NM_003864	8819	Hs.591715	NM_003864	ENSG00000164105	SAP30	-	Sin3A associated protein 30	protein-coding	0.056259	0.549157	318(AGGAAGATCCTGTTCT,-,0.00),319(GGAAGATCCTGTTCTT,+,0.00)
chunk0121_394_1	chr3	25326168	25326673	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	-14382	NM_001290300	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.387352	
chunk0200_453_1	chr9	31438044	31438345	+	0	NA	Intergenic	Intergenic	-946409	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.000000	0.274834	
chunk0151_214_1	chr5	50869076	50869761	+	0	NA	Intergenic	Intergenic	100769	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.008759	0.355685	
chunk0062_343_1	chr14	73660373	73661025	+	0	NA	intron (NM_001201366, intron 4 of 8)	intron (NM_001201366, intron 4 of 8)	15824	NM_031427	83544	Hs.271270	NM_031427	ENSG00000119661	DNAL1	C14orf168|CILD16|LC1	dynein axonemal light chain 1	protein-coding	0.003067	0.378254	319(GAGAACACAGTGTGTC,-,0.00),320(AGAACACAGTGTGTCA,+,0.00)
chunk0174_69_1	chr6	155985389	155986284	+	0	NA	Intergenic	Intergenic	39039	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.006704	0.380580	
chunk0007_51_1	chr1	77832933	77833407	+	0	NA	intron (NM_198549, intron 7 of 15)	intron (NM_198549, intron 7 of 15)	53546	NM_198549	374986	Hs.437755	NM_198549	ENSG00000180488	MIGA1	FAM73A	mitoguardin 1	protein-coding	0.000000	0.368421	344(GAGTACACATTGTACA,-,0.00)
chunk0206_123_1	chr9	120950703	120950902	+	0	NA	Intergenic	Intergenic	-21629	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.000000	0.445000	
chunk0003_282_1	chr1	37448983	37449592	+	0	NA	Intergenic	Intergenic	25156	NR_038842	728431	Hs.380738	NR_038842	ENSG00000233621	LINC01137	-	long intergenic non-protein coding RNA 1137	ncRNA	0.018062	0.504918	
chunk0118_81_1	chr22	28967183	28967423	+	0	NA	intron (NM_032173, intron 1 of 8)	Tigger3|DNA|TcMar-Tigger	49914	NM_032173	84133	Hs.604200	NM_032173	ENSG00000183579	ZNRF3	BK747E2.3|RNF203	zinc and ring finger 3	protein-coding	0.008333	0.356846	
chunk0087_67_1	chr18	31930746	31930998	+	0	NA	intron (NM_014939, intron 2 of 28)	intron (NM_014939, intron 2 of 28)	12256	NM_014939	22878	Hs.202001	NM_014939	ENSG00000153339	TRAPPC8	GSG1|HsT2706|KIAA1012|TRS85	trafficking protein particle complex 8	protein-coding	0.007937	0.292490	
chunk0114_325_1	chr21	17462398	17462845	+	0	NA	Intergenic	Intergenic	23731	NR_037586	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.015660	0.406250	
chunk0099_43_1	chr2	84088719	84089376	+	0	NA	Intergenic	Intergenic	-201635	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.003044	0.335866	172(AAATACATTCTGTACT,-,0.00),277(CAGAACACAATGAGCT,-,0.00),278(AGAACACAATGAGCTT,+,0.00)
chunk0148_384_1	chr5	14721923	14722510	+	0	NA	intron (NM_054027, intron 8 of 11)	intron (NM_054027, intron 8 of 11)	9522	NR_046285	100130744	Hs.660550	NR_046285		LOC100130744	-	uncharacterized LOC100130744	ncRNA	0.010221	0.411565	
chunk0040_190_1	chr11	114109376	114109862	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	49053	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.010288	0.509240	
chunk0137_87_1	chr4	13207280	13207479	+	0	NA	Intergenic	Intergenic	276986	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.000000	0.425000	
chunk0057_96_1	chr13	98901770	98902244	+	0	NA	intron (NM_001130049, intron 12 of 32)	intron (NM_001130049, intron 12 of 32)	69923	NR_046663	100874096	Hs.578066	NR_046663	ENSG00000229918	DOCK9-AS1	-	DOCK9 antisense RNA 1	ncRNA	0.004219	0.370526	
chunk0137_28_1	chr4	10964006	10964205	+	0	NA	Intergenic	(CATGCACACA)n|Simple_repeat|Simple_repeat	-279343	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.010050	0.485000	
chunk0095_416_1	chr2	24596878	24597293	+	0	NA	intron (NM_147223, intron 1 of 21)	intron (NM_147223, intron 1 of 21)	12608	NM_147223	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.000000	0.329327	
chunk0070_307_1	chr15	74986164	74986560	+	0	NA	Intergenic	L2c|LINE|L2	-9173	NR_033660	192683	Hs.374180	NM_138967	ENSG00000198794	SCAMP5	-	secretory carrier membrane protein 5	protein-coding	0.010101	0.544081	68(AAGAGCAGCCTGTACT,-,0.00),69(AGAGCAGCCTGTACTG,+,0.00)
chunk0063_71_1	chr14	77535600	77535872	+	0	NA	intron (NM_004863, intron 9 of 11)	intron (NM_004863, intron 9 of 11)	-36869	NM_182509	145501	Hs.29742	NM_182509	ENSG00000100593	ISM2	TAIL1|THSD3	isthmin 2	protein-coding	0.007353	0.358974	
chunk0127_53_1	chr3	89125814	89126467	+	0	NA	intron (NM_005233, intron 1 of 16)	intron (NM_005233, intron 1 of 16)	18616	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.001531	0.262997	
chunk0098_108_1	chr2	68288165	68288575	+	0	NA	intron (NM_001111101, intron 2 of 2)	L2b|LINE|L2	31681	NM_015463	25927	Hs.212885	NM_015463	ENSG00000119865	CNRIP1	C2orf32|CRIP1	cannabinoid receptor interacting protein 1	protein-coding	0.009756	0.391727	210(GGGAACAGGCTGTGCA,-,0.00),211(GGAACAGGCTGTGCAG,+,0.00)
chunk0114_46_1	chr21	8441080	8441337	+	0	NA	promoter-TSS (NR_003287).2	promoter-TSS (NR_003287).2	62	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.143969	0.689922	
chunk0052_136_1	chr13	23729577	23730210	+	0	NA	TTS (NM_005932)	TTS (NM_005932)	150533	NM_018647	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.000000	0.340694	
chunk0044_201_1	chr12	30792605	30792984	+	0	NA	Intergenic	MIRb|SINE|MIR	-2887	NR_040245	100287314	Hs.355210	NR_040245		LINC00941	lncRNA-MUF	long intergenic non-protein coding RNA 941	ncRNA	0.002639	0.423684	
chunk0116_193_1	chr21	37086065	37086291	+	0	NA	intron (NM_003316, intron 1 of 45)	intron (NM_003316, intron 1 of 45)	3231	NM_003316	7267	Hs.368214	NM_003316	ENSG00000182670	TTC3	DCRR1|RNF105|TPRDIII	tetratricopeptide repeat domain 3	protein-coding	0.000000	0.312775	
chunk0112_279_1	chr20	43590572	43590969	+	0	NA	5' UTR (NM_016004, exon 1 of 14)	5' UTR (NM_016004, exon 1 of 14)	157	NM_001303458	51098	Hs.444332	NM_016004	ENSG00000101052	IFT52	C20orf9|CGI-53|NGD2|NGD5	intraflagellar transport 52	protein-coding	0.070529	0.575377	
chunk0088_370_1	chr18	53947151	53947527	+	0	NA	Intergenic	Intergenic	275073	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.010638	0.429708	
chunk0075_394_1	chr16	56809819	56810324	+	0	NA	intron (NM_014669, intron 5 of 21)	intron (NM_014669, intron 5 of 21)	26570	NM_001242796	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.009901	0.341897	
chunk0171_280_1	chr6	128066861	128067285	+	0	NA	intron (NM_001291981, intron 12 of 32).2	intron (NM_001291981, intron 12 of 32).2	39208	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.011792	0.440000	
chunk0159_213_1	chr5	140710953	140711188	+	0	NA	promoter-TSS (NR_026703)	promoter-TSS (NR_026703)	-206	NR_026703	56664		NR_026703	ENSG00000199990	VTRNA1-1	HVG1|VAULTRC1|VR1|hvg-1|vRNA	vault RNA 1-1	ncRNA	0.042553	0.572034	
chunk0182_205_1	chr7	96245982	96246421	+	0	NA	intron (NM_014251, intron 3 of 17)	intron (NM_014251, intron 3 of 17)	-26445	NR_030322	693176		NR_030322	ENSG00000208025	MIR591	MIRN591|hsa-mir-591	microRNA 591	ncRNA	0.006834	0.393182	269(AGGAACAGAATGTTCC,-,0.00),270(GGAACAGAATGTTCCC,+,0.00)
chunk0204_395_1	chr9	102517797	102518502	+	0	NA	Intergenic	Intergenic	-1488	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.007092	0.362606	545(AAAAACAATCTGTTCT,-,0.00),546(AAAACAATCTGTTCTG,+,0.00)
chunk0130_61_1	chr3	129815039	129815692	+	0	NA	intron (NM_001128224, intron 3 of 5)	L1MA4|LINE|L1	65194	NM_001017395	23023	Hs.477547	NM_015008	ENSG00000172765	TMCC1	-	transmembrane and coiled-coil domain family 1	protein-coding	0.001531	0.356269	
chunk0039_88_1	chr11	97214223	97214679	+	0	NA	Intergenic	L1MC1|LINE|L1	-707574	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.004386	0.343545	
chunk0056_205_1	chr13	85812291	85812529	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-13062	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.004202	0.439331	
chunk0084_7_1	chr17	73278200	73278800	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-16620	NM_001129885	642843	Hs.534707	NM_001129885	ENSG00000187959	CPSF4L	-	cleavage and polyadenylation specific factor 4 like	protein-coding	0.008333	0.475874	
chunk0162_307_1	chr6	6599308	6599843	+	0	NA	intron (NM_004271, intron 1 of 4)	intron (NM_004271, intron 1 of 4)	10874	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.009346	0.511194	
chunk0008_45_1	chr1	89055642	89056049	+	0	NA	intron (NM_002053, intron 8 of 10)	intron (NM_002053, intron 8 of 10)	9515	NM_002053	2633	Hs.62661	NM_002053	ENSG00000117228	GBP1	-	guanylate binding protein 1	protein-coding	0.002457	0.387255	
chunk0011_425_1	chr1	154549219	154549448	+	0	NA	3' UTR (NM_017582, exon 13 of 13)	3' UTR (NM_017582, exon 13 of 13)	-4276	NR_046668	100874097		NR_046668	ENSG00000229780	UBE2Q1-AS1	-	UBE2Q1 antisense RNA 1	ncRNA	0.000000	0.469565	
chunk0186_136_1	chr7	138499427	138499729	+	0	NA	intron (NM_015905, intron 1 of 18)	MER70B|LTR|ERVL	39244	NM_015905	8805	Hs.490287	NM_003852	ENSG00000122779	TRIM24	PTC6|RNF82|TF1A|TIF1|TIF1A|TIF1ALPHA|hTIF1	tripartite motif containing 24	protein-coding	0.009934	0.524752	
chunk0032_64_1	chr11	2176301	2176711	+	0	NA	Intergenic	Intergenic	3443	NR_039834	100616126		NR_039834	ENSG00000265258	MIR4686	-	microRNA 4686	ncRNA	0.021951	0.474453	
chunk0073_74_1	chr16	3820179	3820419	+	0	NA	intron (NM_001079846, intron 2 of 29)	intron (NM_001079846, intron 2 of 29)	59821	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.008333	0.473029	
chunk0095_177_1	chr2	17733741	17733964	+	0	NA	intron (NM_024624, intron 4 of 26)	intron (NM_024624, intron 4 of 26)	19977	NM_024624	79677	Hs.526728	NM_024624	ENSG00000163029	SMC6	SMC-6|SMC6L1|hSMC6	structural maintenance of chromosomes 6	protein-coding	0.000000	0.379464	
chunk0164_302_1	chr6	24920142	24920654	+	0	NA	intron (NM_001286446, intron 1 of 13)	intron (NM_001286446, intron 1 of 13)	-9228	NM_014722	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.000000	0.405458	
chunk0003_354_1	chr1	39142450	39143077	+	0	NA	intron (NM_012090, intron 1 of 92)	intron (NM_012090, intron 1 of 92)	58596	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.004785	0.482484	
chunk0102_258_1	chr2	149427205	149427657	+	0	NA	intron (NM_194317, intron 1 of 4)	intron (NM_194317, intron 1 of 4)	96916	NM_194317	130574	Hs.21929	NM_194317	ENSG00000187123	LYPD6	-	LY6/PLAUR domain containing 6	protein-coding	0.004425	0.375276	
chunk0016_384_1	chr1	202732505	202732921	+	0	NA	intron (NM_001314042, intron 24 of 27)	intron (NM_001314042, intron 24 of 27)	-22290	NM_177402	127833	Hs.25422	NM_177402	ENSG00000143858	SYT2	CMS7|MYSPC|SytII	synaptotagmin 2	protein-coding	0.002404	0.362110	
chunk0080_373_1	chr17	33307716	33308035	+	0	NA	intron (NM_001094, intron 1 of 9)	MIRb|SINE|MIR	-14887	NM_183377	40	Hs.368417	NM_001094	ENSG00000108684	ASIC2	ACCN|ACCN1|ASIC2a|BNC1|BNaC1|MDEG|hBNaC1	acid sensing ion channel subunit 2	protein-coding	0.003135	0.359375	
chunk0095_403_1	chr2	24375439	24376048	+	0	NA	Intergenic	Intergenic	-15215	NM_147152	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.013136	0.478689	
chunk0029_184_1	chr10	100925478	100926325	+	0	NA	intron (NM_001136123, intron 5 of 18)	intron (NM_001136123, intron 5 of 18)	13332	NM_018121	55719	Hs.447458	NM_018121	ENSG00000119906	SLF2	C10orf6|FAM178A	SMC5-SMC6 complex localization factor 2	protein-coding	0.009445	0.369104	
chunk0140_136_1	chr4	69207721	69208068	+	0	NA	intron (NM_001073, intron 3 of 5)	intron (NM_001073, intron 3 of 5)	6837	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.002882	0.321839	
chunk0064_218_1	chr14	93396633	93396983	+	0	NA	intron (NM_020818, intron 1 of 49)	(TG)n|Simple_repeat|Simple_repeat	49617	NM_182971	341947	Hs.666459	NM_182971	ENSG00000187581	COX8C	COX8-3	cytochrome c oxidase subunit 8C	protein-coding	0.000000	0.433048	
chunk0149_243_1	chr5	23535639	23535886	+	0	NA	Intergenic	Intergenic	28107	NM_001310214	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.000000	0.375000	
chunk0175_183_1	chr7	5417819	5418852	+	0	NA	intron (NM_001080495, intron 2 of 29)	intron (NM_001080495, intron 2 of 29)	5211	NM_001080495	84629	Hs.520638	NM_001013722	ENSG00000182095	TNRC18	CAGL79|TNRC18A	trinucleotide repeat containing 18	protein-coding	0.015489	0.540619	
chunk0020_122_1	chr1	233441915	233442504	+	0	NA	Intergenic	Intergenic	114441	NM_032435	84451	Hs.547779	NM_032435	ENSG00000143674	MAP3K21	MLK4|dJ862P8.3	mitogen-activated protein kinase kinase kinase 21	protein-coding	0.010187	0.438983	
chunk0136_34_1	chr4	1054785	1055250	+	0	NA	Intergenic	Intergenic	42553	NM_021923	53834	Hs.193326	NM_021923	ENSG00000127418	FGFRL1	FGFR-5|FGFR5|FHFR	fibroblast growth factor receptor like 1	protein-coding	0.017204	0.650215	16(GGGGACAGTCAGCTCC,-,0.00),17(GGGACAGTCAGCTCCT,+,0.00),39(GGGGACAGTCAGCTCC,-,0.00),40(GGGACAGTCAGCTCCC,+,0.00),79(GGGGACAGTCAGCTCC,-,0.00),80(GGGACAGTCAGCTCCC,+,0.00),119(AGGGACAGTCAGCTCC,-,0.00),120(GGGACAGTCAGCTCCC,+,0.00),139(GGGAACAGTCAGCTCC,-,0.00),140(GGAACAGTCAGCTCCT,+,0.00),159(GGGGACAGTCAGCTCC,-,0.00),160(GGGACAGTCAGCTCCC,+,0.00),199(GGGGACAGCCAGCTCC,-,0.00),200(GGGACAGCCAGCTCCC,+,0.00),222(GGGGACAGTCAGCTCC,-,0.00),223(GGGACAGTCAGCTCCT,+,0.00),245(GGGGACAGTCAGCTCC,-,0.00),246(GGGACAGTCAGCTCCC,+,0.00),265(GGGAACAGTCAGCTCC,-,0.00),266(GGAACAGTCAGCTCCT,+,0.00),285(GGGGACAGTCAGCTCC,-,0.00),286(GGGACAGTCAGCTCCC,+,0.00),308(GGGGACAGTCAGCTCC,-,0.00),309(GGGACAGTCAGCTCCC,+,0.00),368(GAGGACAGCCAGCTCC,-,0.00),369(AGGACAGCCAGCTCCC,+,0.00),391(GGGGACAGTCAGCTCC,-,0.00),392(GGGACAGTCAGCTCCT,+,0.00),414(GGGGACAGTCAGCTCC,-,0.00),415(GGGACAGTCAGCTCCC,+,0.00)
chunk0120_119_1	chr3	4720729	4721260	+	0	NA	intron (NM_001168272, intron 39 of 60)	intron (NM_001168272, intron 39 of 60)	30596	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.015066	0.400376	
chunk0072_28_1	chr16	617122	617658	+	0	NA	intron (NM_021168, intron 2 of 5)	intron (NM_021168, intron 2 of 5)	-13622	NM_053284	117166	Hs.345818	NM_053284	ENSG00000127578	WFIKKN1	C16orf12|RJD2|WFDC20A|WFIKKN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	protein-coding	0.046642	0.594041	321(TGGGACACTGTGTCCC,-,0.00),322(GGGACACTGTGTCCCT,+,0.00)
chunk0211_360_1	chrX	125631251	125631701	+	0	NA	Intergenic	L1PB3|LINE|L1	311356	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.002222	0.317073	
chunk0043_105_1	chr12	14931491	14931728	+	0	NA	intron (NM_152321, intron 3 of 6)	intron (NM_152321, intron 3 of 6)	-2484	NM_001300784	121506	Hs.162143	NM_152321	ENSG00000139055	ERP27	C12orf46|PDIA8	endoplasmic reticulum protein 27	protein-coding	0.012658	0.411765	
chunk0167_61_1	chr6	56073819	56074445	+	0	NA	intron (NM_030820, intron 20 of 29)	intron (NM_030820, intron 20 of 29)	173448	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.001597	0.330144	
chunk0022_149_1	chr10	12377794	12378032	+	0	NA	intron (NM_020397, intron 1 of 9)	intron (NM_020397, intron 1 of 9)	28370	NM_153498	57118	Hs.600547	NM_020397	ENSG00000183049	CAMK1D	CKLiK|CaM-K1|CaMKID	calcium/calmodulin dependent protein kinase ID	protein-coding	0.000000	0.380753	
chunk0198_51_1	chr8	128501195	128501787	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	63188	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.005068	0.355818	
chunk0160_87_1	chr5	150037726	150038312	+	0	NA	intron (NM_014983, intron 13 of 19)	L1ME4a|LINE|L1	-36852	NM_030953	81789	Hs.169333	NM_030953	ENSG00000164296	TIGD6	-	tigger transposable element derived 6	protein-coding	0.003413	0.356048	
chunk0145_255_1	chr4	148938162	148938834	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	-215797	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.008929	0.326895	428(CAGCACTCCCTGTTCA,-,0.00),429(AGCACTCCCTGTTCAT,+,0.00)
chunk0152_190_1	chr5	59829884	59830270	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-61465	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.000000	0.382429	
chunk0147_36_1	chr4	171922867	171923447	+	0	NA	intron (NM_001034845, intron 2 of 12)	intron (NM_001034845, intron 2 of 12)	109733	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.008621	0.330465	
chunk0176_436_1	chr7	19958629	19958899	+	0	NA	intron (NR_110114, intron 5 of 5)	intron (NR_110114, intron 5 of 5)	181662	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.000000	0.287823	221(TAGTACTGCATGTTCC,-,0.00),222(AGTACTGCATGTTCCA,+,0.00)
chunk0074_248_1	chr16	27625173	27625735	+	0	NA	intron (NM_015202, intron 3 of 27)	intron (NM_015202, intron 3 of 27)	75307	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.012456	0.465364	
chunk0188_188_1	chr8	11644110	11644416	+	0	NA	Intergenic	Intergenic	-32656	NM_001308094	2626	Hs.243987	NM_002052	ENSG00000136574	GATA4	ASD2|TACHD|TOF|VSD1	GATA binding protein 4	protein-coding	0.016340	0.540717	
chunk0138_264_1	chr4	40191525	40191970	+	0	NA	intron (NM_001278368, intron 1 of 2)	intron (NM_001278368, intron 1 of 2)	736	NM_001278368	399	Hs.654594	NM_004310	ENSG00000168421	RHOH	ARHH|TTF	ras homolog family member H	protein-coding	0.008989	0.343049	
chunk0118_373_1	chr22	36529098	36529562	+	0	NA	promoter-TSS (NM_003753)	promoter-TSS (NM_003753)	-100	NM_003753	8664	Hs.55682	NM_003753	ENSG00000100353	EIF3D	EIF3S7|eIF3-p66|eIF3-zeta	eukaryotic translation initiation factor 3 subunit D	protein-coding	0.109914	0.623656	
chunk0127_174_1	chr3	95227144	95227369	+	0	NA	Intergenic	LTR33|LTR|ERVL	288993	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.004444	0.415929	
chunk0089_135_1	chr18	58878360	58878601	+	0	NA	intron (NM_018181, intron 3 of 10)	intron (NM_018181, intron 3 of 10)	15651	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.016598	0.520661	
chunk0086_190_1	chr18	22057781	22058482	+	0	NA	Intergenic	Intergenic	110837	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.009986	0.408832	
chunk0159_206_1	chr5	140471053	140471693	+	0	NA	intron (NM_017747, intron 10 of 33)	intron (NM_017747, intron 10 of 33)	69559	NM_017978	54882	Hs.594084	NM_017747	ENSG00000131503	ANKHD1	MASK|MASK1|PP2500|VBARP	ankyrin repeat and KH domain containing 1	protein-coding	0.001563	0.355694	
chunk0160_28_1	chr5	149220697	149221553	+	0	NA	intron (NM_014945, intron 8 of 23)	L2b|LINE|L2	-50713	NM_001146337	134265	Hs.62930	NM_152406	ENSG00000157510	AFAP1L1	-	actin filament associated protein 1 like 1	protein-coding	0.007009	0.493582	470(GAGAACAGTGAGTGCA,-,0.00),471(AGAACAGTGAGTGCAA,+,0.00)
chunk0092_285_1	chr19	33815255	33815503	+	0	NA	3' UTR (NM_001129995, exon 7 of 7)	3' UTR (NM_001129995, exon 7 of 7)	18533	NM_024076	79047	Hs.221873	NM_024076	ENSG00000153885	KCTD15	-	potassium channel tetramerization domain containing 15	protein-coding	0.004032	0.309237	70(GGAAACACTATGTCCC,-,0.00),71(GAAACACTATGTCCCC,+,0.00)
chunk0141_244_1	chr4	85014331	85014548	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	47621	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.000000	0.426606	
chunk0021_183_1	chr10	5573958	5574391	+	0	NA	Intergenic	Intergenic	-47928	NR_120496	100132159	Hs.239600	NR_120496		CALML3-AS1	-	CALML3 antisense RNA 1	ncRNA	0.032333	0.576037	244(TGGTACAGGGTGTTCT,-,0.00),245(GGTACAGGGTGTTCTC,+,0.00)
chunk0124_26_1	chr3	52102898	52103285	+	0	NA	intron (NM_001161581, intron 9 of 10)	L1MCc|LINE|L1	-37979	NR_027331	100128378	Hs.640106	NM_001123039		LINC00696	C3orf74	long intergenic non-protein coding RNA 696	ncRNA	0.010336	0.345361	
chunk0057_37_1	chr13	96020902	96021295	+	0	NA	intron (NM_020121, intron 4 of 38)	LTR40c|LTR|ERVL	32384	NM_020121	55757	Hs.193226	NM_020121	ENSG00000102595	UGGT2	HUGT2|UGCGL2|UGT2	UDP-glucose glycoprotein glucosyltransferase 2	protein-coding	0.005089	0.459391	
chunk0119_3_1	chr22	39992140	39992487	+	0	NA	Intergenic	MIRb|SINE|MIR	-2636	NM_138435	113828	Hs.26192	NM_138435	ENSG00000133477	FAM83F	-	family with sequence similarity 83 member F	protein-coding	0.005764	0.468391	
chunk0137_313_1	chr4	24496537	24497244	+	0	NA	Intergenic	Intergenic	23400	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.018388	0.453390	
chunk0178_222_1	chr7	35647398	35647737	+	0	NA	intron (NM_022373, intron 5 of 8)	intron (NM_022373, intron 5 of 8)	47595	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.008850	0.376471	
chunk0168_310_1	chr6	92085573	92085772	+	0	NA	Intergenic	Intergenic	-395244	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.000000	0.310000	109(AGGGACACACTGTTTT,-,0.00),110(GGGACACACTGTTTTT,+,0.00)
chunk0099_60_1	chr2	84849311	84849741	+	0	NA	intron (NM_001277053, intron 2 of 6)	intron (NM_001277053, intron 2 of 6)	31719	NM_001277053	129293	Hs.469134	NM_001080824	ENSG00000186854	TRABD2A	C2orf89|TIKI1	TraB domain containing 2A	protein-coding	0.006977	0.457077	
chunk0207_276_1	chr9	132409862	132410215	+	0	NA	promoter-TSS (NM_001282957)	promoter-TSS (NM_001282957)	-158	NM_001282957	389799	Hs.201709	NM_207417	ENSG00000188523	CFAP77	C9orf171	cilia and flagella associated protein 77	protein-coding	0.082153	0.661017	
chunk0207_267_1	chr9	132357896	132358358	+	0	NA	Intergenic	L1M4|LINE|L1	-3142	NM_015046	23064	Hs.460317	NM_015046	ENSG00000107290	SETX	ALS4|AOA2|SCAN2|SCAR1|Sen1|bA479K20.2	senataxin	protein-coding	0.010823	0.341253	
chunk0112_360_1	chr20	45419488	45419776	+	0	NA	intron (NR_047694, intron 4 of 10)	intron (NR_047694, intron 4 of 10)	3565	NM_015937	51604	Hs.437388	NM_015937	ENSG00000124155	PIGT	CGI-06|MCAHS3|NDAP|PNH2	phosphatidylinositol glycan anchor biosynthesis class T	protein-coding	0.010417	0.515571	
chunk0169_199_1	chr6	102774376	102774897	+	0	NA	Intergenic	L1M7|LINE|L1	1375651	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001919	0.321839	
chunk0072_306_1	chr15	98763096	98763333	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-21212	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.004219	0.336134	
chunk0207_345_1	chr9	134895169	134895419	+	0	NA	Intergenic	MLT1J2-int|LTR|ERVL-MaLR	14482	NM_004108	2220	Hs.54517	NM_004108	ENSG00000160339	FCN2	EBP-37|FCNL|P35|ficolin-2	ficolin 2	protein-coding	0.012000	0.482072	
chunk0063_335_1	chr14	85345083	85345770	+	0	NA	Intergenic	Intergenic	-48453	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005822	0.295058	
chunk0050_137_1	chr12	102481614	102482402	+	0	NA	Intergenic	Intergenic	-1363	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.000000	0.418251	
chunk0033_394_1	chr11	24485170	24485713	+	0	NA	Intergenic	L1MA1|LINE|L1	-11529	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.007366	0.347426	
chunk0132_298_1	chr3	160185176	160185699	+	0	NA	intron (NR_108088, intron 3 of 9)	intron (NR_108088, intron 3 of 9)	21655	NR_108088	101928376	Hs.565865	NR_108088	ENSG00000244040	IL12A-AS1	ILAS1-AS1	IL12A antisense RNA 1	ncRNA	0.001912	0.385496	
chunk0134_121_1	chr3	177278995	177279737	+	0	NA	Intergenic	Intergenic	-15076	NR_047465	100820709	Hs.518409	NR_047465	ENSG00000203645	LINC00501	-	long intergenic non-protein coding RNA 501	ncRNA	0.010782	0.446837	
chunk0027_444_1	chr10	81192350	81192986	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	651849	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.009434	0.372057	
chunk0197_45_1	chr8	118383252	118383575	+	0	NA	intron (NR_109794, intron 3 of 4)	L2b|LINE|L2	-237588	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.012384	0.456790	91(CAGAACAGGGTGATCT,-,0.00),92(AGAACAGGGTGATCTA,+,0.00)
chunk0058_321_1	chr14	27681777	27682489	+	0	NA	Intergenic	Intergenic	-48855	NR_130461	100422830		NR_130461	ENSG00000264657	MIR3171	-	microRNA 3171	ncRNA	0.014045	0.405330	
chunk0107_108_1	chr2	214293635	214293891	+	0	NA	intron (NR_047659, intron 17 of 17)	L1MA4A|LINE|L1	-117974	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.000000	0.556420	
chunk0035_74_1	chr11	41832164	41832509	+	0	NA	intron (NR_120584, intron 4 of 5)	intron (NR_120584, intron 4 of 5)	117768	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.005797	0.315029	
chunk0160_306_1	chr5	159091171	159091709	+	0	NA	intron (NM_001290360, intron 4 of 15)	intron (NM_001290360, intron 4 of 15)	8340	NM_182708	1879	Hs.573143	NM_024007	ENSG00000164330	EBF1	COE1|EBF|O/E-1|OLF1	EBF transcription factor 1	protein-coding	0.007435	0.395176	
chunk0068_249_1	chr15	55983811	55984518	+	0	NA	intron (NM_006154, intron 1 of 28)	intron (NM_006154, intron 1 of 28)	9582	NM_006154	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.008487	0.371469	
chunk0029_55_1	chr10	96513728	96513927	+	0	NA	promoter-TSS (NM_012465)	promoter-TSS (NM_012465)	99	NM_012465	7093	Hs.154296	NM_012465	ENSG00000095587	TLL2	-	tolloid like 2	protein-coding	0.130653	0.715000	
chunk0083_237_1	chr17	67582779	67583215	+	0	NA	intron (NM_181671, intron 5 of 9)	MER5B|DNA|hAT-Charlie	-111412	NR_030385	693131		NR_030385	ENSG00000263690	MIR548D2	MIRN548D2	microRNA 548d-2	ncRNA	0.013761	0.512586	
chunk0147_425_1	chr4	187388083	187388597	+	0	NA	intron (NR_038931, intron 1 of 4)	intron (NR_038931, intron 1 of 4)	117273	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.003891	0.341748	
chunk0144_132_1	chr4	129663948	129664775	+	0	NA	Intergenic	L2a|LINE|L2	107117	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.001209	0.327295	519(TGATCACTATGTTCCC,+,0.00)
chunk0183_77_1	chr7	104609552	104609751	+	0	NA	intron (NM_199000, intron 1 of 2)	intron (NM_199000, intron 1 of 2)	194441	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.000000	0.335000	
chunk0103_169_1	chr2	162710264	162710781	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-58414	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.005803	0.382239	
chunk0018_345_1	chr1	221556717	221557050	+	0	NA	Intergenic	MIR|SINE|MIR	180017	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.000000	0.344311	
chunk0206_97_1	chr9	120714684	120714883	+	0	NA	promoter-TSS (NM_001080497)	promoter-TSS (NM_001080497)	-296	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.125628	0.745000	
chunk0180_276_1	chr7	69816527	69816819	+	0	NA	intron (NM_015570, intron 1 of 18)	MIRc|SINE|MIR	217754	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.003425	0.392491	
chunk0147_285_1	chr4	184307740	184308300	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	45957	NR_040108	728175	Hs.590107	NR_040108	ENSG00000180712	LINC02363	-	long intergenic non-protein coding RNA 2363	ncRNA	0.016071	0.417112	
chunk0136_387_1	chr3	196792453	196792887	+	0	NA	intron (NM_002577, intron 2 of 14)	intron (NM_002577, intron 2 of 14)	52813	NM_002577	5062	Hs.518530	NM_002577	ENSG00000180370	PAK2	PAK65|PAKgamma	p21 (RAC1) activated kinase 2	protein-coding	0.004608	0.363218	
chunk0121_10_1	chr3	14623552	14624060	+	0	NA	Intergenic	Intergenic	-27940	NM_016474	51244	Hs.517820	NM_016474	ENSG00000154781	CCDC174	C3orf19|HSPC212|IHPM|IHPMR	coiled-coil domain containing 174	protein-coding	0.009843	0.479371	215(TGGCACAGATTGTCCC,-,0.00),216(GGCACAGATTGTCCCA,+,0.00)
chunk0049_346_1	chr12	95243327	95243921	+	0	NA	intron (NM_017599, intron 1 of 11)	MSTB2|LTR|ERVL-MaLR	25878	NM_017599	55591	Hs.24135	NM_017599	ENSG00000028203	VEZT	VEZATIN	vezatin, adherens junctions transmembrane protein	protein-coding	0.005051	0.401681	
chunk0085_63_1	chr18	1170922	1171177	+	0	NA	Intergenic	Intergenic	188580	NR_023927	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.003922	0.359375	
chunk0013_239_1	chr1	169588234	169588688	+	0	NA	TTS (NM_003005)	TTS (NM_003005)	-1930	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.002203	0.325275	
chunk0153_176_1	chr5	71555972	71556342	+	0	NA	intron (NM_018429, intron 35 of 38)	L1ME4b|LINE|L1	-31131	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.000000	0.277628	
chunk0153_167_1	chr5	71441593	71441928	+	0	NA	Intergenic	Intergenic	-13855	NM_018429	55814	Hs.258272	NM_018429	ENSG00000145734	BDP1	DFNB112|HSA238520|TAF3B1|TFC5|TFIIIB''|TFIIIB150|TFIIIB90|TFNR	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.002985	0.410714	
chunk0199_157_1	chr9	4290350	4290927	+	0	NA	intron (NM_001042413, intron 1 of 10)	intron (NM_001042413, intron 1 of 10)	9397	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.008666	0.352941	269(AGAGCTGAATGTTCTT,+,0.00)
chunk0092_36_1	chr19	19192021	19192262	+	0	NA	promoter-TSS (NM_134440)	promoter-TSS (NM_134440)	-58	NM_134440	8625	Hs.153629	NM_003721	ENSG00000064490	RFXANK	ANKRA1|BLS|F14150_1|RFX-B	regulatory factor X associated ankyrin containing protein	protein-coding	0.099585	0.694215	
chunk0156_315_1	chr5	111061472	111061854	+	0	NA	Intergenic	L1ME4b|LINE|L1	-8417	NR_045089	85480	Hs.389874	NM_033035	ENSG00000145777	TSLP	-	thymic stromal lymphopoietin	protein-coding	0.000000	0.336815	
chunk0071_57_1	chr15	80252648	80252939	+	0	NA	promoter-TSS (NR_120317)	promoter-TSS (NR_120317)	-532	NR_120317									0.010309	0.325342	
chunk0201_384_1	chr9	68970251	68970464	+	0	NA	intron (NR_110647, intron 1 of 2)	intron (NR_110647, intron 1 of 2)	5484	NR_110647	101927069	Hs.663405	NR_110647		LOC101927069	-	uncharacterized LOC101927069	ncRNA	0.009390	0.411215	
chunk0001_66_1	chr1	2410668	2411296	+	0	NA	intron (NM_002617, intron 1 of 5)	intron (NM_002617, intron 1 of 5)	1589	NM_153818	5192	Hs.732228	NM_002617	ENSG00000157911	PEX10	NALD|PBD6A|PBD6B|RNF69	peroxisomal biogenesis factor 10	protein-coding	0.009554	0.492846	
chunk0117_161_1	chr22	20132341	20132540	+	0	NA	intron (NM_013373, intron 1 of 10)	intron (NM_013373, intron 1 of 10)	599	NM_001185024	29801	Hs.63128	NM_013373	ENSG00000099904	ZDHHC8	DHHC8|ZDHHCL1|ZNF378	zinc finger DHHC-type containing 8	protein-coding	0.050251	0.700000	
chunk0143_447_1	chr4	124199889	124200336	+	0	NA	Intergenic	Intergenic	358322	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.002237	0.341518	243(AAGTACATTCTGTCAC,-,0.00)
chunk0017_450_1	chr1	214324720	214325365	+	0	NA	intron (NM_020197, intron 6 of 11)	intron (NM_020197, intron 6 of 11)	43820	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.004651	0.363777	
chunk0160_247_1	chr5	156616640	156616953	+	0	NA	intron (NM_000337, intron 6 of 8)	MER58A|DNA|hAT-Charlie	-233742	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.003195	0.404459	102(AAAAACAGCATGTTCC,-,0.00),103(AAAACAGCATGTTCCC,+,0.00)
chunk0100_321_1	chr2	116475947	116476193	+	0	NA	Intergenic	PrimLTR79|LTR|ERV1	1313963	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.004065	0.364372	
chunk0104_257_1	chr2	177622170	177622460	+	0	NA	TTS (NM_001077196)	TTS (NM_001077196)	-3349	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.003448	0.350515	
chunk0177_153_1	chr7	22956970	22957530	+	0	NA	intron (NM_032581, intron 10 of 10)	intron (NM_032581, intron 10 of 10)	56901	NM_032581	84668	Hs.85603	NM_032581	ENSG00000122591	FAM126A	DRCTNNB1A|HCC|HLD5|HYCC1	family with sequence similarity 126 member A	protein-coding	0.008929	0.294118	
chunk0180_345_1	chr7	73518925	73519559	+	0	NA	intron (NM_032408, intron 1 of 19)	intron (NM_032408, intron 1 of 19)	3043	NM_032408	9031	Hs.743372	NM_023005	ENSG00000009954	BAZ1B	WBSCR10|WBSCR9|WSTF	bromodomain adjacent to zinc finger domain 1B	protein-coding	0.001577	0.327559	
chunk0072_365_1	chr15	99857065	99857541	+	0	NA	Intergenic	MIRb|SINE|MIR	-50376	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.000000	0.295597	
chunk0006_360_1	chr1	72924487	72924831	+	0	NA	Intergenic	Intergenic	-381511	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.002907	0.266667	
chunk0144_311_1	chr4	138596017	138596464	+	0	NA	Intergenic	Intergenic	286529	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.004474	0.390625	
chunk0018_267_1	chr1	220458899	220459464	+	0	NA	Intergenic	Intergenic	-69002	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.000000	0.314488	
chunk0007_231_1	chr1	81869407	81869825	+	0	NA	intron (NM_001297706, intron 2 of 18)	intron (NM_001297706, intron 2 of 18)	69219	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.002392	0.281623	
chunk0059_303_1	chr14	36208427	36209195	+	0	NA	Intergenic	Intergenic	-32160	NR_049735	100886964	Hs.742592	NR_049735		PTCSC3	-	papillary thyroid carcinoma susceptibility candidate 3	ncRNA	0.002604	0.335501	
chunk0158_139_1	chr5	127367999	127368387	+	0	NA	intron (NM_001308121, intron 4 of 13)	intron (NM_001308121, intron 4 of 13)	77429	NM_001308121	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.002577	0.401028	182(GGGCCAGTGTGTTCAT,+,0.00)
chunk0082_315_1	chr17	59221723	59222175	+	0	NA	intron (NM_001165993, intron 1 of 9)	intron (NM_001165993, intron 1 of 9)	1482	NM_182569	284161	Hs.631744	NM_182569	ENSG00000153982	GDPD1	GDE4	glycerophosphodiester phosphodiesterase domain containing 1	protein-coding	0.006637	0.331126	
chunk0143_22_1	chr4	105924381	105924937	+	0	NA	intron (NM_001184690, intron 3 of 12)	intron (NM_001184690, intron 3 of 12)	29219	NM_001033047	255743	Hs.518921	NM_198278	ENSG00000168743	NPNT	EGFL6L|POEM	nephronectin	protein-coding	0.003597	0.353680	
chunk0075_10_1	chr16	46785144	46785601	+	0	NA	Intergenic	L1MA8|LINE|L1	-22126	NM_001308301	91807	Hs.130465	NM_182493	ENSG00000140795	MYLK3	MLCK|MLCK2|caMLCK	myosin light chain kinase 3	protein-coding	0.002188	0.465066	253(GGGCACTTCCTGTACC,-,0.00),254(GGCACTTCCTGTACCT,+,0.00)
chunk0134_297_1	chr3	180359699	180360577	+	0	NA	Intergenic	Intergenic	-54035	NR_132416	100505609	Hs.518427	NR_132416	ENSG00000241696	LINC02053	-	long intergenic non-protein coding RNA 2053	ncRNA	0.004556	0.370876	
chunk0028_117_1	chr10	84543008	84543472	+	0	NA	Intergenic	Intergenic	118058	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.023707	0.477419	
chunk0181_120_1	chr7	80781293	80782048	+	0	NA	intron (NM_006379, intron 12 of 17)	intron (NM_006379, intron 12 of 17)	135017	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.003974	0.406085	
chunk0037_216_1	chr11	74773339	74773765	+	0	NA	intron (NM_001098638, intron 1 of 5)	Tigger10|DNA|TcMar-Tigger	24684	NM_001098638	254225	Hs.370145	NM_001098638	ENSG00000166439	RNF169	-	ring finger protein 169	protein-coding	0.002347	0.346604	
chunk0166_15_1	chr6	41652995	41653500	+	0	NA	intron (NM_001300806, intron 3 of 3)	intron (NM_001300806, intron 3 of 3)	14790	NM_001300806	4188	Hs.520119	NM_005586	ENSG00000112559	MDFI	I-MF|I-mfa	MyoD family inhibitor	protein-coding	0.047525	0.586957	
chunk0042_45_1	chr12	1726760	1727288	+	0	NA	intron (NM_024551, intron 1 of 7)	intron (NM_024551, intron 1 of 7)	35943	NM_024551	79602	Hs.371642	NM_024551	ENSG00000006831	ADIPOR2	ACDCR2|PAQR2	adiponectin receptor 2	protein-coding	0.007576	0.362949	
chunk0193_255_1	chr8	76960014	76960236	+	0	NA	Intergenic	Intergenic	6725	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004505	0.381166	
chunk0191_279_1	chr8	53786661	53786985	+	0	NA	intron (NM_015941, intron 9 of 13)	intron (NM_015941, intron 9 of 13)	56219	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.006173	0.369231	
chunk0015_342_1	chr1	189853484	189853872	+	0	NA	Intergenic	L1PB4|LINE|L1	623951	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.005155	0.341902	
chunk0127_211_1	chr3	96455657	96455856	+	0	NA	Intergenic	Intergenic	95792	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.005025	0.300000	
chunk0157_391_1	chr5	124094865	124095151	+	0	NA	intron (NR_125774, intron 4 of 5)	L1PB1|LINE|L1	343512	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.006993	0.327526	
chunk0089_433_1	chr18	70080368	70080567	+	0	NA	intron (NM_173630, intron 32 of 48)	L1MC4|LINE|L1	-123291	NM_006566	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.000000	0.335000	
chunk0069_5_1	chr15	60011908	60012340	+	0	NA	Intergenic	Intergenic	7902	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.006944	0.357968	
chunk0113_397_1	chr20	60300025	60300658	+	0	NA	intron (NR_046099, intron 3 of 4)	Tigger13a|DNA|TcMar-Tigger	-8133	NR_030376	693231		NR_030376	ENSG00000207802	MIR646	MIRN646|hsa-mir-646	microRNA 646	ncRNA	0.023697	0.449527	
chunk0159_347_1	chr5	144328896	144329331	+	0	NA	intron (NM_020768, intron 3 of 3)	intron (NM_020768, intron 3 of 3)	158240	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.002299	0.396789	
chunk0124_385_1	chr3	59610222	59610451	+	0	NA	Intergenic	Intergenic	-560347	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.004367	0.413043	
chunk0095_105_1	chr2	15415205	15415484	+	0	NA	intron (NR_052013, intron 25 of 50)	intron (NR_052013, intron 25 of 50)	146004	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.000000	0.278571	
chunk0072_42_1	chr16	1078556	1078923	+	0	NA	promoter-TSS (NM_001053)	promoter-TSS (NM_001053)	-8	NR_027242	146336	Hs.250557	NM_182510	ENSG00000261713	SSTR5-AS1	-	SSTR5 antisense RNA 1	ncRNA	0.059946	0.652174	
chunk0043_403_1	chr12	25648392	25648869	+	0	NA	promoter-TSS (NM_001145727)	promoter-TSS (NM_001145727)	-68	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.014675	0.493724	
chunk0060_203_1	chr14	48577754	48578029	+	0	NA	Intergenic	Intergenic	-782877	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.003636	0.289855	
chunk0043_166_1	chr12	17047400	17047704	+	0	NA	Intergenic	Intergenic	58805	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.000000	0.334426	
chunk0051_304_1	chr12	118655634	118655935	+	0	NA	Intergenic	MamTip3|DNA|hAT-Tip100	279231	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.003322	0.453642	137(GAGGACAGCCTGAGCA,-,0.00),138(AGGACAGCCTGAGCAC,+,0.00)
chunk0043_177_1	chr12	17322496	17322809	+	0	NA	Intergenic	L1PB1|LINE|L1	333905	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.003195	0.506369	
chunk0184_272_1	chr7	118576375	118576798	+	0	NA	Intergenic	L2a|LINE|L2	351928	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.002364	0.408019	133(ATGGACAGTCTGTACC,-,0.00),134(TGGACAGTCTGTACCA,+,0.00)
chunk0015_220_1	chr1	187626485	187626895	+	0	NA	Intergenic	Intergenic	183062	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.360097	
chunk0077_292_1	chr16	81349340	81350242	+	0	NA	intron (NM_022041, intron 1 of 10)	intron (NM_022041, intron 1 of 10)	34825	NM_022041	8139	Hs.112569	NM_022041	ENSG00000261609	GAN	GAN1|KLHL16	gigaxonin	protein-coding	0.012195	0.368771	
chunk0131_439_1	chr3	153848617	153849017	+	0	NA	Intergenic	Intergenic	-272186	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.005000	0.453865	239(GAGAGCTCTGTGTTCT,-,0.00),240(AGAGCTCTGTGTTCTG,+,0.00)
chunk0206_36_1	chr9	116491391	116491618	+	0	NA	intron (NM_198186, intron 4 of 7)	intron (NM_198186, intron 4 of 7)	-12779	NR_033973	100128505	Hs.675821	NR_033973	ENSG00000229105	ASTN2-AS1	-	ASTN2 antisense RNA 1	ncRNA	0.004405	0.355263	
chunk0082_73_1	chr17	51587865	51588628	+	0	NA	Intergenic	L2a|LINE|L2	251531	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.005242	0.346859	
chunk0119_430_1	chr22	50020549	50020772	+	0	NA	Intergenic	Intergenic	-8034	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.031390	0.508929	
chunk0027_250_1	chr10	77129471	77130048	+	0	NA	intron (NM_001014797, intron 5 of 28)	intron (NM_001014797, intron 5 of 28)	-11072	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.003466	0.271626	
chunk0149_317_1	chr5	26352775	26353392	+	0	NA	Intergenic	L1MA4A|LINE|L1	685499	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.004862	0.318770	
chunk0011_285_1	chr1	151443666	151444147	+	0	NA	intron (NM_001194938, intron 1 of 17)	MER119|DNA|hAT-Charlie	-1701	NM_207171	23126	Hs.489873	NM_015100	ENSG00000143442	POGZ	MRD37|WHSUS|ZNF280E|ZNF635|ZNF635m	pogo transposable element derived with ZNF domain	protein-coding	0.010395	0.398340	
chunk0006_279_1	chr1	70486777	70487060	+	0	NA	Intergenic	Intergenic	75700	NM_001902	1491	Hs.19904	NM_001902	ENSG00000116761	CTH	-	cystathionine gamma-lyase	protein-coding	0.000000	0.542254	
chunk0079_133_1	chr17	12735182	12735381	+	0	NA	intron (NM_001146312, intron 5 of 13)	intron (NM_001146312, intron 5 of 13)	-29146	NR_104605	101928418	Hs.620346	NR_104605	ENSG00000227274	LOC101928418	-	uncharacterized LOC101928418	ncRNA	0.010050	0.425000	102(CAGCACATTGTGTACT,-,0.00),103(AGCACATTGTGTACTG,+,0.00)
chunk0161_56_1	chr5	166163335	166164143	+	0	NA	Intergenic	Intergenic	762631	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.009901	0.414091	
chunk0105_29_1	chr2	182135279	182135795	+	0	NA	Intergenic	Intergenic	106526	NM_001258314	5136	Hs.191046	NM_005019	ENSG00000115252	PDE1A	CAM-PDE 1A|CAM-PDE-1A|HCAM-1|HCAM1|HSPDE1A	phosphodiesterase 1A	protein-coding	0.007752	0.365571	
chunk0171_420_1	chr6	131485797	131486517	+	0	NA	Intergenic	L1M2c|LINE|L1	-87047	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.001389	0.407767	
chunk0178_228_1	chr7	35694832	35695243	+	0	NA	5' UTR (NM_022373, exon 1 of 9)	5' UTR (NM_022373, exon 1 of 9)	125	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.109489	0.728155	
chunk0051_441_1	chr12	123171880	123172396	+	0	NA	intron (NM_022782, intron 16 of 23)	L1ME3C|LINE|L1	61100	NR_103517	10198	Hs.577404	NM_022782	ENSG00000051825	MPHOSPH9	MPP-9|MPP9	M-phase phosphoprotein 9	protein-coding	0.011628	0.373308	
chunk0085_40_1	chr18	650048	650405	+	0	NA	TTS (NM_199167)	TTS (NM_199167)	-7378	NM_001071	7298	Hs.369762	NM_001071	ENSG00000176890	TYMS	HST422|TMS|TS	thymidylate synthetase	protein-coding	0.002801	0.259777	
chunk0162_375_1	chr6	7418184	7418562	+	0	NA	TTS (NM_031480)	TTS (NM_031480)	15726	NM_153005	83732	Hs.437474	NM_031480	ENSG00000124784	RIOK1	AD034|RIO1|RRP10|bA288G3.1	RIO kinase 1	protein-coding	0.007937	0.443272	
chunk0092_97_1	chr19	23113837	23114249	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-2932	NM_001277403	100129543	Hs.427120	NM_001277403	ENSG00000183850	ZNF730	-	zinc finger protein 730	protein-coding	0.000000	0.338983	
chunk0068_200_1	chr15	54944533	54945119	+	0	NA	Intergenic	L1PA6|LINE|L1	252207	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.006826	0.410562	
chunk0109_251_1	chr20	6444777	6444991	+	0	NA	intron (NR_109953, intron 1 of 3)	MER6B|DNA|TcMar-Tigger	18152	NR_109953	101929244	Hs.542488	NR_109953	ENSG00000229876	CASC20	-	cancer susceptibility 20	ncRNA	0.009346	0.320930	
chunk0094_460_1	chr2	11622993	11623192	+	0	NA	intron (NM_014668, intron 23 of 32)	Tigger3b|DNA|TcMar-Tigger	47111	NM_012344	23620	Hs.131138	NM_012344	ENSG00000169006	NTSR2	NTR2	neurotensin receptor 2	protein-coding	0.045226	0.450000	
chunk0144_138_1	chr4	129783502	129783783	+	0	NA	Intergenic	Intergenic	-12164	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.010676	0.336879	
chunk0060_216_1	chr14	48879310	48879509	+	0	NA	Intergenic	Intergenic	707007	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.360000	
chunk0041_161_1	chr11	126050605	126050879	+	0	NA	intron (NM_016952, intron 1 of 19)	intron (NM_016952, intron 1 of 19)	12550	NM_001243597	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.014599	0.483636	100(AAGGACGGGGTGTGCC,-,0.00),101(AGGACGGGGTGTGCCG,+,0.00)
chunk0181_54_1	chr7	80139317	80139960	+	0	NA	intron (NM_001256414, intron 1 of 7)	intron (NM_001256414, intron 1 of 7)	3883	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.001555	0.324534	
chunk0198_231_1	chr8	134120642	134121071	+	0	NA	Intergenic	Intergenic	234360	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006993	0.369767	
chunk0148_258_1	chr5	10323816	10324194	+	0	NA	Intergenic	MIR|SINE|MIR	-15949	NM_138809	134147	Hs.192586	NM_138809	ENSG00000164237	CMBL	JS-1	carboxymethylenebutenolidase homolog	protein-coding	0.007937	0.403694	
chunk0185_223_1	chr7	129144095	129144701	+	0	NA	promoter-TSS (NM_178562)	promoter-TSS (NM_178562)	-318	NM_178562	340348	Hs.27267	NM_178562	ENSG00000158457	TSPAN33	PEN|PEN.|TSPAN-33	tetraspanin 33	protein-coding	0.039604	0.520593	
chunk0156_12_1	chr5	102035868	102036299	+	0	NA	Intergenic	LTR80A|LTR|ERVL	260466	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.314815	
chunk0162_246_1	chr6	4961493	4961692	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-42224	NR_126017	100129461	Hs.131700	NR_126015	ENSG00000272142	LYRM4-AS1	-	LYRM4 antisense RNA 1	ncRNA	0.010050	0.520000	
chunk0194_151_1	chr8	84633914	84634210	+	0	NA	intron (NM_001100393, intron 2 of 8)	intron (NM_001100393, intron 2 of 8)	-71865	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.010135	0.286195	
chunk0082_12_1	chr17	50217934	50218296	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	3421	NR_110806	101927230	Hs.514326	NR_110806		LINC01969	-	long intergenic non-protein coding RNA 1969	ncRNA	0.002762	0.341598	
chunk0097_137_1	chr2	47265307	47265516	+	0	NA	intron (NR_110207, intron 1 of 2)	intron (NR_110207, intron 1 of 2)	-69904	NR_001568	618		NR_001568	ENSG00000236824	BCYRN1	BC200|BC200a|LINC00004|NCRNA00004	brain cytoplasmic RNA 1	ncRNA	0.023923	0.509524	
chunk0146_345_1	chr4	166146924	166147746	+	0	NA	Intergenic	Intergenic	274077	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.007299	0.391252	365(TTGGACATCTTGTGCT,-,0.00),366(TGGACATCTTGTGCTT,+,0.00)
chunk0071_134_1	chr15	81893169	81893431	+	0	NA	Intergenic	Intergenic	152843	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.007634	0.353612	
chunk0151_171_1	chr5	49666839	49667116	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	774423	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.025271	0.431655	
chunk0109_6_1	chr20	238161	238677	+	0	NA	Intergenic	Intergenic	11161	NM_080831	140881	Hs.112087	NM_080831	ENSG00000125903	DEFB129	C20orf87|DEFB-29|DEFB29|bA530N10.3|hBD-29	defensin beta 129	protein-coding	0.009690	0.419729	
chunk0033_10_1	chr11	12388762	12389215	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	11509	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.000000	0.367841	
chunk0164_229_1	chr6	23029392	23029891	+	0	NA	Intergenic	Intergenic	460192	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.004008	0.316000	208(AGGCACGTTCTGTGCT,-,0.00),209(GGCACGTTCTGTGCTT,+,0.00)
chunk0153_417_1	chr5	75623809	75624285	+	0	NA	intron (NM_001276713, intron 3 of 13)	Tigger15a|DNA|TcMar-Tigger	12571	NM_001276713	728780	Hs.370455	NM_001271529	ENSG00000189045	ANKDD1B	-	ankyrin repeat and death domain containing 1B	protein-coding	0.002101	0.389937	
chunk0074_320_1	chr16	30615626	30616317	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	-5196	NR_073481	115509	Hs.454685	NM_138447	ENSG00000156853	ZNF689	TIPUH1	zinc finger protein 689	protein-coding	0.010130	0.452312	
chunk0154_341_1	chr5	86122325	86122548	+	0	NA	Intergenic	Intergenic	-160008	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.004484	0.321429	
chunk0020_128_1	chr1	233588044	233588276	+	0	NA	Intergenic	Intergenic	-25844	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.017241	0.540773	
chunk0038_141_1	chr11	84339731	84340262	+	0	NA	intron (NM_001142699, intron 7 of 27)	intron (NM_001142699, intron 7 of 27)	-22657	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.005650	0.366541	
chunk0026_324_1	chr10	68177716	68178125	+	0	NA	intron (NM_001256268, intron 16 of 23)	intron (NM_001256268, intron 16 of 23)	54193	NM_145178	220202	Hs.175396	NM_145178	ENSG00000179774	ATOH7	Math5|NCRNA|PHPVAR|RNANC|bHLHa13	atonal bHLH transcription factor 7	protein-coding	0.007335	0.360976	
chunk0103_419_1	chr2	169695789	169696075	+	0	NA	intron (NM_001199288, intron 2 of 3)	LTR40b|LTR|ERVL	1478	NM_001199290	100526832		NM_001199290	ENSG00000213160	PHOSPHO2-KLHL23	-	PHOSPHO2-KLHL23 readthrough	protein-coding	0.006993	0.439024	
chunk0102_252_1	chr2	149166923	149167205	+	0	NA	intron (NM_001317002, intron 4 of 7)	intron (NM_001317002, intron 4 of 7)	48890	NM_001317002	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.010638	0.409894	
chunk0164_308_1	chr6	24982706	24983118	+	0	NA	intron (NM_001286446, intron 1 of 13)	LTR23|LTR|ERV1	-46860	NM_001286445	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.002427	0.384988	
chunk0025_420_1	chr10	59831713	59832209	+	0	NA	intron (NM_005436, intron 3 of 8)	MIR3|SINE|MIR	74695	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.006048	0.432596	
chunk0019_124_1	chr1	225508514	225508911	+	0	NA	intron (NM_001008493, intron 10 of 14)	intron (NM_001008493, intron 10 of 14)	-79857	NM_194442	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.005038	0.384422	
chunk0205_236_1	chr9	110050954	110051294	+	0	NA	intron (NM_001004065, intron 1 of 3)	intron (NM_001004065, intron 1 of 3)	2526	NM_001198656	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.000000	0.442815	
chunk0191_360_1	chr8	56741056	56741402	+	0	NA	Intergenic	MIRb|SINE|MIR	-181406	NR_038236	100507632	Hs.583755	NR_038236	ENSG00000246430	LINC00968	-	long intergenic non-protein coding RNA 968	ncRNA	0.011561	0.446686	
chunk0188_182_1	chr8	11361811	11362121	+	0	NA	intron (NR_001578, intron 6 of 8)	intron (NR_001578, intron 6 of 8)	-6436	NR_026814	83656	Hs.583896	NM_054017	ENSG00000184608	FAM167A-AS1	C8orf12	FAM167A antisense RNA 1	ncRNA	0.016129	0.524116	
chunk0059_316_1	chr14	36430448	36431301	+	0	NA	Intergenic	Intergenic	82911	NM_001101341	253970	Hs.509165	NM_001101341	ENSG00000229415	SFTA3	NANCI|SFTPH|SP-H|SPH	surfactant associated 3	ncRNA	0.007034	0.377049	545(CAGAACATGGTGTCCA,-,0.00),546(AGAACATGGTGTCCAC,+,0.00)
chunk0029_296_1	chr10	103951741	103952459	+	0	NA	Intergenic	Intergenic	-15085	NM_001304743	9748	Hs.591922	NM_014720	ENSG00000065613	SLK	LOSK|STK2|bA16H23.1|se20-9	STE20 like kinase	protein-coding	0.006964	0.385257	
chunk0032_153_1	chr11	4848878	4849218	+	0	NA	exon (NM_001004758, exon 1 of 1)	exon (NM_001004758, exon 1 of 1)	160	NM_001004758	119692	Hs.553561	NM_001004758	ENSG00000176922	OR51S1	OR11-24	olfactory receptor family 51 subfamily S member 1	protein-coding	0.008824	0.554252	28(AGGGACAGTGTGAGCA,-,0.00)
chunk0005_114_1	chr1	56639121	56639725	+	0	NA	Intergenic	Intergenic	-5894	NM_006252	5563	Hs.437039	NM_006252	ENSG00000162409	PRKAA2	AMPK|AMPK2|AMPKa2|PRKAA	protein kinase AMP-activated catalytic subunit alpha 2	protein-coding	0.004967	0.333884	
chunk0146_267_1	chr4	163090838	163091413	+	0	NA	Intergenic	L1ME4b|LINE|L1	2503	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003478	0.352431	
chunk0137_365_1	chr4	26124533	26125215	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-194836	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.013196	0.445095	
chunk0074_242_1	chr16	27560393	27561072	+	0	NA	intron (NM_015202, intron 1 of 27)	intron (NM_015202, intron 1 of 27)	10585	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.011782	0.513235	441(GGCACAGGCAGATCCC,+,0.00)
chunk0135_25_1	chr3	184559265	184559673	+	0	NA	Intergenic	Intergenic	-2330	NM_004443	2049	Hs.2913	NM_004443	ENSG00000182580	EPHB3	EK2|ETK2|HEK2|TYRO6	EPH receptor B3	protein-coding	0.024510	0.591687	
chunk0117_411_1	chr21	45751039	45751652	+	0	NA	Intergenic	L1MB4|LINE|L1	85074	NR_038876	100129027	Hs.689591	NR_038876	ENSG00000205424	LOC100129027	-	uncharacterized LOC100129027	ncRNA	0.021207	0.428339	
chunk0146_276_1	chr4	163475526	163476289	+	0	NA	Intergenic	Intergenic	-2012	NM_032136	84076	Hs.303923	NM_032136	ENSG00000151005	TKTL2	-	transketolase like 2	protein-coding	0.001311	0.318063	
chunk0187_453_1	chr7	159201689	159202012	+	0	NA	Intergenic	Intergenic	-56893	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.018576	0.543210	
chunk0209_21_1	chrX	35560933	35561314	+	0	NA	Intergenic	L1P4e|LINE|L1	-237219	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.007874	0.481675	155(GGGAACACCTTGTTCC,-,0.00),156(GGAACACCTTGTTCCC,+,0.00)
chunk0139_291_1	chr4	57430524	57430992	+	0	NA	intron (NR_125907, intron 3 of 5)	MIR|SINE|MIR	4886	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.004274	0.394456	
chunk0005_442_1	chr1	63415231	63415611	+	0	NA	intron (NM_013339, intron 10 of 14)	intron (NM_013339, intron 10 of 14)	47831	NM_013339	29929	Hs.258501	NM_013339	ENSG00000088035	ALG6	CDG1C	ALG6 alpha-1,3-glucosyltransferase	protein-coding	0.000000	0.349081	
chunk0190_353_1	chr8	39668012	39668407	+	0	NA	intron (NM_014237, intron 14 of 19)	intron (NM_014237, intron 14 of 19)	83641	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.007595	0.340909	237(GAGTACATTATGTACC,-,0.00),238(AGTACATTATGTACCA,+,0.00)
chunk0061_432_1	chr14	65423966	65424384	+	0	NA	intron (NR_038170, intron 1 of 10)	Tigger2|DNA|TcMar-Tigger	11445	NR_038170	2530	Hs.597649	NM_004480	ENSG00000033170	FUT8	CDGF|CDGF1	fucosyltransferase 8	protein-coding	0.014354	0.381862	
chunk0185_157_1	chr7	127731536	127732328	+	0	NA	intron (NM_014390, intron 10 of 23)	intron (NM_014390, intron 10 of 23)	79784	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.008838	0.460277	500(GGGAACACGCTGTCTC,-,0.00),501(GGAACACGCTGTCTCT,+,0.00)
chunk0108_175_1	chr2	232069678	232070043	+	0	NA	intron (NR_046476, intron 5 of 20)	intron (NR_046476, intron 5 of 20)	-102793	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.000000	0.379781	173(GTGCACACACTGTCCC,-,0.00),174(TGCACACACTGTCCCA,+,0.00)
chunk0213_24_1	chrY	26663655	26663854	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	935264	NR_001524	114760	Hs.511777	NR_001524	ENSG00000231141	TTTY3	LINC00121|NCRNA00121|TTTY3A|TTY3	testis-specific transcript, Y-linked 3	ncRNA	0.035176	0.400000	
chunk0010_89_1	chr1	113515364	113515970	+	0	NA	intron (NM_152900, intron 1 of 20)	MIRb|SINE|MIR	124814	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.003300	0.326194	
chunk0161_99_1	chr5	167377542	167377741	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	92803	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.000000	0.335000	
chunk0055_194_1	chr13	61812353	61812718	+	0	NA	Intergenic	Intergenic	217013	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.008219	0.396175	
chunk0049_237_1	chr12	93511572	93512255	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	44423	NR_038160	28977	Hs.199579	NM_014050	ENSG00000198015	MRPL42	HSPC204|L31MT|L42MT|MRP-L31|MRP-L42|MRP-S32|MRPL31|MRPS32|PTD007|RPML31|S32MT	mitochondrial ribosomal protein L42	protein-coding	0.007321	0.350877	372(CTGTACAGTGTGTTCA,-,0.00),373(TGTACAGTGTGTTCAG,+,0.00)
chunk0023_440_1	chr10	31947363	31948019	+	0	NA	Intergenic	Intergenic	-18815	NM_001270697	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.012195	0.374429	
chunk0068_393_1	chr15	58620471	58620670	+	0	NA	intron (NM_001110, intron 11 of 15)	intron (NM_001110, intron 11 of 15)	73037	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.000000	0.230000	
chunk0037_390_1	chr11	78905677	78906024	+	0	NA	intron (NM_001098816, intron 6 of 33)	intron (NM_001098816, intron 6 of 33)	-330986	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.008646	0.534483	
chunk0167_16_1	chr6	53651526	53652414	+	0	NA	exon (NM_001003760, exon 3 of 3)	exon (NM_001003760, exon 3 of 3)	13738	NM_001003760	401265	Hs.131064	NM_001003760	ENSG00000124743	KLHL31	BKLHD6|KBTBD1|KLHL|bA345L23.2	kelch like family member 31	protein-coding	0.095721	0.641170	
chunk0072_336_1	chr15	99268440	99268653	+	0	NA	intron (NM_001284400, intron 2 of 8)	intron (NM_001284400, intron 2 of 8)	11021	NR_073383	7190	Hs.656611	NR_073383	ENSG00000259706	HSP90B2P	GRP94P1|GRP94b|HSP|HSPCP2|TRA1P1|TRAP1	heat shock protein 90 beta family member 2, pseudogene	pseudo	0.018779	0.392523	
chunk0193_90_1	chr8	73612888	73613179	+	0	NA	intron (NM_001164384, intron 7 of 10)	intron (NM_001164384, intron 7 of 10)	133894	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.006873	0.369863	
chunk0017_268_1	chr1	209684300	209684851	+	0	NA	Intergenic	Intergenic	-1605	NM_181755	3290	Hs.195040	NM_005525	ENSG00000117594	HSD11B1	11-DH|11-beta-HSD1|CORTRD2|HDL|HSD11|HSD11B|HSD11L|SDR26C1	hydroxysteroid 11-beta dehydrogenase 1	protein-coding	0.001815	0.304348	180(AGGTACTTATTGTTCT,-,0.00),181(GGTACTTATTGTTCTG,+,0.00)
chunk0071_39_1	chr15	79886093	79886559	+	0	NA	intron (NR_037654, intron 2 of 2)	intron (NR_037654, intron 2 of 2)	10671	NR_037654	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.006438	0.385439	
chunk0063_305_1	chr14	84697785	84698091	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-695941	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003268	0.413681	44(GAGGACACAGTGTTTC,-,0.00),45(AGGACACAGTGTTTCA,+,0.00)
chunk0122_352_1	chr3	37466889	37467429	+	0	NA	intron (NM_002207, intron 1 of 27)	intron (NM_002207, intron 1 of 27)	14837	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.012963	0.462107	
chunk0130_41_1	chr3	129195456	129196224	+	0	NA	Intergenic	Intergenic	-11873	NM_001127193	7555	Hs.518249	NM_003418	ENSG00000169714	CNBP	CNBP1|DM2|PROMM|RNF163|ZCCHC22|ZNF9	CCHC-type zinc finger nucleic acid binding protein	protein-coding	0.010417	0.457737	489(TGGTACAGTCAGTGCT,-,0.00),490(GGTACAGTCAGTGCTC,+,0.00),689(TGGCACAGCCAGTACT,-,0.00),690(GGCACAGCCAGTACTG,+,0.00)
chunk0032_44_1	chr11	1502942	1503141	+	0	NA	Intergenic	Intergenic	-16262	NM_001172223	81532	Hs.370360	NM_053005	ENSG00000182208	MOB2	HCCA2	MOB kinase activator 2	protein-coding	0.020101	0.595000	
chunk0006_224_1	chr1	68495427	68495783	+	0	NA	intron (NM_001114120, intron 1 of 11)	L2b|LINE|L2	-1071	NR_110671	101927220	Hs.382856	NR_110671	ENSG00000234264	DEPDC1-AS1	-	DEPDC1 antisense RNA 1	ncRNA	0.002809	0.414566	
chunk0067_226_1	chr15	45372046	45373023	+	0	NA	intron (NM_001482, intron 2 of 8)	intron (NM_001482, intron 2 of 8)	6248	NM_001482	2628	Hs.75335	NM_001482	ENSG00000171766	GATM	AGAT|AT|CCDS3	glycine amidinotransferase	protein-coding	0.007165	0.380368	
chunk0119_449_1	chr22	50310339	50310549	+	0	NA	Intergenic	MIR|SINE|MIR	-2872	NM_012401	23654	Hs.3989	NM_012401	ENSG00000196576	PLXNB2	MM1|Nbla00445|PLEXB2|dJ402G11.3	plexin B2	protein-coding	0.033333	0.597156	62(AGGGACAGGCTGTCCT,-,0.00),63(GGGACAGGCTGTCCTG,+,0.00)
chunk0107_138_1	chr2	214824950	214825798	+	0	NA	intron (NR_110292, intron 1 of 3)	intron (NR_110292, intron 1 of 3)	15145	NR_110292	101928103	Hs.665619	NR_110292	ENSG00000229267	SNHG31	-	small nucleolar RNA host gene 31	ncRNA	0.004717	0.296820	
chunk0160_336_1	chr5	159926205	159926579	+	0	NA	intron (NM_000679, intron 1 of 1)	intron (NM_000679, intron 1 of 1)	9659	NM_000679	147	Hs.368632	NM_000679	ENSG00000170214	ADRA1B	ADRA1|ALPHA1BAR	adrenoceptor alpha 1B	protein-coding	0.018717	0.456000	
chunk0187_14_1	chr8	592500	593207	+	0	NA	Intergenic	AluJb|SINE|Alu	-47072	NM_175075	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.031117	0.553672	
chunk0114_66_1	chr21	9079000	9079258	+	0	NA	intron (NR_038329, intron 2 of 2)	intron (NR_038329, intron 2 of 2)	50632	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.007752	0.324324	
chunk0098_311_1	chr2	76451715	76451938	+	0	NA	Intergenic	L1ME1|LINE|L1	-534139	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.004484	0.294643	
chunk0144_102_1	chr4	128552797	128553574	+	0	NA	Intergenic	Intergenic	125169	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.036036	0.516710	451(CAGAACACACTGGGCC,-,0.00),452(AGAACACACTGGGCCA,+,0.00)
chunk0083_207_1	chr17	66755281	66755819	+	0	NA	intron (NM_002737, intron 13 of 16)	intron (NM_002737, intron 13 of 16)	-31522	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.020446	0.491651	
chunk0011_257_1	chr1	150906323	150906879	+	0	NA	Intergenic	Intergenic	-19738	NM_001243491	9869	Hs.643565	NM_012432	ENSG00000143379	SETDB1	ESET|H3-K9-HMTase4|KG1T|KMT1E|TDRD21	SET domain bifurcated histone lysine methyltransferase 1	protein-coding	0.005396	0.463196	
chunk0188_89_1	chr8	8632561	8633103	+	0	NA	Intergenic	Intergenic	-69324	NM_194284	137075	Hs.183617	NM_194284	ENSG00000253958	CLDN23	CLDNL|hCG1646163	claudin 23	protein-coding	0.003690	0.272560	
chunk0164_332_1	chr6	25282333	25282546	+	0	NA	intron (NM_017640, intron 1 of 36)	intron (NM_017640, intron 1 of 36)	3011	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.014085	0.443925	113(TTGAACAGGCTGTGCT,-,0.00),114(TGAACAGGCTGTGCTT,+,0.00)
chunk0095_433_1	chr2	25086079	25086578	+	0	NA	intron (NM_014971, intron 1 of 22)	L1MC1|LINE|L1	44224	NM_014971	22979	Hs.4892	NM_014971	ENSG00000084710	EFR3B	KIAA0953	EFR3 homolog B	protein-coding	0.008016	0.414000	
chunk0038_69_1	chr11	83052233	83052523	+	0	NA	intron (NM_014488, intron 1 of 5)	MIRc|SINE|MIR	-10780	NR_033347	100379250	Hs.725115	NR_033347	ENSG00000207221	SNORA70E	U70E	small nucleolar RNA, H/ACA box 70E	snoRNA	0.010345	0.467354	
chunk0117_189_1	chr22	21592589	21593264	+	0	NA	exon (NM_003347, exon 2 of 4)	exon (NM_003347, exon 2 of 4)	25196	NR_046082	7332	Hs.108104	NM_003347	ENSG00000185651	UBE2L3	E2-F1|L-UBC|UBCH7|UbcM4	ubiquitin conjugating enzyme E2 L3	protein-coding	0.008889	0.485207	
chunk0189_48_1	chr8	20004768	20005262	+	0	NA	Intergenic	Intergenic	65944	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.008097	0.496970	
chunk0131_388_1	chr3	152459584	152459916	+	0	NA	intron (NM_001314057, intron 11 of 11)	MER58A|DNA|hAT-Charlie	-118760	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.006024	0.396396	
chunk0008_445_1	chr1	99650380	99650695	+	0	NA	intron (NM_017734, intron 1 of 7)	intron (NM_017734, intron 1 of 7)	4662	NM_017734	54873	Hs.483993	NM_017734	ENSG00000099260	PALMD	C1orf11|PALML	palmdelphin	protein-coding	0.003175	0.389241	
chunk0027_118_1	chr10	74135100	74135444	+	0	NA	intron (NM_207012, intron 4 of 9)	intron (NM_207012, intron 4 of 9)	15796	NM_012095	26985	Hs.500104	NM_012095	ENSG00000185009	AP3M1	-	adaptor related protein complex 3 subunit mu 1	protein-coding	0.002907	0.353623	
chunk0105_172_1	chr2	187130575	187130894	+	0	NA	Intergenic	Intergenic	-281564	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.000000	0.318750	
chunk0164_274_1	chr6	23952183	23952671	+	0	NA	Intergenic	X2_LINE|LINE|CR1	-173759	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.008197	0.400818	
chunk0183_243_1	chr7	107118395	107118598	+	0	NA	intron (NM_002736, intron 2 of 10)	intron (NM_002736, intron 2 of 10)	-50465	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.009852	0.446078	
chunk0176_163_1	chr7	13420802	13421373	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	565427	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.001751	0.386364	334(AAGAACATTGTGTCCA,-,0.00),335(AGAACATTGTGTCCAA,+,0.00)
chunk0129_351_1	chr3	124878513	124879212	+	0	NA	intron (NM_002213, intron 1 of 14)	intron (NM_002213, intron 1 of 14)	8443	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.010014	0.461429	
chunk0174_49_1	chr6	154826602	154827191	+	0	NA	intron (NM_014892, intron 17 of 19)	intron (NM_014892, intron 17 of 19)	-26464	NR_036100	100422821		NR_036100	ENSG00000264814	MIR1273C	-	microRNA 1273c	ncRNA	0.013582	0.335593	
chunk0125_39_1	chr3	62718631	62718980	+	0	NA	intron (NM_003716, intron 3 of 29)	intron (NM_003716, intron 3 of 29)	156584	NM_183394	8618	Hs.654933	NM_003716	ENSG00000163618	CADPS	CADPS1|CAPS|CAPS1|UNC-31	calcium dependent secretion activator	protein-coding	0.011461	0.471429	
chunk0116_151_1	chr21	36499890	36500213	+	0	NA	intron (NM_001146077, intron 2 of 2)	intron (NM_001146077, intron 2 of 2)	-19961	NM_001146079	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.030960	0.530864	
chunk0186_113_1	chr7	138038850	138039061	+	0	NA	Intergenic	L1PA6|LINE|L1	-36854	NM_001253775	64764	Hs.490273	NM_194071	ENSG00000182158	CREB3L2	BBF2H7	cAMP responsive element binding protein 3 like 2	protein-coding	0.009479	0.382075	164(AAGAACACAACGTACC,-,0.00)
chunk0087_47_1	chr18	31401896	31402184	+	0	NA	intron (NM_177986, intron 10 of 15)	intron (NM_177986, intron 10 of 15)	24948	NR_110788	101927718	Hs.625473	NR_110788	ENSG00000266729	DSG1-AS1	-	DSG1 antisense RNA 1	ncRNA	0.006944	0.349481	
chunk0019_179_1	chr1	226436729	226437094	+	0	NA	Intergenic	Intergenic	-28811	NM_001618	142	Hs.177766	NM_001618	ENSG00000143799	PARP1	ADPRT|ADPRT 1|ADPRT1|ARTD1|PARP|PARP-1|PPOL|pADPRT-1	poly(ADP-ribose) polymerase 1	protein-coding	0.008219	0.554645	
chunk0052_113_1	chr13	23003411	23003610	+	0	NA	Intergenic	Intergenic	-105329	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.000000	0.325000	
chunk0200_187_1	chr9	19551088	19551423	+	0	NA	intron (NM_020344, intron 6 of 9)	intron (NM_020344, intron 6 of 9)	142328	NM_001010887	340485	Hs.41379	NM_001010887	ENSG00000177076	ACER2	ALKCDase2|ASAH3L	alkaline ceramidase 2	protein-coding	0.011940	0.491071	
chunk0065_456_1	chr14	106681143	106681453	+	0	NA	Intergenic	Intergenic	44587	NR_106988									0.029032	0.459807	
chunk0039_356_1	chr11	105741552	105741890	+	0	NA	intron (NM_001112812, intron 2 of 9)	intron (NM_001112812, intron 2 of 9)	131037	NM_001112812	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.002959	0.383481	
chunk0148_110_1	chr5	4581099	4581298	+	0	NA	Intergenic	(CACGCA)n|Simple_repeat|Simple_repeat	-192283	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.070352	0.580000	
chunk0132_17_1	chr3	154451925	154452253	+	0	NA	Intergenic	Intergenic	-22374	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.003049	0.291793	
chunk0089_105_1	chr18	58456655	58457163	+	0	NA	Intergenic	Intergenic	-5757	NR_039899	100616357		NR_039899	ENSG00000207778	MIR3591	-	microRNA 3591	ncRNA	0.011811	0.451866	271(TGGCACATCCTGTTCT,-,0.00),272(GGCACATCCTGTTCTG,+,0.00)
chunk0110_421_1	chr20	20655915	20656589	+	0	NA	intron (NM_020343, intron 3 of 39)	intron (NM_020343, intron 3 of 39)	56371	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.008902	0.382222	
chunk0059_76_1	chr14	30503616	30504252	+	0	NA	Intergenic	Tigger20a|DNA|TcMar-Tigger	-55189	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.007862	0.350078	
chunk0093_75_1	chr19	40688081	40688353	+	0	NA	intron (NM_004756, intron 1 of 9)	intron (NM_004756, intron 1 of 9)	1905	NM_001289980	9253	Hs.326953	NM_004756	ENSG00000105245	NUMBL	CAG3A|CTG3a|NBL|NUMB-R|NUMBLIKE|NUMBR|TNRC23	NUMB like endocytic adaptor protein	protein-coding	0.011029	0.516484	
chunk0150_143_1	chr5	33586822	33587265	+	0	NA	intron (NM_030955, intron 18 of 23)	(T)n|Simple_repeat|Simple_repeat	146267	NR_047676	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.000000	0.342342	254(GAGAACATCCTGTACA,-,0.00),255(AGAACATCCTGTACAG,+,0.00)
chunk0007_350_1	chr1	84858518	84859049	+	0	NA	intron (NM_012152, intron 2 of 2)	L2c|LINE|L2	34430	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.005650	0.434211	
chunk0168_55_1	chr6	78831544	78831990	+	0	NA	Intergenic	Intergenic	-35777	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.002242	0.395973	244(AATCACAGAATGTTCT,-,0.00),245(ATCACAGAATGTTCTT,+,0.00)
chunk0177_227_1	chr7	24382971	24383207	+	0	NA	Intergenic	L1ME4b|LINE|L1	98901	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.000000	0.409283	
chunk0113_319_1	chr20	58146236	58146772	+	0	NA	Intergenic	Intergenic	-4423	NM_178456	128602	Hs.43977	NM_178456	ENSG00000124237	C20orf85	LLC1|bA196N14.1	chromosome 20 open reading frame 85	protein-coding	0.014925	0.392924	
chunk0129_249_1	chr3	122125319	122125678	+	0	NA	Intergenic	HAL1|LINE|L1	47649	NM_176892	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.002786	0.325000	
chunk0031_170_1	chr10	125538764	125539417	+	0	NA	Intergenic	MER130|DNA|DNA	-35281	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.012251	0.457187	
chunk0055_426_1	chr13	75394586	75395102	+	0	NA	intron (NM_001286659, intron 1 of 18)	intron (NM_001286659, intron 1 of 18)	87324	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.005814	0.307544	
chunk0023_388_1	chr10	30804031	30804244	+	0	NA	Intergenic	Intergenic	111863	NR_036438	645954	Hs.408581	NR_036438		SVIL2P	SVILP1	supervillin family member 2, pseudogene	pseudo	0.014085	0.485981	
chunk0122_284_1	chr3	36058596	36059094	+	0	NA	Intergenic	L1MC3|LINE|L1	314369	NR_029824	406916		NR_029824	ENSG00000207625	MIR128-2	MIR128B|MIRN128-2|MIRN128B|mir-128-2|mir-128b	microRNA 128-2	ncRNA	0.000000	0.324649	
chunk0078_121_1	chr17	2955203	2955507	+	0	NA	intron (NM_015085, intron 3 of 24)	L1MB5|LINE|L1	10540	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.009868	0.386885	
chunk0104_285_1	chr2	178291231	178291688	+	0	NA	intron (NM_001201482, intron 2 of 23)	intron (NM_001201482, intron 2 of 23)	-28785	NM_145739	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.006565	0.373362	118(TAGATCAGTGTGTGCC,-,0.00),119(AGATCAGTGTGTGCCA,+,0.00)
chunk0166_443_1	chr6	53011853	53012114	+	0	NA	intron (NM_016513, intron 11 of 14)	intron (NM_016513, intron 11 of 14)	16363	NR_001445	125050		NR_001445	ENSG00000202198	RN7SK	7SK	RNA component of 7SK nuclear ribonucleoprotein	snRNA	0.007663	0.477099	
chunk0021_457_1	chr1	248923419	248923913	+	0	NA	Intergenic	Intergenic	17423	NM_001017434	267002	Hs.602037	NM_170725	ENSG00000185220	PGBD2	-	piggyBac transposable element derived 2	protein-coding	0.010121	0.444444	
chunk0034_340_1	chr11	35689055	35690019	+	0	NA	intron (NM_017583, intron 2 of 4)	intron (NM_017583, intron 2 of 4)	26785	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.007261	0.395855	
chunk0097_175_1	chr2	49846694	49847123	+	0	NA	Intergenic	Intergenic	500848	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.325581	171(CAGTTCATAATGTTCT,-,0.00)
chunk0070_337_1	chr15	75646777	75647257	+	0	NA	Intergenic	Intergenic	-1990	NM_153271	257364	Hs.8705	NM_153271	ENSG00000173548	SNX33	SH3PX3|SH3PXD3C|SNX30	sorting nexin 33	protein-coding	0.043750	0.563410	232(CAGAACATCCAGTCCC,-,0.00),233(AGAACATCCAGTCCCC,+,0.00)
chunk0090_59_1	chr19	2041961	2042455	+	0	NA	intron (NM_017572, intron 10 of 13)	CpG-13142	9036	NM_199054	2872	Hs.515032	NM_017572	ENSG00000099875	MKNK2	GPRK7|MNK2	MAPK interacting serine/threonine kinase 2	protein-coding	0.115385	0.735354	
chunk0098_138_1	chr2	69570238	69570769	+	0	NA	intron (NM_014911, intron 2 of 21)	intron (NM_014911, intron 2 of 21)	-50332	NR_003705	100124535	Hs.693447	NR_003705	ENSG00000207016	SNORA36C	-	small nucleolar RNA, H/ACA box 36C	snoRNA	0.003766	0.392857	
chunk0141_268_1	chr4	86384138	86384732	+	0	NA	intron (NM_002753, intron 1 of 13)	L2b|LINE|L2	-24213	NM_138980	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.011785	0.433613	
chunk0052_106_1	chr13	22703135	22703991	+	0	NA	Intergenic	Intergenic	194618	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.008178	0.365228	
chunk0044_231_1	chr12	31471944	31472143	+	0	NA	intron (NM_001308339, intron 5 of 22)	MER21-int|LTR|ERVL	-117880	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.030151	0.460000	
chunk0199_185_1	chr9	4663062	4663998	+	0	NA	3' UTR (NM_203453, exon 1 of 1)	3' UTR (NM_203453, exon 1 of 1)	1236	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.011752	0.416222	585(GAAACATGATGTTCAT,+,0.00)
chunk0052_463_1	chr12	133024061	133024260	+	0	NA	Intergenic	MLT1G3-int|LTR|ERVL-MaLR	13062	NR_110091	101928597	Hs.638942	NR_110091	ENSG00000246394	ZNF84-DT	-	ZNF84 divergent transcript	ncRNA	0.010050	0.405000	
chunk0107_311_1	chr2	219524256	219524875	+	0	NA	intron (NM_182847, intron 1 of 8)	MIRb|SINE|MIR	10395	NM_182847	55515	Hs.87469	NM_018674	ENSG00000072182	ASIC4	ACCN4|BNAC4	acid sensing ion channel subunit family member 4	protein-coding	0.012924	0.464516	
chunk0134_219_1	chr3	178736285	178736641	+	0	NA	intron (NM_001278911, intron 1 of 4)	intron (NM_001278911, intron 1 of 4)	123942	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.011236	0.470588	150(AAGAACAGACTGTGCT,-,0.00),151(AGAACAGACTGTGCTC,+,0.00)
chunk0111_78_1	chr20	23162300	23162688	+	0	NA	Intergenic	L2a|LINE|L2	-29858	NR_034149	200261	Hs.352228	NM_182535	ENSG00000233746	LINC00656	-	long intergenic non-protein coding RNA 656	ncRNA	0.028351	0.537275	
chunk0079_405_1	chr17	19508018	19508230	+	0	NA	Intergenic	Intergenic	-25730	NM_018242	55244	Hs.232054	NM_018242	ENSG00000142494	SLC47A1	MATE1	solute carrier family 47 member 1	protein-coding	0.070755	0.563380	
chunk0048_151_1	chr12	80556306	80557264	+	0	NA	intron (NM_001145026, intron 25 of 44)	intron (NM_001145026, intron 25 of 44)	112439	NM_001145026	374462	Hs.539284	NM_001145026	ENSG00000139304	PTPRQ	DFNA73|DFNB84|DFNB84A|PTPGMC1|R-PTP-Q	protein tyrosine phosphatase receptor type Q	protein-coding	0.002088	0.352450	
chunk0199_223_1	chr9	5284835	5285034	+	0	NA	Intergenic	L1M2b|LINE|L1	19677	NM_005059	6019	Hs.127032	NM_005059	ENSG00000107014	RLN2	H2|H2-RLX|RLXH2|bA12D24.1.1|bA12D24.1.2	relaxin 2	protein-coding	0.015075	0.545000	
chunk0016_110_1	chr1	196007564	196008374	+	0	NA	Intergenic	Intergenic	574512	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.003704	0.320592	
chunk0034_222_1	chr11	33064568	33064862	+	0	NA	intron (NM_001145541, intron 7 of 9)	L2c|LINE|L2	-11435	NR_015451	283267	Hs.533701	NR_015451	ENSG00000280798	LINC00294	NCRNA00294	long intergenic non-protein coding RNA 294	ncRNA	0.013605	0.467797	
chunk0162_337_1	chr6	6906664	6907360	+	0	NA	Intergenic	Intergenic	-200585	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.010057	0.407461	
chunk0077_17_1	chr16	75019276	75019685	+	0	NA	intron (NM_032268, intron 1 of 4)	L1ME3E|LINE|L1	20463	NM_032268	84937	Hs.427284	NM_032268	ENSG00000186187	ZNRF1	NIN283	zinc and ring finger 1	protein-coding	0.007335	0.358537	
chunk0176_413_1	chr7	19363349	19363591	+	0	NA	Intergenic	L1ME2|LINE|L1	-218049	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.004132	0.312757	
chunk0029_310_1	chr10	104288164	104288894	+	0	NA	intron (NM_001191014, intron 3 of 4)	L1ME4a|LINE|L1	13400	NM_001191015	119391	Hs.107384	NM_183239	ENSG00000065621	GSTO2	GSTO 2-2|bA127L20.1	glutathione S-transferase omega 2	protein-coding	0.006849	0.372093	
chunk0101_186_1	chr2	129432538	129432741	+	0	NA	Intergenic	Intergenic	-158748	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.024631	0.514706	
chunk0186_106_1	chr7	137942426	137942742	+	0	NA	intron (NM_194071, intron 1 of 11)	(AAAAC)n|Simple_repeat|Simple_repeat	-10764	NM_001243523									0.003165	0.340694	
chunk0059_290_1	chr14	35802849	35803441	+	0	NA	intron (NM_001283043, intron 1 of 41)	L1ME1|LINE|L1	6081	NM_001283044	253959	Hs.113150	NM_014990	ENSG00000174373	RALGAPA1	GARNL1|GRIPE|RalGAPalpha1|TULIP1|p240	Ral GTPase activating protein catalytic alpha subunit 1	protein-coding	0.003378	0.377740	
chunk0013_240_1	chr1	169595907	169596204	+	0	NA	exon (NM_003005, exon 12 of 17)	exon (NM_003005, exon 12 of 17)	-9524	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.010101	0.479866	
chunk0062_299_1	chr14	72894306	72894779	+	0	NA	promoter-TSS (NM_012074)	promoter-TSS (NM_012074)	-426	NM_012074	8110	Hs.162868	NM_012074	ENSG00000205683	DPF3	BAF45C|CERD4	double PHD fingers 3	protein-coding	0.040169	0.485232	
chunk0030_226_1	chr10	114819443	114819823	+	0	NA	Intergenic	Intergenic	-2111	NM_020940	57700	Hs.192619	NM_020940	ENSG00000151553	FAM160B1	KIAA1600|bA106M7.3	family with sequence similarity 160 member B1	protein-coding	0.002632	0.346457	
chunk0084_214_1	chr17	78200717	78201018	+	0	NA	intron (NM_001145526, intron 2 of 10)	intron (NM_001145526, intron 2 of 10)	-13329	NM_001168	332	Hs.744872	NM_001168	ENSG00000089685	BIRC5	API4|EPR-1	baculoviral IAP repeat containing 5	protein-coding	0.016611	0.463576	
chunk0074_264_1	chr16	28151101	28151706	+	0	NA	intron (NM_001270940, intron 9 of 24)	L1ME3A|LINE|L1	60515	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.011570	0.407591	
chunk0167_41_1	chr6	54710355	54710909	+	0	NA	Intergenic	Intergenic	-136139	NM_001010872	222584	Hs.152423	NM_001010872	ENSG00000168143	FAM83B	C6orf143	family with sequence similarity 83 member B	protein-coding	0.003610	0.398198	240(CAGGACAAGTTGTGCC,-,0.00),241(AGGACAAGTTGTGCCT,+,0.00)
chunk0066_407_1	chr15	39360680	39361410	+	0	NA	Intergenic	L1MC4|LINE|L1	110376	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.004110	0.350205	459(AAGTACACTATGTCTC,-,0.00),460(AGTACACTATGTCTCC,+,0.00)
chunk0041_189_1	chr11	126375724	126376244	+	0	NA	intron (NM_006278, intron 1 of 10)	intron (NM_006278, intron 1 of 10)	20090	NM_006278	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.017308	0.401152	
chunk0051_278_1	chr12	118115924	118116182	+	0	NA	Intergenic	MER50|LTR|ERV1	-12048	NM_019086	54621	Hs.187624	NM_019086	ENSG00000176834	VSIG10	-	V-set and immunoglobulin domain containing 10	protein-coding	0.003876	0.494208	
chunk0120_221_1	chr3	7864574	7865069	+	0	NA	Intergenic	Intergenic	151486	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.006061	0.399194	
chunk0057_256_1	chr13	105449156	105449654	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-16462	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.008032	0.338677	123(TGGCACAGGCTGTGTT,-,0.00),124(GGCACAGGCTGTGTTA,+,0.00)
chunk0138_248_1	chr4	39559443	39559951	+	0	NA	intron (NM_174921, intron 3 of 4)	intron (NM_174921, intron 3 of 4)	31858	NR_047679	100885776	Hs.640769	NR_047679	ENSG00000249348	UGDH-AS1	-	UGDH antisense RNA 1	ncRNA	0.013780	0.457760	
chunk0106_395_1	chr2	207744089	207744425	+	0	NA	intron (NM_152523, intron 8 of 10)	L2a|LINE|L2	-10550	NR_039934	100616361		NR_039934	ENSG00000284079	MIR4775	-	microRNA 4775	ncRNA	0.005952	0.462908	
chunk0175_457_1	chr6	170329095	170329347	+	0	NA	intron (NM_032448, intron 3 of 10).2	intron (NM_032448, intron 3 of 10).2	-1540	NR_039787	100616430		NR_039787	ENSG00000266245	MIR4644	-	microRNA 4644	ncRNA	0.003968	0.513834	
chunk0137_336_1	chr4	24973255	24973934	+	0	NA	intron (NM_173463, intron 1 of 12)	MLT1K|LTR|ERVL-MaLR	6610	NM_173463	91050	Hs.106432	NM_173463	ENSG00000181982	CCDC149	-	coiled-coil domain containing 149	protein-coding	0.008837	0.454412	
chunk0145_427_1	chr4	153014129	153014822	+	0	NA	Intergenic	L1ME4c|LINE|L1	71492	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.000000	0.383285	
chunk0143_68_1	chr4	108058595	108059166	+	0	NA	intron (NM_001130714, intron 9 of 9)	intron (NM_001130714, intron 9 of 9)	69166	NM_001184705	3033	Hs.438289	NM_005327	ENSG00000138796	HADH	HAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHAD	hydroxyacyl-CoA dehydrogenase	protein-coding	0.010508	0.426573	307(AAGGACAGTGTGTGCA,-,0.00),308(AGGACAGTGTGTGCAG,+,0.00)
chunk0193_287_1	chr8	77533595	77534159	+	0	NA	Intergenic	Intergenic	83180	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.003546	0.345133	
chunk0170_299_1	chr6	115552879	115553241	+	0	NA	Intergenic	Intergenic	-485671	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.011050	0.338843	
chunk0198_350_1	chr8	140404627	140404826	+	0	NA	intron (NM_001160372, intron 6 of 22)	L1ME3G|LINE|L1	53036	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.040201	0.455000	
chunk0083_98_1	chr17	64515773	64516134	+	0	NA	intron (NM_001316990, intron 4 of 18)	MIRb|SINE|MIR	9217	NM_001316990	90799	Hs.569713	NM_138363	ENSG00000258890	CEP95	CCDC45	centrosomal protein 95	protein-coding	0.002770	0.397790	
chunk0155_383_1	chr5	98276012	98276294	+	0	NA	Intergenic	Intergenic	-493142	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.003546	0.254417	
chunk0130_16_1	chr3	128402528	128402814	+	0	NA	intron (NM_021937, intron 6 of 6)	L1M5|LINE|L1	-60923	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.020979	0.498258	
chunk0060_390_1	chr14	52844465	52845062	+	0	NA	Intergenic	Intergenic	-53095	NM_198066	64841	Hs.478025	NM_198066	ENSG00000100522	GNPNAT1	GNA1|GNPNAT|Gpnat1	glucosamine-phosphate N-acetyltransferase 1	protein-coding	0.010050	0.433110	
chunk0205_347_1	chr9	113357064	113357482	+	0	NA	intron (NM_017688, intron 2 of 5)	L1MD2|LINE|L1	7741	NM_017688	54836	Hs.614517	NM_017688	ENSG00000119411	BSPRY	-	B-box and SPRY domain containing	protein-coding	0.011962	0.403341	119(GAGAGCAGAGTGTCCC,-,0.00),120(AGAGCAGAGTGTCCCA,+,0.00),262(TAGGACTCCTTGTGCT,-,0.00),263(AGGACTCCTTGTGCTA,+,0.00)
chunk0191_224_1	chr8	52714641	52714981	+	0	NA	promoter-TSS (NM_001083617)	promoter-TSS (NM_001083617)	-345	NM_001083617	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.073529	0.630499	
chunk0168_184_1	chr6	85006414	85006721	+	0	NA	Intergenic	Intergenic	-242331	NM_001080508	9096	Hs.251830	NM_001080508	ENSG00000112837	TBX18	CAKUT2	T-box transcription factor 18	protein-coding	0.000000	0.376623	62(AAAAACATGATGTCCT,-,0.00),63(AAAACATGATGTCCTG,+,0.00)
chunk0042_65_1	chr12	2023253	2023772	+	0	NA	Intergenic	Intergenic	-19001	NM_152640	196513	Hs.130934	NM_152640	ENSG00000151065	DCP1B	DCP1	decapping mRNA 1B	protein-coding	0.007707	0.465385	411(AGGTACTTACTGTGCT,-,0.00),412(GGTACTTACTGTGCTT,+,0.00)
chunk0092_257_1	chr19	33037181	33037391	+	0	NA	intron (NM_033103, intron 2 of 14)	LTR12C|LTR|ERV1	27632	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.000000	0.492891	
chunk0027_112_1	chr10	74072506	74073054	+	0	NA	exon (NM_014000, exon 5 of 22)	exon (NM_014000, exon 5 of 22)	74666	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.016423	0.404372	
chunk0071_104_1	chr15	81062524	81062723	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	61669	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.000000	0.480000	
chunk0096_294_1	chr2	32595159	32595688	+	0	NA	intron (NM_016252, intron 68 of 73)	intron (NM_016252, intron 68 of 73)	-20605	NR_125793	103752586	Hs.666092	NR_125793	ENSG00000279897	BIRC6-AS2	linc-birc6|megamind	BIRC6 antisense RNA 2	ncRNA	0.000000	0.307547	
chunk0033_13_1	chr11	12421499	12422043	+	0	NA	intron (NM_018222, intron 1 of 12)	intron (NM_018222, intron 1 of 12)	44292	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.001838	0.420183	
chunk0128_5_1	chr3	103554409	103554896	+	0	NA	Intergenic	LTR30|LTR|ERV1	-30536	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.022587	0.418033	
chunk0201_110_1	chr9	35115886	35116175	+	0	NA	promoter-TSS (NM_025182)	promoter-TSS (NM_025182)	-134	NM_025182	80256	Hs.301696	NM_025182	ENSG00000005238	FAM214B	KIAA1539	family with sequence similarity 214 member B	protein-coding	0.062284	0.651724	
chunk0193_427_1	chr8	80900330	80900529	+	0	NA	Intergenic	L1MB5|LINE|L1	-25648	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.005025	0.345000	
chunk0127_129_1	chr3	94018598	94018797	+	0	NA	intron (NM_001001850, intron 1 of 1)	L2a|LINE|L2	9913	NM_001001850	415117	Hs.679768	NM_001001850	ENSG00000178750	STX19	-	syntaxin 19	protein-coding	0.010050	0.415000	
chunk0164_338_1	chr6	25329844	25330441	+	0	NA	intron (NM_017640, intron 2 of 36)	L2b|LINE|L2	50714	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.010050	0.448161	
chunk0182_95_1	chr7	92953888	92954709	+	0	NA	Intergenic	Intergenic	-117671	NM_001145306	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.006090	0.340633	
chunk0061_361_1	chr14	63893669	63893933	+	0	NA	intron (NM_182914, intron 1 of 115)	intron (NM_182914, intron 1 of 115)	40836	NM_015180	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.011364	0.467925	
chunk0195_68_1	chr8	93868724	93868948	+	0	NA	Intergenic	Charlie15b|DNA|hAT-Charlie	47283	NR_039602	100616169		NR_039602	ENSG00000284288	MIR378D2	mir-378d-2	microRNA 378d-2	ncRNA	0.013393	0.435556	
chunk0145_287_1	chr4	149858909	149859544	+	0	NA	Intergenic	L1MA4|LINE|L1	-219048	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.006299	0.372642	
chunk0179_147_1	chr7	46259974	46260355	+	0	NA	Intergenic	Intergenic	-338892	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.000000	0.410995	
chunk0205_206_1	chr9	109300979	109301655	+	0	NA	intron (NM_018424, intron 1 of 15)	L1MC5a|LINE|L1	19647	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.007396	0.407681	
chunk0084_171_1	chr17	77461403	77461679	+	0	NA	intron (NM_001293698, intron 1 of 9)	intron (NM_001293698, intron 1 of 9)	7548	NM_001293698	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.021739	0.487365	
chunk0197_143_1	chr8	120366441	120366793	+	0	NA	intron (NM_021110, intron 45 of 47)	intron (NM_021110, intron 45 of 47)	-78781	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.008523	0.385269	
chunk0018_35_1	chr1	215621745	215622017	+	0	NA	TTS (NM_016121)	TTS (NM_016121)	54489	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.003676	0.271062	
chunk0081_341_1	chr17	46893864	46894496	+	0	NA	Intergenic	Intergenic	-28940	NM_001012511	9570	Hs.463278	NM_004287	ENSG00000108433	GOSR2	Bos1|EPM6|GS27	golgi SNAP receptor complex member 2	protein-coding	0.017405	0.497630	
chunk0099_326_1	chr2	99864764	99865382	+	0	NA	intron (NM_001025108, intron 6 of 23)	MamRTE1|LINE|RTE-BovB	240510	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.006472	0.458805	
chunk0022_130_1	chr10	11698266	11698603	+	0	NA	Intergenic	L2a|LINE|L2	-43923	NM_024693	79746	Hs.22242	NM_024693	ENSG00000134463	ECHDC3	-	enoyl-CoA hydratase domain containing 3	protein-coding	0.005935	0.443787	
chunk0104_36_1	chr2	171018590	171019075	+	0	NA	intron (NM_001136554, intron 12 of 20)	intron (NM_001136554, intron 12 of 20)	48141	NM_001136555	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.002062	0.347737	127(AAGAACACCAAGTTTC,-,0.00),274(AAGAACAGACTGTATT,-,0.00),275(AGAACAGACTGTATTA,+,0.00)
chunk0173_80_1	chr6	142724853	142725231	+	0	NA	Intergenic	Intergenic	-87153	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.007937	0.503958	134(CAGAACATTCTCTCCT,-,0.00),135(AGAACATTCTCTCCTC,+,0.00)
chunk0012_395_1	chr1	163635410	163635929	+	0	NA	Intergenic	L1MB3|LINE|L1	-212478	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.005780	0.286538	
chunk0003_9_1	chr1	28648531	28648828	+	0	NA	promoter-TSS (NR_004407)	promoter-TSS (NR_004407)	79	NR_004407	26824	Hs.640266	NR_004407	ENSG00000274978	RNU11	RNU11-1|U11	RNA, U11 small nuclear	snRNA	0.043771	0.429530	
chunk0169_117_1	chr6	100831227	100831456	+	0	NA	intron (NM_006828, intron 4 of 41)	L1MEi|LINE|L1	50031	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.000000	0.326087	
chunk0082_70_1	chr17	51433272	51433750	+	0	NA	Intergenic	L1MEi|LINE|L1	96796	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.000000	0.334029	
chunk0178_339_1	chr7	38681736	38682851	+	0	NA	Intergenic	Intergenic	4796	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.002691	0.392473	
chunk0119_400_1	chr22	49277900	49278266	+	0	NA	Intergenic	Intergenic	265383	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.008197	0.435967	105(GAGAACTCCTTGTCCT,-,0.00),106(AGAACTCCTTGTCCTG,+,0.00),194(GGCCCACACTGTCCCT,+,0.00)
chunk0130_323_1	chr3	138118553	138118752	+	0	NA	Intergenic	Intergenic	-3043	NM_173543	199221	Hs.351403	NM_173543	ENSG00000158163	DZIP1L	DZIP2|PKD5	DAZ interacting zinc finger protein 1 like	protein-coding	0.000000	0.460000	
chunk0079_103_1	chr17	12128658	12129630	+	0	NA	exon (NM_003010, exon 9 of 11)	exon (NM_003010, exon 9 of 11)	47245	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.009259	0.417266	
chunk0094_384_1	chr2	9972587	9972843	+	0	NA	intron (NM_198182, intron 8 of 15)	intron (NM_198182, intron 8 of 15)	21052	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.015625	0.517510	
chunk0089_416_1	chr18	68861110	68861391	+	0	NA	intron (NM_024781, intron 4 of 7)	intron (NM_024781, intron 4 of 7)	63170	NM_024781	79839	Hs.280781	NM_024781	ENSG00000150636	CCDC102B	ACY1L|AN|C18orf14|HsT1731	coiled-coil domain containing 102B	protein-coding	0.007117	0.297872	
chunk0173_245_1	chr6	146905231	146905517	+	0	NA	intron (NR_034115, intron 7 of 10)	intron (NR_034115, intron 7 of 10)	-101550	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.000000	0.365854	
chunk0186_165_1	chr7	139290452	139291098	+	0	NA	intron (NM_173569, intron 15 of 17)	intron (NM_173569, intron 15 of 17)	-49584	NM_001244585	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.003096	0.347759	
chunk0157_353_1	chr5	123155021	123155220	+	0	NA	intron (NM_001136239, intron 3 of 7)	intron (NM_001136239, intron 3 of 7)	65974	NM_001136239	93166	Hs.135118	NM_001136239	ENSG00000061455	PRDM6	KMT8C|PDA3|PRISM	PR/SET domain 6	protein-coding	0.005025	0.395000	
chunk0064_150_1	chr14	91760466	91760665	+	0	NA	Intergenic	L1PB4|LINE|L1	-28479	NM_024764	79820	Hs.131755	NM_024764	ENSG00000133962	CATSPERB	C14orf161|CatSper(beta)	cation channel sperm associated auxiliary subunit beta	protein-coding	0.010050	0.510000	
chunk0085_43_1	chr18	765994	766200	+	0	NA	intron (NM_005433, intron 1 of 11)	MLT1L|LTR|ERVL-MaLR	46229	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.009709	0.381643	
chunk0005_448_1	chr1	63479940	63480719	+	0	NA	intron (NM_014288, intron 3 of 8)	intron (NM_014288, intron 3 of 8)	42944	NM_001206739	23421	Hs.166539	NM_014288	ENSG00000142856	ITGB3BP	CENP-R|CENPR|HSU37139|NRIF3|TAP20	integrin subunit beta 3 binding protein	protein-coding	0.002567	0.297436	
chunk0068_230_1	chr15	55387023	55387321	+	0	NA	intron (NM_004748, intron 2 of 7)	intron (NM_004748, intron 2 of 7)	-14138	NR_030358	693213		NR_030358	ENSG00000283891	MIR628	MIRN628|hsa-mir-628|mir-628	microRNA 628	ncRNA	0.000000	0.424749	
chunk0156_70_1	chr5	103647938	103648199	+	0	NA	Intergenic	Intergenic	-85267	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.011494	0.393130	
chunk0037_233_1	chr11	75260976	75261495	+	0	NA	3' UTR (NM_020251, exon 15 of 15)	3' UTR (NM_020251, exon 15 of 15)	20330	NM_001195528	100507050	Hs.577323	NM_001195528	ENSG00000261594	TPBGL	-	trophoblast glycoprotein like	protein-coding	0.011561	0.503846	
chunk0102_110_1	chr2	144457785	144458026	+	0	NA	intron (NM_014795, intron 2 of 9)	intron (NM_014795, intron 2 of 9)	-61709	NR_040248	100303491	Hs.560789	NR_040248	ENSG00000238057	ZEB2-AS1	ZEB2-AS|ZEB2AS|ZEB2NAT	ZEB2 antisense RNA 1	ncRNA	0.004149	0.314050	
chunk0144_108_1	chr4	128635415	128636104	+	0	NA	Intergenic	Intergenic	-173864	NM_024900	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.013062	0.411594	244(TAGCACTGGCTGTCCC,-,0.00),245(AGCACTGGCTGTCCCA,+,0.00)
chunk0173_376_1	chr6	149564447	149564646	+	0	NA	Intergenic	Intergenic	-1846	NM_138785	116254	Hs.438872	NM_138785	ENSG00000055211	GINM1	C6orf72	glycoprotein integral membrane 1	protein-coding	0.005025	0.425000	
chunk0198_201_1	chr8	133721551	133722128	+	0	NA	Intergenic	Intergenic	55513	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.008666	0.418685	
chunk0205_38_1	chr9	105709376	105709940	+	0	NA	intron (NM_018112, intron 2 of 5)	Tigger19b|DNA|TcMar-Tigger	15133	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.008865	0.362832	
chunk0055_286_1	chr13	64542541	64542902	+	0	NA	Intergenic	L2|LINE|L2	-698596	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.002770	0.337017	136(AACACACTATGTACTT,+,0.00)
chunk0140_415_1	chr4	75827170	75827641	+	0	NA	Intergenic	Intergenic	75123	NM_006239	5470	Hs.290873	NM_006239	ENSG00000156194	PPEF2	PPP7CB	protein phosphatase with EF-hand domain 2	protein-coding	0.004246	0.421610	
chunk0120_197_1	chr3	7068230	7068768	+	0	NA	intron (NM_000844, intron 1 of 9)	intron (NM_000844, intron 1 of 9)	-174482	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.007435	0.333952	
chunk0163_215_1	chr6	12058616	12058906	+	0	NA	intron (NM_002114, intron 2 of 8)	intron (NM_002114, intron 2 of 8)	46270	NM_002114	3096	Hs.567284	NM_002114	ENSG00000095951	HIVEP1	CIRIP|CRYBP1|GAAP|MBP-1|PRDII-BF1|Schnurri-1|ZAS1|ZNF40|ZNF40A	human immunodeficiency virus type I enhancer binding protein 1	protein-coding	0.010345	0.446735	
chunk0097_107_1	chr2	46092330	46092869	+	0	NA	intron (NM_005400, intron 11 of 14)	intron (NM_005400, intron 11 of 14)	-204803	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.007421	0.472222	
chunk0184_441_1	chr7	123129101	123129584	+	0	NA	intron (NM_022444, intron 9 of 14)	(TG)n|Simple_repeat|Simple_repeat	70629	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.004141	0.380165	
chunk0193_24_1	chr8	70844515	70844714	+	0	NA	Intergenic	L1M2|LINE|L1	175167	NM_001287260	389668	Hs.458938	NM_001011720	ENSG00000221947	XKR9	XRG9	XK related 9	protein-coding	0.005025	0.585000	
chunk0042_445_1	chr12	12405770	12406290	+	0	NA	intron (NM_058169, intron 2 of 3)	MLT1N2|LTR|ERVL-MaLR	48951	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.009615	0.401152	
chunk0166_145_1	chr6	44983416	44983969	+	0	NA	intron (NM_181356, intron 8 of 12)	intron (NM_181356, intron 8 of 12)	214078	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.001808	0.308664	
chunk0075_13_1	chr16	46809534	46809939	+	0	NA	exon (NM_001001436, exon 3 of 4)	exon (NM_001001436, exon 3 of 4)	21426	NM_001001436	388272	Hs.406551	NM_001001436	ENSG00000155330	C16orf87	-	chromosome 16 open reading frame 87	protein-coding	0.007407	0.366995	
chunk0090_256_1	chr18	74273351	74273675	+	0	NA	intron (NM_001190807, intron 1 of 3)	intron (NM_001190807, intron 1 of 3)	18503	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.006173	0.384615	
chunk0110_281_1	chr20	17587908	17588128	+	0	NA	intron (NM_006870, intron 1 of 3)	MER4C|LTR|ERV1	18064	NM_001011546	11034	Hs.304192	NM_006870	ENSG00000125868	DSTN	ACTDP|ADF|HEL32|bA462D18.2	destrin, actin depolymerizing factor	protein-coding	0.009091	0.407240	100(CAGTACATAATGTACT,-,0.00),101(AGTACATAATGTACTG,+,0.00)
chunk0186_415_1	chr7	146282820	146283509	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	166803	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.008708	0.342029	
chunk0138_242_1	chr4	39539353	39539620	+	0	NA	intron (NR_047679, intron 2 of 4)	LTR3B|LTR|ERVK	11647	NR_047679	100885776	Hs.640769	NR_047679	ENSG00000249348	UGDH-AS1	-	UGDH antisense RNA 1	ncRNA	0.007491	0.462687	
chunk0102_460_1	chr2	158665607	158666288	+	0	NA	intron (NM_001005476, intron 15 of 20)	intron (NM_001005476, intron 15 of 20)	-129370	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.007342	0.375367	
chunk0164_111_1	chr6	20664279	20664717	+	0	NA	intron (NM_017774, intron 5 of 15)	intron (NM_017774, intron 5 of 15)	130041	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.002283	0.298405	
chunk0087_82_1	chr18	32180964	32181362	+	0	NA	Intergenic	L1MC1|LINE|L1	-8861	NM_005925	4225	Hs.194777	NM_005925	ENSG00000141434	MEP1B	-	meprin A subunit beta	protein-coding	0.000000	0.380952	
chunk0211_224_1	chrX	118666476	118666847	+	0	NA	intron (NM_144658, intron 45 of 52)	L1ME2|LINE|L1	-60935	NM_001560	3597	Hs.496646	NM_001560	ENSG00000131724	IL13RA1	CD213A1|CT19|IL-13Ra|NR4	interleukin 13 receptor subunit alpha 1	protein-coding	0.008086	0.317204	
chunk0192_78_1	chr8	60763083	60763524	+	0	NA	intron (NM_017780, intron 2 of 37)	MER33|DNA|hAT-Charlie	22044	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.006803	0.398190	
chunk0109_293_1	chr20	8267130	8267329	+	0	NA	intron (NM_015192, intron 2 of 31)	LTR16A1|LTR|ERVL	134964	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.005025	0.485000	
chunk0202_294_1	chr9	77763523	77763978	+	0	NA	intron (NM_002072, intron 5 of 6)	intron (NM_002072, intron 5 of 6)	-115434	NM_004297	9630	Hs.657795	NM_004297	ENSG00000156049	GNA14	-	G protein subunit alpha 14	protein-coding	0.010989	0.372807	
chunk0184_304_1	chr7	120028770	120029089	+	0	NA	Intergenic	L1MC|LINE|L1	-121554	NR_131963	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.009404	0.290625	
chunk0150_445_1	chr5	40580802	40581270	+	0	NA	Intergenic	L1MA7|LINE|L1	-98894	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.004274	0.334755	180(TTGAGCAGACTGTTCT,-,0.00),181(TGAGCAGACTGTTCTT,+,0.00),284(TGGTTCATCCTGTTCC,-,0.00),285(GGTTCATCCTGTTCCA,+,0.00)
chunk0168_296_1	chr6	91352924	91353308	+	0	NA	Intergenic	Intergenic	-168544	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.013021	0.400000	
chunk0052_415_1	chr12	131512282	131512801	+	0	NA	Intergenic	L2c|LINE|L2	165071	NR_103736	338797	Hs.592007	NM_001025466		LINC02370	-	long intergenic non-protein coding RNA 2370	ncRNA	0.015414	0.528846	
chunk0089_166_1	chr18	59120288	59120530	+	0	NA	Intergenic	Intergenic	-19448	NM_001307941	90701	Hs.45107	NM_033280	ENSG00000166562	SEC11C	SEC11L3|SPC21|SPCS4C	SEC11 homolog C, signal peptidase complex subunit	protein-coding	0.004132	0.370370	
chunk0089_403_1	chr18	68199497	68200048	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	515344	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.000000	0.309783	270(AGGCACATGCTGTATT,-,0.00),271(GGCACATGCTGTATTT,+,0.00)
chunk0172_233_1	chr6	137105038	137105314	+	0	NA	Intergenic	ERVL-int|LTR|ERVL	-59996	NM_001278723	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.010870	0.527076	
chunk0194_193_1	chr8	85312692	85313388	+	0	NA	Intergenic	Intergenic	28674	NM_001164830	759	Hs.23118	NM_001738	ENSG00000133742	CA1	CA-I|CAB|Car1|HEL-S-11	carbonic anhydrase 1	protein-coding	0.011494	0.350072	
chunk0140_165_1	chr4	69683143	69683420	+	0	NA	Intergenic	Intergenic	-30032	NM_001252274	10941	Hs.225950	NM_006798	ENSG00000173610	UGT2A1	UDPGT2A1	UDP glucuronosyltransferase family 2 member A1 complex locus	protein-coding	0.003610	0.262590	
chunk0187_187_1	chr7	151312943	151313218	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-28681	NM_016118	51667	Hs.647082	NM_016118	ENSG00000013374	NUB1	BS4|NUB1L|NYREN18	negative regulator of ubiquitin like proteins 1	protein-coding	0.007273	0.510870	
chunk0001_11_1	chr1	1005366	1005568	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-5295	NM_021170	57801	Hs.154029	NM_021170	ENSG00000188290	HES4	bHLHb42	hes family bHLH transcription factor 4	protein-coding	0.029703	0.591133	
chunk0196_46_1	chr8	101861619	101862013	+	0	NA	intron (NM_001040629, intron 3 of 6)	intron (NM_001040629, intron 3 of 6)	-70605	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.005076	0.341772	
chunk0138_320_1	chr4	41442691	41443144	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	82132	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.323789	
chunk0167_323_1	chr6	72260362	72260844	+	0	NA	intron (NM_014989, intron 18 of 33)	intron (NM_014989, intron 18 of 33)	43843	NM_001168410	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.006224	0.335404	
chunk0054_120_1	chr13	43113650	43114021	+	0	NA	intron (NR_047013, intron 1 of 2)	intron (NR_047013, intron 1 of 2)	670	NR_047013	100874159	Hs.633241	NR_047013		LINC00400	-	long intergenic non-protein coding RNA 400	ncRNA	0.002695	0.419355	
chunk0189_22_1	chr8	19627775	19628321	+	0	NA	intron (NR_024040, intron 1 of 9)	intron (NR_024040, intron 1 of 9)	-25503	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.005495	0.398537	207(GGGAACTCTCTGTACT,-,0.00),208(GGAACTCTCTGTACTA,+,0.00)
chunk0095_135_1	chr2	16720281	16720774	+	0	NA	Intergenic	L1PA16|LINE|L1	-54661	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.016227	0.386640	
chunk0174_141_1	chr6	157570131	157570499	+	0	NA	intron (NM_024630, intron 2 of 8)	intron (NM_024630, intron 2 of 8)	41183	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.010870	0.401084	
chunk0060_233_1	chr14	49641689	49642340	+	0	NA	Intergenic	Intergenic	-6784	NM_001083908	55172	Hs.231761	NM_018139	ENSG00000165506	DNAAF2	C14orf104|CILD10|KTU|PF13	dynein axonemal assembly factor 2	protein-coding	0.012289	0.441718	334(GGGAACACACTGTCTC,-,0.00),335(GGAACACACTGTCTCT,+,0.00)
chunk0069_146_1	chr15	62451981	62452180	+	0	NA	Intergenic	Intergenic	109051	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.015075	0.545000	
chunk0088_281_1	chr18	49461506	49461862	+	0	NA	promoter-TSS (NM_017653)	promoter-TSS (NM_017653)	-975	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.005618	0.364146	
chunk0075_72_1	chr16	48053566	48054229	+	0	NA	Intergenic	Intergenic	92873	NM_033226	94160	Hs.410111	NM_033226	ENSG00000140798	ABCC12	MRP9	ATP binding cassette subfamily C member 12	protein-coding	0.007541	0.472892	
chunk0131_254_1	chr3	149571435	149571713	+	0	NA	intron (NM_015472, intron 3 of 6)	intron (NM_015472, intron 3 of 6)	86451	NM_001168280	25937	Hs.477921	NM_015472	ENSG00000018408	WWTR1	TAZ	WW domain containing transcription regulator 1	protein-coding	0.003597	0.433692	
chunk0008_143_1	chr1	92120352	92120702	+	0	NA	intron (NM_183242, intron 4 of 8)	Tigger3b|DNA|TcMar-Tigger	40222	NM_183242	284697	Hs.676102	NM_183242	ENSG00000189195	BTBD8	-	BTB domain containing 8	protein-coding	0.005714	0.356125	
chunk0131_409_1	chr3	152942929	152943689	+	0	NA	Intergenic	Intergenic	108616	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.005263	0.328515	
chunk0208_268_1	chrX	21489770	21490212	+	0	NA	intron (NM_014927, intron 5 of 21)	intron (NM_014927, intron 5 of 21)	115573	NM_001168648	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.004525	0.367946	
chunk0009_152_1	chr1	104953420	104954145	+	0	NA	Intergenic	Intergenic	665153	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.005517	0.311295	
chunk0189_447_1	chr8	28289942	28290629	+	0	NA	Intergenic	Intergenic	-26847	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.007278	0.380814	
chunk0013_328_1	chr1	171583606	171583805	+	0	NA	intron (NM_015172, intron 28 of 33)	Tigger3b|DNA|TcMar-Tigger	68928	NM_000261	4653	Hs.436037	NM_000261	ENSG00000034971	MYOC	GLC1A|GPOA|JOAG|JOAG1|TIGR	myocilin	protein-coding	0.000000	0.315000	
chunk0050_175_1	chr12	103848915	103849195	+	0	NA	intron (NR_027249, intron 14 of 15)	L2b|LINE|L2	-7858	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.014286	0.491103	108(GGGAACAGATTGTTCT,-,0.00),109(GGAACAGATTGTTCTC,+,0.00)
chunk0121_13_1	chr3	14651511	14651843	+	0	NA	promoter-TSS (NM_016474)	promoter-TSS (NM_016474)	-69	NM_016474	51244	Hs.517820	NM_016474	ENSG00000154781	CCDC174	C3orf19|HSPC212|IHPM|IHPMR	coiled-coil domain containing 174	protein-coding	0.069277	0.540541	
chunk0023_382_1	chr10	30553941	30554312	+	0	NA	Intergenic	Intergenic	75592	NM_183058	119180	Hs.522610	NM_183058	ENSG00000151033	LYZL2	LYZD2	lysozyme like 2	protein-coding	0.029650	0.483871	
chunk0027_462_1	chr10	81840756	81841004	+	0	NA	Intergenic	Intergenic	-34434	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.020161	0.457831	
chunk0081_404_1	chr17	48313945	48314144	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	19697	NR_131240	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.005025	0.235000	
chunk0013_454_1	chr1	174022107	174022348	+	0	NA	Intergenic	CpG	-29155	NM_172071	149041	Hs.30258	NM_172071	ENSG00000135870	RC3H1	RNF198|ROQUIN	ring finger and CCCH-type domains 1	protein-coding	0.112033	0.743802	
chunk0081_259_1	chr17	43361010	43361432	+	0	NA	Intergenic	CpG	27677	NR_027413	100130581	Hs.546897	NR_027412	ENSG00000188825	LINC00910	-	long intergenic non-protein coding RNA 910	ncRNA	0.078199	0.508274	
chunk0176_32_1	chr7	9366255	9366830	+	0	NA	Intergenic	L1PA15|LINE|L1	-267728	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.006957	0.324653	
chunk0145_90_1	chr4	145938778	145939064	+	0	NA	promoter-TSS (NM_001306215)	promoter-TSS (NM_001306215)	39	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.055944	0.585366	
chunk0135_245_1	chr3	188839372	188839571	+	0	NA	intron (NM_001167671, intron 8 of 10)	intron (NM_001167671, intron 8 of 10)	108168	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.015075	0.445000	
chunk0101_294_1	chr2	134491969	134492419	+	0	NA	intron (NM_030923, intron 5 of 7)	intron (NM_030923, intron 5 of 7)	226807	NM_030923	81615	Hs.369471	NM_030923	ENSG00000152128	TMEM163	DC29|SV31	transmembrane protein 163	protein-coding	0.011111	0.423503	
chunk0083_346_1	chr17	70225238	70225822	+	0	NA	Intergenic	Intergenic	55995	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.008562	0.381197	
chunk0200_14_1	chr9	14620859	14621296	+	0	NA	intron (NM_178566, intron 8 of 9)	MIR3|SINE|MIR	72405	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.006865	0.326484	
chunk0108_107_1	chr2	229512467	229513156	+	0	NA	exon (NM_139072, exon 6 of 13)	exon (NM_139072, exon 6 of 13)	201759	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.011611	0.388406	
chunk0129_200_1	chr3	121595042	121595241	+	0	NA	intron (NM_016298, intron 1 of 3)	intron (NM_016298, intron 1 of 3)	1818	NM_016298	51725	Hs.272564	NM_016298	ENSG00000163833	FBXO40	FBX40	F-box protein 40	protein-coding	0.005025	0.455000	
chunk0135_376_1	chr3	190961169	190961728	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	83518	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.001789	0.407143	
chunk0115_159_1	chr21	24042603	24043374	+	0	NA	Intergenic	Intergenic	278389	NR_109963	101927869	Hs.555591	NR_109963	ENSG00000224832	LINC01689	-	long intergenic non-protein coding RNA 1689	ncRNA	0.002594	0.323834	
chunk0034_228_1	chr11	33550730	33551290	+	0	NA	intron (NM_012194, intron 3 of 19)	intron (NM_012194, intron 3 of 19)	8679	NM_012194	25758	Hs.502266	NM_012194	ENSG00000110427	KIAA1549L	C11orf41|C11orf69|G2	KIAA1549 like	protein-coding	0.008929	0.397504	251(AAGAACTTAAAGTGCT,-,0.00)
chunk0205_213_1	chr9	109360573	109361115	+	0	NA	Intergenic	MIR|SINE|MIR	-39880	NM_019114	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.009225	0.381215	
chunk0154_434_1	chr5	89982053	89982473	+	0	NA	Intergenic	Intergenic	34457	NR_037433	100500825		NR_037433	ENSG00000264342	MIR3660	mir-3660	microRNA 3660	ncRNA	0.011905	0.342043	
chunk0122_196_1	chr3	32976042	32976337	+	0	NA	Intergenic	Intergenic	24615	NM_005508	1233	Hs.184926	NM_005508	ENSG00000183813	CCR4	CC-CKR-4|CD194|CKR4|CMKBR4|ChemR13|HGCN:14099|K5-5	C-C motif chemokine receptor 4	protein-coding	0.010169	0.496622	
chunk0007_201_1	chr1	81242491	81243129	+	0	NA	Intergenic	Intergenic	314892	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.004702	0.342723	
chunk0196_325_1	chr8	111935758	111936271	+	0	NA	Intergenic	Intergenic	-699811	NR_125418	101927487	Hs.630004	NR_125418	ENSG00000253103	LINC01609	-	long intergenic non-protein coding RNA 1609	ncRNA	0.005848	0.319066	
chunk0059_333_1	chr14	36874729	36875253	+	0	NA	exon (NM_001171170, exon 2 of 11)	exon (NM_001171170, exon 2 of 11)	77400	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.011450	0.388571	
chunk0098_132_1	chr2	69251001	69251362	+	0	NA	Intergenic	Intergenic	136073	NM_002056	2673	Hs.580300	NM_002056	ENSG00000198380	GFPT1	CMS12|CMSTA1|GFA|GFAT|GFAT 1|GFAT1|GFAT1m|GFPT|GFPT1L|MSLG	glutamine--fructose-6-phosphate transaminase 1	protein-coding	0.002770	0.320442	230(TGCACATTCAGTACTT,+,0.00)
chunk0121_72_1	chr3	15903080	15903643	+	0	NA	Intergenic	Intergenic	29590	NR_030289	693148		NR_030289	ENSG00000207815	MIR563	MIRN563|hsa-mir-563	microRNA 563	ncRNA	0.007105	0.468085	243(TAGCACAGTGTGTATT,-,0.00),244(AGCACAGTGTGTATTG,+,0.00)
chunk0158_109_1	chr5	126875206	126875687	+	0	NA	intron (NM_178450, intron 4 of 4)	intron (NM_178450, intron 4 of 4)	98293	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.024948	0.543568	
chunk0025_371_1	chr10	58747770	58748041	+	0	NA	intron (NM_001080512, intron 3 of 20)	MER58A|DNA|hAT-Charlie	32890	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.007380	0.404412	
chunk0068_157_1	chr15	53930403	53930720	+	0	NA	Intergenic	Intergenic	-82343	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.000000	0.374214	
chunk0064_237_1	chr14	94322474	94323086	+	0	NA	intron (NM_001756, intron 1 of 4)	intron (NM_001756, intron 1 of 4)	571	NM_001756	866	Hs.532635	NM_001756	ENSG00000170099	SERPINA6	CBG	serpin family A member 6	protein-coding	0.013072	0.499184	
chunk0132_322_1	chr3	160973150	160973783	+	0	NA	intron (NM_139245, intron 2 of 3)	intron (NM_139245, intron 2 of 3)	131429	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.003160	0.345426	
chunk0164_77_1	chr6	19796452	19796740	+	0	NA	Intergenic	L1MD2|LINE|L1	-40774	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.006944	0.449827	
chunk0128_201_1	chr3	107717381	107717770	+	0	NA	intron (NM_001276286, intron 5 of 16)	intron (NM_001276286, intron 5 of 16)	160493	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.002571	0.328205	180(TGGAACAGGATGTACT,-,0.00),181(GGAACAGGATGTACTG,+,0.00)
chunk0045_388_1	chr12	52494501	52494845	+	0	NA	Intergenic	Intergenic	-1276	NM_005554	3853	Hs.700779	NM_005554	ENSG00000205420	KRT6A	CK-6C|CK-6E|CK6A|CK6C|CK6D|K6A|K6C|K6D|KRT6C|KRT6D|PC3	keratin 6A	protein-coding	0.014535	0.507246	120(GAGAACAGGGTGTTCC,-,0.00),121(AGAACAGGGTGTTCCC,+,0.00)
chunk0119_31_1	chr22	40327101	40327769	+	0	NA	3' UTR (NM_001162501, exon 23 of 23)	3' UTR (NM_001162501, exon 23 of 23)	-19065	NM_001123378	158	Hs.75527	NM_000026	ENSG00000239900	ADSL	AMPS|ASASE|ASL	adenylosuccinate lyase	protein-coding	0.011976	0.463378	
chunk0093_409_1	chr19	57201458	57201835	+	0	NA	intron (NM_003417, intron 2 of 3)	intron (NM_003417, intron 2 of 3)	10146	NM_003417	9422	Hs.515634	NM_003417	ENSG00000083844	ZNF264	-	zinc finger protein 264	protein-coding	0.015915	0.497354	166(GAGATCAGTCTGTCCC,-,0.00),167(AGATCAGTCTGTCCCA,+,0.00)
chunk0167_251_1	chr6	68145070	68145281	+	0	NA	Intergenic	L1M1|LINE|L1	89824	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.009479	0.495283	
chunk0059_264_1	chr14	35213863	35214615	+	0	NA	intron (NM_014672, intron 5 of 7)	intron (NM_014672, intron 5 of 7)	-64319	NM_001282234	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.001330	0.338645	283(GAAAACAGCATGTTCT,-,0.00),284(AAAACAGCATGTTCTT,+,0.00)
chunk0084_335_1	chr17	81051107	81051569	+	0	NA	intron (NM_006340, intron 1 of 14)	L2|LINE|L2	16191	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.025974	0.535637	
chunk0123_24_1	chr3	40467939	40468533	+	0	NA	Intergenic	L1ME3G|LINE|L1	-8877	NM_001145082	285267	Hs.407159	NM_173656	ENSG00000177873	ZNF619	-	zinc finger protein 619	protein-coding	0.008418	0.425210	
chunk0093_254_1	chr19	50921580	50922534	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	-11319	NM_001302961	9622	Hs.218366	NM_004917	ENSG00000167749	KLK4	AI2A1|ARM1|EMSP|EMSP1|KLK-L1|PRSS17|PSTS|kallikrein	kallikrein related peptidase 4	protein-coding	0.022013	0.485864	
chunk0153_432_1	chr5	76209122	76209346	+	0	NA	intron (NM_014979, intron 3 of 12)	intron (NM_014979, intron 3 of 12)	125820	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.004464	0.422222	
chunk0032_319_1	chr11	10021165	10021547	+	0	NA	intron (NM_030962, intron 6 of 39)	intron (NM_030962, intron 6 of 39)	182214	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.005236	0.342037	
chunk0190_197_1	chr8	33590965	33591356	+	0	NA	TTS (NM_001305116)	TTS (NM_001305116)	6637	NM_001305116	78986	Hs.8719	NM_024025	ENSG00000133878	DUSP26	DSP-4|DUSP24|LDP-4|LDP4|MKP-8|MKP8|NATA1|NEAP|SKRP3	dual specificity phosphatase 26	protein-coding	0.017903	0.492347	81(AGGTACAGGGTGTGCC,-,0.00),82(GGTACAGGGTGTGCCC,+,0.00)
chunk0126_11_1	chr3	73467159	73467761	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	7172	NM_001303141	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.008306	0.409619	
chunk0130_349_1	chr3	138729313	138729698	+	0	NA	intron (NM_006219, intron 6 of 21)	MLT2B4|LTR|ERVL	-21884	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.000000	0.437824	
chunk0142_331_1	chr4	101210355	101210604	+	0	NA	intron (NM_000944, intron 1 of 13)	MIR|SINE|MIR	30393	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.004016	0.348000	
chunk0038_206_1	chr11	86314748	86315114	+	0	NA	intron (NR_024596, intron 2 of 5)	MER5A|DNA|hAT-Charlie	11575	NR_024596	51501	Hs.283322	NM_016401	ENSG00000149196	HIKESHI	C11orf73|HLD13|HSPC138|HSPC179|L7RN6|OPI10	heat shock protein nuclear import factor hikeshi	protein-coding	0.008197	0.400545	
chunk0173_189_1	chr6	145142737	145143480	+	0	NA	Intergenic	Intergenic	-591761	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.004038	0.375000	385(TAGAACAACCTGTTTC,-,0.00),386(AGAACAACCTGTTTCG,+,0.00)
chunk0185_393_1	chr7	133433738	133434250	+	0	NA	intron (NM_001037126, intron 7 of 9)	intron (NM_001037126, intron 7 of 9)	143113	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.000000	0.389864	
chunk0053_99_1	chr13	28646716	28647019	+	0	NA	Intergenic	L1M5|LINE|L1	-12137	NM_015932	51371	Hs.268742	NM_015932	ENSG00000132963	POMP	C13orf12|HSPC014|PNAS-110|PRAAS2|UMP1	proteasome maturation protein	protein-coding	0.006601	0.289474	
chunk0027_107_1	chr10	74014729	74015232	+	0	NA	intron (NM_003373, intron 1 of 20)	AluJb|SINE|Alu	16866	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.007952	0.410714	
chunk0178_398_1	chr7	40804759	40805443	+	0	NA	intron (NM_024728, intron 14 of 14)	intron (NM_024728, intron 14 of 14)	174838	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.008772	0.429197	
chunk0105_32_1	chr2	182659124	182659644	+	0	NA	Intergenic	Intergenic	-56657	NR_073366	54431	Hs.516632	NM_018981	ENSG00000077232	DNAJC10	ERdj5|JPDI|MTHr|PDIA19	DnaJ heat shock protein family (Hsp40) member C10	protein-coding	0.000000	0.297505	
chunk0169_102_1	chr6	100622766	100623104	+	0	NA	intron (NM_006828, intron 30 of 41)	intron (NM_006828, intron 30 of 41)	-159260	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.002959	0.315634	
chunk0030_210_1	chr10	114573345	114573806	+	0	NA	intron (NM_001003407, intron 3 of 21)	intron (NM_001003407, intron 3 of 21)	-46649	NM_006720	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.013015	0.443723	
chunk0195_104_1	chr8	94556737	94557139	+	0	NA	Intergenic	L1PB1|LINE|L1	-3420	NM_183009	25962	Hs.202238	NM_015496	ENSG00000164944	VIRMA	KIAA1429|MSTP054|fSAP121	vir like m6A methyltransferase associated	protein-coding	0.007463	0.349876	
chunk0108_462_1	chr2	238529493	238529692	+	0	NA	intron (NR_037809, intron 2 of 2)	intron (NR_037809, intron 2 of 2)	25907	NR_037809	151171	Hs.652076	NR_037809	ENSG00000225493	LINC01107	-	long intergenic non-protein coding RNA 1107	ncRNA	0.010050	0.455000	
chunk0002_385_1	chr1	26799612	26800594	+	0	NA	Intergenic	Intergenic	11915	NM_001202554	55650	Hs.259605	NM_017837	ENSG00000060642	PIGV	GPI-MT-II|HPMRS1|PIG-V	phosphatidylinositol glycan anchor biosynthesis class V	protein-coding	0.007128	0.485249	
chunk0076_380_1	chr16	72247802	72248536	+	0	NA	Intergenic	Intergenic	-75719	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.008174	0.349660	
chunk0024_384_1	chr10	44752862	44753267	+	0	NA	Intergenic	Intergenic	-158252	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.002469	0.413793	
chunk0151_305_1	chr5	53167860	53168336	+	0	NA	Intergenic	Intergenic	58256	NR_104654	257396	Hs.12326	NR_034107	ENSG00000247796	LOC257396	-	uncharacterized LOC257396	ncRNA	0.002101	0.467505	
chunk0014_452_1	chr1	183902001	183902366	+	0	NA	intron (NM_001297671, intron 11 of 17)	intron (NM_001297671, intron 11 of 17)	97102	NM_001297671	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.002740	0.366120	
chunk0141_273_1	chr4	86494197	86494518	+	0	NA	Intergenic	Intergenic	-41227	NM_002753	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.006231	0.503106	108(ATGGACAGCATGTTCA,-,0.00),109(TGGACAGCATGTTCAG,+,0.00)
chunk0065_89_1	chr15	23773286	23773488	+	0	NA	Intergenic	L1PA16|LINE|L1	-86084	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.000000	0.334975	
chunk0212_352_1	chrX	148632260	148632832	+	0	NA	intron (NM_002025, intron 1 of 20)	intron (NM_002025, intron 1 of 20)	-86545	NM_001170628	2334	Hs.496911	NM_002025	ENSG00000155966	AFF2	FMR2|FMR2P|FRAXE|MRX2|OX19	AF4/FMR2 family member 2	protein-coding	0.006993	0.404887	
chunk0071_68_1	chr15	80535662	80536254	+	0	NA	intron (NM_014862, intron 8 of 18)	intron (NM_014862, intron 8 of 18)	26986	NR_120363	101929586	Hs.569426	NR_120363	ENSG00000259175	LOC101929586	-	uncharacterized LOC101929586	ncRNA	0.016892	0.430017	
chunk0006_72_1	chr1	64872420	64872891	+	0	NA	intron (NM_002227, intron 5 of 24)	L2a|LINE|L2	93849	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.006369	0.319915	
chunk0036_9_1	chr11	58185263	58185888	+	0	NA	Intergenic	Intergenic	-4859	NM_001005283	219957	Hs.553643	NM_001005283	ENSG00000186513	OR9Q2	OR9Q2P	olfactory receptor family 9 subfamily Q member 2	protein-coding	0.008000	0.418530	293(AGGCACTAGGTGTTCC,-,0.00),294(GGCACTAGGTGTTCCT,+,0.00)
chunk0127_143_1	chr3	94333387	94333708	+	0	NA	Intergenic	Intergenic	-270324	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.003115	0.372671	
chunk0118_344_1	chr22	35882329	35882528	+	0	NA	intron (NM_001082579, intron 2 of 13)	L2a|LINE|L2	-41845	NM_014309	23543	Hs.282998	NM_014309	ENSG00000100320	RBFOX2	FOX2|Fox-2|HNRBP2|HRNBP2|RBM9|RTA|dJ106I20.3|fxh	RNA binding fox-1 homolog 2	protein-coding	0.010050	0.385000	
chunk0070_101_1	chr15	70362468	70362792	+	0	NA	Intergenic	Intergenic	-252917	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.009259	0.553846	167(CGGAACAGGATGTCCA,-,0.00),168(GGAACAGGATGTCCAT,+,0.00)
chunk0139_321_1	chr4	58303385	58303905	+	0	NA	Intergenic	MER41B|LTR|ERV1	877773	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003846	0.358925	
chunk0165_421_1	chr6	39465525	39466122	+	0	NA	intron (NM_001289021, intron 12 of 21)	L2c|LINE|L2	-34449	NM_001289024	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.003350	0.429766	232(GGGTACATTGTGTTCT,-,0.00),233(GGTACATTGTGTTCTA,+,0.00)
chunk0042_50_1	chr12	1767652	1768309	+	0	NA	intron (NM_024551, intron 2 of 7)	MER110|LTR|ERV1	-52287	NM_001163925	654429	Hs.585579	NM_001039029	ENSG00000166159	LRTM2	-	leucine rich repeats and transmembrane domains 2	protein-coding	0.003044	0.361702	574(GGCACTTCTTGTACTT,+,0.00)
chunk0089_280_1	chr18	62919212	62919604	+	0	NA	intron (NM_194449, intron 9 of 16)	intron (NM_194449, intron 9 of 16)	203969	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.002551	0.371501	142(AAGTACATGCTGCTCT,-,0.00),143(AGTACATGCTGCTCTT,+,0.00)
chunk0154_18_1	chr5	76727205	76727431	+	0	NA	intron (NM_001992, intron 1 of 1)	MIRc|SINE|MIR	11275	NM_001311313	2149	Hs.482562	NM_001992	ENSG00000181104	F2R	CF2R|HTR|PAR-1|PAR1|TR	coagulation factor II thrombin receptor	protein-coding	0.008850	0.405286	
chunk0016_126_1	chr1	196968344	196968769	+	0	NA	Intergenic	Intergenic	-8981	NM_030787	81494	Hs.282594	NM_030787	ENSG00000134389	CFHR5	CFHL5|CFHR5D|FHR-5|FHR5	complement factor H related 5	protein-coding	0.009412	0.431925	
chunk0038_38_1	chr11	81968167	81968729	+	0	NA	intron (NR_120571, intron 6 of 7)	L1ME2|LINE|L1	-77612	NR_036186	100422823		NR_036186	ENSG00000264110	MIR4300	-	microRNA 4300	ncRNA	0.000000	0.284192	
chunk0092_130_1	chr19	27935310	27935972	+	0	NA	Intergenic	MIR|SINE|MIR	-141701	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.004532	0.399698	
chunk0060_364_1	chr14	52356089	52356326	+	0	NA	Intergenic	Intergenic	41909	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.012658	0.445378	
chunk0066_168_1	chr15	32823649	32824285	+	0	NA	intron (NM_001103184, intron 13 of 16)	intron (NM_001103184, intron 13 of 16)	-105102	NR_109767	100131315	Hs.610545	NR_109767	ENSG00000259721	LOC100131315	-	uncharacterized LOC100131315	ncRNA	0.011006	0.419152	303(TGGAACAGTGTGCCCC,-,0.00),304(GGAACAGTGTGCCCCT,+,0.00)
chunk0051_263_1	chr12	117699360	117699640	+	0	NA	intron (NM_173598, intron 4 of 19)	Tigger3c|DNA|TcMar-Tigger	268723	NM_173598	283455	Hs.375836	NM_173598	ENSG00000171435	KSR2	-	kinase suppressor of ras 2	protein-coding	0.010714	0.362989	
chunk0162_101_1	chr6	2557694	2558025	+	0	NA	Intergenic	Intergenic	76744	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.006042	0.430723	
chunk0046_401_1	chr12	64080292	64081218	+	0	NA	intron (NM_020762, intron 10 of 21)	intron (NM_020762, intron 10 of 21)	141541	NM_001300941	144577	Hs.444671	NM_152440	ENSG00000174206	C12orf66	-	chromosome 12 open reading frame 66	protein-coding	0.007559	0.401294	181(GAGGACACTCTGTGTT,-,0.00),182(AGGACACTCTGTGTTT,+,0.00)
chunk0116_26_1	chr21	33058553	33058825	+	0	NA	intron (NR_104056, intron 2 of 4)	intron (NR_104056, intron 2 of 4)	860	NR_104056	101930746	Hs.580934	NR_104056	ENSG00000232539	LINC00945	-	long intergenic non-protein coding RNA 945	ncRNA	0.014706	0.567766	
chunk0152_148_1	chr5	59240920	59241299	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	35010	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.000000	0.365789	
chunk0114_1_1	chr21	5073401	5073602	+	0	NA	Intergenic	Intergenic	51008	NM_001283052	23308	Hs.14155	NM_015259	ENSG00000160223	ICOSLG	B7-H2|B7H2|B7RP-1|B7RP1|B7h|CD275|GL50|ICOS-L|ICOSL|LICOS	inducible T cell costimulator ligand	protein-coding	0.044776	0.564356	
chunk0055_410_1	chr13	74432845	74433715	+	0	NA	intron (NR_047005, intron 3 of 4)	MER97d|DNA|hAT-Tip100	14107	NR_047005	100874151	Hs.564552	NR_047005	ENSG00000226240	LINC00381	-	long intergenic non-protein coding RNA 381	ncRNA	0.009195	0.369690	
chunk0097_112_1	chr2	46307175	46307614	+	0	NA	intron (NM_001430, intron 1 of 15)	intron (NM_001430, intron 1 of 15)	9992	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.011390	0.479545	
chunk0022_257_1	chr10	14686996	14687905	+	0	NA	intron (NM_001282695, intron 1 of 5)	intron (NM_001282695, intron 1 of 5)	-83032	NM_001282697	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.012101	0.421978	
chunk0183_302_1	chr7	107850802	107851509	+	0	NA	Intergenic	Intergenic	-39952	NM_001289752	1738	Hs.131711	NM_000108	ENSG00000091140	DLD	DLDD|DLDH|E3|GCSL|LAD|PHE3	dihydrolipoamide dehydrogenase	protein-coding	0.009901	0.426554	394(AGGGTCAGACTGTTCT,-,0.00),395(GGGTCAGACTGTTCTA,+,0.00)
chunk0197_129_1	chr8	120019744	120020168	+	0	NA	intron (NM_022783, intron 8 of 8)	intron (NM_022783, intron 8 of 8)	-105152	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.009434	0.463529	256(CAGCACTGCATGTTCC,-,0.00),257(AGCACTGCATGTTCCC,+,0.00)
chunk0073_268_1	chr16	12230352	12230618	+	0	NA	intron (NM_032167, intron 14 of 20)	intron (NM_032167, intron 14 of 20)	253751	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.011278	0.430712	
chunk0006_13_1	chr1	63912463	63913020	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	138722	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.010772	0.453405	
chunk0086_148_1	chr18	21361099	21361660	+	0	NA	intron (NM_001142966, intron 1 of 32)	intron (NM_001142966, intron 1 of 32)	119137	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.003565	0.414591	271(GAGTACAGAGTGTTCC,-,0.00),272(AGTACAGAGTGTTCCT,+,0.00)
chunk0111_352_1	chr20	33434273	33434573	+	0	NA	intron (NM_003098, intron 2 of 7)	intron (NM_003098, intron 2 of 7)	9469	NM_003098	6640	Hs.31121	NM_003098	ENSG00000101400	SNTA1	LQT12|SNT1|TACIP1|dJ1187J4.5	syntrophin alpha 1	protein-coding	0.006667	0.481728	
chunk0083_218_1	chr17	67078638	67079020	+	0	NA	intron (NM_014877, intron 32 of 32)	intron (NM_014877, intron 32 of 32)	34293	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.002618	0.383812	
chunk0164_399_1	chr6	26431444	26431807	+	0	NA	Intergenic	Intergenic	-8847	NM_197974	10384	Hs.167741	NM_006994	ENSG00000111801	BTN3A3	BTF3|BTN3.3	butyrophilin subfamily 3 member A3	protein-coding	0.005510	0.502747	128(GGGAACTAGTTGTTCC,-,0.00),129(GGAACTAGTTGTTCCA,+,0.00)
chunk0123_427_1	chr3	50079441	50080001	+	0	NA	Intergenic	Intergenic	-9187	NR_036627	10181	Hs.439480	NM_005778	ENSG00000003756	RBM5	G15|H37|LUCA-15|LUCA15|RMB5	RNA binding motif protein 5	protein-coding	0.016071	0.452763	
chunk0149_274_1	chr5	24541586	24541958	+	0	NA	intron (NM_006727, intron 2 of 11)	intron (NM_006727, intron 2 of 11)	103204	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.000000	0.284182	
chunk0198_5_1	chr9	288066	288617	+	0	NA	intron (NM_001190458, intron 2 of 45)	MIR|SINE|MIR	15293	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.005445	0.387681	212(TTGAACAACCTGTGCC,-,0.00),213(TGAACAACCTGTGCCT,+,0.00)
chunk0040_148_1	chr11	113564152	113564669	+	0	NA	Intergenic	Intergenic	-89131	NM_016574	1813	Hs.73893	NM_000795	ENSG00000149295	DRD2	D2DR|D2R	dopamine receptor D2	protein-coding	0.003868	0.438224	241(CAACACATGCTGTGCC,-,0.00),242(AACACATGCTGTGCCA,+,0.00)
chunk0199_200_1	chr9	4858914	4859554	+	0	NA	intron (NM_001286699, intron 6 of 6)	intron (NM_001286699, intron 6 of 6)	8937	NR_029836	406894		NR_029836	ENSG00000199065	MIR101-2	MIRN101-2|mir-101-2	microRNA 101-2	ncRNA	0.010937	0.435257	
chunk0063_7_1	chr14	76088299	76088843	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-63314	NM_017926	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.016544	0.440367	
chunk0203_297_1	chr9	89238603	89239135	+	0	NA	Intergenic	Intergenic	-60102	NM_016848	53358	Hs.292737	NM_016848	ENSG00000148082	SHC3	N-Shc|NSHC|RAI|SHCC	SHC adaptor protein 3	protein-coding	0.003759	0.341463	
chunk0085_55_1	chr18	1037078	1037353	+	0	NA	Intergenic	Intergenic	132019	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.007273	0.365942	
chunk0212_284_1	chrX	140838659	140839179	+	0	NA	Intergenic	Intergenic	-54361	NM_004065	1038	Hs.446675	NM_004065	ENSG00000184258	CDR1	CDR|CDR34|CDR62A	cerebellar degeneration related protein 1	protein-coding	0.007692	0.406910	
chunk0045_440_1	chr12	53570400	53570702	+	0	NA	intron (NM_006856, intron 2 of 11)	MLT1C|LTR|ERVL-MaLR	55445	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.003311	0.462046	18(TGGAACTTCCAGTCCT,-,0.00),19(GGAACTTCCAGTCCTC,+,0.00)
chunk0171_135_1	chr6	122897523	122898079	+	0	NA	Intergenic	L2a|LINE|L2	-98170	NM_001010852	134829	Hs.486361	NM_001010852	ENSG00000146352	CLVS2	C6orf212|C6orf213|RLBP1L2|bA160A10.4	clavesin 2	protein-coding	0.000000	0.330341	
chunk0142_118_1	chr4	94553708	94554306	+	0	NA	intron (NM_001011516, intron 3 of 9)	intron (NM_001011516, intron 3 of 9)	102150	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.001672	0.315526	
chunk0066_418_1	chr15	39455317	39456103	+	0	NA	Intergenic	Intergenic	-125369	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.006361	0.387548	
chunk0119_283_1	chr22	46105455	46105792	+	0	NA	intron (NR_027033, intron 4 of 5)	intron (NR_027033, intron 4 of 5)	-7126	NR_029478	406883		NR_029478	ENSG00000283990	MIRLET7A3	LET7A3|MIRNLET7A3|let-7a-3	microRNA let-7a-3	ncRNA	0.047478	0.665680	
chunk0028_132_1	chr10	85381689	85381992	+	0	NA	Intergenic	L1MEc|LINE|L1	50932	NR_120669	101929646	Hs.116129	NR_120669		LINC02647	-	long intergenic non-protein coding RNA 2647	ncRNA	0.003300	0.292763	
chunk0126_325_1	chr3	81713021	81713783	+	0	NA	intron (NM_000158, intron 1 of 15)	intron (NM_000158, intron 1 of 15)	48397	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.007874	0.352556	
chunk0135_189_1	chr3	188206665	188207344	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	-5929	NM_005578	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.010309	0.388235	
chunk0095_371_1	chr2	23445999	23446501	+	0	NA	intron (NM_052920, intron 1 of 13)	L1M5|LINE|L1	60823	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.007968	0.379722	
chunk0191_72_1	chr8	47342575	47343043	+	0	NA	intron (NR_104581, intron 5 of 16)	intron (NR_104581, intron 5 of 16)	81931	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.012821	0.362473	100(TAGCACACATTGTACA,-,0.00),101(AGCACACATTGTACAC,+,0.00)
chunk0100_291_1	chr2	114775604	114776038	+	0	NA	intron (NM_001178036, intron 2 of 26)	L2a|LINE|L2	57727	NR_132105	101927591	Hs.553019	NR_132105	ENSG00000231538	DPP10-AS3	-	DPP10 antisense RNA 3	ncRNA	0.002304	0.379310	
chunk0048_26_1	chr12	77401312	77401726	+	0	NA	Intergenic	MIRb|SINE|MIR	-335939	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.000000	0.371084	
chunk0174_236_1	chr6	160810311	160810591	+	0	NA	Intergenic	Intergenic	108258	NM_000301	5340	Hs.143436	NM_000301	ENSG00000122194	PLG	-	plasminogen	protein-coding	0.007143	0.441281	
chunk0191_13_1	chr8	42501089	42501842	+	0	NA	promoter-TSS (NM_001257180)	promoter-TSS (NM_001257180)	-5	NM_001257180	6575	Hs.653173	NM_006749	ENSG00000168575	SLC20A2	GLVR-2|GLVR2|IBGC1|IBGC3|MLVAR|PIT-2|PIT2|RAM1|Ram-1	solute carrier family 20 member 2	protein-coding	0.014608	0.401857	
chunk0118_401_1	chr22	37904732	37905129	+	0	NA	intron (NR_039973, intron 1 of 1)	intron (NR_039973, intron 1 of 1)	-1218	NM_033386	85377	Hs.517610	NM_033386	ENSG00000100139	MICALL1	MICAL-L1|MIRAB13	MICAL like 1	protein-coding	0.007557	0.469849	
chunk0150_50_1	chr5	31733591	31733894	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-65182	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.023102	0.480263	
chunk0178_156_1	chr7	33536950	33537421	+	0	NA	intron (NM_014451, intron 19 of 20)	intron (NM_014451, intron 19 of 20)	-367726	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.008493	0.389831	
chunk0105_115_1	chr2	185096928	185097285	+	0	NA	Intergenic	Intergenic	498740	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.008403	0.396648	
chunk0084_71_1	chr17	74770381	74770750	+	0	NA	TTS (NM_015654)	TTS (NM_015654)	5860	NM_001305081	26151	Hs.144058	NM_015654	ENSG00000109065	NAT9	EBSP, hNATL	N-acetyltransferase 9 (putative)	protein-coding	0.021680	0.527027	
chunk0017_273_1	chr1	209744953	209745419	+	0	NA	Intergenic	Intergenic	-10846	NM_025228	80342	Hs.147434	NM_025228	ENSG00000009790	TRAF3IP3	T3JAM	TRAF3 interacting protein 3	protein-coding	0.006438	0.432548	231(GGGCACAGCCTGTTCT,-,0.00),232(GGCACAGCCTGTTCTC,+,0.00)
chunk0155_451_1	chr5	101715345	101716043	+	0	NA	Intergenic	L1PA6|LINE|L1	580855	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.008596	0.497854	
chunk0031_427_1	chr10	132418144	132418522	+	0	NA	TTS (NM_138499)	TTS (NM_138499)	21135	NM_138499	170394	Hs.527751	NM_138499	ENSG00000171813	PWWP2B	PWWP2|bA432J24.1|pp8607	PWWP domain containing 2B	protein-coding	0.023810	0.548813	178(TAGAACATTCTGTGCT,-,0.00),179(AGAACATTCTGTGCTC,+,0.00)
chunk0055_160_1	chr13	60347196	60347497	+	0	NA	Intergenic	Intergenic	-49111	NM_001146071	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.006645	0.357616	
chunk0113_44_1	chr20	49982130	49982404	+	0	NA	promoter-TSS (NM_005985)	promoter-TSS (NM_005985)	-709	NM_005985	6615	Hs.48029	NM_005985	ENSG00000124216	SNAI1	SLUGH2|SNA|SNAH|SNAIL|SNAIL1|dJ710H13.1	snail family transcriptional repressor 1	protein-coding	0.051095	0.603636	154(AGGCTCTGAGTGTTCT,-,0.00)
chunk0111_284_1	chr20	31652756	31653388	+	0	NA	Intergenic	L1MC5|LINE|L1	15184	NM_032609	84701	Hs.277101	NM_032609	ENSG00000131055	COX4I2	COX4|COX4-2|COX4B|COX4L2|COXIV-2|dJ857M17.2	cytochrome c oxidase subunit 4I2	protein-coding	0.007911	0.383886	
chunk0015_390_1	chr1	190688967	190689259	+	0	NA	intron (NR_033922, intron 1 of 4)	intron (NR_033922, intron 1 of 4)	64223	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.003425	0.317406	
chunk0038_213_1	chr11	86547878	86548190	+	0	NA	intron (NM_001014811, intron 3 of 13)	intron (NM_001014811, intron 3 of 13)	124164	NM_001014811	10873	Hs.199743	NM_006680	ENSG00000151376	ME3	NADP-ME	malic enzyme 3	protein-coding	0.003205	0.440895	89(CAGAACATCCTGTTCT,-,0.00),90(AGAACATCCTGTTCTA,+,0.00)
chunk0210_221_1	chrX	82318816	82319325	+	0	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-1117128	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.000000	0.358824	291(AAGAACAAACTGTGCT,-,0.00),292(AGAACAAACTGTGCTA,+,0.00)
chunk0126_46_1	chr3	73813267	73813782	+	0	NA	Intergenic	Intergenic	-188603	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.009709	0.403101	293(GTGAACAGGATGTTTT,-,0.00),294(TGAACAGGATGTTTTC,+,0.00)
chunk0158_27_1	chr5	125484993	125485647	+	0	NA	Intergenic	Intergenic	-7941	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.007645	0.433588	362(AGGAACAAAGAGTGCT,-,0.00),363(GGAACAAAGAGTGCTG,+,0.00)
chunk0170_232_1	chr6	113451216	113451550	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	198692	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.008982	0.420896	
chunk0031_24_1	chr10	121900486	121901072	+	0	NA	intron (NR_110006, intron 4 of 9)	intron (NR_110006, intron 4 of 9)	27284	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.013652	0.379898	
chunk0158_88_1	chr5	126566781	126567110	+	0	NA	intron (NM_001202404, intron 9 of 15)	LTR10C|LTR|ERV1	28445	NM_001201377	501	Hs.483239	NM_001182	ENSG00000164904	ALDH7A1	ATQ1|EPD|PDE	aldehyde dehydrogenase 7 family member A1	protein-coding	0.000000	0.333333	
chunk0145_170_1	chr4	147292689	147293114	+	0	NA	Intergenic	L1PA7|LINE|L1	51816	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.009412	0.542254	
chunk0113_227_1	chr20	53871598	53871817	+	0	NA	Intergenic	Intergenic	4002	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.009132	0.404545	
chunk0177_319_1	chr7	26180197	26180396	+	0	NA	intron (NM_004289, intron 2 of 3)	intron (NM_004289, intron 2 of 3)	20497	NM_031243	3181	Hs.487774	NM_002137	ENSG00000122566	HNRNPA2B1	HNRNPA2|HNRNPB1|HNRPA2|HNRPA2B1|HNRPB1|IBMPFD2|RNPA2|SNRPB1	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding	0.000000	0.500000	
chunk0187_369_1	chr7	157482092	157482347	+	0	NA	intron (NR_110157, intron 2 of 3)	(GGTGTGT)n|Simple_repeat|Simple_repeat	15988	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.019608	0.457031	
chunk0080_8_1	chr17	20876263	20876592	+	0	NA	intron (NR_104185, intron 1 of 2)	MLT1A1|LTR|ERVL-MaLR	7994	NR_104185	440416	Hs.661076	NR_104185	ENSG00000233098	CCDC144NL-AS1	-	CCDC144NL antisense RNA 1	ncRNA	0.006079	0.384848	
chunk0163_278_1	chr6	13627986	13628629	+	0	NA	intron (NM_005493, intron 12 of 13)	L2c|LINE|L2	12980	NM_016167	51406	Hs.306242	NM_016167	ENSG00000225921	NOL7	C6orf90|PQBP3|RARG-1|dJ223E5.2	nucleolar protein 7	protein-coding	0.001555	0.329193	
chunk0013_17_1	chr1	165878629	165879188	+	0	NA	intron (NM_012474, intron 1 of 6)	L1MC1|LINE|L1	-29013	NR_037431	100500832		NR_037431	ENSG00000283936	MIR3658	-	microRNA 3658	ncRNA	0.007156	0.380357	
chunk0118_8_1	chr22	25567267	25567533	+	0	NA	intron (NM_005160, intron 1 of 20)	intron (NM_005160, intron 1 of 20)	2506	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.000000	0.370787	
chunk0020_256_1	chr1	236206649	236206848	+	0	NA	intron (NM_003272, intron 6 of 6)	intron (NM_003272, intron 6 of 6)	64216	NM_003272	7107	Hs.498160	NM_003272	ENSG00000077585	GPR137B	TM7SF1	G protein-coupled receptor 137B	protein-coding	0.010050	0.540000	
chunk0050_331_1	chr12	107348702	107349370	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	30616	NM_001018072	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.005988	0.503737	478(ATGAGCAGCCTGTTCT,-,0.00),479(TGAGCAGCCTGTTCTG,+,0.00)
chunk0176_178_1	chr7	13742191	13742790	+	0	NA	Intergenic	Intergenic	244024	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.005008	0.396667	
chunk0143_39_1	chr4	107144175	107144374	+	0	NA	Intergenic	Intergenic	-107978	NM_014421	27123	Hs.211869	NM_014421	ENSG00000155011	DKK2	DKK-2	dickkopf WNT signaling pathway inhibitor 2	protein-coding	0.005025	0.330000	136(AAGCACACAATGTACT,-,0.00),137(AGCACACAATGTACTG,+,0.00)
chunk0085_184_1	chr18	6088447	6088807	+	0	NA	intron (NM_173464, intron 15 of 19)	(GAGAAGT)n|Simple_repeat|Simple_repeat	-168117	NR_110765	101927150		NR_110765		L3MBTL4-AS1	-	L3MBTL4 antisense RNA 1	ncRNA	0.005556	0.445983	
chunk0058_127_1	chr14	22403607	22404082	+	0	NA	Intergenic	Intergenic	185393	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.012632	0.376050	
chunk0122_78_1	chr3	29890911	29891492	+	0	NA	intron (NM_001003793, intron 8 of 14)	intron (NM_001003793, intron 8 of 14)	42955	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.006885	0.383162	320(AAGAACAAACAGTTCA,-,0.00),321(AGAACAAACAGTTCAT,+,0.00)
chunk0035_268_1	chr11	46520255	46520572	+	0	NA	intron (NM_001267782, intron 8 of 19)	intron (NM_001267782, intron 8 of 19)	-68524	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.003155	0.399371	
chunk0130_251_1	chr3	135786687	135787252	+	0	NA	Intergenic	L2a|LINE|L2	-178704	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.008850	0.454064	
chunk0062_232_1	chr14	71123844	71124086	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	216560	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.008264	0.563786	
chunk0134_327_1	chr3	181886231	181886799	+	0	NA	Intergenic	L1ME4b|LINE|L1	-65849	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.003521	0.370826	
chunk0048_385_1	chr12	86876751	86877357	+	0	NA	Intergenic	L1MA3|LINE|L1	-38150	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.003300	0.405272	
chunk0066_162_1	chr15	32657422	32658053	+	0	NA	intron (NM_001144757, intron 2 of 5)	intron (NM_001144757, intron 2 of 5)	16068	NM_001144757	6447	Hs.156540	NM_003020	ENSG00000166922	SCG5	7B2|P7B2|SGNE1|SgV	secretogranin V	protein-coding	0.006339	0.400316	239(GAGAACACACTGTCCT,-,0.00),240(AGAACACACTGTCCTC,+,0.00)
chunk0195_39_1	chr8	93287225	93287483	+	0	NA	Intergenic	Intergenic	-120504	NM_001242668									0.019380	0.436293	
chunk0117_245_1	chr22	23163578	23164123	+	0	NA	3' UTR (NM_004914, exon 11 of 11)	3' UTR (NM_004914, exon 11 of 11)	-16515	NM_021574	613	Hs.517461	NM_004327	ENSG00000186716	BCR	ALL|BCR1|CML|D22S11|D22S662|PHL	BCR activator of RhoGEF and GTPase	protein-coding	0.020183	0.542125	
chunk0149_338_1	chr5	26923276	26923915	+	0	NA	intron (NM_016279, intron 2 of 11)	L1M1|LINE|L1	114987	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.006260	0.296875	
chunk0026_186_1	chr10	63563044	63563599	+	0	NA	intron (NM_001001330, intron 1 of 7)	L1MC3|LINE|L1	41958	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.005405	0.408273	
chunk0200_369_1	chr9	25913872	25914083	+	0	NA	Intergenic	Intergenic	133921	NR_121604	101929582	Hs.140547	NR_121604	ENSG00000236306	LINC01241	-	long intergenic non-protein coding RNA 1241	ncRNA	0.004739	0.353774	
chunk0199_351_1	chr9	12315476	12315675	+	0	NA	Intergenic	L1PA8|LINE|L1	-377811	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.000000	0.560000	
chunk0019_386_1	chr1	230185783	230186517	+	0	NA	intron (NM_001291866, intron 2 of 15)	intron (NM_001291866, intron 2 of 15)	118955	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.013624	0.463946	
chunk0109_61_1	chr20	1345569	1346249	+	0	NA	intron (NR_040047, intron 1 of 2)	L1MC2|LINE|L1	-16674	NM_080489	27111	Hs.657015	NM_015685	ENSG00000125775	SDCBP2	SITAC|SITAC18|ST-2|ST2	syndecan binding protein 2	protein-coding	0.002941	0.368576	
chunk0096_379_1	chr2	36931270	36931686	+	0	NA	intron (NM_003162, intron 1 of 17)	intron (NM_003162, intron 1 of 17)	34994	NM_003162	6801	Hs.127486	NM_003162	ENSG00000115808	STRN	PPP2R6A|SG2NA|STRN1	striatin	protein-coding	0.004808	0.328537	
chunk0023_75_1	chr10	22182753	22183602	+	0	NA	Intergenic	L1M5|LINE|L1	26806	NM_001199938	340900	Hs.450519	NM_001199938	ENSG00000223601	EBLN1	EBLN-1	endogenous Bornavirus like nucleoprotein 1	protein-coding	0.005889	0.354118	
chunk0189_57_1	chr8	20099852	20100361	+	0	NA	Intergenic	Intergenic	83100	NM_001142324	6570	Hs.158322	NM_003053	ENSG00000036565	SLC18A1	CGAT|VAT1|VMAT1	solute carrier family 18 member A1	protein-coding	0.003929	0.345098	
chunk0144_117_1	chr4	128815414	128815931	+	0	NA	intron (NM_001287443, intron 1 of 10)	intron (NM_001287443, intron 1 of 10)	3828	NM_001287443	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.001934	0.362934	
chunk0203_121_1	chr9	84917340	84917908	+	0	NA	intron (NM_001018064, intron 12 of 16)	intron (NM_001018064, intron 12 of 16)	247247	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.010563	0.469244	
chunk0047_196_1	chr12	71141764	71141963	+	0	NA	intron (NM_004616, intron 3 of 8)	intron (NM_004616, intron 3 of 8)	16136	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.000000	0.475000	34(ATGAACACTGTGTCCC,-,0.00),35(TGAACACTGTGTCCCT,+,0.00)
chunk0087_58_1	chr18	31591504	31591773	+	0	NA	promoter-TSS (NM_000371)	promoter-TSS (NM_000371)	-129	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.011152	0.337037	
chunk0111_358_1	chr20	33611938	33612648	+	0	NA	intron (NM_001032999, intron 3 of 10)	intron (NM_001032999, intron 3 of 10)	49928	NM_001039709	9139	Hs.153934	NM_005093	ENSG00000078699	CBFA2T2	EHT|MTGR1|ZMYND3|p85	CBFA2/RUNX1 partner transcriptional co-repressor 2	protein-coding	0.007042	0.350211	334(AAGTACTGCCAGTTCC,-,0.00),335(AGTACTGCCAGTTCCC,+,0.00)
chunk0108_331_1	chr2	235679452	235679849	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	173899	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.012594	0.417085	
chunk0117_367_1	chr21	45009759	45010167	+	0	NA	Intergenic	L1ME1|LINE|L1	-5236	NR_024089	378825	Hs.534828	NR_024089	ENSG00000275874	PICSAR	C21orf113|LINC00162|NCRNA00162|NLC1-C|NLC1C|PRED74	P38 inhibited cutaneous squamous cell carcinoma associated lincRNA	ncRNA	0.014706	0.386308	
chunk0156_459_1	chr5	115052951	115053342	+	0	NA	Intergenic	L2b|LINE|L2	116817	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.005115	0.464286	
chunk0152_142_1	chr5	59204345	59205126	+	0	NA	intron (NM_006203, intron 2 of 14)	intron (NM_006203, intron 2 of 14)	71384	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005122	0.384910	
chunk0097_118_1	chr2	46452769	46453713	+	0	NA	Intergenic	Intergenic	24051	NR_103805	101805491	Hs.304781	NR_103805	ENSG00000187600	LINC02583	-	long intergenic non-protein coding RNA 2583	ncRNA	0.003178	0.411640	451(GAGAGCATAGTGTACC,-,0.00),452(AGAGCATAGTGTACCT,+,0.00)
chunk0137_159_1	chr4	16024122	16024531	+	0	NA	exon (NM_006017, exon 6 of 27)	exon (NM_006017, exon 6 of 27)	51792	NM_001145851	8842	Hs.614734	NM_006017	ENSG00000007062	PROM1	AC133|CD133|CORD12|MCDR2|MSTP061|PROML1|RP41|STGD4	prominin 1	protein-coding	0.009780	0.385366	
chunk0111_424_1	chr20	34907527	34908062	+	0	NA	intron (NM_001076552, intron 2 of 18)	intron (NM_001076552, intron 2 of 18)	31269	NM_001076552	55902	Hs.517034	NM_018677	ENSG00000131069	ACSS2	ACAS2|ACECS|ACS|ACSA|dJ1161H23.1	acyl-CoA synthetase short chain family member 2	protein-coding	0.009346	0.453358	
chunk0019_20_1	chr1	223623241	223623444	+	0	NA	intron (NM_001143962, intron 6 of 20)	MIRb|SINE|MIR	42392	NM_001143962	388743	Hs.291487	NM_001143962	ENSG00000203697	CAPN8	nCL-2	calpain 8	protein-coding	0.019704	0.362745	
chunk0149_461_1	chr5	30194686	30195121	+	0	NA	Intergenic	Intergenic	-798927	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004598	0.305046	
chunk0031_287_1	chr10	128420718	128421145	+	0	NA	Intergenic	Intergenic	134981	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.011710	0.401869	
chunk0132_209_1	chr3	157473569	157474491	+	0	NA	intron (NM_001167911, intron 2 of 12)	L1MCa|LINE|L1	21476	NM_001167917	79674	Hs.658046	NM_024621	ENSG00000197415	VEPH1	MELT|VEPH	ventricular zone expressed PH domain containing 1	protein-coding	0.002169	0.269772	394(TGGAACATGTTGTACT,-,0.00),395(GGAACATGTTGTACTG,+,0.00)
chunk0157_197_1	chr5	118988326	118988605	+	0	NA	promoter-TSS (NM_001308081)	promoter-TSS (NM_001308081)	140	NM_173666	285605	Hs.655891	NM_173666	ENSG00000169570	DTWD2	-	DTW domain containing 2	protein-coding	0.136201	0.725000	
chunk0049_150_1	chr12	91926971	91927214	+	0	NA	Intergenic	Intergenic	214621	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.004115	0.344262	
chunk0138_316_1	chr4	41404692	41405168	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	44145	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.006303	0.354298	
chunk0123_90_1	chr3	42070673	42071178	+	0	NA	Intergenic	MIRb|SINE|MIR	-20329	NM_001042646	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.000000	0.432806	
chunk0208_273_1	chrX	21734031	21734566	+	0	NA	intron (NR_045617, intron 4 of 5)	intron (NR_045617, intron 4 of 5)	23862	NR_045617	23676	Hs.86492	NM_014332	ENSG00000091482	SMPX	DFN6|DFNX4	small muscle protein X-linked	protein-coding	0.003738	0.425373	
chunk0132_328_1	chr3	161083664	161084226	+	0	NA	TTS (NM_033169)	TTS (NM_033169)	20950	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.007117	0.376554	
chunk0033_224_1	chr11	17376401	17376751	+	0	NA	3' UTR (NM_001202439, exon 5 of 5)	3' UTR (NM_001202439, exon 5 of 5)	12083	NM_000525	3767	Hs.248141	NM_000525	ENSG00000187486	KCNJ11	BIR|HHF2|IKATP|KIR6.2|MODY13|PHHI|TNDM3	potassium voltage-gated channel subfamily J member 11	protein-coding	0.008571	0.441595	
chunk0045_382_1	chr12	52298572	52299071	+	0	NA	Intergenic	L1MA4|LINE|L1	-3044	NM_002284	3892	Hs.278658	NM_002284	ENSG00000170442	KRT86	HB6|Hb1|K86|KRTHB1|KRTHB6|MNX	keratin 86	protein-coding	0.004008	0.306000	
chunk0058_291_1	chr14	26820224	26820842	+	0	NA	non-coding (NR_110556, exon 5 of 5)	non-coding (NR_110556, exon 5 of 5)	1587	NR_110033	101927062		NR_110033	ENSG00000257845	LINC02294	-	long intergenic non-protein coding RNA 2294	ncRNA	0.003236	0.334410	
chunk0087_154_1	chr18	34738127	34738894	+	0	NA	intron (NM_032978, intron 1 of 16)	intron (NM_032978, intron 1 of 16)	-17466	NM_001390	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.011734	0.442708	248(AGGTACACACAGTACA,-,0.00)
chunk0028_311_1	chr10	91740400	91740630	+	0	NA	Intergenic	L1PA15|LINE|L1	57681	NR_108070	100507633	Hs.291528	NR_108070	ENSG00000228701	TNKS2-AS1	-	TNKS2 antisense RNA 1 (head to head)	ncRNA	0.000000	0.567100	
chunk0051_215_1	chr12	116599277	116599524	+	0	NA	Intergenic	Intergenic	40019	NM_001085481	643246	Hs.356061	NM_001085481	ENSG00000258102	MAP1LC3B2	ATG8G	microtubule associated protein 1 light chain 3 beta 2	protein-coding	0.036437	0.487903	
chunk0117_80_1	chr22	17158676	17159061	+	0	NA	promoter-TSS (NR_024483)	promoter-TSS (NR_024483)	411	NM_033070	27440	Hs.26890	NM_017829	ENSG00000069998	HDHD5	CECR5	haloacid dehalogenase like hydrolase domain containing 5	protein-coding	0.098701	0.676166	
chunk0043_371_1	chr12	24154144	24154585	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	-58057	NR_030625	100126320		NR_030625	ENSG00000216192	MIR920	MIRN920|hsa-mir-920	microRNA 920	ncRNA	0.002268	0.398190	
chunk0011_130_1	chr1	147163074	147163649	+	0	NA	intron (NR_103870, intron 3 of 5)	L1MB7|LINE|L1	9228	NR_103870	5565	Hs.50732	NM_005399	ENSG00000131791	PRKAB2	-	protein kinase AMP-activated non-catalytic subunit beta 2	protein-coding	0.005217	0.368056	
chunk0212_358_1	chrX	149362968	149363550	+	0	NA	Intergenic	MIR|SINE|MIR	142095	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.005155	0.399657	
chunk0008_50_1	chr1	89248981	89249255	+	0	NA	Intergenic	L1MA2|LINE|L1	23743	NM_001134486	115362	Hs.513726	NM_052942	ENSG00000154451	GBP5	GBP-5	guanylate binding protein 5	protein-coding	0.000000	0.501818	
chunk0120_353_1	chr3	11539728	11540127	+	0	NA	intron (NM_001136031, intron 17 of 17)	L1ME2|LINE|L1	28997	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.030075	0.457500	
chunk0210_197_1	chrX	80319964	80320164	+	0	NA	intron (NR_110646, intron 1 of 5)	L1PA6|LINE|L1	15254	NR_110646	101060146	Hs.546064	NR_110646	ENSG00000278530	CHMP1B2P	-	charged multivesicular body protein 1B2, pseudogene	pseudo	0.015000	0.512438	
chunk0205_69_1	chr9	106816509	106816846	+	0	NA	Intergenic	Intergenic	-46420	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.002967	0.411243	
chunk0113_191_1	chr20	53408675	53409391	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	-143737	NR_110051	101927770		NR_110051		LOC101927770	-	uncharacterized LOC101927770	ncRNA	0.015363	0.400279	
chunk0079_120_1	chr17	12492433	12492976	+	0	NA	Intergenic	L1MD2|LINE|L1	-57264	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.005525	0.365809	
chunk0159_141_1	chr5	139148165	139148862	+	0	NA	intron (NM_022464, intron 1 of 9)	intron (NM_022464, intron 1 of 9)	49863	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.004304	0.505731	
chunk0014_324_1	chr1	181876400	181876643	+	0	NA	Intergenic	L1PB1|LINE|L1	185191	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.012346	0.418033	
chunk0178_392_1	chr7	40490061	40490334	+	0	NA	intron (NM_024728, intron 11 of 14)	L1MA10|LINE|L1	355221	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.003663	0.481752	
chunk0093_440_1	chr19	58362155	58362750	+	0	NA	intron (NM_198458, intron 1 of 2)	CpG	396	NM_001207009	162968	Hs.447840	NM_198458	ENSG00000174586	ZNF497	-	zinc finger protein 497	protein-coding	0.090756	0.652685	
chunk0029_63_1	chr10	96568295	96568803	+	0	NA	intron (NM_020123, intron 2 of 14)	L3|LINE|CR1	18503	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.003937	0.335953	
chunk0015_233_1	chr1	187771942	187772607	+	0	NA	Intergenic	Intergenic	328646	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001504	0.327327	
chunk0128_350_1	chr3	112632961	112633332	+	0	NA	intron (NM_199511, intron 2 of 7)	MIRc|SINE|MIR	7997	NM_199512	151887	Hs.477128	NM_199511	ENSG00000091986	CCDC80	CL2|DRO1|SSG1|URB|okuribin	coiled-coil domain containing 80	protein-coding	0.008086	0.389785	
chunk0041_245_1	chr11	128629674	128629948	+	0	NA	Intergenic	Intergenic	-42253	NM_001143820	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.003650	0.490909	
chunk0170_238_1	chr6	113616710	113617135	+	0	NA	Intergenic	L1ME2|LINE|L1	33153	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.004706	0.338028	
chunk0202_379_1	chr9	80821677	80821949	+	0	NA	Intergenic	L1PA13|LINE|L1	846790	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.003676	0.494505	
chunk0031_90_1	chr10	123393777	123393976	+	0	NA	Intergenic	Intergenic	239632	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.005025	0.390000	
chunk0149_111_1	chr5	19263165	19263750	+	0	NA	Intergenic	LTR40a|LTR|ERVL	622815	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003419	0.363481	
chunk0077_328_1	chr16	82322210	82322436	+	0	NA	Intergenic	L1M2|LINE|L1	-152099	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.000000	0.295154	
chunk0138_303_1	chr4	41132306	41132776	+	0	NA	intron (NM_004307, intron 2 of 17)	intron (NM_004307, intron 2 of 17)	82077	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.000000	0.373673	
chunk0097_331_1	chr2	57516884	57517237	+	0	NA	Intergenic	Intergenic	-390591	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.008499	0.347458	
chunk0035_262_1	chr11	46472025	46473136	+	0	NA	intron (NM_001300731, intron 10 of 16)	intron (NM_001300731, intron 10 of 16)	-20691	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.003600	0.398381	919(TAGAACACAGTGTGAC,-,0.00),920(AGAACACAGTGTGACT,+,0.00)
chunk0133_395_1	chr3	174306617	174307063	+	0	NA	Intergenic	Intergenic	-386044	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004484	0.360179	
chunk0111_196_1	chr20	25744033	25744512	+	0	NA	Intergenic	ERVL47-int|LTR|ERVL	-47368	NM_015655	26152	Hs.61881	NM_015655	ENSG00000130684	ZNF337	-	zinc finger protein 337	protein-coding	0.004175	0.433333	
chunk0108_118_1	chr2	229810765	229811497	+	0	NA	intron (NM_004238, intron 13 of 40)	intron (NM_004238, intron 13 of 40)	68997	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.004098	0.350614	
chunk0062_238_1	chr14	71237510	71238030	+	0	NA	Intergenic	Intergenic	-160567	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.011538	0.435701	
chunk0163_334_1	chr6	15293547	15294006	+	0	NA	intron (NM_001267040, intron 1 of 17)	MER70C|LTR|ERVL	44921	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.004357	0.467391	
chunk0044_146_1	chr12	29725882	29727112	+	0	NA	intron (NM_001193451, intron 5 of 17)	intron (NM_001193451, intron 5 of 17)	57313	NM_001193451	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.007317	0.411860	
chunk0176_172_1	chr7	13641625	13642225	+	0	NA	Intergenic	Intergenic	344589	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.003333	0.361065	
chunk0112_72_1	chr20	37839542	37839836	+	0	NA	intron (NM_030877, intron 11 of 15)	intron (NM_030877, intron 11 of 15)	-63408	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.006803	0.372881	
chunk0047_358_1	chr12	75042025	75042886	+	0	NA	3' UTR (NM_139137, exon 5 of 5)	3' UTR (NM_139137, exon 5 of 5)	167293	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.006969	0.377030	
chunk0165_281_1	chr6	36116257	36116475	+	0	NA	Intergenic	AluJo|SINE|Alu	-14118	NR_072996	5603	Hs.178695	NM_002754	ENSG00000156711	MAPK13	MAPK 13|MAPK-13|PRKM13|SAPK4|p38delta	mitogen-activated protein kinase 13	protein-coding	0.000000	0.342466	
chunk0041_376_1	chr11	131703348	131703624	+	0	NA	intron (NM_001048209, intron 1 of 7)	L1MC5|LINE|L1	-39930	NR_126159	101929637	Hs.730330	NM_207432	ENSG00000224795	NTM-AS1	C11orf39	NTM antisense RNA 1	ncRNA	0.003623	0.335740	
chunk0101_79_1	chr2	124034099	124034831	+	0	NA	intron (NM_130773, intron 1 of 23)	intron (NM_130773, intron 1 of 23)	9178	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.002732	0.424284	
chunk0190_221_1	chr8	35776127	35776697	+	0	NA	intron (NM_080872, intron 16 of 16)	intron (NM_080872, intron 16 of 16)	-66092	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.001754	0.371278	
chunk0181_133_1	chr7	81092651	81092930	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-173439	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.007168	0.357143	
chunk0098_199_1	chr2	72538561	72539044	+	0	NA	intron (NM_015189, intron 8 of 21)	intron (NM_015189, intron 8 of 21)	287246	NM_015189	23233	Hs.303454	NM_015189	ENSG00000144036	EXOC6B	SEC15B|SEC15L2|SEMDJL3	exocyst complex component 6B	protein-coding	0.006211	0.380165	
chunk0038_347_1	chr11	92942647	92942968	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-26816	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.021807	0.518634	
chunk0116_385_1	chr21	42262813	42263321	+	0	NA	intron (NM_207627, intron 3 of 15)	intron (NM_207627, intron 3 of 15)	43169	NM_207174	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.023622	0.542240	
chunk0101_379_1	chr2	138503907	138504239	+	0	NA	intron (NM_001001664, intron 1 of 10)	MER113A|DNA|hAT-Charlie	2293	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.003012	0.285285	
chunk0103_355_1	chr2	168198579	168198801	+	0	NA	intron (NM_013233, intron 1 of 17)	intron (NM_013233, intron 1 of 17)	48905	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.022523	0.434978	
chunk0168_60_1	chr6	79120839	79121151	+	0	NA	Intergenic	L1ME1|LINE|L1	-42701	NM_017934	55023	Hs.511817	NM_017934	ENSG00000146247	PHIP	BRWD2|DCAF14|DIDOD|WDR11|ndrp	pleckstrin homology domain interacting protein	protein-coding	0.003205	0.261981	
chunk0042_129_1	chr12	3698408	3699169	+	0	NA	intron (NM_032680, intron 3 of 10)	intron (NM_032680, intron 3 of 10)	54412	NM_032680	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.006570	0.476378	
chunk0028_138_1	chr10	86437909	86438166	+	0	NA	intron (NM_015045, intron 17 of 18)	intron (NM_015045, intron 17 of 18)	-71544	NM_017551	2894	Hs.530653	NM_017551	ENSG00000182771	GRID1	GluD1	glutamate ionotropic receptor delta type subunit 1	protein-coding	0.011673	0.383721	
chunk0129_185_1	chr3	121027521	121027846	+	0	NA	intron (NM_014980, intron 3 of 27)	MLT1D|LTR|ERVL-MaLR	-21957	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.003077	0.426380	
chunk0204_183_1	chr9	96217943	96218194	+	0	NA	Intergenic	Intergenic	84084	NM_000197	3293	Hs.477	NM_000197	ENSG00000130948	HSD17B3	EDH17B3|SDR12C2	hydroxysteroid 17-beta dehydrogenase 3	protein-coding	0.035857	0.571429	
chunk0099_310_1	chr2	99404469	99404879	+	0	NA	exon (NM_016316, exon 18 of 23)	exon (NM_016316, exon 18 of 23)	67303	NM_015904	9669	Hs.158688	NM_015904	ENSG00000158417	EIF5B	IF2	eukaryotic translation initiation factor 5B	protein-coding	0.014634	0.418491	
chunk0211_13_1	chrX	107716926	107717461	+	0	NA	promoter-TSS (NM_001015881)	promoter-TSS (NM_001015881)	-132	NM_004089	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.033645	0.535448	
chunk0131_75_1	chr3	143041847	143042144	+	0	NA	intron (NM_001080415, intron 23 of 27)	intron (NM_001080415, intron 23 of 27)	40465	NM_001080415	23350	Hs.596572	NM_001080415	ENSG00000163714	U2SURP	SR140|fSAPa	U2 snRNP associated SURP domain containing	protein-coding	0.000000	0.352349	
chunk0142_112_1	chr4	94513407	94514003	+	0	NA	intron (NM_001256428, intron 2 of 11)	L1MA2|LINE|L1	61848	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.003356	0.328308	
chunk0066_412_1	chr15	39449579	39450344	+	0	NA	Intergenic	Intergenic	-131118	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.002614	0.399478	
chunk0040_142_1	chr11	112925531	112925730	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-35617	NM_181351	4684	Hs.503878	NM_000615	ENSG00000149294	NCAM1	CD56|MSK39|NCAM	neural cell adhesion molecule 1	protein-coding	0.015075	0.385000	
chunk0204_225_1	chr9	97484374	97484596	+	0	NA	intron (NM_014290, intron 15 of 16)	(AC)n|Simple_repeat|Simple_repeat	-16695	NM_001166116	7111	Hs.404289	NM_003275	ENSG00000136842	TMOD1	D9S57E|ETMOD|TMOD	tropomodulin 1	protein-coding	0.000000	0.372197	
chunk0160_159_1	chr5	151823822	151824057	+	0	NA	intron (NM_001146040, intron 8 of 8)	intron (NM_001146040, intron 8 of 8)	-51763	NR_132345	100652758	Hs.587054	NM_001278082		LOC100652758	-	uncharacterized LOC100652758	ncRNA	0.008511	0.449153	219(AAGAACACCGTCTTCT,-,0.00),220(AGAACACCGTCTTCTG,+,0.00)
chunk0151_377_1	chr5	55188589	55189144	+	0	NA	Intergenic	Intergenic	-15689	NM_001170402	166979	Hs.669184	NM_152623	ENSG00000164287	CDC20B	G6VTS76519	cell division cycle 20B	protein-coding	0.009009	0.341727	
chunk0104_149_1	chr2	173851233	173851925	+	0	NA	Intergenic	Intergenic	112640	NM_001017371	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.010116	0.445887	
chunk0143_104_1	chr4	108592631	108593194	+	0	NA	intron (NR_026968, intron 1 of 3)	HAL1|LINE|L1	27545	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.007105	0.445035	
chunk0151_366_1	chr5	54802792	54803204	+	0	NA	Intergenic	Intergenic	-58740	NR_104658	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.004854	0.426150	
chunk0045_254_1	chr12	49368077	49368442	+	0	NA	intron (NM_001293286, intron 1 of 12)	intron (NM_001293286, intron 1 of 12)	1354	NR_120663	65244	Hs.654826	NM_023071	ENSG00000123352	SPATS2	Nbla00526|P59SCR|SCR59|SPATA10	spermatogenesis associated serine rich 2	protein-coding	0.013699	0.366120	174(GAGTACAAGCCGTTCT,-,0.00),175(AGTACAAGCCGTTCTT,+,0.00)
chunk0147_130_1	chr4	174400854	174401078	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-22829	NR_036236	100423042		NR_036236	ENSG00000265846	MIR4276	-	microRNA 4276	ncRNA	0.008929	0.471111	
chunk0041_80_1	chr11	124233263	124233831	+	0	NA	Intergenic	L1ME3|LINE|L1	8908	NM_001291438	26492	Hs.381319	NM_001291438		OR8G2P	HSTPCR120|OR8G2|OR8G4|ORL206|ORL486|TPCR120	olfactory receptor family 8 subfamily G member 2 pseudogene	protein-coding	0.001761	0.314587	312(TTGCACAATGTGTACT,-,0.00),313(TGCACAATGTGTACTC,+,0.00)
chunk0045_409_1	chr12	53006384	53006758	+	0	NA	intron (NM_001300821, intron 1 of 14)	CpG	313	NM_001300821	1975	Hs.648394	NM_001417	ENSG00000063046	EIF4B	EIF-4B|PRO1843	eukaryotic translation initiation factor 4B	protein-coding	0.061497	0.602667	
chunk0212_196_1	chrX	134206914	134207538	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-29821	NM_001101357	347475	Hs.679431	NM_001101357	ENSG00000203952	CCDC160	-	coiled-coil domain containing 160	protein-coding	0.001603	0.329600	
chunk0020_59_1	chr1	232544602	232544867	+	0	NA	Intergenic	Intergenic	-29126	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.011321	0.406015	
chunk0189_134_1	chr8	22513395	22513892	+	0	NA	intron (NM_001243974, intron 6 of 14)	intron (NM_001243974, intron 6 of 14)	-38095	NM_005775	10174	Hs.528572	NM_005775	ENSG00000120896	SORBS3	SCAM-1|SCAM1|SH3D4	sorbin and SH3 domain containing 3	protein-coding	0.006036	0.331325	465(CAGGACATTGTGAACT,-,0.00)
chunk0201_126_1	chr9	35465973	35466327	+	0	NA	intron (NR_003581, intron 11 of 17)	L1ME1|LINE|L1	-23802	NM_014806	9853	Hs.493796	NM_014806	ENSG00000198853	RUSC2	Iporin|MRT61	RUN and SH3 domain containing 2	protein-coding	0.000000	0.301408	
chunk0144_467_1	chr4	142556080	142556427	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	290198	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.002882	0.425287	77(AGGAAGACTCTGTCCT,-,0.00),187(AAGTACACTGTGTTCC,-,0.00),188(AGTACACTGTGTTCCC,+,0.00)
chunk0072_159_1	chr15	92908309	92908908	+	0	NA	intron (NM_001042572, intron 2 of 12)	intron (NM_001042572, intron 2 of 12)	4209	NR_036136	100422995		NR_036136	ENSG00000284324	MIR3175	mir-3175	microRNA 3175	ncRNA	0.010017	0.413333	314(GAGCACTTCGTGTACT,-,0.00),315(AGCACTTCGTGTACTT,+,0.00)
chunk0197_50_1	chr8	118488657	118489091	+	0	NA	intron (NR_109794, intron 2 of 4)	L1ME3|LINE|L1	-132127	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.004608	0.358621	
chunk0076_442_1	chr16	73711209	73711636	+	0	NA	Intergenic	Intergenic	324617	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.011710	0.420561	
chunk0093_388_1	chr19	56404814	56405060	+	0	NA	intron (NM_152478, intron 1 of 4)	(TG)n|Simple_repeat|Simple_repeat	588	NM_001159861	147949	Hs.146854	NM_152478	ENSG00000198440	ZNF583	-	zinc finger protein 583	protein-coding	0.016260	0.457490	
chunk0202_79_1	chr9	71799646	71800267	+	0	NA	Intergenic	Intergenic	-31072	NM_001135820	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.001610	0.419614	
chunk0091_457_1	chr19	18029839	18030194	+	0	NA	Intergenic	Intergenic	21848	NM_015683	27106	Hs.515249	NM_015683	ENSG00000105643	ARRDC2	CLONE24945|PP2703	arrestin domain containing 2	protein-coding	0.022535	0.556180	
chunk0122_183_1	chr3	32666965	32667558	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-17884	NM_001256741	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.006745	0.373737	
chunk0025_87_1	chr10	50454931	50455144	+	0	NA	intron (NM_147156, intron 5 of 10)	L2a|LINE|L2	168940	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.000000	0.383178	
chunk0162_402_1	chr5	179820828	179821049	+	0	NA	promoter-TSS (NM_003900)	promoter-TSS (NM_003900)	96	NM_003900	8878	Hs.587290	NM_003900	ENSG00000161011	SQSTM1	A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B	sequestosome 1	protein-coding	0.149321	0.716216	
chunk0046_102_1	chr12	57049939	57050466	+	0	NA	promoter-TSS (NM_005379)	promoter-TSS (NM_005379)	-85	NM_005379	4640	Hs.5394	NM_005379	ENSG00000166866	MYO1A	BBMI|DFNA48|MIHC|MYHL	myosin IA	protein-coding	0.007590	0.520833	214(AAGTCCAGACTGTTCC,-,0.00),215(AGTCCAGACTGTTCCT,+,0.00)
chunk0143_348_1	chr4	121821631	121822322	+	0	NA	intron (NM_001237, intron 2 of 7)	intron (NM_001237, intron 2 of 7)	1957	NM_001237	890	Hs.58974	NM_001237	ENSG00000145386	CCNA2	CCN1|CCNA	cyclin A2	protein-coding	0.001447	0.336705	
chunk0023_455_1	chr10	32213237	32213950	+	0	NA	Intergenic	AluJb|SINE|Alu	133455	NM_001272019	80314	Hs.167805	NM_025209	ENSG00000120616	EPC1	Epl1	enhancer of polycomb homolog 1	protein-coding	0.007013	0.414566	308(AAGCACATTGTGTGCA,-,0.00),309(AGCACATTGTGTGCAG,+,0.00)
chunk0169_8_1	chr6	96433687	96434285	+	0	NA	Intergenic	L1PA10|LINE|L1	-87840	NM_015323	23376	Hs.149367	NM_015323	ENSG00000014123	UFL1	KIAA0776|Maxer|NLBP|RCAD	UFM1 specific ligase 1	protein-coding	0.003344	0.398998	
chunk0016_66_1	chr1	193532660	193532990	+	0	NA	Intergenic	L1PA15|LINE|L1	228080	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.006061	0.368580	
chunk0210_188_1	chrX	79803465	79803962	+	0	NA	Intergenic	L1MA1|LINE|L1	-211043	NM_001109878	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.000000	0.315261	
chunk0203_354_1	chr9	89867950	89868656	+	0	NA	Intergenic	Intergenic	-101113	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.016997	0.514851	
chunk0097_411_1	chr2	62763821	62764225	+	0	NA	intron (NM_001142614, intron 2 of 22)	intron (NM_001142614, intron 2 of 22)	57126	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.000000	0.279012	
chunk0035_53_1	chr11	41294337	41295166	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	164885	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003619	0.314458	
chunk0075_149_1	chr16	50685292	50685711	+	0	NA	Intergenic	Intergenic	-4148	NM_182854	124460	Hs.460777	NM_153337	ENSG00000167208	SNX20	SLIC1	sorting nexin 20	protein-coding	0.016706	0.480952	
chunk0122_225_1	chr3	33650121	33650736	+	0	NA	intron (NM_015097, intron 7 of 38)	intron (NM_015097, intron 7 of 38)	9013	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.003252	0.340909	
chunk0011_360_1	chr1	153049499	153049706	+	0	NA	Intergenic	L1PA11|LINE|L1	7910	NM_005988	6700	Hs.355542	NM_005988	ENSG00000241794	SPRR2A	-	small proline rich protein 2A	protein-coding	0.000000	0.552885	
chunk0025_28_1	chr10	48364926	48365300	+	0	NA	intron (NM_001278547, intron 1 of 11)	intron (NM_001278547, intron 1 of 11)	-36499	NM_001278548	5599	Hs.138211	NM_002750	ENSG00000107643	MAPK8	JNK|JNK-46|JNK1|JNK1A2|JNK21B1/2|PRKM8|SAPK1|SAPK1c	mitogen-activated protein kinase 8	protein-coding	0.005348	0.301333	
chunk0031_298_1	chr10	128662461	128662899	+	0	NA	Intergenic	Intergenic	376730	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.009132	0.339408	
chunk0199_124_1	chr9	3676748	3677087	+	0	NA	intron (NR_121586, intron 3 of 4)	intron (NR_121586, intron 3 of 4)	8831	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.008850	0.476471	
chunk0190_182_1	chr8	33407106	33407401	+	0	NA	intron (NM_032664, intron 3 of 4)	intron (NM_032664, intron 3 of 4)	65893	NM_032664	84750	Hs.458713	NM_032664	ENSG00000172728	FUT10	FUCTX	fucosyltransferase 10	protein-coding	0.010169	0.361486	
chunk0173_444_1	chr6	151568422	151568895	+	0	NA	intron (NM_025059, intron 5 of 10)	L1ME4b|LINE|L1	74618	NM_025059	80129	Hs.660044	NM_025059	ENSG00000120262	CCDC170	C6orf97|bA282P11.1	coiled-coil domain containing 170	protein-coding	0.002114	0.341772	
chunk0109_30_1	chr20	504682	505071	+	0	NA	intron (NM_177559, intron 4 of 13)	MIR3|SINE|MIR	38962	NM_177559	1457	Hs.644056	NM_001895	ENSG00000101266	CSNK2A1	CK2A1|CKII|Cka1|Cka2|OCNDS	casein kinase 2 alpha 1	protein-coding	0.007712	0.361538	180(GAGAAGAGACTGTACC,-,0.00),181(AGAAGAGACTGTACCT,+,0.00)
chunk0165_122_1	chr6	32953154	32953394	+	0	NA	promoter-TSS (NM_006120)	promoter-TSS (NM_006120)	-152	NM_006120	3108	Hs.728759	NM_006120	ENSG00000204257	HLA-DMA	D6S222E|DMA|HLADM|RING6	major histocompatibility complex, class II, DM alpha	protein-coding	0.012500	0.526971	
chunk0211_97_1	chrX	110835892	110836246	+	0	NA	Intergenic	MIR|SINE|MIR	-40011	NM_001143981	91851	Hs.496587	NM_145234	ENSG00000101938	CHRDL1	CHL|MGC1|MGCN|NRLN1|VOPT|dA141H5.1	chordin like 1	protein-coding	0.000000	0.425352	
chunk0070_402_1	chr15	77328691	77329187	+	0	NA	intron (NM_024776, intron 1 of 7)	intron (NM_024776, intron 1 of 7)	91165	NM_024776	79834	Hs.9587	NM_024776	ENSG00000173517	PEAK1	SGK269	pseudopodium enriched atypical kinase 1	protein-coding	0.002016	0.309859	
chunk0065_119_1	chr15	24788033	24788500	+	0	NA	Intergenic	Intergenic	-35381	NM_022808	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.004283	0.329060	
chunk0124_79_1	chr3	53181630	53182286	+	0	NA	intron (NM_001316327, intron 7 of 18)	MER63A|DNA|hAT-Blackjack	20437	NM_001316327	5580	Hs.155342	NM_006254	ENSG00000163932	PRKCD	ALPS3|CVID9|MAY1|PKCD|nPKC-delta	protein kinase C delta	protein-coding	0.024390	0.535769	493(GAGCACACTCTGTCCC,-,0.00),494(AGCACACTCTGTCCCT,+,0.00)
chunk0124_379_1	chr3	59541187	59542010	+	0	NA	Intergenic	L2c|LINE|L2	-491609	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.009721	0.410194	382(AGGCACAGCCTGTACC,-,0.00),383(GGCACAGCCTGTACCC,+,0.00)
chunk0008_450_1	chr1	99737500	99737699	+	0	NA	intron (NM_001013660, intron 7 of 16)	intron (NM_001013660, intron 7 of 16)	-24646	NR_031666	100302152		NR_031666	ENSG00000221669	MIR548N	MIRN548N|hsa-mir-548n	microRNA 548n	ncRNA	0.010050	0.375000	82(TAGGACAGCCTGTTCT,-,0.00),83(AGGACAGCCTGTTCTT,+,0.00)
chunk0135_301_1	chr3	189763738	189764129	+	0	NA	intron (NM_001114978, intron 3 of 12)	intron (NM_001114978, intron 3 of 12)	-25727	NM_001114981	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.005115	0.408163	
chunk0001_258_1	chr1	8463144	8463449	+	0	NA	intron (NM_001042681, intron 11 of 22)	intron (NM_001042681, intron 11 of 22)	31617	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.006557	0.395425	
chunk0117_137_1	chr22	19408781	19409272	+	0	NA	intron (NM_003325, intron 2 of 24)	intron (NM_003325, intron 2 of 24)	22670	NM_003325	7290	Hs.474206	NM_003325	ENSG00000100084	HIRA	DGCR1|TUP1|TUPLE1	histone cell cycle regulator	protein-coding	0.016293	0.475610	
chunk0159_448_1	chr5	148812856	148813931	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-13200	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.009302	0.386617	820(CAAGACATATTGTTCT,-,0.00),821(AAGACATATTGTTCTG,+,0.00)
chunk0014_151_1	chr1	178147342	178147831	+	0	NA	intron (NM_170692, intron 1 of 17)	intron (NM_170692, intron 1 of 17)	-53593	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.008180	0.420408	
chunk0039_270_1	chr11	102378273	102378490	+	0	NA	3' UTR (NM_001166, exon 9 of 9)	3' UTR (NM_001166, exon 9 of 9)	31007	NM_001256163	329	Hs.696238	NM_001166	ENSG00000110330	BIRC2	API1|HIAP2|Hiap-2|MIHB|RNF48|c-IAP1|cIAP1	baculoviral IAP repeat containing 2	protein-coding	0.000000	0.311927	
chunk0025_306_1	chr10	57613229	57613494	+	0	NA	Intergenic	Intergenic	-308802	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.000000	0.323308	
chunk0088_37_1	chr18	43876423	43877737	+	0	NA	Intergenic	Intergenic	-599430	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.009132	0.431939	
chunk0171_28_1	chr6	120372754	120373308	+	0	NA	Intergenic	L2|LINE|L2	357852	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.003610	0.345946	
chunk0084_113_1	chr17	75909549	75910311	+	0	NA	TTS (NM_001080542)	TTS (NM_001080542)	-4830	NM_032478	64978	Hs.442609	NM_032478	ENSG00000204316	MRPL38	HSPC262|L38MT|MRP-L3|MRP-L38|RPML3	mitochondrial ribosomal protein L38	protein-coding	0.022310	0.562254	
chunk0194_186_1	chr8	85220603	85220858	+	0	NA	promoter-TSS (NM_001099672)	promoter-TSS (NM_001099672)	-308	NM_001293320	401466	Hs.443072	NM_001099670	ENSG00000176731	RBIS	C8orf59	ribosomal biogenesis factor	protein-coding	0.066667	0.632812	
chunk0007_267_1	chr1	83154432	83154778	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-168397	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.000000	0.397695	
chunk0121_149_1	chr3	19050462	19050763	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	-97913	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.000000	0.264901	
chunk0074_163_1	chr16	23410050	23410368	+	0	NA	intron (NM_153603, intron 11 of 16)	intron (NM_153603, intron 11 of 16)	42982	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.018868	0.485893	113(AGGTACAGACAGTCCT,-,0.00),114(GGTACAGACAGTCCTC,+,0.00)
chunk0066_274_1	chr15	35102367	35102614	+	0	NA	Intergenic	Intergenic	-114194	NM_014106	54989	Hs.744990	NM_014106	ENSG00000198146	ZNF770	PRO1914	zinc finger protein 770	protein-coding	0.004049	0.258065	
chunk0018_231_1	chr1	219824342	219824820	+	0	NA	Intergenic	Intergenic	104070	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.004184	0.315240	
chunk0007_276_1	chr1	83712127	83712360	+	0	NA	intron (NR_119375, intron 2 of 2)	intron (NR_119375, intron 2 of 2)	148303	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.000000	0.427350	
chunk0076_49_1	chr16	60835620	60835985	+	0	NA	Intergenic	LTR16C|LTR|ERVL	219964	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.008219	0.382514	
chunk0051_190_1	chr12	116222485	116222727	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	54580	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.008264	0.419753	
chunk0109_286_1	chr20	8215485	8215731	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	83343	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.020325	0.457490	
chunk0112_97_1	chr20	38109011	38110570	+	0	NA	Intergenic	Intergenic	55508	NM_004613	7052	Hs.517033	NM_004613	ENSG00000198959	TGM2	TG(C)|TGC	transglutaminase 2	protein-coding	0.007056	0.475000	1321(AAGCACAGAGAGTTCT,-,0.00),1322(AGCACAGAGAGTTCTG,+,0.00)
chunk0180_231_1	chr7	67432902	67433213	+	0	NA	Intergenic	Intergenic	97081	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.025723	0.541667	
chunk0191_123_1	chr8	48430154	48430719	+	0	NA	Intergenic	Intergenic	-121131	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.028319	0.558304	
chunk0137_280_1	chr4	23368313	23368831	+	0	NA	Intergenic	L2c|LINE|L2	521505	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.009653	0.366089	
chunk0007_345_1	chr1	84835119	84835629	+	0	NA	intron (NM_012152, intron 2 of 2)	L3|LINE|CR1	57839	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.013725	0.403131	121(AAAACAATTTGTTCTC,+,0.00)
chunk0087_321_1	chr18	39805171	39805513	+	0	NA	Intergenic	MLT1M|LTR|ERVL-MaLR	-53347	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.002924	0.390671	
chunk0040_19_1	chr11	109071554	109072109	+	0	NA	Intergenic	Intergenic	-350289	NM_207645	399947	Hs.172982	NM_207645	ENSG00000185742	C11orf87	LOH11CR1A|NEURIM1	chromosome 11 open reading frame 87	protein-coding	0.007207	0.447842	235(AAGGACAATGTGTTCC,-,0.00),236(AGGACAATGTGTTCCA,+,0.00)
chunk0200_139_1	chr9	17888048	17888247	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	309193	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.005025	0.475000	
chunk0153_131_1	chr5	68953291	68954049	+	0	NA	Intergenic	Intergenic	76257	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.007916	0.396574	
chunk0168_125_1	chr6	82087046	82087273	+	0	NA	Intergenic	Intergenic	160595	NM_001300906	25998	Hs.306425	NM_015525	ENSG00000005700	IBTK	BTBD26|BTKI	inhibitor of Bruton tyrosine kinase	protein-coding	0.008811	0.434211	
chunk0066_332_1	chr15	36658449	36658763	+	0	NA	intron (NM_032499, intron 6 of 11)	intron (NM_032499, intron 6 of 11)	63737	NM_001290232	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.003185	0.355556	
chunk0023_64_1	chr10	22059319	22059527	+	0	NA	Intergenic	L1ME1|LINE|L1	-55702	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.000000	0.339713	
chunk0149_168_1	chr5	20500395	20501056	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	75148	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004539	0.335347	
chunk0160_280_1	chr5	157795391	157795808	+	0	NA	intron (NM_001195556, intron 8 of 11)	L1MC4|LINE|L1	51904	NM_173491	134353	Hs.23648	NM_173491	ENSG00000155858	LSM11	-	LSM11, U7 small nuclear RNA associated	protein-coding	0.004796	0.349282	
chunk0158_155_1	chr5	127555732	127556146	+	0	NA	TTS (NM_130809)	TTS (NM_130809)	38330	NM_130809	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.002415	0.356627	
chunk0055_293_1	chr13	65228550	65229155	+	0	NA	Intergenic	Intergenic	-637195	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.008264	0.341584	318(TGGGACTCTCTGTTCT,-,0.00),319(GGGACTCTCTGTTCTT,+,0.00)
chunk0084_106_1	chr17	75697539	75697985	+	0	NA	intron (NM_001301855, intron 5 of 11)	intron (NM_001301855, intron 5 of 11)	-23674	NM_000213	3691	Hs.632226	NM_000213	ENSG00000132470	ITGB4	CD104|GP150	integrin subunit beta 4	protein-coding	0.013453	0.530201	
chunk0179_314_1	chr7	50487686	50488303	+	0	NA	intron (NM_001082971, intron 9 of 14)	MER4B-int|LTR|ERV1	-37604	NM_001287494	63979	Hs.137516	NM_022116	ENSG00000132436	FIGNL1	-	fidgetin like 1	protein-coding	0.003241	0.245955	
chunk0154_235_1	chr5	80916968	80917514	+	0	NA	Intergenic	Intergenic	-43448	NM_006909	5924	Hs.162129	NM_006909	ENSG00000113319	RASGRF2	GRF2|RAS-GRF2	Ras protein specific guanine nucleotide releasing factor 2	protein-coding	0.005495	0.318099	
chunk0195_220_1	chr8	97084403	97084973	+	0	NA	intron (NM_016134, intron 7 of 7)	intron (NM_016134, intron 7 of 7)	193260	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.003509	0.381786	208(AGGCACATACAGTGCC,-,0.00),209(GGCACATACAGTGCCA,+,0.00)
chunk0074_413_1	chr16	35600317	35600691	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-93334	NR_034018	100130700	Hs.97712	NR_034018		TP53TG3HP	-	TP53 target 3 family member H, pseudogene	pseudo	0.002674	0.381333	243(AAGAACATAAAGTACA,-,0.00),244(AGAACATAAAGTACAT,+,0.00)
chunk0055_4_1	chr13	51612411	51613030	+	0	NA	intron (NM_052950, intron 1 of 11)	intron (NM_052950, intron 1 of 11)	28372	NM_052950	115825	Hs.46506	NM_052950	ENSG00000139668	WDFY2	PROF|WDF2|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.001616	0.341935	
chunk0036_219_1	chr11	63847228	63847696	+	0	NA	intron (NM_001039469, intron 1 of 18)	intron (NM_001039469, intron 1 of 18)	8534	NM_001163296	2011	Hs.567261	NM_004954	ENSG00000072518	MARK2	EMK-1|EMK1|PAR-1|Par-1b|Par1b	microtubule affinity regulating kinase 2	protein-coding	0.006410	0.473348	
chunk0196_258_1	chr8	108735444	108735921	+	0	NA	Intergenic	L1MB8|LINE|L1	51859	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.004193	0.336820	
chunk0115_105_1	chr21	22757204	22757885	+	0	NA	Intergenic	Intergenic	-321740	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.000000	0.353372	
chunk0185_179_1	chr7	128057974	128058412	+	0	NA	intron (NM_014390, intron 16 of 23)	intron (NM_014390, intron 16 of 23)	-23668	NR_030324	693178		NR_030324	ENSG00000207588	MIR593	MIRN593|hsa-mir-593	microRNA 593	ncRNA	0.002283	0.457859	
chunk0152_19_1	chr5	56422183	56422636	+	0	NA	Intergenic	Intergenic	59360	NR_104664	102467147	Hs.650177	NR_104664	ENSG00000248727	LINC01948	-	long intergenic non-protein coding RNA 1948	ncRNA	0.011038	0.416300	
chunk0147_360_1	chr4	185807881	185808389	+	0	NA	intron (NM_021069, intron 1 of 20)	intron (NM_021069, intron 1 of 20)	2759	NM_001145672	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.000000	0.253438	
chunk0093_397_1	chr19	56855665	56855910	+	0	NA	Intergenic	MADE1|DNA|TcMar-Mariner	14885	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.008163	0.333333	
chunk0033_149_1	chr11	15501429	15501768	+	0	NA	Intergenic	Intergenic	-142287	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.017699	0.364706	
chunk0073_53_1	chr16	3150691	3150977	+	0	NA	TTS (NR_132322)	TTS (NR_132322)	6543	NR_132322	197350	Hs.434132	NR_132322	ENSG00000228146	CASP16P	CASP16	caspase 16, pseudogene	pseudo	0.080420	0.595819	
chunk0108_411_1	chr2	237509876	237510179	+	0	NA	promoter-TSS (NR_106869)	promoter-TSS (NR_106869)	-904	NR_106869	102465486		NR_106869	ENSG00000277842	MIR6811	hsa-mir-6811	microRNA 6811	ncRNA	0.019802	0.427632	
chunk0149_418_1	chr5	29498729	29498955	+	0	NA	Intergenic	L1PA13|LINE|L1	-102866	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.004425	0.528634	
chunk0211_36_1	chrX	108344273	108344554	+	0	NA	intron (NM_001287760, intron 2 of 42)	intron (NM_001287760, intron 2 of 42)	94017	NM_001287760	1288	Hs.145586	NM_001847	ENSG00000197565	COL4A6	CXDELq22.3|DELXq22.3|DFNX6	collagen type IV alpha 6 chain	protein-coding	0.000000	0.390071	
chunk0072_280_1	chr15	97995102	97995594	+	0	NA	Intergenic	Intergenic	34645	NM_183376	91947	Hs.6093	NM_183376	ENSG00000140450	ARRDC4	-	arrestin domain containing 4	protein-coding	0.008130	0.419878	
chunk0136_340_1	chr3	195718311	195718957	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-2248	NM_001291833	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.013932	0.431221	
chunk0013_255_1	chr1	169901155	169901411	+	0	NA	Intergenic	AluJr4|SINE|Alu	-7324	NM_020423	57147	Hs.435560	NM_020423	ENSG00000000457	SCYL3	PACE-1|PACE1	SCY1 like pseudokinase 3	protein-coding	0.000000	0.412451	
chunk0011_279_1	chr1	151372353	151372841	+	0	NA	intron (NM_001258289, intron 1 of 11)	intron (NM_001258289, intron 1 of 11)	137	NM_003944	8991	Hs.632460	NM_003944	ENSG00000143416	SELENBP1	EHMTO|HEL-S-134P|LPSB|MTO|SBP56|SP56|hSBP	selenium binding protein 1	protein-coding	0.016393	0.595092	
chunk0162_389_1	chr5	179559387	179559731	+	0	NA	promoter-TSS (NM_001040452)	promoter-TSS (NM_001040452)	-133	NM_001040451	80230	Hs.306769	NM_025158	ENSG00000176783	RUFY1	RABIP4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding	0.061047	0.608696	
chunk0015_48_1	chr1	184543807	184544006	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	156890	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.310000	
chunk0203_282_1	chr9	88813814	88814111	+	0	NA	Intergenic	Intergenic	-68057	NR_036252	100423015		NR_036252	ENSG00000265873	MIR4289	-	microRNA 4289	ncRNA	0.013468	0.399329	
chunk0006_123_1	chr1	65763986	65764538	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	-28248	NM_001037341	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.001812	0.401447	
chunk0127_74_1	chr3	89493938	89494465	+	0	NA	Intergenic	Intergenic	386677	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.306818	
chunk0112_425_1	chr20	47357449	47358078	+	0	NA	promoter-TSS (NM_001281784)	promoter-TSS (NM_001281784)	-874	NM_001281780	23613	Hs.446240	NM_012408	ENSG00000101040	ZMYND8	PRKCBP1|PRO2893|RACK7	zinc finger MYND-type containing 8	protein-coding	0.039746	0.584127	416(GGGCACAGGCAGTGCC,-,0.00),417(GGCACAGGCAGTGCCT,+,0.00)
chunk0030_2_1	chr10	110784122	110784716	+	0	NA	exon (NM_001134363, exon 4 of 14)	exon (NM_001134363, exon 4 of 14)	86485	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.011785	0.452101	252(GGGAACATTGTGTGCT,-,0.00),253(GGAACATTGTGTGCTT,+,0.00),362(AGGCACATTATGTCCT,-,0.00),363(GGCACATTATGTCCTG,+,0.00)
chunk0159_380_1	chr5	146209782	146210326	+	0	NA	intron (NM_018989, intron 1 of 20)	L2c|LINE|L2	6454	NM_018989	54439	Hs.61441	NM_018989	ENSG00000091009	RBM27	ARRS1|Psc1|ZC3H18|ZC3H20	RNA binding motif protein 27	protein-coding	0.003676	0.354128	
chunk0171_313_1	chr6	129501366	129501968	+	0	NA	intron (NM_001079823, intron 57 of 63)	intron (NM_001079823, intron 57 of 63)	208558	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.006645	0.429519	357(ATGTACTGCATGTTCT,-,0.00)
chunk0198_267_1	chr8	134886335	134887080	+	0	NA	Intergenic	Intergenic	36772	NR_125427	101927845	Hs.559609	NR_125427	ENSG00000251218	LOC101927845	-	uncharacterized LOC101927845	ncRNA	0.010738	0.420912	583(GGTACACTATGAGCTT,+,0.00)
chunk0148_66_1	chr5	2100112	2100688	+	0	NA	Intergenic	Intergenic	211801	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.003472	0.341421	212(AGAACTTCCTGTACAT,+,0.00)
chunk0085_449_1	chr18	11186979	11187301	+	0	NA	Intergenic	Intergenic	-38378	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.012422	0.464396	
chunk0041_137_1	chr11	125274181	125274963	+	0	NA	intron (NM_022062, intron 2 of 12)	intron (NM_022062, intron 2 of 12)	109909	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.019182	0.515964	357(GAGAACAAACTGTGCA,-,0.00),358(AGAACAAACTGTGCAG,+,0.00)
chunk0088_96_1	chr18	44958152	44958844	+	0	NA	intron (NM_015559, intron 4 of 5)	intron (NM_015559, intron 4 of 5)	11668	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.001445	0.396825	
chunk0155_152_1	chr5	93931526	93931912	+	0	NA	intron (NR_028080, intron 4 of 8)	L1ME3A|LINE|L1	179980	NM_001163417	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.000000	0.310078	
chunk0097_161_1	chr2	48732874	48733310	+	0	NA	intron (NM_000233, intron 1 of 10)	UCON29|DNA|PiggyBac?	22649	NM_000233	3973	Hs.468490	NM_000233	ENSG00000138039	LHCGR	HHG|LCGR|LGR2|LH/CG-R|LH/CGR|LHR|LHRHR|LSH-R|ULG5	luteinizing hormone/choriogonadotropin receptor	protein-coding	0.009174	0.414188	
chunk0163_164_1	chr6	11110858	11111257	+	0	NA	intron (NM_207582, intron 1 of 1)	MER50-int|LTR|ERV1	781	NM_207582	405754	Hs.631996	NM_207582	ENSG00000244476	ERVFRD-1	ERVFRDE1|GLLL6191|HERV-FRD|HERV-W/FRD|UNQ6191|envFRD	endogenous retrovirus group FRD member 1, envelope	protein-coding	0.012531	0.472500	
chunk0078_91_1	chr17	2018638	2018983	+	0	NA	intron (NM_178568, intron 1 of 1)	MIRb|SINE|MIR	6535	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.026087	0.595376	
chunk0019_157_1	chr1	225877636	225877890	+	0	NA	intron (NM_014698, intron 2 of 24)	intron (NM_014698, intron 2 of 24)	4957	NM_014698	9725	Hs.119387	NM_014698	ENSG00000196187	TMEM63A	KIAA0792	transmembrane protein 63A	protein-coding	0.019685	0.588235	
chunk0061_86_1	chr14	56984345	56984717	+	0	NA	Intergenic	AluJr4|SINE|Alu	171348	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.002688	0.348525	
chunk0153_318_1	chr5	73729235	73729692	+	0	NA	intron (NM_001080479, intron 2 of 36)	intron (NM_001080479, intron 2 of 36)	-84055	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.004376	0.368996	
chunk0052_214_1	chr13	25305669	25306148	+	0	NA	intron (NM_001008564, intron 1 of 14)	intron (NM_001008564, intron 1 of 14)	4380	NM_001008564	9818	Hs.507537	NM_014089	ENSG00000139496	NUP58	NUP45|NUPL1|PRO2463	nucleoporin 58	protein-coding	0.014614	0.389583	
chunk0110_96_1	chr20	11409126	11410026	+	0	NA	Intergenic	Intergenic	-136193	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.001111	0.335183	261(CTGAACATTTTGTTCT,-,0.00),262(TGAACATTTTGTTCTA,+,0.00)
chunk0112_36_1	chr20	36734283	36734839	+	0	NA	intron (NR_038370, intron 1 of 13)	L2c|LINE|L2	11577	NM_022477	57446	Hs.437338	NM_022477	ENSG00000101079	NDRG3	-	NDRG family member 3	protein-coding	0.005396	0.429084	
chunk0022_394_1	chr10	17840368	17840952	+	0	NA	intron (NM_002438, intron 4 of 29)	intron (NM_002438, intron 4 of 29)	-4447	NR_030167	574445		NR_030167	ENSG00000207938	MIR511	MIR511-1|MIR511-2|MIRN511-1|MIRN511-2|hsa-mir-511|hsa-mir-511-2|mir-511	microRNA 511	ncRNA	0.013699	0.393162	
chunk0039_369_1	chr11	106147887	106148465	+	0	NA	Intergenic	Intergenic	-70438	NM_152433	143879	Hs.101949	NM_152433	ENSG00000182359	KBTBD3	BKLHD3	kelch repeat and BTB domain containing 3	protein-coding	0.000000	0.341969	
chunk0138_436_1	chr4	45643535	45644143	+	0	NA	Intergenic	L2a|LINE|L2	480226	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.001645	0.308703	
chunk0026_357_1	chr10	68957781	68957986	+	0	NA	intron (NM_001256910, intron 1 of 14)	intron (NM_001256910, intron 1 of 14)	1443	NM_001256910	9188	Hs.223141	NM_004728	ENSG00000165732	DDX21	GUA|GURDB|RH-II/GU|RH-II/GuA	DExD-box helicase 21	protein-coding	0.009756	0.427184	
chunk0053_202_1	chr13	31941006	31941212	+	0	NA	intron (NR_027062, intron 1 of 3)	intron (NR_027062, intron 1 of 3)	-90191	NM_023037	10129	Hs.507669	NM_023037	ENSG00000073910	FRY	13CDNA73|214K23.2|C13orf14|CG003|bA207N4.2|bA37E23.1	FRY microtubule binding protein	protein-coding	0.004854	0.478261	
chunk0161_343_1	chr5	174139746	174139945	+	0	NA	Intergenic	Intergenic	94241	NM_015980	51617	Hs.559412	NM_015980	ENSG00000170091	NSG2	CALY3|HMP19	neuronal vesicle trafficking associated 2	protein-coding	0.000000	0.345000	
chunk0150_244_1	chr5	36180188	36181041	+	0	NA	intron (NM_032637, intron 9 of 9)	intron (NM_032637, intron 9 of 9)	28571	NM_005983	6502	Hs.23348	NM_005983	ENSG00000145604	SKP2	FBL1|FBXL1|FLB1|p45	S-phase kinase associated protein 2	protein-coding	0.005862	0.354801	
chunk0105_333_1	chr2	191111813	191112084	+	0	NA	intron (NM_003151, intron 3 of 23)	L1ME1|LINE|L1	39312	NM_003151	6775	Hs.80642	NM_003151	ENSG00000138378	STAT4	SLEB11	signal transducer and activator of transcription 4	protein-coding	0.007380	0.426471	
chunk0193_239_1	chr8	76708357	76708697	+	0	NA	intron (NM_024721, intron 3 of 10)	intron (NM_024721, intron 3 of 10)	-25252	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.002941	0.337243	
chunk0183_144_1	chr7	105826176	105826506	+	0	NA	intron (NM_020725, intron 2 of 11)	MIR3|SINE|MIR	50244	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.000000	0.386707	
chunk0164_173_1	chr6	21958519	21958737	+	0	NA	intron (NR_015410, intron 5 of 11)	L3|LINE|CR1	188565	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.000000	0.383562	
chunk0028_431_1	chr10	93763078	93763439	+	0	NA	intron (NM_001308276, intron 2 of 5)	intron (NM_001308276, intron 2 of 5)	5449	NR_131777	9211	Hs.533670	NM_005097	ENSG00000108231	LGI1	ADLTE|ADPAEF|ADPEAF|EPITEMPIN|EPT|ETL1|IB1099	leucine rich glioma inactivated 1	protein-coding	0.011080	0.477901	
chunk0168_31_1	chr6	77837262	77837734	+	0	NA	intron (NM_001282136, intron 3 of 3)	L1MC5|LINE|L1	146842	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.004237	0.336152	
chunk0176_264_1	chr7	16402090	16402866	+	0	NA	intron (NM_001101426, intron 2 of 9)	L1MEd|LINE|L1	18844	NM_001101417	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.002577	0.361647	
chunk0124_260_1	chr3	57014972	57015219	+	0	NA	intron (NM_001128615, intron 2 of 12)	MER58A|DNA|hAT-Charlie	-45346	NM_181727	353324	Hs.129794	NM_181727	ENSG00000186451	SPATA12	SRG5	spermatogenesis associated 12	protein-coding	0.016194	0.419355	
chunk0208_45_1	chrX	11430859	11431436	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-3362	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.001733	0.368512	
chunk0080_102_1	chr17	26937950	26938253	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	355895	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.003300	0.473684	
chunk0164_407_1	chr6	26612173	26612966	+	0	NA	Intergenic	AluSc|SINE|Alu	15626	NM_013375	29777	Hs.254406	NM_013375	ENSG00000146109	ABT1	Esf2|hABT1	activator of basal transcription 1	protein-coding	0.005044	0.479849	
chunk0057_370_1	chr13	108989975	108990409	+	0	NA	intron (NM_001198950, intron 20 of 34)	intron (NM_001198950, intron 20 of 34)	177111	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.006912	0.379310	
chunk0035_174_1	chr11	43903983	43904521	+	0	NA	intron (NM_139178, intron 8 of 9)	intron (NM_139178, intron 8 of 9)	6949	NR_026952	729799	Hs.368920	NR_026952	ENSG00000213693	SEC14L1P1	-	SEC14 like 1 pseudogene 1	pseudo	0.007435	0.376623	
chunk0068_94_1	chr15	52179859	52180112	+	0	NA	promoter-TSS (NM_006578)	promoter-TSS (NM_006578)	-20	NM_006578	10681	Hs.155090	NM_006578	ENSG00000069966	GNB5	GB5|IDDCA|LADCI	G protein subunit beta 5	protein-coding	0.138340	0.767717	
chunk0186_214_1	chr7	140022596	140022854	+	0	NA	Intergenic	Intergenic	40996	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.000000	0.463320	
chunk0198_345_1	chr8	140265162	140265534	+	0	NA	intron (NM_001160372, intron 15 of 22)	intron (NM_001160372, intron 15 of 22)	192414	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.018817	0.434316	
chunk0125_216_1	chr3	67654822	67655379	+	0	NA	promoter-TSS (NM_003848)	promoter-TSS (NM_003848)	403	NR_109992	101927111	Hs.518057	NR_109992	ENSG00000241316	SUCLG2-AS1	-	SUCLG2 antisense RNA 1 (head to head)	ncRNA	0.025135	0.523297	
chunk0155_396_1	chr5	98785748	98786136	+	0	NA	intron (NM_001012761, intron 4 of 4)	intron (NM_001012761, intron 4 of 4)	-12858	NR_033932	503569	Hs.586188	NR_033932	ENSG00000246763	RGMB-AS1	-	RGMB antisense RNA 1	ncRNA	0.000000	0.344473	
chunk0206_279_1	chr9	124356648	124357360	+	0	NA	non-coding (NR_027406, exon 1 of 1)	non-coding (NR_027406, exon 1 of 1)	3531	NR_027406	100129034	Hs.654980	NR_027406		LOC100129034	-	uncharacterized LOC100129034	ncRNA	0.029494	0.483871	
chunk0089_159_1	chr18	59085648	59086102	+	0	NA	Intergenic	Intergenic	50196	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.002203	0.417582	
chunk0172_134_1	chr6	135310253	135310909	+	0	NA	intron (NM_017651, intron 25 of 27)	intron (NM_017651, intron 25 of 27)	71421	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.001524	0.299848	
chunk0186_171_1	chr7	139341096	139341608	+	0	NA	5' UTR (NM_001244584, exon 1 of 11)	5' UTR (NM_001244584, exon 1 of 11)	220	NM_197964	154791	Hs.718441	NM_197964	ENSG00000164898	FMC1	C7orf55|HSPC268	formation of mitochondrial complex V assembly factor 1 homolog	protein-coding	0.083984	0.598441	
chunk0017_45_1	chr1	205268483	205268929	+	0	NA	intron (NM_001297613, intron 1 of 3)	MIRc|SINE|MIR	12505	NM_001297613	9911	Hs.6360	NM_014858	ENSG00000133069	TMCC2	HUCEP11	transmembrane and coiled-coil domain family 2	protein-coding	0.011211	0.516779	
chunk0129_23_1	chr3	117135948	117136436	+	0	NA	Intergenic	Intergenic	214761	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002049	0.345603	
chunk0035_211_1	chr11	44940487	44940865	+	0	NA	5' UTR (NM_001258320, exon 3 of 10)	5' UTR (NM_001258320, exon 3 of 10)	9532	NM_001258320	9537	Hs.554791	NM_006034	ENSG00000175274	TP53I11	PIG11	tumor protein p53 inducible protein 11	protein-coding	0.021164	0.469657	
chunk0145_239_1	chr4	148648477	148648976	+	0	NA	Intergenic	Intergenic	-206206	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.010020	0.470000	151(GAGATCTGTGTGTCCT,-,0.00),152(AGATCTGTGTGTCCTT,+,0.00),279(TGGAACTTAATGTTCT,-,0.00),280(GGAACTTAATGTTCTG,+,0.00)
chunk0139_58_1	chr4	48902379	48902597	+	0	NA	intron (NM_001014446, intron 2 of 6)	intron (NM_001014446, intron 2 of 6)	4340	NM_001286774	132299	Hs.95835	NM_152398	ENSG00000145247	OCIAD2	-	OCIA domain containing 2	protein-coding	0.000000	0.529680	
chunk0211_123_1	chrX	112305689	112306669	+	0	NA	intron (NM_001004308, intron 2 of 2)	intron (NM_001004308, intron 2 of 2)	223154	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.010204	0.436290	74(TGTACAGTCAGTGCTG,+,0.00),558(AAGCACAATTTGTTCA,-,0.00),559(AGCACAATTTGTTCAG,+,0.00)
chunk0066_338_1	chr15	36806923	36807397	+	0	NA	intron (NR_027320, intron 2 of 3)	intron (NR_027320, intron 2 of 3)	11346	NR_027320	161635	Hs.659822	NR_027320		CSNK1A1P1	CSNK1A1P	casein kinase 1 alpha 1 pseudogene 1	pseudo	0.004219	0.412632	
chunk0015_447_1	chr1	191983639	191983848	+	0	NA	Intergenic	L1MA4A|LINE|L1	-174719	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.014354	0.495238	
chunk0060_134_1	chr14	44701472	44701807	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-194343	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.008955	0.467262	
chunk0092_360_1	chr19	35629661	35629903	+	0	NA	intron (NM_024321, intron 2 of 9)	intron (NM_024321, intron 2 of 9)	704	NM_024321	79171	Hs.5086	NM_024321	ENSG00000126254	RBM42	-	RNA binding motif protein 42	protein-coding	0.016529	0.444444	200(TAGAACATGTTGTCCA,-,0.00),201(AGAACATGTTGTCCAG,+,0.00)
chunk0030_195_1	chr10	114337219	114337617	+	0	NA	intron (NM_001001936, intron 2 of 18)	intron (NM_001001936, intron 2 of 18)	67360	NM_001287824	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.012563	0.511278	
chunk0149_162_1	chr5	20421187	20421650	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	154455	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.008639	0.372845	
chunk0119_60_1	chr22	40958190	40958925	+	0	NA	intron (NM_014248, intron 2 of 4)	intron (NM_014248, intron 2 of 4)	7210	NM_014248	9978	Hs.474949	NM_014248	ENSG00000100387	RBX1	BA554C12.1|RNF75|ROC1	ring-box 1	protein-coding	0.005442	0.381793	
chunk0131_153_1	chr3	146123211	146123879	+	0	NA	intron (NM_000935, intron 2 of 18)	intron (NM_000935, intron 2 of 18)	37950	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.001497	0.303438	
chunk0099_3_1	chr2	82652052	82652668	+	0	NA	Intergenic	(AG)n|Simple_repeat|Simple_repeat	-204443	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.000000	0.333874	
chunk0194_294_1	chr8	87867312	87867616	+	0	NA	Intergenic	Intergenic	6604	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.009868	0.468852	148(TGGAACACAGTGTTTT,-,0.00),149(GGAACACAGTGTTTTT,+,0.00)
chunk0121_100_1	chr3	16995224	16995548	+	0	NA	intron (NM_015184, intron 1 of 5)	intron (NM_015184, intron 1 of 5)	62190	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.009259	0.446154	
chunk0204_78_1	chr9	94002761	94003238	+	0	NA	Intergenic	L1ME2|LINE|L1	-27795	NM_177995	138639	Hs.437943	NM_152422	ENSG00000158079	PTPDC1	PTP9Q22	protein tyrosine phosphatase domain containing 1	protein-coding	0.000000	0.376569	
chunk0027_83_1	chr10	73553300	73553989	+	0	NA	intron (NM_152586, intron 2 of 21)	intron (NM_152586, intron 2 of 21)	22031	NM_152586	159195	Hs.657355	NM_152586	ENSG00000166348	USP54	C10orf29|bA137L10.3|bA137L10.4	ubiquitin specific peptidase 54	protein-coding	0.002903	0.434783	268(AAGAACATTTAGTTCA,-,0.00),269(AGAACATTTAGTTCAG,+,0.00)
chunk0154_95_1	chr5	78090368	78090666	+	0	NA	intron (NM_003664, intron 21 of 26)	intron (NM_003664, intron 21 of 26)	132270	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.006711	0.387960	
chunk0112_285_1	chr20	43731483	43731729	+	0	NA	Intergenic	Intergenic	-4604	NM_001008901	149699	Hs.447626	NM_176791	ENSG00000124196	GTSF1L	C20orf65|FAM112A|dJ1028D15.4	gametocyte specific factor 1 like	protein-coding	0.012195	0.510121	
chunk0203_422_1	chr9	91030016	91030409	+	0	NA	Intergenic	LTR82B|LTR|ERVL	44920	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.015267	0.446701	
chunk0181_73_1	chr7	80277921	80278665	+	0	NA	Intergenic	Intergenic	96146	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.005376	0.351678	
chunk0081_266_1	chr17	43541001	43541476	+	0	NA	intron (NM_001079675, intron 4 of 12)	intron (NM_001079675, intron 4 of 12)	4699	NM_001986	2118	Hs.434059	NM_001986	ENSG00000175832	ETV4	E1A-F|E1AF|PEA3|PEAS3	ETS variant 4	protein-coding	0.014737	0.539916	
chunk0178_387_1	chr7	40286578	40286980	+	0	NA	intron (NM_024728, intron 8 of 14)	intron (NM_024728, intron 8 of 14)	151803	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.004975	0.411911	
chunk0098_373_1	chr2	78568139	78568758	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-277717	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.008078	0.411290	
chunk0015_22_1	chr1	184350769	184351553	+	0	NA	Intergenic	Intergenic	-35855	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.005102	0.364331	
chunk0059_172_1	chr14	32469280	32469648	+	0	NA	intron (NM_004274, intron 2 of 13)	intron (NM_004274, intron 2 of 13)	140191	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.002717	0.300813	
chunk0062_56_1	chr14	67440293	67440750	+	0	NA	Intergenic	AluSz6|SINE|Alu	1409	NR_049879	100847064		NR_049879	ENSG00000265993	MIR5694	-	microRNA 5694	ncRNA	0.021882	0.504367	
chunk0086_441_1	chr18	29085220	29085419	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-907873	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.000000	0.460000	90(GAGAACACAGTGTTCC,-,0.00),91(AGAACACAGTGTTCCT,+,0.00)
chunk0101_193_1	chr2	129731208	129731562	+	0	NA	Intergenic	Intergenic	-191792	NR_110285	101927924	Hs.570248	NR_110285	ENSG00000237574	LINC01856	-	long intergenic non-protein coding RNA 1856	ncRNA	0.014124	0.504225	
chunk0152_441_1	chr5	66203886	66204358	+	0	NA	Intergenic	Intergenic	59287	NM_139168	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.002119	0.467230	295(AAGAACAAACTGTCCA,-,0.00),296(AGAACAAACTGTCCAC,+,0.00)
chunk0072_420_1	chr15	100997504	100997781	+	0	NA	intron (NM_024652, intron 6 of 33)	L1ME4c|LINE|L1	78427	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.003610	0.392086	
chunk0112_123_1	chr20	38479178	38479522	+	0	NA	intron (NM_020336, intron 1 of 29)	L2c|LINE|L2	6544	NM_001282917	57148	Hs.598850	NM_020336	ENSG00000170471	RALGAPB	KIAA1219|RalGAPbeta	Ral GTPase activating protein non-catalytic beta subunit	protein-coding	0.002907	0.327536	
chunk0210_182_1	chrX	79484690	79485146	+	0	NA	Intergenic	L1P2|LINE|L1	-117366	NM_004867	9452	Hs.17109	NM_004867	ENSG00000078596	ITM2A	BRICD2A|E25A	integral membrane protein 2A	protein-coding	0.002193	0.367615	
chunk0162_408_1	chr5	179843854	179844198	+	0	NA	intron (NM_001017987, intron 2 of 4)	intron (NM_001017987, intron 2 of 4)	14814	NM_001017987	51149	Hs.741169	NM_016175	ENSG00000161010	MRNIP	C5orf45	MRN complex interacting protein	protein-coding	0.002907	0.484058	
chunk0046_108_1	chr12	57235276	57235572	+	0	NA	TTS (NM_005412)	TTS (NM_005412)	5058	NR_048562	6472	Hs.741179	NM_005412	ENSG00000182199	SHMT2	GLYA|HEL-S-51e|SHMT	serine hydroxymethyltransferase 2	protein-coding	0.027027	0.666667	
chunk0107_81_1	chr2	212901872	212902144	+	0	NA	Intergenic	Intergenic	-24249	NR_039935	100616267		NR_039935	ENSG00000266354	MIR4776-1	mir-4776-1	microRNA 4776-1	ncRNA	0.000000	0.369963	
chunk0040_304_1	chr11	117230575	117231205	+	0	NA	intron (NM_004716, intron 1 of 16)	intron (NM_004716, intron 1 of 16)	1635	NM_004716	9159	Hs.648612	NM_004716	ENSG00000160613	PCSK7	LPC|PC7|PC8|SPC7	proprotein convertase subtilisin/kexin type 7	protein-coding	0.015873	0.494453	
chunk0143_342_1	chr4	121598734	121599464	+	0	NA	Intergenic	MIR3|SINE|MIR	97893	NM_001154	308	Hs.480653	NM_001154	ENSG00000164111	ANXA5	ANX5|ENX2|HEL-S-7|PP4|RPRGL3	annexin A5	protein-coding	0.004110	0.348837	
chunk0170_56_1	chr6	109499961	109500509	+	0	NA	intron (NM_001145128, intron 35 of 40)	MamGypLTR2c|LTR|Gypsy	-16998	NM_001164313	9841	Hs.409876	NM_014797	ENSG00000112365	ZBTB24	BIF1|ICF2|PATZ2|ZNF450	zinc finger and BTB domain containing 24	protein-coding	0.007299	0.331512	
chunk0205_114_1	chr9	107698639	107699275	+	0	NA	Intergenic	Intergenic	-209237	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.011006	0.411303	
chunk0142_161_1	chr4	95118668	95119227	+	0	NA	intron (NM_001256792, intron 4 of 10)	intron (NM_001256792, intron 4 of 10)	27456	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.007156	0.371429	329(TAATACACAGTGTTCT,-,0.00),330(AATACACAGTGTTCTT,+,0.00)
chunk0054_70_1	chr13	42110578	42111076	+	0	NA	intron (NM_152910, intron 1 of 28)	intron (NM_152910, intron 1 of 28)	-27215	NM_001297429	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.014056	0.370741	246(ATGTACATTTTGTACC,-,0.00),247(TGTACATTTTGTACCT,+,0.00)
chunk0074_115_1	chr16	22385987	22386186	+	0	NA	Intergenic	Intergenic	-11469	NM_001802	1039	Hs.513430	NM_001802	ENSG00000140743	CDR2	CDR62|Yo	cerebellar degeneration related protein 2	protein-coding	0.005025	0.310000	
chunk0139_154_1	chr4	53676215	53676726	+	0	NA	Intergenic	Intergenic	-19431	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.005871	0.410156	246(CAGAACAACATGTTCC,-,0.00),247(AGAACAACATGTTCCC,+,0.00)
chunk0084_165_1	chr17	77286599	77287054	+	0	NA	intron (NM_001293695, intron 1 of 10)	intron (NM_001293695, intron 1 of 10)	-1065	NM_001113492	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.021978	0.603070	
chunk0061_246_1	chr14	61042132	61042608	+	0	NA	intron (NR_033344, intron 8 of 16)	MER131|DNA?|DNA?	61123	NR_033344	145389	Hs.200738	NM_153811	ENSG00000139974	SLC38A6	NAT-1|SNAT6	solute carrier family 38 member 6	protein-coding	0.000000	0.322851	
chunk0045_397_1	chr12	52682747	52683509	+	0	NA	Intergenic	Intergenic	-2721	NM_006121	3848	Hs.80828	NM_006121	ENSG00000167768	KRT1	CK1|EHK|EHK1|EPPK|K1|KRT1A|NEPPK	keratin 1	protein-coding	0.005249	0.453473	392(ATTACAGAATGTTCTC,+,0.00)
chunk0005_236_1	chr1	59463892	59464256	+	0	NA	intron (NM_001244714, intron 4 of 13)	L1PA6|LINE|L1	-51555	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.005495	0.405479	
chunk0166_150_1	chr6	45114179	45114378	+	0	NA	intron (NM_001261823, intron 2 of 9)	L2a|LINE|L2	83492	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.005025	0.315000	
chunk0042_450_1	chr12	12432188	12432802	+	0	NA	intron (NM_058169, intron 2 of 3)	L1MD2|LINE|L1	75416	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.004886	0.364228	
chunk0180_51_1	chr7	54713279	54714282	+	0	NA	Intergenic	AluSp|SINE|Alu	45466	NM_001012456	23480	Hs.488282	NM_014302	ENSG00000132432	SEC61G	SSS1	SEC61 translocon gamma subunit	protein-coding	0.013958	0.446215	789(CTGAACATTCAGTCCC,-,0.00),790(TGAACATTCAGTCCCG,+,0.00)
chunk0165_128_1	chr6	33159059	33159267	+	0	NA	Intergenic	Intergenic	33305	NM_001163771	1302	Hs.390171	NM_080679	ENSG00000204248	COL11A2	DFNA13|DFNB53|FBCG2|HKE5|OSMEDA|OSMEDB|PARP|STL3	collagen type XI alpha 2 chain	protein-coding	0.004808	0.444976	
chunk0070_408_1	chr15	77446862	77447350	+	0	NA	intron (NM_001304504, intron 1 of 9)	intron (NM_001304504, intron 1 of 9)	26455	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.006148	0.400818	
chunk0157_182_1	chr5	118648364	118648563	+	0	NA	Intergenic	Intergenic	52275	NR_104998	102467225	Hs.582523	NR_104998	ENSG00000249128	LINC02215	-	long intergenic non-protein coding RNA 2215	ncRNA	0.005025	0.370000	
chunk0177_439_1	chr7	27999401	28000083	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-180715	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.005865	0.440703	
chunk0009_21_1	chr1	100109437	100109720	+	0	NA	intron (NM_001304829, intron 7 of 15)	L1PA10|LINE|L1	23517	NM_194292	163786	Hs.591447	NM_194292	ENSG00000156876	SASS6	MCPH14|SAS-6|SAS6	SAS-6 centriolar assembly protein	protein-coding	0.000000	0.348592	123(CTGCACATTCTGTACA,-,0.00),124(TGCACATTCTGTACAT,+,0.00)
chunk0115_177_1	chr21	25736804	25737218	+	0	NA	intron (NM_002040, intron 1 of 9)	intron (NM_002040, intron 1 of 9)	-1357	NM_001685	522	Hs.246310	NM_001685	ENSG00000154723	ATP5PF	ATP5|ATP5A|ATP5J|ATPM|CF6|F6	ATP synthase peripheral stalk subunit F6	protein-coding	0.009662	0.334940	168(GGGAACAAAATGTTCT,-,0.00),169(GGAACAAAATGTTCTA,+,0.00)
chunk0196_384_1	chr8	115658478	115658867	+	0	NA	intron (NM_001282903, intron 1 of 6)	intron (NM_001282903, intron 1 of 6)	9340	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.002571	0.315385	233(AAGTACATGATGTACA,-,0.00),234(AGTACATGATGTACAT,+,0.00)
chunk0190_188_1	chr8	33455636	33456341	+	0	NA	intron (NM_032664, intron 2 of 4)	intron (NM_032664, intron 2 of 4)	17158	NM_032664	84750	Hs.458713	NM_032664	ENSG00000172728	FUT10	FUCTX	fucosyltransferase 10	protein-coding	0.011348	0.417847	
chunk0075_100_1	chr16	48470185	48470786	+	0	NA	Intergenic	Intergenic	-85167	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.008319	0.317276	
chunk0191_425_1	chr8	57808636	57809049	+	0	NA	Intergenic	Intergenic	-169516	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.004843	0.490338	
chunk0082_120_1	chr17	55138089	55138416	+	0	NA	intron (NM_178509, intron 16 of 17)	L2a|LINE|L2	-126708	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.006116	0.295732	
chunk0006_97_1	chr1	65157119	65157567	+	0	NA	intron (NM_001005353, intron 2 of 5)	L1ME4b|LINE|L1	9176	NM_013410	205	Hs.10862	NM_013410	ENSG00000162433	AK4	AK 4|AK3|AK3L1|AK3L2	adenylate kinase 4	protein-coding	0.002232	0.436526	210(CTGCACTGAATGTCCT,-,0.00),211(TGCACTGAATGTCCTG,+,0.00)
chunk0025_247_1	chr10	54562672	54563337	+	0	NA	intron (NM_001142769, intron 2 of 35)	intron (NM_001142769, intron 2 of 35)	44953	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.007519	0.330330	
chunk0137_420_1	chr4	28130006	28130382	+	0	NA	Intergenic	L1PB|LINE|L1	-689388	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.005319	0.334218	
chunk0141_45_1	chr4	77190443	77190703	+	0	NA	Intergenic	Intergenic	33369	NM_004354	901	Hs.740456	NM_004354	ENSG00000138764	CCNG2	-	cyclin G2	protein-coding	0.000000	0.444444	
chunk0156_120_1	chr5	105953606	105953846	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	854252	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.004167	0.331950	
chunk0146_51_1	chr4	155674596	155675048	+	0	NA	intron (NM_000856, intron 3 of 10)	Tigger3b|DNA|TcMar-Tigger	7159	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.013274	0.373068	
chunk0096_193_1	chr2	30124973	30125288	+	0	NA	Intergenic	L1MD1|LINE|L1	-21754	NM_001127400	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.000000	0.325949	
chunk0109_426_1	chr2	241297107	241297584	+	0	NA	intron (NM_005336, intron 1 of 27)	L1MC4|LINE|L1	-17842	NM_006155	4735	Hs.721234	NM_004404	ENSG00000168385	SEPTIN2	DIFF6|NEDD-5|NEDD5|Pnutl3|SEPT2|hNedd5	septin 2	protein-coding	0.012579	0.428870	
chunk0094_46_1	chr2	2573505	2574095	+	0	NA	Intergenic	Intergenic	-242487	NM_015025	23040	Hs.434418	NM_015025	ENSG00000186487	MYT1L	MRD39|NZF1|ZC2H2C2|ZC2HC4B|myT1-L	myelin transcription factor 1 like	protein-coding	0.015254	0.475465	
chunk0129_85_1	chr3	119018672	119019202	+	0	NA	intron (NM_152538, intron 3 of 8)	intron (NM_152538, intron 3 of 8)	15892	NM_001015887	152404	Hs.112873	NM_152538	ENSG00000144847	IGSF11	BT-IgSF|CT119|CXADRL1|Igsf13|VSIG3	immunoglobulin superfamily member 11	protein-coding	0.001887	0.401130	
chunk0187_139_1	chr7	149547122	149547550	+	0	NA	non-coding (NR_027789, exon 9 of 9)	non-coding (NR_027789, exon 9 of 9)	-49529	NM_152557	155061	Hs.24643	NM_152557	ENSG00000181220	ZNF746	PARIS	zinc finger protein 746	protein-coding	0.011682	0.519814	253(CAGGACATCCTGTTCT,-,0.00),254(AGGACATCCTGTTCTA,+,0.00)
chunk0068_20_1	chr15	50793965	50794398	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-28468	NM_032802	84888	Hs.401537	NM_032802	ENSG00000138600	SPPL2A	IMP3|PSL2	signal peptide peptidase like 2A	protein-coding	0.004619	0.373272	129(GAGGACTGACTGTACT,-,0.00),130(AGGACTGACTGTACTG,+,0.00)
chunk0085_400_1	chr18	10169101	10169696	+	0	NA	Intergenic	Intergenic	244972	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.011765	0.479866	
chunk0090_370_1	chr18	77127819	77128568	+	0	NA	intron (NM_001025101, intron 1 of 8)	L1MD2|LINE|L1	4625	NM_001025101	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.014686	0.426667	
chunk0053_329_1	chr13	34335350	34336104	+	0	NA	Intergenic	Intergenic	304958	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.022546	0.422517	404(TGGAACAGACAGTTCC,-,0.00),405(GGAACAGACAGTTCCA,+,0.00)
chunk0115_416_1	chr21	31267553	31268189	+	0	NA	intron (NM_003253, intron 4 of 28)	intron (NM_003253, intron 4 of 28)	-229395	NM_001099219	728299	Hs.580875	NM_001099219	ENSG00000206102	KRTAP19-8	-	keratin associated protein 19-8	protein-coding	0.009434	0.401884	275(GGTACAGCATGCCCTG,+,0.00)
chunk0001_384_1	chr1	10516047	10516771	+	0	NA	intron (NM_004565, intron 2 of 8)	intron (NM_004565, intron 2 of 8)	41463	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.008287	0.437241	575(AAGGACAGTCTGGTCT,-,0.00),576(AGGACAGTCTGGTCTC,+,0.00)
chunk0086_304_1	chr18	23992164	23992804	+	0	NA	promoter-TSS (NM_153211)	promoter-TSS (NM_153211)	-289	NM_153211	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.010937	0.435257	
chunk0080_108_1	chr17	26962053	26962591	+	0	NA	Intergenic	Intergenic	331674	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.033457	0.452690	
chunk0152_304_1	chr5	61734038	61734463	+	0	NA	intron (NR_105000, intron 2 of 2)	intron (NR_105000, intron 2 of 2)	1448	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.009412	0.483568	182(TAGGACAGGCTGTTCT,-,0.00),183(AGGACAGGCTGTTCTT,+,0.00)
chunk0066_111_1	chr15	29930031	29930414	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1MEg|LINE|L1	38577	NM_001301025	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.000000	0.296875	
chunk0032_439_1	chr10	132837318	132837607	+	0	NA	intron (NM_001200049, intron 44 of 57)	CpG	-51429	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.069204	0.565517	
chunk0153_312_1	chr5	73631510	73631864	+	0	NA	intron (NM_001080479, intron 1 of 36)	intron (NM_001080479, intron 1 of 36)	5529	NM_001177693	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.000000	0.453521	
chunk0063_241_1	chr14	82328097	82328395	+	0	NA	Intergenic	Intergenic	-705185	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.000000	0.314381	
chunk0025_365_1	chr10	58621727	58622186	+	0	NA	intron (NM_001080512, intron 2 of 20)	(TAGAA)n|Simple_repeat|Simple_repeat	-93059	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.010893	0.456522	
chunk0197_244_1	chr8	123289658	123290027	+	0	NA	Intergenic	Intergenic	-14301	NR_037873	11244	Hs.521800	NM_007222	ENSG00000165156	ZHX1	-	zinc fingers and homeoboxes 1	protein-coding	0.002710	0.386486	
chunk0084_415_1	chr17	82331707	82331906	+	0	NA	intron (NM_003004, intron 1 of 4)	intron (NM_003004, intron 1 of 4)	2239	NM_003004	6398	Hs.558009	NM_003004	ENSG00000141574	SECTM1	K12|SECTM	secreted and transmembrane 1	protein-coding	0.065327	0.690000	
chunk0003_327_1	chr1	38571582	38571993	+	0	NA	Intergenic	Intergenic	288036	NM_001271851	64121	Hs.532461	NM_022157	ENSG00000116954	RRAGC	GTR2|RAGC|TIB929	Ras related GTP binding C	protein-coding	0.002433	0.470874	
chunk0119_43_1	chr22	40632928	40633536	+	0	NA	intron (NM_001282661, intron 1 of 13)	intron (NM_001282661, intron 1 of 13)	3487	NM_001282662	57591	Hs.654688	NM_020831	ENSG00000196588	MRTFA	BSAC|MAL|MKL|MKL1|MRTF-A	myocardin related transcription factor A	protein-coding	0.008224	0.334975	
chunk0123_292_1	chr3	46574319	46575092	+	0	NA	intron (NM_001174136, intron 1 of 5)	LTR90B|LTR|LTR	150	NM_001174136	6997	Hs.385870	NM_003212	ENSG00000241186	TDGF1	CR|CR-1|CRGF|CRIPTO	teratocarcinoma-derived growth factor 1	protein-coding	0.006468	0.423773	
chunk0164_92_1	chr6	20218060	20218991	+	0	NA	Intergenic	L2a|LINE|L2	-6061	NR_073465	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.003222	0.386266	
chunk0171_247_1	chr6	127140880	127141258	+	0	NA	intron (NM_032784, intron 1 of 4)	L2b|LINE|L2	22166	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.002646	0.377309	214(AGGAACTGGATGTCTT,-,0.00)
chunk0055_330_1	chr13	68989799	68990212	+	0	NA	Intergenic	Intergenic	-104680	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.004843	0.289855	
chunk0209_210_1	chrX	44570610	44571460	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-28060	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.005882	0.339600	50(CAGAACAAGCTGTCAT,-,0.00)
chunk0060_57_1	chr14	41552845	41553399	+	0	NA	Intergenic	L1PA15|LINE|L1	-54439	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.007220	0.356757	
chunk0067_195_1	chr15	44849853	44850424	+	0	NA	Intergenic	Intergenic	-106564	NM_152448	145645	Hs.567701	NM_152448	ENSG00000167014	TERB2	C15orf43	telomere repeat binding bouquet formation protein 2	protein-coding	0.008757	0.417832	343(CAGTACACACTGTTCT,-,0.00),344(AGTACACACTGTTCTC,+,0.00)
chunk0056_434_1	chr13	95060159	95060531	+	0	NA	intron (NM_005845, intron 26 of 30)	intron (NM_005845, intron 26 of 30)	100304	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.002688	0.372654	
chunk0022_10_1	chr10	7233370	7233943	+	0	NA	intron (NM_001018039, intron 9 of 20)	intron (NM_001018039, intron 9 of 20)	-46872	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.001745	0.451220	
chunk0135_250_1	chr3	188889322	188889613	+	0	NA	3' UTR (NM_005578, exon 11 of 11)	3' UTR (NM_005578, exon 11 of 11)	58172	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.013746	0.448630	
chunk0037_134_1	chr11	73072798	73073253	+	0	NA	intron (NM_014824, intron 3 of 19)	intron (NM_014824, intron 3 of 19)	69073	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.002198	0.377193	
chunk0044_35_1	chr12	27424187	27424991	+	0	NA	3' UTR (NM_020183, exon 17 of 17)	3' UTR (NM_020183, exon 17 of 17)	22045	NR_109975	101928646	Hs.434269	NR_109975	ENSG00000245311	ARNTL2-AS1	-	ARNTL2 antisense RNA 1	ncRNA	0.004975	0.363975	
chunk0125_203_1	chr3	67201922	67202530	+	0	NA	Intergenic	Intergenic	-23238	NR_036234	100422941		NR_036234	ENSG00000283298	MIR4272	-	microRNA 4272	ncRNA	0.004934	0.338259	
chunk0191_36_1	chr8	43067072	43067759	+	0	NA	intron (NR_033698, intron 2 of 7)	HAL1|LINE|L1	11116	NR_033698	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.008734	0.373547	
chunk0203_288_1	chr9	88936174	88936556	+	0	NA	Intergenic	L1MD3|LINE|L1	-54498	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.005236	0.328982	
chunk0025_42_1	chr10	49207168	49207878	+	0	NA	Intergenic	Intergenic	-19123	NM_001010863	170371	Hs.385493	NM_001010863	ENSG00000204161	TMEM273	C10orf128	transmembrane protein 273	protein-coding	0.014085	0.426160	
chunk0161_217_1	chr5	170878032	170878438	+	0	NA	exon (NM_022897, exon 2 of 28)	exon (NM_022897, exon 2 of 28)	16353	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.002463	0.334152	
chunk0009_383_1	chr1	109991200	109991761	+	0	NA	intron (NM_001242673, intron 1 of 16)	intron (NM_001242673, intron 1 of 16)	6715	NM_006621	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.010695	0.446619	260(GTGGACAGCCTGTACT,-,0.00),261(TGGACAGCCTGTACTC,+,0.00)
chunk0140_171_1	chr4	69726310	69726915	+	0	NA	TTS (NM_014465)	TTS (NM_014465)	34100	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.009917	0.407591	329(TGGAACACAGTGTCCT,-,0.00),330(GGAACACAGTGTCCTG,+,0.00)
chunk0028_362_1	chr10	92692920	92693291	+	0	NA	intron (NM_002729, intron 3 of 3)	intron (NM_002729, intron 3 of 3)	3181	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.002695	0.309140	
chunk0023_153_1	chr10	24251675	24252032	+	0	NA	intron (NM_019590, intron 2 of 20)	MIRb|SINE|MIR	-23832	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.005602	0.427374	
chunk0049_429_1	chr12	97922478	97922927	+	0	NA	Intergenic	Intergenic	16419	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.004454	0.420000	
chunk0074_32_1	chr16	20596779	20597193	+	0	NA	Intergenic	L1MB3|LINE|L1	-20613	NM_001105069	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.007246	0.373494	
chunk0033_100_1	chr11	14273630	14274348	+	0	NA	Intergenic	Intergenic	84496	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.005571	0.369958	
chunk0055_61_1	chr13	52669118	52669446	+	0	NA	intron (NM_006704, intron 10 of 12)	MER53|DNA|hAT	16586	NM_006704	10910	Hs.281902	NM_006704	ENSG00000165416	SUGT1	SGT1	SGT1 homolog, MIS12 kinetochore complex assembly cochaperone	protein-coding	0.006098	0.328267	
chunk0010_119_1	chr1	114462788	114463534	+	0	NA	exon (NM_015906, exon 4 of 20)	exon (NM_015906, exon 4 of 20)	47999	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.002681	0.306560	
chunk0112_149_1	chr20	38870723	38871318	+	0	NA	intron (NM_015568, intron 2 of 10)	intron (NM_015568, intron 2 of 10)	-55292	NM_030919	81610	Hs.726442	NM_030919	ENSG00000101447	FAM83D	C20orf129|CHICA|dJ616B8.3	family with sequence similarity 83 member D	protein-coding	0.021849	0.552013	457(GAGAACAAGGTGTCCT,-,0.00),458(AGAACAAGGTGTCCTG,+,0.00),471(CTGTACACAGAGTCCT,-,0.00),472(TGTACACAGAGTCCTG,+,0.00)
chunk0064_289_1	chr14	95291860	95292233	+	0	NA	intron (NM_024734, intron 1 of 12)	MIR|SINE|MIR	27862	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.016086	0.435829	122(GAGAACTGACTGTGTT,-,0.00),123(AGAACTGACTGTGTTC,+,0.00)
chunk0174_380_1	chr6	164973584	164974094	+	0	NA	Intergenic	Intergenic	-151776	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.001961	0.301370	
chunk0201_295_1	chr9	41121652	41121888	+	0	NA	Intergenic	L1MC5|LINE|L1	7205	NM_001085476	653404	Hs.652377	NM_001085476	ENSG00000273514	FOXD4L6	-	forkhead box D4 like 6	protein-coding	0.008475	0.345992	122(CAGAACAAACAGTTCA,-,0.00),123(AGAACAAACAGTTCAG,+,0.00)
chunk0144_8_1	chr4	124564096	124564734	+	0	NA	Intergenic	Intergenic	-5981	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.004702	0.303599	
chunk0110_122_1	chr20	12946660	12947290	+	0	NA	intron (NR_109868, intron 2 of 11)	intron (NR_109868, intron 2 of 11)	-3365	NR_109870	100505515	Hs.407172	NR_109870	ENSG00000234265	LINC01723	-	long intergenic non-protein coding RNA 1723	ncRNA	0.001587	0.334390	
chunk0212_183_1	chrX	133297100	133297519	+	0	NA	Intergenic	Intergenic	-78961	NM_016521	51270		NM_016521	ENSG00000183434	TFDP3	CT30|DP4|HCA661	transcription factor Dp family member 3	protein-coding	0.007160	0.388095	190(GAGGACAGAGAGATCC,-,0.00),191(AGGACAGAGAGATCCT,+,0.00)
chunk0051_414_1	chr12	122291443	122291843	+	0	NA	intron (NM_001247997, intron 20 of 25)	L1MC4|LINE|L1	-25122	NM_022916	65082	Hs.487883	NM_022916	ENSG00000139719	VPS33A	MPSPS	VPS33A core subunit of CORVET and HOPS complexes	protein-coding	0.017500	0.389027	
chunk0041_301_1	chr11	129779518	129779790	+	0	NA	Intergenic	MER61F|LTR|ERV1	-36192	NM_138788	120224	Hs.504301	NM_138788	ENSG00000151715	TMEM45B	-	transmembrane protein 45B	protein-coding	0.007353	0.472527	
chunk0043_313_1	chr12	22250937	22251641	+	0	NA	intron (NM_001304450, intron 2 of 3)	intron (NM_001304450, intron 2 of 3)	83425	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.002841	0.358865	
chunk0119_184_1	chr22	44028301	44028734	+	0	NA	intron (NM_001243386, intron 1 of 11)	L1MC1|LINE|L1	2213	NM_001243386	29780	Hs.475074	NM_013327	ENSG00000188677	PARVB	CGI-56	parvin beta	protein-coding	0.011547	0.380184	
chunk0028_373_1	chr10	92825335	92825947	+	0	NA	Intergenic	L2a|LINE|L2	-9072	NM_001013848	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.003268	0.383361	
chunk0024_11_1	chr10	32862480	32862925	+	0	NA	intron (NM_024688, intron 21 of 22)	L1M2a|LINE|L1	38770	NR_132768	106633814		NR_132768		SNORA86	-	small nucleolar RNA, H/ACA box 86	snoRNA	0.002247	0.329596	
chunk0138_29_1	chr4	31088823	31089410	+	0	NA	intron (NM_001173523, intron 2 of 2)	L3|LINE|CR1	-82028	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.001704	0.292517	330(AGGGACATTGTGTTAT,-,0.00),331(GGGACATTGTGTTATT,+,0.00)
chunk0189_390_1	chr8	27458981	27459598	+	0	NA	TTS (NM_001282455)	TTS (NM_001282455)	20007	NM_001282455	1135	Hs.57718	NM_000742	ENSG00000120903	CHRNA2	-	cholinergic receptor nicotinic alpha 2 subunit	protein-coding	0.009724	0.487055	
chunk0033_425_1	chr11	24949369	24949937	+	0	NA	intron (NM_001009909, intron 7 of 11)	intron (NM_001009909, intron 7 of 11)	452683	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.012324	0.328647	
chunk0186_335_1	chr7	143244191	143245532	+	0	NA	Intergenic	L1MB7|LINE|L1	-18568	NM_001143681	373156	Hs.390667	NM_015917	ENSG00000197448	GSTK1	GST|GST 13-13|GST13|GST13-13|GSTK1-1|hGSTK1	glutathione S-transferase kappa 1	protein-coding	0.006711	0.353949	318(AAGAACAGTTTGTCCA,-,0.00),319(AGAACAGTTTGTCCAT,+,0.00)
chunk0088_122_1	chr18	45745785	45746173	+	0	NA	intron (NM_001308278, intron 7 of 8)	intron (NM_001308278, intron 7 of 8)	19026	NM_001146037	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.005155	0.439589	
chunk0166_237_1	chr6	47146524	47146762	+	0	NA	Intergenic	Intergenic	-104280	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.000000	0.472803	
chunk0204_196_1	chr9	96609594	96609974	+	0	NA	intron (NM_003671, intron 1 of 12)	intron (NM_003671, intron 1 of 12)	10046	NM_003671	8555	Hs.40582	NM_003671	ENSG00000081377	CDC14B	CDC14B3|Cdc14B1|Cdc14B2|hCDC14B	cell division cycle 14B	protein-coding	0.002632	0.325459	193(AGGAACAAGATGTTTT,-,0.00),194(GGAACAAGATGTTTTT,+,0.00)
chunk0132_255_1	chr3	158860366	158860565	+	0	NA	Intergenic	Intergenic	58539	NR_110328	64747	Hs.58663	NM_022736	ENSG00000118855	MFSD1	SMAP4	major facilitator superfamily domain containing 1	protein-coding	0.000000	0.590000	
chunk0066_399_1	chr15	39231864	39232143	+	0	NA	Intergenic	Intergenic	-18666	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.000000	0.375000	
chunk0022_360_1	chr10	17230462	17230661	+	0	NA	promoter-TSS (NR_108061)	promoter-TSS (NR_108061)	-576	NR_108061	100507347	Hs.740502	NR_108060	ENSG00000229124	VIM-AS1	-	VIM antisense RNA 1	ncRNA	0.085427	0.635000	
chunk0200_192_1	chr9	19810322	19810621	+	0	NA	Intergenic	Intergenic	-23452	NM_001193288	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.010033	0.360000	
chunk0187_356_1	chr7	157200152	157200637	+	0	NA	intron (NM_014671, intron 10 of 22)	intron (NM_014671, intron 10 of 22)	61433	NM_014671	9690	Hs.118351	NM_014671	ENSG00000009335	UBE3C	HECTH2	ubiquitin protein ligase E3C	protein-coding	0.002062	0.306584	
chunk0184_148_1	chr7	116096486	116096935	+	0	NA	Intergenic	L1MDa|LINE|L1	-65897	NM_012252	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.015590	0.371111	
chunk0156_405_1	chr5	114119852	114120118	+	0	NA	Intergenic	Intergenic	-242334	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.007519	0.400749	
chunk0104_13_1	chr2	170455961	170456574	+	0	NA	intron (NR_045684, intron 23 of 34)	LTR48B|LTR|ERV1	-105324	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.003263	0.434853	
chunk0016_1_1	chr1	192666181	192666518	+	0	NA	Intergenic	L1PA6|LINE|L1	30211	NM_144766	6003	Hs.497220	NM_002927	ENSG00000127074	RGS13	-	regulator of G protein signaling 13	protein-coding	0.002967	0.390533	
chunk0165_37_1	chr6	29989248	29990022	+	0	NA	Intergenic	L1ME2|LINE|L1	14520	NR_028032	10255	Hs.656251	NM_005844	ENSG00000204625	HCG9	HCGIX|HCGIX4	HLA complex group 9	ncRNA	0.006460	0.367742	
chunk0111_183_1	chr20	25345615	25346523	+	0	NA	intron (NM_001042472, intron 1 of 12)	L1MC1|LINE|L1	44913	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.002203	0.364136	
chunk0139_47_1	chr4	48659990	48660549	+	0	NA	intron (NM_015030, intron 3 of 63)	L1MC3|LINE|L1	120030	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.000000	0.410714	
chunk0059_413_1	chr14	37894948	37895599	+	0	NA	Intergenic	Intergenic	300074	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.010753	0.398773	
chunk0181_378_1	chr7	89133902	89134356	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	-338412	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.004405	0.331868	306(AGGAACAGAATGTGTT,-,0.00),307(GGAACAGAATGTGTTT,+,0.00)
chunk0038_114_1	chr11	83855798	83856145	+	0	NA	intron (NM_001142699, intron 16 of 27)	L1PA13|LINE|L1	-173546	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.408046	
chunk0124_294_1	chr3	57757137	57757419	+	0	NA	promoter-TSS (NM_007159)	promoter-TSS (NM_007159)	22	NM_001304420	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.046099	0.558304	
chunk0144_401_1	chr4	140254556	140255082	+	0	NA	Intergenic	Intergenic	-2467	NM_032547	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.003802	0.396584	
chunk0097_83_1	chr2	45253268	45253604	+	0	NA	intron (NR_033831, intron 1 of 5)	L2b|LINE|L2	1505	NR_033831	400952	Hs.468368	NR_033831	ENSG00000205054	LINC01121	UNQ6975	long intergenic non-protein coding RNA 1121	ncRNA	0.008929	0.332344	
chunk0014_26_1	chr1	174584180	174584445	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	136238	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.000000	0.349624	
chunk0191_100_1	chr8	47960590	47961057	+	0	NA	promoter-TSS (NM_001081640)	promoter-TSS (NM_001081640)	620	NM_005914	4173	Hs.460184	NM_005914	ENSG00000104738	MCM4	CDC21|CDC54|IMD54|NKCD|NKGCD|P1-CDC21|hCdc21	minichromosome maintenance complex component 4	protein-coding	0.113490	0.655983	
chunk0164_168_1	chr6	21843345	21843756	+	0	NA	intron (NR_015410, intron 4 of 11)	intron (NR_015410, intron 4 of 11)	177106	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.002433	0.351942	
chunk0140_71_1	chr4	67465062	67465284	+	0	NA	Intergenic	L1PBa|LINE|L1	-43173	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.013514	0.533632	
chunk0119_55_1	chr22	40803233	40803547	+	0	NA	intron (NM_006358, intron 1 of 8)	L1MA6|LINE|L1	10568	NR_039923	100616283		NR_039923	ENSG00000266594	MIR4766	mir-4766	microRNA 4766	ncRNA	0.000000	0.380952	
chunk0085_283_1	chr18	7914549	7915930	+	0	NA	intron (NM_001105244, intron 4 of 32)	L4_C_Mam|LINE|RTE-X	347923	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.005793	0.335022	
chunk0195_216_1	chr8	97061963	97062180	+	0	NA	intron (NM_016134, intron 6 of 7)	intron (NM_016134, intron 6 of 7)	215877	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.000000	0.403670	
chunk0056_18_1	chr13	77167521	77168686	+	0	NA	intron (NM_015057, intron 40 of 82)	intron (NM_015057, intron 40 of 82)	92589	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.006867	0.327616	
chunk0114_126_1	chr21	9767570	9767803	+	0	NA	Intergenic	CpG	53375	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.068670	0.658120	
chunk0042_74_1	chr12	2160173	2160463	+	0	NA	intron (NM_001129846, intron 3 of 45)	L2b|LINE|L2	63163	NR_046578	100874234	Hs.372570	NR_046578	ENSG00000256025	CACNA1C-AS4	-	CACNA1C antisense RNA 4	ncRNA	0.013793	0.484536	
chunk0163_190_1	chr6	11635089	11635336	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	96985	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.016194	0.516129	
chunk0134_9_1	chr3	175389048	175389354	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	19661	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.006536	0.286645	
chunk0020_269_1	chr1	236342502	236342912	+	0	NA	Intergenic	Intergenic	-51673	NM_145861	128178	Hs.352224	NM_080738	ENSG00000186197	EDARADD	ECTD11A|ECTD11B|ED3|EDA3	EDAR associated death domain	protein-coding	0.002439	0.330900	
chunk0085_125_1	chr18	3045054	3045813	+	0	NA	Intergenic	Intergenic	-33486	NM_014646	9663	Hs.132342	NM_014646	ENSG00000101577	LPIN2	-	lipin 2	protein-coding	0.015810	0.471053	
chunk0199_23_1	chr9	591247	591756	+	0	NA	intron (NM_001256877, intron 2 of 12)	L2b|LINE|L2	86806	NM_001256877	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.011788	0.447059	261(TTGAACACTATGTTCC,-,0.00),262(TGAACACTATGTTCCA,+,0.00)
chunk0098_362_1	chr2	77832013	77832362	+	0	NA	intron (NR_110288, intron 3 of 3)	MER50-int|LTR|ERV1	-83747	NR_110286	101927926	Hs.149042	NR_110286	ENSG00000233605	LINC01851	-	long intergenic non-protein coding RNA 1851	ncRNA	0.002865	0.460000	
chunk0059_163_1	chr14	32313661	32314314	+	0	NA	Intergenic	Intergenic	-15286	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.006126	0.406728	
chunk0043_28_1	chr12	13127419	13127902	+	0	NA	Intergenic	Intergenic	-23964	NM_001080555	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.010352	0.421488	
chunk0060_48_1	chr14	41349738	41349937	+	0	NA	Intergenic	MER52A|LTR|ERV1	-257724	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.010050	0.525000	
chunk0095_42_1	chr2	13503223	13503772	+	0	NA	Intergenic	L1MEc|LINE|L1	-496484	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.005464	0.363636	
chunk0006_100_1	chr1	65254047	65254246	+	0	NA	Intergenic	Intergenic	-10548	NM_014787	9829	Hs.647643	NM_014787	ENSG00000116675	DNAJC6	DJC6|PARK19	DnaJ heat shock protein family (Hsp40) member C6	protein-coding	0.035176	0.440000	
chunk0081_180_1	chr17	41665781	41665998	+	0	NA	Intergenic	Intergenic	-22986	NM_005801	10209	Hs.150580	NM_005801	ENSG00000173812	EIF1	A121|EIF-1|EIF1A|ISO1|SUI1	eukaryotic translation initiation factor 1	protein-coding	0.041475	0.568807	
chunk0068_179_1	chr15	54386050	54386477	+	0	NA	intron (NM_001080534, intron 15 of 30)	intron (NM_001080534, intron 15 of 30)	373359	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.004684	0.362150	
chunk0135_137_1	chr3	187350584	187351232	+	0	NA	Intergenic	Intergenic	-17472	NM_022147	64108	Hs.43388	NM_022147	ENSG00000136514	RTP4	IFRG28|Z3CXXC4	receptor transporter protein 4	protein-coding	0.004630	0.412943	
chunk0176_76_1	chr7	11367097	11367581	+	0	NA	Intergenic	Intergenic	393467	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.008264	0.358763	
chunk0045_455_1	chr12	53699880	53700079	+	0	NA	Intergenic	Intergenic	-23251	NM_001002031	517	Hs.524464	NM_005176	ENSG00000135390	ATP5MC2	ATP5A|ATP5G2	ATP synthase membrane subunit c locus 2	protein-coding	0.010050	0.500000	
chunk0043_87_1	chr12	14688292	14688805	+	0	NA	intron (NM_004963, intron 1 of 26)	intron (NM_004963, intron 1 of 26)	8037	NM_004963	2984	Hs.524278	NM_004963	ENSG00000070019	GUCY2C	DIAR6|GC-C|GUC2C|MECIL|MUCIL|STAR	guanylate cyclase 2C	protein-coding	0.009747	0.414397	
chunk0153_307_1	chr5	73544490	73545065	+	0	NA	Intergenic	Intergenic	20909	NM_023039	57763	Hs.239154	NM_023039	ENSG00000164331	ANKRA2	ANKRA	ankyrin repeat family A member 2	protein-coding	0.012174	0.446181	
chunk0126_252_1	chr3	79405252	79405524	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-6339	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.003676	0.428571	
chunk0028_81_1	chr10	83820057	83820386	+	0	NA	Intergenic	Intergenic	-319208	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.006079	0.409091	
chunk0075_425_1	chr16	57532008	57532691	+	0	NA	intron (NM_033212, intron 1 of 8)	intron (NM_033212, intron 1 of 8)	4216	NM_033212	92922	Hs.644611	NM_033212	ENSG00000135736	CCDC102A	-	coiled-coil domain containing 102A	protein-coding	0.013177	0.519006	
chunk0160_105_1	chr5	150526630	150526997	+	0	NA	intron (NM_001543, intron 2 of 14)	intron (NM_001543, intron 2 of 14)	18701	NM_001543	3340	Hs.222055	NM_001543	ENSG00000070614	NDST1	HSST|MRT46|NST1	N-deacetylase and N-sulfotransferase 1	protein-coding	0.005450	0.540761	149(AAGGACAAATTGTACC,-,0.00),150(AGGACAAATTGTACCA,+,0.00)
chunk0049_443_1	chr12	98701090	98701718	+	0	NA	intron (NM_181868, intron 17 of 25)	L1MB4|LINE|L1	56104	NM_181861	317	Hs.552567	NM_001160	ENSG00000120868	APAF1	APAF-1|CED4	apoptotic peptidase activating factor 1	protein-coding	0.003185	0.343402	
chunk0207_146_1	chr9	129491015	129491302	+	0	NA	intron (NR_038955, intron 1 of 4)	intron (NR_038955, intron 1 of 4)	2498	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.013937	0.579861	170(TGGGACACTTAGTGCT,-,0.00),171(GGGACACTTAGTGCTG,+,0.00)
chunk0011_394_1	chr1	154006206	154006405	+	0	NA	intron (NM_207308, intron 35 of 39)	A-rich|Low_complexity|Low_complexity	15542	NM_001030	6232	Hs.546291	NM_001030	ENSG00000177954	RPS27	DBA17|MPS-1|MPS1|S27	ribosomal protein S27	protein-coding	0.000000	0.415000	
chunk0063_136_1	chr14	79438009	79438219	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	158775	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.019048	0.540284	
chunk0195_203_1	chr8	96872475	96873155	+	0	NA	intron (NM_016134, intron 3 of 7)	intron (NM_016134, intron 3 of 7)	227588	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.005882	0.306902	
chunk0036_327_1	chr11	66373107	66373765	+	0	NA	promoter-TSS (NM_001300869)	promoter-TSS (NM_001300869)	-960	NM_001300869	3177	Hs.569017	NM_001532	ENSG00000174669	SLC29A2	DER12|ENT2|HNP36	solute carrier family 29 member 2	protein-coding	0.009119	0.393020	297(GAGAACAGCCTGTCCC,-,0.00),298(AGAACAGCCTGTCCCA,+,0.00)
chunk0074_178_1	chr16	23768544	23768967	+	0	NA	Intergenic	L1ME4a|LINE|L1	14128	NM_022097	63928	Hs.178589	NM_022097	ENSG00000166869	CHP2	-	calcineurin like EF-hand protein 2	protein-coding	0.004728	0.438679	
chunk0017_53_1	chr1	205358921	205359329	+	0	NA	Intergenic	Intergenic	-2035	NM_001271863	55220	Hs.10414	NM_018203	ENSG00000162873	KLHDC8A	-	kelch domain containing 8A	protein-coding	0.009804	0.425428	
chunk0168_449_1	chr6	95882071	95882454	+	0	NA	Intergenic	Intergenic	-133707	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.002611	0.408854	
chunk0108_83_1	chr2	227655261	227655523	+	0	NA	Intergenic	MLT1C-int|LTR|ERVL-MaLR	-22072	NM_001162483	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.000000	0.384030	
chunk0020_370_1	chr1	239786428	239786920	+	0	NA	intron (NM_000740, intron 3 of 4)	intron (NM_000740, intron 3 of 4)	-67555	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.024390	0.511156	
chunk0048_452_1	chr12	88723240	88723512	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-142903	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.011029	0.362637	
chunk0051_164_1	chr12	115978858	115979057	+	0	NA	intron (NM_015335, intron 23 of 30)	L2a|LINE|L2	169697	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.005025	0.395000	
chunk0071_348_1	chr15	88467337	88467767	+	0	NA	promoter-TSS (NM_176805)	promoter-TSS (NM_176805)	99	NM_176805	64963	Hs.111286	NM_022839	ENSG00000181991	MRPS11	HCC-2|MRP-S11|S11mt	mitochondrial ribosomal protein S11	protein-coding	0.062791	0.554524	
chunk0165_96_1	chr6	32195758	32195982	+	0	NA	promoter-TSS (NM_022107).2	promoter-TSS (NM_022107).2	-347	NM_022107	63940	Hs.520046	NM_022107	ENSG00000213654	GPSM3	AGS4|C6orf9|G18|G18.1a|G18.1b|G18.2|NG1	G protein signaling modulator 3	protein-coding	0.111607	0.733333	
chunk0097_25_1	chr2	42327152	42327616	+	0	NA	intron (NM_019063, intron 21 of 22)	L1MB8|LINE|L1	33832	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.006466	0.378495	
chunk0095_365_1	chr2	23250501	23250779	+	0	NA	Intergenic	Intergenic	-134787	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.003597	0.505376	90(CGGGGCAGGCTGTTCT,-,0.00),91(GGGGCAGGCTGTTCTG,+,0.00),179(AAGGTCAATGTGTGCC,-,0.00)
chunk0140_335_1	chr4	73829496	73829934	+	0	NA	Intergenic	Intergenic	-6841	NM_002993	6372	Hs.164021	NM_002993	ENSG00000124875	CXCL6	CKA-3|GCP-2|GCP2|SCYB6	C-X-C motif chemokine ligand 6	protein-coding	0.006849	0.293850	
chunk0095_247_1	chr2	19264724	19265237	+	0	NA	Intergenic	Intergenic	-83449	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.011696	0.406615	
chunk0089_336_1	chr18	65575867	65576495	+	0	NA	Intergenic	Intergenic	-174071	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.001592	0.325914	
chunk0149_407_1	chr5	29162297	29162790	+	0	NA	non-coding (NR_130777, exon 5 of 9).2	non-coding (NR_130777, exon 5 of 9).2	19040	NR_130777	101929660	Hs.171348	NR_130777		LINC02109	-	long intergenic non-protein coding RNA 2109	ncRNA	0.002028	0.336032	
chunk0149_173_1	chr5	20709404	20709785	+	0	NA	Intergenic	Intergenic	-133721	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002625	0.264398	
chunk0078_422_1	chr16	89345454	89346063	+	0	NA	intron (NM_001256182, intron 3 of 13)	L1M5|LINE|L1	24625	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.013136	0.472131	316(AGGTACATGCTGTGCA,-,0.00),317(GGTACATGCTGTGCAC,+,0.00)
chunk0033_97_1	chr11	14190074	14190379	+	0	NA	intron (NM_006108, intron 6 of 15)	intron (NM_006108, intron 6 of 15)	168259	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.003279	0.431373	125(AAGAACAAGCTGTACA,-,0.00),126(AGAACAAGCTGTACAA,+,0.00)
chunk0199_85_1	chr9	2613615	2614040	+	0	NA	intron (NR_015375, intron 1 of 3)	intron (NR_015375, intron 1 of 3)	-7966	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.002353	0.474178	
chunk0085_31_1	chr18	491375	491892	+	0	NA	intron (NM_130386, intron 1 of 9)	intron (NM_130386, intron 1 of 9)	9096	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.005803	0.391892	
chunk0024_46_1	chr10	33666882	33667104	+	0	NA	Intergenic	Intergenic	105687	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.000000	0.430493	
chunk0185_94_1	chr7	125492947	125493483	+	0	NA	Intergenic	Intergenic	-228924	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.000000	0.290503	
chunk0053_343_1	chr13	34732591	34732995	+	0	NA	Intergenic	Intergenic	-92108	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.009901	0.395062	
chunk0077_255_1	chr16	80900463	80900826	+	0	NA	Intergenic	Intergenic	-8048	NR_131947	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.027548	0.535714	176(GAGAACAAAATGTTTT,-,0.00),177(AGAACAAAATGTTTTT,+,0.00)
chunk0019_393_1	chr1	230365644	230366092	+	0	NA	intron (NM_001258311, intron 1 of 6)	intron (NM_001258311, intron 1 of 6)	60060	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.013393	0.476615	
chunk0041_444_1	chr11	134703195	134703617	+	0	NA	Intergenic	MER34A|LTR|ERV1	266924	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.007109	0.451537	182(AGGAGCAGAGTGTGCT,-,0.00),183(GGAGCAGAGTGTGCTC,+,0.00),215(AAGGACACTGTGCTCA,-,0.00),216(AGGACACTGTGCTCAG,+,0.00)
chunk0022_279_1	chr10	15232049	15232720	+	0	NA	intron (NM_001010924, intron 5 of 7)	L2a|LINE|L2	-63674	NM_001308295	9397	Hs.60339	NM_004808	ENSG00000152465	NMT2	-	N-myristoyltransferase 2	protein-coding	0.014903	0.438988	
chunk0105_264_1	chr2	189380857	189381326	+	0	NA	Intergenic	L1M6|LINE|L1	-60342	NM_032168	84128	Hs.399984	NM_032168	ENSG00000115368	WDR75	NET16|UTP17	WD repeat domain 75	protein-coding	0.006397	0.297872	
chunk0121_123_1	chr3	17515457	17516097	+	0	NA	intron (NM_014744, intron 2 of 21)	intron (NM_014744, intron 2 of 21)	184243	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.006250	0.341654	
chunk0107_431_1	chr2	224835335	224835780	+	0	NA	intron (NM_014689, intron 25 of 55)	intron (NM_014689, intron 25 of 55)	111508	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.013483	0.367713	269(TAGAACTGAATGTTCC,-,0.00),270(AGAACTGAATGTTCCT,+,0.00)
chunk0181_372_1	chr7	88845897	88846330	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	-50396	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.004619	0.324885	
chunk0050_83_1	chr12	101711875	101712155	+	0	NA	intron (NM_020244, intron 1 of 8)	intron (NM_020244, intron 1 of 8)	14376	NM_020244	56994	Hs.293077	NM_020244	ENSG00000111666	CHPT1	CPT|CPT1	choline phosphotransferase 1	protein-coding	0.014286	0.434164	
chunk0004_457_1	chr1	53586373	53586650	+	0	NA	intron (NM_147193, intron 3 of 9)	intron (NM_147193, intron 3 of 9)	127112	NM_033067	63948	Hs.131654	NM_033067	ENSG00000143006	DMRTB1	-	DMRT like family B with proline rich C-terminal 1	protein-coding	0.021661	0.460432	
chunk0206_394_1	chr9	127024873	127025227	+	0	NA	intron (NM_001190729, intron 4 of 17)	L1ME1|LINE|L1	62825	NM_001190728	9649	Hs.432842	NM_014636	ENSG00000136828	RALGPS1	RALGEF2|RALGPS1A	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.011299	0.394366	
chunk0121_285_1	chr3	23592841	23593622	+	0	NA	Intergenic	Intergenic	-212662	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.006402	0.346547	
chunk0200_198_1	chr9	20179378	20179607	+	0	NA	Intergenic	Intergenic	231746	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.013100	0.500000	
chunk0117_250_1	chr22	23339614	23340100	+	0	NA	Intergenic	MIRb|SINE|MIR	42269	NR_037839	649264	Hs.600549	NR_037839		CES5AP1	-	carboxylesterase 5A pseudogene 1	pseudo	0.008230	0.404517	
chunk0015_134_1	chr1	185627177	185627769	+	0	NA	intron (NR_110793, intron 1 of 3)	L1ME5|LINE|L1	1015	NR_110793	101929093	Hs.535227	NR_110793	ENSG00000228309	LINC01350	GS1-204I12.1	long intergenic non-protein coding RNA 1350	ncRNA	0.006757	0.408094	
chunk0029_430_1	chr10	110010449	110010911	+	0	NA	intron (NM_016824, intron 1 of 14)	MIR|SINE|MIR	-2299	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.004329	0.412527	
chunk0184_142_1	chr7	115724389	115724746	+	0	NA	Intergenic	L1ME3A|LINE|L1	243746	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.002801	0.324022	
chunk0093_64_1	chr19	40443348	40443547	+	0	NA	promoter-TSS (NM_013368)	promoter-TSS (NM_013368)	-849	NM_013368	29946	Hs.515412	NM_013368	ENSG00000167565	SERTAD3	RBT1	SERTA domain containing 3	protein-coding	0.070352	0.690000	
chunk0043_247_1	chr12	20364655	20364880	+	0	NA	Intergenic	L2a|LINE|L2	-4478	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.008889	0.393805	
chunk0147_10_1	chr4	170657608	170658262	+	0	NA	Intergenic	MER63C|DNA|hAT-Blackjack	-382667	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.003058	0.296183	
chunk0043_365_1	chr12	23525276	23525965	+	0	NA	Intergenic	Intergenic	58992	NM_178010	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.007257	0.324638	
chunk0145_292_1	chr4	149995871	149996298	+	0	NA	Intergenic	Charlie6|DNA|hAT-Charlie	-82190	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.004684	0.289720	
chunk0194_379_1	chr8	90620028	90620227	+	0	NA	Intergenic	L1M5|LINE|L1	-14064	NR_104062	101937451	Hs.583685	NR_104062	ENSG00000253799	LINC01030	-	long intergenic non-protein coding RNA 1030	ncRNA	0.000000	0.405000	
chunk0209_226_1	chrX	44954675	44955148	+	0	NA	intron (NR_111960, intron 2 of 27)	intron (NR_111960, intron 2 of 27)	81736	NM_001291421	7403	Hs.522616	NM_021140	ENSG00000147050	KDM6A	KABUK2|UTX|bA386N14.2	lysine demethylase 6A	protein-coding	0.006342	0.377637	
chunk0113_439_1	chr20	62433578	62433933	+	0	NA	Intergenic	Intergenic	-6182	NM_080833	140893	Hs.180374	NM_080833	ENSG00000130701	RBBP8NL	C20orf151	RBBP8 N-terminal like	protein-coding	0.042254	0.584270	
chunk0211_100_1	chrX	110840210	110840992	+	0	NA	Intergenic	Intergenic	-44543	NM_001143981	91851	Hs.496587	NM_145234	ENSG00000101938	CHRDL1	CHL|MGC1|MGCN|NRLN1|VOPT|dA141H5.1	chordin like 1	protein-coding	0.005115	0.353768	
chunk0191_149_1	chr8	48898999	48899327	+	0	NA	Intergenic	Intergenic	22277	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.015244	0.507599	
chunk0131_397_1	chr3	152812299	152812811	+	0	NA	Intergenic	Intergenic	-22138	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.001953	0.352827	
chunk0059_32_1	chr14	29895613	29895934	+	0	NA	intron (NM_002742, intron 1 of 17)	L2a|LINE|L2	31920	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.012461	0.487578	97(TTGCACTGACTGTTCT,-,0.00),98(TGCACTGACTGTTCTT,+,0.00)
chunk0070_417_1	chr15	77596756	77597019	+	0	NA	Intergenic	Intergenic	35640	NM_032808	84894	Hs.656765	NM_032808	ENSG00000169783	LINGO1	LERN1|LRRN6A|MRT64|UNQ201	leucine rich repeat and Ig domain containing 1	protein-coding	0.007605	0.511364	
chunk0095_306_1	chr2	20381547	20382072	+	0	NA	Intergenic	L1M4|LINE|L1	-30959	NM_015317	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.001905	0.450570	
chunk0164_162_1	chr6	21738487	21739277	+	0	NA	intron (NR_015410, intron 2 of 11)	intron (NR_015410, intron 2 of 11)	72438	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.006329	0.383059	
chunk0124_186_1	chr3	55491248	55491600	+	0	NA	Intergenic	Intergenic	-3782	NM_003392	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.017045	0.470255	
chunk0031_239_1	chr10	126759611	126760014	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-145597	NM_001290223	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.012407	0.398515	
chunk0110_128_1	chr20	13262000	13262225	+	0	NA	intron (NM_080826, intron 1 of 5)	intron (NM_080826, intron 1 of 5)	-22425	NR_040043	100505536	Hs.665253	NR_040043		ISM1-AS1	-	ISM1 antisense RNA 1	ncRNA	0.017778	0.446903	
chunk0115_420_1	chr21	31367211	31367579	+	0	NA	intron (NM_003253, intron 2 of 28)	intron (NM_003253, intron 2 of 28)	191582	NM_003253	7074	Hs.517228	NM_003253	ENSG00000156299	TIAM1	TIAM-1	T cell lymphoma invasion and metastasis 1	protein-coding	0.005435	0.414634	
chunk0129_124_1	chr3	119860445	119861055	+	0	NA	intron (NM_001146156, intron 9 of 10)	intron (NM_001146156, intron 9 of 10)	78040	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.001639	0.345336	
chunk0077_93_1	chr16	77625289	77625776	+	0	NA	Intergenic	Intergenic	-96960	NM_001243660	283927	Hs.282665	NM_001105663	ENSG00000140876	NUDT7	-	nudix hydrolase 7	protein-coding	0.008214	0.491803	
chunk0160_166_1	chr5	152393259	152393633	+	0	NA	intron (NM_020167, intron 3 of 3)	intron (NM_020167, intron 3 of 3)	11833	NM_020167	56923	Hs.731911	NM_020167	ENSG00000132911	NMUR2	FM-4|FM4|NMU-R2|NMU2R|TGR-1|TGR1	neuromedin U receptor 2	protein-coding	0.000000	0.352000	
chunk0160_177_1	chr5	153952641	153952899	+	0	NA	Intergenic	MIRb|SINE|MIR	86167	NM_018691	10827	Hs.166551	NM_018691	ENSG00000055147	FAM114A2	133K02|C5orf3	family with sequence similarity 114 member A2	protein-coding	0.011628	0.459459	
chunk0107_368_1	chr2	222795983	222797212	+	0	NA	Intergenic	Intergenic	-64417	NM_004457	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.006509	0.438211	976(GGGAGCTGACTGTTCC,-,0.00),977(GGAGCTGACTGTTCCC,+,0.00)
chunk0075_123_1	chr16	49843093	49843353	+	0	NA	intron (NM_001271620, intron 1 of 7)	L1ME3G|LINE|L1	14696	NM_001271620	23090	Hs.443715	NM_015069	ENSG00000102935	ZNF423	Ebfaz|JBTS19|NPHP14|OAZ|Roaz|ZFP423|Zfp104|hOAZ	zinc finger protein 423	protein-coding	0.007692	0.360153	
chunk0160_403_1	chr5	163562541	163563084	+	0	NA	Intergenic	Intergenic	57284	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.012891	0.441176	
chunk0151_359_1	chr5	54719678	54720341	+	0	NA	intron (NR_104658, intron 1 of 2)	MIR3|SINE|MIR	-16685	NR_104659	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.004525	0.466867	
chunk0116_458_1	chr21	43884006	43884238	+	0	NA	intron (NM_020132, intron 1 of 9)	intron (NM_020132, intron 1 of 9)	18887	NM_020132	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.021552	0.562232	
chunk0101_357_1	chr2	137942287	137942678	+	0	NA	Intergenic	Intergenic	-14550	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.007673	0.415816	
chunk0018_146_1	chr1	218671592	218672070	+	0	NA	intron (NR_031644, intron 3 of 6)	intron (NR_031644, intron 3 of 6)	229205	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.012552	0.432150	
chunk0075_285_1	chr16	53955104	53955355	+	0	NA	intron (NM_001080432, intron 8 of 8)	L2a|LINE|L2	-84164	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.000000	0.396825	
chunk0194_79_1	chr8	82755708	82756209	+	0	NA	Intergenic	Intergenic	-647800	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.011976	0.358566	
chunk0049_145_1	chr12	91902658	91902988	+	0	NA	Intergenic	Intergenic	238890	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.000000	0.389728	
chunk0204_284_1	chr9	98954382	98954656	+	0	NA	intron (NM_001855, intron 2 of 41)	L1ME4a|LINE|L1	10806	NM_001855	1306	Hs.409034	NM_001855	ENSG00000204291	COL15A1	-	collagen type XV alpha 1 chain	protein-coding	0.014599	0.327273	25(CAGAACATTCTGTACA,-,0.00),26(AGAACATTCTGTACAT,+,0.00)
chunk0189_233_1	chr8	24472983	24473437	+	0	NA	intron (NM_003817, intron 7 of 21)	L1MEd|LINE|L1	32214	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.004405	0.360440	
chunk0072_166_1	chr15	93152829	93153411	+	0	NA	Intergenic	Intergenic	-63906	NM_020211	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.013746	0.523156	275(AGGAACAGCCTGTCCT,-,0.00),276(GGAACAGCCTGTCCTC,+,0.00)
chunk0180_146_1	chr7	57404052	57404398	+	0	NA	promoter-TSS (NR_036102)	promoter-TSS (NR_036102)	-542	NR_120505	100653233	Hs.127379	NR_120505	ENSG00000260653	LOC100653233	-	uncharacterized LOC100653233	ncRNA	0.066474	0.593660	
chunk0167_33_1	chr6	53943405	53944010	+	0	NA	intron (NR_125842, intron 1 of 3)	LTR78|LTR|ERV1	13725	NR_125842	101927189	Hs.453592	NR_125842	ENSG00000236740	LOC101927189	-	uncharacterized LOC101927189	ncRNA	0.004959	0.452145	274(TTGTACATCCTGTGCC,-,0.00),275(TGTACATCCTGTGCCT,+,0.00)
chunk0072_177_1	chr15	93994710	93995282	+	0	NA	intron (NR_120320, intron 3 of 8)	intron (NR_120320, intron 3 of 8)	94295	NR_120323	101927129	Hs.652658	NR_120322	ENSG00000258785	LINC01580	-	long intergenic non-protein coding RNA 1580	ncRNA	0.006993	0.420593	
chunk0203_91_1	chr9	84061664	84062126	+	0	NA	Intergenic	Intergenic	-1548	NR_110995	101927575	Hs.459826	NR_110995	ENSG00000227463	LOC101927575	-	uncharacterized LOC101927575	ncRNA	0.008658	0.451404	
chunk0082_116_1	chr17	54979606	54980146	+	0	NA	intron (NM_178509, intron 1 of 17)	intron (NM_178509, intron 1 of 17)	11111	NM_178509	252983	Hs.35199	NM_178509	ENSG00000166263	STXBP4	Synip	syntaxin binding protein 4	protein-coding	0.001852	0.327172	
chunk0142_25_1	chr4	90549014	90549517	+	0	NA	intron (NM_001145065, intron 5 of 10)	intron (NM_001145065, intron 5 of 10)	314234	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.001988	0.345238	
chunk0137_416_1	chr4	28097148	28097865	+	0	NA	Intergenic	Intergenic	-722076	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.004184	0.314763	
chunk0045_153_1	chr12	46508889	46509364	+	0	NA	intron (NR_125380, intron 3 of 3)	intron (NR_125380, intron 3 of 3)	125019	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.008421	0.405462	283(AGGTACTATGTGTGCT,-,0.00),284(GGTACTATGTGTGCTC,+,0.00)
chunk0088_128_1	chr18	45782625	45783057	+	0	NA	Intergenic	Intergenic	-42739	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.002315	0.501155	
chunk0156_116_1	chr5	105898600	105899322	+	0	NA	Intergenic	Intergenic	799487	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.002770	0.406639	
chunk0109_410_1	chr2	240913786	240914203	+	0	NA	Intergenic	Intergenic	-17838	NM_001085437	79919	Hs.193745	NM_024861	ENSG00000172478	MAB21L4	C2orf54	mab-21 like 4	protein-coding	0.038369	0.655502	
chunk0119_296_1	chr22	46335415	46335636	+	0	NA	non-coding (NR_104241, exon 1 of 10)	non-coding (NR_104241, exon 1 of 10)	124	NM_001282782	55687	Hs.439524	NM_018006	ENSG00000100416	TRMU	LCAL3|MTO2|MTU1|TRMT|TRMT1	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	protein-coding	0.090498	0.671171	
chunk0192_225_1	chr8	65334888	65335150	+	0	NA	Intergenic	L2c|LINE|L2	-154679	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.000000	0.349810	
chunk0123_239_1	chr3	45617360	45618468	+	0	NA	intron (NM_014240, intron 1 of 7)	intron (NM_014240, intron 1 of 7)	23083	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.016245	0.519387	307(CTGAACAAAGTGTGCT,-,0.00),308(TGAACAAAGTGTGCTT,+,0.00)
chunk0048_324_1	chr12	83656909	83657171	+	0	NA	Intergenic	Intergenic	969885	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.003817	0.357414	
chunk0132_93_1	chr3	155622188	155622563	+	0	NA	intron (NM_014996, intron 1 of 21)	L1PA7|LINE|L1	53941	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.002667	0.404255	88(AAGAACAACCAGTACC,-,0.00),89(AGAACAACCAGTACCA,+,0.00)
chunk0130_33_1	chr3	128999115	128999454	+	0	NA	Intergenic	Intergenic	-2345	NM_024768	79825	Hs.134807	NM_024768	ENSG00000114654	EFCC1	C3orf73|CCDC48	EF-hand and coiled-coil domain containing 1	protein-coding	0.014749	0.494118	
chunk0193_298_1	chr8	77838974	77839173	+	0	NA	Intergenic	L1ME2z|LINE|L1	388376	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.270000	
chunk0092_394_1	chr19	36938956	36939324	+	0	NA	intron (NM_001204838, intron 6 of 9)	L1M7|LINE|L1	22811	NM_001204836	374900	Hs.404220	NM_198539	ENSG00000198453	ZNF568	ZFP568	zinc finger protein 568	protein-coding	0.002717	0.401084	
chunk0037_22_1	chr11	69368528	69368876	+	0	NA	Intergenic	L1ME3D|LINE|L1	74564	NM_001293291	26579	Hs.523848	NM_138768	ENSG00000172927	MYEOV	OCIM	myeloma overexpressed	protein-coding	0.014368	0.484241	
chunk0146_146_1	chr4	159598506	159599064	+	0	NA	Intergenic	Intergenic	330939	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.005376	0.359571	304(AGGAACATATTGTGCC,-,0.00),305(GGAACATATTGTGCCC,+,0.00)
chunk0062_446_1	chr14	75535662	75536394	+	0	NA	intron (NM_006399, intron 2 of 2)	L2a|LINE|L2	13587	NM_006399	10538	Hs.509964	NM_006399	ENSG00000156127	BATF	B-ATF|BATF1|SFA-2|SFA2	basic leucine zipper ATF-like transcription factor	protein-coding	0.009563	0.440655	370(AGGAACAGTTCGTTCT,-,0.00),371(GGAACAGTTCGTTCTA,+,0.00)
chunk0074_172_1	chr16	23557272	23557512	+	0	NA	promoter-TSS (NM_019116)	promoter-TSS (NM_019116)	-17	NR_003501	124454	Hs.620541	NM_001083614	ENSG00000103356	EARS2	COXPD12|MSE1|gluRS|mtGlnRS	glutamyl-tRNA synthetase 2, mitochondrial	protein-coding	0.091667	0.692946	
chunk0128_345_1	chr3	112408075	112408561	+	0	NA	Intergenic	Intergenic	75249	NM_001004196	4345	Hs.79015	NM_005944	ENSG00000091972	CD200	MOX1|MOX2|MRC|OX-2	CD200 molecule	protein-coding	0.002058	0.318275	
chunk0085_423_1	chr18	10560441	10560640	+	0	NA	Intergenic	Intergenic	34664	NM_003826	8774	Hs.464622	NM_003826	ENSG00000134265	NAPG	GAMMASNAP	NSF attachment protein gamma	protein-coding	0.030151	0.460000	
chunk0048_458_1	chr12	88924031	88924721	+	0	NA	Intergenic	Intergenic	95316	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.007246	0.399421	89(GAGCACTCCCTGTACC,-,0.00),90(AGCACTCCCTGTACCC,+,0.00),369(TAGGGCACCGTGTTCT,-,0.00),370(AGGGCACCGTGTTCTA,+,0.00)
chunk0083_15_1	chr17	62970689	62971224	+	0	NA	Intergenic	Intergenic	26741	NR_030363	693218		NR_030363	ENSG00000207552	MIR633	MIRN633|hsa-mir-633	microRNA 633	ncRNA	0.009346	0.347015	
chunk0200_356_1	chr9	25523964	25524202	+	0	NA	Intergenic	Intergenic	154775	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.000000	0.280335	
chunk0160_416_1	chr5	164156190	164156822	+	0	NA	Intergenic	Intergenic	310896	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.011076	0.383886	
chunk0194_260_1	chr8	86836878	86837589	+	0	NA	Intergenic	Intergenic	-29215	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.001406	0.311798	
chunk0011_10_1	chr1	125176914	125177193	+	0	NA	Intergenic	Intergenic	3657941	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.046595	0.371429	
chunk0137_403_1	chr4	27322054	27322755	+	0	NA	Intergenic	Intergenic	104925	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.007133	0.403134	
chunk0168_400_1	chr6	94572694	94572893	+	0	NA	Intergenic	L1M5|LINE|L1	865710	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.000000	0.280000	
chunk0156_103_1	chr5	105212996	105213567	+	0	NA	Intergenic	L2b|LINE|L2	113807	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.311189	
chunk0185_20_1	chr7	124041573	124041777	+	0	NA	Intergenic	Intergenic	-8206	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.009804	0.458537	
chunk0005_49_1	chr1	54978285	54978543	+	0	NA	Intergenic	MIRb|SINE|MIR	-2250	NM_182532	199964	Hs.663950	NM_182532	ENSG00000143001	TMEM61	-	transmembrane protein 61	protein-coding	0.003876	0.536680	
chunk0071_220_1	chr15	84810921	84811183	+	0	NA	Intergenic	L3|LINE|CR1	-5628	NM_020778	57538	Hs.459183	NM_020778	ENSG00000136383	ALPK3	CMH27|MAK|MIDORI	alpha kinase 3	protein-coding	0.011450	0.452471	
chunk0061_312_1	chr14	62466008	62466265	+	0	NA	Intergenic	Intergenic	-326163	NR_104063	101954204	Hs.607093	NR_104063	ENSG00000259142	LINC00644	-	long intergenic non-protein coding RNA 644	ncRNA	0.003891	0.333333	
chunk0109_160_1	chr20	3976505	3977118	+	0	NA	intron (NM_001134338, intron 1 of 6)	intron (NM_001134338, intron 1 of 6)	38596	NM_007219	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.003263	0.322476	
chunk0016_295_1	chr1	201159819	201160073	+	0	NA	intron (NM_001288564, intron 1 of 5)	intron (NM_001288564, intron 1 of 5)	-5391	NM_001288570	252839	Hs.181444	NM_016456	ENSG00000116857	TMEM9	DERM4|TMEM9A	transmembrane protein 9	protein-coding	0.000000	0.427451	
chunk0072_416_1	chr15	100940745	100941007	+	0	NA	intron (NM_024652, intron 2 of 33)	intron (NM_024652, intron 2 of 33)	21661	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.003817	0.505703	
chunk0139_82_1	chr4	49314074	49314601	+	0	NA	Intergenic	MER21B|LTR|ERVL	327695	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.018975	0.471591	
chunk0161_329_1	chr5	173806988	173807409	+	0	NA	Intergenic	Intergenic	-16256	NR_108028	101928154	Hs.366725	NR_108028		LINC01485	-	long intergenic non-protein coding RNA 1485	ncRNA	0.019002	0.516588	232(AAGAACAGCATGTTCT,-,0.00),233(AGAACAGCATGTTCTT,+,0.00)
chunk0078_354_1	chr16	86952029	86952322	+	0	NA	Intergenic	Intergenic	-105609	NR_126008	440390	Hs.513789	NR_126008	ENSG00000232190	LINC02181	-	long intergenic non-protein coding RNA 2181	ncRNA	0.023891	0.496599	130(GAGATCAGCATGTACT,-,0.00),131(AGATCAGCATGTACTC,+,0.00)
chunk0079_70_1	chr17	11522318	11522922	+	0	NA	intron (NM_001173462, intron 3 of 4)	intron (NM_001173462, intron 3 of 4)	-75811	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.009934	0.423140	
chunk0102_1_1	chr2	140939313	140939848	+	0	NA	intron (NM_018557, intron 20 of 90)	intron (NM_018557, intron 20 of 90)	-352895	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.259328	
chunk0019_230_1	chr1	227351485	227352003	+	0	NA	Intergenic	Intergenic	-33619	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.001931	0.381503	
chunk0059_115_1	chr14	31207501	31208455	+	0	NA	promoter-TSS (NM_015382)	promoter-TSS (NM_015382)	-455	NM_015382	25831	Hs.708017	NM_015382	ENSG00000092148	HECTD1	EULIR	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.111111	0.683770	
chunk0170_446_1	chr6	119240875	119241493	+	0	NA	intron (NM_005907, intron 6 of 12)	intron (NM_005907, intron 6 of 12)	-91991	NM_001288576	79632	Hs.443789	NM_024581	ENSG00000111879	FAM184A	C6orf60	family with sequence similarity 184 member A	protein-coding	0.003236	0.413570	
chunk0125_342_1	chr3	71078277	71078640	+	0	NA	intron (NM_032682, intron 7 of 20)	intron (NM_032682, intron 7 of 20)	-13535	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.005510	0.329670	
chunk0208_174_1	chrX	16873515	16873747	+	0	NA	Intergenic	L2a|LINE|L2	-3220	NM_002893	5931	Hs.495755	NM_002893	ENSG00000102054	RBBP7	RbAp46	RB binding protein 7, chromatin remodeling factor	protein-coding	0.000000	0.394850	
chunk0065_391_1	chr14	104732462	104732661	+	0	NA	intron (NM_199165, intron 1 of 12)	intron (NM_199165, intron 1 of 12)	2670	NM_199165	122622	Hs.592327	NM_152328	ENSG00000185100	ADSSL1	Adss1|MPD5	adenylosuccinate synthase like 1	protein-coding	0.035176	0.670000	
chunk0087_253_1	chr18	36906633	36907026	+	0	NA	intron (NM_020776, intron 5 of 9)	L1MC3|LINE|L1	-77613	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.002545	0.329949	
chunk0069_35_1	chr15	60502583	60503053	+	0	NA	exon (NM_134262, exon 7 of 10)	exon (NM_134262, exon 7 of 10)	23640	NR_120340	101928784	Hs.655155	NR_120339	ENSG00000245534	RORA-AS1	-	RORA antisense RNA 1	ncRNA	0.014894	0.416136	
chunk0162_176_1	chr6	3677228	3677690	+	0	NA	Intergenic	L1PA6|LINE|L1	74553	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.002165	0.483801	
chunk0035_45_1	chr11	41086927	41087149	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	372598	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.004505	0.376682	
chunk0017_211_1	chr1	207849202	207849481	+	0	NA	Intergenic	Intergenic	30962	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.007168	0.475000	206(AATAACATCATGTTCT,-,0.00),207(ATAACATCATGTTCTC,+,0.00)
chunk0162_167_1	chr6	3565169	3565797	+	0	NA	Intergenic	Intergenic	-108924	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.009554	0.451510	259(GGGGTCACTGTGTACC,-,0.00)
chunk0103_340_1	chr2	168039598	168039797	+	0	NA	intron (NM_013233, intron 14 of 17)	L1ME1|LINE|L1	-98553	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.005025	0.400000	
chunk0033_285_1	chr11	19607524	19608335	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	32619	NR_039706	100616118		NR_039706	ENSG00000265210	MIR4486	-	microRNA 4486	ncRNA	0.006165	0.444581	283(AGGTACATCATGTCCT,-,0.00),284(GGTACATCATGTCCTT,+,0.00)
chunk0098_368_1	chr2	78490758	78490957	+	0	NA	Intergenic	Intergenic	-200126	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.005025	0.405000	103(GAGCACATCTAGTTCT,-,0.00),104(AGCACATCTAGTTCTT,+,0.00)
chunk0149_92_1	chr5	18048533	18048787	+	0	NA	Intergenic	Intergenic	-661350	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.003937	0.419608	
chunk0118_117_1	chr22	29394933	29395320	+	0	NA	Intergenic	Intergenic	-6543	NM_001166019	162	Hs.368794	NM_001127	ENSG00000100280	AP1B1	ADTB1|AP105A|BAM22|CLAPB2	adaptor related protein complex 1 subunit beta 1	protein-coding	0.023256	0.497423	
chunk0179_95_1	chr7	44668394	44668767	+	0	NA	intron (NM_001003941, intron 5 of 8)	intron (NM_001003941, intron 5 of 8)	62058	NM_001003941	4967	Hs.488181	NM_002541	ENSG00000105953	OGDH	AKGDH|E1k|OGDC	oxoglutarate dehydrogenase	protein-coding	0.002681	0.475936	
chunk0182_147_1	chr7	95110777	95111062	+	0	NA	intron (NM_001166160, intron 2 of 19)	intron (NM_001166160, intron 2 of 19)	201021	NM_001166162	55607	Hs.21816	NM_017650	ENSG00000158528	PPP1R9A	NRB1|NRBI|Neurabin-I	protein phosphatase 1 regulatory subunit 9A	protein-coding	0.010526	0.377622	
chunk0006_149_1	chr1	66291280	66291929	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-40504	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.003082	0.366154	
chunk0003_219_1	chr1	35463137	35463448	+	0	NA	intron (NM_024874, intron 7 of 20)	intron (NM_024874, intron 7 of 20)	94144	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.006431	0.458333	
chunk0185_386_1	chr7	133383014	133383763	+	0	NA	intron (NM_001037126, intron 7 of 9)	MIR3|SINE|MIR	92507	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.006676	0.354667	
chunk0164_412_1	chr6	26957950	26958149	+	0	NA	intron (NR_026775, intron 1 of 2)	intron (NR_026775, intron 1 of 2)	1056	NR_026775	100133205	Hs.526951	NR_026775	ENSG00000224843	LINC00240	C6orf41|NCRNA00240|bA373D17.1	long intergenic non-protein coding RNA 240	ncRNA	0.005025	0.355000	
chunk0053_217_1	chr13	32087032	32087495	+	0	NA	intron (NM_023037, intron 2 of 60)	intron (NM_023037, intron 2 of 60)	-55624	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.006479	0.435345	
chunk0064_429_1	chr14	99863558	99864025	+	0	NA	intron (NM_004434, intron 2 of 21)	L1MC3|LINE|L1	70383	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.012848	0.386752	
chunk0201_1_1	chr9	31977485	31977905	+	0	NA	Intergenic	Intergenic	-406908	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.002381	0.389549	
chunk0023_397_1	chr10	30942733	30943078	+	0	NA	intron (NM_001143767, intron 1 of 5)	intron (NM_001143767, intron 1 of 5)	56612	NM_001143769	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.008696	0.358382	
chunk0037_447_1	chr11	80550425	80550624	+	0	NA	Intergenic	L1PA16|LINE|L1	212279	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.015075	0.380000	66(AAGTACTGAATGTTCT,-,0.00),67(AGTACTGAATGTTCTC,+,0.00)
chunk0126_258_1	chr3	79553100	79553797	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	45561	NR_037488	100500877		NR_037488	ENSG00000265193	MIR3923	-	microRNA 3923	ncRNA	0.004304	0.329513	
chunk0015_57_1	chr1	184620519	184621179	+	0	NA	3' UTR (NM_030806, exon 6 of 6)	3' UTR (NM_030806, exon 6 of 6)	134058	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.009091	0.399395	479(GAGCACTGTATGTTCC,-,0.00),480(AGCACTGTATGTTCCT,+,0.00)
chunk0040_87_1	chr11	111570005	111570812	+	0	NA	Intergenic	Intergenic	29900	NM_001258390	143903	Hs.503831	NM_178834	ENSG00000204381	LAYN	-	layilin	protein-coding	0.008674	0.428218	
chunk0089_263_1	chr18	62554865	62555503	+	0	NA	intron (NR_126534, intron 5 of 14)	MIRb|SINE|MIR	31759	NR_126534	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.004702	0.363067	
chunk0137_190_1	chr4	17753553	17753994	+	0	NA	intron (NM_015688, intron 1 of 17)	LTR47B3|LTR|ERVL	27739	NM_015688	27146	Hs.744951	NM_015688	ENSG00000047662	FAM184B	-	family with sequence similarity 184 member B	protein-coding	0.004535	0.436652	
chunk0067_36_1	chr15	40479166	40479391	+	0	NA	Intergenic	Intergenic	8317	NM_130468	113189	Hs.442449	NM_130468	ENSG00000169105	CHST14	ATCS|D4ST1|EDSMC1|HNK1ST	carbohydrate sulfotransferase 14	protein-coding	0.000000	0.570796	
chunk0125_214_1	chr3	67562006	67562305	+	0	NA	intron (NM_001177599, intron 2 of 10)	intron (NM_001177599, intron 2 of 10)	92459	NM_001177599	8801	Hs.644919	NM_003848	ENSG00000172340	SUCLG2	G-SCS|GBETA|GTPSCS	succinate-CoA ligase GDP-forming beta subunit	protein-coding	0.003344	0.416667	
chunk0096_423_1	chr2	38258560	38258995	+	0	NA	Intergenic	L1MC1|LINE|L1	117753	NM_001308076	64225	Hs.594950	NM_022374	ENSG00000119787	ATL2	ARL3IP2|ARL6IP2|aip-2|atlastin2	atlastin GTPase 2	protein-coding	0.006897	0.364679	
chunk0109_196_1	chr20	5073318	5073568	+	0	NA	Intergenic	Intergenic	39644	NM_001009923	29058	Hs.472024	NM_014145	ENSG00000089063	TMEM230	C20orf30|HSPC274|dJ1116H23.2.1	transmembrane protein 230	protein-coding	0.004000	0.609562	
chunk0159_435_1	chr5	148379280	148379905	+	0	NA	intron (NR_105057, intron 1 of 4)	MIRb|SINE|MIR	4258	NR_105057	102546294	Hs.660461	NR_105057	ENSG00000247199	LOC102546294	-	uncharacterized LOC102546294	ncRNA	0.000000	0.345048	
chunk0051_280_1	chr12	118209898	118210271	+	0	NA	intron (NM_016281, intron 11 of 20)	intron (NM_016281, intron 11 of 20)	74200	NM_002567	5037	Hs.433863	NM_002567	ENSG00000089220	PEBP1	HCNP|HCNPpp|HEL-210|HEL-S-34|HEL-S-96|PBP|PEBP|PEBP-1|RKIP	phosphatidylethanolamine binding protein 1	protein-coding	0.000000	0.401070	
chunk0008_375_1	chr1	96863397	96863830	+	0	NA	Intergenic	L1MA4A|LINE|L1	140975	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.011547	0.493088	
chunk0191_195_1	chr8	51841594	51842156	+	0	NA	intron (NM_001286783, intron 2 of 5)	MER58A|DNA|hAT-Charlie	-32430	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.005338	0.357016	
chunk0090_153_1	chr18	72363004	72363595	+	0	NA	Intergenic	Intergenic	181189	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.011844	0.312500	
chunk0119_79_1	chr22	41417818	41418453	+	0	NA	Intergenic	Intergenic	28888	NM_016272	10766	Hs.474978	NM_016272	ENSG00000183864	TOB2	APRO5|TOB4|TOBL|TROB2	transducer of ERBB2, 2	protein-coding	0.015748	0.595912	313(CAGGACATTGTGTCCA,-,0.00),314(AGGACATTGTGTCCAG,+,0.00)
chunk0063_48_1	chr14	76968519	76969067	+	0	NA	Intergenic	Intergenic	59906	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.032847	0.551913	
chunk0131_269_1	chr3	150153731	150154322	+	0	NA	Intergenic	L1MC1|LINE|L1	-84493	NR_110168	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.005076	0.314189	
chunk0044_302_1	chr12	32917193	32917554	+	0	NA	Intergenic	Intergenic	-20527	NM_004572	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.000000	0.359116	176(ATGTACAGGTTGTTCT,-,0.00),177(TGTACAGGTTGTTCTG,+,0.00)
chunk0187_91_1	chr8	3596385	3596793	+	0	NA	intron (NM_033225, intron 8 of 69)	intron (NM_033225, intron 8 of 69)	-868138	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.012255	0.437653	
chunk0100_309_1	chr2	115824383	115824784	+	0	NA	intron (NM_001178037, intron 21 of 25)	L1PA8|LINE|L1	662476	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.009975	0.432836	
chunk0177_96_1	chr7	21942829	21943288	+	0	NA	intron (NM_001127370, intron 1 of 10)	intron (NM_001127370, intron 1 of 10)	2866	NM_018719	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.015251	0.476087	
chunk0060_136_1	chr14	44711940	44712635	+	0	NA	Intergenic	Intergenic	-185017	NM_001017923	122525	Hs.82098	NM_001017923	ENSG00000179476	C14orf28	DRIP-1|DRIP1|c14_5270	chromosome 14 open reading frame 28	protein-coding	0.008633	0.416667	
chunk0007_338_1	chr1	84805392	84805739	+	0	NA	Intergenic	L1ME4c|LINE|L1	87648	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.005764	0.347701	
chunk0069_243_1	chr15	64166349	64166626	+	0	NA	3' UTR (NM_022048, exon 12 of 12)	3' UTR (NM_022048, exon 12 of 12)	-3332	NM_000942	5479	Hs.434937	NM_000942	ENSG00000166794	PPIB	B|CYP-S1|CYPB|HEL-S-39|OI9|SCYLP	peptidylprolyl isomerase B	protein-coding	0.014440	0.438849	
chunk0194_296_1	chr8	87886716	87886915	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-12747	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.005025	0.440000	
chunk0163_105_1	chr6	9939380	9939638	+	0	NA	Intergenic	Intergenic	-472809	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003876	0.343629	
chunk0097_217_1	chr2	51632637	51632882	+	0	NA	Intergenic	Intergenic	-600223	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.317073	
chunk0047_61_1	chr12	67515000	67515649	+	0	NA	Intergenic	Intergenic	-4758	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.012327	0.484615	
chunk0143_335_1	chr4	120696411	120696842	+	0	NA	intron (NM_001300824, intron 13 of 13)	MIRb|SINE|MIR	226240	NM_001300824	11107	Hs.666782	NM_018699	ENSG00000138738	PRDM5	BCS2|PFM2	PR/SET domain 5	protein-coding	0.000000	0.358796	
chunk0005_372_1	chr1	61640442	61641209	+	0	NA	Intergenic	Intergenic	-13417	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.018253	0.472656	
chunk0127_318_1	chr3	99925698	99925939	+	0	NA	intron (NM_001042459, intron 3 of 4)	intron (NM_001042459, intron 3 of 4)	38580	NR_037486	100500859		NR_037486	ENSG00000264897	MIR3921	-	microRNA 3921	ncRNA	0.004149	0.516529	
chunk0190_292_1	chr8	37903718	37904415	+	0	NA	Intergenic	Intergenic	-4569	NM_025151	80223	Hs.191179	NM_025151	ENSG00000156675	RAB11FIP1	NOEL1A|RCP|rab11-FIP1	RAB11 family interacting protein 1	protein-coding	0.017217	0.595989	108(CAGAGCACGTTGTTCC,-,0.00),109(AGAGCACGTTGTTCCC,+,0.00)
chunk0209_72_1	chrX	38012149	38012394	+	0	NA	intron (NM_138780, intron 1 of 16)	intron (NM_138780, intron 1 of 16)	5689	NM_138780	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.012245	0.300813	
chunk0081_264_1	chr17	43518013	43518255	+	0	NA	intron (NM_004941, intron 18 of 22)	MIRb|SINE|MIR	12301	NM_001261439	2118	Hs.434059	NM_001986	ENSG00000175832	ETV4	E1A-F|E1AF|PEA3|PEAS3	ETS variant 4	protein-coding	0.004132	0.390947	
chunk0027_202_1	chr10	75772336	75773035	+	0	NA	intron (NR_131178, intron 1 of 7)	intron (NR_131178, intron 1 of 7)	-10076	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.010014	0.407143	387(AGGTACAAAATGTACT,-,0.00),388(GGTACAAAATGTACTG,+,0.00)
chunk0148_249_1	chr5	10199551	10199962	+	0	NA	Intergenic	Intergenic	50153	NM_199133	134145	Hs.481569	NM_199133	ENSG00000150756	ATPSCKMT	FAM173B|JS-2|hFAM173B	ATP synthase c subunit lysine N-methyltransferase	protein-coding	0.004866	0.393204	
chunk0040_306_1	chr11	117256090	117256496	+	0	NA	intron (NM_207343, intron 6 of 14)	MLT1H1|LTR|ERVL-MaLR	23557	NM_001077239	257160	Hs.591934	NM_207343	ENSG00000167257	RNF214	-	ring finger protein 214	protein-coding	0.004926	0.417690	
chunk0166_81_1	chr6	43628345	43628683	+	0	NA	intron (NM_019096, intron 1 of 11)	intron (NM_019096, intron 1 of 11)	732	NM_019096	54676	Hs.485449	NM_019096	ENSG00000172432	GTPBP2	JABELS	GTP binding protein 2	protein-coding	0.029586	0.469027	162(GTGAACATACTGCTCT,-,0.00),163(TGAACATACTGCTCTT,+,0.00),207(GGAACATATTGCTCTT,+,0.00)
chunk0068_252_1	chr15	56059947	56060316	+	0	NA	Intergenic	L1MC1|LINE|L1	-66385	NM_006154	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.005420	0.435135	
chunk0017_389_1	chr1	212286327	212286683	+	0	NA	intron (NM_006243, intron 1 of 12)	intron (NM_006243, intron 1 of 12)	968	NM_006243	5525	Hs.744012	NM_006243	ENSG00000066027	PPP2R5A	B56A|B56alpha|PR61A	protein phosphatase 2 regulatory subunit B'alpha	protein-coding	0.039326	0.554622	
chunk0180_437_1	chr7	76576369	76576620	+	0	NA	intron (NR_029411, intron 2 of 2)	intron (NR_029411, intron 2 of 2)	27153	NR_029411	100133091	Hs.712837	NR_029411	ENSG00000205485	LOC100133091	-	uncharacterized LOC100133091	ncRNA	0.007968	0.452381	
chunk0064_132_1	chr14	91402654	91402922	+	0	NA	intron (NM_001080414, intron 3 of 29)	L1ME3Cz|LINE|L1	15056	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.018657	0.360595	
chunk0067_425_1	chr15	49886256	49886604	+	0	NA	intron (NR_073596, intron 23 of 27)	intron (NR_073596, intron 23 of 27)	226886	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.002874	0.358166	
chunk0208_408_1	chrX	29462103	29462476	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-111989	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.005362	0.334225	
chunk0061_244_1	chr14	60944655	60944955	+	0	NA	intron (NM_002431, intron 7 of 7)	intron (NM_002431, intron 7 of 7)	36274	NM_020810	57570	Hs.380159	NM_020810	ENSG00000126814	TRMT5	COXPD26|KIAA1393|TRM5	tRNA methyltransferase 5	protein-coding	0.003333	0.275748	
chunk0210_298_1	chrX	87484984	87486169	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-32136	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.001688	0.331366	
chunk0126_179_1	chr3	78123044	78123592	+	0	NA	Intergenic	L2c|LINE|L2	896141	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.001825	0.304189	
chunk0134_52_1	chr3	175947963	175948561	+	0	NA	Intergenic	L1PA15|LINE|L1	-171929	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.008361	0.343907	
chunk0005_234_1	chr1	59460599	59460953	+	0	NA	intron (NM_001244714, intron 4 of 13)	L1PA6|LINE|L1	-54853	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.008475	0.470423	
chunk0122_4_1	chr3	27320517	27320773	+	0	NA	intron (NM_199347, intron 7 of 24)	intron (NM_199347, intron 7 of 24)	48815	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.007812	0.431907	83(TGGAACACACAGTTCT,-,0.00),84(GGAACACACAGTTCTG,+,0.00)
chunk0107_150_1	chr2	215125523	215125860	+	0	NA	intron (NR_103740, intron 1 of 54)	L1PB2|LINE|L1	12737	NR_103740	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.008902	0.387574	
chunk0050_343_1	chr12	107515139	107515496	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	-65540	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.005602	0.452514	
chunk0119_379_1	chr22	47914115	47914364	+	0	NA	Intergenic	Intergenic	282565	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.024096	0.508000	191(AGGAACAAGCTGTCCT,-,0.00),192(GGAACAAGCTGTCCTG,+,0.00)
chunk0032_37_1	chr11	1110425	1110685	+	0	NA	TTS (NM_002457)	TTS (NM_002457)	35680	NM_002457	4583	Hs.315	NM_002457		MUC2	MLP|MUC-2|SMUC	mucin 2, oligomeric mucus/gel-forming	protein-coding	0.038462	0.574713	74(GGGGACATGCTGTACT,-,0.00),75(GGGACATGCTGTACTG,+,0.00)
chunk0150_86_1	chr5	32249527	32250152	+	0	NA	intron (NM_001040446, intron 8 of 15)	intron (NM_001040446, intron 8 of 15)	63169	NM_001294343	54545	Hs.481836	NM_019061	ENSG00000150712	MTMR12	3-PAP|PIP3AP	myotubularin related protein 12	protein-coding	0.011200	0.440895	
chunk0122_293_1	chr3	36187149	36187490	+	0	NA	Intergenic	L1PB1|LINE|L1	-193168	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.005865	0.347953	
chunk0016_351_1	chr1	202046968	202047552	+	0	NA	Intergenic	L2b|LINE|L2	36698	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.003425	0.504274	
chunk0025_19_1	chr10	48182806	48183005	+	0	NA	intron (NM_001018071, intron 20 of 28)	intron (NM_001018071, intron 20 of 28)	-7762	NM_001042512	143162	Hs.664786	NM_152428	ENSG00000170324	FRMPD2	PDZD5C|PDZK4|PDZK5C	FERM and PDZ domain containing 2	protein-coding	0.000000	0.510000	
chunk0196_386_1	chr8	115700263	115700505	+	0	NA	Intergenic	Intergenic	-31356	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004132	0.312757	
chunk0029_151_1	chr10	99410752	99410951	+	0	NA	intron (NM_002079, intron 2 of 8)	intron (NM_002079, intron 2 of 8)	19922	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.000000	0.430000	
chunk0076_363_1	chr16	71882734	71882966	+	0	NA	intron (NM_017530, intron 1 of 5)	intron (NM_017530, intron 1 of 5)	691	NM_001201553	55565	Hs.744055	NM_017530	ENSG00000102984	ZNF821	-	zinc finger protein 821	protein-coding	0.004310	0.369099	
chunk0209_13_1	chrX	35280091	35281125	+	0	NA	Intergenic	L1MB5|LINE|L1	337812	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.001934	0.309179	
chunk0067_97_1	chr15	42151814	42152745	+	0	NA	intron (NM_213600, intron 7 of 19)	MLT1H|LTR|ERVL-MaLR	4362	NR_033151	255189	Hs.231873	NM_213600	ENSG00000168907	PLA2G4F	PLA2G4FZ	phospholipase A2 group IVF	protein-coding	0.016112	0.536481	708(AGGGACAGGTTGTTCA,-,0.00),709(GGGACAGGTTGTTCAC,+,0.00)
chunk0170_137_1	chr6	111094080	111095001	+	0	NA	intron (NM_018593, intron 1 of 5)	intron (NM_018593, intron 1 of 5)	6962	NM_018593	117247	Hs.591327	NM_018593	ENSG00000112394	SLC16A10	MCT10|PRO0813|TAT1	solute carrier family 16 member 10	protein-coding	0.005429	0.414317	
chunk0109_358_1	chr2	239151553	239152237	+	0	NA	intron (NM_006037, intron 7 of 26)	intron (NM_006037, intron 7 of 26)	43562	NR_026664	85009	Hs.744565	NM_032923		MGC16025	-	uncharacterized LOC85009	ncRNA	0.014620	0.499270	407(GGGAACGAACTGTGCT,-,0.00),408(GGAACGAACTGTGCTG,+,0.00)
chunk0197_375_1	chr8	126793706	126793977	+	0	NA	Intergenic	MIR3|SINE|MIR	-219313	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.003690	0.400735	
chunk0042_86_1	chr12	2490899	2491241	+	0	NA	intron (NM_001129844, intron 6 of 46)	L1ME1|LINE|L1	181150	NR_046579	100874235	Hs.667644	NR_046579	ENSG00000256271	CACNA1C-AS2	-	CACNA1C antisense RNA 2	ncRNA	0.005848	0.422741	
chunk0113_122_1	chr20	51526015	51526562	+	0	NA	intron (NM_001136021, intron 1 of 10)	MER58A|DNA|hAT-Charlie	16431	NM_001258296	4773	Hs.744148	NM_012340	ENSG00000101096	NFATC2	NFAT1|NFATP	nuclear factor of activated T cells 2	protein-coding	0.023766	0.534672	
chunk0058_340_1	chr14	28763927	28764426	+	0	NA	intron (NR_125758, intron 1 of 6)	intron (NR_125758, intron 1 of 6)	1143	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.022044	0.378000	
chunk0142_343_1	chr4	101349489	101349947	+	0	NA	TTS (NR_033874)	TTS (NR_033874)	1941	NR_033874	90024	Hs.534513	NR_033874	ENSG00000254531	FLJ20021	-	uncharacterized LOC90024	ncRNA	0.006550	0.433551	
chunk0079_38_1	chr17	10224036	10224667	+	0	NA	Intergenic	Intergenic	-25800	NM_201433	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.014263	0.393987	
chunk0016_249_1	chr1	200067780	200067979	+	0	NA	intron (NM_205860, intron 5 of 7)	intron (NM_205860, intron 5 of 7)	25054	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005025	0.390000	89(GAGAACATTTAGTGCT,-,0.00),90(AGAACATTTAGTGCTT,+,0.00)
chunk0202_423_1	chr9	81727174	81727375	+	0	NA	intron (NR_109772, intron 1 of 3)	L1ME4a|LINE|L1	37561	NR_109772	101927502	Hs.528628	NR_109772	ENSG00000233926	LOC101927502	-	uncharacterized LOC101927502	ncRNA	0.000000	0.336634	
chunk0131_370_1	chr3	152026012	152026243	+	0	NA	Intergenic	Intergenic	-97952	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.021645	0.344828	
chunk0013_119_1	chr1	167943697	167943896	+	0	NA	intron (NM_001017977, intron 1 of 18)	L1MA4A|LINE|L1	-6727	NM_015415	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.015075	0.405000	
chunk0004_323_1	chr1	50086504	50087075	+	0	NA	intron (NM_001144777, intron 1 of 6)	intron (NM_001144777, intron 1 of 6)	-17121	NM_001144776	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.005254	0.445804	
chunk0001_386_1	chr1	10523020	10523244	+	0	NA	intron (NM_004565, intron 2 of 8)	Tigger15a|DNA|TcMar-Tigger	48186	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.004464	0.377778	
chunk0086_306_1	chr18	24047628	24048143	+	0	NA	intron (NM_001135993, intron 1 of 13)	L1MA3|LINE|L1	-32425	NR_110796	102724246	Hs.569872	NR_110796	ENSG00000264745	TTC39C-AS1	-	TTC39C antisense RNA 1	ncRNA	0.005825	0.298450	
chunk0084_39_1	chr17	73936793	73937556	+	0	NA	Intergenic	Intergenic	-108637	NR_027146	283982	Hs.464079	NM_182564		LINC00469	C17orf54	long intergenic non-protein coding RNA 469	ncRNA	0.010485	0.493455	10(GGAACAGACAGACCTG,+,0.00),354(CAGAGCAGCGTGTGCA,-,0.00)
chunk0036_155_1	chr11	62341912	62342635	+	0	NA	intron (NM_001083926, intron 2 of 6)	LTR10C|LTR|ERV1	4971	NM_025080	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.013831	0.388122	347(AGGAACAGGCTGTGAC,-,0.00),348(GGAACAGGCTGTGACC,+,0.00),643(AAGAGCAGCCTGTCCA,-,0.00),644(AGAGCAGCCTGTCCAA,+,0.00)
chunk0058_222_1	chr14	25073450	25074182	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-23519	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.001366	0.331514	
chunk0177_37_1	chr7	20896122	20896681	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	60970	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.005367	0.342857	
chunk0062_137_1	chr14	68824951	68825190	+	0	NA	Intergenic	Intergenic	-28827	NM_001244701	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.033473	0.562500	
chunk0128_399_1	chr3	114089597	114090174	+	0	NA	Intergenic	Intergenic	33150	NM_001256837	79691	Hs.477162	NM_024638	ENSG00000151576	QTRT2	QTRTD1	queuine tRNA-ribosyltransferase accessory subunit 2	protein-coding	0.001733	0.384083	296(AGGAACAGGCTGCTCT,-,0.00),297(GGAACAGGCTGCTCTC,+,0.00)
chunk0148_351_1	chr5	14528862	14529608	+	0	NA	Intergenic	L1MC4a|LINE|L1	-52547	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.002681	0.376171	
chunk0158_219_1	chr5	128380659	128380858	+	0	NA	intron (NM_001999, intron 11 of 64)	intron (NM_001999, intron 11 of 64)	157284	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.015075	0.380000	181(AGGAACAGAAAGTACT,-,0.00),182(GGAACAGAAAGTACTT,+,0.00)
chunk0030_425_1	chr10	120392381	120393244	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-37589	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.008111	0.439815	
chunk0152_306_1	chr5	61775065	61775367	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-39518	NR_105000	100506526	Hs.662277	NR_105000		C5orf64-AS1	-	C5orf64 antisense RNA 1	ncRNA	0.009934	0.511551	286(GGAACAGAGAGAGCTT,+,0.00)
chunk0198_338_1	chr8	140114794	140115185	+	0	NA	intron (NM_001160372, intron 17 of 22)	intron (NM_001160372, intron 17 of 22)	342773	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.012788	0.433673	
chunk0007_111_1	chr1	78943985	78944818	+	0	NA	intron (NM_022159, intron 3 of 14)	intron (NM_022159, intron 3 of 14)	62409	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.002401	0.318945	
chunk0111_61_1	chr20	22833519	22833718	+	0	NA	Intergenic	L1MC1|LINE|L1	-201802	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.005025	0.355000	
chunk0099_385_1	chr2	101473140	101473635	+	0	NA	intron (NM_001145664, intron 1 of 11)	intron (NM_001145664, intron 1 of 11)	1316	NM_001145664	731220	Hs.662488	NM_207403	ENSG00000196460	RFX8	-	RFX family member 8, lacking RFX DNA binding domain	protein-coding	0.014141	0.377016	
chunk0056_436_1	chr13	95110913	95111137	+	0	NA	intron (NM_001105515, intron 20 of 20)	intron (NM_001105515, intron 20 of 20)	150984	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.008929	0.346667	
chunk0072_190_1	chr15	94265031	94265738	+	0	NA	Intergenic	Intergenic	-32817	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.007072	0.360169	
chunk0028_237_1	chr10	89972493	89972919	+	0	NA	Intergenic	Intergenic	-15333	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.004695	0.456674	
chunk0037_136_1	chr11	73103783	73104498	+	0	NA	intron (NM_014824, intron 2 of 19)	intron (NM_014824, intron 2 of 19)	37958	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.006993	0.410615	
chunk0164_201_1	chr6	22513940	22514191	+	0	NA	Intergenic	Intergenic	-55384	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007968	0.456349	122(ATGAACAGCACGTTCT,-,0.00),123(TGAACAGCACGTTCTA,+,0.00)
chunk0024_157_1	chr10	35470193	35470392	+	0	NA	intron (NM_001282853, intron 2 of 10)	(GACA)n|Simple_repeat|Simple_repeat	133418	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.020101	0.565000	
chunk0009_130_1	chr1	104081194	104081613	+	0	NA	Intergenic	Intergenic	8380	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.007160	0.354762	213(GGGTACACAATGTACT,-,0.00),214(GGTACACAATGTACTG,+,0.00)
chunk0112_2_1	chr20	35542178	35542377	+	0	NA	intron (NM_015966, intron 1 of 12)	CpG	248	NM_015966	51614	Hs.472558	NM_015966	ENSG00000125991	ERGIC3	C20orf47|C2orf47|CGI-54|Erv46|NY-BR-84|PRO0989|SDBCAG84|dJ477O4.2	ERGIC and golgi 3	protein-coding	0.070352	0.660000	
chunk0154_248_1	chr5	81355797	81356405	+	0	NA	intron (NM_130767, intron 5 of 14)	intron (NM_130767, intron 5 of 14)	38068	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.011513	0.500821	
chunk0166_373_1	chr6	51592984	51593582	+	0	NA	Intergenic	L1MA9|LINE|L1	-28587	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.003344	0.317195	
chunk0141_389_1	chr4	88334721	88335457	+	0	NA	Intergenic	Intergenic	-43650	NM_001165136	55008	Hs.529317	NM_017912	ENSG00000138642	HERC6	-	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	protein-coding	0.008152	0.404342	
chunk0057_64_1	chr13	97972339	97972706	+	0	NA	intron (NM_002271, intron 3 of 28)	intron (NM_002271, intron 3 of 28)	18847	NM_002271	3843	Hs.712598	NM_002271	ENSG00000065150	IPO5	IMB3|KPNB3|Pse1|RANBP5|imp5	importin 5	protein-coding	0.005450	0.421196	
chunk0079_206_1	chr17	14489902	14490451	+	0	NA	Intergenic	Intergenic	186436	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.003643	0.312727	
chunk0181_49_1	chr7	80053184	80053383	+	0	NA	Intergenic	Intergenic	-81541	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.010050	0.465000	76(AGGCCACCTTGTTCTC,+,0.00)
chunk0017_402_1	chr1	212608521	212608857	+	0	NA	promoter-TSS (NM_001206484)	promoter-TSS (NM_001206484)	61	NM_001206488	467	Hs.460	NM_001674	ENSG00000162772	ATF3	-	activating transcription factor 3	protein-coding	0.098214	0.676558	
chunk0023_269_1	chr10	27887999	27888606	+	0	NA	intron (NM_001290020, intron 17 of 19)	L1M2|LINE|L1	93615	NM_001290021	55130	Hs.127530	NM_018076	ENSG00000169126	ARMC4	CILD23	armadillo repeat containing 4	protein-coding	0.004942	0.335526	
chunk0068_384_1	chr15	58384509	58385173	+	0	NA	Intergenic	Intergenic	-47135	NM_000236	3990	Hs.654472	NM_000236	ENSG00000166035	LIPC	HDLCQ12|HL|HTGL|LIPH	lipase C, hepatic type	protein-coding	0.010542	0.425564	
chunk0152_87_1	chr5	58181996	58182195	+	0	NA	Intergenic	Intergenic	-59754	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.005025	0.345000	
chunk0030_36_1	chr10	111482756	111482955	+	0	NA	Intergenic	Intergenic	405823	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.005025	0.470000	
chunk0086_28_1	chr18	12480461	12480662	+	0	NA	intron (NM_001128627, intron 8 of 15)	MIR|SINE|MIR	60372	NM_001142406	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.004975	0.346535	
chunk0001_20_1	chr1	1185022	1185296	+	0	NA	3' UTR (NM_153254, exon 9 of 9)	3' UTR (NM_153254, exon 9 of 9)	5462	NM_153254	254173	Hs.454835	NM_153254	ENSG00000162571	TTLL10	TTLL5	tubulin tyrosine ligase like 10	protein-coding	0.051095	0.636364	
chunk0160_190_1	chr5	154593102	154593499	+	0	NA	Intergenic	Tigger7|DNA|TcMar-Tigger	2772	NR_036094	100422950		NR_036094	ENSG00000264760	MIR3141	mir-3141	microRNA 3141	ncRNA	0.005038	0.329146	216(TAGTACAGCGTGTCCA,-,0.00),217(AGTACAGCGTGTCCAT,+,0.00)
chunk0212_61_1	chrY	11325742	11325982	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1095728	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.012500	0.477178	
chunk0098_150_1	chr2	69781591	69782780	+	0	NA	intron (NM_001153, intron 2 of 12)	intron (NM_001153, intron 2 of 12)	40190	NM_001153	307	Hs.422986	NM_001153	ENSG00000196975	ANXA4	ANX4|HEL-S-274|P32.5|PAP-II|PIG28|PP4-X|ZAP36	annexin A4	protein-coding	0.007569	0.410924	
chunk0152_28_1	chr5	56830390	56830617	+	0	NA	intron (NM_005921, intron 1 of 19)	intron (NM_005921, intron 1 of 19)	15430	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.000000	0.385965	104(TGGGACTTGGTGTTCC,-,0.00),105(GGGACTTGGTGTTCCA,+,0.00)
chunk0198_461_1	chr8	144580857	144581233	+	0	NA	exon (NM_001308207, exon 4 of 12)	exon (NM_001308207, exon 4 of 12)	24650	NM_025251	80728	Hs.148988	NM_025251	ENSG00000147799	ARHGAP39	CrGAP|Vilse	Rho GTPase activating protein 39	protein-coding	0.109043	0.692308	154(GGGGACTCCGTGTTCT,-,0.00),155(GGGACTCCGTGTTCTG,+,0.00)
chunk0055_225_1	chr13	62531591	62531790	+	0	NA	Intergenic	L1MEc|LINE|L1	265002	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.005025	0.350000	84(GGGAACACTTTGATCT,-,0.00),85(GGAACACTTTGATCTC,+,0.00)
chunk0094_230_1	chr2	6955804	6956027	+	0	NA	intron (NM_014746, intron 2 of 8)	intron (NM_014746, intron 2 of 8)	-37233	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.004484	0.428571	
chunk0140_216_1	chr4	70893703	70894331	+	0	NA	Intergenic	Intergenic	-8323	NM_001244767	92597	Hs.691454	NM_173468	ENSG00000173542	MOB1B	MATS2|MOB4A|MOBKL1A	MOB kinase activator 1B	protein-coding	0.020701	0.383148	
chunk0124_60_1	chr3	52869417	52870146	+	0	NA	intron (NM_198563, intron 1 of 8)	intron (NM_198563, intron 1 of 8)	-23229	NR_107031	102465866		NR_107031	ENSG00000275789	MIR8064	hsa-mir-8064	microRNA 8064	ncRNA	0.008230	0.456164	
chunk0064_138_1	chr14	91508999	91509600	+	0	NA	intron (NM_001284280, intron 1 of 14)	intron (NM_001284280, intron 1 of 14)	1181	NM_001284280	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.058236	0.576412	
chunk0027_329_1	chr10	78442998	78443630	+	0	NA	Intergenic	Intergenic	175986	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.015823	0.556082	493(AAGAGCACTGTGTACT,-,0.00),494(AGAGCACTGTGTACTT,+,0.00)
chunk0203_356_1	chr9	89877111	89877456	+	0	NA	Intergenic	Intergenic	-92133	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.008696	0.549133	174(AAGAACATGGTGTACA,-,0.00),175(AGAACATGGTGTACAG,+,0.00)
chunk0161_161_1	chr5	169139748	169139947	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	123847	NR_030311	693170		NR_030311	ENSG00000207619	MIR585	MIRN585|hsa-mir-585|mir-585	microRNA 585	ncRNA	0.020101	0.490000	
chunk0080_15_1	chr17	20936871	20937338	+	0	NA	Intergenic	Intergenic	-1416	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.006424	0.331197	
chunk0195_71_1	chr8	93929285	93929541	+	0	NA	Intergenic	Intergenic	12362	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.007812	0.443580	
chunk0152_42_1	chr5	57189614	57190295	+	0	NA	intron (NM_001203246, intron 2 of 10)	L2c|LINE|L2	14506	NM_001127235	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.004405	0.357771	
chunk0061_450_1	chr14	65854078	65854477	+	0	NA	Intergenic	Intergenic	383175	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.007519	0.407500	
chunk0068_258_1	chr15	56237907	56238440	+	0	NA	intron (NM_022841, intron 1 of 8)	intron (NM_022841, intron 1 of 8)	5112	NM_022841	64864	Hs.745089	NM_022841	ENSG00000181827	RFX7	RFXDC2	regulatory factor X7	protein-coding	0.003752	0.329588	
chunk0190_298_1	chr8	38057446	38057856	+	0	NA	intron (NM_004095, intron 2 of 2)	intron (NM_004095, intron 2 of 2)	27149	NM_004095	1978	Hs.411641	NM_004095	ENSG00000187840	EIF4EBP1	4E-BP1|4EBP1|BP-1|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding	0.014634	0.484185	202(AAAGACACAGTGTACT,-,0.00),203(AAGACACAGTGTACTT,+,0.00)
chunk0171_304_1	chr6	129022105	129022321	+	0	NA	intron (NM_001079823, intron 1 of 63)	intron (NM_001079823, intron 1 of 63)	139072	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.004630	0.304147	
chunk0031_182_1	chr10	125646260	125647003	+	0	NA	Intergenic	Intergenic	36513	NM_001128202	387718	Hs.148259	NM_001128202	ENSG00000175018	TEX36	C10orf122|bA383C5.1	testis expressed 36	protein-coding	0.002692	0.342742	400(AAGGACAGGATGTGAC,-,0.00)
chunk0086_42_1	chr18	12673135	12673665	+	0	NA	non-coding (NR_073537, exon 12 of 13)	non-coding (NR_073537, exon 12 of 13)	14661	NM_147163	56984	Hs.464652	NM_020232	ENSG00000128789	PSMG2	CLAST3|HCCA3|HsT1707|MDS003|PAC2|TNFSF5IP1	proteasome assembly chaperone 2	protein-coding	0.015094	0.338983	
chunk0053_25_1	chr13	26839756	26840337	+	0	NA	Intergenic	Intergenic	-79261	NM_005288	2835	Hs.123034	NM_005288	ENSG00000132975	GPR12	GPCR12|GPCR21|PPP1R84	G protein-coupled receptor 12	protein-coding	0.013769	0.414089	
chunk0157_292_1	chr5	120910221	120910601	+	0	NA	Intergenic	Intergenic	378947	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.002632	0.343832	213(AAGTACAAAATGTACT,-,0.00),214(AGTACAAAATGTACTT,+,0.00)
chunk0104_226_1	chr2	176425367	176425796	+	0	NA	Intergenic	Intergenic	156186	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.000000	0.376744	
chunk0127_312_1	chr3	99568908	99569410	+	0	NA	Intergenic	Intergenic	-69437	NM_020351	1295	Hs.654548	NM_001850	ENSG00000144810	COL8A1	C3orf7	collagen type VIII alpha 1 chain	protein-coding	0.000000	0.339960	
chunk0099_26_1	chr2	83166541	83167517	+	0	NA	Intergenic	MER130|DNA|DNA	310226	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.002049	0.335722	
chunk0005_378_1	chr1	61825385	61825769	+	0	NA	intron (NM_176877, intron 15 of 42)	MER131|DNA?|DNA?	83100	NM_176877	10207	Hs.478125	NM_005799	ENSG00000132849	PATJ	Cipp|INADL|InaD-like|hINADL	PATJ crumbs cell polarity complex component	protein-coding	0.002604	0.363636	
chunk0101_283_1	chr2	134104162	134104509	+	0	NA	Intergenic	Intergenic	-22790	NR_037450	100500878		NR_037450	ENSG00000263813	MIR3679	mir-3679	microRNA 3679	ncRNA	0.000000	0.465517	
chunk0194_55_1	chr8	82175593	82176324	+	0	NA	Intergenic	Intergenic	-333672	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.004104	0.379781	
chunk0006_2_1	chr1	63755222	63755663	+	0	NA	Intergenic	Intergenic	-18577	NM_005012	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.015873	0.475113	
chunk0155_10_1	chr5	90866966	90867501	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	308433	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.003738	0.347015	
chunk0035_417_1	chr11	57101722	57102336	+	0	NA	Intergenic	L3|LINE|CR1	64495	NR_036445	219525	Hs.554519	NR_036445	ENSG00000283307	OR5AK4P	PJCG3	olfactory receptor family 5 subfamily AK member 4 pseudogene	pseudo	0.008143	0.409756	
chunk0069_317_1	chr15	65832644	65833084	+	0	NA	Intergenic	Intergenic	-36595	NM_004663	8766	Hs.321541	NM_004663	ENSG00000103769	RAB11A	YL8	RAB11A, member RAS oncogene family	protein-coding	0.009091	0.517007	
chunk0112_195_1	chr20	40333543	40334121	+	0	NA	Intergenic	L1MA9|LINE|L1	329371	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.003460	0.417962	
chunk0184_371_1	chr7	121314196	121314455	+	0	NA	Intergenic	Intergenic	-11042	NM_016087	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.011583	0.411538	
chunk0201_249_1	chr9	37908751	37908950	+	0	NA	Intergenic	Intergenic	-4497	NR_024873	92014	Hs.634120	NM_033412	ENSG00000122696	SLC25A51	CG7943|MCART1	solute carrier family 25 member 51	protein-coding	0.005025	0.415000	
chunk0079_265_1	chr17	16181472	16182194	+	0	NA	intron (NM_006311, intron 3 of 45)	intron (NM_006311, intron 3 of 45)	12806	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.001385	0.307054	
chunk0118_15_1	chr22	25643527	25644018	+	0	NA	intron (NM_005160, intron 2 of 20)	intron (NM_005160, intron 2 of 20)	78878	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.008147	0.390244	
chunk0101_125_1	chr2	127112165	127112529	+	0	NA	Intergenic	L1MC1|LINE|L1	-5020	NM_139351	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.008242	0.416438	
chunk0097_343_1	chr2	58204412	58204617	+	0	NA	intron (NM_018062, intron 5 of 13)	intron (NM_018062, intron 5 of 13)	36866	NM_001114636	55120	Hs.631890	NM_018062	ENSG00000115392	FANCL	FAAP43|PHF9|POG	FA complementation group L	protein-coding	0.000000	0.398058	
chunk0210_292_1	chrX	85904196	85904407	+	0	NA	promoter-TSS (NR_029848)	promoter-TSS (NR_029848)	-594	NR_029848	494323		NR_029848	ENSG00000199051	MIR361	MIRN361|hsa-mir-361|mir-361	microRNA 361	ncRNA	0.014218	0.396226	
chunk0077_391_1	chr16	84767249	84767490	+	0	NA	intron (NR_073577, intron 8 of 11)	intron (NR_073577, intron 8 of 11)	-52612	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.008299	0.380165	
chunk0089_215_1	chr18	61161111	61161316	+	0	NA	Intergenic	Intergenic	-329329	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.009756	0.504854	
chunk0197_86_1	chr8	119166355	119166882	+	0	NA	Intergenic	Intergenic	-41753	NM_052886	114569	Hs.201083	NM_052886	ENSG00000147676	MAL2	-	mal, T cell differentiation protein 2 (gene/pseudogene)	protein-coding	0.001898	0.363636	
chunk0148_200_1	chr5	8530330	8530806	+	0	NA	Intergenic	HAL1|LINE|L1	69643	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.016807	0.402516	
chunk0114_23_1	chr21	7291910	7292176	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	432872	NR_128718	103504736		NR_128718	ENSG00000278618	MIR8069-2	hsa-mir-8069-2	microRNA 8069-2	ncRNA	0.000000	0.344569	
chunk0076_315_1	chr16	70454589	70454788	+	0	NA	promoter-TSS (NM_145059)	promoter-TSS (NM_145059)	93	NM_145059	197258	Hs.7907	NM_145059	ENSG00000157353	FCSK	1110046B12Rik|CDGF2|FUK	fucose kinase	protein-coding	0.135678	0.740000	
chunk0204_410_1	chr9	102833239	102833458	+	0	NA	Intergenic	Intergenic	-161963	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.000000	0.381818	
chunk0030_285_1	chr10	116962014	116962396	+	0	NA	intron (NM_018330, intron 3 of 14)	intron (NM_018330, intron 3 of 14)	43372	NM_001127211	57698	Hs.501140	NM_018330	ENSG00000187164	SHTN1	KIAA1598|shootin-1	shootin 1	protein-coding	0.005236	0.378590	
chunk0086_365_1	chr18	25984420	25984840	+	0	NA	Intergenic	Intergenic	106017	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.002381	0.315914	
chunk0100_340_1	chr2	116928564	116928864	+	0	NA	Intergenic	L1MC3|LINE|L1	-885965	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.006667	0.358804	126(TGGAACATGGTGTTCT,-,0.00),127(GGAACATGGTGTTCTA,+,0.00)
chunk0074_259_1	chr16	28089453	28089706	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-26070	NM_001109763	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.007905	0.535433	
chunk0205_405_1	chr9	114769197	114769472	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	23196	NM_001204344	9966	Hs.23349	NM_005118	ENSG00000181634	TNFSF15	TL1|TL1A|TNLG1B|VEGI|VEGI192A	TNF superfamily member 15	protein-coding	0.007273	0.449275	
chunk0066_267_1	chr15	34927696	34928138	+	0	NA	intron (NM_014691, intron 12 of 34)	intron (NM_014691, intron 12 of 34)	41877	NM_014691	9716	Hs.510958	NM_014691	ENSG00000021776	AQR	IBP160|fSAP164	aquarius intron-binding spliceosomal factor	protein-coding	0.004525	0.437923	
chunk0152_365_1	chr5	64045181	64045514	+	0	NA	Intergenic	L1M1|LINE|L1	-83055	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.003003	0.311377	185(ATACACATTCTGTTCC,-,0.00),186(TACACATTCTGTTCCT,+,0.00)
chunk0038_54_1	chr11	82864246	82864445	+	0	NA	intron (NM_005040, intron 1 of 8)	intron (NM_005040, intron 1 of 8)	36170	NM_005040	5547	Hs.523936	NM_005040	ENSG00000137509	PRCP	HUMPCP|PCP	prolylcarboxypeptidase	protein-coding	0.010050	0.460000	
chunk0025_304_1	chr10	57526206	57526726	+	0	NA	Intergenic	Intergenic	-221907	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.003846	0.314779	
chunk0078_139_1	chr17	3792611	3792819	+	0	NA	intron (NM_002208, intron 1 of 30)	intron (NM_002208, intron 1 of 30)	8528	NM_002208	3682	Hs.513867	NM_002208	ENSG00000083457	ITGAE	CD103|HUMINAE	integrin subunit alpha E	protein-coding	0.024038	0.411483	
chunk0030_123_1	chr10	113126395	113126868	+	0	NA	intron (NM_001146283, intron 5 of 12)	intron (NM_001146283, intron 5 of 12)	81276	NR_132769	106635520		NR_132769		SNORA87	-	small nucleolar RNA, H/ACA box 87	snoRNA	0.061311	0.565401	
chunk0179_303_1	chr7	50082458	50083216	+	0	NA	intron (NM_001159878, intron 2 of 7)	L1M5|LINE|L1	10427	NM_007009	11055	Hs.388841	NM_007009	ENSG00000042813	ZPBP	ZPBP1	zona pellucida binding protein	protein-coding	0.005277	0.354414	
chunk0152_247_1	chr5	60796376	60796642	+	0	NA	intron (NM_001104558, intron 1 of 7)	MER20|DNA|hAT-Charlie	47765	NM_001297618	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.015038	0.415730	
chunk0066_345_1	chr15	37896169	37896637	+	0	NA	Intergenic	L2c|LINE|L2	-38204	NM_152453	145942	Hs.179646	NM_152453	ENSG00000166069	TMCO5A	TMCO5	transmembrane and coiled-coil domains 5A	protein-coding	0.000000	0.339019	
chunk0022_158_1	chr10	12555065	12555461	+	0	NA	intron (NM_020397, intron 2 of 9)	intron (NM_020397, intron 2 of 9)	-23490	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.015152	0.443325	232(CAGGACAGTCTGTCCT,-,0.00),233(AGGACAGTCTGTCCTC,+,0.00)
chunk0020_397_1	chr1	240667309	240667872	+	0	NA	Intergenic	L2c|LINE|L2	-55428	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.010657	0.464539	258(AGGAACACCGTGCTCC,-,0.00),259(GGAACACCGTGCTCCT,+,0.00)
chunk0100_222_1	chr2	111970831	111971351	+	0	NA	intron (NM_006343, intron 6 of 18)	L1MEc|LINE|L1	72477	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.001923	0.287908	
chunk0109_284_1	chr20	8172564	8173267	+	0	NA	intron (NM_015192, intron 2 of 31)	L1MD2|LINE|L1	40650	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.002845	0.470170	
chunk0197_307_1	chr8	124563353	124564050	+	0	NA	intron (NM_001282974, intron 9 of 13)	intron (NM_001282974, intron 9 of 13)	24599	NM_001278645	4715	Hs.15977	NM_005005	ENSG00000147684	NDUFB9	B22|CI-B22|LYRM3|MC1DN24|UQOR22	NADH:ubiquinone oxidoreductase subunit B9	protein-coding	0.014347	0.485673	
chunk0050_217_1	chr12	104565746	104565963	+	0	NA	intron (NM_018413, intron 1 of 2)	intron (NM_018413, intron 1 of 2)	-25779	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.009217	0.504587	102(AGGAACACTGTGTACC,-,0.00),103(GGAACACTGTGTACCA,+,0.00)
chunk0007_332_1	chr1	84709591	84710352	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	-19414	NM_001166293	117178	Hs.22587	NM_014021	ENSG00000117155	SSX2IP	ADIP|hMsd1	SSX family member 2 interacting protein	protein-coding	0.007884	0.412073	
chunk0144_212_1	chr4	134327549	134327872	+	0	NA	Intergenic	Intergenic	-125962	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.043344	0.574074	
chunk0083_117_1	chr17	64988533	64988776	+	0	NA	Intergenic	Intergenic	-13069	NR_026903	201283	Hs.396447	NM_153032	ENSG00000214174	AMZ2P1	-	archaelysin family metallopeptidase 2 pseudogene 1	pseudo	0.012346	0.536885	82(GGGCACAGCATGTACC,-,0.00),83(GGCACAGCATGTACCA,+,0.00),133(TGGCACACGCTGCTCC,-,0.00),134(GGCACACGCTGCTCCT,+,0.00)
chunk0102_249_1	chr2	149080901	149081408	+	0	NA	intron (NM_001317004, intron 1 of 6)	intron (NM_001317004, intron 1 of 6)	3632	NM_001317004	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.001972	0.413386	
chunk0044_308_1	chr12	33376339	33377003	+	0	NA	3' UTR (NM_198992, exon 7 of 7)	3' UTR (NM_198992, exon 7 of 7)	63148	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.009036	0.324812	
chunk0202_125_1	chr9	73109445	73109661	+	0	NA	Intergenic	Intergenic	-42178	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.009259	0.327189	
chunk0086_247_1	chr18	23237542	23238628	+	0	NA	intron (NM_001100619, intron 7 of 9)	intron (NM_001100619, intron 7 of 9)	82260	NM_138375	91768	Hs.11108	NM_138375	ENSG00000134508	CABLES1	CABL1|CABLES|HsT2563|IK3-1	Cdk5 and Abl enzyme substrate 1	protein-coding	0.023020	0.526219	
chunk0189_377_1	chr8	27354690	27354976	+	0	NA	intron (NM_004103, intron 2 of 31)	intron (NM_004103, intron 2 of 31)	29269	NM_173175	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.010490	0.407666	
chunk0189_366_1	chr8	27250570	27250769	+	0	NA	intron (NM_030795, intron 1 of 6)	intron (NM_030795, intron 1 of 6)	7770	NM_001283055	81551	Hs.201058	NM_030795	ENSG00000015592	STMN4	RB3	stathmin 4	protein-coding	0.005025	0.510000	56(CAGAACAGTGTGTGAT,-,0.00),57(AGAACAGTGTGTGATT,+,0.00)
chunk0192_61_1	chr8	60338177	60338805	+	0	NA	Intergenic	Intergenic	-57096	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.003185	0.327504	
chunk0142_217_1	chr4	97762221	97762447	+	0	NA	intron (NM_174952, intron 9 of 10)	intron (NM_174952, intron 9 of 10)	380906	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.004425	0.400881	102(AGGCACACTCTGTGCT,-,0.00),103(GGCACACTCTGTGCTG,+,0.00)
chunk0040_247_1	chr11	115281593	115282053	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	222700	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.000000	0.299349	281(AAGAACACCATGTCAC,-,0.00)
chunk0090_64_1	chr19	2145672	2146366	+	0	NA	intron (NM_001261826, intron 1 of 31)	intron (NM_001261826, intron 1 of 31)	5538	NM_003938	8943	Hs.512815	NM_003938	ENSG00000065000	AP3D1	ADTD|HPS10|hBLVR	adaptor related protein complex 3 subunit delta 1	protein-coding	0.027378	0.541007	
chunk0063_447_1	chr14	89015980	89016289	+	0	NA	Intergenic	Intergenic	191981	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.006472	0.387097	118(GAGGACAAGTTGTTCC,-,0.00),119(AGGACAAGTTGTTCCC,+,0.00)
chunk0203_198_1	chr9	86499799	86500606	+	0	NA	Intergenic	AluJr4|SINE|Alu	-145715	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.002478	0.377475	
chunk0064_311_1	chr14	95755519	95755914	+	0	NA	Intergenic	Intergenic	-41520	NM_021966	8115	Hs.2484	NM_021966	ENSG00000100721	TCL1A	TCL1	T cell leukemia/lymphoma 1A	protein-coding	0.005063	0.409091	
chunk0124_43_1	chr3	52411205	52411416	+	0	NA	intron (NM_016483, intron 1 of 10)	intron (NM_016483, intron 1 of 10)	749	NM_016483	51533	Hs.372719	NM_016483	ENSG00000010318	PHF7	HSPC045|HSPC226|NYD-SP6	PHD finger protein 7	protein-coding	0.028436	0.523585	
chunk0175_33_1	chr7	817376	817575	+	0	NA	exon (NM_001171945, exon 2 of 7)	exon (NM_001171945, exon 2 of 7)	860	NM_001171945	23353	Hs.438072	NM_025154	ENSG00000164828	SUN1	UNC84A	Sad1 and UNC84 domain containing 1	protein-coding	0.055276	0.620000	
chunk0204_160_1	chr9	95852263	95852462	+	0	NA	intron (NR_023390, intron 1 of 2)	intron (NR_023390, intron 1 of 2)	-23256	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.010050	0.375000	
chunk0067_285_1	chr15	47412159	47412880	+	0	NA	intron (NM_001198999, intron 2 of 19)	intron (NM_001198999, intron 2 of 19)	228313	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.008322	0.383657	
chunk0073_417_1	chr16	18898508	18899072	+	0	NA	intron (NM_015092, intron 1 of 62)	intron (NM_015092, intron 1 of 62)	27614	NM_015092	23049	Hs.460179	NM_015092	ENSG00000157106	SMG1	61E3.4|ATX|LIP	SMG1 nonsense mediated mRNA decay associated PI3K related kinase	protein-coding	0.007092	0.336283	
chunk0008_86_1	chr1	90721537	90721837	+	0	NA	Intergenic	Intergenic	-4450	NM_020063	343472	Hs.451956	NM_020063	ENSG00000143032	BARHL2	-	BarH like homeobox 2	protein-coding	0.030000	0.415282	
chunk0071_171_1	chr15	83210729	83210967	+	0	NA	Intergenic	Intergenic	-2830	NM_016073	50810	Hs.513954	NM_016073	ENSG00000166503	HDGFL3	CGI-142|HDGF-2|HDGF2|HDGFRP3|HRP-3	HDGF like 3	protein-coding	0.008403	0.502092	
chunk0169_346_1	chr6	106540417	106540796	+	0	NA	intron (NM_001624, intron 7 of 19)	intron (NM_001624, intron 7 of 19)	28751	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.000000	0.310526	
chunk0001_94_1	chr1	3114338	3114540	+	0	NA	intron (NM_022114, intron 1 of 16)	(CA)n|Simple_repeat|Simple_repeat	-13536	NR_036215	100422968		NR_036215	ENSG00000283572	MIR4251	-	microRNA 4251	ncRNA	0.099010	0.581281	
chunk0067_123_1	chr15	42764759	42765196	+	0	NA	intron (NM_173500, intron 13 of 14)	L1PA6|LINE|L1	-27758	NM_138477	146059	Hs.599232	NM_138477	ENSG00000140326	CDAN1	CDA1|CDAI|CDAN1A|DLT|PRO1295	codanin 1	protein-coding	0.006865	0.497717	
chunk0074_341_1	chr16	31524478	31524702	+	0	NA	Intergenic	Intergenic	-3292	NM_016633	51327	Hs.274309	NM_016633	ENSG00000169877	AHSP	EDRF|ERAF	alpha hemoglobin stabilizing protein	protein-coding	0.013393	0.484444	
chunk0154_320_1	chr5	84091392	84091975	+	0	NA	intron (NM_001278642, intron 5 of 9)	intron (NM_001278642, intron 5 of 9)	293184	NM_005711	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.005146	0.369863	
chunk0195_335_1	chr8	99217652	99218003	+	0	NA	intron (NM_152564, intron 17 of 61)	MER58A|DNA|hAT-Charlie	204561	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.000000	0.360795	
chunk0114_85_1	chr21	9252363	9252574	+	0	NA	Intergenic	Intergenic	-122707	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.009479	0.377358	
chunk0208_389_1	chrX	28874542	28874741	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	287077	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.000000	0.310000	
chunk0094_393_1	chr2	10302947	10303414	+	0	NA	promoter-TSS (NM_134421)	promoter-TSS (NM_134421)	276	NM_002149	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.122056	0.711538	
chunk0017_408_1	chr1	212858716	212859031	+	0	NA	promoter-TSS (NR_027285)	promoter-TSS (NR_027285)	618	NM_014053	28982	Hs.7055	NM_014053	ENSG00000162769	FLVCR1	AXPC1|FLVCR|MFSD7B|PCA|PCARP|SLC49A1	feline leukemia virus subgroup C cellular receptor 1	protein-coding	0.066667	0.642405	
chunk0139_392_1	chr4	62260507	62260829	+	0	NA	Intergenic	Intergenic	-98903	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.006211	0.315789	
chunk0087_387_1	chr18	41828072	41828684	+	0	NA	Intergenic	Intergenic	-126820	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.008170	0.389886	
chunk0198_274_1	chr8	135481696	135482261	+	0	NA	intron (NM_006558, intron 1 of 8)	intron (NM_006558, intron 1 of 8)	24513	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.010619	0.381625	233(GGGAACAAAATGTGCC,-,0.00),234(GGAACAAAATGTGCCA,+,0.00)
chunk0149_5_1	chr5	15715935	15716454	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-101192	NR_109945	101929472	Hs.662664	NR_109945		CTD-2350J17.1	-	uncharacterized LOC101929472	ncRNA	0.011561	0.382692	
chunk0076_12_1	chr16	58732784	58733001	+	0	NA	intron (NM_001286220, intron 1 of 8)	intron (NM_001286220, intron 1 of 8)	1465	NM_001286220	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.013825	0.472477	
chunk0123_182_1	chr3	44253707	44253967	+	0	NA	intron (NM_001145030, intron 2 of 19)	intron (NM_001145030, intron 2 of 19)	11951	NM_001145030	375337	Hs.132125	NM_001145030	ENSG00000173769	TOPAZ1	C3orf77	testis and ovary specific PAZ domain containing 1	protein-coding	0.003846	0.318008	
chunk0140_203_1	chr4	70488850	70489278	+	0	NA	Intergenic	Intergenic	16947	NM_152291	4589	Hs.631946	NM_152291	ENSG00000171195	MUC7	MG2	mucin 7, secreted	protein-coding	0.009346	0.363636	
chunk0021_33_1	chr10	848281	848787	+	0	NA	intron (NM_015155, intron 5 of 17)	L1MC1|LINE|L1	83171	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.007905	0.357002	
chunk0163_403_1	chr6	16765939	16766552	+	0	NA	Intergenic	Intergenic	-4755	NM_001128164	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.001631	0.366450	
chunk0161_411_1	chr5	177537496	177537902	+	0	NA	intron (NR_024019, intron 4 of 11)	intron (NR_024019, intron 4 of 11)	16848	NM_001190946	54540	Hs.484289	NM_019057	ENSG00000146067	FAM193B	IRIZIO	family with sequence similarity 193 member B	protein-coding	0.009852	0.474201	
chunk0150_375_1	chr5	39187895	39188582	+	0	NA	intron (NM_001465, intron 2 of 18)	intron (NM_001465, intron 2 of 18)	31340	NM_001465	2533	Hs.370503	NM_001465	ENSG00000082074	FYB1	ADAP|FYB|PRO0823|SLAP-130|SLAP130|THC3	FYN binding protein 1	protein-coding	0.010189	0.430233	
chunk0163_177_1	chr6	11304897	11305392	+	0	NA	non-coding (NR_073131, exon 3 of 10)	non-coding (NR_073131, exon 3 of 10)	-72462	NM_006403	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.008081	0.360887	
chunk0201_351_1	chr9	68389450	68389852	+	0	NA	intron (NM_021965, intron 4 of 10)	L1ME1|LINE|L1	-31785	NR_121192	572558	Hs.552819	NR_015423	ENSG00000224958	PGM5-AS1	FAM233A	PGM5 antisense RNA 1	ncRNA	0.012438	0.337469	
chunk0159_133_1	chr5	139108404	139108756	+	0	NA	intron (NM_001037633, intron 4 of 10)	intron (NM_001037633, intron 4 of 10)	89796	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.014205	0.433428	
chunk0040_42_1	chr11	110759853	110760293	+	0	NA	Intergenic	Intergenic	-46884	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.004545	0.399093	
chunk0125_171_1	chr3	66596462	66596690	+	0	NA	Intergenic	Intergenic	-96155	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.013158	0.454148	59(GAGAACAGCATGTACA,-,0.00),60(AGAACAGCATGTACAA,+,0.00)
chunk0058_309_1	chr14	27236780	27237159	+	0	NA	Intergenic	Intergenic	328327	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.002639	0.328947	159(AGGAACAGTTTGTCTC,-,0.00),160(GGAACAGTTTGTCTCC,+,0.00)
chunk0150_246_1	chr5	36239442	36239726	+	0	NA	intron (NM_001287341, intron 1 of 12)	intron (NM_001287341, intron 1 of 12)	1807	NM_001287340	133686	Hs.81907	NM_153013	ENSG00000152620	NADK2	C5orf33|DECRD|MNADK|NADKD1	NAD kinase 2, mitochondrial	protein-coding	0.010563	0.371930	
chunk0052_216_1	chr13	25487984	25488552	+	0	NA	intron (NM_001313741, intron 2 of 35)	L1MB2|LINE|L1	19494	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.012324	0.428822	
chunk0171_441_1	chr6	131743804	131744356	+	0	NA	intron (NR_133007, intron 23 of 23)	MamRep137|DNA|TcMar-Tigger	-33063	NM_001145659	643854	Hs.632613	NM_001145659	ENSG00000236761	CTAGE9	-	CTAGE family member 9	protein-coding	0.000000	0.327306	
chunk0035_176_1	chr11	43926177	43926643	+	0	NA	Intergenic	Intergenic	-5466	NR_038907	100507300	Hs.664588	NR_038907	ENSG00000244926	ALKBH3-AS1	-	ALKBH3 antisense RNA 1	ncRNA	0.021459	0.496788	
chunk0162_45_1	chr6	1251046	1251399	+	0	NA	Intergenic	Intergenic	-61218	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.016997	0.525424	
chunk0090_455_1	chr18	79966631	79966874	+	0	NA	intron (NM_001136180, intron 2 of 3)	intron (NM_001136180, intron 2 of 3)	2170	NM_001136180	440498	Hs.191582	NM_001136180	ENSG00000226742	HSBP1L1	-	heat shock factor binding protein 1 like 1	protein-coding	0.016461	0.393443	
chunk0058_228_1	chr14	25212601	25212974	+	0	NA	Intergenic	L1ME3|LINE|L1	-162490	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.002681	0.326203	
chunk0051_420_1	chr12	122424981	122425508	+	0	NA	Intergenic	Intergenic	-2675	NM_198240	6249	Hs.524809	NM_002956	ENSG00000130779	CLIP1	CLIP|CLIP-170|CLIP170|CYLN1|RSN	CAP-Gly domain containing linker protein 1	protein-coding	0.017078	0.477273	236(AGGACTCAAAGTTCCT,+,0.00)
chunk0015_359_1	chr1	190366980	190367230	+	0	NA	intron (NM_199051, intron 2 of 7)	THE1C-int|LTR|ERVL-MaLR	110524	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.012000	0.529880	
chunk0186_216_1	chr7	140041109	140041435	+	0	NA	intron (NM_022750, intron 6 of 11)	intron (NM_022750, intron 6 of 11)	22449	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.003067	0.373089	
chunk0191_2_1	chr8	42338398	42339289	+	0	NA	intron (NM_002690, intron 1 of 13)	intron (NM_002690, intron 1 of 13)	388	NM_002690	5423	Hs.654484	NM_002690	ENSG00000070501	POLB	-	DNA polymerase beta	protein-coding	0.053872	0.580717	
chunk0200_91_1	chr9	16512194	16512949	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-236258	NR_073471									0.007947	0.349206	
chunk0176_266_1	chr7	16412477	16412835	+	0	NA	intron (NM_001101417, intron 1 of 8)	intron (NM_001101417, intron 1 of 8)	8666	NM_001101417	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.002793	0.345404	
chunk0076_73_1	chr16	63396389	63396852	+	0	NA	Intergenic	MIRb|SINE|MIR	-1359785	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.000000	0.346983	
chunk0183_146_1	chr7	105827015	105827535	+	0	NA	intron (NM_020725, intron 2 of 11)	intron (NM_020725, intron 2 of 11)	49310	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.005769	0.374280	
chunk0004_41_1	chr1	42844758	42844964	+	0	NA	3' UTR (NM_001017922, exon 12 of 12)	3' UTR (NM_001017922, exon 12 of 12)	-1712	NM_015911	51058	Hs.20879	NM_015911	ENSG00000164011	ZNF691	Zfp691	zinc finger protein 691	protein-coding	0.004854	0.396135	
chunk0176_277_1	chr7	16600588	16600839	+	0	NA	3' UTR (NM_020319, exon 10 of 10)	3' UTR (NM_020319, exon 10 of 10)	45104	NM_020319	57037	Hs.157378	NM_020319	ENSG00000106524	ANKMY2	ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding	0.007968	0.484127	
chunk0132_391_1	chr3	163722177	163722387	+	0	NA	Intergenic	LTR2752|LTR|ERV1	-418981	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.004762	0.478673	
chunk0070_53_1	chr15	69587761	69588214	+	0	NA	Intergenic	MIRc|SINE|MIR	-4213	NR_126438	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.004415	0.495595	159(AGGAACATGATGTTCC,-,0.00),160(GGAACATGATGTTCCT,+,0.00)
chunk0188_255_1	chr8	14521390	14521658	+	0	NA	intron (NM_139167, intron 2 of 7)	L1MD1|LINE|L1	331986	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.000000	0.345725	
chunk0166_431_1	chr6	52787843	52788373	+	0	NA	Intergenic	MER65A|LTR|ERV1	15758	NM_145740	2938	Hs.446309	NM_145740	ENSG00000243955	GSTA1	GST-epsilon|GST2|GSTA1-1|GTH1	glutathione S-transferase alpha 1	protein-coding	0.007547	0.312618	
chunk0090_397_1	chr18	78010167	78010401	+	0	NA	Intergenic	(GTG)n|Simple_repeat|Simple_repeat	-16557	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.000000	0.527660	
chunk0056_29_1	chr13	77290588	77290787	+	0	NA	intron (NM_015057, intron 2 of 82)	L1MD2|LINE|L1	36355	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.000000	0.390000	
chunk0054_206_1	chr13	45067914	45068463	+	0	NA	Intergenic	Intergenic	-38091	NR_120424	101929259	Hs.638490	NR_120424		LOC101929259	-	uncharacterized LOC101929259	ncRNA	0.007286	0.385455	
chunk0187_422_1	chr7	158595142	158595381	+	0	NA	Intergenic	(GGTGGT)n|Simple_repeat|Simple_repeat	3645	NR_049893	100847032		NR_049893	ENSG00000265598	MIR5707	-	microRNA 5707	ncRNA	0.008368	0.541667	
chunk0061_74_1	chr14	56660568	56661207	+	0	NA	Intergenic	Intergenic	81094	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.004695	0.451562	
chunk0019_11_1	chr1	223326278	223326813	+	0	NA	intron (NM_001037175, intron 2 of 5)	L1PB3|LINE|L1	37657	NM_017982	55061	Hs.497841	NM_017982	ENSG00000143502	SUSD4	PRO222	sushi domain containing 4	protein-coding	0.003738	0.328358	
chunk0092_158_1	chr19	29676609	29677006	+	0	NA	Intergenic	Intergenic	11387	NM_024310	79156	Hs.466383	NM_024310	ENSG00000166289	PLEKHF1	APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology and FYVE domain containing 1	protein-coding	0.017632	0.603015	
chunk0105_277_1	chr2	189619226	189619678	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-38641	NM_014585	30061	Hs.643005	NM_014585	ENSG00000138449	SLC40A1	FPN1|HFE4|IREG1|MST079|MSTP079|MTP1|SLC11A3	solute carrier family 40 member 1	protein-coding	0.002212	0.366446	
chunk0132_119_1	chr3	155973289	155973811	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	103014	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.000000	0.426386	
chunk0151_48_1	chr5	42369789	42369988	+	0	NA	Intergenic	(TACATA)n|Simple_repeat|Simple_repeat	-53887	NM_000163	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.000000	0.235000	
chunk0005_73_1	chr1	55919978	55920424	+	0	NA	Intergenic	(TAG)n|Simple_repeat|Simple_repeat	659383	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.006726	0.268456	
chunk0032_122_1	chr11	4152131	4152630	+	0	NA	Intergenic	L1MEc|LINE|L1	-34772	NR_047550	100506082	Hs.445705	NR_047550	ENSG00000254480	LINC02749	-	long intergenic non-protein coding RNA 2749	ncRNA	0.002004	0.348000	
chunk0155_279_1	chr5	96030621	96031059	+	0	NA	intron (NR_130776, intron 1 of 4)	AluJr|SINE|Alu	-48298	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.002283	0.384966	
chunk0145_188_1	chr4	147805105	147805463	+	0	NA	intron (NM_024605, intron 1 of 22)	L1PA15|LINE|L1	22689	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.002793	0.398329	
chunk0002_40_1	chr1	12496301	12496908	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-10642	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.009885	0.496711	
chunk0087_419_1	chr18	42260185	42260814	+	0	NA	intron (NR_046454, intron 3 of 6)	L1ME4a|LINE|L1	73831	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.000000	0.279365	
chunk0204_30_1	chr9	92435698	92436545	+	0	NA	intron (NM_001286969, intron 4 of 6)	L1MD1|LINE|L1	-11567	NM_005014	4958	Hs.94070	NM_005014	ENSG00000127083	OMD	OSAD|SLRR2C	osteomodulin	protein-coding	0.003542	0.334906	594(TAGAACAAGGAGTACC,-,0.00),595(AGAACAAGGAGTACCT,+,0.00)
chunk0182_29_1	chr7	91548989	91549589	+	0	NA	Intergenic	Intergenic	284821	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.001667	0.336106	318(AACACATTTTGTTCTT,+,0.00)
chunk0208_417_1	chrX	29570344	29570866	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-3673	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.005747	0.342256	
chunk0015_136_1	chr1	185696611	185697321	+	0	NA	Intergenic	L2b|LINE|L2	-37585	NM_031935	83872	Hs.58877	NM_031935	ENSG00000143341	HMCN1	ARMD1|FBLN6|FIBL-6|FIBL6	hemicentin 1	protein-coding	0.000000	0.367089	
chunk0209_224_1	chrX	44942888	44943487	+	0	NA	intron (NR_111960, intron 2 of 27)	Tigger1a_Art|DNA|TcMar-Tigger	70012	NM_001291421	7403	Hs.522616	NM_021140	ENSG00000147050	KDM6A	KABUK2|UTX|bA386N14.2	lysine demethylase 6A	protein-coding	0.006678	0.311667	
chunk0102_223_1	chr2	148648739	148649200	+	0	NA	intron (NM_015630, intron 1 of 13)	intron (NM_015630, intron 1 of 13)	3978	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.010846	0.378788	
chunk0200_282_1	chr9	22342395	22342850	+	0	NA	Intergenic	Intergenic	-104219	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.002198	0.377193	165(TTGCACATTCTGTCCT,-,0.00),166(TGCACATTCTGTCCTG,+,0.00)
chunk0081_76_1	chr17	39208946	39209773	+	0	NA	Intergenic	MIR3|SINE|MIR	9076	NM_000981	6143	Hs.381061	NM_000981	ENSG00000108298	RPL19	L19	ribosomal protein L19	protein-coding	0.018138	0.579710	
chunk0181_236_1	chr7	85258904	85259583	+	0	NA	Intergenic	L2a|LINE|L2	-137312	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.001473	0.319118	
chunk0071_71_1	chr15	80573082	80573528	+	0	NA	intron (NM_014862, intron 12 of 18)	(TTAT)n|Simple_repeat|Simple_repeat	-7798	NR_049837	100847042		NR_049837	ENSG00000284059	MIR5572	-	microRNA 5572	ncRNA	0.008969	0.324385	
chunk0051_105_1	chr12	114911174	114911726	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-227286	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.003623	0.392405	
chunk0162_53_1	chr6	1298068	1298277	+	0	NA	Intergenic	L1MEc|LINE|L1	-14268	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.000000	0.338095	
chunk0010_255_1	chr1	116619646	116619845	+	0	NA	intron (NM_001007237, intron 2 of 10)	intron (NM_001007237, intron 2 of 10)	47211	NM_001542	3321	Hs.171057	NM_001542	ENSG00000143061	IGSF3	EWI-3|LCDD|V8	immunoglobulin superfamily member 3	protein-coding	0.000000	0.450000	
chunk0176_180_1	chr7	13839019	13839571	+	0	NA	Intergenic	Intergenic	147219	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.001812	0.327306	
chunk0095_304_1	chr2	20351435	20352071	+	0	NA	promoter-TSS (NM_015317)	promoter-TSS (NM_015317)	-903	NM_015317	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.026730	0.485086	
chunk0169_218_1	chr6	104162014	104162614	+	0	NA	Intergenic	L1M1|LINE|L1	697605	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.008333	0.490849	
chunk0003_453_1	chr1	41482435	41482837	+	0	NA	intron (NR_126098, intron 2 of 4)	A-rich|Low_complexity|Low_complexity	2047	NM_001956	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.024876	0.595533	
chunk0111_4_1	chr20	21751026	21751604	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	45656	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.005190	0.350604	
chunk0078_198_1	chr17	5262460	5263215	+	0	NA	Intergenic	L2|LINE|L2	-19426	NM_004703	9135	Hs.584784	NM_004703	ENSG00000029725	RABEP1	RAB5EP|RABPT5	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.005298	0.366402	
chunk0096_400_1	chr2	37679085	37679782	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-6898	NM_001270436	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.002869	0.458453	
chunk0035_402_1	chr11	56706517	56706922	+	0	NA	Intergenic	L1PBb|LINE|L1	6331	NM_001013358	504191		NM_001013358		OR9G9	OR9G1	olfactory receptor family 9 subfamily G member 9	protein-coding	0.004938	0.497537	
chunk0111_293_1	chr20	31738456	31738760	+	0	NA	promoter-TSS (NM_012112)	promoter-TSS (NM_012112)	-493	NM_012112	22974	Hs.244580	NM_012112	ENSG00000088325	TPX2	C20orf1|C20orf2|DIL-2|DIL2|FLS353|GD:C20orf1|HCA519|HCTP4|REPP86|p100	TPX2 microtubule nucleation factor	protein-coding	0.036184	0.445902	
chunk0166_368_1	chr6	51487828	51488395	+	0	NA	Intergenic	Intergenic	-133759	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.007055	0.404930	189(TGAGACACTGTGTGCT,-,0.00),190(GAGACACTGTGTGCTA,+,0.00)
chunk0160_164_1	chr5	152218539	152218820	+	0	NA	intron (NR_109876, intron 1 of 2)	MLT1C|LTR|ERVL-MaLR	186600	NM_020167	56923	Hs.731911	NM_020167	ENSG00000132911	NMUR2	FM-4|FM4|NMU-R2|NMU2R|TGR-1|TGR1	neuromedin U receptor 2	protein-coding	0.007117	0.404255	
chunk0129_126_1	chr3	119932600	119932901	+	0	NA	intron (NM_001146156, intron 3 of 10)	intron (NM_001146156, intron 3 of 10)	150040	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.006645	0.350993	
chunk0192_330_1	chr8	67265837	67266500	+	0	NA	exon (NM_006421, exon 14 of 39)	exon (NM_006421, exon 14 of 39)	77509	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.009050	0.375000	
chunk0049_132_1	chr12	91645979	91646361	+	0	NA	Intergenic	Intergenic	-463046	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.010471	0.375979	
chunk0054_38_1	chr13	41059925	41060518	+	0	NA	Intergenic	CpG	-1340	NM_007187	11193	Hs.411300	NM_007187	ENSG00000120688	WBP4	FBP21	WW domain binding protein 4	protein-coding	0.089376	0.634680	288(AGGCACACTGTGTTCC,-,0.00),289(GGCACACTGTGTTCCG,+,0.00)
chunk0138_18_1	chr4	30642444	30643486	+	0	NA	Intergenic	Intergenic	-77443	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.003839	0.299137	
chunk0185_252_1	chr7	130113866	130114295	+	0	NA	intron (NM_014997, intron 2 of 9)	intron (NM_014997, intron 2 of 9)	43571	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.009324	0.351163	
chunk0039_121_1	chr11	98007616	98008111	+	0	NA	Intergenic	Intergenic	-1013113	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.314516	
chunk0127_86_1	chr3	89707513	89707936	+	0	NA	Intergenic	L1PB2|LINE|L1	600200	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.341981	218(TAGTACTTGATGTCCT,-,0.00),219(AGTACTTGATGTCCTG,+,0.00)
chunk0033_2_1	chr11	12280394	12280761	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-6323	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.002725	0.470109	
chunk0027_343_1	chr10	78589462	78590178	+	0	NA	Intergenic	LTR40a|LTR|ERVL	322492	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.005587	0.383543	
chunk0064_199_1	chr14	92875101	92875336	+	0	NA	Intergenic	Intergenic	-47882	NM_001275	1113	Hs.150793	NM_001275	ENSG00000100604	CHGA	CGA	chromogranin A	protein-coding	0.021277	0.576271	
chunk0082_114_1	chr17	54906830	54907083	+	0	NA	intron (NM_005486, intron 3 of 15)	intron (NM_005486, intron 3 of 15)	6265	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.023715	0.464567	
chunk0125_71_1	chr3	64368252	64369005	+	0	NA	Intergenic	Intergenic	-143173	NM_198859	166336	Hs.148105	NM_198859	ENSG00000163637	PRICKLE2	EPM5	prickle planar cell polarity protein 2	protein-coding	0.013280	0.470822	378(ATGCACACAATGTTCT,-,0.00),379(TGCACACAATGTTCTT,+,0.00)
chunk0038_405_1	chr11	93794649	93795294	+	0	NA	exon (NM_004268, exon 6 of 12)	exon (NM_004268, exon 6 of 12)	10732	NM_004268	9440	Hs.444931	NM_004268	ENSG00000042429	MED17	CRSP6|CRSP77|DRIP80|SRB4|TRAP80	mediator complex subunit 17	protein-coding	0.009302	0.376161	289(CGGCACAGAATGTTCT,-,0.00),290(GGCACAGAATGTTCTC,+,0.00)
chunk0097_329_1	chr2	57351751	57351954	+	0	NA	Intergenic	L1P3|LINE|L1	-555799	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.004926	0.362745	
chunk0194_60_1	chr8	82346003	82346278	+	0	NA	Intergenic	LTR79|LTR|ERVL	-503854	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.394928	122(AGCACAGACTGACCAG,+,0.00)
chunk0083_102_1	chr17	64583289	64583488	+	0	NA	intron (NM_022739, intron 7 of 18)	intron (NM_022739, intron 7 of 18)	76652	NM_001316990	90799	Hs.569713	NM_138363	ENSG00000258890	CEP95	CCDC45	centrosomal protein 95	protein-coding	0.020101	0.375000	
chunk0144_207_1	chr4	134135337	134135594	+	0	NA	Intergenic	L2|LINE|L2	66283	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.011673	0.375969	93(TTGAACTTCATGTTCC,-,0.00),94(TGAACTTCATGTTCCC,+,0.00)
chunk0011_152_1	chr1	147550457	147551048	+	0	NA	intron (NM_004326, intron 1 of 9)	intron (NM_004326, intron 1 of 9)	9251	NM_004326	607	Hs.415209	NM_004326	ENSG00000116128	BCL9	LGS	BCL9 transcription coactivator	protein-coding	0.003384	0.358108	292(TGGAACAGTCTGTCCT,-,0.00),293(GGAACAGTCTGTCCTG,+,0.00)
chunk0106_33_1	chr2	196079740	196080130	+	0	NA	Intergenic	Intergenic	-11123	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.005128	0.437340	
chunk0201_223_1	chr9	37444866	37445308	+	0	NA	intron (NM_014872, intron 1 of 1)	HAL1|LINE|L1	20323	NM_014872	9925	Hs.161276	NM_014872	ENSG00000168795	ZBTB5	-	zinc finger and BTB domain containing 5	protein-coding	0.004525	0.395034	
chunk0180_144_1	chr7	57328425	57328748	+	0	NA	Intergenic	Intergenic	-76181	NR_120505	100653233	Hs.127379	NR_120505	ENSG00000260653	LOC100653233	-	uncharacterized LOC100653233	ncRNA	0.030960	0.635802	161(CAGCACGTTATGTCCC,-,0.00),162(AGCACGTTATGTCCCT,+,0.00)
chunk0119_294_1	chr22	46258854	46259309	+	0	NA	exon (NM_006071, exon 1 of 1)	exon (NM_006071, exon 1 of 1)	4241	NM_006071	10343	Hs.241383	NM_006071	ENSG00000130943	PKDREJ	-	polycystin family receptor for egg jelly	protein-coding	0.010989	0.377193	246(AAGAACATAATGTTAC,-,0.00)
chunk0014_3_1	chr1	174113961	174114683	+	0	NA	Intergenic	Intergenic	44965	NR_121197	102724601	Hs.563791	NR_121197	ENSG00000227373	RABGAP1L-DT	-	RABGAP1L divergent transcript	ncRNA	0.002770	0.301521	319(CAGAACACATTGTCCA,-,0.00),320(AGAACACATTGTCCAT,+,0.00)
chunk0153_244_1	chr5	72319908	72320571	+	0	NA	promoter-TSS (NM_001286751)	promoter-TSS (NM_001286751)	18	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.054299	0.560241	50(AGGAACATACTGTTAT,-,0.00),51(GGAACATACTGTTATT,+,0.00)
chunk0052_348_1	chr12	126582412	126583056	+	0	NA	Intergenic	Intergenic	107584	NR_110036	100996671	Hs.121392	NR_110034	ENSG00000256732	LOC100996671	-	uncharacterized LOC100996671	ncRNA	0.006211	0.370543	
chunk0197_312_1	chr8	124739062	124739659	+	0	NA	Intergenic	Intergenic	-10853	NM_001282971	9788	Hs.336994	NM_014751	ENSG00000170873	MTSS1	MIM|MIMA|MIMB	MTSS I-BAR domain containing 1	protein-coding	0.005025	0.471572	
chunk0029_26_1	chr10	95794520	95794894	+	0	NA	intron (NR_038444, intron 4 of 5)	L2b|LINE|L2	38791	NM_001164182	953	Hs.576612	NM_001776	ENSG00000138185	ENTPD1	ATPDase|CD39|NTPDase-1|SPG64	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding	0.005348	0.434667	
chunk0045_269_1	chr12	49692566	49693125	+	0	NA	intron (NM_198900, intron 1 of 24)	L2c|LINE|L2	14569	NM_175736	91010	Hs.179838	NM_175736	ENSG00000161791	FMNL3	FHOD3|FRL2|WBP-3|WBP3	formin like 3	protein-coding	0.007156	0.371429	
chunk0120_298_1	chr3	9946353	9946552	+	0	NA	promoter-TSS (NR_046734)	promoter-TSS (NR_046734)	-952	NR_046734	100874032	Hs.616388	NR_046734	ENSG00000230082	PRRT3-AS1	-	PRRT3 antisense RNA 1	ncRNA	0.085427	0.655000	28(AGGGGCAGACTGTCCA,-,0.00),29(GGGGCAGACTGTCCAC,+,0.00)
chunk0062_301_1	chr14	72978007	72978352	+	0	NA	exon (NM_001281734, exon 7 of 12)	exon (NM_001281734, exon 7 of 12)	8777	NM_178441	53349	Hs.335106	NM_021260	ENSG00000165861	ZFYVE1	DFCP1|PPP1R172|SR3|TAFF1|ZNFN2A1	zinc finger FYVE-type containing 1	protein-coding	0.020290	0.482659	
chunk0137_414_1	chr4	28065348	28065807	+	0	NA	Intergenic	Intergenic	-754005	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.004357	0.250000	
chunk0201_185_1	chr9	36328675	36328894	+	0	NA	Intergenic	Intergenic	-51728	NM_001128227	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.013699	0.390909	
chunk0113_96_1	chr20	50918753	50919131	+	0	NA	intron (NM_001282531, intron 2 of 5)	intron (NM_001282531, intron 2 of 5)	-9151	NM_001282532	23394	Hs.293736	NM_015339	ENSG00000101126	ADNP	ADNP1|HVDAS|MRD28	activity dependent neuroprotector homeobox	protein-coding	0.005291	0.313984	
chunk0212_4_1	chrY	5870918	5871364	+	0	NA	Intergenic	L1PA13|LINE|L1	372469	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.006726	0.366890	
chunk0156_114_1	chr5	105846483	105846706	+	0	NA	Intergenic	MER66-int|LTR|ERV1	747120	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.013453	0.428571	
chunk0019_325_1	chr1	229191120	229191540	+	0	NA	Intergenic	L1ME5|LINE|L1	-16529	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.004762	0.472684	
chunk0002_63_1	chr1	13859940	13860354	+	0	NA	Intergenic	HAL1|LINE|L1	110766	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.007246	0.397590	
chunk0092_396_1	chr19	37210386	37210839	+	0	NA	promoter-TSS (NM_152279)	promoter-TSS (NM_152279)	-63	NM_152279	92285	Hs.390568	NM_152279	ENSG00000245680	ZNF585B	SZFP41	zinc finger protein 585B	protein-coding	0.050773	0.484581	
chunk0128_332_1	chr3	112025140	112025490	+	0	NA	Intergenic	Intergenic	-14303	NR_026734	344805	Hs.435490	NM_001042575	ENSG00000176040	TMPRSS7	-	transmembrane serine protease 7	protein-coding	0.005714	0.418803	163(GGGGACAATCTGTGCC,-,0.00),164(GGGACAATCTGTGCCT,+,0.00)
chunk0195_171_1	chr8	95905723	95906030	+	0	NA	Intergenic	L1ME4b|LINE|L1	42472	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.003257	0.305195	
chunk0035_389_1	chr11	56351085	56351388	+	0	NA	Intergenic	L1ME2|LINE|L1	5197	NM_001002907	390157	Hs.553748	NM_001002907	ENSG00000150261	OR8K1	OR11-182|OR8N1P	olfactory receptor family 8 subfamily K member 1	protein-coding	0.006601	0.315789	
chunk0079_69_1	chr17	11365813	11366200	+	0	NA	intron (NM_001173461, intron 2 of 3)	L2a|LINE|L2	124583	NM_207386	388336	Hs.592124	NM_175903	ENSG00000188803	SHISA6	-	shisa family member 6	protein-coding	0.000000	0.409794	151(GAGGACAGAGAGTTCC,-,0.00),152(AGGACAGAGAGTTCCA,+,0.00)
chunk0200_354_1	chr9	25465299	25465540	+	0	NA	Intergenic	Intergenic	213439	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.000000	0.322314	
chunk0206_158_1	chr9	121609863	121610320	+	0	NA	intron (NM_032552, intron 1 of 16)	intron (NM_032552, intron 1 of 16)	42989	NM_032552	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.008753	0.521834	
chunk0089_278_1	chr18	62870738	62870957	+	0	NA	intron (NM_194449, intron 4 of 16)	intron (NM_194449, intron 4 of 16)	155408	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.000000	0.372727	
chunk0042_318_1	chr12	8827759	8828223	+	0	NA	intron (NM_144670, intron 3 of 35)	L1MA3|LINE|L1	5519	NM_144670	144568	Hs.620532	NM_144670	ENSG00000166535	A2ML1	CPAMD9|OMS|p170	alpha-2-macroglobulin like 1	protein-coding	0.004310	0.529032	
chunk0071_335_1	chr15	87941648	87942044	+	0	NA	intron (NM_002530, intron 14 of 18)	intron (NM_002530, intron 14 of 18)	-310884	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.015152	0.463476	
chunk0160_414_1	chr5	164062662	164063062	+	0	NA	Intergenic	Intergenic	404540	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.010000	0.411471	124(AAGGACGCGATGTTCT,-,0.00),125(AGGACGCGATGTTCTA,+,0.00)
chunk0020_455_1	chr1	242365468	242365820	+	0	NA	intron (NM_152666, intron 2 of 10)	intron (NM_152666, intron 2 of 10)	83838	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.014205	0.461756	
chunk0146_144_1	chr4	159556088	159556823	+	0	NA	Intergenic	Intergenic	288609	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.002721	0.357337	
chunk0062_444_1	chr14	75450296	75451015	+	0	NA	intron (NM_001135047, intron 2 of 3)	MIRc|SINE|MIR	18521	NM_001135049	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.009736	0.545833	
chunk0140_348_1	chr4	74054593	74054874	+	0	NA	non-coding (NR_026769, exon 1 of 1)	non-coding (NR_026769, exon 1 of 1)	666	NR_026769	10895	Hs.3134	NM_006692	ENSG00000248848	PPBPP2	PPBPL2|SPBPBP	pro-platelet basic protein pseudogene 2	pseudo	0.003559	0.485816	185(GGGCACAAAGTGATCT,-,0.00),186(GGCACAAAGTGATCTG,+,0.00)
chunk0026_283_1	chr10	67410826	67411025	+	0	NA	intron (NM_001291133, intron 6 of 8)	L1MA8|LINE|L1	-7515	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.000000	0.350000	91(GAGAACATTATGTTAC,-,0.00)
chunk0121_2_1	chr3	14336375	14336726	+	0	NA	Intergenic	L1ME5|LINE|L1	16018	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.011396	0.446023	
chunk0142_202_1	chr4	97275460	97276032	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-91180	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.005245	0.406632	
chunk0155_360_1	chr5	97244196	97244715	+	0	NA	Intergenic	Intergenic	-61154	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.001927	0.311538	
chunk0144_98_1	chr4	128504387	128504677	+	0	NA	intron (NR_125882, intron 6 of 8)	LTR1E|LTR|ERV1	76516	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.010345	0.512027	
chunk0202_400_1	chr9	81371941	81372153	+	0	NA	Intergenic	Intergenic	317488	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.028302	0.516432	
chunk0128_274_1	chr3	110710500	110710847	+	0	NA	Intergenic	Intergenic	359286	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.005764	0.393678	
chunk0073_402_1	chr16	16096607	16097387	+	0	NA	intron (NM_004996, intron 19 of 30)	L2a|LINE|L2	126474	NM_001171	368	Hs.442182	NM_001171	ENSG00000091262	ABCC6	ABC34|ARA|EST349056|GACI2|MLP1|MOAT-E|MOATE|MRP6|PXE|PXE1|URG7	ATP binding cassette subfamily C member 6	protein-coding	0.023077	0.481434	
chunk0005_315_1	chr1	60637251	60638140	+	0	NA	Intergenic	Intergenic	187889	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.003375	0.382022	
chunk0078_356_1	chr16	87230991	87231588	+	0	NA	Intergenic	L1ME4b|LINE|L1	19174	NR_110939	101928708	Hs.585717	NR_110939	ENSG00000261095	LOC101928708	-	uncharacterized LOC101928708	ncRNA	0.006700	0.372910	
chunk0047_4_1	chr12	65036724	65037026	+	0	NA	Intergenic	L1PA16|LINE|L1	84691	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.003311	0.363036	
chunk0091_33_1	chr19	3555398	3555600	+	0	NA	intron (NM_001287529, intron 1 of 9)	intron (NM_001287529, intron 1 of 9)	2085	NM_174983	126321	Hs.656901	NM_021731	ENSG00000161091	MFSD12	C19orf28|PP3501	major facilitator superfamily domain containing 12	protein-coding	0.039604	0.546798	
chunk0072_414_1	chr15	100933857	100934128	+	0	NA	intron (NM_024652, intron 2 of 33)	HAL1ME|LINE|L1	14777	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.003690	0.297794	
chunk0193_182_1	chr8	75132744	75133351	+	0	NA	Intergenic	Intergenic	132893	NM_001286777	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.003295	0.315789	
chunk0047_293_1	chr12	73549976	73550375	+	0	NA	Intergenic	Intergenic	390985	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.005013	0.392500	
chunk0087_169_1	chr18	35041297	35041638	+	0	NA	promoter-TSS (NR_046177)	promoter-TSS (NR_046177)	107	NM_001256420	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.082111	0.652047	
chunk0208_176_1	chrX	16971593	16972003	+	0	NA	intron (NM_004726, intron 1 of 17)	L1MB5|LINE|L1	25107	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.004878	0.340633	173(TTGAACAAACTGTTCT,-,0.00),174(TGAACAAACTGTTCTT,+,0.00)
chunk0208_167_1	chrX	16615945	16616401	+	0	NA	intron (NM_019857, intron 16 of 18)	intron (NM_019857, intron 16 of 18)	10912	NR_039762	100616428		NR_039762	ENSG00000265144	MIR548AM	-	microRNA 548am	ncRNA	0.008772	0.424508	
chunk0077_119_1	chr16	78324028	78324258	+	0	NA	intron (NM_016373, intron 5 of 8)	MIRb|SINE|MIR	224730	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.008696	0.450216	
chunk0189_7_1	chr8	19456914	19457150	+	0	NA	intron (NM_001130518, intron 5 of 9)	L3|LINE|CR1	143056	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.008475	0.434599	
chunk0134_88_1	chr3	176722504	176722978	+	0	NA	Intergenic	Intergenic	-87209	NR_109968	100505547	Hs.253350	NR_109968		LINC01208	-	long intergenic non-protein coding RNA 1208	ncRNA	0.008439	0.435789	
chunk0045_370_1	chr12	52093180	52093695	+	0	NA	promoter-TSS (NR_120440)	promoter-TSS (NR_120440)	-132	NR_120440	26628	Hs.524431	NR_120438	ENSG00000257542	OR7E47P	OR7E141	olfactory receptor family 7 subfamily E member 47 pseudogene	pseudo	0.015534	0.447674	
chunk0095_441_1	chr2	25311265	25311526	+	0	NA	intron (NM_175629, intron 2 of 22)	intron (NM_175629, intron 2 of 22)	17326	NR_031570	100302246		NR_031570	ENSG00000221445	MIR1301	MIRN1301|hsa-mir-1301|mir-1301	microRNA 1301	ncRNA	0.019157	0.667939	
chunk0134_27_1	chr3	175552742	175553590	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	183626	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.001179	0.306243	
chunk0024_393_1	chr10	44964146	44964474	+	0	NA	intron (NM_032023, intron 1 of 10)	intron (NM_032023, intron 1 of 10)	4539	NM_032023	83937	Hs.522895	NM_032023	ENSG00000107551	RASSF4	AD037	Ras association domain family member 4	protein-coding	0.018293	0.613982	165(GGGGACAGAGTGTCCT,-,0.00),166(GGGACAGAGTGTCCTC,+,0.00)
chunk0177_122_1	chr7	22334427	22334707	+	0	NA	intron (NM_012294, intron 1 of 25)	intron (NM_012294, intron 1 of 25)	22347	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.003571	0.384342	
chunk0115_190_1	chr21	26124511	26125114	+	0	NA	intron (NM_001136131, intron 1 of 15)	intron (NM_001136131, intron 1 of 15)	15578	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.009950	0.427152	
chunk0125_335_1	chr3	71051851	71052342	+	0	NA	intron (NM_001244812, intron 4 of 15)	intron (NM_001244812, intron 4 of 15)	12827	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.006110	0.418699	
chunk0019_46_1	chr1	224113267	224113532	+	0	NA	promoter-TSS (NM_001136115)	promoter-TSS (NM_001136115)	-688	NM_015176	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.015094	0.315789	
chunk0158_327_1	chr5	132897734	132898408	+	0	NA	intron (NM_014423, intron 10 of 20)	intron (NM_014423, intron 10 of 20)	24405	NM_052971	116842	Hs.337588	NM_052971	ENSG00000164406	LEAP2	LEAP-2	liver enriched antimicrobial peptide 2	protein-coding	0.007418	0.371852	
chunk0081_290_1	chr17	44708411	44708632	+	0	NA	promoter-TSS (NM_145663)	promoter-TSS (NM_145663)	-87	NM_145663	80174	Hs.369998	NM_025104	ENSG00000161692	DBF4B	ASKL1|CHIFB|DRF1|ZDBF1B	DBF4 zinc finger B	protein-coding	0.054299	0.504505	
chunk0185_384_1	chr7	133301066	133301833	+	0	NA	intron (NM_001037126, intron 3 of 9)	intron (NM_001037126, intron 3 of 9)	10568	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.005215	0.395833	44(AGGACTCCCTGATCCT,+,0.00)
chunk0034_127_1	chr11	28483524	28484201	+	0	NA	Intergenic	Intergenic	-6314	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.002954	0.331858	
chunk0008_312_1	chr1	95171855	95172306	+	0	NA	intron (NR_125949, intron 3 of 3)	MLT1C|LTR|ERVL-MaLR	54157	NM_001199691	100527978	Hs.483512	NM_001199691	ENSG00000271092	TLCD4-RWDD3	TMEM56-RWDD3	TLCD4-RWDD3 readthrough	protein-coding	0.006652	0.444690	
chunk0122_61_1	chr3	28810892	28811091	+	0	NA	Intergenic	LTR1A1|LTR|ERV1	235713	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.020101	0.570000	
chunk0203_139_1	chr9	85521195	85522010	+	0	NA	Intergenic	Intergenic	220427	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.029448	0.475490	368(GAGTACACACTGTTAT,-,0.00)
chunk0108_208_1	chr2	233097512	233097924	+	0	NA	intron (NM_001017915, intron 2 of 26)	L1M5|LINE|L1	37751	NM_005541	3635	Hs.262886	NM_005541	ENSG00000168918	INPP5D	SHIP|SHIP-1|SHIP1|SIP-145|hp51CN|p150Ship	inositol polyphosphate-5-phosphatase D	protein-coding	0.007282	0.389831	
chunk0101_400_1	chr2	138831199	138831919	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-51318	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.004167	0.335645	
chunk0147_152_1	chr4	175689395	175689839	+	0	NA	intron (NM_001261448, intron 2 of 6)	L1MB1|LINE|L1	98059	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.006757	0.382022	
chunk0043_19_1	chr12	13039333	13040011	+	0	NA	Intergenic	Intergenic	-4709	NM_020853	57613	Hs.132660	NM_020853	ENSG00000084444	FAM234B	KIAA1467	family with sequence similarity 234 member B	protein-coding	0.008850	0.438881	
chunk0067_149_1	chr15	43294239	43294746	+	0	NA	intron (NM_052955, intron 1 of 12)	MIRb|SINE|MIR	7763	NM_052955	116179	Hs.164661	NM_052955	ENSG00000159495	TGM7	TGMZ	transglutaminase 7	protein-coding	0.015779	0.460630	
chunk0183_231_1	chr7	106912283	106912693	+	0	NA	Intergenic	MIRb|SINE|MIR	47009	NM_002649	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.004878	0.386861	
chunk0113_37_1	chr20	49860766	49861420	+	0	NA	intron (NR_048539, intron 7 of 13)	intron (NR_048539, intron 7 of 13)	48380	NR_048538	23315	Hs.444202	NM_015266	ENSG00000197818	SLC9A8	NHE-8|NHE8	solute carrier family 9 member A8	protein-coding	0.012232	0.490076	
chunk0108_329_1	chr2	235666359	235666691	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	160774	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.012048	0.480480	
chunk0194_43_1	chr8	81939837	81940404	+	0	NA	Intergenic	Charlie9|DNA|hAT-Charlie	-97834	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.299296	
chunk0210_239_1	chrX	82716682	82717253	+	0	NA	Intergenic	Intergenic	-791294	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.000000	0.374126	
chunk0109_78_1	chr20	1928116	1928438	+	0	NA	intron (NM_080792, intron 7 of 8)	L2c|LINE|L2	33097	NM_001040023	140885	Hs.581021	NM_080792	ENSG00000198053	SIRPA	BIT|CD172A|MFR|MYD-1|P84|PTPNS1|SHPS1|SIRP	signal regulatory protein alpha	protein-coding	0.027950	0.495356	
chunk0192_293_1	chr8	66546221	66546745	+	0	NA	Intergenic	Intergenic	53227	NM_152765	254778	Hs.268869	NM_152765	ENSG00000169085	VXN	C8orf46	vexin	protein-coding	0.000000	0.440000	
chunk0070_211_1	chr15	72375688	72376061	+	0	NA	promoter-TSS (NR_027262)	promoter-TSS (NR_027262)	-239	NR_027262	80072	Hs.591113	NM_025005	ENSG00000260339	HEXA-AS1	C15orf34	HEXA antisense RNA 1	ncRNA	0.091153	0.641711	
chunk0172_241_1	chr6	137173754	137174470	+	0	NA	promoter-TSS (NM_181309)	promoter-TSS (NM_181309)	-464	NM_052962	116379	Hs.126891	NM_052962	ENSG00000164485	IL22RA2	CRF2-10|CRF2-S1|CRF2X|IL-22BP|IL-22R-alpha-2|IL-22RA2|ZCYTOR16	interleukin 22 receptor subunit alpha 2	protein-coding	0.006983	0.387727	417(GAAACAACTTGTTCTT,+,0.00)
chunk0080_261_1	chr17	30600462	30600750	+	0	NA	intron (NR_015341, intron 2 of 8)	CpG	-23712	NR_033420	6459	Hs.684860	NR_033420		SH3GL1P2	CNSA-P2|SH3GLP2	SH3 domain containing GRB2 like 1, endophilin A2 pseudogene 2	pseudo	0.107639	0.719723	
chunk0161_25_1	chr5	165781651	165782214	+	0	NA	Intergenic	Intergenic	1144438	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.008881	0.388298	
chunk0185_258_1	chr7	130368612	130369247	+	0	NA	TTS (NM_001127442)	TTS (NM_001127442)	-11442	NM_001868	1357	Hs.2879	NM_001868	ENSG00000091704	CPA1	CPA	carboxypeptidase A1	protein-coding	0.015748	0.542453	315(AGGCACACATTGTCCC,-,0.00),316(GGCACACATTGTCCCA,+,0.00)
chunk0148_223_1	chr5	9032344	9033031	+	0	NA	Intergenic	Intergenic	21208	NR_039779	100616326		NR_039779	ENSG00000266415	MIR4636	mir-4636	microRNA 4636	ncRNA	0.004367	0.417151	
chunk0051_416_1	chr12	122399062	122399261	+	0	NA	intron (NR_045382, intron 2 of 2)	MIR1_Amn|SINE|MIR	3619	NR_045382	100507066	Hs.624253	NR_045382		CLIP1-AS1	-	CLIP1 antisense RNA 1	ncRNA	0.005025	0.385000	
chunk0186_220_1	chr7	140080956	140081203	+	0	NA	Intergenic	Intergenic	-17358	NR_130117	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.024291	0.491935	
chunk0119_186_1	chr22	44126862	44127429	+	0	NA	intron (NM_001003828, intron 5 of 13)	intron (NM_001003828, intron 5 of 13)	-45811	NM_001137605	64098	Hs.658995	NM_022141	ENSG00000138964	PARVG	-	parvin gamma	protein-coding	0.003527	0.411972	
chunk0095_19_1	chr2	12320156	12320779	+	0	NA	intron (NR_110196, intron 4 of 5)	intron (NR_110196, intron 4 of 5)	121337	NR_037452	100500884		NR_037452	ENSG00000264089	MIR3681	-	microRNA 3681	ncRNA	0.012841	0.366987	
chunk0153_450_1	chr5	76404392	76405063	+	0	NA	intron (NM_006633, intron 1 of 35)	intron (NM_006633, intron 1 of 35)	1472	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.008942	0.498512	
chunk0166_362_1	chr6	51459889	51460411	+	0	NA	Intergenic	Intergenic	-161720	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.003831	0.382409	
chunk0148_185_1	chr5	7851562	7852086	+	0	NA	promoter-TSS (NM_001089584)	promoter-TSS (NM_001089584)	-334	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.019084	0.470476	
chunk0126_386_1	chr3	84389630	84389872	+	0	NA	Intergenic	L1PB4|LINE|L1	479824	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.008264	0.378601	
chunk0049_138_1	chr12	91718161	91718982	+	0	NA	Intergenic	Intergenic	423142	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.004872	0.324818	251(CAGAACAAGATGTACC,-,0.00),252(AGAACAAGATGTACCT,+,0.00),404(AAAGACACAGTGTTCC,-,0.00),405(AAGACACAGTGTTCCT,+,0.00),549(AGAAACATACTGTACT,-,0.00),550(GAAACATACTGTACTA,+,0.00)
chunk0199_460_1	chr9	14218378	14218633	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	-37703	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.003922	0.410156	
chunk0004_251_1	chr1	47684883	47685243	+	0	NA	Intergenic	Intergenic	-247746	NR_126355	102724077	Hs.159718	NR_126355		LINC01389	-	long intergenic non-protein coding RNA 1389	ncRNA	0.013889	0.479224	
chunk0120_292_1	chr3	9884512	9884851	+	0	NA	Intergenic	Intergenic	-4427	NM_001199551	63924	Hs.567562	NM_022094	ENSG00000187288	CIDEC	CIDE-3|CIDE3|FPLD5|FSP27	cell death inducing DFFA like effector c	protein-coding	0.014749	0.467647	
chunk0157_239_1	chr5	119555680	119556070	+	0	NA	Intergenic	LTR86A2|LTR|ERVL	-73684	NM_001163991	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.000000	0.427110	27(GGAAACATGCTGTGCC,-,0.00),28(GAAACATGCTGTGCCC,+,0.00)
chunk0150_312_1	chr5	37906165	37906856	+	0	NA	Intergenic	Intergenic	33085	NM_001278094	100861519	Hs.536820	NM_001278094		GDNF-AS1	GDNFOS	GDNF antisense RNA 1	ncRNA	0.007236	0.432081	
chunk0052_342_1	chr12	126521750	126522046	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	79417	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.006757	0.346801	
chunk0008_131_1	chr1	91817060	91817819	+	0	NA	intron (NR_036634, intron 2 of 17)	intron (NR_036634, intron 2 of 17)	68840	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.006588	0.372368	184(AAGAACATAACGTTCA,-,0.00),327(AAGAACACTATGATCA,-,0.00),328(AGAACACTATGATCAT,+,0.00),381(AAGAACACTATGACCT,-,0.00),382(AGAACACTATGACCTT,+,0.00)
chunk0017_176_1	chr1	207054775	207055319	+	0	NA	intron (NM_001018053, intron 2 of 14)	intron (NM_001018053, intron 2 of 14)	1772	NM_006212	5208	Hs.282702	NM_006212	ENSG00000123836	PFKFB2	PFK-2/FBPase-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding	0.001838	0.436697	
chunk0197_318_1	chr8	125029356	125029999	+	0	NA	intron (NM_014846, intron 27 of 28)	L2a|LINE|L2	31199	NM_003129	6713	Hs.71465	NM_003129	ENSG00000104549	SQLE	-	squalene epoxidase	protein-coding	0.010886	0.402174	
chunk0083_108_1	chr17	64626733	64627217	+	0	NA	intron (NM_022739, intron 1 of 18)	intron (NM_022739, intron 1 of 18)	35293	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.008264	0.350515	292(GAGGACAAGCTGATCC,-,0.00),293(AGGACAAGCTGATCCT,+,0.00)
chunk0204_194_1	chr9	96603717	96604338	+	0	NA	intron (NM_003671, intron 1 of 12)	intron (NM_003671, intron 1 of 12)	15803	NM_003671	8555	Hs.40582	NM_003671	ENSG00000081377	CDC14B	CDC14B3|Cdc14B1|Cdc14B2|hCDC14B	cell division cycle 14B	protein-coding	0.014493	0.413183	
chunk0178_253_1	chr7	36266816	36267058	+	0	NA	intron (NM_030636, intron 3 of 7)	L1MB5|LINE|L1	100236	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.012397	0.390947	
chunk0011_158_1	chr1	147612328	147612792	+	0	NA	intron (NM_004326, intron 4 of 9)	intron (NM_004326, intron 4 of 9)	57952	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.008621	0.503226	
chunk0075_195_1	chr16	52477549	52477779	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	69230	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.000000	0.424242	
chunk0186_342_1	chr7	143367876	143368342	+	0	NA	Intergenic	Intergenic	-5362	NM_001278297	9715	Hs.648908	NM_014690	ENSG00000159784	FAM131B	-	family with sequence similarity 131 member B	protein-coding	0.008584	0.513919	
chunk0093_370_1	chr19	55728731	55729014	+	0	NA	intron (NM_176820, intron 3 of 8)	intron (NM_176820, intron 3 of 8)	9530	NM_176820	338321	Hs.661568	NM_176820	ENSG00000185792	NLRP9	CLR19.1|NALP9|NOD6|PAN12	NLR family pyrin domain containing 9	protein-coding	0.007067	0.348592	125(GAGAACAGCATGGCCC,-,0.00)
chunk0174_133_1	chr6	157417385	157417733	+	0	NA	intron (NM_024630, intron 1 of 8)	L1ME4b|LINE|L1	36034	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.014368	0.406877	189(TGGCACATAGTGTGCC,-,0.00),190(GGCACATAGTGTGCCT,+,0.00)
chunk0044_317_1	chr12	33765478	33765957	+	0	NA	Intergenic	Intergenic	-256564	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.006263	0.358333	
chunk0118_261_1	chr22	33246546	33247109	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-188436	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.008881	0.379433	158(CAGCACATATTGTGCT,-,0.00),159(AGCACATATTGTGCTT,+,0.00),341(CAGCACAAAATGTGCT,-,0.00),342(AGCACAAAATGTGCTG,+,0.00)
chunk0147_396_1	chr4	186725724	186726016	+	0	NA	Intergenic	CpG-21708	-2037	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.061644	0.583618	
chunk0014_430_1	chr1	183507628	183507862	+	0	NA	intron (NM_001174061, intron 1 of 21)	intron (NM_001174061, intron 1 of 21)	35374	NM_201569	9887	Hs.591463	NM_014837	ENSG00000116698	SMG7	C1orf16|EST1C|SGA56M	SMG7 nonsense mediated mRNA decay factor	protein-coding	0.008547	0.306383	
chunk0187_354_1	chr7	157186522	157187021	+	0	NA	intron (NM_014671, intron 9 of 22)	intron (NM_014671, intron 9 of 22)	47810	NM_014671	9690	Hs.118351	NM_014671	ENSG00000009335	UBE3C	HECTH2	ubiquitin protein ligase E3C	protein-coding	0.018036	0.440000	
chunk0034_291_1	chr11	34749737	34750780	+	0	NA	Intergenic	Intergenic	117794	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.006711	0.407088	684(TTGTACAAGATGTTCC,-,0.00),685(TGTACAAGATGTTCCC,+,0.00)
chunk0145_182_1	chr4	147752186	147752625	+	0	NA	intron (NM_024605, intron 1 of 22)	intron (NM_024605, intron 1 of 22)	20103	NM_024605	79658	Hs.368631	NM_024605	ENSG00000071205	ARHGAP10	GRAF2|PS-GAP|PSGAP	Rho GTPase activating protein 10	protein-coding	0.011390	0.343182	
chunk0187_428_1	chr7	158662037	158662272	+	0	NA	intron (NR_104054, intron 19 of 30)	intron (NR_104054, intron 19 of 30)	42677	NR_104054	54892	Hs.18616	NM_017760	ENSG00000146918	NCAPG2	3KS|CAP-G2|CAPG2|LUZP5|MTB|hCAP-G2	non-SMC condensin II complex subunit G2	protein-coding	0.008511	0.343220	
chunk0126_20_1	chr3	73543001	73543746	+	0	NA	intron (NR_121660, intron 1 of 1)	intron (NR_121660, intron 1 of 1)	18305	NM_001303140	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.004027	0.426273	
chunk0124_296_1	chr3	57778924	57779192	+	0	NA	intron (NM_001304420, intron 1 of 21)	L1ME3E|LINE|L1	21802	NM_001304420	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.011194	0.342007	
chunk0038_116_1	chr11	83923167	83923491	+	0	NA	intron (NM_001142700, intron 7 of 19)	MIRc|SINE|MIR	-240904	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003086	0.393846	
chunk0149_350_1	chr5	27391328	27391710	+	0	NA	Intergenic	Intergenic	-80773	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.002618	0.347258	
chunk0154_316_1	chr5	83844684	83845042	+	0	NA	Intergenic	Intergenic	-123786	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.008380	0.423398	
chunk0027_217_1	chr10	76189538	76189910	+	0	NA	intron (NR_131178, intron 6 of 7)	MER119|DNA|hAT-Charlie	406963	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.002688	0.423592	
chunk0096_449_1	chr2	39566304	39566901	+	0	NA	intron (NR_037875, intron 5 of 5)	intron (NR_037875, intron 5 of 5)	-98896	NM_001167959	130733	Hs.40808	NM_152390	ENSG00000152154	TMEM178A	TMEM178	transmembrane protein 178A	protein-coding	0.005025	0.396321	
chunk0092_152_1	chr19	29209392	29209691	+	0	NA	intron (NM_006003, intron 1 of 1)	intron (NM_006003, intron 1 of 1)	3688	NM_006003	7386	Hs.743307	NM_006003	ENSG00000169021	UQCRFS1	RIP1|RIS1|RISP|UQCR5	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	protein-coding	0.000000	0.363333	
chunk0078_192_1	chr17	5112076	5112341	+	0	NA	5' UTR (NM_014519, exon 2 of 5)	5' UTR (NM_014519, exon 2 of 5)	-4230	NM_001304284	9098	Hs.448851	NM_004505	ENSG00000129204	USP6	HRP1|TRE17|TRE2|TRESMCR|Tre-2|USP6-short	ubiquitin specific peptidase 6	protein-coding	0.022642	0.526316	
chunk0069_308_1	chr15	65556377	65557071	+	0	NA	intron (NM_016395, intron 3 of 10)	intron (NM_016395, intron 3 of 10)	26235	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.014409	0.469065	
chunk0059_341_1	chr14	37001474	37001897	+	0	NA	intron (NM_030631, intron 1 of 9)	L2c|LINE|L2	-49294	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.004728	0.325472	
chunk0169_212_1	chr6	103111618	103112124	+	0	NA	Intergenic	Intergenic	1712886	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003953	0.353057	
chunk0179_320_1	chr7	50508501	50509261	+	0	NA	intron (NM_001242889, intron 4 of 12)	intron (NM_001242889, intron 4 of 12)	-22878	NR_033845	100129427	Hs.680434	NR_033845	ENSG00000226122	DDC-AS1	-	DDC antisense RNA 1	ncRNA	0.011842	0.501971	
chunk0030_100_1	chr10	112458028	112458400	+	0	NA	intron (NM_145206, intron 1 of 7)	intron (NM_145206, intron 1 of 7)	11216	NM_145206	143187	Hs.194554	NM_145206	ENSG00000151532	VTI1A	MMDS3|MVti1|VTI1RP2|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding	0.005376	0.380697	207(GAGAACAGGATGTTCC,-,0.00),208(AGAACAGGATGTTCCT,+,0.00)
chunk0013_391_1	chr1	172764537	172764736	+	0	NA	Intergenic	Intergenic	105628	NM_001302746	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.010050	0.460000	
chunk0135_56_1	chr3	185716746	185717147	+	0	NA	intron (NR_126326, intron 2 of 7)	intron (NR_126326, intron 2 of 7)	3694	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.014963	0.504975	
chunk0069_229_1	chr15	63891025	63891358	+	0	NA	Intergenic	Intergenic	-20172	NR_029944	494334		NR_029944	ENSG00000199156	MIR422A	MIRN422A	microRNA 422a	ncRNA	0.018018	0.529940	
chunk0020_153_1	chr1	233981180	233981668	+	0	NA	intron (NM_173508, intron 2 of 7)	L1MD2|LINE|L1	76712	NM_173508	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.018443	0.413088	
chunk0004_6_1	chr1	41881389	41882284	+	0	NA	intron (NR_038260, intron 1 of 2)	intron (NR_038260, intron 1 of 2)	36871	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.006704	0.360491	275(CAGAACAATCTGTTCT,-,0.00),276(AGAACAATCTGTTCTT,+,0.00)
chunk0117_446_1	chr21	46509652	46510092	+	0	NA	intron (NM_001146116, intron 7 of 37)	intron (NM_001146116, intron 7 of 37)	47401	NR_046400	100862692	Hs.737163	NR_046400	ENSG00000223692	DIP2A-IT1	-	DIP2A intronic transcript 1	ncRNA	0.015909	0.403628	
chunk0111_330_1	chr20	32744999	32745624	+	0	NA	Intergenic	Intergenic	-1303	NM_053041	149951	Hs.408427	NM_053041	ENSG00000149600	COMMD7	C20orf92|dJ1085F17.3	COMM domain containing 7	protein-coding	0.022400	0.500000	
chunk0143_171_1	chr4	110869367	110869728	+	0	NA	Intergenic	Intergenic	-8900	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.000000	0.350829	
chunk0200_288_1	chr9	22455162	22455757	+	0	NA	Intergenic	MIRb|SINE|MIR	8618	NM_022160	63951	Hs.371976	NM_022160	ENSG00000176399	DMRTA1	DMO|DMRT4	DMRT like family A1	protein-coding	0.016807	0.359060	
chunk0141_417_1	chr4	88614213	88614661	+	0	NA	intron (NM_014606, intron 3 of 25)	intron (NM_014606, intron 3 of 25)	22014	NM_001271602	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.000000	0.320713	
chunk0161_83_1	chr5	167128740	167128939	+	0	NA	Intergenic	Intergenic	-155999	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.015075	0.415000	
chunk0101_449_1	chr2	140013894	140014441	+	0	NA	Intergenic	Intergenic	572518	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.005484	0.372263	
chunk0038_103_1	chr11	83681026	83681314	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	1255	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.006944	0.391003	
chunk0012_33_1	chr1	155077812	155078164	+	0	NA	promoter-TSS (NM_004952)	promoter-TSS (NM_004952)	-884	NM_004952	1944	Hs.516656	NM_004952	ENSG00000143590	EFNA3	EFL2|EPLG3|Ehk1-L|LERK3	ephrin A3	protein-coding	0.005682	0.532578	
chunk0154_303_1	chr5	83418292	83418524	+	0	NA	Intergenic	Intergenic	-53266	NM_001164098	1462	Hs.643801	NM_004385	ENSG00000038427	VCAN	CSPG2|ERVR|GHAP|PG-M|WGN|WGN1	versican	protein-coding	0.000000	0.364807	
chunk0139_339_1	chr4	59409693	59410006	+	0	NA	Intergenic	Intergenic	-1512770	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.331210	
chunk0144_275_1	chr4	137631883	137632247	+	0	NA	Intergenic	L1PA13|LINE|L1	-99567	NM_001300828	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.002747	0.545205	
chunk0177_128_1	chr7	22377734	22378061	+	0	NA	Intergenic	Intergenic	-20983	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.006116	0.484756	130(GGGTACAGGCTGTCCT,-,0.00),131(GGTACAGGCTGTCCTT,+,0.00)
chunk0005_363_1	chr1	61496524	61496723	+	0	NA	Intergenic	Intergenic	-157619	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.015075	0.380000	
chunk0093_269_1	chr19	51364194	51364505	+	0	NA	intron (NM_001985, intron 1 of 5)	intron (NM_001985, intron 1 of 5)	2069	NM_001985	2109	Hs.348531	NM_001985	ENSG00000105379	ETFB	FP585|MADD	electron transfer flavoprotein subunit beta	protein-coding	0.012862	0.548077	
chunk0009_257_1	chr1	107162771	107163553	+	0	NA	intron (NM_001312688, intron 2 of 7)	intron (NM_001312688, intron 2 of 7)	15093	NM_001113226	22854	Hs.133046	NM_014917	ENSG00000162631	NTNG1	Lmnt1	netrin G1	protein-coding	0.001279	0.340996	
chunk0156_271_1	chr5	109529188	109529931	+	0	NA	Intergenic	Intergenic	-119585	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.005384	0.428763	
chunk0076_234_1	chr16	68931126	68931638	+	0	NA	intron (NM_024562, intron 14 of 17)	L1MB8|LINE|L1	87776	NM_024562	79613	Hs.13526	NM_024562	ENSG00000103047	TANGO6	TMCO7	transport and golgi organization 6 homolog	protein-coding	0.009766	0.407407	
chunk0024_230_1	chr10	38094770	38094982	+	0	NA	intron (NM_001178101, intron 1 of 6)	CpG	540	NM_003421	7587	Hs.292575	NM_003421	ENSG00000075407	ZNF37A	KOX21|ZNF37	zinc finger protein 37A	protein-coding	0.094340	0.657277	
chunk0028_150_1	chr10	86779149	86779640	+	0	NA	intron (NM_004329, intron 1 of 12)	L1MA5A|LINE|L1	22755	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.006110	0.367886	
chunk0094_157_1	chr2	5234588	5235008	+	0	NA	Intergenic	Intergenic	456320	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.004762	0.413302	
chunk0002_326_1	chr1	24343440	24344140	+	0	NA	intron (NM_021180, intron 11 of 15)	intron (NM_021180, intron 11 of 15)	20750	NM_021180	57822	Hs.657920	NM_021180	ENSG00000158055	GRHL3	SOM|TFCP2L4|VWS2	grainyhead like transcription factor 3	protein-coding	0.018571	0.556348	
chunk0081_333_1	chr17	46764964	46765192	+	0	NA	intron (NM_030753, intron 4 of 4)	intron (NM_030753, intron 4 of 4)	53682	NM_030753	7473	Hs.445884	NM_030753	ENSG00000108379	WNT3	INT4|TETAMS	Wnt family member 3	protein-coding	0.013158	0.480349	
chunk0048_63_1	chr12	78402556	78402995	+	0	NA	Intergenic	Intergenic	-461218	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.006834	0.377273	
chunk0098_237_1	chr2	74560555	74560761	+	0	NA	intron (NM_138804, intron 8 of 10)	intron (NM_138804, intron 8 of 10)	6273	NM_001381	1796	Hs.103854	NM_001381	ENSG00000115325	DOK1	P62DOK|pp62	docking protein 1	protein-coding	0.014563	0.594203	117(GAGTACATGGAGTTCT,-,0.00),118(AGTACATGGAGTTCTC,+,0.00)
chunk0204_426_1	chr9	103260032	103260307	+	0	NA	intron (NR_121578, intron 6 of 9)	intron (NR_121578, intron 6 of 9)	64864	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.000000	0.311594	213(AAGGACATTGTGTTTT,-,0.00),214(AGGACATTGTGTTTTC,+,0.00)
chunk0141_167_1	chr4	82491487	82492103	+	0	NA	intron (NM_001080506, intron 6 of 7)	FLAM_C|SINE|Alu	61315	NM_001292017	58478	Hs.18442	NM_021204	ENSG00000145293	ENOPH1	E1|MASA|MST145|mtnC	enolase-phosphatase 1	protein-coding	0.017857	0.470016	
chunk0188_93_1	chr8	8655624	8656118	+	0	NA	Intergenic	Intergenic	-46285	NM_194284	137075	Hs.183617	NM_194284	ENSG00000253958	CLDN23	CLDNL|hCG1646163	claudin 23	protein-coding	0.008097	0.438384	
chunk0144_346_1	chr4	139508693	139509373	+	0	NA	3' UTR (NM_030648, exon 8 of 8)	3' UTR (NM_030648, exon 8 of 8)	47736	NM_001306200	80854	Hs.480792	NM_030648	ENSG00000145391	SETD7	KMT7|SET7|SET7/9|SET9	SET domain containing 7, histone lysine methyltransferase	protein-coding	0.016176	0.493392	
chunk0147_158_1	chr4	175713412	175713802	+	0	NA	intron (NM_201592, intron 1 of 6)	intron (NM_201592, intron 1 of 6)	74069	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.010256	0.345269	
chunk0197_131_1	chr8	120069976	120070243	+	0	NA	Intergenic	Intergenic	-54999	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.022472	0.518657	110(GGGAACACACTGTTTA,-,0.00),111(GGAACACACTGTTTAC,+,0.00)
chunk0011_396_1	chr1	154141274	154141593	+	0	NA	exon (NM_001159484, exon 4 of 38)	exon (NM_001159484, exon 4 of 38)	13683	NM_001159484	91181	Hs.67639	NM_207308	ENSG00000143552	NUP210L	-	nucleoporin 210 like	protein-coding	0.009404	0.375000	
chunk0053_411_1	chr13	36907967	36908586	+	0	NA	intron (NM_001127217, intron 1 of 6)	intron (NM_001127217, intron 1 of 6)	11996	NM_005905	4093	Hs.123119	NM_005905	ENSG00000120693	SMAD9	MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B	SMAD family member 9	protein-coding	0.000000	0.343548	28(AAGGACAGCCAGTCCC,-,0.00),29(AGGACAGCCAGTCCCA,+,0.00)
chunk0051_403_1	chr12	122072521	122073114	+	0	NA	Intergenic	HAL1|LINE|L1	-5911	NM_014938	22877	Hs.437153	NM_014938	ENSG00000175727	MLXIP	MIR|MONDOA|bHLHe36	MLX interacting protein	protein-coding	0.006745	0.449495	
chunk0140_342_1	chr4	73899201	73899730	+	0	NA	Intergenic	L2c|LINE|L2	30073	NR_046035	2919	Hs.789	NM_001511	ENSG00000163739	CXCL1	FSP|GRO1|GROa|MGSA|MGSA-a|NAP-3|SCYB1	C-X-C motif chemokine ligand 1	protein-coding	0.007561	0.407547	
chunk0051_166_1	chr12	115998637	115999411	+	0	NA	intron (NM_015335, intron 14 of 30)	intron (NM_015335, intron 14 of 30)	149630	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.011628	0.394839	
chunk0043_304_1	chr12	22149075	22149813	+	0	NA	Intergenic	L1PA7|LINE|L1	103268	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.008130	0.370771	292(CTGAACAACCTGTTCT,-,0.00),293(TGAACAACCTGTTCTT,+,0.00),437(AAAGACACTGTGTACC,-,0.00),438(AAGACACTGTGTACCA,+,0.00)
chunk0004_349_1	chr1	51119103	51119767	+	0	NA	intron (NM_001136508, intron 3 of 4)	intron (NM_001136508, intron 3 of 4)	17201	NM_001136508	284546	Hs.176177	NM_001136508	ENSG00000204006	C1orf185	-	chromosome 1 open reading frame 185	protein-coding	0.007530	0.404511	
chunk0089_272_1	chr18	62744261	62744666	+	0	NA	intron (NM_194449, intron 1 of 16)	intron (NM_194449, intron 1 of 16)	29024	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.000000	0.431034	
chunk0202_449_1	chr9	82418484	82418916	+	0	NA	Intergenic	Intergenic	429928	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.011574	0.378753	
chunk0037_241_1	chr11	75351002	75351307	+	0	NA	intron (NM_004041, intron 1 of 15)	intron (NM_004041, intron 1 of 15)	677	NM_020251	408	Hs.503284	NM_004041	ENSG00000137486	ARRB1	ARB1|ARR1	arrestin beta 1	protein-coding	0.049180	0.571895	
chunk0199_110_1	chr9	3350291	3350996	+	0	NA	intron (NM_001282116, intron 2 of 16)	L1MC1|LINE|L1	44953	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.008511	0.372521	
chunk0128_338_1	chr3	112134584	112135287	+	0	NA	Intergenic	L1ME1|LINE|L1	-1630	NM_001190260	257144	Hs.49614	NM_152785	ENSG00000174500	GCSAM	GCAT2|GCET2|HGAL	germinal center associated signaling and motility	protein-coding	0.004267	0.375000	
chunk0142_329_1	chr4	101176002	101176257	+	0	NA	intron (NM_000944, intron 2 of 13)	intron (NM_000944, intron 2 of 13)	64743	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.011765	0.425781	
chunk0200_422_1	chr9	27689017	27689237	+	0	NA	Intergenic	L2c|LINE|L2	-115261	NM_145005	203228	Hs.493639	NM_018325	ENSG00000147894	C9orf72	ALSFTD|DENND9|DENNL72|FTDALS|FTDALS1	C9orf72-SMCR8 complex subunit	protein-coding	0.018182	0.438914	
chunk0198_399_1	chr8	141732133	141732439	+	0	NA	Intergenic	L2b|LINE|L2	54027	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.032680	0.602606	
chunk0138_147_1	chr4	37192044	37192285	+	0	NA	Intergenic	L2|LINE|L2	49827	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.004149	0.355372	
chunk0054_347_1	chr13	49560271	49560752	+	0	NA	intron (NM_018191, intron 4 of 12)	intron (NM_018191, intron 4 of 12)	25072	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.012474	0.371369	
chunk0127_246_1	chr3	97015651	97016201	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	201345	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.007273	0.348457	
chunk0164_5_1	chr6	17653042	17653774	+	0	NA	intron (NM_001278209, intron 11 of 22)	L1ME2z|LINE|L1	53121	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.010929	0.412005	
chunk0003_155_1	chr1	33178487	33178845	+	0	NA	intron (NM_018207, intron 1 of 4)	intron (NM_018207, intron 1 of 4)	3404	NM_018207	55223	Hs.656006	NM_018207	ENSG00000116525	TRIM62	DEAR1	tripartite motif containing 62	protein-coding	0.005587	0.465181	
chunk0001_179_1	chr1	7004246	7004592	+	0	NA	intron (NM_015215, intron 3 of 22)	intron (NM_015215, intron 3 of 22)	219095	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.002890	0.420749	249(CAGAACTATGTGTTCT,-,0.00),250(AGAACTATGTGTTCTG,+,0.00)
chunk0170_250_1	chr6	113679393	113680282	+	0	NA	Intergenic	AluJb|SINE|Alu	-29762	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.007874	0.379775	
chunk0016_185_1	chr1	198212587	198212898	+	0	NA	intron (NM_133494, intron 1 of 9)	L1PBa|LINE|L1	55764	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.006431	0.519231	
chunk0105_205_1	chr2	187847751	187847953	+	0	NA	Intergenic	Intergenic	-293360	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.330049	
chunk0163_420_1	chr6	17116062	17116261	+	0	NA	intron (NM_001190766, intron 2 of 4)	intron (NM_001190766, intron 2 of 4)	13903	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.005025	0.495000	94(CAGAACAGTCAGTGCT,-,0.00),95(AGAACAGTCAGTGCTG,+,0.00)
chunk0193_188_1	chr8	75317809	75318306	+	0	NA	Intergenic	Intergenic	-39168	NR_103849	101805492	Hs.571424	NR_103848		CASC9	ESCCAL-1|ESSCAL1|LINC00981|linc-JPH1	cancer susceptibility 9	ncRNA	0.002012	0.321285	
chunk0127_375_1	chr3	101978491	101979076	+	0	NA	intron (NR_026934, intron 2 of 3)	L1ME3G|LINE|L1	37924	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.005128	0.380546	
chunk0054_265_1	chr13	46561228	46561733	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	8319	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.007921	0.446640	305(GGCACACGATGTGTTC,+,0.00)
chunk0183_51_1	chr7	103980982	103981326	+	0	NA	intron (NM_005045, intron 1 of 64)	intron (NM_005045, intron 1 of 64)	8362	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.005814	0.379710	
chunk0041_446_1	chr11	134759399	134759722	+	0	NA	Intergenic	Intergenic	323078	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.027864	0.604938	
chunk0104_210_1	chr2	175948133	175948755	+	0	NA	intron (NM_030650, intron 8 of 12)	MER58A|DNA|hAT-Charlie	53901	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.001608	0.324238	
chunk0116_40_1	chr21	33480992	33481824	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-1399	NR_040016	757	Hs.433668	NM_006134	ENSG00000142188	TMEM50B	C21orf4|HCVP7TP3	transmembrane protein 50B	protein-coding	0.009615	0.466987	
chunk0017_417_1	chr1	213099546	213100389	+	0	NA	intron (NM_001287219, intron 4 of 14)	L1ME2z|LINE|L1	48734	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.004745	0.361374	
chunk0046_261_1	chr12	60710099	60710750	+	0	NA	Intergenic	L1M3de|LINE|L1	1021087	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001536	0.434049	
chunk0173_56_1	chr6	142368103	142368813	+	0	NA	intron (NM_020455, intron 3 of 25)	intron (NM_020455, intron 3 of 25)	66539	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.002817	0.278481	
chunk0094_20_1	chr2	1141370	1141569	+	0	NA	intron (NM_018968, intron 6 of 16)	ERVL-E-int|LTR|ERVL	190601	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.010050	0.405000	
chunk0071_106_1	chr15	81087697	81088424	+	0	NA	Intergenic	Intergenic	-46243	NM_173528	161502	Hs.130979	NM_173528	ENSG00000156206	CFAP161	C15orf26	cilia and flagella associated protein 161	protein-coding	0.005502	0.461538	
chunk0111_160_1	chr20	25118701	25118914	+	0	NA	Intergenic	Intergenic	29186	NR_027093	284798	Hs.334934	NR_027091	ENSG00000230725	LOC284798	-	uncharacterized LOC284798	ncRNA	0.018779	0.518692	
chunk0103_291_1	chr2	166156672	166158173	+	0	NA	intron (NR_110260, intron 2 of 11)	MIR3|SINE|MIR	-8290	NM_001202435	6323	Hs.22654	NM_006920	ENSG00000144285	SCN1A	EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI	sodium voltage-gated channel alpha subunit 1	protein-coding	0.003331	0.381491	
chunk0124_449_1	chr3	61576091	61576481	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	14717	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.002564	0.406650	
chunk0175_349_1	chr6	167550795	167551275	+	0	NA	Intergenic	Intergenic	128188	NR_117091	401286	Hs.487182	NR_117091	ENSG00000272549	LINC02538	-	long intergenic non-protein coding RNA 2538	ncRNA	0.035417	0.517672	239(ATACACACCCTGTCCT,-,0.00),240(TACACACCCTGTCCTT,+,0.00)
chunk0081_413_1	chr17	48619530	48619763	+	0	NA	Intergenic	Intergenic	-4707	NM_024016	3218	Hs.514292	NM_024016	ENSG00000120068	HOXB8	HOX2|HOX2D|Hox-2.4	homeobox B8	protein-coding	0.051502	0.474359	
chunk0083_401_1	chr17	71974307	71974695	+	0	NA	Intergenic	Intergenic	51478	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.010309	0.393316	179(GGGAACACGATGATCC,-,0.00),180(GGAACACGATGATCCC,+,0.00)
chunk0088_44_1	chr18	43936161	43936759	+	0	NA	Intergenic	L1PA13|LINE|L1	595237	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.011706	0.333890	
chunk0001_230_1	chr1	8169732	8170437	+	0	NA	Intergenic	Intergenic	-38588	NR_125998	102724539	Hs.516816	NR_125998	ENSG00000227634	LINC01714	-	long intergenic non-protein coding RNA 1714	ncRNA	0.017021	0.491501	169(TGAGACAGGATGTTCT,-,0.00),170(GAGACAGGATGTTCTG,+,0.00)
chunk0046_218_1	chr12	59404069	59404617	+	0	NA	Intergenic	Intergenic	-191697	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.000000	0.284153	
chunk0065_240_1	chr14	101239945	101240323	+	0	NA	Intergenic	Intergenic	167788	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.013228	0.509235	
chunk0146_302_1	chr4	165077051	165077484	+	0	NA	3' UTR (NM_001100389, exon 6 of 6)	3' UTR (NM_001100389, exon 6 of 6)	35605	NM_001100389	201931	Hs.704511	NM_152681	ENSG00000170088	TMEM192	-	transmembrane protein 192	protein-coding	0.006928	0.352535	
chunk0022_383_1	chr10	17606581	17606899	+	0	NA	intron (NM_014241, intron 1 of 6)	Charlie7|DNA|hAT-Charlie	10634	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.000000	0.329154	
chunk0200_297_1	chr9	22893195	22893444	+	0	NA	Intergenic	Intergenic	247119	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.012048	0.392000	
chunk0060_7_1	chr14	39174824	39175336	+	0	NA	promoter-TSS (NM_002687)	promoter-TSS (NM_002687)	-103	NM_002687	5411	Hs.409965	NM_002687	ENSG00000100941	PNN	DRS|DRSP|SDK3|memA	pinin, desmosome associated protein	protein-coding	0.058594	0.559454	
chunk0043_148_1	chr12	16332042	16332425	+	0	NA	Intergenic	Intergenic	-14909	NM_145792	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.010444	0.369792	
chunk0129_66_1	chr3	117609911	117610639	+	0	NA	Intergenic	MER70A|LTR|ERVL	688844	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.009615	0.408779	388(TAGAACAGGATGTCCT,-,0.00),389(AGAACAGGATGTCCTA,+,0.00)
chunk0049_431_1	chr12	97946329	97946718	+	0	NA	Intergenic	L3|LINE|CR1	-7402	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.007712	0.320513	
chunk0074_205_1	chr16	25084439	25085139	+	0	NA	Intergenic	Intergenic	26766	NR_120306	102723510	Hs.569596	NR_120306		LCMT1-AS1	-	LCMT1 antisense RNA 1	ncRNA	0.008571	0.348074	
chunk0009_10_1	chr1	99965620	99965998	+	0	NA	Intergenic	Intergenic	-3980	NM_012243	23443	Hs.448979	NM_012243	ENSG00000117620	SLC35A3	AMRS	solute carrier family 35 member A3	protein-coding	0.000000	0.337731	
chunk0039_422_1	chr11	107808335	107808596	+	0	NA	intron (NM_017515, intron 3 of 7)	intron (NM_017515, intron 3 of 7)	50723	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.003831	0.332061	
chunk0075_210_1	chr16	52578094	52578531	+	0	NA	intron (NR_033920, intron 2 of 3)	intron (NR_033920, intron 2 of 3)	28663	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.013730	0.397260	
chunk0099_324_1	chr2	99861371	99861880	+	0	NA	intron (NM_001025108, intron 6 of 23)	intron (NM_001025108, intron 6 of 23)	243958	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.003929	0.347059	
chunk0068_46_1	chr15	51493356	51493820	+	0	NA	intron (NM_015263, intron 19 of 42)	intron (NM_015263, intron 19 of 42)	129182	NM_015263	23312	Hs.511386	NM_015263	ENSG00000104093	DMXL2	DFNA71|PEPNS|RC3	Dmx like 2	protein-coding	0.006466	0.376344	
chunk0089_414_1	chr18	68715074	68715350	+	0	NA	promoter-TSS (NM_001093729)	promoter-TSS (NM_001093729)	-42	NM_001093729	79839	Hs.280781	NM_024781	ENSG00000150636	CCDC102B	ACY1L|AN|C18orf14|HsT1731	coiled-coil domain containing 102B	protein-coding	0.105072	0.642599	
chunk0074_84_1	chr16	21949126	21949381	+	0	NA	Intergenic	MER4A|LTR|ERV1	-3811	NM_003366	7385	Hs.528803	NM_003366	ENSG00000140740	UQCRC2	MC3DN5|QCR2|UQCR2	ubiquinol-cytochrome c reductase core protein 2	protein-coding	0.000000	0.359375	
chunk0114_351_1	chr21	18107071	18107636	+	0	NA	intron (NM_001204176, intron 2 of 6)	ERVL-E-int|LTR|ERVL	-137480	NM_024944	140578	Hs.283725	NM_024944	ENSG00000154645	CHODL	C21orf68|MT75|PRED12	chondrolectin	protein-coding	0.005310	0.415194	
chunk0110_227_1	chr20	15862088	15862683	+	0	NA	intron (NM_001033087, intron 4 of 13)	intron (NM_001033087, intron 4 of 13)	60929	NR_130925	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.010084	0.348993	
chunk0094_386_1	chr2	9975229	9975711	+	0	NA	intron (NM_198182, intron 8 of 15)	intron (NM_198182, intron 8 of 15)	23807	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.020747	0.422360	
chunk0188_17_1	chr8	6459911	6460185	+	0	NA	intron (NM_024596, intron 9 of 13)	L1MEg|LINE|L1	53456	NM_001172574	79648	Hs.593807	NM_024596	ENSG00000147316	MCPH1	BRIT1|MCT	microcephalin 1	protein-coding	0.036496	0.501818	
chunk0173_232_1	chr6	146542616	146542953	+	0	NA	promoter-TSS (NM_006834)	promoter-TSS (NM_006834)	-908	NM_006834	10981	Hs.287714	NM_006834	ENSG00000118508	RAB32	-	RAB32, member RAS oncogene family	protein-coding	0.011869	0.375740	
chunk0008_361_1	chr1	96632913	96633112	+	0	NA	Intergenic	Intergenic	-88593	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.450000	
chunk0017_337_1	chr1	211602326	211602663	+	0	NA	Intergenic	Intergenic	-23737	NM_021194	7779	Hs.519469	NM_021194	ENSG00000170385	SLC30A1	ZNT1|ZRC1	solute carrier family 30 member 1	protein-coding	0.008902	0.375740	
chunk0024_179_1	chr10	35889917	35890589	+	0	NA	Intergenic	Intergenic	111951	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.019345	0.466568	
chunk0036_52_1	chr11	59031073	59031911	+	0	NA	intron (NR_033853, intron 3 of 5)	intron (NR_033853, intron 3 of 5)	26960	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.003580	0.404052	
chunk0102_85_1	chr2	143426976	143427352	+	0	NA	intron (NM_018460, intron 6 of 13)	intron (NM_018460, intron 6 of 13)	297834	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.002660	0.318302	
chunk0166_132_1	chr6	44730589	44731091	+	0	NA	Intergenic	Intergenic	295199	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.009960	0.493042	
chunk0198_92_1	chr8	130288342	130288650	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	8037	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.003247	0.407767	288(AAGGAGACTCTGTCCT,-,0.00),289(AGGAGACTCTGTCCTC,+,0.00)
chunk0133_251_1	chr3	171677544	171678177	+	0	NA	intron (NM_001130081, intron 15 of 25)	intron (NM_001130081, intron 15 of 25)	132634	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.007899	0.462145	
chunk0068_325_1	chr15	57522316	57522613	+	0	NA	intron (NM_001252335, intron 11 of 19)	intron (NM_001252335, intron 11 of 19)	-69440	NM_001018091	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.020202	0.479866	
chunk0049_368_1	chr12	95717793	95718443	+	0	NA	intron (NM_021229, intron 3 of 9)	intron (NM_021229, intron 3 of 9)	68863	NR_077225	100132594	Hs.676211	NR_077225	ENSG00000257150	PGAM1P5	-	phosphoglycerate mutase 1 pseudogene 5	pseudo	0.009231	0.364055	
chunk0142_99_1	chr4	94334991	94335229	+	0	NA	intron (NM_014485, intron 1 of 5)	intron (NM_014485, intron 1 of 5)	7766	NM_014485	27306	Hs.128433	NM_014485	ENSG00000163106	HPGDS	GSTS|GSTS1|GSTS1-1|PGD2|PGDS	hematopoietic prostaglandin D synthase	protein-coding	0.004202	0.493724	
chunk0064_81_1	chr14	90554333	90554715	+	0	NA	intron (NM_001010854, intron 19 of 19)	intron (NM_001010854, intron 19 of 19)	-88105	NR_110134	101928909	Hs.662545	NR_110134	ENSG00000259163	LOC101928909	-	uncharacterized LOC101928909	ncRNA	0.034031	0.582245	233(TGGCACAGGCTGTCAC,-,0.00),234(GGCACAGGCTGTCACT,+,0.00)
chunk0140_39_1	chr4	66543303	66543570	+	0	NA	Intergenic	L1M1|LINE|L1	266612	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.007491	0.514925	
chunk0156_69_1	chr5	103553375	103554012	+	0	NA	intron (NM_001300741, intron 5 of 6)	L1ME3C|LINE|L1	9108	NM_001300741	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.004710	0.346395	
chunk0053_331_1	chr13	34347857	34348176	+	0	NA	Intergenic	Intergenic	292669	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.012539	0.431250	5(AAGAACTAATTGTGCT,-,0.00),6(AGAACTAATTGTGCTG,+,0.00)
chunk0173_374_1	chr6	149532367	149532633	+	0	NA	intron (NM_139126, intron 7 of 12)	HAL1M8|LINE|L1	13602	NM_139126	85313	Hs.744238	NM_139126	ENSG00000131013	PPIL4	HDCME13P	peptidylprolyl isomerase like 4	protein-coding	0.000000	0.318352	124(AGATACACAGTGTGCT,-,0.00),125(GATACACAGTGTGCTC,+,0.00)
chunk0072_278_1	chr15	97984103	97984433	+	0	NA	Intergenic	Intergenic	23565	NM_183376	91947	Hs.6093	NM_183376	ENSG00000140450	ARRDC4	-	arrestin domain containing 4	protein-coding	0.003030	0.395770	
chunk0107_145_1	chr2	215045516	215046112	+	0	NA	intron (NR_103740, intron 8 of 54)	intron (NR_103740, intron 8 of 54)	-13728	NM_015657	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.005034	0.361809	
chunk0091_323_1	chr19	13240321	13240653	+	0	NA	intron (NM_023035, intron 31 of 46)	intron (NM_023035, intron 31 of 46)	90019	NM_004907	9592	Hs.501629	NM_004907	ENSG00000160888	IER2	ETR101	immediate early response 2	protein-coding	0.009036	0.504505	
chunk0023_256_1	chr10	27542005	27542548	+	0	NA	TTS (NM_021252)	TTS (NM_021252)	38102	NM_001256411	22931	Hs.406799	NM_021252	ENSG00000099246	RAB18	RAB18LI1|WARBM3	RAB18, member RAS oncogene family	protein-coding	0.011050	0.365809	
chunk0151_390_1	chr5	55390485	55390800	+	0	NA	intron (NM_015360, intron 19 of 26)	intron (NM_015360, intron 19 of 26)	82894	NM_015360	23517	Hs.274531	NM_015360	ENSG00000039123	MTREX	Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118	Mtr4 exosome RNA helicase	protein-coding	0.006349	0.401899	
chunk0088_227_1	chr18	48378347	48378923	+	0	NA	Intergenic	HAL1|LINE|L1	-160421	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.001736	0.363951	
chunk0055_284_1	chr13	64498925	64499332	+	0	NA	Intergenic	MER34D|LTR|ERV1	-655003	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.000000	0.360294	
chunk0010_17_1	chr1	112264458	112265019	+	0	NA	Intergenic	Intergenic	-131440	NM_018704	55917	Hs.744100	NM_018704	ENSG00000143079	CTTNBP2NL	-	CTTNBP2 N-terminal like	protein-coding	0.003565	0.446619	
chunk0128_418_1	chr3	114844571	114844882	+	0	NA	intron (NR_121662, intron 2 of 6)	L1MC|LINE|L1	-28307	NR_126422	104413890	Hs.612732	NR_126422	ENSG00000239946	ZBTB20-AS3	-	ZBTB20 antisense RNA 3	ncRNA	0.000000	0.323718	
chunk0121_210_1	chr3	21660205	21660644	+	0	NA	intron (NM_024697, intron 2 of 7)	intron (NM_024697, intron 2 of 7)	90900	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.004556	0.363636	
chunk0197_438_1	chr8	127560162	127560783	+	0	NA	Intergenic	L2|LINE|L2	-78333	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.012882	0.408360	
chunk0052_39_1	chr13	20814077	20814276	+	0	NA	intron (NM_022459, intron 9 of 22)	intron (NM_022459, intron 9 of 22)	-40258	NM_174928	221143	Hs.26674	NM_174928	ENSG00000150456	EEF1AKMT1	ESP13|N6AMT2	EEF1A lysine methyltransferase 1	protein-coding	0.005025	0.340000	
chunk0050_99_1	chr12	101909272	101909672	+	0	NA	intron (NM_018370, intron 4 of 6)	intron (NM_018370, intron 4 of 6)	32145	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.010000	0.356608	
chunk0022_21_1	chr10	7683935	7684334	+	0	NA	Intergenic	L1PA16|LINE|L1	-17136	NM_001001851	80760	Hs.498586	NM_030569	ENSG00000123243	ITIH5	ITI-HC5|PP14776	inter-alpha-trypsin inhibitor heavy chain 5	protein-coding	0.007519	0.345000	
chunk0193_197_1	chr8	75787784	75788241	+	0	NA	Intergenic	Intergenic	248044	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.002188	0.286026	
chunk0133_349_1	chr3	173132240	173132675	+	0	NA	intron (NM_031955, intron 1 of 10)	L1ME3A|LINE|L1	8811	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.000000	0.293578	
chunk0150_432_1	chr5	40414971	40415266	+	0	NA	Intergenic	Intergenic	-264812	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.013559	0.456081	
chunk0015_305_1	chr1	188964865	188965087	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	1512653	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004505	0.430493	
chunk0147_451_1	chr4	188182063	188182582	+	0	NA	Intergenic	L1MC1|LINE|L1	42878	NM_178556	339976	Hs.348618	NM_178556	ENSG00000184108	TRIML1	RNF209	tripartite motif family like 1	protein-coding	0.011561	0.371154	
chunk0090_409_1	chr18	78829135	78829401	+	0	NA	Intergenic	Intergenic	-151007	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.033835	0.602996	167(AGGCTCACGCTGTTCA,-,0.00),168(GGCTCACGCTGTTCAT,+,0.00)
chunk0039_288_1	chr11	102685876	102686429	+	0	NA	Intergenic	Intergenic	19585	NM_022122	64066	Hs.534479	NM_022122	ENSG00000137675	MMP27	MMP-27	matrix metallopeptidase 27	protein-coding	0.001808	0.389892	
chunk0089_164_1	chr18	59098017	59098524	+	0	NA	Intergenic	L1MA2|LINE|L1	-41587	NM_001307941	90701	Hs.45107	NM_033280	ENSG00000166562	SEC11C	SEC11L3|SPC21|SPCS4C	SEC11 homolog C, signal peptidase complex subunit	protein-coding	0.007890	0.395669	
chunk0168_294_1	chr6	91351604	91352096	+	0	NA	Intergenic	Intergenic	-169810	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.006098	0.407708	
chunk0014_310_1	chr1	181101992	181102768	+	0	NA	Intergenic	Intergenic	13878	NM_016545	51278	Hs.15725	NM_016545	ENSG00000162783	IER5	SBBI48	immediate early response 5	protein-coding	0.005155	0.460746	
chunk0125_113_1	chr3	65662022	65662432	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-231589	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.002439	0.396594	168(GGGTACACTCTGTGCC,-,0.00),169(GGTACACTCTGTGCCC,+,0.00)
chunk0202_296_1	chr9	77851840	77852226	+	0	NA	intron (NM_002072, intron 2 of 6)	Tigger19b|DNA|TcMar-Tigger	179416	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.005181	0.403101	
chunk0184_306_1	chr7	120079621	120080163	+	0	NA	Intergenic	LTR53|LTR|ERVL	-172517	NR_131963	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.005535	0.359116	
chunk0186_39_1	chr7	136046053	136046502	+	0	NA	Intergenic	Intergenic	-68821	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.002227	0.446667	171(GGGTACAGCCTGTTCT,-,0.00),172(GGTACAGCCTGTTCTT,+,0.00)
chunk0212_410_1	chrX	151993921	151994519	+	0	NA	Intergenic	Intergenic	-19541	NM_004961	2564	Hs.22785	NM_004961	ENSG00000102287	GABRE	-	gamma-aminobutyric acid type A receptor epsilon subunit	protein-coding	0.005017	0.419032	
chunk0106_323_1	chr2	205637630	205637974	+	0	NA	Intergenic	MIRb|SINE|MIR	-44698	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.017442	0.524638	181(TGAGACACAGTGTCCT,-,0.00),182(GAGACACAGTGTCCTC,+,0.00)
chunk0041_299_1	chr11	129642929	129643641	+	0	NA	Intergenic	Intergenic	-26016	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.011236	0.476858	
chunk0021_251_1	chr1	243363026	243363415	+	0	NA	intron (NM_006642, intron 12 of 17)	intron (NM_006642, intron 12 of 17)	17044	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.007712	0.382051	
chunk0161_107_1	chr5	167448063	167448865	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	163626	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.013716	0.378580	
chunk0062_189_1	chr14	69767744	69768427	+	0	NA	promoter-TSS (NR_029378)	promoter-TSS (NR_029378)	-372	NR_029378	100289511	Hs.729250	NR_029378		LOC100289511	-	uncharacterized LOC100289511	ncRNA	0.051245	0.504386	
chunk0114_249_1	chr21	16035097	16035369	+	0	NA	Intergenic	L2a|LINE|L2	-35289	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.003676	0.296703	
chunk0177_421_1	chr7	27764254	27764453	+	0	NA	intron (NM_001206902, intron 3 of 15)	L1MC4a|LINE|L1	24258	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.005025	0.345000	
chunk0131_256_1	chr3	149658874	149659525	+	0	NA	intron (NR_040250, intron 1 of 2)	intron (NR_040250, intron 1 of 2)	989	NR_040250	100128025	Hs.594912	NR_040250	ENSG00000241313	WWTR1-AS1	-	WWTR1 antisense RNA 1	ncRNA	0.032258	0.507669	418(GAGAACTGTATGTTCT,-,0.00),419(AGAACTGTATGTTCTT,+,0.00)
chunk0034_67_1	chr11	27162219	27162559	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	56379	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.002941	0.422287	162(CTGAACTCTCTGTTCC,-,0.00),163(TGAACTCTCTGTTCCC,+,0.00)
chunk0198_475_1	chr8	145007074	145007312	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-4294	NR_023392	286101	Hs.367856	NR_023392		ZNF252P	ZNF252	zinc finger protein 252, pseudogene	pseudo	0.012605	0.430962	
chunk0197_361_1	chr8	125836039	125836580	+	0	NA	Intergenic	Intergenic	114888	NR_038446	100130231	Hs.729642	NR_038446	ENSG00000245164	LINC00861	-	long intergenic non-protein coding RNA 861	ncRNA	0.007394	0.346863	
chunk0028_289_1	chr10	91433332	91433708	+	0	NA	intron (NM_001284274, intron 2 of 21)	L1ME4b|LINE|L1	23235	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.002660	0.299735	
chunk0162_268_1	chr6	5428290	5428642	+	0	NA	intron (NM_006567, intron 3 of 6)	intron (NM_006567, intron 3 of 6)	29609	NR_125848	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.005682	0.320113	
chunk0063_364_1	chr14	85861858	85862243	+	0	NA	Intergenic	Intergenic	-72628	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.000000	0.349741	
chunk0199_295_1	chr9	6788592	6789052	+	0	NA	intron (NR_130707, intron 1 of 14)	intron (NR_130707, intron 1 of 14)	31181	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.013043	0.509761	
chunk0078_14_1	chr17	434538	435129	+	0	NA	Intergenic	L1M5|LINE|L1	11107	NM_182705	359845	Hs.345588	NM_182705	ENSG00000183688	RFLNB	CFM1|FAM101B	refilin B	protein-coding	0.010152	0.353041	278(AGGAACACGGTGTACT,-,0.00),279(GGAACACGGTGTACTT,+,0.00)
chunk0112_226_1	chr20	41003027	41003417	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-25600	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.007692	0.488491	144(GGAAACACTTTGTGCC,-,0.00),145(GAAACACTTTGTGCCT,+,0.00)
chunk0055_352_1	chr13	70390669	70391000	+	0	NA	Intergenic	Intergenic	-282341	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.009063	0.379518	
chunk0184_87_1	chr7	113176918	113177170	+	0	NA	Intergenic	Intergenic	-58462	NR_015442									0.011905	0.339921	
chunk0141_337_1	chr4	87427489	87427915	+	0	NA	intron (NM_001248011, intron 1 of 6)	intron (NM_001248011, intron 1 of 6)	5105	NM_198038	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.002347	0.316159	
chunk0145_221_1	chr4	148172246	148172526	+	0	NA	intron (NM_000901, intron 4 of 8)	intron (NM_000901, intron 4 of 8)	270134	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.007143	0.362989	
chunk0071_113_1	chr15	81380107	81380393	+	0	NA	non-coding (NR_120365, exon 6 of 7)	non-coding (NR_120365, exon 6 of 7)	-6173	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.010490	0.355401	
chunk0101_296_1	chr2	134778608	134779071	+	0	NA	Intergenic	Intergenic	-59777	NM_138326	130013	Hs.655728	NM_138326	ENSG00000153086	ACMSD	-	aminocarboxymuconate semialdehyde decarboxylase	protein-coding	0.010799	0.392241	
chunk0118_218_1	chr22	32055024	32055468	+	0	NA	intron (NM_000343, intron 2 of 14)	intron (NM_000343, intron 2 of 14)	-3924	NM_001256314	6523	Hs.1964	NM_000343	ENSG00000100170	SLC5A1	D22S675|NAGT|SGLT1	solute carrier family 5 member 1	protein-coding	0.006757	0.426966	
chunk0081_406_1	chr17	48406998	48407469	+	0	NA	intron (NM_001075099, intron 1 of 12)	L1M6|LINE|L1	22999	NM_001075099	8631	Hs.316931	NM_003726	ENSG00000141293	SKAP1	HEL-S-81p|SCAP1|SKAP55	src kinase associated phosphoprotein 1	protein-coding	0.002123	0.317797	
chunk0018_302_1	chr1	220926104	220926446	+	0	NA	Intergenic	Intergenic	-46135	NR_046901	100873924	Hs.645593	NR_046901	ENSG00000257551	HLX-AS1	-	HLX antisense RNA 1	ncRNA	0.008772	0.460641	
chunk0135_374_1	chr3	190874435	190874658	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-3384	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.008969	0.455357	
chunk0120_427_1	chr3	13256018	13256525	+	0	NA	Intergenic	L1MB4|LINE|L1	164048	NM_024923	23225	Hs.475525	NM_024923	ENSG00000132182	NUP210	GP210|POM210	nucleoporin 210	protein-coding	0.013807	0.399606	
chunk0115_263_1	chr21	27816879	27817272	+	0	NA	Intergenic	MIR|SINE|MIR	94696	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.005089	0.451777	
chunk0080_218_1	chr17	29645360	29645846	+	0	NA	intron (NM_001282129, intron 14 of 15)	intron (NM_001282129, intron 14 of 15)	-24180	NM_032854	84940	Hs.143046	NM_032854	ENSG00000167549	CORO6	-	coronin 6	protein-coding	0.006173	0.406571	
chunk0098_145_1	chr2	69674212	69674780	+	0	NA	Intergenic	Intergenic	-30651	NM_014911	22848	Hs.468878	NM_014911	ENSG00000115977	AAK1	-	AP2 associated kinase 1	protein-coding	0.005282	0.377856	272(GGGAACACACTGTGAC,-,0.00)
chunk0068_11_1	chr15	50571340	50572011	+	0	NA	intron (NM_001301212, intron 36 of 38)	intron (NM_001301212, intron 36 of 38)	-24970	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.008942	0.333333	365(GGGAACACTTTGTTCT,-,0.00),366(GGAACACTTTGTTCTT,+,0.00)
chunk0102_23_1	chr2	141565565	141566045	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	565896	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.006250	0.330561	
chunk0182_248_1	chr7	97143978	97144685	+	0	NA	intron (NM_020186, intron 1 of 1)	L1PB1|LINE|L1	27738	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.007072	0.355932	
chunk0070_268_1	chr15	74011327	74012032	+	0	NA	intron (NM_033239, intron 2 of 7)	intron (NM_033239, intron 2 of 7)	17006	NM_033244	5371	Hs.526464	NM_002675	ENSG00000140464	PML	MYL|PP8675|RNF71|TRIM19	promyelocytic leukemia	protein-coding	0.004255	0.447592	
chunk0175_251_1	chr7	7099566	7099973	+	0	NA	Intergenic	Intergenic	-2983	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.002457	0.482843	
chunk0061_143_1	chr14	59448814	59449018	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	16425	NM_022571	64582	Hs.647573	NM_022571	ENSG00000181619	GPR135	HUMNPIIY20	G protein-coupled receptor 135	protein-coding	0.004902	0.419512	
chunk0126_157_1	chr3	77602063	77602262	+	0	NA	intron (NM_001290065, intron 20 of 26)	intron (NM_001290065, intron 20 of 26)	504150	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.015075	0.460000	
chunk0005_133_1	chr1	57085897	57086097	+	0	NA	intron (NM_021080, intron 6 of 16)	intron (NM_021080, intron 6 of 16)	-119857	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.005000	0.422886	47(GGGATCAAGATGTTCT,-,0.00)
chunk0056_248_1	chr13	89301019	89301670	+	0	NA	Intergenic	Intergenic	-64454	NR_131229	105616982	Hs.564527	NR_131229	ENSG00000232225	LINC01047	-	long intergenic non-protein coding RNA 1047	ncRNA	0.003072	0.303681	
chunk0021_6_1	chr10	264096	264342	+	0	NA	Intergenic	LTR56|LTR|ERV1	17867	NR_106988									0.012195	0.489879	
chunk0154_436_1	chr5	90172659	90173064	+	0	NA	intron (NR_120601, intron 4 of 5)	LTR101_Mam|LTR|ERVL	117210	NR_120601	101929495	Hs.346679	NR_120601		LINC01339	-	long intergenic non-protein coding RNA 1339	ncRNA	0.002469	0.374384	
chunk0104_195_1	chr2	175606305	175606983	+	0	NA	Intergenic	Intergenic	395701	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.011799	0.388807	
chunk0085_79_1	chr18	2118428	2118951	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	452814	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.005736	0.320611	
chunk0066_201_1	chr15	33502336	33502740	+	0	NA	intron (NM_001036, intron 2 of 103)	intron (NM_001036, intron 2 of 103)	191576	NM_001036	6263	Hs.709373	NM_001036	ENSG00000198838	RYR3	RYR-3	ryanodine receptor 3	protein-coding	0.007426	0.382716	
chunk0139_169_1	chr4	53927007	53927206	+	0	NA	Intergenic	Intergenic	60176	NR_027153	402176	Hs.452943	NM_001011538		RPL21P44	RPL21_17_477	ribosomal protein L21 pseudogene 44	pseudo	0.005025	0.350000	
chunk0122_194_1	chr3	32794313	32794664	+	0	NA	Intergenic	L2c|LINE|L2	-23530	NM_001039111	131405	Hs.113170	NM_001039111	ENSG00000206557	TRIM71	LIN-41|LIN41	tripartite motif containing 71	protein-coding	0.005698	0.480114	
chunk0016_23_1	chr1	192869293	192869513	+	0	NA	Intergenic	Intergenic	60364	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.009091	0.371041	91(CATTACAGTCTGTTCC,-,0.00),92(ATTACAGTCTGTTCCG,+,0.00)
chunk0086_371_1	chr18	26280234	26280547	+	0	NA	intron (NM_001293725, intron 5 of 14)	L1PA16|LINE|L1	53507	NM_001293725	6875	Hs.369519	NM_005640	ENSG00000141384	TAF4B	SPGF13|TAF2C2|TAFII105	TATA-box binding protein associated factor 4b	protein-coding	0.006390	0.353503	
chunk0098_443_1	chr2	82139841	82140318	+	0	NA	Intergenic	PABL_A|LTR|ERV1	-673133	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.010482	0.405858	
chunk0189_359_1	chr8	26984928	26985431	+	0	NA	Intergenic	HAL1b|LINE|L1	63784	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.001988	0.347222	250(AAGTACATGATGTTCT,-,0.00),251(AGTACATGATGTTCTA,+,0.00)
chunk0173_238_1	chr6	146779739	146779958	+	0	NA	intron (NM_024694, intron 29 of 35)	L1M4|LINE|L1	23976	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.004566	0.281818	
chunk0106_16_1	chr2	195639905	195640875	+	0	NA	Intergenic	Intergenic	-16418	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.005155	0.333677	
chunk0091_41_1	chr19	4053520	4053997	+	0	NA	intron (NM_015898, intron 2 of 2)	(GTGT)n|Simple_repeat|Simple_repeat	13060	NM_015898	51341	Hs.591384	NM_015898	ENSG00000178951	ZBTB7A	FBI-1|FBI1|LRF|TIP21|ZBTB7|ZNF857A|pokemon	zinc finger and BTB domain containing 7A	protein-coding	0.077568	0.577406	
chunk0160_272_1	chr5	157390347	157390957	+	0	NA	exon (NM_014376, exon 30 of 31)	exon (NM_014376, exon 30 of 31)	-44931	NM_001001343	408263	Hs.437066	NM_001001343	ENSG00000172568	FNDC9	C5orf40	fibronectin type III domain containing 9	protein-coding	0.019672	0.559738	
chunk0096_55_1	chr2	27309818	27310034	+	0	NA	exon (NM_002437, exon 8 of 8)	exon (NM_002437, exon 8 of 8)	-1664	NM_003353	7349	Hs.534363	NM_003353	ENSG00000163794	UCN	UI|UROC	urocortin	protein-coding	0.018519	0.516129	
chunk0009_394_1	chr1	110214481	110214832	+	0	NA	intron (NM_001039574, intron 1 of 3)	MIRb|SINE|MIR	3942	NM_004978	3749	Hs.153521	NM_004978	ENSG00000116396	KCNC4	C1orf30|HKSHIIIC|KSHIIIC|KV3.4	potassium voltage-gated channel subfamily C member 4	protein-coding	0.005698	0.443182	
chunk0061_445_1	chr14	65772866	65773272	+	0	NA	Intergenic	Intergenic	301967	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.007389	0.412776	
chunk0084_203_1	chr17	78128325	78128591	+	0	NA	intron (NM_007267, intron 1 of 19)	CpG	322	NM_001127198	11322	Hs.632227	NM_007267	ENSG00000141524	TMC6	EV1|EVER1|EVIN1|LAK-4P	transmembrane channel like 6	protein-coding	0.063910	0.719101	
chunk0120_287_1	chr3	9774351	9774979	+	0	NA	Intergenic	L1ME4c|LINE|L1	-4681	NM_003656	8536	Hs.434875	NM_003656	ENSG00000134072	CAMK1	CAMKI	calcium/calmodulin dependent protein kinase I	protein-coding	0.003185	0.340223	
chunk0055_196_1	chr13	61873632	61873888	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	155788	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.003906	0.443580	
chunk0203_270_1	chr9	88387319	88387810	+	0	NA	promoter-TSS (NM_006717)	promoter-TSS (NM_006717)	-818	NM_006717	10927	Hs.146804	NM_006717	ENSG00000106723	SPIN1	SPIN|TDRD24	spindlin 1	protein-coding	0.036660	0.524390	
chunk0067_224_1	chr15	45367325	45367626	+	0	NA	intron (NM_001482, intron 4 of 8)	intron (NM_001482, intron 4 of 8)	11307	NM_001482	2628	Hs.75335	NM_001482	ENSG00000171766	GATM	AGAT|AT|CCDS3	glycine amidinotransferase	protein-coding	0.013289	0.331126	
chunk0204_61_1	chr9	93443271	93443564	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-8279	NM_001286723	23196	Hs.372003	NM_014612	ENSG00000048828	FAM120A	C9orf10|HBVPTPAP|OSSA	family with sequence similarity 120A	protein-coding	0.000000	0.326531	240(GAGGACTGTCTGTTTT,-,0.00)
chunk0128_412_1	chr3	114704441	114704640	+	0	NA	intron (NM_015642, intron 4 of 9)	intron (NM_015642, intron 4 of 9)	38985	NR_039959	100616166		NR_039959	ENSG00000264623	MIR4796	mir-4796	microRNA 4796	ncRNA	0.000000	0.360000	
chunk0184_42_1	chr7	112239791	112239990	+	0	NA	intron (NM_021994, intron 1 of 11)	L1MA3|LINE|L1	33302	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.000000	0.285000	
chunk0021_300_1	chr1	244719522	244720165	+	0	NA	Intergenic	L1MC2|LINE|L1	66795	NR_123736	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.006221	0.340062	
chunk0092_451_1	chr19	38978189	38978553	+	0	NA	Intergenic	Intergenic	-2558	NM_024907	115290	Hs.531770	NM_024907	ENSG00000269190	FBXO17	FBG4|FBX26|FBXO26|Fbx17	F-box protein 17	protein-coding	0.013736	0.473973	
chunk0192_160_1	chr8	62300615	62300985	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	51858	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.005405	0.318059	
chunk0071_415_1	chr15	89708811	89709026	+	0	NA	intron (NM_020212, intron 4 of 16)	intron (NM_020212, intron 4 of 16)	18121	NM_020212	56964	Hs.177557	NM_020212	ENSG00000140527	WDR93	-	WD repeat domain 93	protein-coding	0.018605	0.560185	
chunk0160_334_1	chr5	159877845	159878190	+	0	NA	Intergenic	Intergenic	-6633	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.020290	0.497110	
chunk0026_60_1	chr10	61118695	61118998	+	0	NA	Intergenic	Intergenic	102571	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.006601	0.335526	281(CTGGACACGATGTGCT,-,0.00),282(TGGACACGATGTGCTT,+,0.00)
chunk0166_138_1	chr6	44836719	44837537	+	0	NA	intron (NM_181356, intron 12 of 12)	intron (NM_181356, intron 12 of 12)	360642	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.002445	0.319902	560(GGGAACTTACTGTTCT,-,0.00),561(GGAACTTACTGTTCTG,+,0.00)
chunk0028_429_1	chr10	93744720	93745336	+	0	NA	Intergenic	AluSq10|SINE|Alu	-12781	NM_001308276	9211	Hs.533670	NM_005097	ENSG00000108231	LGI1	ADLTE|ADPAEF|ADPEAF|EPITEMPIN|EPT|ETL1|IB1099	leucine rich glioma inactivated 1	protein-coding	0.025974	0.445705	
chunk0207_302_1	chr9	133370504	133370892	+	0	NA	intron (NM_001280791, intron 1 of 5)	intron (NM_001280791, intron 1 of 5)	5468	NM_033161	6836	Hs.512465	NM_033161	ENSG00000148248	SURF4	ERV29	surfeit 4	protein-coding	0.015464	0.544987	
chunk0151_233_1	chr5	51054485	51054976	+	0	NA	Intergenic	Intergenic	-84543	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.002037	0.371951	
chunk0140_104_1	chr4	68463798	68464245	+	0	NA	intron (NM_014058, intron 2 of 9)	intron (NM_014058, intron 2 of 9)	16572	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.004474	0.377232	
chunk0108_99_1	chr2	229206463	229206988	+	0	NA	intron (NM_001100818, intron 1 of 2)	intron (NM_001100818, intron 1 of 2)	64616	NM_017933	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.011429	0.395437	
chunk0043_142_1	chr12	16206529	16206835	+	0	NA	intron (NM_001170798, intron 7 of 8)	intron (NM_001170798, intron 7 of 8)	71003	NM_001170798	729025	Hs.692712	NM_001170798	ENSG00000188991	SLC15A5	-	solute carrier family 15 member 5	protein-coding	0.003268	0.381107	269(AGGAACACTGTGTCTT,-,0.00),270(GGAACACTGTGTCTTT,+,0.00)
chunk0161_175_1	chr5	169632834	169633393	+	0	NA	Intergenic	Intergenic	-4134	NM_004946	1794	Hs.586174	NM_004946	ENSG00000134516	DOCK2	IMD40	dedicator of cytokinesis 2	protein-coding	0.001789	0.346429	
chunk0046_212_1	chr12	59284670	59285271	+	0	NA	Intergenic	Intergenic	-311070	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001664	0.338870	
chunk0148_85_1	chr5	3187602	3188002	+	0	NA	Intergenic	Intergenic	9967	NR_104617	102467074	Hs.575250	NR_104617	ENSG00000249808	LINC01377	-	long intergenic non-protein coding RNA 1377	ncRNA	0.020000	0.403990	224(CAGGACGTTTTGTTCT,-,0.00),225(AGGACGTTTTGTTCTT,+,0.00)
chunk0012_323_1	chr1	162388527	162388937	+	0	NA	Intergenic	Intergenic	7002	NM_001085375	400793	Hs.447011	NM_001085375	ENSG00000239887	C1orf226	-	chromosome 1 open reading frame 226	protein-coding	0.017073	0.523114	187(TAGAACTCTCTGTGCT,-,0.00),188(AGAACTCTCTGTGCTT,+,0.00),202(TTGGACTCCCTGTCCT,-,0.00),203(TGGACTCCCTGTCCTC,+,0.00)
chunk0198_173_1	chr8	133297182	133297460	+	0	NA	promoter-TSS (NM_001135242)	promoter-TSS (NM_001135242)	-17	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.125899	0.749104	
chunk0194_31_1	chr8	81775155	81775833	+	0	NA	Intergenic	L1PA14|LINE|L1	43041	NM_152284	92421	Hs.183861	NM_152284	ENSG00000164695	CHMP4C	SNF7-3|Shax3|VPS32C	charged multivesicular body protein 4C	protein-coding	0.008850	0.377025	
chunk0001_393_1	chr1	10665950	10666201	+	0	NA	intron (NM_001079843, intron 4 of 20)	intron (NM_001079843, intron 4 of 20)	130601	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.039841	0.662698	
chunk0198_407_1	chr8	141896995	141897511	+	0	NA	Intergenic	L1MD2|LINE|L1	-110940	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.009690	0.411992	
chunk0100_355_1	chr2	117551833	117552434	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-262546	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.008319	0.390365	
chunk0078_187_1	chr17	4757151	4757586	+	0	NA	Intergenic	L2a|LINE|L2	-14524	NM_003963	9032	Hs.184194	NM_003963	ENSG00000142484	TM4SF5	-	transmembrane 4 L six family member 5	protein-coding	0.011494	0.357798	
chunk0094_94_1	chr2	4077011	4077301	+	0	NA	Intergenic	Intergenic	-103124	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.003448	0.364261	
chunk0164_345_1	chr6	25425036	25425341	+	0	NA	intron (NM_017640, intron 3 of 36)	L2c|LINE|L2	145760	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.003279	0.343137	
chunk0061_65_1	chr14	56546297	56546846	+	0	NA	Intergenic	Intergenic	-33222	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.007286	0.440000	303(CGGGACTGTGAGTCCT,-,0.00),304(GGGACTGTGAGTCCTA,+,0.00)
chunk0090_388_1	chr18	77450084	77450479	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	200229	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.010127	0.388889	
chunk0096_184_1	chr2	29838434	29838845	+	0	NA	intron (NM_004304, intron 1 of 28)	L1ME2|LINE|L1	82972	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.002433	0.334951	
chunk0015_377_1	chr1	190518496	190519095	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	40244	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.006678	0.336667	
chunk0176_259_1	chr7	16296261	16296733	+	0	NA	intron (NM_001101417, intron 4 of 8)	intron (NM_001101417, intron 4 of 8)	86011	NR_038947	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.002119	0.317125	163(GAGTACAAAATGTTCT,-,0.00),164(AGTACAAAATGTTCTT,+,0.00)
chunk0164_276_1	chr6	23988644	23989257	+	0	NA	Intergenic	LTR107_Mam|LTR|LTR	-137236	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.004894	0.374593	
chunk0176_404_1	chr7	19263282	19264136	+	0	NA	Intergenic	Intergenic	-118288	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.008197	0.357895	
chunk0039_428_1	chr11	107840116	107840832	+	0	NA	intron (NM_017515, intron 1 of 7)	intron (NM_017515, intron 1 of 7)	18714	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.008380	0.457462	
chunk0159_234_1	chr5	141616167	141616612	+	0	NA	intron (NM_001314007, intron 1 of 28)	intron (NM_001314007, intron 1 of 28)	2666	NM_005219	1729	Hs.529451	NM_005219	ENSG00000131504	DIAPH1	DFNA1|DIA1|DRF1|LFHL1|SCBMS|hDIA1	diaphanous related formin 1	protein-coding	0.015730	0.446188	
chunk0145_197_1	chr4	147882753	147882952	+	0	NA	intron (NM_024605, intron 10 of 22)	intron (NM_024605, intron 10 of 22)	100257	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.000000	0.365000	
chunk0184_365_1	chr7	121048894	121049213	+	0	NA	intron (NM_001105533, intron 3 of 17)	L2c|LINE|L2	59662	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.000000	0.328125	
chunk0066_350_1	chr15	38187547	38188105	+	0	NA	Intergenic	L2c|LINE|L2	-65025	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.014337	0.459750	252(GAGTACTATGTGTTCT,-,0.00),253(AGTACTATGTGTTCTG,+,0.00),356(AAGGGCATTGTGTGCT,-,0.00),357(AGGGCATTGTGTGCTG,+,0.00)
chunk0134_453_1	chr3	183980457	183980793	+	0	NA	intron (NM_005688, intron 8 of 29)	L3|LINE|CR1	-25713	NR_046570	100873982	Hs.570696	NR_046570	ENSG00000223882	ABCC5-AS1	-	ABCC5 antisense RNA 1	ncRNA	0.008929	0.456973	186(TTGGACATCATGTTCC,-,0.00),187(TGGACATCATGTTCCT,+,0.00)
chunk0038_70_1	chr11	83071682	83071974	+	0	NA	promoter-TSS (NM_001286061)	promoter-TSS (NM_001286061)	95	NM_001286060	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.037671	0.566553	
chunk0042_361_1	chr12	10361915	10362131	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-1746	NR_120430	101928100	Hs.638425	NR_120430	ENSG00000245648	LOC101928100	-	uncharacterized LOC101928100	ncRNA	0.000000	0.345622	160(AGAAACATTCTGTCCA,-,0.00),161(GAAACATTCTGTCCAT,+,0.00)
chunk0065_209_1	chr14	100156144	100157070	+	0	NA	intron (NM_206918, intron 1 of 2)	MIR|SINE|MIR	3068	NM_206918	123099	Hs.159643	NM_206918	ENSG00000168350	DEGS2	C14orf66|DES2|FADS8	delta 4-desaturase, sphingolipid 2	protein-coding	0.011879	0.565264	685(GGGAACAGCTTGTGCC,-,0.00),686(GGAACAGCTTGTGCCG,+,0.00)
chunk0174_315_1	chr6	163059772	163060355	+	0	NA	intron (NM_152410, intron 3 of 6)	A-rich|Low_complexity|Low_complexity	-5902	NR_110871	101929239	Hs.571035	NR_110871	ENSG00000225437	PACRG-AS2	-	PACRG antisense RNA 2	ncRNA	0.001715	0.267123	277(TAGAACATAGTGTACA,-,0.00),278(AGAACATAGTGTACAT,+,0.00)
chunk0065_454_1	chr14	106634558	106634757	+	0	NA	Intergenic	AluJr4|SINE|Alu	-2054	NR_106988									0.020101	0.425000	
chunk0202_55_1	chr9	71382199	71382453	+	0	NA	Intergenic	MIRc|SINE|MIR	-260728	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.003937	0.274510	
chunk0018_308_1	chr1	221135354	221135812	+	0	NA	Intergenic	Intergenic	200713	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.006550	0.416122	250(TGGTACAAGATGTACC,-,0.00),251(GGTACAAGATGTACCT,+,0.00)
chunk0020_75_1	chr1	232695811	232696050	+	0	NA	Intergenic	Intergenic	46785	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.004184	0.495833	
chunk0003_88_1	chr1	31768083	31768425	+	0	NA	Intergenic	L2a|LINE|L2	-4191	NM_001294336	576	Hs.524138	NM_001294335	ENSG00000121753	ADGRB2	BAI2	adhesion G protein-coupled receptor B2	protein-coding	0.011696	0.492711	
chunk0016_85_1	chr1	194256128	194256722	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	951680	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.001684	0.393277	
chunk0118_212_1	chr22	31880060	31880717	+	0	NA	intron (NR_110988, intron 34 of 38)	intron (NR_110988, intron 34 of 38)	58066	NM_001302820	25775	Hs.627602	NM_015372	ENSG00000128254	C22orf24	HSN44A4A	chromosome 22 open reading frame 24	protein-coding	0.010654	0.471125	
chunk0032_281_1	chr11	9183030	9183275	+	0	NA	intron (NM_015213, intron 5 of 22)	intron (NM_015213, intron 5 of 22)	82174	NM_001243254	23258	Hs.501857	NM_015213	ENSG00000184014	DENND5A	EIEE49|RAB6IP1	DENN domain containing 5A	protein-coding	0.004082	0.308943	
chunk0176_341_1	chr7	17696520	17696862	+	0	NA	Intergenic	Intergenic	-137782	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.011696	0.451895	
chunk0003_27_1	chr1	29682496	29683362	+	0	NA	Intergenic	Intergenic	-332815	NR_110758	101928460	Hs.434659	NR_110758	ENSG00000230523	LINC01756	-	long intergenic non-protein coding RNA 1756	ncRNA	0.011547	0.520185	
chunk0018_229_1	chr1	219739524	219739955	+	0	NA	Intergenic	Intergenic	188912	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.002320	0.342593	
chunk0055_358_1	chr13	70607456	70607655	+	0	NA	Intergenic	Intergenic	-407586	NR_047699	100885781	Hs.372660	NR_047699	ENSG00000226846	LINC00348	-	long intergenic non-protein coding RNA 348	ncRNA	0.000000	0.275000	
chunk0051_62_1	chr12	112850334	112850720	+	0	NA	intron (NM_001143854, intron 5 of 21)	intron (NM_001143854, intron 5 of 21)	-56407	NM_016816	4938	Hs.524760	NM_002534	ENSG00000089127	OAS1	E18/E16|IFI-4|OIAS|OIASI	2'-5'-oligoadenylate synthetase 1	protein-coding	0.007772	0.519380	156(GTGACAGAATGTCCCT,+,0.00)
chunk0162_262_1	chr6	5260222	5260497	+	0	NA	promoter-TSS (NM_006567)	promoter-TSS (NM_006567)	591	NR_104417	57128	Hs.387755	NM_020408	ENSG00000214113	LYRM4	C6orf149|CGI-203|COXPD19|ISD11	LYR motif containing 4	protein-coding	0.014545	0.467391	
chunk0107_443_1	chr2	225223313	225223565	+	0	NA	Intergenic	Intergenic	-177447	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.000000	0.284585	
chunk0180_229_1	chr7	67380153	67380545	+	0	NA	Intergenic	(GTGT)n|Simple_repeat|Simple_repeat	44373	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.002551	0.447837	
chunk0053_112_1	chr13	29354350	29354672	+	0	NA	intron (NM_001033602, intron 5 of 13)	intron (NM_001033602, intron 5 of 13)	-74129	NM_015233	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.003106	0.371517	
chunk0103_127_1	chr2	161937464	161937666	+	0	NA	intron (NM_001178016, intron 15 of 26)	intron (NM_001178016, intron 15 of 26)	136977	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.004950	0.369458	
chunk0125_165_1	chr3	66571881	66572676	+	0	NA	Intergenic	Intergenic	-71857	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.010063	0.399497	
chunk0052_104_1	chr13	22513414	22513958	+	0	NA	Intergenic	Intergenic	303401	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.014706	0.433028	
chunk0206_451_1	chr9	128271594	128272152	+	0	NA	intron (NM_004486, intron 2 of 25)	intron (NM_004486, intron 2 of 25)	4116	NM_004486	2801	Hs.155827	NM_004486	ENSG00000167110	GOLGA2	GM130	golgin A2	protein-coding	0.007168	0.407871	
chunk0166_311_1	chr6	49668218	49668612	+	0	NA	Intergenic	Intergenic	-31541	NM_000324	6005	Hs.120950	NM_000324	ENSG00000112077	RHAG	CD241|OHS|OHST|RH2|RH50A|RHNR|Rh50|Rh50GP|SLC42A1	Rh associated glycoprotein	protein-coding	0.002538	0.367089	
chunk0056_242_1	chr13	89143827	89144507	+	0	NA	Intergenic	L1MB7|LINE|L1	-91124	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.001471	0.323054	
chunk0101_184_1	chr2	129370270	129370743	+	0	NA	Intergenic	L1M4|LINE|L1	-96615	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.006342	0.327004	
chunk0182_242_1	chr7	96949673	96950272	+	0	NA	Intergenic	Intergenic	-56006	NM_005222	1750	Hs.249196	NM_005222	ENSG00000006377	DLX6	-	distal-less homeobox 6	protein-coding	0.013356	0.428333	
chunk0070_262_1	chr15	73802710	73803219	+	0	NA	Intergenic	Intergenic	34750	NR_120352	101929221		NR_120352		INSYN1-AS1	C15orf59-AS1	INSYN1 antisense RNA 1	ncRNA	0.009823	0.527451	212(GGGAACTTCTTGTCCC,-,0.00),213(GGAACTTCTTGTCCCT,+,0.00)
chunk0208_337_1	chrX	24883386	24884078	+	0	NA	intron (NM_016937, intron 34 of 36)	intron (NM_016937, intron 34 of 36)	132216	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.005780	0.317460	
chunk0180_308_1	chr7	70679092	70679433	+	0	NA	intron (NM_015570, intron 5 of 18)	intron (NM_015570, intron 5 of 18)	-453275	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.005865	0.400585	
chunk0186_104_1	chr7	137715835	137716082	+	0	NA	intron (NM_004717, intron 1 of 33)	intron (NM_004717, intron 1 of 33)	130905	NM_004717	9162	Hs.242947	NM_004717	ENSG00000157680	DGKI	DGK-IOTA	diacylglycerol kinase iota	protein-coding	0.008097	0.483871	
chunk0087_339_1	chr18	40227675	40228126	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	161614	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.006652	0.318584	
chunk0153_129_1	chr5	68946778	68947027	+	0	NA	Intergenic	Intergenic	83025	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.012048	0.408000	
chunk0190_170_1	chr8	32315797	32316217	+	0	NA	intron (NM_013962, intron 1 of 4)	intron (NM_013962, intron 1 of 4)	-124739	NR_047475	100874286	Hs.147060	NR_047475	ENSG00000254049	NRG1-IT3	-	NRG1 intronic transcript 3	ncRNA	0.019048	0.387173	
chunk0080_212_1	chr17	29546739	29547221	+	0	NA	3' UTR (NM_020791, exon 20 of 20)	3' UTR (NM_020791, exon 20 of 20)	20044	NM_198147	116236	Hs.106510	NM_198147	ENSG00000168792	ABHD15	-	abhydrolase domain containing 15	protein-coding	0.002075	0.360248	
chunk0106_41_1	chr2	196206696	196207301	+	0	NA	intron (NM_020760, intron 28 of 28)	L2b|LINE|L2	-35386	NM_004226	9262	Hs.88297	NM_004226	ENSG00000081320	STK17B	DRAK2	serine/threonine kinase 17b	protein-coding	0.003306	0.460396	
chunk0007_173_1	chr1	80357583	80357829	+	0	NA	Intergenic	Intergenic	-178049	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000000	0.267206	171(TAAAACAGACTGTTCA,-,0.00),172(AAAACAGACTGTTCAG,+,0.00)
chunk0074_277_1	chr16	28538753	28539394	+	0	NA	5' UTR (NM_012385, exon 1 of 3)	5' UTR (NM_012385, exon 1 of 3)	101	NM_001042483	26471	Hs.513463	NM_012385	ENSG00000176046	NUPR1	COM1|P8	nuclear protein 1, transcriptional regulator	protein-coding	0.028081	0.598131	
chunk0074_266_1	chr16	28165712	28165966	+	0	NA	intron (NM_001270940, intron 7 of 24)	intron (NM_001270940, intron 7 of 24)	46079	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.000000	0.360784	
chunk0114_200_1	chr21	15357990	15358289	+	0	NA	Intergenic	Intergenic	-293334	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.013378	0.406667	
chunk0007_407_1	chr1	85629049	85629688	+	0	NA	Intergenic	Intergenic	48607	NM_001554	3491	Hs.8867	NM_001554	ENSG00000142871	CCN1	CYR61|GIG1|IGFBP10	cellular communication network factor 1	protein-coding	0.009390	0.523438	290(AGGAACTCACTGTGCC,-,0.00),291(GGAACTCACTGTGCCT,+,0.00)
chunk0101_55_1	chr2	123157020	123157504	+	0	NA	Intergenic	Intergenic	-868025	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.008264	0.358763	
chunk0194_283_1	chr8	87403817	87404097	+	0	NA	Intergenic	Intergenic	470111	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.003571	0.395018	
chunk0167_395_1	chr6	74805804	74806087	+	0	NA	Intergenic	Intergenic	399962	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.003534	0.295775	226(GGGAACATTTTGTTCC,-,0.00),227(GGAACATTTTGTTCCT,+,0.00)
chunk0097_99_1	chr2	45962629	45962930	+	0	NA	intron (NM_005400, intron 2 of 14)	intron (NM_005400, intron 2 of 14)	310875	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.016611	0.506623	
chunk0137_334_1	chr4	24876361	24876719	+	0	NA	exon (NM_173463, exon 3 of 13)	exon (NM_173463, exon 3 of 13)	36438	NM_001130726	91050	Hs.106432	NM_173463	ENSG00000181982	CCDC149	-	coiled-coil domain containing 149	protein-coding	0.011173	0.454039	
chunk0122_30_1	chr3	27895030	27895683	+	0	NA	Intergenic	L1MB5|LINE|L1	-61220	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.009188	0.368502	
chunk0155_130_1	chr5	93246275	93246489	+	0	NA	Intergenic	Intergenic	324961	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.009346	0.362791	
chunk0194_125_1	chr8	84099184	84099388	+	0	NA	Intergenic	L1PA10|LINE|L1	-83932	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004902	0.385366	
chunk0057_254_1	chr13	105255527	105255854	+	0	NA	Intergenic	L2b|LINE|L2	-210177	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.003058	0.347561	
chunk0036_109_1	chr11	61375635	61375984	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-13526	NM_001300763	220002	Hs.22546	NM_153611	ENSG00000162144	CYB561A3	CYBASC3|LCYTB	cytochrome b561 family member A3	protein-coding	0.014327	0.428571	
chunk0115_215_1	chr21	26939577	26940301	+	0	NA	intron (NM_007038, intron 3 of 7)	intron (NM_007038, intron 3 of 7)	-14022	NR_039916	100616243		NR_039916	ENSG00000266133	MIR4759	-	microRNA 4759	ncRNA	0.005525	0.388966	
chunk0057_409_1	chr13	109796239	109796458	+	0	NA	Intergenic	Intergenic	-9781	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.018265	0.477273	
chunk0090_440_1	chr18	79582097	79582517	+	0	NA	Intergenic	Intergenic	-97494	NM_004715	9150	Hs.465490	NM_004715	ENSG00000060069	CTDP1	CCFDN|FCP1	CTD phosphatase subunit 1	protein-coding	0.014286	0.465558	302(CTGCACACAGTGTACA,-,0.00),303(TGCACACAGTGTACAT,+,0.00)
chunk0081_115_1	chr17	40038748	40039110	+	0	NA	intron (NR_052017, intron 3 of 24)	intron (NR_052017, intron 3 of 24)	-11284	NR_102369	101340251		NR_102369	ENSG00000238793	SNORD124	-	small nucleolar RNA, C/D box 124	snoRNA	0.016575	0.501377	
chunk0095_148_1	chr2	16943291	16944084	+	0	NA	Intergenic	Intergenic	-277821	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.005044	0.416877	464(GAGACCAGTATGTCCC,-,0.00),465(AGACCAGTATGTCCCC,+,0.00)
chunk0110_191_1	chr20	14764640	14765283	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	164557	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.004666	0.433230	
chunk0109_225_1	chr20	5804877	5805076	+	0	NA	intron (NM_001303478, intron 3 of 3)	intron (NM_001303478, intron 3 of 3)	54589	NM_152504	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.005025	0.485000	
chunk0133_300_1	chr3	172234893	172235414	+	0	NA	intron (NM_022763, intron 4 of 25)	Charlie4a|DNA|hAT-Charlie	194599	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.001919	0.304598	
chunk0192_410_1	chr8	69033863	69034300	+	0	NA	intron (NR_039986, intron 2 of 4)	intron (NR_039986, intron 2 of 4)	70109	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.006865	0.349315	
chunk0209_149_1	chrX	42378636	42379342	+	0	NA	Intergenic	L2c|LINE|L2	399246	NR_002191									0.005666	0.356436	414(AGGAACAACCTGATCT,-,0.00),415(GGAACAACCTGATCTT,+,0.00)
chunk0128_162_1	chr3	107257704	107258668	+	0	NA	intron (NR_028302, intron 1 of 3)	intron (NR_028302, intron 1 of 3)	17494	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.002075	0.361658	769(ATGAACTTGCTGTTCC,-,0.00),770(TGAACTTGCTGTTCCC,+,0.00)
chunk0189_241_1	chr8	24682481	24682790	+	0	NA	Intergenic	Intergenic	-134017	NR_125808	101929294	Hs.637673	NR_125808		LOC101929294	-	uncharacterized LOC101929294	ncRNA	0.016181	0.335484	
chunk0174_12_1	chr6	152356607	152357288	+	0	NA	intron (NM_033071, intron 66 of 145)	intron (NM_033071, intron 66 of 145)	-23583	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.005874	0.403226	
chunk0123_353_1	chr3	48087242	48087441	+	0	NA	intron (NM_030885, intron 1 of 3)	intron (NM_030885, intron 1 of 3)	1938	NM_002375	4134	Hs.517949	NM_002375	ENSG00000047849	MAP4	-	microtubule associated protein 4	protein-coding	0.000000	0.410000	
chunk0168_186_1	chr6	85078190	85078397	+	0	NA	Intergenic	Intergenic	-314057	NM_001080508	9096	Hs.251830	NM_001080508	ENSG00000112837	TBX18	CAKUT2	T-box transcription factor 18	protein-coding	0.009662	0.418269	
chunk0202_184_1	chr9	74629620	74630042	+	0	NA	intron (NM_006914, intron 1 of 9)	intron (NM_006914, intron 1 of 9)	-131278	NR_125791	103752585	Hs.635501	NR_125791		RORB-AS1	-	RORB antisense RNA 1	ncRNA	0.002370	0.326241	
chunk0040_371_1	chr11	119021162	119021466	+	0	NA	intron (NM_016146, intron 3 of 4)	intron (NM_016146, intron 3 of 4)	2370	NR_037429									0.013158	0.393443	
chunk0109_183_1	chr20	4813832	4814128	+	0	NA	intron (NM_014737, intron 2 of 11)	intron (NM_014737, intron 2 of 11)	1143	NM_170774	9770	Hs.631504	NM_014737	ENSG00000101265	RASSF2	CENP-34|RASFADIN	Ras association domain family member 2	protein-coding	0.003378	0.464646	
chunk0194_400_1	chr8	91060081	91060303	+	0	NA	non-coding (NR_110438, exon 3 of 3)	non-coding (NR_110438, exon 3 of 3)	9997	NR_110439	100506365	Hs.153412	NR_110438	ENSG00000253738	OTUD6B-AS1	GS1-251I9.4	OTUD6B antisense RNA 1 (head to head)	ncRNA	0.013514	0.412556	94(GTGAACATAGAGTACC,-,0.00),95(TGAACATAGAGTACCT,+,0.00)
chunk0019_384_1	chr1	230158881	230159320	+	0	NA	intron (NM_004481, intron 1 of 15)	intron (NM_004481, intron 1 of 15)	91905	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.015945	0.475000	
chunk0093_59_1	chr19	40304800	40305003	+	0	NA	Intergenic	Charlie15b|DNA|hAT-Charlie	-19506	NM_001626	208	Hs.631535	NM_001626	ENSG00000105221	AKT2	HIHGHH|PKBB|PKBBETA|PRKBB|RAC-BETA	AKT serine/threonine kinase 2	protein-coding	0.009852	0.455882	
chunk0143_113_1	chr4	108961449	108961648	+	0	NA	intron (NM_001256074, intron 6 of 31)	intron (NM_001256074, intron 6 of 31)	-198469	NM_001146627	64850	Hs.106576	NM_031279	ENSG00000164089	ETNPPL	AGXT2L1	ethanolamine-phosphate phospho-lyase	protein-coding	0.010050	0.385000	
chunk0073_337_1	chr16	14516490	14517003	+	0	NA	intron (NM_002582, intron 21 of 23)	L1M8|LINE|L1	113525	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.003899	0.350195	
chunk0074_180_1	chr16	23988203	23988431	+	0	NA	intron (NM_212535, intron 2 of 16)	intron (NM_212535, intron 2 of 16)	152338	NM_002738	5579	Hs.460355	NM_002738	ENSG00000166501	PRKCB	PKC-beta|PKCB|PKCI(2)|PKCbeta|PRKCB1|PRKCB2	protein kinase C beta	protein-coding	0.000000	0.362445	
chunk0020_388_1	chr1	240411391	240412145	+	0	NA	intron (NM_020066, intron 15 of 17)	intron (NM_020066, intron 15 of 17)	200394	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.011936	0.423841	
chunk0055_78_1	chr13	53608633	53609161	+	0	NA	Intergenic	Intergenic	-206522	NR_047488	100861552	Hs.224691	NR_047488	ENSG00000261517	LINC00558	-	long intergenic non-protein coding RNA 558	ncRNA	0.003788	0.366730	
chunk0101_43_1	chr2	122545753	122546217	+	0	NA	Intergenic	LTR24|LTR|ERV1	790440	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.008621	0.402151	
chunk0181_448_1	chr7	90717352	90718201	+	0	NA	intron (NM_001287136, intron 1 of 13)	L2c|LINE|L2	7960	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.007067	0.368235	
chunk0012_349_1	chr1	162693235	162693650	+	0	NA	intron (NM_006182, intron 2 of 17)	L2a|LINE|L2	61004	NM_006182	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.009639	0.372596	
chunk0139_34_1	chr4	48432119	48432604	+	0	NA	Intergenic	AluJr|SINE|Alu	-50982	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.006186	0.393004	
chunk0165_44_1	chr6	30129984	30130406	+	0	NA	Intergenic	Intergenic	-5913	NM_001286633	135644	Hs.509439	NM_138700	ENSG00000204614	TRIM40	RNF35	tripartite motif containing 40	protein-coding	0.007109	0.399527	311(AAGAACACAGTGTACC,-,0.00),312(AGAACACAGTGTACCA,+,0.00)
chunk0117_232_1	chr22	22939537	22940404	+	0	NA	Intergenic	Intergenic	52190	NM_001178126	100423062	Hs.449574	NM_001178126	ENSG00000254709	IGLL5	IGL|IGLV|VL-MAR	immunoglobulin lambda like polypeptide 5	protein-coding	0.013841	0.422811	
chunk0039_91_1	chr11	97248998	97249213	+	0	NA	Intergenic	L1PB4|LINE|L1	-742228	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.004651	0.458333	
chunk0110_319_1	chr20	18721393	18721961	+	0	NA	intron (NM_080820, intron 4 of 5)	L1M5|LINE|L1	-22969	NR_109955	101929526	Hs.639402	NR_109955	ENSG00000233993	LOC101929526	-	uncharacterized LOC101929526	ncRNA	0.010563	0.409490	234(TAGAACGATCTGTTCT,-,0.00),235(AGAACGATCTGTTCTT,+,0.00)
chunk0082_206_1	chr17	56912216	56912579	+	0	NA	intron (NM_005082, intron 1 of 8)	MIR3|SINE|MIR	1651	NM_005082	7706	Hs.528952	NM_005082	ENSG00000121060	TRIM25	EFP|RNF147|Z147|ZNF147	tripartite motif containing 25	protein-coding	0.011019	0.532967	
chunk0078_369_1	chr16	87435635	87436146	+	0	NA	intron (NM_015144, intron 2 of 12)	intron (NM_015144, intron 2 of 12)	43695	NM_022818	81631	Hs.356061	NM_022818	ENSG00000140941	MAP1LC3B	ATG8F|LC3B|MAP1A/1BLC3|MAP1LC3B-a	microtubule associated protein 1 light chain 3 beta	protein-coding	0.021526	0.431641	
chunk0179_436_1	chr7	52259279	52259491	+	0	NA	Intergenic	Intergenic	-776271	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.009434	0.478873	179(GAGCACAAGCTGTACC,-,0.00),180(AGCACAAGCTGTACCT,+,0.00)
chunk0207_317_1	chr9	133941953	133942208	+	0	NA	intron (NM_001134398, intron 1 of 29)	L1MB3|LINE|L1	50244	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.027451	0.488281	73(AAGACCAGAGAGTTCT,-,0.00)
chunk0061_50_1	chr14	56274503	56274805	+	0	NA	intron (NM_021255, intron 2 of 5)	intron (NM_021255, intron 2 of 5)	156279	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.006623	0.402640	167(CAGGACAGCCAGTTCT,-,0.00),168(AGGACAGCCAGTTCTA,+,0.00)
chunk0047_194_1	chr12	71080448	71080647	+	0	NA	Intergenic	FLAM_A|SINE|Alu	77452	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.000000	0.405000	
chunk0152_135_1	chr5	59104660	59105251	+	0	NA	intron (NM_006203, intron 5 of 14)	intron (NM_006203, intron 5 of 14)	-65443	NM_001197222	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.008460	0.435811	
chunk0112_210_1	chr20	40469530	40470171	+	0	NA	Intergenic	Intergenic	219390	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.007800	0.501558	214(AGGGACAATCTGTCCT,-,0.00),215(GGGACAATCTGTCCTT,+,0.00)
chunk0088_319_1	chr18	50838913	50839299	+	0	NA	Intergenic	Intergenic	-13722	NM_001127174	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.002591	0.315245	
chunk0188_322_1	chr8	17488629	17489271	+	0	NA	Intergenic	Intergenic	-8138	NM_001008539	6542	Hs.448520	NM_003046	ENSG00000003989	SLC7A2	ATRC2|CAT2|HCAT2	solute carrier family 7 member 2	protein-coding	0.009346	0.354588	
chunk0086_135_1	chr18	21111169	21111722	+	0	NA	5' UTR (NM_005406, exon 1 of 33)	5' UTR (NM_005406, exon 1 of 33)	406	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.103074	0.696751	
chunk0111_426_1	chr20	34945934	34946133	+	0	NA	exon (NM_000178, exon 3 of 13)	exon (NM_000178, exon 3 of 13)	9765	NM_000178	2937	Hs.82327	NM_000178	ENSG00000100983	GSS	GSHS|HEL-S-64p|HEL-S-88n	glutathione synthetase	protein-coding	0.010050	0.560000	
chunk0024_94_1	chr10	34504594	34505074	+	0	NA	intron (NM_019619, intron 3 of 24)	intron (NM_019619, intron 3 of 24)	310491	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.008333	0.430353	
chunk0175_41_1	chr7	1046713	1047293	+	0	NA	intron (NM_001303473, intron 1 of 1)	intron (NM_001303473, intron 1 of 1)	2430	NM_001303473	115330	Hs.585007	NM_138445	ENSG00000164849	GPR146	PGR8	G protein-coupled receptor 146	protein-coding	0.018966	0.545611	295(AGAGACTCTCTGTTCT,-,0.00),296(GAGACTCTCTGTTCTT,+,0.00)
chunk0185_46_1	chr7	124606371	124606628	+	0	NA	Intergenic	L1M6|LINE|L1	159526	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.003891	0.317829	
chunk0064_431_1	chr14	99894198	99894796	+	0	NA	intron (NM_004434, intron 5 of 21)	intron (NM_004434, intron 5 of 21)	101089	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.006689	0.338898	
chunk0128_173_1	chr3	107284521	107284927	+	0	NA	intron (NR_028302, intron 1 of 3)	intron (NR_028302, intron 1 of 3)	44032	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.002463	0.346437	69(AGGAACATTTTGTTCT,-,0.00),70(GGAACATTTTGTTCTA,+,0.00)
chunk0128_407_1	chr3	114484189	114484552	+	0	NA	intron (NR_121661, intron 1 of 2)	intron (NR_121661, intron 1 of 2)	30777	NR_121661	101929754	Hs.614195	NR_121661	ENSG00000242290	ZBTB20-AS5	-	ZBTB20 antisense RNA 5	ncRNA	0.013774	0.395604	145(CAGTACATTGTGTGCT,-,0.00),146(AGTACATTGTGTGCTC,+,0.00)
chunk0137_263_1	chr4	22137463	22137924	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-188942	NM_147182	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.004338	0.363636	
chunk0156_206_1	chr5	108003238	108003542	+	0	NA	intron (NM_001163315, intron 7 of 8)	L1MEd|LINE|L1	-332495	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.003289	0.383607	
chunk0154_29_1	chr5	76990545	76991305	+	0	NA	Intergenic	MLT2F|LTR|ERVL	38070	NM_001882	1393	Hs.115617	NM_001882	ENSG00000145708	CRHBP	CRF-BP|CRFBP	corticotropin releasing hormone binding protein	protein-coding	0.015789	0.432326	
chunk0205_70_1	chr9	106863111	106863413	+	0	NA	5' UTR (NM_021224, exon 1 of 13)	5' UTR (NM_021224, exon 1 of 13)	165	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.049669	0.570957	
chunk0129_1_1	chr3	115809250	115809577	+	0	NA	3' UTR (NM_002338, exon 7 of 7)	3' UTR (NM_002338, exon 7 of 7)	186109	NM_002045	2596	Hs.134974	NM_002045	ENSG00000172020	GAP43	B-50|PP46	growth associated protein 43	protein-coding	0.018349	0.496951	
chunk0091_300_1	chr19	12750046	12750692	+	0	NA	Intergenic	Intergenic	-2224	NM_017682	54831	Hs.435611	NM_017682	ENSG00000039987	BEST2	VMD2L1	bestrophin 2	protein-coding	0.030960	0.593509	330(GGGAACACGGCGTCCC,-,0.00),331(GGAACACGGCGTCCCA,+,0.00)
chunk0054_114_1	chr13	42914972	42915310	+	0	NA	intron (NM_001002264, intron 9 of 12)	intron (NM_001002264, intron 9 of 12)	-42397	NR_126389	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.005917	0.353982	
chunk0011_383_1	chr1	153848878	153849307	+	0	NA	intron (NM_020699, intron 1 of 10)	FLAM_A|SINE|Alu	55145	NR_126565	343052	Hs.516530	NR_126565	ENSG00000231827	LOC343052	-	immunoglobulin superfamily DCC subclass member 3 pseudogene	pseudo	0.009324	0.481395	
chunk0123_221_1	chr3	45289595	45290207	+	0	NA	Intergenic	Intergenic	-63579	NM_015444	25907	Hs.740403	NM_015444	ENSG00000249992	TMEM158	BBP|RIS1|p40BBP	transmembrane protein 158 (gene/pseudogene)	protein-coding	0.003268	0.448613	
chunk0081_178_1	chr17	41633615	41633901	+	0	NA	intron (NR_033415, intron 4 of 10)	(GT)n|Simple_repeat|Simple_repeat	6441	NR_033415	284116	Hs.725790	NR_033415	ENSG00000214514	KRT42P	-	keratin 42 pseudogene	pseudo	0.020979	0.526132	
chunk0198_412_1	chr8	142677259	142677830	+	0	NA	intron (NR_033343, intron 1 of 2)	intron (NR_033343, intron 1 of 2)	-2912	NM_005672	8000	Hs.652235	NM_005672	ENSG00000167653	PSCA	PRO232	prostate stem cell antigen	protein-coding	0.024518	0.582168	
chunk0096_60_1	chr2	27537494	27537706	+	0	NA	Intergenic	Intergenic	-38922	NM_032266	84226	Hs.131021	NM_032266	ENSG00000221843	C2orf16	-	chromosome 2 open reading frame 16	protein-coding	0.014151	0.511737	
chunk0046_207_1	chr12	59110349	59110591	+	0	NA	Intergenic	L2a|LINE|L2	-189932	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.004132	0.456790	
chunk0037_305_1	chr11	76660647	76661248	+	0	NA	exon (NM_001128922, exon 3 of 3)	exon (NM_001128922, exon 3 of 3)	9053	NM_005512	2615	Hs.151641	NM_005512	ENSG00000137507	LRRC32	D11S833E|GARP	leucine rich repeat containing 32	protein-coding	0.048253	0.651163	176(TGGAGCAGTTTGTTCT,-,0.00),177(GGAGCAGTTTGTTCTC,+,0.00),533(CTGTACAGGCTGTTCC,-,0.00),534(TGTACAGGCTGTTCCC,+,0.00)
chunk0087_156_1	chr18	34755700	34756082	+	0	NA	promoter-TSS (NM_001390)	promoter-TSS (NM_001390)	-85	NM_001390	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.007853	0.334204	
chunk0098_429_1	chr2	81604352	81604784	+	0	NA	Intergenic	Intergenic	-137622	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.002315	0.369515	
chunk0162_273_1	chr6	5537912	5538604	+	0	NA	intron (NM_006567, intron 4 of 6)	intron (NM_006567, intron 4 of 6)	-80183	NR_125847	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.008671	0.382395	
chunk0147_21_1	chr4	171242586	171243032	+	0	NA	Intergenic	L1MD1|LINE|L1	56625	NR_106730	102466953		NR_106730	ENSG00000278502	MIR6082	hsa-mir-6082	microRNA 6082	ncRNA	0.002242	0.366890	
chunk0033_226_1	chr11	17405417	17406171	+	0	NA	intron (NM_001287174, intron 26 of 38)	intron (NM_001287174, intron 26 of 38)	-16463	NM_001166290	3767	Hs.248141	NM_000525	ENSG00000187486	KCNJ11	BIR|HHF2|IKATP|KIR6.2|MODY13|PHHI|TNDM3	potassium voltage-gated channel subfamily J member 11	protein-coding	0.017241	0.515232	424(TGGGACACAGAGTCCT,-,0.00),425(GGGACACAGAGTCCTC,+,0.00)
chunk0202_43_1	chr9	71202863	71203421	+	0	NA	Intergenic	Intergenic	-81544	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.000000	0.388193	
chunk0166_199_1	chr6	46583141	46583900	+	0	NA	intron (NM_016593, intron 10 of 11)	intron (NM_016593, intron 10 of 11)	69310	NM_001278739	51302	Hs.387367	NM_016593	ENSG00000146233	CYP39A1	-	cytochrome P450 family 39 subfamily A member 1	protein-coding	0.007905	0.419737	
chunk0118_98_1	chr22	29210884	29211242	+	0	NA	intron (NM_133455, intron 1 of 14)	intron (NM_133455, intron 1 of 14)	5151	NM_001267895	129080	Hs.289106	NM_133455	ENSG00000186998	EMID1	EMI5|EMU1	EMI domain containing 1	protein-coding	0.016760	0.518106	
chunk0022_451_1	chr10	19904117	19904568	+	0	NA	intron (NM_032812, intron 1 of 13)	L1PB1|LINE|L1	87899	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.004435	0.484513	
chunk0028_443_1	chr10	94005132	94005485	+	0	NA	intron (NM_001288989, intron 1 of 32)	MamRTE1|LINE|RTE-BovB	11319	NM_001288989	51196	Hs.655033	NM_016341	ENSG00000138193	PLCE1	NPHS3|PLCE|PPLC	phospholipase C epsilon 1	protein-coding	0.002833	0.406780	
chunk0158_9_1	chr5	125196503	125197125	+	0	NA	intron (NR_109882, intron 4 of 5)	intron (NR_109882, intron 4 of 5)	159983	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.020900	0.457464	313(GAGAACACAAAGTGCA,-,0.00),314(AGAACACAAAGTGCAT,+,0.00)
chunk0185_325_1	chr7	131612944	131613343	+	0	NA	Intergenic	Intergenic	-56526	NM_005397	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.010025	0.452500	129(AGAACACTTTGGTCTT,+,0.00)
chunk0026_55_1	chr10	61063162	61063452	+	0	NA	Intergenic	Intergenic	47032	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.010345	0.405498	
chunk0156_38_1	chr5	102625372	102626255	+	0	NA	intron (NR_103754, intron 1 of 3)	intron (NR_103754, intron 1 of 3)	44445	NR_047462	100861468	Hs.519483	NR_047462	ENSG00000250958	LINC00492	-	long intergenic non-protein coding RNA 492	ncRNA	0.003398	0.324661	228(TGGAACAGTTTGTTCT,-,0.00),229(GGAACAGTTTGTTCTA,+,0.00)
chunk0014_326_1	chr1	181881452	181881960	+	0	NA	Intergenic	L1MD|LINE|L1	180006	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.003937	0.383104	
chunk0173_299_1	chr6	148345147	148345769	+	0	NA	intron (NM_015278, intron 1 of 19)	intron (NM_015278, intron 1 of 19)	2865	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.006431	0.444623	
chunk0049_81_1	chr12	90635248	90635519	+	0	NA	Intergenic	L1ME1|LINE|L1	-282640	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.007380	0.308824	
chunk0140_68_1	chr4	67403193	67403671	+	0	NA	Intergenic	MER70B|LTR|ERVL	18568	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.004184	0.465553	171(TAAGACATTCTGTTCT,-,0.00),172(AAGACATTCTGTTCTA,+,0.00)
chunk0064_368_1	chr14	98304427	98305115	+	0	NA	Intergenic	L1ME3F|LINE|L1	-326647	NR_015430	388011	Hs.651477	NR_015430	ENSG00000246223	LINC01550	C14orf64	long intergenic non-protein coding RNA 1550	ncRNA	0.005814	0.313498	320(TGACACATTCTGTTCT,-,0.00),321(GACACATTCTGTTCTC,+,0.00)
chunk0070_273_1	chr15	74250400	74251603	+	0	NA	intron (NM_025055, intron 2 of 18)	MIR3|SINE|MIR	14712	NM_025055	80125	Hs.383206	NM_025055	ENSG00000140481	CCDC33	CT61|HP11097	coiled-coil domain containing 33	protein-coding	0.010806	0.544020	858(AGGCCCAGGGTGTCCC,-,0.00)
chunk0165_227_1	chr6	35391933	35392514	+	0	NA	intron (NM_001171819, intron 2 of 6)	intron (NM_001171819, intron 2 of 6)	49665	NM_177435	5467	Hs.696032	NM_006238	ENSG00000112033	PPARD	FAAR|NR1C2|NUC1|NUCI|NUCII|PPARB	peroxisome proliferator activated receptor delta	protein-coding	0.013769	0.561856	
chunk0212_426_1	chrX	153221394	153221705	+	0	NA	Intergenic	Intergenic	42265	NM_004988	4100	Hs.72879	NM_004988	ENSG00000198681	MAGEA1	CT1.1|MAGE1	MAGE family member A1	protein-coding	0.006431	0.400641	
chunk0186_68_1	chr7	137162458	137162657	+	0	NA	intron (NR_046103, intron 1 of 3)	L1M6|LINE|L1	1784	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.010050	0.375000	
chunk0025_148_1	chr10	52255468	52255869	+	0	NA	intron (NM_006258, intron 10 of 17)	L2c|LINE|L2	58460	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.004988	0.340796	
chunk0101_60_1	chr2	123290219	123290532	+	0	NA	Intergenic	Intergenic	-734912	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.003195	0.394904	
chunk0035_337_1	chr11	47984272	47984637	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	3896	NM_002843	5795	Hs.318547	NM_002843	ENSG00000149177	PTPRJ	CD148|DEP1|HPTPeta|R-PTP-ETA|SCC1	protein tyrosine phosphatase receptor type J	protein-coding	0.005479	0.423497	
chunk0031_221_1	chr10	126175917	126176343	+	0	NA	intron (NM_001288973, intron 3 of 22)	intron (NM_001288973, intron 3 of 22)	-202857	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.018779	0.487119	
chunk0069_437_1	chr15	68435009	68435277	+	0	NA	Intergenic	L1MB7|LINE|L1	-2990	NM_001004439	22801	Hs.436416	NM_012211	ENSG00000137809	ITGA11	HsT18964	integrin subunit alpha 11	protein-coding	0.003731	0.364312	
chunk0048_3_1	chr12	76922300	76922548	+	0	NA	Intergenic	Intergenic	-43384	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.008065	0.445783	150(AGGAACAAAATGTTCT,-,0.00),151(GGAACAAAATGTTCTC,+,0.00)
chunk0059_84_1	chr14	30714551	30715192	+	0	NA	intron (NM_182835, intron 18 of 23)	intron (NM_182835, intron 18 of 23)	92552	NM_001257376	23256	Hs.369168	NM_016106	ENSG00000092108	SCFD1	C14orf163|RA410|SLY1|SLY1P|STXBP1L2	sec1 family domain containing 1	protein-coding	0.003120	0.303738	251(CAGAACATCCTGTACA,-,0.00),252(AGAACATCCTGTACAA,+,0.00)
chunk0210_24_1	chrX	67338188	67338577	+	0	NA	Intergenic	Intergenic	-205650	NM_000044	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.002571	0.420513	
chunk0013_89_1	chr1	167681481	167681922	+	0	NA	intron (NM_052862, intron 1 of 6)	intron (NM_052862, intron 1 of 6)	-40249	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.006803	0.472851	331(AATCACACACTGTCCC,-,0.00),332(ATCACACACTGTCCCC,+,0.00)
chunk0106_300_1	chr2	204645253	204645452	+	0	NA	intron (NM_205863, intron 1 of 21)	intron (NM_205863, intron 1 of 21)	99559	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.000000	0.250000	
chunk0118_207_1	chr22	31739475	31740142	+	0	NA	intron (NM_173566, intron 1 of 8)	intron (NM_173566, intron 1 of 8)	10326	NM_173566	253143	Hs.438906	NM_173566	ENSG00000183530	PRR14L	C22orf30	proline rich 14 like	protein-coding	0.005997	0.401198	
chunk0181_380_1	chr7	89308464	89309026	+	0	NA	intron (NM_181646, intron 2 of 3)	MER58A|DNA|hAT-Charlie	-513028	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.000000	0.357016	221(AAGAACAGGGTGTTTC,-,0.00),222(AGAACAGGGTGTTTCT,+,0.00)
chunk0078_270_1	chr17	7851081	7851348	+	0	NA	exon (NM_001080424, exon 14 of 22)	exon (NM_001080424, exon 14 of 22)	-3852	NM_203411	92162	Hs.389669	NM_203411	ENSG00000167874	TMEM88	-	transmembrane protein 88	protein-coding	0.029963	0.611940	
chunk0085_294_1	chr18	7959103	7959597	+	0	NA	intron (NM_001105244, intron 7 of 32)	L3|LINE|CR1	392034	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.002024	0.353535	
chunk0041_232_1	chr11	128413282	128413785	+	0	NA	Intergenic	LTR37-int|LTR|ERV1	108777	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.005964	0.349206	
chunk0105_404_1	chr2	192746992	192747640	+	0	NA	Intergenic	Intergenic	-2529	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.006173	0.346687	327(GAGAACATTCTGTGCT,-,0.00),328(AGAACATTCTGTGCTT,+,0.00)
chunk0198_162_1	chr8	133171033	133171547	+	0	NA	Intergenic	Intergenic	-19749	NM_001204870	8840	Hs.492974	NM_003882	ENSG00000104415	CCN4	WISP1|WISP1-OT1|WISP1-UT1|WISP1c|WISP1i|WISP1tc	cellular communication network factor 4	protein-coding	0.013619	0.520388	
chunk0105_259_1	chr2	189120717	189121112	+	0	NA	intron (NM_000393, intron 1 of 53)	intron (NM_000393, intron 1 of 53)	12197	NR_036076	100422908		NR_036076	ENSG00000264725	MIR3129	mir-3129	microRNA 3129	ncRNA	0.002532	0.320707	
chunk0121_226_1	chr3	21854795	21855157	+	0	NA	Intergenic	L2b|LINE|L2	-102163	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.000000	0.347107	
chunk0003_109_1	chr1	32223992	32224771	+	0	NA	intron (NM_003757, intron 3 of 10)	intron (NM_003757, intron 3 of 10)	-2010	NM_019118	56063	Hs.272299	NM_019118	ENSG00000160055	TMEM234	AASL548|C1orf91|PRO1105|RP4-622L5|dJ622L5.7	transmembrane protein 234	protein-coding	0.015404	0.469231	
chunk0044_144_1	chr12	29589597	29589796	+	0	NA	intron (NM_001193451, intron 7 of 17)	intron (NM_001193451, intron 7 of 17)	-92010	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.010050	0.480000	
chunk0209_285_1	chrX	47562473	47562786	+	0	NA	intron (NM_001256196, intron 1 of 15)	intron (NM_001256196, intron 1 of 15)	1529	NM_001256197	369	Hs.446641	NM_001654	ENSG00000078061	ARAF	A-RAF|ARAF1|PKS2|RAFA1	A-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.009585	0.490446	88(CAGTGCAGTGTGTACT,-,0.00),89(AGTGCAGTGTGTACTG,+,0.00)
chunk0080_207_1	chr17	29387278	29387552	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-3247	NR_039749	100616122		NR_039749	ENSG00000284162	MIR4523	-	microRNA 4523	ncRNA	0.003650	0.414545	
chunk0163_336_1	chr6	15337739	15338149	+	0	NA	intron (NM_001267040, intron 1 of 17)	HUERS-P2-int|LTR|ERV1	89089	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.017073	0.501217	
chunk0111_194_1	chr20	25674338	25674895	+	0	NA	3' UTR (NM_015655, exon 5 of 5)	3' UTR (NM_015655, exon 5 of 5)	12323	NM_001290261	26152	Hs.61881	NM_015655	ENSG00000130684	ZNF337	-	zinc finger protein 337	protein-coding	0.003591	0.471326	15(AGGAGCATTGTGTCCT,-,0.00),16(GGAGCATTGTGTCCTC,+,0.00)
chunk0157_24_1	chr5	115541534	115541890	+	0	NA	intron (NM_020177, intron 2 of 2)	L1ME4b|LINE|L1	3182	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.005618	0.338936	
chunk0209_123_1	chrX	40799677	40799959	+	0	NA	Intergenic	L1PB1|LINE|L1	33378	NR_027761	100132831	Hs.729923	NR_027761		LOC100132831	-	A20-binding inhibitor of NF-kappaB activation 2 pseudogene	pseudo	0.007092	0.395760	
chunk0127_432_1	chr3	102885363	102885562	+	0	NA	Intergenic	MIRb|SINE|MIR	450447	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.005025	0.415000	
chunk0124_125_1	chr3	54281169	54281515	+	0	NA	intron (NM_018398, intron 2 of 37)	intron (NM_018398, intron 2 of 37)	158676	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.014451	0.518732	
chunk0047_426_1	chr12	76259735	76260134	+	0	NA	Intergenic	Intergenic	88508	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.007519	0.387500	182(TTGCACAGATTGTTCC,-,0.00),183(TGCACAGATTGTTCCT,+,0.00)
chunk0027_99_1	chr10	73811614	73811883	+	0	NA	promoter-TSS (NM_003635)	promoter-TSS (NM_003635)	83	NM_003635	8509	Hs.654758	NM_003635	ENSG00000166507	NDST2	HSST2|N-HSST 2|NST2	N-deacetylase and N-sulfotransferase 2	protein-coding	0.148699	0.774074	
chunk0053_107_1	chr13	28877741	28878055	+	0	NA	Intergenic	Intergenic	-146713	NM_001033602	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.009554	0.368254	
chunk0060_305_1	chr14	50900083	50900660	+	0	NA	intron (NM_181814, intron 7 of 10)	L2a|LINE|L2	28211	NM_181814	145447	Hs.271896	NM_181533	ENSG00000131969	ABHD12B	BEM46L3|C14orf29|c14_5314	abhydrolase domain containing 12B	protein-coding	0.006932	0.415225	
chunk0192_30_1	chr8	58613295	58613635	+	0	NA	intron (NM_001144772, intron 9 of 30)	L1MEf|LINE|L1	45942	NM_001144772	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.008824	0.348974	300(AGAAACAATGTGTGCC,-,0.00)
chunk0107_429_1	chr2	224829946	224830977	+	0	NA	intron (NM_014689, intron 27 of 55)	intron (NM_014689, intron 27 of 55)	116604	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.005820	0.353682	
chunk0040_135_1	chr11	112517193	112517661	+	0	NA	intron (NR_120559, intron 2 of 2)	MIR|SINE|MIR	33082	NR_120560	101928823	Hs.126118	NR_120559	ENSG00000254968	LINC02763	-	long intergenic non-protein coding RNA 2763	ncRNA	0.002137	0.362473	
chunk0096_43_1	chr2	26918486	26918840	+	0	NA	intron (NM_020134, intron 2 of 12)	intron (NM_020134, intron 2 of 12)	-51708	NM_012326	22924	Hs.515860	NM_012326	ENSG00000084764	MAPRE3	EB3|EBF3|EBF3-S|RP3	microtubule associated protein RP/EB family member 3	protein-coding	0.011299	0.400000	
chunk0018_243_1	chr1	219990426	219991162	+	0	NA	intron (NM_004446, intron 18 of 31)	intron (NM_004446, intron 18 of 31)	55864	NM_004446	2058	Hs.497788	NM_004446	ENSG00000136628	EPRS	EARS|GLUPRORS|HLD15|PARS|PIG32|QARS|QPRS	glutamyl-prolyl-tRNA synthetase	protein-coding	0.005435	0.321574	
chunk0160_263_1	chr5	157020550	157020749	+	0	NA	Intergenic	Intergenic	37592	NM_012206	26762	Hs.129711	NM_012206	ENSG00000113249	HAVCR1	CD365|HAVCR|HAVCR-1|KIM-1|KIM1|TIM|TIM-1|TIM1|TIMD-1|TIMD1	hepatitis A virus cellular receptor 1	protein-coding	0.005025	0.495000	
chunk0174_378_1	chr6	164964489	164964910	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	-142636	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.019002	0.355450	9(TGGGTCAAGCTGTTCC,-,0.00),10(GGGTCAAGCTGTTCCT,+,0.00)
chunk0151_364_1	chr5	54786648	54786847	+	0	NA	Intergenic	Intergenic	-42489	NR_104658	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.010050	0.425000	
chunk0143_106_1	chr4	108644887	108645402	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-5441	NM_001267818	58505	Hs.445803	NM_021227	ENSG00000198856	OSTC	DC2	oligosaccharyltransferase complex non-catalytic subunit	protein-coding	0.001942	0.453488	
chunk0011_21_1	chr1	143203498	143203907	+	0	NA	Intergenic	Intergenic	218890	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.029340	0.358537	
chunk0087_398_1	chr18	41889141	41889833	+	0	NA	Intergenic	L2b|LINE|L2	-65711	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.004335	0.379509	
chunk0157_427_1	chr5	124689544	124690242	+	0	NA	intron (NM_020747, intron 2 of 8)	L1MC1|LINE|L1	55219	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.000000	0.364807	
chunk0007_412_1	chr1	85934454	85934954	+	0	NA	intron (NM_152890, intron 24 of 59)	MER58A|DNA|hAT-Charlie	221734	NM_152890	255631	Hs.659516	NM_152890	ENSG00000171502	COL24A1	-	collagen type XXIV alpha 1 chain	protein-coding	0.000000	0.325349	
chunk0153_143_1	chr5	69033814	69034035	+	0	NA	Intergenic	Intergenic	-3997	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.004525	0.454955	105(AGGAACAGAGTGACCC,-,0.00),106(GGAACAGAGTGACCCA,+,0.00)
chunk0090_75_1	chr18	70321807	70322023	+	0	NA	intron (NM_004232, intron 1 of 1)	MIRb|SINE|MIR	-13524	NR_126336	101927481	Hs.633706	NR_126336	ENSG00000266258	LINC01909	-	long intergenic non-protein coding RNA 1909	ncRNA	0.000000	0.336406	
chunk0113_421_1	chr20	62087304	62088369	+	0	NA	Intergenic	Intergenic	-22026	NM_003185	6874	Hs.18857	NM_003185	ENSG00000130699	TAF4	TAF2C|TAF2C1|TAF4A|TAFII130|TAFII135	TATA-box binding protein associated factor 4	protein-coding	0.035681	0.554409	167(CGGGACAAGCTGCTCT,-,0.00),168(GGGACAAGCTGCTCTT,+,0.00)
chunk0204_330_1	chr9	101315838	101316077	+	0	NA	intron (NM_017753, intron 6 of 7).2	intron (NM_017753, intron 6 of 7).2	67562	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.004184	0.416667	
chunk0076_435_1	chr16	73171369	73171983	+	0	NA	Intergenic	Intergenic	-27229	NM_207385	388289	Hs.371893	NM_207385		C16orf47	-	chromosome 16 open reading frame 47	protein-coding	0.017915	0.458537	
chunk0045_256_1	chr12	49403966	49404165	+	0	NA	intron (NM_001293285, intron 3 of 14)	L2c|LINE|L2	14891	NR_033267	100335030	Hs.687044	NR_033267		LOC100335030	-	FGFR1 oncogene partner 2 pseudogene	pseudo	0.010050	0.425000	
chunk0002_430_1	chr1	28058356	28058587	+	0	NA	intron (NM_001282560, intron 1 of 16)	intron (NM_001282560, intron 1 of 16)	30166	NR_104214	2140	Hs.185774	NM_001990	ENSG00000158161	EYA3	-	EYA transcriptional coactivator and phosphatase 3	protein-coding	0.008658	0.331897	
chunk0185_11_1	chr7	123824673	123825026	+	0	NA	Intergenic	L2a|LINE|L2	10710	NR_002731	26062	Hs.381305	NR_002731		HYAL6P	HYAL6|HYALP1	hyaluronidase 6, pseudogene	pseudo	0.002833	0.426554	
chunk0192_286_1	chr8	66428882	66429159	+	0	NA	promoter-TSS (NM_015169)	promoter-TSS (NM_015169)	-8	NM_015169	23212	Hs.71827	NM_015169	ENSG00000179041	RRS1	-	ribosome biogenesis regulator 1 homolog	protein-coding	0.079422	0.618705	
chunk0082_213_1	chr17	57035891	57036134	+	0	NA	Intergenic	Intergenic	-9466	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.016461	0.467213	
chunk0100_181_1	chr2	110771972	110772208	+	0	NA	intron (NM_001142807, intron 2 of 17)	MIRb|SINE|MIR	39517	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.000000	0.392405	
chunk0036_88_1	chr11	60866421	60867188	+	0	NA	promoter-TSS (NM_207341)	promoter-TSS (NM_207341)	-738	NM_207341	22917	Hs.172130	NM_207341	ENSG00000149506	ZP1	HEL163|OOMD|OOMD1	zona pellucida glycoprotein 1	protein-coding	0.011734	0.473958	321(TAGTACAGACAGTTCC,-,0.00),322(AGTACAGACAGTTCCC,+,0.00)
chunk0049_373_1	chr12	95738055	95738623	+	0	NA	intron (NM_021229, intron 2 of 9)	intron (NM_021229, intron 2 of 9)	52419	NM_021229	59277	Hs.201034	NM_021229	ENSG00000074527	NTN4	PRO3091	netrin 4	protein-coding	0.015845	0.467487	
chunk0012_251_1	chr1	161165884	161166145	+	0	NA	promoter-TSS (NM_001122764)	promoter-TSS (NM_001122764)	-377	NM_000309	5498	Hs.517373	NM_000309	ENSG00000143224	PPOX	PPO|V290M|VP	protoporphyrinogen oxidase	protein-coding	0.049808	0.583969	
chunk0189_136_1	chr8	22523291	22523886	+	0	NA	intron (NM_001243974, intron 8 of 14)	MARNA|DNA|TcMar-Mariner	-28150	NM_005775	10174	Hs.528572	NM_005775	ENSG00000120896	SORBS3	SCAM-1|SCAM1|SH3D4	sorbin and SH3 domain containing 3	protein-coding	0.008403	0.347315	
chunk0210_427_1	chrX	103191472	103191807	+	0	NA	Intergenic	L1MC5a|LINE|L1	-23453	NM_001127688	56271	Hs.184736	NM_001080425	ENSG00000102409	BEX4	BEXL1	brain expressed X-linked 4	protein-coding	0.005970	0.363095	180(AGGAACTGGGTGTTTT,-,0.00),181(GGAACTGGGTGTTTTG,+,0.00)
chunk0180_243_1	chr7	67693823	67694454	+	0	NA	Intergenic	(CT)n|Simple_repeat|Simple_repeat	-326115	NR_120514	102723427	Hs.583491	NR_120514	ENSG00000225209	LOC102723427	-	uncharacterized LOC102723427	ncRNA	0.004754	0.427215	
chunk0201_124_1	chr9	35427911	35428621	+	0	NA	intron (NR_003582, intron 2 of 10)	intron (NR_003582, intron 2 of 10)	21511	NR_110320	158381	Hs.575661	NR_003581	ENSG00000179766	ATP8B5P	FetA	ATPase phospholipid transporting 8B5, pseudogene	pseudo	0.001408	0.351617	
chunk0072_263_1	chr15	96336856	96337119	+	0	NA	intron (NM_021005, intron 2 of 2)	intron (NM_021005, intron 2 of 2)	3647	NM_001145157	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.015209	0.492424	
chunk0146_317_1	chr4	165398882	165399249	+	0	NA	intron (NM_001873, intron 1 of 8)	intron (NM_001873, intron 1 of 8)	12823	NR_030304	693163		NR_030304	ENSG00000207559	MIR578	MIRN578|hsa-mir-578	microRNA 578	ncRNA	0.000000	0.285326	
chunk0137_215_1	chr4	19615400	19615599	+	0	NA	Intergenic	L1PB4|LINE|L1	-636406	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.010050	0.575000	
chunk0076_133_1	chr16	66767307	66767620	+	0	NA	exon (NM_001136505, exon 16 of 19)	exon (NM_001136505, exon 16 of 19)	15711	NR_133569	106699570	Hs.513658	NR_133569	ENSG00000246777	LOC106699570	-	uncharacterized LOC106699570	ncRNA	0.006390	0.305732	
chunk0209_36_1	chrX	36143054	36143948	+	0	NA	intron (NM_001304548, intron 35 of 63)	intron (NM_001304548, intron 35 of 63)	223767	NM_152632	286464	Hs.376425	NM_152632	ENSG00000165164	CFAP47	CHDC2|CXorf22|CXorf30|CXorf59	cilia and flagella associated protein 47	protein-coding	0.010067	0.395531	212(AAGAACAAACTCTTCT,-,0.00)
chunk0116_430_1	chr21	42981013	42981323	+	0	NA	intron (NM_004571, intron 1 of 10)	intron (NM_004571, intron 1 of 10)	6658	NM_001286258	5316	Hs.431043	NM_004571	ENSG00000160199	PKNOX1	PREP1|pkonx1c	PBX/knotted 1 homeobox 1	protein-coding	0.012903	0.543408	
chunk0128_92_1	chr3	105822883	105823107	+	0	NA	intron (NM_170662, intron 3 of 18)	intron (NM_170662, intron 3 of 18)	46048	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.008929	0.400000	
chunk0084_342_1	chr17	81081887	81082086	+	0	NA	intron (NM_006340, intron 3 of 14)	intron (NM_006340, intron 3 of 14)	43387	NR_030394	724027		NR_030394	ENSG00000207736	MIR657	MIRN657|hsa-mir-657	microRNA 657	ncRNA	0.030151	0.685000	86(AGGTACTGGGTGTGCC,-,0.00),87(GGTACTGGGTGTGCCA,+,0.00)
chunk0192_426_1	chr8	69608817	69609044	+	0	NA	intron (NR_132437, intron 6 of 16)	intron (NR_132437, intron 6 of 16)	16030	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.026432	0.482456	
chunk0115_334_1	chr21	29031955	29032156	+	0	NA	intron (NM_001001992, intron 3 of 17)	L1MD2|LINE|L1	7438	NM_006447	10600	Hs.99819	NM_006447	ENSG00000156256	USP16	UBP-M|UBPM	ubiquitin specific peptidase 16	protein-coding	0.004975	0.420792	
chunk0038_204_1	chr11	86248957	86249176	+	0	NA	intron (NM_001308007, intron 1 of 12)	LTR37A|LTR|ERV1	4682	NM_003797	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.004566	0.377273	
chunk0038_459_1	chr11	94837905	94838592	+	0	NA	intron (NM_130847, intron 6 of 12)	L2a|LINE|L2	69906	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.001456	0.412791	
chunk0198_418_1	chr8	142742501	142742790	+	0	NA	promoter-TSS (NM_020427)	promoter-TSS (NM_020427)	-234	NM_020427	57152	Hs.103505	NM_020427	ENSG00000126233	SLURP1	ANUP|ARS|ArsB|LY6-MT|LY6LS|MDM	secreted LY6/PLAUR domain containing 1	protein-coding	0.006920	0.624138	119(GGGAACTCACTGTTCC,-,0.00),120(GGAACTCACTGTTCCT,+,0.00)
chunk0191_210_1	chr8	52159550	52159749	+	0	NA	intron (NM_014682, intron 14 of 25)	intron (NM_014682, intron 14 of 25)	250230	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.000000	0.340000	
chunk0106_251_1	chr2	203544579	203544884	+	0	NA	Intergenic	L2c|LINE|L2	-9396	NM_203365	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.013115	0.405229	
chunk0059_266_1	chr14	35229600	35230319	+	0	NA	intron (NM_014672, intron 5 of 7)	intron (NM_014672, intron 5 of 7)	-48599	NM_001282234	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.008345	0.406944	
chunk0113_281_1	chr20	56922354	56923085	+	0	NA	Intergenic	Intergenic	-290977	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.016416	0.411202	
chunk0093_256_1	chr19	51050784	51051073	+	0	NA	Intergenic	L1ME5|LINE|L1	14182	NM_015596	26085	Hs.165296	NM_015596	ENSG00000167759	KLK13	KLK-L4|KLKL4	kallikrein related peptidase 13	protein-coding	0.010381	0.372414	
chunk0021_323_1	chr1	245401131	245401689	+	0	NA	intron (NM_018012, intron 3 of 14)	intron (NM_018012, intron 3 of 14)	246425	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.017921	0.422182	
chunk0064_362_1	chr14	97262059	97262545	+	0	NA	Intergenic	L1ME1|LINE|L1	-196514	NR_110166	101929241	Hs.650839	NR_110165	ENSG00000246084	LINC02325	-	long intergenic non-protein coding RNA 2325	ncRNA	0.006173	0.347023	
chunk0195_106_1	chr8	94628631	94629264	+	0	NA	Intergenic	Intergenic	10520	NR_034034	100288748	Hs.608210	NR_034034	ENSG00000261437	LOC100288748	-	uncharacterized LOC100288748	ncRNA	0.011058	0.447950	
chunk0003_52_1	chr1	30823850	30824559	+	0	NA	Intergenic	Intergenic	-66368	NM_006762	7805	Hs.371021	NM_006762	ENSG00000162511	LAPTM5	CLAST6	lysosomal protein transmembrane 5	protein-coding	0.043724	0.602817	
chunk0157_287_1	chr5	120805102	120805728	+	0	NA	Intergenic	Intergenic	273951	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.004792	0.373206	324(AAGAACACTATGTACA,-,0.00),325(AGAACACTATGTACAT,+,0.00)
chunk0031_197_1	chr10	125823161	125823700	+	0	NA	promoter-TSS (NM_000375)	promoter-TSS (NM_000375)	-105	NM_078469	56647	Hs.370292	NM_016567	ENSG00000107949	BCCIP	TOK-1|TOK1	BRCA2 and CDKN1A interacting protein	protein-coding	0.079777	0.627778	
chunk0091_349_1	chr19	14992074	14992460	+	0	NA	intron (NR_073589, intron 1 of 8)	MER96B|DNA|hAT-Tip100	-12532	NM_001272087	6511	Hs.515217	NM_005071	ENSG00000105143	SLC1A6	EAAT4	solute carrier family 1 member 6	protein-coding	0.015544	0.452196	
chunk0063_233_1	chr14	81796233	81796662	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-173386	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.009324	0.358140	
chunk0040_433_1	chr11	121437695	121438086	+	0	NA	Intergenic	Intergenic	-14313	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.012788	0.413265	
chunk0159_12_1	chr5	136130286	136130524	+	0	NA	intron (NR_026763, intron 1 of 1)	intron (NR_026763, intron 1 of 1)	-2440	NM_005903	4090	Hs.167700	NM_005903	ENSG00000113658	SMAD5	DWFC|JV5-1|MADH5	SMAD family member 5	protein-coding	0.000000	0.384937	185(CAGATCATCCTGTTCT,-,0.00),186(AGATCATCCTGTTCTA,+,0.00)
chunk0115_272_1	chr21	28074358	28075179	+	0	NA	intron (NR_126010, intron 1 of 4)	intron (NR_126010, intron 1 of 4)	-15635	NR_126011	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.003654	0.390511	
chunk0207_243_1	chr9	132012575	132013262	+	0	NA	intron (NM_001253881, intron 3 of 6)	intron (NM_001253881, intron 3 of 6)	66969	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.011645	0.457849	
chunk0134_381_1	chr3	182824848	182825470	+	0	NA	intron (NM_014616, intron 2 of 29)	L2c|LINE|L2	31656	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.000000	0.337079	
chunk0094_179_1	chr2	5885328	5885592	+	0	NA	Intergenic	Intergenic	-47227	NR_026832	150622	Hs.560891	NR_026832		SILC1	LINC01105	sciatic injury induced lincRNA upregulator of SOX11	ncRNA	0.000000	0.230189	
chunk0058_181_1	chr14	23977185	23977517	+	0	NA	intron (NM_001193636, intron 1 of 7)	MER102a|DNA|hAT-Charlie	7336	NM_001193635	317749	Hs.647569	NM_198083	ENSG00000187630	DHRS4L2	SDR25C3	dehydrogenase/reductase 4 like 2	protein-coding	0.003012	0.405405	174(TGGAACTGGGTGTGCC,-,0.00),175(GGAACTGGGTGTGCCT,+,0.00)
chunk0143_165_1	chr4	110771927	110772413	+	0	NA	Intergenic	X7C_LINE|LINE|CR1	88477	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.010288	0.375770	
chunk0107_289_1	chr2	218407028	218407520	+	0	NA	Intergenic	L2c|LINE|L2	4628	NR_029500	407017		NR_029500	ENSG00000199121	MIR26B	MIRN26B|hsa-mir-26b|miR-26b	microRNA 26b	ncRNA	0.022358	0.551724	290(AGGACCAGGCTGTGCC,-,0.00),291(GGACCAGGCTGTGCCT,+,0.00)
chunk0029_458_1	chr10	110575680	110576188	+	0	NA	intron (NM_005445, intron 4 of 28)	intron (NM_005445, intron 4 of 28)	8243	NM_005445	9126	Hs.24485	NM_005445	ENSG00000108055	SMC3	BAM|BMH|CDLS3|CSPG6|HCAP|SMC3L1	structural maintenance of chromosomes 3	protein-coding	0.001969	0.332024	
chunk0117_238_1	chr22	23080296	23080523	+	0	NA	intron (NM_002073, intron 1 of 2)	intron (NM_002073, intron 1 of 2)	9926	NM_002073	2781	Hs.584760	NM_002073	ENSG00000128266	GNAZ	gz-alpha	G protein subunit alpha z	protein-coding	0.017621	0.583333	158(GGGGACACTGTGTTCA,-,0.00),159(GGGACACTGTGTTCAC,+,0.00)
chunk0047_286_1	chr12	73389756	73390100	+	0	NA	Intergenic	Intergenic	230738	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.307246	
chunk0181_442_1	chr7	90682686	90683088	+	0	NA	intron (NM_001287135, intron 2 of 14)	L1MC4|LINE|L1	-26511	NM_012395	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.004975	0.364764	
chunk0067_72_1	chr15	41284418	41285024	+	0	NA	intron (NR_026757, intron 1 of 3)	intron (NR_026757, intron 1 of 3)	718	NR_026757	729082	Hs.380164	NR_026757	ENSG00000247556	OIP5-AS1	cyrano|linc-OIP5	OIP5 antisense RNA 1	ncRNA	0.033003	0.443163	
chunk0118_346_1	chr22	35911901	35912423	+	0	NA	intron (NM_001082579, intron 2 of 13)	intron (NM_001082579, intron 2 of 13)	-71579	NM_014309	23543	Hs.282998	NM_014309	ENSG00000100320	RBFOX2	FOX2|Fox-2|HNRBP2|HRNBP2|RBM9|RTA|dJ106I20.3|fxh	RNA binding fox-1 homolog 2	protein-coding	0.005747	0.391969	463(GAACACAGGATGTACC,-,0.00)
chunk0010_209_1	chr1	116171095	116171507	+	0	NA	Intergenic	Intergenic	59546	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.002427	0.382567	
chunk0001_157_1	chr1	6270269	6270636	+	0	NA	intron (NM_181864, intron 8 of 8)	intron (NM_181864, intron 8 of 8)	-9477	NM_207370	387509	Hs.531581	NM_207370	ENSG00000158292	GPR153	PGR1	G protein-coupled receptor 153	protein-coding	0.024523	0.633152	323(CAGGACTCTGAGTCCC,-,0.00)
chunk0007_168_1	chr1	80191342	80191714	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-344227	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000000	0.391421	
chunk0060_377_1	chr14	52577402	52577611	+	0	NA	intron (NM_001099652, intron 1 of 6)	L1P4|LINE|L1	24358	NM_001099652	283554	Hs.416214	NM_001099652	ENSG00000180998	GPR137C	TM7SF1L2	G protein-coupled receptor 137C	protein-coding	0.038278	0.414286	
chunk0060_366_1	chr14	52413571	52414429	+	0	NA	Intergenic	Intergenic	99702	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.012821	0.357392	
chunk0029_324_1	chr10	104473418	104473812	+	0	NA	Intergenic	MER61D|LTR|ERV1	6660	NR_120624	101927523	Hs.407539	NR_120624	ENSG00000225768	LINC02620	-	long intergenic non-protein coding RNA 2620	ncRNA	0.000000	0.417722	
chunk0014_63_1	chr1	175906505	175906725	+	0	NA	Intergenic	MER57B2|LTR|ERV1	29272	NR_125964	101928751		NR_125964	ENSG00000224718	LINC01657	-	long intergenic non-protein coding RNA 1657	ncRNA	0.004545	0.375566	
chunk0175_323_1	chr6	166898649	166899036	+	0	NA	Intergenic	CpG	-4856	NR_046644	100861523	Hs.634640	NR_046644		RPS6KA2-AS1	-	RPS6KA2 antisense RNA 1	ncRNA	0.056848	0.564433	
chunk0016_124_1	chr1	196934018	196934620	+	0	NA	Intergenic	LTR12C|LTR|ERV1	-9449	NM_005666	3080	Hs.632450	NM_005666	ENSG00000080910	CFHR2	CFHL2|FHR2|HFL3	complement factor H related 2	protein-coding	0.014950	0.507463	
chunk0208_101_1	chrX	13758012	13758412	+	0	NA	intron (NM_003611, intron 14 of 22)	intron (NM_003611, intron 14 of 22)	23499	NM_003611	8481	Hs.6483	NM_003611	ENSG00000046651	OFD1	71-7A|CXorf5|JBTS10|RP23|SGBS2	OFD1 centriole and centriolar satellite protein	protein-coding	0.002500	0.369077	
chunk0188_328_1	chr8	17563922	17564441	+	0	NA	intron (NM_001008539, intron 11 of 11)	intron (NM_001008539, intron 11 of 11)	-12252	NM_006207	5157	Hs.458573	NM_006207	ENSG00000104213	PDGFRL	PDGRL|PRLTS	platelet derived growth factor receptor like	protein-coding	0.007707	0.357692	264(AATACAGAGTGTACTT,+,0.00)
chunk0194_449_1	chr8	92587113	92587397	+	0	NA	intron (NR_125827, intron 3 of 4)	intron (NR_125827, intron 3 of 4)	68239	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.007042	0.385965	
chunk0056_316_1	chr13	91068328	91068579	+	0	NA	Intergenic	L1MD|LINE|L1	21164	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.000000	0.357143	
chunk0182_316_1	chr7	98922661	98922987	+	0	NA	intron (NM_003496, intron 21 of 70)	intron (NM_003496, intron 21 of 70)	41127	NR_132754	106633801		NR_132754		SCARNA28	ZL1	small Cajal body-specific RNA 28	ncRNA	0.018405	0.492355	
chunk0206_21_1	chr9	115924204	115924452	+	0	NA	intron (NR_024032, intron 1 of 2)	intron (NR_024032, intron 1 of 2)	770	NR_024032	58483	Hs.23367	NR_024032	ENSG00000204148	LINC00474	C9orf27|EST-YD1	long intergenic non-protein coding RNA 474	ncRNA	0.008065	0.425703	
chunk0092_383_1	chr19	36418599	36419340	+	0	NA	promoter-TSS (NM_133466)	promoter-TSS (NM_133466)	-321	NM_133466	284406	Hs.558734	NM_133466	ENSG00000181007	ZFP82	ZNF545	ZFP82 zinc finger protein	protein-coding	0.066127	0.547170	652(AAATACAGTCAGTTCT,-,0.00),653(AATACAGTCAGTTCTC,+,0.00)
chunk0199_66_1	chr9	2340900	2341353	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	182670	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.011038	0.414097	
chunk0149_267_1	chr5	24088453	24088652	+	0	NA	intron (NR_131245, intron 4 of 4)	L1PA12|LINE|L1	137204	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.005025	0.495000	
chunk0118_275_1	chr22	33620030	33620481	+	0	NA	intron (NM_133642, intron 4 of 14)	intron (NM_133642, intron 4 of 14)	-104731	NR_038949	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.008869	0.393805	
chunk0203_14_1	chr9	82665238	82665588	+	0	NA	Intergenic	Intergenic	397715	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.008571	0.350427	
chunk0067_13_1	chr15	40016415	40016848	+	0	NA	exon (NM_001013703, exon 28 of 39)	exon (NM_001013703, exon 28 of 39)	22571	NM_001309434	6727	Hs.533732	NM_003134	ENSG00000140319	SRP14	ALURBP	signal recognition particle 14	protein-coding	0.006928	0.405530	
chunk0188_209_1	chr8	12735601	12735838	+	0	NA	intron (NM_152271, intron 6 of 11)	MER33|DNA|hAT-Charlie	-8415	NR_037492	100500870		NR_037492	ENSG00000266206	MIR3926-1	mir-3926-1	microRNA 3926-1	ncRNA	0.004219	0.365546	
chunk0012_300_1	chr1	162178966	162179652	+	0	NA	intron (NM_001164757, intron 2 of 9)	MIR|SINE|MIR	22202	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.008746	0.401747	
chunk0080_346_1	chr17	32829329	32829579	+	0	NA	intron (NM_015194, intron 1 of 21)	AluSz6|SINE|Alu	47719	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.008000	0.466135	
chunk0209_97_1	chrX	39732905	39733229	+	0	NA	Intergenic	Intergenic	71851	NR_037501	100500822		NR_037501	ENSG00000263730	MIR3937	-	microRNA 3937	ncRNA	0.009259	0.486154	
chunk0087_392_1	chr18	41849542	41850160	+	0	NA	Intergenic	Intergenic	-105347	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.006472	0.348950	340(AGGAACAAATTGTTTT,-,0.00),341(GGAACAAATTGTTTTT,+,0.00)
chunk0212_286_1	chrX	140869024	140869567	+	0	NA	Intergenic	L1PA15|LINE|L1	56924	NR_031725	100302169		NR_031725	ENSG00000221081	MIR320D2	MIR320D-2|MIRN320D2|hsa-mir-320d-2|mir-320d-2	microRNA 320d-2	ncRNA	0.003683	0.334559	
chunk0139_387_1	chr4	61648835	61649162	+	0	NA	intron (NM_015236, intron 2 of 22)	intron (NM_015236, intron 2 of 22)	151877	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.000000	0.271341	
chunk0007_418_1	chr1	86114892	86115527	+	0	NA	intron (NM_152890, intron 4 of 59)	intron (NM_152890, intron 4 of 59)	41229	NM_152890	255631	Hs.659516	NM_152890	ENSG00000171502	COL24A1	-	collagen type XXIV alpha 1 chain	protein-coding	0.009449	0.405660	347(AAGTACATACTGTACA,-,0.00),348(AGTACATACTGTACAA,+,0.00)
chunk0062_80_1	chr14	67834420	67834766	+	0	NA	intron (NM_133509, intron 3 of 10)	L2c|LINE|L2	14814	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.005780	0.409222	234(TTGTACATTCTGTCCT,-,0.00),235(TGTACATTCTGTCCTC,+,0.00)
chunk0174_372_1	chr6	164871169	164871609	+	0	NA	Intergenic	Intergenic	-49326	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.004545	0.328798	
chunk0163_62_1	chr6	8989924	8990392	+	0	NA	Intergenic	Intergenic	337949	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.006410	0.398721	
chunk0028_145_1	chr10	86734702	86735035	+	0	NA	3' UTR (NM_007078, exon 13 of 13)	3' UTR (NM_007078, exon 13 of 13)	-21771	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.003003	0.455090	
chunk0192_194_1	chr8	63858418	63859082	+	0	NA	intron (NR_125826, intron 4 of 4)	L1MD1|LINE|L1	89320	NR_038875	286184	Hs.586402	NR_038875	ENSG00000253734	LINC01289	-	long intergenic non-protein coding RNA 1289	ncRNA	0.006024	0.338346	
chunk0196_157_1	chr8	104766176	104766585	+	0	NA	Intergenic	L1PA15|LINE|L1	-177356	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.004890	0.390244	
chunk0148_124_1	chr5	5320024	5320729	+	0	NA	TTS (NM_139056)	TTS (NM_139056)	-102297	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.018440	0.488669	
chunk0091_6_1	chr19	2579092	2579468	+	0	NA	intron (NM_052847, intron 2 of 4)	intron (NM_052847, intron 2 of 4)	-51435	NR_107004	102465838		NR_107004	ENSG00000277904	MIR7850	hsa-mir-7850	microRNA 7850	ncRNA	0.061170	0.684350	
chunk0129_295_1	chr3	123602306	123602597	+	0	NA	intron (NR_038266, intron 1 of 2)	LTR57|LTR|ERVL	16938	NR_121654	100506826	Hs.556600	NR_038266	ENSG00000239523	MYLK-AS1	-	MYLK antisense RNA 1	ncRNA	0.003436	0.465753	
chunk0178_154_1	chr7	33511763	33512380	+	0	NA	intron (NM_014451, intron 18 of 20)	intron (NM_014451, intron 18 of 20)	382531	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.004862	0.349515	
chunk0159_315_1	chr5	143227087	143227496	+	0	NA	3' UTR (NM_001135608, exon 23 of 23)	3' UTR (NM_001135608, exon 23 of 23)	34791	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.012225	0.495122	
chunk0002_3_1	chr1	11909571	11909770	+	0	NA	Intergenic	Intergenic	1516	NR_002754	26829		NR_002754	ENSG00000199347	RNU5E-1	RNU5E|U5E	RNA, U5E small nuclear 1	snRNA	0.050251	0.525000	
chunk0030_72_1	chr10	112150949	112151417	+	0	NA	3' UTR (NM_001244949, exon 22 of 22)	3' UTR (NM_001244949, exon 22 of 22)	32596	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.008547	0.362473	
chunk0054_271_1	chr13	46604249	46605537	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	51732	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.006988	0.421257	218(AGGAACACACTGGGCC,-,0.00),219(GGAACACACTGGGCCA,+,0.00)
chunk0174_234_1	chr6	160699473	160699949	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-2482	NM_001168338	5340	Hs.143436	NM_000301	ENSG00000122194	PLG	-	plasminogen	protein-coding	0.014706	0.402516	
chunk0127_361_1	chr3	101561719	101561989	+	0	NA	promoter-TSS (NM_017819)	promoter-TSS (NM_017819)	18	NM_017819	54931	Hs.594839	NM_017819	ENSG00000174173	TRMT10C	COXPD30|HNYA|MRPP1|RG9MTD1	tRNA methyltransferase 10C, mitochondrial RNase P subunit	protein-coding	0.088889	0.601476	
chunk0204_4_1	chr9	91555103	91555817	+	0	NA	Intergenic	L1MC2|LINE|L1	-80791	NR_037472	100500821		NR_037472	ENSG00000266855	MIR3910-1	mir-3910-1	microRNA 3910-1	ncRNA	0.007003	0.359441	
chunk0126_230_1	chr3	79017570	79017896	+	0	NA	intron (NM_002941, intron 3 of 30)	intron (NM_002941, intron 3 of 30)	1726	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.018405	0.394495	59(AGATACAGTGTGTACT,-,0.00),60(GATACAGTGTGTACTC,+,0.00)
chunk0098_289_1	chr2	75809159	75809428	+	0	NA	Intergenic	MIR|SINE|MIR	-98308	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.003717	0.407407	
chunk0061_129_1	chr14	59051351	59051608	+	0	NA	Intergenic	Intergenic	-137184	NM_001270520	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.003891	0.383721	
chunk0057_75_1	chr13	98325750	98326265	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	117483	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.007767	0.391473	
chunk0037_377_1	chr11	78476203	78476697	+	0	NA	intron (NM_024678, intron 9 of 13)	L1M3b|LINE|L1	-46614	NR_120564	101928865	Hs.407574	NR_120564	ENSG00000251323	LINC02728	-	long intergenic non-protein coding RNA 2728	ncRNA	0.004049	0.474747	
chunk0037_366_1	chr11	78100171	78100830	+	0	NA	TTS (NM_001007027)	TTS (NM_001007027)	-20281	NM_001204054	4718	Hs.407860	NM_004549	ENSG00000151366	NDUFC2	B14.5b|CI-B14.5b|HLC-1|NADHDH2	NADH:ubiquinone oxidoreductase subunit C2	protein-coding	0.013657	0.406061	
chunk0056_303_1	chr13	90834568	90835182	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	91722	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.009772	0.338211	
chunk0014_40_1	chr1	175023275	175023528	+	0	NA	promoter-TSS (NR_037606)	promoter-TSS (NR_037606)	54	NR_037606	63931	Hs.654858	NM_022100	ENSG00000120333	MRPS14	COXPD38|DJ262D12.2|HSMRPS14|MRP-S14|S14mt	mitochondrial ribosomal protein S14	protein-coding	0.063241	0.618110	
chunk0198_168_1	chr8	133247600	133247845	+	0	NA	intron (NM_006096, intron 12 of 15)	intron (NM_006096, intron 12 of 15)	49582	NM_001258432	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.008163	0.556911	
chunk0006_210_1	chr1	67832963	67833236	+	0	NA	intron (NR_040077, intron 1 of 9)	CpG	373	NM_018841	55970	Hs.431101	NM_018841	ENSG00000172380	GNG12	-	G protein subunit gamma 12	protein-coding	0.080586	0.715328	
chunk0041_238_1	chr11	128469740	128470357	+	0	NA	intron (NM_001143820, intron 8 of 9)	intron (NM_001143820, intron 8 of 9)	52262	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.012966	0.380259	
chunk0144_261_1	chr4	136829088	136829287	+	0	NA	Intergenic	Intergenic	703311	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.265000	
chunk0018_317_1	chr1	221227349	221227548	+	0	NA	Intergenic	Intergenic	108848	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.000000	0.445000	
chunk0152_433_1	chr5	66021769	66022550	+	0	NA	intron (NM_018695, intron 8 of 24)	intron (NM_018695, intron 8 of 24)	-76586	NR_028474	100303749	Hs.608060	NR_028474		LOC100303749	-	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene	pseudo	0.007682	0.317136	433(AAATACATGCTGTGCT,-,0.00),434(AATACATGCTGTGCTT,+,0.00)
chunk0091_251_1	chr19	10765309	10765913	+	0	NA	intron (NM_001005360, intron 2 of 20)	intron (NM_001005360, intron 2 of 20)	-14643	NR_039903	100616425		NR_039903	ENSG00000265879	MIR4748	mir-4748	microRNA 4748	ncRNA	0.024834	0.583471	
chunk0210_90_1	chrX	71129305	71129532	+	0	NA	exon (NM_005120, exon 26 of 45)	exon (NM_005120, exon 26 of 45)	10862	NM_005120	9968	Hs.409226	NM_005120	ENSG00000184634	MED12	ARC240|CAGH45|FGS1|HOPA|MED12S|OHDOX|OKS|OPA1|TNRC11|TRAP230	mediator complex subunit 12	protein-coding	0.030837	0.565789	
chunk0212_30_1	chrY	10911559	10911824	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1000893	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.018868	0.466165	
chunk0082_265_1	chr17	57872420	57873015	+	0	NA	exon (NM_001271875, exon 5 of 11)	exon (NM_001271875, exon 5 of 11)	-22645	NM_016070	51649	Hs.5836	NM_016070	ENSG00000181610	MRPS23	CGI-138|HSPC329|MRP-S23	mitochondrial ribosomal protein S23	protein-coding	0.026891	0.587248	
chunk0003_140_1	chr1	32937116	32937315	+	0	NA	exon (NM_153341, exon 9 of 9)	exon (NM_153341, exon 9 of 9)	27598	NM_153341	127544	Hs.591504	NM_153341	ENSG00000116514	RNF19B	IBRDC3|NKLAM	ring finger protein 19B	protein-coding	0.015075	0.485000	
chunk0062_367_1	chr14	73987876	73988717	+	0	NA	intron (NM_001249, intron 3 of 15)	intron (NM_001249, intron 3 of 15)	31027	NM_001249	957	Hs.655070	NM_001249	ENSG00000187097	ENTPD5	CD39L4|NTPDase-5|PCPH	ectonucleoside triphosphate diphosphohydrolase 5 (inactive)	protein-coding	0.007134	0.404988	
chunk0062_376_1	chr14	74336892	74337164	+	0	NA	Intergenic	Intergenic	-11435	NM_018228	55237	Hs.578167	NM_018228	ENSG00000133980	VRTN	C14orf115|vertnin	vertebrae development associated	protein-coding	0.007353	0.410256	107(CAGAACATACTGTCCT,-,0.00),108(AGAACATACTGTCCTT,+,0.00)
chunk0025_142_1	chr10	52212752	52213299	+	0	NA	intron (NM_006258, intron 9 of 17)	intron (NM_006258, intron 9 of 17)	101103	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.007313	0.293796	
chunk0165_191_1	chr6	34536441	34537071	+	0	NA	Intergenic	Intergenic	19577	NM_001252294	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.004762	0.586371	
chunk0178_58_1	chr7	30102084	30102763	+	0	NA	intron (NM_001197027, intron 13 of 13)	L1MB4|LINE|L1	-32513	NM_152793	222166	Hs.200100	NM_152793	ENSG00000180354	MTURN	C7orf41|Ells1	maturin, neural progenitor differentiation regulator homolog	protein-coding	0.004418	0.364706	
chunk0062_245_1	chr14	71454478	71455051	+	0	NA	Intergenic	Intergenic	-33097	NR_027046	145474	Hs.658241	NR_027046		LOC145474	-	uncharacterized LOC145474	ncRNA	0.008726	0.385017	
chunk0156_347_1	chr5	111920920	111921119	+	0	NA	intron (NR_046678, intron 1 of 3)	MER61E|LTR|ERV1	8511	NR_046678	100873948	Hs.147716	NR_046678	ENSG00000250095	NREP-AS1	-	NREP antisense RNA 1	ncRNA	0.005025	0.450000	
chunk0127_438_1	chr3	103200711	103201456	+	0	NA	Intergenic	Intergenic	323033	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.006711	0.371314	
chunk0123_197_1	chr3	44466589	44466942	+	0	NA	intron (NM_181489, intron 1 of 7)	HUERS-P1-int|LTR|ERV1	10905	NM_181489	353274	Hs.250481	NM_181489	ENSG00000185219	ZNF445	ZKSCAN15|ZNF168|ZSCAN47	zinc finger protein 445	protein-coding	0.005666	0.307910	
chunk0160_215_1	chr5	154873209	154873408	+	0	NA	intron (NM_001301082, intron 5 of 5)	intron (NM_001301082, intron 5 of 5)	14789	NM_001301080	9337	Hs.26703	NM_004779	ENSG00000155508	CNOT8	CAF1|CALIF|Caf1b|POP2|hCAF1	CCR4-NOT transcription complex subunit 8	protein-coding	0.005025	0.385000	151(CAGAACTTCATGTTCT,-,0.00),152(AGAACTTCATGTTCTT,+,0.00)
chunk0157_90_1	chr5	116631023	116631526	+	0	NA	Intergenic	L1ME3G|LINE|L1	-56348	NM_001300780	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.000000	0.325397	
chunk0092_21_1	chr19	18762541	18762845	+	0	NA	intron (NM_001098482, intron 9 of 14)	intron (NM_001098482, intron 9 of 14)	28612	NM_000095	1311	Hs.1584	NM_000095	ENSG00000105664	COMP	EDM1|EPD1|MED|PSACH|THBS5|TSP5	cartilage oligomeric matrix protein	protein-coding	0.023026	0.629508	
chunk0143_415_1	chr4	123438058	123438348	+	0	NA	Intergenic	Intergenic	38713	NM_005841	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.006897	0.429553	
chunk0114_223_1	chr21	15769316	15770156	+	0	NA	intron (NM_013396, intron 3 of 23)	intron (NM_013396, intron 3 of 23)	39711	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.009524	0.332937	486(CAGAACAAGATGTGCT,-,0.00),487(AGAACAAGATGTGCTA,+,0.00)
chunk0085_186_1	chr18	6120937	6121385	+	0	NA	intron (NM_173464, intron 14 of 19)	intron (NM_173464, intron 14 of 19)	-135583	NR_110765	101927150		NR_110765		L3MBTL4-AS1	-	L3MBTL4 antisense RNA 1	ncRNA	0.008929	0.369710	
chunk0045_59_1	chr12	45304015	45304268	+	0	NA	intron (NM_001142679, intron 2 of 19)	intron (NM_001142679, intron 2 of 19)	11458	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.007905	0.417323	212(GAGAACAGGGTGCCCA,-,0.00),213(AGAACAGGGTGCCCAG,+,0.00)
chunk0180_317_1	chr7	71770374	71770752	+	0	NA	Intergenic	L2c|LINE|L2	-462793	NR_037477	100500836		NR_037477	ENSG00000265878	MIR3914-1	-	microRNA 3914-1	ncRNA	0.007937	0.503958	337(TGGCACACACTGATCC,-,0.00),338(GGCACACACTGATCCC,+,0.00)
chunk0170_367_1	chr6	116888536	116889237	+	0	NA	intron (NM_173560, intron 4 of 18)	intron (NM_173560, intron 4 of 18)	11673	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.002853	0.340456	
chunk0082_347_1	chr17	59869355	59870027	+	0	NA	intron (NM_001193609, intron 5 of 7)	intron (NM_001193609, intron 5 of 7)	23254	NM_001193611	51174	Hs.463638	NM_016261	ENSG00000108423	TUBD1	TUBD	tubulin delta 1	protein-coding	0.010417	0.393759	245(AGGAACATTGTGTTCC,-,0.00),246(GGAACATTGTGTTCCT,+,0.00)
chunk0170_376_1	chr6	116932609	116932808	+	0	NA	TTS (NM_173560)	TTS (NM_173560)	55495	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.005025	0.340000	
chunk0070_356_1	chr15	76111691	76112086	+	0	NA	intron (NM_152335, intron 1 of 10)	L1MC2|LINE|L1	51930	NM_152335	123591	Hs.661411	NM_152335	ENSG00000169758	TMEM266	C15orf27|HVRP1|HsHVRP1|hTMEM266	transmembrane protein 266	protein-coding	0.010127	0.373737	
chunk0189_325_1	chr8	26337474	26337927	+	0	NA	intron (NM_001177591, intron 2 of 9)	Charlie4z|DNA|hAT-Charlie	44484	NM_001177591	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.011038	0.365639	
chunk0154_6_1	chr5	76547384	76548054	+	0	NA	intron (NM_001285460, intron 1 of 34)	intron (NM_001285460, intron 1 of 34)	310	NM_001285460	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.008955	0.430700	
chunk0027_340_1	chr10	78570897	78571345	+	0	NA	Intergenic	L2c|LINE|L2	303793	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.006696	0.510022	172(CAGGACAGACTGCTCT,-,0.00),173(AGGACAGACTGCTCTC,+,0.00)
chunk0021_436_1	chr1	247738981	247739311	+	0	NA	Intergenic	Intergenic	19260	NM_012353	26188	Hs.381306	NM_012353	ENSG00000221888	OR1C1	HSTPCR27|OR1-42|OR1.5.10|ORL211|TPCR27	olfactory receptor family 1 subfamily C member 1	protein-coding	0.003030	0.465257	
chunk0134_50_1	chr3	175941315	175941698	+	0	NA	Intergenic	L1M2|LINE|L1	-165173	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.505208	
chunk0041_419_1	chr11	134258539	134259258	+	0	NA	intron (NM_014384, intron 4 of 10)	intron (NM_014384, intron 4 of 10)	5358	NM_014384	27034	Hs.14791	NM_014384	ENSG00000151498	ACAD8	ACAD-8|ARC42	acyl-CoA dehydrogenase family member 8	protein-coding	0.013908	0.490278	311(AAGTACAGAGAGTTCC,-,0.00),312(AGTACAGAGAGTTCCT,+,0.00)
chunk0045_81_1	chr12	45828399	45828755	+	0	NA	intron (NM_152641, intron 6 of 20)	L1ME3A|LINE|L1	98740	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.005618	0.338936	
chunk0119_278_1	chr22	46060541	46060749	+	0	NA	Intergenic	Intergenic	-6501	NM_018280	55267	Hs.567529	NM_018280		PRR34	C22orf26	PRR34 long non-coding RNA	protein-coding	0.014423	0.358852	
chunk0036_74_1	chr11	59979804	59980102	+	0	NA	intron (NR_130719, intron 8 of 8)	MER67C|LTR|ERV1	37074	NR_130719	255649	Hs.722773	NR_130719		OOSP1	-	oocyte secreted protein 1	pseudo	0.003356	0.381271	
chunk0167_18_1	chr6	53690343	53690871	+	0	NA	Intergenic	Intergenic	-24899	NM_001003760	401265	Hs.131064	NM_001003760	ENSG00000124743	KLHL31	BKLHD6|KBTBD1|KLHL|bA345L23.2	kelch like family member 31	protein-coding	0.007576	0.370510	431(AAAGACAGTCAGTCCT,-,0.00)
chunk0192_333_1	chr8	67344091	67344338	+	0	NA	promoter-TSS (NM_006421)	promoter-TSS (NM_006421)	-537	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.032389	0.520161	
chunk0109_341_1	chr20	9495618	9495817	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-18641	NM_001199897	24141	Hs.22920	NM_012261	ENSG00000125869	LAMP5	BAD-LAMP|BADLAMP|C20orf103|LAMP-5|UNC-46	lysosomal associated membrane protein family member 5	protein-coding	0.020101	0.480000	
chunk0131_431_1	chr3	153666824	153667355	+	0	NA	Intergenic	Intergenic	182594	NM_001101337									0.005650	0.332707	
chunk0210_399_1	chrX	98373472	98373783	+	0	NA	Intergenic	Intergenic	-809092	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.000000	0.333333	
chunk0169_227_1	chr6	104638683	104639350	+	0	NA	Intergenic	L2b|LINE|L2	220903	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.005997	0.432635	228(AGGAACAGCATGTACA,-,0.00),229(GGAACAGCATGTACAA,+,0.00)
chunk0168_414_1	chr6	95340974	95341568	+	0	NA	Intergenic	Intergenic	236180	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.008418	0.300840	
chunk0047_76_1	chr12	67714624	67715104	+	0	NA	intron (NR_110063, intron 4 of 4)	intron (NR_110063, intron 4 of 4)	14611	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.004167	0.390852	
chunk0125_1_1	chr3	61634727	61634962	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	73275	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.004255	0.402542	
chunk0004_316_1	chr1	49584644	49585009	+	0	NA	intron (NM_032785, intron 3 of 13)	MIR|SINE|MIR	-112741	NR_046839	100874313	Hs.551277	NR_046839	ENSG00000225623	AGBL4-IT1	-	AGBL4 intronic transcript 1	ncRNA	0.005479	0.341530	220(GAGAACATCAAGTCCT,-,0.00),221(AGAACATCAAGTCCTC,+,0.00)
chunk0209_70_1	chrX	37994247	37994459	+	0	NA	Intergenic	Intergenic	3536	NM_012274	25763	Hs.122959	NM_012274	ENSG00000187516	HYPM	CXorf27|HIP17	huntingtin interacting protein M	protein-coding	0.014151	0.521127	103(GGAAACAAAATGTTCT,-,0.00),104(GAAACAAAATGTTCTG,+,0.00)
chunk0027_222_1	chr10	76206125	76206609	+	0	NA	intron (NR_131178, intron 6 of 7)	L2c|LINE|L2	423606	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.006198	0.468041	
chunk0208_354_1	chrX	25640378	25640629	+	0	NA	Intergenic	LTR80B|LTR|ERVL	-497840	NM_173699	286514	Hs.350683	NM_173699	ENSG00000176774	MAGEB18	-	MAGE family member B18	protein-coding	0.000000	0.357143	
chunk0017_288_1	chr1	210273094	210273607	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-39229	NR_024337	574036	Hs.446946	NR_024337	ENSG00000203706	SERTAD4-AS1	C1orf133	SERTAD4 antisense RNA 1	ncRNA	0.009747	0.377432	
chunk0162_356_1	chr6	7146997	7147196	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	39243	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.005025	0.535000	
chunk0148_348_1	chr5	14519661	14519897	+	0	NA	Intergenic	L1PREC2|LINE|L1	-62003	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.000000	0.316456	
chunk0212_290_1	chrX	140912676	140913083	+	0	NA	Intergenic	Intergenic	13340	NR_031725	100302169		NR_031725	ENSG00000221081	MIR320D2	MIR320D-2|MIRN320D2|hsa-mir-320d-2|mir-320d-2	microRNA 320d-2	ncRNA	0.000000	0.340686	
chunk0028_455_1	chr10	94779775	94779974	+	0	NA	intron (NM_000769, intron 3 of 8)	intron (NM_000769, intron 3 of 8)	17193	NM_000769	1557	Hs.282409	NM_000769	ENSG00000165841	CYP2C19	CPCJ|CYP2C|CYPIIC17|CYPIIC19|P450C2C|P450IIC19	cytochrome P450 family 2 subfamily C member 19	protein-coding	0.000000	0.375000	
chunk0191_271_1	chr8	53628209	53628543	+	0	NA	Intergenic	L1ME3B|LINE|L1	214666	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.002994	0.370149	108(AAGAACACGGTGTTTC,-,0.00),109(AGAACACGGTGTTTCT,+,0.00)
chunk0067_405_1	chr15	49458264	49458812	+	0	NA	intron (NM_002009, intron 2 of 3)	intron (NM_002009, intron 2 of 3)	35360	NM_002009	2252	Hs.567268	NM_002009	ENSG00000140285	FGF7	HBGF-7|KGF	fibroblast growth factor 7	protein-coding	0.003650	0.298725	350(GGGAACTTTATGTTCC,-,0.00),351(GGAACTTTATGTTCCC,+,0.00)
chunk0171_452_1	chr6	132192983	132193193	+	0	NA	Intergenic	Intergenic	59110	NR_038981	100507254	Hs.103070	NR_038981	ENSG00000228495	LINC01013	-	long intergenic non-protein coding RNA 1013	ncRNA	0.004762	0.364929	174(CAGTACATACCGTGCT,-,0.00),175(AGTACATACCGTGCTC,+,0.00)
chunk0201_220_1	chr9	37373263	37373475	+	0	NA	Intergenic	AluJb|SINE|Alu	-49341	NM_012203	9380	Hs.155742	NM_012203	ENSG00000137106	GRHPR	GLXR|GLYD|PH2	glyoxylate and hydroxypyruvate reductase	protein-coding	0.004717	0.516432	
chunk0022_49_1	chr10	8144305	8145051	+	0	NA	Intergenic	Intergenic	89974	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.017426	0.437751	712(TAGGACTGATTGTCCC,-,0.00),713(AGGACTGATTGTCCCA,+,0.00)
chunk0196_447_1	chr8	116639707	116640379	+	0	NA	Intergenic	X1_LINE|LINE|CR1	115780	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.002976	0.365527	
chunk0040_326_1	chr11	118241206	118241405	+	0	NA	intron (NR_104405, intron 1 of 4)	intron (NR_104405, intron 1 of 4)	11063	NR_104405	196264	Hs.15396	NM_198275	ENSG00000160588	MPZL3	-	myelin protein zero like 3	protein-coding	0.015075	0.465000	
chunk0127_219_1	chr3	96595043	96595578	+	0	NA	Intergenic	Intergenic	-219271	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.003738	0.363806	
chunk0157_399_1	chr5	124225075	124225631	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	213167	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.007194	0.385996	
chunk0120_332_1	chr3	10795496	10796291	+	0	NA	Intergenic	L1MA9|LINE|L1	-20339	NM_014229	6538	Hs.655078	NM_014229	ENSG00000132164	SLC6A11	GAT-3|GAT3|GAT4	solute carrier family 6 member 11	protein-coding	0.006289	0.363065	
chunk0175_436_1	chr6	169653875	169654211	+	0	NA	intron (NM_001202550, intron 10 of 21)	intron (NM_001202550, intron 10 of 21)	48020	NM_182552	253769	Hs.131903	NM_182552	ENSG00000184465	WDR27	-	WD repeat domain 27	protein-coding	0.008929	0.421365	151(GAGAACACAGTGCACT,-,0.00),152(AGAACACAGTGCACTT,+,0.00)
chunk0137_357_1	chr4	25826061	25826602	+	0	NA	intron (NM_001297592, intron 6 of 23)	intron (NM_001297592, intron 6 of 23)	36700	NM_015187	23231	Hs.479384	NM_015187	ENSG00000091490	SEL1L3	Sel-1L3	SEL1L family member 3	protein-coding	0.009242	0.435424	
chunk0146_255_1	chr4	162684176	162684408	+	0	NA	Intergenic	Intergenic	409336	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.004310	0.433476	
chunk0163_283_1	chr6	13725052	13725709	+	0	NA	Intergenic	Intergenic	-13816	NM_005493	10048	Hs.708182	NM_005493	ENSG00000010017	RANBP9	BPM-L|BPM90|RANBPM|RanBP7	RAN binding protein 9	protein-coding	0.010654	0.411854	
chunk0117_169_1	chr22	20390791	20390990	+	0	NA	Intergenic	Intergenic	-3225	NM_003426	7625	Hs.517418	NM_003426	ENSG00000185252	ZNF74	COS52|ZFP520|ZNF520|hZNF7	zinc finger protein 74	protein-coding	0.000000	0.460000	
chunk0019_7_1	chr1	223248384	223248681	+	0	NA	intron (NM_001037175, intron 5 of 5)	intron (NM_001037175, intron 5 of 5)	-105250	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.006734	0.436242	
chunk0044_322_1	chr12	34198948	34199282	+	0	NA	Intergenic	LTR66|LTR|ERVL	176834	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.020958	0.456716	
chunk0157_77_1	chr5	116452939	116453138	+	0	NA	intron (NR_109879, intron 2 of 2)	L2c|LINE|L2	5540	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.005025	0.460000	
chunk0057_237_1	chr13	104466037	104466485	+	0	NA	Intergenic	Intergenic	-999606	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.000000	0.305122	
chunk0124_336_1	chr3	58272021	58272489	+	0	NA	intron (NM_020676, intron 5 of 8)	MIR|SINE|MIR	-33990	NR_049758	11102	Hs.446320	NM_007042	ENSG00000163684	RPP14	P14	ribonuclease P/MRP subunit p14	protein-coding	0.012821	0.428571	
chunk0196_22_1	chr8	101520422	101520964	+	0	NA	intron (NM_024915, intron 1 of 15)	L2b|LINE|L2	28253	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.003690	0.406998	145(GAGAACATCTTGTGTT,-,0.00),146(AGAACATCTTGTGTTT,+,0.00),432(TTGCACATGCTGTTCC,-,0.00),433(TGCACATGCTGTTCCT,+,0.00)
chunk0163_125_1	chr6	10332164	10332582	+	0	NA	Intergenic	AluSx3|SINE|Alu	-79945	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.011962	0.443914	
chunk0144_319_1	chr4	138910850	138911480	+	0	NA	Intergenic	Intergenic	-104594	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.025397	0.529319	
chunk0179_41_1	chr7	43294207	43294574	+	0	NA	intron (NM_015052, intron 3 of 29)	GA-rich|Low_complexity|Low_complexity	143495	NR_037508	100500829		NR_037508	ENSG00000264069	MIR3943	-	microRNA 3943	ncRNA	0.005450	0.519022	
chunk0150_327_1	chr5	38384406	38384605	+	0	NA	intron (NM_152403, intron 6 of 21)	intron (NM_152403, intron 6 of 21)	18966	NR_102749	100506475	Hs.662304	NR_102749	ENSG00000248572	EGFLAM-AS2	-	EGFLAM antisense RNA 2	ncRNA	0.005025	0.490000	
chunk0158_131_1	chr5	127197372	127198266	+	0	NA	Intergenic	L1PA6|LINE|L1	-92945	NM_001308119	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.005593	0.494972	
chunk0131_368_1	chr3	151996460	151996706	+	0	NA	Intergenic	L2b|LINE|L2	-68408	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.004065	0.315789	
chunk0078_174_1	chr17	4415149	4415416	+	0	NA	Intergenic	L1MB7|LINE|L1	-18642	NM_182538	201305	Hs.657543	NM_182538	ENSG00000182557	SPNS3	SLC62A3	sphingolipid transporter 3 (putative)	protein-coding	0.014981	0.451493	
chunk0085_190_1	chr18	6352072	6352843	+	0	NA	intron (NM_173464, intron 1 of 19)	intron (NM_173464, intron 1 of 19)	21968	NR_036205	100422840		NR_036205	ENSG00000283532	MIR4317	-	microRNA 4317	ncRNA	0.000000	0.370466	
chunk0103_161_1	chr2	162579965	162580370	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-188769	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.002469	0.386700	
chunk0096_166_1	chr2	29533574	29533906	+	0	NA	intron (NM_004304, intron 3 of 28)	L2b|LINE|L2	387871	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.003012	0.501502	
chunk0111_290_1	chr20	31699013	31699306	+	0	NA	intron (NM_001191, intron 2 of 2)	intron (NM_001191, intron 2 of 2)	-22348	NR_131907	103021294		NR_131907	ENSG00000281376	ABALON	INXS	apoptotic BCL2L1-antisense long non-coding RNA	ncRNA	0.010239	0.496599	111(AAGGACGCTCTGTTCC,-,0.00),112(AGGACGCTCTGTTCCC,+,0.00)
chunk0101_416_1	chr2	139205116	139205501	+	0	NA	Intergenic	Intergenic	307984	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005195	0.349741	
chunk0210_77_1	chrX	70172304	70172667	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4998	NM_198512	347516	Hs.454355	NM_198512	ENSG00000184210	DGAT2L6	DC3	diacylglycerol O-acyltransferase 2 like 6	protein-coding	0.005510	0.423077	
chunk0003_450_1	chr1	41462293	41462553	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	22260	NM_001956	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.000000	0.406130	
chunk0074_352_1	chr16	33687731	33687963	+	0	NA	Intergenic	Intergenic	-81530	NR_130771	104644205	Hs.742548	NR_130771		ENPP7P13	DUNQU1	ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 13	pseudo	0.000000	0.472103	27(GTGGACACTGTGTGCA,-,0.00),28(TGGACACTGTGTGCAG,+,0.00)
chunk0035_91_1	chr11	42098170	42098583	+	0	NA	Intergenic	L2c|LINE|L2	155314	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.004843	0.398551	
chunk0199_415_1	chr9	13606327	13606997	+	0	NA	Intergenic	Intergenic	-175333	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.008955	0.375559	
chunk0083_37_1	chr17	63364044	63364720	+	0	NA	intron (NM_025185, intron 12 of 24)	intron (NM_025185, intron 12 of 24)	76464	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.007396	0.367799	
chunk0200_167_1	chr9	19049038	19049237	+	0	NA	promoter-TSS (NM_006570)	promoter-TSS (NM_006570)	217	NM_001287049	158297	Hs.731593	NM_153707	ENSG00000155875	SAXO1	C9orf138|FAM154A	stabilizer of axonemal microtubules 1	protein-coding	0.055276	0.615000	
chunk0102_220_1	chr2	148635561	148635938	+	0	NA	Intergenic	Intergenic	-9242	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.002653	0.317460	
chunk0200_176_1	chr9	19246115	19246901	+	0	NA	intron (NR_073201, intron 1 of 31)	AluJr|SINE|Alu	15743	NR_073201	55667	Hs.249591	NM_017925	ENSG00000137145	DENND4C	C9orf55|C9orf55B|RAB10GEF|bA513M16.3	DENN domain containing 4C	protein-coding	0.008906	0.359593	
chunk0176_225_1	chr7	15277875	15278188	+	0	NA	intron (NM_001004320, intron 12 of 12)	L1PA5|LINE|L1	283984	NM_001004320	392636	Hs.670634	NM_001004320	ENSG00000187546	AGMO	TMEM195	alkylglycerol monooxygenase	protein-coding	0.006390	0.490446	
chunk0115_193_1	chr21	26138450	26139190	+	0	NA	intron (NM_001136131, intron 1 of 15)	intron (NM_001136131, intron 1 of 15)	1570	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.012162	0.396761	
chunk0001_22_1	chr1	1237391	1237736	+	0	NA	Intergenic	Intergenic	5314	NM_080605	126792	Hs.284284	NM_080605	ENSG00000176022	B3GALT6	EDSP2|EDSSPD2|SEMDJL1|beta3GalT6	beta-1,3-galactosyltransferase 6	protein-coding	0.049275	0.676301	
chunk0018_255_1	chr1	220238850	220239059	+	0	NA	intron (NM_012414, intron 1 of 34)	L2c|LINE|L2	28761	NR_001587	6791	Hs.654849	NR_001587		AURKAP1	AURKAPS1|AurAps1|STK6P	aurora kinase A pseudogene 1	pseudo	0.014354	0.333333	
chunk0049_256_1	chr12	93712097	93712736	+	0	NA	intron (NR_110092, intron 2 of 2)	L2b|LINE|L2	25407	NR_110092	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.007825	0.331250	23(TAGCACTGACTGTTCT,-,0.00),24(AGCACTGACTGTTCTT,+,0.00)
chunk0070_198_1	chr15	72117756	72117996	+	0	NA	promoter-TSS (NM_001172111)	promoter-TSS (NM_001172111)	223	NM_006901	4649	Hs.513000	NM_006901	ENSG00000066933	MYO9A	CMS24	myosin IXA	protein-coding	0.116667	0.746888	
chunk0076_394_1	chr16	72546377	72546709	+	0	NA	intron (NR_126330, intron 3 of 13)	L1PA7|LINE|L1	118466	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.006024	0.360360	119(AAAGACACAATGTACC,-,0.00)
chunk0054_210_1	chr13	45154288	45154589	+	0	NA	intron (NM_004128, intron 4 of 7)	intron (NM_004128, intron 4 of 7)	33942	NM_004128	2963	Hs.654582	NM_004128	ENSG00000188342	GTF2F2	BTF4|RAP30|TF2F2|TFIIF	general transcription factor IIF subunit 2	protein-coding	0.006645	0.321192	200(TTGGACAGTATGTTCT,-,0.00),201(TGGACAGTATGTTCTT,+,0.00)
chunk0189_11_1	chr8	19491766	19492369	+	0	NA	intron (NM_001130518, intron 4 of 9)	intron (NM_001130518, intron 4 of 9)	110478	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.009950	0.377483	214(AAGTACACTCTGTGCT,-,0.00),215(AGTACACTCTGTGCTA,+,0.00)
chunk0208_282_1	chrX	21900311	21900861	+	0	NA	Intergenic	Intergenic	-39987	NM_001258423	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.010909	0.350272	
chunk0055_205_1	chr13	61995721	61996172	+	0	NA	Intergenic	L2a|LINE|L2	33602	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004435	0.327434	
chunk0185_136_1	chr7	127018598	127018797	+	0	NA	intron (NR_028041, intron 2 of 10)	MLT1J|LTR|ERVL-MaLR	39487	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.005025	0.435000	
chunk0104_265_1	chr2	177797258	177798032	+	0	NA	intron (NM_001077197, intron 10 of 20)	MARNA|DNA|TcMar-Mariner	91094	NM_001077196	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.002584	0.350968	
chunk0012_29_1	chr1	155022784	155023353	+	0	NA	intron (NM_144622, intron 14 of 14)	intron (NM_144622, intron 14 of 14)	10713	NM_144622	127579	Hs.591491	NM_144622	ENSG00000163354	DCST2	-	DC-STAMP domain containing 2	protein-coding	0.010545	0.550877	
chunk0162_198_1	chr6	3943470	3943865	+	0	NA	Intergenic	Intergenic	-77668	NM_003913	8899	Hs.159014	NM_003913	ENSG00000112739	PRPF4B	PR4H|PRP4|PRP4H|PRP4K|dJ1013A10.1	pre-mRNA processing factor 4B	protein-coding	0.032911	0.492424	
chunk0200_417_1	chr9	27560907	27561145	+	0	NA	3' UTR (NM_145005, exon 5 of 5)	3' UTR (NM_145005, exon 5 of 5)	12467	NM_018325	203228	Hs.493639	NM_018325	ENSG00000147894	C9orf72	ALSFTD|DENND9|DENNL72|FTDALS|FTDALS1	C9orf72-SMCR8 complex subunit	protein-coding	0.004202	0.343096	
chunk0153_155_1	chr5	69517664	69518027	+	0	NA	intron (NM_002538, intron 4 of 8)	intron (NM_002538, intron 4 of 8)	13668	NM_001205255	100506658	Hs.592605	NM_002538	ENSG00000197822	OCLN	BLCPMG|PPP1R115|PTORCH1	occludin	protein-coding	0.013774	0.406593	
chunk0151_179_1	chr5	50346696	50347089	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	94508	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.000000	0.314721	
chunk0104_347_1	chr2	179854644	179855461	+	0	NA	intron (NM_152520, intron 1 of 9)	intron (NM_152520, intron 1 of 9)	5856	NR_031659	100302172		NR_031659	ENSG00000221240	MIR1258	MIRN1258|hsa-mir-1258|mir-1258	microRNA 1258	ncRNA	0.004896	0.311736	
chunk0141_288_1	chr4	86824533	86824833	+	0	NA	intron (NM_197965, intron 5 of 5)	L1PA16|LINE|L1	24580	NM_197965	345274	Hs.452996	NM_197965	ENSG00000145283	SLC10A6	SOAT	solute carrier family 10 member 6	protein-coding	0.010000	0.385382	
chunk0211_114_1	chrX	111988327	111988741	+	0	NA	intron (NM_012471, intron 1 of 10)	intron (NM_012471, intron 1 of 10)	94242	NM_012471	7224	Hs.657709	NM_012471	ENSG00000072315	TRPC5	PPP1R159|TRP5	transient receptor potential cation channel subfamily C member 5	protein-coding	0.004831	0.366265	
chunk0199_165_1	chr9	4418659	4418945	+	0	NA	Intergenic	Intergenic	-71625	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.000000	0.404181	
chunk0164_221_1	chr6	22873807	22874207	+	0	NA	Intergenic	Intergenic	304558	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.002500	0.389027	
chunk0160_357_1	chr5	160524215	160524542	+	0	NA	Intergenic	Intergenic	39026	NR_029701	406938		NR_029701	ENSG00000283733	MIR146A	MIRN146|MIRN146A|miR-146a|miRNA146A	microRNA 146a	ncRNA	0.006116	0.411585	
chunk0081_4_1	chr17	37147329	37147716	+	0	NA	intron (NM_198836, intron 45 of 55).2	intron (NM_198836, intron 45 of 55).2	-97279	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.007752	0.435567	
chunk0096_416_1	chr2	38159346	38160048	+	0	NA	intron (NR_027252, intron 2 of 2)	intron (NR_027252, intron 2 of 2)	28592	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.015670	0.453770	523(AAAAACATCCTGTGCT,-,0.00),524(AAAACATCCTGTGCTT,+,0.00)
chunk0101_166_1	chr2	128641026	128641487	+	0	NA	Intergenic	MIR|SINE|MIR	-223344	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.013015	0.495671	219(GAAGACACCTTGTTCC,-,0.00),220(AAGACACCTTGTTCCC,+,0.00)
chunk0154_349_1	chr5	87035453	87035652	+	0	NA	Intergenic	L1PBa|LINE|L1	79402	NR_036243	100422887		NR_036243	ENSG00000265919	MIR4280	-	microRNA 4280	ncRNA	0.005025	0.570000	
chunk0079_226_1	chr17	15385263	15385879	+	0	NA	Intergenic	L1ME1|LINE|L1	-43930	NM_031898	64518	Hs.414648	NM_031898	ENSG00000125409	TEKT3	-	tektin 3	protein-coding	0.003247	0.309562	
chunk0101_403_1	chr2	138893578	138894255	+	0	NA	Intergenic	Intergenic	-3408	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005908	0.380531	365(CTGTACACACAGTTCC,-,0.00),366(TGTACACACAGTTCCT,+,0.00)
chunk0078_53_1	chr17	1413377	1413713	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-13283	NM_006761	7531	Hs.513851	NM_006761	ENSG00000108953	YWHAE	14-3-3E|HEL2|KCIP-1|MDCR|MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	protein-coding	0.002976	0.480712	
chunk0103_411_1	chr2	169441692	169442016	+	0	NA	Intergenic	L1ME1|LINE|L1	-37642	NM_152384	129880	Hs.233398	NM_152384	ENSG00000163093	BBS5	-	Bardet-Biedl syndrome 5	protein-coding	0.018519	0.489231	
chunk0081_293_1	chr17	45043302	45043727	+	0	NA	intron (NM_001288654, intron 1 of 4)	LTR57|LTR|ERVL	8003	NM_001288655	79877	Hs.463148	NM_024819	ENSG00000172992	DCAKD	-	dephospho-CoA kinase domain containing	protein-coding	0.025882	0.525822	
chunk0042_327_1	chr12	9719975	9720229	+	0	NA	intron (NM_001253750, intron 2 of 3)	intron (NM_001253750, intron 2 of 3)	13197	NM_001253750	160365	Hs.560087	NM_172004	ENSG00000184293	CLECL1	DCAL-1|DCAL1	C-type lectin like 1	protein-coding	0.007874	0.501961	
chunk0074_284_1	chr16	29310852	29311199	+	0	NA	intron (NR_002939, intron 1 of 8)	intron (NR_002939, intron 1 of 8)	8738	NR_002939	440352	Hs.658149	NR_002939		SNX29P2	RUNDC2C	sorting nexin 29 pseudogene 2	pseudo	0.028818	0.589080	
chunk0058_202_1	chr14	24806231	24806754	+	0	NA	Intergenic	Intergenic	-172266	NM_004131	3002	Hs.1051	NM_004131	ENSG00000100453	GZMB	C11|CCPI|CGL-1|CGL1|CSP-B|CSPB|CTLA1|CTSGL1|HLP|SECT	granzyme B	protein-coding	0.013384	0.433206	
chunk0198_239_1	chr8	134167506	134168093	+	0	NA	Intergenic	Intergenic	281303	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006814	0.440476	
chunk0205_285_1	chr9	111857494	111857923	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-39058	NM_003358	7357	Hs.304249	NM_003358	ENSG00000148154	UGCG	GCS|GLCT1	UDP-glucose ceramide glucosyltransferase	protein-coding	0.006993	0.439535	
chunk0026_280_1	chr10	67281312	67281600	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	121954	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.003472	0.328720	
chunk0194_159_1	chr8	84803271	84803689	+	0	NA	intron (NM_001287243, intron 3 of 7)	intron (NM_001287243, intron 3 of 7)	97553	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002392	0.367542	
chunk0034_118_1	chr11	28144044	28144268	+	0	NA	intron (NM_001113528, intron 3 of 6)	L2c|LINE|L2	35905	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.004464	0.351111	
chunk0128_298_1	chr3	111402863	111403446	+	0	NA	Intergenic	L1M2a|LINE|L1	-138925	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.008576	0.323630	190(GGGTACAGTGTGCTCT,-,0.00),191(GGTACAGTGTGCTCTG,+,0.00),239(AGGCTCAGTTTGTTCT,-,0.00),240(GGCTCAGTTTGTTCTT,+,0.00)
chunk0086_326_1	chr18	24425234	24425545	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-1256	NM_018439	55364	Hs.515317	NM_018439	ENSG00000154059	IMPACT	RWDD5	impact RWD domain protein	protein-coding	0.009646	0.349359	
chunk0133_436_1	chr3	174955316	174955971	+	0	NA	intron (NM_207015, intron 1 of 13)	intron (NM_207015, intron 1 of 13)	96322	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.003053	0.371951	
chunk0152_326_1	chr5	62145984	62146333	+	0	NA	Intergenic	MIRc|SINE|MIR	-160004	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.002865	0.385714	
chunk0205_123_1	chr9	107935871	107936422	+	0	NA	Intergenic	Intergenic	-446426	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.014519	0.438406	
chunk0063_94_1	chr14	78341783	78342309	+	0	NA	intron (NR_073547, intron 4 of 20)	intron (NR_073547, intron 4 of 20)	-61685	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.003802	0.417457	
chunk0193_345_1	chr8	79454527	79455070	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-156016	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.007366	0.354779	
chunk0188_144_1	chr8	9672697	9673231	+	0	NA	intron (NM_003747, intron 3 of 26)	intron (NM_003747, intron 3 of 26)	-68708	NR_030327	693182		NR_030327	ENSG00000207701	MIR597	MIRN597|hsa-mir-597|mir-597	microRNA 597	ncRNA	0.007491	0.390654	
chunk0030_405_1	chr10	120084981	120085819	+	0	NA	Intergenic	Intergenic	126887	NR_039830	100616322		NR_039830	ENSG00000265370	MIR4682	-	microRNA 4682	ncRNA	0.007160	0.468415	
chunk0178_301_1	chr7	37728654	37728879	+	0	NA	Intergenic	Intergenic	-11628	NM_181791	353345	Hs.563492	NM_181791	ENSG00000187037	GPR141	PGR13	G protein-coupled receptor 141	protein-coding	0.000000	0.530973	
chunk0193_267_1	chr8	77094496	77094900	+	0	NA	Intergenic	L1ME4a|LINE|L1	-93654	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.000000	0.283951	
chunk0193_276_1	chr8	77322523	77323387	+	0	NA	Intergenic	Intergenic	-127742	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.002315	0.328324	
chunk0047_290_1	chr12	73529081	73530066	+	0	NA	Intergenic	L1PB|LINE|L1	370383	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.001015	0.335700	
chunk0181_152_1	chr7	81909054	81909326	+	0	NA	Intergenic	L1PA14|LINE|L1	-99987	NR_110076	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.003676	0.388278	
chunk0016_348_1	chr1	202036923	202037255	+	0	NA	Intergenic	L2a|LINE|L2	26527	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.009036	0.396396	152(GAGAACAGAGTGATCC,-,0.00),153(AGAACAGAGTGATCCC,+,0.00)
chunk0212_76_1	chrY	11531258	11532303	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	889810	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.022967	0.359465	
chunk0065_437_1	chr14	106467267	106467563	+	0	NA	Intergenic	Intergenic	-15024	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.010135	0.484848	
chunk0010_144_1	chr1	115033906	115034119	+	0	NA	promoter-TSS (NM_001277991)	promoter-TSS (NM_001277991)	66	NM_001277991	7252	Hs.406687	NM_000549	ENSG00000134200	TSHB	TSH-B|TSH-BETA	thyroid stimulating hormone subunit beta	protein-coding	0.000000	0.401869	
chunk0113_102_1	chr20	50988266	50988503	+	0	NA	Intergenic	Intergenic	29570	NM_014484	27304	Hs.159410	NM_014484	ENSG00000124217	MOCS3	UBA4	molybdenum cofactor synthesis 3	protein-coding	0.012658	0.487395	136(AGGGACAGCCCGTGCC,-,0.00),137(GGGACAGCCCGTGCCC,+,0.00)
chunk0001_447_1	chr1	11804563	11804778	+	0	NA	intron (NM_005957, intron 1 of 11)	intron (NM_005957, intron 1 of 11)	-1426	NM_001286	1185	Hs.193043	NM_001286	ENSG00000011021	CLCN6	CLC-6	chloride voltage-gated channel 6	protein-coding	0.000000	0.449074	
chunk0089_294_1	chr18	63230430	63230629	+	0	NA	intron (NM_000633, intron 2 of 2)	L1ME3Cz|LINE|L1	88851	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.000000	0.295000	
chunk0168_164_1	chr6	83816253	83816871	+	0	NA	Intergenic	Intergenic	-36704	NM_001009994	134701	Hs.149454	NM_001009994	ENSG00000203877	RIPPLY2	C6orf159|SCDO6|dJ237I15.1	ripply transcriptional repressor 2	protein-coding	0.003236	0.334410	
chunk0184_3_1	chr7	111560775	111561130	+	0	NA	intron (NM_032549, intron 1 of 5)	intron (NM_032549, intron 1 of 5)	1339	NM_032549	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.005634	0.384831	
chunk0051_449_1	chr12	123335411	123335935	+	0	NA	intron (NM_001167856, intron 5 of 30)	MER58A|DNA|hAT-Charlie	14768	NM_018183	55206	Hs.7012	NM_018183	ENSG00000139697	SBNO1	MOP3|Sno	strawberry notch homolog 1	protein-coding	0.009542	0.339048	
chunk0073_91_1	chr16	4183585	4183837	+	0	NA	Intergenic	CpG	58369	NM_001098814	6345	Hs.10041	NM_001098814	ENSG00000185739	SRL	SAR	sarcalumenin	protein-coding	0.123016	0.754941	
chunk0083_96_1	chr17	64506243	64506442	+	0	NA	promoter-TSS (NM_004396)	promoter-TSS (NM_004396)	24	NM_004396	1655	Hs.279806	NM_004396	ENSG00000108654	DDX5	G17P1|HLR1|HUMP68|p68	DEAD-box helicase 5	protein-coding	0.110553	0.645000	
chunk0202_177_1	chr9	74206202	74206538	+	0	NA	Intergenic	Intergenic	-165161	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.000000	0.326409	
chunk0155_363_1	chr5	97433782	97434506	+	0	NA	Intergenic	Intergenic	-70552	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.005525	0.308966	
chunk0173_34_1	chr6	142162007	142162409	+	0	NA	intron (NM_001286372, intron 1 of 5)	intron (NM_001286372, intron 1 of 5)	15046	NM_001286372	51534	Hs.431367	NM_016485	ENSG00000009844	VTA1	C6orf55|DRG-1|DRG1|HSPC228|LIP5|My012|SBP1	vesicle trafficking 1	protein-coding	0.002488	0.347395	
chunk0202_166_1	chr9	73831771	73832081	+	0	NA	Intergenic	Intergenic	-539605	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.006452	0.369775	
chunk0109_259_1	chr20	7988354	7989011	+	0	NA	intron (NM_021156, intron 5 of 7)	intron (NM_021156, intron 5 of 7)	31147	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.016743	0.428571	
chunk0100_202_1	chr2	111205823	111206248	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	85121	NM_001204106	10018	Hs.469658	NM_006538	ENSG00000153094	BCL2L11	BAM|BIM|BOD	BCL2 like 11	protein-coding	0.004706	0.408451	
chunk0102_348_1	chr2	152405174	152405655	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	70177	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.004158	0.427386	
chunk0044_209_1	chr12	30885446	30885721	+	0	NA	Intergenic	L1M2a|LINE|L1	-41321	NM_001080509	441631	Hs.505141	NM_001080509	ENSG00000110900	TSPAN11	VSSW1971	tetraspanin 11	protein-coding	0.003636	0.543478	
chunk0131_362_1	chr3	151969268	151969644	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-41281	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.002660	0.358090	
chunk0197_327_1	chr8	125123101	125123821	+	0	NA	intron (NM_173685, intron 3 of 7)	intron (NM_173685, intron 3 of 7)	31620	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.006944	0.328710	
chunk0206_236_1	chr9	123612004	123612470	+	0	NA	intron (NM_024820, intron 10 of 20)	intron (NM_024820, intron 10 of 20)	-126615	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.004292	0.331906	
chunk0006_114_1	chr1	65557860	65558489	+	0	NA	intron (NM_001198688, intron 1 of 18)	intron (NM_001198688, intron 1 of 18)	32485	NM_001198687	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.001590	0.323810	
chunk0149_353_1	chr5	27590328	27590845	+	0	NA	Intergenic	L1PA16|LINE|L1	118294	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.013540	0.584942	
chunk0067_116_1	chr15	42510289	42510916	+	0	NA	intron (NM_003825, intron 1 of 7)	L2c|LINE|L2	15296	NM_003825	8773	Hs.511149	NM_003825	ENSG00000092531	SNAP23	HsT17016|SNAP-23|SNAP23A|SNAP23B	synaptosome associated protein 23	protein-coding	0.001595	0.418790	289(GAGTACACCCTGTTTT,-,0.00),290(AGTACACCCTGTTTTT,+,0.00)
chunk0164_197_1	chr6	22389810	22390032	+	0	NA	Intergenic	L1PA8A|LINE|L1	-87068	NM_001163558	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.022523	0.609865	
chunk0044_328_1	chr12	37549257	37549713	+	0	NA	Intergenic	Intergenic	-767270	NM_001013620	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.008772	0.345733	
chunk0145_276_1	chr4	149617110	149617627	+	0	NA	Intergenic	Intergenic	-460906	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.001934	0.386100	
chunk0061_381_1	chr14	64164522	64164866	+	0	NA	intron (NM_182914, intron 89 of 115)	intron (NM_182914, intron 89 of 115)	-49447	NM_182913	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.008721	0.414493	
chunk0202_105_1	chr9	72459283	72459510	+	0	NA	Intergenic	Intergenic	-62405	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.000000	0.434211	
chunk0145_267_1	chr4	149120229	149120520	+	0	NA	Intergenic	Intergenic	-33921	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.003436	0.383562	
chunk0195_66_1	chr8	93860254	93860731	+	0	NA	Intergenic	L2b|LINE|L2	55627	NR_039602	100616169		NR_039602	ENSG00000284288	MIR378D2	mir-378d-2	microRNA 378d-2	ncRNA	0.000000	0.412134	159(CAGGACAGAATGTTAT,-,0.00),160(AGGACAGAATGTTATT,+,0.00)
chunk0056_33_1	chr13	77306492	77307080	+	0	NA	intron (NM_015057, intron 1 of 82)	L1MEd|LINE|L1	20256	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.001701	0.385399	
chunk0190_77_1	chr8	29975067	29975629	+	0	NA	Intergenic	Intergenic	-18000	NR_036104	100422876		NR_036104	ENSG00000264788	MIR3148	mir-3148	microRNA 3148	ncRNA	0.003559	0.355240	
chunk0040_63_1	chr11	111232170	111232661	+	0	NA	Intergenic	Intergenic	-23567	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.002037	0.353659	
chunk0120_461_1	chr22	50508169	50508382	+	0	NA	promoter-TSS (NM_033200)	promoter-TSS (NM_033200)	59	NM_014551	29781	Hs.730607	NM_014551	ENSG00000025770	NCAPH2	CAPH2	non-SMC condensin II complex subunit H2	protein-coding	0.107981	0.654206	
chunk0020_150_1	chr1	233805832	233806037	+	0	NA	Intergenic	L1MC2|LINE|L1	-98778	NM_173508	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.004878	0.344660	
chunk0074_358_1	chr16	34071483	34072101	+	0	NA	Intergenic	Intergenic	88244	NR_038368									0.012945	0.420032	
chunk0018_93_1	chr1	217631012	217631666	+	0	NA	promoter-TSS (NM_018040)	promoter-TSS (NM_018040)	15	NM_138796	128153	Hs.171130	NM_138796	ENSG00000162814	SPATA17	IQCH|MSRG-11|MSRG11	spermatogenesis associated 17	protein-coding	0.041284	0.456489	
chunk0030_103_1	chr10	112637806	112638532	+	0	NA	intron (NM_145206, intron 5 of 7)	intron (NM_145206, intron 5 of 7)	3999	NR_036177	100422909		NR_036177	ENSG00000264763	MIR4295	-	microRNA 4295	ncRNA	0.005510	0.349381	
chunk0205_425_1	chr9	115044343	115044875	+	0	NA	intron (NM_002160, intron 17 of 27)	intron (NM_002160, intron 17 of 27)	73648	NM_002160	3371	Hs.143250	NM_002160	ENSG00000041982	TNC	150-225|DFNA56|GMEM|GP|HXB|JI|TN|TN-C	tenascin C	protein-coding	0.009398	0.422139	
chunk0026_420_1	chr10	70583761	70584145	+	0	NA	Intergenic	Intergenic	18822	NM_001083116	5551	Hs.2200	NM_005041	ENSG00000180644	PRF1	HPLH2|P1|PFP	perforin 1	protein-coding	0.005208	0.459740	
chunk0181_396_1	chr7	89739521	89740128	+	0	NA	Intergenic	Intergenic	-379576	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.004942	0.282895	
chunk0104_38_1	chr2	171071708	171072023	+	0	NA	intron (NM_001136554, intron 3 of 20)	L1MA3|LINE|L1	-4892	NM_001136555	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.000000	0.354430	119(TTGAACAGACTGTCCT,-,0.00),120(TGAACAGACTGTCCTT,+,0.00)
chunk0074_424_1	chr16	46388584	46389048	+	0	NA	Intergenic	Intergenic	180281	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.053879	0.372043	
chunk0199_106_1	chr9	3333500	3333980	+	0	NA	intron (NM_001282116, intron 3 of 16)	intron (NM_001282116, intron 3 of 16)	61856	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.006250	0.316008	249(CGGGACATGGTGCCCC,-,0.00),250(GGGACATGGTGCCCCC,+,0.00)
chunk0153_453_1	chr5	76412459	76412982	+	0	NA	intron (NM_006633, intron 1 of 35)	intron (NM_006633, intron 1 of 35)	9465	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.001912	0.353053	
chunk0052_185_1	chr13	24349067	24349623	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	17895	NR_131903	100861547	Hs.585625	NR_131903	ENSG00000261498	LINC00566	-	long intergenic non-protein coding RNA 566	ncRNA	0.007194	0.515260	
chunk0199_463_1	chr9	14268836	14269043	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	45107	NM_005596	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.004831	0.331731	
chunk0141_354_1	chr4	87844085	87844426	+	0	NA	intron (NM_001184696, intron 4 of 4)	intron (NM_001184696, intron 4 of 4)	9552	NM_001291183	56955	Hs.676357	NM_020203	ENSG00000152595	MEPE	OF45	matrix extracellular phosphoglycoprotein	protein-coding	0.005865	0.421053	
chunk0119_272_1	chr22	46013776	46014035	+	0	NA	Intergenic	Intergenic	7289	NR_027240	730668	Hs.640071	NR_027240	ENSG00000280424	LOC730668	-	dynein heavy chain -like pseudogene	pseudo	0.057915	0.673077	
chunk0094_364_1	chr2	9644592	9645145	+	0	NA	Intergenic	Intergenic	-13813	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.019892	0.483755	
chunk0148_220_1	chr5	8934178	8934428	+	0	NA	Intergenic	Intergenic	94571	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.008000	0.513944	
chunk0186_185_1	chr7	139672784	139673460	+	0	NA	intron (NM_001113239, intron 2 of 14)	intron (NM_001113239, intron 2 of 14)	104772	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.011834	0.413589	260(GAGGACAGAAAGTCCT,-,0.00),261(AGGACAGAAAGTCCTA,+,0.00)
chunk0192_290_1	chr8	66522284	66522725	+	0	NA	Intergenic	Intergenic	29248	NM_152765	254778	Hs.268869	NM_152765	ENSG00000169085	VXN	C8orf46	vexin	protein-coding	0.013605	0.540724	
chunk0152_40_1	chr5	57173500	57173731	+	0	NA	promoter-TSS (NM_001203246)	promoter-TSS (NM_001203246)	-333	NM_001203246	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.099567	0.719828	
chunk0005_279_1	chr1	59972642	59973391	+	0	NA	Intergenic	L2b|LINE|L2	-46265	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.016021	0.462667	505(AGGACCACTCTGTGCC,-,0.00),506(GGACCACTCTGTGCCT,+,0.00)
chunk0093_373_1	chr19	55967885	55968084	+	0	NA	intron (NM_001317000, intron 5 of 9)	MER58B|DNA|hAT-Charlie	20152	NM_176811	126205	Hs.446925	NM_176811	ENSG00000179709	NLRP8	CLR19.2|NALP8|NOD16|PAN4	NLR family pyrin domain containing 8	protein-coding	0.010050	0.440000	
chunk0207_255_1	chr9	132166477	132166945	+	0	NA	5' UTR (NM_032536, exon 2 of 8)	5' UTR (NM_032536, exon 2 of 8)	4764	NM_032536	84628	Hs.163642	NM_032536	ENSG00000196358	NTNG2	LHLL9381|Lmnt2|NTNG1|bA479K20.1	netrin G2	protein-coding	0.038462	0.571429	
chunk0014_433_1	chr1	183586853	183587116	+	0	NA	intron (NM_001190794, intron 1 of 13)	intron (NM_001190794, intron 1 of 13)	3620	NM_000433	4688	Hs.587558	NM_000433	ENSG00000116701	NCF2	NCF-2|NOXA2|P67-PHOX|P67PHOX	neutrophil cytosolic factor 2	protein-coding	0.022814	0.560606	
chunk0120_338_1	chr3	11185663	11185965	+	0	NA	intron (NM_001098212, intron 1 of 1)	intron (NM_001098212, intron 1 of 1)	31286	NM_001098212	3269	Hs.1570	NM_000861	ENSG00000196639	HRH1	H1-R|H1R|HH1R|hisH1	histamine receptor H1	protein-coding	0.023179	0.541254	
chunk0124_62_1	chr3	52871989	52872485	+	0	NA	intron (NM_198563, intron 1 of 8)	L2a|LINE|L2	25344	NM_198563	375346	Hs.744189	NM_198563	ENSG00000213533	STIMATE	TMEM110	STIM activating enhancer	protein-coding	0.010081	0.450704	
chunk0212_333_1	chrX	144715323	144715680	+	0	NA	Intergenic	Intergenic	-532086	NM_001009614	494118		NM_001009614	ENSG00000203923	SPANXN1	CT11.6	SPANX family member N1	protein-coding	0.014006	0.402235	183(TAGAACTCCGTGTTCC,-,0.00),184(AGAACTCCGTGTTCCT,+,0.00)
chunk0027_309_1	chr10	77899008	77899437	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	27368	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.009324	0.569767	
chunk0190_399_1	chr8	40210621	40211078	+	0	NA	Intergenic	Intergenic	57381	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.017505	0.432314	
chunk0119_334_1	chr22	46935963	46936351	+	0	NA	intron (NR_104292, intron 10 of 13)	intron (NR_104292, intron 10 of 13)	-20115	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.023196	0.565553	
chunk0106_29_1	chr2	195966217	195966800	+	0	NA	intron (NM_018897, intron 17 of 64)	L1MA3|LINE|L1	102304	NM_018897	56171	Hs.97403	NM_018897	ENSG00000118997	DNAH7	-	dynein axonemal heavy chain 7	protein-coding	0.006861	0.342466	
chunk0104_206_1	chr2	175913818	175914068	+	0	NA	Intergenic	L1P3|LINE|L1	88402	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.012000	0.569721	
chunk0013_51_1	chr1	167165935	167166408	+	0	NA	Intergenic	Intergenic	29634	NR_110811	101928484	Hs.568496	NR_110811		LINC01363	RBSG4	long intergenic non-protein coding RNA 1363	ncRNA	0.016913	0.476793	
chunk0148_342_1	chr5	14407117	14407343	+	0	NA	intron (NM_007118, intron 33 of 56)	MER54A|LTR|ERVL	-174552	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.017699	0.546256	
chunk0068_359_1	chr15	57981109	57981479	+	0	NA	intron (NM_170696, intron 6 of 11)	(AC)n|Simple_repeat|Simple_repeat	32803	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.005405	0.361186	
chunk0187_417_1	chr7	158369934	158370156	+	0	NA	intron (NM_130842, intron 1 of 21)	intron (NM_130842, intron 1 of 21)	162768	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.040541	0.560538	5(GAGGACAGTGTGGTCT,-,0.00),6(AGGACAGTGTGGTCTC,+,0.00)
chunk0155_73_1	chr5	91754065	91754370	+	0	NA	Intergenic	L1MD2|LINE|L1	-370885	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003279	0.294118	
chunk0055_277_1	chr13	64267789	64268027	+	0	NA	Intergenic	Intergenic	-423783	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.004202	0.389121	81(ATGTACACCTTGTCCC,-,0.00),82(TGTACACCTTGTCCCT,+,0.00)
chunk0086_40_1	chr18	12657081	12657289	+	0	NA	promoter-TSS (NM_001128627)	promoter-TSS (NM_001128627)	-453	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.120192	0.760766	
chunk0027_228_1	chr10	76297639	76298134	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	515125	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.018182	0.459677	
chunk0167_147_1	chr6	62446628	62447274	+	0	NA	Intergenic	Intergenic	-160756	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.003096	0.341577	
chunk0170_253_1	chr6	113701893	113702322	+	0	NA	Intergenic	Intergenic	-52032	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.004662	0.406977	75(GAGGGCAGTGTGTTCA,-,0.00),76(AGGGCAGTGTGTTCAG,+,0.00)
chunk0134_129_1	chr3	177372125	177373172	+	0	NA	Intergenic	MamRep1151|LTR?|LTR?	-69273	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.004776	0.305344	
chunk0096_105_1	chr2	28283249	28283758	+	0	NA	intron (NM_199191, intron 10 of 11)	intron (NM_199191, intron 10 of 11)	26956	NR_038319	100505716	Hs.679092	NR_038319	ENSG00000223522	LOC100505716	-	uncharacterized LOC100505716	ncRNA	0.007859	0.439216	277(TGGAACATTCTGTGTT,-,0.00),278(GGAACATTCTGTGTTT,+,0.00)
chunk0063_20_1	chr14	76411888	76412435	+	0	NA	intron (NM_004452, intron 3 of 10)	L2b|LINE|L2	40814	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.010969	0.421533	
chunk0071_295_1	chr15	85918858	85919455	+	0	NA	Intergenic	MIRb|SINE|MIR	93521	NR_049805	100847084		NR_049805	ENSG00000264406	MIR548AP	-	microRNA 548ap	ncRNA	0.005025	0.434783	
chunk0058_329_1	chr14	28652959	28653290	+	0	NA	Intergenic	L2b|LINE|L2	112195	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.003021	0.403614	
chunk0199_113_1	chr9	3421009	3421344	+	0	NA	intron (NM_001282116, intron 1 of 16)	intron (NM_001282116, intron 1 of 16)	-25580	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.005970	0.383929	
chunk0016_220_1	chr1	199065688	199066303	+	0	NA	intron (NR_126351, intron 2 of 2)	intron (NR_126351, intron 2 of 2)	-47031	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.003252	0.285714	265(AAGAACACTAAGTCCT,-,0.00),266(AGAACACTAAGTCCTC,+,0.00)
chunk0158_312_1	chr5	132504784	132505460	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-14349	NM_002198	3659	Hs.436061	NM_002198	ENSG00000125347	IRF1	IRF-1|MAR	interferon regulatory factor 1	protein-coding	0.005917	0.398818	
chunk0034_112_1	chr11	27934771	27935127	+	0	NA	Intergenic	Intergenic	-121866	NR_030341	693195		NR_030341	ENSG00000207874	MIR610	MIRN610|hsa-mir-610	microRNA 610	ncRNA	0.019663	0.431373	
chunk0092_236_1	chr19	32691519	32691890	+	0	NA	promoter-TSS (NM_001105570)	promoter-TSS (NM_001105570)	-257	NM_001105570	390916	Hs.203961	NM_001105570	ENSG00000213965	NUDT19	RP2	nudix hydrolase 19	protein-coding	0.053908	0.594086	
chunk0192_76_1	chr8	60748476	60748690	+	0	NA	intron (NM_017780, intron 2 of 37)	intron (NM_017780, intron 2 of 37)	7324	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.004673	0.413953	
chunk0058_208_1	chr14	24934270	24934720	+	0	NA	intron (NM_014178, intron 2 of 5)	HAL1b|LINE|L1	114505	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.006667	0.356984	
chunk0051_400_1	chr12	122035342	122035616	+	0	NA	intron (NM_001024808, intron 3 of 5)	intron (NM_001024808, intron 3 of 5)	13593	NM_020993	605	Hs.530970	NM_020993	ENSG00000110987	BCL7A	BCL7	BAF chromatin remodeling complex subunit BCL7A	protein-coding	0.029197	0.589091	
chunk0136_83_1	chr4	2480801	2481135	+	0	NA	intron (NM_001185009, intron 2 of 8)	Tigger9b|DNA|TcMar-Tigger	11515	NM_001185009	6047	Hs.66394	NM_002938	ENSG00000063978	RNF4	RES4-26|SLX5|SNURF	ring finger protein 4	protein-coding	0.005988	0.438806	
chunk0047_333_1	chr12	74490489	74490871	+	0	NA	Intergenic	Intergenic	-47091	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.007853	0.381201	
chunk0104_213_1	chr2	176077033	176077569	+	0	NA	Intergenic	Intergenic	6661	NM_001080458	344191	Hs.452341	NM_001080458	ENSG00000174279	EVX2	EVX-2	even-skipped homeobox 2	protein-coding	0.011194	0.314711	
chunk0177_117_1	chr7	22326041	22326719	+	0	NA	intron (NM_012294, intron 1 of 25)	MER58A|DNA|hAT-Charlie	30534	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.005900	0.379971	336(TGGAACACTGTGTGTT,-,0.00),337(GGAACACTGTGTGTTT,+,0.00)
chunk0076_10_1	chr16	58674516	58675079	+	0	NA	intron (NM_018231, intron 8 of 11)	intron (NM_018231, intron 8 of 11)	9910	NM_001308384	55238	Hs.10499	NM_018231	ENSG00000103042	SLC38A7	SNAT7	solute carrier family 38 member 7	protein-coding	0.012433	0.498227	
chunk0091_29_1	chr19	3483107	3483493	+	0	NA	Intergenic	CpG	-2758	NM_001136503	284422	Hs.130714	NM_001136503	ENSG00000095932	SMIM24	C19orf77|HSPC323|MARDI	small integral membrane protein 24	protein-coding	0.077720	0.697674	
chunk0062_253_1	chr14	71538821	71539088	+	0	NA	intron (NM_001284245, intron 1 of 20)	intron (NM_001284245, intron 1 of 20)	9642	NM_001284245	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.003745	0.358209	50(AGTTACAGTCTGTTCT,-,0.00),51(GTTACAGTCTGTTCTT,+,0.00),156(GAGAACACAGTGGTCT,-,0.00),157(AGAACACAGTGGTCTA,+,0.00)
chunk0140_185_1	chr4	69868475	69869316	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-8743	NM_005420	6783	Hs.479898	NM_005420	ENSG00000109193	SULT1E1	EST|EST-1|ST1E1|STE	sulfotransferase family 1E member 1	protein-coding	0.002378	0.320665	
chunk0187_167_1	chr7	150725968	150726588	+	0	NA	intron (NM_001199577, intron 3 of 5)	L1MEd|LINE|L1	9721	NM_001199577	100527949	Hs.647079	NM_001199577	ENSG00000281887	GIMAP1-GIMAP5	-	GIMAP1-GIMAP5 readthrough	protein-coding	0.003226	0.389694	
chunk0196_48_1	chr8	101962057	101962575	+	0	NA	intron (NM_001040629, intron 2 of 6)	intron (NM_001040629, intron 2 of 6)	-22116	NR_126152	104054148	Hs.683917	NR_126152		LOC104054148	-	uncharacterized LOC104054148	ncRNA	0.001931	0.387283	
chunk0187_176_1	chr7	150911578	150912252	+	0	NA	Intergenic	LTR83|LTR|ERVL	43914	NM_001204798	3757	Hs.647099	NM_000238	ENSG00000055118	KCNH2	ERG-1|ERG1|H-ERG|HERG|HERG1|Kv11.1|LQT2|SQT1	potassium voltage-gated channel subfamily H member 2	protein-coding	0.016320	0.487407	355(GGGCACAGAATGTTCT,-,0.00),356(GGCACAGAATGTTCTT,+,0.00)
chunk0078_211_1	chr17	5972019	5972355	+	0	NA	Intergenic	Intergenic	-98427	NM_015253	23302	Hs.370166	NM_015253	ENSG00000179314	WSCD1	-	WSC domain containing 1	protein-coding	0.002976	0.498516	
chunk0016_342_1	chr1	201955495	201955805	+	0	NA	intron (NM_006335, intron 1 of 5)	CpG	159	NM_006335	10440	Hs.20716	NM_006335	ENSG00000134375	TIMM17A	TIM17|TIM17A	translocase of inner mitochondrial membrane 17A	protein-coding	0.058065	0.614148	
chunk0113_108_1	chr20	51210170	51210546	+	0	NA	Intergenic	L1ME3|LINE|L1	-187220	NM_002237	3755	Hs.118695	NM_002237	ENSG00000026559	KCNG1	K13|KCNG|KV6.1|kH2	potassium voltage-gated channel modifier subfamily G member 1	protein-coding	0.002660	0.347480	
chunk0165_15_1	chr6	28810338	28810560	+	0	NA	Intergenic	Intergenic	53228	NR_033379	401242	Hs.448285	NR_033379	ENSG00000225595	LINC01623	-	long intergenic non-protein coding RNA 1623	ncRNA	0.067568	0.591928	
chunk0140_223_1	chr4	70992984	70993381	+	0	NA	promoter-TSS (NM_000788)	promoter-TSS (NM_000788)	-366	NM_000788	1633	Hs.709	NM_000788	ENSG00000156136	DCK	-	deoxycytidine kinase	protein-coding	0.022670	0.487437	
chunk0169_191_1	chr6	102570716	102571146	+	0	NA	Intergenic	LTR16A|LTR|ERVL	1171946	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004651	0.431555	
chunk0125_295_1	chr3	69998674	69999108	+	0	NA	promoter-TSS (NR_110000)	promoter-TSS (NR_110000)	-853	NR_110000	101927152	Hs.382046	NR_110000	ENSG00000240405	SAMMSON	LINC01212	survival associated mitochondrial melanoma specific oncogenic non-coding RNA	ncRNA	0.006912	0.448276	168(GAGCACTACATGTTCC,-,0.00),169(AGCACTACATGTTCCA,+,0.00)
chunk0023_362_1	chr10	29997995	29998327	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	61398	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.009036	0.429429	
chunk0028_153_1	chr10	86851462	86851848	+	0	NA	intron (NM_004329, intron 2 of 12)	intron (NM_004329, intron 2 of 12)	95016	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.018135	0.470284	
chunk0063_386_1	chr14	86766727	86766926	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-138952	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.015075	0.430000	
chunk0155_315_1	chr5	96627849	96628048	+	0	NA	intron (NR_130776, intron 4 of 4)	intron (NR_130776, intron 4 of 4)	-34089	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.010050	0.385000	
chunk0208_288_1	chrX	21961567	21962009	+	0	NA	intron (NM_004595, intron 1 of 10)	intron (NM_004595, intron 1 of 10)	21215	NM_004595	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.009050	0.415350	
chunk0017_428_1	chr1	213210412	213210741	+	0	NA	intron (NM_001287220, intron 8 of 12)	intron (NM_001287220, intron 8 of 12)	159343	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.006079	0.333333	219(GAACACATTGTGTTCT,-,0.00),220(AACACATTGTGTTCTT,+,0.00)
chunk0070_192_1	chr15	72035146	72035420	+	0	NA	intron (NM_006901, intron 2 of 41)	L1ME1|LINE|L1	-78975	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.007299	0.341818	
chunk0038_100_1	chr11	83586005	83586360	+	0	NA	intron (NM_001142699, intron 19 of 27)	intron (NM_001142699, intron 19 of 27)	96243	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.429775	
chunk0154_300_1	chr5	83183404	83183838	+	0	NA	intron (NM_022550, intron 3 of 7)	L1MEb|LINE|L1	106123	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.006912	0.379310	
chunk0093_81_1	chr19	40832059	40832272	+	0	NA	Intergenic	Intergenic	18282	NM_000762	1548	Hs.250615	NM_000762	ENSG00000255974	CYP2A6	CPA6|CYP2A|CYP2A3|CYPIIA6|P450C2A|P450PB	cytochrome P450 family 2 subfamily A member 6	protein-coding	0.000000	0.439252	86(GAAACAGGCAGTGCCC,+,0.00)
chunk0205_97_1	chr9	107432603	107433513	+	0	NA	intron (NR_121581, intron 4 of 7)	intron (NR_121581, intron 4 of 7)	33527	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.012088	0.400659	
chunk0084_124_1	chr17	76157454	76157951	+	0	NA	intron (NM_052916, intron 13 of 18)	L2b|LINE|L2	-16403	NM_001454	2302	Hs.651204	NM_001454	ENSG00000129654	FOXJ1	FKHL13|HFH-4|HFH4	forkhead box J1	protein-coding	0.010060	0.449799	
chunk0086_63_1	chr18	13042800	13043400	+	0	NA	intron (NM_032142, intron 15 of 44)	L1ME3D|LINE|L1	51738	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.010000	0.389351	
chunk0132_146_1	chr3	156513461	156514104	+	0	NA	intron (NM_172159, intron 8 of 13)	intron (NM_172159, intron 8 of 13)	40343	NM_001308205	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.009331	0.430124	315(AAGGACAGGGTGTGTC,-,0.00),316(AGGACAGGGTGTGTCA,+,0.00)
chunk0141_282_1	chr4	86596862	86597140	+	0	NA	intron (NM_006264, intron 1 of 46)	intron (NM_006264, intron 1 of 46)	2686	NM_080685	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.003597	0.358423	
chunk0146_93_1	chr4	158157206	158157812	+	0	NA	intron (NM_001128424, intron 2 of 4)	intron (NM_001128424, intron 2 of 4)	15057	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.006601	0.378913	
chunk0120_111_1	chr3	4642873	4643227	+	0	NA	intron (NM_002222, intron 7 of 57)	intron (NM_002222, intron 7 of 57)	108540	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.005650	0.323944	
chunk0152_63_1	chr5	57793030	57793402	+	0	NA	Intergenic	Intergenic	105946	NR_109900	101928539	Hs.639385	NR_109900	ENSG00000249584	LINC02225	-	long intergenic non-protein coding RNA 2225	ncRNA	0.005376	0.340483	
chunk0162_192_1	chr6	3888061	3888514	+	0	NA	Intergenic	Intergenic	38889	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.017660	0.533040	
chunk0081_330_1	chr17	46225405	46225604	+	0	NA	promoter-TSS (NM_001193465)	promoter-TSS (NM_001193465)	-130	NM_001193465	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.045226	0.605000	
chunk0022_141_1	chr10	12195249	12195484	+	0	NA	promoter-TSS (NM_006023)	promoter-TSS (NM_006023)	-596	NM_006023	8872	Hs.412842	NM_006023	ENSG00000151465	CDC123	C10orf7|D123	cell division cycle 123	protein-coding	0.055319	0.449153	
chunk0038_425_1	chr11	94513062	94513433	+	0	NA	intron (NM_001190462, intron 1 of 3)	intron (NM_001190462, intron 1 of 3)	718	NM_001190462	643037		NM_001190462	ENSG00000257057	C11orf97	LINC01171	chromosome 11 open reading frame 97	protein-coding	0.005391	0.408602	
chunk0097_309_1	chr2	56185590	56186185	+	0	NA	promoter-TSS (NR_125368)	promoter-TSS (NR_125368)	-117	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.023529	0.538591	347(AGGCACAAGCTGTTCT,-,0.00),348(GGCACAAGCTGTTCTT,+,0.00)
chunk0194_62_1	chr8	82396731	82397444	+	0	NA	Intergenic	L1MEd|LINE|L1	-554801	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.247899	
chunk0045_368_1	chr12	52069552	52070122	+	0	NA	promoter-TSS (NM_021934)	promoter-TSS (NM_021934)	-137	NM_001098673	60673	Hs.9911	NM_021934	ENSG00000123395	ATG101	C12orf44	autophagy related 101	protein-coding	0.080702	0.651489	
chunk0120_399_1	chr3	12571500	12571859	+	0	NA	intron (NM_001271707, intron 2 of 6)	intron (NM_001271707, intron 2 of 6)	14665	NM_001271707	23609	Hs.591666	NM_014160	ENSG00000075975	MKRN2	HSPC070|RNF62	makorin ring finger protein 2	protein-coding	0.011142	0.405556	190(GGAAACACTGTGTTCT,-,0.00),191(GAAACACTGTGTTCTA,+,0.00)
chunk0157_332_1	chr5	122327255	122327454	+	0	NA	intron (NM_005460, intron 1 of 10)	intron (NM_005460, intron 1 of 10)	15285	NM_001308100	9627	Hs.426463	NM_005460	ENSG00000064692	SNCAIP	SYPH1|Sph1	synuclein alpha interacting protein	protein-coding	0.010050	0.410000	
chunk0201_203_1	chr9	37055972	37056527	+	0	NA	Intergenic	Intergenic	-21770	NM_001280553	5079	Hs.654464	NM_016734	ENSG00000196092	PAX5	ALL3|BSAP	paired box 5	protein-coding	0.005405	0.392086	
chunk0023_373_1	chr10	30230861	30231240	+	0	NA	non-coding (NR_120653, exon 3 of 3)	non-coding (NR_120653, exon 3 of 3)	19198	NR_120653	101929279	Hs.559153	NR_120653		LOC101929279	-	uncharacterized LOC101929279	ncRNA	0.013193	0.497368	
chunk0037_252_1	chr11	75495419	75495822	+	0	NA	intron (NM_030792, intron 1 of 16)	Zaphod|DNA|hAT-Tip100	29934	NM_030792	81544	Hs.503297	NM_030792	ENSG00000158555	GDPD5	GDE2|PP1665	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding	0.012407	0.361386	
chunk0206_141_1	chr9	121179400	121179622	+	0	NA	3' UTR (NM_016322, exon 8 of 8)	3' UTR (NM_016322, exon 8 of 8)	22576	NM_016322	51552	Hs.371563	NM_016322	ENSG00000119396	RAB14	FBP|RAB-14	RAB14, member RAS oncogene family	protein-coding	0.004505	0.408072	
chunk0190_338_1	chr8	39095560	39095761	+	0	NA	intron (NR_027878, intron 19 of 20)	L1MEd|LINE|L1	-11869	NM_145004	203102	Hs.521545	NM_145004	ENSG00000197140	ADAM32	-	ADAM metallopeptidase domain 32	protein-coding	0.004975	0.366337	
chunk0052_249_1	chr12	123398273	123398985	+	0	NA	intron (NM_020382, intron 5 of 7)	intron (NM_020382, intron 5 of 7)	14472	NM_020382	387893	Hs.443735	NM_020382	ENSG00000183955	KMT5A	PR-Set7|PR/SET07|SET07|SET8|SETD8	lysine methyltransferase 5A	protein-coding	0.019663	0.575035	
chunk0196_134_1	chr8	104264040	104264492	+	0	NA	Intergenic	L1MEf|LINE|L1	40931	NM_001282882	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.000000	0.289183	
chunk0062_321_1	chr14	73329667	73330055	+	0	NA	intron (NM_001005743, intron 4 of 12)	MIR|SINE|MIR	92364	NM_173462	89932	Hs.509909	NM_173462	ENSG00000100767	PAPLN	PPN	papilin, proteoglycan like sulfated glycoprotein	protein-coding	0.002577	0.375321	
chunk0097_228_1	chr2	52857646	52858037	+	0	NA	Intergenic	Intergenic	-155226	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.007673	0.334184	
chunk0002_247_1	chr1	21022327	21022541	+	0	NA	intron (NM_001198801, intron 4 of 34)	intron (NM_001198801, intron 4 of 34)	-34002	NR_031657	100302155		NR_031657	ENSG00000221808	MIR1256	MIRN1256|hsa-mir-1256	microRNA 1256	ncRNA	0.014019	0.400000	
chunk0059_284_1	chr14	35659060	35659542	+	0	NA	intron (NM_001283043, intron 27 of 41)	intron (NM_001283043, intron 27 of 41)	125259	NM_032594	84684	Hs.62813	NM_032594	ENSG00000168348	INSM2	IA-6|IA6|mlt1	INSM transcriptional repressor 2	protein-coding	0.010373	0.310559	
chunk0183_119_1	chr7	105367380	105368032	+	0	NA	intron (NM_182692, intron 2 of 15)	Tigger2|DNA|TcMar-Tigger	21224	NM_182692	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.007669	0.393568	354(GTGTACAGTCTGTACA,-,0.00),355(TGTACAGTCTGTACAC,+,0.00)
chunk0050_222_1	chr12	104733909	104734553	+	0	NA	intron (NM_001173982, intron 2 of 2)	intron (NM_001173982, intron 2 of 2)	142598	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.015528	0.544186	
chunk0141_91_1	chr4	79025154	79025724	+	0	NA	intron (NR_038342, intron 2 of 5)	intron (NR_038342, intron 2 of 5)	53691	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.005263	0.381786	
chunk0116_306_1	chr21	40582781	40583513	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	47620	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.010929	0.402456	6(TAGAACACAGTGCCCT,-,0.00),7(AGAACACAGTGCCCTA,+,0.00),453(CAGTACACATTGTACC,-,0.00),454(AGTACACATTGTACCA,+,0.00)
chunk0114_39_1	chr21	8401603	8401842	+	0	NA	non-coding (NR_003287, exon 3 of 3)	non-coding (NR_003287, exon 3 of 3)	6115	NR_003285	100008587	Hs.426704	NR_003285		RNA5-8SN5	RN5-8S1|RNA5-8S5	RNA, 5.8S ribosomal N5	rRNA	0.175732	0.804167	
chunk0076_360_1	chr16	71805391	71805709	+	0	NA	intron (NM_001128, intron 1 of 22)	intron (NM_001128, intron 1 of 22)	3523	NM_001128	164	Hs.461253	NM_001128	ENSG00000166747	AP1G1	ADTG|CLAPG1	adaptor related protein complex 1 subunit gamma 1	protein-coding	0.006289	0.319749	
chunk0024_364_1	chr10	44191980	44192350	+	0	NA	Intergenic	L1MC1|LINE|L1	-100585	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.013514	0.396226	
chunk0085_414_1	chr18	10454838	10455083	+	0	NA	5' UTR (NM_153000, exon 1 of 5)	5' UTR (NM_153000, exon 1 of 5)	332	NM_153000	147495	Hs.293274	NM_153000	ENSG00000154856	APCDD1	B7323|DRAPC1|FP7019|HHS|HTS|HYPT1	APC down-regulated 1	protein-coding	0.122449	0.756098	
chunk0210_332_1	chrX	95000113	95000366	+	0	NA	Intergenic	L1MC1|LINE|L1	62987	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.000000	0.259843	
chunk0157_274_1	chr5	120264178	120264508	+	0	NA	Intergenic	Intergenic	-199935	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.006061	0.368580	193(GAAGACAGTGTGTTCC,-,0.00),194(AAGACAGTGTGTTCCT,+,0.00)
chunk0077_231_1	chr16	80504734	80505017	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-35859	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.007067	0.345070	
chunk0129_106_1	chr3	119675013	119675457	+	0	NA	intron (NM_005694, intron 1 of 2)	intron (NM_005694, intron 1 of 2)	2161	NM_005694	10063	Hs.534383	NM_005694	ENSG00000138495	COX17	-	cytochrome c oxidase copper chaperone COX17	protein-coding	0.006757	0.348315	
chunk0075_464_1	chr16	58433581	58433831	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	-29939	NM_020465	65009	Hs.322430	NM_020465	ENSG00000103034	NDRG4	BDM1|SMAP-8|SMAP8	NDRG family member 4	protein-coding	0.008000	0.446215	
chunk0086_310_1	chr18	24108532	24109105	+	0	NA	intron (NM_153211, intron 6 of 13)	intron (NM_153211, intron 6 of 13)	-4535	NM_001292030	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.005236	0.346690	
chunk0041_34_1	chr12	828933	829915	+	0	NA	intron (NM_213655, intron 3 of 27)	intron (NM_213655, intron 3 of 27)	76501	NM_018979	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.002037	0.345880	299(ATCACACACTGTGCTC,+,0.00)
chunk0001_57_1	chr1	2082079	2082330	+	0	NA	intron (NM_001242874, intron 1 of 14)	intron (NM_001242874, intron 1 of 14)	8218	NM_001242874	5590	Hs.496255	NM_002744	ENSG00000067606	PRKCZ	PKC-ZETA|PKC2	protein kinase C zeta	protein-coding	0.071713	0.634921	
chunk0044_17_1	chr12	27131919	27132237	+	0	NA	Intergenic	AluJb|SINE|Alu	-49556	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.012579	0.442006	
chunk0081_61_1	chr17	38741885	38742154	+	0	NA	intron (NM_007144, intron 2 of 10)	intron (NM_007144, intron 2 of 10)	6286	NM_007144	7703	Hs.371617	NM_007144	ENSG00000277258	PCGF2	MEL-18|RNF110|TPFS|ZNF144	polycomb group ring finger 2	protein-coding	0.022305	0.600000	
chunk0039_101_1	chr11	97389080	97389804	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-882565	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.002762	0.336552	
chunk0174_257_1	chr6	161130793	161131037	+	0	NA	3' UTR (NM_020133, exon 9 of 9)	3' UTR (NM_020133, exon 9 of 9)	31067	NR_024277	79992	Hs.664873	NM_024929	ENSG00000279355	AGPAT4-IT1	C6orf59|NCRNA00241	AGPAT4 intronic transcript 1	ncRNA	0.008197	0.371429	
chunk0051_125_1	chr12	115354773	115354972	+	0	NA	Intergenic	Intergenic	-670708	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.005025	0.455000	
chunk0045_431_1	chr12	53475495	53476133	+	0	NA	intron (NM_001128914, intron 12 of 12)	intron (NM_001128914, intron 12 of 12)	11346	NR_109828	102157401		NR_109828	ENSG00000282977	PCBP2-OT1	TUC.338|TUC338|uc.338	PCBP2 overlapping transcript 1	ncRNA	0.007837	0.406886	159(TAGTACACTGTGTGCT,-,0.00),160(AGTACACTGTGTGCTG,+,0.00)
chunk0135_419_1	chr3	193509023	193509678	+	0	NA	intron (NM_032279, intron 2 of 29)	intron (NM_032279, intron 2 of 29)	-43863	NR_121666	101929198	Hs.450092	NR_046726		ATP13A4-AS1	-	ATP13A4 antisense RNA 1	ncRNA	0.006107	0.391768	
chunk0209_204_1	chrX	44028149	44028499	+	0	NA	Intergenic	Intergenic	-54649	NM_000266	4693	Hs.522615	NM_000266	ENSG00000124479	NDP	EVR2|FEVR|ND	norrin cystine knot growth factor NDP	protein-coding	0.002857	0.350427	
chunk0047_264_1	chr12	72885872	72886261	+	0	NA	Intergenic	Intergenic	-273124	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.007712	0.402564	
chunk0131_81_1	chr3	143256286	143256773	+	0	NA	Intergenic	Intergenic	-85717	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.000000	0.385246	
chunk0190_461_1	chr8	42297157	42297613	+	0	NA	intron (NR_033818, intron 5 of 21)	intron (NR_033818, intron 5 of 21)	26083	NM_001190720	3551	Hs.597664	NM_001556	ENSG00000104365	IKBKB	IKK-beta|IKK2|IKKB|IMD15|IMD15A|IMD15B|NFKBIKB	inhibitor of nuclear factor kappa B kinase subunit beta	protein-coding	0.013158	0.442013	
chunk0060_384_1	chr14	52713136	52713620	+	0	NA	intron (NM_002806, intron 6 of 13)	intron (NM_002806, intron 6 of 13)	6200	NM_002806	5706	Hs.156171	NM_002806	ENSG00000100519	PSMC6	SUG2|p42	proteasome 26S subunit, ATPase 6	protein-coding	0.004132	0.329897	202(CAGAACATACTGTTCT,-,0.00),203(AGAACATACTGTTCTT,+,0.00)
chunk0005_10_1	chr1	54077424	54078053	+	0	NA	intron (NM_153035, intron 3 of 4)	L2c|LINE|L2	23659	NR_039942	100616315		NR_039942	ENSG00000283749	MIR4781	mir-4781	microRNA 4781	ncRNA	0.003180	0.380952	
chunk0066_188_1	chr15	33140435	33140794	+	0	NA	intron (NM_001277313, intron 4 of 20)	L2c|LINE|L2	54119	NM_001277314	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.019499	0.422222	
chunk0051_283_1	chr12	118228480	118229080	+	0	NA	intron (NM_016281, intron 9 of 20)	L1ME3Cz|LINE|L1	92896	NM_002567	5037	Hs.433863	NM_002567	ENSG00000089220	PEBP1	HCNP|HCNPpp|HEL-210|HEL-S-34|HEL-S-96|PBP|PEBP|PEBP-1|RKIP	phosphatidylethanolamine binding protein 1	protein-coding	0.006667	0.356073	
chunk0156_2_1	chr5	101857535	101857840	+	0	NA	Intergenic	Intergenic	438862	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.003279	0.271242	
chunk0069_322_1	chr15	65936160	65936643	+	0	NA	intron (NM_032445, intron 10 of 22)	L2c|LINE|L2	66942	NM_001206836	8766	Hs.321541	NM_004663	ENSG00000103769	RAB11A	YL8	RAB11A, member RAS oncogene family	protein-coding	0.002070	0.510331	
chunk0079_210_1	chr17	14706005	14706304	+	0	NA	Intergenic	L1MC5a|LINE|L1	-324821	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.006689	0.423333	
chunk0168_190_1	chr6	85409851	85410145	+	0	NA	Intergenic	L1MD2|LINE|L1	-39586	NM_001204813	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.006803	0.349153	
chunk0137_193_1	chr4	17856772	17856971	+	0	NA	intron (NM_153686, intron 6 of 6)	L2c|LINE|L2	46058	NR_073124	64151	Hs.567567	NM_022346	ENSG00000109805	NCAPG	CAPG|CHCG|NY-MEL-3|YCG1	non-SMC condensin I complex subunit G	protein-coding	0.000000	0.355000	
chunk0089_260_1	chr18	62500890	62501928	+	0	NA	Intergenic	Intergenic	-22016	NM_017742	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.000000	0.361886	199(TGGAGCACCATGTTCT,-,0.00),200(GGAGCACCATGTTCTC,+,0.00)
chunk0154_16_1	chr5	76663347	76663653	+	0	NA	intron (NM_006633, intron 21 of 35)	Charlie9|DNA|hAT-Charlie	-40066	NM_004101	2151	Hs.42502	NM_004101	ENSG00000164220	F2RL2	PAR-3|PAR3	coagulation factor II thrombin receptor like 2	protein-coding	0.009804	0.384365	
chunk0012_436_1	chr1	164871402	164872389	+	0	NA	Intergenic	Intergenic	-97254	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.011145	0.446356	
chunk0095_324_1	chr2	20625601	20626122	+	0	NA	intron (NM_022460, intron 4 of 6)	L1ME3|LINE|L1	25243	NM_022460	64342	Hs.531785	NM_022460	ENSG00000118960	HS1BP3	ETM2|HS1-BP3	HCLS1 binding protein 3	protein-coding	0.028791	0.511494	
chunk0038_36_1	chr11	81440361	81440839	+	0	NA	Intergenic	Intergenic	450236	NR_036186	100422823		NR_036186	ENSG00000264110	MIR4300	-	microRNA 4300	ncRNA	0.008368	0.373695	
chunk0121_464_1	chr3	27271917	27272309	+	0	NA	intron (NM_199347, intron 23 of 24)	intron (NM_199347, intron 23 of 24)	-55590	NM_001031741	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.000000	0.437659	
chunk0011_49_1	chr1	143253125	143253627	+	0	NA	Intergenic	Intergenic	169216	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.047809	0.367793	
chunk0155_378_1	chr5	98049246	98049685	+	0	NA	Intergenic	Intergenic	544769	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.002278	0.372727	
chunk0144_44_1	chr4	126168556	126169263	+	0	NA	Intergenic	L1PB4|LINE|L1	661650	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.001414	0.324859	
chunk0179_349_1	chr7	50791880	50792443	+	0	NA	intron (NM_001001555, intron 1 of 16)	intron (NM_001001555, intron 1 of 16)	1301	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.028419	0.439716	256(AGAAACAAAGTGTTCT,-,0.00),257(GAAACAAAGTGTTCTA,+,0.00)
chunk0007_292_1	chr1	84020062	84020261	+	0	NA	Intergenic	Intergenic	-21011	NM_024686	79739	Hs.445826	NM_024686	ENSG00000137941	TTLL7	-	tubulin tyrosine ligase like 7	protein-coding	0.005025	0.275000	
chunk0127_327_1	chr3	100384374	100384882	+	0	NA	intron (NM_014820, intron 3 of 11)	intron (NM_014820, intron 3 of 11)	-16565	NM_001085451	348801	Hs.591294	NM_001085451	ENSG00000206535	LNP1	NP3	leukemia NUP98 fusion partner 1	protein-coding	0.001969	0.367387	
chunk0103_25_1	chr2	159060397	159060884	+	0	NA	intron (NM_001145909, intron 2 of 26)	intron (NM_001145909, intron 2 of 26)	92006	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.006160	0.362705	
chunk0116_28_1	chr21	33273071	33273342	+	0	NA	intron (NM_000628, intron 2 of 6)	Tigger3c|DNA|TcMar-Tigger	6846	NM_000628	3588	Hs.654593	NM_000628	ENSG00000243646	IL10RB	CDW210B|CRF2-4|CRFB4|D21S58|D21S66|IL-10R2	interleukin 10 receptor subunit beta	protein-coding	0.014760	0.426471	
chunk0033_114_1	chr11	14452799	14453330	+	0	NA	Intergenic	MIRb|SINE|MIR	46794	NM_016451	1315	Hs.339278	NM_016451	ENSG00000129083	COPB1	COPB	coatomer protein complex subunit beta 1	protein-coding	0.001883	0.392857	
chunk0204_32_1	chr9	92492564	92492763	+	0	NA	TTS (NM_001197296)	TTS (NM_001197296)	-10101	NM_017680	54829	Hs.435655	NM_017680	ENSG00000106819	ASPN	OS3|PLAP-1|PLAP1|SLRR1C	asporin	protein-coding	0.020101	0.525000	
chunk0069_240_1	chr15	64093154	64093387	+	0	NA	intron (NR_110310, intron 1 of 5)	intron (NR_110310, intron 1 of 5)	738	NR_110310	84191	Hs.439548	NM_032231	ENSG00000166797	CIAO2A	CIA2A|FAM96A	cytosolic iron-sulfur assembly component 2A	protein-coding	0.034335	0.547009	
chunk0120_77_1	chr3	3600605	3600818	+	0	NA	Intergenic	Intergenic	-198726	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.009390	0.406542	
chunk0172_384_1	chr6	139485524	139486193	+	0	NA	Intergenic	Intergenic	-11262	NR_033919	645434	Hs.666240	NR_033919	ENSG00000238099	LINC01625	-	long intergenic non-protein coding RNA 1625	ncRNA	0.004484	0.355224	316(AAGAAGACACTGTTCT,-,0.00),317(AGAAGACACTGTTCTT,+,0.00)
chunk0073_288_1	chr16	13783468	13783698	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-136574	NM_005236	2072	Hs.567265	NM_005236	ENSG00000175595	ERCC4	ERCC11|FANCQ|RAD1|XFEPS|XPF	ERCC excision repair 4, endonuclease catalytic subunit	protein-coding	0.017391	0.489177	
chunk0036_244_1	chr11	64416200	64416462	+	0	NA	Intergenic	Intergenic	-32726	NR_073177	100996455	Hs.634142	NR_073177	ENSG00000181908	LINC02724	-	long intergenic non-protein coding RNA 2724	ncRNA	0.015267	0.555133	
chunk0212_264_1	chrX	139656655	139657099	+	0	NA	intron (NM_001171876, intron 1 of 28)	intron (NM_001171876, intron 1 of 28)	-14036	NM_001171878	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.009009	0.373034	236(ATTACAGCATGTTCCT,+,0.00)
chunk0175_29_1	chr7	738766	739123	+	0	NA	intron (NM_017802, intron 2 of 12)	intron (NM_017802, intron 2 of 12)	-11268	NM_001164758	5575	Hs.520851	NM_002735	ENSG00000188191	PRKAR1B	PRKAR1	protein kinase cAMP-dependent type I regulatory subunit beta	protein-coding	0.028011	0.620112	208(TGGGGCAGAGTGTGCT,-,0.00),209(GGGGCAGAGTGTGCTC,+,0.00)
chunk0101_420_1	chr2	139234690	139234889	+	0	NA	Intergenic	Intergenic	337465	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005025	0.310000	
chunk0119_263_1	chr22	45878915	45879132	+	0	NA	Intergenic	Intergenic	98105	NM_058238	7477	Hs.512714	NM_058238	ENSG00000188064	WNT7B	-	Wnt family member 7B	protein-coding	0.027650	0.623853	
chunk0023_81_1	chr10	22278347	22278585	+	0	NA	Intergenic	MER51B|LTR|ERV1	26394	NR_038921	100130992	Hs.48501	NR_038921		LOC100130992	-	uncharacterized LOC100130992	ncRNA	0.033613	0.485356	
chunk0158_307_1	chr5	132370784	132371052	+	0	NA	intron (NM_003060, intron 1 of 9)	intron (NM_003060, intron 1 of 9)	-1002	NR_110997	553103	Hs.570908	NR_110997	ENSG00000233006	MIR3936HG	SLC22A5-AS1	MIR3936 host gene	ncRNA	0.026119	0.446097	
chunk0108_309_1	chr2	235291541	235291740	+	0	NA	Intergenic	L1MC4a|LINE|L1	-202449	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.015075	0.395000	
chunk0009_133_1	chr1	104472590	104472811	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	399677	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.000000	0.432432	
chunk0190_111_1	chr8	30427207	30427896	+	0	NA	intron (NM_006867, intron 1 of 9)	L2c|LINE|L2	-42150	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.008708	0.455072	238(CAGCACATCTTGTTCT,-,0.00),239(AGCACATCTTGTTCTT,+,0.00)
chunk0068_136_1	chr15	52717673	52717872	+	0	NA	Intergenic	LTR79|LTR|ERVL	-39138	NR_104457	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.015075	0.440000	
chunk0094_233_1	chr2	6977106	6977347	+	0	NA	intron (NM_014746, intron 2 of 8)	MIRc|SINE|MIR	-58544	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.008299	0.450413	
chunk0048_28_1	chr12	77456669	77457450	+	0	NA	Intergenic	Intergenic	-374230	NM_014903	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.006402	0.391304	
chunk0093_362_1	chr19	55653773	55653972	+	0	NA	promoter-TSS (NM_007279)	promoter-TSS (NM_007279)	-178	NM_007279	11338	Hs.528007	NM_007279	ENSG00000063244	U2AF2	U2AF65	U2 small nuclear RNA auxiliary factor 2	protein-coding	0.085427	0.610000	
chunk0074_78_1	chr16	21593592	21593897	+	0	NA	intron (NR_110930, intron 2 of 2)	intron (NR_110930, intron 2 of 2)	-3477	NM_001288659	51108	Hs.279583	NM_016025	ENSG00000197006	METTL9	CGI-81|DREV|DREV1|PAP1	methyltransferase like 9	protein-coding	0.009836	0.395425	
chunk0195_295_1	chr8	98634617	98634891	+	0	NA	intron (NM_001256313, intron 4 of 8)	intron (NM_001256313, intron 4 of 8)	190917	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.000000	0.403636	
chunk0059_352_1	chr14	37246452	37246867	+	0	NA	intron (NM_001195297, intron 3 of 14)	intron (NM_001195297, intron 3 of 14)	48746	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.000000	0.353365	
chunk0098_153_1	chr2	69938688	69939167	+	0	NA	3' UTR (NM_002357, exon 6 of 6)	3' UTR (NM_002357, exon 6 of 6)	23338	NM_152792	151516	Hs.516253	NM_152792	ENSG00000244617	ASPRV1	MUNO|SASP|SASPase|Taps	aspartic peptidase retroviral like 1	protein-coding	0.025052	0.437500	
chunk0149_221_1	chr5	22079818	22080577	+	0	NA	intron (NM_004061, intron 4 of 14)	ORSL-2a|DNA|hAT-Tip100	-62155	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.009223	0.309211	417(CAGAACAATGTGTATT,-,0.00)
chunk0160_193_1	chr5	154660090	154660621	+	0	NA	Intergenic	Intergenic	-25421	NR_031638	100302284		NR_031638	ENSG00000221552	MIR1303	MIRN1303|hsa-mir-1303	microRNA 1303	ncRNA	0.009416	0.445489	
chunk0063_179_1	chr14	80570599	80571027	+	0	NA	intron (NM_152446, intron 19 of 23)	intron (NM_152446, intron 19 of 23)	-339759	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.000000	0.317016	
chunk0037_384_1	chr11	78606857	78607130	+	0	NA	Intergenic	Intergenic	-32129	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.014652	0.375912	
chunk0143_1_1	chr4	105586058	105586525	+	0	NA	intron (NM_017700, intron 1 of 3)	intron (NM_017700, intron 1 of 3)	24700	NR_046840	100874374	Hs.668908	NR_046840	ENSG00000249885	ARHGEF38-IT1	-	ARHGEF38 intronic transcript 1	ncRNA	0.004283	0.333333	
chunk0004_320_1	chr1	49694655	49694883	+	0	NA	intron (NM_032785, intron 3 of 13)	intron (NM_032785, intron 3 of 13)	-222684	NR_046839	100874313	Hs.551277	NR_046839	ENSG00000225623	AGBL4-IT1	-	AGBL4 intronic transcript 1	ncRNA	0.008772	0.358079	
chunk0126_48_1	chr3	74019463	74020082	+	0	NA	Intergenic	L2a|LINE|L2	-394851	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.003231	0.372581	354(TAGAACAGTCTCTGCT,-,0.00),355(AGAACAGTCTCTGCTG,+,0.00)
chunk0051_31_1	chr12	112018553	112019232	+	0	NA	intron (NM_001034025, intron 1 of 1)	L1MB5|LINE|L1	5544	NM_001034025	10961	Hs.75841	NM_006817	ENSG00000089248	ERP29	C12orf8|ERp28|ERp31|HEL-S-107|PDI-DB|PDIA9	endoplasmic reticulum protein 29	protein-coding	0.002946	0.382353	357(GGGCACATATTGTACA,-,0.00),358(GGCACATATTGTACAT,+,0.00)
chunk0172_252_1	chr6	137309348	137309603	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-90045	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.003922	0.496094	
chunk0131_373_1	chr3	152150781	152151251	+	0	NA	Intergenic	MER53|DNA|hAT	-117452	NM_207292	4154	Hs.201858	NM_021038	ENSG00000152601	MBNL1	EXP|MBNL	muscleblind like splicing regulator 1	protein-coding	0.006383	0.335456	
chunk0021_29_1	chr10	700409	700726	+	0	NA	Intergenic	(GTGT)n|Simple_repeat|Simple_repeat	-10899	NM_014974	22982	Hs.432397	NM_014974	ENSG00000151240	DIP2C	KIAA0934	disco interacting protein 2 homolog C	protein-coding	0.018927	0.553459	
chunk0187_389_1	chr7	157687156	157687478	+	0	NA	intron (NM_001308268, intron 12 of 22)	intron (NM_001308268, intron 12 of 22)	-112895	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.015528	0.421053	
chunk0058_343_1	chr14	28867530	28868189	+	0	NA	Intergenic	Intergenic	95155	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.006070	0.395455	257(AAGTACATGCTGTTCT,-,0.00),258(AGTACATGCTGTTCTT,+,0.00)
chunk0099_142_1	chr2	86632656	86633330	+	0	NA	intron (NM_001198954, intron 2 of 7)	MER45C|DNA|hAT-Tip100	-9116	NM_001198951	7844	Hs.469199	NM_005667	ENSG00000239305	RNF103	HKF-1|KF-1|KF1|ZFP-103|ZFP103	ring finger protein 103	protein-coding	0.008902	0.471111	
chunk0142_340_1	chr4	101265408	101266036	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	-24850	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.001592	0.330684	
chunk0201_216_1	chr9	37256396	37256713	+	0	NA	intron (NM_032226, intron 2 of 8)	Charlie1a|DNA|hAT-Charlie	135956	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.006309	0.311321	
chunk0001_134_1	chr1	5586755	5587236	+	0	NA	Intergenic	LTR79|LTR|ERVL	22924	NR_039612									0.008316	0.495851	224(AGGGACAAAGAGTACC,-,0.00),225(GGGACAAAGAGTACCT,+,0.00),453(AAGGACAGAGTGTTCA,-,0.00),454(AGGACAGAGTGTTCAT,+,0.00)
chunk0073_422_1	chr16	19077774	19078358	+	0	NA	intron (NM_016138, intron 5 of 5)	intron (NM_016138, intron 5 of 5)	10149	NM_001190983	10229	Hs.157113	NM_016138	ENSG00000167186	COQ7	CAT5|CLK-1|CLK1|COQ10D8	coenzyme Q7, hydroxylase	protein-coding	0.013699	0.405128	
chunk0038_97_1	chr11	83510814	83511013	+	0	NA	intron (NM_001142699, intron 21 of 27)	intron (NM_001142699, intron 21 of 27)	171512	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.010050	0.330000	
chunk0158_86_1	chr5	126524205	126524611	+	0	NA	Intergenic	Intergenic	59313	NM_001146322	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.007389	0.439803	
chunk0040_310_1	chr11	117673717	117674014	+	0	NA	intron (NM_020693, intron 3 of 32)	intron (NM_020693, intron 3 of 32)	123396	NM_020693	57453	Hs.659513	NM_020693	ENSG00000177103	DSCAML1	DSCAM2	DS cell adhesion molecule like 1	protein-coding	0.026936	0.506711	
chunk0065_144_1	chr15	25345955	25346269	+	0	NA	intron (NM_130838, intron 8 of 9)	L1ME2|LINE|L1	59394	NM_130838	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.006369	0.542857	
chunk0010_437_1	chr1	119958377	119958737	+	0	NA	intron (NM_024408, intron 12 of 33)	intron (NM_024408, intron 12 of 33)	-62033	NM_021794	11085	Hs.283011	NM_021794	ENSG00000134249	ADAM30	svph4	ADAM metallopeptidase domain 30	protein-coding	0.002778	0.426593	181(AAGAACAGAATGTACA,-,0.00),182(AGAACAGAATGTACAG,+,0.00),190(ATGTACAGTGTGTGCC,-,0.00),191(TGTACAGTGTGTGCCT,+,0.00)
chunk0026_105_1	chr10	61821534	61821928	+	0	NA	Intergenic	Intergenic	-79523	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.005076	0.374684	
chunk0205_100_1	chr9	107489865	107490336	+	0	NA	promoter-TSS (NM_004235)	promoter-TSS (NM_004235)	-380	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.133758	0.726695	
chunk0004_242_1	chr1	47313571	47313867	+	0	NA	intron (NM_001282936, intron 1 of 17)	intron (NM_001282936, intron 1 of 17)	428	NM_001282936	6491	Hs.525198	NM_003035	ENSG00000123473	STIL	MCPH7|SIL	STIL centriolar assembly protein	protein-coding	0.030405	0.437710	
chunk0147_49_1	chr4	172410767	172411374	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	277847	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.003295	0.327303	
chunk0196_57_1	chr8	102162478	102163236	+	0	NA	Intergenic	Intergenic	37425	NR_049859	100847001		NR_049859	ENSG00000266756	MIR5680	-	microRNA 5680	ncRNA	0.006596	0.409750	372(ATGACAGTATGTCCCT,+,0.00)
chunk0043_452_1	chr12	26704719	26705007	+	0	NA	intron (NM_002223, intron 9 of 56)	intron (NM_002223, intron 9 of 56)	128335	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.000000	0.321799	
chunk0163_449_1	chr6	17564537	17564786	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-35626	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.012048	0.368000	
chunk0060_252_1	chr14	49999148	49999442	+	0	NA	non-coding (NR_126500, exon 3 of 3)	non-coding (NR_126500, exon 3 of 3)	-6161	NR_126499	283551	Hs.292580	NM_001012706	ENSG00000214900	LINC01588	C14orf182	long intergenic non-protein coding RNA 1588	ncRNA	0.017007	0.552542	151(CAGGACGTCATGTCCT,-,0.00),152(AGGACGTCATGTCCTG,+,0.00)
chunk0132_231_1	chr3	158446568	158447116	+	0	NA	intron (NM_001271834, intron 5 of 8)	intron (NM_001271834, intron 5 of 8)	124224	NR_104147	100996447	Hs.369810	NR_104147	ENSG00000243150	LOC100996447	-	uncharacterized LOC100996447	ncRNA	0.005474	0.333333	209(AAGAACAGAACGTGCC,-,0.00),210(AGAACAGAACGTGCCT,+,0.00)
chunk0048_306_1	chr12	82876186	82876427	+	0	NA	intron (NM_152588, intron 2 of 11)	intron (NM_152588, intron 2 of 11)	189151	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.000000	0.396694	
chunk0019_305_1	chr1	228964356	228964736	+	0	NA	Intergenic	Intergenic	210255	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.007895	0.506562	
chunk0042_219_1	chr12	6182148	6182479	+	0	NA	Intergenic	Intergenic	-18003	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.036254	0.554217	
chunk0200_408_1	chr9	27383661	27384126	+	0	NA	intron (NM_024761, intron 2 of 3)	MER103C|DNA|hAT-Charlie	-86754	NM_001161585	54586	Hs.163070	NM_020641	ENSG00000120160	EQTN	AFAF|C9orf11|SPACA8	equatorin	protein-coding	0.002151	0.362661	
chunk0052_351_1	chr12	126895435	126896438	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-21246	NR_033970	440117	Hs.127100	NR_033970	ENSG00000249873	LINC02372	-	long intergenic non-protein coding RNA 2372	ncRNA	0.010967	0.416335	
chunk0188_437_1	chr8	19179435	19180330	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	65640	NR_038919	100128993	Hs.697742	NR_038919		LOC100128993	-	uncharacterized LOC100128993	ncRNA	0.006704	0.311384	
chunk0089_379_1	chr18	67466298	67466515	+	0	NA	Intergenic	L1MC|LINE|L1	-50140	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.000000	0.321101	
chunk0022_236_1	chr10	14169792	14170216	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	95720	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.004717	0.376471	
chunk0116_313_1	chr21	40680354	40680838	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	-49829	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.004132	0.416495	267(CAGAGCAGTGTGTGCT,-,0.00),268(AGAGCAGTGTGTGCTG,+,0.00)
chunk0035_288_1	chr11	46782246	46783162	+	0	NA	intron (NM_001008938, intron 18 of 43)	MIR|SINE|MIR	-20205	NR_003056	692108	Hs.693252	NR_003056	ENSG00000212135	SNORD67	HBII-166	small nucleolar RNA, C/D box 67	snoRNA	0.006550	0.321701	
chunk0122_76_1	chr3	29609343	29609883	+	0	NA	intron (NM_001003793, intron 4 of 14)	L2b|LINE|L2	324543	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.001852	0.425139	
chunk0186_351_1	chr7	143473926	143474347	+	0	NA	intron (NR_033897, intron 2 of 4)	L1MA9|LINE|L1	-3737	NM_176883	259287	Hs.650648	NM_176883	ENSG00000221855	TAS2R41	T2R41|T2R59	taste 2 receptor member 41	protein-coding	0.007126	0.303318	
chunk0142_222_1	chr4	97903287	97903675	+	0	NA	intron (NM_174952, intron 8 of 10)	L1M5|LINE|L1	239759	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.012887	0.305913	
chunk0204_115_1	chr9	95008141	95008780	+	0	NA	intron (NM_032823, intron 11 of 14)	intron (NM_032823, intron 11 of 14)	-56890	NR_106729	102466518		NR_106729	ENSG00000274115	MIR6081	hsa-mir-6081	microRNA 6081	ncRNA	0.023474	0.485938	
chunk0129_113_1	chr3	119790470	119790910	+	0	NA	intron (NM_022002, intron 1 of 8)	L1MB2|LINE|L1	7980	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.004545	0.374150	
chunk0198_292_1	chr8	135691697	135691962	+	0	NA	Intergenic	Intergenic	234364	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.003774	0.451128	
chunk0075_114_1	chr16	49117052	49117651	+	0	NA	Intergenic	MIRb|SINE|MIR	164480	NM_004352	869	Hs.458423	NM_004352	ENSG00000102924	CBLN1	-	cerebellin 1 precursor	protein-coding	0.011686	0.471667	
chunk0200_389_1	chr9	26855346	26856019	+	0	NA	intron (NM_024828, intron 5 of 5)	L3|LINE|CR1	37146	NM_024828	79886	Hs.178357	NM_024828	ENSG00000120159	CAAP1	C9orf82|CAAP	caspase activity and apoptosis inhibitor 1	protein-coding	0.004458	0.347181	196(GGGAACTCTCTGTACT,-,0.00),197(GGAACTCTCTGTACTT,+,0.00),484(AAGAACTCAGTGTCCC,-,0.00),485(AGAACTCAGTGTCCCA,+,0.00)
chunk0067_54_1	chr15	40894222	40894439	+	0	NA	promoter-TSS (NM_020857)	promoter-TSS (NM_020857)	-100	NM_020857	57617	Hs.23876	NM_020857	ENSG00000104142	VPS18	PEP3	VPS18 core subunit of CORVET and HOPS complexes	protein-coding	0.096774	0.669725	
chunk0118_439_1	chr22	38934873	38935434	+	0	NA	Intergenic	Intergenic	-22369	NM_145699	200315	Hs.226307	NM_145699	ENSG00000128383	APOBEC3A	A3A|ARP3|PHRBN|bK150C2.1	apolipoprotein B mRNA editing enzyme catalytic subunit 3A	protein-coding	0.021390	0.494662	
chunk0019_377_1	chr1	229979821	229980593	+	0	NA	Intergenic	L1MC2|LINE|L1	-77582	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.003886	0.375162	
chunk0179_300_1	chr7	50059091	50059403	+	0	NA	intron (NM_007009, intron 3 of 7)	intron (NM_007009, intron 3 of 7)	34017	NM_007009	11055	Hs.388841	NM_007009	ENSG00000042813	ZPBP	ZPBP1	zona pellucida binding protein	protein-coding	0.000000	0.290735	
chunk0030_120_1	chr10	112965213	112965521	+	0	NA	intron (NM_001198531, intron 4 of 12)	intron (NM_001198531, intron 4 of 12)	15117	NM_001198530	6934	Hs.593995	NM_030756	ENSG00000148737	TCF7L2	TCF-4|TCF4	transcription factor 7 like 2	protein-coding	0.022727	0.462783	
chunk0153_381_1	chr5	74972918	74973509	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	57686	NM_016591	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.003384	0.390203	
chunk0048_365_1	chr12	85948060	85948714	+	0	NA	Intergenic	LTR40a|LTR|ERVL	74092	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.006116	0.406107	259(GAGGACTGGATGTCCT,-,0.00),260(AGGACTGGATGTCCTC,+,0.00)
chunk0035_428_1	chr11	57294637	57295056	+	0	NA	Intergenic	Intergenic	30093	NM_033396	85456	Hs.530730	NM_033396	ENSG00000149115	TNKS1BP1	TAB182	tankyrase 1 binding protein 1	protein-coding	0.000000	0.583333	
chunk0026_177_1	chr10	63435093	63435706	+	0	NA	intron (NM_032776, intron 1 of 25)	intron (NM_032776, intron 1 of 25)	-29830	NR_027182	84989	Hs.659950	NM_032903	ENSG00000272767	JMJD1C-AS1	-	JMJD1C antisense RNA 1	ncRNA	0.011419	0.372964	460(CGGCTCACAGTGTCCC,-,0.00),461(GGCTCACAGTGTCCCA,+,0.00)
chunk0069_328_1	chr15	66116543	66116775	+	0	NA	intron (NM_032445, intron 4 of 22)	intron (NM_032445, intron 4 of 22)	76426	NR_036196	100422905		NR_036196	ENSG00000263512	MIR4311	-	microRNA 4311	ncRNA	0.004310	0.446352	
chunk0026_166_1	chr10	63213953	63214428	+	0	NA	exon (NM_032776, exon 8 of 26)	exon (NM_032776, exon 8 of 26)	55033	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.004211	0.371849	
chunk0129_415_1	chr3	127063947	127064218	+	0	NA	Intergenic	Intergenic	75488	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.014760	0.470588	
chunk0100_343_1	chr2	117144450	117144905	+	0	NA	Intergenic	L1M4a1|LINE|L1	-670002	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.004396	0.274123	
chunk0155_234_1	chr5	95641712	95642334	+	0	NA	Intergenic	Intergenic	-4754	NM_001131066	317671	Hs.399758	NM_173362	ENSG00000175449	RFESD	-	Rieske Fe-S domain containing	protein-coding	0.009646	0.449438	
chunk0149_197_1	chr5	21619671	21620473	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	160592	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.006234	0.313823	
chunk0095_452_1	chr2	25700373	25700621	+	0	NA	Intergenic	Intergenic	-26850	NM_001256303	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.012097	0.369478	
chunk0164_353_1	chr6	25460065	25460306	+	0	NA	intron (NM_017640, intron 8 of 36)	intron (NM_017640, intron 8 of 36)	180757	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.004149	0.404959	
chunk0036_450_1	chr11	68582012	68582397	+	0	NA	intron (NM_018312, intron 14 of 22)	intron (NM_018312, intron 14 of 22)	-102271	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.010390	0.378238	
chunk0069_209_1	chr15	63474298	63474978	+	0	NA	Intergenic	MIRb|SINE|MIR	-29873	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.002941	0.439060	
chunk0136_161_1	chr4	6106919	6107428	+	0	NA	intron (NM_001306133, intron 2 of 12)	intron (NM_001306133, intron 2 of 12)	87446	NM_001306133	152789	Hs.479066	NM_144720	ENSG00000152969	JAKMIP1	Gababrbp|JAMIP1|MARLIN1	janus kinase and microtubule interacting protein 1	protein-coding	0.011788	0.454902	
chunk0035_354_1	chr11	48454178	48454414	+	0	NA	Intergenic	L1P4d|LINE|L1	-34497	NM_001005512	403253	Hs.554532	NM_001005512	ENSG00000237388	OR4A47	OR11-113	olfactory receptor family 4 subfamily A member 47	protein-coding	0.000000	0.303797	
chunk0002_313_1	chr1	23997787	23998078	+	0	NA	Intergenic	L1MB5|LINE|L1	-17469	NM_001191005	10772	Hs.3530	NM_006625	ENSG00000188529	SRSF10	FUSIP1|FUSIP2|NSSR|PPP1R149|SFRS13|SFRS13A|SRp38|SRrp40|TASR|TASR1|TASR2	serine and arginine rich splicing factor 10	protein-coding	0.003436	0.369863	
chunk0157_461_1	chr5	125049586	125050013	+	0	NA	intron (NR_109882, intron 2 of 5)	intron (NR_109882, intron 2 of 5)	12968	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.009368	0.383178	
chunk0032_108_1	chr11	3745719	3746001	+	0	NA	intron (NM_016320, intron 11 of 32)	intron (NM_016320, intron 11 of 32)	-51864	NM_001256235	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.010638	0.374558	
chunk0194_336_1	chr8	88986442	88986888	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-659177	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.006726	0.315436	
chunk0073_282_1	chr16	12803449	12803708	+	0	NA	intron (NM_001099455, intron 1 of 2)	CpG	309	NM_018340	55313	Hs.460002	NM_018340	ENSG00000103381	CPPED1	CSTP1	calcineurin like phosphoesterase domain containing 1	protein-coding	0.057915	0.646154	
chunk0147_141_1	chr4	174617941	174618302	+	0	NA	Intergenic	MER83|LTR|ERV1	-95223	NM_001256305	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.002770	0.430939	
chunk0202_280_1	chr9	77271762	77272256	+	0	NA	intron (NM_001018038, intron 23 of 68)	L1ME2|LINE|L1	-94092	NR_026668	100286938	Hs.662256	NR_026668	ENSG00000232998	VPS13A-AS1	-	VPS13A antisense RNA 1	ncRNA	0.004049	0.331313	
chunk0080_439_1	chr17	36486299	36486674	+	0	NA	promoter-TSS (NM_004773)	promoter-TSS (NM_004773)	-141	NR_104010	9326	Hs.2210	NM_004773	ENSG00000273611	ZNHIT3	PEHO|TRIP3	zinc finger HIT-type containing 3	protein-coding	0.072000	0.545213	
chunk0007_298_1	chr1	84150499	84150710	+	0	NA	intron (NM_001300916, intron 1 of 8)	MSTB|LTR|ERVL-MaLR	6356	NM_182948	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.004739	0.481132	
chunk0187_408_1	chr7	158034990	158035566	+	0	NA	intron (NM_001308268, intron 11 of 22)	intron (NM_001308268, intron 11 of 22)	180693	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.012153	0.466205	
chunk0126_22_1	chr3	73558401	73558943	+	0	NA	intron (NR_121660, intron 1 of 1)	intron (NR_121660, intron 1 of 1)	3006	NM_001303140	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.012915	0.458564	
chunk0117_387_1	chr21	45235088	45235722	+	0	NA	Intergenic	Intergenic	52491	NM_133635	23275	Hs.592164	NM_015227	ENSG00000186866	POFUT2	C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding	0.018927	0.433071	
chunk0210_461_1	chrX	107314532	107314744	+	0	NA	Intergenic	L2a|LINE|L2	108006	NM_173494	139212	Hs.128836	NM_173494	ENSG00000080572	PIH1D3	CILD36|CXorf41|DNAAF6|NYSAR97|TWISTER	PIH1 domain containing 3	protein-coding	0.000000	0.436620	137(TGGTACACTGTGTCCC,-,0.00),138(GGTACACTGTGTCCCT,+,0.00)
chunk0134_445_1	chr3	183765255	183765785	+	0	NA	intron (NM_018023, intron 15 of 30)	intron (NM_018023, intron 15 of 30)	60085	NM_024871	79929	Hs.478465	NM_024871	ENSG00000180834	MAP6D1	MAPO6D1|SL21	MAP6 domain containing 1	protein-coding	0.007547	0.450094	351(GAGTACAGACTGTTCC,-,0.00),352(AGTACAGACTGTTCCT,+,0.00)
chunk0048_247_1	chr12	81603236	81603604	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-5049	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.005435	0.303523	
chunk0050_228_1	chr12	104953425	104953744	+	0	NA	Intergenic	Intergenic	-24890	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.006270	0.428125	112(TGGACTTGCTGTGCCC,+,0.00)
chunk0098_455_1	chr2	82452855	82453241	+	0	NA	Intergenic	L1PA8A|LINE|L1	-403755	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.002591	0.418605	
chunk0134_65_1	chr3	176228102	176228301	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	-286902	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.005025	0.490000	
chunk0195_1_1	chr8	92775034	92775373	+	0	NA	intron (NR_046114, intron 1 of 2)	L1ME4c|LINE|L1	10857	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.002950	0.247059	
chunk0031_276_1	chr10	128109495	128110441	+	0	NA	intron (NM_001145966, intron 11 of 13)	MamRep137|DNA|TcMar-Tigger	16236	NM_001145966	4288	Hs.80976	NM_002417	ENSG00000148773	MKI67	KIA|MIB-|MIB-1|PPP1R105	marker of proliferation Ki-67	protein-coding	0.008457	0.367476	
chunk0097_222_1	chr2	51764731	51765386	+	0	NA	Intergenic	L1ME1|LINE|L1	-732522	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.003053	0.266768	346(GAGAACAGAGAGTCCA,-,0.00),347(AGAACAGAGAGTCCAC,+,0.00)
chunk0158_246_1	chr5	130526487	130526967	+	0	NA	Intergenic	Intergenic	621897	NM_175856	337876	Hs.213137	NM_175856	ENSG00000198108	CHSY3	CHSY2|CSS3	chondroitin sulfate synthase 3	protein-coding	0.006250	0.415800	
chunk0197_219_1	chr8	122752637	122753312	+	0	NA	Intergenic	Intergenic	-28688	NM_014943	22882	Hs.377090	NM_014943	ENSG00000178764	ZHX2	AFR1|RAF	zinc fingers and homeoboxes 2	protein-coding	0.004444	0.405325	323(GGGAAGACCCTGTTCT,-,0.00),324(GGAAGACCCTGTTCTT,+,0.00)
chunk0050_309_1	chr12	106986802	106987001	+	0	NA	intron (NM_001033050, intron 1 of 2)	CpG	265	NM_001033050	80298	Hs.5009	NM_025198	ENSG00000120832	MTERF2	MTERFD3|mTERFL	mitochondrial transcription termination factor 2	protein-coding	0.085427	0.665000	
chunk0048_42_1	chr12	78012641	78013009	+	0	NA	intron (NM_014903, intron 8 of 38)	L2a|LINE|L2	181536	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.002717	0.357724	
chunk0083_128_1	chr17	65312388	65312660	+	0	NA	Intergenic	Intergenic	-145017	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.014706	0.490842	
chunk0130_434_1	chr3	140941729	140941987	+	0	NA	promoter-TSS (NM_001104647)	promoter-TSS (NM_001104647)	38	NM_018155	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.104651	0.675676	
chunk0143_295_1	chr4	118583585	118583784	+	0	NA	Intergenic	Intergenic	-8060	NR_109983	729218	Hs.448518	NR_103825		LOC729218	-	uncharacterized LOC729218	pseudo	0.005025	0.295000	
chunk0157_338_1	chr5	122466307	122466539	+	0	NA	intron (NR_051996, intron 2 of 5)	intron (NR_051996, intron 2 of 5)	12664	NR_051996	153163	Hs.679757	NR_051996	ENSG00000250328	MGC32805	-	uncharacterized LOC153163	ncRNA	0.004310	0.321888	
chunk0045_362_1	chr12	51992997	51993418	+	0	NA	intron (NM_004302, intron 8 of 8)	L1MA9|LINE|L1	-13738	NM_181711	160622	Hs.407202	NM_181711	ENSG00000161835	GRASP	TAMALIN	general receptor for phosphoinositides 1 associated scaffold protein	protein-coding	0.011876	0.445498	
chunk0034_175_1	chr11	31114485	31115250	+	0	NA	Intergenic	L2a|LINE|L2	-122181	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.005229	0.387728	
chunk0158_375_1	chr5	134222453	134222860	+	0	NA	intron (NM_002715, intron 1 of 6)	intron (NM_002715, intron 1 of 6)	-3101	NR_037434	100500905		NR_037434	ENSG00000266751	MIR3661	mir-3661	microRNA 3661	ncRNA	0.004914	0.335784	
chunk0078_45_1	chr17	1167558	1168062	+	0	NA	intron (NM_001159746, intron 1 of 22)	intron (NM_001159746, intron 1 of 22)	12164	NM_021962	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.037698	0.524752	
chunk0003_74_1	chr1	31340782	31341074	+	0	NA	intron (NM_001282572, intron 5 of 5)	MIRb|SINE|MIR	32148	NM_004102	2170	Hs.576372	NM_004102	ENSG00000121769	FABP3	FABP11|H-FABP|M-FABP|MDGI|O-FABP	fatty acid binding protein 3	protein-coding	0.000000	0.327645	
chunk0016_216_1	chr1	199029688	199029909	+	0	NA	intron (NR_126351, intron 1 of 2)	intron (NR_126351, intron 1 of 2)	-10834	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.009050	0.436937	
chunk0185_359_1	chr7	132471465	132472255	+	0	NA	intron (NM_001105543, intron 3 of 3)	intron (NM_001105543, intron 3 of 3)	104704	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.013924	0.462705	
chunk0190_274_1	chr8	37516397	37516820	+	0	NA	non-coding (NR_121621, exon 3 of 3)	non-coding (NR_121621, exon 3 of 3)	4778	NR_121621	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.018913	0.514151	
chunk0031_345_1	chr10	129578934	129579793	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	112179	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.023283	0.468605	
chunk0101_280_1	chr2	134011154	134011518	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-115789	NR_037450	100500878		NR_037450	ENSG00000263813	MIR3679	mir-3679	microRNA 3679	ncRNA	0.019231	0.397260	
chunk0186_200_1	chr7	139781876	139782436	+	0	NA	intron (NM_001130966, intron 2 of 16)	intron (NM_001130966, intron 2 of 16)	3908	NM_001166254	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.000000	0.385027	
chunk0009_435_1	chr1	111180181	111180507	+	0	NA	intron (NM_001007794, intron 5 of 8)	intron (NM_001007794, intron 5 of 8)	20359	NM_024901	79961	Hs.557850	NM_024901	ENSG00000162777	DENND2D	-	DENN domain containing 2D	protein-coding	0.000000	0.418960	
chunk0013_146_1	chr1	168555450	168555726	+	0	NA	Intergenic	Intergenic	-11591	NM_003175	6846	Hs.458346	NM_003175	ENSG00000143185	XCL2	SCM-1b|SCM1B|SCYC2	X-C motif chemokine ligand 2	protein-coding	0.007246	0.397112	
chunk0002_28_1	chr1	12434112	12434631	+	0	NA	intron (NM_018156, intron 64 of 68)	intron (NM_018156, intron 64 of 68)	-72875	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.011561	0.428846	269(GTGCACAGCGTGTGCT,-,0.00),270(TGCACAGCGTGTGCTC,+,0.00)
chunk0110_15_1	chr20	10111045	10111608	+	0	NA	intron (NR_040710, intron 2 of 4)	intron (NR_040710, intron 2 of 4)	76327	NM_022096	63926	Hs.70903	NM_022096	ENSG00000132623	ANKEF1	ANKRD5	ankyrin repeat and EF-hand domain containing 1	protein-coding	0.007105	0.505319	
chunk0163_400_1	chr6	16568197	16568564	+	0	NA	intron (NM_001128164, intron 4 of 7)	intron (NM_001128164, intron 4 of 7)	193110	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.010899	0.345109	203(CGGTACAGGCAGTTCT,-,0.00),204(GGTACAGGCAGTTCTC,+,0.00)
chunk0123_276_1	chr3	46203653	46204239	+	0	NA	exon (NM_001295, exon 2 of 2)	exon (NM_001295, exon 2 of 2)	4395	NM_001295	1230	Hs.301921	NM_001295	ENSG00000163823	CCR1	CD191|CKR-1|CKR1|CMKBR1|HM145|MIP1aR|SCYAR1	C-C motif chemokine receptor 1	protein-coding	0.022184	0.507666	
chunk0123_267_1	chr3	46056629	46057167	+	0	NA	Intergenic	L1ME1|LINE|L1	-29411	NM_005283	2829	Hs.128375	NM_005283	ENSG00000173578	XCR1	CCXCR1|GPR5	X-C motif chemokine receptor 1	protein-coding	0.007435	0.400742	
chunk0140_200_1	chr4	70403178	70403645	+	0	NA	intron (NM_001302807, intron 3 of 3)	MER58A|DNA|hAT-Charlie	5529	NM_001302807	58503	Hs.661425	NM_021225	ENSG00000171199	OPRPN	BPLP|PRL1|PROL1|opiorphin	opiorphin prepropeptide	protein-coding	0.002141	0.346154	452(AAGAACATCATGTGAT,-,0.00)
chunk0099_148_1	chr2	86695024	86695227	+	0	NA	intron (NM_001198954, intron 1 of 7)	LTR10A|LTR|ERV1	-25166	NM_022780	64795	Hs.75277	NM_022780	ENSG00000153561	RMND5A	CTLH|GID2|GID2A|RMD5|p44CTLH	required for meiotic nuclear division 5 homolog A	protein-coding	0.004926	0.436275	32(AAGTACAATGAGTTCT,-,0.00),33(AGTACAATGAGTTCTG,+,0.00)
chunk0205_149_1	chr9	108305409	108305721	+	0	NA	Intergenic	Intergenic	550430	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.006410	0.345048	
chunk0172_258_1	chr6	137371543	137372252	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	122497	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.007052	0.366197	
chunk0116_42_1	chr21	33543901	33544190	+	0	NA	intron (NR_103797, intron 1 of 12)	intron (NR_103797, intron 1 of 12)	1007	NM_001291411	6651	Hs.517262	NM_003103	ENSG00000159140	SON	BASS1|C21orf50|DBP-5|NREBP|SON3|TOKIMS	SON DNA binding protein	protein-coding	0.027682	0.351724	
chunk0185_241_1	chr7	129861120	129861527	+	0	NA	intron (NM_001202498, intron 3 of 6)	L1ME4a|LINE|L1	-86309	NR_029615	406959		NR_029615	ENSG00000207691	MIR183	MIRN183|miR-183|miRNA183	microRNA 183	ncRNA	0.012285	0.399510	
chunk0151_20_1	chr5	41432378	41433111	+	0	NA	intron (NM_001005473, intron 1 of 2)	intron (NM_001005473, intron 1 of 2)	77884	NM_001005473	345557	Hs.145404	NM_001005473	ENSG00000182836	PLCXD3	-	phosphatidylinositol specific phospholipase C X domain containing 3	protein-coding	0.006821	0.414169	340(AAGAACATTCTGTTTA,-,0.00),341(AGAACATTCTGTTTAT,+,0.00)
chunk0033_271_1	chr11	19143109	19143441	+	0	NA	intron (NM_019028, intron 2 of 16)	intron (NM_019028, intron 2 of 16)	26130	NM_019028	54503	Hs.188569	NM_019028	ENSG00000177054	ZDHHC13	HIP14L|HIP3RP	zinc finger DHHC-type containing 13	protein-coding	0.003012	0.372372	
chunk0002_87_1	chr1	14498760	14499312	+	0	NA	Intergenic	LTR33|LTR|ERVL	-99681	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.012681	0.484629	
chunk0144_191_1	chr4	133558038	133558846	+	0	NA	Intergenic	Intergenic	409152	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.004950	0.262052	
chunk0016_203_1	chr1	198697705	198697981	+	0	NA	intron (NM_002838, intron 4 of 32)	intron (NM_002838, intron 4 of 32)	58875	NM_080921	5788	Hs.654514	NM_002838	ENSG00000081237	PTPRC	B220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200	protein tyrosine phosphatase receptor type C	protein-coding	0.003623	0.332130	
chunk0124_159_1	chr3	54950415	54951098	+	0	NA	intron (NM_001304389, intron 1 of 2)	intron (NM_001304389, intron 1 of 2)	16332	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.011713	0.456140	
chunk0198_298_1	chr8	137925850	137926118	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-512396	NR_125428	101927915	Hs.695851	NR_125428		LOC101927915	-	uncharacterized LOC101927915	ncRNA	0.003731	0.513011	
chunk0082_195_1	chr17	56801521	56802133	+	0	NA	intron (NM_001085430, intron 6 of 7)	intron (NM_001085430, intron 6 of 7)	32068	NM_001085430	339210	Hs.658949	NM_001085430	ENSG00000214226	C17orf67	-	chromosome 17 open reading frame 67	protein-coding	0.003268	0.453507	293(AGGAACAACAAGTTCC,-,0.00),294(GGAACAACAAGTTCCC,+,0.00)
chunk0128_239_1	chr3	108424539	108425044	+	0	NA	intron (NM_014981, intron 28 of 41)	intron (NM_014981, intron 28 of 41)	104531	NM_014981	22989	Hs.731060	NM_014981	ENSG00000144821	MYH15	-	myosin heavy chain 15	protein-coding	0.001980	0.367589	
chunk0043_324_1	chr12	22476576	22476775	+	0	NA	intron (NM_001286174, intron 14 of 25)	L2c|LINE|L2	67871	NM_001286174	9847	Hs.271014	NM_014802	ENSG00000111731	C2CD5	CDP138|KIAA0528	C2 calcium dependent domain containing 5	protein-coding	0.000000	0.340000	
chunk0096_280_1	chr2	32063305	32063548	+	0	NA	promoter-TSS (NM_199436)	promoter-TSS (NM_199436)	-185	NM_199436	6683	Hs.468091	NM_014946	ENSG00000021574	SPAST	ADPSP|FSP2|SPG4	spastin	protein-coding	0.106996	0.639344	
chunk0088_15_1	chr18	43263630	43263930	+	0	NA	Intergenic	L1PA7|LINE|L1	13870	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.013333	0.382060	
chunk0093_431_1	chr19	58260871	58261335	+	0	NA	exon (NM_014480, exon 7 of 7)	exon (NM_014480, exon 7 of 7)	-17849	NM_021089	7554	Hs.590941	NM_021089	ENSG00000278129	ZNF8	HF.18|Zfp128	zinc finger protein 8	protein-coding	0.008621	0.427957	196(GGGAACATTGTGAGCT,-,0.00),197(GGAACATTGTGAGCTT,+,0.00)
chunk0014_371_1	chr1	182625062	182625264	+	0	NA	Intergenic	Intergenic	10023	NR_036490	284648	Hs.253475	NR_036490	ENSG00000261504	LINC01686	-	long intergenic non-protein coding RNA 1686	ncRNA	0.000000	0.389163	
chunk0167_434_1	chr6	75849326	75849813	+	0	NA	intron (NM_001300899, intron 11 of 32)	LTR30|LTR|ERV1	100377	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.010267	0.420082	172(AAGTACAGCCAGTACC,-,0.00),173(AGTACAGCCAGTACCT,+,0.00)
chunk0148_216_1	chr5	8825622	8826217	+	0	NA	Intergenic	MIR3|SINE|MIR	-13813	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.001681	0.372483	
chunk0142_309_1	chr4	100593064	100593288	+	0	NA	Intergenic	MamGypLTR1a|LTR|Gypsy	-75083	NM_016242	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.004464	0.471111	
chunk0159_130_1	chr5	139064610	139065047	+	0	NA	intron (NM_001037633, intron 4 of 10)	MIRb|SINE|MIR	133548	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.004577	0.470320	
chunk0165_261_1	chr6	35731815	35732364	+	0	NA	intron (NR_027117, intron 5 of 9)	CpG-23543	-3506	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.098361	0.703636	202(AAGAACATCCTGTGCC,-,0.00),203(AGAACATCCTGTGCCC,+,0.00)
chunk0123_345_1	chr3	47955217	47955495	+	0	NA	intron (NM_001134364, intron 3 of 17)	ERVL-E-int|LTR|ERVL	105801	NR_031595	100302232		NR_031595	ENSG00000221585	MIR1226	MIRN1226|hsa-mir-1226|mir-1226	microRNA 1226	ncRNA	0.017986	0.415771	
chunk0043_458_1	chr12	26733405	26733828	+	0	NA	intron (NM_002223, intron 2 of 56)	intron (NM_002223, intron 2 of 56)	99582	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.000000	0.294811	
chunk0162_139_1	chr6	3149908	3150553	+	0	NA	intron (NR_026649, intron 7 of 7)	intron (NR_026649, intron 7 of 7)	7319	NM_001310315	7280	Hs.654543	NM_001069	ENSG00000137267	TUBB2A	CDCBM5|TUBB|TUBB2	tubulin beta 2A class IIa	protein-coding	0.017054	0.472136	
chunk0008_219_1	chr1	93879781	93880121	+	0	NA	promoter-TSS (NM_014597)	promoter-TSS (NM_014597)	-745	NM_014597	30836	Hs.85769	NM_014597	ENSG00000067334	DNTTIP2	ERBP|FCF2|HSU15552|LPTS-RP2|TdIF2	deoxynucleotidyltransferase terminal interacting protein 2	protein-coding	0.008824	0.372434	
chunk0206_49_1	chr9	117568587	117569035	+	0	NA	Intergenic	Intergenic	-79795	NR_109806	101928797	Hs.382317	NR_109806	ENSG00000233569	LOC101928797	-	uncharacterized LOC101928797	ncRNA	0.002232	0.365256	
chunk0129_165_1	chr3	120689298	120689955	+	0	NA	3' UTR (NM_173825, exon 8 of 8)	3' UTR (NM_173825, exon 8 of 8)	-7055	NM_000187	3081	Hs.368254	NM_000187	ENSG00000113924	HGD	AKU|HGO	homogentisate 1,2-dioxygenase	protein-coding	0.006088	0.379939	
chunk0204_163_1	chr9	95881145	95881596	+	0	NA	intron (NM_001010895, intron 2 of 13)	intron (NM_001010895, intron 2 of 13)	-5393	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.004435	0.340708	
chunk0116_365_1	chr21	41761647	41761980	+	0	NA	intron (NM_020639, intron 1 of 7)	intron (NM_020639, intron 1 of 7)	5276	NM_020639	54101	Hs.517310	NM_020639	ENSG00000183421	RIPK4	ANKK2|ANKRD3|CHANDS|DIK|NKRD3|PKK|PPS2|RIP4	receptor interacting serine/threonine kinase 4	protein-coding	0.024024	0.473054	
chunk0002_306_1	chr1	23784717	23785339	+	0	NA	intron (NM_020362, intron 3 of 5)	intron (NM_020362, intron 3 of 5)	-6128	NM_007260	11313	Hs.533479	NM_007260	ENSG00000011009	LYPLA2	APT-2|APT2|DJ886K2.4	lysophospholipase 2	protein-coding	0.016077	0.412520	
chunk0136_411_1	chr3	197361755	197362310	+	0	NA	Intergenic	MER3|DNA|hAT-Charlie	-62760	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.005405	0.361511	
chunk0107_455_1	chr2	225781021	225781542	+	0	NA	Intergenic	Intergenic	-361513	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003839	0.333333	
chunk0151_386_1	chr5	55306469	55306859	+	0	NA	intron (NM_019030, intron 1 of 26)	intron (NM_019030, intron 1 of 26)	1029	NM_019030	54505	Hs.593268	NM_019030	ENSG00000067248	DHX29	DDX29	DExH-box helicase 29	protein-coding	0.012821	0.378517	
chunk0108_222_1	chr2	233495786	233496176	+	0	NA	intron (NM_018218, intron 23 of 30)	L1ME4b|LINE|L1	69609	NM_018218	55230	Hs.96513	NM_018218	ENSG00000085982	USP40	-	ubiquitin specific peptidase 40	protein-coding	0.007692	0.327366	
chunk0132_51_1	chr3	154980500	154981025	+	0	NA	Intergenic	Intergenic	-98885	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.001905	0.349810	
chunk0177_108_1	chr7	22073242	22074096	+	0	NA	Intergenic	Intergenic	-127745	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.002342	0.378947	
chunk0094_390_1	chr2	10258706	10258905	+	0	NA	Intergenic	L2c|LINE|L2	-44099	NM_002149	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.010050	0.390000	
chunk0059_424_1	chr14	38239659	38240109	+	0	NA	Intergenic	Intergenic	16486	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.004444	0.416851	
chunk0210_111_1	chrX	72227675	72227909	+	0	NA	intron (NM_017669, intron 1 of 1)	LTR10C|LTR|ERV1	11216	NM_017669	54821	Hs.47558	NM_017669	ENSG00000186871	ERCC6L	PICH|RAD26L	ERCC excision repair 6 like, spindle assembly checkpoint helicase	protein-coding	0.008547	0.391489	216(ATGTACTTTATGTTCT,-,0.00),217(TGTACTTTATGTTCTT,+,0.00)
chunk0067_120_1	chr15	42548721	42548920	+	0	NA	promoter-TSS (NM_018097)	promoter-TSS (NM_018097)	7	NM_001130447	55142	Hs.14347	NM_018097	ENSG00000137814	HAUS2	C15orf25|CEP27|HsT17025	HAUS augmin like complex subunit 2	protein-coding	0.150754	0.720000	
chunk0038_123_1	chr11	83964987	83965534	+	0	NA	intron (NM_001142699, intron 13 of 27)	intron (NM_001142699, intron 13 of 27)	-282835	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.001828	0.383212	
chunk0203_174_1	chr9	86093616	86094421	+	0	NA	intron (NM_177937, intron 1 of 9)	intron (NM_177937, intron 1 of 9)	5577	NM_016548	51280	Hs.494337	NM_016548	ENSG00000135052	GOLM1	C9orf155|GOLPH2|GP73|HEL46|PSEC0257|bA379P1.3	golgi membrane protein 1	protein-coding	0.009938	0.405707	758(AAGGTCACTGTGTTCT,-,0.00),759(AGGTCACTGTGTTCTG,+,0.00)
chunk0070_139_1	chr15	71002214	71002893	+	0	NA	intron (NM_017691, intron 11 of 15)	intron (NM_017691, intron 11 of 15)	110110	NM_001199017	54839	Hs.12692	NM_017691	ENSG00000137821	LRRC49	PGs4	leucine rich repeat containing 49	protein-coding	0.004418	0.325000	
chunk0154_323_1	chr5	84131311	84131911	+	0	NA	intron (NM_001278642, intron 4 of 9)	MIR|SINE|MIR	253256	NM_005711	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.000000	0.329451	
chunk0113_117_1	chr20	51486394	51486899	+	0	NA	intron (NM_001136021, intron 3 of 10)	L2a|LINE|L2	-33669	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.013861	0.468379	
chunk0139_238_1	chr4	55438256	55438875	+	0	NA	intron (NM_004898, intron 21 of 22)	intron (NM_004898, intron 21 of 22)	42652	NR_073070	55858	Hs.479766	NM_018475	ENSG00000134851	TMEM165	CDG2K|FT27|GDT1|TMPT27|TPARL	transmembrane protein 165	protein-coding	0.006462	0.400000	
chunk0108_340_1	chr2	235754596	235755075	+	0	NA	intron (NM_001037131, intron 6 of 17)	L2b|LINE|L2	249084	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.027140	0.560417	
chunk0038_285_1	chr11	90103665	90103964	+	0	NA	Intergenic	L1MC|LINE|L1	17864	NM_001143975	642623	Hs.719885	NM_001143975	ENSG00000255009	UBTFL1	C11orf27|HMGPI	upstream binding transcription factor like 1	protein-coding	0.003344	0.326667	
chunk0129_71_1	chr3	117715273	117715785	+	0	NA	Intergenic	MIR|SINE|MIR	794098	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.009766	0.343080	
chunk0187_101_1	chr8	4672974	4673212	+	0	NA	intron (NM_033225, intron 1 of 69)	intron (NM_033225, intron 1 of 69)	321713	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.008403	0.426778	
chunk0003_65_1	chr1	31235552	31235896	+	0	NA	intron (NM_024522, intron 1 of 6)	MIR1_Amn|SINE|MIR	4163	NM_024522	79570	Hs.470259	NM_024522	ENSG00000084628	NKAIN1	FAM77C	sodium/potassium transporting ATPase interacting 1	protein-coding	0.005814	0.486957	
chunk0210_168_1	chrX	78067877	78068123	+	0	NA	Intergenic	Intergenic	-36169	NM_000291	5230	Hs.78771	NM_000291	ENSG00000102144	PGK1	HEL-S-68p|MIG10|PGKA	phosphoglycerate kinase 1	protein-coding	0.004065	0.352227	
chunk0016_68_1	chr1	193597884	193598097	+	0	NA	Intergenic	Charlie2b|DNA|hAT-Charlie	293245	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.000000	0.303738	
chunk0198_90_1	chr8	130255969	130256266	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	40416	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.013468	0.395973	170(ATGAACATTATGTTCC,-,0.00),171(TGAACATTATGTTCCA,+,0.00)
chunk0068_305_1	chr15	57185690	57186165	+	0	NA	intron (NM_003205, intron 6 of 19)	L1MB5|LINE|L1	-33503	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.000000	0.369748	
chunk0122_406_1	chr3	38165872	38166075	+	0	NA	intron (NM_005109, intron 1 of 17)	CpG	438	NM_005109	9943	Hs.475970	NM_005109	ENSG00000172939	OXSR1	OSR1	oxidative stress responsive kinase 1	protein-coding	0.103448	0.705882	
chunk0207_328_1	chr9	134283026	134283624	+	0	NA	Intergenic	L1M5|LINE|L1	-43138	NM_002957	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.045151	0.617696	
chunk0011_380_1	chr1	153768187	153768731	+	0	NA	intron (NM_023015, intron 21 of 29)	intron (NM_023015, intron 21 of 29)	-6833	NM_024330	11000	Hs.438723	NM_024330	ENSG00000143554	SLC27A3	ACSVL3|FATP3|VLCS-3	solute carrier family 27 member 3	protein-coding	0.003676	0.500917	
chunk0115_294_1	chr21	28310086	28310984	+	0	NA	Intergenic	Intergenic	-81868	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.006682	0.351502	
chunk0072_379_1	chr15	100191248	100191500	+	0	NA	intron (NM_139057, intron 8 of 21)	intron (NM_139057, intron 8 of 21)	150604	NM_139057	170691	Hs.513200	NM_139057	ENSG00000140470	ADAMTS17	WMS4	ADAM metallopeptidase with thrombospondin type 1 motif 17	protein-coding	0.019841	0.553360	130(TAGGACTGCATGTGCC,-,0.00),131(AGGACTGCATGTGCCT,+,0.00)
chunk0147_448_1	chr4	187922322	187922607	+	0	NA	Intergenic	Intergenic	-73307	NM_174900	132625	Hs.335787	NM_174900	ENSG00000179059	ZFP42	REX-1|REX1|ZNF754|zfp-42	ZFP42 zinc finger protein	protein-coding	0.021053	0.416084	
chunk0025_26_1	chr10	48337507	48338101	+	0	NA	intron (NM_001278547, intron 1 of 11)	L1PA17|LINE|L1	31165	NM_001278547	5599	Hs.138211	NM_002750	ENSG00000107643	MAPK8	JNK|JNK-46|JNK1|JNK1A2|JNK21B1/2|PRKM8|SAPK1|SAPK1c	mitogen-activated protein kinase 8	protein-coding	0.005051	0.351261	
chunk0183_89_1	chr7	104979514	104979796	+	0	NA	Intergenic	Intergenic	11510	NR_039981	100216546	Hs.369356	NR_039981		LINC01004	-	long intergenic non-protein coding RNA 1004	ncRNA	0.007092	0.484099	
chunk0106_316_1	chr2	205200477	205200754	+	0	NA	intron (NM_205863, intron 15 of 21)	L2a|LINE|L2	-481885	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.007220	0.320144	
chunk0207_209_1	chr9	131373215	131373717	+	0	NA	Intergenic	CpG	-56624	NM_013318	84726	Hs.743955	NM_013318	ENSG00000130723	PRRC2B	BAT2L|BAT2L1|KIAA0515|LQFBS-1	proline rich coiled-coil 2B	protein-coding	0.083665	0.638171	
chunk0032_401_1	chr11	11782488	11782960	+	0	NA	TTS (NR_107037)	TTS (NR_107037)	498	NR_107037	102465870		NR_107037	ENSG00000278529	MIR8070	hsa-mir-8070	microRNA 8070	ncRNA	0.004237	0.486258	178(TGGAACTGCCTGTTCT,-,0.00),179(GGAACTGCCTGTTCTC,+,0.00)
chunk0049_269_1	chr12	93777218	93777582	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-39577	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.008242	0.463014	162(CAGAAGATACTGTTCT,-,0.00),163(AGAAGATACTGTTCTC,+,0.00)
chunk0207_454_1	chr9	137744667	137745339	+	0	NA	intron (NM_001145527, intron 6 of 15)	intron (NM_001145527, intron 6 of 15)	-18019	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.017857	0.456166	
chunk0091_303_1	chr19	12784804	12785357	+	0	NA	Intergenic	Intergenic	-2048	NR_049864	100847071		NR_049864	ENSG00000263800	MIR5684	-	microRNA 5684	ncRNA	0.007233	0.505415	
chunk0093_311_1	chr19	53545761	53545960	+	0	NA	intron (NM_018555, intron 3 of 6)	intron (NM_018555, intron 3 of 6)	7072	NM_001253800	55422	Hs.185674	NM_018555	ENSG00000130844	ZNF331	RITA|ZNF361|ZNF463	zinc finger protein 331	protein-coding	0.040201	0.515000	
chunk0182_6_1	chr7	90945512	90945758	+	0	NA	intron (NM_001287136, intron 7 of 13)	LTR33|LTR|ERVL	235819	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.004065	0.473684	
chunk0103_175_1	chr2	163123475	163123864	+	0	NA	Intergenic	L1MCb|LINE|L1	-284922	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.000000	0.353846	
chunk0070_270_1	chr15	74138308	74138702	+	0	NA	Intergenic	Intergenic	8103	NM_020851	57611	Hs.254775	NM_020851	ENSG00000167178	ISLR2	LINX	immunoglobulin superfamily containing leucine rich repeat 2	protein-coding	0.010152	0.417722	
chunk0125_126_1	chr3	65852177	65852503	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-41476	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.012270	0.458716	
chunk0110_207_1	chr20	15153986	15154425	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	-42653	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.004556	0.443182	
chunk0157_168_1	chr5	118028953	118029441	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	-253377	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.002049	0.339468	
chunk0081_194_1	chr17	42294562	42294770	+	0	NA	intron (NM_001288718, intron 4 of 18)	L2a|LINE|L2	6610	NM_001288720	6776	Hs.437058	NM_003152	ENSG00000126561	STAT5A	MGF|STAT5	signal transducer and activator of transcription 5A	protein-coding	0.009615	0.521531	
chunk0190_162_1	chr8	31795285	31795939	+	0	NA	intron (NM_013962, intron 1 of 4)	intron (NM_013962, intron 1 of 4)	155860	NM_013962	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.010703	0.363359	
chunk0134_74_1	chr3	176421838	176422320	+	0	NA	Intergenic	Intergenic	-93024	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.004149	0.320911	
chunk0063_393_1	chr14	87312119	87312700	+	0	NA	Intergenic	Intergenic	406631	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.006885	0.386598	490(AGGAACAGACTGTCAA,-,0.00)
chunk0042_9_1	chr12	1142464	1142951	+	0	NA	intron (NM_178040, intron 8 of 18)	L1ME4b|LINE|L1	114959	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.008214	0.329918	
chunk0040_3_1	chr11	108606208	108607313	+	0	NA	Intergenic	Intergenic	-13022	NM_001308019	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.003620	0.396022	
chunk0211_213_1	chrX	118335921	118336324	+	0	NA	Intergenic	L1MA7|LINE|L1	-9951	NM_001184965	54521	Hs.98510	NM_019045	ENSG00000131725	WDR44	RAB11BP|RPH11|SYM-4	WD repeat domain 44	protein-coding	0.000000	0.388614	
chunk0028_440_1	chr10	93913085	93913555	+	0	NA	Intergenic	Intergenic	19347	NM_153226	159371	Hs.632085	NM_153226	ENSG00000176273	SLC35G1	C10orf60|POST|TMEM20	solute carrier family 35 member G1	protein-coding	0.002128	0.397028	
chunk0160_379_1	chr5	161295065	161295956	+	0	NA	intron (NM_000813, intron 9 of 9)	intron (NM_000813, intron 9 of 9)	252614	NM_000813	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.001122	0.340807	
chunk0021_248_1	chr1	243275051	243275833	+	0	NA	intron (NM_006642, intron 4 of 17)	intron (NM_006642, intron 4 of 17)	19437	NM_006642	10806	Hs.591530	NM_006642	ENSG00000054282	SDCCAG8	BBS16|CCCAP|CCCAP SLSN7|HSPC085|NPHP10|NY-CO-8|SLSN7|hCCCAP	serologically defined colon cancer antigen 8	protein-coding	0.008951	0.330779	
chunk0108_181_1	chr2	232188686	232189228	+	0	NA	intron (NR_046476, intron 9 of 20)	L1MD2|LINE|L1	16304	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.012915	0.360958	
chunk0074_225_1	chr16	26882331	26882703	+	0	NA	Intergenic	LTR50|LTR|ERVL	-184381	NM_001145545	162083	Hs.120831	NM_182831		C16orf82	TNT	chromosome 16 open reading frame 82	protein-coding	0.010753	0.434316	
chunk0131_199_1	chr3	148655477	148655865	+	0	NA	Intergenic	L1PA16|LINE|L1	-42200	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.000000	0.347044	
chunk0057_289_1	chr13	106226225	106226440	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-150231	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.004651	0.407407	83(GGGACATGGTGAGCCT,+,0.00)
chunk0188_243_1	chr8	13784678	13785327	+	0	NA	Intergenic	L1PA17|LINE|L1	218159	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.001541	0.346154	
chunk0047_178_1	chr12	70640644	70640933	+	0	NA	intron (NR_073474, intron 9 of 10)	intron (NR_073474, intron 9 of 10)	-3348	NM_001109754	5787	Hs.201030	NM_002837	ENSG00000127329	PTPRB	HPTP-BETA|HPTPB|PTPB|R-PTP-BETA|VEPTP	protein tyrosine phosphatase receptor type B	protein-coding	0.000000	0.293103	
chunk0176_352_1	chr7	17844696	17845404	+	0	NA	intron (NM_015132, intron 12 of 25)	L1M4c|LINE|L1	95458	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.008475	0.370945	
chunk0160_79_1	chr5	149937712	149937923	+	0	NA	intron (NM_000440, intron 1 of 21)	MIRb|SINE|MIR	-4840	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.000000	0.419811	
chunk0074_183_1	chr16	24539194	24539481	+	0	NA	promoter-TSS (NM_018703)	promoter-TSS (NM_018703)	-250	NM_032626	5930	Hs.188553	NM_006910	ENSG00000122257	RBBP6	MY038|P2P-R|PACT|RBQ-1|SNAMA	RB binding protein 6, ubiquitin ligase	protein-coding	0.062718	0.621528	
chunk0153_52_1	chr5	67467237	67467488	+	0	NA	Intergenic	Intergenic	-270573	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.003984	0.412698	
chunk0146_240_1	chr4	162274314	162274691	+	0	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	-110468	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.000000	0.439153	
chunk0032_8_1	chr11	470076	470346	+	0	NA	intron (NM_030783, intron 2 of 11)	L1MC3|LINE|L1	19931	NM_030783	81490	Hs.12851	NM_030783	ENSG00000174915	PTDSS2	PSS2	phosphatidylserine synthase 2	protein-coding	0.066667	0.667897	
chunk0098_75_1	chr2	67304628	67304986	+	0	NA	Intergenic	Intergenic	-89488	NR_038844	644838	Hs.145561	NR_038844	ENSG00000236780	LINC01829	-	long intergenic non-protein coding RNA 1829	ncRNA	0.005587	0.348189	
chunk0041_156_1	chr11	125892900	125893573	+	0	NA	TTS (NM_001271985)	TTS (NM_001271985)	6176	NM_001134793	219844	Hs.98133	NM_145014	ENSG00000198331	HYLS1	HLS	HYLS1 centriolar and ciliogenesis associated	protein-coding	0.002972	0.350148	
chunk0165_218_1	chr6	35165718	35166291	+	0	NA	Intergenic	Intergenic	-24594	NM_001261819	6954	Hs.435371	NM_018679	ENSG00000124678	TCP11	D6S230E|FPPR	t-complex 11	protein-coding	0.001745	0.465157	
chunk0009_12_1	chr1	99986668	99987263	+	0	NA	intron (NM_001271685, intron 1 of 7)	intron (NM_001271685, intron 1 of 7)	16529	NM_001271685	23443	Hs.448979	NM_012243	ENSG00000117620	SLC35A3	AMRS	solute carrier family 35 member A3	protein-coding	0.003361	0.409396	263(AGGGACATTATGGTCT,-,0.00),264(GGGACATTATGGTCTT,+,0.00)
chunk0039_402_1	chr11	107425288	107425730	+	0	NA	intron (NM_152434, intron 8 of 17)	Tigger3a|DNA|TcMar-Tigger	32337	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.011312	0.372460	
chunk0117_398_1	chr21	45484304	45484642	+	0	NA	intron (NM_130445, intron 15 of 42)	intron (NM_130445, intron 15 of 42)	6207	NR_106873	102465489		NR_106873	ENSG00000275167	MIR6815	hsa-mir-6815	microRNA 6815	ncRNA	0.011834	0.498525	
chunk0194_177_1	chr8	85078873	85079220	+	0	NA	Intergenic	L1MD|LINE|L1	-28042	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.002882	0.330460	
chunk0065_302_1	chr14	102822524	102822782	+	0	NA	intron (NM_001199427, intron 1 of 7)	intron (NM_001199427, intron 1 of 7)	45174	NM_003300	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.023256	0.413127	72(GAGAACACACTGAACT,-,0.00),73(AGAACACACTGAACTT,+,0.00)
chunk0171_26_1	chr6	120249000	120249427	+	0	NA	Intergenic	L1MA4|LINE|L1	234034	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.000000	0.259346	
chunk0128_170_1	chr3	107274832	107275310	+	0	NA	intron (NR_028302, intron 1 of 3)	ERV3-16A3_I-int|LTR|ERVL	34379	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.002092	0.386221	237(AGACCATCGTGTCCTC,+,0.00)
chunk0136_331_1	chr3	195583835	195584777	+	0	NA	promoter-TSS (NM_001647)	promoter-TSS (NM_001647)	-101	NM_001647	347	Hs.522555	NM_001647	ENSG00000189058	APOD	-	apolipoprotein D	protein-coding	0.021231	0.453871	574(TGGAACATGGAGTTCC,-,0.00),575(GGAACATGGAGTTCCT,+,0.00)
chunk0033_69_1	chr11	13645275	13645629	+	0	NA	Intergenic	Intergenic	-23207	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.011299	0.366197	
chunk0072_79_1	chr15	90557592	90558091	+	0	NA	intron (NM_001042574, intron 2 of 14)	intron (NM_001042574, intron 2 of 14)	27955	NM_001042574	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.010020	0.514000	
chunk0089_193_1	chr18	59963231	59963809	+	0	NA	Intergenic	Intergenic	63560	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.008651	0.360967	
chunk0168_263_1	chr6	89337178	89337478	+	0	NA	intron (NM_016021, intron 5 of 7)	intron (NM_016021, intron 5 of 7)	15572	NM_016021	51465	Hs.163776	NM_016021	ENSG00000198833	UBE2J1	CGI-76|HSPC153|HSPC205|HSU93243|NCUBE-1|NCUBE1|UBC6|UBC6E|Ubc6p	ubiquitin conjugating enzyme E2 J1	protein-coding	0.010000	0.302326	
chunk0137_260_1	chr4	21380896	21381354	+	0	NA	intron (NM_147182, intron 2 of 8)	intron (NM_147182, intron 2 of 8)	-77219	NM_147183	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.006550	0.420479	
chunk0015_11_1	chr1	184171810	184172113	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	120310	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.000000	0.348684	
chunk0094_22_1	chr2	1289234	1289755	+	0	NA	intron (NM_018968, intron 14 of 16)	intron (NM_018968, intron 14 of 16)	-123967	NM_001206745	7173	Hs.467554	NM_000547	ENSG00000115705	TPO	MSA|TDH2A|TPX	thyroid peroxidase	protein-coding	0.021113	0.503831	253(TGGCACACTTTGTGCA,-,0.00),254(GGCACACTTTGTGCAC,+,0.00)
chunk0071_126_1	chr15	81549913	81550222	+	0	NA	Intergenic	L1ME3G|LINE|L1	-175990	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.012945	0.316129	
chunk0056_251_1	chr13	89387167	89387430	+	0	NA	Intergenic	Intergenic	113211	NR_131228	105370308	Hs.599406	NR_131228	ENSG00000226037	LINC01040	TCONS_00021682	long intergenic non-protein coding RNA 1040	ncRNA	0.003802	0.367424	112(AGGTACACTGTGTACC,-,0.00),113(GGTACACTGTGTACCA,+,0.00)
chunk0109_266_1	chr20	8044398	8045019	+	0	NA	Intergenic	L2b|LINE|L2	-24879	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.000000	0.299035	
chunk0191_265_1	chr8	53501147	53501694	+	0	NA	Intergenic	Intergenic	-249723	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.003656	0.399635	
chunk0112_213_1	chr20	40551724	40552082	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	137337	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.005587	0.445682	
chunk0175_248_1	chr7	7096034	7096462	+	0	NA	non-coding (NR_034022, exon 1 of 1)	non-coding (NR_034022, exon 1 of 1)	538	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.007009	0.477855	
chunk0159_279_1	chr5	142507966	142508382	+	0	NA	Intergenic	Intergenic	105987	NM_033137	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.026442	0.443645	
chunk0044_255_1	chr12	32106342	32106541	+	0	NA	promoter-TSS (NM_001714)	promoter-TSS (NM_001714)	-810	NM_001003398	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.095477	0.615000	
chunk0138_457_1	chr4	47639228	47639612	+	0	NA	intron (NM_001278585, intron 14 of 19)	L2b|LINE|L2	-13249	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.002604	0.363636	
chunk0019_136_1	chr1	225694082	225694657	+	0	NA	Intergenic	Intergenic	-41226	NM_018212	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.005217	0.432292	
chunk0003_445_1	chr1	41341997	41342557	+	0	NA	Intergenic	Intergenic	-19654	NM_001291281	100132074	Hs.559677	NM_001291281		FOXO6	-	forkhead box O6	protein-coding	0.023214	0.595365	
chunk0212_178_1	chrX	132698176	132698543	+	0	NA	intron (NM_001077188, intron 4 of 5)	intron (NM_001077188, intron 4 of 5)	30717	NR_046691	100874102	Hs.619341	NR_046691	ENSG00000235849	HS6ST2-AS1	-	HS6ST2 antisense RNA 1	ncRNA	0.002725	0.350543	
chunk0023_199_1	chr10	25176702	25176901	+	0	NA	promoter-TSS (NR_027333)	promoter-TSS (NR_027333)	-525	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.035176	0.555000	48(AGGAACAGAGAGTTCC,-,0.00),49(GGAACAGAGAGTTCCT,+,0.00)
chunk0043_151_1	chr12	16361229	16361458	+	0	NA	intron (NM_001260512, intron 4 of 4)	intron (NM_001260512, intron 4 of 4)	7926	NM_145764	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.008734	0.504348	
chunk0180_322_1	chr7	71969285	71969911	+	0	NA	intron (NM_001017440, intron 4 of 5)	intron (NM_001017440, intron 4 of 5)	367625	NM_001017440	83698	Hs.592750	NM_031468	ENSG00000183166	CALN1	CABP8	calneuron 1	protein-coding	0.006390	0.373206	
chunk0056_349_1	chr13	91797631	91798407	+	0	NA	intron (NM_004466, intron 5 of 7)	intron (NM_004466, intron 5 of 7)	399400	NM_004466	2262	Hs.655675	NM_004466	ENSG00000179399	GPC5	-	glypican 5	protein-coding	0.016753	0.424710	
chunk0194_416_1	chr8	92042622	92043038	+	0	NA	intron (NM_001198633, intron 1 of 10)	intron (NM_001198633, intron 1 of 10)	20133	NM_004349	862	Hs.368431	NM_004349	ENSG00000079102	RUNX1T1	AML1-MTG8|AML1T1|CBFA2T1|CDR|ETO|MTG8|ZMYND2	RUNX1 partner transcriptional co-repressor 1	protein-coding	0.002404	0.378897	
chunk0120_173_1	chr3	5976873	5977273	+	0	NA	Intergenic	Intergenic	-726818	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.000000	0.421446	
chunk0006_347_1	chr1	72579401	72579970	+	0	NA	Intergenic	Intergenic	-297091	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.005272	0.289474	
chunk0147_380_1	chr4	186272700	186273217	+	0	NA	intron (NM_000128, intron 3 of 14)	intron (NM_000128, intron 3 of 14)	6994	NM_000128	2160	Hs.1430	NM_000128	ENSG00000088926	F11	FXI|PTA	coagulation factor XI	protein-coding	0.003868	0.320463	
chunk0066_221_1	chr15	33985054	33985745	+	0	NA	intron (NM_012125, intron 1 of 2)	LTR40c|LTR|ERVL	16511	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.001447	0.445087	
chunk0177_8_1	chr7	20362605	20362841	+	0	NA	intron (NM_002214, intron 1 of 13)	intron (NM_002214, intron 1 of 13)	-30961	NR_110120	101927811	Hs.285724	NR_110119	ENSG00000271133	LOC101927811	-	uncharacterized LOC101927811	ncRNA	0.008475	0.358650	
chunk0182_349_1	chr7	99480937	99481503	+	0	NA	intron (NM_213603, intron 3 of 4)	L1ME4a|LINE|L1	8328	NM_213603	285989	Hs.440384	NM_213603	ENSG00000198556	ZNF789	-	zinc finger protein 789	protein-coding	0.005300	0.333333	
chunk0018_240_1	chr1	219958788	219959366	+	0	NA	Intergenic	Intergenic	-30426	NM_018713	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.029412	0.469775	
chunk0087_232_1	chr18	36455111	36455318	+	0	NA	intron (NM_001281739, intron 3 of 23)	intron (NM_001281739, intron 3 of 23)	157518	NM_001281739	80206	Hs.436636	NM_025135	ENSG00000134775	FHOD3	FHOS2|Formactin2	formin homology 2 domain containing 3	protein-coding	0.004831	0.442308	
chunk0137_79_1	chr4	13024425	13024905	+	0	NA	Intergenic	Intergenic	459700	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.004167	0.378378	
chunk0211_38_1	chrX	108514326	108514778	+	0	NA	intron (NM_033380, intron 1 of 50)	(AAGATAG)n|Simple_repeat|Simple_repeat	74708	NM_000495	1287	Hs.369089	NM_000495	ENSG00000188153	COL4A5	ASLN|ATS|ATS1|CA54	collagen type IV alpha 5 chain	protein-coding	0.006637	0.364238	
chunk0180_240_1	chr7	67666492	67666691	+	0	NA	Intergenic	Intergenic	330615	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.015075	0.415000	
chunk0121_69_1	chr3	15798895	15799423	+	0	NA	promoter-TSS (NM_001195098)	promoter-TSS (NM_001195098)	-975	NM_001195098	23243	Hs.335239	NM_015199	ENSG00000206560	ANKRD28	PITK|PPP1R65	ankyrin repeat domain 28	protein-coding	0.001894	0.294896	
chunk0006_265_1	chr1	70209478	70209715	+	0	NA	intron (NM_001190987, intron 1 of 12)	intron (NM_001190987, intron 1 of 12)	3914	NM_004768	9295	Hs.479693	NM_004768	ENSG00000116754	SRSF11	NET2|SFRS11|dJ677H15.2|p54	serine and arginine rich splicing factor 11	protein-coding	0.004219	0.394958	
chunk0118_319_1	chr22	35257341	35257540	+	0	NA	promoter-TSS (NR_027780)	promoter-TSS (NR_027780)	-12	NR_027780	10042	Hs.588815	NM_005487	ENSG00000100281	HMGXB4	HMG2L1|HMGBCG|THC211630	HMG-box containing 4	protein-coding	0.110553	0.625000	
chunk0185_7_1	chr7	123767996	123768749	+	0	NA	Intergenic	Intergenic	-19301	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.005312	0.340849	
chunk0099_441_1	chr2	103139921	103140453	+	0	NA	Intergenic	Intergenic	378156	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.009398	0.485929	300(GAGTACACACTGTATT,-,0.00)
chunk0079_2_1	chr17	9060887	9061461	+	0	NA	intron (NM_004822, intron 2 of 6)	intron (NM_004822, intron 2 of 6)	39632	NM_004822	9423	Hs.660885	NM_004822	ENSG00000065320	NTN1	MRMV4|NTN1L	netrin 1	protein-coding	0.005226	0.474783	221(AAGATCATCATGTTCT,-,0.00),222(AGATCATCATGTTCTT,+,0.00)
chunk0028_388_1	chr10	92942382	92942626	+	0	NA	intron (NM_019053, intron 13 of 21)	intron (NM_019053, intron 13 of 21)	94036	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.000000	0.293878	
chunk0145_201_1	chr4	147927582	147928047	+	0	NA	intron (NM_024605, intron 13 of 22)	intron (NM_024605, intron 13 of 22)	145219	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.015054	0.502146	
chunk0073_121_1	chr16	4862298	4862969	+	0	NA	intron (NM_001288656, intron 7 of 16)	intron (NM_001288656, intron 7 of 16)	14253	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.008942	0.419643	
chunk0119_190_1	chr22	44561417	44561616	+	0	NA	Intergenic	L1MEc|LINE|L1	-7824	NR_028411	388910	Hs.332685	NM_001012986	ENSG00000187012	LINC00207	NCRNA00207	long intergenic non-protein coding RNA 207	ncRNA	0.015075	0.415000	
chunk0162_369_1	chr6	7241055	7241432	+	0	NA	intron (NM_001003700, intron 11 of 11)	intron (NM_001003700, intron 11 of 11)	72071	NM_003144	6745	Hs.114033	NM_003144	ENSG00000124783	SSR1	TRAPA	signal sequence receptor subunit 1	protein-coding	0.029178	0.494709	
chunk0015_46_1	chr1	184543248	184543643	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	156429	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.002532	0.366162	
chunk0204_333_1	chr9	101339410	101339771	+	0	NA	Intergenic	MIRb|SINE|MIR	43929	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.008310	0.375691	124(AAGTACTCATTGTTCT,-,0.00),125(AGTACTCATTGTTCTC,+,0.00)
chunk0087_374_1	chr18	41507179	41507394	+	0	NA	intron (NR_002838, intron 2 of 5)	intron (NR_002838, intron 2 of 5)	13311	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.000000	0.296296	
chunk0198_287_1	chr8	135593693	135594049	+	0	NA	intron (NM_006558, intron 6 of 8)	L2c|LINE|L2	136406	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.011236	0.473389	
chunk0161_127_1	chr5	168159462	168159715	+	0	NA	intron (NM_001080428, intron 9 of 24)	intron (NM_001080428, intron 9 of 24)	72784	NR_109894	101927862	Hs.659376	NR_109894	ENSG00000253978	CTB-178M22.2	-	uncharacterized LOC101927862	ncRNA	0.007905	0.468504	
chunk0148_68_1	chr5	2142443	2142678	+	0	NA	Intergenic	Intergenic	169641	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.017021	0.504237	
chunk0107_75_1	chr2	212492744	212493161	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	45676	NM_001042599	2066	Hs.390729	NM_005235	ENSG00000178568	ERBB4	ALS19|HER4|p180erbB4	erb-b2 receptor tyrosine kinase 4	protein-coding	0.002398	0.279904	
chunk0193_350_1	chr8	79881751	79882096	+	0	NA	Intergenic	Intergenic	-10186	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.002899	0.424855	142(AGGAACAGATTGTCCT,-,0.00),143(GGAACAGATTGTCCTA,+,0.00)
chunk0111_178_1	chr20	25309687	25310853	+	0	NA	intron (NM_001042472, intron 6 of 12)	intron (NM_001042472, intron 6 of 12)	62200	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.011149	0.571551	855(CAGAACTTGCTGTTTC,-,0.00)
chunk0106_303_1	chr2	204737426	204737801	+	0	NA	intron (NM_205863, intron 2 of 21)	L1PB3|LINE|L1	191820	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.002667	0.335106	
chunk0091_316_1	chr19	13049924	13050149	+	0	NA	intron (NM_001271043, intron 2 of 10)	L1MB7|LINE|L1	25455	NM_001271043	4784	Hs.257970	NM_002501	ENSG00000008441	NFIX	CTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2	nuclear factor I X	protein-coding	0.000000	0.411504	
chunk0086_3_1	chr18	11949177	11949453	+	0	NA	Intergenic	Intergenic	-32113	NM_014214	3613	Hs.743311	NM_014214	ENSG00000141401	IMPA2	-	inositol monophosphatase 2	protein-coding	0.003623	0.418773	
chunk0152_3_1	chr5	56097991	56098417	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	103037	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.011737	0.426230	
chunk0210_418_1	chrX	101150044	101150635	+	0	NA	intron (NM_006733, intron 19 of 20)	L1MC5a|LINE|L1	50530	NM_006733	2491	Hs.348920	NM_006733	ENSG00000102384	CENPI	CENP-I|FSHPRH1|LRPR1	centromere protein I	protein-coding	0.015228	0.383446	
chunk0020_443_1	chr1	242147116	242147724	+	0	NA	intron (NM_001195812, intron 4 of 8)	L1ME1|LINE|L1	-148337	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.006579	0.377668	
chunk0137_379_1	chr4	26372605	26372995	+	0	NA	intron (NM_203284, intron 2 of 11)	intron (NM_203284, intron 2 of 11)	51993	NM_203284	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.007692	0.465473	
chunk0114_348_1	chr21	18080001	18080516	+	0	NA	intron (NM_001204176, intron 2 of 6)	L1PB4|LINE|L1	162918	NM_001204175	140578	Hs.283725	NM_024944	ENSG00000154645	CHODL	C21orf68|MT75|PRED12	chondrolectin	protein-coding	0.003883	0.317829	
chunk0009_315_1	chr1	108598543	108598747	+	0	NA	intron (NM_001010883, intron 1 of 10)	intron (NM_001010883, intron 1 of 10)	38296	NM_001010883	284611	Hs.200230	NM_001010883	ENSG00000162636	FAM102B	SYM-3B	family with sequence similarity 102 member B	protein-coding	0.000000	0.385366	
chunk0163_184_1	chr6	11438913	11439339	+	0	NA	Intergenic	Intergenic	-56778	NR_073131	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.004695	0.372365	
chunk0088_98_1	chr18	44969170	44969842	+	0	NA	TTS (NR_036203)	TTS (NR_036203)	660	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.010417	0.421991	266(TACACAGAATGTTCTT,+,0.00)
chunk0122_413_1	chr3	38468886	38469085	+	0	NA	intron (NM_001106, intron 1 of 10)	intron (NM_001106, intron 1 of 10)	-14165	NR_028389	100128640	Hs.570596	NR_028389	ENSG00000229589	ACVR2B-AS1	-	ACVR2B antisense RNA 1	ncRNA	0.005025	0.500000	
chunk0015_325_1	chr1	189574351	189574992	+	0	NA	Intergenic	Intergenic	902958	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.001560	0.314642	279(GGGCACACAGTGTACT,-,0.00),280(GGCACACAGTGTACTT,+,0.00)
chunk0090_429_1	chr18	79360707	79361341	+	0	NA	intron (NM_001306085, intron 26 of 28)	intron (NM_001306085, intron 26 of 28)	-34748	NM_006162	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.028391	0.444094	
chunk0061_88_1	chr14	57010267	57010466	+	0	NA	Intergenic	Intergenic	197183	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.005025	0.385000	181(AAAAACAAAATGTTCC,-,0.00),182(AAAACAAAATGTTCCT,+,0.00)
chunk0209_120_1	chrX	40738606	40739002	+	0	NA	TTS (NM_001289773)	TTS (NM_001289773)	-3252	NM_004229	9282	Hs.407604	NM_004229	ENSG00000180182	MED14	CRSP150|CRSP2|CSRP|CXorf4|DRIP150|EXLM1|RGR1|TRAP170	mediator complex subunit 14	protein-coding	0.005051	0.345088	
chunk0112_38_1	chr20	36775229	36775620	+	0	NA	Intergenic	Intergenic	-1597	NM_001145318	79980	Hs.632268	NM_024918	ENSG00000149636	DSN1	C20orf172|KNL3|MIS13|dJ469A13.2|hKNL-3	DSN1 component of MIS12 kinetochore complex	protein-coding	0.007673	0.500000	177(GAGAACTCAGTGTTCC,-,0.00),178(AGAACTCAGTGTTCCT,+,0.00)
chunk0110_98_1	chr20	11476164	11476723	+	0	NA	Intergenic	L1MA3|LINE|L1	-203060	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.000000	0.341071	
chunk0039_389_1	chr11	107151030	107151998	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-133069	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.002066	0.316821	
chunk0211_206_1	chrX	118140440	118141138	+	0	NA	Intergenic	Intergenic	-23449	NM_001168301	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.004298	0.412017	
chunk0085_278_1	chr18	7877690	7878010	+	0	NA	intron (NM_001105244, intron 2 of 32)	MIRb|SINE|MIR	310534	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.003125	0.467290	
chunk0130_314_1	chr3	137205478	137206117	+	0	NA	Intergenic	Intergenic	247932	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.007825	0.409375	
chunk0136_118_1	chr4	3468875	3469099	+	0	NA	intron (NM_001301071, intron 2 of 9)	(TGCG)n|Simple_repeat|Simple_repeat	5681	NM_173660	285489	Hs.122110	NM_173660	ENSG00000175920	DOK7	C4orf25|CMS10|CMS1B|FADS3	docking protein 7	protein-coding	0.022321	0.493333	
chunk0096_159_1	chr2	29408861	29409469	+	0	NA	intron (NM_004304, intron 4 of 28)	intron (NM_004304, intron 4 of 28)	293739	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.013158	0.443350	419(GAGAAGAGAGTGTTCT,-,0.00),420(AGAAGAGAGTGTTCTC,+,0.00)
chunk0061_27_1	chr14	55807094	55807426	+	0	NA	Intergenic	Intergenic	-10586	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.027108	0.561562	80(GAGGCCAGGCTGTGCT,-,0.00),81(AGGCCAGGCTGTGCTT,+,0.00)
chunk0176_284_1	chr7	16652054	16652593	+	0	NA	intron (NR_027624, intron 1 of 10)	Charlie15b|DNA|hAT-Charlie	6189	NM_014038	28969	Hs.487635	NM_014038	ENSG00000136261	BZW2	HSPC028|MST017|MSTP017	basic leucine zipper and W2 domains 2	protein-coding	0.020408	0.420370	
chunk0032_344_1	chr11	10307129	10307507	+	0	NA	promoter-TSS (NR_103765)	promoter-TSS (NR_103765)	-995	NR_103765	100130460	Hs.501890	NR_103765		CAND1.11	-	uncharacterized LOC100130460	ncRNA	0.044974	0.469657	
chunk0124_280_1	chr3	57555571	57555978	+	0	NA	promoter-TSS (NM_177966)	promoter-TSS (NM_177966)	-480	NM_177966	201626	Hs.572993	NM_177966	ENSG00000174840	PDE12	2'-PDE|2-PDE	phosphodiesterase 12	protein-coding	0.051597	0.517157	
chunk0081_30_1	chr17	37450085	37450432	+	0	NA	intron (NM_133439, intron 8 of 10)	intron (NM_133439, intron 8 of 10)	-39587	NM_007026	11072	Hs.91448	NM_007026	ENSG00000276023	DUSP14	MKP-L|MKP6	dual specificity phosphatase 14	protein-coding	0.017291	0.445402	
chunk0199_214_1	chr9	5127076	5127625	+	0	NA	3' UTR (NM_004972, exon 25 of 25)	3' UTR (NM_004972, exon 25 of 25)	58268	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.001821	0.287273	
chunk0124_420_1	chr3	61113214	61113590	+	0	NA	intron (NM_001166243, intron 2 of 9)	intron (NM_001166243, intron 2 of 9)	138057	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.000000	0.381963	
chunk0013_35_1	chr1	166825478	166826199	+	0	NA	Intergenic	L2a|LINE|L2	-13566	NM_017542	57645	Hs.432752	NM_017542	ENSG00000143157	POGK	BASS2|KRBOX2|LST003	pogo transposable element derived with KRAB domain	protein-coding	0.004161	0.404432	542(AGGAACAGCAAGTGCC,-,0.00),543(GGAACAGCAAGTGCCA,+,0.00)
chunk0039_408_1	chr11	107494064	107494485	+	0	NA	Intergenic	Intergenic	-36428	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.002375	0.405213	
chunk0065_308_1	chr14	102966184	102966643	+	0	NA	intron (NM_006035, intron 17 of 36)	intron (NM_006035, intron 17 of 36)	43757	NM_030943	81693	Hs.534494	NM_030943	ENSG00000166126	AMN	PRO1028|amnionless	amnion associated transmembrane protein	protein-coding	0.032680	0.441304	
chunk0006_38_1	chr1	64349132	64349565	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-121445	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.006928	0.465438	
chunk0175_320_1	chr6	166874320	166874544	+	0	NA	Intergenic	L2a|LINE|L2	-12149	NM_001006932	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.022321	0.582222	195(GGGAACATACTGTCTT,-,0.00),196(GGAACATACTGTCTTG,+,0.00)
chunk0165_212_1	chr6	35027837	35028250	+	0	NA	intron (NM_015245, intron 11 of 23)	intron (NM_015245, intron 11 of 23)	113367	NM_001093728									0.004843	0.466184	
chunk0055_341_1	chr13	69940724	69941811	+	0	NA	intron (NM_020866, intron 3 of 10)	L1PB|LINE|L1	-165946	NR_002717	6315	Hs.676453	NR_002717		ATXN8OS	KLHL1AS|NCRNA00003|SCA8	ATXN8 opposite strand lncRNA	ncRNA	0.001840	0.296875	404(CAGAACATTCTGCCCC,-,0.00),405(AGAACATTCTGCCCCT,+,0.00)
chunk0038_72_1	chr11	83086906	83087468	+	0	NA	Intergenic	Intergenic	15121	NR_038903	100506233	Hs.503429	NR_038903	ENSG00000246067	RAB30-DT	RAB30-AS1	RAB30 divergent transcript	ncRNA	0.005338	0.349911	
chunk0047_172_1	chr12	70458720	70458962	+	0	NA	Intergenic	Intergenic	92559	NM_014505	27345	Hs.525529	NM_014505	ENSG00000135643	KCNMB4	-	potassium calcium-activated channel subfamily M regulatory beta subunit 4	protein-coding	0.004132	0.366255	168(AAGAACATTAAGTTCA,-,0.00),169(AGAACATTAAGTTCAT,+,0.00)
chunk0065_229_1	chr14	100948121	100948753	+	0	NA	Intergenic	Intergenic	-1396	NR_003193	767577		NR_003193	ENSG00000199575	SNORD114-1	14q(II-1)	small nucleolar RNA, C/D box 114-1	snoRNA	0.004747	0.315956	
chunk0073_297_1	chr16	14085529	14086002	+	0	NA	intron (NM_001308142, intron 2 of 16)	intron (NM_001308142, intron 2 of 16)	14451	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.002114	0.331224	
chunk0012_303_1	chr1	162204412	162204745	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	47471	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.012012	0.479042	155(GGGAAGAGGGTGTTCT,-,0.00),156(GGAAGAGGGTGTTCTG,+,0.00)
chunk0038_13_1	chr11	80899369	80899903	+	0	NA	Intergenic	L1MB8|LINE|L1	-136833	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003745	0.338318	
chunk0140_124_1	chr4	68997141	68997911	+	0	NA	Intergenic	Intergenic	22871	NM_001144767	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.006494	0.360571	
chunk0146_328_1	chr4	165720585	165721127	+	0	NA	intron (NR_121676, intron 3 of 5)	intron (NR_121676, intron 3 of 5)	22215	NR_121677	101928131	Hs.406479	NR_121677		LOC101928131	-	uncharacterized LOC101928131	ncRNA	0.001845	0.360958	
chunk0149_182_1	chr5	21187365	21187685	+	0	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	-271955	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.003125	0.261682	
chunk0175_242_1	chr7	6497439	6497648	+	0	NA	3' UTR (NM_001145118, exon 22 of 22)	3' UTR (NM_001145118, exon 22 of 22)	-13325	NM_001100603	11014	Hs.654552	NM_006854	ENSG00000136240	KDELR2	ELP-1|ERD2.2	KDEL endoplasmic reticulum protein retention receptor 2	protein-coding	0.028708	0.638095	
chunk0145_350_1	chr4	151122548	151122900	+	0	NA	intron (NM_001009555, intron 20 of 20)	L2a|LINE|L2	18897	NR_000007	8944		NR_000007	ENSG00000208797	SNORD73A	RNU73|RNU73A|U73|U73a	small nucleolar RNA, C/D box 73A	snoRNA	0.008523	0.419263	
chunk0206_448_1	chr9	128074610	128074870	+	0	NA	intron (NM_001006641, intron 1 of 9)	intron (NM_001006641, intron 1 of 9)	6540	NM_001006641	114789	Hs.5476	NM_052901	ENSG00000148339	SLC25A25	MCSC|PCSCL|SCAMC-2	solute carrier family 25 member 25	protein-coding	0.019231	0.498084	
chunk0211_347_1	chrX	125247637	125248214	+	0	NA	Intergenic	Intergenic	-72195	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.008666	0.335640	
chunk0066_197_1	chr15	33304902	33305579	+	0	NA	intron (NR_120326, intron 2 of 2)	intron (NR_120326, intron 2 of 2)	5005	NR_120326	101928134	Hs.133851	NR_120326	ENSG00000259446	LOC101928134	-	uncharacterized LOC101928134	ncRNA	0.007386	0.380531	
chunk0122_115_1	chr3	31174288	31174511	+	0	NA	Intergenic	Intergenic	-12612	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.004484	0.294643	
chunk0146_454_1	chr4	170103935	170104150	+	0	NA	Intergenic	L1M1|LINE|L1	-13655	NM_001286683	51166	Hs.529735	NM_016228	ENSG00000109576	AADAT	KAT2|KATII|KYAT2	aminoadipate aminotransferase	protein-coding	0.013953	0.347222	
chunk0062_154_1	chr14	69199798	69200147	+	0	NA	intron (NM_001193363, intron 1 of 8)	Tigger3b|DNA|TcMar-Tigger	8206	NR_034165	55218	Hs.533878	NM_018199	ENSG00000081177	EXD2	C14orf114|EXDL2	exonuclease 3'-5' domain containing 2	protein-coding	0.025788	0.357143	
chunk0123_5_1	chr3	40114115	40114364	+	0	NA	intron (NM_001284426, intron 1 of 14)	Tigger3a|DNA|TcMar-Tigger	14228	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.004016	0.376000	
chunk0198_427_1	chr8	143123657	143123963	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	36230	NM_002347	4062	Hs.159590	NM_002347	ENSG00000176956	LY6H	NMLY6	lymphocyte antigen 6 family member H	protein-coding	0.029412	0.485342	
chunk0146_209_1	chr4	161439116	161439567	+	0	NA	intron (NM_001128427, intron 15 of 15)	intron (NM_001128427, intron 15 of 15)	-583392	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.013304	0.349558	
chunk0188_317_1	chr8	17337942	17338457	+	0	NA	intron (NM_004686, intron 6 of 13)	intron (NM_004686, intron 6 of 13)	75332	NM_004686	9108	Hs.625674	NM_004686	ENSG00000003987	MTMR7	-	myotubularin related protein 7	protein-coding	0.009709	0.405039	
chunk0184_40_1	chr7	112205082	112205309	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	1212	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.026432	0.482456	
chunk0062_58_1	chr14	67490142	67490652	+	0	NA	intron (NM_182526, intron 1 of 2)	intron (NM_182526, intron 1 of 2)	24907	NM_182526	161145	Hs.509707	NM_182526	ENSG00000198133	TMEM229B	C14orf83	transmembrane protein 229B	protein-coding	0.007843	0.477495	253(AGGAACAGACTGTTCC,-,0.00),254(GGAACAGACTGTTCCA,+,0.00)
chunk0021_320_1	chr1	245276758	245277156	+	0	NA	intron (NM_018012, intron 2 of 14)	MLT1C|LTR|ERVL-MaLR	121972	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.005025	0.436090	
chunk0006_206_1	chr1	67760452	67761156	+	0	NA	intron (NM_018841, intron 2 of 3)	L2b|LINE|L2	-71484	NR_040077	100289178	Hs.677603	NR_040077	ENSG00000232284	GNG12-AS1	-	GNG12, DIRAS3 and WLS antisense RNA 1	ncRNA	0.017045	0.429787	
chunk0004_29_1	chr1	42399719	42399939	+	0	NA	intron (NM_173642, intron 2 of 4)	L2b|LINE|L2	19032	NM_173642	284716	Hs.420244	NM_173642	ENSG00000177181	RIMKLA	FAM80A|NAAGS|NAAGS-II	ribosomal modification protein rimK like family member A	protein-coding	0.004545	0.457014	
chunk0178_376_1	chr7	40228854	40229196	+	0	NA	intron (NM_024728, intron 6 of 14)	L1MC5|LINE|L1	94049	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.005848	0.379009	191(AGGAACATTTTGTACC,-,0.00),192(GGAACATTTTGTACCT,+,0.00),241(AAGGACTGTTAGTTCC,-,0.00),242(AGGACTGTTAGTTCCT,+,0.00)
chunk0193_201_1	chr8	75923865	75924096	+	0	NA	Intergenic	L1PA10|LINE|L1	384012	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.012987	0.534483	
chunk0178_367_1	chr7	39663074	39663833	+	0	NA	intron (NM_005402, intron 1 of 4)	Tigger2|DNA|TcMar-Tigger	39900	NM_005402	5898	Hs.6906	NM_005402	ENSG00000006451	RALA	RAL	RAS like proto-oncogene A	protein-coding	0.001318	0.375000	
chunk0191_213_1	chr8	52292285	52292727	+	0	NA	intron (NM_014682, intron 2 of 25)	intron (NM_014682, intron 2 of 25)	117373	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.009050	0.390519	
chunk0081_286_1	chr17	44668134	44668468	+	0	NA	intron (NM_001145080, intron 5 of 7)	intron (NM_001145080, intron 5 of 7)	11907	NM_001145080	284071	Hs.349758	NM_001033659	ENSG00000180336	MEIOC	C17orf104	meiosis specific with coiled-coil domain	protein-coding	0.008982	0.405970	124(AATAACAGTATGTTCC,-,0.00),125(ATAACAGTATGTTCCT,+,0.00)
chunk0067_459_1	chr15	50381889	50382601	+	0	NA	Intergenic	Intergenic	21916	NR_039862	100616396		NR_039862	ENSG00000284284	MIR4712	-	microRNA 4712	ncRNA	0.014045	0.429173	293(AAGAACATGATGTGTC,-,0.00),294(AGAACATGATGTGTCT,+,0.00)
chunk0026_62_1	chr10	61124509	61125220	+	0	NA	Intergenic	Intergenic	108589	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.005626	0.367978	
chunk0028_409_1	chr10	93398078	93398618	+	0	NA	intron (NM_013451, intron 13 of 53)	L2a|LINE|L2	83969	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.009259	0.471349	
chunk0079_195_1	chr17	14325871	14326084	+	0	NA	intron (NR_130138, intron 1 of 2)	intron (NR_130138, intron 1 of 2)	22237	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.018779	0.453271	
chunk0198_24_1	chr8	128141798	128142390	+	0	NA	Intergenic	Intergenic	-8022	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.015203	0.549747	269(TGGGACACGCTGACCC,-,0.00),270(GGGACACGCTGACCCA,+,0.00),284(CAGAACACTGTGACCT,-,0.00),285(AGAACACTGTGACCTT,+,0.00)
chunk0207_322_1	chr9	134182849	134183123	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-18422	NR_023344	100151684	Hs.545589	NR_023344	ENSG00000221676	RNU6ATAC	RNU6ATAC1|U6ATAC	RNA, U6atac small nuclear (U12-dependent splicing)	snRNA	0.008230	0.524590	
chunk0076_130_1	chr16	66703001	66703470	+	0	NA	Intergenic	L2b|LINE|L2	-6528	NM_178818	146223	Hs.643961	NM_178818	ENSG00000183723	CMTM4	CKLFSF4	CKLF like MARVEL transmembrane domain containing 4	protein-coding	0.017058	0.487234	339(GGGAACAGCATGTGCC,-,0.00),340(GGAACAGCATGTGCCA,+,0.00)
chunk0002_135_1	chr1	16883029	16883441	+	0	NA	Intergenic	Intergenic	-12745	NR_004408	26869		NR_004408	ENSG00000207513	RNU1-3	HSD4|RNU1G3	RNA, U1 small nuclear 3	snRNA	0.007282	0.414044	198(AGGTGCATCCTGTTCC,-,0.00),199(GGTGCATCCTGTTCCG,+,0.00)
chunk0116_433_1	chr21	43023225	43023574	+	0	NA	intron (NM_004571, intron 8 of 10)	intron (NM_004571, intron 8 of 10)	48889	NM_001286258	5316	Hs.431043	NM_004571	ENSG00000160199	PKNOX1	PREP1|pkonx1c	PBX/knotted 1 homeobox 1	protein-coding	0.022923	0.468571	
chunk0024_134_1	chr10	35006912	35007320	+	0	NA	Intergenic	Intergenic	67214	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.004902	0.286064	
chunk0084_185_1	chr17	77728369	77729049	+	0	NA	promoter-TSS (NR_104134)	promoter-TSS (NR_104134)	-150	NR_104134	100132174	Hs.640110	NR_104134	ENSG00000267790	LINC01987	-	long intergenic non-protein coding RNA 1987	ncRNA	0.013235	0.475771	175(GGTACACAGCGTGCTG,+,0.00),580(AGGAACACGACGTCCC,-,0.00),581(GGAACACGACGTCCCT,+,0.00)
chunk0021_242_1	chr1	242854910	242855120	+	0	NA	Intergenic	L1PB1|LINE|L1	246729	NR_029401	731275	Hs.722350	NR_029401	ENSG00000214837	LINC01347	-	long intergenic non-protein coding RNA 1347	ncRNA	0.009524	0.563981	
chunk0170_58_1	chr6	109503340	109503898	+	0	NA	intron (NM_001145128, intron 35 of 40)	intron (NM_001145128, intron 35 of 40)	-20382	NM_001164313	9841	Hs.409876	NM_014797	ENSG00000112365	ZBTB24	BIF1|ICF2|PATZ2|ZNF450	zinc finger and BTB domain containing 24	protein-coding	0.014337	0.486583	
chunk0142_181_1	chr4	95820864	95821293	+	0	NA	Intergenic	LTR79|LTR|ERVL	-19010	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.002331	0.330233	
chunk0189_258_1	chr8	25234055	25234579	+	0	NA	intron (NM_024940, intron 1 of 51)	intron (NM_024940, intron 1 of 51)	49545	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.005725	0.365714	
chunk0095_151_1	chr2	16949005	16949557	+	0	NA	Intergenic	Intergenic	-283415	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.007246	0.394213	
chunk0196_364_1	chr8	115163170	115163473	+	0	NA	Intergenic	Intergenic	504691	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.016502	0.365132	
chunk0207_240_1	chr9	131997674	131998156	+	0	NA	intron (NM_001253881, intron 3 of 6)	intron (NM_001253881, intron 3 of 6)	81972	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.018672	0.488613	
chunk0040_430_1	chr11	121409047	121409246	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-43057	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.010050	0.390000	
chunk0084_223_1	chr17	78396788	78397226	+	0	NA	intron (NR_111989, intron 2 of 8)	intron (NR_111989, intron 2 of 8)	18389	NR_111989	9489	Hs.654671	NM_024419	ENSG00000087157	PGS1	-	phosphatidylglycerophosphate synthase 1	protein-coding	0.020548	0.505695	
chunk0190_168_1	chr8	31935864	31936499	+	0	NA	intron (NM_013962, intron 1 of 4)	intron (NM_013962, intron 1 of 4)	-89555	NR_104158	100856811	Hs.97362	NR_104156		NRG1-IT1	-	NRG1 intronic transcript 1	ncRNA	0.006299	0.356918	
chunk0115_186_1	chr21	26085025	26085609	+	0	NA	intron (NM_001136016, intron 3 of 16)	intron (NM_001136016, intron 3 of 16)	55073	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.010274	0.398291	
chunk0063_230_1	chr14	81650579	81650778	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-27617	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.015075	0.470000	
chunk0099_19_1	chr2	82983782	82984491	+	0	NA	Intergenic	Intergenic	127333	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.004231	0.352113	
chunk0157_162_1	chr5	118017671	118017931	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	-264773	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.007692	0.406130	129(GAGAACAGCATGATCC,-,0.00),130(AGAACAGCATGATCCA,+,0.00)
chunk0112_347_1	chr20	45157767	45157986	+	0	NA	Intergenic	L1M3de|LINE|L1	-17023	NM_002638	5266	Hs.112341	NM_002638	ENSG00000124102	PI3	ESI|SKALP|WAP3|WFDC14|cementoin	peptidase inhibitor 3	protein-coding	0.000000	0.440909	
chunk0050_181_1	chr12	103870067	103870797	+	0	NA	intron (NR_027249, intron 9 of 15)	intron (NR_027249, intron 9 of 15)	-29235	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.002740	0.321477	309(AAGGACAGTAAGTTCA,-,0.00),310(AGGACAGTAAGTTCAA,+,0.00),388(AAGAACAAAGAGTACC,-,0.00),389(AGAACAAAGAGTACCC,+,0.00)
chunk0086_430_1	chr18	28149788	28150378	+	0	NA	intron (NM_001792, intron 1 of 15)	intron (NM_001792, intron 1 of 15)	27363	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.022034	0.467005	
chunk0133_320_1	chr3	172513353	172513993	+	0	NA	intron (NM_003810, intron 2 of 4)	Tigger16b|DNA|TcMar-Tigger	9802	NM_001190943	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.004687	0.457098	
chunk0041_392_1	chr11	132779982	132780361	+	0	NA	intron (NM_001012393, intron 2 of 7)	intron (NM_001012393, intron 2 of 7)	162971	NM_002545	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.013193	0.455263	
chunk0114_342_1	chr21	17769181	17769448	+	0	NA	Intergenic	Intergenic	23195	NR_038870	246312	Hs.473425	NR_038870	ENSG00000240770	C21orf91-OT1	D21S2089E|NCRNA00285	C21orf91 overlapping transcript 1	ncRNA	0.007491	0.358209	
chunk0210_412_1	chrX	100745407	100746318	+	0	NA	Intergenic	Intergenic	-13714	NM_001129896	94121	Hs.592224	NM_080737	ENSG00000102362	SYTL4	SLP4	synaptotagmin like 4	protein-coding	0.007684	0.378289	640(GAGAACAAGATGTTCT,-,0.00),641(AGAACAAGATGTTCTA,+,0.00)
chunk0085_334_1	chr18	8555387	8555949	+	0	NA	Intergenic	Intergenic	-53777	NM_001025300	201475	Hs.270074	NM_001025300	ENSG00000206418	RAB12	-	RAB12, member RAS oncogene family	protein-coding	0.005338	0.442274	
chunk0094_48_1	chr2	2982545	2982983	+	0	NA	intron (NR_110228, intron 3 of 6)	L1PB4|LINE|L1	143262	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.002283	0.312073	
chunk0035_297_1	chr11	46985167	46985962	+	0	NA	intron (NM_001278222, intron 1 of 7)	intron (NM_001278222, intron 1 of 7)	48875	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.005031	0.361809	
chunk0006_213_1	chr1	67896620	67896837	+	0	NA	intron (NR_040077, intron 1 of 9)	intron (NR_040077, intron 1 of 9)	-63256	NM_018841	55970	Hs.431101	NM_018841	ENSG00000172380	GNG12	-	G protein subunit gamma 12	protein-coding	0.023041	0.444954	
chunk0048_433_1	chr12	88469894	88470685	+	0	NA	Intergenic	Intergenic	110184	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.003793	0.363636	11(CAGTTCAGGCTGTCCT,-,0.00),12(AGTTCAGGCTGTCCTG,+,0.00)
chunk0152_430_1	chr5	65982465	65983162	+	0	NA	intron (NM_018695, intron 1 of 24)	L1ME2|LINE|L1	-37240	NR_028474	100303749	Hs.608060	NR_028474		LOC100303749	-	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene	pseudo	0.002869	0.333811	418(CAGGACAGGCTGTCTT,-,0.00),419(AGGACAGGCTGTCTTG,+,0.00)
chunk0176_196_1	chr7	14085347	14085926	+	0	NA	Intergenic	L1MEg2|LINE|L1	-94211	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.008636	0.400000	
chunk0191_206_1	chr8	52059515	52059988	+	0	NA	Intergenic	Intergenic	-160565	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.002114	0.364979	
chunk0083_281_1	chr17	68647086	68647601	+	0	NA	intron (NR_110825, intron 2 of 4)	LTR22B|LTR|ERVK	19189	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.021359	0.463178	
chunk0133_242_1	chr3	171506838	171507262	+	0	NA	Intergenic	MIRc|SINE|MIR	-46642	NM_001161563	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.009434	0.355294	
chunk0201_68_1	chr9	34084518	34084901	+	0	NA	Intergenic	Intergenic	-35760	NM_001282529	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.002611	0.492188	169(CAGAACAAGAAGTGCC,-,0.00),170(AGAACAAGAAGTGCCT,+,0.00),190(GAGAACAAGAAGTTCT,-,0.00),191(AGAACAAGAAGTTCTT,+,0.00)
chunk0001_364_1	chr1	10056248	10056823	+	0	NA	intron (NM_001105562, intron 1 of 27)	L2a|LINE|L2	23552	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.012174	0.404514	
chunk0190_418_1	chr8	41225243	41225449	+	0	NA	Intergenic	L1PA6|LINE|L1	45797	NR_049801	100847068		NR_049801	ENSG00000263372	MIR548AO	-	microRNA 548ao	ncRNA	0.019417	0.560386	
chunk0030_204_1	chr10	114460792	114461012	+	0	NA	intron (NM_001003407, intron 12 of 21)	intron (NM_001003407, intron 12 of 21)	-56124	NM_032550	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.000000	0.380090	82(ATGGACACTTTGTGCT,-,0.00),83(TGGACACTTTGTGCTG,+,0.00)
chunk0034_83_1	chr11	27392788	27392987	+	0	NA	intron (NM_018490, intron 2 of 17)	intron (NM_018490, intron 2 of 17)	-29639	NM_080654	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.000000	0.425000	
chunk0157_412_1	chr5	124599384	124600107	+	0	NA	Intergenic	Intergenic	145367	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.008299	0.390884	
chunk0195_110_1	chr8	94719689	94719936	+	0	NA	promoter-TSS (NM_181787)	promoter-TSS (NM_181787)	-63	NM_181787	286148	Hs.567828	NM_181787	ENSG00000156162	DPY19L4	-	dpy-19 like 4	protein-coding	0.121457	0.766129	
chunk0114_220_1	chr21	15694891	15695147	+	0	NA	Intergenic	L1MC2|LINE|L1	-35006	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.003906	0.369650	
chunk0136_112_1	chr4	3343407	3343759	+	0	NA	intron (NM_198229, intron 3 of 17)	L1MC2|LINE|L1	-26414	NM_198227	6002	Hs.527061	NM_002926	ENSG00000159788	RGS12	-	regulator of G protein signaling 12	protein-coding	0.039773	0.481586	82(AAGTACAGAGAGTTCC,-,0.00),83(AGTACAGAGAGTTCCC,+,0.00)
chunk0092_448_1	chr19	38838617	38838819	+	0	NA	intron (NM_001005335, intron 9 of 12)	intron (NM_001005335, intron 9 of 12)	-6861	NM_001398	1891	Hs.196176	NM_001398	ENSG00000104823	ECH1	HPXEL	enoyl-CoA hydratase 1	protein-coding	0.009901	0.561576	
chunk0007_427_1	chr1	86580964	86581341	+	0	NA	TTS (NR_024602)	TTS (NR_024602)	34076	NR_024602	22802	Hs.567422	NM_012128	ENSG00000016602	CLCA4	CaCC|CaCC2	chloride channel accessory 4	protein-coding	0.005305	0.370370	
chunk0194_105_1	chr8	83562972	83563813	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	159634	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.002378	0.336105	142(CAGATCATGTTGTTCC,-,0.00)
chunk0163_296_1	chr6	14128086	14128354	+	0	NA	intron (NM_001040280, intron 2 of 4)	intron (NM_001040280, intron 2 of 4)	10586	NM_001040280	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.011194	0.472119	
chunk0036_129_1	chr11	61830293	61830590	+	0	NA	intron (NM_004265, intron 1 of 11)	intron (NM_004265, intron 1 of 11)	2408	NM_004265	9415	Hs.502745	NM_004265	ENSG00000134824	FADS2	D6D|DES6|FADSD6|LLCDL2|SLL0262|TU13	fatty acid desaturase 2	protein-coding	0.010101	0.389262	
chunk0024_57_1	chr10	33899505	33900165	+	0	NA	Intergenic	Intergenic	-127155	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.007576	0.373676	281(AAGTGCACTATGTTCC,-,0.00),282(AGTGCACTATGTTCCT,+,0.00)
chunk0025_385_1	chr10	59285007	59285669	+	0	NA	intron (NM_001001971, intron 5 of 11)	intron (NM_001001971, intron 5 of 11)	77256	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.006042	0.461538	
chunk0206_380_1	chr9	126673603	126674176	+	0	NA	intron (NM_002316, intron 2 of 7)	intron (NM_002316, intron 2 of 7)	59446	NM_001174147	4010	Hs.129133	NM_002316	ENSG00000136944	LMX1B	LMX1.2|NPS1	LIM homeobox transcription factor 1 beta	protein-coding	0.024433	0.625436	
chunk0057_429_1	chr13	110382304	110382713	+	0	NA	intron (NM_001846, intron 4 of 47)	intron (NM_001846, intron 4 of 47)	41550	NR_107040	102465872		NR_107040	ENSG00000276765	MIR8073	hsa-mir-8073	microRNA 8073	ncRNA	0.007335	0.309756	
chunk0122_32_1	chr3	27918166	27918728	+	0	NA	Intergenic	L1MC4a|LINE|L1	-84311	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.008897	0.335702	
chunk0087_238_1	chr18	36509607	36510099	+	0	NA	intron (NM_001281739, intron 4 of 23)	intron (NM_001281739, intron 4 of 23)	153565	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.020325	0.446247	
chunk0007_24_1	chr1	77538932	77539403	+	0	NA	intron (NM_012093, intron 13 of 13)	LTR54|LTR|ERV1	143491	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.012739	0.442797	
chunk0088_346_1	chr18	51611540	51612030	+	0	NA	Intergenic	L2a|LINE|L2	219743	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.002041	0.350305	217(CATGACATTCTGTTCT,-,0.00),218(ATGACATTCTGTTCTT,+,0.00)
chunk0103_107_1	chr2	161357054	161357469	+	0	NA	intron (NM_005805, intron 3 of 11)	intron (NM_005805, intron 3 of 11)	48986	NM_005805	10213	Hs.740477	NM_005805	ENSG00000115233	PSMD14	PAD1|POH1|RPN11	proteasome 26S subunit, non-ATPase 14	protein-coding	0.000000	0.334135	
chunk0180_454_1	chr7	77492025	77492779	+	0	NA	Intergenic	Intergenic	-45054	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.009284	0.327152	
chunk0191_38_1	chr8	43099613	43100086	+	0	NA	intron (NM_001277971, intron 2 of 3)	L2b|LINE|L2	6343	NM_001277971	84197	Hs.491646	NM_032237	ENSG00000185900	POMK	MDDGA12|MDDGC12|SGK196	protein O-mannose kinase	protein-coding	0.014799	0.518987	
chunk0184_63_1	chr7	112431681	112432113	+	0	NA	intron (NM_001197080, intron 1 of 11)	intron (NM_001197080, intron 1 of 11)	8753	NM_001007245	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.011574	0.374134	
chunk0180_328_1	chr7	72665290	72666082	+	0	NA	intron (NM_001145440, intron 11 of 13)	intron (NM_001145440, intron 11 of 13)	-32217	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.002525	0.341740	
chunk0186_124_1	chr7	138194543	138195426	+	0	NA	Intergenic	L1ME3B|LINE|L1	71226	NR_039678	100616226		NR_039678	ENSG00000284028	MIR4468	-	microRNA 4468	ncRNA	0.012458	0.409502	
chunk0122_465_1	chr3	39982892	39983659	+	0	NA	intron (NM_015460, intron 2 of 16)	intron (NM_015460, intron 2 of 16)	-116736	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.010430	0.361979	
chunk0056_300_1	chr13	90783194	90783729	+	0	NA	Intergenic	Tigger1a_Art|DNA|TcMar-Tigger	143136	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.000000	0.332090	
chunk0068_377_1	chr15	58263434	58263709	+	0	NA	Intergenic	Intergenic	125362	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.007273	0.445652	
chunk0169_439_1	chr6	108752588	108753318	+	0	NA	intron (NR_033376, intron 1 of 4)	intron (NR_033376, intron 1 of 4)	1299	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.008219	0.432285	557(TAAAACTGGCTGTTCT,-,0.00),558(AAAACTGGCTGTTCTC,+,0.00)
chunk0135_339_1	chr3	190306957	190307675	+	0	NA	3' UTR (NM_021101, exon 4 of 4)	3' UTR (NM_021101, exon 4 of 4)	15130	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.004178	0.356050	
chunk0102_68_1	chr2	142982193	142982453	+	0	NA	intron (NM_001032998, intron 8 of 11)	intron (NM_001032998, intron 8 of 11)	104697	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.003846	0.314176	
chunk0009_363_1	chr1	109781912	109782121	+	0	NA	Intergenic	L1ME4b|LINE|L1	-17994	NM_133181	79574	Hs.485352	NM_024526	ENSG00000198758	EPS8L3	EPS8R3	EPS8 like 3	protein-coding	0.000000	0.319048	
chunk0018_328_1	chr1	221316412	221316953	+	0	NA	Intergenic	Intergenic	19614	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.001848	0.389299	
chunk0051_60_1	chr12	112466017	112466548	+	0	NA	intron (NM_002834, intron 6 of 15)	L2a|LINE|L2	47550	NM_080601	5781	Hs.506852	NM_002834	ENSG00000179295	PTPN11	BPTP3|CFC|JMML|METCDS|NS1|PTP-1D|PTP2C|SH-PTP2|SH-PTP3|SHP2	protein tyrosine phosphatase non-receptor type 11	protein-coding	0.001883	0.426692	285(GGGAACAGCAAGTGCA,-,0.00),286(GGAACAGCAAGTGCAA,+,0.00)
chunk0192_178_1	chr8	62929167	62929591	+	0	NA	intron (NR_130764, intron 5 of 6)	intron (NR_130764, intron 5 of 6)	-48482	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.009434	0.381176	83(AAGGGCAGATTGTCCC,-,0.00)
chunk0005_257_1	chr1	59751206	59751773	+	0	NA	intron (NM_001244714, intron 12 of 13)	intron (NM_001244714, intron 12 of 13)	-18193	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.003527	0.329225	
chunk0126_233_1	chr3	79030232	79030455	+	0	NA	intron (NM_002941, intron 3 of 30)	MER20|DNA|hAT-Charlie	-10884	NM_001145845	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.441964	
chunk0018_209_1	chr1	219468434	219468904	+	0	NA	Intergenic	Intergenic	293700	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.008511	0.318471	
chunk0204_290_1	chr9	99345498	99345766	+	0	NA	Intergenic	Intergenic	29625	NR_102270	100996569	Hs.745280	NR_102270	ENSG00000271086	NAMA	-	non-protein coding RNA, associated with MAP kinase pathway and growth arrest	ncRNA	0.003731	0.356877	210(TAGTACATGTTGTTCC,-,0.00),211(AGTACATGTTGTTCCC,+,0.00)
chunk0110_346_1	chr20	19472957	19473364	+	0	NA	intron (NM_020689, intron 2 of 16)	intron (NM_020689, intron 2 of 16)	-188564	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.009828	0.450980	
chunk0088_275_1	chr18	49342603	49343312	+	0	NA	intron (NM_017653, intron 6 of 16)	Tigger3a|DNA|TcMar-Tigger	117752	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.002821	0.381690	
chunk0009_234_1	chr1	106862547	106863005	+	0	NA	Intergenic	Intergenic	-193869	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.010917	0.379085	
chunk0209_116_1	chrX	40518797	40519407	+	0	NA	Intergenic	Intergenic	-61862	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.009836	0.535188	
chunk0115_379_1	chr21	30227651	30228051	+	0	NA	Intergenic	Intergenic	-11700	NM_199328	9073	Hs.162209	NM_012132	ENSG00000156284	CLDN8	HEL-S-79	claudin 8	protein-coding	0.005000	0.438903	
chunk0173_398_1	chr6	150485615	150485929	+	0	NA	Intergenic	Intergenic	-114091	NM_001029884	57480	Hs.189781	NM_001029884	ENSG00000120278	PLEKHG1	ARHGEF41	pleckstrin homology and RhoGEF domain containing G1	protein-coding	0.000000	0.396825	
chunk0185_305_1	chr7	131284542	131285277	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	42870	NR_125364	100506881	Hs.660830	NR_125364	ENSG00000236753	MKLN1-AS	MKLN1-AS2	MKLN1 antisense RNA	ncRNA	0.017687	0.535326	367(TAGAACGCTCTGTCCT,-,0.00),368(AGAACGCTCTGTCCTT,+,0.00)
chunk0135_156_1	chr3	187780625	187780849	+	0	NA	Intergenic	Intergenic	-35012	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.000000	0.257778	
chunk0047_413_1	chr12	75989160	75989398	+	0	NA	Intergenic	L1P3|LINE|L1	42497	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.004202	0.347280	48(AAAAACACAATGTACC,-,0.00),49(AAAACACAATGTACCA,+,0.00)
chunk0212_163_1	chrX	132408417	132408699	+	0	NA	intron (NM_133486, intron 1 of 8)	GA-rich|Low_complexity|Low_complexity	5017	NM_001170702	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.000000	0.303887	164(GAGAACACACTGTATT,-,0.00),165(AGAACACACTGTATTT,+,0.00)
chunk0165_207_1	chr6	34731876	34732095	+	0	NA	Intergenic	Intergenic	-25109	NR_029472	6631	Hs.1063	NM_003093	ENSG00000124562	SNRPC	U1C|Yhc1	small nuclear ribonucleoprotein polypeptide C	protein-coding	0.000000	0.390909	
chunk0212_406_1	chrX	151835220	151835619	+	0	NA	Intergenic	L1MC1|LINE|L1	-77470	NM_001011548	4103	Hs.37107	NM_002362	ENSG00000147381	MAGEA4	CT1.4|MAGE-41|MAGE-X2|MAGE4|MAGE4A|MAGE4B	MAGE family member A4	protein-coding	0.005013	0.337500	
chunk0014_306_1	chr1	181088491	181088760	+	0	NA	5' UTR (NM_016545, exon 1 of 1)	5' UTR (NM_016545, exon 1 of 1)	123	NM_016545	51278	Hs.15725	NM_016545	ENSG00000162783	IER5	SBBI48	immediate early response 5	protein-coding	0.122677	0.681481	
chunk0025_151_1	chr10	52332882	52333349	+	0	NA	Intergenic	Intergenic	18834	NM_012242	22943	Hs.40499	NM_012242	ENSG00000107984	DKK1	DKK-1|SK	dickkopf WNT signaling pathway inhibitor 1	protein-coding	0.008565	0.316239	
chunk0120_168_1	chr3	5798894	5799295	+	0	NA	Intergenic	Intergenic	-548839	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.007481	0.368159	
chunk0126_364_1	chr3	83381784	83382070	+	0	NA	Intergenic	Intergenic	1487648	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.003497	0.264808	
chunk0151_393_1	chr5	55412122	55412498	+	0	NA	intron (NM_015360, intron 23 of 26)	intron (NM_015360, intron 23 of 26)	96616	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.002660	0.294430	102(AAGAACATTGTCTTCT,-,0.00)
chunk0170_47_1	chr6	109440592	109441049	+	0	NA	promoter-TSS (NM_003080)	promoter-TSS (NM_003080)	92	NM_003080	6610	Hs.55235	NM_003080	ENSG00000135587	SMPD2	ISC1|NSMASE|NSMASE1	sphingomyelin phosphodiesterase 2	protein-coding	0.146608	0.766376	
chunk0123_201_1	chr3	44606880	44607307	+	0	NA	Intergenic	L1MB2|LINE|L1	17704	NR_046658	100874094		NR_046658	ENSG00000233509	ZNF197-AS1	-	ZNF197 antisense RNA 1	ncRNA	0.007026	0.320093	
chunk0160_294_1	chr5	158311619	158312278	+	0	NA	Intergenic	Intergenic	97825	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.006070	0.378788	
chunk0205_72_1	chr9	106879143	106879364	+	0	NA	intron (NM_021224, intron 1 of 12)	intron (NM_021224, intron 1 of 12)	16156	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.013575	0.554054	
chunk0063_157_1	chr14	80053892	80054653	+	0	NA	Intergenic	Intergenic	-157147	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.005256	0.332021	
chunk0033_206_1	chr11	16933918	16934265	+	0	NA	intron (NM_175058, intron 3 of 22)	intron (NM_175058, intron 3 of 22)	80325	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.011527	0.531609	
chunk0058_99_1	chr14	21668314	21668901	+	0	NA	Intergenic	Intergenic	3524	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.005111	0.343537	
chunk0094_134_1	chr2	4907926	4908437	+	0	NA	Intergenic	Intergenic	-251959	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.011742	0.402344	6(TGGACAGGCTGGTCTT,+,0.00)
chunk0046_227_1	chr12	59983477	59983881	+	0	NA	Intergenic	AluSx1|SINE|Alu	294342	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.009901	0.392593	285(TAGAACACCCTGCTCC,-,0.00),286(AGAACACCCTGCTCCT,+,0.00)
chunk0098_409_1	chr2	79966697	79967280	+	0	NA	intron (NM_004389, intron 7 of 17)	L2|LINE|L2	-100405	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.013722	0.426370	
chunk0128_24_1	chr3	104215093	104215334	+	0	NA	Intergenic	LTR41C|LTR|ERVL	-691097	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.004149	0.355372	
chunk0158_432_1	chr5	135371742	135372183	+	0	NA	intron (NM_001040158, intron 2 of 8)	intron (NM_001040158, intron 2 of 8)	27276	NM_138609	9555	Hs.420272	NM_004893	ENSG00000113648	H2AFY	H2A.y|H2A/y|H2AF12M|MACROH2A1.1|mH2A1|macroH2A1.2	H2A histone family member Y	protein-coding	0.006803	0.429864	
chunk0098_254_1	chr2	75053401	75053919	+	0	NA	exon (NM_015727, exon 3 of 4)	exon (NM_015727, exon 3 of 4)	-37152	NR_049796	100846995		NR_049796	ENSG00000263909	MIR5000	-	microRNA 5000	ncRNA	0.013514	0.504817	
chunk0022_380_1	chr10	17602526	17602725	+	0	NA	intron (NM_014241, intron 4 of 6)	L1MA8|LINE|L1	14749	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.010050	0.255000	
chunk0134_244_1	chr3	179305523	179305962	+	0	NA	Intergenic	L1MEi|LINE|L1	-17249	NM_001303426	51193	Hs.632578	NM_016331	ENSG00000121864	ZNF639	ANC-2H01|ANC_2H01|ZASC1	zinc finger protein 639	protein-coding	0.004556	0.322727	
chunk0082_226_1	chr17	57256291	57256581	+	0	NA	promoter-TSS (NM_170721)	promoter-TSS (NM_170721)	-134	NM_138962	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.117241	0.756014	
chunk0065_243_1	chr14	101323378	101323763	+	0	NA	Intergenic	LTR10A|LTR|ERV1	84352	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.018182	0.445596	150(AAGTACAATGAGTTCT,-,0.00),151(AGTACAATGAGTTCTG,+,0.00)
chunk0171_151_1	chr6	123910050	123910249	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	106303	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.005025	0.380000	
chunk0162_14_1	chr6	585945	586378	+	0	NA	intron (NR_073064, intron 13 of 29)	intron (NR_073064, intron 13 of 29)	70803	NM_148959	135458	Hs.669039	NM_148959	ENSG00000188996	HUS1B	-	HUS1 checkpoint clamp component B	protein-coding	0.020785	0.444700	
chunk0046_44_1	chr12	54881895	54882416	+	0	NA	Intergenic	L2|LINE|L2	27640	NM_058173	118430	Hs.348419	NM_058173	ENSG00000172551	MUCL1	SBEM	mucin like 1	protein-coding	0.003839	0.363985	
chunk0081_410_1	chr17	48505655	48505898	+	0	NA	Intergenic	MIRc|SINE|MIR	25134	NM_002144	3211	Hs.99992	NM_002144	ENSG00000120094	HOXB1	HCFP3|HOX2|HOX2I|Hox-2.9	homeobox B1	protein-coding	0.000000	0.368852	
chunk0088_218_1	chr18	48206706	48207312	+	0	NA	Intergenic	L1ME3|LINE|L1	-69700	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.011551	0.352554	
chunk0014_28_1	chr1	174711655	174711893	+	0	NA	intron (NM_014857, intron 17 of 20)	LTR12C|LTR|ERV1	-88123	NM_001243765	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.042017	0.673640	
chunk0156_226_1	chr5	108278777	108279155	+	0	NA	intron (NM_001163315, intron 4 of 8)	L1PB4|LINE|L1	103132	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.000000	0.527704	
chunk0188_302_1	chr8	16259409	16259624	+	0	NA	Intergenic	Intergenic	-66725	NM_138716	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.004651	0.333333	
chunk0183_456_1	chr7	111529624	111530516	+	0	NA	intron (NM_032549, intron 1 of 5)	MIRb|SINE|MIR	32221	NM_032549	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.001121	0.354983	
chunk0071_460_1	chr15	90388040	90388259	+	0	NA	promoter-TSS (NM_003870)	promoter-TSS (NM_003870)	-92	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.109589	0.763636	
chunk0078_268_1	chr17	7835274	7835558	+	0	NA	Intergenic	CpG	-4501	NM_001080424	23135	Hs.223678	NM_001080424	ENSG00000132510	KDM6B	JMJD3	lysine demethylase 6B	protein-coding	0.063380	0.645614	
chunk0060_11_1	chr14	39267024	39267576	+	0	NA	promoter-TSS (NR_038935)	promoter-TSS (NR_038935)	176	NM_203355	4253	Hs.287694	NM_005930	ENSG00000150527	MIA2	CTAGE5|MEA6|MGEA|MGEA11|MGEA6|TALI	MIA SH3 domain ER export factor 2	protein-coding	0.099638	0.674503	
chunk0085_263_1	chr18	7646710	7646966	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	79522	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.015625	0.501946	
chunk0056_16_1	chr13	77143388	77144123	+	0	NA	intron (NM_015057, intron 49 of 82)	Tigger3a|DNA|TcMar-Tigger	68241	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.005442	0.417120	
chunk0069_255_1	chr15	64515127	64515511	+	0	NA	intron (NM_015042, intron 1 of 8)	intron (NM_015042, intron 1 of 8)	15899	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.005208	0.431169	
chunk0037_46_1	chr11	70419660	70420199	+	0	NA	intron (NM_005231, intron 9 of 17)	intron (NM_005231, intron 9 of 17)	21423	NM_001184740	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.048237	0.481481	
chunk0164_188_1	chr6	22216071	22216510	+	0	NA	Intergenic	Intergenic	-69097	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.004556	0.406818	191(GGGGTCATCTTGTTCT,-,0.00),192(GGGTCATCTTGTTCTT,+,0.00)
chunk0105_196_1	chr2	187689450	187689750	+	0	NA	Intergenic	Intergenic	-135108	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.289037	
chunk0194_420_1	chr8	92119574	92119989	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-16555	NM_001198633	862	Hs.368431	NM_004349	ENSG00000079102	RUNX1T1	AML1-MTG8|AML1T1|CBFA2T1|CDR|ETO|MTG8|ZMYND2	RUNX1 partner transcriptional co-repressor 1	protein-coding	0.004819	0.300481	
chunk0155_435_1	chr5	100700169	100700465	+	0	NA	Intergenic	L1PA6|LINE|L1	116248	NR_031686	100302288		NR_031686	ENSG00000221263	MIR548P	MIRN548P|hsa-mir-548p	microRNA 548p	ncRNA	0.003378	0.505051	
chunk0010_302_1	chr1	117846844	117847508	+	0	NA	Intergenic	Intergenic	82503	NM_017686	54834	Hs.310809	NM_017686	ENSG00000196505	GDAP2	MACROD3|SCAR27	ganglioside induced differentiation associated protein 2	protein-coding	0.007530	0.383459	
chunk0159_394_1	chr5	147072993	147073490	+	0	NA	intron (NM_181677, intron 2 of 10)	intron (NM_181677, intron 2 of 10)	8229	NM_181678	5521	Hs.627618	NM_181674	ENSG00000156475	PPP2R2B	B55BETA|PP2AB55BETA|PP2ABBETA|PP2APR55B|PP2APR55BETA|PR2AB55BETA|PR2ABBETA|PR2APR55BETA|PR52B|PR55-BETA|PR55BETA|SCA12	protein phosphatase 2 regulatory subunit Bbeta	protein-coding	0.006036	0.423695	
chunk0054_2_1	chr13	40160417	40160686	+	0	NA	Intergenic	MER53|DNA|hAT	-21258	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.003717	0.377778	
chunk0141_121_1	chr4	79895081	79895459	+	0	NA	Intergenic	L1MD1|LINE|L1	67799	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.005291	0.292876	
chunk0012_248_1	chr1	161089062	161089335	+	0	NA	intron (NM_030916, intron 1 of 8)	intron (NM_030916, intron 1 of 8)	397	NM_030916	81607	Hs.492490	NM_030916	ENSG00000143217	NECTIN4	EDSS1|LNIR|PRR4|PVRL4|nectin-4	nectin cell adhesion molecule 4	protein-coding	0.014652	0.558394	
chunk0113_344_1	chr20	58719728	58720366	+	0	NA	Intergenic	Intergenic	27241	NM_024663	79716	Hs.654868	NM_024663	ENSG00000215440	NPEPL1	bA261P9.2	aminopeptidase like 1	protein-coding	0.017241	0.532081	
chunk0075_213_1	chr16	52611901	52612231	+	0	NA	Intergenic	Intergenic	-5091	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.006061	0.456193	
chunk0172_11_1	chr6	132768248	132768447	+	0	NA	Intergenic	Intergenic	-4888	NM_078488	8875	Hs.293130	NM_004665	ENSG00000112303	VNN2	FOAP-4|GPI-80	vanin 2	protein-coding	0.010050	0.545000	63(GTCACACTCTGTCCTG,+,0.00)
chunk0020_289_1	chr1	237069258	237069715	+	0	NA	intron (NM_001035, intron 1 of 104)	intron (NM_001035, intron 1 of 104)	27084	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.000000	0.292576	
chunk0115_79_1	chr21	22005402	22005669	+	0	NA	Intergenic	UCON5|Unknown|Unknown	92924	NR_109959	101927843	Hs.652879	NR_109959	ENSG00000233215	LINC01687	-	long intergenic non-protein coding RNA 1687	ncRNA	0.011236	0.373134	
chunk0182_16_1	chr7	91243878	91244330	+	0	NA	Intergenic	Intergenic	-20364	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.008850	0.448124	
chunk0033_38_1	chr11	13041355	13041728	+	0	NA	Intergenic	Intergenic	32118	NM_001080521	644943	Hs.134650	NM_001080521	ENSG00000189431	RASSF10	-	Ras association domain family member 10	protein-coding	0.002681	0.360963	
chunk0089_357_1	chr18	66831906	66832473	+	0	NA	Intergenic	L1MA4|LINE|L1	-228051	NR_073130	28513	Hs.42771	NM_021153	ENSG00000071991	CDH19	CDH7|CDH7L2	cadherin 19	protein-coding	0.005291	0.292254	
chunk0173_156_1	chr6	144283694	144284041	+	0	NA	Intergenic	L2c|LINE|L2	-7870	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.005764	0.353448	
chunk0135_398_1	chr3	192362674	192363012	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	46206	NM_021032	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.002959	0.342183	
chunk0043_26_1	chr12	13106049	13106516	+	0	NA	Intergenic	L1MC4|LINE|L1	-2586	NM_001080555	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.002141	0.339744	
chunk0071_110_1	chr15	81279757	81280143	+	0	NA	intron (NM_001172128, intron 8 of 18)	intron (NM_001172128, intron 8 of 18)	-16963	NM_004513	3603	Hs.459095	NM_004513	ENSG00000172349	IL16	LCF|NIL16|PRIL16|prIL-16	interleukin 16	protein-coding	0.010363	0.490956	
chunk0098_382_1	chr2	79265781	79266414	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-106343	NM_138937	5068	Hs.567312	NM_002580	ENSG00000172016	REG3A	HIP|HIP/PAP|INGAP|PAP|PAP-H|PAP1|PBCGF|REG-III|REG3	regenerating family member 3 alpha	protein-coding	0.001580	0.392744	
chunk0060_46_1	chr14	41253655	41254292	+	0	NA	Intergenic	MER52A|LTR|ERV1	299262	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.006279	0.551724	
chunk0181_451_1	chr7	90742323	90742624	+	0	NA	intron (NM_001287137, intron 2 of 12)	L1M5|LINE|L1	32657	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.006645	0.258278	
chunk0111_413_1	chr20	34640009	34640478	+	0	NA	intron (NM_080476, intron 4 of 11)	intron (NM_080476, intron 4 of 11)	37042	NM_080476	128869	Hs.253319	NM_080476	ENSG00000101464	PIGU	CDC91L1|GAB1	phosphatidylinositol glycan anchor biosynthesis class U	protein-coding	0.002132	0.468085	
chunk0118_44_1	chr22	27866248	27866846	+	0	NA	intron (NM_001284277, intron 8 of 10)	intron (NM_001284277, intron 8 of 10)	52667	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.005017	0.333890	
chunk0210_173_1	chrX	78333522	78333729	+	0	NA	Intergenic	MIRc|SINE|MIR	-5934	NM_001282186	10800	Hs.733809	NM_006639	ENSG00000173198	CYSLTR1	CYSLT1|CYSLT1R|CYSLTR|HMTMF81	cysteinyl leukotriene receptor 1	protein-coding	0.000000	0.403846	
chunk0201_104_1	chr9	34985109	34985547	+	0	NA	TTS (NR_109756)	TTS (NR_109756)	4051	NR_109756	101926900	Hs.545814	NR_109756	ENSG00000281491	DNAJB5-DT	DNAJB5-AS1	DNAJB5 divergent transcript	ncRNA	0.006849	0.478360	214(AAGCACATTCTGTGCA,-,0.00),215(AGCACATTCTGTGCAT,+,0.00)
chunk0122_178_1	chr3	32616690	32617038	+	0	NA	Intergenic	Intergenic	-45990	NM_016141	51143	Hs.529495	NM_016141	ENSG00000144635	DYNC1LI1	DLC-A|DNCLI1|LIC1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding	0.000000	0.406877	
chunk0059_225_1	chr14	34203313	34203844	+	0	NA	Intergenic	Intergenic	-252500	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.007533	0.359023	
chunk0196_233_1	chr8	107834617	107835249	+	0	NA	Intergenic	Intergenic	248270	NM_001282863	340419	Hs.444834	NM_178565	ENSG00000147655	RSPO2	CRISTIN2|HHRRD|TETAMS2	R-spondin 2	protein-coding	0.007911	0.353870	
chunk0087_299_1	chr18	39221898	39222235	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	400109	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.005935	0.423077	
chunk0107_409_1	chr2	224182410	224183041	+	0	NA	Intergenic	Intergenic	-143406	NM_006216	5270	Hs.38449	NM_006216	ENSG00000135919	SERPINE2	GDN|GDNPF|PI-7|PI7|PN-1|PN1|PNI	serpin family E member 2	protein-coding	0.009509	0.476266	
chunk0182_41_1	chr7	91628600	91629292	+	0	NA	Intergenic	Intergenic	251774	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.008671	0.408369	
chunk0061_140_1	chr14	59290430	59290629	+	0	NA	intron (NM_014992, intron 1 of 24)	MIR|SINE|MIR	27088	NM_014992	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.000000	0.385000	88(CTGCACATAATGTACT,-,0.00),89(TGCACATAATGTACTG,+,0.00)
chunk0068_7_1	chr15	50530637	50531415	+	0	NA	intron (NM_203494, intron 5 of 6)	MER5B|DNA|hAT-Charlie	15679	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.007712	0.379974	
chunk0208_297_1	chrX	22377517	22378171	+	0	NA	intron (NR_073010, intron 5 of 5)	intron (NR_073010, intron 5 of 5)	104931	NM_152577	158506	Hs.132485	NM_152577	ENSG00000175809	CBLL2	CT138|HAKAIL|ZNF645	Cbl proto-oncogene like 2	protein-coding	0.012232	0.383206	
chunk0174_279_1	chr6	161700795	161701128	+	0	NA	intron (NM_013988, intron 4 of 8)	intron (NM_013988, intron 4 of 8)	-426886	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.003003	0.344311	
chunk0157_407_1	chr5	124370517	124371361	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	67581	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004739	0.346746	
chunk0037_11_1	chr11	68973329	68973568	+	0	NA	Intergenic	Intergenic	7538	NM_198923	116512	Hs.527802	NM_198923	ENSG00000172938	MRGPRD	MRGD|TGR7	MAS related GPR family member D	protein-coding	0.008368	0.520833	99(CAGACCATGATGTTCT,-,0.00),100(AGACCATGATGTTCTG,+,0.00)
chunk0136_107_1	chr4	3179221	3180084	+	0	NA	intron (NM_002111, intron 35 of 66)	intron (NM_002111, intron 35 of 66)	-69388	NM_001042690	345222	Hs.442291	NM_001012982	ENSG00000188981	MSANTD1	C4orf44	Myb/SANT DNA binding domain containing 1	protein-coding	0.013905	0.491898	402(GGGGTCAGAGTGTGCC,-,0.00),403(GGGTCAGAGTGTGCCT,+,0.00),453(GGGGTCAGAGTGTGCC,-,0.00),454(GGGTCAGAGTGTGCCT,+,0.00),508(GGGGTCAGAGTGTGCC,-,0.00),509(GGGTCAGAGTGTGCCT,+,0.00),562(GGGGTCAGAGTGTGCC,-,0.00),563(GGGTCAGAGTGTGCCT,+,0.00),618(GGGGTCAGAGTGTGCC,-,0.00),619(GGGTCAGAGTGTGCCT,+,0.00),705(AGGGTCAGAGTGTGCC,-,0.00),706(GGGTCAGAGTGTGCCT,+,0.00)
chunk0056_41_1	chr13	77382911	77383355	+	0	NA	Intergenic	Intergenic	-56091	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.006757	0.352809	
chunk0157_173_1	chr5	118378873	118379487	+	0	NA	intron (NR_104610, intron 9 of 9)	L2a|LINE|L2	96606	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.003257	0.360976	254(TAGTACAGTGTGTTAT,-,0.00)
chunk0023_132_1	chr10	23869461	23870182	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	175075	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.013870	0.368421	
chunk0121_38_1	chr3	15310889	15311295	+	0	NA	intron (NM_001018009, intron 2 of 8)	MIRc|SINE|MIR	21537	NM_004844	9467	Hs.257761	NM_004844	ENSG00000131370	SH3BP5	SAB|SH3BP-5	SH3 domain binding protein 5	protein-coding	0.009852	0.449631	
chunk0143_126_1	chr4	109499615	109499814	+	0	NA	intron (NM_001300813, intron 7 of 24)	Tigger3b|DNA|TcMar-Tigger	11016	NR_030302	693161		NR_030302	ENSG00000207988	MIR576	MIRN576|hsa-mir-576	microRNA 576	ncRNA	0.005025	0.350000	
chunk0115_260_1	chr21	27802794	27802998	+	0	NA	Intergenic	LTR50|LTR|ERVL	80517	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.014706	0.448780	
chunk0211_69_1	chrX	109955000	109955227	+	0	NA	Intergenic	Intergenic	-47522	NM_017698	84187	Hs.496572	NM_017698	ENSG00000157600	TMEM164	bB360B22.3	transmembrane protein 164	protein-coding	0.004405	0.394737	
chunk0113_8_1	chr20	49349774	49350028	+	0	NA	Intergenic	Intergenic	69218	NR_003030	692057		NR_003030	ENSG00000212304	SNORD12	HBII-99|MIR1259|MIRN1259	small nucleolar RNA, C/D box 12	snoRNA	0.011811	0.478431	163(AACACATTTTGTTCCT,+,0.00)
chunk0125_110_1	chr3	65620929	65621595	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-272554	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.007508	0.365817	314(AGGAACACAGTGTGCC,-,0.00),315(GGAACACAGTGTGCCA,+,0.00)
chunk0119_414_1	chr22	49773324	49773610	+	0	NA	3' UTR (NM_001304809, exon 13 of 13)	3' UTR (NM_001304809, exon 13 of 13)	52433	NM_001304809	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.000000	0.324042	
chunk0142_355_1	chr4	101882661	101883021	+	0	NA	intron (NM_017935, intron 5 of 16)	intron (NM_017935, intron 5 of 16)	69015	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.008333	0.354571	
chunk0051_184_1	chr12	116160018	116160807	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	-11758	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.006337	0.379747	
chunk0137_294_1	chr4	23969324	23969770	+	0	NA	Intergenic	Intergenic	-79470	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.013453	0.391499	
chunk0014_313_1	chr1	181250981	181251406	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	14805	NR_046249	100287948	Hs.742594	NR_046249	ENSG00000179452	LINC01699	GM140	long intergenic non-protein coding RNA 1699	ncRNA	0.009412	0.429577	
chunk0003_129_1	chr1	32676945	32677370	+	0	NA	intron (NM_001135256, intron 11 of 11)	intron (NM_001135256, intron 11 of 11)	25603	NM_001161708	81493	Hs.712631	NM_030786	ENSG00000162520	SYNC	SYNC1|SYNCOILIN	syncoilin, intermediate filament protein	protein-coding	0.009412	0.427230	
chunk0167_235_1	chr6	67389413	67389758	+	0	NA	Intergenic	Tigger6b|DNA|TcMar-Tigger	-665766	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.002899	0.361272	
chunk0080_227_1	chr17	29803982	29804297	+	0	NA	intron (NM_033389, intron 1 of 14)	intron (NM_033389, intron 1 of 14)	-42707	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.000000	0.313291	
chunk0187_337_1	chr7	156776614	156776864	+	0	NA	intron (NM_022458, intron 5 of 16)	intron (NM_022458, intron 5 of 16)	116469	NM_022458	64327	Hs.209989	NM_022458	ENSG00000105983	LMBR1	ACHP|C7orf2|DIF14|LSS|PPD2|THYP|TPT|ZRS	limb development membrane protein 1	protein-coding	0.008000	0.458167	
chunk0190_92_1	chr8	30124539	30125244	+	0	NA	intron (NM_001128208, intron 3 of 3)	intron (NM_001128208, intron 3 of 3)	19793	NM_001100916	619373	Hs.627194	NM_001100916	ENSG00000177669	MBOAT4	FKSG89|GOAT|OACT4	membrane bound O-acyltransferase domain containing 4	protein-coding	0.005674	0.327195	
chunk0192_32_1	chr8	58636404	58637060	+	0	NA	intron (NM_001144772, intron 2 of 30)	MER58A|DNA|hAT-Charlie	22675	NM_001144772	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.003049	0.392694	
chunk0209_103_1	chrX	40087694	40087896	+	0	NA	intron (NM_001123383, intron 1 of 14)	intron (NM_001123383, intron 1 of 14)	9671	NM_001123385	54880	Hs.659681	NM_017745	ENSG00000183337	BCOR	ANOP2|MAA2|MCOPS2	BCL6 corepressor	protein-coding	0.009901	0.467980	
chunk0106_242_1	chr2	203081344	203081623	+	0	NA	intron (NM_001114132, intron 8 of 54)	MIR|SINE|MIR	66604	NM_001114132	65065	Hs.648846	NM_198945	ENSG00000144426	NBEAL1	A530083I02Rik|ALS2CR16|ALS2CR17	neurobeachin like 1	protein-coding	0.003584	0.228571	
chunk0047_163_1	chr12	69914920	69915370	+	0	NA	intron (NM_182530, intron 13 of 24)	intron (NM_182530, intron 13 of 24)	89822	NM_182530	196446	Hs.253773	NM_182530	ENSG00000166268	MYRFL	C12orf15|C12orf28|bcm1377	myelin regulatory factor like	protein-coding	0.008889	0.463415	
chunk0148_39_1	chr5	1211657	1211921	+	0	NA	intron (NM_001003841, intron 3 of 11)	(GTGCATGT)n|Simple_repeat|Simple_repeat	10194	NM_001003841	340024	Hs.481478	NM_001003841	ENSG00000174358	SLC6A19	B0AT1|HND	solute carrier family 6 member 19	protein-coding	0.026515	0.524528	
chunk0165_98_1	chr6	32260139	32260574	+	0	NA	Intergenic	L1PA7|LINE|L1	-36289	NM_004557	4855	Hs.436100	NM_004557	ENSG00000204301	NOTCH4	INT3	notch receptor 4	protein-coding	0.006897	0.350917	145(GGTACATTGTGTCTTC,+,0.00),228(AGGAACAGGTTGTTCA,-,0.00),229(GGAACAGGTTGTTCAG,+,0.00)
chunk0102_104_1	chr2	144343039	144343548	+	0	NA	Intergenic	Intergenic	-10759	NM_001284235	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.003929	0.313725	263(GAAACACTATGTACTA,+,0.00)
chunk0094_57_1	chr2	3312801	3313215	+	0	NA	intron (NM_003310, intron 3 of 8)	intron (NM_003310, intron 3 of 8)	64874	NM_003310	7260	Hs.502770	NM_003310	ENSG00000032389	EIPR1	EIPR-1|TSSC1	EARP complex and GARP complex interacting protein 1	protein-coding	0.012077	0.486747	
chunk0047_406_1	chr12	75859292	75859654	+	0	NA	Intergenic	MIRb|SINE|MIR	172303	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.005525	0.358127	
chunk0095_385_1	chr2	23788195	23788603	+	0	NA	intron (NR_125717, intron 21 of 28)	intron (NR_125717, intron 21 of 28)	138715	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.004902	0.391198	
chunk0105_358_1	chr2	191840183	191840844	+	0	NA	intron (NM_004657, intron 1 of 1)	intron (NM_004657, intron 1 of 1)	6767	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.007564	0.404834	
chunk0033_213_1	chr11	17164961	17165247	+	0	NA	intron (NM_002645, intron 1 of 31)	intron (NM_002645, intron 1 of 31)	4703	NM_002645	5286	Hs.175343	NM_002645	ENSG00000011405	PIK3C2A	CPK|OCSKD|PI3-K-C2(ALPHA)|PI3-K-C2A|PI3K-C2-alpha|PI3K-C2alpha	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha	protein-coding	0.003497	0.414634	
chunk0153_27_1	chr5	67074000	67074301	+	0	NA	intron (NM_001290226, intron 2 of 26)	L1ME4a|LINE|L1	69530	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.006645	0.291391	
chunk0057_443_1	chr13	110597158	110597705	+	0	NA	Intergenic	Intergenic	-18029	NM_001242883	55739	Hs.408324	NM_018210	ENSG00000213995	NAXD	CARKD|LP3298|PEBEL2	NAD(P)HX dehydratase	protein-coding	0.025594	0.492701	
chunk0127_9_1	chr3	88030158	88030661	+	0	NA	Intergenic	Intergenic	28587	NM_001008390	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.005964	0.313492	
chunk0036_143_1	chr11	62100824	62101281	+	0	NA	Intergenic	AluSx|SINE|Alu	-22921	NM_001040694	3619	Hs.142179	NM_020238	ENSG00000149503	INCENP	-	inner centromere protein	protein-coding	0.015317	0.500000	
chunk0075_38_1	chr16	46986830	46987375	+	0	NA	Intergenic	Intergenic	-13388	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.007339	0.423077	
chunk0105_424_1	chr2	193256619	193256938	+	0	NA	Intergenic	Intergenic	506933	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.003135	0.431250	
chunk0168_278_1	chr6	90669672	90670312	+	0	NA	Intergenic	Intergenic	-82691	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.006250	0.358814	
chunk0180_17_1	chr7	53439682	53440215	+	0	NA	Intergenic	L1MC3|LINE|L1	371983	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.003752	0.282772	
chunk0172_325_1	chr6	138387523	138388722	+	0	NA	Intergenic	L1MCa|LINE|L1	-16077	NM_014320	23593	Hs.486589	NM_014320	ENSG00000051620	HEBP2	C6ORF34B|C6orf34|PP23|SOUL	heme binding protein 2	protein-coding	0.009174	0.420833	928(CAGAACGTTCTGTTCT,-,0.00),929(AGAACGTTCTGTTCTT,+,0.00)
chunk0106_320_1	chr2	205501590	205501789	+	0	NA	intron (NM_205863, intron 20 of 21)	intron (NM_205863, intron 20 of 21)	-180811	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.010050	0.360000	11(CAGAACACCGTGTCCA,-,0.00),12(AGAACACCGTGTCCAG,+,0.00)
chunk0118_227_1	chr22	32221447	32221895	+	0	NA	intron (NM_014227, intron 13 of 14)	intron (NM_014227, intron 13 of 14)	-16940	NM_001159545	10739	Hs.157427	NM_006605	ENSG00000128253	RFPL2	RNF79	ret finger protein like 2	protein-coding	0.006696	0.369710	
chunk0024_48_1	chr10	33716956	33717174	+	0	NA	Intergenic	MIRb|SINE|MIR	55615	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.004587	0.401826	
chunk0188_308_1	chr8	17016489	17017022	+	0	NA	Intergenic	Intergenic	-10483	NM_181723	286097	Hs.403594	NM_181723	ENSG00000155970	MICU3	EFHA2	mitochondrial calcium uptake family member 3	protein-coding	0.005629	0.320225	
chunk0036_445_1	chr11	68537846	68538534	+	0	NA	intron (NM_018312, intron 4 of 22)	intron (NM_018312, intron 4 of 22)	77472	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.008721	0.378810	
chunk0078_262_1	chr17	7558604	7558914	+	0	NA	TTS (NM_003809)	TTS (NM_003809)	467	NM_172087	8741	Hs.54673	NM_003808	ENSG00000161955	TNFSF13	APRIL|CD256|TALL-2|TALL2|TNLG7B|TRDL-1|UNQ383/PRO715|ZTNF2	TNF superfamily member 13	protein-coding	0.019355	0.614148	
chunk0088_212_1	chr18	48157860	48158281	+	0	NA	Intergenic	Intergenic	-20761	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.007126	0.504739	
chunk0198_170_1	chr8	133272067	133272311	+	0	NA	intron (NM_001258432, intron 1 of 13)	intron (NM_001258432, intron 1 of 13)	25115	NM_001258432	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.008197	0.473469	
chunk0188_229_1	chr8	12891940	12892139	+	0	NA	Intergenic	Intergenic	-53635	NM_020844	57604	Hs.202521	NM_020844	ENSG00000250305	TRMT9B	C8orf79|KIAA1456|TRM9L|hTRM9L	tRNA methyltransferase 9B (putative)	protein-coding	0.010050	0.545000	
chunk0103_331_1	chr2	167789340	167789641	+	0	NA	Intergenic	MIRb|SINE|MIR	-29182	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.006645	0.337748	
chunk0121_265_1	chr3	23219092	23219479	+	0	NA	intron (NM_152653, intron 3 of 5)	intron (NM_152653, intron 3 of 5)	15992	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005168	0.412371	
chunk0034_161_1	chr11	30475485	30475920	+	0	NA	intron (NM_001145399, intron 4 of 6)	L1ME3D|LINE|L1	104791	NM_001584	744	Hs.289795	NM_001584	ENSG00000066382	MPPED2	239FB|C11orf8	metallophosphoesterase domain containing 2	protein-coding	0.004598	0.323394	
chunk0010_229_1	chr1	116330238	116330887	+	0	NA	Intergenic	Intergenic	-42611	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.009245	0.483077	
chunk0213_5_1	chrY	19592646	19592971	+	0	NA	intron (NR_045128, intron 4 of 9)	intron (NR_045128, intron 4 of 9)	25450	NR_045129	246126	Hs.522863	NM_001005852	ENSG00000131002	TXLNGY	CYorf15A|CYorf15B|TXLNG2P	taxilin gamma pseudogene, Y-linked	pseudo	0.000000	0.346626	
chunk0131_138_1	chr3	145650950	145651224	+	0	NA	Intergenic	Intergenic	510408	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.003650	0.247273	
chunk0043_385_1	chr12	25089726	25090073	+	0	NA	intron (NM_001204126, intron 11 of 19)	intron (NM_001204126, intron 11 of 19)	37652	NM_001204127	4033	Hs.124922	NM_006152	ENSG00000118308	LRMP	JAW1	lymphoid restricted membrane protein	protein-coding	0.005764	0.408046	
chunk0121_347_1	chr3	24646521	24647306	+	0	NA	Intergenic	MamGypLTR1a|LTR|Gypsy	-125478	NR_039955									0.008917	0.419847	
chunk0066_353_1	chr15	38217266	38217590	+	0	NA	Intergenic	Intergenic	-35423	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.009259	0.436923	
chunk0010_308_1	chr1	117997518	117998000	+	0	NA	intron (NM_206996, intron 32 of 48)	MER58B|DNA|hAT-Charlie	68010	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.008299	0.343685	
chunk0016_104_1	chr1	195656475	195656705	+	0	NA	Intergenic	Intergenic	925891	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.000000	0.242424	
chunk0124_166_1	chr3	55244406	55244722	+	0	NA	Intergenic	Intergenic	236834	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.003165	0.365931	
chunk0124_177_1	chr3	55402764	55403210	+	0	NA	Intergenic	LTR82A|LTR|ERVL	78411	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.006726	0.420582	
chunk0110_212_1	chr20	15299203	15299690	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	102588	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.004107	0.362705	
chunk0029_304_1	chr10	104256371	104256720	+	0	NA	intron (NM_004832, intron 2 of 5)	intron (NM_004832, intron 2 of 5)	1835	NM_004832	9446	Hs.190028	NM_004832	ENSG00000148834	GSTO1	GSTO 1-1|GSTTLp28|HEL-S-21|P28|SPG-R	glutathione S-transferase omega 1	protein-coding	0.002865	0.437143	
chunk0117_339_1	chr21	43975552	43975805	+	0	NA	intron (NM_020132, intron 7 of 9)	intron (NM_020132, intron 7 of 9)	-36647	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.051383	0.543307	
chunk0175_303_1	chr7	7914368	7914853	+	0	NA	Intergenic	Intergenic	-54133	NM_138426	113263	Hs.131673	NM_138426	ENSG00000106415	GLCCI1	FAM117C|GCTR|GIG18|TSSN1	glucocorticoid induced 1	protein-coding	0.006186	0.405350	
chunk0107_388_1	chr2	223699488	223699880	+	0	NA	Intergenic	Intergenic	-97185	NM_003469	7857	Hs.516726	NM_003469	ENSG00000171951	SCG2	CHGC|EM66|SN|SgII	secretogranin II	protein-coding	0.012755	0.381679	
chunk0039_417_1	chr11	107705085	107705310	+	0	NA	Intergenic	Intergenic	6864	NM_003063	6588	Hs.334629	NM_003063	ENSG00000170290	SLN	-	sarcolipin	protein-coding	0.008889	0.433628	85(AGGGACGCAGAGTTCT,-,0.00)
chunk0065_317_1	chr14	103072013	103072212	+	0	NA	Intergenic	Intergenic	-14707	NM_006035	9578	Hs.654634	NM_006035	ENSG00000198752	CDC42BPB	MRCKB	CDC42 binding protein kinase beta	protein-coding	0.045226	0.610000	
chunk0114_216_1	chr21	15592770	15593472	+	0	NA	Intergenic	Intergenic	-136904	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.005698	0.385491	
chunk0003_50_1	chr1	30815652	30815908	+	0	NA	Intergenic	MIRb|SINE|MIR	-57944	NM_006762	7805	Hs.371021	NM_006762	ENSG00000162511	LAPTM5	CLAST6	lysosomal protein transmembrane 5	protein-coding	0.027344	0.478599	
chunk0017_297_1	chr1	210653865	210654259	+	0	NA	intron (NM_001170580, intron 11 of 11)	intron (NM_001170580, intron 11 of 11)	324766	NM_001170580	55733	Hs.58650	NM_018194	ENSG00000054392	HHAT	MART2|SKI1|Skn	hedgehog acyltransferase	protein-coding	0.017766	0.468354	
chunk0075_265_1	chr16	53708621	53709160	+	0	NA	intron (NM_001080432, intron 1 of 8)	L1MB7|LINE|L1	4927	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.001855	0.307407	
chunk0173_392_1	chr6	150176133	150176578	+	0	NA	intron (NM_030949, intron 1 of 3)	intron (NM_030949, intron 1 of 3)	33303	NM_030949	81706	Hs.486798	NM_030949	ENSG00000198729	PPP1R14C	CPI17-like|KEPI|NY-BR-81	protein phosphatase 1 regulatory inhibitor subunit 14C	protein-coding	0.017978	0.513453	
chunk0077_35_1	chr16	75369526	75369909	+	0	NA	intron (NM_006324, intron 5 of 6)	intron (NM_006324, intron 5 of 6)	63772	NM_006324	10428	Hs.461361	NM_006324	ENSG00000153774	CFDP1	BCNT|BUCENTAUR|CENP-29|CP27|SWC5|Yeti|p97	craniofacial development protein 1	protein-coding	0.013055	0.434896	
chunk0091_248_1	chr19	10749310	10749898	+	0	NA	intron (NM_001005360, intron 1 of 20)	MIRb|SINE|MIR	-30650	NR_039903	100616425		NR_039903	ENSG00000265879	MIR4748	mir-4748	microRNA 4748	ncRNA	0.015306	0.590832	
chunk0136_175_1	chr4	6516245	6516444	+	0	NA	intron (NM_001206995, intron 2 of 9)	intron (NM_001206995, intron 2 of 9)	39334	NM_001206995	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.015075	0.575000	
chunk0118_191_1	chr22	31451784	31452271	+	0	NA	intron (NM_001164502, intron 8 of 16)	intron (NM_001164502, intron 8 of 16)	37534	NM_001164501	56478	Hs.517559	NM_019843	ENSG00000184708	EIF4ENIF1	4E-T|Clast4	eukaryotic translation initiation factor 4E nuclear import factor 1	protein-coding	0.002053	0.368852	
chunk0133_316_1	chr3	172384640	172385329	+	0	NA	intron (NM_022763, intron 25 of 25)	intron (NM_022763, intron 25 of 25)	63472	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.005806	0.365217	411(AGGGACAATTTGTACT,-,0.00),412(GGGACAATTTGTACTG,+,0.00)
chunk0192_163_1	chr8	62499100	62499383	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	250299	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.014134	0.440141	159(CTGTACTTTCTGTTCT,-,0.00),160(TGTACTTTCTGTTCTT,+,0.00)
chunk0128_90_1	chr3	105747186	105747388	+	0	NA	intron (NM_170662, intron 5 of 18)	intron (NM_170662, intron 5 of 18)	121756	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.009901	0.344828	
chunk0151_230_1	chr5	51032893	51033579	+	0	NA	Intergenic	Intergenic	-63049	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.005831	0.387191	
chunk0158_438_1	chr5	135618350	135618779	+	0	NA	Intergenic	L1MA4A|LINE|L1	35371	NR_027127	340074	Hs.434633	NR_027127	ENSG00000251045	SLC25A48-AS1	LINC01959	SLC25A48 antisense RNA 1	ncRNA	0.000000	0.327907	
chunk0075_347_1	chr16	55427130	55427407	+	0	NA	Intergenic	Intergenic	-51562	NM_001302508	4313	Hs.513617	NM_004530	ENSG00000087245	MMP2	CLG4|CLG4A|MMP-2|MMP-II|MONA|TBE-1	matrix metallopeptidase 2	protein-coding	0.010830	0.464029	
chunk0111_115_1	chr20	23965277	23965476	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	21499	NM_178312	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.000000	0.390000	
chunk0072_186_1	chr15	94239858	94240557	+	0	NA	Intergenic	MIRb|SINE|MIR	-57994	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.002861	0.385714	
chunk0047_32_1	chr12	66229586	66229985	+	0	NA	intron (NM_007199, intron 8 of 11)	intron (NM_007199, intron 8 of 11)	-21297	NR_106757	102465249		NR_106757	ENSG00000284011	MIR6502	hsa-mir-6502	microRNA 6502	ncRNA	0.005013	0.397500	218(GAGCACACTAAGTGCT,-,0.00),219(AGCACACTAAGTGCTC,+,0.00)
chunk0053_291_1	chr13	33518599	33518822	+	0	NA	intron (NM_001243476, intron 4 of 17)	intron (NM_001243476, intron 4 of 17)	158125	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.004484	0.459821	
chunk0163_43_1	chr6	8558844	8559601	+	0	NA	intron (NR_038980, intron 3 of 4)	LTR33|LTR|ERVL	-92987	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.011889	0.430079	
chunk0021_303_1	chr1	244792203	244792648	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-42881	NM_001312871	116228	Hs.411490	NM_198076	ENSG00000203667	COX20	FAM36A	cytochrome c oxidase assembly factor COX20	protein-coding	0.004494	0.374439	
chunk0023_311_1	chr10	29022564	29022946	+	0	NA	Intergenic	Intergenic	176347	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.031414	0.530026	
chunk0140_23_1	chr4	65635517	65635733	+	0	NA	intron (NM_001281765, intron 2 of 17)	intron (NM_001281765, intron 2 of 17)	-34336	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.000000	0.359447	
chunk0038_224_1	chr11	86942299	86942543	+	0	NA	intron (NR_120591, intron 3 of 4)	intron (NR_120591, intron 3 of 4)	12977	NM_012193	8322	Hs.591968	NM_012193	ENSG00000174804	FZD4	CD344|EVR1|FEVR|FZD4S|Fz-4|Fz4|FzE4|GPCR|hFz4	frizzled class receptor 4	protein-coding	0.008197	0.383673	
chunk0203_273_1	chr9	88452945	88453577	+	0	NA	intron (NM_006717, intron 3 of 5)	intron (NM_006717, intron 3 of 5)	64879	NM_006717	10927	Hs.146804	NM_006717	ENSG00000106723	SPIN1	SPIN|TDRD24	spindlin 1	protein-coding	0.004747	0.372828	311(GAGTACATAATGTTTC,-,0.00),312(AGTACATAATGTTTCC,+,0.00)
chunk0036_65_1	chr11	59670269	59670627	+	0	NA	Intergenic	Intergenic	-1410	NM_152716	219988	Hs.591960	NM_152716	ENSG00000166889	PATL1	Pat1b|hPat1b	PAT1 homolog 1, processing body mRNA decay factor	protein-coding	0.025140	0.462396	
chunk0097_355_1	chr2	60219900	60220380	+	0	NA	Intergenic	Intergenic	162896	NR_132991	106660609	Hs.565545	NR_132991	ENSG00000228590	MIR4432HG	-	MIR4432 host gene	ncRNA	0.002083	0.340956	183(GAGAACAGTCTGTGTA,-,0.00),184(AGAACAGTCTGTGTAG,+,0.00)
chunk0167_95_1	chr6	57108375	57108916	+	0	NA	3' UTR (NM_001257273, exon 4 of 4)	3' UTR (NM_001257273, exon 4 of 4)	18615	NM_015555	26036	Hs.485628	NM_015555	ENSG00000112200	ZNF451	COASTER|dJ417I1.1	zinc finger protein 451	protein-coding	0.007394	0.354244	
chunk0202_336_1	chr9	78923911	78924363	+	0	NA	Intergenic	MER89-int|LTR|ERV1	221529	NR_109771	101927450	Hs.738041	NR_109771	ENSG00000260995	LOC101927450	-	uncharacterized LOC101927450	ncRNA	0.000000	0.342163	
chunk0155_133_1	chr5	93435918	93436350	+	0	NA	intron (NR_109824, intron 4 of 5)	intron (NR_109824, intron 4 of 5)	135209	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.323326	
chunk0157_92_1	chr5	116663077	116663702	+	0	NA	Intergenic	L2c|LINE|L2	-88463	NM_001300780	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.006400	0.423323	
chunk0138_395_1	chr4	42824367	42825030	+	0	NA	Intergenic	Intergenic	-68568	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.001508	0.362952	
chunk0004_436_1	chr1	52967634	52968034	+	0	NA	intron (NM_001193599, intron 5 of 14)	LTR3B|LTR|ERVK	27520	NR_039972									0.007500	0.466334	
chunk0020_429_1	chr1	241688726	241689251	+	0	NA	intron (NM_144625, intron 7 of 26)	L1MCa|LINE|L1	36710	NM_144625	128025	Hs.97527	NM_144625	ENSG00000162843	WDR64	-	WD repeat domain 64	protein-coding	0.007619	0.437262	217(CAGAACATGTTGTTCT,-,0.00),218(AGAACATGTTGTTCTT,+,0.00)
chunk0116_371_1	chr21	41984794	41986424	+	0	NA	Intergenic	Intergenic	-23585	NR_119384	150142	Hs.143833	NM_198078	ENSG00000237232	ZNF295-AS1	C21orf121|NCRNA00318|PRED87	ZNF295 antisense RNA 1	ncRNA	0.006135	0.416922	1348(TGGTACAGTGTGTTCC,-,0.00),1349(GGTACAGTGTGTTCCA,+,0.00)
chunk0168_334_1	chr6	92686247	92686944	+	0	NA	Intergenic	Intergenic	732987	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.005739	0.346705	
chunk0103_118_1	chr2	161694758	161695102	+	0	NA	intron (NM_001178015, intron 1 of 26)	intron (NM_001178015, intron 1 of 26)	70595	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.000000	0.266667	
chunk0039_167_1	chr11	99524787	99525245	+	0	NA	intron (NM_014361, intron 2 of 24)	intron (NM_014361, intron 2 of 24)	-31129	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.000000	0.278867	
chunk0039_176_1	chr11	100119025	100119352	+	0	NA	intron (NM_014361, intron 13 of 24)	intron (NM_014361, intron 13 of 24)	563043	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003058	0.356707	
chunk0132_35_1	chr3	154765139	154765876	+	0	NA	Intergenic	Intergenic	-314140	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.004071	0.414634	
chunk0019_359_1	chr1	229625051	229625356	+	0	NA	intron (NM_001025247, intron 1 of 3)	intron (NM_001025247, intron 1 of 3)	844	NM_014409	27097	Hs.270621	NM_014409	ENSG00000135801	TAF5L	PAF65B	TATA-box binding protein associated factor 5 like	protein-coding	0.045902	0.519608	
chunk0046_191_1	chr12	58833922	58834130	+	0	NA	Intergenic	Intergenic	-52310	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.009615	0.358852	
chunk0007_170_1	chr1	80251035	80251298	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-284589	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000000	0.333333	
chunk0022_442_1	chr10	19626833	19627148	+	0	NA	intron (NM_001142308, intron 36 of 39)	L1M5|LINE|L1	101560	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.003175	0.265823	
chunk0052_23_1	chr13	20217103	20217399	+	0	NA	Intergenic	L1MD1|LINE|L1	13982	NM_006783	10804	Hs.511757	NM_006783	ENSG00000121742	GJB6	CX30|DFNA3|DFNA3B|DFNB1B|ECTD2|ED2|EDH|HED|HED2	gap junction protein beta 6	protein-coding	0.003378	0.336700	
chunk0145_5_1	chr4	142912889	142913743	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	-66865	NM_001101669	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.005855	0.422222	318(AGGAACAACCTGTGCC,-,0.00),319(GGAACAACCTGTGCCA,+,0.00),359(AAGTACAGTTTGTACC,-,0.00),360(AGTACAGTTTGTACCT,+,0.00)
chunk0051_296_1	chr12	118397764	118398151	+	0	NA	intron (NM_022491, intron 6 of 11)	intron (NM_022491, intron 6 of 11)	21404	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.005168	0.422680	
chunk0210_92_1	chrX	71185190	71185389	+	0	NA	Intergenic	L2c|LINE|L2	-29923	NM_001097642	2705	Hs.333303	NM_000166	ENSG00000169562	GJB1	CMTX|CMTX1|CX32	gap junction protein beta 1	protein-coding	0.010050	0.445000	
chunk0021_316_1	chr1	245205958	245206382	+	0	NA	intron (NM_018012, intron 2 of 14)	intron (NM_018012, intron 2 of 14)	51185	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.002358	0.491765	
chunk0014_42_1	chr1	175040681	175040945	+	0	NA	Intergenic	Intergenic	-17358	NM_022100	63931	Hs.654858	NM_022100	ENSG00000120333	MRPS14	COXPD38|DJ262D12.2|HSMRPS14|MRP-S14|S14mt	mitochondrial ribosomal protein S14	protein-coding	0.018939	0.464151	
chunk0128_287_1	chr3	110927751	110928664	+	0	NA	Intergenic	Intergenic	141752	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.004381	0.307440	
chunk0123_350_1	chr3	48039161	48039461	+	0	NA	intron (NM_030885, intron 1 of 3)	intron (NM_030885, intron 1 of 3)	49968	NM_002375	4134	Hs.517949	NM_002375	ENSG00000047849	MAP4	-	microtubule associated protein 4	protein-coding	0.013333	0.458472	148(AAGCACAAGAAGTGCC,-,0.00),149(AGCACAAGAAGTGCCT,+,0.00)
chunk0137_186_1	chr4	17619794	17620196	+	0	NA	intron (NM_025205, intron 2 of 3)	intron (NM_025205, intron 2 of 3)	5367	NM_025205	80306	Hs.731966	NM_025205	ENSG00000118579	MED28	1500003D12Rik|EG1|magicin	mediator complex subunit 28	protein-coding	0.014925	0.372208	189(GTGTACACAATGTTCT,-,0.00),190(TGTACACAATGTTCTG,+,0.00)
chunk0168_272_1	chr6	90357901	90358186	+	0	NA	Intergenic	Intergenic	45301	NR_039671	100616109		NR_039671	ENSG00000266760	MIR4464	mir-4464	microRNA 4464	ncRNA	0.003509	0.321678	
chunk0166_59_1	chr6	42923216	42924098	+	0	NA	intron (NM_138296, intron 2 of 3)	intron (NM_138296, intron 2 of 3)	-5465	NM_006586	10695	Hs.414099	NM_006586	ENSG00000137161	CNPY3	CAG4A|EIEE60|ERDA5|PRAT4A|TNRC5	canopy FGF signaling regulator 3	protein-coding	0.004535	0.499434	746(GAAGACAGTCAGTTCC,-,0.00),747(AAGACAGTCAGTTCCT,+,0.00)
chunk0192_413_1	chr8	69212237	69212481	+	0	NA	Intergenic	Intergenic	-108169	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.008197	0.432653	
chunk0090_443_1	chr18	79751210	79751613	+	0	NA	intron (NM_004715, intron 12 of 12)	intron (NM_004715, intron 12 of 12)	69981	NM_001202504	9150	Hs.465490	NM_004715	ENSG00000060069	CTDP1	CCFDN|FCP1	CTD phosphatase subunit 1	protein-coding	0.024814	0.596535	200(CAGGACTTGGAGTTCT,-,0.00),201(AGGACTTGGAGTTCTG,+,0.00)
chunk0041_339_1	chr11	130638163	130639218	+	0	NA	Intergenic	Intergenic	-28045	NR_107019	102466873		NR_107019	ENSG00000274999	MIR8052	hsa-mir-8052	microRNA 8052	ncRNA	0.008531	0.450758	
chunk0170_82_1	chr6	109834932	109835253	+	0	NA	Intergenic	L2c|LINE|L2	-81876	NR_106988									0.015576	0.493789	
chunk0162_187_1	chr6	3825535	3826374	+	0	NA	Intergenic	Intergenic	-23444	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.029797	0.485714	351(AAAAACACATTGTGCT,-,0.00),352(AAAACACATTGTGCTT,+,0.00)
chunk0061_109_1	chr14	58073844	58074183	+	0	NA	intron (NM_001001872, intron 5 of 7)	intron (NM_001001872, intron 5 of 7)	78116	NM_001001872	145407	Hs.26766	NM_001001872	ENSG00000139971	ARMH4	C14orf37|UT2|c14_5376	armadillo like helical domain containing 4	protein-coding	0.000000	0.332353	
chunk0182_323_1	chr7	99023896	99024481	+	0	NA	intron (NR_110102, intron 1 of 5)	L1M4c|LINE|L1	11023	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.006838	0.404437	
chunk0101_336_1	chr2	136440380	136441076	+	0	NA	Intergenic	Intergenic	-322573	NM_003467	7852	Hs.593413	NM_003467	ENSG00000121966	CXCR4	CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS	C-X-C motif chemokine receptor 4	protein-coding	0.008621	0.373027	34(AAGTACAGGCTGGGCT,-,0.00),35(AGTACAGGCTGGGCTC,+,0.00)
chunk0141_297_1	chr4	86954982	86955569	+	0	NA	intron (NM_001166693, intron 2 of 20)	intron (NM_001166693, intron 2 of 20)	20273	NM_001166693	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.005111	0.312925	300(TTGAACAGAATGTTCA,-,0.00),301(TGAACAGAATGTTCAT,+,0.00)
chunk0030_70_1	chr10	112077900	112078711	+	0	NA	Intergenic	Intergenic	105474	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.006165	0.365764	
chunk0098_388_1	chr2	79511225	79511665	+	0	NA	Intergenic	Intergenic	-1489	NM_004389	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.025000	0.437642	210(AAGCACATCGTGTGCC,-,0.00),211(AGCACATCGTGTGCCT,+,0.00)
chunk0069_93_1	chr15	61295273	61295705	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-66186	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.004630	0.394919	
chunk0029_441_1	chr10	110248445	110248755	+	0	NA	intron (NM_005962, intron 3 of 5)	intron (NM_005962, intron 3 of 5)	22596	NM_005962	4601	Hs.602078	NM_005962	ENSG00000119950	MXI1	MAD2|MXD2|MXI|bHLHc11	MAX interactor 1, dimerization protein	protein-coding	0.000000	0.331190	
chunk0196_390_1	chr8	115777806	115778389	+	0	NA	Intergenic	Intergenic	-109069	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.010292	0.359589	
chunk0135_392_1	chr3	191473635	191474416	+	0	NA	intron (NR_120606, intron 1 of 6)	intron (NR_120606, intron 1 of 6)	12862	NM_001083308	152138	Hs.690618	NM_001083308	ENSG00000253548	PYDC2	POP2|cPOP2	pyrin domain containing 2	protein-coding	0.005122	0.352941	167(CAGCACAGTTTGTTCC,-,0.00),168(AGCACAGTTTGTTCCC,+,0.00)
chunk0185_366_1	chr7	132874019	132874326	+	0	NA	intron (NM_017812, intron 5 of 7)	L2a|LINE|L2	160743	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.016287	0.405844	
chunk0124_416_1	chr3	60954778	60955271	+	0	NA	intron (NM_001166243, intron 3 of 9)	intron (NM_001166243, intron 3 of 9)	296435	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.004057	0.346154	
chunk0023_138_1	chr10	23999101	23999566	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	-209458	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.006452	0.482833	
chunk0047_115_1	chr12	68937325	68937921	+	0	NA	intron (NM_001874, intron 1 of 8)	L1ME4a|LINE|L1	-4424	NM_001005502	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.001678	0.345059	
chunk0190_173_1	chr8	32449828	32450140	+	0	NA	intron (NM_013962, intron 1 of 4)	L2c|LINE|L2	9238	NR_047475	100874286	Hs.147060	NR_047475	ENSG00000254049	NRG1-IT3	-	NRG1 intronic transcript 3	ncRNA	0.016026	0.444089	129(TGGCACATAAAGTTCC,-,0.00),130(GGCACATAAAGTTCCG,+,0.00)
chunk0111_32_1	chr20	22163898	22164386	+	0	NA	Intergenic	Intergenic	110052	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.006148	0.355828	
chunk0108_355_1	chr2	236319054	236319530	+	0	NA	Intergenic	Intergenic	-54947	NM_212556	401036	Hs.639909	NM_212556	ENSG00000182177	ASB18	ASB-18	ankyrin repeat and SOCS box containing 18	protein-coding	0.023109	0.540881	103(AGGTACAGCCTGCCCC,-,0.00),104(GGTACAGCCTGCCCCA,+,0.00),287(GAGAACGCTGTGTGCT,-,0.00),288(AGAACGCTGTGTGCTG,+,0.00)
chunk0102_39_1	chr2	141899310	141899612	+	0	NA	intron (NM_018557, intron 1 of 90)	intron (NM_018557, intron 1 of 90)	232240	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.003311	0.359736	192(ATAAACACAGTGTGCC,-,0.00),193(TAAACACAGTGTGCCT,+,0.00)
chunk0100_99_1	chr2	108219948	108220595	+	0	NA	Intergenic	Intergenic	-2430	NR_131251	102724774	Hs.626744	NR_131251	ENSG00000225328	LINC01594	TCONS_l2_00015893	long intergenic non-protein coding RNA 1594	ncRNA	0.007728	0.464506	292(AGGTGCAGAGTGTTCC,-,0.00),293(GGTGCAGAGTGTTCCT,+,0.00),316(GATAACACTCTGTCCT,-,0.00),317(ATAACACTCTGTCCTC,+,0.00)
chunk0034_411_1	chr11	38184988	38185640	+	0	NA	Intergenic	L1MC1|LINE|L1	461042	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.003067	0.373660	
chunk0148_104_1	chr5	4481091	4481345	+	0	NA	Intergenic	Intergenic	-292263	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.031496	0.454902	
chunk0014_365_1	chr1	182485635	182486081	+	0	NA	intron (NM_001137669, intron 6 of 21)	MER58B|DNA|hAT-Charlie	35737	NM_001137669	353299	Hs.121200	NM_032267	ENSG00000121446	RGSL1	RGSL|RGSL2	regulator of G protein signaling like 1	protein-coding	0.006726	0.398210	
chunk0165_275_1	chr6	36052102	36052441	+	0	NA	intron (NM_001315, intron 1 of 11)	intron (NM_001315, intron 1 of 11)	24594	NM_139013	1432	Hs.485233	NM_001315	ENSG00000112062	MAPK14	CSBP|CSBP1|CSBP2|CSPB1|EXIP|Mxi2|PRKM14|PRKM15|RK|SAPK2A|p38|p38ALPHA	mitogen-activated protein kinase 14	protein-coding	0.005900	0.429412	
chunk0009_141_1	chr1	104677351	104677869	+	0	NA	Intergenic	MIRb|SINE|MIR	604587	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.000000	0.292871	
chunk0115_55_1	chr21	21357526	21358191	+	0	NA	intron (NM_004540, intron 8 of 17)	A-rich|Low_complexity|Low_complexity	359543	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.010526	0.285285	
chunk0092_133_1	chr19	27940780	27941373	+	0	NA	Intergenic	Intergenic	-147136	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.001686	0.340067	
chunk0026_278_1	chr10	67256908	67257359	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	146277	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.004435	0.296460	
chunk0089_283_1	chr18	62967224	62967457	+	0	NA	intron (NM_194449, intron 14 of 16)	L1ME1|LINE|L1	251901	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.008584	0.384615	
chunk0199_216_1	chr9	5144069	5144611	+	0	NA	Intergenic	L1PA13|LINE|L1	41278	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.012915	0.364641	
chunk0176_426_1	chr7	19700810	19701681	+	0	NA	intron (NM_001002926, intron 2 of 3)	L1MC2|LINE|L1	4191	NR_036101	100422967		NR_036101	ENSG00000265932	MIR3146	mir-3146	microRNA 3146	ncRNA	0.010333	0.344037	
chunk0158_50_1	chr5	125963620	125963957	+	0	NA	Intergenic	Intergenic	-215789	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.002967	0.301775	124(AAGCACAGAATGAACT,-,0.00),125(AGCACAGAATGAACTG,+,0.00)
chunk0063_46_1	chr14	76918765	76919337	+	0	NA	Intergenic	Intergenic	92669	NM_194287	145497	Hs.147276	NM_194287	ENSG00000100565	LRRC74A	C14orf166B|LRRC74	leucine rich repeat containing 74A	protein-coding	0.034965	0.591623	476(CAAAACACCGTGTTCA,-,0.00),477(AAAACACCGTGTTCAC,+,0.00)
chunk0101_215_1	chr2	130624749	130624998	+	0	NA	intron (NM_001277083, intron 6 of 14)	Zaphod2|DNA|hAT-Tip100	13340	NM_001277083	653781	Hs.558829	NM_001277083	ENSG00000222038	POTEJ	POTE2beta	POTE ankyrin domain family member J	protein-coding	0.000000	0.360000	167(AGAACAAGATGCTCTG,+,0.00)
chunk0127_140_1	chr3	94226361	94226656	+	0	NA	Intergenic	Intergenic	-163285	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.006780	0.375000	
chunk0079_97_1	chr17	12094140	12094967	+	0	NA	intron (NM_001281435, intron 4 of 11)	intron (NM_001281435, intron 4 of 11)	12654	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.004837	0.353865	
chunk0170_156_1	chr6	111484035	111484234	+	0	NA	promoter-TSS (NM_002912)	promoter-TSS (NM_002912)	-419	NM_001286432	5980	Hs.232021	NM_002912	ENSG00000009413	REV3L	POLZ|REV3	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding	0.075377	0.580000	
chunk0195_23_1	chr8	93141880	93142187	+	0	NA	intron (NM_001242668, intron 1 of 2)	intron (NM_001242668, intron 1 of 2)	24817	NM_001242668									0.003257	0.496753	
chunk0089_125_1	chr18	58723697	58724146	+	0	NA	intron (NM_006785, intron 10 of 16)	intron (NM_006785, intron 10 of 16)	-52048	NM_001289967	101927322	Hs.644875	NM_001289967		LOC101927322	-	uncharacterized LOC101927322	protein-coding	0.004454	0.337778	191(GGAGACAGAATGTGCT,-,0.00),192(GAGACAGAATGTGCTG,+,0.00)
chunk0177_98_1	chr7	21947079	21947531	+	0	NA	Intergenic	Intergenic	-1381	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.006637	0.373068	
chunk0140_126_1	chr4	69020243	69020903	+	0	NA	promoter-TSS (NM_001075).2	promoter-TSS (NM_001075).2	-176	NM_001075	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.004545	0.335855	
chunk0020_132_1	chr1	233614132	233614519	+	0	NA	exon (NM_002245, exon 1 of 3)	exon (NM_002245, exon 1 of 3)	321	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.082687	0.667526	
chunk0057_199_1	chr13	103394570	103395177	+	0	NA	Intergenic	Intergenic	-30327	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.004942	0.384868	
chunk0032_207_1	chr11	7456235	7456482	+	0	NA	intron (NR_103855, intron 3 of 4)	intron (NR_103855, intron 3 of 4)	9477	NR_103855	100506258	Hs.661614	NR_103855	ENSG00000251364	LOC100506258	-	uncharacterized LOC100506258	ncRNA	0.000000	0.516129	
chunk0131_289_1	chr3	150535378	150536007	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	10949	NM_014445	27230	Hs.518326	NM_014445	ENSG00000120742	SERP1	RAMP4	stress associated endoplasmic reticulum protein 1	protein-coding	0.003180	0.342857	
chunk0108_291_1	chr2	234928413	234928644	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-23456	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.021645	0.534483	
chunk0175_235_1	chr7	6460357	6460617	+	0	NA	TTS (NM_001100603)	TTS (NM_001100603)	-12475	NM_139179	221955	Hs.487498	NM_139179	ENSG00000164535	DAGLB	DAGLBETA|KCCR13L	diacylglycerol lipase beta	protein-coding	0.015385	0.482759	
chunk0062_156_1	chr14	69231372	69231859	+	0	NA	intron (NM_018199, intron 3 of 7)	HAL1|LINE|L1	-28349	NM_020692	57452	Hs.21035	NM_020692	ENSG00000100626	GALNT16	GALNACT16|GALNTL1|GalNAc-T16	polypeptide N-acetylgalactosaminyltransferase 16	protein-coding	0.008214	0.422131	
chunk0169_37_1	chr6	97396304	97396720	+	0	NA	intron (NR_110757, intron 1 of 4)	intron (NR_110757, intron 1 of 4)	90926	NR_110757	101927314	Hs.520283	NR_110757	ENSG00000271860	LOC101927314	-	uncharacterized LOC101927314	ncRNA	0.002404	0.268585	
chunk0094_241_1	chr2	7031683	7032262	+	0	NA	intron (NM_014746, intron 8 of 8)	L1MB8|LINE|L1	45908	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.041451	0.555172	
chunk0135_47_1	chr3	185555961	185556248	+	0	NA	Intergenic	Intergenic	-3523	NM_139248	200879	Hs.68864	NM_139248	ENSG00000163898	LIPH	AH|ARWH2|HYPT7|LAH2|LPDLR|PLA1B|mPA-PLA1	lipase H	protein-coding	0.000000	0.375000	
chunk0187_273_1	chr7	155300616	155300815	+	0	NA	intron (NM_198337, intron 2 of 3)	intron (NM_198337, intron 2 of 3)	2939	NM_005542	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.010050	0.400000	
chunk0055_413_1	chr13	74769351	74769990	+	0	NA	Intergenic	Intergenic	216827	NR_034025	338864	Hs.97408	NR_034024	ENSG00000236678	LINC00347	-	long intergenic non-protein coding RNA 347	ncRNA	0.004695	0.362500	
chunk0048_148_1	chr12	80369362	80369695	+	0	NA	intron (NM_173591, intron 54 of 57)	intron (NM_173591, intron 54 of 57)	-74818	NM_001145026	374462	Hs.539284	NM_001145026	ENSG00000139304	PTPRQ	DFNA73|DFNB84|DFNB84A|PTPGMC1|R-PTP-Q	protein tyrosine phosphatase receptor type Q	protein-coding	0.006006	0.383234	
chunk0025_3_1	chr10	47009543	47009802	+	0	NA	Intergenic	Intergenic	77295	NM_001042357	26095	Hs.440733	NM_015605	ENSG00000204179	PTPN20	CT126|PTPN20A|PTPN20B|bA142I17.1|bA42B19.1	protein tyrosine phosphatase non-receptor type 20	protein-coding	0.011583	0.446154	
chunk0003_438_1	chr1	41215588	41216181	+	0	NA	intron (NM_001172219, intron 1 of 14)	L2c|LINE|L2	26259	NM_001172218	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.001686	0.378788	
chunk0007_197_1	chr1	81223043	81223637	+	0	NA	Intergenic	Intergenic	334362	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.005051	0.339496	
chunk0074_293_1	chr16	29805363	29805615	+	0	NA	promoter-TSS (NM_001276275)	promoter-TSS (NM_001276275)	-607	NM_001276275	4150	Hs.23650	NM_002383	ENSG00000103495	MAZ	PUR1|Pur-1|SAF-1|SAF-2|SAF-3|ZF87|ZNF801|Zif87	MYC associated zinc finger protein	protein-coding	0.103175	0.660079	
chunk0182_457_1	chr7	102157740	102158018	+	0	NA	intron (NM_001202546, intron 7 of 21)	intron (NM_001202546, intron 7 of 21)	-127183	NM_020979	10603	Hs.489448	NM_020979	ENSG00000160999	SH2B2	APS	SH2B adaptor protein 2	protein-coding	0.017986	0.491039	
chunk0006_459_1	chr1	77096011	77096530	+	0	NA	intron (NM_005482, intron 10 of 10)	intron (NM_005482, intron 10 of 10)	36127	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.005780	0.376923	211(AGGAACATAGTGTTCT,-,0.00),212(GGAACATAGTGTTCTA,+,0.00)
chunk0081_284_1	chr17	44411068	44411464	+	0	NA	intron (NM_001002909, intron 6 of 7)	intron (NM_001002909, intron 6 of 7)	-21761	NM_000419	3674	Hs.411312	NM_000419	ENSG00000005961	ITGA2B	BDPLT16|BDPLT2|CD41|CD41B|GP2B|GPIIb|GT|GTA|HPA3|PPP1R93	integrin subunit alpha 2b	protein-coding	0.002525	0.367758	
chunk0002_142_1	chr1	17236976	17237233	+	0	NA	intron (NM_013358, intron 11 of 15)	MIR|SINE|MIR	-11994	NM_016233	51702	Hs.149195	NM_016233	ENSG00000142619	PADI3	PAD3|PDI3|UHS1	peptidyl arginine deiminase 3	protein-coding	0.035019	0.523256	
chunk0178_374_1	chr7	40017274	40017658	+	0	NA	intron (NM_003718, intron 5 of 13)	L1ME3G|LINE|L1	67106	NM_031267	8621	Hs.233552	NM_003718	ENSG00000065883	CDK13	CDC2L|CDC2L5|CHDFIDD|CHED|hCDK13	cyclin dependent kinase 13	protein-coding	0.000000	0.267532	
chunk0031_168_1	chr10	125449072	125449648	+	0	NA	Intergenic	LTR33A|LTR|ERVL	-125011	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.017361	0.435009	
chunk0193_92_1	chr8	73614426	73615029	+	0	NA	intron (NM_001164384, intron 6 of 10)	Tigger15a|DNA|TcMar-Tigger	132200	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.004975	0.332781	293(TAAAACTGTCTGTTCT,-,0.00),294(AAAACTGTCTGTTCTT,+,0.00)
chunk0138_251_1	chr4	39664743	39665247	+	0	NA	Intergenic	Intergenic	-26134	NM_174921	201895	Hs.205952	NM_174921	ENSG00000163683	SMIM14	C4orf34	small integral membrane protein 14	protein-coding	0.000000	0.407921	349(TTGTACATGGTGTTCT,-,0.00),350(TGTACATGGTGTTCTG,+,0.00)
chunk0050_127_1	chr12	102121081	102121504	+	0	NA	intron (NM_017915, intron 1 of 10)	MER58B|DNA|hAT-Charlie	1114	NM_017915	55010	Hs.330663	NM_017915	ENSG00000185480	PARPBP	AROM|C12orf48|PARI	PARP1 binding protein	protein-coding	0.004728	0.410377	
chunk0044_119_1	chr12	29123145	29123419	+	0	NA	Intergenic	Intergenic	-25721	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.000000	0.367273	
chunk0147_435_1	chr4	187480391	187480920	+	0	NA	intron (NR_038931, intron 1 of 4)	L2c|LINE|L2	24958	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.007561	0.400000	
chunk0024_136_1	chr10	35034391	35034997	+	0	NA	intron (NM_001198778, intron 10 of 20)	intron (NM_001198778, intron 10 of 20)	39636	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.009901	0.359143	
chunk0123_418_1	chr3	49562708	49563638	+	0	NA	intron (NM_003458, intron 1 of 11)	intron (NM_003458, intron 1 of 11)	8684	NM_003458	8927	Hs.194684	NM_003458	ENSG00000164061	BSN	ZNF231	bassoon presynaptic cytomatrix protein	protein-coding	0.006452	0.498389	
chunk0037_157_1	chr11	73608043	73608624	+	0	NA	Intergenic	Intergenic	-10144	NM_001286050	23201	Hs.475334	NM_015159	ENSG00000054965	FAM168A	KIAA0280|TCRP1	family with sequence similarity 168 member A	protein-coding	0.006885	0.441581	
chunk0061_9_1	chr14	55588360	55588870	+	0	NA	intron (NM_001079521, intron 1 of 43)	Tigger2b_Pri|DNA|TcMar-Tigger	8408	NR_073128	3895	Hs.509414	NM_004986	ENSG00000126777	KTN1	CG1|KNT|MU-RMS-40.19	kinectin 1	protein-coding	0.003922	0.360078	181(AAGGACAGAATGCTCA,-,0.00),182(AGGACAGAATGCTCAT,+,0.00),294(TGGTACAGTATGTACT,-,0.00),295(GGTACAGTATGTACTG,+,0.00)
chunk0056_457_1	chr13	95267880	95268506	+	0	NA	intron (NM_001105515, intron 1 of 20)	LTR5_Hs|LTR|ERVK	33253	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.012780	0.467305	
chunk0110_8_1	chr20	9594303	9594708	+	0	NA	intron (NM_020341, intron 4 of 10)	LTR44|LTR|ERV1	-79507	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.000000	0.386700	
chunk0202_215_1	chr9	76256203	76256675	+	0	NA	intron (NM_001190482, intron 24 of 36)	intron (NM_001190482, intron 24 of 36)	138089	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.029661	0.443975	
chunk0150_88_1	chr5	32272789	32273062	+	0	NA	intron (NM_001040446, intron 3 of 15)	intron (NM_001040446, intron 3 of 15)	40083	NM_001294343	54545	Hs.481836	NM_019061	ENSG00000150712	MTMR12	3-PAP|PIP3AP	myotubularin related protein 12	protein-coding	0.000000	0.478102	177(GGGCCAGGATGTGCCT,+,0.00)
chunk0059_61_1	chr14	30223987	30224254	+	0	NA	Intergenic	Intergenic	-296427	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.003745	0.421642	
chunk0178_232_1	chr7	35771975	35772194	+	0	NA	intron (NR_120512, intron 3 of 4)	MER113|DNA|hAT-Charlie	28541	NR_120511	101928545	Hs.648103	NR_120511		SEPTIN7-AS1	SEPT7-AS1	SEPT7 antisense RNA 1 (head to head)	ncRNA	0.000000	0.304545	
chunk0141_270_1	chr4	86388146	86388517	+	0	NA	intron (NM_002753, intron 1 of 13)	intron (NM_002753, intron 1 of 13)	-28109	NM_138980	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.005391	0.279570	
chunk0088_8_1	chr18	43174836	43175772	+	0	NA	Intergenic	Intergenic	-59612	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.003205	0.330843	
chunk0035_14_1	chr11	40228621	40229117	+	0	NA	intron (NM_020929, intron 3 of 4)	intron (NM_020929, intron 3 of 4)	64261	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.006048	0.360161	
chunk0171_3_1	chr6	119475924	119476501	+	0	NA	intron (NR_046100, intron 1 of 5)	intron (NR_046100, intron 1 of 5)	15090	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.005199	0.384083	
chunk0076_383_1	chr16	72346598	72347373	+	0	NA	intron (NR_126330, intron 9 of 13)	intron (NR_126330, intron 9 of 13)	-174535	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.003871	0.387887	
chunk0132_243_1	chr3	158685827	158686162	+	0	NA	intron (NM_001308164, intron 16 of 18)	intron (NM_001308164, intron 16 of 18)	-13301	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.000000	0.291667	103(AAGTACTGATTGTTCT,-,0.00),104(AGTACTGATTGTTCTA,+,0.00)
chunk0003_361_1	chr1	39366248	39366798	+	0	NA	intron (NM_012090, intron 43 of 92)	L1MC5a|LINE|L1	-42981	NM_015038	643314	Hs.658760	NM_015038	ENSG00000127603	KIAA0754	-	KIAA0754	protein-coding	0.009091	0.397459	
chunk0150_27_1	chr5	30896225	30896934	+	0	NA	Intergenic	Intergenic	-297076	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.005642	0.342254	178(TAGAACAATATGTCCT,-,0.00),179(AGAACAATATGTCCTG,+,0.00),387(GTAACAGAGTGTCCTA,+,0.00)
chunk0021_235_1	chr10	7011888	7012287	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	174697	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.002506	0.397500	
chunk0196_377_1	chr8	115451635	115451834	+	0	NA	intron (NM_001282903, intron 5 of 6)	intron (NM_001282903, intron 5 of 6)	216278	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.020101	0.425000	
chunk0115_184_1	chr21	25980018	25980591	+	0	NA	intron (NM_001136016, intron 8 of 16)	intron (NM_001136016, intron 8 of 16)	160086	NM_001136016	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.013962	0.442509	
chunk0030_213_1	chr10	114635692	114636726	+	0	NA	intron (NM_001003407, intron 1 of 21)	L2c|LINE|L2	22090	NM_002313	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.007737	0.463768	735(AGGTACAGCATGATCT,-,0.00),736(GGTACAGCATGATCTG,+,0.00)
chunk0085_336_1	chr18	8615421	8616234	+	0	NA	intron (NM_001025300, intron 1 of 5)	intron (NM_001025300, intron 1 of 5)	6382	NM_001025300	201475	Hs.270074	NM_001025300	ENSG00000206418	RAB12	-	RAB12, member RAS oncogene family	protein-coding	0.008610	0.415233	
chunk0123_168_1	chr3	43881679	43882191	+	0	NA	Intergenic	Intergenic	191052	NM_016006	51099	Hs.19385	NM_016006	ENSG00000011198	ABHD5	CGI58|IECN2|NCIE2	abhydrolase domain containing 5	protein-coding	0.019531	0.483431	
chunk0099_247_1	chr2	97811355	97811773	+	0	NA	intron (NM_015348, intron 17 of 40)	intron (NM_015348, intron 17 of 40)	77158	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.004785	0.453461	
chunk0042_88_1	chr12	2586418	2586710	+	0	NA	intron (NM_001129846, intron 18 of 45)	intron (NM_001129846, intron 18 of 45)	85656	NR_046579	100874235	Hs.667644	NR_046579	ENSG00000256271	CACNA1C-AS2	-	CACNA1C antisense RNA 2	ncRNA	0.003425	0.457338	
chunk0145_173_1	chr4	147370968	147371220	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-26377	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.007937	0.411067	127(ATCACAGAGTGTACTT,+,0.00)
chunk0031_418_1	chr10	132265982	132266572	+	0	NA	intron (NM_173575, intron 1 of 11)	L1ME2|LINE|L1	41696	NM_173575	282974	Hs.469002	NM_173575	ENSG00000165752	STK32C	PKE|YANK3	serine/threonine kinase 32C	protein-coding	0.020339	0.434856	
chunk0038_210_1	chr11	86419644	86420481	+	0	NA	intron (NM_001156474, intron 14 of 14)	intron (NM_001156474, intron 14 of 14)	45326	NM_021827	60494	Hs.144913	NM_021827	ENSG00000149201	CCDC81	-	coiled-coil domain containing 81	protein-coding	0.010753	0.414081	
chunk0067_213_1	chr15	45084094	45084566	+	0	NA	Intergenic	Intergenic	29831	NM_014080	50506	Hs.71377	NM_014080	ENSG00000140279	DUOX2	LNOX2|NOXEF2|P138-TOX|TDH6|THOX2	dual oxidase 2	protein-coding	0.008475	0.389006	
chunk0191_204_1	chr8	52034193	52034714	+	0	NA	Intergenic	Intergenic	-135267	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.007678	0.417625	
chunk0089_31_1	chr18	57866308	57866793	+	0	NA	Intergenic	L2b|LINE|L2	-63455	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.008247	0.337449	
chunk0176_194_1	chr7	14034935	14035463	+	0	NA	Intergenic	Intergenic	-43774	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.005682	0.338374	
chunk0189_94_1	chr8	21712974	21713308	+	0	NA	intron (NM_001165038, intron 3 of 7)	MER53|DNA|hAT	75693	NM_001165038	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.020958	0.501493	
chunk0206_133_1	chr9	121035230	121035447	+	0	NA	intron (NM_001735, intron 4 of 40)	intron (NM_001735, intron 4 of 40)	14938	NM_001735	727	Hs.494997	NM_001735	ENSG00000106804	C5	C5D|C5a|C5b|CPAMD4|ECLZB	complement C5	protein-coding	0.004608	0.266055	
chunk0054_149_1	chr13	43980361	43980954	+	0	NA	Intergenic	L2c|LINE|L2	-41678	NR_026955	121838	Hs.201441	NR_026955		LINC00284	NCRNA00284	long intergenic non-protein coding RNA 284	ncRNA	0.005059	0.343434	
chunk0001_366_1	chr1	10101792	10102377	+	0	NA	intron (NM_001105562, intron 4 of 27)	intron (NM_001105562, intron 4 of 27)	69101	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.003419	0.346416	
chunk0001_377_1	chr1	10438542	10439188	+	0	NA	intron (NM_199006, intron 3 of 3)	intron (NM_199006, intron 3 of 3)	8118	NR_036462	378708	Hs.412311	NM_199294	ENSG00000175279	CENPS	APITD1|CENP-S|FAAP16|MHF1	centromere protein S	protein-coding	0.015480	0.414219	
chunk0030_206_1	chr10	114518505	114518717	+	0	NA	intron (NM_001003407, intron 6 of 21)	MER58A|DNA|hAT-Charlie	8315	NM_006720	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.004717	0.427230	
chunk0138_349_1	chr4	41852019	41852771	+	0	NA	Intergenic	MER113A|DNA|hAT-Charlie	30216	NR_104143	101927074	Hs.611425	NR_104143	ENSG00000245870	LINC00682	-	long intergenic non-protein coding RNA 682	ncRNA	0.005319	0.370518	
chunk0198_197_1	chr8	133564011	133565150	+	0	NA	intron (NM_003033, intron 1 of 8)	intron (NM_003033, intron 1 of 8)	7360	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.007024	0.390351	770(CTGTACAAAGTGTGCC,-,0.00),771(TGTACAAAGTGTGCCT,+,0.00)
chunk0004_147_1	chr1	45172067	45172404	+	0	NA	intron (NM_020883, intron 1 of 13)	intron (NM_020883, intron 1 of 13)	34343	NM_020883	57643	Hs.656613	NM_020883	ENSG00000162415	ZSWIM5	-	zinc finger SWIM-type containing 5	protein-coding	0.017804	0.331361	
chunk0051_379_1	chr12	121834158	121834543	+	0	NA	Intergenic	L2a|LINE|L2	24513	NM_002150	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.010390	0.445596	209(GGAAACATACTGTTCT,-,0.00),210(GAAACATACTGTTCTT,+,0.00)
chunk0053_355_1	chr13	35036807	35037118	+	0	NA	intron (NM_015678, intron 1 of 57)	L1M1|LINE|L1	94675	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.003215	0.362179	
chunk0099_365_1	chr2	100935753	100935976	+	0	NA	intron (NM_002518, intron 4 of 20)	intron (NM_002518, intron 4 of 20)	41297	NR_110213	101927142	Hs.656556	NR_110213		LOC101927142	-	uncharacterized LOC101927142	ncRNA	0.008969	0.392857	
chunk0060_157_1	chr14	45134169	45134585	+	0	NA	exon (NM_002013, exon 1 of 7)	exon (NM_002013, exon 1 of 7)	152	NM_002013	2287	Hs.509226	NM_002013	ENSG00000100442	FKBP3	FKBP-25|FKBP-3|FKBP25|PPIase	FKBP prolyl isomerase 3	protein-coding	0.091346	0.685851	
chunk0184_452_1	chr7	123397828	123398855	+	0	NA	Intergenic	Intergenic	134607	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.009737	0.404669	219(TGGCACTGAGTGTACC,-,0.00),220(GGCACTGAGTGTACCG,+,0.00),715(AAGTACACTCTGTCCA,-,0.00),716(AGTACACTCTGTCCAA,+,0.00)
chunk0169_96_1	chr6	100241706	100242015	+	0	NA	Intergenic	Intergenic	221815	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.003236	0.348387	
chunk0120_201_1	chr3	7171442	7171806	+	0	NA	intron (NM_000844, intron 2 of 9)	intron (NM_000844, intron 2 of 9)	-277607	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.010989	0.397260	
chunk0097_291_1	chr2	55290684	55291049	+	0	NA	3' UTR (NM_001254943, exon 34 of 34)	3' UTR (NM_001254943, exon 34 of 34)	8547	NR_027258	344405	Hs.445292	NM_001080459	ENSG00000162997	PRORSD1P	NCRNA00117|PRDXDD1P|Prdxdd1|Ybakd1	prolyl-tRNA synthetase associated domain containing 1, pseudogene	pseudo	0.005479	0.325137	
chunk0133_235_1	chr3	171355267	171355528	+	0	NA	intron (NR_027767, intron 2 of 2)	intron (NR_027767, intron 2 of 2)	105011	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.000000	0.393130	139(TAGAACAAAATGTACT,-,0.00),140(AGAACAAAATGTACTA,+,0.00)
chunk0096_215_1	chr2	30527654	30528529	+	0	NA	intron (NM_001002257, intron 2 of 5)	intron (NM_001002257, intron 2 of 5)	80865	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.003429	0.361872	
chunk0063_11_1	chr14	76199835	76200346	+	0	NA	intron (NM_017972, intron 8 of 8)	L1MB3|LINE|L1	45736	NR_110314	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.005871	0.351562	
chunk0088_344_1	chr18	51537841	51538144	+	0	NA	intron (NR_040074, intron 1 of 2)	LTR106_Mam|LTR|LTR	145950	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.003300	0.325658	
chunk0180_456_1	chr7	77498854	77499053	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-38503	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.005025	0.405000	
chunk0190_5_1	chr8	28712913	28713596	+	0	NA	intron (NR_073468, intron 1 of 4)	MER94|DNA|hAT-Blackjack	11781	NR_073469	2137	Hs.491354	NM_001440	ENSG00000012232	EXTL3	BOTV|EXTL1L|EXTR1|ISDNA|REGR|RPR	exostosin like glycosyltransferase 3	protein-coding	0.013177	0.391813	
chunk0052_126_1	chr13	23488495	23488910	+	0	NA	Intergenic	Intergenic	19190	NR_038995	100506697	Hs.50118	NR_038995	ENSG00000232977	LINC00327	NCRNA00327	long intergenic non-protein coding RNA 327	ncRNA	0.014458	0.432692	
chunk0093_145_1	chr19	46761350	46761855	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	-15139	NM_013403	29888	Hs.631590	NM_013403	ENSG00000090372	STRN4	PPP2R6C|ZIN|zinedin	striatin 4	protein-coding	0.013861	0.409091	
chunk0058_118_1	chr14	22254342	22254696	+	0	NA	Intergenic	Intergenic	334718	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.022599	0.402817	
chunk0045_443_1	chr12	53591217	53591754	+	0	NA	intron (NM_006856, intron 2 of 11)	intron (NM_006856, intron 2 of 11)	34511	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.005587	0.408922	268(AGGGACACTGAGTTTC,-,0.00)
chunk0134_318_1	chr3	181763679	181763941	+	0	NA	Intergenic	L2a|LINE|L2	51886	NM_003106	6657	Hs.518438	NM_003106	ENSG00000181449	SOX2	ANOP3|MCOPS3	SRY-box transcription factor 2	protein-coding	0.003817	0.441065	
chunk0199_203_1	chr9	4895695	4896037	+	0	NA	Intergenic	Intergenic	45569	NR_029836	406894		NR_029836	ENSG00000199065	MIR101-2	MIRN101-2|mir-101-2	microRNA 101-2	ncRNA	0.000000	0.408163	
chunk0034_202_1	chr11	32310159	32310698	+	0	NA	Intergenic	Intergenic	120389	NM_001198552	7490	Hs.591980	NM_000378	ENSG00000184937	WT1	AWT1|GUD|NPHS4|WAGR|WIT-2|WT33	WT1 transcription factor	protein-coding	0.012987	0.396296	
chunk0141_369_1	chr4	88044640	88044842	+	0	NA	intron (NM_000297, intron 5 of 14)	Tigger4b|DNA|TcMar-Tigger	37094	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.014851	0.374384	
chunk0086_26_1	chr18	12430685	12430910	+	0	NA	intron (NM_001142405, intron 6 of 6)	(TG)n|Simple_repeat|Simple_repeat	10608	NM_001142406	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.004444	0.464602	
chunk0032_98_1	chr11	3686059	3686352	+	0	NA	intron (NM_016320, intron 28 of 32)	intron (NM_016320, intron 28 of 32)	-14821	NM_001303035	57053	Hs.732806	NM_020402	ENSG00000129749	CHRNA10	-	cholinergic receptor nicotinic alpha 10 subunit	protein-coding	0.017065	0.472789	
chunk0073_14_1	chr16	2085891	2086650	+	0	NA	exon (NM_001077183, exon 35 of 40)	exon (NM_001077183, exon 35 of 40)	4014	NR_030646	100188847		NR_030646	ENSG00000221656	MIR1225	MIRN1225	microRNA 1225	ncRNA	0.040843	0.675000	347(AGGTACACGGAGTTCC,-,0.00),348(GGTACACGGAGTTCCT,+,0.00)
chunk0055_163_1	chr13	60392284	60392487	+	0	NA	Intergenic	LTR71B|LTR|ERV1	-4072	NM_001146071	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.014778	0.475490	133(TAGTACATCCTGTTTC,-,0.00),134(AGTACATCCTGTTTCT,+,0.00)
chunk0104_103_1	chr2	172522386	172522811	+	0	NA	Intergenic	Intergenic	-32775	NR_103731	5163	Hs.470633	NM_002610	ENSG00000152256	PDK1	-	pyruvate dehydrogenase kinase 1	protein-coding	0.004706	0.460094	
chunk0177_207_1	chr7	24039847	24040509	+	0	NA	Intergenic	L2b|LINE|L2	-244010	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.010574	0.393665	
chunk0099_42_1	chr2	83893924	83894607	+	0	NA	Intergenic	AluSz|SINE|Alu	-396417	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.007321	0.368421	
chunk0023_289_1	chr10	28552926	28553512	+	0	NA	intron (NM_016628, intron 3 of 13)	intron (NM_016628, intron 3 of 13)	19727	NM_100486	51322	Hs.743224	NM_016628	ENSG00000095787	WAC	BM-016|DESSH|PRO1741|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.005119	0.301533	
chunk0068_364_1	chr15	58036574	58036882	+	0	NA	intron (NM_003888, intron 1 of 12)	intron (NM_003888, intron 1 of 12)	-22631	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.009740	0.352751	
chunk0076_21_1	chr16	58848120	58848463	+	0	NA	Intergenic	Intergenic	-113934	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.002915	0.377907	
chunk0084_1_1	chr18	108330	108566	+	0	NA	promoter-TSS (NR_033770)	promoter-TSS (NR_033770)	-617	NR_033770	727758	Hs.585843	NR_033770	ENSG00000263006	ROCK1P1	ROCK1P	Rho associated coiled-coil containing protein kinase 1 pseudogene 1	pseudo	0.004237	0.489451	
chunk0110_344_1	chr20	19459330	19459791	+	0	NA	intron (NM_020689, intron 2 of 16)	intron (NM_020689, intron 2 of 16)	-174964	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.006508	0.413420	
chunk0139_137_1	chr4	53475422	53475792	+	0	NA	intron (NM_032622, intron 8 of 9)	intron (NM_032622, intron 8 of 9)	-24470	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.005405	0.345013	
chunk0081_352_1	chr17	47582277	47582784	+	0	NA	intron (NM_006310, intron 4 of 22)	intron (NM_006310, intron 4 of 22)	51452	NM_006310	9520	Hs.443837	NM_006310	ENSG00000141279	NPEPPS	AAP-S|MP100|PSA	aminopeptidase puromycin sensitive	protein-coding	0.003945	0.336614	250(AGCAGACACTGTTCCT,+,0.00)
chunk0127_52_1	chr3	89111090	89111680	+	0	NA	intron (NM_005233, intron 1 of 16)	intron (NM_005233, intron 1 of 16)	3861	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003390	0.304569	235(AAGAACACACTGTGAT,-,0.00),236(AGAACACACTGTGATT,+,0.00)
chunk0078_101_1	chr17	2111726	2112201	+	0	NA	intron (NM_001256827, intron 6 of 11)	intron (NM_001256827, intron 6 of 11)	-23202	NM_001282326	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.010526	0.422269	
chunk0113_218_1	chr20	53852059	53852552	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	23404	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.014199	0.471660	
chunk0152_26_1	chr5	56727037	56727364	+	0	NA	Intergenic	L2a|LINE|L2	-87873	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.006116	0.399390	129(CAGCACAGAGAGTACC,-,0.00),130(AGCACAGAGAGTACCT,+,0.00)
chunk0122_259_1	chr3	35042363	35042785	+	0	NA	intron (NR_110817, intron 2 of 3)	ERVL-E-int|LTR|ERVL	351449	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.002370	0.420804	
chunk0185_233_1	chr7	129385656	129385964	+	0	NA	intron (NM_001130723, intron 2 of 16)	intron (NM_001130723, intron 2 of 16)	10167	NM_001130722	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.006494	0.359223	
chunk0104_405_1	chr2	180715090	180715694	+	0	NA	intron (NR_104320, intron 1 of 3)	L2a|LINE|L2	23288	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.001656	0.381818	
chunk0156_13_1	chr5	102036967	102037502	+	0	NA	Intergenic	Intergenic	259315	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.003738	0.404851	371(CAGAACAGGCTGTTCT,-,0.00),372(AGAACAGGCTGTTCTG,+,0.00)
chunk0177_275_1	chr7	25543862	25544187	+	0	NA	Intergenic	Intergenic	-315538	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.003077	0.398773	
chunk0142_291_1	chr4	100145487	100145686	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	-44447	NR_125924	101929353	Hs.147584	NR_125924	ENSG00000249710	LOC101929353	-	uncharacterized LOC101929353	ncRNA	0.005025	0.530000	
chunk0208_270_1	chrX	21526789	21527226	+	0	NA	intron (NM_014927, intron 10 of 21)	intron (NM_014927, intron 10 of 21)	131380	NM_153270	257240	Hs.448572	NM_153270	ENSG00000185915	KLHL34	-	kelch like family member 34	protein-coding	0.009153	0.374429	
chunk0144_128_1	chr4	129267008	129267497	+	0	NA	Intergenic	Intergenic	171125	NM_001099783	132321	Hs.567679	NM_173487	ENSG00000151470	C4orf33	-	chromosome 4 open reading frame 33	protein-coding	0.000000	0.236735	
chunk0123_412_1	chr3	49278699	49278958	+	0	NA	exon (NM_199443, exon 20 of 21)	exon (NM_199443, exon 20 of 21)	-1753	NM_198562	375341	Hs.403828	NM_198562	ENSG00000188315	C3orf62	-	chromosome 3 open reading frame 62	protein-coding	0.015444	0.438462	
chunk0084_295_1	chr17	79975213	79975444	+	0	NA	intron (NM_019020, intron 3 of 11)	intron (NM_019020, intron 3 of 11)	-24471	NM_001271845	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.017316	0.521552	
chunk0198_221_1	chr8	133956727	133957195	+	0	NA	Intergenic	L2b|LINE|L2	70465	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.002137	0.324094	
chunk0161_181_1	chr5	169833719	169833999	+	0	NA	intron (NM_004946, intron 26 of 51)	HAL1|LINE|L1	146881	NM_001129891	100131897	Hs.721917	NM_001129891	ENSG00000204767	INSYN2B	C5orf57|FAM196B	inhibitory synaptic factor family member 2B	protein-coding	0.007143	0.487544	
chunk0100_118_1	chr2	108532983	108533447	+	0	NA	Intergenic	Intergenic	-1140	NM_001193483	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.015086	0.352688	
chunk0049_153_1	chr12	91948658	91948909	+	0	NA	Intergenic	Intergenic	192930	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.007968	0.432540	66(GATAACATCCTGTTCT,-,0.00),67(ATAACATCCTGTTCTG,+,0.00)
chunk0064_397_1	chr14	99350435	99350757	+	0	NA	Intergenic	Intergenic	-78883	NM_001282237	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.006211	0.544892	137(AAGAACAGTCTGTTCC,-,0.00),138(AGAACAGTCTGTTCCC,+,0.00)
chunk0207_456_1	chr9	137756125	137756566	+	0	NA	intron (NM_001145527, intron 8 of 15)	L1ME1|LINE|L1	-6677	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.022676	0.513575	
chunk0099_28_1	chr2	83369963	83370218	+	0	NA	Intergenic	LTR37B|LTR|ERV1	513287	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.003922	0.312500	
chunk0115_296_1	chr21	28323544	28323743	+	0	NA	Intergenic	L1MDa|LINE|L1	-94976	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.005025	0.265000	
chunk0082_13_1	chr17	50266752	50267019	+	0	NA	Intergenic	Intergenic	-4521	NM_001168215	162461	Hs.224630	NM_153229	ENSG00000167105	TMEM92	-	transmembrane protein 92	protein-coding	0.022472	0.641791	213(AGGACCACCCTGTCCC,-,0.00),214(GGACCACCCTGTCCCA,+,0.00)
chunk0097_127_1	chr2	46749064	46749269	+	0	NA	intron (NM_144949, intron 1 of 1)	intron (NM_144949, intron 1 of 1)	49956	NM_144949	9655	Hs.468426	NM_014011	ENSG00000171150	SOCS5	CIS6|CISH6|Cish5|SOCS-5	suppressor of cytokine signaling 5	protein-coding	0.004878	0.402913	
chunk0031_162_1	chr10	125289551	125290069	+	0	NA	Intergenic	L1PA15|LINE|L1	-128755	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.011583	0.352601	
chunk0002_148_1	chr1	17632511	17632942	+	0	NA	intron (NM_001011722, intron 14 of 26)	intron (NM_001011722, intron 14 of 26)	52173	NM_001011722	55160	Hs.443460	NM_018125	ENSG00000074964	ARHGEF10L	GrinchGEF	Rho guanine nucleotide exchange factor 10 like	protein-coding	0.023202	0.548611	
chunk0041_58_1	chr11	123314826	123315378	+	0	NA	Intergenic	Intergenic	66410	NR_039714	100616319		NR_039714	ENSG00000265357	MIR4493	-	microRNA 4493	ncRNA	0.023551	0.538879	247(AGGGACGAGCTGTGCC,-,0.00),310(GAGAACATTCAGTACC,-,0.00),311(AGAACATTCAGTACCC,+,0.00)
chunk0004_18_1	chr1	42176626	42177355	+	0	NA	3' UTR (NM_001198852, exon 12 of 12)	3' UTR (NM_001198852, exon 12 of 12)	-12266	NM_033553	2980	Hs.778	NM_033553	ENSG00000197273	GUCA2A	GCAP-I|GUCA2|STARA	guanylate cyclase activator 2A	protein-coding	0.009602	0.404110	364(CTGAACAGAGTGTCCC,-,0.00),365(TGAACAGAGTGTCCCC,+,0.00)
chunk0093_443_1	chr19	58395486	58395791	+	0	NA	promoter-TSS (NM_001195135)	promoter-TSS (NM_001195135)	-452	NM_001195135	646862	Hs.728121	NM_001195135	ENSG00000269855	RNF225	-	ring finger protein 225	protein-coding	0.022951	0.647059	
chunk0082_72_1	chr17	51486073	51486647	+	0	NA	Intergenic	LTR83|LTR|ERVL	149645	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.008711	0.403478	
chunk0119_420_1	chr22	49901438	49901803	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	16838	NM_024105	79087	Hs.526711	NM_024105	ENSG00000182858	ALG12	CDG1G|ECM39|PP14673|hALG12	ALG12 alpha-1,6-mannosyltransferase	protein-coding	0.027397	0.494536	
chunk0130_303_1	chr3	136979362	136979571	+	0	NA	intron (NM_144717, intron 1 of 6)	intron (NM_144717, intron 1 of 6)	21601	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.000000	0.485714	141(GAGTTCAGACTGTACC,-,0.00),142(AGTTCAGACTGTACCT,+,0.00)
chunk0079_123_1	chr17	12536587	12536972	+	0	NA	Intergenic	Intergenic	-13189	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.002597	0.341969	
chunk0120_350_1	chr3	11493465	11493766	+	0	NA	intron (NM_001136031, intron 17 of 17)	intron (NM_001136031, intron 17 of 17)	75309	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.003322	0.473510	
chunk0197_88_1	chr8	119218636	119219957	+	0	NA	intron (NM_052886, intron 1 of 3)	intron (NM_052886, intron 1 of 3)	10925	NM_052886	114569	Hs.201083	NM_052886	ENSG00000147676	MAL2	-	mal, T cell differentiation protein 2 (gene/pseudogene)	protein-coding	0.003028	0.371407	
chunk0156_72_1	chr5	103674192	103674937	+	0	NA	Intergenic	Intergenic	-111763	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.001342	0.386059	
chunk0174_158_1	chr6	158146103	158146302	+	0	NA	intron (NR_073096, intron 6 of 12)	intron (NR_073096, intron 6 of 12)	22078	NR_073096	84947	Hs.154706	NM_032861	ENSG00000122335	SERAC1	-	serine active site containing 1	protein-coding	0.005025	0.320000	
chunk0011_133_1	chr1	147177564	147178032	+	0	NA	promoter-TSS (NR_002305)	promoter-TSS (NR_002305)	-53	NR_002305	171423	Hs.658566	NR_002305		PDIA3P1	ERp60|GRP58P|PDIA3P	protein disulfide isomerase family A member 3 pseudogene 1	pseudo	0.004274	0.362473	
chunk0079_285_1	chr17	16568672	16569377	+	0	NA	5' UTR (NM_020653, exon 1 of 6)	5' UTR (NM_020653, exon 1 of 6)	182	NM_020653	57336	Hs.99724	NM_020653	ENSG00000141040	ZNF287	ZKSCAN13|ZSCAN45	zinc finger protein 287	protein-coding	0.102128	0.695467	424(AAGCACAGAGTGTCCC,-,0.00),425(AGCACAGAGTGTCCCG,+,0.00)
chunk0178_238_1	chr7	36110412	36110769	+	0	NA	Intergenic	Intergenic	15280	NR_108089	101928618	Hs.561704	NR_108089	ENSG00000261184	LOC101928618	-	uncharacterized LOC101928618	ncRNA	0.011204	0.460894	
chunk0030_265_1	chr10	116284518	116284798	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-11044	NM_005264	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.007143	0.466192	
chunk0149_292_1	chr5	25447992	25448872	+	0	NA	Intergenic	Intergenic	-607849	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.013636	0.440409	132(TGGAACAGCATGTATT,-,0.00),133(GGAACAGCATGTATTT,+,0.00),733(GGGCACAGGCTGCTCC,-,0.00),734(GGCACAGGCTGCTCCT,+,0.00)
chunk0028_59_1	chr10	83248224	83248553	+	0	NA	Intergenic	Intergenic	-891041	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.427273	172(AGGCACATGCTGTTCC,-,0.00),173(GGCACATGCTGTTCCT,+,0.00)
chunk0001_305_1	chr1	9150029	9150228	+	0	NA	non-coding (NR_132742, exon 2 of 2)	non-coding (NR_132742, exon 2 of 2)	1649	NR_029610	407040		NR_029610	ENSG00000284357	MIR34A	MIRN34A|miRNA34A|mir-34|mir-34a	microRNA 34a	ncRNA	0.020101	0.555000	
chunk0033_70_1	chr11	13683690	13684223	+	0	NA	intron (NM_032228, intron 1 of 11)	intron (NM_032228, intron 1 of 11)	15297	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.005629	0.342697	
chunk0194_164_1	chr8	84846454	84847130	+	0	NA	intron (NM_001100393, intron 4 of 8)	L1P4d|LINE|L1	140865	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002959	0.354505	
chunk0055_32_1	chr13	51995587	51996144	+	0	NA	intron (NM_001005918, intron 1 of 16)	intron (NM_001005918, intron 1 of 16)	15629	NM_000053	540	Hs.492280	NM_000053	ENSG00000123191	ATP7B	PWD|WC1|WD|WND	ATPase copper transporting beta	protein-coding	0.005386	0.498208	
chunk0066_287_1	chr15	35325430	35325976	+	0	NA	Intergenic	L1M5|LINE|L1	46661	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.005495	0.325411	
chunk0099_306_1	chr2	99160630	99161083	+	0	NA	intron (NM_145198, intron 3 of 3)	L1ME4a|LINE|L1	5782	NM_001204830	51601	Hs.719172	NM_015929	ENSG00000144182	LIPT1	LIPT1D	lipoyltransferase 1	protein-coding	0.011038	0.385463	
chunk0173_82_1	chr6	142778102	142778559	+	0	NA	intron (NM_006734, intron 3 of 9)	intron (NM_006734, intron 3 of 9)	-140441	NR_027312	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.002188	0.312227	
chunk0041_154_1	chr11	125872250	125872469	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-11255	NM_145014	219844	Hs.98133	NM_145014	ENSG00000198331	HYLS1	HLS	HYLS1 centriolar and ciliogenesis associated	protein-coding	0.000000	0.454545	
chunk0058_462_1	chr13	114259477	114259676	+	0	NA	intron (NM_001078645, intron 14 of 17)	intron (NM_001078645, intron 14 of 17)	-14252	NR_039724	100616227		NR_039724	ENSG00000265450	MIR4502	-	microRNA 4502	ncRNA	0.020101	0.390000	
chunk0152_385_1	chr5	64595122	64595321	+	0	NA	intron (NM_001271891, intron 2 of 3)	intron (NM_001271891, intron 2 of 3)	19571	NR_073511	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.005025	0.450000	
chunk0026_272_1	chr10	67085367	67085589	+	0	NA	intron (NR_111909, intron 2 of 2)	intron (NR_111909, intron 2 of 2)	73212	NR_111909	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.004505	0.322870	
chunk0003_432_1	chr1	41109711	41110007	+	0	NA	intron (NM_001172222, intron 2 of 8)	intron (NM_001172222, intron 2 of 8)	50074	NM_001172222	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.003378	0.430976	
chunk0202_263_1	chr9	77003401	77003825	+	0	NA	Intergenic	Intergenic	-16042	NM_001013735	442425	Hs.553843	NM_001013735	ENSG00000204612	FOXB2	bA159H20.4	forkhead box B2	protein-coding	0.009434	0.432941	
chunk0071_124_1	chr15	81491357	81491816	+	0	NA	Intergenic	Intergenic	-117509	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.006536	0.415217	
chunk0143_85_1	chr4	108264609	108265231	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	92800	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.009646	0.386838	
chunk0103_99_1	chr2	161278633	161279015	+	0	NA	Intergenic	L1MB8|LINE|L1	-24181	NR_110593	101929512	Hs.666488	NR_110593		LOC101929512	-	uncharacterized LOC101929512	ncRNA	0.013089	0.438642	
chunk0048_142_1	chr12	80081206	80081720	+	0	NA	Intergenic	L1PA7|LINE|L1	-127990	NM_173591	283310	Hs.723594	NM_173591	ENSG00000165899	OTOGL	C12orf64|DFNB84B	otogelin like	protein-coding	0.005837	0.357282	270(GGTACATTGTGTCTTT,+,0.00)
chunk0127_109_1	chr3	90100002	90100394	+	0	NA	Intergenic	Intergenic	992674	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005102	0.330789	
chunk0019_134_1	chr1	225657470	225658331	+	0	NA	Intergenic	Intergenic	-4757	NM_018212	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.010453	0.417633	
chunk0206_435_1	chr9	127837318	127837978	+	0	NA	intron (NM_001114753, intron 2 of 14)	intron (NM_001114753, intron 2 of 14)	9519	NM_001278138	2022	Hs.76753	NM_000118	ENSG00000106991	ENG	END|HHT1|ORW1	endoglin	protein-coding	0.007576	0.517398	
chunk0030_347_1	chr10	118481851	118482313	+	0	NA	Intergenic	Intergenic	113566	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.015152	0.356371	
chunk0132_317_1	chr3	160796675	160797308	+	0	NA	intron (NM_139245, intron 1 of 3)	L2a|LINE|L2	40783	NM_139245	151742	Hs.389027	NM_139245	ENSG00000163590	PPM1L	PP2C-epsilon|PP2CE|PPM1-LIKE	protein phosphatase, Mg2+/Mn2+ dependent 1L	protein-coding	0.003160	0.381703	332(AGGTACACCTTGTTTT,-,0.00)
chunk0074_330_1	chr16	31094633	31094844	+	0	NA	5' UTR (NM_001311311, exon 1 of 4)	5' UTR (NM_001311311, exon 1 of 4)	261	NM_001311311	79001	Hs.324844	NM_024006	ENSG00000167397	VKORC1	EDTP308|MST134|MST576|VKCFD2|VKOR	vitamin K epoxide reductase complex subunit 1	protein-coding	0.113744	0.716981	
chunk0160_60_1	chr5	149742371	149742781	+	0	NA	intron (NM_133263, intron 1 of 11)	intron (NM_133263, intron 1 of 11)	9751	NR_029870	494327		NR_029870	ENSG00000199047	MIR378A	MIR378|MIRN378|hsa-mir-378|hsa-mir-378a|miRNA378	microRNA 378a	ncRNA	0.004878	0.457421	
chunk0026_334_1	chr10	68400194	68400421	+	0	NA	intron (NR_103475, intron 3 of 18)	AluSz6|SINE|Alu	6882	NM_017987	55680	Hs.653144	NM_017987	ENSG00000204130	RUFY2	RABIP4R|ZFYVE13	RUN and FYVE domain containing 2	protein-coding	0.022026	0.456140	
chunk0194_414_1	chr8	91667099	91667638	+	0	NA	Intergenic	L2b|LINE|L2	350312	NM_175636	862	Hs.368431	NM_004349	ENSG00000079102	RUNX1T1	AML1-MTG8|AML1T1|CBFA2T1|CDR|ETO|MTG8|ZMYND2	RUNX1 partner transcriptional co-repressor 1	protein-coding	0.005566	0.394444	256(AGGATCACTCTGTCCA,-,0.00),257(GGATCACTCTGTCCAT,+,0.00)
chunk0087_245_1	chr18	36764110	36764587	+	0	NA	intron (NM_001281739, intron 22 of 23)	intron (NM_001281739, intron 22 of 23)	-64769	NM_020776	57536	Hs.4045	NM_020776	ENSG00000150477	KIAA1328	-	KIAA1328	protein-coding	0.002096	0.479079	
chunk0175_95_1	chr7	2804076	2804654	+	0	NA	intron (NM_001293092, intron 1 of 2)	intron (NM_001293092, intron 1 of 2)	10894	NM_001282441	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.013841	0.411054	
chunk0034_208_1	chr11	32443303	32443898	+	0	NA	intron (NR_120548, intron 1 of 4)	intron (NR_120548, intron 1 of 4)	7561	NR_120546	51352	Hs.567499	NM_015855	ENSG00000183242	WT1-AS	WIT-1|WIT1|WT1-AS1|WT1AS	WT1 antisense RNA	ncRNA	0.005042	0.338926	
chunk0058_112_1	chr14	21992997	21993405	+	0	NA	Intergenic	L2b|LINE|L2	328118	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.017157	0.410758	
chunk0099_313_1	chr2	99429930	99430478	+	0	NA	intron (NM_016316, intron 8 of 22)	intron (NM_016316, intron 8 of 22)	59814	NM_001037872	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.007299	0.302368	
chunk0189_386_1	chr8	27413698	27414323	+	0	NA	intron (NM_004103, intron 3 of 31)	L1MC4|LINE|L1	-19360	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.006400	0.405751	413(AGGCACATCTTGTACT,-,0.00),414(GGCACATCTTGTACTT,+,0.00)
chunk0108_127_1	chr2	229849153	229849386	+	0	NA	intron (NM_004238, intron 3 of 40)	HAL1|LINE|L1	30859	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.012876	0.371795	
chunk0134_312_1	chr3	180992461	180992969	+	0	NA	Intergenic	LTR33|LTR|ERVL	-2941	NM_145261	131118	Hs.230601	NM_145261	ENSG00000205981	DNAJC19	PAM18|TIM14|TIMM14	DnaJ heat shock protein family (Hsp40) member C19	protein-coding	0.007874	0.444008	219(TGGAACATTTTGTGCC,-,0.00),220(GGAACATTTTGTGCCA,+,0.00)
chunk0137_60_1	chr4	11791352	11792304	+	0	NA	Intergenic	MSTA1|LTR|ERVL-MaLR	-362915	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.005252	0.388248	
chunk0196_305_1	chr8	109784705	109785189	+	0	NA	Intergenic	L1PA10|LINE|L1	-93156	NM_001099744	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.008264	0.364948	214(ATGAACTGACAGTTCT,-,0.00),215(TGAACTGACAGTTCTC,+,0.00)
chunk0066_90_1	chr15	29734981	29735308	+	0	NA	intron (NM_175610, intron 11 of 26)	intron (NM_175610, intron 11 of 26)	86404	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.003058	0.332317	
chunk0204_180_1	chr9	96100614	96101014	+	0	NA	intron (NR_033838, intron 7 of 8)	intron (NR_033838, intron 7 of 8)	15597	NR_132344	158434	Hs.381771	NM_001256408	ENSG00000275465	LOC158434	-	uncharacterized LOC158434	ncRNA	0.010000	0.448878	197(GGGAACAGGAAGTGCC,-,0.00),198(GGAACAGGAAGTGCCT,+,0.00)
chunk0158_129_1	chr5	127185155	127185404	+	0	NA	Intergenic	Intergenic	-105485	NM_001308119	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.012048	0.496000	
chunk0019_57_1	chr1	224182916	224183213	+	0	NA	promoter-TSS (NM_003676)	promoter-TSS (NM_003676)	-144	NM_003676	8560	Hs.299878	NM_003676	ENSG00000143753	DEGS1	DEGS|DEGS-1|DES1|Des-1|FADS7|HLD18|MIG15|MLD	delta 4-desaturase, sphingolipid 1	protein-coding	0.107744	0.714765	
chunk0007_221_1	chr1	81727837	81728518	+	0	NA	intron (NM_001297704, intron 1 of 20)	intron (NM_001297704, intron 1 of 20)	28407	NM_001297704	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.001468	0.321114	
chunk0129_342_1	chr3	124814711	124814987	+	0	NA	intron (NM_002213, intron 8 of 14)	intron (NM_002213, intron 8 of 14)	72456	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.018116	0.487365	
chunk0117_58_1	chr22	16311831	16312030	+	0	NA	Intergenic	Intergenic	280880	NM_014406	150160	Hs.128342	NM_014406	ENSG00000198445	CCT8L2	CESK1	chaperonin containing TCP1 subunit 8 like 2	protein-coding	0.040201	0.325000	
chunk0113_212_1	chr20	53805310	53805563	+	0	NA	Intergenic	Intergenic	70273	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.000000	0.507874	
chunk0069_391_1	chr15	67717143	67717440	+	0	NA	intron (NM_002757, intron 16 of 20)	intron (NM_002757, intron 16 of 20)	-102413	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.000000	0.355705	
chunk0085_62_1	chr18	1099779	1099978	+	0	NA	Intergenic	L2b|LINE|L2	194682	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.015075	0.505000	
chunk0116_142_1	chr21	36332501	36332700	+	0	NA	intron (NM_015358, intron 1 of 16)	MER57C2|LTR|ERV1	12411	NM_015358	23515	Hs.421150	NM_015358	ENSG00000159256	MORC3	NXP2|ZCW5|ZCWCC3	MORC family CW-type zinc finger 3	protein-coding	0.005025	0.370000	
chunk0081_358_1	chr17	47686898	47687512	+	0	NA	Intergenic	Intergenic	-8059	NM_014726	9755	Hs.94790	NM_014726	ENSG00000198933	TBKBP1	ProSAPiP2|SINTBAD	TBK1 binding protein 1	protein-coding	0.008143	0.403252	
chunk0112_459_1	chr20	49026812	49027026	+	0	NA	intron (NM_006420, intron 36 of 38)	intron (NM_006420, intron 36 of 38)	19137	NR_110624	102723483	Hs.209000	NR_110624	ENSG00000227431	CSE1L-AS1	-	CSE1L antisense RNA 1	ncRNA	0.004673	0.376744	
chunk0067_265_1	chr15	45862928	45863304	+	0	NA	Intergenic	MIRc|SINE|MIR	228376	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.010638	0.352785	
chunk0065_35_1	chr15	20732460	20732994	+	0	NA	intron (NR_027992, intron 1 of 2)	L1MEc|LINE|L1	23424	NR_027992	606	Hs.657985	NR_027992		NBEAP1	BCL8|BCL8A	neurobeachin pseudogene 1	pseudo	0.007491	0.315888	
chunk0112_204_1	chr20	40455911	40456258	+	0	NA	Intergenic	L1ME3C|LINE|L1	233156	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.002882	0.359195	
chunk0087_376_1	chr18	41524632	41525432	+	0	NA	Intergenic	Intergenic	-4435	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.001250	0.368290	
chunk0040_385_1	chr11	119608506	119608753	+	0	NA	Intergenic	Intergenic	120096	NM_203286	5818	Hs.334846	NM_002855	ENSG00000110400	NECTIN1	CD111|CLPED1|ED4|HIgR|HV1S|HVEC|OFC7|PRR|PRR1|PVRL1|PVRR|PVRR1|SK-12|nectin-1	nectin cell adhesion molecule 1	protein-coding	0.012146	0.395161	
chunk0087_367_1	chr18	41483627	41484117	+	0	NA	intron (NR_002838, intron 3 of 5)	intron (NR_002838, intron 3 of 5)	36725	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.008163	0.456212	203(CAGAACGTTCTGTTCT,-,0.00),204(AGAACGTTCTGTTCTA,+,0.00)
chunk0077_317_1	chr16	82138399	82138846	+	0	NA	Intergenic	MER89|LTR|ERV1	31602	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.015660	0.437500	
chunk0210_5_1	chrX	66798122	66798403	+	0	NA	Intergenic	MIRc|SINE|MIR	-158964	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.000000	0.404255	
chunk0081_424_1	chr17	48790966	48791199	+	0	NA	intron (NM_001130918, intron 9 of 15)	intron (NM_001130918, intron 9 of 15)	3242	NM_173623	284076	Hs.91930	NM_173623	ENSG00000170703	TTLL6	TTL.6	tubulin tyrosine ligase like 6	protein-coding	0.025751	0.491453	
chunk0208_369_1	chrX	26672637	26673011	+	0	NA	Intergenic	L1MA4|LINE|L1	114487	NR_001559	139538	Hs.447377	NR_001559	ENSG00000259849	VENTXP1	CT18|NA88A|VENTX2P1	VENT homeobox pseudogene 1	pseudo	0.013369	0.322667	
chunk0145_92_1	chr4	145945543	145946165	+	0	NA	Intergenic	Intergenic	-6894	NM_001306215	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.003215	0.423756	
chunk0176_30_1	chr7	9339146	9339594	+	0	NA	Intergenic	L1ME2|LINE|L1	-294900	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.002232	0.302895	
chunk0174_396_1	chr6	165468298	165468965	+	0	NA	intron (NM_006661, intron 4 of 22)	L2c|LINE|L2	59030	NR_106988									0.010495	0.384731	
chunk0167_303_1	chr6	71393605	71394326	+	0	NA	Intergenic	Intergenic	9656	NR_029504	407029		NR_029504	ENSG00000207827	MIR30A	MIRN30A|mir-30a	microRNA 30a	ncRNA	0.001387	0.385042	
chunk0138_300_1	chr4	41129477	41129747	+	0	NA	intron (NM_004307, intron 2 of 17)	intron (NM_004307, intron 2 of 17)	85006	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.003704	0.413284	
chunk0054_100_1	chr13	42747354	42748038	+	0	NA	Intergenic	Intergenic	-33854	NM_182508	144809	Hs.16970	NM_182508	ENSG00000179813	FAM216B	C13orf30	family with sequence similarity 216 member B	protein-coding	0.005848	0.462774	
chunk0189_20_1	chr8	19622023	19622629	+	0	NA	intron (NR_024040, intron 1 of 9)	intron (NR_024040, intron 1 of 9)	-19781	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.004950	0.316310	
chunk0032_275_1	chr11	9103437	9103972	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	9341	NR_027713	283102	Hs.689472	NR_027713	ENSG00000213538	KRT8P41	-	keratin 8 pseudogene 41	pseudo	0.007477	0.460821	
chunk0072_43_1	chr16	1159852	1160187	+	0	NA	intron (NM_021098, intron 2 of 34)	intron (NM_021098, intron 2 of 34)	6778	NM_001005407	8912	Hs.459642	NM_021098	ENSG00000196557	CACNA1H	CACNA1HB|Cav3.2|ECA6|EIG6|HALD4	calcium voltage-gated channel subunit alpha1 H	protein-coding	0.065672	0.672619	
chunk0031_412_1	chr10	132084593	132084813	+	0	NA	Intergenic	L1PB1|LINE|L1	-20106	NM_001105521	282973	Hs.106254	NM_194303	ENSG00000188385	JAKMIP3	C10orf14|C10orf39|Jamip3|NECC2|bA140A10.5	Janus kinase and microtubule interacting protein 3	protein-coding	0.000000	0.398190	
chunk0021_95_1	chr10	2890893	2891182	+	0	NA	Intergenic	Intergenic	-176483	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.024221	0.489655	
chunk0170_392_1	chr6	117309121	117309374	+	0	NA	intron (NM_002944, intron 40 of 42)	(CACATG)n|Simple_repeat|Simple_repeat	43689	NM_153453	245806	Hs.99324	NM_153453	ENSG00000170162	VGLL2	VGL2|VITO1	vestigial like family member 2	protein-coding	0.007905	0.448819	
chunk0105_160_1	chr2	186757725	186758191	+	0	NA	intron (NM_177454, intron 6 of 7)	intron (NM_177454, intron 6 of 7)	63896	NM_177454	165215	Hs.28872	NM_177454	ENSG00000144369	FAM171B	KIAA1946	family with sequence similarity 171 member B	protein-coding	0.008584	0.376874	
chunk0166_75_1	chr6	43145806	43146575	+	0	NA	intron (NR_072997, intron 15 of 18)	intron (NR_072997, intron 15 of 18)	-25105	NM_003131	6722	Hs.520140	NM_003131	ENSG00000112658	SRF	MCM1	serum response factor	protein-coding	0.011704	0.519481	
chunk0131_429_1	chr3	153664165	153664481	+	0	NA	Intergenic	Intergenic	179828	NM_001101337									0.003165	0.397476	168(ATGTACACCCTGTCCC,-,0.00),169(TGTACACCCTGTCCCT,+,0.00)
chunk0123_162_1	chr3	43545909	43546406	+	0	NA	intron (NM_018075, intron 11 of 12)	intron (NM_018075, intron 11 of 12)	75911	NM_001204833	55129	Hs.656657	NM_018075	ENSG00000160746	ANO10	SCAR10|TMEM16K	anoctamin 10	protein-coding	0.002012	0.333333	
chunk0055_115_1	chr13	57325979	57326572	+	0	NA	Intergenic	Charlie4z|DNA|hAT-Charlie	159078	NM_001130405	729240	Hs.525056	NM_001130405	ENSG00000229665	PRR20C	PRR20|PRR20A|PRR20B|PRR20D|PRR20E	proline rich 20C	protein-coding	0.000000	0.306397	
chunk0075_70_1	chr16	48034819	48035564	+	0	NA	Intergenic	Intergenic	111579	NM_033226	94160	Hs.410111	NM_033226	ENSG00000140798	ABCC12	MRP9	ATP binding cassette subfamily C member 12	protein-coding	0.012081	0.407507	
chunk0163_186_1	chr6	11515877	11516086	+	0	NA	Intergenic	Intergenic	-22246	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.009569	0.423810	
chunk0015_230_1	chr1	187759806	187760507	+	0	NA	Intergenic	Intergenic	316528	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001427	0.384615	
chunk0062_392_1	chr14	74793863	74794117	+	0	NA	intron (NM_019589, intron 4 of 20)	intron (NM_019589, intron 4 of 20)	30624	NM_019589	56252	Hs.531111	NM_019589	ENSG00000119596	YLPM1	C14orf170|PPP1R169|ZAP113|ZAP3	YLP motif containing 1	protein-coding	0.000000	0.411765	
chunk0122_341_1	chr3	37245070	37245356	+	0	NA	intron (NM_002078, intron 1 of 23)	MIR|SINE|MIR	2022	NM_001172713	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.010490	0.327526	
chunk0200_273_1	chr9	22098251	22099387	+	0	NA	intron (NR_047532, intron 9 of 13)	MIRb|SINE|MIR	-89506	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.003521	0.367634	320(TAGCACAGGATGTTCC,-,0.00),321(AGCACAGGATGTTCCA,+,0.00),909(GGGAACAACATGTACA,-,0.00),910(GGAACAACATGTACAA,+,0.00)
chunk0211_204_1	chrX	118073970	118074334	+	0	NA	intron (NM_001168301, intron 1 of 7)	intron (NM_001168301, intron 1 of 7)	42713	NM_001168302	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.000000	0.356164	207(AAGAACACTATGACCT,-,0.00),208(AGAACACTATGACCTT,+,0.00)
chunk0181_130_1	chr7	80942465	80943021	+	0	NA	Intergenic	Intergenic	-23392	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.001799	0.353680	
chunk0143_23_1	chr4	105990851	105991356	+	0	NA	Intergenic	Intergenic	31375	NR_125928	101929577	Hs.631131	NR_125928	ENSG00000249635	LOC101929577	-	uncharacterized LOC101929577	ncRNA	0.011881	0.519763	
chunk0092_435_1	chr19	38298654	38299552	+	0	NA	Intergenic	Intergenic	-5061	NM_033520	64073	Hs.631544	NM_022125	ENSG00000167644	C19orf33	H2RSP|IMUP|IMUP-1|IMUP-2	chromosome 19 open reading frame 33	protein-coding	0.017817	0.519466	
chunk0160_43_1	chr5	149514786	149515423	+	0	NA	intron (NM_001271741, intron 4 of 9)	intron (NM_001271741, intron 4 of 9)	35227	NM_001271742	1452	Hs.529862	NM_001892	ENSG00000113712	CSNK1A1	CK1|CK1a|CKIa|HEL-S-77p|HLCDGP1|PRO2975	casein kinase 1 alpha 1	protein-coding	0.004710	0.319749	
chunk0050_291_1	chr12	106702649	106702908	+	0	NA	intron (NM_032491, intron 4 of 13)	L1MEf|LINE|L1	-18078	NR_038912	100505978	Hs.662583	NR_038912	ENSG00000257711	LOC100505978	-	uncharacterized LOC100505978	ncRNA	0.003861	0.461538	
chunk0032_346_1	chr11	10323007	10323206	+	0	NA	intron (NR_103765, intron 1 of 3)	intron (NR_103765, intron 1 of 3)	14793	NR_103765	100130460	Hs.501890	NR_103765		CAND1.11	-	uncharacterized LOC100130460	ncRNA	0.020101	0.425000	
chunk0089_423_1	chr18	69780479	69780745	+	0	NA	intron (NM_152721, intron 7 of 7)	AluSz|SINE|Alu	167241	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.011278	0.397004	
chunk0035_187_1	chr11	44157799	44158058	+	0	NA	intron (NM_001178083, intron 8 of 14)	L1MA3|LINE|L1	61731	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.000000	0.546154	
chunk0184_324_1	chr7	120418593	120418973	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	145115	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.005263	0.396325	
chunk0130_316_1	chr3	137373935	137374336	+	0	NA	Intergenic	L1PA7|LINE|L1	-390157	NM_004189	8403	Hs.248184	NM_004189	ENSG00000168875	SOX14	SOX28	SRY-box transcription factor 14	protein-coding	0.000000	0.333333	
chunk0083_319_1	chr17	69555076	69555813	+	0	NA	Intergenic	Intergenic	-38543	NR_109971	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.002714	0.390244	451(AGACCTGAGTGTTCCT,+,0.00)
chunk0151_46_1	chr5	42273869	42274099	+	0	NA	Intergenic	Intergenic	-98639	NR_104636	101926960	Hs.365692	NR_104635		LOC101926960	-	uncharacterized LOC101926960	ncRNA	0.008696	0.389610	36(AGGTTCAGCATGTTCC,-,0.00),37(GGTTCAGCATGTTCCA,+,0.00)
chunk0164_298_1	chr6	24810404	24810726	+	0	NA	intron (NM_014722, intron 21 of 22)	L2a|LINE|L2	-11669	NM_001282492	101928603	Hs.635133	NM_001282492	ENSG00000260286	ARMH2	C6orf229	armadillo like helical domain containing 2	protein-coding	0.000000	0.352941	
chunk0105_286_1	chr2	189825141	189825376	+	0	NA	intron (NR_110332, intron 6 of 12)	intron (NR_110332, intron 6 of 12)	-40887	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.000000	0.338983	
chunk0073_369_1	chr16	15468842	15469069	+	0	NA	intron (NM_033201, intron 1 of 5)	L1MD2|LINE|L1	-33311	NM_001142469	89927	Hs.401798	NM_033201	ENSG00000166780	BMERB1	C16orf45|MINP	bMERB domain containing 1	protein-coding	0.004405	0.390351	
chunk0067_69_1	chr15	41256205	41256930	+	0	NA	intron (NM_007236, intron 2 of 6)	intron (NM_007236, intron 2 of 6)	25328	NM_007236	11261	Hs.406234	NM_007236	ENSG00000187446	CHP1	CHP|SLC9A1BP|SPAX9|Sid470p|p22|p24	calcineurin like EF-hand protein 1	protein-coding	0.008276	0.389807	
chunk0096_334_1	chr2	35294481	35295228	+	0	NA	Intergenic	Intergenic	-176551	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.008032	0.359626	
chunk0163_260_1	chr6	13007025	13007512	+	0	NA	intron (NM_030948, intron 4 of 14)	L1ME3G|LINE|L1	288318	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.000000	0.309426	
chunk0036_432_1	chr11	68468043	68468755	+	0	NA	intron (NM_001164161, intron 1 of 23)	intron (NM_001164161, intron 1 of 23)	7681	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.008427	0.410940	
chunk0095_430_1	chr2	24996799	24997392	+	0	NA	intron (NR_034113, intron 1 of 2)	intron (NR_034113, intron 1 of 2)	24983	NR_034113	729723	Hs.436366	NR_034113	ENSG00000224165	DNAJC27-AS1	-	DNAJC27 antisense RNA 1	ncRNA	0.008432	0.429293	
chunk0057_132_1	chr13	99677241	99678221	+	0	NA	intron (NR_104592, intron 1 of 9)	intron (NR_104592, intron 1 of 9)	13240	NR_046526	100874063	Hs.577064	NR_046526	ENSG00000227659	CLYBL-AS2	-	CLYBL antisense RNA 2	ncRNA	0.013265	0.353721	
chunk0020_199_1	chr1	234960587	234961073	+	0	NA	intron (NR_125945, intron 1 of 3)	intron (NR_125945, intron 1 of 3)	3169	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.016461	0.443532	111(AAAGACTCCCTGTTCC,-,0.00),112(AAGACTCCCTGTTCCT,+,0.00)
chunk0145_168_1	chr4	147285719	147286147	+	0	NA	Intergenic	Intergenic	58784	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.009346	0.435897	
chunk0139_301_1	chr4	57606819	57607304	+	0	NA	Intergenic	L2c|LINE|L2	181189	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.010309	0.378601	181(TAGTACTCAGTGTCCT,-,0.00),182(AGTACTCAGTGTCCTT,+,0.00),320(AGGCAGAGACTGTTCT,-,0.00),321(GGCAGAGACTGTTCTT,+,0.00)
chunk0165_401_1	chr6	38857719	38858366	+	0	NA	intron (NM_001206927, intron 42 of 92)	intron (NM_001206927, intron 42 of 92)	95065	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.007728	0.370370	
chunk0007_353_1	chr1	84873023	84873775	+	0	NA	intron (NM_012152, intron 1 of 2)	intron (NM_012152, intron 1 of 2)	19814	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.009309	0.345286	295(AGGAACTCTCTGTACT,-,0.00),296(GGAACTCTCTGTACTA,+,0.00)
chunk0042_52_1	chr12	1774277	1774704	+	0	NA	intron (NM_024551, intron 3 of 7)	intron (NM_024551, intron 3 of 7)	-45777	NM_001163925	654429	Hs.585579	NM_001039029	ENSG00000166159	LRTM2	-	leucine rich repeats and transmembrane domains 2	protein-coding	0.004684	0.404206	
chunk0006_70_1	chr1	64864028	64864551	+	0	NA	intron (NM_002227, intron 8 of 24)	intron (NM_002227, intron 8 of 24)	102215	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.019120	0.494275	
chunk0052_110_1	chr13	22812760	22813272	+	0	NA	Intergenic	Intergenic	85165	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.005859	0.391813	
chunk0012_235_1	chr1	160631057	160631256	+	0	NA	intron (NR_104401, intron 3 of 5)	intron (NR_104401, intron 3 of 5)	16155	NR_104401	6504	Hs.523660	NM_003037	ENSG00000117090	SLAMF1	CD150|CDw150|SLAM	signaling lymphocytic activation molecule family member 1	protein-coding	0.015075	0.390000	
chunk0148_113_1	chr5	5119865	5120270	+	0	NA	Intergenic	L1PA14|LINE|L1	19987	NR_109915	101929176	Hs.208717	NR_109915		CTD-2297D10.2	-	uncharacterized LOC101929176	ncRNA	0.002469	0.544335	
chunk0078_337_1	chr17	8872006	8872516	+	0	NA	Intergenic	Intergenic	-4584	NM_001010855	146850	Hs.255809	NM_001010855	ENSG00000276231	PIK3R6	C17orf38|HsT41028|p84 PIKAP|p87(PIKAP)|p87PIKAP	phosphoinositide-3-kinase regulatory subunit 6	protein-coding	0.011765	0.473581	
chunk0081_78_1	chr17	39238537	39238895	+	0	NA	Intergenic	Intergenic	-12929	NM_198993	342667	Hs.145068	NM_198993	ENSG00000141750	STAC2	24b2|24b2/STAC2	SH3 and cysteine rich domain 2	protein-coding	0.027933	0.593315	
chunk0200_262_1	chr9	21856163	21856520	+	0	NA	intron (NM_002451, intron 6 of 7)	intron (NM_002451, intron 6 of 7)	53705	NM_002451	4507	Hs.193268	NM_002451	ENSG00000099810	MTAP	BDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fus	methylthioadenosine phosphorylase	protein-coding	0.008403	0.360335	
chunk0035_270_1	chr11	46547540	46548002	+	0	NA	intron (NM_001300731, intron 3 of 16)	intron (NM_001300731, intron 3 of 16)	43593	NM_017749	55626	Hs.654644	NM_017749	ENSG00000110497	AMBRA1	DCAF3|WDR94	autophagy and beclin 1 regulator 1	protein-coding	0.010823	0.399568	
chunk0029_306_1	chr10	104269287	104269492	+	0	NA	promoter-TSS (NR_039702)	promoter-TSS (NR_039702)	516	NM_001191013	119391	Hs.107384	NM_183239	ENSG00000065621	GSTO2	GSTO 2-2|bA127L20.1	glutathione S-transferase omega 2	protein-coding	0.024390	0.436893	
chunk0186_110_1	chr7	137979153	137979391	+	0	NA	intron (NM_194071, intron 1 of 11)	intron (NM_194071, intron 1 of 11)	22829	NM_194071	64764	Hs.490273	NM_194071	ENSG00000182158	CREB3L2	BBF2H7	cAMP responsive element binding protein 3 like 2	protein-coding	0.008403	0.456067	
chunk0014_19_1	chr1	174475178	174475834	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	27432	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.003049	0.377473	
chunk0102_165_1	chr2	147403130	147403416	+	0	NA	Intergenic	L1PA16|LINE|L1	-441244	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.404181	24(CAGTACTTATTGTCCC,-,0.00),25(AGTACTTATTGTCCCT,+,0.00)
chunk0124_164_1	chr3	55082709	55082908	+	0	NA	Intergenic	Intergenic	-115720	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.010050	0.355000	
chunk0195_124_1	chr8	94943535	94943985	+	0	NA	intron (NM_001135733, intron 1 of 4)	intron (NM_001135733, intron 1 of 4)	5627	NM_033285	94241	Hs.492261	NM_033285	ENSG00000164938	TP53INP1	SIP|TP53DINP1|TP53INP1A|TP53INP1B|Teap|p53DINP1	tumor protein p53 inducible nuclear protein 1	protein-coding	0.002222	0.383592	
chunk0127_27_1	chr3	88575673	88576051	+	0	NA	Intergenic	L2a|LINE|L2	-425996	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.007937	0.356201	280(GAGAACAGTAAGTTCC,-,0.00),281(AGAACAGTAAGTTCCA,+,0.00)
chunk0054_36_1	chr13	41035177	41035376	+	0	NA	Intergenic	Intergenic	-15904	NM_172373	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.010050	0.365000	
chunk0068_390_1	chr15	58611726	58612399	+	0	NA	intron (NM_001110, intron 11 of 15)	intron (NM_001110, intron 11 of 15)	81545	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.005944	0.400593	
chunk0037_393_1	chr11	79088675	79088930	+	0	NA	intron (NM_001098816, intron 4 of 33)	L2b|LINE|L2	313307	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.011765	0.453125	
chunk0138_16_1	chr4	30612529	30612731	+	0	NA	Intergenic	Intergenic	-107778	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.004950	0.428571	
chunk0160_184_1	chr5	154164228	154164544	+	0	NA	Intergenic	Intergenic	-26349	NM_198321	55568	Hs.631797	NM_017540	ENSG00000164574	GALNT10	GALNACT10|PPGALNACT10|PPGANTASE10	polypeptide N-acetylgalactosaminyltransferase 10	protein-coding	0.003165	0.406940	
chunk0153_9_1	chr5	66757159	66757580	+	0	NA	intron (NM_198828, intron 1 of 5)	intron (NM_198828, intron 1 of 5)	-71407	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.002375	0.317536	228(TGGAACATTTTGTTCA,-,0.00),229(GGAACATTTTGTTCAA,+,0.00)
chunk0069_119_1	chr15	61742699	61742931	+	0	NA	Intergenic	Intergenic	317650	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.000000	0.454936	
chunk0151_325_1	chr5	53725913	53726606	+	0	NA	Intergenic	Intergenic	165624	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.005772	0.365994	
chunk0178_299_1	chr7	37713754	37714213	+	0	NA	Intergenic	MIRb|SINE|MIR	-26411	NM_181791	353345	Hs.563492	NM_181791	ENSG00000187037	GPR141	PGR13	G protein-coupled receptor 141	protein-coding	0.008715	0.350000	
chunk0204_266_1	chr9	98211137	98211756	+	0	NA	intron (NR_051978, intron 6 of 11)	L2b|LINE|L2	2105	NM_001267572	55357	Hs.371016	NM_018421	ENSG00000095383	TBC1D2	PARIS-1|PARIS1|TBC1D2A	TBC1 domain family member 2	protein-coding	0.009693	0.541935	
chunk0204_277_1	chr9	98605022	98605271	+	0	NA	intron (NM_005458, intron 1 of 18)	intron (NM_005458, intron 1 of 18)	104051	NM_005458	9568	Hs.198612	NM_005458	ENSG00000136928	GABBR2	EIEE59|GABABR2|GPR51|GPRC3B|HG20|HRIHFB2099|NDPLHS	gamma-aminobutyric acid type B receptor subunit 2	protein-coding	0.012048	0.576000	
chunk0127_88_1	chr3	89710582	89710812	+	0	NA	Intergenic	Intergenic	603173	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.008696	0.311688	
chunk0072_184_1	chr15	94206454	94206917	+	0	NA	Intergenic	Intergenic	-91516	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.010799	0.431034	
chunk0133_314_1	chr3	172370378	172370767	+	0	NA	intron (NM_022763, intron 23 of 25)	intron (NM_022763, intron 23 of 25)	77884	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.007712	0.384615	
chunk0192_404_1	chr8	69009300	69009876	+	0	NA	intron (NR_039986, intron 2 of 4)	L1M5|LINE|L1	94602	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.000000	0.259965	
chunk0079_149_1	chr17	13182598	13182809	+	0	NA	Intergenic	Intergenic	-164639	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.000000	0.518868	
chunk0045_289_1	chr12	50202328	50202595	+	0	NA	promoter-TSS (NM_001243775)	promoter-TSS (NM_001243775)	-928	NM_001243775	51474	Hs.525419	NM_016357	ENSG00000050405	LIMA1	EPLIN|LDLCQ8|SREBP3	LIM domain and actin binding 1	protein-coding	0.011236	0.429104	
chunk0038_226_1	chr11	86976785	86977021	+	0	NA	intron (NR_038905, intron 2 of 2)	MER91A|DNA|hAT-Tip100	21282	NR_038905	100506368	Hs.559920	NR_038905	ENSG00000246523	FZD4-DT	-	FZD4 divergent transcript	ncRNA	0.004237	0.430380	165(CTGTACATGATGTCCT,-,0.00),166(TGTACATGATGTCCTT,+,0.00)
chunk0055_178_1	chr13	61142596	61142842	+	0	NA	Intergenic	Intergenic	57161	NR_036128	100422973		NR_036128	ENSG00000266663	MIR3169	-	microRNA 3169	ncRNA	0.000000	0.425101	
chunk0106_95_1	chr2	197191526	197192054	+	0	NA	intron (NM_001195144, intron 1 of 27)	intron (NM_001195144, intron 1 of 27)	110729	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.001894	0.338374	
chunk0027_127_1	chr10	74242255	74242613	+	0	NA	intron (NM_001123, intron 3 of 10)	L2a|LINE|L2	65945	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.002793	0.364903	136(TGTACACTCAGTGCCT,+,0.00)
chunk0093_429_1	chr19	57957595	57957794	+	0	NA	TTS (NM_152474)	TTS (NM_152474)	-9985	NM_005773	10172	Hs.596242	NM_005773	ENSG00000152454	ZNF256	BMZF-3|BMZF3	zinc finger protein 256	protein-coding	0.030151	0.495000	
chunk0029_28_1	chr10	95818554	95819129	+	0	NA	intron (NM_001312654, intron 2 of 9)	intron (NM_001312654, intron 2 of 9)	62925	NM_001164182	953	Hs.576612	NM_001776	ENSG00000138185	ENTPD1	ATPDase|CD39|NTPDase-1|SPG64	ectonucleoside triphosphate diphosphohydrolase 1	protein-coding	0.003478	0.411458	
chunk0146_89_1	chr4	158120754	158121160	+	0	NA	Intergenic	Intergenic	51609	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.009852	0.405405	
chunk0090_311_1	chr18	75398813	75399266	+	0	NA	Intergenic	Intergenic	28664	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.004415	0.438326	
chunk0172_393_1	chr6	139677088	139677305	+	0	NA	Intergenic	L1MC3|LINE|L1	-93877	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.004608	0.316514	
chunk0022_435_1	chr10	19416520	19416888	+	0	NA	intron (NM_001142308, intron 28 of 39)	L2|LINE|L2	311846	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.000000	0.371274	
chunk0004_434_1	chr1	52940171	52940707	+	0	NA	TTS (NR_039972)	TTS (NR_039972)	125	NR_039972									0.007463	0.448790	
chunk0035_369_1	chr11	49208092	49208419	+	0	NA	intron (NM_001193471, intron 1 of 19)	CpG	415	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.100917	0.673780	
chunk0167_248_1	chr6	67896114	67896443	+	0	NA	Intergenic	Intergenic	-159073	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.003040	0.333333	
chunk0131_443_1	chr3	153961221	153961564	+	0	NA	Intergenic	Intergenic	-159611	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.008746	0.369186	
chunk0202_334_1	chr9	78566717	78567604	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	270085	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.006764	0.441441	
chunk0109_333_1	chr20	9344203	9344931	+	0	NA	intron (NM_001172646, intron 6 of 37)	intron (NM_001172646, intron 6 of 37)	36767	NM_000933	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.013736	0.415638	263(TAGAACTGTCAGTGCC,-,0.00),264(AGAACTGTCAGTGCCC,+,0.00),607(TGGATCATTATGTCCT,-,0.00),608(GGATCATTATGTCCTG,+,0.00)
chunk0058_107_1	chr14	21792202	21792532	+	0	NA	Intergenic	Intergenic	127284	NM_001001912	26686	Hs.547982	NM_001001912	ENSG00000221977	OR4E2	OR14-42	olfactory receptor family 4 subfamily E member 2	protein-coding	0.003030	0.377644	
chunk0134_307_1	chr3	180845656	180845855	+	0	NA	intron (NR_109986, intron 2 of 13)	L1MA8|LINE|L1	24423	NR_109986	101928882	Hs.734668	NR_109986	ENSG00000285336	LOC101928882	-	uncharacterized LOC101928882	ncRNA	0.005025	0.530000	
chunk0039_174_1	chr11	100079311	100079856	+	0	NA	intron (NM_014361, intron 13 of 24)	intron (NM_014361, intron 13 of 24)	523438	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.005505	0.357143	
chunk0163_379_1	chr6	16233929	16234422	+	0	NA	Intergenic	L1PB|LINE|L1	-4405	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.010142	0.380567	
chunk0077_302_1	chr16	81601840	81602286	+	0	NA	intron (NM_030629, intron 1 of 20)	L1ME4c|LINE|L1	-9285	NR_106759	102465251		NR_106759	ENSG00000275109	MIR6504	hsa-mir-6504	microRNA 6504	ncRNA	0.017937	0.465324	
chunk0091_95_1	chr19	5718762	5718968	+	0	NA	intron (NM_001276480, intron 1 of 17)	intron (NM_001276480, intron 1 of 17)	1300	NM_001276479	9361	Hs.350265	NM_004793	ENSG00000196365	LONP1	CODASS|LON|LONP|LonHS|PIM1|PRSS15|hLON	lon peptidase 1, mitochondrial	protein-coding	0.009709	0.478261	
chunk0210_201_1	chrX	80613551	80614067	+	0	NA	Intergenic	L1PA15|LINE|L1	193362	NM_152630	169966	Hs.367959	NM_152630	ENSG00000174016	TENT5D	CT1.26|CT112|FAM46D	terminal nucleotidyltransferase 5D	protein-coding	0.001938	0.363636	
chunk0187_268_1	chr7	155199751	155200272	+	0	NA	Intergenic	MER134|DNA?|DNA?	-97765	NM_198337	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.019194	0.467433	
chunk0201_415_1	chr9	69594157	69594403	+	0	NA	intron (NM_001163, intron 1 of 12)	MER5A1|DNA|hAT-Charlie	78079	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.008130	0.497976	
chunk0155_380_1	chr5	98155869	98156492	+	0	NA	Intergenic	Intergenic	-613115	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.004815	0.439103	
chunk0177_218_1	chr7	24152479	24153480	+	0	NA	Intergenic	Intergenic	-131209	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.007992	0.439122	
chunk0021_314_1	chr1	245062842	245063131	+	0	NA	intron (NM_032328, intron 4 of 7)	ERV3-16A3_I-int|LTR|ERVL	-91999	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.000000	0.475862	
chunk0060_393_1	chr14	52882288	52882653	+	0	NA	intron (NM_001134999, intron 4 of 15)	intron (NM_001134999, intron 4 of 15)	68627	NM_006832	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.002740	0.319672	
chunk0198_353_1	chr8	140496455	140496796	+	0	NA	Intergenic	L1ME1|LINE|L1	-14673	NM_017444	54108	Hs.279704	NM_017444	ENSG00000104472	CHRAC1	CHARC1|CHARC15|CHRAC-1|CHRAC-15|CHRAC15|YCL1	chromatin accessibility complex subunit 1	protein-coding	0.014663	0.438596	
chunk0181_257_1	chr7	85792388	85792587	+	0	NA	Intergenic	L1MA3|LINE|L1	-670556	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.475000	
chunk0018_89_1	chr1	217532383	217532787	+	0	NA	intron (NM_018040, intron 5 of 9)	L2b|LINE|L2	98517	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.000000	0.409877	
chunk0113_207_1	chr20	53744668	53744997	+	0	NA	Intergenic	MIRb|SINE|MIR	130877	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.009119	0.430303	110(GGGAGCAAGGTGTTCC,-,0.00),111(GGAGCAAGGTGTTCCT,+,0.00)
chunk0074_61_1	chr16	21100528	21100779	+	0	NA	intron (NM_017539, intron 16 of 61)	intron (NM_017539, intron 16 of 61)	-57724	NM_001301775	57146	Hs.258212	NM_020422	ENSG00000011638	TMEM159	-	transmembrane protein 159	protein-coding	0.011952	0.452381	
chunk0107_59_1	chr2	211561459	211562110	+	0	NA	intron (NM_001042599, intron 20 of 26)	intron (NM_001042599, intron 20 of 26)	864576	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.006144	0.349693	
chunk0100_175_1	chr2	109721080	109721505	+	0	NA	Intergenic	Intergenic	-71466	NM_001123363	729540	Hs.535589	NM_001037866	ENSG00000183054	RGPD6	RGP6|RGPD7|RanBP2L1|RanBP2L2	RANBP2 like and GRIP domain containing 6	protein-coding	0.021176	0.450704	
chunk0073_270_1	chr16	12262842	12263041	+	0	NA	intron (NM_032167, intron 14 of 20)	L1MB7|LINE|L1	286207	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.000000	0.450000	
chunk0101_334_1	chr2	136241961	136242388	+	0	NA	Intergenic	Intergenic	-124019	NM_003467	7852	Hs.593413	NM_003467	ENSG00000121966	CXCR4	CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS	C-X-C motif chemokine receptor 4	protein-coding	0.009368	0.408879	152(AAGGACAGACAGTTCC,-,0.00),153(AGGACAGACAGTTCCT,+,0.00)
chunk0208_187_1	chrX	17170404	17170848	+	0	NA	Intergenic	Intergenic	-204794	NM_198270	4810	Hs.201623	NM_198270	ENSG00000188158	NHS	CTRCT40|CXN|SCML1	NHS actin remodeling regulator	protein-coding	0.006757	0.420225	
chunk0054_97_1	chr13	42725304	42725628	+	0	NA	Intergenic	Intergenic	-56084	NM_182508	144809	Hs.16970	NM_182508	ENSG00000179813	FAM216B	C13orf30	family with sequence similarity 216 member B	protein-coding	0.003086	0.360000	
chunk0165_344_1	chr6	37942794	37943372	+	0	NA	intron (NM_021943, intron 2 of 5)	intron (NM_021943, intron 2 of 5)	123552	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.003460	0.331606	
chunk0199_342_1	chr9	11244850	11245067	+	0	NA	Intergenic	L1PA11|LINE|L1	631752	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.009217	0.449541	0(ATGTACAGGATGTGCA,-,0.00),1(TGTACAGGATGTGCAG,+,0.00)
chunk0145_418_1	chr4	152962092	152962774	+	0	NA	intron (NM_033393, intron 5 of 10)	intron (NM_033393, intron 5 of 10)	19450	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.011730	0.329429	
chunk0087_189_1	chr18	35610113	35610620	+	0	NA	Intergenic	L2a|LINE|L2	18629	NR_039771	100616257		NR_039771	ENSG00000283514	MIR3975	-	microRNA 3975	ncRNA	0.005917	0.450787	
chunk0158_143_1	chr5	127385880	127386411	+	0	NA	intron (NM_001308121, intron 5 of 13)	intron (NM_001308121, intron 5 of 13)	95381	NM_001308121	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.003766	0.413534	
chunk0118_421_1	chr22	38503774	38504006	+	0	NA	intron (NM_006386, intron 1 of 12)	intron (NM_006386, intron 1 of 12)	2450	NM_006386	10521	Hs.528305	NM_006386	ENSG00000100201	DDX17	P72|RH70	DEAD-box helicase 17	protein-coding	0.004310	0.351931	
chunk0034_343_1	chr11	35743849	35744750	+	0	NA	intron (NM_017583, intron 4 of 4)	MER53|DNA|hAT	81547	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.006659	0.343681	
chunk0042_140_1	chr12	3821372	3821739	+	0	NA	intron (NR_104461, intron 6 of 8)	intron (NR_104461, intron 6 of 8)	51893	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.000000	0.358696	
chunk0150_52_1	chr5	31825064	31825796	+	0	NA	intron (NM_178140, intron 1 of 23)	intron (NM_178140, intron 1 of 23)	26506	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.009563	0.474761	
chunk0151_11_1	chr5	41172168	41172636	+	0	NA	intron (NM_001115131, intron 8 of 17)	intron (NM_001115131, intron 8 of 17)	41191	NM_000065	729	Hs.481992	NM_000065	ENSG00000039537	C6	-	complement C6	protein-coding	0.010684	0.456290	236(AGGAACATGGTGCTCT,-,0.00),237(GGAACATGGTGCTCTG,+,0.00)
chunk0019_48_1	chr1	224132717	224133206	+	0	NA	intron (NR_049764, intron 2 of 3)	L1MB7|LINE|L1	18874	NM_001136115	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.010225	0.377551	
chunk0137_55_1	chr4	11722649	11723261	+	0	NA	Intergenic	Intergenic	-294042	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.001634	0.376835	342(ATGCACTGCTTGTTCT,-,0.00),343(TGCACTGCTTGTTCTG,+,0.00)
chunk0104_120_1	chr2	172995865	172996064	+	0	NA	intron (NM_001282899, intron 12 of 27)	intron (NM_001282899, intron 12 of 27)	67759	NM_001282901	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.010050	0.410000	
chunk0029_313_1	chr10	104309756	104310417	+	0	NA	3' UTR (NM_001272012, exon 2 of 2)	3' UTR (NM_001272012, exon 2 of 2)	-13278	NR_120622	101927472	Hs.670333	NR_120622		ITPRIP-AS1	-	ITPRIP antisense RNA 1	ncRNA	0.015129	0.466767	307(AGGCACACATTGCCCT,-,0.00),308(GGCACACATTGCCCTT,+,0.00)
chunk0186_460_1	chr7	148390261	148391035	+	0	NA	intron (NM_014141, intron 22 of 23)	intron (NM_014141, intron 22 of 23)	-199917	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.003876	0.405161	
chunk0013_243_1	chr1	169673956	169674394	+	0	NA	Intergenic	Intergenic	34681	NR_029467	6402	Hs.728756	NM_000655	ENSG00000188404	SELL	CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1	selectin L	protein-coding	0.002283	0.337130	
chunk0175_314_1	chr6	166667808	166668347	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	-40839	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.020408	0.531481	222(CAGAACACAGTCTCCT,-,0.00),223(AGAACACAGTCTCCTG,+,0.00),244(AAGCACTCAGTGTGCA,-,0.00),245(AGCACTCAGTGTGCAG,+,0.00)
chunk0059_293_1	chr14	35854694	35855058	+	0	NA	intron (NM_032352, intron 4 of 9)	L1MEd|LINE|L1	28485	NM_032352	84312	Hs.525299	NM_032352	ENSG00000100916	BRMS1L	BRMS1	BRMS1 like transcriptional repressor	protein-coding	0.002747	0.416438	
chunk0199_220_1	chr9	5194024	5194599	+	0	NA	Intergenic	Intergenic	-8693	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.005217	0.315972	
chunk0117_47_1	chr22	12602283	12602482	+	0	NA	Intergenic	CpG	704976	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.055276	0.570000	
chunk0016_113_1	chr1	196018114	196018550	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	564149	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.004587	0.425629	210(AGGAACACTCTGTCCT,-,0.00),211(GGAACACTCTGTCCTC,+,0.00)
chunk0124_414_1	chr3	60743266	60743618	+	0	NA	intron (NM_001166243, intron 4 of 9)	L2a|LINE|L2	-125572	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.000000	0.390935	
chunk0185_364_1	chr7	132825126	132825506	+	0	NA	intron (NM_017812, intron 6 of 7)	intron (NM_017812, intron 6 of 7)	176522	NR_046323	286023	Hs.671875	NM_173682	ENSG00000183470	FLJ40288	-	uncharacterized FLJ40288	ncRNA	0.002632	0.377953	
chunk0059_4_1	chr14	29663210	29663541	+	0	NA	intron (NM_002742, intron 4 of 17)	intron (NM_002742, intron 4 of 17)	264318	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.009063	0.361446	
chunk0176_410_1	chr7	19321333	19321788	+	0	NA	Intergenic	Intergenic	-176139	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.002198	0.328947	
chunk0102_415_1	chr2	156568128	156568391	+	0	NA	intron (NM_001083112, intron 9 of 16)	MIRb|SINE|MIR	131871	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.000000	0.378788	
chunk0086_151_1	chr18	21389909	21390108	+	0	NA	intron (NM_001142966, intron 4 of 32)	Tigger3b|DNA|TcMar-Tigger	147766	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.005025	0.410000	
chunk0152_151_1	chr5	59303081	59304447	+	0	NA	intron (NM_001165899, intron 3 of 16)	L1PB1|LINE|L1	-27645	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005857	0.366496	
chunk0126_305_1	chr3	80914694	80915338	+	0	NA	Intergenic	MIRc|SINE|MIR	-78852	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.006211	0.353488	
chunk0148_106_1	chr5	4515509	4515819	+	0	NA	Intergenic	Intergenic	-257817	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.016129	0.389068	
chunk0191_70_1	chr8	47167322	47167521	+	0	NA	Intergenic	Intergenic	-21886	NR_037168	100287846	Hs.21550	NR_037168		LOC100287846	-	uncharacterized LOC100287846	ncRNA	0.025126	0.585000	
chunk0080_421_1	chr17	35788863	35789411	+	0	NA	intron (NR_111988, intron 1 of 8)	intron (NR_111988, intron 1 of 8)	6570	NM_024302	79148	Hs.380710	NM_024302	ENSG00000271447	MMP28	EPILYSIN|MM28|MMP-25|MMP-28|MMP25	matrix metallopeptidase 28	protein-coding	0.001825	0.446266	
chunk0036_361_1	chr11	66985660	66986325	+	0	NA	Intergenic	MIRb|SINE|MIR	10709	NM_001136485	254439	Hs.232604	NM_001136485	ENSG00000173237	C11orf86	-	chromosome 11 open reading frame 86	protein-coding	0.012030	0.582583	292(AGGCACACACTGTGCT,-,0.00),293(GGCACACACTGTGCTG,+,0.00),369(GAGCCCAGTGTGTCCT,-,0.00),370(AGCCCAGTGTGTCCTC,+,0.00)
chunk0080_281_1	chr17	31195320	31195735	+	0	NA	intron (NM_001042492, intron 8 of 57)	L1MB2|LINE|L1	100600	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.012048	0.358173	
chunk0072_296_1	chr15	98727793	98728048	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-56506	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.047059	0.523438	
chunk0037_230_1	chr11	74983775	74984494	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-4771	NM_006656	10825	Hs.191074	NM_006656	ENSG00000162139	NEU3	SIAL3	neuraminidase 3	protein-coding	0.005563	0.411111	
chunk0068_233_1	chr15	55654476	55655207	+	0	NA	intron (NM_173814, intron 11 of 19)	intron (NM_173814, intron 11 of 19)	-65989	NM_015617	26108	Hs.87194	NM_015617	ENSG00000171016	PYGO1	-	pygopus family PHD finger 1	protein-coding	0.006840	0.353825	
chunk0157_350_1	chr5	122991237	122991590	+	0	NA	intron (NM_014035, intron 3 of 6)	Plat_L3|LINE|CR1	45317	NM_000943	5480	Hs.110364	NM_000943	ENSG00000168938	PPIC	CYPC	peptidylprolyl isomerase C	protein-coding	0.008499	0.378531	
chunk0117_82_1	chr22	17159777	17160090	+	0	NA	promoter-TSS (NM_033070)	promoter-TSS (NM_033070)	544	NR_024483	100130717	Hs.660066	NR_024482	ENSG00000185837	HDHD5-AS1	CECR4|CECR5-AS1|NCRNA00017	HDHD5 antisense RNA 1	ncRNA	0.060703	0.554140	
chunk0008_52_1	chr1	89254943	89255438	+	0	NA	Intergenic	L1MA2|LINE|L1	17671	NM_001134486	115362	Hs.513726	NM_052942	ENSG00000154451	GBP5	GBP-5	guanylate binding protein 5	protein-coding	0.008081	0.366935	
chunk0064_153_1	chr14	91816902	91817286	+	0	NA	intron (NM_001128596, intron 1 of 11)	L1MC5|LINE|L1	-13160	NR_106988									0.002604	0.298701	
chunk0091_235_1	chr19	10604106	10604305	+	0	NA	intron (NM_001145056, intron 1 of 21)	L2a|LINE|L2	1760	NM_001145056	57153	Hs.534560	NM_020428	ENSG00000129353	SLC44A2	CTL2|PP1292	solute carrier family 44 member 2	protein-coding	0.025126	0.460000	
chunk0148_165_1	chr5	6830587	6830942	+	0	NA	Intergenic	(ACAC)n|Simple_repeat|Simple_repeat	-2843	NR_036242	100422999		NR_036242	ENSG00000283420	MIR4278	-	microRNA 4278	ncRNA	0.030986	0.533708	
chunk0166_382_1	chr6	51702756	51703332	+	0	NA	intron (NM_138694, intron 60 of 66)	L2c|LINE|L2	81174	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.003472	0.315425	
chunk0126_366_1	chr3	83602028	83602582	+	0	NA	Intergenic	Intergenic	1267270	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.005415	0.381982	
chunk0126_377_1	chr3	84139914	84140581	+	0	NA	Intergenic	L1MD2|LINE|L1	729328	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.005997	0.333832	
chunk0005_21_1	chr1	54314593	54315362	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	78534	NR_103541	619518	Hs.591438	NM_001034847	ENSG00000198711	SSBP3-AS1	C1orf191|MST128|MSTP128	SSBP3 antisense RNA 1	ncRNA	0.011704	0.506494	584(AAGCACTGTCTGTACC,-,0.00),585(AGCACTGTCTGTACCC,+,0.00)
chunk0053_181_1	chr13	30972861	30973342	+	0	NA	intron (NM_152325, intron 6 of 6)	L1ME2|LINE|L1	40404	NM_152325	122046	Hs.124463	NM_152325	ENSG00000175664	TEX26	C13orf26	testis expressed 26	protein-coding	0.002079	0.373444	
chunk0119_166_1	chr22	43295247	43295975	+	0	NA	intron (NM_173050, intron 3 of 21)	intron (NM_173050, intron 3 of 21)	47777	NM_173050	80274	Hs.133995	NM_152514	ENSG00000159307	SCUBE1	-	signal peptide, CUB domain and EGF like domain containing 1	protein-coding	0.017857	0.584362	208(TGGCACAGTTTGTGCT,-,0.00),209(GGCACAGTTTGTGCTT,+,0.00)
chunk0079_100_1	chr17	12107691	12108283	+	0	NA	intron (NM_001281435, intron 6 of 11)	intron (NM_001281435, intron 6 of 11)	26088	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.003378	0.320405	442(CATAACAGACTGTTCT,-,0.00),443(ATAACAGACTGTTCTG,+,0.00)
chunk0212_404_1	chrX	151618606	151618962	+	0	NA	intron (NM_173493, intron 4 of 15)	L2a|LINE|L2	55249	NM_173493	139135	Hs.160594	NM_173493	ENSG00000166049	PASD1	CT63|CT64|OXTES1	PAS domain containing repressor 1	protein-coding	0.002809	0.392157	
chunk0119_177_1	chr22	43643407	43643606	+	0	NA	intron (NM_198856, intron 15 of 29)	intron (NM_198856, intron 15 of 29)	127252	NR_046563	100874197	Hs.627997	NR_046563		EFCAB6-AS1	-	EFCAB6 antisense RNA 1	ncRNA	0.010050	0.570000	
chunk0017_187_1	chr1	207322659	207323176	+	0	NA	intron (NR_125349, intron 2 of 10)	intron (NR_125349, intron 2 of 10)	1445	NM_001300904	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.007737	0.347490	
chunk0158_445_1	chr5	135731672	135731878	+	0	NA	Intergenic	Intergenic	71300	NR_049867	100847082		NR_049867	ENSG00000265924	MIR5692C1	-	microRNA 5692c-1	ncRNA	0.000000	0.454106	
chunk0019_22_1	chr1	223688739	223688938	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-12755	NM_001146068	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.010050	0.520000	
chunk0055_172_1	chr13	60572306	60572976	+	0	NA	intron (NM_030794, intron 13 of 13)	intron (NM_030794, intron 13 of 13)	-100314	NR_047003	101926930	Hs.578045	NR_047003		LINC00378	-	long intergenic non-protein coding RNA 378	ncRNA	0.005970	0.385991	
chunk0160_296_1	chr5	158385981	158386366	+	0	NA	intron (NR_109888, intron 1 of 6)	L1ME4a|LINE|L1	23600	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.007792	0.334197	
chunk0032_212_1	chr11	7520862	7521241	+	0	NA	intron (NM_003621, intron 1 of 23)	intron (NM_003621, intron 1 of 23)	7286	NM_003621	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.005277	0.413158	
chunk0196_7_1	chr8	101423612	101424702	+	0	NA	Intergenic	Intergenic	55264	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.008257	0.442713	797(GGGAACAGCATGTCCC,-,0.00),798(GGAACAGCATGTCCCA,+,0.00)
chunk0118_281_1	chr22	33806340	33806681	+	0	NA	intron (NM_133642, intron 1 of 14)	intron (NM_133642, intron 1 of 14)	81524	NR_038950	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.008798	0.476608	144(GAGGACAAACAGTTCC,-,0.00),145(AGGACAAACAGTTCCT,+,0.00)
chunk0047_341_1	chr12	74624080	74624548	+	0	NA	Intergenic	L1MC1|LINE|L1	86543	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.008547	0.332623	
chunk0130_242_1	chr3	135298670	135298899	+	0	NA	Intergenic	Intergenic	503527	NM_004441	2047	Hs.116092	NM_004441	ENSG00000154928	EPHB1	ELK|EPHT2|Hek6|NET	EPH receptor B1	protein-coding	0.000000	0.452174	
chunk0094_136_1	chr2	4929013	4929497	+	0	NA	Intergenic	Intergenic	-273033	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.033058	0.486598	
chunk0019_447_1	chr1	231326998	231327415	+	0	NA	Intergenic	Intergenic	10666	NM_175876	149371	Hs.356198	NM_175876	ENSG00000116903	EXOC8	EXO84|Exo84p|SEC84	exocyst complex component 8	protein-coding	0.014388	0.389952	
chunk0036_438_1	chr11	68504541	68504918	+	0	NA	intron (NM_001164161, intron 1 of 23)	intron (NM_001164161, intron 1 of 23)	44011	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.010610	0.439153	
chunk0183_328_1	chr7	108195703	108196090	+	0	NA	intron (NM_001193582, intron 14 of 30)	intron (NM_001193582, intron 14 of 30)	44274	NM_001037132	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.007752	0.389175	
chunk0057_138_1	chr13	99856039	99856406	+	0	NA	intron (NR_120421, intron 1 of 4)	intron (NR_120421, intron 1 of 4)	100943	NR_120421	101927437	Hs.619936	NR_120421		LOC101927437	-	uncharacterized LOC101927437	ncRNA	0.008174	0.366848	
chunk0150_109_1	chr5	32831512	32832109	+	0	NA	Intergenic	Intergenic	-115633	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.005025	0.441472	
chunk0090_132_1	chr18	71878802	71879302	+	0	NA	Intergenic	L1M4b|LINE|L1	-96826	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.010000	0.317365	
chunk0134_246_1	chr3	179340323	179341027	+	0	NA	Intergenic	Intergenic	-7017	NM_033540	55669	Hs.478383	NM_017927	ENSG00000171109	MFN1	hfzo1|hfzo2	mitofusin 1	protein-coding	0.002841	0.300709	
chunk0203_101_1	chr9	84319087	84319362	+	0	NA	intron (NM_022127, intron 2 of 18)	MER67A|LTR|ERV1	21555	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.007273	0.380435	
chunk0201_113_1	chr9	35244964	35245371	+	0	NA	intron (NM_006377, intron 6 of 38)	intron (NM_006377, intron 6 of 38)	83175	NM_006377	10497	Hs.493791	NM_006377	ENSG00000198722	UNC13B	MUNC13|UNC13|Unc13h2	unc-13 homolog B	protein-coding	0.004914	0.333333	
chunk0095_3_1	chr2	11669661	11669967	+	0	NA	exon (NM_012344, exon 1 of 4)	exon (NM_012344, exon 1 of 4)	389	NM_012344	23620	Hs.131138	NM_012344	ENSG00000169006	NTSR2	NTR2	neurotensin receptor 2	protein-coding	0.120915	0.732899	
chunk0183_454_1	chr7	111475976	111476590	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	86008	NM_032549	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.004886	0.330081	234(AGAAACAAGATGTCCC,-,0.00)
chunk0113_275_1	chr20	56651909	56652138	+	0	NA	Intergenic	L1ME1|LINE|L1	22721	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.008734	0.395652	
chunk0100_107_1	chr2	108271705	108272415	+	0	NA	Intergenic	Intergenic	-16579	NM_176825	6819	Hs.436123	NM_001056	ENSG00000198203	SULT1C2	ST1C1|ST1C2|SULT1C1|humSULTC2	sulfotransferase family 1C member 2	protein-coding	0.011268	0.462729	254(TAGGACAGGGTGTTTC,-,0.00),255(AGGACAGGGTGTTTCC,+,0.00)
chunk0207_89_1	chrX	9469703	9470237	+	0	NA	intron (NM_005647, intron 1 of 17)	intron (NM_005647, intron 1 of 17)	4809	NM_005647	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.009363	0.444860	
chunk0156_224_1	chr5	108259383	108259629	+	0	NA	intron (NM_001163315, intron 4 of 8)	MIRc|SINE|MIR	122592	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.004065	0.404858	
chunk0164_292_1	chr6	24720921	24721246	+	0	NA	Intergenic	CpG	-1908	NM_030939	81688	Hs.744857	NM_030939	ENSG00000112308	C6orf62	Nbla00237|XTP12|dJ30M3.2	chromosome 6 open reading frame 62	protein-coding	0.036923	0.533742	
chunk0113_346_1	chr20	58779594	58780063	+	0	NA	Intergenic	Intergenic	37866	NR_029844	407022		NR_029844	ENSG00000284040	MIR296	MIRN296|miRNA296|mir-296	microRNA 296	ncRNA	0.006397	0.444681	
chunk0159_396_1	chr5	147243168	147243526	+	0	NA	intron (NM_145001, intron 2 of 6)	intron (NM_145001, intron 2 of 6)	8331	NM_145001	202374	Hs.585069	NM_145001	ENSG00000169302	STK32A	YANK1	serine/threonine kinase 32A	protein-coding	0.011173	0.356546	
chunk0022_133_1	chr10	11824242	11824804	+	0	NA	intron (NM_153256, intron 1 of 3)	intron (NM_153256, intron 1 of 3)	1125	NM_153256	254427	Hs.435775	NM_153256	ENSG00000148426	PROSER2	C10orf47	proline and serine rich 2	protein-coding	0.017794	0.365897	
chunk0096_278_1	chr2	31962442	31963163	+	0	NA	intron (NM_001301852, intron 1 of 7)	MLT2B4|LTR|ERVL	47862	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.000000	0.378116	
chunk0200_268_1	chr9	22041249	22042261	+	0	NA	intron (NR_003529, intron 3 of 18)	intron (NR_003529, intron 3 of 18)	-32442	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.002964	0.372162	
chunk0125_23_1	chr3	62143770	62144492	+	0	NA	intron (NM_002841, intron 6 of 29)	MER58A|DNA|hAT-Charlie	174816	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.008310	0.401107	
chunk0039_211_1	chr11	101092939	101093546	+	0	NA	intron (NM_000926, intron 2 of 7)	intron (NM_000926, intron 2 of 7)	35821	NR_073143	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.008237	0.394737	
chunk0197_140_1	chr8	120306902	120307108	+	0	NA	intron (NM_021110, intron 36 of 47)	intron (NM_021110, intron 36 of 47)	-138393	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.009709	0.396135	
chunk0155_442_1	chr5	101517731	101518208	+	0	NA	Intergenic	Intergenic	-614684	NM_175052	7903	Hs.308628	NM_005668	ENSG00000113532	ST8SIA4	PST|PST1|SIAT8D|ST8SIA-IV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding	0.004193	0.370293	
chunk0134_375_1	chr3	182795429	182795844	+	0	NA	intron (NM_014616, intron 1 of 29)	intron (NM_014616, intron 1 of 29)	2133	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.007229	0.372596	
chunk0135_58_1	chr3	185735417	185735754	+	0	NA	intron (NM_001007225, intron 2 of 14)	intron (NM_001007225, intron 2 of 14)	22333	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.005935	0.423077	
chunk0149_239_1	chr5	23494334	23494954	+	0	NA	Intergenic	Intergenic	-12965	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.004839	0.297907	
chunk0029_42_1	chr10	96275949	96276494	+	0	NA	Intergenic	Intergenic	-4645	NM_013314	29760	Hs.665244	NM_013314	ENSG00000095585	BLNK	AGM4|BASH|BLNK-S|LY57|SLP-65|SLP65|bca	B cell linker	protein-coding	0.001835	0.487179	
chunk0093_289_1	chr19	52193146	52193423	+	0	NA	intron (NM_014225, intron 1 of 14)	intron (NM_014225, intron 1 of 14)	3482	NM_014225	5518	Hs.467192	NM_014225	ENSG00000105568	PPP2R1A	MRD36|PP2A-Aalpha|PP2AA|PP2AAALPHA|PR65A	protein phosphatase 2 scaffold subunit Aalpha	protein-coding	0.003610	0.417266	
chunk0173_154_1	chr6	144213074	144213745	+	0	NA	Intergenic	Intergenic	62892	NM_003764	8676	Hs.118958	NM_003764	ENSG00000135604	STX11	FHL4|HLH4|HPLH4	syntaxin 11	protein-coding	0.010432	0.409226	
chunk0211_70_1	chrX	109995059	109995586	+	0	NA	Intergenic	MIRb|SINE|MIR	-7313	NM_017698	84187	Hs.496572	NM_017698	ENSG00000157600	TMEM164	bB360B22.3	transmembrane protein 164	protein-coding	0.005693	0.414773	
chunk0045_429_1	chr12	53463161	53463985	+	0	NA	promoter-TSS (NR_109828)	promoter-TSS (NR_109828)	-895	NR_109828	102157401		NR_109828	ENSG00000282977	PCBP2-OT1	TUC.338|TUC338|uc.338	PCBP2 overlapping transcript 1	ncRNA	0.009709	0.400000	
chunk0199_348_1	chr9	11996416	11996794	+	0	NA	Intergenic	L1M2a|LINE|L1	-696781	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.010582	0.546174	
chunk0010_35_1	chr1	112594073	112594378	+	0	NA	intron (NM_017744, intron 5 of 14)	Charlie2b|DNA|hAT-Charlie	24914	NM_001308264	54879	Hs.201921	NM_017744	ENSG00000007341	ST7L	FAM4B|ST7R|STLR	suppression of tumorigenicity 7 like	protein-coding	0.000000	0.356209	
chunk0012_95_1	chr1	156302917	156303123	+	0	NA	Intergenic	Intergenic	-3383	NM_001004319	391104	Hs.532378	NM_001004319	ENSG00000189030	VHLL	VHLP|VLP	VHL like	protein-coding	0.009709	0.381643	
chunk0197_52_1	chr8	118522659	118523317	+	0	NA	intron (NR_109794, intron 2 of 4)	intron (NR_109794, intron 2 of 4)	-98013	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.004559	0.364188	283(AAATACACAATGTTCC,-,0.00),284(AATACACAATGTTCCA,+,0.00)
chunk0141_187_1	chr4	83334473	83334958	+	0	NA	promoter-TSS (NM_001199830)	promoter-TSS (NM_001199830)	98	NM_001199830	10855	Hs.44227	NM_006665	ENSG00000173083	HPSE	HPA|HPA1|HPR1|HPSE1|HSE1	heparanase	protein-coding	0.070103	0.679012	
chunk0168_62_1	chr6	79221765	79221966	+	0	NA	intron (NM_001201362, intron 1 of 4)	intron (NM_001201362, intron 1 of 4)	-11809	NR_040671	100288198	Hs.586270	NR_040671	ENSG00000270362	HMGN3-AS1	-	HMGN3 antisense RNA 1	ncRNA	0.004975	0.396040	
chunk0166_409_1	chr6	52115826	52116404	+	0	NA	Intergenic	Intergenic	-28234	NR_029713	406989		NR_029713	ENSG00000207604	MIR206	MIRN206|miRNA206|mir-206	microRNA 206	ncRNA	0.005190	0.326425	
chunk0120_5_1	chr3	380697	381375	+	0	NA	intron (NM_006614, intron 16 of 27)	MER5A1|DNA|hAT-Charlie	4759	NR_110739	101927193	Hs.677744	NR_110739	ENSG00000234661	CHL1-AS1	-	CHL1 antisense RNA 1	ncRNA	0.001475	0.382916	
chunk0042_109_1	chr12	3179263	3179480	+	0	NA	intron (NM_006675, intron 2 of 8)	L3b|LINE|CR1	102016	NM_001168320	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.018433	0.555046	
chunk0166_254_1	chr6	47484698	47485401	+	0	NA	intron (NM_012120, intron 1 of 17)	Tigger3b|DNA|TcMar-Tigger	7260	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.008535	0.380682	
chunk0162_297_1	chr6	6452052	6452355	+	0	NA	intron (NR_026970, intron 3 of 7)	intron (NR_026970, intron 3 of 7)	-131512	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.003300	0.513158	
chunk0205_210_1	chr9	109317284	109317824	+	0	NA	intron (NM_018424, intron 1 of 15)	intron (NM_018424, intron 1 of 15)	3410	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.020370	0.497227	
chunk0188_35_1	chr8	6599230	6599901	+	0	NA	intron (NM_024596, intron 12 of 13)	intron (NM_024596, intron 12 of 13)	22655	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.013413	0.363095	
chunk0129_203_1	chr3	121707404	121708036	+	0	NA	intron (NM_001256488, intron 9 of 20)	intron (NM_001256488, intron 9 of 20)	42047	NM_001256488	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.003165	0.375987	
chunk0075_459_1	chr16	58417525	58418112	+	0	NA	Intergenic	Intergenic	25424	NM_001126130	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.011925	0.486395	
chunk0182_395_1	chr7	100465848	100466346	+	0	NA	TTS (NM_001303043)	TTS (NM_001303043)	-1826	NM_001004323	402573	Hs.632306	NM_001004323	ENSG00000185955	C7orf61	-	chromosome 7 open reading frame 61	protein-coding	0.036145	0.689379	275(AAGGGCACCGTGTGCC,-,0.00),276(AGGGCACCGTGTGCCC,+,0.00)
chunk0204_205_1	chr9	96661752	96662250	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-6684	NM_153698	195827	Hs.44640	NM_153698	ENSG00000158122	PRXL2C	AAED1|C9orf21	peroxiredoxin like 2C	protein-coding	0.010040	0.476954	
chunk0075_204_1	chr16	52526798	52527110	+	0	NA	intron (NM_001146188, intron 1 of 7)	L2b|LINE|L2	19940	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.009615	0.370607	
chunk0143_124_1	chr4	109467998	109468223	+	0	NA	intron (NM_001042734, intron 2 of 22)	intron (NM_001042734, intron 2 of 22)	-20588	NR_030302	693161		NR_030302	ENSG00000207988	MIR576	MIRN576|hsa-mir-576	microRNA 576	ncRNA	0.000000	0.314159	
chunk0044_391_1	chr12	40240321	40240997	+	0	NA	intron (NM_198578, intron 6 of 50)	intron (NM_198578, intron 6 of 50)	15648	NM_198578	120892	Hs.187636	NM_198578	ENSG00000188906	LRRK2	AURA17|DARDARIN|PARK8|RIPK7|ROCO2	leucine rich repeat kinase 2	protein-coding	0.004438	0.320532	
chunk0024_359_1	chr10	43965675	43966391	+	0	NA	intron (NR_033846, intron 6 of 7)	intron (NR_033846, intron 6 of 7)	56729	NR_033846	283033	Hs.178244	NR_033846		LINC00841	-	long intergenic non-protein coding RNA 841	ncRNA	0.012570	0.461646	
chunk0137_296_1	chr4	23982396	23982980	+	0	NA	Intergenic	MIRb|SINE|MIR	-92611	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.006849	0.382906	
chunk0112_70_1	chr20	37790166	37790832	+	0	NA	intron (NM_030877, intron 10 of 15)	intron (NM_030877, intron 10 of 15)	96544	NM_030877	56259	Hs.472667	NM_030877	ENSG00000132792	CTNNBL1	C20orf33|NAP|P14L|PP8304|dJ633O20.1	catenin beta like 1	protein-coding	0.009009	0.401799	
chunk0128_197_1	chr3	107701290	107701966	+	0	NA	intron (NM_001276286, intron 3 of 16)	intron (NM_001276286, intron 3 of 16)	176440	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.004438	0.355982	
chunk0109_290_1	chr20	8225756	8226025	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	93625	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.011152	0.362963	
chunk0051_186_1	chr12	116166968	116167240	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	-18450	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.003676	0.260073	
chunk0190_201_1	chr8	34583931	34584336	+	0	NA	Intergenic	Intergenic	-199788	NR_125746	103689844	Hs.590682	NR_125746	ENSG00000254344	LINC01288	TCONS_00014671	long intergenic non-protein coding RNA 1288	ncRNA	0.002469	0.357143	
chunk0057_311_1	chr13	106564996	106565635	+	0	NA	intron (NM_018011, intron 1 of 3)	intron (NM_018011, intron 1 of 3)	2851	NM_018011	55082	Hs.508644	NM_018011	ENSG00000134884	ARGLU1	-	arginine and glutamate rich 1	protein-coding	0.004695	0.382812	253(TAGAACTTCGTGTTCT,-,0.00),254(AGAACTTCGTGTTCTA,+,0.00)
chunk0167_242_1	chr6	67658507	67658888	+	0	NA	Intergenic	Intergenic	-396654	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.000000	0.301047	
chunk0047_259_1	chr12	72655391	72655731	+	0	NA	intron (NM_013381, intron 17 of 18)	L2c|LINE|L2	-382052	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.005882	0.354839	280(AGGAACAGACTGTACC,-,0.00),281(GGAACAGACTGTACCT,+,0.00)
chunk0102_106_1	chr2	144371731	144372031	+	0	NA	Intergenic	Intergenic	-39347	NM_001284235	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.010000	0.428571	
chunk0047_404_1	chr12	75850475	75850758	+	0	NA	Intergenic	Intergenic	181160	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.003534	0.422535	
chunk0016_165_1	chr1	197783478	197784000	+	0	NA	Intergenic	Intergenic	-8246	NR_125340	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.003831	0.384321	
chunk0027_291_1	chr10	77613316	77613861	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	24231	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.018349	0.494505	
chunk0204_84_1	chr9	94076561	94076845	+	0	NA	intron (NM_177995, intron 2 of 9)	L1MB8|LINE|L1	-7726	NM_152422	138639	Hs.437943	NM_152422	ENSG00000158079	PTPDC1	PTP9Q22	protein tyrosine phosphatase domain containing 1	protein-coding	0.000000	0.347368	
chunk0062_339_1	chr14	73465894	73466174	+	0	NA	Intergenic	Intergenic	-7454	NM_003744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.007143	0.437722	
chunk0115_43_1	chr21	21247529	21247855	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	249377	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.003067	0.290520	
chunk0054_285_1	chr13	47053981	47054260	+	0	NA	Intergenic	L1M5|LINE|L1	-157044	NM_001165947	3356	Hs.72630	NM_000621	ENSG00000102468	HTR2A	5-HT2A|HTR2	5-hydroxytryptamine receptor 2A	protein-coding	0.007168	0.353571	
chunk0008_140_1	chr1	92032021	92032426	+	0	NA	intron (NM_173567, intron 1 of 6)	intron (NM_173567, intron 1 of 6)	2247	NM_173567	253152	Hs.201555	NM_173567	ENSG00000172031	EPHX4	ABHD7|EH4|EPHXRP	epoxide hydrolase 4	protein-coding	0.000000	0.307882	
chunk0001_7_1	chr1	818924	819211	+	0	NA	non-coding (NR_103536, exon 2 of 2)	non-coding (NR_103536, exon 2 of 2)	1696	NR_103536	400728	Hs.568078	NM_207464	ENSG00000177757	FAM87B	-	family with sequence similarity 87 member B	ncRNA	0.013937	0.517361	58(GGGGACAGTGTGTATT,-,0.00),59(GGGACAGTGTGTATTC,+,0.00)
chunk0031_92_1	chr10	123507414	123507813	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-158742	NM_153442	2849	Hs.12751	NM_153442	ENSG00000154478	GPR26	-	G protein-coupled receptor 26	protein-coding	0.005013	0.430000	
chunk0029_247_1	chr10	102775211	102775916	+	0	NA	promoter-TSS (NM_017787)	promoter-TSS (NM_017787)	-568	NM_017787	54838	Hs.500897	NM_017787	ENSG00000166272	WBP1L	C10orf26|OPA1L|OPAL1	WW domain binding protein 1 like	protein-coding	0.021277	0.490085	312(GGGACTTGTTGTACCT,+,0.00)
chunk0060_230_1	chr14	49493509	49494034	+	0	NA	Intergenic	Intergenic	92645	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.005714	0.454373	227(TAGAACACACTGTACC,-,0.00),228(AGAACACACTGTACCC,+,0.00),280(AGGGACTGTATGTTCA,-,0.00),281(GGGACTGTATGTTCAG,+,0.00)
chunk0043_430_1	chr12	26038473	26038829	+	0	NA	intron (NM_001164747, intron 2 of 5)	(AC)n|Simple_repeat|Simple_repeat	-13907	NM_001164746	11228	Hs.696433	NM_007211	ENSG00000123094	RASSF8	C12orf2|HOJ1	Ras association domain family member 8	protein-coding	0.002809	0.344538	
chunk0013_317_1	chr1	171418504	171419060	+	0	NA	Intergenic	MER4D1|LTR|ERV1	-66745	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.005396	0.423698	
chunk0077_229_1	chr16	80503219	80503484	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-37383	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.003774	0.398496	
chunk0159_158_1	chr5	139397891	139398156	+	0	NA	intron (NM_194296, intron 4 of 5)	L2a|LINE|L2	-2827	NM_001161546	389333	Hs.729482	NM_001161546	ENSG00000228672	PROB1	C5orf65	proline rich basic protein 1	protein-coding	0.018868	0.473684	149(ATGAACGGGATGTCCC,-,0.00),150(TGAACGGGATGTCCCT,+,0.00)
chunk0138_323_1	chr4	41445625	41446013	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	85034	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.005155	0.362468	
chunk0177_212_1	chr7	24124589	24124974	+	0	NA	Intergenic	Intergenic	-159407	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.005195	0.373057	
chunk0167_320_1	chr6	72221853	72222248	+	0	NA	intron (NM_001168410, intron 1 of 21)	intron (NM_001168410, intron 1 of 21)	5290	NM_001168410	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.005063	0.247475	
chunk0014_441_1	chr1	183731938	183732165	+	0	NA	intron (NM_001297669, intron 2 of 18)	intron (NM_001297669, intron 2 of 18)	-73030	NM_001297672	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.017621	0.438596	
chunk0054_123_1	chr13	43307998	43308197	+	0	NA	intron (NM_001127615, intron 11 of 16)	intron (NM_001127615, intron 11 of 16)	-140755	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.015075	0.530000	
chunk0046_281_1	chr12	61813879	61814162	+	0	NA	intron (NM_178539, intron 2 of 4)	L2a|LINE|L2	378819	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.007067	0.345070	
chunk0121_459_1	chr3	27060364	27060764	+	0	NA	Intergenic	L1ME3B|LINE|L1	155959	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.005000	0.324190	
chunk0194_190_1	chr8	85260777	85261050	+	0	NA	intron (NM_198584, intron 3 of 6)	intron (NM_198584, intron 3 of 6)	15426	NM_198584	377677	Hs.127189	NM_198584	ENSG00000185015	CA13	CAXIII	carbonic anhydrase 13	protein-coding	0.007326	0.401460	
chunk0105_426_1	chr2	193275266	193275633	+	0	NA	Intergenic	Intergenic	525604	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.002725	0.345109	
chunk0125_85_1	chr3	64954883	64955601	+	0	NA	intron (NR_038264, intron 4 of 5)	intron (NR_038264, intron 4 of 5)	-267553	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.008357	0.454798	
chunk0212_341_1	chrX	146614700	146615464	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-194702	NM_001144064	100129239	Hs.592233	NM_001144064	ENSG00000224440	CXorf51A	CXorf51|CXorf51B	chromosome X open reading frame 51A	protein-coding	0.020942	0.426144	
chunk0187_262_1	chr7	155003613	155003943	+	0	NA	promoter-TSS (NM_007349)	promoter-TSS (NM_007349)	345	NR_028090	202781	Hs.193172	NR_028090	ENSG00000273344	PAXIP1-AS1	-	PAXIP1 antisense RNA 1 (head to head)	ncRNA	0.118182	0.725076	
chunk0067_114_1	chr15	42498659	42499178	+	0	NA	intron (NM_003825, intron 1 of 7)	intron (NM_003825, intron 1 of 7)	3612	NM_003825	8773	Hs.511149	NM_003825	ENSG00000092531	SNAP23	HsT17016|SNAP-23|SNAP23A|SNAP23B	synaptosome associated protein 23	protein-coding	0.005780	0.375000	
chunk0006_116_1	chr1	65584296	65584932	+	0	NA	intron (NM_001003680, intron 5 of 19)	L1MC4a|LINE|L1	58925	NM_001198687	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.004717	0.353218	184(CTGCACAGTCCGTTCT,-,0.00),185(TGCACAGTCCGTTCTA,+,0.00)
chunk0193_111_1	chr8	74043971	74044335	+	0	NA	Intergenic	Intergenic	52824	NM_001195797	23643	Hs.726603	NM_015364	ENSG00000154589	LY96	ESOP-1|MD-2|MD2|ly-96	lymphocyte antigen 96	protein-coding	0.005495	0.430137	
chunk0191_103_1	chr8	48061386	48061618	+	0	NA	3' UTR (NM_003350, exon 4 of 4)	3' UTR (NM_003350, exon 4 of 4)	53067	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.004310	0.313305	
chunk0176_293_1	chr7	16743171	16743749	+	0	NA	Intergenic	Intergenic	-10266	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.006920	0.329879	
chunk0111_180_1	chr20	25339663	25340050	+	0	NA	intron (NM_001042472, intron 1 of 12)	intron (NM_001042472, intron 1 of 12)	51126	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.033592	0.559278	197(TGGCACGGTGTGTCCT,-,0.00),198(GGCACGGTGTGTCCTT,+,0.00)
chunk0206_234_1	chr9	123591395	123591796	+	0	NA	intron (NM_024820, intron 11 of 20)	L2b|LINE|L2	-105973	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.014963	0.544776	
chunk0059_410_1	chr14	37849303	37849570	+	0	NA	Intergenic	Intergenic	254237	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.000000	0.373134	103(AGGAACATTCTGATCT,-,0.00),104(GGAACATTCTGATCTT,+,0.00)
chunk0176_4_1	chr7	8098841	8099193	+	0	NA	Intergenic	L1PA7|LINE|L1	-130265	NR_110018	100505921	Hs.634989	NR_110018		LOC100505921	-	uncharacterized LOC100505921	ncRNA	0.002841	0.359773	230(GAAGACACAATGTACC,-,0.00)
chunk0003_246_1	chr1	36187981	36188654	+	0	NA	Intergenic	Intergenic	-32264	NM_001270895	27095	Hs.523131	NM_014408	ENSG00000054116	TRAPPC3	BET3	trafficking protein particle complex 3	protein-coding	0.013373	0.547478	298(AGGAACATTCAGTCCA,-,0.00),299(GGAACATTCAGTCCAA,+,0.00)
chunk0168_105_1	chr6	80227545	80227817	+	0	NA	intron (NM_000056, intron 8 of 10)	intron (NM_000056, intron 8 of 10)	121054	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.003676	0.351648	124(AATACAATCTGTTCTT,+,0.00)
chunk0022_363_1	chr10	17299535	17300158	+	0	NA	Intergenic	Intergenic	-69861	NR_108061	100507347	Hs.740502	NR_108060	ENSG00000229124	VIM-AS1	-	VIM antisense RNA 1	ncRNA	0.003210	0.301282	
chunk0016_71_1	chr1	193704475	193704998	+	0	NA	Intergenic	Intergenic	399991	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.003824	0.307252	
chunk0020_81_1	chr1	232745756	232746262	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-3294	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.007905	0.406312	189(AAGAACATAAAGTACA,-,0.00),190(AGAACATAAAGTACAT,+,0.00)
chunk0122_84_1	chr3	29969487	29969734	+	0	NA	intron (NM_001003793, intron 12 of 14)	intron (NM_001003793, intron 12 of 14)	-35454	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.004049	0.383065	
chunk0087_301_1	chr18	39276105	39276307	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	345969	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.019802	0.497537	
chunk0145_274_1	chr4	149589696	149590330	+	0	NA	Intergenic	Intergenic	435718	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.004732	0.324409	261(TGGGACACACTGTCCT,-,0.00),262(GGGACACACTGTCCTT,+,0.00)
chunk0077_144_1	chr16	78866271	78867012	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	734084	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.013495	0.448787	501(GGGGACAGTCTGTAAT,-,0.00)
chunk0140_1_1	chr4	65190864	65191211	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-186537	NR_033976	401134	Hs.165899	NR_033976	ENSG00000250125	LINC02232	-	long intergenic non-protein coding RNA 2232	ncRNA	0.005764	0.301724	
chunk0051_357_1	chr12	120700911	120701247	+	0	NA	3' UTR (NM_001303627, exon 5 of 5)	3' UTR (NM_001303627, exon 5 of 5)	-9356	NM_001080533	84747	Hs.127610	NM_032661	ENSG00000175970	UNC119B	POC7B	unc-119 lipid binding chaperone B	protein-coding	0.008929	0.498516	
chunk0060_179_1	chr14	46580991	46581292	+	0	NA	Intergenic	Intergenic	70684	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.013289	0.394040	
chunk0027_67_1	chr10	73124200	73124794	+	0	NA	intron (NR_104264, intron 5 of 8)	intron (NR_104264, intron 5 of 8)	14122	NM_015901	25961	Hs.533657	NM_015901	ENSG00000166321	NUDT13	-	nudix hydrolase 13	protein-coding	0.003367	0.384874	
chunk0163_193_1	chr6	11685874	11686438	+	0	NA	Intergenic	Intergenic	92891	NM_032744	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.008865	0.481416	
chunk0206_372_1	chr9	126081112	126081477	+	0	NA	Intergenic	Intergenic	194621	NR_121584	101929116	Hs.382124	NR_121584	ENSG00000228392	LOC101929116	-	uncharacterized LOC101929116	ncRNA	0.005479	0.445355	
chunk0135_321_1	chr3	190047376	190047575	+	0	NA	intron (NM_001134418, intron 1 of 14)	L1MA5|LINE|L1	-73489	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.000000	0.340000	
chunk0181_394_1	chr7	89694831	89695030	+	0	NA	Intergenic	L1MA1|LINE|L1	-424470	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.005025	0.505000	
chunk0085_280_1	chr18	7883424	7883650	+	0	NA	intron (NM_001105244, intron 2 of 32)	intron (NM_001105244, intron 2 of 32)	316221	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.013274	0.400881	
chunk0003_375_1	chr1	39552921	39553471	+	0	NA	intron (NR_003929, intron 3 of 8)	intron (NR_003929, intron 3 of 8)	6502	NR_003929	728448	Hs.472508	NR_003929	ENSG00000243970	PPIEL	PPIEP1	peptidylprolyl isomerase E like pseudogene	pseudo	0.005455	0.410163	
chunk0001_359_1	chr1	10032709	10032981	+	0	NA	promoter-TSS (NM_006048)	promoter-TSS (NM_006048)	-138	NM_001105562	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.132353	0.761905	
chunk0124_278_1	chr3	57538317	57538843	+	0	NA	intron (NM_198564, intron 2 of 11)	intron (NM_198564, intron 2 of 11)	5764	NM_001291661	201625	Hs.201378	NM_178504	ENSG00000174844	DNAH12	DHC3|DLP12|DLP3|DNAH12L|DNAH7L|DNAHC12|DNAHC3|DNHD2|HDHC3|HL-19|HL19	dynein axonemal heavy chain 12	protein-coding	0.005703	0.392789	235(AAGTACATTGTGTTAT,-,0.00)
chunk0109_32_1	chr20	510527	510832	+	0	NA	intron (NM_001895, intron 1 of 12)	L1MC4|LINE|L1	33159	NM_177559	1457	Hs.644056	NM_001895	ENSG00000101266	CSNK2A1	CK2A1|CKII|Cka1|Cka2|OCNDS	casein kinase 2 alpha 1	protein-coding	0.009836	0.398693	
chunk0013_437_1	chr1	173482302	173482573	+	0	NA	intron (NM_004905, intron 2 of 4)	L2a|LINE|L2	5090	NM_004905	9588	Hs.120	NM_004905	ENSG00000117592	PRDX6	1-Cys|AOP2|HEL-S-128m|NSGPx|PRX|aiPLA2|p29	peroxiredoxin 6	protein-coding	0.007380	0.371324	
chunk0094_366_1	chr2	9661470	9661669	+	0	NA	Intergenic	Intergenic	-30514	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.040201	0.595000	
chunk0043_310_1	chr12	22172856	22173167	+	0	NA	Intergenic	MER30|DNA|hAT-Charlie	126835	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.000000	0.368590	
chunk0165_102_1	chr6	32337209	32337648	+	0	NA	intron (NM_001286475, intron 11 of 23).3	intron (NM_001286475, intron 11 of 23).3	34484	NM_006781	10665	Hs.567414	NM_006781	ENSG00000204296	TSBP1	C6orf10|TSBP	testis expressed basic protein 1	protein-coding	0.009112	0.445455	
chunk0094_377_1	chr2	9939955	9940595	+	0	NA	Intergenic	Intergenic	-11388	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.007812	0.355694	
chunk0017_198_1	chr1	207588815	207589124	+	0	NA	intron (NM_000651, intron 35 of 46)	intron (NM_000651, intron 35 of 46)	-56144	NM_175710	1379	Hs.628568	NM_175710	ENSG00000197721	CR1L	-	complement C3b/C4b receptor 1 like	protein-coding	0.003236	0.390323	171(GAGGGCAACATGTTCC,-,0.00),172(AGGGCAACATGTTCCT,+,0.00)
chunk0070_422_1	chr15	77885575	77885830	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	41144	NR_027024	645752	Hs.546408	NR_027024		LOC645752	-	golgin A6 family member A pseudogene	pseudo	0.023529	0.480469	
chunk0199_104_1	chr9	3239025	3239689	+	0	NA	intron (NM_001282116, intron 15 of 16)	intron (NM_001282116, intron 15 of 16)	57768	NR_121585	101929247	Hs.547178	NR_121585		LINC01231	-	long intergenic non-protein coding RNA 1231	ncRNA	0.007530	0.392481	
chunk0174_383_1	chr6	165027858	165028854	+	0	NA	Intergenic	Intergenic	-206293	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.008032	0.365095	745(AAGCACAAAATGTACA,-,0.00)
chunk0187_53_1	chr8	1803883	1804155	+	0	NA	Intergenic	Intergenic	2894	NR_037445	100500912		NR_037445	ENSG00000283858	MIR3674	-	microRNA 3674	ncRNA	0.003676	0.347985	
chunk0147_378_1	chr4	186109799	186110232	+	0	NA	Intergenic	Intergenic	-34826	NM_015398	25854	Hs.744961	NM_015398	ENSG00000109794	FAM149A	MST119|MSTP119	family with sequence similarity 149 member A	protein-coding	0.000000	0.352535	
chunk0072_449_1	chr15	101694243	101694459	+	0	NA	intron (NM_152334, intron 10 of 18)	intron (NM_152334, intron 10 of 18)	30091	NM_152334	123283	Hs.657163	NM_152334	ENSG00000185418	TARSL2	-	threonyl-tRNA synthetase like 2	protein-coding	0.009259	0.520737	
chunk0069_89_1	chr15	61199568	61200227	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	29406	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.009105	0.454545	305(CAGAACGAGCTGTGCC,-,0.00),306(AGAACGAGCTGTGCCG,+,0.00)
chunk0008_381_1	chr1	96972107	96972557	+	0	NA	Intergenic	Intergenic	-123591	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.013333	0.385809	
chunk0091_147_1	chr19	7346504	7346783	+	0	NA	Intergenic	Intergenic	-48470	NM_015318	23370	Hs.465761	NM_015318	ENSG00000104880	ARHGEF18	P114-RhoGEF|RP78|SA-RhoGEF|p114RhoGEF	Rho/Rac guanine nucleotide exchange factor 18	protein-coding	0.021505	0.539286	
chunk0031_399_1	chr10	131431713	131431917	+	0	NA	Intergenic	L2b|LINE|L2	-120094	NM_174937	256536	Hs.126575	NM_174937	ENSG00000176769	TCERG1L	-	transcription elongation regulator 1 like	protein-coding	0.019608	0.536585	
chunk0024_7_1	chr10	32686775	32687005	+	0	NA	intron (NM_024688, intron 4 of 22)	MER76-int|LTR|ERVL	119167	NM_024688	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.008696	0.437229	201(TAAGACAAACTGTTCC,-,0.00),202(AAGACAAACTGTTCCT,+,0.00)
chunk0119_336_1	chr22	46936518	46936963	+	0	NA	intron (NR_104292, intron 10 of 13)	intron (NR_104292, intron 10 of 13)	-20698	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.020225	0.437220	
chunk0148_335_1	chr5	14265376	14265642	+	0	NA	intron (NM_007118, intron 1 of 56)	intron (NM_007118, intron 1 of 56)	121789	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.003759	0.280899	
chunk0126_136_1	chr3	76154192	76154687	+	0	NA	Intergenic	Intergenic	-368856	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.004040	0.336694	
chunk0115_31_1	chr21	20902438	20903013	+	0	NA	Intergenic	Intergenic	-95590	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.005217	0.314236	304(GAGAACATTTTGACCT,-,0.00)
chunk0203_408_1	chr9	90836251	90836797	+	0	NA	intron (NM_001174167, intron 1 of 13)	Tigger2b_Pri|DNA|TcMar-Tigger	9104	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.007326	0.340037	260(CAGTACACACTGTACT,-,0.00),261(AGTACACACTGTACTG,+,0.00)
chunk0146_119_1	chr4	158997844	158998422	+	0	NA	intron (NM_152543, intron 1 of 4)	MER58B|DNA|hAT-Charlie	37048	NM_152543	152940	Hs.415576	NM_152543	ENSG00000164123	C4orf45	-	chromosome 4 open reading frame 45	protein-coding	0.003460	0.374784	
chunk0063_252_1	chr14	82705631	82705830	+	0	NA	Intergenic	L1PA13|LINE|L1	-1082669	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.010050	0.500000	
chunk0167_29_1	chr6	53837861	53838073	+	0	NA	intron (NM_018214, intron 1 of 13)	intron (NM_018214, intron 1 of 13)	42987	NM_018214	55227	Hs.606493	NM_018214	ENSG00000137269	LRRC1	LANO|dJ523E19.1	leucine rich repeat containing 1	protein-coding	0.004717	0.441315	57(TTGTACAGAATGTGCT,-,0.00),58(TGTACAGAATGTGCTC,+,0.00)
chunk0143_249_1	chr4	114773358	114773557	+	0	NA	Intergenic	Intergenic	116698	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.000000	0.405000	
chunk0036_131_1	chr11	61854041	61854395	+	0	NA	intron (NM_004265, intron 5 of 11)	intron (NM_004265, intron 5 of 11)	24060	NR_106804	102465446		NR_106804	ENSG00000277892	MIR6746	hsa-mir-6746	microRNA 6746	ncRNA	0.028249	0.591549	
chunk0028_370_1	chr10	92758409	92759035	+	0	NA	Intergenic	L1ME4b|LINE|L1	68798	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.004792	0.311005	
chunk0122_205_1	chr3	33167779	33168207	+	0	NA	intron (NM_015551, intron 4 of 4)	intron (NM_015551, intron 4 of 4)	51222	NM_015551	26032	Hs.196647	NM_015551	ENSG00000173705	SUSD5	-	sushi domain containing 5	protein-coding	0.004673	0.489510	
chunk0015_94_1	chr1	185040328	185040527	+	0	NA	Intergenic	Intergenic	-4992	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.000000	0.330000	
chunk0057_431_1	chr13	110431573	110432171	+	0	NA	intron (NM_001846, intron 10 of 47)	intron (NM_001846, intron 10 of 47)	76307	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.015050	0.495826	
chunk0180_119_1	chr7	55464114	55464356	+	0	NA	Intergenic	L1MA4A|LINE|L1	73481	NM_001284284	81552	Hs.488307	NM_030796	ENSG00000154978	VOPP1	ECOP|GASP|WBP1L2	VOPP1 WW domain binding protein	protein-coding	0.004132	0.576132	
chunk0047_180_1	chr12	70696611	70696999	+	0	NA	intron (NM_130846, intron 4 of 9)	L1MB8|LINE|L1	57803	NM_130846	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.000000	0.341902	
chunk0170_169_1	chr6	111662273	111662760	+	0	NA	intron (NM_153048, intron 10 of 10)	L1ME1|LINE|L1	-56242	NM_147686	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.008214	0.401639	
chunk0152_452_1	chr5	66415307	66415544	+	0	NA	Intergenic	L1MB7|LINE|L1	96179	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.000000	0.331933	
chunk0092_234_1	chr19	32539163	32539707	+	0	NA	Intergenic	Intergenic	-41753	NM_004708	9141	Hs.443831	NM_004708	ENSG00000105185	PDCD5	TFAR19	programmed cell death 5	protein-coding	0.016544	0.521101	195(TGACCAGAATGTTCTT,+,0.00)
chunk0130_29_1	chr3	128871690	128872496	+	0	NA	promoter-TSS (NR_034179)	promoter-TSS (NR_034179)	-552	NR_034179	653712	Hs.653243	NR_034179	ENSG00000231305	LOC653712	-	intraflagellar transport 122 homolog (Chlamydomonas) pseudogene	pseudo	0.009926	0.460967	
chunk0137_449_1	chr4	29204792	29205437	+	0	NA	Intergenic	Intergenic	385532	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.006202	0.345201	
chunk0020_373_1	chr1	239805627	239806117	+	0	NA	intron (NM_000740, intron 3 of 4)	intron (NM_000740, intron 3 of 4)	-86753	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.010204	0.356415	
chunk0123_399_1	chr3	48918851	48919127	+	0	NA	exon (NM_001123040, exon 1 of 1)	exon (NM_001123040, exon 1 of 1)	141	NM_006321	10425	Hs.633601	NM_006321	ENSG00000177479	ARIH2	ARI2|TRIAD1	ariadne RBR E3 ubiquitin protein ligase 2	protein-coding	0.141304	0.761733	
chunk0089_184_1	chr18	59866518	59867219	+	0	NA	Intergenic	Intergenic	-33092	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.004280	0.423077	291(GGAAACAGCATGTTCT,-,0.00),292(GAAACAGCATGTTCTT,+,0.00)
chunk0143_351_1	chr4	121957066	121957729	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-5643	NM_001130698	7222	Hs.150981	NM_003305	ENSG00000138741	TRPC3	SCA41|TRP3	transient receptor potential cation channel subfamily C member 3	protein-coding	0.004525	0.426205	
chunk0164_427_1	chr6	27471632	27471831	+	0	NA	intron (NM_007149, intron 2 of 5)	L3|LINE|CR1	1387	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.000000	0.355000	111(AAGAACAGACAGTTTC,-,0.00),112(AGAACAGACAGTTTCC,+,0.00)
chunk0062_169_1	chr14	69451982	69452320	+	0	NA	intron (NM_001252148, intron 3 of 5)	intron (NM_001252148, intron 3 of 5)	-32603	NM_001161498	400224	Hs.509796	NM_001161498	ENSG00000175985	PLEKHD1	UPF0639	pleckstrin homology and coiled-coil domain containing D1	protein-coding	0.002959	0.383481	117(AAGTTCAGTATGTGCC,-,0.00)
chunk0019_390_1	chr1	230215568	230216085	+	0	NA	intron (NM_001291866, intron 3 of 15)	intron (NM_001291866, intron 3 of 15)	148631	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.001934	0.364865	
chunk0053_340_1	chr13	34619628	34619952	+	0	NA	intron (NR_047036, intron 1 of 2)	intron (NR_047036, intron 1 of 2)	20895	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.003086	0.323077	
chunk0128_188_1	chr3	107482524	107482855	+	0	NA	Intergenic	Intergenic	-40247	NM_001276286	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.009063	0.403614	146(CAGAACACCCTGTATT,-,0.00),147(AGAACACCCTGTATTC,+,0.00)
chunk0026_190_1	chr10	63621955	63622324	+	0	NA	3' UTR (NM_001001330, exon 8 of 8)	3' UTR (NM_001001330, exon 8 of 8)	100776	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.002710	0.318919	342(AAGAACATAATGTTTA,-,0.00)
chunk0205_195_1	chr9	109213589	109213921	+	0	NA	exon (NM_019114, exon 17 of 26)	exon (NM_019114, exon 17 of 26)	-46464	NM_014334	23732	Hs.347537	NM_014334	ENSG00000260230	FRRS1L	C9orf4|CG-6|CG6|EIEE37	ferric chelate reductase 1 like	protein-coding	0.012048	0.522523	
chunk0016_335_1	chr1	201778181	201778690	+	0	NA	intron (NM_001167738, intron 1 of 26)	intron (NM_001167738, intron 1 of 26)	-30176	NR_031599	100302158		NR_031599	ENSG00000221028	MIR1231	MIRN1231|hsa-mir-1231	microRNA 1231	ncRNA	0.007859	0.398039	
chunk0118_122_1	chr22	29544822	29545052	+	0	NA	intron (NM_001002877, intron 3 of 20)	intron (NM_001002877, intron 3 of 20)	8718	NM_001002878	8563	Hs.75361	NM_003678	ENSG00000100296	THOC5	C22orf19|Fmip|PK1.3|fSAP79	THO complex 5	protein-coding	0.021739	0.359307	
chunk0074_194_1	chr16	24930459	24930895	+	0	NA	intron (NM_018054, intron 18 of 18)	MER58A|DNA|hAT-Charlie	84446	NM_052944	115584	Hs.164118	NM_052944	ENSG00000158865	SLC5A11	KST1|RKST1|SGLT6|SMIT2	solute carrier family 5 member 11	protein-coding	0.016055	0.482838	
chunk0092_372_1	chr19	36182979	36183222	+	0	NA	exon (NM_152477, exon 5 of 5)	exon (NM_152477, exon 5 of 5)	-30231	NM_001864	1346	Hs.421621	NM_001864	ENSG00000161281	COX7A1	COX7A|COX7AH|COX7AM	cytochrome c oxidase subunit 7A1	protein-coding	0.024691	0.483607	
chunk0149_170_1	chr5	20547693	20547893	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	28080	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.313433	
chunk0014_148_1	chr1	178126036	178126254	+	0	NA	intron (NM_170692, intron 1 of 17)	MIR|SINE|MIR	-32152	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.004587	0.420091	
chunk0109_115_1	chr20	2751297	2751786	+	0	NA	intron (NM_001110514, intron 11 of 17)	intron (NM_001110514, intron 11 of 17)	49105	NM_019609	56265	Hs.659346	NM_019609	ENSG00000088882	CPXM1	CPX1|CPXM	carboxypeptidase X, M14 family member 1	protein-coding	0.042945	0.542857	
chunk0197_381_1	chr8	126951782	126952080	+	0	NA	Intergenic	Intergenic	-61223	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.013423	0.381271	
chunk0052_1_1	chr13	18178910	18179229	+	0	NA	Intergenic	Intergenic	-16228	NR_027278	26080	Hs.448583	NR_027278	ENSG00000279516	FAM230C	LINC00281|NCRNA00281	family with sequence similarity 230 member C	ncRNA	0.000000	0.281250	
chunk0162_288_1	chr6	6259450	6259958	+	0	NA	intron (NM_000129, intron 4 of 14)	intron (NM_000129, intron 4 of 14)	60987	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.005906	0.383104	
chunk0063_384_1	chr14	86730018	86730284	+	0	NA	Intergenic	L1MC4|LINE|L1	-175627	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.003759	0.370787	
chunk0006_103_1	chr1	65427916	65428331	+	0	NA	TTS (NM_001198683)	TTS (NM_001198683)	7407	NM_001198681	54741	Hs.23581	NM_017526	ENSG00000213625	LEPROT	LEPR|OB-RGRP|OBRGRP|VPS55	leptin receptor overlapping transcript	protein-coding	0.004819	0.334135	
chunk0174_21_1	chr6	153044441	153044977	+	0	NA	intron (NM_012419, intron 1 of 4)	MamTip2|DNA|hAT-Tip100	-41894	NM_001301871	54516	Hs.225836	NM_019041	ENSG00000112031	MTRF1L	HMRF1L|MRF1L|mtRF1a	mitochondrial translational release factor 1 like	protein-coding	0.003731	0.340782	340(GGATACAGAATGTCCT,-,0.00),341(GATACAGAATGTCCTA,+,0.00)
chunk0186_1_1	chr7	135477462	135477715	+	0	NA	intron (NM_001008225, intron 1 of 10)	L1ME4b|LINE|L1	32539	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.007905	0.334646	
chunk0081_183_1	chr17	41717754	41718351	+	0	NA	Intergenic	MER34A1|LTR|ERV1	5726	NM_000805	2520	Hs.2681	NM_000805	ENSG00000184502	GAST	GAS	gastrin	protein-coding	0.016750	0.466555	
chunk0112_405_1	chr20	47029775	47030421	+	0	NA	intron (NM_172110, intron 5 of 13)	MER58A|DNA|hAT-Charlie	135474	NM_172110	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.006192	0.420402	
chunk0148_71_1	chr5	2358470	2358704	+	0	NA	Intergenic	Intergenic	-46386	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.017094	0.417021	
chunk0184_26_1	chr7	111958971	111959369	+	0	NA	intron (NM_014705, intron 8 of 51)	intron (NM_014705, intron 8 of 51)	150665	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.017588	0.491228	
chunk0059_160_1	chr14	32308173	32308528	+	0	NA	Intergenic	Intergenic	-20923	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.002817	0.396067	
chunk0093_150_1	chr19	46931014	46931357	+	0	NA	intron (NM_004491, intron 1 of 5)	intron (NM_004491, intron 1 of 5)	12509	NM_004491	2909	Hs.509447	NM_004491	ENSG00000160007	ARHGAP35	GRF-1|GRLF1|P190-A|P190A|p190ARhoGAP|p190RhoGAP	Rho GTPase activating protein 35	protein-coding	0.008746	0.453488	
chunk0001_241_1	chr1	8299970	8300499	+	0	NA	Intergenic	Intergenic	-17851	NM_001080397	50651	Hs.463036	NM_001080397	ENSG00000162426	SLC45A1	DNB5|IDDNPF	solute carrier family 45 member 1	protein-coding	0.007561	0.456604	
chunk0132_144_1	chr3	156464978	156465609	+	0	NA	intron (NM_001308217, intron 6 of 12)	intron (NM_001308217, intron 6 of 12)	-18357	NR_046618	100874084	Hs.131282	NR_046618	ENSG00000242370	KCNAB1-AS1	-	KCNAB1 antisense RNA 1	ncRNA	0.006339	0.376582	
chunk0070_288_1	chr15	74597985	74598574	+	0	NA	TTS (NM_006465)	TTS (NM_006465)	-10093	NM_003992	1198	Hs.511790	NM_001292	ENSG00000179335	CLK3	PHCLK3|PHCLK3/152	CDC like kinase 3	protein-coding	0.025467	0.540678	
chunk0136_202_1	chr4	6966200	6966541	+	0	NA	intron (NM_001113361, intron 2 of 13)	intron (NM_001113361, intron 2 of 13)	-20792	NM_001113363	57533	Hs.518611	NM_020773	ENSG00000132405	TBC1D14	-	TBC1 domain family member 14	protein-coding	0.005865	0.333333	
chunk0049_440_1	chr12	98503840	98504104	+	0	NA	promoter-TSS (NR_038383)	promoter-TSS (NR_038383)	-117	NR_038383	643770	Hs.129589	NR_038383	ENSG00000245017	LINC02453	-	long intergenic non-protein coding RNA 2453	ncRNA	0.087121	0.607547	
chunk0023_237_1	chr10	26976438	26976782	+	0	NA	Intergenic	Intergenic	-34609	NR_026795	387644	Hs.529965	NR_026795	ENSG00000283709	FAM238C	C10orf51|LINC00202|LINC00202-1|NCRNA00202|bB27G4.1	family with sequence similarity 238 member C	ncRNA	0.017442	0.457971	
chunk0030_114_1	chr10	112804455	112804869	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-18834	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.014493	0.455422	159(CAGAACACATTGTCCC,-,0.00),160(AGAACACATTGTCCCG,+,0.00),265(AGGGACTCTGTGTTTC,-,0.00)
chunk0012_18_1	chr1	154885909	154886108	+	0	NA	Intergenic	L1ME4a|LINE|L1	-15730	NM_001204087	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.010050	0.335000	
chunk0100_25_1	chr2	105222161	105222727	+	0	NA	Intergenic	Intergenic	-19299	NM_007227	11250	Hs.590903	NM_007227	ENSG00000135973	GPR45	PSP24|PSP24(ALPHA)|PSP24A	G protein-coupled receptor 45	protein-coding	0.007067	0.432099	
chunk0099_371_1	chr2	101079895	101080840	+	0	NA	intron (NM_001102426, intron 2 of 19)	intron (NM_001102426, intron 2 of 19)	71017	NM_001102426	11138	Hs.442657	NM_007063	ENSG00000204634	TBC1D8	AD3|GRAMD8|HBLP1|TBC1D8A|VRP	TBC1 domain family member 8	protein-coding	0.020106	0.470402	
chunk0208_192_1	chrX	17291439	17292036	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	-83683	NM_198270	4810	Hs.201623	NM_198270	ENSG00000188158	NHS	CTRCT40|CXN|SCML1	NHS actin remodeling regulator	protein-coding	0.003350	0.409699	
chunk0021_434_1	chr1	247680192	247680626	+	0	NA	Intergenic	MER57C1|LTR|ERV1	-7368	NM_001005487	441933	Hs.553834	NM_001005487	ENSG00000197437	OR13G1	OR1-37	olfactory receptor family 13 subfamily G member 1	protein-coding	0.009217	0.383908	
chunk0178_446_1	chr7	41975538	41975865	+	0	NA	intron (NM_000168, intron 12 of 14)	intron (NM_000168, intron 12 of 14)	261318	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.000000	0.347561	
chunk0076_158_1	chr16	67336013	67336782	+	0	NA	intron (NM_018296, intron 1 of 13)	L1MC2|LINE|L1	9553	NM_018296	55282	Hs.125139	NM_018296	ENSG00000159708	LRRC36	RORBP70|XLHSRF2	leucine rich repeat containing 36	protein-coding	0.005202	0.384416	
chunk0070_354_1	chr15	76062328	76062596	+	0	NA	intron (NM_152335, intron 1 of 10)	intron (NM_152335, intron 1 of 10)	2504	NM_152335	123591	Hs.661411	NM_152335	ENSG00000169758	TMEM266	C15orf27|HVRP1|HsHVRP1|hTMEM266	transmembrane protein 266	protein-coding	0.007463	0.408922	
chunk0209_69_1	chrX	37945483	37945765	+	0	NA	Intergenic	Intergenic	-45193	NM_012274	25763	Hs.122959	NM_012274	ENSG00000187516	HYPM	CXorf27|HIP17	huntingtin interacting protein M	protein-coding	0.007092	0.406360	
chunk0115_423_1	chr21	31621379	31621702	+	0	NA	Intergenic	L1MC4a|LINE|L1	-38082	NM_000454	6647	Hs.443914	NM_000454	ENSG00000142168	SOD1	ALS|ALS1|HEL-S-44|IPOA|SOD|hSod1|homodimer	superoxide dismutase 1	protein-coding	0.003096	0.290123	
chunk0155_141_1	chr5	93675130	93676090	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	-54822	NR_031754	100313887		NR_031754	ENSG00000284336	MIR2277	mir-2277	microRNA 2277	ncRNA	0.002083	0.359001	
chunk0143_200_1	chr4	113008207	113008423	+	0	NA	intron (NM_001127493, intron 2 of 46)	intron (NM_001127493, intron 2 of 46)	-41314	NM_020977	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.000000	0.354839	
chunk0120_276_1	chr3	9397046	9397245	+	0	NA	promoter-TSS (NM_001080517)	promoter-TSS (NM_001080517)	349	NR_027007	440944	Hs.598958	NM_001013713	ENSG00000206573	THUMPD3-AS1	SETD5-AS1	THUMPD3 antisense RNA 1	ncRNA	0.095477	0.600000	
chunk0075_120_1	chr16	49717762	49718058	+	0	NA	intron (NM_001271620, intron 3 of 7)	intron (NM_001271620, intron 3 of 7)	104828	NM_015069	23090	Hs.443715	NM_015069	ENSG00000102935	ZNF423	Ebfaz|JBTS19|NPHP14|OAZ|Roaz|ZFP423|Zfp104|hOAZ	zinc finger protein 423	protein-coding	0.010135	0.511785	
chunk0106_18_1	chr2	195656744	195657444	+	0	NA	promoter-TSS (NM_020342)	promoter-TSS (NM_020342)	-34	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.091429	0.584879	
chunk0165_108_1	chr6	32429313	32429905	+	0	NA	Intergenic	MER6|DNA|TcMar-Tigger	-10233	NM_019111	3122	Hs.520048	NM_019111	ENSG00000204287	HLA-DRA	HLA-DRA1	major histocompatibility complex, class II, DR alpha	protein-coding	0.006757	0.369309	
chunk0025_63_1	chr10	49834843	49835409	+	0	NA	intron (NR_130169, intron 13 of 16)	intron (NR_130169, intron 13 of 16)	-72747	NM_001143997	55753	Hs.17860	NM_018245	ENSG00000197444	OGDHL	-	oxoglutarate dehydrogenase like	protein-coding	0.005300	0.396825	
chunk0070_428_1	chr15	78017004	78017247	+	0	NA	intron (NM_015079, intron 7 of 12)	intron (NM_015079, intron 7 of 12)	-22900	NR_026998	91450	Hs.406766	NR_026998		LOC91450	-	uncharacterized LOC91450	ncRNA	0.004115	0.471311	110(TAGGACACTGTGGTCC,-,0.00),111(AGGACACTGTGGTCCA,+,0.00)
chunk0017_192_1	chr1	207352574	207352864	+	0	NA	intron (NR_125349, intron 10 of 10)	MIRb|SINE|MIR	31247	NM_001300904	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.000000	0.340206	
chunk0113_15_1	chr20	49507855	49508058	+	0	NA	exon (NM_000961, exon 10 of 10)	exon (NM_000961, exon 10 of 10)	-25312	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.059113	0.627451	89(GGGCACGTCGTGTTCC,-,0.00),90(GGCACGTCGTGTTCCG,+,0.00)
chunk0109_413_1	chr2	240997226	240997516	+	0	NA	Intergenic	Intergenic	-1467	NM_001080437	25992	Hs.471834	NM_001080437	ENSG00000162804	SNED1	IRE-BP1|SST3|Snep	sushi, nidogen and EGF like domains 1	protein-coding	0.017241	0.584192	
chunk0162_354_1	chr6	7138945	7139524	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	31381	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.001727	0.386207	311(GAGAGCATCCTGTTCT,-,0.00),312(AGAGCATCCTGTTCTG,+,0.00)
chunk0004_314_1	chr1	49346617	49347328	+	0	NA	intron (NM_032785, intron 3 of 13)	MER41C|LTR|ERV1	89561	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.002813	0.383427	
chunk0147_234_1	chr4	182536660	182536903	+	0	NA	intron (NM_001080477, intron 3 of 27)	intron (NM_001080477, intron 3 of 27)	293350	NM_001080477	55714	Hs.130438	NM_001080477	ENSG00000218336	TENM3	MCOPCB9|ODZ3|TNM3|Ten-m3|ten-3	teneurin transmembrane protein 3	protein-coding	0.012346	0.377049	
chunk0045_150_1	chr12	46493709	46494505	+	0	NA	intron (NR_125380, intron 3 of 3)	intron (NR_125380, intron 3 of 3)	110000	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.006281	0.363864	386(AAGCACAGGATGTTCT,-,0.00),387(AGCACAGGATGTTCTT,+,0.00)
chunk0168_416_1	chr6	95366442	95366641	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	210910	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.015075	0.410000	
chunk0208_356_1	chrX	25718778	25719617	+	0	NA	Intergenic	Intergenic	-419146	NM_173699	286514	Hs.350683	NM_173699	ENSG00000176774	MAGEB18	-	MAGE family member B18	protein-coding	0.008343	0.375000	
chunk0203_402_1	chr9	90630015	90630384	+	0	NA	intron (NM_017594, intron 1 of 1)	L2a|LINE|L2	12906	NM_017594	54769	Hs.165636	NM_017594	ENSG00000165023	DIRAS2	Di-Ras2	DIRAS family GTPase 2	protein-coding	0.008130	0.372973	
chunk0090_431_1	chr18	79438992	79439616	+	0	NA	intron (NM_006162, intron 3 of 9)	intron (NM_006162, intron 3 of 9)	39030	NM_001278672	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.049679	0.572800	137(CAGCACGCACTGTTCC,-,0.00),138(AGCACGCACTGTTCCA,+,0.00)
chunk0046_128_1	chr12	57439615	57440127	+	0	NA	intron (NM_005538, intron 1 of 1)	FAM|SINE|Alu	5186	NM_005538	3626	Hs.632722	NM_005538	ENSG00000175189	INHBC	IHBC	inhibin subunit beta C	protein-coding	0.005859	0.403509	
chunk0162_428_1	chr5	180258999	180259877	+	0	NA	intron (NM_001308244, intron 4 of 6)	intron (NM_001308244, intron 4 of 6)	21170	NM_001308244	5601	Hs.484371	NM_002752	ENSG00000050748	MAPK9	JNK-55|JNK2|JNK2A|JNK2ALPHA|JNK2B|JNK2BETA|PRKM9|SAPK|SAPK1a|p54a|p54aSAPK	mitogen-activated protein kinase 9	protein-coding	0.003417	0.403868	
chunk0040_324_1	chr11	118151244	118151715	+	0	NA	intron (NM_174934, intron 1 of 4)	intron (NM_174934, intron 1 of 4)	1436	NM_001142348	6330	Hs.65239	NM_174934	ENSG00000177098	SCN4B	ATFB17|LQT10|Navbeta4	sodium voltage-gated channel beta subunit 4	protein-coding	0.010616	0.497881	
chunk0186_295_1	chr7	142699719	142700255	+	0	NA	Intergenic	Intergenic	33688	NM_001190487	100463482		NM_001190487	ENSG00000270672	MTRNR2L6	HN6	MT-RNR2 like 6	protein-coding	0.000000	0.325885	
chunk0049_382_1	chr12	96047782	96047981	+	0	NA	Intergenic	Intergenic	-4361	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.005025	0.385000	
chunk0072_400_1	chr15	100722979	100723793	+	0	NA	Intergenic	Intergenic	120836	NM_198243	140460	Hs.31845	NM_024708	ENSG00000183475	ASB7	-	ankyrin repeat and SOCS box containing 7	protein-coding	0.009828	0.442945	650(AAGAACAGGCAGTTCT,-,0.00),651(AGAACAGGCAGTTCTG,+,0.00)
chunk0138_33_1	chr4	31193632	31193886	+	0	NA	intron (NR_125935, intron 2 of 4)	intron (NR_125935, intron 2 of 4)	22615	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.000000	0.337255	
chunk0112_103_1	chr20	38259932	38260404	+	0	NA	promoter-TSS (NR_104170)	promoter-TSS (NR_104170)	-7	NR_104170	149684	Hs.628250	NR_104170	ENSG00000285347	LOC149684	-	uncharacterized LOC149684	ncRNA	0.012712	0.528541	
chunk0102_335_1	chr2	152025799	152025998	+	0	NA	intron (NM_001005746, intron 2 of 13)	intron (NM_001005746, intron 2 of 13)	-51927	NM_001005747	785	Hs.120725	NM_000726	ENSG00000182389	CACNB4	CAB4|CACNLB4|EA5|EIG9|EJM|EJM4|EJM6	calcium voltage-gated channel auxiliary subunit beta 4	protein-coding	0.020101	0.400000	
chunk0119_62_1	chr22	40965982	40966330	+	0	NA	intron (NM_014248, intron 3 of 4)	MIRc|SINE|MIR	14809	NM_014248	9978	Hs.474949	NM_014248	ENSG00000100387	RBX1	BA554C12.1|RNF75|ROC1	ring-box 1	protein-coding	0.005747	0.424069	
chunk0176_330_1	chr7	17271195	17271491	+	0	NA	Intergenic	Intergenic	-27309	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.003378	0.511785	
chunk0177_261_1	chr7	25348296	25348932	+	0	NA	Intergenic	Intergenic	-120128	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.006289	0.411303	
chunk0205_2_1	chr9	104767627	104767923	+	0	NA	intron (NR_130760, intron 2 of 5)	intron (NR_130760, intron 2 of 5)	4034	NR_130760	55335	Hs.429294	NM_018376	ENSG00000165028	NIPSNAP3B	FP944|NIPSNAP3|SNAP1	nipsnap homolog 3B	protein-coding	0.006757	0.343434	
chunk0175_434_1	chr6	169617787	169618031	+	0	NA	intron (NM_001202550, intron 18 of 21)	LTR9|LTR|ERV1	84154	NM_182552	253769	Hs.131903	NM_182552	ENSG00000184465	WDR27	-	WD repeat domain 27	protein-coding	0.016393	0.412245	
chunk0179_395_1	chr7	51455902	51456355	+	0	NA	Intergenic	Intergenic	-139310	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.013245	0.418502	
chunk0117_253_1	chr22	23401359	23401762	+	0	NA	intron (NR_003950, intron 2 of 5)	intron (NR_003950, intron 2 of 5)	1052	NR_003950	150244	Hs.386693	NM_152509		ZDHHC8P1	ZDHHC8P	zinc finger DHHC-type containing 8 pseudogene 1	pseudo	0.017370	0.618812	203(CAGGACACCCTGCTCC,-,0.00),204(AGGACACCCTGCTCCT,+,0.00)
chunk0029_433_1	chr10	110045711	110046349	+	0	NA	intron (NM_016824, intron 1 of 14)	Tigger2b_Pri|DNA|TcMar-Tigger	-37649	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.006270	0.322379	
chunk0078_176_1	chr17	4514267	4514497	+	0	NA	intron (NM_001124758, intron 2 of 12)	intron (NM_001124758, intron 2 of 12)	15548	NM_001124758	124976	Hs.22824	NM_001124758	ENSG00000183018	SPNS2	DFNB115|SLC62A2	sphingolipid transporter 2	protein-coding	0.017391	0.614719	
chunk0171_63_1	chr6	121358043	121358368	+	0	NA	Intergenic	Intergenic	-23705	NR_104452	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.003077	0.352761	
chunk0088_117_1	chr18	45651683	45652552	+	0	NA	intron (NM_001242692, intron 11 of 20)	intron (NM_001242692, intron 11 of 20)	37316	NM_007163	8170	Hs.710927	NM_007163	ENSG00000132874	SLC14A2	HUT2|UT-A2|UT2|UTA|UTR|hUT-A6	solute carrier family 14 member 2	protein-coding	0.006904	0.450575	
chunk0066_239_1	chr15	34343161	34343360	+	0	NA	promoter-TSS (NM_001284292)	promoter-TSS (NM_001284292)	-55	NM_001284292	256646	Hs.525769	NM_175741	ENSG00000184507	NUTM1	C15orf55|FAM22H|NUT	NUT midline carcinoma family member 1	protein-coding	0.035176	0.540000	
chunk0121_120_1	chr3	17459662	17460483	+	0	NA	intron (NM_014744, intron 3 of 21)	intron (NM_014744, intron 3 of 21)	239948	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.007308	0.356448	
chunk0199_39_1	chr9	1140778	1140977	+	0	NA	Intergenic	L1M3b|LINE|L1	90257	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.005025	0.535000	
chunk0145_338_1	chr4	150912602	150913193	+	0	NA	intron (NM_001199282, intron 9 of 56)	L1MB2|LINE|L1	102370	NM_001199282	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.008460	0.364865	
chunk0195_351_1	chr8	99634037	99634430	+	0	NA	intron (NM_152564, intron 33 of 61)	intron (NM_152564, intron 33 of 61)	-97372	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.000000	0.347716	
chunk0090_368_1	chr18	77089003	77089431	+	0	NA	intron (NM_001025101, intron 2 of 8)	LTR53|LTR|ERVL	43601	NM_001025101	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.021028	0.578089	
chunk0105_61_1	chr2	183457610	183457908	+	0	NA	Intergenic	L2b|LINE|L2	333404	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.013423	0.371237	
chunk0042_381_1	chr12	10653374	10653934	+	0	NA	intron (NM_018423, intron 1 of 10)	intron (NM_018423, intron 1 of 10)	20638	NM_018423	55359	Hs.24979	NM_018423	ENSG00000060140	STYK1	NOK|SuRTK106	serine/threonine/tyrosine kinase 1	protein-coding	0.003571	0.367201	257(TAGTACAATCTGTACA,-,0.00),258(AGTACAATCTGTACAT,+,0.00)
chunk0033_54_1	chr11	13336470	13336891	+	0	NA	intron (NM_001178, intron 3 of 19)	intron (NM_001178, intron 3 of 19)	58953	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.016627	0.537915	194(CAGCACTGACTGTACT,-,0.00),195(AGCACTGACTGTACTG,+,0.00)
chunk0200_174_1	chr9	19230452	19230694	+	0	NA	promoter-TSS (NM_017925)	promoter-TSS (NM_017925)	-192	NM_017925	55667	Hs.249591	NM_017925	ENSG00000137145	DENND4C	C9orf55|C9orf55B|RAB10GEF|bA513M16.3	DENN domain containing 4C	protein-coding	0.123967	0.711934	
chunk0211_103_1	chrX	111029751	111030030	+	0	NA	intron (NM_001128166, intron 2 of 15)	Tigger2b_Pri|DNA|TcMar-Tigger	-66257	NM_002578	5063	Hs.593599	NM_002578	ENSG00000077264	PAK3	ARA|MRX30|MRX47|OPHN3|PAK-3|PAK3beta|bPAK|beta-PAK	p21 (RAC1) activated kinase 3	protein-coding	0.003584	0.367857	236(CAGTACAGTGTGTACT,-,0.00),237(AGTACAGTGTGTACTA,+,0.00)
chunk0206_378_1	chr9	126389345	126389547	+	0	NA	intron (NM_033446, intron 4 of 9)	intron (NM_033446, intron 4 of 9)	21058	NR_045006	641373	Hs.742606	NR_045006		NRON	NCRNA00194	non-coding repressor of NFAT	ncRNA	0.000000	0.339901	
chunk0185_57_1	chr7	124752333	124752968	+	0	NA	intron (NM_005302, intron 1 of 1)	intron (NM_005302, intron 1 of 1)	13375	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.003150	0.385220	
chunk0078_417_1	chr16	89281410	89281609	+	0	NA	exon (NM_013275, exon 9 of 13)	exon (NM_013275, exon 9 of 13)	-39624	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.040201	0.585000	
chunk0049_254_1	chr12	93711402	93711832	+	0	NA	intron (NR_110092, intron 2 of 2)	L2b|LINE|L2	26206	NR_110092	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.002326	0.431555	237(TGTACTTGCTGTTCCC,+,0.00),259(TGGAACACTCTGACCC,-,0.00),260(GGAACACTCTGACCCT,+,0.00)
chunk0049_409_1	chr12	97159240	97160017	+	0	NA	Intergenic	Intergenic	252162	NM_001135175	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.010296	0.433162	
chunk0074_30_1	chr16	20588507	20588706	+	0	NA	Intergenic	Intergenic	-12233	NM_001105069	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.010050	0.525000	90(AGGGACACTCTGCACC,-,0.00),91(GGGACACTCTGCACCT,+,0.00)
chunk0032_261_1	chr11	8855792	8856326	+	0	NA	intron (NM_005418, intron 2 of 22)	intron (NM_005418, intron 2 of 22)	-44724	NM_139157	6764	Hs.117715	NM_005418	ENSG00000166444	ST5	DENND2B|HTS1|p126	suppression of tumorigenicity 5	protein-coding	0.001873	0.390654	266(GTGAACAGGCTGAACC,-,0.00)
chunk0025_40_1	chr10	49022809	49023127	+	0	NA	intron (NM_001031746, intron 7 of 7)	intron (NM_001031746, intron 7 of 7)	-37381	NR_036182	100422895		NR_036182	ENSG00000264800	MIR4294	-	microRNA 4294	ncRNA	0.003145	0.300940	
chunk0195_249_1	chr8	97763629	97763831	+	0	NA	Intergenic	Intergenic	-11851	NM_018407	55353	Hs.492314	NM_018407	ENSG00000104341	LAPTM4B	LAPTM4beta|LC27	lysosomal protein transmembrane 4 beta	protein-coding	0.019802	0.438424	
chunk0185_134_1	chr7	127008323	127008757	+	0	NA	intron (NR_028041, intron 2 of 10)	intron (NR_028041, intron 2 of 10)	49644	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.000000	0.291954	
chunk0087_250_1	chr18	36886016	36886241	+	0	NA	intron (NM_020776, intron 5 of 9)	intron (NM_020776, intron 5 of 9)	-56912	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.004444	0.393805	
chunk0014_142_1	chr1	177913689	177914049	+	0	NA	Intergenic	Intergenic	56046	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.008333	0.487535	
chunk0162_282_1	chr6	5760605	5761184	+	0	NA	intron (NM_006567, intron 6 of 6)	intron (NM_006567, intron 6 of 6)	-65622	NR_110842	101927950	Hs.571136	NR_110842	ENSG00000270174	LOC101927950	-	uncharacterized LOC101927950	ncRNA	0.018998	0.503448	318(GTACACAGCCTGTCCT,-,0.00),319(TACACAGCCTGTCCTC,+,0.00)
chunk0033_120_1	chr11	14541298	14541758	+	0	NA	intron (NM_148976, intron 2 of 10)	intron (NM_148976, intron 2 of 10)	-21083	NM_001143937	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.008696	0.496746	
chunk0200_53_1	chr9	15552440	15553007	+	0	NA	promoter-TSS (NM_173550)	promoter-TSS (NM_173550)	-376	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.075838	0.630282	57(GGGGACAGGATGCCCT,-,0.00),58(GGGACAGGATGCCCTG,+,0.00)
chunk0203_389_1	chr9	90518550	90518893	+	0	NA	intron (NR_034157, intron 1 of 5)	intron (NR_034157, intron 1 of 5)	64025	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.002915	0.337209	
chunk0141_192_1	chr4	83584697	83585232	+	0	NA	intron (NM_001256421, intron 4 of 12)	Charlie7|DNA|hAT-Charlie	48647	NM_032717	84803	Hs.99196	NM_032717	ENSG00000138678	GPAT3	AGPAT 10|AGPAT10|AGPAT8|AGPAT9|HMFN0839|LPAAT-theta|MAG1	glycerol-3-phosphate acyltransferase 3	protein-coding	0.003738	0.360075	237(GGATACATAATGTTCT,-,0.00),238(GATACATAATGTTCTG,+,0.00)
chunk0068_447_1	chr15	59738673	59739261	+	0	NA	Intergenic	Intergenic	-49524	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.017007	0.483871	
chunk0022_12_1	chr10	7354578	7354894	+	0	NA	intron (NM_001018039, intron 4 of 20)	Zaphod|DNA|hAT-Tip100	54605	NM_001018039	57713	Hs.407983	NM_001018039	ENSG00000198879	SFMBT2	-	Scm like with four mbt domains 2	protein-coding	0.009494	0.400631	
chunk0083_439_1	chr17	72660664	72661113	+	0	NA	intron (NM_001159770, intron 7 of 9)	MER20|DNA|hAT-Charlie	-20416	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.022272	0.517778	
chunk0136_329_1	chr3	195560104	195560303	+	0	NA	Intergenic	Intergenic	-16802	NR_133014	5504	Hs.535731	NM_006241	ENSG00000184203	PPP1R2	IPP-2|IPP2|PPP1R2A	protein phosphatase 1 regulatory inhibitor subunit 2	protein-coding	0.000000	0.540000	
chunk0164_90_1	chr6	20200522	20201180	+	0	NA	intron (NM_001080480, intron 1 of 12)	LTR57|LTR|ERVL	11613	NM_001080480	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.012158	0.490137	
chunk0094_305_1	chr2	8626866	8627281	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	-43281	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.009639	0.471154	
chunk0095_310_1	chr2	20434791	20435355	+	0	NA	Intergenic	MER68|LTR|ERVL	-11998	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.007092	0.449558	
chunk0121_54_1	chr3	15631085	15631419	+	0	NA	intron (NM_001281724, intron 2 of 5)	intron (NM_001281724, intron 2 of 5)	29283	NM_001281725	686	Hs.444197	NM_001281723	ENSG00000169814	BTD	-	biotinidase	protein-coding	0.005988	0.337313	
chunk0201_71_1	chr9	34163572	34163845	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-15297	NM_001171201	51271	Hs.268963	NM_016525	ENSG00000165006	UBAP1	NAG20|SPG80|UAP|UBAP|UBAP-1	ubiquitin associated protein 1	protein-coding	0.003663	0.448905	153(AAGAACATCATGAACT,-,0.00)
chunk0070_282_1	chr15	74546219	74546597	+	0	NA	intron (NM_001307939, intron 2 of 8)	intron (NM_001307939, intron 2 of 8)	5231	NM_001307939	10620	Hs.647642	NM_006465	ENSG00000179361	ARID3B	BDP|DRIL2	AT-rich interaction domain 3B	protein-coding	0.044974	0.583113	
chunk0101_164_1	chr2	128584354	128585070	+	0	NA	Intergenic	L1MEc|LINE|L1	-266115	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.012570	0.345886	210(GAGAACAGACTGTATT,-,0.00),211(AGAACAGACTGTATTC,+,0.00)
chunk0096_414_1	chr2	38152833	38153514	+	0	NA	intron (NR_027252, intron 2 of 2)	Tigger17a|DNA|TcMar-Tigger	22068	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.001468	0.365103	
chunk0058_83_1	chr14	21308250	21308704	+	0	NA	intron (NM_020366, intron 6 of 23)	L2c|LINE|L2	20500	NM_020366	57096	Hs.126035	NM_020366	ENSG00000092200	RPGRIP1	CORD13|LCA6|RGI1|RGRIP|RPGRIP|RPGRIP1d	RPGR interacting protein 1	protein-coding	0.015419	0.421978	
chunk0125_223_1	chr3	67706593	67707403	+	0	NA	intron (NR_109992, intron 3 of 6)	HAL1M8|LINE|L1	52301	NR_109992	101927111	Hs.518057	NR_109992	ENSG00000241316	SUCLG2-AS1	-	SUCLG2 antisense RNA 1 (head to head)	ncRNA	0.006173	0.374846	100(AAAACACAGAGTCCTT,+,0.00),507(GAGTACAGGGAGTTCC,-,0.00),508(AGTACAGGGAGTTCCT,+,0.00)
chunk0136_208_1	chr4	7130854	7131287	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-27694	NR_027441	730971	Hs.591718	NR_027441		LINC02447	-	long intergenic non-protein coding RNA 2447	ncRNA	0.006928	0.486175	
chunk0079_224_1	chr17	15265174	15265789	+	0	NA	promoter-TSS (NM_000304)	promoter-TSS (NM_000304)	-124	NM_000304	5376	Hs.372031	NM_000304	ENSG00000109099	PMP22	CIDP|CMT1A|CMT1E|DSS|GAS-3|GAS3|HMSNIA|HNPP|Sp110	peripheral myelin protein 22	protein-coding	0.008130	0.487013	
chunk0140_295_1	chr4	72884862	72885323	+	0	NA	Intergenic	Intergenic	184667	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.002169	0.320346	178(AAGAAGAGCATGTTCT,-,0.00)
chunk0039_262_1	chr11	102312579	102313153	+	0	NA	Intergenic	Intergenic	-4584	NM_182962	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.006969	0.307826	311(TAGAACAGTATGTTCC,-,0.00),312(AGAACAGTATGTTCCC,+,0.00)
chunk0194_263_1	chr8	86919044	86919913	+	0	NA	intron (NM_173538, intron 3 of 10)	MER57D|LTR|ERV1	53030	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.003452	0.370115	591(AGGAACTCAAAGTACT,-,0.00)
chunk0080_128_1	chr17	27310403	27310644	+	0	NA	intron (NM_015626, intron 7 of 8)	intron (NM_015626, intron 7 of 8)	16443	NM_015626	26118	Hs.446017	NM_015626	ENSG00000109046	WSB1	SWIP1|WSB-1	WD repeat and SOCS box containing 1	protein-coding	0.000000	0.314050	
chunk0152_458_1	chr5	66573831	66574692	+	0	NA	Intergenic	L2a|LINE|L2	-22087	NM_198828	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.005807	0.426914	441(CAGAACTTGCTGTTCT,-,0.00),442(AGAACTTGCTGTTCTG,+,0.00)
chunk0068_22_1	chr15	50834924	50835472	+	0	NA	Intergenic	L1MC5a|LINE|L1	-69485	NM_032802	84888	Hs.401537	NM_032802	ENSG00000138600	SPPL2A	IMP3|PSL2	signal peptide peptidase like 2A	protein-coding	0.005474	0.364299	
chunk0091_18_1	chr19	3176057	3176486	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	-2467	NM_003775	8698	Hs.662006	NM_003775	ENSG00000125910	S1PR4	EDG6|LPC1|S1P4|SLP4	sphingosine-1-phosphate receptor 4	protein-coding	0.025641	0.523256	
chunk0074_286_1	chr16	29740165	29741258	+	0	NA	Intergenic	LTR5B|LTR|ERVK	5308	NM_175900	283897	Hs.331095	NM_175900	ENSG00000185905	C16orf54	-	chromosome 16 open reading frame 54	protein-coding	0.017383	0.472578	350(AGGGACAGAATGCACT,-,0.00),351(GGGACAGAATGCACTG,+,0.00)
chunk0041_253_1	chr11	128916906	128917504	+	0	NA	3' UTR (NM_000890, exon 3 of 3)	3' UTR (NM_000890, exon 3 of 3)	-10974	NR_045767	219833	Hs.689860	NM_145013	ENSG00000174370	C11orf45	-	chromosome 11 open reading frame 45	protein-coding	0.006689	0.530885	
chunk0152_324_1	chr5	62132197	62132884	+	0	NA	Intergenic	Intergenic	-173622	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.002911	0.360465	
chunk0065_51_1	chr15	22745776	22745980	+	0	NA	Intergenic	L1M7|LINE|L1	-11979	NR_040057	283683	Hs.534616	NR_040057	ENSG00000274253	LOC283683	-	uncharacterized LOC283683	ncRNA	0.004902	0.351220	
chunk0082_100_1	chr17	54603372	54603824	+	0	NA	Intergenic	Intergenic	-297093	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.002212	0.353201	
chunk0071_185_1	chr15	83578255	83578560	+	0	NA	intron (NR_125370, intron 6 of 9)	intron (NR_125370, intron 6 of 9)	-75679	NM_207517	57188	Hs.459162	NM_207517	ENSG00000156218	ADAMTSL3	ADAMTSL-3	ADAMTS like 3	protein-coding	0.009836	0.457516	
chunk0092_378_1	chr19	36224486	36224810	+	0	NA	intron (NM_007145, intron 2 of 3)	L1MC5a|LINE|L1	-9564	NM_001042474	147929	Hs.596338	NM_152477	ENSG00000196357	ZNF565	-	zinc finger protein 565	protein-coding	0.015432	0.341538	
chunk0193_274_1	chr8	77282483	77282682	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-168115	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.000000	0.355000	
chunk0191_405_1	chr8	57580488	57580868	+	0	NA	Intergenic	Intergenic	236891	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.007895	0.372703	
chunk0112_116_1	chr20	38455468	38455991	+	0	NA	Intergenic	Intergenic	6360	NR_002986	677837	Hs.16936	NR_002986	ENSG00000199266	SNORA60	ACA60	small nucleolar RNA, H/ACA box 60	snoRNA	0.009560	0.385496	
chunk0067_271_1	chr15	46676608	46676941	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-507432	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.018018	0.443114	
chunk0071_223_1	chr15	84844817	84845496	+	0	NA	intron (NM_020778, intron 5 of 13)	L1MEf|LINE|L1	28476	NM_020778	57538	Hs.459183	NM_020778	ENSG00000136383	ALPK3	CMH27|MAK|MIDORI	alpha kinase 3	protein-coding	0.008837	0.423529	
chunk0145_111_1	chr4	146242188	146242910	+	0	NA	Intergenic	Intergenic	66866	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.030471	0.536653	528(CGGCACATTTTGTGCA,-,0.00),529(GGCACATTTTGTGCAG,+,0.00)
chunk0109_406_1	chr2	240470671	240471346	+	0	NA	Intergenic	Intergenic	-14308	NR_024014	100130449	Hs.655753	NR_024014		LOC100130449	-	uncharacterized LOC100130449	ncRNA	0.010370	0.460059	
chunk0064_75_1	chr14	90384707	90385172	+	0	NA	Intergenic	Intergenic	-12044	NM_006888	801	Hs.282410	NM_006888	ENSG00000198668	CALM1	CALML2|CAM2|CAM3|CAMB|CAMC|CAMI|CAMIII|CPVT4|DD132|LQT14|PHKD|caM	calmodulin 1	protein-coding	0.017204	0.396996	
chunk0109_163_1	chr20	4006621	4007242	+	0	NA	intron (NM_001134338, intron 1 of 6)	intron (NM_001134338, intron 1 of 6)	8476	NM_007219	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.003221	0.421222	
chunk0128_182_1	chr3	107404567	107405164	+	0	NA	Intergenic	Intergenic	-22706	NR_126332	101929579	Hs.552750	NR_126332		LOC101929579	-	uncharacterized LOC101929579	ncRNA	0.001675	0.316054	245(CAGAACATTTTGTGCA,-,0.00),246(AGAACATTTTGTGCAA,+,0.00)
chunk0137_400_1	chr4	27184351	27184973	+	0	NA	Intergenic	Intergenic	-32817	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.016077	0.399679	
chunk0035_139_1	chr11	42843861	42844419	+	0	NA	Intergenic	Intergenic	425229	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.007168	0.425760	
chunk0168_177_1	chr6	84227679	84227944	+	0	NA	promoter-TSS (NM_001286206)	promoter-TSS (NM_001286206)	-176	NM_014895	22832	Hs.485865	NM_014895	ENSG00000135315	CEP162	C6orf84|KIAA1009|QN1	centrosomal protein 162	protein-coding	0.056604	0.560150	
chunk0075_54_1	chr16	47615550	47615970	+	0	NA	intron (NM_001031835, intron 15 of 31)	intron (NM_001031835, intron 15 of 31)	154461	NM_001031835	5257	Hs.78060	NM_000293	ENSG00000102893	PHKB	-	phosphorylase kinase regulatory subunit beta	protein-coding	0.002381	0.344418	
chunk0089_296_1	chr18	63321056	63321792	+	0	NA	Intergenic	Intergenic	-2044	NM_000657	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.025815	0.461330	
chunk0212_84_1	chrY	11690064	11690440	+	0	NA	Intergenic	Intergenic	731338	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.013298	0.379310	
chunk0125_351_1	chr3	71206831	71207226	+	0	NA	intron (NM_032682, intron 5 of 20)	intron (NM_032682, intron 5 of 20)	38137	NM_001244814	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.017722	0.419192	
chunk0116_19_1	chr21	32890323	32890657	+	0	NA	Intergenic	L1MC5a|LINE|L1	-76747	NM_019596	56245	Hs.517235	NM_019596	ENSG00000205929	C21orf62	B37|C21orf120|PRED81	chromosome 21 open reading frame 62	protein-coding	0.008982	0.394030	
chunk0074_160_1	chr16	23362484	23363265	+	0	NA	intron (NM_000336, intron 4 of 12)	intron (NM_000336, intron 4 of 12)	60604	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.012804	0.535806	299(GGGAACACTGTGTCCC,-,0.00),300(GGAACACTGTGTCCCC,+,0.00)
chunk0026_164_1	chr10	63121734	63121933	+	0	NA	Intergenic	Intergenic	-11414	NM_001282405	29982	Hs.449628	NM_030759	ENSG00000148572	NRBF2	COPR|COPR1|COPR2|NRBF-2	nuclear receptor binding factor 2	protein-coding	0.005025	0.450000	
chunk0020_368_1	chr1	239753940	239754624	+	0	NA	intron (NM_000740, intron 3 of 4)	intron (NM_000740, intron 3 of 4)	-35163	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.004386	0.385401	
chunk0006_54_1	chr1	64542097	64542476	+	0	NA	intron (NM_001293274, intron 1 of 25)	intron (NM_001293274, intron 1 of 25)	36372	NM_001293274	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.013193	0.363158	
chunk0039_273_1	chr11	102467375	102467578	+	0	NA	Intergenic	Intergenic	-14432	NM_052932	114908	Hs.503709	NM_052932	ENSG00000152558	TMEM123	KCT3|PORIMIN|PORMIN	transmembrane protein 123	protein-coding	0.000000	0.362745	
chunk0174_451_1	chr6	166472062	166472307	+	0	NA	intron (NM_001006932, intron 11 of 21)	intron (NM_001006932, intron 11 of 21)	-6801	NR_046793	100874353	Hs.675698	NR_046793	ENSG00000232082	RPS6KA2-IT1	-	RPS6KA2 intronic transcript 1	ncRNA	0.012245	0.463415	122(TGGAACAAACAGTTCA,-,0.00),123(GGAACAAACAGTTCAG,+,0.00)
chunk0104_70_1	chr2	171798323	171798877	+	0	NA	intron (NR_047549, intron 12 of 16)	intron (NR_047549, intron 12 of 16)	95706	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.009025	0.394595	
chunk0073_198_1	chr16	9238355	9238935	+	0	NA	Intergenic	Intergenic	146965	NM_014117	29035	Hs.221497	NM_014117	ENSG00000182831	C16orf72	PRO0149	chromosome 16 open reading frame 72	protein-coding	0.001724	0.480207	
chunk0015_179_1	chr1	187085926	187086326	+	0	NA	Intergenic	Intergenic	-6716	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.005000	0.306733	
chunk0046_37_1	chr12	54762418	54762750	+	0	NA	Intergenic	Intergenic	-91931	NM_058173	118430	Hs.348419	NM_058173	ENSG00000172551	MUCL1	SBEM	mucin like 1	protein-coding	0.003012	0.414414	
chunk0085_105_1	chr18	2760326	2761030	+	0	NA	exon (NM_015295, exon 35 of 48)	exon (NM_015295, exon 35 of 48)	-86352	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.004261	0.287943	
chunk0035_356_1	chr11	49069819	49070395	+	0	NA	Intergenic	AluSc|SINE|Alu	-10995	NM_001206631	646754	Hs.740240	NM_001206631	ENSG00000214891	TRIM64C	-	tripartite motif containing 64C	protein-coding	0.012153	0.389948	
chunk0155_236_1	chr5	95646481	95647066	+	0	NA	promoter-TSS (NM_001131065)	promoter-TSS (NM_001131065)	-4	NM_001131066	317671	Hs.399758	NM_173362	ENSG00000175449	RFESD	-	Rieske Fe-S domain containing	protein-coding	0.078632	0.602389	330(GGGGACAGTAAGTTCT,-,0.00),331(GGGACAGTAAGTTCTG,+,0.00)
chunk0008_453_1	chr1	99745046	99745472	+	0	NA	intron (NM_001013660, intron 4 of 16)	Tigger2|DNA|TcMar-Tigger	20534	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.016432	0.447307	
chunk0099_433_1	chr2	102813673	102813900	+	0	NA	intron (NM_144632, intron 4 of 4)	intron (NM_144632, intron 4 of 4)	51755	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.008811	0.407895	
chunk0002_441_1	chr1	28222826	28223202	+	0	NA	intron (NM_014280, intron 2 of 8)	intron (NM_014280, intron 2 of 8)	10017	NM_014280	22826	Hs.433540	NM_014280	ENSG00000126698	DNAJC8	HSPC331|SPF31	DnaJ heat shock protein family (Hsp40) member C8	protein-coding	0.007979	0.533156	
chunk0181_279_1	chr7	86639038	86639444	+	0	NA	Intergenic	Intergenic	-4673	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.002463	0.346437	
chunk0057_81_1	chr13	98473537	98474021	+	0	NA	intron (NM_003576, intron 5 of 10)	intron (NM_003576, intron 5 of 10)	48346	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.014463	0.531959	
chunk0194_334_1	chr8	88985664	88985884	+	0	NA	Intergenic	L1PA13|LINE|L1	-658286	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.004545	0.420814	
chunk0201_171_1	chr9	36102077	36102594	+	0	NA	intron (NM_001316345, intron 14 of 22)	intron (NM_001316345, intron 14 of 22)	-34201	NR_104638	152007	Hs.493819	NM_022343	ENSG00000122694	GLIPR2	C9orf19|GAPR-1|GAPR1	GLI pathogenesis related 2	protein-coding	0.000000	0.376448	
chunk0163_357_1	chr6	15670681	15670924	+	0	NA	Intergenic	Intergenic	-7744	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.000000	0.356557	
chunk0144_421_1	chr4	140596354	140596553	+	0	NA	Intergenic	L1PB2|LINE|L1	-27648	NM_021833	7350	Hs.249211	NM_021833	ENSG00000109424	UCP1	SLC25A7|UCP	uncoupling protein 1	protein-coding	0.010050	0.285000	
chunk0150_155_1	chr5	33959546	33960088	+	0	NA	intron (NM_001297417, intron 2 of 3)	MamRep434|DNA|TcMar-Tigger	23431	NM_016568	51289	Hs.170146	NM_016568	ENSG00000182631	RXFP3	GPCR135|RLN3R1|RXFPR3|SALPR	relaxin family peptide receptor 3	protein-coding	0.012915	0.353591	
chunk0191_120_1	chr8	48303135	48303808	+	0	NA	Intergenic	Intergenic	-248096	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.013373	0.485163	
chunk0082_425_1	chr17	61374927	61375450	+	0	NA	intron (NM_017679, intron 23 of 23)	intron (NM_017679, intron 23 of 23)	24418	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.003824	0.375954	
chunk0051_193_1	chr12	116276634	116276833	+	0	NA	intron (NM_015335, intron 1 of 30)	CpG	453	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.070352	0.595000	
chunk0066_298_1	chr15	35546138	35546359	+	0	NA	promoter-TSS (NM_001141972)	promoter-TSS (NM_001141972)	-45	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.153846	0.765766	
chunk0011_363_1	chr1	153122900	153123428	+	0	NA	Intergenic	L1PBa|LINE|L1	-9649	NM_001014450	6705	Hs.490252	NM_001014450	ENSG00000244094	SPRR2F	-	small proline rich protein 2F	protein-coding	0.005682	0.533081	
chunk0044_89_1	chr12	28278372	28278978	+	0	NA	intron (NM_018318, intron 2 of 11)	L2c|LINE|L2	21475	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.001650	0.324547	303(AAGTACTTGCTGTTCC,-,0.00),304(AGTACTTGCTGTTCCC,+,0.00)
chunk0160_31_1	chr5	149345299	149345760	+	0	NA	5' UTR (NM_152407, exon 1 of 4)	5' UTR (NM_152407, exon 1 of 4)	115	NM_152407	134266	Hs.511816	NM_152407	ENSG00000164284	GRPEL2	Mt-GrpE#2	GrpE like 2, mitochondrial	protein-coding	0.088937	0.636364	
chunk0020_431_1	chr1	241718036	241718355	+	0	NA	intron (NM_144625, intron 8 of 26)	L2c|LINE|L2	65917	NM_144625	128025	Hs.97527	NM_144625	ENSG00000162843	WDR64	-	WD repeat domain 64	protein-coding	0.015674	0.406250	
chunk0092_315_1	chr19	34594776	34595148	+	0	NA	promoter-TSS (NM_001025591)	promoter-TSS (NM_001025591)	-377	NM_001025591	284402	Hs.656990	NM_001025591	ENSG00000205209	SCGB2B2	SCGB4A2|SCGBL	secretoglobin family 2B member 2	protein-coding	0.005376	0.477212	
chunk0031_274_1	chr10	128052561	128052854	+	0	NA	intron (NM_001316676, intron 7 of 21)	intron (NM_001316676, intron 7 of 21)	5158	NM_130435	5791	Hs.127022	NM_006504	ENSG00000132334	PTPRE	HPTPE|PTPE|R-PTP-EPSILON	protein tyrosine phosphatase receptor type E	protein-coding	0.017065	0.537415	
chunk0190_345_1	chr8	39239809	39240338	+	0	NA	intron (NM_001313994, intron 13 of 21)	L1PB1|LINE|L1	-74590	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.007561	0.337736	283(CAGAACATTCTGCCCC,-,0.00),284(AGAACATTCTGCCCCA,+,0.00)
chunk0062_34_1	chr14	67057278	67057944	+	0	NA	intron (NM_001024218, intron 9 of 21)	L1PA10|LINE|L1	-131782	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.001502	0.400300	
chunk0060_94_1	chr14	42608963	42609433	+	0	NA	Intergenic	Intergenic	1001637	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.004255	0.365180	
chunk0130_436_1	chr3	140956767	140957553	+	0	NA	intron (NM_018155, intron 2 of 6)	intron (NM_018155, intron 2 of 6)	15340	NM_018155	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.006361	0.316391	
chunk0118_96_1	chr22	29145388	29145852	+	0	NA	3' UTR (NM_001039570, exon 9 of 9)	3' UTR (NM_001039570, exon 9 of 9)	-60292	NM_133455	129080	Hs.289106	NM_133455	ENSG00000186998	EMID1	EMI5|EMU1	EMI domain containing 1	protein-coding	0.034483	0.602151	231(AGGCACACGGTGCCCT,-,0.00),232(GGCACACGGTGCCCTG,+,0.00)
chunk0212_205_1	chrX	134688267	134688575	+	0	NA	intron (NM_001316887, intron 2 of 3)	intron (NM_001316887, intron 2 of 3)	-29938	NM_001316889	10761	Hs.496811	NM_021796	ENSG00000170965	PLAC1	CT92|OOSP2B|OOSP2L	placenta enriched 1	protein-coding	0.003247	0.394822	
chunk0189_157_1	chr8	23163513	23164035	+	0	NA	intron (NM_003840, intron 1 of 8)	CpG	256	NM_003840	8793	Hs.213467	NM_003840	ENSG00000173530	TNFRSF10D	CD264|DCR2|TRAIL-R4|TRAILR4|TRUNDD	TNF receptor superfamily member 10d	protein-coding	0.093870	0.661568	396(CGGGACGCTTTGTCCC,-,0.00),397(GGGACGCTTTGTCCCC,+,0.00)
chunk0133_18_1	chr3	165700833	165701283	+	0	NA	Intergenic	Intergenic	136407	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.004444	0.368071	
chunk0031_332_1	chr10	129345109	129345482	+	0	NA	Intergenic	Intergenic	-121889	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.010724	0.358289	
chunk0080_96_1	chr17	26870415	26870630	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	423474	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.032558	0.379630	
chunk0170_34_1	chr6	109336620	109337087	+	0	NA	Intergenic	Intergenic	42550	NR_028595	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.006424	0.480769	
chunk0082_36_1	chr17	50866245	50866592	+	0	NA	promoter-TSS (NM_005749)	promoter-TSS (NM_005749)	-64	NM_005749	10140	Hs.703321	NM_005749	ENSG00000141232	TOB1	APRO5|APRO6|PIG49|TOB|TROB|TROB1	transducer of ERBB2, 1	protein-coding	0.146974	0.778736	
chunk0070_91_1	chr15	70291700	70291991	+	0	NA	Intergenic	Intergenic	-193928	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.013746	0.568493	
chunk0110_102_1	chr20	11678771	11679063	+	0	NA	Intergenic	MIRc|SINE|MIR	191798	NR_110635	728450	Hs.560990	NR_110635	ENSG00000228422	LINC00687	C20orf61|dJ1012F16.1	long intergenic non-protein coding RNA 687	ncRNA	0.000000	0.392491	153(AGGCCATGATGTTCCC,+,0.00)
chunk0038_2_1	chr11	80724978	80725551	+	0	NA	Intergenic	L1ME1|LINE|L1	37539	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003490	0.327526	
chunk0005_396_1	chr1	62341705	62342309	+	0	NA	Intergenic	MIR|SINE|MIR	-22595	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.009934	0.418182	
chunk0064_388_1	chr14	99076453	99076834	+	0	NA	Intergenic	L1ME4c|LINE|L1	195070	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.002625	0.369110	
chunk0145_77_1	chr4	145734403	145734844	+	0	NA	Intergenic	Intergenic	54419	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.015873	0.511312	
chunk0013_144_1	chr1	168466312	168466628	+	0	NA	intron (NR_125956, intron 4 of 4)	intron (NR_125956, intron 4 of 4)	29174	NR_125956	101928565	Hs.563806	NR_125956	ENSG00000228697	LOC101928565	-	uncharacterized LOC101928565	ncRNA	0.012658	0.476341	
chunk0059_194_1	chr14	33219989	33220626	+	0	NA	intron (NM_173159, intron 3 of 11)	intron (NM_173159, intron 3 of 11)	281054	NM_001164749	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.007849	0.420063	
chunk0156_36_1	chr5	102595817	102596016	+	0	NA	intron (NR_047462, intron 1 of 1)	intron (NR_047462, intron 1 of 1)	14548	NR_047462	100861468	Hs.519483	NR_047462	ENSG00000250958	LINC00492	-	long intergenic non-protein coding RNA 492	ncRNA	0.015075	0.355000	
chunk0016_214_1	chr1	198995389	198995978	+	0	NA	intron (NR_110525, intron 2 of 2)	intron (NR_110525, intron 2 of 2)	-20450	NR_126351	104266961	Hs.576501	NR_126351	ENSG00000235492	LINC01221	TCONS_00000366	long intergenic non-protein coding RNA 1221	ncRNA	0.003396	0.342373	
chunk0190_276_1	chr8	37608937	37609429	+	0	NA	Intergenic	MIRc|SINE|MIR	-86568	NM_025069	80139	Hs.288042	NM_025069	ENSG00000183779	ZNF703	NLZ1|ZEPPO1|ZNF503L|ZPO1	zinc finger protein 703	protein-coding	0.008130	0.383367	
chunk0140_66_1	chr4	67147453	67147930	+	0	NA	Intergenic	L2a|LINE|L2	274309	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.002096	0.389121	
chunk0022_378_1	chr10	17584897	17585096	+	0	NA	Intergenic	MER57A1|LTR|ERV1	32378	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.010050	0.390000	
chunk0121_405_1	chr3	25597471	25598307	+	0	NA	TTS (NR_110893)	TTS (NR_110893)	66483	NM_001068	7155	Hs.475733	NM_001068	ENSG00000077097	TOP2B	TOPIIB|top2beta	DNA topoisomerase II beta	protein-coding	0.003589	0.350060	
chunk0186_66_1	chr7	137055044	137055385	+	0	NA	intron (NR_046103, intron 1 of 3)	L1M5|LINE|L1	109127	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.002933	0.263158	
chunk0061_219_1	chr14	60562339	60562715	+	0	NA	Intergenic	Intergenic	53307	NM_007374	4990	Hs.194756	NM_007374	ENSG00000184302	SIX6	MCOPCT2|ODRMD|OPTX2|Six9	SIX homeobox 6	protein-coding	0.010638	0.427056	
chunk0046_96_1	chr12	56759227	56759949	+	0	NA	Intergenic	Intergenic	-3630	NM_003725	8630	Hs.524513	NM_003725	ENSG00000025423	HSD17B6	HSE|RODH|SDR9C6	hydroxysteroid 17-beta dehydrogenase 6	protein-coding	0.008310	0.366528	
chunk0171_310_1	chr6	129271119	129271529	+	0	NA	intron (NM_001079823, intron 17 of 63)	intron (NM_001079823, intron 17 of 63)	388183	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.007317	0.372263	
chunk0159_383_1	chr5	146368179	146368476	+	0	NA	Intergenic	Intergenic	29303	NM_002700	5459	Hs.553499	NM_002700	ENSG00000091010	POU4F3	BRN3C|DFNA15|DFNA42|DFNA52	POU class 4 homeobox 3	protein-coding	0.003367	0.406040	
chunk0052_66_1	chr13	21297948	21298151	+	0	NA	promoter-TSS (NR_046461)	promoter-TSS (NR_046461)	-76	NR_046461	650794	Hs.147563	NR_038939		MIPEPP3	-	mitochondrial intermediate peptidase pseudogene 3	pseudo	0.108374	0.656863	
chunk0209_347_1	chrX	53010742	53011137	+	0	NA	Intergenic	L1MEc|LINE|L1	-15467	NM_014138	29057	Hs.6451	NM_014138	ENSG00000268350	FAM156A	PRO0659|TMEM29	family with sequence similarity 156 member A	protein-coding	0.000000	0.272727	
chunk0181_360_1	chr7	88409235	88409434	+	0	NA	Intergenic	Intergenic	-102421	NM_024636	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.015075	0.360000	132(TGGCACATTATGTACC,-,0.00),133(GGCACATTATGTACCT,+,0.00)
chunk0123_332_1	chr3	47521130	47521529	+	0	NA	Intergenic	Intergenic	-7620	NM_001031703	54859	Hs.311100	NM_017713	ENSG00000163832	ELP6	C3orf75|TMEM103	elongator acetyltransferase complex subunit 6	protein-coding	0.017544	0.552500	
chunk0207_391_1	chr9	136625233	136625823	+	0	NA	Intergenic	Intergenic	-33328	NR_046367	51162	Hs.91481	NM_016215	ENSG00000172889	EGFL7	NEU1|VE-STATIN|ZNEU1	EGF like domain multiple 7	protein-coding	0.022034	0.600677	
chunk0137_31_1	chr4	11048655	11049390	+	0	NA	Intergenic	L1MA10|LINE|L1	-319805	NR_030298	693157		NR_030298	ENSG00000207716	MIR572	MIRN572|hsa-mir-572	microRNA 572	ncRNA	0.004082	0.385870	
chunk0209_265_1	chrX	46727391	46727946	+	0	NA	intron (NM_001257291, intron 1 of 16)	intron (NM_001257291, intron 1 of 16)	31504	NM_032591	84679	Hs.91389	NM_032591	ENSG00000065923	SLC9A7	MRX108|NHE-7|NHE7|SLC9A6	solute carrier family 9 member A7	protein-coding	0.012613	0.390288	
chunk0124_263_1	chr3	57134160	57134669	+	0	NA	intron (NM_017563, intron 1 of 12)	intron (NM_017563, intron 1 of 12)	30961	NM_017563	54756	Hs.150725	NM_017563	ENSG00000144730	IL17RD	HH18|IL-17RD|IL17RLM|SEF	interleukin 17 receptor D	protein-coding	0.021611	0.511765	334(ATCACAGCCTGTACCT,+,0.00)
chunk0036_307_1	chr11	66061695	66062159	+	0	NA	exon (NM_006842, exon 16 of 22)	exon (NM_006842, exon 16 of 22)	-8426	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.015086	0.466667	
chunk0161_340_1	chr5	173953412	173954044	+	0	NA	intron (NM_030627, intron 9 of 9)	(T)n|Simple_repeat|Simple_repeat	-35431	NM_001144954	133491	Hs.131469	NM_001144954	ENSG00000185056	C5orf47	-	chromosome 5 open reading frame 47	protein-coding	0.007911	0.366509	
chunk0148_214_1	chr5	8665966	8666229	+	0	NA	Intergenic	Intergenic	-173635	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.007605	0.303030	
chunk0106_434_1	chr2	208481687	208481915	+	0	NA	intron (NM_001309516, intron 10 of 12)	intron (NM_001309516, intron 10 of 12)	74971	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.000000	0.318777	
chunk0167_436_1	chr6	75856879	75857264	+	0	NA	intron (NM_001300899, intron 12 of 32)	intron (NM_001300899, intron 12 of 32)	107879	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.002597	0.357513	
chunk0179_457_1	chr7	52791113	52791832	+	0	NA	Intergenic	Intergenic	-244184	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.005563	0.325000	
chunk0147_363_1	chr4	185817422	185817998	+	0	NA	intron (NM_021069, intron 1 of 20)	intron (NM_021069, intron 1 of 20)	-5454	NM_001145670	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.017361	0.464471	
chunk0024_305_1	chr10	42629504	42629729	+	0	NA	intron (NR_130949, intron 3 of 5)	L1MDa|LINE|L1	9221	NM_001305038	7582	Hs.435774	NM_006955	ENSG00000196693	ZNF33B	KOX2|KOX31|ZNF11B	zinc finger protein 33B	protein-coding	0.004444	0.283186	
chunk0195_185_1	chr8	96448830	96449029	+	0	NA	Intergenic	Intergenic	-44725	NM_002998	6383	Hs.1501	NM_002998	ENSG00000169439	SDC2	CD362|HSPG|HSPG1|SYND2	syndecan 2	protein-coding	0.000000	0.455000	
chunk0208_139_1	chrX	15640778	15641048	+	0	NA	intron (NM_020665, intron 4 of 5)	L2c|LINE|L2	24118	NM_020665	57393	Hs.129614	NM_020665	ENSG00000147003	CLTRN	NX-17|NX17|TMEM27	collectrin, amino acid transport regulator	protein-coding	0.007407	0.453875	101(TGGTACAAAATGTTCT,-,0.00),102(GGTACAAAATGTTCTG,+,0.00)
chunk0048_19_1	chr12	77163034	77163383	+	0	NA	Intergenic	Intergenic	-97628	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.005731	0.348571	
chunk0153_327_1	chr5	74067890	74068298	+	0	NA	Intergenic	HAL1|LINE|L1	240231	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.002451	0.352078	
chunk0204_404_1	chr9	102702229	102702803	+	0	NA	Intergenic	Intergenic	182879	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.010453	0.297391	
chunk0047_84_1	chr12	68024395	68025046	+	0	NA	Intergenic	L2a|LINE|L2	35275	NR_104125	100885789	Hs.439832	NR_104124	ENSG00000255733	IFNG-AS1	GS1-410F4.2|NEST|Tmevpg1	IFNG antisense RNA 1	ncRNA	0.003072	0.400307	
chunk0003_312_1	chr1	37940138	37940748	+	0	NA	intron (NM_005540, intron 6 of 23)	intron (NM_005540, intron 6 of 23)	6614	NM_005540	3633	Hs.449942	NM_005540	ENSG00000204084	INPP5B	5PTase	inositol polyphosphate-5-phosphatase B	protein-coding	0.009836	0.520458	
chunk0195_223_1	chr8	97261535	97261963	+	0	NA	intron (NR_125390, intron 2 of 2)	MLT1K|LTR|ERVL-MaLR	16199	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.007009	0.461538	
chunk0026_414_1	chr10	70448308	70448967	+	0	NA	Intergenic	AluSz|SINE|Alu	-6928	NM_018055	4838	Hs.370414	NM_018055	ENSG00000156574	NODAL	HTX5	nodal growth differentiation factor	protein-coding	0.015175	0.493939	
chunk0118_37_1	chr22	27516484	27516753	+	0	NA	Intergenic	L2|LINE|L2	284880	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.011152	0.455556	
chunk0074_410_1	chr16	35539466	35539908	+	0	NA	Intergenic	Intergenic	-32517	NR_034018	100130700	Hs.97712	NR_034018		TP53TG3HP	-	TP53 target 3 family member H, pseudogene	pseudo	0.000000	0.386005	418(AGGAACTCTCTGTGCT,-,0.00),419(GGAACTCTCTGTGCTG,+,0.00)
chunk0132_437_1	chr3	165100637	165101278	+	0	NA	Intergenic	Intergenic	-22462	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.001560	0.364486	271(CAGAACATTCTGTCCT,-,0.00),272(AGAACATTCTGTCCTT,+,0.00)
chunk0206_315_1	chr9	125160678	125161265	+	0	NA	intron (NM_001123355, intron 3 of 7)	intron (NM_001123355, intron 3 of 7)	-17412	NM_173690	286205	Hs.59504	NM_173690	ENSG00000173611	SCAI	C9orf126|NET40	suppressor of cancer cell invasion	protein-coding	0.005111	0.338435	
chunk0160_283_1	chr5	157912576	157913521	+	0	NA	Intergenic	Intergenic	-53873	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.011640	0.448203	830(AAGTACTCTCTGTTCT,-,0.00),831(AGTACTCTCTGTTCTC,+,0.00)
chunk0151_384_1	chr5	55250146	55250701	+	0	NA	Intergenic	L1MA9|LINE|L1	-16706	NR_125346	10309	Hs.3041	NM_021147	ENSG00000152669	CCNO	CCNU|CILD29|UDG2	cyclin O	protein-coding	0.003604	0.314748	
chunk0055_290_1	chr13	65153188	65153450	+	0	NA	Intergenic	MIRc|SINE|MIR	-712728	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.003817	0.342205	
chunk0188_231_1	chr8	13061313	13061663	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	49224	NM_001099677	57604	Hs.202521	NM_020844	ENSG00000250305	TRMT9B	C8orf79|KIAA1456|TRM9L|hTRM9L	tRNA methyltransferase 9B (putative)	protein-coding	0.005714	0.336182	
chunk0042_155_1	chr12	3897052	3897303	+	0	NA	Intergenic	L3|LINE|CR1	-23729	NM_001286521	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.000000	0.412698	
chunk0203_176_1	chr9	86126930	86127811	+	0	NA	promoter-TSS (NR_110996)	promoter-TSS (NR_110996)	-170	NR_110996	101927623	Hs.575644	NR_110996		LOC101927623	-	uncharacterized LOC101927623	ncRNA	0.014756	0.502268	
chunk0006_120_1	chr1	65754495	65755014	+	0	NA	Intergenic	MIRc|SINE|MIR	-37756	NM_001037341	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.001927	0.357692	
chunk0080_37_1	chr17	21209843	21210142	+	0	NA	intron (NM_003876, intron 1 of 1)	intron (NM_003876, intron 1 of 1)	4603	NM_003876	8834	Hs.592945	NM_003876	ENSG00000178307	TMEM11	C17orf35|PM1|PMI	transmembrane protein 11	protein-coding	0.036789	0.610000	
chunk0082_97_1	chr17	54409909	54410375	+	0	NA	Intergenic	(TGTAT)n|Simple_repeat|Simple_repeat	-490549	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.000000	0.334047	
chunk0125_249_1	chr3	68975110	68975545	+	0	NA	non-coding (NR_103826, exon 16 of 16)	non-coding (NR_103826, exon 16 of 16)	38567	NR_103826	285203	Hs.518059	NM_173654	ENSG00000163378	EOGT	AER61|AOS4|C3orf64|EOGT1	EGF domain specific O-linked N-acetylglucosamine transferase	protein-coding	0.004598	0.293578	
chunk0175_18_1	chr7	342313	342512	+	0	NA	Intergenic	Intergenic	-37013	NR_033960	442497	Hs.704269	NR_033960	ENSG00000249574	LOC442497	-	uncharacterized LOC442497	ncRNA	0.050251	0.610000	
chunk0149_24_1	chr5	16164923	16165657	+	0	NA	intron (NM_001102562, intron 2 of 3)	L1MC3|LINE|L1	14498	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.008174	0.379592	
chunk0010_231_1	chr1	116376288	116376827	+	0	NA	intron (NM_001160233, intron 1 of 22)	intron (NM_001160233, intron 1 of 22)	2690	NM_001160233	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.007421	0.464815	
chunk0059_426_1	chr14	38243537	38244437	+	0	NA	Intergenic	Intergenic	12383	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.003333	0.362930	
chunk0072_283_1	chr15	98256573	98256773	+	0	NA	Intergenic	MIRb|SINE|MIR	-167920	NR_120325	101927332		NR_120325		LINC01582	-	long intergenic non-protein coding RNA 1582	ncRNA	0.010000	0.477612	
chunk0136_343_1	chr3	195736365	195736806	+	0	NA	Intergenic	Intergenic	15703	NM_020790	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.013605	0.321267	
chunk0092_73_1	chr19	20590805	20591031	+	0	NA	Intergenic	Intergenic	-25098	NM_001159293	100129842	Hs.515696	NM_001159293	ENSG00000237440	ZNF737	ZNF102	zinc finger protein 737	protein-coding	0.000000	0.418502	
chunk0142_67_1	chr4	93067536	93067972	+	0	NA	intron (NM_001286838, intron 2 of 14)	L2a|LINE|L2	-761173	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.002294	0.308924	
chunk0192_277_1	chr8	66170721	66171193	+	0	NA	intron (NM_033058, intron 10 of 10)	Charlie24|DNA|hAT-Charlie	7654	NM_000756	1392	Hs.75294	NM_000756	ENSG00000147571	CRH	CRF|CRH1	corticotropin releasing hormone	protein-coding	0.008475	0.380550	
chunk0036_86_1	chr11	60841969	60842232	+	0	NA	5' UTR (NM_024098, exon 1 of 4)	5' UTR (NM_024098, exon 1 of 4)	144	NM_024098	79080	Hs.4253	NM_024098	ENSG00000110104	CCDC86	-	coiled-coil domain containing 86	protein-coding	0.102662	0.670455	
chunk0100_161_1	chr2	109193754	109194262	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	-52420	NR_036223	100422863		NR_036223	ENSG00000264934	MIR4265	-	microRNA 4265	ncRNA	0.011811	0.502947	268(TAGAACAGTCTGTTCT,-,0.00),269(AGAACAGTCTGTTCTG,+,0.00)
chunk0196_136_1	chr8	104278078	104279006	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	55207	NM_001282882	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.004310	0.457481	107(AAGAACATTATGTACT,-,0.00),108(AGAACATTATGTACTA,+,0.00)
chunk0072_423_1	chr15	101027595	101028044	+	0	NA	intron (NM_024652, intron 19 of 33)	intron (NM_024652, intron 19 of 33)	108604	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.040089	0.600000	244(TGGAACTGTCTGTACT,-,0.00),245(GGAACTGTCTGTACTT,+,0.00)
chunk0094_7_1	chr2	776614	776821	+	0	NA	Intergenic	L1M5|LINE|L1	91709	NR_111963	339822	Hs.651879	NR_033880	ENSG00000237667	LINC01115	-	long intergenic non-protein coding RNA 1115	ncRNA	0.024155	0.514423	
chunk0048_441_1	chr12	88552732	88553273	+	0	NA	intron (NM_000899, intron 1 of 9)	intron (NM_000899, intron 1 of 9)	27471	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.003697	0.339483	
chunk0059_286_1	chr14	35669684	35670193	+	0	NA	intron (NM_001283043, intron 26 of 41)	intron (NM_001283043, intron 26 of 41)	135896	NM_032594	84684	Hs.62813	NM_032594	ENSG00000168348	INSM2	IA-6|IA6|mlt1	INSM transcriptional repressor 2	protein-coding	0.005894	0.394118	
chunk0060_20_1	chr14	39621093	39621626	+	0	NA	Intergenic	Intergenic	-188859	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.005629	0.355805	
chunk0043_40_1	chr12	13369653	13369967	+	0	NA	TTS (NR_036555)	TTS (NR_036555)	6935	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.006369	0.476190	
chunk0088_108_1	chr18	45367328	45367767	+	0	NA	intron (NM_001242692, intron 1 of 20)	intron (NM_001242692, intron 1 of 20)	139489	NR_110899	101927980	Hs.591058	NR_110899		SLC14A2-AS1	-	SLC14A2 antisense RNA 1	ncRNA	0.002278	0.404545	
chunk0157_345_1	chr5	122775179	122775380	+	0	NA	5' UTR (NM_001278199, exon 1 of 15)	5' UTR (NM_001278199, exon 1 of 15)	283	NM_001278199	6643	Hs.125352	NM_003100	ENSG00000205302	SNX2	TRG-9	sorting nexin 2	protein-coding	0.074627	0.658416	
chunk0173_253_1	chr6	147049491	147049903	+	0	NA	intron (NR_034115, intron 5 of 10)	L2a|LINE|L2	-109228	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.004854	0.404358	
chunk0129_104_1	chr3	119601919	119602801	+	0	NA	intron (NM_001293225, intron 1 of 10)	L1M5|LINE|L1	2089	NM_001293225	51365	Hs.437451	NM_015900	ENSG00000144837	PLA1A	PS-PLA1|PSPLA1	phospholipase A1 member A	protein-coding	0.003401	0.330691	
chunk0115_400_1	chr21	30574708	30575203	+	0	NA	Intergenic	Intergenic	-13666	NM_181614	337974	Hs.553696	NM_181614	ENSG00000244362	KRTAP19-7	KAP19.7	keratin associated protein 19-7	protein-coding	0.010101	0.340726	
chunk0075_103_1	chr16	48498222	48498774	+	0	NA	Intergenic	Intergenic	111711	NM_153029	9683	Hs.511839	NM_153029	ENSG00000102921	N4BP1	-	NEDD4 binding protein 1	protein-coding	0.010870	0.575045	
chunk0160_423_1	chr5	164331366	164331997	+	0	NA	Intergenic	Intergenic	135721	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.009509	0.311709	
chunk0017_139_1	chr1	206616816	206617502	+	0	NA	Intergenic	L1MD|LINE|L1	-4608	NM_001201478	1939	Hs.497581	NM_006893	ENSG00000143486	EIF2D	HCA56|LGTN	eukaryotic translation initiation factor 2D	protein-coding	0.013120	0.398836	
chunk0143_223_1	chr4	113959265	113959615	+	0	NA	intron (NM_024590, intron 1 of 1)	intron (NM_024590, intron 1 of 1)	20282	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.005714	0.344729	
chunk0116_304_1	chr21	40563959	40564887	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	66344	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.010776	0.433800	
chunk0024_377_1	chr10	44636619	44636818	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-251621	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.005025	0.405000	
chunk0157_267_1	chr5	120100098	120100726	+	0	NA	Intergenic	L1MA5|LINE|L1	-363866	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.003185	0.319555	
chunk0085_416_1	chr18	10469363	10469901	+	0	NA	intron (NM_153000, intron 2 of 4)	L2a|LINE|L2	15004	NM_153000	147495	Hs.293274	NM_153000	ENSG00000154856	APCDD1	B7323|DRAPC1|FP7019|HHS|HTS|HYPT1	APC down-regulated 1	protein-coding	0.003717	0.406308	
chunk0151_258_1	chr5	52404435	52404844	+	0	NA	Intergenic	Intergenic	-383301	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.002445	0.341463	
chunk0107_269_1	chr2	217692208	217692498	+	0	NA	intron (NR_026597, intron 1 of 12)	intron (NR_026597, intron 1 of 12)	64240	NR_026597	729582	Hs.572788	NR_026597		DIRC3	-	disrupted in renal carcinoma 3	ncRNA	0.010345	0.529210	122(TTGAACAACCAGTTCT,-,0.00),123(TGAACAACCAGTTCTC,+,0.00)
chunk0021_147_1	chr10	4238174	4238390	+	0	NA	intron (NR_108040, intron 2 of 2)	intron (NR_108040, intron 2 of 2)	5630	NR_108040	100652988	Hs.433011	NR_108040		LINC00702	-	long intergenic non-protein coding RNA 702	ncRNA	0.013889	0.539171	
chunk0172_20_1	chr6	132893695	132894639	+	0	NA	Intergenic	Intergenic	20161	NR_039664									0.010593	0.413757	
chunk0114_415_1	chr20	63974581	63975085	+	0	NA	3' UTR (NM_080621, exon 5 of 5)	3' UTR (NM_080621, exon 5 of 5)	4809	NM_080621	140700	Hs.27189	NM_080621	ENSG00000130590	SAMD10	C20orf136|dJ591C20|dJ591C20.7	sterile alpha motif domain containing 10	protein-coding	0.021825	0.582178	
chunk0009_448_1	chr1	111576641	111576896	+	0	NA	Intergenic	Intergenic	-12765	NM_001302680	57413	Hs.281342	NM_020683	ENSG00000121933	TMIGD3	AD026	transmembrane and immunoglobulin domain containing 3	protein-coding	0.019608	0.503906	
chunk0089_43_1	chr18	58057314	58057599	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	10230	NM_001144964	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.014035	0.524476	
chunk0058_161_1	chr14	23301550	23301778	+	0	NA	exon (NM_001276318, exon 2 of 5)	exon (NM_001276318, exon 2 of 5)	1184	NM_001276318	90673	Hs.601513	NM_001276318	ENSG00000235194	PPP1R3E	-	protein phosphatase 1 regulatory subunit 3E	protein-coding	0.188596	0.794760	
chunk0031_338_1	chr10	129550131	129550333	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	83048	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.054455	0.581281	74(GGGTTCACAATGTTCC,-,0.00),75(GGTTCACAATGTTCCG,+,0.00)
chunk0147_73_1	chr4	172962386	172963216	+	0	NA	intron (NM_001034845, intron 10 of 12)	intron (NM_001034845, intron 10 of 12)	-205952	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.013253	0.439230	
chunk0047_266_1	chr12	72953321	72953676	+	0	NA	Intergenic	MIR|SINE|MIR	-205692	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.002817	0.351124	
chunk0097_67_1	chr2	44190753	44191009	+	0	NA	intron (NM_177969, intron 1 of 4)	intron (NM_177969, intron 1 of 4)	22078	NM_177969	5495	Hs.416769	NM_002706	ENSG00000138032	PPM1B	PP2C-beta|PP2C-beta-X|PP2CB|PP2CBETA|PPC2BETAX	protein phosphatase, Mg2+/Mn2+ dependent 1B	protein-coding	0.003906	0.291829	
chunk0047_277_1	chr12	73095635	73095881	+	0	NA	Intergenic	Intergenic	-63432	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.400810	
chunk0036_375_1	chr11	67465123	67465636	+	0	NA	intron (NR_073409, intron 4 of 6)	L2c|LINE|L2	3898	NM_001078651	80194	Hs.288761	NM_025124	ENSG00000172663	TMEM134	-	transmembrane protein 134	protein-coding	0.009747	0.570039	
chunk0211_120_1	chrX	112235619	112236018	+	0	NA	intron (NM_001004308, intron 2 of 2)	intron (NM_001004308, intron 2 of 2)	152793	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.000000	0.400000	
chunk0018_391_1	chr1	222546108	222546876	+	0	NA	intron (NM_024746, intron 1 of 8)	intron (NM_024746, intron 1 of 8)	1610	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.014323	0.470741	
chunk0148_171_1	chr5	7497697	7498009	+	0	NA	intron (NM_020546, intron 2 of 24)	Charlie10b|DNA|hAT-Charlie	101623	NM_020546	108	Hs.481545	NM_020546	ENSG00000078295	ADCY2	AC2|HBAC2	adenylate cyclase 2	protein-coding	0.006410	0.357827	
chunk0194_278_1	chr8	87245122	87246174	+	0	NA	intron (NM_173538, intron 6 of 10)	intron (NM_173538, intron 6 of 10)	379200	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.005703	0.260209	
chunk0007_188_1	chr1	80847027	80847352	+	0	NA	Intergenic	MIRb|SINE|MIR	205902	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.003077	0.331288	
chunk0060_386_1	chr14	52815225	52815820	+	0	NA	Intergenic	L1MEc|LINE|L1	-23854	NM_198066	64841	Hs.478025	NM_198066	ENSG00000100522	GNPNAT1	GNA1|GNPNAT|Gpnat1	glucosamine-phosphate N-acetyltransferase 1	protein-coding	0.005042	0.380872	327(AGGAGAGGATGTTCTG,+,0.00)
chunk0202_190_1	chr9	74900902	74901412	+	0	NA	Intergenic	Intergenic	-13063	NM_017662	140803	Hs.272225	NM_017662	ENSG00000119121	TRPM6	CHAK2|HMGX|HOMG|HOMG1|HSH	transient receptor potential cation channel subfamily M member 6	protein-coding	0.000000	0.358121	
chunk0126_241_1	chr3	79343164	79343482	+	0	NA	intron (NM_002941, intron 2 of 30)	L1MC1|LINE|L1	-68404	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.015723	0.329154	
chunk0054_224_1	chr13	45464672	45464944	+	0	NA	promoter-TSS (NM_031431)	promoter-TSS (NM_031431)	-87	NM_031431	83548	Hs.507948	NM_031431	ENSG00000136152	COG3	SEC34	component of oligomeric golgi complex 3	protein-coding	0.069853	0.534799	
chunk0109_178_1	chr20	4678826	4679068	+	0	NA	Intergenic	Intergenic	-7204	NM_001080121	5621	Hs.472010	NM_000311	ENSG00000171867	PRNP	ASCR|AltPrP|CD230|CJD|GSS|KURU|PRIP|PrP|PrP27-30|PrP33-35C|PrPc|p27-30	prion protein	protein-coding	0.012397	0.547325	
chunk0123_111_1	chr3	42254333	42255038	+	0	NA	Intergenic	Intergenic	9262	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.007092	0.502833	
chunk0131_150_1	chr3	146115725	146116097	+	0	NA	intron (NM_000935, intron 3 of 18)	MER58A|DNA|hAT-Charlie	45584	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.002688	0.378016	
chunk0180_391_1	chr7	74643093	74643641	+	0	NA	Intergenic	Intergenic	-14298	NM_033000	2969	Hs.647041	NM_001518	ENSG00000263001	GTF2I	BAP135|BTKAP1|DIWS|GTFII-I|IB291|SPIN|TFII-I|WBS|WBSCR6	general transcription factor IIi	protein-coding	0.027372	0.515483	
chunk0172_386_1	chr6	139512007	139512315	+	0	NA	Intergenic	L1ME3E|LINE|L1	-37565	NR_033919	645434	Hs.666240	NR_033919	ENSG00000238099	LINC01625	-	long intergenic non-protein coding RNA 1625	ncRNA	0.000000	0.294498	
chunk0092_363_1	chr19	35775265	35775464	+	0	NA	promoter-TSS (NM_052948)	promoter-TSS (NM_052948)	-151	NM_001172630	115703	Hs.515364	NM_052948	ENSG00000004777	ARHGAP33	NOMA-GAP|SNX26|TCGAP	Rho GTPase activating protein 33	protein-coding	0.060302	0.620000	
chunk0134_438_1	chr3	183643436	183643985	+	0	NA	intron (NM_017644, intron 2 of 7)	intron (NM_017644, intron 2 of 7)	8087	NM_017644	54800	Hs.407709	NM_017644	ENSG00000114796	KLHL24	DRE1|EBSSH|KRIP6	kelch like family member 24	protein-coding	0.001821	0.310909	
chunk0033_116_1	chr11	14476611	14476908	+	0	NA	intron (NM_001144061, intron 12 of 21)	intron (NM_001144061, intron 12 of 21)	23099	NM_016451	1315	Hs.339278	NM_016451	ENSG00000129083	COPB1	COPB	coatomer protein complex subunit beta 1	protein-coding	0.000000	0.285235	180(CAGAACATTTTGTTCA,-,0.00),181(AGAACATTTTGTTCAA,+,0.00)
chunk0149_287_1	chr5	25345462	25345705	+	0	NA	Intergenic	Intergenic	-505000	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.012346	0.372951	
chunk0199_68_1	chr9	2367878	2368186	+	0	NA	Intergenic	L1MA5A|LINE|L1	209576	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.000000	0.559871	
chunk0011_315_1	chr1	151930038	151930489	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-20378	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.006652	0.382743	
chunk0175_147_1	chr7	3667636	3668108	+	0	NA	intron (NM_152744, intron 4 of 44)	L1ME1|LINE|L1	366424	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.002119	0.348837	
chunk0068_57_1	chr15	51777028	51777379	+	0	NA	intron (NM_014548, intron 5 of 9)	intron (NM_014548, intron 5 of 9)	25642	NM_014548	29767	Hs.513734	NM_014548	ENSG00000128872	TMOD2	N-TMOD|NTMOD	tropomodulin 2	protein-coding	0.005698	0.423295	
chunk0043_63_1	chr12	14195834	14196553	+	0	NA	Intergenic	L1MC1|LINE|L1	-169439	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.012517	0.377778	
chunk0107_370_1	chr2	222884953	222885608	+	0	NA	intron (NM_004457, intron 1 of 16)	L1ME3Cz|LINE|L1	24266	NM_203372	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.004580	0.344512	
chunk0126_359_1	chr3	83046786	83047556	+	0	NA	Intergenic	L1ME3A|LINE|L1	-1285372	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.007792	0.325551	
chunk0212_277_1	chrX	140190352	140190890	+	0	NA	Intergenic	Intergenic	98954	NM_001271560	389895	Hs.127679	NM_001271560		LOC389895	-	chromosome 16 open reading frame 72-like	protein-coding	0.013011	0.376623	255(TGGAACAGTGTGTCCT,-,0.00),256(GGAACAGTGTGTCCTC,+,0.00)
chunk0125_200_1	chr3	67022968	67023257	+	0	NA	Intergenic	Intergenic	24809	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.006920	0.382759	
chunk0139_367_1	chr4	60400452	60400791	+	0	NA	Intergenic	Intergenic	-521998	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.329412	
chunk0038_195_1	chr11	86160683	86160882	+	0	NA	Intergenic	L2c|LINE|L2	-83602	NM_001308007	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.000000	0.375000	
chunk0209_213_1	chrX	44687608	44687936	+	0	NA	Intergenic	Intergenic	-144797	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.006098	0.279635	
chunk0187_45_1	chr8	1588247	1588883	+	0	NA	intron (NM_001277161, intron 3 of 10)	intron (NM_001277161, intron 3 of 10)	33099	NR_103863	100507435	Hs.667133	NR_103863	ENSG00000253267	DLGAP2-AS1	-	DLGAP2 antisense RNA 1	ncRNA	0.014151	0.400314	200(AAAGACAATGTGTTCT,-,0.00),201(AAGACAATGTGTTCTA,+,0.00)
chunk0102_214_1	chr2	148440479	148440937	+	0	NA	intron (NM_018328, intron 5 of 14)	intron (NM_018328, intron 5 of 14)	-204283	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.006550	0.333333	
chunk0003_318_1	chr1	38194473	38195335	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	19863	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.010441	0.432213	
chunk0016_171_1	chr1	197934990	197935739	+	0	NA	Intergenic	Intergenic	17977	NM_020204	56956	Hs.442578	NM_020204	ENSG00000143355	LHX9	-	LIM homeobox 9	protein-coding	0.000000	0.310667	
chunk0154_395_1	chr5	88255935	88256848	+	0	NA	intron (NM_153354, intron 1 of 11)	intron (NM_153354, intron 1 of 11)	12488	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.004381	0.314004	
chunk0055_333_1	chr13	69019049	69019406	+	0	NA	Intergenic	Intergenic	-133902	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.002801	0.296089	
chunk0183_93_1	chr7	105055580	105056178	+	0	NA	intron (NM_018682, intron 2 of 25)	intron (NM_018682, intron 2 of 25)	41689	NM_018682	55904	Hs.592262	NM_018682	ENSG00000005483	KMT2E	HDCMC04P|MLL5|NKp44L	lysine methyltransferase 2E	protein-coding	0.001672	0.355593	
chunk0064_409_1	chr14	99554335	99554582	+	0	NA	intron (NM_001144995, intron 1 of 5)	intron (NM_001144995, intron 1 of 5)	49932	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.032389	0.653226	120(TGGCACAGCGTGATCT,-,0.00),121(GGCACAGCGTGATCTG,+,0.00)
chunk0029_371_1	chr10	107971837	107972344	+	0	NA	intron (NR_125760, intron 4 of 4)	intron (NR_125760, intron 4 of 4)	97203	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.001972	0.336614	
chunk0064_254_1	chr14	94599012	94599688	+	0	NA	Intergenic	Intergenic	-13027	NM_001085	12	Hs.534293	NM_001085	ENSG00000196136	SERPINA3	AACT|ACT|GIG24|GIG25	serpin family A member 3	protein-coding	0.005917	0.536189	
chunk0141_139_1	chr4	81237607	81238010	+	0	NA	Intergenic	L2a|LINE|L2	-22691	NM_001282485	5593	Hs.232044	NM_006259	ENSG00000138669	PRKG2	PKG2|PRKGR2|cGK2|cGKII	protein kinase cGMP-dependent 2	protein-coding	0.002481	0.398515	
chunk0185_447_1	chr7	135008987	135009255	+	0	NA	intron (NM_178563, intron 4 of 16)	L1MB7|LINE|L1	22613	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.007463	0.382900	
chunk0098_269_1	chr2	75362216	75362734	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-161593	NR_110281	101927884	Hs.671110	NR_110281	ENSG00000231172	LOC101927884	-	uncharacterized LOC101927884	ncRNA	0.000000	0.344894	
chunk0033_103_1	chr11	14297983	14298372	+	0	NA	intron (NM_001177314, intron 1 of 5)	intron (NM_001177314, intron 1 of 5)	60308	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.002571	0.333333	
chunk0031_111_1	chr10	124522954	124523250	+	0	NA	intron (NM_022126, intron 6 of 6)	intron (NM_022126, intron 6 of 6)	61330	NM_001167880	64077	Hs.527748	NM_022126	ENSG00000107902	LHPP	HDHD2B	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	protein-coding	0.043919	0.565657	
chunk0211_54_1	chrX	109631680	109632167	+	0	NA	Intergenic	L1ME2z|LINE|L1	-6759	NM_012282	23630	Hs.522753	NM_012282	ENSG00000176076	KCNE5	KCNE1L	potassium voltage-gated channel subfamily E regulatory subunit 5	protein-coding	0.002053	0.358607	
chunk0149_90_1	chr5	17897656	17898101	+	0	NA	Intergenic	Intergenic	-510568	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.011236	0.430493	87(AGGACATTCTGCACCT,+,0.00)
chunk0037_386_1	chr11	78783779	78784261	+	0	NA	intron (NM_001098816, intron 16 of 33)	intron (NM_001098816, intron 16 of 33)	-209156	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.010373	0.395445	
chunk0139_245_1	chr4	55948863	55949106	+	0	NA	5' UTR (NM_025009, exon 1 of 26)	5' UTR (NM_025009, exon 1 of 26)	176	NM_025009	9662	Hs.518767	NM_014645	ENSG00000174799	CEP135	CEP4|KIAA0635|MCPH8	centrosomal protein 135	protein-coding	0.115226	0.709016	
chunk0111_277_1	chr20	31225952	31226182	+	0	NA	Intergenic	Intergenic	-31597	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.026087	0.350649	
chunk0096_190_1	chr2	30048890	30049186	+	0	NA	Intergenic	Intergenic	-97846	NM_001127400	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.016892	0.441077	
chunk0078_408_1	chr16	88944635	88945037	+	0	NA	intron (NM_001290330, intron 1 of 1)	MIR|SINE|MIR	-3636	NM_175931	863	Hs.513811	NM_005187	ENSG00000129993	CBFA2T3	ETO2|MTG16|MTGR2|RUNX1T3|ZMYND4	CBFA2/RUNX1 partner transcriptional co-repressor 3	protein-coding	0.022388	0.565757	
chunk0082_285_1	chr17	58097195	58097819	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	14088	NM_080677	140735	Hs.720595	NM_080677	ENSG00000264364	DYNLL2	DNCL1B|Dlc2|RSPH22	dynein light chain LC8-type 2	protein-coding	0.008013	0.467200	
chunk0198_188_1	chr8	133455475	133456162	+	0	NA	3' UTR (NM_173344, exon 10 of 10)	3' UTR (NM_173344, exon 10 of 10)	116122	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.011645	0.486919	
chunk0161_228_1	chr5	171081245	171081905	+	0	NA	intron (NM_022897, intron 14 of 27)	intron (NM_022897, intron 14 of 27)	219693	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.003030	0.290469	
chunk0168_420_1	chr6	95511676	95511892	+	0	NA	Intergenic	Intergenic	65667	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.267281	
chunk0137_423_1	chr4	28181837	28182131	+	0	NA	Intergenic	L1MA4|LINE|L1	-637598	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.003401	0.325424	
chunk0156_123_1	chr5	106521674	106521919	+	0	NA	Intergenic	Intergenic	489218	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.008163	0.357724	
chunk0144_281_1	chr4	138027151	138027373	+	0	NA	TTS (NR_037866)	TTS (NR_037866)	-61752	NR_038380	641364	Hs.570846	NR_038380	ENSG00000250033	SLC7A11-AS1	-	SLC7A11 antisense RNA 1	ncRNA	0.000000	0.322870	
chunk0108_67_1	chr2	227377635	227377993	+	0	NA	intron (NM_024795, intron 1 of 3)	L1PA13|LINE|L1	1492	NM_024795	79853	Hs.156652	NM_024795	ENSG00000168955	TM4SF20	PRO994|SLI5|TCCE518	transmembrane 4 L six family member 20	protein-coding	0.013966	0.434540	
chunk0082_123_1	chr17	55154770	55155534	+	0	NA	intron (NM_178509, intron 17 of 17)	intron (NM_178509, intron 17 of 17)	-109808	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.001309	0.273203	
chunk0079_72_1	chr17	11529746	11530453	+	0	NA	intron (NM_001173462, intron 3 of 4)	L1M5|LINE|L1	-68332	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.007072	0.354520	
chunk0188_51_1	chr8	6850826	6851025	+	0	NA	Intergenic	(CACACA)n|Simple_repeat|Simple_repeat	-15281	NM_207411	389610	Hs.558840	NM_207411	ENSG00000275591	XKR5	HARL2754|UNQ2754|XRG5A|XRG5BM	XK related 5	protein-coding	0.005025	0.495000	
chunk0022_372_1	chr10	17497537	17498082	+	0	NA	Intergenic	X6B_LINE|LINE|CR1	-43554	NM_001004470	338596	Hs.677766	NM_001004470	ENSG00000148488	ST8SIA6	SIA8F|SIAT8-F|SIAT8F|ST8SIA-VI|ST8SiaVI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	protein-coding	0.011009	0.379121	
chunk0139_80_1	chr4	49150762	49151011	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	164244	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.012048	0.392000	
chunk0201_214_1	chr9	37209867	37210066	+	0	NA	intron (NM_032226, intron 2 of 8)	intron (NM_032226, intron 2 of 8)	89368	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.000000	0.320000	
chunk0062_387_1	chr14	74705416	74705772	+	0	NA	intron (NM_001039479, intron 1 of 19)	intron (NM_001039479, intron 1 of 19)	7510	NM_001039479	9870	Hs.497417	NM_014821	ENSG00000119682	AREL1	FIEL1|KIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding	0.002809	0.380952	
chunk0079_13_1	chr17	9480137	9480738	+	0	NA	intron (NR_033656, intron 4 of 5)	intron (NR_033656, intron 4 of 5)	95521	NM_004853	9482	Hs.431109	NM_004853	ENSG00000170310	STX8	CARB	syntaxin 8	protein-coding	0.008319	0.400332	
chunk0112_54_1	chr20	37192330	37192652	+	0	NA	intron (NM_001135771, intron 2 of 16)	intron (NM_001135771, intron 2 of 16)	-12903	NM_213631	140699	Hs.349125	NM_152503	ENSG00000101353	MROH8	C20orf131|C20orf132	maestro heat like repeat family member 8	protein-coding	0.003106	0.492260	
chunk0206_363_1	chr9	125885797	125886138	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	137768	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.000000	0.353801	
chunk0058_411_1	chr13	112499545	112500098	+	0	NA	intron (NM_006322, intron 19 of 21)	intron (NM_006322, intron 19 of 21)	88364	NM_001286279	10426	Hs.224152	NM_006322	ENSG00000126216	TUBGCP3	104p|ALP6|GCP3|Grip104|SPBC98|Spc98|Spc98p	tubulin gamma complex associated protein 3	protein-coding	0.003617	0.344765	
chunk0049_75_1	chr12	90359783	90360044	+	0	NA	Intergenic	Intergenic	-558110	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.003831	0.251908	
chunk0114_165_1	chr21	13987558	13988153	+	0	NA	Intergenic	L1MB7|LINE|L1	-7411	NR_027270	391267	Hs.364456	NM_153750	ENSG00000215559	ANKRD20A11P	C21orf81	ankyrin repeat domain 20 family member A11, pseudogene	pseudo	0.010084	0.525168	
chunk0002_19_1	chr1	12347647	12347880	+	0	NA	intron (NM_018156, intron 43 of 68)	intron (NM_018156, intron 43 of 68)	117724	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.000000	0.337607	
chunk0170_387_1	chr6	116992262	116992895	+	0	NA	Intergenic	Intergenic	115365	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.001580	0.384858	
chunk0193_399_1	chr8	80551964	80552688	+	0	NA	Intergenic	Intergenic	66113	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.009669	0.386207	
chunk0011_12_1	chr1	125183614	125184176	+	0	NA	Intergenic	Intergenic	3664783	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.044484	0.353464	
chunk0008_155_1	chr1	92473607	92473845	+	0	NA	Intergenic	Intergenic	10073	NM_001127215	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.004202	0.451883	
chunk0085_177_1	chr18	5355059	5355336	+	0	NA	Intergenic	Intergenic	-58144	NM_001243704	7541	Hs.592340	NM_003409	ENSG00000198081	ZBTB14	ZF5|ZFP-161|ZFP-5|ZFP161|ZNF478	zinc finger and BTB domain containing 14	protein-coding	0.003610	0.420863	
chunk0123_338_1	chr3	47744405	47744772	+	0	NA	intron (NM_003074, intron 3 of 27)	intron (NM_003074, intron 3 of 27)	37327	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.000000	0.342391	
chunk0105_4_1	chr2	181660063	181660262	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-3055	NM_001160277	375298	Hs.732358	NM_201548	ENSG00000188452	CERKL	RP26	ceramide kinase like	protein-coding	0.005025	0.495000	
chunk0037_20_1	chr11	69277761	69278544	+	0	NA	Intergenic	Intergenic	-15986	NM_138768	26579	Hs.523848	NM_138768	ENSG00000172927	MYEOV	OCIM	myeloma overexpressed	protein-coding	0.017880	0.585459	
chunk0004_235_1	chr1	47175438	47175643	+	0	NA	Intergenic	Intergenic	-3710	NR_047498	100874253	Hs.435758	NR_047498	ENSG00000224805	LINC00853	PDZK1IP1-AS1|ncRNA-a4	long intergenic non-protein coding RNA 853	ncRNA	0.009756	0.495146	
chunk0090_373_1	chr18	77189625	77190018	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-57003	NM_001025100	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.007634	0.411168	
chunk0136_217_1	chr4	7786661	7786922	+	0	NA	intron (NM_198595, intron 11 of 16)	intron (NM_198595, intron 11 of 16)	32701	NR_026892	84740	Hs.663029	NM_032654	ENSG00000272620	AFAP1-AS1	AFAP1-AS|AFAP1AS	AFAP1 antisense RNA 1	ncRNA	0.011494	0.396947	
chunk0147_315_1	chr4	184937516	184937970	+	0	NA	TTS (NR_039660)	TTS (NR_039660)	697	NR_039660	100616111		NR_039660	ENSG00000263458	MIR4455	-	microRNA 4455	ncRNA	0.013216	0.413187	265(TAGTACTCTCTGTTCC,-,0.00),266(AGTACTCTCTGTTCCC,+,0.00)
chunk0085_403_1	chr18	10235579	10235852	+	0	NA	Intergenic	Intergenic	178655	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.007326	0.448905	
chunk0014_190_1	chr1	178775610	178775828	+	0	NA	intron (NM_001286247, intron 1 of 18)	MIRc|SINE|MIR	50572	NM_152663	55103	Hs.632485	NM_018037	ENSG00000116191	RALGPS2	dJ595C2.1	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.000000	0.319635	
chunk0176_16_1	chr7	8284568	8285099	+	0	NA	intron (NR_125740, intron 3 of 5)	intron (NR_125740, intron 3 of 5)	-22221	NM_001276478	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.001883	0.364662	
chunk0002_334_1	chr1	24570860	24571214	+	0	NA	intron (NM_001010980, intron 1 of 3)	intron (NM_001010980, intron 1 of 3)	14961	NM_001010980	400746	Hs.200253	NM_001010980	ENSG00000184454	NCMAP	C1orf130|MP11	non-compact myelin associated protein	protein-coding	0.014124	0.461972	
chunk0208_109_1	chrX	13811365	13811769	+	0	NA	intron (NM_001001995, intron 1 of 7)	MER58A|DNA|hAT-Charlie	5628	NM_001001995	2824	Hs.495710	NM_005278	ENSG00000046653	GPM6B	M6B	glycoprotein M6B	protein-coding	0.004950	0.338272	
chunk0103_238_1	chr2	164768592	164769022	+	0	NA	intron (NM_001278460, intron 2 of 13)	intron (NM_001278460, intron 2 of 13)	-71942	NR_110574	101929633	Hs.570267	NR_110574		LOC101929633	-	uncharacterized LOC101929633	ncRNA	0.009302	0.317865	
chunk0183_24_1	chr7	103406875	103407383	+	0	NA	intron (NR_120443, intron 7 of 14)	MER119|DNA|hAT-Charlie	36082	NR_120443	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.009843	0.420432	239(TTGAACACTGTGTTCC,-,0.00),240(TGAACACTGTGTTCCT,+,0.00)
chunk0141_140_1	chr4	81238168	81238383	+	0	NA	Intergenic	Intergenic	-23158	NM_001282485	5593	Hs.232044	NM_006259	ENSG00000138669	PRKG2	PKG2|PRKGR2|cGK2|cGKII	protein kinase cGMP-dependent 2	protein-coding	0.000000	0.291667	
chunk0155_213_1	chr5	95123096	95123499	+	0	NA	intron (NM_024717, intron 1 of 22)	intron (NM_024717, intron 1 of 22)	-41431	NM_001297777	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.002481	0.309406	
chunk0174_2_1	chr6	152091144	152091617	+	0	NA	intron (NM_001291230, intron 7 of 8)	intron (NM_001291230, intron 7 of 8)	283701	NM_000125	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.006342	0.436709	
chunk0186_11_1	chr7	135675082	135675611	+	0	NA	3' UTR (NM_001130929, exon 3 of 3)	3' UTR (NM_001130929, exon 3 of 3)	12873	NM_001130929	647087	Hs.200022	NM_001130929	ENSG00000243317	STMP1	C7orf73|PL-5283	short transmembrane mitochondrial protein 1	protein-coding	0.007561	0.330189	
chunk0079_394_1	chr17	19263730	19264282	+	0	NA	intron (NM_001102664, intron 1 of 7)	intron (NM_001102664, intron 1 of 7)	-7387	NR_046824	100874309	Hs.733657	NR_046824		EPN2-IT1	-	EPN2 intronic transcript 1	ncRNA	0.012681	0.446655	
chunk0046_256_1	chr12	60660234	60660613	+	0	NA	Intergenic	Intergenic	971086	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.002639	0.376316	
chunk0125_393_1	chr3	71882776	71883177	+	0	NA	Intergenic	Intergenic	-97770	NM_021935	60675	Hs.528665	NM_021935	ENSG00000163421	PROK2	BV8|HH4|KAL4|MIT1|PK2	prokineticin 2	protein-coding	0.004988	0.383085	
chunk0132_173_1	chr3	156906201	156906873	+	0	NA	intron (NM_001004316, intron 3 of 12)	intron (NM_001004316, intron 3 of 12)	80178	NM_001193283	389170	Hs.478048	NM_001004316	ENSG00000197980	LEKR1	-	leucine, glutamate and lysine rich 1	protein-coding	0.004464	0.320951	
chunk0035_88_1	chr11	42035165	42035364	+	0	NA	Intergenic	L2|LINE|L2	218426	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.005025	0.395000	
chunk0200_65_1	chr9	15836909	15837425	+	0	NA	intron (NM_173550, intron 21 of 25)	intron (NM_173550, intron 21 of 25)	284068	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.011628	0.344294	
chunk0013_168_1	chr1	168758946	168759637	+	0	NA	Intergenic	MIRb|SINE|MIR	-27650	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.005789	0.385838	438(AGGACACTTTGCTCCT,+,0.00)
chunk0132_407_1	chr3	164249257	164249625	+	0	NA	Intergenic	Intergenic	-77885	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.002717	0.338753	185(TGGCACTCTATGTTCT,-,0.00),186(GGCACTCTATGTTCTA,+,0.00)
chunk0136_299_1	chr3	195094821	195095095	+	0	NA	intron (NR_104188, intron 1 of 3)	intron (NR_104188, intron 1 of 3)	370	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.021898	0.563636	
chunk0063_126_1	chr14	79363345	79363684	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	84175	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.005900	0.361765	
chunk0188_201_1	chr8	11863851	11864381	+	0	NA	intron (NM_147781, intron 1 of 10)	L1ME3Cz|LINE|L1	4021	NM_147783	1508	Hs.520898	NM_001908	ENSG00000164733	CTSB	APPS|CPSB|RECEUP	cathepsin B	protein-coding	0.009434	0.423729	
chunk0002_272_1	chr1	21810295	21810872	+	0	NA	Intergenic	AluSx|SINE|Alu	-1682	NM_001013693	401944	Hs.745158	NM_001013693	ENSG00000187942	LDLRAD2	-	low density lipoprotein receptor class A domain containing 2	protein-coding	0.020797	0.461938	
chunk0001_415_1	chr1	11134261	11134620	+	0	NA	exon (NM_004958, exon 37 of 58)	exon (NM_004958, exon 37 of 58)	-9458	NR_046600	100873935	Hs.679133	NR_046600	ENSG00000225602	MTOR-AS1	-	MTOR antisense RNA 1	ncRNA	0.011142	0.552778	
chunk0140_46_1	chr4	66637389	66637645	+	0	NA	Intergenic	Intergenic	360693	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.015625	0.412451	
chunk0163_26_1	chr6	8082870	8083307	+	0	NA	intron (NM_004280, intron 3 of 3)	intron (NM_004280, intron 3 of 3)	3445	NR_003703	100124533		NR_003703		SCARNA27	-	small Cajal body-specific RNA 27	ncRNA	0.011442	0.408676	
chunk0010_201_1	chr1	116123670	116124443	+	0	NA	intron (NM_152367, intron 3 of 6)	intron (NM_152367, intron 3 of 6)	12301	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.020699	0.496124	
chunk0076_226_1	chr16	68722039	68722742	+	0	NA	Intergenic	Intergenic	-14902	NM_004360	999	Hs.461086	NM_004360	ENSG00000039068	CDH1	Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO	cadherin 1	protein-coding	0.007112	0.482955	
chunk0099_416_1	chr2	102342779	102343773	+	0	NA	exon (NM_003856, exon 8 of 8)	exon (NM_003856, exon 8 of 8)	6026	NM_003856	9173	Hs.66	NM_003856	ENSG00000115602	IL1RL1	DER4|FIT-1|IL33R|ST2|ST2L|ST2V|T1	interleukin 1 receptor like 1	protein-coding	0.011066	0.437186	
chunk0051_151_1	chr12	115817249	115817995	+	0	NA	Intergenic	Intergenic	331032	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.013405	0.427041	428(AGGCACATTGAGTACC,-,0.00),429(GGCACATTGAGTACCA,+,0.00)
chunk0092_70_1	chr19	20567780	20568218	+	0	NA	Intergenic	HERVL66-int|LTR|ERVL	-2179	NM_001159293	100129842	Hs.515696	NM_001159293	ENSG00000237440	ZNF737	ZNF102	zinc finger protein 737	protein-coding	0.009132	0.428246	
chunk0029_280_1	chr10	103651648	103651946	+	0	NA	intron (NM_014631, intron 8 of 13)	intron (NM_014631, intron 8 of 13)	-94982	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.010067	0.494983	
chunk0121_435_1	chr3	26068731	26069437	+	0	NA	Intergenic	Intergenic	-195389	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.008499	0.386139	418(AAGCACACTATGTGCC,-,0.00),419(AGCACACTATGTGCCA,+,0.00)
chunk0050_47_1	chr12	100869637	100870198	+	0	NA	intron (NM_001286615, intron 1 of 27)	intron (NM_001286615, intron 1 of 27)	-31729	NM_001286616	121601	Hs.58785	NM_178826	ENSG00000151572	ANO4	TMEM16D	anoctamin 4	protein-coding	0.003565	0.432384	
chunk0071_393_1	chr15	89314653	89314879	+	0	NA	intron (NM_018193, intron 35 of 36)	intron (NM_018193, intron 35 of 36)	12044	NR_106824	102466983		NR_106824	ENSG00000275101	MIR6766	hsa-mir-6766	microRNA 6766	ncRNA	0.000000	0.436123	
chunk0091_341_1	chr19	14496852	14497564	+	0	NA	Intergenic	Intergenic	-1059	NM_202468	10755	Hs.655012	NM_005716	ENSG00000123159	GIPC1	C19orf3|GIPC|GLUT1CBP|Hs.6454|IIP-1|NIP|RGS19IP1|SEMCAP|SYNECTIIN|SYNECTIN|TIP-2	GIPC PDZ domain containing family member 1	protein-coding	0.012640	0.504909	423(CAGGACGCTCAGTTCC,-,0.00),424(AGGACGCTCAGTTCCC,+,0.00)
chunk0170_355_1	chr6	116571050	116571613	+	0	NA	promoter-TSS (NM_001007464)	promoter-TSS (NM_001007464)	-36	NM_016104	51389	Hs.532164	NM_015952	ENSG00000111832	RWDD1	CGI-24|PTD013	RWD domain containing 1	protein-coding	0.092362	0.668440	
chunk0089_326_1	chr18	65398277	65398760	+	0	NA	Intergenic	L2c|LINE|L2	-351734	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.014493	0.367769	
chunk0032_443_1	chr10	132980946	132981414	+	0	NA	Intergenic	L1MEa|LINE|L1	15646	NR_046231	399829	Hs.252872	NR_046231	ENSG00000240707	LINC01168	-	long intergenic non-protein coding RNA 1168	ncRNA	0.021368	0.607676	
chunk0178_99_1	chr7	30671894	30672151	+	0	NA	intron (NM_001202483, intron 2 of 12)	intron (NM_001202483, intron 2 of 12)	10503	NM_001883	1395	Hs.546246	NM_001883	ENSG00000106113	CRHR2	CRF-RB|CRF2|CRFR2|HM-CRF	corticotropin releasing hormone receptor 2	protein-coding	0.023346	0.519380	
chunk0134_389_1	chr3	182913764	182914175	+	0	NA	exon (NM_014616, exon 29 of 30)	exon (NM_014616, exon 29 of 30)	66632	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.012165	0.434466	128(TGGACTCCATGTGCTG,+,0.00),278(TGGAACAGGATGAACC,-,0.00),279(GGAACAGGATGAACCT,+,0.00)
chunk0094_171_1	chr2	5492641	5492840	+	0	NA	Intergenic	Intergenic	198378	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.015075	0.410000	
chunk0058_189_1	chr14	24242203	24242589	+	0	NA	5' UTR (NM_012461, exon 1 of 6)	5' UTR (NM_012461, exon 1 of 6)	278	NM_012461	26277	Hs.496191	NM_012461	ENSG00000092330	TINF2	DKCA3|TIN2	TERF1 interacting nuclear factor 2	protein-coding	0.093264	0.666667	
chunk0187_143_1	chr7	149625944	149626499	+	0	NA	Intergenic	Intergenic	-1431	NR_027788	79970	Hs.520785	NM_024910	ENSG00000133624	ZNF767P	ZNF767	zinc finger family member 767, pseudogene	pseudo	0.016216	0.465827	
chunk0048_278_1	chr12	82457871	82458363	+	0	NA	intron (NM_032230, intron 9 of 11)	intron (NM_032230, intron 9 of 11)	-99312	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.000000	0.292089	
chunk0078_432_1	chr16	89453372	89453958	+	0	NA	non-coding (NR_110932, exon 3 of 3)	non-coding (NR_110932, exon 3 of 3)	22747	NR_110932	101927817	Hs.667942	NR_110931		LOC101927817	-	uncharacterized LOC101927817	ncRNA	0.011945	0.448041	
chunk0009_271_1	chr1	107482533	107482994	+	0	NA	3' UTR (NM_014917, exon 6 of 6)	3' UTR (NM_014917, exon 6 of 6)	205741	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.006508	0.415584	255(AGGAACAGCATGTCTT,-,0.00),256(GGAACAGCATGTCTTA,+,0.00)
chunk0017_52_1	chr1	205344304	205344687	+	0	NA	intron (NM_001271863, intron 3 of 8)	intron (NM_001271863, intron 3 of 8)	12505	NM_018203	55220	Hs.10414	NM_018203	ENSG00000162873	KLHDC8A	-	kelch domain containing 8A	protein-coding	0.062663	0.588542	95(CGGGACACAGCGTGCT,-,0.00),96(GGGACACAGCGTGCTG,+,0.00)
chunk0156_257_1	chr5	109187608	109188334	+	0	NA	3' UTR (NM_001308031, exon 11 of 11)	3' UTR (NM_001308031, exon 11 of 11)	222003	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.012397	0.430536	
chunk0123_302_1	chr3	46948064	46948790	+	0	NA	intron (NM_001277074, intron 1 of 6)	intron (NM_001277074, intron 1 of 6)	28074	NR_102269	151903	Hs.631918	NM_144716	ENSG00000160799	CCDC12	-	coiled-coil domain containing 12	protein-coding	0.023416	0.557084	
chunk0190_35_1	chr8	29286840	29287064	+	0	NA	Intergenic	Intergenic	-23859	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.022321	0.493333	
chunk0026_148_1	chr10	62404780	62405421	+	0	NA	intron (NM_199450, intron 3 of 4)	MamRep137|DNA|TcMar-Tigger	-29973	NR_104162	283045		NR_104162		LOC283045	-	uncharacterized LOC283045	ncRNA	0.006240	0.406542	243(ATGTACATCTTGTACT,-,0.00)
chunk0108_82_1	chr2	227626016	227626400	+	0	NA	intron (NM_001162483, intron 2 of 3)	Tigger3c|DNA|TcMar-Tigger	7112	NM_020161	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.002604	0.384416	
chunk0192_95_1	chr8	61418598	61419128	+	0	NA	intron (NM_173519, intron 3 of 5)	intron (NM_173519, intron 3 of 5)	130897	NM_173519	157807	Hs.591874	NM_173519	ENSG00000177182	CLVS1	C6orf212L|CRALBPL|RLBP1L1	clavesin 1	protein-coding	0.005660	0.421846	345(AGGAACACATTGTCCA,-,0.00),346(GGAACACATTGTCCAT,+,0.00)
chunk0185_68_1	chr7	125032938	125033424	+	0	NA	intron (NR_125718, intron 4 of 10)	intron (NR_125718, intron 4 of 10)	-103198	NR_003102	25913	Hs.31968	NM_015450	ENSG00000128513	POT1	CMM10|GLM9|HPOT1	protection of telomeres 1	protein-coding	0.008230	0.320329	
chunk0062_355_1	chr14	73784498	73784698	+	0	NA	intron (NM_001043318, intron 1 of 11)	intron (NM_001043318, intron 1 of 11)	2660	NM_001043318	91748	Hs.594157	NM_194278	ENSG00000156030	ELMSAN1	C14orf117|C14orf43|LSR68|MIDEAS|c14_5541	ELM2 and Myb/SANT domain containing 1	protein-coding	0.010000	0.512438	
chunk0122_314_1	chr3	36992364	36992773	+	0	NA	promoter-TSS (NM_001258273)	promoter-TSS (NM_001258273)	736	NM_014805	9852	Hs.28020	NM_014805	ENSG00000178567	EPM2AIP1	-	EPM2A interacting protein 1	protein-coding	0.034230	0.531707	
chunk0152_294_1	chr5	61603306	61603799	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-34229	NM_173667									0.006085	0.445344	
chunk0047_235_1	chr12	71949192	71949483	+	0	NA	intron (NM_173353, intron 4 of 10)	MamRep434|DNA|TcMar-Tigger	10491	NM_173353	121278	Hs.736576	NM_173353	ENSG00000139287	TPH2	ADHD7|NTPH	tryptophan hydroxylase 2	protein-coding	0.000000	0.321918	
chunk0183_427_1	chr7	111018903	111019317	+	0	NA	intron (NM_032549, intron 3 of 5)	L2c|LINE|L2	-71896	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.004831	0.387952	
chunk0167_163_1	chr6	62819683	62819945	+	0	NA	Intergenic	Intergenic	500163	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.007634	0.387833	
chunk0138_160_1	chr4	37649655	37649977	+	0	NA	intron (NM_001085399, intron 1 of 6)	intron (NM_001085399, intron 1 of 6)	36561	NM_001085400	768211	Hs.283378	NM_001085399	ENSG00000181826	RELL1	-	RELT like 1	protein-coding	0.003106	0.380805	
chunk0113_289_1	chr20	57311649	57311989	+	0	NA	Intergenic	L1M5|LINE|L1	9772	NR_036219	100422883		NR_036219	ENSG00000266666	MIR4325	-	microRNA 4325	ncRNA	0.023529	0.413490	
chunk0127_270_1	chr3	97678616	97679173	+	0	NA	intron (NM_001080448, intron 14 of 17)	L1MEi|LINE|L1	-85627	NR_103511	84100	Hs.373801	NM_032146	ENSG00000113966	ARL6	BBS3|RP55	ADP ribosylation factor like GTPase 6	protein-coding	0.000000	0.274194	
chunk0167_406_1	chr6	75269442	75269773	+	0	NA	intron (NM_018247, intron 1 of 6)	L1MC1|LINE|L1	15309	NM_018247	55754	Hs.108530	NM_018247	ENSG00000112697	TMEM30A	C6orf67|CDC50A	transmembrane protein 30A	protein-coding	0.009063	0.370482	
chunk0082_257_1	chr17	57574072	57574667	+	0	NA	intron (NM_138962, intron 7 of 13)	intron (NM_138962, intron 7 of 13)	34043	NR_110807	101927539	Hs.680439	NR_110807	ENSG00000263499	LOC101927539	-	uncharacterized LOC101927539	ncRNA	0.008403	0.552013	
chunk0054_360_1	chr13	49689044	49689439	+	0	NA	intron (NR_103802, intron 1 of 4)	intron (NR_103802, intron 1 of 4)	2246	NM_001278636	84650	Hs.433278	NM_032565	ENSG00000123179	EBPL	EBRP	EBP like	protein-coding	0.005063	0.386364	
chunk0045_98_1	chr12	46089487	46090117	+	0	NA	Intergenic	LTR38|LTR|ERV1	-99184	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.007937	0.486529	
chunk0068_39_1	chr15	51303264	51303655	+	0	NA	intron (NM_000103, intron 1 of 9)	intron (NM_000103, intron 1 of 9)	-10575	NR_107012	102466250		NR_107012	ENSG00000278098	MIR7973-1	hsa-mir-7973-1	microRNA 7973-1	ncRNA	0.000000	0.418367	1(CAGGACAGGCTGGGCC,-,0.00),2(AGGACAGGCTGGGCCA,+,0.00)
chunk0033_435_1	chr11	25313283	25313884	+	0	NA	Intergenic	Intergenic	816613	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004992	0.320598	
chunk0186_325_1	chr7	143121019	143121473	+	0	NA	Intergenic	MER4A1_|LTR|ERV1	-10835	NM_002652	5304	Hs.99949	NM_002652	ENSG00000159763	PIP	GCDFP-15|GCDFP15|GPIP4	prolactin induced protein	protein-coding	0.002203	0.364835	192(AGTTCTGTCTGTTCTT,+,0.00)
chunk0020_401_1	chr1	240743380	240744076	+	0	NA	Intergenic	Intergenic	-131566	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.007184	0.410330	
chunk0084_252_1	chr17	79005581	79005804	+	0	NA	intron (NM_001159772, intron 1 of 5)	intron (NM_001159772, intron 1 of 5)	4125	NM_138793	124583	Hs.8859	NM_138793	ENSG00000171302	CANT1	DBQD|DBQD1|EDM7|SCAN-1|SCAN1|SHAPY	calcium activated nucleotidase 1	protein-coding	0.013453	0.584821	
chunk0143_157_1	chr4	110133137	110133559	+	0	NA	intron (NM_001130721, intron 2 of 4)	L2c|LINE|L2	65267	NM_001130721	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.007109	0.427896	
chunk0017_140_1	chr1	206634192	206634405	+	0	NA	Intergenic	Intergenic	-1238	NM_003582	8444	Hs.164267	NM_003582	ENSG00000143479	DYRK3	DYRK5|RED|REDK|hYAK3-2	dual specificity tyrosine phosphorylation regulated kinase 3	protein-coding	0.009390	0.308411	
chunk0130_406_1	chr3	140439020	140439850	+	0	NA	intron (NM_022131, intron 5 of 16)	intron (NM_022131, intron 5 of 16)	69354	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.009639	0.490975	
chunk0039_74_1	chr11	96422996	96423348	+	0	NA	Intergenic	Intergenic	33178	NM_001261833	8690	Hs.105940	NM_003772	ENSG00000183340	JRKL	HHMJG	JRK like	protein-coding	0.005682	0.303116	
chunk0116_278_1	chr21	39779896	39780407	+	0	NA	intron (NM_001080444, intron 5 of 8)	L1MA7|LINE|L1	34744	NM_001080444	150084	Hs.422120	NM_001080444	ENSG00000183067	IGSF5	GSF5|JAM4	immunoglobulin superfamily member 5	protein-coding	0.007828	0.357422	
chunk0093_346_1	chr19	55002276	55002871	+	0	NA	Intergenic	L1MC3|LINE|L1	35691	NM_001083899	51206	Hs.661752	NM_016363	ENSG00000088053	GP6	BDPLT11|GPIV|GPVI	glycoprotein VI platelet	protein-coding	0.018487	0.436242	
chunk0166_227_1	chr6	46982619	46983440	+	0	NA	Intergenic	L3|LINE|CR1	-28091	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.002436	0.411192	
chunk0073_88_1	chr16	4097853	4098077	+	0	NA	intron (NM_001116, intron 2 of 10)	L2a|LINE|L2	18220	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.008929	0.382222	
chunk0052_325_1	chr12	125812804	125813204	+	0	NA	Intergenic	Intergenic	170370	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.017500	0.446384	
chunk0171_184_1	chr6	125198689	125198999	+	0	NA	intron (NM_001003395, intron 1 of 6)	MER20|DNA|hAT-Charlie	44570	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.019355	0.459807	186(GTGAACACACAGTTCC,-,0.00),187(TGAACACACAGTTCCC,+,0.00)
chunk0212_235_1	chrX	136523744	136524029	+	0	NA	Intergenic	L1M3|LINE|L1	-8266	NM_016267	51442	Hs.496843	NM_016267	ENSG00000102243	VGLL1	TDU|VGL1	vestigial like family member 1	protein-coding	0.000000	0.332168	
chunk0144_269_1	chr4	137212778	137213285	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	319467	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.003945	0.356299	
chunk0031_302_1	chr10	128752180	128752535	+	0	NA	Intergenic	L1ME1|LINE|L1	466407	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.000000	0.314607	164(AGGCACATCATGTTCA,-,0.00),165(GGCACATCATGTTCAT,+,0.00)
chunk0206_70_1	chr9	119866326	119866798	+	0	NA	Intergenic	L1PA16|LINE|L1	-68498	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.004237	0.319239	
chunk0142_47_1	chr4	91256060	91256454	+	0	NA	intron (NM_001145065, intron 10 of 10)	MER11B|LTR|ERVK	1021045	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.012690	0.473418	
chunk0115_3_1	chr21	20292260	20292637	+	0	NA	Intergenic	Intergenic	510660	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.007958	0.328042	
chunk0138_410_1	chr4	43799225	43799424	+	0	NA	Intergenic	L1M1|LINE|L1	-217537	NR_131959	100506827	Hs.156197	NR_131958	ENSG00000251350	LINC02475	LVCAT1	long intergenic non-protein coding RNA 2475	ncRNA	0.000000	0.365000	
chunk0066_17_1	chr15	27282983	27283188	+	0	NA	intron (NM_033223, intron 3 of 9)	L1MD2|LINE|L1	-121766	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.009756	0.490291	
chunk0093_275_1	chr19	51700365	51700947	+	0	NA	intron (NM_001316972, intron 2 of 8)	intron (NM_001316972, intron 2 of 8)	-7200	NR_108100	102238594	Hs.640185	NR_108100	ENSG00000269959	SPACA6P-AS	LINC01129	SPACA6P antisense RNA	ncRNA	0.006873	0.411664	
chunk0091_259_1	chr19	11064858	11065083	+	0	NA	Intergenic	L1M4a2|LINE|L1	-24392	NM_000527	3949	Hs.213289	NM_000527	ENSG00000130164	LDLR	FH|FHC|LDLCQ2	low density lipoprotein receptor	protein-coding	0.026667	0.575221	
chunk0173_127_1	chr6	143691066	143691693	+	0	NA	intron (NM_001100164, intron 1 of 12)	intron (NM_001100164, intron 1 of 12)	13414	NM_001100165	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.004785	0.350318	
chunk0095_60_1	chr2	14240653	14241015	+	0	NA	intron (NR_103814, intron 2 of 3)	intron (NR_103814, intron 2 of 3)	160124	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.019337	0.377410	
chunk0045_207_1	chr12	47820172	47820708	+	0	NA	promoter-TSS (NM_001098416)	promoter-TSS (NM_001098416)	-460	NM_001308090	51564	Hs.200063	NM_015401	ENSG00000061273	HDAC7	HD7|HD7A|HDAC7A	histone deacetylase 7	protein-coding	0.046642	0.567970	405(GGGTCCAGCCTGTTCC,-,0.00),406(GGTCCAGCCTGTTCCT,+,0.00)
chunk0199_447_1	chr9	14066790	14067167	+	0	NA	Intergenic	Intergenic	113824	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.007958	0.383598	
chunk0165_199_1	chr6	34598552	34599192	+	0	NA	intron (NM_022758, intron 3 of 3)	intron (NM_022758, intron 3 of 3)	-42539	NM_012391	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.004687	0.430577	372(TGGTACACAGTGTGCT,-,0.00),373(GGTACACAGTGTGCTA,+,0.00)
chunk0052_46_1	chr13	20881575	20881834	+	0	NA	intron (NM_022459, intron 1 of 22)	L1ME2|LINE|L1	21070	NM_022459	64328	Hs.507452	NM_022459	ENSG00000132953	XPO4	exp4	exportin 4	protein-coding	0.003861	0.280769	
chunk0013_418_1	chr1	173287974	173288328	+	0	NA	intron (NR_037845, intron 2 of 2)	L1ME1|LINE|L1	-80838	NM_003326	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.002825	0.385915	
chunk0149_255_1	chr5	23876126	23876784	+	0	NA	Intergenic	Intergenic	-74893	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.004559	0.330804	
chunk0118_256_1	chr22	33044095	33044356	+	0	NA	intron (NM_001135774, intron 1 of 13)	intron (NM_001135774, intron 1 of 13)	14166	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.022989	0.507634	128(AGGTACAGTGCGTTCT,-,0.00),129(GGTACAGTGCGTTCTT,+,0.00)
chunk0044_188_1	chr12	30436925	30437748	+	0	NA	Intergenic	LTR82B|LTR|ERVL	239908	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.006075	0.425971	
chunk0127_369_1	chr3	101849019	101849247	+	0	NA	promoter-TSS (NM_031419)	promoter-TSS (NM_031419)	-381	NM_031419	64332	Hs.319171	NM_031419	ENSG00000144802	NFKBIZ	IKBZ|INAP|MAIL	NFKB inhibitor zeta	protein-coding	0.096491	0.777293	
chunk0016_7_1	chr1	192690821	192691683	+	0	NA	Intergenic	Intergenic	-25076	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.001160	0.347625	
chunk0061_121_1	chr14	58537054	58537272	+	0	NA	TTS (NM_001244193)	TTS (NM_001244193)	-96905	NR_046093	51339	Hs.48950	NM_016651	ENSG00000165617	DACT1	DAPPER|DAPPER1|DPR1|FRODO|HDPR1|TBS2|THYEX3	dishevelled binding antagonist of beta catenin 1	protein-coding	0.013761	0.374429	
chunk0098_281_1	chr2	75709148	75709665	+	0	NA	intron (NM_001201335, intron 1 of 2)	intron (NM_001201335, intron 1 of 2)	1200	NM_001201334	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.005803	0.349421	273(GAGGACATTATGTTAC,-,0.00)
chunk0004_277_1	chr1	48433161	48433424	+	0	NA	intron (NM_019073, intron 3 of 12)	L1MB3|LINE|L1	38916	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.000000	0.276515	
chunk0176_41_1	chr7	10524986	10525216	+	0	NA	Intergenic	Intergenic	415085	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.008696	0.406926	58(CAGCACGGCTTGTCCC,-,0.00),59(AGCACGGCTTGTCCCT,+,0.00)
chunk0077_173_1	chr16	79452085	79452500	+	0	NA	Intergenic	Intergenic	148433	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.002410	0.326923	
chunk0085_135_1	chr18	3226036	3226361	+	0	NA	Intergenic	Intergenic	-6090	NM_019856	8736	Hs.464469	NM_003803	ENSG00000101605	MYOM1	SKELEMIN	myomesin 1	protein-coding	0.012308	0.435583	128(AGGAACATTGTGTTCC,-,0.00),129(GGAACATTGTGTTCCA,+,0.00),266(GAGCTCACTATGTCCT,-,0.00),267(AGCTCACTATGTCCTC,+,0.00)
chunk0184_193_1	chr7	116923400	116923679	+	0	NA	Intergenic	Intergenic	-29788	NM_021908	7982	Hs.368131	NM_018412	ENSG00000004866	ST7	ETS7q|FAM4A|FAM4A1|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding	0.000000	0.400000	
chunk0197_187_1	chr8	121403850	121404144	+	0	NA	Intergenic	Intergenic	-235349	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.003401	0.335593	
chunk0171_55_1	chr6	121176203	121176513	+	0	NA	intron (NR_104452, intron 24 of 35)	L2a|LINE|L2	158142	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.003226	0.418006	
chunk0186_46_1	chr7	136168877	136169599	+	0	NA	Intergenic	Intergenic	-191782	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.008310	0.377593	
chunk0141_52_1	chr4	77563976	77564765	+	0	NA	intron (NM_006419, intron 1 of 4)	intron (NM_006419, intron 1 of 4)	52617	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.007605	0.413924	330(CAGGACGTTCTGTACT,-,0.00),331(AGGACGTTCTGTACTA,+,0.00),472(TTGAACTAGCTGTTCT,-,0.00),473(TGAACTAGCTGTTCTG,+,0.00)
chunk0099_166_1	chr2	88602147	88602591	+	0	NA	intron (NM_001313915, intron 2 of 16)	intron (NM_001313915, intron 2 of 16)	22560	NM_001313915	9451	Hs.591589	NM_004836	ENSG00000172071	EIF2AK3	PEK|PERK|WRS	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding	0.002252	0.400000	185(GAGACCAGTGTGTTCC,-,0.00),186(AGACCAGTGTGTTCCC,+,0.00),207(AGGAACACACTGGCCC,-,0.00),208(GGAACACACTGGCCCT,+,0.00)
chunk0099_177_1	chr2	89828535	89828772	+	0	NA	Intergenic	(ATTCC)n|Simple_repeat|Simple_repeat	1016283	NR_039635	100616399		NR_039635	ENSG00000265510	MIR4436A	mir-4436a	microRNA 4436a	ncRNA	0.008439	0.399160	
chunk0099_403_1	chr2	102032483	102032721	+	0	NA	Intergenic	L1ME3F|LINE|L1	33640	NR_048564	7850	Hs.25333	NM_004633	ENSG00000115590	IL1R2	CD121b|CDw121b|IL-1R-2|IL-1RT-2|IL-1RT2|IL1R2c|IL1RB	interleukin 1 receptor type 2	protein-coding	0.000000	0.326360	
chunk0053_156_1	chr13	30289680	30290054	+	0	NA	intron (NM_032116, intron 1 of 10)	Cheshire|DNA|hAT-Charlie	17187	NM_001014380	84056	Hs.243596	NM_032116	ENSG00000102781	KATNAL1	-	katanin catalytic subunit A1 like 1	protein-coding	0.000000	0.328000	
chunk0104_12_1	chr2	170419019	170419368	+	0	NA	intron (NR_045684, intron 22 of 34)	intron (NR_045684, intron 22 of 34)	-68250	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.008596	0.420000	
chunk0182_78_1	chr7	92421936	92422267	+	0	NA	Intergenic	LTR33|LTR|ERVL	-25347	NR_052016	57798	Hs.21145	NM_021167	ENSG00000157259	GATAD1	CMD2B|ODAG|RG083M05.2	GATA zinc finger domain containing 1	protein-coding	0.003021	0.524096	
chunk0025_184_1	chr10	53214647	53215128	+	0	NA	Intergenic	Intergenic	-443187	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.006237	0.390041	
chunk0194_304_1	chr8	88041313	88041829	+	0	NA	exon (NM_005941, exon 10 of 10)	exon (NM_005941, exon 10 of 10)	-167503	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.007752	0.452611	
chunk0145_243_1	chr4	148692053	148692714	+	0	NA	Intergenic	Intergenic	-249863	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.012103	0.383686	331(AGGGACGCAGTGTTCC,-,0.00),332(GGGACGCAGTGTTCCT,+,0.00)
chunk0151_110_1	chr5	43453779	43454150	+	0	NA	exon (NM_022483, exon 2 of 3)	exon (NM_022483, exon 2 of 3)	29926	NM_022483	64417	Hs.732093	NM_022483	ENSG00000151881	TMEM267	C5orf28	transmembrane protein 267	protein-coding	0.008086	0.379032	
chunk0042_14_1	chr12	1220047	1220636	+	0	NA	intron (NR_027946, intron 12 of 18)	L2a|LINE|L2	192593	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.003396	0.354237	
chunk0166_44_1	chr6	42339553	42340058	+	0	NA	intron (NM_001297573, intron 3 of 17)	intron (NM_001297573, intron 3 of 17)	112246	NM_033502	55809	Hs.485392	NM_018415	ENSG00000124496	TRERF1	BCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5	transcriptional regulating factor 1	protein-coding	0.005941	0.399209	
chunk0097_82_1	chr2	44775636	44775849	+	0	NA	Intergenic	Intergenic	165765	NR_103785	100506108	Hs.503113	NR_103785	ENSG00000236502	SIX3-AS1	SIX3OS	SIX3 antisense RNA 1	ncRNA	0.004695	0.373832	83(ATGCTCACAGTGTTCT,-,0.00),84(TGCTCACAGTGTTCTC,+,0.00)
chunk0056_78_1	chr13	79514851	79515409	+	0	NA	intron (NM_019080, intron 1 of 7)	Tigger3a|DNA|TcMar-Tigger	-33899	NR_046685	100874208	Hs.602801	NR_046685	ENSG00000232132	NDFIP2-AS1	-	NDFIP2 antisense RNA 1	ncRNA	0.008961	0.350626	
chunk0080_256_1	chr17	30470656	30470997	+	0	NA	Intergenic	Intergenic	-6582	NM_001007024	9527	Hs.462680	NM_004871	ENSG00000108587	GOSR1	GOLIM2|GOS-28|GOS28|GOS28/P28|GS28|P28	golgi SNAP receptor complex member 1	protein-coding	0.008798	0.377193	
chunk0196_415_1	chr8	116052725	116053143	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	272125	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.016746	0.384248	
chunk0071_230_1	chr15	85041206	85041405	+	0	NA	intron (NM_002605, intron 1 of 21)	intron (NM_002605, intron 1 of 21)	59331	NM_173454	5151	Hs.9333	NM_002605	ENSG00000073417	PDE8A	HsT19550	phosphodiesterase 8A	protein-coding	0.020101	0.390000	
chunk0083_75_1	chr17	64150274	64150576	+	0	NA	intron (NM_018469, intron 11 of 11)	L2c|LINE|L2	4086	NR_002995	677842	Hs.405444	NR_002995	ENSG00000277887	SNORA50C	ACA62|SNORA76|SNORA76C	small nucleolar RNA, H/ACA box 50C	snoRNA	0.003311	0.537954	
chunk0129_57_1	chr3	117507993	117508197	+	0	NA	Intergenic	Intergenic	586664	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.370732	
chunk0048_272_1	chr12	82354231	82354430	+	0	NA	intron (NR_033192, intron 3 of 3)	intron (NR_033192, intron 3 of 3)	4090	NM_014167	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.000000	0.375000	
chunk0099_105_1	chr2	85708448	85709221	+	0	NA	Intergenic	L1MC4a|LINE|L1	14543	NM_001302758	10578	Hs.105806	NM_006433	ENSG00000115523	GNLY	D2S69E|LAG-2|LAG2|NKG5|TLA519	granulysin	protein-coding	0.003881	0.372093	340(AGGAACAAGATGTACC,-,0.00),341(GGAACAAGATGTACCA,+,0.00),389(AAGGACTCACTGTCCC,-,0.00),390(AGGACTCACTGTCCCT,+,0.00)
chunk0001_106_1	chr1	3473738	3474067	+	0	NA	intron (NM_014448, intron 8 of 14)	intron (NM_014448, intron 8 of 14)	19319	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.021277	0.575758	
chunk0046_59_1	chr12	55759039	55759461	+	0	NA	intron (NR_026722, intron 9 of 10)	intron (NR_026722, intron 9 of 10)	15970	NM_005811	10220	Hs.600883	NM_005811	ENSG00000135414	GDF11	BMP-11|BMP11	growth differentiation factor 11	protein-coding	0.002370	0.366430	153(AAGAACAGGAAGTCTC,-,0.00),203(AGGCACAACCAGTTCT,-,0.00),204(GGCACAACCAGTTCTT,+,0.00)
chunk0196_113_1	chr8	103316862	103317301	+	0	NA	intron (NM_001164615, intron 2 of 6)	L2a|LINE|L2	18250	NM_001164616	8323	Hs.591863	NM_003506	ENSG00000164930	FZD6	FZ-6|FZ6|HFZ6|NDNC10	frizzled class receptor 6	protein-coding	0.002278	0.390909	313(GGGAACAGCAAGTGCA,-,0.00),314(GGAACAGCAAGTGCAA,+,0.00)
chunk0019_220_1	chr1	227282614	227283526	+	0	NA	intron (NM_014826, intron 1 of 34)	Charlie22a|DNA|hAT-Charlie	35055	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.001096	0.293538	273(AAACACAAAATGTTCT,-,0.00),274(AACACAAAATGTTCTG,+,0.00)
chunk0097_47_1	chr2	43370851	43371162	+	0	NA	intron (NR_073394, intron 27 of 35)	intron (NR_073394, intron 27 of 35)	143795	NR_027251	100129726	Hs.194480	NM_178529	ENSG00000279873	LINC01126	-	long intergenic non-protein coding RNA 1126	ncRNA	0.000000	0.323718	
chunk0086_186_1	chr18	22021580	22022344	+	0	NA	Intergenic	Intergenic	147006	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.014398	0.490196	
chunk0212_95_1	chrY	12774595	12775108	+	0	NA	intron (NM_004654, intron 17 of 45)	intron (NM_004654, intron 17 of 45)	73620	NM_004654	8287	Hs.598540	NM_004654	ENSG00000114374	USP9Y	DFFRY|SPGFY2	ubiquitin specific peptidase 9 Y-linked	protein-coding	0.003899	0.305447	
chunk0139_83_1	chr4	49321090	49321543	+	0	NA	Intergenic	Intergenic	334674	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.044150	0.548458	
chunk0132_92_1	chr3	155602097	155602381	+	0	NA	intron (NM_014996, intron 1 of 21)	L1MC4a|LINE|L1	74077	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.007042	0.319298	
chunk0130_32_1	chr3	128976654	128977035	+	0	NA	intron (NM_020741, intron 6 of 7)	intron (NM_020741, intron 6 of 7)	17299	NM_020741	57501	Hs.518247	NM_020741	ENSG00000114656	KIAA1257	-	KIAA1257	protein-coding	0.013123	0.403141	
chunk0005_210_1	chr1	59106061	59106347	+	0	NA	Intergenic	MIRc|SINE|MIR	40603	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.013986	0.519164	
chunk0048_334_1	chr12	83907538	83908013	+	0	NA	Intergenic	L1PB4|LINE|L1	1005054	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.004211	0.399160	
chunk0023_212_1	chr10	25493621	25494152	+	0	NA	intron (NM_020752, intron 5 of 10)	intron (NM_020752, intron 5 of 10)	-157826	NR_108067	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.001883	0.319549	
chunk0053_392_1	chr13	36302236	36302950	+	0	NA	3' UTR (NM_001142296, exon 10 of 10)	3' UTR (NM_001142296, exon 10 of 10)	-4738	NM_001144985	728591	Hs.656745	NM_001144981	ENSG00000242715	CCDC169	C13orf38	coiled-coil domain containing 169	protein-coding	0.008403	0.356643	
chunk0157_35_1	chr5	115762512	115762711	+	0	NA	Intergenic	THE1D-int|LTR|ERVL-MaLR	54097	NM_001801	1036	Hs.442378	NM_001801	ENSG00000129596	CDO1	CDO-I	cysteine dioxygenase type 1	protein-coding	0.000000	0.535000	
chunk0027_58_1	chr10	72952534	72953070	+	0	NA	intron (NM_032562, intron 1 of 3)	intron (NM_032562, intron 1 of 3)	1950	NM_032562	84647	Hs.333175	NM_032562	ENSG00000138308	PLA2G12B	FKSG71|GXIIB|GXIIIsPLA2|PLA2G13|sPLA2-GXIIB	phospholipase A2 group XIIB	protein-coding	0.013060	0.437616	
chunk0037_23_1	chr11	69507702	69508200	+	0	NA	Intergenic	L1MB7|LINE|L1	22390	NR_120543	101928292	Hs.736219	NR_120542		LINC01488	BRCAT8	long intergenic non-protein coding RNA 1488	ncRNA	0.004016	0.362725	248(AGGTACAGGAAGTACC,-,0.00),249(GGTACAGGAAGTACCT,+,0.00)
chunk0123_308_1	chr3	47035644	47036058	+	0	NA	intron (NM_014159, intron 18 of 20)	intron (NM_014159, intron 18 of 20)	24309	NR_024046	100129354	Hs.201522	NR_024046		NRADDP	-	neurotrophin receptor associated death domain, pseudogene	pseudo	0.004831	0.363855	
chunk0166_191_1	chr6	46222507	46223226	+	0	NA	3' UTR (NM_001251974, exon 5 of 5)	3' UTR (NM_001251974, exon 5 of 5)	-51856	NM_001290073	59084	Hs.35198	NM_021572	ENSG00000112796	ENPP5	NPP-5|NPP5	ectonucleotide pyrophosphatase/phosphodiesterase family member 5	protein-coding	0.009736	0.419444	
chunk0004_205_1	chr1	46666420	46666722	+	0	NA	promoter-TSS (NM_001243728)	promoter-TSS (NM_001243728)	-693	NM_001256418	64756	Hs.100874	NM_022745	ENSG00000123472	ATPAF1	ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding	0.000000	0.432343	
chunk0026_142_1	chr10	62291920	62292327	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-23260	NM_145307	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.000000	0.311275	
chunk0085_433_1	chr18	10908136	10908811	+	0	NA	intron (NM_022068, intron 4 of 51)	intron (NM_022068, intron 4 of 51)	-148824	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.007407	0.389053	
chunk0022_459_1	chr10	20105179	20105488	+	0	NA	intron (NM_032812, intron 4 of 13)	Tigger16a|DNA|TcMar-Tigger	288890	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.012945	0.345161	
chunk0093_207_1	chr19	49613421	49613837	+	0	NA	intron (NM_020719, intron 6 of 13)	intron (NM_020719, intron 6 of 13)	21974	NM_020719	57479	Hs.590971	NM_020719	ENSG00000126464	PRR12	KIAA1205	proline rich 12	protein-coding	0.009615	0.501199	
chunk0167_115_1	chr6	57497907	57498509	+	0	NA	intron (NM_000947, intron 7 of 13)	intron (NM_000947, intron 7 of 13)	108076	NR_036097	100422884		NR_036097	ENSG00000212017	MIR548U	-	microRNA 548u	ncRNA	0.001661	0.305141	199(TTGAACAACCTGTTCT,-,0.00),200(TGAACAACCTGTTCTC,+,0.00)
chunk0027_154_1	chr10	74786013	74786670	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-40072	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.010654	0.402736	
chunk0197_14_1	chr8	117060324	117060923	+	0	NA	intron (NM_001172815, intron 2 of 10)	intron (NM_001172815, intron 2 of 10)	-74475	NM_173851	169026	Hs.532270	NM_173851	ENSG00000164756	SLC30A8	ZNT8|ZnT-8	solute carrier family 30 member 8	protein-coding	0.001669	0.360000	
chunk0142_82_1	chr4	93903012	93903471	+	0	NA	Intergenic	Intergenic	74314	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.004357	0.297826	
chunk0013_162_1	chr1	168737770	168738231	+	0	NA	Intergenic	LTR33|LTR|ERVL	-8796	NM_001937	1805	Hs.80552	NM_001937	ENSG00000143196	DPT	TRAMP	dermatopontin	protein-coding	0.008677	0.463203	
chunk0104_363_1	chr2	180001602	180002017	+	0	NA	intron (NM_020943, intron 1 of 19)	L2a|LINE|L2	5244	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.000000	0.399038	
chunk0068_104_1	chr15	52295632	52295911	+	0	NA	promoter-TSS (NM_018728)	promoter-TSS (NM_018728)	27	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.111111	0.746429	
chunk0009_464_1	chr1	111673637	111674118	+	0	NA	intron (NM_001010935, intron 2 of 8)	intron (NM_001010935, intron 2 of 8)	53730	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.004158	0.367220	
chunk0004_84_1	chr1	43732052	43732367	+	0	NA	intron (NM_174963, intron 1 of 12)	LTR33|LTR|ERVL	-4866	NR_125986	101929592		NR_125986	ENSG00000229444	LOC101929592	-	uncharacterized LOC101929592	ncRNA	0.003175	0.465190	
chunk0064_439_1	chr14	99966610	99967311	+	0	NA	Intergenic	Intergenic	-98454	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.037090	0.613960	
chunk0045_275_1	chr12	49757308	49757949	+	0	NA	intron (NM_003217, intron 4 of 9)	intron (NM_003217, intron 4 of 9)	15819	NM_001098576	7009	Hs.743965	NM_003217	ENSG00000139644	TMBIM6	BAXI1|BI-1|TEGT	transmembrane BAX inhibitor motif containing 6	protein-coding	0.006240	0.386293	265(TAGAACAGCTTGTTCT,-,0.00),266(AGAACAGCTTGTTCTG,+,0.00),437(TGGAACAGGTTGCCCT,-,0.00),438(GGAACAGGTTGCCCTC,+,0.00)
chunk0060_85_1	chr14	42317490	42317697	+	0	NA	Intergenic	Intergenic	710032	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.004831	0.264423	
chunk0158_262_1	chr5	131109783	131110219	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	55347	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.002294	0.409611	
chunk0042_187_1	chr12	5133289	5133590	+	0	NA	Intergenic	Intergenic	89520	NM_002234	3741	Hs.150208	NM_002234	ENSG00000130037	KCNA5	ATFB7|HCK1|HK2|HPCN1|KV1.5|PCN1	potassium voltage-gated channel subfamily A member 5	protein-coding	0.009967	0.350993	
chunk0208_140_1	chrX	15650567	15650813	+	0	NA	intron (NM_020665, intron 3 of 5)	intron (NM_020665, intron 3 of 5)	14341	NM_020665	57393	Hs.129614	NM_020665	ENSG00000147003	CLTRN	NX-17|NX17|TMEM27	collectrin, amino acid transport regulator	protein-coding	0.008130	0.340081	
chunk0201_7_1	chr9	32128544	32128801	+	0	NA	Intergenic	L1PA10|LINE|L1	-255931	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.011673	0.585271	
chunk0033_133_1	chr11	15277809	15278016	+	0	NA	Intergenic	Intergenic	128810	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.004831	0.504808	
chunk0061_297_1	chr14	61712105	61712374	+	0	NA	intron (NM_001243084, intron 1 of 14)	L2a|LINE|L2	14617	NM_001243084	3091	Hs.597216	NM_001530	ENSG00000100644	HIF1A	HIF-1-alpha|HIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78	hypoxia inducible factor 1 subunit alpha	protein-coding	0.003717	0.459259	
chunk0172_85_1	chr6	134531984	134532216	+	0	NA	intron (NR_125856, intron 1 of 2)	intron (NR_125856, intron 1 of 2)	7905	NR_125855	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.012931	0.390558	
chunk0081_395_1	chr17	48233777	48234106	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-60406	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.000000	0.384848	
chunk0149_93_1	chr5	18507293	18507492	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-1120082	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.005025	0.410000	
chunk0110_311_1	chr20	18496015	18496366	+	0	NA	intron (NM_006606, intron 1 of 4)	intron (NM_006606, intron 1 of 4)	1053	NM_006606	10741	Hs.69330	NM_006606	ENSG00000089050	RBBP9	BOG|RBBP10	RB binding protein 9, serine hydrolase	protein-coding	0.014245	0.480114	
chunk0103_374_1	chr2	168559049	168559452	+	0	NA	intron (NM_001256126, intron 2 of 10)	intron (NM_001256126, intron 2 of 10)	-23693	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.004963	0.371287	211(CAGTACATTTTGTACC,-,0.00),212(AGTACATTTTGTACCC,+,0.00)
chunk0002_278_1	chr1	22348297	22348768	+	0	NA	Intergenic	Intergenic	82293	NR_039613	100616433		NR_039613	ENSG00000266564	MIR4418	-	microRNA 4418	ncRNA	0.021231	0.516949	
chunk0208_52_1	chrX	11464201	11464885	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-36758	NM_001287242	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.002924	0.350365	299(AGGCACAGGATGTTCC,-,0.00),300(GGCACAGGATGTTCCT,+,0.00)
chunk0209_236_1	chrX	45301559	45301851	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-100804	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.006849	0.358362	
chunk0108_47_1	chr2	226867041	226867411	+	0	NA	exon (NM_001167608, exon 5 of 9)	exon (NM_001167608, exon 5 of 9)	31271	NM_001167608	84236	Hs.471514	NM_032276	ENSG00000144468	RHBDD1	RHBDL4|RRP4	rhomboid domain containing 1	protein-coding	0.008108	0.345013	
chunk0200_143_1	chr9	18053541	18053972	+	0	NA	Intergenic	L2b|LINE|L2	-420325	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.011601	0.379630	
chunk0113_429_1	chr20	62237947	62238431	+	0	NA	promoter-TSS (NM_014835)	promoter-TSS (NM_014835)	-296	NM_001278649	9885	Hs.473254	NM_014835	ENSG00000130703	OSBPL2	DFNA67|DNFA67|ORP-2|ORP2	oxysterol binding protein like 2	protein-coding	0.061983	0.637113	
chunk0093_98_1	chr19	43380769	43381134	+	0	NA	Intergenic	Intergenic	-7660	NM_031451	83639	Hs.97978	NM_031451	ENSG00000131126	TEX101	CT131|GTPR867|NYD-SP8|PRO1884|SGRG|SPATA44|TES101RP	testis expressed 101	protein-coding	0.008219	0.483607	
chunk0055_316_1	chr13	68122119	68122587	+	0	NA	Intergenic	Intergenic	749966	NR_130792	100874145	Hs.508194	NR_130792	ENSG00000230040	LINC00364	LncRNA00364	long intergenic non-protein coding RNA 364	ncRNA	0.002137	0.292111	323(CTGGACAAGCTGTTCA,-,0.00),324(TGGACAAGCTGTTCAT,+,0.00)
chunk0163_385_1	chr6	16396853	16397057	+	0	NA	intron (NM_001128164, intron 6 of 7)	Tigger3|DNA|TcMar-Tigger	158375	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.009804	0.429268	
chunk0150_187_1	chr5	34582230	34582524	+	0	NA	Intergenic	Intergenic	-73951	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.006803	0.477966	
chunk0146_353_1	chr4	167216662	167217342	+	0	NA	intron (NM_001204352, intron 2 of 11)	intron (NM_001204352, intron 2 of 11)	17424	NM_001204353	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.007353	0.303965	
chunk0025_296_1	chr10	57015802	57016339	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	288489	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.011173	0.496283	375(AGGAACAGTTTGTCTT,-,0.00),376(GGAACAGTTTGTCTTC,+,0.00)
chunk0139_25_1	chr4	48340373	48341263	+	0	NA	promoter-TSS (NM_020846)	promoter-TSS (NM_020846)	-778	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.038202	0.475870	
chunk0183_287_1	chr7	107623110	107623817	+	0	NA	TTS (NM_018844)	TTS (NM_018844)	-37172	NM_000441	5172	Hs.571246	NM_000441	ENSG00000091137	SLC26A4	DFNB4|EVA|PDS|TDH2B	solute carrier family 26 member 4	protein-coding	0.008487	0.409605	
chunk0044_182_1	chr12	30313360	30313751	+	0	NA	Intergenic	L1PA10|LINE|L1	363689	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.007673	0.369898	
chunk0100_189_1	chr2	110984395	110985191	+	0	NA	intron (NM_001142807, intron 12 of 17)	intron (NM_001142807, intron 12 of 17)	130795	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.010050	0.392723	
chunk0205_21_1	chr9	105154705	105155033	+	0	NA	Intergenic	L2a|LINE|L2	-89744	NM_080546	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.006098	0.428571	
chunk0012_259_1	chr1	161439741	161440066	+	0	NA	Intergenic	Intergenic	-65512	NM_021642	2212	Hs.352642	NM_021642	ENSG00000143226	FCGR2A	CD32|CD32A|CDw32|FCG2|FCGR2|FCGR2A1|FcGR|IGFR2	Fc fragment of IgG receptor IIa	protein-coding	0.043077	0.616564	
chunk0188_350_1	chr8	17896053	17896252	+	0	NA	promoter-TSS (NM_004467)	promoter-TSS (NM_004467)	-614	NM_201552	2267	Hs.491143	NM_004467	ENSG00000104760	FGL1	HFREP1|HP-041|HPS|LFIRE-1|LFIRE1	fibrinogen like 1	protein-coding	0.010050	0.360000	14(CTGGACAAGTTGTTCC,-,0.00),15(TGGACAAGTTGTTCCT,+,0.00)
chunk0013_412_1	chr1	173134324	173134523	+	0	NA	Intergenic	Intergenic	71135	NM_001297562	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.005025	0.355000	
chunk0135_291_1	chr3	189508920	189509229	+	0	NA	Intergenic	Intergenic	-122353	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.000000	0.393548	87(TAGCACACTCTGTCCT,-,0.00),88(AGCACACTCTGTCCTT,+,0.00)
chunk0107_421_1	chr2	224607968	224608567	+	0	NA	Intergenic	Intergenic	-22870	NM_001257197	8452	Hs.372286	NM_003590	ENSG00000036257	CUL3	CUL-3|PHA2E	cullin 3	protein-coding	0.005008	0.410000	
chunk0010_350_1	chr1	118618112	118618311	+	0	NA	Intergenic	L1MA2|LINE|L1	371345	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.000000	0.450000	
chunk0050_82_1	chr12	101685030	101685373	+	0	NA	intron (NM_206819, intron 30 of 30)	intron (NM_206819, intron 30 of 30)	-12438	NM_020244	56994	Hs.293077	NM_020244	ENSG00000111666	CHPT1	CPT|CPT1	choline phosphotransferase 1	protein-coding	0.005831	0.334302	117(GAAACTCTCTGTGCCT,+,0.00)
chunk0034_56_1	chr11	27089821	27090120	+	0	NA	intron (NR_125766, intron 3 of 4)	intron (NR_125766, intron 3 of 4)	49008	NM_003986	8424	Hs.591996	NM_003986	ENSG00000129151	BBOX1	BBH|BBOX|G-BBH|gamma-BBH	gamma-butyrobetaine hydroxylase 1	protein-coding	0.003344	0.360000	
chunk0105_6_1	chr2	181743399	181743598	+	0	NA	Intergenic	Intergenic	-62833	NM_002500	4760	Hs.574626	NM_002500	ENSG00000162992	NEUROD1	BETA2|BHF-1|MODY6|NEUROD|bHLHa3	neuronal differentiation 1	protein-coding	0.000000	0.370000	
chunk0176_323_1	chr7	17063388	17063587	+	0	NA	Intergenic	Intergenic	-181498	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.005025	0.405000	
chunk0029_420_1	chr10	109977249	109977616	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-28536	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.008174	0.478261	
chunk0015_124_1	chr1	185477825	185478264	+	0	NA	Intergenic	Intergenic	-143005	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.004556	0.388636	
chunk0187_445_1	chr7	159024424	159024895	+	0	NA	intron (NR_024394, intron 4 of 4)	CpG	16305	NR_024394	154822	Hs.544783	NM_198345	ENSG00000231419	LINC00689	-	long intergenic non-protein coding RNA 689	ncRNA	0.082803	0.644068	
chunk0094_214_1	chr2	6624293	6624817	+	0	NA	Intergenic	Intergenic	9232	NR_110500	102800315	Hs.729713	NR_110498	ENSG00000236172	LINC01246	-	long intergenic non-protein coding RNA 1246	ncRNA	0.005725	0.373333	
chunk0001_113_1	chr1	3773342	3773722	+	0	NA	intron (NM_001288583, intron 2 of 3)	intron (NM_001288583, intron 2 of 3)	745	NM_001163724	388588	Hs.22047	NM_001163724	ENSG00000235169	SMIM1	Vel	small integral membrane protein 1 (Vel blood group)	protein-coding	0.031579	0.606299	97(GGGAACAACGTGTTCT,-,0.00),98(GGAACAACGTGTTCTA,+,0.00)
chunk0003_101_1	chr1	31938370	31938854	+	0	NA	promoter-TSS (NM_080391)	promoter-TSS (NM_080391)	-225	NM_080391	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.097107	0.719588	
chunk0196_106_1	chr8	103075097	103075330	+	0	NA	Intergenic	Intergenic	54193	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.004292	0.418803	
chunk0187_65_1	chr8	2007179	2007880	+	0	NA	TTS (NM_014867)	TTS (NM_014867)	33651	NM_014867	9920	Hs.5333	NM_014867	ENSG00000176595	KBTBD11	KLHDC7C	kelch repeat and BTB domain containing 11	protein-coding	0.022825	0.605413	329(GAGGACAGCCTGTCCC,-,0.00),330(AGGACAGCCTGTCCCT,+,0.00)
chunk0194_19_1	chr8	81593228	81593655	+	0	NA	Intergenic	Intergenic	-62126	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.002342	0.364486	
chunk0171_296_1	chr6	128492163	128492845	+	0	NA	intron (NM_001291981, intron 1 of 32).2	MIR|SINE|MIR	28170	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.004399	0.390922	
chunk0116_272_1	chr21	39275408	39275885	+	0	NA	intron (NM_018963, intron 12 of 41)	L1MA7|LINE|L1	38140	NM_001007246	54014	Hs.627139	NM_018963	ENSG00000185658	BRWD1	C21orf107|DCAF19|N143|WDR9|WRD9	bromodomain and WD repeat domain containing 1	protein-coding	0.012579	0.368201	
chunk0189_223_1	chr8	24391227	24391902	+	0	NA	intron (NM_001145271, intron 2 of 14)	intron (NM_001145271, intron 2 of 14)	7279	NM_001145271	27299	Hs.521459	NM_014479	ENSG00000134028	ADAMDEC1	M12.219	ADAM like decysin 1	protein-coding	0.001481	0.315089	345(AAGAACATTGTGTCCA,-,0.00),346(AGAACATTGTGTCCAT,+,0.00)
chunk0167_32_1	chr6	53886738	53887175	+	0	NA	intron (NM_018214, intron 4 of 13)	intron (NM_018214, intron 4 of 13)	-43026	NR_125842	101927189	Hs.453592	NR_125842	ENSG00000236740	LOC101927189	-	uncharacterized LOC101927189	ncRNA	0.004577	0.404110	164(GGGATCAGCTTGTACT,-,0.00),165(GGATCAGCTTGTACTC,+,0.00)
chunk0118_59_1	chr22	27965522	27965770	+	0	NA	intron (NR_026963, intron 2 of 4)	L1ME3C|LINE|L1	-45034	NR_036169	100423034		NR_036169	ENSG00000264073	MIR3199-1	mir-3199-1	microRNA 3199-1	ncRNA	0.008065	0.361446	
chunk0060_23_1	chr14	39771199	39771717	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-338958	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.003861	0.339114	
chunk0007_89_1	chr1	78549166	78550332	+	0	NA	Intergenic	L1PA16|LINE|L1	58706	NM_000959	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.006861	0.379606	
chunk0043_43_1	chr12	13431529	13431787	+	0	NA	Intergenic	L2c|LINE|L2	-54913	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.003876	0.359073	
chunk0088_138_1	chr18	45975676	45976010	+	0	NA	Intergenic	LTR8A|LTR|ERV1	-8504	NM_020964	57724	Hs.514843	NM_020964	ENSG00000152223	EPG5	HEEW1|KIAA1632|VICIS	ectopic P-granules autophagy protein 5 homolog	protein-coding	0.008982	0.417910	
chunk0008_14_1	chr1	87385953	87386297	+	0	NA	Intergenic	Intergenic	-14470	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.011628	0.391304	
chunk0115_430_1	chr21	31846766	31847064	+	0	NA	Intergenic	Charlie15a|DNA|hAT-Charlie	-26400	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.000000	0.444816	
chunk0087_175_1	chr18	35241516	35242009	+	0	NA	intron (NM_032347, intron 1 of 5)	intron (NM_032347, intron 1 of 5)	732	NM_001135178	84307	Hs.591061	NM_032347	ENSG00000186812	ZNF397	ZNF47|ZSCAN15	zinc finger protein 397	protein-coding	0.012170	0.315789	
chunk0129_134_1	chr3	120093858	120094190	+	0	NA	5' UTR (NM_002093, exon 1 of 12)	5' UTR (NM_002093, exon 1 of 12)	393	NM_002093	2932	Hs.445733	NM_002093	ENSG00000082701	GSK3B	-	glycogen synthase kinase 3 beta	protein-coding	0.099398	0.702703	
chunk0077_92_1	chr16	77607940	77608403	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-114321	NM_001243660	283927	Hs.282665	NM_001105663	ENSG00000140876	NUDT7	-	nudix hydrolase 7	protein-coding	0.008639	0.385776	
chunk0040_186_1	chr11	114080269	114080792	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	19964	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.009560	0.416031	
chunk0145_317_1	chr4	150540651	150540923	+	0	NA	intron (NM_001199282, intron 40 of 56)	intron (NM_001199282, intron 40 of 56)	-41138	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.000000	0.315018	
chunk0017_109_1	chr1	205958755	205959568	+	0	NA	TTS (NR_110982)	TTS (NR_110982)	1236	NR_110982	103021295	Hs.741319	NR_110982		LOC103021295	-	uncharacterized LOC103021295	ncRNA	0.009840	0.491400	
chunk0116_334_1	chr21	41346013	41346724	+	0	NA	intron (NM_058186, intron 5 of 7)	intron (NM_058186, intron 5 of 7)	-15655	NM_002463	4600	Hs.926	NM_002463	ENSG00000183486	MX2	MXB	MX dynamin like GTPase 2	protein-coding	0.018284	0.445225	
chunk0168_371_1	chr6	93723750	93724184	+	0	NA	intron (NR_015362, intron 2 of 9)	intron (NR_015362, intron 2 of 9)	16884	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.004608	0.365517	
chunk0110_138_1	chr20	13551712	13552327	+	0	NA	intron (NM_017714, intron 8 of 13)	HAL1M8|LINE|L1	86917	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.004878	0.366883	259(AGGAACATGCTGAACT,-,0.00),260(GGAACATGCTGAACTT,+,0.00),322(CAGGACAAACAGTCCA,-,0.00),323(AGGACAAACAGTCCAG,+,0.00)
chunk0109_29_1	chr20	496237	496568	+	0	NA	intron (NM_177559, intron 7 of 13)	MER58A|DNA|hAT-Charlie	-33849	NM_144628	128637	Hs.590876	NM_144628	ENSG00000125875	TBC1D20	C20orf140|WARBM4	TBC1 domain family member 20	protein-coding	0.006042	0.391566	
chunk0131_212_1	chr3	148979713	148979924	+	0	NA	Intergenic	L1ME4b|LINE|L1	-11590	NM_001184721	2992	Hs.477892	NM_004130	ENSG00000163754	GYG1	GSD15|GYG	glycogenin 1	protein-coding	0.004739	0.334906	105(TGGCACAAACAGTGCT,-,0.00),106(GGCACAAACAGTGCTG,+,0.00)
chunk0089_40_1	chr18	58020540	58020929	+	0	NA	Intergenic	Intergenic	-23644	NM_001243960	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.005141	0.433333	
chunk0031_308_1	chr10	128866140	128866679	+	0	NA	Intergenic	Intergenic	580459	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.007421	0.387037	
chunk0105_251_1	chr2	188811474	188811815	+	0	NA	Intergenic	Intergenic	-21540	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.002933	0.406433	
chunk0116_263_1	chr21	39046806	39047084	+	0	NA	Intergenic	Intergenic	-69171	NR_109962	101928435	Hs.385528	NR_109962	ENSG00000232837	LINC01700	-	long intergenic non-protein coding RNA 1700	ncRNA	0.000000	0.462366	
chunk0152_79_1	chr5	58090723	58090922	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	31519	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.010050	0.380000	
chunk0130_178_1	chr3	133452725	133453373	+	0	NA	intron (NM_003571, intron 4 of 6)	intron (NM_003571, intron 4 of 6)	53054	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.007716	0.416025	
chunk0043_55_1	chr12	13941626	13942306	+	0	NA	intron (NM_000834, intron 1 of 12)	intron (NM_000834, intron 1 of 12)	38122	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.014706	0.459618	
chunk0176_251_1	chr7	16202231	16202578	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-8082	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.002882	0.333333	
chunk0151_126_1	chr5	43870345	43870607	+	0	NA	Intergenic	Intergenic	-267246	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.003817	0.292776	
chunk0006_133_1	chr1	65978862	65979573	+	0	NA	intron (NM_002600, intron 3 of 16)	intron (NM_002600, intron 3 of 16)	-13399	NM_001037340	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.007032	0.379213	
chunk0125_157_1	chr3	66463026	66463545	+	0	NA	intron (NM_015541, intron 1 of 18)	intron (NM_015541, intron 1 of 18)	37136	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.013487	0.461538	
chunk0112_435_1	chr20	47605896	47606153	+	0	NA	intron (NM_001174087, intron 2 of 22)	AluJo|SINE|Alu	104167	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.000000	0.414729	
chunk0042_369_1	chr12	10435847	10436076	+	0	NA	promoter-TSS (NM_002260)	promoter-TSS (NM_002260)	32	NM_002260	3822	Hs.591157	NM_002260	ENSG00000205809	KLRC2	CD159c|NKG2-C|NKG2C	killer cell lectin like receptor C2	protein-coding	0.008734	0.417391	
chunk0086_79_1	chr18	13306064	13306566	+	0	NA	intron (NM_181481, intron 1 of 5)	Tigger2|DNA|TcMar-Tigger	28210	NM_181481	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.003984	0.419483	
chunk0097_154_1	chr2	48305428	48306008	+	0	NA	Intergenic	Intergenic	-8938	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.010345	0.397590	
chunk0195_230_1	chr8	97431821	97432056	+	0	NA	intron (NR_125390, intron 1 of 2)	intron (NR_125390, intron 1 of 2)	14559	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.004255	0.444915	
chunk0136_232_1	chr4	8428346	8428545	+	0	NA	intron (NM_003501, intron 1 of 17)	CpG	12280	NM_001101667	8310	Hs.479122	NM_003501	ENSG00000087008	ACOX3	-	acyl-CoA oxidase 3, pristanoyl	protein-coding	0.115578	0.735000	
chunk0131_98_1	chr3	143644432	143644752	+	0	NA	intron (NM_173653, intron 6 of 15)	intron (NM_173653, intron 6 of 15)	203939	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.003125	0.492212	
chunk0201_366_1	chr9	68573701	68573943	+	0	NA	Intergenic	Intergenic	-27220	NR_109769	101927015	Hs.406454	NR_109769	ENSG00000234506	LINC01506	-	long intergenic non-protein coding RNA 1506	ncRNA	0.000000	0.386831	
chunk0128_89_1	chr3	105689705	105690054	+	0	NA	intron (NM_170662, intron 13 of 18)	intron (NM_170662, intron 13 of 18)	179164	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.248571	
chunk0177_289_1	chr7	25756920	25757290	+	0	NA	Intergenic	Intergenic	192881	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.000000	0.353100	
chunk0038_383_1	chr11	93498131	93498477	+	0	NA	intron (NM_020179, intron 2 of 2)	intron (NM_020179, intron 2 of 2)	45076	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.008671	0.446686	
chunk0067_380_1	chr15	49068092	49068630	+	0	NA	Intergenic	MIR3|SINE|MIR	-21798	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.001859	0.389610	
chunk0182_352_1	chr7	99551991	99552199	+	0	NA	promoter-TSS (NM_145111)	promoter-TSS (NM_145111)	39	NM_145111	221786	Hs.596587	NM_145111	ENSG00000221909	FAM200A	C7orf38	family with sequence similarity 200 member A	protein-coding	0.057692	0.617225	
chunk0146_221_1	chr4	161842920	161843237	+	0	NA	intron (NM_001128427, intron 4 of 15)	intron (NM_001128427, intron 4 of 15)	-179655	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.298742	
chunk0073_52_1	chr16	3129488	3129753	+	0	NA	non-coding (NR_110900, exon 4 of 6)	non-coding (NR_110900, exon 4 of 6)	5262	NR_110900	100507458	Hs.522143	NR_110900		ZNF213-AS1	-	ZNF213 antisense RNA 1 (head to head)	ncRNA	0.045283	0.597744	
chunk0204_147_1	chr9	95683767	95684278	+	0	NA	Intergenic	L1MA9|LINE|L1	-167057	NM_001083603	5727	Hs.494538	NM_000264	ENSG00000185920	PTCH1	BCNS|NBCCS|PTC|PTC1|PTCH	patched 1	protein-coding	0.011742	0.378906	
chunk0077_168_1	chr16	79416137	79416541	+	0	NA	Intergenic	L2b|LINE|L2	184386	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.014851	0.432099	
chunk0129_48_1	chr3	117444026	117444553	+	0	NA	Intergenic	LTR1E|LTR|ERV1	522858	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.007590	0.475379	
chunk0105_323_1	chr2	190964743	190965504	+	0	NA	3' UTR (NM_014905, exon 18 of 18)	3' UTR (NM_014905, exon 18 of 18)	49127	NM_139266	6772	Hs.642990	NM_007315	ENSG00000115415	STAT1	CANDF7|IMD31A|IMD31B|IMD31C|ISGF-3|STAT91	signal transducer and activator of transcription 1	protein-coding	0.010512	0.362205	
chunk0150_270_1	chr5	36837012	36837393	+	0	NA	Intergenic	Intergenic	39492	NR_046262	646719	Hs.355684	NR_046262	ENSG00000285967	NIPBL-DT	NIPBL-AS|NIPBL-AS1	NIPBL divergent transcript	ncRNA	0.002625	0.348168	
chunk0141_88_1	chr4	78687870	78688144	+	0	NA	Intergenic	Intergenic	42013	NR_038305	100505702	Hs.235795	NR_038303		LINC01094	-	long intergenic non-protein coding RNA 1094	ncRNA	0.010949	0.403636	
chunk0138_426_1	chr4	45140419	45141057	+	0	NA	Intergenic	Intergenic	-414104	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.001567	0.306729	
chunk0087_118_1	chr18	32787563	32787964	+	0	NA	Intergenic	Intergenic	-14752	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.002494	0.303483	
chunk0092_204_1	chr19	31113353	31113843	+	0	NA	Intergenic	Intergenic	235686	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.004082	0.395112	
chunk0096_142_1	chr2	28894539	28894807	+	0	NA	promoter-TSS (NM_015131)	promoter-TSS (NM_015131)	30	NM_015131	23160	Hs.622982	NM_015131	ENSG00000163811	WDR43	NET12|UTP5	WD repeat domain 43	protein-coding	0.111940	0.724907	
chunk0141_27_1	chr4	76873704	76874208	+	0	NA	Intergenic	Intergenic	23893	NM_001029870	345079	Hs.257292	NM_001029870	ENSG00000186212	SOWAHB	ANKRD56	sosondowah ankyrin repeat domain family member B	protein-coding	0.005952	0.390099	
chunk0132_418_1	chr3	164533309	164533666	+	0	NA	Intergenic	Intergenic	297993	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.008403	0.391061	
chunk0176_6_1	chr7	8136801	8137278	+	0	NA	intron (NM_001136020, intron 12 of 13)	intron (NM_001136020, intron 12 of 13)	125013	NM_022307	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.010482	0.341004	
chunk0093_212_1	chr19	49765504	49765818	+	0	NA	Intergenic	Intergenic	-1262	NM_014203	160	Hs.467125	NM_014203	ENSG00000196961	AP2A1	ADTAA|AP2-ALPHA|CLAPA1	adaptor related protein complex 2 subunit alpha 1	protein-coding	0.003185	0.482540	
chunk0028_421_1	chr10	93591757	93592149	+	0	NA	3' UTR (NM_006744, exon 6 of 6)	3' UTR (NM_006744, exon 6 of 6)	9283	NM_006744	5950	Hs.50223	NM_006744	ENSG00000138207	RBP4	MCOPCB10|RDCCAS	retinol binding protein 4	protein-coding	0.017857	0.419847	
chunk0183_170_1	chr7	106117637	106118318	+	0	NA	Intergenic	MER83A-int|LTR|ERV1	-5330	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.014684	0.419355	305(AGGTACACAGTGAACT,-,0.00),306(GGTACACAGTGAACTT,+,0.00)
chunk0030_448_1	chr10	121021936	121022241	+	0	NA	Intergenic	HAL1|LINE|L1	-170909	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.003279	0.362745	
chunk0211_435_1	chrX	129525213	129525412	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-1807	NM_001282874	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.015075	0.415000	
chunk0097_58_1	chr2	43531736	43532197	+	0	NA	intron (NR_073394, intron 21 of 35)	L1M4|LINE|L1	64008	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.004338	0.346320	
chunk0199_57_1	chr9	2029765	2030286	+	0	NA	intron (NM_003070, intron 2 of 33)	intron (NM_003070, intron 2 of 33)	8080	NM_001289396	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.005758	0.400383	
chunk0068_68_1	chr15	51907341	51907912	+	0	NA	intron (NM_014547, intron 9 of 9)	MIRb|SINE|MIR	16494	NR_109775	100422556	Hs.664788	NR_109775		LOC100422556	-	LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene	pseudo	0.014011	0.452797	
chunk0029_105_1	chr10	97687180	97687426	+	0	NA	promoter-TSS (NM_021732)	promoter-TSS (NM_021732)	-45	NM_021732	60370	Hs.23918	NM_021732	ENSG00000119986	AVPI1	PP5395|VIP32|VIT32	arginine vasopressin induced 1	protein-coding	0.093496	0.684211	
chunk0086_379_1	chr18	26449318	26449526	+	0	NA	Intergenic	Intergenic	26427	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.009615	0.377990	
chunk0016_305_1	chr1	201309335	201310472	+	0	NA	intron (NM_001005337, intron 2 of 13)	MER20B|DNA|hAT-Charlie	26451	NM_001005337	5317	Hs.497350	NM_000299	ENSG00000081277	PKP1	B6P	plakophilin 1	protein-coding	0.014952	0.515817	
chunk0102_377_1	chr2	153519113	153519670	+	0	NA	Intergenic	Intergenic	-40583	NM_019845	56475	Hs.100890	NM_019845	ENSG00000177519	RPRM	REPRIMO	reprimo, TP53 dependent G2 arrest mediator homolog	protein-coding	0.007181	0.345878	
chunk0102_366_1	chr2	152730915	152731393	+	0	NA	intron (NM_152522, intron 2 of 3)	MamGypLTR1c|LTR|Gypsy	13261	NR_024526	151188	Hs.643580	NM_152522	ENSG00000177917	ARL6IP6	AIP-6|AIP6|PFAAP1	ADP ribosylation factor like GTPase 6 interacting protein 6	protein-coding	0.002092	0.377871	
chunk0189_351_1	chr8	26811536	26812188	+	0	NA	intron (NM_033302, intron 1 of 2)	L1ME3|LINE|L1	53543	NM_033302	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.013804	0.364472	
chunk0123_243_1	chr3	45689134	45689471	+	0	NA	promoter-TSS (NM_014016)	promoter-TSS (NM_014016)	40	NM_014016	22908	Hs.156509	NM_014016	ENSG00000211456	SACM1L	SAC1	SAC1 like phosphatidylinositide phosphatase	protein-coding	0.112760	0.680473	
chunk0137_3_1	chr4	10496412	10497151	+	0	NA	intron (NM_052964, intron 18 of 18)	MER51B|LTR|ERV1	-39373	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.014885	0.431081	
chunk0119_313_1	chr22	46686078	46686359	+	0	NA	3' UTR (NM_022766, exon 13 of 13)	3' UTR (NM_022766, exon 13 of 13)	52037	NM_022766	64781	Hs.200668	NM_022766	ENSG00000100422	CERK	LK4|dA59H18.2|dA59H18.3|hCERK	ceramide kinase	protein-coding	0.046263	0.549645	94(AAGGACAAGATGTTCA,-,0.00),95(AGGACAAGATGTTCAA,+,0.00)
chunk0161_398_1	chr5	177197600	177197961	+	0	NA	intron (NM_022455, intron 3 of 22)	intron (NM_022455, intron 3 of 22)	63948	NM_022455	64324	Hs.106861	NM_022455	ENSG00000165671	NSD1	ARA267|KMT3B|SOTOS|SOTOS1|STO	nuclear receptor binding SET domain protein 1	protein-coding	0.019391	0.417127	
chunk0126_113_1	chr3	75314930	75315132	+	0	NA	Intergenic	Intergenic	100555	NR_039646	100616394		NR_039646	ENSG00000284252	MIR4444-1	MIR4444|hsa-mir-4444-1|miR-4444-1	microRNA 4444-1	ncRNA	0.004950	0.458128	
chunk0132_168_1	chr3	156755179	156755571	+	0	NA	intron (NR_038387, intron 1 of 2)	MER34C_|LTR|ERV1	56646	NR_003284	647033	Hs.745109	NR_003284		PA2G4P4	PA2G4L1	proliferation-associated 2G4 pseudogene 4	pseudo	0.005102	0.379135	
chunk0101_142_1	chr2	127527037	127527448	+	0	NA	promoter-TSS (NM_017969)	promoter-TSS (NM_017969)	-731	NM_017969	55677	Hs.469879	NM_017969	ENSG00000163166	IWS1	-	interacts with SUPT6H, CTD assembly factor 1	protein-coding	0.019465	0.463592	
chunk0013_407_1	chr1	173061933	173062288	+	0	NA	Intergenic	Intergenic	-11147	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.005634	0.351124	
chunk0081_457_1	chr17	49369634	49370271	+	0	NA	intron (NR_110883, intron 2 of 4)	intron (NR_110883, intron 2 of 4)	-7479	NM_014897	22834	Hs.463375	NM_014897	ENSG00000198740	ZNF652	-	zinc finger protein 652	protein-coding	0.004710	0.427900	17(TGCCCAGGCTGTTCTC,+,0.00)
chunk0165_132_1	chr6	33323268	33323582	+	0	NA	promoter-TSS (NM_001350)	promoter-TSS (NM_001350)	-409	NM_001254717	1616	Hs.336916	NM_001350	ENSG00000204209	DAXX	BING2|DAP6|EAP1|SMIM40	death domain associated protein	protein-coding	0.044586	0.580952	
chunk0199_134_1	chr9	3881982	3882575	+	0	NA	intron (NM_001042413, intron 7 of 10)	LTR16E2|LTR|ERVL	-16368	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.013491	0.461279	
chunk0155_69_1	chr5	91643751	91644253	+	0	NA	Intergenic	Intergenic	-260670	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003984	0.347913	181(AGGAACAGTGTGATCC,-,0.00),182(GGAACAGTGTGATCCT,+,0.00)
chunk0110_199_1	chr20	14845530	14845897	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	83805	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.005450	0.404891	
chunk0187_50_1	chr8	1760229	1760520	+	0	NA	Intergenic	Intergenic	-3330	NM_018941	2055	Hs.127675	NM_018941	ENSG00000182372	CLN8	C8orf61|EPMR|TLCD6	CLN8 transmembrane ER and ERGIC protein	protein-coding	0.030928	0.489726	
chunk0189_249_1	chr8	25057384	25058116	+	0	NA	Intergenic	L1PA16|LINE|L1	-100881	NM_006158	4747	Hs.521461	NM_006158	ENSG00000277586	NEFL	CMT1F|CMT2E|CMTDIG|NF-L|NF68|NFL|PPP1R110	neurofilament light	protein-coding	0.004098	0.342428	
chunk0162_9_1	chr6	355965	356316	+	0	NA	Intergenic	Intergenic	-35599	NM_002460	3662	Hs.401013	NM_002460	ENSG00000137265	IRF4	LSIRF|MUM1|NF-EM5|SHEP8	interferon regulatory factor 4	protein-coding	0.008547	0.420455	
chunk0056_284_1	chr13	90426114	90426547	+	0	NA	Intergenic	L1MCb|LINE|L1	-66958	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.004619	0.354839	
chunk0119_306_1	chr22	46607433	46607842	+	0	NA	Intergenic	L2a|LINE|L2	-19124	NM_015124	23151	Hs.475150	NM_015124	ENSG00000075240	GRAMD4	DIP	GRAM domain containing 4	protein-coding	0.036675	0.612195	
chunk0079_360_1	chr17	17913862	17914244	+	0	NA	intron (NM_001033551, intron 1 of 13)	intron (NM_001033551, intron 1 of 13)	58417	NM_001033551	146691	Hs.462379	NM_144678	ENSG00000175662	TOM1L2	-	target of myb1 like 2 membrane trafficking protein	protein-coding	0.005236	0.566580	
chunk0014_164_1	chr1	178289820	178290374	+	0	NA	intron (NM_170692, intron 2 of 17)	L2a|LINE|L2	-51374	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.003610	0.340541	
chunk0158_273_1	chr5	131435943	131436513	+	0	NA	exon (NM_001164389, exon 25 of 25)	exon (NM_001164389, exon 25 of 25)	172219	NM_001038702	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.007018	0.402802	310(CAGTACTGTCTGTTCT,-,0.00),311(AGTACTGTCTGTTCTT,+,0.00)
chunk0124_19_1	chr3	51926062	51926577	+	0	NA	Intergenic	L1ME1|LINE|L1	15622	NM_004704	9136	Hs.153768	NM_004704	ENSG00000114767	RRP9	RNU3IP2|U3-55K	ribosomal RNA processing 9, U3 small nucleolar RNA binding protein	protein-coding	0.005825	0.375969	
chunk0126_106_1	chr3	75089665	75090322	+	0	NA	Intergenic	Intergenic	-124483	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.004566	0.344985	
chunk0038_21_1	chr11	80958471	80958729	+	0	NA	Intergenic	Intergenic	-195797	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003876	0.362934	
chunk0042_270_1	chr12	6961210	6961525	+	0	NA	TTS (NM_002831)	TTS (NM_002831)	-2332	NR_029779	406985		NR_029779	ENSG00000207713	MIR200C	MIRN200C|mir-200c	microRNA 200c	ncRNA	0.050794	0.617089	
chunk0108_154_1	chr2	231050370	231050709	+	0	NA	TTS (NM_001144994)	TTS (NM_001144994)	-6325	NM_001191037	5707	Hs.3887	NM_002807	ENSG00000173692	PSMD1	P112|Rpn2|S1	proteasome 26S subunit, non-ATPase 1	protein-coding	0.008850	0.523529	
chunk0203_438_1	chr9	91327929	91328128	+	0	NA	intron (NM_001698, intron 3 of 9)	LTR27D|LTR|ERV1	33896	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.015075	0.600000	
chunk0031_243_1	chr10	126895214	126895680	+	0	NA	Intergenic	Intergenic	-9962	NM_001290223	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.012876	0.573876	213(CTGTACACTCAGTTCC,-,0.00),214(TGTACACTCAGTTCCC,+,0.00)
chunk0067_448_1	chr15	50228867	50229273	+	0	NA	intron (NM_003645, intron 8 of 9)	intron (NM_003645, intron 8 of 9)	36895	NM_001306146	3067	Hs.1481	NM_002112	ENSG00000140287	HDC	-	histidine decarboxylase	protein-coding	0.007389	0.459459	
chunk0072_3_1	chr16	181783	181982	+	0	NA	TTS (NM_005331)	TTS (NM_005331)	1548	NM_005331	3049	Hs.247921	NM_005331	ENSG00000086506	HBQ1	HBQ	hemoglobin subunit theta 1	protein-coding	0.020101	0.480000	
chunk0088_199_1	chr18	47858523	47859180	+	0	NA	intron (NM_001003652, intron 6 of 10)	L1MEf|LINE|L1	71748	NM_005901	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.006088	0.278116	
chunk0169_269_1	chr6	105544435	105544884	+	0	NA	Intergenic	Intergenic	-141535	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.008909	0.400000	
chunk0100_80_1	chr2	106970851	106971100	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-83868	NM_032528	84620	Hs.98265	NM_032528	ENSG00000144057	ST6GAL2	SIAT2|ST6GalII	ST6 beta-galactoside alpha-2,6-sialyltransferase 2	protein-coding	0.008032	0.408000	
chunk0122_235_1	chr3	33810710	33810927	+	0	NA	intron (NM_001162429, intron 1 of 17)	AluJr4|SINE|Alu	12247	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.004608	0.403670	
chunk0057_401_1	chr13	109644022	109644481	+	0	NA	Intergenic	L2a|LINE|L2	-84023	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.006536	0.441304	
chunk0184_357_1	chr7	120854756	120855031	+	0	NA	intron (NM_012338, intron 2 of 7)	intron (NM_012338, intron 2 of 7)	3230	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.010909	0.369565	
chunk0152_260_1	chr5	60979729	60980073	+	0	NA	intron (NM_174889, intron 1 of 3)	L1M1|LINE|L1	34772	NM_174889	91942	Hs.591757	NM_174889	ENSG00000164182	NDUFAF2	B17.2L|MC1DN10|MMTN|NDUFA12L|mimitin	NADH:ubiquinone oxidoreductase complex assembly factor 2	protein-coding	0.008721	0.501449	
chunk0206_459_1	chr9	128433550	128433854	+	0	NA	intron (NM_001286760, intron 9 of 12)	MIRb|SINE|MIR	13222	NM_016174	51148	Hs.495230	NM_016174	ENSG00000167123	CERCAM	CEECAM1|GLT25D3	cerebral endothelial cell adhesion molecule	protein-coding	0.016447	0.567213	
chunk0202_142_1	chr9	73454689	73455126	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	303176	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.009153	0.342466	
chunk0166_319_1	chr6	49760683	49760900	+	0	NA	Intergenic	Intergenic	-16336	NM_006061	10321	Hs.404466	NM_006061	ENSG00000096006	CRISP3	Aeg2|CRISP-3|CRS3|SGP28|dJ442L6.3	cysteine rich secretory protein 3	protein-coding	0.000000	0.403670	
chunk0002_215_1	chr1	19639993	19640510	+	0	NA	intron (NM_001204088, intron 2 of 4)	L2a|LINE|L2	-2978	NM_001278164	4681	Hs.654502	NM_005380	ENSG00000158747	NBL1	D1S1733E|DAN|DAND1|NB|NO3	NBL1, DAN family BMP antagonist	protein-coding	0.011605	0.465251	
chunk0054_394_1	chr13	50365964	50367064	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	160935	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.006364	0.402361	
chunk0024_214_1	chr10	36924664	36925000	+	0	NA	Intergenic	Intergenic	-201025	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.005952	0.323442	
chunk0017_27_1	chr1	204741363	204741782	+	0	NA	Intergenic	HAL1|LINE|L1	-56103	NM_201630	10446	Hs.26312	NM_006338	ENSG00000170382	LRRN2	FIGLER7|GAC1|LRANK1|LRRN5	leucine rich repeat neuronal 2	protein-coding	0.007160	0.357143	
chunk0099_420_1	chr2	102539169	102539743	+	0	NA	Intergenic	Intergenic	66153	NM_001011552	389015	Hs.447686	NM_001011552	ENSG00000180251	SLC9A4	NHE4	solute carrier family 9 member A4	protein-coding	0.012195	0.353043	
chunk0069_188_1	chr15	63164091	63164585	+	0	NA	Intergenic	Intergenic	-6796	NM_015920	51065	Hs.108957	NM_015920	ENSG00000185088	RPS27L	-	ribosomal protein S27 like	protein-coding	0.008097	0.404040	
chunk0087_331_1	chr18	40017064	40017437	+	0	NA	Intergenic	Intergenic	-49036	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.018767	0.393048	
chunk0200_129_1	chr9	17482044	17482889	+	0	NA	intron (NM_017738, intron 23 of 25)	L1M3b|LINE|L1	-96488	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.002367	0.294326	
chunk0086_260_1	chr18	23442766	23443169	+	0	NA	Intergenic	Intergenic	-5006	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.004963	0.309406	
chunk0153_121_1	chr5	68713505	68713792	+	0	NA	Intergenic	MIRb|SINE|MIR	316279	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.000000	0.399306	
chunk0117_127_1	chr22	19104512	19104868	+	0	NA	intron (NM_005137, intron 1 of 9)	intron (NM_005137, intron 1 of 9)	17764	NM_001184781	9993	Hs.517357	NM_005137	ENSG00000070413	DGCR2	DGS-C|IDD|LAN|SEZ-12	DiGeorge syndrome critical region gene 2	protein-coding	0.005618	0.521008	
chunk0023_98_1	chr10	22683239	22683631	+	0	NA	intron (NM_005028, intron 1 of 9)	MIRc|SINE|MIR	31139	NM_005028	5305	Hs.57079	NM_005028	ENSG00000150867	PIP4K2A	PI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK	phosphatidylinositol-5-phosphate 4-kinase type 2 alpha	protein-coding	0.015306	0.465649	
chunk0119_28_1	chr22	40277371	40277655	+	0	NA	intron (NM_001024843, intron 10 of 23)	intron (NM_001024843, intron 10 of 23)	-68987	NM_001123378	158	Hs.75527	NM_000026	ENSG00000239900	ADSL	AMPS|ASASE|ASL	adenylosuccinate lyase	protein-coding	0.021127	0.371930	201(GGGGACACCCTGTCCC,-,0.00),202(GGGACACCCTGTCCCT,+,0.00)
chunk0167_178_1	chr6	63671130	63671543	+	0	NA	intron (NM_001290260, intron 2 of 3)	L2a|LINE|L2	24810	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.009685	0.381643	
chunk0100_376_1	chr2	118056266	118056670	+	0	NA	Intergenic	MIRb|SINE|MIR	-32006	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.012376	0.476543	
chunk0176_349_1	chr7	17815355	17815815	+	0	NA	intron (NM_015132, intron 19 of 25)	AluJr4|SINE|Alu	124923	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.008696	0.394794	
chunk0032_289_1	chr11	9486410	9486787	+	0	NA	intron (NM_001282657, intron 6 of 14)	intron (NM_001282657, intron 6 of 14)	25633	NM_003442	7702	Hs.523471	NM_003442	ENSG00000166478	ZNF143	SBF|STAF|pHZ-1	zinc finger protein 143	protein-coding	0.013263	0.383598	242(TAGAACAATGTGTTTT,-,0.00),243(AGAACAATGTGTTTTG,+,0.00)
chunk0131_207_1	chr3	148915074	148915273	+	0	NA	Intergenic	L1MEh|LINE|L1	49917	NM_001870	1359	Hs.646	NM_001870	ENSG00000163751	CPA3	MC-CPA	carboxypeptidase A3	protein-coding	0.005025	0.345000	
chunk0150_369_1	chr5	39063135	39063397	+	0	NA	intron (NM_001285439, intron 2 of 38)	intron (NM_001285439, intron 2 of 38)	11142	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.003817	0.357414	
chunk0066_240_1	chr15	34447588	34447980	+	0	NA	Intergenic	L1MC4|LINE|L1	-10318	NR_027409	23015	Hs.182982	NM_181077	ENSG00000175265	GOLGA8A	GM88|GOLGA8B	golgin A8 family member A	protein-coding	0.005102	0.363868	
chunk0057_8_1	chr13	95535146	95535629	+	0	NA	intron (NM_182848, intron 1 of 4)	L2c|LINE|L2	-1477	NR_046533	100874194	Hs.569229	NR_046533	ENSG00000223392	CLDN10-AS1	-	CLDN10 antisense RNA 1	ncRNA	0.008282	0.473140	
chunk0018_221_1	chr1	219656697	219657406	+	0	NA	Intergenic	Intergenic	271600	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.005642	0.352113	
chunk0161_156_1	chr5	169031861	169032692	+	0	NA	intron (NR_109897, intron 3 of 4)	intron (NR_109897, intron 3 of 4)	19049	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.006017	0.338942	
chunk0119_87_1	chr22	41638115	41638511	+	0	NA	intron (NM_001288978, intron 5 of 11)	Tigger3c|DNA|TcMar-Tigger	16971	NM_001288976	2547	Hs.292493	NM_001469	ENSG00000196419	XRCC6	CTC75|CTCBF|G22P1|KU70|ML8|TLAA	X-ray repair cross complementing 6	protein-coding	0.007576	0.397985	
chunk0063_110_1	chr14	79074407	79074899	+	0	NA	intron (NR_073547, intron 14 of 20)	intron (NR_073547, intron 14 of 20)	-204686	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.006098	0.436105	
chunk0145_302_1	chr4	150112234	150112433	+	0	NA	intron (NR_036614, intron 2 of 16)	L1PB3|LINE|L1	34059	NM_001040261	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.000000	0.350000	
chunk0171_43_1	chr6	120933925	120934260	+	0	NA	Intergenic	L1PB4|LINE|L1	400408	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.000000	0.303571	
chunk0030_442_1	chr10	120857772	120858056	+	0	NA	intron (NM_018117, intron 2 of 28)	L2a|LINE|L2	-6735	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.000000	0.364912	
chunk0131_275_1	chr3	150228054	150228253	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-10366	NR_110168	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.010050	0.565000	
chunk0192_314_1	chr8	66970618	66971173	+	0	NA	Intergenic	Intergenic	-8305	NM_001193502	100129654	Hs.120040	NM_001193502	ENSG00000261787	TCF24	TCF-24|bHLHa25	transcription factor 24	protein-coding	0.007207	0.411871	
chunk0093_218_1	chr19	49987100	49987556	+	0	NA	intron (NM_001308420, intron 12 of 12)	intron (NM_001308420, intron 12 of 12)	17728	NR_002825									0.024123	0.557987	
chunk0133_404_1	chr3	174356609	174357029	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-436023	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.002381	0.368171	
chunk0193_302_1	chr8	77998367	77998947	+	0	NA	Intergenic	L1MC1|LINE|L1	-517444	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.000000	0.342513	468(GGGAACTCTTTGTACC,-,0.00),469(GGAACTCTTTGTACCT,+,0.00)
chunk0120_35_1	chr3	2574319	2574556	+	0	NA	intron (NM_001206955, intron 3 of 23)	intron (NM_001206955, intron 3 of 23)	-317778	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.004219	0.378151	
chunk0096_148_1	chr2	29165527	29165913	+	0	NA	intron (NR_109844, intron 12 of 13)	intron (NR_109844, intron 12 of 13)	50294	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.010363	0.382429	
chunk0132_412_1	chr3	164360677	164361054	+	0	NA	Intergenic	Intergenic	-189309	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.007958	0.298942	
chunk0050_58_1	chr12	101141194	101141502	+	0	NA	Intergenic	LTR79|LTR|ERVL	68890	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.003247	0.401294	
chunk0207_221_1	chr9	131708274	131708554	+	0	NA	intron (NM_001304275, intron 1 of 23)	intron (NM_001304275, intron 1 of 23)	1428	NM_198679	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.017857	0.533808	
chunk0032_429_1	chr11	12247564	12247938	+	0	NA	intron (NM_001282664, intron 20 of 25)	intron (NM_001282664, intron 20 of 25)	-39149	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.000000	0.464000	180(GAGAACTGGCTGTTCC,-,0.00),181(AGAACTGGCTGTTCCT,+,0.00)
chunk0087_112_1	chr18	32612594	32613100	+	0	NA	Intergenic	Intergenic	101184	NR_003558	441818	Hs.549773	NR_003558	ENSG00000260389	WBP11P1	HsT3017	WW domain binding protein 11 pseudogene 1	pseudo	0.005929	0.370809	
chunk0003_337_1	chr1	38986602	38986889	+	0	NA	Intergenic	L2c|LINE|L2	-4499	NM_024595	79647	Hs.293563	NM_024595	ENSG00000174574	AKIRIN1	C1orf108|STRF2	akirin 1	protein-coding	0.000000	0.409722	
chunk0197_270_1	chr8	123761775	123762252	+	0	NA	Intergenic	Intergenic	-6629	NM_144963	157769	Hs.459174	NM_144963	ENSG00000176853	FAM91A1	-	family with sequence similarity 91 member A1	protein-coding	0.004193	0.332636	
chunk0119_42_1	chr22	40625574	40626090	+	0	NA	intron (NM_001282661, intron 1 of 13)	intron (NM_001282661, intron 1 of 13)	10887	NM_001282662	57591	Hs.654688	NM_020831	ENSG00000196588	MRTFA	BSAC|MAL|MKL|MKL1|MRTF-A	myocardin related transcription factor A	protein-coding	0.011628	0.427466	
chunk0077_162_1	chr16	79171741	79172282	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	428714	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.016636	0.433579	272(AGGAACACGGAGCTCC,-,0.00),273(GGAACACGGAGCTCCT,+,0.00)
chunk0019_203_1	chr1	226945345	226945676	+	0	NA	intron (NM_020247, intron 1 of 14)	intron (NM_020247, intron 1 of 14)	5273	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.021148	0.503012	
chunk0105_41_1	chr2	182900025	182900542	+	0	NA	Intergenic	Intergenic	-33513	NM_001463	2487	Hs.128453	NM_001463	ENSG00000162998	FRZB	FRE|FRITZ|FRP-3|FRZB-1|FRZB-PEN|FRZB1|FZRB|OS1|SFRP3|SRFP3|hFIZ	frizzled related protein	protein-coding	0.011605	0.445946	
chunk0099_280_1	chr2	98339973	98340172	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-6083	NM_001298	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.010050	0.540000	
chunk0058_367_1	chr14	29118242	29118748	+	0	NA	Intergenic	Intergenic	345791	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.007905	0.368836	
chunk0058_376_1	chr14	29305862	29306165	+	0	NA	Intergenic	Intergenic	533309	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.006601	0.302632	
chunk0208_88_1	chrX	13372974	13373589	+	0	NA	Intergenic	Intergenic	38040	NR_045260	100133123	Hs.449499	NR_045260	ENSG00000226985	LINC01203	-	long intergenic non-protein coding RNA 1203	ncRNA	0.004878	0.378247	
chunk0114_359_1	chr21	19566892	19567718	+	0	NA	Intergenic	Intergenic	-807493	NR_109925	101927797	Hs.551743	NR_109925		MIR548XHG	-	MIR548X host gene	ncRNA	0.001211	0.403869	
chunk0191_435_1	chr8	57861105	57861531	+	0	NA	Intergenic	Intergenic	-117040	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.009390	0.491803	
chunk0134_167_1	chr3	177937375	177937574	+	0	NA	Intergenic	Intergenic	120609	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.000000	0.295000	
chunk0008_369_1	chr1	96772347	96772948	+	0	NA	intron (NM_001300987, intron 6 of 14)	L1MA7|LINE|L1	50009	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.008319	0.395349	
chunk0109_436_1	chr2	241358220	241358495	+	0	NA	intron (NM_014808, intron 1 of 26)	intron (NM_014808, intron 1 of 26)	2108	NM_001282983	9855	Hs.726316	NM_014808	ENSG00000006607	FARP2	FIR|FRG|PLEKHC3	FERM, ARH/RhoGEF and pleckstrin domain protein 2	protein-coding	0.003636	0.358696	
chunk0010_5_1	chr1	111841018	111841850	+	0	NA	intron (NM_172198, intron 2 of 6)	L3|LINE|CR1	15471	NR_046783	100874295	Hs.738190	NR_046783	ENSG00000232558	KCND3-IT1	-	KCND3 intronic transcript 1	ncRNA	0.010817	0.436975	
chunk0208_27_1	chrX	11091676	11092041	+	0	NA	Intergenic	Intergenic	-19428	NM_001171991	3052	Hs.211571	NM_005333	ENSG00000004961	HCCS	CCHL|LSDMCA1|MCOPS7|MLS	holocytochrome c synthase	protein-coding	0.005479	0.355191	
chunk0131_346_1	chr3	151552421	151552820	+	0	NA	Intergenic	MER87|LTR|ERV1	13375	NR_049818	100847036		NR_049818	ENSG00000264330	MIR5186	-	microRNA 5186	ncRNA	0.007519	0.382500	202(CAGGTCACAATGTTCC,-,0.00),203(AGGTCACAATGTTCCT,+,0.00)
chunk0024_171_1	chr10	35719124	35719602	+	0	NA	Intergenic	L2|LINE|L2	-58939	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.010460	0.492693	213(TAGGACACCCTGGCCC,-,0.00),214(AGGACACCCTGGCCCT,+,0.00)
chunk0137_430_1	chr4	28358913	28359192	+	0	NA	Intergenic	Intergenic	-460530	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.003584	0.285714	
chunk0035_109_1	chr11	42498749	42499520	+	0	NA	Intergenic	L2a|LINE|L2	-245444	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.005188	0.389896	
chunk0156_130_1	chr5	106780327	106780558	+	0	NA	Intergenic	L1MA3|LINE|L1	230572	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.008658	0.495690	
chunk0148_377_1	chr5	14683872	14684615	+	0	NA	intron (NM_138348, intron 4 of 6)	intron (NM_138348, intron 4 of 6)	19569	NM_138348	90268	Hs.406335	NM_138348	ENSG00000154124	OTULIN	AIPDS|FAM105B|GUM	OTU deubiquitinase with linear linkage specificity	protein-coding	0.008075	0.416667	317(GAAAACACAGTGTACC,-,0.00),318(AAAACACAGTGTACCT,+,0.00)
chunk0049_439_1	chr12	98445326	98445546	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	11709	NR_033801	121456	Hs.620643	NR_033801	ENSG00000227825	SLC9A7P1	-	solute carrier family 9 member 7 pseudogene 1	pseudo	0.022727	0.484163	
chunk0074_33_1	chr16	20622225	20622471	+	0	NA	TTS (NM_052956)	TTS (NM_052956)	-45975	NM_001105069	348158	Hs.298252	NM_182617	ENSG00000066813	ACSM2B	ACSM2|HXMA|HYST1046	acyl-CoA synthetase medium chain family member 2B	protein-coding	0.004065	0.542510	173(GGGGACAATATGTGCT,-,0.00),174(GGGACAATATGTGCTC,+,0.00)
chunk0148_366_1	chr5	14626133	14626580	+	0	NA	Intergenic	Intergenic	26026	NR_132980	106635683		NR_132980		SNORD141A	-	small nucleolar RNA, C/D box 141A	snoRNA	0.011186	0.406250	
chunk0119_365_1	chr22	47487060	47487302	+	0	NA	promoter-TSS (NR_109967)	promoter-TSS (NR_109967)	-70	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.016529	0.473251	
chunk0139_411_1	chr4	63415424	63416102	+	0	NA	Intergenic	Intergenic	993697	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.004425	0.332842	
chunk0165_311_1	chr6	36987014	36987251	+	0	NA	promoter-TSS (NM_014341)	promoter-TSS (NM_014341)	-581	NM_001271641	23787	Hs.485262	NM_014341	ENSG00000137409	MTCH1	CGI-64|PIG60|PSAP|SLC25A49	mitochondrial carrier 1	protein-coding	0.033755	0.466387	47(TAGGACAGCAAGTGCC,-,0.00),48(AGGACAGCAAGTGCCC,+,0.00)
chunk0205_451_1	chr9	115496304	115496755	+	0	NA	Intergenic	Intergenic	247710	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.002217	0.356195	221(CAGAACAATCAGTCCA,-,0.00),222(AGAACAATCAGTCCAT,+,0.00)
chunk0185_104_1	chr7	125640776	125641174	+	0	NA	Intergenic	L2c|LINE|L2	-376684	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.002513	0.280702	
chunk0029_416_1	chr10	109965495	109965803	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-40319	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.032468	0.517799	
chunk0130_172_1	chr3	133330380	133330769	+	0	NA	intron (NM_001282865, intron 2 of 3)	intron (NM_001282865, intron 2 of 3)	-69421	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.000000	0.343590	
chunk0180_197_1	chr7	66205133	66205683	+	0	NA	5' UTR (NM_003596, exon 1 of 6)	5' UTR (NM_003596, exon 1 of 6)	136	NM_003596	8460	Hs.421194	NM_003596	ENSG00000169902	TPST1	TANGO13A	tyrosylprotein sulfotransferase 1	protein-coding	0.114545	0.731397	
chunk0056_424_1	chr13	94612684	94613001	+	0	NA	intron (NM_180989, intron 3 of 8)	intron (NM_180989, intron 3 of 8)	10992	NM_180989	160897	Hs.439363	NM_180989	ENSG00000152749	GPR180	ITR	G protein-coupled receptor 180	protein-coding	0.000000	0.289308	
chunk0103_299_1	chr2	166599657	166599879	+	0	NA	Intergenic	L1MA3|LINE|L1	-112797	NM_002976	6332	Hs.596087	NM_002976	ENSG00000136546	SCN7A	NaG|Nav2.1|Nav2.2|SCN6A	sodium voltage-gated channel alpha subunit 7	protein-coding	0.000000	0.286996	
chunk0195_393_1	chr8	100269844	100270148	+	0	NA	exon (NM_015435, exon 5 of 11)	exon (NM_015435, exon 5 of 11)	33263	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003289	0.344262	
chunk0037_124_1	chr11	72862694	72863141	+	0	NA	intron (NM_014824, intron 13 of 19)	L1MEc|LINE|L1	-17003	NR_039664									0.006711	0.372768	
chunk0124_441_1	chr3	61368053	61368285	+	0	NA	Intergenic	Intergenic	-116710	NM_001166243	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.008621	0.446352	
chunk0175_341_1	chr6	167432014	167432276	+	0	NA	Intergenic	Intergenic	-47635	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.007634	0.387833	
chunk0083_409_1	chr17	72130949	72131465	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	10187	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.005814	0.433269	
chunk0094_335_1	chr2	9212151	9212689	+	0	NA	intron (NM_003887, intron 1 of 27)	intron (NM_003887, intron 1 of 27)	5655	NM_003887	8853	Hs.555902	NM_003887	ENSG00000151693	ASAP2	AMAP2|CENTB3|DDEF2|PAG3|PAP|Pap-alpha|SHAG1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding	0.016729	0.523191	
chunk0083_254_1	chr17	68101557	68101819	+	0	NA	non-coding (NR_027418, exon 1 of 6)	non-coding (NR_027418, exon 1 of 6)	133	NR_027418	100499466	Hs.591212	NR_027418		LINC00674	-	long intergenic non-protein coding RNA 674	ncRNA	0.114504	0.722433	
chunk0056_358_1	chr13	92320292	92320869	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	31627	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.005199	0.316609	253(TAGTACACAGTGTTCC,-,0.00),254(AGTACACAGTGTTCCC,+,0.00)
chunk0034_446_1	chr11	39491357	39491856	+	0	NA	Intergenic	L2c|LINE|L2	801524	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.010020	0.356000	
chunk0050_154_1	chr12	102924601	102924831	+	0	NA	Intergenic	LTR40b|LTR|ERVL	-7113	NM_000277	5053	Hs.560019	NM_000277	ENSG00000171759	PAH	PH|PKU|PKU1	phenylalanine hydroxylase	protein-coding	0.000000	0.424242	
chunk0058_80_1	chr14	21279943	21280233	+	0	NA	Intergenic	Intergenic	-7889	NM_020366	57096	Hs.126035	NM_020366	ENSG00000092200	RPGRIP1	CORD13|LCA6|RGI1|RGRIP|RPGRIP|RPGRIP1d	RPGR interacting protein 1	protein-coding	0.003448	0.384880	
chunk0123_317_1	chr3	47275124	47275357	+	0	NA	intron (NM_182902, intron 3 of 20)	intron (NM_182902, intron 3 of 20)	-7600	NM_025010	23276	Hs.517946	NM_025010	ENSG00000114648	KLHL18	-	kelch like family member 18	protein-coding	0.008584	0.367521	
chunk0182_424_1	chr7	101216839	101217038	+	0	NA	promoter-TSS (NM_006349)	promoter-TSS (NM_006349)	-766	NM_006349	10467	Hs.211079	NM_006349	ENSG00000106400	ZNHIT1	CG1I|ZNFN4A1	zinc finger HIT-type containing 1	protein-coding	0.030151	0.580000	74(AGGAACACTCTGACCC,-,0.00),75(GGAACACTCTGACCCC,+,0.00)
chunk0136_238_1	chr4	8795816	8796419	+	0	NA	Intergenic	Intergenic	75700	NM_001306142	3166	Hs.104134	NM_018942	ENSG00000215612	HMX1	H6|NKX5-3	H6 family homeobox 1	protein-coding	0.021559	0.521523	
chunk0119_247_1	chr22	45742883	45743570	+	0	NA	intron (NM_001167621, intron 8 of 10)	intron (NM_001167621, intron 8 of 10)	-17298	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.014556	0.425872	
chunk0095_184_1	chr2	17879709	17880346	+	0	NA	intron (NM_002252, intron 1 of 2)	intron (NM_002252, intron 1 of 2)	1370	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.029827	0.529781	
chunk0176_300_1	chr7	16814193	16814545	+	0	NA	Intergenic	L1MEd|LINE|L1	-9255	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.005682	0.325779	
chunk0016_366_1	chr1	202405880	202406441	+	0	NA	intron (NM_002481, intron 1 of 23)	intron (NM_002481, intron 1 of 23)	-56583	NM_032103	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.003565	0.387900	267(GGGCACAGAGTGATCT,-,0.00),268(GGCACAGAGTGATCTG,+,0.00)
chunk0008_270_1	chr1	94663752	94664119	+	0	NA	intron (NR_104131, intron 4 of 4)	MER4-int|LTR|ERV1	81965	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.005450	0.274457	
chunk0066_328_1	chr15	36582252	36582452	+	0	NA	intron (NM_001130010, intron 1 of 11)	Charlie1a|DNA|hAT-Charlie	2749	NM_001290233	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.005000	0.343284	
chunk0029_177_1	chr10	100691506	100691712	+	0	NA	Intergenic	Intergenic	-44100	NM_001304569	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.004854	0.536232	
chunk0029_166_1	chr10	99894303	99894883	+	0	NA	intron (NM_015221, intron 11 of 16)	intron (NM_015221, intron 11 of 16)	-32616	NR_024130	100188954	Hs.656104	NR_024130		DNMBP-AS1	NCRNA00093	DNMBP antisense RNA 1	ncRNA	0.005172	0.371773	
chunk0069_182_1	chr15	63072364	63072583	+	0	NA	TTS (NM_001018020)	TTS (NM_001018020)	24036	NM_001301289	7168	Hs.133892	NM_000366	ENSG00000140416	TPM1	C15orf13|CMD1Y|CMH3|HEL-S-265|HTM-alpha|LVNC9|TMSA	tropomyosin 1	protein-coding	0.004566	0.354545	
chunk0029_403_1	chr10	109650205	109650675	+	0	NA	Intergenic	L1MEc|LINE|L1	273113	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.006383	0.473461	
chunk0039_450_1	chr11	108370358	108371304	+	0	NA	Intergenic	L1M5|LINE|L1	96700	NM_152587	160140	Hs.653180	NM_152587	ENSG00000166323	C11orf65	-	chromosome 11 open reading frame 65	protein-coding	0.006342	0.333685	
chunk0126_415_1	chr3	85781634	85782241	+	0	NA	intron (NM_153184, intron 1 of 9)	intron (NM_153184, intron 1 of 9)	46113	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.001647	0.327303	
chunk0146_197_1	chr4	161345076	161346089	+	0	NA	Intergenic	Intergenic	-677151	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.003949	0.332347	
chunk0051_385_1	chr12	121841192	121841721	+	0	NA	intron (NM_001171993, intron 14 of 15)	L1MB7|LINE|L1	17407	NM_002150	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.018904	0.439623	
chunk0066_209_1	chr15	33837851	33838084	+	0	NA	exon (NM_001243996, exon 88 of 103)	exon (NM_001243996, exon 88 of 103)	-130921	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.034335	0.444444	
chunk0027_82_1	chr10	73503225	73503424	+	0	NA	intron (NM_152586, intron 20 of 21)	L2c|LINE|L2	-7300	NM_001289968	5532	Hs.500067	NM_021132	ENSG00000107758	PPP3CB	CALNA2|CALNB|CNA2|PP2Bbeta	protein phosphatase 3 catalytic subunit beta	protein-coding	0.005025	0.395000	
chunk0139_161_1	chr4	53776094	53776593	+	0	NA	Intergenic	L1MA10|LINE|L1	80442	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.010020	0.340000	
chunk0028_281_1	chr10	91051891	91052296	+	0	NA	intron (NR_047467, intron 3 of 3)	intron (NR_047467, intron 3 of 3)	6285	NR_047467	100874184	Hs.512240	NR_047467		LINC00502	-	long intergenic non-protein coding RNA 502	ncRNA	0.004938	0.406404	
chunk0172_124_1	chr6	135225763	135226438	+	0	NA	Intergenic	Intergenic	-13060	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.011852	0.343195	
chunk0204_18_1	chr9	91994406	91994919	+	0	NA	Intergenic	MER34A1|LTR|ERV1	-44500	NM_004560	4920	Hs.98255	NM_004560	ENSG00000169071	ROR2	BDB|BDB1|NTRKR2	receptor tyrosine kinase like orphan receptor 2	protein-coding	0.007797	0.422179	
chunk0145_229_1	chr4	148397222	148397830	+	0	NA	intron (NM_000901, intron 2 of 8)	intron (NM_000901, intron 2 of 8)	44994	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.004934	0.408867	
chunk0138_286_1	chr4	40747465	40747846	+	0	NA	Intergenic	Intergenic	-2242	NM_024677	79730	Hs.479602	NM_024677	ENSG00000179299	NSUN7	-	NOP2/Sun RNA methyltransferase family member 7	protein-coding	0.002625	0.353403	
chunk0167_172_1	chr6	63487362	63487631	+	0	NA	Intergenic	Intergenic	-84516	NM_003463	7803	Hs.227777	NM_003463	ENSG00000112245	PTP4A1	HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1	protein tyrosine phosphatase 4A1	protein-coding	0.003717	0.359259	
chunk0211_133_1	chrX	112756452	112757094	+	0	NA	Intergenic	Intergenic	24015	NR_036255	100423009		NR_036255	ENSG00000283775	MIR4329	-	microRNA 4329	ncRNA	0.003115	0.401244	
chunk0127_187_1	chr3	95728562	95728761	+	0	NA	Intergenic	L1PA16|LINE|L1	-45468	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.010050	0.395000	
chunk0031_317_1	chr10	129123409	129123696	+	0	NA	Intergenic	Intergenic	-343632	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.013937	0.451389	
chunk0087_462_1	chr18	42803470	42803816	+	0	NA	intron (NM_002930, intron 4 of 4)	intron (NM_002930, intron 4 of 4)	312049	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.002890	0.345821	
chunk0041_291_1	chr11	129538137	129538976	+	0	NA	Intergenic	Intergenic	78713	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.007151	0.461905	365(AGGCACAAGCTGTACA,-,0.00),366(GGCACAAGCTGTACAC,+,0.00)
chunk0104_378_1	chr2	180257910	180258810	+	0	NA	Intergenic	Intergenic	-251307	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.002222	0.346282	
chunk0023_275_1	chr10	28263242	28263767	+	0	NA	intron (NM_173496, intron 2 of 18)	intron (NM_173496, intron 2 of 18)	18634	NM_173496	143098	Hs.499159	NM_173496	ENSG00000150054	MPP7	-	membrane palmitoylated protein 7	protein-coding	0.015238	0.475285	
chunk0021_259_1	chr1	243462561	243463083	+	0	NA	intron (NM_006642, intron 16 of 17)	intron (NM_006642, intron 16 of 17)	116646	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.001916	0.390057	
chunk0062_181_1	chr14	69685568	69686098	+	0	NA	intron (NM_014734, intron 2 of 5)	Tigger8|DNA|TcMar-Tigger	74240	NM_014734	9766	Hs.440025	NM_014734	ENSG00000100647	SUSD6	DRAGO|KIAA0247	sushi domain containing 6	protein-coding	0.015094	0.457627	246(GGGAACAACCTGTACT,-,0.00),247(GGAACAACCTGTACTC,+,0.00)
chunk0201_305_1	chr9	42268684	42269117	+	0	NA	Intergenic	Intergenic	70038	NR_126166	100996582		NR_126166		FAM74A7	-	family with sequence similarity 74 member A7	ncRNA	0.011547	0.398618	251(GGGTCAGGATGTACTG,+,0.00)
chunk0114_241_1	chr21	15994128	15994327	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-76295	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.000000	0.325000	
chunk0077_412_1	chr16	85064915	85065324	+	0	NA	intron (NM_001286565, intron 1 of 12)	intron (NM_001286565, intron 1 of 12)	1907	NM_001286565	9764	Hs.301658	NM_014732	ENSG00000135709	KIAA0513	-	KIAA0513	protein-coding	0.039120	0.507317	
chunk0177_429_1	chr7	27919769	27920460	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	180019	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.004342	0.355491	364(TAGTACAGTGAGTCCT,-,0.00),365(AGTACAGTGAGTCCTT,+,0.00)
chunk0143_230_1	chr4	114250379	114250883	+	0	NA	Intergenic	Intergenic	-270909	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.003968	0.388119	291(CTGAACTCTGTGTTCT,-,0.00),292(TGAACTCTGTGTTCTG,+,0.00)
chunk0094_71_1	chr2	3483763	3484089	+	0	NA	Intergenic	Intergenic	33821	NM_001306077	55256	Hs.502773	NM_018269	ENSG00000182551	ADI1	APL1|ARD|Fe-ARD|HMFT1638|MTCBP1|Ni-ARD|SIPL|mtnD	acireductone dioxygenase 1	protein-coding	0.015337	0.507645	
chunk0160_430_1	chr5	164517958	164518968	+	0	NA	intron (NR_105065, intron 2 of 3)	intron (NR_105065, intron 2 of 3)	48184	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.002970	0.373887	
chunk0129_447_1	chr3	128146552	128146838	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-6762	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.048951	0.547038	
chunk0083_382_1	chr17	71512482	71513048	+	0	NA	Intergenic	Intergenic	-310586	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.001767	0.358025	
chunk0101_148_1	chr2	127913903	127914142	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-28082	NM_001199140	83607	Hs.546449	NM_031445	ENSG00000144233	AMMECR1L	-	AMMECR1 like	protein-coding	0.020921	0.404167	
chunk0132_162_1	chr3	156676176	156676518	+	0	NA	promoter-TSS (NM_001184718)	promoter-TSS (NM_001184718)	-317	NM_001184718	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.008772	0.341108	248(GGGGACACTCAGTTTT,-,0.00)
chunk0181_13_1	chr7	77727519	77729101	+	0	NA	intron (NM_198467, intron 1 of 7)	HAL1|LINE|L1	-30965	NR_038361	100505854	Hs.72451	NR_038361	ENSG00000214293	APTR	RSBN1L-AS1	Alu-mediated CDKN1A/p21 transcriptional regulator	ncRNA	0.008850	0.403664	1128(GGCACTTGCAGTGCTT,+,0.00)
chunk0025_60_1	chr10	49539295	49539797	+	0	NA	promoter-TSS (NM_000124)	promoter-TSS (NM_000124)	-8	NM_001277059	2074	Hs.49063	NM_000124	ENSG00000225830	ERCC6	ARMD5|CKN2|COFS|COFS1|CSB|CSB-PGBD3|POF11|RAD26|UVSS1	ERCC excision repair 6, chromatin remodeling factor	protein-coding	0.043825	0.536779	
chunk0015_23_1	chr1	184362795	184363458	+	0	NA	Intergenic	Intergenic	-23890	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.003017	0.432229	297(CAGCACAGAGTGTCCT,-,0.00),298(AGCACAGAGTGTCCTC,+,0.00)
chunk0170_181_1	chr6	111851055	111851402	+	0	NA	intron (NM_002037, intron 1 of 13)	intron (NM_002037, intron 1 of 13)	22224	NM_002037	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.011527	0.422414	
chunk0142_58_1	chr4	92069464	92070155	+	0	NA	Intergenic	MSTA-int|LTR|ERVL-MaLR	207493	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.001447	0.404624	
chunk0182_196_1	chr7	95974145	95974496	+	0	NA	intron (NM_001278421, intron 5 of 15)	L2a|LINE|L2	201814	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.002849	0.357955	
chunk0133_341_1	chr3	172875015	172875277	+	0	NA	Intergenic	Intergenic	124461	NM_001258316	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.000000	0.307985	
chunk0147_204_1	chr4	178147072	178147627	+	0	NA	Intergenic	Intergenic	-239413	NR_108093	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.000000	0.271583	
chunk0067_442_1	chr15	50163651	50164037	+	0	NA	Intergenic	L1M1|LINE|L1	-18352	NM_001159629	11001	Hs.11729	NM_003645	ENSG00000140284	SLC27A2	ACSVL1|FACVL1|FATP2|HsT17226|VLACS|VLCS|hFACVL1	solute carrier family 27 member 2	protein-coding	0.000000	0.521964	
chunk0203_432_1	chr9	91208358	91208564	+	0	NA	Intergenic	Intergenic	-133329	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.009709	0.483092	35(AGGTACACACTGTGCC,-,0.00),36(GGTACACACTGTGCCG,+,0.00)
chunk0002_263_1	chr1	21338697	21338932	+	0	NA	intron (NM_001113348, intron 1 of 18)	intron (NM_001113348, intron 1 of 18)	6727	NM_001113348	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.008511	0.601695	
chunk0181_72_1	chr7	80259316	80259720	+	0	NA	Intergenic	Intergenic	114921	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.009901	0.360494	
chunk0090_401_1	chr18	78542138	78542769	+	0	NA	Intergenic	Intergenic	-437822	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.011094	0.457278	
chunk0023_346_1	chr10	29643733	29644412	+	0	NA	intron (NM_003174, intron 3 of 35)	intron (NM_003174, intron 3 of 35)	-9100	NM_021738	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.016200	0.510294	
chunk0006_435_1	chr1	76562308	76562928	+	0	NA	intron (NM_152996, intron 3 of 4)	L3|LINE|CR1	-304883	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.004839	0.384863	
chunk0189_200_1	chr8	23680370	23681029	+	0	NA	non-coding (NR_046072, exon 2 of 2)	non-coding (NR_046072, exon 2 of 2)	2190	NM_001256339	4824	Hs.55999	NM_006167	ENSG00000167034	NKX3-1	BAPX2|NKX3|NKX3.1|NKX3A	NK3 homeobox 1	protein-coding	0.006070	0.451515	
chunk0095_55_1	chr2	13791015	13791404	+	0	NA	Intergenic	Intergenic	609749	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.005141	0.346154	
chunk0138_30_1	chr4	31104650	31104849	+	0	NA	intron (NM_001173523, intron 2 of 2)	intron (NM_001173523, intron 2 of 2)	-66395	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.015075	0.425000	
chunk0112_133_1	chr20	38569754	38570102	+	0	NA	exon (NM_001282917, exon 27 of 30)	exon (NM_001282917, exon 27 of 30)	-11267	NM_001018082	149685	Hs.368028	NM_174906	ENSG00000182035	ADIG	SMAF1	adipogenin	protein-coding	0.008621	0.452722	
chunk0110_373_1	chr20	19964419	19965015	+	0	NA	intron (NM_018993, intron 4 of 10)	intron (NM_018993, intron 4 of 10)	-52573	NM_016100	51126	Hs.368783	NM_016100	ENSG00000173418	NAA20	NAT3|NAT3P|NAT5|NAT5P|dJ1002M8.1	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding	0.018456	0.495812	
chunk0101_304_1	chr2	135047362	135047657	+	0	NA	Intergenic	Intergenic	-4756	NM_012233	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.000000	0.395270	
chunk0130_264_1	chr3	136166559	136166864	+	0	NA	intron (NM_018133, intron 1 of 1)	intron (NM_018133, intron 1 of 1)	27757	NM_001145417	55167	Hs.18631	NM_018133	ENSG00000174579	MSL2	MSL-2|MSL2L1|RNF184	MSL complex subunit 2	protein-coding	0.009836	0.382353	
chunk0180_188_1	chr7	66114883	66115111	+	0	NA	intron (NM_001040648, intron 1 of 2)	CpG	179	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.096491	0.668122	
chunk0174_226_1	chr6	160439357	160439838	+	0	NA	intron (NM_021977, intron 7 of 10)	intron (NM_021977, intron 7 of 10)	71527	NR_028093	80350	Hs.654503	NM_024492	ENSG00000213071	LPAL2	APOA2|APOAL|APOARGC|apo(a)rg-C	lipoprotein(a) like 2, pseudogene	pseudo	0.006237	0.340249	259(AAGAACAGACTGTTCT,-,0.00),260(AGAACAGACTGTTCTC,+,0.00)
chunk0168_28_1	chr6	77624667	77625109	+	0	NA	Intergenic	Intergenic	-65768	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.011312	0.275395	
chunk0013_399_1	chr1	172933904	172934299	+	0	NA	Intergenic	Intergenic	116862	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.010127	0.421717	
chunk0069_221_1	chr15	63677897	63678130	+	0	NA	exon (NM_003922, exon 37 of 78)	exon (NM_003922, exon 37 of 78)	-77186	NR_034080	100130855	Hs.631163	NR_034080	ENSG00000259248	USP3-AS1	-	USP3 antisense RNA 1	ncRNA	0.025751	0.534188	
chunk0094_165_1	chr2	5433822	5434320	+	0	NA	Intergenic	Intergenic	257047	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.004016	0.358717	
chunk0031_437_1	chr10	132495995	132496194	+	0	NA	Intergenic	HAL1M8|LINE|L1	-41755	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.000000	0.335000	148(AGGTACACAGTGTGCT,-,0.00),149(GGTACACAGTGTGCTT,+,0.00)
chunk0009_347_1	chr1	109483852	109484355	+	0	NA	intron (NM_153340, intron 1 of 10)	CpG	164	NM_153340	127002	Hs.118248	NM_153340	ENSG00000162650	ATXN7L2	-	ataxin 7 like 2	protein-coding	0.115308	0.722222	
chunk0168_87_1	chr6	79878292	79878543	+	0	NA	Intergenic	L1MA2|LINE|L1	-66171	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.003984	0.503968	
chunk0190_51_1	chr8	29479182	29479441	+	0	NA	Intergenic	Intergenic	-128561	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.003861	0.457692	
chunk0141_155_1	chr4	81677953	81678532	+	0	NA	Intergenic	Intergenic	-206314	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.001727	0.337931	
chunk0153_288_1	chr5	73307301	73308106	+	0	NA	Intergenic	Intergenic	134507	NM_153217	134288	Hs.508588	NM_153217	ENSG00000164325	TMEM174	-	transmembrane protein 174	protein-coding	0.006211	0.468983	
chunk0063_1_1	chr14	75854081	75854302	+	0	NA	intron (NM_015072, intron 28 of 31)	L1ME2|LINE|L1	127831	NM_003239	7043	Hs.592317	NM_003239	ENSG00000119699	TGFB3	ARVD|ARVD1|LDS5|RNHF|TGF-beta3	transforming growth factor beta 3	protein-coding	0.009050	0.378378	
chunk0009_265_1	chr1	107454048	107454328	+	0	NA	intron (NM_001312688, intron 7 of 7)	intron (NM_001312688, intron 7 of 7)	234316	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.000000	0.395018	
chunk0181_97_1	chr7	80465466	80465696	+	0	NA	intron (NM_001102386, intron 5 of 7)	intron (NM_001102386, intron 5 of 7)	46345	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.013043	0.411255	
chunk0171_125_1	chr6	122696960	122697342	+	0	NA	intron (NM_181794, intron 5 of 6)	LTR53|LTR|ERVL	44422	NM_001270395	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.000000	0.467363	
chunk0128_119_1	chr3	106370311	106370719	+	0	NA	Intergenic	Intergenic	-501472	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.014706	0.356968	
chunk0007_391_1	chr1	85423568	85424008	+	0	NA	intron (NM_001134445, intron 2 of 6)	L1MC3|LINE|L1	41418	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.004545	0.328798	
chunk0103_446_1	chr2	170148121	170148457	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-29856	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.000000	0.418398	
chunk0159_210_1	chr5	140640758	140641114	+	0	NA	intron (NM_018502, intron 2 of 11)	intron (NM_018502, intron 2 of 11)	1509	NM_001300980	55374	Hs.534333	NM_018502	ENSG00000113119	TMCO6	PRO1580	transmembrane and coiled-coil domains 6	protein-coding	0.011236	0.383754	
chunk0084_11_1	chr17	73341820	73342033	+	0	NA	intron (NM_001144952, intron 44 of 44)	MIR|SINE|MIR	-29922	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.032864	0.518692	
chunk0088_373_1	chr18	54175032	54175354	+	0	NA	intron (NM_003927, intron 3 of 6)	intron (NM_003927, intron 3 of 6)	47219	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.003106	0.359133	138(AGGAACATGCTGAACT,-,0.00),139(GGAACATGCTGAACTT,+,0.00)
chunk0119_135_1	chr22	42940176	42940526	+	0	NA	intron (NM_001184970, intron 1 of 10)	L2c|LINE|L2	6690	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.011429	0.415954	
chunk0129_390_1	chr3	126347351	126348080	+	0	NA	intron (NM_014079, intron 2 of 2)	intron (NM_014079, intron 2 of 2)	9678	NM_014079	28999	Hs.272215	NM_014079	ENSG00000163884	KLF15	KKLF	Kruppel like factor 15	protein-coding	0.012346	0.556164	243(TGGAACAGGACGTTCT,-,0.00),244(GGAACAGGACGTTCTG,+,0.00),409(AGGGACAGGGAGTACT,-,0.00),410(GGGACAGGGAGTACTC,+,0.00)
chunk0096_441_1	chr2	39138988	39139306	+	0	NA	Intergenic	(GTTTT)n|Simple_repeat|Simple_repeat	-18684	NM_005633	6654	Hs.709893	NM_005633	ENSG00000115904	SOS1	GF1|GGF1|GINGF|HGF|NS4|SOS-1	SOS Ras/Rac guanine nucleotide exchange factor 1	protein-coding	0.018868	0.363636	
chunk0144_256_1	chr4	136570256	136570501	+	0	NA	Intergenic	Intergenic	-656698	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.004082	0.300813	
chunk0028_122_1	chr10	84668060	84668821	+	0	NA	Intergenic	Intergenic	243258	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.009198	0.455381	
chunk0091_277_1	chr19	11597337	11597758	+	0	NA	5' UTR (NM_145295, exon 1 of 4)	5' UTR (NM_145295, exon 1 of 4)	127	NM_001290083	199692	Hs.526665	NM_145295	ENSG00000198551	ZNF627	-	zinc finger protein 627	protein-coding	0.083135	0.687204	
chunk0148_136_1	chr5	5819235	5819660	+	0	NA	Intergenic	Intergenic	396774	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.002353	0.478873	
chunk0116_190_1	chr21	37064872	37065354	+	0	NA	TTS (NR_028352)	TTS (NR_028352)	-1047	NR_131189	105372795	Hs.528019	NR_131189		LOC105372795	-	uncharacterized LOC105372795	ncRNA	0.000000	0.399586	338(AAGTACTAACTGTACC,-,0.00),339(AGTACTAACTGTACCC,+,0.00)
chunk0091_266_1	chr19	11323736	11324064	+	0	NA	3' UTR (NM_004283, exon 5 of 5)	3' UTR (NM_004283, exon 5 of 5)	15768	NM_004283	9545	Hs.744916	NM_004283	ENSG00000105514	RAB3D	D2-2|GOV|RAB16|RAD3D	RAB3D, member RAS oncogene family	protein-coding	0.015244	0.531915	
chunk0157_231_1	chr5	119452635	119453585	+	0	NA	intron (NM_001292028, intron 1 of 23)	intron (NM_001292028, intron 1 of 23)	613	NM_001292028	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.034737	0.511041	
chunk0203_312_1	chr9	89470501	89470908	+	0	NA	intron (NM_006378, intron 1 of 17)	L1ME1|LINE|L1	8992	NM_006378	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.014742	0.406863	
chunk0004_259_1	chr1	47875849	47876276	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	120828	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.004684	0.469626	
chunk0077_274_1	chr16	81006772	81007335	+	0	NA	promoter-TSS (NM_020188)	promoter-TSS (NM_020188)	-156	NM_020188	56942	Hs.55028	NM_020188	ENSG00000103121	CMC2	2310061C15Rik|C16orf61|DC13	C-X9-C motif containing 2	protein-coding	0.085258	0.671986	193(AGGCACAGTGAGTCCA,-,0.00),194(GGCACAGTGAGTCCAC,+,0.00)
chunk0156_360_1	chr5	112479617	112479828	+	0	NA	Intergenic	Intergenic	60139	NR_027706	54508	Hs.591264	NR_027706	ENSG00000278921	EPB41L4A-DT	EPB41L4A-AS2	EPB41L4A divergent transcript	ncRNA	0.000000	0.518868	
chunk0168_306_1	chr6	91704466	91704681	+	0	NA	Intergenic	L1PA16|LINE|L1	-14145	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.009302	0.310185	
chunk0121_378_1	chr3	25080039	25080238	+	0	NA	Intergenic	L1MB4|LINE|L1	-94194	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.005025	0.375000	
chunk0140_252_1	chr4	71467815	71468655	+	0	NA	intron (NM_001098484, intron 13 of 25)	intron (NM_001098484, intron 13 of 25)	129182	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.002381	0.324614	
chunk0004_404_1	chr1	52257919	52258629	+	0	NA	intron (NM_007324, intron 4 of 17)	intron (NM_007324, intron 4 of 17)	107931	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.000000	0.378340	
chunk0163_452_1	chr6	17583583	17584142	+	0	NA	Intergenic	Intergenic	-16425	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.016100	0.442857	
chunk0067_49_1	chr15	40830717	40830916	+	0	NA	Intergenic	MIRb|SINE|MIR	-2107	NM_001130143	54866	Hs.192927	NM_017726	ENSG00000166143	PPP1R14D	CPI17-like|GBPI-1|GBPI1	protein phosphatase 1 regulatory inhibitor subunit 14D	protein-coding	0.000000	0.445000	
chunk0008_139_1	chr1	92015995	92016558	+	0	NA	Intergenic	Intergenic	-13700	NM_173567	253152	Hs.201555	NM_173567	ENSG00000172031	EPHX4	ABHD7|EH4|EPHXRP	epoxide hydrolase 4	protein-coding	0.003552	0.370567	198(CAGTACAGATTGTCCT,-,0.00),199(AGTACAGATTGTCCTA,+,0.00)
chunk0184_294_1	chr7	119256679	119257187	+	0	NA	Intergenic	Intergenic	650442	NR_131960	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.005906	0.349705	
chunk0155_464_1	chr5	101785284	101785527	+	0	NA	Intergenic	L2c|LINE|L2	511144	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.008230	0.418033	
chunk0151_66_1	chr5	42514868	42515359	+	0	NA	intron (NM_001242400, intron 2 of 10)	intron (NM_001242400, intron 2 of 10)	-32930	NM_001242402	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.002037	0.402439	
chunk0134_337_1	chr3	182163282	182163687	+	0	NA	Intergenic	Intergenic	211120	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.004938	0.320197	
chunk0006_315_1	chr1	71462904	71463224	+	0	NA	intron (NM_173808, intron 6 of 6)	L2a|LINE|L2	373948	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.006250	0.364486	
chunk0170_340_1	chr6	116311271	116311849	+	0	NA	intron (NM_001080976, intron 1 of 5)	L1ME4b|LINE|L1	31440	NM_001080976	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.005190	0.383420	381(CAGAACATTGTGCTCC,-,0.00),382(AGAACATTGTGCTCCA,+,0.00)
chunk0082_360_1	chr17	60176956	60177302	+	0	NA	TTS (NM_032582)	TTS (NM_032582)	27188	NM_000717	762	Hs.89485	NM_000717	ENSG00000167434	CA4	CAIV|Car4|RP17	carbonic anhydrase 4	protein-coding	0.008671	0.449568	
chunk0077_332_1	chr16	82358673	82358927	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-188576	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.019685	0.431373	
chunk0210_231_1	chrX	82463837	82464384	+	0	NA	Intergenic	Intergenic	-1044151	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.007313	0.341241	
chunk0122_18_1	chr3	27512782	27513237	+	0	NA	Intergenic	Intergenic	-28589	NM_001258379	9497	Hs.250072	NM_003615	ENSG00000033867	SLC4A7	NBC2|NBC3|NBCN1|SBC2|SLC4A6	solute carrier family 4 member 7	protein-coding	0.002198	0.326754	
chunk0070_219_1	chr15	72724061	72724408	+	0	NA	intron (NR_045565, intron 8 of 16)	intron (NR_045565, intron 8 of 16)	38055	NM_001252678	585	Hs.208681	NM_033028	ENSG00000140463	BBS4	-	Bardet-Biedl syndrome 4	protein-coding	0.002882	0.408046	
chunk0172_249_1	chr6	137241405	137242038	+	0	NA	Intergenic	Intergenic	-22291	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.004739	0.378549	
chunk0196_171_1	chr8	105847393	105847977	+	0	NA	intron (NR_125796, intron 2 of 7)	L1M3de|LINE|L1	212818	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.003425	0.490598	
chunk0003_176_1	chr1	33640277	33640646	+	0	NA	intron (NM_052896, intron 29 of 69)	MER58A|DNA|hAT-Charlie	167830	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.005420	0.394595	
chunk0206_120_1	chr9	120936155	120936525	+	0	NA	Intergenic	Intergenic	-7167	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.013514	0.512129	
chunk0099_159_1	chr2	88209673	88209872	+	0	NA	Intergenic	L3|LINE|CR1	36633	NM_018271	55258	Hs.739080	NM_018271	ENSG00000144115	THNSL2	SOFAT|THS2|TSH2	threonine synthase like 2	protein-coding	0.015075	0.530000	
chunk0139_118_1	chr4	52848314	52848633	+	0	NA	Intergenic	Intergenic	-13855	NM_023940	65997	Hs.8035	NM_023940	ENSG00000128045	RASL11B	-	RAS like family 11 member B	protein-coding	0.018809	0.415625	
chunk0205_158_1	chr9	108567953	108568596	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	287721	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.006221	0.413043	315(CAGTACACTATGTCCC,-,0.00),316(AGTACACTATGTCCCC,+,0.00)
chunk0062_340_1	chr14	73519974	73520443	+	0	NA	intron (NM_001220484, intron 4 of 17)	intron (NM_001220484, intron 4 of 17)	-17016	NM_001037161	641371	Hs.446685	NM_001037161	ENSG00000184227	ACOT1	ACH2|CTE-1|LACH2	acyl-CoA thioesterase 1	protein-coding	0.004264	0.380851	
chunk0170_222_1	chr6	113279707	113280109	+	0	NA	Intergenic	L1MC3|LINE|L1	370167	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.007463	0.362283	
chunk0160_310_1	chr5	159175657	159175899	+	0	NA	intron (NM_144726, intron 5 of 10)	intron (NM_144726, intron 5 of 10)	31870	NM_001199382	153830	Hs.349306	NM_144726	ENSG00000145860	RNF145	-	ring finger protein 145	protein-coding	0.004132	0.419753	
chunk0025_283_1	chr10	56400997	56401551	+	0	NA	Intergenic	Intergenic	-40001	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.003610	0.308108	
chunk0113_237_1	chr20	54084926	54085282	+	0	NA	Intergenic	Intergenic	-14339	NM_003657	8537	Hs.400556	NM_003657	ENSG00000064787	BCAS1	AIBC1|NABC1	breast carcinoma amplified sequence 1	protein-coding	0.002809	0.425770	
chunk0145_144_1	chr4	147022199	147022764	+	0	NA	Intergenic	L1PREC2|LINE|L1	-76599	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.001770	0.349823	
chunk0013_77_1	chr1	167600212	167600439	+	0	NA	Intergenic	Intergenic	-29912	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.013216	0.469298	
chunk0179_284_1	chr7	49606781	49607270	+	0	NA	Intergenic	L1PB1|LINE|L1	-166636	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.002045	0.353061	201(AGGGACATTATGTACT,-,0.00),202(GGGACATTATGTACTT,+,0.00)
chunk0200_450_1	chr9	31335559	31336299	+	0	NA	Intergenic	MIR|SINE|MIR	-927475	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.005405	0.442645	441(TAGGACATCCTGTGCC,-,0.00),442(AGGACATCCTGTGCCT,+,0.00)
chunk0191_315_1	chr8	55681306	55681843	+	0	NA	Intergenic	Intergenic	82406	NM_001286657	137695	Hs.420076	NM_152417	ENSG00000167904	TMEM68	-	transmembrane protein 68	protein-coding	0.005587	0.353160	
chunk0110_81_1	chr20	11178541	11179332	+	0	NA	Intergenic	Intergenic	94447	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.001264	0.327020	
chunk0132_274_1	chr3	159644292	159644682	+	0	NA	intron (NM_001197108, intron 1 of 6)	intron (NM_001197108, intron 1 of 6)	124125	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.005128	0.332481	
chunk0061_91_1	chr14	57402202	57402556	+	0	NA	intron (NM_001011713, intron 4 of 4)	L2a|LINE|L2	11826	NM_001011713	122830	Hs.165465	NM_001011713	ENSG00000139977	NAA30	C14orf35|MAK3|Mak3p|NAT12|NAT12P	N(alpha)-acetyltransferase 30, NatC catalytic subunit	protein-coding	0.000000	0.332394	
chunk0126_71_1	chr3	74585917	74586390	+	0	NA	Intergenic	Intergenic	-65013	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002114	0.352321	
chunk0206_54_1	chr9	117944940	117945158	+	0	NA	Intergenic	LTR10C|LTR|ERV1	240874	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.004587	0.347032	
chunk0185_348_1	chr7	132242196	132242790	+	0	NA	intron (NM_020911, intron 4 of 31)	intron (NM_020911, intron 4 of 31)	332273	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.008418	0.426891	
chunk0207_182_1	chr9	130731327	130731814	+	0	NA	intron (NM_007313, intron 1 of 10)	L1M5|LINE|L1	17689	NM_007313	25	Hs.431048	NM_005157	ENSG00000097007	ABL1	ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-abl	ABL proto-oncogene 1, non-receptor tyrosine kinase	protein-coding	0.004107	0.354508	
chunk0012_84_1	chr1	156115226	156115446	+	0	NA	intron (NM_001282625, intron 4 of 12)	CpG	666	NM_005572	4000	Hs.594444	NM_005572	ENSG00000160789	LMNA	CDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1	lamin A/C	protein-coding	0.068182	0.669683	
chunk0208_453_1	chrX	33050906	33051142	+	0	NA	intron (NM_000109, intron 1 of 78)	intron (NM_000109, intron 1 of 78)	77403	NM_004010	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.008475	0.329114	
chunk0168_313_1	chr6	92220481	92221183	+	0	NA	Intergenic	Intergenic	-530404	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.001425	0.321479	268(AAGGACACCCTGTTCT,-,0.00),269(AGGACACCCTGTTCTT,+,0.00)
chunk0017_155_1	chr1	206916047	206916340	+	0	NA	intron (NM_005449, intron 1 of 7)	L3|LINE|CR1	5697	NM_001193338	9214	Hs.58831	NM_005449	ENSG00000162894	FCMR	FAIM3|TOSO	Fc fragment of IgM receptor	protein-coding	0.010239	0.489796	
chunk0021_180_1	chr10	5513265	5513683	+	0	NA	TTS (NR_120497)	TTS (NR_120497)	-11415	NM_005185	810	Hs.239600	NM_005185	ENSG00000178363	CALML3	CLP	calmodulin like 3	protein-coding	0.011962	0.455847	255(AAGATCAACTTGTTCT,-,0.00)
chunk0109_316_1	chr20	9114776	9115039	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	45853	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.015209	0.477273	
chunk0046_269_1	chr12	61274867	61275329	+	0	NA	Intergenic	Intergenic	917741	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.004329	0.354212	
chunk0181_36_1	chr7	78524245	78524954	+	0	NA	intron (NM_001301128, intron 3 of 20)	intron (NM_001301128, intron 3 of 20)	177357	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.008463	0.339437	
chunk0053_419_1	chr13	37294946	37295965	+	0	NA	Intergenic	Intergenic	189329	NR_125762	103695431	Hs.550637	NR_125762	ENSG00000230390	LINC01048	-	long intergenic non-protein coding RNA 1048	ncRNA	0.013739	0.430392	240(CTGTACAGTATGTGCA,-,0.00),241(TGTACAGTATGTGCAG,+,0.00)
chunk0071_94_1	chr15	80913398	80914075	+	0	NA	intron (NM_001293304, intron 14 of 29)	intron (NM_001293304, intron 14 of 29)	-71663	NR_030393	693132		NR_030393	ENSG00000208003	MIR549A	MIR549|MIRN549|hsa-mir-549|hsa-mir-549a|mir-549a	microRNA 549a	ncRNA	0.008863	0.417404	
chunk0004_341_1	chr1	50701409	50702038	+	0	NA	intron (NM_007051, intron 7 of 18)	intron (NM_007051, intron 7 of 18)	258541	NM_007051	11124	Hs.530402	NM_007051	ENSG00000185104	FAF1	CGI-03|HFAF1s|UBXD12|UBXN3A|hFAF1	Fas associated factor 1	protein-coding	0.004769	0.325397	
chunk0165_368_1	chr6	38188803	38189472	+	0	NA	intron (NM_001099272, intron 10 of 10)	intron (NM_001099272, intron 10 of 10)	369606	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.017937	0.526866	
chunk0202_441_1	chr9	82108524	82108939	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	119959	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.002410	0.353365	
chunk0014_278_1	chr1	180522505	180522832	+	0	NA	Intergenic	L2b|LINE|L2	-19781	NM_032360	84320	Hs.200051	NM_032360	ENSG00000230124	ACBD6	-	acyl-CoA binding domain containing 6	protein-coding	0.000000	0.381098	
chunk0030_49_1	chr10	111787767	111788335	+	0	NA	Intergenic	Intergenic	395728	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.010563	0.398946	
chunk0052_252_1	chr12	123512925	123513241	+	0	NA	intron (NM_178314, intron 2 of 6)	(TG)n|Simple_repeat|Simple_repeat	20635	NM_178314	353116	Hs.530315	NM_178314	ENSG00000188026	RILPL1	GOSPEL|RLP1	Rab interacting lysosomal protein like 1	protein-coding	0.022152	0.536278	
chunk0192_434_1	chr8	69684711	69685645	+	0	NA	intron (NM_030958, intron 6 of 9)	intron (NM_030958, intron 6 of 9)	92278	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.005353	0.408556	210(TGAGACACTCTGTTCT,-,0.00),211(GAGACACTCTGTTCTA,+,0.00)
chunk0115_326_1	chr21	28859213	28859428	+	0	NA	Intergenic	L1MEj|LINE|L1	26053	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.004651	0.337963	
chunk0142_321_1	chr4	100898406	100899199	+	0	NA	Intergenic	Intergenic	-223689	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.002522	0.340050	
chunk0039_50_1	chr11	96145131	96145671	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-196037	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.007407	0.395564	
chunk0088_81_1	chr18	44779952	44780157	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	99156	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.024390	0.533981	
chunk0186_252_1	chr7	141057084	141057567	+	0	NA	Intergenic	LTR33A_|LTR|ERVL	-16907	NM_001195278	100507421	Hs.283851	NM_001195278	ENSG00000261115	TMEM178B	-	transmembrane protein 178B	protein-coding	0.012422	0.522727	208(CAGTTCACCGTGTCCT,-,0.00),209(AGTTCACCGTGTCCTG,+,0.00)
chunk0178_343_1	chr7	38756346	38757019	+	0	NA	intron (NM_080631, intron 18 of 27)	intron (NM_080631, intron 18 of 27)	-69593	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.010401	0.318991	349(AGGGTCAGAGTGTTCT,-,0.00),350(GGGTCAGAGTGTTCTA,+,0.00)
chunk0003_417_1	chr1	40508496	40508705	+	0	NA	promoter-TSS (NM_022774)	promoter-TSS (NM_022774)	-161	NM_022774	64789	Hs.59584	NM_022774	ENSG00000164002	EXO5	C1orf176|DEM1|Exo V|hExo5	exonuclease 5	protein-coding	0.076555	0.604762	
chunk0198_391_1	chr8	141378306	141378889	+	0	NA	Intergenic	MIR3|SINE|MIR	-11332	NM_005293	2843	Hs.152432	NM_005293	ENSG00000204882	GPR20	-	G protein-coupled receptor 20	protein-coding	0.015437	0.616438	
chunk0084_325_1	chr17	80751000	80751747	+	0	NA	intron (NM_020761, intron 5 of 33)	intron (NM_020761, intron 5 of 33)	54259	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.030790	0.483957	382(GGGGACTCTGTGTCCT,-,0.00),383(GGGACTCTGTGTCCTC,+,0.00)
chunk0078_86_1	chr17	1996513	1996853	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	28662	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.017647	0.451613	
chunk0117_67_1	chr22	16977735	16978128	+	0	NA	intron (NM_001037814, intron 3 of 9)	L1PA7|LINE|L1	30291	NM_001037814	128954	Hs.434113	NM_001037814	ENSG00000215568	GAB4	-	GRB2 associated binding protein family member 4	protein-coding	0.007634	0.360406	169(CTGAACAACCTGTTCC,-,0.00),170(TGAACAACCTGTTCCT,+,0.00),255(AAAGACACAATGTACC,-,0.00)
chunk0001_171_1	chr1	6811593	6811884	+	0	NA	intron (NR_038934, intron 1 of 3)	Tigger15a|DNA|TcMar-Tigger	26414	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.027491	0.465753	
chunk0187_244_1	chr7	152974592	152974936	+	0	NA	Intergenic	Intergenic	215015	NR_073001									0.008721	0.463768	
chunk0094_415_1	chr2	10486492	10486829	+	0	NA	Intergenic	Intergenic	36932	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.011869	0.538462	24(AGGCACAAAGTGTCCA,-,0.00),25(GGCACAAAGTGTCCAG,+,0.00)
chunk0138_61_1	chr4	32130884	32131457	+	0	NA	intron (NR_125936, intron 1 of 2)	Tigger2|DNA|TcMar-Tigger	133791	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.003490	0.386760	
chunk0179_352_1	chr7	50857847	50858574	+	0	NA	Intergenic	L1MA4A|LINE|L1	-64748	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.008253	0.502747	
chunk0211_363_1	chrX	125806784	125807327	+	0	NA	Intergenic	Intergenic	-302707	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.000000	0.316176	
chunk0154_78_1	chr5	77620476	77620834	+	0	NA	Intergenic	Intergenic	18042	NM_032109	23440	Hs.202247	NM_032109	ENSG00000171540	OTP	-	orthopedia homeobox	protein-coding	0.011173	0.420613	
chunk0127_198_1	chr3	96111858	96112431	+	0	NA	Intergenic	L1MB8|LINE|L1	-247820	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.001745	0.289199	
chunk0096_304_1	chr2	32916148	32916670	+	0	NA	intron (NR_027099, intron 5 of 5)	(G)n|Simple_repeat|Simple_repeat	-10718	NR_027097	285045	Hs.434660	NR_027097	ENSG00000230876	LINC00486	-	long intergenic non-protein coding RNA 486	ncRNA	0.023061	0.933054	
chunk0123_437_1	chr3	50334366	50334753	+	0	NA	intron (NM_001206957, intron 1 of 4)	intron (NM_001206957, intron 1 of 4)	2905	NM_170713	11186	Hs.476270	NM_007182	ENSG00000068028	RASSF1	123F2|NORE2A|RASSF1A|RDA32|REH3P21	Ras association domain family member 1	protein-coding	0.005168	0.520619	
chunk0175_180_1	chr7	5307831	5308179	+	0	NA	3' UTR (NM_001080495, exon 30 of 30)	3' UTR (NM_001080495, exon 30 of 30)	25075	NM_153247	222962	Hs.4302	NM_153247	ENSG00000164638	SLC29A4	ENT4|PMAT	solute carrier family 29 member 4	protein-coding	0.074713	0.681948	
chunk0197_139_1	chr8	120268616	120269011	+	0	NA	intron (NM_021110, intron 25 of 47)	intron (NM_021110, intron 25 of 47)	143705	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.007595	0.277778	
chunk0095_400_1	chr2	24288801	24289247	+	0	NA	intron (NM_019595, intron 15 of 38)	L1MA9|LINE|L1	71504	NM_019595	50618	Hs.432562	NM_006277	ENSG00000198399	ITSN2	PRO2015|SH3D1B|SH3P18|SWA|SWAP	intersectin 2	protein-coding	0.006726	0.337808	
chunk0086_193_1	chr18	22169555	22169886	+	0	NA	promoter-TSS (NR_102763)	promoter-TSS (NR_102763)	283	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.123867	0.716867	
chunk0101_441_1	chr2	139501904	139502384	+	0	NA	Intergenic	L1PA14|LINE|L1	604820	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.004167	0.351351	
chunk0055_29_1	chr13	51971363	51972002	+	0	NA	intron (NM_001005918, intron 2 of 16)	intron (NM_001005918, intron 2 of 16)	39812	NM_000053	540	Hs.492280	NM_000053	ENSG00000123191	ATP7B	PWD|WC1|WD|WND	ATPase copper transporting beta	protein-coding	0.009390	0.414062	
chunk0025_31_1	chr10	48518158	48518605	+	0	NA	intron (NR_045675, intron 4 of 10)	L2a|LINE|L2	-24732	NM_001256026	58504	Hs.655672	NM_021226	ENSG00000128805	ARHGAP22	RhoGAP2|RhoGap22	Rho GTPase activating protein 22	protein-coding	0.013423	0.522321	216(GGGAACAGATTGTGCA,-,0.00),217(GGAACAGATTGTGCAA,+,0.00)
chunk0139_331_1	chr4	58826173	58826752	+	0	NA	Intergenic	Intergenic	1400590	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.000000	0.281034	297(TAGTACTGATTGTTCC,-,0.00),298(AGTACTGATTGTTCCA,+,0.00)
chunk0165_431_1	chr6	39772749	39773222	+	0	NA	Intergenic	Intergenic	-19398	NM_001201427	23500	Hs.357128	NM_015345	ENSG00000146122	DAAM2	dJ90A20A.1	dishevelled associated activator of morphogenesis 2	protein-coding	0.008457	0.417722	190(GGATACACTGTGTGCT,-,0.00),191(GATACACTGTGTGCTT,+,0.00)
chunk0006_73_1	chr1	64898108	64898480	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	68210	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.010753	0.455764	
chunk0167_264_1	chr6	69642348	69642779	+	0	NA	Intergenic	Intergenic	154594	NM_018368	55788	Hs.271643	NM_018368	ENSG00000168216	LMBRD1	C6orf209|LMBD1|MAHCF|NESI	LMBR1 domain containing 1	protein-coding	0.009281	0.337963	
chunk0059_251_1	chr14	35068187	35068566	+	0	NA	intron (NM_173607, intron 2 of 4)	LTR33|LTR|ERVL	-12705	NR_110415	101927178	Hs.617139	NR_110415	ENSG00000151327	LOC101927178	-	uncharacterized LOC101927178	ncRNA	0.007916	0.384211	
chunk0106_277_1	chr2	204060072	204060724	+	0	NA	Intergenic	Intergenic	123650	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.009202	0.362940	
chunk0125_94_1	chr3	65326561	65326800	+	0	NA	Intergenic	Intergenic	-567136	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.008368	0.408333	
chunk0209_442_1	chrX	64422935	64423153	+	0	NA	Intergenic	Intergenic	-27591	NM_017677	55613	Hs.442892	NM_017677	ENSG00000102043	MTMR8	-	myotubularin related protein 8	protein-coding	0.004587	0.452055	
chunk0092_120_1	chr19	27780893	27781180	+	0	NA	Intergenic	(TTATTG)n|Simple_repeat|Simple_repeat	-12431	NR_110689	101927151	Hs.567934	NR_110687	ENSG00000267575	LOC101927151	-	uncharacterized LOC101927151	ncRNA	0.006969	0.381944	
chunk0029_336_1	chr10	105239750	105240270	+	0	NA	intron (NM_014978, intron 20 of 26)	intron (NM_014978, intron 20 of 26)	-573794	NR_104028	100505890	Hs.348526	NR_104028	ENSG00000226387	SORCS3-AS1	-	SORCS3 antisense RNA 1	ncRNA	0.001923	0.464491	
chunk0156_279_1	chr5	109897023	109897508	+	0	NA	Intergenic	L1M5|LINE|L1	14083	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.002062	0.263374	
chunk0140_384_1	chr4	74943850	74944728	+	0	NA	intron (NM_015393, intron 1 of 3)	intron (NM_015393, intron 1 of 3)	11214	NM_015393	25849	Hs.105460	NM_015393	ENSG00000169116	PARM1	Cipar1|DKFZP564O0823|PARM-1|WSC4	prostate androgen-regulated mucin-like protein 1	protein-coding	0.009112	0.443686	
chunk0149_322_1	chr5	26504439	26505037	+	0	NA	Intergenic	Intergenic	533844	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.003344	0.407346	
chunk0205_396_1	chr9	114555593	114555792	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-32022	NM_004888	9550	Hs.388654	NM_004888	ENSG00000136888	ATP6V1G1	ATP6G|ATP6G1|ATP6GL|ATP6J|Vma10	ATPase H+ transporting V1 subunit G1	protein-coding	0.005025	0.440000	
chunk0152_193_1	chr5	59893985	59894191	+	0	NA	promoter-TSS (NM_001104631)	promoter-TSS (NM_001104631)	-294	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.067961	0.647343	
chunk0172_200_1	chr6	136655946	136656481	+	0	NA	intron (NM_005923, intron 10 of 29)	intron (NM_005923, intron 10 of 29)	27099	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.005607	0.376866	302(CAGTACAAGATGTTCT,-,0.00),303(AGTACAAGATGTTCTT,+,0.00)
chunk0012_266_1	chr1	161749291	161749500	+	0	NA	promoter-TSS (NM_007240)	promoter-TSS (NM_007240)	-373	NM_007240	11266	Hs.416216	NM_007240	ENSG00000081721	DUSP12	DUSP1|YVH1	dual specificity phosphatase 12	protein-coding	0.004785	0.309524	
chunk0112_73_1	chr20	37845242	37845706	+	0	NA	intron (NM_030877, intron 13 of 15)	intron (NM_030877, intron 13 of 15)	-57623	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.023707	0.526882	
chunk0089_430_1	chr18	70005611	70005851	+	0	NA	intron (NM_173630, intron 47 of 48)	L2b|LINE|L2	-48555	NM_006566	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.008333	0.456432	
chunk0106_205_1	chr2	202326773	202326997	+	0	NA	Intergenic	Intergenic	33834	NR_003031	692058		NR_003031	ENSG00000238317	SNORD11	HBII-95	small nucleolar RNA, C/D box 11	snoRNA	0.026786	0.466667	
chunk0158_45_1	chr5	125833746	125834148	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	340686	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.000000	0.424318	176(AAGAACACTGTGTCCT,-,0.00),177(AGAACACTGTGTCCTC,+,0.00)
chunk0163_324_1	chr6	14889634	14889985	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-356166	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.019943	0.420455	
chunk0062_228_1	chr14	71060130	71060675	+	0	NA	intron (NM_001308160, intron 24 of 33)	Tigger3|DNA|TcMar-Tigger	152997	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.005505	0.349817	268(TAGAACAGTATGTCTT,-,0.00),269(AGAACAGTATGTCTTG,+,0.00)
chunk0190_231_1	chr8	35861534	35862301	+	0	NA	Intergenic	Intergenic	-151597	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.003911	0.385417	
chunk0181_123_1	chr7	80802589	80803039	+	0	NA	intron (NM_006379, intron 8 of 17)	intron (NM_006379, intron 8 of 17)	116537	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.011111	0.325942	
chunk0200_244_1	chr9	20876217	20876733	+	0	NA	intron (NM_017794, intron 21 of 45)	intron (NM_017794, intron 21 of 45)	155161	NM_001010915	401494	Hs.716678	NM_001010915	ENSG00000188921	HACD4	PTPLAD2	3-hydroxyacyl-CoA dehydratase 4	protein-coding	0.005814	0.396518	258(CAGTACAGAATGTGCA,-,0.00),259(AGTACAGAATGTGCAG,+,0.00)
chunk0102_136_1	chr2	145874349	145874956	+	0	NA	Intergenic	Intergenic	-712405	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.001647	0.375000	
chunk0047_434_1	chr12	76385899	76386459	+	0	NA	exon (NM_020841, exon 14 of 24)	exon (NM_020841, exon 14 of 24)	-37737	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.005357	0.272727	
chunk0203_318_1	chr9	89556601	89556954	+	0	NA	Intergenic	L1M5|LINE|L1	-48235	NM_006705	10912	Hs.9701	NM_006705	ENSG00000130222	GADD45G	CR6|DDIT2|GADD45gamma|GRP17	growth arrest and DNA damage inducible gamma	protein-coding	0.016997	0.519774	
chunk0161_387_1	chr5	176957600	176958582	+	0	NA	intron (NM_016290, intron 7 of 14)	intron (NM_016290, intron 7 of 14)	48351	NM_016290	51720	Hs.232721	NM_016290	ENSG00000087206	UIMC1	RAP80|X2HRIP110	ubiquitin interaction motif containing 1	protein-coding	0.003055	0.350966	
chunk0179_196_1	chr7	47254205	47254793	+	0	NA	Intergenic	CpG	327645	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.093537	0.694397	317(CGGAACACGGCGTCCT,-,0.00),318(GGAACACGGCGTCCTC,+,0.00)
chunk0115_40_1	chr21	21190685	21190957	+	0	NA	intron (NM_004540, intron 1 of 17)	MIR|SINE|MIR	192506	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.000000	0.329670	
chunk0121_372_1	chr3	25018051	25018438	+	0	NA	Intergenic	Intergenic	-156088	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.347938	
chunk0060_200_1	chr14	48105236	48105753	+	0	NA	Intergenic	LTR9|LTR|ERV1	-310480	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.013540	0.391892	139(GTGAACAGCATGTACT,-,0.00),140(TGAACAGCATGTACTC,+,0.00)
chunk0043_400_1	chr12	25585121	25585439	+	0	NA	intron (NM_001145727, intron 1 of 7)	intron (NM_001145727, intron 1 of 7)	-31997	NM_152590	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.006289	0.420063	
chunk0098_37_1	chr2	66161067	66161518	+	0	NA	Intergenic	L1MEf|LINE|L1	197036	NR_039938	100616464		NR_039938	ENSG00000264525	MIR4778	-	microRNA 4778	ncRNA	0.002217	0.309735	
chunk0184_186_1	chr7	116780836	116781350	+	0	NA	intron (NM_000245, intron 17 of 20)	MER74A|LTR|ERVL	-81416	NM_006136	830	Hs.446123	NM_006136	ENSG00000198898	CAPZA2	CAPPA2|CAPZ	capping actin protein of muscle Z-line subunit alpha 2	protein-coding	0.001946	0.497087	453(ATGACAGGGTGTGCCT,+,0.00)
chunk0209_380_1	chrX	54360292	54360847	+	0	NA	Intergenic	Intergenic	-2564	NM_020922	65267	Hs.92423	NM_020922	ENSG00000196632	WNK3	PRKWNK3	WNK lysine deficient protein kinase 3	protein-coding	0.005405	0.361511	
chunk0112_12_1	chr20	35900873	35901140	+	0	NA	intron (NM_016436, intron 10 of 17)	L1ME3A|LINE|L1	53620	NM_033630	51282	Hs.584909	NM_016558	ENSG00000171222	SCAND1	RAZ1|SDP1	SCAN domain containing 1	protein-coding	0.003745	0.380597	
chunk0107_96_1	chr2	213316284	213316948	+	0	NA	intron (NR_047659, intron 6 of 17)	L2a|LINE|L2	32237	NM_024532	79582	Hs.743365	NM_024532	ENSG00000144451	SPAG16	PF20|WDR29	sperm associated antigen 16	protein-coding	0.001506	0.434586	
chunk0015_185_1	chr1	187209515	187210106	+	0	NA	intron (NR_126347, intron 1 of 3)	intron (NR_126347, intron 1 of 3)	116968	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.001692	0.297297	
chunk0121_234_1	chr3	22091053	22091840	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	134307	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.002541	0.406091	427(CAGAACACCCTGGTCT,-,0.00),428(AGAACACCCTGGTCTG,+,0.00),466(CTGAACACTGTGTTCC,-,0.00),467(TGAACACTGTGTTCCT,+,0.00)
chunk0147_120_1	chr4	174249865	174250164	+	0	NA	intron (NM_012180, intron 3 of 5)	intron (NM_012180, intron 3 of 5)	-29616	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.006689	0.350000	
chunk0211_73_1	chrX	110012986	110013416	+	0	NA	intron (NM_032227, intron 2 of 6)	intron (NM_032227, intron 2 of 6)	10087	NM_032227	84187	Hs.496572	NM_017698	ENSG00000157600	TMEM164	bB360B22.3	transmembrane protein 164	protein-coding	0.004651	0.473318	
chunk0001_214_1	chr1	8004732	8005460	+	0	NA	Intergenic	Intergenic	21237	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.024725	0.525377	
chunk0189_124_1	chr8	22279383	22279582	+	0	NA	exon (NM_001135721, exon 2 of 23)	exon (NM_001135721, exon 2 of 23)	3915	NM_001135721	55124	Hs.614809	NM_018068	ENSG00000197181	PIWIL2	CT80|HILI|PIWIL1L|mili	piwi like RNA-mediated gene silencing 2	protein-coding	0.015075	0.585000	
chunk0201_136_1	chr9	35732086	35732285	+	0	NA	promoter-TSS (NM_006368)	promoter-TSS (NM_006368)	-135	NM_006368	10488	Hs.522110	NM_006368	ENSG00000107175	CREB3	LUMAN|LZIP|sLZIP	cAMP responsive element binding protein 3	protein-coding	0.140704	0.775000	
chunk0180_182_1	chr7	65907478	65907993	+	0	NA	intron (NM_001284342, intron 1 of 1)	intron (NM_001284342, intron 1 of 1)	34465	NM_173517	154807	Hs.427232	NM_173517	ENSG00000196715	VKORC1L1	-	vitamin K epoxide reductase complex subunit 1 like 1	protein-coding	0.007767	0.375969	
chunk0073_381_1	chr16	15942801	15943489	+	0	NA	Intergenic	Intergenic	-6432	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.010174	0.438316	
chunk0059_300_1	chr14	35949820	35950398	+	0	NA	Intergenic	UCON105|Unknown|Unknown	-120318	NR_073454	101101773	Hs.640678	NR_073454	ENSG00000257585	LINC00609	-	long intergenic non-protein coding RNA 609	ncRNA	0.001730	0.367876	
chunk0202_19_1	chr9	70455908	70456555	+	0	NA	Intergenic	Intergenic	-41574	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.010819	0.489198	
chunk0030_141_1	chr10	113705131	113705330	+	0	NA	intron (NM_001267056, intron 2 of 6)	intron (NM_001267056, intron 2 of 6)	-4115	NM_001267058	840	Hs.9216	NM_001227	ENSG00000165806	CASP7	CASP-7|CMH-1|ICE-LAP3|LICE2|MCH3	caspase 7	protein-coding	0.005025	0.420000	
chunk0166_439_1	chr6	52953658	52954272	+	0	NA	Intergenic	Intergenic	41415	NM_001512	2941	Hs.485557	NM_001512	ENSG00000170899	GSTA4	GSTA4-4|GTA4	glutathione S-transferase alpha 4	protein-coding	0.006515	0.352846	
chunk0028_128_1	chr10	85009629	85010138	+	0	NA	Intergenic	Intergenic	189022	NR_120668	101929624	Hs.588831	NR_120667	ENSG00000237267	LINC01519	-	long intergenic non-protein coding RNA 1519	ncRNA	0.013752	0.398039	
chunk0210_51_1	chrX	68757449	68758151	+	0	NA	Intergenic	Intergenic	64160	NM_001142504	9754	Hs.95140	NM_014725	ENSG00000130052	STARD8	ARHGAP38|DLC3|STARTGAP3	StAR related lipid transfer domain containing 8	protein-coding	0.008547	0.460882	282(AGGAACATTTTGTTCT,-,0.00),283(GGAACATTTTGTTCTG,+,0.00)
chunk0017_453_1	chr1	214414642	214415024	+	0	NA	intron (NM_005401, intron 3 of 18)	intron (NM_005401, intron 3 of 18)	133611	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.015707	0.428198	
chunk0129_233_1	chr3	121969932	121970599	+	0	NA	Intergenic	MER31-int|LTR|ERV1	52015	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.004498	0.347305	
chunk0204_235_1	chr9	97860013	97860422	+	0	NA	Intergenic	Intergenic	6962	NM_004473	2304		NM_004473	ENSG00000178919	FOXE1	FKHL15|FOXE2|HFKH4|HFKL5|NMTC4|TITF2|TTF-2|TTF2	forkhead box E1	protein-coding	0.002445	0.431707	
chunk0177_150_1	chr7	22920922	22921537	+	0	NA	Intergenic	L1M4b|LINE|L1	64616	NR_003075	692210		NR_003075	ENSG00000221740	SNORD93	HBII-336	small nucleolar RNA, C/D box 93	snoRNA	0.000000	0.345779	
chunk0075_234_1	chr16	52984936	52985453	+	0	NA	Intergenic	Intergenic	-69839	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.009671	0.388031	
chunk0087_411_1	chr18	42177823	42178320	+	0	NA	Intergenic	L2a|LINE|L2	-8597	NR_046456	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.002012	0.389558	
chunk0022_116_1	chr10	11228057	11228577	+	0	NA	intron (NM_001083591, intron 3 of 13)	MIR|SINE|MIR	63287	NM_001083591	10659	Hs.309288	NM_006561	ENSG00000048740	CELF2	BRUNOL3|CELF-2|CUG-BP2|CUGBP2|ETR-3|ETR3|NAPOR	CUGBP Elav-like family member 2	protein-coding	0.000000	0.312860	
chunk0211_12_1	chrX	107715814	107716142	+	0	NA	intron (NM_198057, intron 1 of 2)	intron (NM_198057, intron 1 of 2)	503	NM_001015881	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.027439	0.550152	
chunk0208_155_1	chrX	16140740	16141457	+	0	NA	intron (NM_005314, intron 1 of 2)	intron (NM_005314, intron 1 of 2)	17797	NM_005314	2925	Hs.567282	NM_005314	ENSG00000126010	GRPR	BB2|BB2R	gastrin releasing peptide receptor	protein-coding	0.008368	0.388579	350(ATGAACAATGTGTGCC,-,0.00),351(TGAACAATGTGTGCCA,+,0.00)
chunk0179_424_1	chr7	51866324	51866662	+	0	NA	Intergenic	Intergenic	-549675	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.002959	0.486726	
chunk0010_276_1	chr1	117321971	117322170	+	0	NA	TTS (NR_126408)	TTS (NR_126408)	26604	NR_126408	104355292	Hs.576446	NR_126408	ENSG00000235202	LINC01525	lnc-MAN1A2-1	long intergenic non-protein coding RNA 1525	ncRNA	0.000000	0.420000	
chunk0009_38_1	chr1	100419343	100419664	+	0	NA	intron (NM_003672, intron 4 of 15)	intron (NM_003672, intron 4 of 15)	67036	NM_003672	8556	Hs.127411	NM_003672	ENSG00000079335	CDC14A	DFNB105|DFNB32|DFNB35|cdc14|hCDC14	cell division cycle 14A	protein-coding	0.003115	0.422360	
chunk0010_267_1	chr1	116988779	116989333	+	0	NA	3' UTR (NM_020440, exon 9 of 9)	3' UTR (NM_020440, exon 9 of 9)	-12694	NM_001256106	9398	Hs.654598	NM_004258	ENSG00000134256	CD101	EWI-101|IGSF2|V7	CD101 molecule	protein-coding	0.009025	0.488288	
chunk0036_408_1	chr11	68099374	68100061	+	0	NA	intron (NM_001277, intron 1 of 11)	intron (NM_001277, intron 1 of 11)	21674	NM_001277	1119	Hs.77221	NM_001277	ENSG00000110721	CHKA	CHK|CK|CKI|EK	choline kinase alpha	protein-coding	0.013100	0.402616	
chunk0025_423_1	chr10	59866843	59867283	+	0	NA	intron (NM_005436, intron 1 of 8)	intron (NM_005436, intron 1 of 8)	39593	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.006818	0.453515	
chunk0196_214_1	chr8	106761249	106761472	+	0	NA	exon (NM_139166, exon 2 of 2)	exon (NM_139166, exon 2 of 2)	8884	NM_139166	137735	Hs.374668	NM_139166	ENSG00000174429	ABRA	STARS	actin binding Rho activating protein	protein-coding	0.017937	0.513393	
chunk0057_108_1	chr13	99093917	99094445	+	0	NA	Intergenic	L1MC4a|LINE|L1	7458	NR_047482	100861541	Hs.344872	NR_047482		DOCK9-DT	DOCK9-AS2	DOCK9 divergent transcript	ncRNA	0.005682	0.455577	477(CAGCTCAGTGTGTGCT,-,0.00),478(AGCTCAGTGTGTGCTC,+,0.00)
chunk0074_323_1	chr16	30823203	30823464	+	0	NA	Intergenic	L1MC|LINE|L1	-36131	NM_001080417	23361	Hs.301094	NM_001080417	ENSG00000102870	ZNF629	ZNF|ZNF65	zinc finger protein 629	protein-coding	0.007663	0.309160	
chunk0150_139_1	chr5	33549860	33550551	+	0	NA	intron (NM_030955, intron 20 of 23)	intron (NM_030955, intron 20 of 23)	109429	NR_047676	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.008683	0.518786	346(TTGCACAGCCTGTTCC,-,0.00),347(TGCACAGCCTGTTCCA,+,0.00)
chunk0023_15_1	chr10	20936190	20936829	+	0	NA	intron (NM_213569, intron 4 of 6)	intron (NM_213569, intron 4 of 6)	-38907	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.001565	0.365625	
chunk0115_63_1	chr21	21461207	21461611	+	0	NA	intron (NM_004540, intron 12 of 17)	intron (NM_004540, intron 12 of 17)	275910	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.002475	0.246914	
chunk0090_102_1	chr18	70942583	70942906	+	0	NA	Intergenic	L1M1|LINE|L1	-291887	NM_001278515									0.000000	0.509259	
chunk0203_131_1	chr9	85331785	85332331	+	0	NA	Intergenic	Intergenic	409971	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.009158	0.404022	
chunk0179_358_1	chr7	50928354	50928745	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-135087	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.010230	0.372449	
chunk0100_137_1	chr2	108798976	108799207	+	0	NA	intron (NR_130121, intron 6 of 13)	L1MC4|LINE|L1	12341	NM_001303106	165055	Hs.362702	NM_144978	ENSG00000163006	CCDC138	-	coiled-coil domain containing 138	protein-coding	0.008658	0.366379	
chunk0111_434_1	chr20	35191596	35192096	+	0	NA	Intergenic	L2a|LINE|L2	19909	NM_006404	10544	Hs.647450	NM_006404	ENSG00000101000	PROCR	CCCA|CCD41|EPCR	protein C receptor	protein-coding	0.008000	0.425150	
chunk0183_239_1	chr7	107041157	107041356	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-3477	NM_002736	5577	Hs.433068	NM_002736	ENSG00000005249	PRKAR2B	PRKAR2|RII-BETA	protein kinase cAMP-dependent type II regulatory subunit beta	protein-coding	0.010050	0.435000	
chunk0136_56_1	chr4	1554786	1555346	+	0	NA	Intergenic	Intergenic	128925	NM_001013622	152877	Hs.143314	NM_001013622	ENSG00000174137	FAM53A	DNTNP	family with sequence similarity 53 member A	protein-coding	0.039286	0.606061	
chunk0108_321_1	chr2	235541814	235542281	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	36296	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.010707	0.420940	
chunk0147_54_1	chr4	172586390	172587077	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	102184	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.008734	0.347384	
chunk0087_161_1	chr18	34868689	34868975	+	0	NA	TTS (NM_001391)	TTS (NM_001391)	50494	NM_032981	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.006993	0.310105	
chunk0022_103_1	chr10	10049596	10050030	+	0	NA	Intergenic	Intergenic	-8909	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.002304	0.413793	
chunk0098_96_1	chr2	67885094	67885603	+	0	NA	Intergenic	L1ME3G|LINE|L1	-59786	NR_110271	101927701	Hs.348697	NR_110271	ENSG00000237013	LINC01812	-	long intergenic non-protein coding RNA 1812	ncRNA	0.003929	0.307843	263(CAGAACAATTTGTACA,-,0.00)
chunk0146_182_1	chr4	160806446	160806807	+	0	NA	Intergenic	Intergenic	-1216107	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.334254	
chunk0077_111_1	chr16	78230889	78231201	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	131632	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.009615	0.428115	
chunk0149_328_1	chr5	26641412	26641972	+	0	NA	Intergenic	L1PREC2|LINE|L1	396890	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.005357	0.342246	
chunk0187_450_1	chr7	159177112	159177677	+	0	NA	Intergenic	Intergenic	-32437	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.003540	0.356890	
chunk0069_197_1	chr15	63362129	63362552	+	0	NA	intron (NM_206925, intron 2 of 9)	MIR|SINE|MIR	19770	NM_206925	771	Hs.210995	NM_001218	ENSG00000074410	CA12	CA-XII|CAXII|HsT18816|T18816	carbonic anhydrase 12	protein-coding	0.007092	0.452830	154(ATAGACACTGTGTTCC,-,0.00),155(TAGACACTGTGTTCCT,+,0.00)
chunk0095_449_1	chr2	25618724	25619039	+	0	NA	intron (NM_001256303, intron 4 of 19)	intron (NM_001256303, intron 4 of 19)	31341	NM_001256308	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.006349	0.420886	49(AGGGACATGATGATCC,-,0.00),50(GGGACATGATGATCCC,+,0.00)
chunk0188_267_1	chr8	14831125	14831570	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	22163	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.004494	0.378924	324(TGGGACACAGTGCTCC,-,0.00),325(GGGACACAGTGCTCCA,+,0.00)
chunk0188_276_1	chr8	15493436	15494267	+	0	NA	Intergenic	Intergenic	-46236	NM_178234	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.014440	0.395433	
chunk0091_84_1	chr19	5340395	5340669	+	0	NA	intron (NM_130853, intron 1 of 28)	CpG	271	NM_002850	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.083942	0.658182	
chunk0032_150_1	chr11	4769484	4769920	+	0	NA	exon (NM_001004752, exon 1 of 1)	exon (NM_001004752, exon 1 of 1)	215	NM_001004752	256892		NM_001004752	ENSG00000280021	OR51F1	OR11-21|OR51F1P	olfactory receptor family 51 subfamily F member 1 (gene/pseudogene)	protein-coding	0.009174	0.443936	291(AGGATCACGCTGTTCC,-,0.00),292(GGATCACGCTGTTCCC,+,0.00)
chunk0010_345_1	chr1	118590893	118591669	+	0	NA	Intergenic	Intergenic	398275	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.003866	0.391248	597(TAGCACAGAATGTCCT,-,0.00),598(AGCACAGAATGTCCTG,+,0.00)
chunk0149_209_1	chr5	21708495	21708818	+	0	NA	Intergenic	MER70A|LTR|ERVL	-175798	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.015480	0.419753	
chunk0149_454_1	chr5	29993438	29993686	+	0	NA	Intergenic	L2|LINE|L2	-597586	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.008065	0.405622	
chunk0191_363_1	chr8	56747395	56747902	+	0	NA	Intergenic	Intergenic	-187825	NR_038236	100507632	Hs.583755	NR_038236	ENSG00000246430	LINC00968	-	long intergenic non-protein coding RNA 968	ncRNA	0.000000	0.377953	242(GAGGACACACAGATCT,-,0.00),243(AGGACACACAGATCTC,+,0.00)
chunk0068_203_1	chr15	54968229	54968506	+	0	NA	Intergenic	L1PA7|LINE|L1	228666	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.000000	0.334532	
chunk0037_200_1	chr11	74377498	74378104	+	0	NA	intron (NM_173582, intron 1 of 13)	intron (NM_173582, intron 1 of 13)	20664	NM_173582	283209	Hs.26612	NM_173582	ENSG00000165434	PGM2L1	BM32A|PMMLP	phosphoglucomutase 2 like 1	protein-coding	0.004950	0.359143	
chunk0011_120_1	chr1	147053950	147054371	+	0	NA	Intergenic	Intergenic	-11121	NR_024442	728989	Hs.537068	NR_024442		LOC728989	-	phosphodiesterase 4D interacting protein pseudogene	pseudo	0.002375	0.343602	153(TAGGACTTTTTGTGCT,-,0.00),154(AGGACTTTTTGTGCTA,+,0.00)
chunk0171_423_1	chr6	131493837	131494247	+	0	NA	Intergenic	Intergenic	-79162	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.002439	0.316302	
chunk0076_195_1	chr16	67816529	67816961	+	0	NA	intron (NM_001288994, intron 2 of 10)	intron (NM_001288994, intron 2 of 10)	9867	NM_001288994	55815	Hs.632212	NM_018430	ENSG00000102904	TSNAXIP1	TXI1	translin associated factor X interacting protein 1	protein-coding	0.048611	0.579677	
chunk0091_205_1	chr19	9407043	9407423	+	0	NA	Intergenic	CpG	28345	NM_001271314	10781	Hs.656185	NM_006631	ENSG00000174652	ZNF266	HZF1	zinc finger protein 266	protein-coding	0.068421	0.635171	
chunk0014_334_1	chr1	182163663	182163955	+	0	NA	Intergenic	Intergenic	-102097	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.006849	0.443686	
chunk0027_253_1	chr10	77179158	77179415	+	0	NA	intron (NM_001014797, intron 5 of 28)	MIR|SINE|MIR	38455	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.019455	0.531008	
chunk0033_372_1	chr11	23442755	23443244	+	0	NA	Intergenic	Intergenic	-23809	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.008180	0.369388	217(GAGTACACTATGTCTC,-,0.00),218(AGTACACTATGTCTCT,+,0.00)
chunk0153_428_1	chr5	76028374	76028881	+	0	NA	Intergenic	Intergenic	-54787	NM_001297716	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.003945	0.397638	
chunk0199_364_1	chr9	12759608	12760276	+	0	NA	intron (NR_125775, intron 2 of 3)	intron (NR_125775, intron 2 of 3)	-15071	NM_203403	286343	Hs.445356	NM_203403	ENSG00000153714	LURAP1L	C9orf150|HYST0841|LRAP35b|bA3L8.2	leucine rich adaptor protein 1 like	protein-coding	0.002994	0.385650	
chunk0014_272_1	chr1	180352510	180352790	+	0	NA	intron (NM_032360, intron 6 of 7)	intron (NM_032360, intron 6 of 7)	-77969	NR_037642	100527964	Hs.496545	NR_037642	ENSG00000230124	LHX4-AS1	-	LHX4 antisense RNA 1	ncRNA	0.000000	0.391459	
chunk0168_42_1	chr6	78462244	78462863	+	0	NA	Intergenic	Intergenic	-404991	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.006462	0.422581	
chunk0052_258_1	chr12	123686615	123687062	+	0	NA	exon (NM_001143850, exon 6 of 18)	exon (NM_001143850, exon 6 of 18)	15725	NM_024809	79867	Hs.167165	NM_024809	ENSG00000168778	TCTN2	C12orf38|JBTS24|MKS8|TECT2	tectonic family member 2	protein-coding	0.029083	0.479911	
chunk0125_386_1	chr3	71684864	71685085	+	0	NA	intron (NM_173359, intron 7 of 7)	intron (NM_173359, intron 7 of 7)	40401	NM_001134651	317649	Hs.581355	NM_173359	ENSG00000163412	EIF4E3	eIF-4E3|eIF4E-3	eukaryotic translation initiation factor 4E family member 3	protein-coding	0.018100	0.454955	
chunk0033_234_1	chr11	17812557	17812901	+	0	NA	intron (NM_012139, intron 10 of 10)	L2b|LINE|L2	76781	NM_004976	3746	Hs.552896	NM_004976	ENSG00000129159	KCNC1	EPM7|KV3.1|KV4|NGK2	potassium voltage-gated channel subfamily C member 1	protein-coding	0.000000	0.426087	
chunk0165_362_1	chr6	38150681	38151006	+	0	NA	intron (NM_021943, intron 5 of 5)	intron (NM_021943, intron 5 of 5)	331312	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.003077	0.518405	
chunk0094_106_1	chr2	4243844	4244043	+	0	NA	Intergenic	Intergenic	-269911	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.030151	0.545000	
chunk0020_117_1	chr1	233348096	233348684	+	0	NA	intron (NM_032435, intron 2 of 9)	L1MB8|LINE|L1	20622	NM_032435	84451	Hs.547779	NM_032435	ENSG00000143674	MAP3K21	MLK4|dJ862P8.3	mitogen-activated protein kinase kinase kinase 21	protein-coding	0.008503	0.392190	
chunk0063_295_1	chr14	84500898	84501097	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	-892882	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005025	0.400000	
chunk0071_20_1	chr15	78990914	78991529	+	0	NA	intron (NM_153815, intron 8 of 13)	intron (NM_153815, intron 8 of 13)	14439	NM_153815	5923	Hs.459035	NM_002891	ENSG00000058335	RASGRF1	CDC25|CDC25L|GNRP|GRF1|GRF55|H-GRF55|PP13187|ras-GRF1	Ras protein specific guanine nucleotide releasing factor 1	protein-coding	0.014634	0.467532	
chunk0042_198_1	chr12	5617021	5617845	+	0	NA	intron (NM_001278596, intron 17 of 25)	intron (NM_001278596, intron 17 of 25)	123301	NM_002527	4908	Hs.99171	NM_002527	ENSG00000185652	NTF3	HDNF|NGF-2|NGF2|NT-3|NT3	neurotrophin 3	protein-coding	0.021845	0.489697	19(CAGATCACAGTGTACC,-,0.00),20(AGATCACAGTGTACCA,+,0.00),67(CAGATCACACTGTACC,-,0.00),68(AGATCACACTGTACCA,+,0.00),91(AAGATCACACTGTACC,-,0.00),92(AGATCACACTGTACCA,+,0.00),115(CAGACCACAGTGTACC,-,0.00),163(CAGATCACACTGTACC,-,0.00),164(AGATCACACTGTACCA,+,0.00),187(AAGATCACAATGTACC,-,0.00),235(CAGATCACAGTGTACC,-,0.00),236(AGATCACAGTGTACCA,+,0.00),331(TGGATCACAGTGTGCC,-,0.00),332(GGATCACAGTGTGCCA,+,0.00),355(CAGATCACACTGTACC,-,0.00),356(AGATCACACTGTACCA,+,0.00),379(AAGATCACAATGTACC,-,0.00),427(CAGATCACAGTGTGCC,-,0.00),428(AGATCACAGTGTGCCA,+,0.00),547(CAGACCACACTGTACC,-,0.00),548(AGACCACACTGTACCA,+,0.00),571(AAGATCACGATGTACC,-,0.00),619(CAGATCACAGTGTGCC,-,0.00),620(AGATCACAGTGTGCCA,+,0.00),691(AAGATCACACTGTACC,-,0.00),692(AGATCACACTGTACCA,+,0.00),715(CGGATCACAGTGTGCC,-,0.00),716(GGATCACAGTGTGCCA,+,0.00)
chunk0098_128_1	chr2	69039727	69040249	+	0	NA	intron (NM_053034, intron 1 of 14)	intron (NM_053034, intron 1 of 14)	26844	NM_018153	84168	Hs.165859	NM_018153	ENSG00000169604	ANTXR1	ATR|GAPO|TEM8	ANTXR cell adhesion molecule 1	protein-coding	0.011494	0.395793	
chunk0061_288_1	chr14	61585935	61586437	+	0	NA	intron (NR_039985, intron 1 of 2)	intron (NR_039985, intron 1 of 2)	-15533	NR_110416	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.005976	0.451292	
chunk0044_221_1	chr12	31357420	31358014	+	0	NA	Intergenic	AluJb|SINE|Alu	-31492	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.015152	0.431933	
chunk0085_28_1	chr18	428880	429498	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	71540	NM_130386	81035	Hs.464422	NM_030781	ENSG00000158270	COLEC12	CLP1|NSR2|SCARA4|SRCL	collectin subfamily member 12	protein-coding	0.006472	0.340872	352(AAGAACACGTTGTCTC,-,0.00),353(AGAACACGTTGTCTCT,+,0.00),411(CAGAACAATGTGTACA,-,0.00),412(AGAACAATGTGTACAA,+,0.00)
chunk0085_87_1	chr18	2518533	2518772	+	0	NA	Intergenic	Intergenic	52851	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.020921	0.512500	
chunk0011_405_1	chr1	154272658	154272857	+	0	NA	exon (NM_006118, exon 1 of 7)	exon (NM_006118, exon 1 of 7)	194	NM_006118	10456	Hs.199625	NM_006118	ENSG00000143575	HAX1	HCLSBP1|HS1BP1|SCN3	HCLS1 associated protein X-1	protein-coding	0.065327	0.570000	
chunk0092_116_1	chr19	27392219	27392608	+	0	NA	Intergenic	LTR12C|LTR|ERV1	-401054	NR_110689	101927151	Hs.567934	NR_110687	ENSG00000267575	LOC101927151	-	uncharacterized LOC101927151	ncRNA	0.007712	0.497436	
chunk0083_455_1	chr17	73205615	73205927	+	0	NA	intron (NM_018714, intron 10 of 13)	intron (NM_018714, intron 10 of 13)	12737	NM_018714	9382	Hs.103555	NM_018714	ENSG00000166685	COG1	CDG2G|LDLB	component of oligomeric golgi complex 1	protein-coding	0.016026	0.482428	180(TTGAACAGTAAGTGCT,-,0.00),181(TGAACAGTAAGTGCTC,+,0.00)
chunk0179_78_1	chr7	44320833	44321078	+	0	NA	intron (NM_172084, intron 1 of 15)	intron (NM_172084, intron 1 of 15)	4676	NM_172078	816	Hs.351887	NM_001220	ENSG00000058404	CAMK2B	CAM2|CAMK2|CAMKB|MRD54	calcium/calmodulin dependent protein kinase II beta	protein-coding	0.016327	0.658537	
chunk0038_152_1	chr11	84608574	84609136	+	0	NA	intron (NM_001142699, intron 6 of 27)	MIR|SINE|MIR	-291516	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.007117	0.397869	
chunk0102_241_1	chr2	149005687	149006125	+	0	NA	intron (NR_111932, intron 15 of 19)	MIRc|SINE|MIR	-32561	NM_001317003	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.011416	0.469248	
chunk0133_84_1	chr3	167346316	167346591	+	0	NA	intron (NM_001199202, intron 9 of 20)	intron (NM_001199202, intron 9 of 20)	33830	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.007273	0.347826	
chunk0199_233_1	chr9	5389270	5389529	+	0	NA	intron (NM_018465, intron 3 of 5)	MER90|LTR|ERV1	48538	NM_018465	55848	Hs.584242	NM_018465	ENSG00000107020	PLGRKT	AD025|C9orf46|MDS030|PLG-RKT|Plg-R(KT)	plasminogen receptor with a C-terminal lysine	protein-coding	0.007722	0.423077	
chunk0190_146_1	chr8	30924935	30925495	+	0	NA	Intergenic	Intergenic	-76198	NM_031271									0.007143	0.333333	
chunk0162_327_1	chr6	6782885	6783372	+	0	NA	Intergenic	Intergenic	-160302	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.006160	0.375000	25(GGGGACAGTCAGTACA,-,0.00),26(GGGACAGTCAGTACAC,+,0.00)
chunk0184_79_1	chr7	112848468	112848718	+	0	NA	intron (NM_152556, intron 3 of 4)	intron (NM_152556, intron 3 of 4)	-58170	NR_109840	64418	Hs.606345	NM_022484	ENSG00000146802	TMEM168	-	transmembrane protein 168	protein-coding	0.012000	0.434263	
chunk0031_144_1	chr10	125023949	125024388	+	0	NA	intron (NM_001290215, intron 3 of 10)	intron (NM_001290215, intron 3 of 10)	3716	NM_022802	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.043280	0.554545	
chunk0055_436_1	chr13	75549310	75549814	+	0	NA	promoter-TSS (NM_006002)	promoter-TSS (NM_006002)	82	NM_001270952	7347	Hs.162241	NM_006002	ENSG00000118939	UCHL3	UCH-L3	ubiquitin C-terminal hydrolase L3	protein-coding	0.091270	0.615842	
chunk0104_133_1	chr2	173287524	173287972	+	0	NA	Intergenic	Intergenic	-5712	NR_033882	339751	Hs.570083	NR_033882	ENSG00000238133	MAP3K20-AS1	MLK7-AS1	MAP3K20 antisense RNA 1	ncRNA	0.004464	0.416481	286(AGGACCAGAATGTTCT,-,0.00),287(GGACCAGAATGTTCTA,+,0.00)
chunk0177_237_1	chr7	24690224	24690699	+	0	NA	3' UTR (NM_016447, exon 13 of 13)	3' UTR (NM_016447, exon 13 of 13)	67003	NM_001127453	1687	Hs.520708	NM_004403	ENSG00000105928	GSDME	DFNA5|ICERE-1	gasdermin E	protein-coding	0.008421	0.409664	223(GGAAACATGATGTGCC,-,0.00)
chunk0169_256_1	chr6	105321121	105321583	+	0	NA	intron (NM_002726, intron 10 of 14)	intron (NM_002726, intron 10 of 14)	81772	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.015152	0.388769	
chunk0074_251_1	chr16	27703792	27704025	+	0	NA	exon (NM_015202, exon 12 of 28)	exon (NM_015202, exon 12 of 28)	153761	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.017167	0.448718	
chunk0059_41_1	chr14	29916101	29916300	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	11493	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005025	0.450000	
chunk0013_332_1	chr1	171671635	171671939	+	0	NA	Intergenic	L1ME1|LINE|L1	-19154	NM_000261	4653	Hs.436037	NM_000261	ENSG00000034971	MYOC	GLC1A|GPOA|JOAG|JOAG1|TIGR	myocilin	protein-coding	0.003289	0.360656	
chunk0165_373_1	chr6	38272901	38273373	+	0	NA	intron (NM_001099272, intron 8 of 10)	intron (NM_001099272, intron 8 of 10)	322930	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.000000	0.401691	197(GAGCACTCCCTGTTCC,-,0.00),198(AGCACTCCCTGTTCCC,+,0.00)
chunk0014_263_1	chr1	180173668	180174507	+	0	NA	intron (NM_001004128, intron 2 of 12)	intron (NM_001004128, intron 2 of 12)	19254	NM_001004128	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.013111	0.522619	
chunk0158_174_1	chr5	127707288	127707600	+	0	NA	Intergenic	Intergenic	54429	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.006410	0.345048	159(CAGAACAGATTGTACT,-,0.00),160(AGAACAGATTGTACTG,+,0.00)
chunk0078_131_1	chr17	3636080	3636305	+	0	NA	promoter-TSS (NM_004937)	promoter-TSS (NM_004937)	130	NM_013276	23729	Hs.579217	NM_013276	ENSG00000197417	SHPK	CARKL|SHK	sedoheptulokinase	protein-coding	0.102222	0.721239	
chunk0034_374_1	chr11	36271820	36272332	+	0	NA	TTS (NM_001307932)	TTS (NM_001307932)	17373	NM_001307937	29099	Hs.99443	NM_014186	ENSG00000110442	COMMD9	C11orf55|HSPC166|LINC00610	COMM domain containing 9	protein-coding	0.005859	0.475634	
chunk0085_306_1	chr18	8148894	8149169	+	0	NA	intron (NM_001105244, intron 14 of 32)	L1PA7|LINE|L1	218003	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.003636	0.373188	
chunk0035_155_1	chr11	43359783	43360013	+	0	NA	intron (NM_018259, intron 1 of 23)	intron (NM_018259, intron 1 of 23)	1013	NM_018259	55761	Hs.191186	NM_018259	ENSG00000052841	TTC17	-	tetratricopeptide repeat domain 17	protein-coding	0.034783	0.424242	
chunk0063_66_1	chr14	77321272	77321504	+	0	NA	promoter-TSS (NM_013382)	promoter-TSS (NM_013382)	501	NM_145871	2954	Hs.655292	NM_001513	ENSG00000100577	GSTZ1	GSTZ1-1|MAAI|MAAID|MAI	glutathione S-transferase zeta 1	protein-coding	0.090517	0.678112	
chunk0138_293_1	chr4	40975344	40975832	+	0	NA	intron (NM_004307, intron 6 of 17)	MIRb|SINE|MIR	-118396	NM_001166053	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.006148	0.390593	
chunk0024_113_1	chr10	34704748	34705125	+	0	NA	intron (NM_019619, intron 1 of 24)	intron (NM_019619, intron 1 of 24)	110389	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.002653	0.304233	
chunk0116_414_1	chr21	42662548	42662951	+	0	NA	intron (NM_001001575, intron 1 of 14)	(AC)n|Simple_repeat|Simple_repeat	8997	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.027295	0.537129	
chunk0181_149_1	chr7	81837204	81837696	+	0	NA	Intergenic	Intergenic	-67314	NM_001010934	3082	Hs.396530	NM_000601	ENSG00000019991	HGF	DFNB39|F-TCF|HGFB|HPTA|SF	hepatocyte growth factor	protein-coding	0.008130	0.286004	
chunk0138_4_1	chr4	30255253	30255646	+	0	NA	Intergenic	L1PB3|LINE|L1	-464959	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.005089	0.482234	
chunk0201_241_1	chr9	37782381	37783204	+	0	NA	intron (NM_016042, intron 2 of 3)	L2c|LINE|L2	2300	NM_001002269	51010	Hs.602571	NM_016042	ENSG00000107371	EXOSC3	CGI-102|PCH1B|RRP40|Rrp40p|bA3J10.7|hRrp-40|p10	exosome component 3	protein-coding	0.012151	0.391990	649(GGGAACAGCATGTGCA,-,0.00),650(GGAACAGCATGTGCAA,+,0.00)
chunk0184_379_1	chr7	121434905	121435519	+	0	NA	Intergenic	Intergenic	-38844	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.004886	0.338211	
chunk0191_234_1	chr8	52832733	52833136	+	0	NA	Intergenic	Intergenic	-106974	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.000000	0.289604	
chunk0048_164_1	chr12	80712810	80713250	+	0	NA	Intergenic	Intergenic	-3899	NM_005593	4617	Hs.178023	NM_005593	ENSG00000111049	MYF5	EORVA|bHLHc2	myogenic factor 5	protein-coding	0.000000	0.410431	
chunk0114_305_1	chr21	17089011	17089561	+	0	NA	Intergenic	Intergenic	-349604	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.003636	0.348457	
chunk0109_242_1	chr20	6005747	6006172	+	0	NA	promoter-TSS (NM_019095)	promoter-TSS (NM_019095)	-134	NM_019095	54675	Hs.743956	NM_019095	ENSG00000088766	CRLS1	C20orf155|CLS|CLS1|GCD10|dJ967N21.6	cardiolipin synthase 1	protein-coding	0.096471	0.673709	
chunk0027_321_1	chr10	78277779	78278369	+	0	NA	intron (NR_073447, intron 1 of 2)	intron (NR_073447, intron 1 of 2)	10746	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.020339	0.541455	267(CAGAACAGGCTGTCCT,-,0.00),268(AGAACAGGCTGTCCTG,+,0.00)
chunk0058_444_1	chr13	113640429	113640869	+	0	NA	non-coding (NR_026580, exon 11 of 11)	non-coding (NR_026580, exon 11 of 11)	17549	NM_000705	496	Hs.434202	NM_000705	ENSG00000186009	ATP4B	ATP6B	ATPase H+/K+ transporting subunit beta	protein-coding	0.015909	0.405896	
chunk0135_67_1	chr3	185866531	185866974	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-41713	NM_001007225	10644	Hs.35354	NM_006548	ENSG00000073792	IGF2BP2	IMP-2|IMP2|VICKZ2	insulin like growth factor 2 mRNA binding protein 2	protein-coding	0.002257	0.461712	222(GGGAACAGTGAGTGCT,-,0.00),223(GGAACAGTGAGTGCTG,+,0.00)
chunk0083_64_1	chr17	63989856	63990139	+	0	NA	Intergenic	Intergenic	-8354	NM_001164257	92340	Hs.708161	NM_001164257	ENSG00000224383	PRR29	C17orf72	proline rich 29	protein-coding	0.028269	0.531690	
chunk0030_236_1	chr10	114981052	114981609	+	0	NA	Intergenic	L1MEd|LINE|L1	-13327	NR_120677	102724589		NR_120677	ENSG00000236799	LINC02626	-	long intergenic non-protein coding RNA 2626	ncRNA	0.005386	0.344086	
chunk0130_76_1	chr3	130494786	130495003	+	0	NA	Intergenic	HAL1|LINE|L1	-65440	NM_001102608	131873	Hs.591282	NM_001102608	ENSG00000206384	COL6A6	-	collagen type VI alpha 6 chain	protein-coding	0.004608	0.426606	
chunk0191_372_1	chr8	56974421	56974713	+	0	NA	intron (NM_017813, intron 3 of 4)	intron (NM_017813, intron 3 of 4)	19304	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.017123	0.392491	
chunk0043_31_1	chr12	13135609	13136430	+	0	NA	Intergenic	Intergenic	-32323	NM_001080555	83445	Hs.240053	NM_031289	ENSG00000111305	GSG1	-	germ cell associated 1	protein-coding	0.021924	0.496350	427(TGGAACACTGTGTGCC,-,0.00),428(GGAACACTGTGTGCCC,+,0.00)
chunk0120_231_1	chr3	8293799	8294129	+	0	NA	intron (NR_033378, intron 3 of 3)	intron (NR_033378, intron 3 of 3)	207694	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.000000	0.329305	
chunk0212_18_1	chrY	8777438	8777762	+	0	NA	Intergenic	Intergenic	39782	NR_001548	83866	Hs.122396	NR_001548	ENSG00000180910	TTTY11	NCRNA00134|TTY11	testis-specific transcript, Y-linked 11	ncRNA	0.003086	0.289231	
chunk0079_257_1	chr17	16160834	16161404	+	0	NA	intron (NM_006311, intron 5 of 45)	intron (NM_006311, intron 5 of 45)	33520	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.003509	0.399299	
chunk0134_101_1	chr3	176943769	176944212	+	0	NA	Intergenic	L1PB1|LINE|L1	-126989	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.002257	0.319820	
chunk0067_236_1	chr15	45497326	45498037	+	0	NA	intron (NM_013309, intron 3 of 7)	intron (NM_013309, intron 3 of 7)	-13455	NR_022014	283651	Hs.574240	NM_173609		HMGN2P46	C15orf21|D-PCa-2	high mobility group nucleosomal binding domain 2 pseudogene 46	pseudo	0.005626	0.318820	
chunk0006_234_1	chr1	68725406	68725605	+	0	NA	Intergenic	Intergenic	-228284	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.010050	0.470000	
chunk0167_76_1	chr6	56521264	56521837	+	0	NA	intron (NM_183380, intron 60 of 93)	intron (NM_183380, intron 60 of 93)	121346	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.003490	0.311847	
chunk0125_179_1	chr3	66625700	66626376	+	0	NA	Intergenic	L2b|LINE|L2	-125617	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.007396	0.460857	
chunk0058_301_1	chr14	26967071	26967423	+	0	NA	Intergenic	Intergenic	58605	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.008523	0.424929	119(AAGTACTTTCTGTTCT,-,0.00),120(AGTACTTTCTGTTCTA,+,0.00)
chunk0149_17_1	chr5	15904018	15904622	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-30862	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.008278	0.323967	
chunk0206_116_1	chr9	120916394	120917145	+	0	NA	intron (NM_005658, intron 3 of 7)	intron (NM_005658, intron 3 of 7)	-2197	NM_001190947	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.013316	0.458777	322(AGGGACAAGTTGTTCC,-,0.00),323(GGGACAAGTTGTTCCC,+,0.00)
chunk0068_348_1	chr15	57761449	57762038	+	0	NA	Intergenic	Tigger14a|DNA|TcMar-Tigger	55222	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.001698	0.384746	369(AAGAACAGAATGTCTC,-,0.00),370(AGAACAGAATGTCTCA,+,0.00)
chunk0147_405_1	chr4	186825829	186826513	+	0	NA	Intergenic	Intergenic	-102338	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.005848	0.345985	
chunk0110_368_1	chr20	19935957	19936296	+	0	NA	intron (NM_018993, intron 2 of 10)	intron (NM_018993, intron 2 of 10)	46560	NM_018993	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.017699	0.535294	
chunk0195_386_1	chr8	100219881	100220270	+	0	NA	intron (NM_003114, intron 12 of 18)	intron (NM_003114, intron 12 of 18)	61740	NM_003114	6674	Hs.591866	NM_003114	ENSG00000104450	SPAG1	CILD28|CT140|HEL-S-268|HSD-3.8|SP75|TPIS	sperm associated antigen 1	protein-coding	0.012853	0.407692	
chunk0085_313_1	chr18	8261015	8261424	+	0	NA	intron (NM_001105244, intron 19 of 32)	(ACAAA)n|Simple_repeat|Simple_repeat	105815	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.009780	0.463415	
chunk0116_164_1	chr21	36615714	36616110	+	0	NA	Intergenic	Intergenic	-39343	NM_001146077	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.005051	0.433249	
chunk0026_19_1	chr10	60625632	60625850	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	-52785	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.004587	0.315068	
chunk0015_351_1	chr1	190186314	190186686	+	0	NA	intron (NM_199051, intron 6 of 7)	intron (NM_199051, intron 6 of 7)	291129	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.010753	0.361930	
chunk0129_364_1	chr3	125356620	125356822	+	0	NA	intron (NM_021964, intron 1 of 8)	intron (NM_021964, intron 1 of 8)	18633	NM_021964	7707	Hs.592591	NM_021964	ENSG00000163848	ZNF148	BERF-1|BFCOL1|GDACCF|HT-BETA|ZBP-89|ZFP148|pHZ-52	zinc finger protein 148	protein-coding	0.004950	0.334975	
chunk0019_39_1	chr1	224013788	224014113	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	-21306	NR_132119	441124	Hs.520589	NR_132119		GTF2IP20	-	general transcription factor IIi pseudogene 20	pseudo	0.052308	0.441718	
chunk0053_34_1	chr13	27295549	27295866	+	0	NA	Intergenic	Intergenic	25380	NM_206827	387496	Hs.192131	NM_206827	ENSG00000122035	RASL11A	-	RAS like family 11 member A	protein-coding	0.012618	0.465409	170(AAGAACTCTGTGCCCT,-,0.00),171(AGAACTCTGTGCCCTT,+,0.00)
chunk0075_363_1	chr16	56262326	56262964	+	0	NA	intron (NM_020988, intron 2 of 8)	intron (NM_020988, intron 2 of 8)	17125	NR_037499	100500891		NR_037499	ENSG00000265281	MIR3935	-	microRNA 3935	ncRNA	0.012539	0.416275	
chunk0088_368_1	chr18	53838567	53839277	+	0	NA	Intergenic	Intergenic	-257863	NR_110800	101928167	Hs.382012	NR_110800	ENSG00000260433	LINC01917	-	long intergenic non-protein coding RNA 1917	ncRNA	0.007042	0.376934	
chunk0154_284_1	chr5	82605342	82605698	+	0	NA	Intergenic	L1MA4A|LINE|L1	-234635	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.002809	0.549020	
chunk0130_290_1	chr3	136617190	136617746	+	0	NA	intron (NM_005862, intron 3 of 33)	intron (NM_005862, intron 3 of 33)	134935	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.000000	0.438061	
chunk0078_318_1	chr17	8510645	8511042	+	0	NA	intron (NM_001256095, intron 23 of 41)	MamRep137|DNA|TcMar-Tigger	74991	NM_030808	81565	Hs.372123	NM_030808	ENSG00000166579	NDEL1	EOPA|MITAP1|NDE1L1|NDE2|NUDEL	nudE neurodevelopment protein 1 like 1	protein-coding	0.010076	0.331658	
chunk0061_422_1	chr14	65168992	65169259	+	0	NA	Intergenic	Intergenic	53222	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.011236	0.436567	135(GGGTACGGTTTGTTCT,-,0.00),136(GGTACGGTTTGTTCTT,+,0.00)
chunk0187_74_1	chr8	2719460	2719855	+	0	NA	intron (NR_125426, intron 1 of 2)	intron (NR_125426, intron 1 of 2)	8794	NR_125426	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.010127	0.391414	
chunk0097_253_1	chr2	54099449	54099727	+	0	NA	Intergenic	L1MA8|LINE|L1	-15685	NM_138448	98	Hs.516173	NM_138448	ENSG00000170634	ACYP2	ACYM|ACYP	acylphosphatase 2	protein-coding	0.010791	0.379928	
chunk0203_375_1	chr9	90249044	90249532	+	0	NA	Intergenic	L2a|LINE|L2	184201	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.000000	0.392638	
chunk0165_81_1	chr6	31293229	31293669	+	0	NA	Intergenic	Intergenic	-21313	NM_001243042	3107	Hs.656020	NM_002117	ENSG00000204525	HLA-C	D6S204|HLA-JY3|HLAC|HLC-C|MHC|PSORS1	major histocompatibility complex, class I, C	protein-coding	0.011364	0.378685	
chunk0072_326_1	chr15	99137144	99137373	+	0	NA	non-coding (NR_109947, exon 13 of 13)	non-coding (NR_109947, exon 13 of 13)	32178	NM_145728	23336	Hs.207106	NM_015286	ENSG00000182253	SYNM	DMN|SYN	synemin	protein-coding	0.034934	0.591304	
chunk0049_227_1	chr12	93431488	93431687	+	0	NA	intron (NM_003348, intron 1 of 3)	MIR|SINE|MIR	10663	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.010050	0.350000	
chunk0092_103_1	chr19	23350745	23350945	+	0	NA	Intergenic	MER48|LTR|ERV1	44715	NM_003430	7644	Hs.58834	NM_003430	ENSG00000167232	ZNF91	HPF7|HTF10	zinc finger protein 91	protein-coding	0.020000	0.532338	
chunk0164_240_1	chr6	23289807	23290191	+	0	NA	Intergenic	L1MC|LINE|L1	720550	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.002604	0.309091	
chunk0012_180_1	chr1	159294299	159294848	+	0	NA	intron (NM_002001, intron 1 of 5)	L2a|LINE|L2	4859	NM_002001	2205	Hs.897	NM_002001	ENSG00000179639	FCER1A	FCE1A|FcERI	Fc fragment of IgE receptor Ia	protein-coding	0.005464	0.334545	183(TAAAACAGATTGTCCT,-,0.00),184(AAAACAGATTGTCCTT,+,0.00)
chunk0100_250_1	chr2	113046453	113047351	+	0	NA	intron (NM_014438, intron 1 of 5)	L1MC3|LINE|L1	5965	NM_014438	27177	Hs.278909	NM_014438	ENSG00000136696	IL36B	FIL1|FIL1-(ETA)|FIL1H|FILI-(ETA)|IL-1F8|IL-1H2|IL1-ETA|IL1F8|IL1H2	interleukin 36 beta	protein-coding	0.007795	0.361513	
chunk0110_431_1	chr20	20816184	20816476	+	0	NA	Intergenic	MER4D1|LTR|ERV1	-103707	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.003425	0.389078	
chunk0208_381_1	chrX	28587488	28588173	+	0	NA	5' UTR (NM_014271, exon 1 of 11)	5' UTR (NM_014271, exon 1 of 11)	266	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.013139	0.399417	
chunk0195_20_1	chr8	93115213	93115741	+	0	NA	Intergenic	Intergenic	51373	NM_001242668									0.001894	0.338374	238(ATGAACACTGTGTTCC,-,0.00),239(TGAACACTGTGTTCCT,+,0.00),284(CAGAACATGCTGTTTT,-,0.00),285(AGAACATGCTGTTTTG,+,0.00)
chunk0021_84_1	chr10	1732825	1733218	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	4455	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.027990	0.461929	
chunk0066_255_1	chr15	34790031	34790284	+	0	NA	3' UTR (NM_005159, exon 7 of 7)	3' UTR (NM_005159, exon 7 of 7)	5569	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.007905	0.381890	
chunk0093_15_1	chr2	168478	169008	+	0	NA	Intergenic	L1MC2|LINE|L1	87597	NM_001282687	26751	Hs.515951	NM_015677	ENSG00000035115	SH3YL1	RAY	SH3 and SYLF domain containing 1	protein-coding	0.003774	0.372881	
chunk0123_144_1	chr3	42838450	42838934	+	0	NA	intron (NM_001296, intron 2 of 2)	L1MD|LINE|L1	29220	NM_001296	1238	Hs.146346	NM_001296	ENSG00000144648	ACKR2	CCBP2|CCR10|CCR9|CMKBR9|D6|hD6	atypical chemokine receptor 2	protein-coding	0.008264	0.354639	
chunk0059_16_1	chr14	29800103	29800527	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	127378	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.011792	0.392941	255(TTAACACTCTGTTCCT,+,0.00)
chunk0174_210_1	chr6	160305927	160306572	+	0	NA	Intergenic	Intergenic	-42124	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.009302	0.434985	
chunk0032_237_1	chr11	7694111	7694465	+	0	NA	intron (NM_198185, intron 12 of 14)	intron (NM_198185, intron 12 of 14)	12106	NM_198185	341277	Hs.532475	NM_198185	ENSG00000183378	OVCH2	OVTN	ovochymase 2 (gene/pseudogene)	protein-coding	0.011299	0.433803	
chunk0156_394_1	chr5	113371697	113372134	+	0	NA	intron (NM_001085377, intron 2 of 18)	intron (NM_001085377, intron 2 of 18)	63116	NM_032028	83942	Hs.519507	NM_032028	ENSG00000212122	TSSK1B	FKSG81|SPOGA4|STK22D|TSK1|TSSK1	testis specific serine kinase 1B	protein-coding	0.004577	0.333333	
chunk0173_67_1	chr6	142570377	142570771	+	0	NA	intron (NR_027312, intron 1 of 2)	intron (NR_027312, intron 1 of 2)	67262	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.000000	0.392405	206(GTCACATGGTGTTCTG,+,0.00)
chunk0103_56_1	chr2	159605721	159606113	+	0	NA	intron (NM_001289975, intron 1 of 35)	intron (NM_001289975, intron 1 of 35)	-9377	NR_110588	643072	Hs.632541	NR_110587		LOC643072	-	uncharacterized LOC643072	ncRNA	0.005102	0.356234	
chunk0175_205_1	chr7	6012495	6012694	+	0	NA	intron (NM_006303, intron 1 of 3)	AluSx1|SINE|Alu	3343	NM_006303	7965	Hs.301613	NM_006303	ENSG00000106305	AIMP2	HLD17|JTV-1|JTV1|P38	aminoacyl tRNA synthetase complex interacting multifunctional protein 2	protein-coding	0.020101	0.475000	
chunk0043_125_1	chr12	15703150	15703581	+	0	NA	intron (NM_004447, intron 1 of 20)	L2c|LINE|L2	86211	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.000000	0.328704	123(GGGAACATTCAGTTCA,-,0.00),124(GGAACATTCAGTTCAG,+,0.00)
chunk0183_298_1	chr7	107799737	107800170	+	0	NA	intron (NM_000111, intron 1 of 20)	intron (NM_000111, intron 1 of 20)	3280	NM_000111	1811	Hs.1650	NM_000111	ENSG00000091138	SLC26A3	CLD|DRA	solute carrier family 26 member 3	protein-coding	0.006928	0.384793	
chunk0082_394_1	chr17	60748831	60749261	+	0	NA	intron (NM_017679, intron 6 of 23)	HY1|scRNA|scRNA	71235	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.011628	0.324826	150(TAGAACAAGGAGTTCC,-,0.00),151(AGAACAAGGAGTTCCA,+,0.00)
chunk0003_408_1	chr1	40176124	40176433	+	0	NA	intron (NM_012421, intron 1 of 7)	L1ME1|LINE|L1	14909	NM_012421	6018	Hs.205627	NM_012421	ENSG00000117000	RLF	ZN-15L|ZNF292L	rearranged L-myc fusion	protein-coding	0.003236	0.358065	
chunk0086_357_1	chr18	25883007	25883488	+	0	NA	Intergenic	MIRb|SINE|MIR	207400	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.010395	0.400415	
chunk0102_359_1	chr2	152631856	152632289	+	0	NA	exon (NM_052905, exon 21 of 26)	exon (NM_052905, exon 21 of 26)	85389	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.016166	0.435484	
chunk0167_333_1	chr6	72500722	72501408	+	0	NA	Intergenic	L1MC4|LINE|L1	-120778	NM_001160133	56479	Hs.445324	NM_019842	ENSG00000185760	KCNQ5	Kv7.5|MRD46	potassium voltage-gated channel subfamily Q member 5	protein-coding	0.002915	0.388646	298(ATCACAGTGTGTGCTT,+,0.00)
chunk0095_125_1	chr2	16031872	16032124	+	0	NA	Intergenic	Intergenic	-18429	NR_126559	104797537	Hs.435748	NR_126559	ENSG00000236289	GACAT3	LINC01458|lncRNA-AC130710	gastric cancer associated transcript 3	ncRNA	0.031746	0.494071	114(CAGCACTGCCTGTGCT,-,0.00),115(AGCACTGCCTGTGCTC,+,0.00)
chunk0054_130_1	chr13	43501297	43501622	+	0	NA	intron (NM_001242863, intron 2 of 16)	L1MA10|LINE|L1	52607	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.000000	0.319018	
chunk0014_215_1	chr1	179331724	179331976	+	0	NA	intron (NM_001252512, intron 2 of 14)	intron (NM_001252512, intron 2 of 14)	-33870	NM_144696	126859	Hs.658505	NM_144696	ENSG00000162779	AXDND1	C1orf125	axonemal dynein light chain domain containing 1	protein-coding	0.000000	0.363636	
chunk0109_248_1	chr20	6305511	6305900	+	0	NA	Intergenic	Intergenic	-121027	NR_109953	101929244	Hs.542488	NR_109953	ENSG00000229876	CASC20	-	cancer susceptibility 20	ncRNA	0.000000	0.361538	
chunk0211_372_1	chrX	126533361	126533576	+	0	NA	Intergenic	Intergenic	19391	NM_178470	139170	Hs.120403	NM_178470	ENSG00000198889	DCAF12L1	KIAA1892L|WDR40B	DDB1 and CUL4 associated factor 12 like 1	protein-coding	0.000000	0.388889	
chunk0053_387_1	chr13	36163646	36164115	+	0	NA	Intergenic	Intergenic	-32503	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.012793	0.444681	253(GAGAACTGGGAGTACT,-,0.00),254(AGAACTGGGAGTACTT,+,0.00)
chunk0142_253_1	chr4	98986809	98987096	+	0	NA	Intergenic	L2a|LINE|L2	-8685	NM_015143	23173	Hs.480364	NM_015143	ENSG00000164024	METAP1	MAP1A|MetAP1A	methionyl aminopeptidase 1	protein-coding	0.000000	0.416667	
chunk0203_86_1	chr9	83986570	83987233	+	0	NA	intron (NM_024945, intron 1 of 2)	intron (NM_024945, intron 1 of 2)	6179	NM_024945	80010	Hs.726327	NM_024945	ENSG00000178966	RMI1	BLAP75|C9orf76|FAAP75	RecQ mediated genome instability 1	protein-coding	0.007541	0.379518	306(AAGTACACTTTGTCCT,-,0.00),307(AGTACACTTTGTCCTC,+,0.00)
chunk0119_371_1	chr22	47631482	47631681	+	0	NA	promoter-TSS (NR_033377)	promoter-TSS (NR_033377)	-12	NR_033377	400932	Hs.561058	NM_001001693	ENSG00000205634	LINC00898	-	long intergenic non-protein coding RNA 898	ncRNA	0.035176	0.585000	
chunk0060_185_1	chr14	46964267	46964875	+	0	NA	intron (NM_182830, intron 8 of 16)	intron (NM_182830, intron 8 of 16)	-312746	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.006579	0.351396	
chunk0058_250_1	chr14	25672818	25673289	+	0	NA	Intergenic	Intergenic	-622756	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.014862	0.377119	
chunk0003_389_1	chr1	39859759	39860229	+	0	NA	intron (NR_132406, intron 1 of 8)	intron (NR_132406, intron 1 of 8)	23517	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.002128	0.343949	
chunk0016_359_1	chr1	202348490	202348689	+	0	NA	promoter-TSS (NM_001167858)	promoter-TSS (NM_001167858)	-113	NM_002481	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.065327	0.595000	
chunk0185_216_1	chr7	128827031	128827242	+	0	NA	Intergenic	Intergenic	-3293	NM_001458	2318	Hs.58414	NM_001458	ENSG00000128591	FLNC	ABP-280|ABP280A|ABPA|ABPL|CMH26|FLN2|MFM5|MPD4|RCM5	filamin C	protein-coding	0.000000	0.490566	
chunk0036_167_1	chr11	62540711	62540910	+	0	NA	intron (NM_024060, intron 1 of 5)	intron (NM_024060, intron 1 of 5)	6050	NM_024060	79026	Hs.502756	NM_001620	ENSG00000124942	AHNAK	AHNAKRS|PM227	AHNAK nucleoprotein	protein-coding	0.030151	0.555000	89(CGGGACAGACTGTAAT,-,0.00),90(GGGACAGACTGTAATT,+,0.00)
chunk0045_15_1	chr12	43099637	43100007	+	0	NA	Intergenic	L2c|LINE|L2	452099	NM_025003	80070	Hs.287554	NM_025003	ENSG00000173157	ADAMTS20	ADAM-TS20|ADAMTS-20|GON-1	ADAM metallopeptidase with thrombospondin type 1 motif 20	protein-coding	0.002703	0.401617	
chunk0036_176_1	chr11	62592981	62593289	+	0	NA	TTS (NM_004739)	TTS (NM_004739)	-1498	NM_022830	64852	Hs.728983	NM_022830	ENSG00000149016	TUT1	PAPD2|RBM21|STARPAP|TENT1|TUTase|URLC6	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding	0.009740	0.482201	
chunk0043_423_1	chr12	25914827	25915156	+	0	NA	Intergenic	Intergenic	-40912	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.000000	0.342424	
chunk0060_223_1	chr14	49280455	49281072	+	0	NA	Intergenic	Intergenic	305653	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.004862	0.438511	
chunk0175_277_1	chr7	7572879	7573190	+	0	NA	exon (NM_019005, exon 4 of 13)	exon (NM_019005, exon 4 of 13)	6049	NM_019005	54468	Hs.520215	NM_019005	ENSG00000164654	MIOS	MIO|Sea4|Yulink	meiosis regulator for oocyte development	protein-coding	0.019293	0.400641	
chunk0051_324_1	chr12	120067283	120067640	+	0	NA	intron (NM_207311, intron 4 of 8)	intron (NM_207311, intron 4 of 8)	49378	NM_001167606	11021	Hs.524788	NM_006861	ENSG00000111737	RAB35	H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding	0.005602	0.424581	
chunk0175_266_1	chr7	7454049	7454452	+	0	NA	intron (NM_001037763, intron 16 of 34)	intron (NM_001037763, intron 16 of 34)	81579	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.000000	0.289604	
chunk0015_200_1	chr1	187358190	187359155	+	0	NA	intron (NR_126347, intron 3 of 3)	intron (NR_126347, intron 3 of 3)	-84956	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.002073	0.338509	
chunk0106_180_1	chr2	201117291	201117490	+	0	NA	intron (NM_001202517, intron 1 of 8)	intron (NM_001202517, intron 1 of 8)	-1156	NM_001127183	8837	Hs.390736	NM_003879	ENSG00000003402	CFLAR	CASH|CASP8AP1|CLARP|Casper|FLAME|FLAME-1|FLAME1|FLIP|I-FLICE|MRIT|c-FLIP|c-FLIPL|c-FLIPR|c-FLIPS|cFLIP	CASP8 and FADD like apoptosis regulator	protein-coding	0.025126	0.425000	
chunk0113_150_1	chr20	52596353	52596667	+	0	NA	Intergenic	Intergenic	-24328	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.006369	0.377778	
chunk0211_234_1	chrX	118969052	118969251	+	0	NA	Intergenic	L2c|LINE|L2	-5463	NM_024778	79836	Hs.144266	NM_024778	ENSG00000175556	LONRF3	RNF127	LON peptidase N-terminal domain and ring finger 3	protein-coding	0.010050	0.430000	102(GTGGACACACTGTTCC,-,0.00),103(TGGACACACTGTTCCC,+,0.00)
chunk0181_100_1	chr7	80505916	80506561	+	0	NA	intron (NM_001102386, intron 1 of 7)	intron (NM_001102386, intron 1 of 7)	5688	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.012403	0.325077	
chunk0143_20_1	chr4	105912597	105913040	+	0	NA	intron (NM_001184690, intron 3 of 12)	intron (NM_001184690, intron 3 of 12)	17378	NM_001033047	255743	Hs.518921	NM_198278	ENSG00000168743	NPNT	EGFL6L|POEM	nephronectin	protein-coding	0.013544	0.380631	257(AAGAAGACAATGTTCT,-,0.00),258(AGAAGACAATGTTCTT,+,0.00)
chunk0092_405_1	chr19	37469296	37469561	+	0	NA	5' UTR (NM_144694, exon 1 of 5)	5' UTR (NM_144694, exon 1 of 5)	370	NM_144694	148268	Hs.126962	NM_144694	ENSG00000171827	ZNF570	-	zinc finger protein 570	protein-coding	0.075472	0.657895	
chunk0011_116_1	chr1	146650559	146650758	+	0	NA	intron (NR_103556, intron 13 of 45)	intron (NR_103556, intron 13 of 45)	103169	NR_103556	100288805	Hs.648712	NR_049745		HYDIN2	HYDINP1	HYDIN axonemal central pair apparatus protein 2 (pseudogene)	pseudo	0.005025	0.305000	149(AGAAACACAGTGTGCA,-,0.00),150(GAAACACAGTGTGCAT,+,0.00)
chunk0075_12_1	chr16	46788916	46789624	+	0	NA	Intergenic	L1MA8|LINE|L1	-26024	NM_001308301	91807	Hs.130465	NM_182493	ENSG00000140795	MYLK3	MLCK|MLCK2|caMLCK	myosin light chain kinase 3	protein-coding	0.005650	0.377997	
chunk0033_315_1	chr11	20696860	20697278	+	0	NA	intron (NM_006157, intron 2 of 19)	MER57B2|LTR|ERV1	27518	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.004785	0.357995	
chunk0191_378_1	chr8	57023508	57024009	+	0	NA	Intergenic	L1PA4|LINE|L1	-29887	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.005988	0.368526	
chunk0148_241_1	chr5	9633803	9634054	+	0	NA	Intergenic	L1PB2|LINE|L1	-3577	NM_019599	50834	Hs.567492	NM_019599	ENSG00000169777	TAS2R1	T2R1|TRB7	taste 2 receptor member 1	protein-coding	0.000000	0.345238	
chunk0169_59_1	chr6	98594077	98594721	+	0	NA	Intergenic	HAL1|LINE|L1	-240305	NM_005604	5454	Hs.182505	NM_005604	ENSG00000184486	POU3F2	BRN2|N-Oct3|OCT7|OTF-7|OTF7|POUF3|brn-2|oct-7	POU class 3 homeobox 2	protein-coding	0.004658	0.339535	
chunk0017_381_1	chr1	212189262	212189779	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	45216	NR_125982	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.009671	0.540541	
chunk0172_223_1	chr6	137004862	137005206	+	0	NA	intron (NM_014432, intron 5 of 6)	Tigger19b|DNA|TcMar-Tigger	-11803	NR_027994	100294720	Hs.520412	NR_027994	ENSG00000225391	NHEG1	-	neuroblastoma highly expressed 1	ncRNA	0.014535	0.391304	
chunk0001_71_1	chr1	2453970	2454463	+	0	NA	Intergenic	Intergenic	-13243	NM_001303012	9651	Hs.170156	NM_014638	ENSG00000149527	PLCH2	PLC-L4|PLC-eta2|PLCL4|PLCeta2	phospholipase C eta 2	protein-coding	0.026369	0.661943	222(AGGAACTGCCTGTTCC,-,0.00),223(GGAACTGCCTGTTCCC,+,0.00)
chunk0131_261_1	chr3	149890208	149890786	+	0	NA	intron (NM_183381, intron 4 of 9)	MIR|SINE|MIR	77809	NM_007282	11342	Hs.12333	NM_007282	ENSG00000082996	RNF13	EIEE73|RZF	ring finger protein 13	protein-coding	0.001730	0.348877	166(CTGCACAGTCTGTCCT,-,0.00),167(TGCACAGTCTGTCCTT,+,0.00)
chunk0034_238_1	chr11	34002557	34002756	+	0	NA	Intergenic	Intergenic	-49027	NM_005898	4076	Hs.471818	NM_005898	ENSG00000135387	CAPRIN1	GPIAP1|GPIP137|GRIP137|M11S1|RNG105|p137GPI	cell cycle associated protein 1	protein-coding	0.010050	0.490000	
chunk0136_446_1	chr3	197960955	197961251	+	0	NA	intron (NM_001136049, intron 1 of 16)	L2c|LINE|L2	903	NR_026786	89782	Hs.518540	NM_033029	ENSG00000185621	LMLN	GP63|INV|IX14|LMNL1|MSP	leishmanolysin like peptidase	protein-coding	0.027027	0.434343	
chunk0198_119_1	chr8	131882827	131883526	+	0	NA	Intergenic	L1PA6|LINE|L1	-20933	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.010014	0.507143	
chunk0038_158_1	chr11	84824983	84825268	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	98296	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003509	0.419580	
chunk0112_372_1	chr20	46085232	46085583	+	0	NA	intron (NM_020967, intron 1 of 7)	intron (NM_020967, intron 1 of 7)	4534	NM_020967	57727	Hs.654991	NM_020967	ENSG00000124160	NCOA5	CIA|bA465L10.6	nuclear receptor coactivator 5	protein-coding	0.002849	0.471591	
chunk0196_335_1	chr8	113486279	113486599	+	0	NA	Intergenic	L1M1|LINE|L1	-49426	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.000000	0.495327	
chunk0137_63_1	chr4	11842603	11843374	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-380463	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.001297	0.308290	
chunk0066_93_1	chr15	29776794	29777386	+	0	NA	intron (NM_175610, intron 2 of 26)	Charlie1a|DNA|hAT-Charlie	44458	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.010135	0.349073	
chunk0021_266_1	chr1	243698895	243699282	+	0	NA	intron (NM_181690, intron 1 of 13)	intron (NM_181690, intron 1 of 13)	144194	NM_005465	10000	Hs.498292	NM_005465	ENSG00000117020	AKT3	MPPH|MPPH2|PKB-GAMMA|PKBG|PRKBG|RAC-PK-gamma|RAC-gamma|STK-2	AKT serine/threonine kinase 3	protein-coding	0.007752	0.368557	181(ATGGACAGAAAGTCCT,-,0.00),182(TGGACAGAAAGTCCTA,+,0.00)
chunk0021_277_1	chr1	244280930	244281222	+	0	NA	Intergenic	Intergenic	-71559	NM_001012970	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.003425	0.372014	
chunk0203_307_1	chr9	89359921	89360318	+	0	NA	TTS (NM_001282689)	TTS (NM_001282689)	41268	NM_001282690	79048	Hs.59804	NM_024077	ENSG00000187742	SECISBP2	SBP2	SECIS binding protein 2	protein-coding	0.010076	0.474874	
chunk0199_390_1	chr9	13214695	13214947	+	0	NA	intron (NM_003829, intron 10 of 45)	intron (NM_003829, intron 10 of 45)	64743	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.011905	0.399209	
chunk0026_441_1	chr10	71391681	71392147	+	0	NA	Intergenic	L2c|LINE|L2	-5020	NM_001171931	64072	Hs.656032	NM_022124	ENSG00000107736	CDH23	CDHR23|PITA5|USH1D	cadherin related 23	protein-coding	0.010730	0.479657	
chunk0121_12_1	chr3	14634955	14635245	+	0	NA	Intergenic	L2b|LINE|L2	-16646	NM_016474	51244	Hs.517820	NM_016474	ENSG00000154781	CCDC174	C3orf19|HSPC212|IHPM|IHPMR	coiled-coil domain containing 174	protein-coding	0.003448	0.405498	
chunk0210_146_1	chrX	75359267	75359510	+	0	NA	Intergenic	Intergenic	85329	NR_030774	139596	Hs.91612	NM_145052	ENSG00000094841	UPRT	FUR1|UPP	uracil phosphoribosyltransferase homolog	protein-coding	0.008230	0.385246	
chunk0112_234_1	chr20	41143408	41143607	+	0	NA	intron (NM_002660, intron 1 of 31)	intron (NM_002660, intron 1 of 31)	-5507	NR_109889	101927117	Hs.668593	NR_109889	ENSG00000226648	PLCG1-AS1	TOP1-AS1	PLCG1 antisense RNA 1	ncRNA	0.010050	0.525000	124(GGGAACAGTGCGTCCT,-,0.00),125(GGAACAGTGCGTCCTT,+,0.00)
chunk0022_54_1	chr10	8272846	8273137	+	0	NA	Intergenic	Intergenic	-4686	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.020619	0.421233	
chunk0147_103_1	chr4	173448047	173448588	+	0	NA	Intergenic	Intergenic	-48851	NM_007281	11341	Hs.7122	NM_007281	ENSG00000164106	SCRG1	SCRG-1	stimulator of chondrogenesis 1	protein-coding	0.009242	0.448339	
chunk0024_165_1	chr10	35621579	35621798	+	0	NA	Intergenic	Intergenic	16278	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.009132	0.531818	
chunk0120_51_1	chr3	3015415	3015897	+	0	NA	intron (NM_001206955, intron 13 of 23)	intron (NM_001206955, intron 13 of 23)	45489	NR_046554	100873975	Hs.581502	NR_046554		CNTN4-AS1	-	CNTN4 antisense RNA 1	ncRNA	0.008299	0.383023	
chunk0002_164_1	chr1	18440582	18441007	+	0	NA	Intergenic	MER74A|LTR|ERVL	-40136	NM_152375	127707	Hs.406913	NM_152375	ENSG00000179023	KLHDC7A	-	kelch domain containing 7A	protein-coding	0.009412	0.462441	
chunk0200_74_1	chr9	16203713	16204343	+	0	NA	TTS (NR_073471)	TTS (NR_073471)	49079	NM_001271829	100129385	Hs.586441	NM_001271829	ENSG00000205549	C9orf92	Em:AL513424.1	chromosome 9 open reading frame 92	protein-coding	0.020635	0.429477	
chunk0039_445_1	chr11	108333481	108333784	+	0	NA	intron (NM_000051, intron 53 of 62)	intron (NM_000051, intron 53 of 62)	110800	NM_000051	472	Hs.367437	NM_000051	ENSG00000149311	ATM	AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1	ATM serine/threonine kinase	protein-coding	0.006601	0.378289	
chunk0065_345_1	chr14	103572166	103572571	+	0	NA	intron (NR_126432, intron 2 of 3)	intron (NR_126432, intron 2 of 3)	9411	NM_001302653	84334	Hs.598441	NM_001302652	ENSG00000256053	COA8	APOP|APOP1|APOPT1|C14orf153	cytochrome c oxidase assembly factor 8	protein-coding	0.014815	0.423645	
chunk0001_335_1	chr1	9596351	9596692	+	0	NA	intron (NM_001010866, intron 2 of 5)	MER58A|DNA|hAT-Charlie	7647	NM_001130924	199953	Hs.632365	NM_001010866	ENSG00000188807	TMEM201	Ima1|NET5|SAMP1	transmembrane protein 201	protein-coding	0.017595	0.543860	159(CGGGTCATAGTGTGCT,-,0.00),160(GGGTCATAGTGTGCTG,+,0.00)
chunk0189_85_1	chr8	21266200	21266804	+	0	NA	Intergenic	Intergenic	-31737	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.003311	0.479339	
chunk0095_31_1	chr2	13243132	13243425	+	0	NA	Intergenic	MIR|SINE|MIR	-236265	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.010239	0.428571	
chunk0133_266_1	chr3	171806204	171806665	+	0	NA	intron (NM_001130081, intron 1 of 25)	intron (NM_001130081, intron 1 of 25)	4060	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.004338	0.359307	
chunk0072_63_1	chr16	1651371	1651587	+	0	NA	intron (NM_020825, intron 5 of 19)	intron (NM_020825, intron 5 of 19)	-26798	NM_144570	90861	Hs.513261	NM_144570	ENSG00000206053	JPT2	C16orf34|HN1L|L11	Jupiter microtubule associated homolog 2	protein-coding	0.013889	0.529954	
chunk0033_73_1	chr11	13762169	13762582	+	0	NA	Intergenic	LTR33|LTR|ERVL	93716	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.007264	0.425121	153(TGTACATCGTGTTCAT,+,0.00)
chunk0133_277_1	chr3	172040318	172040626	+	0	NA	promoter-TSS (NM_001135095)	promoter-TSS (NM_001135095)	-82	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.146104	0.822006	
chunk0085_247_1	chr18	7487878	7488240	+	0	NA	Intergenic	Intergenic	-79257	NM_001105244	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.008287	0.369146	
chunk0198_469_1	chr8	144798796	144798995	+	0	NA	promoter-TSS (NM_213605)	promoter-TSS (NM_213605)	19	NM_213605	340385	Hs.521942	NM_213605	ENSG00000197363	ZNF517	-	zinc finger protein 517	protein-coding	0.165829	0.795000	
chunk0099_336_1	chr2	100065147	100065580	+	0	NA	intron (NM_001025108, intron 2 of 23)	intron (NM_001025108, intron 2 of 23)	40220	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.006928	0.294931	
chunk0009_69_1	chr1	100900171	100900446	+	0	NA	intron (NM_001144884, intron 2 of 11)	intron (NM_001144884, intron 2 of 11)	4230	NM_133496	148867	Hs.533903	NM_133496	ENSG00000162695	SLC30A7	ZNT7|ZnT-7|ZnTL2	solute carrier family 30 member 7	protein-coding	0.000000	0.286232	
chunk0164_454_1	chr6	28380859	28381622	+	0	NA	intron (NR_028077, intron 5 of 5)	intron (NR_028077, intron 5 of 5)	18527	NR_028077	9753	Hs.134816	NM_014724	ENSG00000158691	ZSCAN12	ZFP96|ZNF29K1|ZNF305|ZNF96|dJ29K1.2	zinc finger and SCAN domain containing 12	protein-coding	0.003932	0.352094	
chunk0111_147_1	chr20	25036420	25036859	+	0	NA	intron (NM_032501, intron 2 of 13)	intron (NM_032501, intron 2 of 13)	-3933	NM_001252676	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.009112	0.452273	
chunk0008_356_1	chr1	96465612	96465847	+	0	NA	Intergenic	Intergenic	-91604	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.029787	0.491525	
chunk0100_444_1	chr2	120783438	120783822	+	0	NA	Intergenic	Intergenic	-13661	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.020833	0.472727	
chunk0035_453_1	chr11	57772377	57772974	+	0	NA	intron (NM_001085467, intron 1 of 16)	intron (NM_001085467, intron 1 of 16)	10913	NM_001206883	1500	Hs.166011	NM_001331	ENSG00000198561	CTNND1	BCDS2|CAS|CTNND|P120CAS|P120CTN|p120|p120(CAS)|p120(CTN)	catenin delta 1	protein-coding	0.008375	0.428094	215(AAGCACATCCTGAGCC,-,0.00)
chunk0002_414_1	chr1	27570350	27570770	+	0	NA	intron (NM_001029882, intron 1 of 6)	intron (NM_001029882, intron 1 of 6)	32934	NM_001029882	27245	Hs.469280	NM_001029882	ENSG00000126705	AHDC1	MRD25	AT-hook DNA binding motif containing 1	protein-coding	0.004762	0.532067	152(AGCACAGCTTGATCCG,+,0.00)
chunk0069_353_1	chr15	66750977	66751228	+	0	NA	intron (NR_027654, intron 4 of 4)	intron (NR_027654, intron 4 of 4)	48766	NR_027654	4091	Hs.153863	NM_005585	ENSG00000137834	SMAD6	AOVD2|HsT17432|MADH6|MADH7	SMAD family member 6	protein-coding	0.011952	0.531746	
chunk0183_292_1	chr7	107742440	107742934	+	0	NA	Intergenic	Intergenic	-1010	NM_001284291	79872	Hs.592271	NM_024814	ENSG00000105879	CBLL1	HAKAI|RNF188	Cbl proto-oncogene like 1	protein-coding	0.008097	0.357576	
chunk0085_365_1	chr18	9366178	9366682	+	0	NA	intron (NM_020648, intron 3 of 4)	intron (NM_020648, intron 3 of 4)	31663	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.011905	0.465347	
chunk0024_415_1	chr10	45473990	45474343	+	0	NA	intron (NM_001002266, intron 3 of 6)	intron (NM_001002266, intron 3 of 6)	-21045	NR_120674	102724323	Hs.559151	NR_120674	ENSG00000231964	LOC102724323	-	uncharacterized LOC102724323	ncRNA	0.016997	0.500000	277(CAGGACACAACGTCCT,-,0.00),278(AGGACACAACGTCCTG,+,0.00)
chunk0127_139_1	chr3	94177931	94178625	+	0	NA	Intergenic	Intergenic	-115055	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.012968	0.400000	
chunk0164_328_1	chr6	25226184	25226582	+	0	NA	Intergenic	Intergenic	35024	NR_110862	101928663	Hs.561600	NR_110862		LOC101928663	-	uncharacterized LOC101928663	ncRNA	0.010050	0.370927	
chunk0019_104_1	chr1	224935400	224935849	+	0	NA	intron (NM_001145154, intron 1 of 10)	L1MA4|LINE|L1	5963	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.004454	0.335556	331(CAGAACGTTCTGTCCA,-,0.00)
chunk0065_276_1	chr14	102140593	102140869	+	0	NA	promoter-TSS (NM_001017963)	promoter-TSS (NM_001017963)	879	NM_001242416	91833	Hs.36859	NM_144574	ENSG00000140153	WDR20	DMR	WD repeat domain 20	protein-coding	0.050725	0.534296	
chunk0114_366_1	chr21	19923746	19923984	+	0	NA	Intergenic	MLT1A0-int|LTR|ERVL-MaLR	879243	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.004202	0.372385	
chunk0074_300_1	chr16	29961617	29961978	+	0	NA	promoter-TSS (NM_001083613)	promoter-TSS (NM_001083613)	-233	NM_194280	124446	Hs.460574	NM_194280	ENSG00000149932	TMEM219	IGFBP-3R	transmembrane protein 219	protein-coding	0.066482	0.640884	
chunk0114_377_1	chr20	62957744	62957943	+	0	NA	intron (NM_022082, intron 3 of 12)	(GTGC)n|Simple_repeat|Simple_repeat	5196	NM_001302643	63910	Hs.512686	NM_022082	ENSG00000101194	SLC17A9	C20orf59|POROK8|VNUT	solute carrier family 17 member 9	protein-coding	0.065327	0.590000	
chunk0197_198_1	chr8	121850017	121850386	+	0	NA	Intergenic	Intergenic	-208811	NM_005328	3037	Hs.159226	NM_005328	ENSG00000170961	HAS2	-	hyaluronan synthase 2	protein-coding	0.008130	0.364865	
chunk0020_108_1	chr1	233052474	233052779	+	0	NA	intron (NM_014801, intron 25 of 33)	intron (NM_014801, intron 25 of 33)	102002	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.003279	0.467320	
chunk0185_203_1	chr7	128455452	128455806	+	0	NA	promoter-TSS (NM_013332)	promoter-TSS (NM_013332)	-201	NM_001098786	29923	Hs.706124	NM_013332	ENSG00000135245	HILPDA	C7orf68|HIG-2|HIG2	hypoxia inducible lipid droplet associated	protein-coding	0.081921	0.588732	
chunk0036_417_1	chr11	68200143	68200603	+	0	NA	intron (NM_001300909, intron 1 of 8)	intron (NM_001300909, intron 1 of 8)	12944	NM_016028	51111	Hs.632120	NM_016028	ENSG00000110066	KMT5B	CGI-85|CGI85|MRD51|SUV420H1	lysine methyltransferase 5B	protein-coding	0.013043	0.453362	
chunk0104_435_1	chr2	181223860	181224103	+	0	NA	intron (NR_130784, intron 1 of 4)	MER5A1|DNA|hAT-Charlie	81671	NR_039637	100616213		NR_039637	ENSG00000266705	MIR4437	mir-4437	microRNA 4437	ncRNA	0.004115	0.368852	
chunk0156_10_1	chr5	102029188	102029475	+	0	NA	Intergenic	Intergenic	267218	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.326389	
chunk0005_2_1	chr1	53942569	53942876	+	0	NA	intron (NM_001316935, intron 1 of 5)	L2c|LINE|L2	3101	NR_133633	51668	Hs.525462	NM_016126	ENSG00000081870	HSPB11	C1orf41|HSPCO34|IFT25|PP25	heat shock protein family B (small) member 11	protein-coding	0.000000	0.379870	
chunk0110_362_1	chr20	19794968	19795189	+	0	NA	Intergenic	Intergenic	-91443	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.013575	0.441441	
chunk0158_211_1	chr5	128316887	128317688	+	0	NA	intron (NM_001999, intron 36 of 64)	L2a|LINE|L2	220755	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.006242	0.441397	
chunk0082_10_1	chr17	49821407	49821644	+	0	NA	intron (NM_007067, intron 10 of 14)	intron (NM_007067, intron 10 of 14)	-24385	NM_001242791	729220	Hs.434138	NM_001242791		FLJ45513	-	uncharacterized LOC729220	protein-coding	0.000000	0.361345	
chunk0007_119_1	chr1	79010612	79010919	+	0	NA	Intergenic	Intergenic	-3955	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.006515	0.373377	
chunk0037_185_1	chr11	74108172	74108558	+	0	NA	intron (NM_001286577, intron 12 of 32)	intron (NM_001286577, intron 12 of 32)	62654	NM_015531	26005	Hs.557938	NM_015531	ENSG00000168014	C2CD3	OFD14	C2 domain containing 3 centriole elongation regulator	protein-coding	0.000000	0.291990	172(GAAAACAAGATGTTCT,-,0.00),173(AAAACAAGATGTTCTT,+,0.00)
chunk0061_354_1	chr14	63683123	63683796	+	0	NA	TTS (NM_030791)	TTS (NM_030791)	-41536	NM_001258272	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.005944	0.311573	
chunk0178_329_1	chr7	38273539	38273967	+	0	NA	promoter-TSS (NM_001003799)	promoter-TSS (NM_001003799)	-106	NM_001003806	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.004673	0.368298	
chunk0196_71_1	chr8	102511599	102512131	+	0	NA	Intergenic	Intergenic	-39755	NM_024410	4956	Hs.159274	NM_024410	ENSG00000155087	ODF1	CT133|HSPB10|ODF|ODF2|ODF27|ODFP|ODFPG|ODFPGA|ODFPGB|RT7|SODF	outer dense fiber of sperm tails 1	protein-coding	0.011278	0.491557	22(GGGAAGACTCTGTCCC,-,0.00),23(GGAAGACTCTGTCCCC,+,0.00)
chunk0085_42_1	chr18	745239	745701	+	0	NA	intron (NM_005433, intron 6 of 11)	intron (NM_005433, intron 6 of 11)	-32808	NM_017512	55556	Hs.658550	NM_017512	ENSG00000132199	ENOSF1	FUCD|RTS|TYMSAS	enolase superfamily member 1	protein-coding	0.004329	0.328294	
chunk0091_180_1	chr19	8221192	8221825	+	0	NA	intron (NM_024552, intron 2 of 11)	MER113|DNA|hAT-Charlie	12175	NM_024552	79603	Hs.515111	NM_024552	ENSG00000090661	CERS4	LASS4|Trh1	ceramide synthase 4	protein-coding	0.018957	0.495268	
chunk0068_220_1	chr15	55255768	55256358	+	0	NA	intron (NM_183234, intron 1 of 6)	MIRc|SINE|MIR	14223	NM_183234	5873	Hs.654978	NM_004580	ENSG00000069974	RAB27A	GS2|HsT18676|RAB27|RAM	RAB27A, member RAS oncogene family	protein-coding	0.010169	0.443316	76(TGGTACACCATGTGCA,-,0.00),77(GGTACACCATGTGCAC,+,0.00)
chunk0078_312_1	chr17	8345987	8346316	+	0	NA	TTS (NM_153007)	TTS (NM_153007)	6281	NM_153007	146852	Hs.186045	NM_153007	ENSG00000184650	ODF4	CT134|CT136|OPPO1	outer dense fiber of sperm tails 4	protein-coding	0.009119	0.472727	
chunk0011_103_1	chr1	145978862	145979332	+	0	NA	TTS (NM_032305)	TTS (NM_032305)	14394	NM_032305	84265	Hs.591456	NM_032305	ENSG00000121851	POLR3GL	RPC32HOM|flj32422	RNA polymerase III subunit G like	protein-coding	0.008511	0.496815	
chunk0039_65_1	chr11	96317603	96318204	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-23535	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.003328	0.440199	
chunk0013_111_1	chr1	167899328	167899701	+	0	NA	exon (NM_001297772, exon 6 of 33)	exon (NM_001297772, exon 6 of 33)	14712	NM_001167749	55811	Hs.320892	NM_018417	ENSG00000143199	ADCY10	HCA2|HEL-S-7a|SAC|SACI|Sacy|hsAC	adenylate cyclase 10	protein-coding	0.010724	0.497326	
chunk0088_362_1	chr18	53234534	53235232	+	0	NA	intron (NM_005215, intron 12 of 28)	intron (NM_005215, intron 12 of 28)	-2218	NR_130465	100616232		NR_130465	ENSG00000263872	MIR4528	-	microRNA 4528	ncRNA	0.002865	0.349070	
chunk0006_378_1	chr1	74222579	74223315	+	0	NA	intron (NM_001199327, intron 3 of 23)	intron (NM_001199327, intron 3 of 23)	-12440	NM_015978	51086	Hs.480085	NM_015978	ENSG00000116783	TNNI3K	CARK|CCDD	TNNI3 interacting kinase	protein-coding	0.012228	0.430122	
chunk0178_208_1	chr7	34940006	34940586	+	0	NA	TTS (NR_031666)	TTS (NR_031666)	538	NR_031666	100302152		NR_031666	ENSG00000221669	MIR548N	MIRN548N|hsa-mir-548n	microRNA 548n	ncRNA	0.000000	0.345955	
chunk0050_34_1	chr12	100200631	100200931	+	0	NA	promoter-TSS (NR_048569)	promoter-TSS (NR_048569)	4	NR_048568	64431	Hs.115088	NM_022496	ENSG00000075089	ACTR6	ARP6|CDA12|HSPC281|MSTP136|hARP6|hARPX	actin related protein 6	protein-coding	0.063333	0.514950	
chunk0052_94_1	chr13	22265450	22266090	+	0	NA	intron (NR_103810, intron 1 of 1)	intron (NR_103810, intron 1 of 1)	55485	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.010937	0.390016	237(AAGACCACTATGTTCC,-,0.00),238(AGACCACTATGTTCCG,+,0.00),332(AAGTACAACGAGTACT,-,0.00),333(AGTACAACGAGTACTT,+,0.00)
chunk0163_326_1	chr6	15026940	15027384	+	0	NA	Intergenic	Intergenic	-218813	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.013514	0.460674	
chunk0027_419_1	chr10	80781662	80782011	+	0	NA	Intergenic	L1M5|LINE|L1	241017	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.002865	0.271429	
chunk0046_64_1	chr12	55920657	55921097	+	0	NA	intron (NM_032345, intron 1 of 2)	L1ME4a|LINE|L1	6248	NM_001143853	84305	Hs.505687	NM_032345	ENSG00000170473	PYM1	PYM|WIBG	PYM homolog 1, exon junction complex associated factor	protein-coding	0.004545	0.310658	
chunk0044_170_1	chr12	29980019	29980233	+	0	NA	Intergenic	Intergenic	-195367	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.009346	0.400000	
chunk0032_373_1	chr11	11136509	11136708	+	0	NA	Intergenic	Intergenic	216749	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.010050	0.360000	
chunk0167_205_1	chr6	65050658	65050987	+	0	NA	intron (NM_001142800, intron 13 of 42)	intron (NM_001142800, intron 13 of 42)	-250596	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.000000	0.339394	181(CATAACAGAGTGTCCC,-,0.00),182(ATAACAGAGTGTCCCT,+,0.00)
chunk0152_31_1	chr5	56849502	56850260	+	0	NA	intron (NM_005921, intron 1 of 19)	MIRb|SINE|MIR	34808	NM_005921	4214	Hs.653654	NM_005921	ENSG00000095015	MAP3K1	MAPKKK1|MEKK|MEKK 1|MEKK1|SRXY6	mitogen-activated protein kinase kinase kinase 1	protein-coding	0.005277	0.379447	
chunk0150_91_1	chr5	32388044	32388363	+	0	NA	intron (NM_016107, intron 13 of 19)	intron (NM_016107, intron 13 of 19)	6272	NR_030305	693164		NR_030305	ENSG00000207956	MIR579	MIRN579|hsa-mir-579	microRNA 579	ncRNA	0.009404	0.343750	
chunk0113_368_1	chr20	59253217	59253416	+	0	NA	intron (NM_178457, intron 4 of 4)	intron (NM_178457, intron 4 of 4)	-47111	NM_207034	1908	Hs.1408	NM_000114	ENSG00000124205	EDN3	ET-3|ET3|HSCR4|PPET3|WS4B	endothelin 3	protein-coding	0.015075	0.395000	
chunk0128_255_1	chr3	109093401	109093910	+	0	NA	intron (NM_014429, intron 7 of 27)	intron (NM_014429, intron 7 of 27)	24491	NM_014429	27136	Hs.591296	NM_014429	ENSG00000114487	MORC1	CT33|MORC|ZCW6	MORC family CW-type zinc finger 1	protein-coding	0.000000	0.347059	
chunk0086_31_1	chr18	12573243	12573675	+	0	NA	intron (NM_001128627, intron 2 of 15)	L1MC2|LINE|L1	83273	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.006944	0.346420	
chunk0041_340_1	chr11	130645416	130645653	+	0	NA	Intergenic	L2c|LINE|L2	-21201	NR_107019	102466873		NR_107019	ENSG00000274999	MIR8052	hsa-mir-8052	microRNA 8052	ncRNA	0.008439	0.474790	
chunk0025_193_1	chr10	53327206	53327481	+	0	NA	Intergenic	Intergenic	-555643	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.351449	
chunk0187_307_1	chr7	156399574	156400075	+	0	NA	Intergenic	Intergenic	45764	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.017964	0.382470	
chunk0209_133_1	chrX	41488355	41488709	+	0	NA	Intergenic	L1MD|LINE|L1	41072	NM_022567	60506	Hs.302019	NM_022567	ENSG00000188937	NYX	CLRP|CSNB1|CSNB1A|CSNB4|NBM1	nyctalopin	protein-coding	0.008475	0.408451	119(AGAGACATACTGTGCT,-,0.00),120(GAGACATACTGTGCTC,+,0.00)
chunk0047_436_1	chr12	76402332	76402715	+	0	NA	intron (NM_001003712, intron 5 of 22)	Charlie17a|DNA|hAT-Charlie	-54081	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.000000	0.377604	
chunk0186_94_1	chr7	137484106	137484421	+	0	NA	intron (NM_004717, intron 24 of 33)	intron (NM_004717, intron 24 of 33)	-140463	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.003175	0.357595	
chunk0102_134_1	chr2	145769133	145769574	+	0	NA	Intergenic	Intergenic	-817704	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.006803	0.361991	
chunk0114_390_1	chr20	63208862	63209124	+	0	NA	intron (NM_017798, intron 3 of 4)	Tigger3b|DNA|TcMar-Tigger	7193	NM_017798	54915	Hs.744852	NM_017798	ENSG00000149658	YTHDF1	C20orf21	YTH N6-methyladenosine RNA binding protein 1	protein-coding	0.019084	0.403042	
chunk0200_246_1	chr9	20990851	20991050	+	0	NA	intron (NM_017794, intron 44 of 45)	intron (NM_017794, intron 44 of 45)	40686	NM_001010915	401494	Hs.716678	NM_001010915	ENSG00000188921	HACD4	PTPLAD2	3-hydroxyacyl-CoA dehydratase 4	protein-coding	0.005025	0.480000	
chunk0076_36_1	chr16	59693786	59693985	+	0	NA	Intergenic	Intergenic	61306	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.005025	0.395000	
chunk0035_327_1	chr11	47553102	47553321	+	0	NA	promoter-TSS (NM_006560)	promoter-TSS (NM_006560)	29	NM_006560	10658	Hs.595333	NM_006560	ENSG00000149187	CELF1	BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50	CUGBP Elav-like family member 1	protein-coding	0.146119	0.768182	
chunk0069_427_1	chr15	68188238	68188636	+	0	NA	TTS (NM_016166)	TTS (NM_016166)	17673	NM_001031733	91860	Hs.709550	NM_033429	ENSG00000129007	CALML4	NY-BR-20	calmodulin like 4	protein-coding	0.020101	0.421053	
chunk0184_184_1	chr7	116730648	116730955	+	0	NA	intron (NM_000245, intron 2 of 20)	L2c|LINE|L2	58396	NM_000245	4233	Hs.132966	NM_000245	ENSG00000105976	MET	AUTS9|DFNB97|HGFR|RCCP2|c-Met	MET proto-oncogene, receptor tyrosine kinase	protein-coding	0.006515	0.444805	
chunk0200_375_1	chr9	26352379	26352600	+	0	NA	Intergenic	L1PB1|LINE|L1	285814	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.000000	0.369369	
chunk0151_351_1	chr5	54399161	54399503	+	0	NA	intron (NR_126379, intron 1 of 4)	intron (NR_126379, intron 1 of 4)	-56269	NM_006308	8988	Hs.41707	NM_006308	ENSG00000169271	HSPB3	DHMN2C|HMN2C|HSPL27	heat shock protein family B (small) member 3	protein-coding	0.011696	0.399417	206(GGAGCAAACTGTGCTT,+,0.00)
chunk0096_365_1	chr2	36482597	36482874	+	0	NA	intron (NM_016441, intron 7 of 16)	intron (NM_016441, intron 7 of 16)	115454	NM_005102	9637	Hs.258563	NM_005102	ENSG00000171055	FEZ2	HUM3CL	fasciculation and elongation protein zeta 2	protein-coding	0.010830	0.392086	
chunk0166_96_1	chr6	43745342	43745608	+	0	NA	Intergenic	Intergenic	-24734	NM_001025367	7422	Hs.73793	NM_003376	ENSG00000112715	VEGFA	MVCD1|VEGF|VPF	vascular endothelial growth factor A	protein-coding	0.022556	0.445693	
chunk0021_76_1	chr10	1519248	1519452	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	-7280	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.019608	0.424390	
chunk0121_236_1	chr3	22104760	22105407	+	0	NA	Intergenic	Intergenic	147944	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.004637	0.314815	
chunk0078_244_1	chr17	7045724	7046069	+	0	NA	Intergenic	Intergenic	-1973	NM_153357	162515	Hs.336564	NM_153357	ENSG00000174326	SLC16A11	MCT 11|MCT11	solute carrier family 16 member 11	protein-coding	0.002899	0.346821	
chunk0076_425_1	chr16	72995808	72996017	+	0	NA	intron (NM_006885, intron 1 of 9)	intron (NM_006885, intron 1 of 9)	52463	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.033493	0.447619	
chunk0099_215_1	chr2	95384726	95385212	+	0	NA	3' UTR (NM_001034914, exon 8 of 8)	3' UTR (NM_001034914, exon 8 of 8)	-17731	NM_016044	51011	Hs.531247	NM_016044	ENSG00000115042	FAHD2A	CGI-105	fumarylacetoacetate hydrolase domain containing 2A	protein-coding	0.020576	0.626283	176(CAGCACAGACTGTTCC,-,0.00),177(AGCACAGACTGTTCCC,+,0.00)
chunk0187_86_1	chr8	3172958	3173157	+	0	NA	intron (NM_033225, intron 37 of 69)	intron (NM_033225, intron 37 of 69)	-444606	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.005025	0.410000	
chunk0034_189_1	chr11	31627270	31627482	+	0	NA	intron (NM_019040, intron 6 of 9)	intron (NM_019040, intron 6 of 9)	117647	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.000000	0.352113	
chunk0177_81_1	chr7	21579230	21579794	+	0	NA	intron (NM_001277115, intron 8 of 81)	L2b|LINE|L2	36297	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.005319	0.375221	215(GAGTACAGAGTGCTCT,-,0.00),216(AGTACAGAGTGCTCTG,+,0.00)
chunk0113_431_1	chr20	62247008	62247207	+	0	NA	intron (NM_001278649, intron 1 of 12)	intron (NM_001278649, intron 1 of 12)	8622	NM_144498	9885	Hs.473254	NM_014835	ENSG00000130703	OSBPL2	DFNA67|DNFA67|ORP-2|ORP2	oxysterol binding protein like 2	protein-coding	0.040201	0.610000	
chunk0204_320_1	chr9	100556015	100556367	+	0	NA	intron (NM_003692, intron 7 of 9)	L2a|LINE|L2	-21888	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.008523	0.373938	
chunk0087_343_1	chr18	40273230	40273528	+	0	NA	Intergenic	Intergenic	207093	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.003356	0.364548	188(CAGTACAACATGTGCA,-,0.00),189(AGTACAACATGTGCAC,+,0.00)
chunk0070_155_1	chr15	71218303	71218720	+	0	NA	intron (NM_024817, intron 3 of 16)	intron (NM_024817, intron 3 of 16)	-29452	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.007194	0.461722	
chunk0191_141_1	chr8	48818432	48819228	+	0	NA	Intergenic	Intergenic	-83519	NR_024605	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.015075	0.552070	463(AGGTGCAACCTGTTCT,-,0.00),464(GGTGCAACCTGTTCTT,+,0.00)
chunk0210_437_1	chrX	103699073	103699695	+	0	NA	Intergenic	L2c|LINE|L2	-11226	NM_001142419	9643	Hs.326387	NM_012286	ENSG00000123562	MORF4L2	MORFL2|MRGX	mortality factor 4 like 2	protein-coding	0.016077	0.452648	
chunk0184_55_1	chr7	112360818	112361195	+	0	NA	Intergenic	Intergenic	-62138	NM_001197080	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.015915	0.378307	
chunk0001_216_1	chr1	8026854	8027179	+	0	NA	promoter-TSS (NM_018948)	promoter-TSS (NM_018948)	-683	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.040000	0.604294	
chunk0018_298_1	chr1	220812188	220812798	+	0	NA	intron (NM_022746, intron 6 of 6)	L2a|LINE|L2	-16762	NR_110797	101929730	Hs.398159	NR_110797	ENSG00000238078	LINC01352	-	long intergenic non-protein coding RNA 1352	ncRNA	0.014754	0.472995	
chunk0171_193_1	chr6	125267751	125268137	+	0	NA	Intergenic	LTR18A|LTR|ERVL	34192	NM_016063	51020	Hs.32826	NM_016063	ENSG00000111906	HDDC2	C6orf74|CGI-130|NS5ATP2|dJ167O5.2	HD domain containing 2	protein-coding	0.010363	0.493540	
chunk0067_363_1	chr15	48681313	48681720	+	0	NA	Intergenic	Intergenic	-35728	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.007371	0.401961	
chunk0038_360_1	chr11	93257394	93258901	+	0	NA	Intergenic	Intergenic	-60172	NM_152313	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.003318	0.342175	344(AGGAACACTGTGTTAT,-,0.00),345(GGAACACTGTGTTATG,+,0.00),1218(AGGCACACACAGATCT,-,0.00)
chunk0089_26_1	chr18	57789431	57789736	+	0	NA	intron (NM_005603, intron 1 of 27)	intron (NM_005603, intron 1 of 27)	13512	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.013115	0.431373	
chunk0154_160_1	chr5	79507866	79508727	+	0	NA	intron (NM_001277077, intron 1 of 5)	MER112|DNA|hAT-Charlie	5540	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.006969	0.404872	
chunk0167_84_1	chr6	56637193	56637940	+	0	NA	intron (NM_001723, intron 8 of 23)	intron (NM_001723, intron 8 of 23)	5330	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.009371	0.334225	
chunk0107_439_1	chr2	224934464	224934991	+	0	NA	intron (NM_014689, intron 1 of 55)	intron (NM_014689, intron 1 of 55)	12338	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.007590	0.424242	
chunk0054_451_1	chr13	51458608	51459123	+	0	NA	Intergenic	Intergenic	5520	NR_103812	100507398	Hs.594897	NR_103812	ENSG00000236778	INTS6-AS1	-	INTS6 antisense RNA 1	ncRNA	0.005825	0.325581	
chunk0040_125_1	chr11	112310099	112310584	+	0	NA	intron (NR_126004, intron 2 of 3)	intron (NR_126004, intron 2 of 3)	39592	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.004124	0.397119	
chunk0204_242_1	chr9	98045370	98045572	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-11206	NM_018946	54187	Hs.522310	NM_018946	ENSG00000095380	NANS	HEL-S-100|SAS|SEMDCG|SEMDG	N-acetylneuraminate synthase	protein-coding	0.009901	0.408867	
chunk0005_100_1	chr1	56557895	56558519	+	0	NA	intron (NM_003713, intron 1 of 5)	intron (NM_003713, intron 1 of 5)	21377	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.003205	0.409600	293(GAGAACTTCTTGTTCT,-,0.00),294(AGAACTTCTTGTTCTC,+,0.00)
chunk0100_56_1	chr2	106269618	106270234	+	0	NA	Intergenic	CpG	-75587	NM_025076	80146	Hs.469561	NM_025076	ENSG00000115652	UXS1	SDR6E1|UGD	UDP-glucuronate decarboxylase 1	protein-coding	0.063312	0.609400	
chunk0157_437_1	chr5	124847809	124848170	+	0	NA	Intergenic	UCON29|DNA|PiggyBac?	-102877	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.008310	0.348066	
chunk0022_114_1	chr10	10778228	10778474	+	0	NA	Intergenic	Intergenic	16563	NR_027082	207107	Hs.31562	NR_027082	ENSG00000225383	SFTA1P	SFTPF	surfactant associated 1, pseudogene	pseudo	0.004065	0.437247	
chunk0136_137_1	chr4	3945701	3946317	+	0	NA	intron (NR_130742, intron 3 of 3)	intron (NR_130742, intron 3 of 3)	9419	NR_130741	348926	Hs.591720	NR_024253	ENSG00000251669	FAM86EP	-	family with sequence similarity 86, member A pseudogene	pseudo	0.034091	0.598055	
chunk0170_67_1	chr6	109691117	109691664	+	0	NA	promoter-TSS (NM_001145128)	promoter-TSS (NM_001145128)	169	NM_014845	9896	Hs.529959	NM_014845	ENSG00000112367	FIG4	ALS11|BTOP|CMT4J|KIAA0274|SAC3|YVS|dJ249I4.1	FIG4 phosphoinositide 5-phosphatase	protein-coding	0.058501	0.627737	
chunk0153_198_1	chr5	71714764	71715497	+	0	NA	Intergenic	Intergenic	-4033	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.002729	0.382834	
chunk0004_115_1	chr1	44537624	44538044	+	0	NA	intron (NM_018150, intron 2 of 14)	L3|LINE|CR1	-7659	NR_049849	100847089		NR_049849	ENSG00000263381	MIR5584	-	microRNA 5584	ncRNA	0.016667	0.448931	159(AAGTGCAGAATGTTCC,-,0.00),160(AGTGCAGAATGTTCCC,+,0.00)
chunk0119_148_1	chr22	42995086	42995727	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	19772	NM_001184970	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.012480	0.453271	240(AAGAACAGGCTGCTTT,-,0.00)
chunk0162_155_1	chr6	3399332	3399643	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	45526	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.016077	0.419872	
chunk0046_455_1	chr12	64941659	64941858	+	0	NA	intron (NR_033988, intron 2 of 2)	MLT1D|LTR|ERVL-MaLR	57984	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.005025	0.420000	
chunk0120_144_1	chr3	5188804	5189368	+	0	NA	intron (NM_014674, intron 1 of 11)	intron (NM_014674, intron 1 of 11)	1412	NM_014674	9695	Hs.224616	NM_014674	ENSG00000134109	EDEM1	EDEM	ER degradation enhancing alpha-mannosidase like protein 1	protein-coding	0.017730	0.518584	
chunk0075_236_1	chr16	53045767	53046154	+	0	NA	Intergenic	Intergenic	-9073	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.002584	0.484536	
chunk0126_348_1	chr3	82731333	82731579	+	0	NA	Intergenic	Intergenic	-969657	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004065	0.344130	
chunk0130_84_1	chr3	130697539	130698230	+	0	NA	intron (NM_014602, intron 13 of 19)	L1MB7|LINE|L1	48968	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.000000	0.322254	
chunk0152_125_1	chr5	58843391	58843842	+	0	NA	intron (NM_138453, intron 4 of 4)	MamRep434|DNA|TcMar-Tigger	156316	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.006652	0.323009	
chunk0006_141_1	chr1	66266309	66266781	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-65563	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.012712	0.450317	
chunk0003_211_1	chr1	35306847	35307230	+	0	NA	intron (NM_005095, intron 1 of 29)	intron (NM_005095, intron 1 of 29)	38071	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.002611	0.322917	158(CAGCACTGTTTGTGCC,-,0.00),159(AGCACTGTTTGTGCCT,+,0.00)
chunk0010_274_1	chr1	117318014	117318393	+	0	NA	intron (NR_126408, intron 2 of 2)	L1MB5|LINE|L1	22737	NR_126408	104355292	Hs.576446	NR_126408	ENSG00000235202	LINC01525	lnc-MAN1A2-1	long intergenic non-protein coding RNA 1525	ncRNA	0.002639	0.344737	152(ATGAACATTGTGTGCA,-,0.00),153(TGAACATTGTGTGCAA,+,0.00)
chunk0030_363_1	chr10	118740128	118740327	+	0	NA	intron (NM_153810, intron 1 of 8)	HAL1|LINE|L1	15019	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.010050	0.325000	
chunk0196_216_1	chr8	107044514	107044713	+	0	NA	Intergenic	L1PB1|LINE|L1	-274369	NM_139166	137735	Hs.374668	NM_139166	ENSG00000174429	ABRA	STARS	actin binding Rho activating protein	protein-coding	0.005025	0.400000	
chunk0086_283_1	chr18	23704284	23704545	+	0	NA	intron (NR_130106, intron 1 of 12)	MIRb|SINE|MIR	14971	NR_130106	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.011494	0.450382	216(AAGTTCACAGTGTTCT,-,0.00),217(AGTTCACAGTGTTCTG,+,0.00)
chunk0152_283_1	chr5	61449833	61450032	+	0	NA	intron (NM_020928, intron 1 of 13)	intron (NM_020928, intron 1 of 13)	117659	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.000000	0.445000	
chunk0043_357_1	chr12	23193995	23194375	+	0	NA	Intergenic	Intergenic	18549	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.005263	0.364829	
chunk0188_332_1	chr8	17647629	17648174	+	0	NA	intron (NM_001001924, intron 13 of 14)	intron (NM_001001924, intron 13 of 14)	33756	NR_036103	100422850		NR_036103	ENSG00000265520	MIR548V	-	microRNA 548v	ncRNA	0.014679	0.423077	342(CAGGACAACCTGTTCA,-,0.00),343(AGGACAACCTGTTCAG,+,0.00)
chunk0086_125_1	chr18	21019829	21020163	+	0	NA	intron (NM_005406, intron 12 of 32)	intron (NM_005406, intron 12 of 32)	91855	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.002994	0.280597	
chunk0076_97_1	chr16	65734131	65734630	+	0	NA	Intergenic	Intergenic	-158080	NR_027755	283867	Hs.444774	NM_001101346	ENSG00000261742	LINC00922	-	long intergenic non-protein coding RNA 922	ncRNA	0.004008	0.402000	208(TAGAACAGTAAGTGCC,-,0.00),209(AGAACAGTAAGTGCCC,+,0.00)
chunk0111_436_1	chr20	35207853	35208639	+	0	NA	Intergenic	Intergenic	-18490	NM_006690	10893	Hs.715494	NM_006690	ENSG00000125966	MMP24	MMP-24|MMP25|MT-MMP 5|MT-MMP5|MT5-MMP|MT5MMP|MTMMP5	matrix metallopeptidase 24	protein-coding	0.011450	0.442186	345(AAGGACATCCTGTGCT,-,0.00),346(AGGACATCCTGTGCTG,+,0.00)
chunk0146_298_1	chr4	164989546	164990239	+	0	NA	Intergenic	Intergenic	-12226	NM_001012414	391712	Hs.654633	NM_001012414	ENSG00000183439	TRIM61	RNF35	tripartite motif containing 61	protein-coding	0.008658	0.390490	
chunk0112_49_1	chr20	37095906	37096169	+	0	NA	promoter-TSS (NM_002895)	promoter-TSS (NM_002895)	-37	NM_183404	5933	Hs.207745	NM_002895	ENSG00000080839	RBL1	CP107|PRB1|p107	RB transcriptional corepressor like 1	protein-coding	0.079848	0.594697	
chunk0065_399_1	chr14	105119134	105119333	+	0	NA	Intergenic	Intergenic	25086	NR_110546	102723354	Hs.569410	NR_110546		LINC02298	-	long intergenic non-protein coding RNA 2298	ncRNA	0.030151	0.560000	
chunk0155_405_1	chr5	99109616	99109884	+	0	NA	Intergenic	Intergenic	180616	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.011194	0.327138	
chunk0024_68_1	chr10	34152293	34153071	+	0	NA	intron (NM_019619, intron 22 of 24)	intron (NM_019619, intron 22 of 24)	-380002	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.002571	0.392811	
chunk0017_219_1	chr1	207963611	207964179	+	0	NA	Intergenic	Intergenic	-52557	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.077465	0.673111	
chunk0154_410_1	chr5	88925701	88926186	+	0	NA	intron (NR_109941, intron 3 of 3)	Tigger3b|DNA|TcMar-Tigger	-21838	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.004124	0.341564	
chunk0117_222_1	chr22	22559301	22560464	+	0	NA	promoter-TSS (NM_206956)	promoter-TSS (NM_206956)	-521	NM_206956	23532	Hs.30743	NM_006115	ENSG00000185686	PRAME	CT130|MAPE|OIP-4|OIP4	preferentially expressed antigen in melanoma	protein-coding	0.023216	0.524055	
chunk0015_1_1	chr1	184073700	184074147	+	0	NA	non-coding (NR_023349, exon 6 of 6)	non-coding (NR_023349, exon 6 of 6)	22272	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.006711	0.321429	
chunk0188_274_1	chr8	15422096	15422505	+	0	NA	Intergenic	L1M5|LINE|L1	-117787	NM_178234	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.004890	0.331707	
chunk0101_42_1	chr2	122539899	122540435	+	0	NA	Intergenic	L2a|LINE|L2	784622	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.011194	0.383613	184(AGGAACAGGTTGTGAT,-,0.00)
chunk0201_57_1	chr9	33898845	33899212	+	0	NA	intron (NM_017811, intron 2 of 4)	intron (NM_017811, intron 2 of 4)	35336	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.002725	0.315217	
chunk0131_102_1	chr3	143826364	143826676	+	0	NA	intron (NM_173653, intron 2 of 15)	intron (NM_173653, intron 2 of 15)	22011	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.003205	0.469649	
chunk0127_288_1	chr3	97926659	97927360	+	0	NA	intron (NM_153605, intron 17 of 21)	L1PA15|LINE|L1	45442	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.007133	0.377493	
chunk0118_64_1	chr22	28424672	28424937	+	0	NA	intron (NM_001145418, intron 2 of 22)	intron (NM_001145418, intron 2 of 22)	-35065	NR_106713	102466081		NR_106713	ENSG00000276162	MIR5739	hsa-mir-5739	microRNA 5739	ncRNA	0.000000	0.383459	
chunk0009_204_1	chr1	106084778	106085441	+	0	NA	Intergenic	Intergenic	-466174	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001508	0.307229	
chunk0151_249_1	chr5	51845865	51846352	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-462776	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.006160	0.385246	
chunk0177_373_1	chr7	26777445	26778040	+	0	NA	intron (NM_001303468, intron 4 of 12)	intron (NM_001303468, intron 4 of 12)	79981	NM_001303468	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.000000	0.325503	285(AAGTCCAGAGTGTTCT,-,0.00),286(AGTCCAGAGTGTTCTG,+,0.00)
chunk0185_335_1	chr7	131960983	131961592	+	0	NA	Intergenic	Intergenic	51067	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.016420	0.490164	294(GGGACACTCTCTTCTT,+,0.00)
chunk0144_388_1	chr4	140122878	140123455	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	30913	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.001733	0.311419	
chunk0101_247_1	chr2	131895165	131895555	+	0	NA	Intergenic	(TTTAA)n|Simple_repeat|Simple_repeat	-93699	NM_214461									0.000000	0.301790	168(CAGAACATTCAGTTTC,-,0.00)
chunk0038_279_1	chr11	89676918	89677729	+	0	NA	intron (NM_153696, intron 7 of 13)	intron (NM_153696, intron 7 of 13)	18026	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.012330	0.362069	316(AGGAACAGACAGTATC,-,0.00)
chunk0161_321_1	chr5	173662353	173663472	+	0	NA	Intergenic	Intergenic	-46249	NM_138369	91272	Hs.425091	NM_138369	ENSG00000145919	BOD1	FAM44B	biorientation of chromosomes in cell division 1	protein-coding	0.015192	0.467857	887(CAGAACAGAGAGTACC,-,0.00),888(AGAACAGAGAGTACCT,+,0.00)
chunk0106_471_1	chr2	209501620	209502054	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	77790	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.004608	0.360920	280(CAGGACAGCTTGAGCC,-,0.00),281(AGGACAGCTTGAGCCC,+,0.00)
chunk0130_205_1	chr3	133805651	133805850	+	0	NA	5' UTR (NM_021203, exon 2 of 8)	5' UTR (NM_021203, exon 2 of 8)	21717	NM_021203	58477	Hs.12152	NM_021203	ENSG00000144867	SRPRB	APMCF1|SR-beta	SRP receptor subunit beta	protein-coding	0.075377	0.615000	
chunk0207_292_1	chr9	133114470	133114998	+	0	NA	intron (NM_001042368, intron 1 of 17)	intron (NM_001042368, intron 1 of 17)	6516	NM_006266	5900	Hs.106185	NM_006266	ENSG00000160271	RALGDS	RGDS|RGF|RalGEF	ral guanine nucleotide dissociation stimulator	protein-coding	0.017045	0.620038	266(AAGAACACCACGTGCT,-,0.00),267(AGAACACCACGTGCTT,+,0.00)
chunk0042_91_1	chr12	2662322	2663030	+	0	NA	intron (NM_001129846, intron 33 of 45)	L1ME3C|LINE|L1	9544	NR_046579	100874235	Hs.667644	NR_046579	ENSG00000256271	CACNA1C-AS2	-	CACNA1C antisense RNA 2	ncRNA	0.005650	0.334274	
chunk0040_31_1	chr11	110305364	110305887	+	0	NA	Intergenic	Intergenic	-8913	NM_001260493	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.000000	0.322519	
chunk0101_365_1	chr2	138025985	138026607	+	0	NA	Intergenic	Intergenic	62058	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.003215	0.338684	
chunk0142_34_1	chr4	90709934	90710212	+	0	NA	intron (NM_001145065, intron 6 of 10)	L1PA11|LINE|L1	475042	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.000000	0.347670	
chunk0115_452_1	chr21	32495417	32495785	+	0	NA	intron (NM_058187, intron 5 of 7)	intron (NM_058187, intron 5 of 7)	83164	NM_001286556	59271	Hs.208358	NM_058187	ENSG00000166979	EVA1C	B18|B19|C21orf63|C21orf64|FAM176C|PRED34|SUE21	eva-1 homolog C	protein-coding	0.013587	0.387534	
chunk0172_66_1	chr6	134300941	134301457	+	0	NA	intron (NM_001143676, intron 1 of 13)	L2|LINE|L2	16859	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.001938	0.411992	
chunk0125_384_1	chr3	71658037	71658644	+	0	NA	Intergenic	Intergenic	67035	NM_001134651	317649	Hs.581355	NM_173359	ENSG00000163412	EIF4E3	eIF-4E3|eIF4E-3	eukaryotic translation initiation factor 4E family member 3	protein-coding	0.016474	0.485197	
chunk0033_236_1	chr11	17921882	17922356	+	0	NA	intron (NR_104040, intron 9 of 11)	intron (NR_104040, intron 9 of 11)	91043	NR_104041	26297	Hs.32470	NM_012139	ENSG00000129158	SERGEF	DELGEF|Gnefr	secretion regulating guanine nucleotide exchange factor	protein-coding	0.006329	0.452632	258(GGAAACAGAGTGTCCT,-,0.00),259(GAAACAGAGTGTCCTT,+,0.00)
chunk0133_76_1	chr3	167094529	167094770	+	0	NA	Intergenic	Intergenic	285634	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.012448	0.330579	
chunk0021_290_1	chr1	244545630	244545829	+	0	NA	intron (NM_001130957, intron 8 of 21)	ERVL-B4-int|LTR|ERVL	84358	NM_001242340	257044	Hs.459534	NM_173807	ENSG00000179397	CATSPERE	C10orf101|C1orf101	catsper channel auxiliary subunit epsilon	protein-coding	0.005025	0.435000	
chunk0079_383_1	chr17	18530494	18530775	+	0	NA	Intergenic	L1MC4a|LINE|L1	-3788	NR_026809									0.000000	0.411348	
chunk0051_310_1	chr12	119479251	119479542	+	0	NA	intron (NM_178499, intron 4 of 13)	intron (NM_178499, intron 4 of 13)	-114063	NM_001136534	387890	Hs.530965	NM_001136534	ENSG00000224982	TMEM233	DSPB2|IFITMD2	transmembrane protein 233	protein-coding	0.017182	0.458904	
chunk0102_57_1	chr2	142823703	142824140	+	0	NA	Intergenic	Intergenic	-53705	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.000000	0.264840	
chunk0098_439_1	chr2	82109726	82110341	+	0	NA	Intergenic	MER110-int|LTR|ERV1	-643087	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.001626	0.379870	
chunk0004_32_1	chr1	42570835	42571524	+	0	NA	intron (NM_001080850, intron 6 of 15)	intron (NM_001080850, intron 6 of 15)	36290	NM_001080850	728621	Hs.729640	NM_001080850	ENSG00000186409	CCDC30	PFD6L|PFDN6L	coiled-coil domain containing 30	protein-coding	0.005806	0.366667	
chunk0153_356_1	chr5	74415690	74416243	+	0	NA	intron (NR_126354, intron 2 of 2)	intron (NR_126354, intron 2 of 2)	93480	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.014467	0.429603	
chunk0182_61_1	chr7	92044822	92045330	+	0	NA	exon (NM_005751, exon 21 of 50)	exon (NM_005751, exon 21 of 50)	89450	NM_000786	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.001969	0.337917	
chunk0158_402_1	chr5	134705380	134705983	+	0	NA	intron (NM_021982, intron 17 of 22)	L1MB8|LINE|L1	-32799	NM_001745	819	Hs.529846	NM_001745	ENSG00000164615	CAMLG	CAML|GET2	calcium modulating ligand	protein-coding	0.003317	0.341060	
chunk0018_292_1	chr1	220784975	220785682	+	0	NA	Intergenic	Intergenic	-1369	NM_022746	64757	Hs.497816	NM_022746	ENSG00000186205	MARC1	MOSC1	mitochondrial amidoxime reducing component 1	protein-coding	0.012730	0.508475	
chunk0005_149_1	chr1	58092795	58093192	+	0	NA	intron (NM_021080, intron 1 of 16)	intron (NM_021080, intron 1 of 16)	157546	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.015113	0.432161	
chunk0126_220_1	chr3	78838330	78839176	+	0	NA	intron (NM_133631, intron 2 of 28)	MSTB1|LTR|ERVL-MaLR	180706	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004728	0.415584	
chunk0101_306_1	chr2	135125076	135125357	+	0	NA	intron (NM_001172435, intron 9 of 24)	L1MB7|LINE|L1	72951	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.003559	0.390071	
chunk0202_28_1	chr9	70593197	70593569	+	0	NA	intron (NM_024971, intron 21 of 25)	intron (NM_024971, intron 21 of 25)	-178726	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.000000	0.319035	
chunk0130_266_1	chr3	136232250	136232857	+	0	NA	Intergenic	Intergenic	-17772	NM_000532	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.006590	0.422697	
chunk0186_386_1	chr7	144448677	144449039	+	0	NA	Intergenic	Intergenic	-38631	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.008287	0.407713	147(CGGTACAGTATGTTCC,-,0.00),148(GGTACAGTATGTTCCC,+,0.00)
chunk0096_313_1	chr2	33161505	33161888	+	0	NA	intron (NM_000627, intron 1 of 29)	intron (NM_000627, intron 1 of 29)	27099	NM_001166266	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.013055	0.346354	
chunk0202_87_1	chr9	71962308	71962662	+	0	NA	intron (NM_182505, intron 2 of 3)	intron (NM_182505, intron 2 of 3)	50978	NM_182505	138241	Hs.534190	NM_182505	ENSG00000155621	C9orf85	-	chromosome 9 open reading frame 85	protein-coding	0.011299	0.349296	
chunk0052_386_1	chr12	129704269	129705032	+	0	NA	intron (NM_133448, intron 1 of 8)	intron (NM_133448, intron 1 of 8)	199017	NM_133448	121256	Hs.507268	NM_133448	ENSG00000151952	TMEM132D	MOLT|PPP1R153	transmembrane protein 132D	protein-coding	0.014417	0.459424	
chunk0199_305_1	chr9	7037763	7038227	+	0	NA	intron (NM_015061, intron 15 of 21)	intron (NM_015061, intron 15 of 21)	280354	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.006466	0.320430	
chunk0016_57_1	chr1	193306397	193306851	+	0	NA	intron (NR_125789, intron 1 of 3)	L3|LINE|CR1	1879	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.008811	0.437363	
chunk0055_147_1	chr13	59780901	59781329	+	0	NA	intron (NM_001258369, intron 25 of 26)	HAL1|LINE|L1	-231603	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004673	0.354312	
chunk0020_261_1	chr1	236297968	236298525	+	0	NA	Intergenic	L2b|LINE|L2	-16207	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.016158	0.435484	
chunk0125_258_1	chr3	69171926	69172394	+	0	NA	intron (NM_015123, intron 22 of 22)	LTR37B|LTR|ERV1	-49565	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.000000	0.336887	
chunk0066_391_1	chr15	39040825	39041437	+	0	NA	Intergenic	Tigger5b|DNA|TcMar-Tigger	-209538	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.009804	0.409462	269(TAGTACAGACAGTCCC,-,0.00),270(AGTACAGACAGTCCCT,+,0.00)
chunk0190_437_1	chr8	41609907	41610558	+	0	NA	intron (NM_178819, intron 4 of 12)	intron (NM_178819, intron 4 of 12)	-31864	NR_125824	102723729	Hs.586384	NR_125824		LOC102723729	-	uncharacterized LOC102723729	ncRNA	0.013825	0.552147	305(GGGAACATTGTGTGCT,-,0.00),306(GGAACATTGTGTGCTT,+,0.00)
chunk0023_108_1	chr10	22980729	22981312	+	0	NA	intron (NM_173081, intron 8 of 18)	L3|LINE|CR1	52996	NM_001282746	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.005146	0.318493	
chunk0163_63_1	chr6	9019234	9019466	+	0	NA	Intergenic	Intergenic	367141	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.008621	0.412017	
chunk0031_51_1	chr10	122665157	122665356	+	0	NA	Intergenic	Intergenic	34566	NM_001010912	399814	Hs.363649	NM_001010912	ENSG00000183559	C10orf120	bA318C4.1	chromosome 10 open reading frame 120	protein-coding	0.005025	0.395000	
chunk0045_467_1	chr12	53887147	53887594	+	0	NA	Intergenic	Intergenic	-51422	NM_017410	3229	Hs.118608	NM_017410	ENSG00000123364	HOXC13	ECTD9|HOX3|HOX3G	homeobox C13	protein-coding	0.008949	0.392857	234(GGGGACTGTCTGTACC,-,0.00),235(GGGACTGTCTGTACCA,+,0.00)
chunk0036_45_1	chr11	59012838	59013250	+	0	NA	intron (NR_033853, intron 3 of 5)	L1M1|LINE|L1	45408	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.009709	0.518160	
chunk0180_292_1	chr7	70150184	70150744	+	0	NA	intron (NM_015570, intron 4 of 18)	MER92-int|LTR|ERV1	551545	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.000000	0.335116	295(TAGACATGCTGTTCTT,+,0.00)
chunk0091_264_1	chr19	11189734	11190120	+	0	NA	intron (NM_015493, intron 2 of 10)	intron (NM_015493, intron 2 of 10)	4663	NM_015493	25959	Hs.284208	NM_015493	ENSG00000197256	KANK2	ANKRD25|MXRA3|NPHS16|PPKWH|SIP	KN motif and ankyrin repeat domains 2	protein-coding	0.023316	0.596899	
chunk0148_134_1	chr5	5617100	5617436	+	0	NA	Intergenic	L1ME2|LINE|L1	194595	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.000000	0.382789	
chunk0179_30_1	chr7	42993676	42994515	+	0	NA	Intergenic	L1M5|LINE|L1	61755	NM_031903	64983	Hs.50252	NM_031903	ENSG00000106591	MRPL32	HSPC283|L32mt|MRP-L32|bMRP-59b	mitochondrial ribosomal protein L32	protein-coding	0.003576	0.369048	
chunk0144_409_1	chr4	140363536	140363738	+	0	NA	intron (NM_001153446, intron 2 of 4)	Tigger2|DNA|TcMar-Tigger	9755	NR_033939	100129858	Hs.660477	NR_033939	ENSG00000196951	SCOC-AS1	-	SCOC antisense RNA 1	ncRNA	0.000000	0.374384	109(TAGTACATACTGTACT,-,0.00),110(AGTACATACTGTACTA,+,0.00)
chunk0202_306_1	chr9	77979660	77980117	+	0	NA	intron (NM_002072, intron 1 of 6)	intron (NM_002072, intron 1 of 6)	51561	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.008753	0.362445	
chunk0155_103_1	chr5	92552229	92553106	+	0	NA	Intergenic	Intergenic	1018676	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.006842	0.375854	
chunk0087_217_1	chr18	36073336	36073890	+	0	NA	Intergenic	Intergenic	-6019	NM_018170	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.003610	0.349550	
chunk0169_75_1	chr6	99308540	99309088	+	0	NA	intron (NM_032511, intron 4 of 5)	intron (NM_032511, intron 4 of 5)	40841	NM_032511	84553	Hs.573245	NM_032511	ENSG00000146267	FAXC	C6orf168|dJ273F20	failed axon connections homolog, metaxin like GST domain containing	protein-coding	0.007299	0.309654	
chunk0077_276_1	chr16	81067138	81067592	+	0	NA	intron (NM_152337, intron 1 of 3)	L1MC5|LINE|L1	9902	NM_152337	123775	Hs.658684	NM_152337	ENSG00000166455	C16orf46	-	chromosome 16 open reading frame 46	protein-coding	0.004405	0.327473	
chunk0006_49_1	chr1	64495621	64496383	+	0	NA	intron (NM_020925, intron 1 of 26)	intron (NM_020925, intron 1 of 26)	-9912	NM_001293274	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.002625	0.355177	
chunk0004_406_1	chr1	52302939	52303153	+	0	NA	intron (NM_007324, intron 11 of 17)	AluSx|SINE|Alu	63159	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.023364	0.474419	
chunk0168_304_1	chr6	91661602	91662098	+	0	NA	intron (NR_104154, intron 2 of 3)	intron (NR_104154, intron 2 of 3)	28578	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.000000	0.301811	
chunk0097_34_1	chr2	42546392	42547047	+	0	NA	intron (NM_001282755, intron 2 of 17)	intron (NM_001282755, intron 2 of 17)	-21326	NM_001282756	57504	Hs.435413	NM_020744	ENSG00000057935	MTA3	-	metastasis associated 1 family member 3	protein-coding	0.010687	0.431402	
chunk0127_354_1	chr3	101072293	101072576	+	0	NA	Intergenic	Intergenic	-78944	NM_015429	25890	Hs.477015	NM_015429	ENSG00000154175	ABI3BP	NESHBP|TARSH	ABI family member 3 binding protein	protein-coding	0.010601	0.369718	
chunk0118_153_1	chr22	30202568	30202983	+	0	NA	Intergenic	L3|LINE|CR1	44076	NM_002309	3976	Hs.2250	NM_002309	ENSG00000128342	LIF	CDF|DIA|HILDA|MLPLI	LIF interleukin 6 family cytokine	protein-coding	0.019277	0.548077	
chunk0113_362_1	chr20	59084511	59084817	+	0	NA	Intergenic	Intergenic	-41818	NM_001256403	51012	Hs.656865	NM_016045	ENSG00000101166	PRELID3B	C20orf45|SLMO2|dJ543J19.5	PRELI domain containing 3B	protein-coding	0.016340	0.456026	
chunk0188_111_1	chr8	9037789	9038068	+	0	NA	Intergenic	Intergenic	-10517	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.000000	0.357143	
chunk0071_258_1	chr15	85500027	85500596	+	0	NA	intron (NM_007200, intron 2 of 36)	intron (NM_007200, intron 2 of 36)	-119639	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.007030	0.377193	279(TGGAACACTCTGTGTT,-,0.00),280(GGAACACTCTGTGTTT,+,0.00)
chunk0078_450_1	chr16	89909704	89909979	+	0	NA	intron (NM_014972, intron 16 of 17)	L2c|LINE|L2	-8038	NM_002386	4157	Hs.513829	NM_002386	ENSG00000258839	MC1R	CMM5|MSH-R|SHEP2	melanocortin 1 receptor	protein-coding	0.036364	0.590580	
chunk0178_161_1	chr7	33832174	33832814	+	0	NA	Intergenic	Intergenic	-72417	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.018750	0.463339	
chunk0067_315_1	chr15	47908984	47909428	+	0	NA	Intergenic	Intergenic	-62970	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.006757	0.350562	
chunk0197_91_1	chr8	119338462	119338684	+	0	NA	Intergenic	L2c|LINE|L2	13402	NR_106755	102466162		NR_106755	ENSG00000276479	MIR548AZ	hsa-mir-548az	microRNA 548az	ncRNA	0.004505	0.367713	
chunk0080_153_1	chr17	28041187	28041388	+	0	NA	Intergenic	Intergenic	-1375	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.014925	0.445545	
chunk0003_174_1	chr1	33634719	33635155	+	0	NA	intron (NM_052896, intron 31 of 69)	intron (NM_052896, intron 31 of 69)	162306	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.020642	0.558352	
chunk0095_357_1	chr2	22773813	22774162	+	0	NA	Intergenic	L1ME3A|LINE|L1	237508	NR_110577	102723362	Hs.502887	NR_110577	ENSG00000233587	LINC01884	-	long intergenic non-protein coding RNA 1884	ncRNA	0.014327	0.391429	
chunk0010_111_1	chr1	114416692	114417073	+	0	NA	intron (NM_033020, intron 11 of 18)	MSTB|LTR|ERVL-MaLR	94278	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.002625	0.327225	
chunk0048_420_1	chr12	88306438	88306867	+	0	NA	Intergenic	Intergenic	164356	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.004662	0.353488	
chunk0041_228_1	chr11	128282122	128282506	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	239996	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.013021	0.431169	
chunk0064_281_1	chr14	95193265	95193502	+	0	NA	intron (NM_024734, intron 12 of 12)	intron (NM_024734, intron 12 of 12)	-35373	NM_030621	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.008439	0.491597	
chunk0152_423_1	chr5	65781523	65781874	+	0	NA	intron (NM_020726, intron 6 of 12)	intron (NM_020726, intron 6 of 12)	59502	NM_020726	57486	Hs.247460	NM_020726	ENSG00000123213	NLN	AGTBP|EP24.16|MEP|MOP	neurolysin	protein-coding	0.002849	0.392045	
chunk0181_195_1	chr7	83643814	83644246	+	0	NA	intron (NM_012431, intron 1 of 16)	intron (NM_012431, intron 1 of 16)	-2599	NM_001178129	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.002315	0.346420	
chunk0133_333_1	chr3	172691880	172692419	+	0	NA	intron (NM_001146276, intron 1 of 4)	intron (NM_001146276, intron 1 of 4)	19069	NM_001146278	57552	Hs.444099	NM_020792	ENSG00000144959	NCEH1	AADACL1|NCEH	neutral cholesterol ester hydrolase 1	protein-coding	0.011132	0.394444	
chunk0086_423_1	chr18	27072254	27072453	+	0	NA	intron (NM_031422, intron 2 of 5)	intron (NM_031422, intron 2 of 5)	112985	NM_001256316	83539	Hs.44584	NM_031422	ENSG00000154080	CHST9	GALNAC4ST-2|GalNAc4ST2	carbohydrate sulfotransferase 9	protein-coding	0.000000	0.410000	
chunk0179_286_1	chr7	49631393	49631796	+	0	NA	Intergenic	Intergenic	-142067	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.425743	
chunk0099_263_1	chr2	98070973	98071568	+	0	NA	Intergenic	(TCCTTTG)n|Simple_repeat|Simple_repeat	-15862	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.003361	0.377517	
chunk0134_262_1	chr3	179454965	179455228	+	0	NA	Intergenic	Intergenic	-3513	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.003802	0.431818	72(AAGTACAGTTTGTACT,-,0.00),73(AGTACAGTTTGTACTT,+,0.00)
chunk0142_387_1	chr4	102537323	102537677	+	0	NA	intron (NM_003998, intron 4 of 23)	MamRTE1|LINE|RTE-BovB	36171	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.005650	0.397183	23(TAGCACAGGGTGTGTT,-,0.00),24(AGCACAGGGTGTGTTC,+,0.00)
chunk0063_223_1	chr14	81551776	81552060	+	0	NA	Intergenic	L1ME2|LINE|L1	-18057	NM_001244984	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.003521	0.312281	
chunk0084_230_1	chr17	78697242	78697719	+	0	NA	intron (NM_004762, intron 9 of 12)	intron (NM_004762, intron 9 of 12)	19552	NM_001292019	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.004193	0.414226	
chunk0088_150_1	chr18	46273900	46274186	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	-60181	NM_001256758	494470	Hs.501114	NM_152470	ENSG00000141622	RNF165	ARKL2|Ark2C|RNF111L2	ring finger protein 165	protein-coding	0.000000	0.487805	
chunk0178_411_1	chr7	40984803	40985250	+	0	NA	Intergenic	Intergenic	-5087	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.004474	0.408482	
chunk0063_185_1	chr14	80618140	80618535	+	0	NA	intron (NM_152446, intron 18 of 23)	intron (NM_152446, intron 18 of 23)	321203	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.017722	0.325758	
chunk0096_28_1	chr2	26635554	26635978	+	0	NA	intron (NM_001029881, intron 2 of 6)	L1ME4b|LINE|L1	5577	NM_001029881	130106	Hs.591579	NM_001029881	ENSG00000157884	CIB4	KIP4	calcium and integrin binding family member 4	protein-coding	0.004717	0.456471	
chunk0202_313_1	chr9	78177150	78177502	+	0	NA	Intergenic	L1M5|LINE|L1	-58749	NM_032171	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.000000	0.314448	
chunk0200_86_1	chr9	16461735	16462293	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-185701	NR_073471									0.007168	0.398927	
chunk0046_153_1	chr12	58205899	58206098	+	0	NA	Intergenic	L2b|LINE|L2	264336	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.005025	0.445000	48(CTGAACACACTGTGCT,-,0.00),49(TGAACACACTGTGCTG,+,0.00)
chunk0050_387_1	chr12	109052450	109052663	+	0	NA	promoter-TSS (NM_032663)	promoter-TSS (NM_032663)	-14	NM_032663	84749	Hs.486434	NM_032663	ENSG00000135093	USP30	-	ubiquitin specific peptidase 30	protein-coding	0.103286	0.668224	
chunk0191_49_1	chr8	43372177	43373257	+	0	NA	Intergenic	AluSz|SINE|Alu	80275	NM_001005365	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.006481	0.408881	
chunk0004_413_1	chr1	52366291	52366567	+	0	NA	promoter-TSS (NM_032449)	promoter-TSS (NM_032449)	-224	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.097826	0.722022	
chunk0022_271_1	chr10	15097273	15097612	+	0	NA	promoter-TSS (NM_153244)	promoter-TSS (NM_153244)	-123	NM_153244	221060	Hs.567777	NM_153244		RPP38-DT	C10orf111	RPP38 divergent transcript	ncRNA	0.132743	0.755882	
chunk0158_408_1	chr5	134838576	134838863	+	0	NA	Intergenic	AluJr|SINE|Alu	-6961	NM_152409	134553	Hs.708536	NM_152409	ENSG00000181904	C5orf24	-	chromosome 5 open reading frame 24	protein-coding	0.010453	0.434028	
chunk0076_123_1	chr16	66660417	66660947	+	0	NA	intron (NM_181521, intron 1 of 3)	L1ME4a|LINE|L1	36025	NM_181521	146223	Hs.643961	NM_178818	ENSG00000183723	CMTM4	CKLFSF4	CKLF like MARVEL transmembrane domain containing 4	protein-coding	0.013208	0.397363	
chunk0168_441_1	chr6	95730898	95731276	+	0	NA	Intergenic	Intergenic	153590	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.000000	0.340369	
chunk0116_420_1	chr21	42721414	42721723	+	0	NA	intron (NM_001001576, intron 2 of 14)	intron (NM_001001576, intron 2 of 14)	67816	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.003236	0.467742	
chunk0058_56_1	chr14	20591160	20591904	+	0	NA	promoter-TSS (NM_001024822)	promoter-TSS (NM_001024822)	-709	NM_001024822	493901	Hs.729466	NM_001024822	ENSG00000258436	RNASE12	HEL-S-85p|RAI1	ribonuclease A family member 12 (inactive)	protein-coding	0.014785	0.444295	
chunk0030_315_1	chr10	117921449	117921722	+	0	NA	Intergenic	L2a|LINE|L2	125018	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.021978	0.540146	
chunk0163_40_1	chr6	8468318	8468690	+	0	NA	intron (NR_038979, intron 2 of 3)	intron (NR_038979, intron 2 of 3)	32881	NR_038979	100506207	Hs.311049	NR_038979	ENSG00000285219	LOC100506207	-	uncharacterized LOC100506207	ncRNA	0.008065	0.359249	
chunk0021_333_1	chr1	245768407	245769040	+	0	NA	intron (NM_001167740, intron 10 of 11)	MLT1A1|LTR|ERVL-MaLR	613738	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.009479	0.422713	344(AAGGACACAGTGTTCC,-,0.00),345(AGGACACAGTGTTCCT,+,0.00)
chunk0207_298_1	chr9	133334194	133334393	+	0	NA	intron (NM_006753, intron 2 of 4)	intron (NM_006753, intron 2 of 4)	1917	NR_103874	6838	Hs.274430	NM_006753	ENSG00000148296	SURF6	RRP14	surfeit 6	protein-coding	0.020101	0.575000	
chunk0002_280_1	chr1	22412655	22412860	+	0	NA	Intergenic	Intergenic	-39094	NM_014870	9923	Hs.418966	NM_014870	ENSG00000184677	ZBTB40	ZNF923	zinc finger and BTB domain containing 40	protein-coding	0.014634	0.480583	
chunk0076_285_1	chr16	69706667	69706993	+	0	NA	Intergenic	MIR|SINE|MIR	19800	NM_001025434	1728	Hs.406515	NM_000903	ENSG00000181019	NQO1	DHQU|DIA4|DTD|NMOR1|NMORI|QR1	NAD(P)H quinone dehydrogenase 1	protein-coding	0.003067	0.379205	215(TGGCACAGTAAGTGCC,-,0.00),216(GGCACAGTAAGTGCCT,+,0.00)
chunk0110_150_1	chr20	13705091	13705445	+	0	NA	Intergenic	L1MD|LINE|L1	-66332	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.000000	0.323944	
chunk0132_345_1	chr3	161356352	161356704	+	0	NA	intron (NM_001040100, intron 2 of 2)	intron (NM_001040100, intron 2 of 2)	15555	NM_001040100	165679	Hs.369104	NM_145035	ENSG00000196542	SPTSSB	ADMP|C3orf57|SSSPTB	serine palmitoyltransferase small subunit B	protein-coding	0.002841	0.334278	
chunk0188_338_1	chr8	17782999	17783599	+	0	NA	intron (NM_001001924, intron 1 of 14)	intron (NM_001001924, intron 1 of 14)	17618	NM_001001925	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.013333	0.467554	
chunk0187_246_1	chr7	153032449	153033015	+	0	NA	Intergenic	L1MEd|LINE|L1	272983	NR_073001									0.003534	0.345679	238(AAGCACACTGAGTCCA,-,0.00),239(AGCACACTGAGTCCAG,+,0.00)
chunk0101_313_1	chr2	135201773	135201972	+	0	NA	intron (NM_001286568, intron 20 of 20)	intron (NM_001286568, intron 20 of 20)	149607	NM_001172435	22930	Hs.306327	NM_012233	ENSG00000115839	RAB3GAP1	P130|RAB3GAP|RAB3GAP130|WARBM1	RAB3 GTPase activating protein catalytic subunit 1	protein-coding	0.010050	0.405000	
chunk0103_301_1	chr2	166654913	166655356	+	0	NA	Intergenic	MER4D1|LTR|ERV1	-168163	NM_002976	6332	Hs.596087	NM_002976	ENSG00000136546	SCN7A	NaG|Nav2.1|Nav2.2|SCN6A	sodium voltage-gated channel alpha subunit 7	protein-coding	0.000000	0.362613	
chunk0029_272_1	chr10	103297456	103297818	+	0	NA	Intergenic	Intergenic	20474	NM_032727	9118	Hs.500916	NM_032727	ENSG00000148798	INA	NEF5|NF-66|TXBP-1	internexin neuronal intermediate filament protein alpha	protein-coding	0.005525	0.349862	
chunk0203_74_1	chr9	83707941	83708332	+	0	NA	5' UTR (NM_013438, exon 1 of 11)	5' UTR (NM_013438, exon 1 of 11)	117	NM_013438	29979	Hs.9589	NM_013438	ENSG00000135018	UBQLN1	DA41|DSK2|PLIC-1|UBQN|XDRP1	ubiquilin 1	protein-coding	0.094629	0.612245	
chunk0106_264_1	chr2	203722128	203722847	+	0	NA	intron (NM_001243078, intron 1 of 2)	intron (NM_001243078, intron 1 of 2)	16012	NM_001243078	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.005563	0.379167	
chunk0067_73_1	chr15	41337648	41337847	+	0	NA	intron (NM_001243144, intron 1 of 8)	L2a|LINE|L2	5053	NM_001301136	51203	Hs.615092	NM_016359	ENSG00000137804	NUSAP1	ANKT|BM037|LNP|NUSAP|PRO0310p1|Q0310|SAPL	nucleolar and spindle associated protein 1	protein-coding	0.005025	0.485000	81(AGGCACTTTCTGTTCT,-,0.00),82(GGCACTTTCTGTTCTA,+,0.00)
chunk0123_51_1	chr3	41130942	41131194	+	0	NA	Intergenic	Intergenic	-68383	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.007937	0.442688	
chunk0127_282_1	chr3	97839064	97839575	+	0	NA	intron (NM_153605, intron 1 of 21)	(TTTTA)n|Simple_repeat|Simple_repeat	17279	NM_153605	131544	Hs.733378	NM_153605	ENSG00000080200	CRYBG3	DKFZp667G2110|vlAKAP	crystallin beta-gamma domain containing 3	protein-coding	0.001957	0.335938	
chunk0131_108_1	chr3	143912860	143913059	+	0	NA	Intergenic	L1MA2|LINE|L1	-58839	NM_173552	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.360000	
chunk0124_433_1	chr3	61232509	61233295	+	0	NA	intron (NM_001166243, intron 1 of 9)	L1ME4b|LINE|L1	18557	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.002545	0.374841	388(CAGAACAATGTGTATT,-,0.00)
chunk0010_338_1	chr1	118503264	118503740	+	0	NA	Intergenic	Intergenic	-318277	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.000000	0.381551	
chunk0209_435_1	chrX	63282175	63282582	+	0	NA	Intergenic	MER83|LTR|ERV1	68961	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.004914	0.397059	
chunk0016_134_1	chr1	197042804	197043488	+	0	NA	intron (NM_001994, intron 10 of 11)	L1MEg|LINE|L1	24121	NM_001994	2165	Hs.435782	NM_001994	ENSG00000143278	F13B	FXIIIB	coagulation factor XIII B chain	protein-coding	0.002924	0.370803	
chunk0205_394_1	chr9	114503749	114503948	+	0	NA	promoter-TSS (NM_001083885)	promoter-TSS (NM_001083885)	-633	NM_001083885	25861	Hs.93836	NM_015404	ENSG00000095397	WHRN	CIP98|DFNB31|PDZD7B|USH2D|WI	whirlin	protein-coding	0.005025	0.400000	
chunk0029_334_1	chr10	104926843	104927207	+	0	NA	intron (NM_014978, intron 3 of 26)	intron (NM_014978, intron 3 of 26)	-260809	NR_104028	100505890	Hs.348526	NR_104028	ENSG00000226387	SORCS3-AS1	-	SORCS3 antisense RNA 1	ncRNA	0.005495	0.271233	
chunk0187_375_1	chr7	157571313	157571709	+	0	NA	intron (NM_001308268, intron 19 of 22)	intron (NM_001308268, intron 19 of 22)	2911	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.022727	0.314861	
chunk0117_309_1	chr22	24578811	24579432	+	0	NA	Intergenic	MER74B|LTR|ERVL	-4629	NM_013430	2678	Hs.595809	NM_005265	ENSG00000100031	GGT1	CD224|D22S672|D22S732|GGT|GGT 1|GGTD|GTG	gamma-glutamyltransferase 1	protein-coding	0.004831	0.403537	
chunk0014_62_1	chr1	175903791	175904047	+	0	NA	Intergenic	MER67C|LTR|ERV1	26576	NR_125964	101928751		NR_125964	ENSG00000224718	LINC01657	-	long intergenic non-protein coding RNA 1657	ncRNA	0.003906	0.416342	
chunk0201_22_1	chr9	33161744	33161977	+	0	NA	intron (NM_001497, intron 1 of 5)	intron (NM_001497, intron 1 of 5)	-5088	NR_108109	101929639	Hs.545818	NR_108108	ENSG00000233554	B4GALT1-AS1	-	B4GALT1 antisense RNA 1	ncRNA	0.004292	0.461538	
chunk0025_357_1	chr10	58363097	58363604	+	0	NA	intron (NM_003338, intron 3 of 6)	intron (NM_003338, intron 3 of 6)	-21793	NR_073073	7019	Hs.594250	NM_003201	ENSG00000108064	TFAM	MTDPS15|MTTF1|MTTFA|TCF6|TCF6L1|TCF6L2|TCF6L3	transcription factor A, mitochondrial	protein-coding	0.009862	0.320866	
chunk0029_263_1	chr10	103121360	103121757	+	0	NA	intron (NM_001134373, intron 3 of 17)	intron (NM_001134373, intron 3 of 17)	71748	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.005038	0.402010	
chunk0212_29_1	chrY	10907570	10907862	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	996918	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.013699	0.457338	
chunk0175_264_1	chr7	7438792	7439257	+	0	NA	intron (NM_001037763, intron 21 of 34)	intron (NM_001037763, intron 21 of 34)	96805	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.012903	0.452790	
chunk0069_170_1	chr15	62788171	62789001	+	0	NA	intron (NM_015059, intron 42 of 55)	MIRb|SINE|MIR	-35371	NR_029709	406965		NR_029709	ENSG00000211137	MIR190A	MIR190|MIRN190|hsa-mir-190a|miR-190|mir-190a	microRNA 190a	ncRNA	0.012048	0.454874	185(TAAAACAAAATGTTCT,-,0.00),186(AAAACAAAATGTTCTG,+,0.00)
chunk0051_326_1	chr12	120086969	120087318	+	0	NA	intron (NM_207311, intron 7 of 8)	CpG	29696	NM_001167606	11021	Hs.524788	NM_006861	ENSG00000111737	RAB35	H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding	0.091691	0.682857	
chunk0185_214_1	chr7	128785565	128786362	+	0	NA	Intergenic	L1MEd|LINE|L1	-5447	NM_001201372	64753	Hs.521178	NM_022742	ENSG00000128596	CCDC136	NAG6	coiled-coil domain containing 136	protein-coding	0.006274	0.373434	
chunk0036_174_1	chr11	62587563	62588269	+	0	NA	intron (NM_022830, intron 2 of 8)	intron (NM_022830, intron 2 of 8)	3721	NM_022830	64852	Hs.728983	NM_022830	ENSG00000149016	TUT1	PAPD2|RBM21|STARPAP|TENT1|TUTase|URLC6	terminal uridylyl transferase 1, U6 snRNA-specific	protein-coding	0.000000	0.408769	352(AAGGACAGGGTGTTCT,-,0.00),353(AGGACAGGGTGTTCTA,+,0.00)
chunk0030_378_1	chr10	119284737	119285353	+	0	NA	intron (NM_005308, intron 1 of 15)	L5|LINE|RTE-X	77360	NM_005308	2869	Hs.524625	NM_005308	ENSG00000198873	GRK5	FP2025|GPRK5	G protein-coupled receptor kinase 5	protein-coding	0.016234	0.554295	285(AGGTACGATGTGTTCC,-,0.00),286(GGTACGATGTGTTCCT,+,0.00)
chunk0150_422_1	chr5	40374849	40375322	+	0	NA	Intergenic	MIR3|SINE|MIR	-304845	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.012685	0.400844	203(CGAAACAGTCTGTTCC,-,0.00),204(GAAACAGTCTGTTCCT,+,0.00)
chunk0011_114_1	chr1	146317852	146318156	+	0	NA	Intergenic	Intergenic	20187	NR_002212									0.003289	0.396721	
chunk0197_428_1	chr8	127428519	127428981	+	0	NA	intron (NR_117100, intron 4 of 5)	MIRb|SINE|MIR	13138	NM_001159542	5462	Hs.450254	NM_001159542	ENSG00000212993	POU5F1B	OCT4-PG1|OCT4PG1|OTF3C|OTF3P1|POU5F1P1|POU5F1P4|POU5FLC20|POU5FLC8	POU class 5 homeobox 1B	protein-coding	0.002165	0.397408	
chunk0167_180_1	chr6	63806156	63807112	+	0	NA	intron (NM_001142800, intron 36 of 42)	intron (NM_001142800, intron 36 of 42)	160108	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.006276	0.367816	618(TTGAACAAACTGTGCT,-,0.00),619(TGAACAAACTGTGCTT,+,0.00)
chunk0138_183_1	chr4	37968800	37969350	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	8640	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.005455	0.435572	
chunk0054_383_1	chr13	50223016	50223447	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	51213	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.002320	0.400463	
chunk0211_236_1	chrX	119003460	119003717	+	0	NA	intron (NM_001031855, intron 5 of 10)	L1ME3B|LINE|L1	27256	NM_001289109	79836	Hs.144266	NM_024778	ENSG00000175556	LONRF3	RNF127	LON peptidase N-terminal domain and ring finger 3	protein-coding	0.011673	0.403101	
chunk0082_152_1	chr17	55588426	55588667	+	0	NA	Intergenic	L2b|LINE|L2	134318	NM_018286	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.000000	0.367769	
chunk0156_152_1	chr5	107381174	107381388	+	0	NA	exon (NM_001962, exon 5 of 5)	exon (NM_001962, exon 5 of 5)	289614	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.042056	0.511628	
chunk0152_449_1	chr5	66365675	66366363	+	0	NA	Intergenic	Intergenic	145585	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.007267	0.445573	335(GGAGACAGGGTGTTCC,-,0.00),336(GAGACAGGGTGTTCCA,+,0.00)
chunk0137_452_1	chr4	29229945	29230339	+	0	NA	Intergenic	L1PA7|LINE|L1	410560	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.015228	0.541772	
chunk0127_91_1	chr3	89852493	89853270	+	0	NA	Intergenic	Intergenic	745357	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.006435	0.332905	
chunk0197_354_1	chr8	125579684	125580460	+	0	NA	Intergenic	L2a|LINE|L2	147863	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.012887	0.495495	
chunk0027_34_1	chr10	72331589	72331927	+	0	NA	Intergenic	Intergenic	23391	NM_001002762	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.020710	0.563422	
chunk0044_427_1	chr12	42034010	42034288	+	0	NA	Intergenic	MIR|SINE|MIR	110722	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.000000	0.362007	
chunk0050_419_1	chr12	109900122	109900622	+	0	NA	promoter-TSS (NM_001143852)	promoter-TSS (NM_001143852)	98	NM_001143852	84260	Hs.410924	NM_032300	ENSG00000139437	TCHP	TpMs	trichoplein keratin filament binding	protein-coding	0.106000	0.654691	
chunk0063_351_1	chr14	85501603	85502343	+	0	NA	Intergenic	Intergenic	-28171	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.002703	0.356275	
chunk0083_370_1	chr17	71111551	71111809	+	0	NA	intron (NR_104152, intron 3 of 3)	intron (NR_104152, intron 3 of 3)	90499	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.003876	0.366795	
chunk0102_22_1	chr2	141530480	141530785	+	0	NA	intron (NM_018557, intron 2 of 90)	L2a|LINE|L2	601069	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.006557	0.369281	
chunk0136_444_1	chr3	197941694	197942217	+	0	NA	intron (NM_032263, intron 4 of 11)	intron (NM_032263, intron 4 of 11)	7970	NM_001134435	84223	Hs.591675	NM_032263	ENSG00000114473	IQCG	CFAP122|DRC9	IQ motif containing G	protein-coding	0.009560	0.383588	
chunk0171_357_1	chr6	130602496	130602716	+	0	NA	Intergenic	Intergenic	165489	NM_052913	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.018182	0.384615	
chunk0157_144_1	chr5	117560690	117561290	+	0	NA	intron (NR_046089, intron 5 of 5)	intron (NR_046089, intron 5 of 5)	145478	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.005000	0.319468	
chunk0135_340_1	chr3	190326868	190327297	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-4636	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.009324	0.376744	
chunk0120_437_1	chr3	13517255	13517571	+	0	NA	Intergenic	Intergenic	-31712	NM_001998	2199	Hs.198862	NM_001998	ENSG00000163520	FBLN2	-	fibulin 2	protein-coding	0.041139	0.675079	198(GGGAACAGGCTGTCCC,-,0.00),199(GGAACAGGCTGTCCCG,+,0.00)
chunk0016_48_1	chr1	193218581	193219260	+	0	NA	intron (NM_024529, intron 13 of 16)	L1PA15|LINE|L1	-32307	NM_003783	8707	Hs.518834	NM_003783	ENSG00000162630	B3GALT2	BETA3GALT2|GLCT2|beta3Gal-T2	beta-1,3-galactosyltransferase 2	protein-coding	0.004418	0.377941	
chunk0003_45_1	chr1	30735151	30735381	+	0	NA	intron (NM_006762, intron 6 of 7)	intron (NM_006762, intron 6 of 7)	3966	NR_039616	100616164		NR_039616	ENSG00000264773	MIR4420	mir-4420	microRNA 4420	ncRNA	0.021739	0.558442	128(CAGGTCAGGCTGTGCT,-,0.00),129(AGGTCAGGCTGTGCTT,+,0.00)
chunk0044_24_1	chr12	27224150	27224365	+	0	NA	Intergenic	L1MC1|LINE|L1	-19888	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.004651	0.361111	
chunk0007_93_1	chr1	78627215	78627800	+	0	NA	intron (NM_006820, intron 1 of 8)	MER58A|DNA|hAT-Charlie	7125	NM_006820	10964	Hs.744918	NM_006820	ENSG00000137959	IFI44L	C1orf29|GS3686	interferon induced protein 44 like	protein-coding	0.001709	0.283276	
chunk0111_29_1	chr20	22066452	22066796	+	0	NA	intron (NR_038394, intron 1 of 3)	intron (NR_038394, intron 1 of 3)	12534	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.005814	0.443478	118(AAGCACAAAGTGTGCT,-,0.00),119(AGCACAAAGTGTGCTT,+,0.00)
chunk0177_368_1	chr7	26735373	26735660	+	0	NA	intron (NM_001303468, intron 6 of 12)	intron (NM_001303468, intron 6 of 12)	96431	NM_001302625									0.003484	0.336806	
chunk0021_264_1	chr1	243553240	243553706	+	0	NA	intron (NM_181690, intron 9 of 13)	intron (NM_181690, intron 9 of 13)	207297	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.004292	0.334047	
chunk0085_19_1	chr18	364351	364794	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	-96513	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.000000	0.427928	158(GGGCACAGAGTGAACT,-,0.00),159(GGCACAGAGTGAACTG,+,0.00)
chunk0056_293_1	chr13	90532690	90533414	+	0	NA	intron (NR_120414, intron 5 of 5)	intron (NR_120414, intron 5 of 5)	39764	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.002762	0.376552	427(GAGAACAAGCTGTACA,-,0.00),428(AGAACAAGCTGTACAA,+,0.00)
chunk0026_313_1	chr10	68065635	68066574	+	0	NA	intron (NM_022079, intron 3 of 25)	intron (NM_022079, intron 3 of 25)	9242	NM_015601	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.005325	0.358511	
chunk0112_236_1	chr20	41213490	41213866	+	0	NA	intron (NM_015035, intron 2 of 3)	intron (NM_015035, intron 2 of 3)	44655	NR_106931	102466912		NR_106931	ENSG00000276169	MIR6871	hsa-mir-6871	microRNA 6871	ncRNA	0.002660	0.472149	
chunk0210_144_1	chrX	75092864	75093322	+	0	NA	intron (NM_001271699, intron 3 of 14)	L1MC2|LINE|L1	63247	NM_001271698	22	Hs.370480	NM_004299	ENSG00000131269	ABCB7	ABC7|ASAT|Atm1p|EST140535	ATP binding cassette subfamily B member 7	protein-coding	0.002183	0.346405	
chunk0012_76_1	chr1	155800941	155801316	+	0	NA	intron (NM_001282858, intron 11 of 31)	(A)n|Simple_repeat|Simple_repeat	-17296	NR_132767	106633816		NR_132767		SCARNA26B	-	small Cajal body-specific RNA 26B	ncRNA	0.005333	0.356383	77(TAGAACTATCTGTCCT,-,0.00),78(AGAACTATCTGTCCTT,+,0.00),193(AAGAACTCTCTGTCCT,-,0.00),194(AGAACTCTCTGTCCTG,+,0.00)
chunk0179_410_1	chr7	51640459	51640658	+	0	NA	Intergenic	Intergenic	-323740	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.015075	0.435000	
chunk0056_4_1	chr13	76993498	76994068	+	0	NA	intron (NM_006493, intron 1 of 3)	intron (NM_006493, intron 1 of 3)	1859	NM_006493	1203	Hs.30213	NM_006493	ENSG00000102805	CLN5	-	CLN5 intracellular trafficking protein	protein-coding	0.012281	0.367776	
chunk0206_271_1	chr9	124077920	124078191	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	66445	NM_004789	9355	Hs.696425	NM_004789	ENSG00000106689	LHX2	LH2|hLhx2	LIM homeobox 2	protein-coding	0.003690	0.481618	161(GGGGACAGCCTGGCCT,-,0.00),162(GGGACAGCCTGGCCTT,+,0.00)
chunk0089_151_1	chr18	59065518	59066145	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	30152	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.009569	0.348726	
chunk0196_220_1	chr8	107417675	107418320	+	0	NA	intron (NM_001146, intron 1 of 8)	intron (NM_001146, intron 1 of 8)	80058	NM_001199859	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.007752	0.351393	
chunk0019_113_1	chr1	225208557	225209114	+	0	NA	intron (NM_001373, intron 40 of 83)	L1MCc|LINE|L1	219278	NM_002296	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.000000	0.331541	
chunk0037_1_1	chr11	68735470	68735913	+	0	NA	TTS (NM_001039656)	TTS (NM_001039656)	15829	NM_001039656	9633	Hs.145932	NM_004923	ENSG00000132749	TESMIN	CXCDC2|MTL5|MTLT	testis expressed metallothionein like protein	protein-coding	0.011287	0.457207	
chunk0052_179_1	chr13	24203640	24204137	+	0	NA	intron (NM_153023, intron 1 of 11)	L2b|LINE|L2	41472	NR_031753	100313842		NR_031753	ENSG00000252695	MIR2276	-	microRNA 2276	ncRNA	0.004024	0.385542	
chunk0090_261_1	chr18	74453155	74453459	+	0	NA	intron (NM_001044369, intron 1 of 3)	intron (NM_001044369, intron 1 of 3)	3961	NM_001044369	125704	Hs.371690	NM_001044369	ENSG00000187773	DIPK1C	C18orf51|FAM69C	divergent protein kinase domain 1C	protein-coding	0.019737	0.455738	
chunk0186_179_1	chr7	139447148	139447383	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-19739	NR_033999	100129148	Hs.744449	NR_033999		LOC100129148	-	uncharacterized LOC100129148	ncRNA	0.017021	0.368644	
chunk0068_71_1	chr15	51924571	51925366	+	0	NA	promoter-TSS (NR_109775)	promoter-TSS (NR_109775)	-848	NR_109775	100422556	Hs.664788	NR_109775		LOC100422556	-	LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene	pseudo	0.011321	0.438442	
chunk0002_166_1	chr1	18464327	18464816	+	0	NA	Intergenic	Intergenic	-16359	NM_152375	127707	Hs.406913	NM_152375	ENSG00000179023	KLHDC7A	-	kelch domain containing 7A	protein-coding	0.016360	0.520408	
chunk0195_258_1	chr8	97940481	97940869	+	0	NA	intron (NM_030583, intron 3 of 18)	intron (NM_030583, intron 3 of 18)	71592	NM_030583	4147	Hs.189445	NM_002380	ENSG00000132561	MATN2	-	matrilin 2	protein-coding	0.002577	0.313625	
chunk0035_219_1	chr11	45062919	45063715	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-30696	NR_046338									0.008794	0.381430	
chunk0116_105_1	chr21	35416649	35417155	+	0	NA	intron (NR_073512, intron 2 of 2)	intron (NR_073512, intron 2 of 2)	163862	NR_073512	100506403	Hs.536609	NR_073512	ENSG00000159216	LOC100506403	-	uncharacterized LOC100506403	ncRNA	0.011858	0.449704	
chunk0182_4_1	chr7	90902463	90902968	+	0	NA	intron (NM_001287136, intron 6 of 13)	L1MA4A|LINE|L1	192899	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.007921	0.341897	
chunk0145_231_1	chr4	148418930	148419353	+	0	NA	intron (NM_000901, intron 2 of 8)	intron (NM_000901, intron 2 of 8)	23379	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.007092	0.382075	
chunk0129_305_1	chr3	123680705	123680982	+	0	NA	intron (NM_053025, intron 20 of 33)	(TTGT)n|Simple_repeat|Simple_repeat	-8801	NR_046629	100873940	Hs.667316	NR_046629	ENSG00000250174	MYLK-AS2	-	MYLK antisense RNA 2	ncRNA	0.007220	0.384892	141(AAACACAGCATGTGCT,-,0.00),142(AACACAGCATGTGCTG,+,0.00)
chunk0060_1_1	chr14	39024075	39024480	+	0	NA	Intergenic	Intergenic	78956	NM_006364	10484	Hs.272927	NM_006364	ENSG00000100934	SEC23A	CLSD|hSec23A	Sec23 homolog A, coat complex II component	protein-coding	0.004938	0.391626	113(GTGCACTGAATGTTCT,-,0.00),114(TGCACTGAATGTTCTT,+,0.00)
chunk0150_288_1	chr5	37249093	37249292	+	0	NA	intron (NM_023073, intron 1 of 51)	CpG	236	NM_023073	65250	Hs.586199	NM_023073	ENSG00000197603	CPLANE1	C5orf42|Hug|JBTS17|OFD6	ciliogenesis and planar polarity effector 1	protein-coding	0.115578	0.720000	
chunk0049_421_1	chr12	97694587	97694812	+	0	NA	Intergenic	L1PA5|LINE|L1	58899	NR_077241	643711	Hs.585557	NR_077240	ENSG00000257501	LOC643711	-	platelet activating factor acetylhydrolase 1b catalytic subunit 2 pseudogene	pseudo	0.000000	0.362832	
chunk0010_399_1	chr1	119508939	119509138	+	0	NA	intron (NM_000862, intron 2 of 3)	intron (NM_000862, intron 2 of 3)	1835	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.000000	0.400000	
chunk0099_334_1	chr2	100055594	100055885	+	0	NA	intron (NM_001025108, intron 2 of 23)	MER58A|DNA|hAT-Charlie	49844	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.006873	0.397260	
chunk0139_99_1	chr4	49709155	49711820	+	0	NA	Intergenic	SAR|Satellite|Satellite	723845	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.003752	0.234434	
chunk0001_342_1	chr1	9746554	9747145	+	0	NA	intron (NM_001009566, intron 7 of 18)	MIR|SINE|MIR	-59275	NR_126367	101929074	Hs.661762	NR_126366	ENSG00000231789	PIK3CD-AS2	-	PIK3CD antisense RNA 2	ncRNA	0.018613	0.489865	
chunk0194_433_1	chr8	92486158	92486842	+	0	NA	Intergenic	LTR40a|LTR|ERVL	168994	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.004386	0.407299	
chunk0032_368_1	chr11	10927602	10927845	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	69506	NR_034137	729013	Hs.726427	NR_034137	ENSG00000247271	ZBED5-AS1	-	ZBED5 antisense RNA 1	ncRNA	0.004115	0.475410	
chunk0065_332_1	chr14	103259967	103260607	+	0	NA	Intergenic	LTR66|LTR|ERVL	-71259	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.021875	0.474259	
chunk0002_416_1	chr1	27608707	27609015	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-5367	NM_001029882	27245	Hs.469280	NM_001029882	ENSG00000126705	AHDC1	MRD25	AT-hook DNA binding motif containing 1	protein-coding	0.012987	0.511327	
chunk0136_301_1	chr3	195110845	195111158	+	0	NA	intron (NM_001308069, intron 3 of 3)	MLT1C|LTR|ERVL-MaLR	16413	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.028754	0.541401	
chunk0188_399_1	chr8	18691421	18691798	+	0	NA	intron (NM_015310, intron 9 of 15)	intron (NM_015310, intron 9 of 15)	117286	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.005305	0.367725	
chunk0008_354_1	chr1	96298587	96298924	+	0	NA	intron (NR_110693, intron 5 of 5)	L1M4|LINE|L1	75370	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.005935	0.263314	
chunk0164_456_1	chr6	28443328	28443537	+	0	NA	promoter-TSS (NM_001012455)	promoter-TSS (NM_001012455)	70	NM_001012455	222696	Hs.721841	NM_001012455	ENSG00000187987	ZSCAN23	ZNF390|ZNF453|dJ29K1.3|dJ29K1.3.1	zinc finger and SCAN domain containing 23	protein-coding	0.081340	0.600000	
chunk0172_1_1	chr6	132286554	132287488	+	0	NA	Intergenic	L1MD2|LINE|L1	114513	NM_015529	26002	Hs.6909	NM_015529	ENSG00000079931	MOXD1	MOX|PRO5780|dJ248E1.1	monooxygenase DBH like 1	protein-coding	0.004283	0.371123	
chunk0204_316_1	chr9	100425702	100426228	+	0	NA	Intergenic	L1MB5|LINE|L1	-1248	NM_001198807	91283	Hs.530272	NM_080655	ENSG00000066697	MSANTD3	C9orf30|L8	Myb/SANT DNA binding domain containing 3	protein-coding	0.005703	0.379507	
chunk0100_446_1	chr2	120934958	120935347	+	0	NA	intron (NM_005270, intron 2 of 12)	intron (NM_005270, intron 2 of 12)	137861	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.023136	0.530769	
chunk0079_451_1	chr17	20291692	20292282	+	0	NA	intron (NM_001033553, intron 12 of 14)	intron (NM_001033553, intron 12 of 14)	-29187	NR_023380	348254	Hs.462475	NR_023380		CCDC144CP	CCDC144C	coiled-coil domain containing 144C, pseudogene	pseudo	0.015254	0.497462	
chunk0054_21_1	chr13	40648086	40648533	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	18288	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.002237	0.354911	
chunk0026_306_1	chr10	67981377	67981735	+	0	NA	intron (NM_022079, intron 15 of 25)	L1MA2|LINE|L1	29327	NR_131184	100009667		NR_131184		POU5F1P5	Oct4-pg5	POU class 5 homeobox 1 pseudogene 5	pseudo	0.005587	0.398329	
chunk0024_39_1	chr10	33472090	33472498	+	0	NA	Intergenic	L1MA2|LINE|L1	-137389	NM_001024628	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.004902	0.374083	
chunk0134_273_1	chr3	179571654	179572124	+	0	NA	intron (NM_177989, intron 3 of 13)	MER68|LTR|ERVL	9009	NM_178042	86	Hs.435326	NM_004301	ENSG00000136518	ACTL6A	ACTL6|ARPN-BETA|Arp4|BAF53A|INO80K	actin like 6A	protein-coding	0.004255	0.394904	
chunk0019_463_1	chr1	231513701	231513944	+	0	NA	Intergenic	L1ME3G|LINE|L1	-14831	NR_028399	100303453	Hs.13318	NR_028393	ENSG00000270106	TSNAX-DISC1	-	TSNAX-DISC1 readthrough (NMD candidate)	ncRNA	0.000000	0.286885	123(TAGTACATACAGTTCT,-,0.00),124(AGTACATACAGTTCTA,+,0.00)
chunk0001_220_1	chr1	8058378	8058659	+	0	NA	Intergenic	Intergenic	-32185	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.014235	0.478723	
chunk0008_428_1	chr1	99345641	99345840	+	0	NA	Intergenic	MIRb|SINE|MIR	81448	NM_001166252	9890	Hs.13245	NM_014839	ENSG00000117600	PLPPR4	LPPR4|LPR4|PHP1|PRG-1|PRG1	phospholipid phosphatase related 4	protein-coding	0.005025	0.365000	
chunk0065_274_1	chr14	102056988	102057382	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	29990	NM_005348	3320	Hs.525600	NM_005348	ENSG00000080824	HSP90AA1	EL52|HEL-S-65p|HSP86|HSP89A|HSP90A|HSP90N|HSPC1|HSPCA|HSPCAL1|HSPCAL4|HSPN|Hsp103|Hsp89|Hsp90|LAP-2|LAP2	heat shock protein 90 alpha family class A member 1	protein-coding	0.058376	0.567089	
chunk0019_106_1	chr1	225036716	225037140	+	0	NA	intron (NM_001373, intron 11 of 83)	L1PA14|LINE|L1	107267	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.000000	0.367059	
chunk0173_340_1	chr6	149019355	149019703	+	0	NA	intron (NM_005715, intron 6 of 7)	intron (NM_005715, intron 6 of 7)	-54845	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.008621	0.406877	
chunk0154_194_1	chr5	80229457	80229871	+	0	NA	intron (NM_178276, intron 1 of 12)	intron (NM_178276, intron 1 of 12)	26418	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.002415	0.356627	
chunk0042_422_1	chr12	11842246	11842609	+	0	NA	intron (NM_001987, intron 3 of 7)	(AC)n|Simple_repeat|Simple_repeat	192573	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.008264	0.475275	
chunk0198_93_1	chr8	130302292	130302618	+	0	NA	intron (NM_001247996, intron 4 of 30)	intron (NM_001247996, intron 4 of 30)	-5922	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.006135	0.422018	
chunk0169_388_1	chr6	107881611	107881844	+	0	NA	intron (NM_007214, intron 17 of 20)	L2c|LINE|L2	-57410	NM_001286408	256380	Hs.486109	NM_198081	ENSG00000146285	SCML4	dJ47M23.1	Scm polycomb group protein like 4	protein-coding	0.000000	0.393162	
chunk0122_436_1	chr3	39290847	39291114	+	0	NA	Intergenic	MER4C|LTR|ERV1	-9245	NM_001171174	1524	Hs.78913	NM_001337	ENSG00000168329	CX3CR1	CCRL1|CMKBRL1|CMKDR1|GPR13|GPRV28|V28	C-X3-C motif chemokine receptor 1	protein-coding	0.018727	0.429104	
chunk0088_237_1	chr18	48515413	48515690	+	0	NA	Intergenic	Intergenic	-23505	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.007220	0.517986	
chunk0188_77_1	chr8	8406658	8407952	+	0	NA	Intergenic	Intergenic	-25471	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.007728	0.372973	
chunk0207_239_1	chr9	131976375	131976933	+	0	NA	intron (NM_001253881, intron 3 of 6)	intron (NM_001253881, intron 3 of 6)	103233	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.003584	0.354204	
chunk0032_431_1	chr11	12248094	12248888	+	0	NA	intron (NM_001282664, intron 20 of 25)	intron (NM_001282664, intron 20 of 25)	-38409	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.010076	0.525786	
chunk0063_249_1	chr14	82503489	82503848	+	0	NA	Intergenic	Intergenic	-880607	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.002786	0.361111	
chunk0143_252_1	chr4	115054174	115054581	+	0	NA	intron (NM_022569, intron 2 of 13)	intron (NM_022569, intron 2 of 13)	59499	NM_022569	64579	Hs.591700	NM_022569	ENSG00000138653	NDST4	N-HSST|N-HSST 4|NDST-4|NHSST4	N-deacetylase and N-sulfotransferase 4	protein-coding	0.000000	0.276961	
chunk0084_157_1	chr17	76914974	76915338	+	0	NA	intron (NM_198955, intron 7 of 15)	L2|LINE|L2	42509	NM_198955	146664	Hs.144531	NM_144677	ENSG00000167889	MGAT5B	GnT-IX|GnT-VB	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B	protein-coding	0.013736	0.512329	
chunk0047_29_1	chr12	65891924	65892432	+	0	NA	intron (NM_001300918, intron 3 of 4)	intron (NM_001300918, intron 3 of 4)	-10011	NM_001292024									0.019685	0.479371	
chunk0104_442_1	chr2	181496669	181497320	+	0	NA	intron (NM_000885, intron 14 of 27)	intron (NM_000885, intron 14 of 27)	40102	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.006144	0.361963	272(AGGTACACAATGAGCC,-,0.00),273(GGTACACAATGAGCCT,+,0.00),298(AGGTACACAATGAGCC,-,0.00),299(GGTACACAATGAGCCT,+,0.00)
chunk0200_312_1	chr9	23229354	23229818	+	0	NA	Intergenic	Intergenic	442813	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.006466	0.309677	191(GAGATCAACATGTTCT,-,0.00),192(AGATCAACATGTTCTG,+,0.00)
chunk0091_333_1	chr19	14103041	14103439	+	0	NA	intron (NM_001304349, intron 3 of 9)	L2b|LINE|L2	5150	NM_001304349	5566	Hs.631630	NM_002730	ENSG00000072062	PRKACA	PKACA|PPNAD4	protein kinase cAMP-activated catalytic subunit alpha	protein-coding	0.012563	0.566416	
chunk0010_77_1	chr1	113255711	113256129	+	0	NA	Intergenic	Intergenic	-49667	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.011962	0.415274	
chunk0203_450_1	chr9	91456865	91457075	+	0	NA	Intergenic	L1ME1|LINE|L1	-32344	NM_001290000	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.000000	0.293839	
chunk0110_237_1	chr20	16303316	16303896	+	0	NA	intron (NM_001199865, intron 24 of 24)	intron (NM_001199865, intron 24 of 24)	269828	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.005172	0.376936	
chunk0045_102_1	chr12	46157247	46157802	+	0	NA	Intergenic	Intergenic	108971	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.000000	0.390288	
chunk0163_310_1	chr6	14673213	14673422	+	0	NA	Intergenic	Intergenic	-387863	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.004785	0.447619	
chunk0173_222_1	chr6	145928414	145928613	+	0	NA	intron (NM_173082, intron 14 of 29)	intron (NM_173082, intron 14 of 29)	35584	NM_001042683	257218	Hs.723297	NM_173082	ENSG00000146414	SHPRH	bA545I5.2	SNF2 histone linker PHD RING helicase	protein-coding	0.000000	0.260000	
chunk0050_169_1	chr12	103802055	103802284	+	0	NA	intron (NM_001031701, intron 4 of 13)	intron (NM_001031701, intron 4 of 13)	39028	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.008734	0.495652	
chunk0015_66_1	chr1	184686378	184686943	+	0	NA	Intergenic	Intergenic	68247	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.007080	0.434629	129(AAGTACAGTATGTATT,-,0.00),474(GAGCACATTCAGTTCT,-,0.00),475(AGCACATTCAGTTCTG,+,0.00)
chunk0061_356_1	chr14	63710069	63710275	+	0	NA	intron (NM_030791, intron 1 of 2)	L1M5|LINE|L1	17923	NM_030791	81537	Hs.24678	NM_030791	ENSG00000126821	SGPP1	SPP-1|SPPase1	sphingosine-1-phosphate phosphatase 1	protein-coding	0.004854	0.333333	
chunk0121_49_1	chr3	15565156	15565572	+	0	NA	intron (NR_104315, intron 12 of 14)	intron (NR_104315, intron 12 of 14)	-35988	NM_001281723	686	Hs.444197	NM_001281723	ENSG00000169814	BTD	-	biotinidase	protein-coding	0.002404	0.364508	
chunk0109_95_1	chr20	2244462	2245223	+	0	NA	Intergenic	MER68-int|LTR|ERVL	37914	NM_001287682									0.013141	0.501312	453(GGGCACATGTTGTACC,-,0.00),454(GGCACATGTTGTACCC,+,0.00)
chunk0067_378_1	chr15	49032133	49032479	+	0	NA	intron (NM_001193489, intron 4 of 17)	intron (NM_001193489, intron 4 of 17)	14257	NM_001193489	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.000000	0.311239	
chunk0072_452_1	chr15	101724044	101724359	+	0	NA	exon (NM_152334, exon 1 of 19)	exon (NM_152334, exon 1 of 19)	241	NM_152334	123283	Hs.657163	NM_152334	ENSG00000185418	TARSL2	-	threonyl-tRNA synthetase like 2	protein-coding	0.126984	0.753165	
chunk0092_271_1	chr19	33302411	33302690	+	0	NA	promoter-TSS (NM_001285829)	promoter-TSS (NM_001285829)	14	NM_001287424	1050	Hs.76171	NM_004364	ENSG00000245848	CEBPA	C/EBP-alpha|CEBP	CCAAT enhancer binding protein alpha	protein-coding	0.161290	0.785714	
chunk0076_149_1	chr16	67177868	67178153	+	0	NA	exon (NM_001040715, exon 6 of 7)	exon (NM_001040715, exon 6 of 7)	4157	NM_003946	8996	Hs.513667	NM_003946	ENSG00000140939	NOL3	ARC|FCM|MYOCL1|MYP|NOP|NOP30	nucleolar protein 3	protein-coding	0.049123	0.636364	
chunk0036_53_1	chr11	59045575	59045908	+	0	NA	intron (NR_033853, intron 3 of 5)	L1ME3G|LINE|L1	12711	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.009009	0.389222	
chunk0073_219_1	chr16	10871689	10872066	+	0	NA	Intergenic	Intergenic	-5321	NM_000246	4261	Hs.592051	NM_000246	ENSG00000179583	CIITA	C2TA|CIITAIV|MHC2TA|NLRA	class II major histocompatibility complex transactivator	protein-coding	0.013263	0.550265	203(CAGGCCAGCCTGTTCC,-,0.00),204(AGGCCAGCCTGTTCCA,+,0.00)
chunk0148_447_1	chr4	190177808	190178198	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	4229	NM_001306068	100288687	Hs.728749	NM_001205218	ENSG00000260596	DUX4	DUX4L	double homeobox 4	protein-coding	0.010256	0.491049	
chunk0104_380_1	chr2	180314078	180314551	+	0	NA	Intergenic	Intergenic	-307261	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.004228	0.337553	
chunk0087_208_1	chr18	35962384	35962737	+	0	NA	Intergenic	Intergenic	-10065	NM_001201475	83608	Hs.37883	NM_031446	ENSG00000141428	C18orf21	HsT3108|PNAS-124|PNAS-131|XTP13	chromosome 18 open reading frame 21	protein-coding	0.005666	0.435028	
chunk0026_42_1	chr10	60817057	60817750	+	0	NA	Intergenic	Intergenic	38949	NM_001170407	983	Hs.732435	NM_001786	ENSG00000170312	CDK1	CDC2|CDC28A|P34CDC2	cyclin dependent kinase 1	protein-coding	0.008658	0.416427	314(AGGAACTGAAAGTTCC,-,0.00),315(GGAACTGAAAGTTCCC,+,0.00)
chunk0180_239_1	chr7	67504227	67504881	+	0	NA	Intergenic	Intergenic	168578	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.007645	0.396947	
chunk0044_90_1	chr12	28279967	28280188	+	0	NA	intron (NM_018318, intron 2 of 11)	intron (NM_018318, intron 2 of 11)	22877	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.000000	0.319820	161(TAGAACAGAAAGTACA,-,0.00),162(AGAACAGAAAGTACAC,+,0.00)
chunk0187_312_1	chr7	156460802	156461405	+	0	NA	Intergenic	Intergenic	-15515	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.014925	0.473510	
chunk0087_329_1	chr18	40009597	40009820	+	0	NA	Intergenic	Intergenic	-56578	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.004484	0.361607	
chunk0093_102_1	chr19	43455538	43455855	+	0	NA	Intergenic	Intergenic	9983	NM_014400	27076	Hs.631594	NM_014400	ENSG00000124466	LYPD3	C4.4A	LY6/PLAUR domain containing 3	protein-coding	0.012618	0.415094	
chunk0200_131_1	chr9	17486466	17486741	+	0	NA	intron (NM_017738, intron 24 of 25)	intron (NM_017738, intron 24 of 25)	-92351	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.003636	0.355072	
chunk0153_139_1	chr5	69020015	69020214	+	0	NA	intron (NR_130778, intron 1 of 3)	intron (NR_130778, intron 1 of 3)	9813	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.000000	0.395000	
chunk0196_348_1	chr8	114454473	114454672	+	0	NA	Intergenic	Intergenic	-1017559	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.005025	0.350000	138(CAGAACAAATTGTTCC,-,0.00),139(AGAACAAATTGTTCCT,+,0.00)
chunk0020_15_1	chr1	231707475	231707963	+	0	NA	intron (NM_001012957, intron 3 of 12)	intron (NM_001012957, intron 3 of 12)	80904	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.000000	0.359918	
chunk0190_144_1	chr8	30807455	30807982	+	0	NA	intron (NM_001009552, intron 1 of 6)	intron (NM_001009552, intron 1 of 6)	5118	NM_001009552	5516	Hs.491440	NM_004156	ENSG00000104695	PPP2CB	PP2Abeta|PP2CB	protein phosphatase 2 catalytic subunit beta	protein-coding	0.005693	0.375000	256(AGTCACAGAGTGTCCT,-,0.00),257(GTCACAGAGTGTCCTG,+,0.00)
chunk0092_114_1	chr19	24102840	24103318	+	0	NA	intron (NM_001278662, intron 2 of 4)	intron (NM_001278662, intron 2 of 4)	15919	NM_001278664	9534	Hs.434406	NM_004876	ENSG00000213096	ZNF254	BMZF-5|HD-ZNF1|ZNF539|ZNF91L	zinc finger protein 254	protein-coding	0.000000	0.342380	
chunk0208_327_1	chrX	24642558	24642938	+	0	NA	intron (NM_001163264, intron 1 of 7)	intron (NM_001163264, intron 1 of 7)	4590	NM_001163265	9468	Hs.660708	NM_004845	ENSG00000102230	PCYT1B	CCTB|CTB	phosphate cytidylyltransferase 1, choline, beta	protein-coding	0.007895	0.396325	
chunk0013_267_1	chr1	170115604	170115805	+	0	NA	Intergenic	Intergenic	-30343	NM_001136107	149281	Hs.553612	NM_001136107	ENSG00000203740	METTL11B	C1orf184|HOMT1B|NTM1B	methyltransferase like 11B	protein-coding	0.009950	0.559406	123(AGGGACTGTGTGTCTC,-,0.00)
chunk0013_276_1	chr1	170477490	170477852	+	0	NA	intron (NR_125958, intron 1 of 2)	L1ME1|LINE|L1	-54451	NM_152281	92344	Hs.183702	NM_152281	ENSG00000120370	GORAB	GO|NTKLBP1|SCYL1BP1	golgin, RAB6 interacting	protein-coding	0.005525	0.338843	219(CAGTACATACTGTTAT,-,0.00)
chunk0124_371_1	chr3	59311136	59311687	+	0	NA	Intergenic	Intergenic	-261422	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.007260	0.302536	
chunk0056_330_1	chr13	91203356	91203770	+	0	NA	intron (NR_047004, intron 1 of 3)	L2b|LINE|L2	8135	NR_047004	100874150	Hs.711947	NR_047004		LINC00379	-	long intergenic non-protein coding RNA 379	ncRNA	0.002415	0.390361	
chunk0169_409_1	chr6	108523502	108523803	+	0	NA	TTS (NM_145315)	TTS (NM_145315)	-36171	NM_201559	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.003322	0.357616	190(GGCACAGCATGGCCCT,+,0.00)
chunk0135_309_1	chr3	189949912	189950697	+	0	NA	Intergenic	Intergenic	120382	NR_030642	100126340		NR_030642	ENSG00000216058	MIR944	MIRN944|hsa-mir-944|mir-944	microRNA 944	ncRNA	0.016561	0.438931	
chunk0059_395_1	chr14	37544519	37544750	+	0	NA	intron (NM_001195296, intron 14 of 14)	intron (NM_001195296, intron 14 of 14)	50486	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.004329	0.400862	
chunk0136_250_1	chr4	10162457	10162965	+	0	NA	Intergenic	Intergenic	-45762	NM_017491	9948	Hs.128548	NM_005112	ENSG00000071127	WDR1	AIP1|HEL-S-52|NORI-1	WD repeat domain 1	protein-coding	0.007874	0.449902	
chunk0013_345_1	chr1	172158092	172158291	+	0	NA	intron (NM_001136127, intron 14 of 19)	L2a|LINE|L2	-13356	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.005025	0.465000	87(GGGAACAGTATGTGCA,-,0.00),88(GGAACAGTATGTGCAA,+,0.00)
chunk0055_434_1	chr13	75466854	75467585	+	0	NA	intron (NM_001286659, intron 1 of 18)	intron (NM_001286659, intron 1 of 18)	14949	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.005472	0.329235	
chunk0195_252_1	chr8	97797673	97798321	+	0	NA	intron (NM_018407, intron 1 of 6)	intron (NM_018407, intron 1 of 6)	22416	NM_018407	55353	Hs.492314	NM_018407	ENSG00000104341	LAPTM4B	LAPTM4beta|LC27	lysosomal protein transmembrane 4 beta	protein-coding	0.004630	0.385208	277(GGAACAGTTTGCTCAT,+,0.00)
chunk0031_146_1	chr10	125034684	125034919	+	0	NA	intron (NM_001290215, intron 3 of 10)	intron (NM_001290215, intron 3 of 10)	-1931	NR_036178	100423041		NR_036178	ENSG00000264572	MIR4296	-	microRNA 4296	ncRNA	0.004255	0.372881	
chunk0029_215_1	chr10	102235663	102236042	+	0	NA	intron (NM_005029, intron 1 of 3)	intron (NM_005029, intron 1 of 3)	5622	NM_005029	5309	Hs.137568	NM_005029	ENSG00000107859	PITX3	ASGD1|ASMD|ASOD|CTPP4|CTRCT11|PTX3	paired like homeodomain 3	protein-coding	0.005277	0.510526	179(GTGAACACTCTGTCCT,-,0.00),180(TGAACACTCTGTCCTG,+,0.00)
chunk0051_63_1	chr12	112863710	112864048	+	0	NA	intron (NM_001143854, intron 5 of 21)	L2b|LINE|L2	-43055	NM_016816	4938	Hs.524760	NM_002534	ENSG00000089127	OAS1	E18/E16|IFI-4|OIAS|OIASI	2'-5'-oligoadenylate synthetase 1	protein-coding	0.005917	0.448378	
chunk0014_159_1	chr1	178230985	178231287	+	0	NA	intron (NM_170692, intron 1 of 17)	MER50|LTR|ERV1	-110335	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.003311	0.488449	
chunk0158_167_1	chr5	127667813	127668431	+	0	NA	Intergenic	Intergenic	15107	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.006472	0.345719	
chunk0135_228_1	chr3	188589894	188590628	+	0	NA	intron (NM_001167671, intron 5 of 10)	intron (NM_001167671, intron 5 of 10)	-21595	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.014986	0.401361	
chunk0034_367_1	chr11	36132012	36132211	+	0	NA	intron (NM_174902, intron 4 of 5)	intron (NM_174902, intron 4 of 5)	122013	NR_039769	100616311		NR_039769	ENSG00000263389	MIR3973	-	microRNA 3973	ncRNA	0.005025	0.350000	109(CAGAACAGTGTGTCCC,-,0.00),110(AGAACAGTGTGTCCCT,+,0.00)
chunk0034_376_1	chr11	36289320	36289611	+	0	NA	promoter-TSS (NM_001307932)	promoter-TSS (NM_001307932)	-16	NM_001307932	29099	Hs.99443	NM_014186	ENSG00000110442	COMMD9	C11orf55|HSPC166|LINC00610	COMM domain containing 9	protein-coding	0.072165	0.619863	
chunk0121_141_1	chr3	18811594	18812133	+	0	NA	Intergenic	Intergenic	-336662	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.001855	0.351852	259(GAACACAGAGTGTTCT,-,0.00),260(AACACAGAGTGTTCTA,+,0.00)
chunk0018_239_1	chr1	219928593	219928792	+	0	NA	promoter-TSS (NR_046437)	promoter-TSS (NR_046437)	-41	NM_018713	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.080402	0.685000	
chunk0182_330_1	chr7	99128206	99129000	+	0	NA	intron (NM_020429, intron 1 of 18)	intron (NM_020429, intron 1 of 18)	15517	NM_020429	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.013854	0.369811	
chunk0061_192_1	chr14	60191096	60191376	+	0	NA	Intergenic	Intergenic	-25743	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.003571	0.387900	
chunk0109_235_1	chr20	5970369	5970894	+	0	NA	intron (NM_001281521, intron 10 of 18)	LTR16C|LTR|ERVL	19979	NM_001281520	84515	Hs.597484	NM_032485	ENSG00000125885	MCM8	C20orf154|POF10|dJ967N21.5	minichromosome maintenance 8 homologous recombination repair factor	protein-coding	0.005714	0.454373	269(CTGAACAGTGAGTGCC,-,0.00),270(TGAACAGTGAGTGCCA,+,0.00)
chunk0086_400_1	chr18	26745151	26745951	+	0	NA	Intergenic	Intergenic	-41913	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.007500	0.459426	
chunk0030_372_1	chr10	119166591	119167134	+	0	NA	TTS (NM_001302272)	TTS (NM_001302272)	-1170	NM_213649	119559	Hs.655168	NM_178867	ENSG00000183605	SFXN4	BCRM1|COXPD18|SLC56A4	sideroflexin 4	protein-coding	0.018416	0.520221	
chunk0008_288_1	chr1	94875821	94876098	+	0	NA	intron (NM_001258342, intron 11 of 13)	intron (NM_001258342, intron 11 of 13)	49849	NM_001286056	1266	Hs.483454	NM_001839	ENSG00000117519	CNN3	-	calponin 3	protein-coding	0.000000	0.453237	170(GAAAACACTGTGTTCT,-,0.00),171(AAAACACTGTGTTCTG,+,0.00)
chunk0118_397_1	chr22	37855053	37855262	+	0	NA	intron (NM_016091, intron 3 of 12)	intron (NM_016091, intron 3 of 12)	5785	NM_001242923	51386	Hs.446852	NM_016091	ENSG00000100129	EIF3L	EIF3EIP|EIF3S11|EIF3S6IP|HSPC021|HSPC025|MSTP005	eukaryotic translation initiation factor 3 subunit L	protein-coding	0.009569	0.447619	
chunk0116_416_1	chr21	42671851	42672464	+	0	NA	intron (NM_001001575, intron 1 of 14)	intron (NM_001001575, intron 1 of 14)	18405	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.017945	0.485342	
chunk0106_290_1	chr2	204370143	204370526	+	0	NA	Intergenic	Intergenic	-175459	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.005222	0.460938	
chunk0065_111_1	chr15	24625242	24625691	+	0	NA	Intergenic	Intergenic	-49928	NM_018958	23742	Hs.649663	NM_018958	ENSG00000185823	NPAP1	C15orf2	nuclear pore associated protein 1	protein-coding	0.004454	0.373333	
chunk0019_165_1	chr1	226026676	226027272	+	0	NA	Intergenic	Intergenic	-27609	NM_152608	163859	Hs.520192	NM_152608	ENSG00000143751	SDE2	C1orf55|dJ671D7.1	SDE2 telomere maintenance homolog	protein-coding	0.005034	0.378559	
chunk0205_360_1	chr9	113580478	113580877	+	0	NA	promoter-TSS (NM_001282922)	promoter-TSS (NM_001282922)	-200	NM_001282922	5998	Hs.494875	NM_017790	ENSG00000138835	RGS3	C2PA|RGP3	regulator of G protein signaling 3	protein-coding	0.012531	0.557500	
chunk0026_365_1	chr10	69282046	69282396	+	0	NA	intron (NM_033497, intron 1 of 20)	MIRb|SINE|MIR	12221	NM_033498	3098	Hs.370365	NM_000188	ENSG00000156515	HK1	HK|HK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1|RP79|hexokinase	hexokinase 1	protein-coding	0.008571	0.484330	145(GGGCACATGAAGTCCT,-,0.00),146(GGCACATGAAGTCCTT,+,0.00)
chunk0152_400_1	chr5	64823965	64824164	+	0	NA	intron (NM_001297644, intron 10 of 12)	intron (NM_001297644, intron 10 of 12)	55146	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.005025	0.280000	
chunk0048_177_1	chr12	80917663	80918184	+	0	NA	intron (NM_004664, intron 1 of 5)	L1MEd|LINE|L1	17910	NR_030349	693203		NR_030349	ENSG00000208022	MIR618	MIRN618|hsa-mir-618|mir-618	microRNA 618	ncRNA	0.005758	0.385057	
chunk0174_13_1	chr6	152368881	152369322	+	0	NA	exon (NM_182961, exon 61 of 146)	exon (NM_182961, exon 61 of 146)	-11429	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.024943	0.488688	
chunk0191_236_1	chr8	52918891	52919261	+	0	NA	Intergenic	Intergenic	-20832	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.005405	0.444744	
chunk0023_117_1	chr10	23326464	23326794	+	0	NA	intron (NM_153714, intron 2 of 4)	L1MEf|LINE|L1	18214	NM_153714	256815	Hs.132442	NM_153714	ENSG00000179133	C10orf67	C10orf115|LINC01552	chromosome 10 open reading frame 67	protein-coding	0.006061	0.314199	
chunk0060_295_1	chr14	50746419	50746865	+	0	NA	intron (NM_016350, intron 21 of 28)	intron (NM_016350, intron 21 of 28)	-78289	NM_021818	60485	Hs.642842	NM_021818	ENSG00000151748	SAV1	SAV|WW45|WWP4	salvador family WW domain containing protein 1	protein-coding	0.002242	0.319911	
chunk0192_29_1	chr8	58560149	58560415	+	0	NA	intron (NM_001007067, intron 1 of 8)	L1MB7|LINE|L1	7113	NM_001007070	6386	Hs.200804	NM_005625	ENSG00000137575	SDCBP	MDA-9|MDA9|ST1|SYCL|TACIP18	syndecan binding protein	protein-coding	0.003759	0.516854	
chunk0034_80_1	chr11	27227776	27228048	+	0	NA	Intergenic	Intergenic	-7799	NR_125767	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.014706	0.534799	
chunk0150_354_1	chr5	38692697	38693250	+	0	NA	TTS (NR_109951)	TTS (NR_109951)	27300	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.010850	0.413357	191(TAAAACACTCTGTTCC,-,0.00),192(AAAACACTCTGTTCCA,+,0.00)
chunk0148_22_1	chr5	529566	530141	+	0	NA	Intergenic	L1M5|LINE|L1	-5419	NM_004174	6550	Hs.658120	NM_004174	ENSG00000066230	SLC9A3	DIAR8|NHE-3|NHE3	solute carrier family 9 member A3	protein-coding	0.001739	0.329861	
chunk0156_158_1	chr5	107413134	107413641	+	0	NA	intron (NM_001962, intron 2 of 4)	intron (NM_001962, intron 2 of 4)	257508	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.001972	0.340551	
chunk0174_72_1	chr6	156045617	156046268	+	0	NA	Intergenic	Intergenic	99145	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.006144	0.388037	
chunk0005_97_1	chr1	56473588	56473858	+	0	NA	Intergenic	L2a|LINE|L2	105861	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.003704	0.394834	
chunk0137_458_1	chr4	29853868	29854218	+	0	NA	Intergenic	Intergenic	-866365	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.005714	0.433048	
chunk0097_419_1	chr2	62858311	62858554	+	0	NA	exon (NM_015252, exon 8 of 25)	exon (NM_015252, exon 8 of 25)	151535	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.004115	0.393443	
chunk0155_120_1	chr5	93051356	93051555	+	0	NA	Intergenic	Intergenic	519888	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.300000	
chunk0197_422_1	chr8	127395576	127396358	+	0	NA	intron (NR_117100, intron 5 of 5)	L2c|LINE|L2	-4432	NR_109834	101805488	Hs.745578	NR_109834	ENSG00000280997	CCAT2	LINC00873|NCCP1	colon cancer associated transcript 2	ncRNA	0.007673	0.444444	
chunk0075_141_1	chr16	50261773	50262303	+	0	NA	Intergenic	Intergenic	-4502	NM_001286057	113	Hs.513578	NM_001114	ENSG00000121281	ADCY7	AC7	adenylate cyclase 7	protein-coding	0.018868	0.553672	
chunk0082_158_1	chr17	55668041	55668540	+	0	NA	Intergenic	Intergenic	54574	NM_018286	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.010020	0.450000	
chunk0150_428_1	chr5	40382813	40383045	+	0	NA	Intergenic	Intergenic	-297001	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.000000	0.321888	
chunk0080_397_1	chr17	35096226	35096696	+	0	NA	intron (NR_037714, intron 5 of 6)	MLT1L|LTR|ERVL-MaLR	-7132	NR_037713	117584	Hs.13680	NM_057178	ENSG00000092871	RFFL	CARP-2|CARP2|FRING|RIFIFYLIN|RNF189|RNF34L	ring finger and FYVE like domain containing E3 ubiquitin protein ligase	protein-coding	0.014894	0.494692	
chunk0137_324_1	chr4	24782253	24782686	+	0	NA	Intergenic	Intergenic	-12994	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.011547	0.440092	
chunk0145_51_1	chr4	145063048	145063677	+	0	NA	intron (NM_001256711, intron 5 of 6)	intron (NM_001256711, intron 5 of 6)	-34642	NM_002940	6059	Hs.12013	NM_002940	ENSG00000164163	ABCE1	ABC38|OABP|RLI|RLI1|RNASEL1|RNASELI|RNS4I	ATP binding cassette subfamily E member 1	protein-coding	0.003180	0.295238	
chunk0095_193_1	chr2	18118611	18118986	+	0	NA	Intergenic	Intergenic	240141	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.010667	0.375000	
chunk0151_185_1	chr5	50420330	50421085	+	0	NA	intron (NM_198449, intron 2 of 8)	L2a|LINE|L2	20693	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.006623	0.383598	
chunk0200_318_1	chr9	23540206	23540683	+	0	NA	intron (NR_121602, intron 16 of 27)	intron (NR_121602, intron 16 of 27)	131955	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.002096	0.420502	
chunk0039_361_1	chr11	106032882	106033394	+	0	NA	Intergenic	Intergenic	-10911	NM_032424	84437	Hs.266782	NM_032424	ENSG00000170903	MSANTD4	KIAA1826	Myb/SANT DNA binding domain containing 4 with coiled-coils	protein-coding	0.003906	0.329435	
chunk0184_43_1	chr7	112254408	112254700	+	0	NA	intron (NM_021994, intron 1 of 11)	intron (NM_021994, intron 1 of 11)	47966	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.000000	0.348123	
chunk0019_415_1	chr1	230730987	230731570	+	0	NA	Intergenic	Intergenic	-16106	NM_006615	10753	Hs.498021	NM_006615	ENSG00000135773	CAPN9	GC36|nCL-4	calpain 9	protein-coding	0.012007	0.481164	
chunk0104_448_1	chr2	181526051	181526314	+	0	NA	intron (NM_000885, intron 21 of 27)	intron (NM_000885, intron 21 of 27)	69290	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.011407	0.367424	
chunk0106_76_1	chr2	197006442	197006991	+	0	NA	intron (NM_001195144, intron 20 of 27)	intron (NM_001195144, intron 20 of 27)	-79986	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.005464	0.425455	
chunk0067_234_1	chr15	45449912	45450212	+	0	NA	Intergenic	Intergenic	17012	NR_030599	100126311		NR_030599	ENSG00000284386	MIR147B	MIRN147B|mir-147b	microRNA 147b	ncRNA	0.030000	0.594684	
chunk0006_236_1	chr1	68887331	68887824	+	0	NA	Intergenic	HAL1|LINE|L1	-390356	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.000000	0.352227	
chunk0203_244_1	chr9	87337078	87337740	+	0	NA	Intergenic	Intergenic	-159819	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.024169	0.431373	
chunk0046_397_1	chr12	63974370	63974937	+	0	NA	intron (NM_020762, intron 1 of 21)	intron (NM_020762, intron 1 of 21)	129892	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.001764	0.325704	
chunk0037_295_1	chr11	76148346	76149038	+	0	NA	Intergenic	Intergenic	57838	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.017341	0.548341	
chunk0160_324_1	chr5	159481871	159482333	+	0	NA	Intergenic	L1PREC2|LINE|L1	-15826	NR_027110	285627	Hs.552766	NR_027110	ENSG00000253298	LINC01845	-	long intergenic non-protein coding RNA 1845	ncRNA	0.004329	0.397408	
chunk0028_439_1	chr10	93909448	93909892	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	15697	NM_153226	159371	Hs.632085	NM_153226	ENSG00000176273	SLC35G1	C10orf60|POST|TMEM20	solute carrier family 35 member G1	protein-coding	0.004505	0.337079	216(CAGCACTCCTTGTTCT,-,0.00),217(AGCACTCCTTGTTCTT,+,0.00)
chunk0166_128_1	chr6	44668739	44669596	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	233526	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.014002	0.423077	
chunk0042_428_1	chr12	12076721	12076952	+	0	NA	intron (NM_030766, intron 1 of 5)	intron (NM_030766, intron 1 of 5)	5368	NM_138722	79370	Hs.210343	NM_030766	ENSG00000121380	BCL2L14	BCLG	BCL2 like 14	protein-coding	0.012987	0.482759	
chunk0169_382_1	chr6	107495106	107495305	+	0	NA	intron (NM_018013, intron 1 of 6)	intron (NM_018013, intron 1 of 6)	5092	NM_018013	55084	Hs.445244	NM_018013	ENSG00000112320	SOBP	JXC1|MRAMS	sine oculis binding protein homolog	protein-coding	0.005025	0.545000	
chunk0151_223_1	chr5	50900149	50900750	+	0	NA	Intergenic	Intergenic	69738	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.001664	0.333887	
chunk0116_166_1	chr21	36741087	36741392	+	0	NA	intron (NM_005069, intron 7 of 10)	intron (NM_005069, intron 7 of 10)	42106	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.000000	0.401961	
chunk0155_54_1	chr5	91235063	91235769	+	0	NA	Intergenic	Intergenic	78986	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.004249	0.381895	
chunk0091_290_1	chr19	12325584	12326241	+	0	NA	intron (NM_145276, intron 1 of 3)	L1MB4|LINE|L1	7808	NM_145276	147837	Hs.663510	NM_145276	ENSG00000188868	ZNF563	-	zinc finger protein 563	protein-coding	0.000000	0.351064	
chunk0195_384_1	chr8	100213310	100213622	+	0	NA	intron (NM_003114, intron 11 of 18)	CpG-27473	55131	NM_003114	6674	Hs.591866	NM_003114	ENSG00000104450	SPAG1	CILD28|CT140|HEL-S-268|HSD-3.8|SP75|TPIS	sperm associated antigen 1	protein-coding	0.108974	0.709265	
chunk0116_177_1	chr21	36835627	36835842	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	130922	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.009302	0.523148	
chunk0116_403_1	chr21	42520589	42521078	+	0	NA	intron (NM_018964, intron 3 of 20)	L1MC4a|LINE|L1	21201	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.030675	0.495918	246(CAGAACATCTTGTGCC,-,0.00),247(AGAACATCTTGTGCCA,+,0.00)
chunk0024_104_1	chr10	34625988	34626767	+	0	NA	intron (NM_019619, intron 2 of 24)	intron (NM_019619, intron 2 of 24)	188948	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.003851	0.408974	447(GAATACAGCTTGTTCT,-,0.00),448(AATACAGCTTGTTCTT,+,0.00)
chunk0051_40_1	chr12	112243539	112243779	+	0	NA	exon (NM_001109662, exon 31 of 76)	exon (NM_001109662, exon 31 of 76)	-80338	NR_106921	102465519		NR_106921	ENSG00000283793	MIR6861	hsa-mir-6861	microRNA 6861	ncRNA	0.045833	0.580913	
chunk0067_372_1	chr15	48908422	48908621	+	0	NA	intron (NM_203349, intron 2 of 11)	L1PB1|LINE|L1	30428	NM_014335	23741	Hs.255973	NM_014335	ENSG00000255302	EID1	C15orf3|CRI1|EID-1|IRO45620|PNAS-22|PTD014|RBP21	EP300 interacting inhibitor of differentiation 1	protein-coding	0.010050	0.370000	
chunk0154_286_1	chr5	82684409	82684786	+	0	NA	Intergenic	Intergenic	-155558	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.002653	0.386243	174(AAGGACAGCATGTTTT,-,0.00),175(AGGACAGCATGTTTTG,+,0.00)
chunk0027_387_1	chr10	79884594	79884838	+	0	NA	Intergenic	L1MA9|LINE|L1	-20182	NR_033857	100288974	Hs.733579	NR_033857		BMS1P21	-	BMS1 pseudogene 21	pseudo	0.004098	0.248980	
chunk0072_458_1	chr15	101903925	101904128	+	0	NA	Intergenic	L2c|LINE|L2	19033	NM_001004195	26682	Hs.554420	NM_001004195	ENSG00000177693	OR4F4	OLA-7501|OR4F18	olfactory receptor family 4 subfamily F member 4	protein-coding	0.000000	0.372549	77(TGCTCATGCTGTTCCT,+,0.00)
chunk0040_400_1	chr11	120522790	120523666	+	0	NA	intron (NM_014619, intron 1 of 20)	intron (NM_014619, intron 1 of 20)	11482	NM_014619	2900	Hs.538738	NM_014619	ENSG00000149403	GRIK4	EAA1|GRIK|GluK4|KA1	glutamate ionotropic receptor kainate type subunit 4	protein-coding	0.018265	0.548461	
chunk0063_200_1	chr14	81184026	81184269	+	0	NA	intron (NM_001278940, intron 9 of 9)	intron (NM_001278940, intron 9 of 9)	18687	NR_003021	677845	Hs.693251	NR_003021	ENSG00000221303	SNORA79	ACA65|SNORA79A	small nucleolar RNA, H/ACA box 79	snoRNA	0.004115	0.323770	119(GAGTACAGTTTGTGCC,-,0.00),120(AGTACAGTTTGTGCCA,+,0.00)
chunk0097_169_1	chr2	49694675	49695068	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	-540344	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.000000	0.370558	
chunk0173_228_1	chr6	146303101	146303376	+	0	NA	intron (NM_001278064, intron 2 of 7)	intron (NM_001278064, intron 2 of 7)	-240454	NM_006834	10981	Hs.287714	NM_006834	ENSG00000118508	RAB32	-	RAB32, member RAS oncogene family	protein-coding	0.000000	0.423913	
chunk0072_324_1	chr15	98980197	98980458	+	0	NA	intron (NM_001167902, intron 2 of 4)	intron (NM_001167902, intron 2 of 4)	25329	NM_001102612	145814	Hs.592021	NM_001102612	ENSG00000183571	PGPEP1L	-	pyroglutamyl-peptidase I like	protein-coding	0.007663	0.408397	
chunk0102_48_1	chr2	142696504	142696940	+	0	NA	Intergenic	L1PBa|LINE|L1	-180904	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.004587	0.379863	
chunk0045_108_1	chr12	46209985	46210586	+	0	NA	intron (NM_001077484, intron 5 of 16)	intron (NM_001077484, intron 5 of 16)	56210	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.008319	0.473422	
chunk0081_33_1	chr17	37453197	37453752	+	0	NA	intron (NM_133439, intron 8 of 10)	intron (NM_133439, intron 8 of 10)	-36371	NM_007026	11072	Hs.91448	NM_007026	ENSG00000276023	DUSP14	MKP-L|MKP6	dual specificity phosphatase 14	protein-coding	0.001802	0.384892	
chunk0001_348_1	chr1	9825233	9825453	+	0	NA	promoter-TSS (NM_001302883)	promoter-TSS (NM_001302883)	-817	NM_001009566	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.027273	0.552036	
chunk0183_182_1	chr7	106205758	106206282	+	0	NA	Intergenic	Intergenic	79172	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.009542	0.428571	
chunk0044_287_1	chr12	32739782	32740103	+	0	NA	intron (NM_001278464, intron 17 of 20)	intron (NM_001278464, intron 17 of 20)	16011	NM_001040436	51067	Hs.505231	NM_015936	ENSG00000139131	YARS2	CGI-04|MLASA2|MT-TYRRS|TYRRS	tyrosyl-tRNA synthetase 2	protein-coding	0.003115	0.360248	
chunk0016_447_1	chr1	204126314	204126858	+	0	NA	3' UTR (NM_005686, exon 14 of 14)	3' UTR (NM_005686, exon 14 of 14)	-14822	NR_123739	101929441	Hs.736889	NR_123739	ENSG00000230550	ERLNC1	ElncRNA1|TC0101441	estrogen receptor responsive lncRNA 1	ncRNA	0.014706	0.548624	281(AGGGTCTGGCTGTCCC,-,0.00),282(GGGTCTGGCTGTCCCT,+,0.00)
chunk0039_438_1	chr11	108067395	108067615	+	0	NA	intron (NM_003478, intron 7 of 18)	MER112|DNA|hAT-Charlie	-54026	NM_000019	38	Hs.232375	NM_000019	ENSG00000075239	ACAT1	ACAT|MAT|T2|THIL	acetyl-CoA acetyltransferase 1	protein-coding	0.000000	0.289593	
chunk0065_338_1	chr14	103500145	103500641	+	0	NA	intron (NM_001128919, intron 16 of 16)	intron (NM_001128919, intron 16 of 16)	22466	NM_001823	1152	Hs.173724	NM_001823	ENSG00000166165	CKB	B-CK|BCK|CKBB|CPK-B|HEL-211|HEL-S-29	creatine kinase B	protein-coding	0.018145	0.444668	
chunk0011_271_1	chr1	151165826	151166167	+	0	NA	promoter-TSS (NR_037937)	promoter-TSS (NR_037937)	-26	NR_037937	79005	Hs.732060	NM_024041	ENSG00000163156	SCNM1	-	sodium channel modifier 1	protein-coding	0.064516	0.555556	
chunk0162_381_1	chr6	7548716	7549048	+	0	NA	intron (NM_001008844, intron 1 of 23)	intron (NM_001008844, intron 1 of 23)	7245	NM_004415	1832	Hs.519873	NM_004415	ENSG00000096696	DSP	DCWHKTA|DP	desmoplakin	protein-coding	0.003012	0.435435	
chunk0159_224_1	chr5	141119702	141120271	+	0	NA	Intergenic	Intergenic	-1764	NM_018938	56131	Hs.591250	NM_018938	ENSG00000081818	PCDHB4	PCDH-BETA4	protocadherin beta 4	protein-coding	0.005272	0.319298	
chunk0178_83_1	chr7	30476714	30477162	+	0	NA	intron (NM_006092, intron 1 of 13)	intron (NM_006092, intron 1 of 13)	1839	NM_006092	10392	Hs.405153	NM_006092	ENSG00000106100	NOD1	CARD4|CLR7.1|NLRC1	nucleotide binding oligomerization domain containing 1	protein-coding	0.020089	0.494432	
chunk0150_282_1	chr5	37029091	37029389	+	0	NA	intron (NM_015384, intron 32 of 45)	L1ME1|LINE|L1	152481	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.003356	0.344482	
chunk0156_396_1	chr5	113427370	113427569	+	0	NA	intron (NM_001085377, intron 1 of 18)	intron (NM_001085377, intron 1 of 18)	7562	NM_032028	83942	Hs.519507	NM_032028	ENSG00000212122	TSSK1B	FKSG81|SPOGA4|STK22D|TSK1|TSSK1	testis specific serine kinase 1B	protein-coding	0.000000	0.350000	
chunk0012_333_1	chr1	162557533	162557880	+	0	NA	Intergenic	Intergenic	-3800	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.008646	0.454023	
chunk0126_216_1	chr3	78814990	78815229	+	0	NA	intron (NM_133631, intron 2 of 28)	Tigger1|DNA|TcMar-Tigger	204350	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004184	0.387500	74(AGGTTCAGACTGTTCT,-,0.00),75(GGTTCAGACTGTTCTA,+,0.00)
chunk0038_10_1	chr11	80826332	80826638	+	0	NA	Intergenic	(TAGA)n|Simple_repeat|Simple_repeat	-63682	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.003268	0.381107	
chunk0158_417_1	chr5	135049470	135049985	+	0	NA	intron (NM_001277348, intron 1 of 5)	L1MD2|LINE|L1	-9680	NR_105050	101927953	Hs.436898	NR_105049	ENSG00000249082	C5orf66-AS1	Epist	C5orf66 antisense RNA 1	ncRNA	0.009709	0.408915	
chunk0099_278_1	chr2	98307278	98307853	+	0	NA	intron (NM_144992, intron 26 of 27)	LTR10C|LTR|ERV1	-38590	NM_001298	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.010435	0.369792	278(AAGAACATAAAGTACA,-,0.00),279(AGAACATAAAGTACAT,+,0.00)
chunk0007_255_1	chr1	82806623	82807099	+	0	NA	Intergenic	L2a|LINE|L2	178061	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.004202	0.312369	
chunk0205_279_1	chr9	111601514	111601938	+	0	NA	Intergenic	Intergenic	-1871	NM_001146108	22949	Hs.584864	NM_012212	ENSG00000106853	PTGR1	LTB4DH|PGR1|ZADH3	prostaglandin reductase 1	protein-coding	0.011792	0.350588	
chunk0036_211_1	chr11	63575145	63575437	+	0	NA	intron (NM_007069, intron 3 of 3)	intron (NM_007069, intron 3 of 3)	-11908	NM_017878	54979	Hs.272805	NM_017878	ENSG00000133328	PLAAT2	HRASLS2|PLA1/2-2|PLAAT-2	phospholipase A and acyltransferase 2	protein-coding	0.013699	0.508532	
chunk0185_171_1	chr7	127898034	127898336	+	0	NA	intron (NM_014390, intron 13 of 23)	intron (NM_014390, intron 13 of 23)	-99324	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.006623	0.438944	
chunk0201_48_1	chr9	33817789	33817988	+	0	NA	exon (NM_017811, exon 1 of 5)	exon (NM_017811, exon 1 of 5)	704	NM_017811	54926	Hs.643648	NM_017811	ENSG00000107341	UBE2R2	CDC34B|E2-CDC34B|UBC3B	ubiquitin conjugating enzyme E2 R2	protein-coding	0.065327	0.655000	
chunk0033_141_1	chr11	15466875	15467074	+	0	NA	Intergenic	Intergenic	-176911	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.000000	0.515000	
chunk0146_239_1	chr4	162259152	162259435	+	0	NA	Intergenic	Intergenic	-95259	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.003534	0.341549	
chunk0152_184_1	chr5	59790809	59791336	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-22460	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.013283	0.414773	
chunk0043_379_1	chr12	24665666	24666070	+	0	NA	Intergenic	L2b|LINE|L2	-81700	NR_029451	144360	Hs.350668	NM_144667	ENSG00000197503	LINC00477	C12orf67|FAM191B	long intergenic non-protein coding RNA 477	ncRNA	0.007426	0.375309	
chunk0163_3_1	chr6	7658466	7658822	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-68134	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.011236	0.509804	
chunk0064_96_1	chr14	90975277	90975551	+	0	NA	intron (NM_182398, intron 3 of 12)	MLT1B|LTR|ERVL-MaLR	85235	NM_004755	9252	Hs.510225	NM_004755	ENSG00000100784	RPS6KA5	MSK1|MSPK1|RLPK	ribosomal protein S6 kinase A5	protein-coding	0.003650	0.447273	
chunk0194_365_1	chr8	89825125	89825706	+	0	NA	Intergenic	Intergenic	67668	NM_003821	8767	Hs.103755	NM_003821	ENSG00000104312	RIPK2	CARD3|CARDIAK|CCK|GIG30|RICK|RIP2	receptor interacting serine/threonine kinase 2	protein-coding	0.012048	0.376289	
chunk0140_393_1	chr4	75365249	75365629	+	0	NA	Intergenic	Intergenic	11363	NR_033964	441025	Hs.407667	NR_033964	ENSG00000251383	LINC02483	-	long intergenic non-protein coding RNA 2483	ncRNA	0.010526	0.414698	
chunk0109_147_1	chr20	3559192	3559510	+	0	NA	intron (NM_001207047, intron 6 of 24)	intron (NM_001207047, intron 6 of 24)	88333	NM_139321	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.003145	0.420063	
chunk0091_32_1	chr19	3513417	3513756	+	0	NA	intron (NM_016263, intron 1 of 13)	intron (NM_016263, intron 1 of 13)	7289	NM_016263	51343	Hs.413133	NM_016263	ENSG00000105325	FZR1	CDC20C|CDH1|FZR|FZR2|HCDH|HCDH1	fizzy and cell division cycle 20 related 1	protein-coding	0.023599	0.632353	158(AAGCACACTGAGTGCT,-,0.00),159(AGCACACTGAGTGCTT,+,0.00)
chunk0175_178_1	chr7	5202793	5203230	+	0	NA	intron (NM_001033518, intron 3 of 12)	intron (NM_001033518, intron 3 of 12)	-11258	NM_001033520	26100	Hs.122363	NM_015610	ENSG00000157954	WIPI2	ATG18B|Atg21|CGI-50|IDDSSA|WIPI-2	WD repeat domain, phosphoinositide interacting 2	protein-coding	0.009153	0.378995	
chunk0001_104_1	chr1	3444123	3444322	+	0	NA	Intergenic	L1MC1|LINE|L1	-10361	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.015075	0.510000	
chunk0010_173_1	chr1	115725716	115726443	+	0	NA	intron (NM_001232, intron 6 of 10)	intron (NM_001232, intron 6 of 10)	42726	NM_001232	845	Hs.57975	NM_001232	ENSG00000118729	CASQ2	PDIB2	calsequestrin 2	protein-coding	0.006878	0.472527	
chunk0080_388_1	chr17	34916118	34916452	+	0	NA	Intergenic	Intergenic	45224	NM_006584	10693	Hs.73072	NM_006584	ENSG00000132141	CCT6B	CCT-zeta-2|CCTZ-2|Cctz2|TCP-1-zeta-2|TSA303	chaperonin containing TCP1 subunit 6B	protein-coding	0.002994	0.447761	
chunk0205_130_1	chr9	108071657	108072114	+	0	NA	Intergenic	Intergenic	-582165	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.002188	0.373362	
chunk0128_322_1	chr3	111883575	111883985	+	0	NA	intron (NM_001134439, intron 1 of 17)	intron (NM_001134439, intron 1 of 17)	24059	NM_001134439	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.007317	0.367397	
chunk0084_94_1	chr17	75459320	75459691	+	0	NA	intron (NM_014738, intron 1 of 31)	intron (NM_014738, intron 1 of 31)	2922	NM_014738	9772	Hs.514474	NM_014738	ENSG00000177728	TMEM94	IDDCDF|KIAA0195	transmembrane protein 94	protein-coding	0.005391	0.465054	
chunk0103_80_1	chr2	160582988	160583582	+	0	NA	Intergenic	Intergenic	-89478	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.003367	0.388235	
chunk0174_36_1	chr6	154329771	154330115	+	0	NA	intron (NM_001130699, intron 1 of 12)	intron (NM_001130699, intron 1 of 12)	138	NM_001130699	26034	Hs.146100	NM_015553	ENSG00000074706	IPCEF1	PIP3-E	interaction protein for cytohesin exchange factors 1	protein-coding	0.008721	0.443478	
chunk0016_390_1	chr1	202926804	202927379	+	0	NA	5' UTR (NM_021633, exon 1 of 12)	5' UTR (NM_021633, exon 1 of 12)	181	NM_021633	59349	Hs.706793	NM_021633	ENSG00000117153	KLHL12	C3IP1|DKIR	kelch like family member 12	protein-coding	0.071304	0.656250	
chunk0132_201_1	chr3	157284473	157285350	+	0	NA	intron (NM_001167911, intron 11 of 12)	intron (NM_001167911, intron 11 of 12)	-124151	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.005701	0.341686	477(AGGAACACTTTGTGTT,-,0.00),478(GGAACACTTTGTGTTT,+,0.00)
chunk0002_62_1	chr1	13832233	13832456	+	0	NA	Intergenic	MIR|SINE|MIR	82963	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.013453	0.495536	
chunk0188_173_1	chr8	11148533	11148926	+	0	NA	intron (NM_173683, intron 1 of 2)	L1ME1|LINE|L1	52637	NM_173683	286046	Hs.657083	NM_173683	ENSG00000171044	XKR6	C8orf21|C8orf5|C8orf7|XRG6	XK related 6	protein-coding	0.007634	0.342640	
chunk0047_248_1	chr12	72346248	72347032	+	0	NA	intron (NM_013381, intron 2 of 18)	L2b|LINE|L2	-73131	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.008929	0.450955	
chunk0029_190_1	chr10	101377087	101377394	+	0	NA	intron (NM_003939, intron 1 of 13)	L1ME1|LINE|L1	23207	NM_033637	8945	Hs.643802	NM_003939	ENSG00000166167	BTRC	BETA-TRCP|FBW1A|FBXW1|FBXW1A|FWD1|bTrCP|bTrCP1|betaTrCP	beta-transducin repeat containing E3 ubiquitin protein ligase	protein-coding	0.009772	0.340909	
chunk0188_407_1	chr8	18818393	18818745	+	0	NA	intron (NM_015310, intron 4 of 15)	intron (NM_015310, intron 4 of 15)	-9674	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.008523	0.399433	209(CAGGACAATCTGCTCT,-,0.00),210(AGGACAATCTGCTCTG,+,0.00)
chunk0118_388_1	chr22	37196841	37197585	+	0	NA	Intergenic	Intergenic	-8923	NM_031910	114904	Hs.22011	NM_031910	ENSG00000133466	C1QTNF6	CTFP6|CTRP6|ZACRP6	C1q and TNF related 6	protein-coding	0.010753	0.562416	150(AGGGACACTGTGGCCC,-,0.00)
chunk0107_191_1	chr2	216140372	216140571	+	0	NA	intron (NM_021141, intron 12 of 20)	intron (NM_021141, intron 12 of 20)	31174	NM_021141	7520	Hs.388739	NM_021141	ENSG00000079246	XRCC5	KARP-1|KARP1|KU80|KUB2|Ku86|NFIV	X-ray repair cross complementing 5	protein-coding	0.010050	0.365000	
chunk0011_69_1	chr1	143924112	143924442	+	0	NA	Intergenic	MamRep1527|LTR|LTR	47729	NM_001287385	554282		NM_001287385	ENSG00000263513	FAM72C	-	family with sequence similarity 72 member C	protein-coding	0.006061	0.365559	
chunk0022_206_1	chr10	13796183	13796591	+	0	NA	intron (NM_018027, intron 5 of 24)	intron (NM_018027, intron 5 of 24)	209448	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.009804	0.447433	127(AGGCACACCCTGCACC,-,0.00),128(GGCACACCCTGCACCC,+,0.00)
chunk0146_170_1	chr4	160252255	160252486	+	0	NA	Intergenic	Intergenic	984524	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.004329	0.439655	
chunk0144_64_1	chr4	127223865	127224367	+	0	NA	Intergenic	L1PA8A|LINE|L1	-408816	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.001992	0.351889	9(CAGAACAAAGAGTACC,-,0.00),10(AGAACAAAGAGTACCA,+,0.00)
chunk0028_319_1	chr10	91864063	91864674	+	0	NA	3' UTR (NM_025235, exon 27 of 27)	3' UTR (NM_025235, exon 27 of 27)	45133	NM_152429	143282	Hs.466120	NM_152429	ENSG00000174721	FGFBP3	C10orf13|FGF-BP3	fibroblast growth factor binding protein 3	protein-coding	0.004910	0.390523	
chunk0071_325_1	chr15	86948413	86949052	+	0	NA	intron (NM_152336, intron 22 of 23)	intron (NM_152336, intron 22 of 23)	-628197	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.010955	0.367188	585(AGGAACTGTGTGGTCC,-,0.00)
chunk0182_160_1	chr7	95510564	95511005	+	0	NA	intron (NM_145872, intron 2 of 2)	intron (NM_145872, intron 2 of 2)	24883	NM_016116	51666	Hs.602765	NM_016116	ENSG00000005981	ASB4	ASB-4	ankyrin repeat and SOCS box containing 4	protein-coding	0.004535	0.364253	
chunk0033_380_1	chr11	23797725	23798003	+	0	NA	Intergenic	Intergenic	-378674	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.000000	0.397849	
chunk0150_121_1	chr5	33011564	33012074	+	0	NA	Intergenic	Intergenic	64376	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.001961	0.332681	216(TAAACATTGTGTTCCT,+,0.00)
chunk0203_129_1	chr9	85200804	85201417	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	530733	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.003263	0.442997	
chunk0110_443_1	chr20	21088362	21088931	+	0	NA	Intergenic	Intergenic	-37337	NM_001276389	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.005272	0.363158	
chunk0038_257_1	chr11	88598021	88598364	+	0	NA	intron (NM_001143831, intron 4 of 8)	intron (NM_001143831, intron 4 of 8)	93616	NR_049724	100873989	Hs.616625	NR_049724	ENSG00000255082	GRM5-AS1	-	GRM5 antisense RNA 1	ncRNA	0.002915	0.354651	121(AGGTACACACTGTGTT,-,0.00),122(GGTACACACTGTGTTC,+,0.00)
chunk0024_348_1	chr10	43499049	43499266	+	0	NA	Intergenic	L1MEd|LINE|L1	62031	NR_026693									0.009217	0.311927	
chunk0144_455_1	chr4	142193204	142193625	+	0	NA	intron (NM_001101669, intron 14 of 25)	intron (NM_001101669, intron 14 of 25)	556818	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.004751	0.308057	244(TAGAACAGTGTGTTCT,-,0.00),245(AGAACAGTGTGTTCTC,+,0.00)
chunk0158_337_1	chr5	133242484	133242952	+	0	NA	intron (NM_015082, intron 7 of 15)	intron (NM_015082, intron 7 of 15)	184988	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.010684	0.466951	244(AAGAACTGGATGTTCA,-,0.00),245(AGAACTGGATGTTCAG,+,0.00)
chunk0012_413_1	chr1	164190958	164191202	+	0	NA	Intergenic	L1M1|LINE|L1	-368280	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.004098	0.326531	
chunk0075_448_1	chr16	58126019	58126235	+	0	NA	intron (NM_013242, intron 1 of 5)	MIRb|SINE|MIR	3265	NM_013242	29105	Hs.532755	NM_013242	ENSG00000070761	CFAP20	BUG22|C16orf80|EVORF|GTL3|fSAP23	cilia and flagella associated protein 20	protein-coding	0.023148	0.447005	
chunk0082_451_1	chr17	62218727	62219357	+	0	NA	Intergenic	Intergenic	56613	NR_027486	440452	Hs.448884	NR_027486	ENSG00000188755	TBC1D3P2	-	TBC1 domain family member 3 pseudogene 2	pseudo	0.006349	0.374010	
chunk0106_115_1	chr2	197613088	197614033	+	0	NA	intron (NM_144629, intron 7 of 8)	MamRTE1|LINE|RTE-BovB	62300	NM_144629	130132	Hs.591615	NM_144629	ENSG00000162944	RFTN2	C2orf11|Raftlin-2	raftlin family member 2	protein-coding	0.004233	0.355180	529(AAGAACAGCATGTGAC,-,0.00),530(AGAACAGCATGTGACT,+,0.00)
chunk0172_110_1	chr6	135032463	135032770	+	0	NA	intron (NM_001145158, intron 3 of 16)	intron (NM_001145158, intron 3 of 16)	22282	NM_001145158	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.003257	0.285714	
chunk0108_339_1	chr2	235733701	235734055	+	0	NA	intron (NM_001037131, intron 3 of 17)	intron (NM_001037131, intron 3 of 17)	228127	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.008475	0.352113	
chunk0189_1_1	chr8	19395890	19396505	+	0	NA	TTS (NM_022071)	TTS (NM_022071)	82221	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.013008	0.461039	
chunk0156_451_1	chr5	114921124	114921575	+	0	NA	Intergenic	L1P1|LINE|L1	-147936	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.002217	0.380531	
chunk0137_151_1	chr4	15707303	15707521	+	0	NA	intron (NM_004334, intron 2 of 8)	intron (NM_004334, intron 2 of 8)	4462	NM_004334	683	Hs.720344	NM_004334	ENSG00000109743	BST1	CD157	bone marrow stromal cell antigen 1	protein-coding	0.013761	0.406393	
chunk0021_178_1	chr10	5503413	5503942	+	0	NA	Intergenic	Intergenic	-4107	NM_017422	51806	Hs.180142	NM_017422	ENSG00000178372	CALML5	CLSP	calmodulin like 5	protein-coding	0.009452	0.537736	
chunk0183_221_1	chr7	106705235	106705561	+	0	NA	Intergenic	HAL1|LINE|L1	-44210	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.003067	0.336391	
chunk0068_106_1	chr15	52306286	52306594	+	0	NA	TTS (NM_000259)	TTS (NM_000259)	-10642	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.003247	0.378641	
chunk0071_46_1	chr15	79932493	79932914	+	0	NA	Intergenic	Intergenic	-8949	NR_037652	400410	Hs.729127	NM_001100879	ENSG00000180953	ST20	HCCS-1	suppressor of tumorigenicity 20	protein-coding	0.014252	0.478673	
chunk0086_55_1	chr18	13007347	13007745	+	0	NA	intron (NM_032142, intron 3 of 44)	intron (NM_032142, intron 3 of 44)	16184	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.005025	0.426065	
chunk0060_110_1	chr14	43460675	43461018	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	1046450	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.002915	0.380814	
chunk0139_202_1	chr4	54814129	54814489	+	0	NA	Intergenic	Intergenic	156381	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.005556	0.357341	
chunk0045_344_1	chr12	51405837	51406174	+	0	NA	intron (NM_001258401, intron 1 of 24)	intron (NM_001258401, intron 1 of 24)	-14589	NM_007210	11226	Hs.505575	NM_007210	ENSG00000139629	GALNT6	GALNAC-T6|GalNAcT6	polypeptide N-acetylgalactosaminyltransferase 6	protein-coding	0.008902	0.434911	
chunk0199_359_1	chr9	12658086	12658361	+	0	NA	Intergenic	MER52D|LTR|ERV1	-35163	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.007273	0.579710	
chunk0200_361_1	chr9	25674170	25674436	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	4555	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.011278	0.434457	
chunk0065_418_1	chr14	105916140	105916372	+	0	NA	Intergenic	Intergenic	-1723	NR_026800	9834	Hs.649259	NM_014151	ENSG00000226777	FAM30A	C14orf110|HSPC053|KIAA0125	family with sequence similarity 30 member A	ncRNA	0.000000	0.506438	93(AGGTACACACTGTACT,-,0.00),94(GGTACACACTGTACTT,+,0.00)
chunk0014_280_1	chr1	180528543	180529366	+	0	NA	Intergenic	Intergenic	-26067	NM_032360	84320	Hs.200051	NM_032360	ENSG00000230124	ACBD6	-	acyl-CoA binding domain containing 6	protein-coding	0.015796	0.430825	423(CGAGACATCGTGTTCT,-,0.00),424(GAGACATCGTGTTCTC,+,0.00),684(GGAGCTGGGTGTCCTT,+,0.00)
chunk0046_440_1	chr12	64836088	64836550	+	0	NA	intron (NM_015279, intron 5 of 11)	intron (NM_015279, intron 5 of 11)	11747	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.019481	0.416847	
chunk0162_140_1	chr6	3155474	3155812	+	0	NA	exon (NM_001069, exon 3 of 4)	exon (NM_001069, exon 3 of 4)	1906	NM_001310315	7280	Hs.654543	NM_001069	ENSG00000137267	TUBB2A	CDCBM5|TUBB|TUBB2	tubulin beta 2A class IIa	protein-coding	0.014793	0.536873	
chunk0153_369_1	chr5	74766934	74767345	+	0	NA	non-coding (NR_104006, exon 1 of 20)	non-coding (NR_104006, exon 1 of 20)	148	NR_073403	10412	Hs.482526	NM_014886	ENSG00000164346	NSA2	CDK105|HCL-G1|HCLG1|HUSSY-29|HUSSY29|TINP1	NSA2 ribosome biogenesis factor	protein-coding	0.080292	0.597087	
chunk0096_371_1	chr2	36663968	36664471	+	0	NA	Intergenic	L2a|LINE|L2	-32471	NM_053276	5212	Hs.137415	NM_053276	ENSG00000205221	VIT	VIT1	vitrin	protein-coding	0.017893	0.416667	
chunk0043_79_1	chr12	14442331	14442701	+	0	NA	intron (NM_001286514, intron 5 of 14)	Merlin1_HS|DNA|Merlin	57452	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.010811	0.371968	339(AGGGACAATTTGTTCA,-,0.00),340(GGGACAATTTGTTCAG,+,0.00)
chunk0125_325_1	chr3	70983792	70984182	+	0	NA	intron (NM_032682, intron 14 of 20)	intron (NM_032682, intron 14 of 20)	80936	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.007692	0.347826	
chunk0103_376_1	chr2	168627371	168627774	+	0	NA	intron (NM_001256126, intron 3 of 10)	L1M6|LINE|L1	44629	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.002481	0.297030	
chunk0103_367_1	chr2	168478277	168478476	+	0	NA	intron (NM_001256126, intron 1 of 10)	HAL1|LINE|L1	22127	NM_203463	253782	Hs.506829	NM_203463	ENSG00000172292	CERS6	CERS5|LASS6	ceramide synthase 6	protein-coding	0.005025	0.540000	
chunk0174_425_1	chr6	165925347	165925727	+	0	NA	intron (NR_026861, intron 1 of 1)	L1MD2|LINE|L1	-62014	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.000000	0.356955	
chunk0177_132_1	chr7	22442177	22442750	+	0	NA	intron (NM_001164460, intron 4 of 4)	intron (NM_001164460, intron 4 of 4)	57819	NM_001164460	256227	Hs.729825	NM_207342	ENSG00000105889	STEAP1B	-	STEAP family member 1B	protein-coding	0.012216	0.486063	
chunk0022_38_1	chr10	8006968	8007553	+	0	NA	intron (NM_031923, intron 4 of 6)	L1ME3Cz|LINE|L1	45231	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.000000	0.385666	
chunk0152_55_1	chr5	57561767	57562078	+	0	NA	Intergenic	L2a|LINE|L2	-8420	NR_120607	100996645	Hs.582496	NR_120607		LINCR-0003	-	uncharacterized LincR-0003	ncRNA	0.003215	0.336538	150(TAGAACACAATGTTTC,-,0.00),151(AGAACACAATGTTTCT,+,0.00)
chunk0179_293_1	chr7	49770260	49770804	+	0	NA	Intergenic	MIR3|SINE|MIR	-3129	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.003676	0.467890	
chunk0055_314_1	chr13	68066993	68067635	+	0	NA	Intergenic	MER70A|LTR|ERVL	694927	NR_130792	100874145	Hs.508194	NR_130792	ENSG00000230040	LINC00364	LncRNA00364	long intergenic non-protein coding RNA 364	ncRNA	0.004673	0.395023	94(AGAAACAGGATGTACT,-,0.00),95(GAAACAGGATGTACTT,+,0.00)
chunk0115_26_1	chr21	20877204	20877824	+	0	NA	Intergenic	Intergenic	-74406	NR_109788	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.003226	0.399356	
chunk0045_401_1	chr12	52814332	52814997	+	0	NA	promoter-TSS (NM_002272)	promoter-TSS (NM_002272)	-548	NM_002272	3851	Hs.654610	NM_002272	ENSG00000170477	KRT4	CK-4|CK4|CYK4|K4|WSN1	keratin 4	protein-coding	0.012030	0.516517	
chunk0121_380_1	chr3	25189286	25189548	+	0	NA	intron (NM_001290216, intron 1 of 7)	L4_A_Mam|LINE|RTE-X	15085	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.003817	0.429658	
chunk0056_410_1	chr13	94178952	94179162	+	0	NA	intron (NR_046535, intron 3 of 3)	intron (NR_046535, intron 3 of 3)	8934	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.019048	0.454976	
chunk0179_4_1	chr7	42392520	42393024	+	0	NA	Intergenic	Intergenic	-155753	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.007937	0.378218	
chunk0199_241_1	chr9	5510622	5511097	+	0	NA	intron (NM_025239, intron 1 of 6)	intron (NM_025239, intron 1 of 6)	314	NM_025239	80380	Hs.532279	NM_025239	ENSG00000197646	PDCD1LG2	B7DC|Btdc|CD273|PD-L2|PDCD1L2|PDL2|bA574F11.2	programmed cell death 1 ligand 2	protein-coding	0.002105	0.418067	
chunk0102_233_1	chr2	148793042	148793403	+	0	NA	Intergenic	Intergenic	-82001	NM_004522	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.005540	0.381215	168(AAGAACACTGTGTTCT,-,0.00),169(AGAACACTGTGTTCTT,+,0.00)
chunk0037_110_1	chr11	72348616	72348893	+	0	NA	intron (NM_030813, intron 6 of 16)	intron (NM_030813, intron 6 of 16)	85930	NM_001258394	81570	Hs.523877	NM_030813	ENSG00000162129	CLPB	ANKCLB|HSP78|MEGCANN|MGCA7|SKD3	ClpB homolog, mitochondrial AAA ATPase chaperonin	protein-coding	0.000000	0.438849	
chunk0126_68_1	chr3	74559211	74559708	+	0	NA	Intergenic	Intergenic	-38319	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.012072	0.443775	
chunk0061_14_1	chr14	55654025	55655125	+	0	NA	intron (NR_073128, intron 28 of 43)	intron (NR_073128, intron 28 of 43)	74368	NR_073128	3895	Hs.509414	NM_004986	ENSG00000126777	KTN1	CG1|KNT|MU-RMS-40.19	kinectin 1	protein-coding	0.007273	0.366031	1046(CAGGACATCCTGGGCT,-,0.00),1047(AGGACATCCTGGGCTC,+,0.00)
chunk0072_151_1	chr15	92805088	92805481	+	0	NA	Intergenic	MIRb|SINE|MIR	9800	NR_033769	728619	Hs.684129	NR_033769		ASB9P1	-	ankyrin repeat and SOCS box containing 9 pseudogene 1	pseudo	0.017812	0.439086	
chunk0106_465_1	chr2	209457841	209458249	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	33998	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.000000	0.369193	
chunk0080_440_1	chr17	36534470	36534734	+	0	NA	promoter-TSS (NM_178517).2	promoter-TSS (NM_178517).2	855	NM_001033580	80179	Hs.302051	NM_025109	ENSG00000278259	MYO19	MYOHD1	myosin XIX	protein-coding	0.041667	0.607547	
chunk0091_115_1	chr19	6229567	6229793	+	0	NA	intron (NM_005934, intron 4 of 11)	(AC)n|Simple_repeat|Simple_repeat	50268	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.039823	0.546256	
chunk0012_406_1	chr1	164061437	164061654	+	0	NA	Intergenic	L1PA13|LINE|L1	-497815	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.004608	0.591743	
chunk0133_178_1	chr3	170070461	170070771	+	0	NA	intron (NM_014373, intron 2 of 3)	L1MC5|LINE|L1	32669	NM_014373	26996	Hs.231320	NM_014373	ENSG00000173890	GPR160	GPCR1|GPCR150	G protein-coupled receptor 160	protein-coding	0.003226	0.376206	
chunk0184_125_1	chr7	114653462	114653661	+	0	NA	TTS (NR_037439)	TTS (NR_037439)	216	NR_037439	100500896		NR_037439	ENSG00000272230	MIR3666	-	microRNA 3666	ncRNA	0.005025	0.485000	
chunk0101_371_1	chr2	138177626	138178313	+	0	NA	Intergenic	Intergenic	213731	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.005822	0.386628	
chunk0035_9_1	chr11	40073669	40074047	+	0	NA	Intergenic	L2a|LINE|L2	219272	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.308707	
chunk0005_72_1	chr1	55903977	55904240	+	0	NA	Intergenic	L1ME1|LINE|L1	675476	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.000000	0.291667	
chunk0209_372_1	chrX	54045398	54045986	+	0	NA	promoter-TSS (NM_001184896)	promoter-TSS (NM_001184896)	-556	NM_001184896	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.011905	0.410866	
chunk0070_52_1	chr15	69576824	69577306	+	0	NA	Intergenic	Intergenic	-15135	NR_126438	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.004149	0.530021	
chunk0166_421_1	chr6	52591792	52592041	+	0	NA	Intergenic	Intergenic	14618	NR_103447	401264	Hs.544586	NR_103446	ENSG00000225791	TRAM2-AS1	-	TRAM2 antisense RNA 1 (head to head)	ncRNA	0.004016	0.476000	
chunk0042_121_1	chr12	3365386	3365738	+	0	NA	Intergenic	Intergenic	-15787	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.022727	0.572238	
chunk0078_143_1	chr17	3895040	3895325	+	0	NA	Intergenic	L2b|LINE|L2	-2139	NM_172207	84254	Hs.8417	NM_032294	ENSG00000004660	CAMKK1	CAMKKA	calcium/calmodulin dependent protein kinase kinase 1	protein-coding	0.003509	0.566434	
chunk0020_207_1	chr1	235078237	235078679	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-8640	NR_027454	731656	Hs.702477	NR_027454		LINC01348	-	long intergenic non-protein coding RNA 1348	ncRNA	0.006787	0.383747	
chunk0094_216_1	chr2	6648677	6649025	+	0	NA	TTS (NR_110497)	TTS (NR_110497)	-1522	NR_106986	102466235		NR_106986	ENSG00000283394	MIR7515	hsa-mir-7515	microRNA 7515	ncRNA	0.014368	0.441261	193(AAGAACGGTCTGTTCT,-,0.00),194(AGAACGGTCTGTTCTG,+,0.00)
chunk0071_11_1	chr15	78866812	78867211	+	0	NA	Intergenic	L1MC5a|LINE|L1	-5770	NM_001265603	10933	Hs.374503	NM_006791	ENSG00000185787	MORF4L1	Eaf3|FWP006|HsT17725|MEAF3|MORFRG15|MRG15|S863-6	mortality factor 4 like 1	protein-coding	0.012531	0.370000	
chunk0160_151_1	chr5	151493185	151493384	+	0	NA	TTS (NM_078483)	TTS (NM_078483)	28864	NR_106752	102465246		NR_106752	ENSG00000276622	MIR6499	hsa-mir-6499|mir-6499	microRNA 6499	ncRNA	0.020101	0.475000	
chunk0032_132_1	chr11	4494867	4495487	+	0	NA	Intergenic	HERVK13-int|LTR|ERVK	6298	NM_001005171	390036	Hs.553726	NM_001005171	ENSG00000196778	OR52K1	OR11-8	olfactory receptor family 52 subfamily K member 1	protein-coding	0.008065	0.409018	
chunk0065_168_1	chr15	25829546	25829849	+	0	NA	intron (NM_024490, intron 1 of 20)	intron (NM_024490, intron 1 of 20)	19128	NR_039865	100616474		NR_039865	ENSG00000266517	MIR4715	-	microRNA 4715	ncRNA	0.019802	0.588816	267(AGGGACACAGTGGGCC,-,0.00)
chunk0104_141_1	chr2	173474697	173475082	+	0	NA	Intergenic	Intergenic	120056	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.002597	0.448187	228(AGGAACACCTTGTTCA,-,0.00),229(GGAACACCTTGTTCAC,+,0.00)
chunk0097_339_1	chr2	58080923	58081549	+	0	NA	intron (NM_001288836, intron 3 of 13)	Kanga1|DNA|TcMar-Tc2	34524	NM_001130481	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.000000	0.306220	
chunk0033_448_1	chr11	25515747	25516114	+	0	NA	Intergenic	LTR1B1|LTR|ERV1	-673193	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.035422	0.529891	
chunk0180_170_1	chr7	65308317	65308670	+	0	NA	Intergenic	PABL_B-int|LTR|ERV1	-65306	NM_001287534	168374	Hs.9521	NM_007139	ENSG00000146757	ZNF92	HEL-203|HPF12|HTF12|TF12	zinc finger protein 92	protein-coding	0.005666	0.460452	
chunk0090_212_1	chr18	73381621	73382015	+	0	NA	Intergenic	Intergenic	56877	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.000000	0.329114	
chunk0201_233_1	chr9	37602738	37603266	+	0	NA	Intergenic	Intergenic	-10363	NM_001001790	401505	Hs.130774	NM_001001790	ENSG00000175768	TOMM5	C9orf105|Tom5|bA613M10.3	translocase of outer mitochondrial membrane 5	protein-coding	0.011364	0.480151	
chunk0157_302_1	chr5	121105800	121106288	+	0	NA	Intergenic	Intergenic	-216506	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.004098	0.284254	
chunk0161_47_1	chr5	166045973	166046405	+	0	NA	Intergenic	Intergenic	880181	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004630	0.341801	
chunk0192_242_1	chr8	65586236	65586440	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-23672	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.000000	0.439024	
chunk0027_398_1	chr10	80319766	80319965	+	0	NA	Intergenic	Intergenic	-24880	NR_070309	84332	Hs.741500	NM_032372	ENSG00000133665	DYDC2	-	DPY30 domain containing 2	protein-coding	0.000000	0.505000	
chunk0045_8_1	chr12	42921941	42922611	+	0	NA	Intergenic	Intergenic	-275778	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.010448	0.426230	
chunk0057_218_1	chr13	104024269	104024981	+	0	NA	Intergenic	Intergenic	599425	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.004213	0.389902	
chunk0075_380_1	chr16	56643286	56643568	+	0	NA	promoter-TSS (NR_003658)	promoter-TSS (NR_003658)	-260	NR_027781	326343	Hs.679600	NM_175620		MT1DP	MTM	metallothionein 1D, pseudogene	pseudo	0.088652	0.689046	
chunk0190_308_1	chr8	38381714	38382035	+	0	NA	5' UTR (NM_023034, exon 1 of 24)	5' UTR (NM_023034, exon 1 of 24)	398	NM_023034	54904	Hs.434966	NM_017778	ENSG00000147548	NSD3	KMT3F|KMT3G|WHISTLE|WHSC1L1|pp14328	nuclear receptor binding SET domain protein 3	protein-coding	0.105919	0.677019	
chunk0171_294_1	chr6	128483682	128483997	+	0	NA	intron (NM_001291981, intron 1 of 32).2	intron (NM_001291981, intron 1 of 32).2	36835	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.006349	0.379747	
chunk0196_104_1	chr8	103052120	103052422	+	0	NA	intron (NM_001695, intron 5 of 12)	intron (NM_001695, intron 5 of 12)	31251	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.006623	0.326733	
chunk0138_78_1	chr4	35039769	35040264	+	0	NA	Intergenic	L1ME1|LINE|L1	-1000123	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.006061	0.312500	
chunk0190_229_1	chr8	35826294	35826500	+	0	NA	Intergenic	HAL1|LINE|L1	-116077	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.004854	0.434783	
chunk0154_61_1	chr5	77305319	77305827	+	0	NA	intron (NM_001029853, intron 1 of 20)	intron (NM_001029853, intron 1 of 20)	94692	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.003937	0.546169	159(AGGAAGAGAGTGTTCT,-,0.00),160(GGAAGAGAGTGTTCTG,+,0.00)
chunk0212_248_1	chrX	138556455	138556958	+	0	NA	Intergenic	L2a|LINE|L2	60932	NR_026935	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.001988	0.345238	314(GAAGACAGAATGTGCC,-,0.00),315(AAGACAGAATGTGCCC,+,0.00)
chunk0116_336_1	chr21	41396487	41396699	+	0	NA	intron (NM_002463, intron 7 of 13)	MIRb|SINE|MIR	-23965	NM_001144925	4599	Hs.517307	NM_002462	ENSG00000157601	MX1	IFI-78K|IFI78|MX|MxA	MX dynamin like GTPase 1	protein-coding	0.033019	0.488263	
chunk0210_302_1	chrX	88631906	88632155	+	0	NA	Intergenic	L1MA2|LINE|L1	-115195	NM_033048	53336	Hs.458292	NM_033048	ENSG00000147183	CPXCR1	CT77	CPX chromosome region candidate 1	protein-coding	0.004016	0.300000	
chunk0202_371_1	chr9	80567111	80567670	+	0	NA	Intergenic	L1MB7|LINE|L1	592367	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.001789	0.330357	
chunk0120_243_1	chr3	8582879	8583223	+	0	NA	Intergenic	L2a|LINE|L2	11269	NR_024065	29931	Hs.433151	NM_013343		LINC00312	ERR-10|ERR10|LMCD1DN|LOH3CR2A|NAG-7|NAG7|NCRNA00312	long intergenic non-protein coding RNA 312	ncRNA	0.005814	0.428986	
chunk0049_122_1	chr12	91440846	91441261	+	0	NA	Intergenic	L1PA15|LINE|L1	-257929	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.007229	0.401442	
chunk0149_119_1	chr5	19454969	19455322	+	0	NA	Intergenic	L1MC3|LINE|L1	431127	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.005666	0.344633	
chunk0178_473_1	chr7	42292998	42293511	+	0	NA	Intergenic	Intergenic	-56235	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.015595	0.521401	
chunk0178_107_1	chr7	30896846	30897232	+	0	NA	Intergenic	Intergenic	-14761	NM_198098	358	Hs.76152	NM_000385	ENSG00000240583	AQP1	AQP-CHIP|CHIP28|CO	aquaporin 1 (Colton blood group)	protein-coding	0.010363	0.586563	
chunk0018_170_1	chr1	219013969	219014531	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	159538	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.003559	0.339254	
chunk0039_131_1	chr11	98316685	98317083	+	0	NA	Intergenic	Intergenic	-704092	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.010050	0.383459	175(CAACACACAGTGTTCC,-,0.00),176(AACACACAGTGTTCCT,+,0.00)
chunk0046_409_1	chr12	64403202	64403529	+	0	NA	Intergenic	MIR|SINE|MIR	-1008	NM_007235	11260	Hs.85951	NM_007235	ENSG00000184575	XPOT	XPO3	exportin for tRNA	protein-coding	0.012232	0.390244	142(GAGCACATTGTGTGTC,-,0.00)
chunk0162_109_1	chr6	2708488	2708913	+	0	NA	intron (NM_001012418, intron 2 of 12)	intron (NM_001012418, intron 2 of 12)	42220	NM_001012418	340156	Hs.127830	NM_001012418	ENSG00000145949	MYLK4	SgK085	myosin light chain kinase family member 4	protein-coding	0.009412	0.363850	156(CAGGACTATATGTTCT,-,0.00),157(AGGACTATATGTTCTA,+,0.00)
chunk0061_187_1	chr14	60157520	60157956	+	0	NA	intron (NM_016029, intron 1 of 6)	L2b|LINE|L2	7755	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.002294	0.379863	
chunk0098_227_1	chr2	73874140	73874767	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-18513	NM_001199893	72	Hs.516105	NM_001615	ENSG00000163017	ACTG2	ACT|ACTA3|ACTE|ACTL3|ACTSG|VSCM	actin gamma 2, smooth muscle	protein-coding	0.004785	0.393312	318(AGATACAGGATGTCCT,-,0.00),319(GATACAGGATGTCCTT,+,0.00)
chunk0204_436_1	chr9	103942693	103943092	+	0	NA	Intergenic	Intergenic	-56817	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.002506	0.385000	
chunk0021_172_1	chr10	5446266	5446832	+	0	NA	promoter-TSS (NM_005863)	promoter-TSS (NM_005863)	-2	NM_005863	10276	Hs.25155	NM_005863	ENSG00000173848	NET1	ARHGEF8|NET1A	neuroepithelial cell transforming 1	protein-coding	0.038869	0.532628	
chunk0046_254_1	chr12	60544869	60545469	+	0	NA	Intergenic	L1MC3|LINE|L1	855832	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.010000	0.317804	218(ATACACACGGTGTTCT,-,0.00),219(TACACACGGTGTTCTC,+,0.00)
chunk0092_69_1	chr19	20565764	20566023	+	0	NA	promoter-TSS (NM_001159293)	promoter-TSS (NM_001159293)	-73	NM_001159293	100129842	Hs.515696	NM_001159293	ENSG00000237440	ZNF737	ZNF102	zinc finger protein 737	protein-coding	0.030888	0.569231	
chunk0002_336_1	chr1	24645143	24645522	+	0	NA	intron (NM_001303449, intron 1 of 17)	intron (NM_001303449, intron 1 of 17)	1773	NM_001303449	10250	Hs.18192	NM_005839	ENSG00000133226	SRRM1	160-KD|POP101|SRM160	serine and arginine repetitive matrix 1	protein-coding	0.013193	0.386842	
chunk0081_323_1	chr17	46121214	46121552	+	0	NA	intron (NM_001193465, intron 3 of 15)	L2a|LINE|L2	71417	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.002959	0.457227	226(TGGCACTGGCTGTTCT,-,0.00),227(GGCACTGGCTGTTCTT,+,0.00)
chunk0075_442_1	chr16	58021763	58022327	+	0	NA	TTS (NM_024598)	TTS (NM_024598)	-3333	NM_002428	4324	Hs.80343	NM_002428	ENSG00000102996	MMP15	MMP-15|MT2-MMP|MT2MMP|MTMMP2|SMCP-2	matrix metallopeptidase 15	protein-coding	0.008865	0.562832	496(AGGCACATTCTGTGCC,-,0.00),497(GGCACATTCTGTGCCT,+,0.00)
chunk0197_121_1	chr8	119956343	119956607	+	0	NA	intron (NM_022783, intron 3 of 8)	intron (NM_022783, intron 3 of 8)	82820	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.000000	0.513208	239(AGGGACAGAGTGGTCA,-,0.00)
chunk0063_124_1	chr14	79329432	79329768	+	0	NA	intron (NM_138970, intron 1 of 5)	MER58A|DNA|hAT-Charlie	50261	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.005952	0.418398	
chunk0207_170_1	chr9	130451783	130452446	+	0	NA	intron (NM_000050, intron 2 of 15)	intron (NM_000050, intron 2 of 15)	7407	NM_000050	445	Hs.160786	NM_000050	ENSG00000130707	ASS1	ASS|CTLN1	argininosuccinate synthase 1	protein-coding	0.030166	0.621988	293(GTGAACATCCTGTTCC,-,0.00),294(TGAACATCCTGTTCCC,+,0.00)
chunk0178_175_1	chr7	34130680	34131083	+	0	NA	intron (NM_133468, intron 14 of 15)	MIRb|SINE|MIR	225970	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.002481	0.482673	182(AGGAACAGCATGTGCT,-,0.00),183(GGAACAGCATGTGCTT,+,0.00)
chunk0024_342_1	chr10	43353605	43353953	+	0	NA	Intergenic	Intergenic	-17865	NM_001184963	53828	Hs.130497	NM_173160	ENSG00000150201	FXYD4	CHIF	FXYD domain containing ion transport regulator 4	protein-coding	0.002874	0.378223	
chunk0177_138_1	chr7	22607357	22607644	+	0	NA	Intergenic	Intergenic	44163	NR_038393	100506178	Hs.668122	NR_038393	ENSG00000232759	LOC100506178	-	uncharacterized LOC100506178	ncRNA	0.013937	0.361111	
chunk0115_385_1	chr21	30338426	30339075	+	0	NA	Intergenic	Intergenic	-1056	NM_001077711	643812	Hs.580881	NM_001077711	ENSG00000206107	KRTAP27-1	-	keratin associated protein 27-1	protein-coding	0.009245	0.349231	
chunk0161_82_1	chr5	167103925	167104744	+	0	NA	Intergenic	L2b|LINE|L2	-177964	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.009768	0.382927	
chunk0010_92_1	chr1	113739463	113739963	+	0	NA	intron (NM_006608, intron 2 of 17)	L1MA5|LINE|L1	19442	NM_006608	10745	Hs.655824	NM_006608	ENSG00000116793	PHTF1	PHTF	putative homeodomain transcription factor 1	protein-coding	0.010000	0.339321	
chunk0012_32_1	chr1	155049618	155050012	+	0	NA	intron (NR_040773, intron 1 of 3)	intron (NR_040773, intron 1 of 3)	1350	NR_040772	100505666	Hs.657533	NR_040772		DCST1-AS1	-	DCST1 antisense RNA 1	ncRNA	0.005076	0.450633	
chunk0139_329_1	chr4	58688608	58689004	+	0	NA	Intergenic	Intergenic	1262934	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.002525	0.322418	
chunk0070_109_1	chr15	70445765	70446042	+	0	NA	Intergenic	Intergenic	-169644	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.003610	0.338129	
chunk0039_312_1	chr11	103335946	103336451	+	0	NA	intron (NM_001377, intron 82 of 88)	L1MA4|LINE|L1	226767	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.005941	0.337945	
chunk0065_412_1	chr14	105660742	105661184	+	0	NA	Intergenic	Intergenic	11844	NR_046211	2003	Hs.744419	NR_046211		ELK2AP	ELK2|ELK2.1|ELK2P1	ETS transcription factor ELK2A, pseudogene	pseudo	0.011312	0.487585	
chunk0001_39_1	chr1	1577125	1577626	+	0	NA	Intergenic	MER52A|LTR|ERV1	-2493	NM_014188	29101	Hs.30026	NM_014188	ENSG00000160075	SSU72	HSPC182|PNAS-120	SSU72 homolog, RNA polymerase II CTD phosphatase	protein-coding	0.007984	0.545817	
chunk0084_386_1	chr17	81991795	81992146	+	0	NA	intron (NM_024083, intron 4 of 15)	intron (NM_024083, intron 4 of 15)	14420	NM_024083	79058	Hs.298351	NM_024083	ENSG00000169696	ASPSCR1	ASPCR1|ASPL|ASPS|RCC17|TUG|UBXD9|UBXN9	ASPSCR1 tether for SLC2A4, UBX domain containing	protein-coding	0.056980	0.644886	
chunk0194_313_1	chr8	88256993	88257605	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	70189	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.001634	0.350734	
chunk0198_17_1	chr9	312385	313091	+	0	NA	intron (NM_001190458, intron 5 of 45)	L4_B_Mam|LINE|RTE-X	39690	NM_001193536	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.004249	0.396040	
chunk0076_224_1	chr16	68696634	68696900	+	0	NA	intron (NM_001793, intron 15 of 15)	intron (NM_001793, intron 15 of 15)	-40525	NM_004360	999	Hs.461086	NM_004360	ENSG00000039068	CDH1	Arc-1|BCDS1|CD324|CDHE|ECAD|LCAM|UVO	cadherin 1	protein-coding	0.022556	0.471910	
chunk0078_65_1	chr17	1504412	1504949	+	0	NA	intron (NM_001135642, intron 9 of 13)	MIRb|SINE|MIR	-11973	NM_001080779	4641	Hs.286226	NM_033375	ENSG00000197879	MYO1C	MMI-beta|MMIb|NMI|myr2	myosin IC	protein-coding	0.020484	0.520446	
chunk0095_260_1	chr2	19552408	19552607	+	0	NA	Intergenic	Intergenic	-193896	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.005025	0.340000	
chunk0078_445_1	chr16	89682051	89682601	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-4342	NM_052987	8558	Hs.699177	NM_003674	ENSG00000185324	CDK10	ALSAS|PISSLRE	cyclin dependent kinase 10	protein-coding	0.003636	0.377495	
chunk0036_262_1	chr11	65027390	65027802	+	0	NA	exon (NM_013306, exon 1 of 8)	exon (NM_013306, exon 1 of 8)	188	NM_013306	29907	Hs.80132	NM_013306	ENSG00000110025	SNX15	HSAF001435	sorting nexin 15	protein-coding	0.072816	0.605327	
chunk0163_430_1	chr6	17239194	17239668	+	0	NA	Intergenic	Intergenic	-42147	NM_001143942	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.008439	0.414737	222(AGGTACGGTATGTGCT,-,0.00),223(GGTACGGTATGTGCTG,+,0.00)
chunk0184_423_1	chr7	122834033	122834446	+	0	NA	intron (NM_017954, intron 1 of 29)	intron (NM_017954, intron 1 of 29)	52520	NM_001009571	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.009685	0.408213	
chunk0175_172_1	chr7	4783752	4783982	+	0	NA	intron (NM_014855, intron 5 of 16)	intron (NM_014855, intron 5 of 16)	4772	NR_039800	100616465		NR_039800	ENSG00000264474	MIR4656	-	microRNA 4656	ncRNA	0.052174	0.692641	
chunk0047_320_1	chr12	74194263	74194927	+	0	NA	intron (NR_038300, intron 3 of 6)	L1P4|LINE|L1	98036	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.003012	0.363910	411(TAGATCAAGATGTTCT,-,0.00),412(AGATCAAGATGTTCTC,+,0.00)
chunk0166_281_1	chr6	48290565	48291296	+	0	NA	Intergenic	Intergenic	-222241	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.005472	0.367486	
chunk0031_35_1	chr10	122112427	122112745	+	0	NA	promoter-TSS (NM_001291879)	promoter-TSS (NM_001291879)	-453	NM_001291879	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.062893	0.573668	
chunk0151_23_1	chr5	41609328	41609688	+	0	NA	Intergenic	L1PA5|LINE|L1	-98880	NM_001005473	345557	Hs.145404	NM_001005473	ENSG00000182836	PLCXD3	-	phosphatidylinositol specific phospholipase C X domain containing 3	protein-coding	0.011111	0.440443	
chunk0020_275_1	chr1	236415903	236416148	+	0	NA	intron (NM_080738, intron 3 of 5)	intron (NM_080738, intron 3 of 5)	20609	NM_080738	128178	Hs.352224	NM_080738	ENSG00000186197	EDARADD	ECTD11A|ECTD11B|ED3|EDA3	EDAR associated death domain	protein-coding	0.012245	0.540650	
chunk0121_442_1	chr3	26374754	26375049	+	0	NA	Intergenic	L1PREC2|LINE|L1	-247908	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.006780	0.371622	
chunk0016_233_1	chr1	199774549	199775222	+	0	NA	Intergenic	Intergenic	-252717	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.004458	0.372404	
chunk0152_296_1	chr5	61610101	61610682	+	0	NA	Intergenic	Intergenic	-27390	NM_173667									0.013769	0.431271	
chunk0128_209_1	chr3	107987017	107987408	+	0	NA	Intergenic	Intergenic	103876	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.010230	0.428571	
chunk0020_346_1	chr1	239226740	239227231	+	0	NA	Intergenic	L1M2|LINE|L1	-402088	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.000000	0.504065	370(TGGCACTGCTTGTTCC,-,0.00),371(GGCACTGCTTGTTCCC,+,0.00)
chunk0077_350_1	chr16	83740823	83741100	+	0	NA	intron (NM_001220488, intron 11 of 14)	intron (NM_001220488, intron 11 of 14)	63015	NR_120308	102724163		NR_120308	ENSG00000260228	LOC102724163	-	uncharacterized LOC102724163	ncRNA	0.003610	0.492806	
chunk0093_401_1	chr19	56934814	56935038	+	0	NA	Intergenic	L1MB3|LINE|L1	94024	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.013393	0.426667	
chunk0091_413_1	chr19	16719659	16720090	+	0	NA	promoter-TSS (NM_001290355)	promoter-TSS (NM_001290355)	-102	NM_001290355	284434	Hs.406014	NM_001007525	ENSG00000188039	NWD1	-	NACHT and WD repeat domain containing 1	protein-coding	0.023202	0.516204	
chunk0047_242_1	chr12	72241558	72241854	+	0	NA	Intergenic	L1ME1|LINE|L1	-31043	NM_013381	29953	Hs.199814	NM_013381	ENSG00000072657	TRHDE	PAP-II|PGPEP2|TRH-DE	thyrotropin releasing hormone degrading enzyme	protein-coding	0.010135	0.390572	
chunk0106_163_1	chr2	200742007	200742240	+	0	NA	intron (NR_001557, intron 7 of 30)	intron (NR_001557, intron 7 of 30)	-6946	NR_037886	100507140	Hs.382116	NR_037886	ENSG00000237166	LINC01792	-	long intergenic non-protein coding RNA 1792	ncRNA	0.008584	0.482906	
chunk0012_465_1	chr1	165616112	165616815	+	0	NA	Intergenic	Intergenic	-14410	NM_004528	4259	Hs.191734	NM_004528	ENSG00000143198	MGST3	GST-III	microsomal glutathione S-transferase 3	protein-coding	0.001422	0.417614	
chunk0104_49_1	chr2	171321752	171321951	+	0	NA	3' UTR (NM_024770, exon 10 of 10)	3' UTR (NM_024770, exon 10 of 10)	-90537	NM_001136554	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.000000	0.330000	
chunk0106_406_1	chr2	207896467	207897074	+	0	NA	intron (NM_001080475, intron 6 of 7)	intron (NM_001080475, intron 6 of 7)	-127351	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.008237	0.429276	
chunk0130_341_1	chr3	138686880	138687145	+	0	NA	intron (NM_001256045, intron 5 of 12)	intron (NM_001256045, intron 5 of 12)	20609	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.000000	0.387218	
chunk0086_296_1	chr18	23852309	23852525	+	0	NA	intron (NM_001127717, intron 32 of 73)	intron (NM_001127717, intron 32 of 73)	-20603	NM_001127718	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.000000	0.313364	
chunk0159_100_1	chr5	138337683	138338495	+	0	NA	promoter-TSS (NM_016605)	promoter-TSS (NM_016605)	74	NM_016605	51307	Hs.54056	NM_016605	ENSG00000120709	FAM53C	C5orf6	family with sequence similarity 53 member C	protein-coding	0.077586	0.671587	
chunk0173_181_1	chr6	144816903	144817432	+	0	NA	intron (NM_007124, intron 64 of 73)	intron (NM_007124, intron 64 of 73)	411512	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.001890	0.316981	
chunk0174_285_1	chr6	161944563	161945077	+	0	NA	intron (NM_013988, intron 3 of 8)	intron (NM_013988, intron 3 of 8)	-670745	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.001946	0.357282	181(AAGAACACACTGTCAC,-,0.00)
chunk0123_35_1	chr3	40722964	40723429	+	0	NA	Intergenic	Intergenic	198318	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.002151	0.418455	
chunk0027_392_1	chr10	79996446	79996708	+	0	NA	Intergenic	L1PA14|LINE|L1	-47472	NM_003019	6441	Hs.253495	NM_003019	ENSG00000133661	SFTPD	COLEC7|PSP-D|SFTP4|SP-D	surfactant protein D	protein-coding	0.000000	0.517110	
chunk0053_58_1	chr13	27960637	27960999	+	0	NA	Intergenic	CpG	8550	NM_001265	1045	Hs.127383	NM_001265	ENSG00000165556	CDX2	CDX-3|CDX2/AS|CDX3	caudal type homeobox 2	protein-coding	0.074586	0.617080	
chunk0050_339_1	chr12	107487184	107487724	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	-93403	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.005556	0.462107	
chunk0192_248_1	chr8	65726169	65726784	+	0	NA	intron (NM_002603, intron 9 of 12)	intron (NM_002603, intron 9 of 12)	56603	NM_001145838	9650	Hs.584788	NM_014637	ENSG00000066855	MTFR1	CHPPR|FAM54A2	mitochondrial fission regulator 1	protein-coding	0.006504	0.305195	
chunk0093_344_1	chr19	54867758	54868266	+	0	NA	TTS (NM_001282171).4	TTS (NM_001282171).4	-6081	NM_133278	2204	Hs.659872	NM_002000	ENSG00000186431	FCAR	CD89|CTB-61M7.2|FcalphaRI	Fc fragment of IgA receptor	protein-coding	0.003937	0.373281	317(AAGGACTGTGTGTACA,-,0.00),318(AGGACTGTGTGTACAC,+,0.00)
chunk0014_420_1	chr1	183262892	183263092	+	0	NA	intron (NM_170706, intron 8 of 10)	intron (NM_170706, intron 8 of 10)	41882	NM_170706	23057	Hs.497123	NM_015039	ENSG00000157064	NMNAT2	C1orf15|PNAT2	nicotinamide nucleotide adenylyltransferase 2	protein-coding	0.005000	0.437811	
chunk0206_69_1	chr9	119861578	119861939	+	0	NA	Intergenic	MIR|SINE|MIR	-73302	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.005540	0.345304	
chunk0057_212_1	chr13	104007710	104008074	+	0	NA	Intergenic	Intergenic	582692	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.008242	0.328767	
chunk0190_302_1	chr8	38231404	38231628	+	0	NA	promoter-TSS (NM_001164234)	promoter-TSS (NM_001164234)	25	NM_001164234	23259	Hs.434966	NM_015214	ENSG00000085788	DDHD2	SAMWD1|SPG54|iPLA(1)gamma	DDHD domain containing 2	protein-coding	0.098214	0.675556	
chunk0109_18_1	chr20	370748	371089	+	0	NA	Intergenic	Intergenic	-9711	NM_021158	57761	Hs.516826	NM_021158	ENSG00000101255	TRIB3	C20orf97|NIPK|SINK|SKIP3|TRB3	tribbles pseudokinase 3	protein-coding	0.005865	0.461988	145(AAGAACAGGATGCTCT,-,0.00),146(AGAACAGGATGCTCTG,+,0.00)
chunk0130_404_1	chr3	140387279	140387609	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	121345	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.003030	0.413897	
chunk0130_259_1	chr3	135964022	135964586	+	0	NA	Intergenic	Intergenic	-1369	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.001773	0.389381	256(TGGTACATTGTGTACT,-,0.00),257(GGTACATTGTGTACTT,+,0.00)
chunk0090_218_1	chr18	73509307	73509790	+	0	NA	Intergenic	L1MCa|LINE|L1	184607	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.004141	0.334711	
chunk0088_145_1	chr18	46173950	46174182	+	0	NA	promoter-TSS (NM_001008239)	promoter-TSS (NM_001008239)	44	NM_001008239	147339	Hs.116486	NM_145055	ENSG00000152242	C18orf25	ARKL1|Ark2N|RNF111L1	chromosome 18 open reading frame 25	protein-coding	0.112069	0.699571	
chunk0157_308_1	chr5	121542253	121542496	+	0	NA	Intergenic	Intergenic	219824	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.000000	0.254098	
chunk0012_115_1	chr1	156806127	156806482	+	0	NA	TTS (NM_001161441)	TTS (NM_001161441)	-9446	NM_001007792	4914	Hs.406293	NM_002529	ENSG00000198400	NTRK1	MTC|TRK|TRK1|TRKA|Trk-A|p140-TrkA	neurotrophic receptor tyrosine kinase 1	protein-coding	0.000000	0.497191	
chunk0091_406_1	chr19	16608151	16608696	+	0	NA	intron (NM_004831, intron 1 of 2)	MER63D|DNA|hAT-Blackjack	19781	NM_004831	9441	Hs.715040	NM_004831	ENSG00000105085	MED26	CRSP7|CRSP70	mediator complex subunit 26	protein-coding	0.003670	0.397436	257(GAGGACATGGTGTGCT,-,0.00),258(AGGACATGGTGTGCTA,+,0.00)
chunk0052_230_1	chr13	25683916	25684144	+	0	NA	intron (NM_001313741, intron 24 of 35)	intron (NM_001313741, intron 24 of 35)	215256	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.008772	0.301310	
chunk0148_233_1	chr5	9516840	9517350	+	0	NA	non-coding (NR_109935, exon 3 of 3)	non-coding (NR_109935, exon 3 of 3)	5762	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.003922	0.405088	264(AAGTACGATCTGTTCT,-,0.00),265(AGTACGATCTGTTCTT,+,0.00)
chunk0007_17_1	chr1	77380300	77380813	+	0	NA	intron (NM_012093, intron 6 of 13)	intron (NM_012093, intron 6 of 13)	97954	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.001949	0.431907	
chunk0171_186_1	chr6	125202000	125202404	+	0	NA	intron (NM_001003395, intron 1 of 6)	intron (NM_001003395, intron 1 of 6)	47928	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.009901	0.419753	
chunk0169_397_1	chr6	108155651	108156688	+	0	NA	Intergenic	Intergenic	-9889	NM_003269	7101	Hs.157688	NM_003269	ENSG00000112333	NR2E1	TLL|TLX|XTLL	nuclear receptor subfamily 2 group E member 1	protein-coding	0.005786	0.419075	
chunk0210_229_1	chrX	82398380	82399044	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-1109549	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.006024	0.332331	
chunk0194_28_1	chr8	81731837	81732267	+	0	NA	promoter-TSS (NM_152284)	promoter-TSS (NM_152284)	-401	NM_152284	92421	Hs.183861	NM_152284	ENSG00000164695	CHMP4C	SNF7-3|Shax3|VPS32C	charged multivesicular body protein 4C	protein-coding	0.013953	0.464037	285(AGGAACACTATGCTCA,-,0.00),286(GGAACACTATGCTCAC,+,0.00)
chunk0013_5_1	chr1	165689163	165689636	+	0	NA	intron (NM_000696, intron 2 of 10)	LTR40A1|LTR|ERVL	9264	NM_000696	223	Hs.2533	NM_000696	ENSG00000143149	ALDH9A1	ALDH4|ALDH7|ALDH9|E3|TMABADH	aldehyde dehydrogenase 9 family member A1	protein-coding	0.010571	0.400844	
chunk0132_350_1	chr3	161407067	161407491	+	0	NA	Intergenic	Intergenic	-19148	NR_102265	101243545	Hs.737526	NR_102265	ENSG00000240567	LINC02067	-	long intergenic non-protein coding RNA 2067	ncRNA	0.000000	0.341176	
chunk0046_382_1	chr12	63682830	63683107	+	0	NA	Intergenic	Intergenic	-14394	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.010830	0.428058	
chunk0194_87_1	chr8	82964641	82965419	+	0	NA	Intergenic	Intergenic	-438728	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003856	0.310655	
chunk0177_311_1	chr7	26078628	26079141	+	0	NA	Intergenic	Intergenic	-73343	NM_004289	9603	Hs.404741	NM_004289	ENSG00000050344	NFE2L3	NRF3	nuclear factor, erythroid 2 like 3	protein-coding	0.023392	0.414397	
chunk0186_230_1	chr7	140604713	140604950	+	0	NA	Intergenic	L2c|LINE|L2	-2289	NM_015689	27147	Hs.6385	NM_015689	ENSG00000146966	DENND2A	FAM31D|KIAA1277	DENN domain containing 2A	protein-coding	0.000000	0.361345	
chunk0210_308_1	chrX	90058771	90058981	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	136935	NM_138960	90316	Hs.592220	NM_138960	ENSG00000153779	TGIF2LX	TGIFLX	TGFB induced factor homeobox 2 like X-linked	protein-coding	0.004762	0.364929	
chunk0133_172_1	chr3	169967255	169967816	+	0	NA	promoter-TSS (NR_024409)	promoter-TSS (NR_024409)	743	NM_003262	7095	Hs.744859	NM_003262	ENSG00000008952	SEC62	Dtrp1|HTP1|TLOC1|TP-1	SEC62 homolog, preprotein translocation factor	protein-coding	0.032086	0.457295	
chunk0118_254_1	chr22	33036985	33037270	+	0	NA	intron (NM_001135774, intron 1 of 13)	MER34A1|LTR|ERV1	21264	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.014035	0.419580	
chunk0116_62_1	chr21	34054266	34054752	+	0	NA	Intergenic	Intergenic	-19014	NM_006933	6526	Hs.302742	NM_006933	ENSG00000198743	SLC5A3	BCW2|SMIT|SMIT1|SMIT2	solute carrier family 5 member 3	protein-coding	0.014403	0.451745	
chunk0118_409_1	chr22	38113847	38114118	+	0	NA	intron (NM_001004426, intron 13 of 15)	intron (NM_001004426, intron 13 of 15)	-3313	NM_025045	80115	Hs.474822	NM_025045	ENSG00000128298	BAIAP2L2	-	BAI1 associated protein 2 like 2	protein-coding	0.018450	0.547794	
chunk0179_330_1	chr7	50653872	50654419	+	0	NA	intron (NM_001001549, intron 4 of 14)	intron (NM_001001549, intron 4 of 14)	51156	NM_001001550	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.020110	0.518248	238(TTGCACAGTGTGTTCT,-,0.00),239(TGCACAGTGTGTTCTG,+,0.00)
chunk0102_390_1	chr2	154750375	154750750	+	0	NA	intron (NM_002239, intron 2 of 2)	intron (NM_002239, intron 2 of 2)	51981	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.008000	0.279255	
chunk0114_134_1	chr21	9983370	9983569	+	0	NA	Intergenic	Intergenic	-162408	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.405000	
chunk0176_395_1	chr7	18857030	18857767	+	0	NA	intron (NM_178425, intron 20 of 24)	Charlie9|DNA|hAT-Charlie	260274	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.001357	0.313008	
chunk0085_142_1	chr18	3260517	3261026	+	0	NA	intron (NR_130144, intron 1 of 2)	intron (NR_130144, intron 1 of 2)	1059	NR_130143	104968399	Hs.464472	NR_130143	ENSG00000264235	LOC104968399	-	uncharacterized LOC104968399	ncRNA	0.019646	0.413725	
chunk0111_320_1	chr20	32325822	32326709	+	0	NA	intron (NM_004798, intron 5 of 8)	intron (NM_004798, intron 5 of 8)	-32079	NM_001164603	171023	Hs.374043	NM_015338	ENSG00000171456	ASXL1	BOPS|MDS	ASXL transcriptional regulator 1	protein-coding	0.006764	0.453829	50(TGGCCAGGCTGTTCTC,+,0.00)
chunk0151_85_1	chr5	42819609	42820191	+	0	NA	Intergenic	Intergenic	-7978	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.008591	0.411664	
chunk0155_204_1	chr5	94941278	94941477	+	0	NA	intron (NM_024717, intron 4 of 22)	intron (NM_024717, intron 4 of 22)	140489	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.005025	0.445000	
chunk0004_264_1	chr1	47972783	47973115	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	23941	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.009036	0.471471	
chunk0069_239_1	chr15	64072511	64073303	+	0	NA	non-coding (NR_110310, exon 6 of 6)	non-coding (NR_110310, exon 6 of 6)	21101	NR_110310	84191	Hs.439548	NM_032231	ENSG00000166797	CIAO2A	CIA2A|FAM96A	cytosolic iron-sulfur assembly component 2A	protein-coding	0.005051	0.317781	432(AAGGACACACTGTTCC,-,0.00),433(AGGACACACTGTTCCA,+,0.00)
chunk0022_265_1	chr10	14922604	14923240	+	0	NA	intron (NM_022487, intron 11 of 12)	intron (NM_022487, intron 11 of 12)	31510	NM_001289079	64421	Hs.655932	NM_022487	ENSG00000152457	DCLRE1C	A-SCID|DCLREC1C|RS-SCID|SCIDA|SNM1C	DNA cross-link repair 1C	protein-coding	0.007862	0.437991	342(GGGGACACCAAGTCCC,-,0.00),343(GGGACACCAAGTCCCA,+,0.00)
chunk0025_186_1	chr10	53217796	53218110	+	0	NA	Intergenic	Intergenic	-446253	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.006369	0.203175	
chunk0032_138_1	chr11	4636069	4636782	+	0	NA	Intergenic	L2|LINE|L2	-3290	NM_001004751	390038	Hs.553728	NM_001004751	ENSG00000197428	OR51D1	OR11-14|OR51D1Q	olfactory receptor family 51 subfamily D member 1	protein-coding	0.007013	0.401961	
chunk0150_297_1	chr5	37494783	37495085	+	0	NA	intron (NM_018034, intron 8 of 17)	MER58A|DNA|hAT-Charlie	115624	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.000000	0.386139	
chunk0196_39_1	chr8	101635703	101636137	+	0	NA	intron (NM_024915, intron 11 of 15)	intron (NM_024915, intron 11 of 15)	143480	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.000000	0.402299	
chunk0194_306_1	chr8	88063061	88063260	+	0	NA	intron (NM_005941, intron 7 of 9)	L3|LINE|CR1	-189092	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.000000	0.320000	
chunk0120_317_1	chr3	10285993	10286298	+	0	NA	TTS (NR_026829)	TTS (NR_026829)	1726	NR_026829	84657	Hs.302131	NM_001039102	ENSG00000231177	LINC00852	C3orf42|GHRL-AS2|GHRLOS2|NAG73	long intergenic non-protein coding RNA 852	ncRNA	0.019672	0.526144	
chunk0065_162_1	chr15	25660898	25661296	+	0	NA	Intergenic	L1M6B|LINE|L1	187728	NR_039865	100616474		NR_039865	ENSG00000266517	MIR4715	-	microRNA 4715	ncRNA	0.005025	0.360902	
chunk0099_164_1	chr2	88553109	88553559	+	0	NA	intron (NR_110236, intron 2 of 2)	AluJb|SINE|Alu	14614	NR_110236	101928371	Hs.738045	NR_110236	ENSG00000225420	LOC101928371	-	uncharacterized LOC101928371	ncRNA	0.006667	0.490022	190(AGGCACATACTGTTCC,-,0.00),191(GGCACATACTGTTCCT,+,0.00)
chunk0053_154_1	chr13	30257701	30258298	+	0	NA	intron (NM_001014380, intron 3 of 10)	MamRTE1|LINE|RTE-BovB	49055	NM_001014380	84056	Hs.243596	NM_032116	ENSG00000102781	KATNAL1	-	katanin catalytic subunit A1 like 1	protein-coding	0.006700	0.406355	
chunk0209_378_1	chrX	54093163	54093649	+	0	NA	intron (NM_017848, intron 10 of 15)	L2c|LINE|L2	-48270	NM_001184896	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.004115	0.394251	203(TTGAACAGATTGTTCT,-,0.00),204(TGAACAGATTGTTCTG,+,0.00)
chunk0111_242_1	chr20	29781892	29782091	+	0	NA	Intergenic	Intergenic	-98393	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.020101	0.480000	
chunk0095_379_1	chr2	23593996	23594677	+	0	NA	intron (NM_052920, intron 3 of 13)	intron (NM_052920, intron 3 of 13)	208909	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.029369	0.516129	398(AGGGACATTTCGTTCC,-,0.00),399(GGGACATTTCGTTCCT,+,0.00)
chunk0135_181_1	chr3	188076901	188077644	+	0	NA	Intergenic	L2c|LINE|L2	-76601	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.013459	0.479839	352(TGGACTGTGAGTTCTT,+,0.00)
chunk0080_409_1	chr17	35664410	35664826	+	0	NA	intron (NM_001282, intron 14 of 20)	intron (NM_001282, intron 14 of 20)	-67042	NM_033315	91608	Hs.744994	NM_033315	ENSG00000270885	RASL10B	RRP17|VTS58635	RAS like family 10 member B	protein-coding	0.009615	0.354916	
chunk0107_44_1	chr2	211206201	211206905	+	0	NA	Intergenic	Intergenic	588982	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.004261	0.356028	
chunk0100_299_1	chr2	115174765	115174970	+	0	NA	intron (NM_001004360, intron 1 of 25)	MamRTE1|LINE|RTE-BovB	12760	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.004878	0.432039	
chunk0198_454_1	chr8	144253338	144254007	+	0	NA	intron (NM_032450, intron 33 of 43)	L1MEd|LINE|L1	9065	NR_107057	102465906		NR_107057	ENSG00000284054	MIR7112	MIR7112-1|MIR7112-2|hsa-mir-7112|hsa-mir-7112-1|hsa-mir-7112-2	microRNA 7112	ncRNA	0.028401	0.574627	
chunk0058_232_1	chr14	25457524	25457877	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	-407403	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.008499	0.333333	
chunk0070_88_1	chr15	70177707	70178062	+	0	NA	Intergenic	L1ME4a|LINE|L1	-79967	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.005634	0.379213	
chunk0146_427_1	chr4	169219411	169219886	+	0	NA	intron (NM_020870, intron 2 of 11)	intron (NM_020870, intron 2 of 11)	51450	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.006316	0.355042	
chunk0192_316_1	chr8	67047628	67048029	+	0	NA	intron (NM_006837, intron 6 of 7)	Tigger15a|DNA|TcMar-Tigger	14499	NM_006837	10987	Hs.491912	NM_006837	ENSG00000121022	COPS5	CSN5|JAB1|MOV-34|SGN5	COP9 signalosome subunit 5	protein-coding	0.004988	0.395522	149(AGGTTCAGACTGTTCT,-,0.00),150(GGTTCAGACTGTTCTG,+,0.00)
chunk0054_152_1	chr13	44051348	44051863	+	0	NA	Intergenic	Intergenic	29270	NR_026955	121838	Hs.201441	NR_026955		LINC00284	NCRNA00284	long intergenic non-protein coding RNA 284	ncRNA	0.003883	0.360465	
chunk0138_352_1	chr4	41897599	41897869	+	0	NA	Intergenic	Intergenic	-15123	NR_104143	101927074	Hs.611425	NR_104143	ENSG00000245870	LINC00682	-	long intergenic non-protein coding RNA 682	ncRNA	0.000000	0.309963	154(AAGAACATAAAGTGCC,-,0.00),155(AGAACATAAAGTGCCT,+,0.00)
chunk0012_178_1	chr1	159246846	159247300	+	0	NA	Intergenic	L1MA7|LINE|L1	41814	NM_001122951	2532	Hs.153381	NM_002036	ENSG00000213088	ACKR1	CCBP1|CD234|DARC|DARC/ACKR1|Dfy|FY|GPD|GpFy|WBCQ1	atypical chemokine receptor 1 (Duffy blood group)	protein-coding	0.002203	0.507692	
chunk0198_328_1	chr8	139958643	139958886	+	0	NA	intron (NM_001160372, intron 19 of 22)	intron (NM_001160372, intron 19 of 22)	-255708	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.024691	0.557377	95(CAGGACAGGGTGTGCA,-,0.00),96(AGGACAGGGTGTGCAG,+,0.00)
chunk0184_449_1	chr7	123328425	123328923	+	0	NA	Intergenic	Intergenic	-128703	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.000000	0.304609	
chunk0049_96_1	chr12	90851664	90852296	+	0	NA	Intergenic	Intergenic	-66043	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.004747	0.315956	
chunk0156_383_1	chr5	112958316	112958863	+	0	NA	Intergenic	Intergenic	-18121	NM_001242377	167227	Hs.443875	NM_152624	ENSG00000172795	DCP2	NUDT20	decapping mRNA 2	protein-coding	0.005484	0.401460	
chunk0211_448_1	chrX	129698012	129698584	+	0	NA	Intergenic	Intergenic	-40672	NM_003399	7512	Hs.170499	NM_003399	ENSG00000122121	XPNPEP2	AEACEI|APP2	X-prolyl aminopeptidase 2	protein-coding	0.003497	0.364747	271(TAGAACACAGTGTGTC,-,0.00),272(AGAACACAGTGTGTCC,+,0.00),274(AACACAGTGTGTCCAT,+,0.00)
chunk0043_294_1	chr12	21766143	21766428	+	0	NA	exon (NM_004982, exon 3 of 3)	exon (NM_004982, exon 3 of 3)	8536	NM_004982	3764	Hs.102308	NM_004982	ENSG00000121361	KCNJ8	KIR6.1|uKATP-1	potassium voltage-gated channel subfamily J member 8	protein-coding	0.028070	0.493007	
chunk0142_398_1	chr4	102674416	102674774	+	0	NA	intron (NM_005908, intron 7 of 16)	intron (NM_005908, intron 7 of 16)	86399	NM_005908	4126	Hs.480415	NM_005908	ENSG00000109323	MANBA	MANB1	mannosidase beta	protein-coding	0.005587	0.401114	202(ATGTACATGGTGTTCT,-,0.00),203(TGTACATGGTGTTCTA,+,0.00)
chunk0021_413_1	chr1	246814012	246814613	+	0	NA	Intergenic	Intergenic	24695	NR_015422	149134	Hs.720494	NM_207326		LINC01341	-	long intergenic non-protein coding RNA 1341	ncRNA	0.016639	0.423588	
chunk0023_401_1	chr10	31042744	31042980	+	0	NA	Intergenic	Intergenic	-10925	NR_026560	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.004237	0.341772	98(TAGAACATGAAGTACC,-,0.00),99(AGAACATGAAGTACCT,+,0.00)
chunk0070_27_1	chr15	69288789	69289197	+	0	NA	Intergenic	MIRb|SINE|MIR	-9962	NM_017705	54852	Hs.591096	NM_017705	ENSG00000137819	PAQR5	MPRG	progestin and adipoQ receptor family member 5	protein-coding	0.017157	0.567237	222(GAGGACACGAAGTACC,-,0.00),223(AGGACACGAAGTACCT,+,0.00)
chunk0030_435_1	chr10	120727038	120727594	+	0	NA	Intergenic	Charlie8|DNA|hAT-Charlie	-123859	NM_018117	55717	Hs.144447	NM_018117	ENSG00000120008	WDR11	BRWD2|DR11|HH14|SRI1|WDR15	WD repeat domain 11	protein-coding	0.005396	0.407540	
chunk0169_64_1	chr6	98871016	98871634	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	36621	NM_005604	5454	Hs.182505	NM_005604	ENSG00000184486	POU3F2	BRN2|N-Oct3|OCT7|OTF-7|OTF7|POUF3|brn-2|oct-7	POU class 3 homeobox 2	protein-coding	0.006472	0.350565	
chunk0058_374_1	chr14	29239819	29240467	+	0	NA	Intergenic	Intergenic	467439	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.006173	0.325116	
chunk0134_174_1	chr3	178085087	178086682	+	0	NA	Intergenic	Intergenic	269019	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.004389	0.413534	72(AGGCACATAATGAGCC,-,0.00),429(TGAACATGCAGTACTG,+,0.00),1487(CAGAACATCCTGTGAT,-,0.00),1488(AGAACATCCTGTGATT,+,0.00)
chunk0206_265_1	chr9	123960987	123961233	+	0	NA	Intergenic	Intergenic	-30972	NM_024820	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.008130	0.465587	
chunk0170_127_1	chr6	110897637	110897884	+	0	NA	Intergenic	Intergenic	22976	NM_001287216	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.012146	0.399194	
chunk0039_307_1	chr11	103160624	103161447	+	0	NA	exon (NM_001080463, exon 29 of 90)	exon (NM_001080463, exon 29 of 90)	51604	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.001215	0.276699	
chunk0065_407_1	chr14	105582678	105582984	+	0	NA	Intergenic	Intergenic	-38285	NR_107059	102466889		NR_107059	ENSG00000277030	MIR8071-2	hsa-mir-8071-2	microRNA 8071-2	ncRNA	0.009804	0.599349	
chunk0065_173_1	chr15	26096299	26096750	+	0	NA	Intergenic	MER90|LTR|ERV1	-19289	NR_038852	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.006652	0.396018	273(TAGACCATCCTGTTCT,-,0.00),274(AGACCATCCTGTTCTC,+,0.00)
chunk0011_38_1	chr1	143237504	143237709	+	0	NA	Intergenic	Intergenic	184986	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.024390	0.349515	
chunk0162_88_1	chr6	2105262	2105716	+	0	NA	intron (NM_001253846, intron 4 of 10)	intron (NM_001253846, intron 4 of 10)	70502	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.002203	0.345055	
chunk0147_213_1	chr4	180482659	180483017	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	676311	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.008380	0.323120	
chunk0162_27_1	chr6	901703	902319	+	0	NA	Intergenic	Intergenic	33513	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.012987	0.388979	
chunk0176_457_1	chr7	20140309	20140608	+	0	NA	promoter-TSS (NR_110114)	promoter-TSS (NR_110114)	-32	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.010033	0.463333	
chunk0057_98_1	chr13	98963890	98964229	+	0	NA	intron (NM_001130049, intron 1 of 32)	L2c|LINE|L2	14025	NM_001130050	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.014749	0.505882	
chunk0148_364_1	chr5	14594380	14594657	+	0	NA	intron (NM_019018, intron 1 of 7)	intron (NM_019018, intron 1 of 7)	12736	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.007220	0.586331	135(GAGGACACTGTGTCCC,-,0.00),136(AGGACACTGTGTCCCC,+,0.00)
chunk0112_448_1	chr20	48485321	48485526	+	0	NA	Intergenic	Intergenic	125512	NR_026958	284749	Hs.299080	NR_026958	ENSG00000235621	LINC00494	-	long intergenic non-protein coding RNA 494	ncRNA	0.024390	0.427184	
chunk0081_349_1	chr17	47291313	47291920	+	0	NA	intron (NM_000212, intron 9 of 14)	intron (NM_000212, intron 9 of 14)	31997	NR_110881	102724508	Hs.661005	NR_110880	ENSG00000263293	THCAT158	-	thyroid cancer-associated transcript 158	ncRNA	0.009885	0.401316	
chunk0094_220_1	chr2	6735244	6735472	+	0	NA	intron (NR_038369, intron 2 of 5)	intron (NR_038369, intron 2 of 5)	34953	NR_038369	400941	Hs.446195	NM_001001695	ENSG00000205837	LINC00487	-	long intergenic non-protein coding RNA 487	ncRNA	0.000000	0.318777	
chunk0137_26_1	chr4	10950024	10950662	+	0	NA	Intergenic	Intergenic	-265581	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.006270	0.367762	
chunk0135_355_1	chr3	190566655	190566919	+	0	NA	intron (NM_134470, intron 3 of 8)	intron (NM_134470, intron 3 of 8)	52736	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.011364	0.460377	
chunk0128_17_1	chr3	104061402	104061604	+	0	NA	Intergenic	Intergenic	-537387	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.354680	
chunk0209_315_1	chrX	50282128	50282585	+	0	NA	Intergenic	Intergenic	-2184	NM_033670	85417	Hs.130310	NM_033031	ENSG00000147082	CCNB3	-	cyclin B3	protein-coding	0.004376	0.489083	
chunk0124_313_1	chr3	58025980	58026333	+	0	NA	intron (NM_001164317, intron 1 of 46)	intron (NM_001164317, intron 1 of 46)	17756	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.014164	0.548023	
chunk0010_418_1	chr1	119669697	119669996	+	0	NA	Intergenic	Intergenic	-22079	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.010033	0.523333	92(AGAGACACCCTGTACT,-,0.00),93(GAGACACCCTGTACTT,+,0.00)
chunk0022_69_1	chr10	8614099	8614749	+	0	NA	Intergenic	Intergenic	-283565	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.009231	0.345622	
chunk0143_11_1	chr4	105836642	105837403	+	0	NA	intron (NM_001031720, intron 9 of 11)	intron (NM_001031720, intron 9 of 11)	-9850	NR_125927	101929529	Hs.603751	NR_125927	ENSG00000251175	LOC101929529	-	uncharacterized LOC101929529	ncRNA	0.002628	0.392388	
chunk0178_468_1	chr7	42234693	42235204	+	0	NA	intron (NM_000168, intron 1 of 14)	intron (NM_000168, intron 1 of 14)	2071	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.005871	0.330078	
chunk0011_206_1	chr1	150014489	150015172	+	0	NA	Intergenic	L1ME3A|LINE|L1	-4093	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.005857	0.321637	
chunk0171_260_1	chr6	127420571	127420962	+	0	NA	Intergenic	Intergenic	38624	NM_014702	9729	Hs.319247	NM_014702	ENSG00000189367	KIAA0408	-	KIAA0408	protein-coding	0.005115	0.464286	
chunk0009_120_1	chr1	102897492	102897931	+	0	NA	intron (NM_080630, intron 55 of 64)	intron (NM_080630, intron 55 of 64)	210785	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.006834	0.354545	238(GAGAACAATTTGTTTC,-,0.00)
chunk0056_426_1	chr13	94646876	94647219	+	0	NA	Intergenic	Intergenic	45197	NM_180989	160897	Hs.439363	NM_180989	ENSG00000152749	GPR180	ITR	G protein-coupled receptor 180	protein-coding	0.011662	0.383721	
chunk0114_48_1	chr21	8443191	8443450	+	0	NA	non-coding (NR_003287, exon 1 of 1)	non-coding (NR_003287, exon 1 of 1)	2174	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.173745	0.815385	
chunk0108_392_1	chr2	237097867	237098352	+	0	NA	3' UTR (NM_198189, exon 9 of 9)	3' UTR (NM_198189, exon 9 of 9)	12668	NM_198189	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.004124	0.358025	203(CAGCACATGCCGTACT,-,0.00),204(AGCACATGCCGTACTC,+,0.00)
chunk0028_227_1	chr10	89648150	89648379	+	0	NA	Intergenic	Intergenic	-2692	NM_148977	53354	Hs.163555	NM_138316	ENSG00000152782	PANK1	PANK	pantothenate kinase 1	protein-coding	0.008734	0.526087	110(TGGGACAGAACGTCCT,-,0.00),111(GGGACAGAACGTCCTC,+,0.00)
chunk0037_126_1	chr11	72943368	72944048	+	0	NA	intron (NM_014824, intron 8 of 19)	L2a|LINE|L2	63788	NR_039664									0.002941	0.317181	
chunk0091_172_1	chr19	7986719	7987023	+	0	NA	intron (NM_001419, intron 2 of 5)	L1ME4a|LINE|L1	18774	NM_001419	1994	Hs.184492	NM_001419	ENSG00000066044	ELAVL1	ELAV1|HUR|Hua|MelG	ELAV like RNA binding protein 1	protein-coding	0.026316	0.419672	
chunk0165_443_1	chr6	40436173	40436633	+	0	NA	intron (NM_020737, intron 1 of 2)	MER58A|DNA|hAT-Charlie	57979	NR_024015									0.006522	0.438178	
chunk0139_343_1	chr4	59688888	59689493	+	0	NA	Intergenic	Intergenic	-1233429	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.013223	0.410891	
chunk0078_50_1	chr17	1347738	1348200	+	0	NA	intron (NR_024058, intron 6 of 6)	intron (NR_024058, intron 6 of 6)	52293	NR_024058	7531	Hs.513851	NM_006761	ENSG00000108953	YWHAE	14-3-3E|HEL2|KCIP-1|MDCR|MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	protein-coding	0.017316	0.429806	
chunk0101_433_1	chr2	139360713	139361029	+	0	NA	Intergenic	Intergenic	463547	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.003165	0.359621	
chunk0182_426_1	chr7	101335677	101335953	+	0	NA	Intergenic	L1MD3|LINE|L1	-13992	NM_001130821	64792	Hs.389104	NM_022777	ENSG00000128581	IFT22	RABL5	intraflagellar transport 22	protein-coding	0.014493	0.350181	160(TGGTACAGAGTGTTCT,-,0.00),161(GGTACAGAGTGTTCTT,+,0.00)
chunk0034_444_1	chr11	39463736	39464099	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	815059	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.002755	0.293956	
chunk0039_86_1	chr11	97202390	97202694	+	0	NA	Intergenic	L1PBb|LINE|L1	-695665	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.006579	0.534426	
chunk0159_97_1	chr5	138245912	138246193	+	0	NA	Intergenic	Intergenic	28512	NM_001496	2676	Hs.58042	NM_001496	ENSG00000146013	GFRA3	GDNFR3	GDNF family receptor alpha 3	protein-coding	0.007117	0.570922	
chunk0061_369_1	chr14	64088437	64089095	+	0	NA	intron (NM_182914, intron 58 of 115)	intron (NM_182914, intron 58 of 115)	6359	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.007599	0.361153	
chunk0017_9_1	chr1	204398301	204398516	+	0	NA	Intergenic	AluJr|SINE|Alu	13409	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.009302	0.472222	
chunk0175_406_1	chr6	168628095	168628571	+	0	NA	intron (NM_022138, intron 9 of 12)	intron (NM_022138, intron 9 of 12)	187182	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.018908	0.431866	
chunk0060_126_1	chr14	44010110	44010348	+	0	NA	Intergenic	Intergenic	497067	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.008403	0.334728	
chunk0032_199_1	chr11	6806888	6807349	+	0	NA	Intergenic	L1PA16|LINE|L1	-11210	NM_003696	8590	Hs.652252	NM_003696	ENSG00000184933	OR6A2	I7|OR11-55|OR6A1|OR6A2P	olfactory receptor family 6 subfamily A member 2	protein-coding	0.000000	0.335498	
chunk0092_347_1	chr19	35353812	35354145	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	2436	NM_005303	2864	Hs.248127	NM_005303	ENSG00000126266	FFAR1	FFA1R|GPCR40|GPR40	free fatty acid receptor 1	protein-coding	0.018018	0.392216	84(CTGTACACAGTGTACT,-,0.00),85(TGTACACAGTGTACTG,+,0.00)
chunk0175_163_1	chr7	4317274	4317681	+	0	NA	Intergenic	L1ME4a|LINE|L1	187792	NM_001079653	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.002457	0.330882	
chunk0153_14_1	chr5	66876436	66877018	+	0	NA	intron (NM_015183, intron 1 of 27)	intron (NM_015183, intron 1 of 27)	47951	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.010309	0.439108	221(AAGTACAGCCAGTACT,-,0.00),222(AGTACAGCCAGTACTT,+,0.00)
chunk0119_19_1	chr22	40194828	40195422	+	0	NA	intron (NM_015088, intron 1 of 20)	intron (NM_015088, intron 1 of 20)	17200	NM_015088	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.006734	0.406723	
chunk0016_364_1	chr1	202379877	202380535	+	0	NA	intron (NM_002481, intron 1 of 23)	L2c|LINE|L2	31504	NM_001167858	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.006079	0.396055	
chunk0156_21_1	chr5	102222645	102223256	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	73599	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.001637	0.348039	
chunk0095_186_1	chr2	17887955	17888391	+	0	NA	intron (NM_002252, intron 1 of 2)	L1PB1|LINE|L1	9516	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.004587	0.327231	
chunk0185_113_1	chr7	125834256	125834803	+	0	NA	Intergenic	MER76|LTR|ERVL	-570238	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.009141	0.467153	
chunk0010_168_1	chr1	115665400	115665759	+	0	NA	intron (NM_138959, intron 4 of 7)	intron (NM_138959, intron 4 of 7)	22950	NM_001172412	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.013928	0.513889	
chunk0115_151_1	chr21	23754158	23754481	+	0	NA	Intergenic	LTR80A|LTR|ERVL	-369484	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.003096	0.376543	
chunk0009_54_1	chr1	100570589	100570884	+	0	NA	Intergenic	L1PREC2|LINE|L1	32564	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.003390	0.351351	
chunk0057_207_1	chr13	103844441	103844859	+	0	NA	Intergenic	Intergenic	419450	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.004785	0.348449	
chunk0124_306_1	chr3	57972443	57973187	+	0	NA	Intergenic	Intergenic	-35585	NM_001164317	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.013441	0.522148	488(AGGCACACCCAGTACA,-,0.00),489(GGCACACCCAGTACAT,+,0.00)
chunk0190_317_1	chr8	38734678	38734958	+	0	NA	intron (NM_001146216, intron 1 of 12)	intron (NM_001146216, intron 1 of 12)	6632	NM_001146216	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.035714	0.604982	
chunk0049_37_1	chr12	89770278	89770477	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	61422	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.000000	0.420000	
chunk0131_8_1	chr3	141743933	141744743	+	0	NA	intron (NR_037702, intron 3 of 3)	intron (NR_037702, intron 3 of 3)	6129	NM_001201370	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.006173	0.340321	
chunk0168_148_1	chr6	83182352	83183015	+	0	NA	intron (NM_001199917, intron 6 of 13)	intron (NM_001199917, intron 6 of 13)	10610	NM_015599	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.010558	0.373494	
chunk0082_21_1	chr17	50532596	50532811	+	0	NA	promoter-TSS (NM_017957)	promoter-TSS (NM_017957)	16	NM_017957	55040	Hs.670090	NM_017957	ENSG00000049283	EPN3	-	epsin 3	protein-coding	0.037209	0.648148	
chunk0072_26_1	chr16	599974	600406	+	0	NA	intron (NM_021168, intron 1 of 5)	intron (NM_021168, intron 1 of 5)	10017	NM_021168	57799	Hs.459630	NM_021168	ENSG00000197562	RAB40C	RARL|RASL8C	RAB40C, member RAS oncogene family	protein-coding	0.023148	0.484988	230(TGGAACAGTCTGTACT,-,0.00),231(GGAACAGTCTGTACTT,+,0.00)
chunk0180_24_1	chr7	53796743	53797013	+	0	NA	intron (NR_038371, intron 1 of 5)	LTR47A|LTR|ERVL	15053	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.000000	0.450185	127(GGGGACAGAATGTCCA,-,0.00),128(GGGACAGAATGTCCAT,+,0.00)
chunk0034_301_1	chr11	34948990	34949189	+	0	NA	intron (NM_001166158, intron 3 of 5)	intron (NM_001166158, intron 3 of 5)	7252	NR_039836	100616437		NR_039836	ENSG00000251862	MIR1343	-	microRNA 1343	ncRNA	0.000000	0.420000	
chunk0100_238_1	chr2	112644143	112644648	+	0	NA	promoter-TSS (NR_033871)	promoter-TSS (NR_033871)	-215	NR_033871	400999	Hs.585221	NR_033871		FLJ42351	-	uncharacterized LOC400999	ncRNA	0.013861	0.418972	
chunk0025_379_1	chr10	59191809	59192371	+	0	NA	intron (NM_001143774, intron 1 of 4)	intron (NM_001143774, intron 1 of 4)	14623	NM_001143774	84457	Hs.499704	NM_032439	ENSG00000165443	PHYHIPL	-	phytanoyl-CoA 2-hydroxylase interacting protein like	protein-coding	0.003559	0.310835	
chunk0211_380_1	chrX	127032614	127032856	+	0	NA	Intergenic	Intergenic	212971	NM_001122716	100130613	Hs.130370	NM_001122716	ENSG00000183631	PRR32	CXorf64	proline rich 32	protein-coding	0.004132	0.349794	
chunk0096_433_1	chr2	38562117	38562449	+	0	NA	TTS (NM_138394)	TTS (NM_138394)	40753	NM_001142650	92906	Hs.445497	NM_138394	ENSG00000143889	HNRNPLL	HNRPLL|SRRF	heterogeneous nuclear ribonucleoprotein L like	protein-coding	0.000000	0.351351	
chunk0159_425_1	chr5	148104105	148104652	+	0	NA	intron (NM_006846, intron 15 of 32)	Tigger12|DNA|TcMar-Tigger	40406	NM_001127699	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.001828	0.372263	
chunk0171_79_1	chr6	121663193	121663792	+	0	NA	Intergenic	L2a|LINE|L2	227915	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.000000	0.395000	
chunk0018_24_1	chr1	215539910	215540837	+	0	NA	Intergenic	LTR57|LTR|ERVL	-27019	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.005394	0.408405	
chunk0172_126_1	chr6	135244822	135245172	+	0	NA	Intergenic	Intergenic	5837	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.017143	0.455840	
chunk0013_201_1	chr1	169250604	169251178	+	0	NA	intron (NR_104229, intron 7 of 12)	L1PB3|LINE|L1	-117065	NM_003666	8548	Hs.130746	NM_003666	ENSG00000117475	BLZF1	GOLGIN-45|JEM-1|JEM-1s|JEM1	basic leucine zipper nuclear factor 1	protein-coding	0.005226	0.318261	
chunk0081_251_1	chr17	43315863	43316277	+	0	NA	Intergenic	Intergenic	-15839	NR_002716	6066		NR_002716	ENSG00000274585	RNU2-1	RNU2|U2	RNA, U2 small nuclear 1	snRNA	0.024155	0.402410	
chunk0092_265_1	chr19	33184369	33184568	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-10225	NM_002333	4037	Hs.515340	NM_002333	ENSG00000130881	LRP3	-	LDL receptor related protein 3	protein-coding	0.055276	0.555000	
chunk0178_118_1	chr7	31271688	31271887	+	0	NA	Intergenic	Intergenic	69137	NM_022728	63974	Hs.45152	NM_022728	ENSG00000164600	NEUROD6	Atoh2|MATH2|Math-2|NEX1M|Nex1|bHLHa2	neuronal differentiation 6	protein-coding	0.010050	0.435000	
chunk0143_46_1	chr4	107635710	107636242	+	0	NA	intron (NM_005443, intron 10 of 11)	intron (NM_005443, intron 10 of 11)	84287	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.005639	0.350844	
chunk0106_172_1	chr2	200800495	200801049	+	0	NA	intron (NR_110275, intron 1 of 3)	L1PB3|LINE|L1	-10774	NM_001207067	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.007220	0.358559	
chunk0069_298_1	chr15	65396844	65397098	+	0	NA	exon (NM_020962, exon 6 of 20)	exon (NM_020962, exon 6 of 20)	-18931	NM_004884	9543	Hs.128292	NM_004884	ENSG00000174498	IGDCC3	HsT18880|PUNC	immunoglobulin superfamily DCC subclass member 3	protein-coding	0.082677	0.631373	216(AGGAACACTCTGCACC,-,0.00),217(GGAACACTCTGCACCC,+,0.00)
chunk0138_284_1	chr4	40612611	40613321	+	0	NA	intron (NM_001098634, intron 1 of 6)	intron (NM_001098634, intron 1 of 6)	16900	NM_001098634	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.002817	0.355837	
chunk0021_406_1	chr1	246709863	246710424	+	0	NA	Intergenic	MER67A|LTR|ERV1	-13933	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.007130	0.435943	
chunk0134_53_1	chr3	175977683	175977992	+	0	NA	Intergenic	Intergenic	-201504	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.016181	0.535484	
chunk0005_224_1	chr1	59355395	59355619	+	0	NA	intron (NM_001113411, intron 4 of 16)	intron (NM_001113411, intron 4 of 16)	45429	NM_001244714	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.000000	0.342222	
chunk0174_149_1	chr6	157818744	157819154	+	0	NA	Intergenic	Intergenic	-4222	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.014634	0.467153	233(CTGGACACTATGTCCC,-,0.00),234(TGGACACTATGTCCCG,+,0.00)
chunk0173_355_1	chr6	149132937	149133580	+	0	NA	Intergenic	Intergenic	-84666	NM_001292035	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.009331	0.431677	309(AGGACATTGTGCTCAT,+,0.00)
chunk0209_12_1	chrX	35219902	35220304	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	277307	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.004975	0.367246	147(TGGGACACTGCGTGCC,-,0.00),148(GGGACACTGCGTGCCA,+,0.00)
chunk0112_380_1	chr20	46255309	46255755	+	0	NA	intron (NM_021248, intron 1 of 11)	intron (NM_021248, intron 1 of 11)	52966	NM_021248	64405	Hs.472861	NM_021248	ENSG00000149654	CDH22	C20orf25|dJ998H6.1	cadherin 22	protein-coding	0.008969	0.572707	207(GGGCACAATCTGTACT,-,0.00),208(GGCACAATCTGTACTA,+,0.00)
chunk0088_289_1	chr18	49727748	49728255	+	0	NA	Intergenic	MIRb|SINE|MIR	85880	NM_006111	10449	Hs.200136	NM_006111	ENSG00000167315	ACAA2	DSAEC	acetyl-CoA acyltransferase 2	protein-coding	0.023669	0.511811	
chunk0053_47_1	chr13	27549125	27549551	+	0	NA	intron (NM_153371, intron 9 of 9)	intron (NM_153371, intron 9 of 9)	71245	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.009390	0.423888	
chunk0131_401_1	chr3	152835829	152836029	+	0	NA	exon (NM_002563, exon 1 of 1)	exon (NM_002563, exon 1 of 1)	1236	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.075000	0.592040	
chunk0133_413_1	chr3	174537435	174537721	+	0	NA	Intergenic	L2c|LINE|L2	-321743	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.013986	0.376307	
chunk0147_206_1	chr4	178833321	178833614	+	0	NA	Intergenic	L1MC1|LINE|L1	-925531	NR_108093	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.006826	0.340136	
chunk0186_157_1	chr7	139242715	139243452	+	0	NA	intron (NM_173569, intron 2 of 17)	intron (NM_173569, intron 2 of 17)	11598	NM_173569	254048	Hs.153458	NM_173569	ENSG00000157741	UBN2	-	ubinuclein 2	protein-coding	0.001357	0.372629	
chunk0209_73_1	chrX	38041188	38041608	+	0	NA	intron (NM_138780, intron 2 of 16)	intron (NM_138780, intron 2 of 16)	7864	NM_001163334	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.004762	0.356295	
chunk0110_289_1	chr20	17722113	17722375	+	0	NA	intron (NM_001014977, intron 1 of 2)	intron (NM_001014977, intron 1 of 2)	22296	NM_178477	140836	Hs.115366	NM_178477	ENSG00000125888	BANF2	BAF-L|BAF2|BAFL|C20orf179	barrier to autointegration factor 2	protein-coding	0.011450	0.444867	
chunk0006_442_1	chr1	76715840	76716039	+	0	NA	Intergenic	Intergenic	-151562	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.010050	0.345000	
chunk0081_6_1	chr17	37168634	37169334	+	0	NA	intron (NM_198836, intron 41 of 55).2	AmnSINE1|SINE|5S-Deu-L2	-75817	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.005714	0.343795	
chunk0143_325_1	chr4	119742381	119742846	+	0	NA	Intergenic	Intergenic	61902	NR_110660	101927007	Hs.143958	NR_110660	ENSG00000250772	LINC01365	-	long intergenic non-protein coding RNA 1365	ncRNA	0.008602	0.377682	
chunk0164_119_1	chr6	20812569	20813489	+	0	NA	intron (NM_017774, intron 8 of 15)	L1ME1|LINE|L1	278572	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.003261	0.351792	
chunk0025_79_1	chr10	50362598	50362862	+	0	NA	intron (NM_147156, intron 6 of 10)	intron (NM_147156, intron 6 of 10)	-114120	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.003788	0.350943	
chunk0203_445_1	chr9	91355346	91356093	+	0	NA	intron (NM_001698, intron 3 of 9)	intron (NM_001698, intron 3 of 9)	6205	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.012048	0.371658	
chunk0180_427_1	chr7	76302223	76302678	+	0	NA	promoter-TSS (NM_001540)	promoter-TSS (NM_001540)	-108	NM_001540	3315	Hs.520973	NM_001540	ENSG00000106211	HSPB1	CMT2F|HEL-S-102|HMN2B|HS.76067|HSP27|HSP28|Hsp25|SRP27	heat shock protein family B (small) member 1	protein-coding	0.057143	0.594298	
chunk0056_194_1	chr13	85687253	85687941	+	0	NA	Intergenic	Intergenic	111751	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.005814	0.380261	
chunk0064_122_1	chr14	91367298	91367927	+	0	NA	intron (NM_001080414, intron 3 of 29)	L2c|LINE|L2	50232	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.027027	0.546032	321(CAGCACAGGGAGTACT,-,0.00),322(AGCACAGGGAGTACTG,+,0.00)
chunk0210_243_1	chrX	82765873	82766231	+	0	NA	Intergenic	Intergenic	-742209	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.002793	0.356546	
chunk0023_344_1	chr10	29627908	29628170	+	0	NA	intron (NM_003174, intron 3 of 35)	intron (NM_003174, intron 3 of 35)	6933	NM_021738	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.007634	0.338403	
chunk0097_392_1	chr2	61986171	61986636	+	0	NA	intron (NM_152516, intron 1 of 2)	L1MA2|LINE|L1	80735	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.002151	0.379828	
chunk0019_214_1	chr1	227114257	227114876	+	0	NA	intron (NM_003607, intron 12 of 35)	L1MEd|LINE|L1	174329	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.001616	0.295161	
chunk0052_157_1	chr13	23889368	23889567	+	0	NA	promoter-TSS (NM_001135816)	promoter-TSS (NM_001135816)	14	NM_001135816	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.120603	0.690000	
chunk0149_391_1	chr5	28788910	28789300	+	0	NA	Intergenic	Intergenic	-137765	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.000000	0.291560	
chunk0151_124_1	chr5	43839161	43839692	+	0	NA	Intergenic	MIRc|SINE|MIR	-236196	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.000000	0.360902	
chunk0024_203_1	chr10	36420234	36420856	+	0	NA	Intergenic	Intergenic	642243	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.011254	0.391653	
chunk0180_287_1	chr7	70036871	70037107	+	0	NA	intron (NM_015570, intron 2 of 18)	intron (NM_015570, intron 2 of 18)	438070	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.004237	0.379747	
chunk0147_265_1	chr4	183660951	183661431	+	0	NA	intron (NM_199053, intron 1 of 30)	intron (NM_199053, intron 1 of 30)	1924	NM_021942	60684	Hs.443240	NM_021942	ENSG00000168538	TRAPPC11	C4orf41|FOIGR|GRY|LGMD2S|LGMDR18	trafficking protein particle complex 11	protein-coding	0.014583	0.388773	
chunk0136_367_1	chr3	196081456	196081720	+	0	NA	intron (NM_001313965, intron 1 of 17)	CpG	502	NM_003234	7037	Hs.529618	NM_003234	ENSG00000072274	TFRC	CD71|IMD46|T9|TFR|TFR1|TR|TRFR|p90	transferrin receptor	protein-coding	0.113636	0.724528	
chunk0019_171_1	chr1	226151074	226151273	+	0	NA	intron (NM_022735, intron 7 of 7)	intron (NM_022735, intron 7 of 7)	35549	NM_022735	64746	Hs.520207	NM_022735	ENSG00000182827	ACBD3	GCP60|GOCAP1|GOLPH1|PAP7	acyl-CoA binding domain containing 3	protein-coding	0.000000	0.385000	
chunk0153_187_1	chr5	71632064	71632710	+	0	NA	intron (NM_022132, intron 8 of 16)	intron (NM_022132, intron 8 of 16)	45099	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.012384	0.417311	
chunk0034_250_1	chr11	34271646	34272154	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	86108	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.001969	0.422397	
chunk0160_385_1	chr5	161548284	161548486	+	0	NA	promoter-TSS (NM_000813)	promoter-TSS (NM_000813)	-261	NM_021911	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.059406	0.620690	
chunk0206_213_1	chr9	123216443	123217124	+	0	NA	intron (NR_033234, intron 1 of 18)	MIRb|SINE|MIR	51781	NM_018387	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.005874	0.372434	
chunk0090_98_1	chr18	70777487	70777901	+	0	NA	Intergenic	L2|LINE|L2	-126837	NM_001278515									0.012077	0.395181	
chunk0026_371_1	chr10	69360604	69361722	+	0	NA	intron (NM_033497, intron 6 of 20)	intron (NM_033497, intron 6 of 20)	42316	NM_000188	3098	Hs.370365	NM_000188	ENSG00000156515	HK1	HK|HK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1|RP79|hexokinase	hexokinase 1	protein-coding	0.009839	0.552279	
chunk0038_130_1	chr11	84089662	84089861	+	0	NA	intron (NM_001142699, intron 10 of 27)	intron (NM_001142699, intron 10 of 27)	183519	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.350000	
chunk0203_143_1	chr9	85536015	85536418	+	0	NA	Intergenic	Intergenic	205813	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.007444	0.495050	196(TGGCACATCATGTTCT,-,0.00),197(GGCACATCATGTTCTG,+,0.00)
chunk0110_429_1	chr20	20759216	20759973	+	0	NA	Intergenic	Intergenic	-46971	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.006605	0.356201	
chunk0065_92_1	chr15	23789909	23790382	+	0	NA	Intergenic	Intergenic	-102842	NM_002487	4692	Hs.50130	NM_002487	ENSG00000182636	NDN	HsT16328|PWCR	necdin, MAGE family member	protein-coding	0.004228	0.286920	
chunk0154_330_1	chr5	85337696	85338309	+	0	NA	Intergenic	Intergenic	-944442	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.009788	0.333876	321(GAGGACACGTAGTTCT,-,0.00),322(AGGACACGTAGTTCTA,+,0.00)
chunk0195_325_1	chr8	99002624	99002938	+	0	NA	Intergenic	Intergenic	-10485	NM_181661	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.009554	0.514286	
chunk0207_427_1	chr9	137279288	137279487	+	0	NA	exon (NM_017723, exon 2 of 2)	exon (NM_017723, exon 2 of 2)	1559	NM_017723	54863	Hs.495541	NM_017723	ENSG00000198113	TOR4A	C9orf167	torsin family 4 member A	protein-coding	0.140704	0.735000	
chunk0097_156_1	chr2	48444627	48445262	+	0	NA	intron (NM_001135629, intron 1 of 21)	intron (NM_001135629, intron 1 of 21)	4175	NM_152994	129285	Hs.654619	NM_152994	ENSG00000162869	PPP1R21	CCDC128|KLRAQ1	protein phosphatase 1 regulatory subunit 21	protein-coding	0.000000	0.364780	
chunk0088_429_1	chr18	55578591	55578919	+	0	NA	intron (NM_003199, intron 3 of 19)	intron (NM_003199, intron 3 of 19)	7364	NM_001306207	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.012195	0.361702	
chunk0201_364_1	chr9	68520627	68521028	+	0	NA	intron (NM_021965, intron 10 of 10)	intron (NM_021965, intron 10 of 10)	20040	NM_153237	169693	Hs.663056	NM_153237	ENSG00000181778	TMEM252	C9orf71	transmembrane protein 252	protein-coding	0.009975	0.300995	
chunk0117_181_1	chr22	20885402	20885951	+	0	NA	intron (NM_004782, intron 4 of 4)	intron (NM_004782, intron 4 of 4)	26672	NM_004782	9342	Hs.108002	NM_004782	ENSG00000099940	SNAP29	CEDNIK|SNAP-29	synaptosome associated protein 29	protein-coding	0.018215	0.574545	
chunk0094_348_1	chr2	9339813	9340012	+	0	NA	intron (NM_003887, intron 9 of 27)	intron (NM_003887, intron 9 of 27)	83602	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.010050	0.520000	
chunk0001_68_1	chr1	2437782	2438372	+	0	NA	Intergenic	Intergenic	-25506	NM_002617	5192	Hs.732228	NM_002617	ENSG00000157911	PEX10	NALD|PBD6A|PBD6B|RNF69	peroxisomal biogenesis factor 10	protein-coding	0.040678	0.622673	
chunk0175_32_1	chr7	768864	769103	+	0	NA	intron (NM_017802, intron 8 of 12)	CpG	-41307	NM_001164758	5575	Hs.520851	NM_002735	ENSG00000188191	PRKAR1B	PRKAR1	protein kinase cAMP-dependent type I regulatory subunit beta	protein-coding	0.066946	0.633333	
chunk0133_115_1	chr3	168123615	168123983	+	0	NA	Intergenic	Intergenic	-27874	NM_001308155	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.000000	0.344173	
chunk0091_178_1	chr19	8201160	8201914	+	0	NA	Intergenic	Intergenic	-7796	NM_024552	79603	Hs.515111	NM_024552	ENSG00000090661	CERS4	LASS4|Trh1	ceramide synthase 4	protein-coding	0.007958	0.446358	410(AAGATCACACTGTACC,-,0.00),411(AGATCACACTGTACCT,+,0.00)
chunk0188_412_1	chr8	18879208	18879671	+	0	NA	intron (NM_015310, intron 2 of 15)	intron (NM_015310, intron 2 of 15)	-70544	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.015119	0.443966	
chunk0072_385_1	chr15	100504465	100504946	+	0	NA	intron (NM_001290341, intron 3 of 13)	intron (NM_001290341, intron 3 of 13)	39581	NM_001290342	204219	Hs.662371	NM_178842	ENSG00000154227	CERS3	ARCI9|LASS3	ceramide synthase 3	protein-coding	0.012474	0.448133	
chunk0178_462_1	chr7	42207109	42207382	+	0	NA	intron (NM_000168, intron 2 of 14)	L1ME3A|LINE|L1	29774	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.007326	0.427007	
chunk0136_245_1	chr4	10019318	10019999	+	0	NA	intron (NM_001001290, intron 2 of 12)	intron (NM_001001290, intron 2 of 12)	1832	NM_020041	56606	Hs.444612	NM_020041	ENSG00000109667	SLC2A9	GLUT9|GLUTX|UAQTL2|URATv1	solute carrier family 2 member 9	protein-coding	0.024963	0.574780	388(ATGCACATACTGTTCC,-,0.00),389(TGCACATACTGTTCCA,+,0.00)
chunk0013_350_1	chr1	172201459	172201678	+	0	NA	intron (NM_001136127, intron 14 of 19)	L1PA14|LINE|L1	-56733	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.000000	0.522727	
chunk0053_82_1	chr13	28411675	28412172	+	0	NA	intron (NM_001159920, intron 10 of 12)	intron (NM_001159920, intron 10 of 12)	83205	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.010060	0.403614	
chunk0018_287_1	chr1	220734429	220735074	+	0	NA	Intergenic	Intergenic	-13583	NM_017898	54996	Hs.369042	NM_017898	ENSG00000117791	MARC2	MOSC2	mitochondrial amidoxime reducing component 2	protein-coding	0.015504	0.410217	
chunk0124_42_1	chr3	52343604	52343842	+	0	NA	intron (NM_015512, intron 8 of 77)	L2a|LINE|L2	27404	NM_015512	25981	Hs.655469	NM_015512	ENSG00000114841	DNAH1	CILD37|DNAHC1|HDHC7|HL-11|HL11|HSRF-1|SPGF18|XLHSRF-1	dynein axonemal heavy chain 1	protein-coding	0.021008	0.564854	
chunk0195_46_1	chr8	93404362	93404967	+	0	NA	intron (NR_033858, intron 7 of 10)	intron (NR_033858, intron 7 of 10)	-237814	NM_001242668									0.009917	0.496700	
chunk0211_442_1	chrX	129644911	129645369	+	0	NA	TTS (NM_017413)	TTS (NM_017413)	9816	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.004367	0.337691	
chunk0138_424_1	chr4	45130938	45131711	+	0	NA	Intergenic	L1MC5|LINE|L1	-404690	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.006468	0.354005	
chunk0099_190_1	chr2	90390565	90391150	+	0	NA	Intergenic	Intergenic	1269092	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.051282	0.385666	
chunk0207_24_1	chrM	14738	16536	+	0	NA	NA	Intergenic	NA	NA									0.025584	0.456365	
chunk0096_135_1	chr2	28746355	28747021	+	0	NA	Intergenic	Tigger16b|DNA|TcMar-Tigger	-5060	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.004505	0.397301	
chunk0054_158_1	chr13	44151652	44151851	+	0	NA	intron (NR_104064, intron 4 of 4)	intron (NR_104064, intron 4 of 4)	-4016	NR_132368	105370183	Hs.652552	NR_132368		LINC00390	-	long intergenic non-protein coding RNA 390	ncRNA	0.005025	0.435000	
chunk0012_172_1	chr1	158699886	158700151	+	0	NA	exon (NM_001005279, exon 1 of 1)	exon (NM_001005279, exon 1 of 1)	634	NM_001005279	81448	Hs.554489	NM_001005279	ENSG00000196171	OR6K2	OR1-17	olfactory receptor family 6 subfamily K member 2	protein-coding	0.037736	0.477444	
chunk0057_346_1	chr13	107962074	107962825	+	0	NA	Intergenic	Intergenic	-95337	NM_001080396	728215	Hs.535394	NM_001080396	ENSG00000204442	FAM155A	-	family with sequence similarity 155 member A	protein-coding	0.005326	0.340426	
chunk0098_319_1	chr2	76680395	76681005	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-305265	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.006557	0.412439	213(CGGTACACCATGTCCC,-,0.00),214(GGTACACCATGTCCCA,+,0.00),567(GAGAACACAATGACCC,-,0.00),568(AGAACACAATGACCCT,+,0.00)
chunk0092_206_1	chr19	31223395	31223840	+	0	NA	Intergenic	Intergenic	125667	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.006742	0.392377	
chunk0058_238_1	chr14	25509742	25510153	+	0	NA	Intergenic	Intergenic	-459650	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004866	0.337379	
chunk0051_430_1	chr12	122895868	122896357	+	0	NA	promoter-TSS (NM_024667)	promoter-TSS (NM_024667)	53	NM_024667	79720	Hs.507162	NM_024667	ENSG00000139722	VPS37B	-	VPS37B subunit of ESCRT-I	protein-coding	0.124744	0.700000	
chunk0136_80_1	chr4	2235579	2236217	+	0	NA	intron (NM_024511, intron 4 of 4)	L1ME3D|LINE|L1	6266	NM_001303143	79441	Hs.665869	NM_024511	ENSG00000214367	HAUS3	C4orf15|IT1|dgt3	HAUS augmin like complex subunit 3	protein-coding	0.006270	0.289515	120(CAGCACATAAAGTTCA,-,0.00)
chunk0159_285_1	chr5	142690378	142690676	+	0	NA	intron (NM_001144935, intron 1 of 3)	intron (NM_001144935, intron 1 of 3)	-4032	NM_001257207	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.010067	0.377926	
chunk0185_415_1	chr7	134297243	134297819	+	0	NA	intron (NM_032826, intron 8 of 9)	L1ME4c|LINE|L1	19544	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.003472	0.339688	
chunk0047_303_1	chr12	73834954	73835610	+	0	NA	Intergenic	Intergenic	457349	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.003049	0.354642	
chunk0057_275_1	chr13	105917219	105917786	+	0	NA	Intergenic	LTR102_Mam|LTR|ERVL	210672	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.015873	0.464789	186(GAAACATTCAGTCCTT,+,0.00)
chunk0076_13_1	chr16	58734168	58734461	+	0	NA	promoter-TSS (NM_002080)	promoter-TSS (NM_002080)	43	NM_001286220	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.098976	0.714286	
chunk0102_364_1	chr2	152717418	152717657	+	0	NA	promoter-TSS (NR_024526)	promoter-TSS (NR_024526)	-76	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.087866	0.679167	
chunk0014_416_1	chr1	183142939	183143203	+	0	NA	3' UTR (NM_002293, exon 28 of 28)	3' UTR (NM_002293, exon 28 of 28)	-42968	NM_005562	3918	Hs.591484	NM_005562	ENSG00000058085	LAMC2	B2T|BM600|CSF|EBR2|EBR2A|LAMB2T|LAMNB2	laminin subunit gamma 2	protein-coding	0.026515	0.449057	
chunk0184_400_1	chr7	122128120	122128450	+	0	NA	intron (NM_005763, intron 3 of 23)	L2a|LINE|L2	16005	NM_005763	10157	Hs.156738	NM_005763	ENSG00000008311	AASS	LKR/SDH|LKRSDH|LORSDH	aminoadipate-semialdehyde synthase	protein-coding	0.006061	0.450151	195(CTGAACATGGTGTACT,-,0.00),196(TGAACATGGTGTACTC,+,0.00)
chunk0021_32_1	chr10	825154	825374	+	0	NA	exon (NM_015155, exon 13 of 18)	exon (NM_015155, exon 13 of 18)	106441	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.022727	0.389140	
chunk0083_59_1	chr17	63752751	63753074	+	0	NA	intron (NM_020198, intron 9 of 12)	intron (NM_020198, intron 9 of 12)	-10942	NM_001003788	92335	Hs.514402	NM_153335	ENSG00000266173	STRADA	LYK5|NY-BR-96|PMSE|STRAD|STRAD alpha|Stlk	STE20 related adaptor alpha	protein-coding	0.003096	0.413580	
chunk0205_257_1	chr9	110776620	110776933	+	0	NA	intron (NM_005592, intron 10 of 13)	intron (NM_005592, intron 10 of 13)	108005	NM_005592	4593	Hs.521653	NM_005592	ENSG00000030304	MUSK	CMS9|FADS|FADS1	muscle associated receptor tyrosine kinase	protein-coding	0.006390	0.359873	123(CAGAACAGAATGTACA,-,0.00),124(AGAACAGAATGTACAG,+,0.00)
chunk0199_136_1	chr9	3944563	3944765	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	46018	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.004950	0.364532	
chunk0161_58_1	chr5	166280714	166281404	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	645311	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.001449	0.439942	
chunk0190_243_1	chr8	36845275	36845572	+	0	NA	intron (NM_001031836, intron 16 of 26)	intron (NM_001031836, intron 16 of 26)	61099	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.016835	0.446309	
chunk0182_286_1	chr7	98226022	98226707	+	0	NA	intron (NM_015395, intron 17 of 25)	intron (NM_015395, intron 17 of 25)	14110	NM_177455	168620	Hs.511979	NM_177455	ENSG00000180535	BHLHA15	BHLHB8|MIST1	basic helix-loop-helix family member a15	protein-coding	0.026277	0.532070	
chunk0206_38_1	chr9	116571553	116571778	+	0	NA	intron (NM_198186, intron 4 of 7)	intron (NM_198186, intron 4 of 7)	67382	NR_033973	100128505	Hs.675821	NR_033973	ENSG00000229105	ASTN2-AS1	-	ASTN2 antisense RNA 1	ncRNA	0.017778	0.469027	
chunk0170_291_1	chr6	115328634	115329143	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-709843	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.001965	0.337255	
chunk0195_11_1	chr8	92992198	92992418	+	0	NA	Intergenic	L1MCc|LINE|L1	-26164	NM_001171795	286144	Hs.440643	NM_001171795	ENSG00000205133	TRIQK	C8orf83|PRO0845|UPF0599	triple QxxK/R motif containing	protein-coding	0.004545	0.542986	
chunk0056_286_1	chr13	90447456	90447655	+	0	NA	Intergenic	MER45C|DNA|hAT-Tip100	-45733	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.000000	0.485000	
chunk0165_145_1	chr6	33631998	33632555	+	0	NA	intron (NM_002224, intron 1 of 57)	MIR3|SINE|MIR	10897	NM_002224	3710	Hs.65758	NM_002224	ENSG00000096433	ITPR3	IP3R|IP3R3	inositol 1,4,5-trisphosphate receptor type 3	protein-coding	0.007181	0.525090	49(GAAACAGTTTGTGCCT,+,0.00),144(TGGAACTTGCTGTTCC,-,0.00),145(GGAACTTGCTGTTCCA,+,0.00)
chunk0080_75_1	chr17	22127768	22128470	+	0	NA	Intergenic	Intergenic	-170645	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.002849	0.307255	103(CAGTACACCCAGTTCA,-,0.00),104(AGTACACCCAGTTCAC,+,0.00)
chunk0101_135_1	chr2	127418229	127418526	+	0	NA	promoter-TSS (NM_000312)	promoter-TSS (NM_000312)	-43	NM_000312	5624	Hs.224698	NM_000312	ENSG00000115718	PROC	APC|PC|PROC1|THPH3|THPH4	protein C, inactivator of coagulation factors Va and VIIIa	protein-coding	0.030303	0.580537	90(CAGAACAAGCCGTGCT,-,0.00),91(AGAACAAGCCGTGCTG,+,0.00)
chunk0208_9_1	chrX	10457985	10458184	+	0	NA	intron (NM_001193277, intron 8 of 9)	L2b|LINE|L2	109519	NM_001193280	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.000000	0.355000	
chunk0014_177_1	chr1	178537067	178537362	+	0	NA	Intergenic	Intergenic	-5582	NR_033186	400798	Hs.668085	NM_207467	ENSG00000213057	C1orf220	-	chromosome 1 open reading frame 220 (putative)	ncRNA	0.016949	0.530405	191(CTGAACAGGCAGTGCC,-,0.00),192(TGAACAGGCAGTGCCA,+,0.00)
chunk0122_242_1	chr3	34007686	34008140	+	0	NA	Intergenic	L2b|LINE|L2	209342	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.006608	0.479121	
chunk0174_100_1	chr6	156850935	156851577	+	0	NA	intron (NM_017519, intron 2 of 18)	intron (NM_017519, intron 2 of 18)	-71525	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.012461	0.421462	
chunk0126_104_1	chr3	75043196	75043446	+	0	NA	Intergenic	L1PA8A|LINE|L1	-171155	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.008000	0.557769	
chunk0062_291_1	chr14	72500096	72500917	+	0	NA	intron (NM_001204418, intron 13 of 16)	intron (NM_001204418, intron 13 of 16)	-16314	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.007308	0.453771	
chunk0120_308_1	chr3	10189704	10189969	+	0	NA	intron (NM_001570, intron 2 of 12)	intron (NM_001570, intron 2 of 12)	24957	NM_001570	3656	Hs.449207	NM_001570	ENSG00000134070	IRAK2	IRAK-2	interleukin 1 receptor associated kinase 2	protein-coding	0.015094	0.567669	
chunk0118_75_1	chr22	28821868	28822092	+	0	NA	Intergenic	Intergenic	-21408	NM_005080	7494	Hs.437638	NM_005080	ENSG00000100219	XBP1	TREB-5|TREB5|XBP-1|XBP2	X-box binding protein 1	protein-coding	0.022321	0.466667	49(GAAACTTTCTGTTCCT,+,0.00)
chunk0212_303_1	chrX	142245700	142246241	+	0	NA	Intergenic	L1MA9|LINE|L1	-40680	NM_016249	51438	Hs.123536	NM_016249	ENSG00000046774	MAGEC2	CT10|HCA587|MAGEE1	MAGE family member C2	protein-coding	0.007394	0.356089	
chunk0050_392_1	chr12	109148097	109148389	+	0	NA	intron (NM_001093, intron 1 of 51)	intron (NM_001093, intron 1 of 51)	8846	NM_001093	32	Hs.234898	NM_001093	ENSG00000076555	ACACB	ACC2|ACCB|HACC275	acetyl-CoA carboxylase beta	protein-coding	0.003425	0.464164	
chunk0020_212_1	chr1	235149704	235150161	+	0	NA	intron (NR_027762, intron 4 of 9)	intron (NR_027762, intron 4 of 9)	11324	NM_001161533	23029	Hs.535224	NM_015014	ENSG00000188739	RBM34	-	RNA binding motif protein 34	protein-coding	0.017505	0.371179	
chunk0041_181_1	chr11	126267802	126268001	+	0	NA	intron (NM_001177842, intron 1 of 12)	intron (NM_001177842, intron 1 of 12)	1081	NM_003139	6734	Hs.368376	NM_003139	ENSG00000182934	SRPRA	DP|SRPR|Sralpha	SRP receptor subunit alpha	protein-coding	0.015075	0.480000	
chunk0047_316_1	chr12	74141605	74142263	+	0	NA	intron (NR_038300, intron 6 of 6)	intron (NR_038300, intron 6 of 6)	150697	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.004559	0.298938	
chunk0004_76_1	chr1	43559279	43560105	+	0	NA	intron (NM_130440, intron 5 of 32)	intron (NM_130440, intron 5 of 32)	28816	NM_002840	5792	Hs.272062	NM_002840	ENSG00000142949	PTPRF	BNAH2|LAR	protein tyrosine phosphatase receptor type F	protein-coding	0.024213	0.538089	
chunk0104_236_1	chr2	176556226	176557033	+	0	NA	Intergenic	MIR3|SINE|MIR	44423	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.008674	0.389851	
chunk0120_229_1	chr3	8220117	8220708	+	0	NA	TTS (NR_033378)	TTS (NR_033378)	-204105	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.000000	0.337838	
chunk0185_165_1	chr7	127831434	127831693	+	0	NA	intron (NM_014390, intron 11 of 23)	intron (NM_014390, intron 11 of 23)	-165946	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.003861	0.496154	
chunk0144_397_1	chr4	140228745	140229368	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-28230	NM_032547	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.006421	0.371795	240(TGTACTTGGTGTTCTG,+,0.00)
chunk0108_156_1	chr2	231102586	231103096	+	0	NA	intron (NR_034059, intron 15 of 23)	intron (NR_034059, intron 15 of 23)	22269	NM_000867	3357	Hs.421649	NM_000867	ENSG00000135914	HTR2B	5-HT(2B)|5-HT-2B|5-HT2B	5-hydroxytryptamine receptor 2B	protein-coding	0.005882	0.375734	
chunk0175_115_1	chr7	3273980	3274558	+	0	NA	Intergenic	Intergenic	-27179	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005190	0.392055	
chunk0133_32_1	chr3	165953748	165954668	+	0	NA	Intergenic	Intergenic	-116743	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.004348	0.375679	
chunk0063_85_1	chr14	77934910	77935240	+	0	NA	Intergenic	Intergenic	134992	NM_020421	57143	Hs.413208	NM_020421	ENSG00000063761	ADCK1	-	aarF domain containing kinase 1	protein-coding	0.003030	0.432024	
chunk0107_319_1	chr2	219836648	219837009	+	0	NA	Intergenic	L1MB4|LINE|L1	69737	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.008310	0.381215	
chunk0180_90_1	chr7	55075400	55076101	+	0	NA	intron (NM_201283, intron 1 of 9)	intron (NM_201283, intron 1 of 9)	56718	NM_005228	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.007133	0.418803	
chunk0204_29_1	chr9	92424319	92424761	+	0	NA	promoter-TSS (NM_005014)	promoter-TSS (NM_005014)	14	NM_005014	4958	Hs.94070	NM_005014	ENSG00000127083	OMD	OSAD|SLRR2C	osteomodulin	protein-coding	0.004525	0.370203	236(TGAAACAGCATGTACT,-,0.00),237(GAAACAGCATGTACTG,+,0.00)
chunk0206_206_1	chr9	123089040	123089632	+	0	NA	intron (NM_012197, intron 19 of 25)	MIR|SINE|MIR	22307	NR_030331	693185		NR_030331	ENSG00000283941	MIR600	MIRN600|hsa-mir-600	microRNA 600	ncRNA	0.005068	0.443508	
chunk0134_211_1	chr3	178584832	178585170	+	0	NA	intron (NM_001278911, intron 1 of 4)	intron (NM_001278911, intron 1 of 4)	26301	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.002959	0.389381	
chunk0048_159_1	chr12	80632489	80632977	+	0	NA	intron (NM_001145026, intron 34 of 44)	intron (NM_001145026, intron 34 of 44)	-74896	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.010246	0.413088	
chunk0202_135_1	chr9	73326985	73327718	+	0	NA	Intergenic	Intergenic	175620	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.002729	0.366485	385(AGGAACTCAATGTGCT,-,0.00),386(GGAACTCAATGTGCTT,+,0.00)
chunk0056_30_1	chr13	77291823	77292218	+	0	NA	intron (NM_015057, intron 2 of 82)	intron (NM_015057, intron 2 of 82)	35022	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.005063	0.411616	
chunk0054_396_1	chr13	50385869	50386129	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	141450	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.003846	0.463602	182(CAGTACAGCCTGGGCC,-,0.00),183(AGTACAGCCTGGGCCT,+,0.00)
chunk0007_322_1	chr1	84510722	84511037	+	0	NA	intron (NM_001310156, intron 1 of 13)	L1MA3|LINE|L1	-4300	NM_005274	2787	Hs.645427	NM_005274	ENSG00000174021	GNG5	-	G protein subunit gamma 5	protein-coding	0.006349	0.392405	
chunk0040_60_1	chr11	111201782	111202247	+	0	NA	Intergenic	L1MEd|LINE|L1	-53968	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.006452	0.330472	
chunk0157_317_1	chr5	121979638	121979991	+	0	NA	intron (NM_152546, intron 3 of 7)	LTR80A|LTR|ERVL	17853	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.008499	0.418079	
chunk0138_196_1	chr4	38099088	38099524	+	0	NA	intron (NM_015173, intron 14 of 19)	L1ME3G|LINE|L1	-10875	NM_001253913	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.009174	0.400458	240(GAGTACAGCATGGTCT,-,0.00),241(AGTACAGCATGGTCTC,+,0.00)
chunk0100_374_1	chr2	117997278	117997769	+	0	NA	intron (NM_019044, intron 4 of 23)	intron (NM_019044, intron 4 of 23)	16640	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.014257	0.463415	
chunk0069_292_1	chr15	65304820	65305556	+	0	NA	TTS (NR_002757)	TTS (NR_002757)	511	NR_002757	26832		NR_002757	ENSG00000200156	RNU5B-1	RNU5B|RNU5B-1P|U5B1	RNA, U5B small nuclear 1	snRNA	0.027174	0.436906	
chunk0111_303_1	chr20	32067312	32068016	+	0	NA	intron (NM_001172132, intron 2 of 13)	L2b|LINE|L2	15476	NM_001172130	3055	Hs.655210	NM_002110	ENSG00000101336	HCK	JTK9|p59Hck|p61Hck	HCK proto-oncogene, Src family tyrosine kinase	protein-coding	0.008523	0.402837	
chunk0188_162_1	chr8	10760336	10760757	+	0	NA	Intergenic	L2b|LINE|L2	-29972	NM_031439	83595	Hs.709543	NM_031439	ENSG00000171056	SOX7	-	SRY-box transcription factor 7	protein-coding	0.023753	0.471564	
chunk0113_311_1	chr20	58017516	58018029	+	0	NA	Intergenic	Intergenic	122378	NR_039757									0.019493	0.585603	307(CGGAACACAGCGTCCT,-,0.00),308(GGAACACAGCGTCCTT,+,0.00)
chunk0183_353_1	chr7	108613966	108614768	+	0	NA	Intergenic	Intergenic	-44599	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.006234	0.413450	
chunk0191_380_1	chr8	57025532	57026125	+	0	NA	Intergenic	Intergenic	-31957	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.001686	0.301347	
chunk0095_294_1	chr2	20207961	20208646	+	0	NA	intron (NM_001006946, intron 2 of 5)	MamRep434|DNA|TcMar-Tigger	16863	NM_002997	6382	Hs.224607	NM_002997	ENSG00000115884	SDC1	CD138|SDC|SYND1|syndecan	syndecan 1	protein-coding	0.017518	0.545190	336(AAAAACAATTTGTTCC,-,0.00)
chunk0021_115_1	chr10	3472060	3472599	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	153634	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.025974	0.487037	
chunk0078_129_1	chr17	3471637	3472005	+	0	NA	promoter-TSS (NM_001170697)	promoter-TSS (NM_001170697)	11	NM_001170697	84690	Hs.351068	NM_032598	ENSG00000141255	SPATA22	NYD-SP20|NYDSP20	spermatogenesis associated 22	protein-coding	0.097826	0.653117	
chunk0039_246_1	chr11	102147160	102147399	+	0	NA	intron (NM_001282098, intron 2 of 6)	intron (NM_001282098, intron 2 of 6)	34839	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.012552	0.333333	
chunk0030_133_1	chr10	113463814	113464094	+	0	NA	Intergenic	L1MEc|LINE|L1	-86877	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.010714	0.469751	46(CTGGACTTACTGTGCT,-,0.00),47(TGGACTTACTGTGCTA,+,0.00)
chunk0018_90_1	chr1	217534497	217534963	+	0	NA	intron (NM_018040, intron 5 of 9)	intron (NM_018040, intron 5 of 9)	96372	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.002146	0.351178	
chunk0137_385_1	chr4	26663877	26664166	+	0	NA	intron (NM_018317, intron 8 of 20)	L2c|LINE|L2	80097	NM_001292054	55296	Hs.479403	NM_018317	ENSG00000109680	TBC1D19	-	TBC1 domain family member 19	protein-coding	0.000000	0.372414	
chunk0196_68_1	chr8	102405959	102406372	+	0	NA	intron (NM_015902, intron 1 of 58)	intron (NM_015902, intron 1 of 58)	6524	NM_015902	51366	Hs.492445	NM_015902	ENSG00000104517	UBR5	DD5|EDD|EDD1|HYD	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.007264	0.357488	274(AGGCCAGACTGTACTT,+,0.00)
chunk0007_240_1	chr1	82347559	82348025	+	0	NA	Intergenic	Intergenic	547395	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.002146	0.314775	
chunk0210_317_1	chrX	92221238	92221846	+	0	NA	intron (NM_032969, intron 3 of 5)	intron (NM_032969, intron 3 of 5)	386081	NM_001168360	27328	Hs.655673	NM_014522	ENSG00000102290	PCDH11X	PCDH-X|PCDH-Y|PCDH11|PCDH11Y|PCDH22|PCDHX|PPP1R119	protocadherin 11 X-linked	protein-coding	0.003289	0.334975	
chunk0161_154_1	chr5	169010236	169010659	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	-2780	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.004728	0.441038	219(CTGTACTGGGTGTCCT,-,0.00),220(TGTACTGGGTGTCCTG,+,0.00)
chunk0077_5_1	chr16	74501589	74502112	+	0	NA	intron (NR_027264, intron 4 of 26)	intron (NR_027264, intron 4 of 26)	-80380	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.011472	0.438931	
chunk0174_308_1	chr6	162725918	162726307	+	0	NA	intron (NM_013988, intron 1 of 8)	intron (NM_013988, intron 1 of 8)	-1020	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.000000	0.279487	
chunk0084_262_1	chr17	79167212	79167453	+	0	NA	intron (NM_001082575, intron 4 of 14)	intron (NM_001082575, intron 4 of 14)	92395	NM_001042573	64772	Hs.29288	NM_022759	ENSG00000167280	ENGASE	-	endo-beta-N-acetylglucosaminidase	protein-coding	0.008299	0.640496	
chunk0136_423_1	chr3	197539852	197540051	+	0	NA	intron (NM_203314, intron 3 of 7).2	LTR8|LTR|ERV1	16036	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.015075	0.465000	
chunk0083_333_1	chr17	70137425	70137698	+	0	NA	Intergenic	Intergenic	31841	NR_036534	400617	Hs.225661	NR_036534	ENSG00000267365	KCNJ2-AS1	-	KCNJ2 antisense RNA 1	ncRNA	0.018315	0.434307	
chunk0064_320_1	chr14	95918405	95918901	+	0	NA	intron (NR_132398, intron 2 of 2)	intron (NR_132398, intron 2 of 2)	41881	NR_038861	100507043	Hs.455955	NR_038861	ENSG00000250366	TUNAR	HI-LNC78|LINC00617|TUNA	TCL1 upstream neural differentiation-associated RNA	ncRNA	0.012097	0.462777	
chunk0074_212_1	chr16	25298284	25298956	+	0	NA	Intergenic	MIR|SINE|MIR	-41086	NM_001012981	342357	Hs.513451	NM_001012981	ENSG00000155592	ZKSCAN2	ZNF694|ZSCAN31|ZSCAN34	zinc finger with KRAB and SCAN domains 2	protein-coding	0.008929	0.413076	
chunk0209_24_1	chrX	35726393	35726810	+	0	NA	Intergenic	Intergenic	-71741	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.007194	0.354067	136(GTGTACATGGTGTCCT,-,0.00),137(TGTACATGGTGTCCTT,+,0.00)
chunk0157_123_1	chr5	117129236	117129701	+	0	NA	Intergenic	Intergenic	-286044	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.006452	0.334764	168(AAGAACAAAATGTTTT,-,0.00),169(AGAACAAAATGTTTTT,+,0.00)
chunk0125_408_1	chr3	72274576	72274941	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	123501	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.016438	0.450820	
chunk0013_396_1	chr1	172886108	172886479	+	0	NA	Intergenic	L1M4b|LINE|L1	164670	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.002695	0.405914	
chunk0174_229_1	chr6	160553147	160553750	+	0	NA	intron (NM_005577, intron 31 of 39)	L1ME2|LINE|L1	-42324	NR_028092	80350	Hs.654503	NM_024492	ENSG00000213071	LPAL2	APOA2|APOAL|APOARGC|apo(a)rg-C	lipoprotein(a) like 2, pseudogene	pseudo	0.009950	0.304636	
chunk0005_144_1	chr1	57673353	57673816	+	0	NA	intron (NM_021080, intron 2 of 16)	intron (NM_021080, intron 2 of 16)	-186959	NR_104362	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.002160	0.334052	
chunk0130_153_1	chr3	132327734	132328119	+	0	NA	intron (NM_001099, intron 1 of 9)	intron (NM_001099, intron 1 of 9)	10559	NM_001134194	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.005195	0.391192	
chunk0202_67_1	chr9	71722903	71723398	+	0	NA	intron (NM_001135820, intron 10 of 22)	L2c|LINE|L2	45734	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.006061	0.387097	
chunk0091_269_1	chr19	11482570	11483120	+	0	NA	TTS (NM_138783)	TTS (NM_138783)	-1857	NM_001420	1995	Hs.1701	NM_001420	ENSG00000196361	ELAVL3	HUC|HUCL|PLE21	ELAV like RNA binding protein 3	protein-coding	0.080000	0.662432	370(TGGCACTGGTTGTTCC,-,0.00),371(GGCACTGGTTGTTCCT,+,0.00)
chunk0122_128_1	chr3	31531917	31532127	+	0	NA	promoter-TSS (NM_178862)	promoter-TSS (NM_178862)	-479	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.119048	0.691943	
chunk0148_139_1	chr5	6018848	6019572	+	0	NA	Intergenic	L1MA7|LINE|L1	318082	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.005525	0.368276	
chunk0049_303_1	chr12	94535489	94536261	+	0	NA	Intergenic	Intergenic	-25914	NR_049885	100847031		NR_049885	ENSG00000266099	MIR5700	-	microRNA 5700	ncRNA	0.015544	0.508409	
chunk0207_363_1	chr9	135774269	135774621	+	0	NA	intron (NM_001272003, intron 18 of 30)	(TGTGTGT)n|Simple_repeat|Simple_repeat	72260	NM_001272003	57582	Hs.104950	NM_020822	ENSG00000107147	KCNT1	EIEE14|ENFL5|KCa4.1|SLACK|Slo2.2|bA100C15.2	potassium sodium-activated channel subfamily T member 1	protein-coding	0.019886	0.504249	
chunk0064_242_1	chr14	94395777	94396472	+	0	NA	Intergenic	Intergenic	-5432	NM_001127707	5265	Hs.525557	NM_000295	ENSG00000197249	SERPINA1	A1A|A1AT|AAT|PI|PI1|PRO2275|alpha1AT|nNIF	serpin family A member 1	protein-coding	0.008633	0.478448	
chunk0038_111_1	chr11	83778461	83778664	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	-96137	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.009852	0.313725	
chunk0112_182_1	chr20	40047786	40048071	+	0	NA	Intergenic	Intergenic	43467	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.000000	0.332168	
chunk0210_123_1	chrX	73159902	73160305	+	0	NA	Intergenic	L1M1|LINE|L1	-32023	NR_027291	645996	Hs.617486	NR_027291	ENSG00000204118	NAP1L6	-	nucleosome assembly protein 1 like 6	pseudo	0.002481	0.321782	105(TGTACATTTTGTACTT,+,0.00)
chunk0103_449_1	chr2	170248891	170249092	+	0	NA	intron (NR_045684, intron 7 of 34)	intron (NR_045684, intron 7 of 34)	70846	NM_001083615	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.009950	0.420792	
chunk0153_447_1	chr5	76387922	76388621	+	0	NA	Intergenic	Intergenic	-14984	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.004292	0.378571	
chunk0036_20_1	chr11	58402199	58402398	+	0	NA	TTS (NM_001005469)	TTS (NM_001005469)	1111	NM_001005469	441608	Hs.553826	NM_001005469	ENSG00000172769	OR5B3	OR11-239|OR5B13|OST129	olfactory receptor family 5 subfamily B member 3	protein-coding	0.000000	0.315000	
chunk0034_296_1	chr11	34874883	34875112	+	0	NA	Intergenic	LTR1F|LTR|ERV1	-41133	NM_001166158	8050	Hs.502315	NM_003477	ENSG00000110435	PDHX	DLDBP|E3BP|OPDX|PDHXD|PDX1|proX	pyruvate dehydrogenase complex component X	protein-coding	0.017467	0.539130	
chunk0210_285_1	chrX	84959331	84959603	+	0	NA	Intergenic	LTR10C|LTR|ERV1	25316	NR_024062	100131816	Hs.460809	NM_178567	ENSG00000229547	UBE2DNL	-	ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)	pseudo	0.003676	0.395604	
chunk0146_315_1	chr4	165380878	165381216	+	0	NA	intron (NM_001873, intron 1 of 8)	intron (NM_001873, intron 1 of 8)	2102	NM_001873	1363	Hs.75360	NM_001873	ENSG00000109472	CPE	CPH	carboxypeptidase E	protein-coding	0.002959	0.300885	
chunk0137_217_1	chr4	19767723	19768073	+	0	NA	Intergenic	L1M2|LINE|L1	-484007	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.011429	0.538462	
chunk0180_12_1	chr7	53223159	53223501	+	0	NA	Intergenic	Intergenic	187674	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008772	0.346939	
chunk0147_391_1	chr4	186666226	186666679	+	0	NA	intron (NM_005245, intron 2 of 26)	intron (NM_005245, intron 2 of 26)	57381	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.008830	0.389868	213(GATAACAGAATGTTCT,-,0.00),214(ATAACAGAATGTTCTC,+,0.00)
chunk0071_408_1	chr15	89680517	89680916	+	0	NA	TTS (NM_003847)	TTS (NM_003847)	-1299	NM_002666	5346	Hs.103253	NM_002666	ENSG00000166819	PLIN1	FPLD4|PERI|PLIN	perilipin 1	protein-coding	0.005013	0.492500	
chunk0118_266_1	chr22	33338524	33338845	+	0	NA	intron (NM_133642, intron 9 of 14)	MIR|SINE|MIR	97985	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.003115	0.409938	
chunk0127_359_1	chr3	101505091	101505752	+	0	NA	intron (NM_001077203, intron 1 of 22)	intron (NM_001077203, intron 1 of 22)	7820	NM_001077203	57337	Hs.529551	NM_020654	ENSG00000138468	SENP7	-	SUMO specific peptidase 7	protein-coding	0.003026	0.339879	
chunk0118_277_1	chr22	33720665	33720864	+	0	NA	intron (NM_133642, intron 2 of 14)	intron (NM_133642, intron 2 of 14)	-4222	NR_038949	100506195	Hs.658872	NR_038949	ENSG00000224973	LARGE-AS1	-	LARGE antisense RNA 1	ncRNA	0.005025	0.465000	
chunk0052_45_1	chr13	20860556	20860780	+	0	NA	intron (NM_022459, intron 3 of 22)	intron (NM_022459, intron 3 of 22)	42106	NM_022459	64328	Hs.507452	NM_022459	ENSG00000132953	XPO4	exp4	exportin 4	protein-coding	0.000000	0.391111	
chunk0168_228_1	chr6	87196478	87196701	+	0	NA	intron (NM_015021, intron 1 of 7)	Tigger6a|DNA|TcMar-Tigger	41038	NM_015021	23036	Hs.444800	NM_015021	ENSG00000188994	ZNF292	Nbla00365|ZFP292|ZN-16|Zn-15|bA393I2.3	zinc finger protein 292	protein-coding	0.000000	0.375000	
chunk0191_188_1	chr8	51630151	51630704	+	0	NA	intron (NM_144651, intron 2 of 22)	L1PA15|LINE|L1	179018	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.007233	0.337545	
chunk0161_420_1	chr5	178249573	178250928	+	0	NA	intron (NM_173465, intron 17 of 28)	intron (NM_173465, intron 17 of 28)	-17428	NM_001278346	85007	Hs.248746	NM_153373	ENSG00000175309	PHYKPL	AGXT2L2|PHLU	5-phosphohydroxy-L-lysine phospho-lyase	protein-coding	0.014022	0.500000	239(CTGCACTGAGTGTTCT,-,0.00),240(TGCACTGAGTGTTCTC,+,0.00),602(CAGGACACACTGTGCA,-,0.00),603(AGGACACACTGTGCAC,+,0.00)
chunk0171_56_1	chr6	121211677	121212175	+	0	NA	intron (NM_152730, intron 21 of 31)	L2a|LINE|L2	122574	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.012048	0.464930	228(CTGCACACACAGTTCC,-,0.00),229(TGCACACACAGTTCCT,+,0.00)
chunk0008_136_1	chr1	92004212	92004531	+	0	NA	intron (NM_001726, intron 16 of 18)	intron (NM_001726, intron 16 of 18)	-25605	NM_173567	253152	Hs.201555	NM_173567	ENSG00000172031	EPHX4	ABHD7|EH4|EPHXRP	epoxide hydrolase 4	protein-coding	0.000000	0.300000	
chunk0162_216_1	chr6	4285851	4286050	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-95921	NR_125874	102724096	Hs.571140	NR_125874		LOC102724096	-	uncharacterized LOC102724096	ncRNA	0.005025	0.360000	
chunk0101_67_1	chr2	123678742	123679239	+	0	NA	Intergenic	Intergenic	-346297	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.295181	
chunk0043_446_1	chr12	26508594	26508951	+	0	NA	intron (NM_002223, intron 37 of 56)	L1MB7|LINE|L1	313199	NM_005086	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.008403	0.382682	342(TTGTACAGAATGTTCA,-,0.00)
chunk0168_309_1	chr6	91902690	91903363	+	0	NA	Intergenic	Intergenic	-212598	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.007429	0.338279	
chunk0208_214_1	chrX	18302510	18303006	+	0	NA	intron (NM_006089, intron 7 of 14)	L2c|LINE|L2	51966	NR_033717	10389	Hs.495774	NM_006089	ENSG00000102098	SCML2	-	Scm polycomb group protein like 2	protein-coding	0.004032	0.406439	
chunk0060_246_1	chr14	49926857	49927235	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	34028	NM_001663	382	Hs.525330	NM_001663	ENSG00000165527	ARF6	-	ADP ribosylation factor 6	protein-coding	0.005291	0.393140	
chunk0181_51_1	chr7	80088843	80089068	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-45869	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.000000	0.407080	
chunk0004_256_1	chr1	47809752	47809977	+	0	NA	intron (NM_001194986, intron 2 of 6)	MIR3|SINE|MIR	187026	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.004444	0.455752	
chunk0153_22_1	chr5	67042556	67043161	+	0	NA	intron (NM_001297651, intron 1 of 25)	intron (NM_001297651, intron 1 of 25)	38238	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.014876	0.407591	
chunk0209_427_1	chrX	57643592	57644192	+	0	NA	Intergenic	L1MA2|LINE|L1	52056	NM_007157	158586	Hs.156257	NM_007157	ENSG00000198455	ZXDB	ZNF905|dJ83L6.1	zinc finger X-linked duplicated B	protein-coding	0.001667	0.299501	
chunk0094_52_1	chr2	3110329	3110772	+	0	NA	intron (NR_110228, intron 3 of 6)	(GT)n|Simple_repeat|Simple_repeat	15476	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.009029	0.416667	
chunk0211_182_1	chrX	117204174	117204588	+	0	NA	Intergenic	Intergenic	-741348	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.002415	0.356627	
chunk0119_181_1	chr22	43956352	43956755	+	0	NA	intron (NM_015380, intron 1 of 14)	LTR26C|LTR|ERV1	1172	NM_015380	25813	Hs.505824	NM_015380	ENSG00000100347	SAMM50	CGI-51|OMP85|SAM50|TOB55|TRG-3|YNL026W	SAMM50 sorting and assembly machinery component	protein-coding	0.017370	0.435644	
chunk0053_166_1	chr13	30690570	30691084	+	0	NA	Intergenic	LTR78B|LTR|ERV1	-22651	NM_001204406	241	Hs.507658	NM_001629	ENSG00000132965	ALOX5AP	FLAP	arachidonate 5-lipoxygenase activating protein	protein-coding	0.019455	0.524272	
chunk0041_304_1	chr11	129808109	129808697	+	0	NA	Intergenic	L1PB1|LINE|L1	-7443	NM_138788	120224	Hs.504301	NM_138788	ENSG00000151715	TMEM45B	-	transmembrane protein 45B	protein-coding	0.003401	0.393888	
chunk0099_156_1	chr2	87745469	87745668	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-2519	NM_002665	5342	Hs.652169	NM_002665	ENSG00000125551	PLGLB2	PLGLA|PLGLA1|PLGP1|PLGP2|PRGA	plasminogen like B2	protein-coding	0.020101	0.465000	
chunk0190_97_1	chr8	30254862	30255279	+	0	NA	Intergenic	Intergenic	98773	NM_006571	10671	Hs.158427	NM_006571	ENSG00000104671	DCTN6	WS-3|WS3|p27	dynactin subunit 6	protein-coding	0.011990	0.409091	
chunk0053_403_1	chr13	36393282	36394200	+	0	NA	Intergenic	L1PA15|LINE|L1	-23561	NM_001142294	23111	Hs.440414	NM_015087	ENSG00000133104	SPART	SPG20|TAHCCP1	spartin	protein-coding	0.003268	0.368879	
chunk0051_411_1	chr12	122203309	122203633	+	0	NA	promoter-TSS (NM_030765)	promoter-TSS (NM_030765)	-210	NM_030765	79369	Hs.363315	NM_030765	ENSG00000176383	B3GNT4	B3GN-T4|beta3Gn-T4	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	protein-coding	0.120370	0.698462	
chunk0001_155_1	chr1	6259476	6260018	+	0	NA	intron (NM_207370, intron 1 of 5)	intron (NM_207370, intron 1 of 5)	1228	NM_207370	387509	Hs.531581	NM_207370	ENSG00000158292	GPR153	PGR1	G protein-coupled receptor 153	protein-coding	0.022140	0.572744	276(GGGAACAAAGTGTCCC,-,0.00),277(GGAACAAAGTGTCCCT,+,0.00)
chunk0003_179_1	chr1	33659599	33660806	+	0	NA	intron (NM_052896, intron 26 of 69)	MIR|SINE|MIR	187571	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.008285	0.431291	
chunk0080_277_1	chr17	31128254	31128522	+	0	NA	intron (NM_001042492, intron 1 of 57)	L1PA13|LINE|L1	33461	NM_001128147	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.007463	0.390335	
chunk0036_386_1	chr11	67649618	67649931	+	0	NA	intron (NM_080658, intron 1 of 7)	(GT)n|Simple_repeat|Simple_repeat	885	NM_080658	91703	Hs.126265	NM_080658	ENSG00000132744	ACY3	ACY-3|HCBP1	aminoacylase 3	protein-coding	0.041534	0.509554	
chunk0080_266_1	chr17	30950853	30951065	+	0	NA	intron (NM_018404, intron 7 of 10)	intron (NM_018404, intron 7 of 10)	-19979	NM_197939	84282	Hs.29874	NM_032322	ENSG00000181481	RNF135	L13|MMFD|REUL|Riplet	ring finger protein 135	protein-coding	0.009434	0.488263	
chunk0180_73_1	chr7	54967390	54967914	+	0	NA	Intergenic	Intergenic	-51380	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.017176	0.434286	
chunk0070_216_1	chr15	72496812	72497117	+	0	NA	intron (NM_005744, intron 1 of 13)	intron (NM_005744, intron 1 of 13)	22638	NM_005744	25820	Hs.268787	NM_005744	ENSG00000166233	ARIH1	ARI|HARI|HHARI|UBCH7BP	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding	0.003279	0.379085	
chunk0149_347_1	chr5	27369195	27369484	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-102953	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.003460	0.355172	
chunk0100_193_1	chr2	111071604	111072241	+	0	NA	intron (NM_001142807, intron 16 of 17)	L2c|LINE|L2	43666	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.007849	0.452978	441(AAGAACAGGGAGATCC,-,0.00),442(AGAACAGGGAGATCCT,+,0.00)
chunk0046_266_1	chr12	61098242	61098441	+	0	NA	Intergenic	L1PA17|LINE|L1	1094498	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.015075	0.575000	
chunk0109_319_1	chr20	9155687	9156187	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	-61453	NM_182797	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.008000	0.405190	
chunk0037_375_1	chr11	78279937	78280433	+	0	NA	intron (NM_012296, intron 2 of 9)	intron (NM_012296, intron 2 of 9)	61695	NM_012296	9846	Hs.429434	NM_012296	ENSG00000033327	GAB2	-	GRB2 associated binding protein 2	protein-coding	0.006048	0.428571	342(TGGGACACAGAGTGCT,-,0.00),343(GGGACACAGAGTGCTG,+,0.00)
chunk0046_277_1	chr12	61584671	61585464	+	0	NA	Intergenic	Intergenic	607772	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.005044	0.360202	422(AGGTACATTTTGTACC,-,0.00),423(GGTACATTTTGTACCT,+,0.00)
chunk0162_203_1	chr6	4052890	4053675	+	0	NA	intron (NM_003913, intron 11 of 14)	intron (NM_003913, intron 11 of 14)	-25924	NR_104464	404220	Hs.716731	NM_206834	ENSG00000185689	C6orf201	dJ1013A10.5	chromosome 6 open reading frame 201	protein-coding	0.008917	0.370229	
chunk0041_441_1	chr11	134565463	134565682	+	0	NA	Intergenic	(ATGATG)n|Simple_repeat|Simple_repeat	129090	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.041096	0.463636	
chunk0108_190_1	chr2	232282840	232283346	+	0	NA	intron (NR_046476, intron 13 of 20)	MIRb|SINE|MIR	-95441	NM_001632	250	Hs.284255	NM_001632	ENSG00000163283	ALPP	ALP|ALPI|IAP|PALP|PLAP|PLAP-1	alkaline phosphatase, placental	protein-coding	0.011858	0.469428	
chunk0091_370_1	chr19	15595044	15595644	+	0	NA	Intergenic	LTR44|LTR|ERV1	-19874	NM_007253	11283	Hs.268554	NM_007253	ENSG00000186526	CYP4F8	CPF8|CYPIVF8	cytochrome P450 family 4 subfamily F member 8	protein-coding	0.011667	0.396007	
chunk0006_188_1	chr1	67434524	67434933	+	0	NA	Intergenic	L1MB7|LINE|L1	-4288	NM_015640	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.004890	0.351220	
chunk0065_10_1	chr15	20275723	20276428	+	0	NA	Intergenic	Intergenic	-6669	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.015603	0.416431	
chunk0170_42_1	chr6	109382327	109382860	+	0	NA	promoter-TSS (NM_001142402)	promoter-TSS (NM_001142402)	-34	NM_001142402	8763	Hs.520313	NM_006016	ENSG00000135535	CD164	DFNA66|MGC-24|MGC-24v|MUC-24|endolyn	CD164 molecule	protein-coding	0.090056	0.647940	
chunk0159_317_1	chr5	143418028	143418336	+	0	NA	intron (NM_001018075, intron 1 of 8)	intron (NM_001018075, intron 1 of 8)	-13702	NM_001018076	2908	Hs.122926	NM_000176	ENSG00000113580	NR3C1	GCCR|GCR|GCRST|GR|GRL	nuclear receptor subfamily 3 group C member 1	protein-coding	0.003247	0.362460	
chunk0129_297_1	chr3	123613007	123613314	+	0	NA	3' UTR (NM_053032, exon 3 of 3)	3' UTR (NM_053032, exon 3 of 3)	7523	NM_053032	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.006515	0.363636	136(AAGTACATGGAGTTCT,-,0.00),137(AGTACATGGAGTTCTC,+,0.00)
chunk0081_108_1	chr17	39934207	39934666	+	0	NA	Intergenic	Intergenic	-6805	NM_139280	94103	Hs.514151	NM_016471	ENSG00000172057	ORMDL3	-	ORMDL sphingolipid biosynthesis regulator 3	protein-coding	0.006536	0.450000	
chunk0127_241_1	chr3	96931456	96931875	+	0	NA	intron (NM_001080448, intron 2 of 17)	L1PA10|LINE|L1	117084	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.007160	0.538095	
chunk0140_45_1	chr4	66626514	66627083	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	349974	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.003515	0.392982	
chunk0163_25_1	chr6	8080145	8080779	+	0	NA	intron (NM_004280, intron 3 of 3)	intron (NM_004280, intron 3 of 3)	6071	NR_003703	100124533		NR_003703		SCARNA27	-	small Cajal body-specific RNA 27	ncRNA	0.004732	0.368504	
chunk0115_208_1	chr21	26815130	26815365	+	0	NA	Intergenic	(ATGTTT)n|Simple_repeat|Simple_repeat	30162	NM_006988	9510	Hs.643357	NM_006988	ENSG00000154734	ADAMTS1	C3-C5|METH1	ADAM metallopeptidase with thrombospondin type 1 motif 1	protein-coding	0.000000	0.296610	
chunk0196_155_1	chr8	104731851	104732247	+	0	NA	Intergenic	Intergenic	-143025	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.020202	0.493703	87(GAGAACACAGTGTGAT,-,0.00)
chunk0070_203_1	chr15	72155074	72155696	+	0	NA	Intergenic	Intergenic	37095	NM_001172111	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.027331	0.544141	
chunk0015_312_1	chr1	189154953	189155469	+	0	NA	Intergenic	Intergenic	1322418	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003876	0.317215	
chunk0028_147_1	chr10	86737956	86738407	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-18458	NM_004329	657	Hs.524477	NM_004329	ENSG00000107779	BMPR1A	10q23del|ACVRLK3|ALK3|CD292|SKR5	bone morphogenetic protein receptor type 1A	protein-coding	0.006652	0.453540	
chunk0146_12_1	chr4	155029978	155030519	+	0	NA	Intergenic	Intergenic	-178381	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.003697	0.361624	
chunk0037_246_1	chr11	75422215	75422759	+	0	NA	TTS (NM_001256802)	TTS (NM_001256802)	8142	NM_001039548	283212	Hs.292451	NM_173583	ENSG00000149243	KLHL35	-	kelch like family member 35	protein-coding	0.020221	0.519266	297(GGGAGCAGAGTGTGCA,-,0.00),298(GGAGCAGAGTGTGCAT,+,0.00)
chunk0158_258_1	chr5	131014989	131015349	+	0	NA	Intergenic	L1PB1|LINE|L1	150179	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.000000	0.340720	
chunk0079_5_1	chr17	9151253	9151494	+	0	NA	intron (NM_004822, intron 2 of 6)	intron (NM_004822, intron 2 of 6)	27745	NR_110828	101928266	Hs.639880	NR_110828	ENSG00000262966	LOC101928266	-	uncharacterized LOC101928266	ncRNA	0.020747	0.504132	
chunk0139_385_1	chr4	61638402	61638875	+	0	NA	intron (NM_015236, intron 2 of 22)	intron (NM_015236, intron 2 of 22)	141517	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.002114	0.305907	
chunk0053_416_1	chr13	37106708	37106976	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-1178	NM_145203	122011	Hs.512897	NM_145203	ENSG00000180138	CSNK1A1L	CK1	casein kinase 1 alpha 1 like	protein-coding	0.000000	0.408922	115(AGGAGCATGCTGTTCT,-,0.00),116(GGAGCATGCTGTTCTC,+,0.00)
chunk0011_391_1	chr1	153986326	153986631	+	0	NA	promoter-TSS (NM_002870)	promoter-TSS (NM_002870)	-101	NR_073553	5872	Hs.151536	NM_002870	ENSG00000143545	RAB13	GIG4	RAB13, member RAS oncogene family	protein-coding	0.039344	0.584967	
chunk0197_136_1	chr8	120204388	120204909	+	0	NA	intron (NM_021110, intron 9 of 47)	L1MD1|LINE|L1	79540	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.007678	0.450192	
chunk0170_365_1	chr6	116810953	116811174	+	0	NA	intron (NM_001286354, intron 1 of 5)	L1MA4A|LINE|L1	17994	NM_001286355	222545	Hs.266745	NM_148963	ENSG00000173612	GPRC6A	GPCR|bA86F4.3	G protein-coupled receptor class C group 6 member A	protein-coding	0.000000	0.495495	
chunk0180_315_1	chr7	71251593	71252120	+	0	NA	intron (NM_022479, intron 1 of 10)	Charlie7|DNA|hAT-Charlie	-55818	NR_037479	100500920		NR_037479	ENSG00000283278	MIR3914-2	-	microRNA 3914-2	ncRNA	0.015180	0.501894	
chunk0143_417_1	chr4	123588003	123588607	+	0	NA	Intergenic	Intergenic	-64480	NR_027105	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.013245	0.439669	
chunk0204_421_1	chr9	103036878	103037262	+	0	NA	Intergenic	Intergenic	41759	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.010417	0.361039	
chunk0062_247_1	chr14	71457013	71457397	+	0	NA	Intergenic	L3|LINE|CR1	-30656	NR_027046	145474	Hs.658241	NR_027046		LOC145474	-	uncharacterized LOC145474	ncRNA	0.010417	0.418182	
chunk0045_33_1	chr12	44174442	44174892	+	0	NA	intron (NM_032256, intron 4 of 7)	L2b|LINE|L2	338806	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.006667	0.294900	
chunk0016_139_1	chr1	197212007	197212408	+	0	NA	intron (NM_001257965, intron 1 of 14)	L1ME1|LINE|L1	10745	NM_001257965	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.004988	0.310945	
chunk0117_304_1	chr22	24553617	24553922	+	0	NA	intron (NM_001284251, intron 1 of 5)	intron (NM_001284251, intron 1 of 5)	1538	NM_001284254	83606	Hs.9850	NM_031444	ENSG00000138867	GUCD1	C22orf13|LLN4	guanylyl cyclase domain containing 1	protein-coding	0.019672	0.565359	
chunk0190_36_1	chr8	29314410	29314716	+	0	NA	Intergenic	SATR2|Satellite|Satellite	34242	NM_057158	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.019608	0.381107	
chunk0156_276_1	chr5	109691153	109691527	+	0	NA	intron (NM_002372, intron 1 of 21)	intron (NM_002372, intron 1 of 21)	1974	NM_002372	4124	Hs.432822	NM_002372	ENSG00000112893	MAN2A1	AMan II|GOLIM7|MANA2|MANII	mannosidase alpha class 2A member 1	protein-coding	0.048128	0.477333	147(GGACACAGTCTGTTCC,-,0.00),148(GACACAGTCTGTTCCC,+,0.00)
chunk0156_267_1	chr5	109468850	109469095	+	0	NA	Intergenic	Intergenic	-58998	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.008163	0.418699	
chunk0029_339_1	chr10	106162598	106162911	+	0	NA	Intergenic	L1M4b|LINE|L1	-342421	NR_120625	101927549	Hs.556885	NR_120625		LINC02627	-	long intergenic non-protein coding RNA 2627	ncRNA	0.000000	0.353503	
chunk0170_247_1	chr6	113668946	113670145	+	0	NA	Intergenic	Intergenic	-19470	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.003336	0.422500	
chunk0014_82_1	chr1	176530828	176531414	+	0	NA	intron (NM_020318, intron 1 of 22)	intron (NM_020318, intron 1 of 22)	67950	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.003413	0.405451	249(TGGAACTGAATGTTCT,-,0.00),250(GGAACTGAATGTTCTA,+,0.00)
chunk0082_276_1	chr17	57988398	57988597	+	0	NA	promoter-TSS (NM_007146)	promoter-TSS (NM_007146)	-243	NM_007146	7716	Hs.463569	NM_007146	ENSG00000136451	VEZF1	DB1|ZNF161	vascular endothelial zinc finger 1	protein-coding	0.085427	0.785000	
chunk0049_316_1	chr12	94596533	94596994	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	19388	NM_001301036	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.004338	0.432900	
chunk0167_153_1	chr6	62612404	62612778	+	0	NA	Intergenic	MER50-int|LTR|ERV1	-326396	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.005348	0.466667	
chunk0106_269_1	chr2	203775198	203775560	+	0	NA	Intergenic	LTR33|LTR|ERVL	68904	NM_001243078	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.011050	0.528926	
chunk0038_461_1	chr11	94845425	94846214	+	0	NA	intron (NM_130847, intron 6 of 12)	intron (NM_130847, intron 6 of 12)	77477	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.006337	0.455696	
chunk0018_315_1	chr1	221203987	221204734	+	0	NA	Intergenic	Intergenic	131936	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.004016	0.382353	367(AAGAACACACAGTACC,-,0.00),368(AGAACACACAGTACCT,+,0.00)
chunk0072_217_1	chr15	95629451	95629859	+	0	NA	Intergenic	Intergenic	196562	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.004902	0.376528	
chunk0128_405_1	chr3	114445966	114446530	+	0	NA	intron (NM_001164343, intron 8 of 11)	intron (NM_001164343, intron 8 of 11)	-7345	NR_121661	101929754	Hs.614195	NR_121661	ENSG00000242290	ZBTB20-AS5	-	ZBTB20 antisense RNA 5	ncRNA	0.005319	0.323894	
chunk0062_306_1	chr14	73090955	73091240	+	0	NA	intron (NM_021239, intron 6 of 18)	intron (NM_021239, intron 6 of 18)	32584	NM_021239	58517	Hs.531106	NM_021239	ENSG00000119707	RBM25	NET52|RED120|RNPC7|S164|Snu71|fSAP94	RNA binding motif protein 25	protein-coding	0.003509	0.314685	104(AGGACTCACTGTTTTC,+,0.00)
chunk0179_199_1	chr7	47333535	47333738	+	0	NA	intron (NM_022748, intron 20 of 30)	intron (NM_022748, intron 20 of 30)	248508	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.004926	0.328431	
chunk0035_71_1	chr11	41779320	41779899	+	0	NA	intron (NR_120584, intron 2 of 5)	MER4C|LTR|ERV1	65041	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.001727	0.391379	
chunk0046_84_1	chr12	56291540	56291757	+	0	NA	intron (NM_004077, intron 1 of 10)	L3|LINE|CR1	8743	NM_004077	1431	Hs.743252	NM_004077	ENSG00000062485	CS	-	citrate synthase	protein-coding	0.004608	0.490826	
chunk0102_139_1	chr2	146120992	146121403	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	-465860	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.002433	0.276699	
chunk0068_219_1	chr15	55240109	55240522	+	0	NA	intron (NM_183234, intron 1 of 6)	intron (NM_183234, intron 1 of 6)	29971	NM_183234	5873	Hs.654978	NM_004580	ENSG00000069974	RAB27A	GS2|HsT18676|RAB27|RAM	RAB27A, member RAS oncogene family	protein-coding	0.007264	0.420290	139(GAGAACACACAGTACC,-,0.00),140(AGAACACACAGTACCA,+,0.00)
chunk0086_137_1	chr18	21168922	21169342	+	0	NA	Intergenic	L2c|LINE|L2	-57281	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.004762	0.339667	
chunk0030_298_1	chr10	117362751	117363029	+	0	NA	intron (NM_173791, intron 1 of 4)	intron (NM_173791, intron 1 of 4)	12577	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.003597	0.304659	
chunk0191_182_1	chr8	51339481	51339755	+	0	NA	intron (NM_144651, intron 21 of 22)	intron (NM_144651, intron 21 of 22)	469827	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.010949	0.363636	
chunk0178_310_1	chr7	38051759	38051997	+	0	NA	Intergenic	L1MA4A|LINE|L1	-126328	NM_032016	83930	Hs.309753	NM_032016	ENSG00000010270	STARD3NL	MENTHO	STARD3 N-terminal like	protein-coding	0.004202	0.552301	
chunk0168_222_1	chr6	86380755	86380994	+	0	NA	Intergenic	Intergenic	-556432	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.008368	0.425000	
chunk0093_33_1	chr19	39402221	39402826	+	0	NA	Intergenic	Intergenic	-4324	NM_003407	7538	Hs.534052	NM_003407	ENSG00000128016	ZFP36	G0S24|GOS24|NUP475|RNF162A|TIS11|TTP|zfp-36	ZFP36 ring finger protein	protein-coding	0.066116	0.605611	
chunk0207_315_1	chr9	133915690	133916011	+	0	NA	intron (NM_001134398, intron 2 of 29)	CpG	76474	NM_003371	7410	Hs.369921	NM_003371	ENSG00000160293	VAV2	VAV-2	vav guanine nucleotide exchange factor 2	protein-coding	0.059190	0.493789	237(ATGCACACGATGTACA,-,0.00),238(TGCACACGATGTACAT,+,0.00)
chunk0188_360_1	chr8	18073394	18074024	+	0	NA	intron (NM_001127505, intron 2 of 13)	7SK|RNA|RNA	10661	NM_177924	427	Hs.527412	NM_004315	ENSG00000104763	ASAH1	AC|ACDase|ASAH|PHP|PHP32|SMAPME	N-acylsphingosine amidohydrolase 1	protein-coding	0.009524	0.412044	
chunk0139_26_1	chr4	48343444	48343689	+	0	NA	intron (NM_020846, intron 1 of 7)	intron (NM_020846, intron 1 of 7)	1970	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.004082	0.414634	123(TAGAACAAAGAGTACT,-,0.00),124(AGAACAAAGAGTACTG,+,0.00),132(GAGTACTGACAGTGCT,-,0.00),133(AGTACTGACAGTGCTC,+,0.00)
chunk0212_37_1	chrY	11282067	11282444	+	0	NA	Intergenic	Intergenic	1139335	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.007958	0.412698	
chunk0210_97_1	chrX	71378841	71379114	+	0	NA	exon (NM_001286074, exon 8 of 38)	exon (NM_001286074, exon 8 of 38)	12738	NR_104389	6872	Hs.158560	NM_004606	ENSG00000147133	TAF1	BA2R|CCG1|CCGS|DYT3|DYT3/TAF1|KAT4|MRXS33|N-TAF1|NSCL2|OF|P250|TAF(II)250|TAF2A|TAFII-250|TAFII250|XDP	TATA-box binding protein associated factor 1	protein-coding	0.007326	0.478102	
chunk0007_120_1	chr1	79017218	79017769	+	0	NA	Intergenic	Intergenic	-10683	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.001815	0.324275	
chunk0034_55_1	chr11	27088406	27088826	+	0	NA	intron (NR_125766, intron 3 of 4)	intron (NR_125766, intron 3 of 4)	47654	NM_003986	8424	Hs.591996	NM_003986	ENSG00000129151	BBOX1	BBH|BBOX|G-BBH|gamma-BBH	gamma-butyrobetaine hydroxylase 1	protein-coding	0.000000	0.353919	
chunk0028_18_1	chr10	82463433	82464050	+	0	NA	intron (NM_001010848, intron 2 of 8)	MIRb|SINE|MIR	-230821	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.003241	0.385113	
chunk0195_417_1	chr8	100680927	100681692	+	0	NA	Intergenic	Intergenic	21715	NR_106992	102466854		NR_106992	ENSG00000284570	MIR7705	hsa-mir-7705	microRNA 7705	ncRNA	0.011765	0.455614	277(AGGAACATTTAGTCCT,-,0.00),278(GGAACATTTAGTCCTA,+,0.00)
chunk0078_249_1	chr17	7159474	7160131	+	0	NA	Intergenic	LTR5B|LTR|ERVK	19762	NM_001197216	432	Hs.12056	NM_001671	ENSG00000141505	ASGR1	ASGPR|ASGPR1|CLEC4H1|HL-1	asialoglycoprotein receptor 1	protein-coding	0.019787	0.460486	
chunk0010_360_1	chr1	118825852	118826252	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	163504	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.000000	0.438903	
chunk0170_306_1	chr6	115916106	115916450	+	0	NA	Intergenic	Intergenic	-122453	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.002907	0.391304	
chunk0039_126_1	chr11	98231399	98231971	+	0	NA	Intergenic	Intergenic	-789291	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.006993	0.291449	
chunk0184_189_1	chr7	116788354	116789047	+	0	NA	intron (NM_000245, intron 19 of 20)	intron (NM_000245, intron 19 of 20)	-73809	NM_006136	830	Hs.446123	NM_006136	ENSG00000198898	CAPZA2	CAPPA2|CAPZ	capping actin protein of muscle Z-line subunit alpha 2	protein-coding	0.007215	0.396254	
chunk0123_2_1	chr3	40057524	40057723	+	0	NA	intron (NM_001284425, intron 3 of 15)	intron (NM_001284425, intron 3 of 15)	-42388	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.000000	0.470000	
chunk0168_340_1	chr6	92864921	92865586	+	0	NA	Intergenic	L1MCa|LINE|L1	554329	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.006015	0.423423	416(AGGAACAGGAAGTCCA,-,0.00),417(GGAACAGGAAGTCCAC,+,0.00)
chunk0137_343_1	chr4	25099403	25099859	+	0	NA	Intergenic	Intergenic	60951	NM_016955	51091	Hs.253305	NM_016955	ENSG00000109618	SEPSECS	LP|PCH2D|SLA|SLA/LP	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	protein-coding	0.010965	0.522976	
chunk0073_335_1	chr16	14513347	14513737	+	0	NA	intron (NM_002582, intron 21 of 23)	intron (NM_002582, intron 21 of 23)	116729	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.015385	0.485934	
chunk0019_9_1	chr1	223319407	223319731	+	0	NA	intron (NM_001037175, intron 2 of 5)	intron (NM_001037175, intron 2 of 5)	44633	NM_017982	55061	Hs.497841	NM_017982	ENSG00000143502	SUSD4	PRO222	sushi domain containing 4	protein-coding	0.006173	0.446154	
chunk0157_97_1	chr5	116734389	116734934	+	0	NA	Intergenic	Intergenic	27548	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.009174	0.521978	
chunk0037_86_1	chr11	71464166	71464632	+	0	NA	intron (NM_018161, intron 5 of 20)	MER51B|LTR|ERV1	-9104	NR_106812	102466728		NR_106812	ENSG00000278349	MIR6754	hsa-mir-6754	microRNA 6754	ncRNA	0.021459	0.488223	
chunk0041_19_1	chr12	456039	456415	+	0	NA	Intergenic	MIRc|SINE|MIR	-4150	NM_173593	283358	Hs.504416	NM_173593	ENSG00000139044	B4GALNT3	-	beta-1,4-N-acetyl-galactosaminyltransferase 3	protein-coding	0.007979	0.416446	
chunk0103_400_1	chr2	169063414	169063859	+	0	NA	Intergenic	Intergenic	-3399	NM_001289763	10170	Hs.179608	NM_005771	ENSG00000073737	DHRS9	3-alpha-HSD|3ALPHA-HSD|RDH-E2|RDH-TBE|RDH15|RDHL|RDHTBE|RETSDR8|SDR9C4	dehydrogenase/reductase 9	protein-coding	0.006742	0.349776	
chunk0165_225_1	chr6	35359941	35360148	+	0	NA	intron (NM_001171819, intron 2 of 6)	intron (NM_001171819, intron 2 of 6)	17486	NM_177435	5467	Hs.696032	NM_006238	ENSG00000112033	PPARD	FAAR|NR1C2|NUC1|NUCI|NUCII|PPARB	peroxisome proliferator activated receptor delta	protein-coding	0.004831	0.514423	
chunk0201_139_1	chr9	35770980	35772143	+	0	NA	Intergenic	Intergenic	-17284	NM_001044264	692094	Hs.571601	NM_001044264	ENSG00000215183	MSMP	PSMP	microseminoprotein, prostate associated	protein-coding	0.004299	0.392612	
chunk0177_61_1	chr7	21163290	21163777	+	0	NA	Intergenic	L1M5|LINE|L1	-264538	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.004107	0.270492	
chunk0190_285_1	chr8	37765317	37765516	+	0	NA	intron (NM_007198, intron 1 of 7)	intron (NM_007198, intron 1 of 7)	2833	NM_007198	11212	Hs.304792	NM_007198	ENSG00000147471	PLPBP	EPVB6D|PROSC	pyridoxal phosphate binding protein	protein-coding	0.005025	0.400000	
chunk0196_453_1	chr8	116667152	116667975	+	0	NA	intron (NM_003756, intron 2 of 7)	intron (NM_003756, intron 2 of 7)	88260	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.001215	0.342233	
chunk0047_96_1	chr12	68621721	68622165	+	0	NA	intron (NM_001251917, intron 1 of 5)	intron (NM_001251917, intron 1 of 5)	5432	NR_033335	100379132	Hs.724530	NR_033335	ENSG00000206650	SNORA70G	U70G	small nucleolar RNA, H/ACA box 70G	snoRNA	0.000000	0.370787	
chunk0209_90_1	chrX	39241772	39242496	+	0	NA	Intergenic	Intergenic	85228	NR_038968	286442	Hs.638478	NR_038968	ENSG00000235304	LINC01281	-	long intergenic non-protein coding RNA 1281	ncRNA	0.006906	0.445517	312(GAACACAGGGTGTTCT,-,0.00),313(AACACAGGGTGTTCTT,+,0.00)
chunk0050_190_1	chr12	103957286	103957718	+	0	NA	promoter-TSS (NM_001135570)	promoter-TSS (NM_001135570)	-287	NM_001135570	728568	Hs.42547	NM_001135570	ENSG00000204954	C12orf73	-	chromosome 12 open reading frame 73	protein-coding	0.023148	0.461894	287(AGGCACTCACTGTCCC,-,0.00),288(GGCACTCACTGTCCCT,+,0.00)
chunk0125_402_1	chr3	72129392	72130022	+	0	NA	Intergenic	Intergenic	-21550	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.007937	0.434231	
chunk0111_37_1	chr20	22223474	22223751	+	0	NA	Intergenic	Intergenic	59189	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.014440	0.456835	
chunk0185_327_1	chr7	131665463	131666038	+	0	NA	Intergenic	Intergenic	-109133	NM_005397	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.010435	0.529514	
chunk0181_231_1	chr7	85230637	85231109	+	0	NA	Intergenic	Intergenic	-108942	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.008475	0.363636	
chunk0174_302_1	chr6	162683274	162683501	+	0	NA	intron (NM_013988, intron 1 of 8)	intron (NM_013988, intron 1 of 8)	-43745	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.008811	0.364035	
chunk0034_184_1	chr11	31551869	31552559	+	0	NA	intron (NM_019040, intron 3 of 9)	L2a|LINE|L2	42485	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.005797	0.374819	
chunk0190_123_1	chr8	30589502	30590020	+	0	NA	intron (NM_002095, intron 6 of 7)	intron (NM_002095, intron 6 of 7)	-48839	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.007722	0.385356	263(CAGCACTTGCTGTTCT,-,0.00),264(AGCACTTGCTGTTCTT,+,0.00)
chunk0084_268_1	chr17	79620147	79620386	+	0	NA	Intergenic	Intergenic	86983	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.062762	0.533333	
chunk0015_131_1	chr1	185545170	185545462	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	83172	NR_110793	101929093	Hs.535227	NR_110793	ENSG00000228309	LINC01350	GS1-204I12.1	long intergenic non-protein coding RNA 1350	ncRNA	0.003425	0.324232	16(AGAACACAATCTCCTT,+,0.00)
chunk0206_391_1	chr9	127011729	127012203	+	0	NA	intron (NM_001190729, intron 4 of 17)	intron (NM_001190729, intron 4 of 17)	49741	NM_001190728	9649	Hs.432842	NM_014636	ENSG00000136828	RALGPS1	RALGEF2|RALGPS1A	Ral GEF with PH domain and SH3 binding motif 1	protein-coding	0.014768	0.452632	
chunk0167_64_1	chr6	56156466	56156714	+	0	NA	intron (NM_030820, intron 10 of 29)	MER67D|LTR|ERV1	90990	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.000000	0.429719	47(AGGAAGATAGTGTCCC,-,0.00)
chunk0022_119_1	chr10	11522765	11523467	+	0	NA	intron (NM_001080491, intron 3 of 13)	intron (NM_001080491, intron 3 of 13)	9164	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.005698	0.391181	
chunk0136_31_1	chr4	869821	870020	+	0	NA	intron (NM_001286833, intron 16 of 24)	(CACA)n|Simple_repeat|Simple_repeat	-43763	NM_006651	10815	Hs.478930	NM_006651	ENSG00000168993	CPLX1	CPX-I|CPX1|EIEE63	complexin 1	protein-coding	0.045226	0.515000	
chunk0120_149_1	chr3	5265181	5265641	+	0	NA	Intergenic	L2c|LINE|L2	-15156	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.006522	0.375271	
chunk0056_373_1	chr13	93073034	93073444	+	0	NA	Intergenic	Intergenic	27898	NR_126360	104326053	Hs.578064	NR_126360		LINC00363	TCONS_00021586	long intergenic non-protein coding RNA 363	ncRNA	0.000000	0.243309	
chunk0037_307_1	chr11	76688117	76688409	+	0	NA	intron (NR_024042, intron 19 of 20)	L2b|LINE|L2	-17516	NM_001128922	2615	Hs.151641	NM_005512	ENSG00000137507	LRRC32	D11S833E|GARP	leucine rich repeat containing 32	protein-coding	0.020548	0.614334	167(AAGAACATGGTGTGCT,-,0.00),168(AGAACATGGTGTGCTT,+,0.00)
chunk0064_248_1	chr14	94447894	94448377	+	0	NA	exon (NM_001080451, exon 2 of 5)	exon (NM_001080451, exon 2 of 5)	4650	NM_001080451	256394	Hs.145890	NM_001080451	ENSG00000186910	SERPINA11	-	serpin family A member 11	protein-coding	0.016563	0.462810	453(AGGAACAGGGAGTTTC,-,0.00),454(GGAACAGGGAGTTTCC,+,0.00)
chunk0149_213_1	chr5	21774674	21775240	+	0	NA	intron (NM_004061, intron 11 of 14)	MER5A|DNA|hAT-Charlie	-109497	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.003534	0.375661	
chunk0170_87_1	chr6	110141314	110141794	+	0	NA	intron (NM_001024936, intron 1 of 8)	L2c|LINE|L2	38450	NM_001024935	8936	Hs.75850	NM_003931	ENSG00000112290	WASF1	SCAR1|WAVE|WAVE1	WASP family member 1	protein-coding	0.006250	0.365904	
chunk0054_201_1	chr13	45006497	45007073	+	0	NA	intron (NM_001316952, intron 3 of 8)	MIRb|SINE|MIR	17255	NM_001316952	55425	Hs.731811	NM_018559	ENSG00000133114	GPALPP1	AD029|KIAA1704|LSR7|bA245H20.2	GPALPP motifs containing 1	protein-coding	0.003472	0.324090	266(ATAACAGCATGTACTT,+,0.00)
chunk0107_434_1	chr2	224882510	224883171	+	0	NA	intron (NM_014689, intron 7 of 55)	intron (NM_014689, intron 7 of 55)	64225	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.006051	0.386707	
chunk0166_436_1	chr6	52946407	52946843	+	0	NA	Intergenic	MER83|LTR|ERV1	-36927	NM_000847	2940	Hs.102484	NM_000847	ENSG00000174156	GSTA3	GSTA3-3|GTA3	glutathione S-transferase alpha 3	protein-coding	0.006881	0.386728	
chunk0042_136_1	chr12	3791413	3792267	+	0	NA	Intergenic	LTR50|LTR|ERVL	-38640	NM_001144958	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.015222	0.447953	
chunk0060_307_1	chr14	50947463	50948124	+	0	NA	Intergenic	Intergenic	-3263	NM_001163940	5836	Hs.282417	NM_002863	ENSG00000100504	PYGL	GSD6	glycogen phosphorylase L	protein-coding	0.012103	0.463746	
chunk0053_105_1	chr13	28826327	28826794	+	0	NA	Intergenic	Intergenic	-107547	NM_001135919	283537	Hs.117167	NM_181785	ENSG00000139508	SLC46A3	FKSG16	solute carrier family 46 member 3	protein-coding	0.004283	0.365385	
chunk0032_61_1	chr11	2131560	2132134	+	0	NA	non-coding (NR_003512, exon 7 of 7)	non-coding (NR_003512, exon 7 of 7)	2362	NR_030158	619552		NR_030158	ENSG00000207805	MIR483	MIRN483|hsa-mir-483|mir-483	microRNA 483	ncRNA	0.034843	0.533913	
chunk0073_71_1	chr16	3696842	3697352	+	0	NA	intron (NM_016292, intron 1 of 17)	L1ME4b|LINE|L1	20500	NM_016292	10131	Hs.30345	NM_016292	ENSG00000126602	TRAP1	HSP 75|HSP75|HSP90L|TRAP-1	TNF receptor associated protein 1	protein-coding	0.015686	0.422701	
chunk0183_236_1	chr7	107017930	107018192	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-26672	NM_002736	5577	Hs.433068	NM_002736	ENSG00000005249	PRKAR2B	PRKAR2|RII-BETA	protein kinase cAMP-dependent type II regulatory subunit beta	protein-coding	0.003817	0.433460	
chunk0083_76_1	chr17	64151960	64152325	+	0	NA	intron (NM_018469, intron 10 of 11)	intron (NM_018469, intron 10 of 11)	5803	NR_002995	677842	Hs.405444	NR_002995	ENSG00000277887	SNORA50C	ACA62|SNORA76|SNORA76C	small nucleolar RNA, H/ACA box 50C	snoRNA	0.008219	0.344262	
chunk0207_12_1	chrM	11170	11420	+	0	NA	NA	Intergenic	NA	NA									0.016000	0.446215	
chunk0159_243_1	chr5	141865083	141865934	+	0	NA	intron (NM_032420, intron 2 of 4)	MER117|DNA|hAT-Charlie	694	NM_001278615	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.022327	0.511737	
chunk0150_136_1	chr5	33470262	33470520	+	0	NA	Intergenic	Intergenic	29615	NR_047676	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.007752	0.355212	
chunk0212_96_1	chrY	12934850	12935357	+	0	NA	Intergenic	Intergenic	29398	NM_001302552	8653	Hs.99120	NM_004660	ENSG00000067048	DDX3Y	DBY	DEAD-box helicase 3 Y-linked	protein-coding	0.003945	0.318898	311(ATGAACAGGATGTACT,-,0.00),312(TGAACAGGATGTACTT,+,0.00)
chunk0113_4_1	chr20	49210299	49211070	+	0	NA	Intergenic	Intergenic	-8611	NM_017895	55661	Hs.65234	NM_017895	ENSG00000124228	DDX27	DRS1|Drs1p|HSPC259|PP3241|RHLP|dJ686N3.1	DEAD-box helicase 27	protein-coding	0.002594	0.357513	
chunk0210_36_1	chrX	67774249	67774532	+	0	NA	Intergenic	L1PREC2|LINE|L1	205549	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.000000	0.366197	
chunk0209_287_1	chrX	48021223	48021713	+	0	NA	Intergenic	Intergenic	13696	NM_001079900	729201	Hs.319319	NM_001079900	ENSG00000171478	SPACA5B	LYZL5B	sperm acrosome associated 5B	protein-coding	0.040816	0.517312	
chunk0010_279_1	chr1	117405031	117405237	+	0	NA	intron (NM_006699, intron 2 of 12)	MER58A|DNA|hAT-Charlie	37671	NM_006699	10905	Hs.435938	NM_006699	ENSG00000198162	MAN1A2	MAN1B	mannosidase alpha class 1A member 2	protein-coding	0.004854	0.362319	
chunk0153_48_1	chr5	67302535	67302764	+	0	NA	Intergenic	Intergenic	-105860	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.004367	0.365217	
chunk0063_74_1	chr14	77542514	77543515	+	0	NA	intron (NM_004863, intron 9 of 11)	intron (NM_004863, intron 9 of 11)	-44147	NM_182509	145501	Hs.29742	NM_182509	ENSG00000100593	ISM2	TAIL1|THSD3	isthmin 2	protein-coding	0.013986	0.457086	
chunk0024_88_1	chr10	34420390	34420736	+	0	NA	intron (NM_001184790, intron 4 of 22)	intron (NM_001184790, intron 4 of 22)	394762	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.005780	0.354467	
chunk0149_206_1	chr5	21686942	21687377	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-197295	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.004598	0.321101	
chunk0207_73_1	chrX	9183510	9184012	+	0	NA	Intergenic	Intergenic	-149634	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.003984	0.439364	
chunk0118_205_1	chr22	31714969	31715431	+	0	NA	exon (NM_173566, exon 4 of 9)	exon (NM_173566, exon 4 of 9)	34934	NM_173566	253143	Hs.438906	NM_173566	ENSG00000183530	PRR14L	C22orf30	proline rich 14 like	protein-coding	0.004329	0.401728	
chunk0012_370_1	chr1	162994160	162994440	+	0	NA	Intergenic	Intergenic	-74306	NM_001102445	5999	Hs.386726	NM_005613	ENSG00000117152	RGS4	RGP4|SCZD9	regulator of G protein signaling 4	protein-coding	0.003571	0.384342	88(AGGGACAATCTGTCCC,-,0.00),89(GGGACAATCTGTCCCT,+,0.00)
chunk0188_279_1	chr8	15517950	15518311	+	0	NA	Intergenic	L1MB7|LINE|L1	-21957	NM_178234	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.008310	0.361878	
chunk0071_389_1	chr15	89243764	89244113	+	0	NA	promoter-TSS (NM_001113378)	promoter-TSS (NM_001113378)	-25	NM_001113378	55215	Hs.513126	NM_018193	ENSG00000140525	FANCI	KIAA1794	FA complementation group I	protein-coding	0.108883	0.685714	
chunk0095_446_1	chr2	25499586	25499887	+	0	NA	intron (NM_001256303, intron 9 of 19)	L2a|LINE|L2	150486	NM_001256308	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.003322	0.317881	
chunk0172_307_1	chr6	138161322	138161597	+	0	NA	promoter-TSS (NM_020340)	promoter-TSS (NM_020340)	-457	NM_020340	57221	Hs.194408	NM_020340	ENSG00000112379	ARFGEF3	A7322|BIG3|C6orf92|KIAA1244|PPP1R33|dJ171N11.1	ARFGEF family member 3	protein-coding	0.061818	0.623188	132(GGGCACAGTGTGTGCA,-,0.00),133(GGCACAGTGTGTGCAA,+,0.00)
chunk0198_120_1	chr8	131904033	131904312	+	0	NA	promoter-TSS (NM_015137)	promoter-TSS (NM_015137)	63	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.186380	0.785714	
chunk0065_394_1	chr14	104791953	104792231	+	0	NA	intron (NM_001014431, intron 2 of 13)	intron (NM_001014431, intron 2 of 13)	1509	NM_005163	207	Hs.525622	NM_005163	ENSG00000142208	AKT1	AKT|CWS6|PKB|PKB-ALPHA|PRKBA|RAC|RAC-ALPHA	AKT serine/threonine kinase 1	protein-coding	0.010791	0.666667	
chunk0208_171_1	chrX	16693279	16693842	+	0	NA	intron (NM_019857, intron 4 of 18)	intron (NM_019857, intron 4 of 18)	18657	NM_001144002	56474	Hs.227049	NM_019857	ENSG00000047230	CTPS2	-	CTP synthase 2	protein-coding	0.019538	0.423759	
chunk0017_214_1	chr1	207884049	207884767	+	0	NA	Intergenic	L2a|LINE|L2	26930	NM_001773	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.005571	0.425591	
chunk0155_255_1	chr5	95759630	95760059	+	0	NA	intron (NM_014899, intron 6 of 11)	intron (NM_014899, intron 6 of 11)	28698	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.004662	0.360465	
chunk0024_27_1	chr10	33179095	33179554	+	0	NA	non-coding (NR_045259, exon 16 of 16)	non-coding (NR_045259, exon 16 of 16)	155581	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.021786	0.454348	
chunk0099_392_1	chr2	101822018	101822491	+	0	NA	intron (NM_145686, intron 3 of 30)	Tigger3b|DNA|TcMar-Tigger	124178	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.008457	0.339662	
chunk0058_193_1	chr14	24310826	24311185	+	0	NA	promoter-TSS (NM_001143919)	promoter-TSS (NM_001143919)	365	NM_014430	27141	Hs.642693	NM_014430	ENSG00000136305	CIDEB	-	cell death inducing DFFA like effector b	protein-coding	0.111421	0.738889	
chunk0203_223_1	chr9	86968666	86969032	+	0	NA	intron (NR_049794, intron 2 of 6)	intron (NR_049794, intron 2 of 6)	20151	NR_049794	100506834	Hs.553987	NR_049794	ENSG00000226237	GAS1RR	LncRNA-Hh	GAS1 adjacent regulatory RNA	ncRNA	0.010929	0.427793	
chunk0038_274_1	chr11	89671480	89672087	+	0	NA	intron (NM_153696, intron 4 of 13)	intron (NM_153696, intron 4 of 13)	12486	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.004942	0.332237	
chunk0006_182_1	chr1	67260229	67260576	+	0	NA	TTS (NM_144701)	TTS (NM_144701)	-46962	NR_047584	3595	Hs.479347	NM_001559	ENSG00000081985	IL12RB2	-	interleukin 12 receptor subunit beta 2	protein-coding	0.002882	0.410920	
chunk0013_152_1	chr1	168627800	168628087	+	0	NA	Intergenic	Intergenic	51470	NM_002995	6375	Hs.546295	NM_002995	ENSG00000143184	XCL1	ATAC|LPTN|LTN|SCM-1|SCM-1a|SCM1|SCM1A|SCYC1	X-C motif chemokine ligand 1	protein-coding	0.000000	0.329861	82(ATGACAGAGTGTTCCA,+,0.00)
chunk0027_164_1	chr10	74875841	74876330	+	0	NA	intron (NM_001256468, intron 3 of 17)	intron (NM_001256468, intron 3 of 17)	49672	NM_001256468	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.002045	0.373469	
chunk0210_425_1	chrX	102829211	102829677	+	0	NA	intron (NR_038988, intron 4 of 7)	MamGypLTR1a|LTR|Gypsy	60277	NR_038988	100287765	Hs.556850	NR_038988		LINC00630	-	long intergenic non-protein coding RNA 630	ncRNA	0.000000	0.451820	
chunk0018_363_1	chr1	221774473	221774860	+	0	NA	Intergenic	Intergenic	-32490	NM_007207	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.007752	0.422680	
chunk0081_102_1	chr17	39812348	39812846	+	0	NA	intron (NM_001257408, intron 2 of 6)	intron (NM_001257408, intron 2 of 6)	-34372	NM_001284516	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.012048	0.464930	
chunk0009_328_1	chr1	108966758	108967147	+	0	NA	Intergenic	Intergenic	-3453	NM_015127	23155	Hs.658489	NM_015127	ENSG00000121940	CLCC1	MCLC	chloride channel CLIC like 1	protein-coding	0.002571	0.443590	
chunk0007_54_1	chr1	77859301	77859706	+	0	NA	intron (NM_198549, intron 10 of 15)	intron (NM_198549, intron 10 of 15)	-29012	NM_001172309	91624	Hs.612385	NM_144573	ENSG00000162614	NEXN	CMH20|NELIN	nexilin F-actin binding protein	protein-coding	0.004938	0.376847	
chunk0059_207_1	chr14	33521794	33522177	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-186952	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.018277	0.364583	
chunk0078_351_1	chr16	86614732	86615072	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	36393	NM_005250	2300	Hs.533830	NM_005250	ENSG00000176678	FOXL1	FKH6|FKHL11|FREAC7	forkhead box L1	protein-coding	0.014706	0.480938	158(TAGTACTGAGTGTCCC,-,0.00),159(AGTACTGAGTGTCCCT,+,0.00)
chunk0118_84_1	chr22	29023315	29023669	+	0	NA	intron (NM_032173, intron 2 of 8)	intron (NM_032173, intron 2 of 8)	7984	NR_046851	100874123	Hs.674708	NR_046851	ENSG00000177993	ZNRF3-AS1	-	ZNRF3 antisense RNA 1	ncRNA	0.002825	0.526761	4(CAGCACACTCTGACCT,-,0.00),5(AGCACACTCTGACCTC,+,0.00),55(TGGGACTAGGTGTGCT,-,0.00),56(GGGACTAGGTGTGCTT,+,0.00)
chunk0060_86_1	chr14	42344467	42344883	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	737114	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.002404	0.364508	221(GGGAACAGCCTGTTAA,-,0.00)
chunk0111_96_1	chr20	23595837	23596263	+	0	NA	Intergenic	MER57D|LTR|ERV1	9923	NM_001008693	128822	Hs.698020	NM_001008693	ENSG00000173335	CST9	CLM|CTES7A	cystatin 9	protein-coding	0.004695	0.407494	
chunk0009_209_1	chr1	106153900	106154724	+	0	NA	Intergenic	Intergenic	-535377	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002427	0.328485	
chunk0203_185_1	chr9	86369821	86370057	+	0	NA	Intergenic	L1M2|LINE|L1	-15452	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.012712	0.392405	
chunk0062_313_1	chr14	73143479	73143756	+	0	NA	intron (NM_007318, intron 1 of 11)	intron (NM_007318, intron 1 of 11)	7182	NM_007318	5663	Hs.3260	NM_000021	ENSG00000080815	PSEN1	ACNINV3|AD3|FAD|PS-1|PS1|S182	presenilin 1	protein-coding	0.003610	0.381295	
chunk0047_37_1	chr12	66639346	66639609	+	0	NA	intron (NM_021150, intron 1 of 23)	L2b|LINE|L2	39668	NM_021150	23426	Hs.505946	NM_021150	ENSG00000155974	GRIP1	FRASRS3|GRIP	glutamate receptor interacting protein 1	protein-coding	0.003802	0.435606	
chunk0009_454_1	chr1	111602019	111602295	+	0	NA	intron (NR_034126, intron 4 of 4)	intron (NR_034126, intron 4 of 4)	6161	NR_034126	100129269	Hs.689728	NR_034126		LINC01160	-	long intergenic non-protein coding RNA 1160	ncRNA	0.007246	0.447653	
chunk0076_437_1	chr16	73463923	73464580	+	0	NA	Intergenic	Intergenic	77446	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.009132	0.376900	
chunk0151_244_1	chr5	51278971	51279733	+	0	NA	Intergenic	Intergenic	-103772	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.003937	0.311927	
chunk0094_109_1	chr2	4255076	4255742	+	0	NA	Intergenic	Intergenic	-281377	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.012012	0.451274	
chunk0154_132_1	chr5	79152032	79152325	+	0	NA	Intergenic	L2a|LINE|L2	40397	NM_001713	635	Hs.80756	NM_001713	ENSG00000145692	BHMT	BHMT1|HEL-S-61p	betaine--homocysteine S-methyltransferase	protein-coding	0.010239	0.486395	
chunk0157_425_1	chr5	124686324	124686811	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	58545	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.000000	0.440574	
chunk0149_38_1	chr5	16485375	16485868	+	0	NA	intron (NM_001034850, intron 3 of 8)	intron (NM_001034850, intron 3 of 8)	-19836	NM_033414	90441	Hs.60300	NM_033414	ENSG00000173545	ZNF622	ZPR9	zinc finger protein 622	protein-coding	0.004057	0.331984	
chunk0164_69_1	chr6	19537386	19537612	+	0	NA	Intergenic	Intergenic	-299871	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.000000	0.383260	136(GGGAACAAGGTGTTCC,-,0.00),137(GGAACAAGGTGTTCCA,+,0.00)
chunk0158_252_1	chr5	130913726	130914472	+	0	NA	Intergenic	L1MA4|LINE|L1	251249	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.002681	0.326640	
chunk0056_81_1	chr13	79644533	79644795	+	0	NA	Intergenic	Kanga11a|DNA|TcMar-Tc2	77937	NR_125772	103724388	Hs.434862	NR_125772	ENSG00000227676	LINC01068	-	long intergenic non-protein coding RNA 1068	ncRNA	0.000000	0.365019	
chunk0195_176_1	chr8	96225471	96226043	+	0	NA	TTS (NR_045639)	TTS (NR_045639)	9877	NM_006294	7381	Hs.131255	NM_006294	ENSG00000156467	UQCRB	MC3DN3|QCR7|QP-C|QPC|UQBC|UQBP|UQCR6|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding	0.005245	0.445026	106(CAAAACTGCCTGTCCT,-,0.00),107(AAAACTGCCTGTCCTT,+,0.00)
chunk0048_321_1	chr12	83339237	83339534	+	0	NA	Intergenic	L1MA2|LINE|L1	652230	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.003367	0.516779	
chunk0182_81_1	chr7	92633441	92633794	+	0	NA	intron (NM_001145306, intron 5 of 7)	intron (NM_001145306, intron 5 of 7)	-43223	NR_109929	257415	Hs.18564	NM_152789	ENSG00000234545	FAM133B	-	family with sequence similarity 133 member B	protein-coding	0.002833	0.364407	249(GTGGACAAACTGTTCT,-,0.00),250(TGGACAAACTGTTCTG,+,0.00)
chunk0195_167_1	chr8	95868958	95869682	+	0	NA	Intergenic	L1MC3|LINE|L1	79028	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.004144	0.318621	
chunk0180_363_1	chr7	73863701	73863900	+	0	NA	intron (NM_182504, intron 1 of 2)	intron (NM_182504, intron 1 of 2)	2641	NM_182504	135886	Hs.647026	NM_182504	ENSG00000175877	TMEM270	WBSCR28	transmembrane protein 270	protein-coding	0.010050	0.545000	
chunk0072_343_1	chr15	99524230	99524515	+	0	NA	Intergenic	Intergenic	-41556	NM_001130927	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.003509	0.349650	
chunk0015_318_1	chr1	189357315	189357773	+	0	NA	Intergenic	Intergenic	1120085	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004367	0.339869	
chunk0136_283_1	chr3	194851198	194851775	+	0	NA	Intergenic	L2|LINE|L2	143065	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.010399	0.534602	
chunk0170_313_1	chr6	116071063	116071582	+	0	NA	Intergenic	Intergenic	-10564	NM_002031	2444	Hs.89426	NM_002031	ENSG00000111816	FRK	GTK|PTK5|RAK	fyn related Src family tyrosine kinase	protein-coding	0.005780	0.369231	
chunk0092_391_1	chr19	36620244	36620567	+	0	NA	intron (NM_001256838, intron 4 of 4)	intron (NM_001256838, intron 4 of 4)	15100	NM_032825	84911	Hs.631591	NM_032825	ENSG00000161298	ZNF382	KS1	zinc finger protein 382	protein-coding	0.000000	0.348765	
chunk0172_86_1	chr6	134571770	134572102	+	0	NA	Intergenic	L1PB1|LINE|L1	-31931	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.003012	0.369369	
chunk0067_298_1	chr15	47726022	47726352	+	0	NA	intron (NM_020858, intron 1 of 16)	MIRb|SINE|MIR	7698	NM_024966	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.018182	0.444109	
chunk0115_202_1	chr21	26399283	26399498	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	173872	NM_052954	116159	Hs.37445	NM_052954	ENSG00000166265	CYYR1	C21orf95	cysteine and tyrosine rich 1	protein-coding	0.004651	0.490741	
chunk0130_397_1	chr3	140224301	140224591	+	0	NA	intron (NM_022131, intron 2 of 16)	L2a|LINE|L2	284343	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.003448	0.374570	
chunk0087_324_1	chr18	39863996	39864406	+	0	NA	Intergenic	Intergenic	-112206	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.004878	0.457421	
chunk0071_417_1	chr15	89739165	89739460	+	0	NA	intron (NM_020212, intron 16 of 16)	MER58A|DNA|hAT-Charlie	11997	NM_018670	55897	Hs.447531	NM_018670	ENSG00000166823	MESP1	bHLHc5	mesoderm posterior bHLH transcription factor 1	protein-coding	0.010169	0.418919	
chunk0081_467_1	chr17	49565986	49566522	+	0	NA	intron (NR_103773, intron 1 of 2)	L2c|LINE|L2	7810	NR_103773	100288866	Hs.720309	NR_103773	ENSG00000249906	LOC100288866	-	uncharacterized LOC100288866	ncRNA	0.026119	0.534451	251(GGGAACACTGTGTACA,-,0.00),252(GGAACACTGTGTACAA,+,0.00)
chunk0092_119_1	chr19	27773394	27773799	+	0	NA	Intergenic	Intergenic	-19871	NR_110689	101927151	Hs.567934	NR_110687	ENSG00000267575	LOC101927151	-	uncharacterized LOC101927151	ncRNA	0.007407	0.490148	
chunk0103_31_1	chr2	159083240	159083493	+	0	NA	intron (NM_001145909, intron 3 of 26)	intron (NM_001145909, intron 3 of 26)	-103469	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.000000	0.381890	
chunk0049_320_1	chr12	94634524	94635304	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	15648	NM_020698	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.006410	0.395647	
chunk0087_458_1	chr18	42765021	42765865	+	0	NA	intron (NM_002930, intron 4 of 4)	intron (NM_002930, intron 4 of 4)	350249	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.004739	0.360947	593(AAGAACAAAGTGTGTT,-,0.00),594(AGAACAAAGTGTGTTG,+,0.00)
chunk0148_192_1	chr5	8225116	8225534	+	0	NA	Intergenic	L1PA7|LINE|L1	232239	NR_039984	729506	Hs.566412	NR_039984	ENSG00000245729	LINC02226	-	long intergenic non-protein coding RNA 2226	ncRNA	0.002392	0.355609	
chunk0184_80_1	chr7	112881250	112881449	+	0	NA	intron (NM_152556, intron 3 of 4)	MER52A|LTR|ERV1	58528	NM_152556	154743	Hs.489734	NM_152556	ENSG00000164603	BMT2	C7orf60|SAMTOR	base methyltransferase of 25S rRNA 2 homolog	protein-coding	0.000000	0.560000	
chunk0005_437_1	chr1	63269546	63270153	+	0	NA	intron (NR_038252, intron 3 of 11)	intron (NR_038252, intron 3 of 11)	47408	NR_038252	199899	Hs.116210	NR_038252	ENSG00000224209	LINC00466	-	long intergenic non-protein coding RNA 466	ncRNA	0.004942	0.355263	310(TGGGACACAATGTACC,-,0.00),311(GGGACACAATGTACCA,+,0.00)
chunk0201_198_1	chr9	36621393	36621835	+	0	NA	intron (NR_046337, intron 8 of 17)	intron (NR_046337, intron 8 of 17)	48752	NM_014791	9833	Hs.184339	NM_014791	ENSG00000165304	MELK	HPK38	maternal embryonic leucine zipper kinase	protein-coding	0.002262	0.349887	
chunk0120_285_1	chr3	9716103	9716388	+	0	NA	intron (NM_001308388, intron 13 of 19)	intron (NM_001308388, intron 13 of 19)	12419	NM_153635	151835	Hs.121335	NM_153635	ENSG00000144550	CPNE9	-	copine family member 9	protein-coding	0.003509	0.454545	
chunk0014_154_1	chr1	178192202	178192801	+	0	NA	intron (NM_170692, intron 1 of 17)	intron (NM_170692, intron 1 of 17)	-98508	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.003339	0.320000	
chunk0061_447_1	chr14	65818164	65818370	+	0	NA	Intergenic	(ACACC)n|Simple_repeat|Simple_repeat	347165	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.004854	0.449275	
chunk0126_453_1	chr3	87247209	87247617	+	0	NA	intron (NM_001244644, intron 2 of 4)	Tigger17a|DNA|TcMar-Tigger	20150	NM_014043	25978	Hs.476930	NM_014043	ENSG00000083937	CHMP2B	ALS17|CHMP2.5|DMT1|VPS2-2|VPS2B	charged multivesicular body protein 2B	protein-coding	0.002451	0.361858	155(AAGCACATCATGTCCT,-,0.00),156(AGCACATCATGTCCTT,+,0.00)
chunk0066_271_1	chr15	34988294	34988534	+	0	NA	promoter-TSS (NM_014106)	promoter-TSS (NM_014106)	-118	NM_014106	54989	Hs.744990	NM_014106	ENSG00000198146	ZNF770	PRO1914	zinc finger protein 770	protein-coding	0.087500	0.634855	
chunk0128_54_1	chr3	104820459	104820783	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	-546092	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.003086	0.421538	
chunk0169_404_1	chr6	108297948	108298267	+	0	NA	intron (NM_145315, intron 1 of 12)	intron (NM_145315, intron 1 of 12)	3213	NM_145315	246269	Hs.259666	NM_145315	ENSG00000135537	AFG1L	AFG1|LACE1|c222389	AFG1 like ATPase	protein-coding	0.000000	0.353125	
chunk0135_304_1	chr3	189903778	189904212	+	0	NA	Intergenic	MIRb|SINE|MIR	74073	NR_030642	100126340		NR_030642	ENSG00000216058	MIR944	MIRN944|hsa-mir-944|mir-944	microRNA 944	ncRNA	0.011521	0.347126	
chunk0075_182_1	chr16	52100148	52100619	+	0	NA	Intergenic	MIR|SINE|MIR	15102	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.004246	0.349576	225(AAGTACTGCCTGTGCC,-,0.00),226(AGTACTGCCTGTGCCC,+,0.00)
chunk0120_123_1	chr3	4848220	4848570	+	0	NA	TTS (NM_001099952)	TTS (NM_001099952)	58106	NR_125914	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.008571	0.441595	
chunk0055_439_1	chr13	75610341	75610838	+	0	NA	intron (NR_120412, intron 1 of 1)	intron (NR_120412, intron 1 of 1)	-9845	NM_005358	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.000000	0.293173	
chunk0064_303_1	chr14	95531013	95531281	+	0	NA	Intergenic	Intergenic	2482	NR_003002	677768	Hs.448753	NR_003002	ENSG00000252481	SCARNA13	U93	small Cajal body-specific RNA 13	ncRNA	0.026119	0.498141	
chunk0051_83_1	chr12	114028247	114028574	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-62039	NM_001146699	9904	Hs.7482	NM_016196	ENSG00000122965	RBM19	Mrd1	RNA binding motif protein 19	protein-coding	0.003058	0.432927	
chunk0180_372_1	chr7	74085171	74085648	+	0	NA	intron (NM_002314, intron 1 of 15)	intron (NM_002314, intron 1 of 15)	1632	NM_002314	3984	Hs.647035	NM_002314	ENSG00000106683	LIMK1	LIMK|LIMK-1	LIM domain kinase 1	protein-coding	0.012579	0.566946	
chunk0157_100_1	chr5	116738863	116739176	+	0	NA	Intergenic	Intergenic	23190	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.000000	0.433121	
chunk0195_402_1	chr8	100465580	100466258	+	0	NA	Intergenic	Intergenic	83156	NR_039681	100616451		NR_039681	ENSG00000265599	MIR4471	-	microRNA 4471	ncRNA	0.010324	0.512518	
chunk0108_164_1	chr2	231305218	231305643	+	0	NA	intron (NM_001291656, intron 19 of 20)	Charlie1|DNA|hAT-Charlie	-57278	NR_039937	100616317		NR_039937	ENSG00000263641	MIR4777	-	microRNA 4777	ncRNA	0.011765	0.392019	
chunk0044_133_1	chr12	29381220	29381437	+	0	NA	promoter-TSS (NM_016570)	promoter-TSS (NM_016570)	-118	NM_016570	51290	Hs.339453	NM_016570	ENSG00000087502	ERGIC2	CDA14|Erv41|PTX1|cd002	ERGIC and golgi 2	protein-coding	0.059908	0.472477	
chunk0178_40_1	chr7	29538518	29538843	+	0	NA	Intergenic	L1MA2|LINE|L1	-25131	NM_175887	222171	Hs.91109	NM_175887	ENSG00000176532	PRR15	-	proline rich 15	protein-coding	0.015385	0.549080	
chunk0048_253_1	chr12	81737647	81738292	+	0	NA	intron (NM_003625, intron 3 of 32)	L1MEg|LINE|L1	20538	NM_001220475	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003101	0.294118	
chunk0085_228_1	chr18	6926852	6927217	+	0	NA	non-coding (NR_034100, exon 4 of 7)	non-coding (NR_034100, exon 4 of 7)	2835	NR_034100	400643	Hs.253920	NM_001103383	ENSG00000265933	LINC00668	-	long intergenic non-protein coding RNA 668	ncRNA	0.010959	0.428962	142(AGGATCTTTCTGTTCT,-,0.00),143(GGATCTTTCTGTTCTT,+,0.00)
chunk0061_22_1	chr14	55789453	55789848	+	0	NA	intron (NR_026796, intron 3 of 3)	Charlie7|DNA|hAT-Charlie	7024	NR_026797	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.005063	0.381313	
chunk0184_367_1	chr7	121102520	121102758	+	0	NA	intron (NM_001105533, intron 6 of 17)	L1MEh|LINE|L1	113248	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.008403	0.464435	
chunk0184_376_1	chr7	121382742	121383266	+	0	NA	5' UTR (NM_001040020, exon 2 of 10)	5' UTR (NM_001040020, exon 2 of 10)	13364	NM_001040020	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.000000	0.318095	
chunk0145_195_1	chr4	147841541	147841740	+	0	NA	intron (NM_024605, intron 3 of 22)	intron (NM_024605, intron 3 of 22)	59045	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.005025	0.295000	
chunk0181_146_1	chr7	81658870	81659313	+	0	NA	intron (NR_126025, intron 1 of 10)	L1M2|LINE|L1	32315	NR_126025	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.004515	0.560811	
chunk0199_121_1	chr9	3603389	3603946	+	0	NA	Intergenic	Intergenic	-64419	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.003591	0.379928	
chunk0193_2_1	chr8	70411238	70411481	+	0	NA	Intergenic	L1ME3A|LINE|L1	-7574	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.000000	0.290984	20(TTGTACAGGCAGTTCT,-,0.00),21(TGTACAGGCAGTTCTA,+,0.00)
chunk0015_375_1	chr1	190488019	190488525	+	0	NA	Intergenic	L2a|LINE|L2	9721	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.001976	0.317554	
chunk0085_309_1	chr18	8162791	8163903	+	0	NA	intron (NM_001105244, intron 14 of 32)	intron (NM_001105244, intron 14 of 32)	203687	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.007194	0.419587	
chunk0054_5_1	chr13	40181498	40181892	+	0	NA	promoter-TSS (NR_046870)	promoter-TSS (NR_046870)	-114	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.007614	0.407595	
chunk0078_185_1	chr17	4721645	4721898	+	0	NA	TTS (NM_001257330)	TTS (NM_001257330)	-9637	NM_001305000	400569	Hs.513885	NM_001001683	ENSG00000161920	MED11	HSPC296	mediator complex subunit 11	protein-coding	0.035573	0.523622	
chunk0179_138_1	chr7	45983014	45983351	+	0	NA	Intergenic	Intergenic	-61910	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.017804	0.473373	
chunk0137_329_1	chr4	24832075	24832705	+	0	NA	intron (NM_001130726, intron 8 of 11)	intron (NM_001130726, intron 8 of 11)	36927	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.004762	0.358162	
chunk0102_198_1	chr2	147904490	147904701	+	0	NA	intron (NM_001616, intron 4 of 10)	intron (NM_001616, intron 4 of 10)	59600	NM_001616	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.330189	
chunk0015_246_1	chr1	187967920	187968586	+	0	NA	Intergenic	L1PA8|LINE|L1	524625	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.009009	0.332834	
chunk0042_241_1	chr12	6342323	6342761	+	0	NA	promoter-TSS (NM_001065)	promoter-TSS (NM_001065)	-425	NM_001065	7132	Hs.279594	NM_001065	ENSG00000067182	TNFRSF1A	CD120a|FPF|TBP1|TNF-R|TNF-R-I|TNF-R55|TNFAR|TNFR1|TNFR55|TNFR60|p55|p55-R|p60	TNF receptor superfamily member 1A	protein-coding	0.006849	0.478360	211(AGGTACTCCATGTCCC,-,0.00),212(GGTACTCCATGTCCCT,+,0.00)
chunk0030_239_1	chr10	115061037	115061529	+	0	NA	Intergenic	Intergenic	-32082	NM_001276282	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.008130	0.393509	
chunk0078_223_1	chr17	6451355	6451686	+	0	NA	TTS (NM_001195228)	TTS (NM_001195228)	7105	NM_001195228	54478	Hs.592116	NM_019013	ENSG00000129195	PIMREG	CATS|FAM64A|RCS1	PICALM interacting mitotic regulator	protein-coding	0.018127	0.469880	
chunk0161_166_1	chr5	169218944	169219200	+	0	NA	intron (NM_003062, intron 3 of 35)	intron (NM_003062, intron 3 of 35)	44622	NR_030311	693170		NR_030311	ENSG00000207619	MIR585	MIRN585|hsa-mir-585|mir-585	microRNA 585	ncRNA	0.007812	0.498054	
chunk0184_245_1	chr7	117862383	117862718	+	0	NA	intron (NM_033427, intron 1 of 22)	intron (NM_033427, intron 1 of 22)	10957	NM_033427	83992	Hs.592285	NM_033427	ENSG00000077063	CTTNBP2	C7orf8|CORTBP2|Orf4	cortactin binding protein 2	protein-coding	0.008955	0.455357	209(AGGCACACTCTGCTCC,-,0.00),210(GGCACACTCTGCTCCT,+,0.00)
chunk0203_351_1	chr9	89862536	89863249	+	0	NA	Intergenic	L2b|LINE|L2	-106524	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.012623	0.495798	
chunk0161_177_1	chr5	169633932	169634457	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	-3053	NM_004946	1794	Hs.586174	NM_004946	ENSG00000134516	DOCK2	IMD40	dedicator of cytokinesis 2	protein-coding	0.003810	0.365019	
chunk0097_414_1	chr2	62789477	62790526	+	0	NA	intron (NM_001142614, intron 4 of 22)	intron (NM_001142614, intron 4 of 22)	83104	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.006673	0.370476	14(GAGGACAGAATGTTAT,-,0.00)
chunk0161_403_1	chr5	177376207	177376499	+	0	NA	Intergenic	L1ME3G|LINE|L1	-8078	NM_003052	6569	Hs.936	NM_003052	ENSG00000131183	SLC34A1	FRTS2|HCINF2|NAPI-3|NPHLOP1|NPT2|NPTIIa|SLC11|SLC17A2	solute carrier family 34 member 1	protein-coding	0.023973	0.464164	91(GGGTACAGCGTGTTCT,-,0.00),92(GGTACAGCGTGTTCTA,+,0.00)
chunk0163_411_1	chr6	16901545	16902090	+	0	NA	Intergenic	Intergenic	-140327	NM_001128164	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.011009	0.406593	
chunk0150_359_1	chr5	38907643	38907966	+	0	NA	intron (NM_003999, intron 9 of 17)	L1PA16|LINE|L1	61805	NM_003999	9180	Hs.120658	NM_003999	ENSG00000145623	OSMR	IL-31R-beta|IL-31RB|OSMRB|PLCA1	oncostatin M receptor	protein-coding	0.006192	0.552469	
chunk0023_33_1	chr10	21166725	21167265	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	-6995	NR_046283	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.024074	0.451017	52(TAGAACATGTTGTACT,-,0.00),53(AGAACATGTTGTACTT,+,0.00)
chunk0137_208_1	chr4	18710685	18711156	+	0	NA	Intergenic	HAL1|LINE|L1	-689060	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.006369	0.307203	
chunk0140_211_1	chr4	70704232	70704562	+	0	NA	promoter-TSS (NM_001130709)	promoter-TSS (NM_001130709)	-540	NM_001130709	22902	Hs.740904	NM_014961	ENSG00000018189	RUFY3	RIPX|SINGAR1|ZFYVE30	RUN and FYVE domain containing 3	protein-coding	0.042424	0.504532	
chunk0183_141_1	chr7	105805818	105806017	+	0	NA	intron (NM_020725, intron 2 of 11)	intron (NM_020725, intron 2 of 11)	70668	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.010050	0.535000	
chunk0132_396_1	chr3	163940166	163940378	+	0	NA	Intergenic	LTR33|LTR|ERVL	231284	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.014151	0.455399	
chunk0160_329_1	chr5	159787191	159787656	+	0	NA	intron (NR_109891, intron 2 of 2)	intron (NR_109891, intron 2 of 2)	83961	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.019355	0.465665	208(GAGGACATTCTGTACT,-,0.00),209(AGGACATTCTGTACTT,+,0.00),318(AAGCACAGCCTGCGCT,-,0.00),319(AGCACAGCCTGCGCTC,+,0.00)
chunk0028_434_1	chr10	93797355	93798380	+	0	NA	non-coding (NR_131777, exon 6 of 6)	non-coding (NR_131777, exon 6 of 6)	40058	NR_131777	9211	Hs.533670	NM_005097	ENSG00000108231	LGI1	ADLTE|ADPAEF|ADPEAF|EPITEMPIN|EPT|ETL1|IB1099	leucine rich glioma inactivated 1	protein-coding	0.009756	0.358674	
chunk0195_389_1	chr8	100238230	100239029	+	0	NA	intron (NM_003114, intron 16 of 18)	intron (NM_003114, intron 16 of 18)	64630	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003755	0.386250	
chunk0171_446_1	chr6	131854655	131855228	+	0	NA	exon (NM_006208, exon 6 of 25)	exon (NM_006208, exon 6 of 25)	46925	NM_006208	5167	Hs.527295	NM_006208	ENSG00000197594	ENPP1	ARHR2|COLED|M6S1|NPP1|NPPS|PC-1|PCA1|PDNP1	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding	0.008726	0.355401	
chunk0208_335_1	chrX	24773045	24773616	+	0	NA	intron (NM_016937, intron 26 of 36)	L3|LINE|CR1	28889	NR_003007	677773	Hs.689695	NR_003007	ENSG00000251869	SCARNA23	ACA12	small Cajal body-specific RNA 23	ncRNA	0.005254	0.395105	
chunk0160_208_1	chr5	154833943	154834626	+	0	NA	intron (NM_032385, intron 4 of 8)	L2a|LINE|L2	4826	NR_039667	100616306		NR_039667	ENSG00000263361	MIR378H	-	microRNA 378h	ncRNA	0.005857	0.342105	315(AAGCACTGACTGTACC,-,0.00),316(AGCACTGACTGTACCA,+,0.00)
chunk0022_391_1	chr10	17794261	17794460	+	0	NA	intron (NM_001098844, intron 3 of 3)	intron (NM_001098844, intron 3 of 3)	-14983	NM_002438	4360	Hs.75182	NM_002438	ENSG00000260314	MRC1	CD206|CLEC13D|CLEC13DL|MMR|MRC1L1|bA541I19.1|hMR	mannose receptor C-type 1	protein-coding	0.010050	0.345000	
chunk0206_119_1	chr9	120935377	120935624	+	0	NA	Intergenic	Intergenic	-6327	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.000000	0.604839	
chunk0143_408_1	chr4	123344542	123345379	+	0	NA	Intergenic	Intergenic	-51835	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.011947	0.449881	
chunk0162_342_1	chr6	6942626	6943202	+	0	NA	Intergenic	Intergenic	-164683	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.031250	0.497400	
chunk0042_359_1	chr12	10267263	10267682	+	0	NA	Intergenic	L2a|LINE|L2	-36979	NM_001114396	3824	Hs.562457	NM_002262	ENSG00000134539	KLRD1	CD94	killer cell lectin like receptor D1	protein-coding	0.002387	0.288095	
chunk0052_211_1	chr13	25233842	25234646	+	0	NA	Intergenic	Intergenic	52912	NR_120427	102723318	Hs.549877	NR_120427		LINC01053	-	long intergenic non-protein coding RNA 1053	ncRNA	0.007463	0.414907	
chunk0070_220_1	chr15	72727313	72727567	+	0	NA	intron (NR_045565, intron 9 of 16)	intron (NR_045565, intron 9 of 16)	41261	NM_001252678	585	Hs.208681	NM_033028	ENSG00000140463	BBS4	-	Bardet-Biedl syndrome 4	protein-coding	0.000000	0.392157	
chunk0060_312_1	chr14	51116661	51117082	+	0	NA	Intergenic	Intergenic	-21167	NM_052978	114088	Hs.654750	NM_015163	ENSG00000100505	TRIM9	RNF91|SPRING	tripartite motif containing 9	protein-coding	0.002375	0.405213	
chunk0125_176_1	chr3	66608169	66608657	+	0	NA	Intergenic	MIR|SINE|MIR	-107992	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.010246	0.374233	251(AAGCACACGGTGTACT,-,0.00),252(AGCACACGGTGTACTA,+,0.00)
chunk0103_125_1	chr2	161844857	161845309	+	0	NA	intron (NM_001178016, intron 5 of 26)	intron (NM_001178016, intron 5 of 26)	220748	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.002212	0.337748	
chunk0067_239_1	chr15	45500121	45500646	+	0	NA	intron (NM_013309, intron 3 of 7)	MIRb|SINE|MIR	-10753	NR_022014	283651	Hs.574240	NM_173609		HMGN2P46	C15orf21|D-PCa-2	high mobility group nucleosomal binding domain 2 pseudogene 46	pseudo	0.003810	0.365019	
chunk0188_10_1	chr8	6334828	6335259	+	0	NA	Intergenic	L1M7|LINE|L1	71505	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.011601	0.386574	
chunk0203_249_1	chr9	87422923	87423329	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-74102	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.002463	0.422604	
chunk0056_362_1	chr13	92413215	92413679	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	-61240	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.002155	0.331183	237(AAGAACAATGTGTACA,-,0.00),238(AGAACAATGTGTACAC,+,0.00)
chunk0040_250_1	chr11	115421441	115421757	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	82924	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.009494	0.422713	
chunk0072_329_1	chr15	99156161	99156428	+	0	NA	exon (NM_001288616, exon 10 of 12)	exon (NM_001288616, exon 10 of 12)	51214	NM_145728	23336	Hs.207106	NM_015286	ENSG00000182253	SYNM	DMN|SYN	synemin	protein-coding	0.029963	0.518657	
chunk0201_356_1	chr9	68443459	68444137	+	0	NA	intron (NM_021965, intron 6 of 10)	intron (NM_021965, intron 6 of 10)	-85932	NR_121192	572558	Hs.552819	NR_015423	ENSG00000224958	PGM5-AS1	FAM233A	PGM5 antisense RNA 1	ncRNA	0.004425	0.384389	
chunk0161_416_1	chr5	178069926	178070134	+	0	NA	Intergenic	MIR3|SINE|MIR	-43525	NM_015111	23138	Hs.101761	NM_015111	ENSG00000145911	N4BP3	LZTS4	NEDD4 binding protein 3	protein-coding	0.019231	0.559809	
chunk0051_25_1	chr12	111856957	111857587	+	0	NA	intron (NM_003668, intron 1 of 13)	AluSx|SINE|Alu	-14370	NR_015404	51275	Hs.333120	NR_015404	ENSG00000234608	MAPKAPK5-AS1	C12orf47	MAPKAPK5 antisense RNA 1	ncRNA	0.015873	0.412044	244(TAGTACTTTCTGTTCC,-,0.00),245(AGTACTTTCTGTTCCT,+,0.00)
chunk0207_378_1	chr9	136036875	136037116	+	0	NA	intron (NM_144653, intron 2 of 5)	L1MEf|LINE|L1	58290	NM_144653	138151	Hs.112895	NM_144653	ENSG00000148411	NACC2	BEND9|BTBD14|BTBD14A|BTBD31|NAC-2|RBB	NACC family member 2	protein-coding	0.008299	0.355372	
chunk0162_220_1	chr6	4322921	4323269	+	0	NA	Intergenic	Intergenic	-104907	NR_106988									0.000000	0.424069	
chunk0172_312_1	chr6	138231401	138232098	+	0	NA	intron (NM_020340, intron 5 of 33)	intron (NM_020340, intron 5 of 33)	-13259	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.005739	0.363897	
chunk0131_33_1	chr3	142484986	142485467	+	0	NA	exon (NM_001184, exon 36 of 47)	exon (NM_001184, exon 36 of 47)	-37164	NM_001282859	54464	Hs.435103	NM_019001	ENSG00000114127	XRN1	SEP1	5'-3' exoribonuclease 1	protein-coding	0.008316	0.373444	
chunk0182_362_1	chr7	99883166	99883499	+	0	NA	Intergenic	L1M3|LINE|L1	-6299	NM_001005276	81392	Hs.647523	NM_001005276	ENSG00000244623	OR2AE1	OR2AE2	olfactory receptor family 2 subfamily AE member 1	protein-coding	0.012012	0.395210	
chunk0173_304_1	chr6	148441138	148441554	+	0	NA	intron (NM_015278, intron 4 of 19)	intron (NM_015278, intron 4 of 19)	98753	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.019231	0.489209	
chunk0072_208_1	chr15	95556803	95557427	+	0	NA	Intergenic	Intergenic	124022	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.024038	0.436800	
chunk0025_446_1	chr10	60235177	60235376	+	0	NA	intron (NM_001204403, intron 8 of 43)	intron (NM_001204403, intron 8 of 43)	-94260	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005025	0.410000	
chunk0200_1_1	chr9	14407012	14407641	+	0	NA	Intergenic	Intergenic	-8343	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.007949	0.353968	
chunk0074_346_1	chr16	33336682	33336956	+	0	NA	Intergenic	(TGGCTTGGC)n|Simple_repeat|Simple_repeat	-24058	NM_016212	24150	Hs.592038	NM_015369	ENSG00000183632	TP53TG3	P53TG3|TP53TG3A|TP53TG3E|TP53TG3F	TP53 target 3	protein-coding	0.007299	0.672727	
chunk0094_88_1	chr2	3844063	3844262	+	0	NA	intron (NM_001287444, intron 10 of 10)	intron (NM_001287444, intron 10 of 10)	129870	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.005025	0.425000	
chunk0135_441_1	chr3	194003373	194003824	+	0	NA	promoter-TSS (NR_033944)	promoter-TSS (NR_033944)	61	NR_033944	647323	Hs.652830	NR_033944	ENSG00000214146	LINC02026	-	long intergenic non-protein coding RNA 2026	ncRNA	0.059867	0.617257	137(AAGAGCAGCATGTTCT,-,0.00),138(AGAGCAGCATGTTCTC,+,0.00)
chunk0094_27_1	chr2	1618017	1618511	+	0	NA	Intergenic	Intergenic	126283	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.022267	0.591919	
chunk0178_63_1	chr7	30177903	30178251	+	0	NA	Intergenic	Intergenic	43141	NM_152793	222166	Hs.200100	NM_152793	ENSG00000180354	MTURN	C7orf41|Ells1	maturin, neural progenitor differentiation regulator homolog	protein-coding	0.008621	0.398281	
chunk0169_341_1	chr6	106473964	106474319	+	0	NA	Intergenic	Intergenic	-37714	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.002817	0.396067	
chunk0059_212_1	chr14	33794479	33794688	+	0	NA	intron (NM_022123, intron 9 of 10)	intron (NM_022123, intron 9 of 10)	85646	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.014354	0.371429	
chunk0071_167_1	chr15	83067215	83067521	+	0	NA	promoter-TSS (NR_039740)	promoter-TSS (NR_039740)	-14	NM_025238	53339	Hs.459149	NM_025238	ENSG00000064726	BTBD1	C15orf1|NS5ATP8	BTB domain containing 1	protein-coding	0.088235	0.732899	
chunk0029_392_1	chr10	109574819	109575340	+	0	NA	Intergenic	Intergenic	348474	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.005758	0.398467	123(GAGAACAAAAAGTACT,-,0.00),124(AGAACAAAAAGTACTT,+,0.00)
chunk0109_227_1	chr20	5843134	5843703	+	0	NA	intron (NM_001303478, intron 3 of 3)	L1MEd|LINE|L1	-67910	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.007030	0.394737	
chunk0159_308_1	chr5	143076301	143076853	+	0	NA	intron (NM_015071, intron 17 of 22)	intron (NM_015071, intron 17 of 22)	-115923	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.003623	0.329114	282(TGGCACACCCTGTTCA,-,0.00),283(GGCACACCCTGTTCAG,+,0.00)
chunk0205_332_1	chr9	113121334	113121533	+	0	NA	Intergenic	Intergenic	8537	NR_024366	286333	Hs.99052	NR_024366	ENSG00000231528	FAM225A	C9orf109|LINC00256A|NCRNA00256A	family with sequence similarity 225 member A	ncRNA	0.005025	0.390000	
chunk0128_120_1	chr3	106401783	106401994	+	0	NA	Intergenic	Intergenic	-532845	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.339623	
chunk0016_192_1	chr1	198302713	198303061	+	0	NA	intron (NM_133494, intron 9 of 9)	intron (NM_133494, intron 9 of 9)	145909	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.005747	0.386819	
chunk0081_117_1	chr17	40066588	40066977	+	0	NA	intron (NM_199334, intron 1 of 8)	MIR|SINE|MIR	3967	NM_199334	7067	Hs.724	NM_003250	ENSG00000126351	THRA	AR7|CHNG6|EAR7|ERB-T-1|ERBA|ERBA1|NR1A1|THRA1|THRA2|c-ERBA-1	thyroid hormone receptor alpha	protein-coding	0.015424	0.417949	
chunk0009_17_1	chr1	100006753	100007012	+	0	NA	intron (NM_001271684, intron 3 of 5)	intron (NM_001271684, intron 3 of 5)	-31351	NM_033055	64645	Hs.124156	NM_033055	ENSG00000156875	MFSD14A	HIAT1	major facilitator superfamily domain containing 14A	protein-coding	0.003861	0.369231	
chunk0115_217_1	chr21	26950004	26950463	+	0	NA	intron (NM_007038, intron 2 of 7)	intron (NM_007038, intron 2 of 7)	-3728	NR_039916	100616243		NR_039916	ENSG00000266133	MIR4759	-	microRNA 4759	ncRNA	0.006536	0.354348	
chunk0108_414_1	chr2	237582381	237582666	+	0	NA	intron (NM_022449, intron 2 of 5)	intron (NM_022449, intron 2 of 5)	8603	NM_022449	64284	Hs.44278	NM_022449	ENSG00000124839	RAB17	-	RAB17, member RAS oncogene family	protein-coding	0.017544	0.587413	
chunk0153_57_1	chr5	67648152	67648797	+	0	NA	Intergenic	Intergenic	-144739	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.010853	0.436533	
chunk0146_234_1	chr4	162165746	162166371	+	0	NA	Intergenic	Intergenic	-2024	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.004800	0.353035	
chunk0167_397_1	chr6	74969939	74970384	+	0	NA	Intergenic	MER110|LTR|ERV1	235746	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.004494	0.363229	
chunk0189_361_1	chr8	27000973	27001204	+	0	NA	Intergenic	L1MEf|LINE|L1	47875	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.000000	0.370690	
chunk0034_43_1	chr11	26853110	26853932	+	0	NA	Intergenic	Intergenic	-131494	NM_178498	159963	Hs.148907	NM_178498	ENSG00000148942	SLC5A12	SMCT2	solute carrier family 5 member 12	protein-coding	0.014599	0.379101	
chunk0074_275_1	chr16	28526986	28527425	+	0	NA	Intergenic	L2a|LINE|L2	11969	NM_001042483	26471	Hs.513463	NM_012385	ENSG00000176046	NUPR1	COM1|P8	nuclear protein 1, transcriptional regulator	protein-coding	0.004556	0.375000	311(AAGGACAGTATGTCTA,-,0.00)
chunk0175_269_1	chr7	7492669	7492910	+	0	NA	intron (NM_001037763, intron 11 of 34)	intron (NM_001037763, intron 11 of 34)	43040	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.000000	0.380165	120(AAGTACTTACTGTGCA,-,0.00),121(AGTACTTACTGTGCAT,+,0.00)
chunk0032_293_1	chr11	9563454	9563712	+	0	NA	Intergenic	L1MA2|LINE|L1	-10098	NM_003390	7465	Hs.249441	NM_003390	ENSG00000166483	WEE1	WEE1A|WEE1hu	WEE1 G2 checkpoint kinase	protein-coding	0.003876	0.559846	
chunk0029_156_1	chr10	99454580	99454800	+	0	NA	Intergenic	Intergenic	-23917	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.013636	0.438914	54(TAGGACACCTAGTTCT,-,0.00),55(AGGACACCTAGTTCTC,+,0.00)
chunk0122_37_1	chr3	28019324	28019553	+	0	NA	Intergenic	Intergenic	-185302	NR_132438	100996624	Hs.275746	NR_132438	ENSG00000229243	LINC01981	-	long intergenic non-protein coding RNA 1981	ncRNA	0.013100	0.521739	
chunk0036_179_1	chr11	62653200	62653610	+	0	NA	promoter-TSS (NM_030628)	promoter-TSS (NM_030628)	-103	NM_030628	80789	Hs.458390	NM_030628	ENSG00000185085	INTS5	INT5|KIAA1698	integrator complex subunit 5	protein-coding	0.087805	0.613139	
chunk0196_381_1	chr8	115484665	115484977	+	0	NA	intron (NM_001282903, intron 5 of 6)	intron (NM_001282903, intron 5 of 6)	183191	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.000000	0.383387	163(AAGAACACAATGTTCT,-,0.00),164(AGAACACAATGTTCTT,+,0.00)
chunk0185_219_1	chr7	129054757	129055223	+	0	NA	promoter-TSS (NR_002187)	promoter-TSS (NR_002187)	183	NM_012470	23534	Hs.193613	NM_012470	ENSG00000064419	TNPO3	IPO12|LGMD1F|LGMDD2|MTR10A|TRN-SR|TRN-SR2|TRNSR	transportin 3	protein-coding	0.066524	0.588865	
chunk0016_356_1	chr1	202287208	202287687	+	0	NA	intron (NM_001017403, intron 6 of 17)	L2a|LINE|L2	54519	NM_014176	29089	Hs.5199	NM_014176	ENSG00000077152	UBE2T	FANCT|HSPC150|PIG50	ubiquitin conjugating enzyme E2 T	protein-coding	0.004175	0.441667	
chunk0003_386_1	chr1	39852977	39853388	+	0	NA	intron (NM_001312692, intron 1 of 8)	intron (NM_001312692, intron 1 of 8)	30329	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.004866	0.388350	
chunk0032_4_1	chr11	280847	281052	+	0	NA	exon (NM_138329, exon 4 of 8)	exon (NM_138329, exon 4 of 8)	2379	NM_001276700	171389	Hs.352611	NM_138329	ENSG00000174885	NLRP6	AVR|CLR11.4|NALP6|NAVR|NAVR/AVR|PAN3|PYPAF5	NLR family pyrin domain containing 6	protein-coding	0.112195	0.640777	
chunk0024_52_1	chr10	33756084	33756539	+	0	NA	Intergenic	L2a|LINE|L2	16369	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.000000	0.344298	
chunk0114_270_1	chr21	16243340	16243583	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	49082	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.008230	0.319672	
chunk0085_222_1	chr18	6782902	6783316	+	0	NA	Intergenic	Intergenic	-51324	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.004831	0.431325	172(GAGGCCACTGTGTTCT,-,0.00),173(AGGCCACTGTGTTCTT,+,0.00)
chunk0074_207_1	chr16	25135359	25135625	+	0	NA	intron (NM_016309, intron 3 of 10)	MER58A|DNA|hAT-Charlie	13540	NR_039998	100506655	Hs.657576	NR_039998	ENSG00000260034	LCMT1-AS2	-	LCMT1 antisense RNA 2	ncRNA	0.003759	0.404494	
chunk0007_103_1	chr1	78855921	78856756	+	0	NA	Intergenic	Intergenic	150472	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.003593	0.372010	
chunk0142_164_1	chr4	95240493	95240692	+	0	NA	intron (NM_003728, intron 7 of 15)	intron (NM_003728, intron 7 of 15)	149101	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.010050	0.330000	
chunk0135_19_1	chr3	184345750	184345976	+	0	NA	TTS (NM_004366)	TTS (NM_004366)	8375	NM_144635	131408	Hs.591307	NM_144635	ENSG00000175182	FAM131A	C3orf40|FLAT715|PRO1378	family with sequence similarity 131 member A	protein-coding	0.013274	0.550661	60(TGGGACTTCATGTTCT,-,0.00),61(GGGACTTCATGTTCTT,+,0.00)
chunk0065_360_1	chr14	103824682	103825257	+	0	NA	intron (NM_015316, intron 1 of 16)	Tigger1|DNA|TcMar-Tigger	22621	NM_015316	23368	Hs.709297	NM_015316	ENSG00000088808	PPP1R13B	ASPP1|p53BP2-like|p85	protein phosphatase 1 regulatory subunit 13B	protein-coding	0.010435	0.394097	
chunk0121_188_1	chr3	20098903	20099689	+	0	NA	intron (NM_003884, intron 3 of 17)	intron (NM_003884, intron 3 of 17)	-38269	NR_036086	100422901		NR_036086	ENSG00000266745	MIR3135A	MIR3135|hsa-mir-3135a	microRNA 3135a	ncRNA	0.011450	0.451080	
chunk0111_122_1	chr20	24165544	24166074	+	0	NA	Intergenic	Charlie7a|DNA|hAT-Charlie	-33958	NR_040102	400839	Hs.651965	NR_040102	ENSG00000230133	LINC01721	-	long intergenic non-protein coding RNA 1721	ncRNA	0.001887	0.406780	
chunk0213_2_1	chrY	19544468	19545005	+	0	NA	Intergenic	MER92-int|LTR|ERV1	-22622	NR_045128	246126	Hs.522863	NM_001005852	ENSG00000131002	TXLNGY	CYorf15A|CYorf15B|TXLNG2P	taxilin gamma pseudogene, Y-linked	pseudo	0.005587	0.280669	
chunk0050_414_1	chr12	109823164	109823409	+	0	NA	intron (NM_021625, intron 1 of 15)	intron (NM_021625, intron 1 of 15)	-8459	NM_147204	59341	Hs.506713	NM_021625	ENSG00000111199	TRPV4	BCYM3|CMT2C|HMSN2C|OTRPC4|SMAL|SPSMA|SSQTL1|TRP12|VRL2|VROAC	transient receptor potential cation channel subfamily V member 4	protein-coding	0.032653	0.658537	
chunk0197_359_1	chr8	125735261	125735707	+	0	NA	Intergenic	LTR27B|LTR|ERV1	215713	NR_038446	100130231	Hs.729642	NR_038446	ENSG00000245164	LINC00861	-	long intergenic non-protein coding RNA 861	ncRNA	0.006726	0.487696	
chunk0102_192_1	chr2	147716929	147717514	+	0	NA	Intergenic	Intergenic	-127296	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.337884	
chunk0011_119_1	chr1	146989546	146989764	+	0	NA	exon (NM_001278141, exon 31 of 37)	exon (NM_001278141, exon 31 of 37)	51110	NM_001278141	149013	Hs.666981	NM_001278141	ENSG00000268043	NBPF12	COAS1|KIAA1245	NBPF member 12	protein-coding	0.013761	0.479452	
chunk0179_132_1	chr7	45924146	45924872	+	0	NA	Intergenic	Intergenic	-3237	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.009642	0.489684	
chunk0148_198_1	chr5	8501233	8501795	+	0	NA	Intergenic	Intergenic	40589	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.007117	0.373002	256(CTGGACATTGTGTCCT,-,0.00),257(TGGACATTGTGTCCTA,+,0.00)
chunk0192_128_1	chr8	61805521	61805994	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	90969	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.000000	0.402954	
chunk0046_180_1	chr12	58745351	58745588	+	0	NA	intron (NR_120452, intron 1 of 7)	intron (NR_120452, intron 1 of 7)	36247	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.012658	0.558824	
chunk0107_147_1	chr2	215097584	215097874	+	0	NA	intron (NR_103740, intron 2 of 54)	intron (NR_103740, intron 2 of 54)	40699	NR_103740	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.010345	0.333333	
chunk0087_452_1	chr18	42695384	42695913	+	0	NA	Intergenic	Intergenic	420044	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.286792	
chunk0141_71_1	chr4	77927951	77928409	+	0	NA	intron (NM_020236, intron 7 of 8)	intron (NM_020236, intron 7 of 8)	65529	NM_020236	65008	Hs.532019	NM_020236	ENSG00000169288	MRPL1	BM022|L1MT|MRP-L1	mitochondrial ribosomal protein L1	protein-coding	0.002183	0.339869	
chunk0157_149_1	chr5	117726257	117726516	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-3975	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.000000	0.342308	173(GTGTACATAATGTCCC,-,0.00),174(TGTACATAATGTCCCA,+,0.00)
chunk0018_378_1	chr1	222241952	222242624	+	0	NA	Intergenic	Intergenic	305814	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.007440	0.365527	135(CAACACAGCATGTTCT,-,0.00),136(AACACAGCATGTTCTG,+,0.00)
chunk0136_449_1	chr3	197994806	197995171	+	0	NA	intron (NR_026786, intron 9 of 16)	L1MA7|LINE|L1	34788	NR_026786	89782	Hs.518540	NM_033029	ENSG00000185621	LMLN	GP63|INV|IX14|LMNL1|MSP	leishmanolysin like peptidase	protein-coding	0.002740	0.420765	
chunk0060_131_1	chr14	44626595	44627189	+	0	NA	Intergenic	LTR18B|LTR|ERVL	-119596	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.011785	0.497479	
chunk0132_152_1	chr3	156576729	156577169	+	0	NA	Intergenic	Intergenic	-21749	NM_001308197	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.002273	0.428571	
chunk0008_241_1	chr1	94246557	94246880	+	0	NA	Intergenic	Intergenic	-8967	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.021672	0.509259	
chunk0068_327_1	chr15	57528752	57529491	+	0	NA	intron (NM_001252335, intron 14 of 19)	intron (NM_001252335, intron 14 of 19)	-62783	NM_001018091	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.006766	0.462162	352(GGGCACAGATAGTTCC,-,0.00),353(GGCACAGATAGTTCCT,+,0.00)
chunk0110_183_1	chr20	14425261	14425571	+	0	NA	intron (NM_080676, intron 3 of 16)	HAL1|LINE|L1	-87749	NM_013281	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.009677	0.321543	
chunk0212_122_1	chrX	130877896	130878662	+	0	NA	intron (NM_006375, intron 2 of 14)	intron (NM_006375, intron 2 of 14)	25038	NM_001281736	10495	Hs.171458	NM_006375	ENSG00000165675	ENOX2	APK1|COVA1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.005222	0.415906	
chunk0035_214_1	chr11	44978929	44979486	+	0	NA	Intergenic	Intergenic	5305	NR_026681	221122	Hs.551656	NR_026681	ENSG00000254654	LINC02685	-	long intergenic non-protein coding RNA 2685	ncRNA	0.005386	0.543011	
chunk0002_253_1	chr1	21267808	21268501	+	0	NA	intron (NM_001113348, intron 4 of 18)	intron (NM_001113348, intron 4 of 18)	11536	NM_001113347	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.014430	0.492795	273(GTGCACACAGTGTACT,-,0.00),274(TGCACACAGTGTACTT,+,0.00)
chunk0195_408_1	chr8	100539815	100540374	+	0	NA	intron (NM_001270377, intron 1 of 4)	MIR|SINE|MIR	19617	NM_001270378	157567	Hs.530199	NM_198401	ENSG00000186106	ANKRD46	ANK-S|GENX-115279	ankyrin repeat domain 46	protein-coding	0.005367	0.326786	
chunk0075_188_1	chr16	52253382	52253646	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	168233	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.007576	0.433962	114(AGGAACAGTCAGTTCT,-,0.00),115(GGAACAGTCAGTTCTT,+,0.00)
chunk0049_248_1	chr12	93679533	93679782	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	2282	NM_003805	8738	Hs.38533	NM_003805	ENSG00000169372	CRADD	MRT34|RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.016064	0.504000	
chunk0095_56_1	chr2	14051037	14051249	+	0	NA	Intergenic	Intergenic	349815	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.004717	0.356808	
chunk0210_149_1	chrX	76423412	76423763	+	0	NA	Intergenic	Intergenic	-4066	NM_020932	57692	Hs.8453	NM_020932	ENSG00000198934	MAGEE1	DAMAGE|HCA1	MAGE family member E1	protein-coding	0.008547	0.397727	
chunk0110_225_1	chr20	15818588	15819046	+	0	NA	intron (NM_001033087, intron 4 of 13)	L2c|LINE|L2	104497	NR_130925	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.008734	0.440087	
chunk0109_191_1	chr20	4972955	4973296	+	0	NA	intron (NM_203327, intron 1 of 16)	intron (NM_203327, intron 1 of 16)	28374	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.002933	0.327485	
chunk0201_192_1	chr9	36428663	36429012	+	0	NA	Intergenic	L2b|LINE|L2	-27639	NM_194330	152006	Hs.333503	NM_022781	ENSG00000137075	RNF38	-	ring finger protein 38	protein-coding	0.002865	0.420000	
chunk0143_389_1	chr4	122895824	122896086	+	0	NA	3' UTR (NM_002006, exon 3 of 3)	3' UTR (NM_002006, exon 3 of 3)	26651	NM_007083	11162	Hs.558459	NM_007083	ENSG00000170917	NUDT6	ASFGF2|FGF-AS|FGF2AS|GFG-1|GFG1	nudix hydrolase 6	protein-coding	0.000000	0.304183	
chunk0172_131_1	chr6	135274691	135275097	+	0	NA	Intergenic	Intergenic	35734	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.007389	0.385749	
chunk0052_174_1	chr13	24171279	24171594	+	0	NA	intron (NM_153023, intron 1 of 11)	intron (NM_153023, intron 1 of 11)	9020	NR_031753	100313842		NR_031753	ENSG00000252695	MIR2276	-	microRNA 2276	ncRNA	0.019048	0.522152	
chunk0122_96_1	chr3	30362284	30362759	+	0	NA	Intergenic	L1MC4a|LINE|L1	-243981	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.004211	0.334034	175(AGGAACATTATGTGAT,-,0.00)
chunk0198_103_1	chr8	130733692	130734617	+	0	NA	Intergenic	Intergenic	-290494	NM_001247996	50807	Hs.655552	NM_018482	ENSG00000153317	ASAP1	AMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14P	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	protein-coding	0.007568	0.340173	
chunk0205_338_1	chr9	113243056	113243493	+	0	NA	intron (NM_001859, intron 1 of 4)	intron (NM_001859, intron 1 of 4)	21746	NM_001859	1317	Hs.532315	NM_001859	ENSG00000136868	SLC31A1	COPT1|CTR1	solute carrier family 31 member 1	protein-coding	0.002288	0.331050	
chunk0159_302_1	chr5	142942996	142943411	+	0	NA	intron (NM_015071, intron 11 of 22)	intron (NM_015071, intron 11 of 22)	-74293	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.004819	0.415865	
chunk0010_394_1	chr1	119471139	119471470	+	0	NA	Intergenic	Intergenic	-35899	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.015106	0.481928	
chunk0198_477_1	chr8	145021792	145022200	+	0	NA	Intergenic	LTR5A|LTR|ERVK	-19097	NR_023392	286101	Hs.367856	NR_023392		ZNF252P	ZNF252	zinc finger protein 252, pseudogene	pseudo	0.009804	0.449878	
chunk0099_339_1	chr2	100067639	100068339	+	0	NA	intron (NM_001025108, intron 2 of 23)	intron (NM_001025108, intron 2 of 23)	37594	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.010000	0.385164	407(AGGAACAGTTTGTTCT,-,0.00),408(GGAACAGTTTGTTCTT,+,0.00)
chunk0059_218_1	chr14	33943503	33943859	+	0	NA	intron (NM_001308103, intron 1 of 4)	intron (NM_001308103, intron 1 of 4)	7145	NM_001308103	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.005618	0.417367	
chunk0118_180_1	chr22	31082480	31082817	+	0	NA	promoter-TSS (NM_001207017)	promoter-TSS (NM_001207017)	-212	NM_001207017	6525	Hs.149098	NM_006932	ENSG00000183963	SMTN	-	smoothelin	protein-coding	0.008902	0.571006	185(GAAGACACAGTGTACC,-,0.00),186(AAGACACAGTGTACCT,+,0.00)
chunk0029_398_1	chr10	109616089	109616625	+	0	NA	Intergenic	Intergenic	307196	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.003731	0.452514	249(CAGGGCACTCTGTTCT,-,0.00),250(AGGGCACTCTGTTCTC,+,0.00)
chunk0186_53_1	chr7	136349018	136349282	+	0	NA	Intergenic	Intergenic	-371694	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.000000	0.332075	
chunk0133_269_1	chr3	171917822	171918057	+	0	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-17199	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.004255	0.453390	
chunk0052_53_1	chr13	21013257	21013704	+	0	NA	intron (NM_014572, intron 2 of 7)	intron (NM_014572, intron 2 of 7)	48103	NM_014572	26524	Hs.78960	NM_014572	ENSG00000150457	LATS2	KPM	large tumor suppressor kinase 2	protein-coding	0.013423	0.412946	
chunk0146_378_1	chr4	168440987	168441507	+	0	NA	intron (NM_001291510, intron 10 of 29)	intron (NM_001291510, intron 10 of 29)	39267	NM_001012967	91351	Hs.535011	NM_001012967	ENSG00000181381	DDX60L	-	DExD/H-box 60 like	protein-coding	0.005769	0.368522	
chunk0173_19_1	chr6	141420904	141421210	+	0	NA	Intergenic	L1ME3A|LINE|L1	667742	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.003268	0.296417	
chunk0161_105_1	chr5	167416354	167416553	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	131615	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.015075	0.350000	
chunk0077_152_1	chr16	78924639	78924844	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	675984	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.004878	0.330097	
chunk0134_157_1	chr3	177809491	177809690	+	0	NA	Intergenic	Intergenic	-7275	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.005025	0.330000	
chunk0079_201_1	chr17	14417458	14417942	+	0	NA	Intergenic	MER57C2|LTR|ERV1	113960	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.002066	0.360825	
chunk0114_369_1	chr20	62887133	62887800	+	0	NA	3' UTR (NM_001193370, exon 15 of 15)	3' UTR (NM_001193370, exon 15 of 15)	-25703	NM_001301726	10732	Hs.126248	NM_006602	ENSG00000101190	TCFL5	CHA|E2BP-1|Figlb|SOSF1|bHLHe82	transcription factor like 5	protein-coding	0.019490	0.479042	402(GAGAACAGACTGTGCA,-,0.00),403(AGAACAGACTGTGCAC,+,0.00)
chunk0065_279_1	chr14	102439782	102440287	+	0	NA	intron (NM_001172631, intron 10 of 16)	intron (NM_001172631, intron 10 of 16)	69757	NM_152326	122416	Hs.432945	NM_152326	ENSG00000156381	ANKRD9	-	ankyrin repeat domain 9	protein-coding	0.019802	0.535573	
chunk0138_237_1	chr4	39375363	39375839	+	0	NA	Intergenic	Intergenic	-9220	NM_002913	5981	Hs.507475	NM_002913	ENSG00000035928	RFC1	A1|CANVAS|MHCBFB|PO-GA|RECC1|RFC|RFC140	replication factor C subunit 1	protein-coding	0.008403	0.339623	
chunk0044_435_1	chr12	42260276	42260898	+	0	NA	Intergenic	Intergenic	-22235	NM_005748	10138	Hs.649195	NM_005748	ENSG00000015153	YAF2	-	YY1 associated factor 2	protein-coding	0.014469	0.481541	
chunk0145_2_1	chr4	142697286	142698075	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	148771	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.002535	0.324051	
chunk0127_136_1	chr3	94158966	94159408	+	0	NA	Intergenic	Intergenic	-95964	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.009050	0.435666	194(GTGGACATCGTGTGCC,-,0.00),195(TGGACATCGTGTGCCT,+,0.00)
chunk0061_48_1	chr14	56219949	56220185	+	0	NA	intron (NM_021255, intron 2 of 5)	intron (NM_021255, intron 2 of 5)	101692	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.008475	0.405063	
chunk0147_119_1	chr4	174248491	174248804	+	0	NA	intron (NM_012180, intron 3 of 5)	intron (NM_012180, intron 3 of 5)	-28249	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.003195	0.353503	62(GAGCACACACTGTCCA,-,0.00),63(AGCACACACTGTCCAC,+,0.00)
chunk0193_195_1	chr8	75780562	75780848	+	0	NA	Intergenic	Intergenic	240737	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.006993	0.334495	
chunk0166_29_1	chr6	42045560	42046212	+	0	NA	intron (NM_001287434, intron 1 of 4)	intron (NM_001287434, intron 1 of 4)	3008	NM_001287434	896	Hs.534307	NM_001760	ENSG00000112576	CCND3	-	cyclin D3	protein-coding	0.018405	0.534456	296(GAGTACAACCTGTTCT,-,0.00),297(AGTACAACCTGTTCTC,+,0.00)
chunk0164_206_1	chr6	22603227	22603482	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	33905	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007843	0.332031	
chunk0008_359_1	chr1	96552437	96552795	+	0	NA	Intergenic	Intergenic	-168989	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.364903	
chunk0080_180_1	chr17	28807713	28808217	+	0	NA	intron (NM_001288635, intron 1 of 3)	intron (NM_001288635, intron 1 of 3)	4470	NM_001288634	55731	Hs.564533	NM_018182	ENSG00000173065	FAM222B	C17orf63	family with sequence similarity 222 member B	protein-coding	0.005952	0.362376	
chunk0060_318_1	chr14	51341520	51341805	+	0	NA	intron (NR_038358, intron 1 of 4)	intron (NR_038358, intron 1 of 4)	8269	NR_038358	283553	Hs.325752	NR_038358	ENSG00000258479	LINC00640	-	long intergenic non-protein coding RNA 640	ncRNA	0.007018	0.381119	
chunk0066_114_1	chr15	30039146	30039410	+	0	NA	Intergenic	Intergenic	-43677	NM_001282472	653073	Hs.574257	NM_001282472	ENSG00000179938	GOLGA8J	-	golgin A8 family member J	protein-coding	0.007576	0.535849	
chunk0007_116_1	chr1	78983714	78984281	+	0	NA	intron (NM_022159, intron 2 of 14)	L1MEd|LINE|L1	22813	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.005291	0.302817	
chunk0177_293_1	chr7	25794432	25794897	+	0	NA	Intergenic	L1M5|LINE|L1	155322	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.002151	0.319742	218(AAGCACACAGTGTTCC,-,0.00),219(AGCACACAGTGTTCCA,+,0.00)
chunk0104_197_1	chr2	175770963	175771266	+	0	NA	Intergenic	Intergenic	231231	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.006601	0.421053	
chunk0119_355_1	chr22	47351472	47352097	+	0	NA	Intergenic	Intergenic	135327	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.017600	0.551118	
chunk0197_241_1	chr8	123268053	123268377	+	0	NA	intron (NR_037873, intron 1 of 3)	intron (NR_037873, intron 1 of 3)	6272	NM_007222	11244	Hs.521800	NM_007222	ENSG00000165156	ZHX1	-	zinc fingers and homeoboxes 1	protein-coding	0.003086	0.313846	
chunk0039_110_1	chr11	97656389	97656907	+	0	NA	Intergenic	Intergenic	-1149771	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.007722	0.325626	
chunk0148_356_1	chr5	14564645	14565052	+	0	NA	Intergenic	HAL1|LINE|L1	-16934	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.009828	0.367647	
chunk0126_155_1	chr3	76954693	76955052	+	0	NA	Intergenic	Intergenic	-85271	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.000000	0.333333	
chunk0084_273_1	chr17	79691791	79692084	+	0	NA	Intergenic	Intergenic	15312	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.020478	0.510204	
chunk0063_244_1	chr14	82379914	82380274	+	0	NA	Intergenic	L1MB8|LINE|L1	-757033	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.002778	0.265928	
chunk0086_301_1	chr18	23956462	23957043	+	0	NA	Intergenic	Intergenic	-36021	NM_153211	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.015491	0.472509	
chunk0038_399_1	chr11	93651044	93651508	+	0	NA	Intergenic	L2a|LINE|L2	-10374	NM_033395	85459	Hs.458418	NM_033395	ENSG00000166004	CEP295	KIAA1731	centrosomal protein 295	protein-coding	0.008621	0.359140	
chunk0120_425_1	chr3	13106618	13106909	+	0	NA	Intergenic	Intergenic	-33646	NM_001134382	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.010309	0.417808	
chunk0001_381_1	chr1	10507313	10507623	+	0	NA	intron (NM_004565, intron 2 of 8)	intron (NM_004565, intron 2 of 8)	32522	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.025806	0.511254	
chunk0076_144_1	chr16	67109295	67109752	+	0	NA	promoter-TSS (NM_025187)	promoter-TSS (NM_025187)	-489	NM_025187	80262	Hs.513666	NM_025187	ENSG00000125149	C16orf70	C16orf6|LIN10|lin-10	chromosome 16 open reading frame 70	protein-coding	0.052516	0.606987	
chunk0033_188_1	chr11	16092881	16093457	+	0	NA	intron (NM_001145811, intron 8 of 14)	intron (NM_001145811, intron 8 of 14)	-123548	NR_106721	102464826		NR_106721	ENSG00000284094	MIR6073	hsa-mir-6073	microRNA 6073	ncRNA	0.005208	0.350087	
chunk0189_432_1	chr8	28092975	28093599	+	0	NA	intron (NM_001284225, intron 1 of 12)	CpG	220	NM_001284224	55140	Hs.491336	NM_018091	ENSG00000134014	ELP3	KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.060897	0.532800	383(AGGGTCAGTGTGTCCA,-,0.00),384(GGGTCAGTGTGTCCAT,+,0.00)
chunk0024_140_1	chr10	35130477	35130971	+	0	NA	intron (NM_183060, intron 1 of 5)	Tigger3c|DNA|TcMar-Tigger	3267	NM_183060	1390	Hs.200250	NM_001881	ENSG00000095794	CREM	CREM-2|ICER|hCREM-2	cAMP responsive element modulator	protein-coding	0.006073	0.371717	
chunk0072_202_1	chr15	94819599	94819999	+	0	NA	Intergenic	Intergenic	-35564	NR_077061	440311	Hs.745156	NR_077061	ENSG00000277654	LOC440311	-	NOP53 ribosome biogenesis factor pseudogene	pseudo	0.010000	0.364090	
chunk0207_372_1	chr9	136023859	136024758	+	0	NA	intron (NM_144653, intron 2 of 5)	intron (NM_144653, intron 2 of 5)	-62928	NM_016172	10422	Hs.9194	NM_016172	ENSG00000130560	UBAC1	GBDR1|KPC2|UBADC1	UBA domain containing 1	protein-coding	0.013348	0.528889	687(GAGGACAGTGTGTGTA,-,0.00),721(AAGGACAGAGTGTGCA,-,0.00),722(AGGACAGAGTGTGCAT,+,0.00)
chunk0115_343_1	chr21	29182153	29182905	+	0	NA	Intergenic	Intergenic	-10965	NR_027072	193629	Hs.720711	NM_138968	ENSG00000215533	LINC00189	C21orf109|NCRNA00189	long intergenic non-protein coding RNA 189	ncRNA	0.011968	0.381142	
chunk0073_214_1	chr16	10594663	10594933	+	0	NA	Intergenic	Intergenic	-14082	NM_001424	2013	Hs.531561	NM_001424	ENSG00000213853	EMP2	XMP	epithelial membrane protein 2	protein-coding	0.025926	0.634686	
chunk0089_99_1	chr18	58402310	58402753	+	0	NA	TTS (NM_001144966)	TTS (NM_001144966)	-48543	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.018059	0.452703	
chunk0203_200_1	chr9	86508878	86509356	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-154630	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.004184	0.354906	
chunk0178_326_1	chr7	38261168	38261646	+	0	NA	intron (NM_001003806, intron 3 of 3)	MIRb|SINE|MIR	12240	NM_001003799	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.014644	0.407098	
chunk0149_69_1	chr5	17114295	17114494	+	0	NA	Intergenic	Intergenic	-102429	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.015075	0.430000	
chunk0164_38_1	chr6	18431511	18432021	+	0	NA	intron (NM_182757, intron 3 of 7)	intron (NM_182757, intron 3 of 7)	44416	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.003922	0.385519	
chunk0056_368_1	chr13	92823098	92823516	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	-101693	NR_046520	100873969	Hs.577863	NR_046520	ENSG00000235984	GPC5-AS1	-	GPC5 antisense RNA 1	ncRNA	0.002392	0.293556	
chunk0021_370_1	chr1	246381211	246381902	+	0	NA	intron (NM_001167740, intron 1 of 11)	intron (NM_001167740, intron 1 of 11)	35856	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.013025	0.421965	397(GAGTACATCCAGTACC,-,0.00),398(AGTACATCCAGTACCT,+,0.00)
chunk0050_164_1	chr12	103672696	103673157	+	0	NA	intron (NM_017564, intron 22 of 68)	intron (NM_017564, intron 22 of 68)	85635	NM_017564	55576	Hs.408249	NM_017564	ENSG00000136011	STAB2	FEEL2|FELE-2|FELL2|FEX2|HARE|SCARH1	stabilin 2	protein-coding	0.013015	0.415584	
chunk0063_129_1	chr14	79382307	79382506	+	0	NA	intron (NM_138970, intron 1 of 5)	MER83C|LTR|ERV1	103067	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.010050	0.475000	160(GGGAACATGATGTTCT,-,0.00),161(GGAACATGATGTTCTG,+,0.00)
chunk0172_361_1	chr6	139173981	139174622	+	0	NA	intron (NM_016217, intron 2 of 3)	intron (NM_016217, intron 2 of 3)	39189	NM_016217	51696	Hs.197644	NM_016217	ENSG00000112406	HECA	HDC|HDCL|HHDC|dJ225E12.1	hdc homolog, cell cycle regulator	protein-coding	0.009360	0.423676	
chunk0107_235_1	chr2	217100868	217101304	+	0	NA	Intergenic	Intergenic	-181647	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.009174	0.418764	
chunk0092_89_1	chr19	21986732	21987049	+	0	NA	intron (NM_007153, intron 3 of 3)	intron (NM_007153, intron 3 of 3)	24053	NM_007153	7757	Hs.732975	NM_007153	ENSG00000160321	ZNF208	PMIDP|ZNF95	zinc finger protein 208	protein-coding	0.000000	0.311321	
chunk0149_271_1	chr5	24502425	24502664	+	0	NA	intron (NM_006727, intron 8 of 11)	intron (NM_006727, intron 8 of 11)	142432	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.008368	0.375000	
chunk0075_197_1	chr16	52481138	52481768	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	65441	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.001587	0.316957	
chunk0112_353_1	chr20	45329521	45330003	+	0	NA	intron (NM_002999, intron 4 of 4)	intron (NM_002999, intron 4 of 4)	18662	NM_002999	6385	Hs.632267	NM_002999	ENSG00000124145	SDC4	SYND4	syndecan 4	protein-coding	0.010373	0.507246	
chunk0048_82_1	chr12	79075862	79076061	+	0	NA	intron (NM_001135805, intron 4 of 11)	MER39|LTR|ERV1	30308	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.000000	0.285000	
chunk0046_259_1	chr12	60704237	60705032	+	0	NA	Intergenic	L2b|LINE|L2	1015297	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.005031	0.350503	
chunk0166_242_1	chr6	47268947	47269615	+	0	NA	intron (NM_014452, intron 3 of 5)	intron (NM_014452, intron 3 of 5)	40666	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.002994	0.393124	427(TTGAACATGGTGTTCA,-,0.00),428(TGAACATGGTGTTCAA,+,0.00)
chunk0046_404_1	chr12	64237338	64237747	+	0	NA	Intergenic	Intergenic	-15246	NM_001300940	144577	Hs.444671	NM_152440	ENSG00000174206	C12orf66	-	chromosome 12 open reading frame 66	protein-coding	0.000000	0.324390	
chunk0026_291_1	chr10	67737931	67738474	+	0	NA	Intergenic	L1PA4|LINE|L1	-42011	NM_013266	29119	Hs.21375	NM_013266	ENSG00000183230	CTNNA3	ARVD13|VR22	catenin alpha 3	protein-coding	0.011050	0.492647	
chunk0105_98_1	chr2	184482408	184482973	+	0	NA	Intergenic	Intergenic	103715	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.003540	0.293286	
chunk0017_165_1	chr1	207009833	207010645	+	0	NA	Intergenic	Intergenic	22517	NM_001083924	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.018473	0.462485	342(CAGCACACCCTGTTCT,-,0.00),343(AGCACACCCTGTTCTT,+,0.00)
chunk0208_106_1	chrX	13765664	13765974	+	0	NA	intron (NM_003611, intron 19 of 22)	intron (NM_003611, intron 19 of 22)	31106	NM_003611	8481	Hs.6483	NM_003611	ENSG00000046651	OFD1	71-7A|CXorf5|JBTS10|RP23|SGBS2	OFD1 centriole and centriolar satellite protein	protein-coding	0.000000	0.411576	
chunk0052_262_1	chr12	123690039	123690687	+	0	NA	intron (NM_024809, intron 7 of 17)	intron (NM_024809, intron 7 of 17)	19250	NM_024809	79867	Hs.167165	NM_024809	ENSG00000168778	TCTN2	C12orf38|JBTS24|MKS8|TECT2	tectonic family member 2	protein-coding	0.010802	0.409861	
chunk0161_62_1	chr5	166399932	166400131	+	0	NA	Intergenic	Intergenic	526339	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.010050	0.395000	
chunk0200_110_1	chr9	16931188	16931544	+	0	NA	Intergenic	Intergenic	-60578	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.002809	0.380952	
chunk0165_358_1	chr6	38107083	38107544	+	0	NA	intron (NM_021943, intron 4 of 5)	intron (NM_021943, intron 4 of 5)	287782	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.002169	0.439394	
chunk0113_30_1	chr20	49728387	49728943	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-14781	NM_004776	9334	Hs.370487	NM_004776	ENSG00000158470	B4GALT5	B4Gal-T5|BETA4-GALT-IV|beta4Gal-T5|beta4GalT-V|gt-V	beta-1,4-galactosyltransferase 5	protein-coding	0.001799	0.400359	
chunk0099_419_1	chr2	102505401	102505607	+	0	NA	intron (NM_001011552, intron 4 of 11)	intron (NM_001011552, intron 4 of 11)	32201	NM_001011552	389015	Hs.447686	NM_001011552	ENSG00000180251	SLC9A4	NHE4	solute carrier family 9 member A4	protein-coding	0.024272	0.507246	
chunk0060_361_1	chr14	52343388	52343777	+	0	NA	Intergenic	Intergenic	29284	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.000000	0.379487	174(AGTACACATTGTTTCT,+,0.00)
chunk0076_229_1	chr16	68775318	68775627	+	0	NA	intron (NM_004360, intron 2 of 15)	intron (NM_004360, intron 2 of 15)	32956	NR_106988									0.009709	0.409677	
chunk0166_320_1	chr6	49764220	49764512	+	0	NA	Intergenic	Intergenic	-19911	NM_006061	10321	Hs.404466	NM_006061	ENSG00000096006	CRISP3	Aeg2|CRISP-3|CRS3|SGP28|dJ442L6.3	cysteine rich secretory protein 3	protein-coding	0.017123	0.344710	
chunk0078_85_1	chr17	1981534	1981898	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	43629	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.008242	0.542466	142(TGGTACACACTGCCCT,-,0.00),143(GGTACACACTGCCCTG,+,0.00)
chunk0118_341_1	chr22	35654768	35655512	+	0	NA	intron (NM_030641, intron 1 of 2)	MER34B|LTR|ERV1	6763	NM_030641	80830	Hs.257352	NM_030641	ENSG00000221963	APOL6	APOL-VI|APOLVI	apolipoprotein L6	protein-coding	0.006720	0.386577	
chunk0199_422_1	chr9	13652738	13653227	+	0	NA	Intergenic	Intergenic	-221653	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.008180	0.338776	
chunk0047_281_1	chr12	73143533	73144384	+	0	NA	Intergenic	Intergenic	-15232	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.002350	0.368545	
chunk0165_424_1	chr6	39488466	39488864	+	0	NA	intron (NM_001289021, intron 12 of 21)	L2b|LINE|L2	-57291	NM_001289024	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.002513	0.398496	
chunk0139_324_1	chr4	58313558	58313787	+	0	NA	Intergenic	Intergenic	887800	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.013100	0.317391	
chunk0076_308_1	chr16	70331856	70332403	+	0	NA	intron (NM_001014449, intron 8 of 9)	intron (NM_001014449, intron 8 of 9)	14618	NR_039997	100506083	Hs.635008	NR_039997	ENSG00000261777	LOC100506083	-	uncharacterized LOC100506083	ncRNA	0.010969	0.509124	297(CAGAACATTGTGTCTC,-,0.00),298(AGAACATTGTGTCTCC,+,0.00)
chunk0173_142_1	chr6	143950678	143951324	+	0	NA	intron (NM_001289047, intron 2 of 3)	intron (NM_001289047, intron 2 of 3)	57403	NM_001080956	5325	Hs.743225	NM_002656	ENSG00000118495	PLAGL1	LOT1|ZAC|ZAC1	PLAG1 like zinc finger 1	protein-coding	0.004644	0.408037	
chunk0130_382_1	chr3	139934125	139934348	+	0	NA	promoter-TSS (NM_022131)	promoter-TSS (NM_022131)	-949	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.004484	0.303571	
chunk0186_262_1	chr7	141492135	141492334	+	0	NA	Intergenic	L2a|LINE|L2	-59044	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.010050	0.490000	
chunk0108_278_1	chr2	234587752	234587974	+	0	NA	Intergenic	Intergenic	-90810	NM_001282431	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.004505	0.421525	
chunk0211_353_1	chrX	125449547	125450257	+	0	NA	Intergenic	L1PA10|LINE|L1	129782	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.004225	0.343179	363(ATGAACAGACAGTTCT,-,0.00),364(TGAACAGACAGTTCTC,+,0.00)
chunk0089_208_1	chr18	60675825	60676092	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-303190	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.007491	0.395522	
chunk0121_197_1	chr3	20786874	20787412	+	0	NA	Intergenic	Intergenic	444675	NR_110814	101927829	Hs.639381	NR_110814	ENSG00000231304	LOC101927829	-	uncharacterized LOC101927829	ncRNA	0.009294	0.382189	249(AAGCTCAGCATGTTCA,-,0.00)
chunk0189_312_1	chr8	26151364	26151674	+	0	NA	Intergenic	Intergenic	-106395	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.000000	0.453376	
chunk0058_186_1	chr14	24131272	24131471	+	0	NA	promoter-TSS (NM_203402)	promoter-TSS (NM_203402)	-95	NM_203402	161247	Hs.128060	NM_203402	ENSG00000139914	FITM1	FIT1	fat storage inducing transmembrane protein 1	protein-coding	0.020101	0.620000	
chunk0134_386_1	chr3	182889730	182890522	+	0	NA	intron (NM_014616, intron 25 of 29)	intron (NM_014616, intron 25 of 29)	90475	NM_020640	54165	Hs.592789	NM_020640	ENSG00000043093	DCUN1D1	DCNL1|DCUN1L1|RP42|SCCRO|SCRO|Tes3	defective in cullin neddylation 1 domain containing 1	protein-coding	0.003788	0.372005	413(GTTACACTGTGTTCTG,+,0.00)
chunk0204_96_1	chr9	94507896	94508277	+	0	NA	Intergenic	L1MA7|LINE|L1	-46959	NR_121566	101928099	Hs.674409	NR_121566		PCAT7	PCAN-R2	prostate cancer associated transcript 7	ncRNA	0.010499	0.390052	
chunk0142_272_1	chr4	99436485	99436990	+	0	NA	Intergenic	Intergenic	-1227	NM_000673	131	Hs.389	NM_000673	ENSG00000196344	ADH7	ADH4	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding	0.003960	0.337945	
chunk0089_329_1	chr18	65471069	65471500	+	0	NA	Intergenic	Intergenic	-278968	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.002320	0.324074	157(CAAAACATAGTGTACT,-,0.00),158(AAAACATAGTGTACTT,+,0.00)
chunk0024_381_1	chr10	44688457	44688722	+	0	NA	Intergenic	Intergenic	-222727	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.000000	0.293233	
chunk0195_101_1	chr8	94457241	94457466	+	0	NA	intron (NM_001205262, intron 3 of 3)	intron (NM_001205262, intron 3 of 3)	17762	NM_012415	25788	Hs.30561	NM_006550	ENSG00000197275	RAD54B	RDH54	RAD54 homolog B	protein-coding	0.004444	0.442478	
chunk0196_52_1	chr8	102030258	102030592	+	0	NA	intron (NM_001040628, intron 1 of 7)	L1MC5|LINE|L1	45993	NR_126152	104054148	Hs.683917	NR_126152		LOC104054148	-	uncharacterized LOC104054148	ncRNA	0.005988	0.340299	
chunk0001_140_1	chr1	5727143	5727990	+	0	NA	Intergenic	L2b|LINE|L2	135175	NR_039838	100616421		NR_039838	ENSG00000264101	MIR4689	mir-4689	microRNA 4689	ncRNA	0.005903	0.437500	219(GAGGACACAGTGTTCA,-,0.00),220(AGGACACAGTGTTCAC,+,0.00)
chunk0038_92_1	chr11	83410773	83411396	+	0	NA	Intergenic	Intergenic	-124677	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.000000	0.485577	293(CAGTACAGGCTGTTCT,-,0.00),294(AGTACAGGCTGTTCTT,+,0.00)
chunk0008_7_1	chr1	87213960	87214504	+	0	NA	intron (NM_001290053, intron 1 of 3)	intron (NM_001290053, intron 1 of 3)	1563	NM_001290053	101927844	Hs.694591	NM_001290053		LINC02801	-	long intergenic non-protein coding RNA 2801	protein-coding	0.007353	0.379817	244(AAGTACTGTGTGTTCC,-,0.00),245(AGTACTGTGTGTTCCA,+,0.00)
chunk0093_251_1	chr19	50880107	50880808	+	0	NA	non-coding (NR_045763, exon 5 of 5)	non-coding (NR_045763, exon 5 of 5)	7024	NR_045763	3817	Hs.515560	NM_005551	ENSG00000167751	KLK2	KLK2A2|hGK-1|hK2	kallikrein related peptidase 2	protein-coding	0.009986	0.448718	
chunk0167_254_1	chr6	69189524	69190063	+	0	NA	intron (NM_001704, intron 17 of 31)	intron (NM_001704, intron 17 of 31)	554053	NM_001704	577	Hs.13261	NM_001704	ENSG00000135298	ADGRB3	BAI3	adhesion G protein-coupled receptor B3	protein-coding	0.012987	0.350000	
chunk0084_45_1	chr17	74176973	74177295	+	0	NA	Intergenic	Intergenic	-26522	NM_001035258	6169	Hs.380953	NM_000999	ENSG00000172809	RPL38	L38	ribosomal protein L38	protein-coding	0.006211	0.557276	
chunk0043_238_1	chr12	20175655	20176486	+	0	NA	Intergenic	L1M7|LINE|L1	161385	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.004813	0.337740	490(ATTACATTCTGTTCTG,+,0.00)
chunk0057_395_1	chr13	109564497	109564841	+	0	NA	Intergenic	L1MD|LINE|L1	-163605	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.000000	0.315942	167(TGAAACACTGTGTGCT,-,0.00),168(GAAACACTGTGTGCTT,+,0.00)
chunk0060_438_1	chr14	54488781	54489166	+	0	NA	promoter-TSS (NM_004124)	promoter-TSS (NM_004124)	53	NM_004124	2764	Hs.151413	NM_004124	ENSG00000197045	GMFB	GMF	glia maturation factor beta	protein-coding	0.103896	0.652850	
chunk0131_323_1	chr3	151101257	151101456	+	0	NA	intron (NM_053002, intron 1 of 42)	MIR|SINE|MIR	14558	NM_053002	116931	Hs.744234	NM_053002	ENSG00000144893	MED12L	NOPAR|TNRC11L|TRALP|TRALPUSH	mediator complex subunit 12L	protein-coding	0.005025	0.435000	
chunk0128_204_1	chr3	107762486	107762808	+	0	NA	intron (NM_001276286, intron 10 of 16)	intron (NM_001276286, intron 10 of 16)	115421	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.006211	0.337461	
chunk0004_370_1	chr1	51639157	51639356	+	0	NA	intron (NM_148906, intron 1 of 22)	L1ME2|LINE|L1	22382	NM_148909	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.010050	0.460000	
chunk0037_438_1	chr11	80343636	80344069	+	0	NA	Intergenic	Intergenic	418951	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.002309	0.391705	
chunk0050_334_1	chr12	107400421	107400702	+	0	NA	intron (NM_001018072, intron 1 of 16)	MIR|SINE|MIR	82141	NM_001018072	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.010676	0.425532	
chunk0093_349_1	chr19	55027883	55028456	+	0	NA	intron (NM_001083899, intron 3 of 7).10	MIRb|SINE|MIR	10095	NM_001083899	51206	Hs.661752	NM_016363	ENSG00000088053	GP6	BDPLT11|GPIV|GPVI	glycoprotein VI platelet	protein-coding	0.010471	0.484321	
chunk0033_197_1	chr11	16487740	16488193	+	0	NA	Intergenic	Intergenic	-11578	NM_033326	55553	Hs.368226	NM_017508	ENSG00000110693	SOX6	HSSOX6|SOXD	SRY-box transcription factor 6	protein-coding	0.006623	0.345815	
chunk0056_138_1	chr13	83344387	83344979	+	0	NA	Intergenic	L1P4|LINE|L1	537710	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.003378	0.345700	
chunk0130_254_1	chr3	135884449	135884937	+	0	NA	Intergenic	Intergenic	-80980	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.006148	0.372188	225(TAGTACAAAATGTACT,-,0.00),226(AGTACAAAATGTACTG,+,0.00)
chunk0001_52_1	chr1	1894585	1894883	+	0	NA	Intergenic	Intergenic	-3617	NM_001282538	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.026846	0.652174	
chunk0085_181_1	chr18	5788064	5788317	+	0	NA	intron (NR_038839, intron 3 of 4)	LTR49-int|LTR|ERV1	39371	NR_038839	645355	Hs.632356	NR_038839	ENSG00000261738	MIR3976HG	LINC01469	MIR3976 host gene	ncRNA	0.003953	0.417323	
chunk0130_409_1	chr3	140488476	140488984	+	0	NA	intron (NM_022131, intron 8 of 16)	intron (NM_022131, intron 8 of 16)	20059	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.005906	0.387033	
chunk0044_12_1	chr12	27076944	27077752	+	0	NA	Intergenic	Intergenic	5174	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.007426	0.374536	
chunk0199_288_1	chr9	6658586	6659136	+	0	NA	Intergenic	Intergenic	-13169	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.005455	0.375681	
chunk0012_59_1	chr1	155521818	155522496	+	0	NA	intron (NM_018489, intron 1 of 27)	intron (NM_018489, intron 1 of 27)	-39824	NR_027023	645676	Hs.568693	NR_027023	ENSG00000235919	ASH1L-AS1	-	ASH1L antisense RNA 1	ncRNA	0.004425	0.310751	
chunk0141_165_1	chr4	82374288	82375074	+	0	NA	promoter-TSS (NM_002138)	promoter-TSS (NM_002138)	-685	NM_001003810	3184	Hs.480073	NM_002138	ENSG00000138668	HNRNPD	AUF1|AUF1A|HNRPD|P37|hnRNPD0	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.063613	0.504447	
chunk0098_235_1	chr2	74486285	74486601	+	0	NA	intron (NR_027749, intron 2 of 11)	L2a|LINE|L2	-3213	NM_032779	84865	Hs.430199	NM_032779	ENSG00000135637	CCDC142	-	coiled-coil domain containing 142	protein-coding	0.000000	0.403785	
chunk0182_138_1	chr7	94682884	94683458	+	0	NA	Intergenic	Intergenic	26846	NM_001172438	23089	Hs.147492	NM_015068	ENSG00000242265	PEG10	EDR|HB-1|MEF3L|Mar2|Mart2|RGAG3|RTL2|SIRH1	paternally expressed 10	protein-coding	0.005226	0.384348	
chunk0206_89_1	chr9	120618281	120618480	+	0	NA	intron (NM_001080497, intron 3 of 5)	L2|LINE|L2	-38210	NR_073554	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.000000	0.370000	
chunk0094_155_1	chr2	5214718	5215031	+	0	NA	Intergenic	L1MC4|LINE|L1	476244	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.012780	0.423567	
chunk0165_196_1	chr6	34595551	34596199	+	0	NA	intron (NM_022758, intron 3 of 3)	intron (NM_022758, intron 3 of 3)	-39542	NM_012391	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.007716	0.405239	
chunk0050_272_1	chr12	106205326	106205756	+	0	NA	Intergenic	LTR16C|LTR|ERVL	42394	NM_006825	10970	Hs.74368	NM_006825	ENSG00000136026	CKAP4	CLIMP-63|ERGIC-63|p63	cytoskeleton associated protein 4	protein-coding	0.009302	0.535963	
chunk0062_371_1	chr14	74207007	74207218	+	0	NA	Intergenic	Intergenic	-32360	NM_182894	338917	Hs.449771	NM_182894	ENSG00000119614	VSX2	CHX10|HOX10|MCOP2|MCOPCB3|RET1	visual system homeobox 2	protein-coding	0.014218	0.566038	
chunk0097_278_1	chr2	54990022	54990664	+	0	NA	intron (NM_153828, intron 1 of 6)	L1MA7|LINE|L1	19991	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.004673	0.284603	
chunk0009_255_1	chr1	107099940	107100517	+	0	NA	Intergenic	MIR|SINE|MIR	-39690	NM_014917	22854	Hs.133046	NM_014917	ENSG00000162631	NTNG1	Lmnt1	netrin G1	protein-coding	0.005199	0.326990	
chunk0091_256_1	chr19	10952843	10953175	+	0	NA	Intergenic	Intergenic	-7913	NM_001128844	6597	Hs.327527	NM_003072	ENSG00000127616	SMARCA4	BAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2L4|SNF2LB|SWI2|hSNF2b	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	protein-coding	0.012048	0.510511	
chunk0023_323_1	chr10	29191831	29192030	+	0	NA	Intergenic	Intergenic	-97131	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.015075	0.380000	
chunk0135_142_1	chr3	187409079	187409448	+	0	NA	Intergenic	L1MEc|LINE|L1	40883	NM_022147	64108	Hs.43388	NM_022147	ENSG00000136514	RTP4	IFRG28|Z3CXXC4	receptor transporter protein 4	protein-coding	0.002710	0.389189	
chunk0196_140_1	chr8	104416962	104417453	+	0	NA	intron (NM_001385, intron 7 of 9)	intron (NM_001385, intron 7 of 9)	49842	NM_001385	1807	Hs.443161	NM_001385	ENSG00000147647	DPYS	DHP|DHPase	dihydropyrimidinase	protein-coding	0.008147	0.369919	
chunk0078_23_1	chr17	794813	795143	+	0	NA	Intergenic	Intergenic	-12647	NM_016080	51031	Hs.279061	NM_016080	ENSG00000167699	GLOD4	C17orf25|CGI-150|HC71	glyoxalase domain containing 4	protein-coding	0.033333	0.501511	
chunk0194_67_1	chr8	82501854	82502252	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-659767	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.005025	0.401003	163(CAGATCATCCTGTTCC,-,0.00),164(AGATCATCCTGTTCCA,+,0.00),208(ATGTACAGACTGTGCC,-,0.00),209(TGTACAGACTGTGCCT,+,0.00)
chunk0083_172_1	chr17	66275526	66275996	+	0	NA	Intergenic	Intergenic	-27047	NM_002737	5578	Hs.531704	NM_002737	ENSG00000154229	PRKCA	AAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACA	protein kinase C alpha	protein-coding	0.010638	0.460722	
chunk0193_210_1	chr8	76266506	76266705	+	0	NA	Intergenic	MIRb|SINE|MIR	-140049	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.005025	0.310000	
chunk0144_266_1	chr4	137206955	137207432	+	0	NA	Intergenic	Intergenic	325305	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.341004	
chunk0044_73_1	chr12	28013995	28014564	+	0	NA	Intergenic	Intergenic	-42296	NM_002820	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.003515	0.398246	
chunk0037_361_1	chr11	78079762	78080036	+	0	NA	5' UTR (NM_001203262, exon 1 of 3)	5' UTR (NM_001203262, exon 1 of 3)	320	NM_001204055	4718	Hs.407860	NM_004549	ENSG00000151366	NDUFC2	B14.5b|CI-B14.5b|HLC-1|NADHDH2	NADH:ubiquinone oxidoreductase subunit C2	protein-coding	0.109489	0.636364	
chunk0036_230_1	chr11	64106179	64106671	+	0	NA	intron (NM_013280, intron 1 of 1)	L2a|LINE|L2	2535	NM_013280	23769	Hs.584876	NM_013280	ENSG00000126500	FLRT1	SPG68	fibronectin leucine rich transmembrane protein 1	protein-coding	0.004065	0.557809	235(GAGCACTTTCTGTGCC,-,0.00),236(AGCACTTTCTGTGCCA,+,0.00)
chunk0002_47_1	chr1	12677547	12677990	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	33221	NM_001013630	343066	Hs.209954	NM_001013630	ENSG00000204518	AADACL4	-	arylacetamide deacetylase like 4	protein-coding	0.002257	0.466216	234(CAGAACACTGTGTACC,-,0.00),235(AGAACACTGTGTACCA,+,0.00)
chunk0155_209_1	chr5	95031673	95032090	+	0	NA	intron (NM_024717, intron 1 of 22)	L1PA17|LINE|L1	49985	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.009592	0.361244	
chunk0116_82_1	chr21	34730182	34730632	+	0	NA	intron (NR_024351, intron 4 of 5)	L3b|LINE|CR1	6775	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.015556	0.410200	
chunk0140_262_1	chr4	71586258	71586667	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	197900	NM_000583	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.009780	0.363415	
chunk0156_350_1	chr5	112012227	112012435	+	0	NA	intron (NR_046678, intron 3 of 3)	intron (NR_046678, intron 3 of 3)	-35400	NM_001142475	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.004808	0.368421	
chunk0069_234_1	chr15	64005350	64005549	+	0	NA	intron (NM_014326, intron 2 of 11)	intron (NM_014326, intron 2 of 11)	40873	NM_014326	23604	Hs.237886	NM_014326	ENSG00000035664	DAPK2	DRP-1|DRP1	death associated protein kinase 2	protein-coding	0.005025	0.480000	
chunk0118_404_1	chr22	37933736	37934314	+	0	NA	intron (NM_033386, intron 13 of 15)	intron (NM_033386, intron 13 of 15)	19622	NM_032561	84645	Hs.517612	NM_032561	ENSG00000128346	C22orf23	EVG1|dJ1039K5.6	chromosome 22 open reading frame 23	protein-coding	0.020761	0.614853	
chunk0201_14_1	chr9	33013141	33013421	+	0	NA	Intergenic	MIR|SINE|MIR	-11640	NM_175069	54840	Hs.20158	NM_017692	ENSG00000137074	APTX	AOA|AOA1|AXA1|EAOH|EOAHA|FHA-HIT	aprataxin	protein-coding	0.003571	0.362989	
chunk0167_382_1	chr6	73893533	73894017	+	0	NA	Intergenic	L1MA6|LINE|L1	-175676	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.004132	0.329897	
chunk0155_328_1	chr5	96807510	96807723	+	0	NA	intron (NM_001198541, intron 1 of 18)	CpG	573	NM_016442	51752	Hs.666524	NM_016442	ENSG00000164307	ERAP1	A-LAP|ALAP|APPILS|ARTS-1|ARTS1|ERAAP|ERAAP1|PILS-AP|PILSAP	endoplasmic reticulum aminopeptidase 1	protein-coding	0.145540	0.794393	
chunk0054_267_1	chr13	46565916	46566356	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	12975	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.004545	0.417234	
chunk0082_350_1	chr17	60037383	60037628	+	0	NA	Intergenic	L1MD2|LINE|L1	5600	NR_039890	100616210		NR_039890	ENSG00000264049	MIR4737	-	microRNA 4737	ncRNA	0.012245	0.495935	
chunk0054_276_1	chr13	46655482	46655690	+	0	NA	intron (NM_001164213, intron 2 of 18)	intron (NM_001164213, intron 2 of 18)	102425	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.000000	0.349282	
chunk0118_259_1	chr22	33094304	33094914	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-36218	NM_001135774	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.019672	0.454992	
chunk0151_65_1	chr5	42506020	42506219	+	0	NA	intron (NM_001242401, intron 2 of 10)	intron (NM_001242401, intron 2 of 10)	-41924	NM_001242402	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.010050	0.345000	
chunk0105_207_1	chr2	187853354	187853897	+	0	NA	Intergenic	L1MC1|LINE|L1	-299133	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.001842	0.334559	
chunk0095_374_1	chr2	23493087	23493510	+	0	NA	intron (NM_052920, intron 2 of 13)	intron (NM_052920, intron 2 of 13)	107871	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.014184	0.431604	
chunk0003_157_1	chr1	33240394	33240935	+	0	NA	Intergenic	MER97c|DNA|hAT-Tip100	-15909	NM_152493	149076	Hs.743358	NM_152493	ENSG00000160094	ZNF362	RN|lin-29	zinc finger protein 362	protein-coding	0.009242	0.378229	
chunk0016_187_1	chr1	198233055	198233315	+	0	NA	intron (NM_133494, intron 2 of 9)	intron (NM_133494, intron 2 of 9)	76207	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.003846	0.379310	80(CAGTACATTTTGTACC,-,0.00),81(AGTACATTTTGTACCT,+,0.00)
chunk0054_345_1	chr13	49490713	49490914	+	0	NA	intron (NM_001160308, intron 11 of 12)	intron (NM_001160308, intron 11 of 12)	-4852	NM_001040443	51131	Hs.369039	NM_001040443	ENSG00000136147	PHF11	APY|BCAP|IGEL|IGER|IGHER|NY-REN-34|NYREN34	PHD finger protein 11	protein-coding	0.000000	0.331683	131(TGGTACAGAATGTTTT,-,0.00),132(GGTACAGAATGTTTTT,+,0.00)
chunk0080_404_1	chr17	35463335	35463673	+	0	NA	Intergenic	LTR57|LTR|ERVL	-14667	NM_144682	146857	Hs.462833	NM_144682	ENSG00000154760	SLFN13	SLFN10|hSLFN13	schlafen family member 13	protein-coding	0.008876	0.477876	
chunk0080_259_1	chr17	30599150	30599349	+	0	NA	intron (NR_015341, intron 1 of 8)	intron (NR_015341, intron 1 of 8)	22784	NR_015341	107133515	Hs.568209	NR_015341		SMURF2P1-LRRC37BP1	-	SMURF2P1-LRRC37BP1 readthrough transcribed pseudogene	pseudo	0.015075	0.315000	
chunk0138_145_1	chr4	37014414	37014723	+	0	NA	Intergenic	L1ME1|LINE|L1	227423	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.000000	0.296774	
chunk0183_442_1	chr7	111192682	111193343	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	102006	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.003026	0.418429	
chunk0069_372_1	chr15	67268327	67268633	+	0	NA	intron (NM_022784, intron 3 of 5)	intron (NM_022784, intron 3 of 5)	-13282	NM_001271885	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.003268	0.361564	130(CTGCTCACACTGTTCT,-,0.00),131(TGCTCACACTGTTCTT,+,0.00)
chunk0100_294_1	chr2	114909568	114910020	+	0	NA	intron (NM_001178036, intron 2 of 26)	L1MEd|LINE|L1	-76246	NR_132105	101927591	Hs.553019	NR_132105	ENSG00000231538	DPP10-AS3	-	DPP10 antisense RNA 3	ncRNA	0.006637	0.350993	
chunk0197_7_1	chr8	116865090	116865573	+	0	NA	intron (NM_006265, intron 2 of 13)	intron (NM_006265, intron 2 of 13)	-9093	NR_033886	644660	Hs.706174	NR_033886	ENSG00000253327	RAD21-AS1	C8orf81|NCRNA00255	RAD21 antisense RNA 1	ncRNA	0.012422	0.336777	
chunk0046_341_1	chr12	62912412	62913166	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	22096	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.006631	0.421192	150(ATGTACAGAATGTACA,-,0.00)
chunk0120_13_1	chr3	1184749	1185192	+	0	NA	intron (NM_001289080, intron 2 of 22)	intron (NM_001289080, intron 2 of 22)	92312	NM_014461	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.004515	0.288288	202(AGGAACAAGCTGTACT,-,0.00),203(GGAACAAGCTGTACTC,+,0.00)
chunk0053_159_1	chr13	30403420	30404034	+	0	NA	Intergenic	Intergenic	18517	NR_125771	103724387		NR_125771	ENSG00000225039	LINC01058	-	long intergenic non-protein coding RNA 1058	ncRNA	0.014658	0.426016	
chunk0051_175_1	chr12	116099297	116099909	+	0	NA	intron (NM_015335, intron 3 of 30)	intron (NM_015335, intron 3 of 30)	49051	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.009804	0.357259	
chunk0099_169_1	chr2	88666628	88667181	+	0	NA	Intergenic	Intergenic	-24754	NM_144563	22934	Hs.469264	NM_144563	ENSG00000153574	RPIA	RPI|RPIAD	ribose 5-phosphate isomerase A	protein-coding	0.009042	0.525271	
chunk0113_194_1	chr20	53425823	53426267	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	-126725	NR_110051	101927770		NR_110051		LOC101927770	-	uncharacterized LOC101927770	ncRNA	0.006757	0.379775	
chunk0159_144_1	chr5	139168068	139168651	+	0	NA	intron (NM_022464, intron 1 of 9)	L1M4c|LINE|L1	30017	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.005146	0.426370	384(AAGAACACTGTCTTCC,-,0.00)
chunk0212_421_1	chrX	152863589	152864001	+	0	NA	intron (NM_015922, intron 5 of 7)	intron (NM_015922, intron 5 of 7)	32828	NM_001129765	50814	Hs.57698	NM_015922	ENSG00000147383	NSDHL	H105E3|SDR31E1|XAP104	NAD(P) dependent steroid dehydrogenase-like	protein-coding	0.019417	0.547215	246(CGGTACATGCTGTACT,-,0.00),247(GGTACATGCTGTACTG,+,0.00)
chunk0161_336_1	chr5	173926047	173926701	+	0	NA	intron (NM_001308191, intron 2 of 7)	intron (NM_001308191, intron 2 of 7)	33323	NM_001308193	80315	Hs.127126	NM_030627	ENSG00000113742	CPEB4	CPE-BP4|hCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding	0.004587	0.369466	316(TAGTACATACTGTTCT,-,0.00),317(AGTACATACTGTTCTT,+,0.00)
chunk0105_346_1	chr2	191358345	191358928	+	0	NA	intron (NM_001130158, intron 7 of 30)	intron (NM_001130158, intron 7 of 30)	113108	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.017153	0.438356	
chunk0001_109_1	chr1	3547465	3547678	+	0	NA	intron (NM_001409, intron 4 of 36)	intron (NM_001409, intron 4 of 36)	13219	NR_030277	693135		NR_030277	ENSG00000207776	MIR551A	MIRN551A|mir-551a	microRNA 551a	ncRNA	0.046948	0.635514	
chunk0167_440_1	chr6	75870251	75870920	+	0	NA	intron (NM_001300899, intron 18 of 32)	intron (NM_001300899, intron 18 of 32)	121393	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.001495	0.286567	339(ATGACACTGTGTACTT,+,0.00)
chunk0010_257_1	chr1	116632461	116632820	+	0	NA	intron (NM_001007237, intron 2 of 10)	intron (NM_001007237, intron 2 of 10)	34316	NM_001542	3321	Hs.171057	NM_001542	ENSG00000143061	IGSF3	EWI-3|LCDD|V8	immunoglobulin superfamily member 3	protein-coding	0.019499	0.480556	
chunk0189_318_1	chr8	26204192	26204761	+	0	NA	Intergenic	Intergenic	-87015	NM_002717	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.024605	0.456140	
chunk0072_99_1	chr15	91065407	91065861	+	0	NA	Intergenic	L2b|LINE|L2	-34318	NM_001167580	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.008811	0.509890	198(CAGGACTTGATGTGCT,-,0.00),199(AGGACTTGATGTGCTT,+,0.00)
chunk0070_39_1	chr15	69467618	69468226	+	0	NA	Intergenic	Intergenic	15102	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.019737	0.492611	
chunk0152_189_1	chr5	59812626	59813492	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-44447	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004619	0.389850	
chunk0131_41_1	chr3	142577609	142577963	+	0	NA	intron (NM_001184, intron 1 of 46)	intron (NM_001184, intron 1 of 46)	1040	NM_001184	545	Hs.271791	NM_001184	ENSG00000175054	ATR	FCTCS|FRP1|MEC1|SCKL|SCKL1	ATR serine/threonine kinase	protein-coding	0.011299	0.400000	
chunk0142_278_1	chr4	99617516	99618071	+	0	NA	intron (NM_001300785, intron 15 of 17)	intron (NM_001300785, intron 15 of 17)	53715	NM_000253	4547	Hs.195799	NM_000253	ENSG00000138823	MTTP	ABL|MTP	microsomal triglyceride transfer protein	protein-coding	0.007207	0.366906	
chunk0043_374_1	chr12	24308135	24308334	+	0	NA	intron (NM_152989, intron 3 of 17)	MER50|LTR|ERV1	84963	NR_120472	101928471	Hs.569156	NR_120472	ENSG00000256120	SOX5-AS1	-	SOX5 antisense RNA 1	ncRNA	0.020101	0.520000	70(GTGAACACACTGCTCC,-,0.00),71(TGAACACACTGCTCCC,+,0.00)
chunk0172_432_1	chr6	140772682	140772932	+	0	NA	Intergenic	Intergenic	88993	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.004000	0.346614	
chunk0089_202_1	chr18	60471488	60471925	+	0	NA	Intergenic	Intergenic	-98938	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.000000	0.390411	
chunk0179_368_1	chr7	51140670	51141020	+	0	NA	intron (NM_001287436, intron 5 of 13)	intron (NM_001287436, intron 5 of 13)	175973	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.020000	0.498575	87(GAGTGCAGGGTGTTCC,-,0.00),88(AGTGCAGGGTGTTCCT,+,0.00),134(GAGAACACGTTGTCTC,-,0.00),135(AGAACACGTTGTCTCC,+,0.00),332(GGATCAATCTGTTCAT,+,0.00)
chunk0022_456_1	chr10	19979854	19980441	+	0	NA	intron (NM_032812, intron 1 of 13)	intron (NM_032812, intron 1 of 13)	163704	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.005111	0.355442	
chunk0208_415_1	chrX	29542655	29543349	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-31276	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.005764	0.375540	
chunk0187_460_1	chr7	159330353	159330833	+	0	NA	Intergenic	Intergenic	-185636	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.008333	0.384615	
chunk0098_95_1	chr2	67845991	67846427	+	0	NA	Intergenic	Intergenic	-20647	NR_110271	101927701	Hs.348697	NR_110271	ENSG00000237013	LINC01812	-	long intergenic non-protein coding RNA 1812	ncRNA	0.009174	0.432494	
chunk0168_355_1	chr6	93207287	93207835	+	0	NA	Intergenic	L1M2|LINE|L1	212021	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.003650	0.393443	253(AAGGACAGTATCTTCC,-,0.00),254(AGGACAGTATCTTCCT,+,0.00)
chunk0033_221_1	chr11	17308041	17308259	+	0	NA	intron (NM_005013, intron 5 of 13)	L1MC4|LINE|L1	-23892	NR_132751	4925	Hs.654599	NM_005013	ENSG00000070081	NUCB2	HEL-S-109|NEFA	nucleobindin 2	protein-coding	0.000000	0.392694	
chunk0116_47_1	chr21	33678187	33678552	+	0	NA	intron (NM_001001132, intron 1 of 29)	L2a|LINE|L2	35891	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.008219	0.439891	240(GAGGACACTCTGTTTT,-,0.00),241(AGGACACTCTGTTTTG,+,0.00)
chunk0017_113_1	chr1	205983879	205984078	+	0	NA	intron (NM_001304839, intron 4 of 4)	intron (NM_001304839, intron 4 of 4)	10461	NM_177403	338382	Hs.534612	NM_177403	ENSG00000276600	RAB7B	RAB7	RAB7B, member RAS oncogene family	protein-coding	0.010050	0.495000	
chunk0039_1_1	chr11	94880197	94880587	+	0	NA	Intergenic	Intergenic	93220	NM_016403	51503	Hs.503597	NM_016403	ENSG00000150316	CWC15	AD002|C11orf5|Cwf15|HSPC148|ORF5	CWC15 spliceosome associated protein homolog	protein-coding	0.007692	0.424552	
chunk0028_314_1	chr10	91788528	91788909	+	0	NA	intron (NR_108071, intron 1 of 1)	L1MA3|LINE|L1	9478	NR_108070	100507633	Hs.291528	NR_108070	ENSG00000228701	TNKS2-AS1	-	TNKS2 antisense RNA 1 (head to head)	ncRNA	0.010499	0.520942	
chunk0087_151_1	chr18	34631552	34632081	+	0	NA	intron (NM_001128175, intron 1 of 11)	intron (NM_001128175, intron 1 of 11)	38498	NM_001198940	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.003781	0.324528	
chunk0058_294_1	chr14	26863162	26863623	+	0	NA	Intergenic	Intergenic	-9741	NR_110041	101927081	Hs.97955	NR_110041	ENSG00000257612	MIR4307HG	-	MIR4307 host gene	ncRNA	0.000000	0.294372	
chunk0144_84_1	chr4	128168632	128168970	+	0	NA	intron (NM_018078, intron 12 of 19)	L1ME1|LINE|L1	107535	NM_001278604	55132	Hs.654971	NM_018078	ENSG00000138709	LARP1B	LARP2	La ribonucleoprotein domain family member 1B	protein-coding	0.002959	0.324484	
chunk0191_353_1	chr8	56439705	56439904	+	0	NA	Intergenic	Intergenic	-6003	NR_125813	101929415	Hs.701520	NR_125813	ENSG00000254254	LOC101929415	-	uncharacterized LOC101929415	ncRNA	0.020101	0.540000	
chunk0105_275_1	chr2	189555965	189556336	+	0	NA	Intergenic	Intergenic	24661	NM_014585	30061	Hs.643005	NM_014585	ENSG00000138449	SLC40A1	FPN1|HFE4|IREG1|MST079|MSTP079|MTP1|SLC11A3	solute carrier family 40 member 1	protein-coding	0.005391	0.435484	
chunk0060_432_1	chr14	54333564	54333798	+	0	NA	Intergenic	Intergenic	-63274	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.000000	0.370213	
chunk0043_232_1	chr12	20011100	20011564	+	0	NA	Intergenic	Intergenic	-3353	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.008621	0.354839	
chunk0184_137_1	chr7	115649309	115649910	+	0	NA	Intergenic	LTR40a|LTR|ERVL	318704	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.003328	0.382060	
chunk0044_363_1	chr12	39284716	39284915	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	158575	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.005025	0.450000	
chunk0183_380_1	chr7	109660000	109660301	+	0	NA	Intergenic	Intergenic	300063	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.003322	0.344371	
chunk0011_89_1	chr1	145542701	145542909	+	0	NA	Intergenic	Intergenic	65053	NR_104217	101929780	Hs.534675	NR_104217	ENSG00000272150	NBPF25P	WI2-925H4.1	NBPF member 25, pseudogene	pseudo	0.000000	0.320574	
chunk0090_395_1	chr18	77769444	77769661	+	0	NA	Intergenic	Intergenic	224175	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.013825	0.582569	
chunk0160_99_1	chr5	150436598	150436827	+	0	NA	Intergenic	L2a|LINE|L2	13044	NM_001025071	6208	Hs.744846	NM_005617	ENSG00000164587	RPS14	EMTB|S14	ribosomal protein S14	protein-coding	0.021834	0.443478	
chunk0108_334_1	chr2	235715202	235715904	+	0	NA	intron (NM_001037131, intron 2 of 17)	intron (NM_001037131, intron 2 of 17)	209802	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.015670	0.557610	372(GGAGACAGTTTGTTCC,-,0.00),373(GAGACAGTTTGTTCCT,+,0.00)
chunk0201_187_1	chr9	36392124	36392509	+	0	NA	intron (NM_194330, intron 1 of 11)	intron (NM_194330, intron 1 of 11)	7983	NM_022781	152006	Hs.333503	NM_022781	ENSG00000137075	RNF38	-	ring finger protein 38	protein-coding	0.005195	0.380829	189(CTGTACAGAATGTTCT,-,0.00),190(TGTACAGAATGTTCTG,+,0.00)
chunk0163_118_1	chr6	10258400	10258660	+	0	NA	Intergenic	L1MC1|LINE|L1	-153788	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003846	0.379310	
chunk0064_436_1	chr14	99956537	99956924	+	0	NA	Intergenic	L1M5|LINE|L1	-108684	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.007752	0.376289	
chunk0166_248_1	chr6	47455742	47455941	+	0	NA	Intergenic	Intergenic	-21948	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.000000	0.395000	
chunk0151_143_1	chr5	45646495	45647024	+	0	NA	intron (NM_021072, intron 1 of 7)	intron (NM_021072, intron 1 of 7)	49359	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.003781	0.296226	
chunk0203_124_1	chr9	85108245	85108498	+	0	NA	Intergenic	Intergenic	437994	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.015810	0.503937	
chunk0038_173_1	chr11	85581605	85582117	+	0	NA	intron (NM_001142699, intron 3 of 27)	L2a|LINE|L2	45409	NM_001142699	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.005859	0.372320	
chunk0067_170_1	chr15	44102574	44103198	+	0	NA	intron (NM_001286490, intron 1 of 15)	UCON8|DNA|DNA	91560	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.000000	0.440000	
chunk0034_31_1	chr11	26465543	26465743	+	0	NA	intron (NM_031418, intron 4 of 26)	intron (NM_031418, intron 4 of 26)	-8259	NM_001313727	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.005000	0.313433	
chunk0144_205_1	chr4	133914970	133915169	+	0	NA	Intergenic	L1MEd|LINE|L1	286679	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.005025	0.255000	
chunk0158_11_1	chr5	125207915	125208152	+	0	NA	intron (NR_109882, intron 4 of 5)	intron (NR_109882, intron 4 of 5)	171202	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.000000	0.323529	
chunk0038_407_1	chr11	93876549	93876774	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-26159	NM_001144871	387804	Hs.512252	NM_001144871	ENSG00000214376	VSTM5	C11orf90	V-set and transmembrane domain containing 5	protein-coding	0.000000	0.358407	
chunk0179_431_1	chr7	52044001	52044229	+	0	NA	Intergenic	L1ME3A|LINE|L1	-727297	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.013158	0.314410	
chunk0082_201_1	chr17	56837503	56837709	+	0	NA	intron (NM_003647, intron 2 of 11)	intron (NM_003647, intron 2 of 11)	3507	NM_003647	8526	Hs.239514	NM_003647	ENSG00000153933	DGKE	AHUS7|DAGK5|DAGK6|DGK|NPHS7	diacylglycerol kinase epsilon	protein-coding	0.000000	0.367150	22(GAGACCACAGTGTCCT,-,0.00),23(AGACCACAGTGTCCTG,+,0.00)
chunk0076_302_1	chr16	70250226	70250449	+	0	NA	3' UTR (NM_058219, exon 1 of 1)	3' UTR (NM_058219, exon 1 of 1)	1593	NM_058219	118460	Hs.660633	NM_058219	ENSG00000223496	EXOSC6	EAP4|MTR3|Mtr3p|hMtr3p|p11	exosome component 6	protein-coding	0.026906	0.441964	
chunk0186_268_1	chr7	141649762	141650402	+	0	NA	intron (NM_018238, intron 14 of 15)	intron (NM_018238, intron 14 of 15)	52071	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.004687	0.421217	64(CAGTTCACCATGTCCT,-,0.00),65(AGTTCACCATGTCCTC,+,0.00)
chunk0130_388_1	chr3	140015063	140015814	+	0	NA	intron (NM_022131, intron 1 of 16)	L2a|LINE|L2	80253	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.003995	0.476064	
chunk0108_272_1	chr2	234464013	234464324	+	0	NA	Intergenic	Intergenic	32881	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.038585	0.487179	
chunk0136_184_1	chr4	6728559	6729560	+	0	NA	Intergenic	Intergenic	12944	NM_018366	55330	Hs.7570	NM_018366	ENSG00000186222	BLOC1S4	BCAS4L|BLOS4|CNO	biogenesis of lysosomal organelles complex 1 subunit 4	protein-coding	0.016983	0.556886	229(CAGGACAGTGTGGGCT,-,0.00),230(AGGACAGTGTGGGCTC,+,0.00)
chunk0173_148_1	chr6	144134720	144135335	+	0	NA	Intergenic	L1MC2|LINE|L1	-15490	NM_003764	8676	Hs.118958	NM_003764	ENSG00000135604	STX11	FHL4|HLH4|HPLH4	syntaxin 11	protein-coding	0.004878	0.319805	
chunk0199_428_1	chr9	13732294	13732501	+	0	NA	Intergenic	L2c|LINE|L2	-195574	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.000000	0.427885	
chunk0169_180_1	chr6	102347745	102347949	+	0	NA	Intergenic	L1PA12|LINE|L1	948862	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.400000	
chunk0165_352_1	chr6	38069137	38069573	+	0	NA	intron (NM_021943, intron 3 of 5)	intron (NM_021943, intron 3 of 5)	249824	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.004587	0.347826	
chunk0129_91_1	chr3	119345954	119346322	+	0	NA	intron (NM_020754, intron 1 of 11)	intron (NM_020754, intron 1 of 11)	-23378	NR_046748	100874246	Hs.607097	NR_046748	ENSG00000241155	ARHGAP31-AS1	-	ARHGAP31 antisense RNA 1	ncRNA	0.002717	0.504065	
chunk0045_349_1	chr12	51489725	51490082	+	0	NA	exon (NM_001258401, exon 19 of 25)	exon (NM_001258401, exon 19 of 25)	64786	NM_001258403	9498	Hs.4749	NM_004858	ENSG00000050438	SLC4A8	NBC3|NDCBE	solute carrier family 4 member 8	protein-coding	0.005602	0.480447	
chunk0205_412_1	chr9	114928988	114929450	+	0	NA	intron (NM_001252290, intron 1 of 4)	intron (NM_001252290, intron 1 of 4)	1376	NM_001244	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.008658	0.360691	271(CTGTACAGTGTGTACC,-,0.00),272(TGTACAGTGTGTACCC,+,0.00)
chunk0013_21_1	chr1	166032743	166033141	+	0	NA	Intergenic	Intergenic	121856	NR_030626	100126349		NR_030626	ENSG00000215952	MIR921	MIRN921|hsa-mir-921	microRNA 921	ncRNA	0.007538	0.516291	222(GTGACATGCTGTTCCT,+,0.00)
chunk0052_268_1	chr12	124130530	124131165	+	0	NA	intron (NM_001204299, intron 2 of 4)	intron (NM_001204299, intron 2 of 4)	157632	NM_001204298	144348	Hs.524828	NM_152437	ENSG00000179195	ZNF664	ZFOC1|ZNF176	zinc finger protein 664	protein-coding	0.012598	0.490566	
chunk0153_364_1	chr5	74527626	74528328	+	0	NA	intron (NR_126354, intron 1 of 2)	intron (NR_126354, intron 1 of 2)	8999	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.008547	0.492176	
chunk0106_59_1	chr2	196403253	196403786	+	0	NA	intron (NM_020760, intron 2 of 28)	intron (NM_020760, intron 2 of 28)	-41395	NM_001304840	57520	Hs.633212	NM_020760	ENSG00000138411	HECW2	NDHSAL|NEDL2	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.003752	0.352060	
chunk0029_34_1	chr10	96124387	96124935	+	0	NA	Intergenic	L1M4c|LINE|L1	-5054	NM_014803	9849	Hs.600823	NM_014803	ENSG00000177853	ZNF518A	ZNF518	zinc finger protein 518A	protein-coding	0.007299	0.510018	
chunk0126_27_1	chr3	73666649	73666903	+	0	NA	Intergenic	Intergenic	-41855	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.003937	0.349020	
chunk0158_46_1	chr5	125913533	125913878	+	0	NA	Intergenic	L1MA3|LINE|L1	-265872	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.002899	0.514451	
chunk0063_50_1	chr14	77007854	77008348	+	0	NA	Intergenic	Intergenic	20598	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.002024	0.595960	
chunk0167_388_1	chr6	74618425	74618624	+	0	NA	intron (NR_110856, intron 2 of 3)	intron (NR_110856, intron 2 of 3)	549073	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.010050	0.490000	
chunk0012_256_1	chr1	161389809	161390008	+	0	NA	Intergenic	CpG	-22025	NM_001013625	257177	Hs.534593	NM_001013625	ENSG00000188931	CFAP126	C1orf192|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding	0.100503	0.625000	
chunk0100_186_1	chr2	110796687	110797119	+	0	NA	intron (NM_001142807, intron 5 of 17)	intron (NM_001142807, intron 5 of 17)	64330	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.006944	0.448037	
chunk0005_317_1	chr1	60715903	60716494	+	0	NA	intron (NR_110628, intron 4 of 5)	L1MC1|LINE|L1	109386	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.003384	0.354730	
chunk0192_281_1	chr8	66317140	66317470	+	0	NA	Intergenic	L1MD1|LINE|L1	111672	NR_040434	100505676	Hs.121613	NM_001242759	ENSG00000246145	RRS1-AS1	-	RRS1 antisense RNA 1 (head to head)	ncRNA	0.012121	0.392749	
chunk0025_299_1	chr10	57168952	57169384	+	0	NA	Intergenic	L1PA15|LINE|L1	135391	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.009259	0.351039	239(TAGTACTGTATGTCCT,-,0.00),240(AGTACTGTATGTCCTA,+,0.00)
chunk0140_268_1	chr4	72003084	72003497	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-28514	NM_004885	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.004843	0.328502	
chunk0045_251_1	chr12	49130532	49130771	+	0	NA	intron (NM_006082, intron 1 of 3)	CpG	870	NM_006082	10376	Hs.524390	NM_006082	ENSG00000123416	TUBA1B	K-ALPHA-1	tubulin alpha 1b	protein-coding	0.033473	0.508333	
chunk0055_319_1	chr13	68475570	68475842	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	409619	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.003676	0.333333	
chunk0110_78_1	chr20	11157420	11158388	+	0	NA	Intergenic	Intergenic	115479	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.008264	0.357069	
chunk0095_238_1	chr2	19126647	19127022	+	0	NA	Intergenic	Intergenic	-221595	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.013333	0.484043	167(GTGTACAAAGTGTGCC,-,0.00),168(TGTACAAAGTGTGCCT,+,0.00)
chunk0113_426_1	chr20	62202117	62202590	+	0	NA	3' UTR (NM_015666, exon 7 of 7)	3' UTR (NM_015666, exon 7 of 7)	17914	NM_007232	11255	Hs.251399	NM_007232	ENSG00000101180	HRH3	GPCR97|HH3R	histamine receptor H3	protein-coding	0.012685	0.554852	
chunk0209_239_1	chrX	45328401	45328744	+	0	NA	Intergenic	L1MD2|LINE|L1	-127671	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.002915	0.360465	
chunk0126_88_1	chr3	74740517	74740779	+	0	NA	Intergenic	L1M4|LINE|L1	-219508	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.007634	0.296578	154(GTGAACTCCCTGTTCT,-,0.00),155(TGAACTCCCTGTTCTG,+,0.00)
chunk0049_29_1	chr12	89660474	89660736	+	0	NA	Intergenic	L3|LINE|CR1	-4538	NM_001682	490	Hs.506276	NM_001682	ENSG00000070961	ATP2B1	PMCA1|PMCA1kb	ATPase plasma membrane Ca2+ transporting 1	protein-coding	0.003817	0.361217	
chunk0205_162_1	chr9	108607617	108607957	+	0	NA	Intergenic	MIRb|SINE|MIR	248208	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.011765	0.410557	
chunk0088_78_1	chr18	44715395	44715796	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	34697	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.004988	0.395522	
chunk0075_221_1	chr16	52805689	52806154	+	0	NA	Intergenic	Intergenic	-198946	NR_033920	643714	Hs.662199	NR_033920	ENSG00000249231	CASC16	LINC00918	cancer susceptibility 16	ncRNA	0.004301	0.461373	341(GGGTCAAAGTGTTCTG,+,0.00)
chunk0155_240_1	chr5	95664476	95665039	+	0	NA	intron (NR_125330, intron 2 of 7)	intron (NR_125330, intron 2 of 7)	17878	NM_001131065	317671	Hs.399758	NM_173362	ENSG00000175449	RFESD	-	Rieske Fe-S domain containing	protein-coding	0.008881	0.367021	400(ATGCACATAATGTTCA,-,0.00),401(TGCACATAATGTTCAT,+,0.00)
chunk0141_113_1	chr4	79665576	79666252	+	0	NA	Intergenic	Intergenic	-161557	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.002959	0.289513	
chunk0091_59_1	chr19	4815645	4816306	+	0	NA	TTS (NM_182919)	TTS (NM_182919)	15767	NM_182919	148022	Hs.29344	NM_014261	ENSG00000127666	TICAM1	IIAE6|MyD88-3|PRVTIRB|TICAM-1|TRIF	toll like receptor adaptor molecule 1	protein-coding	0.040847	0.546828	
chunk0148_14_1	chr5	271279	271790	+	0	NA	promoter-TSS (NM_001267559)	promoter-TSS (NM_001267559)	-10	NR_104613	102467073	Hs.368328	NR_104613		HRAT5	-	heart tissue-associated transcript 5	ncRNA	0.084149	0.664062	
chunk0069_378_1	chr15	67405569	67406053	+	0	NA	non-coding (NR_040052, exon 6 of 6)	non-coding (NR_040052, exon 6 of 6)	115162	NR_040055	100506686	Hs.656245	NR_040051	ENSG00000259673	IQCH-AS1	-	IQCH antisense RNA 1	ncRNA	0.004132	0.470103	
chunk0030_170_1	chr10	114142075	114142527	+	0	NA	intron (NM_018017, intron 6 of 15)	intron (NM_018017, intron 6 of 15)	31878	NR_031747	100302224		NR_031747	ENSG00000284442	MIR2110	hsa-mir-2110|mir-2110	microRNA 2110	ncRNA	0.011062	0.437086	
chunk0103_43_1	chr2	159273050	159273611	+	0	NA	intron (NM_001128213, intron 4 of 10)	intron (NM_001128213, intron 4 of 10)	13222	NM_152528	151525	Hs.20848	NM_152528	ENSG00000196151	WDSUB1	UBOX6|WDSAM1	WD repeat, sterile alpha motif and U-box domain containing 1	protein-coding	0.007130	0.370107	
chunk0182_132_1	chr7	94509372	94509674	+	0	NA	promoter-TSS (NM_022900)	promoter-TSS (NM_022900)	-335	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.039735	0.590759	
chunk0131_16_1	chr3	142067862	142068507	+	0	NA	intron (NM_001178138, intron 3 of 13)	L1MC|LINE|L1	-39519	NM_006286	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.003101	0.359133	235(AGGACAGACAGCCCTG,+,0.00)
chunk0061_390_1	chr14	64514991	64515620	+	0	NA	intron (NR_110550, intron 3 of 3)	intron (NR_110550, intron 3 of 3)	-10092	NM_001304508	7597	Hs.654571	NM_006977	ENSG00000089775	ZBTB25	C14orf51|KUP|ZNF46	zinc finger and BTB domain containing 25	protein-coding	0.007949	0.363492	405(TAGAACATAAAGTTCA,-,0.00),406(AGAACATAAAGTTCAT,+,0.00)
chunk0165_284_1	chr6	36220220	36220443	+	0	NA	intron (NM_015695, intron 9 of 12)	intron (NM_015695, intron 9 of 12)	-22837	NM_173676	285848	Hs.407002	NM_173676	ENSG00000180316	PNPLA1	ARCI10|dJ50J22.1	patatin like phospholipase domain containing 1	protein-coding	0.013453	0.357143	
chunk0047_421_1	chr12	76106695	76107172	+	0	NA	Intergenic	Intergenic	-21900	NM_139207	4673	Hs.524599	NM_004537	ENSG00000187109	NAP1L1	NAP1|NAP1L|NRP	nucleosome assembly protein 1 like 1	protein-coding	0.010482	0.341004	
chunk0034_283_1	chr11	34667971	34668626	+	0	NA	Intergenic	Intergenic	35834	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.003053	0.449695	
chunk0190_224_1	chr8	35786959	35787604	+	0	NA	intron (NM_080872, intron 16 of 16)	intron (NM_080872, intron 16 of 16)	-76961	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.007752	0.391641	
chunk0163_331_1	chr6	15264972	15265279	+	0	NA	intron (NM_001267040, intron 1 of 17)	intron (NM_001267040, intron 1 of 17)	16270	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.013029	0.467532	
chunk0023_41_1	chr10	21241324	21241833	+	0	NA	Intergenic	Intergenic	67276	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.019646	0.484314	
chunk0097_334_1	chr2	57776586	57776787	+	0	NA	Intergenic	Intergenic	-130965	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.004975	0.341584	
chunk0154_81_1	chr5	77729367	77729923	+	0	NA	intron (NM_001297738, intron 1 of 2)	intron (NM_001297738, intron 1 of 2)	46716	NM_004607	6902	Hs.291212	NM_004607	ENSG00000171530	TBCA	-	tubulin folding cofactor A	protein-coding	0.003597	0.348294	
chunk0034_125_1	chr11	28357571	28357770	+	0	NA	Intergenic	Intergenic	119878	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.005025	0.385000	
chunk0037_432_1	chr11	80223564	80224061	+	0	NA	Intergenic	Intergenic	538991	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.010060	0.393574	
chunk0171_299_1	chr6	128598997	128599472	+	0	NA	Intergenic	MIR|SINE|MIR	-78560	NM_001291981	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.004211	0.361345	
chunk0196_109_1	chr8	103152147	103152505	+	0	NA	intron (NM_001024372, intron 1 of 1)	L2b|LINE|L2	-2288	NR_036106	100422992		NR_036106	ENSG00000265657	MIR3151	mir-3151	microRNA 3151	ncRNA	0.013966	0.523677	125(TGCTCAGCGTGTTCCG,+,0.00)
chunk0158_325_1	chr5	132866298	132866800	+	0	NA	promoter-TSS (NM_001288828)	promoter-TSS (NM_001288828)	30	NM_001288828	2661	Hs.25022	NM_005260	ENSG00000164404	GDF9	POF14	growth differentiation factor 9	protein-coding	0.057769	0.624254	
chunk0185_9_1	chr7	123795923	123796200	+	0	NA	Intergenic	Intergenic	-5350	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.003610	0.388489	
chunk0130_440_1	chr3	141228308	141228994	+	0	NA	Intergenic	Intergenic	-3174	NM_152282	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.005831	0.420670	
chunk0083_178_1	chr17	66348353	66348742	+	0	NA	intron (NM_002737, intron 2 of 16)	intron (NM_002737, intron 2 of 16)	45739	NM_002737	5578	Hs.531704	NM_002737	ENSG00000154229	PRKCA	AAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACA	protein kinase C alpha	protein-coding	0.005141	0.407692	
chunk0121_221_1	chr3	21828862	21829404	+	0	NA	Intergenic	Intergenic	-77809	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.000000	0.406998	
chunk0149_114_1	chr5	19281726	19282313	+	0	NA	Intergenic	Intergenic	604253	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.001704	0.253401	
chunk0013_383_1	chr1	172559010	172559303	+	0	NA	intron (NM_014283, intron 6 of 23)	intron (NM_014283, intron 6 of 23)	26038	NM_001282751	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.006826	0.360544	
chunk0135_148_1	chr3	187640112	187640602	+	0	NA	Intergenic	Intergenic	30056	NM_001048	6750	Hs.12409	NM_001048	ENSG00000157005	SST	SMST	somatostatin	protein-coding	0.008163	0.433809	
chunk0048_47_1	chr12	78094347	78094846	+	0	NA	intron (NM_014903, intron 12 of 38)	intron (NM_014903, intron 12 of 38)	263307	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.006012	0.320000	
chunk0174_437_1	chr6	166087011	166087833	+	0	NA	Intergenic	Intergenic	81247	NM_001270484	6862	Hs.389457	NM_003181	ENSG00000164458	TBXT	SAVA|T|TFT	T-box transcription factor T	protein-coding	0.020681	0.540705	450(AAGAACACACTGGACT,-,0.00),451(AGAACACACTGGACTT,+,0.00)
chunk0097_272_1	chr2	54899565	54900153	+	0	NA	intron (NM_001039753, intron 21 of 40)	L2b|LINE|L2	110475	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.008503	0.422750	465(GGGGCAATATGTCCTT,+,0.00)
chunk0208_165_1	chrX	16473846	16474486	+	0	NA	Intergenic	Intergenic	152919	NR_039762	100616428		NR_039762	ENSG00000265144	MIR548AM	-	microRNA 548am	ncRNA	0.007812	0.408736	
chunk0187_110_1	chr8	5990740	5991477	+	0	NA	Intergenic	L1ME2|LINE|L1	415440	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.006784	0.296748	
chunk0104_182_1	chr2	174825870	174826367	+	0	NA	intron (NM_001025201, intron 7 of 12)	MamRTE1|LINE|RTE-BovB	21500	NM_001206602	1123	Hs.380138	NM_001822	ENSG00000128656	CHN1	ARHGAP2|CHN|DURS2|NC|RHOGAP2	chimerin 1	protein-coding	0.004024	0.381526	
chunk0017_463_1	chr1	214568106	214568651	+	0	NA	Intergenic	Intergenic	-16697	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.005505	0.441392	106(CAGAACAGCCTGTCCT,-,0.00),107(AGAACAGCCTGTCCTT,+,0.00)
chunk0050_278_1	chr12	106302475	106302827	+	0	NA	promoter-TSS (NM_152772)	promoter-TSS (NM_152772)	-140	NM_152772	255394	Hs.696047	NM_152772	ENSG00000166046	TCP11L2	-	t-complex 11 like 2	protein-coding	0.096591	0.654391	
chunk0034_400_1	chr11	37230012	37230602	+	0	NA	Intergenic	Intergenic	-632028	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.005085	0.333333	205(AAATACAGGATGTCCT,-,0.00),206(AATACAGGATGTCCTC,+,0.00)
chunk0042_377_1	chr12	10623478	10624232	+	0	NA	intron (NM_018423, intron 8 of 10)	Tigger13a|DNA|TcMar-Tigger	-10246	NM_018048	55110	Hs.104650	NM_018048	ENSG00000111196	MAGOHB	MGN2|mago|magoh	mago homolog B, exon junction complex subunit	protein-coding	0.002653	0.308609	
chunk0133_59_1	chr3	166809402	166809981	+	0	NA	Intergenic	Intergenic	570592	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.006908	0.294828	
chunk0051_112_1	chr12	115089311	115089841	+	0	NA	Intergenic	(GTGGCGC)n|Simple_repeat|Simple_repeat	-405412	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.022642	0.510358	
chunk0110_424_1	chr20	20700940	20701186	+	0	NA	intron (NM_020343, intron 1 of 39)	L2a|LINE|L2	11560	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.008130	0.396761	
chunk0128_70_1	chr3	105153149	105153348	+	0	NA	Intergenic	Intergenic	-213465	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.005025	0.275000	
chunk0112_197_1	chr20	40359444	40359949	+	0	NA	Intergenic	Intergenic	329544	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.003960	0.440711	
chunk0075_353_1	chr16	55928896	55929216	+	0	NA	intron (NM_001190158, intron 2 of 13)	intron (NM_001190158, intron 2 of 13)	26975	NM_001190158	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.012500	0.551402	
chunk0151_129_1	chr5	44001046	44001589	+	0	NA	Intergenic	Intergenic	387365	NM_004465	2255	Hs.248049	NM_004465	ENSG00000070193	FGF10	-	fibroblast growth factor 10	protein-coding	0.003683	0.352941	
chunk0164_271_1	chr6	23715015	23715819	+	0	NA	Intergenic	L1ME3|LINE|L1	-410769	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.003731	0.385093	
chunk0129_354_1	chr3	124920805	124921039	+	0	NA	intron (NM_033049, intron 4 of 11)	MIRb|SINE|MIR	13829	NM_033049	56667	Hs.5940	NM_033049	ENSG00000173702	MUC13	DRCC1|MUC-13	mucin 13, cell surface associated	protein-coding	0.017094	0.506383	
chunk0035_415_1	chr11	57083577	57084017	+	0	NA	Intergenic	LTR42|LTR|ERVL	46263	NR_036445	219525	Hs.554519	NR_036445	ENSG00000283307	OR5AK4P	PJCG3	olfactory receptor family 5 subfamily AK member 4 pseudogene	pseudo	0.002273	0.428571	
chunk0069_315_1	chr15	65790851	65791410	+	0	NA	intron (NM_001144823, intron 1 of 32)	intron (NM_001144823, intron 1 of 32)	1163	NM_001144823	10260	Hs.654567	NM_005848	ENSG00000174485	DENND4A	IRLB|MYCPBP	DENN domain containing 4A	protein-coding	0.025045	0.394643	
chunk0110_358_1	chr20	19775551	19775856	+	0	NA	Intergenic	MIRb|SINE|MIR	-110818	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.003279	0.454248	
chunk0103_184_1	chr2	163367655	163368330	+	0	NA	Intergenic	Intergenic	368011	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.001481	0.353550	
chunk0001_88_1	chr1	2795437	2796044	+	0	NA	Intergenic	Intergenic	-6075	NM_001242672	100287898	Hs.632363	NM_001242672	ENSG00000215912	TTC34	-	tetratricopeptide repeat domain 34	protein-coding	0.009885	0.470395	
chunk0088_358_1	chr18	52748149	52748705	+	0	NA	intron (NM_005215, intron 1 of 28)	LTR2752|LTR|ERV1	408255	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.026978	0.581688	
chunk0045_323_1	chr12	50835276	50835808	+	0	NA	Intergenic	L1PB1|LINE|L1	-7376	NM_182559	283471	Hs.125571	NM_182559	ENSG00000186452	TMPRSS12	CT151	transmembrane serine protease 12	protein-coding	0.001880	0.322702	
chunk0053_62_1	chr13	28035430	28035726	+	0	NA	exon (NM_004119, exon 12 of 24)	exon (NM_004119, exon 12 of 24)	-46941	NM_001105577	646625	Hs.705356	NM_001105577	ENSG00000183463	URAD	PRHOXNB	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	protein-coding	0.010135	0.430976	
chunk0201_369_1	chr9	68668181	68668652	+	0	NA	Intergenic	Intergenic	-36998	NM_003558	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.010616	0.463983	
chunk0152_80_1	chr5	58107717	58108215	+	0	NA	non-coding (NR_104669, exon 5 of 5)	non-coding (NR_104669, exon 5 of 5)	14375	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.006024	0.394790	
chunk0088_424_1	chr18	55225971	55226460	+	0	NA	3' UTR (NM_001083962, exon 20 of 20)	3' UTR (NM_001083962, exon 20 of 20)	76406	NM_001243236	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.006135	0.302041	
chunk0001_27_1	chr1	1281721	1282073	+	0	NA	intron (NM_001130413, intron 3 of 17)	intron (NM_001130413, intron 3 of 17)	1461	NR_037668	6339	Hs.512681	NM_002978	ENSG00000162572	SCNN1D	ENaCd|ENaCdelta|SCNED|dNaCh	sodium channel epithelial 1 delta subunit	protein-coding	0.034091	0.677054	
chunk0086_245_1	chr18	23073859	23074154	+	0	NA	Intergenic	Intergenic	-60558	NM_001256438	91768	Hs.11108	NM_138375	ENSG00000134508	CABLES1	CABL1|CABLES|HsT2563|IK3-1	Cdk5 and Abl enzyme substrate 1	protein-coding	0.003390	0.314189	
chunk0098_314_1	chr2	76549764	76550329	+	0	NA	Intergenic	Intergenic	-435919	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.007080	0.397527	307(AGGCACTGGTTGTTCT,-,0.00),308(GGCACTGGTTGTTCTC,+,0.00)
chunk0202_127_1	chr9	73148253	73148828	+	0	NA	Intergenic	L1MC2|LINE|L1	-3191	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.006957	0.324653	
chunk0100_260_1	chr2	113229252	113229640	+	0	NA	intron (NM_013953, intron 7 of 9)	intron (NM_013953, intron 7 of 9)	-6081	NR_047570	654433	Hs.656660	NR_015377	ENSG00000189223	PAX8-AS1	-	PAX8 antisense RNA 1	ncRNA	0.002577	0.411311	
chunk0131_300_1	chr3	150637683	150638083	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	34604	NM_016275	51714	Hs.369052	NM_016275	ENSG00000198843	SELENOT	SELT	selenoprotein T	protein-coding	0.012500	0.386534	
chunk0082_5_1	chr17	49708350	49708598	+	0	NA	promoter-TSS (NM_005827)	promoter-TSS (NM_005827)	-523	NM_001278784	10237	Hs.154073	NM_005827	ENSG00000121073	SLC35B1	UGTREL1	solute carrier family 35 member B1	protein-coding	0.036290	0.534137	
chunk0092_456_1	chr19	39142961	39143178	+	0	NA	intron (NM_001014834, intron 1 of 7)	L2a|LINE|L2	17289	NM_001014834	10298	Hs.20447	NM_005884	ENSG00000130669	PAK4	-	p21 (RAC1) activated kinase 4	protein-coding	0.009217	0.541284	
chunk0083_115_1	chr17	64919440	64919744	+	0	NA	promoter-TSS (NM_199340)	promoter-TSS (NM_199340)	-112	NM_001303255	374819	Hs.551962	NM_199340	ENSG00000176809	LRRC37A3	LRRC37|LRRC37A	leucine rich repeat containing 37 member A3	protein-coding	0.131579	0.727869	
chunk0038_412_1	chr11	94144990	94145439	+	0	NA	intron (NM_015368, intron 1 of 4)	intron (NM_015368, intron 1 of 4)	16286	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.011136	0.386667	
chunk0028_95_1	chr10	84196243	84196762	+	0	NA	intron (NM_033100, intron 2 of 16)	intron (NM_033100, intron 2 of 16)	1867	NM_033100	92211	Hs.137556	NM_033100	ENSG00000148600	CDHR1	CORD15|PCDH21|PRCAD|RP65	cadherin related family member 1	protein-coding	0.013487	0.513462	
chunk0050_215_1	chr12	104487456	104487932	+	0	NA	intron (NM_018413, intron 1 of 2)	intron (NM_018413, intron 1 of 2)	30780	NM_001173982	50515	Hs.17569	NM_018413	ENSG00000171310	CHST11	C4ST|C4ST-1|C4ST1|HSA269537|OCBMD	carbohydrate sulfotransferase 11	protein-coding	0.014706	0.366876	255(CGAAACAGTATGTACC,-,0.00),256(GAAACAGTATGTACCT,+,0.00)
chunk0067_90_1	chr15	41972782	41973074	+	0	NA	promoter-TSS (NM_139265)	promoter-TSS (NM_139265)	165	NR_120334	101928388	Hs.738043	NR_120334	ENSG00000246740	PLA2G4E-AS1	-	PLA2G4E antisense RNA 1	ncRNA	0.051370	0.600683	
chunk0010_130_1	chr1	114593743	114593997	+	0	NA	intron (NM_001256404, intron 18 of 20)	MIR|SINE|MIR	-12226	NM_005872	10286	Hs.22960	NM_005872	ENSG00000116752	BCAS2	DAM1|SPF27|Snt309	BCAS2 pre-mRNA processing factor	protein-coding	0.003937	0.325490	
chunk0020_395_1	chr1	240572207	240572821	+	0	NA	intron (NM_022469, intron 1 of 1)	intron (NM_022469, intron 1 of 1)	39648	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.004886	0.369106	
chunk0121_353_1	chr3	24771008	24771622	+	0	NA	Intergenic	MER97d|DNA|hAT-Tip100	-249880	NR_039955									0.001629	0.266667	
chunk0193_226_1	chr8	76615456	76615684	+	0	NA	intron (NR_024360, intron 3 of 3)	intron (NR_024360, intron 3 of 3)	-65710	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.004386	0.353712	78(AAGAACATTGTGTACC,-,0.00),79(AGAACATTGTGTACCC,+,0.00)
chunk0015_438_1	chr1	191767479	191768067	+	0	NA	Intergenic	Intergenic	-390689	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.003401	0.324278	
chunk0211_197_1	chrX	117792632	117792912	+	0	NA	Intergenic	Intergenic	180966	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.007143	0.391459	
chunk0152_245_1	chr5	60767832	60768485	+	0	NA	intron (NM_001297618, intron 4 of 8)	intron (NM_001297618, intron 4 of 8)	-67992	NM_018369	55789	Hs.482233	NM_018369	ENSG00000035499	DEPDC1B	BRCC3|XTP1	DEP domain containing 1B	protein-coding	0.004594	0.368502	
chunk0188_130_1	chr8	9207923	9208596	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	19260	NR_125431	101929128		NR_125431	ENSG00000248538	LOC101929128	-	uncharacterized LOC101929128	ncRNA	0.005944	0.362018	258(TAGGACAATGTGTACT,-,0.00),259(AGGACAATGTGTACTG,+,0.00)
chunk0116_58_1	chr21	33932074	33932400	+	0	NA	intron (NR_038883, intron 1 of 2)	intron (NR_038883, intron 1 of 2)	1025	NR_038883	100506334	Hs.532855	NM_207472	ENSG00000237945	LINC00649	-	long intergenic non-protein coding RNA 649	ncRNA	0.018405	0.486239	
chunk0205_173_1	chr9	108863276	108863572	+	0	NA	exon (NM_006687, exon 1 of 1)	exon (NM_006687, exon 1 of 1)	1196	NM_006687	10881	Hs.123530	NM_006687	ENSG00000187003	ACTL7A	-	actin like 7A	protein-coding	0.037162	0.572391	112(GGGAACATCCTGCTCT,-,0.00),113(GGAACATCCTGCTCTG,+,0.00)
chunk0117_142_1	chr22	19544090	19544417	+	0	NA	Intergenic	Intergenic	-18916	NM_001130861	7122	Hs.505337	NM_003277	ENSG00000184113	CLDN5	AWAL|BEC1|CPETRL1|TMDVCF|TMVCF	claudin 5	protein-coding	0.015291	0.615854	
chunk0152_376_1	chr5	64490046	64490245	+	0	NA	Intergenic	L1PA13|LINE|L1	-15802	NM_001029875	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.020101	0.580000	
chunk0093_16_1	chr2	215873	216072	+	0	NA	Intergenic	L1ME1|LINE|L1	40368	NM_001282687	26751	Hs.515951	NM_015677	ENSG00000035115	SH3YL1	RAY	SH3 and SYLF domain containing 1	protein-coding	0.015075	0.415000	
chunk0066_265_1	chr15	34911926	34912217	+	0	NA	intron (NM_014691, intron 16 of 34)	L1MA9|LINE|L1	57723	NM_014691	9716	Hs.510958	NM_014691	ENSG00000021776	AQR	IBP160|fSAP164	aquarius intron-binding spliceosomal factor	protein-coding	0.006873	0.339041	
chunk0205_407_1	chr9	114785991	114786686	+	0	NA	3' UTR (NM_005118, exon 4 of 4)	3' UTR (NM_005118, exon 4 of 4)	6192	NM_001204344	9966	Hs.23349	NM_005118	ENSG00000181634	TNFSF15	TL1|TL1A|TNLG1B|VEGI|VEGI192A	TNF superfamily member 15	protein-coding	0.010072	0.426724	
chunk0102_369_1	chr2	152921011	152921477	+	0	NA	Intergenic	Intergenic	203351	NR_024526	151188	Hs.643580	NM_152522	ENSG00000177917	ARL6IP6	AIP-6|AIP6|PFAAP1	ADP ribosylation factor like GTPase 6 interacting protein 6	protein-coding	0.006438	0.458244	
chunk0086_376_1	chr18	26440323	26441017	+	0	NA	Intergenic	Intergenic	17675	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.017291	0.450360	463(TGGAACAGTATGTTCT,-,0.00),464(GGAACAGTATGTTCTG,+,0.00)
chunk0030_287_1	chr10	116963669	116964066	+	0	NA	intron (NM_018330, intron 3 of 14)	intron (NM_018330, intron 3 of 14)	41710	NM_001127211	57698	Hs.501140	NM_018330	ENSG00000187164	SHTN1	KIAA1598|shootin-1	shootin 1	protein-coding	0.007557	0.356784	
chunk0076_317_1	chr16	70565109	70565501	+	0	NA	intron (NM_012426, intron 19 of 25)	intron (NM_012426, intron 19 of 25)	-14590	NM_152456	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.007653	0.519084	112(GGGAACACACTGGACC,-,0.00),113(GGAACACACTGGACCT,+,0.00)
chunk0062_433_1	chr14	75340872	75341374	+	0	NA	Intergenic	Intergenic	46719	NR_038421	731223	Hs.534624	NR_038421		LINC01220	-	long intergenic non-protein coding RNA 1220	ncRNA	0.017928	0.493042	286(AGGAACAGGACGTCCT,-,0.00),287(GGAACAGGACGTCCTT,+,0.00)
chunk0040_367_1	chr11	118916780	118917107	+	0	NA	Intergenic	Intergenic	-6039	NM_182557	283149	Hs.414740	NM_182557	ENSG00000186174	BCL9L	B9L|BCL9-2|DLNB11	BCL9 like	protein-coding	0.012232	0.585366	
chunk0087_385_1	chr18	41751146	41751878	+	0	NA	Intergenic	Intergenic	-203686	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.004098	0.384720	355(GAGAACAAAGTGTCCT,-,0.00),356(AGAACAAAGTGTCCTA,+,0.00)
chunk0195_337_1	chr8	99281393	99281592	+	0	NA	intron (NM_152564, intron 19 of 61)	LTR40b|LTR|ERVL	255238	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.010050	0.415000	
chunk0168_181_1	chr6	84540131	84540392	+	0	NA	Intergenic	Intergenic	-65332	NR_132100	105377880	Hs.171384	NR_132100	ENSG00000231776	LINC01611	TCONS_l2_00025430	long intergenic non-protein coding RNA 1611	ncRNA	0.000000	0.286260	
chunk0191_221_1	chr8	52695634	52695908	+	0	NA	intron (NM_014781, intron 1 of 23)	MER77|LTR|ERVL	18695	NM_014781	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.010949	0.450909	
chunk0175_59_1	chr7	1790084	1790290	+	0	NA	Intergenic	L1MEc|LINE|L1	-47877	NR_120509	101927125	Hs.633957	NR_120508	ENSG00000236081	ELFN1-AS1	MYCLo-2	ELFN1 antisense RNA 1	ncRNA	0.000000	0.362319	
chunk0189_246_1	chr8	24929553	24929752	+	0	NA	Intergenic	Intergenic	14710	NM_001105541	4741	Hs.458657	NM_005382	ENSG00000104722	NEFM	NEF3|NF-M|NFM	neurofilament medium	protein-coding	0.000000	0.385000	
chunk0180_133_1	chr7	56051251	56051734	+	0	NA	promoter-TSS (NM_001009186)	promoter-TSS (NM_001009186)	83	NM_004577	5723	Hs.512656	NM_004577	ENSG00000146733	PSPH	PSP|PSPHD	phosphoserine phosphatase	protein-coding	0.099379	0.652893	
chunk0201_270_1	chr9	38633082	38633552	+	0	NA	Intergenic	Intergenic	12229	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.014894	0.380042	
chunk0153_233_1	chr5	72228165	72228750	+	0	NA	intron (NM_015084, intron 7 of 10)	L1ME4a|LINE|L1	58990	NR_039967	100616377		NR_039967	ENSG00000264099	MIR4803	-	microRNA 4803	ncRNA	0.006838	0.320819	
chunk0069_12_1	chr15	60200565	60201288	+	0	NA	Intergenic	MIR|SINE|MIR	196704	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.004149	0.324586	
chunk0110_196_1	chr20	14792707	14793358	+	0	NA	intron (NM_080676, intron 5 of 16)	L2b|LINE|L2	136486	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.004608	0.354294	
chunk0073_415_1	chr16	18882907	18883183	+	0	NA	intron (NM_015092, intron 9 of 62)	intron (NM_015092, intron 9 of 62)	43359	NM_015092	23049	Hs.460179	NM_015092	ENSG00000157106	SMG1	61E3.4|ATX|LIP	SMG1 nonsense mediated mRNA decay associated PI3K related kinase	protein-coding	0.014493	0.389892	
chunk0005_302_1	chr1	60388090	60388400	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-314475	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.006452	0.482315	
chunk0038_162_1	chr11	84866856	84867273	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	56357	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004796	0.339713	
chunk0105_218_1	chr2	188053624	188054364	+	0	NA	intron (NR_126396, intron 2 of 2)	intron (NR_126396, intron 2 of 2)	233697	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.004054	0.272605	
chunk0033_353_1	chr11	22963924	22964134	+	0	NA	Intergenic	L1PA6|LINE|L1	-103603	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.000000	0.393365	117(TAGTACTGGTTGTTCC,-,0.00),118(AGTACTGGTTGTTCCT,+,0.00)
chunk0129_282_1	chr3	123185025	123185224	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-16803	NM_012430	26984	Hs.477361	NM_012430	ENSG00000121542	SEC22A	SEC22L2	SEC22 homolog A, vesicle trafficking protein	protein-coding	0.035176	0.540000	
chunk0169_266_1	chr6	105514295	105514996	+	0	NA	Intergenic	Intergenic	-111521	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.009986	0.444444	
chunk0088_196_1	chr18	47643889	47644258	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	263577	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.008130	0.545946	
chunk0048_58_1	chr12	78325544	78325916	+	0	NA	Intergenic	Intergenic	494441	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.002688	0.402145	
chunk0069_73_1	chr15	60984393	60984902	+	0	NA	intron (NM_134261, intron 1 of 10)	MER5C|DNA|hAT-Charlie	244656	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.001965	0.325490	
chunk0119_228_1	chr22	45238371	45239171	+	0	NA	intron (NM_001009880, intron 1 of 9)	intron (NM_001009880, intron 1 of 9)	1998	NM_001009880	23313	Hs.592207	NM_015264	ENSG00000100364	KIAA0930	C22orf9|LSC3	KIAA0930	protein-coding	0.013750	0.539326	
chunk0126_109_1	chr3	75101805	75102103	+	0	NA	Intergenic	L1MA3|LINE|L1	-112522	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.020134	0.551839	
chunk0014_253_1	chr1	180114460	180115057	+	0	NA	3' UTR (NM_014810, exon 38 of 38)	3' UTR (NM_014810, exon 38 of 38)	-40075	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.006700	0.364548	
chunk0040_245_1	chr11	115220358	115220975	+	0	NA	intron (NM_001301043, intron 5 of 11)	intron (NM_001301043, intron 5 of 11)	283857	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.011345	0.367314	
chunk0207_435_1	chr9	137422788	137423197	+	0	NA	promoter-TSS (NM_001256068)	promoter-TSS (NM_001256068)	270	NR_104598	54932	Hs.495553	NM_017820	ENSG00000187609	EXD3	mut-7	exonuclease 3'-5' domain containing 3	protein-coding	0.132029	0.790244	
chunk0142_215_1	chr4	97641868	97642145	+	0	NA	intron (NM_174952, intron 10 of 10)	intron (NM_174952, intron 10 of 10)	275080	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.000000	0.298561	
chunk0093_41_1	chr19	39532794	39533047	+	0	NA	promoter-TSS (NM_152361)	promoter-TSS (NM_152361)	-53	NM_152361	126272	Hs.135181	NM_152361	ENSG00000176401	EID2B	EID-2B|EID-3	EP300 interacting inhibitor of differentiation 2B	protein-coding	0.090909	0.586614	
chunk0178_430_1	chr7	41178465	41178677	+	0	NA	Intergenic	Intergenic	76967	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.000000	0.276995	50(AAAAACACAGTGTTCT,-,0.00),51(AAAACACAGTGTTCTG,+,0.00)
chunk0074_261_1	chr16	28121590	28121941	+	0	NA	intron (NM_001270940, intron 14 of 24)	intron (NM_001270940, intron 14 of 24)	-58256	NM_001109763	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.005698	0.375000	
chunk0030_90_1	chr10	112384797	112385073	+	0	NA	intron (NM_016234, intron 1 of 20)	L1ME4b|LINE|L1	8737	NM_016234	51703	Hs.11638	NM_016234	ENSG00000197142	ACSL5	ACS2|ACS5|FACL5	acyl-CoA synthetase long chain family member 5	protein-coding	0.010870	0.368231	97(ATGTACACACTGTCCA,-,0.00),98(TGTACACACTGTCCAA,+,0.00)
chunk0027_334_1	chr10	78485711	78486085	+	0	NA	Intergenic	Intergenic	218570	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.000000	0.306667	
chunk0032_30_1	chr11	955478	955727	+	0	NA	intron (NM_001242837, intron 1 of 21)	L2a|LINE|L2	29793	NM_001242837	161	Hs.19121	NM_012305	ENSG00000183020	AP2A2	ADTAB|CLAPA2|HIP-9|HIP9|HYPJ	adaptor related protein complex 2 subunit alpha 2	protein-coding	0.012048	0.552000	
chunk0021_59_1	chr10	1119099	1119733	+	0	NA	intron (NM_014023, intron 11 of 13)	intron (NM_014023, intron 11 of 13)	-40352	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.012618	0.467717	340(CTGAACTAAATGTTCT,-,0.00),341(TGAACTAAATGTTCTC,+,0.00)
chunk0008_305_1	chr1	95053699	95054112	+	0	NA	intron (NM_001305242, intron 2 of 4)	L1MEd|LINE|L1	-7691	NR_132786	101928098	Hs.730090	NR_132786	ENSG00000230427	LOC101928098	-	uncharacterized LOC101928098	ncRNA	0.000000	0.350242	
chunk0157_13_1	chr5	115292702	115292943	+	0	NA	intron (NM_001040440, intron 1 of 9)	L1M4|LINE|L1	3468	NM_152549	153733	Hs.436121	NM_152549	ENSG00000164221	CCDC112	MBC1	coiled-coil domain containing 112	protein-coding	0.000000	0.450413	
chunk0200_126_1	chr9	17373771	17373970	+	0	NA	intron (NM_017738, intron 13 of 25)	L1MA3|LINE|L1	-205084	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.010050	0.355000	
chunk0176_275_1	chr7	16599407	16600370	+	0	NA	3' UTR (NM_020319, exon 10 of 10)	3' UTR (NM_020319, exon 10 of 10)	45929	NM_020319	57037	Hs.157378	NM_020319	ENSG00000106524	ANKMY2	ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding	0.013499	0.376556	778(AAGTTCAGAGTGTTCA,-,0.00)
chunk0102_270_1	chr2	150100682	150101410	+	0	NA	Intergenic	Intergenic	386649	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.000000	0.358025	
chunk0136_43_1	chr4	1191805	1192161	+	0	NA	intron (NM_001199021, intron 1 of 7)	intron (NM_001199021, intron 1 of 7)	16979	NM_001199021	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.011236	0.593838	85(AGGACAGCCAGCCCCT,+,0.00)
chunk0083_32_1	chr17	63258646	63259262	+	0	NA	intron (NM_025185, intron 6 of 24)	L1MA4A|LINE|L1	181892	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.004870	0.523501	
chunk0090_457_1	chr18	80145291	80145513	+	0	NA	Intergenic	Intergenic	-2522	NR_028340	100130522	Hs.352602	NM_001145731	ENSG00000267270	PARD6G-AS1	-	PARD6G antisense RNA 1	ncRNA	0.004505	0.381166	
chunk0035_165_1	chr11	43649921	43650530	+	0	NA	Intergenic	L1M5|LINE|L1	-30368	NM_016142	51144	Hs.132513	NM_016142	ENSG00000149084	HSD17B12	KAR|SDR12C1	hydroxysteroid 17-beta dehydrogenase 12	protein-coding	0.003284	0.378689	
chunk0063_65_1	chr14	77314093	77314407	+	0	NA	intron (NM_013382, intron 1 of 20)	LTR40c|LTR|ERVL	6632	NM_013382	29954	Hs.132989	NM_013382	ENSG00000009830	POMT2	LGMD2N|LGMDR14|MDDGA2|MDDGB2|MDDGC2	protein O-mannosyltransferase 2	protein-coding	0.006369	0.485714	
chunk0044_234_1	chr12	31517915	31518518	+	0	NA	intron (NM_001308339, intron 1 of 22)	intron (NM_001308339, intron 1 of 22)	-71707	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.001658	0.432119	
chunk0166_316_1	chr6	49722803	49723286	+	0	NA	Intergenic	Intergenic	-9454	NM_001142408	7180	Hs.2042	NM_003296	ENSG00000124490	CRISP2	CRISP-2|CT36|GAPDL5|TPX1|TSP1	cysteine rich secretory protein 2	protein-coding	0.004141	0.355372	
chunk0040_80_1	chr11	111390050	111390715	+	0	NA	Intergenic	Intergenic	-10950	NM_006235	5450	Hs.654525	NM_006235	ENSG00000110777	POU2AF1	BOB1|OBF-1|OBF1|OCAB	POU class 2 homeobox associating factor 1	protein-coding	0.001504	0.414414	
chunk0210_72_1	chrX	69971628	69971968	+	0	NA	intron (NM_001005612, intron 2 of 7)	L2b|LINE|L2	-51059	NR_037494	100500887		NR_037494	ENSG00000211991	MIR676	hsa-mir-676|mir-676	microRNA 676	ncRNA	0.011765	0.378299	
chunk0210_13_1	chrX	66902004	66902486	+	0	NA	Intergenic	Intergenic	-262947	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.008299	0.422360	
chunk0130_75_1	chr3	130473418	130473717	+	0	NA	intron (NM_001278298, intron 40 of 40)	LTR3B_|LTR|ERVK	-86767	NM_001102608	131873	Hs.591282	NM_001102608	ENSG00000206384	COL6A6	-	collagen type VI alpha 6 chain	protein-coding	0.003344	0.420000	186(CAGAGCAAACTGTTCT,-,0.00),187(AGAGCAAACTGTTCTC,+,0.00)
chunk0122_281_1	chr3	35944979	35945482	+	0	NA	Intergenic	Intergenic	200754	NR_029824	406916		NR_029824	ENSG00000207625	MIR128-2	MIR128B|MIRN128-2|MIRN128B|mir-128-2|mir-128b	microRNA 128-2	ncRNA	0.003976	0.329365	
chunk0078_124_1	chr17	2975525	2976092	+	0	NA	intron (NM_015085, intron 8 of 24)	LTR79|LTR|ERVL	-9913	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.024691	0.498239	
chunk0161_159_1	chr5	169099746	169100286	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	86789	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.011111	0.517560	273(TGGAACGCCTTGTTCT,-,0.00),274(GGAACGCCTTGTTCTG,+,0.00)
chunk0163_175_1	chr6	11287860	11288556	+	0	NA	intron (NM_001142393, intron 2 of 7)	intron (NM_001142393, intron 2 of 7)	-55526	NM_006403	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.012931	0.457676	253(TAGAACATCCTGATCT,-,0.00),254(AGAACATCCTGATCTT,+,0.00),409(GAGTACACCCTGGTCT,-,0.00)
chunk0041_142_1	chr11	125338535	125338746	+	0	NA	intron (NM_022062, intron 3 of 12)	intron (NM_022062, intron 3 of 12)	-156574	NM_001301851	403312	Hs.450611	NM_203452		LOC403312	-	putative uncharacterized protein MGC39545	protein-coding	0.009479	0.509434	75(AGAGACACTTTGTTCC,-,0.00),76(GAGACACTTTGTTCCT,+,0.00)
chunk0150_377_1	chr5	39209913	39210228	+	0	NA	intron (NM_001243093, intron 1 of 18)	intron (NM_001243093, intron 1 of 18)	9508	NM_001465	2533	Hs.370503	NM_001465	ENSG00000082074	FYB1	ADAP|FYB|PRO0823|SLAP-130|SLAP130|THC3	FYN binding protein 1	protein-coding	0.025397	0.550633	
chunk0150_366_1	chr5	39056044	39056287	+	0	NA	intron (NM_001285439, intron 2 of 38)	L2|LINE|L2	18243	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.008230	0.385246	
chunk0044_372_1	chr12	39763273	39763557	+	0	NA	intron (NM_052885, intron 9 of 9)	intron (NM_052885, intron 9 of 9)	137245	NM_001031748	283461	Hs.648205	NM_001031748	ENSG00000180116	C12orf40	HEL-206|HEL-S-94	chromosome 12 open reading frame 40	protein-coding	0.000000	0.357895	
chunk0176_346_1	chr7	17770104	17770425	+	0	NA	Intergenic	MIRb|SINE|MIR	170244	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.009346	0.350932	
chunk0196_88_1	chr8	102864341	102864597	+	0	NA	promoter-TSS (NM_148174)	promoter-TSS (NM_148174)	198	NR_126339	100506753	Hs.602901	NR_126338		AZIN1-AS1	-	AZIN1 antisense RNA 1	ncRNA	0.136719	0.766537	
chunk0157_72_1	chr5	116382535	116382894	+	0	NA	Intergenic	Intergenic	-8144	NR_104675	101927190	Hs.639849	NR_104675		LOC101927190	-	uncharacterized LOC101927190	ncRNA	0.002786	0.422222	
chunk0095_299_1	chr2	20315080	20315521	+	0	NA	intron (NM_001282752, intron 2 of 19)	L2b|LINE|L2	12086	NM_001282791	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.002268	0.402715	214(GAGAACATGATGAACC,-,0.00),215(AGAACATGATGAACCT,+,0.00)
chunk0209_298_1	chrX	48626820	48627096	+	0	NA	Intergenic	Intergenic	29122	NM_001166426	64743	Hs.521973	NM_017883	ENSG00000101940	WDR13	MG21	WD repeat domain 13	protein-coding	0.010870	0.425993	
chunk0150_305_1	chr5	37730910	37731654	+	0	NA	intron (NM_018034, intron 17 of 17)	intron (NM_018034, intron 17 of 17)	103540	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.004032	0.402685	
chunk0097_215_1	chr2	51437438	51437841	+	0	NA	Intergenic	L1MC2|LINE|L1	-405103	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.007444	0.331683	
chunk0015_432_1	chr1	191636436	191637014	+	0	NA	Intergenic	L1MA7|LINE|L1	-521737	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.001730	0.336788	
chunk0140_273_1	chr4	72145078	72145482	+	0	NA	intron (NM_004885, intron 3 of 3)	(AT)n|Simple_repeat|Simple_repeat	106148	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.000000	0.190123	
chunk0163_107_1	chr6	10007240	10007584	+	0	NA	Intergenic	Intergenic	-404906	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.000000	0.347826	
chunk0115_99_1	chr21	22535590	22535903	+	0	NA	Intergenic	L1PA15|LINE|L1	437129	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.006390	0.525478	252(GAGAACATCTTGACCC,-,0.00),253(AGAACATCTTGACCCC,+,0.00)
chunk0089_343_1	chr18	65876336	65876681	+	0	NA	intron (NM_004361, intron 11 of 11)	intron (NM_004361, intron 11 of 11)	125587	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.008696	0.416185	
chunk0067_24_1	chr15	40350729	40351277	+	0	NA	promoter-TSS (NM_001145643)	promoter-TSS (NM_001145643)	-30	NM_001145643	644844	Hs.447537	NM_001145643	ENSG00000233041	PHGR1	-	proline, histidine and glycine rich 1	protein-coding	0.009124	0.548270	286(GAGGACAGACAGTGCC,-,0.00),287(AGGACAGACAGTGCCC,+,0.00)
chunk0043_299_1	chr12	22043791	22044381	+	0	NA	Intergenic	L2c|LINE|L2	-2090	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.005085	0.402707	
chunk0203_23_1	chr9	82878501	82878700	+	0	NA	Intergenic	Intergenic	184528	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.015075	0.345000	102(CTGTACACACAGTTCT,-,0.00),103(TGTACACACAGTTCTT,+,0.00)
chunk0032_426_1	chr11	12233440	12233942	+	0	NA	intron (NM_001282663, intron 15 of 27)	Charlie19a|DNA|hAT-Charlie	-53209	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.005976	0.330020	
chunk0070_68_1	chr15	69807836	69808117	+	0	NA	Intergenic	Intergenic	-27258	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.017794	0.539007	
chunk0053_336_1	chr13	34459003	34459461	+	0	NA	intron (NR_047036, intron 2 of 2)	intron (NR_047036, intron 2 of 2)	181453	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.004367	0.372549	278(CAGAACAAACTGTTAT,-,0.00)
chunk0198_459_1	chr8	144443263	144443512	+	0	NA	intron (NM_013432, intron 3 of 25)	intron (NM_013432, intron 3 of 25)	1042	NM_013432	4796	Hs.675285	NM_013432	ENSG00000160949	TONSL	IKBR|NFKBIL2	tonsoku like, DNA repair protein	protein-coding	0.032129	0.612000	
chunk0038_418_1	chr11	94237520	94238657	+	0	NA	Intergenic	L1PA2|LINE|L1	-67549	NM_001199206	390243	Hs.553758	NM_001080486	ENSG00000183560	IZUMO1R	FOLR4|Folbp3|JUNO	IZUMO1 receptor, JUNO	protein-coding	0.033421	0.528998	
chunk0187_126_1	chr7	149147993	149148298	+	0	NA	intron (NM_170686, intron 1 of 5)	CpG	677	NM_170686	57541	Hs.632032	NM_020781	ENSG00000197024	ZNF398	P51|P71|ZER6	zinc finger protein 398	protein-coding	0.118033	0.702614	
chunk0122_421_1	chr3	39051652	39052010	+	0	NA	promoter-TSS (NM_020839)	promoter-TSS (NM_020839)	-155	NM_020839	57599	Hs.109778	NM_020839	ENSG00000114742	WDR48	P80|SPG60|UAF1	WD repeat domain 48	protein-coding	0.039106	0.545961	
chunk0133_256_1	chr3	171725954	171726688	+	0	NA	intron (NM_001130081, intron 6 of 25)	intron (NM_001130081, intron 6 of 25)	84173	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.002725	0.364626	
chunk0087_26_1	chr18	31061109	31061383	+	0	NA	Intergenic	Intergenic	-18431	NM_001941	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.003650	0.400000	
chunk0035_106_1	chr11	42355815	42356188	+	0	NA	Intergenic	Intergenic	-102311	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002681	0.312834	
chunk0085_355_1	chr18	9174391	9174658	+	0	NA	intron (NM_001204056, intron 1 of 11)	L1PREC2|LINE|L1	36961	NM_001204056	23253	Hs.464585	NM_015208	ENSG00000101745	ANKRD12	ANCO-2|ANCO1|GAC-1|Nbla00144	ankyrin repeat domain 12	protein-coding	0.011236	0.559701	
chunk0176_207_1	chr7	14717134	14717800	+	0	NA	intron (NM_145695, intron 5 of 23)	intron (NM_145695, intron 5 of 23)	123983	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.001502	0.305847	
chunk0191_197_1	chr8	51858984	51859273	+	0	NA	intron (NM_001286783, intron 1 of 5)	intron (NM_001286783, intron 1 of 5)	40058	NM_052937	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.003460	0.472414	
chunk0131_349_1	chr3	151632101	151632969	+	0	NA	Intergenic	Intergenic	-66540	NR_049818	100847036		NR_049818	ENSG00000264330	MIR5186	-	microRNA 5186	ncRNA	0.005760	0.378596	
chunk0109_439_1	chr2	241384808	241385114	+	0	NA	intron (NM_014808, intron 2 of 26)	intron (NM_014808, intron 2 of 26)	28712	NM_001282983	9855	Hs.726316	NM_014808	ENSG00000006607	FARP2	FIR|FRG|PLEKHC3	FERM, ARH/RhoGEF and pleckstrin domain protein 2	protein-coding	0.003268	0.260586	
chunk0169_84_1	chr6	99562696	99563265	+	0	NA	intron (NM_001013399, intron 1 of 11)	intron (NM_001013399, intron 1 of 11)	5834	NM_001013399	892	Hs.430646	NM_005190	ENSG00000112237	CCNC	CycC|SRB11|hSRB11	cyclin C	protein-coding	0.007030	0.310526	310(TTGAACACATTGTTCA,-,0.00),311(TGAACACATTGTTCAT,+,0.00)
chunk0008_377_1	chr1	96865621	96866245	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	143295	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.004808	0.403200	
chunk0008_366_1	chr1	96750053	96750534	+	0	NA	intron (NM_001300987, intron 3 of 14)	intron (NM_001300987, intron 3 of 14)	27655	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.331950	
chunk0134_179_1	chr3	178111004	178111387	+	0	NA	Intergenic	L1MEf|LINE|L1	294330	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.002611	0.283854	
chunk0117_148_1	chr22	19681326	19681984	+	0	NA	Intergenic	L1MDa|LINE|L1	-32809	NM_002688	5413	Hs.728762	NM_002688	ENSG00000184702	SEPTIN5	CDCREL|CDCREL-1|CDCREL1|H5|HCDCREL-1|PNUTL1|SEPT5	septin 5	protein-coding	0.009119	0.361153	
chunk0114_356_1	chr21	18959218	18959493	+	0	NA	Intergenic	Intergenic	-199543	NR_109925	101927797	Hs.551743	NR_109925		MIR548XHG	-	MIR548X host gene	ncRNA	0.010909	0.322464	
chunk0126_52_1	chr3	74182233	74182719	+	0	NA	Intergenic	Intergenic	338664	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002058	0.375770	442(CTGAACAGTATGTCCC,-,0.00),443(TGAACAGTATGTCCCC,+,0.00)
chunk0159_437_1	chr5	148384992	148385618	+	0	NA	intron (NM_030793, intron 1 of 21)	intron (NM_030793, intron 1 of 21)	1370	NM_001271723	81545	Hs.483772	NM_030793	ENSG00000145868	FBXO38	Fbx38|HMN2D|MOKA|SP329	F-box protein 38	protein-coding	0.003195	0.389155	
chunk0125_101_1	chr3	65503858	65504140	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-389817	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.003546	0.399293	
chunk0065_257_1	chr14	101722045	101722443	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-8193	NR_026774	145200	Hs.150840	NR_026774	ENSG00000258512	LINC00239	C14orf72|NCRNA00239	long intergenic non-protein coding RNA 239	ncRNA	0.032663	0.413534	
chunk0029_419_1	chr10	109972463	109972675	+	0	NA	intron (NR_038943, intron 2 of 4)	LTR33|LTR|ERVL	-33399	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.000000	0.389671	
chunk0081_344_1	chr17	46972408	46972733	+	0	NA	promoter-TSS (NR_049812)	promoter-TSS (NR_049812)	-447	NR_049812	100847067		NR_049812	ENSG00000264999	MIR5089	-	microRNA 5089	ncRNA	0.018462	0.585890	
chunk0058_79_1	chr14	21246460	21246942	+	0	NA	intron (NM_001077442, intron 1 of 7)	intron (NM_001077442, intron 1 of 7)	22778	NM_001077443	3183	Hs.508848	NM_004500	ENSG00000092199	HNRNPC	C1|C2|HNRNP|HNRPC|SNRPC	heterogeneous nuclear ribonucleoprotein C (C1/C2)	protein-coding	0.010373	0.409938	
chunk0110_352_1	chr20	19710494	19710693	+	0	NA	intron (NM_020689, intron 15 of 16)	intron (NM_020689, intron 15 of 16)	-175928	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.010050	0.450000	102(TGGCACTTAATGTTCC,-,0.00),103(GGCACTTAATGTTCCT,+,0.00)
chunk0169_205_1	chr6	102882907	102883500	+	0	NA	Intergenic	Intergenic	1484218	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.005059	0.319865	
chunk0045_41_1	chr12	44710745	44711184	+	0	NA	intron (NM_001145108, intron 11 of 19)	intron (NM_001145108, intron 11 of 19)	164697	NM_001145109	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.000000	0.365909	
chunk0066_213_1	chr15	33889169	33889672	+	0	NA	intron (NM_020371, intron 2 of 5)	intron (NM_020371, intron 2 of 5)	-79468	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.003976	0.333333	
chunk0177_194_1	chr7	23703548	23703845	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-6471	NM_031414	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.003367	0.496644	77(CAGGGCAGACTGTGCT,-,0.00),78(AGGGCAGACTGTGCTG,+,0.00)
chunk0051_118_1	chr12	115257782	115257981	+	0	NA	Intergenic	Intergenic	-573717	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.005025	0.320000	
chunk0205_92_1	chr9	107387305	107387750	+	0	NA	Intergenic	Intergenic	79058	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.006742	0.486547	217(GAGCTCACAGTGTTCT,-,0.00),218(AGCTCACAGTGTTCTA,+,0.00)
chunk0023_6_1	chr10	20878669	20878880	+	0	NA	intron (NM_006393, intron 5 of 27)	intron (NM_006393, intron 5 of 27)	18828	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.004739	0.358491	
chunk0207_133_1	chr9	129166998	129167197	+	0	NA	Intergenic	Intergenic	11164	NM_203434	389792	Hs.529857	NM_203434	ENSG00000188483	IER5L	bA247A12.2	immediate early response 5 like	protein-coding	0.025126	0.605000	
chunk0084_174_1	chr17	77478882	77479326	+	0	NA	intron (NM_001113495, intron 1 of 9)	L1MB2|LINE|L1	3861	NM_001113495	10801	Hs.440932	NM_006640	ENSG00000184640	SEPTIN9	AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1	septin 9	protein-coding	0.027027	0.474157	166(GAGGACAGTTTGTTTT,-,0.00),167(AGGACAGTTTGTTTTA,+,0.00)
chunk0129_422_1	chr3	127303954	127304852	+	0	NA	Intergenic	Intergenic	86267	NR_110147	101927123	Hs.526761	NR_110147	ENSG00000244215	LINC02016	-	long intergenic non-protein coding RNA 2016	ncRNA	0.033408	0.591769	389(CAGAACACACAGTTCT,-,0.00),390(AGAACACACAGTTCTG,+,0.00),497(CAGTACATACTGTACT,-,0.00),498(AGTACATACTGTACTG,+,0.00),828(GGGCACAGTCTGCACT,-,0.00),829(GGCACAGTCTGCACTT,+,0.00)
chunk0067_427_1	chr15	49918052	49918552	+	0	NA	intron (NR_073596, intron 19 of 27)	MamRep38|DNA|hAT	195014	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.002000	0.363273	
chunk0180_435_1	chr7	76482245	76482969	+	0	NA	exon (NM_001102594, exon 4 of 11)	exon (NM_001102594, exon 4 of 11)	2097	NM_001102596	113878	Hs.187058	NM_020892	ENSG00000091073	DTX2	RNF58	deltex E3 ubiquitin ligase 2	protein-coding	0.040055	0.575172	
chunk0061_364_1	chr14	63920039	63920400	+	0	NA	intron (NM_182914, intron 2 of 115)	L2c|LINE|L2	67254	NM_015180	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.016620	0.441989	
chunk0022_89_1	chr10	9209257	9209683	+	0	NA	intron (NR_120635, intron 4 of 4)	intron (NR_120635, intron 4 of 4)	-66143	NR_108039	100507163	Hs.649223	NR_108039		LINC00709	-	long intergenic non-protein coding RNA 709	ncRNA	0.018779	0.370023	181(TTGGACACCGTGTCCT,-,0.00),182(TGGACACCGTGTCCTA,+,0.00)
chunk0034_449_1	chr11	39625234	39625875	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	667576	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001560	0.281931	
chunk0050_263_1	chr12	105934262	105934599	+	0	NA	Intergenic	Intergenic	205603	NM_014840	9891	Hs.524692	NM_014840	ENSG00000074590	NUAK1	ARK5	NUAK family kinase 1	protein-coding	0.017804	0.482249	
chunk0132_383_1	chr3	163247008	163247691	+	0	NA	intron (NR_033945, intron 2 of 6)	intron (NR_033945, intron 2 of 6)	55952	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.001464	0.277778	
chunk0083_163_1	chr17	65990530	65990736	+	0	NA	intron (NM_001302891, intron 15 of 24)	L1M1|LINE|L1	-164090	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.004854	0.545894	
chunk0144_180_1	chr4	133298428	133298960	+	0	NA	Intergenic	Intergenic	149404	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.003759	0.279550	
chunk0088_352_1	chr18	52245965	52246360	+	0	NA	Intergenic	Intergenic	-94010	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.002532	0.297980	
chunk0103_296_1	chr2	166278142	166278599	+	0	NA	intron (NM_002977, intron 14 of 26)	MIRb|SINE|MIR	97617	NM_002977	6335	Hs.439145	NM_002977	ENSG00000169432	SCN9A	ETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP	sodium voltage-gated channel alpha subunit 9	protein-coding	0.002188	0.340611	
chunk0096_291_1	chr2	32440421	32440739	+	0	NA	intron (NM_016252, intron 16 of 73)	MIRc|SINE|MIR	83552	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.006289	0.354232	
chunk0071_101_1	chr15	81013672	81013932	+	0	NA	Intergenic	L2c|LINE|L2	12848	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.007692	0.486590	51(TTGCACAAGCTGTCCC,-,0.00),52(TGCACAAGCTGTCCCT,+,0.00)
chunk0143_337_1	chr4	121182052	121182251	+	0	NA	intron (NM_001128843, intron 3 of 12)	intron (NM_001128843, intron 3 of 12)	-17811	NM_024873	79931	Hs.208206	NM_024873	ENSG00000050730	TNIP3	ABIN-3|LIND	TNFAIP3 interacting protein 3	protein-coding	0.005025	0.340000	
chunk0058_260_1	chr14	25941780	25942193	+	0	NA	Intergenic	Intergenic	655768	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.012107	0.420290	
chunk0064_29_1	chr14	89429710	89430159	+	0	NA	intron (NM_001085471, intron 1 of 6)	intron (NM_001085471, intron 1 of 6)	12580	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.011136	0.366667	
chunk0066_206_1	chr15	33754209	33754460	+	0	NA	intron (NM_001036, intron 57 of 103)	L2a|LINE|L2	-214554	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.007968	0.460317	
chunk0007_204_1	chr1	81407502	81407847	+	0	NA	Intergenic	Intergenic	150028	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.000000	0.381503	
chunk0099_387_1	chr2	101566701	101567217	+	0	NA	Intergenic	Intergenic	-92256	NM_001145664	731220	Hs.662488	NM_207403	ENSG00000196460	RFX8	-	RFX family member 8, lacking RFX DNA binding domain	protein-coding	0.011628	0.408124	
chunk0154_431_1	chr5	89530806	89531249	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	485693	NR_037433	100500825		NR_037433	ENSG00000264342	MIR3660	mir-3660	microRNA 3660	ncRNA	0.002257	0.299550	
chunk0142_263_1	chr4	99230137	99230701	+	0	NA	intron (NR_037884, intron 4 of 9)	L1PA7|LINE|L1	-11173	NM_000672	130	Hs.586161	NM_000672	ENSG00000172955	ADH6	ADH-5	alcohol dehydrogenase 6 (class V)	protein-coding	0.000000	0.355752	257(AGGAGCAGGTTGTTCT,-,0.00),258(GGAGCAGGTTGTTCTG,+,0.00)
chunk0030_427_1	chr10	120409509	120409708	+	0	NA	Intergenic	Intergenic	-47346	NM_001030059	196051	Hs.40479	NM_001030059	ENSG00000203805	PLPP4	DPPL2|PPAPDC1|PPAPDC1A	phospholipid phosphatase 4	protein-coding	0.020101	0.470000	
chunk0025_374_1	chr10	59058040	59058428	+	0	NA	Intergenic	Intergenic	58716	NR_108046	100507008	Hs.170953	NR_108046		LINC00844	-	long intergenic non-protein coding RNA 844	ncRNA	0.012887	0.408740	
chunk0179_373_1	chr7	51186615	51187085	+	0	NA	intron (NM_001287436, intron 4 of 13)	intron (NM_001287436, intron 4 of 13)	129968	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.008511	0.471338	220(GAGAACTCAGTGTTCC,-,0.00),221(AGAACTCAGTGTTCCC,+,0.00)
chunk0108_215_1	chr2	233381632	233381980	+	0	NA	intron (NM_152879, intron 1 of 29)	MIRc|SINE|MIR	-6348	NM_003648	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.011494	0.375358	
chunk0062_135_1	chr14	68778600	68779186	+	0	NA	Intergenic	Intergenic	15021	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.008532	0.402044	
chunk0175_256_1	chr7	7117726	7118024	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-21089	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.003356	0.331104	194(AAGCACATCTTGATCT,-,0.00),195(AGCACATCTTGATCTT,+,0.00)
chunk0032_194_1	chr11	6587588	6587877	+	0	NA	Intergenic	MER52D|LTR|ERV1	15918	NM_015324	23378	Hs.652255	NM_015324	ENSG00000132275	RRP8	KIAA0409|NML	ribosomal RNA processing 8	protein-coding	0.017301	0.613793	
chunk0151_50_1	chr5	42426297	42427105	+	0	NA	intron (NM_001242401, intron 1 of 10)	intron (NM_001242401, intron 1 of 10)	1709	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.004950	0.336218	445(CAGTACAGAATGTCTT,-,0.00),446(AGTACAGAATGTCTTT,+,0.00)
chunk0036_157_1	chr11	62369054	62369419	+	0	NA	intron (NM_001083926, intron 4 of 6)	LTR5_Hs|LTR|ERVK	31934	NM_025080	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.010959	0.439891	
chunk0127_7_1	chr3	87927564	87928074	+	0	NA	Intergenic	Intergenic	-54757	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.001961	0.266145	
chunk0045_16_1	chr12	43200103	43200302	+	0	NA	Intergenic	MIR|SINE|MIR	351719	NM_025003	80070	Hs.287554	NM_025003	ENSG00000173157	ADAMTS20	ADAM-TS20|ADAMTS-20|GON-1	ADAM metallopeptidase with thrombospondin type 1 motif 20	protein-coding	0.000000	0.335000	
chunk0016_369_1	chr1	202508727	202509249	+	0	NA	intron (NM_002481, intron 18 of 23)	MER58A|DNA|hAT-Charlie	-31126	NM_001197131	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.013410	0.434034	
chunk0131_6_1	chr3	141716834	141717530	+	0	NA	Intergenic	L1MEc|LINE|L1	-21027	NM_014245	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.004310	0.295552	
chunk0209_292_1	chrX	48589715	48590162	+	0	NA	Intergenic	LTR75|LTR|ERVL	-7554	NR_029427	64743	Hs.521973	NM_017883	ENSG00000101940	WDR13	MG21	WD repeat domain 13	protein-coding	0.024609	0.524554	
chunk0081_401_1	chr17	48283552	48284143	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-10500	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.003384	0.474662	201(GAGGACAATGTGCTCT,-,0.00),202(AGGACAATGTGCTCTC,+,0.00),307(GAGATCAGACTGTACT,-,0.00),308(AGATCAGACTGTACTT,+,0.00)
chunk0190_72_1	chr8	29850392	29851178	+	0	NA	Intergenic	Intergenic	-22281	NR_125817	101929470	Hs.204721	NR_125817	ENSG00000248964	LOC101929470	-	uncharacterized LOC101929470	ncRNA	0.007634	0.416773	
chunk0055_44_1	chr13	52194135	52194572	+	0	NA	non-coding (NR_002816, exon 1 of 9)	non-coding (NR_002816, exon 1 of 9)	114	NR_002816	100887750	Hs.553878	NR_002816	ENSG00000243406	MRPS31P5	MRPS31P3	mitochondrial ribosomal protein S31 pseudogene 5	pseudo	0.070938	0.605023	
chunk0044_378_1	chr12	39888568	39888767	+	0	NA	intron (NM_052885, intron 4 of 9)	intron (NM_052885, intron 4 of 9)	217192	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.000000	0.325000	
chunk0101_291_1	chr2	134433400	134433853	+	0	NA	intron (NM_002410, intron 14 of 15)	intron (NM_002410, intron 14 of 15)	179367	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.015453	0.444934	
chunk0025_232_1	chr10	54091253	54091706	+	0	NA	intron (NM_001142769, intron 17 of 35)	intron (NM_001142769, intron 17 of 35)	516478	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.004415	0.405286	195(AGGAACGTATTGTTCT,-,0.00),196(GGAACGTATTGTTCTT,+,0.00)
chunk0113_160_1	chr20	52818460	52818742	+	0	NA	Intergenic	Intergenic	-153806	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.028369	0.505300	
chunk0073_106_1	chr16	4556662	4556861	+	0	NA	exon (NM_001145011, exon 1 of 16)	exon (NM_001145011, exon 1 of 16)	271	NM_001145011	342346	Hs.684212	NM_001145011	ENSG00000205832	C16orf96	-	chromosome 16 open reading frame 96	protein-coding	0.035176	0.640000	
chunk0145_226_1	chr4	148302434	148302633	+	0	NA	intron (NM_000901, intron 2 of 8)	MER61-int|LTR|ERV1	139987	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.000000	0.370000	
chunk0138_289_1	chr4	40842647	40842941	+	0	NA	intron (NM_001166051, intron 1 of 6)	intron (NM_001166051, intron 1 of 6)	14361	NM_001166051	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.013605	0.484746	
chunk0077_383_1	chr16	84716096	84716589	+	0	NA	intron (NM_001272075, intron 2 of 14)	MIRb|SINE|MIR	16393	NR_073577	9100	Hs.136778	NM_005153	ENSG00000103194	USP10	UBPO	ubiquitin specific peptidase 10	protein-coding	0.006085	0.419028	
chunk0112_221_1	chr20	40686243	40686814	+	0	NA	3' UTR (NM_005461, exon 1 of 1)	3' UTR (NM_005461, exon 1 of 1)	2712	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.010508	0.465035	
chunk0084_53_1	chr17	74431949	74432464	+	0	NA	intron (NM_022036, intron 1 of 3)	CpG	678	NM_022036	55890	Hs.446438	NM_018653	ENSG00000170412	GPRC5C	RAIG-3|RAIG3	G protein-coupled receptor class C group 5 member C	protein-coding	0.100971	0.720930	
chunk0114_198_1	chr21	15285529	15285936	+	0	NA	Intergenic	Intergenic	-220927	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.009828	0.387255	195(TGGAACACACTGTACT,-,0.00),196(GGAACACACTGTACTC,+,0.00)
chunk0170_135_1	chr6	110965769	110966173	+	0	NA	intron (NM_138408, intron 5 of 5)	MLT1F|LTR|ERVL-MaLR	7411	NM_138408	112495	Hs.418520	NM_138408	ENSG00000155115	GTF3C6	C6orf51|TFIIIC35|bA397G5.3	general transcription factor IIIC subunit 6	protein-coding	0.004950	0.414815	
chunk0003_230_1	chr1	35688028	35688534	+	0	NA	Intergenic	L2|LINE|L2	30908	NM_152374	127703	Hs.112023	NM_152374	ENSG00000142686	C1orf216	-	chromosome 1 open reading frame 216	protein-coding	0.013834	0.526627	
chunk0197_377_1	chr8	126821564	126822062	+	0	NA	Intergenic	Intergenic	-191341	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.014056	0.406814	1(GAGAACAATTTGTTCT,-,0.00),2(AGAACAATTTGTTCTC,+,0.00),185(TAGGACTTGCTGTTCT,-,0.00),186(AGGACTTGCTGTTCTC,+,0.00)
chunk0055_227_1	chr13	62662191	62662576	+	0	NA	Intergenic	L2a|LINE|L2	134309	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.000000	0.378238	
chunk0038_168_1	chr11	85030132	85030496	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	-106893	NM_001300983	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.002747	0.309589	
chunk0051_331_1	chr12	120237329	120237700	+	0	NA	intron (NM_001243756, intron 1 of 10)	intron (NM_001243756, intron 1 of 10)	12647	NM_025157	5829	Hs.446336	NM_002859	ENSG00000089159	PXN	-	paxillin	protein-coding	0.013477	0.500000	
chunk0088_284_1	chr18	49534545	49534934	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-27292	NM_001308006	9388	Hs.465102	NM_006033	ENSG00000101670	LIPG	EDL|EL|PRO719	lipase G, endothelial type	protein-coding	0.002571	0.315385	209(AGAACTCTGAGTACTC,+,0.00)
chunk0027_278_1	chr10	77485926	77486805	+	0	NA	intron (NM_001014797, intron 1 of 28)	MIR|SINE|MIR	135493	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.007964	0.479545	661(AAGAACAGTGAGCTCT,-,0.00),662(AGAACAGTGAGCTCTC,+,0.00)
chunk0105_212_1	chr2	187958504	187959040	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	328919	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.000000	0.245810	
chunk0154_368_1	chr5	87640021	87640485	+	0	NA	Intergenic	L1MEf|LINE|L1	-227220	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.004310	0.294624	
chunk0066_38_1	chr15	27715037	27715298	+	0	NA	Intergenic	Intergenic	384145	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.019157	0.458015	
chunk0123_210_1	chr3	44933658	44933969	+	0	NA	intron (NM_016598, intron 4 of 7)	intron (NM_016598, intron 4 of 7)	42369	NM_016598	51304	Hs.61430	NM_016598	ENSG00000163812	ZDHHC3	DHHC-3|DHHC3|GODZ|ZNF373	zinc finger DHHC-type containing 3	protein-coding	0.016077	0.471154	171(AGGAACAAAGTGCTCC,-,0.00),172(GGAACAAAGTGCTCCA,+,0.00)
chunk0124_67_1	chr3	53005956	53006433	+	0	NA	intron (NM_016329, intron 1 of 20)	intron (NM_016329, intron 1 of 20)	39879	NM_016329	51460	Hs.343679	NM_016329	ENSG00000163935	SFMBT1	RU1|SFMBT|hSFMBT	Scm like with four mbt domains 1	protein-coding	0.014675	0.495816	
chunk0119_340_1	chr22	47033202	47033534	+	0	NA	intron (NM_014346, intron 10 of 12)	intron (NM_014346, intron 10 of 12)	-117326	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.024096	0.486486	115(AAGAACGTCATGTTCT,-,0.00),116(AGAACGTCATGTTCTA,+,0.00)
chunk0093_323_1	chr19	54048547	54048756	+	0	NA	intron (NR_110142, intron 4 of 9)	L1MB7|LINE|L1	15302	NR_110142	284415	Hs.444431	NM_198481	ENSG00000189068	VSTM1	SIRL-1|SIRL1|UNQ3033	V-set and transmembrane domain containing 1	protein-coding	0.014354	0.390476	
chunk0126_140_1	chr3	76364017	76364673	+	0	NA	Intergenic	L2a|LINE|L2	-578762	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.004573	0.339422	
chunk0171_232_1	chr6	126438852	126439547	+	0	NA	intron (NR_104462, intron 3 of 3)	intron (NR_104462, intron 3 of 3)	-45432	NR_030316	693173		NR_030316	ENSG00000207632	MIR588	MIRN588|hsa-mir-588	microRNA 588	ncRNA	0.001439	0.349138	
chunk0184_301_1	chr7	119964992	119965762	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-58002	NR_131963	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.000000	0.430610	
chunk0202_291_1	chr9	77523901	77524221	+	0	NA	intron (NR_121184, intron 4 of 4)	intron (NR_121184, intron 4 of 4)	76412	NR_121184	101927422	Hs.434324	NR_121184	ENSG00000231373	GNA14-AS1	-	GNA14 antisense RNA 1	ncRNA	0.000000	0.339564	
chunk0052_273_1	chr12	124188511	124188902	+	0	NA	intron (NM_001204299, intron 3 of 4)	L2a|LINE|L2	-100458	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.010230	0.502551	
chunk0081_8_1	chr17	37170224	37170473	+	0	NA	intron (NM_198836, intron 41 of 55).2	intron (NM_198836, intron 41 of 55).2	-74453	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.004016	0.384000	
chunk0023_349_1	chr10	29686941	29687436	+	0	NA	intron (NM_003174, intron 1 of 35)	LTR34|LTR|ERV1	48613	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.010101	0.391129	
chunk0204_128_1	chr9	95282335	95282921	+	0	NA	intron (NM_001243744, intron 1 of 13)	L1M1|LINE|L1	34626	NM_001243743	2176	Hs.494529	NM_000136	ENSG00000158169	FANCC	FA3|FAC|FACC	FA complementation group C	protein-coding	0.001706	0.320273	
chunk0186_273_1	chr7	141695689	141696236	+	0	NA	intron (NM_001080392, intron 1 of 8)	intron (NM_001080392, intron 1 of 8)	6191	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.010969	0.509124	
chunk0178_3_1	chr7	28964030	28964577	+	0	NA	Intergenic	Intergenic	-5890	NM_014817	9865	Hs.744120	NM_014817	ENSG00000255690	TRIL	-	TLR4 interactor with leucine rich repeats	protein-coding	0.007313	0.454380	
chunk0024_155_1	chr10	35440064	35440406	+	0	NA	intron (NM_001282853, intron 2 of 10)	L1MDa|LINE|L1	103361	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.005848	0.486880	
chunk0155_17_1	chr5	90894886	90895695	+	0	NA	intron (NR_003149, intron 83 of 89)	L2b|LINE|L2	336490	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.003708	0.412346	
chunk0119_222_1	chr22	45190342	45190990	+	0	NA	Intergenic	Intergenic	10353	NR_031651	100302149		NR_031651	ENSG00000221598	MIR1249	MIRN1249|hsa-mir-1249	microRNA 1249	ncRNA	0.003086	0.391371	315(AAGTACAGCATGTTAC,-,0.00)
chunk0164_114_1	chr6	20740465	20741239	+	0	NA	intron (NM_017774, intron 6 of 15)	intron (NM_017774, intron 6 of 15)	206395	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.006460	0.348387	698(GAGGACACTTAGTGCT,-,0.00),699(AGGACACTTAGTGCTA,+,0.00)
chunk0182_199_1	chr7	95975182	95975693	+	0	NA	intron (NM_001278421, intron 5 of 15)	MLT1C|LTR|ERVL-MaLR	202931	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.003914	0.408203	188(AGGAAGAATCTGTTCT,-,0.00)
chunk0129_288_1	chr3	123285907	123286108	+	0	NA	intron (NM_001199642, intron 20 of 20)	intron (NM_001199642, intron 20 of 20)	84080	NM_012430	26984	Hs.477361	NM_012430	ENSG00000121542	SEC22A	SEC22L2	SEC22 homolog A, vesicle trafficking protein	protein-coding	0.009950	0.569307	
chunk0028_235_1	chr10	89908239	89908609	+	0	NA	Intergenic	L1PA13|LINE|L1	48949	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.005405	0.404313	
chunk0006_197_1	chr1	67579689	67580009	+	0	NA	Intergenic	L2c|LINE|L2	-105328	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.006250	0.408100	
chunk0030_353_1	chr10	118590552	118590761	+	0	NA	Intergenic	Intergenic	4992	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.004785	0.423810	
chunk0172_445_1	chr6	140981663	140982663	+	0	NA	Intergenic	L1M5|LINE|L1	298349	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.003000	0.324675	
chunk0159_146_1	chr5	139225922	139226541	+	0	NA	Intergenic	MER50|LTR|ERV1	-27855	NM_022464	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.008078	0.487097	
chunk0161_334_1	chr5	173918023	173918334	+	0	NA	intron (NM_001308191, intron 2 of 7)	intron (NM_001308191, intron 2 of 7)	25127	NM_001308193	80315	Hs.127126	NM_030627	ENSG00000113742	CPEB4	CPE-BP4|hCPEB-4	cytoplasmic polyadenylation element binding protein 4	protein-coding	0.012862	0.416667	
chunk0113_196_1	chr20	53597065	53597633	+	0	NA	Intergenic	Intergenic	-14252	NM_006526	7764	Hs.155040	NM_006526	ENSG00000171940	ZNF217	ZABC1	zinc finger protein 217	protein-coding	0.007042	0.337434	
chunk0150_233_1	chr5	35889813	35890684	+	0	NA	Intergenic	MER21C|LTR|ERVL	33373	NM_002185	3575	Hs.591742	NM_002185	ENSG00000168685	IL7R	CD127|CDW127|IL-7R-alpha|IL7RA|ILRA	interleukin 7 receptor	protein-coding	0.005741	0.408257	
chunk0183_133_1	chr7	105685111	105685674	+	0	NA	intron (NM_020725, intron 3 of 11)	intron (NM_020725, intron 3 of 11)	-6230	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.005329	0.459220	
chunk0139_63_1	chr4	49091837	49092127	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	105340	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.013793	0.422680	
chunk0057_323_1	chr13	106824401	106824786	+	0	NA	Intergenic	Intergenic	170713	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.000000	0.391192	224(AAGTACAAAATGTACC,-,0.00),225(AGTACAAAATGTACCC,+,0.00)
chunk0197_390_1	chr8	127042979	127043679	+	0	NA	Intergenic	L2a|LINE|L2	30175	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.000000	0.369472	
chunk0074_108_1	chr16	22232527	22233245	+	0	NA	intron (NM_013302, intron 2 of 17)	intron (NM_013302, intron 2 of 17)	26615	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.020891	0.493741	
chunk0043_376_1	chr12	24541460	24541935	+	0	NA	intron (NM_152989, intron 1 of 17)	intron (NM_152989, intron 1 of 17)	20752	NM_152989	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.010526	0.329832	278(GAGAACATAACGTGCT,-,0.00),279(AGAACATAACGTGCTG,+,0.00)
chunk0043_367_1	chr12	23896036	23896235	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	53568	NM_006940	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.005025	0.410000	
chunk0020_300_1	chr1	237283333	237283606	+	0	NA	intron (NM_001035, intron 2 of 104)	L2b|LINE|L2	-187650	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.010989	0.390511	
chunk0033_90_1	chr11	14117463	14118031	+	0	NA	intron (NM_006108, intron 5 of 15)	intron (NM_006108, intron 5 of 15)	155110	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.001761	0.360281	
chunk0162_415_1	chr5	179955163	179955534	+	0	NA	3' UTR (NM_001280801, exon 8 of 8)	3' UTR (NM_001280801, exon 8 of 8)	-47492	NM_198868	23061	Hs.155829	NM_015043	ENSG00000197226	TBC1D9B	GRAMD9B	TBC1 domain family member 9B	protein-coding	0.013477	0.448925	212(GAGCACATTCTGTCTC,-,0.00),213(AGCACATTCTGTCTCT,+,0.00)
chunk0046_115_1	chr12	57278346	57278975	+	0	NA	intron (NM_014925, intron 12 of 21)	intron (NM_014925, intron 12 of 21)	-27467	NR_104422	246329	Hs.417595	NM_145064	ENSG00000185482	STAC3	MYPBB|NAM	SH3 and cysteine rich domain 3	protein-coding	0.006359	0.398413	
chunk0090_41_1	chr19	1479257	1479767	+	0	NA	promoter-TSS (NM_152482)	promoter-TSS (NM_152482)	-283	NM_152482	148223	Hs.532840	NM_152482	ENSG00000119559	C19orf25	-	chromosome 19 open reading frame 25	protein-coding	0.072549	0.600783	
chunk0043_245_1	chr12	20304862	20305294	+	0	NA	Intergenic	L1M2a|LINE|L1	-64167	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.011574	0.540416	
chunk0161_272_1	chr5	172560195	172560503	+	0	NA	Intergenic	L1ME1|LINE|L1	-80917	NM_001308177	54492	Hs.91521	NM_001142651	ENSG00000214357	NEURL1B	NEURL3|RNF67B|hNeur2|neur2	neuralized E3 ubiquitin protein ligase 1B	protein-coding	0.003247	0.336570	
chunk0060_445_1	chr14	54669853	54670463	+	0	NA	intron (NM_015589, intron 1 of 11)	intron (NM_015589, intron 1 of 11)	-84630	NM_001161577	23034	Hs.98259	NM_015589	ENSG00000020577	SAMD4A	SAMD4|SMAUG|SMAUG1|SMG|SMGA	sterile alpha motif domain containing 4A	protein-coding	0.021311	0.454992	258(CAGAACATTTAGTTCT,-,0.00),259(AGAACATTTAGTTCTC,+,0.00)
chunk0022_454_1	chr10	19956416	19956984	+	0	NA	intron (NM_032812, intron 1 of 13)	L2a|LINE|L2	140257	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.005282	0.335677	263(AGGCACAGACTGTATC,-,0.00),264(GGCACAGACTGTATCT,+,0.00),309(TAGAACATTCTGTGTC,-,0.00),310(AGAACATTCTGTGTCT,+,0.00)
chunk0121_287_1	chr3	23600238	23600539	+	0	NA	Intergenic	Intergenic	-205505	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.013289	0.410596	
chunk0048_339_1	chr12	84284289	84284800	+	0	NA	Intergenic	Intergenic	628285	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.001957	0.306641	
chunk0149_103_1	chr5	18988672	18989110	+	0	NA	Intergenic	Intergenic	897381	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.006849	0.318907	
chunk0192_227_1	chr8	65395301	65396022	+	0	NA	Intergenic	L2a|LINE|L2	167005	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.002774	0.451524	
chunk0068_109_1	chr15	52355423	52355748	+	0	NA	intron (NM_001142495, intron 25 of 39)	intron (NM_001142495, intron 25 of 39)	-59787	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.006154	0.312883	
chunk0187_23_1	chr8	694226	694659	+	0	NA	intron (NM_001303100, intron 2 of 5)	intron (NM_001303100, intron 2 of 5)	36797	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.032333	0.486175	
chunk0169_333_1	chr6	106388526	106389120	+	0	NA	Intergenic	Intergenic	-63003	NM_001286111	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.001684	0.319328	
chunk0156_92_1	chr5	104795023	104795328	+	0	NA	Intergenic	Intergenic	-304299	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.352941	
chunk0135_433_1	chr3	193850721	193851114	+	0	NA	Intergenic	L1ME4a|LINE|L1	143321	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.005089	0.393401	
chunk0198_69_1	chr8	129977122	129977636	+	0	NA	intron (NR_046360, intron 1 of 14)	intron (NR_046360, intron 1 of 14)	31074	NR_049826	100847051		NR_049826	ENSG00000264653	MIR5194	mir-5194	microRNA 5194	ncRNA	0.017510	0.466019	
chunk0148_297_1	chr5	12208479	12208678	+	0	NA	Intergenic	L1PA15|LINE|L1	-304535	NM_001288717	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.005025	0.555000	
chunk0009_469_1	chr1	111755782	111755981	+	0	NA	promoter-TSS (NM_198926)	promoter-TSS (NM_198926)	-84	NM_198926	55924	Hs.193406	NM_019099	ENSG00000197852	INKA2	C1orf183|FAM212B	inka box actin regulator 2	protein-coding	0.090452	0.595000	
chunk0064_434_1	chr14	99928261	99928511	+	0	NA	intron (NM_004434, intron 17 of 21)	L1MC5|LINE|L1	134978	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.004000	0.434263	
chunk0108_336_1	chr2	235725548	235726263	+	0	NA	intron (NM_001037131, intron 3 of 17)	intron (NM_001037131, intron 3 of 17)	220154	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.009790	0.399441	462(CAGGACAAAGTGTGTT,-,0.00),463(AGGACAAAGTGTGTTT,+,0.00)
chunk0060_65_1	chr14	41833399	41833739	+	0	NA	intron (NM_152447, intron 2 of 5)	ERVL-E-int|LTR|ERVL	226008	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.005882	0.351906	
chunk0091_388_1	chr19	16068900	16069329	+	0	NA	intron (NM_001145160, intron 1 of 8)	intron (NM_001145160, intron 1 of 8)	1607	NM_001145160	7171	Hs.631618	NM_003290	ENSG00000167460	TPM4	HEL-S-108	tropomyosin 4	protein-coding	0.016317	0.488372	
chunk0082_92_1	chr17	53336273	53336472	+	0	NA	Intergenic	L1PA15|LINE|L1	350852	NM_001243552	100506650	Hs.146556	NM_001243552		C17orf112	-	chromosome 17 open reading frame 112	protein-coding	0.010050	0.540000	
chunk0072_175_1	chr15	93783989	93784343	+	0	NA	Intergenic	L2c|LINE|L2	-72394	NR_120321	101927153	Hs.371900	NR_120321		LINC02207	-	long intergenic non-protein coding RNA 2207	ncRNA	0.011299	0.498592	
chunk0047_191_1	chr12	70993989	70994700	+	0	NA	Intergenic	Intergenic	-73540	NM_002849	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.007032	0.358146	290(AAATACACACTGTTCC,-,0.00),291(AATACACACTGTTCCT,+,0.00)
chunk0006_170_1	chr1	66696779	66697416	+	0	NA	intron (NM_032291, intron 18 of 24)	intron (NM_032291, intron 18 of 24)	-55360	NM_152665	200132	Hs.479226	NM_152665	ENSG00000152760	TCTEX1D1	-	Tctex1 domain containing 1	protein-coding	0.001570	0.343260	
chunk0075_287_1	chr16	53964112	53964577	+	0	NA	intron (NM_001080432, intron 8 of 8)	MER58A|DNA|hAT-Charlie	-75049	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.000000	0.381974	
chunk0049_147_1	chr12	91914165	91914770	+	0	NA	Intergenic	Intergenic	227246	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.004959	0.386139	
chunk0118_32_1	chr22	27116394	27116593	+	0	NA	Intergenic	Intergenic	213201	NR_110540	101929539	Hs.517505	NR_110540	ENSG00000235271	LINC01422	-	long intergenic non-protein coding RNA 1422	ncRNA	0.005025	0.500000	
chunk0103_379_1	chr2	168653460	168653703	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	70638	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.004115	0.331967	
chunk0141_104_1	chr4	79426880	79427449	+	0	NA	Intergenic	LTR50|LTR|ERVL	-18946	NM_033214	2712	Hs.98008	NM_033214	ENSG00000196475	GK2	GKP2|GKTA	glycerol kinase 2	protein-coding	0.000000	0.433333	
chunk0153_366_1	chr5	74538337	74538597	+	0	NA	Intergenic	Intergenic	-1491	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.007692	0.524904	138(GAGCACAGGCTGAGCT,-,0.00),139(AGCACAGGCTGAGCTG,+,0.00)
chunk0019_381_1	chr1	230101403	230101943	+	0	NA	intron (NM_004481, intron 1 of 15)	intron (NM_004481, intron 1 of 15)	34478	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.009259	0.417745	290(TGGAACTGTGTGTTCT,-,0.00),291(GGAACTGTGTGTTCTG,+,0.00)
chunk0153_377_1	chr5	74895936	74896165	+	0	NA	Intergenic	Intergenic	-29212	NM_015566	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.004367	0.473913	
chunk0160_175_1	chr5	153576585	153576921	+	0	NA	intron (NM_001258020, intron 3 of 16)	intron (NM_001258020, intron 3 of 16)	84581	NM_001258021	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.005952	0.350148	
chunk0167_59_1	chr6	55901681	55902003	+	0	NA	Intergenic	Intergenic	-26265	NM_021073	653	Hs.296648	NM_021073	ENSG00000112175	BMP5	-	bone morphogenetic protein 5	protein-coding	0.000000	0.334365	
chunk0026_181_1	chr10	63487318	63488352	+	0	NA	Intergenic	Intergenic	-21834	NM_032776	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.006770	0.405797	
chunk0133_75_1	chr3	167091363	167092361	+	0	NA	Intergenic	Intergenic	288421	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.004008	0.336336	
chunk0213_13_1	chrY	20777582	20777857	+	0	NA	intron (NM_001039567, intron 5 of 6)	intron (NM_001039567, intron 5 of 6)	21651	NM_001039567	140032	Hs.367761	NM_001039567	ENSG00000280969	RPS4Y2	RPS4Y2P	ribosomal protein S4 Y-linked 2	protein-coding	0.003636	0.362319	154(AGTCCATAGTGTTCCC,+,0.00)
chunk0059_117_1	chr14	31229507	31230116	+	0	NA	Intergenic	Intergenic	-22288	NM_015382	25831	Hs.708017	NM_015382	ENSG00000092148	HECTD1	EULIR	HECT domain E3 ubiquitin protein ligase 1	protein-coding	0.011494	0.398361	
chunk0100_184_1	chr2	110782289	110782718	+	0	NA	intron (NM_001142807, intron 2 of 17)	Mam_R4|LINE|Dong-R4	49930	NM_001142807	55289	Hs.253320	NM_018308	ENSG00000153093	ACOXL	-	acyl-CoA oxidase like	protein-coding	0.002331	0.334884	
chunk0012_254_1	chr1	161318348	161318623	+	0	NA	intron (NM_001035513, intron 1 of 3)	intron (NM_001035513, intron 1 of 3)	4109	NM_001035513	6391	Hs.444472	NM_003001	ENSG00000143252	SDHC	CYB560|CYBL|PGL3|QPS1|SDH3	succinate dehydrogenase complex subunit C	protein-coding	0.003636	0.391304	
chunk0113_358_1	chr20	59012462	59012863	+	0	NA	Intergenic	Intergenic	-5408	NM_001336	1522	Hs.252549	NM_001336	ENSG00000101160	CTSZ	CTSX	cathepsin Z	protein-coding	0.012469	0.487562	
chunk0165_30_1	chr6	29844608	29844807	+	0	NA	Intergenic	Intergenic	17728	NM_002127	3135	Hs.512152	NM_002127	ENSG00000204632	HLA-G	MHC-G	major histocompatibility complex, class I, G	protein-coding	0.000000	0.435000	
chunk0181_308_1	chr7	87303276	87303475	+	0	NA	Intergenic	Intergenic	42117	NR_015381	11257	Hs.274329	NM_007233	ENSG00000182165	TP53TG1	LINC00096|NCRNA00096|P53TG1|P53TG1-D|TP53AP1	TP53 target 1	ncRNA	0.010050	0.500000	
chunk0012_409_1	chr1	164101787	164102116	+	0	NA	Intergenic	L1MA9|LINE|L1	-457409	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.006079	0.584848	
chunk0008_390_1	chr1	97184555	97185047	+	0	NA	intron (NM_000110, intron 20 of 22)	L1M5|LINE|L1	88878	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.008130	0.286004	
chunk0191_170_1	chr8	50630336	50630873	+	0	NA	intron (NM_018967, intron 13 of 18)	intron (NM_018967, intron 13 of 18)	718825	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.000000	0.371747	
chunk0016_297_1	chr1	201245118	201245317	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-38235	NM_000299	5317	Hs.497350	NM_000299	ENSG00000081277	PKP1	B6P	plakophilin 1	protein-coding	0.005025	0.540000	
chunk0113_424_1	chr20	62149875	62150188	+	0	NA	intron (NR_125981, intron 1 of 11)	intron (NR_125981, intron 1 of 11)	6311	NR_125981	26039	Hs.154429	NM_015558	ENSG00000184402	SS18L1	CREST|LP2261	SS18L1 subunit of BAF chromatin remodeling complex	protein-coding	0.035144	0.509554	
chunk0076_35_1	chr16	59635006	59635295	+	0	NA	Intergenic	Intergenic	120041	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.003460	0.413793	
chunk0212_191_1	chrX	134089400	134089599	+	0	NA	Intergenic	L1PA17|LINE|L1	79953	NR_029852	574031		NR_029852	ENSG00000284499	MIR363	MIR-363|MIRN363|hsa-mir-363	microRNA 363	ncRNA	0.005025	0.435000	
chunk0194_340_1	chr8	89038399	89038653	+	0	NA	Intergenic	Intergenic	-711038	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.007874	0.368627	
chunk0137_175_1	chr4	17432626	17432825	+	0	NA	Intergenic	L1PB3|LINE|L1	79509	NM_001306140	5860	Hs.75438	NM_000320	ENSG00000151552	QDPR	DHPR|HDHPR|PKU2|SDR33C1	quinoid dihydropteridine reductase	protein-coding	0.000000	0.345000	
chunk0130_59_1	chr3	129790850	129791142	+	0	NA	intron (NM_001128224, intron 3 of 5)	intron (NM_001128224, intron 3 of 5)	89563	NM_001017395	23023	Hs.477547	NM_015008	ENSG00000172765	TMCC1	-	transmembrane and coiled-coil domain family 1	protein-coding	0.013699	0.337884	
chunk0128_265_1	chr3	110464238	110464629	+	0	NA	Intergenic	Intergenic	605526	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.007673	0.487245	
chunk0151_361_1	chr5	54738947	54739370	+	0	NA	intron (NR_104658, intron 1 of 2)	MLT1C|LTR|ERVL-MaLR	5100	NR_104658	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.009456	0.389151	153(CTGCACAGTGTGATCC,-,0.00),154(TGCACAGTGTGATCCC,+,0.00)
chunk0138_138_1	chr4	36891140	36891367	+	0	NA	Intergenic	L1PA15|LINE|L1	350738	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.000000	0.548246	
chunk0105_8_1	chr2	181810605	181811474	+	0	NA	Intergenic	Intergenic	-80677	NM_001287504	6744	Hs.196983	NM_006751	ENSG00000138434	ITPRID2	CS-1|CS1|KRAP|SPAG13|SSFA2	ITPR interacting domain containing 2	protein-coding	0.010357	0.414943	
chunk0039_185_1	chr11	100697441	100697640	+	0	NA	intron (NM_152432, intron 1 of 23)	intron (NM_152432, intron 1 of 23)	-9585	NR_133571	100128386	Hs.635125	NR_133571	ENSG00000248027	LOC100128386	-	uncharacterized LOC100128386	ncRNA	0.030151	0.430000	
chunk0050_62_1	chr12	101268752	101269145	+	0	NA	Intergenic	L1MC2|LINE|L1	-11179	NM_014503	27340	Hs.295732	NM_014503	ENSG00000120800	UTP20	1A6/DRIM|DRIM	UTP20 small subunit processome component	protein-coding	0.005089	0.370558	
chunk0134_258_1	chr3	179431545	179431927	+	0	NA	intron (NM_021629, intron 1 of 9)	L1MC5a|LINE|L1	19847	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.002618	0.375979	
chunk0094_219_1	chr2	6692107	6692620	+	0	NA	Intergenic	Intergenic	-41844	NR_110497	102800314	Hs.258100	NR_110497	ENSG00000236172	MIR7515HG	-	MIR7515 host gene	ncRNA	0.011696	0.348249	
chunk0075_90_1	chr16	48313254	48313494	+	0	NA	intron (NM_031490, intron 11 of 14)	L1PA11|LINE|L1	-42311	NR_040677	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.000000	0.394191	
chunk0115_112_1	chr21	22869187	22869431	+	0	NA	Intergenic	L1MA2|LINE|L1	-209975	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.000000	0.334694	
chunk0021_75_1	chr10	1495099	1495496	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	-31333	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.005038	0.324121	
chunk0096_355_1	chr2	36360707	36361349	+	0	NA	intron (NM_016441, intron 1 of 16)	intron (NM_016441, intron 1 of 16)	4801	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.006231	0.398134	
chunk0014_387_1	chr1	182754269	182754634	+	0	NA	Intergenic	Intergenic	-34998	NM_001200056	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.016438	0.527322	
chunk0084_408_1	chr17	82258983	82259468	+	0	NA	intron (NR_110578, intron 2 of 8)	L1M5|LINE|L1	14493	NM_001893	1453	Hs.631725	NM_001893	ENSG00000141551	CSNK1D	ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID	casein kinase 1 delta	protein-coding	0.004124	0.366255	
chunk0102_121_1	chr2	144953216	144953765	+	0	NA	intron (NR_033870, intron 3 of 4)	intron (NR_033870, intron 3 of 4)	285523	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.003643	0.400000	
chunk0190_226_1	chr8	35793435	35793962	+	0	NA	3' UTR (NM_080872, exon 17 of 17)	3' UTR (NM_080872, exon 17 of 17)	-83378	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.001898	0.333333	
chunk0037_445_1	chr11	80431969	80432548	+	0	NA	Intergenic	L2a|LINE|L2	330545	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.005181	0.365517	
chunk0173_433_1	chr6	151319005	151319497	+	0	NA	intron (NM_005100, intron 3 of 4)	intron (NM_005100, intron 3 of 4)	-6280	NM_144497	9590	Hs.371240	NM_005100	ENSG00000131016	AKAP12	AKAP250|SSeCKS	A-kinase anchoring protein 12	protein-coding	0.002033	0.314402	
chunk0125_262_1	chr3	69200687	69200949	+	0	NA	intron (NM_015123, intron 11 of 22)	intron (NM_015123, intron 11 of 22)	-78223	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.011450	0.452471	
chunk0013_130_1	chr1	168137231	168137875	+	0	NA	promoter-TSS (NM_153832)	promoter-TSS (NM_153832)	20	NM_001267614	23432	Hs.271809	NM_007369	ENSG00000143147	GPR161	RE2	G protein-coupled receptor 161	protein-coding	0.038820	0.528682	
chunk0041_371_1	chr11	131498732	131499290	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	41856	NR_110140	101929653	Hs.559159	NR_110140	ENSG00000237654	LOC101929653	-	uncharacterized LOC101929653	ncRNA	0.014337	0.518784	
chunk0145_72_1	chr4	145679448	145680635	+	0	NA	promoter-TSS (NM_001080531)	promoter-TSS (NM_001080531)	-163	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.006740	0.402357	961(CAGGACAGCATGAGCC,-,0.00),962(AGGACAGCATGAGCCT,+,0.00)
chunk0053_215_1	chr13	32080288	32080646	+	0	NA	intron (NM_023037, intron 2 of 60)	MIR|SINE|MIR	-48828	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.002793	0.403900	
chunk0098_248_1	chr2	74867723	74868019	+	0	NA	intron (NM_000189, intron 3 of 17)	intron (NM_000189, intron 3 of 17)	35216	NM_000189	3099	Hs.406266	NM_000189	ENSG00000159399	HK2	HKII|HXK2	hexokinase 2	protein-coding	0.013514	0.508418	215(GAGCTCAGGCTGTTCT,-,0.00),216(AGCTCAGGCTGTTCTG,+,0.00)
chunk0184_56_1	chr7	112381720	112382186	+	0	NA	Intergenic	L1PA16|LINE|L1	-41191	NM_001197080	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.004292	0.336188	
chunk0007_69_1	chr1	78325498	78325880	+	0	NA	intron (NR_027310, intron 3 of 5)	ERVL-E-int|LTR|ERVL	96090	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.007853	0.422977	275(TTGCACATTCTGTGCC,-,0.00),276(TGCACATTCTGTGCCC,+,0.00)
chunk0111_191_1	chr20	25517724	25518010	+	0	NA	intron (NM_025176, intron 2 of 23)	intron (NM_025176, intron 2 of 23)	67650	NM_025176	22981	Hs.631508	NM_025176	ENSG00000101004	NINL	NLP	ninein like	protein-coding	0.006993	0.351916	
chunk0097_336_1	chr2	57921560	57922247	+	0	NA	intron (NM_001288837, intron 1 of 15)	X2_LINE|LINE|CR1	14252	NM_001288837	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.002911	0.335756	124(GGGAACAGTAAGTTCC,-,0.00),125(GGAACAGTAAGTTCCC,+,0.00)
chunk0118_115_1	chr22	29377210	29377485	+	0	NA	intron (NM_145730, intron 1 of 20)	intron (NM_145730, intron 1 of 20)	11236	NM_001127	162	Hs.368794	NM_001127	ENSG00000100280	AP1B1	ADTB1|AP105A|BAM22|CLAPB2	adaptor related protein complex 1 subunit beta 1	protein-coding	0.003636	0.387681	
chunk0066_70_1	chr15	29207853	29208283	+	0	NA	intron (NM_015307, intron 3 of 10)	intron (NM_015307, intron 3 of 10)	61748	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.011628	0.570766	
chunk0085_291_1	chr18	7946694	7947070	+	0	NA	intron (NM_001105244, intron 5 of 32)	intron (NM_001105244, intron 5 of 32)	379566	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.005319	0.477454	
chunk0151_438_1	chr5	56029805	56030276	+	0	NA	Intergenic	MIR3|SINE|MIR	34873	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.000000	0.434322	
chunk0121_90_1	chr3	16456910	16457268	+	0	NA	intron (NM_015150, intron 2 of 9)	intron (NM_015150, intron 2 of 9)	56626	NM_015150	23180	Hs.98910	NM_015150	ENSG00000131378	RFTN1	MIG2|PIB10|PIG9|RAFTLIN	raftlin, lipid raft linker 1	protein-coding	0.005587	0.378830	
chunk0042_233_1	chr12	6266885	6267592	+	0	NA	Intergenic	L1ME4b|LINE|L1	-43198	NM_018173	55200	Hs.631660	NM_018173	ENSG00000008323	PLEKHG6	MyoGEF	pleckstrin homology and RhoGEF domain containing G6	protein-coding	0.015559	0.488701	
chunk0154_150_1	chr5	79442486	79442733	+	0	NA	intron (NM_001277078, intron 4 of 5)	intron (NM_001277078, intron 4 of 5)	71227	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.004049	0.415323	
chunk0206_17_1	chr9	115740589	115740886	+	0	NA	intron (NR_109805, intron 2 of 2)	L3|LINE|CR1	3502	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.010101	0.422819	
chunk0033_287_1	chr11	19627957	19628512	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	52924	NR_039706	100616118		NR_039706	ENSG00000265210	MIR4486	-	microRNA 4486	ncRNA	0.012613	0.546763	276(GTGGACATTATGTTCC,-,0.00),277(TGGACATTATGTTCCT,+,0.00)
chunk0149_116_1	chr5	19318136	19318609	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	567900	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002114	0.318565	280(AGAGACTGTGTGTTCC,-,0.00),281(GAGACTGTGTGTTCCT,+,0.00)
chunk0067_353_1	chr15	48507150	48507903	+	0	NA	intron (NM_000138, intron 15 of 65)	intron (NM_000138, intron 15 of 65)	138262	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.001328	0.396552	
chunk0038_350_1	chr11	93188598	93189028	+	0	NA	intron (NM_152313, intron 1 of 10)	MLT1C|LTR|ERVL-MaLR	8642	NM_001286139	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.002326	0.387471	
chunk0162_165_1	chr6	3509175	3509441	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-52749	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.018797	0.505618	
chunk0090_16_1	chr19	707218	707725	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-1482	NM_001040134	5064	Hs.631841	NM_002579	ENSG00000099864	PALM	PALM1	paralemmin	protein-coding	0.019724	0.500000	
chunk0175_75_1	chr7	2196252	2196786	+	0	NA	intron (NM_003550, intron 10 of 18)	intron (NM_003550, intron 10 of 18)	36429	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.029963	0.502804	284(GTGGGCAGACTGTGCT,-,0.00),285(TGGGCAGACTGTGCTG,+,0.00)
chunk0129_139_1	chr3	120419049	120419270	+	0	NA	intron (NM_007085, intron 2 of 10)	intron (NM_007085, intron 2 of 10)	-23430	NR_029584	406975		NR_029584	ENSG00000284121	MIR198	MIRN198|miR-198	microRNA 198	ncRNA	0.013575	0.554054	
chunk0164_54_1	chr6	19165414	19165796	+	0	NA	intron (NR_110860, intron 3 of 10)	L1MC2|LINE|L1	14875	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.002618	0.328982	
chunk0145_13_1	chr4	143376449	143377014	+	0	NA	intron (NM_002039, intron 1 of 9)	intron (NM_002039, intron 1 of 9)	33271	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.005310	0.349823	
chunk0031_224_1	chr10	126249885	126250599	+	0	NA	intron (NM_001288973, intron 3 of 22)	intron (NM_001288973, intron 3 of 22)	138316	NM_001288975	8038	Hs.594351	NM_003474	ENSG00000148848	ADAM12	ADAM12-OT1|CAR10|MCMP|MCMPMltna|MLTN|MLTNA	ADAM metallopeptidase domain 12	protein-coding	0.009804	0.423776	417(GAGAACAAACAGTGCT,-,0.00),418(AGAACAAACAGTGCTC,+,0.00)
chunk0199_198_1	chr9	4811261	4811645	+	0	NA	intron (NM_001286699, intron 1 of 6)	L1MA5|LINE|L1	18619	NM_001286700	10171	Hs.194121	NM_005772	ENSG00000120158	RCL1	RNAC|RPCL1	RNA terminal phosphate cyclase like 1	protein-coding	0.007812	0.340260	
chunk0169_290_1	chr6	105894168	105894429	+	0	NA	Intergenic	Intergenic	-192022	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.003831	0.362595	
chunk0132_257_1	chr3	158914746	158914955	+	0	NA	Intergenic	MER66-int|LTR|ERV1	112924	NR_110328	64747	Hs.58663	NM_022736	ENSG00000118855	MFSD1	SMAP4	major facilitator superfamily domain containing 1	protein-coding	0.000000	0.338095	
chunk0052_337_1	chr12	126262894	126263093	+	0	NA	Intergenic	Intergenic	167001	NR_110053	101927464	Hs.443932	NR_110053	ENSG00000284848	LINC02359	-	long intergenic non-protein coding RNA 2359	ncRNA	0.015075	0.550000	
chunk0136_294_1	chr3	194984931	194985401	+	0	NA	Intergenic	LTR50|LTR|ERVL	-109422	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.063830	0.656051	
chunk0193_13_1	chr8	70571302	70571986	+	0	NA	Intergenic	L1M3|LINE|L1	36815	NM_014294	23471	Hs.491988	NM_014294	ENSG00000067167	TRAM1	PNAS8|TRAM|TRAMP	translocation associated membrane protein 1	protein-coding	0.005848	0.375182	
chunk0166_235_1	chr6	47131667	47132042	+	0	NA	Intergenic	L2a|LINE|L2	-89491	NM_025048	266977	Hs.733762	NM_025048	ENSG00000153292	ADGRF1	GPR110|KPG_012|PGR19|hGPCR36	adhesion G protein-coupled receptor F1	protein-coding	0.008000	0.367021	
chunk0078_110_1	chr17	2511776	2512053	+	0	NA	promoter-TSS (NM_024086)	promoter-TSS (NM_024086)	-8	NM_024086	79066	Hs.632237	NM_024086	ENSG00000127804	METTL16	METT10D	methyltransferase like 16	protein-coding	0.075812	0.579137	
chunk0091_382_1	chr19	15934970	15935474	+	0	NA	promoter-TSS (NM_001128932)	promoter-TSS (NM_001128932)	-356	NM_021187	57834	Hs.187393	NM_021187	ENSG00000171903	CYP4F11	CYPIVF11	cytochrome P450 family 4 subfamily F member 11	protein-coding	0.009921	0.540594	
chunk0208_104_1	chrX	13764880	13765406	+	0	NA	intron (NM_003611, intron 19 of 22)	intron (NM_003611, intron 19 of 22)	30430	NM_003611	8481	Hs.6483	NM_003611	ENSG00000046651	OFD1	71-7A|CXorf5|JBTS10|RP23|SGBS2	OFD1 centriole and centriolar satellite protein	protein-coding	0.011407	0.436433	
chunk0002_339_1	chr1	24893497	24893851	+	0	NA	Intergenic	Intergenic	25742	NR_106789	102465437		NR_106789	ENSG00000278034	MIR6731	hsa-mir-6731	microRNA 6731	ncRNA	0.008475	0.507042	
chunk0111_44_1	chr20	22346673	22347034	+	0	NA	Intergenic	Intergenic	-64052	NR_110615	101929663	Hs.143562	NR_110615	ENSG00000225321	LINC01427	-	long intergenic non-protein coding RNA 1427	ncRNA	0.008310	0.414365	
chunk0033_427_1	chr11	25022476	25022825	+	0	NA	intron (NM_001009909, intron 9 of 11)	intron (NM_001009909, intron 9 of 11)	525680	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002865	0.297143	
chunk0107_242_1	chr2	217220538	217221232	+	0	NA	Intergenic	Intergenic	-61848	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.004323	0.424460	
chunk0035_68_1	chr11	41765579	41765912	+	0	NA	intron (NR_120584, intron 2 of 5)	intron (NR_120584, intron 2 of 5)	51177	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.000000	0.293413	
chunk0046_406_1	chr12	64282065	64282440	+	0	NA	intron (NM_001099676, intron 6 of 10)	MER58A|DNA|hAT-Charlie	-59956	NM_001300940	144577	Hs.444671	NM_152440	ENSG00000174206	C12orf66	-	chromosome 12 open reading frame 66	protein-coding	0.016000	0.438830	
chunk0162_106_1	chr6	2642966	2643638	+	0	NA	Intergenic	L1ME1|LINE|L1	-8699	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.004464	0.407132	
chunk0079_399_1	chr17	19359756	19360027	+	0	NA	intron (NM_001243473, intron 2 of 5)	intron (NM_001243473, intron 2 of 5)	2842	NM_015681	27077	Hs.309467	NM_015681	ENSG00000108641	B9D1	B9|EPPB9|JBTS27|MKS9|MKSR-1|MKSR1	B9 domain containing 1	protein-coding	0.007380	0.514706	
chunk0044_49_1	chr12	27679116	27679695	+	0	NA	intron (NM_003622, intron 19 of 29)	intron (NM_003622, intron 19 of 29)	-17090	NM_001029874	387849	Hs.269836	NM_001029874	ENSG00000174236	REP15	RAB15EP	RAB15 effector protein	protein-coding	0.006908	0.379310	
chunk0173_135_1	chr6	143755260	143755864	+	0	NA	intron (NM_001100166, intron 4 of 11)	intron (NM_001100166, intron 4 of 11)	77597	NM_001100165	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.014901	0.421488	
chunk0029_321_1	chr10	104368292	104368901	+	0	NA	intron (NM_001008723, intron 6 of 17)	intron (NM_001008723, intron 6 of 17)	14832	NM_001008723	159686	Hs.253576	NM_001008723	ENSG00000120051	CFAP58	C10orf80|CCDC147|bA127L20.4|bA127L20.5|bA554P13.1	cilia and flagella associated protein 58	protein-coding	0.004926	0.419672	206(CAGCACAGTTTGGTCT,-,0.00)
chunk0056_443_1	chr13	95152042	95152473	+	0	NA	intron (NM_001105515, intron 19 of 20)	intron (NM_001105515, intron 19 of 20)	149189	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.004640	0.358796	
chunk0126_9_1	chr3	73453713	73454187	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-19954	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.008439	0.404211	
chunk0201_297_1	chr9	41224315	41224860	+	0	NA	Intergenic	Intergenic	-9168	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.009174	0.395604	
chunk0068_140_1	chr15	53549794	53550434	+	0	NA	intron (NR_102334, intron 18 of 19)	L2b|LINE|L2	-9011	NR_102335	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.004687	0.404056	335(AGACACAGTCTGTGCC,-,0.00),336(GACACAGTCTGTGCCT,+,0.00)
chunk0061_7_1	chr14	55543353	55543983	+	0	NA	Intergenic	Intergenic	36424	NR_027123	100129075	Hs.633724	NR_027123	ENSG00000186615	KTN1-AS1	C14orf33|MYCLo-3	KTN1 antisense RNA 1	ncRNA	0.020635	0.521395	
chunk0016_121_1	chr1	196812517	196812716	+	0	NA	Intergenic	Intergenic	-7115	NM_002113	3078	Hs.575869	NM_002113	ENSG00000244414	CFHR1	CFHL|CFHL1|CFHL1P|CFHR1P|FHR1|H36-1|H36-2|HFL1|HFL2	complement factor H related 1	protein-coding	0.005025	0.425000	
chunk0212_227_1	chrX	136247688	136247953	+	0	NA	intron (NM_001173516, intron 1 of 18)	intron (NM_001173516, intron 1 of 18)	3759	NM_024597	79649	Hs.446275	NM_024597	ENSG00000129680	MAP7D3	MDP3	MAP7 domain containing 3	protein-coding	0.003774	0.353383	
chunk0139_326_1	chr4	58648594	58648962	+	0	NA	Intergenic	Intergenic	1222906	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.002717	0.338753	
chunk0110_160_1	chr20	13963208	13963412	+	0	NA	intron (NR_073207, intron 1 of 18)	intron (NR_073207, intron 1 of 18)	27309	NR_073206	80343	Hs.590879	NM_025229	ENSG00000101251	SEL1L2	C20orf50|sel-1L2	SEL1L2 adaptor subunit of ERAD E3 ligase	protein-coding	0.004902	0.360976	
chunk0070_106_1	chr15	70396382	70397151	+	0	NA	Intergenic	Intergenic	-218781	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.015605	0.379221	
chunk0182_443_1	chr7	101779204	101779552	+	0	NA	Intergenic	Intergenic	-36526	NM_001202545	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.008621	0.530086	183(CAGGACACACAGTCCC,-,0.00),184(AGGACACACAGTCCCT,+,0.00)
chunk0193_72_1	chr8	73147945	73148358	+	0	NA	Intergenic	L2c|LINE|L2	-54879	NM_153225	157869	Hs.439040	NM_153225	ENSG00000164764	SBSPON	C8orf84|RPESP	somatomedin B and thrombospondin type 1 domain containing	protein-coding	0.002421	0.458937	
chunk0010_451_1	chr1	121476497	121476696	+	0	NA	Intergenic	Intergenic	-42516	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.000000	0.360000	
chunk0022_240_1	chr10	14198081	14198395	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	123954	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.028662	0.526984	
chunk0058_184_1	chr14	24102723	24103133	+	0	NA	intron (NM_001308054, intron 8 of 9)	intron (NM_001308054, intron 8 of 9)	8647	NM_001308054	5106	Hs.75812	NM_004563	ENSG00000100889	PCK2	PEPCK|PEPCK-M|PEPCK2	phosphoenolpyruvate carboxykinase 2, mitochondrial	protein-coding	0.014634	0.540146	
chunk0085_127_1	chr18	3093857	3094533	+	0	NA	exon (NM_003803, exon 26 of 38)	exon (NM_003803, exon 26 of 38)	-82248	NM_014646	9663	Hs.132342	NM_014646	ENSG00000101577	LPIN2	-	lipin 2	protein-coding	0.010355	0.403250	
chunk0090_323_1	chr18	75776280	75776596	+	0	NA	Intergenic	Intergenic	-346560	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.003165	0.482650	
chunk0205_5_1	chr9	104918247	104918904	+	0	NA	intron (NM_005502, intron 1 of 49)	intron (NM_005502, intron 1 of 49)	9671	NM_005502	19	Hs.659274	NM_005502	ENSG00000165029	ABCA1	ABC-1|ABC1|CERP|HDLDT1|TGD	ATP binding cassette subfamily A member 1	protein-coding	0.001522	0.398176	
chunk0134_384_1	chr3	182869481	182869887	+	0	NA	intron (NM_014616, intron 17 of 29)	L1MB7|LINE|L1	76181	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.007389	0.363636	
chunk0011_17_1	chr1	143193433	143193655	+	0	NA	Intergenic	Intergenic	229048	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.049550	0.367713	
chunk0065_383_1	chr14	104582616	104583158	+	0	NA	intron (NM_001286400, intron 1 of 4)	intron (NM_001286400, intron 1 of 4)	1746	NM_001286400	400258	Hs.153827	NM_001008404	ENSG00000184601	C14orf180	C14orf77|NRAC	chromosome 14 open reading frame 180	protein-coding	0.031365	0.642726	247(GTTACACACTGTCCCT,+,0.00)
chunk0120_210_1	chr3	7382189	7383015	+	0	NA	intron (NM_000844, intron 4 of 9)	L2a|LINE|L2	152682	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.002421	0.357920	
chunk0014_34_1	chr1	174911649	174912047	+	0	NA	intron (NM_001243763, intron 2 of 3)	MamSINE1|SINE|tRNA-RTE	36330	NM_001035230	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.005025	0.411028	
chunk0114_91_1	chr21	9318138	9318516	+	0	NA	Intergenic	MER52A|LTR|ERV1	-188566	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.015873	0.583113	
chunk0212_44_1	chrY	11305166	11305619	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1116198	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.006623	0.464758	
chunk0197_233_1	chr8	123074720	123075024	+	0	NA	intron (NM_001145088, intron 1 of 19)	L2b|LINE|L2	2192	NM_001145088	93594	Hs.492716	NM_145647	ENSG00000156787	TBC1D31	Gm85|WDR67	TBC1 domain family member 31	protein-coding	0.013158	0.393443	
chunk0022_322_1	chr10	16310131	16310793	+	0	NA	Intergenic	L1MEc|LINE|L1	-126481	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.004532	0.319759	340(TGGAACATAATGTTCA,-,0.00),341(GGAACATAATGTTCAA,+,0.00)
chunk0086_299_1	chr18	23923341	23923608	+	0	NA	intron (NM_001127718, intron 24 of 36)	L2a|LINE|L2	50454	NM_000227	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.007491	0.500000	
chunk0142_336_1	chr4	101244447	101244756	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	-3729	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.012945	0.390323	
chunk0038_201_1	chr11	86218614	86218814	+	0	NA	Intergenic	Intergenic	-25670	NM_001308007	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.030000	0.487562	
chunk0106_409_1	chr2	207907806	207908030	+	0	NA	intron (NM_001080475, intron 6 of 7)	L1MB7|LINE|L1	117642	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.013393	0.382222	
chunk0185_88_1	chr7	125478615	125479370	+	0	NA	Intergenic	Intergenic	-214701	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.001325	0.301587	
chunk0179_237_1	chr7	48059708	48060348	+	0	NA	intron (NM_001100159, intron 8 of 8)	intron (NM_001100159, intron 8 of 8)	24517	NM_001267865	136288	Hs.258357	NM_001100159	ENSG00000164746	C7orf57	-	chromosome 7 open reading frame 57	protein-coding	0.007812	0.368175	
chunk0113_284_1	chr20	57049668	57050017	+	0	NA	Intergenic	MER53|DNA|hAT	-163854	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.017192	0.431429	
chunk0012_388_1	chr1	163583670	163584287	+	0	NA	Intergenic	Intergenic	-160787	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.009724	0.389968	
chunk0082_407_1	chr17	60919721	60920620	+	0	NA	intron (NM_017679, intron 12 of 23)	L1PA16|LINE|L1	242359	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.003337	0.331111	
chunk0156_407_1	chr5	114188292	114188859	+	0	NA	Intergenic	L1M5|LINE|L1	-173744	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.003527	0.299296	
chunk0020_349_1	chr1	239419116	239419447	+	0	NA	Intergenic	Intergenic	-209792	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.009063	0.325301	
chunk0128_206_1	chr3	107861448	107861676	+	0	NA	intron (NR_024276, intron 3 of 7)	intron (NR_024276, intron 3 of 7)	16506	NR_024276	151658	Hs.159043	NR_015414	ENSG00000241469	LINC00635	-	long intergenic non-protein coding RNA 635	ncRNA	0.004386	0.379913	
chunk0161_278_1	chr5	172775639	172775877	+	0	NA	Intergenic	MIR3|SINE|MIR	-4558	NM_004417	1843	Hs.171695	NM_004417	ENSG00000120129	DUSP1	CL100|HVH1|MKP-1|MKP1|PTPN10	dual specificity phosphatase 1	protein-coding	0.004202	0.476987	
chunk0185_27_1	chr7	124279618	124279935	+	0	NA	Intergenic	Intergenic	72320	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.003155	0.424528	
chunk0115_331_1	chr21	28957537	28958239	+	0	NA	intron (NM_015565, intron 14 of 29)	intron (NM_015565, intron 14 of 29)	35068	NM_015565	26046	Hs.288773	NM_015565	ENSG00000198862	LTN1	C21orf10|C21orf98|RNF160|ZNF294	listerin E3 ubiquitin protein ligase 1	protein-coding	0.002849	0.364154	377(AAGAACAATCAGTACA,-,0.00),378(AGAACAATCAGTACAT,+,0.00)
chunk0111_227_1	chr20	29084823	29085193	+	0	NA	intron (NR_132316, intron 2 of 5)	L1MEc|LINE|L1	4618	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.005405	0.328841	
chunk0122_319_1	chr3	37041228	37042032	+	0	NA	intron (NM_001167618, intron 14 of 18)	MIRc|SINE|MIR	47853	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.002488	0.390062	
chunk0033_24_1	chr11	12700886	12701222	+	0	NA	intron (NM_021961, intron 2 of 12)	intron (NM_021961, intron 2 of 12)	26632	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.011905	0.412463	82(AAGCACAGAGTCTCCT,-,0.00)
chunk0130_256_1	chr3	135908405	135908733	+	0	NA	Intergenic	L3|LINE|CR1	-57104	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.018293	0.586626	
chunk0050_336_1	chr12	107480642	107481177	+	0	NA	intron (NM_001018072, intron 1 of 16)	intron (NM_001018072, intron 1 of 16)	-99948	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.009346	0.460821	
chunk0032_78_1	chr11	2778892	2779580	+	0	NA	intron (NM_181798, intron 15 of 15)	intron (NM_181798, intron 15 of 15)	-79238	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.029070	0.648766	385(GGGAACACGGTGTTTC,-,0.00),386(GGAACACGGTGTTTCC,+,0.00)
chunk0125_268_1	chr3	69271015	69271561	+	0	NA	intron (NM_015123, intron 5 of 22)	intron (NM_015123, intron 5 of 22)	115016	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.009158	0.378428	
chunk0073_68_1	chr16	3646048	3646837	+	0	NA	Intergenic	Intergenic	-6497	NM_005223	1773	Hs.629638	NM_005223	ENSG00000213918	DNASE1	DNL1|DRNI	deoxyribonuclease 1	protein-coding	0.020279	0.553165	
chunk0040_299_1	chr11	117176010	117176582	+	0	NA	3' UTR (NM_001184748, exon 6 of 6)	3' UTR (NM_001184748, exon 6 of 6)	-2927	NM_001040455	51092	Hs.712144	NM_015996	ENSG00000149577	SIDT2	CGI-40	SID1 transmembrane family member 2	protein-coding	0.005245	0.448517	
chunk0157_226_1	chr5	119434278	119434622	+	0	NA	Intergenic	MER51B|LTR|ERV1	-17993	NM_001292027	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.005814	0.423188	
chunk0104_292_1	chr2	178453012	178453412	+	0	NA	intron (NM_001042702, intron 1 of 6)	intron (NM_001042702, intron 1 of 6)	1776	NM_001042702	494513	Hs.87734	NM_001042702	ENSG00000204311	PJVK	DFNB59	pejvakin	protein-coding	0.007500	0.346633	
chunk0020_251_1	chr1	236123531	236123743	+	0	NA	Intergenic	MIR|SINE|MIR	-18895	NM_003272	7107	Hs.498160	NM_003272	ENSG00000077585	GPR137B	TM7SF1	G protein-coupled receptor 137B	protein-coding	0.009434	0.460094	
chunk0075_427_1	chr16	57596499	57596761	+	0	NA	Intergenic	L1ME3B|LINE|L1	-23063	NM_001290142	9289	Hs.513633	NM_005682	ENSG00000205336	ADGRG1	BFPP|BPPR|GPR56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding	0.015267	0.338403	
chunk0160_107_1	chr5	150700681	150700880	+	0	NA	intron (NM_018047, intron 1 of 10)	CpG	327	NM_018047	55696	Hs.713564	NM_018047	ENSG00000086589	RBM22	Cwc2|ZC3H16|fSAP47	RNA binding motif protein 22	protein-coding	0.065327	0.675000	
chunk0084_402_1	chr17	82152351	82153213	+	0	NA	TTS (NM_001316321)	TTS (NM_001316321)	-54552	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.025522	0.623407	391(CAGCACACCCTGTCCC,-,0.00),392(AGCACACCCTGTCCCC,+,0.00)
chunk0153_305_1	chr5	73515167	73515717	+	0	NA	Intergenic	Intergenic	17017	NM_001207	689	Hs.591768	NM_001207	ENSG00000145741	BTF3	BETA-NAC|BTF3a|BTF3b|NACB	basic transcription factor 3	protein-coding	0.014545	0.431942	
chunk0042_390_1	chr12	10890249	10890497	+	0	NA	intron (NM_001291314, intron 3 of 6).3	intron (NM_001291314, intron 3 of 6).3	19189	NM_023920	50838	Hs.679407	NM_023920	ENSG00000212128	TAS2R13	T2R13|TRB3	taste 2 receptor member 13	protein-coding	0.004032	0.389558	
chunk0128_213_1	chr3	108052911	108053498	+	0	NA	intron (NM_198793, intron 7 of 8)	intron (NM_198793, intron 7 of 8)	37884	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.013629	0.469388	
chunk0034_193_1	chr11	31819303	31819585	+	0	NA	intron (NR_033971, intron 1 of 2)	intron (NR_033971, intron 1 of 2)	-1483	NM_001127612	5080	Hs.270303	NM_000280	ENSG00000007372	PAX6	AN|AN2|ASGD5|D11S812E|FVH1|MGDA|WAGR	paired box 6	protein-coding	0.024823	0.558304	
chunk0158_393_1	chr5	134613479	134613681	+	0	NA	intron (NM_001033503, intron 4 of 7)	intron (NM_001033503, intron 4 of 7)	19263	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.000000	0.261084	
chunk0199_192_1	chr9	4772778	4773131	+	0	NA	Intergenic	Intergenic	-19880	NM_001286699	10171	Hs.194121	NM_005772	ENSG00000120158	RCL1	RNAC|RPCL1	RNA terminal phosphate cyclase like 1	protein-coding	0.008499	0.341808	
chunk0036_46_1	chr11	59014106	59014867	+	0	NA	intron (NR_033853, intron 3 of 5)	L1M1|LINE|L1	43966	NR_033853	283194		NR_033853	ENSG00000255240	LOC283194	-	uncharacterized LOC283194	ncRNA	0.003942	0.311024	
chunk0165_194_1	chr6	34557428	34557642	+	0	NA	Intergenic	Intergenic	-1202	NM_012391	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.028037	0.558140	
chunk0135_135_1	chr3	187335739	187336528	+	0	NA	Intergenic	Intergenic	-32247	NM_022147	64108	Hs.43388	NM_022147	ENSG00000136514	RTP4	IFRG28|Z3CXXC4	receptor transporter protein 4	protein-coding	0.008872	0.448101	
chunk0144_264_1	chr4	137153809	137154033	+	0	NA	Intergenic	Intergenic	378577	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.293333	
chunk0051_99_1	chr12	114798547	114798855	+	0	NA	Intergenic	Intergenic	-114537	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.006494	0.446602	
chunk0072_107_1	chr15	91294065	91294766	+	0	NA	3' UTR (NM_014848, exon 14 of 14)	3' UTR (NM_014848, exon 14 of 14)	-168924	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.009986	0.376068	
chunk0171_189_1	chr6	125234051	125234326	+	0	NA	intron (NM_001003395, intron 3 of 6)	intron (NM_001003395, intron 3 of 6)	67948	NM_016063	51020	Hs.32826	NM_016063	ENSG00000111906	HDDC2	C6orf74|CGI-130|NS5ATP2|dJ167O5.2	HD domain containing 2	protein-coding	0.000000	0.394928	
chunk0112_170_1	chr20	39861322	39861815	+	0	NA	Intergenic	Intergenic	-142893	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.002028	0.455466	
chunk0091_254_1	chr19	10896813	10897153	+	0	NA	intron (NM_199141, intron 1 of 15)	MER58A|DNA|hAT-Charlie	25406	NM_199141	10498	Hs.323213	NM_199141	ENSG00000142453	CARM1	PRMT4	coactivator associated arginine methyltransferase 1	protein-coding	0.014706	0.510264	
chunk0121_24_1	chr3	15038264	15038784	+	0	NA	intron (NM_001291694, intron 12 of 13)	intron (NM_001291694, intron 12 of 13)	26785	NM_022497	64432	Hs.657764	NM_022497	ENSG00000131368	MRPS25	MRP-S25|RPMS25	mitochondrial ribosomal protein S25	protein-coding	0.013462	0.416507	
chunk0095_80_1	chr2	14815178	14815597	+	0	NA	Intergenic	Intergenic	180296	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.002387	0.388095	
chunk0091_409_1	chr19	16652978	16653343	+	0	NA	intron (NM_001300925, intron 4 of 4)	intron (NM_001300925, intron 4 of 4)	6997	NM_001300925	79086	Hs.356467	NM_024104	ENSG00000214046	SMIM7	C19orf42	small integral membrane protein 7	protein-coding	0.019178	0.516393	208(GAGAACTCCATGTTCC,-,0.00),209(AGAACTCCATGTTCCA,+,0.00)
chunk0060_143_1	chr14	44997442	44997703	+	0	NA	intron (NR_131765, intron 2 of 19)	intron (NR_131765, intron 2 of 19)	35382	NM_001308120	23116	Hs.371078	NM_015091	ENSG00000198718	TOGARAM1	FAM179B|KIAA0423	TOG array regulator of axonemal microtubules 1	protein-coding	0.007663	0.347328	
chunk0077_257_1	chr16	80909615	80910298	+	0	NA	Intergenic	Charlie22a|DNA|hAT-Charlie	-17360	NR_131947	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.010249	0.453216	
chunk0004_153_1	chr1	45360221	45360462	+	0	NA	intron (NM_007170, intron 4 of 10)	intron (NM_007170, intron 4 of 10)	-19871	NM_001293192	4595	Hs.271353	NM_012222	ENSG00000132781	MUTYH	MYH	mutY DNA glycosylase	protein-coding	0.004149	0.458678	
chunk0068_52_1	chr15	51676022	51676357	+	0	NA	Intergenic	L2c|LINE|L2	-5164	NM_001165257	29106	Hs.232618	NM_013243	ENSG00000104112	SCG3	SGIII	secretogranin III	protein-coding	0.011940	0.416667	
chunk0069_236_1	chr15	64019837	64020146	+	0	NA	intron (NM_014326, intron 2 of 11)	intron (NM_014326, intron 2 of 11)	26331	NM_014326	23604	Hs.237886	NM_014326	ENSG00000035664	DAPK2	DRP-1|DRP1	death associated protein kinase 2	protein-coding	0.006472	0.461290	
chunk0169_76_1	chr6	99341927	99342294	+	0	NA	intron (NM_032511, intron 2 of 5)	intron (NM_032511, intron 2 of 5)	7545	NM_032511	84553	Hs.573245	NM_032511	ENSG00000146267	FAXC	C6orf168|dJ273F20	failed axon connections homolog, metaxin like GST domain containing	protein-coding	0.008174	0.380435	210(CAGAACATGGAGTGCT,-,0.00),211(AGAACATGGAGTGCTG,+,0.00)
chunk0155_456_1	chr5	101753195	101753605	+	0	NA	Intergenic	HAL1b|LINE|L1	543149	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.296837	
chunk0046_413_1	chr12	64437470	64438160	+	0	NA	intron (NM_007235, intron 22 of 24)	intron (NM_007235, intron 22 of 24)	-14245	NM_013254	29110	Hs.505874	NM_013254	ENSG00000183735	TBK1	FTDALS4|IIAE8|NAK|T2K	TANK binding kinase 1	protein-coding	0.007246	0.419682	
chunk0147_17_1	chr4	170734880	170735379	+	0	NA	Intergenic	Intergenic	-305473	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.000000	0.380000	259(AAGAACAGTTTGTTCC,-,0.00),260(AGAACAGTTTGTTCCT,+,0.00)
chunk0008_233_1	chr1	94050770	94050991	+	0	NA	intron (NM_000350, intron 17 of 49)	intron (NM_000350, intron 17 of 49)	70269	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.004525	0.423423	
chunk0121_427_1	chr3	25906976	25907549	+	0	NA	Intergenic	Intergenic	-33567	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.006981	0.325784	
chunk0065_21_1	chr15	20361059	20361394	+	0	NA	Intergenic	L1MD2|LINE|L1	78482	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.000000	0.473214	
chunk0149_405_1	chr5	29136386	29136685	+	0	NA	Intergenic	Intergenic	-6968	NR_130777	101929660	Hs.171348	NR_130777		LINC02109	-	long intergenic non-protein coding RNA 2109	ncRNA	0.003344	0.283333	
chunk0088_410_1	chr18	54767061	54767555	+	0	NA	Intergenic	Intergenic	-61169	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.002024	0.359596	
chunk0178_151_1	chr7	33467110	33467603	+	0	NA	intron (NM_014451, intron 17 of 20)	intron (NM_014451, intron 17 of 20)	337816	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.008114	0.390688	
chunk0113_352_1	chr20	58942564	58943007	+	0	NA	Intergenic	L1MB7|LINE|L1	-38423	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.009029	0.414414	
chunk0017_39_1	chr1	205146881	205147149	+	0	NA	3' UTR (NM_015375, exon 13 of 13)	3' UTR (NM_015375, exon 13 of 13)	-24993	NM_005057	5929	Hs.519230	NM_005057	ENSG00000117222	RBBP5	RBQ3|SWD1	RB binding protein 5, histone lysine methyltransferase complex subunit	protein-coding	0.000000	0.442379	
chunk0106_382_1	chr2	207447400	207447800	+	0	NA	Intergenic	Intergenic	-82292	NM_004379	1385	Hs.516646	NM_004379	ENSG00000118260	CREB1	CREB|CREB-1	cAMP responsive element binding protein 1	protein-coding	0.000000	0.369077	
chunk0118_406_1	chr22	37943152	37943929	+	0	NA	3' UTR (NM_001207062, exon 6 of 6)	3' UTR (NM_001207062, exon 6 of 6)	10107	NM_032561	84645	Hs.517612	NM_032561	ENSG00000128346	C22orf23	EVG1|dJ1039K5.6	chromosome 22 open reading frame 23	protein-coding	0.015444	0.473008	
chunk0071_268_1	chr15	85567545	85568191	+	0	NA	intron (NM_007200, intron 5 of 36)	intron (NM_007200, intron 5 of 36)	-52082	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.013932	0.428130	
chunk0174_231_1	chr6	160686022	160686471	+	0	NA	Intergenic	Intergenic	-15947	NM_001168338	5340	Hs.143436	NM_000301	ENSG00000122194	PLG	-	plasminogen	protein-coding	0.008909	0.442222	
chunk0109_128_1	chr20	2941310	2941590	+	0	NA	intron (NM_080840, intron 2 of 22)	intron (NM_080840, intron 2 of 22)	18243	NM_080841	5786	Hs.269577	NM_002836	ENSG00000132670	PTPRA	HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA	protein tyrosine phosphatase receptor type A	protein-coding	0.003571	0.444840	
chunk0054_274_1	chr13	46624001	46624524	+	0	NA	intron (NM_001164213, intron 1 of 18)	intron (NM_001164213, intron 1 of 18)	71101	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.003824	0.425573	
chunk0181_302_1	chr7	87028756	87029507	+	0	NA	intron (NM_001142749, intron 1 of 21)	L2a|LINE|L2	11103	NM_001291991	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.003995	0.412234	
chunk0118_163_1	chr22	30422697	30423317	+	0	NA	3' UTR (NM_001291932, exon 11 of 11)	3' UTR (NM_001291932, exon 11 of 11)	-2616	NM_001003704	51537	Hs.713636	NM_016498	ENSG00000242114	MTFP1	HSPC242|MTP18	mitochondrial fission process 1	protein-coding	0.020968	0.533011	
chunk0095_245_1	chr2	19204316	19204582	+	0	NA	Intergenic	Intergenic	-143980	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.018797	0.565543	
chunk0192_191_1	chr8	63593664	63593932	+	0	NA	Intergenic	L1M3c|LINE|L1	127949	NR_125825	102724612	Hs.97639	NR_125825	ENSG00000253894	LOC102724612	-	uncharacterized LOC102724612	ncRNA	0.003731	0.494424	
chunk0070_113_1	chr15	70552096	70552477	+	0	NA	Intergenic	L2c|LINE|L2	-63261	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.000000	0.431937	
chunk0110_410_1	chr20	20571359	20571829	+	0	NA	exon (NM_020343, exon 23 of 40)	exon (NM_020343, exon 23 of 40)	141029	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.014894	0.401274	
chunk0012_440_1	chr1	165001016	165001713	+	0	NA	Intergenic	L2b|LINE|L2	-226723	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.000000	0.368195	
chunk0189_74_1	chr8	20938976	20939294	+	0	NA	Intergenic	L2a|LINE|L2	-14498	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.015723	0.473354	
chunk0095_376_1	chr2	23554469	23554871	+	0	NA	intron (NM_052920, intron 2 of 13)	intron (NM_052920, intron 2 of 13)	169243	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.034826	0.565757	84(GTGTACAGTGTGTACA,-,0.00),85(TGTACAGTGTGTACAC,+,0.00)
chunk0080_163_1	chr17	28221865	28222202	+	0	NA	Intergenic	Intergenic	-4530	NR_003064	23615	Hs.157195	NM_021093	ENSG00000237575	PYY2	-	peptide YY 2 (pseudogene)	pseudo	0.005935	0.511834	
chunk0049_18_1	chr12	89383133	89383630	+	0	NA	Intergenic	Intergenic	-30522	NM_022652	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.004024	0.391566	
chunk0053_263_1	chr13	33090660	33091230	+	0	NA	Intergenic	Intergenic	74512	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.007018	0.429072	
chunk0183_435_1	chr7	111164269	111164735	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	73496	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.002146	0.453961	328(CAGTACACAGTGACCT,-,0.00),329(AGTACACAGTGACCTA,+,0.00)
chunk0097_62_1	chr2	44102798	44103344	+	0	NA	Intergenic	Intergenic	-65732	NM_177968	5495	Hs.416769	NM_002706	ENSG00000138032	PPM1B	PP2C-beta|PP2C-beta-X|PP2CB|PP2CBETA|PPC2BETAX	protein phosphatase, Mg2+/Mn2+ dependent 1B	protein-coding	0.010989	0.383912	252(GAGGACAGGCCGTTCT,-,0.00),253(AGGACAGGCCGTTCTG,+,0.00)
chunk0036_325_1	chr11	66348080	66348320	+	0	NA	promoter-TSS (NM_006876)	promoter-TSS (NM_006876)	-510	NM_006876	11041	Hs.8526	NM_006876	ENSG00000174684	B4GAT1	B3GN-T1|B3GNT1|B3GNT6|BETA3GNTI|MDDGA13|iGAT|iGNT	beta-1,4-glucuronyltransferase 1	protein-coding	0.041667	0.518672	
chunk0194_309_1	chr8	88204914	88205113	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	122475	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.000000	0.410000	
chunk0054_332_1	chr13	49312480	49313092	+	0	NA	intron (NM_001079670, intron 10 of 10)	L1ME3Cz|LINE|L1	64875	NR_036439	81602	Hs.388220	NM_030911	ENSG00000102543	CDADC1	NYD-SP15|bA103J18.1	cytidine and dCMP deaminase domain containing 1	protein-coding	0.009804	0.388254	
chunk0211_170_1	chrX	115385908	115386165	+	0	NA	Intergenic	Intergenic	96319	NM_016383	51213	Hs.242183	NM_016383	ENSG00000102021	LUZP4	CT-28|CT-8|CT28|HOM-TES-85	leucine zipper protein 4	protein-coding	0.011673	0.352713	
chunk0025_189_1	chr10	53269594	53270146	+	0	NA	Intergenic	Intergenic	-498170	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.007246	0.316456	
chunk0048_392_1	chr12	87348071	87348602	+	0	NA	Intergenic	L1ME3E|LINE|L1	436375	NR_033410	400058	Hs.572212	NR_033410		MKRN9P	MKRN5|MKRN9|MKRNP6|RNF65|ZNF127L3	makorin ring finger protein 9, pseudogene	pseudo	0.005650	0.319549	
chunk0032_424_1	chr11	12227335	12227690	+	0	NA	intron (NM_001282663, intron 15 of 27)	intron (NM_001282663, intron 15 of 27)	-59388	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.008451	0.404494	
chunk0006_24_1	chr1	64006696	64007253	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	105231	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.007181	0.451613	
chunk0184_446_1	chr7	123202972	123203528	+	0	NA	Intergenic	Intergenic	-3279	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.001799	0.341113	
chunk0055_281_1	chr13	64420473	64420890	+	0	NA	Intergenic	Intergenic	-576556	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.009592	0.306220	
chunk0133_409_1	chr3	174409000	174409231	+	0	NA	Intergenic	L2a|LINE|L2	-450206	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.004329	0.267241	
chunk0118_172_1	chr22	30764272	30764654	+	0	NA	intron (NM_001282740, intron 1 of 12)	intron (NM_001282740, intron 1 of 12)	210	NM_001282740	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.010471	0.530026	
chunk0192_319_1	chr8	67068638	67069108	+	0	NA	intron (NM_024790, intron 1 of 28)	MER90a|LTR|ERV1	4505	NM_024790	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.010638	0.397028	
chunk0133_254_1	chr3	171678855	171679455	+	0	NA	intron (NM_001130081, intron 15 of 25)	L2c|LINE|L2	131339	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.005000	0.407654	
chunk0032_358_1	chr11	10669608	10670554	+	0	NA	intron (NM_001206880, intron 1 of 19)	intron (NM_001206880, intron 1 of 19)	-17780	NM_001098579	10335	Hs.501898	NM_130385	ENSG00000072952	MRVI1	IRAG|JAW1L	murine retrovirus integration site 1 homolog	protein-coding	0.007400	0.441394	
chunk0030_197_1	chr10	114347994	114348725	+	0	NA	intron (NM_001001936, intron 1 of 18)	L1ME1|LINE|L1	56419	NM_001287824	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.013680	0.424863	
chunk0198_206_1	chr8	133778882	133779360	+	0	NA	Intergenic	L1PB1|LINE|L1	-1769	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.006276	0.340292	
chunk0152_238_1	chr5	60540611	60540810	+	0	NA	intron (NR_024617, intron 3 of 3)	intron (NR_024617, intron 3 of 3)	-52612	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.010050	0.385000	
chunk0053_334_1	chr13	34412011	34412286	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	228537	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.007273	0.369565	
chunk0015_445_1	chr1	191963927	191964570	+	0	NA	Intergenic	MIR|SINE|MIR	-194214	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.004666	0.329193	
chunk0187_124_1	chr7	149130561	149130792	+	0	NA	intron (NM_020781, intron 2 of 6)	L1ME1|LINE|L1	4260	NM_020781	57541	Hs.632032	NM_020781	ENSG00000197024	ZNF398	P51|P71|ZER6	zinc finger protein 398	protein-coding	0.017316	0.413793	
chunk0041_433_1	chr11	134476468	134476719	+	0	NA	intron (NR_033852, intron 3 of 5)	intron (NR_033852, intron 3 of 5)	40111	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.027888	0.527778	
chunk0164_103_1	chr6	20560885	20561268	+	0	NA	intron (NM_017774, intron 4 of 15)	intron (NM_017774, intron 4 of 15)	26619	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.020888	0.437500	
chunk0190_210_1	chr8	35693820	35694333	+	0	NA	intron (NM_080872, intron 7 of 16)	intron (NM_080872, intron 7 of 16)	16244	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.011696	0.406615	
chunk0057_300_1	chr13	106420883	106421274	+	0	NA	Intergenic	Intergenic	44515	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.002558	0.380102	209(GAGAACTGAGTGTGTT,-,0.00),210(AGAACTGAGTGTGTTT,+,0.00)
chunk0080_172_1	chr17	28684825	28685493	+	0	NA	intron (NM_003170, intron 19 of 36)	intron (NM_003170, intron 19 of 36)	22875	NM_003170	6830	Hs.250429	NM_003170	ENSG00000109111	SUPT6H	SPT6|SPT6H|emb-5	SPT6 homolog, histone chaperone and transcription elongation factor	protein-coding	0.011976	0.424514	406(TGGGTCAGGCTGTTCC,-,0.00),407(GGGTCAGGCTGTTCCA,+,0.00)
chunk0208_68_1	chrX	11899245	11899710	+	0	NA	Intergenic	Intergenic	139861	NM_006800	10943	Hs.655288	NM_006800	ENSG00000005302	MSL3	MSL3L1	MSL complex subunit 3	protein-coding	0.008602	0.326180	
chunk0035_104_1	chr11	42340623	42341351	+	0	NA	Intergenic	MIRb|SINE|MIR	-87297	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.006868	0.397805	
chunk0092_240_1	chr19	32740578	32740809	+	0	NA	intron (NM_001110822, intron 3 of 12)	intron (NM_001110822, intron 3 of 12)	20920	NM_001110822	91646	Hs.646351	NM_001015890	ENSG00000173809	TDRD12	ECAT8	tudor domain containing 12	protein-coding	0.008658	0.547414	
chunk0175_382_1	chr6	168238983	168239356	+	0	NA	Intergenic	Intergenic	-3769	NR_110870	101929420	Hs.571211	NR_110870	ENSG00000234647	LOC101929420	-	uncharacterized LOC101929420	ncRNA	0.026810	0.510695	
chunk0179_150_1	chr7	46281044	46281570	+	0	NA	Intergenic	Intergenic	-360035	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.003802	0.358634	
chunk0019_453_1	chr1	231358559	231358791	+	0	NA	Intergenic	Intergenic	20739	NM_001010984	83932	Hs.554892	NM_032018	ENSG00000010072	SPRTN	C1orf124|DVC1|PRO4323|spartan	SprT-like N-terminal domain	protein-coding	0.008621	0.347639	
chunk0053_272_1	chr13	33196814	33197136	+	0	NA	intron (NM_001243476, intron 5 of 17)	Charlie7a|DNA|hAT-Charlie	9075	NM_001243474	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.006211	0.380805	
chunk0114_354_1	chr21	18936565	18936928	+	0	NA	Intergenic	Intergenic	-176934	NR_109925	101927797	Hs.551743	NR_109925		MIR548XHG	-	MIR548X host gene	ncRNA	0.000000	0.326923	
chunk0196_9_1	chr8	101434016	101434337	+	0	NA	Intergenic	Intergenic	-58264	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.006231	0.419255	
chunk0087_430_1	chr18	42378658	42379475	+	0	NA	intron (NR_046174, intron 4 of 9)	L1PA17|LINE|L1	192398	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.001224	0.367971	316(TGGTACAGTGTGTCTT,-,0.00),317(GGTACAGTGTGTCTTT,+,0.00)
chunk0115_175_1	chr21	25607481	25607751	+	0	NA	promoter-TSS (NM_080794)	promoter-TSS (NM_080794)	-127	NM_017446	54148	Hs.420696	NM_017446	ENSG00000154719	MRPL39	C21orf92|L39mt|MRP-L5|MRPL5|MSTP003|PRED22|PRED66|RPML5	mitochondrial ribosomal protein L39	protein-coding	0.107407	0.701107	
chunk0099_321_1	chr2	99800469	99801035	+	0	NA	intron (NM_001025108, intron 7 of 23)	L1ME1|LINE|L1	304831	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.003534	0.358025	
chunk0049_434_1	chr12	98180742	98180981	+	0	NA	Intergenic	Intergenic	-185413	NR_036189	100422924		NR_036189	ENSG00000263890	MIR4303	-	microRNA 4303	ncRNA	0.016736	0.387500	
chunk0123_72_1	chr3	41532935	41533457	+	0	NA	intron (NM_017886, intron 32 of 36)	MLT1H|LTR|ERVL-MaLR	333745	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005747	0.413002	
chunk0045_395_1	chr12	52655771	52656025	+	0	NA	Intergenic	Intergenic	-3723	NM_000423	3849	Hs.707	NM_000423	ENSG00000172867	KRT2	CK-2e|K2e|KRT2A|KRT2E|KRTE	keratin 2	protein-coding	0.011811	0.552941	
chunk0160_462_1	chr5	165201825	165202378	+	0	NA	Intergenic	L3b|LINE|CR1	731822	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.000000	0.379061	
chunk0143_262_1	chr4	116248584	116249211	+	0	NA	Intergenic	Intergenic	-50828	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.003190	0.308917	
chunk0074_117_1	chr16	22409582	22409781	+	0	NA	Intergenic	L1MC1|LINE|L1	-27327	NR_027154	641298	Hs.552700	NM_199284	ENSG00000237296	SMG1P1	-	SMG1 pseudogene 1	pseudo	0.005025	0.380000	
chunk0007_213_1	chr1	81523013	81523672	+	0	NA	intron (NR_125943, intron 1 of 3)	L1M5|LINE|L1	34360	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.004552	0.289394	
chunk0177_196_1	chr7	23742684	23743058	+	0	NA	intron (NM_001260505, intron 8 of 22)	L1M2|LINE|L1	32545	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.005348	0.408000	
chunk0061_366_1	chr14	63960058	63960698	+	0	NA	intron (NM_182914, intron 8 of 115)	L2b|LINE|L2	107413	NM_015180	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.006250	0.329173	
chunk0123_13_1	chr3	40263509	40263992	+	0	NA	intron (NR_033965, intron 2 of 2)	MER34B-int|LTR|ERV1	-45932	NM_005875	10289	Hs.315230	NM_005875	ENSG00000114784	EIF1B	GC20	eukaryotic translation initiation factor 1B	protein-coding	0.012422	0.417355	
chunk0137_112_1	chr4	13886828	13887415	+	0	NA	intron (NR_121681, intron 3 of 3)	intron (NR_121681, intron 3 of 3)	-224847	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.003407	0.363946	
chunk0103_294_1	chr2	166178885	166179317	+	0	NA	intron (NR_110260, intron 3 of 11)	intron (NR_110260, intron 3 of 11)	-29969	NM_001202435	6323	Hs.22654	NM_006920	ENSG00000144285	SCN1A	EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI	sodium voltage-gated channel alpha subunit 1	protein-coding	0.009259	0.374134	
chunk0002_398_1	chr1	27272681	27272880	+	0	NA	intron (NM_015023, intron 3 of 15)	AluJr|SINE|Alu	38264	NM_001276252	23038	Hs.469154	NM_015023	ENSG00000142784	WDTC1	ADP|DCAF9	WD and tetratricopeptide repeats 1	protein-coding	0.000000	0.480000	
chunk0037_129_1	chr11	72985625	72986026	+	0	NA	intron (NM_014824, intron 6 of 19)	intron (NM_014824, intron 6 of 19)	105905	NR_039664									0.000000	0.437811	
chunk0207_380_1	chr9	136199621	136199884	+	0	NA	exon (NM_178138, exon 3 of 6)	exon (NM_178138, exon 3 of 6)	3406	NM_014564	8022	Hs.148427	NM_014564	ENSG00000107187	LHX3	CPHD3|LIM3|M2-LHX3	LIM homeobox 3	protein-coding	0.098859	0.662879	176(TGGTACACGAAGTCCT,-,0.00),177(GGTACACGAAGTCCTG,+,0.00)
chunk0058_60_1	chr14	20628897	20629114	+	0	NA	Intergenic	L1MC1|LINE|L1	12686	NM_001001968	341799	Hs.513132	NM_001001968	ENSG00000181803	OR6S1	OR14-37|OR6S1Q	olfactory receptor family 6 subfamily S member 1	protein-coding	0.000000	0.362385	68(AAGTACAGAGAGTTCC,-,0.00),69(AGTACAGAGAGTTCCT,+,0.00),120(AAGGACATCCTGCACC,-,0.00)
chunk0056_429_1	chr13	94917834	94918161	+	0	NA	intron (NR_110754, intron 3 of 4)	intron (NR_110754, intron 3 of 4)	-42044	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.003058	0.496951	
chunk0180_442_1	chr7	77237407	77237616	+	0	NA	intron (NM_020879, intron 3 of 18)	LTR16C|LTR|ERVL	-37678	NM_006682	10875	Hs.520989	NM_006682	ENSG00000127951	FGL2	T49|pT49	fibrinogen like 2	protein-coding	0.014354	0.519048	
chunk0081_275_1	chr17	44028869	44029068	+	0	NA	Intergenic	Intergenic	-5817	NM_001304813	84336	Hs.514211	NM_032376	ENSG00000091947	TMEM101	-	transmembrane protein 101	protein-coding	0.010050	0.455000	
chunk0083_259_1	chr17	68296693	68297514	+	0	NA	intron (NM_001267727, intron 1 of 11)	intron (NM_001267727, intron 1 of 11)	5608	NM_001267727	22901	Hs.437249	NM_014960	ENSG00000141337	ARSG	USH4	arylsulfatase G	protein-coding	0.013398	0.434307	451(CTGGACAAAGAGTTCT,-,0.00),452(TGGACAAAGAGTTCTT,+,0.00)
chunk0064_147_1	chr14	91652773	91653076	+	0	NA	intron (NM_024764, intron 15 of 26)	intron (NM_024764, intron 15 of 26)	79162	NM_024764	79820	Hs.131755	NM_024764	ENSG00000133962	CATSPERB	C14orf161|CatSper(beta)	cation channel sperm associated auxiliary subunit beta	protein-coding	0.000000	0.345395	
chunk0011_209_1	chr1	150067352	150067758	+	0	NA	promoter-TSS (NM_001279354)	promoter-TSS (NM_001279354)	-113	NM_001279354	11311	Hs.443750	NM_007259	ENSG00000136631	VPS45	H1|H1VPS45|SCN5|VPS45A|VPS45B|VPS54A|VSP45|VSP45A	vacuolar protein sorting 45 homolog	protein-coding	0.064039	0.621622	
chunk0079_338_1	chr17	17685448	17685716	+	0	NA	intron (NM_030665, intron 1 of 5)	L2b|LINE|L2	4109	NM_030665	10743	Hs.655395	NM_030665	ENSG00000108557	RAI1	SMCR|SMS	retinoic acid induced 1	protein-coding	0.022388	0.587361	
chunk0003_325_1	chr1	38413143	38413645	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-198627	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.005976	0.425447	
chunk0039_200_1	chr11	100902913	100903164	+	0	NA	intron (NM_152432, intron 4 of 23)	LTR16D|LTR|ERVL	-89042	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.015936	0.500000	
chunk0160_112_1	chr5	150815500	150815699	+	0	NA	Intergenic	L1M4|LINE|L1	-30924	NM_001145805	345611	Hs.519680	NM_001145805	ENSG00000237693	IRGM	IFI1|IRGM1|LRG-47|LRG47	immunity related GTPase M	protein-coding	0.010050	0.335000	98(CAGTACTGAAAGTTCT,-,0.00),99(AGTACTGAAAGTTCTG,+,0.00)
chunk0025_376_1	chr10	59061980	59062426	+	0	NA	Intergenic	Intergenic	62685	NR_108046	100507008	Hs.170953	NR_108046		LINC00844	-	long intergenic non-protein coding RNA 844	ncRNA	0.008969	0.458613	
chunk0025_367_1	chr10	58638993	58639494	+	0	NA	intron (NM_001080512, intron 2 of 20)	intron (NM_001080512, intron 2 of 20)	-75772	NR_027508	728640	Hs.729209	NR_027508		FAM133CP	-	family with sequence similarity 133, member A pseudogene	pseudo	0.003992	0.344622	
chunk0084_417_1	chr17	82384824	82385381	+	0	NA	Intergenic	Intergenic	10825	NM_018949	2837	Hs.192720	NM_018949	ENSG00000181408	UTS2R	GPR14|UR-2-R|UTR|UTR2	urotensin 2 receptor	protein-coding	0.030521	0.652330	
chunk0124_228_1	chr3	56607317	56607826	+	0	NA	intron (NR_024460, intron 10 of 17)	L1PBa1|LINE|L1	50415	NR_024460	285331	Hs.476399	NM_001012506	ENSG00000180376	CCDC66	-	coiled-coil domain containing 66	protein-coding	0.007859	0.384314	
chunk0066_204_1	chr15	33597727	33598563	+	0	NA	intron (NM_001036, intron 16 of 103)	MER4-int|LTR|ERV1	287183	NM_001036	6263	Hs.709373	NM_001036	ENSG00000198838	RYR3	RYR-3	ryanodine receptor 3	protein-coding	0.007177	0.304659	
chunk0007_206_1	chr1	81431938	81432275	+	0	NA	Intergenic	Intergenic	125596	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.011869	0.399408	
chunk0114_282_1	chr21	16419559	16420114	+	0	NA	intron (NR_027791, intron 3 of 5)	intron (NR_027791, intron 3 of 5)	-119253	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.016216	0.359712	
chunk0146_442_1	chr4	169770324	169771089	+	0	NA	Intergenic	Intergenic	-12764	NM_017867	54969	Hs.406756	NM_017867	ENSG00000056050	HPF1	C4orf27	histone PARylation factor 1	protein-coding	0.001307	0.360313	
chunk0062_142_1	chr14	68947706	68948220	+	0	NA	intron (NM_001130004, intron 1 of 21)	intron (NM_001130004, intron 1 of 21)	31403	NM_001130005	87	Hs.235750	NM_001102	ENSG00000072110	ACTN1	BDPLT15	actinin alpha 1	protein-coding	0.015564	0.545631	195(GAGAACACGGTGTATC,-,0.00),196(AGAACACGGTGTATCT,+,0.00)
chunk0124_309_1	chr3	57998722	57998933	+	0	NA	Intergenic	Intergenic	-9573	NM_001164317	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.023697	0.485849	8(ATAAACACTCTGTTCT,-,0.00),9(TAAACACTCTGTTCTC,+,0.00)
chunk0027_62_1	chr10	73087076	73087275	+	0	NA	intron (NM_001142595, intron 1 of 15)	L1MD|LINE|L1	9799	NM_001142595	5033	Hs.500047	NM_000917	ENSG00000122884	P4HA1	P4HA	prolyl 4-hydroxylase subunit alpha 1	protein-coding	0.005025	0.310000	
chunk0209_188_1	chrX	43803868	43804133	+	0	NA	intron (NM_000898, intron 3 of 14)	intron (NM_000898, intron 3 of 14)	78475	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.007547	0.413534	165(GGGAACACATTGTTCC,-,0.00),166(GGAACACATTGTTCCA,+,0.00)
chunk0095_189_1	chr2	17977562	17978099	+	0	NA	Intergenic	Intergenic	99173	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.007449	0.440520	
chunk0001_9_1	chr1	933038	933426	+	0	NA	intron (NM_152486, intron 4 of 13)	intron (NM_152486, intron 4 of 13)	7491	NM_152486	148398	Hs.335293	NM_152486	ENSG00000187634	SAMD11	MRS	sterile alpha motif domain containing 11	protein-coding	0.030928	0.642674	
chunk0175_254_1	chr7	7114672	7115228	+	0	NA	Intergenic	Intergenic	-18164	NR_034022	100131257	Hs.551110	NR_034022		LOC100131257	-	zinc finger protein 655 pseudogene	pseudo	0.008993	0.418312	
chunk0077_130_1	chr16	78522180	78522701	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	423027	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.009597	0.402299	
chunk0171_80_1	chr6	121733850	121734198	+	0	NA	Intergenic	Intergenic	298447	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.000000	0.289398	
chunk0029_253_1	chr10	102837242	102837530	+	0	NA	5' UTR (NM_000102, exon 1 of 8)	5' UTR (NM_000102, exon 1 of 8)	147	NM_000102	1586	Hs.438016	NM_000102	ENSG00000148795	CYP17A1	CPT7|CYP17|P450C17|S17AH	cytochrome P450 family 17 subfamily A member 1	protein-coding	0.006944	0.564014	
chunk0117_433_1	chr21	46240886	46241178	+	0	NA	non-coding (NR_110566, exon 3 of 3)	non-coding (NR_110566, exon 3 of 3)	11801	NR_110565	114044	Hs.655095	NR_002776	ENSG00000215424	MCM3AP-AS1	C21orf85|MCM3AP-AS|MCM3APAS|MCM3APASB|NCRNA00031	MCM3AP antisense RNA 1	ncRNA	0.006849	0.443686	37(GAGCACACTCTGTGCT,-,0.00),38(AGCACACTCTGTGCTC,+,0.00)
chunk0060_129_1	chr14	44154843	44155373	+	0	NA	Intergenic	L1M1|LINE|L1	352188	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.000000	0.433145	
chunk0175_409_1	chr6	168725793	168726169	+	0	NA	Intergenic	Intergenic	284830	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.029255	0.586207	145(AGGGACTGACTGTTCC,-,0.00),146(GGGACTGACTGTTCCC,+,0.00)
chunk0083_341_1	chr17	70206896	70207349	+	0	NA	Intergenic	Intergenic	37587	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.004415	0.350220	
chunk0133_382_1	chr3	173939273	173939681	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	-18681	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.004902	0.354523	237(AGGCACATAATGATCT,-,0.00),238(GGCACATAATGATCTT,+,0.00)
chunk0170_142_1	chr6	111234954	111235224	+	0	NA	Intergenic	L1PB1|LINE|L1	-24190	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.000000	0.365314	
chunk0145_224_1	chr4	148268855	148269283	+	0	NA	intron (NM_000901, intron 2 of 8)	intron (NM_000901, intron 2 of 8)	173451	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.007009	0.412587	190(AAGGACTCCATGTTCT,-,0.00),191(AGGACTCCATGTTCTG,+,0.00)
chunk0090_6_1	chr19	437040	437431	+	0	NA	intron (NM_012435, intron 4 of 12)	intron (NM_012435, intron 4 of 12)	23761	NM_012435	25759	Hs.30965	NM_012435	ENSG00000129946	SHC2	SCK|SHCB|SLI	SHC adaptor protein 2	protein-coding	0.056266	0.540816	
chunk0172_129_1	chr6	135254364	135254859	+	0	NA	Intergenic	Intergenic	15451	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.004040	0.497984	262(AGGGACAGGCTGCTCC,-,0.00),263(GGGACAGGCTGCTCCC,+,0.00)
chunk0206_240_1	chr9	123642378	123642982	+	0	NA	intron (NM_024820, intron 9 of 20)	intron (NM_024820, intron 9 of 20)	-157058	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.011589	0.421488	
chunk0137_462_1	chr4	30153180	30153379	+	0	NA	Intergenic	MER52C|LTR|ERV1	-567129	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.000000	0.530000	
chunk0203_110_1	chr9	84615053	84615660	+	0	NA	Intergenic	Intergenic	-53102	NM_001291937	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.000000	0.391447	
chunk0156_162_1	chr5	107462100	107462804	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	208443	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.005682	0.408511	
chunk0028_320_1	chr10	91881474	91881673	+	0	NA	Intergenic	L2a|LINE|L2	27928	NM_152429	143282	Hs.466120	NM_152429	ENSG00000174721	FGFBP3	C10orf13|FGF-BP3	fibroblast growth factor binding protein 3	protein-coding	0.005025	0.505000	
chunk0007_38_1	chr1	77683620	77683916	+	0	NA	promoter-TSS (NM_001308237)	promoter-TSS (NM_001308237)	-341	NM_001308237	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.047297	0.569024	
chunk0116_392_1	chr21	42366317	42366587	+	0	NA	promoter-TSS (NM_003225)	promoter-TSS (NM_003225)	83	NM_003225	7031	Hs.162807	NM_003225	ENSG00000160182	TFF1	BCEI|D21S21|HP1.A|HPS2|pNR-2|pS2	trefoil factor 1	protein-coding	0.037037	0.601476	150(CAGATCACCTTGTTCT,-,0.00),151(AGATCACCTTGTTCTC,+,0.00)
chunk0171_367_1	chr6	130847470	130847883	+	0	NA	intron (NM_001199388, intron 17 of 17)	intron (NM_001199388, intron 17 of 17)	20271	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.012107	0.347826	
chunk0088_286_1	chr18	49639212	49639439	+	0	NA	Intergenic	MIRb|SINE|MIR	77294	NM_006033	9388	Hs.465102	NM_006033	ENSG00000101670	LIPG	EDL|EL|PRO719	lipase G, endothelial type	protein-coding	0.008811	0.464912	202(ATGTACATAATGTCCT,-,0.00),203(TGTACATAATGTCCTT,+,0.00)
chunk0069_141_1	chr15	62385143	62385746	+	0	NA	Intergenic	Intergenic	42415	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.003317	0.321192	
chunk0171_376_1	chr6	130947057	130947771	+	0	NA	intron (NM_001199388, intron 3 of 17)	intron (NM_001199388, intron 3 of 17)	53353	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.005602	0.406993	
chunk0129_192_1	chr3	121269722	121270088	+	0	NA	intron (NM_014980, intron 18 of 27)	intron (NM_014980, intron 18 of 27)	220265	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.002732	0.348774	
chunk0174_146_1	chr6	157602953	157603489	+	0	NA	intron (NM_024630, intron 3 of 8)	L2c|LINE|L2	74089	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.020522	0.515829	
chunk0046_172_1	chr12	58532922	58533746	+	0	NA	Intergenic	Intergenic	-58368	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.002427	0.398788	
chunk0161_215_1	chr5	170862958	170863625	+	0	NA	intron (NM_022897, intron 1 of 27)	L2c|LINE|L2	1409	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.008996	0.425150	260(AAGAACATGGTGTACT,-,0.00),261(AGAACATGGTGTACTG,+,0.00)
chunk0003_46_1	chr1	30735543	30735842	+	0	NA	intron (NM_006762, intron 6 of 7)	intron (NM_006762, intron 6 of 7)	3540	NR_039616	100616164		NR_039616	ENSG00000264773	MIR4420	mir-4420	microRNA 4420	ncRNA	0.006689	0.470000	172(AGGAACAGTTAGTACA,-,0.00)
chunk0058_43_1	chr14	20191332	20191832	+	0	NA	Intergenic	Intergenic	-5754	NM_001005503	390439	Hs.554582	NM_001005503	ENSG00000196832	OR11G2	OR14-34	olfactory receptor family 11 subfamily G member 2	protein-coding	0.008000	0.419162	
chunk0028_242_1	chr10	90179621	90180043	+	0	NA	Intergenic	Intergenic	-222459	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.009479	0.486998	47(AGGCCCACACTGTCCC,-,0.00),48(GGCCCACACTGTCCCT,+,0.00),119(AAGAACAGAGTGTCTC,-,0.00),120(AGAACAGAGTGTCTCA,+,0.00),194(GAGCTCATTCTGTACT,-,0.00),195(AGCTCATTCTGTACTG,+,0.00)
chunk0168_291_1	chr6	91174254	91174453	+	0	NA	Intergenic	Intergenic	-347307	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.005025	0.355000	
chunk0012_75_1	chr1	155772827	155773525	+	0	NA	exon (NM_032292, exon 18 of 21)	exon (NM_032292, exon 18 of 21)	10656	NR_132767	106633816		NR_132767		SCARNA26B	-	small Cajal body-specific RNA 26B	ncRNA	0.010029	0.403433	
chunk0079_111_1	chr17	12374181	12375055	+	0	NA	Intergenic	L1MEj|LINE|L1	-175350	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.001144	0.280000	380(ATTACACAATGTTCCT,+,0.00)
chunk0147_328_1	chr4	185204049	185204263	+	0	NA	promoter-TSS (NM_001292033)	promoter-TSS (NM_001292033)	-128	NM_001292033	57587	Hs.535734	NM_020827	ENSG00000164323	CFAP97	KIAA1430|hmw	cilia and flagella associated protein 97	protein-coding	0.149533	0.781395	
chunk0189_450_1	chr8	28324095	28324481	+	0	NA	intron (NM_006228, intron 1 of 3)	intron (NM_006228, intron 1 of 3)	7156	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.012953	0.467700	
chunk0063_438_1	chr14	88780184	88780383	+	0	NA	intron (NM_183387, intron 1 of 42)	LTR40a|LTR|ERVL	12469	NM_183387	161436	Hs.325846	NM_183387	ENSG00000165521	EML5	EMAP-2|EMAP-5	EMAP like 5	protein-coding	0.005025	0.405000	
chunk0040_238_1	chr11	114504229	114504428	+	0	NA	Intergenic	L1PA13|LINE|L1	55567	NM_152315	120400	Hs.550126	NM_152315	ENSG00000095110	NXPE1	FAM55A	neurexophilin and PC-esterase domain family member 1	protein-coding	0.000000	0.595000	
chunk0207_448_1	chr9	137690064	137690524	+	0	NA	intron (NM_001145527, intron 1 of 15)	L1ME3G|LINE|L1	71302	NM_001145527	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.017391	0.453362	
chunk0147_454_1	chr4	188433129	188433618	+	0	NA	Intergenic	Intergenic	-22205	NR_033869	401164	Hs.435756	NR_033869	ENSG00000249378	LINC01060	-	long intergenic non-protein coding RNA 1060	ncRNA	0.014315	0.404082	
chunk0109_37_1	chr20	694846	695836	+	0	NA	Intergenic	Intergenic	-19162	NM_033129	85508	Hs.355284	NM_033129	ENSG00000215397	SCRT2	ZNF898B	scratch family transcriptional repressor 2	protein-coding	0.006061	0.432896	
chunk0002_156_1	chr1	18165589	18166134	+	0	NA	intron (NM_032880, intron 1 of 9)	LTR10C|LTR|ERV1	58115	NM_032880	84966	Hs.212511	NM_032880	ENSG00000117154	IGSF21	-	immunoglobin superfamily member 21	protein-coding	0.005505	0.375458	131(TGCACTTTATGTTCTT,+,0.00)
chunk0090_251_1	chr18	74234213	74234710	+	0	NA	Intergenic	Intergenic	57555	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.010060	0.413655	
chunk0211_90_1	chrX	110421648	110422310	+	0	NA	intron (NM_020769, intron 1 of 3)	intron (NM_020769, intron 1 of 3)	2922	NM_020769	57529	Hs.201071	NM_020769	ENSG00000243978	RTL9	MAR9|MART9|RGAG1|SIRH10	retrotransposon Gag like 9	protein-coding	0.003021	0.472097	
chunk0094_327_1	chr2	9029871	9030075	+	0	NA	Intergenic	Intergenic	-26226	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.014706	0.463415	
chunk0147_209_1	chr4	180446123	180446544	+	0	NA	Intergenic	Intergenic	712816	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.014252	0.367299	
chunk0125_273_1	chr3	69299477	69300097	+	0	NA	intron (NM_015123, intron 4 of 22)	intron (NM_015123, intron 4 of 22)	86517	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.008065	0.423510	
chunk0113_78_1	chr20	50592132	50592590	+	0	NA	non-coding (NR_110890, exon 19 of 22)	non-coding (NR_110890, exon 19 of 22)	6575	NR_030375	693230		NR_030375	ENSG00000208018	MIR645	MIRN645|hsa-mir-645	microRNA 645	ncRNA	0.028384	0.588235	
chunk0079_274_1	chr17	16380932	16381187	+	0	NA	promoter-TSS (NM_001281720)	promoter-TSS (NM_001281720)	-38	NM_001281720	7314	Hs.356190	NM_018955	ENSG00000170315	UBB	HEL-S-50	ubiquitin B	protein-coding	0.070588	0.562500	
chunk0065_451_1	chr14	106562974	106563660	+	0	NA	Intergenic	L1ME1|LINE|L1	-73394	NR_106988									0.010204	0.352256	
chunk0039_351_1	chr11	105500636	105501237	+	0	NA	Intergenic	L1MC|LINE|L1	-109137	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.004992	0.285714	
chunk0042_364_1	chr12	10385343	10385585	+	0	NA	intron (NR_120430, intron 3 of 3)	L1MA5|LINE|L1	4590	NM_007360	22914	Hs.387787	NM_007360	ENSG00000213809	KLRK1	CD314|D12S2489E|KLR|NKG2-D|NKG2D	killer cell lectin like receptor K1	protein-coding	0.004132	0.358025	
chunk0143_268_1	chr4	116485416	116485693	+	0	NA	Intergenic	L1PA16|LINE|L1	185829	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.000000	0.316547	
chunk0018_448_1	chr1	223109663	223110262	+	0	NA	3' UTR (NM_003268, exon 6 of 6)	3' UTR (NM_003268, exon 6 of 6)	33320	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.008347	0.445000	207(AAGAACATGAAGTGCA,-,0.00),208(AGAACATGAAGTGCAG,+,0.00)
chunk0011_240_1	chr1	150561103	150561672	+	0	NA	TTS (NM_001288608)	TTS (NM_001288608)	9458	NR_036211	100422997		NR_036211	ENSG00000264553	MIR4257	-	microRNA 4257	ncRNA	0.050967	0.642105	339(CAGCACTGGATGTCCT,-,0.00),340(AGCACTGGATGTCCTG,+,0.00)
chunk0136_379_1	chr3	196568353	196568644	+	0	NA	promoter-TSS (NM_182627)	promoter-TSS (NM_182627)	44	NM_182627	348793	Hs.385865	NM_182627	ENSG00000185798	WDR53	-	WD repeat domain 53	protein-coding	0.089347	0.623288	
chunk0176_401_1	chr7	19210912	19211215	+	0	NA	Intergenic	Intergenic	-65642	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.013201	0.384868	
chunk0060_50_1	chr14	41359517	41360435	+	0	NA	Intergenic	Intergenic	-247585	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.009804	0.365615	
chunk0144_290_1	chr4	138253407	138253811	+	0	NA	Intergenic	L1M5|LINE|L1	-11260	NM_014331	23657	Hs.390594	NM_014331	ENSG00000151012	SLC7A11	CCBR1|xCT	solute carrier family 7 member 11	protein-coding	0.002475	0.251852	
chunk0129_356_1	chr3	125006339	125006743	+	0	NA	intron (NM_020733, intron 8 of 16)	intron (NM_020733, intron 8 of 16)	49417	NM_020733	57493	Hs.477420	NM_020733	ENSG00000173706	HEG1	HEG|MST112|MSTP112	heart development protein with EGF like domains 1	protein-coding	0.009901	0.400000	
chunk0022_17_1	chr10	7555686	7556103	+	0	NA	Intergenic	Intergenic	63779	NM_032817	80760	Hs.498586	NM_030569	ENSG00000123243	ITIH5	ITI-HC5|PP14776	inter-alpha-trypsin inhibitor heavy chain 5	protein-coding	0.000000	0.325359	
chunk0128_69_1	chr3	105151590	105152039	+	0	NA	Intergenic	Intergenic	-214899	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.006682	0.393333	
chunk0180_448_1	chr7	77444125	77444780	+	0	NA	Intergenic	Intergenic	-28052	NM_017439	54103	Hs.186649	NM_017439	ENSG00000186088	GSAP	PION	gamma-secretase activating protein	protein-coding	0.007634	0.422256	
chunk0033_170_1	chr11	15695050	15695472	+	0	NA	intron (NM_001293172, intron 1 of 2)	intron (NM_001293172, intron 1 of 2)	51376	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.002370	0.420804	
chunk0079_332_1	chr17	17533996	17534380	+	0	NA	intron (NM_148172, intron 2 of 6)	L1ME1|LINE|L1	-37793	NM_016084	51655	Hs.25829	NM_016084	ENSG00000108551	RASD1	AGS1|DEXRAS1|MGC:26290	ras related dexamethasone induced 1	protein-coding	0.002604	0.405195	
chunk0185_140_1	chr7	127376264	127376729	+	0	NA	intron (NM_176814, intron 4 of 5)	intron (NM_176814, intron 4 of 5)	16228	NM_176814	168850	Hs.159006	NM_176814	ENSG00000048405	ZNF800	-	zinc finger protein 800	protein-coding	0.002151	0.306867	
chunk0082_418_1	chr17	61291066	61292182	+	0	NA	intron (NM_017679, intron 22 of 23)	intron (NM_017679, intron 22 of 23)	107982	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.015233	0.432408	
chunk0156_418_1	chr5	114346063	114347178	+	0	NA	Intergenic	L1MC4a|LINE|L1	-15699	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.004484	0.362903	
chunk0011_322_1	chr1	152003787	152004185	+	0	NA	Intergenic	Intergenic	-9748	NM_002966	6281	Hs.143873	NM_002966	ENSG00000197747	S100A10	42C|ANX2L|ANX2LG|CAL1L|CLP11|Ca[1]|GP11|P11|p10	S100 calcium binding protein A10	protein-coding	0.005025	0.513784	140(CTGGACACCTTGTGCT,-,0.00),141(TGGACACCTTGTGCTC,+,0.00)
chunk0140_101_1	chr4	68407690	68408163	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-39523	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.006342	0.337553	
chunk0088_426_1	chr18	55334898	55335504	+	0	NA	intron (NM_001243228, intron 8 of 19)	intron (NM_001243228, intron 8 of 19)	-13342	NM_001243235	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.008251	0.369028	467(AGTTCATTGTGTCCTG,+,0.00)
chunk0172_50_1	chr6	134103035	134103547	+	0	NA	Intergenic	MER89|LTR|ERV1	14389	NR_037938	387065	Hs.571061	NR_037938		HMGA1P7	HMGA1L7	high mobility group AT-hook 1 pseudogene 7	pseudo	0.011719	0.475634	133(CTGGACATTTTGTGCC,-,0.00),134(TGGACATTTTGTGCCA,+,0.00)
chunk0137_118_1	chr4	14365056	14365388	+	0	NA	Intergenic	Intergenic	253254	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.000000	0.444444	103(AAGGACAGAATGTTTC,-,0.00),104(AGGACAGAATGTTTCC,+,0.00)
chunk0097_159_1	chr2	48525272	48525655	+	0	NA	Intergenic	Intergenic	-4462	NM_001198593	286749	Hs.732016	NM_172311	ENSG00000068781	STON1-GTF2A1L	ALF|GTF2A1L|GTF2A1LF|SALF	STON1-GTF2A1L readthrough	protein-coding	0.007833	0.361979	
chunk0023_457_1	chr10	32313152	32313624	+	0	NA	intron (NM_001282391, intron 1 of 13)	L2a|LINE|L2	33660	NM_001272019	80314	Hs.167805	NM_025209	ENSG00000120616	EPC1	Epl1	enhancer of polycomb homolog 1	protein-coding	0.006356	0.350951	
chunk0177_284_1	chr7	25676131	25676417	+	0	NA	Intergenic	Intergenic	273712	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.006993	0.519164	
chunk0153_7_1	chr5	66741365	66741827	+	0	NA	intron (NM_198828, intron 1 of 5)	intron (NM_198828, intron 1 of 5)	-87180	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.006494	0.455724	
chunk0021_388_1	chr1	246582913	246584026	+	0	NA	intron (NM_001139459, intron 1 of 8)	intron (NM_001139459, intron 1 of 8)	17132	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.008086	0.406643	914(AGGAGCATCGTGTTCC,-,0.00),915(GGAGCATCGTGTTCCC,+,0.00)
chunk0092_454_1	chr19	39126542	39127033	+	0	NA	intron (NM_001014834, intron 1 of 7)	MIRb|SINE|MIR	1007	NM_001014834	10298	Hs.20447	NM_005884	ENSG00000130669	PAK4	-	p21 (RAC1) activated kinase 4	protein-coding	0.032587	0.530488	222(GGGCTCACACTGTGCT,-,0.00),223(GGCTCACACTGTGCTC,+,0.00)
chunk0152_232_1	chr5	60489993	60490220	+	0	NA	non-coding (NR_028508, exon 2 of 2)	non-coding (NR_028508, exon 2 of 2)	-2008	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.008811	0.421053	95(GTTACAGACTGTCCCC,+,0.00)
chunk0122_44_1	chr3	28279815	28280162	+	0	NA	intron (NM_182523, intron 2 of 3)	L1ME2z|LINE|L1	38355	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.008646	0.347701	
chunk0191_287_1	chr8	53920254	53920759	+	0	NA	intron (NR_104579, intron 1 of 3)	L1MB7|LINE|L1	39634	NR_104578	8601	Hs.368733	NM_003702	ENSG00000147509	RGS20	RGSZ1|ZGAP1|g(z)GAP|gz-GAP	regulator of G protein signaling 20	protein-coding	0.001980	0.286561	
chunk0141_68_1	chr4	77880836	77881058	+	0	NA	intron (NM_020236, intron 2 of 8)	MLT1H|LTR|ERVL-MaLR	18296	NM_020236	65008	Hs.532019	NM_020236	ENSG00000169288	MRPL1	BM022|L1MT|MRP-L1	mitochondrial ribosomal protein L1	protein-coding	0.000000	0.452915	
chunk0168_127_1	chr6	82178470	82179557	+	0	NA	intron (NM_015525, intron 26 of 28)	L2b|LINE|L2	68741	NM_001300906	25998	Hs.306425	NM_015525	ENSG00000005700	IBTK	BTBD26|BTKI	inhibitor of Bruton tyrosine kinase	protein-coding	0.004600	0.347426	809(AAAAACAGGCTGTTCT,-,0.00),810(AAAACAGGCTGTTCTA,+,0.00)
chunk0092_209_1	chr19	31293045	31293444	+	0	NA	intron (NM_020856, intron 1 of 1)	intron (NM_020856, intron 1 of 1)	56040	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.007519	0.417500	
chunk0057_349_1	chr13	108218135	108218597	+	0	NA	promoter-TSS (NM_032859)	promoter-TSS (NM_032859)	2	NM_001098268	3981	Hs.166091	NM_002312	ENSG00000174405	LIG4	LIG4S	DNA ligase 4	protein-coding	0.095238	0.686825	
chunk0071_273_1	chr15	85648950	85649320	+	0	NA	intron (NM_007200, intron 10 of 36)	MIRb|SINE|MIR	29185	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.000000	0.388140	
chunk0032_352_1	chr11	10519311	10519832	+	0	NA	intron (NM_016422, intron 4 of 5)	Tigger3c|DNA|TcMar-Tigger	-10395	NM_001190702	100463486		NM_001190702	ENSG00000255823	MTRNR2L8	HN8	MT-RNR2 like 8	protein-coding	0.007678	0.342912	
chunk0020_41_1	chr1	232274162	232274452	+	0	NA	Intergenic	Intergenic	241301	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.003448	0.384880	
chunk0007_347_1	chr1	84843750	84844396	+	0	NA	intron (NM_012152, intron 2 of 2)	L2a|LINE|L2	49140	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.001548	0.454405	
chunk0146_380_1	chr4	168468914	168469402	+	0	NA	intron (NM_001291510, intron 4 of 29)	L1ME2z|LINE|L1	11356	NM_001012967	91351	Hs.535011	NM_001012967	ENSG00000181381	DDX60L	-	DExD/H-box 60 like	protein-coding	0.006148	0.329243	221(AAGAACAAAGTGGGCT,-,0.00)
chunk0092_328_1	chr19	34919981	34920588	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	6542	NR_110749	102723513	Hs.149702	NR_110749		ZNF30-AS1	-	ZNF30 antisense RNA 1	ncRNA	0.004942	0.460526	
chunk0067_221_1	chr15	45279072	45279485	+	0	NA	promoter-TSS (NR_120335)	promoter-TSS (NR_120335)	-56	NR_120335	101928414		NR_120335	ENSG00000259520	LOC101928414	-	uncharacterized LOC101928414	ncRNA	0.060533	0.591787	115(AGGAACTCACTGTCTC,-,0.00)
chunk0176_8_1	chr7	8191154	8191668	+	0	NA	intron (NM_001136020, intron 6 of 13)	MER47A|DNA|TcMar-Tigger	70641	NM_022307	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.003891	0.357282	136(TTGTACAGACAGTCCT,-,0.00),137(TGTACAGACAGTCCTG,+,0.00)
chunk0048_398_1	chr12	87960570	87961582	+	0	NA	Intergenic	Intergenic	68323	NM_152589	160419	Hs.112930	NM_152589	ENSG00000165805	C12orf50	-	chromosome 12 open reading frame 50	protein-coding	0.003953	0.338598	251(TGGCACAAATTGTCCT,-,0.00),252(GGCACAAATTGTCCTT,+,0.00)
chunk0006_90_1	chr1	65072853	65073226	+	0	NA	Intergenic	Intergenic	-14531	NR_029516	406893		NR_029516	ENSG00000199135	MIR101-1	MIRN101-1|mir-101-1	microRNA 101-1	ncRNA	0.008043	0.510695	
chunk0081_98_1	chr17	39776623	39776927	+	0	NA	intron (NM_001257413, intron 3 of 3)	intron (NM_001257413, intron 3 of 3)	1450	NM_001284516	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.003289	0.314754	
chunk0053_278_1	chr13	33279345	33279838	+	0	NA	non-coding (NR_046693, exon 2 of 3)	non-coding (NR_046693, exon 2 of 3)	2037	NR_046693	100874241	Hs.662433	NR_046693	ENSG00000236581	STARD13-AS	STARD13-AS2	STARD13 antisense RNA	ncRNA	0.002028	0.366397	240(CTGTACACCCTGTGCT,-,0.00),241(TGTACACCCTGTGCTA,+,0.00)
chunk0152_374_1	chr5	64360898	64361304	+	0	NA	intron (NM_001113561, intron 7 of 7)	LTR40b|LTR|ERVL	-144846	NM_001029875	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.002463	0.329238	185(AGGCACACATTGATCC,-,0.00)
chunk0072_331_1	chr15	99180743	99180995	+	0	NA	intron (NR_109947, intron 8 of 12)	L3|LINE|CR1	68750	NM_001288615	64927	Hs.513195	NM_022905	ENSG00000103852	TTC23	HCC-8	tetratricopeptide repeat domain 23	protein-coding	0.007937	0.450593	
chunk0043_189_1	chr12	18953442	18953947	+	0	NA	Intergenic	Intergenic	-175998	NM_001190860	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.005941	0.401186	
chunk0212_319_1	chrX	143769096	143769317	+	0	NA	Intergenic	L1PREC2|LINE|L1	-48538	NM_001009615	494119		NM_001009615	ENSG00000268988	SPANXN2	CT11.7|SPANX-N2	SPANX family member N2	protein-coding	0.009050	0.364865	
chunk0005_35_1	chr1	54869034	54869473	+	0	NA	intron (NM_014762, intron 5 of 8)	L1ME3G|LINE|L1	17995	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.006834	0.368182	
chunk0007_265_1	chr1	83086046	83086849	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-100239	NR_110633	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.006227	0.378109	367(AGGCACTGGCTGTCCT,-,0.00),368(GGCACTGGCTGTCCTT,+,0.00)
chunk0014_419_1	chr1	183169110	183169393	+	0	NA	Intergenic	Intergenic	-16788	NM_005562	3918	Hs.591484	NM_005562	ENSG00000058085	LAMC2	B2T|BM600|CSF|EBR2|EBR2A|LAMB2T|LAMNB2	laminin subunit gamma 2	protein-coding	0.003534	0.419014	
chunk0009_391_1	chr1	110049313	110049736	+	0	NA	exon (NM_033088, exon 17 of 21)	exon (NM_033088, exon 17 of 21)	14923	NM_033088	85369	Hs.584996	NM_033088	ENSG00000143093	STRIP1	FAM40A|FAR11A	striatin interacting protein 1	protein-coding	0.009456	0.495283	213(CAAAACATCATGTCCT,-,0.00),214(AAAACATCATGTCCTA,+,0.00)
chunk0127_390_1	chr3	102197460	102197659	+	0	NA	Intergenic	LTR33A|LTR|ERVL	-237456	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.480000	
chunk0090_300_1	chr18	75208322	75208521	+	0	NA	intron (NM_175907, intron 1 of 1)	CpG	927	NM_175907	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.090452	0.655000	
chunk0114_422_1	chr20	64164043	64164479	+	0	NA	promoter-TSS (NM_004535)	promoter-TSS (NM_004535)	-213	NM_004535	4661	Hs.279562	NM_004535	ENSG00000196132	MYT1	C20orf36|MTF1|MYTI|NZF2|PLPB1|ZC2H2C1|ZC2HC4A	myelin transcription factor 1	protein-coding	0.016055	0.462243	
chunk0117_135_1	chr22	19390634	19391017	+	0	NA	intron (NM_003325, intron 9 of 24)	L1ME2|LINE|L1	40871	NM_003325	7290	Hs.474206	NM_003325	ENSG00000100084	HIRA	DGCR1|TUP1|TUPLE1	histone cell cycle regulator	protein-coding	0.015666	0.437500	
chunk0010_383_1	chr1	119298712	119299255	+	0	NA	Intergenic	Intergenic	-69793	NM_001005783	51179	Hs.659767	NM_016527	ENSG00000116882	HAO2	GIG16|HAOX2	hydroxyacid oxidase 2	protein-coding	0.000000	0.400735	
chunk0133_440_1	chr3	175091272	175092003	+	0	NA	intron (NR_046390, intron 2 of 3)	LTR106_Mam|LTR|LTR	23605	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.006840	0.300546	359(ATAAACATGGTGTTCT,-,0.00)
chunk0086_374_1	chr18	26345087	26345367	+	0	NA	intron (NM_001293725, intron 13 of 14)	L1MA5A|LINE|L1	-77768	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.010714	0.555160	
chunk0112_427_1	chr20	47464297	47464964	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-37227	NM_006534	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.014993	0.429641	281(GGGTACAGCCTGTGAT,-,0.00)
chunk0155_89_1	chr5	92289822	92290232	+	0	NA	Intergenic	L1MC2|LINE|L1	-906695	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.002439	0.257908	
chunk0040_374_1	chr11	119121512	119121711	+	0	NA	promoter-TSS (NM_001243259)	promoter-TSS (NM_001243259)	88	NM_198971	25988	Hs.504091	NM_015517	ENSG00000172273	HINFP	HiNF-P|MIZF|ZNF743	histone H4 transcription factor	protein-coding	0.060302	0.600000	
chunk0056_289_1	chr13	90491072	90491808	+	0	NA	Intergenic	L1MA6|LINE|L1	-1848	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.001359	0.321574	
chunk0046_178_1	chr12	58656094	58656599	+	0	NA	intron (NR_120452, intron 1 of 7)	MER52A|LTR|ERV1	64644	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.003960	0.573123	
chunk0202_181_1	chr9	74357665	74358043	+	0	NA	Intergenic	Intergenic	-13677	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.007937	0.356201	
chunk0177_352_1	chr7	26616350	26616611	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-21391	NM_001145531									0.019157	0.557252	155(TGGGACATGCTGTCTT,-,0.00),156(GGGACATGCTGTCTTG,+,0.00)
chunk0073_39_1	chr16	2799904	2800277	+	0	NA	intron (NM_001135086, intron 3 of 4)	Tigger3|DNA|TcMar-Tigger	1605	NM_001135086	360226	Hs.647401	NM_001135086	ENSG00000215148	PRSS41	TESSP1	serine protease 41	protein-coding	0.005362	0.430481	
chunk0191_90_1	chr8	47643723	47644402	+	0	NA	intron (NM_001080394, intron 10 of 19)	intron (NM_001080394, intron 10 of 19)	94102	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.007364	0.429412	
chunk0006_287_1	chr1	70717995	70718428	+	0	NA	intron (NR_125938, intron 5 of 6)	MIR|SINE|MIR	11758	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.002309	0.382488	
chunk0013_257_1	chr1	169942286	169942875	+	0	NA	intron (NM_001204514, intron 20 of 20)	intron (NM_001204514, intron 20 of 20)	-48621	NM_020423	57147	Hs.435560	NM_020423	ENSG00000000457	SCYL3	PACE-1|PACE1	SCY1 like pseudokinase 3	protein-coding	0.003396	0.389831	
chunk0147_240_1	chr4	182905954	182906153	+	0	NA	intron (NM_001921, intron 3 of 5)	L2c|LINE|L2	11424	NM_001012732	1635	Hs.183850	NM_001921	ENSG00000129187	DCTD	-	dCMP deaminase	protein-coding	0.035176	0.580000	
chunk0129_198_1	chr3	121430550	121431079	+	0	NA	TTS (NM_199420)	TTS (NM_199420)	115192	NM_199420	10721	Hs.241517	NM_199420	ENSG00000051341	POLQ	PRO0327	DNA polymerase theta	protein-coding	0.000000	0.411321	
chunk0182_289_1	chr7	98258555	98258914	+	0	NA	Intergenic	L1ME3B|LINE|L1	-6483	NM_015395	25851	Hs.592281	NM_015395	ENSG00000205356	TECPR1	-	tectonin beta-propeller repeat containing 1	protein-coding	0.013928	0.391667	
chunk0081_207_1	chr17	42441590	42441826	+	0	NA	Intergenic	L1MDa|LINE|L1	-17136	NM_001130020	535	Hs.463074	NM_005177	ENSG00000033627	ATP6V0A1	ATP6N1|ATP6N1A|Stv1|VPP1|Vph1|a1	ATPase H+ transporting V0 subunit a1	protein-coding	0.000000	0.379747	
chunk0020_16_1	chr1	231720930	231721455	+	0	NA	intron (NM_001164550, intron 4 of 4)	MIRc|SINE|MIR	94377	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.001905	0.363118	
chunk0059_102_1	chr14	30986851	30987305	+	0	NA	intron (NM_001083893, intron 1 of 17)	intron (NM_001083893, intron 1 of 17)	27664	NR_030354	693209		NR_030354	ENSG00000207952	MIR624	MIRN624|hsa-mir-624|mir-624	microRNA 624	ncRNA	0.015419	0.375824	252(TAGTACAGGCTGTACA,-,0.00),253(AGTACAGGCTGTACAC,+,0.00)
chunk0116_398_1	chr21	42462801	42463467	+	0	NA	Intergenic	Tigger18a|DNA|TcMar-Tigger	33220	NM_001286506	89765	Hs.661069	NM_080860	ENSG00000160188	RSPH1	CT79|RSP44|RSPH10A|TSA2|TSGA2	radial spoke head component 1	protein-coding	0.003003	0.326837	
chunk0199_139_1	chr9	4004004	4004473	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	105592	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.006397	0.370213	
chunk0195_262_1	chr8	97972800	97973303	+	0	NA	intron (NM_030583, intron 5 of 18)	intron (NM_030583, intron 5 of 18)	69166	NR_002581	26775	Hs.684855	NR_002581	ENSG00000207067	SNORA72	RNU72|U72	small nucleolar RNA, H/ACA box 72	snoRNA	0.003976	0.432540	
chunk0093_395_1	chr19	56834801	56835007	+	0	NA	intron (NM_001146326, intron 2 of 11)	intron (NM_001146326, intron 2 of 11)	5822	NM_001146185	5178	Hs.731875	NM_006210	ENSG00000198300	PEG3	PW1|ZKSCAN22|ZNF904|ZSCAN24	paternally expressed 3	protein-coding	0.000000	0.454106	
chunk0211_24_1	chrX	107897333	107897808	+	0	NA	intron (NR_110395, intron 3 of 3)	intron (NR_110395, intron 3 of 3)	38410	NR_110395	101928335	Hs.657090	NR_110395	ENSG00000236064	LOC101928335	-	uncharacterized LOC101928335	ncRNA	0.004211	0.382353	
chunk0136_260_1	chr4	10422219	10422543	+	0	NA	Intergenic	Intergenic	35027	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.006173	0.393846	
chunk0108_159_1	chr2	231130141	231130536	+	0	NA	intron (NR_034059, intron 15 of 23)	intron (NR_034059, intron 15 of 23)	-5228	NM_000867	3357	Hs.421649	NM_000867	ENSG00000135914	HTR2B	5-HT(2B)|5-HT-2B|5-HT2B	5-hydroxytryptamine receptor 2B	protein-coding	0.005063	0.338384	
chunk0040_232_1	chr11	114459783	114459982	+	0	NA	Intergenic	Intergenic	20496	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.000000	0.375000	
chunk0207_442_1	chr9	137592682	137593052	+	0	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-2382	NM_138462	116225	Hs.128096	NM_138462	ENSG00000165724	ZMYND19	MIZIP	zinc finger MYND-type containing 19	protein-coding	0.024324	0.576819	
chunk0063_432_1	chr14	88613491	88614160	+	0	NA	TTS (NM_207662)	TTS (NM_207662)	19439	NM_207662	79882	Hs.684046	NM_024824	ENSG00000100722	ZC3H14	MRT56|MSUT-2|NY-REN-37|SUT2|UKp68	zinc finger CCCH-type containing 14	protein-coding	0.007474	0.394030	217(GAGGGCACAGTGTGCT,-,0.00),218(AGGGCACAGTGTGCTT,+,0.00)
chunk0075_170_1	chr16	51956906	51957142	+	0	NA	Intergenic	Intergenic	116911	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.000000	0.396624	
chunk0057_251_1	chr13	105165671	105165962	+	0	NA	Intergenic	MER73|LTR|ERVL	-300051	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.003436	0.458904	
chunk0169_264_1	chr6	105503616	105504032	+	0	NA	Intergenic	Intergenic	-100700	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.007212	0.393285	
chunk0147_322_1	chr4	185077307	185077507	+	0	NA	Intergenic	Intergenic	58566	NM_001300781	391723	Hs.531242	NM_001029887	ENSG00000187821	HELT	HCM1228|HESL|Mgn|bHLHb44	helt bHLH transcription factor	protein-coding	0.005000	0.502488	
chunk0027_336_1	chr10	78513065	78513581	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	245995	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.005814	0.446809	
chunk0154_237_1	chr5	80976601	80977270	+	0	NA	intron (NM_006909, intron 1 of 26)	intron (NM_006909, intron 1 of 26)	-16028	NR_105015	102524628	Hs.737159	NR_105015	ENSG00000251450	RASGRF2-AS1	-	RASGRF2 antisense RNA 1	ncRNA	0.010463	0.467164	
chunk0100_60_1	chr2	106334711	106334918	+	0	NA	Intergenic	Intergenic	-47300	NR_003506	285189	Hs.143436	NR_003506	ENSG00000240935	PLGLA	PLGLA1|PLGP2|PRGA	plasminogen like A (pseudogene)	pseudo	0.009662	0.432692	
chunk0054_77_1	chr13	42271539	42271738	+	0	NA	promoter-TSS (NM_016248)	promoter-TSS (NM_016248)	-515	NM_016248	11215	Hs.105105	NM_016248	ENSG00000023516	AKAP11	AKAP-11|AKAP220|PPP1R44|PRKA11	A-kinase anchoring protein 11	protein-coding	0.035176	0.585000	
chunk0030_221_1	chr10	114722595	114723035	+	0	NA	Intergenic	L2c|LINE|L2	-38160	NM_001003408	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.002273	0.421769	
chunk0034_357_1	chr11	35969538	35970249	+	0	NA	intron (NM_001304263, intron 1 of 4)	intron (NM_001304263, intron 1 of 4)	25912	NM_001304264	143458	Hs.745134	NM_174902	ENSG00000179241	LDLRAD3	LRAD3	low density lipoprotein receptor class A domain containing 3	protein-coding	0.007032	0.466292	
chunk0021_440_1	chr1	248229346	248229637	+	0	NA	Intergenic	L1PA15|LINE|L1	-9438	NM_017504	26245	Hs.381309	NM_017504	ENSG00000171180	OR2M4	HSHTPCRX18|HTPCRX18|OR1-55|OST710|TPCR100	olfactory receptor family 2 subfamily M member 4	protein-coding	0.013746	0.565068	
chunk0028_248_1	chr10	90450468	90451095	+	0	NA	intron (NR_110657, intron 3 of 6)	intron (NR_110657, intron 3 of 6)	90024	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.000000	0.296178	
chunk0014_169_1	chr1	178337134	178337812	+	0	NA	intron (NM_170692, intron 3 of 17)	intron (NM_170692, intron 3 of 17)	-3998	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.002950	0.360825	
chunk0158_157_1	chr5	127556616	127557060	+	0	NA	Intergenic	MIRb|SINE|MIR	39229	NM_130809	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.004505	0.330337	
chunk0138_199_1	chr4	38365208	38365637	+	0	NA	Intergenic	Intergenic	157758	NR_110951	101928776	Hs.586147	NR_110951	ENSG00000249534	LINC01258	-	long intergenic non-protein coding RNA 1258	ncRNA	0.002331	0.327907	255(TAGAACTCTTTGTACC,-,0.00),256(AGAACTCTTTGTACCC,+,0.00)
chunk0185_52_1	chr7	124737576	124738151	+	0	NA	Intergenic	L1MCa|LINE|L1	28162	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.003478	0.322917	
chunk0186_101_1	chr7	137622457	137622824	+	0	NA	intron (NM_004717, intron 7 of 33)	MER58A|DNA|hAT-Charlie	224223	NM_004717	9162	Hs.242947	NM_004717	ENSG00000157680	DGKI	DGK-IOTA	diacylglycerol kinase iota	protein-coding	0.005450	0.375000	
chunk0017_68_1	chr1	205556720	205556919	+	0	NA	promoter-TSS (NR_027086)	promoter-TSS (NR_027086)	-184	NR_027086	284578	Hs.537020	NR_027086		MFSD4A-AS1	-	MFSD4A antisense RNA 1	ncRNA	0.005025	0.415000	
chunk0101_181_1	chr2	129347888	129348192	+	0	NA	Intergenic	Intergenic	-74149	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.003289	0.396721	
chunk0211_427_1	chrX	129320098	129320384	+	0	NA	Intergenic	Intergenic	203264	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.003497	0.390244	
chunk0206_328_1	chr9	125341468	125341953	+	0	NA	intron (NM_001282679, intron 18 of 27)	intron (NM_001282679, intron 18 of 27)	42820	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.008247	0.370370	
chunk0200_124_1	chr9	17332578	17333025	+	0	NA	intron (NM_017738, intron 10 of 25)	intron (NM_017738, intron 10 of 25)	197810	NM_017738	54875	Hs.435381	NM_017738	ENSG00000044459	CNTLN	C9orf101|C9orf39|bA340N12.1	centlein	protein-coding	0.004474	0.308036	
chunk0181_243_1	chr7	85328471	85328969	+	0	NA	Intergenic	Intergenic	-206789	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.006024	0.310621	
chunk0048_156_1	chr12	80612447	80613252	+	0	NA	intron (NM_001145026, intron 28 of 44)	L1MD2|LINE|L1	-94780	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.003727	0.343672	
chunk0139_310_1	chr4	58022130	58022740	+	0	NA	Intergenic	Intergenic	596563	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.004918	0.338789	
chunk0165_410_1	chr6	39019880	39020079	+	0	NA	intron (NM_001206927, intron 91 of 92)	L2b|LINE|L2	-28802	NM_002062	2740	Hs.351883	NM_002062	ENSG00000112164	GLP1R	GLP-1|GLP-1-R|GLP-1R	glucagon like peptide 1 receptor	protein-coding	0.015075	0.485000	
chunk0114_288_1	chr21	16526398	16526744	+	0	NA	intron (NR_111004, intron 5 of 5)	HSMAR1|DNA|TcMar-Mariner	-12518	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.017341	0.446686	
chunk0091_75_1	chr19	5017150	5017703	+	0	NA	intron (NM_015015, intron 2 of 22)	MER58A|DNA|hAT-Charlie	48313	NM_015015	23030	Hs.654816	NM_015015	ENSG00000127663	KDM4B	JMJD2B|TDRD14B	lysine demethylase 4B	protein-coding	0.012658	0.489170	427(AGGTCTGTCTGTGCCT,+,0.00)
chunk0146_448_1	chr4	169941658	169942132	+	0	NA	intron (NR_037878, intron 2 of 4)	LTR26C|LTR|ERV1	34007	NR_037878	100506085	Hs.649173	NR_037878	ENSG00000248319	LINC02275	-	long intergenic non-protein coding RNA 2275	ncRNA	0.008439	0.494737	
chunk0026_355_1	chr10	68871960	68872435	+	0	NA	intron (NM_001130159, intron 1 of 3)	intron (NM_001130159, intron 1 of 3)	-29081	NM_024045	79009	Hs.522984	NM_024045	ENSG00000107625	DDX50	GU2|GUB|RH-II/GuB|mcdrh	DExD-box helicase 50	protein-coding	0.016842	0.378151	294(AGGGACTAAATGTTCT,-,0.00),295(GGGACTAAATGTTCTT,+,0.00)
chunk0188_21_1	chr8	6526422	6526734	+	0	NA	intron (NM_001147, intron 3 of 8)	Charlie9|DNA|hAT-Charlie	36685	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.000000	0.265176	
chunk0206_209_1	chr9	123104709	123105219	+	0	NA	TTS (NM_012197)	TTS (NM_012197)	6679	NR_030331	693185		NR_030331	ENSG00000283941	MIR600	MIRN600|hsa-mir-600	microRNA 600	ncRNA	0.013725	0.442270	
chunk0178_26_1	chr7	29349182	29349788	+	0	NA	intron (NM_001293070, intron 2 of 13)	MIR|SINE|MIR	-130227	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.008251	0.337727	403(ATGAACATCTTGTTCA,-,0.00),404(TGAACATCTTGTTCAT,+,0.00)
chunk0166_314_1	chr6	49703630	49703840	+	0	NA	intron (NM_001142417, intron 4 of 9)	L1PB1|LINE|L1	9855	NM_001142417	7180	Hs.2042	NM_003296	ENSG00000124490	CRISP2	CRISP-2|CT36|GAPDL5|TPX1|TSP1	cysteine rich secretory protein 2	protein-coding	0.004762	0.383886	
chunk0044_236_1	chr12	31589837	31590168	+	0	NA	promoter-TSS (NR_046909)	promoter-TSS (NR_046909)	79	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.081571	0.626506	
chunk0144_76_1	chr4	127954781	127955233	+	0	NA	intron (NM_152778, intron 3 of 12)	L1MB2|LINE|L1	-10299	NM_001039717	80167	Hs.143995	NM_025097	ENSG00000164074	ABHD18	C4orf29	abhydrolase domain containing 18	protein-coding	0.004425	0.348786	
chunk0004_397_1	chr1	52125925	52126279	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-15992	NM_004799	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.000000	0.326761	
chunk0206_454_1	chr9	128322429	128322731	+	0	NA	promoter-TSS (NM_015679)	promoter-TSS (NM_015679)	72	NM_001305942	51117	Hs.98541	NM_016035	ENSG00000167113	COQ4	CGI-92|COQ10D7	coenzyme Q4	protein-coding	0.082781	0.597360	
chunk0010_21_1	chr1	112383459	112383701	+	0	NA	Intergenic	L1MB1|LINE|L1	-12598	NM_018704	55917	Hs.744100	NM_018704	ENSG00000143079	CTTNBP2NL	-	CTTNBP2 N-terminal like	protein-coding	0.004132	0.436214	
chunk0150_364_1	chr5	39049366	39049730	+	0	NA	intron (NM_001285439, intron 2 of 38)	MER58A|DNA|hAT-Charlie	24860	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.002747	0.369863	
chunk0112_24_1	chr20	36112005	36112354	+	0	NA	intron (NM_001258329, intron 1 of 22)	intron (NM_001258329, intron 1 of 22)	19469	NM_001258329	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.014327	0.494286	
chunk0064_18_1	chr14	89337964	89338202	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	79027	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.008403	0.489540	
chunk0039_249_1	chr11	102161667	102162116	+	0	NA	intron (NM_001282098, intron 2 of 6)	intron (NM_001282098, intron 2 of 6)	49451	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.004454	0.315556	
chunk0078_126_1	chr17	2996163	2996889	+	0	NA	intron (NM_015085, intron 13 of 24)	intron (NM_015085, intron 13 of 24)	-30631	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.016529	0.521320	
chunk0055_421_1	chr13	75025938	75026204	+	0	NA	Intergenic	Intergenic	214310	NR_027466	647288	Hs.567920	NR_027466	ENSG00000214249	CTAGE11P	-	CTAGE family member 11, pseudogene	pseudo	0.003759	0.344569	
chunk0175_440_1	chr6	169814391	169814619	+	0	NA	Intergenic	Intergenic	-15680	NR_026781	401288	Hs.556095	NM_207502	ENSG00000229214	LINC00242	C6orf122|NCRNA00242|dJ266L20.5	long intergenic non-protein coding RNA 242	ncRNA	0.035088	0.628821	
chunk0041_135_1	chr11	125260683	125260962	+	0	NA	intron (NM_022062, intron 2 of 12)	intron (NM_022062, intron 2 of 12)	96159	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.010753	0.492857	
chunk0037_50_1	chr11	70517105	70517534	+	0	NA	intron (NR_110766, intron 2 of 8)	L1MC2|LINE|L1	-113775	NR_046567	100874198	Hs.656610	NR_046567	ENSG00000226627	SHANK2-AS1	-	SHANK2 antisense RNA 1	ncRNA	0.016317	0.423256	
chunk0072_118_1	chr15	92227005	92227204	+	0	NA	Intergenic	Intergenic	-166806	NM_006011	8128	Hs.302341	NM_006011	ENSG00000140557	ST8SIA2	HsT19690|SIAT8-B|SIAT8B|ST8SIA-II|ST8SiaII|STX	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	protein-coding	0.005025	0.460000	
chunk0015_143_1	chr1	186082238	186082572	+	0	NA	intron (NM_031935, intron 56 of 106)	MLT1H|LTR|ERVL-MaLR	-213868	NM_005807	10216	Hs.647723	NM_005807	ENSG00000116690	PRG4	CACP|HAPO|JCAP|MSF|SZP	proteoglycan 4	protein-coding	0.014970	0.480597	
chunk0198_265_1	chr8	134866760	134867459	+	0	NA	intron (NR_125427, intron 1 of 2)	L2b|LINE|L2	17174	NR_125427	101927845	Hs.559609	NR_125427	ENSG00000251218	LOC101927845	-	uncharacterized LOC101927845	ncRNA	0.008584	0.504286	347(GGGAACAGCGTGTGCA,-,0.00),348(GGAACAGCGTGTGCAT,+,0.00),380(AAGCACGGCATGTTCA,-,0.00)
chunk0082_168_1	chr17	55785469	55785921	+	0	NA	Intergenic	L2a|LINE|L2	34590	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.002212	0.331126	
chunk0176_344_1	chr7	17725746	17726013	+	0	NA	Intergenic	Intergenic	-166970	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.007491	0.358209	
chunk0032_284_1	chr11	9364335	9364567	+	0	NA	Intergenic	CpG	-20171	NM_006391	10527	Hs.744911	NM_006391	ENSG00000205339	IPO7	Imp7|RANBP7	importin 7	protein-coding	0.125000	0.708155	
chunk0133_388_1	chr3	174191648	174192188	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	-271122	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.005556	0.330869	
chunk0119_67_1	chr22	41106479	41106809	+	0	NA	intron (NM_001429, intron 1 of 30)	AluJr|SINE|Alu	14034	NM_001429	2033	Hs.517517	NM_001429	ENSG00000100393	EP300	KAT3B|MKHK2|RSTS2|p300	E1A binding protein p300	protein-coding	0.015152	0.468278	
chunk0124_340_1	chr3	58350371	58350620	+	0	NA	intron (NM_001289101, intron 1 of 14)	intron (NM_001289101, intron 1 of 14)	17605	NM_001289101	54899	Hs.190544	NM_017771	ENSG00000168297	PXK	MONAKA|SLOB	PX domain containing serine/threonine kinase like	protein-coding	0.012048	0.516000	
chunk0131_457_1	chr3	154120142	154120577	+	0	NA	promoter-TSS (NM_001251962)	promoter-TSS (NM_001251962)	-644	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.013793	0.389908	
chunk0047_439_1	chr12	76419890	76420704	+	0	NA	intron (NM_001003712, intron 3 of 22)	intron (NM_001003712, intron 3 of 22)	-71855	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.006143	0.295706	
chunk0207_49_1	chrX	7103840	7104346	+	0	NA	intron (NM_001178136, intron 2 of 3)	L1MB2|LINE|L1	-43767	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.000000	0.351085	
chunk0073_220_1	chr16	10895801	10896031	+	0	NA	intron (NM_001286402, intron 3 of 19)	intron (NM_001286402, intron 3 of 19)	18718	NM_001286402	4261	Hs.592051	NM_000246	ENSG00000179583	CIITA	C2TA|CIITAIV|MHC2TA|NLRA	class II major histocompatibility complex transactivator	protein-coding	0.017391	0.515152	
chunk0063_312_1	chr14	85031518	85031809	+	0	NA	Intergenic	Intergenic	-362216	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003436	0.304795	
chunk0119_291_1	chr22	46196201	46196761	+	0	NA	intron (NM_005036, intron 3 of 8)	L2a|LINE|L2	45885	NM_005036	5465	Hs.103110	NM_005036	ENSG00000186951	PPARA	NR1C1|PPAR|PPARalpha|hPPAR	peroxisome proliferator activated receptor alpha	protein-coding	0.019643	0.522282	308(TGCACTTGGTGTTCTC,+,0.00)
chunk0100_125_1	chr2	108616789	108617319	+	0	NA	intron (NM_001193482, intron 1 of 9)	intron (NM_001193482, intron 1 of 9)	-4192	NM_001193484	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.001887	0.369115	
chunk0145_100_1	chr4	146040401	146041065	+	0	NA	Intergenic	Intergenic	81180	NR_038331	100505545	Hs.122199	NR_038331	ENSG00000248809	LINC01095	-	long intergenic non-protein coding RNA 1095	ncRNA	0.004518	0.415038	337(GGGCCATATTGTTCTT,+,0.00),447(CAGCACACAAAGTTCA,-,0.00),448(AGCACACAAAGTTCAT,+,0.00)
chunk0153_241_1	chr5	72282741	72283300	+	0	NA	intron (NM_001286748, intron 4 of 11)	intron (NM_001286748, intron 4 of 11)	37237	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.003578	0.358929	
chunk0156_111_1	chr5	105569694	105569987	+	0	NA	Intergenic	L1MB7|LINE|L1	470366	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.272109	
chunk0117_365_1	chr21	44938490	44938903	+	0	NA	intron (NR_027129, intron 1 of 3)	intron (NR_027129, intron 1 of 3)	-1001	NM_001316988	85395	Hs.410830	NM_058190	ENSG00000160256	FAM207A	C21orf70|PRED56	family with sequence similarity 207 member A	protein-coding	0.021792	0.483092	
chunk0115_25_1	chr21	20856911	20857330	+	0	NA	Intergenic	Intergenic	-54012	NR_109788	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.014320	0.390476	
chunk0163_208_1	chr6	11938377	11938811	+	0	NA	Intergenic	Intergenic	62650	NR_125853	101928253	Hs.128163	NR_125853		LOC101928253	-	uncharacterized LOC101928253	ncRNA	0.016129	0.508046	106(AAGATCACAGAGTCCC,-,0.00)
chunk0012_153_1	chr1	157938556	157938957	+	0	NA	Intergenic	Intergenic	-54517	NM_018240	55243	Hs.272234	NM_018240	ENSG00000183853	KIRREL1	KIRREL|NEPH1	kirre like nephrin family adhesion molecule 1	protein-coding	0.002494	0.435323	
chunk0106_455_1	chr2	209395693	209395964	+	0	NA	Intergenic	Intergenic	-28219	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.000000	0.356618	
chunk0040_56_1	chr11	111171748	111172003	+	0	NA	Intergenic	Tigger17b|DNA|TcMar-Tigger	-84107	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.007843	0.355469	
chunk0072_161_1	chr15	92914738	92915061	+	0	NA	intron (NM_001042572, intron 2 of 12)	LTR54B|LTR|ERV1	10500	NR_036136	100422995		NR_036136	ENSG00000284324	MIR3175	mir-3175	microRNA 3175	ncRNA	0.003096	0.370370	
chunk0180_141_1	chr7	56447853	56448104	+	0	NA	intron (NR_029420, intron 1 of 5)	CpG	397	NR_029420	650226	Hs.448401	NR_029420		LOC650226	-	ankyrin repeat domain 26 pseudogene	pseudo	0.067729	0.674603	
chunk0163_329_1	chr6	15213688	15214394	+	0	NA	Intergenic	L2a|LINE|L2	-31934	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.009915	0.380481	
chunk0144_115_1	chr4	128725538	128725957	+	0	NA	Intergenic	Intergenic	-83876	NM_024900	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.004773	0.423810	
chunk0176_108_1	chr7	11716259	11716532	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	115803	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.000000	0.434307	
chunk0039_124_1	chr11	98086981	98087734	+	0	NA	Intergenic	Intergenic	-933619	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003984	0.344828	
chunk0170_304_1	chr6	115841849	115842274	+	0	NA	Intergenic	L1MC2|LINE|L1	-196670	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.004706	0.340376	
chunk0030_182_1	chr10	114204070	114204501	+	0	NA	intron (NM_198795, intron 9 of 25)	intron (NM_198795, intron 9 of 25)	25015	NM_198795	56165	Hs.333132	NM_198795	ENSG00000095627	TDRD1	CT41.1	tudor domain containing 1	protein-coding	0.002320	0.333333	
chunk0018_141_1	chr1	218650486	218651086	+	0	NA	intron (NR_031644, intron 3 of 6)	L1PA7|LINE|L1	208160	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.008333	0.386023	180(GGTACATTGTGTCTTT,+,0.00),263(AGGAGCAGGTTGTTCT,-,0.00),264(GGAGCAGGTTGTTCTG,+,0.00)
chunk0121_239_1	chr3	22475505	22475802	+	0	NA	Intergenic	MIRb|SINE|MIR	518514	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.013468	0.426174	
chunk0142_420_1	chr4	103418346	103418901	+	0	NA	Intergenic	Intergenic	-6419	NR_125925	101929448	Hs.570839	NR_125925	ENSG00000248740	LINC02428	-	long intergenic non-protein coding RNA 2428	ncRNA	0.000000	0.357914	
chunk0066_120_1	chr15	30905893	30906588	+	0	NA	intron (NM_001146094, intron 2 of 3)	intron (NM_001146094, intron 2 of 3)	2367	NM_014967	22909	Hs.584863	NM_014967	ENSG00000198690	FAN1	KIAA1018|KMIN|MTMR15|hFAN1	FANCD2 and FANCI associated nuclease 1	protein-coding	0.010072	0.415230	
chunk0013_10_1	chr1	165809238	165809715	+	0	NA	Intergenic	Intergenic	-18019	NM_012474	7371	Hs.458360	NM_012474	ENSG00000143179	UCK2	TSA903|UK|UMPK	uridine-cytidine kinase 2	protein-coding	0.000000	0.382845	
chunk0141_216_1	chr4	84638307	84638523	+	0	NA	intron (NM_001263, intron 8 of 12)	intron (NM_001263, intron 8 of 12)	55511	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.000000	0.350230	
chunk0065_158_1	chr15	25528068	25528376	+	0	NA	Intergenic	Intergenic	-89194	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.035714	0.631068	
chunk0202_340_1	chr9	79451228	79451740	+	0	NA	Intergenic	L1MC3|LINE|L1	-120289	NM_001282749	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.007812	0.325536	
chunk0081_15_1	chr17	37274266	37274995	+	0	NA	intron (NM_198836, intron 8 of 55).2	intron (NM_198836, intron 8 of 55).2	25137	NM_198837	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.009602	0.419178	
chunk0160_161_1	chr5	151847996	151848458	+	0	NA	intron (NM_001292000, intron 6 of 7)	MER68B|LTR|ERVL	-76051	NR_132345	100652758	Hs.587054	NM_001278082		LOC100652758	-	uncharacterized LOC100652758	ncRNA	0.006494	0.453564	
chunk0060_450_1	chr14	54877922	54878207	+	0	NA	TTS (NR_036194)	TTS (NR_036194)	129	NR_036194	100422984		NR_036194	ENSG00000265432	MIR4308	-	microRNA 4308	ncRNA	0.003509	0.398601	
chunk0004_440_1	chr1	53125660	53125859	+	0	NA	intron (NM_001287595, intron 2 of 10)	intron (NM_001287595, intron 2 of 10)	16873	NM_001287596	6512	Hs.104637	NM_006671	ENSG00000162383	SLC1A7	AAAT|EAAT5	solute carrier family 1 member 7	protein-coding	0.030151	0.630000	
chunk0048_387_1	chr12	87087091	87087427	+	0	NA	Intergenic	MIRb|SINE|MIR	-248355	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.002976	0.267062	
chunk0112_292_1	chr20	44018155	44018649	+	0	NA	intron (NM_001098796, intron 3 of 8)	intron (NM_001098796, intron 3 of 8)	72506	NM_001098798	84969	Hs.26608	NM_032883	ENSG00000124191	TOX2	C20orf100|GCX-1|GCX1|dJ1108D11.2|dJ495O3.1	TOX high mobility group box family member 2	protein-coding	0.020243	0.488889	
chunk0124_181_1	chr3	55436387	55437011	+	0	NA	Intergenic	L1ME4a|LINE|L1	44699	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.000000	0.342400	
chunk0117_42_1	chr22	12176132	12176582	+	0	NA	Intergenic	ACRO1|Satellite|acro	278951	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.033333	0.560976	
chunk0209_221_1	chrX	44891627	44892262	+	0	NA	intron (NR_111960, intron 2 of 27)	LTR10C|LTR|ERV1	18769	NM_001291421	7403	Hs.522616	NM_021140	ENSG00000147050	KDM6A	KABUK2|UTX|bA386N14.2	lysine demethylase 6A	protein-coding	0.011024	0.393082	351(AAGAACATAAAGTACA,-,0.00),352(AGAACATAAAGTACAT,+,0.00)
chunk0101_222_1	chr2	130885013	130885481	+	0	NA	Intergenic	Intergenic	-31404	NM_015320	50649	Hs.469935	NM_015320	ENSG00000136002	ARHGEF4	ASEF|ASEF1|GEF4|SMIM39|STM6	Rho guanine nucleotide exchange factor 4	protein-coding	0.014957	0.424307	
chunk0203_1_1	chr9	82580938	82581712	+	0	NA	Intergenic	Intergenic	481803	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002584	0.360000	
chunk0051_217_1	chr12	116609543	116609945	+	0	NA	Intergenic	Intergenic	50363	NM_001085481	643246	Hs.356061	NM_001085481	ENSG00000258102	MAP1LC3B2	ATG8G	microtubule associated protein 1 light chain 3 beta 2	protein-coding	0.002488	0.498759	262(GGGGACAGGCTGTCCT,-,0.00),263(GGGACAGGCTGTCCTG,+,0.00)
chunk0079_162_1	chr17	13528363	13528562	+	0	NA	intron (NM_006042, intron 1 of 1)	ERV3-16A3_LTR|LTR|ERVL	15184	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.015075	0.540000	
chunk0075_239_1	chr16	53094142	53094426	+	0	NA	intron (NM_025134, intron 1 of 38)	intron (NM_025134, intron 1 of 38)	39251	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.021127	0.603509	
chunk0104_170_1	chr2	174503118	174503916	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-16429	NM_001267051	151556	Hs.516604	NM_152529	ENSG00000163328	GPR155	DEP.7|DEPDC3|PGR22	G protein-coupled receptor 155	protein-coding	0.003759	0.377972	
chunk0017_203_1	chr1	207680155	207680593	+	0	NA	intron (NM_175710, intron 3 of 11)	L1MD2|LINE|L1	35261	NM_175710	1379	Hs.628568	NM_175710	ENSG00000197721	CR1L	-	complement C3b/C4b receptor 1 like	protein-coding	0.004566	0.355353	
chunk0031_123_1	chr10	124748178	124748579	+	0	NA	Intergenic	Intergenic	-4017	NM_014661	9679	Hs.129195	NM_014661	ENSG00000189319	FAM53B	KIAA0140|bA12J10.2|smp	family with sequence similarity 53 member B	protein-coding	0.007481	0.405473	
chunk0097_280_1	chr2	55013024	55013266	+	0	NA	intron (NM_153828, intron 1 of 6)	intron (NM_153828, intron 1 of 6)	-2811	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.000000	0.382716	
chunk0106_64_1	chr2	196876059	196876267	+	0	NA	intron (NM_024989, intron 13 of 26)	intron (NM_024989, intron 13 of 26)	50567	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.000000	0.277512	
chunk0150_57_1	chr5	31895317	31895595	+	0	NA	intron (NM_178140, intron 1 of 23)	MLT1A0|LTR|ERVL-MaLR	40703	NR_036241	100422874		NR_036241	ENSG00000266243	MIR4279	-	microRNA 4279	ncRNA	0.000000	0.455197	
chunk0157_195_1	chr5	118967053	118967657	+	0	NA	intron (NM_173666, intron 1 of 5)	L1MC4a|LINE|L1	-7231	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.003311	0.345455	
chunk0166_434_1	chr6	52876413	52876832	+	0	NA	Intergenic	MER89-int|LTR|ERV1	-30527	NM_153699	221357	Hs.646984	NM_153699	ENSG00000182793	GSTA5	-	glutathione S-transferase alpha 5	protein-coding	0.004773	0.411905	
chunk0101_340_1	chr2	137140769	137140968	+	0	NA	intron (NM_001316349, intron 5 of 27)	L2a|LINE|L2	375306	NM_001316349	80731	Hs.68533	NM_001080427	ENSG00000144229	THSD7B	-	thrombospondin type 1 domain containing 7B	protein-coding	0.005025	0.310000	
chunk0054_92_1	chr13	42575823	42576451	+	0	NA	intron (NM_003701, intron 1 of 4)	intron (NM_003701, intron 1 of 4)	1982	NM_003701	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.015924	0.437202	
chunk0165_330_1	chr6	37262462	37263111	+	0	NA	intron (NR_130108, intron 1 of 12)	intron (NR_130108, intron 1 of 12)	-4631	NR_104442	221468	Hs.520101	NM_145316	ENSG00000172738	TMEM217	C6orf128|dJ355M6.2	transmembrane protein 217	protein-coding	0.013867	0.400000	
chunk0082_338_1	chr17	59825632	59825857	+	0	NA	intron (NM_030938, intron 10 of 11)	intron (NM_030938, intron 10 of 11)	-15522	NR_029493	406991	Hs.444569	NR_029493	ENSG00000284190	MIR21	MIRN21|hsa-mir-21|miR-21|miRNA21	microRNA 21	ncRNA	0.000000	0.433628	97(AGATACAGAATGTTCC,-,0.00),98(GATACAGAATGTTCCA,+,0.00)
chunk0064_95_1	chr14	90858635	90858900	+	0	NA	Intergenic	L1ME3|LINE|L1	-42350	NM_001010854	145567	Hs.655697	NM_001010854	ENSG00000165914	TTC7B	TTC7L1|c14_5685	tetratricopeptide repeat domain 7B	protein-coding	0.007547	0.432331	
chunk0194_355_1	chr8	89534065	89534740	+	0	NA	Intergenic	Intergenic	223309	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.002963	0.363905	
chunk0079_412_1	chr17	19641484	19641829	+	0	NA	Intergenic	L1MC|LINE|L1	-7095	NM_001031806	224	Hs.499886	NM_000382	ENSG00000072210	ALDH3A2	ALDH10|FALDH|SLS	aldehyde dehydrogenase 3 family member A2	protein-coding	0.002899	0.280347	
chunk0035_220_1	chr11	45147050	45147264	+	0	NA	promoter-TSS (NM_001256695)	promoter-TSS (NM_001256695)	-186	NM_001256695	56981	Hs.178715	NM_001256695	ENSG00000019485	PRDM11	PFM8	PR/SET domain 11	protein-coding	0.140187	0.758140	
chunk0204_44_1	chr9	92761532	92761767	+	0	NA	intron (NM_001003800, intron 1 of 6)	intron (NM_001003800, intron 1 of 6)	3152	NM_001003800	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.008511	0.567797	147(CAGAACAAAGTGTCTC,-,0.00)
chunk0041_365_1	chr11	131310227	131310705	+	0	NA	Intergenic	L2b|LINE|L2	-60010	NM_001048209	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.004184	0.384134	
chunk0096_222_1	chr2	30604256	30605209	+	0	NA	intron (NM_001304446, intron 5 of 5)	intron (NM_001304446, intron 5 of 5)	157506	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.012592	0.392034	
chunk0100_31_1	chr2	105303794	105304375	+	0	NA	intron (NM_001142621, intron 2 of 11)	L1MC5|LINE|L1	25630	NM_004257	9392	Hs.446350	NM_004257	ENSG00000135966	TGFBRAP1	TRAP-1|TRAP1|VPS3	transforming growth factor beta receptor associated protein 1	protein-coding	0.001721	0.302405	
chunk0036_258_1	chr11	64939474	64940077	+	0	NA	intron (NM_001300803, intron 7 of 8)	intron (NM_001300803, intron 7 of 8)	-3887	NM_130769	170589	Hs.436119	NM_130769	ENSG00000149735	GPHA2	A2|GPA2|ZSIG51	glycoprotein hormone subunit alpha 2	protein-coding	0.013267	0.456954	
chunk0144_32_1	chr4	125062344	125062704	+	0	NA	Intergenic	Intergenic	-253888	NM_024582	79633	Hs.563205	NM_024582	ENSG00000196159	FAT4	CDHF14|CDHR11|FAT-J|FATJ|HKLLS2|NBLA00548|VMLDS2	FAT atypical cadherin 4	protein-coding	0.008333	0.332410	
chunk0185_381_1	chr7	133239896	133240297	+	0	NA	Intergenic	Helitron1Na_Mam|RC|Helitron	-12971	NM_021807	60412	Hs.321273	NM_021807	ENSG00000131558	EXOC4	SEC8|SEC8L1|Sec8p	exocyst complex component 4	protein-coding	0.007481	0.298507	
chunk0193_149_1	chr8	74576233	74577019	+	0	NA	Intergenic	Intergenic	-23240	NR_033830	441355	Hs.647162	NR_033830	ENSG00000254349	MIR2052HG	-	MIR2052 host gene	ncRNA	0.003817	0.470140	
chunk0133_397_1	chr3	174316794	174317268	+	0	NA	Intergenic	Intergenic	-396235	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.006329	0.336842	
chunk0183_372_1	chr7	109496314	109496805	+	0	NA	Intergenic	L1ME2|LINE|L1	463654	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.002037	0.247967	
chunk0095_444_1	chr2	25479310	25479698	+	0	NA	intron (NM_001256303, intron 10 of 19)	intron (NM_001256303, intron 10 of 19)	-136914	NM_175629	1788	Hs.515840	NM_022552	ENSG00000119772	DNMT3A	DNMT3A2|M.HsaIIIA|TBRS	DNA methyltransferase 3 alpha	protein-coding	0.010309	0.354756	
chunk0125_45_1	chr3	63886541	63887075	+	0	NA	intron (NM_000333, intron 1 of 12)	intron (NM_000333, intron 1 of 12)	-11591	NM_001177387	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.001873	0.386916	
chunk0174_35_1	chr6	154301183	154301575	+	0	NA	intron (NM_001130700, intron 1 of 11)	intron (NM_001130700, intron 1 of 11)	28702	NM_001130699	26034	Hs.146100	NM_015553	ENSG00000074706	IPCEF1	PIP3-E	interaction protein for cytohesin exchange factors 1	protein-coding	0.017857	0.458015	
chunk0035_342_1	chr11	48041727	48042477	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	-54680	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.008000	0.447403	330(AGGCCACGGTGTACTT,+,0.00),593(TAGAACACTCTGTGTC,-,0.00),594(AGAACACTCTGTGTCC,+,0.00)
chunk0149_459_1	chr5	30045722	30046252	+	0	NA	Intergenic	MIR|SINE|MIR	-650011	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.003774	0.327684	
chunk0123_123_1	chr3	42562332	42563036	+	0	NA	intron (NM_032970, intron 3 of 6)	intron (NM_032970, intron 3 of 6)	19344	NM_004206	9117	Hs.445892	NM_004206	ENSG00000093183	SEC22C	SEC22L3	SEC22 homolog C, vesicle trafficking protein	protein-coding	0.002841	0.466667	353(GAGCACAGACTGTCCC,-,0.00),354(AGCACAGACTGTCCCC,+,0.00)
chunk0069_442_1	chr15	68529022	68529252	+	0	NA	Intergenic	Intergenic	-49832	NM_006091	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.013043	0.419913	
chunk0096_340_1	chr2	35575333	35575654	+	0	NA	Intergenic	L1MA5|LINE|L1	104088	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.006231	0.568323	101(AGGCACATGGTGATCC,-,0.00),102(GGCACATGGTGATCCC,+,0.00)
chunk0017_216_1	chr1	207938140	207938508	+	0	NA	Intergenic	MER57C2|LTR|ERV1	-26986	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.005435	0.395664	
chunk0114_297_1	chr21	16906883	16907195	+	0	NA	Intergenic	L1MA4A|LINE|L1	316802	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.003205	0.376997	
chunk0091_64_1	chr19	4933533	4933799	+	0	NA	TTS (NR_039902)	TTS (NR_039902)	979	NR_039902	100616337		NR_039902	ENSG00000263409	MIR4747	mir-4747	microRNA 4747	ncRNA	0.022556	0.486891	142(AGGGACATTCTGTTCA,-,0.00),143(GGGACATTCTGTTCAT,+,0.00)
chunk0041_247_1	chr11	128761246	128761578	+	0	NA	intron (NM_001271012, intron 2 of 6)	L2a|LINE|L2	-65389	NR_038908	100507392	Hs.657715	NR_038908	ENSG00000254703	SENCR	FLI1-AS1|lncRNA9	smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA	ncRNA	0.021084	0.498498	
chunk0004_388_1	chr1	51916875	51917174	+	0	NA	3' UTR (NM_002867, exon 5 of 5)	3' UTR (NM_002867, exon 5 of 5)	-38087	NM_002525	4898	Hs.584782	NM_002525	ENSG00000078618	NRDC	NRD1|hNRD1|hNRD2	nardilysin convertase	protein-coding	0.003344	0.440000	
chunk0065_396_1	chr14	104979764	104980421	+	0	NA	Intergenic	Intergenic	-1735	NM_138420	113146	Hs.441783	NM_138420	ENSG00000185567	AHNAK2	C14orf78	AHNAK nucleoprotein 2	protein-coding	0.022831	0.527356	333(GAGGCCAGGCTGTACC,-,0.00),334(AGGCCAGGCTGTACCG,+,0.00)
chunk0170_441_1	chr6	119171163	119171362	+	0	NA	Intergenic	Intergenic	-22069	NM_001288576	79632	Hs.443789	NM_024581	ENSG00000111879	FAM184A	C6orf60	family with sequence similarity 184 member A	protein-coding	0.010050	0.405000	
chunk0050_420_1	chr12	109940518	109940836	+	0	NA	intron (NM_057170, intron 14 of 17)	AluSz|SINE|Alu	40159	NM_032300	84260	Hs.410924	NM_032300	ENSG00000139437	TCHP	TpMs	trichoplein keratin filament binding	protein-coding	0.018868	0.492163	
chunk0066_54_1	chr15	28225803	28226002	+	0	NA	intron (NM_004667, intron 35 of 92)	L1MB5|LINE|L1	96250	NM_004667	8924	Hs.434890	NM_004667	ENSG00000128731	HERC2	D15F37S1|MRT38|SHEP1|jdf2|p528	HECT and RLD domain containing E3 ubiquitin protein ligase 2	protein-coding	0.010050	0.320000	0(AGAACACTGTGAACTA,+,0.00)
chunk0201_91_1	chr9	34674354	34674973	+	0	NA	Intergenic	Intergenic	-11971	NM_006664	10850	Hs.648124	NM_006664	ENSG00000213927	CCL27	ALP|CTACK|CTAK|ESKINE|ILC|PESKY|SCYA27	C-C motif chemokine ligand 27	protein-coding	0.009693	0.417742	323(ATGAACAGGGAGTGCC,-,0.00),324(TGAACAGGGAGTGCCC,+,0.00)
chunk0190_2_1	chr8	28631325	28631524	+	0	NA	Intergenic	Intergenic	70040	NR_126027	101929402	Hs.667366	NR_126027	ENSG00000246339	EXTL3-AS1	C8orf50	EXTL3 antisense RNA 1	ncRNA	0.005025	0.460000	
chunk0055_128_1	chr13	57708757	57709103	+	0	NA	intron (NM_001040429, intron 3 of 3)	intron (NM_001040429, intron 3 of 3)	77275	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.000000	0.270893	
chunk0067_182_1	chr15	44519467	44519890	+	0	NA	intron (NM_016396, intron 11 of 12)	intron (NM_016396, intron 11 of 12)	17222	NR_034171	645212	Hs.594287	NR_034170		EIF3J-DT	EIF3J-AS1	EIF3J divergent transcript	ncRNA	0.009456	0.320755	
chunk0212_439_1	chrX	154524893	154525283	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-8846	NM_001171134	60343	Hs.289108	NM_021806	ENSG00000071889	FAM3A	2.19|DLD|DXS560S|XAP-7	family with sequence similarity 3 member A	protein-coding	0.007692	0.429668	
chunk0144_465_1	chr4	142525975	142526616	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	320156	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.007800	0.381620	232(AAGAACATGCTGTATC,-,0.00),233(AGAACATGCTGTATCT,+,0.00)
chunk0027_177_1	chr10	75127332	75128116	+	0	NA	intron (NM_144660, intron 1 of 4)	intron (NM_144660, intron 1 of 4)	16089	NM_001174156	142891	Hs.744986	NM_144660	ENSG00000156671	SAMD8	HEL-177|SMSr	sterile alpha motif domain containing 8	protein-coding	0.006378	0.335032	507(AGGAACAACATGTACT,-,0.00),508(GGAACAACATGTACTT,+,0.00)
chunk0041_42_1	chr12	990388	990965	+	0	NA	promoter-TSS (NM_001297419)	promoter-TSS (NM_001297419)	-532	NM_178040	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.102253	0.652249	307(GGGACAAAGCGTCCCC,+,0.00)
chunk0056_150_1	chr13	84010874	84011369	+	0	NA	Intergenic	L2|LINE|L2	-128728	NM_001281503	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.320565	
chunk0151_246_1	chr5	51567183	51567468	+	0	NA	Intergenic	Intergenic	-183993	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.007018	0.360140	126(CAGAACATACTGTACA,-,0.00),127(AGAACATACTGTACAA,+,0.00)
chunk0068_453_1	chr15	59862602	59863122	+	0	NA	Intergenic	Intergenic	-141360	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.009615	0.458733	157(ATGAACACTCTGCCCT,-,0.00),158(TGAACACTCTGCCCTC,+,0.00)
chunk0164_70_1	chr6	19556365	19556894	+	0	NA	Intergenic	Intergenic	-280741	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.009452	0.401887	265(ATGTGCAGAGTGTTCT,-,0.00),266(TGTGCAGAGTGTTCTT,+,0.00)
chunk0009_456_1	chr1	111613478	111613860	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	-5351	NR_034126	100129269	Hs.689728	NR_034126		LINC01160	-	long intergenic non-protein coding RNA 1160	ncRNA	0.013089	0.422977	
chunk0128_271_1	chr3	110589510	110589854	+	0	NA	Intergenic	Intergenic	480277	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.002907	0.417391	
chunk0143_211_1	chr4	113616390	113616947	+	0	NA	intron (NM_172114, intron 3 of 17)	intron (NM_172114, intron 3 of 17)	145259	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.001795	0.299283	271(AAGAACAATCAGTTCT,-,0.00),272(AGAACAATCAGTTCTT,+,0.00)
chunk0141_203_1	chr4	84319129	84319586	+	0	NA	Intergenic	Intergenic	-20188	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.010941	0.445415	
chunk0076_51_1	chr16	61099765	61100380	+	0	NA	Intergenic	Intergenic	-44306	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.000000	0.353896	
chunk0151_375_1	chr5	55107511	55107963	+	0	NA	intron (NM_006144, intron 2 of 4)	intron (NM_006144, intron 2 of 4)	5091	NM_006144	3001	Hs.90708	NM_006144	ENSG00000145649	GZMA	CTLA3|HFSP	granzyme A	protein-coding	0.008850	0.366446	
chunk0160_411_1	chr5	163967182	163967912	+	0	NA	Intergenic	Intergenic	462019	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.002740	0.366621	
chunk0153_359_1	chr5	74499389	74500014	+	0	NA	intron (NR_126354, intron 1 of 2)	A-rich|Low_complexity|Low_complexity	37275	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.006400	0.373802	
chunk0022_93_1	chr10	9596614	9596863	+	0	NA	Intergenic	Intergenic	-301145	NR_120635	101928272	Hs.650697	NR_120635		LOC101928272	-	uncharacterized LOC101928272	ncRNA	0.004016	0.440000	78(TATACAGAATGTTCTT,+,0.00)
chunk0020_33_1	chr1	232085248	232085447	+	0	NA	Intergenic	MIRb|SINE|MIR	159513	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.010050	0.470000	
chunk0052_408_1	chr12	131010160	131010420	+	0	NA	intron (NM_198827, intron 12 of 24)	intron (NM_198827, intron 12 of 24)	-16314	NR_131951	105755954	Hs.677534	NR_131950		ADGRD1-AS1	LACAT8	ADGRD1 antisense RNA 1	ncRNA	0.019231	0.501916	
chunk0204_227_1	chr9	97557554	97558204	+	0	NA	intron (NM_001166116, intron 4 of 9)	intron (NM_001166116, intron 4 of 9)	56240	NM_003275	7111	Hs.404289	NM_003275	ENSG00000136842	TMOD1	D9S57E|ETMOD|TMOD	tropomodulin 1	protein-coding	0.012308	0.480799	249(CAGAACTCAATGTTCT,-,0.00),250(AGAACTCAATGTTCTT,+,0.00)
chunk0199_369_1	chr9	12817704	12818081	+	0	NA	intron (NM_203403, intron 1 of 1)	intron (NM_203403, intron 1 of 1)	-3503	NR_125775	101929467	Hs.586443	NR_125775	ENSG00000235448	LURAP1L-AS1	-	LURAP1L antisense RNA 1	ncRNA	0.023873	0.478836	197(CAGGACTCTCTGTGCC,-,0.00),198(AGGACTCTCTGTGCCT,+,0.00)
chunk0200_351_1	chr9	25207605	25207804	+	0	NA	Intergenic	Intergenic	471154	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.010050	0.450000	
chunk0098_436_1	chr2	81894474	81895011	+	0	NA	Intergenic	Intergenic	-427796	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.005587	0.356877	210(AAGAACACTCTGTACT,-,0.00),211(AGAACACTCTGTACTC,+,0.00)
chunk0033_239_1	chr11	17938599	17938972	+	0	NA	intron (NR_104040, intron 9 of 11)	intron (NR_104040, intron 9 of 11)	74377	NR_104041	26297	Hs.32470	NM_012139	ENSG00000129158	SERGEF	DELGEF|Gnefr	secretion regulating guanine nucleotide exchange factor	protein-coding	0.000000	0.403743	
chunk0152_56_1	chr5	57650400	57650637	+	0	NA	promoter-TSS (NR_104668)	promoter-TSS (NR_104668)	-142	NR_104668	101928505	Hs.119998	NR_104668		LOC101928505	-	uncharacterized LOC101928505	ncRNA	0.004219	0.470588	
chunk0129_187_1	chr3	121042528	121043213	+	0	NA	intron (NM_014980, intron 4 of 27)	intron (NM_014980, intron 4 of 27)	-6770	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.005839	0.380466	
chunk0169_172_1	chr6	102181263	102181687	+	0	NA	Intergenic	L1MEi|LINE|L1	782490	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.284706	
chunk0006_298_1	chr1	71247268	71247735	+	0	NA	Intergenic	LTR48B|LTR|ERV1	166177	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.002141	0.367521	
chunk0116_387_1	chr21	42315246	42315712	+	0	NA	5' UTR (NM_003226, exon 1 of 3)	5' UTR (NM_003226, exon 1 of 3)	117	NM_003226	7033	Hs.82961	NM_003226	ENSG00000160180	TFF3	ITF|P1B|TFI	trefoil factor 3	protein-coding	0.027897	0.605996	
chunk0186_408_1	chr7	145409242	145409871	+	0	NA	Intergenic	Intergenic	-573503	NM_022445	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.001590	0.336508	
chunk0127_22_1	chr3	88328967	88329421	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-179328	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.008811	0.351648	
chunk0108_420_1	chr2	237714150	237714645	+	0	NA	intron (NM_001137550, intron 3 of 23)	intron (NM_001137550, intron 3 of 23)	22233	NM_004735	9208	Hs.471779	NM_004735	ENSG00000124831	LRRFIP1	FLAP-1|FLAP1|FLIIAP1|GCF-2|GCF2|HUFI-1|TRIP	LRR binding FLII interacting protein 1	protein-coding	0.002020	0.330645	
chunk0127_48_1	chr3	88982121	88982471	+	0	NA	Intergenic	Intergenic	-125228	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.327635	
chunk0089_118_1	chr18	58591093	58591462	+	0	NA	intron (NM_052947, intron 3 of 12)	MIRc|SINE|MIR	-9343	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.005420	0.437838	
chunk0015_74_1	chr1	184790821	184791408	+	0	NA	TTS (NM_052966)	TTS (NM_052966)	-36207	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.013629	0.375850	
chunk0143_174_1	chr4	110917414	110917639	+	0	NA	Intergenic	Intergenic	-56879	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.004444	0.283186	
chunk0052_389_1	chr12	130038134	130038333	+	0	NA	intron (NR_024457, intron 1 of 2)	L2c|LINE|L2	4109	NR_024457	100190940	Hs.625993	NR_024457	ENSG00000214039	LINC02418	-	long intergenic non-protein coding RNA 2418	ncRNA	0.020101	0.550000	
chunk0186_389_1	chr7	144510585	144511430	+	0	NA	intron (NM_001042482, intron 7 of 7)	intron (NM_001042482, intron 7 of 7)	-100780	NM_001080413	135935	Hs.558628	NM_001080413	ENSG00000106410	NOBOX	OG-2|OG2|OG2X|POF5|TCAG_12042	NOBOX oogenesis homeobox	protein-coding	0.014201	0.449173	222(GGTACTGTGAGTTCTG,+,0.00)
chunk0002_387_1	chr1	26826130	26826512	+	0	NA	promoter-TSS (NM_032283)	promoter-TSS (NM_032283)	-389	NM_032283	84243	Hs.523710	NM_032283	ENSG00000204160	ZDHHC18	DHHC-18|DHHC18	zinc finger DHHC-type containing 18	protein-coding	0.039267	0.577023	
chunk0195_211_1	chr8	96998544	96999166	+	0	NA	intron (NM_016134, intron 5 of 7)	intron (NM_016134, intron 5 of 7)	279093	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.003215	0.354735	
chunk0059_344_1	chr14	37047108	37047319	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	-94822	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.014218	0.433962	
chunk0061_136_1	chr14	59244570	59244854	+	0	NA	intron (NM_001270520, intron 1 of 24)	(TG)n|Simple_repeat|Simple_repeat	-18729	NM_014992	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.007042	0.424561	
chunk0013_394_1	chr1	172859287	172859707	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	191466	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.000000	0.349169	
chunk0099_58_1	chr2	84643759	84644255	+	0	NA	intron (NM_001370, intron 33 of 76)	L1MCa|LINE|L1	127552	NM_001370	1768	Hs.249972	NM_001370	ENSG00000115423	DNAH6	DNHL1|Dnahc6|HL-2|HL2	dynein axonemal heavy chain 6	protein-coding	0.006048	0.412475	216(CTGGACATGATGTACT,-,0.00),217(TGGACATGATGTACTG,+,0.00)
chunk0005_146_1	chr1	57726917	57727444	+	0	NA	intron (NM_021080, intron 2 of 16)	intron (NM_021080, intron 2 of 16)	-133363	NR_104362	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.013283	0.435606	302(TGGGACAGGAAGTTCA,-,0.00),303(GGGACAGGAAGTTCAA,+,0.00)
chunk0144_163_1	chr4	131662291	131662987	+	0	NA	Intergenic	MER70A|LTR|ERVL	-102199	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.011494	0.403156	321(AGGTACACTGTGTACT,-,0.00),322(GGTACACTGTGTACTA,+,0.00)
chunk0027_105_1	chr10	73999716	74000166	+	0	NA	intron (NM_003373, intron 1 of 20)	intron (NM_003373, intron 1 of 20)	1827	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.002222	0.368071	
chunk0083_180_1	chr17	66373105	66373462	+	0	NA	intron (NM_002737, intron 2 of 16)	MIRb|SINE|MIR	43571	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.008403	0.365922	
chunk0132_360_1	chr3	161586677	161587401	+	0	NA	Intergenic	Intergenic	90231	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.001381	0.390345	
chunk0062_19_1	chr14	66508220	66508441	+	0	NA	5' UTR (NM_020806, exon 1 of 23)	5' UTR (NM_020806, exon 1 of 23)	923	NM_020806	10243	Hs.208765	NM_020806	ENSG00000171723	GPHN	GEPH|GPH|GPHRYN|HKPX1|MOCODC	gephyrin	protein-coding	0.122172	0.743243	
chunk0146_49_1	chr4	155667075	155667274	+	0	NA	promoter-TSS (NM_001130684)	promoter-TSS (NM_001130684)	177	NM_001130685	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.085427	0.625000	
chunk0041_28_1	chr12	744056	744772	+	0	NA	Intergenic	AluJo|SINE|Alu	-8509	NM_001184985	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.006983	0.376569	
chunk0041_87_1	chr11	124460799	124461092	+	0	NA	Intergenic	Intergenic	-19860	NM_012378	26493	Hs.351822	NM_012378	ENSG00000197125	OR8B8	TPCR85	olfactory receptor family 8 subfamily B member 8	protein-coding	0.010239	0.462585	
chunk0139_3_1	chr4	47728850	47729236	+	0	NA	intron (NM_001278585, intron 4 of 19)	intron (NM_001278585, intron 4 of 19)	76374	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.010363	0.392765	
chunk0128_114_1	chr3	106285035	106285405	+	0	NA	Intergenic	L1PREC2|LINE|L1	-416177	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.002703	0.331536	
chunk0165_4_1	chr6	28587117	28587713	+	0	NA	promoter-TSS (NM_052923)	promoter-TSS (NM_052923)	-80	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.055369	0.571189	
chunk0117_313_1	chr22	24727050	24727497	+	0	NA	intron (NM_001008496, intron 16 of 20)	MLT1E2|LTR|ERVL-MaLR	-37228	NR_001283	7152	Hs.381281	NR_001283		TOP1P2	-	DNA topoisomerase I pseudogene 2	pseudo	0.002237	0.417411	
chunk0187_351_1	chr7	157151995	157152875	+	0	NA	intron (NM_014671, intron 1 of 22)	intron (NM_014671, intron 1 of 22)	13474	NM_014671	9690	Hs.118351	NM_014671	ENSG00000009335	UBE3C	HECTH2	ubiquitin protein ligase E3C	protein-coding	0.011364	0.493757	
chunk0029_47_1	chr10	96370705	96371047	+	0	NA	intron (NM_012465, intron 19 of 20)	intron (NM_012465, intron 19 of 20)	-11511	NM_033207	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.023392	0.495627	
chunk0050_280_1	chr12	106342703	106343241	+	0	NA	intron (NM_152772, intron 9 of 9)	intron (NM_152772, intron 9 of 9)	-14686	NM_018082	55703	Hs.62696	NM_018082	ENSG00000013503	POLR3B	C128|HLD8|INMAP|RPC2	RNA polymerase III subunit B	protein-coding	0.013011	0.471243	
chunk0068_155_1	chr15	53877664	53878313	+	0	NA	Intergenic	L1ME2|LINE|L1	-115110	NR_102334	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.004622	0.344615	
chunk0158_94_1	chr5	126628642	126629061	+	0	NA	Intergenic	Intergenic	-2871	NM_207408	389320	Hs.177983	NM_207408	ENSG00000196900	TEX43	C5orf48|Tseg7	testis expressed 43	protein-coding	0.007160	0.378571	
chunk0123_425_1	chr3	49990131	49990330	+	0	NA	intron (NM_005777, intron 5 of 20)	Tigger3a|DNA|TcMar-Tigger	50186	NM_005777	10180	Hs.696735	NM_005777	ENSG00000004534	RBM6	3G2|DEF-3|DEF3|HLC-11|NY-LU-12|g16	RNA binding motif protein 6	protein-coding	0.005025	0.350000	
chunk0204_191_1	chr9	96435260	96435783	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-14634	NM_014282	22927	Hs.494567	NM_014282	ENSG00000130956	HABP4	IHABP-4|IHABP4|Ki-1/57|SERBP1L	hyaluronan binding protein 4	protein-coding	0.007648	0.461832	
chunk0028_29_1	chr10	82825858	82826109	+	0	NA	intron (NM_001165972, intron 3 of 8)	intron (NM_001165972, intron 3 of 8)	-593063	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.003984	0.273810	
chunk0138_373_1	chr4	42460072	42460431	+	0	NA	intron (NM_006095, intron 27 of 36)	intron (NM_006095, intron 27 of 36)	62412	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.008357	0.363889	
chunk0167_370_1	chr6	73650522	73651106	+	0	NA	intron (NM_012434, intron 1 of 10)	L2a|LINE|L2	3200	NM_012434	26503	Hs.597422	NM_012434	ENSG00000119899	SLC17A5	AST|ISSD|NSD|SD|SIALIN|SIASD|SLD	solute carrier family 17 member 5	protein-coding	0.005137	0.388034	
chunk0054_173_1	chr13	44378311	44378789	+	0	NA	intron (NM_001010897, intron 1 of 2)	intron (NM_001010897, intron 1 of 2)	4708	NM_001010897	387923	Hs.377972	NM_001010897	ENSG00000151778	SERP2	C13orf21|bA269C23.1	stress associated endoplasmic reticulum protein family member 2	protein-coding	0.006276	0.327766	
chunk0118_264_1	chr22	33327732	33328193	+	0	NA	intron (NM_133642, intron 10 of 14)	L2a|LINE|L2	108707	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.004338	0.426407	
chunk0058_31_1	chr14	19965226	19965506	+	0	NA	Intergenic	L1MB7|LINE|L1	-10153	NM_001005486	81127	Hs.554583	NM_001005486	ENSG00000169488	OR4K15	OR14-20|OR4K15Q	olfactory receptor family 4 subfamily K member 15	protein-coding	0.007143	0.295374	
chunk0208_216_1	chrX	18596220	18596436	+	0	NA	intron (NM_001037343, intron 11 of 21)	intron (NM_001037343, intron 11 of 21)	75775	NM_000330	6247	Hs.715725	NM_000330	ENSG00000102104	RS1	RS|XLRS1	retinoschisin 1	protein-coding	0.018519	0.437788	81(GGGAACATAGTGTACA,-,0.00),82(GGAACATAGTGTACAT,+,0.00)
chunk0022_255_1	chr10	14666859	14667694	+	0	NA	intron (NM_001282695, intron 2 of 5)	intron (NM_001282695, intron 2 of 5)	-62858	NM_001282697	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.014371	0.351675	
chunk0004_409_1	chr1	52308667	52309167	+	0	NA	intron (NM_007324, intron 12 of 17)	L2b|LINE|L2	57288	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.004000	0.335329	
chunk0211_298_1	chrX	122966563	122967003	+	0	NA	Intergenic	(TTAT)n|Simple_repeat|Simple_repeat	-217460	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.006818	0.349206	50(TAGAACACTATGTTCT,-,0.00),51(AGAACACTATGTTCTT,+,0.00)
chunk0163_202_1	chr6	11854864	11855284	+	0	NA	Intergenic	Intergenic	-76027	NM_001143948	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.007143	0.375297	
chunk0077_279_1	chr16	81077270	81077540	+	0	NA	promoter-TSS (NM_152337)	promoter-TSS (NM_152337)	-138	NM_001100873	123775	Hs.658684	NM_152337	ENSG00000166455	C16orf46	-	chromosome 16 open reading frame 46	protein-coding	0.088889	0.649446	
chunk0051_343_1	chr12	120302173	120302650	+	0	NA	promoter-TSS (NM_012240)	promoter-TSS (NM_012240)	90	NM_012240	23409	Hs.50861	NM_012240	ENSG00000089163	SIRT4	SIR2L4	sirtuin 4	protein-coding	0.035639	0.491632	
chunk0140_402_1	chr4	75530908	75531416	+	0	NA	Intergenic	MER68|LTR|ERVL	16718	NM_144721	152815	Hs.479971	NM_144721	ENSG00000174796	THAP6	-	THAP domain containing 6	protein-coding	0.001969	0.444008	265(CAGAACACCCAGTTTC,-,0.00),266(AGAACACCCAGTTTCC,+,0.00)
chunk0151_86_1	chr5	42840442	42840977	+	0	NA	Intergenic	Intergenic	-28787	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.009346	0.470149	
chunk0031_97_1	chr10	124035893	124036419	+	0	NA	intron (NM_014863, intron 5 of 5)	intron (NM_014863, intron 5 of 5)	56268	NM_015892	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.036122	0.611006	
chunk0008_134_1	chr1	91886005	91886281	+	0	NA	non-coding (NR_036634, exon 1 of 18)	non-coding (NR_036634, exon 1 of 18)	136	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.123188	0.729242	
chunk0184_299_1	chr7	119893629	119894252	+	0	NA	intron (NR_131960, intron 1 of 4)	L1MEc|LINE|L1	13435	NR_131960	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.003210	0.315705	324(AAAAACAGTATGTTCC,-,0.00),325(AAAACAGTATGTTCCA,+,0.00)
chunk0053_164_1	chr13	30617676	30617895	+	0	NA	promoter-TSS (NM_005800)	promoter-TSS (NM_005800)	92	NM_005800	10208	Hs.533831	NM_005800	ENSG00000132952	USPL1	C13orf22|D13S106E|bA121O19.1	ubiquitin specific peptidase like 1	protein-coding	0.095890	0.681818	
chunk0041_306_1	chr11	129836337	129836577	+	0	NA	intron (NM_138788, intron 1 of 5)	MLT1B-int|LTR|ERVL-MaLR	20611	NM_138788	120224	Hs.504301	NM_138788	ENSG00000151715	TMEM45B	-	transmembrane protein 45B	protein-coding	0.004167	0.414938	133(GAGGACAGGGTGTTAT,-,0.00),134(AGGACAGGGTGTTATG,+,0.00)
chunk0129_14_1	chr3	117034204	117034584	+	0	NA	Intergenic	L1ME1|LINE|L1	112963	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.007895	0.396325	
chunk0181_437_1	chr7	90563127	90563480	+	0	NA	Intergenic	Intergenic	-33059	NM_001287135	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.011331	0.336158	
chunk0065_152_1	chr15	25426284	25427098	+	0	NA	intron (NM_130839, intron 1 of 12)	intron (NM_130839, intron 1 of 12)	12337	NM_130839	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.009828	0.366871	
chunk0179_289_1	chr7	49639059	49639655	+	0	NA	Intergenic	LTR80A|LTR|ERVL	-134304	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.001678	0.475712	
chunk0116_34_1	chr21	33324741	33325170	+	0	NA	promoter-TSS (NM_000629)	promoter-TSS (NM_000629)	46	NM_000629	3454	Hs.529400	NM_000629	ENSG00000142166	IFNAR1	AVP|IFN-alpha-REC|IFNAR|IFNBR|IFRC	interferon alpha and beta receptor subunit 1	protein-coding	0.102564	0.665116	
chunk0200_200_1	chr9	20382725	20383228	+	0	NA	intron (NM_001286691, intron 5 of 10)	intron (NM_001286691, intron 5 of 10)	28262	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.000000	0.351190	
chunk0070_214_1	chr15	72493218	72493628	+	0	NA	intron (NM_005744, intron 1 of 13)	Charlie15b|DNA|hAT-Charlie	19097	NM_005744	25820	Hs.268787	NM_005744	ENSG00000166233	ARIH1	ARI|HARI|HHARI|UBCH7BP	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding	0.004878	0.377129	
chunk0069_380_1	chr15	67416888	67417358	+	0	NA	intron (NM_001284348, intron 12 of 16)	intron (NM_001284348, intron 12 of 16)	103850	NR_040055	100506686	Hs.656245	NR_040051	ENSG00000259673	IQCH-AS1	-	IQCH antisense RNA 1	ncRNA	0.012766	0.426752	
chunk0176_102_1	chr7	11707156	11707652	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	124794	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.002016	0.382294	
chunk0191_292_1	chr8	54191826	54192070	+	0	NA	Intergenic	Intergenic	56727	NM_014175	29088	Hs.18349	NM_014175	ENSG00000137547	MRPL15	HSPC145|L15mt|MRP-L15|MRP-L7|RPML7	mitochondrial ribosomal protein L15	protein-coding	0.028689	0.628571	
chunk0080_264_1	chr17	30906165	30906552	+	0	NA	promoter-TSS (NM_024683)	promoter-TSS (NM_024683)	-90	NM_024683	79736	Hs.317340	NM_024683	ENSG00000172171	TEFM	C17orf42	transcription elongation factor, mitochondrial	protein-coding	0.082687	0.639175	
chunk0030_188_1	chr10	114239019	114239836	+	0	NA	5' UTR (NM_001272046, exon 1 of 14)	5' UTR (NM_001272046, exon 1 of 14)	173	NM_001272046	340706	Hs.197741	NM_198496	ENSG00000165816	VWA2	AMACO|CCSP-2|CCSP2|NET42	von Willebrand factor A domain containing 2	protein-coding	0.088127	0.621027	
chunk0012_64_1	chr1	155648577	155648949	+	0	NA	Intergenic	Intergenic	30492	NR_132762	106633810		NR_132762		SCARNA26A	-	small Cajal body-specific RNA 26A	ncRNA	0.008065	0.423592	
chunk0031_425_1	chr10	132364327	132364572	+	0	NA	intron (NM_030626, intron 9 of 10)	(CACTCA)n|Simple_repeat|Simple_repeat	27342	NM_001309474	80313	Hs.119897	NM_030626	ENSG00000148814	LRRC27	-	leucine rich repeat containing 27	protein-coding	0.028571	0.548780	
chunk0046_264_1	chr12	60844791	60845253	+	0	NA	Intergenic	Intergenic	1155685	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.002165	0.330454	
chunk0019_88_1	chr1	224540484	224540765	+	0	NA	Intergenic	Intergenic	-75853	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.003559	0.372340	
chunk0110_61_1	chr20	10861386	10862104	+	0	NA	Intergenic	Intergenic	47527	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.006964	0.365786	270(GAGTACAGTGTGTTAT,-,0.00),271(AGTACAGTGTGTTATT,+,0.00)
chunk0155_119_1	chr5	93022560	93023096	+	0	NA	Intergenic	Intergenic	548515	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.001866	0.303538	
chunk0019_27_1	chr1	223707334	223707588	+	0	NA	intron (NM_001146068, intron 1 of 20)	intron (NM_001146068, intron 1 of 20)	-4956	NM_001748	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.003937	0.450980	
chunk0097_420_1	chr2	62917713	62917960	+	0	NA	intron (NM_001142614, intron 9 of 22)	LTR40c|LTR|ERVL	129875	NR_027069	100132215	Hs.656781	NR_027069	ENSG00000231609	LOC100132215	-	uncharacterized LOC100132215	ncRNA	0.008097	0.387097	
chunk0055_122_1	chr13	57414624	57414964	+	0	NA	Intergenic	Intergenic	-216861	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.002941	0.275660	
chunk0157_2_1	chr5	115138513	115138868	+	0	NA	intron (NM_001300759, intron 5 of 9)	intron (NM_001300759, intron 5 of 9)	31273	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.005634	0.339888	
chunk0123_97_1	chr3	42130379	42130636	+	0	NA	intron (NM_001042646, intron 2 of 15)	intron (NM_001042646, intron 2 of 15)	-18728	NM_001265609	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.007782	0.368217	
chunk0089_331_1	chr18	65487437	65488041	+	0	NA	Intergenic	Intergenic	-262513	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.003311	0.370248	
chunk0134_46_1	chr3	175794037	175794500	+	0	NA	intron (NM_207015, intron 13 of 13)	intron (NM_207015, intron 13 of 13)	-17935	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.008639	0.321121	
chunk0186_402_1	chr7	144761549	144761811	+	0	NA	intron (NM_001042482, intron 3 of 7)	intron (NM_001042482, intron 3 of 7)	74373	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.011450	0.444867	113(AGGAACAGGCTGCACT,-,0.00),114(GGAACAGGCTGCACTT,+,0.00)
chunk0119_127_1	chr22	42844837	42845147	+	0	NA	intron (NM_001142293, intron 2 of 14)	intron (NM_001142293, intron 2 of 14)	12410	NM_014570	26286	Hs.685225	NM_014570	ENSG00000242247	ARFGAP3	ARFGAP1	ADP ribosylation factor GTPase activating protein 3	protein-coding	0.012903	0.411576	
chunk0148_91_1	chr5	3501573	3501788	+	0	NA	intron (NR_104618, intron 1 of 2)	L1ME2|LINE|L1	2324	NR_104618	102467075	Hs.652949	NR_104618	ENSG00000250716	LINC01017	-	long intergenic non-protein coding RNA 1017	ncRNA	0.009302	0.379630	
chunk0048_34_1	chr12	77752763	77753181	+	0	NA	Intergenic	Intergenic	-78317	NM_014903	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.002392	0.365155	
chunk0117_28_1	chr22	11900636	11900857	+	0	NA	intron (NR_110761, intron 1 of 2)	AluJr|SINE|Alu	3340	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.000000	0.472973	
chunk0169_178_1	chr6	102279249	102279568	+	0	NA	Intergenic	Intergenic	880423	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003135	0.265625	
chunk0006_292_1	chr1	71030427	71030706	+	0	NA	intron (NM_198719, intron 1 of 3)	intron (NM_198719, intron 1 of 3)	-15940	NR_038420	100132618	Hs.720513	NR_038420		ZRANB2-AS1	-	ZRANB2 antisense RNA 1	ncRNA	0.007168	0.321429	
chunk0126_327_1	chr3	81729431	81729755	+	0	NA	intron (NM_000158, intron 1 of 15)	ERVL-E-int|LTR|ERVL	32206	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.406154	
chunk0043_301_1	chr12	22081570	22081794	+	0	NA	Intergenic	Intergenic	35506	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.008929	0.391111	
chunk0078_66_1	chr17	1515495	1516018	+	0	NA	intron (NM_001135642, intron 2 of 13)	intron (NM_001135642, intron 2 of 13)	1132	NM_130766	51763	Hs.632238	NM_016532	ENSG00000132376	INPP5K	MDCCAID|PPS|SKIP	inositol polyphosphate-5-phosphatase K	protein-coding	0.028681	0.500000	
chunk0171_137_1	chr6	123482273	123482549	+	0	NA	intron (NM_001256020, intron 8 of 8)	intron (NM_001256020, intron 8 of 8)	42807	NR_110844	101927990	Hs.660877	NR_110844		TRDN-AS1	HRAT13	TRDN antisense RNA 1	ncRNA	0.000000	0.303249	
chunk0210_2_1	chrX	66733473	66734011	+	0	NA	Intergenic	Intergenic	-94444	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.000000	0.322820	
chunk0008_57_1	chr1	89446801	89447000	+	0	NA	Intergenic	L1M1|LINE|L1	39221	NR_003133	400759	Hs.661968	NR_003133	ENSG00000225492	GBP1P1	-	guanylate binding protein 1 pseudogene 1	pseudo	0.000000	0.505000	44(GGGTCAAGCTGTACTT,+,0.00)
chunk0053_414_1	chr13	36999319	36999687	+	0	NA	promoter-TSS (NM_001142364)	promoter-TSS (NM_001142364)	-136	NM_013338	29880	Hs.507769	NM_013338	ENSG00000120697	ALG5	bA421P11.2	ALG5 dolichyl-phosphate beta-glucosyltransferase	protein-coding	0.084239	0.520325	
chunk0192_439_1	chr8	69764089	69764729	+	0	NA	intron (NM_030958, intron 2 of 9)	intron (NM_030958, intron 2 of 9)	68760	NM_001146009	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.007812	0.365055	
chunk0203_295_1	chr9	89150407	89150889	+	0	NA	intron (NM_016848, intron 1 of 11)	L1MB7|LINE|L1	28119	NM_016848	53358	Hs.292737	NM_016848	ENSG00000148082	SHC3	N-Shc|NSHC|RAI|SHCC	SHC adaptor protein 3	protein-coding	0.004149	0.364389	46(TAGTACAATATGTGCC,-,0.00),47(AGTACAATATGTGCCG,+,0.00)
chunk0037_244_1	chr11	75399747	75399971	+	0	NA	promoter-TSS (NR_000005)	promoter-TSS (NR_000005)	368	NM_001005	6188	Hs.546286	NM_001005	ENSG00000149273	RPS3	S3	ribosomal protein S3	protein-coding	0.053571	0.537778	
chunk0088_61_1	chr18	44270071	44270712	+	0	NA	Intergenic	Intergenic	261306	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.003120	0.344237	
chunk0096_309_1	chr2	32997781	32998080	+	0	NA	intron (NM_206943, intron 2 of 33)	intron (NM_206943, intron 2 of 33)	50628	NM_206943	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.003344	0.406667	
chunk0134_325_1	chr3	181880294	181880631	+	0	NA	Intergenic	Intergenic	-71902	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.008902	0.437870	
chunk0156_332_1	chr5	111655100	111655630	+	0	NA	intron (NR_040093, intron 1 of 6)	intron (NR_040093, intron 1 of 6)	100886	NM_001142483	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.003774	0.393597	
chunk0063_131_1	chr14	79405819	79406308	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	126724	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004090	0.404082	243(AAGTACAGAATGTTTT,-,0.00),244(AGTACAGAATGTTTTG,+,0.00)
chunk0207_141_1	chr9	129456503	129456726	+	0	NA	Intergenic	Intergenic	-32046	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.004484	0.482143	
chunk0138_81_1	chr4	35456018	35456381	+	0	NA	Intergenic	L1PA16|LINE|L1	-787917	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.011019	0.365385	
chunk0036_252_1	chr11	64560711	64561701	+	0	NA	intron (NM_001307985, intron 2 of 7)	intron (NM_001307985, intron 2 of 7)	5605	NM_018484	55867	Hs.220844	NM_018484	ENSG00000168065	SLC22A11	OAT4|hOAT4	solute carrier family 22 member 11	protein-coding	0.022222	0.548940	
chunk0197_134_1	chr8	120202645	120202918	+	0	NA	intron (NM_021110, intron 8 of 47)	L2a|LINE|L2	77673	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.003663	0.386861	
chunk0095_250_1	chr2	19284691	19285051	+	0	NA	Intergenic	L1PREC2|LINE|L1	-63558	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.005556	0.340720	
chunk0058_283_1	chr14	26481815	26482057	+	0	NA	intron (NM_002515, intron 2 of 4)	intron (NM_002515, intron 2 of 4)	115818	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.000000	0.308642	48(AATACAAAGTGTTCTT,+,0.00)
chunk0187_249_1	chr7	153562117	153562705	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-150177	NR_125776	103724390	Hs.614280	NR_125776	ENSG00000234722	LINC01287	TCONS_l2_00027522	long intergenic non-protein coding RNA 1287	ncRNA	0.015306	0.483871	
chunk0180_49_1	chr7	54664486	54664956	+	0	NA	Intergenic	CpG	94525	NM_001012456	23480	Hs.488282	NM_014302	ENSG00000132432	SEC61G	SSS1	SEC61 translocon gamma subunit	protein-coding	0.061702	0.619958	
chunk0096_228_1	chr2	30641991	30642311	+	0	NA	3' UTR (NM_182551, exon 7 of 7)	3' UTR (NM_182551, exon 7 of 7)	165294	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.006250	0.417445	
chunk0142_280_1	chr4	99854019	99854516	+	0	NA	intron (NM_001306151, intron 4 of 9)	intron (NM_001306151, intron 4 of 9)	37434	NM_001306151	27071	Hs.436271	NM_014395	ENSG00000070190	DAPP1	BAM32	dual adaptor of phosphotyrosine and 3-phosphoinositides 1	protein-coding	0.002012	0.345382	
chunk0031_36_1	chr10	122120836	122121621	+	0	NA	intron (NM_001291879, intron 1 of 16)	intron (NM_001291879, intron 1 of 16)	8189	NM_001291879	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.015287	0.510178	283(AGGAGCAGCCTGTGCA,-,0.00),284(GGAGCAGCCTGTGCAC,+,0.00),361(AGTACATTCTGTATTT,+,0.00)
chunk0082_332_1	chr17	59723585	59723893	+	0	NA	intron (NM_030938, intron 1 of 11)	L2|LINE|L2	-16141	NM_001015509	51651	Hs.12677	NM_016077	ENSG00000141378	PTRH2	BIT1|CFAP37|CGI-147|IMNEPD|PTH|PTH 2|PTH2	peptidyl-tRNA hydrolase 2	protein-coding	0.003247	0.368932	
chunk0161_190_1	chr5	170195391	170195591	+	0	NA	intron (NR_108022, intron 3 of 4)	intron (NR_108022, intron 3 of 4)	3650	NR_108022	100507267	Hs.634846	NR_108022		LINC01187	CTB-27N1.1|KIDR	long intergenic non-protein coding RNA 1187	ncRNA	0.010000	0.288557	
chunk0018_49_1	chr1	216316684	216317060	+	0	NA	intron (NM_206933, intron 9 of 71)	L1P3|LINE|L1	106524	NM_206933	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.005319	0.376658	156(ATGAACAGACAGTTCT,-,0.00),157(TGAACAGACAGTTCTC,+,0.00)
chunk0077_360_1	chr16	84096483	84097104	+	0	NA	intron (NM_003791, intron 3 of 22)	intron (NM_003791, intron 3 of 22)	20150	NM_003791	8720	Hs.75890	NM_003791	ENSG00000140943	MBTPS1	PCSK8|S1P|SEDKF|SKI-1	membrane bound transcription factor peptidase, site 1	protein-coding	0.004831	0.395498	
chunk0117_306_1	chr22	24555650	24555966	+	0	NA	promoter-TSS (NM_031444)	promoter-TSS (NM_031444)	127	NR_104286	83606	Hs.9850	NM_031444	ENSG00000138867	GUCD1	C22orf13|LLN4	guanylyl cyclase domain containing 1	protein-coding	0.069620	0.671924	
chunk0076_231_1	chr16	68834523	68835038	+	0	NA	3' UTR (NM_004360, exon 16 of 16)	3' UTR (NM_004360, exon 16 of 16)	-8826	NM_024562	79613	Hs.13526	NM_024562	ENSG00000103047	TANGO6	TMCO7	transport and golgi organization 6 homolog	protein-coding	0.003883	0.434109	
chunk0140_389_1	chr4	74990106	74990555	+	0	NA	intron (NM_015393, intron 1 of 3)	intron (NM_015393, intron 1 of 3)	-19968	NR_121617	100507388	Hs.570765	NR_121617	ENSG00000249717	LOC100507388	-	uncharacterized LOC100507388	ncRNA	0.000000	0.426667	
chunk0113_225_1	chr20	53869711	53870275	+	0	NA	Intergenic	Intergenic	5716	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.008865	0.362832	
chunk0087_310_1	chr18	39474449	39475103	+	0	NA	intron (NR_024391, intron 3 of 3)	MIR3|SINE|MIR	147399	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.009174	0.393893	
chunk0193_100_1	chr8	73669910	73670109	+	0	NA	intron (NM_001164383, intron 1 of 9)	intron (NM_001164383, intron 1 of 9)	76918	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.000000	0.300000	
chunk0069_448_1	chr15	68674249	68674455	+	0	NA	intron (NM_001190456, intron 2 of 11)	intron (NM_001190456, intron 2 of 11)	42364	NM_001190457	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.033981	0.584541	
chunk0144_413_1	chr4	140426236	140426802	+	0	NA	intron (NM_004362, intron 1 of 14)	intron (NM_004362, intron 1 of 14)	1142	NM_001130675	1047	Hs.86368	NM_004362	ENSG00000153132	CLGN	-	calmegin	protein-coding	0.012367	0.356261	
chunk0012_455_1	chr1	165178500	165178805	+	0	NA	Intergenic	Intergenic	177589	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.006557	0.428105	
chunk0082_274_1	chr17	57939850	57940504	+	0	NA	intron (NM_001271875, intron 1 of 10)	MIRc|SINE|MIR	15146	NM_001271875	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.015291	0.496183	
chunk0025_137_1	chr10	52136843	52137144	+	0	NA	intron (NM_006258, intron 8 of 17)	intron (NM_006258, intron 8 of 17)	177135	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.003322	0.374172	
chunk0059_401_1	chr14	37641295	37641525	+	0	NA	intron (NM_001310135, intron 3 of 32)	intron (NM_001310135, intron 3 of 32)	46211	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.000000	0.337662	
chunk0113_183_1	chr20	53258678	53259246	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	73679	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.010563	0.391916	
chunk0115_161_1	chr21	24319583	24320025	+	0	NA	intron (NR_109963, intron 1 of 3)	intron (NR_109963, intron 1 of 3)	1573	NR_109963	101927869	Hs.555591	NR_109963	ENSG00000224832	LINC01689	-	long intergenic non-protein coding RNA 1689	ncRNA	0.004525	0.376975	
chunk0169_115_1	chr6	100799770	100800226	+	0	NA	intron (NM_006828, intron 6 of 41)	intron (NM_006828, intron 6 of 41)	81374	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.004386	0.280088	
chunk0016_354_1	chr1	202217671	202218179	+	0	NA	intron (NM_001017404, intron 1 of 15)	intron (NM_001017404, intron 1 of 15)	3770	NM_001017404	59352	Hs.497402	NM_021636	ENSG00000133067	LGR6	GPCR|VTS20631	leucine rich repeat containing G protein-coupled receptor 6	protein-coding	0.001969	0.453831	206(GAGAACAGGTTGTGCT,-,0.00),207(AGAACAGGTTGTGCTC,+,0.00)
chunk0203_66_1	chr9	83538158	83538825	+	0	NA	promoter-TSS (NM_174938)	promoter-TSS (NM_174938)	-58	NM_174938	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.122939	0.739521	
chunk0173_42_1	chr6	142285421	142286248	+	0	NA	Intergenic	Intergenic	-16085	NM_001032395	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.007255	0.371981	387(AAGAACTCTGTGTCCT,-,0.00),388(AGAACTCTGTGTCCTG,+,0.00)
chunk0012_397_1	chr1	163688359	163688611	+	0	NA	Intergenic	Intergenic	-265294	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.003968	0.343874	161(AAGAACACTGAGTTTT,-,0.00)
chunk0015_450_1	chr1	192389977	192390367	+	0	NA	Intergenic	Intergenic	73180	NM_001039152	431704	Hs.558673	NM_001039152	ENSG00000253148	RGS21	-	regulator of G protein signaling 21	protein-coding	0.002564	0.360614	166(AAGCACACTCTGTGAC,-,0.00)
chunk0121_292_1	chr3	23724014	23724627	+	0	NA	Intergenic	Intergenic	-81573	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.001631	0.451140	
chunk0001_327_1	chr1	9518558	9518800	+	0	NA	Intergenic	Intergenic	-20790	NM_032315	84275	Hs.568613	NM_032315	ENSG00000171612	SLC25A33	BMSC-MCP|PNC1	solute carrier family 25 member 33	protein-coding	0.020661	0.596708	149(TAGGACACCAAGTTCC,-,0.00),150(AGGACACCAAGTTCCC,+,0.00)
chunk0061_241_1	chr14	60794945	60795201	+	0	NA	intron (NM_002431, intron 1 of 7)	intron (NM_002431, intron 1 of 7)	60332	NM_002431	4331	Hs.509523	NM_002431	ENSG00000020426	MNAT1	CAP35|MAT1|RNF66|TFB3	MNAT1 component of CDK activating kinase	protein-coding	0.007812	0.365759	
chunk0072_25_1	chr16	591365	591577	+	0	NA	intron (NM_021168, intron 1 of 5)	intron (NM_021168, intron 1 of 5)	1298	NM_021168	57799	Hs.459630	NM_021168	ENSG00000197562	RAB40C	RARL|RASL8C	RAB40C, member RAS oncogene family	protein-coding	0.028302	0.530516	
chunk0016_428_1	chr1	203686220	203686694	+	0	NA	intron (NM_001001396, intron 2 of 21)	intron (NM_001001396, intron 2 of 21)	-43124	NR_003019	677843	Hs.676135	NR_003019	ENSG00000221643	SNORA77	ACA63|SNORA77A	small nucleolar RNA, H/ACA box 77	snoRNA	0.004219	0.444211	
chunk0151_312_1	chr5	53355161	53355801	+	0	NA	Intergenic	Intergenic	-124953	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.007812	0.361934	
chunk0142_403_1	chr4	102781569	102782096	+	0	NA	intron (NR_125932, intron 4 of 4)	MER70A|LTR|ERVL	4795	NR_125932	102723704	Hs.638374	NR_125932		LOC102723704	-	uncharacterized LOC102723704	ncRNA	0.001898	0.456439	230(CAGAACAGGATGTCCT,-,0.00),231(AGAACAGGATGTCCTT,+,0.00)
chunk0142_166_1	chr4	95284722	95284949	+	0	NA	intron (NM_003728, intron 3 of 15)	intron (NM_003728, intron 3 of 15)	193344	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.004405	0.447368	
chunk0145_285_1	chr4	149749738	149750072	+	0	NA	Intergenic	L2b|LINE|L2	-328369	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.002994	0.361194	
chunk0179_145_1	chr7	46255266	46255899	+	0	NA	Intergenic	L1MDa|LINE|L1	-334310	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.003160	0.304416	
chunk0098_29_1	chr2	65612422	65612940	+	0	NA	Intergenic	Intergenic	-180159	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.007722	0.400771	
chunk0042_22_1	chr12	1350264	1350949	+	0	NA	intron (NM_178040, intron 15 of 18)	intron (NM_178040, intron 15 of 18)	-149885	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.007299	0.448980	380(AGGGACTTACAGTTCT,-,0.00),381(GGGACTTACAGTTCTA,+,0.00)
chunk0087_63_1	chr18	31641354	31641857	+	0	NA	intron (NM_004775, intron 4 of 8)	L3b|LINE|CR1	43118	NM_004775	9331	Hs.591063	NM_004775	ENSG00000118276	B4GALT6	B4Gal-T6|beta4Gal-T6	beta-1,4-galactosyltransferase 6	protein-coding	0.001988	0.351190	187(AAGATCTCAGTGTTCT,-,0.00),188(AGATCTCAGTGTTCTG,+,0.00)
chunk0193_425_1	chr8	80807776	80808423	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	66682	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.004637	0.370370	
chunk0152_446_1	chr5	66361159	66361450	+	0	NA	Intergenic	MER57C2|LTR|ERV1	150300	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.010309	0.438356	
chunk0147_93_1	chr4	173278501	173278735	+	0	NA	intron (NM_017423, intron 2 of 11)	L3|LINE|CR1	10458	NR_036093	100422849		NR_036093	ENSG00000221296	MIR548T	-	microRNA 548t	ncRNA	0.000000	0.302128	
chunk0211_239_1	chrX	119460234	119460704	+	0	NA	Intergenic	Intergenic	-7931	NM_001152	292	Hs.632282	NM_001152	ENSG00000005022	SLC25A5	2F1|AAC2|ANT2|T2|T3	solute carrier family 25 member 5	protein-coding	0.008511	0.371550	
chunk0188_158_1	chr8	10510545	10511059	+	0	NA	Intergenic	Intergenic	-14744	NM_198464	203074	Hs.591394	NM_198464	ENSG00000184647	PRSS55	CT153|T-SP1|TSP1|UNQ9391	serine protease 55	protein-coding	0.013619	0.440777	
chunk0071_211_1	chr15	84633541	84633919	+	0	NA	intron (NR_003654, intron 1 of 3)	CpG	2270	NR_004859	54581	Hs.658114	NM_022050		SCAND2P	SCAND2	SCAN domain containing 2 pseudogene	pseudo	0.132275	0.754617	
chunk0073_203_1	chr16	9543569	9544169	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	-88364	NR_126349	104266959	Hs.578888	NR_126349	ENSG00000261075	LINC01195	-	long intergenic non-protein coding RNA 1195	ncRNA	0.008333	0.429285	
chunk0160_25_1	chr5	149160618	149161635	+	0	NA	intron (NM_014945, intron 2 of 23)	intron (NM_014945, intron 2 of 23)	19117	NM_001301018	22885	Hs.49688	NM_014945	ENSG00000173210	ABLIM3	HMFN1661	actin binding LIM protein family member 3	protein-coding	0.010816	0.504912	88(TAGGACATCCTGTGCT,-,0.00),89(AGGACATCCTGTGCTT,+,0.00)
chunk0081_261_1	chr17	43419223	43419422	+	0	NA	Intergenic	Intergenic	20337	NM_001661	379	Hs.183153	NM_001661	ENSG00000175906	ARL4D	ARF4L|ARL6	ADP ribosylation factor like GTPase 4D	protein-coding	0.020101	0.545000	
chunk0143_45_1	chr4	107603428	107603919	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	116590	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.008147	0.359756	
chunk0092_255_1	chr19	33032346	33032936	+	0	NA	intron (NM_033103, intron 2 of 14)	MER112|DNA|hAT-Charlie	32277	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.005085	0.445008	
chunk0104_24_1	chr2	170651476	170652224	+	0	NA	intron (NR_045684, intron 33 of 34)	intron (NR_045684, intron 33 of 34)	62717	NR_027433	440925	Hs.668461	NM_001013712	ENSG00000222033	LINC01124	-	long intergenic non-protein coding RNA 1124	ncRNA	0.013369	0.411215	229(GAGGACACCATGTACT,-,0.00),230(AGGACACCATGTACTA,+,0.00)
chunk0184_238_1	chr7	117619331	117619609	+	0	NA	intron (NM_000492, intron 21 of 26)	intron (NM_000492, intron 21 of 26)	139507	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.003597	0.387097	
chunk0042_447_1	chr12	12415781	12416452	+	0	NA	intron (NM_058169, intron 2 of 3)	L1PA6|LINE|L1	59037	NM_058169	118426	Hs.504805	NM_058169	ENSG00000165714	BORCS5	LOH12CR1|LOH1CR12	BLOC-1 related complex subunit 5	protein-coding	0.002981	0.316964	
chunk0166_147_1	chr6	45039602	45040179	+	0	NA	intron (NM_181356, intron 5 of 12)	intron (NM_181356, intron 5 of 12)	157880	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.005199	0.394464	300(ATGCACAAGATGTTCC,-,0.00),301(TGCACAAGATGTTCCA,+,0.00)
chunk0021_153_1	chr10	4662012	4662324	+	0	NA	non-coding (NR_015425, exon 3 of 3)	non-coding (NR_015425, exon 3 of 3)	6012	NR_015425	338588	Hs.121365	NR_015425		LINC00705	-	long intergenic non-protein coding RNA 705	ncRNA	0.009615	0.466454	
chunk0097_105_1	chr2	46038134	46038637	+	0	NA	intron (NM_005400, intron 10 of 14)	intron (NM_005400, intron 10 of 14)	-259017	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.009940	0.369048	
chunk0120_195_1	chr3	7058734	7059184	+	0	NA	intron (NM_000844, intron 1 of 9)	LTR10C|LTR|ERV1	-164942	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.002222	0.365854	272(AAGAACATAAAGTACA,-,0.00)
chunk0154_429_1	chr5	89374508	89375030	+	0	NA	Intergenic	Intergenic	-470664	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.000000	0.363289	
chunk0140_417_1	chr4	75921214	75921643	+	0	NA	intron (NM_014435, intron 5 of 10)	intron (NM_014435, intron 5 of 10)	-18900	NM_006239	5470	Hs.290873	NM_006239	ENSG00000156194	PPEF2	PPP7CB	protein phosphatase with EF-hand domain 2	protein-coding	0.011655	0.469767	203(AAGGACTTTTTGTGCT,-,0.00),204(AGGACTTTTTGTGCTT,+,0.00)
chunk0127_57_1	chr3	89186523	89186870	+	0	NA	intron (NM_005233, intron 2 of 16)	intron (NM_005233, intron 2 of 16)	79172	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005764	0.336207	
chunk0183_315_1	chr7	108017379	108017691	+	0	NA	Intergenic	Intergenic	-14176	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.003205	0.415335	
chunk0198_114_1	chr8	131835022	131835300	+	0	NA	Intergenic	Intergenic	-68948	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.007194	0.311828	
chunk0173_365_1	chr6	149387801	149388450	+	0	NA	intron (NM_001292034, intron 3 of 6)	MLT1I|LTR|ERVL-MaLR	-12234	NM_001002255	387082	Hs.657168	NM_001002255	ENSG00000177688	SUMO4	IDDM5|SMT3H4|SUMO-4|dJ281H8.4	small ubiquitin like modifier 4	protein-coding	0.001541	0.410769	
chunk0075_292_1	chr16	54075934	54076404	+	0	NA	intron (NM_001080432, intron 8 of 8)	intron (NM_001080432, intron 8 of 8)	36776	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.010638	0.418259	
chunk0137_83_1	chr4	13109096	13109983	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	374826	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.002255	0.386261	
chunk0031_100_1	chr10	124088985	124089254	+	0	NA	intron (NM_001270764, intron 1 of 7)	intron (NM_001270764, intron 1 of 7)	3305	NM_015892	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.007435	0.481481	127(TGGAACAGAGTGACCC,-,0.00),128(GGAACAGAGTGACCCT,+,0.00)
chunk0046_333_1	chr12	62832210	62832723	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	102419	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.007797	0.412451	192(AAGAACATTATGGTCT,-,0.00),193(AGAACATTATGGTCTT,+,0.00)
chunk0002_169_1	chr1	18902497	18902853	+	0	NA	5' UTR (NM_170726, exon 1 of 16)	5' UTR (NM_170726, exon 1 of 16)	124	NM_170726	8659	Hs.77448	NM_003748	ENSG00000159423	ALDH4A1	ALDH4|P5CD|P5CDh	aldehyde dehydrogenase 4 family member A1	protein-coding	0.084270	0.582633	
chunk0197_48_1	chr8	118412965	118413270	+	0	NA	intron (NR_109794, intron 3 of 4)	MLT1H|LTR|ERVL-MaLR	-207884	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.009836	0.473856	
chunk0186_176_1	chr7	139431091	139431350	+	0	NA	Intergenic	L1ME1|LINE|L1	-3694	NR_033999	100129148	Hs.744449	NR_033999		LOC100129148	-	uncharacterized LOC100129148	ncRNA	0.007722	0.423077	
chunk0159_35_1	chr5	136985731	136986189	+	0	NA	intron (NM_004598, intron 8 of 10)	intron (NM_004598, intron 8 of 10)	513369	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.002183	0.420479	202(GGTTCATCCTGTCCTT,+,0.00)
chunk0029_58_1	chr10	96532300	96532998	+	0	NA	intron (NM_020123, intron 10 of 14)	MER58A|DNA|hAT-Charlie	-18723	NM_012465	7093	Hs.154296	NM_012465	ENSG00000095587	TLL2	-	tolloid like 2	protein-coding	0.002865	0.331903	
chunk0017_342_1	chr1	211728820	211729468	+	0	NA	Intergenic	Intergenic	-53514	NM_001204182	4751	Hs.153704	NM_002497	ENSG00000117650	NEK2	HsPK21|NEK2A|NLK1|PPP1R111|RP67	NIMA related kinase 2	protein-coding	0.015432	0.395994	
chunk0148_282_1	chr5	10982566	10983036	+	0	NA	intron (NM_001288717, intron 19 of 20)	L1MA4|LINE|L1	-221526	NM_004394	1611	Hs.75189	NM_004394	ENSG00000112977	DAP	-	death associated protein	protein-coding	0.006383	0.405520	
chunk0193_36_1	chr8	71341390	71342065	+	0	NA	intron (NM_172060, intron 1 of 15)	intron (NM_172060, intron 1 of 15)	14784	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.002963	0.316568	
chunk0094_9_1	chr2	942633	943408	+	0	NA	Intergenic	Intergenic	-7848	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.012903	0.412371	292(AGAACATGGTCTTCCC,+,0.00)
chunk0112_239_1	chr20	41268320	41268771	+	0	NA	intron (NM_015035, intron 2 of 3)	intron (NM_015035, intron 2 of 3)	31554	NM_015035	23051	Hs.380133	NM_015035	ENSG00000174306	ZHX3	TIX1	zinc fingers and homeoboxes 3	protein-coding	0.004435	0.318584	
chunk0155_391_1	chr5	98635766	98636282	+	0	NA	Intergenic	Intergenic	-133271	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.005814	0.417795	
chunk0125_211_1	chr3	67516521	67516978	+	0	NA	intron (NM_001177599, intron 6 of 10)	L2a|LINE|L2	137865	NM_001177599	8801	Hs.644919	NM_003848	ENSG00000172340	SUCLG2	G-SCS|GBETA|GTPSCS	succinate-CoA ligase GDP-forming beta subunit	protein-coding	0.004376	0.456332	
chunk0138_362_1	chr4	42149362	42150120	+	0	NA	intron (NM_001159547, intron 2 of 5)	intron (NM_001159547, intron 2 of 5)	3137	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.007916	0.397892	
chunk0189_65_1	chr8	20418376	20418741	+	0	NA	Intergenic	Intergenic	142785	NR_047509	100874051	Hs.385799	NR_047509	ENSG00000253733	LZTS1-AS1	-	LZTS1 antisense RNA 1	ncRNA	0.013699	0.439891	
chunk0133_153_1	chr3	169515258	169515581	+	0	NA	intron (NM_004991, intron 1 of 16)	MIRb|SINE|MIR	148356	NM_004991	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.006192	0.391975	
chunk0135_42_1	chr3	185424376	185425032	+	0	NA	intron (NM_004721, intron 1 of 13)	intron (NM_004721, intron 1 of 13)	61656	NM_004721	9175	Hs.591306	NM_004721	ENSG00000073803	MAP3K13	LZK|MEKK13|MLK	mitogen-activated protein kinase kinase kinase 13	protein-coding	0.004573	0.372907	
chunk0169_32_1	chr6	97267799	97268171	+	0	NA	exon (NM_198468, exon 8 of 25)	exon (NM_198468, exon 8 of 25)	15191	NM_198468	253714	Hs.444292	NM_198468	ENSG00000146263	MMS22L	C6orf167|dJ39B17.2	MMS22 like, DNA repair protein	protein-coding	0.005376	0.294906	
chunk0105_102_1	chr2	184555342	184555697	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-42847	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.008451	0.331461	
chunk0198_464_1	chr8	144614688	144614964	+	0	NA	intron (NM_001308208, intron 1 of 10)	L1MEc|LINE|L1	-1323	NM_001308207	80728	Hs.148988	NM_025251	ENSG00000147799	ARHGAP39	CrGAP|Vilse	Rho GTPase activating protein 39	protein-coding	0.003623	0.451264	177(GAGTACTTACTGTTCC,-,0.00),178(AGTACTTACTGTTCCC,+,0.00)
chunk0187_223_1	chr7	152255336	152255809	+	0	NA	intron (NM_170606, intron 9 of 58)	L1MC4a|LINE|L1	180433	NM_170606	58508	Hs.647120	NM_021230	ENSG00000055609	KMT2C	HALR|KLEFS2|MLL3	lysine methyltransferase 2C	protein-coding	0.004228	0.392405	
chunk0068_381_1	chr15	58332912	58333551	+	0	NA	Intergenic	Intergenic	-98745	NM_000236	3990	Hs.654472	NM_000236	ENSG00000166035	LIPC	HDLCQ12|HL|HTGL|LIPH	lipase C, hepatic type	protein-coding	0.001565	0.437500	
chunk0080_333_1	chr17	32592735	32593293	+	0	NA	intron (NM_015194, intron 21 of 21)	intron (NM_015194, intron 21 of 21)	105927	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.008961	0.441860	
chunk0140_176_1	chr4	69775553	69775894	+	0	NA	Intergenic	Intergenic	-15011	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.002933	0.342105	
chunk0187_185_1	chr7	151304740	151305294	+	0	NA	Intergenic	HAL1|LINE|L1	-27872	NM_003078	6604	Hs.647067	NM_003078	ENSG00000082014	SMARCD3	BAF60C|CRACD3|Rsc6p	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	protein-coding	0.027076	0.450450	
chunk0140_167_1	chr4	69707742	69708358	+	0	NA	Intergenic	Intergenic	52662	NM_014465	27284	Hs.129742	NM_014465	ENSG00000173597	SULT1B1	ST1B1|ST1B2|SULT1B2	sulfotransferase family 1B member 1	protein-coding	0.000000	0.346840	
chunk0123_100_1	chr3	42190287	42190486	+	0	NA	intron (NM_001042646, intron 6 of 15)	intron (NM_001042646, intron 6 of 15)	30217	NM_014965	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.005025	0.475000	97(CTGCACATCTTGTTCT,-,0.00),98(TGCACATCTTGTTCTG,+,0.00)
chunk0072_83_1	chr15	90624333	90624573	+	0	NA	intron (NR_120372, intron 3 of 3)	(TCCC)n|Simple_repeat|Simple_repeat	-35781	NR_120371	101929765	Hs.615348	NR_120371	ENSG00000245479	LINC01585	-	long intergenic non-protein coding RNA 1585	ncRNA	0.016667	0.568465	
chunk0102_422_1	chr2	157037839	157038361	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-219728	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.000000	0.369025	
chunk0127_134_1	chr3	94062525	94062886	+	0	NA	promoter-TSS (NM_022072)	promoter-TSS (NM_022072)	282	NM_176815	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.060942	0.519337	
chunk0206_255_1	chr9	123795475	123795849	+	0	NA	intron (NM_024820, intron 2 of 20)	intron (NM_024820, intron 2 of 20)	134476	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.013369	0.357333	
chunk0025_250_1	chr10	54750640	54751173	+	0	NA	intron (NM_001142769, intron 1 of 35)	intron (NM_001142769, intron 1 of 35)	50385	NM_001142771	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.003752	0.245318	
chunk0132_10_1	chr3	154330289	154330497	+	0	NA	Intergenic	Intergenic	-5896	NM_020865	170506	Hs.446270	NM_020865	ENSG00000174953	DHX36	DDX36|G4R1|MLEL1|RHAU	DEAH-box helicase 36	protein-coding	0.004808	0.406699	
chunk0079_92_1	chr17	11997319	11997636	+	0	NA	promoter-TSS (NM_001303282)	promoter-TSS (NM_001303282)	33	NM_001303281	7566	Hs.370473	NM_144680	ENSG00000154957	ZNF18	HDSG1|KOX11|ZKSCAN6|ZNF535|ZSCAN38|Zfp535	zinc finger protein 18	protein-coding	0.129338	0.748428	
chunk0118_333_1	chr22	35480147	35480525	+	0	NA	Intergenic	Intergenic	-60969	NM_014310	23551	Hs.474711	NM_014310	ENSG00000100302	RASD2	Rhes|TEM2	RASD family member 2	protein-coding	0.029101	0.583113	
chunk0026_309_1	chr10	68047522	68048030	+	0	NA	intron (NM_022079, intron 3 of 25)	L1MC1|LINE|L1	27570	NM_015601	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.005906	0.400786	
chunk0164_204_1	chr6	22599139	22599747	+	0	NA	Intergenic	Intergenic	29994	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.006579	0.333333	
chunk0011_93_1	chr1	145806984	145807259	+	0	NA	intron (NM_014455, intron 1 of 8)	intron (NM_014455, intron 1 of 8)	-16948	NM_006468	10623	Hs.515768	NM_006468	ENSG00000186141	POLR3C	RPC3|RPC62	RNA polymerase III subunit C	protein-coding	0.003636	0.340580	
chunk0016_282_1	chr1	200732373	200732781	+	0	NA	Intergenic	L2|LINE|L2	-6981	NM_001297707	23271	Hs.23585	NM_203459	ENSG00000118200	CAMSAP2	CAMSAP1L1	calmodulin regulated spectrin associated protein family member 2	protein-coding	0.012255	0.464548	
chunk0164_459_1	chr6	28458308	28458975	+	0	NA	Intergenic	Intergenic	-15139	NM_001012455	222696	Hs.721841	NM_001012455	ENSG00000187987	ZSCAN23	ZNF390|ZNF453|dJ29K1.3|dJ29K1.3.1	zinc finger and SCAN domain containing 23	protein-coding	0.001499	0.360778	
chunk0044_442_1	chr12	42324813	42325196	+	0	NA	intron (NM_033114, intron 1 of 7)	Tigger3a|DNA|TcMar-Tigger	1126	NM_033114	85437	Hs.496279	NM_033114	ENSG00000139168	ZCRB1	MADP-1|MADP1|RBM36|SNRNP31|ZCCHC19	zinc finger CCHC-type and RNA binding motif containing 1	protein-coding	0.005222	0.393229	
chunk0035_203_1	chr11	44659462	44660098	+	0	NA	Intergenic	Intergenic	94189	NM_002231	3732	Hs.527778	NM_002231	ENSG00000085117	CD82	4F9|C33|GR15|IA4|KAI1|R2|SAR2|ST6|TSPAN27	CD82 molecule	protein-coding	0.009434	0.569859	146(TGAAACATTCTGTTCT,-,0.00),147(GAAACATTCTGTTCTG,+,0.00),364(GGGCACAGAGTGTTCC,-,0.00),365(GGCACAGAGTGTTCCC,+,0.00)
chunk0186_417_1	chr7	146471090	146471390	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	354879	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.003333	0.352159	
chunk0026_228_1	chr10	65155897	65156262	+	0	NA	Intergenic	L2c|LINE|L2	330551	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.005479	0.355191	
chunk0087_40_1	chr18	31274138	31274572	+	0	NA	Intergenic	Intergenic	-43734	NM_001942	1828	Hs.2633	NM_001942	ENSG00000134760	DSG1	CDHF4|DG1|DSG|EPKHE|EPKHIA|PPKS1|SPPK1	desmoglein 1	protein-coding	0.009217	0.354023	
chunk0002_419_1	chr1	27784445	27784791	+	0	NA	intron (NM_177424, intron 1 of 8)	intron (NM_177424, intron 1 of 8)	11435	NM_177424	23673	Hs.523855	NM_177424	ENSG00000117758	STX12	STX13|STX14	syntaxin 12	protein-coding	0.005780	0.397695	
chunk0148_354_1	chr5	14534731	14535170	+	0	NA	Intergenic	Intergenic	-46832	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.015945	0.484091	
chunk0149_70_1	chr5	17115765	17116136	+	0	NA	Intergenic	Intergenic	-100873	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.000000	0.387097	
chunk0040_446_1	chr11	121585502	121586307	+	0	NA	intron (NM_003105, intron 26 of 47)	L1ME4b|LINE|L1	133701	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.008696	0.370968	
chunk0142_416_1	chr4	103198304	103198878	+	0	NA	promoter-TSS (NM_001286734)	promoter-TSS (NM_001286734)	-182	NM_001286734	1062	Hs.75573	NM_001813	ENSG00000138778	CENPE	CENP-E|KIF10|MCPH13|PPP1R61	centromere protein E	protein-coding	0.048780	0.523478	
chunk0208_348_1	chrX	25288616	25289162	+	0	NA	Intergenic	Intergenic	-272941	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.001832	0.365631	
chunk0185_453_1	chr7	135099077	135099477	+	0	NA	intron (NM_001305630, intron 2 of 2)	intron (NM_001305630, intron 2 of 2)	-48737	NM_018295	55281	Hs.521213	NM_018295	ENSG00000146859	TMEM140	-	transmembrane protein 140	protein-coding	0.000000	0.266833	
chunk0148_428_1	chr5	15356500	15357322	+	0	NA	Intergenic	L1PA6|LINE|L1	-90351	NR_109944	101929454	Hs.453273	NR_109944		LINC02149	-	long intergenic non-protein coding RNA 2149	ncRNA	0.004866	0.493317	
chunk0141_220_1	chr4	84651344	84651840	+	0	NA	TTS (NM_001263)	TTS (NM_001263)	68688	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.004032	0.424547	
chunk0033_292_1	chr11	19670053	19670766	+	0	NA	intron (NM_001111018, intron 1 of 37)	L2b|LINE|L2	-42926	NM_001244963	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.016830	0.558824	
chunk0135_365_1	chr3	190709328	190710145	+	0	NA	Intergenic	Intergenic	152940	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.006120	0.356968	
chunk0183_12_1	chr7	102989029	102989678	+	0	NA	intron (NM_145032, intron 6 of 19)	L3|LINE|CR1	15916	NM_001085386	58160	Hs.621233	NM_001085386	ENSG00000230257	NFE4	NF-E4	nuclear factor, erythroid 4	protein-coding	0.007704	0.444615	328(CAGCACAGAAAGTACT,-,0.00),329(AGCACAGAAAGTACTA,+,0.00)
chunk0103_193_1	chr2	163646363	163646917	+	0	NA	intron (NM_018086, intron 2 of 2)	intron (NM_018086, intron 2 of 2)	89363	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.000000	0.320721	
chunk0135_247_1	chr3	188868919	188869373	+	0	NA	intron (NM_001167671, intron 9 of 10)	intron (NM_001167671, intron 9 of 10)	78493	NR_046873	100874043	Hs.616287	NR_046873	ENSG00000234076	TPRG1-AS1	-	TPRG1 antisense RNA 1	ncRNA	0.002203	0.468132	
chunk0109_421_1	chr2	241173733	241174450	+	0	NA	intron (NM_002712, intron 9 of 9)	L1MEc|LINE|L1	-14418	NM_001001891									0.005579	0.387187	
chunk0083_266_1	chr17	68386492	68386918	+	0	NA	intron (NM_014960, intron 9 of 11)	intron (NM_014960, intron 9 of 11)	-26918	NM_001278433	5573	Hs.280342	NM_002734	ENSG00000108946	PRKAR1A	ACRDYS1|ADOHR|CAR|CNC|CNC1|PKR1|PPNAD1|PRKAR1|TSE1	protein kinase cAMP-dependent type I regulatory subunit alpha	protein-coding	0.011737	0.543326	
chunk0183_73_1	chr7	104327623	104327954	+	0	NA	promoter-TSS (NM_199000)	promoter-TSS (NM_199000)	-868	NM_199000	375612	Hs.659164	NM_199000	ENSG00000187416	LHFPL3	LHFPL4	LHFPL tetraspan subfamily member 3	protein-coding	0.018127	0.466867	
chunk0076_146_1	chr16	67111145	67111605	+	0	NA	intron (NM_025187, intron 1 of 15)	intron (NM_025187, intron 1 of 15)	1363	NM_025187	80262	Hs.513666	NM_025187	ENSG00000125149	C16orf70	C16orf6|LIN10|lin-10	chromosome 16 open reading frame 70	protein-coding	0.004348	0.451193	
chunk0144_172_1	chr4	132912394	132912767	+	0	NA	Intergenic	Intergenic	236536	NR_125885	101927359	Hs.649960	NR_125885	ENSG00000250241	LOC101927359	-	uncharacterized LOC101927359	ncRNA	0.010724	0.304813	
chunk0083_277_1	chr17	68549776	68550016	+	0	NA	intron (NM_001243746, intron 5 of 11)	intron (NM_001243746, intron 5 of 11)	8531	NR_027751	54757	Hs.268874	NM_017565	ENSG00000108950	FAM20A	AI1G|AIGFS|FP2747	FAM20A golgi associated secretory pathway pseudokinase	protein-coding	0.000000	0.381743	83(AGGAACACAATGTATT,-,0.00),84(GGAACACAATGTATTT,+,0.00)
chunk0141_342_1	chr4	87456827	87457258	+	0	NA	intron (NM_001248011, intron 6 of 6)	L2a|LINE|L2	34445	NM_198038	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.011601	0.347222	
chunk0063_375_1	chr14	86146953	86147193	+	0	NA	Intergenic	Intergenic	212395	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.004167	0.253112	
chunk0050_403_1	chr12	109445087	109445519	+	0	NA	intron (NM_001101421, intron 29 of 30)	intron (NM_001101421, intron 29 of 30)	32047	NM_031954	83892	Hs.524731	NM_031954	ENSG00000110906	KCTD10	BTBD28|MSTP028|ULRO61|hBACURD3	potassium channel tetramerization domain containing 10	protein-coding	0.000000	0.381062	197(AAGAACTGAATGTGCT,-,0.00),198(AGAACTGAATGTGCTC,+,0.00)
chunk0061_359_1	chr14	63735712	63736017	+	0	NA	Intergenic	Intergenic	-7769	NM_030791	81537	Hs.24678	NM_030791	ENSG00000126821	SGPP1	SPP-1|SPPase1	sphingosine-1-phosphate phosphatase 1	protein-coding	0.013115	0.415033	
chunk0193_97_1	chr8	73634841	73635337	+	0	NA	intron (NM_001164383, intron 1 of 9)	L1ME4b|LINE|L1	111838	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.004032	0.340040	
chunk0050_166_1	chr12	103725322	103725757	+	0	NA	intron (NM_017564, intron 45 of 68)	intron (NM_017564, intron 45 of 68)	115658	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.016092	0.417431	156(AAGGACACAGAGTGCT,-,0.00),157(AGGACACAGAGTGCTC,+,0.00)
chunk0027_420_1	chr10	80783698	80784096	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	243078	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.007538	0.365915	
chunk0189_445_1	chr8	28277773	28278019	+	0	NA	Intergenic	L1MB3|LINE|L1	-39236	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.008130	0.396761	
chunk0014_392_1	chr1	182780303	182780851	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-8872	NM_001200056	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.010949	0.398907	
chunk0008_48_1	chr1	89169196	89169597	+	0	NA	intron (NM_207398, intron 2 of 10)	MER65-int|LTR|ERV1	6644	NM_207398	388646	Hs.591450	NM_207398	ENSG00000213512	GBP7	GBP4L	guanylate binding protein 7	protein-coding	0.004988	0.310945	
chunk0011_255_1	chr1	150817113	150817498	+	0	NA	intron (NM_178427, intron 15 of 20)	intron (NM_178427, intron 15 of 20)	-8864	NM_000396	1513	Hs.632466	NM_000396	ENSG00000143387	CTSK	CTS02|CTSO|CTSO1|CTSO2|PKND|PYCD	cathepsin K	protein-coding	0.005195	0.393782	
chunk0145_97_1	chr4	145982252	145982774	+	0	NA	Intergenic	Intergenic	-43553	NM_001306215	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.005747	0.332696	
chunk0213_36_1	chrY	56856912	56857310	+	0	NA	Intergenic	L1MD2|LINE|L1	-97144	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.002513	0.283208	
chunk0083_205_1	chr17	66725050	66725391	+	0	NA	intron (NM_002737, intron 8 of 16)	intron (NM_002737, intron 8 of 16)	-61852	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.002933	0.500000	
chunk0054_418_1	chr13	50910444	50910726	+	0	NA	non-coding (NR_046552, exon 1 of 3)	non-coding (NR_046552, exon 1 of 3)	127	NR_046552	100874255	Hs.741501	NR_046552		RNASEH2B-AS1	-	RNASEH2B antisense RNA 1	ncRNA	0.046099	0.614841	
chunk0153_136_1	chr5	69007629	69008184	+	0	NA	intron (NR_130778, intron 1 of 3)	intron (NR_130778, intron 1 of 3)	22021	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.014414	0.438849	
chunk0087_326_1	chr18	39949138	39949388	+	0	NA	Intergenic	MIRc|SINE|MIR	-117023	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.362550	
chunk0110_293_1	chr20	17875282	17875564	+	0	NA	Intergenic	Intergenic	87523	NR_003045	692086	Hs.680747	NR_003045	ENSG00000212232	SNORD17	HBI-43	small nucleolar RNA, C/D box 17	snoRNA	0.024823	0.568905	
chunk0180_236_1	chr7	67470154	67470908	+	0	NA	Intergenic	Intergenic	134555	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.013263	0.496689	369(TAAAACAGCATGTTCC,-,0.00),370(AAAACAGCATGTTCCT,+,0.00)
chunk0133_64_1	chr3	166845161	166845737	+	0	NA	Intergenic	L1PA10|LINE|L1	534834	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.000000	0.374350	
chunk0080_76_1	chr17	22139344	22139694	+	0	NA	Intergenic	Intergenic	-159245	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.000000	0.373219	
chunk0005_51_1	chr1	54987217	54988006	+	0	NA	intron (NM_182532, intron 2 of 2)	intron (NM_182532, intron 2 of 2)	6947	NM_182532	199964	Hs.663950	NM_182532	ENSG00000143001	TMEM61	-	transmembrane protein 61	protein-coding	0.007605	0.458228	397(AAGTACAGAGTGTGCC,-,0.00),398(AGTACAGAGTGTGCCT,+,0.00)
chunk0070_71_1	chr15	69910183	69910619	+	0	NA	Intergenic	Intergenic	75167	NR_026764	414926	Hs.569502	NR_026764	ENSG00000245750	LINC00593	C15orf50	long intergenic non-protein coding RNA 593	ncRNA	0.004587	0.466819	204(AGGAACAGAGAGATCT,-,0.00),205(GGAACAGAGAGATCTG,+,0.00)
chunk0109_281_1	chr20	8126083	8126531	+	0	NA	Intergenic	Intergenic	-5958	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.004464	0.380846	
chunk0085_67_1	chr18	1347776	1347975	+	0	NA	intron (NR_023926, intron 2 of 5)	L1ME4b|LINE|L1	11754	NR_023927	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.005025	0.250000	
chunk0063_307_1	chr14	84803099	84803726	+	0	NA	Intergenic	MER6|DNA|TcMar-Tigger	-590467	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.011164	0.375796	
chunk0074_401_1	chr16	35450744	35451004	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	29722	NR_026980	146481	Hs.316564	NR_026980		FRG2DP	-	FSHD region gene 2 family member D, pseudogene	pseudo	0.000000	0.505747	
chunk0118_76_1	chr22	28822847	28823124	+	0	NA	Intergenic	Intergenic	-22413	NM_005080	7494	Hs.437638	NM_005080	ENSG00000100219	XBP1	TREB-5|TREB5|XBP-1|XBP2	X-box binding protein 1	protein-coding	0.003610	0.406475	
chunk0018_236_1	chr1	219900193	219900730	+	0	NA	Intergenic	Intergenic	28190	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.003724	0.436803	
chunk0007_271_1	chr1	83545693	83545892	+	0	NA	Intergenic	Intergenic	314754	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.010050	0.470000	
chunk0046_290_1	chr12	62044801	62045463	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	147707	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.007553	0.386124	
chunk0017_348_1	chr1	211808425	211808956	+	0	NA	intron (NM_014873, intron 2 of 7)	L1MD|LINE|L1	22082	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.007533	0.379699	
chunk0034_379_1	chr11	36425569	36425911	+	0	NA	intron (NM_001160167, intron 4 of 8)	intron (NM_001160167, intron 4 of 8)	24743	NM_001160169	79899	Hs.19987	NM_024841	ENSG00000135362	PRR5L	PROTOR2	proline rich 5 like	protein-coding	0.008772	0.437318	
chunk0194_181_1	chr8	85177560	85177862	+	0	NA	intron (NM_001083588, intron 1 of 7)	CpG	327	NM_001951	1875	Hs.445758	NM_001951	ENSG00000133740	E2F5	E2F-5	E2F transcription factor 5	protein-coding	0.105960	0.709571	
chunk0049_235_1	chr12	93490014	93490572	+	0	NA	intron (NR_038160, intron 6 of 6)	intron (NR_038160, intron 6 of 6)	22803	NR_038160	28977	Hs.199579	NM_014050	ENSG00000198015	MRPL42	HSPC204|L31MT|L42MT|MRP-L31|MRP-L42|MRP-S32|MRPL31|MRPS32|PTD007|RPML31|S32MT	mitochondrial ribosomal protein L42	protein-coding	0.005376	0.323792	
chunk0158_179_1	chr5	127827238	127827965	+	0	NA	Intergenic	Intergenic	174586	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.011004	0.398352	381(AAGAACGCCTTGTGCT,-,0.00),382(AGAACGCCTTGTGCTG,+,0.00)
chunk0014_156_1	chr1	178198691	178198922	+	0	NA	intron (NM_170692, intron 1 of 17)	L1P2|LINE|L1	-104813	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.004329	0.538793	
chunk0071_53_1	chr15	80105262	80105674	+	0	NA	intron (NM_001242919, intron 1 of 5)	MamRTE1|LINE|RTE-BovB	7052	NM_001242919	54469	Hs.596679	NM_019006	ENSG00000086666	ZFAND6	AWP1|ZA20D3|ZFAND5B	zinc finger AN1-type containing 6	protein-coding	0.007282	0.387409	
chunk0108_403_1	chr2	237468040	237468618	+	0	NA	Intergenic	L1MD2|LINE|L1	-18081	NM_001281474	79083	Hs.102406	NM_024101	ENSG00000115648	MLPH	SLAC2-A	melanophilin	protein-coding	0.012111	0.350604	
chunk0031_149_1	chr10	125117445	125117788	+	0	NA	intron (NM_001083914, intron 1 of 10)	intron (NM_001083914, intron 1 of 10)	41199	NM_001290215	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.020408	0.456395	210(ATGAACAGGGTGTACC,-,0.00),211(TGAACAGGGTGTACCC,+,0.00)
chunk0162_71_1	chr6	1768052	1768339	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	157749	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.003484	0.302083	
chunk0088_4_1	chr18	43074146	43074545	+	0	NA	intron (NM_001272077, intron 1 of 5)	L1ME3G|LINE|L1	41347	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.007519	0.317500	
chunk0108_177_1	chr2	232148341	232148822	+	0	NA	intron (NR_046476, intron 8 of 20)	intron (NR_046476, intron 8 of 20)	-24072	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.006237	0.317427	
chunk0135_306_1	chr3	189944160	189944845	+	0	NA	Intergenic	Intergenic	114580	NR_030642	100126340		NR_030642	ENSG00000216058	MIR944	MIRN944|hsa-mir-944|mir-944	microRNA 944	ncRNA	0.018978	0.460641	
chunk0088_293_1	chr18	49731472	49731821	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	82235	NM_006111	10449	Hs.200136	NM_006111	ENSG00000167315	ACAA2	DSAEC	acetyl-CoA acyltransferase 2	protein-coding	0.011461	0.454286	
chunk0004_75_1	chr1	43550196	43550578	+	0	NA	intron (NM_130440, intron 3 of 32)	intron (NM_130440, intron 3 of 32)	19511	NM_002840	5792	Hs.272062	NM_002840	ENSG00000142949	PTPRF	BNAH2|LAR	protein tyrosine phosphatase receptor type F	protein-coding	0.052356	0.673629	
chunk0191_239_1	chr8	52993075	52993572	+	0	NA	Intergenic	Intergenic	53415	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.002012	0.321285	
chunk0048_169_1	chr12	80838149	80838683	+	0	NA	intron (NM_004664, intron 4 of 5)	intron (NM_004664, intron 4 of 5)	-5787	NR_030348	693202		NR_030348	ENSG00000207763	MIR617	MIRN617|hsa-mir-617	microRNA 617	ncRNA	0.007491	0.409346	
chunk0184_374_1	chr7	121344047	121344246	+	0	NA	Intergenic	Intergenic	15110	NM_057168	51384	Hs.272375	NM_016087	ENSG00000002745	WNT16	-	Wnt family member 16	protein-coding	0.005025	0.330000	72(GTTACAGGATGTTCTT,+,0.00)
chunk0163_343_1	chr6	15435410	15435707	+	0	NA	intron (NM_001267040, intron 3 of 17)	intron (NM_001267040, intron 3 of 17)	186703	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.000000	0.432886	
chunk0051_202_1	chr12	116405145	116405967	+	0	NA	Intergenic	Tigger6b|DNA|TcMar-Tigger	22762	NR_039683	100616309		NR_039683	ENSG00000264037	MIR4472-2	-	microRNA 4472-2	ncRNA	0.006083	0.426488	316(AGAACAAGATGCTCCC,+,0.00)
chunk0089_107_1	chr18	58514364	58514831	+	0	NA	intron (NM_052947, intron 10 of 12)	intron (NM_052947, intron 10 of 12)	-63445	NR_039899	100616357		NR_039899	ENSG00000207778	MIR3591	-	microRNA 3591	ncRNA	0.002141	0.335470	
chunk0077_394_1	chr16	84823196	84823763	+	0	NA	intron (NM_031476, intron 1 of 14)	intron (NM_031476, intron 1 of 14)	3498	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.012346	0.475352	487(GAGGACATCATGGTCC,-,0.00)
chunk0063_86_1	chr14	77946095	77946369	+	0	NA	Intergenic	Intergenic	146149	NM_020421	57143	Hs.413208	NM_020421	ENSG00000063761	ADCK1	-	aarF domain containing kinase 1	protein-coding	0.000000	0.494545	
chunk0010_152_1	chr1	115349564	115350193	+	0	NA	Intergenic	Intergenic	-11642	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.006359	0.380952	
chunk0200_223_1	chr9	20630756	20631116	+	0	NA	Intergenic	Intergenic	-8393	NM_004529	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.002778	0.398892	138(ATGAACAGATTGCTCT,-,0.00),139(TGAACAGATTGCTCTT,+,0.00)
chunk0181_144_1	chr7	81491418	81492064	+	0	NA	Intergenic	Intergenic	134475	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.009288	0.357032	
chunk0102_282_1	chr2	150328042	150328535	+	0	NA	Intergenic	Intergenic	159407	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.010142	0.423077	261(AAGTACAGGCTGTGCT,-,0.00),262(AGTACAGGCTGTGCTG,+,0.00)
chunk0043_137_1	chr12	16030723	16030976	+	0	NA	intron (NM_015954, intron 6 of 8)	L2a|LINE|L2	119677	NM_001300779	51071	Hs.39429	NM_015954	ENSG00000023697	DERA	CGI-26|DEOC	deoxyribose-phosphate aldolase	protein-coding	0.000000	0.429134	52(AGGAACTTTTTGTTCA,-,0.00),53(GGAACTTTTTGTTCAT,+,0.00)
chunk0184_232_1	chr7	117562780	117563120	+	0	NA	intron (NM_000492, intron 11 of 26)	intron (NM_000492, intron 11 of 26)	82987	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.002941	0.422287	
chunk0171_301_1	chr6	128642281	128642769	+	0	NA	Intergenic	Intergenic	-121851	NM_001291981	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.004098	0.361963	
chunk0173_313_1	chr6	148560298	148560497	+	0	NA	Intergenic	Intergenic	-186738	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.020101	0.495000	
chunk0183_363_1	chr7	108997727	108998228	+	0	NA	Intergenic	Intergenic	-113390	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.007984	0.328685	
chunk0044_380_1	chr12	39892693	39893038	+	0	NA	intron (NM_052885, intron 4 of 9)	intron (NM_052885, intron 4 of 9)	212994	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.000000	0.254335	
chunk0135_87_1	chr3	186381994	186382683	+	0	NA	Intergenic	MIRb|SINE|MIR	-20104	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.007257	0.405797	
chunk0055_96_1	chr13	55378318	55378567	+	0	NA	Intergenic	Intergenic	203988	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.008032	0.252000	
chunk0133_455_1	chr3	175223978	175224498	+	0	NA	intron (NM_207015, intron 2 of 13)	LTR46|LTR|ERV1	46858	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.011538	0.470250	
chunk0074_8_1	chr16	19676643	19676888	+	0	NA	intron (NM_001300743, intron 24 of 27)	intron (NM_001300743, intron 24 of 27)	-39691	NR_130967	124152	Hs.460217	NM_153208	ENSG00000174628	IQCK	-	IQ motif containing K	protein-coding	0.012245	0.410569	
chunk0058_449_1	chr13	113868733	113869079	+	0	NA	Intergenic	L1ME1|LINE|L1	4729	NR_044993	100506394	Hs.132168	NR_044993	ENSG00000272695	GAS6-DT	GAS6-AS2	GAS6 divergent transcript	ncRNA	0.005780	0.337176	
chunk0161_164_1	chr5	169142179	169142978	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	121116	NR_030311	693170		NR_030311	ENSG00000207619	MIR585	MIRN585|hsa-mir-585|mir-585	microRNA 585	ncRNA	0.005006	0.456250	
chunk0125_53_1	chr3	63975695	63976219	+	0	NA	intron (NM_001128149, intron 1 of 8)	intron (NM_001128149, intron 1 of 8)	8213	NM_001128149	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.005725	0.472381	290(AGGGACAGAGTGTGCT,-,0.00),291(GGGACAGAGTGTGCTT,+,0.00)
chunk0145_36_1	chr4	143907599	143907959	+	0	NA	Intergenic	Intergenic	-2216	NM_002102	2996	Hs.654368	NM_002102	ENSG00000197465	GYPE	GPE|GYPA|MNS|MiIX	glycophorin E (MNS blood group)	protein-coding	0.002778	0.445983	221(GTGAACAATCTGTTCC,-,0.00),222(TGAACAATCTGTTCCT,+,0.00)
chunk0171_444_1	chr6	131825689	131826205	+	0	NA	intron (NM_006208, intron 1 of 24)	intron (NM_006208, intron 1 of 24)	17931	NM_006208	5167	Hs.527295	NM_006208	ENSG00000197594	ENPP1	ARHR2|COLED|M6S1|NPP1|NPPS|PC-1|PCA1|PDNP1	ectonucleotide pyrophosphatase/phosphodiesterase 1	protein-coding	0.003876	0.317215	
chunk0116_169_1	chr21	36768667	36769301	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	69851	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.018927	0.497638	
chunk0148_422_1	chr5	15043110	15043420	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-171487	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.003226	0.372990	
chunk0092_93_1	chr19	22825855	22826054	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-41783	NM_001080409	7652	Hs.737077	NM_001080409	ENSG00000213973	ZNF99	C19orf9|F8281	zinc finger protein 99	protein-coding	0.005025	0.470000	
chunk0162_335_1	chr6	6832490	6832787	+	0	NA	Intergenic	Intergenic	-209812	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.010101	0.553691	176(CAGGACACTGAGTCCT,-,0.00),177(AGGACACTGAGTCCTC,+,0.00)
chunk0033_298_1	chr11	19829120	19829581	+	0	NA	intron (NM_001244963, intron 1 of 39)	intron (NM_001244963, intron 1 of 39)	-69267	NR_039843	100616426		NR_039843	ENSG00000264309	MIR4694	-	microRNA 4694	ncRNA	0.010846	0.437229	
chunk0056_237_1	chr13	89046362	89046966	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-188627	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.008278	0.305785	
chunk0208_342_1	chrX	25081061	25081426	+	0	NA	Intergenic	Intergenic	-65295	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.013699	0.396175	212(GGGAACTGTATGTGCA,-,0.00),213(GGAACTGTATGTGCAG,+,0.00)
chunk0197_22_1	chr8	117906810	117907023	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	204903	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.004695	0.439252	
chunk0138_431_1	chr4	45294491	45294918	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-568070	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.002342	0.383178	
chunk0175_64_1	chr7	1993211	1993680	+	0	NA	intron (NM_003550, intron 14 of 18)	intron (NM_003550, intron 14 of 18)	-52895	NM_001304525	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.012793	0.489362	
chunk0201_354_1	chr9	68437837	68438039	+	0	NA	intron (NM_021965, intron 6 of 10)	MER102c|DNA|hAT-Charlie	-80072	NR_121192	572558	Hs.552819	NR_015423	ENSG00000224958	PGM5-AS1	FAM233A	PGM5 antisense RNA 1	ncRNA	0.009901	0.492611	
chunk0097_166_1	chr2	49306669	49307437	+	0	NA	Intergenic	L2c|LINE|L2	-152526	NM_181446	2492	Hs.1428	NM_000145	ENSG00000170820	FSHR	FSHR1|FSHRO|LGR1|ODG1	follicle stimulating hormone receptor	protein-coding	0.005208	0.368010	405(AAGGACAGTTTGTACT,-,0.00),406(AGGACAGTTTGTACTC,+,0.00)
chunk0161_414_1	chr5	177837528	177837739	+	0	NA	Intergenic	Intergenic	-37628	NR_003615	728554	Hs.535769	NR_003615	ENSG00000170089	LOC728554	-	THO complex 3 pseudogene	pseudo	0.009479	0.542453	
chunk0014_398_1	chr1	182893498	182893726	+	0	NA	Intergenic	MER50|LTR|ERV1	54308	NM_001357	1660	Hs.191518	NM_001357	ENSG00000135829	DHX9	DDX9|LKP|NDH2|NDHII|RHA	DExH-box helicase 9	protein-coding	0.004386	0.493450	
chunk0021_455_1	chr1	248906042	248906504	+	0	NA	promoter-TSS (NM_170725)	promoter-TSS (NM_170725)	30	NM_001017434	267002	Hs.602037	NM_170725	ENSG00000185220	PGBD2	-	piggyBac transposable element derived 2	protein-coding	0.119048	0.688985	
chunk0104_287_1	chr2	178317662	178318243	+	0	NA	intron (NM_001201482, intron 3 of 23)	intron (NM_001201482, intron 3 of 23)	-2292	NM_145739	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.006885	0.350515	
chunk0141_348_1	chr4	87559294	87559571	+	0	NA	Intergenic	Intergenic	-29929	NM_001291976	8404	Hs.62886	NM_004684	ENSG00000152583	SPARCL1	MAST 9|MAST9|PIG33|SC1	SPARC like 1	protein-coding	0.003610	0.413669	
chunk0177_183_1	chr7	23430988	23431192	+	0	NA	intron (NM_006547, intron 2 of 14)	intron (NM_006547, intron 2 of 14)	39286	NM_006547	10643	Hs.700696	NM_006547	ENSG00000136231	IGF2BP3	CT98|IMP-3|IMP3|KOC|KOC1|VICKZ3	insulin like growth factor 2 mRNA binding protein 3	protein-coding	0.014706	0.360976	96(AGGAACAAAATGTACA,-,0.00),97(GGAACAAAATGTACAT,+,0.00)
chunk0120_2_1	chr3	356946	357278	+	0	NA	intron (NM_006614, intron 11 of 27)	MIRc|SINE|MIR	28683	NR_110739	101927193	Hs.677744	NR_110739	ENSG00000234661	CHL1-AS1	-	CHL1 antisense RNA 1	ncRNA	0.012048	0.459459	
chunk0208_220_1	chrX	18722285	18722894	+	0	NA	intron (NM_152224, intron 4 of 18)	intron (NM_152224, intron 4 of 18)	-29902	NR_046642	100874004		NR_046642		PPEF1-AS1	-	PPEF1 antisense RNA 1	ncRNA	0.008210	0.401639	
chunk0154_289_1	chr5	82753999	82754808	+	0	NA	Intergenic	Intergenic	-85752	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.003708	0.324691	
chunk0173_306_1	chr6	148497260	148497694	+	0	NA	intron (NM_015278, intron 8 of 19)	MIR|SINE|MIR	154884	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.004608	0.455172	
chunk0013_360_1	chr1	172359712	172359982	+	0	NA	intron (NM_015569, intron 17 of 20)	intron (NM_015569, intron 17 of 20)	-60841	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.011111	0.380074	
chunk0165_61_1	chr6	30821976	30823090	+	0	NA	intron (NR_130726, intron 1 of 1).3	intron (NR_130726, intron 1 of 1).3	8126	NR_130726	401247		NR_130726	ENSG00000214894	LINC00243	C6orf214|NCRNA00243	long intergenic non-protein coding RNA 243	ncRNA	0.007181	0.412556	968(GGGAACACTCAGTGCC,-,0.00),969(GGAACACTCAGTGCCT,+,0.00)
chunk0177_225_1	chr7	24311408	24311653	+	0	NA	Intergenic	LTR33|LTR|ERVL	27342	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.004082	0.500000	
chunk0074_344_1	chr16	31557227	31557511	+	0	NA	Intergenic	L1PA15-16|LINE|L1	12155	NR_027011	440359	Hs.650902	NR_027011		YBX3P1	CSDAP1	Y-box binding protein 3 pseudogene 1	pseudo	0.017606	0.585965	
chunk0193_123_1	chr8	74250644	74251318	+	0	NA	intron (NM_020647, intron 3 of 5)	MamRep605|LTR?|LTR?	70346	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.004451	0.441481	
chunk0026_340_1	chr10	68516288	68516760	+	0	NA	intron (NM_152707, intron 2 of 8)	LTR10C|LTR|ERV1	10999	NM_152707	8034	Hs.180408	NM_152707	ENSG00000122912	SLC25A16	D10S105E|GDA|GDC|HGT.1|ML7|hML7	solute carrier family 25 member 16	protein-coding	0.002119	0.359408	
chunk0205_345_1	chr9	113339995	113340465	+	0	NA	5' UTR (NM_145241, exon 1 of 11)	5' UTR (NM_145241, exon 1 of 11)	110	NM_145241	114987	Hs.133331	NM_145241	ENSG00000148225	WDR31	-	WD repeat domain 31	protein-coding	0.082979	0.653928	
chunk0179_443_1	chr7	52450952	52451188	+	0	NA	Intergenic	Intergenic	-584586	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.004237	0.396624	
chunk0053_190_1	chr13	31562122	31562650	+	0	NA	Intergenic	L1PA7|LINE|L1	-177156	NM_130806	122042	Hs.680763	NM_130806	ENSG00000133105	RXFP2	GPR106|GREAT|INSL3R|LGR8|LGR8.1|RXFPR2	relaxin family peptide receptor 2	protein-coding	0.003788	0.355388	
chunk0080_290_1	chr17	31409495	31409865	+	0	NA	intron (NM_032932, intron 1 of 14)	intron (NM_032932, intron 1 of 14)	18056	NM_032932	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.008108	0.539084	
chunk0021_64_1	chr10	1320657	1321366	+	0	NA	intron (NM_018702, intron 3 of 9)	intron (NM_018702, intron 3 of 9)	161243	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.005642	0.418310	
chunk0105_108_1	chr2	184730536	184731021	+	0	NA	intron (NM_194250, intron 1 of 3)	L1MC2|LINE|L1	132412	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.002062	0.378601	
chunk0166_18_1	chr6	41728222	41728944	+	0	NA	intron (NM_001167827, intron 1 of 8)	intron (NM_001167827, intron 1 of 8)	5818	NM_001271945	7942	Hs.485360	NM_007162	ENSG00000112561	TFEB	ALPHATFEB|BHLHE35|TCFEB	transcription factor EB	protein-coding	0.019391	0.605809	377(AAGGACAGGCTGTGAC,-,0.00),378(AGGACAGGCTGTGACT,+,0.00)
chunk0042_48_1	chr12	1751094	1751387	+	0	NA	intron (NM_024551, intron 1 of 7)	intron (NM_024551, intron 1 of 7)	60159	NM_024551	79602	Hs.371642	NM_024551	ENSG00000006831	ADIPOR2	ACDCR2|PAQR2	adiponectin receptor 2	protein-coding	0.000000	0.309524	
chunk0138_368_1	chr4	42306492	42306872	+	0	NA	Intergenic	Intergenic	-91157	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.002632	0.488189	85(AGGGACACTGTGTTTT,-,0.00),86(GGGACACTGTGTTTTG,+,0.00)
chunk0151_131_1	chr5	44002567	44002950	+	0	NA	Intergenic	Intergenic	385924	NM_004465	2255	Hs.248049	NM_004465	ENSG00000070193	FGF10	-	fibroblast growth factor 10	protein-coding	0.000000	0.359375	
chunk0071_174_1	chr15	83295294	83295901	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-10881	NM_001717	646	Hs.459153	NM_001717	ENSG00000169594	BNC1	BNC|BSN1|HsT19447	basonuclin 1	protein-coding	0.009885	0.442434	370(AGGTCCAGGCTGTCCT,-,0.00),371(GGTCCAGGCTGTCCTG,+,0.00)
chunk0100_400_1	chr2	119303996	119304601	+	0	NA	intron (NM_001017927, intron 6 of 6)	intron (NM_001017927, intron 6 of 6)	-55227	NR_046721	100874111	Hs.704682	NR_046721	ENSG00000229867	STEAP3-AS1	-	STEAP3 antisense RNA 1	ncRNA	0.003306	0.366337	221(AAAGACACCCTGTTCT,-,0.00),222(AAGACACCCTGTTCTT,+,0.00)
chunk0145_425_1	chr4	153001944	153002700	+	0	NA	Intergenic	Intergenic	59339	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.003968	0.466314	
chunk0146_236_1	chr4	162238927	162239188	+	0	NA	Intergenic	L1PA8|LINE|L1	-75023	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.000000	0.389313	
chunk0108_416_1	chr2	237590248	237590529	+	0	NA	intron (NR_033308, intron 1 of 4)	(AC)n|Simple_repeat|Simple_repeat	738	NM_022449	64284	Hs.44278	NM_022449	ENSG00000124839	RAB17	-	RAB17, member RAS oncogene family	protein-coding	0.014235	0.507092	
chunk0046_76_1	chr12	56079699	56080290	+	0	NA	promoter-TSS (NM_001982)	promoter-TSS (NM_001982)	-31	NM_001982	2065	Hs.118681	NM_001982	ENSG00000065361	ERBB3	ErbB-3|FERLK|HER3|LCCS2|MDA-BF-1|c-erbB-3|c-erbB3|erbB3-S|p180-ErbB3|p45-sErbB3|p85-sErbB3	erb-b2 receptor tyrosine kinase 3	protein-coding	0.059222	0.614865	
chunk0082_399_1	chr17	60815815	60816184	+	0	NA	intron (NM_017679, intron 7 of 23)	intron (NM_017679, intron 7 of 23)	138188	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.010840	0.375676	
chunk0118_290_1	chr22	34037276	34037660	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-117040	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.005208	0.420779	
chunk0175_455_1	chr6	170276740	170276994	+	0	NA	promoter-TSS (NR_126021)	promoter-TSS (NR_126021)	-105	NR_126021	285804	Hs.651959	NR_126021	ENSG00000271820	LOC285804	-	uncharacterized LOC285804	ncRNA	0.051181	0.541176	
chunk0064_314_1	chr14	95886034	95886378	+	0	NA	intron (NR_038861, intron 1 of 1)	intron (NR_038861, intron 1 of 1)	9434	NR_038861	100507043	Hs.455955	NR_038861	ENSG00000250366	TUNAR	HI-LNC78|LINC00617|TUNA	TCL1 upstream neural differentiation-associated RNA	ncRNA	0.014535	0.556522	
chunk0106_397_1	chr2	207776945	207777150	+	0	NA	Intergenic	Intergenic	-7628	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.009756	0.500000	
chunk0003_258_1	chr1	36239541	36240505	+	0	NA	intron (NM_005119, intron 1 of 11)	intron (NM_005119, intron 1 of 11)	15607	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.004149	0.402073	
chunk0169_413_1	chr6	108587482	108587938	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	26844	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.010965	0.400438	
chunk0102_354_1	chr2	152486122	152486321	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	150984	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.015075	0.405000	
chunk0016_288_1	chr1	200951059	200951370	+	0	NA	Intergenic	Intergenic	56393	NM_001142569	55765	Hs.518997	NM_018265	ENSG00000163362	INAVA	C1orf106	innate immunity activator	protein-coding	0.003215	0.416667	
chunk0124_355_1	chr3	58646490	58647177	+	0	NA	intron (NM_138805, intron 4 of 9)	intron (NM_138805, intron 4 of 9)	-19223	NM_001282714	11170	Hs.506357	NM_007177	ENSG00000168309	FAM107A	DRR1|TU3A	family with sequence similarity 107 member A	protein-coding	0.004367	0.539244	
chunk0078_1_1	chr17	142288	142588	+	0	NA	Intergenic	Intergenic	4867	NM_001097610	653486	Hs.127059	NM_001097610	ENSG00000268320	SCGB1C2	SCGB1C1	secretoglobin family 1C member 2	protein-coding	0.043333	0.544850	
chunk0044_448_1	chr12	42574791	42575462	+	0	NA	intron (NM_153026, intron 1 of 7)	intron (NM_153026, intron 1 of 7)	14644	NM_153026	144165	Hs.524348	NM_153026	ENSG00000139174	PRICKLE1	EPM1B|RILP	prickle planar cell polarity protein 1	protein-coding	0.004471	0.349702	
chunk0209_353_1	chrX	53086382	53086978	+	0	NA	intron (NM_022117, intron 6 of 6)	intron (NM_022117, intron 6 of 6)	4320	NM_022117	64061	Hs.136164	NM_022117	ENSG00000184205	TSPYL2	CDA1|CINAP|CTCL|DENTT|HRIHFB2216|NP79|SE204|TSPX	TSPY like 2	protein-coding	0.011745	0.462312	256(CAGCACAGTCTGTACC,-,0.00),257(AGCACAGTCTGTACCC,+,0.00),324(GTGAACAGTGTGCTCT,-,0.00),325(TGAACAGTGTGCTCTC,+,0.00)
chunk0142_105_1	chr4	94412922	94413446	+	0	NA	Intergenic	Intergenic	-38673	NM_001256425	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.005725	0.354286	
chunk0205_276_1	chr9	111525605	111525804	+	0	NA	intron (NM_133464, intron 1 of 5)	intron (NM_133464, intron 1 of 5)	545	NM_001007169	158399	Hs.584864	NM_133464	ENSG00000173258	ZNF483	ZKSCAN16|ZSCAN48	zinc finger protein 483	protein-coding	0.050251	0.560000	
chunk0123_149_1	chr3	42935076	42935275	+	0	NA	non-coding (NR_122033, exon 2 of 2)	non-coding (NR_122033, exon 2 of 2)	-1167	NM_001205272	100506243	Hs.720172	NM_015673	ENSG00000240747	KRBOX1	-	KRAB box domain containing 1	protein-coding	0.005025	0.385000	
chunk0197_447_1	chr8	127801546	127801860	+	0	NA	intron (NR_003367, intron 1 of 8)	intron (NR_003367, intron 1 of 8)	5741	NR_031609	100302185		NR_031609	ENSG00000283710	MIR1204	hsa-mir-1204	microRNA 1204	ncRNA	0.006369	0.463492	
chunk0084_101_1	chr17	75679829	75680159	+	0	NA	intron (NR_126036, intron 3 of 9)	intron (NR_126036, intron 3 of 9)	-12805	NM_004259	9400	Hs.632229	NM_004259	ENSG00000108469	RECQL5	RECQ5	RecQ like helicase 5	protein-coding	0.021212	0.534743	
chunk0173_28_1	chr6	141995144	141995394	+	0	NA	Intergenic	L1M2|LINE|L1	93530	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.008000	0.593625	
chunk0102_428_1	chr2	157283334	157284020	+	0	NA	intron (NM_014568, intron 1 of 9)	intron (NM_014568, intron 1 of 9)	25849	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.002915	0.420670	
chunk0149_73_1	chr5	17172796	17173214	+	0	NA	intron (NR_027253, intron 1 of 2)	L1ME1|LINE|L1	-43818	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.007177	0.360382	
chunk0168_58_1	chr6	78900458	78900861	+	0	NA	3' UTR (NM_001010844, exon 4 of 4)	3' UTR (NM_001010844, exon 4 of 4)	33115	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.002481	0.371287	
chunk0049_266_1	chr12	93758934	93759330	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-21309	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.002525	0.337531	
chunk0049_277_1	chr12	93823791	93824333	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-86239	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.011070	0.418048	185(GAGAACACAGTGACCC,-,0.00),186(AGAACACAGTGACCCA,+,0.00)
chunk0207_206_1	chr9	131349610	131350030	+	0	NA	Intergenic	Intergenic	60126	NM_032728	84814	Hs.134292	NM_032728	ENSG00000160539	PLPP7	C9orf67|NET39|PPAPDC3	phospholipid phosphatase 7 (inactive)	protein-coding	0.019048	0.600950	
chunk0023_424_1	chr10	31596440	31596639	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	275404	NM_001174094	6935	Hs.124503	NM_030751	ENSG00000148516	ZEB1	AREB6|BZP|DELTAEF1|FECD6|NIL2A|PPCD3|TCF8|ZFHEP|ZFHX1A	zinc finger E-box binding homeobox 1	protein-coding	0.000000	0.390000	94(TAGGACATGGAGTTCC,-,0.00),95(AGGACATGGAGTTCCA,+,0.00)
chunk0106_319_1	chr2	205498568	205498798	+	0	NA	intron (NM_001302769, intron 20 of 22)	L2c|LINE|L2	-183817	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.004348	0.467532	
chunk0175_191_1	chr7	5495383	5496330	+	0	NA	promoter-TSS (NR_030318)	promoter-TSS (NR_030318)	61	NR_030318	693174		NR_030318	ENSG00000207973	MIR589	MIRN589|hsa-mir-589|mir-589	microRNA 589	ncRNA	0.040127	0.614979	471(CTGAACAGGCAGTACC,-,0.00),472(TGAACAGGCAGTACCC,+,0.00)
chunk0072_376_1	chr15	100060312	100060977	+	0	NA	intron (NM_139057, intron 15 of 21)	intron (NM_139057, intron 15 of 21)	-253717	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.015038	0.519520	
chunk0179_15_1	chr7	42597398	42597604	+	0	NA	Intergenic	Intergenic	108946	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.004854	0.342995	
chunk0104_255_1	chr2	177616191	177616559	+	0	NA	3' UTR (NM_152275, exon 1 of 1)	3' UTR (NM_152275, exon 1 of 1)	2591	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.008152	0.409214	
chunk0122_409_1	chr3	38298219	38298435	+	0	NA	Intergenic	L1MC4|LINE|L1	-7627	NM_004803	9389	Hs.165559	NM_004803	ENSG00000144671	SLC22A14	OCTL2|OCTL4|ORCTL4	solute carrier family 22 member 14	protein-coding	0.004630	0.396313	119(GAGTACTAGGTGTGCT,-,0.00),120(AGTACTAGGTGTGCTC,+,0.00)
chunk0160_245_1	chr5	156584599	156585088	+	0	NA	intron (NM_000337, intron 4 of 8)	Tigger19b|DNA|TcMar-Tigger	258086	NM_000337	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.000000	0.377551	
chunk0143_445_1	chr4	124133682	124134275	+	0	NA	Intergenic	LTR40a|LTR|ERVL	359714	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.003373	0.373737	
chunk0006_322_1	chr1	71642668	71642915	+	0	NA	intron (NM_173808, intron 4 of 6)	intron (NM_173808, intron 4 of 6)	194221	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.000000	0.334677	
chunk0126_297_1	chr3	80662214	80662975	+	0	NA	Intergenic	Intergenic	-331274	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.002628	0.300525	313(AAGAACATTAAGTGCT,-,0.00),314(AGAACATTAAGTGCTT,+,0.00)
chunk0108_135_1	chr2	230423881	230424080	+	0	NA	intron (NM_001080391, intron 2 of 28)	L1M5|LINE|L1	7224	NM_001206704	6672	Hs.369056	NM_003113	ENSG00000067066	SP100	lysp100b	SP100 nuclear antigen	protein-coding	0.000000	0.415000	
chunk0062_215_1	chr14	70933330	70933850	+	0	NA	intron (NM_001308160, intron 1 of 33)	MER58B|DNA|hAT-Charlie	26185	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.000000	0.314779	
chunk0160_367_1	chr5	161172065	161172804	+	0	NA	Intergenic	L1MC1|LINE|L1	-233808	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.005413	0.340541	
chunk0153_165_1	chr5	71089718	71089987	+	0	NA	intron (NR_026578, intron 1 of 4)	Tigger3b|DNA|TcMar-Tigger	3218	NR_026578	647859	Hs.671081	NR_026578		OCLNP1	-	OCLN pseudogene 1	pseudo	0.003717	0.337037	
chunk0183_70_1	chr7	104203019	104203353	+	0	NA	intron (NM_002553, intron 2 of 13)	L2c|LINE|L2	4861	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.008982	0.456716	
chunk0048_181_1	chr12	80936563	80936762	+	0	NA	promoter-TSS (NR_030349)	promoter-TSS (NR_030349)	-829	NR_030349	693203		NR_030349	ENSG00000208022	MIR618	MIRN618|hsa-mir-618|mir-618	microRNA 618	ncRNA	0.050251	0.635000	
chunk0111_75_1	chr20	23092246	23092735	+	0	NA	Intergenic	Intergenic	-6150	NM_012072	22918	Hs.97199	NM_012072	ENSG00000125810	CD93	C1QR1|C1qR(P)|C1qRP|CDw93|ECSM3|MXRA4|dJ737E23.1	CD93 molecule	protein-coding	0.008180	0.428571	
chunk0094_288_1	chr2	8306607	8307529	+	0	NA	intron (NR_034135, intron 2 of 8)	intron (NR_034135, intron 2 of 8)	21351	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.014100	0.418202	
chunk0050_433_1	chr12	110270261	110270586	+	0	NA	Intergenic	Intergenic	-10804	NM_170665	488	Hs.506759	NM_001681	ENSG00000174437	ATP2A2	ATP2B|DAR|DD|SERCA2	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2	protein-coding	0.009231	0.542945	165(GATACATGGTGTCCTC,+,0.00)
chunk0149_12_1	chr5	15886146	15886603	+	0	NA	intron (NM_012304, intron 2 of 3)	intron (NM_012304, intron 2 of 3)	-48808	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.002188	0.421397	
chunk0003_110_1	chr1	32290398	32290772	+	0	NA	Intergenic	Intergenic	-1522	NM_004964	3065	Hs.88556	NM_004964	ENSG00000116478	HDAC1	GON-10|HD1|KDAC1|RPD3|RPD3L1	histone deacetylase 1	protein-coding	0.002674	0.424000	
chunk0136_385_1	chr3	196787734	196788307	+	0	NA	intron (NM_002577, intron 2 of 14)	intron (NM_002577, intron 2 of 14)	48163	NM_002577	5062	Hs.518530	NM_002577	ENSG00000180370	PAK2	PAK65|PAKgamma	p21 (RAC1) activated kinase 2	protein-coding	0.012216	0.444251	
chunk0197_68_1	chr8	118863890	118864096	+	0	NA	Intergenic	L1MC4|LINE|L1	88151	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.014563	0.371981	
chunk0076_5_1	chr16	58492355	58492958	+	0	NA	intron (NM_020465, intron 2 of 15)	AluJo|SINE|Alu	-7487	NM_001242833	65009	Hs.322430	NM_020465	ENSG00000103034	NDRG4	BDM1|SMAP-8|SMAP8	NDRG family member 4	protein-coding	0.014925	0.549669	
chunk0161_142_1	chr5	168591949	168592411	+	0	NA	Intergenic	Intergenic	-12571	NM_024594	79646	Hs.388400	NM_024594	ENSG00000120137	PANK3	-	pantothenate kinase 3	protein-coding	0.002165	0.395248	
chunk0207_38_1	chrX	5928085	5928584	+	0	NA	intron (NM_181332, intron 3 of 5)	intron (NM_181332, intron 3 of 5)	298869	NM_001282146	57502	Hs.21107	NM_020742	ENSG00000146938	NLGN4X	ASPGX2|AUTSX2|HLNX|HNL4X|NLGN4	neuroligin 4 X-linked	protein-coding	0.008016	0.366000	223(TTGAACTCTGTGTTCT,-,0.00),224(TGAACTCTGTGTTCTT,+,0.00)
chunk0041_159_1	chr11	125967274	125967492	+	0	NA	intron (NM_016952, intron 18 of 19)	intron (NM_016952, intron 18 of 19)	63017	NM_013264	29118	Hs.420263	NM_013264	ENSG00000109832	DDX25	GRTH	DEAD-box helicase 25	protein-coding	0.000000	0.333333	
chunk0043_175_1	chr12	17206483	17206895	+	0	NA	Intergenic	Intergenic	217942	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.000000	0.314770	
chunk0105_132_1	chr2	185795815	185796034	+	0	NA	exon (NM_173651, exon 16 of 23)	exon (NM_173651, exon 16 of 23)	-55447	NR_110217	101927196	Hs.244783	NR_110214	ENSG00000226747	FSIP2-AS2	-	FSIP2 antisense RNA 2	ncRNA	0.004566	0.350000	
chunk0021_191_1	chr10	5744885	5745266	+	0	NA	intron (NM_017782, intron 14 of 20)	intron (NM_017782, intron 14 of 20)	60237	NM_017782	54906	Hs.610717	NM_017782	ENSG00000108021	TASOR2	C10orf18|FAM208B|bA318E3.2	transcription activation suppressor family member 2	protein-coding	0.010499	0.392670	
chunk0173_62_1	chr6	142406111	142406593	+	0	NA	intron (NM_020455, intron 15 of 25)	intron (NM_020455, intron 15 of 25)	104433	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.006224	0.341615	
chunk0203_46_1	chr9	83076409	83076851	+	0	NA	Intergenic	Intergenic	-13502	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.000000	0.325056	
chunk0102_9_1	chr2	141134530	141134878	+	0	NA	intron (NM_018557, intron 7 of 90)	intron (NM_018557, intron 7 of 90)	-548019	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.295129	
chunk0164_372_1	chr6	25863102	25863301	+	0	NA	intron (NM_001098486, intron 2 of 12)	intron (NM_001098486, intron 2 of 12)	11042	NM_001098486	10786	Hs.327179	NM_006632	ENSG00000124564	SLC17A3	GOUT4|NPT4|UAQTL4	solute carrier family 17 member 3	protein-coding	0.015075	0.360000	
chunk0095_107_1	chr2	15437050	15437680	+	0	NA	intron (NR_052013, intron 21 of 50)	intron (NR_052013, intron 21 of 50)	123983	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.006349	0.424723	
chunk0080_303_1	chr17	31654988	31655188	+	0	NA	Intergenic	Intergenic	79677	NR_029856	100126356		NR_029856	ENSG00000283978	MIR365B	MIR365-2|MIRN365-2|hsa-mir-365b|mir-365b	microRNA 365b	ncRNA	0.025000	0.626866	
chunk0124_387_1	chr3	59641466	59641976	+	0	NA	Intergenic	Intergenic	-591732	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.013725	0.487280	
chunk0057_286_1	chr13	106144006	106144750	+	0	NA	Intergenic	Intergenic	-232185	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.004032	0.362416	
chunk0131_196_1	chr3	148625065	148625814	+	0	NA	Intergenic	Intergenic	-72432	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.005340	0.345333	
chunk0159_345_1	chr5	144187900	144188373	+	0	NA	intron (NM_020768, intron 2 of 3)	AmnSINE1|SINE|5S-Deu-L2	17263	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.006342	0.386076	
chunk0015_262_1	chr1	188175720	188176141	+	0	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	732302	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.002375	0.303318	276(GGAACACAGTCTGCTT,+,0.00)
chunk0113_395_1	chr20	60078578	60078777	+	0	NA	Intergenic	Intergenic	-9009	NR_109918	729296	Hs.534781	NR_109916		LOC729296	-	uncharacterized LOC729296	ncRNA	0.010050	0.485000	
chunk0019_139_1	chr1	225705414	225705734	+	0	NA	Intergenic	Intergenic	-52431	NM_018212	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.018750	0.498442	152(AAGCACAGTCTGTGCC,-,0.00),153(AGCACAGTCTGTGCCA,+,0.00)
chunk0090_194_1	chr18	73057691	73057965	+	0	NA	Intergenic	Kanga2_a|DNA|TcMar-Tc2	-190253	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.007299	0.305455	
chunk0127_104_1	chr3	90019928	90020630	+	0	NA	Intergenic	L1MEh|LINE|L1	912755	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004274	0.293030	219(AAGGACAAAATGTCTT,-,0.00)
chunk0181_162_1	chr7	82511324	82512063	+	0	NA	Intergenic	L1MEg|LINE|L1	-67887	NM_001302890	781	Hs.282151	NM_000722	ENSG00000153956	CACNA2D1	CACNA2|CACNL2A|CCHL2A|LINC01112|lncRNA-N3	calcium voltage-gated channel auxiliary subunit alpha2delta 1	protein-coding	0.002706	0.297297	
chunk0118_303_1	chr22	35021144	35021662	+	0	NA	Intergenic	Intergenic	-44733	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.017375	0.526012	
chunk0159_276_1	chr5	142443877	142444101	+	0	NA	intron (NR_120664, intron 3 of 3)	MIR|SINE|MIR	118696	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.000000	0.364444	
chunk0159_267_1	chr5	142290964	142291397	+	0	NA	Intergenic	MIR|SINE|MIR	27142	NR_131221	100642175	Hs.684549	NR_131221		SPRY4-IT1	SPRIGHTLY	SPRY4 intronic transcript 1	ncRNA	0.002309	0.382488	
chunk0171_112_1	chr6	122428953	122429609	+	0	NA	intron (NM_004506, intron 11 of 12)	intron (NM_004506, intron 11 of 12)	29730	NM_001135564	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.001524	0.331811	323(CTGGACATTGAGTCCT,-,0.00),324(TGGACATTGAGTCCTT,+,0.00)
chunk0193_257_1	chr8	76963375	76963991	+	0	NA	Intergenic	Intergenic	3167	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004870	0.346840	
chunk0109_269_1	chr20	8053027	8053226	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-33297	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.015075	0.520000	
chunk0011_90_1	chr1	145747725	145747944	+	0	NA	intron (NM_014455, intron 8 of 8)	MER58A|DNA|hAT-Charlie	28388	NM_007053	11126	Hs.488237	NM_007053	ENSG00000117281	CD160	BY55|NK1|NK28	CD160 molecule	protein-coding	0.009132	0.368182	84(CAGGACACAATGACCT,-,0.00),85(AGGACACAATGACCTG,+,0.00)
chunk0155_353_1	chr5	97136294	97136784	+	0	NA	intron (NM_153234, intron 1 of 5)	L2c|LINE|L2	6277	NM_153234	167410	Hs.656702	NM_153234	ENSG00000145721	LIX1	C5orf11|Lft	limb and CNS expressed 1	protein-coding	0.012245	0.423625	
chunk0083_95_1	chr17	64450705	64450942	+	0	NA	intron (NM_001291317, intron 2 of 8)	L1ME3G|LINE|L1	1708	NM_001085423	284021	Hs.631749	NM_001085423	ENSG00000271605	MILR1	Allergin-1|C17orf60|MCA-32|MCA32	mast cell immunoglobulin like receptor 1	protein-coding	0.012658	0.453782	
chunk0202_156_1	chr9	73689989	73690222	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	538374	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.380342	
chunk0134_295_1	chr3	180165800	180166038	+	0	NA	Intergenic	L1PA17|LINE|L1	-128866	NM_001256750	51555	Hs.235331	NM_016559	ENSG00000114757	PEX5L	PEX5R|PEX5RP|PXR2|PXR2B|TRIP8b	peroxisomal biogenesis factor 5 like	protein-coding	0.000000	0.552301	
chunk0028_115_1	chr10	84479448	84479721	+	0	NA	intron (NM_001284240, intron 9 of 9)	L2a|LINE|L2	54402	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.000000	0.343066	
chunk0168_154_1	chr6	83226582	83227284	+	0	NA	intron (NM_002395, intron 11 of 13)	intron (NM_002395, intron 11 of 13)	-32997	NM_001199917	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.001425	0.317212	
chunk0007_448_1	chr1	86960622	86961202	+	0	NA	intron (NM_012262, intron 1 of 6)	L1MC2|LINE|L1	46260	NM_012262	9653	Hs.743280	NM_012262	ENSG00000153936	HS2ST1	dJ604K5.2	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.003448	0.361446	
chunk0092_427_1	chr19	38095527	38095743	+	0	NA	intron (NM_015073, intron 4 of 21)	L2a|LINE|L2	128615	NM_001135155	8193	Hs.631576	NM_004647	ENSG00000011332	DPF1	BAF45b|NEUD4|neuro-d4	double PHD fingers 1	protein-coding	0.004630	0.580645	
chunk0185_187_1	chr7	128229775	128230335	+	0	NA	Intergenic	Intergenic	-11223	NM_000230	3952	Hs.194236	NM_000230	ENSG00000174697	LEP	LEPD|OB|OBS	leptin	protein-coding	0.012500	0.488414	
chunk0203_11_1	chr9	82632456	82633243	+	0	NA	Intergenic	L1PA15|LINE|L1	430279	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.006353	0.368020	
chunk0133_191_1	chr3	170631648	170632290	+	0	NA	Intergenic	Intergenic	-45895	NM_020949	57709	Hs.596660	NM_020949	ENSG00000013293	SLC7A14	PPP1R142	solute carrier family 7 member 14	protein-coding	0.004673	0.339036	
chunk0070_366_1	chr15	76273962	76274602	+	0	NA	intron (NM_000126, intron 9 of 11)	intron (NM_000126, intron 9 of 11)	-14130	NR_028510	7302	Hs.684881	NR_002721		TYRO3P	-	TYRO3P protein tyrosine kinase pseudogene	pseudo	0.003125	0.330733	
chunk0206_24_1	chr9	116087171	116087389	+	0	NA	Intergenic	Intergenic	-66512	NM_002581	5069	Hs.643599	NM_002581	ENSG00000182752	PAPPA	ASBABP2|DIPLA1|IGFBP-4ase|PAPA|PAPP-A|PAPPA1	pappalysin 1	protein-coding	0.000000	0.333333	
chunk0110_300_1	chr20	17975651	17976164	+	0	NA	intron (NM_001310338, intron 4 of 5)	intron (NM_001310338, intron 4 of 5)	-6916	NM_001282454	27131	Hs.316890	NM_014426	ENSG00000089006	SNX5	-	sorting nexin 5	protein-coding	0.015595	0.437743	
chunk0070_377_1	chr15	76390521	76390827	+	0	NA	intron (NM_020843, intron 26 of 30)	MIRc|SINE|MIR	53950	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.000000	0.498371	
chunk0094_422_1	chr2	10590565	10591250	+	0	NA	intron (NR_048552, intron 16 of 19)	intron (NR_048552, intron 16 of 19)	99080	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.005839	0.368805	
chunk0097_135_1	chr2	47195039	47195738	+	0	NA	intron (NR_110208, intron 4 of 4)	intron (NR_110208, intron 4 of 4)	-18452	NM_001305625	805	Hs.468442	NM_001743	ENSG00000143933	CALM2	CALM|CALML2|CAM1|CAM3|CAMC|CAMII|CAMIII|LQT15|PHKD|PHKD2|caM	calmodulin 2	protein-coding	0.008584	0.417143	
chunk0165_323_1	chr6	37167230	37167662	+	0	NA	Intergenic	MIR|SINE|MIR	-2700	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.013889	0.355658	
chunk0139_423_1	chr4	64144914	64145366	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	264320	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.004425	0.421634	
chunk0023_196_1	chr10	25162042	25162849	+	0	NA	intron (NR_027333, intron 1 of 1)	L2a|LINE|L2	-12916	NM_020752	57512	Hs.499108	NM_020752	ENSG00000151025	GPR158	-	G protein-coupled receptor 158	protein-coding	0.006196	0.368812	
chunk0137_80_1	chr4	13054571	13054797	+	0	NA	Intergenic	Intergenic	429681	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.004425	0.422907	59(ATTACACTCTGTTCTT,+,0.00)
chunk0031_130_1	chr10	124913177	124913630	+	0	NA	Intergenic	Intergenic	-28720	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.006623	0.409692	
chunk0056_275_1	chr13	90331725	90332558	+	0	NA	Intergenic	Intergenic	100959	NR_030754	693207		NR_030754	ENSG00000283783	MIR622	MIRN622|hsa-mir-622	microRNA 622	ncRNA	0.003601	0.269784	
chunk0162_366_1	chr6	7201046	7201656	+	0	NA	intron (NM_001003698, intron 6 of 11)	intron (NM_001003698, intron 6 of 11)	93498	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.016393	0.515548	
chunk0077_13_1	chr16	74812046	74812277	+	0	NA	Intergenic	Intergenic	-37330	NM_024306	79152	Hs.461329	NM_024306	ENSG00000103089	FA2H	FAAH|FAH1|FAXDC1|SCS7|SPG35	fatty acid 2-hydroxylase	protein-coding	0.008658	0.525862	
chunk0162_377_1	chr6	7418958	7419534	+	0	NA	Intergenic	Intergenic	16599	NM_153005	83732	Hs.437474	NM_031480	ENSG00000124784	RIOK1	AD034|RIO1|RRP10|bA288G3.1	RIO kinase 1	protein-coding	0.003472	0.395147	
chunk0008_68_1	chr1	89717686	89718205	+	0	NA	3' UTR (NM_032270, exon 3 of 3)	3' UTR (NM_032270, exon 3 of 3)	84860	NM_032270	84230	Hs.412836	NM_032270	ENSG00000171488	LRRC8C	AD158|FAD158	leucine rich repeat containing 8 VRAC subunit C	protein-coding	0.001927	0.346154	
chunk0208_364_1	chrX	26166155	26166418	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-26154	NM_173523	158809	Hs.376011	NM_173523	ENSG00000176746	MAGEB6	CT3.4|MAGE-B6|MAGEB6A	MAGE family member B6	protein-coding	0.000000	0.356061	
chunk0112_328_1	chr20	44960300	44960812	+	0	NA	promoter-TSS (NM_006809)	promoter-TSS (NM_006809)	-83	NM_006809	10953	Hs.517066	NM_006809	ENSG00000025772	TOMM34	HTOM34P|TOM34|URCC3	translocase of outer mitochondrial membrane 34	protein-coding	0.064453	0.596491	
chunk0013_224_1	chr1	169527796	169528109	+	0	NA	exon (NM_000130, exon 17 of 25)	exon (NM_000130, exon 17 of 25)	-41982	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.009585	0.480892	
chunk0181_412_1	chr7	90213545	90213994	+	0	NA	promoter-TSS (NM_001040666)	promoter-TSS (NM_001040666)	-51	NM_001040666	261729	Hs.489051	NM_152999	ENSG00000157214	STEAP2	IPCA1|PCANAP1|PUMPCn|STAMP1|STMP	STEAP2 metalloreductase	protein-coding	0.008909	0.375556	
chunk0098_178_1	chr2	71241397	71241691	+	0	NA	Intergenic	MamTip3|DNA|hAT-Tip100	-14441	NM_020459	400961	Hs.416735	NM_020459	ENSG00000124374	PAIP2B	-	poly(A) binding protein interacting protein 2B	protein-coding	0.000000	0.383051	
chunk0044_271_1	chr12	32435708	32436429	+	0	NA	Intergenic	Intergenic	-49904	NM_001304481	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.008322	0.386427	
chunk0149_315_1	chr5	26343531	26344321	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	694656	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.003797	0.343869	
chunk0011_287_1	chr1	151454050	151454376	+	0	NA	intron (NM_001194938, intron 1 of 17)	intron (NM_001194938, intron 1 of 17)	5252	NM_145796	23126	Hs.489873	NM_015100	ENSG00000143442	POGZ	MRD37|WHSUS|ZNF280E|ZNF635|ZNF635m	pogo transposable element derived with ZNF domain	protein-coding	0.003067	0.311927	
chunk0088_300_1	chr18	49996799	49997077	+	0	NA	intron (NM_001080467, intron 5 of 39)	intron (NM_001080467, intron 5 of 39)	129625	NR_036204	100422865		NR_036204	ENSG00000283343	MIR4320	-	microRNA 4320	ncRNA	0.007194	0.426523	
chunk0039_20_1	chr11	95641588	95641799	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	148097	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.009479	0.471698	
chunk0117_159_1	chr22	20040770	20041239	+	0	NA	intron (NR_104275, intron 1 of 5)	intron (NR_104275, intron 1 of 5)	4244	NR_104275	128989	Hs.474233	NM_152906	ENSG00000183597	TANGO2	C22orf25|MECRCN	transport and golgi organization 2 homolog	protein-coding	0.008529	0.587234	
chunk0137_376_1	chr4	26227997	26228259	+	0	NA	Intergenic	Intergenic	-91582	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.015267	0.520913	
chunk0191_322_1	chr8	55872452	55873051	+	0	NA	Intergenic	MIRb|SINE|MIR	-7076	NM_002350	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.005008	0.438333	
chunk0005_201_1	chr1	59062061	59062423	+	0	NA	intron (NR_110626, intron 2 of 2)	MLT1J2|LTR|ERVL-MaLR	41766	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.008287	0.443526	
chunk0091_319_1	chr19	13134731	13135006	+	0	NA	intron (NM_052876, intron 1 of 5)	intron (NM_052876, intron 1 of 5)	15506	NM_003765	8677	Hs.43812	NM_003765	ENSG00000104915	STX10	SYN10|hsyn10	syntaxin 10	protein-coding	0.007273	0.489130	118(TAGCACACTGTGTCCT,-,0.00),119(AGCACACTGTGTCCTA,+,0.00)
chunk0131_358_1	chr3	151890763	151891262	+	0	NA	intron (NR_110202, intron 1 of 3)	LTR88b|LTR|Gypsy?	17369	NM_033050	56670	Hs.133181	NM_033050	ENSG00000198829	SUCNR1	GPR91	succinate receptor 1	protein-coding	0.008016	0.404000	196(CAGAGCAGCCTGTGCT,-,0.00),197(AGAGCAGCCTGTGCTT,+,0.00)
chunk0189_45_1	chr8	19929943	19930306	+	0	NA	Intergenic	Intergenic	-8947	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.002755	0.461538	
chunk0207_213_1	chr9	131422431	131422839	+	0	NA	Intergenic	Intergenic	-7455	NM_013318	84726	Hs.743955	NM_013318	ENSG00000130723	PRRC2B	BAT2L|BAT2L1|KIAA0515|LQFBS-1	proline rich coiled-coil 2B	protein-coding	0.017157	0.515892	
chunk0142_433_1	chr4	104922322	104922853	+	0	NA	Intergenic	Intergenic	-223288	NM_017628	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.003766	0.312030	
chunk0066_133_1	chr15	31159216	31159612	+	0	NA	intron (NM_001252020, intron 1 of 26).2	intron (NM_001252020, intron 1 of 26).2	1859	NM_001252020	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.015152	0.508816	156(AAGAACAGTGTGGGCC,-,0.00),157(AGAACAGTGTGGGCCA,+,0.00)
chunk0027_371_1	chr10	79264801	79265006	+	0	NA	intron (NM_020338, intron 7 of 24)	intron (NM_020338, intron 7 of 24)	-82561	NM_005729	10105	Hs.381072	NM_005729	ENSG00000108179	PPIF	CYP3|CyP-M|Cyp-D|CypD	peptidylprolyl isomerase F	protein-coding	0.004878	0.524272	
chunk0154_261_1	chr5	81794061	81794308	+	0	NA	Intergenic	L2b|LINE|L2	-42931	NM_001256735	23635	Hs.102735	NM_012446	ENSG00000145687	SSBP2	HSPC116|SOSS-B2	single stranded DNA binding protein 2	protein-coding	0.004049	0.427419	
chunk0058_430_1	chr13	113139535	113140019	+	0	NA	intron (NM_001312674, intron 4 of 6)	intron (NM_001312674, intron 4 of 6)	-9731	NR_126424	104413892		NR_126424		F10-AS1	-	F10 antisense RNA 1	ncRNA	0.012397	0.385567	
chunk0135_62_1	chr3	185757814	185758544	+	0	NA	intron (NM_001007225, intron 2 of 14)	intron (NM_001007225, intron 2 of 14)	9725	NR_049838	100847078		NR_049838	ENSG00000265470	MIR548AQ	-	microRNA 548aq	ncRNA	0.006849	0.422709	287(CAGGACAAGGTGTACT,-,0.00),288(AGGACAAGGTGTACTT,+,0.00)
chunk0206_427_1	chr9	127583453	127583984	+	0	NA	Intergenic	L1ME2|LINE|L1	-4711	NM_001035534	64855	Hs.522401	NM_022833	ENSG00000136830	NIBAN2	C9orf88|FAM129B|MEG-3|MINERVA|OC58|bA356B19.6	niban apoptosis regulator 2	protein-coding	0.003766	0.360902	
chunk0087_60_1	chr18	31630589	31630891	+	0	NA	intron (NM_004775, intron 6 of 8)	MIRb|SINE|MIR	38973	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.009934	0.465347	
chunk0096_156_1	chr2	29314802	29315418	+	0	NA	intron (NM_004304, intron 8 of 28)	intron (NM_004304, intron 8 of 28)	199684	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.025974	0.531605	
chunk0184_329_1	chr7	120502911	120503201	+	0	NA	intron (NM_012281, intron 1 of 5)	LTR78|LTR|ERV1	229388	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.336770	
chunk0191_240_1	chr8	53006150	53006473	+	0	NA	Intergenic	Intergenic	66403	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.006192	0.447531	
chunk0103_151_1	chr2	162244612	162245148	+	0	NA	Intergenic	Intergenic	-1345	NM_004460	2191	Hs.654370	NM_004460	ENSG00000078098	FAP	DPPIV|FAPA|FAPalpha|SIMP	fibroblast activation protein alpha	protein-coding	0.003731	0.433892	363(GAACACACCGTGTTCT,-,0.00),364(AACACACCGTGTTCTC,+,0.00)
chunk0116_181_1	chr21	36854335	36854653	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	112162	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.015723	0.501567	
chunk0147_90_1	chr4	173239292	173239673	+	0	NA	intron (NM_017423, intron 1 of 11)	L2c|LINE|L2	-28678	NR_036093	100422849		NR_036093	ENSG00000221296	MIR548T	-	microRNA 548t	ncRNA	0.010499	0.418848	
chunk0211_209_1	chrX	118210003	118210422	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	-92872	NM_001168301	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.004773	0.411905	
chunk0039_386_1	chr11	107128547	107129055	+	0	NA	Intergenic	L2c|LINE|L2	-110356	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.005906	0.438114	116(AAGCACACGAAGTCCT,-,0.00),117(AGCACACGAAGTCCTC,+,0.00),207(AGGCACAGCATGCACT,-,0.00),208(GGCACAGCATGCACTT,+,0.00),241(GGTTCATGCTGTCCCT,+,0.00)
chunk0073_233_1	chr16	11353539	11353893	+	0	NA	Intergenic	MIR|SINE|MIR	8278	NR_130754	116028	Hs.347524	NM_152308	ENSG00000175643	RMI2	BLAP18|C16orf75	RecQ mediated genome instability 2	protein-coding	0.008475	0.411268	209(AGGATCAGTATGTTCT,-,0.00),210(GGATCAGTATGTTCTT,+,0.00),291(TAGTACAAAGAGTTCC,-,0.00),292(AGTACAAAGAGTTCCC,+,0.00)
chunk0090_426_1	chr18	79329229	79329750	+	0	NA	intron (NM_001306085, intron 16 of 28)	intron (NM_001306085, intron 16 of 28)	-66283	NM_006162	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.015355	0.360153	
chunk0137_245_1	chr4	20616273	20616880	+	0	NA	intron (NM_001289135, intron 33 of 35)	intron (NM_001289135, intron 33 of 35)	-83837	NM_001258345	133015	Hs.479298	NM_145048	ENSG00000163138	PACRGL	C4orf28	parkin coregulated like	protein-coding	0.000000	0.462171	
chunk0202_398_1	chr9	81279947	81280526	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	409299	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.001727	0.377586	
chunk0184_208_1	chr7	117123510	117124056	+	0	NA	intron (NM_021908, intron 3 of 15)	intron (NM_021908, intron 3 of 15)	21809	NR_109981	93654	Hs.628891	NR_002331	ENSG00000226367	ST7-AS2	ST7AS2|ST7OT2	ST7 antisense RNA 2	ncRNA	0.001832	0.338208	
chunk0110_251_1	chr20	16604326	16604653	+	0	NA	Intergenic	Intergenic	-31055	NM_001199865	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.009174	0.329268	
chunk0114_327_1	chr21	17472071	17472738	+	0	NA	Intergenic	Intergenic	33514	NR_037586	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.002999	0.411677	
chunk0002_181_1	chr1	19073824	19074246	+	0	NA	TTS (NM_020765)	TTS (NM_020765)	-117703	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.023697	0.579196	
chunk0015_268_1	chr1	188363830	188364041	+	0	NA	Intergenic	Intergenic	920307	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.301887	17(CAGCACACATAGTACC,-,0.00),18(AGCACACATAGTACCT,+,0.00)
chunk0180_213_1	chr7	66781617	66781829	+	0	NA	intron (NM_001287060, intron 5 of 9)	L1MEc|LINE|L1	25841	NM_001287061	27342	Hs.530053	NM_014504	ENSG00000154710	RABGEF1	RABEX5|RAP1|rabex-5	RAB guanine nucleotide exchange factor 1	protein-coding	0.014151	0.474178	
chunk0164_378_1	chr6	25922200	25922712	+	0	NA	intron (NM_005835, intron 3 of 10)	intron (NM_005835, intron 3 of 10)	3423	NM_001286123	10246	Hs.591802	NM_005835	ENSG00000112337	SLC17A2	NPT3	solute carrier family 17 member 2	protein-coding	0.003906	0.372320	
chunk0065_226_1	chr14	100822066	100822578	+	0	NA	Intergenic	Intergenic	-3786	NR_046473	55384	Hs.654863	NR_002766	ENSG00000214548	MEG3	FP504|GTL2|LINC00023|NCRNA00023|PRO0518|PRO2160|onco-lncRNA-83|prebp1	maternally expressed 3	ncRNA	0.019531	0.483431	272(GGGAGCAGAGTGTTCC,-,0.00),273(GGAGCAGAGTGTTCCC,+,0.00)
chunk0045_78_1	chr12	45771766	45771981	+	0	NA	intron (NM_152641, intron 3 of 20)	L1M4b|LINE|L1	42036	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.004651	0.305556	
chunk0161_148_1	chr5	168799328	168799544	+	0	NA	intron (NM_003062, intron 9 of 35)	intron (NM_003062, intron 9 of 35)	-31181	NR_029632	407001		NR_029632	ENSG00000207739	MIR218-2	MIRN218-2|mir-218-2	microRNA 218-2	ncRNA	0.004630	0.405530	
chunk0192_75_1	chr8	60718870	60719187	+	0	NA	intron (NM_017780, intron 1 of 37)	Tigger3b|DNA|TcMar-Tigger	-22231	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.003155	0.402516	
chunk0138_8_1	chr4	30315079	30315278	+	0	NA	Intergenic	AluSq|SINE|Alu	-405230	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.005025	0.435000	
chunk0185_14_1	chr7	123915144	123915376	+	0	NA	Intergenic	Intergenic	-9972	NM_153189	6677	Hs.121494	NM_003117	ENSG00000106304	SPAM1	HEL-S-96n|HYA1|HYAL1|HYAL3|HYAL5|PH-20|PH20|SPAG15	sperm adhesion molecule 1	protein-coding	0.000000	0.304721	
chunk0156_243_1	chr5	108661611	108662314	+	0	NA	Intergenic	Intergenic	66299	NR_046368	100652853	Hs.133009	NR_046368	ENSG00000272523	LINC01023	HP07349	long intergenic non-protein coding RNA 1023	ncRNA	0.011380	0.430398	
chunk0153_113_1	chr5	68554872	68555398	+	0	NA	Intergenic	Intergenic	262567	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.013308	0.497154	
chunk0100_430_1	chr2	120291423	120291766	+	0	NA	intron (NM_002881, intron 4 of 4)	intron (NM_002881, intron 4 of 4)	38756	NM_002881	5899	Hs.469820	NM_002881	ENSG00000144118	RALB	-	RAS like proto-oncogene B	protein-coding	0.005831	0.450581	
chunk0033_17_1	chr11	12503024	12503523	+	0	NA	intron (NM_018222, intron 5 of 12)	intron (NM_018222, intron 5 of 12)	125794	NM_018222	55742	Hs.432914	NM_018222	ENSG00000197702	PARVA	CH-ILKBP|MXRA2	parvin alpha	protein-coding	0.006012	0.498000	
chunk0187_157_1	chr7	150360002	150360892	+	0	NA	Intergenic	MER67C|LTR|ERV1	-8343	NM_001099695	29803	Hs.647086	NM_013400	ENSG00000214022	REPIN1	AP4|RIP60|ZNF464|Zfp464	replication initiator 1	protein-coding	0.002247	0.439955	477(AGGGACACTGTCTTCC,-,0.00),478(GGGACACTGTCTTCCT,+,0.00)
chunk0146_206_1	chr4	161399626	161400070	+	0	NA	intron (NM_001128427, intron 15 of 15)	Tigger2b_Pri|DNA|TcMar-Tigger	-622885	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.013514	0.316854	208(TAGTACAGTATGTACT,-,0.00),209(AGTACAGTATGTACTA,+,0.00)
chunk0178_79_1	chr7	30450185	30450757	+	0	NA	intron (NM_006092, intron 6 of 13)	intron (NM_006092, intron 6 of 13)	28306	NM_006092	10392	Hs.405153	NM_006092	ENSG00000106100	NOD1	CARD4|CLR7.1|NLRC1	nucleotide binding oligomerization domain containing 1	protein-coding	0.008741	0.460733	
chunk0062_263_1	chr14	71689456	71689991	+	0	NA	intron (NM_001284245, intron 10 of 20)	intron (NM_001284245, intron 10 of 20)	102152	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.009346	0.395522	
chunk0133_227_1	chr3	171248169	171248841	+	0	NA	intron (NM_001161560, intron 2 of 31)	L2|LINE|L2	-141746	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.002976	0.429421	
chunk0011_24_1	chr1	143207709	143207912	+	0	NA	Intergenic	Intergenic	214782	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.064039	0.352941	
chunk0171_118_1	chr6	122603835	122604133	+	0	NA	intron (NM_181794, intron 3 of 6)	intron (NM_181794, intron 3 of 6)	-6248	NM_032471	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.003356	0.341137	
chunk0088_251_1	chr18	48733749	48734304	+	0	NA	intron (NM_014772, intron 7 of 11)	intron (NM_014772, intron 7 of 11)	63426	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.018018	0.561151	299(AGGGACGCTGTGTTCT,-,0.00),300(GGGACGCTGTGTTCTT,+,0.00)
chunk0066_435_1	chr15	39732900	39733117	+	0	NA	intron (NM_152597, intron 8 of 11)	intron (NM_152597, intron 8 of 11)	49830	NM_152597	161835	Hs.129598	NM_152597	ENSG00000150667	FSIP1	HSD10	fibrous sheath interacting protein 1	protein-coding	0.013825	0.412844	
chunk0057_194_1	chr13	103175809	103176020	+	0	NA	Intergenic	Intergenic	-109068	NM_000452	6555	Hs.194783	NM_000452	ENSG00000125255	SLC10A2	ASBT|IBAT|ISBT|NTCP2|PBAM	solute carrier family 10 member 2	protein-coding	0.009479	0.320755	
chunk0165_16_1	chr6	28825312	28825883	+	0	NA	Intergenic	Intergenic	38080	NR_033379	401242	Hs.448285	NR_033379	ENSG00000225595	LINC01623	-	long intergenic non-protein coding RNA 1623	ncRNA	0.043783	0.496503	
chunk0032_457_1	chr10	133526978	133527177	+	0	NA	promoter-TSS (NM_000773)	promoter-TSS (NM_000773)	-286	NM_000773	1571	Hs.12907	NM_000773	ENSG00000130649	CYP2E1	CPE1|CYP2E|P450-J|P450C2E	cytochrome P450 family 2 subfamily E member 1	protein-coding	0.015075	0.510000	
chunk0096_392_1	chr2	37631071	37631907	+	0	NA	Intergenic	Intergenic	40710	NM_001270438	10602	Hs.369574	NM_006449	ENSG00000163171	CDC42EP3	BORG2|CEP3|UB1	CDC42 effector protein 3	protein-coding	0.008373	0.389486	
chunk0131_284_1	chr3	150316650	150317188	+	0	NA	intron (NR_110187, intron 1 of 1)	intron (NR_110187, intron 1 of 1)	6828	NR_110186	101928022	Hs.555199	NR_110186		LINC01214	-	long intergenic non-protein coding RNA 1214	ncRNA	0.001859	0.354360	
chunk0035_390_1	chr11	56416062	56416474	+	0	NA	TTS (NM_001004744)	TTS (NM_001004744)	1964	NM_001004744	219479	Hs.553630	NM_001004744	ENSG00000279961	OR5R1	OR11-185|OR5R1P	olfactory receptor family 5 subfamily R member 1 (gene/pseudogene)	protein-coding	0.000000	0.244552	
chunk0181_168_1	chr7	82678334	82679379	+	0	NA	Intergenic	Intergenic	-235050	NM_001302890	781	Hs.282151	NM_000722	ENSG00000153956	CACNA2D1	CACNA2|CACNL2A|CCHL2A|LINC01112|lncRNA-N3	calcium voltage-gated channel auxiliary subunit alpha2delta 1	protein-coding	0.008612	0.376673	
chunk0133_44_1	chr3	166304535	166304997	+	0	NA	Intergenic	Mam_R4|LINE|Dong-R4	-467301	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.010823	0.373650	
chunk0006_328_1	chr1	71821116	71821846	+	0	NA	intron (NR_046218, intron 1 of 2)	ERV3-16A3_I-int|LTR|ERVL	15531	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005479	0.392613	234(AGGGTCAGGCTGTCCA,-,0.00)
chunk0011_427_1	chr1	154558659	154559042	+	0	NA	promoter-TSS (NM_017582)	promoter-TSS (NM_017582)	-206	NM_017582	55585	Hs.607928	NM_017582	ENSG00000160714	UBE2Q1	GTAP|NICE-5|NICE5|PRO3094|UBE2Q	ubiquitin conjugating enzyme E2 Q1	protein-coding	0.101828	0.718750	
chunk0009_182_1	chr1	105702129	105702511	+	0	NA	Intergenic	Intergenic	-83385	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002618	0.318538	196(TAGAACTTGGTGTTCT,-,0.00),197(AGAACTTGGTGTTCTT,+,0.00)
chunk0157_21_1	chr5	115497511	115497710	+	0	NA	Intergenic	LTR67B|LTR|ERVL	47284	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.005025	0.470000	
chunk0092_90_1	chr19	22118165	22118524	+	0	NA	Intergenic	Intergenic	65896	NM_033468	113835	Hs.283900	NM_033468	ENSG00000197134	ZNF257	BMZF-4|BMZF4	zinc finger protein 257	protein-coding	0.002786	0.408333	
chunk0028_163_1	chr10	87091409	87091894	+	0	NA	intron (NM_005271, intron 1 of 12)	intron (NM_005271, intron 1 of 12)	3368	NM_005271	2746	Hs.500409	NM_005271	ENSG00000148672	GLUD1	GDH|GDH1|GLUD	glutamate dehydrogenase 1	protein-coding	0.004124	0.370370	
chunk0090_30_1	chr19	1213544	1213971	+	0	NA	intron (NM_000455, intron 1 of 9)	intron (NM_000455, intron 1 of 9)	7958	NM_000455	6794	Hs.515005	NM_000455	ENSG00000118046	STK11	LKB1|PJS|hLKB1	serine/threonine kinase 11	protein-coding	0.044496	0.623832	276(GGAGCTGGGTGTTCCT,+,0.00)
chunk0017_364_1	chr1	211967657	211967990	+	0	NA	intron (NR_037667, intron 16 of 20)	intron (NR_037667, intron 16 of 20)	-67730	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.012012	0.329341	187(AAGAACAAGAAGTACT,-,0.00)
chunk0162_305_1	chr6	6570954	6571316	+	0	NA	intron (NR_026970, intron 1 of 7)	intron (NR_026970, intron 1 of 7)	-17566	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.005525	0.338843	
chunk0028_406_1	chr10	93300836	93301238	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	181280	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.012438	0.426799	
chunk0037_273_1	chr11	75722324	75722697	+	0	NA	intron (NM_025098, intron 2 of 5)	intron (NM_025098, intron 2 of 5)	4621	NM_025098	80168	Hs.288568	NM_025098	ENSG00000166391	MOGAT2	DGAT2L5|DGAT2L5.|MGAT2|hDC5	monoacylglycerol O-acyltransferase 2	protein-coding	0.018767	0.588235	
chunk0068_270_1	chr15	56668059	56668646	+	0	NA	intron (NM_001002843, intron 13 of 20)	intron (NM_001002843, intron 13 of 20)	65734	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.000000	0.353741	
chunk0127_39_1	chr3	88747271	88747821	+	0	NA	Intergenic	L1PA6|LINE|L1	-359978	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.016364	0.542650	
chunk0023_352_1	chr10	29731019	29731404	+	0	NA	intron (NM_003174, intron 1 of 35)	L2c|LINE|L2	4590	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.010390	0.424870	
chunk0056_207_1	chr13	85985577	85986101	+	0	NA	Intergenic	L1ME3G|LINE|L1	-186491	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.003817	0.323810	276(TGGAACAAAGTGTACA,-,0.00),277(GGAACAAAGTGTACAC,+,0.00)
chunk0006_454_1	chr1	77043014	77043307	+	0	NA	intron (NM_030965, intron 2 of 4)	intron (NM_030965, intron 2 of 4)	-16983	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.017065	0.384354	
chunk0204_397_1	chr9	102521073	102521761	+	0	NA	intron (NR_103830, intron 1 of 4)	intron (NR_103830, intron 1 of 4)	1780	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.007267	0.362845	208(AAGAACAAACTGTACT,-,0.00),209(AGAACAAACTGTACTC,+,0.00)
chunk0081_289_1	chr17	44689697	44689989	+	0	NA	promoter-TSS (NM_001099225)	promoter-TSS (NM_001099225)	-46	NM_144609	124808	Hs.579115	NM_144609	ENSG00000180329	CCDC43	-	coiled-coil domain containing 43	protein-coding	0.095890	0.627986	
chunk0079_437_1	chr17	20059782	20060291	+	0	NA	intron (NM_001243439, intron 1 of 14)	Charlie25|DNA|hAT-Charlie	-26986	NM_152904	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.005894	0.400000	
chunk0006_209_1	chr1	67824851	67825109	+	0	NA	intron (NM_018841, intron 1 of 3)	intron (NM_018841, intron 1 of 3)	-7308	NR_040077	100289178	Hs.677603	NR_040077	ENSG00000232284	GNG12-AS1	-	GNG12, DIRAS3 and WLS antisense RNA 1	ncRNA	0.003876	0.440154	
chunk0005_350_1	chr1	61299478	61299928	+	0	NA	intron (NM_001145511, intron 3 of 10)	intron (NM_001145511, intron 3 of 10)	-46185	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.004444	0.345898	
chunk0138_401_1	chr4	42907841	42908427	+	0	NA	intron (NM_001080476, intron 1 of 3)	ERV3-16A3_I-int|LTR|ERVL	14868	NM_001080476	389207	Hs.162559	NM_001080476	ENSG00000215203	GRXCR1	DFNB25|PPP1R88	glutaredoxin and cysteine rich domain containing 1	protein-coding	0.006826	0.480409	
chunk0044_114_1	chr12	29033302	29033556	+	0	NA	Intergenic	Intergenic	-115574	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.003937	0.380392	
chunk0097_433_1	chr2	63871911	63872284	+	0	NA	intron (NM_001001521, intron 3 of 9)	MER58A|DNA|hAT-Charlie	30217	NM_006759	7360	Hs.516217	NM_006759	ENSG00000169764	UGP2	UDPG|UDPGP|UDPGP2|UGP1|UGPP1|UGPP2|pHC379	UDP-glucose pyrophosphorylase 2	protein-coding	0.010724	0.374332	
chunk0070_305_1	chr15	74937450	74937790	+	0	NA	intron (NM_004255, intron 1 of 4)	CpG	534	NM_004255	9377	Hs.401903	NM_004255	ENSG00000178741	COX5A	COX|COX-VA|VA	cytochrome c oxidase subunit 5A	protein-coding	0.102941	0.686217	
chunk0139_125_1	chr4	53149165	53149592	+	0	NA	intron (NM_152540, intron 4 of 8)	L1MC3|LINE|L1	216697	NM_152540	152579	Hs.302287	NM_152540	ENSG00000184178	SCFD2	STXBP1L1	sec1 family domain containing 2	protein-coding	0.000000	0.341121	
chunk0150_68_1	chr5	32129150	32129745	+	0	NA	intron (NM_022130, intron 3 of 3)	intron (NM_022130, intron 3 of 3)	44872	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.006723	0.338926	
chunk0210_21_1	chrX	67105225	67105944	+	0	NA	Intergenic	Intergenic	-438448	NM_000044	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.006954	0.437500	403(AGGGACACGCTGTTCT,-,0.00),404(GGGACACGCTGTTCTA,+,0.00)
chunk0020_410_1	chr1	241392015	241392356	+	0	NA	Intergenic	Intergenic	-34955	NM_001282773	6000	Hs.655739	NM_002924	ENSG00000182901	RGS7	-	regulator of G protein signaling 7	protein-coding	0.005865	0.423977	
chunk0139_283_1	chr4	57125267	57125469	+	0	NA	intron (NR_034081, intron 1 of 4)	MER58A|DNA|hAT-Charlie	-14983	NM_001553	3490	Hs.479808	NM_001553	ENSG00000163453	IGFBP7	AGM|FSTL2|IBP-7|IGFBP-7|IGFBP-7v|IGFBPRP1|MAC25|PSF|RAMSVPS|TAF	insulin like growth factor binding protein 7	protein-coding	0.004950	0.379310	
chunk0094_282_1	chr2	8249890	8250152	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	78398	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.007634	0.406844	
chunk0107_172_1	chr2	215543696	215544511	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	90396	NR_110607	102724849	Hs.116161	NR_110607	ENSG00000225166	LOC102724849	-	uncharacterized LOC102724849	ncRNA	0.003681	0.401961	
chunk0122_440_1	chr3	39298096	39298398	+	0	NA	Intergenic	L1M2|LINE|L1	-16512	NM_001171174	1524	Hs.78913	NM_001337	ENSG00000168329	CX3CR1	CCRL1|CMKBRL1|CMKDR1|GPR13|GPRV28|V28	C-X3-C motif chemokine receptor 1	protein-coding	0.009934	0.590759	
chunk0191_209_1	chr8	52151135	52151682	+	0	NA	intron (NM_014682, intron 15 of 25)	intron (NM_014682, intron 15 of 25)	-252222	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.018282	0.395985	
chunk0042_68_1	chr12	2038786	2039651	+	0	NA	Intergenic	Intergenic	-9134	NR_046768	100874369	Hs.208723	NR_046768	ENSG00000256257	CACNA1C-IT2	-	CACNA1C intronic transcript 2	ncRNA	0.001156	0.384527	
chunk0176_199_1	chr7	14112499	14112981	+	0	NA	Intergenic	Intergenic	-121315	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.006224	0.360248	67(ATGAACAACATGTACT,-,0.00),68(TGAACAACATGTACTA,+,0.00)
chunk0105_311_1	chr2	190417107	190417475	+	0	NA	intron (NM_017694, intron 2 of 7)	intron (NM_017694, intron 2 of 7)	8936	NM_017694	54842	Hs.418581	NM_017694	ENSG00000151690	MFSD6	MMR2|hMMR2	major facilitator superfamily domain containing 6	protein-coding	0.010870	0.417344	103(AAGTACTGTTTGTTCT,-,0.00),104(AGTACTGTTTGTTCTG,+,0.00)
chunk0021_44_1	chr10	917257	917942	+	0	NA	intron (NM_015155, intron 1 of 17)	LTR49-int|LTR|ERV1	14106	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.007299	0.358601	
chunk0149_363_1	chr5	27850259	27850633	+	0	NA	Intergenic	Intergenic	378154	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.000000	0.280000	
chunk0051_232_1	chr12	116972665	116972987	+	0	NA	intron (NM_012174, intron 5 of 10)	L1MC4|LINE|L1	14511	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.009317	0.452012	
chunk0191_454_1	chr8	58067455	58068106	+	0	NA	intron (NM_147189, intron 3 of 4)	L2a|LINE|L2	73226	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.003072	0.426380	
chunk0089_137_1	chr18	58881732	58882048	+	0	NA	intron (NM_018181, intron 3 of 10)	intron (NM_018181, intron 3 of 10)	19061	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.003165	0.397476	
chunk0131_352_1	chr3	151751782	151752156	+	0	NA	intron (NR_110203, intron 2 of 2)	intron (NR_110203, intron 2 of 2)	18053	NM_207365	344752	Hs.144710	NM_207365	ENSG00000197953	AADACL2	-	arylacetamide deacetylase like 2	protein-coding	0.002674	0.312000	200(AAGAACTCAGTGTACT,-,0.00),201(AGAACTCAGTGTACTT,+,0.00)
chunk0172_273_1	chr6	137587503	137588307	+	0	NA	Intergenic	Intergenic	-77741	NR_125867	102723649	Hs.129235	NR_125867		LOC102723649	-	uncharacterized LOC102723649	ncRNA	0.002488	0.336646	502(TTGTACAATGTGTGCT,-,0.00),503(TGTACAATGTGTGCTT,+,0.00)
chunk0049_84_1	chr12	90712751	90713060	+	0	NA	Intergenic	Intergenic	-205118	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.006472	0.351613	
chunk0058_3_1	chr14	18592516	18592769	+	0	NA	Intergenic	L1M2|LINE|L1	-8475	NM_001013354	440153	Hs.534880	NM_001013354	ENSG00000257115	OR11H12	-	olfactory receptor family 11 subfamily H member 12	protein-coding	0.011858	0.303150	
chunk0191_328_1	chr8	55956726	55957029	+	0	NA	intron (NM_001111097, intron 8 of 12)	intron (NM_001111097, intron 8 of 12)	77050	NM_001111097	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.023102	0.470395	
chunk0134_1_1	chr3	175329226	175329683	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	-40086	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.002188	0.340611	
chunk0136_26_1	chr4	693122	693670	+	0	NA	Intergenic	Intergenic	-3955	NM_001294341	84179	Hs.567612	NM_032219	ENSG00000169026	SLC49A3	LP2561|MFSD7	solute carrier family 49 member 3	protein-coding	0.038321	0.599271	
chunk0180_38_1	chr7	54349077	54349642	+	0	NA	non-coding (NR_120515, exon 3 of 3)	non-coding (NR_120515, exon 3 of 3)	18662	NR_120516	102723605	Hs.154626	NR_120515	ENSG00000231427	LINC01445	-	long intergenic non-protein coding RNA 1445	ncRNA	0.007080	0.362191	265(AGGAACATTATGCTCC,-,0.00),266(GGAACATTATGCTCCA,+,0.00)
chunk0182_98_1	chr7	93203217	93204011	+	0	NA	intron (NM_001039372, intron 4 of 9)	intron (NM_001039372, intron 4 of 9)	15981	NM_001288810	253012	Hs.443169	NM_198151	ENSG00000188175	HEPACAM2	MIKI	HEPACAM family member 2	protein-coding	0.003778	0.435220	
chunk0145_257_1	chr4	148939721	148939989	+	0	NA	Intergenic	Intergenic	-214440	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.000000	0.349442	
chunk0195_65_1	chr8	93827822	93828121	+	0	NA	Intergenic	Intergenic	73127	NM_001142301	91147	Hs.116240	NM_153704	ENSG00000164953	TMEM67	JBTS6|MECKELIN|MKS3|NPHP11|TNEM67	transmembrane protein 67	protein-coding	0.003344	0.490000	
chunk0211_240_1	chrX	119561858	119562195	+	0	NA	intron (NM_022101, intron 1 of 6)	L2a|LINE|L2	3383	NM_001170569	63932	Hs.248572	NM_022101	ENSG00000018610	CXorf56	MRX107	chromosome X open reading frame 56	protein-coding	0.020772	0.449704	115(AAGCACATGCTGTTTC,-,0.00),116(AGCACATGCTGTTTCC,+,0.00)
chunk0074_368_1	chr16	34585801	34586361	+	0	NA	Intergenic	Intergenic	-426045	NR_038368									0.033929	0.356506	
chunk0043_107_1	chr12	15085617	15085992	+	0	NA	Intergenic	Intergenic	-66119	NR_046559	100873980	Hs.569154	NR_046559	ENSG00000255660	RERG-AS1	-	RERG antisense RNA 1	ncRNA	0.005333	0.377660	
chunk0202_392_1	chr9	81183775	81184182	+	0	NA	Intergenic	Intergenic	505557	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002457	0.340686	
chunk0184_202_1	chr7	117062608	117063091	+	0	NA	intron (NM_021908, intron 1 of 15)	intron (NM_021908, intron 1 of 15)	27932	NR_109980	93654	Hs.628891	NR_002331	ENSG00000226367	ST7-AS2	ST7AS2|ST7OT2	ST7 antisense RNA 2	ncRNA	0.002070	0.307851	184(GGTACATCCTGAACTT,+,0.00)
chunk0020_160_1	chr1	234345348	234345621	+	0	NA	Intergenic	Intergenic	27919	NR_125962	101927765	Hs.596703	NR_125961	ENSG00000231663	COA6-AS1	-	COA6 antisense RNA 1	ncRNA	0.003663	0.510949	
chunk0051_374_1	chr12	121610162	121610442	+	0	NA	Intergenic	Intergenic	13773	NR_049838	100847078		NR_049838	ENSG00000265470	MIR548AQ	-	microRNA 548aq	ncRNA	0.017857	0.523132	106(TTGACAGGCTGTTCCC,+,0.00)
chunk0057_426_1	chr13	110055276	110055840	+	0	NA	TTS (NR_126387)	TTS (NR_126387)	2273	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.017730	0.463717	
chunk0036_126_1	chr11	61800389	61800699	+	0	NA	3' UTR (NM_013402, exon 12 of 12)	3' UTR (NM_013402, exon 12 of 12)	7907	NM_004111	2237	Hs.409065	NM_004111	ENSG00000168496	FEN1	FEN-1|MF1|RAD2	flap structure-specific endonuclease 1	protein-coding	0.003226	0.440514	
chunk0163_299_1	chr6	14317016	14317327	+	0	NA	Intergenic	Intergenic	-31717	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.012862	0.516026	
chunk0084_318_1	chr17	80634107	80634499	+	0	NA	intron (NM_020761, intron 2 of 33)	intron (NM_020761, intron 2 of 33)	89478	NM_001163034	57521	Hs.133044	NM_020761	ENSG00000141564	RPTOR	KOG1|Mip1	regulatory associated protein of MTOR complex 1	protein-coding	0.048469	0.508906	
chunk0147_24_1	chr4	171589894	171590404	+	0	NA	Intergenic	Intergenic	-223275	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.001961	0.291585	
chunk0119_321_1	chr22	46788895	46789168	+	0	NA	intron (NM_001284305, intron 1 of 12)	intron (NM_001284305, intron 1 of 12)	15104	NM_001284305	25771	Hs.435044	NM_014346	ENSG00000054611	TBC1D22A	C22orf4|HSC79E021	TBC1 domain family member 22A	protein-coding	0.014652	0.489051	
chunk0073_390_1	chr16	16029510	16029734	+	0	NA	intron (NM_004996, intron 5 of 30)	L1MC4a|LINE|L1	80045	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.013393	0.346667	
chunk0198_442_1	chr8	143856826	143857161	+	0	NA	TTS (NM_031308)	TTS (NM_031308)	-16019	NM_178564	340371	Hs.521926	NM_178564	ENSG00000185189	NRBP2	TRG16|pp9320	nuclear receptor binding protein 2	protein-coding	0.017910	0.559524	
chunk0211_322_1	chrX	123873931	123874211	+	0	NA	intron (NR_037916, intron 1 of 5)	LTR83|LTR|ERVL	13904	NR_037916	331	Hs.356076	NM_001167	ENSG00000101966	XIAP	API3|BIRC4|IAP-3|ILP1|MIHA|XLP2|hIAP-3|hIAP3	X-linked inhibitor of apoptosis	protein-coding	0.000000	0.395018	
chunk0016_9_1	chr1	192715231	192715430	+	0	NA	promoter-TSS (NR_039624)	promoter-TSS (NR_039624)	-998	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.000000	0.510000	
chunk0030_456_1	chr10	121155789	121156296	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	-304863	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.007890	0.442913	
chunk0095_175_1	chr2	17719836	17720223	+	0	NA	intron (NM_024624, intron 10 of 26)	intron (NM_024624, intron 10 of 26)	33800	NM_024624	79677	Hs.526728	NM_024624	ENSG00000163029	SMC6	SMC-6|SMC6L1|hSMC6	structural maintenance of chromosomes 6	protein-coding	0.002584	0.389175	
chunk0124_34_1	chr3	52216790	52217026	+	0	NA	Intergenic	L2b|LINE|L2	9255	NM_017442	54106	Hs.87968	NM_017442	ENSG00000239732	TLR9	CD289	toll like receptor 9	protein-coding	0.004237	0.481013	
chunk0199_453_1	chr9	14119872	14120171	+	0	NA	intron (NM_001190737, intron 8 of 10)	intron (NM_001190737, intron 8 of 10)	60781	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.003344	0.346667	
chunk0175_44_1	chr7	1096997	1097856	+	0	NA	intron (NM_032350, intron 2 of 4)	L1MC4|LINE|L1	9339	NM_001098201	2852	Hs.20961	NM_001505	ENSG00000164850	GPER1	CEPR|CMKRL2|DRY12|FEG-1|GPCR-Br|GPER|GPR30|LERGU|LERGU2|LyGPR|mER	G protein-coupled estrogen receptor 1	protein-coding	0.032596	0.552326	362(AAGGACACGGTGTCCT,-,0.00),363(AGGACACGGTGTCCTC,+,0.00)
chunk0034_452_1	chr11	39731960	39732450	+	0	NA	Intergenic	L2a|LINE|L2	560925	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.366599	
chunk0024_91_1	chr10	34469327	34470307	+	0	NA	intron (NM_019619, intron 4 of 24)	L1ME4b|LINE|L1	345508	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.011224	0.395515	291(AAGTTCATAATGTTCT,-,0.00)
chunk0064_180_1	chr14	92659614	92660224	+	0	NA	intron (NM_024832, intron 7 of 9)	MLT1C|LTR|ERVL-MaLR	88783	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.008197	0.487725	
chunk0094_428_1	chr2	10730294	10730734	+	0	NA	intron (NM_001039362, intron 3 of 13)	intron (NM_001039362, intron 3 of 13)	8865	NM_001039362	245973	Hs.580464	NM_144583	ENSG00000143882	ATP6V1C2	ATP6C2|VMA5	ATPase H+ transporting V1 subunit C2	protein-coding	0.002273	0.426304	
chunk0112_240_1	chr20	41292112	41292469	+	0	NA	intron (NM_015035, intron 1 of 3)	intron (NM_015035, intron 1 of 3)	7809	NM_015035	23051	Hs.380133	NM_015035	ENSG00000174306	ZHX3	TIX1	zinc fingers and homeoboxes 3	protein-coding	0.002801	0.346369	
chunk0206_90_1	chr9	120620454	120620690	+	0	NA	intron (NM_001080497, intron 3 of 5)	L2c|LINE|L2	-40402	NR_073554	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.008475	0.375527	
chunk0088_349_1	chr18	52139314	52139950	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-200540	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.006289	0.370487	
chunk0121_17_1	chr3	14724807	14725563	+	0	NA	intron (NM_001184957, intron 10 of 16)	intron (NM_001184957, intron 10 of 16)	50086	NM_001184957	84077	Hs.661452	NM_032137	ENSG00000131379	C3orf20	-	chromosome 3 open reading frame 20	protein-coding	0.007937	0.434610	
chunk0050_135_1	chr12	102438822	102439323	+	0	NA	intron (NM_001111284, intron 2 of 3)	L2a|LINE|L2	39579	NM_001111284	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.005988	0.414343	
chunk0195_445_1	chr8	101280435	101280694	+	0	NA	Intergenic	Intergenic	-74500	NM_001267709	51123	Hs.374485	NM_016096	ENSG00000120963	ZNF706	HSPC038|PNAS-106|PNAS-113	zinc finger protein 706	protein-coding	0.000000	0.461538	
chunk0209_391_1	chrX	54930870	54931665	+	0	NA	exon (NM_016157, exon 13 of 13)	exon (NM_016157, exon 13 of 13)	10443	NM_001271184	7216	Hs.633653	NM_016157	ENSG00000067445	TRO	MAGE-d3|MAGED3	trophinin	protein-coding	0.012579	0.471106	
chunk0110_349_1	chr20	19531549	19531874	+	0	NA	intron (NM_020689, intron 3 of 16)	intron (NM_020689, intron 3 of 16)	-247115	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.018462	0.444785	278(GAGATCAGAGTGTCCC,-,0.00),279(AGATCAGAGTGTCCCA,+,0.00)
chunk0018_206_1	chr1	219414168	219414630	+	0	NA	Intergenic	L2b|LINE|L2	239430	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.006494	0.352052	305(TGAACATTCTGAGCCT,+,0.00)
chunk0207_265_1	chr9	132309017	132309672	+	0	NA	intron (NM_015046, intron 11 of 25)	L1M5|LINE|L1	45641	NM_015046	23064	Hs.460317	NM_015046	ENSG00000107290	SETX	ALS4|AOA2|SCAN2|SCAR1|Sen1|bA479K20.2	senataxin	protein-coding	0.013740	0.454268	
chunk0205_35_1	chr9	105697841	105698373	+	0	NA	intron (NM_018112, intron 1 of 5)	intron (NM_018112, intron 1 of 5)	3582	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.009398	0.350844	
chunk0012_319_1	chr1	162353676	162354419	+	0	NA	intron (NM_001164757, intron 6 of 9)	intron (NM_001164757, intron 6 of 9)	-8936	NM_001126060	9722	Hs.731942	NM_014697	ENSG00000198929	NOS1AP	6330408P19Rik|CAPON	nitric oxide synthase 1 adaptor protein	protein-coding	0.009421	0.478495	439(TAGAACAATTTGTTCT,-,0.00),440(AGAACAATTTGTTCTA,+,0.00)
chunk0181_418_1	chr7	90231079	90231852	+	0	NA	intron (NM_001244946, intron 5 of 5)	Tigger3a|DNA|TcMar-Tigger	-13709	NM_001160138	79846	Hs.521014	NM_024788	ENSG00000105792	CFAP69	C7orf63|FAP69|SPGF24	cilia and flagella associated protein 69	protein-coding	0.005175	0.302326	
chunk0049_205_1	chr12	93146522	93146721	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-27745	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.005025	0.455000	
chunk0188_210_1	chr8	12736793	12737201	+	0	NA	exon (NM_152271, exon 5 of 12)	exon (NM_152271, exon 5 of 12)	-9693	NR_037492	100500870		NR_037492	ENSG00000266206	MIR3926-1	mir-3926-1	microRNA 3926-1	ncRNA	0.002451	0.342298	147(AATCACATCCTGTTCT,-,0.00),148(ATCACATCCTGTTCTA,+,0.00)
chunk0139_31_1	chr4	48419609	48419826	+	0	NA	intron (NM_020846, intron 6 of 7)	intron (NM_020846, intron 6 of 7)	-63626	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.004608	0.339450	
chunk0025_331_1	chr10	57925060	57925307	+	0	NA	Intergenic	Intergenic	342751	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.004049	0.379032	
chunk0101_392_1	chr2	138713529	138713908	+	0	NA	intron (NM_007226, intron 1 of 1)	intron (NM_007226, intron 1 of 1)	66523	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.013193	0.421053	
chunk0071_50_1	chr15	80023168	80023518	+	0	NA	Intergenic	Intergenic	-36225	NM_001242912	54469	Hs.596679	NM_019006	ENSG00000086666	ZFAND6	AWP1|ZA20D3|ZFAND5B	zinc finger AN1-type containing 6	protein-coding	0.005714	0.521368	
chunk0108_433_1	chr2	237898302	237898699	+	0	NA	intron (NM_001308353, intron 3 of 3)	intron (NM_001308353, intron 3 of 3)	38956	NM_005855	10267	Hs.471783	NM_005855	ENSG00000132329	RAMP1	-	receptor activity modifying protein 1	protein-coding	0.012594	0.527638	
chunk0146_213_1	chr4	161643622	161644282	+	0	NA	intron (NM_001128427, intron 7 of 15)	L2c|LINE|L2	-378781	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004545	0.332829	423(GAGAACAGTCAGTTTT,-,0.00),424(AGAACAGTCAGTTTTA,+,0.00)
chunk0112_322_1	chr20	44714099	44714824	+	0	NA	promoter-TSS (NM_003881)	promoter-TSS (NM_003881)	-783	NM_003881	8839	Hs.592145	NM_003881	ENSG00000064205	CCN5	CT58|CTGF-L|WISP2	cellular communication network factor 5	protein-coding	0.022069	0.552342	273(TGGTACGTACTGTTCC,-,0.00),274(GGTACGTACTGTTCCC,+,0.00),296(TGGAACATTCTGCCCT,-,0.00),297(GGAACATTCTGCCCTC,+,0.00)
chunk0055_256_1	chr13	63361564	63361773	+	0	NA	Intergenic	L1MA6|LINE|L1	-33574	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.004785	0.242857	
chunk0023_284_1	chr10	28463767	28464106	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	68418	NR_033805	220906	Hs.403253	NR_033805		WAC-AS1	-	WAC antisense RNA 1 (head to head)	ncRNA	0.014749	0.497059	
chunk0068_369_1	chr15	58095506	58095705	+	0	NA	Intergenic	Intergenic	-29682	NM_003888	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.005025	0.425000	
chunk0177_457_1	chr7	28553342	28553620	+	0	NA	intron (NM_182899, intron 3 of 9)	intron (NM_182899, intron 3 of 9)	117866	NM_004904	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.000000	0.379928	
chunk0085_58_1	chr18	1075340	1075913	+	0	NA	Intergenic	Intergenic	170430	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.008726	0.404181	
chunk0117_62_1	chr22	16699377	16699717	+	0	NA	Intergenic	Intergenic	-24007	NR_040115	23783	Hs.627452	NR_040115		ANKRD62P1-PARP4P3	VWFP1-ANKRD62P1-PARP4P3	ANKRD62P1-PARP4P3 readthrough, transcribed pseudogene	pseudo	0.014706	0.454545	
chunk0208_390_1	chrX	28886946	28887162	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	299490	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.004630	0.350230	
chunk0142_371_1	chr4	102036468	102037040	+	0	NA	intron (NM_017935, intron 10 of 16)	intron (NM_017935, intron 10 of 16)	222928	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.008741	0.397906	299(TAGAACATCATGATCC,-,0.00),300(AGAACATCATGATCCC,+,0.00)
chunk0027_433_1	chr10	81002438	81002647	+	0	NA	Intergenic	Intergenic	461723	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.000000	0.419048	
chunk0212_254_1	chrX	139126517	139126820	+	0	NA	intron (NM_001139501, intron 2 of 7)	intron (NM_001139501, intron 2 of 7)	78355	NM_001139500	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.006601	0.480263	220(AGTACAACCTGCTCCT,+,0.00)
chunk0189_211_1	chr8	24302820	24303324	+	0	NA	intron (NR_125808, intron 3 of 5)	L1PA10|LINE|L1	9032	NM_021777	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.001984	0.354455	
chunk0014_228_1	chr1	179847451	179847784	+	0	NA	exon (NM_001199260, exon 6 of 7)	exon (NM_001199260, exon 6 of 7)	30189	NM_145034	163590	Hs.571797	NM_022347	ENSG00000169905	TOR1AIP2	IFRG15|LULL1|NET9	torsin 1A interacting protein 2	protein-coding	0.003003	0.377246	
chunk0115_367_1	chr21	30119545	30120202	+	0	NA	Intergenic	Intergenic	46780	NM_012131	26285	Hs.258589	NM_012131	ENSG00000156282	CLDN17	-	claudin 17	protein-coding	0.006088	0.392097	
chunk0192_440_1	chr8	69766106	69766311	+	0	NA	intron (NM_030958, intron 2 of 9)	L2a|LINE|L2	66961	NM_001146009	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.000000	0.514563	
chunk0209_119_1	chrX	40544841	40545062	+	0	NA	Intergenic	Intergenic	-36013	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.013575	0.504505	
chunk0115_376_1	chr21	30226962	30227507	+	0	NA	Intergenic	Intergenic	-11083	NM_199328	9073	Hs.162209	NM_012132	ENSG00000156284	CLDN8	HEL-S-79	claudin 8	protein-coding	0.000000	0.395604	
chunk0164_73_1	chr6	19669003	19669253	+	0	NA	Intergenic	Intergenic	-168242	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.004000	0.370518	
chunk0064_266_1	chr14	94813701	94813964	+	0	NA	Intergenic	Intergenic	-43670	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.019011	0.500000	
chunk0064_277_1	chr14	95146096	95146342	+	0	NA	intron (NM_030621, intron 1 of 28)	LTR27C|LTR|ERV1	-8233	NR_036131	100422981		NR_036131	ENSG00000264607	MIR3173	mir-3173	microRNA 3173	ncRNA	0.008130	0.445344	
chunk0081_145_1	chr17	40718518	40719225	+	0	NA	Intergenic	Intergenic	-15121	NM_019016	192666	Hs.87383	NM_019016	ENSG00000167916	KRT24	K24|KA24	keratin 24	protein-coding	0.016973	0.408192	
chunk0090_410_1	chr18	78925905	78926453	+	0	NA	Intergenic	L1MB7|LINE|L1	-54096	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.067518	0.619308	
chunk0024_282_1	chr10	41903408	41903622	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	464530	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.018692	0.423256	
chunk0141_233_1	chr4	84886827	84887269	+	0	NA	intron (NM_014991, intron 3 of 67)	intron (NM_014991, intron 3 of 67)	79343	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.002262	0.365688	
chunk0022_90_1	chr10	9229773	9229972	+	0	NA	intron (NR_120635, intron 4 of 4)	intron (NR_120635, intron 4 of 4)	-45741	NR_108039	100507163	Hs.649223	NR_108039		LINC00709	-	long intergenic non-protein coding RNA 709	ncRNA	0.015075	0.465000	
chunk0115_245_1	chr21	27492772	27493461	+	0	NA	Intergenic	Intergenic	-229263	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.005806	0.347826	
chunk0059_362_1	chr14	37303473	37304000	+	0	NA	intron (NM_001195296, intron 9 of 14)	L2a|LINE|L2	105823	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.000000	0.321970	
chunk0020_30_1	chr1	232029445	232029783	+	0	NA	intron (NM_001012957, intron 12 of 12)	intron (NM_001012957, intron 12 of 12)	103780	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.005917	0.418879	
chunk0093_352_1	chr19	55258934	55259721	+	0	NA	promoter-TSS (NM_014931)	promoter-TSS (NM_014931)	-657	NM_014931	22870	Hs.515610	NM_014931	ENSG00000105063	PPP6R1	KIAA1115|PP6R1|SAP190|SAPS1	protein phosphatase 6 regulatory subunit 1	protein-coding	0.085133	0.618020	
chunk0197_39_1	chr8	118168356	118168555	+	0	NA	Intergenic	Intergenic	-56636	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.010050	0.415000	
chunk0052_438_1	chr12	132338680	132338947	+	0	NA	Intergenic	Intergenic	8963	NR_120467	101928416		NR_120467	ENSG00000255916	LOC101928416	-	uncharacterized LOC101928416	ncRNA	0.056180	0.604478	120(GTGAACATCATGTTCT,-,0.00),121(TGAACATCATGTTCTG,+,0.00)
chunk0098_406_1	chr2	79890546	79890910	+	0	NA	intron (NM_004389, intron 6 of 17)	MLT1A0|LTR|ERVL-MaLR	-24145	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.005495	0.386301	
chunk0178_186_1	chr7	34261352	34261621	+	0	NA	Intergenic	LTR85c|LTR|Gypsy?	356575	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.007435	0.400000	
chunk0164_12_1	chr6	17835499	17835916	+	0	NA	intron (NM_022113, intron 11 of 38)	L2c|LINE|L2	-128873	NM_001278210	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.000000	0.318182	
chunk0033_209_1	chr11	16999228	16999427	+	0	NA	intron (NM_175058, intron 3 of 22)	intron (NM_175058, intron 3 of 22)	15089	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.005025	0.530000	
chunk0084_246_1	chr17	78933438	78933637	+	0	NA	Intergenic	Intergenic	-8147	NM_003255	7077	Hs.633514	NM_003255	ENSG00000035862	TIMP2	CSC-21K|DDC8	TIMP metallopeptidase inhibitor 2	protein-coding	0.015075	0.555000	
chunk0106_44_1	chr2	196233060	196233259	+	0	NA	intron (NM_020760, intron 21 of 28)	intron (NM_020760, intron 21 of 28)	-26865	NR_110225	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.020101	0.435000	
chunk0033_328_1	chr11	22160234	22160433	+	0	NA	Intergenic	MER67C|LTR|ERV1	-32843	NM_213599	203859	Hs.154329	NM_213599	ENSG00000171714	ANO5	GDD1|LGMD2L|LGMDR12|TMEM16E	anoctamin 5	protein-coding	0.000000	0.445000	
chunk0186_438_1	chr7	147040040	147040239	+	0	NA	intron (NM_014141, intron 3 of 23)	L1PA14|LINE|L1	57470	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.005025	0.345000	
chunk0132_224_1	chr3	157981757	157982518	+	0	NA	Intergenic	Intergenic	124026	NM_001163678	6474	Hs.55967	NM_003030	ENSG00000168779	SHOX2	OG12|OG12X|SHOT	short stature homeobox 2	protein-coding	0.005256	0.391076	
chunk0111_409_1	chr20	34533050	34533629	+	0	NA	intron (NM_001281729, intron 3 of 4)	intron (NM_001281729, intron 3 of 4)	-13545	NM_181509	84557	Hs.632273	NM_032514	ENSG00000101460	MAP1LC3A	ATG8E|LC3|LC3A|MAP1ALC3|MAP1BLC3	microtubule associated protein 1 light chain 3 alpha	protein-coding	0.020725	0.503448	302(AGGGTCAACATGTTCC,-,0.00)
chunk0111_254_1	chr20	30811946	30812519	+	0	NA	Intergenic	Intergenic	-408770	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.036649	0.585366	
chunk0080_242_1	chr17	30253239	30253761	+	0	NA	intron (NM_000386, intron 11 of 11)	intron (NM_000386, intron 11 of 11)	-17532	NM_001045	6532	Hs.29792	NM_001045	ENSG00000108576	SLC6A4	5-HTT|5-HTTLPR|5HTT|HTT|OCD1|SERT|SERT1|hSERT	solute carrier family 6 member 4	protein-coding	0.013410	0.447419	
chunk0172_262_1	chr6	137448317	137448792	+	0	NA	Intergenic	Intergenic	45840	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.006316	0.355042	
chunk0115_80_1	chr21	22033063	22033323	+	0	NA	intron (NR_109959, intron 4 of 5)	ERV3-16A3_I-int|LTR|ERVL	65266	NR_109959	101927843	Hs.652879	NR_109959	ENSG00000233215	LINC01687	-	long intergenic non-protein coding RNA 1687	ncRNA	0.003846	0.417625	
chunk0156_229_1	chr5	108286169	108286392	+	0	NA	intron (NM_001163315, intron 4 of 8)	L1PA15|LINE|L1	95818	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.000000	0.383929	63(AAGAACAGGATGTCCT,-,0.00),64(AGAACAGGATGTCCTC,+,0.00)
chunk0182_212_1	chr7	96319432	96319952	+	0	NA	intron (NR_027662, intron 1 of 16)	L4_A_Mam|LINE|RTE-X	2455	NM_014251	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.000000	0.391555	234(AAGCACATAATGTTCC,-,0.00),235(AGCACATAATGTTCCA,+,0.00)
chunk0092_170_1	chr19	29912754	29913338	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-10598	NM_001252641	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.015411	0.410256	285(TGGCACTGACTGTACT,-,0.00),286(GGCACTGACTGTACTA,+,0.00)
chunk0106_227_1	chr2	202601940	202602309	+	0	NA	Intergenic	Intergenic	-33054	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.008130	0.375676	
chunk0207_69_1	chrX	9102790	9103508	+	0	NA	Intergenic	L1MC4|LINE|L1	-69022	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.006964	0.344924	354(ATGCACACTGTGTTCT,-,0.00),355(TGCACACTGTGTTCTT,+,0.00)
chunk0166_341_1	chr6	50978106	50978652	+	0	NA	Intergenic	Intergenic	159653	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.007326	0.414991	219(CAGGACAGAATGTCCC,-,0.00),220(AGGACAGAATGTCCCC,+,0.00)
chunk0056_212_1	chr13	86414904	86415144	+	0	NA	Intergenic	Intergenic	-496896	NR_132371	106144533	Hs.525107	NR_132371		LINC00430	-	long intergenic non-protein coding RNA 430	ncRNA	0.004167	0.402490	
chunk0158_85_1	chr5	126518883	126519087	+	0	NA	Intergenic	AluSx1|SINE|Alu	53890	NM_001146322	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.014706	0.492683	
chunk0019_192_1	chr1	226709021	226709348	+	0	NA	intron (NM_002221, intron 2 of 7)	MER53|DNA|hAT	29991	NM_002221	3707	Hs.528087	NM_002221	ENSG00000143772	ITPKB	IP3-3KB|IP3K|IP3K-B|IP3KB|PIG37	inositol-trisphosphate 3-kinase B	protein-coding	0.009174	0.542683	
chunk0156_308_1	chr5	110703506	110704060	+	0	NA	intron (NM_001039763, intron 1 of 13)	ERV24B_Prim-int|LTR|ERV1	22966	NM_001039763	642987	Hs.729154	NM_001039763	ENSG00000186952	TMEM232	-	transmembrane protein 232	protein-coding	0.005415	0.362162	237(TGGGACAGATAGTTCT,-,0.00),238(GGGACAGATAGTTCTC,+,0.00)
chunk0150_104_1	chr5	32791201	32791999	+	0	NA	3' UTR (NM_001204376, exon 8 of 8)	3' UTR (NM_001204376, exon 8 of 8)	80268	NM_001204375	4883	Hs.13528	NM_000908	ENSG00000113389	NPR3	ANP-C|ANPR-C|ANPRC|C5orf23|GUCY2B|NPR-C|NPRC	natriuretic peptide receptor 3	protein-coding	0.011278	0.369212	480(ATAACAATGTGTTCTC,+,0.00)
chunk0080_320_1	chr17	32157041	32157662	+	0	NA	intron (NM_001288755, intron 1 of 18)	L2a|LINE|L2	-5780	NR_002222	503640	Hs.631752	NR_002222		ARGFXP2	-	arginine-fifty homeobox pseudogene 2	pseudo	0.009662	0.392283	
chunk0052_361_1	chr12	127401681	127401978	+	0	NA	Intergenic	MER57A1|LTR|ERV1	-61757	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.010101	0.402685	
chunk0107_413_1	chr2	224268345	224268721	+	0	NA	Intergenic	Intergenic	133461	NM_024785	79843	Hs.147585	NM_024785	ENSG00000124019	FAM124B	-	family with sequence similarity 124 member B	protein-coding	0.005319	0.363395	
chunk0006_17_1	chr1	63928512	63929265	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	154869	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.005312	0.431034	394(AAGGACACAGTGTGCC,-,0.00),395(AGGACACAGTGTGCCC,+,0.00)
chunk0043_462_1	chr12	26769195	26769575	+	0	NA	intron (NM_002223, intron 2 of 56)	intron (NM_002223, intron 2 of 56)	63813	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.002632	0.367454	
chunk0020_286_1	chr1	237002457	237002728	+	0	NA	Intergenic	Intergenic	1826	NM_001276687	645745	Hs.632513	NM_001039954	ENSG00000244020	MT1HL1	MT1P2	metallothionein 1H like 1	protein-coding	0.014760	0.522059	82(AGGGACAGACTGTGCT,-,0.00),83(GGGACAGACTGTGCTC,+,0.00)
chunk0149_234_1	chr5	23324988	23325551	+	0	NA	Intergenic	Intergenic	-182340	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.005329	0.400709	
chunk0155_197_1	chr5	94757036	94757391	+	0	NA	intron (NM_024717, intron 19 of 22)	intron (NM_024717, intron 19 of 22)	138527	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.011268	0.412921	
chunk0047_382_1	chr12	75270644	75271270	+	0	NA	Intergenic	L2b|LINE|L2	59099	NM_032606	84698	Hs.733835	NM_032606	ENSG00000180881	CAPS2	UG0636c06	calcyphosine 2	protein-coding	0.007987	0.377990	
chunk0118_242_1	chr22	32680292	32680501	+	0	NA	intron (NM_003490, intron 5 of 12)	L2c|LINE|L2	-120420	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.000000	0.409524	
chunk0176_311_1	chr7	16905186	16905712	+	0	NA	Intergenic	L1MEc|LINE|L1	-23460	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.007605	0.409867	
chunk0186_361_1	chr7	143896312	143896633	+	0	NA	intron (NM_001206938, intron 1 of 8)	L1ME3D|LINE|L1	5607	NM_014719	9747	Hs.735149	NM_014719	ENSG00000198420	TCAF1	FAM115A	TRPM8 channel associated factor 1	protein-coding	0.006231	0.301242	
chunk0085_154_1	chr18	3530450	3530848	+	0	NA	intron (NM_001308390, intron 8 of 10)	intron (NM_001308390, intron 8 of 10)	-63465	NR_024101	649446	Hs.19872	NM_001039796		DLGAP1-AS1	HsT914	DLGAP1 antisense RNA 1	ncRNA	0.002513	0.433584	
chunk0187_230_1	chr7	152436126	152436482	+	0	NA	promoter-TSS (NR_002935)	promoter-TSS (NR_002935)	-299	NM_170606	58508	Hs.647120	NM_021230	ENSG00000055609	KMT2C	HALR|KLEFS2|MLL3	lysine methyltransferase 2C	protein-coding	0.162921	0.803922	
chunk0095_331_1	chr2	20704438	20704777	+	0	NA	intron (NM_001282723, intron 4 of 5)	L1ME4a|LINE|L1	37943	NM_182828	151449	Hs.447688	NM_182828	ENSG00000143869	GDF7	BMP12	growth differentiation factor 7	protein-coding	0.002950	0.288235	124(TAGTACAGTATGATCC,-,0.00),125(AGTACAGTATGATCCC,+,0.00)
chunk0068_187_1	chr15	54793440	54793671	+	0	NA	Intergenic	Intergenic	403478	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004329	0.254310	
chunk0037_262_1	chr11	75637047	75637633	+	0	NA	intron (NM_207577, intron 1 of 2)	intron (NM_207577, intron 1 of 2)	31094	NM_033063	4135	Hs.585540	NM_033063	ENSG00000171533	MAP6	MAP6-N|MTAP6|N-STOP|STOP	microtubule associated protein 6	protein-coding	0.003413	0.373083	
chunk0045_358_1	chr12	51975318	51975577	+	0	NA	exon (NM_020328, exon 2 of 10)	exon (NM_020328, exon 2 of 10)	22067	NM_020327	91	Hs.438918	NM_004302	ENSG00000135503	ACVR1B	ACTRIB|ACVRLK4|ALK4|SKR2	activin A receptor type 1B	protein-coding	0.023166	0.561538	
chunk0088_323_1	chr18	50970012	50970235	+	0	NA	intron (NM_018696, intron 1 of 3)	AluJr|SINE|Alu	2106	NM_018696	55520	Hs.657360	NM_018696	ENSG00000141642	ELAC1	D29	elaC ribonuclease Z 1	protein-coding	0.000000	0.446429	
chunk0125_445_1	chr3	72820981	72821588	+	0	NA	intron (NM_018130, intron 6 of 10)	intron (NM_018130, intron 6 of 10)	27163	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.011532	0.434211	
chunk0140_361_1	chr4	74253485	74253916	+	0	NA	intron (NM_001144978, intron 6 of 7)	L1M3e|LINE|L1	-54770	NM_001270991	255324	Hs.401237	NM_001013442	ENSG00000182585	EPGN	ALGV3072|EPG|PRO9904	epithelial mitogen	protein-coding	0.006961	0.574074	
chunk0192_388_1	chr8	68731628	68732319	+	0	NA	intron (NM_052958, intron 10 of 13)	Charlie17a|DNA|hAT-Charlie	372217	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.007236	0.345376	
chunk0046_320_1	chr12	62533320	62534120	+	0	NA	intron (NM_001278469, intron 12 of 35)	L1MC4|LINE|L1	66903	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.005000	0.392010	287(TAGAACAAGATGTTCC,-,0.00),288(AGAACAAGATGTTCCA,+,0.00)
chunk0045_424_1	chr12	53250535	53250847	+	0	NA	promoter-TSS (NM_001170790)	promoter-TSS (NM_001170790)	-895	NM_001170790	84975	Hs.654660	NM_032889	ENSG00000182544	MFSD5	hsMOT2	major facilitator superfamily domain containing 5	protein-coding	0.003205	0.424920	
chunk0171_175_1	chr6	125113035	125113234	+	0	NA	Intergenic	Intergenic	-40595	NM_001300994	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.000000	0.560000	
chunk0181_92_1	chr7	80386185	80386394	+	0	NA	Intergenic	MIRb|SINE|MIR	-11850	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.004785	0.319048	
chunk0129_453_1	chr3	128241598	128242137	+	0	NA	intron (NM_021937, intron 1 of 6)	MIR|SINE|MIR	88410	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.009276	0.411111	
chunk0017_233_1	chr1	208055609	208056026	+	0	NA	intron (NM_025179, intron 13 of 31)	UCON7|DNA?|DNA?	-144479	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.023981	0.373206	
chunk0094_91_1	chr2	4054529	4054728	+	0	NA	Intergenic	Intergenic	-80596	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.010050	0.400000	
chunk0164_315_1	chr6	25051038	25051567	+	0	NA	Intergenic	Intergenic	-9134	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.003781	0.383019	
chunk0075_454_1	chr16	58384364	58384769	+	0	NA	Intergenic	HAL1ME|LINE|L1	-7828	NM_001126129	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.012346	0.460591	
chunk0024_354_1	chr10	43703837	43704059	+	0	NA	Intergenic	Intergenic	-55070	NM_006973	7580	Hs.522885	NM_006973	ENSG00000169740	ZNF32	KOX30	zinc finger protein 32	protein-coding	0.009009	0.408072	
chunk0002_355_1	chr1	25872338	25872537	+	0	NA	Intergenic	L2c|LINE|L2	-1184	NM_178422	164091	Hs.523652	NM_178422	ENSG00000182749	PAQR7	MPRA|PGLP|mSR	progestin and adipoQ receptor family member 7	protein-coding	0.010050	0.450000	
chunk0191_17_1	chr8	42660640	42661018	+	0	NA	Intergenic	Intergenic	-36590	NM_000749	1142	Hs.654576	NM_000749	ENSG00000147432	CHRNB3	-	cholinergic receptor nicotinic beta 3 subunit	protein-coding	0.021164	0.464380	
chunk0166_259_1	chr6	47634309	47634886	+	0	NA	Intergenic	MER110|LTR|ERV1	-21993	NM_153839	222611	Hs.724860	NM_153839	ENSG00000164393	ADGRF2	GPR111|PGR20|hGPCR35	adhesion G protein-coupled receptor F2	protein-coding	0.005199	0.371972	
chunk0107_163_1	chr2	215397702	215397901	+	0	NA	exon (NM_212482, exon 22 of 46)	exon (NM_212482, exon 22 of 46)	38267	NM_212476	2335	Hs.203717	NM_002026	ENSG00000115414	FN1	CIG|ED-B|FINC|FN|FNZ|GFND|GFND2|LETS|MSF|SMDCF	fibronectin 1	protein-coding	0.030151	0.510000	
chunk0075_328_1	chr16	54655665	54655967	+	0	NA	Intergenic	Intergenic	272962	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.016556	0.386139	
chunk0008_39_1	chr1	88891413	88891839	+	0	NA	promoter-TSS (NM_001514)	promoter-TSS (NM_001514)	-8	NM_001514	2959	Hs.481852	NM_001514	ENSG00000137947	GTF2B	TF2B|TFIIB	general transcription factor IIB	protein-coding	0.079812	0.548009	239(AAGAACAGTGAGATCC,-,0.00),240(AGAACAGTGAGATCCC,+,0.00)
chunk0107_406_1	chr2	224086135	224086607	+	0	NA	Intergenic	Intergenic	-47052	NM_006216	5270	Hs.38449	NM_006216	ENSG00000135919	SERPINE2	GDN|GDNPF|PI-7|PI7|PN-1|PN1|PNI	serpin family E member 2	protein-coding	0.006356	0.350951	
chunk0042_104_1	chr12	3047943	3048642	+	0	NA	Intergenic	L2a|LINE|L2	-29063	NM_006675	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.012876	0.528571	
chunk0071_65_1	chr15	80520560	80521207	+	0	NA	intron (NM_014862, intron 8 of 18)	MER75|DNA|PiggyBac	42061	NR_120363	101929586	Hs.569426	NR_120363	ENSG00000259175	LOC101929586	-	uncharacterized LOC101929586	ncRNA	0.006182	0.311728	
chunk0212_382_1	chrX	150270686	150270942	+	0	NA	Intergenic	Intergenic	42810	NR_031748	100313839		NR_031748	ENSG00000252454	MIR2114	-	microRNA 2114	ncRNA	0.011719	0.482490	
chunk0184_217_1	chr7	117379666	117379952	+	0	NA	intron (NM_130768, intron 10 of 12)	intron (NM_130768, intron 10 of 12)	47714	NM_001301821	136991	Hs.352412	NM_130768	ENSG00000154438	ASZ1	ALP1|ANKL1|C7orf7|CT1.19|GASZ|Orf3	ankyrin repeat, SAM and basic leucine zipper domain containing 1	protein-coding	0.000000	0.254355	
chunk0139_400_1	chr4	63260985	63261184	+	0	NA	Intergenic	Intergenic	-1099319	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.005025	0.295000	
chunk0165_300_1	chr6	36679069	36679928	+	0	NA	intron (NM_001220778, intron 1 of 2)	CpG	788	NM_001220778	1026	Hs.370771	NM_000389	ENSG00000124762	CDKN1A	CAP20|CDKN1|CIP1|MDA-6|P21|SDI1|WAF1|p21CIP1	cyclin dependent kinase inhibitor 1A	protein-coding	0.074505	0.679070	513(TGGAACAGTTTGTTCC,-,0.00),514(GGAACAGTTTGTTCCC,+,0.00),700(CGGCCCAGCCTGTCCT,-,0.00),701(GGCCCAGCCTGTCCTC,+,0.00)
chunk0047_409_1	chr12	75893590	75894169	+	0	NA	Intergenic	Intergenic	137897	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.008636	0.346552	
chunk0013_72_1	chr1	167542619	167542964	+	0	NA	intron (NM_003851, intron 3 of 3)	intron (NM_003851, intron 3 of 3)	11028	NM_003851	8804	Hs.5710	NM_003851	ENSG00000143162	CREG1	CREG	cellular repressor of E1A stimulated genes 1	protein-coding	0.005797	0.450867	
chunk0047_254_1	chr12	72482539	72483374	+	0	NA	intron (NM_013381, intron 5 of 18)	intron (NM_013381, intron 5 of 18)	-209447	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.001198	0.333732	232(ATTACATTCTGTTCCT,+,0.00)
chunk0145_130_1	chr4	146379786	146379999	+	0	NA	intron (NM_001029998, intron 5 of 11)	intron (NM_001029998, intron 5 of 11)	-28691	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.004695	0.373832	
chunk0032_395_1	chr11	11616035	11616572	+	0	NA	intron (NM_198516, intron 1 of 10)	L1ME4c|LINE|L1	5711	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.003724	0.388476	
chunk0090_160_1	chr18	72483909	72484676	+	0	NA	Intergenic	Intergenic	60196	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.007823	0.319010	
chunk0195_50_1	chr8	93496575	93496784	+	0	NA	intron (NR_033858, intron 7 of 10)	MER63A|DNA|hAT-Blackjack	203754	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.019139	0.385714	
chunk0196_121_1	chr8	103613965	103614320	+	0	NA	intron (NM_001100117, intron 1 of 23)	L1MA2|LINE|L1	113394	NM_001100117	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.011268	0.519663	
chunk0038_35_1	chr11	81217631	81218007	+	0	NA	Intergenic	Intergenic	-455016	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.005319	0.371353	
chunk0025_175_1	chr10	52837412	52837959	+	0	NA	Intergenic	LTR37A|LTR|ERV1	-65985	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.007313	0.328467	
chunk0003_126_1	chr1	32570566	32570778	+	0	NA	intron (NR_111980, intron 2 of 3)	L1ME2|LINE|L1	31527	NM_001291496	653121	Hs.546479	NM_144621	ENSG00000160062	ZBTB8A	BOZF1|ZBTB8|ZNF916A	zinc finger and BTB domain containing 8A	protein-coding	0.004717	0.272300	
chunk0204_64_1	chr9	93523529	93523846	+	0	NA	intron (NM_001286723, intron 7 of 9)	intron (NM_001286723, intron 7 of 9)	-52940	NM_005392	5253	Hs.211441	NM_005392	ENSG00000197724	PHF2	CENP-35|GRC5|JHDM1E|KDM7C	PHD finger protein 2	protein-coding	0.015773	0.437107	
chunk0128_442_1	chr3	115062069	115062329	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	9215	NM_001164343	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.007692	0.448276	
chunk0170_334_1	chr6	116258882	116259081	+	0	NA	Intergenic	Intergenic	-4883	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.010050	0.495000	
chunk0121_209_1	chr3	21643610	21644339	+	0	NA	intron (NM_024697, intron 2 of 7)	intron (NM_024697, intron 2 of 7)	101185	NR_046731	100874216	Hs.661720	NR_046731	ENSG00000225542	ZNF385D-AS1	-	ZNF385D antisense RNA 1	ncRNA	0.002743	0.379452	383(AAGAACAGGATGTCTC,-,0.00),384(AGAACAGGATGTCTCC,+,0.00)
chunk0022_287_1	chr10	15461364	15461579	+	0	NA	Intergenic	Intergenic	-90412	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.009302	0.453704	
chunk0200_393_1	chr9	27054962	27055161	+	0	NA	intron (NM_001099222, intron 16 of 19)	Tigger17a|DNA|TcMar-Tigger	-49368	NM_022901	64922	Hs.128071	NM_022901	ENSG00000184434	LRRC19	-	leucine rich repeat containing 19	protein-coding	0.000000	0.325000	
chunk0121_454_1	chr3	26958810	26959305	+	0	NA	Intergenic	L1PA6|LINE|L1	257466	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.008081	0.508065	
chunk0091_44_1	chr19	4268225	4268662	+	0	NA	intron (NM_018074, intron 7 of 7)	intron (NM_018074, intron 7 of 7)	-10158	NM_020209	56961	Hs.7423	NM_020209	ENSG00000105251	SHD	-	Src homology 2 domain containing transforming protein D	protein-coding	0.036613	0.573059	
chunk0062_272_1	chr14	71985736	71986130	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	52864	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.002538	0.394937	
chunk0125_65_1	chr3	64266352	64267122	+	0	NA	Intergenic	Intergenic	-41282	NM_198859	166336	Hs.148105	NM_198859	ENSG00000163637	PRICKLE2	EPM5	prickle planar cell polarity protein 2	protein-coding	0.006494	0.433204	
chunk0098_413_1	chr2	79994209	79994410	+	0	NA	intron (NM_004389, intron 7 of 17)	intron (NM_004389, intron 7 of 17)	-127726	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.019900	0.400990	
chunk0053_148_1	chr13	30192631	30193048	+	0	NA	Intergenic	Intergenic	-83964	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.016787	0.500000	
chunk0156_302_1	chr5	110391562	110392001	+	0	NA	Intergenic	Intergenic	122134	NR_031644	100302159		NR_031644	ENSG00000221436	MIR548F3	MIR548F-3|MIRN548F3|hsa-mir-548f-3	microRNA 548f-3	ncRNA	0.006834	0.327273	
chunk0107_32_1	chr2	210440208	210440492	+	0	NA	intron (NM_001136574, intron 6 of 9)	intron (NM_001136574, intron 6 of 9)	36355	NM_001136574	10314	Hs.13351	NM_006055	ENSG00000115365	LANCL1	GPR69A|p40	LanC like 1	protein-coding	0.010563	0.371930	
chunk0123_257_1	chr3	45861386	45861846	+	0	NA	intron (NM_001276378, intron 2 of 11)	(TG)n|Simple_repeat|Simple_repeat	-19458	NR_075080	54585	Hs.30824	NM_020347	ENSG00000163818	LZTFL1	BBS17	leucine zipper transcription factor like 1	protein-coding	0.004348	0.383948	
chunk0061_113_1	chr14	58272523	58272783	+	0	NA	TTS (NM_152132)	TTS (NM_152132)	25484	NR_029435	379025	Hs.531089	NR_029434	ENSG00000257621	PSMA3-AS1	-	PSMA3 antisense RNA 1	ncRNA	0.007692	0.409962	
chunk0188_226_1	chr8	12829218	12829456	+	0	NA	Intergenic	Intergenic	-17936	NR_015383	340357	Hs.434302	NR_015383	ENSG00000254813	LOC340357	-	uncharacterized LOC340357	ncRNA	0.008403	0.364017	
chunk0020_194_1	chr1	234918021	234918621	+	0	NA	Intergenic	Intergenic	45678	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.035000	0.537438	
chunk0063_101_1	chr14	78654545	78654927	+	0	NA	intron (NR_073547, intron 6 of 20)	L2a|LINE|L2	251005	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.007853	0.378590	
chunk0189_53_1	chr8	20016611	20017106	+	0	NA	Intergenic	Intergenic	77787	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.004040	0.350806	
chunk0026_398_1	chr10	69769306	69769806	+	0	NA	Intergenic	Intergenic	-32332	NM_001130103	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.014000	0.542914	
chunk0110_16_1	chr20	10185767	10186550	+	0	NA	intron (NR_040710, intron 2 of 4)	MLT1H|LTR|ERVL-MaLR	-32671	NM_003081	6616	Hs.167317	NM_003081	ENSG00000132639	SNAP25	CMS18|RIC-4|RIC4|SEC9|SNAP|SNAP-25|SUP|bA416N4.2|dJ1068F16.2	synaptosome associated protein 25	protein-coding	0.001277	0.457908	
chunk0197_104_1	chr8	119746811	119747080	+	0	NA	intron (NM_003184, intron 22 of 25)	intron (NM_003184, intron 22 of 25)	85889	NM_003184	6873	Hs.122752	NM_003184	ENSG00000064313	TAF2	CIF150|MRT40|TAF2B|TAFII150	TATA-box binding protein associated factor 2	protein-coding	0.003717	0.377778	
chunk0149_378_1	chr5	28387123	28387328	+	0	NA	Intergenic	LTR80A|LTR|ERVL	-539645	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.000000	0.339806	
chunk0022_427_1	chr10	19184947	19185411	+	0	NA	intron (NM_001142308, intron 14 of 39)	intron (NM_001142308, intron 14 of 39)	136408	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.004310	0.286022	
chunk0082_302_1	chr17	58666117	58667646	+	0	NA	intron (NM_001201457, intron 1 of 32)	intron (NM_001201457, intron 1 of 32)	25174	NM_001201457	56155	Hs.390221	NM_031272	ENSG00000121101	TEX14	CT113|SPGF23	testis expressed 14, intercellular bridge forming factor	protein-coding	0.028777	0.450327	
chunk0073_364_1	chr16	15060279	15060942	+	0	NA	3' UTR (NM_018427, exon 18 of 18)	3' UTR (NM_018427, exon 18 of 18)	-4531	NM_001270767	123803	Hs.592045	NM_173474	ENSG00000157045	NTAN1	PNAA|PNAD	N-terminal asparagine amidase	protein-coding	0.009050	0.352410	
chunk0067_89_1	chr15	41925278	41925619	+	0	NA	intron (NR_120332, intron 1 of 3)	intron (NR_120332, intron 1 of 3)	4031	NR_120332	101928363	Hs.680195	NR_120332		EHD4-AS1	-	EHD4 antisense RNA 1	ncRNA	0.017595	0.438596	
chunk0098_115_1	chr2	68538900	68539109	+	0	NA	intron (NM_173545, intron 7 of 9)	intron (NM_173545, intron 7 of 9)	71445	NM_173545	200558	Hs.720369	NM_173545	ENSG00000169621	APLF	APFL|C2orf13|PALF|Xip1|ZCCHH1	aprataxin and PNKP like factor	protein-coding	0.000000	0.300000	54(AAAACATTCAGTTCCC,+,0.00)
chunk0117_336_1	chr22	25148467	25148681	+	0	NA	intron (NM_001145206, intron 4 of 10)	intron (NM_001145206, intron 4 of 10)	-35882	NR_038941	100128531	Hs.662126	NR_038941	ENSG00000203280	LOC100128531	-	uncharacterized LOC100128531	ncRNA	0.014019	0.567442	
chunk0076_201_1	chr16	68047986	68048580	+	0	NA	intron (NM_017803, intron 3 of 16)	intron (NM_017803, intron 3 of 16)	-24416	NM_018380	55794	Hs.458313	NM_018380	ENSG00000182810	DDX28	MDDX28	DEAD-box helicase 28	protein-coding	0.003367	0.442017	
chunk0091_191_1	chr19	8421963	8422314	+	0	NA	intron (NM_001005415, intron 2 of 4)	intron (NM_001005415, intron 2 of 4)	8835	NM_001005415	51257	Hs.631861	NM_016496	ENSG00000099785	MARCH2	HSPC240|MARCH-II|RNF172	membrane associated ring-CH-type finger 2	protein-coding	0.028490	0.517045	
chunk0071_143_1	chr15	82726236	82726522	+	0	NA	non-coding (NR_036446, exon 3 of 3)	non-coding (NR_036446, exon 3 of 3)	-12386	NR_034139	338963	Hs.254464	NR_034139	ENSG00000228141	LOC338963	-	epididymal protein pseudogene	pseudo	0.010490	0.512195	
chunk0047_388_1	chr12	75492570	75492999	+	0	NA	intron (NM_006851, intron 3 of 5)	L2c|LINE|L2	12051	NM_006851	11010	Hs.205558	NM_006851	ENSG00000139278	GLIPR1	CRISP7|GLIPR|RTVP1	GLI pathogenesis related 1	protein-coding	0.000000	0.297674	
chunk0124_169_1	chr3	55279221	55279738	+	0	NA	Intergenic	Intergenic	201919	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.011605	0.370656	
chunk0111_440_1	chr20	35269055	35269523	+	0	NA	intron (NM_006690, intron 6 of 8)	MIRb|SINE|MIR	8868	NR_102706									0.019231	0.558635	
chunk0118_248_1	chr22	32791055	32791411	+	0	NA	intron (NM_003490, intron 5 of 12)	MIR|SINE|MIR	-9583	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.014045	0.420168	
chunk0193_130_1	chr8	74377847	74378206	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	27643	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.005571	0.394444	49(ATGAACAAACTGTTCT,-,0.00),50(TGAACAAACTGTTCTA,+,0.00)
chunk0060_268_1	chr14	50339012	50339684	+	0	NA	intron (NM_001282236, intron 6 of 8)	intron (NM_001282236, intron 6 of 8)	27019	NM_015684	27109	Hs.438489	NM_015684	ENSG00000125375	DMAC2L	ATP5S|ATPW|FB|HSU79253	distal membrane arm assembly complex 2 like	protein-coding	0.004464	0.429421	
chunk0165_251_1	chr6	35687673	35688113	+	0	NA	intron (NM_001145775, intron 2 of 11)	CpG	1022	NM_001145776	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.063636	0.498866	83(CTGAACACACTGTCCT,-,0.00),84(TGAACACACTGTCCTG,+,0.00)
chunk0025_107_1	chr10	50884463	50884721	+	0	NA	intron (NM_014576, intron 1 of 12)	intron (NM_014576, intron 1 of 12)	1083	NM_138933	29974	Hs.282795	NM_014576	ENSG00000148584	A1CF	ACF|ACF64|ACF65|APOBEC1CF|ASP	APOBEC1 complementation factor	protein-coding	0.007752	0.339768	
chunk0010_226_1	chr1	116322952	116324036	+	0	NA	Intergenic	Intergenic	-49679	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.003690	0.379724	303(AAGAACAGACAGTTCA,-,0.00),304(AGAACAGACAGTTCAT,+,0.00)
chunk0187_393_1	chr7	157777132	157777789	+	0	NA	intron (NM_001308268, intron 12 of 22)	intron (NM_001308268, intron 12 of 22)	-77125	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.024353	0.519757	198(GAGGACACGCAGTGCC,-,0.00),199(AGGACACGCAGTGCCC,+,0.00),254(GAGGACACGCAGTGCC,-,0.00),255(AGGACACGCAGTGCCC,+,0.00),310(GAGGACACGCAGTGCC,-,0.00),311(AGGACACGCAGTGCCC,+,0.00),366(GAGGACACGCAGTGCC,-,0.00),367(AGGACACGCAGTGCCC,+,0.00)
chunk0059_431_1	chr14	38314036	38314403	+	0	NA	Intergenic	Intergenic	-57849	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.002725	0.301630	217(GTGTACAATTTGTTCT,-,0.00),218(TGTACAATTTGTTCTT,+,0.00)
chunk0169_29_1	chr6	97089902	97090101	+	0	NA	intron (NM_001286254, intron 5 of 8)	intron (NM_001286254, intron 5 of 8)	79802	NM_001286254	114792	Hs.45056	NM_052904	ENSG00000186231	KLHL32	BKLHD5|KIAA1900|UG0030H05|dJ21F7.1	kelch like family member 32	protein-coding	0.010050	0.455000	
chunk0088_16_1	chr18	43389279	43389478	+	0	NA	Intergenic	L1ME3|LINE|L1	-111728	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.000000	0.420000	
chunk0208_233_1	chrX	19343472	19343825	+	0	NA	promoter-TSS (NM_000284)	promoter-TSS (NM_000284)	-245	NM_001173455	5160	Hs.530331	NM_000284	ENSG00000131828	PDHA1	PDHA|PDHAD|PDHCE1A|PHE1A	pyruvate dehydrogenase E1 alpha 1 subunit	protein-coding	0.062323	0.601695	
chunk0024_288_1	chr10	42079934	42080144	+	0	NA	Intergenic	(ATCGAATGGAATC)n|Simple_repeat|Simple_repeat	288006	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.047619	0.364929	
chunk0069_114_1	chr15	61682570	61683929	+	0	NA	Intergenic	Intergenic	377216	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.006623	0.422059	1049(AAGCACATTCCGTGCT,-,0.00),1050(AGCACATTCCGTGCTT,+,0.00)
chunk0185_270_1	chr7	130786174	130786598	+	0	NA	Intergenic	L1ME2|LINE|L1	-52353	NM_138693	136259	Hs.125240	NM_138693	ENSG00000266265	KLF14	BTEB5	Kruppel like factor 14	protein-coding	0.004717	0.517647	
chunk0014_222_1	chr1	179657935	179658501	+	0	NA	intron (NM_001199089, intron 14 of 17)	L1MA8|LINE|L1	51991	NM_001199092	163589	Hs.197354	NM_173533	ENSG00000162782	TDRD5	TUDOR3	tudor domain containing 5	protein-coding	0.003534	0.326279	178(GTAACATAATGTCCTC,+,0.00)
chunk0178_294_1	chr7	37535788	37536269	+	0	NA	Intergenic	Intergenic	-86702	NM_001206480	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.000000	0.394191	
chunk0129_155_1	chr3	120590968	120591509	+	0	NA	Intergenic	L1M5|LINE|L1	-5043	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.007394	0.332103	
chunk0095_112_1	chr2	15580337	15580875	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-11015	NM_004939	1653	Hs.440599	NM_004939	ENSG00000079785	DDX1	DBP-RB|UKVH5d	DEAD-box helicase 1	protein-coding	0.007435	0.411874	
chunk0204_153_1	chr9	95767737	95768000	+	0	NA	Intergenic	L2a|LINE|L2	-107750	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.003802	0.375000	160(GAGCACAGCATGTGCT,-,0.00),161(AGCACAGCATGTGCTC,+,0.00)
chunk0057_410_1	chr13	109799452	109799955	+	0	NA	Intergenic	Intergenic	-13136	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.001988	0.380952	
chunk0036_110_1	chr11	61424013	61424308	+	0	NA	intron (NM_024811, intron 2 of 9)	intron (NM_024811, intron 2 of 9)	5751	NM_024811	79869	Hs.718984	NM_024811	ENSG00000149532	CPSF7	CFIm59	cleavage and polyadenylation specific factor 7	protein-coding	0.006780	0.368243	
chunk0168_47_1	chr6	78577856	78578093	+	0	NA	Intergenic	Intergenic	-289570	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.000000	0.424370	
chunk0127_68_1	chr3	89358754	89359271	+	0	NA	intron (NM_005233, intron 5 of 16)	intron (NM_005233, intron 5 of 16)	251488	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003868	0.277992	
chunk0195_129_1	chr8	94991058	94992102	+	0	NA	Intergenic	L1ME4b|LINE|L1	-33406	NM_152416	137682	Hs.435500	NM_152416	ENSG00000156170	NDUFAF6	C8orf38|MC1DN17	NADH:ubiquinone oxidoreductase complex assembly factor 6	protein-coding	0.004789	0.357895	
chunk0131_78_1	chr3	143209788	143210238	+	0	NA	Intergenic	Intergenic	90237	NM_004267	9435	Hs.8786	NM_004267	ENSG00000175040	CHST2	C6ST|GST-2|GST2|Gn6ST-1|HEL-S-75|glcNAc6ST-1	carbohydrate sulfotransferase 2	protein-coding	0.006667	0.416851	
chunk0160_189_1	chr5	154504288	154504773	+	0	NA	Intergenic	L1ME3G|LINE|L1	-26266	NM_004821	9421	Hs.152531	NM_004821	ENSG00000113196	HAND1	Hxt|Thing1|bHLHa27|eHand	heart and neural crest derivatives expressed 1	protein-coding	0.006186	0.395062	
chunk0125_143_1	chr3	66133184	66133562	+	0	NA	promoter-TSS (NM_173471)	promoter-TSS (NM_173471)	-237	NM_173471	115286	Hs.379386	NM_173471	ENSG00000144741	SLC25A26	COXPD28|SAMC	solute carrier family 25 member 26	protein-coding	0.010582	0.414248	
chunk0186_432_1	chr7	146701429	146701628	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	396081	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.000000	0.265000	
chunk0033_322_1	chr11	21075601	21075815	+	0	NA	intron (NM_006157, intron 12 of 19)	AluJr|SINE|Alu	406157	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.004673	0.404651	
chunk0165_6_1	chr6	28674401	28674614	+	0	NA	Intergenic	Intergenic	-87172	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.056338	0.560748	
chunk0079_144_1	chr17	13146319	13146584	+	0	NA	Intergenic	L1MC|LINE|L1	-128387	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.000000	0.327068	
chunk0212_440_1	chrX	154607611	154607810	+	0	NA	Intergenic	AluJo|SINE|Alu	11561	NM_001327	1485	Hs.534310	NM_001327	ENSG00000184033	CTAG1B	CT6.1|CTAG|CTAG1|ESO1|LAGE-2|LAGE2B|NY-ESO-1	cancer/testis antigen 1B	protein-coding	0.010050	0.420000	
chunk0086_99_1	chr18	13909702	13909986	+	0	NA	intron (NM_001291911, intron 1 of 1)	L1MC3|LINE|L1	5692	NM_000529	4158	Hs.248144	NM_000529	ENSG00000185231	MC2R	ACTHR	melanocortin 2 receptor	protein-coding	0.003521	0.403509	
chunk0167_421_1	chr6	75488872	75489575	+	0	NA	intron (NR_110608, intron 1 of 1)	intron (NR_110608, intron 1 of 1)	4606	NM_001289987	27145	Hs.201488	NM_015687	ENSG00000118407	FILIP1	FILIP	filamin A interacting protein 1	protein-coding	0.004267	0.319602	319(TAGAACAGTCTGTGCT,-,0.00),320(AGAACAGTCTGTGCTG,+,0.00)
chunk0093_424_1	chr19	57810951	57811252	+	0	NA	intron (NM_024762, intron 2 of 2)	LTR5_Hs|LTR|ERVK	3812	NM_024762	79818	Hs.560727	NM_024762	ENSG00000178935	ZNF552	-	zinc finger protein 552	protein-coding	0.029900	0.480132	
chunk0029_67_1	chr10	96581714	96582149	+	0	NA	intron (NM_020123, intron 1 of 14)	intron (NM_020123, intron 1 of 14)	5121	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.009195	0.383028	
chunk0011_170_1	chr1	147681692	147682030	+	0	NA	Intergenic	L1MA8|LINE|L1	-11349	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.005917	0.581121	
chunk0043_331_1	chr12	22664912	22665457	+	0	NA	intron (NM_018638, intron 4 of 7)	intron (NM_018638, intron 4 of 7)	40042	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.003670	0.305861	297(AAACACAGACTGTTCT,-,0.00),298(AACACAGACTGTTCTT,+,0.00)
chunk0072_189_1	chr15	94248281	94249362	+	0	NA	Intergenic	Intergenic	-49380	NM_001159643	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.011101	0.394640	
chunk0196_297_1	chr8	109607812	109608239	+	0	NA	intron (NM_017786, intron 5 of 8)	intron (NM_017786, intron 5 of 8)	35165	NM_001099756	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.002342	0.471963	
chunk0120_21_1	chr3	1950202	1950652	+	0	NA	Intergenic	L1MEg|LINE|L1	-148439	NM_175607	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.004444	0.341463	
chunk0171_107_1	chr6	122145818	122146092	+	0	NA	Intergenic	Intergenic	-253596	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.000000	0.367273	142(CTGATCACAGTGTTCC,-,0.00),143(TGATCACAGTGTTCCT,+,0.00)
chunk0152_99_1	chr5	58323423	58323845	+	0	NA	Intergenic	Intergenic	136505	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.011848	0.354610	
chunk0022_24_1	chr10	7773928	7774137	+	0	NA	intron (NR_045609, intron 7 of 13)	MER58A|DNA|hAT-Charlie	13995	NM_012311	22944	Hs.397918	NM_012311	ENSG00000151657	KIN	BTCD|KIN17|Rts2	Kin17 DNA and RNA binding protein	protein-coding	0.009569	0.476190	
chunk0052_432_1	chr12	131896394	131896977	+	0	NA	intron (NM_003565, intron 3 of 27)	intron (NM_003565, intron 3 of 27)	1951	NM_003565	8408	Hs.47061	NM_003565	ENSG00000177169	ULK1	ATG1|ATG1A|UNC51|Unc51.1|hATG1	unc-51 like autophagy activating kinase 1	protein-coding	0.024014	0.660959	286(AGGCACACTGTGTCCT,-,0.00),287(GGCACACTGTGTCCTG,+,0.00)
chunk0093_358_1	chr19	55526879	55527578	+	0	NA	Intergenic	(CACACT)n|Simple_repeat|Simple_repeat	9066	NM_001101401	646643	Hs.532676	NM_001101401	ENSG00000187550	SBK2	SGK069	SH3 domain binding kinase family member 2	protein-coding	0.022890	0.471429	
chunk0026_156_1	chr10	62771829	62772296	+	0	NA	Intergenic	Intergenic	-32694	NM_032804	84890	Hs.99821	NM_032804	ENSG00000181915	ADO	C10orf22	2-aminoethanethiol dioxygenase	protein-coding	0.002141	0.324786	
chunk0180_69_1	chr7	54917463	54918012	+	0	NA	Intergenic	AluJb|SINE|Alu	-101295	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.014572	0.487273	200(TGGAGCATTCTGTTCT,-,0.00),201(GGAGCATTCTGTTCTT,+,0.00)
chunk0048_355_1	chr12	85362331	85362605	+	0	NA	Intergenic	Intergenic	82210	NM_006982	8092	Hs.41683	NM_006982	ENSG00000180318	ALX1	CART1|FND3|HEL23	ALX homeobox 1	protein-coding	0.010949	0.378182	
chunk0128_448_1	chr3	115200106	115200761	+	0	NA	Intergenic	Intergenic	-53153	NM_015642	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.010687	0.342988	
chunk0130_421_1	chr3	140815483	140816308	+	0	NA	Intergenic	L1MC1|LINE|L1	-125925	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.001212	0.330508	
chunk0121_240_1	chr3	22491313	22491829	+	0	NA	Intergenic	L2a|LINE|L2	534432	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.001938	0.365571	
chunk0054_437_1	chr13	51380285	51380669	+	0	NA	intron (NM_001306091, intron 12 of 19)	MIR|SINE|MIR	-31838	NR_049878	100847003		NR_049878	ENSG00000266072	MIR5693	-	microRNA 5693	ncRNA	0.010417	0.337662	
chunk0112_17_1	chr20	36066702	36067192	+	0	NA	Intergenic	L2a|LINE|L2	-15987	NR_027451	647979	Hs.743232	NR_027451	ENSG00000260032	NORAD	LINC00657	non-coding RNA activated by DNA damage	ncRNA	0.006122	0.490835	
chunk0039_179_1	chr11	100434972	100435377	+	0	NA	Intergenic	LTR18B|LTR|ERVL	-252502	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.019753	0.517241	
chunk0199_381_1	chr9	13140899	13141098	+	0	NA	intron (NM_001261406, intron 26 of 45)	intron (NM_001261406, intron 26 of 45)	138566	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.015075	0.475000	
chunk0157_451_1	chr5	124980596	124981373	+	0	NA	Intergenic	Intergenic	-55847	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.012870	0.368895	
chunk0023_78_1	chr10	22247489	22248104	+	0	NA	Intergenic	Intergenic	-4276	NR_038921	100130992	Hs.48501	NR_038921		LOC100130992	-	uncharacterized LOC100130992	ncRNA	0.004878	0.370130	
chunk0035_364_1	chr11	49172417	49172676	+	0	NA	intron (NM_001014986, intron 10 of 17)	MIRc|SINE|MIR	36124	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.000000	0.307692	
chunk0004_439_1	chr1	53107593	53107992	+	0	NA	TTS (NM_001287596)	TTS (NM_001287596)	34840	NM_001287596	6512	Hs.104637	NM_006671	ENSG00000162383	SLC1A7	AAAT|EAAT5	solute carrier family 1 member 7	protein-coding	0.022556	0.425000	
chunk0163_232_1	chr6	12297583	12298033	+	0	NA	TTS (NM_001168319)	TTS (NM_001168319)	7512	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.008889	0.432373	131(AGGAACATTGAGTACC,-,0.00),132(GGAACATTGAGTACCA,+,0.00)
chunk0098_32_1	chr2	65708919	65709535	+	0	NA	Intergenic	Intergenic	-276705	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.003247	0.418152	414(GGGAACAGTGTGTACA,-,0.00),415(GGAACAGTGTGTACAA,+,0.00)
chunk0136_151_1	chr4	4672032	4672739	+	0	NA	intron (NR_037888, intron 4 of 5)	L2b|LINE|L2	-89375	NR_125892	101928279	Hs.586152	NR_125892		LOC101928279	-	uncharacterized LOC101928279	ncRNA	0.015559	0.490113	207(GTGGACAGGGAGTGCC,-,0.00),208(TGGACAGGGAGTGCCT,+,0.00)
chunk0015_273_1	chr1	188458689	188459118	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	1015275	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.434884	
chunk0140_432_1	chr4	76187136	76187772	+	0	NA	intron (NM_005506, intron 2 of 11)	L1ME4c|LINE|L1	26445	NM_005506	950	Hs.349656	NM_005506	ENSG00000138760	SCARB2	AMRF|CD36L2|EPM4|HLGP85|LGP85|LIMP-2|LIMPII|SR-BII	scavenger receptor class B member 2	protein-coding	0.004717	0.326531	
chunk0164_363_1	chr6	25616605	25617055	+	0	NA	intron (NM_017640, intron 36 of 36)	intron (NM_017640, intron 36 of 36)	-35371	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.017778	0.359202	
chunk0170_278_1	chr6	114172653	114173382	+	0	NA	intron (NR_125845, intron 6 of 9)	intron (NR_125845, intron 6 of 9)	-110140	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.002743	0.320548	
chunk0042_39_1	chr12	1574931	1575299	+	0	NA	intron (NM_152441, intron 1 of 1)	intron (NM_152441, intron 1 of 1)	19050	NM_152441	144699	Hs.367956	NM_152441	ENSG00000171823	FBXL14	Fbl14	F-box and leucine rich repeat protein 14	protein-coding	0.000000	0.330623	
chunk0057_160_1	chr13	100680287	100680782	+	0	NA	Intergenic	Intergenic	-5599	NM_032813	84899	Hs.190983	NM_032813	ENSG00000125247	TMTC4	-	transmembrane O-mannosyltransferase targeting cadherins 4	protein-coding	0.002020	0.441532	
chunk0008_104_1	chr1	91268078	91268670	+	0	NA	intron (NM_001017975, intron 34 of 38)	L2|LINE|L2	136495	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.003378	0.298482	
chunk0041_336_1	chr11	130557555	130557772	+	0	NA	Intergenic	Intergenic	108689	NM_139055	170689	Hs.534221	NM_139055	ENSG00000166106	ADAMTS15	-	ADAM metallopeptidase with thrombospondin type 1 motif 15	protein-coding	0.004608	0.353211	23(AAGAACAGTCTGTACT,-,0.00),24(AGAACAGTCTGTACTA,+,0.00)
chunk0087_55_1	chr18	31575397	31576104	+	0	NA	Intergenic	MIRb|SINE|MIR	-16017	NM_000371	7276	Hs.427202	NM_000371	ENSG00000118271	TTR	ATTR|CTS|CTS1|HEL111|HsT2651|PALB|TBPA	transthyretin	protein-coding	0.007072	0.396893	
chunk0121_322_1	chr3	24326444	24326861	+	0	NA	intron (NM_001128177, intron 2 of 10)	intron (NM_001128177, intron 2 of 10)	-167435	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.011990	0.442584	
chunk0001_297_1	chr1	9027341	9027784	+	0	NA	Intergenic	L1PA14|LINE|L1	-1217	NM_207420	155184	Hs.531239	NM_207420	ENSG00000197241	SLC2A7	GLUT-7|GLUT7	solute carrier family 2 member 7	protein-coding	0.006772	0.360360	
chunk0181_407_1	chr7	90084640	90084874	+	0	NA	intron (NR_110029, intron 2 of 2)	intron (NR_110029, intron 2 of 2)	-34643	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.004274	0.348936	
chunk0111_388_1	chr20	34101365	34101626	+	0	NA	intron (NM_001316364, intron 3 of 7)	intron (NM_001316364, intron 3 of 7)	10861	NM_001316363	8894	Hs.429180	NM_003908	ENSG00000125977	EIF2S2	EIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta	eukaryotic translation initiation factor 2 subunit beta	protein-coding	0.015326	0.385496	
chunk0047_440_1	chr12	76430075	76430342	+	0	NA	intron (NM_001003712, intron 3 of 22)	L1MA9|LINE|L1	-81766	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.007491	0.500000	
chunk0200_230_1	chr9	20718688	20719056	+	0	NA	intron (NM_017794, intron 5 of 45)	intron (NM_017794, intron 5 of 45)	2767	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.002717	0.336043	234(CTGAACACAATGTCCT,-,0.00),235(TGAACACAATGTCCTT,+,0.00)
chunk0181_173_1	chr7	82945092	82945806	+	0	NA	intron (NM_014510, intron 6 of 19)	MLT1B|LTR|ERVL-MaLR	217432	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.008403	0.345455	
chunk0074_81_1	chr16	21598521	21598791	+	0	NA	promoter-TSS (NM_001077180)	promoter-TSS (NM_001077180)	729	NR_110930	101927814	Hs.555158	NR_110930		LOC101927814	-	uncharacterized LOC101927814	ncRNA	0.011111	0.402214	115(AGGAACACAGTGTAAC,-,0.00)
chunk0210_451_1	chrX	106328332	106328806	+	0	NA	Intergenic	Intergenic	160264	NM_001171020	139221	Hs.592221	NM_152423	ENSG00000157502	PWWP3B	MUM1L1	PWWP domain containing 3B	protein-coding	0.004219	0.332632	
chunk0137_189_1	chr4	17752761	17753174	+	0	NA	intron (NM_015688, intron 1 of 17)	intron (NM_015688, intron 1 of 17)	28545	NM_015688	27146	Hs.744951	NM_015688	ENSG00000047662	FAM184B	-	family with sequence similarity 184 member B	protein-coding	0.007264	0.420290	
chunk0097_371_1	chr2	61037398	61037688	+	0	NA	intron (NM_002618, intron 2 of 3)	L1PA6|LINE|L1	-19313	NM_144709	150962	Hs.368348	NM_144709	ENSG00000162927	PUS10	CCDC139|DOBI	pseudouridine synthase 10	protein-coding	0.003448	0.367698	
chunk0184_343_1	chr7	120729144	120729839	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	128632	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.002878	0.408046	331(GGGCTCAGGCTGTCCT,-,0.00),332(GGCTCAGGCTGTCCTT,+,0.00),361(CAGGACAGCCTGGACT,-,0.00),362(AGGACAGCCTGGACTG,+,0.00),540(ATGAACACTTTGTGCC,-,0.00),541(TGAACACTTTGTGCCC,+,0.00)
chunk0078_325_1	chr17	8593795	8594227	+	0	NA	intron (NM_001256095, intron 3 of 41)	L1MC|LINE|L1	36750	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.004630	0.334873	197(AGGAACAGAGAGTCCT,-,0.00),198(GGAACAGAGAGTCCTG,+,0.00)
chunk0176_132_1	chr7	12640193	12640392	+	0	NA	intron (NM_033128, intron 8 of 13)	intron (NM_033128, intron 8 of 13)	-46535	NM_212460	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.005025	0.365000	
chunk0051_299_1	chr12	118567546	118568752	+	0	NA	Intergenic	AluJr|SINE|Alu	191596	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.002488	0.302403	
chunk0084_86_1	chr17	75182570	75182898	+	0	NA	intron (NM_001005849, intron 1 of 2)	CpG	269	NM_006937	6613	Hs.380973	NM_006937	ENSG00000188612	SUMO2	HSMT3|SMT3B|SMT3H2|SUMO3|Smt3A	small ubiquitin like modifier 2	protein-coding	0.140244	0.759878	
chunk0211_17_1	chrX	107741577	107742303	+	0	NA	intron (NM_198057, intron 1 of 2)	intron (NM_198057, intron 1 of 2)	-24879	NM_004089	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.013774	0.529574	377(CAGTACTCCCAGTTCT,-,0.00),378(AGTACTCCCAGTTCTG,+,0.00)
chunk0031_257_1	chr10	127219617	127220037	+	0	NA	intron (NM_001290223, intron 27 of 51)	intron (NM_001290223, intron 27 of 51)	-23669	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.002381	0.463183	
chunk0070_7_1	chr15	68821923	68822506	+	0	NA	Intergenic	Intergenic	-1292	NM_006305	8125	Hs.458747	NM_006305	ENSG00000140350	ANP32A	C15orf1|HPPCn|I1PP2A|LANP|MAPM|PHAP1|PHAPI|PP32	acidic nuclear phosphoprotein 32 family member A	protein-coding	0.018868	0.402397	
chunk0192_382_1	chr8	68598671	68599182	+	0	NA	intron (NM_052958, intron 7 of 13)	intron (NM_052958, intron 7 of 13)	-267435	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.001957	0.269531	207(GAGGACAAGATGTGCT,-,0.00),208(AGGACAAGATGTGCTC,+,0.00)
chunk0005_5_1	chr1	54001535	54002157	+	0	NA	Intergenic	Intergenic	16340	NM_001276393	388633	Hs.439583	NM_001010978	ENSG00000203985	LDLRAD1	-	low density lipoprotein receptor class A domain containing 1	protein-coding	0.004823	0.504013	
chunk0134_66_1	chr3	176231807	176232006	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-283197	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.005025	0.400000	
chunk0049_180_1	chr12	92543229	92543649	+	0	NA	Intergenic	Intergenic	-115291	NM_001025232	574016	Hs.551199	NM_001025232	ENSG00000205057	CLLU1OS	-	chronic lymphocytic leukemia up-regulated 1 opposite strand	protein-coding	0.002381	0.418052	
chunk0151_337_1	chr5	54196913	54197674	+	0	NA	intron (NM_019087, intron 1 of 4)	intron (NM_019087, intron 1 of 4)	113280	NM_019087	54622	Hs.659125	NM_019087	ENSG00000185305	ARL15	ARFRP2	ADP ribosylation factor like GTPase 15	protein-coding	0.000000	0.354331	293(AAGAACACAATGTTAT,-,0.00),294(AGAACACAATGTTATC,+,0.00)
chunk0165_349_1	chr6	37988069	37988787	+	0	NA	intron (NM_021943, intron 2 of 5)	intron (NM_021943, intron 2 of 5)	168897	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.002786	0.343533	
chunk0012_44_1	chr1	155262916	155263364	+	0	NA	promoter-TSS (NM_005698)	promoter-TSS (NM_005698)	-755	NM_052837	10067	Hs.200600	NM_005698	ENSG00000116521	SCAMP3	C1orf3	secretory carrier membrane protein 3	protein-coding	0.026786	0.503341	
chunk0101_339_1	chr2	136905708	136906158	+	0	NA	intron (NM_001316349, intron 2 of 27)	intron (NM_001316349, intron 2 of 27)	140371	NM_001316349	80731	Hs.68533	NM_001080427	ENSG00000144229	THSD7B	-	thrombospondin type 1 domain containing 7B	protein-coding	0.004444	0.430155	
chunk0028_178_1	chr10	88244235	88244449	+	0	NA	Intergenic	Intergenic	338983	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.028037	0.576744	
chunk0061_106_1	chr14	57782344	57782717	+	0	NA	intron (NM_001306087, intron 1 of 7)	Tigger2|DNA|TcMar-Tigger	83344	NM_001206920	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.005362	0.339572	253(TAGTACATACTGTACT,-,0.00),254(AGTACATACTGTACTA,+,0.00)
chunk0037_268_1	chr11	75692426	75693327	+	0	NA	Intergenic	L1MD2|LINE|L1	-24442	NM_207577	4135	Hs.585540	NM_033063	ENSG00000171533	MAP6	MAP6-N|MTAP6|N-STOP|STOP	microtubule associated protein 6	protein-coding	0.011099	0.374723	
chunk0087_184_1	chr18	35525814	35526154	+	0	NA	Intergenic	Intergenic	-27993	NM_194281	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.014706	0.516129	
chunk0024_422_1	chr10	45896896	45897109	+	0	NA	intron (NR_029388, intron 8 of 12)	intron (NR_029388, intron 8 of 12)	-43125	NM_001291379	119016	Hs.314437	NM_133446	ENSG00000188234	AGAP4	AGAP-4|AGAP-8|AGAP8|CTGLF1|CTGLF5|MRIP2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	protein-coding	0.004695	0.303738	
chunk0189_174_1	chr8	23525776	23526018	+	0	NA	Intergenic	LTR67B|LTR|ERVL	-2953	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.016529	0.559671	
chunk0027_135_1	chr10	74420040	74420429	+	0	NA	intron (NM_001202450, intron 6 of 9)	intron (NM_001202450, intron 6 of 9)	109090	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.005141	0.369231	
chunk0017_390_1	chr1	212341058	212341368	+	0	NA	intron (NM_006243, intron 3 of 12)	intron (NM_006243, intron 3 of 12)	-11605	NR_004389	692157	Hs.707958	NR_004389	ENSG00000201544	SNORA16B	U98b	small nucleolar RNA, H/ACA box 16B	snoRNA	0.003226	0.353698	
chunk0043_118_1	chr12	15539786	15540043	+	0	NA	intron (NM_030667, intron 12 of 26)	intron (NM_030667, intron 12 of 26)	-6430	NM_030671	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.000000	0.255814	
chunk0088_41_1	chr18	43919510	43920008	+	0	NA	Intergenic	Intergenic	611938	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.000000	0.380762	
chunk0162_7_1	chr6	330962	331225	+	0	NA	intron (NR_104473, intron 3 of 5)	intron (NR_104473, intron 3 of 5)	39036	NR_104474	56940	Hs.29106	NM_020185	ENSG00000112679	DUSP22	JKAP|JSP-1|JSP1|LMW-DSP2|LMWDSP2|MKP-x|MKPX|VHX	dual specificity phosphatase 22	protein-coding	0.026616	0.412879	
chunk0046_248_1	chr12	60479125	60479561	+	0	NA	Intergenic	Intergenic	790006	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.002294	0.315789	
chunk0120_383_1	chr3	12273422	12273681	+	0	NA	Intergenic	Intergenic	-14299	NM_005037	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.007722	0.346154	
chunk0075_322_1	chr16	54578757	54578956	+	0	NA	Intergenic	Intergenic	-292390	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.005025	0.475000	
chunk0065_210_1	chr14	100172875	100173168	+	0	NA	Intergenic	HERVL74-int|LTR|ERVL	-13346	NM_206918	123099	Hs.159643	NM_206918	ENSG00000168350	DEGS2	C14orf66|DES2|FADS8	delta 4-desaturase, sphingolipid 2	protein-coding	0.017065	0.438776	
chunk0030_89_1	chr10	112362470	112362869	+	0	NA	Intergenic	Intergenic	-6074	NR_028134	390003	Hs.534691	NR_028134	ENSG00000243316	GUCY2GP	GUCY2G	guanylate cyclase 2G, pseudogene	pseudo	0.000000	0.397500	
chunk0081_443_1	chr17	49076965	49077343	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	-55306	NM_001159388	124872	Hs.374679	NM_153446	ENSG00000167080	B4GALNT2	B4GALT|GALGT2	beta-1,4-N-acetyl-galactosaminyltransferase 2	protein-coding	0.013228	0.453826	
chunk0175_319_1	chr6	166836450	166837114	+	0	NA	intron (NM_001006932, intron 2 of 21)	L1ME3|LINE|L1	25501	NM_001006932	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.033133	0.502256	
chunk0147_170_1	chr4	176274498	176274805	+	0	NA	Intergenic	Intergenic	-5429	NM_080874	140458	Hs.591712	NM_080874	ENSG00000164122	ASB5	ASB-5	ankyrin repeat and SOCS box containing 5	protein-coding	0.000000	0.412338	
chunk0064_205_1	chr14	92987232	92987993	+	0	NA	intron (NM_001142594, intron 5 of 10)	MIRb|SINE|MIR	64512	NM_001301690	1113	Hs.150793	NM_001275	ENSG00000100604	CHGA	CGA	chromogranin A	protein-coding	0.022339	0.602362	371(GGGAACAGGGTGAGCT,-,0.00),372(GGAACAGGGTGAGCTT,+,0.00)
chunk0124_419_1	chr3	60992361	60992740	+	0	NA	intron (NM_001166243, intron 3 of 9)	intron (NM_001166243, intron 3 of 9)	258909	NM_002012	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.010554	0.410526	
chunk0185_369_1	chr7	132894512	132894791	+	0	NA	intron (NM_017812, intron 4 of 7)	L2b|LINE|L2	140264	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.003584	0.414286	
chunk0104_240_1	chr2	176729741	176730171	+	0	NA	Intergenic	Intergenic	92202	NR_110599	102724224	Hs.663125	NR_110599	ENSG00000224577	LINC01117	-	long intergenic non-protein coding RNA 1117	ncRNA	0.002326	0.422274	
chunk0210_396_1	chrX	98068085	98068865	+	0	NA	Intergenic	Intergenic	-503940	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.003846	0.370038	380(ATGAGCAGAGTGTTCT,-,0.00),381(TGAGCAGAGTGTTCTT,+,0.00)
chunk0035_57_1	chr11	41400735	41401484	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	58527	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.002670	0.330667	
chunk0160_250_1	chr5	156670567	156671146	+	0	NA	intron (NM_000337, intron 7 of 8)	intron (NM_000337, intron 7 of 8)	-179682	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.003454	0.360345	
chunk0017_447_1	chr1	214268302	214268598	+	0	NA	Intergenic	Intergenic	-12772	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.000000	0.269360	
chunk0158_185_1	chr5	127899529	127899986	+	0	NA	Intergenic	Intergenic	183317	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.008753	0.414847	
chunk0041_416_1	chr11	134227755	134228931	+	0	NA	intron (NM_052875, intron 1 of 5)	intron (NM_052875, intron 1 of 5)	3738	NM_052875	112936	Hs.334684	NM_052875	ENSG00000151502	VPS26B	Pep8b	VPS26, retromer complex component B	protein-coding	0.008503	0.403568	
chunk0158_223_1	chr5	128499409	128500045	+	0	NA	intron (NM_001999, intron 5 of 64)	intron (NM_001999, intron 5 of 64)	38315	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.011006	0.357928	
chunk0042_220_1	chr12	6201004	6201489	+	0	NA	intron (NM_001769, intron 1 of 7)	intron (NM_001769, intron 1 of 7)	930	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.055670	0.644033	
chunk0021_439_1	chr1	248205191	248205629	+	0	NA	Intergenic	L1PB1|LINE|L1	2342	NM_001004689	127062	Hs.553581	NM_001004689	ENSG00000228198	OR2M3	OR1-54|OR2M3P|OR2M6|OST003	olfactory receptor family 2 subfamily M member 3	protein-coding	0.004566	0.369021	
chunk0098_290_1	chr2	75882373	75883027	+	0	NA	Intergenic	L1ME1|LINE|L1	-171715	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.003058	0.338931	
chunk0058_40_1	chr14	20180276	20180754	+	0	NA	Intergenic	MER67C|LTR|ERV1	-16821	NM_001005503	390439	Hs.554582	NM_001005503	ENSG00000196832	OR11G2	OR14-34	olfactory receptor family 11 subfamily G member 2	protein-coding	0.004184	0.367432	
chunk0104_322_1	chr2	179302847	179303606	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-38603	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.005270	0.417105	
chunk0138_117_1	chr4	36320196	36320498	+	0	NA	intron (NM_001170700, intron 7 of 8)	L2b|LINE|L2	36325	NM_001170700	401124	Hs.363407	NM_001136536	ENSG00000197057	DTHD1	-	death domain containing 1	protein-coding	0.013245	0.382838	
chunk0157_396_1	chr5	124137583	124137796	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	300831	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.000000	0.294393	
chunk0054_317_1	chr13	48949670	48950259	+	0	NA	Intergenic	MIRb|SINE|MIR	-25948	NM_001079673	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.005093	0.354237	296(AAGAACACTGAGATCT,-,0.00)
chunk0163_56_1	chr6	8851490	8852104	+	0	NA	Intergenic	Intergenic	199588	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.000000	0.373984	293(TGGAACATCCAGTTCT,-,0.00),294(GGAACATCCAGTTCTT,+,0.00)
chunk0072_250_1	chr15	96170863	96171494	+	0	NA	intron (NR_125738, intron 3 of 4)	intron (NR_125738, intron 3 of 4)	-154750	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.015848	0.436709	
chunk0006_255_1	chr1	69428104	69428768	+	0	NA	Intergenic	Intergenic	-331739	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.004518	0.338346	
chunk0202_419_1	chr9	81712814	81713040	+	0	NA	intron (NR_109772, intron 1 of 3)	intron (NR_109772, intron 1 of 3)	23214	NR_109772	101927502	Hs.528628	NR_109772	ENSG00000233926	LOC101927502	-	uncharacterized LOC101927502	ncRNA	0.008850	0.396476	
chunk0037_211_1	chr11	74657854	74658149	+	0	NA	Intergenic	L1M1|LINE|L1	53366	NM_001304417	25884	Hs.432379	NM_015424	ENSG00000054938	CHRDL2	BNF1|CHL2	chordin like 2	protein-coding	0.000000	0.368243	
chunk0199_140_1	chr9	4028766	4029156	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	123222	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.000000	0.340153	
chunk0042_342_1	chr12	10003346	10003813	+	0	NA	Intergenic	Intergenic	-4279	NM_016509	51266	Hs.409794	NM_016509	ENSG00000165682	CLEC1B	1810061I13Rik|CLEC2|CLEC2B|PRO1384|QDED721	C-type lectin domain family 1 member B	protein-coding	0.012848	0.414530	
chunk0053_441_1	chr13	39363288	39363487	+	0	NA	intron (NM_005780, intron 3 of 3)	MIR3|SINE|MIR	239832	NM_005780	10186	Hs.507798	NM_005780	ENSG00000183722	LHFPL6	LHFP	LHFPL tetraspan subfamily member 6	protein-coding	0.005025	0.425000	
chunk0140_312_1	chr4	73223048	73223475	+	0	NA	promoter-TSS (NM_001286771)	promoter-TSS (NM_001286771)	-147	NM_001286771	26057	Hs.601206	NM_015574	ENSG00000132466	ANKRD17	GTAR|MASK2|NY-BR-16	ankyrin repeat domain 17	protein-coding	0.007026	0.359813	
chunk0173_420_1	chr6	151036276	151036626	+	0	NA	intron (NM_001242767, intron 25 of 27)	intron (NM_001242767, intron 25 of 27)	170118	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.005714	0.430199	41(AGGAACACTGTGTGCC,-,0.00),42(GGAACACTGTGTGCCA,+,0.00)
chunk0211_93_1	chrX	110669333	110670119	+	0	NA	Intergenic	Intergenic	126122	NM_145234	91851	Hs.496587	NM_145234	ENSG00000101938	CHRDL1	CHL|MGC1|MGCN|NRLN1|VOPT|dA141H5.1	chordin like 1	protein-coding	0.002545	0.350699	
chunk0147_239_1	chr4	182854416	182854700	+	0	NA	Intergenic	Intergenic	62919	NM_001012732	1635	Hs.183850	NM_001921	ENSG00000129187	DCTD	-	dCMP deaminase	protein-coding	0.007042	0.487719	
chunk0013_123_1	chr1	167965919	167966354	+	0	NA	intron (NM_001198957, intron 2 of 20)	L1MC1|LINE|L1	-29067	NM_015415	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.016092	0.435780	
chunk0039_230_1	chr11	101765988	101766447	+	0	NA	Intergenic	Intergenic	-148798	NM_020802	57562	Hs.156352	NM_020802	ENSG00000110318	CEP126	KIAA1377	centrosomal protein 126	protein-coding	0.008715	0.395652	
chunk0088_33_1	chr18	43828859	43829257	+	0	NA	Intergenic	MIR|SINE|MIR	-551408	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.012563	0.416040	152(AAGAACAAAGTGTTCT,-,0.00),153(AGAACAAAGTGTTCTT,+,0.00)
chunk0007_236_1	chr1	82299553	82300081	+	0	NA	Intergenic	UCON78|DNA|DNA	499420	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.003788	0.330813	171(AGGCACACAATGTTCT,-,0.00),172(GGCACACAATGTTCTT,+,0.00)
chunk0066_234_1	chr15	34216300	34216995	+	0	NA	Intergenic	L1ME3G|LINE|L1	-6551	NM_024713	79768	Hs.633566	NM_024713	ENSG00000134152	KATNBL1	C15orf29	katanin regulatory subunit B1 like 1	protein-coding	0.002878	0.347701	
chunk0107_76_1	chr2	212537492	212537691	+	0	NA	intron (NM_001042599, intron 1 of 26)	CpG	1037	NM_001042599	2066	Hs.390729	NM_005235	ENSG00000178568	ERBB4	ALS19|HER4|p180erbB4	erb-b2 receptor tyrosine kinase 4	protein-coding	0.065327	0.615000	
chunk0144_316_1	chr4	138837960	138838343	+	0	NA	Intergenic	Intergenic	-177608	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.013055	0.463542	
chunk0193_360_1	chr8	79924723	79925250	+	0	NA	intron (NM_014018, intron 2 of 2)	intron (NM_014018, intron 2 of 2)	-53249	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.001898	0.316288	
chunk0047_397_1	chr12	75673171	75673570	+	0	NA	Intergenic	Intergenic	-161732	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.005013	0.280000	245(TTGAACTTTGTGTCCT,-,0.00),246(TGAACTTTGTGTCCTT,+,0.00)
chunk0036_295_1	chr11	65575028	65575346	+	0	NA	promoter-TSS (NM_001099409)	promoter-TSS (NM_001099409)	-851	NM_001099409	254102	Hs.502867	NM_001099409	ENSG00000173442	EHBP1L1	-	EH domain binding protein 1 like 1	protein-coding	0.028302	0.557994	134(AGGAACAAACTGACCT,-,0.00),135(GGAACAAACTGACCTA,+,0.00)
chunk0119_82_1	chr22	41442421	41442639	+	0	NA	intron (NM_016272, intron 1 of 1)	intron (NM_016272, intron 1 of 1)	4493	NM_016272	10766	Hs.474978	NM_016272	ENSG00000183864	TOB2	APRO5|TOB4|TOBL|TROB2	transducer of ERBB2, 2	protein-coding	0.004587	0.442922	156(GAGAACAGGCTGGACC,-,0.00)
chunk0100_326_1	chr2	116613682	116613966	+	0	NA	Intergenic	L1MB5|LINE|L1	-1200855	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.007042	0.417544	
chunk0124_339_1	chr3	58322747	58323071	+	0	NA	Intergenic	Intergenic	-9981	NM_001289095	54899	Hs.190544	NM_017771	ENSG00000168297	PXK	MONAKA|SLOB	PX domain containing serine/threonine kinase like	protein-coding	0.009259	0.424615	
chunk0155_182_1	chr5	94438631	94439008	+	0	NA	intron (NM_001145678, intron 14 of 20)	intron (NM_001145678, intron 14 of 20)	179785	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.010610	0.431217	
chunk0077_100_1	chr16	78099877	78100147	+	0	NA	non-coding (NR_120435, exon 1 of 1)	non-coding (NR_120435, exon 1 of 1)	599	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.096296	0.697417	
chunk0117_177_1	chr22	20777506	20778090	+	0	NA	intron (NM_000185, intron 1 of 4)	Tigger15a|DNA|TcMar-Tigger	3703	NM_000185	3053	Hs.474270	NM_000185	ENSG00000099937	SERPIND1	D22S673|HC2|HCF2|HCII|HLS2|LS2|THPH10	serpin family D member 1	protein-coding	0.008562	0.449573	
chunk0194_398_1	chr8	91040669	91041274	+	0	NA	promoter-TSS (NM_018710)	promoter-TSS (NM_018710)	4	NM_018710	55529	Hs.202517	NM_018710	ENSG00000155099	PIP4P2	TMEM55A	phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2	protein-coding	0.049587	0.620462	
chunk0175_439_1	chr6	169800782	169800981	+	0	NA	non-coding (NR_026780, exon 3 of 3).2	non-coding (NR_026780, exon 3 of 3).2	-2056	NR_026781	401288	Hs.556095	NM_207502	ENSG00000229214	LINC00242	C6orf122|NCRNA00242|dJ266L20.5	long intergenic non-protein coding RNA 242	ncRNA	0.015075	0.585000	
chunk0200_179_1	chr9	19331954	19332434	+	0	NA	intron (NM_017925, intron 17 of 31)	intron (NM_017925, intron 17 of 31)	48043	NM_001010	6194	Hs.408073	NM_001010	ENSG00000137154	RPS6	S6	ribosomal protein S6	protein-coding	0.006250	0.355509	
chunk0151_417_1	chr5	55638453	55639072	+	0	NA	intron (NR_047649, intron 10 of 13)	intron (NR_047649, intron 10 of 13)	54291	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.012924	0.385484	
chunk0031_10_1	chr10	121523785	121523984	+	0	NA	intron (NM_001144916, intron 3 of 14)	intron (NM_001144916, intron 3 of 14)	70083	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.025126	0.415000	134(TGAACAATGAGTGCTT,+,0.00)
chunk0153_171_1	chr5	71482077	71482526	+	0	NA	intron (NM_018429, intron 7 of 38)	L1MEf|LINE|L1	26686	NM_018429	55814	Hs.258272	NM_018429	ENSG00000145734	BDP1	DFNB112|HSA238520|TAF3B1|TFC5|TFIIIB''|TFIIIB150|TFIIIB90|TFNR	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.004454	0.437778	
chunk0073_134_1	chr16	5064983	5065242	+	0	NA	intron (NM_001098514, intron 1 of 7)	(TGTG)n|Simple_repeat|Simple_repeat	1033	NM_152459	146556	Hs.11782	NM_152459	ENSG00000153446	C16orf89	-	chromosome 16 open reading frame 89	protein-coding	0.023166	0.523077	
chunk0001_422_1	chr1	11169902	11170493	+	0	NA	intron (NM_004958, intron 28 of 57)	intron (NM_004958, intron 28 of 57)	-19092	NM_021146	10218	Hs.146559	NM_021146	ENSG00000171819	ANGPTL7	AngX|CDT6|dJ647M16.1	angiopoietin like 7	protein-coding	0.011844	0.442568	
chunk0066_372_1	chr15	38490024	38490814	+	0	NA	3' UTR (NM_005739, exon 17 of 17)	3' UTR (NM_005739, exon 17 of 17)	36292	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.002532	0.376738	
chunk0026_387_1	chr10	69538670	69538974	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	34632	NM_020999	50674	Hs.532682	NM_020999	ENSG00000122859	NEUROG3	Atoh5|Math4B|NGN-3|bHLHa7|ngn3	neurogenin 3	protein-coding	0.006579	0.498361	
chunk0017_22_1	chr1	204494290	204494726	+	0	NA	Intergenic	CpG	-4162	NM_002646	5287	Hs.497487	NM_002646	ENSG00000133056	PIK3C2B	C2-PI3K	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta	protein-coding	0.089450	0.702517	
chunk0049_341_1	chr12	95085683	95086102	+	0	NA	exon (NM_018351, exon 19 of 21)	exon (NM_018351, exon 19 of 21)	-12264	NM_001032287	7181	Hs.108301	NM_003297	ENSG00000120798	NR2C1	TR2	nuclear receptor subfamily 2 group C member 1	protein-coding	0.000000	0.307143	
chunk0112_93_1	chr20	38082836	38083035	+	0	NA	intron (NM_021215, intron 6 of 6)	intron (NM_021215, intron 6 of 6)	49389	NM_021215	58490	Hs.278839	NM_021215	ENSG00000101413	RPRD1B	C20orf77|CREPT|K-H|Kub5-Hera|NET60|dJ1057B20.2	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.000000	0.375000	
chunk0110_33_1	chr20	10523856	10524325	+	0	NA	intron (NM_001009608, intron 2 of 7)	intron (NM_001009608, intron 2 of 7)	88787	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.017058	0.510638	
chunk0105_81_1	chr2	183926386	183926827	+	0	NA	Intergenic	MER77|LTR|ERVL	-452369	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.002268	0.371041	217(GTGCACACTGTGTACC,-,0.00),218(TGCACACTGTGTACCT,+,0.00)
chunk0087_400_1	chr18	41899116	41899367	+	0	NA	Intergenic	Intergenic	-55957	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.003984	0.448413	
chunk0122_153_1	chr3	32133669	32134464	+	0	NA	intron (NM_015141, intron 2 of 7)	intron (NM_015141, intron 2 of 7)	27555	NM_015141	23171	Hs.82432	NM_015141	ENSG00000152642	GPD1L	GPD1-L	glycerol-3-phosphate dehydrogenase 1 like	protein-coding	0.007547	0.422111	
chunk0212_397_1	chrX	150898120	150898357	+	0	NA	intron (NM_001242614, intron 1 of 11)	intron (NM_001242614, intron 1 of 11)	578	NM_031462	83692	Hs.522805	NM_031462	ENSG00000102181	CD99L2	CD99B|MIC2L1	CD99 molecule like 2	protein-coding	0.050633	0.588235	
chunk0139_296_1	chr4	57487079	57487724	+	0	NA	Intergenic	L2a|LINE|L2	61529	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.006202	0.371517	
chunk0210_158_1	chrX	77691817	77692490	+	0	NA	intron (NM_138270, intron 5 of 33)	intron (NM_138270, intron 5 of 33)	94116	NM_138270	546	Hs.533526	NM_000489	ENSG00000085224	ATRX	JMS|MRX52|RAD54|RAD54L|XH2|XNP|ZNF-HX	ATRX chromatin remodeler	protein-coding	0.004458	0.347181	
chunk0073_57_1	chr16	3400934	3401209	+	0	NA	promoter-TSS (NM_003450)	promoter-TSS (NM_003450)	-6	NM_017810	54925	Hs.592078	NM_017810	ENSG00000140987	ZSCAN32	HCCS-5|ZNF434	zinc finger and SCAN domain containing 32	protein-coding	0.098182	0.655797	
chunk0029_291_1	chr10	103890150	103890559	+	0	NA	intron (NM_024928, intron 8 of 9)	intron (NM_024928, intron 8 of 9)	27933	NM_024928	79991	Hs.62314	NM_024928	ENSG00000107960	STN1	AAF-44|AAF44|OBFC1|RPA-32|bA541N10.2	STN1 subunit of CST complex	protein-coding	0.007335	0.482927	
chunk0169_242_1	chr6	105144618	105144818	+	0	NA	intron (NR_037157, intron 1 of 3)	L1MC2|LINE|L1	7031	NR_037157	154442	Hs.586271	NR_037157	ENSG00000203808	BVES-AS1	C6orf112|bA99L11.2	BVES antisense RNA 1	ncRNA	0.000000	0.333333	
chunk0025_25_1	chr10	48295760	48295959	+	0	NA	Intergenic	Intergenic	-10780	NM_001278547	5599	Hs.138211	NM_002750	ENSG00000107643	MAPK8	JNK|JNK-46|JNK1|JNK1A2|JNK21B1/2|PRKM8|SAPK1|SAPK1c	mitogen-activated protein kinase 8	protein-coding	0.005025	0.520000	
chunk0027_365_1	chr10	79086952	79087856	+	0	NA	intron (NM_020338, intron 1 of 24)	intron (NM_020338, intron 1 of 24)	18369	NM_020338	57178	Hs.193118	NM_020338	ENSG00000108175	ZMIZ1	MIZ|RAI17|TRAFIP10|ZIMP10	zinc finger MIZ-type containing 1	protein-coding	0.008850	0.489503	
chunk0144_303_1	chr4	138413285	138413696	+	0	NA	intron (NR_051987, intron 2 of 2)	intron (NR_051987, intron 2 of 2)	103779	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.002433	0.308252	
chunk0190_152_1	chr8	31165569	31165935	+	0	NA	intron (NM_000553, intron 33 of 34)	intron (NM_000553, intron 33 of 34)	-132037	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.005464	0.297003	
chunk0123_10_1	chr3	40231230	40231765	+	0	NA	intron (NM_001284424, intron 11 of 15)	intron (NM_001284424, intron 11 of 15)	-78185	NM_005875	10289	Hs.315230	NM_005875	ENSG00000114784	EIF1B	GC20	eukaryotic translation initiation factor 1B	protein-coding	0.007477	0.442164	
chunk0079_229_1	chr17	15463468	15463688	+	0	NA	intron (NM_001204477, intron 1 of 3)	intron (NM_001204477, intron 1 of 3)	4033	NM_001204477	284040	Hs.164595	NM_173622	ENSG00000239704	CDRT4	-	CMT1A duplicated region transcript 4	protein-coding	0.018182	0.497738	
chunk0038_146_1	chr11	84412301	84412516	+	0	NA	intron (NM_001142699, intron 7 of 27)	intron (NM_001142699, intron 7 of 27)	-95069	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004651	0.361111	
chunk0154_346_1	chr5	86881306	86881505	+	0	NA	Intergenic	Intergenic	134587	NR_105017	100505878	Hs.246405	NR_105017		LINC02059	-	long intergenic non-protein coding RNA 2059	ncRNA	0.010050	0.480000	
chunk0027_247_1	chr10	77078566	77079114	+	0	NA	intron (NM_001014797, intron 13 of 28)	intron (NM_001014797, intron 13 of 28)	-61991	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.018248	0.448087	
chunk0101_169_1	chr2	129036090	129036320	+	0	NA	Intergenic	L1MD|LINE|L1	171605	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.008696	0.402597	
chunk0196_422_1	chr8	116170371	116171018	+	0	NA	intron (NR_046215, intron 4 of 13)	intron (NR_046215, intron 4 of 13)	154365	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.006182	0.342593	
chunk0135_420_1	chr3	193552953	193553249	+	0	NA	promoter-TSS (NR_046726)	promoter-TSS (NR_046726)	-112	NR_121666	101929198	Hs.450092	NR_046726		ATP13A4-AS1	-	ATP13A4 antisense RNA 1	ncRNA	0.003378	0.474747	177(GAAAACACAGTGTCCC,-,0.00),178(AAAACACAGTGTCCCT,+,0.00)
chunk0169_320_1	chr6	106247110	106247771	+	0	NA	intron (NR_104402, intron 4 of 5)	intron (NR_104402, intron 4 of 5)	68826	NR_104403	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.004539	0.344411	
chunk0179_212_1	chr7	47660986	47661200	+	0	NA	3' UTR (NM_001123065, exon 3 of 3)	3' UTR (NM_001123065, exon 3 of 3)	5849	NM_001123065	401335	Hs.520816	NM_001123065		C7orf65	-	chromosome 7 open reading frame 65	protein-coding	0.014019	0.488372	
chunk0058_63_1	chr14	20687613	20687978	+	0	NA	promoter-TSS (NM_001097577)	promoter-TSS (NM_001097577)	-978	NM_001097577	283	Hs.283749	NM_001145	ENSG00000214274	ANG	ALS9|HEL168|RAA1|RNASE4|RNASE5	angiogenin	protein-coding	0.000000	0.426230	
chunk0136_324_1	chr3	195419299	195419748	+	0	NA	intron (NM_012287, intron 1 of 22)	HY1|scRNA|scRNA	23565	NM_012287	23527	Hs.593373	NM_012287	ENSG00000114331	ACAP2	CENTB2|CNT-B2	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	protein-coding	0.002227	0.355556	314(TAGACAGACTGTCCTG,+,0.00)
chunk0079_308_1	chr17	17191625	17191917	+	0	NA	3' UTR (NM_201274, exon 24 of 24)	3' UTR (NM_201274, exon 24 of 24)	14561	NM_178836	201164	Hs.729079	NM_178836	ENSG00000179598	PLD6	ZUC	phospholipase D family member 6	protein-coding	0.027397	0.453925	162(AAGAACACTCAGTTCA,-,0.00),163(AGAACACTCAGTTCAC,+,0.00)
chunk0130_128_1	chr3	131728863	131729250	+	0	NA	intron (NM_130808, intron 2 of 15)	intron (NM_130808, intron 2 of 15)	-226040	NM_007208	11222	Hs.205163	NM_007208	ENSG00000114686	MRPL3	COXPD9|MRL3|RPML3	mitochondrial ribosomal protein L3	protein-coding	0.007752	0.453608	
chunk0128_141_1	chr3	106776752	106777288	+	0	NA	Intergenic	Intergenic	463618	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.009328	0.415270	
chunk0001_288_1	chr1	8788727	8788971	+	0	NA	intron (NM_001042681, intron 1 of 22)	L2b|LINE|L2	28791	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.008197	0.514286	
chunk0027_42_1	chr10	72693220	72693419	+	0	NA	intron (NM_001270680, intron 1 of 7)	intron (NM_001270680, intron 1 of 7)	700	NM_001270680	90550	Hs.591366	NM_138357	ENSG00000156026	MCU	C10orf42|CCDC109A|HsMCU	mitochondrial calcium uniporter	protein-coding	0.000000	0.420000	
chunk0152_329_1	chr5	62194858	62195384	+	0	NA	Intergenic	MamRep1527|LTR|LTR	-111041	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.003802	0.459203	
chunk0052_312_1	chr12	125014554	125014792	+	0	NA	intron (NM_080626, intron 2 of 2)	MER68B|LTR|ERVL	12750	NR_110375	102659353	Hs.596464	NR_110375	ENSG00000280634	THRIL	BRI3BP-AS1|BRI3BPAS1|Linc1992|TCONS_00020260	TNF and HNRNPL related immunoregulatory long non-coding RNA	ncRNA	0.008403	0.531381	
chunk0171_25_1	chr6	120247172	120247723	+	0	NA	Intergenic	LTR86C|LTR|ERVL	232268	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.003630	0.346014	
chunk0162_241_1	chr6	4904609	4904967	+	0	NA	intron (NR_026590, intron 4 of 8)	intron (NR_026590, intron 4 of 8)	14796	NM_001143971	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.016760	0.451253	
chunk0102_327_1	chr2	151824886	151825426	+	0	NA	intron (NM_177985, intron 1 of 5)	L2a|LINE|L2	3339	NM_177985	26225	Hs.470233	NM_012097	ENSG00000162980	ARL5A	ARFLP5|ARL5	ADP ribosylation factor like GTPase 5A	protein-coding	0.003704	0.371534	
chunk0022_292_1	chr10	15509685	15509924	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-138745	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.016736	0.441667	155(GGGAACACGGTGTGAT,-,0.00)
chunk0098_76_1	chr2	67319217	67319799	+	0	NA	Intergenic	Intergenic	-77802	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.013746	0.382504	
chunk0041_177_1	chr11	126221813	126222167	+	0	NA	intron (NM_024556, intron 1 of 8)	intron (NM_024556, intron 1 of 8)	10266	NM_024556	79607	Hs.276315	NM_024556	ENSG00000197798	FAM118B	-	family with sequence similarity 118 member B	protein-coding	0.008475	0.402817	
chunk0199_52_1	chr9	1856615	1857191	+	0	NA	Intergenic	MIR|SINE|MIR	-158316	NM_001289397	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.003472	0.358752	
chunk0041_166_1	chr11	126071959	126072535	+	0	NA	Intergenic	Intergenic	-8955	NM_016952	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.005208	0.353553	
chunk0053_304_1	chr13	33817910	33818197	+	0	NA	promoter-TSS (NM_002915)	promoter-TSS (NM_002915)	-16	NM_181558	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.094077	0.538194	
chunk0060_211_1	chr14	48842760	48843292	+	0	NA	Intergenic	L2a|LINE|L2	743390	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.003759	0.422139	
chunk0150_342_1	chr5	38600319	38600799	+	0	NA	intron (NR_103554, intron 2 of 8)	L2|LINE|L2	-5154	NM_002310	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.002083	0.422037	
chunk0041_403_1	chr11	133817489	133817954	+	0	NA	Intergenic	Intergenic	-7345	NR_120444	646522	Hs.560000	NR_120444	ENSG00000255258	LINC02743	-	long intergenic non-protein coding RNA 2743	ncRNA	0.015054	0.581545	255(AGGGACAGCGTGTGCT,-,0.00),256(GGGACAGCGTGTGCTC,+,0.00)
chunk0043_411_1	chr12	25813596	25814230	+	0	NA	Intergenic	Intergenic	60166	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.007886	0.404724	
chunk0183_120_1	chr7	105388093	105388292	+	0	NA	intron (NM_182692, intron 2 of 15)	CpG	738	NM_182692	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.100503	0.730000	
chunk0056_261_1	chr13	89980765	89981521	+	0	NA	Intergenic	Intergenic	138574	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.001323	0.284016	
chunk0109_256_1	chr20	7387929	7388217	+	0	NA	Intergenic	Intergenic	16465	NR_107029	102465865		NR_107029	ENSG00000278159	MIR8062	hsa-mir-8062	microRNA 8062	ncRNA	0.003472	0.352941	
chunk0164_133_1	chr6	21103564	21104053	+	0	NA	intron (NM_017774, intron 12 of 15)	intron (NM_017774, intron 12 of 15)	408084	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.012270	0.385714	
chunk0035_134_1	chr11	42794602	42795449	+	0	NA	Intergenic	L1ME3G|LINE|L1	474344	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.003542	0.287736	
chunk0168_253_1	chr6	88973052	88973452	+	0	NA	Intergenic	MER67C|LTR|ERV1	-9623	NM_001286426	8732	Hs.567378	NM_003800	ENSG00000111880	RNGTT	CAP1A|HCE|HCE1|hCAP	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0.002500	0.384040	
chunk0051_446_1	chr12	123259820	123260465	+	0	NA	TTS (NM_001270434)	TTS (NM_001270434)	8112	NM_001270434	8099	Hs.433201	NM_004642	ENSG00000111328	CDK2AP1	DOC1|DORC1|ST19|doc-1|p12DOC-1	cyclin dependent kinase 2 associated protein 1	protein-coding	0.015504	0.402477	334(ATGTACTTTATGTTCT,-,0.00),335(TGTACTTTATGTTCTT,+,0.00)
chunk0141_22_1	chr4	76738271	76738470	+	0	NA	intron (NM_020859, intron 4 of 10)	intron (NM_020859, intron 4 of 10)	159479	NM_001029870	345079	Hs.257292	NM_001029870	ENSG00000186212	SOWAHB	ANKRD56	sosondowah ankyrin repeat domain family member B	protein-coding	0.005025	0.400000	
chunk0172_211_1	chr6	136720218	136720710	+	0	NA	exon (NM_005923, exon 2 of 30)	exon (NM_005923, exon 2 of 30)	72054	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.018293	0.395538	
chunk0127_203_1	chr3	96272395	96272719	+	0	NA	Intergenic	Intergenic	-87407	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.307692	213(TGGCACAAACAGTTCT,-,0.00),214(GGCACAAACAGTTCTT,+,0.00)
chunk0044_265_1	chr12	32277339	32277941	+	0	NA	intron (NM_001003398, intron 2 of 8)	intron (NM_001003398, intron 2 of 8)	170389	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.004983	0.354892	
chunk0090_4_1	chr19	372368	372649	+	0	NA	intron (NM_199202, intron 4 of 6)	intron (NM_199202, intron 4 of 6)	3505	NM_199202	51298	Hs.250002	NM_016585	ENSG00000105549	THEG	CT56|THEG1	theg spermatid protein	protein-coding	0.017794	0.592199	
chunk0105_373_1	chr2	192062367	192062566	+	0	NA	intron (NM_016192, intron 4 of 9)	L1ME2|LINE|L1	132467	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.000000	0.315000	
chunk0150_220_1	chr5	35363615	35364029	+	0	NA	Intergenic	Intergenic	-133233	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.007246	0.378313	143(GAAAACAGGATGTTCT,-,0.00),144(AAAACAGGATGTTCTT,+,0.00)
chunk0182_261_1	chr7	97555847	97556513	+	0	NA	Intergenic	Intergenic	-175779	NM_013996	6863	Hs.2563	NM_003182	ENSG00000006128	TAC1	Hs.2563|NK2|NKNA|NPK|TAC2	tachykinin precursor 1	protein-coding	0.015015	0.442279	
chunk0070_241_1	chr15	73111225	73111427	+	0	NA	intron (NM_002499, intron 1 of 28)	intron (NM_002499, intron 1 of 28)	58842	NM_002499	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.014851	0.300493	
chunk0194_392_1	chr8	90987362	90987565	+	0	NA	Intergenic	L2b|LINE|L2	-2206	NM_001190972	100127983	Hs.733266	NM_001190972	ENSG00000253250	C8orf88	-	chromosome 8 open reading frame 88	protein-coding	0.000000	0.411765	
chunk0129_27_1	chr3	117170001	117170584	+	0	NA	Intergenic	Intergenic	248861	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001715	0.416096	310(CAGCACAGCCTGTTCA,-,0.00),311(AGCACAGCCTGTTCAC,+,0.00)
chunk0039_393_1	chr11	107161520	107162225	+	0	NA	Intergenic	L1MA7|LINE|L1	-143427	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.001418	0.327195	
chunk0164_435_1	chr6	27542457	27542892	+	0	NA	Intergenic	Intergenic	-69556	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.004598	0.371560	
chunk0167_122_1	chr6	60870385	60871289	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-703266	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.008850	0.434254	195(GTCACACTGTGTTCTT,+,0.00)
chunk0155_188_1	chr5	94605004	94605255	+	0	NA	intron (NM_001145678, intron 1 of 20)	L1PA10|LINE|L1	13475	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.000000	0.333333	
chunk0065_2_1	chr15	17081318	17081872	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-3201149	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.009025	0.472072	
chunk0013_97_1	chr1	167715571	167715799	+	0	NA	Intergenic	Intergenic	-6265	NM_001146191	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.030702	0.366812	
chunk0141_48_1	chr4	77386804	77387048	+	0	NA	Intergenic	Intergenic	-124827	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.004098	0.448980	
chunk0020_61_1	chr1	232557543	232558171	+	0	NA	Intergenic	Intergenic	-42249	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.003185	0.414944	324(CTGAACATCCTGTACC,-,0.00),325(TGAACATCCTGTACCA,+,0.00)
chunk0129_88_1	chr3	119130522	119131111	+	0	NA	intron (NM_152538, intron 1 of 8)	L1PA6|LINE|L1	15235	NM_152538	152404	Hs.112873	NM_152538	ENSG00000144847	IGSF11	BT-IgSF|CT119|CXADRL1|Igsf13|VSIG3	immunoglobulin superfamily member 11	protein-coding	0.008489	0.489831	
chunk0172_174_1	chr6	136351670	136351885	+	0	NA	intron (NM_001198619, intron 16 of 17)	LTR41|LTR|ERVL	-61926	NM_001077440	9774	Hs.486542	NM_014739	ENSG00000029363	BCLAF1	BTF|bK211L9.1	BCL2 associated transcription factor 1	protein-coding	0.009302	0.430556	
chunk0052_131_1	chr13	23577579	23577825	+	0	NA	intron (NM_001204459, intron 1 of 7)	L2c|LINE|L2	-1658	NM_001204458	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.036585	0.510121	
chunk0008_342_1	chr1	95888861	95889629	+	0	NA	Intergenic	Intergenic	-102823	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.010417	0.384915	
chunk0181_399_1	chr7	89928689	89929287	+	0	NA	intron (NR_110029, intron 2 of 2)	intron (NR_110029, intron 2 of 2)	-190412	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.000000	0.350584	
chunk0060_174_1	chr14	46122712	46122914	+	0	NA	intron (NR_102701, intron 1 of 5)	intron (NR_102701, intron 1 of 5)	58654	NR_102701	100506412	Hs.207545	NR_102699	ENSG00000258700	LINC00871	-	long intergenic non-protein coding RNA 871	ncRNA	0.009901	0.325123	
chunk0029_127_1	chr10	98582112	98582324	+	0	NA	intron (NM_001166246, intron 9 of 12)	MER97a|DNA|hAT-Tip100	-135255	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.009434	0.305164	
chunk0066_378_1	chr15	38819083	38819871	+	0	NA	Intergenic	Intergenic	122879	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.013959	0.433460	
chunk0041_105_1	chr11	124837103	124837302	+	0	NA	Intergenic	Intergenic	-28207	NM_022370	64221	Hs.435621	NM_022370	ENSG00000154134	ROBO3	HGPPS|HGPPS1|HGPS|RBIG1|RIG1	roundabout guidance receptor 3	protein-coding	0.010050	0.445000	
chunk0037_53_1	chr11	70739797	70740466	+	0	NA	intron (NM_012309, intron 13 of 24)	L2a|LINE|L2	-78291	NM_133266	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.028401	0.573134	265(TAGGACAGACAGTGCC,-,0.00),266(AGGACAGACAGTGCCT,+,0.00),320(TAGGACAGACAGTGCC,-,0.00),321(AGGACAGACAGTGCCT,+,0.00),375(TAGGACAGACAGTGCC,-,0.00),376(AGGACAGACAGTGCCT,+,0.00)
chunk0027_28_1	chr10	72273516	72274036	+	0	NA	promoter-TSS (NM_019058)	promoter-TSS (NM_019058)	-143	NM_019058	54541	Hs.744875	NM_019058	ENSG00000168209	DDIT4	Dig2|REDD-1|REDD1	DNA damage inducible transcript 4	protein-coding	0.084615	0.664107	
chunk0008_220_1	chr1	93899334	93899857	+	0	NA	intron (NM_001308253, intron 2 of 5)	L1ME4c|LINE|L1	10003	NM_002061	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.007648	0.311069	
chunk0001_428_1	chr1	11292460	11292892	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	19478	NM_013319	29914	Hs.522933	NM_013319	ENSG00000120942	UBIAD1	SCCD|TERE1	UbiA prenyltransferase domain containing 1	protein-coding	0.011574	0.478060	
chunk0072_444_1	chr15	101639620	101640120	+	0	NA	intron (NM_001307960, intron 4 of 4)	L2a|LINE|L2	12521	NM_025141	80213	Hs.288912	NM_025141	ENSG00000184277	TM2D3	BLP2	TM2 domain containing 3	protein-coding	0.008000	0.413174	
chunk0005_345_1	chr1	61187824	61188091	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	65561	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.014981	0.511194	139(GTGGACTCCGTGTTCC,-,0.00),140(TGGACTCCGTGTTCCC,+,0.00)
chunk0170_414_1	chr6	118075338	118075788	+	0	NA	intron (NM_001029858, intron 1 of 7)	intron (NM_001029858, intron 1 of 7)	168037	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.002222	0.310421	279(CAGGACATCCTGTTAT,-,0.00)
chunk0061_335_1	chr14	63370803	63371161	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-52103	NM_145171	122876	Hs.375028	NM_145171	ENSG00000179600	GPHB5	B5|GPB5|ZLUT1	glycoprotein hormone subunit beta 5	protein-coding	0.008380	0.467967	274(AGAGACACGATGTTCT,-,0.00),275(GAGACACGATGTTCTT,+,0.00)
chunk0191_93_1	chr8	47659107	47659909	+	0	NA	intron (NM_001080394, intron 10 of 19)	intron (NM_001080394, intron 10 of 19)	78656	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.032419	0.499377	416(AAGAACACAATGTCCT,-,0.00),417(AGAACACAATGTCCTG,+,0.00)
chunk0044_38_1	chr12	27478293	27478530	+	0	NA	intron (NM_001145010, intron 5 of 8)	L1M2|LINE|L1	11601	NM_001145010	341346	Hs.282121	NM_001145010	ENSG00000165935	SMCO2	C12orf70	single-pass membrane protein with coiled-coil domains 2	protein-coding	0.000000	0.575630	149(GGGTCATCATGTCCCT,+,0.00)
chunk0069_69_1	chr15	60913814	60914749	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	232712	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.008556	0.425214	
chunk0181_77_1	chr7	80304046	80304322	+	0	NA	Intergenic	Intergenic	70255	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.007246	0.277978	
chunk0081_237_1	chr17	42918875	42919162	+	0	NA	Intergenic	Intergenic	18221	NM_000151	2538	Hs.212293	NM_000151	ENSG00000131482	G6PC	G6PC1|G6PT|G6Pase|GSD1|GSD1a	glucose-6-phosphatase catalytic subunit	protein-coding	0.006969	0.395833	
chunk0098_333_1	chr2	77013313	77013697	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	27540	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.013021	0.425974	
chunk0146_114_1	chr4	158851866	158852333	+	0	NA	intron (NM_020840, intron 8 of 16)	intron (NM_020840, intron 8 of 16)	83069	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.004283	0.376068	
chunk0062_414_1	chr14	75120359	75120861	+	0	NA	intron (NM_033116, intron 3 of 21)	intron (NM_033116, intron 3 of 21)	6465	NM_033116	91754	Hs.7200	NM_033116	ENSG00000119638	NEK9	APUG|LCCS10|NC|NERCC|NERCC1	NIMA related kinase 9	protein-coding	0.001992	0.351889	
chunk0140_318_1	chr4	73285809	73286020	+	0	NA	Intergenic	Intergenic	-27129	NM_198889	26057	Hs.601206	NM_015574	ENSG00000132466	ANKRD17	GTAR|MASK2|NY-BR-16	ankyrin repeat domain 17	protein-coding	0.000000	0.433962	
chunk0203_258_1	chr9	87714700	87715264	+	0	NA	Intergenic	Intergenic	-11077	NM_001912	1514	Hs.731507	NM_001912	ENSG00000135047	CTSL	CATL|CTSL1|MEP	cathepsin L	protein-coding	0.003546	0.415929	
chunk0055_269_1	chr13	63926615	63927066	+	0	NA	Intergenic	L1M5|LINE|L1	-82715	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.004435	0.254425	
chunk0068_356_1	chr15	57973070	57973376	+	0	NA	intron (NM_170696, intron 6 of 11)	intron (NM_170696, intron 6 of 11)	40874	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.000000	0.328990	
chunk0023_183_1	chr10	24681136	24681630	+	0	NA	intron (NM_020824, intron 2 of 25)	intron (NM_020824, intron 2 of 25)	42285	NM_020824	57584	Hs.524195	NM_020824	ENSG00000107863	ARHGAP21	ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.002024	0.331313	
chunk0040_202_1	chr11	114149177	114149830	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	88937	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.007657	0.388379	
chunk0063_402_1	chr14	88174668	88174879	+	0	NA	Intergenic	Intergenic	96138	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.009479	0.533019	
chunk0143_244_1	chr4	114695879	114696253	+	0	NA	Intergenic	Intergenic	39307	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.005348	0.282667	
chunk0160_444_1	chr5	164871388	164871739	+	0	NA	Intergenic	Intergenic	401284	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.005698	0.309659	
chunk0115_137_1	chr21	23417699	23418248	+	0	NA	Intergenic	Intergenic	-33138	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.005464	0.300000	
chunk0190_396_1	chr8	40181272	40181892	+	0	NA	Intergenic	Intergenic	28114	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.004839	0.384863	
chunk0027_306_1	chr10	77887266	77888028	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	38943	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.010499	0.458716	
chunk0154_207_1	chr5	80403335	80403722	+	0	NA	Intergenic	Intergenic	-4485	NM_001284237	9765	Hs.482660	NM_014733	ENSG00000039319	ZFYVE16	PPP1R69	zinc finger FYVE-type containing 16	protein-coding	0.007752	0.365979	184(ATAACAGCCTGTACTT,+,0.00)
chunk0128_49_1	chr3	104810889	104811570	+	0	NA	Intergenic	L1MA6|LINE|L1	-555484	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.001468	0.379765	
chunk0100_63_1	chr2	106551580	106552147	+	0	NA	Intergenic	Intergenic	-83518	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.010582	0.515845	
chunk0023_225_1	chr10	26733943	26734525	+	0	NA	intron (NM_014317, intron 8 of 11)	intron (NM_014317, intron 8 of 11)	36568	NM_014317	23590	Hs.558468	NM_014317	ENSG00000148459	PDSS1	COQ1|COQ10D2|COQ1A|DPS|SPS|TPRT|TPT|TPT 1|hDPS1	decaprenyl diphosphate synthase subunit 1	protein-coding	0.015464	0.504288	
chunk0005_267_1	chr1	59815891	59816274	+	0	NA	intron (NM_015888, intron 1 of 21)	intron (NM_015888, intron 1 of 21)	1221	NM_015888	51361	Hs.378836	NM_015888	ENSG00000134709	HOOK1	HK1	hook microtubule tethering protein 1	protein-coding	0.007833	0.408854	
chunk0137_444_1	chr4	28923008	28923517	+	0	NA	Intergenic	Intergenic	103680	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.005894	0.388235	
chunk0114_9_1	chr21	6371198	6371674	+	0	NA	Intergenic	Intergenic	96172	NM_000071	875	Hs.533013	NM_000071	ENSG00000160200	CBS	CBSL|HIP4	cystathionine-beta-synthase	protein-coding	0.027311	0.545073	
chunk0156_144_1	chr5	107230263	107230525	+	0	NA	Intergenic	Intergenic	-219380	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.007634	0.490494	
chunk0092_239_1	chr19	32717371	32717700	+	0	NA	Intergenic	Intergenic	-2238	NM_001110822	91646	Hs.646351	NM_001015890	ENSG00000173809	TDRD12	ECAT8	tudor domain containing 12	protein-coding	0.015198	0.460606	166(GTGAGCATTCTGTTCC,-,0.00),167(TGAGCATTCTGTTCCC,+,0.00)
chunk0052_318_1	chr12	125096421	125096926	+	0	NA	intron (NM_023928, intron 5 of 17)	intron (NM_023928, intron 5 of 17)	31294	NM_023928	65985	Hs.656073	NM_023928	ENSG00000081760	AACS	ACSF1|SUR-5	acetoacetyl-CoA synthetase	protein-coding	0.011881	0.559289	
chunk0022_298_1	chr10	15548362	15548694	+	0	NA	exon (NM_003638, exon 27 of 30)	exon (NM_003638, exon 27 of 30)	171807	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.021084	0.411411	
chunk0160_301_1	chr5	158905327	158905740	+	0	NA	intron (NM_182708, intron 5 of 14)	intron (NM_182708, intron 5 of 14)	194247	NM_182708	1879	Hs.573143	NM_024007	ENSG00000164330	EBF1	COE1|EBF|O/E-1|OLF1	EBF transcription factor 1	protein-coding	0.012107	0.367150	
chunk0123_394_1	chr3	48885657	48886265	+	0	NA	intron (NM_000387, intron 2 of 8)	HAL1|LINE|L1	13032	NM_000387	788	Hs.13845	NM_000387	ENSG00000178537	SLC25A20	CAC|CACT	solute carrier family 25 member 20	protein-coding	0.006579	0.385878	
chunk0208_22_1	chrX	11053157	11053822	+	0	NA	Intergenic	Intergenic	-57797	NM_001171991	3052	Hs.211571	NM_005333	ENSG00000004961	HCCS	CCHL|LSDMCA1|MCOPS7|MLS	holocytochrome c synthase	protein-coding	0.000000	0.352853	
chunk0211_255_1	chrX	120672325	120672776	+	0	NA	Intergenic	Intergenic	-42400	NM_152692	29071	Hs.643920	NM_152692	ENSG00000171155	C1GALT1C1	C1GALT2|C38H2-L1|COSMC|HSPC067|MST143|TNPS	C1GALT1 specific chaperone 1	protein-coding	0.006652	0.400442	161(AAGAACACTGTGCTCC,-,0.00),162(AGAACACTGTGCTCCT,+,0.00)
chunk0089_189_1	chr18	59902208	59902478	+	0	NA	intron (NM_021127, intron 1 of 1)	intron (NM_021127, intron 1 of 1)	2383	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.011111	0.350554	
chunk0186_318_1	chr7	143063590	143064436	+	0	NA	promoter-TSS (NR_002140)	promoter-TSS (NR_002140)	-228	NR_002140	89883	Hs.339818	NR_002140		OR6W1P	OR6W1|sdolf	olfactory receptor family 6 subfamily W member 1 pseudogene	pseudo	0.005910	0.429752	
chunk0134_126_1	chr3	177359744	177360240	+	0	NA	Intergenic	Intergenic	65550	NR_047465	100820709	Hs.518409	NR_047465	ENSG00000203645	LINC00501	-	long intergenic non-protein coding RNA 501	ncRNA	0.070565	0.619718	
chunk0001_282_1	chr1	8729881	8730371	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	87514	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.002041	0.338086	
chunk0170_164_1	chr6	111602080	111602467	+	0	NA	TTS (NR_034109)	TTS (NR_034109)	3678	NM_147200	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.007752	0.422680	
chunk0082_144_1	chr17	55452385	55452858	+	0	NA	Intergenic	Intergenic	-30641	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.008457	0.455696	
chunk0125_74_1	chr3	64514700	64514931	+	0	NA	TTS (NM_182920)	TTS (NM_182920)	-46531	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.004329	0.443966	
chunk0176_368_1	chr7	18420055	18420447	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-75495	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.007653	0.371501	
chunk0139_55_1	chr4	48777488	48777990	+	0	NA	intron (NM_015030, intron 1 of 63)	intron (NM_015030, intron 1 of 63)	2560	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.007968	0.351889	
chunk0072_301_1	chr15	98751798	98752333	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-32361	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.009346	0.438433	
chunk0034_26_1	chr11	26264152	26264558	+	0	NA	intron (NM_001313726, intron 1 of 27)	intron (NM_001313726, intron 1 of 27)	23652	NR_132968	105376599	Hs.125537	NR_132968	ENSG00000254819	ANO3-AS1	-	ANO3 antisense RNA 1	ncRNA	0.002463	0.324324	
chunk0057_293_1	chr13	106284240	106284878	+	0	NA	Intergenic	Intergenic	-92004	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.007837	0.375587	
chunk0027_313_1	chr10	78010128	78010677	+	0	NA	intron (NM_007055, intron 12 of 30)	intron (NM_007055, intron 12 of 30)	19138	NM_007055	11128	Hs.436896	NM_007055	ENSG00000148606	POLR3A	ADDH|HLD7|RPC1|RPC155|WDRTS|hRPC155	RNA polymerase III subunit A	protein-coding	0.014572	0.407273	288(AGGAACACTGTGTTCC,-,0.00),289(GGAACACTGTGTTCCA,+,0.00)
chunk0207_271_1	chr9	132381462	132382653	+	0	NA	intron (NM_007344, intron 9 of 10)	intron (NM_007344, intron 9 of 10)	24794	NM_001205296	7270	Hs.54780	NM_007344	ENSG00000125482	TTF1	TTF-1|TTF-I	transcription termination factor 1	protein-coding	0.017632	0.458054	
chunk0131_183_1	chr3	147664698	147665126	+	0	NA	Intergenic	Intergenic	243585	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.000000	0.351981	
chunk0119_47_1	chr22	40711449	40712028	+	0	NA	Intergenic	LTR81A|LTR|Gypsy	32560	NM_005297	2847	Hs.248122	NM_005297	ENSG00000128285	MCHR1	GPR24|MCH-1R|MCH1R|SLC-1|SLC1	melanin concentrating hormone receptor 1	protein-coding	0.027634	0.505172	
chunk0204_75_1	chr9	93886076	93886816	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	67089	NR_036254	100422927		NR_036254	ENSG00000265347	MIR4291	-	microRNA 4291	ncRNA	0.008108	0.360324	380(TAGTACAGAATGTGCT,-,0.00),381(AGTACAGAATGTGCTA,+,0.00)
chunk0090_330_1	chr18	76112288	76112487	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-10611	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.015075	0.435000	
chunk0117_105_1	chr22	17877424	17877638	+	0	NA	intron (NM_001136004, intron 17 of 21)	intron (NM_001136004, intron 17 of 21)	29355	NM_001122731	57553	Hs.528024	NM_015241	ENSG00000243156	MICAL3	MICAL-3	microtubule associated monooxygenase, calponin and LIM domain containing 3	protein-coding	0.000000	0.497674	
chunk0131_225_1	chr3	149259247	149259459	+	0	NA	Intergenic	L1MA4A|LINE|L1	-37308	NM_000096	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.009434	0.591549	
chunk0145_360_1	chr4	151284433	151285068	+	0	NA	intron (NM_183375, intron 4 of 4)	L1MEf|LINE|L1	7577	NM_183375	345062	Hs.651266	NM_183375	ENSG00000189099	PRSS48	ESSPL	serine protease 48	protein-coding	0.004724	0.374214	
chunk0178_357_1	chr7	38877000	38877227	+	0	NA	intron (NM_080631, intron 2 of 27)	intron (NM_080631, intron 2 of 27)	32087	NM_080631	27072	Hs.592184	NM_014396	ENSG00000006715	VPS41	HVPS41|HVSP41|hVps41p	VPS41 subunit of HOPS complex	protein-coding	0.008811	0.425439	
chunk0159_201_1	chr5	140412630	140413116	+	0	NA	intron (NM_024668, intron 1 of 10)	intron (NM_024668, intron 1 of 10)	11059	NM_017978	54882	Hs.594084	NM_017747	ENSG00000131503	ANKHD1	MASK|MASK1|PP2500|VBARP	ankyrin repeat and KH domain containing 1	protein-coding	0.000000	0.328542	278(AGCACATTTTGCTCTT,+,0.00)
chunk0173_280_1	chr6	147898186	147898693	+	0	NA	Intergenic	Intergenic	389747	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.003945	0.379921	
chunk0107_333_1	chr2	220969289	220969488	+	0	NA	Intergenic	Intergenic	602970	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.015075	0.420000	
chunk0044_213_1	chr12	31022070	31022494	+	0	NA	intron (NR_038927, intron 2 of 2)	LTR40a|LTR|ERVL	-51563	NM_001257144	1663	Hs.443960	NM_004399	ENSG00000013573	DDX11	CHL1|CHLR1|KRG2|WABS	DEAD/H-box helicase 11	protein-coding	0.007075	0.449412	
chunk0055_370_1	chr13	73001970	73002201	+	0	NA	intron (NM_006346, intron 17 of 17)	intron (NM_006346, intron 17 of 17)	-52891	NM_001286818	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.000000	0.349138	96(AGGCACTTAGTGTACC,-,0.00),97(GGCACTTAGTGTACCA,+,0.00)
chunk0071_74_1	chr15	80715723	80716455	+	0	NA	intron (NM_021214, intron 1 of 2)	intron (NM_021214, intron 1 of 2)	20778	NM_021214	58489	Hs.459072	NM_021214	ENSG00000136379	ABHD17C	FAM108C1	abhydrolase domain containing 17C	protein-coding	0.009563	0.402456	
chunk0013_425_1	chr1	173445562	173446495	+	0	NA	intron (NR_125960, intron 1 of 1)	L1MEf|LINE|L1	15334	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.005359	0.377944	
chunk0028_264_1	chr10	90887549	90888779	+	0	NA	intron (NM_006413, intron 6 of 10)	intron (NM_006413, intron 6 of 10)	16212	NM_006413	10556	Hs.139120	NM_006413	ENSG00000148688	RPP30	TSG15	ribonuclease P/MRP subunit p30	protein-coding	0.011382	0.434606	
chunk0176_431_1	chr7	19845895	19846507	+	0	NA	Intergenic	Intergenic	-73420	NM_152774	256130	Hs.487670	NM_152774	ENSG00000173452	TMEM196	-	transmembrane protein 196	protein-coding	0.011438	0.402936	
chunk0063_389_1	chr14	87020863	87021117	+	0	NA	Intergenic	Intergenic	115212	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.039370	0.462745	
chunk0060_53_1	chr14	41445457	41445668	+	0	NA	Intergenic	Intergenic	-161999	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.004739	0.405660	
chunk0139_184_1	chr4	54281323	54281808	+	0	NA	intron (NM_006206, intron 16 of 22)	intron (NM_006206, intron 16 of 22)	52468	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.014433	0.430041	
chunk0130_122_1	chr3	131502721	131503208	+	0	NA	promoter-TSS (NM_007208)	promoter-TSS (NM_007208)	52	NM_007208	11222	Hs.205163	NM_007208	ENSG00000114686	MRPL3	COXPD9|MRL3|RPML3	mitochondrial ribosomal protein L3	protein-coding	0.080082	0.600410	
chunk0079_302_1	chr17	17053674	17054063	+	0	NA	intron (NM_015134, intron 1 of 22)	intron (NM_015134, intron 1 of 22)	11108	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.005141	0.441026	234(AAGTACAGTAAGTCCT,-,0.00),235(AGTACAGTAAGTCCTC,+,0.00)
chunk0208_447_1	chrX	31423850	31424049	+	0	NA	intron (NM_004021, intron 17 of 34)	intron (NM_004021, intron 17 of 34)	84349	NM_004014	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.005025	0.405000	
chunk0166_180_1	chr6	46098711	46099091	+	0	NA	Intergenic	Intergenic	-18553	NM_001114086	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.007895	0.514436	
chunk0196_428_1	chr8	116318865	116319272	+	0	NA	intron (NR_046215, intron 1 of 13)	L1PA11|LINE|L1	5991	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.002457	0.333333	
chunk0080_29_1	chr17	21052736	21053120	+	0	NA	Intergenic	L1MEc|LINE|L1	-9889	NM_015276	23326	Hs.462492	NM_015276	ENSG00000124422	USP22	USP3L	ubiquitin specific peptidase 22	protein-coding	0.018229	0.350649	
chunk0179_218_1	chr7	47774812	47775575	+	0	NA	intron (NM_138295, intron 56 of 56)	L1M5|LINE|L1	13717	NR_038407	84847	Hs.488236	NR_038407	ENSG00000146666	LINC00525	-	long intergenic non-protein coding RNA 525	ncRNA	0.005242	0.376963	611(AGACACAGGATGTTCT,-,0.00),612(GACACAGGATGTTCTC,+,0.00)
chunk0053_19_1	chr13	26571502	26571798	+	0	NA	intron (NM_006646, intron 1 of 9)	L1MC4a|LINE|L1	13947	NM_001291965	10810	Hs.618732	NM_006646	ENSG00000132970	WASF3	Brush-1|SCAR3|WAVE3	WASP family member 3	protein-coding	0.003378	0.360269	
chunk0019_14_1	chr1	223419693	223420352	+	0	NA	Intergenic	MIRb|SINE|MIR	26649	NM_152610	164127	Hs.192090	NM_152610	ENSG00000178395	CCDC185	C1orf65	coiled-coil domain containing 185	protein-coding	0.018209	0.493939	433(AGGTACTATTTGTTCT,-,0.00),434(GGTACTATTTGTTCTT,+,0.00)
chunk0061_71_1	chr14	56651047	56651446	+	0	NA	Intergenic	Intergenic	71453	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.000000	0.365000	
chunk0136_452_1	chr3	198149965	198150219	+	0	NA	Intergenic	Intergenic	-2274	NM_001145248	728262	Hs.744675	NM_001145248	ENSG00000236438	FAM157A	GTF2IP18	family with sequence similarity 157 member A	ncRNA	0.019685	0.403922	
chunk0126_91_1	chr3	74801903	74802267	+	0	NA	Intergenic	Intergenic	-280945	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.005495	0.353425	254(AGGGACAGTCTGTAAT,-,0.00),255(GGGACAGTCTGTAATT,+,0.00)
chunk0140_131_1	chr4	69125590	69126030	+	0	NA	Intergenic	Intergenic	29335	NM_001074	7364	Hs.654424	NM_001074	ENSG00000171234	UGT2B7	UDPGT 2B7|UDPGT 2B9|UDPGT2B7|UDPGTH2|UDPGTh-2|UGT2B9	UDP glucuronosyltransferase family 2 member B7	protein-coding	0.004545	0.349206	
chunk0132_149_1	chr3	156542307	156543162	+	0	NA	3' UTR (NM_007107, exon 5 of 5)	3' UTR (NM_007107, exon 5 of 5)	11391	NM_001308205	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.004678	0.370327	232(TGGAACAGTGTGTTCT,-,0.00),233(GGAACAGTGTGTTCTT,+,0.00)
chunk0172_53_1	chr6	134109625	134109990	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	7873	NR_037938	387065	Hs.571061	NR_037938		HMGA1P7	HMGA1L7	high mobility group AT-hook 1 pseudogene 7	pseudo	0.013699	0.360656	
chunk0190_158_1	chr8	31299134	31299414	+	0	NA	Intergenic	Intergenic	-265559	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.007143	0.505338	
chunk0026_34_1	chr10	60726040	60726777	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	7118	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.002714	0.340108	
chunk0030_119_1	chr10	112945632	112946149	+	0	NA	Intergenic	Intergenic	-4360	NM_001198529	6934	Hs.593995	NM_030756	ENSG00000148737	TCF7L2	TCF-4|TCF4	transcription factor 7 like 2	protein-coding	0.011605	0.438224	
chunk0148_327_1	chr5	14107219	14107436	+	0	NA	Intergenic	L1MEd|LINE|L1	-36393	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.004608	0.284404	
chunk0084_438_1	chr17	82838078	82838394	+	0	NA	intron (NM_024702, intron 1 of 2)	intron (NM_024702, intron 1 of 2)	1819	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.022152	0.435331	
chunk0183_116_1	chr7	105364712	105365080	+	0	NA	intron (NM_182692, intron 2 of 15)	Tigger2|DNA|TcMar-Tigger	24034	NM_182692	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.000000	0.449864	
chunk0093_183_1	chr19	48784746	48784945	+	0	NA	Intergenic	Intergenic	26218	NM_001284325	587	Hs.512670	NM_001190	ENSG00000105552	BCAT2	BCAM|BCATM|BCT2|PP18	branched chain amino acid transaminase 2	protein-coding	0.020101	0.465000	
chunk0004_44_1	chr1	42937886	42938132	+	0	NA	intron (NM_006516, intron 2 of 9)	MIR3|SINE|MIR	-21040	NR_033967	440584	Hs.260928	NR_033967	ENSG00000227533	SLC2A1-AS1	-	SLC2A1 antisense RNA 1	ncRNA	0.004065	0.526316	
chunk0192_455_1	chr8	70230632	70231034	+	0	NA	intron (NM_006540, intron 2 of 22)	intron (NM_006540, intron 2 of 22)	-159506	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.000000	0.263027	
chunk0147_292_1	chr4	184400071	184400758	+	0	NA	intron (NM_002199, intron 6 of 8)	L1MD2|LINE|L1	-18108	NR_125933	102723766	Hs.432281	NR_125933	ENSG00000249096	LINC02362	-	long intergenic non-protein coding RNA 2362	ncRNA	0.014556	0.409884	
chunk0060_45_1	chr14	41167235	41167552	+	0	NA	Intergenic	MER76|LTR|ERVL	212682	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.006309	0.367925	
chunk0173_403_1	chr6	150668503	150668759	+	0	NA	intron (NM_001029884, intron 2 of 16)	intron (NM_001029884, intron 2 of 16)	68768	NM_001029884	57480	Hs.189781	NM_001029884	ENSG00000120278	PLEKHG1	ARHGEF41	pleckstrin homology and RhoGEF domain containing G1	protein-coding	0.019531	0.431907	
chunk0171_411_1	chr6	131311401	131311850	+	0	NA	Intergenic	L1M4|LINE|L1	61466	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.000000	0.297778	
chunk0081_150_1	chr17	40803690	40804049	+	0	NA	Intergenic	Intergenic	-3910	NM_181535	162605	Hs.59736	NM_181535	ENSG00000173908	KRT28	K25IRS4|KRT25D	keratin 28	protein-coding	0.019499	0.452778	
chunk0013_100_1	chr1	167749776	167750201	+	0	NA	intron (NM_024569, intron 1 of 4)	Tigger15a|DNA|TcMar-Tigger	28038	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.002353	0.375587	
chunk0030_391_1	chr10	119658303	119658683	+	0	NA	intron (NM_004281, intron 1 of 3)	intron (NM_004281, intron 1 of 3)	7123	NM_004281	9531	Hs.523309	NM_004281	ENSG00000151929	BAG3	BAG-3|BIS|CAIR-1|MFM6	BCL2 associated athanogene 3	protein-coding	0.034211	0.572178	203(TTGAACTGAATGTTCC,-,0.00),204(TGAACTGAATGTTCCA,+,0.00)
chunk0202_34_1	chr9	70805895	70806449	+	0	NA	intron (NM_024971, intron 6 of 25)	intron (NM_024971, intron 6 of 25)	3912	NR_029621	406987		NR_029621	ENSG00000207935	MIR204	MIRN204|RDICC|miRNA204|mir-204	microRNA 204	ncRNA	0.016245	0.482883	334(GAGAACAGCCTGTTCA,-,0.00),335(AGAACAGCCTGTTCAT,+,0.00)
chunk0186_246_1	chr7	140931757	140932313	+	0	NA	Intergenic	L2a|LINE|L2	-7271	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.010791	0.348294	
chunk0200_94_1	chr9	16531407	16531738	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-255259	NR_073471									0.009063	0.298193	
chunk0093_225_1	chr19	50135904	50136393	+	0	NA	Intergenic	L1PB1|LINE|L1	-2284	NR_024230	100170217	Hs.723095	NR_024230		SNAR-B2	-	small NF90 (ILF3) associated RNA B2	snRNA	0.020450	0.375510	
chunk0066_12_1	chr15	27006457	27007129	+	0	NA	intron (NM_033223, intron 2 of 9)	L1PA15|LINE|L1	35511	NM_001270873	2567	Hs.569475	NM_033223	ENSG00000182256	GABRG3	-	gamma-aminobutyric acid type A receptor gamma3 subunit	protein-coding	0.008929	0.433878	
chunk0120_396_1	chr3	12486870	12487252	+	0	NA	intron (NM_001145395, intron 1 of 8)	L1MB7|LINE|L1	2550	NM_025265	80746	Hs.335550	NM_025265	ENSG00000154743	TSEN2	PCH2B|SEN2|SEN2L	tRNA splicing endonuclease subunit 2	protein-coding	0.010471	0.409922	
chunk0166_277_1	chr6	48272711	48273357	+	0	NA	Intergenic	Intergenic	-204345	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.007740	0.352396	
chunk0066_73_1	chr15	29337318	29337839	+	0	NA	intron (NM_015307, intron 2 of 10)	intron (NM_015307, intron 2 of 10)	-67762	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.009597	0.473180	
chunk0166_266_1	chr6	47762245	47762739	+	0	NA	Intergenic	L1MC1|LINE|L1	-19547	NM_181744	221391	Hs.213717	NM_181744	ENSG00000124818	OPN5	GPR136|GRP136|PGR12|TMEM13	opsin 5	protein-coding	0.006073	0.355556	
chunk0107_264_1	chr2	217463273	217463607	+	0	NA	intron (NR_026597, intron 3 of 12)	MIR3|SINE|MIR	180707	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.002994	0.447761	
chunk0121_93_1	chr3	16623057	16623258	+	0	NA	Intergenic	Intergenic	-17658	NM_001351	1618	Hs.131179	NM_001351	ENSG00000092345	DAZL	DAZH|DAZL1|DAZLA|SPGYLA	deleted in azoospermia like	protein-coding	0.000000	0.311881	
chunk0052_375_1	chr12	128932522	128932730	+	0	NA	intron (NR_133646, intron 7 of 10)	intron (NR_133646, intron 7 of 10)	79192	NM_144669	144423	Hs.655668	NM_144669	ENSG00000151948	GLT1D1	-	glycosyltransferase 1 domain containing 1	protein-coding	0.048077	0.531100	
chunk0161_441_1	chr5	178585447	178585833	+	0	NA	intron (NM_173465, intron 1 of 28)	intron (NM_173465, intron 1 of 28)	4915	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.031088	0.614987	
chunk0105_431_1	chr2	193585973	193586379	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-758093	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.009852	0.343980	
chunk0017_134_1	chr1	206560135	206560352	+	0	NA	intron (NM_182665, intron 1 of 4)	intron (NM_182665, intron 1 of 4)	3079	NM_182665	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.018433	0.550459	
chunk0028_333_1	chr10	92103543	92104173	+	0	NA	intron (NM_001178137, intron 7 of 9)	intron (NM_001178137, intron 7 of 9)	139421	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.001587	0.378764	
chunk0051_56_1	chr12	112375159	112375442	+	0	NA	intron (NM_001109662, intron 1 of 75)	L1ME1|LINE|L1	6792	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.017668	0.415493	
chunk0204_388_1	chr9	102206223	102206961	+	0	NA	Intergenic	Intergenic	-313045	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.008130	0.395129	372(TTGCACAGAATGTACT,-,0.00),373(TGCACAGAATGTACTC,+,0.00)
chunk0073_22_1	chr16	2260361	2260623	+	0	NA	intron (NM_080594, intron 6 of 7)	PABL_A-int|LTR|ERV1	6845	NM_001286625	10921	Hs.355643	NM_006711	ENSG00000205937	RNPS1	E5.1	RNA binding protein with serine rich domain 1	protein-coding	0.019084	0.399240	
chunk0186_375_1	chr7	144174021	144174234	+	0	NA	Intergenic	Intergenic	-8843	NM_001278507	100142659	Hs.661442	NM_001278507	ENSG00000244693	CTAGE8	CTAGE4	CTAGE family member 8	protein-coding	0.000000	0.336449	
chunk0145_10_1	chr4	143352140	143352572	+	0	NA	intron (NM_002039, intron 1 of 9)	intron (NM_002039, intron 1 of 9)	8896	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.000000	0.411085	
chunk0116_309_1	chr21	40641842	40642508	+	0	NA	intron (NR_073202, intron 3 of 32)	MIRb|SINE|MIR	-11408	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.013514	0.479760	
chunk0179_275_1	chr7	49430128	49430370	+	0	NA	Intergenic	Intergenic	-343412	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.000000	0.349794	
chunk0139_43_1	chr4	48635770	48636423	+	0	NA	intron (NM_015030, intron 3 of 63)	intron (NM_015030, intron 3 of 63)	144203	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.004594	0.293578	373(TTGAACACAGTGTACA,-,0.00),374(TGAACACAGTGTACAT,+,0.00)
chunk0025_411_1	chr10	59682604	59683135	+	0	NA	intron (NM_194298, intron 2 of 5)	intron (NM_194298, intron 2 of 5)	27022	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.001883	0.298872	
chunk0084_361_1	chr17	81400283	81400482	+	0	NA	TTS (NR_039894)	TTS (NR_039894)	396	NR_039894	100616294		NR_039894	ENSG00000266392	MIR4740	-	microRNA 4740	ncRNA	0.080402	0.565000	
chunk0012_439_1	chr1	164974756	164975214	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-200344	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.010917	0.477124	
chunk0181_338_1	chr7	88198267	88198889	+	0	NA	3' UTR (NM_016351, exon 30 of 30)	3' UTR (NM_016351, exon 30 of 30)	-18082	NR_120517	102723885	Hs.489040	NR_120517		LOC102723885	-	uncharacterized LOC102723885	ncRNA	0.006431	0.364366	
chunk0001_91_1	chr1	2896799	2897126	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-107297	NM_001242672	100287898	Hs.632363	NM_001242672	ENSG00000215912	TTC34	-	tetratricopeptide repeat domain 34	protein-coding	0.012232	0.448171	
chunk0142_365_1	chr4	101945987	101946607	+	0	NA	intron (NM_017935, intron 7 of 16)	L3|LINE|CR1	132471	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.012903	0.314010	
chunk0074_311_1	chr16	30445771	30445970	+	0	NA	5' UTR (NM_012248, exon 1 of 1)	5' UTR (NM_012248, exon 1 of 1)	105	NM_012248	22928	Hs.118725	NM_012248	ENSG00000179918	SEPHS2	SPS2	selenophosphate synthetase 2	protein-coding	0.055276	0.515000	
chunk0097_87_1	chr2	45388824	45389067	+	0	NA	3' UTR (NM_018079, exon 21 of 21)	3' UTR (NM_018079, exon 21 of 21)	-134004	NR_033831	400952	Hs.468368	NR_033831	ENSG00000205054	LINC01121	UNQ6975	long intergenic non-protein coding RNA 1121	ncRNA	0.004115	0.319672	
chunk0097_28_1	chr2	42379442	42379876	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-18443	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.006912	0.441379	
chunk0209_456_1	chrX	66633034	66633372	+	0	NA	intron (NM_001199687, intron 1 of 6)	A-rich|Low_complexity|Low_complexity	5847	NM_021783	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.008876	0.339233	
chunk0047_153_1	chr12	69719109	69719805	+	0	NA	intron (NR_110072, intron 3 of 3)	intron (NR_110072, intron 3 of 3)	19111	NR_110072	101928002	Hs.569096	NR_110072		LOC101928002	-	uncharacterized LOC101928002	ncRNA	0.001437	0.397418	
chunk0099_127_1	chr2	86102963	86103162	+	0	NA	intron (NM_015425, intron 1 of 33)	L2a|LINE|L2	3093	NM_015425	25885	Hs.531818	NM_015425	ENSG00000068654	POLR1A	A190|AFDCIN|RPA1|RPA194|RPO1-4|RPO14	RNA polymerase I subunit A	protein-coding	0.015075	0.430000	
chunk0141_57_1	chr4	77621165	77621404	+	0	NA	Intergenic	Intergenic	109531	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.004184	0.358333	
chunk0104_17_1	chr2	170530091	170530854	+	0	NA	intron (NR_045682, intron 31 of 35)	intron (NR_045682, intron 31 of 35)	-179529	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.013106	0.465969	299(AAGAACAGCCAGTGCT,-,0.00),300(AGAACAGCCAGTGCTC,+,0.00)
chunk0108_313_1	chr2	235468821	235469052	+	0	NA	Intergenic	Intergenic	-25153	NM_014914	116987	Hs.435039	NM_014914	ENSG00000157985	AGAP1	AGAP-1|CENTG2|GGAP1|cnt-g2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	protein-coding	0.017316	0.396552	134(AAGGACAGCGTGCACC,-,0.00),135(AGGACAGCGTGCACCT,+,0.00)
chunk0138_108_1	chr4	36196803	36197206	+	0	NA	intron (NM_015230, intron 6 of 32)	L2c|LINE|L2	-47112	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.012407	0.386139	
chunk0054_308_1	chr13	48493461	48494224	+	0	NA	intron (NM_001286831, intron 11 of 11)	L2a|LINE|L2	39414	NM_001268	1102	Hs.652712	NM_001268	ENSG00000136161	RCBTB2	CHC1L|RLG	RCC1 and BTB domain containing protein 2	protein-coding	0.006553	0.437173	
chunk0077_123_1	chr16	78385751	78385958	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	286441	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.024155	0.461538	
chunk0004_227_1	chr1	46942051	46942531	+	0	NA	promoter-TSS (NM_000778)	promoter-TSS (NM_000778)	-807	NM_000778	1579	Hs.1645	NM_000778	ENSG00000187048	CYP4A11	CP4Y|CYP4A2|CYP4AII|CYPIVA11	cytochrome P450 family 4 subfamily A member 11	protein-coding	0.002083	0.336798	274(AAGGACAATCTGTACT,-,0.00),275(AGGACAATCTGTACTA,+,0.00)
chunk0124_392_1	chr3	59664375	59664766	+	0	NA	Intergenic	Intergenic	-614581	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.002558	0.456633	
chunk0105_368_1	chr2	192008968	192009333	+	0	NA	intron (NM_016192, intron 5 of 9)	L4_C_Mam|LINE|RTE-X	-161870	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.005479	0.349727	
chunk0199_27_1	chr9	708838	709318	+	0	NA	intron (NM_153186, intron 1 of 10)	intron (NM_153186, intron 1 of 10)	2272	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.010417	0.399168	267(CAAAACAAGGTGTTCC,-,0.00),268(AAAACAAGGTGTTCCT,+,0.00)
chunk0117_420_1	chr21	45916156	45916614	+	0	NA	intron (NM_020528, intron 8 of 13)	intron (NM_020528, intron 8 of 13)	-56585	NR_109931	101928796	Hs.130919	NR_109931		LOC101928796	-	uncharacterized LOC101928796	ncRNA	0.019651	0.562092	
chunk0075_93_1	chr16	48365254	48365924	+	0	NA	5' UTR (NM_001006610, exon 1 of 2)	5' UTR (NM_001006610, exon 1 of 2)	284	NM_001006610	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.029851	0.536513	
chunk0040_217_1	chr11	114221169	114221406	+	0	NA	intron (NM_006006, intron 4 of 6)	intron (NM_006006, intron 4 of 6)	-74526	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.008439	0.436975	
chunk0063_417_1	chr14	88463381	88463746	+	0	NA	Intergenic	Intergenic	77919	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.008219	0.407104	
chunk0061_171_1	chr14	59897748	59898017	+	0	NA	Intergenic	Intergenic	-21831	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.018587	0.477778	
chunk0135_177_1	chr3	188061053	188061647	+	0	NA	Intergenic	Intergenic	-92523	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.003367	0.415126	
chunk0187_20_1	chr8	640176	640801	+	0	NA	intron (NM_001303100, intron 5 of 5)	intron (NM_001303100, intron 5 of 5)	90751	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.017600	0.450479	223(AGGAACATTCTGTAAT,-,0.00)
chunk0068_139_1	chr15	53523152	53523534	+	0	NA	intron (NR_102334, intron 18 of 19)	(AG)n|Simple_repeat|Simple_repeat	17509	NR_102336	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.007853	0.381201	
chunk0086_217_1	chr18	22510478	22510766	+	0	NA	Intergenic	L1M4|LINE|L1	-92707	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.003472	0.335640	90(AAGAACAGTCTCTACT,-,0.00),91(AGAACAGTCTCTACTG,+,0.00)
chunk0011_292_1	chr1	151513084	151513374	+	0	NA	intron (NM_020770, intron 1 of 20)	intron (NM_020770, intron 1 of 20)	1843	NM_020770	57530	Hs.591464	NM_020770	ENSG00000143375	CGN	-	cingulin	protein-coding	0.006897	0.577320	
chunk0135_403_1	chr3	192613233	192613635	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	114165	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.007463	0.310174	
chunk0076_267_1	chr16	69424514	69424751	+	0	NA	promoter-TSS (NM_030579)	promoter-TSS (NM_030579)	37	NM_030579	80777	Hs.461131	NM_030579	ENSG00000103018	CYB5B	CYB5-M|CYPB5M|OMB5	cytochrome b5 type B	protein-coding	0.067511	0.554622	
chunk0144_242_1	chr4	135290830	135291185	+	0	NA	Intergenic	MIRb|SINE|MIR	597086	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.000000	0.342697	
chunk0083_147_1	chr17	65784861	65785652	+	0	NA	intron (NM_001302891, intron 19 of 24)	L1MB7|LINE|L1	41287	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.003793	0.343434	
chunk0076_276_1	chr16	69574293	69574624	+	0	NA	intron (NM_138713, intron 2 of 14)	intron (NM_138713, intron 2 of 14)	8492	NM_006599	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.003021	0.277108	
chunk0043_83_1	chr12	14537444	14537801	+	0	NA	intron (NM_024829, intron 4 of 10)	intron (NM_024829, intron 4 of 10)	-30110	NR_120465	101928290	Hs.131933	NR_120465	ENSG00000256751	PLBD1-AS1	-	PLBD1 antisense RNA 1	ncRNA	0.005602	0.382682	
chunk0064_404_1	chr14	99467443	99467642	+	0	NA	intron (NM_032233, intron 1 of 12)	intron (NM_032233, intron 1 of 12)	13347	NM_032233	84193	Hs.510407	NM_032233	ENSG00000183576	SETD3	C14orf154|hSETD3	SET domain containing 3, actin histidine methyltransferase	protein-coding	0.020101	0.510000	
chunk0007_49_1	chr1	77796465	77797188	+	0	NA	intron (NM_198549, intron 2 of 15)	L1MC4a|LINE|L1	17202	NM_198549	374986	Hs.437755	NM_198549	ENSG00000180488	MIGA1	FAM73A	mitoguardin 1	protein-coding	0.008299	0.410221	363(GAGCACAATTTGTTCT,-,0.00),364(AGCACAATTTGTTCTT,+,0.00)
chunk0103_452_1	chr2	170293857	170294321	+	0	NA	intron (NR_045684, intron 7 of 34)	L1MD2|LINE|L1	56854	NR_110576	101929753	Hs.534101	NR_110576		MYO3B-AS1	-	MYO3B antisense RNA 1	ncRNA	0.004310	0.359140	
chunk0096_34_1	chr2	26867089	26867473	+	0	NA	intron (NM_001253724, intron 1 of 12)	intron (NM_001253724, intron 1 of 12)	18857	NM_001253724	56896	Hs.299315	NM_020134	ENSG00000157851	DPYSL5	CRAM|CRMP-5|CRMP5|Ulip6	dihydropyrimidinase like 5	protein-coding	0.007812	0.335065	
chunk0174_350_1	chr6	164317741	164318046	+	0	NA	Intergenic	Intergenic	504170	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.003279	0.343137	
chunk0025_161_1	chr10	52566398	52567266	+	0	NA	Intergenic	Intergenic	-96299	NR_120641	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.006912	0.327963	
chunk0152_217_1	chr5	60325932	60326490	+	0	NA	intron (NM_001165899, intron 1 of 16)	L1MD1|LINE|L1	-161502	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.003584	0.354204	
chunk0119_154_1	chr22	43114931	43115419	+	0	NA	intron (NM_001197, intron 1 of 4)	L2c|LINE|L2	4427	NM_001197	638	Hs.475055	NM_001197	ENSG00000100290	BIK	BIP1|BP4|NBK	BCL2 interacting killer	protein-coding	0.014344	0.582822	
chunk0125_450_1	chr3	72948988	72949391	+	0	NA	intron (NM_001080393, intron 3 of 6)	L2c|LINE|L2	-47779	NM_174907	151987	Hs.431092	NM_174907	ENSG00000163605	PPP4R2	PP4R2	protein phosphatase 4 regulatory subunit 2	protein-coding	0.009926	0.507426	201(TTGGACAGCCTGATCT,-,0.00),202(TGGACAGCCTGATCTC,+,0.00)
chunk0066_315_1	chr15	35773775	35774071	+	0	NA	intron (NR_038251, intron 2 of 2)	intron (NR_038251, intron 2 of 2)	-152933	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.006757	0.313131	
chunk0002_222_1	chr1	19889734	19890075	+	0	NA	intron (NM_015207, intron 1 of 7)	intron (NM_015207, intron 1 of 7)	7509	NM_015207	23252	Hs.374987	NM_015207	ENSG00000169914	OTUD3	DUBA4	OTU deubiquitinase 3	protein-coding	0.000000	0.406433	
chunk0038_51_1	chr11	82574200	82574769	+	0	NA	Intergenic	L1MC4|LINE|L1	159380	NM_175885	220382	Hs.448218	NM_175885	ENSG00000182103	FAM181B	-	family with sequence similarity 181 member B	protein-coding	0.003515	0.298246	
chunk0089_80_1	chr18	58237421	58237946	+	0	NA	intron (NM_001144971, intron 3 of 30)	intron (NM_001144971, intron 3 of 30)	16161	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.001905	0.366920	
chunk0063_176_1	chr14	80427230	80427445	+	0	NA	intron (NR_038355, intron 8 of 8)	intron (NR_038355, intron 8 of 8)	-196283	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.004651	0.398148	
chunk0132_123_1	chr3	156009786	156010309	+	0	NA	Intergenic	Intergenic	-110501	NM_172160	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.005736	0.333969	
chunk0204_440_1	chr9	103972818	103973404	+	0	NA	Intergenic	Intergenic	-26598	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.006826	0.359455	
chunk0087_423_1	chr18	42264772	42265033	+	0	NA	intron (NR_046454, intron 3 of 6)	intron (NR_046454, intron 3 of 6)	78234	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.007663	0.339695	
chunk0100_310_1	chr2	115899926	115900363	+	0	NA	Intergenic	Intergenic	738037	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.006865	0.321918	
chunk0035_22_1	chr11	40328831	40329406	+	0	NA	intron (NM_020929, intron 2 of 4)	intron (NM_020929, intron 2 of 4)	-35988	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003478	0.378472	
chunk0213_10_1	chrY	20360057	20360646	+	0	NA	Intergenic	L1MA3|LINE|L1	158877	NR_001542	246119	Hs.461175	NR_001542	ENSG00000229236	TTTY10	NCRNA00133|TTY10	testis-specific transcript, Y-linked 10	ncRNA	0.005093	0.296610	
chunk0076_345_1	chr16	71593741	71594452	+	0	NA	Intergenic	Intergenic	-17001	NM_000353	6898	Hs.161640	NM_000353	ENSG00000198650	TAT	-	tyrosine aminotransferase	protein-coding	0.005626	0.463483	
chunk0185_192_1	chr7	128343701	128343910	+	0	NA	5' UTR (NM_018077, exon 1 of 19)	5' UTR (NM_018077, exon 1 of 19)	103	NM_001166135	55131	Hs.274263	NM_018077	ENSG00000106344	RBM28	ANES	RNA binding motif protein 28	protein-coding	0.095694	0.642857	
chunk0161_304_1	chr5	173408890	173409287	+	0	NA	Intergenic	L1ME4a|LINE|L1	61633	NR_107023	102465862		NR_107023	ENSG00000274994	MIR8056	hsa-mir-8056	microRNA 8056	ncRNA	0.002519	0.276382	
chunk0201_219_1	chr9	37324798	37325552	+	0	NA	intron (NM_032226, intron 5 of 8)	intron (NM_032226, intron 5 of 8)	-97535	NM_012203	9380	Hs.155742	NM_012203	ENSG00000137106	GRHPR	GLXR|GLYD|PH2	glyoxylate and hydroxypyruvate reductase	protein-coding	0.006631	0.349669	
chunk0140_375_1	chr4	74771227	74772303	+	0	NA	intron (NM_001729, intron 1 of 5)	L1ME4a|LINE|L1	22921	NM_001316963	685	Hs.591704	NM_001729	ENSG00000174808	BTC	-	betacellulin	protein-coding	0.002788	0.332405	
chunk0097_313_1	chr2	56230065	56230654	+	0	NA	intron (NM_001080433, intron 2 of 5)	intron (NM_001080433, intron 2 of 5)	-44589	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.005093	0.384746	
chunk0078_258_1	chr17	7329412	7329732	+	0	NA	promoter-TSS (NM_001005408)	promoter-TSS (NM_001005408)	-253	NM_001005408	84461	Hs.654794	NM_032442	ENSG00000215041	NEURL4	-	neuralized E3 ubiquitin protein ligase 4	protein-coding	0.090625	0.632399	
chunk0071_450_1	chr15	90160430	90160629	+	0	NA	Intergenic	Intergenic	-24391	NM_020210	10509	Hs.474935	NM_020210	ENSG00000185033	SEMA4B	SEMAC|SemC	semaphorin 4B	protein-coding	0.025126	0.400000	
chunk0183_103_1	chr7	105248878	105249329	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	19974	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.011086	0.411504	234(GAGCACATCCTGTTTC,-,0.00),235(AGCACATCCTGTTTCA,+,0.00)
chunk0181_111_1	chr7	80641405	80642006	+	0	NA	intron (NM_001001548, intron 1 of 14)	intron (NM_001001548, intron 1 of 14)	3189	NM_000072	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.003328	0.372093	
chunk0111_153_1	chr20	25067719	25067966	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-9660	NM_032501	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.036437	0.524194	
chunk0003_1_1	chr1	28512284	28512753	+	0	NA	intron (NM_001048199, intron 3 of 11)	L1MEc|LINE|L1	3960	NR_004404	26768		NR_004404	ENSG00000200087	SNORA73B	105A|E1c|RNU105A|RNU17B|U17B	small nucleolar RNA, H/ACA box 73B	snoRNA	0.000000	0.346809	
chunk0017_57_1	chr1	205370849	205371158	+	0	NA	Intergenic	Intergenic	-2249	NR_038425	284576	Hs.585440	NR_038425	ENSG00000226235	LEMD1-AS1	-	LEMD1 antisense RNA 1	ncRNA	0.000000	0.461290	
chunk0173_416_1	chr6	151024675	151025570	+	0	NA	intron (NM_001242767, intron 24 of 27)	intron (NM_001242767, intron 24 of 27)	158789	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.027933	0.464286	
chunk0009_221_1	chr1	106541403	106542038	+	0	NA	Intergenic	Intergenic	-514925	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.003150	0.306604	
chunk0074_138_1	chr16	23072028	23072378	+	0	NA	intron (NM_020718, intron 14 of 15)	intron (NM_020718, intron 14 of 15)	77067	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.037143	0.592593	
chunk0159_5_1	chr5	136041203	136041402	+	0	NA	intron (NM_000358, intron 2 of 16)	intron (NM_000358, intron 2 of 16)	12407	NM_000358	7045	Hs.369397	NM_000358	ENSG00000120708	TGFBI	BIGH3|CDB1|CDG2|CDGG1|CSD|CSD1|CSD2|CSD3|EBMD|LCD1	transforming growth factor beta induced	protein-coding	0.010050	0.545000	
chunk0171_161_1	chr6	124294714	124294913	+	0	NA	intron (NM_001300740, intron 1 of 5)	intron (NM_001300740, intron 1 of 5)	11808	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.005025	0.375000	
chunk0035_447_1	chr11	57624917	57625255	+	0	NA	Intergenic	Intergenic	-16112	NR_029673	406919		NR_029673	ENSG00000208009	MIR130A	MIRN130A|miRNA130A|mir-130a	microRNA 130a	ncRNA	0.005917	0.430678	
chunk0069_347_1	chr15	66593384	66593764	+	0	NA	intron (NR_110372, intron 1 of 4)	intron (NR_110372, intron 1 of 4)	11384	NR_110372	102723165	Hs.636703	NR_110372	ENSG00000259471	LINC01169	-	long intergenic non-protein coding RNA 1169	ncRNA	0.005263	0.514436	
chunk0067_391_1	chr15	49112585	49112784	+	0	NA	Intergenic	L1MA4A|LINE|L1	42973	NM_004236	9318	Hs.369614	NM_004236	ENSG00000166200	COPS2	ALIEN|CSN2|SGN2|TRIP15	COP9 signalosome subunit 2	protein-coding	0.000000	0.300000	
chunk0092_298_1	chr19	34254358	34254572	+	0	NA	promoter-TSS (NM_014686)	promoter-TSS (NM_014686)	-86	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.107477	0.730233	
chunk0193_394_1	chr8	80440976	80441525	+	0	NA	Intergenic	Intergenic	-44369	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.003643	0.445455	
chunk0119_58_1	chr22	40947673	40948043	+	0	NA	Intergenic	Intergenic	-3489	NM_014248	9978	Hs.474949	NM_014248	ENSG00000100387	RBX1	BA554C12.1|RNF75|ROC1	ring-box 1	protein-coding	0.002703	0.390836	
chunk0069_265_1	chr15	64640207	64640439	+	0	NA	intron (NM_015042, intron 2 of 8)	AluJo|SINE|Alu	62958	NM_001301302	4947	Hs.744924	NM_002537	ENSG00000180304	OAZ2	AZ2	ornithine decarboxylase antizyme 2	protein-coding	0.008621	0.446352	
chunk0188_195_1	chr8	11800422	11800812	+	0	NA	intron (NM_001287744, intron 1 of 7)	LTR10C|LTR|ERV1	-1994	NM_001287756	2222	Hs.593928	NM_004462	ENSG00000079459	FDFT1	DGPT|ERG9|SQS|SQSD|SS	farnesyl-diphosphate farnesyltransferase 1	protein-coding	0.007692	0.391304	256(AAGAACATGAAGTACA,-,0.00),257(AGAACATGAAGTACAT,+,0.00)
chunk0015_211_1	chr1	187520030	187520557	+	0	NA	Intergenic	Intergenic	76665	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001898	0.301136	
chunk0037_45_1	chr11	70402676	70403124	+	0	NA	intron (NM_005231, intron 1 of 17)	L1MB7|LINE|L1	4394	NM_001184740	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.002232	0.400891	
chunk0195_74_1	chr8	93983077	93983559	+	0	NA	Intergenic	Intergenic	66267	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.022822	0.492754	155(TTGTACACGCTGTTCC,-,0.00),156(TGTACACGCTGTTCCT,+,0.00)
chunk0182_15_1	chr7	91209642	91210005	+	0	NA	3' UTR (NM_012395, exon 14 of 14)	3' UTR (NM_012395, exon 14 of 14)	-54645	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.008264	0.392857	
chunk0042_216_1	chr12	6089133	6089490	+	0	NA	intron (NM_000552, intron 6 of 51)	intron (NM_000552, intron 6 of 51)	35359	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.025210	0.516760	
chunk0140_246_1	chr4	71350943	71351293	+	0	NA	intron (NM_001098484, intron 5 of 25)	intron (NM_001098484, intron 5 of 25)	12065	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.008571	0.455840	
chunk0048_309_1	chr12	82931043	82931893	+	0	NA	intron (NM_152588, intron 4 of 11)	intron (NM_152588, intron 4 of 11)	244313	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004706	0.390129	
chunk0079_317_1	chr17	17253364	17253886	+	0	NA	intron (NM_001316356, intron 8 of 10)	intron (NM_001316356, intron 8 of 10)	-16437	NM_144997	201163	Hs.31652	NM_144606	ENSG00000154803	FLCN	BHD|DENND8B|FLCL	folliculin	protein-coding	0.009579	0.434034	
chunk0050_42_1	chr12	100605801	100606142	+	0	NA	intron (NM_001303130, intron 4 of 8)	L1MA2|LINE|L1	12353	NM_001303131	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.000000	0.347953	
chunk0149_133_1	chr5	19855492	19855788	+	0	NA	intron (NM_001167667, intron 2 of 12)	intron (NM_001167667, intron 2 of 12)	30632	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.336700	
chunk0050_28_1	chr12	99983521	99983720	+	0	NA	intron (NM_152788, intron 1 of 25)	intron (NM_152788, intron 1 of 25)	1034	NM_152788	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.020101	0.500000	
chunk0015_174_1	chr1	186848600	186848834	+	0	NA	intron (NM_001311193, intron 1 of 15)	intron (NM_001311193, intron 1 of 15)	19817	NM_024420	5321	Hs.497200	NM_024420	ENSG00000116711	PLA2G4A	GURDP|PLA2G4|cPLA2|cPLA2-alpha	phospholipase A2 group IVA	protein-coding	0.000000	0.387234	
chunk0143_74_1	chr4	108118559	108118805	+	0	NA	intron (NM_016269, intron 3 of 11)	intron (NM_016269, intron 3 of 11)	48115	NM_001166119	51176	Hs.743478	NM_016269	ENSG00000138795	LEF1	LEF-1|TCF10|TCF1ALPHA|TCF7L3	lymphoid enhancer binding factor 1	protein-coding	0.004065	0.388664	
chunk0212_64_1	chrY	11328843	11329162	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1092588	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.003135	0.437500	
chunk0145_394_1	chr4	152487143	152487532	+	0	NA	intron (NM_001257069, intron 2 of 3)	L1MC4|LINE|L1	2079	NR_036092	100422896		NR_036092	ENSG00000264678	MIR3140	mir-3140	microRNA 3140	ncRNA	0.000000	0.294872	
chunk0118_436_1	chr22	38755153	38755733	+	0	NA	promoter-TSS (NM_001199580)	promoter-TSS (NM_001199580)	19	NM_001199580	25777	Hs.517622	NM_015374	ENSG00000100242	SUN2	UNC84B	Sad1 and UNC84 domain containing 2	protein-coding	0.075862	0.685026	257(GGGAACTGCCTGTCCC,-,0.00),258(GGAACTGCCTGTCCCT,+,0.00)
chunk0039_157_1	chr11	98867934	98868629	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-152695	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004317	0.408046	
chunk0050_87_1	chr12	101761309	101761760	+	0	NA	intron (NM_024312, intron 14 of 20)	intron (NM_024312, intron 14 of 20)	-22062	NM_153694	50511	Hs.506504	NM_153694	ENSG00000139351	SYCP3	COR1|RPRGL4|SCP3|SPGF4	synaptonemal complex protein 3	protein-coding	0.013304	0.353982	
chunk0132_36_1	chr3	154772237	154772468	+	0	NA	Intergenic	L1PA14|LINE|L1	-307295	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.012987	0.538793	
chunk0057_61_1	chr13	97724351	97724773	+	0	NA	Intergenic	Intergenic	-229113	NM_002271	3843	Hs.712598	NM_002271	ENSG00000065150	IPO5	IMB3|KPNB3|Pse1|RANBP5|imp5	importin 5	protein-coding	0.007109	0.385343	184(AGGTACACCATGTACT,-,0.00),185(GGTACACCATGTACTT,+,0.00)
chunk0140_307_1	chr4	73047663	73048385	+	0	NA	Intergenic	LTR47B3|LTR|ERVL	21735	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.005540	0.399723	
chunk0206_292_1	chr9	124563242	124563816	+	0	NA	intron (NM_033334, intron 2 of 9)	MIR|SINE|MIR	-56109	NM_004959	2516	Hs.495108	NM_004959	ENSG00000136931	NR5A1	AD4BP|ELP|FTZ1|FTZF1|POF7|SF-1|SF1|SPGF8|SRXX4|SRXY3|hSF-1	nuclear receptor subfamily 5 group A member 1	protein-coding	0.005226	0.354783	
chunk0003_295_1	chr1	37513497	37513696	+	0	NA	intron (NR_073090, intron 1 of 8)	intron (NR_073090, intron 1 of 8)	1223	NR_073092	64769	Hs.17118	NM_022756	ENSG00000163875	MEAF6	C1orf149|CENP-28|EAF6|NY-SAR-91	MYST/Esa1 associated factor 6	protein-coding	0.025126	0.425000	
chunk0105_362_1	chr2	191895019	191895266	+	0	NA	Intergenic	LTR16B1|LTR|ERVL	-47862	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.012146	0.411290	55(CTGTACATTCTGTCCT,-,0.00),56(TGTACATTCTGTCCTC,+,0.00)
chunk0183_405_1	chr7	110394505	110395056	+	0	NA	Intergenic	L1MA10|LINE|L1	-434567	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.003630	0.329710	
chunk0138_102_1	chr4	36084844	36085263	+	0	NA	intron (NM_015230, intron 28 of 32)	intron (NM_015230, intron 28 of 32)	-159063	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.011933	0.304762	
chunk0054_302_1	chr13	48384492	48384817	+	0	NA	intron (NM_000321, intron 17 of 26)	intron (NM_000321, intron 17 of 26)	28863	NM_001162498	10161	Hs.123464	NM_005767	ENSG00000139679	LPAR6	ARWH1|HYPT8|LAH3|P2RY5|P2Y5	lysophosphatidic acid receptor 6	protein-coding	0.006154	0.365031	
chunk0078_384_1	chr16	87788860	87789226	+	0	NA	Intergenic	L1M5|LINE|L1	-9895	NR_120309	102724467	Hs.587857	NR_120309		LOC102724467	-	uncharacterized LOC102724467	ncRNA	0.010929	0.395095	
chunk0181_274_1	chr7	86248917	86249447	+	0	NA	Intergenic	Intergenic	-394732	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.001887	0.299435	
chunk0132_425_1	chr3	164640367	164641078	+	0	NA	Intergenic	Intergenic	190758	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.002813	0.307584	
chunk0007_141_1	chr1	79323534	79324147	+	0	NA	Intergenic	AluJb|SINE|Alu	-317030	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.001631	0.421824	
chunk0111_64_1	chr20	22961238	22961744	+	0	NA	Intergenic	Intergenic	-73929	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.007905	0.469428	
chunk0069_38_1	chr15	60529229	60529803	+	0	NA	intron (NR_120339, intron 5 of 5)	intron (NR_120339, intron 5 of 5)	50338	NR_120340	101928784	Hs.655155	NR_120339	ENSG00000245534	RORA-AS1	-	RORA antisense RNA 1	ncRNA	0.001742	0.309565	
chunk0035_48_1	chr11	41232722	41232945	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	226803	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.004484	0.357143	
chunk0087_283_1	chr18	38764083	38764308	+	0	NA	Intergenic	L1PB1|LINE|L1	857980	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.000000	0.358407	
chunk0197_216_1	chr8	122728353	122728944	+	0	NA	Intergenic	Intergenic	-34542	NR_126348	104266958	Hs.575540	NR_126348	ENSG00000253819	LINC01151	-	long intergenic non-protein coding RNA 1151	ncRNA	0.005076	0.442568	
chunk0158_249_1	chr5	130893884	130894232	+	0	NA	Intergenic	L1PA6|LINE|L1	271290	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.011494	0.507163	
chunk0184_99_1	chr7	113382884	113383177	+	0	NA	Intergenic	MIR|SINE|MIR	-264448	NR_015442									0.006826	0.282313	
chunk0200_20_1	chr9	14659654	14660105	+	0	NA	intron (NM_178566, intron 6 of 9)	intron (NM_178566, intron 6 of 9)	33603	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.013304	0.358407	
chunk0116_340_1	chr21	41491413	41491700	+	0	NA	intron (NM_001135099, intron 3 of 13)	intron (NM_001135099, intron 3 of 13)	16509	NM_001135099	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.017422	0.506944	97(AGGCACACGATGTTCT,-,0.00),98(GGCACACGATGTTCTC,+,0.00)
chunk0031_279_1	chr10	128140603	128140956	+	0	NA	Intergenic	Intergenic	-14575	NM_002417	4288	Hs.80976	NM_002417	ENSG00000148773	MKI67	KIA|MIB-|MIB-1|PPP1R105	marker of proliferation Ki-67	protein-coding	0.011331	0.485876	
chunk0168_321_1	chr6	92422652	92422989	+	0	NA	Intergenic	L1PA5|LINE|L1	-732392	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.008902	0.387574	117(AAGAACAACCAGTACC,-,0.00),118(AGAACAACCAGTACCA,+,0.00)
chunk0108_247_1	chr2	233912919	233913185	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-4346	NM_024080	79054	Hs.366053	NM_024080	ENSG00000144481	TRPM8	LTRPC6|LTrpC-6|TRPP8|trp-p8	transient receptor potential cation channel subfamily M member 8	protein-coding	0.030075	0.546816	
chunk0115_444_1	chr21	32232987	32233342	+	0	NA	Intergenic	Intergenic	45901	NM_018944	54069	Hs.190518	NM_018944	ENSG00000159055	MIS18A	B28|C21orf45|C21orf46|FASP1|MIS18alpha|hMis18alpha	MIS18 kinetochore protein A	protein-coding	0.000000	0.365169	
chunk0129_140_1	chr3	120433511	120433775	+	0	NA	intron (NM_007085, intron 2 of 10)	L2a|LINE|L2	17428	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.000000	0.418868	
chunk0084_432_1	chr17	82648218	82648685	+	0	NA	promoter-TSS (NM_019613)	promoter-TSS (NM_019613)	84	NM_019613	56270	Hs.132161	NM_019613	ENSG00000141580	WDR45B	NEDSBAS|WDR45L|WIPI-3|WIPI3	WD repeat domain 45B	protein-coding	0.141328	0.747863	
chunk0153_335_1	chr5	74111556	74112180	+	0	NA	Intergenic	L1ME3|LINE|L1	196457	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.004808	0.336000	
chunk0108_365_1	chr2	236660674	236661359	+	0	NA	Intergenic	Intergenic	91279	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.001460	0.393586	246(GGGTACAGTGTGTATT,-,0.00),247(GGTACAGTGTGTATTT,+,0.00)
chunk0013_149_1	chr1	168606119	168606529	+	0	NA	Intergenic	L1MB4|LINE|L1	29851	NM_002995	6375	Hs.546295	NM_002995	ENSG00000143184	XCL1	ATAC|LPTN|LTN|SCM-1|SCM-1a|SCM1|SCM1A|SCYC1	X-C motif chemokine ligand 1	protein-coding	0.000000	0.287105	
chunk0059_199_1	chr14	33439034	33439393	+	0	NA	intron (NM_022123, intron 3 of 10)	MIRc|SINE|MIR	-269724	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.002786	0.313889	
chunk0179_98_1	chr7	44707509	44707853	+	0	NA	exon (NM_002541, exon 22 of 23)	exon (NM_002541, exon 22 of 23)	-40885	NM_001300959	83637	Hs.77978	NM_031449	ENSG00000122515	ZMIZ2	NET27|TRAFIP20|ZIMP7|hZIMP7	zinc finger MIZ-type containing 2	protein-coding	0.017442	0.591304	
chunk0185_356_1	chr7	132356113	132356787	+	0	NA	intron (NM_020911, intron 3 of 31)	intron (NM_020911, intron 3 of 31)	220114	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.007418	0.428148	
chunk0204_382_1	chr9	102177228	102177617	+	0	NA	Intergenic	L1MA6|LINE|L1	-342215	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.005141	0.512821	
chunk0135_105_1	chr3	186743149	186743828	+	0	NA	TTS (NM_001102416)	TTS (NM_001102416)	26179	NM_000893	3827	Hs.77741	NM_000893	ENSG00000113889	KNG1	BDK|BK|HMWK|KNG	kininogen 1	protein-coding	0.007364	0.375000	
chunk0189_273_1	chr8	25331974	25332566	+	0	NA	exon (NM_024940, exon 19 of 52)	exon (NM_024940, exon 19 of 52)	-13132	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.003378	0.317032	
chunk0140_86_1	chr4	68076698	68077262	+	0	NA	intron (NM_207407, intron 3 of 9)	intron (NM_207407, intron 3 of 9)	-13683	NR_027094	401135	Hs.130270	NM_001014372		SYT14P1	CHR415SYT|SYT14L|SYTDEP	synaptotagmin 14 pseudogene 1	pseudo	0.005319	0.456637	
chunk0116_222_1	chr21	38080746	38081511	+	0	NA	intron (NM_005867, intron 2 of 2)	intron (NM_005867, intron 2 of 2)	40232	NM_005867	10281	Hs.23251	NM_005867	ENSG00000184029	DSCR4	DCRB|DSCRB	Down syndrome critical region 4	ncRNA	0.018301	0.473890	
chunk0058_310_1	chr14	27251835	27252039	+	0	NA	Intergenic	L1MEb|LINE|L1	343295	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.014706	0.356098	
chunk0134_110_1	chr3	177047935	177048340	+	0	NA	intron (NM_024665, intron 7 of 15)	intron (NM_024665, intron 7 of 15)	149123	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.007407	0.339901	
chunk0028_290_1	chr10	91433922	91434217	+	0	NA	intron (NM_001284274, intron 2 of 21)	intron (NM_001284274, intron 2 of 21)	23784	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.000000	0.314189	
chunk0142_313_1	chr4	100672531	100672943	+	0	NA	intron (NR_046811, intron 2 of 3)	intron (NR_046811, intron 2 of 3)	2376	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.007282	0.418886	
chunk0167_37_1	chr6	54050741	54051114	+	0	NA	intron (NM_138569, intron 1 of 12)	intron (NM_138569, intron 1 of 12)	32011	NM_001281746	90523	Hs.449276	NM_138569	ENSG00000146147	MLIP	C6orf142|CIP	muscular LMNA interacting protein	protein-coding	0.005362	0.395722	187(CTGAACTTTCTGTCCT,-,0.00),188(TGAACTTTCTGTCCTC,+,0.00)
chunk0151_402_1	chr5	55569146	55569909	+	0	NA	Intergenic	Intergenic	-34449	NM_003711	8611	Hs.696231	NM_003711	ENSG00000067113	PLPP1	LLP1a|LPP1|PAP-2a|PAP2|PPAP2A	phospholipid phosphatase 1	protein-coding	0.014417	0.379581	443(AAGTACATGTTGTACC,-,0.00),444(AGTACATGTTGTACCC,+,0.00)
chunk0014_355_1	chr1	182363489	182364003	+	0	NA	Intergenic	L1ME4b|LINE|L1	27658	NM_001033056	2752	Hs.132016	NM_002065	ENSG00000135821	GLUL	GLNS|GS|PIG43|PIG59	glutamate-ammonia ligase	protein-coding	0.009728	0.388350	
chunk0095_83_1	chr2	14984687	14985104	+	0	NA	Intergenic	Intergenic	349804	NM_001291410	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.011990	0.459330	
chunk0091_439_1	chr19	17108239	17108478	+	0	NA	intron (NM_004145, intron 2 of 39)	intron (NM_004145, intron 2 of 39)	32577	NM_004145	4650	Hs.123198	NM_004145	ENSG00000099331	MYO9B	CELIAC4|MYR5	myosin IXB	protein-coding	0.037657	0.566667	
chunk0077_425_1	chr16	85351017	85351355	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-44861	NR_049816	100847022		NR_049816	ENSG00000266307	MIR5093	-	microRNA 5093	ncRNA	0.008876	0.557522	
chunk0186_86_1	chr7	137331465	137332153	+	0	NA	intron (NM_002825, intron 1 of 4)	intron (NM_002825, intron 1 of 4)	11991	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.010174	0.428157	
chunk0078_252_1	chr17	7234084	7234283	+	0	NA	TTS (NM_024297)	TTS (NM_024297)	361	NM_004422	1856	Hs.118640	NM_004422	ENSG00000004975	DVL2	-	dishevelled segment polarity protein 2	protein-coding	0.090452	0.635000	
chunk0086_343_1	chr18	24930835	24931275	+	0	NA	Intergenic	Intergenic	302873	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.020455	0.439909	
chunk0152_343_1	chr5	62569013	62569285	+	0	NA	intron (NM_016338, intron 27 of 29)	intron (NM_016338, intron 27 of 29)	-9586	NM_181506	100130733	Hs.721348	NM_181506	ENSG00000186105	LRRC70	SLRN	leucine rich repeat containing 70	protein-coding	0.003676	0.490842	
chunk0205_146_1	chr9	108250819	108251188	+	0	NA	Intergenic	L1MC1|LINE|L1	604992	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.002710	0.335135	
chunk0048_340_1	chr12	84290199	84290708	+	0	NA	Intergenic	Intergenic	622376	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.000000	0.268627	
chunk0123_279_1	chr3	46271240	46271678	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	29078	NM_001164680	1232	Hs.506190	NM_001837	ENSG00000183625	CCR3	CC-CKR-3|CD193|CKR3|CMKBR3	C-C motif chemokine receptor 3	protein-coding	0.009132	0.455581	
chunk0121_255_1	chr3	23078637	23078848	+	0	NA	Intergenic	Intergenic	-124551	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.009479	0.363208	
chunk0020_293_1	chr1	237176543	237177279	+	0	NA	intron (NM_001035, intron 1 of 104)	intron (NM_001035, intron 1 of 104)	134509	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.004076	0.317503	131(CAATACATTCTGTGCC,-,0.00),132(AATACATTCTGTGCCT,+,0.00),330(AGGAACATACAGTACT,-,0.00),331(GGAACATACAGTACTT,+,0.00)
chunk0132_97_1	chr3	155643541	155643856	+	0	NA	intron (NM_014996, intron 1 of 21)	L2a|LINE|L2	32618	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.009524	0.389241	
chunk0052_86_1	chr13	21983392	21983897	+	0	NA	Intergenic	Intergenic	-105484	NR_047040	100874182	Hs.148951	NR_047040	ENSG00000226722	LINC00424	-	long intergenic non-protein coding RNA 424	ncRNA	0.009901	0.478261	260(CAGGACACAATGCCCT,-,0.00),261(AGGACACAATGCCCTA,+,0.00)
chunk0197_203_1	chr8	122518744	122519313	+	0	NA	intron (NR_131202, intron 2 of 3)	intron (NR_131202, intron 2 of 3)	49616	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.003515	0.366667	
chunk0050_313_1	chr12	107057026	107057543	+	0	NA	intron (NM_004075, intron 1 of 12)	intron (NM_004075, intron 1 of 12)	36573	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.005803	0.339768	
chunk0066_363_1	chr15	38369652	38370099	+	0	NA	Intergenic	Intergenic	-84252	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.006711	0.366071	283(AGGGACAGAATGTTAT,-,0.00),284(GGGACAGAATGTTATT,+,0.00)
chunk0142_306_1	chr4	100581381	100581727	+	0	NA	Intergenic	Intergenic	-63461	NM_016242	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.002890	0.461095	211(ATCACATCCTGTCCTC,+,0.00)
chunk0038_231_1	chr11	87005241	87006004	+	0	NA	Intergenic	Intergenic	-32222	NM_022918	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.013106	0.388743	
chunk0148_219_1	chr5	8930631	8931247	+	0	NA	Intergenic	L1MC3|LINE|L1	91207	NR_109932	101929284	Hs.403715	NR_109932		LINC02199	-	long intergenic non-protein coding RNA 2199	ncRNA	0.009740	0.359806	
chunk0106_439_1	chr2	208552757	208553331	+	0	NA	Intergenic	L1M3d|LINE|L1	146214	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.005226	0.446957	
chunk0166_84_1	chr6	43699498	43700128	+	0	NA	Intergenic	Intergenic	-12001	NM_018135	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.012698	0.519810	
chunk0158_351_1	chr5	133506763	133507061	+	0	NA	intron (NM_015082, intron 3 of 15)	intron (NM_015082, intron 3 of 15)	-79206	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.010067	0.444816	
chunk0097_42_1	chr2	43053443	43053909	+	0	NA	Intergenic	L1ME3|LINE|L1	-14133	NR_110585	102723854	Hs.570165	NR_110585	ENSG00000231826	LINC01819	-	long intergenic non-protein coding RNA 1819	ncRNA	0.015021	0.368308	
chunk0082_437_1	chr17	61561589	61561928	+	0	NA	Intergenic	Intergenic	29444	NM_199290	342538	Hs.591178	NM_199290	ENSG00000253506	NACA2	ANAC|NACAL	nascent polypeptide associated complex subunit alpha 2	protein-coding	0.002950	0.405882	
chunk0028_76_1	chr10	83790367	83790669	+	0	NA	Intergenic	L1PB4|LINE|L1	-348911	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.003311	0.521452	
chunk0128_236_1	chr3	108406471	108406924	+	0	NA	intron (NM_014981, intron 33 of 41)	intron (NM_014981, intron 33 of 41)	94912	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.011038	0.394273	
chunk0137_137_1	chr4	15240761	15241116	+	0	NA	intron (NR_125911, intron 2 of 5)	intron (NR_125911, intron 2 of 5)	-98998	NM_001135170	114905	Hs.153714	NM_031911	ENSG00000163145	C1QTNF7	CTRP7|ZACRP7	C1q and TNF related 7	protein-coding	0.008451	0.466292	
chunk0048_222_1	chr12	81464172	81464494	+	0	NA	intron (NM_001220474, intron 2 of 30)	MIRb|SINE|MIR	48058	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003106	0.371517	
chunk0124_156_1	chr3	54888732	54889320	+	0	NA	intron (NM_018398, intron 24 of 37)	L2b|LINE|L2	12229	NR_046666	100874237	Hs.570583	NR_046666	ENSG00000243715	CACNA2D3-AS1	-	CACNA2D3 antisense RNA 1	ncRNA	0.003401	0.415959	319(AGGAACAGCATGTACA,-,0.00),320(GGAACAGCATGTACAA,+,0.00)
chunk0071_244_1	chr15	85340229	85340655	+	0	NA	Intergenic	Intergenic	-40154	NR_106993	102465803		NR_106993	ENSG00000284160	MIR7706	hsa-mir-7706	microRNA 7706	ncRNA	0.002347	0.473068	
chunk0047_455_1	chr12	76719132	76719380	+	0	NA	Intergenic	L1M1|LINE|L1	-44818	NM_015336	23390	Hs.4014	NM_015336	ENSG00000186908	ZDHHC17	DHHC-17|HIP14|HIP3|HSPC294|HYPH	zinc finger DHHC-type containing 17	protein-coding	0.004032	0.506024	
chunk0127_348_1	chr3	100717531	100718006	+	0	NA	intron (NM_001007565, intron 2 of 7)	L1MA5A|LINE|L1	8226	NM_001195478	10342	Hs.518123	NM_006070	ENSG00000114354	TFG	HMSNP|SPG57|TF6|TRKT3	trafficking from ER to golgi regulator	protein-coding	0.002105	0.325630	
chunk0002_228_1	chr1	20032364	20033013	+	0	NA	Intergenic	LTR46-int|LTR|ERV1	-37520	NM_000929	5322	Hs.319438	NM_000929	ENSG00000127472	PLA2G5	FRFB|GV-PLA2|PLA2-10|hVPLA(2)	phospholipase A2 group V	protein-coding	0.001541	0.446154	
chunk0073_48_1	chr16	2977387	2977781	+	0	NA	intron (NM_001258451, intron 2 of 8)	L1M4b|LINE|L1	2955	NM_001258450	9088	Hs.732385	NM_004203	ENSG00000127564	PKMYT1	MYT1|PPP1R126	protein kinase, membrane associated tyrosine/threonine 1	protein-coding	0.020305	0.544304	
chunk0097_247_1	chr2	53654540	53655069	+	0	NA	Intergenic	L1M5|LINE|L1	-112988	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.000000	0.341509	
chunk0052_307_1	chr12	124827706	124828256	+	0	NA	intron (NM_001082959, intron 1 of 11)	L2a|LINE|L2	35992	NM_005505	949	Hs.731377	NM_005505	ENSG00000073060	SCARB1	CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1	scavenger receptor class B member 1	protein-coding	0.023636	0.466425	
chunk0151_389_1	chr5	55358792	55359273	+	0	NA	intron (NM_015360, intron 15 of 26)	intron (NM_015360, intron 15 of 26)	51284	NM_015360	23517	Hs.274531	NM_015360	ENSG00000039123	MTREX	Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118	Mtr4 exosome RNA helicase	protein-coding	0.006237	0.377593	205(CTGCACAAGTTGTTCT,-,0.00),206(TGCACAAGTTGTTCTT,+,0.00),229(TAGAACAGGAAGTTCT,-,0.00),230(AGAACAGGAAGTTCTG,+,0.00)
chunk0193_10_1	chr8	70492234	70492433	+	0	NA	Intergenic	L1M5|LINE|L1	21199	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.000000	0.290000	
chunk0166_205_1	chr6	46655872	46656263	+	0	NA	intron (NM_001204051, intron 2 of 8)	intron (NM_001204051, intron 2 of 8)	3152	NM_004277	9481	Hs.40510	NM_004277	ENSG00000153291	SLC25A27	UCP4	solute carrier family 25 member 27	protein-coding	0.020460	0.436224	
chunk0087_31_1	chr18	31190912	31191426	+	0	NA	Intergenic	Intergenic	-28313	NM_004948	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.003891	0.372816	
chunk0144_248_1	chr4	136060569	136061182	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	-147195	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.001631	0.293160	
chunk0198_141_1	chr8	132887371	132887600	+	0	NA	exon (NM_003235, exon 9 of 48)	exon (NM_003235, exon 9 of 48)	20525	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.008734	0.521739	
chunk0069_213_1	chr15	63514405	63514738	+	0	NA	intron (NR_046342, intron 1 of 15)	intron (NR_046342, intron 1 of 15)	10060	NR_046341	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.009009	0.344311	
chunk0204_254_1	chr9	98121065	98121860	+	0	NA	3' UTR (NM_052820, exon 12 of 12)	3' UTR (NM_052820, exon 12 of 12)	-2109	NM_014788	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.006289	0.417085	703(TAGAACAGCATGTGTC,-,0.00),704(AGAACAGCATGTGTCA,+,0.00)
chunk0126_422_1	chr3	86054385	86055342	+	0	NA	intron (NM_153184, intron 8 of 9)	intron (NM_153184, intron 8 of 9)	-226813	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.002090	0.298539	
chunk0204_409_1	chr9	102820448	102820647	+	0	NA	Intergenic	Intergenic	-174764	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.010050	0.345000	
chunk0008_216_1	chr1	93779860	93780081	+	0	NA	intron (NM_001261408, intron 2 of 13)	intron (NM_001261408, intron 2 of 13)	-66862	NR_030621	100126348		NR_030621	ENSG00000211575	MIR760	MIRN760|hsa-mir-760|mir-760	microRNA 760	ncRNA	0.004525	0.527027	
chunk0077_36_1	chr16	75433619	75433991	+	0	NA	promoter-TSS (NM_006324)	promoter-TSS (NM_006324)	-316	NM_006324	10428	Hs.461361	NM_006324	ENSG00000153774	CFDP1	BCNT|BUCENTAUR|CENP-29|CP27|SWC5|Yeti|p97	craniofacial development protein 1	protein-coding	0.032258	0.428954	
chunk0046_436_1	chr12	64812180	64812395	+	0	NA	Intergenic	MIRb|SINE|MIR	-12285	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.000000	0.324074	
chunk0187_94_1	chr8	3900403	3900602	+	0	NA	intron (NM_033225, intron 5 of 69)	intron (NM_033225, intron 5 of 69)	1094304	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.000000	0.545000	
chunk0153_71_1	chr5	67978103	67978302	+	0	NA	Intergenic	Intergenic	184989	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.005025	0.380000	
chunk0045_225_1	chr12	48157472	48157678	+	0	NA	promoter-TSS (NM_024095)	promoter-TSS (NM_024095)	19	NM_024095	140461	Hs.432699	NM_024095	ENSG00000177981	ASB8	PP14212	ankyrin repeat and SOCS box containing 8	protein-coding	0.063107	0.599034	
chunk0173_105_1	chr6	143286228	143286442	+	0	NA	intron (NM_001286587, intron 5 of 6)	intron (NM_001286587, intron 5 of 6)	156342	NM_001286259	134637	Hs.709561	NM_182503	ENSG00000189007	ADAT2	DEADC1|TAD2|dJ20N2|dJ20N2.1	adenosine deaminase tRNA specific 2	protein-coding	0.004673	0.409302	
chunk0031_360_1	chr10	130137266	130137476	+	0	NA	intron (NM_006541, intron 1 of 10)	intron (NM_006541, intron 1 of 10)	996	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.038095	0.459716	
chunk0185_198_1	chr7	128435030	128435700	+	0	NA	Intergenic	L1MEd|LINE|L1	-20465	NM_001098786	29923	Hs.706124	NM_013332	ENSG00000135245	HILPDA	C7orf68|HIG-2|HIG2	hypoxia inducible lipid droplet associated	protein-coding	0.008955	0.432191	
chunk0142_28_1	chr4	90550004	90550668	+	0	NA	intron (NM_001145065, intron 5 of 10)	intron (NM_001145065, intron 5 of 10)	315305	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.003012	0.299248	
chunk0015_53_1	chr1	184581491	184581872	+	0	NA	intron (NM_030806, intron 3 of 5)	intron (NM_030806, intron 3 of 5)	173226	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.002625	0.287958	
chunk0192_153_1	chr8	62102176	62102819	+	0	NA	Intergenic	HUERS-P3-int|LTR|ERV1	-146445	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.004666	0.453416	517(AAGAGCAGGGTGTGCA,-,0.00),518(AGAGCAGGGTGTGCAT,+,0.00)
chunk0036_66_1	chr11	59678116	59678413	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-9226	NM_152716	219988	Hs.591960	NM_152716	ENSG00000166889	PATL1	Pat1b|hPat1b	PAT1 homolog 1, processing body mRNA decay factor	protein-coding	0.006734	0.345638	
chunk0097_365_1	chr2	60579055	60579275	+	0	NA	Intergenic	Intergenic	-25667	NM_018014	53335	Hs.370549	NM_018014	ENSG00000119866	BCL11A	BCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856	BAF chromatin remodeling complex subunit BCL11A	protein-coding	0.013636	0.470588	
chunk0125_244_1	chr3	68699051	68699703	+	0	NA	Intergenic	Intergenic	233233	NM_001005527	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.006135	0.415008	
chunk0095_25_1	chr2	12750340	12750895	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	13250	NR_036072	100422986		NR_036072	ENSG00000264370	MIR3125	mir-3125	microRNA 3125	ncRNA	0.010811	0.431655	
chunk0070_136_1	chr15	70965733	70966249	+	0	NA	intron (NM_017691, intron 9 of 15)	MER58A|DNA|hAT-Charlie	73548	NM_001199017	54839	Hs.12692	NM_017691	ENSG00000137821	LRRC49	PGs4	leucine rich repeat containing 49	protein-coding	0.001938	0.324952	
chunk0079_243_1	chr17	16044555	16044826	+	0	NA	intron (NM_006311, intron 42 of 45)	intron (NM_006311, intron 42 of 45)	-44998	NM_001042697	125150	Hs.593985	NM_001042697	ENSG00000214941	ZSWIM7	SWS1	zinc finger SWIM-type containing 7	protein-coding	0.029520	0.547794	
chunk0045_183_1	chr12	47088215	47088447	+	0	NA	intron (NM_001281429, intron 1 of 2)	intron (NM_001281429, intron 1 of 2)	-8380	NM_181847	347902	Hs.121520	NM_181847	ENSG00000139211	AMIGO2	ALI1|AMIGO-2|DEGA	adhesion molecule with Ig like domain 2	protein-coding	0.004310	0.480687	
chunk0142_87_1	chr4	93960938	93961194	+	0	NA	Intergenic	Intergenic	132139	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.003906	0.459144	
chunk0099_291_1	chr2	98779868	98780182	+	0	NA	Intergenic	LTR47A2|LTR|ERVL	-8127	NR_126337	101927070	Hs.469395	NR_126337		LINC02611	-	long intergenic non-protein coding RNA 2611	ncRNA	0.009554	0.434921	
chunk0037_417_1	chr11	79920494	79921250	+	0	NA	Intergenic	Intergenic	-480221	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.002646	0.372523	197(TAGAACATTATGTCTT,-,0.00),198(AGAACATTATGTCTTC,+,0.00)
chunk0008_335_1	chr1	95575170	95575888	+	0	NA	Intergenic	LTR33B|LTR|ERVL	65413	NR_110621	100996635	Hs.639548	NR_110621	ENSG00000228971	LINC02607	-	long intergenic non-protein coding RNA 2607	ncRNA	0.009749	0.432545	
chunk0157_10_1	chr5	115202778	115203065	+	0	NA	Intergenic	Intergenic	-22375	NM_018700	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.010453	0.517361	
chunk0106_122_1	chr2	198290933	198291532	+	0	NA	Intergenic	L2a|LINE|L2	83865	NR_110267	101927619	Hs.632942	NR_110267		LINC01923	-	long intergenic non-protein coding RNA 1923	ncRNA	0.013356	0.463333	
chunk0109_388_1	chr2	240098435	240098675	+	0	NA	Intergenic	L1PB3|LINE|L1	37775	NM_001163424	150678	Hs.293884	NM_138336	ENSG00000172428	COPS9	CSNAP|MYEOV2	COP9 signalosome subunit 9	protein-coding	0.000000	0.336100	
chunk0136_40_1	chr4	1155082	1155726	+	0	NA	Intergenic	MIR|SINE|MIR	17465	NM_012445	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.009317	0.479070	
chunk0053_247_1	chr13	32852503	32853064	+	0	NA	intron (NR_047020, intron 4 of 4)	intron (NR_047020, intron 4 of 4)	58869	NR_047020	100874167	Hs.406290	NR_047020		LINC00423	-	long intergenic non-protein coding RNA 423	ncRNA	0.001783	0.373665	243(AGTAACAGATTGTTCT,-,0.00),244(GTAACAGATTGTTCTG,+,0.00)
chunk0019_297_1	chr1	228867600	228868060	+	0	NA	Intergenic	Intergenic	132753	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.010870	0.438178	
chunk0095_343_1	chr2	20860825	20861071	+	0	NA	Intergenic	Intergenic	-37818	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.000000	0.311741	
chunk0040_83_1	chr11	111430226	111430707	+	0	NA	Intergenic	MER4A|LTR|ERV1	-12280	NR_046085	100132078	Hs.672662	NR_046085	ENSG00000255428	LOC100132078	-	uncharacterized LOC100132078	ncRNA	0.002079	0.402490	
chunk0100_452_1	chr2	121035881	121036631	+	0	NA	Intergenic	Intergenic	238965	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.014667	0.439414	
chunk0080_147_1	chr17	27820816	27821096	+	0	NA	Intergenic	L1ME3|LINE|L1	-20427	NM_000625	4843	Hs.709191	NM_000625	ENSG00000007171	NOS2	HEP-NOS|INOS|NOS|NOS2A	nitric oxide synthase 2	protein-coding	0.003571	0.437722	
chunk0172_167_1	chr6	136031936	136032411	+	0	NA	intron (NM_018945, intron 2 of 12)	intron (NM_018945, intron 2 of 12)	180477	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.002105	0.363445	
chunk0079_35_1	chr17	10210045	10210533	+	0	NA	Intergenic	Intergenic	-11738	NM_201433	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.012295	0.494888	
chunk0172_176_1	chr6	136365825	136366271	+	0	NA	intron (NM_001198619, intron 9 of 17)	intron (NM_001198619, intron 9 of 17)	-76197	NM_001077440	9774	Hs.486542	NM_014739	ENSG00000029363	BCLAF1	BTF|bK211L9.1	BCL2 associated transcription factor 1	protein-coding	0.020179	0.485459	
chunk0182_117_1	chr7	93895875	93896173	+	0	NA	Intergenic	Intergenic	-5033	NM_001271003	7980	Hs.438231	NM_006528	ENSG00000105825	TFPI2	PP5|REF1|TFPI-2	tissue factor pathway inhibitor 2	protein-coding	0.000000	0.364548	
chunk0195_86_1	chr8	94199230	94199739	+	0	NA	intron (NM_001144663, intron 1 of 17)	intron (NM_001144663, intron 1 of 17)	9103	NM_004063	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.005894	0.339216	
chunk0006_119_1	chr1	65719330	65719582	+	0	NA	Intergenic	L1M1|LINE|L1	-73054	NM_001037341	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.007937	0.529644	
chunk0075_391_1	chr16	56806994	56807323	+	0	NA	intron (NM_014669, intron 5 of 21)	L2a|LINE|L2	23657	NM_001242796	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.006079	0.506061	
chunk0036_185_1	chr11	62860662	62861086	+	0	NA	intron (NM_001012664, intron 1 of 9)	LTR5B|LTR|ERVK	4862	NM_001012662	6520	Hs.502769	NM_002394	ENSG00000168003	SLC3A2	4F2|4F2HC|4T2HC|CD98|CD98HC|MDU1|NACAE	solute carrier family 3 member 2	protein-coding	0.018868	0.468235	127(CAGTGCACTGTGTCCC,-,0.00),128(AGTGCACTGTGTCCCT,+,0.00)
chunk0118_147_1	chr22	29961747	29961946	+	0	NA	intron (NM_021090, intron 2 of 19)	Tigger3c|DNA|TcMar-Tigger	-45203	NR_106876	102466742		NR_106876	ENSG00000275818	MIR6818	hsa-mir-6818	microRNA 6818	ncRNA	0.000000	0.370000	
chunk0049_32_1	chr12	89706002	89706670	+	0	NA	Intergenic	Intergenic	-2619	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.002994	0.327354	
chunk0103_310_1	chr2	167248665	167249273	+	0	NA	exon (NM_152381, exon 9 of 11)	exon (NM_152381, exon 9 of 11)	61686	NM_001199145	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.008224	0.376026	
chunk0197_71_1	chr8	118894190	118894509	+	0	NA	Intergenic	L1ME4b|LINE|L1	57795	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.009404	0.281250	
chunk0148_381_1	chr5	14716613	14717546	+	0	NA	TTS (NR_046285)	TTS (NR_046285)	4385	NR_046285	100130744	Hs.660550	NR_046285		LOC100130744	-	uncharacterized LOC100130744	ncRNA	0.012862	0.466809	554(CAGCTCAGCCAGTTCC,-,0.00)
chunk0099_355_1	chr2	100415437	100415670	+	0	NA	intron (NM_004854, intron 1 of 6)	intron (NM_004854, intron 1 of 6)	2115	NM_004854	9486	Hs.516370	NM_004854	ENSG00000115526	CHST10	HNK-1ST|HNK1ST	carbohydrate sulfotransferase 10	protein-coding	0.008584	0.388889	
chunk0125_312_1	chr3	70765555	70766145	+	0	NA	Intergenic	Intergenic	299073	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.005085	0.318105	
chunk0060_176_1	chr14	46144772	46145343	+	0	NA	intron (NR_102701, intron 1 of 5)	intron (NR_102701, intron 1 of 5)	80898	NR_102701	100506412	Hs.207545	NR_102699	ENSG00000258700	LINC00871	-	long intergenic non-protein coding RNA 871	ncRNA	0.005254	0.346154	400(TGGGACATACTGTACT,-,0.00),401(GGGACATACTGTACTT,+,0.00)
chunk0184_462_1	chr7	123637372	123637796	+	0	NA	3' UTR (NM_080928, exon 10 of 10)	3' UTR (NM_080928, exon 10 of 10)	-12627	NR_111922	102724555	Hs.83916	NR_111922	ENSG00000230442	LOC102724555	-	uncharacterized LOC102724555	ncRNA	0.004717	0.418824	211(CTGGACACTCTGTCTC,-,0.00),212(TGGACACTCTGTCTCT,+,0.00)
chunk0169_95_1	chr6	100177974	100178180	+	0	NA	Intergenic	Intergenic	-183839	NM_032503	84539	Hs.591342	NM_032503	ENSG00000152034	MCHR2	GPR145|GPRv17|MCH-2R|MCH-R2|MCH2|MCH2R|MCHR-2|SLT	melanin concentrating hormone receptor 2	protein-coding	0.004854	0.487923	
chunk0155_292_1	chr5	96245352	96245976	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	166526	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.004808	0.387200	
chunk0053_365_1	chr13	35362488	35362821	+	0	NA	intron (NM_015678, intron 38 of 57)	intron (NM_015678, intron 38 of 57)	114041	NM_005584	4081	Hs.584776	NM_005584	ENSG00000180660	MAB21L1	CAGR1|Nbla00126	mab-21 like 1	protein-coding	0.003003	0.320359	
chunk0023_330_1	chr10	29303731	29304004	+	0	NA	intron (NM_032517, intron 3 of 4)	intron (NM_032517, intron 3 of 4)	14806	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.014652	0.434307	
chunk0013_195_1	chr1	169209295	169209714	+	0	NA	intron (NR_104229, intron 10 of 12)	L2b|LINE|L2	102795	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.004773	0.319048	
chunk0141_359_1	chr4	87929147	87929750	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-46202	NM_001251829	6696	Hs.313	NM_000582	ENSG00000118785	SPP1	BNSP|BSPI|ETA-1|OPN	secreted phosphoprotein 1	protein-coding	0.001658	0.331126	
chunk0143_375_1	chr4	122588389	122588632	+	0	NA	Intergenic	Intergenic	-30473	NR_104126	100996941	Hs.439487	NR_104126	ENSG00000227145	IL21-AS1	-	IL21 antisense RNA 1	ncRNA	0.012346	0.459016	
chunk0061_342_1	chr14	63477192	63477583	+	0	NA	intron (NM_001282180, intron 2 of 13)	MIR|SINE|MIR	30851	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.000000	0.359694	
chunk0121_391_1	chr3	25280691	25280979	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	-59967	NM_001290300	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.006944	0.415225	
chunk0094_369_1	chr2	9699036	9699594	+	0	NA	Intergenic	Intergenic	-68260	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.023297	0.504472	
chunk0053_42_1	chr13	27426121	27426615	+	0	NA	intron (NM_002097, intron 1 of 8)	intron (NM_002097, intron 1 of 8)	1824	NM_002097	2971	Hs.445977	NM_002097	ENSG00000122034	GTF3A	AP2|TFIIIA	general transcription factor IIIA	protein-coding	0.018219	0.470707	226(TAGCTCACTGTGTTCC,-,0.00),227(AGCTCACTGTGTTCCT,+,0.00)
chunk0160_446_1	chr5	164973045	164973321	+	0	NA	Intergenic	LTR25-int|LTR|ERV1	502904	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.000000	0.407942	
chunk0124_82_1	chr3	53270062	53270417	+	0	NA	Intergenic	Intergenic	-14125	NR_047580	7086	Hs.89643	NM_001064	ENSG00000163931	TKT	HEL-S-48|HEL107|SDDHD|TK|TKT1	transketolase	protein-coding	0.022535	0.615169	
chunk0158_295_1	chr5	132219058	132219572	+	0	NA	intron (NM_001017974, intron 1 of 14)	intron (NM_001017974, intron 1 of 14)	-1397	NR_106888	102465498		NR_106888	ENSG00000283678	MIR6830	hsa-mir-6830	microRNA 6830	ncRNA	0.005837	0.495146	236(GGCAGACACTGTTCTC,+,0.00)
chunk0086_25_1	chr18	12413901	12414515	+	0	NA	intron (NM_001142405, intron 1 of 6)	Charlie1a|DNA|hAT-Charlie	-5981	NM_001142406	10650	Hs.514718	NM_006553	ENSG00000141391	PRELID3A	C18orf43|HFL-EDDG1|SLMO1	PRELI domain containing 3A	protein-coding	0.014658	0.486179	
chunk0055_153_1	chr13	60009406	60009922	+	0	NA	intron (NM_001258369, intron 8 of 26)	intron (NM_001258369, intron 8 of 26)	-3054	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.009690	0.431335	
chunk0171_329_1	chr6	129859212	129859965	+	0	NA	intron (NM_001010876, intron 1 of 4)	intron (NM_001010876, intron 1 of 4)	1683	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.003984	0.363395	65(AAGTACTGTATGTTCC,-,0.00),66(AGTACTGTATGTTCCC,+,0.00)
chunk0071_312_1	chr15	86217103	86217466	+	0	NA	intron (NM_152336, intron 4 of 23)	L2a|LINE|L2	75273	NM_152336	123624	Hs.31795	NM_152336	ENSG00000273540	AGBL1	CCP4|FECD8	ATP/GTP binding protein like 1	protein-coding	0.002755	0.346154	
chunk0098_180_1	chr2	71333074	71333592	+	0	NA	intron (NM_014497, intron 1 of 27)	intron (NM_014497, intron 1 of 27)	1578	NM_001252612	27332	Hs.434401	NM_014497	ENSG00000075292	ZNF638	NP220|ZFML|Zfp638	zinc finger protein 638	protein-coding	0.007722	0.306358	
chunk0126_139_1	chr3	76239841	76240196	+	0	NA	Intergenic	Intergenic	-454435	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.008451	0.443820	208(GAGCACAGGCCGTTCT,-,0.00),209(AGCACAGGCCGTTCTA,+,0.00)
chunk0152_25_1	chr5	56669121	56669557	+	0	NA	Intergenic	Intergenic	-63107	NM_001287053	101928448	Hs.208052	NM_001287053	ENSG00000225940	C5orf67	-	chromosome 5 open reading frame 67	ncRNA	0.011468	0.450801	
chunk0207_405_1	chr9	136950023	136950370	+	0	NA	Intergenic	CpG	-2120	NM_178536	286256	Hs.440519	NM_178536	ENSG00000184925	LCN12	-	lipocalin 12	protein-coding	0.074928	0.718391	
chunk0190_394_1	chr8	40174601	40175073	+	0	NA	Intergenic	Intergenic	21369	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.012712	0.441860	141(AGGAACATTTTGCCCT,-,0.00),142(GGAACATTTTGCCCTT,+,0.00)
chunk0119_339_1	chr22	46997200	46997519	+	0	NA	intron (NM_014346, intron 9 of 12)	intron (NM_014346, intron 9 of 12)	-81317	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.031348	0.503125	
chunk0196_198_1	chr8	106373172	106373527	+	0	NA	intron (NM_001198533, intron 2 of 16)	intron (NM_001198533, intron 2 of 16)	-74575	NM_001198532	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.002817	0.351124	
chunk0178_400_1	chr7	40865519	40865722	+	0	NA	Intergenic	Intergenic	114319	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.024631	0.524510	
chunk0171_208_1	chr6	125892709	125892956	+	0	NA	intron (NM_001122842, intron 10 of 15)	intron (NM_001122842, intron 10 of 15)	-26392	NM_001199622	135112	Hs.171426	NM_181782	ENSG00000111912	NCOA7	ERAP140|ESNA1|NCOA7-AS|Nbla00052|Nbla10993|TLDC4|dJ187J11.3	nuclear receptor coactivator 7	protein-coding	0.008097	0.334677	
chunk0030_93_1	chr10	112391407	112391827	+	0	NA	intron (NM_016234, intron 1 of 20)	intron (NM_016234, intron 1 of 20)	15419	NM_016234	51703	Hs.11638	NM_016234	ENSG00000197142	ACSL5	ACS2|ACS5|FACL5	acyl-CoA synthetase long chain family member 5	protein-coding	0.007143	0.382423	
chunk0018_103_1	chr1	218150828	218151513	+	0	NA	Intergenic	Intergenic	107665	NR_110794	101929631	Hs.407614	NR_110794	ENSG00000232100	LINC01653	-	long intergenic non-protein coding RNA 1653	ncRNA	0.007299	0.330904	
chunk0032_33_1	chr11	1017411	1017610	+	0	NA	exon (NM_005961, exon 31 of 33)	exon (NM_005961, exon 31 of 33)	19196	NM_005961	4588	Hs.528432	NM_005961	ENSG00000184956	MUC6	MUC-6	mucin 6, oligomeric mucus/gel-forming	protein-coding	0.020101	0.570000	
chunk0027_304_1	chr10	77881721	77882089	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	44685	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.010870	0.517615	175(GGGGACATTCTGTCCA,-,0.00),176(GGGACATTCTGTCCAC,+,0.00)
chunk0153_216_1	chr5	72010199	72010888	+	0	NA	Intergenic	Intergenic	-96748	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.005806	0.352174	348(TGGTACAGTCTGTTCC,-,0.00),349(GGTACAGTCTGTTCCT,+,0.00)
chunk0109_440_1	chr2	241461848	241462453	+	0	NA	intron (NM_014808, intron 14 of 26)	intron (NM_014808, intron 14 of 26)	-15755	NR_036083	100422942		NR_036083	ENSG00000263752	MIR3133	-	microRNA 3133	ncRNA	0.011570	0.471947	
chunk0065_285_1	chr14	102524977	102525480	+	0	NA	Intergenic	MER113B|DNA|hAT-Charlie	-14416	NR_036192	100422954		NR_036192	ENSG00000266015	MIR4309	-	microRNA 4309	ncRNA	0.035785	0.494048	
chunk0131_330_1	chr3	151146868	151147320	+	0	NA	intron (NM_053002, intron 4 of 42)	L1MC5|LINE|L1	56107	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.000000	0.386313	
chunk0137_446_1	chr4	29119045	29119646	+	0	NA	Intergenic	L1MC1|LINE|L1	299763	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.004992	0.320598	
chunk0058_458_1	chr13	114030645	114030844	+	0	NA	intron (NM_007368, intron 4 of 23)	intron (NM_007368, intron 4 of 23)	-101753	NR_047495	100861555	Hs.353773	NR_047495	ENSG00000260910	LINC00565	-	long intergenic non-protein coding RNA 565	ncRNA	0.025126	0.565000	
chunk0162_22_1	chr6	868177	868569	+	0	NA	promoter-TSS (NR_110853)	promoter-TSS (NR_110853)	-125	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.017857	0.488550	
chunk0115_56_1	chr21	21368805	21369104	+	0	NA	intron (NM_004540, intron 8 of 17)	intron (NM_004540, intron 8 of 17)	368365	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.003344	0.350000	
chunk0136_63_1	chr4	1808412	1808905	+	0	NA	3' UTR (NM_022965, exon 16 of 16)	3' UTR (NM_022965, exon 16 of 16)	15346	NM_022965	2261	Hs.1420	NM_000142	ENSG00000068078	FGFR3	ACH|CD333|CEK2|HSFGFR3EX|JTK4	fibroblast growth factor receptor 3	protein-coding	0.022312	0.473684	
chunk0170_177_1	chr6	111767994	111768525	+	0	NA	intron (NM_002037, intron 3 of 13)	L2c|LINE|L2	-9128	NM_153048	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.007533	0.392857	
chunk0203_94_1	chr9	84163592	84163802	+	0	NA	Intergenic	Intergenic	100254	NR_110995	101927575	Hs.459826	NR_110995	ENSG00000227463	LOC101927575	-	uncharacterized LOC101927575	ncRNA	0.004762	0.279621	
chunk0010_100_1	chr1	114007908	114008299	+	0	NA	Intergenic	Intergenic	28712	NM_001286352	56944	Hs.9315	NM_020190	ENSG00000116774	OLFML3	HNOEL-iso|OLF44	olfactomedin like 3	protein-coding	0.002558	0.484694	
chunk0033_391_1	chr11	24428018	24429056	+	0	NA	Intergenic	MER34B|LTR|ERV1	-68433	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.007707	0.339750	80(GAGAGCACAATGTACC,-,0.00),180(AAGGACAGAAAGTACT,-,0.00),181(AGGACAGAAAGTACTC,+,0.00)
chunk0170_403_1	chr6	117603078	117603588	+	0	NA	promoter-TSS (NM_001017408)	promoter-TSS (NM_001017408)	-791	NM_001017408	57120	Hs.191539	NM_020399	ENSG00000047932	GOPC	CAL|FIG|GOPC1|PIST|dJ94G16.2	golgi associated PDZ and coiled-coil motif containing	protein-coding	0.015686	0.385519	
chunk0065_123_1	chr15	24851545	24851772	+	0	NA	intron (NM_022807, intron 2 of 12)	intron (NM_022807, intron 2 of 12)	-4893	NM_022805	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.013216	0.539474	
chunk0015_408_1	chr1	191152937	191153234	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	528195	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.010101	0.416107	
chunk0085_387_1	chr18	9874643	9875034	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-10888	NM_001098529	84203	Hs.98712	NM_032243	ENSG00000168454	TXNDC2	SPTRX|SPTRX1	thioredoxin domain containing 2	protein-coding	0.012788	0.410714	130(GGCACTTTCTGTACAT,+,0.00)
chunk0058_324_1	chr14	28141778	28142042	+	0	NA	Intergenic	Intergenic	-508632	NR_130461	100422830		NR_130461	ENSG00000264657	MIR3171	-	microRNA 3171	ncRNA	0.003788	0.392453	
chunk0040_25_1	chr11	110206318	110206712	+	0	NA	intron (NM_001260496, intron 6 of 7)	L1ME3E|LINE|L1	90197	NM_001260496	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.007614	0.296203	229(AGGAACATGCAGTGCC,-,0.00),230(GGAACATGCAGTGCCA,+,0.00)
chunk0027_441_1	chr10	81119850	81120126	+	0	NA	Intergenic	Intergenic	579169	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.000000	0.444043	174(GAGGACACCCTGTCCT,-,0.00),175(AGGACACCCTGTCCTT,+,0.00)
chunk0090_183_1	chr18	72902933	72903300	+	0	NA	Intergenic	L1PB4|LINE|L1	-35541	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.002725	0.328804	
chunk0134_124_1	chr3	177307389	177307673	+	0	NA	intron (NR_047465, intron 1 of 1)	intron (NR_047465, intron 1 of 1)	13089	NR_047465	100820709	Hs.518409	NR_047465	ENSG00000203645	LINC00501	-	long intergenic non-protein coding RNA 501	ncRNA	0.003521	0.361404	
chunk0188_100_1	chr8	8856023	8856582	+	0	NA	intron (NM_004225, intron 1 of 2)	intron (NM_004225, intron 1 of 2)	37319	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.012522	0.469643	
chunk0049_115_1	chr12	91348652	91349133	+	0	NA	Intergenic	MER31B|LTR|ERV1	-165768	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.006237	0.410788	
chunk0070_22_1	chr15	69172888	69173282	+	0	NA	intron (NM_015554, intron 1 of 4)	L3|LINE|CR1	12451	NM_015554	26035	Hs.183006	NM_015554	ENSG00000138604	GLCE	HSEPI	glucuronic acid epimerase	protein-coding	0.005076	0.367089	
chunk0001_198_1	chr1	7717617	7718326	+	0	NA	intron (NM_015215, intron 11 of 22)	L2b|LINE|L2	-53298	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.029619	0.442254	
chunk0205_437_1	chr9	115262438	115262835	+	0	NA	intron (NM_017418, intron 2 of 7)	intron (NM_017418, intron 2 of 7)	120818	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.000000	0.459799	
chunk0018_116_1	chr1	218332471	218332951	+	0	NA	3' UTR (NM_016052, exon 5 of 5)	3' UTR (NM_016052, exon 5 of 5)	-12623	NM_003238	7042	Hs.133379	NM_003238	ENSG00000092969	TGFB2	G-TSF|LDS4|TGF-beta2	transforming growth factor beta 2	protein-coding	0.000000	0.303534	
chunk0012_128_1	chr1	157088631	157089160	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	10913	NM_001004341	440695	Hs.127138	NM_001004341	ENSG00000253831	ETV3L	-	ETS variant 3 like	protein-coding	0.005671	0.377358	
chunk0022_182_1	chr10	13206077	13206276	+	0	NA	intron (NM_182751, intron 18 of 19)	L1M5|LINE|L1	-11093	NR_104080	101954271		NR_104080	ENSG00000207507	RNU6-9	U6-9	RNA, U6 small nuclear 9	snRNA	0.030151	0.455000	
chunk0014_291_1	chr1	180663991	180664274	+	0	NA	intron (NM_001135669, intron 1 of 13)	L1MA3|LINE|L1	32122	NM_001135669	9213	Hs.227656	NM_004736	ENSG00000143324	XPR1	IBGC6|SLC53A1|SYG1|X3	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.014134	0.528169	
chunk0062_403_1	chr14	74945487	74946113	+	0	NA	intron (NM_001207012, intron 5 of 5)	intron (NM_001207012, intron 5 of 5)	9964	NM_001207012	5228	Hs.252820	NM_002632	ENSG00000119630	PGF	D12S1900|PGFL|PIGF|PLGF|PlGF-2|SHGC-10760	placental growth factor	protein-coding	0.014377	0.502392	
chunk0146_103_1	chr4	158758718	158758933	+	0	NA	Intergenic	Intergenic	-10205	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.004651	0.365741	
chunk0062_177_1	chr14	69648579	69648997	+	0	NA	intron (NM_014734, intron 1 of 5)	intron (NM_014734, intron 1 of 5)	37195	NM_014734	9766	Hs.440025	NM_014734	ENSG00000100647	SUSD6	DRAGO|KIAA0247	sushi domain containing 6	protein-coding	0.004785	0.422434	
chunk0177_33_1	chr7	20737864	20738289	+	0	NA	intron (NM_001163941, intron 23 of 27)	intron (NM_001163941, intron 23 of 27)	48813	NM_182700	221833	Hs.195922	NM_182700	ENSG00000164651	SP8	BTD	Sp8 transcription factor	protein-coding	0.009412	0.366197	
chunk0008_71_1	chr1	89805997	89806196	+	0	NA	Intergenic	Intergenic	-14918	NM_001134479	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.005025	0.535000	
chunk0062_166_1	chr14	69424057	69424613	+	0	NA	intron (NM_001252150, intron 2 of 6)	intron (NM_001252150, intron 2 of 6)	25667	NM_001252148	55334	Hs.432690	NM_018375	ENSG00000029364	SLC39A9	ZIP-9|ZIP9	solute carrier family 39 member 9	protein-coding	0.003597	0.366248	
chunk0034_430_1	chr11	38769327	38769526	+	0	NA	Intergenic	L1PREC2|LINE|L1	120568	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.010050	0.510000	
chunk0172_417_1	chr6	140317163	140317510	+	0	NA	Intergenic	Intergenic	112084	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.008646	0.373563	
chunk0127_171_1	chr3	95140533	95141220	+	0	NA	Intergenic	L1MC2|LINE|L1	202613	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.004367	0.357558	
chunk0159_92_1	chr5	137899846	137900380	+	0	NA	intron (NM_001258448, intron 5 of 14)	Tigger2|DNA|TcMar-Tigger	10677	NM_001300921	27039	Hs.716884	NM_014386	ENSG00000078795	PKD2L2	TRPP5	polycystin 2 like 2, transient receptor potential cation channel	protein-coding	0.007491	0.306542	316(GAGTACGTACTGTACT,-,0.00)
chunk0138_261_1	chr4	40174739	40174996	+	0	NA	Intergenic	L1MA6|LINE|L1	-16144	NM_001278368	399	Hs.654594	NM_004310	ENSG00000168421	RHOH	ARHH|TTF	ras homolog family member H	protein-coding	0.019455	0.426357	
chunk0031_158_1	chr10	125184171	125184733	+	0	NA	Intergenic	L1PA6|LINE|L1	-23397	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.014235	0.522202	
chunk0028_277_1	chr10	91023298	91023913	+	0	NA	Intergenic	MamGypsy2-LTR|LTR|Gypsy	-22203	NR_047467	100874184	Hs.512240	NR_047467		LINC00502	-	long intergenic non-protein coding RNA 502	ncRNA	0.009756	0.456169	
chunk0017_359_1	chr1	211920181	211920828	+	0	NA	Intergenic	Intergenic	-89732	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.007728	0.436728	
chunk0068_282_1	chr15	56918304	56918532	+	0	NA	promoter-TSS (NM_207036)	promoter-TSS (NM_207036)	81	NR_015419	145783	Hs.620525	NR_015419	ENSG00000285331	LOC145783	-	uncharacterized LOC145783	ncRNA	0.127193	0.742358	
chunk0091_122_1	chr19	6259278	6260118	+	0	NA	intron (NM_005934, intron 3 of 11)	intron (NM_005934, intron 3 of 11)	20250	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.017857	0.508918	
chunk0037_176_1	chr11	74049635	74049834	+	0	NA	intron (NM_001286577, intron 26 of 32)	intron (NM_001286577, intron 26 of 32)	-40497	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.000000	0.465000	
chunk0009_170_1	chr1	105395903	105396604	+	0	NA	Intergenic	L1MA2|LINE|L1	222682	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004280	0.427350	
chunk0174_162_1	chr6	158337352	158337829	+	0	NA	intron (NM_001007466, intron 1 of 12)	intron (NM_001007466, intron 1 of 12)	24930	NM_001007466	56995	Hs.486993	NM_020245	ENSG00000130338	TULP4	TUSP	TUB like protein 4	protein-coding	0.004193	0.405858	
chunk0046_147_1	chr12	58158425	58159171	+	0	NA	Intergenic	L1ME3|LINE|L1	217136	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.002681	0.382865	
chunk0128_12_1	chr3	103708656	103709121	+	0	NA	Intergenic	Intergenic	-184772	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.296137	
chunk0139_186_1	chr4	54346375	54346886	+	0	NA	Intergenic	L1PB1|LINE|L1	117533	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.000000	0.341797	
chunk0094_270_1	chr2	8059187	8059590	+	0	NA	intron (NR_034135, intron 8 of 8)	intron (NR_034135, intron 8 of 8)	-82574	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.007444	0.383663	
chunk0043_217_1	chr12	19719628	19719827	+	0	NA	Intergenic	MER117|DNA|hAT-Charlie	279146	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.005025	0.425000	
chunk0016_381_1	chr1	202709482	202709696	+	0	NA	intron (NM_177402, intron 1 of 8)	intron (NM_177402, intron 1 of 8)	834	NM_177402	127833	Hs.25422	NM_177402	ENSG00000143858	SYT2	CMS7|MYSPC|SytII	synaptotagmin 2	protein-coding	0.042056	0.651163	
chunk0029_181_1	chr10	100802210	100802564	+	0	NA	intron (NM_003987, intron 6 of 10)	intron (NM_003987, intron 6 of 10)	56676	NM_003990	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.005650	0.543662	174(AGGAACACAGTGTTCT,-,0.00),175(GGAACACAGTGTTCTC,+,0.00)
chunk0051_301_1	chr12	118589057	118589638	+	0	NA	Intergenic	L2a|LINE|L2	212794	NM_022491	64426	Hs.416630	NM_022491	ENSG00000111707	SUDS3	SAP45|SDS3	SDS3 homolog, SIN3A corepressor complex component	protein-coding	0.008606	0.475945	
chunk0133_37_1	chr3	166052154	166052493	+	0	NA	Intergenic	Intergenic	-214858	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.532353	
chunk0041_414_1	chr11	134008698	134008898	+	0	NA	Intergenic	Intergenic	-23474	NR_027276	100128239	Hs.423734	NR_027276	ENSG00000204241	LINC02731	-	long intergenic non-protein coding RNA 2731	ncRNA	0.010000	0.527363	
chunk0154_8_1	chr5	76561500	76561699	+	0	NA	intron (NM_001285460, intron 1 of 34)	intron (NM_001285460, intron 1 of 34)	14190	NM_001285460	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.005025	0.515000	
chunk0005_338_1	chr1	61143753	61144180	+	0	NA	intron (NM_001145511, intron 2 of 10)	Tigger15a|DNA|TcMar-Tigger	61658	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.009368	0.390187	
chunk0023_4_1	chr10	20622789	20623389	+	0	NA	Intergenic	Intergenic	71119	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.010000	0.361065	
chunk0175_96_1	chr7	2805687	2806177	+	0	NA	intron (NM_001293092, intron 1 of 2)	MER33|DNA|hAT-Charlie	9327	NM_001282441	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.018367	0.378819	
chunk0064_178_1	chr14	92619695	92620209	+	0	NA	intron (NM_024832, intron 4 of 9)	MER41-int|LTR|ERV1	106171	NM_024832	79890	Hs.326822	NM_024832	ENSG00000100599	RIN3	-	Ras and Rab interactor 3	protein-coding	0.013619	0.366990	
chunk0178_449_1	chr7	42039868	42040565	+	0	NA	exon (NM_000168, exon 7 of 15)	exon (NM_000168, exon 7 of 15)	196803	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.015782	0.431232	
chunk0045_61_1	chr12	45352826	45353127	+	0	NA	intron (NM_001142679, intron 7 of 19)	L1MC5|LINE|L1	60293	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.006645	0.350993	
chunk0102_381_1	chr2	154413776	154414428	+	0	NA	intron (NM_052917, intron 11 of 12)	L1M5|LINE|L1	43336	NM_001256368									0.003067	0.281776	
chunk0014_127_1	chr1	177601008	177601345	+	0	NA	Intergenic	Intergenic	-99348	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.002967	0.494083	
chunk0196_192_1	chr8	106186210	106186873	+	0	NA	Intergenic	Intergenic	-83637	NM_001198533	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.001508	0.293675	
chunk0039_46_1	chr11	96095806	96096312	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-171852	NM_016156	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.003953	0.443787	
chunk0065_36_1	chr15	21242366	21242661	+	0	NA	Intergenic	Intergenic	55316	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.000000	0.280405	
chunk0184_331_1	chr7	120547329	120548014	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	274003	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.007299	0.384840	66(AGGTCATATTGTCCCT,+,0.00),200(TAGAACTCTCTGTTCC,-,0.00),201(AGAACTCTCTGTTCCC,+,0.00)
chunk0157_394_1	chr5	124134912	124135353	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	303388	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004535	0.298643	
chunk0042_335_1	chr12	9801671	9801928	+	0	NA	Intergenic	L1PA8|LINE|L1	-25682	NM_016523	51348	Hs.183125	NM_016523	ENSG00000150045	KLRF1	CLEC5C|NKp80	killer cell lectin like receptor F1	protein-coding	0.003891	0.352713	
chunk0071_318_1	chr15	86712152	86712351	+	0	NA	intron (NM_152336, intron 22 of 23)	intron (NM_152336, intron 22 of 23)	-395283	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.005025	0.305000	
chunk0068_422_1	chr15	59333458	59334049	+	0	NA	intron (NM_004998, intron 1 of 27)	intron (NM_004998, intron 1 of 27)	39119	NM_004998	4643	Hs.654506	NM_004998	ENSG00000157483	MYO1E	FSGS6|HuncM-IC|MYO1C	myosin IE	protein-coding	0.008460	0.430743	
chunk0127_214_1	chr3	96493566	96493869	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	133753	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.016502	0.595395	
chunk0114_88_1	chr21	9259058	9259401	+	0	NA	Intergenic	Intergenic	-129468	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.008746	0.325581	
chunk0168_419_1	chr6	95423521	95423878	+	0	NA	Intergenic	Intergenic	153752	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.002801	0.349162	
chunk0122_370_1	chr3	37627341	37627717	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	175207	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.021277	0.503979	
chunk0087_357_1	chr18	40982834	40983267	+	0	NA	Intergenic	MER92-int|LTR|ERV1	537547	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.004619	0.364055	
chunk0028_205_1	chr10	89132788	89133016	+	0	NA	Intergenic	MER110A|LTR|ERV1	-69491	NR_039827	100616192		NR_039827	ENSG00000265375	MIR4679-2	-	microRNA 4679-2	ncRNA	0.004386	0.379913	
chunk0166_76_1	chr6	43172402	43172639	+	0	NA	intron (NM_001292001, intron 1 of 6)	CpG	130	NM_001292001	6722	Hs.520140	NM_003131	ENSG00000112658	SRF	MCM1	serum response factor	protein-coding	0.054852	0.609244	
chunk0105_150_1	chr2	186533301	186534156	+	0	NA	Intergenic	Intergenic	47570	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.000000	0.323598	430(AAGAACACCCTGCCCT,-,0.00),431(AGAACACCCTGCCCTT,+,0.00),605(GAGTACACCATGCTCT,-,0.00),606(AGTACACCATGCTCTC,+,0.00)
chunk0066_236_1	chr15	34262739	34263080	+	0	NA	intron (NM_001042497, intron 1 of 23)	LTR28C|LTR|ERV1	37912	NM_016454	51234	Hs.250905	NM_016454	ENSG00000128463	EMC4	PIG17|TMEM85	ER membrane protein complex subunit 4	protein-coding	0.017595	0.561404	
chunk0078_179_1	chr17	4653373	4654028	+	0	NA	Intergenic	Intergenic	-12035	NM_001140	246	Hs.73809	NM_001140	ENSG00000161905	ALOX15	12-LOX|15-LOX|15-LOX-1|LOG15	arachidonate 15-lipoxygenase	protein-coding	0.004580	0.338415	319(GGCTCAAACTGTGCCT,+,0.00)
chunk0049_413_1	chr12	97368960	97369338	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-95872	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.013228	0.451187	
chunk0207_116_1	chr9	128874531	128874787	+	0	NA	intron (NM_001287390, intron 1 of 14)	Tigger6a|DNA|TcMar-Tigger	7416	NM_001287390	883	Hs.495250	NM_004059	ENSG00000171097	KYAT1	CCBL1|GTK|KAT1|KATI	kynurenine aminotransferase 1	protein-coding	0.015625	0.439689	
chunk0164_448_1	chr6	28080050	28080272	+	0	NA	promoter-TSS (NM_003447)	promoter-TSS (NM_003447)	-543	NM_003447	7718	Hs.55481	NM_003447	ENSG00000197279	ZNF165	CT53|LD65|ZSCAN7	zinc finger protein 165	protein-coding	0.031532	0.538117	
chunk0201_381_1	chr9	68904190	68904677	+	0	NA	intron (NM_003558, intron 8 of 15)	intron (NM_003558, intron 8 of 15)	71408	NR_110647	101927069	Hs.663405	NR_110647		LOC101927069	-	uncharacterized LOC101927069	ncRNA	0.006160	0.411885	204(CAGGACAATGAGTTCA,-,0.00),205(AGGACAATGAGTTCAT,+,0.00)
chunk0146_405_1	chr4	168931776	168932172	+	0	NA	Intergenic	L1M2c|LINE|L1	78343	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.002525	0.387909	
chunk0062_105_1	chr14	68214384	68215038	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	394932	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.006116	0.386260	245(GGTTCATCATGTTCTG,+,0.00),606(AAGAACAATTTGTTTT,-,0.00)
chunk0117_164_1	chr22	20221522	20221721	+	0	NA	Intergenic	Intergenic	15289	NR_026919	150197	Hs.635544	NM_152508	ENSG00000236499	LINC00896	-	long intergenic non-protein coding RNA 896	ncRNA	0.015075	0.555000	
chunk0190_10_1	chr8	28810495	28810795	+	0	NA	intron (NR_026826, intron 6 of 14)	intron (NR_026826, intron 6 of 14)	79270	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.006667	0.395349	
chunk0027_19_1	chr10	72223376	72223620	+	0	NA	intron (NM_001242546, intron 2 of 4)	intron (NM_001242546, intron 2 of 4)	-6364	NR_045564	51008	Hs.500007	NM_015947	ENSG00000138303	ASCC1	ASC1p50|CGI-18|SMABF2|p50	activating signal cointegrator 1 complex subunit 1	protein-coding	0.004098	0.363265	54(CAGAACACAGTGTTAT,-,0.00),55(AGAACACAGTGTTATT,+,0.00)
chunk0123_152_1	chr3	43295059	43295878	+	0	NA	intron (NM_001100594, intron 1 of 5)	intron (NM_001100594, intron 1 of 5)	8956	NM_001100594	54861	Hs.476052	NM_017719	ENSG00000163788	SNRK	HSNFRK	SNF related kinase	protein-coding	0.006105	0.397561	
chunk0151_53_1	chr5	42429627	42430074	+	0	NA	intron (NM_001242401, intron 1 of 10)	intron (NM_001242401, intron 1 of 10)	4858	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.002237	0.370536	
chunk0070_48_1	chr15	69554359	69554558	+	0	NA	Intergenic	Intergenic	-7262	NR_026979	145837	Hs.410126	NR_026979		DRAIC	-	downregulated RNA in cancer, inhibitor of cell invasion and migration	ncRNA	0.010050	0.475000	
chunk0106_128_1	chr2	199358151	199358582	+	0	NA	intron (NM_015265, intron 7 of 11)	intron (NM_015265, intron 7 of 11)	99730	NM_001172509	23314	Hs.516617	NM_015265	ENSG00000119042	SATB2	GLSS	SATB homeobox 2	protein-coding	0.004640	0.328704	
chunk0100_324_1	chr2	116514081	116514280	+	0	NA	Intergenic	Intergenic	-1300499	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.010050	0.425000	
chunk0109_382_1	chr2	239881798	239882219	+	0	NA	Intergenic	Intergenic	61086	NR_039949	100616417		NR_039949	ENSG00000264279	MIR4786	mir-4786	microRNA 4786	ncRNA	0.030879	0.563981	
chunk0007_372_1	chr1	85220584	85221297	+	0	NA	Intergenic	Intergenic	-19895	NM_032184	84144	Hs.533853	NM_032184	ENSG00000097096	SYDE2	-	synapse defective Rho GTPase homolog 2	protein-coding	0.012623	0.425770	238(AAGTACACCGTGTACT,-,0.00),239(AGTACACCGTGTACTT,+,0.00)
chunk0155_298_1	chr5	96331626	96332100	+	0	NA	intron (NR_130776, intron 3 of 4)	intron (NR_130776, intron 3 of 4)	100296	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.000000	0.389474	
chunk0073_136_1	chr16	5944142	5944657	+	0	NA	Intergenic	Intergenic	-74732	NM_001142333	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.021359	0.457364	
chunk0186_74_1	chr7	137197373	137197713	+	0	NA	Intergenic	L1MD1|LINE|L1	-33202	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.005882	0.328446	
chunk0052_74_1	chr13	21481327	21481628	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-22107	NR_104486	253832	Hs.564611	NM_153251	ENSG00000180776	ZDHHC20	4933421L13Rik|DHHC-20|DHHC20	zinc finger DHHC-type containing 20	protein-coding	0.016611	0.400662	80(CAGAACAAGGTGTACT,-,0.00),81(AGAACAAGGTGTACTA,+,0.00)
chunk0015_389_1	chr1	190688556	190688949	+	0	NA	intron (NR_033922, intron 1 of 4)	MLT1I|LTR|ERVL-MaLR	63862	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.000000	0.342640	
chunk0162_48_1	chr6	1290705	1291304	+	0	NA	Intergenic	Intergenic	-21436	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.006678	0.443333	
chunk0039_325_1	chr11	104271139	104271374	+	0	NA	Intergenic	Intergenic	18665	NR_106987									0.004255	0.322034	
chunk0170_105_1	chr6	110593734	110593950	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	-117201	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.004630	0.516129	
chunk0003_200_1	chr1	34840880	34841079	+	0	NA	Intergenic	Intergenic	18066	NM_001164824	113444	Hs.27160	NM_138428	ENSG00000163866	SMIM12	C1orf212	small integral membrane protein 12	protein-coding	0.005025	0.530000	
chunk0150_71_1	chr5	32145362	32146171	+	0	NA	intron (NM_022130, intron 1 of 3)	intron (NM_022130, intron 1 of 3)	28553	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.011125	0.427160	484(GGGAACGGACAGTTCT,-,0.00),485(GGAACGGACAGTTCTG,+,0.00)
chunk0133_96_1	chr3	167886852	167887051	+	0	NA	Intergenic	Intergenic	-8997	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.005025	0.295000	
chunk0053_87_1	chr13	28478036	28478446	+	0	NA	intron (NM_001159920, intron 1 of 12)	intron (NM_001159920, intron 1 of 12)	16887	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.004878	0.343066	
chunk0203_386_1	chr9	90455495	90456405	+	0	NA	Intergenic	Intergenic	-22461	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.012088	0.425906	621(GAGTACAGTAAGTCCT,-,0.00),622(AGTACAGTAAGTCCTC,+,0.00)
chunk0080_18_1	chr17	20955146	20955842	+	0	NA	intron (NR_123730, intron 2 of 5)	intron (NR_123730, intron 2 of 5)	16974	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.001437	0.348637	
chunk0124_47_1	chr3	52573798	52574455	+	0	NA	intron (NM_018313, intron 23 of 29)	MSTD|LTR|ERVL-MaLR	37521	NM_001124767	440957	Hs.660577	NM_001124767	ENSG00000168273	SMIM4	C3orf78	small integral membrane protein 4	protein-coding	0.003044	0.422492	
chunk0117_414_1	chr21	45818408	45818854	+	0	NA	Intergenic	L1MC1|LINE|L1	17788	NR_038876	100129027	Hs.689591	NR_038876	ENSG00000205424	LOC100129027	-	uncharacterized LOC100129027	ncRNA	0.008969	0.427293	
chunk0169_235_1	chr6	104996112	104996775	+	0	NA	intron (NM_001004317, intron 2 of 3)	MER90|LTR|ERV1	39395	NM_001004317	389421	Hs.23616	NM_001004317	ENSG00000187772	LIN28B	CSDD2	lin-28 homolog B	protein-coding	0.001508	0.390060	255(GTCACAGAATGTTCTT,+,0.00)
chunk0158_1_1	chr5	125114704	125115318	+	0	NA	intron (NR_109882, intron 2 of 5)	intron (NR_109882, intron 2 of 5)	78180	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.009772	0.377236	
chunk0175_37_1	chr7	884651	885276	+	0	NA	intron (NM_015949, intron 1 of 8)	AluJb|SINE|Alu	8409	NM_015949	51608	Hs.107387	NM_015949	ENSG00000239857	GET4	C7orf20|CEE|CGI-20|TRC35	guided entry of tail-anchored proteins factor 4	protein-coding	0.027200	0.501597	
chunk0139_294_1	chr4	57462314	57463410	+	0	NA	intron (NR_125907, intron 4 of 5)	intron (NR_125907, intron 4 of 5)	36990	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003650	0.365542	
chunk0034_3_1	chr11	25768086	25768348	+	0	NA	Intergenic	Intergenic	-420906	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.003817	0.376426	
chunk0091_128_1	chr19	6362326	6362927	+	0	NA	intron (NM_006012, intron 3 of 5)	intron (NM_006012, intron 3 of 5)	1174	NM_006012	8192	Hs.515092	NM_006012	ENSG00000125656	CLPP	DFNB81|PRLTS3	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding	0.028286	0.561462	422(CTGCACATACTGTTCT,-,0.00),423(TGCACATACTGTTCTG,+,0.00)
chunk0195_246_1	chr8	97658144	97658516	+	0	NA	intron (NM_178812, intron 1 of 11)	intron (NM_178812, intron 1 of 11)	14151	NM_178812	92140	Hs.377155	NM_178812	ENSG00000147649	MTDH	3D3|AEG-1|AEG1|LYRIC|LYRIC/3D3	metadherin	protein-coding	0.005376	0.380697	206(GGGAACTGAATGTTCC,-,0.00),207(GGAACTGAATGTTCCT,+,0.00)
chunk0042_71_1	chr12	2126388	2127155	+	0	NA	intron (NM_001129846, intron 3 of 45)	MIR|SINE|MIR	73486	NM_001167624	775	Hs.118262	NM_000719	ENSG00000151067	CACNA1C	CACH2|CACN2|CACNL1A1|CCHL1A1|CaV1.2|LQT8|TS|TS. LQT8	calcium voltage-gated channel subunit alpha1 C	protein-coding	0.010430	0.509115	
chunk0140_74_1	chr4	67558118	67558770	+	0	NA	promoter-TSS (NM_012108)	promoter-TSS (NM_012108)	-284	NM_012108	26228	Hs.435579	NM_012108	ENSG00000035720	STAP1	BRDG1|STAP-1	signal transducing adaptor family member 1	protein-coding	0.004601	0.330781	
chunk0076_399_1	chr16	72619278	72619703	+	0	NA	intron (NR_126330, intron 1 of 13)	intron (NR_126330, intron 1 of 13)	45519	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.002353	0.330986	20(TACACATTCTGTTCTT,+,0.00)
chunk0049_406_1	chr12	97042280	97042773	+	0	NA	Intergenic	Intergenic	135060	NM_001135175	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.006085	0.408907	114(AAGGACACATAGTCCA,-,0.00),200(AAGCCCAGAATGTTCT,-,0.00),201(AGCCCAGAATGTTCTT,+,0.00)
chunk0053_28_1	chr13	26910808	26911393	+	0	NA	Intergenic	Intergenic	-150315	NM_005288	2835	Hs.123034	NM_005288	ENSG00000132975	GPR12	GPCR12|GPCR21|PPP1R84	G protein-coupled receptor 12	protein-coding	0.020513	0.552901	
chunk0026_321_1	chr10	68125847	68126317	+	0	NA	intron (NM_001256267, intron 3 of 20)	L2c|LINE|L2	16649	NM_001256268	84665	Hs.55205	NM_032578	ENSG00000138347	MYPN	CMD1DD|CMH22|MYOP|NEM11|RCM4	myopalladin	protein-coding	0.004255	0.424628	
chunk0101_253_1	chr2	132616916	132617412	+	0	NA	intron (NM_001508, intron 1 of 1)	L1M5|LINE|L1	53744	NM_144586	116372	Hs.432395	NM_144586	ENSG00000150551	LYPD1	LYPDC1|PHTS	LY6/PLAUR domain containing 1	protein-coding	0.006048	0.376258	
chunk0194_58_1	chr8	82273279	82273478	+	0	NA	Intergenic	L1MA1|LINE|L1	-431092	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.505000	
chunk0195_375_1	chr8	100026109	100026485	+	0	NA	intron (NM_001286692, intron 14 of 27)	intron (NM_001286692, intron 14 of 27)	-2213	NR_031675									0.005319	0.371353	
chunk0154_344_1	chr5	86618137	86618432	+	0	NA	intron (NM_001867, intron 1 of 2)	intron (NM_001867, intron 1 of 2)	317	NM_001867	1350	Hs.430075	NM_001867	ENSG00000127184	COX7C	-	cytochrome c oxidase subunit 7C	protein-coding	0.061017	0.645270	
chunk0180_405_1	chr7	75796072	75796457	+	0	NA	Intergenic	Intergenic	-6518	NM_006072	10344	Hs.131342	NM_006072	ENSG00000006606	CCL26	IMAC|MIP-4a|MIP-4alpha|SCYA26|TSC-1	C-C motif chemokine ligand 26	protein-coding	0.018182	0.494819	164(AAGAACTGAATGTTCC,-,0.00),165(AGAACTGAATGTTCCT,+,0.00)
chunk0065_97_1	chr15	23961329	23961832	+	0	NA	Intergenic	L1MC3|LINE|L1	-13567	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.017893	0.376984	
chunk0059_443_1	chr14	38721518	38721849	+	0	NA	Intergenic	Intergenic	195199	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.015106	0.379518	
chunk0129_9_1	chr3	116367781	116367980	+	0	NA	intron (NR_109998, intron 1 of 3)	intron (NR_109998, intron 1 of 3)	7856	NR_109998	101926903	Hs.26479	NR_109998	ENSG00000240922	LSAMP-AS1	-	LSAMP antisense RNA 1	ncRNA	0.015075	0.395000	
chunk0184_118_1	chr7	113839924	113840405	+	0	NA	Intergenic	Intergenic	78863	NM_002711	5506	Hs.458309	NM_002711	ENSG00000154415	PPP1R3A	GM|PP1G|PPP1R3	protein phosphatase 1 regulatory subunit 3A	protein-coding	0.002079	0.367220	
chunk0136_326_1	chr3	195516683	195517283	+	0	NA	intron (NR_133014, intron 4 of 4)	intron (NR_133014, intron 4 of 4)	26418	NM_001291504	5504	Hs.535731	NM_006241	ENSG00000184203	PPP1R2	IPP-2|IPP2|PPP1R2A	protein phosphatase 1 regulatory inhibitor subunit 2	protein-coding	0.008333	0.321131	
chunk0083_436_1	chr17	72614552	72614972	+	0	NA	intron (NR_033876, intron 3 of 4)	intron (NR_033876, intron 3 of 4)	-21958	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.007143	0.410926	
chunk0211_119_1	chrX	112205782	112206244	+	0	NA	intron (NM_001004308, intron 2 of 2)	intron (NM_001004308, intron 2 of 2)	122988	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.008658	0.356371	
chunk0151_174_1	chr5	50325060	50325590	+	0	NA	Intergenic	Intergenic	116075	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.005660	0.274953	268(AAGTACTGTATGTTCT,-,0.00),269(AGTACTGTATGTTCTT,+,0.00)
chunk0071_131_1	chr15	81766763	81767333	+	0	NA	Intergenic	Intergenic	279095	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.003509	0.415061	
chunk0143_307_1	chr4	118904310	118904747	+	0	NA	intron (NM_133477, intron 1 of 4)	intron (NM_133477, intron 1 of 4)	15687	NM_133477	171024	Hs.655519	NM_133477	ENSG00000172403	SYNPO2	-	synaptopodin 2	protein-coding	0.004577	0.385845	
chunk0150_335_1	chr5	38555653	38555862	+	0	NA	intron (NM_002310, intron 1 of 19)	intron (NM_002310, intron 1 of 19)	889	NM_001127671	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.014354	0.400000	
chunk0021_37_1	chr10	855805	856757	+	0	NA	intron (NM_015155, intron 5 of 17)	L1MC1|LINE|L1	75424	NM_015155	23185	Hs.159069	NM_015155	ENSG00000107929	LARP4B	KIAA0217|LARP5	La ribonucleoprotein domain family member 4B	protein-coding	0.013655	0.394544	83(CAGAACAGACAGTCCA,-,0.00),84(AGAACAGACAGTCCAA,+,0.00)
chunk0131_293_1	chr3	150546515	150546732	+	0	NA	promoter-TSS (NM_032025)	promoter-TSS (NM_032025)	18	NM_014445	27230	Hs.518326	NM_014445	ENSG00000120742	SERP1	RAMP4	stress associated endoplasmic reticulum protein 1	protein-coding	0.115207	0.637615	
chunk0163_137_1	chr6	10682392	10683084	+	0	NA	intron (NR_026736, intron 4 of 5)	intron (NR_026736, intron 4 of 5)	11868	NR_026737	347744	Hs.61389	NM_001145020	ENSG00000137434	C6orf52	-	chromosome 6 open reading frame 52	protein-coding	0.000000	0.405483	
chunk0131_4_1	chr3	141703343	141703590	+	0	NA	Intergenic	L1PB1|LINE|L1	-34743	NM_014245	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.008097	0.395161	
chunk0188_149_1	chr8	10260527	10260939	+	0	NA	intron (NM_001135671, intron 3 of 5)	intron (NM_001135671, intron 3 of 5)	165181	NM_001199729	4482	Hs.490981	NM_012331	ENSG00000175806	MSRA	PMSR	methionine sulfoxide reductase A	protein-coding	0.009709	0.394673	
chunk0030_255_1	chr10	115666174	115666483	+	0	NA	intron (NM_207303, intron 26 of 28)	intron (NM_207303, intron 26 of 28)	572963	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.009709	0.316129	
chunk0203_20_1	chr9	82832571	82833059	+	0	NA	Intergenic	Intergenic	230313	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002049	0.429448	
chunk0198_234_1	chr8	134139957	134140571	+	0	NA	Intergenic	L2a|LINE|L2	253768	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.003257	0.463415	
chunk0058_452_1	chr13	113870808	113871026	+	0	NA	Intergenic	L1ME1|LINE|L1	6740	NR_044993	100506394	Hs.132168	NR_044993	ENSG00000272695	GAS6-DT	GAS6-AS2	GAS6 divergent transcript	ncRNA	0.004587	0.369863	
chunk0074_289_1	chr16	29765401	29766004	+	0	NA	Intergenic	Intergenic	-12538	NM_152338	653808	Hs.632195	NM_152338	ENSG00000174992	ZG16	JCLN|JCLN1|ZG16A	zymogen granule protein 16	protein-coding	0.014925	0.519868	
chunk0208_241_1	chrX	20007372	20007639	+	0	NA	3' UTR (NM_001168465, exon 17 of 17)	3' UTR (NM_001168465, exon 17 of 17)	9682	NR_037414	100500809		NR_037414	ENSG00000264566	MIR23C	hsa-mir-23c|mir-23c	microRNA 23c	ncRNA	0.011236	0.384328	
chunk0057_225_1	chr13	104170988	104171706	+	0	NA	Intergenic	Intergenic	746147	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.013928	0.383866	
chunk0024_14_1	chr10	32953006	32953716	+	0	NA	intron (NM_002211, intron 1 of 15)	intron (NM_002211, intron 1 of 15)	4533	NM_133376	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.008451	0.410689	393(GGTACTCAATGTACTG,+,0.00)
chunk0089_299_1	chr18	63460406	63461029	+	0	NA	Intergenic	L1ME1|LINE|L1	-16194	NM_002639	5268	Hs.55279	NM_002639	ENSG00000206075	SERPINB5	PI5|maspin	serpin family B member 5	protein-coding	0.001605	0.301282	259(TGGTACAGTCTGTACT,-,0.00),260(GGTACAGTCTGTACTC,+,0.00)
chunk0035_136_1	chr11	42823901	42824697	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	445070	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.006281	0.432873	
chunk0022_188_1	chr10	13399535	13400378	+	0	NA	Intergenic	Intergenic	-51658	NM_001195602	22929	Hs.124027	NM_012247	ENSG00000086475	SEPHS1	SELD|SPS|SPS1	selenophosphate synthetase 1	protein-coding	0.008304	0.382701	
chunk0043_343_1	chr12	22917430	22918020	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-257911	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.003390	0.304569	
chunk0176_237_1	chr7	15875495	15875744	+	0	NA	Intergenic	Intergenic	187241	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.000000	0.368000	
chunk0109_254_1	chr20	7069079	7069678	+	0	NA	Intergenic	Intergenic	184824	NR_110609	101929265	Hs.637730	NR_110609	ENSG00000228888	LINC01428	-	long intergenic non-protein coding RNA 1428	ncRNA	0.003339	0.398333	299(GTAACATCATGTTCCT,+,0.00)
chunk0076_77_1	chr16	63621140	63621486	+	0	NA	Intergenic	Intergenic	1500824	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.008671	0.380403	
chunk0143_86_1	chr4	108271921	108272446	+	0	NA	Intergenic	Intergenic	100063	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.007619	0.414449	
chunk0202_253_1	chr9	76825439	76825659	+	0	NA	intron (NM_015225, intron 5 of 18)	intron (NM_015225, intron 5 of 18)	61113	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.000000	0.484163	
chunk0012_122_1	chr1	157010989	157011494	+	0	NA	intron (NM_198236, intron 1 of 40)	L1MB8|LINE|L1	34129	NM_014784	9826	Hs.516954	NM_014784	ENSG00000132694	ARHGEF11	GTRAP48|PDZ-RHOGEF	Rho guanine nucleotide exchange factor 11	protein-coding	0.003960	0.345850	
chunk0112_119_1	chr20	38457360	38458033	+	0	NA	Intergenic	L2a|LINE|L2	8327	NR_002986	677837	Hs.16936	NR_002986	ENSG00000199266	SNORA60	ACA60	small nucleolar RNA, H/ACA box 60	snoRNA	0.010401	0.485163	
chunk0159_173_1	chr5	139883058	139883430	+	0	NA	intron (NM_004883, intron 2 of 9)	intron (NM_004883, intron 2 of 9)	87423	NM_032289	84249	Hs.21963	NM_032289	ENSG00000146005	PSD2	EFA6C	pleckstrin and Sec7 domain containing 2	protein-coding	0.021505	0.646113	
chunk0001_192_1	chr1	7572145	7572535	+	0	NA	intron (NM_015215, intron 6 of 22)	L1PREC2|LINE|L1	-198929	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.005128	0.337596	
chunk0039_11_1	chr11	95120704	95120942	+	0	NA	intron (NM_015036, intron 1 of 1)	L1MA2|LINE|L1	-29716	NR_110303	101929295	Hs.735838	NR_110303	ENSG00000245552	LOC101929295	-	uncharacterized LOC101929295	ncRNA	0.008403	0.506276	
chunk0125_131_1	chr3	65889750	65890094	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-3894	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.008721	0.431884	
chunk0055_64_1	chr13	52725275	52725828	+	0	NA	intron (NM_007015, intron 3 of 6)	intron (NM_007015, intron 3 of 6)	14261	NM_007015	11061	Hs.421391	NM_007015	ENSG00000136110	CNMD	BRICD3|CHM-I|CHM1|LECT1|MYETS1	chondromodulin	protein-coding	0.001808	0.413357	
chunk0010_149_1	chr1	115317629	115318060	+	0	NA	intron (NM_002506, intron 1 of 2)	intron (NM_002506, intron 1 of 2)	20392	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.013921	0.425926	
chunk0181_345_1	chr7	88281190	88282154	+	0	NA	intron (NM_001205316, intron 2 of 3)	intron (NM_001205316, intron 2 of 3)	25241	NM_001205316	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.003112	0.330570	
chunk0036_200_1	chr11	63280779	63281377	+	0	NA	Intergenic	L1M2|LINE|L1	-8880	NM_001039752	387775	Hs.188982	NM_001039752	ENSG00000184999	SLC22A10	OAT5|hOAT5	solute carrier family 22 member 10	protein-coding	0.001672	0.330551	
chunk0035_359_1	chr11	49159847	49160454	+	0	NA	intron (NM_001014986, intron 13 of 17)	L1PA10|LINE|L1	48520	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.011532	0.366776	
chunk0015_176_1	chr1	186894728	186895001	+	0	NA	intron (NM_001311193, intron 5 of 15)	intron (NM_001311193, intron 5 of 15)	65964	NM_024420	5321	Hs.497200	NM_024420	ENSG00000116711	PLA2G4A	GURDP|PLA2G4|cPLA2|cPLA2-alpha	phospholipase A2 group IVA	protein-coding	0.003663	0.332117	
chunk0069_204_1	chr15	63466311	63466957	+	0	NA	Intergenic	Intergenic	-37877	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.007740	0.452859	
chunk0015_167_1	chr1	186634735	186635000	+	0	NA	Intergenic	Intergenic	45560	NM_000963	5743	Hs.196384	NM_000963	ENSG00000073756	PTGS2	COX-2|COX2|GRIPGHS|PGG/HS|PGHS-2|PHS-2|hCox-2	prostaglandin-endoperoxide synthase 2	protein-coding	0.007547	0.379699	
chunk0118_434_1	chr22	38700957	38701156	+	0	NA	promoter-TSS (NM_014876)	promoter-TSS (NM_014876)	-602	NM_014876	9929	Hs.3094	NM_014876	ENSG00000100221	JOSD1	dJ508I15.2	Josephin domain containing 1	protein-coding	0.145729	0.725000	
chunk0077_195_1	chr16	79800061	79800453	+	0	NA	intron (NR_104660, intron 3 of 3)	intron (NR_104660, intron 3 of 3)	5008	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.007653	0.407125	
chunk0042_171_1	chr12	4606875	4607130	+	0	NA	intron (NM_003845, intron 9 of 12)	intron (NM_003845, intron 9 of 12)	2139	NM_001282285	8798	Hs.439530	NM_003845	ENSG00000010219	DYRK4	-	dual specificity tyrosine phosphorylation regulated kinase 4	protein-coding	0.003922	0.406250	
chunk0206_188_1	chr9	122912735	122912936	+	0	NA	intron (NM_006626, intron 1 of 1)	intron (NM_006626, intron 1 of 1)	493	NM_006626	10773	Hs.654596	NM_006626	ENSG00000186130	ZBTB6	ZID|ZNF482	zinc finger and BTB domain containing 6	protein-coding	0.024876	0.366337	
chunk0026_253_1	chr10	66565046	66565245	+	0	NA	intron (NM_001127384, intron 10 of 17)	intron (NM_001127384, intron 10 of 17)	-360889	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.000000	0.290000	
chunk0174_92_1	chr6	156719814	156720015	+	0	NA	Intergenic	CpG	-58016	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.054726	0.554455	
chunk0161_247_1	chr5	171753603	171754074	+	0	NA	Intergenic	Intergenic	-32034	NM_001289970	644994	Hs.591740	NM_001289970	ENSG00000185662	SMIM23	C5orf50	small integral membrane protein 23	protein-coding	0.008493	0.423729	
chunk0145_396_1	chr4	152524810	152525307	+	0	NA	intron (NM_001257069, intron 2 of 3)	intron (NM_001257069, intron 2 of 3)	9975	NM_033632	55294	Hs.561245	NM_018315	ENSG00000109670	FBXW7	AGO|CDC4|FBW6|FBW7|FBX30|FBXO30|FBXW6|SEL-10|SEL10|hAgo|hCdc4	F-box and WD repeat domain containing 7	protein-coding	0.004024	0.327309	221(GAGAACATGCTCTTCT,-,0.00),222(AGAACATGCTCTTCTT,+,0.00)
chunk0105_237_1	chr2	188399504	188400153	+	0	NA	intron (NR_045563, intron 3 of 12)	intron (NR_045563, intron 3 of 12)	102336	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.000000	0.343077	
chunk0101_321_1	chr2	135926415	135926893	+	0	NA	intron (NM_001293312, intron 6 of 14)	intron (NM_001293312, intron 6 of 14)	-50177	NM_005915	4175	Hs.444118	NM_005915	ENSG00000076003	MCM6	MCG40308|Mis5|P105MCM	minichromosome maintenance complex component 6	protein-coding	0.008368	0.340292	
chunk0144_95_1	chr4	128426781	128427201	+	0	NA	Intergenic	Intergenic	-1025	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.009524	0.296912	
chunk0187_258_1	chr7	154847797	154848360	+	0	NA	intron (NM_001290252, intron 14 of 23)	L1MA7|LINE|L1	-80439	NR_024476	100132707	Hs.586358	NR_024476	ENSG00000214106	PAXIP1-AS2	PAXIP1OS	PAXIP1 antisense RNA 2	ncRNA	0.010657	0.393617	337(AGTACAGACAGCTCTT,+,0.00)
chunk0161_365_1	chr5	175890435	175890670	+	0	NA	Intergenic	Intergenic	19054	NM_001008220	10814	Hs.193235	NM_006650	ENSG00000145920	CPLX2	921-L|CPX-2|CPX2|Hfb1	complexin 2	protein-coding	0.029787	0.546610	
chunk0209_240_1	chrX	45330913	45331569	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-130340	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.006098	0.375951	
chunk0181_276_1	chr7	86472562	86472921	+	0	NA	Intergenic	MIRc|SINE|MIR	-171173	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.005571	0.319444	
chunk0078_386_1	chr16	87864693	87865044	+	0	NA	intron (NM_003486, intron 1 of 9)	LTR22B|LTR|ERVK	4626	NM_003486	8140	Hs.513797	NM_003486	ENSG00000103257	SLC7A5	4F2LC|CD98|D16S469E|E16|LAT1|MPE16	solute carrier family 7 member 5	protein-coding	0.019943	0.394886	
chunk0181_267_1	chr7	86111049	86111623	+	0	NA	Intergenic	Intergenic	-532578	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.005226	0.354783	
chunk0120_10_1	chr3	990660	990900	+	0	NA	Intergenic	(ATGG)n|Simple_repeat|Simple_repeat	-101878	NM_001289080	27255	Hs.387300	NM_014461	ENSG00000134115	CNTN6	NB3	contactin 6	protein-coding	0.000000	0.448133	
chunk0159_162_1	chr5	139561092	139561371	+	0	NA	promoter-TSS (NM_003339)	promoter-TSS (NM_003339)	65	NM_181838	7322	Hs.108332	NM_003339	ENSG00000131508	UBE2D2	E2(17)KB2|PUBC1|UBC4|UBC4/5|UBCH4|UBCH5B	ubiquitin conjugating enzyme E2 D2	protein-coding	0.150538	0.764286	
chunk0171_217_1	chr6	126112977	126113176	+	0	NA	Intergenic	L2c|LINE|L2	126646	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.005025	0.435000	
chunk0198_363_1	chr8	140931077	140931416	+	0	NA	intron (NM_153831, intron 1 of 31)	L1ME4b|LINE|L1	70067	NM_005607	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.000000	0.314706	
chunk0162_57_1	chr6	1394828	1395191	+	0	NA	3' UTR (NM_001452, exon 2 of 2)	3' UTR (NM_001452, exon 2 of 2)	-4598	NR_106778	102466720		NR_106778	ENSG00000275859	MIR6720	hsa-mir-6720|mir-6720	microRNA 6720	ncRNA	0.038567	0.538462	
chunk0193_152_1	chr8	74663034	74663656	+	0	NA	intron (NR_033830, intron 2 of 5)	intron (NR_033830, intron 2 of 5)	-42348	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.003215	0.337079	327(AAGAACACCGTGTTTT,-,0.00),328(AGAACACCGTGTTTTG,+,0.00)
chunk0097_19_1	chr2	42190622	42190928	+	0	NA	intron (NM_019063, intron 1 of 22)	MER58B|DNA|hAT-Charlie	-20544	NR_110584	102723824	Hs.639826	NR_110584		LOC102723824	-	uncharacterized LOC102723824	ncRNA	0.000000	0.335505	
chunk0153_342_1	chr5	74206557	74206777	+	0	NA	Intergenic	Intergenic	101658	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.018182	0.493213	
chunk0040_411_1	chr11	121072304	121072503	+	0	NA	intron (NM_152715, intron 7 of 7)	intron (NM_152715, intron 7 of 7)	-30263	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.005025	0.260000	
chunk0037_408_1	chr11	79729507	79729927	+	0	NA	Intergenic	Intergenic	-289066	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.004762	0.308789	
chunk0050_304_1	chr12	106793607	106794012	+	0	NA	intron (NM_018157, intron 2 of 8)	L1MB7|LINE|L1	-18978	NR_040246	100287944	Hs.742087	NR_040246	ENSG00000257545	LOC100287944	-	uncharacterized LOC100287944	ncRNA	0.002469	0.455665	
chunk0084_445_1	chr17	82889021	82889270	+	0	NA	intron (NM_005993, intron 15 of 38)	intron (NM_005993, intron 15 of 38)	-49090	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.028112	0.620000	
chunk0134_85_1	chr3	176572680	176573379	+	0	NA	Intergenic	Intergenic	57926	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.004292	0.401429	
chunk0018_120_1	chr1	218446945	218447529	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	4611	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.008562	0.384615	257(GGGAACAGAATGTACT,-,0.00),258(GGAACAGAATGTACTG,+,0.00)
chunk0130_439_1	chr3	141204580	141204779	+	0	NA	Intergenic	MER57A1|LTR|ERV1	-27146	NM_152282	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.010050	0.440000	
chunk0211_391_1	chrX	128437322	128437902	+	0	NA	Intergenic	Intergenic	-385209	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.003448	0.337349	
chunk0066_141_1	chr15	31365618	31366122	+	0	NA	intron (NM_001302461, intron 1 of 1).2	intron (NM_001302461, intron 1 of 1).2	39015	NM_001302461	51621	Hs.376443	NM_015995	ENSG00000169926	KLF13	BTEB3|FKLF2|NSLP1|RFLAT-1|RFLAT1	Kruppel like factor 13	protein-coding	0.043651	0.641584	292(GAGAACACGTTGTCCC,-,0.00),293(AGAACACGTTGTCCCC,+,0.00),342(TGGGACGCTGTGTTCC,-,0.00),343(GGGACGCTGTGTTCCT,+,0.00)
chunk0142_441_1	chr4	105345187	105345874	+	0	NA	intron (NR_126420, intron 1 of 5)	intron (NR_126420, intron 1 of 5)	7351	NR_126420	104384744	Hs.624109	NR_126420		TET2-AS1	-	TET2 antisense RNA 1	ncRNA	0.005822	0.405523	
chunk0192_370_1	chr8	68325522	68325734	+	0	NA	intron (NR_038877, intron 1 of 2)	intron (NR_038877, intron 1 of 2)	-5094	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.014151	0.417840	
chunk0115_446_1	chr21	32278921	32279183	+	0	NA	promoter-TSS (NM_018944)	promoter-TSS (NM_018944)	13	NM_018944	54069	Hs.190518	NM_018944	ENSG00000159055	MIS18A	B28|C21orf45|C21orf46|FASP1|MIS18alpha|hMis18alpha	MIS18 kinetochore protein A	protein-coding	0.114504	0.676806	
chunk0049_172_1	chr12	92312958	92313157	+	0	NA	Intergenic	Intergenic	-108474	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.005025	0.365000	
chunk0202_321_1	chr9	78296315	78296536	+	0	NA	promoter-TSS (NM_058179)	promoter-TSS (NM_058179)	-650	NM_058179	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.058824	0.549550	
chunk0098_205_1	chr2	72689537	72689925	+	0	NA	intron (NM_015189, intron 6 of 21)	intron (NM_015189, intron 6 of 21)	136317	NM_015189	23233	Hs.303454	NM_015189	ENSG00000144036	EXOC6B	SEC15B|SEC15L2|SEMDJL3	exocyst complex component 6B	protein-coding	0.012887	0.452442	
chunk0182_108_1	chr7	93307031	93307673	+	0	NA	intron (NM_001257998, intron 19 of 28)	Tigger17c|DNA|TcMar-Tigger	75012	NM_024553	55610	Hs.202424	NM_017667	ENSG00000004766	VPS50	CCDC132|VPS54L	VPS50 subunit of EARP/GARPII complex	protein-coding	0.009346	0.368585	
chunk0004_421_1	chr1	52523349	52523791	+	0	NA	intron (NM_001009881, intron 2 of 29)	AluSz|SINE|Alu	29520	NM_015269	23318	Hs.655407	NM_015269	ENSG00000134744	TUT4	PAPD3|TENT3A|ZCCHC11	terminal uridylyl transferase 4	protein-coding	0.006787	0.426637	
chunk0086_161_1	chr18	21612147	21612370	+	0	NA	promoter-TSS (NM_006938)	promoter-TSS (NM_006938)	-11	NM_001291916	6632	Hs.464734	NM_006938	ENSG00000167088	SNRPD1	HsT2456|SMD1|SNRPD|Sm-D1	small nuclear ribonucleoprotein D1 polypeptide	protein-coding	0.107623	0.665179	
chunk0190_279_1	chr8	37736321	37736608	+	0	NA	promoter-TSS (NM_007175)	promoter-TSS (NM_007175)	-115	NM_001003791	11160	Hs.669261	NM_007175	ENSG00000147475	ERLIN2	C8orf2|Erlin-2|NET32|SPFH2|SPG18	ER lipid raft associated 2	protein-coding	0.121951	0.694444	
chunk0153_220_1	chr5	72026750	72027235	+	0	NA	Intergenic	L1ME3|LINE|L1	-80299	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.002062	0.302469	
chunk0185_354_1	chr7	132307720	132308037	+	0	NA	intron (NM_020911, intron 3 of 31)	intron (NM_020911, intron 3 of 31)	268686	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.015773	0.465409	
chunk0147_182_1	chr4	177303331	177303876	+	0	NA	Intergenic	Intergenic	-6234	NM_018248	55247	Hs.405467	NM_018248	ENSG00000109674	NEIL3	FGP2|FPG2|NEI3|ZGRF3|hFPG2|hNEI3	nei like DNA glycosylase 3	protein-coding	0.005505	0.366300	
chunk0005_399_1	chr1	62367173	62367387	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	-47868	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.014019	0.465116	
chunk0093_293_1	chr19	52371641	52371980	+	0	NA	intron (NM_001145434, intron 1 of 3)	MIR|SINE|MIR	1893	NM_001145434	400713	Hs.502314	NM_001145434	ENSG00000221923	ZNF880	-	zinc finger protein 880	protein-coding	0.017699	0.482353	162(GGGAACAGATTGTTCT,-,0.00),163(GGAACAGATTGTTCTT,+,0.00)
chunk0186_450_1	chr7	148191095	148191653	+	0	NA	intron (NM_014141, intron 18 of 23)	MSTD|LTR|ERVL-MaLR	-399191	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.003584	0.459750	
chunk0052_450_1	chr12	132565513	132565752	+	0	NA	intron (NM_001142641, intron 5 of 16)	intron (NM_001142641, intron 5 of 16)	-16365	NR_106821	102465975		NR_106821	ENSG00000277052	MIR6763	hsa-mir-6763	microRNA 6763	ncRNA	0.050209	0.525000	
chunk0055_397_1	chr13	73977514	73977755	+	0	NA	intron (NM_007249, intron 2 of 7)	L1MC1|LINE|L1	156295	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.000000	0.289256	
chunk0078_20_1	chr17	729272	729529	+	0	NA	Intergenic	Intergenic	-3207	NM_024792	79850	Hs.154396	NM_024792	ENSG00000167695	TLCD3A	CT120|FAM57A	TLC domain containing 3A	protein-coding	0.011673	0.406977	
chunk0044_70_1	chr12	27944154	27944444	+	0	NA	Intergenic	MIRb|SINE|MIR	25662	NM_198964	5744	Hs.591159	NM_002820	ENSG00000087494	PTHLH	BDE2|HHM|PLP|PTHR|PTHRP	parathyroid hormone like hormone	protein-coding	0.013793	0.439863	
chunk0152_161_1	chr5	59441523	59442510	+	0	NA	intron (NM_001165899, intron 3 of 16)	L3|LINE|CR1	-85115	NM_001197219	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002026	0.357287	
chunk0180_120_1	chr7	55532328	55532723	+	0	NA	intron (NM_030796, intron 1 of 4)	intron (NM_030796, intron 1 of 4)	5191	NM_001284284	81552	Hs.488307	NM_030796	ENSG00000154978	VOPP1	ECOP|GASP|WBP1L2	VOPP1 WW domain binding protein	protein-coding	0.012658	0.421717	
chunk0089_238_1	chr18	61922678	61923113	+	0	NA	Intergenic	Intergenic	-29824	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.006897	0.428899	196(CAGGTCAGCCTGTGCA,-,0.00),197(AGGTCAGCCTGTGCAC,+,0.00),207(GTGCACAGAATGTACA,-,0.00),208(TGCACAGAATGTACAT,+,0.00),226(CAGGTCAGCCTGTGCA,-,0.00),227(AGGTCAGCCTGTGCAC,+,0.00),237(GTGCACAGAATGTACC,-,0.00),238(TGCACAGAATGTACCT,+,0.00)
chunk0009_24_1	chr1	100202607	100203082	+	0	NA	intron (NM_001918, intron 10 of 10)	L1PA7|LINE|L1	-24571	NM_001256387	127495	Hs.44277	NM_144620	ENSG00000122477	LRRC39	-	leucine rich repeat containing 39	protein-coding	0.006316	0.363445	
chunk0172_408_1	chr6	140042505	140043141	+	0	NA	intron (NR_121623, intron 1 of 1)	intron (NR_121623, intron 1 of 1)	-51562	NR_121624	103352541	Hs.582647	NR_121624		LOC103352541	-	uncharacterized LOC103352541	ncRNA	0.006289	0.321821	
chunk0071_375_1	chr15	89117810	89118301	+	0	NA	intron (NM_007011, intron 7 of 14)	intron (NM_007011, intron 7 of 14)	29905	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.010183	0.418699	251(AAGGACATGGTGTTCT,-,0.00),252(AGGACATGGTGTTCTT,+,0.00)
chunk0073_359_1	chr16	14989012	14989211	+	0	NA	intron (NM_001285448, intron 2 of 21)	intron (NM_001285448, intron 2 of 21)	14148	NM_001285444	23042	Hs.370781	NM_015027	ENSG00000179889	PDXDC1	LP8165	pyridoxal dependent decarboxylase domain containing 1	protein-coding	0.035176	0.610000	
chunk0156_51_1	chr5	103109830	103110029	+	0	NA	intron (NM_017676, intron 1 of 7)	L1M5|LINE|L1	10209	NM_017676	54826	Hs.24088	NM_017676	ENSG00000145723	GIN1	GIN-1|TGIN1|ZH2C2	gypsy retrotransposon integrase 1	protein-coding	0.005025	0.310000	
chunk0062_420_1	chr14	75196463	75196838	+	0	NA	Intergenic	Intergenic	-20004	NM_006827	10972	Hs.74137	NM_006827	ENSG00000170348	TMED10	P24(DELTA)|S31I125|S31III125|TMP21|Tmp-21-I|p23|p24d1	transmembrane p24 trafficking protein 10	protein-coding	0.008000	0.550532	
chunk0151_45_1	chr5	42266999	42267490	+	0	NA	Intergenic	HAL1b|LINE|L1	-91899	NR_104636	101926960	Hs.365692	NR_104635		LOC101926960	-	uncharacterized LOC101926960	ncRNA	0.002037	0.319106	252(GGGAACTGAGTGTTCC,-,0.00),253(GGAACTGAGTGTTCCT,+,0.00)
chunk0188_123_1	chr8	9128713	9129215	+	0	NA	Intergenic	L1MD1|LINE|L1	21746	NM_024607	79660	Hs.458513	NM_024607	ENSG00000173281	PPP1R3B	GL|PPP1R4|PTG	protein phosphatase 1 regulatory subunit 3B	protein-coding	0.007968	0.339960	
chunk0061_216_1	chr14	60551529	60552114	+	0	NA	Intergenic	Intergenic	42601	NM_007374	4990	Hs.194756	NM_007374	ENSG00000184302	SIX6	MCOPCT2|ODRMD|OPTX2|Six9	SIX homeobox 6	protein-coding	0.008547	0.416382	
chunk0040_161_1	chr11	113838411	113838912	+	0	NA	intron (NM_020886, intron 5 of 24)	L2a|LINE|L2	36909	NM_001301029	57646	Hs.503891	NM_020886	ENSG00000048028	USP28	-	ubiquitin specific peptidase 28	protein-coding	0.005988	0.472112	
chunk0072_56_1	chr16	1563413	1563678	+	0	NA	intron (NM_014714, intron 17 of 30)	intron (NM_014714, intron 17 of 30)	29888	NM_024600	79652	Hs.459652	NM_024600	ENSG00000131634	TMEM204	C16orf30|CLP24	transmembrane protein 204	protein-coding	0.011321	0.451128	
chunk0180_54_1	chr7	54785283	54785482	+	0	NA	intron (NR_110040, intron 2 of 2)	intron (NR_110040, intron 2 of 2)	26069	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.025126	0.580000	
chunk0140_450_1	chr4	76397374	76397650	+	0	NA	intron (NM_001042784, intron 2 of 23)	L1MC4|LINE|L1	9793	NM_001042784	339965	Hs.529680	NM_178555	ENSG00000163749	CCDC158	-	coiled-coil domain containing 158	protein-coding	0.000000	0.274368	
chunk0128_372_1	chr3	113274904	113275479	+	0	NA	intron (NM_033254, intron 9 of 19)	intron (NM_033254, intron 9 of 19)	62694	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.019130	0.526042	480(CTGGACACTGTGTCCT,-,0.00),481(TGGACACTGTGTCCTG,+,0.00)
chunk0205_144_1	chr9	108247696	108247895	+	0	NA	Intergenic	Intergenic	608200	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.005025	0.505000	
chunk0082_51_1	chr17	51080279	51080555	+	0	NA	intron (NM_001130528, intron 1 of 29)	L2a|LINE|L2	-33449	NM_001251971	9043	Hs.463439	NM_003971	ENSG00000008294	SPAG9	CT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6	sperm associated antigen 9	protein-coding	0.025362	0.404332	
chunk0163_250_1	chr6	12532962	12533580	+	0	NA	Intergenic	Intergenic	-183534	NM_001242648	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.006472	0.369952	259(AAGAACACAGTGTTCA,-,0.00),260(AGAACACAGTGTTCAA,+,0.00)
chunk0168_387_1	chr6	94029579	94029778	+	0	NA	Intergenic	L1MA2|LINE|L1	322595	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.000000	0.425000	49(AGTACACTATGATCCT,+,0.00)
chunk0010_123_1	chr1	114506760	114507311	+	0	NA	intron (NM_033020, intron 1 of 18)	intron (NM_033020, intron 1 of 18)	4125	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.012704	0.375000	
chunk0200_252_1	chr9	21335801	21336058	+	0	NA	promoter-TSS (NM_018847)	promoter-TSS (NM_018847)	-499	NM_018847	55958	Hs.701778	NM_018847	ENSG00000198642	KLHL9	-	kelch like family member 9	protein-coding	0.003891	0.271318	
chunk0167_439_1	chr6	75860216	75860825	+	0	NA	intron (NM_001300899, intron 14 of 32)	intron (NM_001300899, intron 14 of 32)	111328	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.001642	0.300000	
chunk0170_420_1	chr6	118342696	118343202	+	0	NA	Intergenic	L1PA7|LINE|L1	-158424	NR_002730	23629	Hs.648050	NR_002730		BRD7P3	BP75	bromodomain containing 7 pseudogene 3	pseudo	0.009881	0.463511	
chunk0050_441_1	chr12	110450185	110450384	+	0	NA	5' UTR (NM_001287222, exon 1 of 7)	5' UTR (NM_001287222, exon 1 of 7)	127	NM_001287222	10094	Hs.524741	NM_001278556	ENSG00000111229	ARPC3	ARC21|p21-Arc	actin related protein 2/3 complex subunit 3	protein-coding	0.095477	0.655000	
chunk0143_312_1	chr4	119049624	119049823	+	0	NA	intron (NM_133477, intron 4 of 4)	intron (NM_133477, intron 4 of 4)	-86061	NM_016599	51778	Hs.732122	NM_016599	ENSG00000172399	MYOZ2	C4orf5|CMH16|CS-1|FATZ-2	myozenin 2	protein-coding	0.000000	0.395000	
chunk0007_363_1	chr1	84941457	84942119	+	0	NA	intron (NM_153259, intron 7 of 13)	intron (NM_153259, intron 7 of 13)	-48575	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.004532	0.420814	
chunk0091_37_1	chr19	3721374	3721736	+	0	NA	promoter-TSS (NM_001267561)	promoter-TSS (NM_001267561)	-144	NM_001267561	27134	Hs.25527	NM_014428	ENSG00000105289	TJP3	ZO-3|ZO3	tight junction protein 3	protein-coding	0.069061	0.652893	
chunk0043_208_1	chr12	19550753	19551188	+	0	NA	Intergenic	Intergenic	110389	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.006897	0.330275	
chunk0060_408_1	chr14	53090770	53091302	+	0	NA	intron (NM_030637, intron 4 of 11)	L4_B_Mam|LINE|RTE-X	62292	NM_001160147	80821	Hs.125525	NM_030637	ENSG00000100523	DDHD1	PA-PLA1|PAPLA1|SPG28	DDHD domain containing 1	protein-coding	0.005639	0.335835	
chunk0175_128_1	chr7	3373585	3373822	+	0	NA	intron (NM_152744, intron 1 of 44)	L1ME4a|LINE|L1	72255	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.004219	0.294118	
chunk0094_14_1	chr2	1041002	1041247	+	0	NA	intron (NM_018968, intron 1 of 16)	intron (NM_018968, intron 1 of 16)	90256	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.016327	0.471545	
chunk0016_453_1	chr1	204195996	204196541	+	0	NA	intron (NM_002256, intron 1 of 2)	intron (NM_002256, intron 1 of 2)	223	NM_002256	3814	Hs.95008	NM_002256	ENSG00000170498	KISS1	HH13|KiSS-1	KiSS-1 metastasis suppressor	protein-coding	0.023853	0.576923	
chunk0010_285_1	chr1	117546990	117547604	+	0	NA	Intergenic	Intergenic	58473	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.004886	0.341463	
chunk0102_155_1	chr2	147203637	147204249	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	616886	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.001634	0.384992	
chunk0086_411_1	chr18	26863112	26863678	+	0	NA	promoter-TSS (NM_004028)	promoter-TSS (NM_004028)	-784	NM_004028	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.061837	0.664903	428(AAGGACAGCCTCTCCT,-,0.00),429(AGGACAGCCTCTCCTC,+,0.00)
chunk0043_329_1	chr12	22640604	22640803	+	0	NA	intron (NM_001039481, intron 1 of 2)	MIR|SINE|MIR	15561	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.015075	0.385000	
chunk0128_234_1	chr3	108405692	108406281	+	0	NA	intron (NM_014981, intron 33 of 41)	intron (NM_014981, intron 33 of 41)	94201	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.003396	0.342373	
chunk0160_56_1	chr5	149634079	149634796	+	0	NA	3' UTR (NM_001001669, exon 13 of 13)	3' UTR (NM_001001669, exon 13 of 13)	52865	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.008368	0.455432	280(GGGGACAGCCTGTTCT,-,0.00),281(GGGACAGCCTGTTCTG,+,0.00)
chunk0107_205_1	chr2	216560367	216560806	+	0	NA	Intergenic	UCON47|Unknown|Unknown	46352	NR_110392	101928232	Hs.694592	NR_110392		LINC01280	-	long intergenic non-protein coding RNA 1280	ncRNA	0.004556	0.406818	
chunk0138_15_1	chr4	30500271	30501042	+	0	NA	Intergenic	Intergenic	-219752	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.009079	0.393782	
chunk0096_321_1	chr2	33511979	33512221	+	0	NA	intron (NM_170672, intron 3 of 18)	intron (NM_170672, intron 3 of 18)	-1775	NM_015376	25780	Hs.143674	NM_015376	ENSG00000152689	RASGRP3	GRP3	RAS guanyl releasing protein 3	protein-coding	0.012397	0.415638	
chunk0103_326_1	chr2	167740122	167740693	+	0	NA	Intergenic	Intergenic	-78265	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.000000	0.316434	246(TGGTACATGCTGTTCC,-,0.00),247(GGTACATGCTGTTCCT,+,0.00)
chunk0125_375_1	chr3	71542656	71542949	+	0	NA	promoter-TSS (NR_031697)	promoter-TSS (NR_031697)	-713	NR_031697	100302112		NR_031697	ENSG00000221264	MIR1284	MIRN1284|hsa-mir-1284|mir-1284	microRNA 1284	ncRNA	0.027304	0.564626	
chunk0054_35_1	chr13	41025277	41025896	+	0	NA	Intergenic	MIR3|SINE|MIR	-6214	NM_172373	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.009693	0.409677	
chunk0204_256_1	chr9	98135356	98136531	+	0	NA	intron (NM_003389, intron 3 of 11)	intron (NM_003389, intron 3 of 11)	-16590	NM_014788	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.011915	0.511054	282(AGTACAAGGTGATCCT,+,0.00),960(GGCAGACACTGTCCTT,+,0.00)
chunk0185_282_1	chr7	130942073	130942524	+	0	NA	intron (NR_109855, intron 4 of 4)	intron (NR_109855, intron 4 of 4)	28834	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.017738	0.391593	149(CGGGACACTTTGACCT,-,0.00),150(GGGACACTTTGACCTT,+,0.00)
chunk0132_195_1	chr3	157174891	157175299	+	0	NA	Intergenic	CpG	-14335	NM_001308185	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.100490	0.596577	
chunk0046_434_1	chr12	64805355	64805596	+	0	NA	Intergenic	Intergenic	-19097	NM_015279	23329	Hs.192492	NM_015279	ENSG00000111490	TBC1D30	-	TBC1 domain family member 30	protein-coding	0.000000	0.417355	
chunk0008_214_1	chr1	93714934	93715364	+	0	NA	intron (NM_001261408, intron 2 of 13)	intron (NM_001261408, intron 2 of 13)	-33311	NM_003567	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.000000	0.357309	
chunk0208_136_1	chrX	15621112	15621873	+	0	NA	TTS (NR_126564)	TTS (NR_126564)	18611	NR_126564	104798195	Hs.131674	NR_126564	ENSG00000225833	GS1-594A7.3	-	uncharacterized LOC104798195	ncRNA	0.001314	0.350394	
chunk0015_417_1	chr1	191460325	191460619	+	0	NA	Intergenic	Intergenic	-697990	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.000000	0.345763	
chunk0183_271_1	chr7	107527138	107527829	+	0	NA	intron (NM_006348, intron 5 of 21)	L1PA10|LINE|L1	-36474	NR_073003	11062	Hs.97627	NM_181581	ENSG00000105865	DUS4L	DUS4|PP35	dihydrouridine synthase 4 like	protein-coding	0.007236	0.364162	
chunk0011_182_1	chr1	148451197	148451396	+	0	NA	intron (NR_027468, intron 1 of 4)	AluSq|SINE|Alu	8624	NR_027468	388685	Hs.713362	NM_207400	ENSG00000274020	LINC01138	LINC00875	long intergenic non-protein coding RNA 1138	ncRNA	0.040201	0.520000	
chunk0009_427_1	chr1	111099296	111099543	+	0	NA	Intergenic	LTR22A|LTR|ERVK	-40208	NM_001007794	10390	Hs.363572	NM_006090	ENSG00000134255	CEPT1	-	choline/ethanolamine phosphotransferase 1	protein-coding	0.004049	0.443548	
chunk0113_33_1	chr20	49831212	49831420	+	0	NA	intron (NM_015266, intron 3 of 15)	intron (NM_015266, intron 3 of 15)	18603	NR_048538	23315	Hs.444202	NM_015266	ENSG00000197818	SLC9A8	NHE-8|NHE8	solute carrier family 9 member A8	protein-coding	0.014423	0.559809	
chunk0159_412_1	chr5	147892475	147892872	+	0	NA	TTS (NM_206966)	TTS (NM_206966)	13865	NM_206966	389336	Hs.660038	NM_206966	ENSG00000178776	C5orf46	SSSP1	chromosome 5 open reading frame 46	protein-coding	0.007557	0.364322	
chunk0194_47_1	chr8	82031536	82032274	+	0	NA	Intergenic	L1MA9|LINE|L1	-189619	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.004065	0.343708	
chunk0035_241_1	chr11	46100603	46101222	+	0	NA	intron (NM_016621, intron 1 of 17)	intron (NM_016621, intron 1 of 17)	20522	NM_001101802	51317	Hs.502458	NM_016621	ENSG00000135365	PHF21A	BHC80|BM-006	PHD finger protein 21A	protein-coding	0.006462	0.375806	
chunk0059_429_1	chr14	38290762	38290961	+	0	NA	Intergenic	Intergenic	-34491	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.005025	0.340000	
chunk0150_171_1	chr5	34245835	34246205	+	0	NA	Intergenic	Intergenic	-121492	NR_037951	100534612	Hs.171929	NR_037951	ENSG00000273294	C1QTNF3-AMACR	-	C1QTNF3-AMACR readthrough (NMD candidate)	ncRNA	0.002703	0.407008	
chunk0070_134_1	chr15	70913784	70913992	+	0	NA	intron (NM_017691, intron 6 of 15)	Charlie14a|DNA|hAT-Charlie	21445	NM_001199017	54839	Hs.12692	NM_017691	ENSG00000137821	LRRC49	PGs4	leucine rich repeat containing 49	protein-coding	0.000000	0.282297	
chunk0106_96_1	chr2	197213471	197214145	+	0	NA	intron (NM_001195144, intron 1 of 27)	intron (NM_001195144, intron 1 of 27)	88711	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.004451	0.343704	
chunk0203_179_1	chr9	86170702	86171175	+	0	NA	Intergenic	L1M4|LINE|L1	43398	NR_110996	101927623	Hs.575644	NR_110996		LOC101927623	-	uncharacterized LOC101927623	ncRNA	0.010571	0.409283	
chunk0201_155_1	chr9	35969206	35969670	+	0	NA	Intergenic	L1MA5|LINE|L1	-11284	NM_019897	56656	Hs.553540	NM_019897	ENSG00000278889	OR2S2	OR37A|OST715	olfactory receptor family 2 subfamily S member 2 (gene/pseudogene)	protein-coding	0.006466	0.350538	
chunk0182_102_1	chr7	93232039	93232647	+	0	NA	promoter-TSS (NM_017667)	promoter-TSS (NM_017667)	3	NM_024553	55610	Hs.202424	NM_017667	ENSG00000004766	VPS50	CCDC132|VPS54L	VPS50 subunit of EARP/GARPII complex	protein-coding	0.049342	0.546798	
chunk0068_91_1	chr15	52132006	52132696	+	0	NA	intron (NM_016194, intron 9 of 12)	L2a|LINE|L2	-19576	NM_020396	10017	Hs.283672	NM_020396	ENSG00000137875	BCL2L10	BCL-B|Boo|Diva|bcl2-L-10	BCL2 like 10	protein-coding	0.007246	0.447178	
chunk0186_244_1	chr7	140920295	140920771	+	0	NA	intron (NM_004333, intron 1 of 17)	intron (NM_004333, intron 1 of 17)	4231	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.002101	0.379455	
chunk0198_315_1	chr8	139705864	139706197	+	0	NA	Intergenic	CpG-27595	-2974	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.114114	0.697605	156(AAGTCCAGGCTGTCCC,-,0.00),157(AGTCCAGGCTGTCCCC,+,0.00)
chunk0173_164_1	chr6	144321926	144322579	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	30515	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.009188	0.435780	
chunk0183_114_1	chr7	105345754	105346160	+	0	NA	intron (NM_182692, intron 2 of 15)	MER3|DNA|hAT-Charlie	42973	NM_182692	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.007389	0.361179	
chunk0168_34_1	chr6	78098323	78098856	+	0	NA	Intergenic	Intergenic	407933	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.003752	0.337079	174(AAGAGCATTCTGTTCC,-,0.00),175(AGAGCATTCTGTTCCA,+,0.00)
chunk0059_289_1	chr14	35786549	35786862	+	0	NA	intron (NM_001283043, intron 1 of 41)	intron (NM_001283043, intron 1 of 41)	22521	NM_001283044	253959	Hs.113150	NM_014990	ENSG00000174373	RALGAPA1	GARNL1|GRIPE|RalGAPalpha1|TULIP1|p240	Ral GTPase activating protein catalytic alpha subunit 1	protein-coding	0.019169	0.391720	
chunk0194_82_1	chr8	82882114	82882601	+	0	NA	Intergenic	L1MB4|LINE|L1	-521401	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.000000	0.405738	
chunk0049_178_1	chr12	92382405	92382676	+	0	NA	Intergenic	Intergenic	-38991	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.003690	0.371324	
chunk0126_198_1	chr3	78541135	78541570	+	0	NA	Intergenic	LTR43-int|LTR|ERV1	478107	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.419725	
chunk0210_279_1	chrX	84842577	84843294	+	0	NA	Intergenic	HAL1ME|LINE|L1	-91216	NR_024062	100131816	Hs.460809	NM_178567	ENSG00000229547	UBE2DNL	-	ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)	pseudo	0.005579	0.378830	
chunk0120_394_1	chr3	12410046	12410898	+	0	NA	intron (NM_138711, intron 6 of 7)	intron (NM_138711, intron 6 of 7)	58970	NM_015869	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.011737	0.395076	114(TGGAACTGACTGTCCC,-,0.00),115(GGAACTGACTGTCCCC,+,0.00)
chunk0012_96_1	chr1	156311076	156311275	+	0	NA	exon (NM_001008800, exon 10 of 12)	exon (NM_001008800, exon 10 of 12)	-11538	NM_001004319	391104	Hs.532378	NM_001004319	ENSG00000189030	VHLL	VHLP|VLP	VHL like	protein-coding	0.020101	0.525000	
chunk0150_214_1	chr5	35211226	35211449	+	0	NA	intron (NM_000949, intron 1 of 9)	X6A_LINE|LINE|CR1	19252	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.000000	0.446429	109(TGGAACACCATGTTCC,-,0.00),110(GGAACACCATGTTCCA,+,0.00)
chunk0009_287_1	chr1	107676579	107676933	+	0	NA	intron (NM_006113, intron 19 of 26)	intron (NM_006113, intron 19 of 26)	11748	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002825	0.335211	
chunk0010_36_1	chr1	112641795	112642356	+	0	NA	intron (NM_006135, intron 1 of 9)	intron (NM_006135, intron 1 of 9)	22622	NM_006135	829	Hs.744974	NM_006135	ENSG00000116489	CAPZA1	CAPPA1|CAPZ|CAZ1	capping actin protein of muscle Z-line subunit alpha 1	protein-coding	0.012478	0.386121	
chunk0037_402_1	chr11	79449284	79449772	+	0	NA	Intergenic	Intergenic	-8877	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.006148	0.323108	
chunk0119_398_1	chr22	48982348	48982707	+	0	NA	Intergenic	L2c|LINE|L2	115757	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.019499	0.552778	
chunk0153_348_1	chr5	74330135	74330624	+	0	NA	Intergenic	Intergenic	7893	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.006135	0.448980	
chunk0052_244_1	chr12	123365827	123366030	+	0	NA	Intergenic	Intergenic	-1085	NR_107039	102466877		NR_107039	ENSG00000284425	MIR8072	hsa-mir-8072	microRNA 8072	ncRNA	0.019704	0.465686	
chunk0028_180_1	chr10	88373007	88373673	+	0	NA	intron (NM_001031709, intron 4 of 6)	intron (NM_001031709, intron 4 of 6)	209985	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.000000	0.301349	
chunk0196_139_1	chr8	104305132	104305402	+	0	NA	Intergenic	MER50|LTR|ERV1	-34529	NM_030788	81501	Hs.652230	NM_030788	ENSG00000164935	DCSTAMP	FIND|TM7SF4|hDC-STAMP	dendrocyte expressed seven transmembrane protein	protein-coding	0.011111	0.472325	
chunk0007_12_1	chr1	77293194	77293714	+	0	NA	intron (NM_012093, intron 2 of 13)	MER58A|DNA|hAT-Charlie	10852	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.009615	0.389635	
chunk0056_102_1	chr13	82470005	82470551	+	0	NA	Intergenic	L1MA2|LINE|L1	-1243295	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.000000	0.294333	
chunk0087_193_1	chr18	35695886	35696248	+	0	NA	intron (NM_020474, intron 8 of 10)	intron (NM_020474, intron 8 of 10)	41498	NM_020474	2589	Hs.514806	NM_020474	ENSG00000141429	GALNT1	GALNAC-T1	polypeptide N-acetylgalactosaminyltransferase 1	protein-coding	0.019337	0.471074	
chunk0125_307_1	chr3	70716698	70717247	+	0	NA	Intergenic	Intergenic	347951	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.009107	0.332727	266(AGGAACATAAAGTTCA,-,0.00),267(GGAACATAAAGTTCAA,+,0.00),287(TGAAACATCCTGTCCC,-,0.00),288(GAAACATCCTGTCCCT,+,0.00)
chunk0188_36_1	chr8	6602605	6602804	+	0	NA	intron (NM_024596, intron 12 of 13)	intron (NM_024596, intron 12 of 13)	19516	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.005025	0.440000	
chunk0094_187_1	chr2	6128334	6129242	+	0	NA	Intergenic	Intergenic	146810	NR_026833	400940	Hs.378814	NM_207479		LOC400940	-	uncharacterized LOC400940	ncRNA	0.007709	0.385039	
chunk0178_31_1	chr7	29442163	29442865	+	0	NA	intron (NM_001293069, intron 7 of 13)	intron (NM_001293069, intron 7 of 13)	-37198	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.009972	0.418208	
chunk0107_266_1	chr2	217656689	217656982	+	0	NA	intron (NR_026597, intron 1 of 12)	intron (NR_026597, intron 1 of 12)	99758	NR_026597	729582	Hs.572788	NR_026597		DIRC3	-	disrupted in renal carcinoma 3	ncRNA	0.013652	0.479592	130(AAGTACTGTGTGTTCC,-,0.00),131(AGTACTGTGTGTTCCT,+,0.00),165(TGAAACACTGTGTCCC,-,0.00),166(GAAACACTGTGTCCCC,+,0.00)
chunk0166_264_1	chr6	47698895	47699236	+	0	NA	intron (NM_153838, intron 1 of 9)	intron (NM_153838, intron 1 of 9)	512	NM_153838	221393	Hs.150131	NM_153838	ENSG00000153294	ADGRF4	GPR115|PGR18	adhesion G protein-coupled receptor F4	protein-coding	0.002933	0.353801	
chunk0174_173_1	chr6	158799298	158799682	+	0	NA	intron (NM_003379, intron 1 of 12)	intron (NM_003379, intron 1 of 12)	-18489	NR_102425	101409257	Hs.571207	NR_102425	ENSG00000233893	EZR-AS1	-	EZR antisense RNA 1	ncRNA	0.015625	0.423377	
chunk0093_330_1	chr19	54209992	54210443	+	0	NA	Intergenic	Intergenic	9359	NM_001013	6203	Hs.467284	NM_001013	ENSG00000170889	RPS9	S9	ribosomal protein S9	protein-coding	0.017738	0.515487	
chunk0107_277_1	chr2	218052122	218052485	+	0	NA	intron (NR_034176, intron 2 of 13)	MER101-int|LTR|ERV1	8987	NR_002712	3580	Hs.647858	NR_002712		CXCR2P1	CXCR2P|IL8RBP	C-X-C motif chemokine receptor 2 pseudogene 1	pseudo	0.013774	0.390110	139(GAGGACAACGTGTCCT,-,0.00),140(AGGACAACGTGTCCTC,+,0.00)
chunk0174_407_1	chr6	165634599	165634908	+	0	NA	intron (NM_006661, intron 1 of 22)	L4_A_Mam|LINE|RTE-X	27347	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.016181	0.432258	
chunk0185_422_1	chr7	134491679	134492102	+	0	NA	Intergenic	Intergenic	-32754	NM_001628	231	Hs.521212	NM_001628	ENSG00000085662	AKR1B1	ADR|ALDR1|ALR2|AR	aldo-keto reductase family 1 member B	protein-coding	0.011820	0.422170	
chunk0147_188_1	chr4	177489183	177489382	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-46779	NM_000027	175	Hs.207776	NM_000027	ENSG00000038002	AGA	AGU|ASRG|GA	aspartylglucosaminidase	protein-coding	0.005025	0.385000	
chunk0085_419_1	chr18	10519874	10520343	+	0	NA	Intergenic	Intergenic	-5768	NM_003826	8774	Hs.464622	NM_003826	ENSG00000134265	NAPG	GAMMASNAP	NSF attachment protein gamma	protein-coding	0.025586	0.412766	
chunk0171_343_1	chr6	130007840	130008675	+	0	NA	Intergenic	L1MB3|LINE|L1	-10326	NM_032438	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.004790	0.355263	
chunk0157_279_1	chr5	120600590	120600984	+	0	NA	intron (NM_001308088, intron 1 of 3)	L1PA16|LINE|L1	69323	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.010152	0.394937	
chunk0191_391_1	chr8	57225174	57225807	+	0	NA	intron (NR_038235, intron 8 of 9).2	intron (NR_038235, intron 8 of 9).2	7214	NR_038235	100507651	Hs.371831	NR_038235	ENSG00000253301	LINC01606	-	long intergenic non-protein coding RNA 1606	ncRNA	0.012638	0.421136	
chunk0131_61_1	chr3	142846849	142847119	+	0	NA	intron (NM_013363, intron 3 of 8)	L1ME2z|LINE|L1	42219	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.000000	0.321033	
chunk0127_71_1	chr3	89427233	89427769	+	0	NA	intron (NM_005233, intron 11 of 16)	intron (NM_005233, intron 11 of 16)	319977	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005597	0.305400	
chunk0207_54_1	chrX	7946712	7947275	+	0	NA	Intergenic	L1M1|LINE|L1	-19254	NM_001142389	8228	Hs.264	NM_004650	ENSG00000006757	PNPLA4	DXS1283E|GS2|iPLA2eta	patatin like phospholipase domain containing 4	protein-coding	0.007105	0.473404	282(AGAGCTTTCTGTTCTG,+,0.00)
chunk0209_328_1	chrX	50801094	50801524	+	0	NA	intron (NR_027121, intron 1 of 9)	intron (NR_027121, intron 1 of 9)	12735	NR_027121	57477	Hs.420541	NM_020717	ENSG00000158352	SHROOM4	SHAP|shrm4	shroom family member 4	protein-coding	0.004651	0.487239	
chunk0010_425_1	chr1	119766380	119766823	+	0	NA	intron (NM_001166107, intron 1 of 8)	intron (NM_001166107, intron 1 of 8)	2331	NM_001166107	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.009029	0.448198	
chunk0206_182_1	chr9	122815667	122816112	+	0	NA	Intergenic	MIR|SINE|MIR	12767	NM_005388	5082	Hs.271749	NM_005388	ENSG00000136940	PDCL	PhLP	phosducin like	protein-coding	0.006742	0.405830	
chunk0003_223_1	chr1	35514136	35514464	+	0	NA	intron (NM_024874, intron 2 of 20)	L1ME4c|LINE|L1	43136	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.012195	0.346505	
chunk0095_329_1	chr2	20699278	20699687	+	0	NA	intron (NM_001282721, intron 5 of 5)	intron (NM_001282721, intron 5 of 5)	32818	NM_182828	151449	Hs.447688	NM_182828	ENSG00000143869	GDF7	BMP12	growth differentiation factor 7	protein-coding	0.004890	0.351220	
chunk0149_448_1	chr5	29913605	29913804	+	0	NA	Intergenic	L1PA13|LINE|L1	-517728	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.010050	0.565000	
chunk0195_312_1	chr8	98899689	98900130	+	0	NA	intron (NM_001256312, intron 1 of 12)	MIR|SINE|MIR	42662	NM_001256312	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004535	0.402715	
chunk0136_310_1	chr3	195198781	195199243	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	48908	NM_001308069	152002	Hs.478741	NM_152531	ENSG00000173950	XXYLT1	C3orf21	xyloside xylosyltransferase 1	protein-coding	0.019481	0.483801	
chunk0064_413_1	chr14	99565997	99566564	+	0	NA	intron (NM_001144995, intron 1 of 5)	MIRb|SINE|MIR	38110	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.021164	0.554577	
chunk0003_185_1	chr1	33711313	33711595	+	0	NA	intron (NM_052896, intron 21 of 69)	intron (NM_052896, intron 21 of 69)	-149021	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.003546	0.424028	
chunk0209_454_1	chrX	66196153	66196517	+	0	NA	intron (NM_001282141, intron 9 of 17)	L1ME2z|LINE|L1	32105	NM_014799	9843	Hs.31720	NM_014799	ENSG00000089472	HEPH	CPL	hephaestin	protein-coding	0.005495	0.301370	
chunk0170_280_1	chr6	114193820	114194182	+	0	NA	intron (NR_125845, intron 8 of 9)	L4_C_Mam|LINE|RTE-X	-131124	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.002762	0.352617	181(AGGAACATACTGTCAC,-,0.00),182(GGAACATACTGTCACT,+,0.00)
chunk0095_208_1	chr2	18625525	18625788	+	0	NA	Intergenic	Intergenic	-36076	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.003802	0.306818	
chunk0016_155_1	chr1	197557373	197557737	+	0	NA	intron (NM_001300858, intron 15 of 15)	intron (NM_001300858, intron 15 of 15)	217938	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.005495	0.315068	
chunk0209_209_1	chrX	44545750	44546017	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-2908	NM_173794	139341	Hs.7549	NM_173794	ENSG00000069509	FUNDC1	-	FUN14 domain containing 1	protein-coding	0.007491	0.347015	
chunk0047_269_1	chr12	72971428	72971897	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-187528	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.338298	
chunk0159_168_1	chr5	139660128	139660435	+	0	NA	intron (NM_016463, intron 1 of 2)	intron (NM_016463, intron 1 of 2)	11565	NM_016463	51523	Hs.189119	NM_016463	ENSG00000171604	CXXC5	CF5|HSPC195|RINF|WID	CXXC finger protein 5	protein-coding	0.026059	0.629870	
chunk0033_119_1	chr11	14538095	14538372	+	0	NA	intron (NM_148976, intron 2 of 10)	intron (NM_148976, intron 2 of 10)	-17788	NM_001143937	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.010830	0.316547	
chunk0108_441_1	chr2	238079729	238080345	+	0	NA	intron (NM_016510, intron 4 of 11)	L1MB7|LINE|L1	19113	NM_016510	51540	Hs.731909	NM_016510	ENSG00000132330	SCLY	SCL|hSCL	selenocysteine lyase	protein-coding	0.003247	0.372771	
chunk0071_307_1	chr15	86164446	86164645	+	0	NA	intron (NM_152336, intron 4 of 23)	intron (NM_152336, intron 4 of 23)	22534	NM_152336	123624	Hs.31795	NM_152336	ENSG00000273540	AGBL1	CCP4|FECD8	ATP/GTP binding protein like 1	protein-coding	0.020101	0.470000	
chunk0172_389_1	chr6	139588674	139589309	+	0	NA	Intergenic	Intergenic	-114395	NR_033919	645434	Hs.666240	NR_033919	ENSG00000238099	LINC01625	-	long intergenic non-protein coding RNA 1625	ncRNA	0.006299	0.347484	316(AAGCAGAGACTGTTCC,-,0.00),317(AGCAGAGACTGTTCCT,+,0.00)
chunk0143_131_1	chr4	109666034	109666610	+	0	NA	intron (NM_017918, intron 4 of 7)	L1MC1|LINE|L1	37151	NR_133012	839	Hs.654616	NM_001226	ENSG00000138794	CASP6	MCH2	caspase 6	protein-coding	0.006944	0.381282	
chunk0111_370_1	chr20	33802120	33802396	+	0	NA	intron (NR_110623, intron 1 of 3)	L1MB5|LINE|L1	8841	NR_110623	101929746	Hs.504633	NR_110623	ENSG00000230753	ZNF341-AS1	-	ZNF341 antisense RNA 1	ncRNA	0.003623	0.393502	
chunk0114_140_1	chr21	10132114	10132371	+	0	NA	Intergenic	Intergenic	-281278	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.003891	0.519380	
chunk0187_252_1	chr7	153842996	153843316	+	0	NA	Intergenic	(CACA)n|Simple_repeat|Simple_repeat	-43941	NM_001039350	1804	Hs.490684	NM_001936	ENSG00000130226	DPP6	DPL1|DPPX|MRD33|VF2	dipeptidyl peptidase like 6	protein-coding	0.059375	0.492212	
chunk0062_280_1	chr14	72128218	72129027	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	195553	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.014833	0.366667	
chunk0188_425_1	chr8	19010073	19010659	+	0	NA	intron (NM_015310, intron 1 of 15)	intron (NM_015310, intron 1 of 15)	3320	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.011945	0.429302	
chunk0025_343_1	chr10	58086164	58086558	+	0	NA	Intergenic	Intergenic	181573	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.005076	0.384810	
chunk0041_190_1	chr11	126381858	126382235	+	0	NA	intron (NM_006278, intron 1 of 10)	intron (NM_006278, intron 1 of 10)	-21370	NM_001254758	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.018568	0.634921	
chunk0103_40_1	chr2	159214399	159214598	+	0	NA	intron (NM_001145909, intron 19 of 26)	intron (NM_001145909, intron 19 of 26)	27663	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.005025	0.560000	
chunk0116_67_1	chr21	34156262	34156482	+	0	NA	Intergenic	Intergenic	-24305	NR_027267	114036	Hs.720230	NM_153751	ENSG00000227456	LINC00310	C21orf82|NCRNA00310	long intergenic non-protein coding RNA 310	ncRNA	0.009091	0.479638	
chunk0156_231_1	chr5	108315743	108316590	+	0	NA	intron (NM_001163315, intron 4 of 8)	intron (NM_001163315, intron 4 of 8)	65932	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.002361	0.278302	
chunk0064_163_1	chr14	92100516	92100855	+	0	NA	intron (NR_028460, intron 1 of 5)	L1ME3A|LINE|L1	5936	NR_028453	4287	Hs.532632	NM_004993	ENSG00000066427	ATXN3	AT3|ATX3|JOS|MJD|MJD1|SCA3	ataxin 3	protein-coding	0.005900	0.352941	
chunk0023_61_1	chr10	21992899	21993368	+	0	NA	intron (NM_022365, intron 1 of 11)	intron (NM_022365, intron 1 of 11)	10588	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.012793	0.312766	
chunk0135_164_1	chr3	187871687	187871899	+	0	NA	Intergenic	L2c|LINE|L2	-126068	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.000000	0.417840	
chunk0185_288_1	chr7	131040589	131040788	+	0	NA	intron (NR_109850, intron 3 of 5)	intron (NR_109850, intron 3 of 5)	66342	NR_024153	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.015075	0.455000	
chunk0036_351_1	chr11	66887023	66887264	+	0	NA	intron (NM_000920, intron 2 of 21)	HAL1|LINE|L1	20726	NM_022172	5091	Hs.89890	NM_000920	ENSG00000173599	PC	PCB	pyruvate carboxylase	protein-coding	0.016598	0.582645	
chunk0161_28_1	chr5	165786031	165786461	+	0	NA	Intergenic	L2a|LINE|L2	1140124	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.006977	0.348028	
chunk0045_4_1	chr12	42888006	42888253	+	0	NA	Intergenic	Intergenic	-241631	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.000000	0.387097	
chunk0119_156_1	chr22	43130488	43130743	+	0	NA	TTS (NM_001197)	TTS (NM_001197)	12782	NR_046423	27349	Hs.349111	NM_014507	ENSG00000100294	MCAT	FASN2C|MCT|MCT1|MT|NET62|fabD	malonyl-CoA-acyl carrier protein transacylase	protein-coding	0.039216	0.550781	
chunk0212_269_1	chrX	139683875	139684204	+	0	NA	intron (NM_001171876, intron 1 of 28)	L1MB8|LINE|L1	24183	NM_001099855	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.009119	0.309091	
chunk0038_437_1	chr11	94659749	94660483	+	0	NA	Intergenic	L2c|LINE|L2	92808	NM_152431	143689	Hs.660188	NM_152431	ENSG00000134627	PIWIL4	HIWI2|MIWI2	piwi like RNA-mediated gene silencing 4	protein-coding	0.004087	0.420408	367(TTGTACACACTGTTCC,-,0.00),368(TGTACACACTGTTCCC,+,0.00)
chunk0099_181_1	chr2	90381022	90381229	+	0	NA	Intergenic	Intergenic	1278824	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.038647	0.350962	
chunk0139_379_1	chr4	61221094	61221543	+	0	NA	Intergenic	Intergenic	-275803	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.006682	0.322222	
chunk0007_315_1	chr1	84426288	84426908	+	0	NA	Intergenic	Intergenic	18247	NM_058248	58511	Hs.129142	NM_021233	ENSG00000137976	DNASE2B	DLAD	deoxyribonuclease 2 beta	protein-coding	0.006452	0.378422	
chunk0114_52_1	chr21	8464651	8465008	+	0	NA	Intergenic	(CTCT)n|Simple_repeat|Simple_repeat	23683	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.005602	0.486034	
chunk0179_401_1	chr7	51578792	51579217	+	0	NA	Intergenic	L1M4|LINE|L1	-262186	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.000000	0.265258	
chunk0148_155_1	chr5	6585729	6585992	+	0	NA	non-coding (NR_024424, exon 2 of 3)	non-coding (NR_024424, exon 2 of 3)	2584	NR_024424	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.022814	0.511364	
chunk0082_231_1	chr17	57288069	57288379	+	0	NA	intron (NM_138962, intron 5 of 13)	MIRb|SINE|MIR	31211	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.019355	0.504823	133(GGAACAGACAGAACTT,+,0.00)
chunk0076_332_1	chr16	71060222	71060430	+	0	NA	intron (NM_001270974, intron 18 of 85)	intron (NM_001270974, intron 18 of 85)	170396	NM_001270974	54768	Hs.351914	NM_017558	ENSG00000157423	HYDIN	CILD5|HYDIN1|HYDIN2|PPP1R31	HYDIN axonemal central pair apparatus protein	protein-coding	0.004808	0.315789	9(ATGCACACTGTGTTTC,-,0.00),10(TGCACACTGTGTTTCT,+,0.00)
chunk0178_125_1	chr7	31730373	31730854	+	0	NA	Intergenic	Intergenic	43596	NM_006658	10842	Hs.227011	NM_006658	ENSG00000106341	PPP1R17	C7orf16|GSBS	protein phosphatase 1 regulatory subunit 17	protein-coding	0.010395	0.450207	
chunk0210_360_1	chrX	96432716	96433161	+	0	NA	Intergenic	Intergenic	-95036	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.002247	0.381166	148(AAGAACAAAATGTTAC,-,0.00)
chunk0197_171_1	chr8	120985551	120985861	+	0	NA	Intergenic	MIRb|SINE|MIR	-173637	NM_021021	6641	Hs.46701	NM_021021	ENSG00000172164	SNTB1	59-DAP|A1B|BSYN2|DAPA1B|SNT2|SNT2B1|TIP-43	syntrophin beta 1	protein-coding	0.016129	0.424437	
chunk0207_120_1	chr9	128879898	128880434	+	0	NA	intron (NM_001287390, intron 1 of 14)	MIRc|SINE|MIR	1909	NM_001287390	883	Hs.495250	NM_004059	ENSG00000171097	KYAT1	CCBL1|GTK|KAT1|KATI	kynurenine aminotransferase 1	protein-coding	0.014925	0.506518	
chunk0081_373_1	chr17	47955387	47956122	+	0	NA	intron (NM_024320, intron 1 of 1)	intron (NM_024320, intron 1 of 1)	2123	NM_024320	79170	Hs.368260	NM_024320	ENSG00000167183	PRR15L	ATAD4	proline rich 15 like	protein-coding	0.006803	0.548913	325(CAGAACTTAGTGTTCC,-,0.00),326(AGAACTTAGTGTTCCA,+,0.00)
chunk0159_418_1	chr5	147981032	147981542	+	0	NA	Intergenic	Intergenic	-74749	NM_206966	389336	Hs.660038	NM_206966	ENSG00000178776	C5orf46	SSSP1	chromosome 5 open reading frame 46	protein-coding	0.001961	0.420744	212(AGGCTCACCCTGTACT,-,0.00)
chunk0198_73_1	chr8	129996497	129997361	+	0	NA	intron (NR_046360, intron 1 of 14)	L2a|LINE|L2	11524	NR_049826	100847051		NR_049826	ENSG00000264653	MIR5194	mir-5194	microRNA 5194	ncRNA	0.006944	0.464740	
chunk0098_266_1	chr2	75321591	75322318	+	0	NA	Intergenic	Intergenic	-122435	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.008253	0.462912	
chunk0048_67_1	chr12	78669779	78670338	+	0	NA	Intergenic	Intergenic	-193935	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.003578	0.362500	
chunk0098_277_1	chr2	75516554	75516767	+	0	NA	intron (NM_032181, intron 3 of 3)	intron (NM_032181, intron 3 of 3)	-7408	NR_110281	101927884	Hs.671110	NR_110281	ENSG00000231172	LOC101927884	-	uncharacterized LOC101927884	ncRNA	0.009390	0.462617	
chunk0161_306_1	chr5	173453329	173453607	+	0	NA	Intergenic	Intergenic	106013	NR_107023	102465862		NR_107023	ENSG00000274994	MIR8056	hsa-mir-8056	microRNA 8056	ncRNA	0.003597	0.448029	
chunk0187_384_1	chr7	157676858	157677094	+	0	NA	intron (NM_001308268, intron 13 of 22)	intron (NM_001308268, intron 13 of 22)	-102554	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.033898	0.620253	
chunk0204_59_1	chr9	93393200	93393556	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	-46964	NM_001098808	445577	Hs.575636	NM_001098808	ENSG00000204352	C9orf129	bA165J3.3	chromosome 9 open reading frame 129	protein-coding	0.028090	0.515406	
chunk0145_152_1	chr4	147079268	147079479	+	0	NA	Intergenic	Intergenic	-133491	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.037915	0.575472	
chunk0065_149_1	chr15	25417793	25418258	+	0	NA	intron (NM_130839, intron 1 of 12)	Tigger3a|DNA|TcMar-Tigger	-12519	NM_130838	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.008602	0.343348	
chunk0001_139_1	chr1	5688457	5689077	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	124696	NR_039612									0.033871	0.505636	
chunk0179_8_1	chr7	42426067	42426587	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-189308	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.009615	0.374280	465(CTGGACAGAATGTCCC,-,0.00),466(TGGACAGAATGTCCCC,+,0.00)
chunk0173_414_1	chr6	151004446	151005155	+	0	NA	intron (NM_001242767, intron 20 of 27)	intron (NM_001242767, intron 20 of 27)	138467	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.009873	0.383099	
chunk0092_182_1	chr19	30060556	30061118	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	118598	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.016014	0.452931	
chunk0158_66_1	chr5	126182981	126183677	+	0	NA	intron (NR_105042, intron 1 of 3)	intron (NR_105042, intron 1 of 3)	3752	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.007184	0.418938	
chunk0149_380_1	chr5	28500508	28500799	+	0	NA	Intergenic	MER67C|LTR|ERV1	-426217	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.006873	0.400685	
chunk0172_402_1	chr6	139977824	139978594	+	0	NA	TTS (NR_121624)	TTS (NR_121624)	1890	NR_121622	100507477	Hs.179213	NR_121622	ENSG00000236013	LOC100507477	-	uncharacterized LOC100507477	ncRNA	0.002597	0.355383	
chunk0089_232_1	chr18	61802606	61802928	+	0	NA	Intergenic	Charlie20a|DNA|hAT-Charlie	54591	NR_103449	100996669	Hs.586981	NR_103449		LINC01544	-	long intergenic non-protein coding RNA 1544	ncRNA	0.006211	0.297214	
chunk0009_90_1	chr1	101239373	101239638	+	0	NA	exon (NM_001400, exon 2 of 2)	exon (NM_001400, exon 2 of 2)	2756	NM_001400	1901	Hs.154210	NM_001400	ENSG00000170989	S1PR1	CD363|CHEDG1|D1S3362|ECGF1|EDG-1|EDG1|S1P1	sphingosine-1-phosphate receptor 1	protein-coding	0.045283	0.556391	
chunk0139_79_1	chr4	49140977	49141214	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	154453	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.033755	0.428571	
chunk0103_63_1	chr2	159897099	159897478	+	0	NA	intron (NM_001198759, intron 2 of 38)	intron (NM_001198759, intron 2 of 38)	7468	NM_001198759	100526664	Hs.153563	NM_001198759	ENSG00000248672	LY75-CD302	CD205|CLEC13B|DEC-205|LY75|Ly-75|gp200-MR6	LY75-CD302 readthrough	protein-coding	0.002639	0.368421	
chunk0047_370_1	chr12	75138406	75138735	+	0	NA	intron (NM_139136, intron 2 of 5)	MER5A|DNA|hAT-Charlie	71178	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.015198	0.348485	
chunk0075_119_1	chr16	49674229	49674568	+	0	NA	intron (NM_001271620, intron 3 of 7)	intron (NM_001271620, intron 3 of 7)	148340	NM_015069	23090	Hs.443715	NM_015069	ENSG00000102935	ZNF423	Ebfaz|JBTS19|NPHP14|OAZ|Roaz|ZFP423|Zfp104|hOAZ	zinc finger protein 423	protein-coding	0.029499	0.550000	
chunk0006_391_1	chr1	75067929	75068164	+	0	NA	Intergenic	L1PA17|LINE|L1	-60388	NM_001001933	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.004255	0.525424	
chunk0193_396_1	chr8	80502734	80503045	+	0	NA	intron (NM_001105539, intron 2 of 5)	MER5B|DNA|hAT-Charlie	16676	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.009646	0.375000	
chunk0163_444_1	chr6	17491526	17492300	+	0	NA	intron (NM_006366, intron 4 of 12)	intron (NM_006366, intron 4 of 12)	19352	NR_110855	101928491	Hs.622876	NR_110855		LOC101928491	-	uncharacterized LOC101928491	ncRNA	0.014212	0.407742	517(GAGTACTTAATGTGCC,-,0.00)
chunk0077_2_1	chr16	74449835	74450191	+	0	NA	non-coding (NR_027265, exon 21 of 21)	non-coding (NR_027265, exon 21 of 21)	-28543	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.014045	0.532213	
chunk0140_244_1	chr4	71336019	71336347	+	0	NA	intron (NM_001098484, intron 3 of 25)	intron (NM_001098484, intron 3 of 25)	-2870	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.003049	0.331307	
chunk0060_402_1	chr14	53033265	53033522	+	0	NA	Intergenic	Intergenic	-82296	NM_001135000	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.003891	0.360465	
chunk0184_107_1	chr7	113490306	113490650	+	0	NA	Intergenic	Intergenic	-371896	NR_015442									0.000000	0.298551	
chunk0043_202_1	chr12	19389613	19389905	+	0	NA	Intergenic	Intergenic	-49915	NM_001114176	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.003425	0.382253	256(AAAACAATATGTCCTG,+,0.00)
chunk0020_183_1	chr1	234689208	234689502	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-34687	NR_038856	100506810	Hs.586634	NR_038856	ENSG00000227630	LINC01132	-	long intergenic non-protein coding RNA 1132	ncRNA	0.010204	0.471186	198(AGGAACACTGTGTCCT,-,0.00),199(GGAACACTGTGTCCTC,+,0.00)
chunk0097_441_1	chr2	64281534	64281735	+	0	NA	Intergenic	Intergenic	53233	NR_120420	100507006	Hs.442789	NR_120420		LOC100507006	-	uncharacterized LOC100507006	ncRNA	0.004975	0.371287	
chunk0127_335_1	chr3	100484073	100484689	+	0	NA	Intergenic	L1MEg|LINE|L1	-8238	NM_018004	55076	Hs.658956	NM_018004	ENSG00000181458	TMEM45A	DERP7|DNAPTP4	transmembrane protein 45A	protein-coding	0.001623	0.316045	
chunk0089_374_1	chr18	67344493	67344825	+	0	NA	Intergenic	(AT)n|Simple_repeat|Simple_repeat	-171887	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.006024	0.300300	
chunk0042_214_1	chr12	6072293	6072886	+	0	NA	intron (NM_000552, intron 8 of 51)	intron (NM_000552, intron 8 of 51)	52081	NM_000552	7450	Hs.440848	NM_000552	ENSG00000110799	VWF	F8VWF|VWD	von Willebrand factor	protein-coding	0.018550	0.483165	
chunk0143_318_1	chr4	119284655	119285298	+	0	NA	intron (NM_019050, intron 16 of 17)	intron (NM_019050, intron 16 of 17)	15837	NM_001001701	401152	Hs.173705	NM_001001701	ENSG00000164096	C4orf3	ALN|HCVFTP1	chromosome 4 open reading frame 3	protein-coding	0.003110	0.335404	139(AAGTACATTATGTACT,-,0.00),140(AGTACATTATGTACTT,+,0.00)
chunk0170_159_1	chr6	111528087	111528492	+	0	NA	intron (NR_034109, intron 1 of 1)	intron (NR_034109, intron 1 of 1)	39071	NM_001164283	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.004938	0.327586	
chunk0065_224_1	chr14	100762053	100762555	+	0	NA	Intergenic	L1MB8|LINE|L1	35439	NM_003836	8788	Hs.116631	NM_003836	ENSG00000185559	DLK1	DLK|DLK-1|Delta1|FA1|PREF1|Pref-1|ZOG|pG2	delta like non-canonical Notch ligand 1	protein-coding	0.009960	0.383698	
chunk0099_222_1	chr2	96162109	96163040	+	0	NA	Intergenic	L1ME3G|LINE|L1	-17134	NM_004418	1844	Hs.1183	NM_004418	ENSG00000158050	DUSP2	PAC-1|PAC1	dual specificity phosphatase 2	protein-coding	0.017186	0.436695	
chunk0090_284_1	chr18	74930829	74931048	+	0	NA	intron (NM_017757, intron 7 of 7)	L1MC4a|LINE|L1	274575	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.004566	0.413636	
chunk0134_223_1	chr3	178803300	178803595	+	0	NA	intron (NR_126561, intron 2 of 5)	intron (NR_126561, intron 2 of 5)	56958	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.000000	0.435811	
chunk0176_429_1	chr7	19739898	19740268	+	0	NA	intron (NM_152774, intron 1 of 3)	L1ME4b|LINE|L1	-31046	NM_001002926	221830	Hs.353035	NM_001002926	ENSG00000105849	TWISTNB	-	TWIST neighbor	protein-coding	0.000000	0.334232	
chunk0178_60_1	chr7	30140208	30140849	+	0	NA	intron (NM_152793, intron 1 of 2)	intron (NM_152793, intron 1 of 2)	5592	NM_152793	222166	Hs.200100	NM_152793	ENSG00000180354	MTURN	C7orf41|Ells1	maturin, neural progenitor differentiation regulator homolog	protein-coding	0.006240	0.397196	
chunk0039_258_1	chr11	102306125	102306721	+	0	NA	Intergenic	Intergenic	-11027	NM_182962	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.006711	0.435511	
chunk0205_302_1	chr9	112184963	112185299	+	0	NA	Intergenic	L1ME3|LINE|L1	-9834	NM_001282640	64420	Hs.494827	NM_022486	ENSG00000106868	SUSD1	-	sushi domain containing 1	protein-coding	0.002976	0.362018	
chunk0159_338_1	chr5	144032368	144032727	+	0	NA	Intergenic	Intergenic	138167	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.016713	0.525000	150(GGAACGCTCTGTGCAG,+,0.00)
chunk0021_281_1	chr1	244327174	244327971	+	0	NA	Intergenic	L1ME1|LINE|L1	-25063	NM_001012970	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.002509	0.320802	
chunk0040_112_1	chr11	111988594	111989080	+	0	NA	intron (NM_001037954, intron 9 of 19)	intron (NM_001037954, intron 9 of 19)	11528	NM_033425	85458	Hs.655626	NM_033425	ENSG00000150764	DIXDC1	CCD1	DIX domain containing 1	protein-coding	0.006173	0.383984	242(TGGATCAGCCTGTACT,-,0.00),243(GGATCAGCCTGTACTG,+,0.00)
chunk0113_323_1	chr20	58331943	58332349	+	0	NA	intron (NM_020673, intron 2 of 6)	L1MEf|LINE|L1	22431	NM_020673	57403	Hs.529044	NM_020673	ENSG00000124209	RAB22A	-	RAB22A, member RAS oncogene family	protein-coding	0.007389	0.380835	
chunk0104_119_1	chr2	172946944	172947473	+	0	NA	intron (NM_001282901, intron 1 of 24)	Helitron1Na_Mam|RC|Helitron	19003	NM_001282901	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.005671	0.326415	
chunk0142_142_1	chr4	94865940	94866139	+	0	NA	intron (NM_001203, intron 1 of 12)	intron (NM_001203, intron 1 of 12)	108062	NM_001203	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.000000	0.365000	
chunk0066_442_1	chr15	39869355	39869674	+	0	NA	intron (NM_001271854, intron 1 of 3)	intron (NM_001271854, intron 1 of 3)	-40238	NM_001271855	11245	Hs.37196	NM_007223	ENSG00000166073	GPR176	HB-954	G protein-coupled receptor 176	protein-coding	0.012539	0.440625	
chunk0131_286_1	chr3	150410952	150411169	+	0	NA	exon (NM_014779, exon 1 of 4)	exon (NM_014779, exon 1 of 4)	2725	NM_014779	9819	Hs.722470	NM_014779	ENSG00000196428	TSC22D2	TILZ4a|TILZ4b|TILZ4c	TSC22 domain family member 2	protein-coding	0.032258	0.541284	
chunk0057_196_1	chr13	103296913	103297242	+	0	NA	Intergenic	MER70A|LTR|ERVL	-128123	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.003040	0.400000	121(AGGTTCACTGTGTACT,-,0.00)
chunk0004_122_1	chr1	44660089	44660622	+	0	NA	intron (NM_001300748, intron 1 of 2)	intron (NM_001300748, intron 1 of 2)	14253	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.022514	0.595506	
chunk0140_129_1	chr4	69095389	69095731	+	0	NA	promoter-TSS (NM_001074)	promoter-TSS (NM_001074)	-915	NM_001074	7364	Hs.654424	NM_001074	ENSG00000171234	UGT2B7	UDPGT 2B7|UDPGT 2B9|UDPGT2B7|UDPGTH2|UDPGTh-2|UGT2B9	UDP glucuronosyltransferase family 2 member B7	protein-coding	0.005848	0.361516	
chunk0034_40_1	chr11	26815377	26815682	+	0	NA	Intergenic	L1PB1|LINE|L1	-93502	NM_178498	159963	Hs.148907	NM_178498	ENSG00000148942	SLC5A12	SMCT2	solute carrier family 5 member 12	protein-coding	0.000000	0.382353	
chunk0154_117_1	chr5	78739803	78740002	+	0	NA	Intergenic	Intergenic	-91077	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.015075	0.475000	
chunk0028_259_1	chr10	90641909	90642573	+	0	NA	Intergenic	Intergenic	-101436	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.009036	0.362406	
chunk0017_377_1	chr1	212133124	212133832	+	0	NA	Intergenic	L1MD2|LINE|L1	55865	NR_036068	100422947		NR_036068	ENSG00000264358	MIR3122	mir-3122	microRNA 3122	ncRNA	0.002825	0.380818	
chunk0055_382_1	chr13	73300764	73301283	+	0	NA	Intergenic	Intergenic	242231	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.003854	0.325000	
chunk0092_221_1	chr19	31926352	31926555	+	0	NA	Intergenic	L1PB3|LINE|L1	-99409	NR_110674	100996665	Hs.443685	NR_110673	ENSG00000267779	LINC01533	CTC-360P9.3	long intergenic non-protein coding RNA 1533	ncRNA	0.000000	0.348039	
chunk0208_305_1	chrX	23736070	23736594	+	0	NA	intron (NM_001037171, intron 1 of 15)	intron (NM_001037171, intron 1 of 15)	6958	NM_001033583	23597	Hs.298885	NM_001033583	ENSG00000123130	ACOT9	ACATE2|CGI-16|MT-ACT48|MTACT48	acyl-CoA thioesterase 9	protein-coding	0.009542	0.350476	
chunk0160_238_1	chr5	155761463	155761846	+	0	NA	Intergenic	(CATCATCCT)n|Simple_repeat|Simple_repeat	-565103	NM_172244	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.002611	0.492188	
chunk0143_438_1	chr4	123924443	123925033	+	0	NA	intron (NR_027105, intron 3 of 4)	MLT1H2|LTR|ERVL-MaLR	150474	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.006780	0.375635	
chunk0147_197_1	chr4	177785424	177785686	+	0	NA	intron (NR_028342, intron 2 of 5)	L1PB|LINE|L1	56798	NR_028342	285501	Hs.722466	NM_001085490	ENSG00000231171	LINC01098	-	long intergenic non-protein coding RNA 1098	ncRNA	0.000000	0.349810	
chunk0067_454_1	chr15	50257870	50258539	+	0	NA	intron (NM_002112, intron 3 of 11)	MIRb|SINE|MIR	7761	NM_001306146	3067	Hs.1481	NM_002112	ENSG00000140287	HDC	-	histidine decarboxylase	protein-coding	0.011958	0.452239	
chunk0010_72_1	chr1	113155125	113155872	+	0	NA	Intergenic	L1MC1|LINE|L1	50755	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.006693	0.407754	
chunk0006_456_1	chr1	77071846	77072395	+	0	NA	Intergenic	L1ME3F|LINE|L1	11977	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.005464	0.283636	
chunk0193_451_1	chr8	81173817	81174016	+	0	NA	Intergenic	L1M7|LINE|L1	-61848	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.000000	0.380000	
chunk0173_272_1	chr6	147735535	147736093	+	0	NA	Intergenic	Intergenic	227122	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.003584	0.341682	
chunk0067_209_1	chr15	45024793	45024992	+	0	NA	intron (NR_034039, intron 1 of 8)	intron (NR_034039, intron 1 of 8)	1788	NR_034039	6652	Hs.878	NM_003104	ENSG00000140263	SORD	HEL-S-95n|RDH|SDH|SORD1|XDH	sorbitol dehydrogenase	protein-coding	0.010050	0.500000	
chunk0026_82_1	chr10	61342869	61343252	+	0	NA	Intergenic	LTR33|LTR|ERVL	-109579	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.013055	0.458333	
chunk0108_148_1	chr2	231029430	231030014	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-7844	NM_001144994	257407	Hs.526596	NM_001144994	ENSG00000204128	C2orf72	-	chromosome 2 open reading frame 72	protein-coding	0.017123	0.538462	252(AGGAACACTGCGTCCC,-,0.00),253(GGAACACTGCGTCCCT,+,0.00)
chunk0175_281_1	chr7	7589311	7589837	+	0	NA	intron (NM_019005, intron 9 of 12)	intron (NM_019005, intron 9 of 12)	22589	NM_019005	54468	Hs.520215	NM_019005	ENSG00000164654	MIOS	MIO|Sea4|Yulink	meiosis regulator for oocyte development	protein-coding	0.001901	0.339658	
chunk0149_141_1	chr5	20008635	20008989	+	0	NA	intron (NM_001291956, intron 2 of 14)	intron (NM_001291956, intron 2 of 14)	-20568	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.008475	0.377465	
chunk0089_56_1	chr18	58140113	58140334	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	-9110	NM_001144969	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.013575	0.486486	58(AAGGACAGAGCGTGCA,-,0.00)
chunk0010_13_1	chr1	112054463	112055154	+	0	NA	Intergenic	L1MC4|LINE|L1	64240	NM_001270945									0.004342	0.434971	
chunk0166_172_1	chr6	46012721	46013043	+	0	NA	intron (NM_001114086, intron 1 of 5)	intron (NM_001114086, intron 1 of 5)	3007	NM_016929	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.006211	0.359133	
chunk0009_298_1	chr1	107811619	107811822	+	0	NA	intron (NM_006113, intron 2 of 26)	intron (NM_006113, intron 2 of 26)	-85503	NR_107006	102465839		NR_107006	ENSG00000275455	MIR7852	hsa-mir-7852	microRNA 7852	ncRNA	0.004926	0.294118	
chunk0126_187_1	chr3	78304714	78304921	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	714642	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.009662	0.394231	
chunk0053_371_1	chr13	35704342	35704703	+	0	NA	Intergenic	Intergenic	6795	NR_132115	100507114	Hs.236298	NR_132115	ENSG00000236036	LINC00445	-	long intergenic non-protein coding RNA 445	ncRNA	0.002770	0.414365	
chunk0189_408_1	chr8	27616959	27617331	+	0	NA	Intergenic	L3b|LINE|CR1	-2334	NM_001831	1191	Hs.436657	NM_001831	ENSG00000120885	CLU	AAG4|APO-J|APOJ|CLI|CLU1|CLU2|KUB1|NA1/NA2|SGP-2|SGP2|SP-40|TRPM-2|TRPM2	clusterin	protein-coding	0.008065	0.522788	
chunk0119_387_1	chr22	48395710	48395948	+	0	NA	Intergenic	L1ME4c|LINE|L1	-93631	NM_001082967	25817	Hs.436854	NM_015381	ENSG00000219438	TAFA5	FAM19A5|QLLK5208|TAFA-5|UNQ5208	TAFA chemokine like family member 5	protein-coding	0.012605	0.468619	
chunk0041_215_1	chr11	127205994	127206276	+	0	NA	Intergenic	L1PA14|LINE|L1	-64935	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.003546	0.551237	
chunk0100_26_1	chr2	105249688	105250535	+	0	NA	Intergenic	Intergenic	8368	NM_007227	11250	Hs.590903	NM_007227	ENSG00000135973	GPR45	PSP24|PSP24(ALPHA)|PSP24A	G protein-coupled receptor 45	protein-coding	0.012987	0.470519	379(GGGAACAAGGTGTTCT,-,0.00),380(GGAACAAGGTGTTCTA,+,0.00)
chunk0116_291_1	chr21	40315737	40316113	+	0	NA	intron (NR_073202, intron 8 of 32)	intron (NR_073202, intron 8 of 32)	-67158	NR_038896	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.007979	0.328912	
chunk0181_5_1	chr7	77614885	77615356	+	0	NA	intron (NM_001131008, intron 11 of 17)	intron (NM_001131008, intron 11 of 17)	77085	NM_001131008	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.004246	0.283898	
chunk0032_300_1	chr11	9700079	9700574	+	0	NA	intron (NM_001297714, intron 2 of 10)	intron (NM_001297714, intron 2 of 10)	36249	NM_015055	23075	Hs.153026	NM_015055	ENSG00000133789	SWAP70	HSPC321|SWAP-70	switching B cell complex subunit SWAP70	protein-coding	0.002020	0.334677	184(GGAACAGTGAGCCCTT,+,0.00)
chunk0138_275_1	chr4	40476386	40476869	+	0	NA	intron (NM_001098634, intron 2 of 6)	intron (NM_001098634, intron 2 of 6)	25492	NR_039966	100616274		NR_039966	ENSG00000263642	MIR4802	-	microRNA 4802	ncRNA	0.002070	0.419421	
chunk0093_410_1	chr19	57240552	57240789	+	0	NA	promoter-TSS (NM_001145078)	promoter-TSS (NM_001145078)	-15	NM_001023563	390980	Hs.22488	NM_001023563	ENSG00000204524	ZNF805	-	zinc finger protein 805	protein-coding	0.101266	0.651261	
chunk0191_456_1	chr8	58073489	58073910	+	0	NA	intron (NM_147189, intron 3 of 4)	intron (NM_147189, intron 3 of 4)	79145	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.002375	0.329384	
chunk0159_111_1	chr5	138566298	138566554	+	0	NA	intron (NM_004134, intron 9 of 16)	intron (NM_004134, intron 9 of 16)	-5316	NR_002913	26785		NR_002913	ENSG00000206989	SNORD63	RNU63|SNORD63A|U63	small nucleolar RNA, C/D box 63	snoRNA	0.000000	0.346304	
chunk0109_455_1	chr2	241882454	241882803	+	0	NA	non-coding (NR_110220, exon 2 of 4)	non-coding (NR_110220, exon 2 of 4)	1265	NR_110220	101927289	Hs.130180	NR_110220	ENSG00000233806	LINC01237	-	long intergenic non-protein coding RNA 1237	ncRNA	0.025788	0.471429	
chunk0051_245_1	chr12	117130091	117130510	+	0	NA	intron (NR_120464, intron 2 of 2)	intron (NR_120464, intron 2 of 2)	30833	NR_120464	101928244	Hs.742266	NR_120464		TESC-AS1	-	TESC antisense RNA 1 (head to head)	ncRNA	0.007160	0.488095	165(CAGAACAGCATGAGCT,-,0.00),166(AGAACAGCATGAGCTT,+,0.00)
chunk0022_353_1	chr10	17143947	17144754	+	0	NA	3' UTR (NM_004412, exon 11 of 11)	3' UTR (NM_004412, exon 11 of 11)	-14533	NM_001081	8029	Hs.166206	NM_001081	ENSG00000107611	CUBN	IFCR|MGA1|gp280	cubilin	protein-coding	0.003717	0.361386	
chunk0168_392_1	chr6	94448721	94448983	+	0	NA	Intergenic	L1MD2|LINE|L1	741769	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.003817	0.346008	
chunk0028_341_1	chr10	92148204	92148618	+	0	NA	intron (NM_001178137, intron 4 of 9)	L2c|LINE|L2	94868	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.009662	0.414458	114(AAGGACAATGTGTTCC,-,0.00),115(AGGACAATGTGTTCCC,+,0.00)
chunk0030_328_1	chr10	118253327	118254010	+	0	NA	Intergenic	Intergenic	88659	NM_022063	63877	Hs.105575	NM_022063	ENSG00000165669	FAM204A	C10orf84|bA319I23.1	family with sequence similarity 204 member A	protein-coding	0.014641	0.450292	
chunk0198_435_1	chr8	143553536	143553846	+	0	NA	5' UTR (NM_001166237, exon 1 of 14).2	5' UTR (NM_001166237, exon 1 of 14).2	304	NM_001166237	79792	Hs.118983	NM_024736	ENSG00000104518	GSDMD	DF5L|DFNA5L|FKSG10|GSDMDC1	gasdermin D	protein-coding	0.064516	0.681672	
chunk0051_376_1	chr12	121648461	121649404	+	0	NA	Intergenic	L1ME4b|LINE|L1	20722	NM_173855	283385	Hs.434154	NM_173855	ENSG00000139714	MORN3	-	MORN repeat containing 3	protein-coding	0.015907	0.462924	456(AAGCACACCCTCTTCC,-,0.00)
chunk0069_120_1	chr15	61750131	61751042	+	0	NA	Intergenic	Intergenic	309879	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.015368	0.475877	
chunk0051_367_1	chr12	121336617	121336994	+	0	NA	intron (NM_001137559, intron 6 of 16)	intron (NM_001137559, intron 6 of 16)	15657	NM_016237	51433	Hs.7101	NM_016237	ENSG00000089053	ANAPC5	APC5	anaphase promoting complex subunit 5	protein-coding	0.031830	0.486772	
chunk0138_346_1	chr4	41696195	41696429	+	0	NA	intron (NM_001112717, intron 25 of 25)	intron (NM_001112717, intron 25 of 25)	52658	NM_003924	8929	Hs.87202	NM_003924	ENSG00000109132	PHOX2B	CCHS|NBLST2|NBPhox|PMX2B	paired like homeobox 2B	protein-coding	0.012821	0.404255	106(TTGTACATGGTGTTCT,-,0.00),107(TGTACATGGTGTTCTG,+,0.00)
chunk0057_358_1	chr13	108919380	108919834	+	0	NA	intron (NM_001198950, intron 16 of 34)	intron (NM_001198950, intron 16 of 34)	247696	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.017621	0.406593	
chunk0201_27_1	chr9	33249505	33249736	+	0	NA	Intergenic	Intergenic	9422	NM_014471	27290	Hs.555934	NM_014471	ENSG00000122711	SPINK4	HEL136|PEC-60|PEC60	serine peptidase inhibitor, Kazal type 4	protein-coding	0.004329	0.508621	
chunk0054_146_1	chr13	43804572	43805464	+	0	NA	Intergenic	Intergenic	-18038	NM_001242863	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.008969	0.390817	
chunk0105_443_1	chr2	194895346	194895545	+	0	NA	Intergenic	L1MA3|LINE|L1	164850	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.000000	0.370000	
chunk0090_352_1	chr18	76611542	76612033	+	0	NA	Intergenic	Intergenic	-7990	NR_120419	400660	Hs.131718	NR_120419	ENSG00000266256	LINC00683	-	long intergenic non-protein coding RNA 683	ncRNA	0.089613	0.676829	
chunk0137_238_1	chr4	20429418	20429645	+	0	NA	intron (NM_001289135, intron 4 of 35)	L2a|LINE|L2	37342	NR_037876	100505893	Hs.665305	NR_037876	ENSG00000248228	SLIT2-IT1	-	SLIT2 intronic transcript 1	ncRNA	0.004405	0.368421	
chunk0023_30_1	chr10	21142149	21142803	+	0	NA	intron (NM_001177483, intron 1 of 1)	L3b|LINE|CR1	4083	NM_001010896	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.012232	0.465649	149(TAGCACAGCCTGAGCC,-,0.00),150(AGCACAGCCTGAGCCA,+,0.00)
chunk0141_366_1	chr4	88042892	88043467	+	0	NA	intron (NM_000297, intron 4 of 14)	intron (NM_000297, intron 4 of 14)	35532	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.006957	0.447917	
chunk0153_104_1	chr5	68426831	68427075	+	0	NA	Intergenic	Intergenic	134385	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.004098	0.400000	
chunk0141_377_1	chr4	88148625	88148824	+	0	NA	intron (NM_001257386, intron 1 of 15)	intron (NM_001257386, intron 1 of 15)	10135	NM_004827	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.010050	0.345000	
chunk0094_356_1	chr2	9580166	9580790	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-24690	NM_003183	6868	Hs.404914	NM_003183	ENSG00000151694	ADAM17	ADAM18|CD156B|CSVP|NISBD|NISBD1|TACE	ADAM metallopeptidase domain 17	protein-coding	0.022436	0.438400	
chunk0186_129_1	chr7	138243153	138243661	+	0	NA	Intergenic	Intergenic	119649	NR_039678	100616226		NR_039678	ENSG00000284028	MIR4468	-	microRNA 4468	ncRNA	0.005906	0.353635	
chunk0152_112_1	chr5	58506157	58506532	+	0	NA	Intergenic	Intergenic	14909	NM_152687	202309	Hs.547697	NM_152687	ENSG00000175857	GAPT	C5orf29	GRB2 binding adaptor protein, transmembrane	protein-coding	0.005333	0.343085	
chunk0002_127_1	chr1	16604245	16604748	+	0	NA	intron (NM_017940, intron 2 of 28)	intron (NM_017940, intron 2 of 28)	9109	NM_017940	55672	Hs.467587	NM_017940	ENSG00000219481	NBPF1	AB13|AB14|AB23|AD2|NBG|NBPF	NBPF member 1	protein-coding	0.007952	0.382937	
chunk0114_381_1	chr20	63069803	63070138	+	0	NA	intron (NR_033370, intron 1 of 4)	intron (NR_033370, intron 1 of 4)	-31322	NR_003244	768096	Hs.549606	NR_003244		HAR1A	HAR1F|LINC00064|NCRNA00064	highly accelerated region 1A	ncRNA	0.038806	0.642857	
chunk0097_148_1	chr2	48197177	48197468	+	0	NA	Intergenic	MER115|DNA|hAT-Tip100	-117334	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.010309	0.568493	50(CAGAACATGGTGTCCT,-,0.00),51(AGAACATGGTGTCCTG,+,0.00),153(GAGGACACCCCGTCCT,-,0.00),154(AGGACACCCCGTCCTT,+,0.00)
chunk0011_197_1	chr1	149993918	149994199	+	0	NA	intron (NM_020205, intron 1 of 11)	intron (NM_020205, intron 1 of 11)	16679	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.000000	0.375887	
chunk0196_270_1	chr8	108978424	108978630	+	0	NA	Intergenic	Intergenic	-108897	NM_003301	7201	Hs.3022	NM_003301	ENSG00000174417	TRHR	TRH-R	thyrotropin releasing hormone receptor	protein-coding	0.000000	0.357488	
chunk0076_162_1	chr16	67350405	67350604	+	0	NA	intron (NM_018296, intron 5 of 13)	intron (NM_018296, intron 5 of 13)	3149	NM_001161575	55282	Hs.125139	NM_018296	ENSG00000159708	LRRC36	RORBP70|XLHSRF2	leucine rich repeat containing 36	protein-coding	0.005025	0.420000	84(AAGCACAAGCTGTACT,-,0.00),85(AGCACAAGCTGTACTT,+,0.00)
chunk0180_459_1	chr7	77548399	77548598	+	0	NA	intron (NM_001131008, intron 1 of 17)	intron (NM_001131008, intron 1 of 17)	10463	NM_001131008	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.005025	0.380000	
chunk0210_130_1	chrX	74231800	74232114	+	0	NA	intron (NR_028379, intron 5 of 6)	intron (NR_028379, intron 5 of 6)	-13339	NR_030620	100126317		NR_030620	ENSG00000212027	MIR374B	MIRN374B|mir-374b	microRNA 374b	ncRNA	0.009554	0.358730	
chunk0180_204_1	chr7	66382607	66382956	+	0	NA	intron (NR_026873, intron 3 of 4)	intron (NR_026873, intron 3 of 4)	17627	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.005731	0.354286	
chunk0184_83_1	chr7	113034342	113034820	+	0	NA	Intergenic	Intergenic	-38938	NR_110162	101928036	Hs.120006	NR_110162	ENSG00000234520	HRAT17	-	heart tissue-associated transcript 17	ncRNA	0.002092	0.354906	
chunk0005_173_1	chr1	58620259	58620530	+	0	NA	Intergenic	MIRb|SINE|MIR	-42900	NM_002353	4070	Hs.23582	NM_002353	ENSG00000184292	TACSTD2	EGP-1|EGP1|GA733-1|GA7331|GP50|M1S1|TROP2	tumor associated calcium signal transducer 2	protein-coding	0.018450	0.503676	
chunk0133_281_1	chr3	172074933	172075283	+	0	NA	intron (NM_001135095, intron 1 of 25)	intron (NM_001135095, intron 1 of 25)	34554	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.008571	0.313390	
chunk0109_64_1	chr20	1381411	1381979	+	0	NA	intron (NM_000801, intron 2 of 4)	L1ME1|LINE|L1	11266	NR_106929	102465524		NR_106929	ENSG00000284436	MIR6869	hsa-mir-6869	microRNA 6869	ncRNA	0.007042	0.340949	
chunk0185_297_1	chr7	131145107	131145383	+	0	NA	intron (NM_001145354, intron 2 of 18)	CR1-3_Croc|LINE|CR1	35149	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.018116	0.400722	
chunk0023_286_1	chr10	28543903	28544460	+	0	NA	intron (NM_016628, intron 3 of 13)	intron (NM_016628, intron 3 of 13)	10689	NM_100486	51322	Hs.743224	NM_016628	ENSG00000095787	WAC	BM-016|DESSH|PRO1741|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.017953	0.444444	
chunk0063_262_1	chr14	83550896	83551591	+	0	NA	Intergenic	Intergenic	-1842636	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.004317	0.320402	261(GAGAACACTAAGTCCT,-,0.00),262(AGAACACTAAGTCCTT,+,0.00)
chunk0055_409_1	chr13	74420634	74420913	+	0	NA	intron (NR_047005, intron 2 of 4)	intron (NR_047005, intron 2 of 4)	1600	NR_047005	100874151	Hs.564552	NR_047005	ENSG00000226240	LINC00381	-	long intergenic non-protein coding RNA 381	ncRNA	0.010753	0.428571	
chunk0102_27_1	chr2	141666130	141667412	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	464930	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.003120	0.374903	
chunk0051_80_1	chr12	113846947	113847474	+	0	NA	intron (NM_001146699, intron 22 of 24)	intron (NM_001146699, intron 22 of 24)	-73527	NR_110026	100506465	Hs.211461	NR_110025	ENSG00000249550	LINC01234	LCAL84|onco-lncRNA-32	long intergenic non-protein coding RNA 1234	ncRNA	0.018975	0.439394	
chunk0117_215_1	chr22	22224904	22225103	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-19777	NM_007128	7441	Hs.247979	NM_007128	ENSG00000169575	VPREB1	CD179a|IGI|IGVPB|VPREB	V-set pre-B cell surrogate light chain 1	protein-coding	0.015075	0.500000	101(TGGAACATGCTGTTCC,-,0.00),102(GGAACATGCTGTTCCC,+,0.00)
chunk0195_432_1	chr8	100988817	100989241	+	0	NA	Intergenic	Intergenic	-35634	NM_003406	7534	Hs.492407	NM_003406	ENSG00000164924	YWHAZ	14-3-3-zeta|HEL-S-3|HEL-S-93|HEL4|KCIP-1|POPCHAS|YWHAD	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	protein-coding	0.000000	0.390588	175(TAGAACAATCTGTGTT,-,0.00),176(AGAACAATCTGTGTTT,+,0.00)
chunk0202_58_1	chr9	71652667	71652931	+	0	NA	Intergenic	MLT2D|LTR|ERVL	116085	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.007576	0.456604	146(CTGCACATTTTGTACT,-,0.00),147(TGCACATTTTGTACTT,+,0.00)
chunk0043_99_1	chr12	14825593	14826036	+	0	NA	Intergenic	Intergenic	-11632	NM_001013698	440087	Hs.220931	NM_001013698	ENSG00000179256	SMCO3	C12orf69	single-pass membrane protein with coiled-coil domains 3	protein-coding	0.002257	0.297297	239(GAGAACACCTTGTTAT,-,0.00)
chunk0108_142_1	chr2	230777712	230778007	+	0	NA	intron (NM_016289, intron 2 of 8)	L1ME4a|LINE|L1	64311	NM_001130849	51719	Hs.603930	NM_016289	ENSG00000135932	CAB39	CGI-66|MO25	calcium binding protein 39	protein-coding	0.010169	0.358108	
chunk0072_374_1	chr15	100041068	100041629	+	0	NA	intron (NM_139057, intron 18 of 21)	intron (NM_139057, intron 18 of 21)	-234421	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.010695	0.437722	213(CAGTACAGCATGTACT,-,0.00),214(AGTACAGCATGTACTG,+,0.00)
chunk0173_278_1	chr6	147776572	147777124	+	0	NA	Intergenic	Eulor5A|DNA?|DNA?	268156	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.007246	0.396022	
chunk0143_432_1	chr4	123856734	123857440	+	0	NA	intron (NR_027105, intron 3 of 4)	intron (NR_027105, intron 3 of 4)	82823	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.012748	0.388967	
chunk0016_88_1	chr1	194570504	194570772	+	0	NA	Intergenic	Intergenic	1265893	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.000000	0.356877	
chunk0032_251_1	chr11	8596755	8597050	+	0	NA	Intergenic	L2a|LINE|L2	-2613	NM_001289058	65975	Hs.501833	NM_030906	ENSG00000130413	STK33	-	serine/threonine kinase 33	protein-coding	0.000000	0.429054	
chunk0207_459_1	chr9	137785589	137786130	+	0	NA	intron (NM_024757, intron 15 of 26)	intron (NM_024757, intron 15 of 26)	22837	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.027726	0.498155	
chunk0167_319_1	chr6	72194260	72194844	+	0	NA	intron (NM_014989, intron 6 of 33)	L2a|LINE|L2	-18259	NM_001168408	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.001712	0.297436	
chunk0207_204_1	chr9	131227181	131227384	+	0	NA	intron (NM_005085, intron 32 of 35)	intron (NM_005085, intron 32 of 35)	49237	NM_033387	286336	Hs.143878	NM_033387	ENSG00000126882	FAM78A	C9orf59	family with sequence similarity 78 member A	protein-coding	0.009852	0.563725	
chunk0049_264_1	chr12	93749865	93750110	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-12164	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.000000	0.390244	163(AATACATTATGTTCCT,+,0.00)
chunk0055_388_1	chr13	73451321	73451855	+	0	NA	Intergenic	Intergenic	-112656	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.013109	0.437383	
chunk0077_210_1	chr16	79970490	79970834	+	0	NA	Intergenic	Intergenic	175413	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.014535	0.469565	
chunk0067_322_1	chr15	48016808	48017363	+	0	NA	Intergenic	Intergenic	-103887	NM_205850	283652	Hs.710240	NM_205850	ENSG00000188467	SLC24A5	JSX|NCKX5|OCA6|SHEP4	solute carrier family 24 member 5	protein-coding	0.005405	0.402878	
chunk0016_27_1	chr1	193007708	193008409	+	0	NA	Intergenic	MIRc|SINE|MIR	51335	NM_001199261	51377	Hs.145469	NM_015984	ENSG00000116750	UCHL5	CGI-70|INO80R|UCH-L5|UCH37	ubiquitin C-terminal hydrolase L5	protein-coding	0.000000	0.351852	
chunk0183_69_1	chr7	104191760	104192085	+	0	NA	intron (NM_002553, intron 5 of 13)	L1MEc|LINE|L1	16125	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.006154	0.380368	
chunk0094_192_1	chr2	6207518	6207922	+	0	NA	Intergenic	L2c|LINE|L2	167702	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.007426	0.395062	
chunk0087_260_1	chr18	37080145	37080504	+	0	NA	intron (NM_020776, intron 7 of 9)	intron (NM_020776, intron 7 of 9)	-251108	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.005571	0.402778	
chunk0122_256_1	chr3	34893959	34894526	+	0	NA	intron (NR_110817, intron 2 of 3)	AluJo|SINE|Alu	499781	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.005291	0.387324	
chunk0166_178_1	chr6	46088531	46089021	+	0	NA	Intergenic	Intergenic	-8428	NM_001114086	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.002041	0.303462	
chunk0129_327_1	chr3	124520988	124521475	+	0	NA	intron (NM_001024660, intron 33 of 59)	L2c|LINE|L2	-63428	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.010267	0.471311	
chunk0031_21_1	chr10	121874327	121874526	+	0	NA	intron (NM_001001976, intron 7 of 11)	intron (NM_001001976, intron 7 of 11)	53637	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.005025	0.305000	
chunk0160_374_1	chr5	161207458	161208214	+	0	NA	Intergenic	L1PA15|LINE|L1	-269210	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.005291	0.343461	
chunk0151_273_1	chr5	52707613	52708007	+	0	NA	Intergenic	Intergenic	-80130	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.005076	0.405063	
chunk0141_305_1	chr4	87067015	87067641	+	0	NA	intron (NM_001313959, intron 3 of 19)	intron (NM_001313959, intron 3 of 19)	60327	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.003195	0.384370	
chunk0067_240_1	chr15	45503103	45503354	+	0	NA	intron (NM_013309, intron 3 of 7)	intron (NM_013309, intron 3 of 7)	-7908	NR_022014	283651	Hs.574240	NM_173609		HMGN2P46	C15orf21|D-PCa-2	high mobility group nucleosomal binding domain 2 pseudogene 46	pseudo	0.000000	0.297619	
chunk0110_457_1	chr20	21298116	21298315	+	0	NA	Intergenic	Intergenic	-5089	NM_012255	22803	Hs.255932	NM_012255	ENSG00000088930	XRN2	-	5'-3' exoribonuclease 2	protein-coding	0.000000	0.380000	
chunk0038_243_1	chr11	87173150	87173501	+	0	NA	intron (NM_022918, intron 5 of 14)	intron (NM_022918, intron 5 of 14)	135481	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.005698	0.355114	
chunk0056_8_1	chr13	77055046	77056327	+	0	NA	exon (NM_015057, exon 80 of 83)	exon (NM_015057, exon 80 of 83)	-19828	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.003903	0.361154	
chunk0203_230_1	chr9	87028555	87028983	+	0	NA	intron (NR_027471, intron 1 of 1)	intron (NR_027471, intron 1 of 1)	13357	NR_027471	440173	Hs.127361	NR_027471	ENSG00000269994	LOC440173	-	uncharacterized LOC440173	ncRNA	0.002336	0.358974	
chunk0081_199_1	chr17	42384862	42385174	+	0	NA	intron (NM_139276, intron 1 of 23)	MER3|DNA|hAT-Charlie	3369	NM_213662	6774	Hs.463059	NM_003150	ENSG00000168610	STAT3	ADMIO|ADMIO1|APRF|HIES	signal transducer and activator of transcription 3	protein-coding	0.003205	0.392971	165(CTGTACTGTATGTTCT,-,0.00),166(TGTACTGTATGTTCTT,+,0.00)
chunk0041_263_1	chr11	129055079	129055800	+	0	NA	intron (NM_001142685, intron 9 of 21)	L1MC2|LINE|L1	-31246	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.002774	0.360111	
chunk0198_133_1	chr8	132487136	132487394	+	0	NA	Intergenic	Intergenic	-6508	NM_004519	3786	Hs.374023	NM_004519	ENSG00000184156	KCNQ3	BFNC2|EBN2|KV7.3	potassium voltage-gated channel subfamily Q member 3	protein-coding	0.003876	0.490347	76(AAGCACTCTGTGTTCT,-,0.00),77(AGCACTCTGTGTTCTT,+,0.00)
chunk0159_332_1	chr5	143680667	143681257	+	0	NA	TTS (NR_049829)	TTS (NR_049829)	1102	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.008475	0.394247	
chunk0205_308_1	chr9	112486315	112486752	+	0	NA	promoter-TSS (NM_133465)	promoter-TSS (NM_133465)	-435	NM_001287038	158405	Hs.656619	NM_133465	ENSG00000165185	KIAA1958	-	KIAA1958	protein-coding	0.096110	0.625571	
chunk0099_309_1	chr2	99396876	99397123	+	0	NA	intron (NM_015904, intron 22 of 23)	intron (NM_015904, intron 22 of 23)	59628	NM_015904	9669	Hs.158688	NM_015904	ENSG00000158417	EIF5B	IF2	eukaryotic translation initiation factor 5B	protein-coding	0.004049	0.403226	
chunk0113_41_1	chr20	49899428	49900171	+	0	NA	Intergenic	Intergenic	13940	NM_001135773	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.012113	0.428763	
chunk0101_58_1	chr2	123159116	123159623	+	0	NA	Intergenic	L1MA3|LINE|L1	-865918	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.314961	
chunk0039_252_1	chr11	102201820	102202149	+	0	NA	intron (NM_001130145, intron 4 of 8)	L1MC5a|LINE|L1	89544	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.006079	0.381818	
chunk0144_18_1	chr4	124863670	124864178	+	0	NA	Intergenic	LTR48B|LTR|ERV1	-151192	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.003937	0.390963	
chunk0186_50_1	chr7	136334499	136334760	+	0	NA	Intergenic	Intergenic	-357173	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.003831	0.354962	
chunk0052_50_1	chr13	20953479	20953778	+	0	NA	Intergenic	Intergenic	-4200	NR_104058	101930748	Hs.637638	NR_104058	ENSG00000233780	LINC00367	-	long intergenic non-protein coding RNA 367	ncRNA	0.006689	0.396667	
chunk0099_228_1	chr2	96338143	96338664	+	0	NA	intron (NM_001281712, intron 1 of 16)	L2|LINE|L2	2662	NM_015341	23397	Hs.308045	NM_015341	ENSG00000121152	NCAPH	BRRN1|CAP-H|CAPH|MCPH23	non-SMC condensin I complex subunit H	protein-coding	0.007678	0.440613	
chunk0105_145_1	chr2	186440486	186440989	+	0	NA	Intergenic	Intergenic	-45421	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.005964	0.359127	
chunk0131_194_1	chr3	148603404	148603825	+	0	NA	Intergenic	Intergenic	-94257	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.002375	0.305687	253(ATGAACATTATGTCCT,-,0.00),254(TGAACATTATGTCCTT,+,0.00)
chunk0161_135_1	chr5	168367142	168367355	+	0	NA	intron (NM_001161661, intron 1 of 22)	intron (NM_001161661, intron 1 of 22)	75188	NM_001161661	23286	Hs.484047	NM_015238	ENSG00000113645	WWC1	HBEBP3|HBEBP36|KIBRA|MEMRYQTL|PPP1R168	WW and C2 domain containing 1	protein-coding	0.009390	0.406542	126(AGCACAGCTTGCTCTG,+,0.00)
chunk0205_229_1	chr9	109912258	109912485	+	0	NA	intron (NM_053016, intron 3 of 6)	intron (NM_053016, intron 3 of 6)	132074	NM_053016	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.008811	0.403509	
chunk0032_6_1	chr11	410086	410285	+	0	NA	intron (NM_021805, intron 1 of 9)	intron (NM_021805, intron 1 of 9)	4814	NM_001135054	59307	Hs.501624	NM_021805	ENSG00000185187	SIGIRR	IL-1R8|TIR8	single Ig and TIR domain containing	protein-coding	0.040201	0.660000	
chunk0073_7_1	chr16	1971799	1972107	+	0	NA	promoter-TSS (NM_006453)	promoter-TSS (NM_006453)	-110	NM_006453	10607	Hs.513267	NM_006453	ENSG00000183751	TBL3	SAZD|UTP13	transducin beta like 3	protein-coding	0.110390	0.653722	
chunk0057_284_1	chr13	106129350	106129549	+	0	NA	Intergenic	Intergenic	-247114	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.000000	0.365000	
chunk0159_274_1	chr5	142421318	142421641	+	0	NA	intron (NR_120664, intron 3 of 3)	intron (NR_120664, intron 3 of 3)	96186	NR_120664	101926941	Hs.658945	NR_120664	ENSG00000231185	SPRY4-AS1	THCAT68	SPRY4 antisense RNA 1	ncRNA	0.012384	0.462963	
chunk0079_231_1	chr17	15649821	15650302	+	0	NA	intron (NM_006470, intron 4 of 8)	intron (NM_006470, intron 4 of 8)	-30357	NM_001282540	374286	Hs.548021	NM_006382	ENSG00000241322	CDRT1	C170RF1|C17ORF1|C17ORF1A|FBXW10B|FBXW10P1|HREP|SM25H2	CMT1A duplicated region transcript 1	protein-coding	0.010395	0.464730	
chunk0004_128_1	chr1	44701139	44701477	+	0	NA	intron (NM_001145636, intron 5 of 11)	intron (NM_001145636, intron 5 of 11)	20593	NR_002753	26828		NR_002753	ENSG00000199377	RNU5F-1	RNU5F|U5F	RNA, U5F small nuclear 1	snRNA	0.011834	0.448378	
chunk0138_207_1	chr4	38692579	38693149	+	0	NA	intron (NM_016531, intron 4 of 5)	intron (NM_016531, intron 4 of 5)	-28236	NR_026804	79667	Hs.29725	NM_024614	ENSG00000231160	KLF3-AS1	-	KLF3 antisense RNA 1	ncRNA	0.008772	0.322242	
chunk0002_291_1	chr1	22967503	22968173	+	0	NA	Intergenic	L2a|LINE|L2	-2408	NM_001289974	646262		NM_001289974	ENSG00000215906	LACTBL1	-	lactamase beta like 1	protein-coding	0.004478	0.359165	
chunk0206_197_1	chr9	123026313	123026830	+	0	NA	intron (NM_012197, intron 13 of 25)	intron (NM_012197, intron 13 of 25)	-7072	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.001934	0.361004	
chunk0045_410_1	chr12	53008164	53008459	+	0	NA	intron (NM_001300821, intron 1 of 14)	intron (NM_001300821, intron 1 of 14)	2053	NM_001300821	1975	Hs.648394	NM_001417	ENSG00000063046	EIF4B	EIF-4B|PRO1843	eukaryotic translation initiation factor 4B	protein-coding	0.020339	0.402027	
chunk0168_156_1	chr6	83274657	83274976	+	0	NA	intron (NM_002395, intron 6 of 13)	Tigger6b|DNA|TcMar-Tigger	-80880	NM_001199917	5238	Hs.661665	NM_015599	ENSG00000013375	PGM3	AGM1|IMD23|PAGM|PGM 3	phosphoglucomutase 3	protein-coding	0.012539	0.334375	
chunk0123_383_1	chr3	48738934	48739340	+	0	NA	Intergenic	Intergenic	-21859	NM_001146179	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.012315	0.555283	193(GGGAACACAATGGTCC,-,0.00),194(GGAACACAATGGTCCC,+,0.00)
chunk0015_337_1	chr1	189840675	189840990	+	0	NA	Intergenic	Intergenic	636797	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.306962	
chunk0011_221_1	chr1	150207590	150207789	+	0	NA	Intergenic	MER89|LTR|ERV1	26989	NM_001136479	81611	Hs.656466	NM_030920	ENSG00000143401	ANP32E	LANP-L|LANPL	acidic nuclear phosphoprotein 32 family member E	protein-coding	0.020101	0.470000	
chunk0142_148_1	chr4	94951724	94952157	+	0	NA	intron (NM_001203, intron 2 of 12)	L1PA7|LINE|L1	-44292	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.004619	0.373272	
chunk0040_118_1	chr11	112216412	112216620	+	0	NA	intron (NM_001037290, intron 11 of 11)	intron (NM_001037290, intron 11 of 11)	-9849	NM_000317	5805	Hs.503860	NM_000317	ENSG00000150787	PTS	PTPS	6-pyruvoyltetrahydropterin synthase	protein-coding	0.009615	0.306220	
chunk0164_236_1	chr6	23263079	23263326	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	693753	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.000000	0.383065	
chunk0109_153_1	chr20	3846169	3846373	+	0	NA	promoter-TSS (NM_020746)	promoter-TSS (NM_020746)	-528	NM_020746	57506	Hs.570362	NM_020746	ENSG00000088888	MAVS	CARDIF|IPS-1|IPS1|VISA	mitochondrial antiviral signaling protein	protein-coding	0.044118	0.673171	
chunk0046_314_1	chr12	62500669	62500945	+	0	NA	exon (NM_001278472, exon 7 of 36)	exon (NM_001278472, exon 7 of 36)	33990	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.000000	0.267148	120(TAGAACAACCAGTACT,-,0.00),121(AGAACAACCAGTACTG,+,0.00)
chunk0037_101_1	chr11	72070923	72071184	+	0	NA	intron (NM_006185, intron 1 of 26)	intron (NM_006185, intron 1 of 26)	1249	NR_036123	100422953		NR_036123	ENSG00000263742	MIR3165	mir-3165	microRNA 3165	ncRNA	0.000000	0.438931	
chunk0202_154_1	chr9	73631840	73632499	+	0	NA	Intergenic	MIR|SINE|MIR	480438	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.009105	0.333333	
chunk0076_168_1	chr16	67404691	67405053	+	0	NA	intron (NM_013304, intron 3 of 10)	intron (NM_013304, intron 3 of 10)	-11337	NM_016140	51673	Hs.534458	NM_015964	ENSG00000159713	TPPP3	CGI-38|TPPP/p20|p20|p25gamma	tubulin polymerization promoting protein family member 3	protein-coding	0.008287	0.482094	
chunk0003_23_1	chr1	29271684	29271966	+	0	NA	intron (NM_133177, intron 7 of 30)	intron (NM_133177, intron 7 of 30)	35309	NM_133178	10076	Hs.19718	NM_005704	ENSG00000060656	PTPRU	FMI|PCP-2|PTP|PTP-J|PTP-PI|PTP-RO|PTPPSI|PTPRO|PTPU2|R-PTP-PSI|R-PTP-U|hPTP-J	protein tyrosine phosphatase receptor type U	protein-coding	0.014184	0.544170	
chunk0083_248_1	chr17	67963331	67964174	+	0	NA	intron (NM_182641, intron 24 of 27)	intron (NM_182641, intron 24 of 27)	29897	NM_181655	284018	Hs.90790	NM_181655	ENSG00000186665	C17orf58	-	chromosome 17 open reading frame 58	protein-coding	0.001186	0.312796	667(ATTACACAGTGTTCTT,+,0.00)
chunk0158_126_1	chr5	127038724	127039122	+	0	NA	Intergenic	Intergenic	-8115	NM_178450	115123	Hs.132441	NM_178450	ENSG00000173926	MARCH3	MARCH-III|RNF173	membrane associated ring-CH-type finger 3	protein-coding	0.005025	0.353383	
chunk0086_118_1	chr18	14946679	14947124	+	0	NA	intron (NR_104164, intron 1 of 3)	intron (NR_104164, intron 1 of 3)	634	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.008989	0.479821	46(GGGCACTGAGTGTTCT,-,0.00),47(GGCACTGAGTGTTCTC,+,0.00)
chunk0113_16_1	chr20	49510450	49510807	+	0	NA	intron (NM_000961, intron 9 of 9)	intron (NM_000961, intron 9 of 9)	-27984	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.014006	0.494413	
chunk0152_118_1	chr5	58699014	58699875	+	0	NA	intron (NM_138453, intron 2 of 4)	L1PA6|LINE|L1	116332	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.009292	0.497680	
chunk0189_389_1	chr8	27437771	27438042	+	0	NA	intron (NM_004103, intron 19 of 31)	intron (NM_004103, intron 19 of 31)	4536	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.014760	0.573529	
chunk0097_142_1	chr2	47759922	47760573	+	0	NA	Intergenic	MER34B|LTR|ERV1	-22835	NM_000179	2956	Hs.445052	NM_000179	ENSG00000116062	MSH6	GTBP|GTMBP|HNPCC5|HSAP|p160	mutS homolog 6	protein-coding	0.007680	0.423313	295(GAGGGCAGAGAGTTCT,-,0.00),296(AGGGCAGAGAGTTCTC,+,0.00)
chunk0055_440_1	chr13	75631840	75632044	+	0	NA	intron (NM_005358, intron 2 of 29)	L1ME4a|LINE|L1	4052	NR_120410	101927155	Hs.564550	NR_120410	ENSG00000261105	LMO7-AS1	UCHL3-AS1	LMO7 antisense RNA 1	ncRNA	0.009804	0.424390	
chunk0175_421_1	chr6	168913105	168913455	+	0	NA	Intergenic	Intergenic	249021	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.005714	0.467236	
chunk0060_101_1	chr14	43377794	43378264	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	1129267	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.004255	0.288747	
chunk0023_194_1	chr10	25135006	25135448	+	0	NA	intron (NR_120649, intron 6 of 7)	L1MB3|LINE|L1	22169	NR_120649	101929025	Hs.553324	NR_120649	ENSG00000231422	LINC01516	-	long intergenic non-protein coding RNA 1516	ncRNA	0.006787	0.381490	
chunk0124_321_1	chr3	58120240	58120996	+	0	NA	intron (NM_001164317, intron 19 of 46)	intron (NM_001164317, intron 19 of 46)	90385	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.011905	0.466314	340(CGGTACAGTCAGTTCT,-,0.00),341(GGTACAGTCAGTTCTC,+,0.00)
chunk0177_6_1	chr7	20330432	20330688	+	0	NA	promoter-TSS (NM_002214)	promoter-TSS (NM_002214)	-542	NM_002214	3696	Hs.592171	NM_002214	ENSG00000105855	ITGB8	-	integrin subunit beta 8	protein-coding	0.074219	0.610895	
chunk0120_257_1	chr3	9054662	9055321	+	0	NA	intron (NM_001033117, intron 8 of 21)	L4_B_Mam|LINE|RTE-X	-91516	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.007587	0.381818	428(GAAAACACTCTGTTCA,-,0.00),429(AAAACACTCTGTTCAT,+,0.00)
chunk0056_344_1	chr13	91565390	91565589	+	0	NA	intron (NM_004466, intron 2 of 7)	intron (NM_004466, intron 2 of 7)	166870	NM_004466	2262	Hs.655675	NM_004466	ENSG00000179399	GPC5	-	glypican 5	protein-coding	0.010050	0.390000	
chunk0096_58_1	chr2	27420689	27421400	+	0	NA	Intergenic	Intergenic	-7562	NM_013392	29959	Hs.515876	NM_013392	ENSG00000115216	NRBP1	BCON3|MADM|MUDPNP|NRBP	nuclear receptor binding protein 1	protein-coding	0.011252	0.432584	
chunk0050_148_1	chr12	102694127	102694753	+	0	NA	Intergenic	L1MA2|LINE|L1	129959	NR_033855	283432	Hs.382110	NR_033855	ENSG00000258169	LINC00485	-	long intergenic non-protein coding RNA 485	ncRNA	0.003195	0.513557	
chunk0149_49_1	chr5	16674837	16675061	+	0	NA	exon (NM_012334, exon 35 of 41)	exon (NM_012334, exon 35 of 41)	-57891	NM_001034850	54463	Hs.481704	NM_019000	ENSG00000154153	RETREG1	FAM134B|JK-1|JK1	reticulophagy regulator 1	protein-coding	0.026786	0.546667	
chunk0174_399_1	chr6	165487675	165488243	+	0	NA	intron (NM_006661, intron 3 of 22)	intron (NM_006661, intron 3 of 22)	78358	NR_106988									0.001761	0.356766	
chunk0208_366_1	chrX	26257980	26258613	+	0	NA	Intergenic	MER67D|LTR|ERV1	42127	NM_001271752	347541	Hs.224079	NM_001271752	ENSG00000188408	MAGEB5	CT3.3|MAGE-B5	MAGE family member B5	protein-coding	0.001580	0.351735	364(AAGAACAGGTTGATCA,-,0.00)
chunk0195_438_1	chr8	101120597	101121118	+	0	NA	Intergenic	Intergenic	68803	NR_033962	441374	Hs.652045	NR_033962	ENSG00000248599	FLJ42969	-	uncharacterized LOC441374	ncRNA	0.017274	0.519157	198(GAGACCACGGTGTGCC,-,0.00),199(AGACCACGGTGTGCCA,+,0.00)
chunk0013_226_1	chr1	169545424	169545930	+	0	NA	intron (NM_000130, intron 11 of 24)	intron (NM_000130, intron 11 of 24)	40854	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.005929	0.394477	
chunk0045_160_1	chr12	46685920	46686372	+	0	NA	Intergenic	Intergenic	139851	NM_018018	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.006637	0.434879	
chunk0087_379_1	chr18	41594872	41595095	+	0	NA	Intergenic	Intergenic	-74386	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.013453	0.566964	
chunk0017_305_1	chr1	211179924	211180673	+	0	NA	Intergenic	L1MC2|LINE|L1	-46183	NM_002238	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.005340	0.362667	
chunk0190_130_1	chr8	30642101	30642399	+	0	NA	intron (NM_001206847, intron 1 of 2)	intron (NM_001206847, intron 1 of 2)	3650	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.003356	0.304348	
chunk0162_364_1	chr6	7199294	7199770	+	0	NA	intron (NM_001003698, intron 6 of 11)	intron (NM_001003698, intron 6 of 11)	91679	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.008403	0.417191	
chunk0031_383_1	chr10	130941436	130941847	+	0	NA	Intergenic	Intergenic	21027	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.014599	0.327670	220(GAGGACAAGCTGTGCT,-,0.00),221(AGGACAAGCTGTGCTG,+,0.00)
chunk0140_50_1	chr4	66648686	66649343	+	0	NA	Intergenic	MIR|SINE|MIR	372190	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.003044	0.310030	294(TAAACACTCTGTGCCT,+,0.00)
chunk0172_101_1	chr6	134853376	134853636	+	0	NA	Intergenic	Intergenic	96616	NM_170771	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.003846	0.432950	168(CTGTACATACTGTACC,-,0.00),169(TGTACATACTGTACCT,+,0.00)
chunk0058_26_1	chr14	19917978	19918478	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-2379	NM_001005483	79317	Hs.554585	NM_001005483	ENSG00000176281	OR4K5	OR14-16	olfactory receptor family 4 subfamily K member 5	protein-coding	0.002000	0.415170	
chunk0127_113_1	chr3	90192852	90193530	+	0	NA	Intergenic	L1PA6|LINE|L1	1085667	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.010324	0.530191	
chunk0163_189_1	chr6	11621058	11621506	+	0	NA	Intergenic	Intergenic	83055	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.011161	0.501114	
chunk0117_263_1	chr22	23678962	23679161	+	0	NA	intron (NR_024448, intron 10 of 11)	intron (NR_024448, intron 10 of 11)	-11800	NM_153615	266747	Hs.658997	NM_153615	ENSG00000159496	RGL4	Rgr	ral guanine nucleotide dissociation stimulator like 4	protein-coding	0.015075	0.415000	
chunk0137_374_1	chr4	26206397	26206771	+	0	NA	Intergenic	Intergenic	-113126	NM_203283	3516	Hs.479396	NM_005349	ENSG00000168214	RBPJ	AOS3|CBF1|IGKJRB|IGKJRB1|KBF2|RBP-J|RBPJK|RBPSUH|SUH|csl	recombination signal binding protein for immunoglobulin kappa J region	protein-coding	0.005348	0.373333	
chunk0131_426_1	chr3	153528572	153528877	+	0	NA	Intergenic	LTR40A1|LTR|ERVL	44229	NM_001101337									0.000000	0.300654	
chunk0177_251_1	chr7	25128164	25128363	+	0	NA	Intergenic	L1M1|LINE|L1	-2902	NM_018947	54205	Hs.437060	NM_018947	ENSG00000172115	CYCS	CYC|HCS|THC4	cytochrome c, somatic	protein-coding	0.005025	0.520000	
chunk0155_170_1	chr5	94368009	94368239	+	0	NA	intron (NM_001145678, intron 20 of 20)	L1ME4c|LINE|L1	250480	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.000000	0.333333	
chunk0148_88_1	chr5	3414356	3414856	+	0	NA	Intergenic	Intergenic	89398	NR_104618	102467075	Hs.652949	NR_104618	ENSG00000250716	LINC01017	-	long intergenic non-protein coding RNA 1017	ncRNA	0.016000	0.431138	
chunk0174_77_1	chr6	156199187	156199475	+	0	NA	Intergenic	Intergenic	252534	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.017361	0.394464	
chunk0074_237_1	chr16	27354676	27354875	+	0	NA	intron (NM_000418, intron 7 of 10)	intron (NM_000418, intron 7 of 10)	40866	NM_001257406	3566	Hs.513457	NM_000418	ENSG00000077238	IL4R	CD124|IL-4RA|IL4RA	interleukin 4 receptor	protein-coding	0.020101	0.540000	
chunk0132_210_1	chr3	157490439	157490844	+	0	NA	intron (NM_001167911, intron 2 of 12)	L1ME3C|LINE|L1	4865	NM_001167917	79674	Hs.658046	NM_024621	ENSG00000197415	VEPH1	MELT|VEPH	ventricular zone expressed PH domain containing 1	protein-coding	0.000000	0.334975	
chunk0007_133_1	chr1	79193131	79193446	+	0	NA	Intergenic	Intergenic	-186478	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.012698	0.389241	
chunk0035_7_1	chr11	39944103	39944542	+	0	NA	Intergenic	L1MA8|LINE|L1	348808	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.002278	0.295455	
chunk0005_92_1	chr1	56372394	56372927	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	206924	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.001876	0.346442	
chunk0087_79_1	chr18	32097236	32097455	+	0	NA	intron (NM_198128, intron 1 of 4)	intron (NM_198128, intron 1 of 4)	4739	NM_001191324	51444	Hs.302408	NM_016271	ENSG00000134758	RNF138	HSD-4|NARF|STRIN|hNARF	ring finger protein 138	protein-coding	0.000000	0.318182	182(TTGAACATCCAGTTCC,-,0.00),183(TGAACATCCAGTTCCT,+,0.00)
chunk0021_421_1	chr1	246950698	246951270	+	0	NA	intron (NM_001204221, intron 5 of 5)	intron (NM_001204221, intron 5 of 5)	-19560	NM_015446	25909	Hs.300887	NM_015446	ENSG00000153207	AHCTF1	ELYS|MST108|MSTP108|TMBS62	AT-hook containing transcription factor 1	protein-coding	0.005245	0.382199	
chunk0090_358_1	chr18	76850197	76850438	+	0	NA	intron (NM_001306089, intron 2 of 30)	intron (NM_001306089, intron 2 of 30)	26157	NM_007345	7776	Hs.719137	NM_007345	ENSG00000130856	ZNF236	ZNF236A|ZNF236B	zinc finger protein 236	protein-coding	0.004149	0.363636	111(GAGAACAGGATGTGAC,-,0.00)
chunk0130_319_1	chr3	137843865	137844292	+	0	NA	Intergenic	Intergenic	72167	NR_109987	100507274	Hs.360349	NR_109987	ENSG00000239513	LINC01210	-	long intergenic non-protein coding RNA 1210	ncRNA	0.000000	0.341121	
chunk0075_89_1	chr16	48295631	48296133	+	0	NA	intron (NM_031490, intron 8 of 14)	intron (NM_031490, intron 8 of 14)	51715	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.001992	0.347913	
chunk0096_154_1	chr2	29234619	29234855	+	0	NA	intron (NM_004304, intron 13 of 28)	intron (NM_004304, intron 13 of 28)	119311	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.029661	0.518987	
chunk0019_91_1	chr1	224579358	224579615	+	0	NA	Intergenic	HAL1|LINE|L1	-36991	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.000000	0.430233	185(AGGGACTGAGTGTACT,-,0.00),186(GGGACTGAGTGTACTA,+,0.00)
chunk0119_34_1	chr22	40396894	40397191	+	0	NA	intron (NM_015705, intron 1 of 21)	intron (NM_015705, intron 1 of 21)	26480	NM_015705	27352	Hs.474914	NM_015705	ENSG00000100359	SGSM3	CIP85|MAP|RABGAP5|RUSC3|RUTBC3|RabGAP-5|rabGAPLP	small G protein signaling modulator 3	protein-coding	0.010101	0.459732	
chunk0153_39_1	chr5	67215559	67216177	+	0	NA	Intergenic	Intergenic	-19079	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.022654	0.534733	
chunk0057_352_1	chr13	108501624	108501911	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	-94385	NM_015011	23026	Hs.656587	NM_015011	ENSG00000041515	MYO16	MYAP3|MYR8|Myo16b|NYAP3|PPP1R107	myosin XVI	protein-coding	0.017422	0.420139	
chunk0123_21_1	chr3	40396442	40396757	+	0	NA	intron (NR_040100, intron 3 of 3)	intron (NR_040100, intron 3 of 3)	9354	NM_001291960	956	Hs.441145	NM_001248	ENSG00000168032	ENTPD3	CD39L3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding	0.012698	0.458861	
chunk0176_289_1	chr7	16725985	16726291	+	0	NA	Intergenic	LTR106_Mam|LTR|LTR	-27588	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.000000	0.289902	
chunk0032_349_1	chr11	10390264	10390816	+	0	NA	intron (NR_103765, intron 2 of 3)	intron (NR_103765, intron 2 of 3)	-59781	NM_001172431	272	Hs.501890	NM_000480	ENSG00000133805	AMPD3	-	adenosine monophosphate deaminase 3	protein-coding	0.000000	0.437613	
chunk0147_221_1	chr4	181506009	181506475	+	0	NA	Intergenic	Intergenic	-347093	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.006438	0.349036	367(CAGGACGGAATGTTCA,-,0.00),368(AGGACGGAATGTTCAT,+,0.00)
chunk0179_102_1	chr7	44795837	44796076	+	0	NA	promoter-TSS (NM_001300981)	promoter-TSS (NM_001300981)	-680	NM_021130	5478	Hs.356331	NM_021130	ENSG00000196262	PPIA	CYPA|CYPH|HEL-S-69p	peptidylprolyl isomerase A	protein-coding	0.020921	0.479167	
chunk0030_322_1	chr10	118119287	118119506	+	0	NA	intron (NR_026940, intron 3 of 3)	intron (NR_026940, intron 3 of 3)	72575	NR_026941	255082	Hs.89387	NM_178816	ENSG00000177640	CASC2	C10orf5	cancer susceptibility 2	ncRNA	0.000000	0.377273	
chunk0155_287_1	chr5	96157376	96158274	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	78687	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.005568	0.385984	
chunk0197_463_1	chr8	127928599	127929067	+	0	NA	intron (NR_003367, intron 2 of 8)	intron (NR_003367, intron 2 of 8)	19890	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.012821	0.522388	
chunk0101_47_1	chr2	122969014	122969507	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-1056027	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.004057	0.346154	
chunk0188_224_1	chr8	12817744	12818116	+	0	NA	intron (NR_102423, intron 1 of 1)	intron (NR_102423, intron 1 of 1)	-6529	NR_015383	340357	Hs.434302	NR_015383	ENSG00000254813	LOC340357	-	uncharacterized LOC340357	ncRNA	0.010753	0.356568	
chunk0197_106_1	chr8	119767645	119768201	+	0	NA	intron (NM_003184, intron 18 of 25)	L1PA15-16|LINE|L1	64911	NM_003184	6873	Hs.122752	NM_003184	ENSG00000064313	TAF2	CIF150|MRT40|TAF2B|TAFII150	TATA-box binding protein associated factor 2	protein-coding	0.023381	0.588869	
chunk0117_272_1	chr22	24060430	24060661	+	0	NA	intron (NM_012295, intron 12 of 36)	intron (NM_012295, intron 12 of 36)	49175	NM_001199281	23523	Hs.517478	NM_012295	ENSG00000099991	CABIN1	CAIN|KB-318B8.7|PPP3IN	calcineurin binding protein 1	protein-coding	0.004329	0.504310	
chunk0205_243_1	chr9	110188901	110189566	+	0	NA	Intergenic	Intergenic	18900	NM_001012993	401546	Hs.125608	NM_001012993	ENSG00000188959	C9orf152	bA470J20.2	chromosome 9 open reading frame 152	protein-coding	0.009023	0.438438	
chunk0166_32_1	chr6	42083352	42083856	+	0	NA	Intergenic	Intergenic	33091	NM_138572	129685	Hs.520122	NM_138572	ENSG00000137413	TAF8	II|TAF|TAF(II)43|TAFII-43|TAFII43|TBN	TATA-box binding protein associated factor 8	protein-coding	0.009921	0.475248	185(TAGAACACTGTGTCTT,-,0.00),186(AGAACACTGTGTCTTA,+,0.00)
chunk0181_350_1	chr7	88304955	88305487	+	0	NA	intron (NM_001205315, intron 1 of 5)	intron (NM_001205315, intron 1 of 5)	1692	NM_001205316	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.005639	0.371482	
chunk0130_191_1	chr3	133608536	133608809	+	0	NA	exon (NM_007027, exon 27 of 28)	exon (NM_007027, exon 27 of 28)	34238	NM_001282765	55573	Hs.518265	NM_017548	ENSG00000091527	CDV3	H41	CDV3 homolog	protein-coding	0.003663	0.364964	
chunk0113_300_1	chr20	57757334	57758358	+	0	NA	Intergenic	Intergenic	-46310	NM_199171	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.003906	0.468293	561(AGGAACAGGCTGCACA,-,0.00)
chunk0006_89_1	chr1	65051623	65052186	+	0	NA	Intergenic	Intergenic	5938	NR_037443	100500854		NR_037443	ENSG00000265996	MIR3671	-	microRNA 3671	ncRNA	0.010657	0.382979	
chunk0073_366_1	chr16	15435215	15435518	+	0	NA	intron (NM_033201, intron 1 of 5)	intron (NM_033201, intron 1 of 5)	898	NM_033201	89927	Hs.401798	NM_033201	ENSG00000166780	BMERB1	C16orf45|MINP	bMERB domain containing 1	protein-coding	0.036304	0.470395	92(AGGCACACACCGTTCT,-,0.00),93(GGCACACACCGTTCTC,+,0.00)
chunk0105_289_1	chr2	189866436	189867247	+	0	NA	intron (NM_001128143, intron 9 of 11)	MIR|SINE|MIR	-82470	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.008631	0.386700	
chunk0193_383_1	chr8	80173386	80173997	+	0	NA	Intergenic	Intergenic	-2032	NM_005079	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.003273	0.374183	
chunk0200_11_1	chr9	14607943	14608936	+	0	NA	Intergenic	Intergenic	85043	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.008056	0.354125	
chunk0212_59_1	chrY	11323429	11323755	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1097998	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.024540	0.483180	33(CTGGACTCTCTGTGCC,-,0.00),34(TGGACTCTCTGTGCCC,+,0.00)
chunk0076_92_1	chr16	64959684	64960249	+	0	NA	intron (NM_001797, intron 11 of 12)	intron (NM_001797, intron 11 of 12)	162171	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.005310	0.363958	
chunk0086_175_1	chr18	21849809	21850039	+	0	NA	intron (NM_020774, intron 17 of 20)	L1MC5a|LINE|L1	-18518	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.004348	0.350649	
chunk0209_255_1	chrX	46185780	46186459	+	0	NA	Intergenic	Intergenic	141555	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.005891	0.388235	
chunk0124_253_1	chr3	56866936	56867403	+	0	NA	intron (NM_001128615, intron 4 of 12)	intron (NM_001128615, intron 4 of 12)	49302	NM_001289698	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.002141	0.329060	
chunk0135_215_1	chr3	188454799	188455337	+	0	NA	intron (NM_001167671, intron 3 of 10)	intron (NM_001167671, intron 3 of 10)	113598	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.005576	0.376623	
chunk0128_133_1	chr3	106590219	106590454	+	0	NA	Intergenic	Intergenic	650302	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.004255	0.372881	
chunk0117_334_1	chr22	25134004	25134458	+	0	NA	intron (NM_001145206, intron 4 of 10)	intron (NM_001145206, intron 4 of 10)	-21539	NR_038941	100128531	Hs.662126	NR_038941	ENSG00000203280	LOC100128531	-	uncharacterized LOC100128531	ncRNA	0.011013	0.476923	
chunk0029_228_1	chr10	102432510	102432801	+	0	NA	promoter-TSS (NM_024040)	promoter-TSS (NM_024040)	11	NM_024040	79004	Hs.500874	NM_024040	ENSG00000107874	CUEDC2	C10orf66|bA18I14.5	CUE domain containing 2	protein-coding	0.082474	0.643836	
chunk0189_417_1	chr8	27838011	27838256	+	0	NA	promoter-TSS (NM_018492)	promoter-TSS (NM_018492)	-38	NM_001278945	55872	Hs.104741	NM_018492	ENSG00000168078	PBK	CT84|HEL164|Nori-3|SPK|TOPK	PDZ binding kinase	protein-coding	0.024490	0.373984	
chunk0134_200_1	chr3	178444316	178444826	+	0	NA	intron (NR_046786, intron 1 of 2)	intron (NR_046786, intron 1 of 2)	25370	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.005882	0.391389	
chunk0146_70_1	chr4	157052064	157052853	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-23667	NM_001166061	2743	Hs.32973	NM_000824	ENSG00000109738	GLRB	HKPX2	glycine receptor beta	protein-coding	0.019011	0.487342	53(GTTACACCGTGTTCTT,+,0.00)
chunk0204_269_1	chr9	98230204	98230733	+	0	NA	intron (NR_051978, intron 3 of 11)	intron (NR_051978, intron 3 of 11)	-1251	NR_106913	102465514		NR_106913	ENSG00000278412	MIR6854	hsa-mir-6854	microRNA 6854	ncRNA	0.015123	0.441509	
chunk0199_327_1	chr9	8547716	8548281	+	0	NA	intron (NM_001040712, intron 3 of 29)	intron (NM_001040712, intron 3 of 29)	185948	NM_130393	5789	Hs.446083	NM_002839	ENSG00000153707	PTPRD	HPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA	protein tyrosine phosphatase receptor type D	protein-coding	0.008850	0.360424	
chunk0178_296_1	chr7	37578252	37578786	+	0	NA	Intergenic	Intergenic	-129193	NM_001206480	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.005618	0.308411	
chunk0004_37_1	chr1	42693338	42694122	+	0	NA	intron (NR_132737, intron 2 of 6)	intron (NR_132737, intron 2 of 6)	10743	NR_132737	4904	Hs.473583	NM_004559	ENSG00000065978	YBX1	BP-8|CBF-A|CSDA2|CSDB|DBPB|EFI-A|MDR-NF1|NSEP-1|NSEP1|YB-1|YB1	Y-box binding protein 1	protein-coding	0.002551	0.349045	
chunk0202_47_1	chr9	71263310	71263926	+	0	NA	Intergenic	Intergenic	-142020	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.001623	0.410049	373(AGGTACAAGATGTCCA,-,0.00),374(GGTACAAGATGTCCAT,+,0.00)
chunk0069_116_1	chr15	61702527	61703257	+	0	NA	Intergenic	Intergenic	357573	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.005479	0.462380	434(GTAACTGGCTGTTCCT,+,0.00)
chunk0147_353_1	chr4	185695674	185696150	+	0	NA	intron (NM_001145672, intron 1 of 20)	intron (NM_001145672, intron 1 of 20)	-38943	NM_001145675	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.010504	0.383648	284(AAGAACACCAAGTACC,-,0.00),285(AGAACACCAAGTACCT,+,0.00)
chunk0042_165_1	chr12	4472780	4473085	+	0	NA	Intergenic	Intergenic	-27318	NM_020996	2251	Hs.166015	NM_020996	ENSG00000111241	FGF6	HBGF-6|HST2	fibroblast growth factor 6	protein-coding	0.003279	0.447712	177(GGGACACAGTCTTCTG,+,0.00),266(CAGAACAGAGTGTTCC,-,0.00),267(AGAACAGAGTGTTCCT,+,0.00)
chunk0084_450_1	chr17	83031861	83032067	+	0	NA	intron (NM_001009905, intron 4 of 12)	intron (NM_001009905, intron 4 of 12)	19846	NM_001009905	146712	Hs.607824	NM_001009905	ENSG00000175711	B3GNTL1	3-Gn-T8|B3GNT8|BGnT-8|beta-1|beta3Gn-T8|beta3GnTL1	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1	protein-coding	0.043689	0.603865	
chunk0111_59_1	chr20	22811133	22811713	+	0	NA	Intergenic	Intergenic	-203906	NR_109883	101929685	Hs.563018	NR_109883	ENSG00000237396	LNCNEF	LINC01384|lncRNA-NEF	lncRNA neighboring enhancer of FOXA2	ncRNA	0.006897	0.454389	
chunk0174_111_1	chr6	156997256	156997742	+	0	NA	intron (NM_017519, intron 4 of 18)	MIRc|SINE|MIR	-217768	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.006173	0.314168	
chunk0044_54_1	chr12	27704036	27704321	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-6595	NM_001190864	60488	Hs.714076	NM_021821	ENSG00000061794	MRPS35	HDCMD11P|MDS023|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding	0.000000	0.356643	
chunk0001_14_1	chr1	1074746	1075091	+	0	NA	promoter-TSS (NM_001205252)	promoter-TSS (NM_001205252)	-611	NM_001205252	401934	Hs.568137	NM_001205252	ENSG00000237330	RNF223	-	ring finger protein 223	protein-coding	0.031884	0.580925	
chunk0052_445_1	chr12	132466754	132467055	+	0	NA	Intergenic	Intergenic	-23667	NM_001142641	57666	Hs.411138	NM_001142641	ENSG00000112787	FBRSL1	-	fibrosin like 1	protein-coding	0.019934	0.612583	142(AGGAACACCCTGTGCC,-,0.00),143(GGAACACCCTGTGCCT,+,0.00),175(AGGAACACTGTGACCA,-,0.00),176(GGAACACTGTGACCAG,+,0.00)
chunk0106_421_1	chr2	208055178	208055825	+	0	NA	Intergenic	Intergenic	-29941	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.010819	0.362654	341(GAGAACAGGGAGTCCA,-,0.00),342(AGAACAGGGAGTCCAA,+,0.00)
chunk0090_78_1	chr18	70381593	70382060	+	0	NA	non-coding (NR_110764, exon 3 of 3)	non-coding (NR_110764, exon 3 of 3)	2765	NR_110764	101060542	Hs.586967	NR_110764	ENSG00000266278	LINC01910	-	long intergenic non-protein coding RNA 1910	ncRNA	0.017131	0.455128	
chunk0093_426_1	chr19	57823701	57824126	+	0	NA	Intergenic	LTR5B|LTR|ERVK	3549	NR_024162	2282	Hs.720356	NR_024162		FKBP1AP1	FKBP12|FKBP1P1	FKBP prolyl isomerase 1A pseudogene 1	pseudo	0.009412	0.502347	199(AGGGACACAATGCACT,-,0.00),200(GGGACACAATGCACTG,+,0.00),312(AAGATCTTACTGTTCC,-,0.00),313(AGATCTTACTGTTCCC,+,0.00)
chunk0115_238_1	chr21	27406397	27406694	+	0	NA	Intergenic	Intergenic	-315834	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.000000	0.389262	
chunk0070_233_1	chr15	72980021	72980355	+	0	NA	Intergenic	L1ME1|LINE|L1	-72296	NM_001172624	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.008982	0.388060	
chunk0065_72_1	chr15	23471357	23471691	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-24281	NM_001304388	283685		NM_182561	ENSG00000174450	GOLGA6L2	CT105	golgin A6 family like 2	protein-coding	0.002994	0.394030	
chunk0045_286_1	chr12	50172952	50173371	+	0	NA	Intergenic	Intergenic	-5628	NR_104035	91012	Hs.270525	NM_147190	ENSG00000139624	CERS5	LASS5|Trh4	ceramide synthase 5	protein-coding	0.002387	0.402381	
chunk0079_146_1	chr17	13159631	13160442	+	0	NA	Intergenic	L2a|LINE|L2	-141972	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.003699	0.432266	
chunk0024_192_1	chr10	36172982	36173823	+	0	NA	Intergenic	Intergenic	395100	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.011891	0.374109	
chunk0177_323_1	chr7	26311433	26312081	+	0	NA	intron (NM_001199835, intron 1 of 6)	intron (NM_001199835, intron 1 of 6)	19862	NM_001199835	29887	Hs.741316	NM_013322	ENSG00000086300	SNX10	OPTB8	sorting nexin 10	protein-coding	0.006173	0.406780	
chunk0036_85_1	chr11	60775501	60775751	+	0	NA	exon (NM_001278242, exon 6 of 6)	exon (NM_001278242, exon 6 of 6)	-9722	NM_206893	341116	Hs.591956	NM_206893	ENSG00000172689	MS4A10	CD20L7|MS4A9	membrane spanning 4-domains A10	protein-coding	0.036000	0.581673	
chunk0005_168_1	chr1	58547045	58547840	+	0	NA	promoter-TSS (NM_145243)	promoter-TSS (NM_145243)	-643	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.008805	0.369347	
chunk0038_308_1	chr11	91292025	91292374	+	0	NA	Intergenic	Intergenic	-422997	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.002865	0.322857	191(AGGAACATTGTGTTTT,-,0.00),192(GGAACATTGTGTTTTA,+,0.00)
chunk0154_108_1	chr5	78546561	78546852	+	0	NA	intron (NM_005779, intron 3 of 4)	intron (NM_005779, intron 3 of 4)	102119	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.013746	0.410959	
chunk0186_445_1	chr7	148129007	148129523	+	0	NA	intron (NM_014141, intron 16 of 23)	intron (NM_014141, intron 16 of 23)	-461300	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.011628	0.442940	
chunk0019_354_1	chr1	229563331	229563545	+	0	NA	Intergenic	Intergenic	-4743	NM_012089	23456	Hs.17614	NM_012089	ENSG00000135776	ABCB10	EST20237|M-ABC2|MTABC2	ATP binding cassette subfamily B member 10	protein-coding	0.018692	0.479070	
chunk0071_438_1	chr15	89958274	89958484	+	0	NA	Intergenic	Intergenic	-43112	NM_198526	374655	Hs.459311	NM_198526	ENSG00000140548	ZNF710	-	zinc finger protein 710	protein-coding	0.023810	0.597156	
chunk0078_230_1	chr17	6587454	6587653	+	0	NA	intron (NM_014804, intron 18 of 18)	intron (NM_014804, intron 18 of 18)	-30996	NM_001165966	83394	Hs.183983	NM_031220	ENSG00000091622	PITPNM3	ACKR6|CORD5|NIR1|RDGBA3	PITPNM family member 3	protein-coding	0.020101	0.425000	
chunk0042_415_1	chr12	11745502	11745987	+	0	NA	intron (NM_001987, intron 1 of 7)	intron (NM_001987, intron 1 of 7)	95890	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.008247	0.446502	
chunk0166_115_1	chr6	44415531	44415836	+	0	NA	intron (NM_001253, intron 8 of 15)	MLT1J|LTR|ERVL-MaLR	-19958	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.006557	0.486928	
chunk0026_154_1	chr10	62488719	62489016	+	0	NA	intron (NM_199451, intron 4 of 7)	intron (NM_199451, intron 4 of 7)	-31581	NM_199452	22891	Hs.22653	NM_014951	ENSG00000138311	ZNF365	Su48|UAN|ZNF365D	zinc finger protein 365	protein-coding	0.010101	0.392617	
chunk0140_445_1	chr4	76280532	76280841	+	0	NA	intron (NM_001242936, intron 7 of 7)	intron (NM_001242936, intron 7 of 7)	-25340	NM_003943	8987	Hs.109590	NM_003943	ENSG00000118804	STBD1	GENEX3414|GENX-3414	starch binding domain 1	protein-coding	0.006472	0.435484	
chunk0196_14_1	chr8	101460075	101460851	+	0	NA	Intergenic	Intergenic	-31977	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.005155	0.423423	
chunk0041_272_1	chr11	129233792	129234358	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-41877	NM_001142685	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.003534	0.261023	
chunk0020_358_1	chr1	239583520	239583899	+	0	NA	Intergenic	Intergenic	-45364	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.002639	0.310526	
chunk0163_245_1	chr6	12416776	12417053	+	0	NA	Intergenic	Intergenic	126618	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.010830	0.413669	
chunk0125_361_1	chr3	71375270	71375955	+	0	NA	intron (NM_032682, intron 3 of 20)	intron (NM_032682, intron 3 of 20)	-70852	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.008759	0.341108	
chunk0074_150_1	chr16	23256343	23256963	+	0	NA	Intergenic	L2a|LINE|L2	-45617	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.008065	0.405797	248(CAGAACAGGCAGTTCA,-,0.00),249(AGAACAGGCAGTTCAC,+,0.00),284(GAGTACACCTTGTTCC,-,0.00),285(AGTACACCTTGTTCCT,+,0.00)
chunk0200_325_1	chr9	23663410	23663855	+	0	NA	intron (NR_121602, intron 3 of 27)	intron (NR_121602, intron 3 of 27)	8767	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.015730	0.412556	
chunk0183_347_1	chr7	108600381	108601066	+	0	NA	Intergenic	Intergenic	-30955	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.001460	0.326531	
chunk0008_106_1	chr1	91385598	91385797	+	0	NA	exon (NM_001017975, exon 5 of 39)	exon (NM_001017975, exon 5 of 39)	19172	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.005025	0.345000	
chunk0035_366_1	chr11	49195206	49195414	+	0	NA	intron (NM_001193473, intron 2 of 16)	L1M5|LINE|L1	13360	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.000000	0.248804	
chunk0020_424_1	chr1	241616246	241616934	+	0	NA	intron (NM_014322, intron 1 of 3)	intron (NM_014322, intron 1 of 3)	19340	NM_001821	1122	Hs.654545	NM_001821	ENSG00000203668	CHML	REP2	CHM like Rab escort protein	protein-coding	0.007267	0.354136	
chunk0035_377_1	chr11	50068629	50069214	+	0	NA	Intergenic	Intergenic	36047	NM_001005513	403257	Hs.554533	NM_001005513	ENSG00000260811	OR4C45	-	olfactory receptor family 4 subfamily C member 45 (gene/pseudogene)	protein-coding	0.003419	0.366894	
chunk0085_392_1	chr18	9954199	9954495	+	0	NA	3' UTR (NM_003574, exon 7 of 7)	3' UTR (NM_003574, exon 7 of 7)	40389	NM_003574	9218	Hs.165195	NM_003574	ENSG00000101558	VAPA	VAP-33|VAP-A|VAP33|hVAP-33	VAMP associated protein A	protein-coding	0.013514	0.353535	246(TGCACATTGAGTCCTT,+,0.00)
chunk0176_145_1	chr7	12941400	12942094	+	0	NA	Intergenic	Intergenic	254461	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.012968	0.346763	
chunk0173_215_1	chr6	145587297	145587727	+	0	NA	Intergenic	Intergenic	-147357	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.357309	
chunk0053_433_1	chr13	38907134	38907791	+	0	NA	Intergenic	L1MC4|LINE|L1	83397	NM_145286	161003	Hs.327794	NM_145286	ENSG00000133115	STOML3	Epb7.2l|SRO	stomatin like 3	protein-coding	0.010654	0.484802	
chunk0032_323_1	chr11	10058226	10058834	+	0	NA	intron (NM_030962, intron 2 of 39)	L1PA14|LINE|L1	219388	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.001645	0.369458	
chunk0044_120_1	chr12	29127056	29127286	+	0	NA	Intergenic	L1MC1|LINE|L1	-21832	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.008696	0.333333	
chunk0054_51_1	chr13	41674687	41675280	+	0	NA	intron (NM_015058, intron 36 of 44)	intron (NM_015058, intron 36 of 44)	-106588	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.001686	0.301347	
chunk0163_367_1	chr6	15906364	15906589	+	0	NA	Intergenic	Intergenic	-222610	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.008889	0.442478	
chunk0110_395_1	chr20	20354689	20354948	+	0	NA	intron (NM_015585, intron 26 of 26)	intron (NM_015585, intron 26 of 26)	-13303	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.003861	0.538462	
chunk0174_338_1	chr6	163958049	163958363	+	0	NA	Intergenic	Intergenic	543563	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.012739	0.412698	
chunk0004_96_1	chr1	43841925	43842148	+	0	NA	intron (NM_001270466, intron 4 of 4)	MSTA-int|LTR|ERVL-MaLR	3414	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.000000	0.415179	
chunk0169_147_1	chr6	101516572	101517038	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	117820	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.310493	
chunk0071_361_1	chr15	88930683	88931044	+	0	NA	Intergenic	Intergenic	-17394	NM_001310319	4240	Hs.3745	NM_005928	ENSG00000140545	MFGE8	BA46|EDIL1|HMFG|HsT19888|MFG-E8|MFGM|OAcGD3S|SED1|SPAG10|hP47	milk fat globule-EGF factor 8 protein	protein-coding	0.005540	0.378453	
chunk0081_311_1	chr17	45654968	45655403	+	0	NA	intron (NM_001256299, intron 3 of 14).2	intron (NM_001256299, intron 3 of 14).2	16210	NR_026906	147081	Hs.128813	NM_152466	ENSG00000204650	LINC02210	C17orf69|CRHR1-IT1	long intergenic non-protein coding RNA 2210	ncRNA	0.004598	0.463303	215(GGATACACACTGTACT,-,0.00),216(GATACACACTGTACTG,+,0.00)
chunk0083_303_1	chr17	69367407	69367951	+	0	NA	Intergenic	Intergenic	-40497	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.007353	0.383486	260(GAGTACTGAGTGTCCT,-,0.00),261(AGTACTGAGTGTCCTG,+,0.00)
chunk0125_438_1	chr3	72743612	72744066	+	0	NA	Intergenic	L2c|LINE|L2	104608	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.013216	0.432967	
chunk0103_3_1	chr2	158735846	158736099	+	0	NA	Intergenic	L1ME4a|LINE|L1	-59345	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.007905	0.350394	
chunk0011_353_1	chr1	152513072	152513271	+	0	NA	TTS (NM_178438)	TTS (NM_178438)	-1331	NM_019060	54544	Hs.110196	NM_019060	ENSG00000169509	CRCT1	C1orf42|NICE-1|NICE1	cysteine rich C-terminal 1	protein-coding	0.005025	0.365000	
chunk0061_104_1	chr14	57717908	57718352	+	0	NA	intron (NM_001306087, intron 1 of 7)	L1MA2|LINE|L1	147744	NM_001206920	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.000000	0.377528	
chunk0087_186_1	chr18	35596755	35596955	+	0	NA	Intergenic	Intergenic	5118	NR_039771	100616257		NR_039771	ENSG00000283514	MIR3975	-	microRNA 3975	ncRNA	0.000000	0.437811	62(AAGACTTGCTGTTCTT,+,0.00),113(CAGCACAGTATGTTCA,-,0.00),114(AGCACAGTATGTTCAT,+,0.00)
chunk0197_113_1	chr8	119891358	119891754	+	0	NA	intron (NM_001283012, intron 1 of 6)	intron (NM_001283012, intron 1 of 6)	17901	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.005051	0.387909	150(GTGTACATTTTGTTCT,-,0.00),151(TGTACATTTTGTTCTT,+,0.00),211(GAGGACGGCCTGTTCA,-,0.00),212(AGGACGGCCTGTTCAT,+,0.00)
chunk0096_47_1	chr2	27015057	27015523	+	0	NA	intron (NM_001303050, intron 1 of 6)	MIR|SINE|MIR	536	NM_001303050	22924	Hs.515860	NM_012326	ENSG00000084764	MAPRE3	EB3|EBF3|EBF3-S|RP3	microtubule associated protein RP/EB family member 3	protein-coding	0.006438	0.498929	
chunk0062_62_1	chr14	67524524	67524930	+	0	NA	Intergenic	Intergenic	-8564	NM_020715	57475	Hs.594236	NM_020715	ENSG00000054690	PLEKHH1	-	pleckstrin homology, MyTH4 and FERM domain containing H1	protein-coding	0.012315	0.457002	197(AAGAACATACTGTATA,-,0.00)
chunk0151_262_1	chr5	52473708	52474313	+	0	NA	Intergenic	L1MA5A|LINE|L1	-313930	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.001653	0.331683	
chunk0068_297_1	chr15	57081933	57082132	+	0	NA	intron (NM_003205, intron 4 of 19)	intron (NM_003205, intron 4 of 19)	-137398	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.000000	0.375000	
chunk0189_167_1	chr8	23410270	23410469	+	0	NA	Intergenic	Intergenic	-6160	NM_002318	4017	Hs.626637	NM_002318	ENSG00000134013	LOXL2	LOR|LOR2|WS9-14	lysyl oxidase like 2	protein-coding	0.020101	0.445000	
chunk0082_35_1	chr17	50828816	50829156	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-6258	NM_175575	124857	Hs.211475	NM_175575	ENSG00000173714	WFIKKN2	GASP-1|WFDC20B|WFIKKNRP|hGASP-1	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	protein-coding	0.011765	0.498534	
chunk0080_95_1	chr17	26854797	26855042	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	439077	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.044898	0.406504	
chunk0201_140_1	chr9	35790080	35790693	+	0	NA	Intergenic	L2c|LINE|L2	-2023	NM_003995	4882	Hs.78518	NM_000907	ENSG00000159899	NPR2	AMDM|ANPRB|ANPb|ECDM|GUC2B|GUCY2B|NPRB|NPRBi|SNSK	natriuretic peptide receptor 2	protein-coding	0.021207	0.490228	297(AGGTACAGCTTGTGCT,-,0.00),298(GGTACAGCTTGTGCTA,+,0.00)
chunk0144_434_1	chr4	140955685	140956040	+	0	NA	intron (NM_020724, intron 2 of 6)	intron (NM_020724, intron 2 of 6)	177600	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.002817	0.367978	
chunk0208_7_1	chrX	10136000	10136423	+	0	NA	intron (NM_015691, intron 19 of 22)	intron (NM_015691, intron 19 of 22)	-20734	NM_001256944	1183	Hs.495674	NM_001830	ENSG00000073464	CLCN4	CLC4|ClC-4|ClC-4A|MRX15|MRX49|MRXSRC	chloride voltage-gated channel 4	protein-coding	0.016548	0.478774	141(AAGCACGCCCTGTCCT,-,0.00),142(AGCACGCCCTGTCCTT,+,0.00)
chunk0163_80_1	chr6	9407935	9409177	+	0	NA	Intergenic	Intergenic	756347	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.006441	0.370877	
chunk0088_395_1	chr18	54424954	54425362	+	0	NA	Intergenic	Intergenic	64630	NM_001288982	162681	Hs.208701	NM_173529	ENSG00000166845	C18orf54	LAS2	chromosome 18 open reading frame 54	protein-coding	0.004902	0.315403	
chunk0194_321_1	chr8	88441767	88442155	+	0	NA	Intergenic	Intergenic	-114473	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.005155	0.321337	
chunk0190_257_1	chr8	37097223	37097776	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	313175	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.014467	0.474729	
chunk0140_65_1	chr4	67092515	67092714	+	0	NA	Intergenic	Intergenic	329386	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.015075	0.445000	
chunk0026_58_1	chr10	61099111	61099417	+	0	NA	Intergenic	Intergenic	82989	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.003268	0.364821	
chunk0204_370_1	chr9	101967437	101968002	+	0	NA	Intergenic	Intergenic	-229139	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.001770	0.300353	289(AAGGACATGTTGTTCT,-,0.00),290(AGGACATGTTGTTCTG,+,0.00)
chunk0156_35_1	chr5	102543826	102544064	+	0	NA	Intergenic	Intergenic	-37423	NR_047462	100861468	Hs.519483	NR_047462	ENSG00000250958	LINC00492	-	long intergenic non-protein coding RNA 492	ncRNA	0.000000	0.397490	81(AAGGACAGAGTGACCA,-,0.00),82(AGGACAGAGTGACCAT,+,0.00)
chunk0036_23_1	chr11	58444155	58444457	+	0	NA	Intergenic	Intergenic	-4133	NM_001004733	390191	Hs.553754	NM_001004733	ENSG00000172362	OR5B12	OR11-241|OR5B12P|OR5B16|OST743	olfactory receptor family 5 subfamily B member 12	protein-coding	0.006623	0.524752	
chunk0167_191_1	chr6	64431455	64432420	+	0	NA	intron (NM_001142800, intron 28 of 42)	intron (NM_001142800, intron 28 of 42)	785411	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.004145	0.347826	138(AAGGACAGTGAGTACT,-,0.00),139(AGGACAGTGAGTACTC,+,0.00)
chunk0093_194_1	chr19	49256756	49257025	+	0	NA	Intergenic	Intergenic	51978	NR_036209	100422979		NR_036209	ENSG00000265407	MIR4324	mir-4324	microRNA 4324	ncRNA	0.003717	0.422222	
chunk0027_142_1	chr10	74593185	74593833	+	0	NA	intron (NM_001123, intron 8 of 10)	L2b|LINE|L2	-64185	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.003086	0.368259	365(GAGAACTTAATGTACT,-,0.00),366(AGAACTTAATGTACTA,+,0.00)
chunk0205_317_1	chr9	112751407	112751683	+	0	NA	intron (NM_001012994, intron 1 of 8)	intron (NM_001012994, intron 1 of 8)	691	NM_001012994	401548	Hs.522350	NM_001012994	ENSG00000148158	SNX30	ATG24A	sorting nexin family member 30	protein-coding	0.036232	0.588448	
chunk0119_169_1	chr22	43354534	43354838	+	0	NA	Intergenic	L1MB4|LINE|L1	-11298	NM_173050	80274	Hs.133995	NM_152514	ENSG00000159307	SCUBE1	-	signal peptide, CUB domain and EGF like domain containing 1	protein-coding	0.013158	0.449180	
chunk0162_390_1	chr5	179595868	179596345	+	0	NA	non-coding (NR_110560, exon 9 of 9)	non-coding (NR_110560, exon 9 of 9)	7635	NR_110560	101928445	Hs.663255	NR_110560	ENSG00000244945	LOC101928445	-	uncharacterized LOC101928445	ncRNA	0.014675	0.395397	
chunk0165_457_1	chr6	40962135	40962656	+	0	NA	intron (NR_110873, intron 1 of 5)	intron (NR_110873, intron 1 of 5)	60885	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.007678	0.473180	
chunk0139_357_1	chr4	60245042	60245535	+	0	NA	Intergenic	Intergenic	-677331	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.004057	0.305668	
chunk0212_256_1	chrX	139200879	139201103	+	0	NA	intron (NM_001139501, intron 2 of 7)	intron (NM_001139501, intron 2 of 7)	4032	NM_001139500	2258	Hs.6540	NM_004114	ENSG00000129682	FGF13	FGF-13|FGF2|FHF-2|FHF2|LINC00889	fibroblast growth factor 13	protein-coding	0.017857	0.373333	
chunk0159_77_1	chr5	137609818	137610352	+	0	NA	Intergenic	L1MB7|LINE|L1	37564	NR_030588	100126343		NR_030588	ENSG00000216009	MIR874	MIRN874|hsa-mir-874|mir-874	microRNA 874	ncRNA	0.000000	0.342056	189(CAGAACTGCCAGTCCA,-,0.00),190(AGAACTGCCAGTCCAT,+,0.00)
chunk0059_237_1	chr14	34374946	34375341	+	0	NA	Intergenic	Intergenic	87119	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.005063	0.391414	295(TTGAACAGTTTGTTCT,-,0.00),296(TGAACAGTTTGTTCTC,+,0.00)
chunk0045_194_1	chr12	47393663	47393888	+	0	NA	Intergenic	Intergenic	-29506	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.008889	0.345133	
chunk0076_173_1	chr16	67441327	67441915	+	0	NA	intron (NM_004691, intron 4 of 7)	intron (NM_004691, intron 4 of 7)	10488	NM_000196	3291	Hs.1376	NM_000196	ENSG00000176387	HSD11B2	AME|AME1|HSD11K|HSD2|SDR9C3	hydroxysteroid 11-beta dehydrogenase 2	protein-coding	0.030612	0.572156	
chunk0064_264_1	chr14	94730493	94731304	+	0	NA	Intergenic	L1MC3|LINE|L1	39264	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.006165	0.357143	
chunk0135_263_1	chr3	189104307	189104705	+	0	NA	Intergenic	Intergenic	-67468	NM_198485	285386	Hs.729544	NM_198485	ENSG00000188001	TPRG1	FAM79B	tumor protein p63 regulated 1	protein-coding	0.015075	0.380952	
chunk0115_374_1	chr21	30223801	30224253	+	0	NA	Intergenic	L2b|LINE|L2	-7876	NM_199328	9073	Hs.162209	NM_012132	ENSG00000156284	CLDN8	HEL-S-79	claudin 8	protein-coding	0.013274	0.403974	
chunk0072_299_1	chr15	98749021	98749641	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-35095	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.006452	0.322061	
chunk0196_187_1	chr8	106103273	106103786	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-43026	NR_125797	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.003899	0.426070	
chunk0187_46_1	chr8	1634332	1634961	+	0	NA	intron (NM_001277161, intron 5 of 10)	intron (NM_001277161, intron 5 of 10)	-12982	NR_103863	100507435	Hs.667133	NR_103863	ENSG00000253267	DLGAP2-AS1	-	DLGAP2 antisense RNA 1	ncRNA	0.011129	0.420635	
chunk0038_302_1	chr11	90765428	90765705	+	0	NA	intron (NR_104190, intron 3 of 6)	intron (NR_104190, intron 3 of 6)	103636	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.003610	0.298561	
chunk0094_139_1	chr2	4954160	4954750	+	0	NA	Intergenic	Intergenic	-298233	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.001695	0.355330	
chunk0033_456_1	chr11	25677604	25677967	+	0	NA	Intergenic	L1MA4|LINE|L1	-511338	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.005510	0.332418	
chunk0178_184_1	chr7	34246403	34246899	+	0	NA	Intergenic	MER3|DNA|hAT-Charlie	341740	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.002016	0.374245	302(TGGGCAGGCTGTGCTC,+,0.00)
chunk0154_102_1	chr5	78294066	78294461	+	0	NA	intron (NM_003664, intron 1 of 26)	intron (NM_003664, intron 1 of 26)	492	NM_001271769	8546	Hs.532091	NM_003664	ENSG00000132842	AP3B1	ADTB3|ADTB3A|HPS|HPS2|PE	adaptor related protein complex 3 subunit beta 1	protein-coding	0.040506	0.547980	
chunk0024_198_1	chr10	36375146	36375345	+	0	NA	Intergenic	Intergenic	596943	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.000000	0.335000	
chunk0138_218_1	chr4	38925829	38926364	+	0	NA	intron (NR_033290, intron 7 of 12)	MIRc|SINE|MIR	58064	NR_030300	693159		NR_030300	ENSG00000207944	MIR574	MIR574-3p|MIRN574|hsa-mir-574|mir-574	microRNA 574	ncRNA	0.003738	0.423507	418(CAGAACTCTCTGTGCT,-,0.00),419(AGAACTCTCTGTGCTC,+,0.00)
chunk0098_259_1	chr2	75261696	75262226	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-62442	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.001887	0.391714	
chunk0005_162_1	chr1	58446482	58447083	+	0	NA	Intergenic	Intergenic	100017	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.001664	0.426910	75(AAGTGCATGCTGTTCT,-,0.00),76(AGTGCATGCTGTTCTC,+,0.00)
chunk0098_404_1	chr2	79850587	79850818	+	0	NA	intron (NM_004389, intron 3 of 17)	MIR|SINE|MIR	15881	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.004329	0.379310	
chunk0070_390_1	chr15	76799741	76799940	+	0	NA	intron (NM_020843, intron 6 of 30)	MER70A|LTR|ERVL	62104	NM_001145923	49855	Hs.458986	NM_020843	ENSG00000140386	SCAPER	IDDRP|MSTP063|ZNF291|Zfp291	S-phase cyclin A associated protein in the ER	protein-coding	0.010050	0.465000	
chunk0132_226_1	chr3	158098014	158098464	+	0	NA	exon (NM_003030, exon 6 of 6)	exon (NM_003030, exon 6 of 6)	7924	NM_001163678	6474	Hs.55967	NM_003030	ENSG00000168779	SHOX2	OG12|OG12X|SHOT	short stature homeobox 2	protein-coding	0.080000	0.618625	
chunk0167_44_1	chr6	55447864	55448295	+	0	NA	intron (NR_109869, intron 3 of 4)	L1M5|LINE|L1	120610	NM_207410	389400	Hs.526967	NM_207410	ENSG00000187871	GFRAL	C6orf144|GRAL|UNQ9356|bA360D14.1	GDNF family receptor alpha like	protein-coding	0.006961	0.314815	
chunk0123_451_1	chr3	50963404	50963635	+	0	NA	intron (NM_004947, intron 5 of 52)	L1M5|LINE|L1	288278	NM_004947	1795	Hs.476284	NM_004947	ENSG00000088538	DOCK3	MOCA|NEDIDHA|PBP	dedicator of cytokinesis 3	protein-coding	0.004329	0.301724	
chunk0115_232_1	chr21	27325950	27326695	+	0	NA	Intergenic	Intergenic	-359202	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.008054	0.300268	
chunk0063_273_1	chr14	84124588	84125189	+	0	NA	Intergenic	Intergenic	-1268991	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.004992	0.315615	
chunk0187_325_1	chr7	156656064	156656387	+	0	NA	intron (NR_131778, intron 4 of 8)	MIRc|SINE|MIR	12424	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.012384	0.345679	
chunk0060_337_1	chr14	51626311	51626534	+	0	NA	intron (NM_001042481, intron 2 of 14)	MIRb|SINE|MIR	25322	NR_037676	145438	Hs.645410	NR_037676	ENSG00000273888	FRMD6-AS1	C14orf82	FRMD6 antisense RNA 1	ncRNA	0.008969	0.366071	
chunk0053_135_1	chr13	29917374	29917584	+	0	NA	Intergenic	Intergenic	9172	NR_047501	100861573	Hs.585619	NR_047501	ENSG00000224405	LINC00572	-	long intergenic non-protein coding RNA 572	ncRNA	0.004762	0.417062	
chunk0013_210_1	chr1	169467800	169468780	+	0	NA	intron (NM_006996, intron 4 of 5)	intron (NM_006996, intron 4 of 5)	-7621	NM_001300968	57821	Hs.567557	NM_021179	ENSG00000117477	CCDC181	C1orf114	coiled-coil domain containing 181	protein-coding	0.006122	0.373089	
chunk0183_206_1	chr7	106417466	106417665	+	0	NA	Intergenic	Intergenic	-132373	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.010050	0.480000	
chunk0068_121_1	chr15	52568403	52568985	+	0	NA	intron (NM_001306191, intron 3 of 5)	CpG	438	NM_006628	10776	Hs.512908	NM_006628	ENSG00000128989	ARPP19	ARPP-16|ARPP-19|ARPP16|ENSAL	cAMP regulated phosphoprotein 19	protein-coding	0.092784	0.631218	
chunk0091_281_1	chr19	11713497	11714041	+	0	NA	Intergenic	L1M4b|LINE|L1	25240	NM_017507	55552	Hs.142167	NM_017507	ENSG00000197933	ZNF823	HSZFP36	zinc finger protein 823	protein-coding	0.003676	0.330275	
chunk0016_140_1	chr1	197222248	197222649	+	0	NA	intron (NM_001257965, intron 1 of 14)	intron (NM_001257965, intron 1 of 14)	20986	NM_001257965	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.024938	0.477612	
chunk0176_443_1	chr7	20006982	20007918	+	0	NA	intron (NR_110114, intron 3 of 5)	MLT1J1|LTR|ERVL-MaLR	132976	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.003205	0.394877	
chunk0111_256_1	chr20	30813783	30814120	+	0	NA	Intergenic	CpG	-410489	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.094955	0.704142	
chunk0117_278_1	chr22	24207939	24208675	+	0	NA	Intergenic	L1ME4b|LINE|L1	26831	NM_019601	56241	Hs.131819	NM_019601	ENSG00000099994	SUSD2	BK65A6.2|W5C5	sushi domain containing 2	protein-coding	0.002717	0.401628	
chunk0169_18_1	chr6	96765156	96765409	+	0	NA	Intergenic	Intergenic	72195	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.007905	0.492126	
chunk0167_227_1	chr6	67143531	67144148	+	0	NA	Intergenic	L1MD1|LINE|L1	-911512	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.003241	0.320388	367(TGCACAATATGTACCT,+,0.00)
chunk0178_55_1	chr7	30027314	30027513	+	0	NA	promoter-TSS (NM_001197026)	promoter-TSS (NM_001197026)	-612	NR_046479	55033	Hs.390838	NM_017946	ENSG00000106080	FKBP14	EDSKMH|EDSKSCL2|FKBP22|IPBP12	FKBP prolyl isomerase 14	protein-coding	0.025126	0.355000	
chunk0107_341_1	chr2	221514920	221515119	+	0	NA	intron (NM_001304536, intron 4 of 18)	intron (NM_001304536, intron 4 of 18)	57339	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.005025	0.320000	17(AAGAACAGCATGTCAC,-,0.00),18(AGAACAGCATGTCACT,+,0.00)
chunk0029_222_1	chr10	102280581	102281089	+	0	NA	intron (NM_001199378, intron 3 of 39)	intron (NM_001199378, intron 3 of 39)	35337	NM_001199379	8729	Hs.290243	NM_004193	ENSG00000107862	GBF1	ARF1GEF	golgi brefeldin A resistant guanine nucleotide exchange factor 1	protein-coding	0.003937	0.445972	
chunk0114_155_1	chr21	10430077	10430365	+	0	NA	intron (NM_001187, intron 3 of 4)	MER20|DNA|hAT-Charlie	16689	NM_182484	85316	Hs.545789	NM_182484		BAGE5	CT2.5	BAGE family member 5	protein-coding	0.003472	0.463668	
chunk0140_143_1	chr4	69280029	69280663	+	0	NA	promoter-TSS (NM_001207004)	promoter-TSS (NM_001207004)	-153	NM_053039	54490	Hs.653154	NM_053039	ENSG00000135226	UGT2B28	-	UDP glucuronosyltransferase family 2 member B28	protein-coding	0.009464	0.360630	
chunk0149_236_1	chr5	23420629	23420851	+	0	NA	Intergenic	Intergenic	-86869	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.000000	0.331839	
chunk0148_52_1	chr5	1507561	1507776	+	0	NA	intron (NM_024830, intron 1 of 13)	intron (NM_024830, intron 1 of 13)	3188	NR_106723	102466103		NR_106723	ENSG00000273742	MIR6075	hsa-mir-6075	microRNA 6075	ncRNA	0.060465	0.648148	
chunk0020_284_1	chr1	236860609	236860934	+	0	NA	intron (NM_001291939, intron 19 of 31)	intron (NM_001291939, intron 19 of 31)	65490	NM_001291939	4548	Hs.498187	NM_000254	ENSG00000116984	MTR	HMAG|MS|cblG	5-methyltetrahydrofolate-homocysteine methyltransferase	protein-coding	0.003077	0.300613	
chunk0118_235_1	chr22	32474477	32474710	+	0	NA	promoter-TSS (NM_001257990)	promoter-TSS (NM_001257990)	-127	NM_012179	25793	Hs.5912	NM_012179	ENSG00000100225	FBXO7	FBX|FBX07|FBX7|PARK15|PKPS	F-box protein 7	protein-coding	0.090129	0.641026	117(AAGTACTGGGAGTCCC,-,0.00)
chunk0019_288_1	chr1	228781068	228781582	+	0	NA	Intergenic	Intergenic	46248	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.011673	0.419417	
chunk0166_413_1	chr6	52475321	52476120	+	0	NA	intron (NM_018100, intron 7 of 10)	Charlie7a|DNA|hAT-Charlie	54713	NM_001172420	114327	Hs.403171	NM_018100	ENSG00000096093	EFHC1	EJM1|dJ304B14.2	EF-hand domain containing 1	protein-coding	0.006258	0.385000	
chunk0042_113_1	chr12	3233905	3234184	+	0	NA	intron (NM_001168320, intron 2 of 7)	intron (NM_001168320, intron 2 of 7)	-147305	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.017921	0.485714	
chunk0172_337_1	chr6	138645277	138645581	+	0	NA	Intergenic	L2a|LINE|L2	-46239	NR_033896	441172	Hs.92290	NR_033896		FLJ46906	-	uncharacterized LOC441172	ncRNA	0.013158	0.445902	
chunk0034_310_1	chr11	35074167	35074496	+	0	NA	Intergenic	L1ME1|LINE|L1	63701	NR_120528	100507144	Hs.673491	NR_120528	ENSG00000255521	LOC100507144	-	uncharacterized LOC100507144	ncRNA	0.003040	0.348485	
chunk0035_305_1	chr11	47189245	47189915	+	0	NA	Intergenic	L2c|LINE|L2	-3121	NM_016223	29763	Hs.334639	NM_016223	ENSG00000165912	PACSIN3	SDPIII	protein kinase C and casein kinase substrate in neurons 3	protein-coding	0.008955	0.432191	
chunk0085_156_1	chr18	3595859	3596072	+	0	NA	intron (NR_024101, intron 2 of 2)	intron (NR_024101, intron 2 of 2)	1851	NR_024101	649446	Hs.19872	NM_001039796		DLGAP1-AS1	HsT914	DLGAP1 antisense RNA 1	ncRNA	0.000000	0.443925	
chunk0069_405_1	chr15	67917459	67918020	+	0	NA	Intergenic	LTR23|LTR|ERV1	-77694	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.001783	0.380783	
chunk0113_349_1	chr20	58941627	58942184	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	-39303	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.003591	0.344086	
chunk0008_165_1	chr1	92792017	92792249	+	0	NA	intron (NM_001308248, intron 1 of 18)	intron (NM_001308248, intron 1 of 18)	271	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.017241	0.339056	
chunk0129_219_1	chr3	121844720	121845309	+	0	NA	intron (NM_018456, intron 2 of 5)	L2c|LINE|L2	9827	NM_018456	55840	Hs.477325	NM_018456	ENSG00000145088	EAF2	BM040|TRAITS|U19	ELL associated factor 2	protein-coding	0.013582	0.381356	
chunk0210_257_1	chrX	83896138	83896382	+	0	NA	Intergenic	L1M1|LINE|L1	35134	NM_001271680	1538	Hs.444230	NM_021118	ENSG00000183035	CYLC1	CYCL1	cylicin 1	protein-coding	0.004098	0.338776	
chunk0201_109_1	chr9	35103146	35103345	+	0	NA	promoter-TSS (NM_013442)	promoter-TSS (NM_013442)	-50	NM_001287031	30968	Hs.3439	NM_013442	ENSG00000165283	STOML2	HSPC108|SLP-2	stomatin like 2	protein-coding	0.070352	0.585000	
chunk0150_113_1	chr5	32887389	32887835	+	0	NA	Intergenic	Intergenic	-59831	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.006726	0.375839	
chunk0052_143_1	chr13	23756025	23756229	+	0	NA	intron (NM_005932, intron 18 of 18)	intron (NM_005932, intron 18 of 18)	-132762	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.004902	0.356098	
chunk0045_426_1	chr12	53382321	53382902	+	0	NA	exon (NM_001251825, exon 3 of 6)	exon (NM_001251825, exon 3 of 6)	1967	NM_003109	6667	Hs.620754	NM_003109	ENSG00000185591	SP1	-	Sp1 transcription factor	protein-coding	0.010327	0.522337	
chunk0209_93_1	chrX	39336651	39337645	+	0	NA	Intergenic	Intergenic	-9786	NR_038968	286442	Hs.638478	NR_038968	ENSG00000235304	LINC01281	-	long intergenic non-protein coding RNA 1281	ncRNA	0.008048	0.470352	
chunk0125_432_1	chr3	72628196	72628407	+	0	NA	Intergenic	Intergenic	-181678	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.023697	0.599057	
chunk0186_143_1	chr7	138755429	138755631	+	0	NA	intron (NM_130840, intron 9 of 20)	intron (NM_130840, intron 9 of 20)	18507	NM_130841	50617	Hs.98967	NM_020632	ENSG00000105929	ATP6V0A4	A4|ATP6N1B|ATP6N2|RDRTA2|RTA1C|RTADR|STV1|VPH1|VPP2	ATPase H+ transporting V0 subunit a4	protein-coding	0.009901	0.536946	
chunk0155_24_1	chr5	90981731	90982002	+	0	NA	intron (NR_003149, intron 84 of 89)	MER6|DNA|TcMar-Tigger	332536	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.000000	0.367647	
chunk0181_201_1	chr7	84022663	84022877	+	0	NA	intron (NM_006080, intron 6 of 16)	intron (NM_006080, intron 6 of 16)	172131	NM_006080	10371	Hs.252451	NM_006080	ENSG00000075213	SEMA3A	COLL1|HH16|Hsema-I|Hsema-III|SEMA1|SEMAD|SEMAIII|SEMAL|SemD|coll-1	semaphorin 3A	protein-coding	0.004673	0.381395	
chunk0183_213_1	chr7	106466925	106467547	+	0	NA	Intergenic	LTR56|LTR|ERV1	-182044	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.008039	0.398074	
chunk0174_332_1	chr6	163627498	163627997	+	0	NA	Intergenic	Intergenic	213104	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.012024	0.464000	271(CTGCACACACTGTTCT,-,0.00),272(TGCACACACTGTTCTT,+,0.00),320(TGGAACTCCGTGTGCA,-,0.00),321(GGAACTCCGTGTGCAG,+,0.00)
chunk0025_99_1	chr10	50579882	50580456	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	43808	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.005226	0.356522	
chunk0015_101_1	chr1	185091562	185091816	+	0	NA	exon (NM_007212, exon 3 of 7)	exon (NM_007212, exon 3 of 7)	46270	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.011811	0.384314	
chunk0016_52_1	chr1	193269537	193270168	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	-34893	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.006339	0.325949	
chunk0157_257_1	chr5	119916229	119916529	+	0	NA	Intergenic	Intergenic	286820	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.000000	0.308970	162(TGGTACACTTTGTGCT,-,0.00),163(GGTACACTTTGTGCTA,+,0.00)
chunk0202_82_1	chr9	71911723	71912254	+	0	NA	promoter-TSS (NM_016014)	promoter-TSS (NM_016014)	481	NM_182505	138241	Hs.534190	NM_182505	ENSG00000155621	C9orf85	-	chromosome 9 open reading frame 85	protein-coding	0.030132	0.471805	
chunk0037_337_1	chr11	77316646	77316952	+	0	NA	Intergenic	Intergenic	-29381	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.009804	0.364821	
chunk0046_235_1	chr12	60255991	60256444	+	0	NA	Intergenic	Intergenic	566880	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.004415	0.301762	
chunk0008_415_1	chr1	98409872	98410521	+	0	NA	Intergenic	Intergenic	199485	NR_046088	729987	Hs.683961	NR_046088	ENSG00000226053	LINC01776	-	long intergenic non-protein coding RNA 1776	ncRNA	0.004622	0.332308	372(CAGCACACAGTGTGCT,-,0.00),373(AGCACACAGTGTGCTA,+,0.00)
chunk0087_294_1	chr18	38980358	38980817	+	0	NA	Intergenic	L2|LINE|L2	641588	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.000000	0.408696	
chunk0058_151_1	chr14	23153869	23154400	+	0	NA	intron (NM_012244, intron 3 of 10)	intron (NM_012244, intron 3 of 10)	316	NM_001267037	23428	Hs.596643	NM_012244	ENSG00000092068	SLC7A8	LAT2|LPI-PC1	solute carrier family 7 member 8	protein-coding	0.013183	0.541353	261(CAGAACGCCCTGTTCC,-,0.00),262(AGAACGCCCTGTTCCT,+,0.00)
chunk0211_89_1	chrX	110229960	110230394	+	0	NA	intron (NM_001025580, intron 1 of 4)	L1PA6|LINE|L1	-5117	NR_004379	692226		NR_004379	ENSG00000208883	SNORD96B	U96b	small nucleolar RNA, C/D box 96B	snoRNA	0.020737	0.537931	
chunk0130_227_1	chr3	134374943	134375339	+	0	NA	promoter-TSS (NM_016201)	promoter-TSS (NM_016201)	276	NM_001278683	51421	Hs.426312	NM_016201	ENSG00000114019	AMOTL2	LCCP	angiomotin like 2	protein-coding	0.042929	0.561713	
chunk0134_351_1	chr3	182571145	182571508	+	0	NA	Intergenic	MIRb|SINE|MIR	-84964	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.002755	0.387363	
chunk0042_463_1	chr12	12606762	12607045	+	0	NA	Intergenic	Intergenic	-4930	NM_001310	1389	Hs.591156	NM_001310	ENSG00000111269	CREBL2	-	cAMP responsive element binding protein like 2	protein-coding	0.000000	0.390845	
chunk0166_163_1	chr6	45748797	45749364	+	0	NA	Intergenic	Intergenic	188517	NR_045674	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.003527	0.295775	
chunk0174_274_1	chr6	161548660	161549160	+	0	NA	exon (NM_004562, exon 9 of 12)	exon (NM_004562, exon 9 of 12)	-274835	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.014000	0.471058	
chunk0164_49_1	chr6	19002524	19002900	+	0	NA	Intergenic	Intergenic	177768	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.000000	0.312997	
chunk0166_406_1	chr6	52078275	52078538	+	0	NA	intron (NM_138694, intron 5 of 66)	intron (NM_138694, intron 5 of 66)	9219	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.011407	0.477273	
chunk0042_106_1	chr12	3069409	3070316	+	0	NA	Intergenic	Intergenic	-7493	NM_006675	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.011025	0.432819	
chunk0126_270_1	chr3	79909237	79909717	+	0	NA	Intergenic	MER41A|LTR|ERV1	-141568	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002083	0.461538	
chunk0177_16_1	chr7	20534206	20534804	+	0	NA	Intergenic	Intergenic	-81117	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.001672	0.330551	242(AAGAACACTGTGTACT,-,0.00),243(AGAACACTGTGTACTT,+,0.00)
chunk0001_187_1	chr1	7331909	7332772	+	0	NA	intron (NM_015215, intron 5 of 22)	intron (NM_015215, intron 5 of 22)	-438929	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.016222	0.444444	
chunk0113_6_1	chr20	49287048	49287320	+	0	NA	intron (NR_003604, intron 4 of 4)	LTR10B1|LTR|ERV1	6501	NR_003030	692057		NR_003030	ENSG00000212304	SNORD12	HBII-99|MIR1259|MIRN1259	small nucleolar RNA, C/D box 12	snoRNA	0.003676	0.450549	
chunk0047_256_1	chr12	72485514	72485727	+	0	NA	intron (NM_013381, intron 5 of 18)	L1MA9|LINE|L1	-212111	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.014085	0.588785	
chunk0098_341_1	chr2	77203447	77203946	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	217731	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.002004	0.390000	305(AGGTACAGCCAGTGCA,-,0.00),306(GGTACAGCCAGTGCAT,+,0.00),383(AGAAACATACTGTTCC,-,0.00),384(GAAACATACTGTTCCA,+,0.00)
chunk0020_352_1	chr1	239448836	239449356	+	0	NA	Intergenic	Intergenic	-179977	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.005769	0.318618	
chunk0032_41_1	chr11	1261923	1262292	+	0	NA	TTS (NM_002458)	TTS (NM_002458)	5502	NR_106802	102466725		NR_106802	ENSG00000275669	MIR6744	hsa-mir-6744	microRNA 6744	ncRNA	0.048780	0.648649	
chunk0051_189_1	chr12	116221442	116221974	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	55478	NM_015335	23389	Hs.603766	NM_015335	ENSG00000123066	MED13L	MRFACD|PROSIT240|THRAP2|TRAP240L	mediator complex subunit 13L	protein-coding	0.003759	0.285178	
chunk0152_107_1	chr5	58460295	58460843	+	0	NA	promoter-TSS (NM_006622)	promoter-TSS (NM_006622)	-430	NM_006622	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.105839	0.719490	
chunk0093_30_1	chr19	39304295	39304633	+	0	NA	Intergenic	Intergenic	8139	NM_172140	282618	Hs.406745	NM_172140	ENSG00000182393	IFNL1	IL-29|IL29	interferon lambda 1	protein-coding	0.002959	0.463127	61(TTGCACATGCTGTTCC,-,0.00),62(TGCACATGCTGTTCCC,+,0.00)
chunk0119_419_1	chr22	49831591	49832377	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-4436	NM_001304808	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.012723	0.514612	
chunk0071_432_1	chr15	89858541	89859167	+	0	NA	intron (NM_001199058, intron 8 of 9)	intron (NM_001199058, intron 8 of 9)	-8133	NR_049817	100847059		NR_049817	ENSG00000264966	MIR5094	-	microRNA 5094	ncRNA	0.009585	0.384370	521(TGCTCAGGCTGTTCTC,+,0.00)
chunk0130_44_1	chr3	129225122	129225416	+	0	NA	Intergenic	Intergenic	-24341	NM_016128	22820	Hs.518250	NM_016128	ENSG00000181789	COPG1	COPG	coatomer protein complex subunit gamma 1	protein-coding	0.023810	0.515254	
chunk0121_456_1	chr3	26978700	26979292	+	0	NA	Intergenic	Intergenic	237527	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.001689	0.269815	
chunk0197_165_1	chr8	120778086	120778367	+	0	NA	intron (NM_021021, intron 1 of 6)	intron (NM_021021, intron 1 of 6)	16973	NR_125419	101927543	Hs.371902	NR_125419	ENSG00000248318	LOC101927543	-	uncharacterized LOC101927543	ncRNA	0.007117	0.375887	
chunk0145_383_1	chr4	151664211	151664751	+	0	NA	TTS (NM_001109977)	TTS (NM_001109977)	96542	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.005556	0.475046	
chunk0077_226_1	chr16	80414165	80414555	+	0	NA	intron (NR_120307, intron 2 of 5)	L2c|LINE|L2	-126374	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.005128	0.460358	
chunk0031_451_1	chr10	132679911	132680371	+	0	NA	intron (NM_005539, intron 4 of 15)	L1MB3|LINE|L1	105892	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.028261	0.416486	
chunk0213_21_1	chrY	22211785	22212103	+	0	NA	Intergenic	Intergenic	-29002	NM_152585	159163	Hs.567746	NM_152585	ENSG00000169800	RBMY1F	YRRM2	RNA binding motif protein, Y-linked, family 1, member F	protein-coding	0.000000	0.307210	
chunk0092_353_1	chr19	35437250	35437683	+	0	NA	Intergenic	Intergenic	-12249	NM_005306	2867	Hs.248056	NM_005306	ENSG00000126262	FFAR2	FFA2R|GPR43	free fatty acid receptor 2	protein-coding	0.006928	0.495392	
chunk0153_68_1	chr5	67921158	67921357	+	0	NA	Intergenic	L2c|LINE|L2	128044	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.010050	0.430000	
chunk0005_412_1	chr1	62613968	62614340	+	0	NA	intron (NM_001272001, intron 14 of 47)	intron (NM_001272001, intron 14 of 47)	16667	NM_014495	27329	Hs.209153	NM_014495	ENSG00000132855	ANGPTL3	ANG-5|ANGPT5|ANL3|FHBL2	angiopoietin like 3	protein-coding	0.002688	0.316354	
chunk0061_39_1	chr14	56056730	56057506	+	0	NA	Intergenic	Intergenic	-61257	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.010309	0.442728	
chunk0073_305_1	chr16	14117063	14117515	+	0	NA	intron (NM_001308142, intron 2 of 16)	L2c|LINE|L2	45975	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.002212	0.439294	22(GATCACACTCTGTTCT,-,0.00),23(ATCACACTCTGTTCTT,+,0.00)
chunk0112_89_1	chr20	38059789	38060369	+	0	NA	intron (NM_021215, intron 5 of 6)	intron (NM_021215, intron 5 of 6)	26533	NM_021215	58490	Hs.278839	NM_021215	ENSG00000101413	RPRD1B	C20orf77|CREPT|K-H|Kub5-Hera|NET60|dJ1057B20.2	regulation of nuclear pre-mRNA domain containing 1B	protein-coding	0.010345	0.444062	
chunk0085_398_1	chr18	10040969	10041669	+	0	NA	Intergenic	MER70B|LTR|ERVL	127361	NM_003574	9218	Hs.165195	NM_003574	ENSG00000101558	VAPA	VAP-33|VAP-A|VAP33|hVAP-33	VAMP associated protein A	protein-coding	0.000000	0.415121	340(CAGAACAGGATGTTCT,-,0.00),341(AGAACAGGATGTTCTG,+,0.00)
chunk0131_160_1	chr3	146473633	146474286	+	0	NA	intron (NM_020359, intron 1 of 8)	intron (NM_020359, intron 1 of 8)	-4658	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.003063	0.337920	286(AAGAACAATATGTTCT,-,0.00),287(AGAACAATATGTTCTT,+,0.00)
chunk0155_427_1	chr5	100526328	100526527	+	0	NA	Intergenic	L1PB|LINE|L1	-8878	NM_198507	345757	Hs.356108	NM_198507	ENSG00000174132	FAM174A	HGS_RE408|NS5ATP6|TMEM157|UNQ1912	family with sequence similarity 174 member A	protein-coding	0.000000	0.330000	
chunk0018_285_1	chr1	220727348	220727641	+	0	NA	Intergenic	L1ME3B|LINE|L1	-20840	NM_017898	54996	Hs.369042	NM_017898	ENSG00000117791	MARC2	MOSC2	mitochondrial amidoxime reducing component 2	protein-coding	0.003413	0.316327	
chunk0027_458_1	chr10	81775706	81776420	+	0	NA	Intergenic	PrimLTR79|LTR|ERV1	-99251	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.007003	0.386014	
chunk0136_247_1	chr4	10102779	10103124	+	0	NA	intron (NM_017491, intron 3 of 14)	(ATGA)n|Simple_repeat|Simple_repeat	13998	NM_005112	9948	Hs.128548	NM_005112	ENSG00000071127	WDR1	AIP1|HEL-S-52|NORI-1	WD repeat domain 1	protein-coding	0.005797	0.505780	
chunk0053_40_1	chr13	27393230	27393859	+	0	NA	Intergenic	L1MD1|LINE|L1	-31000	NM_002097	2971	Hs.445977	NM_002097	ENSG00000122034	GTF3A	AP2|TFIIIA	general transcription factor IIIA	protein-coding	0.015898	0.392063	
chunk0133_117_1	chr3	168186656	168186855	+	0	NA	Intergenic	Charlie8|DNA|hAT-Charlie	-62767	NR_021485	93556	Hs.478158	NR_021485		EGFEM1P	C3orf50|NCRNA00259	EGF like and EMI domain containing 1, pseudogene	pseudo	0.010050	0.435000	
chunk0192_373_1	chr8	68429387	68429600	+	0	NA	intron (NM_052958, intron 1 of 13)	L1ME3B|LINE|L1	-98002	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.009390	0.373832	
chunk0049_286_1	chr12	93983674	93983991	+	0	NA	Intergenic	Intergenic	-164891	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.000000	0.474843	
chunk0124_80_1	chr3	53243991	53244190	+	0	NA	intron (NR_047580, intron 1 of 13)	intron (NR_047580, intron 1 of 13)	12024	NM_001135055	7086	Hs.89643	NM_001064	ENSG00000163931	TKT	HEL-S-48|HEL107|SDDHD|TK|TKT1	transketolase	protein-coding	0.015075	0.545000	
chunk0168_56_1	chr6	78875372	78876231	+	0	NA	intron (NM_001010844, intron 1 of 3)	L1PA17|LINE|L1	8257	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.006985	0.373256	
chunk0075_146_1	chr16	50530859	50531103	+	0	NA	Intergenic	Intergenic	-17349	NM_033119	85407	Hs.187578	NM_033119	ENSG00000140807	NKD1	Naked1	NKD inhibitor of WNT signaling pathway 1	protein-coding	0.024590	0.551020	
chunk0178_420_1	chr7	41114662	41115184	+	0	NA	intron (NR_110832, intron 3 of 5)	intron (NR_110832, intron 3 of 5)	13319	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.005747	0.357553	
chunk0208_252_1	chrX	20311196	20311395	+	0	NA	Intergenic	Intergenic	-44663	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.030151	0.430000	89(CTGGACACTCTGTACC,-,0.00),90(TGGACACTCTGTACCC,+,0.00)
chunk0018_123_1	chr1	218480610	218481137	+	0	NA	intron (NR_031644, intron 2 of 6)	intron (NR_031644, intron 2 of 6)	38247	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.003795	0.337121	
chunk0027_324_1	chr10	78303127	78303631	+	0	NA	Intergenic	CpG	36051	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.113095	0.752475	
chunk0061_200_1	chr14	60278565	60279240	+	0	NA	intron (NM_177951, intron 2 of 3)	L1ME3Cz|LINE|L1	29654	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.005926	0.381657	
chunk0100_19_1	chr2	105137667	105138316	+	0	NA	Intergenic	Intergenic	-35047	NR_110227	101927492	Hs.469537	NR_110227	ENSG00000231851	UTAT33	-	uncharacterized LOC101927492	ncRNA	0.007704	0.436923	
chunk0112_51_1	chr20	37097266	37097683	+	0	NA	Intergenic	AluSz6|SINE|Alu	-1474	NM_183404	5933	Hs.207745	NM_002895	ENSG00000080839	RBL1	CP107|PRB1|p107	RB transcriptional corepressor like 1	protein-coding	0.011990	0.433014	
chunk0207_425_1	chr9	137254978	137255344	+	0	NA	promoter-TSS (NM_015456)	promoter-TSS (NM_015456)	-139	NM_015456	25920	Hs.521809	NM_015456	ENSG00000188986	NELFB	COBRA1|NELF-B	negative elongation factor complex member B	protein-coding	0.144809	0.743869	
chunk0204_132_1	chr9	95298435	95298755	+	0	NA	intron (NM_001243744, intron 1 of 13)	intron (NM_001243744, intron 1 of 13)	18659	NM_001243743	2176	Hs.494529	NM_000136	ENSG00000158169	FANCC	FA3|FAC|FACC	FA complementation group C	protein-coding	0.003125	0.448598	
chunk0188_54_1	chr8	6889252	6889542	+	0	NA	Intergenic	Intergenic	-11390	NM_005218	1672	Hs.32949	NM_005218	ENSG00000164825	DEFB1	BD1|DEFB-1|DEFB101|HBD1	defensin beta 1	protein-coding	0.013793	0.453608	92(GGGACTTAGAGTTCTG,+,0.00)
chunk0195_327_1	chr8	99046297	99046813	+	0	NA	intron (NM_015243, intron 3 of 17)	L1PB1|LINE|L1	33289	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.003876	0.353965	
chunk0191_231_1	chr8	52818791	52819277	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-104568	NM_001083617	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.006173	0.449692	
chunk0048_161_1	chr12	80673731	80674316	+	0	NA	intron (NM_001145026, intron 43 of 44)	MIR|SINE|MIR	-33606	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.003419	0.322526	
chunk0180_123_1	chr7	55598026	55598225	+	0	NA	Intergenic	L1PA16|LINE|L1	-25618	NM_030796	81552	Hs.488307	NM_030796	ENSG00000154978	VOPP1	ECOP|GASP|WBP1L2	VOPP1 WW domain binding protein	protein-coding	0.010050	0.405000	
chunk0201_244_1	chr9	37818927	37819447	+	0	NA	intron (NM_024345, intron 1 of 6)	intron (NM_024345, intron 1 of 6)	18401	NM_024345	79269	Hs.118394	NM_024345	ENSG00000122741	DCAF10	WDR32	DDB1 and CUL4 associated factor 10	protein-coding	0.003846	0.324376	
chunk0094_268_1	chr2	7992760	7992973	+	0	NA	Intergenic	L2b|LINE|L2	-16052	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.004695	0.443925	
chunk0052_453_1	chr12	132687242	132687550	+	0	NA	promoter-TSS (NM_018663)	promoter-TSS (NM_018663)	128	NM_006231	5426	Hs.524871	NM_006231	ENSG00000177084	POLE	CRCS12|FILS|IMAGEI|POLE1	DNA polymerase epsilon, catalytic subunit	protein-coding	0.133117	0.747573	
chunk0160_387_1	chr5	161857132	161857680	+	0	NA	intron (NM_001127643, intron 4 of 10)	intron (NM_001127643, intron 4 of 10)	6709	NM_001127648	2554	Hs.175934	NM_000806	ENSG00000022355	GABRA1	ECA4|EIEE19|EJM|EJM5	gamma-aminobutyric acid type A receptor alpha1 subunit	protein-coding	0.003650	0.324226	
chunk0141_258_1	chr4	85751861	85752060	+	0	NA	intron (NM_001025616, intron 3 of 9)	intron (NM_001025616, intron 3 of 9)	-26738	NM_001042669	83478	Hs.444229	NM_031305	ENSG00000138639	ARHGAP24	FILGAP|RC-GAP72|RCGAP72|p73|p73RhoGAP	Rho GTPase activating protein 24	protein-coding	0.000000	0.410000	
chunk0180_285_1	chr7	69934417	69934648	+	0	NA	intron (NM_015570, intron 2 of 18)	intron (NM_015570, intron 2 of 18)	335613	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.000000	0.418103	
chunk0197_66_1	chr8	118845436	118845832	+	0	NA	Intergenic	Intergenic	106510	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.000000	0.294710	
chunk0136_365_1	chr3	196048475	196048844	+	0	NA	TTS (NM_001128148)	TTS (NM_001128148)	33431	NM_003234	7037	Hs.529618	NM_003234	ENSG00000072274	TFRC	CD71|IMD46|T9|TFR|TFR1|TR|TRFR|p90	transferrin receptor	protein-coding	0.013550	0.429730	
chunk0147_276_1	chr4	184014422	184014765	+	0	NA	intron (NM_020225, intron 3 of 3)	(A)n|Simple_repeat|Simple_repeat	109237	NM_020225	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.014577	0.360465	
chunk0116_411_1	chr21	42655440	42656096	+	0	NA	intron (NM_001001575, intron 1 of 14)	intron (NM_001001575, intron 1 of 14)	2016	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.030488	0.566210	
chunk0186_453_1	chr7	148282252	148282820	+	0	NA	intron (NM_014141, intron 21 of 23)	MIR|SINE|MIR	-308029	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.005282	0.360281	
chunk0093_290_1	chr19	52269725	52270015	+	0	NA	intron (NM_001010851, intron 1 of 3)	CpG	299	NM_001010851	90321	Hs.439662	NM_001010851	ENSG00000196214	ZNF766	-	zinc finger protein 766	protein-coding	0.106897	0.666667	
chunk0153_223_1	chr5	72106403	72106721	+	0	NA	promoter-TSS (NM_005909)	promoter-TSS (NM_005909)	-729	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.003145	0.373041	
chunk0069_13_1	chr15	60264368	60264849	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	133378	NM_001136015	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.008316	0.379668	
chunk0207_36_1	chrX	4876161	4876783	+	0	NA	Intergenic	MIRb|SINE|MIR	-242900	NR_110390	101928201	Hs.586488	NR_110390	ENSG00000236513	LOC101928201	-	uncharacterized LOC101928201	ncRNA	0.004823	0.348315	257(CAGTACAAAGTGTCCT,-,0.00),258(AGTACAAAGTGTCCTC,+,0.00)
chunk0049_30_1	chr12	89676668	89676907	+	0	NA	Intergenic	Intergenic	-20720	NM_001682	490	Hs.506276	NM_001682	ENSG00000070961	ATP2B1	PMCA1|PMCA1kb	ATPase plasma membrane Ca2+ transporting 1	protein-coding	0.004184	0.312500	
chunk0026_250_1	chr10	66487527	66488038	+	0	NA	intron (NM_001127384, intron 11 of 17)	intron (NM_001127384, intron 11 of 17)	-438252	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.005871	0.339844	
chunk0007_279_1	chr1	83754125	83754656	+	0	NA	intron (NR_119375, intron 1 of 2)	intron (NR_119375, intron 1 of 2)	106156	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.003766	0.332707	
chunk0139_215_1	chr4	55025181	55025919	+	0	NA	Intergenic	LTR10C|LTR|ERV1	100045	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.010840	0.350474	326(AAGTACTTTATGTTCT,-,0.00),327(AGTACTTTATGTTCTT,+,0.00),406(GGTCACAGCCTGTTCC,-,0.00),407(GTCACAGCCTGTTCCT,+,0.00)
chunk0121_146_1	chr3	18904573	18905181	+	0	NA	Intergenic	L1ME2|LINE|L1	-243648	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.001645	0.354680	397(CAGAGCACTGTGTTCC,-,0.00),398(AGAGCACTGTGTTCCT,+,0.00)
chunk0194_189_1	chr8	85233150	85233874	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-11975	NM_198584	377677	Hs.127189	NM_198584	ENSG00000185015	CA13	CAXIII	carbonic anhydrase 13	protein-coding	0.006906	0.431724	
chunk0078_134_1	chr17	3660012	3660806	+	0	NA	3' UTR (NM_004937, exon 12 of 12)	3' UTR (NM_004937, exon 12 of 12)	8270	NM_014604	30851	Hs.12956	NM_014604	ENSG00000213977	TAX1BP3	TIP-1|TIP1	Tax1 binding protein 3	protein-coding	0.042821	0.633962	
chunk0015_282_1	chr1	188595461	188595839	+	0	NA	Intergenic	Intergenic	1152022	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.005291	0.313984	160(TAGGACATAATGTCTT,-,0.00)
chunk0203_48_1	chr9	83107674	83108032	+	0	NA	Intergenic	Intergenic	-44725	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.002793	0.353760	302(AAGTACACACTGGTCT,-,0.00)
chunk0057_277_1	chr13	105962065	105962426	+	0	NA	Intergenic	L1ME2|LINE|L1	255415	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.013850	0.436464	
chunk0185_417_1	chr7	134445582	134445909	+	0	NA	intron (NM_001628, intron 8 of 9)	intron (NM_001628, intron 8 of 9)	13391	NM_001628	231	Hs.521212	NM_001628	ENSG00000085662	AKR1B1	ADR|ALDR1|ALR2|AR	aldo-keto reductase family 1 member B	protein-coding	0.009174	0.423780	
chunk0124_367_1	chr3	59243710	59244156	+	0	NA	Intergenic	L2a|LINE|L2	-193944	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.004484	0.447427	
chunk0157_73_1	chr5	116424048	116424442	+	0	NA	Intergenic	Intergenic	-23253	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.007614	0.443038	66(AAGGACATACAGTTCT,-,0.00),67(AGGACATACAGTTCTG,+,0.00)
chunk0198_360_1	chr8	140802728	140803043	+	0	NA	intron (NM_001316342, intron 9 of 32)	Tigger3b|DNA|TcMar-Tigger	-70232	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.006349	0.344937	143(AAGAACAGTCTGTGAT,-,0.00),144(AGAACAGTCTGTGATG,+,0.00)
chunk0159_287_1	chr5	142720830	142721159	+	0	NA	Intergenic	Intergenic	-22924	NM_001144935	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.024316	0.512121	
chunk0124_245_1	chr3	56812251	56812590	+	0	NA	intron (NM_001128615, intron 4 of 12)	intron (NM_001128615, intron 4 of 12)	-10453	NM_019555	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.002950	0.391176	
chunk0157_12_1	chr5	115290733	115291284	+	0	NA	intron (NM_001040440, intron 1 of 9)	L1M4|LINE|L1	5282	NM_152549	153733	Hs.436121	NM_152549	ENSG00000164221	CCDC112	MBC1	coiled-coil domain containing 112	protein-coding	0.007260	0.317029	
chunk0106_102_1	chr2	197312143	197312703	+	0	NA	Intergenic	Intergenic	-1626	NM_001195144	91526	Hs.432706	NM_153697	ENSG00000065413	ANKRD44	PP6-ARS-B	ankyrin repeat domain 44	protein-coding	0.005357	0.393939	
chunk0003_348_1	chr1	39076300	39076856	+	0	NA	Intergenic	L2c|LINE|L2	-7589	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.010791	0.493716	
chunk0181_182_1	chr7	83162300	83162566	+	0	NA	exon (NM_033026, exon 1 of 25)	exon (NM_033026, exon 1 of 25)	448	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.082707	0.666667	
chunk0200_136_1	chr9	17671618	17672077	+	0	NA	intron (NM_003026, intron 1 of 8)	intron (NM_003026, intron 1 of 8)	92893	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.006536	0.332609	
chunk0136_42_1	chr4	1160069	1160984	+	0	NA	Intergenic	L1MEc|LINE|L1	12343	NM_012445	10417	Hs.302963	NM_012445	ENSG00000159674	SPON2	DIL-1|DIL1|M-SPONDIN|MINDIN	spondin 2	protein-coding	0.003279	0.311135	
chunk0210_73_1	chrX	70138518	70138950	+	0	NA	intron (NM_001551, intron 3 of 6)	L1ME4a|LINE|L1	5266	NM_001551	3476	Hs.496267	NM_001551	ENSG00000089289	IGBP1	ALPHA-4|IBP1	immunoglobulin binding protein 1	protein-coding	0.004630	0.311778	
chunk0070_386_1	chr15	76695812	76696293	+	0	NA	intron (NM_020843, intron 19 of 30)	intron (NM_020843, intron 19 of 30)	109405	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.002079	0.321577	
chunk0082_391_1	chr17	60656811	60657192	+	0	NA	intron (NM_003620, intron 5 of 5)	intron (NM_003620, intron 5 of 5)	-20810	NM_017679	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.007874	0.324607	
chunk0090_84_1	chr18	70519338	70519791	+	0	NA	Intergenic	Intergenic	131293	NM_001278515									0.000000	0.359031	
chunk0175_117_1	chr7	3321293	3321501	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	19949	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.009615	0.430622	
chunk0185_176_1	chr7	127909646	127910128	+	0	NA	intron (NM_014390, intron 14 of 23)	intron (NM_014390, intron 14 of 23)	-87622	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.002075	0.409938	
chunk0144_395_1	chr4	140195097	140195456	+	0	NA	Intergenic	L2a|LINE|L2	-41197	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.005571	0.505556	
chunk0192_81_1	chr8	60850669	60851294	+	0	NA	intron (NM_017780, intron 26 of 37)	intron (NM_017780, intron 26 of 37)	109722	NM_001316690	55636	Hs.20395	NM_017780	ENSG00000171316	CHD7	CRG|HH5|IS3|KAL5	chromodomain helicase DNA binding protein 7	protein-coding	0.004800	0.353035	31(CAGTACACACTGTATT,-,0.00),32(AGTACACACTGTATTG,+,0.00)
chunk0185_167_1	chr7	127883945	127884577	+	0	NA	intron (NM_014390, intron 12 of 23)	L1MC4|LINE|L1	-113248	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.006329	0.385466	
chunk0190_363_1	chr8	39831848	39832577	+	0	NA	intron (NM_001464, intron 3 of 20).2	intron (NM_001464, intron 3 of 20).2	6077	NM_001278114	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.002743	0.360274	285(AAGGACACCTTGTGCA,-,0.00),286(AGGACACCTTGTGCAA,+,0.00)
chunk0128_10_1	chr3	103696433	103696870	+	0	NA	Intergenic	Intergenic	-172535	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.342466	
chunk0063_192_1	chr14	80878521	80878867	+	0	NA	intron (NM_152446, intron 7 of 23)	L1MA2|LINE|L1	60846	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.005780	0.544669	
chunk0167_15_1	chr6	53603631	53604028	+	0	NA	Intergenic	Intergenic	-24551	NR_125841	101927171	Hs.334005	NR_125841	ENSG00000235899	LINC01564	TCONS_00011314|XLOC_005327	long intergenic non-protein coding RNA 1564	ncRNA	0.007557	0.389447	
chunk0084_109_1	chr17	75776651	75776980	+	0	NA	3' UTR (NM_005324, exon 4 of 4)	3' UTR (NM_005324, exon 4 of 4)	3120	NM_005324	3021	Hs.180877	NM_005324	ENSG00000132475	H3F3B	H3.3B	H3 histone family member 3B	protein-coding	0.015198	0.439394	
chunk0126_211_1	chr3	78766272	78766471	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	253088	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.005025	0.390000	
chunk0156_391_1	chr5	113151173	113151556	+	0	NA	exon (NM_001085377, exon 4 of 19)	exon (NM_001085377, exon 4 of 19)	143551	NM_002387	4163	Hs.593171	NM_002387	ENSG00000171444	MCC	MCC1	MCC regulator of WNT signaling pathway	protein-coding	0.007833	0.385417	
chunk0053_63_1	chr13	28097588	28097849	+	0	NA	intron (NR_130706, intron 1 of 24)	intron (NR_130706, intron 1 of 24)	2874	NM_004119	2322	Hs.507590	NM_004119	ENSG00000122025	FLT3	CD135|FLK-2|FLK2|STK1	fms related tyrosine kinase 3	protein-coding	0.003831	0.419847	
chunk0014_175_1	chr1	178436026	178436324	+	0	NA	intron (NM_170692, intron 5 of 17)	intron (NM_170692, intron 5 of 17)	-76902	NM_001170724	84066	Hs.534501	NM_032126	ENSG00000240021	TEX35	C1orf49|TSC24	testis expressed 35	protein-coding	0.003356	0.354515	
chunk0008_66_1	chr1	89623950	89624473	+	0	NA	TTS (NR_033981)	TTS (NR_033981)	8683	NR_033981	400761	Hs.741594	NR_033981	ENSG00000231999	LRRC8C-DT	-	LRRC8C divergent transcript	ncRNA	0.007648	0.387405	
chunk0208_384_1	chrX	28693095	28693591	+	0	NA	intron (NM_014271, intron 1 of 10)	intron (NM_014271, intron 1 of 10)	105779	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.004032	0.386318	
chunk0078_57_1	chr17	1454787	1455006	+	0	NA	intron (NM_005206, intron 1 of 2)	intron (NM_005206, intron 1 of 2)	1371	NM_005206	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.027397	0.481818	
chunk0110_434_1	chr20	20823357	20823651	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-110881	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.023810	0.562712	
chunk0122_362_1	chr3	37595346	37595722	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	143212	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.013298	0.466844	
chunk0017_258_1	chr1	209377973	209378479	+	0	NA	Intergenic	Intergenic	-50597	NM_001104548									0.005929	0.398422	
chunk0129_438_1	chr3	127971615	127971869	+	0	NA	intron (NM_207335, intron 4 of 4)	intron (NM_207335, intron 4 of 4)	48683	NM_207335	166348	Hs.132087	NM_207335	ENSG00000187715	KBTBD12	KLHDC6	kelch repeat and BTB domain containing 12	protein-coding	0.003937	0.545098	
chunk0011_276_1	chr1	151260339	151260596	+	0	NA	intron (NM_002810, intron 1 of 9)	intron (NM_002810, intron 1 of 9)	5746	NM_002810	5710	Hs.505059	NM_002810	ENSG00000159352	PSMD4	AF|AF-1|ASF|MCB1|Rpn10|S5A|pUB-R5	proteasome 26S subunit, non-ATPase 4	protein-coding	0.007782	0.395349	
chunk0011_267_1	chr1	151070364	151071205	+	0	NA	5' UTR (NM_144618, exon 1 of 9)	5' UTR (NM_144618, exon 1 of 9)	180	NM_144618	126626	Hs.15671	NM_144618	ENSG00000143458	GABPB2	GABPB-2	GA binding protein transcription factor subunit beta 2	protein-coding	0.058264	0.587886	
chunk0114_65_1	chr21	9074958	9075233	+	0	NA	intron (NR_038327, intron 2 of 3)	intron (NR_038327, intron 2 of 3)	54666	NR_038328	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.032727	0.626812	
chunk0151_139_1	chr5	45134398	45134888	+	0	NA	Intergenic	MER34B|LTR|ERV1	325718	NM_016640	10884	Hs.124165	NM_016640	ENSG00000112996	MRPS30	MRP-S30|PAP|PDCD9|S30mt	mitochondrial ribosomal protein S30	protein-coding	0.004082	0.344196	
chunk0076_292_1	chr16	69861698	69862231	+	0	NA	intron (NM_007014, intron 7 of 24)	intron (NM_007014, intron 7 of 24)	23227	NM_001270453	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.016886	0.451311	
chunk0091_102_1	chr19	5827892	5828251	+	0	NA	exon (NM_004558, exon 2 of 2)	exon (NM_004558, exon 2 of 2)	4264	NM_004558	4902	Hs.234775	NM_004558	ENSG00000171119	NRTN	NTN	neurturin	protein-coding	0.167131	0.752778	198(GAGGACGAGGTGTCCT,-,0.00),199(AGGACGAGGTGTCCTT,+,0.00)
chunk0163_253_1	chr6	12920066	12920503	+	0	NA	intron (NM_030948, intron 4 of 14)	intron (NM_030948, intron 4 of 14)	203479	NM_030948	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.006865	0.335616	
chunk0140_453_1	chr4	76443564	76444073	+	0	NA	intron (NM_020859, intron 1 of 10)	intron (NM_020859, intron 1 of 10)	8718	NM_020859	57619	Hs.683808	NM_020859	ENSG00000138771	SHROOM3	APXL3|MSTP013|SHRM|ShrmL	shroom family member 3	protein-coding	0.003929	0.429412	239(CAGAACACTCTGTCCT,-,0.00),240(AGAACACTCTGTCCTG,+,0.00)
chunk0210_315_1	chrX	91395151	91395750	+	0	NA	Intergenic	L1MCa|LINE|L1	-39148	NM_080832	140886	Hs.246590	NM_080832	ENSG00000174740	PABPC5	PABP5	poly(A) binding protein cytoplasmic 5	protein-coding	0.003339	0.320000	
chunk0207_97_1	chrX	9787023	9787731	+	0	NA	intron (NM_001649, intron 1 of 9)	intron (NM_001649, intron 1 of 9)	921	NM_001649	357	Hs.567236	NM_001649	ENSG00000146950	SHROOM2	APXL|HSAPXL	shroom family member 2	protein-coding	0.032486	0.466855	
chunk0146_285_1	chr4	164008095	164008408	+	0	NA	intron (NM_001166373, intron 2 of 7)	L1M1|LINE|L1	189460	NM_012403	23520	Hs.661161	NM_012403		ANP32C	PP32R1	acidic nuclear phosphoprotein 32 family member C	protein-coding	0.000000	0.305732	
chunk0137_387_1	chr4	26822229	26822450	+	0	NA	Intergenic	Intergenic	-38352	NM_020860	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.009050	0.436937	
chunk0188_120_1	chr8	9102524	9102925	+	0	NA	Intergenic	Intergenic	47986	NM_024607	79660	Hs.458513	NM_024607	ENSG00000173281	PPP1R3B	GL|PPP1R4|PTG	protein phosphatase 1 regulatory subunit 3B	protein-coding	0.002494	0.490050	
chunk0021_117_1	chr10	3524222	3525109	+	0	NA	intron (NR_131187, intron 1 of 1)	L1PB3|LINE|L1	205970	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.005637	0.371622	
chunk0154_281_1	chr5	82537641	82537881	+	0	NA	Intergenic	Intergenic	258299	NM_001017971	92270	Hs.676227	NM_001017971	ENSG00000205464	ATP6AP1L	-	ATPase H+ transporting accessory protein 1 like	protein-coding	0.000000	0.290456	
chunk0062_423_1	chr14	75206291	75206860	+	0	NA	Intergenic	Intergenic	-29929	NM_006827	10972	Hs.74137	NM_006827	ENSG00000170348	TMED10	P24(DELTA)|S31I125|S31III125|TMP21|Tmp-21-I|p23|p24d1	transmembrane p24 trafficking protein 10	protein-coding	0.005272	0.456140	
chunk0085_446_1	chr18	11177449	11177849	+	0	NA	Intergenic	MIRb|SINE|MIR	-28887	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.012500	0.471322	297(GGCCCATCCTGTCCTC,+,0.00)
chunk0090_205_1	chr18	73245548	73246081	+	0	NA	intron (NR_034133, intron 2 of 5)	MLT1K|LTR|ERVL-MaLR	18684	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.007505	0.385768	
chunk0015_354_1	chr1	190226108	190226371	+	0	NA	exon (NM_199051, exon 6 of 8)	exon (NM_199051, exon 6 of 8)	251390	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.007605	0.397727	
chunk0116_161_1	chr21	36584811	36585333	+	0	NA	Intergenic	Intergenic	-8503	NM_001146077	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.005747	0.413002	
chunk0127_295_1	chr3	98161952	98162343	+	0	NA	Intergenic	MLT1A1-int|LTR|ERVL-MaLR	-6553	NM_001005515	403274	Hs.554713	NM_001005515	ENSG00000233412	OR5H15	-	olfactory receptor family 5 subfamily H member 15	protein-coding	0.005115	0.334184	
chunk0016_450_1	chr1	204150051	204150664	+	0	NA	intron (NM_018208, intron 1 of 7)	intron (NM_018208, intron 1 of 7)	1825	NM_001297760	55224	Hs.497469	NM_018208	ENSG00000143845	ETNK2	EKI2|HMFT1716	ethanolamine kinase 2	protein-coding	0.011419	0.547231	302(CAGAACACTATGTCCT,-,0.00),303(AGAACACTATGTCCTG,+,0.00)
chunk0093_76_1	chr19	40715519	40715809	+	0	NA	promoter-TSS (NM_001142555)	promoter-TSS (NM_001142555)	-558	NM_001142555	79934	Hs.130712	NM_024876	ENSG00000123815	COQ8B	ADCK4|NPHS9	coenzyme Q8B	protein-coding	0.024138	0.560137	
chunk0058_304_1	chr14	27051168	27051828	+	0	NA	Intergenic	Intergenic	142856	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.000000	0.295008	
chunk0134_104_1	chr3	176974196	176974720	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-157457	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.011450	0.462857	214(GGGACCACTATGTGCT,-,0.00),215(GGACCACTATGTGCTT,+,0.00)
chunk0048_411_1	chr12	88190102	88190488	+	0	NA	intron (NM_181783, intron 11 of 13)	intron (NM_181783, intron 11 of 13)	47999	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.000000	0.297158	
chunk0006_231_1	chr1	68696407	68696651	+	0	NA	Intergenic	Intergenic	-199308	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.004098	0.436735	96(AAGCACAGAATGTCCA,-,0.00),97(AGCACAGAATGTCCAC,+,0.00)
chunk0039_377_1	chr11	106436194	106436751	+	0	NA	Intergenic	Intergenic	185065	NR_120551	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.003591	0.349462	
chunk0065_103_1	chr15	24051081	24051561	+	0	NA	intron (NR_126392, intron 4 of 5)	L1MEc|LINE|L1	76174	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.006250	0.413721	
chunk0170_283_1	chr6	114301946	114302166	+	0	NA	intron (NR_125845, intron 9 of 9)	intron (NR_125845, intron 9 of 9)	-239179	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.009091	0.361991	
chunk0105_397_1	chr2	192547365	192547606	+	0	NA	Intergenic	Intergenic	-202360	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.000000	0.280992	
chunk0045_76_1	chr12	45743285	45743972	+	0	NA	intron (NM_152641, intron 3 of 20)	L1MC|LINE|L1	13791	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.002911	0.369186	
chunk0127_1_1	chr3	87756553	87757065	+	0	NA	Intergenic	L1MC1|LINE|L1	-225767	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.003906	0.360624	
chunk0145_236_1	chr4	148514734	148515249	+	0	NA	Intergenic	Intergenic	-72471	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.003883	0.337209	
chunk0056_37_1	chr13	77330280	77330481	+	0	NA	Intergenic	Intergenic	-3338	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.014925	0.361386	
chunk0064_410_1	chr14	99555844	99556200	+	0	NA	intron (NM_001144995, intron 1 of 5)	L1MC4|LINE|L1	48368	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.022472	0.481793	
chunk0040_67_1	chr11	111258642	111259114	+	0	NA	intron (NM_198498, intron 1 of 3)	intron (NM_198498, intron 1 of 3)	2896	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.000000	0.369979	
chunk0090_277_1	chr18	74694377	74694828	+	0	NA	intron (NM_001146189, intron 2 of 6)	L1MEf|LINE|L1	63639	NM_001146190	55628	Hs.536490	NM_017757	ENSG00000215421	ZNF407	-	zinc finger protein 407	protein-coding	0.002217	0.420354	196(CTGAACACCAAGTTCC,-,0.00),197(TGAACACCAAGTTCCA,+,0.00)
chunk0190_73_1	chr8	29897808	29898042	+	0	NA	Intergenic	Intergenic	-23588	NR_024473	286135	Hs.376840	NR_024473	ENSG00000253279	LINC02209	FAM183CP	long intergenic non-protein coding RNA 2209	ncRNA	0.008547	0.502128	
chunk0149_21_1	chr5	16135902	16136546	+	0	NA	intron (NM_001102562, intron 2 of 3)	L1M7|LINE|L1	43564	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.001553	0.361240	
chunk0206_276_1	chr9	124225925	124226378	+	0	NA	Intergenic	L1MC4|LINE|L1	-31455	NM_001166167	10783	Hs.197071	NM_014397	ENSG00000119408	NEK6	SID6-1512	NIMA related kinase 6	protein-coding	0.000000	0.409692	
chunk0182_37_1	chr7	91597238	91597532	+	0	NA	Intergenic	Intergenic	283335	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.003401	0.481356	
chunk0089_156_1	chr18	59075901	59076337	+	0	NA	Intergenic	Intergenic	40440	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.006881	0.427918	
chunk0170_125_1	chr6	110763633	110764157	+	0	NA	intron (NM_001300964, intron 1 of 12)	L1MA5|LINE|L1	-50726	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.015267	0.339048	
chunk0039_305_1	chr11	103050315	103051180	+	0	NA	TTS (NM_032299)	TTS (NM_032299)	41468	NM_032299	84259	Hs.503716	NM_032299	ENSG00000137692	DCUN1D5	SCCRO5	defective in cullin neddylation 1 domain containing 5	protein-coding	0.000000	0.341801	477(AAAAACACACAGTCCC,-,0.00),478(AAAACACACAGTCCCT,+,0.00)
chunk0003_220_1	chr1	35499917	35500503	+	0	NA	intron (NM_024874, intron 3 of 20)	intron (NM_024874, intron 3 of 20)	57226	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.008532	0.424191	
chunk0065_405_1	chr14	105398497	105398696	+	0	NA	promoter-TSS (NM_001195082)	promoter-TSS (NM_001195082)	13	NM_001195082	647310	Hs.729499	NM_001195082	ENSG00000226174	TEX22	-	testis expressed 22	protein-coding	0.125628	0.745000	
chunk0155_399_1	chr5	98793151	98793356	+	0	NA	exon (NM_001012761, exon 5 of 5)	exon (NM_001012761, exon 5 of 5)	-20169	NR_033932	503569	Hs.586188	NR_033932	ENSG00000246763	RGMB-AS1	-	RGMB antisense RNA 1	ncRNA	0.053659	0.606796	
chunk0112_231_1	chr20	41086756	41087242	+	0	NA	intron (NM_003286, intron 8 of 20)	intron (NM_003286, intron 8 of 20)	-50522	NM_002660	5335	Hs.268177	NM_002660	ENSG00000124181	PLCG1	NCKAP3|PLC-II|PLC1|PLC148|PLCgamma1	phospholipase C gamma 1	protein-coding	0.012346	0.404517	
chunk0125_219_1	chr3	67691597	67692033	+	0	NA	intron (NR_109992, intron 3 of 6)	intron (NR_109992, intron 3 of 6)	37118	NR_109992	101927111	Hs.518057	NR_109992	ENSG00000241316	SUCLG2-AS1	-	SUCLG2 antisense RNA 1 (head to head)	ncRNA	0.006881	0.448513	
chunk0084_52_1	chr17	74430144	74430600	+	0	NA	Intergenic	Intergenic	-1156	NM_022036	55890	Hs.446438	NM_018653	ENSG00000170412	GPRC5C	RAIG-3|RAIG3	G protein-coupled receptor class C group 5 member C	protein-coding	0.028509	0.536105	151(CAGCACACTGTGTTCA,-,0.00),152(AGCACACTGTGTTCAG,+,0.00)
chunk0206_345_1	chr9	125561816	125562128	+	0	NA	intron (NM_001006618, intron 5 of 7)	intron (NM_001006618, intron 5 of 7)	145262	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.000000	0.418530	99(CTGAGCAGCATGTTCT,-,0.00)
chunk0018_97_1	chr1	217764480	217764679	+	0	NA	intron (NM_138796, intron 6 of 10)	L1MC1|LINE|L1	20541	NR_125784	103752555	Hs.602803	NR_125784	ENSG00000234070	SPATA17-AS1	-	SPATA17 antisense RNA 1	ncRNA	0.005025	0.345000	
chunk0191_51_1	chr8	43410978	43411177	+	0	NA	Intergenic	L1P4d|LINE|L1	118635	NM_001005365	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.000000	0.495000	
chunk0041_193_1	chr11	126451258	126451529	+	0	NA	intron (NM_032531, intron 7 of 16)	intron (NM_032531, intron 7 of 16)	45211	NM_001254759	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.029520	0.518382	
chunk0026_444_1	chr10	71473972	71474361	+	0	NA	intron (NM_001171931, intron 3 of 24)	intron (NM_001171931, intron 3 of 24)	37754	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.007712	0.541026	172(CAGTACAGCCTGTTCC,-,0.00),173(AGTACAGCCTGTTCCC,+,0.00),199(AGGGCCAGCTTGTTCT,-,0.00),200(GGGCCAGCTTGTTCTG,+,0.00)
chunk0196_45_1	chr8	101829293	101829607	+	0	NA	intron (NM_001040629, intron 3 of 6)	Charlie7|DNA|hAT-Charlie	-38239	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.000000	0.311111	
chunk0114_143_1	chr21	10272336	10272575	+	0	NA	Intergenic	AluSx3|SINE|Alu	-141065	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.012552	0.395833	
chunk0154_421_1	chr5	89053354	89053946	+	0	NA	Intergenic	Intergenic	-149545	NM_001131005	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.008446	0.328836	
chunk0106_108_1	chr2	197502098	197502711	+	0	NA	intron (NM_001202485, intron 2 of 8)	intron (NM_001202485, intron 2 of 8)	-2130	NM_199440	3329	Hs.595053	NM_002156	ENSG00000144381	HSPD1	CPN60|GROEL|HLD4|HSP-60|HSP60|HSP65|HuCHA60|SPG13	heat shock protein family D (Hsp60) member 1	protein-coding	0.008157	0.413681	
chunk0165_18_1	chr6	28982968	28983352	+	0	NA	Intergenic	Intergenic	22100	NM_001010877	282890	Hs.148218	NM_001010877	ENSG00000197935	ZNF311	zf31	zinc finger protein 311	protein-coding	0.015625	0.418182	
chunk0100_304_1	chr2	115433776	115434001	+	0	NA	intron (NM_001178037, intron 3 of 25)	intron (NM_001178037, intron 3 of 25)	271781	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.004444	0.296460	
chunk0131_264_1	chr3	150039704	150040227	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-56599	NM_001079809	653659	Hs.652908	NM_001079809		TMEM183B	C1ORF37DUP|C1orf37-DUP	transmembrane protein 183B	protein-coding	0.003824	0.309160	263(AGGAACACCCAGTTCC,-,0.00),264(GGAACACCCAGTTCCT,+,0.00)
chunk0181_188_1	chr7	83369560	83370067	+	0	NA	intron (NM_001178129, intron 16 of 16)	intron (NM_001178129, intron 16 of 16)	-206932	NM_033026	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.003945	0.405512	207(AAGGACTTTGTGTACC,-,0.00),208(AGGACTTTGTGTACCT,+,0.00)
chunk0146_425_1	chr4	169202855	169203373	+	0	NA	intron (NM_020870, intron 2 of 11)	MER103C|DNA|hAT-Charlie	67984	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.005792	0.387283	285(AAGAACATGCTGTTAT,-,0.00),286(AGAACATGCTGTTATT,+,0.00)
chunk0190_12_1	chr8	28836325	28836735	+	0	NA	intron (NR_026826, intron 3 of 14)	(TTCAT)n|Simple_repeat|Simple_repeat	53385	NM_001172562	55756	Hs.162397	NM_018250	ENSG00000104299	INTS9	CPSF2L|INT9|RC74	integrator complex subunit 9	protein-coding	0.004878	0.391727	
chunk0017_384_1	chr1	212208786	212209425	+	0	NA	Intergenic	Intergenic	25631	NR_125982	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.001565	0.450000	
chunk0148_244_1	chr5	9836460	9836946	+	0	NA	intron (NR_027112, intron 4 of 12)	intron (NR_027112, intron 4 of 12)	67121	NR_027112	285692	Hs.651487	NR_027112	ENSG00000249781	LINC02112	-	long intergenic non-protein coding RNA 2112	ncRNA	0.008230	0.408624	
chunk0171_222_1	chr6	126273783	126274177	+	0	NA	Intergenic	Intergenic	-65809	NR_104462	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.002538	0.293671	
chunk0161_310_1	chr5	173472122	173472814	+	0	NA	Intergenic	Intergenic	-107166	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.008671	0.425685	331(CGGAACAGCATGTGTC,-,0.00),332(GGAACAGCATGTGTCT,+,0.00)
chunk0009_162_1	chr1	105263793	105264153	+	0	NA	Intergenic	L1PA7|LINE|L1	354962	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002778	0.346260	169(GGTACATTGTGTCTTT,+,0.00)
chunk0137_34_1	chr4	11281342	11281939	+	0	NA	Intergenic	Intergenic	-87187	NR_030298	693157		NR_030298	ENSG00000207716	MIR572	MIRN572|hsa-mir-572	microRNA 572	ncRNA	0.000000	0.367893	
chunk0071_219_1	chr15	84789280	84789688	+	0	NA	intron (NM_014630, intron 4 of 10)	L1MB2|LINE|L1	-27196	NM_020778	57538	Hs.459183	NM_020778	ENSG00000136383	ALPK3	CMH27|MAK|MIDORI	alpha kinase 3	protein-coding	0.000000	0.359413	
chunk0081_269_1	chr17	43749462	43750018	+	0	NA	Intergenic	L2a|LINE|L2	9048	NM_025237	50964	Hs.349204	NM_025237	ENSG00000167941	SOST	CDD|DAND6|SOST1|VBCH	sclerostin	protein-coding	0.012590	0.536804	
chunk0054_89_1	chr13	42553170	42554167	+	0	NA	Intergenic	Intergenic	-9068	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.004012	0.436874	
chunk0166_61_1	chr6	42939405	42939998	+	0	NA	TTS (NM_006586)	TTS (NM_006586)	10579	NM_006586	10695	Hs.414099	NM_006586	ENSG00000137161	CNPY3	CAG4A|EIEE60|ERDA5|PRAT4A|TNRC5	canopy FGF signaling regulator 3	protein-coding	0.010118	0.537037	325(GTCACACCATGTTCCT,+,0.00)
chunk0027_452_1	chr10	81304893	81305722	+	0	NA	Intergenic	L1MC5|LINE|L1	-570007	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.006031	0.336145	
chunk0037_91_1	chr11	71943385	71943775	+	0	NA	intron (NR_024147, intron 1 of 7)	L2c|LINE|L2	14858	NM_001300926	55298	Hs.368554	NM_018320	ENSG00000137522	RNF121	-	ring finger protein 121	protein-coding	0.005128	0.398977	
chunk0123_49_1	chr3	41097907	41098194	+	0	NA	Intergenic	L2a|LINE|L2	-101401	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.006969	0.503472	
chunk0119_232_1	chr22	45314442	45315056	+	0	NA	intron (NM_001104595, intron 2 of 9)	intron (NM_001104595, intron 2 of 9)	4845	NM_017911	55007	Hs.265018	NM_017911	ENSG00000100376	FAM118A	C22orf8	family with sequence similarity 118 member A	protein-coding	0.019544	0.450407	
chunk0115_169_1	chr21	25296455	25296654	+	0	NA	Intergenic	MER70A|LTR|ERVL	135147	NR_024027	54072	Hs.234016	NM_058184	ENSG00000185433	LINC00158	C21orf42|NCRNA00158	long intergenic non-protein coding RNA 158	ncRNA	0.015075	0.475000	
chunk0150_66_1	chr5	32108222	32108669	+	0	NA	3' UTR (NM_178140, exon 24 of 24)	3' UTR (NM_178140, exon 24 of 24)	65874	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.008949	0.426339	
chunk0135_357_1	chr3	190591144	190591446	+	0	NA	intron (NM_134470, intron 3 of 8)	MIRb|SINE|MIR	77244	NM_001167929	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.013245	0.405941	
chunk0177_436_1	chr7	27976400	27976658	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	-203928	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.007752	0.420849	
chunk0146_36_1	chr4	155423347	155424060	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-46733	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.008415	0.343137	
chunk0155_77_1	chr5	91831708	91832749	+	0	NA	Intergenic	Intergenic	-448896	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.001921	0.382917	709(GGGGACAGGTTGTTCT,-,0.00),710(GGGACAGGTTGTTCTT,+,0.00)
chunk0093_333_1	chr19	54462731	54463283	+	0	NA	TTS (NM_052925)	TTS (NM_052925)	704	NM_198988	94059	Hs.590976	NM_198988	ENSG00000275183	LENG9	-	leukocyte receptor cluster member 9	protein-coding	0.088768	0.707052	
chunk0005_239_1	chr1	59516610	59517274	+	0	NA	intron (NM_001278224, intron 1 of 9)	intron (NM_001278224, intron 1 of 9)	1313	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.000000	0.434586	400(AAGAACATTTTGTTCT,-,0.00),401(AGAACATTTTGTTCTT,+,0.00)
chunk0141_252_1	chr4	85566781	85567410	+	0	NA	intron (NM_001025616, intron 1 of 9)	L2a|LINE|L2	91964	NM_001025616	83478	Hs.444229	NM_031305	ENSG00000138639	ARHGAP24	FILGAP|RC-GAP72|RCGAP72|p73|p73RhoGAP	Rho GTPase activating protein 24	protein-coding	0.003180	0.404762	
chunk0120_378_1	chr3	12189702	12189990	+	0	NA	intron (NM_133625, intron 12 of 12)	intron (NM_133625, intron 12 of 12)	-30495	NM_003256	7079	Hs.591665	NM_003256	ENSG00000157150	TIMP4	TIMP-4	TIMP metallopeptidase inhibitor 4	protein-coding	0.020833	0.439446	
chunk0061_249_1	chr14	61170795	61171253	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	110788	NM_001017970	161291	Hs.146180	NM_001017970	ENSG00000182107	TMEM30B	CDC50B	transmembrane protein 30B	protein-coding	0.008734	0.409586	
chunk0126_174_1	chr3	78031811	78032258	+	0	NA	Intergenic	Intergenic	934022	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.011186	0.337054	
chunk0212_373_1	chrX	150065397	150065658	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	126979	NR_027456	100272228	Hs.496916	NR_027456	ENSG00000235703	LINC00894	-	long intergenic non-protein coding RNA 894	ncRNA	0.019157	0.435115	
chunk0094_262_1	chr2	7745314	7745703	+	0	NA	Intergenic	L2c|LINE|L2	154147	NR_110256	101929551	Hs.116006	NR_110256	ENSG00000226506	LOC101929551	-	uncharacterized LOC101929551	ncRNA	0.010283	0.371795	
chunk0119_374_1	chr22	47647491	47647712	+	0	NA	intron (NR_122046, intron 2 of 8)	(CA)n|Simple_repeat|Simple_repeat	15927	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.004525	0.477477	
chunk0016_244_1	chr1	199947768	199947967	+	0	NA	Intergenic	L1PA12|LINE|L1	-79735	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005025	0.345000	
chunk0092_267_1	chr19	33234601	33235022	+	0	NA	Intergenic	L2c|LINE|L2	-8961	NM_019849	56301	Hs.58679	NM_019849	ENSG00000130876	SLC7A10	ASC1|HASC-1|asc-1	solute carrier family 7 member 10	protein-coding	0.019002	0.568720	
chunk0092_276_1	chr19	33376692	33376911	+	0	NA	intron (NM_001252296, intron 1 of 1)	intron (NM_001252296, intron 1 of 1)	2277	NM_001252296	1054	Hs.429666	NM_001806	ENSG00000153879	CEBPG	GPE1BP|IG/EBP-1	CCAAT enhancer binding protein gamma	protein-coding	0.004566	0.395455	54(TAGGACTGAGTGTCCA,-,0.00),55(AGGACTGAGTGTCCAG,+,0.00)
chunk0149_383_1	chr5	28523375	28524337	+	0	NA	Intergenic	MER67C|LTR|ERV1	-403014	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.003119	0.359294	
chunk0136_87_1	chr4	2533853	2534212	+	0	NA	Intergenic	AluSx1|SINE|Alu	64579	NM_001185009	6047	Hs.66394	NM_002938	ENSG00000063978	RNF4	RES4-26|SLX5|SNURF	ring finger protein 4	protein-coding	0.011142	0.427778	
chunk0056_96_1	chr13	82306327	82306724	+	0	NA	Intergenic	Intergenic	-1079542	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.005038	0.278894	61(GTGAACTCAATGTACC,-,0.00)
chunk0070_94_1	chr15	70321201	70321745	+	0	NA	Intergenic	Intergenic	-223556	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.003676	0.491743	
chunk0136_28_1	chr4	765915	766114	+	0	NA	intron (NM_006315, intron 10 of 10)	intron (NM_006315, intron 10 of 10)	15834	NR_036512	100129917	Hs.731755	NR_036511	ENSG00000249592	LOC100129917	-	uncharacterized LOC100129917	ncRNA	0.045226	0.605000	89(AGGCACTGTGCGTTCT,-,0.00),90(GGCACTGTGCGTTCTT,+,0.00)
chunk0072_34_1	chr16	751320	751519	+	0	NA	Intergenic	Intergenic	-9346	NM_005823	10232	Hs.408488	NM_005823	ENSG00000102854	MSLN	MPF|SMRP	mesothelin	protein-coding	0.035176	0.600000	
chunk0031_49_1	chr10	122655894	122656426	+	0	NA	Intergenic	Intergenic	43662	NM_001010912	399814	Hs.363649	NM_001010912	ENSG00000183559	C10orf120	bA318C4.1	chromosome 10 open reading frame 120	protein-coding	0.007519	0.437148	
chunk0009_412_1	chr1	110577940	110578687	+	0	NA	Intergenic	L1ME1|LINE|L1	28040	NM_004974	3737	Hs.248139	NM_004974	ENSG00000177301	KCNA2	EIEE32|HBK5|HK4|HUKIV|KV1.2|MK2|NGK1|RBK2	potassium voltage-gated channel subfamily A member 2	protein-coding	0.004016	0.344920	
chunk0089_398_1	chr18	68150860	68151459	+	0	NA	Intergenic	L1MA2|LINE|L1	563957	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.003339	0.368333	
chunk0126_53_1	chr3	74229190	74229523	+	0	NA	Intergenic	Intergenic	291784	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.311377	7(AAGCACATTCTGTTCC,-,0.00),8(AGCACATTCTGTTCCC,+,0.00)
chunk0170_31_1	chr6	109300313	109300582	+	0	NA	intron (NR_028595, intron 2 of 3)	intron (NR_028595, intron 2 of 3)	6144	NR_028595	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.022305	0.474074	
chunk0018_36_1	chr1	215631529	215632020	+	0	NA	intron (NM_206933, intron 70 of 71)	intron (NM_206933, intron 70 of 71)	64382	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.008147	0.500000	297(AGGAACAGGGTGTTTA,-,0.00),298(GGAACAGGGTGTTTAC,+,0.00)
chunk0117_193_1	chr22	21615870	21616069	+	0	NA	intron (NR_028436, intron 4 of 4)	Tigger17a|DNA|TcMar-Tigger	14082	NM_001017964	150223	Hs.355952	NM_001017964	ENSG00000161179	YDJC	-	YdjC chitooligosaccharide deacetylase homolog	protein-coding	0.005025	0.395000	
chunk0203_22_1	chr9	82875384	82875875	+	0	NA	Intergenic	Tigger4|DNA|TcMar-Tigger	187499	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.010183	0.392276	
chunk0032_436_1	chr10	132756268	132756563	+	0	NA	intron (NM_005539, intron 11 of 15)	(GT)n|Simple_repeat|Simple_repeat	29618	NM_177400	84504	Hs.134013	NM_177400	ENSG00000148826	NKX6-2	GTX|NKX6.2|NKX6B|SPAX8	NK6 homeobox 2	protein-coding	0.044068	0.472973	
chunk0015_422_1	chr1	191533242	191533553	+	0	NA	Intergenic	L1M2|LINE|L1	-625065	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.012862	0.554487	
chunk0020_180_1	chr1	234610825	234611027	+	0	NA	Intergenic	CpG	-1401	NM_001077397	359948	Hs.350268	NM_182972	ENSG00000168264	IRF2BP2	CVID14	interferon regulatory factor 2 binding protein 2	protein-coding	0.163366	0.748768	
chunk0057_205_1	chr13	103817647	103818188	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	392717	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.016636	0.472325	296(GAGGACACTGAGTCCT,-,0.00),297(AGGACACTGAGTCCTC,+,0.00)
chunk0190_315_1	chr8	38546278	38546651	+	0	NA	Intergenic	HAL1|LINE|L1	-17802	NM_207412	389649	Hs.546586	NM_207412	ENSG00000196166	C8orf86	-	chromosome 8 open reading frame 86	protein-coding	0.002681	0.409091	
chunk0047_373_1	chr12	75160951	75161150	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	48698	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.000000	0.300000	
chunk0062_31_1	chr14	67003675	67004099	+	0	NA	intron (NM_001024218, intron 8 of 21)	MIR3|SINE|MIR	-185506	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.007075	0.334118	
chunk0060_91_1	chr14	42543842	42544393	+	0	NA	Intergenic	L1MA9|LINE|L1	936556	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.005445	0.320652	314(CTGAACAGACTGTCCT,-,0.00),315(TGAACAGACTGTCCTT,+,0.00)
chunk0053_326_1	chr13	34322908	34323711	+	0	NA	Intergenic	Intergenic	317376	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.011208	0.374378	
chunk0104_35_1	chr2	171003410	171004062	+	0	NA	intron (NM_001136554, intron 18 of 20)	Tigger2|DNA|TcMar-Tigger	63237	NM_001136555	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.016871	0.361409	402(AGGTACAGTCTGTGTT,-,0.00),403(GGTACAGTCTGTGTTT,+,0.00)
chunk0162_94_1	chr6	2209136	2209549	+	0	NA	intron (NM_001500, intron 1 of 10)	intron (NM_001500, intron 1 of 10)	-33351	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.002421	0.427536	195(CTGAACACAATGTACT,-,0.00),196(TGAACACAATGTACTC,+,0.00)
chunk0092_345_1	chr19	35297987	35298264	+	0	NA	intron (NM_002361, intron 4 of 10)	(AC)n|Simple_repeat|Simple_repeat	6039	NM_001199216	4099	Hs.643440	NM_002361	ENSG00000105695	MAG	GMA|S-MAG|SIGLEC-4A|SIGLEC4A|SPG75	myelin associated glycoprotein	protein-coding	0.007220	0.482014	
chunk0052_155_1	chr13	23852554	23852753	+	0	NA	intron (NM_005932, intron 10 of 18)	Tigger3b|DNA|TcMar-Tigger	-36236	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.005025	0.370000	
chunk0141_384_1	chr4	88216440	88216655	+	0	NA	intron (NM_001257386, intron 1 of 15)	ERVL-E-int|LTR|ERVL	14775	NM_001257386	9429	Hs.480218	NM_004827	ENSG00000118777	ABCG2	ABC15|ABCP|BCRP|BCRP1|BMDP|CD338|CDw338|EST157481|GOUT1|MRX|MXR|MXR-1|MXR1|UAQTL1	ATP binding cassette subfamily G member 2 (Junior blood group)	protein-coding	0.023256	0.509259	
chunk0019_101_1	chr1	224884328	224884706	+	0	NA	Intergenic	LTR40A1|LTR|ERVL	-45137	NM_001145154	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.002646	0.427441	
chunk0063_198_1	chr14	81144466	81144957	+	0	NA	3' UTR (NM_000369, exon 10 of 10)	3' UTR (NM_000369, exon 10 of 10)	58123	NR_003021	677845	Hs.693251	NR_003021	ENSG00000221303	SNORA79	ACA65|SNORA79A	small nucleolar RNA, H/ACA box 79	snoRNA	0.004073	0.359756	
chunk0026_301_1	chr10	67917026	67917706	+	0	NA	3' UTR (NM_001142498, exon 8 of 8)	3' UTR (NM_001142498, exon 8 of 8)	25964	NM_001314049	23411	Hs.369779	NM_012238	ENSG00000096717	SIRT1	SIR2|SIR2L1|SIR2alpha	sirtuin 1	protein-coding	0.004412	0.353891	
chunk0203_447_1	chr9	91413024	91413265	+	0	NA	intron (NM_001290000, intron 1 of 1)	intron (NM_001290000, intron 1 of 1)	10718	NM_005384	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.004149	0.318182	
chunk0180_425_1	chr7	76249302	76249893	+	0	NA	intron (NM_001110199, intron 3 of 14)	L3|LINE|CR1	47704	NM_001291831	222183	Hs.511025	NM_001039212	ENSG00000177679	SRRM3	-	serine/arginine repetitive matrix 3	protein-coding	0.027073	0.516892	288(GGGAACAGCCTGTGCC,-,0.00),289(GGAACAGCCTGTGCCT,+,0.00)
chunk0204_311_1	chr9	100285540	100286226	+	0	NA	intron (NR_051962, intron 14 of 17)	MER68|LTR|ERVL	66688	NM_001161584	54881	Hs.494648	NM_017746	ENSG00000136891	TEX10	Ipi1|bA208F1.2	testis expressed 10	protein-coding	0.010204	0.395924	
chunk0057_84_1	chr13	98535426	98535944	+	0	NA	intron (NM_001286649, intron 1 of 9)	MIRb|SINE|MIR	-13560	NM_003576	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.013514	0.468208	
chunk0164_451_1	chr6	28323845	28324270	+	0	NA	TTS (NM_001135216)	TTS (NM_001135216)	12077	NM_001135216	64288	Hs.656413	NM_030899	ENSG00000235109	ZSCAN31	ZNF20-Lp|ZNF310P|ZNF323	zinc finger and SCAN domain containing 31	protein-coding	0.002353	0.511737	
chunk0058_19_1	chr14	19726680	19727104	+	0	NA	Intergenic	L1MA3|LINE|L1	-12560	NM_001197287	79334	Hs.554706	NM_001197287	ENSG00000258453	OR11H2	C14orf15|OR11H13|OR11H2P|OR11H8P	olfactory receptor family 11 subfamily H member 2	protein-coding	0.002358	0.289412	
chunk0064_160_1	chr14	91985613	91985975	+	0	NA	intron (NM_004239, intron 16 of 20)	intron (NM_004239, intron 16 of 20)	-38092	NM_006329	10516	Hs.332708	NM_006329	ENSG00000140092	FBLN5	ADCL2|ARCL1A|ARMD3|DANCE|EVEC|FIBL-5|HNARMD|UP50	fibulin 5	protein-coding	0.005525	0.294766	
chunk0024_273_1	chr10	41875045	41875560	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	492743	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.017476	0.412791	
chunk0002_411_1	chr1	27522283	27522560	+	0	NA	Intergenic	Intergenic	-32234	NM_001201404	10163	Hs.469244	NM_006990	ENSG00000158195	WASF2	IMD2|SCAR2|WASF4|WAVE2|dJ393P12.2	WASP family member 2	protein-coding	0.021661	0.543165	128(GGGAACACTGTGTGAC,-,0.00),129(GGAACACTGTGTGACT,+,0.00)
chunk0157_363_1	chr5	123423363	123423562	+	0	NA	intron (NM_153223, intron 1 of 20)	CpG	130	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.070352	0.635000	
chunk0186_155_1	chr7	139133713	139133912	+	0	NA	promoter-TSS (NM_001287512)	promoter-TSS (NM_001287512)	68	NM_024926	79989	Hs.133020	NM_024926	ENSG00000105948	TTC26	DYF13|IFT56|dyf-13	tetratricopeptide repeat domain 26	protein-coding	0.080402	0.585000	
chunk0136_306_1	chr3	195181765	195182066	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	34044	NR_102710	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.003322	0.413907	
chunk0134_39_1	chr3	175695365	175695667	+	0	NA	intron (NM_207015, intron 11 of 13)	intron (NM_207015, intron 11 of 13)	80817	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.003311	0.346535	228(AGTACTATTTGTTCTT,+,0.00)
chunk0207_285_1	chr9	132871142	132871733	+	0	NA	intron (NM_152572, intron 2 of 12)	intron (NM_152572, intron 2 of 12)	-6883	NR_133631	11092	Hs.62595	NM_018956	ENSG00000165698	SPACA9	C9orf9|Mast	sperm acrosome associated 9	protein-coding	0.020305	0.538851	287(AAGGACAAAATGTTCT,-,0.00),288(AGGACAAAATGTTCTA,+,0.00)
chunk0146_97_1	chr4	158176757	158177213	+	0	NA	Intergenic	Intergenic	-3935	NM_001128424	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.367615	
chunk0152_67_1	chr5	58024064	58024427	+	0	NA	Intergenic	Intergenic	98096	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.000000	0.343407	
chunk0076_298_1	chr16	69909609	69910569	+	0	NA	3' UTR (NM_001270455, exon 9 of 9)	3' UTR (NM_001270455, exon 9 of 9)	-14894	NM_199424	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.012500	0.364204	
chunk0091_108_1	chr19	5959369	5959620	+	0	NA	intron (NM_007320, intron 1 of 15)	intron (NM_007320, intron 1 of 15)	18815	NM_001300865	8498	Hs.531752	NM_003624	ENSG00000031823	RANBP3	-	RAN binding protein 3	protein-coding	0.027888	0.603175	
chunk0173_357_1	chr6	149243012	149243252	+	0	NA	intron (NM_001292035, intron 2 of 6)	intron (NM_001292035, intron 2 of 6)	25208	NR_125861	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.020833	0.439834	
chunk0178_280_1	chr7	37201354	37201920	+	0	NA	intron (NM_001206482, intron 13 of 21)	intron (NM_001206482, intron 13 of 21)	152031	NM_001206482	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.008834	0.462081	335(GTAACAGAATGTCCCA,+,0.00)
chunk0122_368_1	chr3	37622888	37623341	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	170792	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.011038	0.378855	
chunk0023_264_1	chr10	27699709	27700968	+	0	NA	intron (NM_173576, intron 5 of 6)	intron (NM_173576, intron 5 of 6)	-44277	NR_121652	101929202	Hs.568843	NR_121652		MKX-AS1	-	MKX antisense RNA 1	ncRNA	0.007149	0.338889	
chunk0049_426_1	chr12	97871729	97872038	+	0	NA	Intergenic	Intergenic	67238	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.003236	0.351613	38(TAGGGCATTCTGTGCT,-,0.00),39(AGGGCATTCTGTGCTT,+,0.00)
chunk0159_24_1	chr5	136490440	136491027	+	0	NA	Intergenic	L1M4|LINE|L1	-125257	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.001704	0.382653	
chunk0084_140_1	chr17	76382904	76383261	+	0	NA	Intergenic	CpG	-1527	NM_001142601	8877	Hs.68061	NM_021972	ENSG00000176170	SPHK1	SPHK	sphingosine kinase 1	protein-coding	0.114846	0.726257	
chunk0207_123_1	chr9	128920411	128920993	+	0	NA	promoter-TSS (NM_001100876)	promoter-TSS (NM_001100876)	-193	NM_174933	254295	Hs.709447	NM_174933	ENSG00000175287	PHYHD1	-	phytanoyl-CoA dioxygenase domain containing 1	protein-coding	0.018900	0.559177	550(GAAACACTTTGTCCCT,+,0.00)
chunk0017_252_1	chr1	208949042	208949464	+	0	NA	Intergenic	Intergenic	-479570	NM_001104548									0.004739	0.304965	
chunk0129_432_1	chr3	127612273	127612658	+	0	NA	intron (NM_004526, intron 8 of 15)	MIR|SINE|MIR	14108	NR_073375	4171	Hs.477481	NM_004526	ENSG00000073111	MCM2	BM28|CCNL1|CDCL1|D3S3194|DFNA70|MITOTIN|cdc19	minichromosome maintenance complex component 2	protein-coding	0.005195	0.396373	
chunk0212_81_1	chrY	11556997	11557246	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	864469	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.028112	0.388000	
chunk0086_67_1	chr18	13111783	13112487	+	0	NA	intron (NM_032142, intron 40 of 44)	L1MB5|LINE|L1	-106595	NM_181482	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.004261	0.375887	
chunk0210_363_1	chrX	96563509	96563964	+	0	NA	Intergenic	Intergenic	-120927	NM_006729	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.000000	0.390351	
chunk0001_45_1	chr1	1841412	1842019	+	0	NA	intron (NM_002074, intron 1 of 11)	intron (NM_002074, intron 1 of 11)	49402	NM_002074	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.009885	0.406250	
chunk0018_425_1	chr1	222797237	222797577	+	0	NA	Intergenic	L2b|LINE|L2	-17682	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.002941	0.351906	
chunk0029_99_1	chr10	97407765	97408249	+	0	NA	Intergenic	MIRb|SINE|MIR	-6637	NM_015179	23223	Hs.434251	NM_015179	ENSG00000052749	RRP12	KIAA0690	ribosomal RNA processing 12 homolog	protein-coding	0.004132	0.447423	
chunk0075_51_1	chr16	47516215	47516774	+	0	NA	intron (NM_001031835, intron 7 of 31)	intron (NM_001031835, intron 7 of 31)	55195	NM_001031835	5257	Hs.78060	NM_000293	ENSG00000102893	PHKB	-	phosphorylase kinase regulatory subunit beta	protein-coding	0.008945	0.348214	
chunk0102_74_1	chr2	143125762	143126223	+	0	NA	Intergenic	Intergenic	-3338	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.004338	0.348485	
chunk0085_56_1	chr18	1073273	1073602	+	0	NA	Intergenic	Intergenic	168241	NM_001117	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.000000	0.306061	
chunk0179_281_1	chr7	49564079	49564342	+	0	NA	Intergenic	L1PA16|LINE|L1	-209451	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.015209	0.568182	44(AGGAGCAGAGTGTACC,-,0.00),45(GGAGCAGAGTGTACCT,+,0.00)
chunk0153_200_1	chr5	71748234	71748896	+	0	NA	Intergenic	Intergenic	29402	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.018127	0.511312	249(GAGGACGTGCTGTTCC,-,0.00),250(AGGACGTGCTGTTCCA,+,0.00),418(TGGGACTCAGTGTTCC,-,0.00),419(GGGACTCAGTGTTCCC,+,0.00)
chunk0005_298_1	chr1	60315717	60315969	+	0	NA	Intergenic	Intergenic	-242073	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.000000	0.292490	
chunk0078_22_1	chr17	782142	782432	+	0	NA	promoter-TSS (NM_018146)	promoter-TSS (NM_018146)	14	NM_018146	55178	Hs.182729	NM_018146	ENSG00000171861	MRM3	RMTL1|RNMTL1	mitochondrial rRNA methyltransferase 3	protein-coding	0.127586	0.670103	
chunk0157_372_1	chr5	123574603	123575282	+	0	NA	intron (NM_001031812, intron 5 of 12)	intron (NM_001031812, intron 5 of 12)	29525	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.002946	0.344118	
chunk0024_262_1	chr10	41846015	41846227	+	0	NA	Intergenic	Intergenic	521924	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.042453	0.347418	
chunk0180_100_1	chr7	55185127	55185675	+	0	NA	intron (NR_047551, intron 1 of 1)	intron (NR_047551, intron 1 of 1)	3548	NR_047551	100507500	Hs.720489	NR_047551	ENSG00000224057	EGFR-AS1	-	EGFR antisense RNA 1	ncRNA	0.010949	0.466302	
chunk0112_146_1	chr20	38813106	38813420	+	0	NA	intron (NM_015568, intron 1 of 10)	intron (NM_015568, intron 1 of 10)	7570	NM_001172735	26051	Hs.45719	NM_015568	ENSG00000101445	PPP1R16B	ANKRD4|TIMAP	protein phosphatase 1 regulatory subunit 16B	protein-coding	0.003185	0.504762	187(AGGTACATGGTGTTCC,-,0.00),188(GGTACATGGTGTTCCT,+,0.00)
chunk0210_234_1	chrX	82682060	82682688	+	0	NA	Intergenic	L1PA16|LINE|L1	-825887	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.006369	0.386328	
chunk0010_116_1	chr1	114452721	114453127	+	0	NA	intron (NM_033020, intron 4 of 18)	intron (NM_033020, intron 4 of 18)	58236	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.012315	0.439803	
chunk0196_174_1	chr8	105892128	105892401	+	0	NA	intron (NR_125796, intron 2 of 7)	L1MA6|LINE|L1	168239	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.000000	0.383212	108(GAGAACATTATGTTAC,-,0.00)
chunk0115_387_1	chr21	30408810	30409249	+	0	NA	Intergenic	L1PA16|LINE|L1	12955	NM_181599	140258	Hs.407653	NM_181599	ENSG00000198390	KRTAP13-1	KAP13.1|KRTAP13.1	keratin associated protein 13-1	protein-coding	0.025057	0.525000	
chunk0001_53_1	chr1	1898272	1898761	+	0	NA	Intergenic	Intergenic	-7399	NM_001282538	2782	Hs.430425	NM_002074	ENSG00000078369	GNB1	MRD42	G protein subunit beta 1	protein-coding	0.010225	0.451020	
chunk0178_403_1	chr7	40941366	40941875	+	0	NA	Intergenic	L1PB3|LINE|L1	38319	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.003929	0.329412	
chunk0178_166_1	chr7	33967271	33967591	+	0	NA	intron (NM_133468, intron 5 of 15)	intron (NM_133468, intron 5 of 15)	62520	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.006250	0.283489	
chunk0065_54_1	chr15	22821500	22821702	+	0	NA	intron (NM_001142275, intron 4 of 4)	intron (NM_001142275, intron 4 of 4)	-17040	NM_001184888	81614	Hs.591003	NM_030922	ENSG00000140157	NIPA2	SLC57A2	NIPA magnesium transporter 2	protein-coding	0.024752	0.512315	
chunk0018_100_1	chr1	218081422	218081643	+	0	NA	Intergenic	Intergenic	38027	NR_110794	101929631	Hs.407614	NR_110794	ENSG00000232100	LINC01653	-	long intergenic non-protein coding RNA 1653	ncRNA	0.000000	0.369369	
chunk0178_177_1	chr7	34156658	34156897	+	0	NA	TTS (NM_133468)	TTS (NM_133468)	251866	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.008368	0.370833	
chunk0037_428_1	chr11	80195142	80195348	+	0	NA	Intergenic	Intergenic	567558	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.391304	85(TAGCACATTCTGTTCC,-,0.00),86(AGCACATTCTGTTCCC,+,0.00)
chunk0059_382_1	chr14	37426856	37427336	+	0	NA	intron (NM_001195296, intron 13 of 14)	L1MB4|LINE|L1	168024	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.006250	0.365904	
chunk0188_116_1	chr8	9082073	9082313	+	0	NA	Intergenic	Intergenic	33748	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.004167	0.410788	
chunk0048_25_1	chr12	77345890	77346127	+	0	NA	Intergenic	Intergenic	-280428	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.008439	0.361345	
chunk0074_75_1	chr16	21520117	21520710	+	0	NA	promoter-TSS (NR_002594)	promoter-TSS (NR_002594)	31	NR_002594	387254	Hs.448808	NR_002594		SLC7A5P2	IMAA|MMAA	solute carrier family 7 member 5 pseudogene 2	pseudo	0.143339	0.757576	
chunk0004_401_1	chr1	52209704	52209932	+	0	NA	intron (NM_007324, intron 1 of 17)	L2c|LINE|L2	67724	NM_007324	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.000000	0.344978	
chunk0077_271_1	chr16	81002573	81002772	+	0	NA	intron (NM_020188, intron 1 of 3)	intron (NM_020188, intron 1 of 3)	-3826	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.005025	0.320000	
chunk0055_150_1	chr13	59946075	59946627	+	0	NA	intron (NM_001258369, intron 17 of 26)	intron (NM_001258369, intron 17 of 26)	-66367	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.003623	0.311031	419(GAAACACAATGTTCAC,+,0.00)
chunk0097_452_1	chr2	64607826	64608041	+	0	NA	intron (NR_034023, intron 1 of 3)	intron (NR_034023, intron 1 of 3)	621	NR_034023	339807	Hs.434736	NR_034023	ENSG00000233694	LINC02579	-	long intergenic non-protein coding RNA 2579	ncRNA	0.027907	0.601852	
chunk0210_372_1	chrX	97094602	97094851	+	0	NA	intron (NM_006729, intron 19 of 26)	intron (NM_006729, intron 19 of 26)	210818	NM_013347	29935	Hs.659349	NM_013347	ENSG00000204086	RPA4	HSU24186	replication protein A4	protein-coding	0.004016	0.388000	
chunk0037_354_1	chr11	77637581	77637882	+	0	NA	promoter-TSS (NM_001311200)	promoter-TSS (NM_001311200)	75	NM_001311199	1207	Hs.430733	NM_001293	ENSG00000074201	CLNS1A	CLCI|CLNS1B|ICln	chloride nucleotide-sensitive channel 1A	protein-coding	0.059801	0.609272	
chunk0155_461_1	chr5	101782272	101783093	+	0	NA	Intergenic	Intergenic	513867	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.012180	0.375912	
chunk0202_301_1	chr9	77898789	77899159	+	0	NA	intron (NM_002072, intron 2 of 6)	L1ME3G|LINE|L1	132475	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.005405	0.312668	148(CAGGACATATAGTTCT,-,0.00),149(AGGACATATAGTTCTA,+,0.00)
chunk0050_458_1	chr12	111067405	111068103	+	0	NA	intron (NM_015267, intron 1 of 21)	intron (NM_015267, intron 1 of 21)	33730	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.014327	0.510730	
chunk0098_225_1	chr2	73780068	73780365	+	0	NA	promoter-TSS (NM_003584)	promoter-TSS (NM_003584)	-59	NM_003584	8446	Hs.14611	NM_003584	ENSG00000144048	DUSP11	PIR1	dual specificity phosphatase 11	protein-coding	0.063973	0.563758	
chunk0096_444_1	chr2	39289132	39289397	+	0	NA	intron (NM_003618, intron 19 of 33)	intron (NM_003618, intron 19 of 33)	-59732	NM_001009565	344387	Hs.403201	NM_001009565	ENSG00000205111	CDKL4	-	cyclin dependent kinase like 4	protein-coding	0.011321	0.296992	
chunk0133_108_1	chr3	168018773	168019297	+	0	NA	intron (NM_001308155, intron 13 of 14)	MER58A|DNA|hAT-Charlie	76890	NM_014498	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.005725	0.354286	
chunk0012_467_1	chr1	165617459	165617699	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-13294	NM_004528	4259	Hs.191734	NM_004528	ENSG00000143198	MGST3	GST-III	microsomal glutathione S-transferase 3	protein-coding	0.000000	0.473029	
chunk0121_51_1	chr3	15611932	15612419	+	0	NA	intron (NM_001281725, intron 1 of 3)	L1M7|LINE|L1	10206	NM_001281725	686	Hs.444197	NM_001281723	ENSG00000169814	BTD	-	biotinidase	protein-coding	0.004107	0.311475	
chunk0172_282_1	chr6	137732037	137732409	+	0	NA	intron (NR_121618, intron 1 of 2)	intron (NR_121618, intron 1 of 2)	6814	NR_121619	100507406	Hs.556703	NR_121618	ENSG00000234956	LINC02539	-	long intergenic non-protein coding RNA 2539	ncRNA	0.005376	0.386059	
chunk0036_342_1	chr11	66768774	66769241	+	0	NA	intron (NM_001302084, intron 2 of 14)	intron (NM_001302084, intron 2 of 14)	24271	NM_024650	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.000000	0.414530	246(GGGCACTTACTGTTCC,-,0.00),247(GGCACTTACTGTTCCA,+,0.00)
chunk0187_359_1	chr7	157259843	157260509	+	0	NA	intron (NM_014671, intron 22 of 22)	intron (NM_014671, intron 22 of 22)	-76840	NM_005494	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.022523	0.434783	
chunk0068_417_1	chr15	59158285	59158700	+	0	NA	intron (NM_004998, intron 24 of 27)	intron (NM_004998, intron 24 of 27)	12770	NR_031750	100313886		NR_031750	ENSG00000253030	MIR2116	mir-2116	microRNA 2116	ncRNA	0.002410	0.432692	
chunk0007_394_1	chr1	85464591	85464904	+	0	NA	exon (NM_012137, exon 1 of 6)	exon (NM_012137, exon 1 of 6)	459	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.115016	0.716561	
chunk0066_396_1	chr15	39088142	39088659	+	0	NA	Intergenic	Intergenic	-162269	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.001934	0.333977	
chunk0064_30_1	chr14	89432325	89432588	+	0	NA	intron (NM_001085471, intron 1 of 6)	MIRb|SINE|MIR	15102	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.011407	0.443182	64(ATGAACACCAAGTACC,-,0.00)
chunk0211_146_1	chrX	113455111	113455580	+	0	NA	intron (NR_110399, intron 3 of 3)	L1PB2|LINE|L1	412618	NR_110399	101928437	Hs.640112	NR_110399		LOC101928437	-	uncharacterized LOC101928437	ncRNA	0.002132	0.327660	126(GAGCACAGGATGTGTT,-,0.00),127(AGCACAGGATGTGTTT,+,0.00)
chunk0120_73_1	chr3	3464653	3465035	+	0	NA	Intergenic	Intergenic	-285127	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.000000	0.391645	
chunk0069_224_1	chr15	63759688	63760005	+	0	NA	intron (NM_003922, intron 3 of 77)	intron (NM_003922, intron 3 of 77)	74102	NM_003922	8925	Hs.210385	NM_003922	ENSG00000103657	HERC1	MDFPMR|p532|p619	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding	0.003155	0.367925	
chunk0197_1_1	chr8	116690344	116690831	+	0	NA	intron (NM_003756, intron 2 of 7)	intron (NM_003756, intron 2 of 7)	65236	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.002053	0.375000	282(GGGCACAGAATGTACT,-,0.00),283(GGCACAGAATGTACTA,+,0.00)
chunk0052_381_1	chr12	129146252	129146974	+	0	NA	intron (NM_133448, intron 5 of 8)	intron (NM_133448, intron 5 of 8)	36923	NR_104172	283352	Hs.665667	NR_104172	ENSG00000249196	TMEM132D-AS1	-	TMEM132D antisense RNA 1	ncRNA	0.009695	0.428769	
chunk0174_90_1	chr6	156600218	156600680	+	0	NA	Intergenic	Intergenic	-177481	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.012987	0.425486	220(AAGAACACCGTGTCCC,-,0.00),221(AGAACACCGTGTCCCT,+,0.00)
chunk0114_129_1	chr21	9843724	9844628	+	0	NA	Intergenic	MER70A|LTR|ERVL	-23115	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.004425	0.391160	417(AGGTACACTGTGTACT,-,0.00),418(GGTACACTGTGTACTA,+,0.00)
chunk0195_219_1	chr8	97077320	97077573	+	0	NA	intron (NM_016134, intron 7 of 7)	Tigger2b_Pri|DNA|TcMar-Tigger	200502	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.003953	0.377953	125(TAGTACAGTATGTACT,-,0.00),126(AGTACAGTATGTACTA,+,0.00)
chunk0035_258_1	chr11	46461244	46461924	+	0	NA	intron (NM_001300731, intron 10 of 16)	intron (NM_001300731, intron 10 of 16)	-9695	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.002941	0.381791	
chunk0103_313_1	chr2	167397228	167397760	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	210211	NM_001199145	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.001880	0.352720	264(TGGCACATTCTGTTCT,-,0.00),265(GGCACATTCTGTTCTC,+,0.00)
chunk0047_362_1	chr12	75048759	75049189	+	0	NA	intron (NM_139136, intron 3 of 5)	intron (NM_139136, intron 3 of 5)	160774	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.004651	0.359629	
chunk0078_447_1	chr16	89722712	89722927	+	0	NA	exon (NM_001113525, exon 2 of 11)	exon (NM_001113525, exon 2 of 11)	1275	NM_001113525	92822	Hs.290154	NM_152287	ENSG00000158805	ZNF276	CENP-Z|CENPZ|ZADT|ZFP276|ZNF477	zinc finger protein 276	protein-coding	0.055814	0.611111	188(AGGGACAGGGCGTGCC,-,0.00),189(GGGACAGGGCGTGCCT,+,0.00)
chunk0155_338_1	chr5	96934497	96935911	+	0	NA	promoter-TSS (NM_005575)	promoter-TSS (NM_005575)	-438	NM_005575	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.079208	0.624735	
chunk0209_302_1	chrX	48898030	48898288	+	0	NA	promoter-TSS (NM_001167992)	promoter-TSS (NM_001167992)	-16	NM_005834	10245	Hs.30570	NM_005834	ENSG00000126768	TIMM17B	DXS9822|JM3|TIM17B	translocase of inner mitochondrial membrane 17B	protein-coding	0.046512	0.629344	
chunk0004_8_1	chr1	41950231	41951054	+	0	NA	intron (NR_038261, intron 1 of 3)	intron (NR_038261, intron 1 of 3)	-31817	NR_038260	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.002430	0.372573	
chunk0151_192_1	chr5	50575829	50576054	+	0	NA	Intergenic	Intergenic	-89958	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.008889	0.314159	
chunk0009_407_1	chr1	110414612	110414913	+	0	NA	intron (NR_102697, intron 2 of 2)	MLT1B|LTR|ERVL-MaLR	-6838	NM_006402	10542	Hs.439815	NM_006402	ENSG00000134248	LAMTOR5	HBXIP|XIP	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	protein-coding	0.000000	0.456954	
chunk0009_173_1	chr1	105479249	105479462	+	0	NA	Intergenic	L1MEg|LINE|L1	139580	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004695	0.359813	
chunk0105_64_1	chr2	183603993	183604576	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	479929	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.008576	0.347603	324(TAGTACAGTATGTACT,-,0.00),325(AGTACAGTATGTACTA,+,0.00)
chunk0161_63_1	chr5	166416627	166416914	+	0	NA	Intergenic	L1MEf|LINE|L1	509600	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.000000	0.274306	
chunk0068_176_1	chr15	54212639	54213236	+	0	NA	intron (NM_001080534, intron 3 of 30)	intron (NM_001080534, intron 3 of 30)	200033	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.005025	0.336120	246(AGGAACAAACAGTACT,-,0.00),247(GGAACAAACAGTACTT,+,0.00)
chunk0037_282_1	chr11	75876352	75876584	+	0	NA	intron (NM_003369, intron 3 of 14)	intron (NM_003369, intron 3 of 14)	61301	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.000000	0.386266	
chunk0165_434_1	chr6	39964835	39965572	+	0	NA	Intergenic	L1MEd|LINE|L1	-30652	NR_033233	4337	Hs.357128	NM_005942	ENSG00000124615	MOCS1	MIG11|MOCOD|MOCS1A|MOCS1B	molybdenum cofactor synthesis 1	protein-coding	0.000000	0.292683	
chunk0139_334_1	chr4	59298706	59299164	+	0	NA	Intergenic	L1MB7|LINE|L1	-1623684	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.004367	0.409586	
chunk0101_444_1	chr2	139617359	139617749	+	0	NA	Intergenic	L1PBa|LINE|L1	720230	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.002564	0.355499	
chunk0169_395_1	chr6	108127901	108128387	+	0	NA	Intergenic	Intergenic	-37914	NM_003269	7101	Hs.157688	NM_003269	ENSG00000112333	NR2E1	TLL|TLX|XTLL	nuclear receptor subfamily 2 group E member 1	protein-coding	0.002058	0.359343	
chunk0099_99_1	chr2	85549034	85549520	+	0	NA	3' UTR (NM_000821, exon 15 of 15)	3' UTR (NM_000821, exon 15 of 15)	10299	NM_005911	4144	Hs.516157	NM_005911	ENSG00000168906	MAT2A	MATA2|MATII|SAMS2	methionine adenosyltransferase 2A	protein-coding	0.022634	0.431211	
chunk0034_433_1	chr11	39194914	39195289	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	546243	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.005333	0.414894	
chunk0059_409_1	chr14	37826751	37827269	+	0	NA	intron (NM_001310135, intron 30 of 32)	intron (NM_001310135, intron 30 of 32)	231811	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.001931	0.331407	
chunk0093_264_1	chr19	51207591	51208096	+	0	NA	promoter-TSS (NR_107041)	promoter-TSS (NR_107041)	-834	NR_107041	102465873		NR_107041	ENSG00000278617	MIR8074	hsa-mir-8074	microRNA 8074	ncRNA	0.007921	0.466403	
chunk0167_261_1	chr6	69594218	69594856	+	0	NA	Intergenic	Intergenic	202620	NM_018368	55788	Hs.271643	NM_018368	ENSG00000168216	LMBRD1	C6orf209|LMBD1|MAHCF|NESI	LMBR1 domain containing 1	protein-coding	0.004702	0.367762	
chunk0199_432_1	chr9	13801392	13801705	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-126423	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.009585	0.334395	
chunk0059_254_1	chr14	35108859	35109074	+	0	NA	intron (NR_130972, intron 4 of 11)	intron (NR_130972, intron 4 of 11)	-13355	NM_001256678	9692	Hs.458487	NM_014672	ENSG00000100890	PRORP	KIAA0391|MRPP3	protein only RNase P catalytic subunit	protein-coding	0.013953	0.361111	
chunk0012_117_1	chr1	156912969	156913359	+	0	NA	intron (NM_001080471, intron 18 of 22)	intron (NM_001080471, intron 18 of 22)	-7468	NM_144702	149499	Hs.491734	NM_144702	ENSG00000160838	LRRC71	C1orf92	leucine rich repeat containing 71	protein-coding	0.015385	0.601023	193(GAGCTCACCCTGTGCT,-,0.00),194(AGCTCACCCTGTGCTT,+,0.00)
chunk0096_301_1	chr2	32727086	32727713	+	0	NA	intron (NM_017735, intron 10 of 19)	Charlie1a|DNA|hAT-Charlie	92144	NR_039922	100616219		NR_039922	ENSG00000265057	MIR4765	-	microRNA 4765	ncRNA	0.003190	0.318471	
chunk0048_83_1	chr12	79093757	79094332	+	0	NA	intron (NM_001135805, intron 4 of 11)	LTR49-int|LTR|ERV1	48391	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.000000	0.246528	
chunk0103_306_1	chr2	166853026	166853451	+	0	NA	Intergenic	L1MA8|LINE|L1	-35249	NM_001199143	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.002353	0.298122	
chunk0063_139_1	chr14	79509907	79510384	+	0	NA	intron (NR_073547, intron 15 of 20)	intron (NR_073547, intron 15 of 20)	230806	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.010482	0.410042	
chunk0207_149_1	chr9	129687594	129687830	+	0	NA	intron (NM_016307, intron 1 of 3)	intron (NM_016307, intron 1 of 3)	22071	NM_016307	51450	Hs.660115	NM_016307	ENSG00000167157	PRRX2	PMX2|PRX2	paired related homeobox 2	protein-coding	0.021186	0.565401	
chunk0107_225_1	chr2	216985493	216986055	+	0	NA	Intergenic	Intergenic	115002	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.016014	0.547069	
chunk0187_241_1	chr7	152899819	152900141	+	0	NA	Intergenic	Intergenic	140231	NR_073001									0.015528	0.492260	
chunk0212_362_1	chrX	149400258	149400769	+	0	NA	Intergenic	L1PB1|LINE|L1	104841	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.003914	0.337891	
chunk0094_273_1	chr2	8103390	8103644	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	-126703	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.007874	0.329412	
chunk0174_287_1	chr6	162103102	162103986	+	0	NA	intron (NM_004562, intron 4 of 11)	L1M5|LINE|L1	-623588	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.010181	0.376271	
chunk0183_195_1	chr7	106313397	106314073	+	0	NA	Intergenic	Intergenic	-28543	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.005917	0.355982	
chunk0142_324_1	chr4	100982327	100982677	+	0	NA	Intergenic	Intergenic	258370	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.008571	0.404558	209(AAGAACAGGACGTGCT,-,0.00),210(AGAACAGGACGTGCTT,+,0.00)
chunk0060_428_1	chr14	53963250	53963479	+	0	NA	Intergenic	Intergenic	-6528	NM_001202	652	Hs.68879	NM_001202	ENSG00000125378	BMP4	BMP2B|BMP2B1|MCOPS6|OFC11|ZYME	bone morphogenetic protein 4	protein-coding	0.061135	0.591304	167(AGGGGCAGACTGTACT,-,0.00),168(GGGGCAGACTGTACTT,+,0.00)
chunk0175_108_1	chr7	3106343	3106696	+	0	NA	Intergenic	Intergenic	52054	NR_126024	100129603	Hs.652997	NR_126024		LOC100129603	-	uncharacterized LOC100129603	ncRNA	0.002833	0.500000	
chunk0010_103_1	chr1	114093750	114094431	+	0	NA	intron (NM_205848, intron 6 of 7)	intron (NM_205848, intron 6 of 7)	58350	NM_205848	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.008811	0.434018	
chunk0001_174_1	chr1	6902495	6903263	+	0	NA	intron (NM_015215, intron 3 of 22)	L1ME2|LINE|L1	117555	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.005208	0.374512	
chunk0060_354_1	chr14	52291146	52291567	+	0	NA	Intergenic	L1ME3B|LINE|L1	-22942	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.009501	0.362559	
chunk0022_345_1	chr10	16957146	16957631	+	0	NA	intron (NM_001081, intron 31 of 66)	L1MA6|LINE|L1	-139934	NM_012425	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.004124	0.380658	172(ATGAACATAAAGTCCT,-,0.00),173(TGAACATAAAGTCCTT,+,0.00)
chunk0066_158_1	chr15	32091921	32092561	+	0	NA	intron (NR_046324, intron 2 of 7)	HAL1b|LINE|L1	61758	NR_046324	1139	Hs.511772	NM_000746	ENSG00000175344	CHRNA7	CHRNA7-2|NACHRA7	cholinergic receptor nicotinic alpha 7 subunit	protein-coding	0.003125	0.355694	
chunk0109_443_1	chr2	241550210	241550956	+	0	NA	intron (NR_033346, intron 1 of 1)	intron (NR_033346, intron 1 of 1)	-8148	NM_032515	666	Hs.293753	NM_032515	ENSG00000176720	BOK	BCL2L9|BOKL	BCL2 family apoptosis regulator BOK	protein-coding	0.017426	0.585007	
chunk0120_315_1	chr3	10248629	10248887	+	0	NA	5' UTR (NM_014760, exon 1 of 8)	5' UTR (NM_014760, exon 1 of 8)	265	NM_014760	9797	Hs.475401	NM_014760	ENSG00000157014	TATDN2	-	TatD DNase domain containing 2	protein-coding	0.100775	0.687259	
chunk0150_295_1	chr5	37401802	37402341	+	0	NA	intron (NM_018034, intron 5 of 17)	L1MA5|LINE|L1	22761	NM_018034	55100	Hs.213690	NM_018034	ENSG00000082068	WDR70	-	WD repeat domain 70	protein-coding	0.003711	0.337037	
chunk0131_333_1	chr3	151171005	151171854	+	0	NA	intron (NM_053002, intron 10 of 42)	intron (NM_053002, intron 10 of 42)	31772	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.009423	0.483529	508(CTGGACAGAGTGTTCC,-,0.00),509(TGGACAGAGTGTTCCT,+,0.00),721(TGGCACAGAGTGTCCC,-,0.00),722(GGCACAGAGTGTCCCA,+,0.00)
chunk0146_100_1	chr4	158645489	158645688	+	0	NA	intron (NR_045580, intron 15 of 17)	intron (NR_045580, intron 15 of 17)	26462	NM_001008393	201725	Hs.380920	NM_001008393	ENSG00000205208	C4orf46	RCDG1	chromosome 4 open reading frame 46	protein-coding	0.005025	0.310000	
chunk0062_400_1	chr14	74890329	74890764	+	0	NA	intron (NM_001933, intron 6 of 14)	intron (NM_001933, intron 6 of 14)	8655	NR_033814	1743	Hs.525459	NM_001933	ENSG00000119689	DLST	DLTS	dihydrolipoamide S-succinyltransferase	protein-coding	0.013793	0.438073	
chunk0103_28_1	chr2	159062955	159063396	+	0	NA	intron (NM_001145909, intron 2 of 26)	MamRep605|LTR?|LTR?	94541	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.009070	0.423077	146(AGCACACTCTCTCCCT,+,0.00)
chunk0172_428_1	chr6	140731905	140732418	+	0	NA	Intergenic	(AATATGA)n|Simple_repeat|Simple_repeat	48347	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.005848	0.291829	
chunk0155_111_1	chr5	92896725	92896937	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	674512	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.267606	
chunk0105_455_1	chr2	195140859	195141058	+	0	NA	Intergenic	Intergenic	410363	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.005025	0.415000	
chunk0176_397_1	chr7	18866356	18866592	+	0	NA	intron (NM_178425, intron 20 of 24)	intron (NM_178425, intron 20 of 24)	251198	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.004237	0.451477	
chunk0132_271_1	chr3	159626741	159626940	+	0	NA	intron (NM_001197108, intron 1 of 6)	intron (NM_001197108, intron 1 of 6)	141772	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.000000	0.435000	
chunk0103_87_1	chr2	160793619	160793880	+	0	NA	Intergenic	L1M4b|LINE|L1	-299942	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.003831	0.339695	
chunk0196_53_1	chr8	102095861	102096078	+	0	NA	intron (NM_001040628, intron 1 of 7)	intron (NM_001040628, intron 1 of 7)	28365	NM_001040625	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.000000	0.454128	
chunk0172_354_1	chr6	139069009	139069547	+	0	NA	Intergenic	Intergenic	40596	NM_021243	58527	Hs.600861	NM_021243	ENSG00000146386	ABRACL	C6orf115|Costars|HSPC280|PRO2013	ABRA C-terminal like	protein-coding	0.005576	0.332096	474(GACACAAAATGTTCTG,+,0.00)
chunk0073_258_1	chr16	11912809	11913523	+	0	NA	intron (NM_001130007, intron 1 of 14)	intron (NM_001130007, intron 1 of 14)	2802	NM_001130006	2935	Hs.528780	NM_002094	ENSG00000103342	GSPT1	551G9.2|ETF3A|GST1|eRF3a	G1 to S phase transition 1	protein-coding	0.011204	0.377622	347(AAGCACTGATTGTTCT,-,0.00),348(AGCACTGATTGTTCTC,+,0.00)
chunk0111_362_1	chr20	33644947	33645693	+	0	NA	3' UTR (NM_001039709, exon 11 of 11)	3' UTR (NM_001039709, exon 11 of 11)	-16966	NM_080825	128864	Hs.324104	NM_080825	ENSG00000149609	C20orf144	dJ63M2.6	chromosome 20 open reading frame 144	protein-coding	0.013405	0.503347	
chunk0188_103_1	chr8	8874938	8875625	+	0	NA	intron (NM_004225, intron 1 of 2)	intron (NM_004225, intron 1 of 2)	18340	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.010189	0.324128	
chunk0089_339_1	chr18	65757917	65758254	+	0	NA	intron (NM_004361, intron 1 of 11)	intron (NM_004361, intron 1 of 11)	7164	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.000000	0.325444	
chunk0155_274_1	chr5	95989316	95990187	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	-27680	NM_012081	22936	Hs.192221	NM_012081	ENSG00000118985	ELL2	MRCCAT1	elongation factor for RNA polymerase II 2	protein-coding	0.001148	0.327982	518(CAGAACAGAAAGTCCT,-,0.00),519(AGAACAGAAAGTCCTG,+,0.00)
chunk0075_231_1	chr16	52929358	52929692	+	0	NA	Intergenic	L2b|LINE|L2	-125508	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.000000	0.328358	179(ATGCACAGCAAGTGCT,-,0.00)
chunk0087_414_1	chr18	42207313	42208011	+	0	NA	intron (NR_046455, intron 1 of 4)	intron (NR_046455, intron 1 of 4)	20994	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.002865	0.311874	
chunk0002_25_1	chr1	12381152	12381760	+	0	NA	intron (NM_018156, intron 56 of 68)	intron (NM_018156, intron 56 of 68)	-125790	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.006579	0.392447	
chunk0110_18_1	chr20	10264987	10265624	+	0	NA	intron (NM_003081, intron 1 of 7)	intron (NM_003081, intron 1 of 7)	-45799	NR_040710	100131208	Hs.658178	NR_040710	ENSG00000227906	SNAP25-AS1	-	SNAP25 antisense RNA 1	ncRNA	0.004710	0.360502	
chunk0128_360_1	chr3	113084185	113084643	+	0	NA	Intergenic	AluJr4|SINE|Alu	-64706	NM_015412	25871	Hs.591288	NM_015412	ENSG00000163608	NEPRO	C3orf17|NET17	nucleolus and neural progenitor protein	protein-coding	0.008734	0.413943	
chunk0164_21_1	chr6	17984980	17985939	+	0	NA	intron (NM_001243423, intron 2 of 2)	intron (NM_001243423, intron 2 of 2)	2164	NM_022113	63971	Hs.94499	NM_022113	ENSG00000137177	KIF13A	RBKIN|bA500C11.2	kinesin family member 13A	protein-coding	0.012513	0.375000	
chunk0203_57_1	chr9	83380525	83380855	+	0	NA	intron (NM_001244959, intron 2 of 14)	intron (NM_001244959, intron 2 of 14)	-48729	NM_001244961	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.006061	0.350453	
chunk0036_348_1	chr11	66801711	66802222	+	0	NA	intron (NM_024650, intron 8 of 16)	intron (NM_024650, intron 8 of 16)	-41446	NM_001032279	9986	Hs.654972	NM_005133	ENSG00000173653	RCE1	FACE2|RCE1A|RCE1B	Ras converting CAAX endopeptidase 1	protein-coding	0.015656	0.437500	
chunk0073_384_1	chr16	15975200	15975417	+	0	NA	intron (NM_004996, intron 1 of 30)	intron (NM_004996, intron 1 of 30)	25731	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.013825	0.486239	174(TTGTACACGTTGTTCC,-,0.00),175(TGTACACGTTGTTCCT,+,0.00)
chunk0019_337_1	chr1	229273661	229274349	+	0	NA	intron (NM_001271998, intron 1 of 5)	intron (NM_001271998, intron 1 of 5)	2943	NM_004578	5867	Hs.296169	NM_004578	ENSG00000168118	RAB4A	HRES-1|HRES-1/RAB4|HRES1|RAB4	RAB4A, member RAS oncogene family	protein-coding	0.008721	0.454282	
chunk0030_144_1	chr10	113720557	113720986	+	0	NA	intron (NM_001267058, intron 1 of 5)	L1ME3A|LINE|L1	11426	NM_001267058	840	Hs.9216	NM_001227	ENSG00000165806	CASP7	CASP-7|CMH-1|ICE-LAP3|LICE2|MCH3	caspase 7	protein-coding	0.018648	0.430233	
chunk0132_114_1	chr3	155917714	155918210	+	0	NA	intron (NM_003875, intron 9 of 15)	L1MB2|LINE|L1	47426	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.006048	0.382294	309(AGGAACTTATTGTCCA,-,0.00),310(GGAACTTATTGTCCAT,+,0.00)
chunk0008_295_1	chr1	94980138	94980414	+	0	NA	Intergenic	Intergenic	52248	NR_033998	729970	Hs.297988	NR_033998	ENSG00000235501	LOC729970	-	hCG2028352-like	ncRNA	0.007246	0.429603	
chunk0026_137_1	chr10	62166728	62167037	+	0	NA	Intergenic	Intergenic	101981	NM_001282941	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.009709	0.374194	
chunk0183_2_1	chr7	102395937	102396204	+	0	NA	promoter-TSS (NM_024653)	promoter-TSS (NM_024653)	-287	NM_024653	79706	Hs.722104	NM_024653	ENSG00000128563	PRKRIP1	C114|KRBOX3	PRKR interacting protein 1	protein-coding	0.059925	0.619403	
chunk0209_308_1	chrX	49699836	49700138	+	0	NA	Intergenic	L1MB7|LINE|L1	-3994	NM_003785	8712	Hs.128231	NM_003785	ENSG00000068985	PAGE1	AL5|CT16.3|GAGE-9|GAGEB1|PAGE-1	PAGE family member 1	protein-coding	0.006623	0.346535	
chunk0155_332_1	chr5	96887359	96887968	+	0	NA	intron (NM_001130140, intron 4 of 18)	intron (NM_001130140, intron 4 of 18)	11723	NM_022350	64167	Hs.482910	NM_022350	ENSG00000164308	ERAP2	L-RAP|LRAP	endoplasmic reticulum aminopeptidase 2	protein-coding	0.014778	0.426230	
chunk0124_189_1	chr3	55614778	55615506	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	44327	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.004121	0.370370	
chunk0010_405_1	chr1	119567613	119567945	+	0	NA	non-coding (NR_033781, exon 1 of 1)	non-coding (NR_033781, exon 1 of 1)	3899	NR_033781	128102	Hs.681806	NR_033781		HSD3BP4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 4	pseudo	0.006024	0.447447	
chunk0003_203_1	chr1	34851037	34851275	+	0	NA	3' UTR (NM_138428, exon 2 of 2)	3' UTR (NM_138428, exon 2 of 2)	7889	NM_001164824	113444	Hs.27160	NM_138428	ENSG00000163866	SMIM12	C1orf212	small integral membrane protein 12	protein-coding	0.004202	0.384937	142(TAGCACAGTCTGTGAC,-,0.00)
chunk0001_211_1	chr1	7982403	7982694	+	0	NA	intron (NM_007262, intron 6 of 6)	intron (NM_007262, intron 6 of 6)	20894	NM_001123377	11315	Hs.419640	NM_007262	ENSG00000116288	PARK7	DJ-1|DJ1|GATD2|HEL-S-67p	Parkinsonism associated deglycase	protein-coding	0.027491	0.486301	
chunk0095_309_1	chr2	20405035	20405408	+	0	NA	Intergenic	Intergenic	-41850	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.002681	0.385027	
chunk0096_250_1	chr2	31233932	31234155	+	0	NA	promoter-TSS (NM_014600)	promoter-TSS (NM_014600)	29	NM_014600	30845	Hs.368808	NM_014600	ENSG00000013016	EHD3	PAST3	EH domain containing 3	protein-coding	0.085202	0.691964	
chunk0174_24_1	chr6	153170564	153170851	+	0	NA	Intergenic	LTR78B|LTR|ERV1	-39453	NM_012419	26575	Hs.166313	NM_012419	ENSG00000091844	RGS17	RGS-17|RGSZ2|hRGS17	regulator of G protein signaling 17	protein-coding	0.003484	0.503472	
chunk0035_252_1	chr11	46273800	46274351	+	0	NA	Intergenic	Intergenic	-3563	NM_052854	90993	Hs.405961	NM_052854	ENSG00000157613	CREB3L1	OASIS|OI16	cAMP responsive element binding protein 3 like 1	protein-coding	0.012704	0.550725	
chunk0109_145_1	chr20	3553578	3554008	+	0	NA	intron (NM_001207047, intron 6 of 24)	L2c|LINE|L2	82775	NM_139321	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.004651	0.454756	
chunk0014_118_1	chr1	177413573	177413772	+	0	NA	Intergenic	Intergenic	62086	NR_126001	102724661	Hs.146628	NR_126001		LINC01645	-	long intergenic non-protein coding RNA 1645	ncRNA	0.000000	0.370000	
chunk0095_228_1	chr2	18970769	18971083	+	0	NA	Intergenic	Intergenic	-377503	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.009554	0.412698	
chunk0194_367_1	chr8	89946641	89947054	+	0	NA	intron (NM_001024688, intron 13 of 16)	intron (NM_001024688, intron 13 of 16)	37824	NM_002485	4683	Hs.492208	NM_002485	ENSG00000104320	NBN	AT-V1|AT-V2|ATV|NBS|NBS1|P95	nibrin	protein-coding	0.002421	0.314010	
chunk0209_229_1	chrX	45063541	45064305	+	0	NA	intron (NR_111960, intron 15 of 27)	intron (NR_111960, intron 15 of 27)	136978	NM_176819	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.014398	0.410458	
chunk0194_376_1	chr8	90036821	90037113	+	0	NA	intron (NM_001359, intron 6 of 9)	intron (NM_001359, intron 6 of 9)	35615	NM_001359	1666	Hs.492212	NM_001359	ENSG00000104325	DECR1	DECR|NADPH|SDR18C1	2,4-dienoyl-CoA reductase 1	protein-coding	0.003425	0.409556	
chunk0060_288_1	chr14	50544744	50545320	+	0	NA	intron (NM_001127713, intron 1 of 13)	LTR57|LTR|ERVL	11950	NM_001127713	51062	Hs.584905	NM_015915	ENSG00000198513	ATL1	AD-FSP|FSP1|GBP3|HSN1D|SPG3|SPG3A|atlastin1	atlastin GTPase 1	protein-coding	0.006944	0.461005	
chunk0041_357_1	chr11	130876229	130876428	+	0	NA	3' UTR (NM_014758, exon 11 of 11)	3' UTR (NM_014758, exon 11 of 11)	-6081	NR_125382	103611081	Hs.430300	NR_125382	ENSG00000255455	LOC103611081	-	uncharacterized LOC103611081	ncRNA	0.010050	0.460000	
chunk0190_372_1	chr8	39918859	39919087	+	0	NA	intron (NM_002164, intron 4 of 9)	intron (NM_002164, intron 4 of 9)	5164	NM_002164	3620	Hs.840	NM_002164	ENSG00000131203	IDO1	IDO|IDO-1|INDO	indoleamine 2,3-dioxygenase 1	protein-coding	0.017544	0.436681	
chunk0185_402_1	chr7	133945763	133945962	+	0	NA	intron (NM_021807, intron 14 of 17)	intron (NM_021807, intron 14 of 17)	-120974	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.005025	0.350000	
chunk0005_292_1	chr1	60126816	60127136	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-53206	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.009375	0.408100	
chunk0121_231_1	chr3	22067162	22067575	+	0	NA	Intergenic	Intergenic	110229	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.000000	0.330918	
chunk0024_268_1	chr10	41859444	41859643	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	508502	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.020101	0.410000	
chunk0151_356_1	chr5	54656046	54656609	+	0	NA	Intergenic	MER90a|LTR|ERV1	46997	NR_104659	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.001776	0.406028	290(AAGAACACTATGACCC,-,0.00),291(AGAACACTATGACCCA,+,0.00)
chunk0053_310_1	chr13	34035959	34036612	+	0	NA	Intergenic	Intergenic	218216	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.004594	0.394495	
chunk0127_66_1	chr3	89344535	89345051	+	0	NA	intron (NM_005233, intron 5 of 16)	intron (NM_005233, intron 5 of 16)	237269	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.007752	0.352031	
chunk0023_290_1	chr10	28575120	28576092	+	0	NA	intron (NM_016628, intron 3 of 13)	L1MB8|LINE|L1	42114	NM_100486	51322	Hs.743224	NM_016628	ENSG00000095787	WAC	BM-016|DESSH|PRO1741|Wwp4	WW domain containing adaptor with coiled-coil	protein-coding	0.008230	0.374101	
chunk0131_76_1	chr3	143043229	143043455	+	0	NA	intron (NM_001080415, intron 24 of 27)	L2b|LINE|L2	41812	NM_001080415	23350	Hs.596572	NM_001080415	ENSG00000163714	U2SURP	SR140|fSAPa	U2 snRNP associated SURP domain containing	protein-coding	0.017699	0.409692	133(TAGTACATACTGTTCC,-,0.00),134(AGTACATACTGTTCCT,+,0.00)
chunk0031_236_1	chr10	126634887	126635098	+	0	NA	Intergenic	Intergenic	-113551	NM_001004298	118611	Hs.587663	NM_001004298	ENSG00000154493	C10orf90	FATS|bA422P15.2	chromosome 10 open reading frame 90	protein-coding	0.014218	0.485849	
chunk0047_431_1	chr12	76266733	76267150	+	0	NA	Intergenic	Intergenic	81501	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.004796	0.428230	192(AAGACAAAGTGTTCTC,+,0.00)
chunk0032_29_1	chr11	954767	955074	+	0	NA	intron (NM_001242837, intron 1 of 21)	HAL1ME|LINE|L1	29111	NM_001242837	161	Hs.19121	NM_012305	ENSG00000183020	AP2A2	ADTAB|CLAPA2|HIP-9|HIP9|HYPJ	adaptor related protein complex 2 subunit alpha 2	protein-coding	0.003257	0.418831	
chunk0119_299_1	chr22	46464009	46464208	+	0	NA	exon (NM_014246, exon 2 of 35)	exon (NM_014246, exon 2 of 35)	73062	NM_014246	9620	Hs.252387	NM_014246	ENSG00000075275	CELSR1	ADGRC1|CDHF9|FMI2|HFMI2|ME2	cadherin EGF LAG seven-pass G-type receptor 1	protein-coding	0.100503	0.635000	
chunk0050_452_1	chr12	110738511	110739230	+	0	NA	intron (NM_001244974, intron 1 of 7)	intron (NM_001244974, intron 1 of 7)	4108	NM_001244974	5501	Hs.79081	NM_002710	ENSG00000186298	PPP1CC	PP-1G|PP1C|PPP1G	protein phosphatase 1 catalytic subunit gamma	protein-coding	0.013908	0.488889	
chunk0190_234_1	chr8	36139473	36139735	+	0	NA	Intergenic	Intergenic	-429284	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.015267	0.349810	
chunk0194_80_1	chr8	82845604	82846175	+	0	NA	Intergenic	Intergenic	-557869	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.001751	0.277972	
chunk0182_122_1	chr7	94145459	94146252	+	0	NA	Intergenic	Intergenic	-141477	NM_005868	10282	Hs.489132	NM_005868	ENSG00000105829	BET1	HBET1	Bet1 golgi vesicular membrane trafficking protein	protein-coding	0.006305	0.351385	
chunk0156_119_1	chr5	105952580	105953302	+	0	NA	Intergenic	Intergenic	853467	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.004155	0.343015	
chunk0210_378_1	chrX	97409914	97410599	+	0	NA	intron (NM_006729, intron 25 of 26)	L1PA6|LINE|L1	154279	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.010219	0.495627	
chunk0045_264_1	chr12	49567458	49567725	+	0	NA	intron (NM_006337, intron 1 of 14)	intron (NM_006337, intron 1 of 14)	554	NM_006337	10445	Hs.25313	NM_006337	ENSG00000187778	MCRS1	ICP22BP|INO80Q|MCRS2|MSP58|P78	microspherule protein 1	protein-coding	0.048689	0.608209	
chunk0097_458_1	chr2	64751530	64751757	+	0	NA	Intergenic	CpG	-97731	NM_014755	9792	Hs.591569	NM_014755	ENSG00000179833	SERTAD2	Sei-2|TRIP-Br2|TRIPBR2	SERTA domain containing 2	protein-coding	0.083700	0.706140	42(GGGGACTGGCTGTGCT,-,0.00),43(GGGACTGGCTGTGCTG,+,0.00)
chunk0137_419_1	chr4	28128720	28129073	+	0	NA	Intergenic	L1MC4a|LINE|L1	-690686	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.000000	0.265537	
chunk0059_388_1	chr14	37511178	37511392	+	0	NA	intron (NM_001195296, intron 14 of 14)	MamTip2|DNA|hAT-Tip100	83835	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.000000	0.358140	196(TGGTACTGAATGTGCT,-,0.00),197(GGTACTGAATGTGCTT,+,0.00)
chunk0034_135_1	chr11	28682382	28682581	+	0	NA	Intergenic	Intergenic	-204933	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.000000	0.310000	
chunk0037_422_1	chr11	80043374	80043847	+	0	NA	Intergenic	Intergenic	-602959	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.014799	0.445148	
chunk0106_117_1	chr2	197722817	197723193	+	0	NA	Intergenic	Intergenic	17701	NM_138395	92935	Hs.744330	NM_138395	ENSG00000247626	MARS2	COXPD25|MetRS|mtMetRS	methionyl-tRNA synthetase 2, mitochondrial	protein-coding	0.005319	0.350133	
chunk0064_194_1	chr14	92737657	92738172	+	0	NA	intron (NM_005606, intron 1 of 13)	intron (NM_005606, intron 1 of 13)	10788	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.007767	0.410853	
chunk0082_119_1	chr17	55116685	55116962	+	0	NA	intron (NM_178509, intron 16 of 17)	intron (NM_178509, intron 16 of 17)	148058	NM_178509	252983	Hs.35199	NM_178509	ENSG00000166263	STXBP4	Synip	syntaxin binding protein 4	protein-coding	0.003610	0.341727	
chunk0158_335_1	chr5	133236645	133237106	+	0	NA	intron (NM_015082, intron 7 of 15)	L2a|LINE|L2	184905	NM_002154	3308	Hs.90093	NM_002154	ENSG00000170606	HSPA4	APG-2|HEL-S-5a|HS24/P52|HSPH2|RY|hsp70|hsp70RY	heat shock protein family A (Hsp70) member 4	protein-coding	0.015184	0.588745	
chunk0038_255_1	chr11	88519532	88519769	+	0	NA	intron (NR_049724, intron 4 of 5)	intron (NR_049724, intron 4 of 5)	15074	NR_049724	100873989	Hs.616625	NR_049724	ENSG00000255082	GRM5-AS1	-	GRM5 antisense RNA 1	ncRNA	0.000000	0.315126	
chunk0163_321_1	chr6	14791652	14792401	+	0	NA	Intergenic	Intergenic	-453949	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.005340	0.346667	
chunk0180_149_1	chr7	60928403	60928639	+	0	NA	Intergenic	Intergenic	2375535	NR_003952	643955	Hs.583308	NR_003952	ENSG00000185037	ZNF733P	ZNF733	zinc finger protein 733, pseudogene	pseudo	0.046610	0.392405	
chunk0072_169_1	chr15	93280268	93280484	+	0	NA	Intergenic	Intergenic	-191162	NM_020211	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.050926	0.608295	28(GGGAACAGCCTGCCCT,-,0.00),29(GGAACAGCCTGCCCTT,+,0.00)
chunk0135_193_1	chr3	188230995	188231327	+	0	NA	intron (NM_005578, intron 2 of 10)	MLT1F2|LTR|ERVL-MaLR	5756	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.015060	0.495495	136(GGTGACACACTGTTCC,-,0.00),137(GTGACACACTGTTCCC,+,0.00)
chunk0160_419_1	chr5	164191316	164191912	+	0	NA	Intergenic	Intergenic	275788	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.008389	0.395310	
chunk0199_361_1	chr9	12759117	12759398	+	0	NA	intron (NR_125775, intron 3 of 3)	intron (NR_125775, intron 3 of 3)	-15756	NM_203403	286343	Hs.445356	NM_203403	ENSG00000153714	LURAP1L	C9orf150|HYST0841|LRAP35b|bA3L8.2	leucine rich adaptor protein 1 like	protein-coding	0.024911	0.368794	
chunk0200_359_1	chr9	25549351	25549896	+	0	NA	Intergenic	Intergenic	129235	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.001835	0.336996	
chunk0015_91_1	chr1	185010904	185011702	+	0	NA	Intergenic	L2a|LINE|L2	-34116	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.011278	0.391740	
chunk0115_34_1	chr21	20997845	20998344	+	0	NA	promoter-TSS (NM_004540)	promoter-TSS (NM_004540)	-221	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.118236	0.712000	
chunk0020_205_1	chr1	234997119	234997744	+	0	NA	Intergenic	Intergenic	-33432	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.020800	0.559105	217(GAGAACATCCTGGTCC,-,0.00),218(AGAACATCCTGGTCCT,+,0.00)
chunk0142_452_1	chr4	105552208	105552503	+	0	NA	promoter-TSS (NM_001242729)	promoter-TSS (NM_001242729)	-265	NM_017700	54848	Hs.585224	NM_017700	ENSG00000236699	ARHGEF38	-	Rho guanine nucleotide exchange factor 38	protein-coding	0.016949	0.523649	
chunk0002_83_1	chr1	14421897	14422508	+	0	NA	Intergenic	Intergenic	-176515	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.014730	0.434641	
chunk0164_383_1	chr6	26026936	26027184	+	0	NA	exon (NM_003544, exon 1 of 1)	exon (NM_003544, exon 1 of 1)	192	NM_003544	8366	Hs.143080	NM_003544	ENSG00000278705	HIST1H4B	H4/I|H4FI	histone cluster 1 H4 family member b	protein-coding	0.092742	0.558233	
chunk0123_236_1	chr3	45560837	45561037	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-33894	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.005000	0.398010	
chunk0060_422_1	chr14	53714722	53715058	+	0	NA	Intergenic	Intergenic	233594	NR_049843	100847076		NR_049843	ENSG00000266431	MIR5580	-	microRNA 5580	ncRNA	0.011905	0.376855	
chunk0184_127_1	chr7	114848214	114848508	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-73793	NM_001166346	29969	Hs.741413	NM_199072	ENSG00000135272	MDFIC	HIC|MDFIC1	MyoD family inhibitor domain containing	protein-coding	0.000000	0.393220	
chunk0170_449_1	chr6	119255094	119255491	+	0	NA	intron (NM_005907, intron 5 of 12)	intron (NM_005907, intron 5 of 12)	94474	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.000000	0.331658	
chunk0177_29_1	chr7	20692332	20692822	+	0	NA	intron (NM_001163941, intron 16 of 27)	L1ME1|LINE|L1	45234	NM_001163942	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.000000	0.279022	
chunk0073_252_1	chr16	11782855	11783277	+	0	NA	intron (NM_014153, intron 1 of 22)	intron (NM_014153, intron 1 of 22)	14192	NM_014153	29066	Hs.371856	NM_014153	ENSG00000122299	ZC3H7A	HSPC055|ZC3H7|ZC3HDC7	zinc finger CCCH-type containing 7A	protein-coding	0.014218	0.437352	
chunk0091_117_1	chr19	6236879	6237262	+	0	NA	intron (NM_005934, intron 3 of 11)	intron (NM_005934, intron 3 of 11)	42878	NM_005934	4298	Hs.10095	NM_005934	ENSG00000130382	MLLT1	ENL|LTG19|YEATS1	MLLT1 super elongation complex subunit	protein-coding	0.052219	0.661458	
chunk0106_467_1	chr2	209495630	209496372	+	0	NA	intron (NM_001039538, intron 1 of 14)	intron (NM_001039538, intron 1 of 14)	71954	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.004043	0.367429	
chunk0014_331_1	chr1	182083740	182084274	+	0	NA	Intergenic	Intergenic	-22295	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.005618	0.469159	250(AAGAACATTGAGTTCC,-,0.00),251(AGAACATTGAGTTCCT,+,0.00)
chunk0212_431_1	chrX	153765581	153765786	+	0	NA	intron (NM_005393, intron 2 of 35)	intron (NM_005393, intron 2 of 35)	1487	NM_001163257	5365	Hs.632833	NM_005393	ENSG00000198753	PLXNB3	PLEXB3|PLEXR|PLXN6	plexin B3	protein-coding	0.029268	0.650485	
chunk0161_326_1	chr5	173767424	173768420	+	0	NA	Intergenic	L2c|LINE|L2	-21713	NR_108027	101928136	Hs.449267	NR_108027	ENSG00000253686	LINC01484	-	long intergenic non-protein coding RNA 1484	ncRNA	0.014056	0.497492	348(GAGAACAAGGTGGCCT,-,0.00)
chunk0072_419_1	chr15	100986480	100986980	+	0	NA	intron (NM_024652, intron 4 of 33)	LTR22A|LTR|ERVK	67515	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.008000	0.479042	
chunk0172_422_1	chr6	140427663	140427892	+	0	NA	Intergenic	L1M1|LINE|L1	222525	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.004367	0.517391	
chunk0009_92_1	chr1	101245113	101245772	+	0	NA	Intergenic	Intergenic	8693	NM_001400	1901	Hs.154210	NM_001400	ENSG00000170989	S1PR1	CD363|CHEDG1|D1S3362|ECGF1|EDG-1|EDG1|S1P1	sphingosine-1-phosphate receptor 1	protein-coding	0.003035	0.356061	
chunk0039_7_1	chr11	95076299	95076968	+	0	NA	Intergenic	Intergenic	9756	NR_103726	10929	Hs.476680	NM_032102	ENSG00000263465	SRSF8	DSM-1|SFRS2B|SRP46	serine and arginine rich splicing factor 8	protein-coding	0.001495	0.368657	
chunk0202_250_1	chr9	76799269	76800021	+	0	NA	intron (NM_015225, intron 6 of 18)	intron (NM_015225, intron 6 of 18)	35209	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.002660	0.386454	
chunk0084_88_1	chr17	75189310	75189718	+	0	NA	Intergenic	MIR|SINE|MIR	-6511	NM_001005849	6613	Hs.380973	NM_006937	ENSG00000188612	SUMO2	HSMT3|SMT3B|SMT3H2|SUMO3|Smt3A	small ubiquitin like modifier 2	protein-coding	0.002451	0.430318	
chunk0137_169_1	chr4	16550474	16551142	+	0	NA	intron (NM_001290, intron 5 of 7)	L1ME3C|LINE|L1	324145	NR_027697	202020	Hs.445315	NM_152684	ENSG00000263327	TAPT1-AS1	-	TAPT1 antisense RNA 1 (head to head)	ncRNA	0.004491	0.328849	
chunk0043_340_1	chr12	22804484	22804870	+	0	NA	Intergenic	Intergenic	179535	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.007772	0.395349	
chunk0128_279_1	chr3	110859828	110860580	+	0	NA	Intergenic	Intergenic	209755	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.006649	0.354582	
chunk0117_357_1	chr21	44736446	44737080	+	0	NA	Intergenic	Intergenic	-25183	NM_001272037	54084	Hs.660703	NM_144991	ENSG00000175894	TSPEAR	C21orf29|DFNB98|ECTD14|TSP-EAR	thrombospondin type laminin G domain and EAR repeats	protein-coding	0.014196	0.584252	
chunk0192_362_1	chr8	68172359	68172608	+	0	NA	intron (NM_024870, intron 35 of 39)	intron (NM_024870, intron 35 of 39)	-158239	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.008032	0.364000	
chunk0145_49_1	chr4	145056918	145057250	+	0	NA	intron (NM_001256711, intron 5 of 6)	intron (NM_001256711, intron 5 of 6)	-40920	NM_002940	6059	Hs.12013	NM_002940	ENSG00000164163	ABCE1	ABC38|OABP|RLI|RLI1|RNASEL1|RNASELI|RNS4I	ATP binding cassette subfamily E member 1	protein-coding	0.003012	0.342342	
chunk0049_160_1	chr12	92049703	92049986	+	0	NA	intron (NR_132341, intron 1 of 4)	MLT1J|LTR|ERVL-MaLR	91869	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.007067	0.450704	
chunk0207_100_1	chrX	9917981	9918532	+	0	NA	intron (NM_001649, intron 5 of 9)	intron (NM_001649, intron 5 of 9)	-49102	NM_001195081	100288814		NM_001195081	ENSG00000234469	CLDN34	-	claudin 34	protein-coding	0.009074	0.471014	
chunk0199_438_1	chr9	13947212	13947595	+	0	NA	Intergenic	L1M6|LINE|L1	19432	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.000000	0.299479	
chunk0149_451_1	chr5	29955396	29956089	+	0	NA	Intergenic	Intergenic	-559766	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.008658	0.425072	337(TGGTACACCATGTACA,-,0.00),338(GGTACACCATGTACAT,+,0.00)
chunk0162_179_1	chr6	3718473	3718672	+	0	NA	Intergenic	MER74A|LTR|ERVL	33440	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.015075	0.505000	
chunk0042_1_1	chr12	1040681	1041167	+	0	NA	intron (NR_027949, intron 2 of 15)	intron (NR_027949, intron 2 of 15)	13176	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.006173	0.347023	153(ATGTACACAGTGTACC,-,0.00),154(TGTACACAGTGTACCA,+,0.00)
chunk0166_4_1	chr6	41373063	41373262	+	0	NA	Intergenic	CpG	37372	NM_004828	9436	Hs.194721	NM_004828	ENSG00000096264	NCR2	CD336|LY95|NK-p44|NKP44|dJ149M18.1	natural cytotoxicity triggering receptor 2	protein-coding	0.130653	0.660000	
chunk0087_164_1	chr18	34917709	34918140	+	0	NA	Intergenic	Intergenic	-59004	NM_001143826	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.000000	0.363426	
chunk0151_198_1	chr5	50654932	50655484	+	0	NA	Intergenic	Intergenic	-10691	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.001812	0.392405	341(AGGCACATCCTGTTCA,-,0.00),342(GGCACATCCTGTTCAA,+,0.00)
chunk0111_431_1	chr20	35085031	35085362	+	0	NA	intron (NM_199368, intron 1 of 18)	intron (NM_199368, intron 1 of 18)	7619	NM_015638	26133	Hs.168073	NM_015638	ENSG00000100991	TRPC4AP	C20orf188|PPP1R158|TRRP4AP|TRUSS	transient receptor potential cation channel subfamily C member 4 associated protein	protein-coding	0.006042	0.373494	
chunk0120_363_1	chr3	11660254	11660601	+	0	NA	intron (NM_014667, intron 2 of 5)	intron (NM_014667, intron 2 of 5)	-16450	NM_001128219	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.005764	0.413793	
chunk0212_368_1	chrX	149689613	149690048	+	0	NA	intron (NM_001011544, intron 2 of 4)	intron (NM_001011544, intron 2 of 4)	1593	NM_001011544	4110	Hs.670252	NM_005366	ENSG00000185247	MAGEA11	CT1.11|MAGE-11|MAGE11|MAGEA-11	MAGE family member A11	protein-coding	0.004598	0.490826	256(AGGCACACACTGTTCT,-,0.00),257(GGCACACACTGTTCTT,+,0.00)
chunk0139_278_1	chr4	57008471	57008804	+	0	NA	intron (NM_000938, intron 10 of 24)	L2c|LINE|L2	29997	NM_000938	5431	Hs.602757	NM_000938	ENSG00000047315	POLR2B	POL2RB|RPB2|hRPB140	RNA polymerase II subunit B	protein-coding	0.009009	0.464072	
chunk0108_324_1	chr2	235606498	235606753	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	100874	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.015686	0.433594	
chunk0020_84_1	chr1	232764379	232765173	+	0	NA	Intergenic	Intergenic	-22061	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.002519	0.389937	
chunk0078_48_1	chr17	1226514	1226902	+	0	NA	Intergenic	(TGCATG)n|Simple_repeat|Simple_repeat	-39386	NM_001159746	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.010309	0.452442	
chunk0196_211_1	chr8	106657508	106657914	+	0	NA	promoter-TSS (NM_181354)	promoter-TSS (NM_181354)	-97	NM_181354	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.068966	0.624079	
chunk0114_50_1	chr21	8453796	8454186	+	0	NA	Intergenic	L1PREC2|LINE|L1	12845	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.035897	0.503836	
chunk0173_193_1	chr6	145204711	145205303	+	0	NA	Intergenic	MIRc|SINE|MIR	-529862	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.005068	0.340641	199(AAGGACATTGTGTTCT,-,0.00),200(AGGACATTGTGTTCTC,+,0.00)
chunk0179_421_1	chr7	51827797	51828269	+	0	NA	Intergenic	Intergenic	-511215	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.002119	0.355180	
chunk0185_389_1	chr7	133405826	133406100	+	0	NA	intron (NM_001037126, intron 7 of 9)	L2a|LINE|L2	115082	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.000000	0.352727	
chunk0003_216_1	chr1	35355407	35355654	+	0	NA	intron (NM_005095, intron 2 of 29)	intron (NM_005095, intron 2 of 29)	86563	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.004049	0.286290	
chunk0059_440_1	chr14	38671692	38671923	+	0	NA	Intergenic	L1PA6|LINE|L1	245075	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.004329	0.478448	
chunk0203_134_1	chr9	85392184	85392431	+	0	NA	Intergenic	Intergenic	349722	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.012146	0.467742	
chunk0067_144_1	chr15	43135233	43135655	+	0	NA	intron (NM_024956, intron 2 of 13)	intron (NM_024956, intron 2 of 13)	1920	NM_024956	80021	Hs.511175	NM_024956	ENSG00000137842	TMEM62	-	transmembrane protein 62	protein-coding	0.009479	0.385343	
chunk0006_146_1	chr1	66281789	66282222	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-50103	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.006928	0.400922	
chunk0193_141_1	chr8	74512234	74512593	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-36130	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.008357	0.308333	
chunk0070_179_1	chr15	71710130	71710903	+	0	NA	intron (NM_001286429, intron 2 of 11)	intron (NM_001286429, intron 2 of 11)	-18977	NR_120346	101929173	Hs.680593	NR_120346		THSD4-AS2	-	THSD4 antisense RNA 2	ncRNA	0.002587	0.397933	649(TGGTACGTTCTGTTCC,-,0.00),650(GGTACGTTCTGTTCCA,+,0.00)
chunk0108_458_1	chr2	238404577	238404932	+	0	NA	Intergenic	L1MCc|LINE|L1	-22231	NM_001040445	51665	Hs.516788	NM_016114	ENSG00000065802	ASB1	ASB-1	ankyrin repeat and SOCS box containing 1	protein-coding	0.025352	0.567416	165(TAGACACCGTGTCCCT,+,0.00),241(GTGGACACCGTGTCCC,-,0.00),242(TGGACACCGTGTCCCT,+,0.00)
chunk0101_250_1	chr2	132287984	132288188	+	0	NA	Intergenic	Intergenic	-19058	NM_001304449	646915		NM_001304449		ZNF806	-	zinc finger protein 806	protein-coding	0.014706	0.570732	
chunk0072_339_1	chr15	99372334	99372769	+	0	NA	intron (NM_144598, intron 9 of 9)	intron (NM_144598, intron 9 of 9)	115026	NR_073383	7190	Hs.656611	NR_073383	ENSG00000259706	HSP90B2P	GRP94P1|GRP94b|HSP|HSPCP2|TRA1P1|TRAP1	heat shock protein 90 beta family member 2, pseudogene	pseudo	0.006897	0.376147	
chunk0043_181_1	chr12	17602835	17603059	+	0	NA	Intergenic	Intergenic	-70352	NR_039770	100616279		NR_039770	ENSG00000283665	MIR3974	-	microRNA 3974	ncRNA	0.008929	0.337778	
chunk0189_354_1	chr8	26955072	26955630	+	0	NA	Intergenic	Intergenic	-89946	NM_033303	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.000000	0.345259	277(GTTACAGAGTGTTCTC,+,0.00)
chunk0212_311_1	chrX	143580871	143581070	+	0	NA	Intergenic	Intergenic	53533	NM_001184750	139065	Hs.272284	NM_173078	ENSG00000179542	SLITRK4	-	SLIT and NTRK like family member 4	protein-coding	0.000000	0.380000	
chunk0034_365_1	chr11	36099304	36099756	+	0	NA	intron (NM_174902, intron 4 of 5)	L1ME3F|LINE|L1	89432	NR_039769	100616311		NR_039769	ENSG00000263389	MIR3973	-	microRNA 3973	ncRNA	0.004425	0.306843	
chunk0158_165_1	chr5	127666143	127666754	+	0	NA	Intergenic	Intergenic	13433	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.003273	0.416667	226(GAGGTCACACTGTTCC,-,0.00),227(AGGTCACACTGTTCCT,+,0.00)
chunk0009_399_1	chr1	110242696	110243446	+	0	NA	Intergenic	MIRb|SINE|MIR	32357	NM_004978	3749	Hs.153521	NM_004978	ENSG00000116396	KCNC4	C1orf30|HKSHIIIC|KSHIIIC|KV3.4	potassium voltage-gated channel subfamily C member 4	protein-coding	0.016000	0.529960	
chunk0084_453_1	chr17	83053549	83054093	+	0	NA	Intergenic	Intergenic	-2011	NM_001009905	146712	Hs.607824	NM_001009905	ENSG00000175711	B3GNTL1	3-Gn-T8|B3GNT8|BGnT-8|beta-1|beta3Gn-T8|beta3GnTL1	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1	protein-coding	0.009191	0.438532	217(AGGGACTTCATGTTCT,-,0.00),218(GGGACTTCATGTTCTC,+,0.00),379(CAGCACATGGTGTCCA,-,0.00),380(AGCACATGGTGTCCAG,+,0.00)
chunk0131_32_1	chr3	142447951	142448199	+	0	NA	promoter-TSS (NM_019001)	promoter-TSS (NM_019001)	-13	NM_001282859	54464	Hs.435103	NM_019001	ENSG00000114127	XRN1	SEP1	5'-3' exoribonuclease 1	protein-coding	0.129032	0.710843	
chunk0013_347_1	chr1	172164522	172164721	+	0	NA	intron (NM_001136127, intron 14 of 19)	intron (NM_001136127, intron 14 of 19)	-19786	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.010050	0.460000	
chunk0189_428_1	chr8	27969525	27969852	+	0	NA	intron (NM_173833, intron 2 of 8)	L1MC1|LINE|L1	23164	NM_173833	286133	Hs.591833	NM_173833	ENSG00000168079	SCARA5	NET33|Tesr	scavenger receptor class A member 5	protein-coding	0.006116	0.417683	
chunk0147_350_1	chr4	185652611	185653232	+	0	NA	intron (NM_003603, intron 7 of 22)	intron (NM_003603, intron 7 of 22)	4048	NM_001145674	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.009662	0.364952	
chunk0059_397_1	chr14	37566618	37567491	+	0	NA	Intergenic	AmnSINE2|SINE|tRNA-Deu	28066	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.006873	0.384439	
chunk0008_110_1	chr1	91502032	91502541	+	0	NA	intron (NM_001134420, intron 2 of 11)	intron (NM_001134420, intron 2 of 11)	1178	NM_001134420	8317	Hs.533573	NM_003503	ENSG00000097046	CDC7	CDC7L1|HsCDC7|Hsk1|huCDC7	cell division cycle 7	protein-coding	0.005894	0.354902	
chunk0162_230_1	chr6	4693212	4693558	+	0	NA	Intergenic	HAL1ME|LINE|L1	-12774	NR_026590									0.005780	0.363112	
chunk0067_308_1	chr15	47845744	47846137	+	0	NA	intron (NR_120336, intron 1 of 4)	intron (NR_120336, intron 1 of 4)	296	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.005089	0.418782	
chunk0208_325_1	chrX	24566186	24566673	+	0	NA	intron (NM_001163264, intron 7 of 7)	L1ME4a|LINE|L1	80909	NM_001163265	9468	Hs.660708	NM_004845	ENSG00000102230	PCYT1B	CCTB|CTB	phosphate cytidylyltransferase 1, choline, beta	protein-coding	0.008214	0.360656	224(TAGAACACTATGTTCT,-,0.00),225(AGAACACTATGTTCTG,+,0.00)
chunk0057_341_1	chr13	107287178	107287503	+	0	NA	intron (NM_001080396, intron 1 of 2)	intron (NM_001080396, intron 1 of 2)	243908	NR_031671	100302286		NR_031671	ENSG00000221650	MIR1267	MIRN1267|hsa-mir-1267	microRNA 1267	ncRNA	0.012308	0.423313	
chunk0177_320_1	chr7	26200624	26201189	+	0	NA	promoter-TSS (NM_007276)	promoter-TSS (NM_007276)	-113	NM_002137	3181	Hs.487774	NM_002137	ENSG00000122566	HNRNPA2B1	HNRNPA2|HNRNPB1|HNRPA2|HNRPA2B1|HNRPB1|IBMPFD2|RNPA2|SNRPB1	heterogeneous nuclear ribonucleoprotein A2/B1	protein-coding	0.090265	0.600707	
chunk0167_212_1	chr6	66084628	66085021	+	0	NA	Intergenic	L1PA15|LINE|L1	296945	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.002545	0.548223	227(GGCACTTTCTGTGCAT,+,0.00)
chunk0160_339_1	chr5	160023903	160024166	+	0	NA	intron (NM_003314, intron 2 of 7)	intron (NM_003314, intron 2 of 7)	14934	NM_001282500	7265	Hs.519718	NM_003314	ENSG00000113312	TTC1	TPR1	tetratricopeptide repeat domain 1	protein-coding	0.000000	0.454545	
chunk0163_58_1	chr6	8921835	8922428	+	0	NA	Intergenic	L1MC2|LINE|L1	269922	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.010118	0.345118	
chunk0204_81_1	chr9	94056361	94057030	+	0	NA	intron (NM_177995, intron 1 of 9)	intron (NM_177995, intron 1 of 9)	25886	NM_001253830	138639	Hs.437943	NM_152422	ENSG00000158079	PTPDC1	PTP9Q22	protein tyrosine phosphatase domain containing 1	protein-coding	0.007474	0.382090	286(CAGAACACCATGTGTC,-,0.00),287(AGAACACCATGTGTCT,+,0.00)
chunk0119_446_1	chr22	50206557	50206810	+	0	NA	intron (NM_031454, intron 2 of 8)	intron (NM_031454, intron 2 of 8)	5704	NM_031454	83642	Hs.365405	NM_031454	ENSG00000073169	SELENOO	SELO	selenoprotein O	protein-coding	0.031621	0.582677	85(AAGTCCAGCCTGTCCC,-,0.00),86(AGTCCAGCCTGTCCCT,+,0.00)
chunk0070_230_1	chr15	72897266	72897979	+	0	NA	Intergenic	L1MC2|LINE|L1	-113837	NR_023319									0.008415	0.379552	487(AAGAACAAAGAGTGCA,-,0.00)
chunk0010_70_1	chr1	113114541	113114887	+	0	NA	exon (NM_014813, exon 15 of 18)	exon (NM_014813, exon 15 of 18)	41544	NM_014813	9860	Hs.448972	NM_014813	ENSG00000198799	LRIG2	LIG-2|LIG2|UFS2	leucine rich repeats and immunoglobulin like domains 2	protein-coding	0.008671	0.440922	
chunk0067_229_1	chr15	45387121	45387918	+	0	NA	Intergenic	L2c|LINE|L2	-8737	NM_001482	2628	Hs.75335	NM_001482	ENSG00000171766	GATM	AGAT|AT|CCDS3	glycine amidinotransferase	protein-coding	0.001255	0.360902	
chunk0034_247_1	chr11	34249414	34249713	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	108445	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.013378	0.460000	
chunk0148_445_1	chr4	189895279	189895492	+	0	NA	Intergenic	Intergenic	13870	NR_132380	105377617	Hs.662618	NR_132380	ENSG00000250666	LINC01596	-	long intergenic non-protein coding RNA 1596	ncRNA	0.000000	0.285047	
chunk0107_78_1	chr2	212746745	212747220	+	0	NA	Intergenic	Intergenic	-48349	NR_131941	102725079	Hs.176124	NR_131941	ENSG00000234308	LINC01878	-	long intergenic non-protein coding RNA 1878	ncRNA	0.002105	0.281513	
chunk0193_380_1	chr8	80147270	80147870	+	0	NA	intron (NR_105035, intron 1 of 6)	intron (NR_105035, intron 1 of 6)	23630	NR_105036	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.015000	0.477537	
chunk0146_224_1	chr4	161881813	161882934	+	0	NA	intron (NM_001128427, intron 4 of 15)	intron (NM_001128427, intron 4 of 15)	-140360	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.003568	0.314617	
chunk0198_257_1	chr8	134740194	134740678	+	0	NA	Intergenic	Intergenic	-27387	NR_110323	57623	Hs.446172	NM_020863	ENSG00000066827	ZFAT	AITD3|ZFAT1|ZNF406	zinc finger and AT-hook domain containing	protein-coding	0.008264	0.426804	332(TAGAACACCTAGTTCC,-,0.00),333(AGAACACCTAGTTCCC,+,0.00)
chunk0181_353_1	chr7	88357244	88357668	+	0	NA	Intergenic	Intergenic	-50543	NM_024636	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.002358	0.418824	
chunk0113_303_1	chr20	57773092	57773743	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-61881	NM_199171	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.013825	0.458589	
chunk0194_137_1	chr8	84368937	84369486	+	0	NA	intron (NM_001100392, intron 2 of 9)	intron (NM_001100392, intron 2 of 9)	184346	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005464	0.363636	
chunk0117_186_1	chr22	21256975	21257195	+	0	NA	Intergenic	Intergenic	-25340	NR_024583	29797	Hs.396963	NM_001029950		POM121L8P	DKFZp434K191	POM121 transmembrane nucleoporin like 8, pseudogene	pseudo	0.013636	0.542986	
chunk0004_102_1	chr1	44004598	44005080	+	0	NA	intron (NM_001024845, intron 5 of 13)	intron (NM_001024845, intron 5 of 13)	12501	NM_006934	6536	Hs.442590	NM_006934	ENSG00000196517	SLC6A9	GCENSG|GLYT1	solute carrier family 6 member 9	protein-coding	0.012448	0.440994	
chunk0163_154_1	chr6	11020808	11021489	+	0	NA	intron (NM_017770, intron 1 of 7)	L2b|LINE|L2	-22610	NR_038963	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.002937	0.410557	390(CAACACATCCTGTTCT,-,0.00),391(AACACATCCTGTTCTC,+,0.00)
chunk0205_240_1	chr9	110089991	110090227	+	0	NA	intron (NM_001004065, intron 1 of 3)	intron (NM_001004065, intron 1 of 3)	-35392	NM_001136562	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.033898	0.464135	
chunk0026_245_1	chr10	66350567	66351233	+	0	NA	intron (NM_001127384, intron 12 of 17)	intron (NM_001127384, intron 12 of 17)	-575134	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.001502	0.343328	
chunk0140_109_1	chr4	68496893	68497630	+	0	NA	3' UTR (NM_014058, exon 10 of 10)	3' UTR (NM_014058, exon 10 of 10)	49812	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.001357	0.314363	
chunk0022_5_1	chr10	7196323	7196611	+	0	NA	intron (NM_001018039, intron 15 of 20)	intron (NM_001018039, intron 15 of 20)	-9683	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.010417	0.494810	165(CAGGACACTGTGTTCC,-,0.00),166(AGGACACTGTGTTCCT,+,0.00)
chunk0155_162_1	chr5	94206377	94206810	+	0	NA	intron (NM_001145678, intron 20 of 20)	intron (NM_001145678, intron 20 of 20)	-94894	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.000000	0.343318	
chunk0197_460_1	chr8	127895739	127896294	+	0	NA	intron (NR_003367, intron 2 of 8)	intron (NR_003367, intron 2 of 8)	52707	NR_103558	641384	Hs.629674	NM_001037234	ENSG00000280055	TMEM75	-	transmembrane protein 75	ncRNA	0.005405	0.392086	
chunk0023_115_1	chr10	23081392	23081918	+	0	NA	Intergenic	Intergenic	-13843	NM_012228	22921	Hs.461420	NM_012228	ENSG00000148450	MSRB2	CBS-1|CBS1|CGI-131|MSRB|PILB	methionine sulfoxide reductase B2	protein-coding	0.009506	0.426945	227(CAGAACACCCTGAACT,-,0.00),228(AGAACACCCTGAACTC,+,0.00)
chunk0048_175_1	chr12	80906656	80906944	+	0	NA	intron (NM_004664, intron 1 of 5)	L1PA15|LINE|L1	29033	NR_030349	693203		NR_030349	ENSG00000208022	MIR618	MIRN618|hsa-mir-618|mir-618	microRNA 618	ncRNA	0.017361	0.449827	
chunk0159_239_1	chr5	141821985	141822583	+	0	NA	Intergenic	Intergenic	43918	NM_001278615	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.005017	0.479132	315(CTGTACATCCTGTGCC,-,0.00),316(TGTACATCCTGTGCCG,+,0.00)
chunk0134_203_1	chr3	178453852	178454526	+	0	NA	intron (NR_046786, intron 1 of 2)	L1ME1|LINE|L1	34988	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.002967	0.312593	
chunk0039_359_1	chr11	105962101	105962375	+	0	NA	intron (NR_046356, intron 14 of 16)	intron (NR_046356, intron 14 of 16)	59989	NM_032424	84437	Hs.266782	NM_032424	ENSG00000170903	MSANTD4	KIAA1826	Myb/SANT DNA binding domain containing 4 with coiled-coils	protein-coding	0.000000	0.301818	
chunk0199_318_1	chr9	7237408	7238022	+	0	NA	Intergenic	LTR40a|LTR|ERVL	480074	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.000000	0.413008	
chunk0145_442_1	chr4	153486252	153486915	+	0	NA	intron (NM_001131007, intron 3 of 34)	MLT1L|LTR|ERVL-MaLR	20237	NM_001131007	23240	Hs.732450	NM_015196	ENSG00000121210	TMEM131L	KIAA0922	transmembrane 131 like	protein-coding	0.010558	0.501506	313(GGACCTGTCTGTTCTG,+,0.00),330(TGGACTCTGTGTGCCG,+,0.00)
chunk0019_167_1	chr1	226110048	226110248	+	0	NA	Intergenic	CpG	47421	NR_002315	440926	Hs.533624	NR_002315		H3F3AP4	p13	H3 histone, family 3A, pseudogene 4	pseudo	0.170000	0.805970	
chunk0061_85_1	chr14	56971851	56972343	+	0	NA	Intergenic	L1M5|LINE|L1	158914	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.002033	0.267748	
chunk0019_176_1	chr1	226420793	226421298	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-12945	NM_001618	142	Hs.177766	NM_001618	ENSG00000143799	PARP1	ADPRT|ADPRT 1|ADPRT1|ARTD1|PARP|PARP-1|PPOL|pADPRT-1	poly(ADP-ribose) polymerase 1	protein-coding	0.007921	0.448617	
chunk0112_35_1	chr20	36733162	36733378	+	0	NA	intron (NR_038370, intron 1 of 13)	intron (NR_038370, intron 1 of 13)	12868	NM_022477	57446	Hs.437338	NM_022477	ENSG00000101079	NDRG3	-	NDRG family member 3	protein-coding	0.004630	0.322581	
chunk0065_204_1	chr14	100091371	100091598	+	0	NA	intron (NM_016337, intron 2 of 13)	MER21A|LTR|ERVL	18030	NR_039601	100616247		NR_039601	ENSG00000265154	MIR151B	-	microRNA 151b	ncRNA	0.008811	0.521930	
chunk0205_322_1	chr9	112781997	112782835	+	0	NA	intron (NM_001012994, intron 1 of 8)	MER58B|DNA|hAT-Charlie	31562	NM_001012994	401548	Hs.522350	NM_001012994	ENSG00000148158	SNX30	ATG24A	sorting nexin family member 30	protein-coding	0.005967	0.399285	
chunk0136_371_1	chr3	196175586	196175897	+	0	NA	Intergenic	Intergenic	33105	NR_034088	401109	Hs.280133	NM_001001699	ENSG00000224652	LINC00885	-	long intergenic non-protein coding RNA 885	ncRNA	0.012862	0.554487	
chunk0096_189_1	chr2	29967519	29967718	+	0	NA	Intergenic	Intergenic	-46007	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.000000	0.375000	150(AGGGACAAAATGTACT,-,0.00),151(GGGACAAAATGTACTT,+,0.00)
chunk0118_395_1	chr22	37784867	37785103	+	0	NA	intron (NR_039973, intron 1 of 1)	L2b|LINE|L2	-20122	NM_005318	3005	Hs.745024	NM_005318	ENSG00000189060	H1F0	H10|H1FV	H1 histone family member 0	protein-coding	0.021186	0.594937	
chunk0009_77_1	chr1	100995496	100996039	+	0	NA	intron (NM_015958, intron 5 of 7)	intron (NM_015958, intron 5 of 7)	30039	NM_001077395	51611	Hs.440776	NM_015958	ENSG00000117543	DPH5	AD-018|CGI-30|HSPC143|NPD015	diphthamide biosynthesis 5	protein-coding	0.007366	0.352941	
chunk0203_364_1	chr9	89926311	89927030	+	0	NA	Intergenic	HAL1|LINE|L1	-42746	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.012517	0.422222	
chunk0174_292_1	chr6	162436411	162436893	+	0	NA	intron (NM_013987, intron 2 of 10)	intron (NM_013987, intron 2 of 10)	-290480	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.016598	0.424431	
chunk0005_427_1	chr1	62834179	62834545	+	0	NA	intron (NM_032852, intron 8 of 10)	intron (NM_032852, intron 8 of 10)	50256	NM_178221	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.005464	0.329700	
chunk0087_272_1	chr18	37477981	37478704	+	0	NA	intron (NM_001025088, intron 2 of 12)	intron (NM_001025088, intron 2 of 12)	-11838	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.015214	0.534530	
chunk0155_412_1	chr5	99443512	99444151	+	0	NA	Intergenic	Intergenic	-90159	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.006260	0.403125	
chunk0197_110_1	chr8	119873747	119874604	+	0	NA	intron (NM_001283012, intron 1 of 6)	CpG	520	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.078180	0.632867	114(CAGCACTGGCAGTGCT,-,0.00),115(AGCACTGGCAGTGCTG,+,0.00)
chunk0212_138_1	chrX	131778143	131778407	+	0	NA	intron (NR_026975, intron 6 of 12)	intron (NR_026975, intron 6 of 12)	52368	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.000000	0.403774	
chunk0083_300_1	chr17	69334832	69335259	+	0	NA	Intergenic	Intergenic	-7863	NM_172232	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.004684	0.299065	
chunk0027_385_1	chr10	79615012	79615425	+	0	NA	3' UTR (NM_005411, exon 6 of 6)	3' UTR (NM_005411, exon 6 of 6)	4279	NM_001093770	653509	Hs.535295	NM_005411	ENSG00000122852	SFTPA1	COLEC4|PSAP|PSP-A|PSPA|SFTP1|SFTPA1B|SP-A|SP-A1|SPA|SPA1	surfactant protein A1	protein-coding	0.002421	0.398551	
chunk0051_82_1	chr12	113940064	113940263	+	0	NA	intron (NM_001146699, intron 14 of 24)	intron (NM_001146699, intron 14 of 24)	26208	NM_016196	9904	Hs.7482	NM_016196	ENSG00000122965	RBM19	Mrd1	RNA binding motif protein 19	protein-coding	0.025126	0.605000	
chunk0129_246_1	chr3	122086379	122086815	+	0	NA	intron (NM_006889, intron 1 of 6)	intron (NM_006889, intron 1 of 6)	8748	NM_176892	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.006881	0.530892	250(AAGTACTCTCTGTACC,-,0.00),251(AGTACTCTCTGTACCT,+,0.00)
chunk0093_178_1	chr19	48567494	48567740	+	0	NA	intron (NM_177973, intron 1 of 6)	intron (NM_177973, intron 1 of 6)	-8119	NM_004605	6820	Hs.369331	NM_004605	ENSG00000088002	SULT2B1	ARCI14|HSST2	sulfotransferase family 2B member 1	protein-coding	0.024390	0.510121	68(AAGAACACAGTGTTAC,-,0.00),69(AGAACACAGTGTTACC,+,0.00)
chunk0113_316_1	chr20	58123184	58123853	+	0	NA	Intergenic	L1MC3|LINE|L1	-27409	NM_178456	128602	Hs.43977	NM_178456	ENSG00000124237	C20orf85	LLC1|bA196N14.1	chromosome 20 open reading frame 85	protein-coding	0.004484	0.346269	164(AAAACATAGAGTTCTT,+,0.00)
chunk0120_133_1	chr3	4979200	4979399	+	0	NA	promoter-TSS (NM_003670)	promoter-TSS (NM_003670)	-113	NM_003670	8553	Hs.744856	NM_003670	ENSG00000134107	BHLHE40	BHLHB2|Clast5|DEC1|HLHB2|SHARP-2|SHARP2|STRA13|Stra14	basic helix-loop-helix family member e40	protein-coding	0.055276	0.670000	
chunk0024_211_1	chr10	36811710	36811990	+	0	NA	Intergenic	L2b|LINE|L2	-314007	NM_052997	91074	Hs.373787	NM_052997	ENSG00000148513	ANKRD30A	NY-BR-1	ankyrin repeat domain 30A	protein-coding	0.010714	0.387900	
chunk0138_191_1	chr4	38009806	38010605	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	49770	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.007509	0.416250	
chunk0186_109_1	chr7	137953972	137954314	+	0	NA	intron (NM_001243523, intron 1 of 3)	intron (NM_001243523, intron 1 of 3)	795	NM_001243523									0.008772	0.402332	
chunk0101_189_1	chr2	129529170	129529846	+	0	NA	Intergenic	L1MA3|LINE|L1	-255617	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.002959	0.305761	
chunk0116_175_1	chr21	36790657	36791078	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	91734	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.011876	0.481043	
chunk0054_391_1	chr13	50354075	50354528	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	173148	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.002208	0.433921	
chunk0195_9_1	chr8	92964688	92965393	+	0	NA	intron (NM_001171796, intron 1 of 5)	intron (NM_001171796, intron 1 of 5)	549	NM_001191036	286144	Hs.440643	NM_001171795	ENSG00000205133	TRIQK	C8orf83|PRO0845|UPF0599	triple QxxK/R motif containing	protein-coding	0.007092	0.399433	
chunk0153_124_1	chr5	68782929	68783604	+	0	NA	Intergenic	L2|LINE|L2	246661	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.004444	0.368343	
chunk0208_11_1	chrX	10519094	10519720	+	0	NA	intron (NM_001193281, intron 2 of 2)	intron (NM_001193281, intron 2 of 2)	48196	NM_001193280	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.000000	0.355662	
chunk0087_334_1	chr18	40108625	40109270	+	0	NA	Intergenic	Intergenic	42661	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.010853	0.396285	
chunk0129_375_1	chr3	125652330	125652603	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-56929	NM_022776	114885	Hs.477440	NM_022776	ENSG00000144909	OSBPL11	ORP-11|ORP11|OSBP12|TCCCIA00292	oxysterol binding protein like 11	protein-coding	0.007326	0.500000	
chunk0204_373_1	chr9	102021100	102021373	+	0	NA	Intergenic	Intergenic	-282656	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.003663	0.259124	
chunk0046_395_1	chr12	63955832	63956143	+	0	NA	intron (NM_020762, intron 1 of 21)	intron (NM_020762, intron 1 of 21)	111226	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.016077	0.403846	96(AAGTACTCTGTGTTCT,-,0.00),97(AGTACTCTGTGTTCTC,+,0.00)
chunk0201_143_1	chr9	35795756	35796191	+	0	NA	intron (NM_003995, intron 2 of 21)	L2a|LINE|L2	3564	NM_003995	4882	Hs.78518	NM_000907	ENSG00000159899	NPR2	AMDM|ANPRB|ANPb|ECDM|GUC2B|GUCY2B|NPRB|NPRBi|SNSK	natriuretic peptide receptor 2	protein-coding	0.000000	0.392202	
chunk0028_196_1	chr10	88856028	88856290	+	0	NA	Intergenic	LTR47B3|LTR|ERVL	-4184	NM_144590	118932	Hs.217484	NM_144590	ENSG00000152766	ANKRD22	-	ankyrin repeat domain 22	protein-coding	0.003817	0.391635	
chunk0019_417_1	chr1	230751762	230752238	+	0	NA	intron (NM_016452, intron 1 of 18)	intron (NM_016452, intron 1 of 18)	4585	NM_016452	10753	Hs.498021	NM_006615	ENSG00000135773	CAPN9	GC36|nCL-4	calpain 9	protein-coding	0.016807	0.555556	
chunk0192_132_1	chr8	61844220	61844568	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	129606	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.005747	0.386819	102(ATAAACAGCCTGTACC,-,0.00),103(TAAACAGCCTGTACCT,+,0.00)
chunk0049_330_1	chr12	94764315	94764637	+	0	NA	Intergenic	Intergenic	-69922	NR_030171	574449		NR_030171	ENSG00000283998	MIR492	MIRN492|hsa-mir-492	microRNA 492	ncRNA	0.009317	0.380805	
chunk0193_448_1	chr8	81123107	81123853	+	0	NA	Intergenic	Intergenic	-11412	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.009383	0.369478	421(CAGAGCATTATGTTCT,-,0.00),422(AGAGCATTATGTTCTT,+,0.00)
chunk0130_212_1	chr3	133973259	133973648	+	0	NA	intron (NM_005630, intron 3 of 13)	intron (NM_005630, intron 3 of 13)	-43641	NM_025041	80111	Hs.287691	NM_025041	ENSG00000174640	C3orf36	-	chromosome 3 open reading frame 36	ncRNA	0.002571	0.482051	
chunk0069_100_1	chr15	61393828	61394135	+	0	NA	Intergenic	Intergenic	-164678	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.006515	0.370130	
chunk0108_151_1	chr2	231030224	231030672	+	0	NA	Intergenic	Intergenic	-7118	NM_001144994	257407	Hs.526596	NM_001144994	ENSG00000204128	C2orf72	-	chromosome 2 open reading frame 72	protein-coding	0.006696	0.400891	
chunk0032_242_1	chr11	8105862	8106413	+	0	NA	TTS (NM_001206672)	TTS (NM_001206672)	24775	NM_177972	7275	Hs.568986	NM_003320	ENSG00000166402	TUB	RDOB|rd5	TUB bipartite transcription factor	protein-coding	0.007260	0.369565	
chunk0057_404_1	chr13	109656944	109657581	+	0	NA	Intergenic	Intergenic	-71012	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.007849	0.369906	
chunk0001_268_1	chr1	8598204	8598550	+	0	NA	intron (NM_001042681, intron 4 of 22)	intron (NM_001042681, intron 4 of 22)	-103464	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.031792	0.556196	
chunk0057_259_1	chr13	105463968	105464708	+	0	NA	intron (NR_040247, intron 5 of 6)	L2a|LINE|L2	-1529	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.004054	0.380567	593(TAGAACACCAAGTTCC,-,0.00),594(AGAACACCAAGTTCCT,+,0.00)
chunk0179_128_1	chr7	45889255	45889835	+	0	NA	intron (NM_000596, intron 1 of 3)	intron (NM_000596, intron 1 of 3)	1185	NM_000596	3484	Hs.642938	NM_000596	ENSG00000146678	IGFBP1	AFBP|IBP1|IGF-BP25|PP12|hIGFBP-1	insulin like growth factor binding protein 1	protein-coding	0.013793	0.519793	248(GGATACAGTATGTGCT,-,0.00),249(GATACAGTATGTGCTT,+,0.00)
chunk0104_231_1	chr2	176466925	176467491	+	0	NA	Intergenic	Intergenic	133844	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.010601	0.396825	
chunk0030_308_1	chr10	117763432	117764424	+	0	NA	Intergenic	L2b|LINE|L2	-218860	NR_002791	196047	Hs.312592	NR_002791	ENSG00000229847	EMX2OS	EMX2-AS1|NCRNA00045	EMX2 opposite strand/antisense RNA	ncRNA	0.008065	0.452165	
chunk0036_104_1	chr11	61165116	61165315	+	0	NA	Intergenic	Intergenic	-3771	NM_017966	55048	Hs.523715	NM_017966	ENSG00000167987	VPS37C	-	VPS37C subunit of ESCRT-I	protein-coding	0.020101	0.440000	
chunk0098_78_1	chr2	67327152	67327466	+	0	NA	Intergenic	Intergenic	-70001	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.000000	0.323810	
chunk0081_59_1	chr17	38693823	38694084	+	0	NA	Intergenic	Intergenic	8378	NR_039887	100616203		NR_039887	ENSG00000275238	MIR4734	mir-4734	microRNA 4734	ncRNA	0.011494	0.606870	
chunk0041_186_1	chr11	126364799	126365043	+	0	NA	intron (NM_006278, intron 1 of 10)	intron (NM_006278, intron 1 of 10)	9027	NM_006278	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.020492	0.624490	
chunk0074_153_1	chr16	23324601	23325234	+	0	NA	intron (NM_000336, intron 1 of 12)	intron (NM_000336, intron 1 of 12)	22647	NM_000336	6338	Hs.414614	NM_000336	ENSG00000168447	SCNN1B	BESC1|ENaCb|ENaCbeta|LIDLS1|SCNEB	sodium channel epithelial 1 beta subunit	protein-coding	0.006319	0.518927	
chunk0023_32_1	chr10	21154356	21154659	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	-7948	NM_001177483	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.009901	0.417763	
chunk0007_257_1	chr1	82943251	82943628	+	0	NA	Intergenic	Intergenic	41483	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.002653	0.462963	
chunk0062_296_1	chr14	72583343	72583733	+	0	NA	Intergenic	Intergenic	66718	NR_106994	102465832		NR_106994	ENSG00000273830	MIR7843	hsa-mir-7843	microRNA 7843	ncRNA	0.007692	0.447570	210(AAGAACACAGTCTTCT,-,0.00),211(AGAACACAGTCTTCTG,+,0.00)
chunk0158_415_1	chr5	134943721	134944076	+	0	NA	intron (NM_032151, intron 2 of 3)	intron (NM_032151, intron 2 of 3)	15859	NR_039666									0.000000	0.390449	
chunk0030_229_1	chr10	114857799	114858808	+	0	NA	intron (NM_020940, intron 14 of 16)	intron (NM_020940, intron 14 of 16)	36559	NM_001135051	57700	Hs.192619	NM_020940	ENSG00000151553	FAM160B1	KIAA1600|bA106M7.3	family with sequence similarity 160 member B1	protein-coding	0.002973	0.302970	
chunk0111_138_1	chr20	24930561	24930923	+	0	NA	Intergenic	HERVE-int|LTR|ERV1	-18488	NM_003650	8530	Hs.143212	NM_003650	ENSG00000077984	CST7	CMAP	cystatin F	protein-coding	0.019337	0.465565	
chunk0014_161_1	chr1	178275079	178275649	+	0	NA	intron (NM_170692, intron 1 of 17)	intron (NM_170692, intron 1 of 17)	-66107	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.003509	0.408056	
chunk0078_233_1	chr17	6672487	6672842	+	0	NA	Intergenic	L1ME4a|LINE|L1	14945	NR_045985	100652883	Hs.549540	NR_045985		ALOX15P1	ALOX15P	arachidonate 15-lipoxygenase pseudogene 1	pseudo	0.019718	0.334270	
chunk0005_24_1	chr1	54374567	54374877	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	31673	NM_145716	23648	Hs.476706	NM_018070	ENSG00000157216	SSBP3	CSDP|SSDP|SSDP1	single stranded DNA binding protein 3	protein-coding	0.006452	0.472669	69(TGGAACAAGCTGTCCC,-,0.00),70(GGAACAAGCTGTCCCC,+,0.00)
chunk0085_238_1	chr18	7067561	7067846	+	0	NA	intron (NM_005559, intron 3 of 62)	intron (NM_005559, intron 3 of 62)	50111	NM_005559	284217	Hs.270364	NM_005559	ENSG00000101680	LAMA1	LAMA|PTBHS|S-LAM-alpha	laminin subunit alpha 1	protein-coding	0.017544	0.433566	162(TAGGACTGAATGTACT,-,0.00),163(AGGACTGAATGTACTA,+,0.00)
chunk0056_281_1	chr13	90416495	90417061	+	0	NA	Intergenic	Intergenic	-76510	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.008834	0.368607	276(AAGAACAAGATGTGCT,-,0.00),277(AGAACAAGATGTGCTT,+,0.00)
chunk0032_320_1	chr11	10039786	10039985	+	0	NA	intron (NM_030962, intron 3 of 39)	L1MC4|LINE|L1	200743	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.005025	0.315000	
chunk0202_189_1	chr9	74887699	74888094	+	0	NA	promoter-TSS (NM_001177311)	promoter-TSS (NM_001177311)	-176	NM_001177310	140803	Hs.272225	NM_017662	ENSG00000119121	TRPM6	CHAK2|HMGX|HOMG|HOMG1|HSH	transient receptor potential cation channel subfamily M member 6	protein-coding	0.030380	0.507576	137(CAAGACAGGTTGTTCT,-,0.00),138(AAGACAGGTTGTTCTT,+,0.00)
chunk0149_158_1	chr5	20340000	20340557	+	0	NA	intron (NM_001291956, intron 1 of 14)	MER52-int|LTR|ERV1	235595	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.005386	0.446237	
chunk0053_430_1	chr13	38898311	38898696	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	92356	NM_145286	161003	Hs.327794	NM_145286	ENSG00000133115	STOML3	Epb7.2l|SRO	stomatin like 3	protein-coding	0.005195	0.362694	
chunk0170_296_1	chr6	115360950	115361404	+	0	NA	Intergenic	MIR|SINE|MIR	-677554	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.006608	0.345055	
chunk0209_144_1	chrX	41993999	41994426	+	0	NA	Intergenic	L1MB8|LINE|L1	-71178	NM_001126055	8573	Hs.495984	NM_003688	ENSG00000147044	CASK	CAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK	calcium/calmodulin dependent serine protein kinase	protein-coding	0.002342	0.327103	
chunk0016_445_1	chr1	204088834	204089482	+	0	NA	intron (NM_005686, intron 1 of 13)	intron (NM_005686, intron 1 of 13)	16040	NM_005686	9580	Hs.201671	NM_005686	ENSG00000143842	SOX13	ICA12|Sox-13	SRY-box transcription factor 13	protein-coding	0.016975	0.519260	311(AAGCACATTCTGTTCT,-,0.00),312(AGCACATTCTGTTCTC,+,0.00)
chunk0102_143_1	chr2	146315916	146316158	+	0	NA	Intergenic	Intergenic	-271020	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.008264	0.341564	
chunk0044_285_1	chr12	32692581	32693251	+	0	NA	intron (NM_001278464, intron 1 of 20)	L1ME3C|LINE|L1	13716	NM_012062	10059	Hs.556296	NM_005690	ENSG00000087470	DNM1L	DLP1|DRP1|DVLP|DYMPLE|EMPF|EMPF1|HDYNIV|OPA5	dynamin 1 like	protein-coding	0.002985	0.345753	31(AAGAACACAGAGTCCA,-,0.00),32(AGAACACAGAGTCCAT,+,0.00)
chunk0199_131_1	chr9	3857578	3857807	+	0	NA	intron (NM_001042413, intron 8 of 10)	intron (NM_001042413, intron 8 of 10)	-40954	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.013100	0.408696	
chunk0044_425_1	chr12	42023878	42024378	+	0	NA	Intergenic	Intergenic	120743	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.032000	0.475050	
chunk0047_132_1	chr12	69470189	69470497	+	0	NA	promoter-TSS (NM_001278357)	promoter-TSS (NM_001278357)	-6	NM_001278354	10818	Hs.593446	NM_006654	ENSG00000166225	FRS2	FRS1A|FRS2A|FRS2alpha|SNT|SNT-1|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.081169	0.676375	
chunk0050_151_1	chr12	102892507	102892786	+	0	NA	intron (NM_000277, intron 3 of 12)	L1MC2|LINE|L1	24957	NM_000277	5053	Hs.560019	NM_000277	ENSG00000171759	PAH	PH|PKU|PKU1	phenylalanine hydroxylase	protein-coding	0.000000	0.360714	
chunk0182_421_1	chr7	101163010	101163417	+	0	NA	exon (NM_003378, exon 2 of 2)	exon (NM_003378, exon 2 of 2)	2358	NM_003378	7425	Hs.587325	NM_003378	ENSG00000128564	VGF	SCG7|SgVII	VGF nerve growth factor inducible	protein-coding	0.122850	0.742647	
chunk0004_108_1	chr1	44327745	44327944	+	0	NA	intron (NM_001301701, intron 2 of 7)	intron (NM_001301701, intron 2 of 7)	27435	NM_001301700	79033	Hs.731413	NM_024066	ENSG00000117419	ERI3	PINT1|PRNPIP	ERI1 exoribonuclease family member 3	protein-coding	0.005025	0.455000	
chunk0094_45_1	chr2	2512678	2513155	+	0	NA	Intergenic	LTR16|LTR|ERVL	-181603	NM_015025	23040	Hs.434418	NM_015025	ENSG00000186487	MYT1L	MRD39|NZF1|ZC2H2C2|ZC2HC4B|myT1-L	myelin transcription factor 1 like	protein-coding	0.020964	0.556485	
chunk0016_143_1	chr1	197285658	197285869	+	0	NA	intron (NM_201253, intron 1 of 11)	intron (NM_201253, intron 1 of 11)	17559	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.004739	0.448113	
chunk0124_444_1	chr3	61462393	61462665	+	0	NA	Intergenic	MIR|SINE|MIR	-99040	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.003676	0.435897	
chunk0056_421_1	chr13	94544405	94544626	+	0	NA	Intergenic	Intergenic	51760	NM_014305	23483	Hs.12393	NM_014305	ENSG00000088451	TGDS	CATMANS|SDR2E1|TDPGD	TDP-glucose 4,6-dehydratase	protein-coding	0.009050	0.445946	
chunk0102_445_1	chr2	158183312	158183568	+	0	NA	intron (NM_001301684, intron 9 of 11)	intron (NM_001301684, intron 9 of 11)	16790	NR_038850	554201	Hs.570262	NR_038850	ENSG00000227480	CCDC148-AS1	-	CCDC148 antisense RNA 1	ncRNA	0.007812	0.404669	
chunk0083_251_1	chr17	67992992	67993254	+	0	NA	exon (NM_181656, exon 2 of 3)	exon (NM_181656, exon 2 of 3)	526	NM_181655	284018	Hs.90790	NM_181655	ENSG00000186665	C17orf58	-	chromosome 17 open reading frame 58	protein-coding	0.068702	0.555133	
chunk0013_213_1	chr1	169485140	169485440	+	0	NA	intron (NM_006996, intron 1 of 5)	intron (NM_006996, intron 1 of 5)	680	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.043333	0.504983	
chunk0011_201_1	chr1	150001488	150001937	+	0	NA	intron (NM_020205, intron 1 of 11)	intron (NM_020205, intron 1 of 11)	9025	NM_020205	56957	Hs.98322	NM_020205	ENSG00000264522	OTUD7B	CEZANNE|ZA20D1	OTU deubiquitinase 7B	protein-coding	0.002227	0.442222	
chunk0201_65_1	chr9	34035618	34036194	+	0	NA	intron (NM_018449, intron 1 of 28)	intron (NM_018449, intron 1 of 28)	13043	NM_018449	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.013889	0.391681	
chunk0185_101_1	chr7	125578994	125579193	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-314802	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.005025	0.380000	
chunk0186_52_1	chr7	136348177	136348783	+	0	NA	Intergenic	Intergenic	-371024	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.009901	0.474465	
chunk0151_14_1	chr5	41193693	41194248	+	0	NA	intron (NM_001115131, intron 5 of 17)	intron (NM_001115131, intron 5 of 17)	19623	NM_000065	729	Hs.481992	NM_000065	ENSG00000039537	C6	-	complement C6	protein-coding	0.010811	0.410072	238(GAGGACTGGTTGTCCC,-,0.00),239(AGGACTGGTTGTCCCG,+,0.00)
chunk0205_328_1	chr9	112842601	112843027	+	0	NA	intron (NM_001012994, intron 6 of 8)	intron (NM_001012994, intron 6 of 8)	48099	NM_033051	57864	Hs.512668	NM_033051	ENSG00000119457	SLC46A2	Ly110|TSCOT	solute carrier family 46 member 2	protein-coding	0.009390	0.437939	247(GAGAACAGCTTGTACT,-,0.00),248(AGAACAGCTTGTACTA,+,0.00)
chunk0099_329_1	chr2	99940942	99941321	+	0	NA	intron (NM_001025108, intron 6 of 23)	intron (NM_001025108, intron 6 of 23)	164452	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.021108	0.552632	127(CAGCACAGGCTGTGCT,-,0.00),128(AGCACAGGCTGTGCTT,+,0.00)
chunk0206_350_1	chr9	125600280	125600875	+	0	NA	intron (NM_001006618, intron 4 of 7)	intron (NM_001006618, intron 4 of 7)	106657	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.001681	0.377517	325(TTGGACAAAATGTTCC,-,0.00),326(TGGACAAAATGTTCCT,+,0.00)
chunk0025_355_1	chr10	58353193	58353765	+	0	NA	intron (NM_001204880, intron 1 of 5)	MamSINE1|SINE|tRNA-RTE	18500	NM_003338	7321	Hs.129683	NM_003338	ENSG00000072401	UBE2D1	E2(17)KB1|SFT|UBC4/5|UBCH5|UBCH5A	ubiquitin conjugating enzyme E2 D1	protein-coding	0.003497	0.352531	
chunk0154_37_1	chr5	77087376	77087685	+	0	NA	promoter-TSS (NM_032367)	promoter-TSS (NM_032367)	-325	NM_032367	84327	Hs.584988	NM_032367	ENSG00000132846	ZBED3	-	zinc finger BED-type containing 3	protein-coding	0.025890	0.477419	
chunk0199_312_1	chr9	7169981	7170317	+	0	NA	intron (NM_001304339, intron 21 of 21)	intron (NM_001304339, intron 21 of 21)	412508	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.005952	0.347181	
chunk0027_26_1	chr10	72254913	72255644	+	0	NA	Intergenic	Intergenic	-18641	NM_019058	54541	Hs.744875	NM_019058	ENSG00000168209	DDIT4	Dig2|REDD-1|REDD1	DNA damage inducible transcript 4	protein-coding	0.017784	0.588798	356(CAGAACGGTCTGTACC,-,0.00),357(AGAACGGTCTGTACCC,+,0.00)
chunk0158_113_1	chr5	126883789	126884135	+	0	NA	intron (NM_178450, intron 3 of 4)	intron (NM_178450, intron 3 of 4)	106809	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.005780	0.417867	
chunk0117_294_1	chr22	24402602	24403144	+	0	NA	intron (NM_001254732, intron 13 of 14)	intron (NM_001254732, intron 13 of 14)	-20724	NM_001278500	135	Hs.197029	NM_000675	ENSG00000128271	ADORA2A	A2aR|ADORA2|RDC8	adenosine A2a receptor	protein-coding	0.003690	0.460405	
chunk0042_110_1	chr12	3200904	3201421	+	0	NA	intron (NM_006675, intron 2 of 8)	intron (NM_006675, intron 2 of 8)	123807	NM_001168320	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.065764	0.565637	317(AAGTACATGATGTTCC,-,0.00),318(AGTACATGATGTTCCT,+,0.00)
chunk0166_410_1	chr6	52156181	52156380	+	0	NA	Intergenic	Intergenic	-5257	NR_131248	101154644	Hs.582788	NR_131248		LINCMD1	LINC-MD1|MIR133BHG	long intergenic non-protein coding RNA, muscle differentiation 1	ncRNA	0.005025	0.500000	
chunk0038_17_1	chr11	80928702	80929047	+	0	NA	Intergenic	L1PA15|LINE|L1	-166071	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.002899	0.372832	
chunk0140_140_1	chr4	69219317	69219531	+	0	NA	Intergenic	L1MB8|LINE|L1	-4693	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.014019	0.320930	
chunk0052_52_1	chr13	20995465	20995785	+	0	NA	intron (NM_014572, intron 2 of 7)	intron (NM_014572, intron 2 of 7)	-46197	NR_104058	101930748	Hs.637638	NR_104058	ENSG00000233780	LINC00367	-	long intergenic non-protein coding RNA 367	ncRNA	0.009375	0.451713	
chunk0205_454_1	chr9	115498062	115498702	+	0	NA	Intergenic	Intergenic	245857	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.009375	0.429017	
chunk0099_208_1	chr2	94960863	94961396	+	0	NA	Intergenic	Intergenic	-13787	NR_037597	442028	Hs.611545	NR_037597	ENSG00000259848	LOC442028	-	uncharacterized LOC442028	ncRNA	0.011257	0.483146	231(AGGTACAGTGAGTTCT,-,0.00),232(GGTACAGTGAGTTCTT,+,0.00)
chunk0133_8_1	chr3	165268874	165269073	+	0	NA	intron (NR_125764, intron 1 of 5)	intron (NR_125764, intron 1 of 5)	62013	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.005025	0.265000	
chunk0165_314_1	chr6	37069698	37069913	+	0	NA	Intergenic	L2b|LINE|L2	64158	NM_173558	221472	Hs.509664	NM_173558	ENSG00000146192	FGD2	ZFYVE4	FYVE, RhoGEF and PH domain containing 2	protein-coding	0.013953	0.439815	
chunk0205_209_1	chr9	109316356	109316654	+	0	NA	intron (NM_018424, intron 1 of 15)	L3b|LINE|CR1	4459	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.026846	0.588629	
chunk0139_414_1	chr4	63766250	63766552	+	0	NA	Intergenic	Intergenic	643059	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.000000	0.369637	
chunk0129_307_1	chr3	123758311	123758600	+	0	NA	intron (NM_053025, intron 4 of 33)	intron (NM_053025, intron 4 of 33)	68811	NR_046629	100873940	Hs.667316	NR_046629	ENSG00000250174	MYLK-AS2	-	MYLK antisense RNA 2	ncRNA	0.010381	0.465517	
chunk0135_260_1	chr3	189061377	189061683	+	0	NA	Intergenic	L1PREC2|LINE|L1	-110444	NM_198485	285386	Hs.729544	NM_198485	ENSG00000188001	TPRG1	FAM79B	tumor protein p63 regulated 1	protein-coding	0.000000	0.325733	
chunk0074_64_1	chr16	21214977	21215248	+	0	NA	promoter-TSS (NM_003460)	promoter-TSS (NM_003460)	-602	NM_003460	7783	Hs.73982	NM_003460	ENSG00000103310	ZP2	OOMD6|ZPA|Zp-2	zona pellucida glycoprotein 2	protein-coding	0.007380	0.360294	
chunk0141_325_1	chr4	87304625	87305225	+	0	NA	3' UTR (NM_001136230, exon 6 of 6)	3' UTR (NM_001136230, exon 6 of 6)	-4342	NR_049891	100847027		NR_049891	ENSG00000263981	MIR5705	-	microRNA 5705	ncRNA	0.006667	0.344426	
chunk0196_262_1	chr8	108798060	108798286	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-10632	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.008850	0.370044	
chunk0002_175_1	chr1	18988797	18989473	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	-32803	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.014793	0.505170	
chunk0083_6_1	chr17	62718181	62718639	+	0	NA	intron (NM_001100875, intron 8 of 10)	intron (NM_001100875, intron 8 of 10)	88243	NM_001100875	162333	Hs.665663	NM_152598	ENSG00000173838	MARCH10	MARCH-X|RNF190	membrane associated ring-CH-type finger 10	protein-coding	0.017467	0.490196	
chunk0076_170_1	chr16	67423537	67424095	+	0	NA	Intergenic	Intergenic	-7317	NM_000196	3291	Hs.1376	NM_000196	ENSG00000176387	HSD11B2	AME|AME1|HSD11K|HSD2|SDR9C3	hydroxysteroid 11-beta dehydrogenase 2	protein-coding	0.010753	0.400716	
chunk0024_174_1	chr10	35721157	35721673	+	0	NA	Intergenic	Intergenic	-56887	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.003876	0.315280	
chunk0189_422_1	chr8	27911933	27912595	+	0	NA	intron (NM_173833, intron 4 of 8)	intron (NM_173833, intron 4 of 8)	-26148	NR_036249	100422828		NR_036249	ENSG00000265847	MIR4287	-	microRNA 4287	ncRNA	0.015106	0.450980	
chunk0017_11_1	chr1	204404761	204405021	+	0	NA	3' UTR (NM_032833, exon 2 of 2)	3' UTR (NM_032833, exon 2 of 2)	6926	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.007692	0.360153	
chunk0143_9_1	chr4	105805441	105805796	+	0	NA	intron (NM_001031720, intron 5 of 11)	intron (NM_001031720, intron 5 of 11)	21554	NR_125927	101929529	Hs.603751	NR_125927	ENSG00000251175	LOC101929529	-	uncharacterized LOC101929529	ncRNA	0.002817	0.320225	
chunk0089_419_1	chr18	69659474	69659689	+	0	NA	intron (NM_152721, intron 3 of 7)	Eulor5B|DNA?|DNA?	258533	NM_152721	220164	Hs.278285	NM_152721	ENSG00000206052	DOK6	DOK5L|HsT3226	docking protein 6	protein-coding	0.018605	0.444444	
chunk0177_248_1	chr7	25062104	25062330	+	0	NA	Intergenic	Intergenic	63144	NM_018947	54205	Hs.437060	NM_018947	ENSG00000172115	CYCS	CYC|HCS|THC4	cytochrome c, somatic	protein-coding	0.017699	0.488987	
chunk0021_344_1	chr1	246037584	246038313	+	0	NA	intron (NM_001167740, intron 5 of 11)	MER58A|DNA|hAT-Charlie	379464	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.008230	0.412329	
chunk0162_393_1	chr5	179678434	179678991	+	0	NA	exon (NM_001164444, exon 2 of 2)	exon (NM_001164444, exon 2 of 2)	2262	NM_001164444	646019	Hs.535767	NM_001164444	ENSG00000204659	CBY3	-	chibby family member 3	protein-coding	0.113106	0.691756	
chunk0178_336_1	chr7	38335668	38335928	+	0	NA	Intergenic	Intergenic	-5779	NR_040085	100506776	Hs.173034	NR_040085	ENSG00000281103	TRG-AS1	TCRGV	T cell receptor gamma locus antisense RNA 1	ncRNA	0.011538	0.647510	
chunk0156_89_1	chr5	104652810	104653067	+	0	NA	Intergenic	L1MA4A|LINE|L1	-446536	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.003891	0.550388	
chunk0023_163_1	chr10	24306580	24306996	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	31103	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.014423	0.422062	200(AGGGACATCGTGTCTT,-,0.00),201(GGGACATCGTGTCTTT,+,0.00)
chunk0063_270_1	chr14	83982674	83983090	+	0	NA	Intergenic	Intergenic	-1410997	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.004808	0.263789	239(AGGACATTCTGTCTAT,+,0.00)
chunk0023_406_1	chr10	31104671	31105340	+	0	NA	Intergenic	AluJr4|SINE|Alu	-73068	NR_026560	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.014948	0.462687	
chunk0064_61_1	chr14	90037288	90037958	+	0	NA	intron (NM_018319, intron 16 of 16)	L1MC4|LINE|L1	-24142	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.002985	0.308495	
chunk0045_178_1	chr12	46952576	46953324	+	0	NA	Intergenic	Intergenic	-126653	NM_138371	91523	Hs.560100	NM_138371	ENSG00000179715	PCED1B	FAM113B	PC-esterase domain containing 1B	protein-coding	0.002674	0.376502	
chunk0102_65_1	chr2	142915646	142915947	+	0	NA	intron (NM_001032998, intron 2 of 11)	intron (NM_001032998, intron 2 of 11)	38170	NM_003937	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.003322	0.367550	
chunk0055_289_1	chr13	65095176	65095389	+	0	NA	Intergenic	Intergenic	-770765	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.009390	0.364486	
chunk0167_218_1	chr6	66478812	66479218	+	0	NA	Intergenic	LTR18A|LTR|ERVL	691136	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.009852	0.474201	
chunk0051_47_1	chr12	112305707	112306392	+	0	NA	intron (NM_001109662, intron 7 of 75)	intron (NM_001109662, intron 7 of 75)	76043	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.004380	0.395044	378(GAAGACAGAATGTCCC,-,0.00),379(AAGACAGAATGTCCCT,+,0.00)
chunk0070_393_1	chr15	77001670	77001881	+	0	NA	intron (NM_003978, intron 1 of 14)	L1ME4b|LINE|L1	6651	NM_003978	9051	Hs.129758	NM_003978	ENSG00000140368	PSTPIP1	CD2BP1|CD2BP1L|CD2BP1S|H-PIP|PAPAS|PSTPIP	proline-serine-threonine phosphatase interacting protein 1	protein-coding	0.018957	0.466981	
chunk0120_435_1	chr3	13475989	13476739	+	0	NA	TTS (NR_046690)	TTS (NR_046690)	3689	NR_046690	100874101	Hs.535701	NR_046690	ENSG00000244502	HDAC11-AS1	-	HDAC11 antisense RNA 1	ncRNA	0.010667	0.545939	
chunk0192_311_1	chr8	66839731	66840123	+	0	NA	intron (NM_001033578, intron 10 of 16)	intron (NM_001033578, intron 10 of 16)	-30822	NM_173518	157777	Hs.437006	NM_173518	ENSG00000178460	MCMDC2	C8orf45	minichromosome maintenance domain containing 2	protein-coding	0.010204	0.391858	
chunk0005_287_1	chr1	60097677	60098042	+	0	NA	Intergenic	Intergenic	-24089	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.016438	0.434426	
chunk0090_341_1	chr18	76376153	76376747	+	0	NA	intron (NM_014643, intron 4 of 6)	intron (NM_014643, intron 4 of 6)	118740	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.013468	0.406723	
chunk0173_379_1	chr6	149855120	149856035	+	0	NA	intron (NM_032832, intron 1 of 6)	PABL_B|LTR|ERV1	-7921	NR_045126	100652739	Hs.642734	NR_045126	ENSG00000223701	RAET1E-AS1	RAET1G-AS1	RAET1E antisense RNA 1	ncRNA	0.007650	0.414847	
chunk0171_355_1	chr6	130558270	130558696	+	0	NA	Intergenic	Intergenic	121366	NM_052913	114801	Hs.591341	NM_052913	ENSG00000164484	TMEM200A	KIAA1913|TTMA|TTMC	transmembrane protein 200A	protein-coding	0.002347	0.325527	
chunk0082_89_1	chr17	52774917	52775309	+	0	NA	Intergenic	Intergenic	-210407	NM_001243552	100506650	Hs.146556	NM_001243552		C17orf112	-	chromosome 17 open reading frame 112	protein-coding	0.007653	0.374046	
chunk0006_35_1	chr1	64321530	64321810	+	0	NA	Intergenic	L2c|LINE|L2	117863	NM_152489	148581	Hs.388746	NM_152489	ENSG00000177414	UBE2U	-	ubiquitin conjugating enzyme E2 U	protein-coding	0.000000	0.402135	
chunk0135_79_1	chr3	186109949	186110515	+	0	NA	Intergenic	Intergenic	-1120	NM_004454	2119	Hs.43697	NM_004454	ENSG00000244405	ETV5	ERM	ETS variant 5	protein-coding	0.042403	0.566138	
chunk0187_7_1	chr8	473159	473460	+	0	NA	Intergenic	Intergenic	66501	NM_012173	26260	Hs.438454	NM_012173	ENSG00000147364	FBXO25	FBX25	F-box protein 25	protein-coding	0.016611	0.556291	165(TGAGACAGTGTGTTCT,-,0.00),166(GAGACAGTGTGTTCTA,+,0.00)
chunk0048_107_1	chr12	79421917	79422144	+	0	NA	intron (NM_001291901, intron 8 of 9)	L1ME3C|LINE|L1	2773	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.008811	0.355263	
chunk0170_184_1	chr6	111870813	111871225	+	0	NA	intron (NM_002037, intron 1 of 13)	intron (NM_002037, intron 1 of 13)	2433	NM_002037	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.014563	0.336562	
chunk0001_262_1	chr1	8483588	8484059	+	0	NA	intron (NM_001042681, intron 10 of 22)	intron (NM_001042681, intron 10 of 22)	11090	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.006369	0.338983	
chunk0179_122_1	chr7	45631463	45631933	+	0	NA	intron (NM_021116, intron 4 of 19)	intron (NM_021116, intron 4 of 19)	57172	NM_021116	107	Hs.192215	NM_021116	ENSG00000164742	ADCY1	AC1|DFNB44	adenylate cyclase 1	protein-coding	0.002128	0.320594	
chunk0030_302_1	chr10	117391812	117392167	+	0	NA	Intergenic	Intergenic	-16522	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.011268	0.500000	
chunk0078_390_1	chr16	87925207	87925980	+	0	NA	intron (NM_001739, intron 2 of 6)	intron (NM_001739, intron 2 of 6)	10913	NM_001739	763	Hs.177446	NM_001739	ENSG00000174990	CA5A	CA5|CA5AD|CAV|CAVA|GS1-21A4.1	carbonic anhydrase 5A	protein-coding	0.032342	0.571059	681(CTGCTCAGTCTGTCCT,-,0.00),682(TGCTCAGTCTGTCCTC,+,0.00)
chunk0085_374_1	chr18	9568336	9568578	+	0	NA	intron (NM_001042388, intron 11 of 19)	intron (NM_001042388, intron 11 of 19)	46150	NM_001042388	9989	Hs.743236	NM_005134	ENSG00000154845	PPP4R1	MEG1|PP4(Rmeg)|PP4R1	protein phosphatase 4 regulatory subunit 1	protein-coding	0.000000	0.333333	
chunk0090_404_1	chr18	78780827	78781117	+	0	NA	Intergenic	MER119|DNA|hAT-Charlie	-199303	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.037931	0.570447	
chunk0090_259_1	chr18	74300557	74300823	+	0	NA	Intergenic	MER34|LTR|ERV1	-8674	NM_001190807	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.007519	0.363296	
chunk0130_218_1	chr3	134076554	134076997	+	0	NA	Intergenic	Intergenic	-46699	NM_005630	6578	Hs.518270	NM_005630	ENSG00000174640	SLCO2A1	MATR1|OATP2A1|PGT|PHOAR2|SLC21A2	solute carrier organic anion transporter family member 2A1	protein-coding	0.006772	0.490991	
chunk0147_201_1	chr4	178094519	178095150	+	0	NA	Intergenic	Intergenic	-186898	NR_108093	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.004754	0.270570	
chunk0193_442_1	chr8	81104288	81104770	+	0	NA	intron (NM_018440, intron 1 of 8)	L2b|LINE|L2	7539	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.012448	0.447205	
chunk0131_406_1	chr3	152911114	152911393	+	0	NA	Intergenic	Intergenic	76560	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.007168	0.421429	
chunk0131_163_1	chr3	146496114	146496367	+	0	NA	promoter-TSS (NM_020359)	promoter-TSS (NM_020359)	-249	NM_020359	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.003953	0.397638	
chunk0149_152_1	chr5	20228994	20230220	+	0	NA	intron (NM_001291956, intron 2 of 14)	intron (NM_001291956, intron 2 of 14)	-241363	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002447	0.309698	682(TAAAACATTTTGTTCT,-,0.00),683(AAAACATTTTGTTCTT,+,0.00)
chunk0069_149_1	chr15	62489244	62489530	+	0	NA	Intergenic	Intergenic	146358	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.003497	0.351916	
chunk0034_28_1	chr11	26332036	26332282	+	0	NA	promoter-TSS (NM_031418)	promoter-TSS (NM_031418)	28	NM_031418	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.097561	0.659919	
chunk0092_350_1	chr19	35388275	35388802	+	0	NA	Intergenic	LTR8B|LTR|ERV1	-17069	NR_040046	100128682	Hs.570008	NR_040046	ENSG00000205786	LINC01531	-	long intergenic non-protein coding RNA 1531	ncRNA	0.007590	0.446970	126(AAGAACATCATGTACT,-,0.00),127(AGAACATCATGTACTA,+,0.00)
chunk0023_413_1	chr10	31233342	31233665	+	0	NA	Intergenic	L1MA5|LINE|L1	85592	NR_024284	220930	Hs.372654	NR_024284	ENSG00000237036	ZEB1-AS1	-	ZEB1 antisense RNA 1	ncRNA	0.012384	0.561728	
chunk0021_401_1	chr1	246657618	246657929	+	0	NA	intron (NM_152609, intron 9 of 10)	intron (NM_152609, intron 9 of 10)	-66303	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.006431	0.458333	156(GGCTCATTCTGTGCCT,+,0.00)
chunk0034_87_1	chr11	27401828	27402412	+	0	NA	intron (NM_018490, intron 2 of 17)	MLT1L|LTR|ERVL-MaLR	-38872	NM_080654	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.008562	0.456410	
chunk0145_380_1	chr4	151618135	151618845	+	0	NA	intron (NM_001109977, intron 7 of 13)	intron (NM_001109977, intron 7 of 13)	142533	NM_004564	5188	Hs.119316	NM_004564	ENSG00000059691	GATB	HSPC199|PET112|PET112L	glutamyl-tRNA amidotransferase subunit B	protein-coding	0.005634	0.379747	
chunk0041_294_1	chr11	129586035	129586535	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	30984	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.006000	0.415170	
chunk0053_3_1	chr13	26103531	26103730	+	0	NA	Intergenic	L1P3|LINE|L1	-52570	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.020101	0.535000	
chunk0085_232_1	chr18	6961300	6961781	+	0	NA	intron (NM_005559, intron 53 of 62)	intron (NM_005559, intron 53 of 62)	6863	NR_126040	101927188	Hs.680444	NR_126040	ENSG00000265069	LOC101927188	-	uncharacterized LOC101927188	ncRNA	0.022869	0.443983	
chunk0005_90_1	chr1	56340050	56340519	+	0	NA	Intergenic	L1M2c|LINE|L1	239300	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.004264	0.525532	
chunk0184_67_1	chr7	112488962	112489252	+	0	NA	intron (NM_182597, intron 3 of 3)	intron (NM_182597, intron 3 of 3)	8096	NM_182597	286006	Hs.396189	NM_182597	ENSG00000181016	LSMEM1	C7orf53	leucine rich single-pass membrane protein 1	protein-coding	0.003448	0.316151	
chunk0093_172_1	chr19	48427699	48428140	+	0	NA	intron (NM_000836, intron 10 of 12)	MLT1B|LTR|ERVL-MaLR	-17854	NM_031485	83743	Hs.400625	NM_031485	ENSG00000105447	GRWD1	CDW4|GRWD|RRB1|WDR28	glutamate rich WD repeat containing 1	protein-coding	0.011338	0.454751	
chunk0062_55_1	chr14	67437989	67438247	+	0	NA	Intergenic	Intergenic	3812	NR_049879	100847064		NR_049879	ENSG00000265993	MIR5694	-	microRNA 5694	ncRNA	0.007752	0.555985	152(CAGGACAGTATGCTCT,-,0.00),153(AGGACAGTATGCTCTG,+,0.00)
chunk0183_210_1	chr7	106433030	106434145	+	0	NA	Intergenic	L1MC4a|LINE|L1	-148395	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.001794	0.324373	
chunk0017_325_1	chr1	211474064	211475008	+	0	NA	Intergenic	Intergenic	18381	NM_001164688	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.005297	0.379894	571(AGGAACAGCTTGTTCC,-,0.00),572(GGAACAGCTTGTTCCT,+,0.00)
chunk0212_132_1	chrX	131566668	131566950	+	0	NA	Intergenic	MIRb|SINE|MIR	22735	NM_001004486	347468	Hs.553711	NM_001004486	ENSG00000171054	OR13H1	ORX1	olfactory receptor family 13 subfamily H member 1	protein-coding	0.000000	0.268551	
chunk0104_51_1	chr2	171348205	171348632	+	0	NA	intron (NM_024770, intron 3 of 9)	MER58A|DNA|hAT-Charlie	-85833	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.004684	0.425234	
chunk0077_69_1	chr16	76956158	76956627	+	0	NA	Intergenic	Intergenic	87456	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.014925	0.393617	209(ATAAACACGGTGTTCT,-,0.00),210(TAAACACGGTGTTCTG,+,0.00)
chunk0173_260_1	chr6	147152655	147152877	+	0	NA	intron (NR_034115, intron 3 of 10)	L2c|LINE|L2	-6159	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.000000	0.452915	125(GAGATCACTTTGTTCT,-,0.00),126(AGATCACTTTGTTCTC,+,0.00)
chunk0141_11_1	chr4	76601844	76602489	+	0	NA	intron (NM_020859, intron 2 of 10)	intron (NM_020859, intron 2 of 10)	26615	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.003101	0.345201	
chunk0028_284_1	chr10	91261606	91261881	+	0	NA	intron (NM_001257101, intron 7 of 9)	intron (NM_001257101, intron 7 of 9)	41141	NM_032373	84333	Hs.500512	NM_032373	ENSG00000180628	PCGF5	RNF159	polycomb group ring finger 5	protein-coding	0.003636	0.286232	
chunk0140_52_1	chr4	66657723	66658333	+	0	NA	Intergenic	Intergenic	381204	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.004918	0.371522	369(AAAGACAGTCTGTCCA,-,0.00),370(AAGACAGTCTGTCCAA,+,0.00)
chunk0172_121_1	chr6	135129442	135129732	+	0	NA	Intergenic	LTR16D|LTR|ERVL	-51728	NM_001161660	4602	Hs.606320	NM_005375	ENSG00000118513	MYB	Cmyb|c-myb|c-myb_CDS|efg	MYB proto-oncogene, transcription factor	protein-coding	0.006897	0.453608	
chunk0063_369_1	chr14	85880578	85881093	+	0	NA	Intergenic	Intergenic	-53843	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.003883	0.416667	
chunk0148_143_1	chr5	6064741	6065049	+	0	NA	Intergenic	L1MC1|LINE|L1	272397	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.000000	0.258900	
chunk0155_418_1	chr5	99721464	99721883	+	0	NA	Intergenic	Intergenic	187683	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.000000	0.359524	
chunk0087_278_1	chr18	38517567	38517787	+	0	NA	Intergenic	Intergenic	860542	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.013636	0.425339	
chunk0103_433_1	chr2	169943782	169944363	+	0	NA	intron (NM_172070, intron 20 of 38)	intron (NM_172070, intron 20 of 38)	116564	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.003442	0.266323	
chunk0044_97_1	chr12	28454291	28454603	+	0	NA	intron (NM_018318, intron 10 of 11)	L1M3d|LINE|L1	197247	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.009615	0.466454	114(TAGTACATGGTGTTCC,-,0.00),115(AGTACATGGTGTTCCA,+,0.00)
chunk0174_298_1	chr6	162653090	162653355	+	0	NA	intron (NM_013988, intron 1 of 8)	intron (NM_013988, intron 1 of 8)	-73910	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.007547	0.360902	
chunk0110_235_1	chr20	16288245	16288472	+	0	NA	intron (NM_001199865, intron 24 of 24)	intron (NM_001199865, intron 24 of 24)	285076	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.000000	0.377193	157(AAGTACAGTATGTACT,-,0.00),158(AGTACAGTATGTACTG,+,0.00)
chunk0192_138_1	chr8	61979043	61979447	+	0	NA	Intergenic	Intergenic	264457	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.000000	0.335802	229(TGGCACAGTGTGTCTT,-,0.00),230(GGCACAGTGTGTCTTA,+,0.00)
chunk0105_75_1	chr2	183813776	183814068	+	0	NA	Intergenic	Intergenic	-565053	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.003425	0.262799	
chunk0042_460_1	chr12	12568221	12568831	+	0	NA	Intergenic	Intergenic	-6012	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.009836	0.476268	
chunk0166_160_1	chr6	45554658	45554985	+	0	NA	Intergenic	Intergenic	132244	NM_001278478	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.003058	0.378049	215(CAGGTCATTCTGTCCC,-,0.00),216(AGGTCATTCTGTCCCA,+,0.00)
chunk0034_306_1	chr11	35016814	35017355	+	0	NA	Intergenic	Intergenic	75247	NR_039836	100616437		NR_039836	ENSG00000251862	MIR1343	-	microRNA 1343	ncRNA	0.007394	0.341328	
chunk0084_155_1	chr17	76860372	76860660	+	0	NA	Intergenic	MER87B|LTR|ERV1	-8200	NM_001199172	146664	Hs.144531	NM_144677	ENSG00000167889	MGAT5B	GnT-IX|GnT-VB	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B	protein-coding	0.010417	0.411765	
chunk0126_273_1	chr3	79992314	79992513	+	0	NA	Intergenic	Intergenic	-224504	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.010050	0.340000	
chunk0170_55_1	chr6	109486048	109486469	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-3021	NM_001164313	9841	Hs.409876	NM_014797	ENSG00000112365	ZBTB24	BIF1|ICF2|PATZ2|ZNF450	zinc finger and BTB domain containing 24	protein-coding	0.002375	0.386256	
chunk0142_151_1	chr4	95012560	95012951	+	0	NA	intron (NM_001256792, intron 1 of 10)	intron (NM_001256792, intron 1 of 10)	16523	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.005115	0.298469	
chunk0115_156_1	chr21	24027363	24027732	+	0	NA	Intergenic	Intergenic	293830	NR_109963	101927869	Hs.555591	NR_109963	ENSG00000224832	LINC01689	-	long intergenic non-protein coding RNA 1689	ncRNA	0.005420	0.367568	155(GTGAACAATTTGTCCC,-,0.00),156(TGAACAATTTGTCCCA,+,0.00)
chunk0095_181_1	chr2	17795302	17795794	+	0	NA	Intergenic	Intergenic	-20971	NM_001105569	343930		NM_001105569	ENSG00000151379	MSGN1	MSOG|pMsgn1	mesogenin 1	protein-coding	0.014228	0.490872	266(AGGAACAGCCTGTACT,-,0.00),267(GGAACAGCCTGTACTG,+,0.00)
chunk0068_337_1	chr15	57673772	57674316	+	0	NA	intron (NR_104369, intron 11 of 12)	L2c|LINE|L2	-32477	NM_015532	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.007353	0.335780	
chunk0049_293_1	chr12	94089983	94090662	+	0	NA	Intergenic	Intergenic	-58401	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.007364	0.422059	
chunk0021_8_1	chr10	274424	275092	+	0	NA	3' UTR (NM_014974, exon 37 of 37)	3' UTR (NM_014974, exon 37 of 37)	7328	NR_106988									0.008982	0.385650	
chunk0175_401_1	chr6	168584258	168584859	+	0	NA	intron (NM_022138, intron 7 of 12)	intron (NM_022138, intron 7 of 12)	143407	NM_001166412	64094	Hs.487200	NM_022138	ENSG00000112562	SMOC2	DTDP1|MST117|MSTP117|MSTP140|SMAP2|bA270C4A.1|bA37D8.1|dJ421D16.1	SPARC related modular calcium binding 2	protein-coding	0.014975	0.405316	
chunk0083_349_1	chr17	70327505	70328147	+	0	NA	Intergenic	Intergenic	158291	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.018692	0.396579	
chunk0060_121_1	chr14	43845847	43846389	+	0	NA	Intergenic	Intergenic	661178	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.003690	0.311234	
chunk0038_454_1	chr11	94832732	94833375	+	0	NA	intron (NM_130847, intron 6 of 12)	intron (NM_130847, intron 6 of 12)	64711	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.004666	0.403727	545(CAGGACACTTTGTGCC,-,0.00),546(AGGACACTTTGTGCCT,+,0.00)
chunk0086_291_1	chr18	23818817	23819275	+	0	NA	intron (NM_001127717, intron 18 of 73)	L1ME4a|LINE|L1	-53974	NM_001127718	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.002183	0.311547	
chunk0011_5_1	chr1	125170047	125170364	+	0	NA	Intergenic	Intergenic	3651093	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.053628	0.374214	
chunk0173_186_1	chr6	145102142	145102577	+	0	NA	Intergenic	MIR|SINE|MIR	-632510	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.004598	0.314220	
chunk0065_70_1	chr15	23403379	23404074	+	0	NA	Intergenic	Intergenic	43517	NM_001304388	283685		NM_182561	ENSG00000174450	GOLGA6L2	CT105	golgin A6 family like 2	protein-coding	0.012950	0.489943	383(AGTCCACAATGTTCCC,+,0.00)
chunk0032_316_1	chr11	9978710	9979364	+	0	NA	intron (NM_030962, intron 13 of 39)	intron (NM_030962, intron 13 of 39)	139895	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.018349	0.462595	
chunk0059_153_1	chr14	32202689	32202964	+	0	NA	TTS (NR_104084).3	TTS (NR_104084).3	443	NR_104088	101954278		NR_104088	ENSG00000202337	RNU6-8	U6-8	RNA, U6 small nuclear 8	snRNA	0.010909	0.394928	252(AGGCACAAGGTGACCT,-,0.00),253(GGCACAAGGTGACCTT,+,0.00)
chunk0098_352_1	chr2	77391072	77391652	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	131006	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.001724	0.313253	
chunk0093_406_1	chr19	57128620	57129203	+	0	NA	exon (NM_020903, exon 4 of 4)	exon (NM_020903, exon 4 of 4)	8770	NM_020903	57663	Hs.515632	NM_020903	ENSG00000131864	USP29	HOM-TES-84/86	ubiquitin specific peptidase 29	protein-coding	0.003431	0.352740	284(AAAAACAACGTGTTCT,-,0.00),285(AAAACAACGTGTTCTT,+,0.00)
chunk0038_328_1	chr11	92640153	92640581	+	0	NA	intron (NM_001008781, intron 2 of 24)	MIRb|SINE|MIR	288271	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.000000	0.400932	
chunk0176_75_1	chr7	11331517	11332028	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	357900	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.003914	0.394531	
chunk0045_465_1	chr12	53835573	53836049	+	0	NA	Intergenic	Intergenic	-78777	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.004202	0.480084	
chunk0160_392_1	chr5	163370972	163371194	+	0	NA	Intergenic	Intergenic	-66488	NM_199246	900	Hs.79101	NM_004060	ENSG00000113328	CCNG1	CCNG	cyclin G1	protein-coding	0.000000	0.538117	
chunk0177_303_1	chr7	25964451	25964943	+	0	NA	Intergenic	Intergenic	-14711	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.014228	0.436105	
chunk0152_291_1	chr5	61582922	61583255	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-54693	NM_173667									0.006006	0.437126	152(TGGATCATCCTGTTCC,-,0.00),153(GGATCATCCTGTTCCA,+,0.00)
chunk0115_339_1	chr21	29150010	29150578	+	0	NA	intron (NM_020152, intron 8 of 9)	intron (NM_020152, intron 8 of 9)	4735	NM_001286624	56911	Hs.222802	NM_020152	ENSG00000156265	MAP3K7CL	C21orf7|HC21ORF7|TAK1L|TAKL|TAKL-1|TAKL-2|TAKL-4	MAP3K7 C-terminal like	protein-coding	0.007042	0.458699	
chunk0122_311_1	chr3	36922820	36923097	+	0	NA	intron (NM_014831, intron 1 of 22)	MER83|LTR|ERV1	22099	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.014440	0.453237	161(CAGGACACACAGTGCT,-,0.00),162(AGGACACACAGTGCTC,+,0.00)
chunk0190_435_1	chr8	41604114	41604600	+	0	NA	intron (NM_178819, intron 2 of 12)	intron (NM_178819, intron 2 of 12)	-25989	NR_125824	102723729	Hs.586384	NR_125824		LOC102723729	-	uncharacterized LOC102723729	ncRNA	0.000000	0.425051	
chunk0055_145_1	chr13	59770726	59771099	+	0	NA	intron (NM_001258366, intron 26 of 26)	intron (NM_001258366, intron 26 of 26)	-241806	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.000000	0.374332	
chunk0102_50_1	chr2	142724723	142725339	+	0	NA	Intergenic	Intergenic	-152595	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.003247	0.312804	
chunk0094_174_1	chr2	5553220	5553644	+	0	NA	Intergenic	Intergenic	137686	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.007075	0.477647	159(AGAAACATTTTGTTCC,-,0.00)
chunk0199_307_1	chr9	7103942	7104196	+	0	NA	intron (NM_015061, intron 18 of 21)	L2b|LINE|L2	346428	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.011811	0.458824	
chunk0166_286_1	chr6	48426944	48427646	+	0	NA	Intergenic	Intergenic	-358606	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.005698	0.338549	
chunk0031_442_1	chr10	132566415	132566614	+	0	NA	intron (NM_005539, intron 1 of 15)	intron (NM_005539, intron 1 of 15)	28665	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.020101	0.405000	
chunk0170_43_1	chr6	109414147	109414497	+	0	NA	intron (NR_104429, intron 6 of 8)	L1MC5|LINE|L1	-26406	NM_003080	6610	Hs.55235	NM_003080	ENSG00000135587	SMPD2	ISC1|NSMASE|NSMASE1	sphingomyelin phosphodiesterase 2	protein-coding	0.000000	0.307692	
chunk0130_275_1	chr3	136343332	136344195	+	0	NA	intron (NM_005862, intron 30 of 33)	intron (NM_005862, intron 30 of 33)	93438	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.005794	0.387731	
chunk0009_332_1	chr1	109096228	109096427	+	0	NA	3' UTR (NM_020141, exon 3 of 3)	3' UTR (NM_020141, exon 3 of 3)	-3866	NR_003023	677766	Hs.550815	NR_003023	ENSG00000278249	SCARNA2	HBII-382|mgU2-25/61	small Cajal body-specific RNA 2	ncRNA	0.005025	0.400000	
chunk0091_344_1	chr19	14518693	14518923	+	0	NA	promoter-TSS (NM_006145)	promoter-TSS (NM_006145)	-249	NM_006145	3337	Hs.515210	NM_006145	ENSG00000132002	DNAJB1	HSPF1|Hdj1|Hsp40|RSPH16B|Sis1	DnaJ heat shock protein family (Hsp40) member B1	protein-coding	0.073913	0.679654	
chunk0204_368_1	chr9	101946464	101946672	+	0	NA	Intergenic	Intergenic	-207988	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.009615	0.382775	69(AAGTACATGTAGTCCC,-,0.00),70(AGTACATGTAGTCCCC,+,0.00)
chunk0051_58_1	chr12	112422311	112422953	+	0	NA	intron (NM_002834, intron 1 of 15)	intron (NM_002834, intron 1 of 15)	3900	NM_080601	5781	Hs.506852	NM_002834	ENSG00000179295	PTPN11	BPTP3|CFC|JMML|METCDS|NS1|PTP-1D|PTP2C|SH-PTP2|SH-PTP3|SHP2	protein tyrosine phosphatase non-receptor type 11	protein-coding	0.012461	0.452566	278(AAGTACATTTTGTCCT,-,0.00),279(AGTACATTTTGTCCTG,+,0.00)
chunk0121_35_1	chr3	15232768	15233190	+	0	NA	intron (NM_014296, intron 10 of 20)	intron (NM_014296, intron 10 of 20)	-21205	NR_046084	100505696	Hs.745026	NR_046084	ENSG00000224660	SH3BP5-AS1	-	SH3BP5 antisense RNA 1	ncRNA	0.004739	0.364066	
chunk0048_462_1	chr12	89056621	89056906	+	0	NA	Intergenic	Intergenic	-37071	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.007018	0.381119	
chunk0142_385_1	chr4	102404520	102404719	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-59121	NM_001135146	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.000000	0.435000	
chunk0051_154_1	chr12	115829778	115830646	+	0	NA	Intergenic	L1MC1|LINE|L1	318442	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.006912	0.407365	
chunk0029_329_1	chr10	104520731	104520936	+	0	NA	Intergenic	MIRb|SINE|MIR	-40558	NR_120624	101927523	Hs.407539	NR_120624	ENSG00000225768	LINC02620	-	long intergenic non-protein coding RNA 2620	ncRNA	0.029268	0.563107	12(GGCCCAAACTGTTCTG,+,0.00)
chunk0045_32_1	chr12	44159209	44159490	+	0	NA	intron (NM_032256, intron 4 of 7)	intron (NM_032256, intron 4 of 7)	323488	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.000000	0.358156	
chunk0084_381_1	chr17	81924944	81925260	+	0	NA	intron (NM_002359, intron 1 of 2)	intron (NM_002359, intron 1 of 2)	-1534	NM_032711	4097	Hs.252229	NM_002359	ENSG00000197063	MAFG	hMAF	MAF bZIP transcription factor G	protein-coding	0.031646	0.656151	
chunk0029_208_1	chr10	101867969	101868497	+	0	NA	intron (NM_024541, intron 24 of 25)	Tigger2|DNA|TcMar-Tigger	-24313	NM_173197	30819	Hs.97044	NM_014591	ENSG00000120049	KCNIP2	KCHIP2	potassium voltage-gated channel interacting protein 2	protein-coding	0.003788	0.353497	
chunk0134_220_1	chr3	178778580	178778958	+	0	NA	intron (NR_126560, intron 2 of 7)	intron (NR_126560, intron 2 of 7)	81636	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.010582	0.461741	
chunk0129_312_1	chr3	123919179	123919418	+	0	NA	intron (NM_001308317, intron 11 of 11)	L1MA7|LINE|L1	-34996	NM_053026	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.004184	0.525000	
chunk0165_95_1	chr6	32155393	32155620	+	0	NA	intron (NR_037861, intron 3 of 15)	MIRc|SINE|MIR	-1141	NR_037170	100507547	Hs.549204	NR_037169	ENSG00000284954	LOC100507547	-	uncharacterized LOC100507547	ncRNA	0.004405	0.495614	121(TGGCACAGGGTGTGCC,-,0.00),122(GGCACAGGGTGTGCCT,+,0.00)
chunk0097_26_1	chr2	42348839	42349169	+	0	NA	Intergenic	L1MC4|LINE|L1	12212	NM_004718	9167	Hs.339639	NM_004718	ENSG00000115944	COX7A2L	COX7AR|COX7RP|EB1|SIG81	cytochrome c oxidase subunit 7A2 like	protein-coding	0.009091	0.416918	157(AGGAACTGCATGTGCT,-,0.00),158(GGAACTGCATGTGCTG,+,0.00)
chunk0014_83_1	chr1	176545929	176546302	+	0	NA	intron (NM_020318, intron 1 of 22)	Charlie16a|DNA|hAT-Charlie	82944	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.387701	146(ATGGACAGGTTGTACT,-,0.00),147(TGGACAGGTTGTACTG,+,0.00)
chunk0001_273_1	chr1	8629387	8629690	+	0	NA	intron (NM_001042681, intron 2 of 22)	intron (NM_001042681, intron 2 of 22)	-134625	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.003300	0.444079	
chunk0095_355_1	chr2	21833437	21833698	+	0	NA	Intergenic	Intergenic	-122915	NR_038837	645949	Hs.456782	NR_038837	ENSG00000229621	LINC01822	-	long intergenic non-protein coding RNA 1822	ncRNA	0.011494	0.423664	87(AGGTTCATGCTGTTCC,-,0.00),88(GGTTCATGCTGTTCCC,+,0.00)
chunk0113_242_1	chr20	54158761	54159123	+	0	NA	intron (NM_000782, intron 8 of 11)	intron (NM_000782, intron 8 of 11)	15035	NM_001128915	1591	Hs.89663	NM_000782	ENSG00000019186	CYP24A1	CP24|CYP24|HCAI|HCINF1|P450-CC24	cytochrome P450 family 24 subfamily A member 1	protein-coding	0.013812	0.385675	
chunk0159_292_1	chr5	142771219	142771727	+	0	NA	intron (NM_015071, intron 1 of 22)	intron (NM_015071, intron 1 of 22)	746	NM_015071	23092	Hs.654668	NM_015071	ENSG00000145819	ARHGAP26	GRAF|GRAF1|OPHN1L|OPHN1L1	Rho GTPase activating protein 26	protein-coding	0.037402	0.540275	
chunk0067_317_1	chr15	47944538	47945101	+	0	NA	Intergenic	L1ME3D|LINE|L1	-98583	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.008881	0.381206	297(TAGGACAGGCTGATCT,-,0.00),298(AGGACAGGCTGATCTT,+,0.00)
chunk0015_297_1	chr1	188855655	188856207	+	0	NA	Intergenic	L1ME2|LINE|L1	1412303	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007246	0.341772	
chunk0197_126_1	chr8	119982781	119982985	+	0	NA	intron (NM_022783, intron 4 of 8)	MLT1J|LTR|ERVL-MaLR	109228	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.004902	0.492683	27(AAGGGCAGTCTGTCCC,-,0.00),28(AGGGCAGTCTGTCCCA,+,0.00)
chunk0002_331_1	chr1	24398870	24399493	+	0	NA	intron (NM_001199014, intron 2 of 9)	L1ME3A|LINE|L1	14591	NM_178122	90529	Hs.403187	NM_178122	ENSG00000001460	STPG1	C1orf201|MAPO2	sperm tail PG-rich repeat containing 1	protein-coding	0.003210	0.304487	
chunk0058_142_1	chr14	22982492	22983012	+	0	NA	promoter-TSS (NM_001289097)	promoter-TSS (NM_001289097)	-110	NM_001289097	84962	Hs.655832	NM_032876	ENSG00000129474	AJUBA	JUB	ajuba LIM protein	protein-coding	0.075000	0.633397	
chunk0099_343_1	chr2	100107135	100107452	+	0	NA	intron (NM_002285, intron 1 of 23)	intron (NM_002285, intron 1 of 23)	-1710	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.000000	0.345912	
chunk0075_35_1	chr16	46976427	46976888	+	0	NA	Intergenic	Intergenic	-2943	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.006508	0.383117	142(AAGAACTTTGTGTGCT,-,0.00),143(AGAACTTTGTGTGCTT,+,0.00)
chunk0194_444_1	chr8	92555677	92556244	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	99534	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.005291	0.427817	269(AAGCCCAGGCTGTCCT,-,0.00),270(AGCCCAGGCTGTCCTG,+,0.00)
chunk0087_215_1	chr18	36066050	36066436	+	0	NA	intron (NM_001303412, intron 1 of 8)	intron (NM_001303412, intron 1 of 8)	1351	NM_001303411	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.012953	0.366925	179(AAGGACAGATTGTCTC,-,0.00),180(AGGACAGATTGTCTCC,+,0.00)
chunk0024_45_1	chr10	33649538	33649818	+	0	NA	Intergenic	Intergenic	123002	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.010714	0.473310	
chunk0204_431_1	chr9	103517605	103517804	+	0	NA	Intergenic	L1ME2|LINE|L1	-192671	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.005025	0.295000	
chunk0153_85_1	chr5	68171044	68171558	+	0	NA	Intergenic	Intergenic	-18575	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.017510	0.467961	250(CAGAACATCGTGTTCC,-,0.00),251(AGAACATCGTGTTCCG,+,0.00)
chunk0113_320_1	chr20	58248008	58248428	+	0	NA	non-coding (NR_003505, exon 7 of 17)	non-coding (NR_003505, exon 7 of 17)	-19565	NM_001304369	140731	Hs.266571	NM_080674	ENSG00000124227	ANKRD60	C20orf86|bA196N14.3	ankyrin repeat domain 60	protein-coding	0.021429	0.472684	
chunk0076_287_1	chr16	69763474	69763997	+	0	NA	intron (NM_001270454, intron 1 of 23)	L2c|LINE|L2	1451	NM_001270454	11060	Hs.408458	NM_007014	ENSG00000198373	WWP2	AIP2|WWp2-like	WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.013384	0.387405	
chunk0116_462_1	chr21	43929062	43930101	+	0	NA	intron (NM_001037553, intron 1 of 8)	intron (NM_001037553, intron 1 of 8)	4183	NM_001037553	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.039461	0.608654	
chunk0122_138_1	chr3	31804524	31804794	+	0	NA	intron (NM_001174060, intron 3 of 10)	intron (NM_001174060, intron 3 of 10)	100446	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.025926	0.416974	
chunk0148_129_1	chr5	5467447	5467879	+	0	NA	intron (NM_015325, intron 14 of 18)	L2a|LINE|L2	44990	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.000000	0.341801	
chunk0062_60_1	chr14	67492701	67493021	+	0	NA	intron (NM_182526, intron 1 of 2)	L2a|LINE|L2	22443	NM_182526	161145	Hs.509707	NM_182526	ENSG00000198133	TMEM229B	C14orf83	transmembrane protein 229B	protein-coding	0.003125	0.433022	
chunk0196_273_1	chr8	109255753	109256098	+	0	NA	intron (NM_001128211, intron 8 of 9)	L2b|LINE|L2	74008	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.005797	0.430636	104(GGGAACAGCATGTTTC,-,0.00),105(GGAACAGCATGTTTCA,+,0.00)
chunk0030_317_1	chr10	117981287	117981520	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	65200	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.012876	0.435897	89(AGGTTCATGGTGTTCT,-,0.00),90(GGTTCATGGTGTTCTC,+,0.00)
chunk0091_8_1	chr19	2634440	2635150	+	0	NA	intron (NM_052847, intron 2 of 4)	intron (NM_052847, intron 2 of 4)	4080	NR_107004	102465838		NR_107004	ENSG00000277904	MIR7850	hsa-mir-7850	microRNA 7850	ncRNA	0.040845	0.554149	
chunk0194_301_1	chr8	88006601	88006911	+	0	NA	Intergenic	Intergenic	-132688	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.000000	0.395498	
chunk0107_352_1	chr2	221942837	221943610	+	0	NA	Intergenic	Intergenic	-354924	NM_153038	151278	Hs.350729	NM_153038	ENSG00000163081	CCDC140	-	coiled-coil domain containing 140	ncRNA	0.002587	0.409561	582(AAGAGCACAGTGTACC,-,0.00),583(AGAGCACAGTGTACCC,+,0.00)
chunk0155_92_1	chr5	92330103	92330575	+	0	NA	Intergenic	Intergenic	-947007	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.004237	0.304440	
chunk0136_433_1	chr3	197725444	197725962	+	0	NA	intron (NM_001145642, intron 1 of 20)	intron (NM_001145642, intron 1 of 20)	11223	NM_014687	9711	Hs.478868	NM_014687	ENSG00000145016	RUBCN	KIAA0226|RUBICON|SCAR15	rubicon autophagy regulator	protein-coding	0.013514	0.433526	
chunk0064_330_1	chr14	96417289	96417708	+	0	NA	intron (NM_152327, intron 4 of 17)	intron (NM_152327, intron 4 of 17)	25387	NM_152327	122481	Hs.667462	NM_152327	ENSG00000140057	AK7	AK 7|SPGF27	adenylate kinase 7	protein-coding	0.004773	0.421429	
chunk0170_60_1	chr6	109511947	109512991	+	0	NA	intron (NM_001145128, intron 32 of 40)	MER41A|LTR|ERV1	-29232	NM_001164313	9841	Hs.409876	NM_014797	ENSG00000112365	ZBTB24	BIF1|ICF2|PATZ2|ZNF450	zinc finger and BTB domain containing 24	protein-coding	0.003831	0.404785	
chunk0050_385_1	chr12	108985661	108986134	+	0	NA	intron (NM_018711, intron 1 of 15)	intron (NM_018711, intron 1 of 15)	35343	NM_018711	55530	Hs.4221	NM_018711	ENSG00000166111	SVOP	-	SV2 related protein	protein-coding	0.004228	0.411392	
chunk0023_172_1	chr10	24410886	24411503	+	0	NA	intron (NM_019590, intron 3 of 20)	intron (NM_019590, intron 3 of 20)	-38239	NM_001282769	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.006483	0.344660	
chunk0063_187_1	chr14	80637628	80638172	+	0	NA	intron (NM_152446, intron 18 of 23)	MLT1D|LTR|ERVL-MaLR	301640	NM_152446	145508	Hs.162889	NM_152446	ENSG00000100629	CEP128	C14orf145|C14orf61|LEDP/132	centrosomal protein 128	protein-coding	0.009191	0.412844	212(AAGAACACAGTGTAAC,-,0.00)
chunk0178_159_1	chr7	33819063	33819523	+	0	NA	Intergenic	Intergenic	-85618	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.000000	0.268980	
chunk0098_284_1	chr2	75752380	75752661	+	0	NA	Intergenic	Intergenic	-41535	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.003559	0.382979	
chunk0005_170_1	chr1	58577867	58578103	+	0	NA	promoter-TSS (NM_002353)	promoter-TSS (NM_002353)	-491	NM_002353	4070	Hs.23582	NM_002353	ENSG00000184292	TACSTD2	EGP-1|EGP1|GA733-1|GA7331|GP50|M1S1|TROP2	tumor associated calcium signal transducer 2	protein-coding	0.012712	0.413502	
chunk0174_239_1	chr6	160954175	160954830	+	0	NA	Intergenic	L2a|LINE|L2	-37225	NM_006724	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.009160	0.460366	284(AGGCACTGGCTGCTCC,-,0.00)
chunk0022_350_1	chr10	17049529	17049728	+	0	NA	intron (NM_001081, intron 22 of 66)	intron (NM_001081, intron 22 of 66)	80189	NM_001081	8029	Hs.166206	NM_001081	ENSG00000107611	CUBN	IFCR|MGA1|gp280	cubilin	protein-coding	0.005025	0.380000	
chunk0187_377_1	chr7	157620980	157621666	+	0	NA	intron (NM_001308268, intron 15 of 22)	CpG	-46901	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.053936	0.646288	
chunk0187_366_1	chr7	157433200	157433578	+	0	NA	Intergenic	Intergenic	-32842	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.018519	0.548813	
chunk0108_26_1	chr2	226549848	226550294	+	0	NA	Intergenic	Intergenic	108722	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.000000	0.438479	
chunk0177_316_1	chr7	26097072	26097401	+	0	NA	Intergenic	Intergenic	-54991	NM_004289	9603	Hs.404741	NM_004289	ENSG00000050344	NFE2L3	NRF3	nuclear factor, erythroid 2 like 3	protein-coding	0.003040	0.315152	
chunk0094_53_1	chr2	3137863	3138701	+	0	NA	Intergenic	Intergenic	-12256	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.011933	0.438617	
chunk0209_437_1	chrX	63360238	63360636	+	0	NA	Intergenic	HERVK22-int|LTR|ERVK	-9098	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.007538	0.438596	
chunk0171_181_1	chr6	125191098	125191559	+	0	NA	intron (NM_001003395, intron 1 of 6)	intron (NM_001003395, intron 1 of 6)	37054	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.008677	0.387446	174(AAGAACAAATTGTCCT,-,0.00),175(AGAACAAATTGTCCTT,+,0.00)
chunk0018_13_1	chr1	215146285	215146873	+	0	NA	intron (NM_001017424, intron 3 of 6)	MamSINE1|SINE|tRNA-RTE	63362	NM_001017425	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.008503	0.342954	
chunk0044_100_1	chr12	28505507	28506220	+	0	NA	intron (NM_018318, intron 11 of 11)	intron (NM_018318, intron 11 of 11)	248663	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.002805	0.362745	
chunk0091_401_1	chr19	16442482	16442836	+	0	NA	intron (NR_047665, intron 1 of 22)	intron (NR_047665, intron 1 of 22)	29353	NM_021235	58513	Hs.654639	NM_021235	ENSG00000127527	EPS15L1	EPS15R	epidermal growth factor receptor pathway substrate 15 like 1	protein-coding	0.025424	0.538028	
chunk0093_413_1	chr19	57310828	57311027	+	0	NA	Intergenic	Intergenic	-9570	NM_213598	125919	Hs.202544	NM_213598	ENSG00000178229	ZNF543	-	zinc finger protein 543	protein-coding	0.010050	0.480000	
chunk0167_275_1	chr6	70388381	70388580	+	0	NA	Intergenic	Intergenic	-5722	NR_125857	101928353		NR_125857		EVADR	-	uncharacterized LOC101928353	ncRNA	0.005025	0.380000	
chunk0069_285_1	chr15	65165755	65166288	+	0	NA	intron (NM_006660, intron 4 of 13)	intron (NM_006660, intron 4 of 13)	19204	NM_006660	10845	Hs.113823	NM_006660	ENSG00000166855	CLPX	EPP2	caseinolytic mitochondrial matrix peptidase chaperone subunit	protein-coding	0.003752	0.380150	
chunk0105_440_1	chr2	194258882	194259271	+	0	NA	Intergenic	Intergenic	-85193	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.000000	0.289744	
chunk0161_430_1	chr5	178444698	178445225	+	0	NA	intron (NM_173465, intron 2 of 28)	MIR|SINE|MIR	145594	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.009488	0.352273	
chunk0180_13_1	chr7	53223830	53224059	+	0	NA	Intergenic	Intergenic	188288	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.000000	0.313043	
chunk0106_344_1	chr2	206708140	206708754	+	0	NA	intron (NM_001093730, intron 2 of 11)	intron (NM_001093730, intron 2 of 11)	9949	NM_001093730	391475	Hs.640667	NM_001093730	ENSG00000232125	DYTN	-	dystrotelin	protein-coding	0.011401	0.382114	
chunk0018_72_1	chr1	217119513	217119865	+	0	NA	intron (NM_001134285, intron 1 of 8)	intron (NM_001134285, intron 1 of 8)	18066	NM_001134285	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.331445	
chunk0164_158_1	chr6	21588490	21588736	+	0	NA	Intergenic	CpG	-5128	NM_003107	6659	Hs.643910	NM_003107	ENSG00000124766	SOX4	EVI16	SRY-box transcription factor 4	protein-coding	0.085366	0.623482	
chunk0119_56_1	chr22	40852575	40853211	+	0	NA	intron (NM_003932, intron 1 of 11)	intron (NM_003932, intron 1 of 11)	4115	NM_001278589	6767	Hs.712713	NM_003932	ENSG00000100380	ST13	AAG2|FAM10A1|FAM10A4|HIP|HOP|HSPABP|HSPABP1|P48|PRO0786|SNC6	ST13 Hsp70 interacting protein	protein-coding	0.004717	0.340659	
chunk0020_404_1	chr1	240794315	240794788	+	0	NA	intron (NM_001282778, intron 16 of 16)	intron (NM_001282778, intron 16 of 16)	-182389	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.008457	0.428270	
chunk0040_291_1	chr11	117071215	117071974	+	0	NA	intron (NM_025164, intron 1 of 23)	intron (NM_025164, intron 1 of 23)	26821	NM_001281748	23387	Hs.167451	NM_025164	ENSG00000160584	SIK3	L19|QSK|SEMDK|SIK-3	SIK family kinase 3	protein-coding	0.005270	0.418421	
chunk0069_123_1	chr15	61796110	61796462	+	0	NA	Intergenic	L1ME1|LINE|L1	264179	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.008523	0.351275	
chunk0153_23_1	chr5	67045716	67045997	+	0	NA	intron (NM_001297651, intron 1 of 25)	LTR23|LTR|ERV1	41236	NM_001290227	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.010676	0.368794	
chunk0200_305_1	chr9	22979629	22979835	+	0	NA	Intergenic	L1MC4a|LINE|L1	333532	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.000000	0.318841	
chunk0137_392_1	chr4	27011476	27011793	+	0	NA	intron (NM_020860, intron 10 of 11)	L1ME3Cz|LINE|L1	150943	NM_001169117	57620	Hs.744950	NM_020860	ENSG00000109689	STIM2	-	stromal interaction molecule 2	protein-coding	0.009464	0.399371	
chunk0033_35_1	chr11	12997079	12997733	+	0	NA	Intergenic	Intergenic	-7858	NR_038904	100506305	Hs.153408	NR_038904	ENSG00000251381	LINC00958	BLACAT2	long intergenic non-protein coding RNA 958	ncRNA	0.003058	0.377099	
chunk0019_408_1	chr1	230665906	230666120	+	0	NA	intron (NM_001145036, intron 5 of 17)	L2c|LINE|L2	23557	NM_007357	22796	Hs.211800	NM_007357	ENSG00000135775	COG2	CDG2Q|LDLC	component of oligomeric golgi complex 2	protein-coding	0.009346	0.502326	
chunk0089_387_1	chr18	67717765	67717969	+	0	NA	intron (NR_033921, intron 1 of 4)	intron (NR_033921, intron 1 of 4)	-201137	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.009804	0.341463	
chunk0008_126_1	chr1	91761373	91761707	+	0	NA	intron (NR_036634, intron 4 of 17)	intron (NR_036634, intron 4 of 17)	124739	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.002994	0.435821	165(AGGGACAATGAGTCCT,-,0.00),166(GGGACAATGAGTCCTG,+,0.00)
chunk0129_318_1	chr3	124100699	124101409	+	0	NA	intron (NM_003947, intron 1 of 33)	intron (NM_003947, intron 1 of 33)	6343	NM_003947	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.005634	0.419128	
chunk0113_248_1	chr20	54968266	54968725	+	0	NA	Intergenic	MER97c|DNA|hAT-Tip100	-454548	NR_110629	102723578	Hs.446269	NR_110629	ENSG00000235166	LINC01440	-	long intergenic non-protein coding RNA 1440	ncRNA	0.010893	0.323913	
chunk0012_344_1	chr1	162609124	162609329	+	0	NA	Intergenic	Intergenic	-23212	NM_001014796	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.000000	0.364078	110(TGTACTTACTGTTCTT,+,0.00)
chunk0110_314_1	chr20	18635873	18636326	+	0	NA	intron (NM_080820, intron 4 of 5)	intron (NM_080820, intron 4 of 5)	48187	NM_080820	92675	Hs.659442	NM_080820	ENSG00000125821	DTD1	C20orf88|DTD|DUE-B|DUEB|HARS2|pqn-68	D-aminoacyl-tRNA deacylase 1	protein-coding	0.002208	0.332599	
chunk0029_202_1	chr10	101685466	101686133	+	0	NA	intron (NM_022039, intron 1 of 8)	intron (NM_022039, intron 1 of 8)	9187	NM_022039	6468	Hs.500822	NM_022039	ENSG00000107829	FBXW4	DAC|FBW4|FBWD4|SHFM3|SHSF3	F-box and WD repeat domain containing 4	protein-coding	0.002999	0.359281	
chunk0116_118_1	chr21	35873866	35874265	+	0	NA	Intergenic	Intergenic	130602	NR_110418	101928269	Hs.589909	NR_110418		LOC101928269	-	uncharacterized LOC101928269	ncRNA	0.015038	0.412500	
chunk0148_50_1	chr5	1416260	1417062	+	0	NA	intron (NM_001044, intron 6 of 14)	intron (NM_001044, intron 6 of 14)	28767	NM_001044	6531	Hs.406	NM_001044	ENSG00000142319	SLC6A3	DAT|DAT1|PKDYS|PKDYS1	solute carrier family 6 member 3	protein-coding	0.036160	0.551681	243(CAGAACAGCATGGACT,-,0.00),738(CAGAACAGCATGGACT,-,0.00),739(AGAACAGCATGGACTT,+,0.00)
chunk0207_72_1	chrX	9178432	9178631	+	0	NA	Intergenic	Intergenic	-144404	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.020101	0.495000	
chunk0200_377_1	chr9	26453473	26454052	+	0	NA	Intergenic	Intergenic	387087	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.008636	0.375862	
chunk0076_24_1	chr16	59211648	59211988	+	0	NA	Intergenic	MIR3|SINE|MIR	-477461	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.002941	0.357771	
chunk0200_366_1	chr9	25733660	25733859	+	0	NA	Intergenic	Intergenic	-46297	NR_121604	101929582	Hs.140547	NR_121604	ENSG00000236306	LINC01241	-	long intergenic non-protein coding RNA 1241	ncRNA	0.010050	0.450000	56(AGAACTTACTGACCTT,+,0.00)
chunk0130_98_1	chr3	130888097	130888305	+	0	NA	intron (NM_001199181, intron 1 of 26)	L1M1|LINE|L1	-5790	NM_001199179	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.009615	0.511962	
chunk0026_189_1	chr10	63586697	63587406	+	0	NA	intron (NM_001001330, intron 2 of 7)	Tigger15a|DNA|TcMar-Tigger	65688	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.007052	0.398592	
chunk0198_130_1	chr8	132217751	132218175	+	0	NA	intron (NM_004519, intron 1 of 14)	MamRep434|DNA|TcMar-Tigger	-112698	NM_001145095	10086	Hs.285026	NM_005712	ENSG00000132297	HHLA1	PLA2L	HERV-H LTR-associating 1	protein-coding	0.007075	0.404706	186(AAAAACAGTTTGTTCT,-,0.00),187(AAAACAGTTTGTTCTC,+,0.00)
chunk0041_260_1	chr11	129041010	129042081	+	0	NA	intron (NM_001142685, intron 9 of 21)	intron (NM_001142685, intron 9 of 21)	-17352	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.004669	0.337687	
chunk0069_425_1	chr15	68109294	68109786	+	0	NA	intron (NM_016166, intron 2 of 13)	intron (NM_016166, intron 2 of 13)	55306	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.002033	0.367140	
chunk0068_101_1	chr15	52289715	52290245	+	0	NA	intron (NM_018728, intron 1 of 40)	intron (NM_018728, intron 1 of 40)	5818	NM_018728	55930	Hs.487036	NM_018728	ENSG00000128833	MYO5C	-	myosin VC	protein-coding	0.003774	0.519774	
chunk0183_226_1	chr7	106869782	106869981	+	0	NA	intron (NM_002649, intron 2 of 10)	MIR|SINE|MIR	4402	NM_002649	5294	Hs.32942	NM_002649	ENSG00000105851	PIK3CG	PI3CG|PI3K|PI3Kgamma|PIK3|p110gamma|p120-PI3K	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	protein-coding	0.000000	0.360000	
chunk0109_150_1	chr20	3738364	3739098	+	0	NA	intron (NM_052970, intron 2 of 12)	intron (NM_052970, intron 2 of 12)	6061	NM_001197327	116835	Hs.516854	NM_052970	ENSG00000132622	HSPA12B	C20orf60	heat shock protein family A (Hsp70) member 12B	protein-coding	0.012262	0.482993	
chunk0058_148_1	chr14	23145906	23146180	+	0	NA	intron (NM_012244, intron 3 of 10)	intron (NM_012244, intron 3 of 10)	8407	NM_001267037	23428	Hs.596643	NM_012244	ENSG00000092068	SLC7A8	LAT2|LPI-PC1	solute carrier family 7 member 8	protein-coding	0.010949	0.461818	
chunk0123_380_1	chr3	48711792	48712200	+	0	NA	intron (NM_016291, intron 1 of 5)	intron (NM_016291, intron 1 of 5)	5282	NM_001005910	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.007353	0.481663	
chunk0045_413_1	chr12	53073928	53074177	+	0	NA	intron (NM_032840, intron 5 of 10)	intron (NM_032840, intron 5 of 10)	5368	NM_032840	84926	Hs.343334	NM_032840	ENSG00000167778	SPRYD3	-	SPRY domain containing 3	protein-coding	0.012048	0.500000	
chunk0009_461_1	chr1	111643039	111643762	+	0	NA	intron (NM_001010935, intron 2 of 8)	intron (NM_001010935, intron 2 of 8)	23253	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.008299	0.389503	
chunk0117_379_1	chr21	45121586	45121894	+	0	NA	intron (NM_015834, intron 1 of 12)	L1MEd|LINE|L1	47162	NM_001160230	104	Hs.474018	NM_001112	ENSG00000197381	ADARB1	ADAR2|DRABA2|DRADA2|RED1	adenosine deaminase RNA specific B1	protein-coding	0.016234	0.423948	
chunk0128_257_1	chr3	109119006	109119415	+	0	NA	Intergenic	Intergenic	-1064	NM_014429	27136	Hs.591296	NM_014429	ENSG00000114487	MORC1	CT33|MORC|ZCW6	MORC family CW-type zinc finger 1	protein-coding	0.004890	0.331707	254(AGGAACATGATGTTCT,-,0.00),255(GGAACATGATGTTCTA,+,0.00)
chunk0134_348_1	chr3	182501097	182501503	+	0	NA	Intergenic	Intergenic	-14938	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.009852	0.307125	
chunk0167_207_1	chr6	65127518	65127838	+	0	NA	intron (NM_001142800, intron 12 of 42)	intron (NM_001142800, intron 12 of 42)	-173740	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.000000	0.330218	
chunk0093_115_1	chr19	44558063	44558283	+	0	NA	Intergenic	(AATC)n|Simple_repeat|Simple_repeat	-1256	NR_027754	388550	Hs.446909	NR_027754	ENSG00000230666	CEACAM22P	-	carcinoembryonic antigen related cell adhesion molecule 22, pseudogene	pseudo	0.000000	0.307692	
chunk0131_178_1	chr3	147456591	147457058	+	0	NA	intron (NR_121655, intron 1 of 2)	intron (NR_121655, intron 1 of 2)	35497	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.000000	0.393162	
chunk0078_364_1	chr16	87364100	87364299	+	0	NA	intron (NM_001282683, intron 2 of 9)	intron (NM_001282683, intron 2 of 9)	19594	NM_024735	79791	Hs.567582	NM_024735	ENSG00000103264	FBXO31	FBX14|FBXO14|Fbx31|MRT45|pp2386	F-box protein 31	protein-coding	0.030151	0.560000	4(CAACACAATCTGTCCT,-,0.00),5(AACACAATCTGTCCTT,+,0.00)
chunk0047_199_1	chr12	71162965	71163693	+	0	NA	Intergenic	Intergenic	-5330	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.008242	0.393690	
chunk0063_14_1	chr14	76313929	76314179	+	0	NA	Intergenic	Intergenic	-57293	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.008000	0.414343	
chunk0207_13_1	chrM	11744	12160	+	0	NA	NA	Intergenic	NA	NA									0.021635	0.443645	145(GAGAACTCTCTGTGCT,-,0.00),146(AGAACTCTCTGTGCTA,+,0.00)
chunk0088_314_1	chr18	50773822	50774141	+	0	NA	Intergenic	L1MA4A|LINE|L1	46083	NM_001127175	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.000000	0.321875	
chunk0027_151_1	chr10	74778292	74778609	+	0	NA	Intergenic	PRIMA41-int|LTR|ERV1	-47963	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.009464	0.440252	
chunk0105_382_1	chr2	192345310	192345515	+	0	NA	Intergenic	L1MC1|LINE|L1	-150479	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.004878	0.441748	
chunk0098_424_1	chr2	80717492	80717852	+	0	NA	Intergenic	Intergenic	404293	NM_001282599	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.008333	0.290859	
chunk0139_190_1	chr4	54355550	54356486	+	0	NA	Intergenic	L2a|LINE|L2	126921	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.011752	0.442903	808(GGCCCAGCATGTTCTA,+,0.00)
chunk0038_322_1	chr11	91839913	91840260	+	0	NA	Intergenic	Intergenic	-512010	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.000000	0.307471	
chunk0077_213_1	chr16	80014250	80014541	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	219146	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.000000	0.376712	
chunk0004_117_1	chr1	44618176	44618376	+	0	NA	intron (NM_018150, intron 3 of 14)	(CA)n|Simple_repeat|Simple_repeat	56332	NM_001300747	79639	Hs.22157	NM_024587	ENSG00000126106	TMEM53	NET4	transmembrane protein 53	protein-coding	0.010000	0.532338	
chunk0136_135_1	chr4	3932015	3932290	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	23276	NR_130741	348926	Hs.591720	NR_024253	ENSG00000251669	FAM86EP	-	family with sequence similarity 86, member A pseudogene	pseudo	0.010909	0.442029	
chunk0022_201_1	chr10	13586747	13587667	+	0	NA	intron (NM_003675, intron 1 of 9)	CpG	268	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.053261	0.585233	
chunk0166_194_1	chr6	46453645	46454148	+	0	NA	intron (NM_001251973, intron 2 of 4)	intron (NM_001251973, intron 2 of 4)	37427	NM_001251974	10231	Hs.440168	NM_005822	ENSG00000172348	RCAN2	CSP2|DSCR1L1|MCIP2|RCN2|ZAKI-4|ZAKI4	regulator of calcineurin 2	protein-coding	0.003976	0.382937	
chunk0157_435_1	chr5	124841834	124842407	+	0	NA	Intergenic	Intergenic	-97008	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.012216	0.397213	
chunk0154_122_1	chr5	78830174	78830373	+	0	NA	intron (NM_198709, intron 7 of 7)	intron (NM_198709, intron 7 of 7)	155670	NM_198709	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.010050	0.470000	
chunk0054_119_1	chr13	43096351	43096626	+	0	NA	intron (NM_013238, intron 5 of 5)	CR1-3_Croc|LINE|CR1	-16677	NR_047013	100874159	Hs.633241	NR_047013		LINC00400	-	long intergenic non-protein coding RNA 400	ncRNA	0.000000	0.333333	
chunk0040_127_1	chr11	112343236	112343992	+	0	NA	intron (NR_126004, intron 2 of 3)	intron (NR_126004, intron 2 of 3)	72865	NR_126004	283140	Hs.651827	NR_126004	ENSG00000250303	LINC02762	-	long intergenic non-protein coding RNA 2762	ncRNA	0.009259	0.468956	149(TGGAACTGTCTGTCTT,-,0.00),150(GGAACTGTCTGTCTTC,+,0.00)
chunk0138_319_1	chr4	41429128	41429722	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	68640	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.010101	0.363025	291(GTGAACAGACTGTTCT,-,0.00),292(TGAACAGACTGTTCTC,+,0.00)
chunk0048_331_1	chr12	83817676	83818302	+	0	NA	Intergenic	Intergenic	1094840	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.003195	0.414673	
chunk0132_206_1	chr3	157369646	157369894	+	0	NA	intron (NM_001167911, intron 7 of 12)	intron (NM_001167911, intron 7 of 12)	-67021	NM_002852	5806	Hs.591286	NM_002852	ENSG00000163661	PTX3	TNFAIP5|TSG-14	pentraxin 3	protein-coding	0.004032	0.341365	
chunk0096_80_1	chr2	27943975	27944557	+	0	NA	intron (NM_199191, intron 3 of 11)	L1ME1|LINE|L1	-52101	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.003436	0.288165	
chunk0117_79_1	chr22	17152913	17153414	+	0	NA	intron (NM_017829, intron 1 of 7)	intron (NM_017829, intron 1 of 7)	6116	NM_033070	27440	Hs.26890	NM_017829	ENSG00000069998	HDHD5	CECR5	haloacid dehalogenase like hydrolase domain containing 5	protein-coding	0.007984	0.490040	
chunk0072_398_1	chr15	100694315	100694678	+	0	NA	Intergenic	Intergenic	91946	NM_198243	140460	Hs.31845	NM_024708	ENSG00000183475	ASB7	-	ankyrin repeat and SOCS box containing 7	protein-coding	0.002755	0.412088	217(AGGAACGTGCTGTACC,-,0.00),218(GGAACGTGCTGTACCA,+,0.00)
chunk0173_294_1	chr6	148342612	148342830	+	0	NA	5' UTR (NM_015278, exon 1 of 20)	5' UTR (NM_015278, exon 1 of 20)	128	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.073394	0.598174	
chunk0204_362_1	chr9	101771762	101772094	+	0	NA	Intergenic	Intergenic	-33348	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.000000	0.444444	
chunk0140_27_1	chr4	65780454	65780844	+	0	NA	Intergenic	MER39|LTR|ERV1	-110154	NM_004439	2044	Hs.654492	NM_004439	ENSG00000145242	EPHA5	CEK7|EHK-1|EHK1|EK7|HEK7|TYRO4	EPH receptor A5	protein-coding	0.005128	0.393862	251(AGAAACATCTTGTTCT,-,0.00),252(GAAACATCTTGTTCTC,+,0.00)
chunk0163_47_1	chr6	8639783	8640335	+	0	NA	intron (NR_038980, intron 3 of 4)	intron (NR_038980, intron 3 of 4)	-12150	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.005435	0.421338	313(AGGTACAGTTTGTTCA,-,0.00),314(GGTACAGTTTGTTCAG,+,0.00)
chunk0203_233_1	chr9	87119126	87119337	+	0	NA	Intergenic	Intergenic	-29413	NM_001001709									0.004739	0.344340	
chunk0031_448_1	chr10	132634411	132635249	+	0	NA	intron (NM_005539, intron 2 of 15)	L1MC4|LINE|L1	96981	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.022673	0.499404	
chunk0067_243_1	chr15	45518014	45518263	+	0	NA	intron (NR_022014, intron 3 of 5)	L2a|LINE|L2	4666	NM_013309	7782	Hs.162989	NM_013309	ENSG00000104154	SLC30A4	ZNT4|znT-4	solute carrier family 30 member 4	protein-coding	0.004016	0.436000	134(TGGTACATGCTGTTCT,-,0.00),135(GGTACATGCTGTTCTC,+,0.00)
chunk0038_240_1	chr11	87144267	87144785	+	0	NA	intron (NM_001168724, intron 4 of 13)	intron (NM_001168724, intron 4 of 13)	106682	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.003861	0.348748	
chunk0089_34_1	chr18	57885822	57886218	+	0	NA	Intergenic	Intergenic	-82925	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.005051	0.387909	
chunk0210_435_1	chrX	103658532	103659312	+	0	NA	Intergenic	MER66-int|LTR|ERV1	27896	NM_012286	9643	Hs.326387	NM_012286	ENSG00000123562	MORF4L2	MORFL2|MRGX	mortality factor 4 like 2	protein-coding	0.003846	0.466069	226(AGGAACTCCCTGTTCC,-,0.00),227(GGAACTCCCTGTTCCT,+,0.00)
chunk0070_157_1	chr15	71252042	71252397	+	0	NA	intron (NM_024817, intron 4 of 16)	UCON43|Unknown|Unknown	-63160	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.002817	0.424157	
chunk0009_338_1	chr1	109161910	109162490	+	0	NA	intron (NM_001267048, intron 2 of 19)	intron (NM_001267048, intron 2 of 19)	-24349	NM_001284353	57535	Hs.708190	NM_020775	ENSG00000116299	KIAA1324	EIG121	KIAA1324	protein-coding	0.015517	0.476764	
chunk0151_270_1	chr5	52548505	52548704	+	0	NA	Intergenic	LTR1D1|LTR|ERV1	-239336	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.000000	0.510000	
chunk0049_61_1	chr12	90129067	90129446	+	0	NA	Intergenic	Intergenic	420301	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.002639	0.347368	
chunk0140_88_1	chr4	68129710	68130495	+	0	NA	promoter-TSS (NM_207407)	promoter-TSS (NM_207407)	-233	NM_207407	389208	Hs.677557	NM_207407	ENSG00000198092	TMPRSS11F	-	transmembrane serine protease 11F	protein-coding	0.007643	0.407125	
chunk0076_427_1	chr16	72996551	72997282	+	0	NA	intron (NM_006885, intron 1 of 9)	intron (NM_006885, intron 1 of 9)	51459	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.017784	0.489071	
chunk0085_299_1	chr18	8079927	8080666	+	0	NA	intron (NM_001105244, intron 9 of 32)	intron (NM_001105244, intron 9 of 32)	286738	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.000000	0.348649	
chunk0118_457_1	chr22	39777970	39778504	+	0	NA	intron (NM_152512, intron 5 of 6)	intron (NM_152512, intron 5 of 6)	115553	NM_152512	150350	Hs.474869	NM_152512	ENSG00000176177	ENTHD1	CACNA1I|dJ370M22.3	ENTH domain containing 1	protein-coding	0.007491	0.413084	
chunk0007_130_1	chr1	79151108	79151342	+	0	NA	Intergenic	Intergenic	-144415	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.008547	0.395745	
chunk0105_254_1	chr2	189001083	189001282	+	0	NA	intron (NM_000090, intron 32 of 50)	intron (NM_000090, intron 32 of 50)	5552	NR_037401	100500837		NR_037401	ENSG00000284180	MIR3606	mir-3606	microRNA 3606	ncRNA	0.000000	0.315000	
chunk0052_27_1	chr13	20498231	20498430	+	0	NA	intron (NM_015974, intron 2 of 7)	intron (NM_015974, intron 2 of 7)	27543	NM_015974	51084	Hs.370703	NM_015974	ENSG00000165475	CRYL1	GDH|HEL30|gul3DH|lambda-CRY	crystallin lambda 1	protein-coding	0.005025	0.435000	
chunk0105_409_1	chr2	192813383	192814218	+	0	NA	Intergenic	L1MC2|LINE|L1	63955	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.002395	0.356459	
chunk0202_367_1	chr9	80399582	80399797	+	0	NA	Intergenic	Intergenic	424666	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.004651	0.361111	
chunk0202_376_1	chr9	80749430	80749972	+	0	NA	Intergenic	Intergenic	774678	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.003690	0.290976	
chunk0129_131_1	chr3	119981513	119982381	+	0	NA	intron (NM_001146156, intron 2 of 10)	L1PA6|LINE|L1	112470	NM_002093	2932	Hs.445733	NM_002093	ENSG00000082701	GSK3B	-	glycogen synthase kinase 3 beta	protein-coding	0.021889	0.516686	
chunk0035_11_1	chr11	40144611	40145200	+	0	NA	intron (NM_020929, intron 3 of 4)	intron (NM_020929, intron 3 of 4)	148225	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005093	0.349153	
chunk0155_407_1	chr5	99155648	99155865	+	0	NA	Intergenic	Intergenic	226622	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.009217	0.298165	
chunk0117_260_1	chr22	23535968	23536364	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-1936	NR_109832	101978785	Hs.575107	NR_109832		PCAT14	-	prostate cancer associated transcript 14	ncRNA	0.005051	0.468514	
chunk0077_206_1	chr16	79887433	79888685	+	0	NA	Intergenic	Intergenic	92810	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.006390	0.420591	852(CTGCACATCCTGTCCT,-,0.00),853(TGCACATCCTGTCCTC,+,0.00)
chunk0059_64_1	chr14	30267303	30267928	+	0	NA	Intergenic	Intergenic	-291508	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.004800	0.418530	97(CAAGACAAAATGTTCT,-,0.00),98(AAGACAAAATGTTCTG,+,0.00)
chunk0013_69_1	chr1	167410007	167410442	+	0	NA	intron (NR_037163, intron 14 of 16)	intron (NR_037163, intron 14 of 16)	81180	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.002299	0.364679	207(AAGAACATTATGTTTA,-,0.00)
chunk0137_398_1	chr4	27096513	27096827	+	0	NA	Intergenic	Intergenic	-120809	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.006369	0.346032	
chunk0019_402_1	chr1	230634172	230634441	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-8150	NM_001145036	22796	Hs.211800	NM_007357	ENSG00000135775	COG2	CDG2Q|LDLC	component of oligomeric golgi complex 2	protein-coding	0.007435	0.448148	
chunk0102_129_1	chr2	145232947	145233639	+	0	NA	Intergenic	HAL1|LINE|L1	565326	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.004335	0.324675	
chunk0202_245_1	chr9	76729980	76730257	+	0	NA	intron (NM_015225, intron 6 of 18)	Tigger13a|DNA|TcMar-Tigger	-34318	NR_132312	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.007220	0.348921	
chunk0012_8_1	chr1	154784855	154785167	+	0	NA	intron (NM_170782, intron 2 of 7)	intron (NM_170782, intron 2 of 7)	74851	NM_170782	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.006410	0.498403	
chunk0041_379_1	chr11	131932721	131933168	+	0	NA	intron (NM_001144058, intron 1 of 7)	intron (NM_001144058, intron 1 of 7)	22126	NM_001144059	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.022371	0.486607	
chunk0123_448_1	chr3	50674845	50675044	+	0	NA	promoter-TSS (NM_004947)	promoter-TSS (NM_004947)	-136	NR_039950	100616138		NR_039950	ENSG00000272543	MIR4787	mir-4787	microRNA 4787	ncRNA	0.195980	0.815000	
chunk0100_142_1	chr2	108833219	108833503	+	0	NA	intron (NR_130121, intron 10 of 13)	L1MC2|LINE|L1	46611	NM_001303106	165055	Hs.362702	NM_144978	ENSG00000163006	CCDC138	-	coiled-coil domain containing 138	protein-coding	0.000000	0.382456	
chunk0164_152_1	chr6	21479114	21479511	+	0	NA	Intergenic	Intergenic	32580	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.022670	0.419598	
chunk0003_104_1	chr1	32032493	32032765	+	0	NA	intron (NM_006559, intron 3 of 8)	intron (NM_006559, intron 3 of 8)	18935	NR_073498	10657	Hs.445893	NM_006559	ENSG00000121774	KHDRBS1	Sam68|p62|p68	KH RNA binding domain containing, signal transduction associated 1	protein-coding	0.000000	0.380952	
chunk0111_199_1	chr20	26101161	26101458	+	0	NA	Intergenic	L1MEd|LINE|L1	12732	NR_003678	149934	Hs.711274	NM_001039379	ENSG00000240108	NCOR1P1	C20orf191|bB329D4.2	nuclear receptor corepressor 1 pseudogene 1	pseudo	0.010101	0.295302	
chunk0028_78_1	chr10	83808880	83809410	+	0	NA	Intergenic	L2c|LINE|L2	-330284	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.005660	0.355932	
chunk0002_112_1	chr1	15854285	15854487	+	0	NA	intron (NM_015001, intron 1 of 14)	intron (NM_015001, intron 1 of 14)	-6239	NR_024279	729614	Hs.119298	NR_024279	ENSG00000179743	FLJ37453	-	uncharacterized LOC729614	ncRNA	0.000000	0.266010	
chunk0093_32_1	chr19	39341853	39342070	+	0	NA	promoter-TSS (NM_001303614)	promoter-TSS (NM_001303614)	-498	NM_018028	55095	Hs.612332	NM_018028	ENSG00000179134	SAMD4B	SMGB|Smaug2	sterile alpha motif domain containing 4B	protein-coding	0.087558	0.660550	
chunk0104_146_1	chr2	173649769	173650082	+	0	NA	Intergenic	Intergenic	295092	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.012780	0.426752	
chunk0202_80_1	chr9	71891672	71892026	+	0	NA	intron (NM_001025780, intron 1 of 3)	intron (NM_001025780, intron 1 of 3)	19383	NM_001025780	51104	Hs.380389	NM_016014	ENSG00000107362	ABHD17B	C9orf77|CGI-67|FAM108B1	abhydrolase domain containing 17B	protein-coding	0.011299	0.385915	
chunk0160_156_1	chr5	151742823	151743078	+	0	NA	3' UTR (NM_004045, exon 4 of 4)	3' UTR (NM_004045, exon 4 of 4)	15699	NM_004045	475	Hs.125213	NM_004045	ENSG00000177556	ATOX1	ATX1|HAH1	antioxidant 1 copper chaperone	protein-coding	0.019608	0.507812	
chunk0107_358_1	chr2	222698673	222698976	+	0	NA	intron (NM_058165, intron 5 of 5)	intron (NM_058165, intron 5 of 5)	27086	NM_058165	116255	Hs.344090	NM_058165	ENSG00000124003	MOGAT1	DGAT2L|DGAT2L1|MGAT1	monoacylglycerol O-acyltransferase 1	protein-coding	0.006601	0.457237	
chunk0199_375_1	chr9	12946132	12946443	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	26346	NR_132976	106635615		NR_132976		SNORD137	-	small nucleolar RNA, C/D box 137	snoRNA	0.003215	0.407051	
chunk0015_121_1	chr1	185358734	185359052	+	0	NA	Intergenic	L1P4a|LINE|L1	-23854	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.003145	0.595611	
chunk0016_50_1	chr1	193261354	193261626	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-43255	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.003676	0.304029	
chunk0073_46_1	chr16	2952769	2953175	+	0	NA	Intergenic	Intergenic	-11244	NM_024507	79412	Hs.661128	NM_024507	ENSG00000131650	KREMEN2	KRM2	kringle containing transmembrane protein 2	protein-coding	0.024631	0.614251	187(GAGAACAGGATGAGCT,-,0.00),188(AGAACAGGATGAGCTC,+,0.00)
chunk0122_132_1	chr3	31648516	31648786	+	0	NA	Intergenic	L1MA4A|LINE|L1	-55562	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.007407	0.579336	
chunk0114_74_1	chr21	9133783	9134016	+	0	NA	Intergenic	L1MA3|LINE|L1	-4138	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.000000	0.358974	
chunk0042_126_1	chr12	3451675	3451923	+	0	NA	intron (NM_001256536, intron 1 of 9)	intron (NM_001256536, intron 1 of 9)	-39399	NM_019854	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.016129	0.453815	
chunk0107_424_1	chr2	224626247	224627001	+	0	NA	Intergenic	Intergenic	-41227	NM_001257197	8452	Hs.372286	NM_003590	ENSG00000036257	CUL3	CUL-3|PHA2E	cullin 3	protein-coding	0.002653	0.369536	
chunk0101_376_1	chr2	138310319	138310826	+	0	NA	Intergenic	Intergenic	-191208	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.000000	0.370079	
chunk0041_79_1	chr11	124195178	124195408	+	0	NA	Intergenic	Intergenic	-29346	NM_001291438	26492	Hs.381319	NM_001291438		OR8G2P	HSTPCR120|OR8G2|OR8G4|ORL206|ORL486|TPCR120	olfactory receptor family 8 subfamily G member 2 pseudogene	protein-coding	0.013043	0.458874	
chunk0130_207_1	chr3	133863248	133863814	+	0	NA	intron (NM_016577, intron 2 of 7)	MER103C|DNA|hAT-Charlie	32316	NM_016577	51560	Hs.715344	NM_016577	ENSG00000154917	RAB6B	-	RAB6B, member RAS oncogene family	protein-coding	0.007067	0.417989	
chunk0064_293_1	chr14	95319341	95319540	+	0	NA	intron (NM_024734, intron 1 of 12)	CpG	468	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.065327	0.650000	
chunk0012_401_1	chr1	163875621	163876279	+	0	NA	Intergenic	Intergenic	-452759	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.016717	0.447648	358(AAGGTCACGTTGTGCT,-,0.00)
chunk0072_156_1	chr15	92855955	92856221	+	0	NA	Intergenic	Intergenic	-26755	NR_037600	100507217	Hs.622504	NR_037600		LINC01578	-	long intergenic non-protein coding RNA 1578	ncRNA	0.007519	0.385768	
chunk0165_235_1	chr6	35590413	35591232	+	0	NA	intron (NM_001145777, intron 6 of 6)	intron (NM_001145777, intron 6 of 6)	73967	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.013431	0.430488	513(AAGAACACGGAGCTCC,-,0.00),514(AGAACACGGAGCTCCT,+,0.00)
chunk0201_129_1	chr9	35511176	35511585	+	0	NA	intron (NR_052015, intron 1 of 11)	intron (NR_052015, intron 1 of 11)	21428	NR_052015	9853	Hs.493796	NM_014806	ENSG00000198853	RUSC2	Iporin|MRT61	RUN and SH3 domain containing 2	protein-coding	0.004890	0.465854	
chunk0031_380_1	chr10	130790504	130790704	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	172064	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.005000	0.512438	
chunk0135_294_1	chr3	189586618	189587382	+	0	NA	Intergenic	L3|LINE|CR1	-44427	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.013089	0.383007	
chunk0064_4_1	chr14	89186081	89186937	+	0	NA	intron (NM_005197, intron 4 of 5)	intron (NM_005197, intron 4 of 5)	230601	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.014019	0.514586	787(CAAGACATGGTGTGCT,-,0.00),788(AAGACATGGTGTGCTG,+,0.00)
chunk0181_221_1	chr7	85156824	85157258	+	0	NA	Intergenic	Intergenic	-35110	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.002304	0.317241	
chunk0199_246_1	chr9	5621377	5621644	+	0	NA	Intergenic	Intergenic	-7609	NM_001206557	57589	Hs.211520	NM_020829	ENSG00000107036	RIC1	CIP150|KIAA1432|bA207C16.1	RIC1 homolog, RAB6A GEF complex partner 1	protein-coding	0.014981	0.462687	
chunk0009_111_1	chr1	102724607	102725310	+	0	NA	Intergenic	(A)n|Simple_repeat|Simple_repeat	383538	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.004267	0.301136	
chunk0097_385_1	chr2	61707853	61708341	+	0	NA	Intergenic	Intergenic	146046	NR_037710	84140	Hs.440466	NM_032180	ENSG00000170264	FAM161A	RP28	FAM161 centrosomal protein A	protein-coding	0.010246	0.425358	
chunk0036_68_1	chr11	59762033	59762441	+	0	NA	intron (NM_004177, intron 1 of 10)	intron (NM_004177, intron 1 of 10)	7178	NM_004177	6809	Hs.180711	NM_004177	ENSG00000166900	STX3	STX3A	syntaxin 3	protein-coding	0.014706	0.520782	
chunk0002_99_1	chr1	14965395	14965839	+	0	NA	intron (NM_001017999, intron 2 of 7)	L1ME4a|LINE|L1	19698	NM_001017999	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.009009	0.355056	
chunk0102_432_1	chr2	157742016	157742616	+	0	NA	intron (NM_001111067, intron 9 of 10)	intron (NM_001111067, intron 9 of 10)	-113429	NM_001111032	130399	Hs.562901	NM_145259	ENSG00000123612	ACVR1C	ACVRLK7|ALK7	activin A receptor type 1C	protein-coding	0.018333	0.479201	380(CGGAACAGACTGAGCC,-,0.00),381(GGAACAGACTGAGCCA,+,0.00)
chunk0195_27_1	chr8	93165088	93165831	+	0	NA	intron (NM_001242668, intron 1 of 2)	intron (NM_001242668, intron 1 of 2)	1391	NM_001242668									0.001346	0.314516	
chunk0127_124_1	chr3	93934372	93934795	+	0	NA	intron (NM_001314077, intron 1 of 15)	intron (NM_001314077, intron 1 of 15)	39498	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.004728	0.337264	156(AAGAACATTCTGTAAT,-,0.00)
chunk0079_93_1	chr17	12010676	12011296	+	0	NA	Intergenic	Intergenic	-9832	NM_003010	6416	Hs.514681	NM_003010	ENSG00000065559	MAP2K4	JNKK|JNKK1|MAPKK4|MEK4|MKK4|PRKMK4|SAPKK-1|SAPKK1|SEK1|SERK1|SKK1	mitogen-activated protein kinase kinase 4	protein-coding	0.016129	0.423510	
chunk0118_323_1	chr22	35292845	35293044	+	0	NA	intron (NM_001003681, intron 9 of 10)	intron (NM_001003681, intron 9 of 10)	-6331	NM_001135729	10043	Hs.474705	NM_005488	ENSG00000100284	TOM1	-	target of myb1 membrane trafficking protein	protein-coding	0.005025	0.425000	
chunk0092_173_1	chr19	29945377	29945756	+	0	NA	intron (NR_045557, intron 1 of 9)	intron (NR_045557, intron 1 of 9)	3327	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.007916	0.357895	
chunk0026_238_1	chr10	65907785	65907984	+	0	NA	Intergenic	Intergenic	336459	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.005025	0.275000	
chunk0092_407_1	chr19	37594679	37595189	+	0	NA	promoter-TSS (NM_016536)	promoter-TSS (NM_016536)	104	NM_001172226	163255	Hs.728927	NM_152606	ENSG00000171817	ZNF540	Nbla10512	zinc finger protein 540	protein-coding	0.072549	0.567515	
chunk0160_82_1	chr5	149953374	149953600	+	0	NA	Intergenic	Intergenic	-7250	NM_000112	1836	Hs.302738	NM_000112	ENSG00000155850	SLC26A2	D5S1708|DTD|DTDST|EDM4|MST153|MSTP157	solute carrier family 26 member 2	protein-coding	0.004425	0.317181	85(CAGAACAAGGTGATCC,-,0.00),86(AGAACAAGGTGATCCT,+,0.00)
chunk0011_92_1	chr1	145803682	145803881	+	0	NA	intron (NM_014455, intron 1 of 8)	intron (NM_014455, intron 1 of 8)	-20288	NM_006468	10623	Hs.515768	NM_006468	ENSG00000186141	POLR3C	RPC3|RPC62	RNA polymerase III subunit C	protein-coding	0.000000	0.390000	
chunk0071_109_1	chr15	81275085	81275290	+	0	NA	intron (NM_001172128, intron 6 of 18)	intron (NM_001172128, intron 6 of 18)	-21726	NM_004513	3603	Hs.459095	NM_004513	ENSG00000172349	IL16	LCF|NIL16|PRIL16|prIL-16	interleukin 16	protein-coding	0.024390	0.495146	
chunk0096_299_1	chr2	32711991	32712475	+	0	NA	intron (NM_017735, intron 10 of 19)	intron (NM_017735, intron 10 of 19)	76978	NR_039922	100616219		NR_039922	ENSG00000265057	MIR4765	-	microRNA 4765	ncRNA	0.008264	0.364948	
chunk0135_43_1	chr3	185444358	185444557	+	0	NA	intron (NM_001242314, intron 5 of 14)	L4_A_Mam|LINE|RTE-X	54600	NM_080652	90407	Hs.677570	NM_080652	ENSG00000163900	TMEM41A	2900010K02Rik	transmembrane protein 41A	protein-coding	0.010050	0.315000	
chunk0169_33_1	chr6	97270225	97270901	+	0	NA	intron (NM_198468, intron 6 of 24)	intron (NM_198468, intron 6 of 24)	12613	NM_198468	253714	Hs.444292	NM_198468	ENSG00000146263	MMS22L	C6orf167|dJ39B17.2	MMS22 like, DNA repair protein	protein-coding	0.002959	0.304284	
chunk0175_275_1	chr7	7553343	7553864	+	0	NA	intron (NR_110084, intron 3 of 4)	intron (NR_110084, intron 3 of 4)	12462	NR_110084	101927391	Hs.223837	NR_110084		LOC101927391	-	uncharacterized LOC101927391	ncRNA	0.001919	0.350575	253(AGGTACAATGTGTACC,-,0.00),254(GGTACAATGTGTACCT,+,0.00)
chunk0187_233_1	chr7	152504286	152504877	+	0	NA	Intergenic	Intergenic	40457	NR_027387	100128822	Hs.647112	NR_027387	ENSG00000261455	LINC01003	-	long intergenic non-protein coding RNA 1003	ncRNA	0.008460	0.513514	409(GGGCACACTTAGTCCC,-,0.00),410(GGCACACTTAGTCCCT,+,0.00)
chunk0036_165_1	chr11	62509681	62510051	+	0	NA	intron (NM_024060, intron 4 of 5)	AluSx1|SINE|Alu	36994	NM_024060	79026	Hs.502756	NM_001620	ENSG00000124942	AHNAK	AHNAKRS|PM227	AHNAK nucleoprotein	protein-coding	0.016216	0.447439	
chunk0139_416_1	chr4	63954917	63955247	+	0	NA	Intergenic	L1MEf|LINE|L1	454378	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.000000	0.290030	
chunk0072_82_1	chr15	90617755	90618191	+	0	NA	intron (NM_001042574, intron 8 of 14)	intron (NM_001042574, intron 8 of 14)	-42261	NR_120371	101929765	Hs.615348	NR_120371	ENSG00000245479	LINC01585	-	long intergenic non-protein coding RNA 1585	ncRNA	0.018349	0.446224	
chunk0020_172_1	chr1	234458358	234459052	+	0	NA	intron (NM_005646, intron 8 of 29)	intron (NM_005646, intron 8 of 29)	20398	NM_005646	6894	Hs.498115	NM_005646	ENSG00000059588	TARBP1	TRM3|TRMT3|TRP-185|TRP185	TAR (HIV-1) RNA binding protein 1	protein-coding	0.008646	0.435971	
chunk0165_316_1	chr6	37109339	37110586	+	0	NA	Intergenic	MIRc|SINE|MIR	-60184	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.016038	0.486378	
chunk0053_385_1	chr13	36111620	36111948	+	0	NA	intron (NM_004734, intron 3 of 17)	intron (NM_004734, intron 3 of 17)	19593	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.021341	0.419453	
chunk0014_217_1	chr1	179399436	179399771	+	0	NA	intron (NR_073544, intron 11 of 25)	L1PB1|LINE|L1	33631	NR_073544	126859	Hs.658505	NM_144696	ENSG00000162779	AXDND1	C1orf125	axonemal dynein light chain domain containing 1	protein-coding	0.005970	0.357143	
chunk0173_60_1	chr6	142375423	142376601	+	0	NA	intron (NM_020455, intron 4 of 25)	intron (NM_020455, intron 4 of 25)	74093	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.005093	0.295165	825(AAGAACAGACAGTGCC,-,0.00),826(AGAACAGACAGTGCCT,+,0.00)
chunk0132_70_1	chr3	155196889	155197609	+	0	NA	Intergenic	Intergenic	-43696	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.004167	0.345354	
chunk0080_323_1	chr17	32317201	32317689	+	0	NA	intron (NM_138328, intron 8 of 8)	intron (NM_138328, intron 8 of 8)	24764	NM_022344	64149	Hs.655257	NM_022344	ENSG00000108666	C17orf75	NJMU-R1|SRI2	chromosome 17 open reading frame 75	protein-coding	0.008197	0.421268	225(AGGAACAAGATGTCTT,-,0.00),226(GGAACAAGATGTCTTC,+,0.00)
chunk0024_176_1	chr10	35783217	35784002	+	0	NA	intron (NR_110138, intron 1 of 2)	intron (NR_110138, intron 1 of 2)	5307	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.012739	0.400763	
chunk0131_341_1	chr3	151356536	151357163	+	0	NA	intron (NM_053002, intron 17 of 42)	intron (NM_053002, intron 17 of 42)	-15994	NM_176876	64805	Hs.591281	NM_022788	ENSG00000169313	P2RY12	ADPG-R|BDPLT8|HORK3|P2T(AC)|P2Y(12)R|P2Y(AC)|P2Y(ADP)|P2Y(cyc)|P2Y12|SP1999	purinergic receptor P2Y12	protein-coding	0.000000	0.299363	
chunk0192_443_1	chr8	69893248	69893960	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	-58540	NM_030958	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.004213	0.420757	
chunk0027_430_1	chr10	80966458	80966737	+	0	NA	Intergenic	L1ME3A|LINE|L1	425778	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.003584	0.432143	
chunk0094_389_1	chr2	10047837	10048134	+	0	NA	exon (NM_003597, exon 3 of 4)	exon (NM_003597, exon 3 of 4)	3740	NM_001177718	8462	Hs.12229	NM_003597	ENSG00000172059	KLF11	FKLF|FKLF1|MODY7|TIEG2|Tieg3	Kruppel like factor 11	protein-coding	0.013468	0.553691	
chunk0178_334_1	chr7	38305919	38306433	+	0	NA	Intergenic	Intergenic	-32529	NM_001003806	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.005837	0.485437	
chunk0149_10_1	chr5	15833267	15833702	+	0	NA	intron (NM_012304, intron 2 of 3)	MLT1A0|LTR|ERVL-MaLR	-101698	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.011494	0.435780	
chunk0208_393_1	chrX	28970179	28970760	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	382905	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.006885	0.326460	
chunk0021_346_1	chr1	246166192	246166740	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	250946	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.010949	0.435337	51(GGGCACAGGCTGCACC,-,0.00),52(GGCACAGGCTGCACCA,+,0.00)
chunk0030_35_1	chr10	111409753	111409965	+	0	NA	Intergenic	Intergenic	332827	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.004717	0.530516	
chunk0022_412_1	chr10	18413874	18414545	+	0	NA	intron (NM_001167945, intron 3 of 13)	intron (NM_001167945, intron 3 of 13)	13625	NM_201570	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.007452	0.447917	
chunk0032_95_1	chr11	3159195	3159776	+	0	NA	intron (NM_145638, intron 1 of 20)	MIRc|SINE|MIR	5867	NM_020896	114879	Hs.436166	NM_020896	ENSG00000021762	OSBPL5	OBPH1|ORP5	oxysterol binding protein like 5	protein-coding	0.018933	0.611684	275(AGGGACACCATGTACT,-,0.00),276(GGGACACCATGTACTA,+,0.00)
chunk0203_305_1	chr9	89328896	89329134	+	0	NA	intron (NM_001282690, intron 5 of 16)	intron (NM_001282690, intron 5 of 16)	10164	NM_001282690	79048	Hs.59804	NM_024077	ENSG00000187742	SECISBP2	SBP2	SECIS binding protein 2	protein-coding	0.004202	0.355649	
chunk0023_259_1	chr10	27546987	27547920	+	0	NA	Intergenic	L2a|LINE|L2	43279	NM_001256411	22931	Hs.406799	NM_021252	ENSG00000099246	RAB18	RAB18LI1|WARBM3	RAB18, member RAS oncogene family	protein-coding	0.005359	0.383298	
chunk0150_23_1	chr5	30638899	30639527	+	0	NA	Intergenic	Intergenic	-554442	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.001592	0.282989	
chunk0120_442_1	chr3	13896480	13896814	+	0	NA	Intergenic	Intergenic	-16526	NM_004625	7476	Hs.72290	NM_004625	ENSG00000154764	WNT7A	Wnt-7a	Wnt family member 7A	protein-coding	0.026946	0.507463	
chunk0043_291_1	chr12	21614174	21614408	+	0	NA	Intergenic	Intergenic	-9444	NM_021957	2998	Hs.82614	NM_021957	ENSG00000111713	GYS2	-	glycogen synthase 2	protein-coding	0.004274	0.293617	
chunk0207_226_1	chr9	131732121	131732522	+	0	NA	intron (NM_001304275, intron 1 of 23)	intron (NM_001304275, intron 1 of 23)	5217	NM_005312	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.017456	0.504975	
chunk0196_337_1	chr8	113897691	113898229	+	0	NA	Intergenic	Intergenic	-460947	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.007435	0.352505	
chunk0057_32_1	chr13	95831350	95831646	+	0	NA	intron (NM_020121, intron 38 of 38)	L1ME3G|LINE|L1	154359	NM_006260	5611	Hs.59214	NM_006260	ENSG00000102580	DNAJC3	ACPHD|ERdj6|HP58|P58|P58IPK|PRKRI	DnaJ heat shock protein family (Hsp40) member C3	protein-coding	0.003378	0.272727	
chunk0178_272_1	chr7	36957404	36957760	+	0	NA	intron (NM_001206482, intron 16 of 21)	L2a|LINE|L2	27530	NM_001039459	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.005618	0.411765	
chunk0198_451_1	chr8	144182067	144182385	+	0	NA	intron (NM_032450, intron 7 of 43)	intron (NM_032450, intron 7 of 43)	33581	NM_001288814	727957	Hs.443139	NM_032450	ENSG00000179832	MROH1	HEATR7A	maestro heat like repeat family member 1	protein-coding	0.034591	0.661442	
chunk0098_160_1	chr2	70461979	70462479	+	0	NA	intron (NM_001308158, intron 3 of 5)	intron (NM_001308158, intron 3 of 5)	19411	NR_046798	100874273	Hs.682157	NR_046798	ENSG00000224606	TGFA-IT1	-	TGFA intronic transcript 1	ncRNA	0.010000	0.512974	199(AGGGACAGAGTGTTCT,-,0.00),200(GGGACAGAGTGTTCTA,+,0.00)
chunk0148_438_1	chr4	189265825	189266221	+	0	NA	Intergenic	L2a|LINE|L2	-393583	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.010101	0.385390	123(GGGTACTCCCTGTTCC,-,0.00),124(GGTACTCCCTGTTCCT,+,0.00)
chunk0193_435_1	chr8	80994019	80994542	+	0	NA	intron (NM_018440, intron 3 of 8)	intron (NM_018440, intron 3 of 8)	117788	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.003824	0.419847	
chunk0184_309_1	chr7	120148211	120148810	+	0	NA	Intergenic	L1MD2|LINE|L1	-125158	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.011686	0.341667	
chunk0202_299_1	chr9	77886499	77886812	+	0	NA	intron (NM_002072, intron 2 of 6)	intron (NM_002072, intron 2 of 6)	144794	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.003195	0.324841	
chunk0114_375_1	chr20	62929685	62930096	+	0	NA	intron (NM_022105, intron 1 of 5)	intron (NM_022105, intron 1 of 5)	-3339	NM_001193369	11083	Hs.517172	NM_022105	ENSG00000101191	DIDO1	BYE1|C20orf158|DATF-1|DATF1|DIDO2|DIDO3|DIO-1|DIO1|dJ885L7.8	death inducer-obliterator 1	protein-coding	0.017032	0.398058	
chunk0056_191_1	chr13	85653715	85654123	+	0	NA	Intergenic	L2a|LINE|L2	145429	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.007353	0.432763	
chunk0206_407_1	chr9	127311463	127311742	+	0	NA	intron (NR_104591, intron 2 of 26)	intron (NR_104591, intron 2 of 26)	47125	NR_104591	84253	Hs.29304	NM_032293	ENSG00000136895	GARNL3	bA356B19.1	GTPase activating Rap/RanGAP domain like 3	protein-coding	0.014337	0.414286	
chunk0163_392_1	chr6	16454074	16454402	+	0	NA	intron (NM_001128164, intron 6 of 7)	L2a|LINE|L2	215658	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.006098	0.410334	
chunk0067_35_1	chr15	40460843	40461178	+	0	NA	intron (NM_001301132, intron 2 of 6)	MIR|SINE|MIR	-9951	NM_130468	113189	Hs.442449	NM_130468	ENSG00000169105	CHST14	ATCS|D4ST1|EDSMC1|HNK1ST	carbohydrate sulfotransferase 14	protein-coding	0.005970	0.455357	
chunk0023_341_1	chr10	29534474	29535009	+	0	NA	intron (NM_021738, intron 7 of 37)	MIRb|SINE|MIR	10356	NR_030335	693189		NR_030335	ENSG00000207612	MIR604	MIRN604|hsa-mir-604	microRNA 604	ncRNA	0.003738	0.391791	
chunk0211_308_1	chrX	123476301	123476543	+	0	NA	intron (NM_000828, intron 14 of 15)	intron (NM_000828, intron 14 of 15)	256632	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.004132	0.399177	
chunk0089_253_1	chr18	62426167	62426514	+	0	NA	Intergenic	Intergenic	-97085	NM_017742	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.011527	0.468391	129(CTGGACAGTCTGTGCC,-,0.00),130(TGGACAGTCTGTGCCA,+,0.00)
chunk0206_173_1	chr9	122291902	122292101	+	0	NA	intron (NM_199177, intron 4 of 4)	L2a|LINE|L2	21137	NM_199177	92399	Hs.368011	NM_138777	ENSG00000148187	MRRF	MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding	0.010050	0.395000	
chunk0199_74_1	chr9	2427119	2427995	+	0	NA	Intergenic	Intergenic	-194236	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.011416	0.464082	414(GGGAACAGGCAGTCCC,-,0.00),415(GGAACAGGCAGTCCCA,+,0.00),709(CTGCACACAGTGTACA,-,0.00)
chunk0044_195_1	chr12	30548124	30548781	+	0	NA	Intergenic	MIRc|SINE|MIR	128792	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.001522	0.320669	
chunk0085_376_1	chr18	9608764	9609191	+	0	NA	intron (NM_001042388, intron 2 of 19)	intron (NM_001042388, intron 2 of 19)	5630	NM_001042388	9989	Hs.743236	NM_005134	ENSG00000154845	PPP4R1	MEG1|PP4(Rmeg)|PP4R1	protein phosphatase 4 regulatory subunit 1	protein-coding	0.002342	0.366822	
chunk0028_30_1	chr10	82830688	82831018	+	0	NA	intron (NM_001165972, intron 3 of 8)	intron (NM_001165972, intron 3 of 8)	-597933	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.003030	0.383686	
chunk0090_163_1	chr18	72518949	72519344	+	0	NA	Intergenic	L1ME1|LINE|L1	25342	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.010127	0.368687	
chunk0184_228_1	chr7	117490028	117490340	+	0	NA	intron (NM_000492, intron 1 of 26)	MIRb|SINE|MIR	10221	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.003205	0.367412	
chunk0147_92_1	chr4	173274962	173275220	+	0	NA	intron (NM_017423, intron 2 of 11)	intron (NM_017423, intron 2 of 11)	6931	NR_036093	100422849		NR_036093	ENSG00000221296	MIR548T	-	microRNA 548t	ncRNA	0.015504	0.467181	
chunk0133_346_1	chr3	173026619	173027108	+	0	NA	intron (NM_031955, intron 3 of 10)	L1ME1|LINE|L1	114405	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.004090	0.281633	
chunk0145_133_1	chr4	146383294	146383594	+	0	NA	intron (NM_001029998, intron 5 of 11)	MER51B|LTR|ERV1	-25139	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.016667	0.441860	102(TGTACAGGGTGTACAC,+,0.00)
chunk0075_317_1	chr16	54509128	54509887	+	0	NA	Intergenic	Intergenic	-223041	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.025033	0.484211	336(CGGGTCAGTTTGTTCT,-,0.00),337(GGGTCAGTTTGTTCTC,+,0.00)
chunk0111_145_1	chr20	25017299	25017774	+	0	NA	intron (NM_032501, intron 7 of 13)	MER68C|LTR|ERVL	15170	NM_001252676	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.025263	0.579832	
chunk0051_339_1	chr12	120291491	120291952	+	0	NA	TTS (NR_003137)	TTS (NR_003137)	182	NR_003137	26834		NR_003137	ENSG00000202538	RNU4-2	RNU4-1B|RNU4B1|RNU4C|U4A|U4b|U4c	RNA, U4 small nuclear 2	snRNA	0.039046	0.424242	
chunk0191_302_1	chr8	54789683	54789882	+	0	NA	Intergenic	L1M3b|LINE|L1	173715	NM_006269	6101	Hs.732820	NM_006269	ENSG00000104237	RP1	DCDC4A|ORP1	RP1 axonemal microtubule associated	protein-coding	0.005025	0.525000	
chunk0085_245_1	chr18	7231808	7232691	+	0	NA	TTS (NM_001105581)	TTS (NM_001105581)	1110	NM_001105581	339291	Hs.647588	NM_001105581	ENSG00000206422	LRRC30	-	leucine rich repeat containing 30	protein-coding	0.018120	0.487557	489(GAGAACTAACAGTTCT,-,0.00),490(AGAACTAACAGTTCTG,+,0.00)
chunk0131_259_1	chr3	149791478	149791727	+	0	NA	intron (NM_001315506, intron 1 of 4)	intron (NM_001315506, intron 1 of 4)	1221	NM_001144960	389161	Hs.665988	NM_001144960	ENSG00000206199	ANKUB1	C3orf16	ankyrin repeat and ubiquitin domain containing 1	protein-coding	0.004016	0.292000	
chunk0173_43_1	chr6	142300894	142301363	+	0	NA	promoter-TSS (NM_198569)	promoter-TSS (NM_198569)	-791	NM_001032395	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.010661	0.491489	
chunk0062_186_1	chr14	69732939	69733174	+	0	NA	Intergenic	Intergenic	-34056	NM_001039465	6430	Hs.632326	NM_006925	ENSG00000100650	SRSF5	HRS|SFRS5|SRP40	serine and arginine rich splicing factor 5	protein-coding	0.012766	0.500000	
chunk0135_60_1	chr3	185736959	185737797	+	0	NA	intron (NM_001007225, intron 2 of 14)	MIR1_Amn|SINE|MIR	24126	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.005967	0.350417	
chunk0039_447_1	chr11	108346408	108346770	+	0	NA	intron (NM_000051, intron 58 of 62)	intron (NM_000051, intron 58 of 62)	120942	NM_152587	160140	Hs.653180	NM_152587	ENSG00000166323	C11orf65	-	chromosome 11 open reading frame 65	protein-coding	0.000000	0.352617	
chunk0041_296_1	chr11	129621967	129622371	+	0	NA	Intergenic	Intergenic	-4900	NR_120582	101929557	Hs.385785	NR_120582	ENSG00000281097	LINC01395	-	long intergenic non-protein coding RNA 1395	ncRNA	0.012376	0.466667	
chunk0065_347_1	chr14	103620613	103621233	+	0	NA	Intergenic	AluSz6|SINE|Alu	-8265	NM_005552	3831	Hs.20107	NM_005552	ENSG00000126214	KLC1	KLC|KNS2|KNS2A	kinesin light chain 1	protein-coding	0.012903	0.444444	
chunk0016_438_1	chr1	204060890	204061201	+	0	NA	Intergenic	L2a|LINE|L2	-12073	NM_005686	9580	Hs.201671	NM_005686	ENSG00000143842	SOX13	ICA12|Sox-13	SRY-box transcription factor 13	protein-coding	0.003215	0.358974	
chunk0155_5_1	chr5	90782753	90783236	+	0	NA	intron (NR_003149, intron 65 of 89)	intron (NR_003149, intron 65 of 89)	224194	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.002070	0.371901	
chunk0110_242_1	chr20	16424903	16425507	+	0	NA	intron (NM_001199865, intron 15 of 24)	L1MC4|LINE|L1	148229	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.006623	0.342149	
chunk0085_80_1	chr18	2198322	2198629	+	0	NA	Intergenic	Intergenic	373028	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.006515	0.373377	124(GGGAACAAGCTGTTTT,-,0.00),125(GGAACAAGCTGTTTTG,+,0.00)
chunk0013_204_1	chr1	169383322	169383726	+	0	NA	intron (NM_003666, intron 6 of 7)	L2a|LINE|L2	-15561	NM_197972	29922	Hs.706952	NM_013330	ENSG00000143156	NME7	CFAP67|MN23H7|NDK 7|NDK7|nm23-H7	NME/NM23 family member 7	protein-coding	0.004950	0.407407	
chunk0112_308_1	chr20	44467190	44467688	+	0	NA	Intergenic	Intergenic	-2095	NR_132343	140834	Hs.357589	NM_001287807	ENSG00000168746	LINC01620	C20orf62|dJ1013A22.3	long intergenic non-protein coding RNA 1620	ncRNA	0.020080	0.535070	210(GAGGACATACTGTACC,-,0.00),211(AGGACATACTGTACCT,+,0.00)
chunk0081_409_1	chr17	48483669	48484325	+	0	NA	Intergenic	Intergenic	39164	NR_110804	101927166	Hs.149244	NR_110804		LOC101927166	-	uncharacterized LOC101927166	ncRNA	0.007622	0.499239	364(TGGGACAGAATGTGCC,-,0.00),365(GGGACAGAATGTGCCT,+,0.00)
chunk0046_323_1	chr12	62562654	62563114	+	0	NA	intron (NM_001278469, intron 26 of 35)	intron (NM_001278469, intron 26 of 35)	40550	NR_121682	283416	Hs.375881	NM_175895	ENSG00000221949	LINC01465	C12orf61	long intergenic non-protein coding RNA 1465	ncRNA	0.006522	0.357918	180(AGGACTTCAAGTTCTC,+,0.00)
chunk0101_299_1	chr2	134823202	134823921	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-15055	NM_138326	130013	Hs.655728	NM_138326	ENSG00000153086	ACMSD	-	aminocarboxymuconate semialdehyde decarboxylase	protein-coding	0.004172	0.398611	
chunk0138_281_1	chr4	40559564	40560260	+	0	NA	intron (NM_001098634, intron 1 of 6)	intron (NM_001098634, intron 1 of 6)	-43939	NM_019027	54502	Hs.518727	NM_019027	ENSG00000163694	RBM47	NET18	RNA binding motif protein 47	protein-coding	0.007184	0.406026	
chunk0151_297_1	chr5	52929005	52929359	+	0	NA	intron (NM_181501, intron 20 of 28)	MLT1A0|LTR|ERVL-MaLR	-60144	NR_073104	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.000000	0.419718	
chunk0112_229_1	chr20	41066813	41067218	+	0	NA	intron (NM_003286, intron 3 of 20)	intron (NM_003286, intron 3 of 20)	38193	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.012346	0.396552	
chunk0212_145_1	chrX	131885448	131886066	+	0	NA	Intergenic	L1PA15|LINE|L1	-55114	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.001618	0.342488	
chunk0028_286_1	chr10	91404901	91405409	+	0	NA	intron (NR_024467, intron 3 of 4)	intron (NR_024467, intron 3 of 4)	-5130	NR_104291	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.007874	0.339882	
chunk0068_262_1	chr15	56422273	56422639	+	0	NA	intron (NM_198524, intron 10 of 12)	L1MEc|LINE|L1	42681	NM_018365	55329	Hs.444483	NM_018365	ENSG00000138587	MNS1	SPATA40	meiosis specific nuclear structural 1	protein-coding	0.002732	0.291553	
chunk0150_85_1	chr5	32233557	32234245	+	0	NA	exon (NM_001040446, exon 15 of 16)	exon (NM_001040446, exon 15 of 16)	-59582	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.015988	0.490566	
chunk0139_166_1	chr4	53801331	53801917	+	0	NA	Intergenic	Intergenic	105723	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.005119	0.362862	366(AAGGACAACATGTTCA,-,0.00),367(AGGACAACATGTTCAA,+,0.00)
chunk0139_177_1	chr4	54144657	54145335	+	0	NA	Intergenic	Intergenic	44915	NM_133267	170825	Hs.371899	NM_133267	ENSG00000180613	GSX2	GSH2	GS homeobox 2	protein-coding	0.008850	0.418262	
chunk0094_402_1	chr2	10405996	10406499	+	0	NA	intron (NM_001258357, intron 2 of 4)	L2c|LINE|L2	37483	NM_001258359	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.025845	0.565476	242(TGGCACACACTGTTCC,-,0.00),243(GGCACACACTGTTCCC,+,0.00)
chunk0165_303_1	chr6	36874704	36874903	+	0	NA	5' UTR (NM_016059, exon 1 of 4)	5' UTR (NM_016059, exon 1 of 4)	221	NM_016059	51645	Hs.27693	NM_016059	ENSG00000137168	PPIL1	CGI-124|CYPL1|PPIase|hCyPX	peptidylprolyl isomerase like 1	protein-coding	0.075377	0.580000	
chunk0107_160_1	chr2	215268957	215269471	+	0	NA	Intergenic	MIRc|SINE|MIR	-42742	NM_004044	471	Hs.90280	NM_004044	ENSG00000138363	ATIC	AICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	protein-coding	0.003891	0.314563	
chunk0158_104_1	chr5	126796229	126796483	+	0	NA	intron (NM_005573, intron 1 of 10)	intron (NM_005573, intron 1 of 10)	19203	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.000000	0.450980	
chunk0174_182_1	chr6	159740268	159740768	+	0	NA	intron (NM_001270531, intron 3 of 7)	intron (NM_001270531, intron 3 of 7)	13018	NM_152857	9589	Hs.446091	NM_004906	ENSG00000146457	WTAP	Mum2	WT1 associated protein	protein-coding	0.014000	0.333333	
chunk0034_304_1	chr11	34995049	34995576	+	0	NA	3' UTR (NM_003477, exon 11 of 11)	3' UTR (NM_003477, exon 11 of 11)	53475	NR_039836	100616437		NR_039836	ENSG00000251862	MIR1343	-	microRNA 1343	ncRNA	0.007590	0.333333	
chunk0076_353_1	chr16	71712038	71712684	+	0	NA	intron (NM_001289003, intron 2 of 17)	(ATAA)n|Simple_repeat|Simple_repeat	3479	NM_001289003	23035	Hs.709458	NM_015020	ENSG00000040199	PHLPP2	PHLPPL|PPM3B	PH domain and leucine rich repeat protein phosphatase 2	protein-coding	0.006192	0.333849	
chunk0115_154_1	chr21	23837467	23838207	+	0	NA	Intergenic	Intergenic	-453002	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.005405	0.330634	
chunk0129_450_1	chr3	128235547	128235843	+	0	NA	intron (NM_021937, intron 1 of 6)	L1ME3G|LINE|L1	82238	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.016892	0.454545	
chunk0057_115_1	chr13	99269273	99269481	+	0	NA	intron (NM_001144072, intron 4 of 8)	intron (NM_001144072, intron 4 of 8)	-10949	NM_001098200	2841	Hs.741589	NM_005292	ENSG00000125245	GPR18	-	G protein-coupled receptor 18	protein-coding	0.004808	0.358852	
chunk0104_437_1	chr2	181232300	181233132	+	0	NA	intron (NR_130784, intron 2 of 4)	intron (NR_130784, intron 2 of 4)	72936	NR_039637	100616213		NR_039637	ENSG00000266705	MIR4437	mir-4437	microRNA 4437	ncRNA	0.002404	0.346939	
chunk0016_361_1	chr1	202349333	202349859	+	0	NA	intron (NM_002481, intron 1 of 23)	intron (NM_002481, intron 1 of 23)	894	NM_001167858	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.015209	0.413662	352(TAGAACACGCTGGACC,-,0.00),353(AGAACACGCTGGACCT,+,0.00)
chunk0036_415_1	chr11	68166687	68166971	+	0	NA	3' UTR (NM_016028, exon 10 of 10)	3' UTR (NM_016028, exon 10 of 10)	-45438	NM_212469	1119	Hs.77221	NM_001277	ENSG00000110721	CHKA	CHK|CK|CKI|EK	choline kinase alpha	protein-coding	0.007042	0.357895	119(GGATACAGACTGTGCC,-,0.00),120(GATACAGACTGTGCCT,+,0.00)
chunk0010_69_1	chr1	113089033	113089293	+	0	NA	intron (NM_001312686, intron 1 of 18)	intron (NM_001312686, intron 1 of 18)	15993	NM_014813	9860	Hs.448972	NM_014813	ENSG00000198799	LRIG2	LIG-2|LIG2|UFS2	leucine rich repeats and immunoglobulin like domains 2	protein-coding	0.003846	0.402299	76(GAGAACAAATTGTTCT,-,0.00),77(AGAACAAATTGTTCTA,+,0.00)
chunk0055_199_1	chr13	61929334	61929992	+	0	NA	Intergenic	Intergenic	99885	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004559	0.314112	
chunk0082_17_1	chr17	50352487	50352686	+	0	NA	intron (NR_110010, intron 1 of 9)	intron (NR_110010, intron 1 of 9)	6554	NR_110010	64132	Hs.463416	NM_022167	ENSG00000015532	XYLT2	PXYLT2|SOS|XT-II|XT2|xylT-II	xylosyltransferase 2	protein-coding	0.005025	0.575000	114(CTGGACATGCTGTTCA,-,0.00),115(TGGACATGCTGTTCAG,+,0.00)
chunk0139_105_1	chr4	51906990	51907433	+	0	NA	intron (NM_015115, intron 8 of 9)	intron (NM_015115, intron 8 of 9)	63632	NM_001287755	23142	Hs.605388	NM_015115	ENSG00000109184	DCUN1D4	-	defective in cullin neddylation 1 domain containing 4	protein-coding	0.004515	0.322072	
chunk0156_17_1	chr5	102138368	102138655	+	0	NA	Intergenic	Intergenic	158038	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.006969	0.440972	
chunk0057_413_1	chr13	109816632	109816831	+	0	NA	Intergenic	Intergenic	-30164	NM_003749	8660	Hs.442344	NM_003749	ENSG00000185950	IRS2	IRS-2	insulin receptor substrate 2	protein-coding	0.000000	0.450000	
chunk0185_273_1	chr7	130890846	130891163	+	0	NA	intron (NR_110472, intron 2 of 3)	intron (NR_110472, intron 2 of 3)	-13465	NR_029517	407024		NR_029517	ENSG00000283797	MIR29B1	MIRN29B1|miR-29b|miRNA29B1|mir-29b-1	microRNA 29b-1	ncRNA	0.006309	0.374214	86(GAGGACAGCCTGTTCT,-,0.00),87(AGGACAGCCTGTTCTT,+,0.00)
chunk0036_113_1	chr11	61488965	61489305	+	0	NA	intron (NM_145017, intron 11 of 13)	intron (NM_145017, intron 11 of 13)	8022	NM_001170753	220004	Hs.729003	NM_145017	ENSG00000162148	PPP1R32	C11orf66|IIIG9	protein phosphatase 1 regulatory subunit 32	protein-coding	0.029412	0.607038	
chunk0137_47_1	chr4	11505441	11506004	+	0	NA	Intergenic	Intergenic	-76809	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.005329	0.423759	
chunk0033_243_1	chr11	18071282	18071665	+	0	NA	Intergenic	Intergenic	-30685	NM_004179	7166	Hs.591999	NM_004179	ENSG00000129167	TPH1	TPRH|TRPH	tryptophan hydroxylase 1	protein-coding	0.005222	0.380208	
chunk0099_83_1	chr2	85396640	85397219	+	0	NA	intron (NM_001747, intron 8 of 9)	intron (NM_001747, intron 8 of 9)	13768	NM_001256140	822	Hs.516155	NM_001747	ENSG00000042493	CAPG	AFCP|HEL-S-66|MCP	capping actin protein, gelsolin like	protein-coding	0.005181	0.482759	379(CAGAACAGGCTCTGCC,-,0.00),380(AGAACAGGCTCTGCCC,+,0.00)
chunk0208_230_1	chrX	19331005	19331345	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-12718	NM_001173455	5160	Hs.530331	NM_000284	ENSG00000131828	PDHA1	PDHA|PDHAD|PDHCE1A|PHE1A	pyruvate dehydrogenase E1 alpha 1 subunit	protein-coding	0.008824	0.445748	141(GTAACATGTTGTTCTT,+,0.00)
chunk0201_438_1	chr9	70141658	70142306	+	0	NA	intron (NR_125850, intron 8 of 13)	MER34A|LTR|ERV1	33906	NR_040076	100507244	Hs.556816	NR_040076	ENSG00000204706	MAMDC2-AS1	-	MAMDC2 antisense RNA 1	ncRNA	0.003086	0.432974	238(AGGGACAGAATGTTCC,-,0.00),239(GGGACAGAATGTTCCT,+,0.00),271(GAGAACACCTTGTTCA,-,0.00),272(AGAACACCTTGTTCAC,+,0.00)
chunk0027_3_1	chr10	71761147	71761454	+	0	NA	intron (NM_022153, intron 2 of 6)	intron (NM_022153, intron 2 of 6)	12280	NM_022153	64115	Hs.47382	NM_022153	ENSG00000107738	VSIR	B7-H5|B7H5|C10orf54|DD1alpha|Dies1|GI24|PD-1H|PP2135|SISP1|VISTA	V-set immunoregulatory receptor	protein-coding	0.006515	0.532468	
chunk0092_92_1	chr19	22628253	22628507	+	0	NA	Intergenic	Intergenic	-5944	NM_020855	57615	Hs.232108	NM_020855	ENSG00000229676	ZNF492	ZNF115	zinc finger protein 492	protein-coding	0.019685	0.596078	
chunk0008_85_1	chr1	90160736	90161378	+	0	NA	Intergenic	Intergenic	165938	NM_182976	284695	Hs.306221	NM_181781	ENSG00000162664	ZNF326	ZAN75|ZIRD|Zfp326|dJ871E2.1	zinc finger protein 326	protein-coding	0.009346	0.382582	436(ATGAACAGGAAGTTCT,-,0.00),437(TGAACAGGAAGTTCTG,+,0.00)
chunk0106_212_1	chr2	202449515	202449753	+	0	NA	intron (NM_001204, intron 1 of 12)	MER68|LTR|ERVL	73307	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.008403	0.410042	
chunk0090_32_1	chr19	1245858	1246369	+	0	NA	Intergenic	Intergenic	-2440	NM_177401	90007	Hs.465529	NM_177401	ENSG00000167470	MIDN	-	midnolin	protein-coding	0.025440	0.632812	222(GGGAACAGCCCGTGCT,-,0.00),223(GGAACAGCCCGTGCTG,+,0.00)
chunk0162_325_1	chr6	6766572	6766776	+	0	NA	Intergenic	Intergenic	-143848	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.009804	0.439024	
chunk0056_227_1	chr13	88590775	88591030	+	0	NA	Intergenic	Intergenic	50073	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.003922	0.257812	
chunk0117_55_1	chr22	12869878	12870220	+	0	NA	Intergenic	Intergenic	972643	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.011696	0.364431	
chunk0083_457_1	chr17	73215437	73216009	+	0	NA	intron (NM_001098832, intron 2 of 3)	intron (NM_001098832, intron 2 of 3)	11994	NM_001289412	84923	Hs.741276	NM_032837	ENSG00000133193	FAM104A	-	family with sequence similarity 104 member A	protein-coding	0.003497	0.492147	199(AGGTGCAGCTTGTTCT,-,0.00)
chunk0006_308_1	chr1	71417465	71417795	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	336306	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.006061	0.344411	
chunk0039_48_1	chr11	96142947	96143397	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-198266	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.004444	0.356984	
chunk0011_173_1	chr1	147777663	147778173	+	0	NA	Intergenic	Intergenic	-4556	NM_005266	2702	Hs.447968	NM_005266	ENSG00000265107	GJA5	ATFB11|CX40	gap junction protein alpha 5	protein-coding	0.009804	0.457926	54(AAGAACGGTGAGTCCT,-,0.00),55(AGAACGGTGAGTCCTC,+,0.00),207(AAGAACACTCTGTTCC,-,0.00),208(AGAACACTCTGTTCCA,+,0.00)
chunk0011_407_1	chr1	154334664	154335048	+	0	NA	intron (NM_001005855, intron 11 of 11)	intron (NM_001005855, intron 11 of 11)	7056	NM_020452	57198	Hs.435700	NM_020452	ENSG00000143515	ATP8B2	ATPID	ATPase phospholipid transporting 8B2	protein-coding	0.005208	0.405195	
chunk0081_388_1	chr17	48199217	48199542	+	0	NA	intron (NM_001075099, intron 4 of 12)	L2c|LINE|L2	-42868	NR_031607	100302211		NR_031607	ENSG00000221739	MIR1203	MIRN1203|hsa-mir-1203	microRNA 1203	ncRNA	0.003077	0.420245	
chunk0103_142_1	chr2	162119929	162120128	+	0	NA	intron (NR_110255, intron 1 of 3)	intron (NR_110255, intron 1 of 3)	5587	NR_110255	101929532	Hs.639883	NR_110255	ENSG00000236841	LOC101929532	-	uncharacterized LOC101929532	ncRNA	0.010050	0.440000	
chunk0178_278_1	chr7	37186699	37187104	+	0	NA	intron (NM_001206482, intron 13 of 21)	L1MB8|LINE|L1	166767	NM_001206482	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.000000	0.364532	
chunk0014_343_1	chr1	182249919	182250253	+	0	NA	intron (NR_104175, intron 2 of 2)	intron (NR_104175, intron 2 of 2)	63975	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.005988	0.453731	
chunk0040_355_1	chr11	118770963	118771162	+	0	NA	intron (NM_001257191, intron 4 of 13)	intron (NM_001257191, intron 4 of 13)	19886	NM_001257191	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.000000	0.420000	
chunk0188_69_1	chr8	8362228	8362427	+	0	NA	intron (NM_001080826, intron 2 of 4)	HERVI-int|LTR|ERV1	19507	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.015075	0.525000	
chunk0114_86_1	chr21	9257897	9258264	+	0	NA	Intergenic	MER21C|LTR|ERVL	-128319	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.005450	0.456522	
chunk0125_140_1	chr3	66053764	66054348	+	0	NA	Intergenic	L2a|LINE|L2	-15222	NM_001033057	9223	Hs.476636	NM_004742	ENSG00000151276	MAGI1	AIP-3|AIP3|BAIAP1|BAP-1|BAP1|MAGI-1|MAGI-1b|Magi1d|TNRC19|WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.011986	0.452991	525(GGGAGACAGTGTTCTG,+,0.00)
chunk0212_443_1	chrX	155234416	155234961	+	0	NA	intron (NM_001303544, intron 5 of 6)	HAL1M8|LINE|L1	18264	NM_003372	7411	Hs.436803	NM_003372	ENSG00000155959	VBP1	HIBBJ46|PFD3|PFDN3|VBP-1	VHL binding protein 1	protein-coding	0.005505	0.371795	
chunk0141_393_1	chr4	88361901	88362443	+	0	NA	Intergenic	MER34C|LTR|ERV1	-16567	NM_001165136	55008	Hs.529317	NM_017912	ENSG00000138642	HERC6	-	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	protein-coding	0.011070	0.338858	
chunk0022_418_1	chr10	18640570	18640769	+	0	NA	intron (NM_182543, intron 3 of 10)	L1ME2|LINE|L1	10968	NM_182543	221078	Hs.396175	NM_182543	ENSG00000241058	NSUN6	4933414E04Rik|ARL5B-AS1|NOPD1	NOP2/Sun RNA methyltransferase 6	protein-coding	0.005025	0.395000	
chunk0133_207_1	chr3	170876541	170877033	+	0	NA	Intergenic	Intergenic	-6531	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.008130	0.361055	
chunk0146_226_1	chr4	161983211	161983556	+	0	NA	intron (NM_001128427, intron 3 of 15)	MamGypLTR1c|LTR|Gypsy	-39350	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.008696	0.390173	
chunk0166_78_1	chr6	43367508	43367804	+	0	NA	intron (NM_014345, intron 1 of 9)	L2b|LINE|L2	1787	NM_014345	24149	Hs.509718	NM_014345	ENSG00000171467	ZNF318	HRIHFB2436|TZF|ZFP318	zinc finger protein 318	protein-coding	0.010135	0.420875	
chunk0021_98_1	chr10	2995439	2995705	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	-71948	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.000000	0.367041	
chunk0026_232_1	chr10	65497931	65498345	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-73287	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.004831	0.400000	
chunk0056_44_1	chr13	77460235	77460528	+	0	NA	Intergenic	Intergenic	-75293	NM_001160706	8796	Hs.534699	NM_003843	ENSG00000136155	SCEL	-	sciellin	protein-coding	0.006826	0.448980	
chunk0070_46_1	chr15	69482673	69483098	+	0	NA	Intergenic	Intergenic	30065	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.007059	0.500000	
chunk0182_44_1	chr7	91654465	91655098	+	0	NA	Intergenic	Intergenic	225939	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.004739	0.350158	
chunk0061_110_1	chr14	58097014	58097535	+	0	NA	intron (NM_001001872, intron 4 of 7)	intron (NM_001001872, intron 4 of 7)	54855	NM_001001872	145407	Hs.26766	NM_001001872	ENSG00000139971	ARMH4	C14orf37|UT2|c14_5376	armadillo like helical domain containing 4	protein-coding	0.000000	0.333333	
chunk0201_361_1	chr9	68500577	68501111	+	0	NA	intron (NM_021965, intron 10 of 10)	intron (NM_021965, intron 10 of 10)	40023	NM_153237	169693	Hs.663056	NM_153237	ENSG00000181778	TMEM252	C9orf71	transmembrane protein 252	protein-coding	0.009363	0.435514	
chunk0117_184_1	chr22	21103029	21103264	+	0	NA	non-coding (NR_037566, exon 1 of 6)	non-coding (NR_037566, exon 1 of 6)	130	NR_037566	400892	Hs.745077	NM_207474		BCRP2	BCR-2|BCR2|BCRL2	BCR pseudogene 2	pseudo	0.025532	0.567797	
chunk0065_206_1	chr14	100103640	100104646	+	0	NA	intron (NM_016337, intron 3 of 13)	MIRb|SINE|MIR	5371	NR_039601	100616247		NR_039601	ENSG00000265154	MIR151B	-	microRNA 151b	ncRNA	0.012922	0.473684	
chunk0019_174_1	chr1	226400865	226401075	+	0	NA	intron (NM_001618, intron 2 of 22)	LTR16D|LTR|ERVL	7130	NM_001618	142	Hs.177766	NM_001618	ENSG00000143799	PARP1	ADPRT|ADPRT 1|ADPRT1|ARTD1|PARP|PARP-1|PPOL|pADPRT-1	poly(ADP-ribose) polymerase 1	protein-coding	0.014286	0.521327	
chunk0114_307_1	chr21	17105857	17106481	+	0	NA	Intergenic	L1PA11|LINE|L1	-332721	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.000000	0.376000	
chunk0118_41_1	chr22	27764642	27765425	+	0	NA	intron (NM_002430, intron 1 of 1)	MLT2B4|LTR|ERVL	36465	NM_002430	4330	Hs.268515	NM_002430	ENSG00000169184	MN1	MGCR|MGCR1|MGCR1-PEN|dJ353E16.2	MN1 proto-oncogene, transcriptional regulator	protein-coding	0.007663	0.422194	
chunk0020_178_1	chr1	234563576	234563854	+	0	NA	Intergenic	L1ME4a|LINE|L1	-31936	NR_038426	100506795	Hs.448989	NR_038426	ENSG00000231768	LINC01354	-	long intergenic non-protein coding RNA 1354	ncRNA	0.000000	0.286738	
chunk0078_7_1	chr17	348443	349170	+	0	NA	intron (NM_006987, intron 1 of 9)	intron (NM_006987, intron 1 of 9)	4036	NM_006987	9501	Hs.651925	NM_006987	ENSG00000181031	RPH3AL	NOC2	rabphilin 3A like (without C2 domains)	protein-coding	0.017882	0.446429	
chunk0071_140_1	chr15	82268347	82268968	+	0	NA	intron (NM_001008226, intron 1 of 2)	intron (NM_001008226, intron 1 of 2)	5846	NM_001008226	283726	Hs.459117	NM_001008226	ENSG00000188659	SAXO2	FAM154B	stabilizer of axonemal microtubules 2	protein-coding	0.003221	0.376206	
chunk0044_2_1	chr12	26805361	26805937	+	0	NA	intron (NM_002223, intron 1 of 56)	L2a|LINE|L2	27549	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.006944	0.395147	
chunk0151_121_1	chr5	43704169	43704595	+	0	NA	exon (NM_012343, exon 22 of 22)	exon (NM_012343, exon 22 of 22)	-101152	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.009390	0.395785	
chunk0149_394_1	chr5	28828493	28828701	+	0	NA	Intergenic	Intergenic	-98273	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.004808	0.248804	
chunk0164_279_1	chr6	24069639	24069862	+	0	NA	Intergenic	Intergenic	-56436	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.008969	0.415179	
chunk0145_435_1	chr4	153340513	153340774	+	0	NA	Intergenic	L2c|LINE|L2	-4006	NR_045605	84057	Hs.294088	NM_032117	ENSG00000121211	MND1	GAJ	meiotic nuclear divisions 1	protein-coding	0.011494	0.435115	
chunk0015_369_1	chr1	190453515	190453867	+	0	NA	intron (NM_199051, intron 2 of 7)	intron (NM_199051, intron 2 of 7)	23938	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.002841	0.314448	
chunk0162_46_1	chr6	1278025	1278550	+	0	NA	Intergenic	Intergenic	-34153	NM_033260	94234	Hs.591352	NM_033260	ENSG00000164379	FOXQ1	HFH1	forkhead box Q1	protein-coding	0.007619	0.435361	
chunk0046_16_1	chr12	54191513	54191716	+	0	NA	Intergenic	Intergenic	-2620	NM_001243791	23583	Hs.632721	NM_014311	ENSG00000123415	SMUG1	FDG|HMUDG|UNG3	single-strand-selective monofunctional uracil-DNA glycosylase 1	protein-coding	0.029557	0.563725	
chunk0035_157_1	chr11	43376574	43376976	+	0	NA	intron (NM_018259, intron 1 of 23)	intron (NM_018259, intron 1 of 23)	17890	NM_018259	55761	Hs.191186	NM_018259	ENSG00000052841	TTC17	-	tetratricopeptide repeat domain 17	protein-coding	0.004975	0.387097	
chunk0070_11_1	chr15	68897135	68897531	+	0	NA	Intergenic	Intergenic	-33167	NR_033672	79400	Hs.657932	NM_024505	ENSG00000255346	NOX5	-	NADPH oxidase 5	protein-coding	0.002525	0.400504	213(GAGAACATGTTGTTCA,-,0.00),214(AGAACATGTTGTTCAG,+,0.00)
chunk0021_207_1	chr10	5910167	5910670	+	0	NA	intron (NM_178150, intron 5 of 20)	intron (NM_178150, intron 5 of 20)	16032	NM_032807	84893	Hs.498543	NM_032807	ENSG00000134452	FBH1	FBXO18|Fbx18|hFBH1	F-box DNA helicase 1	protein-coding	0.017893	0.470238	
chunk0068_268_1	chr15	56658801	56659179	+	0	NA	intron (NM_001002843, intron 15 of 20)	intron (NM_001002843, intron 15 of 20)	75096	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.005291	0.369393	
chunk0203_366_1	chr9	89964531	89964964	+	0	NA	Intergenic	L1ME4b|LINE|L1	-4669	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.011547	0.389401	
chunk0133_98_1	chr3	167900887	167901480	+	0	NA	intron (NR_033843, intron 1 of 7)	intron (NR_033843, intron 1 of 7)	5235	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.001686	0.340067	
chunk0080_16_1	chr17	20944363	20944627	+	0	NA	intron (NR_123730, intron 1 of 5)	L1M1|LINE|L1	5975	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.015152	0.547170	
chunk0172_14_1	chr6	132814094	132814385	+	0	NA	promoter-TSS (NM_001016)	promoter-TSS (NM_001016)	-330	NM_001016	6206	Hs.546289	NM_001016	ENSG00000112306	RPS12	S12	ribosomal protein S12	protein-coding	0.065292	0.568493	47(AGGAACAAAGTGCGCT,-,0.00),48(GGAACAAAGTGCGCTG,+,0.00)
chunk0203_377_1	chr9	90295998	90296542	+	0	NA	Intergenic	L3|LINE|CR1	137219	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.003676	0.341284	191(GAGCACACCCAGTTCC,-,0.00),192(AGCACACCCAGTTCCC,+,0.00)
chunk0018_226_1	chr1	219713213	219713658	+	0	NA	Intergenic	Charlie21a|DNA|hAT-Charlie	215216	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.002247	0.260090	
chunk0019_53_1	chr1	224142819	224143477	+	0	NA	intron (NM_001136115, intron 3 of 3)	AluSx|SINE|Alu	29061	NM_001136115	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.021277	0.496206	
chunk0099_25_1	chr2	83151878	83152414	+	0	NA	Intergenic	MIRb|SINE|MIR	295343	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.005597	0.337058	
chunk0129_244_1	chr3	122085253	122085852	+	0	NA	intron (NM_006889, intron 1 of 6)	intron (NM_006889, intron 1 of 6)	7703	NM_176892	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.011686	0.500000	200(AGGTACAGAGAGTTCT,-,0.00),201(GGTACAGAGAGTTCTT,+,0.00)
chunk0100_371_1	chr2	117981736	117982174	+	0	NA	intron (NM_019044, intron 7 of 23)	intron (NM_019044, intron 7 of 23)	32208	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.004566	0.343964	
chunk0012_218_1	chr1	160172519	160172810	+	0	NA	intron (NM_144699, intron 12 of 21)	intron (NM_144699, intron 12 of 21)	-4747	NM_001001734	480	Hs.662219	NM_144699	ENSG00000132681	ATP1A4	ATP1A1|ATP1AL2	ATPase Na+/K+ transporting subunit alpha 4	protein-coding	0.003436	0.448630	199(GAGAACTAGGTGTTCT,-,0.00),200(AGAACTAGGTGTTCTC,+,0.00)
chunk0113_314_1	chr20	58048139	58048368	+	0	NA	Intergenic	Intergenic	-102674	NM_178456	128602	Hs.43977	NM_178456	ENSG00000124237	C20orf85	LLC1|bA196N14.1	chromosome 20 open reading frame 85	protein-coding	0.004367	0.508696	
chunk0075_243_1	chr16	53131621	53132002	+	0	NA	intron (NM_025134, intron 1 of 38)	CpG	-24115	NM_001308319	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.104987	0.714660	
chunk0049_183_1	chr12	92602850	92603119	+	0	NA	Intergenic	L2c|LINE|L2	-99859	NM_001037671	338809	Hs.326303	NM_001037671	ENSG00000187510	C12orf74	-	chromosome 12 open reading frame 74	protein-coding	0.003717	0.396296	43(AAGAACACAGTGTGAC,-,0.00)
chunk0110_248_1	chr20	16553442	16553878	+	0	NA	intron (NM_001199865, intron 1 of 24)	intron (NM_001199865, intron 1 of 24)	19774	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.006881	0.475973	
chunk0112_302_1	chr20	44319767	44320257	+	0	NA	Intergenic	MER57D|LTR|ERV1	-8763	NM_001080472	128486	Hs.632269	NM_001080472	ENSG00000197296	FITM2	C20orf142|Fit2|dJ881L22.2	fat storage inducing transmembrane protein 2	protein-coding	0.002041	0.405295	
chunk0004_15_1	chr1	42146972	42147362	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-6254	NM_007102	2981	Hs.32966	NM_007102	ENSG00000044012	GUCA2B	GCAP-II|UGN	guanylate cyclase activator 2B	protein-coding	0.017949	0.488491	
chunk0041_55_1	chr11	123267950	123268626	+	0	NA	Intergenic	Intergenic	-72983	NM_024769	79827	Hs.591949	NM_024769	ENSG00000166250	CLMP	ACAM|ASAM|CSBM|CSBS	CXADR like membrane protein	protein-coding	0.019231	0.494830	
chunk0087_336_1	chr18	40150471	40150670	+	0	NA	Intergenic	MIR|SINE|MIR	84284	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.005025	0.335000	
chunk0008_23_1	chr1	87830282	87830607	+	0	NA	Intergenic	Intergenic	-458789	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.009231	0.319018	
chunk0162_11_1	chr6	581109	581502	+	0	NA	intron (NR_073064, intron 13 of 29)	AluSz|SINE|Alu	75659	NM_148959	135458	Hs.669039	NM_148959	ENSG00000188996	HUS1B	-	HUS1 checkpoint clamp component B	protein-coding	0.015267	0.403553	95(GAGAACTGCTTGTACC,-,0.00),96(AGAACTGCTTGTACCT,+,0.00)
chunk0046_41_1	chr12	54870561	54871069	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	16300	NM_058173	118430	Hs.348419	NM_058173	ENSG00000172551	MUCL1	SBEM	mucin like 1	protein-coding	0.009843	0.357564	
chunk0147_173_1	chr4	176339292	176339806	+	0	NA	Intergenic	Intergenic	19610	NM_021928	60559	Hs.42194	NM_021928	ENSG00000129128	SPCS3	PRO3567|SPC22/23|SPC3|YLR066W	signal peptidase complex subunit 3	protein-coding	0.003891	0.361165	
chunk0081_440_1	chr17	49020323	49020915	+	0	NA	intron (NM_001160423, intron 2 of 12)	intron (NM_001160423, intron 2 of 12)	23207	NM_001160423	10642	Hs.144936	NM_006546	ENSG00000159217	IGF2BP1	CRD-BP|CRDBP|IMP-1|IMP1|VICKZ1|ZBP1	insulin like growth factor 2 mRNA binding protein 1	protein-coding	0.013514	0.426644	
chunk0090_115_1	chr18	71372075	71372325	+	0	NA	Intergenic	L2a|LINE|L2	206756	NR_038326	100505776	Hs.202072	NR_038325	ENSG00000260676	LINC01541	UTAT39	long intergenic non-protein coding RNA 1541	ncRNA	0.004000	0.350598	
chunk0088_248_1	chr18	48714934	48715724	+	0	NA	intron (NM_014772, intron 7 of 11)	intron (NM_014772, intron 7 of 11)	44729	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.015190	0.508217	
chunk0174_188_1	chr6	159953391	159954073	+	0	NA	Intergenic	Intergenic	-15367	NM_000876	3482	Hs.487062	NM_000876	ENSG00000197081	IGF2R	CD222|CI-M6PR|CIMPR|M6P-R|M6P/IGF2R|MPR 300|MPR1|MPR300|MPRI	insulin like growth factor 2 receptor	protein-coding	0.008798	0.415813	
chunk0094_408_1	chr2	10452098	10452746	+	0	NA	non-coding (NR_110597, exon 3 of 5)	non-coding (NR_110597, exon 3 of 5)	2694	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.006173	0.520801	
chunk0118_16_1	chr22	25663562	25664160	+	0	NA	intron (NM_005160, intron 5 of 20)	intron (NM_005160, intron 5 of 20)	-78292	NM_032608	84700	Hs.417959	NM_032608	ENSG00000133454	MYO18B	KFS4	myosin XVIIIB	protein-coding	0.006689	0.343907	380(GTAACATTATGTTCTA,+,0.00)
chunk0028_194_1	chr10	88814075	88814501	+	0	NA	intron (NM_001128215, intron 3 of 8)	intron (NM_001128215, intron 3 of 8)	11558	NM_001128215	340654	Hs.55118	NM_001128215	ENSG00000173239	LIPM	LIPL3|bA304I5.1	lipase family member M	protein-coding	0.014085	0.402810	
chunk0017_393_1	chr1	212481284	212481777	+	0	NA	Intergenic	Intergenic	48643	NR_026598	29937	Hs.461787	NM_013349	ENSG00000117691	NENF	CIR2|SCIRP10|SPUF	neudesin neurotrophic factor	protein-coding	0.008114	0.400810	
chunk0206_92_1	chr9	120628422	120629257	+	0	NA	intron (NM_001080497, intron 2 of 5)	LTR40a|LTR|ERVL	-48669	NR_073554	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.004790	0.411483	
chunk0057_406_1	chr13	109730413	109731032	+	0	NA	TTS (NR_103846)	TTS (NR_103846)	2448	NR_103846	101409253	Hs.578072	NR_103846	ENSG00000234854	LINC00676	-	long intergenic non-protein coding RNA 676	ncRNA	0.006462	0.358065	
chunk0158_39_1	chr5	125612359	125612845	+	0	NA	Intergenic	Intergenic	119341	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.022634	0.478439	
chunk0036_106_1	chr11	61309903	61310115	+	0	NA	intron (NM_001923, intron 19 of 26)	intron (NM_001923, intron 19 of 26)	-14693	NM_152718	220001	Hs.60640	NM_152718	ENSG00000167992	VWCE	URG11|VWC1	von Willebrand factor C and EGF domains	protein-coding	0.018868	0.502347	
chunk0086_355_1	chr18	25854547	25854775	+	0	NA	Intergenic	Intergenic	235986	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.008772	0.493450	
chunk0128_21_1	chr3	104165884	104166207	+	0	NA	Intergenic	Intergenic	-641929	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.006192	0.330247	
chunk0057_163_1	chr13	101232818	101233371	+	0	NA	intron (NM_052867, intron 12 of 43)	intron (NM_052867, intron 12 of 43)	183368	NM_052867	259232	Hs.525146	NM_052867	ENSG00000102452	NALCN	CLIFAHDD|CanIon|IHPRF|IHPRF1|INNFD|VGCNL1|bA430M15.1	sodium leak channel, non-selective	protein-coding	0.005425	0.324910	377(CAGAACATTTTGTCTC,-,0.00),378(AGAACATTTTGTCTCT,+,0.00)
chunk0184_222_1	chr7	117470652	117471105	+	0	NA	Intergenic	Intergenic	-9085	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.011038	0.471366	201(TGGGACTGGGTGTTCC,-,0.00),202(GGGACTGGGTGTTCCA,+,0.00)
chunk0015_270_1	chr1	188408712	188408981	+	0	NA	Intergenic	Intergenic	965218	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.229630	
chunk0175_207_1	chr7	6020729	6021238	+	0	NA	intron (NM_006303, intron 3 of 3)	Tigger2|DNA|TcMar-Tigger	-10393	NM_001271700	100310846	Hs.744468	NM_001271700	ENSG00000157999	ANKRD61	-	ankyrin repeat domain 61	protein-coding	0.017682	0.466667	
chunk0084_219_1	chr17	78360785	78361041	+	0	NA	promoter-TSS (NM_003955)	promoter-TSS (NM_003955)	-89	NR_110846	101928674	Hs.637297	NR_110845	ENSG00000266970	LOC101928674	-	uncharacterized LOC101928674	ncRNA	0.066406	0.673152	
chunk0072_47_1	chr16	1238025	1238479	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-2425	NM_003294	7177	Hs.405479	NM_003294	ENSG00000172236	TPSAB1	TPS1|TPS2|TPSB1|TPSB2|Tryptase-2	tryptase alpha/beta 1	protein-coding	0.019824	0.498901	
chunk0032_235_1	chr11	7635608	7636234	+	0	NA	intron (NM_003621, intron 14 of 23)	intron (NM_003621, intron 14 of 23)	30187	NM_001256569	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.009585	0.379585	359(GTGTACACTCAGTCCC,-,0.00),360(TGTACACTCAGTCCCG,+,0.00)
chunk0119_301_1	chr22	46478164	46478634	+	0	NA	intron (NM_014246, intron 1 of 34)	intron (NM_014246, intron 1 of 34)	58771	NM_014246	9620	Hs.252387	NM_014246	ENSG00000075275	CELSR1	ADGRC1|CDHF9|FMI2|HFMI2|ME2	cadherin EGF LAG seven-pass G-type receptor 1	protein-coding	0.036170	0.558386	
chunk0041_184_1	chr11	126340076	126340275	+	0	NA	intron (NM_014026, intron 4 of 5)	intron (NM_014026, intron 4 of 5)	15412	NR_033839	399972	Hs.585206	NR_033839		GSEC	DCPS-AS1|ST3GAL4-AS1	G-quadruplex forming sequence containing lncRNA	ncRNA	0.015075	0.545000	
chunk0152_355_1	chr5	63400002	63400623	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	561980	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.008052	0.384244	
chunk0074_269_1	chr16	28189586	28189834	+	0	NA	intron (NM_015171, intron 1 of 23)	intron (NM_015171, intron 1 of 23)	22208	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.012097	0.405622	
chunk0016_432_1	chr1	203839075	203839443	+	0	NA	intron (NM_014827, intron 13 of 19)	FLAM_A|SINE|Alu	-22326	NM_003094	6635	Hs.334612	NM_003094	ENSG00000182004	SNRPE	HYPT11|SME|Sm-E|snRNP-E	small nuclear ribonucleoprotein polypeptide E	protein-coding	0.013587	0.406504	
chunk0143_88_1	chr4	108292222	108292701	+	0	NA	Intergenic	MER131|DNA?|DNA?	120341	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.002088	0.368750	
chunk0168_189_1	chr6	85395167	85395541	+	0	NA	Intergenic	Intergenic	-54230	NM_001204813	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.000000	0.373333	
chunk0184_340_1	chr7	120709972	120710616	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	147829	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.001553	0.367442	
chunk0073_157_1	chr16	7620735	7620999	+	0	NA	intron (NM_001142333, intron 10 of 14)	intron (NM_001142333, intron 10 of 14)	288117	NM_145892	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.003788	0.396226	
chunk0200_233_1	chr9	20745493	20745971	+	0	NA	intron (NM_017794, intron 7 of 45)	intron (NM_017794, intron 7 of 45)	29627	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.006276	0.346555	
chunk0047_443_1	chr12	76455540	76455950	+	0	NA	intron (NM_020841, intron 3 of 23)	intron (NM_020841, intron 3 of 23)	104064	NM_001003712	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.007317	0.360097	
chunk0123_133_1	chr3	42653324	42653581	+	0	NA	promoter-TSS (NM_145166)	promoter-TSS (NM_145166)	-232	NM_145166	92999	Hs.409561	NM_145166	ENSG00000114853	ZBTB47	ZNF651	zinc finger and BTB domain containing 47	protein-coding	0.007782	0.581395	
chunk0090_178_1	chr18	72780051	72780474	+	0	NA	intron (NM_138966, intron 7 of 10)	intron (NM_138966, intron 7 of 10)	73120	NR_049858	100847083		NR_049858	ENSG00000263750	MIR548AV	-	microRNA 548av	ncRNA	0.007092	0.375000	247(AAGAACACCCTGTGTC,-,0.00),248(AGAACACCCTGTGTCT,+,0.00)
chunk0015_187_1	chr1	187244465	187245011	+	0	NA	intron (NR_126347, intron 1 of 3)	intron (NR_126347, intron 1 of 3)	151896	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.009158	0.363803	
chunk0096_374_1	chr2	36779456	36779655	+	0	NA	intron (NM_001177970, intron 9 of 13)	L1PA11|LINE|L1	82865	NM_001177971	5212	Hs.137415	NM_053276	ENSG00000205221	VIT	VIT1	vitrin	protein-coding	0.010050	0.460000	
chunk0080_300_1	chr17	31560474	31561263	+	0	NA	TTS (NR_029710)	TTS (NR_029710)	872	NR_029710	406968		NR_029710	ENSG00000207614	MIR193A	MIRN193|MIRN193A|mir-193a	microRNA 193a	ncRNA	0.019011	0.521519	
chunk0057_172_1	chr13	102236309	102237264	+	0	NA	intron (NM_175929, intron 1 of 4)	intron (NM_175929, intron 1 of 4)	-130744	NR_125912	100874081	Hs.569296	NR_125912	ENSG00000234445	FGF14-AS1	-	FGF14 antisense RNA 1	ncRNA	0.016754	0.512552	
chunk0109_81_1	chr20	2005872	2006426	+	0	NA	Intergenic	Intergenic	-11864	NM_024411	5173	Hs.22584	NM_024411	ENSG00000101327	PDYN	ADCA|PENKB|SCA23	prodynorphin	protein-coding	0.021661	0.450450	
chunk0206_168_1	chr9	122248736	122248980	+	0	NA	intron (NR_027125, intron 3 of 6)	intron (NR_027125, intron 3 of 6)	-15745	NM_138777	92399	Hs.368011	NM_138777	ENSG00000148187	MRRF	MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding	0.004098	0.461224	60(AGGAACAGGATGTCCC,-,0.00),61(GGAACAGGATGTCCCA,+,0.00)
chunk0035_230_1	chr11	45842068	45842424	+	0	NA	Intergenic	MER83|LTR|ERV1	-4872	NM_001127457	1408	Hs.532491	NM_021117	ENSG00000121671	CRY2	HCRY2|PHLL2	cryptochrome circadian regulator 2	protein-coding	0.000000	0.450980	
chunk0096_232_1	chr2	30755337	30755729	+	0	NA	intron (NM_144575, intron 8 of 22)	intron (NM_144575, intron 8 of 22)	51912	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.005102	0.506361	171(TGGAACGATGTGTTCC,-,0.00),172(GGAACGATGTGTTCCA,+,0.00)
chunk0091_98_1	chr19	5798035	5798284	+	0	NA	Intergenic	Intergenic	-6921	NM_020175	56931	Hs.284297	NM_020175	ENSG00000141994	DUS3L	DUS3	dihydrouridine synthase 3 like	protein-coding	0.012048	0.596000	
chunk0183_224_1	chr7	106752424	106752659	+	0	NA	Intergenic	Intergenic	-91353	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.000000	0.483051	
chunk0082_328_1	chr17	59643370	59643766	+	0	NA	intron (NM_004859, intron 1 of 31)	L2c|LINE|L2	23879	NM_001288653	1213	Hs.491351	NM_004859	ENSG00000141367	CLTC	CHC|CHC17|CLH-17|CLTCL2|Hc|MRD56	clathrin heavy chain	protein-coding	0.007576	0.380353	
chunk0088_316_1	chr18	50807302	50807881	+	0	NA	intron (NM_001127175, intron 2 of 5)	intron (NM_001127175, intron 2 of 5)	12473	NM_001127175	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.008636	0.424138	458(GGGAACACTGTGTGTC,-,0.00),459(GGAACACTGTGTGTCT,+,0.00)
chunk0159_182_1	chr5	140220772	140221062	+	0	NA	intron (NM_032412, intron 2 of 2)	intron (NM_032412, intron 2 of 2)	45849	NM_032412	84418	Hs.529798	NM_032412	ENSG00000120306	CYSTM1	C5orf32|ORF1-FL49	cysteine rich transmembrane module containing 1	protein-coding	0.003448	0.505155	152(CAGAACATCCTGAGCC,-,0.00),153(AGAACATCCTGAGCCA,+,0.00)
chunk0156_328_1	chr5	111549162	111549619	+	0	NA	intron (NR_040093, intron 1 of 6)	intron (NR_040093, intron 1 of 6)	-36793	NM_001308057	134429	Hs.93842	NM_139164	ENSG00000164211	STARD4	-	StAR related lipid transfer domain containing 4	protein-coding	0.013129	0.438865	
chunk0150_124_1	chr5	33148210	33148627	+	0	NA	Intergenic	Intergenic	200975	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.004796	0.401914	
chunk0078_377_1	chr16	87727709	87727995	+	0	NA	intron (NM_001184856, intron 5 of 10)	intron (NM_001184856, intron 5 of 10)	38140	NM_017566	54758	Hs.123450	NM_017566	ENSG00000104731	KLHDC4	-	kelch domain containing 4	protein-coding	0.010490	0.505226	
chunk0179_439_1	chr7	52272199	52272483	+	0	NA	Intergenic	Intergenic	-763315	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.000000	0.336842	
chunk0181_287_1	chr7	86910829	86911091	+	0	NA	intron (NM_001291990, intron 15 of 21)	intron (NM_001291990, intron 15 of 21)	55015	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.000000	0.338403	
chunk0082_209_1	chr17	57021401	57022088	+	0	NA	Intergenic	L2a|LINE|L2	-23734	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.007278	0.428779	286(AAGAACAGAATGTGTC,-,0.00),287(AGAACAGAATGTGTCT,+,0.00)
chunk0107_194_1	chr2	216200094	216200800	+	0	NA	intron (NM_021141, intron 19 of 20)	intron (NM_021141, intron 19 of 20)	-16442	NR_037701	150967	Hs.56876	NM_001199924	ENSG00000260804	LINC01963	PKI55	long intergenic non-protein coding RNA 1963	ncRNA	0.005666	0.405941	
chunk0166_196_1	chr6	46493136	46493659	+	0	NA	intron (NR_125837, intron 1 of 2)	A-rich|Low_complexity|Low_complexity	-1330	NM_001251973	10231	Hs.440168	NM_005822	ENSG00000172348	RCAN2	CSP2|DSCR1L1|MCIP2|RCN2|ZAKI-4|ZAKI4	regulator of calcineurin 2	protein-coding	0.001912	0.354962	296(AAGAACAAAATGTTAC,-,0.00)
chunk0164_10_1	chr6	17764628	17764903	+	0	NA	exon (NM_001105568, exon 37 of 38)	exon (NM_001105568, exon 37 of 38)	-57931	NM_001278210	9972	Hs.601591	NM_005124	ENSG00000124789	NUP153	HNUP153|N153	nucleoporin 153	protein-coding	0.014545	0.500000	
chunk0033_229_1	chr11	17531597	17532029	+	0	NA	intron (NR_123738, intron 2 of 19)	intron (NR_123738, intron 2 of 19)	12603	NM_001297764	10083	Hs.502072	NM_005709	ENSG00000006611	USH1C	AIE-75|DFNB18|DFNB18A|NY-CO-37|NY-CO-38|PDZ-45|PDZ-73|PDZ-73/NY-CO-38|PDZ73|PDZD7C|ush1cpst	USH1 protein network component harmonin	protein-coding	0.013889	0.501155	
chunk0022_92_1	chr10	9542558	9542884	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-247128	NR_120635	101928272	Hs.650697	NR_120635		LOC101928272	-	uncharacterized LOC101928272	ncRNA	0.009202	0.345566	
chunk0020_32_1	chr1	232059837	232060095	+	0	NA	Intergenic	Intergenic	134132	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.015504	0.544402	
chunk0204_237_1	chr9	97922144	97922452	+	0	NA	intron (NM_016481, intron 1 of 4)	CpG	272	NM_016481	51531	Hs.9196	NM_016481	ENSG00000136932	TRMO	C9orf156|HSPC219|NAP1	tRNA methyltransferase O	protein-coding	0.084416	0.582524	
chunk0098_426_1	chr2	81165634	81166105	+	0	NA	Intergenic	Intergenic	301077	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.292373	
chunk0087_159_1	chr18	34765603	34766154	+	0	NA	intron (NM_032975, intron 3 of 21)	intron (NM_032975, intron 3 of 21)	9902	NM_001391	1837	Hs.643454	NM_001390	ENSG00000134769	DTNA	D18S892E|DRP3|DTN|DTN-A|LVNC1	dystrobrevin alpha	protein-coding	0.007260	0.356884	
chunk0157_442_1	chr5	124886467	124887101	+	0	NA	Intergenic	Intergenic	-141672	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.004732	0.348031	
chunk0195_140_1	chr8	95126987	95127795	+	0	NA	Intergenic	Intergenic	-6330	NM_024613	79666	Hs.29724	NM_024613	ENSG00000175895	PLEKHF2	EAPF|PHAFIN2|ZFYVE18	pleckstrin homology and FYVE domain containing 2	protein-coding	0.004950	0.377009	495(GGGAACATCTTGTCTT,-,0.00)
chunk0127_23_1	chr3	88340631	88341241	+	0	NA	Intergenic	Intergenic	-191070	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.001639	0.281506	
chunk0033_308_1	chr11	20450926	20451375	+	0	NA	intron (NM_001145166, intron 8 of 13)	intron (NM_001145166, intron 8 of 13)	63620	NM_005788	10196	Hs.152337	NM_005788	ENSG00000185238	PRMT3	HRMT1L3	protein arginine methyltransferase 3	protein-coding	0.004454	0.364444	
chunk0019_45_1	chr1	224106909	224107198	+	0	NA	Intergenic	LTR41|LTR|ERVL	-7034	NM_015176	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.006920	0.362069	
chunk0136_142_1	chr4	4507103	4507309	+	0	NA	intron (NM_016930, intron 1 of 10)	Tigger5|DNA|TcMar-Tigger	-25506	NR_126434	104472519	Hs.691848	NR_126434	ENSG00000248221	STX18-IT1	-	STX18 intronic transcript 1	ncRNA	0.019417	0.497585	
chunk0092_418_1	chr19	37969606	37970153	+	0	NA	intron (NM_015073, intron 1 of 21)	L2c|LINE|L2	62658	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.012797	0.421533	
chunk0133_212_1	chr3	170949149	170949753	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-40814	NM_020390	56648	Hs.164144	NM_020390	ENSG00000163577	EIF5A2	EIF-5A2|eIF5AII	eukaryotic translation initiation factor 5A2	protein-coding	0.006623	0.366942	
chunk0190_448_1	chr8	42010044	42010674	+	0	NA	intron (NM_001305878, intron 2 of 13)	intron (NM_001305878, intron 2 of 13)	41667	NM_001305878	7994	Hs.491577	NM_006766	ENSG00000083168	KAT6A	MOZ|MRD32|MYST-3|MYST3|RUNXBP2|ZC2HC6A|ZNF220	lysine acetyltransferase 6A	protein-coding	0.014286	0.467512	
chunk0137_58_1	chr4	11730628	11730844	+	0	NA	Intergenic	Intergenic	-301823	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.000000	0.433180	
chunk0039_57_1	chr11	96235085	96235470	+	0	NA	intron (NM_032427, intron 1 of 4)	MER58A|DNA|hAT-Charlie	-106161	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.002597	0.411917	
chunk0212_429_1	chrX	153592729	153593454	+	0	NA	intron (NM_152274, intron 3 of 4)	intron (NM_152274, intron 3 of 4)	6086	NM_001130997	92002	Hs.496943	NM_152274	ENSG00000262919	CCNQ	FAM58A	cyclin Q	protein-coding	0.015172	0.589532	426(GGGCACATGCTGTCCT,-,0.00),427(GGCACATGCTGTCCTC,+,0.00)
chunk0147_162_1	chr4	175909855	175910346	+	0	NA	intron (NR_048571, intron 1 of 5)	MER63A|DNA|hAT-Blackjack	92591	NM_005277	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.002037	0.388211	
chunk0050_430_1	chr12	110199765	110200003	+	0	NA	intron (NM_001143779, intron 14 of 18)	intron (NM_001143779, intron 14 of 18)	75549	NM_031473	28981	Hs.528382	NM_014055	ENSG00000122970	IFT81	CDV-1|CDV-1R|CDV1|CDV1R|DV1|SRTD19	intraflagellar transport 81	protein-coding	0.012605	0.439331	
chunk0086_181_1	chr18	21972310	21972949	+	0	NA	Intergenic	Intergenic	-141223	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.014085	0.481250	200(AGGGCCACCGTGTCCT,-,0.00),201(GGGCCACCGTGTCCTC,+,0.00)
chunk0001_101_1	chr1	3359711	3359911	+	0	NA	intron (NM_022114, intron 3 of 16)	intron (NM_022114, intron 3 of 16)	-94772	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.055000	0.567164	
chunk0014_329_1	chr1	182066249	182066782	+	0	NA	Intergenic	Intergenic	-4803	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.001876	0.436330	
chunk0114_312_1	chr21	17161196	17161822	+	0	NA	Intergenic	Intergenic	-277381	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.001597	0.427432	378(AAGCACATTTTGTACA,-,0.00)
chunk0029_83_1	chr10	96863780	96864748	+	0	NA	intron (NM_032440, intron 2 of 7)	intron (NM_032440, intron 2 of 7)	31309	NM_032440	84458	Hs.427927	NM_015652	ENSG00000196233	LCOR	C10orf12|MLR2	ligand dependent nuclear receptor corepressor	protein-coding	0.004132	0.355005	721(AAGCAGACTCTGTTCC,-,0.00),722(AGCAGACTCTGTTCCT,+,0.00)
chunk0210_442_1	chrX	104165745	104166171	+	0	NA	promoter-TSS (NM_207318)	promoter-TSS (NM_207318)	-517	NM_207318	139231	Hs.496535	NM_207318	ENSG00000123575	FAM199X	CXorf39	family with sequence similarity 199, X-linked	protein-coding	0.023474	0.498829	
chunk0097_3_1	chr2	41052595	41053338	+	0	NA	Intergenic	Intergenic	-540531	NM_001112802	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.002692	0.364247	
chunk0014_208_1	chr1	179229950	179230149	+	0	NA	promoter-TSS (NM_001136001)	promoter-TSS (NM_001136001)	-365	NM_007314	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.055276	0.590000	
chunk0092_168_1	chr19	29905008	29905732	+	0	NA	Intergenic	L1ME3G|LINE|L1	-18274	NM_001252641	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.002762	0.333793	
chunk0178_215_1	chr7	35552702	35553161	+	0	NA	Intergenic	L2c|LINE|L2	142231	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.004357	0.413043	
chunk0121_229_1	chr3	21901629	21901828	+	0	NA	Intergenic	Intergenic	-55411	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.015075	0.355000	
chunk0105_256_1	chr2	189060014	189060787	+	0	NA	intron (NM_000393, intron 31 of 53)	intron (NM_000393, intron 31 of 53)	64770	NR_037401	100500837		NR_037401	ENSG00000284180	MIR3606	mir-3606	microRNA 3606	ncRNA	0.001294	0.365633	
chunk0066_130_1	chr15	31099151	31099908	+	0	NA	intron (NM_001252024, intron 1 of 27)	intron (NM_001252024, intron 1 of 27)	2197	NM_001252024	4308	Hs.155942	NM_002420	ENSG00000134160	TRPM1	CSNB1C|LTRPC1|MLSN1	transient receptor potential cation channel subfamily M member 1	protein-coding	0.003963	0.403694	
chunk0039_134_1	chr11	98444903	98445174	+	0	NA	Intergenic	L2|LINE|L2	-575938	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.007380	0.360294	
chunk0069_195_1	chr15	63340700	63341259	+	0	NA	intron (NM_206925, intron 5 of 9)	intron (NM_206925, intron 5 of 9)	41131	NM_206925	771	Hs.210995	NM_001218	ENSG00000074410	CA12	CA-XII|CAXII|HsT18816|T18816	carbonic anhydrase 12	protein-coding	0.008945	0.458929	
chunk0188_265_1	chr8	14801408	14801615	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	51999	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.009662	0.312500	
chunk0168_367_1	chr6	93477892	93478375	+	0	NA	Intergenic	MIR3|SINE|MIR	-58551	NM_001288629	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.004141	0.326446	
chunk0121_308_1	chr3	24139868	24140595	+	0	NA	intron (NM_000461, intron 7 of 9)	intron (NM_000461, intron 7 of 9)	-11093	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.004127	0.383242	368(TGGAACTGTATGTTCA,-,0.00),369(GGAACTGTATGTTCAG,+,0.00)
chunk0051_392_1	chr12	121931531	121932155	+	0	NA	exon (NM_144668, exon 4 of 22)	exon (NM_144668, exon 4 of 22)	13286	NM_001178003	144406	Hs.709837	NM_144668	ENSG00000158023	WDR66	CFAP251|CaM-IP4|SPGF33	WD repeat domain 66	protein-coding	0.022436	0.444800	
chunk0040_181_1	chr11	114059377	114059791	+	0	NA	promoter-TSS (NM_001018011)	promoter-TSS (NM_001018011)	-125	NM_006006	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.111111	0.737349	
chunk0021_212_1	chr10	5971450	5972060	+	0	NA	intron (NM_001256765, intron 1 of 7)	intron (NM_001256765, intron 1 of 7)	5856	NM_172200	3601	Hs.445124	NM_002189	ENSG00000134470	IL15RA	CD215	interleukin 15 receptor subunit alpha	protein-coding	0.016393	0.476268	329(AAGTACAGACTGTCTC,-,0.00),330(AGTACAGACTGTCTCC,+,0.00)
chunk0109_373_1	chr2	239365567	239365766	+	0	NA	intron (NM_006037, intron 1 of 26)	intron (NM_006037, intron 1 of 26)	-13862	NR_039948	100616360		NR_039948	ENSG00000264292	MIR2467	mir-2467	microRNA 2467	ncRNA	0.025126	0.605000	
chunk0007_383_1	chr1	85313707	85314361	+	0	NA	Intergenic	Intergenic	-37130	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.004587	0.409160	
chunk0168_245_1	chr6	88490540	88491193	+	0	NA	Intergenic	Intergenic	48503	NR_110867	101928936	Hs.533080	NR_110867		LOC101928936	-	uncharacterized LOC101928936	ncRNA	0.007657	0.428135	
chunk0047_429_1	chr12	76264661	76264981	+	0	NA	Intergenic	Tigger4|DNA|TcMar-Tigger	83621	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.000000	0.373832	
chunk0081_75_1	chr17	39199991	39200459	+	0	NA	promoter-TSS (NM_000981)	promoter-TSS (NM_000981)	-58	NM_000981	6143	Hs.381061	NM_000981	ENSG00000108298	RPL19	L19	ribosomal protein L19	protein-coding	0.057692	0.530917	
chunk0073_230_1	chr16	11258936	11259296	+	0	NA	Intergenic	Intergenic	-2934	NM_003745	8651	Hs.50640	NM_003745	ENSG00000185338	SOCS1	CIS1|CISH1|JAB|SOCS-1|SSI-1|SSI1|TIP-3|TIP3	suppressor of cytokine signaling 1	protein-coding	0.013889	0.573407	
chunk0013_70_1	chr1	167417578	167418094	+	0	NA	non-coding (NR_037163, exon 17 of 17)	non-coding (NR_037163, exon 17 of 17)	88792	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.003876	0.382979	
chunk0198_21_1	chr8	128067809	128068127	+	0	NA	intron (NR_003367, intron 5 of 8)	intron (NR_003367, intron 5 of 8)	18816	NR_031612	100302175		NR_031612	ENSG00000221176	MIR1207	MIRN1207|hsa-mir-1207	microRNA 1207	ncRNA	0.000000	0.394984	
chunk0163_339_1	chr6	15411009	15411355	+	0	NA	intron (NM_001267040, intron 3 of 17)	intron (NM_001267040, intron 3 of 17)	162327	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.005780	0.342939	
chunk0191_243_1	chr8	53051785	53052099	+	0	NA	Intergenic	L1PA15|LINE|L1	112034	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.003185	0.536508	
chunk0147_412_1	chr4	186952086	186952587	+	0	NA	Intergenic	MIRb|SINE|MIR	-228503	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.001996	0.378486	
chunk0195_52_1	chr8	93588031	93588534	+	0	NA	intron (NR_033858, intron 5 of 10)	L2a|LINE|L2	112151	NR_033858	642924	Hs.434882	NR_033858	ENSG00000246662	LINC00535	-	long intergenic non-protein coding RNA 535	ncRNA	0.009940	0.446429	
chunk0202_232_1	chr9	76504954	76505399	+	0	NA	3' UTR (NM_001490, exon 4 of 4)	3' UTR (NM_001490, exon 4 of 4)	4543	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.004494	0.329596	
chunk0003_463_1	chr1	41823282	41823653	+	0	NA	intron (NM_024503, intron 1 of 8)	MIRb|SINE|MIR	95240	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.005391	0.491935	
chunk0196_101_1	chr8	103048825	103049358	+	0	NA	intron (NM_001695, intron 4 of 12)	intron (NM_001695, intron 4 of 12)	28071	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.000000	0.325843	291(AGGTACATCCTGTTCC,-,0.00),292(GGTACATCCTGTTCCC,+,0.00)
chunk0010_265_1	chr1	116931552	116931853	+	0	NA	intron (NM_020440, intron 1 of 8)	intron (NM_020440, intron 1 of 8)	21779	NM_020440	5738	Hs.418093	NM_020440	ENSG00000134247	PTGFRN	CD315|CD9P-1|EWI-F|FPRP|SMAP-6	prostaglandin F2 receptor inhibitor	protein-coding	0.003322	0.427152	
chunk0063_297_1	chr14	84578920	84579258	+	0	NA	Intergenic	LTR27D|LTR|ERV1	-814790	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005917	0.498525	
chunk0031_133_1	chr10	124926420	124926966	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-15430	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.014652	0.385740	82(CTGTACATCTTGTCCC,-,0.00)
chunk0168_80_1	chr6	79788833	79789476	+	0	NA	Intergenic	Intergenic	23092	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.004666	0.374224	273(CAGAACATCCTGGACC,-,0.00),274(AGAACATCCTGGACCT,+,0.00)
chunk0124_56_1	chr3	52829749	52830650	+	0	NA	intron (NM_001166449, intron 1 of 21)	MIR|SINE|MIR	502	NM_001166449	3700	Hs.709406	NM_002218	ENSG00000055955	ITIH4	GP120|H4P|IHRP|ITI-HC4|ITIHL1|PK-120|PK120	inter-alpha-trypsin inhibitor heavy chain 4	protein-coding	0.023307	0.527716	
chunk0075_229_1	chr16	52924776	52925272	+	0	NA	Intergenic	L1MEd|LINE|L1	-130009	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.000000	0.323944	
chunk0104_144_1	chr2	173589465	173590140	+	0	NA	Intergenic	MIR|SINE|MIR	234969	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.008889	0.415680	
chunk0206_418_1	chr9	127540451	127540982	+	0	NA	intron (NM_001035534, intron 1 of 13)	intron (NM_001035534, intron 1 of 13)	28401	NM_022833	64855	Hs.522401	NM_022833	ENSG00000136830	NIBAN2	C9orf88|FAM129B|MEG-3|MINERVA|OC58|bA356B19.6	niban apoptosis regulator 2	protein-coding	0.037665	0.610902	
chunk0143_109_1	chr4	108769371	108769734	+	0	NA	Intergenic	L2a|LINE|L2	-6473	NM_001146627	64850	Hs.106576	NM_031279	ENSG00000164089	ETNPPL	AGXT2L1	ethanolamine-phosphate phospho-lyase	protein-coding	0.005510	0.412088	
chunk0166_358_1	chr6	51416090	51416575	+	0	NA	Intergenic	Intergenic	-205538	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.002062	0.427984	
chunk0122_145_1	chr3	31978684	31978965	+	0	NA	intron (NM_017784, intron 1 of 11)	intron (NM_017784, intron 1 of 11)	-2950	NM_001137674	344787	Hs.585139	NM_001137674	ENSG00000197385	ZNF860	-	zinc finger protein 860	protein-coding	0.003559	0.368794	
chunk0160_154_1	chr5	151679398	151679790	+	0	NA	intron (NR_109873, intron 2 of 4)	intron (NR_109873, intron 2 of 4)	2649	NR_109873	101927096	Hs.571023	NR_109873	ENSG00000249035	CLMAT3	CTB-113P19.1|SPARC-AS1	colorectal liver metastasis associated transcript 3	ncRNA	0.012755	0.549618	
chunk0101_374_1	chr2	138275797	138276003	+	0	NA	Intergenic	Intergenic	-225880	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.009709	0.304348	
chunk0110_303_1	chr20	18005857	18006537	+	0	NA	Intergenic	Intergenic	-37206	NM_001282454	27131	Hs.316890	NM_014426	ENSG00000089006	SNX5	-	sorting nexin 5	protein-coding	0.019118	0.477239	416(CAGAACAGCGTGTGCC,-,0.00),417(AGAACAGCGTGTGCCC,+,0.00)
chunk0098_194_1	chr2	72274495	72275001	+	0	NA	intron (NM_015189, intron 20 of 21)	intron (NM_015189, intron 20 of 21)	-126886	NM_001277742	56603	Hs.91546	NM_019885	ENSG00000003137	CYP26B1	CYP26A2|P450RAI-2|P450RAI2|RHFCA	cytochrome P450 family 26 subfamily B member 1	protein-coding	0.009881	0.347140	
chunk0054_93_1	chr13	42584913	42585184	+	0	NA	intron (NM_003701, intron 2 of 4)	intron (NM_003701, intron 2 of 4)	10893	NM_003701	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.007380	0.378676	
chunk0139_420_1	chr4	64115087	64115435	+	0	NA	Intergenic	Intergenic	294199	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.014368	0.303725	
chunk0175_212_1	chr7	6050993	6051192	+	0	NA	intron (NM_001134335, intron 2 of 14)	intron (NM_001134335, intron 2 of 14)	8137	NM_014413	27102	Hs.520205	NM_014413	ENSG00000086232	EIF2AK1	HCR|HRI	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.015075	0.385000	
chunk0165_320_1	chr6	37128081	37128512	+	0	NA	Intergenic	L2c|LINE|L2	-41850	NM_002648	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.004640	0.479167	
chunk0185_262_1	chr7	130417210	130417520	+	0	NA	intron (NM_018718, intron 2 of 10)	intron (NM_018718, intron 2 of 10)	23845	NM_001257158	95681	Hs.368315	NM_018718	ENSG00000106477	CEP41	JBTS15|TSGA14	centrosomal protein 41	protein-coding	0.016129	0.443730	
chunk0127_85_1	chr3	89683782	89684047	+	0	NA	Intergenic	Intergenic	576390	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.007547	0.315789	
chunk0083_395_1	chr17	71681674	71681873	+	0	NA	Intergenic	Intergenic	344206	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.005025	0.420000	
chunk0190_380_1	chr8	40041503	40042169	+	0	NA	Intergenic	Intergenic	106881	NM_194294	169355	Hs.676257	NM_194294	ENSG00000188676	IDO2	INDOL1	indoleamine 2,3-dioxygenase 2	protein-coding	0.015015	0.457271	
chunk0075_308_1	chr16	54422071	54422716	+	0	NA	Intergenic	Intergenic	-135927	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.007752	0.527864	
chunk0166_424_1	chr6	52617107	52617472	+	0	NA	Intergenic	Intergenic	39991	NR_103447	401264	Hs.544586	NR_103446	ENSG00000225791	TRAM2-AS1	-	TRAM2 antisense RNA 1 (head to head)	ncRNA	0.010959	0.415301	
chunk0107_426_1	chr2	224775775	224775974	+	0	NA	intron (NM_014689, intron 51 of 55)	intron (NM_014689, intron 51 of 55)	171191	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.005025	0.360000	
chunk0088_303_1	chr18	50216309	50216648	+	0	NA	Intergenic	MamRep1879|DNA|hAT-Tip100?	-21397	NM_001080467	4645	Hs.720076	NM_001080467	ENSG00000167306	MYO5B	-	myosin VB	protein-coding	0.011799	0.423529	
chunk0072_154_1	chr15	92840383	92840605	+	0	NA	Intergenic	MIRb|SINE|MIR	-42349	NR_037600	100507217	Hs.622504	NR_037600		LINC01578	-	long intergenic non-protein coding RNA 1578	ncRNA	0.009009	0.520179	
chunk0135_296_1	chr3	189628317	189628556	+	0	NA	Intergenic	Intergenic	-2991	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.004184	0.412500	145(AAGAACAAAGTGTCCC,-,0.00),146(AGAACAAAGTGTCCCT,+,0.00)
chunk0192_289_1	chr8	66462595	66462820	+	0	NA	intron (NM_144650, intron 13 of 13)	intron (NM_144650, intron 13 of 13)	30224	NM_144650	137872	Hs.720023	NM_144650	ENSG00000147576	ADHFE1	ADH8|HMFT2263|HOT	alcohol dehydrogenase iron containing 1	protein-coding	0.004444	0.438053	
chunk0076_197_1	chr16	67940122	67940483	+	0	NA	exon (NM_000229, exon 6 of 6)	exon (NM_000229, exon 6 of 6)	-3425	NM_002801	5699	Hs.9661	NM_002801	ENSG00000205220	PSMB10	LMP10|MECL1|beta2i	proteasome subunit beta 10	protein-coding	0.038781	0.582873	
chunk0041_60_1	chr11	123321750	123322016	+	0	NA	Intergenic	Intergenic	59629	NR_039714	100616319		NR_039714	ENSG00000265357	MIR4493	-	microRNA 4493	ncRNA	0.007519	0.475655	
chunk0091_207_1	chr19	9431288	9431487	+	0	NA	intron (NM_001271314, intron 4 of 10)	LTR41B|LTR|ERVL	4191	NM_001271314	10781	Hs.656185	NM_006631	ENSG00000174652	ZNF266	HZF1	zinc finger protein 266	protein-coding	0.025126	0.565000	
chunk0106_98_1	chr2	197229431	197229972	+	0	NA	intron (NM_001195144, intron 1 of 27)	MIR|SINE|MIR	72818	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.001848	0.359779	
chunk0101_232_1	chr2	131141655	131141978	+	0	NA	intron (NM_001309451, intron 6 of 6)	MER6A|DNA|TcMar-Tigger	36969	NM_001267067	55041	Hs.469944	NM_017958	ENSG00000115762	PLEKHB2	EVT2	pleckstrin homology domain containing B2	protein-coding	0.000000	0.296296	
chunk0025_291_1	chr10	56823856	56824055	+	0	NA	Intergenic	L1PB4|LINE|L1	-462682	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.520000	
chunk0045_404_1	chr12	52896226	52896593	+	0	NA	TTS (NM_001256282)	TTS (NM_001256282)	8675	NM_002273	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.002725	0.532609	
chunk0165_242_1	chr6	35623379	35623602	+	0	NA	intron (NM_001145777, intron 3 of 6)	L1ME4b|LINE|L1	41299	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.004484	0.325893	
chunk0045_259_1	chr12	49460961	49461462	+	0	NA	intron (NM_001293286, intron 2 of 12)	intron (NM_001293286, intron 2 of 12)	72037	NR_033267	100335030	Hs.687044	NR_033267		LOC100335030	-	FGFR1 oncogene partner 2 pseudogene	pseudo	0.007984	0.334661	
chunk0055_311_1	chr13	66809578	66809815	+	0	NA	intron (NM_020403, intron 2 of 3)	L2c|LINE|L2	-15473	NR_046527	100874064	Hs.569284	NR_046527	ENSG00000228842	PCDH9-AS2	-	PCDH9 antisense RNA 2	ncRNA	0.000000	0.348739	
chunk0199_244_1	chr9	5620311	5620859	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-8534	NM_001206557	57589	Hs.211520	NM_020829	ENSG00000107036	RIC1	CIP150|KIAA1432|bA207C16.1	RIC1 homolog, RAB6A GEF complex partner 1	protein-coding	0.007299	0.391621	
chunk0029_25_1	chr10	95693870	95694264	+	0	NA	promoter-TSS (NM_001143973)	promoter-TSS (NM_001143973)	76	NM_001143973	26123	Hs.438991	NM_015631	ENSG00000119977	TCTN3	C10orf61|JBTS18|OFD4|TECT3	tectonic family member 3	protein-coding	0.093909	0.643038	
chunk0209_231_1	chrX	45202944	45203333	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-2237	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.000000	0.369231	254(GAGCACATCTTGTTCT,-,0.00),255(AGCACATCTTGTTCTG,+,0.00)
chunk0190_442_1	chr8	41630643	41631171	+	0	NA	Intergenic	Intergenic	16452	NM_152568	157848		NM_152568	ENSG00000165066	NKX6-3	NKX6.3	NK6 homeobox 3	protein-coding	0.030303	0.551985	
chunk0032_314_1	chr11	9910150	9910453	+	0	NA	intron (NM_030962, intron 16 of 39)	Tigger3b|DNA|TcMar-Tigger	71159	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.000000	0.328947	
chunk0093_259_1	chr19	51070851	51071585	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-6108	NM_015596	26085	Hs.165296	NM_015596	ENSG00000167759	KLK13	KLK-L4|KLKL4	kallikrein related peptidase 13	protein-coding	0.010899	0.402721	
chunk0133_218_1	chr3	171133854	171134170	+	0	NA	intron (NM_001161560, intron 15 of 31)	intron (NM_001161560, intron 15 of 31)	-27253	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.003165	0.372240	
chunk0059_269_1	chr14	35336690	35336984	+	0	NA	Intergenic	Intergenic	44520	NM_001282232	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.034014	0.637288	
chunk0126_337_1	chr3	82103316	82103605	+	0	NA	Intergenic	L1ME1|LINE|L1	-341661	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.344828	
chunk0033_302_1	chr11	20070290	20070900	+	0	NA	intron (NM_001244963, intron 24 of 39)	intron (NM_001244963, intron 24 of 39)	-21292	NR_046672	100874014	Hs.557916	NR_046672	ENSG00000254453	NAV2-AS2	-	NAV2 antisense RNA 2	ncRNA	0.008197	0.423895	
chunk0038_456_1	chr11	94835071	94835342	+	0	NA	intron (NM_130847, intron 6 of 12)	intron (NM_130847, intron 6 of 12)	66864	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.003690	0.408088	
chunk0130_344_1	chr3	138718435	138719060	+	0	NA	intron (NM_006219, intron 6 of 21)	L1PA14|LINE|L1	-11126	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.006400	0.372204	
chunk0119_137_1	chr22	42944352	42944852	+	0	NA	intron (NM_001184970, intron 1 of 10)	L1ME4c|LINE|L1	2439	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.016000	0.399202	242(TGGACAAAATGTTCAT,+,0.00)
chunk0192_429_1	chr8	69639283	69639778	+	0	NA	intron (NR_132437, intron 14 of 16)	intron (NR_132437, intron 14 of 16)	46630	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.006061	0.457661	
chunk0037_270_1	chr11	75714975	75715380	+	0	NA	Intergenic	L1MC|LINE|L1	-2712	NM_025098	80168	Hs.288568	NM_025098	ENSG00000166391	MOGAT2	DGAT2L5|DGAT2L5.|MGAT2|hDC5	monoacylglycerol O-acyltransferase 2	protein-coding	0.027160	0.475369	
chunk0010_38_1	chr1	112674016	112674464	+	0	NA	promoter-TSS (NM_020963)	promoter-TSS (NM_020963)	-72	NM_001286072	4343	Hs.514941	NM_020963	ENSG00000155363	MOV10	fSAP113|gb110	Mov10 RISC complex RNA helicase	protein-coding	0.037946	0.507795	
chunk0009_267_1	chr1	107473844	107474716	+	0	NA	intron (NM_001312688, intron 7 of 7)	intron (NM_001312688, intron 7 of 7)	214224	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002294	0.359679	
chunk0012_98_1	chr1	156457037	156457556	+	0	NA	Intergenic	CpG	-27904	NM_006365	10485	Hs.380027	NM_006365	ENSG00000125462	C1orf61	CROC4	chromosome 1 open reading frame 61	protein-coding	0.069364	0.598077	
chunk0128_451_1	chr3	115234663	115234902	+	0	NA	Intergenic	Intergenic	-87502	NM_015642	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.008368	0.412500	
chunk0046_6_1	chr12	54016417	54017063	+	0	NA	promoter-TSS (NM_153693)	promoter-TSS (NM_153693)	-112	NR_003084	3222	Hs.549040	NM_018953	ENSG00000172789	HOXC5	CP11|HOX3|HOX3D	homeobox C5	protein-coding	0.041796	0.514683	
chunk0014_202_1	chr1	179125634	179126166	+	0	NA	intron (NM_007314, intron 4 of 11)	intron (NM_007314, intron 4 of 11)	17189	NM_001168239	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.005639	0.348968	
chunk0107_286_1	chr2	218326231	218326709	+	0	NA	non-coding (NR_125777, exon 4 of 4)	non-coding (NR_125777, exon 4 of 4)	3291	NM_022572	25953	Hs.98475	NM_015488	ENSG00000127838	PNKD	BRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|TAHCCP2	PNKD metallo-beta-lactamase domain containing	protein-coding	0.004184	0.459290	
chunk0166_284_1	chr6	48378775	48379348	+	0	NA	Intergenic	Intergenic	-310372	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.000000	0.337979	
chunk0122_443_1	chr3	39383820	39384132	+	0	NA	intron (NM_017875, intron 1 of 6)	CpG	652	NM_017875	54977	Hs.369615	NM_017875	ENSG00000144659	SLC25A38	SIDBA2	solute carrier family 25 member 38	protein-coding	0.083333	0.690096	
chunk0141_157_1	chr4	81725005	81725219	+	0	NA	Intergenic	Intergenic	-253184	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.000000	0.511628	
chunk0052_9_1	chr13	19624287	19624766	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-9122	NM_017520	54737	Hs.269654	NM_017520	ENSG00000196199	MPHOSPH8	HSMPP8|TWA3|mpp8	M-phase phosphoprotein 8	protein-coding	0.006263	0.383333	
chunk0139_280_1	chr4	57063389	57063637	+	0	NA	intron (NM_001253835, intron 1 of 3)	intron (NM_001253835, intron 1 of 3)	-46249	NR_034081	255130	Hs.691061	NR_034081	ENSG00000245067	IGFBP7-AS1	-	IGFBP7 antisense RNA 1	ncRNA	0.008065	0.397590	
chunk0020_413_1	chr1	241531129	241531442	+	0	NA	promoter-TSS (NM_003679)	promoter-TSS (NM_003679)	-849	NM_003679	8564	Hs.731056	NM_003679	ENSG00000117009	KMO	dJ317G22.1	kynurenine 3-monooxygenase	protein-coding	0.009585	0.366242	
chunk0009_345_1	chr1	109392990	109393345	+	0	NA	5' UTR (NM_001205228, exon 1 of 20)	5' UTR (NM_001205228, exon 1 of 20)	190	NM_001205228	6272	Hs.485195	NM_002959	ENSG00000134243	SORT1	Gp95|LDLCQ6|NT3|NTR3	sortilin 1	protein-coding	0.019718	0.497191	122(AGGCACACTCAGTCCT,-,0.00),123(GGCACACTCAGTCCTG,+,0.00)
chunk0114_318_1	chr21	17285104	17285691	+	0	NA	Intergenic	L1PA10|LINE|L1	-153493	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.003407	0.358844	
chunk0071_27_1	chr15	79314926	79315125	+	0	NA	intron (NR_125394, intron 3 of 3)	intron (NR_125394, intron 3 of 3)	3963	NR_125394	23423	Hs.71608	NM_007364	ENSG00000166557	TMED3	C15orf22|P24B|p24g4|p24gamma4|p26	transmembrane p24 trafficking protein 3	protein-coding	0.020101	0.520000	
chunk0094_176_1	chr2	5780800	5781040	+	0	NA	Intergenic	Intergenic	88253	NM_003108	6664	Hs.432638	NM_003108	ENSG00000176887	SOX11	MRD27	SRY-box transcription factor 11	protein-coding	0.012500	0.377593	137(CAGCACAGAAAGTTCC,-,0.00),138(AGCACAGAAAGTTCCA,+,0.00)
chunk0091_346_1	chr19	14595865	14596064	+	0	NA	intron (NR_109784, intron 8 of 13)	(TGA)n|Simple_repeat|Simple_repeat	12880	NM_207390	388512	Hs.567933	NM_207390	ENSG00000187912	CLEC17A	-	C-type lectin domain containing 17A	protein-coding	0.000000	0.435000	
chunk0186_9_1	chr7	135642338	135642752	+	0	NA	intron (NM_015135, intron 38 of 42)	intron (NM_015135, intron 38 of 42)	-19928	NM_001130929	647087	Hs.200022	NM_001130929	ENSG00000243317	STMP1	C7orf73|PL-5283	short transmembrane mitochondrial protein 1	protein-coding	0.007246	0.390361	
chunk0024_389_1	chr10	44874088	44874549	+	0	NA	intron (NR_033842, intron 2 of 7)	intron (NR_033842, intron 2 of 7)	-36998	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.002169	0.426407	
chunk0097_430_1	chr2	63610595	63610896	+	0	NA	Intergenic	L1ME4b|LINE|L1	21594	NM_001199112	4190	Hs.526521	NM_005917	ENSG00000014641	MDH1	HEL-S-32|MDH-s|MDHA|MGC:1375|MOR2	malate dehydrogenase 1	protein-coding	0.009967	0.417219	148(TATAACACACTGTTCT,-,0.00),149(ATAACACACTGTTCTG,+,0.00)
chunk0055_132_1	chr13	59322112	59322362	+	0	NA	Intergenic	L3b|LINE|CR1	-690481	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004000	0.358566	
chunk0195_109_1	chr8	94693245	94693483	+	0	NA	intron (NM_001122826, intron 14 of 14)	intron (NM_001122826, intron 14 of 14)	-26511	NM_181787	286148	Hs.567828	NM_181787	ENSG00000156162	DPY19L4	-	dpy-19 like 4	protein-coding	0.008403	0.405858	
chunk0153_110_1	chr5	68544524	68544977	+	0	NA	Intergenic	Intergenic	252182	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.017660	0.433921	
chunk0113_235_1	chr20	54071231	54072056	+	0	NA	promoter-TSS (NM_001316361)	promoter-TSS (NM_001316361)	-878	NM_003657	8537	Hs.400556	NM_003657	ENSG00000064787	BCAS1	AIBC1|NABC1	breast carcinoma amplified sequence 1	protein-coding	0.008485	0.420097	
chunk0206_162_1	chr9	121732103	121732314	+	0	NA	intron (NM_032552, intron 3 of 16)	intron (NM_032552, intron 3 of 16)	-10577	NM_138709	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.018957	0.448113	
chunk0099_411_1	chr2	102198107	102198399	+	0	NA	intron (NM_003854, intron 4 of 11)	intron (NM_003854, intron 4 of 11)	11280	NM_003854	8808	Hs.659863	NM_003854	ENSG00000115598	IL1RL2	IL-1Rrp2|IL-36R|IL1R-rp2|IL1RRP2	interleukin 1 receptor like 2	protein-coding	0.013699	0.344710	
chunk0156_240_1	chr5	108644680	108645421	+	0	NA	Intergenic	Intergenic	83211	NR_046368	100652853	Hs.133009	NR_046368	ENSG00000272523	LINC01023	HP07349	long intergenic non-protein coding RNA 1023	ncRNA	0.004049	0.425876	
chunk0076_221_1	chr16	68416168	68416839	+	0	NA	intron (NM_018667, intron 1 of 8)	intron (NM_018667, intron 1 of 8)	32003	NM_018667	55512	Hs.368421	NM_018667	ENSG00000103056	SMPD3	NSMASE2	sphingomyelin phosphodiesterase 3	protein-coding	0.017884	0.534226	
chunk0143_52_1	chr4	107682116	107682824	+	0	NA	intron (NM_005443, intron 4 of 11)	Tigger17c|DNA|TcMar-Tigger	37793	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.007062	0.361072	
chunk0025_127_1	chr10	51770761	51771247	+	0	NA	intron (NM_006258, intron 3 of 17)	Tigger3a|DNA|TcMar-Tigger	-71409	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.006173	0.377823	
chunk0082_240_1	chr17	57360053	57360420	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	103223	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.010899	0.513587	
chunk0170_260_1	chr6	113836918	113837582	+	0	NA	Intergenic	Intergenic	-20085	NM_002356	4082	Hs.519909	NM_002356	ENSG00000277443	MARCKS	80K-L|MACS|PKCSL|PRKCSL	myristoylated alanine rich protein kinase C substrate	protein-coding	0.006024	0.386466	
chunk0010_206_1	chr1	116133621	116134540	+	0	NA	3' UTR (NM_152367, exon 7 of 7)	3' UTR (NM_152367, exon 7 of 7)	22325	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.010881	0.478261	257(CAACACAAAGTGTTCC,-,0.00),258(AACACAAAGTGTTCCT,+,0.00),625(CTGCTCAGTGTGTTCC,-,0.00),626(TGCTCAGTGTGTTCCT,+,0.00)
chunk0118_349_1	chr22	36027561	36028037	+	0	NA	intron (NM_001082579, intron 1 of 13)	intron (NM_001082579, intron 1 of 13)	738	NM_001082579	23543	Hs.282998	NM_014309	ENSG00000100320	RBFOX2	FOX2|Fox-2|HNRBP2|HRNBP2|RBM9|RTA|dJ106I20.3|fxh	RNA binding fox-1 homolog 2	protein-coding	0.021008	0.507338	
chunk0003_165_1	chr1	33454012	33454211	+	0	NA	Intergenic	Intergenic	-18520	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.020101	0.550000	
chunk0047_289_1	chr12	73507429	73507819	+	0	NA	Intergenic	Intergenic	348434	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.007692	0.445013	
chunk0180_210_1	chr7	66640720	66641342	+	0	NA	3' UTR (NM_153033, exon 4 of 4)	3' UTR (NM_153033, exon 4 of 4)	12150	NM_153033	154881	Hs.546627	NM_153033	ENSG00000243335	KCTD7	CLN14|EPM3	potassium channel tetramerization domain containing 7	protein-coding	0.012862	0.452648	
chunk0090_172_1	chr18	72690352	72691078	+	0	NA	Intergenic	Intergenic	-146227	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.011019	0.345254	
chunk0080_349_1	chr17	32839354	32839939	+	0	NA	intron (NM_015194, intron 1 of 21)	intron (NM_015194, intron 1 of 21)	37527	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.005128	0.397611	
chunk0188_206_1	chr8	12583704	12583906	+	0	NA	intron (NR_047662, intron 6 of 8)	intron (NR_047662, intron 6 of 8)	81806	NR_047662	729732	Hs.322761	NR_047662	ENSG00000283674	LOC729732	-	uncharacterized LOC729732	ncRNA	0.029703	0.487685	
chunk0035_393_1	chr11	56538941	56539472	+	0	NA	Intergenic	L2a|LINE|L2	4051	NM_001005245	219487	Hs.553632	NM_001005245	ENSG00000255223	OR5M11	OR11-199	olfactory receptor family 5 subfamily M member 11	protein-coding	0.001883	0.304511	
chunk0054_255_1	chr13	46260460	46260666	+	0	NA	intron (NM_001282460, intron 7 of 9)	L2b|LINE|L2	37281	NR_047493	100861554	Hs.90866	NR_047493	ENSG00000261097	LINC00563	-	long intergenic non-protein coding RNA 563	ncRNA	0.019417	0.420290	
chunk0197_124_1	chr8	119977307	119977872	+	0	NA	intron (NM_022783, intron 4 of 8)	intron (NM_022783, intron 4 of 8)	103934	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.007080	0.356890	
chunk0149_279_1	chr5	25004792	25005403	+	0	NA	Intergenic	(TGTATA)n|Simple_repeat|Simple_repeat	-164514	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.008183	0.312092	
chunk0159_188_1	chr5	140262836	140263265	+	0	NA	intron (NM_002622, intron 3 of 3)	MIRb|SINE|MIR	40054	NM_002622	5201	Hs.483564	NM_002622	ENSG00000113068	PFDN1	PDF|PFD1	prefoldin subunit 1	protein-coding	0.006993	0.402326	
chunk0134_335_1	chr3	182041302	182041725	+	0	NA	Intergenic	Intergenic	89149	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.014184	0.365566	
chunk0058_135_1	chr14	22817816	22818365	+	0	NA	intron (NM_001126106, intron 1 of 10)	intron (NM_001126106, intron 1 of 10)	1721	NM_001126106	9056	Hs.513147	NM_003982	ENSG00000155465	SLC7A7	LAT3|LPI|MOP-2|Y+LAT1|y+LAT-1	solute carrier family 7 member 7	protein-coding	0.012750	0.476364	
chunk0011_418_1	chr1	154427709	154428119	+	0	NA	intron (NM_181359, intron 1 of 8)	intron (NM_181359, intron 1 of 8)	22721	NM_000565	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.004878	0.496350	
chunk0182_319_1	chr7	98985960	98986694	+	0	NA	intron (NM_003496, intron 60 of 70)	L1MB7|LINE|L1	-26838	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.002725	0.349660	
chunk0156_322_1	chr5	111495648	111495847	+	0	NA	TTS (NM_139164)	TTS (NM_139164)	-16479	NR_040093	100505678	Hs.745061	NR_040093	ENSG00000246859	STARD4-AS1	-	STARD4 antisense RNA 1	ncRNA	0.005025	0.280000	
chunk0018_210_1	chr1	219506397	219507014	+	0	NA	Intergenic	Intergenic	331736	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.006483	0.475728	432(GGATACACTGTGTTCT,-,0.00),433(GATACACTGTGTTCTT,+,0.00)
chunk0107_30_1	chr2	210431080	210431681	+	0	NA	3' UTR (NM_006055, exon 10 of 10)	3' UTR (NM_006055, exon 10 of 10)	45325	NM_001136574	10314	Hs.13351	NM_006055	ENSG00000115365	LANCL1	GPR69A|p40	LanC like 1	protein-coding	0.009983	0.365449	
chunk0056_319_1	chr13	91079136	91079798	+	0	NA	Intergenic	Intergenic	10150	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.003021	0.343891	
chunk0194_446_1	chr8	92561902	92562482	+	0	NA	Intergenic	L1PA6|LINE|L1	93302	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.006897	0.487091	
chunk0125_88_1	chr3	64964218	64964474	+	0	NA	intron (NR_038264, intron 4 of 5)	AluSx1|SINE|Alu	-276657	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.023438	0.392996	
chunk0096_238_1	chr2	30956962	30957446	+	0	NA	intron (NR_045602, intron 5 of 15)	MIR|SINE|MIR	-149759	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.000000	0.441237	
chunk0062_260_1	chr14	71651243	71651854	+	0	NA	intron (NM_001284245, intron 5 of 20)	intron (NM_001284245, intron 5 of 20)	63977	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.003273	0.364379	
chunk0135_184_1	chr3	188164337	188164754	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	-10457	NR_036497	339929	Hs.596639	NR_036497	ENSG00000270959	LPP-AS2	MYCLo-5|MYCLo-6	LPP antisense RNA 2	ncRNA	0.004796	0.444976	
chunk0185_268_1	chr7	130659301	130660000	+	0	NA	intron (NM_012133, intron 4 of 23)	AluSc8|SINE|Alu	9108	NM_001290033	26958	Hs.6421	NM_012133	ENSG00000158623	COPG2	2-COP|gamma-2-COP	coatomer protein complex subunit gamma 2	protein-coding	0.017167	0.408571	
chunk0010_213_1	chr1	116178752	116179516	+	0	NA	Intergenic	Intergenic	67379	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.003927	0.487582	
chunk0080_251_1	chr17	30376824	30377076	+	0	NA	Intergenic	Intergenic	-1974	NM_001304	1362	Hs.446079	NM_001304	ENSG00000108582	CPD	GP180	carboxypeptidase D	protein-coding	0.011905	0.458498	
chunk0084_327_1	chr17	80773603	80774015	+	0	NA	intron (NM_020761, intron 6 of 33)	intron (NM_020761, intron 6 of 33)	31823	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.033981	0.590799	
chunk0003_415_1	chr1	40374248	40374555	+	0	NA	promoter-TSS (NM_001198978)	promoter-TSS (NM_001198978)	-232	NM_001198978	64744	Hs.15200	NM_022733	ENSG00000084070	SMAP2	SMAP1L	small ArfGAP2	protein-coding	0.052117	0.607143	
chunk0075_302_1	chr16	54326034	54326527	+	0	NA	Intergenic	Intergenic	-39814	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.010142	0.445344	285(AAGAACACGCTCTTCC,-,0.00),286(AGAACACGCTCTTCCC,+,0.00)
chunk0024_402_1	chr10	45164974	45165276	+	0	NA	intron (NR_033891, intron 2 of 7)	intron (NR_033891, intron 2 of 7)	1111	NR_036112	100422988		NR_036112	ENSG00000263476	MIR3156-1	mir-3156-1	microRNA 3156-1	ncRNA	0.003311	0.287129	
chunk0064_183_1	chr14	92698281	92698747	+	0	NA	Intergenic	L1MC3|LINE|L1	50188	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.002146	0.374732	
chunk0157_380_1	chr5	123813950	123814703	+	0	NA	Intergenic	Intergenic	268909	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.011952	0.411141	
chunk0015_14_1	chr1	184222609	184223008	+	0	NA	Intergenic	Intergenic	-164208	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.017544	0.450000	
chunk0170_79_1	chr6	109816434	109817368	+	0	NA	intron (NM_014845, intron 22 of 22)	intron (NM_014845, intron 22 of 22)	-63685	NR_106988									0.014989	0.447059	250(AGGAACTCTCTGTCCT,-,0.00),251(GGAACTCTCTGTCCTC,+,0.00)
chunk0046_349_1	chr12	62966889	62967176	+	0	NA	Intergenic	Intergenic	-32147	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.003484	0.388889	
chunk0053_151_1	chr13	30241835	30242372	+	0	NA	intron (NM_001014380, intron 4 of 10)	intron (NM_001014380, intron 4 of 10)	64951	NM_001014380	84056	Hs.243596	NM_032116	ENSG00000102781	KATNAL1	-	katanin catalytic subunit A1 like 1	protein-coding	0.007449	0.342007	304(AGGAACATTCTGTAAT,-,0.00)
chunk0105_59_1	chr2	183426378	183427091	+	0	NA	Intergenic	HAL1ME|LINE|L1	302379	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.002805	0.320728	
chunk0212_289_1	chrX	140879264	140879657	+	0	NA	Intergenic	L2c|LINE|L2	46759	NR_031725	100302169		NR_031725	ENSG00000221081	MIR320D2	MIR320D-2|MIRN320D2|hsa-mir-320d-2|mir-320d-2	microRNA 320d-2	ncRNA	0.000000	0.368020	154(CAGTGCACACTGTACT,-,0.00),155(AGTGCACACTGTACTT,+,0.00)
chunk0064_225_1	chr14	93860786	93861350	+	0	NA	Intergenic	Intergenic	-57826	NM_138344	90050	Hs.525550	NM_138344	ENSG00000140067	FAM181A	C14orf152	family with sequence similarity 181 member A	protein-coding	0.007092	0.410619	293(AAATACATTATGTCCT,-,0.00),294(AATACATTATGTCCTC,+,0.00)
chunk0099_161_1	chr2	88406917	88407116	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	45519	NM_001135649	344167	Hs.131262	NM_001135649	ENSG00000214336	FOXI3	-	forkhead box I3	protein-coding	0.000000	0.400000	167(TAGGACAATGTGTACT,-,0.00),168(AGGACAATGTGTACTA,+,0.00)
chunk0155_201_1	chr5	94903621	94904349	+	0	NA	intron (NM_024717, intron 10 of 22)	intron (NM_024717, intron 10 of 22)	177881	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.008242	0.395062	260(AAAAACAACTTGTTCC,-,0.00)
chunk0143_140_1	chr4	109873236	109873803	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	25335	NM_198506	345193	Hs.308127	NM_198506	ENSG00000183423	LRIT3	CSNB1F|FIGLER4	leucine rich repeat, Ig-like and transmembrane domains 3	protein-coding	0.008818	0.426056	
chunk0181_24_1	chr7	77834018	77834925	+	0	NA	intron (NM_001127358, intron 1 of 17)	LTR23|LTR|ERV1	-5659	NM_020432	57157	Hs.203965	NM_020432	ENSG00000006576	PHTF2	-	putative homeodomain transcription factor 2	protein-coding	0.008820	0.404185	
chunk0146_210_1	chr4	161507669	161507871	+	0	NA	intron (NM_001128428, intron 10 of 14)	intron (NM_001128428, intron 10 of 14)	-514963	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004950	0.241379	10(GAGGACATTGCGTTCC,-,0.00),11(AGGACATTGCGTTCCA,+,0.00)
chunk0004_261_1	chr1	47963384	47964167	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	33115	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.011494	0.450255	325(TGGTACATTATGTACC,-,0.00),326(GGTACATTATGTACCC,+,0.00)
chunk0188_213_1	chr8	12765506	12765938	+	0	NA	TTS (NR_015383)	TTS (NR_015383)	-10239	NM_152271	91694	Hs.180178	NM_152271	ENSG00000154359	LONRF1	RNF191	LON peptidase N-terminal domain and ring finger 1	protein-coding	0.011574	0.501155	157(TGGGACACTATGTTCC,-,0.00),158(GGGACACTATGTTCCT,+,0.00)
chunk0061_126_1	chr14	58808703	58809253	+	0	NA	Intergenic	Intergenic	-19310	NR_110547	102723742	Hs.232734	NR_110547	ENSG00000258583	LINC01500	-	long intergenic non-protein coding RNA 1500	ncRNA	0.007273	0.384755	
chunk0098_286_1	chr2	75788132	75788653	+	0	NA	Intergenic	Intergenic	-77407	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.009597	0.494253	
chunk0118_251_1	chr22	32889317	32889556	+	0	NA	intron (NM_003490, intron 3 of 12)	(A)n|Simple_repeat|Simple_repeat	88620	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.008368	0.379167	
chunk0114_131_1	chr21	9873279	9873478	+	0	NA	Intergenic	L1P4e|LINE|L1	-52317	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.020101	0.585000	
chunk0178_263_1	chr7	36390417	36390683	+	0	NA	promoter-TSS (NM_001100425)	promoter-TSS (NM_001100425)	-425	NM_001100425	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.048872	0.486891	
chunk0191_317_1	chr8	55685325	55685959	+	0	NA	Intergenic	MIRb|SINE|MIR	78338	NM_001286657	137695	Hs.420076	NM_152417	ENSG00000167904	TMEM68	-	transmembrane protein 68	protein-coding	0.006309	0.489764	
chunk0051_398_1	chr12	121969229	121969623	+	0	NA	intron (NM_144668, intron 17 of 21)	intron (NM_144668, intron 17 of 21)	50869	NM_001178003	144406	Hs.709837	NM_144668	ENSG00000158023	WDR66	CFAP251|CaM-IP4|SPGF33	WD repeat domain 66	protein-coding	0.010152	0.526582	
chunk0211_243_1	chrX	120245023	120245347	+	0	NA	promoter-TSS (NR_027131)	promoter-TSS (NR_027131)	82	NR_027131	158801	Hs.442518	NM_173522	ENSG00000233382	NKAPP1	CXorf42	NFKB activating protein pseudogene 1	pseudo	0.061728	0.569231	
chunk0062_379_1	chr14	74373062	74373403	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	24769	NM_018228	55237	Hs.578167	NM_018228	ENSG00000133980	VRTN	C14orf115|vertnin	vertebrae development associated	protein-coding	0.008798	0.333333	
chunk0121_302_1	chr3	24018914	24019454	+	0	NA	Intergenic	LTR2752|LTR|ERV1	73063	NM_001145425	9975	Hs.37288	NM_005126	ENSG00000174738	NR1D2	BD73|EAR-1R|REVERBB|REVERBbeta|RVR	nuclear receptor subfamily 1 group D member 2	protein-coding	0.031481	0.613678	
chunk0187_364_1	chr7	157384142	157384748	+	0	NA	intron (NM_058246, intron 6 of 9)	intron (NM_058246, intron 6 of 9)	47428	NM_058246	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.021452	0.474465	234(GAGGTCACTCTGTTCC,-,0.00),235(AGGTCACTCTGTTCCT,+,0.00)
chunk0140_9_1	chr4	65342674	65342910	+	0	NA	intron (NM_001281765, intron 15 of 17)	intron (NM_001281765, intron 15 of 17)	-327169	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.000000	0.316456	158(AGGCACACCCAGTACA,-,0.00)
chunk0142_3_1	chr4	89680999	89681477	+	0	NA	Intergenic	L1MEd|LINE|L1	-155163	NR_045481	644248	Hs.553954	NR_045481	ENSG00000247775	SNCA-AS1	-	SNCA antisense RNA 1	ncRNA	0.014644	0.425887	213(AGGACATTGTGTTACT,+,0.00)
chunk0078_305_1	chr17	8280950	8281186	+	0	NA	Intergenic	MER21C|LTR|ERVL	-7583	NM_001177801	29098	Hs.408233	NM_016492	ENSG00000108961	RANGRF	HSPC165|HSPC236|MOG1|RANGNRF	RAN guanine nucleotide release factor	protein-coding	0.016949	0.510549	
chunk0012_207_1	chr1	160073158	160073357	+	0	NA	Intergenic	Intergenic	-2996	NM_002241	3766	Hs.408960	NM_002241	ENSG00000177807	KCNJ10	BIRK-10|KCNJ13-PEN|KIR1.2|KIR4.1|SESAME	potassium voltage-gated channel subfamily J member 10	protein-coding	0.005025	0.420000	
chunk0106_275_1	chr2	204030962	204031247	+	0	NA	Intergenic	Intergenic	94356	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.017544	0.363636	
chunk0080_6_1	chr17	20840037	20840451	+	0	NA	Intergenic	Intergenic	-28189	NR_104185	440416	Hs.661076	NR_104185	ENSG00000233098	CCDC144NL-AS1	-	CCDC144NL antisense RNA 1	ncRNA	0.000000	0.322892	
chunk0092_162_1	chr19	29720734	29721206	+	0	NA	Intergenic	Intergenic	-5181	NM_001256047	83636	Hs.529094	NM_031448	ENSG00000131943	C19orf12	MPAN|NBIA3|NBIA4|SPG43	chromosome 19 open reading frame 12	protein-coding	0.004237	0.441860	
chunk0149_360_1	chr5	27788013	27788690	+	0	NA	Intergenic	L2b|LINE|L2	316059	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.004431	0.346608	
chunk0158_68_1	chr5	126219602	126219826	+	0	NA	Intergenic	L1PA14|LINE|L1	40137	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.000000	0.386667	
chunk0106_346_1	chr2	206749401	206749761	+	0	NA	intron (NR_104261, intron 4 of 9)	Tigger4b|DNA|TcMar-Tigger	-15807	NM_014929	22868	Hs.5930	NM_014929	ENSG00000118246	FASTKD2	KIAA0971	FAST kinase domains 2	protein-coding	0.002778	0.318560	190(AGGACCAGAGTGTTCC,-,0.00),191(GGACCAGAGTGTTCCA,+,0.00)
chunk0202_238_1	chr9	76586109	76587271	+	0	NA	Intergenic	Intergenic	86057	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.006885	0.418745	
chunk0093_341_1	chr19	54831362	54831637	+	0	NA	TTS (NM_013289).10	TTS (NM_013289).10	-1177	NM_012314	3809	Hs.654608	NM_012314	ENSG00000221957	KIR2DS4	CD158I|KIR-2DS4|KIR1D|KIR412|KKA3|NKAT-8|NKAT8	killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4	protein-coding	0.014545	0.315217	
chunk0123_435_1	chr3	50321423	50321830	+	0	NA	5' UTR (NM_033158, exon 2 of 5)	5' UTR (NM_033158, exon 2 of 5)	1224	NM_033158	8692	Hs.76873	NM_003773	ENSG00000068001	HYAL2	LUCA2	hyaluronidase 2	protein-coding	0.078624	0.683824	
chunk0147_418_1	chr4	187207911	187208479	+	0	NA	Intergenic	L2b|LINE|L2	297418	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.010563	0.423550	
chunk0085_189_1	chr18	6337304	6337632	+	0	NA	intron (NM_173464, intron 1 of 19)	L1ME3A|LINE|L1	36957	NR_036205	100422840		NR_036205	ENSG00000283532	MIR4317	-	microRNA 4317	ncRNA	0.000000	0.285714	
chunk0008_124_1	chr1	91757999	91758396	+	0	NA	intron (NR_036634, intron 5 of 17)	intron (NR_036634, intron 5 of 17)	128082	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.015113	0.432161	
chunk0209_51_1	chrX	36849362	36849924	+	0	NA	Intergenic	Intergenic	-158716	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.005338	0.412078	
chunk0094_417_1	chr2	10490855	10491175	+	0	NA	Intergenic	L2c|LINE|L2	41287	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.015625	0.545171	171(GAGTTCACAGTGTCCT,-,0.00),172(AGTTCACAGTGTCCTG,+,0.00)
chunk0020_406_1	chr1	241144582	241144812	+	0	NA	intron (NM_001282775, intron 2 of 17)	intron (NM_001282775, intron 2 of 17)	12425	NR_036069	100422856		NR_036069	ENSG00000265831	MIR3123	mir-3123	microRNA 3123	ncRNA	0.021739	0.510823	
chunk0135_55_1	chr3	185708789	185709392	+	0	NA	intron (NM_001007225, intron 2 of 14)	intron (NM_001007225, intron 2 of 14)	-4162	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.004975	0.380795	
chunk0020_163_1	chr1	234371292	234371815	+	0	NA	Intergenic	Intergenic	1850	NR_125962	101927765	Hs.596703	NR_125961	ENSG00000231663	COA6-AS1	-	COA6 antisense RNA 1	ncRNA	0.003824	0.358779	
chunk0181_292_1	chr7	86953336	86954140	+	0	NA	intron (NM_001291990, intron 2 of 21)	intron (NM_001291990, intron 2 of 21)	12237	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.003731	0.354037	450(AGAACAGAAAGACCTT,+,0.00),601(CTGCACTCACTGTTCT,-,0.00),602(TGCACTCACTGTTCTT,+,0.00)
chunk0090_264_1	chr18	74468585	74468816	+	0	NA	Intergenic	Intergenic	-11432	NM_001044369	125704	Hs.371690	NM_001044369	ENSG00000187773	DIPK1C	C18orf51|FAM69C	divergent protein kinase domain 1C	protein-coding	0.004329	0.474138	
chunk0031_12_1	chr10	121589255	121590101	+	0	NA	intron (NM_022970, intron 2 of 17)	intron (NM_022970, intron 2 of 17)	4289	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.011820	0.350649	
chunk0159_197_1	chr5	140340776	140340975	+	0	NA	intron (NM_001945, intron 3 of 5)	MIRc|SINE|MIR	5728	NM_001945	1839	Hs.799	NM_001945	ENSG00000113070	HBEGF	DTR|DTS|DTSF|HEGFL	heparin binding EGF like growth factor	protein-coding	0.000000	0.430000	
chunk0145_234_1	chr4	148503508	148504218	+	0	NA	Intergenic	Intergenic	-61343	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.002817	0.324895	
chunk0047_150_1	chr12	69703200	69703725	+	0	NA	Intergenic	Charlie22a|DNA|hAT-Charlie	-4046	NM_032735	144453	Hs.280782	NM_032735	ENSG00000127325	BEST3	VMD2L3	bestrophin 3	protein-coding	0.005714	0.477186	
chunk0113_147_1	chr20	52443069	52443421	+	0	NA	Intergenic	Intergenic	-177593	NR_110038	101927700	Hs.434465	NR_110038	ENSG00000234948	LINC01524	-	long intergenic non-protein coding RNA 1524	ncRNA	0.002841	0.317280	
chunk0001_402_1	chr1	10796780	10797242	+	0	NA	promoter-TSS (NM_017766)	promoter-TSS (NM_017766)	-335	NM_017766	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.045455	0.548596	329(AGGAACGAAATGTTCT,-,0.00),330(GGAACGAAATGTTCTC,+,0.00)
chunk0210_141_1	chrX	74669988	74670702	+	0	NA	Intergenic	Intergenic	-55719	NM_016120	51132	Hs.653288	NM_016120	ENSG00000131263	RLIM	MRX61|NY-REN-43|RNF12|TOKAS	ring finger protein, LIM domain interacting	protein-coding	0.005602	0.370629	
chunk0030_51_1	chr10	111789748	111790264	+	0	NA	Intergenic	L1MD2|LINE|L1	393773	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.001938	0.315280	
chunk0058_365_1	chr14	29037393	29037629	+	0	NA	Intergenic	Intergenic	264807	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.000000	0.396624	
chunk0143_381_1	chr4	122666581	122667276	+	0	NA	intron (NR_104126, intron 10 of 10)	intron (NR_104126, intron 10 of 10)	-45871	NM_001207006	59067	Hs.567559	NM_021803	ENSG00000138684	IL21	CVID11|IL-21|Za11	interleukin 21	protein-coding	0.002878	0.323276	352(AGGAACATTAAGTACT,-,0.00),353(GGAACATTAAGTACTT,+,0.00)
chunk0132_54_1	chr3	155082377	155082976	+	0	NA	intron (NM_007289, intron 1 of 22)	intron (NM_007289, intron 1 of 22)	2386	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.005008	0.371667	329(GGGGACAGCATGTTTA,-,0.00)
chunk0172_139_1	chr6	135378424	135378773	+	0	NA	intron (NM_017651, intron 22 of 27)	intron (NM_017651, intron 22 of 27)	119167	NM_001134831	54806	Hs.386684	NM_017651	ENSG00000135541	AHI1	AHI-1|JBTS3|ORF1|dJ71N10.1	Abelson helper integration site 1	protein-coding	0.005731	0.265714	
chunk0089_154_1	chr18	59074201	59074623	+	0	NA	Intergenic	Intergenic	38733	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.004739	0.288416	
chunk0058_247_1	chr14	25658936	25659652	+	0	NA	Intergenic	LTR80B|LTR|ERVL	-608997	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004190	0.386332	
chunk0026_446_1	chr10	71512867	71513425	+	0	NA	intron (NM_001171931, intron 6 of 24)	intron (NM_001171931, intron 6 of 24)	-1226	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.008961	0.556351	250(AAGGACACACCGTCCT,-,0.00),251(AGGACACACCGTCCTT,+,0.00)
chunk0128_158_1	chr3	107192714	107193025	+	0	NA	intron (NR_028303, intron 1 of 3)	intron (NR_028303, intron 1 of 3)	47769	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.009646	0.384615	
chunk0194_299_1	chr8	87915019	87915728	+	0	NA	Intergenic	Intergenic	-41305	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.011283	0.370423	278(CAGTACACGCTGACCT,-,0.00),279(AGTACACGCTGACCTA,+,0.00)
chunk0021_261_1	chr1	243542223	243542497	+	0	NA	intron (NM_181690, intron 11 of 13)	MIRc|SINE|MIR	196184	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.003650	0.385455	
chunk0145_372_1	chr4	151519485	151519930	+	0	NA	intron (NM_001109977, intron 3 of 13)	L1ME2z|LINE|L1	110461	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.002247	0.343049	
chunk0077_120_1	chr16	78340710	78340982	+	0	NA	intron (NM_016373, intron 5 of 8)	HAL1|LINE|L1	241433	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.000000	0.432234	
chunk0117_423_1	chr21	46068966	46069601	+	0	NA	Intergenic	(TGTG)n|Simple_repeat|Simple_repeat	-28836	NM_058174	1292	Hs.420269	NM_001849	ENSG00000142173	COL6A2	BTHLM1|PP3610|UCMD1	collagen type VI alpha 2 chain	protein-coding	0.025197	0.561321	
chunk0136_441_1	chr3	197882666	197882918	+	0	NA	Intergenic	Intergenic	67133	NM_001134435	84223	Hs.591675	NM_032263	ENSG00000114473	IQCG	CFAP122|DRC9	IQ motif containing G	protein-coding	0.007937	0.347826	
chunk0008_249_1	chr1	94415421	94415690	+	0	NA	Intergenic	LTR65|LTR|ERV1	-2822	NM_002858	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.000000	0.337037	
chunk0027_63_1	chr10	73096706	73096997	+	0	NA	5' UTR (NM_001142596, exon 1 of 14)	5' UTR (NM_001142596, exon 1 of 14)	123	NM_001142595	5033	Hs.500047	NM_000917	ENSG00000122884	P4HA1	P4HA	prolyl 4-hydroxylase subunit alpha 1	protein-coding	0.099656	0.684932	
chunk0015_192_1	chr1	187321902	187322515	+	0	NA	intron (NR_126347, intron 2 of 3)	intron (NR_126347, intron 2 of 3)	-121420	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004894	0.311075	259(TGGGACACAGTGTTCA,-,0.00),260(GGGACACAGTGTTCAA,+,0.00)
chunk0031_73_1	chr10	123034170	123034789	+	0	NA	exon (NM_001609, exon 2 of 11)	exon (NM_001609, exon 2 of 11)	25566	NM_001609	36	Hs.81934	NM_001609	ENSG00000196177	ACADSB	2-MEBCAD|ACAD7|SBCAD	acyl-CoA dehydrogenase short/branched chain	protein-coding	0.001616	0.362903	
chunk0131_266_1	chr3	150061602	150061801	+	0	NA	Intergenic	Intergenic	-78335	NM_001079809	653659	Hs.652908	NM_001079809		TMEM183B	C1ORF37DUP|C1orf37-DUP	transmembrane protein 183B	protein-coding	0.010050	0.465000	
chunk0055_362_1	chr13	71285044	71285309	+	0	NA	Intergenic	L1M1|LINE|L1	270035	NR_047699	100885781	Hs.372660	NR_047699	ENSG00000226846	LINC00348	-	long intergenic non-protein coding RNA 348	ncRNA	0.000000	0.304511	166(TGGTTCAGGATGTTCT,-,0.00),167(GGTTCAGGATGTTCTC,+,0.00)
chunk0119_245_1	chr22	45691863	45692310	+	0	NA	intron (NM_013236, intron 2 of 11)	MIRb|SINE|MIR	20288	NM_013236	25814	Hs.475125	NM_013236	ENSG00000130638	ATXN10	E46L|HUMEEP|SCA10	ataxin 10	protein-coding	0.004474	0.386161	229(ATGCACATTGTGTGCT,-,0.00),230(TGCACATTGTGTGCTC,+,0.00)
chunk0004_218_1	chr1	46806806	46807021	+	0	NA	intron (NM_000779, intron 1 of 11)	intron (NM_000779, intron 1 of 11)	7915	NM_000779	1580	Hs.436317	NM_000779	ENSG00000142973	CYP4B1	CYPIVB1|P-450HP	cytochrome P450 family 4 subfamily B member 1	protein-coding	0.013953	0.564815	26(CAGAACTTCCAGTCCT,-,0.00),27(AGAACTTCCAGTCCTG,+,0.00)
chunk0147_338_1	chr4	185457120	185457372	+	0	NA	intron (NM_152775, intron 6 of 6)	LTR40a|LTR|ERVL	14513	NM_152775	256309	Hs.41101	NM_152775	ENSG00000168491	CCDC110	CT52|KM-HN-1|KMHN1	coiled-coil domain containing 110	protein-coding	0.007937	0.418972	
chunk0123_315_1	chr3	47235193	47235461	+	0	NA	intron (NR_033373, intron 3 of 6)	intron (NR_033373, intron 3 of 6)	-47513	NM_025010	23276	Hs.517946	NM_025010	ENSG00000114648	KLHL18	-	kelch like family member 18	protein-coding	0.011194	0.561338	
chunk0162_258_1	chr6	5167295	5168302	+	0	NA	intron (NM_001164841, intron 2 of 3)	intron (NM_001164841, intron 2 of 3)	-19476	NR_037462	100500900		NR_037462	ENSG00000265083	MIR3691	mir-3691	microRNA 3691	ncRNA	0.010924	0.381944	418(ATGGACAGGAAGTCCC,-,0.00),419(TGGACAGGAAGTCCCT,+,0.00)
chunk0063_354_1	chr14	85562656	85562922	+	0	NA	intron (NM_013231, intron 1 of 1)	intron (NM_013231, intron 1 of 1)	32645	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.015038	0.389513	
chunk0017_386_1	chr1	212228636	212229300	+	0	NA	intron (NR_125984, intron 3 of 3)	intron (NR_125984, intron 3 of 3)	5768	NR_125982	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.012048	0.412030	
chunk0197_351_1	chr8	125451977	125452314	+	0	NA	Intergenic	Intergenic	19936	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.035608	0.559172	
chunk0173_400_1	chr6	150526624	150527647	+	0	NA	Intergenic	Intergenic	-72728	NM_001029884	57480	Hs.189781	NM_001029884	ENSG00000120278	PLEKHG1	ARHGEF41	pleckstrin homology and RhoGEF domain containing G1	protein-coding	0.012708	0.419922	
chunk0094_337_1	chr2	9226454	9226983	+	0	NA	intron (NM_003887, intron 1 of 27)	intron (NM_003887, intron 1 of 27)	19953	NM_003887	8853	Hs.555902	NM_003887	ENSG00000151693	ASAP2	AMAP2|CENTB3|DDEF2|PAG3|PAP|Pap-alpha|SHAG1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding	0.015123	0.547170	
chunk0107_61_1	chr2	211563068	211563398	+	0	NA	intron (NM_001042599, intron 19 of 26)	intron (NM_001042599, intron 19 of 26)	863127	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.009091	0.283988	
chunk0013_103_1	chr1	167793790	167794105	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	71997	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.003175	0.351266	
chunk0063_428_1	chr14	88584348	88584884	+	0	NA	intron (NM_207660, intron 9 of 13)	Tigger2|DNA|TcMar-Tigger	-9770	NM_207662	79882	Hs.684046	NM_024824	ENSG00000100722	ZC3H14	MRT56|MSUT-2|NY-REN-37|SUT2|UKp68	zinc finger CCCH-type containing 14	protein-coding	0.005597	0.344507	210(TAGTACATACTGTACT,-,0.00),211(AGTACATACTGTACTA,+,0.00)
chunk0040_228_1	chr11	114423787	114424294	+	0	NA	Intergenic	L1M1|LINE|L1	-15346	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.003945	0.336614	
chunk0187_57_1	chr8	1920495	1920913	+	0	NA	intron (NM_001308152, intron 17 of 27).2	intron (NM_001308152, intron 17 of 27).2	-50693	NR_126346	104266957	Hs.734498	NR_126346	ENSG00000253696	KBTBD11-OT1	-	KBTBD11 overlapping transcript 1	ncRNA	0.011962	0.400955	
chunk0180_195_1	chr7	66167951	66168477	+	0	NA	Intergenic	L1MB4|LINE|L1	-37058	NM_003596	8460	Hs.421194	NM_003596	ENSG00000169902	TPST1	TANGO13A	tyrosylprotein sulfotransferase 1	protein-coding	0.007605	0.383302	
chunk0175_261_1	chr7	7321471	7322003	+	0	NA	Intergenic	Intergenic	66583	NR_108073	101927354	Hs.520664	NR_108073		LOC101927354	-	uncharacterized LOC101927354	ncRNA	0.016917	0.478424	247(CAGCACAGAATGTGCT,-,0.00),248(AGCACAGAATGTGCTG,+,0.00)
chunk0049_196_1	chr12	93087302	93087765	+	0	NA	intron (NR_040096, intron 3 of 4)	MER110|LTR|ERV1	-86833	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.004320	0.387931	
chunk0089_58_1	chr18	58148909	58149491	+	0	NA	promoter-TSS (NM_001144969)	promoter-TSS (NM_001144969)	-133	NM_001144969	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.012027	0.469983	221(TAAAACAGAGTGTACT,-,0.00),222(AAAACAGAGTGTACTT,+,0.00)
chunk0036_171_1	chr11	62553496	62553792	+	0	NA	Intergenic	Intergenic	6662	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.027027	0.595960	
chunk0177_434_1	chr7	27936270	27937151	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	196615	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.004540	0.387755	
chunk0018_195_1	chr1	219310182	219310868	+	0	NA	Intergenic	Intergenic	135556	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.002915	0.391557	
chunk0185_211_1	chr7	128747173	128747823	+	0	NA	intron (NR_074086, intron 1 of 4)	intron (NR_074086, intron 1 of 4)	8206	NR_074086	813	Hs.7753	NM_001219	ENSG00000128595	CALU	-	calumenin	protein-coding	0.006154	0.403994	
chunk0099_118_1	chr2	85954535	85955199	+	0	NA	Intergenic	Intergenic	65587	NR_110569	101928113	Hs.625888	NR_110569		ST3GAL5-AS1	-	ST3GAL5 antisense RNA 1 (head to head)	ncRNA	0.009036	0.476692	86(CAGTACACGTTGTCCC,-,0.00),87(AGTACACGTTGTCCCC,+,0.00)
chunk0119_376_1	chr22	47736104	47736394	+	0	NA	intron (NR_122046, intron 7 of 8)	intron (NR_122046, intron 7 of 8)	104575	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.024138	0.512027	
chunk0205_119_1	chr9	107830600	107830959	+	0	NA	Intergenic	L1MA4|LINE|L1	-341059	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.005571	0.358333	
chunk0012_15_1	chr1	154877340	154877937	+	0	NA	Intergenic	Intergenic	-7360	NM_001204087	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.026801	0.550167	236(AGGAACTTGTTGTTCT,-,0.00),237(GGAACTTGTTGTTCTA,+,0.00)
chunk0119_367_1	chr22	47575392	47575791	+	0	NA	Intergenic	Intergenic	55978	NR_033377	400932	Hs.561058	NM_001001693	ENSG00000205634	LINC00898	-	long intergenic non-protein coding RNA 898	ncRNA	0.017544	0.480000	
chunk0100_28_1	chr2	105296064	105296286	+	0	NA	intron (NM_001142621, intron 4 of 11)	MIRb|SINE|MIR	33539	NM_004257	9392	Hs.446350	NM_004257	ENSG00000135966	TGFBRAP1	TRAP-1|TRAP1|VPS3	transforming growth factor beta receptor associated protein 1	protein-coding	0.013514	0.408072	
chunk0158_203_1	chr5	128085150	128085457	+	0	NA	intron (NR_046207, intron 1 of 26)	intron (NR_046207, intron 1 of 26)	1512	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.016287	0.383117	122(TGGGACACGCTGTTCC,-,0.00),123(GGGACACGCTGTTCCT,+,0.00)
chunk0148_375_1	chr5	14664662	14664979	+	0	NA	5' UTR (NM_138348, exon 1 of 7)	5' UTR (NM_138348, exon 1 of 7)	146	NM_138348	90268	Hs.406335	NM_138348	ENSG00000154124	OTULIN	AIPDS|FAM105B|GUM	OTU deubiquitinase with linear linkage specificity	protein-coding	0.160883	0.779874	
chunk0042_200_1	chr12	5871924	5872333	+	0	NA	intron (NM_001278596, intron 3 of 25)	intron (NM_001278596, intron 3 of 25)	73131	NM_001278596	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.007335	0.480488	
chunk0126_176_1	chr3	78064516	78064929	+	0	NA	Intergenic	Intergenic	954737	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002421	0.357488	
chunk0013_116_1	chr1	167931584	167931968	+	0	NA	intron (NR_026550, intron 1 of 4)	intron (NR_026550, intron 1 of 4)	4425	NR_026550	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.002604	0.254545	
chunk0141_20_1	chr4	76717847	76718492	+	0	NA	intron (NM_020859, intron 3 of 10)	intron (NM_020859, intron 3 of 10)	142618	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.004651	0.311146	
chunk0183_100_1	chr7	105202671	105202990	+	0	NA	intron (NM_001278273, intron 4 of 16)	L4_C_Mam|LINE|RTE-X	66247	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.009404	0.371875	
chunk0127_185_1	chr3	95689622	95689901	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-6568	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.007168	0.353571	
chunk0016_246_1	chr1	200049319	200049619	+	0	NA	intron (NM_205860, intron 5 of 7)	intron (NM_205860, intron 5 of 7)	6644	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.003333	0.345515	
chunk0071_453_1	chr15	90221155	90221426	+	0	NA	intron (NM_020210, intron 6 of 14)	intron (NM_020210, intron 6 of 14)	12757	NM_001277764	10519	Hs.715556	NM_006384	ENSG00000185043	CIB1	CIB|CIBP|KIP1|PRKDCIP|SIP2-28	calcium and integrin binding 1	protein-coding	0.018450	0.577206	
chunk0111_150_1	chr20	25048434	25048764	+	0	NA	intron (NM_032501, intron 1 of 13)	intron (NM_032501, intron 1 of 13)	9583	NM_001252675	84532	Hs.529353	NM_032501	ENSG00000154930	ACSS1	ACAS2L|ACECS1|AceCS2L	acyl-CoA synthetase short chain family member 1	protein-coding	0.012121	0.567976	135(AAGAACACTCAGTGCA,-,0.00),136(AGAACACTCAGTGCAA,+,0.00)
chunk0150_200_1	chr5	34900806	34901092	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	14677	NR_026591	5810	Hs.38114	NM_002853	ENSG00000113456	RAD1	HRAD1|REC1	RAD1 checkpoint DNA exonuclease	protein-coding	0.017483	0.383275	137(AGTACAGTACGTACTC,+,0.00)
chunk0003_71_1	chr1	31294851	31295259	+	0	NA	intron (NM_004814, intron 1 of 9)	L2a|LINE|L2	1742	NM_004814	9410	Hs.33962	NM_004814	ENSG00000060688	SNRNP40	40K|HPRP8BP|PRP8BP|PRPF8BP|SPF38|WDR57	small nuclear ribonucleoprotein U5 subunit 40	protein-coding	0.022059	0.476773	
chunk0127_223_1	chr3	96683633	96684102	+	0	NA	Intergenic	L1MA1|LINE|L1	-130714	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002132	0.312766	
chunk0092_332_1	chr19	35048146	35048398	+	0	NA	intron (NM_002151, intron 3 of 13)	MIR|SINE|MIR	7766	NM_182983	3249	Hs.182385	NM_002151	ENSG00000105707	HPN	TMPRSS1	hepsin	protein-coding	0.015873	0.505929	
chunk0201_86_1	chr9	34593132	34593331	+	0	NA	Intergenic	Intergenic	-3091	NM_001207011	1271	Hs.129966	NM_001842	ENSG00000122756	CNTFR	-	ciliary neurotrophic factor receptor	protein-coding	0.080402	0.755000	
chunk0149_130_1	chr5	19734983	19735346	+	0	NA	intron (NM_001167667, intron 4 of 12)	intron (NM_001167667, intron 4 of 12)	151108	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.008264	0.392857	
chunk0051_387_1	chr12	121860156	121860694	+	0	NA	intron (NM_001171993, intron 2 of 15)	intron (NM_001171993, intron 2 of 15)	-1562	NM_002150	3242	Hs.2899	NM_002150	ENSG00000158104	HPD	4-HPPD|4HPPD|GLOD3|HPPDASE|PPD	4-hydroxyphenylpyruvate dioxygenase	protein-coding	0.001859	0.539889	
chunk0158_216_1	chr5	128353310	128353815	+	0	NA	intron (NM_001999, intron 20 of 64)	intron (NM_001999, intron 20 of 64)	184480	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.000000	0.363636	
chunk0197_249_1	chr8	123405354	123406107	+	0	NA	Intergenic	L1ME4b|LINE|L1	-9265	NM_014109	29028	Hs.370834	NM_014109	ENSG00000156802	ATAD2	ANCCA|CT137|PRO2000	ATPase family AAA domain containing 2	protein-coding	0.006640	0.380637	304(CTGTACACTCTGTTCT,-,0.00),305(TGTACACTCTGTTCTG,+,0.00)
chunk0146_195_1	chr4	161288055	161288268	+	0	NA	Intergenic	L1MC1|LINE|L1	-734572	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004695	0.373832	
chunk0190_49_1	chr8	29401343	29402216	+	0	NA	Intergenic	(C)n|Simple_repeat|Simple_repeat	-51029	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.016037	0.438215	214(CGGACCACTGTGTCCT,-,0.00),215(GGACCACTGTGTCCTT,+,0.00),322(AGGTACAAGAAGTTCC,-,0.00),323(GGTACAAGAAGTTCCC,+,0.00)
chunk0126_417_1	chr3	85803568	85804288	+	0	NA	intron (NM_153184, intron 2 of 9)	intron (NM_153184, intron 2 of 9)	24122	NR_046752	100874037	Hs.570566	NR_046752	ENSG00000241648	CADM2-AS2	-	CADM2 antisense RNA 2	ncRNA	0.002778	0.320388	
chunk0086_228_1	chr18	22773947	22774513	+	0	NA	intron (NR_110782, intron 1 of 1)	intron (NR_110782, intron 1 of 1)	12607	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.007067	0.365079	
chunk0187_134_1	chr7	149271723	149271939	+	0	NA	intron (NM_001195220, intron 4 of 5)	L1MC5|LINE|L1	9660	NM_001195220	100289678	Hs.490512	NM_001195220	ENSG00000204946	ZNF783	-	zinc finger family member 783	protein-coding	0.000000	0.345622	
chunk0029_175_1	chr10	100636491	100636963	+	0	NA	Intergenic	MIR|SINE|MIR	-98982	NM_001304569	5076	Hs.155644	NM_000278	ENSG00000075891	PAX2	FSGS7|PAPRS	paired box 2	protein-coding	0.012712	0.414376	
chunk0085_250_1	chr18	7492331	7492858	+	0	NA	Intergenic	MIRb|SINE|MIR	-74722	NM_001105244	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.007590	0.397727	
chunk0041_423_1	chr11	134283909	134284108	+	0	NA	intron (NM_001080407, intron 6 of 19)	intron (NM_001080407, intron 6 of 19)	7627	NM_001080407	112937	Hs.721382	NM_138416	ENSG00000166105	GLB1L3	-	galactosidase beta 1 like 3	protein-coding	0.005025	0.485000	166(AGGGACTGGTTGTCCA,-,0.00),167(GGGACTGGTTGTCCAC,+,0.00)
chunk0086_309_1	chr18	24071202	24071500	+	0	NA	intron (NM_153211, intron 4 of 13)	L2b|LINE|L2	-42002	NM_001292030	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.013423	0.361204	
chunk0208_94_1	chrX	13523789	13524228	+	0	NA	Intergenic	LTR50|LTR|ERVL	-45567	NM_001167890	25975	Hs.12844	NM_015507	ENSG00000198759	EGFL6	MAEG|W80	EGF like domain multiple 6	protein-coding	0.002278	0.438636	
chunk0038_391_1	chr11	93586852	93587266	+	0	NA	Intergenic	Intergenic	-43679	NM_020179	56935	Hs.438064	NM_020179	ENSG00000166002	SMCO4	C11orf75|FN5	single-pass membrane protein with coiled-coil domains 4	protein-coding	0.004831	0.361446	
chunk0154_191_1	chr5	80207406	80208415	+	0	NA	intron (NM_178276, intron 1 of 12)	intron (NM_178276, intron 1 of 12)	48172	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.006938	0.374257	
chunk0016_375_1	chr1	202568357	202569269	+	0	NA	intron (NM_001197131, intron 5 of 6)	intron (NM_001197131, intron 5 of 6)	28699	NM_001197131	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.006579	0.409639	
chunk0102_307_1	chr2	150973519	150973735	+	0	NA	Intergenic	Intergenic	288248	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.009259	0.317972	
chunk0125_453_1	chr3	73014876	73015294	+	0	NA	intron (NM_174907, intron 2 of 8)	intron (NM_174907, intron 2 of 8)	18117	NM_174907	151987	Hs.431092	NM_174907	ENSG00000163605	PPP4R2	PP4R2	protein phosphatase 4 regulatory subunit 2	protein-coding	0.009569	0.453461	
chunk0182_439_1	chr7	101644926	101645472	+	0	NA	Intergenic	MER121|DNA|hAT?	-15903	NM_138403	93408	Hs.247831	NM_138403	ENSG00000106436	MYL10	MYLC2PL|PLRLC	myosin light chain 10	protein-coding	0.040293	0.590494	
chunk0079_209_1	chr17	14631567	14632157	+	0	NA	Intergenic	Intergenic	328122	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.005085	0.360406	
chunk0134_415_1	chr3	183268551	183269148	+	0	NA	intron (NM_032047, intron 1 of 1)	intron (NM_032047, intron 1 of 1)	15605	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.010050	0.391304	
chunk0006_437_1	chr1	76569199	76569646	+	0	NA	intron (NM_152996, intron 3 of 4)	intron (NM_152996, intron 3 of 4)	-298079	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.008949	0.357143	
chunk0114_361_1	chr21	19807350	19807687	+	0	NA	Intergenic	Intergenic	995590	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005935	0.322485	
chunk0076_182_1	chr16	67624247	67624670	+	0	NA	intron (NM_001191022, intron 5 of 9)	L2|LINE|L2	-20669	NM_001317026	146206	Hs.611432	NM_001013838	ENSG00000159753	CARMIL2	CARMIL2b|IMD58|LRRC16C|RLTPR	capping protein regulator and myosin 1 linker 2	protein-coding	0.004728	0.426887	
chunk0136_304_1	chr3	195155150	195155435	+	0	NA	intron (NM_001308069, intron 3 of 3)	intron (NM_001308069, intron 3 of 3)	7421	NR_102710	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.031579	0.566434	
chunk0147_111_1	chr4	174206750	174207451	+	0	NA	intron (NR_125896, intron 1 of 4)	L1ME4b|LINE|L1	13298	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.004280	0.370370	24(TGCCCAGGCTGTTCTC,+,0.00)
chunk0130_108_1	chr3	131164056	131164490	+	0	NA	intron (NM_145910, intron 11 of 14)	MER63A|DNA|hAT-Blackjack	-137419	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.004608	0.360920	
chunk0079_328_1	chr17	17460007	17460238	+	0	NA	Intergenic	(CCATCA)n|Simple_repeat|Simple_repeat	-16864	NM_018019	55090	Hs.244595	NM_018019	ENSG00000141026	MED9	MED25	mediator complex subunit 9	protein-coding	0.012987	0.508621	
chunk0077_54_1	chr16	76346707	76346925	+	0	NA	intron (NM_138994, intron 2 of 22)	intron (NM_138994, intron 2 of 22)	36978	NM_138994	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.000000	0.319635	
chunk0196_402_1	chr8	115947196	115947633	+	0	NA	Intergenic	MIRb|SINE|MIR	-278386	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004577	0.365297	
chunk0037_139_1	chr11	73227371	73227838	+	0	NA	intron (NM_176071, intron 1 of 2)	intron (NM_176071, intron 1 of 2)	9147	NM_176071	5029	Hs.339	NM_002564	ENSG00000175591	P2RY2	HP2U|P2RU1|P2U|P2U1|P2UR|P2Y2|P2Y2R	purinergic receptor P2Y2	protein-coding	0.012848	0.534188	
chunk0135_400_1	chr3	192469370	192469800	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	-60536	NM_021032	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.002326	0.382831	
chunk0008_351_1	chr1	96208800	96209393	+	0	NA	Intergenic	Intergenic	165029	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.008432	0.367003	
chunk0169_300_1	chr6	106040984	106041256	+	0	NA	Intergenic	Intergenic	-45200	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.003676	0.373626	
chunk0099_331_1	chr2	99998773	99999509	+	0	NA	intron (NM_001025108, intron 6 of 23)	intron (NM_001025108, intron 6 of 23)	106442	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.016304	0.451832	354(GAGAACACAGCGTCCC,-,0.00),355(AGAACACAGCGTCCCA,+,0.00)
chunk0002_343_1	chr1	25080593	25081582	+	0	NA	Intergenic	L2c|LINE|L2	57584	NR_039623	100616365		NR_039623	ENSG00000264371	MIR4425	-	microRNA 4425	ncRNA	0.008089	0.490909	454(TGTACAGGCTGCTCCT,+,0.00),943(AGGTACATTATGTGCT,-,0.00),944(GGTACATTATGTGCTG,+,0.00)
chunk0204_443_1	chr9	104049067	104049554	+	0	NA	Intergenic	Intergenic	43164	NR_121580	101928550	Hs.144722	NR_121580	ENSG00000270332	SMC2-AS1	-	SMC2 antisense RNA 1 (head to head)	ncRNA	0.006160	0.356557	
chunk0049_358_1	chr12	95484480	95485061	+	0	NA	intron (NM_006838, intron 3 of 10)	L4_A_Mam|LINE|RTE-X	10724	NM_006838	10988	Hs.444986	NM_006838	ENSG00000111142	METAP2	MAP2|MNPEP|p67eIF2	methionyl aminopeptidase 2	protein-coding	0.000000	0.319588	
chunk0133_261_1	chr3	171765049	171765591	+	0	NA	intron (NM_001130081, intron 1 of 25)	intron (NM_001130081, intron 1 of 25)	45174	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.007380	0.373849	295(AAGAACAAAATGTTCC,-,0.00),296(AGAACAAAATGTTCCA,+,0.00)
chunk0144_323_1	chr4	139011300	139011625	+	0	NA	Intergenic	Intergenic	-4297	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.018462	0.481595	166(CAGCACTTGCTGTTCC,-,0.00),167(AGCACTTGCTGTTCCT,+,0.00)
chunk0201_307_1	chr9	42433297	42434041	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	135680	NR_126050	103908605	Hs.721139	NR_126050		LOC103908605	-	uncharacterized LOC103908605	ncRNA	0.009409	0.413423	
chunk0049_424_1	chr12	97856622	97857402	+	0	NA	Intergenic	L1MA6|LINE|L1	82109	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.006410	0.326504	
chunk0023_277_1	chr10	28274499	28274722	+	0	NA	intron (NM_173496, intron 2 of 18)	intron (NM_173496, intron 2 of 18)	7528	NM_173496	143098	Hs.499159	NM_173496	ENSG00000150054	MPP7	-	membrane palmitoylated protein 7	protein-coding	0.000000	0.366071	
chunk0023_266_1	chr10	27811393	27811872	+	0	NA	TTS (NM_018076)	TTS (NM_018076)	-65783	NM_001242702	283078	Hs.128193	NM_173576	ENSG00000150051	MKX	C10orf48|IFRX|IRXL1	mohawk homeobox	protein-coding	0.016701	0.316667	182(TGGGACAGTGAGTTCC,-,0.00),183(GGGACAGTGAGTTCCC,+,0.00),302(AAGTACTTTGTGTGCT,-,0.00),303(AGTACTTTGTGTGCTG,+,0.00)
chunk0063_282_1	chr14	84268033	84268456	+	0	NA	Intergenic	Intergenic	-1125635	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.007092	0.429245	200(GGGAACAGGTTGCTCC,-,0.00),201(GGAACAGGTTGCTCCT,+,0.00)
chunk0040_222_1	chr11	114315692	114316465	+	0	NA	Intergenic	Intergenic	20265	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.016818	0.467700	
chunk0204_145_1	chr9	95674225	95674808	+	0	NA	Intergenic	Intergenic	-157551	NM_001083603	5727	Hs.494538	NM_000264	ENSG00000185920	PTCH1	BCNS|NBCCS|PTC|PTC1|PTCH	patched 1	protein-coding	0.008576	0.296233	
chunk0063_422_1	chr14	88468765	88469423	+	0	NA	intron (NM_007039, intron 17 of 18)	intron (NM_007039, intron 17 of 18)	83450	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.018237	0.444613	453(AGGGACAGTGTGACCC,-,0.00),454(GGGACAGTGTGACCCT,+,0.00)
chunk0129_143_1	chr3	120462644	120462843	+	0	NA	Intergenic	Intergenic	-11672	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.000000	0.450000	
chunk0104_229_1	chr2	176465131	176465468	+	0	NA	Intergenic	Intergenic	135753	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.008902	0.470414	
chunk0120_236_1	chr3	8500609	8500914	+	0	NA	intron (NR_033378, intron 1 of 3)	intron (NR_033378, intron 1 of 3)	897	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.016393	0.490196	
chunk0020_76_1	chr1	232704757	232705224	+	0	NA	Intergenic	Intergenic	37725	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.006424	0.431624	
chunk0169_6_1	chr6	96240272	96240731	+	0	NA	Intergenic	L1ME3D|LINE|L1	224532	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.000000	0.300000	
chunk0075_144_1	chr16	50360576	50361023	+	0	NA	intron (NM_001173984, intron 2 of 16)	7SK|RNA|RNA	8135	NM_013263	29117	Hs.437894	NM_013263	ENSG00000166164	BRD7	BP75|CELTIX1|NAG4	bromodomain containing 7	protein-coding	0.006711	0.428571	
chunk0049_284_1	chr12	93943532	93944177	+	0	NA	Intergenic	LTR33|LTR|ERVL	-204869	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.003101	0.475232	279(AGGAACAAAGTGTGCT,-,0.00),280(GGAACAAAGTGTGCTA,+,0.00)
chunk0202_56_1	chr9	71565390	71565924	+	0	NA	Intergenic	Intergenic	203227	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.003745	0.319626	185(AGGAACTTGGTGTGCA,-,0.00),186(GGAACTTGGTGTGCAT,+,0.00)
chunk0137_321_1	chr4	24774676	24775294	+	0	NA	Intergenic	Intergenic	-20478	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.004854	0.382876	
chunk0116_343_1	chr21	41520466	41521078	+	0	NA	Intergenic	MIRb|SINE|MIR	-12614	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.003268	0.466558	
chunk0030_231_1	chr10	114859448	114859662	+	0	NA	intron (NM_020940, intron 14 of 16)	intron (NM_020940, intron 14 of 16)	37811	NM_001135051	57700	Hs.192619	NM_020940	ENSG00000151553	FAM160B1	KIAA1600|bA106M7.3	family with sequence similarity 160 member B1	protein-coding	0.004673	0.493023	
chunk0162_252_1	chr6	5133900	5134319	+	0	NA	intron (NR_104417, intron 2 of 3)	L1MB5|LINE|L1	14213	NR_037462	100500900		NR_037462	ENSG00000265083	MIR3691	mir-3691	microRNA 3691	ncRNA	0.007160	0.380952	
chunk0042_249_1	chr12	6430506	6431333	+	0	NA	Intergenic	L1ME3G|LINE|L1	-13966	NM_001242	939	Hs.355307	NM_001242	ENSG00000139193	CD27	S152|S152. LPFS2|T14|TNFRSF7|Tp55	CD27 molecule	protein-coding	0.022975	0.448068	
chunk0023_205_1	chr10	25328274	25328559	+	0	NA	intron (NM_020752, intron 2 of 10)	intron (NM_020752, intron 2 of 10)	-152140	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.000000	0.258741	
chunk0147_332_1	chr4	185267941	185268658	+	0	NA	intron (NM_031953, intron 5 of 18)	intron (NM_031953, intron 5 of 18)	58169	NM_031953	83891	Hs.369091	NM_031953	ENSG00000109762	SNX25	MSTP043|SBBI31	sorting nexin 25	protein-coding	0.002789	0.357939	419(GGGAGCACAGTGTCCC,-,0.00),420(GGAGCACAGTGTCCCT,+,0.00)
chunk0201_375_1	chr9	68780008	68780578	+	0	NA	exon (NM_138333, exon 1 of 1)	exon (NM_138333, exon 1 of 1)	245	NM_138333	116224	Hs.655572	NM_138333	ENSG00000187866	FAM122A	C9orf42	family with sequence similarity 122A	protein-coding	0.092982	0.672504	
chunk0203_359_1	chr9	89878693	89879304	+	0	NA	Intergenic	Intergenic	-90418	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.014730	0.565359	245(AGGGACACCGTGTACA,-,0.00),246(GGGACACCGTGTACAG,+,0.00)
chunk0004_212_1	chr1	46687389	46687723	+	0	NA	intron (NM_014774, intron 7 of 10)	intron (NM_014774, intron 7 of 10)	13520	NR_038827	100130197	Hs.568643	NR_038827	ENSG00000228237	EFCAB14-AS1	KIAA0494-AS1	EFCAB14 antisense RNA 1	ncRNA	0.000000	0.408955	
chunk0027_326_1	chr10	78383287	78383716	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	116173	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.000000	0.383721	
chunk0163_419_1	chr6	17097915	17098456	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-4073	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.007394	0.357934	
chunk0150_351_1	chr5	38672401	38672696	+	0	NA	Intergenic	Intergenic	47725	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.000000	0.439189	
chunk0140_219_1	chr4	70930360	70930902	+	0	NA	intron (NM_173468, intron 1 of 5)	intron (NM_173468, intron 1 of 5)	28291	NM_173468	92597	Hs.691454	NM_173468	ENSG00000173542	MOB1B	MATS2|MOB4A|MOBKL1A	MOB kinase activator 1B	protein-coding	0.005535	0.331492	
chunk0040_340_1	chr11	118402215	118402743	+	0	NA	intron (NM_006476, intron 1 of 2)	intron (NM_006476, intron 1 of 2)	1090	NM_006476	10632	Hs.486360	NM_006476	ENSG00000167283	ATP5MG	ATP5JG|ATP5L	ATP synthase membrane subunit g	protein-coding	0.022727	0.376181	
chunk0028_4_1	chr10	82004817	82005137	+	0	NA	intron (NM_001165973, intron 1 of 10)	MLT1B|LTR|ERVL-MaLR	127290	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.009375	0.417445	
chunk0065_114_1	chr15	24647279	24647478	+	0	NA	Intergenic	L1MC|LINE|L1	-28016	NM_018958	23742	Hs.649663	NM_018958	ENSG00000185823	NPAP1	C15orf2	nuclear pore associated protein 1	protein-coding	0.010050	0.360000	
chunk0054_17_1	chr13	40577939	40578239	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	88508	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.006667	0.435216	
chunk0125_155_1	chr3	66460582	66460831	+	0	NA	intron (NM_015541, intron 2 of 18)	MLT1B|LTR|ERVL-MaLR	39715	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.008032	0.496000	
chunk0112_437_1	chr20	47642362	47643070	+	0	NA	intron (NM_001174087, intron 17 of 22)	intron (NM_001174087, intron 17 of 22)	140859	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.019774	0.394922	
chunk0028_293_1	chr10	91490063	91490533	+	0	NA	intron (NM_001284274, intron 12 of 21)	L1ME4c|LINE|L1	80013	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.002128	0.276008	
chunk0201_246_1	chr9	37870591	37871306	+	0	NA	Intergenic	Intergenic	33405	NR_024872	92014	Hs.634120	NM_033412	ENSG00000122696	SLC25A51	CG7943|MCART1	solute carrier family 25 member 51	protein-coding	0.012587	0.435754	507(GAGAACAGCCTGGGCA,-,0.00)
chunk0134_113_1	chr3	177073790	177074048	+	0	NA	intron (NM_024665, intron 2 of 15)	intron (NM_024665, intron 2 of 15)	123341	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.015504	0.451737	
chunk0051_34_1	chr12	112134629	112135363	+	0	NA	intron (NM_006700, intron 3 of 11)	intron (NM_006700, intron 3 of 11)	9451	NM_001143906	10906	Hs.5148	NM_006700	ENSG00000135148	TRAFD1	FLN29	TRAF-type zinc finger domain containing 1	protein-coding	0.009537	0.435374	
chunk0199_129_1	chr9	3834998	3835333	+	0	NA	intron (NM_001042413, intron 9 of 10)	intron (NM_001042413, intron 9 of 10)	-63481	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.005970	0.467262	
chunk0147_274_1	chr4	183922063	183922304	+	0	NA	intron (NM_020225, intron 1 of 3)	intron (NM_020225, intron 1 of 3)	16827	NM_020225	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.008299	0.322314	
chunk0070_252_1	chr15	73601327	73602027	+	0	NA	intron (NM_012428, intron 1 of 8)	intron (NM_012428, intron 1 of 8)	31735	NM_012428	27020	Hs.744867	NM_012428	ENSG00000156642	NPTN	GP55|GP65|SDFR1|SDR1|np55|np65	neuroplastin	protein-coding	0.004286	0.445078	
chunk0173_449_1	chr6	151752739	151753072	+	0	NA	intron (NM_001122742, intron 2 of 9)	intron (NM_001122742, intron 2 of 9)	-52768	NM_001122741	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.003003	0.302395	
chunk0151_91_1	chr5	42858671	42859363	+	0	NA	Intergenic	Intergenic	-47095	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.011561	0.434343	409(TGGAACAGTCTGTGTT,-,0.00),410(GGAACAGTCTGTGTTC,+,0.00)
chunk0085_301_1	chr18	8114490	8114776	+	0	NA	intron (NM_001105244, intron 12 of 32)	intron (NM_001105244, intron 12 of 32)	252401	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.006993	0.407666	189(CAGAACAGTGAGATCC,-,0.00),190(AGAACAGTGAGATCCT,+,0.00)
chunk0062_193_1	chr14	69922019	69922658	+	0	NA	intron (NM_022137, intron 1 of 11)	intron (NM_022137, intron 1 of 11)	42941	NM_022137	64093	Hs.497349	NM_022137	ENSG00000198732	SMOC1	OAS	SPARC related modular calcium binding 1	protein-coding	0.012520	0.495312	221(ATGCACTTAATGTTCT,-,0.00),222(TGCACTTAATGTTCTT,+,0.00),358(GGGCACAGTACGTGCT,-,0.00),359(GGCACAGTACGTGCTG,+,0.00)
chunk0078_136_1	chr17	3705274	3705558	+	0	NA	Intergenic	Intergenic	-9012	NM_002561	5026	Hs.731607	NM_002561	ENSG00000083454	P2RX5	LRH-1|P2X5|P2X5R	purinergic receptor P2X 5	protein-coding	0.021127	0.529825	
chunk0144_16_1	chr4	124813833	124814302	+	0	NA	Intergenic	L2b|LINE|L2	-101335	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.002132	0.340426	
chunk0146_2_1	chr4	154569207	154569988	+	0	NA	exon (NM_001184741, exon 7 of 8)	exon (NM_001184741, exon 7 of 8)	6617	NM_005141	2244	Hs.300774	NM_005141	ENSG00000171564	FGB	HEL-S-78p	fibrinogen beta chain	protein-coding	0.008963	0.387468	
chunk0041_283_1	chr11	129380536	129380753	+	0	NA	intron (NM_003658, intron 1 of 3)	intron (NM_003658, intron 1 of 3)	4658	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.009217	0.408257	
chunk0091_15_1	chr19	2953160	2953411	+	0	NA	Intergenic	LTR43B|LTR|ERV1	-8314	NM_021217	58492	Hs.38004	NM_021217	ENSG00000175691	ZNF77	pT1	zinc finger protein 77	protein-coding	0.011952	0.444444	
chunk0074_256_1	chr16	27880167	27880757	+	0	NA	intron (NM_144675, intron 2 of 5)	MIRb|SINE|MIR	7695	NM_144675	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.008475	0.499154	
chunk0176_370_1	chr7	18440783	18441453	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-54628	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.002985	0.307004	
chunk0102_375_1	chr2	153495728	153496128	+	0	NA	Intergenic	LTR33|LTR|ERVL	-17120	NM_019845	56475	Hs.100890	NM_019845	ENSG00000177519	RPRM	REPRIMO	reprimo, TP53 dependent G2 arrest mediator homolog	protein-coding	0.002500	0.453865	
chunk0016_307_1	chr1	201358540	201358901	+	0	NA	TTS (NM_001276345)	TTS (NM_001276345)	18980	NM_001276347	7139	Hs.533613	NM_000364	ENSG00000118194	TNNT2	CMD1D|CMH2|CMPD2|LVNC6|RCM3|TnTC|cTnT	troponin T2, cardiac type	protein-coding	0.005540	0.569061	101(AAGAGCTCCCTGTCCC,-,0.00),102(AGAGCTCCCTGTCCCT,+,0.00),213(GGGAACACTCTGTCCC,-,0.00),214(GGAACACTCTGTCCCC,+,0.00)
chunk0117_31_1	chr22	11910018	11910232	+	0	NA	intron (NR_110761, intron 1 of 2)	intron (NR_110761, intron 1 of 2)	12719	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.004673	0.320930	
chunk0008_200_1	chr1	93471726	93472235	+	0	NA	intron (NM_017737, intron 1 of 14)	intron (NM_017737, intron 1 of 14)	23849	NM_017737	54874	Hs.134060	NM_017737	ENSG00000137942	FNBP1L	C1orf39|TOCA1	formin binding protein 1 like	protein-coding	0.001965	0.347059	
chunk0057_264_1	chr13	105720925	105721432	+	0	NA	intron (NR_046391, intron 3 of 3)	intron (NR_046391, intron 3 of 3)	14348	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.007890	0.381890	
chunk0124_374_1	chr3	59320287	59320618	+	0	NA	Intergenic	Intergenic	-270463	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.006042	0.439759	
chunk0181_298_1	chr7	87003775	87004503	+	0	NA	intron (NM_001142749, intron 1 of 21)	intron (NM_001142749, intron 1 of 21)	36095	NM_001291991	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.008242	0.423868	275(AGGTACTGGCTGTGCC,-,0.00),276(GGTACTGGCTGTGCCA,+,0.00)
chunk0017_94_1	chr1	205813607	205813819	+	0	NA	promoter-TSS (NM_173854)	promoter-TSS (NM_173854)	-517	NM_173854	254428	Hs.20274	NM_173854	ENSG00000133065	SLC41A1	MgtE	solute carrier family 41 member 1	protein-coding	0.056604	0.619718	
chunk0029_107_1	chr10	97834566	97835140	+	0	NA	intron (NR_108035, intron 1 of 2)	intron (NR_108035, intron 1 of 2)	14945	NR_108035	100505561	Hs.351904	NR_108035	ENSG00000227356	LINC00866	-	long intergenic non-protein coding RNA 866	ncRNA	0.005226	0.459130	295(GTGTACATCCTGTTCT,-,0.00),296(TGTACATCCTGTTCTT,+,0.00)
chunk0165_29_1	chr6	29810330	29810813	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-16408	NM_002127	3135	Hs.512152	NM_002127	ENSG00000204632	HLA-G	MHC-G	major histocompatibility complex, class I, G	protein-coding	0.004141	0.415289	
chunk0073_179_1	chr16	8915719	8916131	+	0	NA	intron (NM_003470, intron 8 of 30)	intron (NM_003470, intron 8 of 30)	20804	NM_001286458	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.014563	0.414044	
chunk0167_102_1	chr6	57127635	57128234	+	0	NA	intron (NM_001031623, intron 4 of 14)	MER58A|DNA|hAT-Charlie	37904	NM_015555	26036	Hs.485628	NM_015555	ENSG00000112200	ZNF451	COASTER|dJ417I1.1	zinc finger protein 451	protein-coding	0.000000	0.341667	
chunk0190_141_1	chr8	30727760	30728158	+	0	NA	promoter-TSS (NM_001195102)	promoter-TSS (NM_001195102)	10	NM_001195103	2936	Hs.271510	NM_000637	ENSG00000104687	GSR	GR|HEL-75|HEL-S-122m	glutathione-disulfide reductase	protein-coding	0.125628	0.744361	
chunk0211_437_1	chrX	129548970	129549659	+	0	NA	intron (NM_000276, intron 4 of 23)	intron (NM_000276, intron 4 of 23)	9039	NM_001587	4952	Hs.126357	NM_000276	ENSG00000122126	OCRL	INPP5F|LOCR|NPHL2|OCRL-1|OCRL1	OCRL inositol polyphosphate-5-phosphatase	protein-coding	0.002903	0.363768	197(GGAACATGATCTTCTT,+,0.00)
chunk0206_338_1	chr9	125529230	125529605	+	0	NA	intron (NM_001006618, intron 7 of 7)	intron (NM_001006618, intron 7 of 7)	177817	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.002667	0.356383	
chunk0200_134_1	chr9	17637287	17637594	+	0	NA	intron (NM_003026, intron 1 of 8)	L2c|LINE|L2	58486	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.009772	0.389610	
chunk0092_111_1	chr19	23822732	23823295	+	0	NA	intron (NR_003662, intron 3 of 3)	HERV3-int|LTR|ERV1	59999	NR_003662									0.005329	0.468085	
chunk0064_78_1	chr14	90402690	90403058	+	0	NA	intron (NM_006888, intron 3 of 5)	intron (NM_006888, intron 3 of 5)	5891	NM_006888	801	Hs.282410	NM_006888	ENSG00000198668	CALM1	CALML2|CAM2|CAM3|CAMB|CAMC|CAMI|CAMIII|CPVT4|DD132|LQT14|PHKD|caM	calmodulin 1	protein-coding	0.005435	0.414634	
chunk0044_226_1	chr12	31390966	31391165	+	0	NA	intron (NM_001308339, intron 21 of 22)	L2a|LINE|L2	-64840	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.005025	0.480000	
chunk0123_363_1	chr3	48242508	48243051	+	0	NA	intron (NM_016089, intron 1 of 3)	MER58B|DNA|hAT-Charlie	1673	NM_016089	51385	Hs.172602	NM_016089	ENSG00000164048	ZNF589	SZF1	zinc finger protein 589	protein-coding	0.023941	0.494485	
chunk0128_152_1	chr3	106989208	106989433	+	0	NA	Intergenic	L1MA6|LINE|L1	251318	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.000000	0.504425	
chunk0022_77_1	chr10	8837841	8838154	+	0	NA	Intergenic	L3|LINE|CR1	-59992	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.006390	0.353503	
chunk0196_408_1	chr8	115991890	115992754	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	-323294	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.009259	0.398844	474(TGGGACTGGGTGTTCT,-,0.00),475(GGGACTGGGTGTTCTC,+,0.00)
chunk0178_190_1	chr7	34307563	34308038	+	0	NA	Intergenic	Intergenic	-350439	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.004211	0.306723	
chunk0100_42_1	chr2	105713281	105713718	+	0	NA	Intergenic	Intergenic	-31564	NM_001004722	8440	Hs.529244	NM_003581	ENSG00000071051	NCK2	GRB4|NCKbeta	NCK adaptor protein 2	protein-coding	0.009153	0.484018	173(AGGAACTGGGTGTCCT,-,0.00),174(GGAACTGGGTGTCCTT,+,0.00)
chunk0070_384_1	chr15	76655603	76656231	+	0	NA	intron (NM_020843, intron 20 of 30)	L1PA15|LINE|L1	69270	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.004777	0.375199	
chunk0130_102_1	chr3	131083281	131083679	+	0	NA	intron (NM_145910, intron 4 of 14)	intron (NM_145910, intron 4 of 14)	-56626	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.007538	0.463659	
chunk0069_210_1	chr15	63497742	63498045	+	0	NA	Intergenic	L2c|LINE|L2	-6618	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.006601	0.493421	194(AGAAACATCCTGTACT,-,0.00),195(GAAACATCCTGTACTT,+,0.00)
chunk0079_322_1	chr17	17315315	17315746	+	0	NA	intron (NM_020201, intron 2 of 4)	L2b|LINE|L2	12164	NM_020201	56953	Hs.513977	NM_020201	ENSG00000205309	NT5M	dNT-2|dNT2|mdN	5',3'-nucleotidase, mitochondrial	protein-coding	0.004640	0.493056	
chunk0018_2_1	chr1	214820736	214821023	+	0	NA	Intergenic	L1PB1|LINE|L1	-184663	NM_001017424	3776	Hs.497745	NM_014217	ENSG00000082482	KCNK2	K2p2.1|TPKC1|TREK|TREK-1|TREK1|hTREK-1c|hTREK-1e	potassium two pore domain channel subfamily K member 2	protein-coding	0.003484	0.385417	
chunk0207_195_1	chr9	130961806	130962206	+	0	NA	Intergenic	(CAGGTA)n|Simple_repeat|Simple_repeat	-22938	NM_001145106	84929	Hs.133205	NM_032843	ENSG00000130720	FIBCD1	-	fibrinogen C domain containing 1	protein-coding	0.000000	0.546135	104(AGGGACAGGTTGTGCT,-,0.00),105(GGGACAGGTTGTGCTG,+,0.00),135(GGGGACAAGTTGTGCA,-,0.00),136(GGGACAAGTTGTGCAG,+,0.00),166(AGGGACAGGCTGTGCT,-,0.00),167(GGGACAGGCTGTGCTG,+,0.00),197(AGGTACAGGGTGTGCT,-,0.00),198(GGTACAGGGTGTGCTG,+,0.00),215(AGGGACAGGTTGTGCT,-,0.00),216(GGGACAGGTTGTGCTG,+,0.00),233(AGGGACAGGTTGTGCT,-,0.00),234(GGGACAGGTTGTGCTG,+,0.00)
chunk0144_41_1	chr4	125695429	125695799	+	0	NA	Intergenic	Intergenic	188355	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.010811	0.398922	
chunk0148_307_1	chr5	12787814	12788432	+	0	NA	intron (NR_033383, intron 3 of 3)	intron (NR_033383, intron 3 of 3)	120264	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.004854	0.271405	
chunk0096_56_1	chr2	27380808	27381176	+	0	NA	promoter-TSS (NM_144631)	promoter-TSS (NM_144631)	-248	NM_144631	130557	Hs.515872	NM_144631	ENSG00000163795	ZNF513	HMFT0656|RP58	zinc finger protein 513	protein-coding	0.081522	0.677507	
chunk0106_15_1	chr2	195560270	195560576	+	0	NA	Intergenic	L2c|LINE|L2	-96385	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.013072	0.335505	
chunk0113_18_1	chr20	49515533	49516151	+	0	NA	intron (NM_000961, intron 6 of 9)	L1ME4b|LINE|L1	-33198	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.006472	0.441034	
chunk0011_332_1	chr1	152146046	152146777	+	0	NA	Intergenic	Intergenic	12817	NM_001122965	126638	Hs.376144	NM_152364	ENSG00000215853	RPTN	-	repetin	protein-coding	0.004104	0.435792	
chunk0088_436_1	chr18	55815545	55815868	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	104493	NR_110755	101927273	Hs.434335	NR_110755	ENSG00000260930	LINC01416	-	long intergenic non-protein coding RNA 1416	ncRNA	0.003096	0.339506	
chunk0063_288_1	chr14	84315055	84315477	+	0	NA	Intergenic	L1MA4A|LINE|L1	-1078613	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.392435	
chunk0058_87_1	chr14	21477044	21477453	+	0	NA	promoter-TSS (NM_001163380)	promoter-TSS (NM_001163380)	72	NM_001303523	9878	Hs.555910	NM_014828	ENSG00000092203	TOX4	C14orf92|KIAA0737|LCP1|MIG7	TOX high mobility group box family member 4	protein-coding	0.066015	0.612195	
chunk0138_96_1	chr4	35836522	35837005	+	0	NA	Intergenic	Intergenic	-407353	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.000000	0.384298	
chunk0009_5_1	chr1	99835968	99836586	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-13807	NM_000642	178	Hs.904	NM_000028	ENSG00000162688	AGL	GDE	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	protein-coding	0.008091	0.462036	
chunk0159_221_1	chr5	140882780	140882993	+	0	NA	exon (NM_031865, exon 1 of 1)	exon (NM_031865, exon 1 of 1)	617	NM_031865	56136	Hs.199343	NM_018904	ENSG00000239389	PCDHA13	CNR5|CNRN5|CNRS5|CRNR5|PCDH-ALPHA13	protocadherin alpha 13	protein-coding	0.032864	0.453271	
chunk0110_436_1	chr20	20844949	20845349	+	0	NA	Intergenic	Intergenic	-132526	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.010000	0.508728	86(CGGAGCAGGCTGTGCC,-,0.00),87(GGAGCAGGCTGTGCCA,+,0.00)
chunk0045_180_1	chr12	47033021	47033708	+	0	NA	Intergenic	Intergenic	-46239	NM_138371	91523	Hs.560100	NM_138371	ENSG00000179715	PCED1B	FAM113B	PC-esterase domain containing 1B	protein-coding	0.010189	0.414244	187(GTGCACAGAGTGTTCC,-,0.00),188(TGCACAGAGTGTTCCT,+,0.00)
chunk0079_240_1	chr17	15966010	15966784	+	0	NA	intron (NM_000676, intron 1 of 1)	intron (NM_000676, intron 1 of 1)	21480	NM_000676	136	Hs.167046	NM_000676	ENSG00000170425	ADORA2B	ADORA2	adenosine A2b receptor	protein-coding	0.014212	0.468387	224(TAGAACTCTGTGTGCA,-,0.00),225(AGAACTCTGTGTGCAT,+,0.00)
chunk0135_449_1	chr3	194243340	194243542	+	0	NA	intron (NR_125403, intron 1 of 2)	L1MC1|LINE|L1	-4207	NR_125402	101929337	Hs.548086	NR_125402	ENSG00000238097	LINC02037	-	long intergenic non-protein coding RNA 2037	ncRNA	0.004950	0.403941	
chunk0131_84_1	chr3	143286222	143287038	+	0	NA	intron (NM_173653, intron 14 of 15)	intron (NM_173653, intron 14 of 15)	-55616	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.006127	0.485924	
chunk0058_28_1	chr14	19941868	19942163	+	0	NA	Intergenic	L1M2a|LINE|L1	6407	NM_001004063	79544	Hs.554584	NM_001004063	ENSG00000155249	OR4K1	OR14-19	olfactory receptor family 4 subfamily K member 1	protein-coding	0.000000	0.513514	
chunk0092_461_1	chr19	39167022	39167292	+	0	NA	intron (NM_001014834, intron 1 of 7)	intron (NM_001014834, intron 1 of 7)	-29807	NM_001001414	342897	Hs.726934	NM_001001414	ENSG00000188505	NCCRP1	FBXO50|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding	0.051852	0.708487	
chunk0011_274_1	chr1	151206243	151206692	+	0	NA	intron (NM_001135637, intron 1 of 13)	intron (NM_001135637, intron 1 of 13)	7922	NM_001135638	8394	Hs.655131	NM_003557	ENSG00000143398	PIP5K1A	-	phosphatidylinositol-4-phosphate 5-kinase type 1 alpha	protein-coding	0.008909	0.402222	
chunk0013_405_1	chr1	173034922	173035318	+	0	NA	Intergenic	L1PA7|LINE|L1	15843	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.005051	0.355164	
chunk0180_2_1	chr7	52971871	52972365	+	0	NA	Intergenic	Intergenic	-63538	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.002024	0.248485	
chunk0031_363_1	chr10	130221807	130222502	+	0	NA	Intergenic	LTR57|LTR|ERVL	85779	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.017266	0.527299	
chunk0081_64_1	chr17	38799621	38800239	+	0	NA	promoter-TSS (NM_003559)	promoter-TSS (NM_003559)	-25	NM_003559	8396	Hs.260603	NM_003559	ENSG00000276293	PIP4K2B	PI5P4KB|PIP5K2B|PIP5KIIB|PIP5KIIbeta|PIP5P4KB	phosphatidylinositol-5-phosphate 4-kinase type 2 beta	protein-coding	0.093851	0.728595	
chunk0020_290_1	chr1	237070523	237070996	+	0	NA	intron (NM_001035, intron 1 of 104)	MER52A|LTR|ERV1	28357	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.004228	0.605485	
chunk0050_310_1	chr12	107027823	107028112	+	0	NA	intron (NM_004075, intron 1 of 12)	intron (NM_004075, intron 1 of 12)	-40801	NM_025198	80298	Hs.5009	NM_025198	ENSG00000120832	MTERF2	MTERFD3|mTERFL	mitochondrial transcription termination factor 2	protein-coding	0.000000	0.320690	
chunk0148_86_1	chr5	3211997	3212299	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	34313	NR_104617	102467074	Hs.575250	NR_104617	ENSG00000249808	LINC01377	-	long intergenic non-protein coding RNA 1377	ncRNA	0.016556	0.518152	
chunk0163_169_1	chr6	11186875	11187204	+	0	NA	intron (NM_001142393, intron 7 of 7)	intron (NM_001142393, intron 7 of 7)	45643	NM_182966	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.009119	0.403030	
chunk0072_321_1	chr15	98952404	98953245	+	0	NA	intron (NM_001291858, intron 20 of 20)	intron (NM_001291858, intron 20 of 20)	52832	NM_001102612	145814	Hs.592021	NM_001102612	ENSG00000183571	PGPEP1L	-	pyroglutamyl-peptidase I like	protein-coding	0.013080	0.469121	338(GGGCACTTCCTGTTCT,-,0.00),339(GGCACTTCCTGTTCTC,+,0.00)
chunk0152_340_1	chr5	62563940	62564708	+	0	NA	intron (NM_016338, intron 27 of 29)	intron (NM_016338, intron 27 of 29)	-14411	NM_181506	100130733	Hs.721348	NM_181506	ENSG00000186105	LRRC70	SLRN	leucine rich repeat containing 70	protein-coding	0.005208	0.336801	
chunk0117_283_1	chr22	24291986	24292666	+	0	NA	intron (NM_015330, intron 2 of 16)	intron (NM_015330, intron 2 of 16)	21509	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.004412	0.425844	
chunk0131_205_1	chr3	148830733	148831061	+	0	NA	intron (NM_001871, intron 2 of 10)	L3|LINE|CR1	3096	NM_001871	1360	Hs.477891	NM_001871	ENSG00000153002	CPB1	CPB|PASP|PCPB	carboxypeptidase B1	protein-coding	0.003049	0.379939	
chunk0014_99_1	chr1	176717159	176717413	+	0	NA	intron (NM_020318, intron 12 of 22)	MER66C|LTR|ERV1	254115	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.003937	0.454902	
chunk0041_31_1	chr12	775687	776160	+	0	NA	intron (NM_213655, intron 1 of 27)	MIR|SINE|MIR	23000	NM_018979	65125	Hs.744906	NM_014823	ENSG00000060237	WNK1	HSAN2|HSN2|KDP|PPP1R167|PRKWNK1|PSK|p65	WNK lysine deficient protein kinase 1	protein-coding	0.008457	0.402954	
chunk0100_365_1	chr2	117943222	117943438	+	0	NA	intron (NM_019044, intron 18 of 23)	intron (NM_019044, intron 18 of 23)	70833	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.004630	0.382488	
chunk0141_94_1	chr4	79098391	79098682	+	0	NA	intron (NR_038342, intron 3 of 5)	HAL1ME|LINE|L1	126788	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.000000	0.291096	
chunk0193_372_1	chr8	80084156	80084606	+	0	NA	intron (NM_001025253, intron 1 of 7)	intron (NM_001025253, intron 1 of 7)	-3550	NM_001287140	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.004444	0.547672	
chunk0085_444_1	chr18	11146602	11147060	+	0	NA	intron (NM_022068, intron 1 of 51)	intron (NM_022068, intron 1 of 51)	1931	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.030568	0.586057	
chunk0117_125_1	chr22	19086809	19087119	+	0	NA	intron (NR_033674, intron 1 of 8)	intron (NR_033674, intron 1 of 8)	35490	NM_001184781	9993	Hs.517357	NM_005137	ENSG00000070413	DGCR2	DGS-C|IDD|LAN|SEZ-12	DiGeorge syndrome critical region gene 2	protein-coding	0.006452	0.440514	
chunk0100_247_1	chr2	112966103	112966905	+	0	NA	Intergenic	Charlie17|DNA|hAT-Charlie	-11515	NM_001278568	56300	Hs.211238	NM_019618	ENSG00000136688	IL36G	IL-1F9|IL-1H1|IL-1RP2|IL1E|IL1F9|IL1H1|IL1RP2	interleukin 36 gamma	protein-coding	0.003741	0.276463	
chunk0183_149_1	chr7	105831932	105832681	+	0	NA	intron (NM_020725, intron 2 of 11)	MER46C|DNA|TcMar-Tigger	44279	NM_152749	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.008011	0.408000	
chunk0176_269_1	chr7	16439008	16439611	+	0	NA	Intergenic	Intergenic	-17987	NM_001101426	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.000000	0.347682	
chunk0186_219_1	chr7	140062872	140063117	+	0	NA	non-coding (NR_130117, exon 1 of 11)	non-coding (NR_130117, exon 1 of 11)	727	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.159184	0.756098	
chunk0152_222_1	chr5	60386858	60387591	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-100489	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.005457	0.415531	3(GACACAGTTTGTGCTT,+,0.00),290(AAGGACAAGGTGATCT,-,0.00),291(AGGACAAGGTGATCTG,+,0.00)
chunk0015_356_1	chr1	190274027	190274490	+	0	NA	intron (NM_199051, intron 3 of 7)	intron (NM_199051, intron 3 of 7)	203371	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.008639	0.364224	
chunk0024_101_1	chr10	34583499	34583957	+	0	NA	intron (NM_019619, intron 2 of 24)	MIRc|SINE|MIR	231597	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.002183	0.307190	
chunk0061_66_1	chr14	56579437	56579906	+	0	NA	promoter-TSS (NM_017799)	promoter-TSS (NM_017799)	-122	NM_017799	54916	Hs.497253	NM_017799	ENSG00000070269	TMEM260	C14orf101|SHDRA	transmembrane protein 260	protein-coding	0.072495	0.617021	
chunk0035_179_1	chr11	43995437	43995636	+	0	NA	Intergenic	L2b|LINE|L2	-52445	NM_001031854	390110	Hs.558851	NM_001031854	ENSG00000205126	ACCSL	-	1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like	protein-coding	0.005025	0.495000	
chunk0002_217_1	chr1	19674155	19674450	+	0	NA	intron (NM_000871, intron 1 of 2)	L1ME3G|LINE|L1	9015	NM_000871	3362	Hs.22180	NM_000871	ENSG00000158748	HTR6	5-HT6|5-HT6R	5-hydroxytryptamine receptor 6	protein-coding	0.006780	0.327703	
chunk0206_111_1	chr9	120856783	120857164	+	0	NA	non-coding (NR_104601, exon 9 of 9)	non-coding (NR_104601, exon 9 of 9)	11938	NM_001286842	26147	Hs.460124	NM_015651	ENSG00000119403	PHF19	MTF2L1|PCL3|TDRD19B	PHD finger protein 19	protein-coding	0.013123	0.581152	
chunk0042_351_1	chr12	10168930	10169468	+	0	NA	intron (NM_002543, intron 1 of 5)	intron (NM_002543, intron 1 of 5)	-1400	NM_001079815	120939	Hs.226422	NM_153022	ENSG00000165685	TMEM52B	C12orf59	transmembrane protein 52B	protein-coding	0.005576	0.380334	
chunk0019_273_1	chr1	228490647	228491008	+	0	NA	intron (NM_001010858, intron 2 of 3)	intron (NM_001010858, intron 2 of 3)	3460	NM_001010858	149603	Hs.356377	NM_001010858	ENSG00000168159	RNF187	RACO-1|RACO1	ring finger protein 187	protein-coding	0.002770	0.552486	
chunk0086_222_1	chr18	22604364	22604646	+	0	NA	Intergenic	Intergenic	182332	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.000000	0.441696	
chunk0052_219_1	chr13	25494926	25495434	+	0	NA	intron (NM_001313741, intron 2 of 35)	intron (NM_001313741, intron 2 of 35)	26406	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.009843	0.504912	302(AAGGCCAGAGTGTGCC,-,0.00),303(AGGCCAGAGTGTGCCA,+,0.00)
chunk0066_360_1	chr15	38295278	38295484	+	0	NA	intron (NM_152594, intron 1 of 6)	Tigger3a|DNA|TcMar-Tigger	42530	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.014563	0.362319	
chunk0053_452_1	chr13	40093229	40093428	+	0	NA	Intergenic	Intergenic	-88481	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.010050	0.480000	
chunk0193_234_1	chr8	76671844	76672374	+	0	NA	intron (NR_024360, intron 2 of 3)	intron (NR_024360, intron 2 of 3)	-9171	NM_024721	79776	Hs.458973	NM_024721	ENSG00000091656	ZFHX4	ZFH4|ZHF4	zinc finger homeobox 4	protein-coding	0.005660	0.350282	
chunk0067_231_1	chr15	45423703	45423995	+	0	NA	Intergenic	Intergenic	-6680	NM_032413	84419	Hs.112242	NM_032413	ENSG00000166920	C15orf48	FOAP-11|MIR147BHG|NMES1	chromosome 15 open reading frame 48	protein-coding	0.000000	0.419795	
chunk0184_355_1	chr7	120852523	120853060	+	0	NA	intron (NM_012338, intron 2 of 7)	MIR|SINE|MIR	5332	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.001862	0.373606	
chunk0203_241_1	chr9	87293764	87294131	+	0	NA	Intergenic	Intergenic	145303	NM_001001709									0.000000	0.369565	216(CAGGTCACTGTGTTCC,-,0.00),217(AGGTCACTGTGTTCCA,+,0.00)
chunk0050_63_1	chr12	101302550	101302767	+	0	NA	intron (NM_014503, intron 15 of 61)	intron (NM_014503, intron 15 of 61)	22531	NM_014503	27340	Hs.295732	NM_014503	ENSG00000120800	UTP20	1A6/DRIM|DRIM	UTP20 small subunit processome component	protein-coding	0.004608	0.284404	
chunk0004_207_1	chr1	46668413	46668873	+	0	NA	promoter-TSS (NM_022745)	promoter-TSS (NM_022745)	-216	NM_001042546	64756	Hs.100874	NM_022745	ENSG00000123472	ATPAF1	ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding	0.080435	0.609544	
chunk0206_399_1	chr9	127113240	127113462	+	0	NA	intron (NM_012098, intron 1 of 4)	intron (NM_012098, intron 1 of 4)	9414	NM_012098	23452	Hs.653262	NM_012098	ENSG00000136859	ANGPTL2	ARP2|HARP	angiopoietin like 2	protein-coding	0.009009	0.493274	
chunk0046_33_1	chr12	54512330	54512976	+	0	NA	intron (NM_005337, intron 9 of 30)	L2c|LINE|L2	13869	NM_001184976	3071	Hs.182014	NM_005337	ENSG00000123338	NCKAP1L	HEM1	NCK associated protein 1 like	protein-coding	0.001548	0.394127	
chunk0155_267_1	chr5	95924705	95925174	+	0	NA	intron (NM_012081, intron 2 of 11)	intron (NM_012081, intron 2 of 11)	-37062	NR_130776	101929710		NR_130776	ENSG00000251314	LOC101929710	-	uncharacterized LOC101929710	ncRNA	0.006397	0.380851	
chunk0120_141_1	chr3	5168434	5168699	+	0	NA	intron (NM_018184, intron 1 of 6)	intron (NM_018184, intron 1 of 6)	-19108	NM_014674	9695	Hs.224616	NM_014674	ENSG00000134109	EDEM1	EDEM	ER degradation enhancing alpha-mannosidase like protein 1	protein-coding	0.007547	0.394737	
chunk0087_416_1	chr18	42217685	42217969	+	0	NA	intron (NR_046174, intron 2 of 9)	HERV16-int|LTR|ERVL	31159	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.000000	0.396491	
chunk0138_128_1	chr4	36579995	36580325	+	0	NA	Intergenic	L1MA9|LINE|L1	-153732	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.000000	0.244713	
chunk0060_192_1	chr14	47668256	47668596	+	0	NA	intron (NM_001113498, intron 1 of 16)	intron (NM_001113498, intron 1 of 16)	6528	NM_001113498	161357	Hs.436380	NM_182830	ENSG00000139915	MDGA2	MAMDC1|c14_5286	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.005882	0.304985	
chunk0193_363_1	chr8	79951198	79951438	+	0	NA	intron (NM_014018, intron 2 of 2)	MER45C|DNA|hAT-Tip100	78953	NM_014018	28957	Hs.521124	NM_014018	ENSG00000147586	MRPS28	HSPC007|MRP-S28|MRP-S35|MRPS35	mitochondrial ribosomal protein S28	protein-coding	0.012500	0.535270	
chunk0105_269_1	chr2	189424375	189425185	+	0	NA	Intergenic	L1MA6|LINE|L1	-16653	NM_032168	84128	Hs.399984	NM_032168	ENSG00000115368	WDR75	NET16|UTP17	WD repeat domain 75	protein-coding	0.002469	0.316893	
chunk0093_84_1	chr19	40886759	40887167	+	0	NA	Intergenic	Intergenic	-3863	NR_040249	22952	Hs.738699	NR_040249	ENSG00000130612	CYP2G1P	CYP2G1|CYP2G2P|CYP2GP1	cytochrome P450 family 2 subfamily G member 1, pseudogene	pseudo	0.004902	0.425428	
chunk0054_209_1	chr13	45150179	45150635	+	0	NA	intron (NM_004128, intron 3 of 7)	intron (NM_004128, intron 3 of 7)	29911	NM_004128	2963	Hs.654582	NM_004128	ENSG00000188342	GTF2F2	BTF4|RAP30|TF2F2|TFIIF	general transcription factor IIF subunit 2	protein-coding	0.000000	0.306346	
chunk0054_454_1	chr13	51519772	51520409	+	0	NA	Intergenic	Intergenic	-32499	NR_039852	100616423		NR_039852	ENSG00000266611	MIR4703	-	microRNA 4703	ncRNA	0.004710	0.413793	
chunk0030_146_1	chr10	113739369	113739676	+	0	NA	Intergenic	L2a|LINE|L2	-11932	NM_001193435	79949	Hs.228320	NM_024889	ENSG00000148735	PLEKHS1	C10orf81|HEL185	pleckstrin homology domain containing S1	protein-coding	0.016287	0.405844	218(GAAGACAGACAGTTCT,-,0.00),219(AAGACAGACAGTTCTA,+,0.00)
chunk0073_386_1	chr16	15998322	15998883	+	0	NA	intron (NM_004996, intron 1 of 30)	intron (NM_004996, intron 1 of 30)	49025	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.016043	0.514235	
chunk0172_192_1	chr6	136604880	136605296	+	0	NA	intron (NM_005923, intron 19 of 29)	intron (NM_005923, intron 19 of 29)	-24026	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.009615	0.388489	
chunk0201_131_1	chr9	35603868	35604343	+	0	NA	Intergenic	CpG	-1179	NM_006285	7016	Hs.708096	NM_006285	ENSG00000107140	TESK1	-	testis associated actin remodelling kinase 1	protein-coding	0.086316	0.607143	
chunk0021_15_1	chr10	435997	436531	+	0	NA	intron (NM_014974, intron 4 of 36)	intron (NM_014974, intron 4 of 36)	-154178	NR_106988									0.029963	0.478505	
chunk0191_144_1	chr8	48849297	48849551	+	0	NA	Intergenic	Intergenic	72016	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.003937	0.349020	
chunk0109_132_1	chr20	3156752	3157069	+	0	NA	intron (NM_021826, intron 1 of 1)	intron (NM_021826, intron 1 of 1)	2976	NM_021826	60493	Hs.741168	NM_021826	ENSG00000215251	FASTKD5	dJ1187M17.5	FAST kinase domains 5	protein-coding	0.009464	0.433962	
chunk0113_434_1	chr20	62358266	62358798	+	0	NA	intron (NM_005560, intron 2 of 79)	intron (NM_005560, intron 2 of 79)	5522	NR_109923	101928158	Hs.473256	NR_109922	ENSG00000228812	LAMA5-AS1	-	LAMA5 antisense RNA 1	ncRNA	0.030075	0.664165	156(CTGCACTTCCTGTCCT,-,0.00),157(TGCACTTCCTGTCCTT,+,0.00),299(GAGAGCAGGCAGTCCT,-,0.00),300(AGAGCAGGCAGTCCTG,+,0.00)
chunk0181_239_1	chr7	85284829	85285128	+	0	NA	Intergenic	Intergenic	-163047	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.290000	
chunk0019_262_1	chr1	228090540	228091490	+	0	NA	intron (NM_001024227, intron 1 of 4)	intron (NM_001024227, intron 1 of 4)	-6248	NR_037415	100500810		NR_037415	ENSG00000284163	MIR3620	mir-3620	microRNA 3620	ncRNA	0.007368	0.493165	
chunk0195_155_1	chr8	95423994	95424391	+	0	NA	intron (NR_038209, intron 2 of 3)	intron (NR_038209, intron 2 of 3)	-154958	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.007557	0.379397	
chunk0029_112_1	chr10	97963506	97963895	+	0	NA	intron (NM_018058, intron 2 of 14)	intron (NM_018058, intron 2 of 14)	67128	NM_018058	55118	Hs.500736	NM_018058	ENSG00000095713	CRTAC1	ASPIC|ASPIC1|CEP-68|CEP68|LOTUS	cartilage acidic protein 1	protein-coding	0.007712	0.376923	
chunk0078_241_1	chr17	6977065	6977554	+	0	NA	Intergenic	Intergenic	-18756	NM_000697	239	Hs.654431	NM_000697	ENSG00000108839	ALOX12	12-LOX|12S-LOX|LOG12	arachidonate 12-lipoxygenase, 12S type	protein-coding	0.008180	0.389796	
chunk0158_220_1	chr5	128441786	128442393	+	0	NA	intron (NM_001999, intron 7 of 64)	intron (NM_001999, intron 7 of 64)	95953	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.004942	0.335526	
chunk0081_397_1	chr17	48241152	48241383	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-53080	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.004329	0.508621	
chunk0151_428_1	chr5	55823120	55823446	+	0	NA	Intergenic	Intergenic	-28096	NM_001242638	133396	Hs.55378	NM_139017	ENSG00000164509	IL31RA	CRL|CRL3|GLM-R|GLMR|GPL|IL-31RA|PLCA2|PRO21384|hGLM-R	interleukin 31 receptor A	protein-coding	0.003067	0.376147	
chunk0016_312_1	chr1	201495849	201496328	+	0	NA	intron (NM_004078, intron 2 of 5)	intron (NM_004078, intron 2 of 5)	485	NM_001193572	1465	Hs.108080	NM_004078	ENSG00000159176	CSRP1	CRP|CRP1|CSRP|CYRP|D1S181E|HEL-141|HEL-S-286	cysteine and glycine rich protein 1	protein-coding	0.022965	0.535417	
chunk0098_4_1	chr2	64955028	64955293	+	0	NA	Intergenic	MIR|SINE|MIR	-22713	NR_036586	400958	Hs.591565	NR_036586		LINC02245	-	long intergenic non-protein coding RNA 2245	ncRNA	0.000000	0.334586	
chunk0042_223_1	chr12	6229538	6230110	+	0	NA	intron (NM_001769, intron 2 of 7)	(T)n|Simple_repeat|Simple_repeat	29508	NM_001769	928	Hs.114286	NM_001769	ENSG00000010278	CD9	BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29	CD9 molecule	protein-coding	0.019231	0.465969	
chunk0061_295_1	chr14	61647799	61648304	+	0	NA	intron (NR_039985, intron 1 of 2)	L1MC3|LINE|L1	-47350	NM_001530	3091	Hs.597216	NM_001530	ENSG00000100644	HIF1A	HIF-1-alpha|HIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78	hypoxia inducible factor 1 subunit alpha	protein-coding	0.011881	0.369565	
chunk0073_20_1	chr16	2251716	2252463	+	0	NA	promoter-TSS (NM_001919)	promoter-TSS (NM_001919)	-488	NM_001178029	1632	Hs.403436	NM_001919	ENSG00000167969	ECI1	DCI	enoyl-CoA delta isomerase 1	protein-coding	0.045515	0.602941	465(GAATACAGTCTGTTCC,-,0.00),466(AATACAGTCTGTTCCC,+,0.00)
chunk0145_12_1	chr4	143358969	143359249	+	0	NA	intron (NM_002039, intron 1 of 9)	intron (NM_002039, intron 1 of 9)	15649	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.010714	0.419929	
chunk0116_329_1	chr21	41260672	41261308	+	0	NA	intron (NM_138991, intron 7 of 7)	L1ME3E|LINE|L1	-55744	NM_206964	54097	Hs.473877	NM_058186	ENSG00000183844	FAM3B	2-21|C21orf11|C21orf76|ORF9|PANDER|PRED44	family with sequence similarity 3 member B	protein-coding	0.014151	0.367347	
chunk0151_354_1	chr5	54545785	54545988	+	0	NA	3' UTR (NM_001102575, exon 2 of 2)	3' UTR (NM_001102575, exon 2 of 2)	28123	NM_052870	112574	Hs.432755	NM_052870	ENSG00000178996	SNX18	SH3PX2|SH3PXD3B|SNAG1	sorting nexin 18	protein-coding	0.000000	0.333333	
chunk0104_243_1	chr2	177192632	177192927	+	0	NA	Intergenic	Intergenic	-19915	NM_194247	220988	Hs.516539	NM_194247	ENSG00000170144	HNRNPA3	2610510D13Rik|D10S102|FBRNP|HNRPA3	heterogeneous nuclear ribonucleoprotein A3	protein-coding	0.003390	0.320946	
chunk0160_253_1	chr5	156778122	156778354	+	0	NA	Intergenic	MIRc|SINE|MIR	-72300	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.004310	0.343348	
chunk0173_423_1	chr6	151044508	151045210	+	0	NA	intron (NM_001242767, intron 26 of 27)	intron (NM_001242767, intron 26 of 27)	178526	NM_001242768	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.027066	0.527738	
chunk0013_120_1	chr1	167949624	167950105	+	0	NA	intron (NM_001017977, intron 1 of 18)	intron (NM_001017977, intron 1 of 18)	-12795	NM_015415	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.004158	0.340249	
chunk0095_67_1	chr2	14493018	14493653	+	0	NA	Intergenic	Intergenic	-92377	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.009449	0.360063	
chunk0045_277_1	chr12	49801409	49802001	+	0	NA	intron (NM_001037806, intron 6 of 12)	intron (NM_001037806, intron 6 of 12)	26720	NM_001037806	57701	Hs.143067	NM_001037806	ENSG00000167566	NCKAP5L	Cep169|FP1193|KIAA1602	NCK associated protein 5 like	protein-coding	0.025338	0.576728	
chunk0179_191_1	chr7	47181734	47182310	+	0	NA	Intergenic	Intergenic	400122	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.006944	0.521664	
chunk0045_266_1	chr12	49609727	49609926	+	0	NA	Intergenic	L1ME1|LINE|L1	-4176	NM_032130	84070	Hs.524406	NM_032130	ENSG00000135436	FAM186B	C12orf25	family with sequence similarity 186 member B	protein-coding	0.000000	0.585000	
chunk0158_342_1	chr5	133275662	133276414	+	0	NA	intron (NM_015082, intron 6 of 15)	Charlie29a|DNA|hAT-Charlie	151668	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.015957	0.483400	
chunk0068_211_1	chr15	55102404	55103054	+	0	NA	Intergenic	Intergenic	94304	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004615	0.391705	
chunk0102_131_1	chr2	145648753	145649135	+	0	NA	Intergenic	Intergenic	-938113	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.002618	0.326371	
chunk0034_142_1	chr11	29360617	29360816	+	0	NA	Intergenic	Intergenic	621677	NR_132652	106456574	Hs.128812	NR_132652	ENSG00000261340	LINC01616	n341006	long intergenic non-protein coding RNA 1616	ncRNA	0.000000	0.495000	
chunk0190_236_1	chr8	36573729	36574152	+	0	NA	Intergenic	LTR18A|LTR|ERVL	-210384	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.011820	0.490566	
chunk0206_77_1	chr9	119991964	119992485	+	0	NA	Intergenic	(CACA)n|Simple_repeat|Simple_repeat	57164	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.009597	0.524904	
chunk0097_326_1	chr2	57164601	57165000	+	0	NA	Intergenic	Intergenic	-742851	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.002506	0.350000	252(AGGAACACAAAGATCT,-,0.00)
chunk0167_117_1	chr6	57767490	57768008	+	0	NA	Intergenic	L1ME3B|LINE|L1	169180	NR_132999	375513	Hs.561539	NM_206908		GUSBP4	C6orf216|GUSBL2|SMA3-L|SMAC3L	GUSB pseudogene 4	pseudo	0.001931	0.271676	296(TGTACTGGATGTCCTT,+,0.00)
chunk0012_261_1	chr1	161612490	161612870	+	0	NA	Intergenic	Intergenic	6621	NR_024151	3311	Hs.662180	NR_024151		HSPA7	HSP70B	heat shock protein family A (Hsp70) member 7	pseudo	0.076316	0.519685	
chunk0093_205_1	chr19	49554004	49554279	+	0	NA	Intergenic	Intergenic	26431	NM_015953	51070	Hs.7236	NM_015953	ENSG00000142546	NOSIP	CGI-25	nitric oxide synthase interacting protein	protein-coding	0.021818	0.525362	
chunk0142_40_1	chr4	90959234	90959433	+	0	NA	intron (NM_001145065, intron 9 of 10)	MIRb|SINE|MIR	724302	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.010050	0.335000	
chunk0064_196_1	chr14	92783580	92784147	+	0	NA	Intergenic	Intergenic	-10368	NM_005113	9950	Hs.104320	NM_005113	ENSG00000066455	GOLGA5	GOLIM5|RFG5|ret-II	golgin A5	protein-coding	0.008818	0.438380	
chunk0094_101_1	chr2	4221190	4221684	+	0	NA	Intergenic	L1ME3A|LINE|L1	-247405	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.006073	0.379798	
chunk0125_381_1	chr3	71611160	71611410	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	-27296	NM_032682	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.008000	0.406375	
chunk0007_152_1	chr1	79657678	79658286	+	0	NA	Intergenic	Intergenic	-651172	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.004934	0.354680	
chunk0148_312_1	chr5	13403832	13404054	+	0	NA	Intergenic	L2|LINE|L2	540537	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.009009	0.484305	
chunk0035_386_1	chr11	55545081	55545373	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	-9080	NM_001001920	81309		NM_001001920	ENSG00000181939	OR4C15	OR11-127|OR11-134	olfactory receptor family 4 subfamily C member 15	protein-coding	0.013699	0.433447	
chunk0130_117_1	chr3	131421940	131422351	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	40364	NR_033268	131870	Hs.282050	NM_152395	ENSG00000198585	NUDT16	-	nudix hydrolase 16	protein-coding	0.000000	0.468447	
chunk0050_40_1	chr12	100601494	100602004	+	0	NA	exon (NM_174942, exon 5 of 10)	exon (NM_174942, exon 5 of 10)	8131	NM_001303131	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.001961	0.287671	
chunk0029_462_1	chr10	110614553	110614757	+	0	NA	Intergenic	Intergenic	-29742	NM_001134363	282996	Hs.116630	NM_001134363	ENSG00000203867	RBM20	-	RNA binding motif protein 20	protein-coding	0.009804	0.448780	
chunk0092_399_1	chr19	37332696	37333171	+	0	NA	Intergenic	Intergenic	-1745	NM_181786	284459	Hs.640243	NM_181786	ENSG00000181666	ZNF875	HKR1	zinc finger protein 875	protein-coding	0.002105	0.357143	
chunk0032_147_1	chr11	4742006	4742378	+	0	NA	Intergenic	L2c|LINE|L2	27725	NM_001004752	256892		NM_001004752	ENSG00000280021	OR51F1	OR11-21|OR51F1P	olfactory receptor family 51 subfamily F member 1 (gene/pseudogene)	protein-coding	0.008065	0.399464	
chunk0161_324_1	chr5	173671008	173671486	+	0	NA	Intergenic	Intergenic	-54584	NM_138369	91272	Hs.425091	NM_138369	ENSG00000145919	BOD1	FAM44B	biorientation of chromosomes in cell division 1	protein-coding	0.025105	0.534447	269(AAGGACTTTGTGTCCC,-,0.00),270(AGGACTTTGTGTCCCC,+,0.00)
chunk0105_370_1	chr2	192027516	192027932	+	0	NA	intron (NM_016192, intron 5 of 9)	MER45B|DNA|hAT-Tip100	167209	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.004808	0.462830	176(GGGCACACAGAGTCCT,-,0.00),177(GGCACACAGAGTCCTG,+,0.00)
chunk0090_290_1	chr18	75010590	75011145	+	0	NA	intron (NM_017757, intron 7 of 7)	intron (NM_017757, intron 7 of 7)	194646	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.003604	0.404676	328(AAGTACAGTCAGATCT,-,0.00)
chunk0078_359_1	chr16	87332148	87332818	+	0	NA	intron (NM_024735, intron 8 of 8)	intron (NM_024735, intron 8 of 8)	-15063	NM_001256917	100506581	Hs.729380	NM_001195124	ENSG00000260456	C16orf95	-	chromosome 16 open reading frame 95	protein-coding	0.023881	0.566319	
chunk0127_200_1	chr3	96198982	96199241	+	0	NA	Intergenic	L1MEc|LINE|L1	-160853	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.334615	
chunk0123_372_1	chr3	48558310	48558887	+	0	NA	Intergenic	Intergenic	-1804	NM_004567	5210	Hs.476217	NM_004567	ENSG00000114268	PFKFB4	-	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	protein-coding	0.012132	0.574394	368(GGGAACACCCTGCCCC,-,0.00),369(GGAACACCCTGCCCCA,+,0.00)
chunk0161_458_1	chr5	179406414	179407062	+	0	NA	Intergenic	Intergenic	-61308	NM_021599	9509	Hs.23871	NM_014244	ENSG00000087116	ADAMTS2	ADAM-TS2|ADAMTS-2|ADAMTS-3|EDSDERMS|NPI|PC I-NP|PCI-NP|PCINP|PCPNI|PNPI	ADAM metallopeptidase with thrombospondin type 1 motif 2	protein-coding	0.016975	0.517720	
chunk0150_185_1	chr5	34551029	34551258	+	0	NA	Intergenic	MIR|SINE|MIR	-105185	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.008734	0.413043	
chunk0168_250_1	chr6	88796917	88797445	+	0	NA	intron (NM_001286426, intron 11 of 14)	intron (NM_001286426, intron 11 of 14)	166448	NM_003800	8732	Hs.567378	NM_003800	ENSG00000111880	RNGTT	CAP1A|HCE|HCE1|hCAP	RNA guanylyltransferase and 5'-phosphatase	protein-coding	0.007576	0.328922	
chunk0137_253_1	chr4	20788069	20788903	+	0	NA	intron (NM_147181, intron 1 of 6)	intron (NM_147181, intron 1 of 6)	62182	NM_147181	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.002398	0.348503	
chunk0163_387_1	chr6	16402084	16402875	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	163899	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.006321	0.420455	
chunk0201_318_1	chr9	62798837	62799043	+	0	NA	Intergenic	Intergenic	-2525	NR_121647	103352539	Hs.351215	NR_121647	ENSG00000238113	LINC01410	-	long intergenic non-protein coding RNA 1410	ncRNA	0.029126	0.516908	
chunk0185_45_1	chr7	124542874	124543073	+	0	NA	Intergenic	L1MA10|LINE|L1	-190877	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.000000	0.300000	
chunk0164_130_1	chr6	20982988	20983195	+	0	NA	intron (NM_017774, intron 10 of 15)	intron (NM_017774, intron 10 of 15)	448634	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.004831	0.307692	
chunk0183_123_1	chr7	105468782	105469076	+	0	NA	intron (NM_019042, intron 11 of 15)	AluJo|SINE|Alu	53309	NM_019042	54517	Hs.520619	NM_019042	ENSG00000091127	PUS7	IDDABS	pseudouridine synthase 7	protein-coding	0.013605	0.450847	
chunk0139_62_1	chr4	49091231	49091620	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	104783	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.020566	0.415385	
chunk0144_300_1	chr4	138398215	138398931	+	0	NA	intron (NR_051987, intron 2 of 2)	intron (NR_051987, intron 2 of 2)	88862	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.002793	0.379358	
chunk0118_33_1	chr22	27121960	27122159	+	0	NA	Intergenic	L2a|LINE|L2	218767	NR_110540	101929539	Hs.517505	NR_110540	ENSG00000235271	LINC01422	-	long intergenic non-protein coding RNA 1422	ncRNA	0.000000	0.415000	
chunk0132_103_1	chr3	155689224	155689527	+	0	NA	intron (NM_014996, intron 1 of 21)	L1M1|LINE|L1	-13059	NM_001130960	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.006601	0.384868	
chunk0200_48_1	chr9	15491306	15491672	+	0	NA	intron (NM_021144, intron 2 of 9)	Tigger17a|DNA|TcMar-Tigger	18800	NM_021144	11168	Hs.658434	NM_021144	ENSG00000164985	PSIP1	DFS70|LEDGF|PAIP|PSIP2|p52|p75	PC4 and SFRS1 interacting protein 1	protein-coding	0.005464	0.370572	
chunk0089_82_1	chr18	58285497	58286310	+	0	NA	intron (NM_001144970, intron 4 of 28)	intron (NM_001144970, intron 4 of 28)	64381	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.007380	0.353808	422(TAGAACATTATGTTCT,-,0.00),423(AGAACATTATGTTCTA,+,0.00)
chunk0071_381_1	chr15	89129564	89130268	+	0	NA	intron (NM_007011, intron 7 of 14)	intron (NM_007011, intron 7 of 14)	41766	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.009943	0.380142	
chunk0022_461_1	chr10	20195945	20196344	+	0	NA	intron (NM_032812, intron 9 of 13)	intron (NM_032812, intron 9 of 13)	-355826	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.007519	0.402500	
chunk0077_116_1	chr16	78258564	78259075	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	159406	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.011742	0.369141	
chunk0213_12_1	chrY	20568552	20568767	+	0	NA	Intergenic	L1PA10|LINE|L1	-7052	NM_004681	9086	Hs.461178	NM_004681	ENSG00000198692	EIF1AY	eIF-4C	eukaryotic translation initiation factor 1A Y-linked	protein-coding	0.013953	0.328704	
chunk0208_179_1	chrX	16979286	16979869	+	0	NA	intron (NM_004726, intron 1 of 17)	intron (NM_004726, intron 1 of 17)	32886	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.005146	0.340753	16(GGGAACTGAATGTTTT,-,0.00),17(GGAACTGAATGTTTTC,+,0.00)
chunk0145_315_1	chr4	150519329	150519643	+	0	NA	intron (NM_001199282, intron 40 of 56)	L1ME2|LINE|L1	-62439	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.009554	0.333333	
chunk0087_166_1	chr18	34979134	34979437	+	0	NA	intron (NM_001143827, intron 1 of 7)	intron (NM_001143827, intron 1 of 7)	1041	NM_001143827	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.016502	0.467105	
chunk0087_177_1	chr18	35470333	35471164	+	0	NA	intron (NM_194281, intron 4 of 4)	intron (NM_194281, intron 4 of 4)	26901	NM_001308064	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.013237	0.485577	414(CTGAACAGACTGCACT,-,0.00),415(TGAACAGACTGCACTG,+,0.00)
chunk0107_4_1	chr2	209735164	209735792	+	0	NA	Intergenic	Intergenic	-36515	NM_032504	285175	Hs.396201	NM_032504	ENSG00000144406	UNC80	C2orf21|UNC-80	unc-80 homolog, NALCN channel complex subunit	protein-coding	0.003185	0.356121	
chunk0035_20_1	chr11	40313846	40314096	+	0	NA	intron (NM_001258419, intron 4 of 6)	L1MA5A|LINE|L1	-20841	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.036000	0.458167	
chunk0133_15_1	chr3	165665114	165665677	+	0	NA	Intergenic	Intergenic	172070	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.003552	0.326241	
chunk0064_424_1	chr14	99780990	99781284	+	0	NA	Intergenic	Intergenic	-12271	NM_001008707	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.023810	0.566102	
chunk0142_63_1	chr4	92409655	92410119	+	0	NA	intron (NM_001286838, intron 1 of 14)	intron (NM_001286838, intron 1 of 14)	105488	NM_001510	2895	Hs.162727	NM_001510	ENSG00000152208	GRID2	GluD2|SCAR18	glutamate ionotropic receptor delta type subunit 2	protein-coding	0.000000	0.346237	191(TGGGACAGACTGTGCT,-,0.00),192(GGGACAGACTGTGCTG,+,0.00)
chunk0192_237_1	chr8	65500521	65501371	+	0	NA	Intergenic	Intergenic	61720	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.004706	0.396005	
chunk0126_408_1	chr3	85335340	85336160	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	-49960	NR_049870	100847077		NR_049870	ENSG00000264084	MIR5688	-	microRNA 5688	ncRNA	0.003659	0.325213	590(AAAGACAGCCTGTTCT,-,0.00),591(AAGACAGCCTGTTCTC,+,0.00)
chunk0187_22_1	chr8	687280	687808	+	0	NA	intron (NM_001303100, intron 3 of 5)	CpG	43695	NM_207332	157697	Hs.655310	NM_207332	ENSG00000104714	ERICH1	HSPC319	glutamate rich 1	protein-coding	0.085227	0.646503	
chunk0092_77_1	chr19	20704098	20704458	+	0	NA	Intergenic	Intergenic	-42682	NM_145297	199777	Hs.657001	NM_145297	ENSG00000188171	ZNF626	-	zinc finger protein 626	protein-coding	0.008333	0.465374	
chunk0067_146_1	chr15	43235408	43235697	+	0	NA	exon (NM_004245, exon 9 of 12)	exon (NM_004245, exon 9 of 12)	-14427	NM_001114134	2038	Hs.368642	NM_000119	ENSG00000166947	EPB42	PA|SPH5	erythrocyte membrane protein band 4.2	protein-coding	0.024221	0.544828	81(ATGAACGCTGTGTCCT,-,0.00),82(TGAACGCTGTGTCCTG,+,0.00)
chunk0006_144_1	chr1	66278619	66279016	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-53291	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.012594	0.442211	
chunk0082_93_1	chr17	53370249	53370822	+	0	NA	Intergenic	Intergenic	385015	NM_001243552	100506650	Hs.146556	NM_001243552		C17orf112	-	chromosome 17 open reading frame 112	protein-coding	0.012216	0.402439	
chunk0080_33_1	chr17	21162222	21162701	+	0	NA	intron (NM_015510, intron 1 of 6)	intron (NM_015510, intron 1 of 6)	35533	NM_015510	25979	Hs.386989	NM_015510	ENSG00000109016	DHRS7B	CGI-93|SDR32C1	dehydrogenase/reductase 7B	protein-coding	0.008351	0.404167	
chunk0203_136_1	chr9	85431412	85432054	+	0	NA	Intergenic	Intergenic	310296	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.003115	0.377916	
chunk0064_358_1	chr14	96859136	96859455	+	0	NA	intron (NM_003384, intron 10 of 12)	L1ME3A|LINE|L1	61948	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.006270	0.303125	
chunk0002_202_1	chr1	19504632	19505354	+	0	NA	Intergenic	Intergenic	-19352	NM_004930	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.002770	0.376210	
chunk0102_318_1	chr2	151409927	151410126	+	0	NA	promoter-TSS (NM_001177665)	promoter-TSS (NM_001177665)	-64	NM_001177665	55183	Hs.536537	NM_018151	ENSG00000080345	RIF1	-	replication timing regulatory factor 1	protein-coding	0.090452	0.660000	
chunk0003_214_1	chr1	35326203	35326868	+	0	NA	intron (NM_005095, intron 2 of 29)	MER6|DNA|TcMar-Tigger	57568	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.004511	0.378378	
chunk0026_56_1	chr10	61066607	61066899	+	0	NA	Intergenic	Intergenic	50478	NR_108052	100507058	Hs.145227	NR_108052	ENSG00000227244	LINC00845	-	long intergenic non-protein coding RNA 845	ncRNA	0.000000	0.361775	
chunk0010_271_1	chr1	117148075	117148274	+	0	NA	intron (NM_001253850, intron 3 of 4)	intron (NM_001253850, intron 3 of 4)	-26385	NM_001145635	80263	Hs.301526	NM_025188	ENSG00000134253	TRIM45	RNF99	tripartite motif containing 45	protein-coding	0.010050	0.395000	
chunk0173_31_1	chr6	142044211	142044632	+	0	NA	Intergenic	Intergenic	44378	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.004751	0.379147	195(CAGAACATCTCGTCCT,-,0.00),196(AGAACATCTCGTCCTC,+,0.00)
chunk0084_9_1	chr17	73310614	73310878	+	0	NA	intron (NM_012121, intron 1 of 1)	(CA)n|Simple_repeat|Simple_repeat	1258	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.030303	0.581132	
chunk0135_125_1	chr3	187104352	187104796	+	0	NA	Intergenic	Intergenic	34901	NM_052969	116832	Hs.647900	NM_052969	ENSG00000163923	RPL39L	L39-2|RPL39L1	ribosomal protein L39 like	protein-coding	0.018018	0.478652	
chunk0073_94_1	chr16	4368902	4369306	+	0	NA	intron (NM_001201473, intron 7 of 25)	intron (NM_001201473, intron 7 of 25)	-2744	NM_138440	114990	Hs.372579	NM_138440	ENSG00000168140	VASN	SLITL2	vasorin	protein-coding	0.014851	0.639506	
chunk0183_36_1	chr7	103691290	103691751	+	0	NA	intron (NM_005045, intron 10 of 64)	intron (NM_005045, intron 10 of 64)	-245343	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.008677	0.430736	
chunk0003_171_1	chr1	33510362	33510561	+	0	NA	Intergenic	Intergenic	37830	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.005025	0.470000	65(AGGGACACTCTGTTCT,-,0.00),66(GGGACACTCTGTTCTC,+,0.00)
chunk0151_422_1	chr5	55689712	55690151	+	0	NA	intron (NM_173514, intron 3 of 15)	intron (NM_173514, intron 3 of 15)	3122	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.000000	0.318182	237(TAGAACAGATTGATCT,-,0.00),238(AGAACAGATTGATCTA,+,0.00)
chunk0010_114_1	chr1	114434801	114435581	+	0	NA	intron (NM_033020, intron 4 of 18)	L2c|LINE|L2	75969	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.001282	0.353393	
chunk0196_167_1	chr8	105770670	105771032	+	0	NA	intron (NM_012082, intron 5 of 7)	intron (NM_012082, intron 5 of 7)	289652	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.002762	0.402204	
chunk0187_48_1	chr8	1663203	1663402	+	0	NA	intron (NM_001277161, intron 5 of 10)	intron (NM_001277161, intron 5 of 10)	-41638	NR_103863	100507435	Hs.667133	NR_103863	ENSG00000253267	DLGAP2-AS1	-	DLGAP2 antisense RNA 1	ncRNA	0.025126	0.530000	
chunk0196_176_1	chr8	105913000	105913519	+	0	NA	intron (NR_125796, intron 2 of 7)	intron (NR_125796, intron 2 of 7)	147244	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.000000	0.326923	
chunk0029_118_1	chr10	98332964	98333198	+	0	NA	Intergenic	Intergenic	62226	NR_031619	100302133		NR_031619	ENSG00000284415	MIR1287	MIRN1287|hsa-mir-1287|mir-1287	microRNA 1287	ncRNA	0.017094	0.365957	
chunk0144_6_1	chr4	124484992	124485918	+	0	NA	Intergenic	Intergenic	72979	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.003240	0.269687	
chunk0116_202_1	chr21	37428348	37428694	+	0	NA	intron (NM_130436, intron 1 of 10)	intron (NM_130436, intron 1 of 10)	8221	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.000000	0.311239	
chunk0064_284_1	chr14	95259706	95260024	+	0	NA	intron (NM_024734, intron 1 of 12)	intron (NM_024734, intron 1 of 12)	60043	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.015723	0.536050	213(TTGCACACGCTGTTCC,-,0.00),214(TGCACACGCTGTTCCT,+,0.00)
chunk0210_236_1	chrX	82694632	82695293	+	0	NA	Intergenic	Intergenic	-813299	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.007564	0.398792	
chunk0188_114_1	chr8	9059540	9059870	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	11260	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.012121	0.410876	
chunk0050_326_1	chr12	107175813	107176203	+	0	NA	Intergenic	L2a|LINE|L2	-82151	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.000000	0.375959	
chunk0127_351_1	chr3	100940950	100941755	+	0	NA	intron (NM_015429, intron 1 of 34)	intron (NM_015429, intron 1 of 34)	52138	NM_015429	25890	Hs.477015	NM_015429	ENSG00000154175	ABI3BP	NESHBP|TARSH	ABI family member 3 binding protein	protein-coding	0.006211	0.388337	261(CAGAACAGCACGTTCC,-,0.00),262(AGAACAGCACGTTCCC,+,0.00)
chunk0132_405_1	chr3	164196956	164197285	+	0	NA	Intergenic	L1PA16|LINE|L1	-25564	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.006079	0.381818	195(TAGTACTGGATGTCCT,-,0.00),196(AGTACTGGATGTCCTA,+,0.00)
chunk0089_47_1	chr18	58088241	58089106	+	0	NA	intron (NM_001144964, intron 1 of 30)	L4_B_Mam|LINE|RTE-X	41447	NM_001144964	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.008092	0.383372	
chunk0178_164_1	chr7	33929669	33930091	+	0	NA	intron (NM_133468, intron 3 of 15)	intron (NM_133468, intron 3 of 15)	24969	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.007109	0.427896	
chunk0031_378_1	chr10	130787125	130787643	+	0	NA	Intergenic	Intergenic	175284	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.011583	0.387283	301(GGGACACCACGTGCCT,+,0.00)
chunk0193_315_1	chr8	78530336	78530875	+	0	NA	intron (NM_181839, intron 1 of 2)	intron (NM_181839, intron 1 of 2)	14504	NM_181839	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.000000	0.318519	
chunk0087_105_1	chr18	32495751	32496245	+	0	NA	Intergenic	L1MA2|LINE|L1	-15665	NR_003558	441818	Hs.549773	NR_003558	ENSG00000260389	WBP11P1	HsT3017	WW domain binding protein 11 pseudogene 1	pseudo	0.002024	0.345455	
chunk0037_356_1	chr11	77827695	77827972	+	0	NA	intron (NR_133637, intron 1 of 4)	L1M4|LINE|L1	6719	NM_001316957	28971	Hs.745040	NM_024684	ENSG00000087884	AAMDC	C11orf67|CK067|PTD015	adipogenesis associated Mth938 domain containing	protein-coding	0.000000	0.338129	
chunk0034_148_1	chr11	30008932	30009416	+	0	NA	TTS (NM_002233)	TTS (NM_002233)	7856	NM_002233	3739	Hs.592002	NM_002233	ENSG00000182255	KCNA4	HBK4|HK1|HPCN2|HUKII|KCNA4L|KCNA8|KV1.4|MCIDDS|PCN2	potassium voltage-gated channel subfamily A member 4	protein-coding	0.006198	0.352577	
chunk0017_179_1	chr1	207088825	207089117	+	0	NA	promoter-TSS (NM_000716)	promoter-TSS (NM_000716)	129	NM_001017366	725	Hs.99886	NM_000716	ENSG00000123843	C4BPB	C4BP	complement component 4 binding protein beta	protein-coding	0.010274	0.498294	
chunk0168_301_1	chr6	91501300	91501628	+	0	NA	Intergenic	Intergenic	-20196	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.000000	0.313070	
chunk0057_76_1	chr13	98329954	98330265	+	0	NA	intron (NM_001286839, intron 2 of 27)	L2a|LINE|L2	121585	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.012862	0.512821	145(GGGGACAGAGTGTTCC,-,0.00),146(GGGACAGAGTGTTCCA,+,0.00)
chunk0091_261_1	chr19	11102914	11103113	+	0	NA	intron (NM_001195800, intron 3 of 15)	intron (NM_001195800, intron 3 of 15)	-10461	NR_106946	102465534		NR_106946	ENSG00000284553	MIR6886	hsa-mir-6886	microRNA 6886	ncRNA	0.045226	0.610000	
chunk0148_131_1	chr5	5510787	5511470	+	0	NA	Intergenic	Intergenic	88455	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.019034	0.475146	
chunk0194_238_1	chr8	86343165	86343364	+	0	NA	intron (NM_007013, intron 1 of 24)	intron (NM_007013, intron 1 of 24)	499	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.035176	0.525000	
chunk0144_251_1	chr4	136328886	136329197	+	0	NA	Intergenic	L1PA16|LINE|L1	-415361	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.006431	0.532051	
chunk0038_119_1	chr11	83951100	83951760	+	0	NA	intron (NM_001142699, intron 14 of 27)	L2a|LINE|L2	-269005	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003030	0.379728	
chunk0198_158_1	chr8	133139293	133139871	+	0	NA	Intergenic	Intergenic	-36516	NM_001282965	6503	Hs.75367	NM_006748	ENSG00000155926	SLA	SLA1|SLAP	Src like adaptor	protein-coding	0.006920	0.464594	
chunk0103_441_1	chr2	170095824	170096185	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-82141	NR_045684	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.011080	0.381215	119(GTGATCATTCTGTTCT,-,0.00),120(TGATCATTCTGTTCTT,+,0.00)
chunk0200_447_1	chr9	31253950	31254151	+	0	NA	Intergenic	CpG	-845596	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.069652	0.633663	
chunk0138_122_1	chr4	36399593	36399918	+	0	NA	Intergenic	Intergenic	26673	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.000000	0.334356	
chunk0054_322_1	chr13	49003659	49003998	+	0	NA	intron (NM_001278438, intron 1 of 25)	L1MC4|LINE|L1	27219	NM_001278438	22862	Hs.508010	NM_014923	ENSG00000102531	FNDC3A	FNDC3|HUGO|bA203I16.1|bA203I16.5	fibronectin type III domain containing 3A	protein-coding	0.000000	0.302941	
chunk0211_144_1	chrX	113417527	113417997	+	0	NA	intron (NR_110399, intron 3 of 3)	L1MA2|LINE|L1	375035	NR_110399	101928437	Hs.640112	NR_110399		LOC101928437	-	uncharacterized LOC101928437	ncRNA	0.004255	0.320594	
chunk0007_396_1	chr1	85494672	85494921	+	0	NA	intron (NM_001134445, intron 2 of 6)	intron (NM_001134445, intron 2 of 6)	-29590	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.004016	0.480000	
chunk0066_394_1	chr15	39064022	39064390	+	0	NA	Intergenic	Intergenic	-186463	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.002717	0.387534	132(TAGGACATTGAGTTCC,-,0.00),133(AGGACATTGAGTTCCA,+,0.00)
chunk0060_198_1	chr14	47915506	47916111	+	0	NA	Intergenic	Intergenic	-120794	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.003306	0.318482	
chunk0062_357_1	chr14	73863881	73864423	+	0	NA	intron (NM_001146155, intron 3 of 9)	L1MB7|LINE|L1	12234	NM_152444	145482	Hs.632344	NM_152444	ENSG00000140043	PTGR2	HEL-S-298|PGR2|ZADH1	prostaglandin reductase 2	protein-coding	0.003690	0.406998	
chunk0169_16_1	chr6	96739133	96739654	+	0	NA	Intergenic	(TTCTATT)n|Simple_repeat|Simple_repeat	98084	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.003839	0.310345	
chunk0039_390_1	chr11	107159397	107159737	+	0	NA	Intergenic	MER21-int|LTR|ERVL	-141122	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.005882	0.381232	
chunk0019_268_1	chr1	228232442	228232858	+	0	NA	intron (NM_052843, intron 9 of 80)	L1MB7|LINE|L1	-18986	NR_073154	574407	Hs.650039	NM_001025495	ENSG00000162913	OBSCN-AS1	C1orf145	OBSCN antisense RNA 1	ncRNA	0.004808	0.465228	
chunk0008_223_1	chr1	93944883	93945208	+	0	NA	Intergenic	L1MA6|LINE|L1	-35447	NM_001308253	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.006154	0.389571	
chunk0110_29_1	chr20	10506099	10506801	+	0	NA	intron (NM_001009608, intron 2 of 7)	L2a|LINE|L2	71147	NM_001009608	128710	Hs.668782	NM_001009608	ENSG00000149346	SLX4IP	C20orf94|bA204H22.1|bA254M13.1|dJ1099D15.3	SLX4 interacting protein	protein-coding	0.004274	0.375533	
chunk0117_449_1	chr21	46534760	46534971	+	0	NA	intron (NM_206889, intron 13 of 21)	intron (NM_206889, intron 13 of 21)	70257	NM_006272	6285	Hs.422181	NM_006272	ENSG00000160307	S100B	NEF|S100|S100-B|S100beta	S100 calcium binding protein B	protein-coding	0.009479	0.509434	126(GGGCACACGGTGTCTC,-,0.00),127(GGCACACGGTGTCTCT,+,0.00)
chunk0068_53_1	chr15	51678933	51679324	+	0	NA	Intergenic	Charlie14a|DNA|hAT-Charlie	-2225	NM_001165257	29106	Hs.232618	NM_013243	ENSG00000104112	SCG3	SGIII	secretogranin III	protein-coding	0.002558	0.285714	
chunk0049_78_1	chr12	90574634	90575080	+	0	NA	Intergenic	L1MA3|LINE|L1	-343166	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.004484	0.411633	
chunk0069_226_1	chr15	63802258	63802489	+	0	NA	intron (NM_003922, intron 1 of 77)	intron (NM_003922, intron 1 of 77)	31575	NM_003922	8925	Hs.210385	NM_003922	ENSG00000103657	HERC1	MDFPMR|p532|p619	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding	0.012987	0.318966	
chunk0020_264_1	chr1	236320457	236321292	+	0	NA	Intergenic	Intergenic	-38835	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.004790	0.400718	357(CAGAACATTCTGTAAT,-,0.00)
chunk0008_185_1	chr1	93138027	93138353	+	0	NA	3' UTR (NM_001164391, exon 16 of 16)	3' UTR (NM_001164391, exon 16 of 16)	42499	NM_001167830	50999	Hs.482873	NM_016040	ENSG00000117500	TMED5	CGI-100|p24g2|p28	transmembrane p24 trafficking protein 5	protein-coding	0.000000	0.293578	
chunk0109_138_1	chr20	3342410	3342654	+	0	NA	intron (NM_001009984, intron 9 of 36)	intron (NM_001009984, intron 9 of 36)	65130	NM_001009984	25943	Hs.516853	NM_001009984	ENSG00000088854	C20orf194	-	chromosome 20 open reading frame 194	protein-coding	0.008197	0.355102	
chunk0170_357_1	chr6	116631419	116631958	+	0	NA	intron (NM_001010892, intron 5 of 5)	MER76|LTR|ERVL	15209	NM_001161664	345895	Hs.160380	NM_001010892	ENSG00000111834	RSPH4A	CILD11|RSHL3|RSPH6B|dJ412I7.1	radial spoke head component 4A	protein-coding	0.009276	0.462963	
chunk0189_14_1	chr8	19505404	19505629	+	0	NA	exon (NM_018371, exon 4 of 10)	exon (NM_018371, exon 4 of 10)	97029	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.031111	0.619469	
chunk0035_94_1	chr11	42175545	42175928	+	0	NA	Intergenic	Intergenic	77954	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002611	0.401042	
chunk0199_445_1	chr9	14041165	14041643	+	0	NA	Intergenic	Intergenic	113433	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.006276	0.484342	
chunk0068_174_1	chr15	54173965	54174440	+	0	NA	intron (NM_001080534, intron 3 of 30)	L1ME2z|LINE|L1	161298	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.006316	0.302521	
chunk0016_131_1	chr1	196991480	196992240	+	0	NA	intron (NM_030787, intron 3 of 9)	L1PA6|LINE|L1	14323	NM_030787	81494	Hs.282594	NM_030787	ENSG00000134389	CFHR5	CFHL5|CFHR5D|FHR-5|FHR5	complement factor H related 5	protein-coding	0.011842	0.526938	
chunk0045_205_1	chr12	47753270	47753860	+	0	NA	intron (NM_006105, intron 2 of 27)	intron (NM_006105, intron 2 of 27)	4833	NM_001098532	10411	Hs.8578	NM_006105	ENSG00000079337	RAPGEF3	CAMP-GEFI|EPAC|EPAC1|HSU79275|bcm910	Rap guanine nucleotide exchange factor 3	protein-coding	0.010169	0.605753	150(CAGTACAACCAGTCCT,-,0.00),151(AGTACAACCAGTCCTG,+,0.00),422(CGGAACAAACAGTGCC,-,0.00),423(GGAACAAACAGTGCCT,+,0.00)
chunk0173_125_1	chr6	143655630	143655867	+	0	NA	intron (NM_001100166, intron 1 of 11)	intron (NM_001100166, intron 1 of 11)	-22217	NM_001100164	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.012658	0.336134	
chunk0183_97_1	chr7	105137321	105137842	+	0	NA	intron (NM_001278273, intron 12 of 16)	intron (NM_001278273, intron 12 of 16)	123391	NM_018682	55904	Hs.592262	NM_018682	ENSG00000005483	KMT2E	HDCMC04P|MLL5|NKp44L	lysine methyltransferase 2E	protein-coding	0.005758	0.477011	
chunk0135_31_1	chr3	184970415	184970769	+	0	NA	intron (NM_001009921, intron 38 of 46)	intron (NM_001009921, intron 38 of 46)	158449	NM_001009921	23355	Hs.269263	NM_015303	ENSG00000156931	VPS8	KIAA0804	VPS8 subunit of CORVET complex	protein-coding	0.002825	0.400000	
chunk0169_41_1	chr6	97407544	97407914	+	0	NA	intron (NR_110757, intron 1 of 4)	intron (NR_110757, intron 1 of 4)	102143	NR_110757	101927314	Hs.520283	NR_110757	ENSG00000271860	LOC101927314	-	uncharacterized LOC101927314	ncRNA	0.005405	0.336927	
chunk0044_210_1	chr12	30908627	30909187	+	0	NA	Intergenic	Intergenic	-17997	NM_001080509	441631	Hs.505141	NM_001080509	ENSG00000110900	TSPAN11	VSSW1971	tetraspanin 11	protein-coding	0.003571	0.422460	
chunk0193_73_1	chr8	73160109	73160597	+	0	NA	Intergenic	Intergenic	-67081	NM_153225	157869	Hs.439040	NM_153225	ENSG00000164764	SBSPON	C8orf84|RPESP	somatomedin B and thrombospondin type 1 domain containing	protein-coding	0.008197	0.398773	238(CAGAACAATTTGTTCT,-,0.00),239(AGAACAATTTGTTCTT,+,0.00)
chunk0093_277_1	chr19	51780631	51780962	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-14362	NM_002030	2359	Hs.445466	NM_002030	ENSG00000187474	FPR3	FML2_HUMAN|FMLP-R-II|FMLPY|FPRH1|FPRH2|FPRL2|RMLP-R-I	formyl peptide receptor 3	protein-coding	0.006042	0.451807	2(ATGGACACTGAGTCCC,-,0.00),3(TGGACACTGAGTCCCT,+,0.00)
chunk0106_261_1	chr2	203676307	203676507	+	0	NA	Intergenic	Intergenic	-30068	NM_001243077	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.005000	0.313433	15(AGGAACAAACTGACCT,-,0.00),16(GGAACAAACTGACCTC,+,0.00)
chunk0139_336_1	chr4	59343612	59343821	+	0	NA	Intergenic	Intergenic	-1578903	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.357143	
chunk0165_436_1	chr6	40295270	40295469	+	0	NA	Intergenic	LTR16E2|LTR|ERVL	60637	NR_038887	401260	Hs.654837	NM_001001705		LINC00951	-	long intergenic non-protein coding RNA 951	ncRNA	0.005025	0.535000	
chunk0173_283_1	chr6	147977513	147977939	+	0	NA	Intergenic	Intergenic	-364867	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.021127	0.491803	
chunk0052_327_1	chr12	125904952	125905900	+	0	NA	Intergenic	Intergenic	77948	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.007384	0.441517	398(AAGAACAGTCTGCCCA,-,0.00),399(AGAACAGTCTGCCCAC,+,0.00)
chunk0166_225_1	chr6	46972751	46973670	+	0	NA	Intergenic	Intergenic	-18272	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.004353	0.346739	
chunk0102_312_1	chr2	151241362	151241664	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	20362	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.006623	0.353135	130(AAGAACAACGAGTCCA,-,0.00),131(AGAACAACGAGTCCAC,+,0.00)
chunk0179_44_1	chr7	43369812	43370525	+	0	NA	intron (NM_015052, intron 6 of 29)	L1MC1|LINE|L1	152374	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.007013	0.350140	
chunk0144_349_1	chr4	139535114	139536153	+	0	NA	intron (NM_001306200, intron 2 of 2)	intron (NM_001306200, intron 2 of 2)	21136	NM_001306200	80854	Hs.480792	NM_030648	ENSG00000145391	SETD7	KMT7|SET7|SET7/9|SET9	SET domain containing 7, histone lysine methyltransferase	protein-coding	0.005775	0.378846	
chunk0028_61_1	chr10	83275333	83275883	+	0	NA	Intergenic	Intergenic	-863821	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.001818	0.343013	
chunk0103_304_1	chr2	166812035	166812612	+	0	NA	Intergenic	L1MC3|LINE|L1	-76164	NM_001199143	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.006932	0.371972	
chunk0002_208_1	chr1	19613271	19613849	+	0	NA	intron (NM_001204088, intron 2 of 4)	L2b|LINE|L2	5753	NR_077246	644068	Hs.660760	NR_077246		RPS14P3	RPS14_1_16	ribosomal protein S14 pseudogene 3	pseudo	0.013841	0.459413	266(TAGTACATCCTGTTTC,-,0.00),267(AGTACATCCTGTTTCT,+,0.00)
chunk0061_1_1	chr14	55344631	55345218	+	0	NA	intron (NM_152231, intron 1 of 1)	L2c|LINE|L2	66934	NM_014924	22863	Hs.414809	NM_014924	ENSG00000126775	ATG14	ATG14L|BARKOR|KIAA0831	autophagy related 14	protein-coding	0.008518	0.484694	
chunk0126_402_1	chr3	85007143	85007843	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	48511	NM_001167675	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.008571	0.330956	
chunk0204_429_1	chr9	103290507	103291008	+	0	NA	intron (NR_121578, intron 3 of 9)	intron (NR_121578, intron 3 of 9)	34276	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.005988	0.310757	
chunk0141_179_1	chr4	82859405	82859656	+	0	NA	intron (NM_016211, intron 12 of 24)	intron (NM_016211, intron 12 of 24)	31652	NM_001191049	22872	Hs.370024	NM_014933	ENSG00000138674	SEC31A	ABP125|ABP130|HSPC275|HSPC334|SEC31L1	SEC31 homolog A, COPII coat complex component	protein-coding	0.000000	0.289683	
chunk0143_155_1	chr4	110121984	110122402	+	0	NA	intron (NM_001130721, intron 2 of 4)	intron (NM_001130721, intron 2 of 4)	76422	NM_001130721	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.004785	0.338902	
chunk0037_198_1	chr11	74347415	74347725	+	0	NA	intron (NM_173582, intron 6 of 13)	intron (NM_173582, intron 6 of 13)	-35894	NM_182904	283208	Hs.660541	NM_182904	ENSG00000149380	P4HA3	-	prolyl 4-hydroxylase subunit alpha 3	protein-coding	0.006452	0.385852	
chunk0186_327_1	chr7	143141242	143141742	+	0	NA	Intergenic	L2a|LINE|L2	9411	NM_002652	5304	Hs.99949	NM_002652	ENSG00000159763	PIP	GCDFP-15|GCDFP15|GPIP4	prolactin induced protein	protein-coding	0.004000	0.347305	
chunk0033_437_1	chr11	25336357	25336556	+	0	NA	Intergenic	L1ME2z|LINE|L1	839486	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.010050	0.295000	
chunk0108_63_1	chr2	227223811	227224299	+	0	NA	intron (NR_102371, intron 12 of 13)	intron (NR_102371, intron 12 of 13)	59490	NM_000091	1285	Hs.570065	NM_000091	ENSG00000169031	COL4A3	ATS2|ATS3	collagen type IV alpha 3 chain	protein-coding	0.016393	0.447853	
chunk0001_176_1	chr1	6909840	6910327	+	0	NA	intron (NM_015215, intron 3 of 22)	intron (NM_015215, intron 3 of 22)	124759	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.002053	0.487705	
chunk0127_249_1	chr3	97024171	97024785	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	209897	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.001629	0.297561	
chunk0001_167_1	chr1	6412753	6413378	+	0	NA	Intergenic	Intergenic	6854	NM_019089	54626	Hs.118727	NM_019089	ENSG00000069812	HES2	bHLHb40	hes family bHLH transcription factor 2	protein-coding	0.011200	0.468051	
chunk0198_396_1	chr8	141529536	141529776	+	0	NA	Intergenic	Intergenic	-22426	NM_207414	389690	Hs.689547	NM_207414	ENSG00000226807	MROH5	-	maestro heat like repeat family member 5 (gene/pseudogene)	protein-coding	0.029167	0.514523	166(TGGCACACGCAGTACT,-,0.00),167(GGCACACGCAGTACTG,+,0.00)
chunk0179_227_1	chr7	47853762	47854013	+	0	NA	intron (NM_138295, intron 30 of 56)	intron (NM_138295, intron 30 of 56)	58596	NM_001302627	80099	Hs.287647	NM_025031		C7orf69	-	chromosome 7 open reading frame 69	ncRNA	0.011952	0.392857	
chunk0097_40_1	chr2	42910566	42911169	+	0	NA	Intergenic	L2b|LINE|L2	-118256	NM_012205	23498	Hs.368805	NM_012205	ENSG00000162882	HAAO	3-HAO|HAO|VCRL1|h3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding	0.003317	0.445364	
chunk0022_332_1	chr10	16602240	16602901	+	0	NA	intron (NM_152724, intron 7 of 7)	intron (NM_152724, intron 7 of 7)	-80565	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.013616	0.403323	350(AAACACATTGTGTGCT,-,0.00)
chunk0177_18_1	chr7	20542565	20542985	+	0	NA	Intergenic	Intergenic	-72847	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.002381	0.349169	
chunk0142_326_1	chr4	101021028	101021265	+	0	NA	Intergenic	L2c|LINE|L2	219726	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.008439	0.411765	
chunk0011_77_1	chr1	144551217	144551862	+	0	NA	Intergenic	Intergenic	-41329	NM_001164261	645142	Hs.730589	NM_001164261	ENSG00000256374	PPIAL4D	-	peptidylprolyl isomerase A like 4D	protein-coding	0.038760	0.496904	
chunk0115_321_1	chr21	28772080	28772564	+	0	NA	Intergenic	Intergenic	113051	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.004132	0.352577	
chunk0111_237_1	chr20	29438169	29438520	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-21383	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.005698	0.440341	
chunk0148_318_1	chr5	13755086	13755389	+	0	NA	intron (NM_001369, intron 61 of 78)	intron (NM_001369, intron 61 of 78)	189243	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.006601	0.309211	
chunk0168_444_1	chr6	95805197	95805532	+	0	NA	Intergenic	Intergenic	-210605	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.002985	0.363095	
chunk0129_50_1	chr3	117448916	117449417	+	0	NA	Intergenic	Intergenic	527735	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001996	0.274900	
chunk0051_169_1	chr12	116018194	116018634	+	0	NA	intron (NM_015335, intron 7 of 30)	intron (NM_015335, intron 7 of 30)	130240	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.013636	0.333333	
chunk0099_175_1	chr2	89821705	89821905	+	0	NA	Intergenic	(ATTCC)n|Simple_repeat|Simple_repeat	1009435	NR_039635	100616399		NR_039635	ENSG00000265510	MIR4436A	mir-4436a	microRNA 4436a	ncRNA	0.015000	0.388060	
chunk0007_158_1	chr1	79859385	79859961	+	0	NA	Intergenic	L1MC5|LINE|L1	-676082	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.012153	0.376083	
chunk0060_356_1	chr14	52325606	52326093	+	0	NA	intron (NM_000956, intron 1 of 1)	intron (NM_000956, intron 1 of 1)	11551	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.006160	0.434426	
chunk0048_202_1	chr12	81262577	81263047	+	0	NA	intron (NM_003625, intron 31 of 32)	intron (NM_003625, intron 31 of 32)	-16377	NR_120491	102724663	Hs.667264	NR_120491	ENSG00000257467	PPFIA2-AS1	-	PPFIA2 antisense RNA 1	ncRNA	0.004255	0.322718	
chunk0109_311_1	chr20	8955941	8956398	+	0	NA	Intergenic	L1MA8|LINE|L1	-112885	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.000000	0.379913	
chunk0145_363_1	chr4	151321962	151322161	+	0	NA	Intergenic	Intergenic	44888	NM_183375	345062	Hs.651266	NM_183375	ENSG00000189099	PRSS48	ESSPL	serine protease 48	protein-coding	0.005025	0.400000	
chunk0077_405_1	chr16	84976652	84977231	+	0	NA	intron (NM_001145548, intron 8 of 8)	intron (NM_001145548, intron 8 of 8)	34594	NM_001145548	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.027634	0.517241	
chunk0161_452_1	chr5	178893590	178894077	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-2082	NM_030613	80108	Hs.654533	NM_030613	ENSG00000198939	ZFP2	ZNF751|zfp-2	ZFP2 zinc finger protein	protein-coding	0.012320	0.463115	221(AAGAACAGAAAGTTCA,-,0.00),222(AGAACAGAAAGTTCAT,+,0.00)
chunk0041_449_1	chr11	134877437	134877669	+	0	NA	Intergenic	Intergenic	441071	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.012931	0.476395	159(AGGAACACTCTGTATT,-,0.00),160(GGAACACTCTGTATTC,+,0.00)
chunk0123_378_1	chr3	48662839	48663158	+	0	NA	promoter-TSS (NM_001407)	promoter-TSS (NM_001407)	-83	NM_001407	1951	Hs.631926	NM_001407	ENSG00000008300	CELSR3	ADGRC3|CDHF11|EGFL1|FMI1|HFMI1|MEGF2|RESDA1	cadherin EGF LAG seven-pass G-type receptor 3	protein-coding	0.094044	0.656250	
chunk0085_137_1	chr18	3247449	3247982	+	0	NA	5' UTR (NM_006471, exon 1 of 4)	5' UTR (NM_006471, exon 1 of 4)	185	NM_001303047	10627	Hs.190086	NM_006471	ENSG00000101608	MYL12A	HEL-S-24|MLC-2B|MLCB|MRCL3|MRLC3|MYL2B	myosin light chain 12A	protein-coding	0.071295	0.602996	
chunk0045_84_1	chr12	45850340	45850869	+	0	NA	exon (NM_152641, exon 15 of 21)	exon (NM_152641, exon 15 of 21)	120767	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.000000	0.447170	
chunk0090_333_1	chr18	76265480	76266264	+	0	NA	Intergenic	Intergenic	142874	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.011480	0.471338	
chunk0201_312_1	chr9	43130598	43131261	+	0	NA	Intergenic	Intergenic	342529	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.004525	0.415663	172(AGGAACACTGTGTGCC,-,0.00),173(GGAACACTGTGTGCCA,+,0.00)
chunk0079_17_1	chr17	9684870	9685952	+	0	NA	intron (NM_153210, intron 7 of 14)	intron (NM_153210, intron 7 of 14)	39874	NM_153210	124739	Hs.709621	NM_153210	ENSG00000154914	USP43	-	ubiquitin specific peptidase 43	protein-coding	0.012939	0.409972	
chunk0172_356_1	chr6	139115815	139116014	+	0	NA	Intergenic	Intergenic	-19198	NM_016217	51696	Hs.197644	NM_016217	ENSG00000112406	HECA	HDC|HDCL|HHDC|dJ225E12.1	hdc homolog, cell cycle regulator	protein-coding	0.005025	0.440000	
chunk0131_180_1	chr3	147509337	147509864	+	0	NA	non-coding (NR_121655, exon 3 of 3)	non-coding (NR_121655, exon 3 of 3)	88273	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.007590	0.359848	
chunk0197_223_1	chr8	122875142	122875668	+	0	NA	intron (NM_014943, intron 2 of 3)	MER58C|DNA|hAT-Charlie	93743	NM_014943	22882	Hs.377090	NM_014943	ENSG00000178764	ZHX2	AFR1|RAF	zinc fingers and homeoboxes 2	protein-coding	0.009506	0.415560	
chunk0027_310_1	chr10	77911690	77911990	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	14750	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.016667	0.514950	
chunk0153_66_1	chr5	67875456	67876005	+	0	NA	Intergenic	MER121|DNA|hAT?	82517	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.007286	0.401818	
chunk0144_330_1	chr4	139085081	139085586	+	0	NA	promoter-TSS (NM_001276457)	promoter-TSS (NM_001276457)	-919	NM_001276459	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.009901	0.304348	
chunk0118_30_1	chr22	26742139	26742515	+	0	NA	intron (NR_110543, intron 2 of 5)	intron (NR_110543, intron 2 of 5)	69484	NR_110543	102724827	Hs.642767	NR_110543		MIATNB	-	MIAT neighbor	ncRNA	0.010638	0.448276	
chunk0007_210_1	chr1	81517980	81518509	+	0	NA	intron (NR_125943, intron 1 of 3)	intron (NR_125943, intron 1 of 3)	39458	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.015123	0.430189	
chunk0132_133_1	chr3	156230486	156230864	+	0	NA	intron (NM_003471, intron 1 of 13)	L2a|LINE|L2	-2792	NR_046617	100874083	Hs.603823	NR_046617	ENSG00000240596	KCNAB1-AS2	-	KCNAB1 antisense RNA 2	ncRNA	0.002646	0.335092	
chunk0210_347_1	chrX	95885190	95885574	+	0	NA	Intergenic	Intergenic	452520	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.007812	0.420779	
chunk0114_417_1	chr20	64080436	64080743	+	0	NA	promoter-TSS (NM_001039467)	promoter-TSS (NM_001039467)	471	NM_000913	4987	Hs.2859	NM_000913	ENSG00000125510	OPRL1	KOR-3|NOCIR|NOP|NOPr|OOR|ORL1	opioid related nociceptin receptor 1	protein-coding	0.035831	0.594156	147(AAGGCCACACTGTCCC,-,0.00),148(AGGCCACACTGTCCCC,+,0.00)
chunk0021_145_1	chr10	4183441	4184051	+	0	NA	Intergenic	Intergenic	60166	NR_108040	100652988	Hs.433011	NR_108040		LINC00702	-	long intergenic non-protein coding RNA 702	ncRNA	0.011475	0.412439	
chunk0039_216_1	chr11	101187392	101187609	+	0	NA	Intergenic	Intergenic	-57687	NM_000926	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.004608	0.339450	
chunk0084_282_1	chr17	79851284	79851851	+	0	NA	Intergenic	L2a|LINE|L2	-12153	NM_003655	8535	Hs.405046	NM_003655	ENSG00000141582	CBX4	NBP16|PC2	chromobox 4	protein-coding	0.021164	0.484155	
chunk0143_187_1	chr4	112251012	112251663	+	0	NA	intron (NM_001128426, intron 1 of 8)	intron (NM_001128426, intron 1 of 8)	19598	NM_001128426	55435	Hs.435991	NM_018569	ENSG00000138660	AP1AR	2C18|C4orf16|GBAR|PRO0971|gamma-BAR	adaptor related protein complex 1 associated regulatory protein	protein-coding	0.004608	0.418712	374(TAGAACATGGTGTTCT,-,0.00),375(AGAACATGGTGTTCTG,+,0.00)
chunk0155_35_1	chr5	91078714	91079473	+	0	NA	intron (NR_003149, intron 86 of 89)	intron (NR_003149, intron 86 of 89)	235309	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.002635	0.393421	375(GTAACAGTATGTACTT,+,0.00)
chunk0024_375_1	chr10	44596832	44597244	+	0	NA	Intergenic	L1PA8|LINE|L1	-211941	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.002427	0.384988	
chunk0178_142_1	chr7	33052672	33052964	+	0	NA	intron (NM_001002009, intron 1 of 9)	MER5A|DNA|hAT-Charlie	9979	NM_001002010	51251	Hs.487933	NM_016489	ENSG00000122643	NT5C3A	NT5C3|P5'N-1|P5N-1|PN-I|POMP|PSN1|UMPH|UMPH1|cN-III|hUMP1|p36	5'-nucleotidase, cytosolic IIIA	protein-coding	0.003425	0.372014	
chunk0103_278_1	chr2	165896605	165896804	+	0	NA	intron (NM_024753, intron 22 of 28)	L2a|LINE|L2	-24763	NR_045375	100506124	Hs.709870	NR_045375		LOC100506124	-	uncharacterized LOC100506124	ncRNA	0.005025	0.435000	
chunk0159_391_1	chr5	146966234	146966527	+	0	NA	intron (NM_001271900, intron 2 of 10)	intron (NM_001271900, intron 2 of 10)	-46874	NR_047115	100874361	Hs.193825	NR_047115	ENSG00000249553	PPP2R2B-IT1	-	PPP2R2B intronic transcript 1	ncRNA	0.017065	0.510204	
chunk0098_6_1	chr2	65097640	65097972	+	0	NA	intron (NM_004161, intron 3 of 5)	intron (NM_004161, intron 3 of 5)	32495	NM_004161	5861	Hs.310645	NM_004161	ENSG00000138069	RAB1A	RAB1|YPT1	RAB1A, member RAS oncogene family	protein-coding	0.000000	0.261261	
chunk0073_85_1	chr16	4046191	4046624	+	0	NA	intron (NM_001116, intron 2 of 10)	intron (NM_001116, intron 2 of 10)	69778	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.023095	0.481567	
chunk0113_341_1	chr20	58690226	58691208	+	0	NA	intron (NM_001204872, intron 1 of 12)	intron (NM_001204872, intron 1 of 12)	1586	NM_001204872	79716	Hs.654868	NM_024663	ENSG00000215440	NPEPL1	bA261P9.2	aminopeptidase like 1	protein-coding	0.009165	0.392675	
chunk0129_211_1	chr3	121749640	121750076	+	0	NA	promoter-TSS (NM_001256487)	promoter-TSS (NM_001256487)	-91	NM_001256487	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.055046	0.567506	
chunk0035_23_1	chr11	40354915	40355114	+	0	NA	intron (NM_020929, intron 2 of 4)	L1MA3|LINE|L1	-61884	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.010050	0.505000	
chunk0171_154_1	chr6	124008146	124008616	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	204535	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.010638	0.397028	
chunk0024_246_1	chr10	38878779	38879026	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	182306	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.032389	0.383065	
chunk0112_162_1	chr20	39463658	39464237	+	0	NA	Intergenic	Intergenic	-239199	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.003454	0.365517	111(GAGCACAGTCTGACCT,-,0.00),112(AGCACAGTCTGACCTT,+,0.00)
chunk0157_347_1	chr5	122858131	122858912	+	0	NA	intron (NM_014035, intron 1 of 6)	L1MC5|LINE|L1	13056	NM_014035	28966	Hs.483200	NM_014035	ENSG00000064652	SNX24	PRO1284|SBBI31	sorting nexin 24	protein-coding	0.005122	0.351662	
chunk0192_207_1	chr8	64984471	64984904	+	0	NA	Intergenic	Intergenic	-185896	NM_004820	9420	Hs.657330	NM_004820	ENSG00000172817	CYP7B1	CBAS3|CP7B|SPG5A	cytochrome P450 family 7 subfamily B member 1	protein-coding	0.000000	0.267281	
chunk0091_289_1	chr19	12294795	12295129	+	0	NA	promoter-TSS (NM_001164276)	promoter-TSS (NM_001164276)	-63	NM_016264	51710	Hs.296731	NM_016264	ENSG00000197857	ZNF44	GIOT-2|KOX7|ZNF|ZNF504|ZNF55|ZNF58	zinc finger protein 44	protein-coding	0.053892	0.591045	
chunk0068_129_1	chr15	52656386	52656879	+	0	NA	intron (NM_019600, intron 2 of 12)	intron (NM_019600, intron 2 of 12)	-4582	NM_001286495	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.002028	0.311741	
chunk0126_438_1	chr3	87115742	87116129	+	0	NA	intron (NR_104153, intron 1 of 2)	intron (NR_104153, intron 1 of 2)	26655	NR_047469	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.002584	0.337629	
chunk0156_90_1	chr5	104698714	104699092	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-400571	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.007937	0.551451	
chunk0207_383_1	chr9	136282426	136282754	+	0	NA	intron (NR_111982, intron 9 of 9)	intron (NR_111982, intron 9 of 9)	21504	NR_111982	399693	Hs.530383	NM_001291516	ENSG00000260220	CCDC187	-	coiled-coil domain containing 187	protein-coding	0.024390	0.623100	
chunk0082_90_1	chr17	53321680	53322324	+	0	NA	Intergenic	L1MC1|LINE|L1	336482	NM_001243552	100506650	Hs.146556	NM_001243552		C17orf112	-	chromosome 17 open reading frame 112	protein-coding	0.006211	0.334884	
chunk0080_30_1	chr17	21126761	21126985	+	0	NA	promoter-TSS (NM_015510)	promoter-TSS (NM_015510)	-55	NM_015510	25979	Hs.386989	NM_015510	ENSG00000109016	DHRS7B	CGI-93|SDR32C1	dehydrogenase/reductase 7B	protein-coding	0.080357	0.595556	
chunk0203_106_1	chr9	84519379	84519866	+	0	NA	Intergenic	Intergenic	-148836	NM_001291937	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.010267	0.405738	
chunk0168_112_1	chr6	81086898	81087302	+	0	NA	Intergenic	Intergenic	665611	NM_017633	55603	Hs.10784	NM_017633	ENSG00000112773	TENT5A	C6orf37|FAM46A|OI18|XTP11	terminal nucleotidyltransferase 5A	protein-coding	0.004950	0.360494	160(AGGAACTGCTTGTTCC,-,0.00),161(GGAACTGCTTGTTCCC,+,0.00)
chunk0002_232_1	chr1	20302103	20302336	+	0	NA	intron (NM_001039500, intron 1 of 21)	intron (NM_001039500, intron 1 of 21)	11300	NM_001039500	127731	Hs.205178	NM_144623	ENSG00000158816	VWA5B1	-	von Willebrand factor A domain containing 5B1	protein-coding	0.004292	0.538462	
chunk0079_292_1	chr17	16900285	16900595	+	0	NA	Intergenic	Intergenic	-67607	NR_029392	400578	Hs.723586	NR_029392		KRT16P2	-	keratin 16 pseudogene 2	pseudo	0.006452	0.527331	
chunk0107_349_1	chr2	221741768	221742225	+	0	NA	Intergenic	L2c|LINE|L2	-167794	NM_001304536	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.004376	0.388646	
chunk0094_131_1	chr2	4863030	4863564	+	0	NA	Intergenic	Intergenic	-207075	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.001873	0.386916	
chunk0011_317_1	chr1	151950187	151950416	+	0	NA	Intergenic	Intergenic	-40416	NM_053055	117145	Hs.164070	NM_053055	ENSG00000159445	THEM4	CTMP	thioesterase superfamily member 4	protein-coding	0.021834	0.513043	
chunk0175_145_1	chr7	3610013	3610352	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	308734	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005900	0.329412	
chunk0006_418_1	chr1	76081064	76081603	+	0	NA	intron (NM_152996, intron 1 of 4)	MER30|DNA|hAT-Charlie	6629	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.012987	0.392593	
chunk0041_430_1	chr11	134398048	134398600	+	0	NA	intron (NM_054025, intron 1 of 5)	intron (NM_054025, intron 1 of 5)	13594	NM_054025	27087	Hs.381050	NM_018644	ENSG00000109956	B3GAT1	CD57|GLCATP|GLCUATP|HNK1|LEU7|NK-1|NK1	beta-1,3-glucuronyltransferase 1	protein-coding	0.023551	0.524412	
chunk0048_238_1	chr12	81565337	81565849	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	32778	NM_001220478	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.007812	0.384016	
chunk0191_168_1	chr8	50483452	50483893	+	0	NA	intron (NM_018967, intron 8 of 18)	intron (NM_018967, intron 8 of 18)	571893	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.004535	0.359729	
chunk0047_346_1	chr12	74817402	74817702	+	0	NA	Intergenic	MER52A|LTR|ERV1	279781	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.013333	0.564784	140(GGGCACACCGTGTTCC,-,0.00),141(GGCACACCGTGTTCCC,+,0.00)
chunk0003_7_1	chr1	28643085	28643284	+	0	NA	promoter-TSS (NM_001135218)	promoter-TSS (NM_001135218)	-92	NM_005644	6883	Hs.530251	NM_005644	ENSG00000120656	TAF12	TAF2J|TAFII20	TATA-box binding protein associated factor 12	protein-coding	0.110553	0.640000	
chunk0033_92_1	chr11	14144841	14145408	+	0	NA	intron (NM_006108, intron 6 of 15)	intron (NM_006108, intron 6 of 15)	182487	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.003527	0.413732	
chunk0098_251_1	chr2	75035407	75036133	+	0	NA	Intergenic	MIR|SINE|MIR	-55042	NR_049796	100846995		NR_049796	ENSG00000263909	MIR5000	-	microRNA 5000	ncRNA	0.002755	0.310867	357(CAGAACATGCTGAACC,-,0.00),358(AGAACATGCTGAACCC,+,0.00)
chunk0118_286_1	chr22	33860872	33861169	+	0	NA	intron (NM_004737, intron 1 of 15)	intron (NM_004737, intron 1 of 15)	59408	NM_004737	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.033670	0.570470	
chunk0044_158_1	chr12	29843582	29843878	+	0	NA	Intergenic	L1ME4a|LINE|L1	-58971	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.010135	0.353535	
chunk0022_308_1	chr10	15796997	15797789	+	0	NA	intron (NM_024948, intron 10 of 14)	Tigger20a|DNA|TcMar-Tigger	63127	NM_024948	80013	Hs.158870	NM_024948	ENSG00000148481	MINDY3	C10orf97|CARP|DERP5|FAM188A|MST126|MSTP126|my042	MINDY lysine 48 deubiquitinase 3	protein-coding	0.003788	0.365700	
chunk0050_43_1	chr12	100609453	100609745	+	0	NA	intron (NM_001303130, intron 4 of 8)	L1MA2|LINE|L1	15981	NM_001303131	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.006849	0.546075	
chunk0149_123_1	chr5	19497148	19498366	+	0	NA	intron (NM_004934, intron 11 of 12)	intron (NM_004934, intron 11 of 12)	388515	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004926	0.351928	453(TGGAACATTGTGTTAC,-,0.00)
chunk0197_157_1	chr8	120455705	120456081	+	0	NA	intron (NM_022045, intron 6 of 21)	intron (NM_022045, intron 6 of 21)	-10486	NM_014078	28998	Hs.333823	NM_014078	ENSG00000172172	MRPL13	L13|L13A|L13mt|RPL13|RPML13	mitochondrial ribosomal protein L13	protein-coding	0.002660	0.278515	134(AAGCACACTGTGTGCT,-,0.00),135(AGCACACTGTGTGCTT,+,0.00)
chunk0122_212_1	chr3	33273541	33274173	+	0	NA	Intergenic	FLAM_C|SINE|Alu	-3585	NM_012157	25827	Hs.475872	NM_012157	ENSG00000153558	FBXL2	FBL2|FBL3	F-box and leucine rich repeat protein 2	protein-coding	0.007911	0.377567	
chunk0165_115_1	chr6	32901084	32901289	+	0	NA	non-coding (NR_037178, exon 2 of 2)	non-coding (NR_037178, exon 2 of 2)	7010	NR_037177	100294145	Hs.559456	NR_037177		LOC100294145	-	uncharacterized LOC100294145	ncRNA	0.004878	0.388350	
chunk0053_186_1	chr13	31092765	31093540	+	0	NA	Intergenic	Intergenic	68869	NM_001286503	10808	Hs.743267	NM_006644	ENSG00000120694	HSPH1	HSP105|HSP105A|HSP105B|NY-CO-25	heat shock protein family H (Hsp110) member 1	protein-coding	0.007742	0.487113	236(GAGCTCATGGTGTGCT,-,0.00),380(CTGAACAGCATGTTCT,-,0.00),381(TGAACAGCATGTTCTG,+,0.00)
chunk0119_161_1	chr22	43185594	43186375	+	0	NA	intron (NM_015140, intron 1 of 13)	intron (NM_015140, intron 1 of 13)	1147	NM_015140	23170	Hs.517670	NM_015140	ENSG00000100304	TTLL12	dJ526I14.2	tubulin tyrosine ligase like 12	protein-coding	0.032010	0.588235	
chunk0126_361_1	chr3	83214696	83215232	+	0	NA	Intergenic	L1MC1|LINE|L1	-1453165	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.005597	0.320298	
chunk0182_75_1	chr7	92296961	92297419	+	0	NA	intron (NM_019004, intron 2 of 19)	MIR|SINE|MIR	50956	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.006550	0.372549	
chunk0195_14_1	chr8	93007883	93008244	+	0	NA	Intergenic	L1PA10|LINE|L1	-21688	NR_107051	102467005		NR_107051	ENSG00000277063	MIR8084	hsa-mir-8084	microRNA 8084	ncRNA	0.005540	0.444751	
chunk0025_154_1	chr10	52415827	52416036	+	0	NA	Intergenic	L1MC4|LINE|L1	39341	NR_120642	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.009569	0.371429	
chunk0211_162_1	chrX	114797504	114797797	+	0	NA	intron (NM_001256760, intron 5 of 6)	intron (NM_001256760, intron 5 of 6)	-25804	NR_029955	554212		NR_029955	ENSG00000199001	MIR448	MIRN448|hsa-mir-448|miRNA448	microRNA 448	ncRNA	0.000000	0.397959	132(AGGAGCACATTGTTCC,-,0.00),133(GGAGCACATTGTTCCA,+,0.00)
chunk0127_230_1	chr3	96777597	96778183	+	0	NA	Intergenic	Intergenic	-36691	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.010239	0.395230	
chunk0074_128_1	chr16	22717775	22718260	+	0	NA	Intergenic	Intergenic	-96522	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.006186	0.353909	
chunk0020_320_1	chr1	237706272	237706471	+	0	NA	intron (NM_001035, intron 67 of 104)	intron (NM_001035, intron 67 of 104)	-155804	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.005025	0.440000	
chunk0164_100_1	chr6	20441953	20442308	+	0	NA	intron (NM_001243076, intron 1 of 6)	intron (NM_001243076, intron 1 of 6)	38451	NM_001243076	1871	Hs.269408	NM_001949	ENSG00000112242	E2F3	E2F-3	E2F transcription factor 3	protein-coding	0.016901	0.488764	
chunk0047_275_1	chr12	73072521	73072742	+	0	NA	Intergenic	L1PA14|LINE|L1	-86559	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.004525	0.554054	
chunk0036_377_1	chr11	67512794	67513347	+	0	NA	Intergenic	L1MC3|LINE|L1	-4342	NM_005851	10263	Hs.523835	NM_005851	ENSG00000167797	CDK2AP2	DOC-1R|p14	cyclin dependent kinase 2 associated protein 2	protein-coding	0.012658	0.456679	
chunk0057_303_1	chr13	106437460	106437905	+	0	NA	Intergenic	Intergenic	61119	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.011236	0.369955	287(CAGTACAAGTTGTTCT,-,0.00),288(AGTACAAGTTGTTCTT,+,0.00)
chunk0036_366_1	chr11	67136669	67137136	+	0	NA	intron (NR_027473, intron 2 of 20)	L2c|LINE|L2	17633	NM_012308	22992	Hs.124147	NM_012308	ENSG00000173120	KDM2A	CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA	lysine demethylase 2A	protein-coding	0.002141	0.414530	
chunk0116_238_1	chr21	38312690	38313168	+	0	NA	Intergenic	Intergenic	33147	NR_110545	102724678	Hs.635675	NR_110545		LINC01423	-	long intergenic non-protein coding RNA 1423	ncRNA	0.002092	0.413361	
chunk0212_346_1	chrX	147219975	147220284	+	0	NA	Intergenic	L1M5|LINE|L1	5823	NR_030232	574510		NR_030232	ENSG00000207984	MIR513A2	MIRN513-2|MIRN513A-2|MIRN513A2|hsa-mir-513a-2	microRNA 513a-2	ncRNA	0.006472	0.306452	
chunk0105_421_1	chr2	193162451	193162998	+	0	NA	Intergenic	Intergenic	412879	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.001828	0.348540	
chunk0107_6_1	chr2	209946582	209946999	+	0	NA	intron (NM_032504, intron 46 of 63)	intron (NM_032504, intron 46 of 63)	-55775	NM_006916	6120	Hs.282260	NM_006916	ENSG00000197713	RPE	RPE2-1	ribulose-5-phosphate-3-epimerase	protein-coding	0.004796	0.377990	
chunk0066_72_1	chr15	29275822	29276300	+	0	NA	intron (NM_015307, intron 2 of 10)	intron (NM_015307, intron 2 of 10)	-6245	NM_138704	56160	Hs.94011	NM_138704	ENSG00000185115	NSMCE3	HCA4|LICS|MAGEG1|MAGEL3|NDNL2|NSE3	NSE3 homolog, SMC5-SMC6 complex component	protein-coding	0.002092	0.434238	271(ATAACACTTTGTCCCT,+,0.00)
chunk0121_92_1	chr3	16576528	16576888	+	0	NA	Intergenic	L1MA4|LINE|L1	28082	NM_001190811	1618	Hs.131179	NM_001351	ENSG00000092345	DAZL	DAZH|DAZL1|DAZLA|SPGYLA	deleted in azoospermia like	protein-coding	0.005556	0.551247	
chunk0073_23_1	chr16	2264766	2265064	+	0	NA	intron (NM_080594, intron 1 of 7)	intron (NM_080594, intron 1 of 7)	2422	NM_001286625	10921	Hs.355643	NM_006711	ENSG00000205937	RNPS1	E5.1	RNA binding protein with serine rich domain 1	protein-coding	0.020134	0.464883	
chunk0006_168_1	chr1	66538397	66538934	+	0	NA	intron (NM_032291, intron 1 of 24)	Tigger16a|DNA|TcMar-Tigger	4709	NM_032291	84251	Hs.132121	NM_032291	ENSG00000118473	SGIP1	-	SH3 domain GRB2 like endophilin interacting protein 1	protein-coding	0.000000	0.323420	
chunk0198_210_1	chr8	133824627	133825267	+	0	NA	Intergenic	MIRb|SINE|MIR	-47595	NR_125422	101927798	Hs.615036	NR_125422	ENSG00000253165	LOC101927798	-	uncharacterized LOC101927798	ncRNA	0.012500	0.449298	
chunk0185_445_1	chr7	134966701	134967113	+	0	NA	intron (NM_033157, intron 14 of 14)	intron (NM_033157, intron 14 of 14)	-19601	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.007282	0.430993	
chunk0017_124_1	chr1	206416129	206416373	+	0	NA	intron (NM_001170637, intron 10 of 21)	intron (NM_001170637, intron 10 of 21)	-53992	NM_001193322	9641	Hs.321045	NM_014002	ENSG00000263528	IKBKE	IKK-E|IKK-i|IKKE|IKKI	inhibitor of nuclear factor kappa B kinase subunit epsilon	protein-coding	0.020492	0.502041	
chunk0028_323_1	chr10	91968057	91968806	+	0	NA	intron (NM_003972, intron 14 of 37)	L1MC2|LINE|L1	44452	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.005340	0.362667	
chunk0145_70_1	chr4	145670437	145671054	+	0	NA	Intergenic	Intergenic	-9459	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.001621	0.378641	
chunk0154_397_1	chr5	88306036	88306755	+	0	NA	intron (NR_105019, intron 6 of 7)	L1P2|LINE|L1	37379	NR_105019	100505894	Hs.559426	NR_039993	ENSG00000247828	TMEM161B-AS1	linc-POLR3G-8	TMEM161B antisense RNA 1	ncRNA	0.015299	0.525000	
chunk0084_428_1	chr17	82584791	82585211	+	0	NA	intron (NM_004514, intron 6 of 8)	intron (NM_004514, intron 6 of 8)	63534	NM_019613	56270	Hs.132161	NM_019613	ENSG00000141580	WDR45B	NEDSBAS|WDR45L|WIPI-3|WIPI3	WD repeat domain 45B	protein-coding	0.014286	0.536817	
chunk0102_101_1	chr2	144303730	144304739	+	0	NA	intron (NM_001164629, intron 1 of 11)	L1ME1|LINE|L1	-9741	NM_001006636	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.006938	0.371287	
chunk0190_206_1	chr8	35575021	35575547	+	0	NA	intron (NM_080872, intron 3 of 16)	intron (NM_080872, intron 3 of 16)	135036	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.005703	0.383302	
chunk0124_217_1	chr3	56141204	56141563	+	0	NA	intron (NR_132749, intron 5 of 17)	MLT1G|LTR|ERVL-MaLR	-288789	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.002786	0.486111	
chunk0057_316_1	chr13	106731588	106731984	+	0	NA	Intergenic	Intergenic	77906	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.010101	0.367758	156(TGGCACTCACTGTCCT,-,0.00),157(GGCACTCACTGTCCTA,+,0.00)
chunk0038_197_1	chr11	86198207	86198827	+	0	NA	Intergenic	L1MC1|LINE|L1	-45867	NM_001308007	8726	Hs.503510	NM_003797	ENSG00000074266	EED	COGIS|HEED|WAIT1	embryonic ectoderm development	protein-coding	0.001613	0.346216	
chunk0098_349_1	chr2	77340178	77341032	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	181763	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.003513	0.321637	
chunk0189_453_1	chr8	28348041	28348728	+	0	NA	3' UTR (NM_018660, exon 10 of 10)	3' UTR (NM_018660, exon 10 of 10)	9736	NM_001284244	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.017467	0.452035	325(CAGAACGAGCTGTTCC,-,0.00),326(AGAACGAGCTGTTCCT,+,0.00)
chunk0051_181_1	chr12	116131292	116131657	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	17180	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.010959	0.379781	
chunk0139_365_1	chr4	60383100	60383620	+	0	NA	Intergenic	Intergenic	-539259	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.312860	
chunk0040_392_1	chr11	120146455	120146816	+	0	NA	Intergenic	MIR|SINE|MIR	-8480	NM_012101	23650	Hs.504115	NM_012101	ENSG00000137699	TRIM29	ATDC	tripartite motif containing 29	protein-coding	0.019391	0.469613	158(TGGAACTCCATGTACT,-,0.00),159(GGAACTCCATGTACTC,+,0.00)
chunk0165_465_1	chr6	41288509	41288816	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-1943	NM_001242589	54210	Hs.283022	NM_018643	ENSG00000124731	TREM1	CD354|TREM-1	triggering receptor expressed on myeloid cells 1	protein-coding	0.013029	0.435065	
chunk0119_411_1	chr22	49698036	49698463	+	0	NA	Intergenic	L1MEd|LINE|L1	-40707	NR_110522	348645	Hs.133159	NM_198851	ENSG00000188511	C22orf34	-	chromosome 22 open reading frame 34	protein-coding	0.014052	0.408879	
chunk0212_275_1	chrX	139870482	139870799	+	0	NA	Intergenic	L1ME3G|LINE|L1	-38352	NM_001010986	286410	Hs.88252	NM_173694	ENSG00000101974	ATP11C	ATPIG|ATPIQ|HACXL	ATPase phospholipid transporting 11C	protein-coding	0.022082	0.323899	
chunk0084_354_1	chr17	81335430	81335753	+	0	NA	Intergenic	MIRb|SINE|MIR	-4917	NM_178520	284186	Hs.364191	NM_178520		TMEM105	-	TMEM105 long non-coding RNA	ncRNA	0.009288	0.512346	
chunk0137_291_1	chr4	23951110	23951544	+	0	NA	Intergenic	L2b|LINE|L2	-61250	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.002304	0.411494	
chunk0093_235_1	chr19	50690437	50690636	+	0	NA	intron (NM_016148, intron 14 of 22)	intron (NM_016148, intron 14 of 22)	26402	NM_016148	50944	Hs.274255	NM_016148	ENSG00000161681	SHANK1	SPANK-1|SSTRIP|synamon	SH3 and multiple ankyrin repeat domains 1	protein-coding	0.010050	0.535000	
chunk0142_43_1	chr4	91019446	91019700	+	0	NA	intron (NM_001145065, intron 9 of 10)	intron (NM_001145065, intron 9 of 10)	784542	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.000000	0.294118	
chunk0015_109_1	chr1	185170192	185170617	+	0	NA	intron (NM_017673, intron 4 of 18)	intron (NM_017673, intron 4 of 18)	13245	NM_017673	54823	Hs.134183	NM_017673	ENSG00000116668	SWT1	C1orf26|HsSwt1	SWT1 RNA endoribonuclease homolog	protein-coding	0.011765	0.495305	
chunk0147_317_1	chr4	184962315	184962615	+	0	NA	Intergenic	Intergenic	-24025	NR_039660	100616111		NR_039660	ENSG00000263458	MIR4455	-	microRNA 4455	ncRNA	0.030000	0.508306	114(GAGTGCACACTGTACC,-,0.00)
chunk0050_60_1	chr12	101210763	101211278	+	0	NA	promoter-TSS (NM_145913).2	promoter-TSS (NM_145913).2	-782	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.005825	0.327519	
chunk0077_133_1	chr16	78568758	78569044	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	469488	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.013986	0.428571	
chunk0004_237_1	chr1	47249800	47250212	+	0	NA	TTS (NM_001282937)	TTS (NM_001282937)	-17671	NM_001290406	6886	Hs.705618	NM_003189	ENSG00000162367	TAL1	SCL|TCL5|bHLHa17|tal-1	TAL bHLH transcription factor 1, erythroid differentiation factor	protein-coding	0.007282	0.334140	
chunk0029_250_1	chr10	102799969	102800277	+	0	NA	intron (NM_017787, intron 2 of 3)	intron (NM_017787, intron 2 of 3)	23992	NM_017787	54838	Hs.500897	NM_017787	ENSG00000166272	WBP1L	C10orf26|OPA1L|OPAL1	WW domain binding protein 1 like	protein-coding	0.000000	0.472492	142(GAGGACACACAGTGCC,-,0.00),143(AGGACACACAGTGCCA,+,0.00)
chunk0046_30_1	chr12	54445193	54445672	+	0	NA	intron (NR_120487, intron 3 of 3)	MIRb|SINE|MIR	25647	NR_120488	102724050	Hs.670941	NR_120486	ENSG00000258137	LOC102724050	-	uncharacterized LOC102724050	ncRNA	0.004175	0.404167	
chunk0075_92_1	chr16	48357348	48357659	+	0	NA	intron (NR_040677, intron 1 of 1)	intron (NR_040677, intron 1 of 1)	1818	NR_040677	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.012862	0.410256	
chunk0008_157_1	chr1	92538331	92538658	+	0	NA	intron (NM_001308248, intron 18 of 18)	intron (NM_001308248, intron 18 of 18)	-51618	NM_005263	2672	Hs.73172	NM_005263	ENSG00000162676	GFI1	GFI-1|GFI1A|SCN2|ZNF163	growth factor independent 1 transcriptional repressor	protein-coding	0.000000	0.344512	
chunk0030_5_1	chr10	110824010	110824589	+	0	NA	intron (NM_001134363, intron 12 of 13)	intron (NM_001134363, intron 12 of 13)	46605	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.012090	0.439655	
chunk0111_346_1	chr20	33281869	33282068	+	0	NA	Intergenic	Intergenic	-1167	NM_033197	92747	Hs.65551	NM_033197	ENSG00000125999	BPIFB1	C20orf114|LPLUNC1	BPI fold containing family B member 1	protein-coding	0.015075	0.530000	
chunk0133_145_1	chr3	169294331	169294867	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-146865	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.003731	0.443203	
chunk0170_385_1	chr6	116991442	116991944	+	0	NA	Intergenic	Intergenic	114480	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.005976	0.335984	
chunk0188_442_1	chr8	19291583	19291837	+	0	NA	Intergenic	Intergenic	-21860	NM_001174160	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.015748	0.462745	
chunk0058_159_1	chr14	23255198	23255535	+	0	NA	intron (NM_001282322, intron 4 of 14)	intron (NM_001282322, intron 4 of 14)	17448	NM_001282322	100507650		NM_001282322	ENSG00000215277	RNF212B	C14orf164	ring finger protein 212B	protein-coding	0.000000	0.325444	
chunk0114_176_1	chr21	14863540	14863754	+	0	NA	Intergenic	Intergenic	201158	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.004673	0.306977	
chunk0114_167_1	chr21	14266913	14267674	+	0	NA	Intergenic	Intergenic	-6506	NR_003088	150000	Hs.366575	NM_138726	ENSG00000243064	ABCC13	ABCC13P|C21orf73|PRED6	ATP binding cassette subfamily C member 13 (pseudogene)	pseudo	0.006570	0.391076	
chunk0134_359_1	chr3	182651459	182651825	+	0	NA	Intergenic	Intergenic	-141861	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.021858	0.465940	
chunk0094_318_1	chr2	8957452	8957651	+	0	NA	intron (NM_138799, intron 2 of 12)	intron (NM_138799, intron 2 of 12)	46196	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.000000	0.365000	
chunk0039_203_1	chr11	100919113	100919540	+	0	NA	intron (NM_152432, intron 5 of 23)	MER68|LTR|ERVL	-72754	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.007026	0.446262	
chunk0054_239_1	chr13	46120101	46120613	+	0	NA	Intergenic	Intergenic	-15281	NM_001872	1361	Hs.512937	NM_001872	ENSG00000080618	CPB2	CPU|PCPB|TAFI	carboxypeptidase B2	protein-coding	0.005859	0.469786	
chunk0194_202_1	chr8	85660088	85660339	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	2300	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.019920	0.380952	
chunk0190_38_1	chr8	29316463	29316978	+	0	NA	Intergenic	Intergenic	32085	NM_057158	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.015534	0.432171	
chunk0192_98_1	chr8	61496169	61496488	+	0	NA	intron (NM_173519, intron 5 of 5)	intron (NM_173519, intron 5 of 5)	193521	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.006270	0.471875	
chunk0185_65_1	chr7	124919558	124920421	+	0	NA	intron (NR_003102, intron 2 of 19)	LTR75B|LTR|ERVL	-9884	NR_125718	401398	Hs.658551	NM_001023566	ENSG00000224897	POT1-AS1	-	POT1 antisense RNA 1	ncRNA	0.005794	0.393519	
chunk0062_385_1	chr14	74680382	74680965	+	0	NA	intron (NM_001039479, intron 5 of 19)	L1MD1|LINE|L1	32431	NM_001039479	9870	Hs.497417	NM_014821	ENSG00000119682	AREL1	FIEL1|KIAA0317	apoptosis resistant E3 ubiquitin protein ligase 1	protein-coding	0.001715	0.373288	
chunk0156_287_1	chr5	109987754	109988503	+	0	NA	Intergenic	Intergenic	104946	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.008011	0.372000	380(GGGAACAGCTTGTGCC,-,0.00),381(GGAACAGCTTGTGCCT,+,0.00)
chunk0165_32_1	chr6	29905124	29905422	+	0	NA	Intergenic	Intergenic	17513	NR_001434	3136	Hs.728808	NR_001434		HLA-H	HLAHP	major histocompatibility complex, class I, H (pseudogene)	pseudo	0.003356	0.431438	
chunk0012_429_1	chr1	164704260	164704929	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	70047	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.004484	0.328358	390(TAGGACTCTATGTACC,-,0.00),391(AGGACTCTATGTACCA,+,0.00)
chunk0109_102_1	chr20	2320944	2321555	+	0	NA	intron (NM_003245, intron 7 of 12)	intron (NM_003245, intron 7 of 12)	25282	NM_003245	7053	Hs.2022	NM_003245	ENSG00000125780	TGM3	TGE|UHS2	transglutaminase 3	protein-coding	0.006547	0.486928	
chunk0005_89_1	chr1	56311762	56312085	+	0	NA	Intergenic	L2c|LINE|L2	267661	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.003096	0.404321	
chunk0082_287_1	chr17	58110488	58111145	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	27397	NM_080677	140735	Hs.720595	NM_080677	ENSG00000264364	DYNLL2	DNCL1B|Dlc2|RSPH22	dynein light chain LC8-type 2	protein-coding	0.001522	0.430091	460(CTGGACATGCTGTGCT,-,0.00),461(TGGACATGCTGTGCTG,+,0.00)
chunk0045_95_1	chr12	46024304	46024712	+	0	NA	Intergenic	L1PB2|LINE|L1	-33890	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.002451	0.518337	104(GAGGACATAAAGTTCC,-,0.00),105(AGGACATAAAGTTCCC,+,0.00)
chunk0010_442_1	chr1	120176101	120176300	+	0	NA	intron (NM_004892, intron 1 of 4)	CpG	321	NM_004892	9554	Hs.632438	NM_004892	ENSG00000265808	SEC22B	ERS-24|SEC22L1	SEC22 homolog B, vesicle trafficking protein (gene/pseudogene)	protein-coding	0.060302	0.530000	
chunk0111_275_1	chr20	31184951	31185246	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-72566	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.020339	0.402027	
chunk0181_454_1	chr7	90754553	90755018	+	0	NA	intron (NM_001287136, intron 3 of 13)	L1PA16|LINE|L1	44969	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.012903	0.360515	
chunk0113_259_1	chr20	56248012	56248465	+	0	NA	promoter-TSS (NM_019888)	promoter-TSS (NM_019888)	-494	NM_019888	4159	Hs.248018	NM_019888	ENSG00000124089	MC3R	BMIQ9|MC3|MC3-R|OB20|OQTL	melanocortin 3 receptor	protein-coding	0.013245	0.495595	
chunk0106_289_1	chr2	204246404	204246649	+	0	NA	Intergenic	Intergenic	-299267	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.012245	0.369919	
chunk0023_314_1	chr10	29056772	29056986	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	210471	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.004673	0.437209	
chunk0108_60_1	chr2	227199642	227200070	+	0	NA	intron (NM_000091, intron 1 of 51)	intron (NM_000091, intron 1 of 51)	35291	NM_000091	1285	Hs.570065	NM_000091	ENSG00000169031	COL4A3	ATS2|ATS3	collagen type IV alpha 3 chain	protein-coding	0.007009	0.386946	
chunk0122_218_1	chr3	33499561	33500131	+	0	NA	intron (NM_015097, intron 38 of 38)	MIR|SINE|MIR	-59441	NM_001128161	7342	Hs.729120	NM_014517	ENSG00000153560	UBP1	LBP-1B|LBP-1a|LBP1A|LBP1B	upstream binding protein 1	protein-coding	0.007018	0.395797	
chunk0019_244_1	chr1	227442450	227442649	+	0	NA	Intergenic	L2c|LINE|L2	-120970	NR_102302	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.005025	0.345000	164(TTGTACACAATGTGCC,-,0.00),165(TGTACACAATGTGCCA,+,0.00)
chunk0053_294_1	chr13	33642756	33643066	+	0	NA	intron (NM_001243476, intron 3 of 17)	intron (NM_001243476, intron 3 of 17)	33924	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.009677	0.446945	
chunk0097_43_1	chr2	43106117	43106347	+	0	NA	Intergenic	Intergenic	-66689	NR_110585	102723854	Hs.570165	NR_110585	ENSG00000231826	LINC01819	-	long intergenic non-protein coding RNA 1819	ncRNA	0.008696	0.484848	188(GGAGACATCATGTTCC,-,0.00),189(GAGACATCATGTTCCC,+,0.00)
chunk0203_415_1	chr9	90929529	90929984	+	0	NA	Intergenic	L2b|LINE|L2	102336	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.010989	0.423246	226(GAGAACACTGTGTCCA,-,0.00),227(AGAACACTGTGTCCAA,+,0.00)
chunk0146_383_1	chr4	168524032	168524519	+	0	NA	intron (NM_016081, intron 2 of 20)	intron (NM_016081, intron 2 of 20)	27209	NM_001166108	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.000000	0.327869	
chunk0139_87_1	chr4	49510748	49511144	+	0	NA	Intergenic	Intergenic	524304	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.012626	0.372796	
chunk0022_302_1	chr10	15603395	15604001	+	0	NA	intron (NM_001291494, intron 19 of 28)	intron (NM_001291494, intron 19 of 28)	116637	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.006601	0.415157	284(AAGACCAGGCTGTTCC,-,0.00),285(AGACCAGGCTGTTCCT,+,0.00)
chunk0093_95_1	chr19	43342133	43342365	+	0	NA	Intergenic	L1MB3|LINE|L1	-6807	NR_026881	23574	Hs.721578	NR_026881		PRG1	-	p53-responsive gene 1	ncRNA	0.025862	0.403433	
chunk0020_248_1	chr1	236097231	236097488	+	0	NA	Intergenic	LTR10A|LTR|ERV1	-32178	NM_002508	4811	Hs.356624	NM_002508	ENSG00000116962	NID1	NID	nidogen 1	protein-coding	0.015564	0.550388	
chunk0038_221_1	chr11	86790342	86790574	+	0	NA	promoter-TSS (NM_001293180)	promoter-TSS (NM_001293180)	-601	NM_001293180	11098	Hs.25338	NM_007173	ENSG00000150687	PRSS23	SIG13|SPUVE|ZSIG13	serine protease 23	protein-coding	0.000000	0.356223	
chunk0163_355_1	chr6	15638504	15638822	+	0	NA	intron (NM_001271669, intron 1 of 7)	L1MC4|LINE|L1	24395	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.000000	0.335423	
chunk0188_380_1	chr8	18390020	18390219	+	0	NA	Intergenic	Intergenic	-1126	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.005025	0.495000	
chunk0111_207_1	chr20	26358674	26358873	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-149540	NR_040095	284801	Hs.370699	NR_040095	ENSG00000227195	MIR663AHG	-	MIR663A host gene	ncRNA	0.015075	0.370000	
chunk0139_28_1	chr4	48396083	48396404	+	0	NA	intron (NM_020846, intron 6 of 7)	intron (NM_020846, intron 6 of 7)	54647	NM_020846	57606	Hs.479677	NM_020846	ENSG00000109171	SLAIN2	KIAA1458	SLAIN motif family member 2	protein-coding	0.003115	0.369565	
chunk0164_149_1	chr6	21451349	21451721	+	0	NA	Intergenic	L1MEh|LINE|L1	60357	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.008065	0.364611	
chunk0183_257_1	chr7	107234613	107234885	+	0	NA	intron (NM_006348, intron 18 of 21)	intron (NM_006348, intron 18 of 21)	65734	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.000000	0.391941	
chunk0044_152_1	chr12	29734628	29735249	+	0	NA	intron (NM_001193451, intron 5 of 17)	intron (NM_001193451, intron 5 of 17)	48872	NM_001193451	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.011272	0.371383	281(CAGAACATAACGTGCT,-,0.00),282(AGAACATAACGTGCTG,+,0.00)
chunk0129_53_1	chr3	117463185	117463846	+	0	NA	Intergenic	Intergenic	542084	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.003026	0.368580	100(GAAAACACATTGTTCT,-,0.00),101(AAAACACATTGTTCTC,+,0.00)
chunk0086_398_1	chr18	26687379	26688426	+	0	NA	non-coding (NR_024259, exon 2 of 2)	non-coding (NR_024259, exon 2 of 2)	15736	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.004776	0.370229	
chunk0128_226_1	chr3	108243016	108243752	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-20814	NM_018010	55081	Hs.412196	NM_018010	ENSG00000114446	IFT57	ESRRBL1|HIPPI|MHS4R2|OFD18	intraflagellar transport 57	protein-coding	0.002717	0.358209	
chunk0191_162_1	chr8	49343681	49343951	+	0	NA	Intergenic	Intergenic	271475	NM_001256597	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.011111	0.317343	
chunk0137_127_1	chr4	15005813	15006020	+	0	NA	intron (NR_125911, intron 5 of 5)	intron (NR_125911, intron 5 of 5)	3242	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.004831	0.322115	
chunk0006_412_1	chr1	75969547	75969811	+	0	NA	Intergenic	L2c|LINE|L2	-37248	NM_080868	127247	Hs.125423	NM_080868	ENSG00000154007	ASB17	Asb-17	ankyrin repeat and SOCS box containing 17	protein-coding	0.007576	0.471698	
chunk0048_232_1	chr12	81543556	81544149	+	0	NA	intron (NM_001220474, intron 2 of 30)	L1MC3|LINE|L1	-31461	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.006745	0.355219	
chunk0010_380_1	chr1	119238743	119239100	+	0	NA	intron (NR_125975, intron 4 of 6)	intron (NR_125975, intron 4 of 6)	-98249	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.000000	0.287709	
chunk0204_261_1	chr9	98158226	98158848	+	0	NA	intron (NM_052820, intron 1 of 11)	L2b|LINE|L2	14355	NM_003389	7464	Hs.113094	NM_003389	ENSG00000106789	CORO2A	CLIPINB|IR10|WDR2	coronin 2A	protein-coding	0.006431	0.460674	
chunk0077_435_1	chr16	85589864	85590122	+	0	NA	Intergenic	Intergenic	-21430	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.019380	0.432432	
chunk0118_194_1	chr22	31530505	31530944	+	0	NA	intron (NM_001258325, intron 3 of 30)	intron (NM_001258325, intron 3 of 30)	34585	NM_001258326	9814	Hs.62209	NM_014775	ENSG00000198089	SFI1	PISD|PPP1R139|hSfi1p	SFI1 centrin binding protein	protein-coding	0.004556	0.386364	
chunk0127_393_1	chr3	102257210	102257488	+	0	NA	Intergenic	Intergenic	-177666	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.003597	0.336918	
chunk0037_27_1	chr11	69675032	69675433	+	0	NA	exon (NM_153451, exon 1 of 5)	exon (NM_153451, exon 1 of 5)	165	NM_153451	220064	Hs.667996	NM_153451	ENSG00000149716	LTO1	CIAB1|ORAOV1|TAOS1	LTO1 maturation factor of ABCE1	protein-coding	0.099751	0.706468	
chunk0090_303_1	chr18	75321040	75321779	+	0	NA	Intergenic	Intergenic	106294	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.018945	0.477027	
chunk0157_213_1	chr5	119290505	119290704	+	0	NA	intron (NM_001077654, intron 1 of 1)	MLT1F|LTR|ERVL-MaLR	21912	NM_001286817	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.005025	0.460000	
chunk0028_16_1	chr10	82455219	82455636	+	0	NA	intron (NM_001010848, intron 2 of 8)	Tigger3b|DNA|TcMar-Tigger	-222507	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.004796	0.373206	
chunk0037_88_1	chr11	71679478	71679923	+	0	NA	Intergenic	L1M2|LINE|L1	-96825	NM_001005405	440051	Hs.679617	NM_001005405	ENSG00000204571	KRTAP5-11	KRTAP5-5|KRTAP5-6|KRTAP5.11	keratin associated protein 5-11	protein-coding	0.002247	0.331839	
chunk0211_168_1	chrX	115240617	115241076	+	0	NA	Intergenic	MER101B|LTR|ERV1	-6774	NM_001243963	57631	Hs.65366	NM_020871	ENSG00000130224	LRCH2	dA204F4.4	leucine rich repeats and calponin homology domain containing 2	protein-coding	0.004357	0.397826	
chunk0174_119_1	chr6	157246817	157247337	+	0	NA	Intergenic	Intergenic	77182	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.021154	0.512476	
chunk0187_68_1	chr8	2050053	2050599	+	0	NA	intron (NM_003970, intron 1 of 36)	intron (NM_003970, intron 1 of 36)	5283	NM_003970	9172	Hs.443683	NM_003970	ENSG00000036448	MYOM2	TTNAP	myomesin 2	protein-coding	0.021978	0.513711	
chunk0190_265_1	chr8	37310413	37311113	+	0	NA	Intergenic	Intergenic	183150	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.010000	0.435093	
chunk0062_26_1	chr14	66933597	66933911	+	0	NA	intron (NM_020806, intron 8 of 22)	intron (NM_020806, intron 8 of 22)	-255639	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.003185	0.339683	
chunk0016_101_1	chr1	195307629	195307926	+	0	NA	Intergenic	Intergenic	1274704	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.000000	0.322148	
chunk0045_235_1	chr12	48716398	48717072	+	0	NA	5' UTR (NM_001240, exon 1 of 9)	5' UTR (NM_001240, exon 1 of 9)	263	NM_001277842	904	Hs.92308	NM_001240	ENSG00000129315	CCNT1	CCNT|CYCT1|HIVE1	cyclin T1	protein-coding	0.075668	0.579259	
chunk0076_456_1	chr16	74343410	74343846	+	0	NA	intron (NR_026950, intron 8 of 14)	L1MB3|LINE|L1	24627	NR_026950	283922	Hs.558726	NR_026950	ENSG00000214331	LOC283922	-	pyruvate dehydrogenase phosphatase regulatory subunit pseudogene	pseudo	0.011468	0.391304	
chunk0011_243_1	chr1	150575830	150576238	+	0	NA	3' UTR (NM_021960, exon 3 of 3)	3' UTR (NM_021960, exon 3 of 3)	-1482	NR_104133	574406	Hs.516243	NM_001025493	ENSG00000203804	ADAMTSL4-AS1	C1orf138	ADAMTSL4 antisense RNA 1	ncRNA	0.000000	0.354523	
chunk0103_272_1	chr2	165804840	165805039	+	0	NA	Intergenic	Intergenic	-10646	NM_004482	2591	Hs.170986	NM_004482	ENSG00000115339	GALNT3	GalNAc-T3|HFTC|HFTC1|HHS	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.005025	0.355000	
chunk0029_301_1	chr10	104110476	104110835	+	0	NA	Intergenic	Charlie22a|DNA|hAT-Charlie	-11403	NM_145247	119392	Hs.93667	NM_145247	ENSG00000156384	SFR1	C10orf78|MEI5|MEIR5|bA373N18.1	SWI5 dependent homologous recombination repair protein 1	protein-coding	0.005571	0.394444	
chunk0178_148_1	chr7	33382460	33382850	+	0	NA	intron (NM_014451, intron 15 of 20)	intron (NM_014451, intron 15 of 20)	253115	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.005128	0.347826	
chunk0158_364_1	chr5	133884704	133885323	+	0	NA	Intergenic	Intergenic	-28664	NR_131252	105664404	Hs.582536	NR_131252	ENSG00000249073	WSPAR	LncTCF7|TCONS_00009511	WNT signaling pathway activating non-coding RNA	ncRNA	0.009693	0.483871	
chunk0047_98_1	chr12	68725522	68725721	+	0	NA	intron (NM_020401, intron 17 of 27)	intron (NM_020401, intron 17 of 27)	-20535	NM_018656	55508	Hs.506011	NM_018656	ENSG00000175782	SLC35E3	BLOV1	solute carrier family 35 member E3	protein-coding	0.000000	0.290000	
chunk0070_126_1	chr15	70762675	70762948	+	0	NA	intron (NM_018003, intron 1 of 18)	CpG	700	NM_018003	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.080586	0.678832	
chunk0189_155_1	chr8	23067913	23068129	+	0	NA	promoter-TSS (NR_038873)	promoter-TSS (NR_038873)	-208	NR_038873	286059	Hs.306673	NR_038873	ENSG00000246130	LOC286059	-	TNF receptor superfamily member 10d pseudogene	pseudo	0.023148	0.543779	
chunk0180_21_1	chr7	53645724	53645923	+	0	NA	Intergenic	L1MC3|LINE|L1	166108	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.000000	0.305000	
chunk0079_298_1	chr17	17018339	17019193	+	0	NA	Intergenic	Intergenic	-23994	NM_201274	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.014052	0.594152	407(AGGGACACGCTGTTCT,-,0.00),408(GGGACACGCTGTTCTG,+,0.00)
chunk0149_97_1	chr5	18639557	18639942	+	0	NA	Intergenic	Intergenic	1246523	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.007792	0.290155	
chunk0040_156_1	chr11	113773823	113774233	+	0	NA	promoter-TSS (NM_004724)	promoter-TSS (NM_004724)	-265	NM_004724	9183	Hs.503886	NM_004724	ENSG00000086827	ZW10	HZW10|KNTC1AP	zw10 kinetochore protein	protein-coding	0.043902	0.408759	
chunk0168_118_1	chr6	81947233	81947505	+	0	NA	Intergenic	Intergenic	-133177	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.007353	0.362637	
chunk0002_238_1	chr1	20356812	20357232	+	0	NA	Intergenic	MamRep434|DNA|TcMar-Tigger	66103	NM_001039500	127731	Hs.205178	NM_144623	ENSG00000158816	VWA5B1	-	von Willebrand factor A domain containing 5B1	protein-coding	0.009524	0.456057	181(GGGAACACATTGCCCC,-,0.00),182(GGAACACATTGCCCCT,+,0.00)
chunk0170_26_1	chr6	109256279	109256675	+	0	NA	intron (NM_001277339, intron 5 of 9)	intron (NM_001277339, intron 5 of 9)	19863	NM_001277339	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.007576	0.403023	
chunk0082_24_1	chr17	50641237	50641785	+	0	NA	intron (NM_001144070, intron 1 of 11)	intron (NM_001144070, intron 1 of 11)	6654	NM_003786	8714	Hs.463421	NM_003786	ENSG00000108846	ABCC3	ABC31|EST90757|MLP2|MOAT-D|MRP3|cMOAT2	ATP binding cassette subfamily C member 3	protein-coding	0.009124	0.497268	284(GAGAACACTGTGTTCC,-,0.00),285(AGAACACTGTGTTCCT,+,0.00)
chunk0156_24_1	chr5	102246567	102246861	+	0	NA	intron (NM_180991, intron 10 of 12)	intron (NM_180991, intron 10 of 12)	49835	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.000000	0.332203	
chunk0009_51_1	chr1	100502442	100502785	+	0	NA	intron (NM_003672, intron 15 of 15)	intron (NM_003672, intron 15 of 15)	-35559	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.005831	0.375000	
chunk0130_199_1	chr3	133731165	133731364	+	0	NA	Intergenic	Intergenic	-14869	NM_001063	7018	Hs.518267	NM_001063	ENSG00000091513	TF	HEL-S-71p|PRO1557|PRO2086|TFQTL1	transferrin	protein-coding	0.000000	0.435000	
chunk0190_347_1	chr8	39255571	39256233	+	0	NA	intron (NM_001313994, intron 15 of 21)	L1PB1|LINE|L1	-58761	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.007553	0.355958	
chunk0162_126_1	chr6	2960288	2960669	+	0	NA	intron (NM_001297700, intron 1 of 6)	intron (NM_001297700, intron 1 of 6)	1692	NM_001271825	5269	Hs.519523	NM_004568	ENSG00000124570	SERPINB6	CAP|DFNB91|MSTP057|PI-6|PI6|PTI|SPI3	serpin family B member 6	protein-coding	0.015748	0.549738	
chunk0026_99_1	chr10	61732493	61733291	+	0	NA	intron (NM_173554, intron 4 of 6)	intron (NM_173554, intron 4 of 6)	69931	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.005013	0.302879	
chunk0208_124_1	chrX	15358226	15358767	+	0	NA	intron (NR_037859, intron 10 of 14)	intron (NR_037859, intron 10 of 14)	-22942	NR_033836	5277	Hs.137154	NM_002641	ENSG00000165195	PIGA	GPI3|MCAHS2|PIG-A|PNH1	phosphatidylinositol glycan anchor biosynthesis class A	protein-coding	0.005545	0.352399	213(TAGAACACCATGTCCT,-,0.00),214(AGAACACCATGTCCTG,+,0.00)
chunk0092_317_1	chr19	34654793	34655317	+	0	NA	Intergenic	LTR33|LTR|ERVL	9182	NR_045208	100130342	Hs.679909	NR_045208		SCGB2B3P	C2B|SCGB4A3P	secretoglobin family 2B member 3, pseudogene	pseudo	0.003817	0.432381	
chunk0153_11_1	chr5	66802170	66802755	+	0	NA	intron (NM_198828, intron 3 of 5)	intron (NM_198828, intron 3 of 5)	-26314	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.003419	0.327645	256(TGGGACTTAGTGTTCT,-,0.00),257(GGGACTTAGTGTTCTT,+,0.00)
chunk0083_78_1	chr17	64206021	64206220	+	0	NA	intron (NM_018469, intron 2 of 11)	intron (NM_018469, intron 2 of 11)	24636	NM_001288733	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.005025	0.460000	
chunk0034_414_1	chr11	38326472	38326773	+	0	NA	Intergenic	Intergenic	319734	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.003322	0.341060	
chunk0148_101_1	chr5	4042331	4042912	+	0	NA	Intergenic	Intergenic	446567	NM_024337	79192	Hs.424156	NM_024337	ENSG00000170549	IRX1	IRX-5|IRXA1	iroquois homeobox 1	protein-coding	0.006885	0.415808	
chunk0165_413_1	chr6	39062330	39062606	+	0	NA	intron (NM_002062, intron 3 of 12)	intron (NM_002062, intron 3 of 12)	13687	NM_002062	2740	Hs.351883	NM_002062	ENSG00000112164	GLP1R	GLP-1|GLP-1-R|GLP-1R	glucagon like peptide 1 receptor	protein-coding	0.010870	0.559567	148(AGGGACACAGTGATCC,-,0.00),149(GGGACACAGTGATCCT,+,0.00)
chunk0139_313_1	chr4	58113638	58113837	+	0	NA	Intergenic	Intergenic	687865	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.005025	0.345000	
chunk0097_60_1	chr2	43898347	43898991	+	0	NA	intron (NM_133259, intron 34 of 37)	intron (NM_133259, intron 34 of 37)	59705	NM_022437	64241	Hs.413931	NM_022437	ENSG00000143921	ABCG8	GBD4|STSL	ATP binding cassette subfamily G member 8	protein-coding	0.026398	0.443411	
chunk0210_38_1	chrX	68148476	68148679	+	0	NA	intron (NM_002547, intron 15 of 24)	intron (NM_002547, intron 15 of 24)	284880	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.009852	0.392157	
chunk0209_267_1	chrX	46730855	46731200	+	0	NA	intron (NM_001257291, intron 1 of 16)	L1ME4b|LINE|L1	28145	NM_032591	84679	Hs.91389	NM_032591	ENSG00000065923	SLC9A7	MRX108|NHE-7|NHE7|SLC9A6	solute carrier family 9 member A7	protein-coding	0.002899	0.349711	285(CAGAACAGAAAGTCCA,-,0.00),286(AGAACAGAAAGTCCAG,+,0.00)
chunk0194_329_1	chr8	88896998	88897500	+	0	NA	Intergenic	L1MA1|LINE|L1	-569761	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.003984	0.397614	
chunk0212_98_1	chrY	13358267	13358477	+	0	NA	non-coding (NR_047607, exon 14 of 30)	non-coding (NR_047607, exon 14 of 30)	122298	NR_047606	7404	Hs.115277	NM_007125	ENSG00000183878	UTY	KDM6AL|KDM6C|UTY1	ubiquitously transcribed tetratricopeptide repeat containing, Y-linked	protein-coding	0.004762	0.331754	
chunk0188_448_1	chr8	19330439	19330686	+	0	NA	intron (NM_001174159, intron 2 of 9)	intron (NM_001174159, intron 2 of 9)	16586	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.004049	0.524194	23(ATGGTCACTGTGTTCT,-,0.00),24(TGGTCACTGTGTTCTC,+,0.00)
chunk0181_240_1	chr7	85288832	85289564	+	0	NA	Intergenic	Intergenic	-167267	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.008197	0.392906	
chunk0120_69_1	chr3	3323440	3323672	+	0	NA	Intergenic	Intergenic	-143839	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.008621	0.360515	
chunk0143_14_1	chr4	105899463	105899969	+	0	NA	intron (NM_001033047, intron 2 of 11)	intron (NM_001033047, intron 2 of 11)	4276	NM_001033047	255743	Hs.518921	NM_198278	ENSG00000168743	NPNT	EGFL6L|POEM	nephronectin	protein-coding	0.007905	0.384615	
chunk0167_199_1	chr6	64774851	64775139	+	0	NA	intron (NM_001142800, intron 22 of 42)	intron (NM_001142800, intron 22 of 42)	-526423	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.013889	0.359862	
chunk0209_345_1	chrX	52995618	52996050	+	0	NA	promoter-TSS (NM_001242497)	promoter-TSS (NM_001242497)	-362	NM_014138	29057	Hs.6451	NM_014138	ENSG00000268350	FAM156A	PRO0659|TMEM29	family with sequence similarity 156 member A	protein-coding	0.041667	0.547344	
chunk0010_448_1	chr1	120973028	120973302	+	0	NA	Intergenic	Intergenic	30565	NR_125392	101954268		NR_125392		RNVU1-20	RNU1-110|vU1.20	RNA, variant U1 small nuclear 20	snRNA	0.003650	0.480000	112(AGGAACACCCTGTCCA,-,0.00),113(GGAACACCCTGTCCAG,+,0.00)
chunk0071_369_1	chr15	89096597	89097192	+	0	NA	intron (NM_007011, intron 2 of 14)	intron (NM_007011, intron 2 of 14)	8744	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.008403	0.401007	
chunk0175_443_1	chr6	169944477	169944981	+	0	NA	Intergenic	L1ME1|LINE|L1	-17894	NR_027434	100131532	Hs.703417	NR_027434		LOC100131532	-	uncharacterized LOC100131532	ncRNA	0.005952	0.388119	
chunk0029_444_1	chr10	110279227	110279568	+	0	NA	intron (NM_001008541, intron 3 of 4)	intron (NM_001008541, intron 3 of 4)	25552	NM_005871	10285	Hs.632093	NM_005871	ENSG00000119953	SMNDC1	SMNR|SPF30|TDRD16C	survival motor neuron domain containing 1	protein-coding	0.008798	0.409357	
chunk0015_140_1	chr1	185926811	185927055	+	0	NA	intron (NM_031935, intron 9 of 106)	intron (NM_031935, intron 9 of 106)	192382	NM_031935	83872	Hs.58877	NM_031935	ENSG00000143341	HMCN1	ARMD1|FBLN6|FIBL-6|FIBL6	hemicentin 1	protein-coding	0.012295	0.342857	
chunk0199_45_1	chr9	1388698	1389009	+	0	NA	Intergenic	Intergenic	338233	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.016077	0.426282	85(TGGAACAGAATGCTCT,-,0.00),86(GGAACAGAATGCTCTA,+,0.00)
chunk0157_38_1	chr5	115794327	115794674	+	0	NA	Intergenic	Intergenic	22208	NM_001801	1036	Hs.442378	NM_001801	ENSG00000129596	CDO1	CDO-I	cysteine dioxygenase type 1	protein-coding	0.002882	0.433908	29(ATAACACATTGTTCTT,+,0.00),67(GGGATCATCTTGTCCT,-,0.00)
chunk0027_55_1	chr10	72912845	72913181	+	0	NA	intron (NR_130125, intron 5 of 7)	intron (NR_130125, intron 5 of 7)	19457	NM_152635	170392	Hs.8366	NM_152635	ENSG00000138315	OIT3	LZP	oncoprotein induced transcript 3	protein-coding	0.011905	0.362018	
chunk0118_426_1	chr22	38554229	38554699	+	0	NA	intron (NM_007068, intron 6 of 13)	intron (NM_007068, intron 6 of 13)	13945	NM_001278208	11144	Hs.339396	NM_007068	ENSG00000100206	DMC1	DMC1H|LIM15|dJ199H16.1	DNA meiotic recombinase 1	protein-coding	0.008511	0.384289	
chunk0109_108_1	chr20	2470699	2471050	+	0	NA	promoter-TSS (NM_198216)	promoter-TSS (NM_198216)	-21	NM_003091	6628	Hs.83753	NM_003091	ENSG00000125835	SNRPB	CCMS|COD|SNRPB1|Sm-B/B'|SmB/B'|SmB/SmB'|snRNP-B	small nuclear ribonucleoprotein polypeptides B and B1	protein-coding	0.065527	0.579545	
chunk0181_322_1	chr7	87704443	87704806	+	0	NA	intron (NM_138290, intron 4 of 11)	intron (NM_138290, intron 4 of 11)	8699	NM_000927	5243	Hs.489033	NM_000927	ENSG00000085563	ABCB1	ABC20|CD243|CLCS|GP170|MDR1|P-GP|PGY1	ATP binding cassette subfamily B member 1	protein-coding	0.000000	0.368132	
chunk0161_260_1	chr5	172043872	172044248	+	0	NA	3' UTR (NM_005990, exon 19 of 19)	3' UTR (NM_005990, exon 19 of 19)	-37187	NM_033645	23291	Hs.484138	NM_012300	ENSG00000072803	FBXW11	BTRC2|BTRCP2|FBW1B|FBXW1B|Fbw11|Hos	F-box and WD repeat domain containing 11	protein-coding	0.034574	0.607427	152(CAGTACAGCCTGTGCT,-,0.00),153(AGTACAGCCTGTGCTT,+,0.00)
chunk0121_407_1	chr3	25611409	25611945	+	0	NA	intron (NM_001068, intron 28 of 35)	intron (NM_001068, intron 28 of 35)	52695	NM_001068	7155	Hs.475733	NM_001068	ENSG00000077097	TOP2B	TOPIIB|top2beta	DNA topoisomerase II beta	protein-coding	0.005597	0.368715	316(GACACAGGATGTGCTT,+,0.00)
chunk0121_173_1	chr3	19946911	19947297	+	0	NA	promoter-TSS (NM_001292048)	promoter-TSS (NM_001292048)	24	NM_004162	5868	Hs.475663	NM_004162	ENSG00000144566	RAB5A	RAB5	RAB5A, member RAS oncogene family	protein-coding	0.106218	0.679587	
chunk0098_300_1	chr2	76239308	76239625	+	0	NA	Intergenic	L1M5|LINE|L1	-528481	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.006309	0.270440	
chunk0192_275_1	chr8	66114267	66114568	+	0	NA	Intergenic	Intergenic	-12626	NM_184085	84675	Hs.85524	NM_033058	ENSG00000147573	TRIM55	MURF-2|RNF29|muRF2	tripartite motif containing 55	protein-coding	0.029900	0.430464	
chunk0131_314_1	chr3	150773563	150774105	+	0	NA	Intergenic	LTR40c|LTR|ERVL	-10358	NM_005067	6478	Hs.477959	NM_005067	ENSG00000181788	SIAH2	hSiah2	siah E3 ubiquitin protein ligase 2	protein-coding	0.020295	0.539595	263(AAGGACATGGTGTCTC,-,0.00),264(AGGACATGGTGTCTCG,+,0.00)
chunk0060_27_1	chr14	40172048	40172694	+	0	NA	Intergenic	L1MD2|LINE|L1	-739871	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.001548	0.332303	295(AGGTACAGATAGTTCC,-,0.00),296(GGTACAGATAGTTCCA,+,0.00)
chunk0147_243_1	chr4	183042080	183042359	+	0	NA	Intergenic	L1MEd|LINE|L1	4554	NR_003612	403315	Hs.652187	NR_003612	ENSG00000230219	FAM92A1P2	FAM92A3	family with sequence similarity 92, member A3	pseudo	0.003584	0.310714	
chunk0191_412_1	chr8	57702952	57703496	+	0	NA	Intergenic	Intergenic	-275134	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.007353	0.467890	
chunk0088_178_1	chr18	47336609	47336956	+	0	NA	Intergenic	Intergenic	-43714	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.002882	0.468391	144(CTGGACAGACAGTTCC,-,0.00),145(TGGACAGACAGTTCCC,+,0.00),183(GGGAACAGCATGTGCT,-,0.00),184(GGAACAGCATGTGCTC,+,0.00)
chunk0006_162_1	chr1	66403854	66404682	+	0	NA	Intergenic	Intergenic	49890	NM_001297442	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.010870	0.411339	
chunk0018_383_1	chr1	222347561	222348198	+	0	NA	Intergenic	Intergenic	200223	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.006279	0.424765	
chunk0027_184_1	chr10	75225358	75225817	+	0	NA	intron (NM_003375, intron 8 of 9)	LTR23|LTR|ERV1	10425	NM_144589	118881	Hs.355333	NM_144589	ENSG00000165644	COMTD1	-	catechol-O-methyltransferase domain containing 1	protein-coding	0.006536	0.397826	277(AAGAACAAAGTGTTTT,-,0.00),278(AGAACAAAGTGTTTTT,+,0.00)
chunk0091_429_1	chr19	16986186	16986889	+	0	NA	intron (NM_015692, intron 13 of 41)	intron (NM_015692, intron 13 of 41)	40278	NM_015692	27151	Hs.631644	NM_015692	ENSG00000160111	CPAMD8	ASGD8|K-CAP|VIP	C3 and PZP like alpha-2-macroglobulin domain containing 8	protein-coding	0.018492	0.562500	322(AAGAACAGTGTGTTCA,-,0.00),323(AGAACAGTGTGTTCAG,+,0.00)
chunk0169_61_1	chr6	98820789	98821277	+	0	NA	Intergenic	LTR50|LTR|ERVL	-13671	NM_005604	5454	Hs.182505	NM_005604	ENSG00000184486	POU3F2	BRN2|N-Oct3|OCT7|OTF-7|OTF7|POUF3|brn-2|oct-7	POU class 3 homeobox 2	protein-coding	0.008197	0.435583	
chunk0060_88_1	chr14	42364401	42364903	+	0	NA	Intergenic	Intergenic	757091	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.001992	0.341948	208(AAGTACAGTATGTACC,-,0.00),209(AGTACAGTATGTACCA,+,0.00)
chunk0116_232_1	chr21	38240830	38241427	+	0	NA	intron (NM_001276438, intron 1 of 2)	intron (NM_001276438, intron 1 of 2)	11213	NM_001276437	3772	Hs.411299	NM_002243	ENSG00000157551	KCNJ15	IRKK|KIR1.3|KIR4.2	potassium voltage-gated channel subfamily J member 15	protein-coding	0.008375	0.416388	258(TGGAACATATTGTACT,-,0.00),259(GGAACATATTGTACTT,+,0.00)
chunk0210_206_1	chrX	80715069	80715434	+	0	NA	intron (NM_153252, intron 20 of 40)	intron (NM_153252, intron 20 of 40)	94483	NM_153252	254065	Hs.147027	NM_153252	ENSG00000165288	BRWD3	BRODL|MRX93	bromodomain and WD repeat domain containing 3	protein-coding	0.000000	0.281421	
chunk0203_165_1	chr9	86045809	86046565	+	0	NA	intron (NM_177937, intron 5 of 9)	intron (NM_177937, intron 5 of 9)	53408	NM_016548	51280	Hs.494337	NM_016548	ENSG00000135052	GOLM1	C9orf155|GOLPH2|GP73|HEL46|PSEC0257|bA379P1.3	golgi membrane protein 1	protein-coding	0.019841	0.441215	
chunk0151_9_1	chr5	40895846	40896507	+	0	NA	Intergenic	L1P2|LINE|L1	-13321	NM_000587	730	Hs.78065	NM_000587	ENSG00000112936	C7	-	complement C7	protein-coding	0.009077	0.496979	
chunk0166_457_1	chr6	53300849	53301476	+	0	NA	intron (NM_001242828, intron 1 of 8)	intron (NM_001242828, intron 1 of 8)	24169	NR_049866	100847075		NR_049866	ENSG00000264056	MIR5685	-	microRNA 5685	ncRNA	0.007974	0.501592	
chunk0149_36_1	chr5	16466105	16466377	+	0	NA	promoter-TSS (NM_033414)	promoter-TSS (NM_033414)	-456	NM_033414	90441	Hs.60300	NM_033414	ENSG00000173545	ZNF622	ZPR9	zinc finger protein 622	protein-coding	0.106618	0.673993	
chunk0021_443_1	chr1	248404103	248404353	+	0	NA	Intergenic	Intergenic	-1767	NM_030904	26696	Hs.626885	NM_030904	ENSG00000175143	OR2T1	OR1-25	olfactory receptor family 2 subfamily T member 1	protein-coding	0.020000	0.398406	
chunk0184_419_1	chr7	122773579	122774031	+	0	NA	intron (NM_017954, intron 1 of 29)	intron (NM_017954, intron 1 of 29)	-70838	NM_198085	378925	Hs.675191	NM_198085	ENSG00000235631	RNF148	-	ring finger protein 148	protein-coding	0.002212	0.311258	
chunk0046_194_1	chr12	58894656	58895129	+	0	NA	intron (NM_001136051, intron 3 of 18)	intron (NM_001136051, intron 3 of 18)	24654	NM_001136051	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.010571	0.383966	219(TAGTACAGGGAGTTCC,-,0.00),220(AGTACAGGGAGTTCCA,+,0.00)
chunk0075_407_1	chr16	57156204	57156570	+	0	NA	intron (NM_024946, intron 6 of 6)	intron (NM_024946, intron 6 of 6)	29677	NM_024946	80011	Hs.396740	NM_024946	ENSG00000172775	FAM192A	C16orf94|CDA018|CDA10|NIP30|PIP30	family with sequence similarity 192 member A	protein-coding	0.013661	0.408719	
chunk0160_127_1	chr5	151023325	151024000	+	0	NA	intron (NM_002084, intron 1 of 4)	intron (NM_002084, intron 1 of 4)	3224	NM_002084	2878	Hs.386793	NM_002084	ENSG00000211445	GPX3	GPx-P|GSHPx-3|GSHPx-P	glutathione peroxidase 3	protein-coding	0.013333	0.511834	
chunk0084_422_1	chr17	82502220	82502456	+	0	NA	Intergenic	L1MC3|LINE|L1	-17380	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.033898	0.527426	
chunk0172_88_1	chr6	134621659	134622324	+	0	NA	Intergenic	Intergenic	-81986	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.006015	0.454955	346(AAGAACATCCAGTCTC,-,0.00)
chunk0153_325_1	chr5	73998309	73998967	+	0	NA	Intergenic	Intergenic	185120	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.009119	0.370258	
chunk0075_173_1	chr16	51980480	51980682	+	0	NA	Intergenic	Intergenic	93354	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.024752	0.472906	
chunk0110_178_1	chr20	14385247	14385879	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	-47896	NM_013281	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.004747	0.296998	
chunk0195_187_1	chr8	96575576	96575878	+	0	NA	intron (NM_002998, intron 1 of 4)	intron (NM_002998, intron 1 of 4)	-69500	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.003311	0.376238	
chunk0028_41_1	chr10	83103124	83103434	+	0	NA	Intergenic	Intergenic	-870359	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.006452	0.405145	
chunk0179_64_1	chr7	43896532	43897143	+	0	NA	intron (NM_001077664, intron 1 of 5)	intron (NM_001077664, intron 1 of 5)	9795	NM_001204871	100534592		NM_001204871	ENSG00000270617	URGCP-MRPS24	-	URGCP-MRPS24 readthrough	protein-coding	0.000000	0.364379	
chunk0168_331_1	chr6	92681268	92681881	+	0	NA	Intergenic	L1ME3C|LINE|L1	738008	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.001631	0.301303	
chunk0090_316_1	chr18	75653139	75653425	+	0	NA	Intergenic	Intergenic	-225579	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.003497	0.379791	115(ATGAGCACTGTGTTCT,-,0.00),116(TGAGCACTGTGTTCTT,+,0.00)
chunk0180_383_1	chr7	74464729	74465315	+	0	NA	intron (NM_001199207, intron 1 of 26)	intron (NM_001199207, intron 1 of 26)	11232	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.013652	0.591141	
chunk0136_263_1	chr3	194351931	194352130	+	0	NA	promoter-TSS (NM_001291988)	promoter-TSS (NM_001291988)	-702	NM_001291988	1370	Hs.528368	NM_001309	ENSG00000178772	CPN2	ACBP	carboxypeptidase N subunit 2	protein-coding	0.035176	0.580000	
chunk0024_307_1	chr10	42640905	42641312	+	0	NA	Intergenic	LTR10B1|LTR|ERV1	-2271	NM_001305036	7582	Hs.435774	NM_006955	ENSG00000196693	ZNF33B	KOX2|KOX31|ZNF11B	zinc finger protein 33B	protein-coding	0.012285	0.424020	
chunk0182_409_1	chr7	100912776	100913109	+	0	NA	Intergenic	Intergenic	-16809	NM_001302622	43	Hs.154495	NM_000665	ENSG00000087085	ACHE	ACEE|ARACHE|N-ACHE|YT	acetylcholinesterase (Cartwright blood group)	protein-coding	0.000000	0.305389	
chunk0011_308_1	chr1	151829764	151830152	+	0	NA	intron (NM_005060, intron 1 of 10)	L2c|LINE|L2	1914	NM_005060	6097	Hs.256022	NM_005060	ENSG00000143365	RORC	IMD42|NR1F3|RORG|RZR-GAMMA|RZRG|TOR	RAR related orphan receptor C	protein-coding	0.000000	0.465296	
chunk0006_173_1	chr1	66867346	66868128	+	0	NA	intron (NM_207014, intron 6 of 9)	L1MEd|LINE|L1	57150	NM_024763	79819	Hs.49421	NM_024763	ENSG00000152763	WDR78	DIC4	WD repeat domain 78	protein-coding	0.003836	0.310345	218(AAGAACATTCTGTTCT,-,0.00),219(AGAACATTCTGTTCTT,+,0.00),514(AGTGACACTATGTTCT,-,0.00),515(GTGACACTATGTTCTG,+,0.00)
chunk0083_358_1	chr17	70579406	70579700	+	0	NA	Intergenic	L2c|LINE|L2	410018	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.003401	0.406780	
chunk0182_254_1	chr7	97201350	97201777	+	0	NA	Intergenic	L2a|LINE|L2	84970	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.004684	0.373832	
chunk0006_407_1	chr1	75733501	75734087	+	0	NA	intron (NM_001127328, intron 5 of 11)	intron (NM_001127328, intron 5 of 11)	9447	NM_001286044	34	Hs.445040	NM_000016	ENSG00000117054	ACADM	ACAD1|MCAD|MCADH	acyl-CoA dehydrogenase medium chain	protein-coding	0.008532	0.420784	344(AGTACTCGGAGTTCTG,+,0.00)
chunk0186_297_1	chr7	142778491	142778733	+	0	NA	Intergenic	Intergenic	7669	NR_130149	5645	Hs.449281	NM_002770	ENSG00000275896	PRSS2	TRY2|TRY8|TRYP2	serine protease 2	protein-coding	0.016529	0.567901	
chunk0111_212_1	chr20	28816480	28816703	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-213926	NR_132315	100289097	Hs.529357	NR_132315	ENSG00000282826	FRG1CP	-	FSHD region gene 1 family member C, pseudogene	pseudo	0.004484	0.370536	
chunk0002_299_1	chr1	23303451	23304067	+	0	NA	TTS (NM_005826)	TTS (NM_005826)	-18241	NR_110616	100996511	Hs.99836	NR_110616		LINC01355	-	long intergenic non-protein coding RNA 1355	ncRNA	0.006494	0.343598	
chunk0166_395_1	chr6	51933512	51934225	+	0	NA	intron (NM_138694, intron 37 of 66)	intron (NM_138694, intron 37 of 66)	153757	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.014025	0.462185	
chunk0022_317_1	chr10	16166600	16166799	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-270244	NM_001001484	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.020101	0.470000	
chunk0083_424_1	chr17	72428475	72429058	+	0	NA	intron (NR_036488, intron 2 of 3)	MIRb|SINE|MIR	164038	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.005146	0.330479	311(AGGAACATCTAGTGCC,-,0.00),312(GGAACATCTAGTGCCA,+,0.00)
chunk0011_229_1	chr1	150375463	150376037	+	0	NA	intron (NM_001297673, intron 1 of 10)	intron (NM_001297673, intron 1 of 10)	11639	NM_015203	23248	Hs.213666	NM_015203	ENSG00000163125	RPRD2	HSPC099|KIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding	0.005226	0.335652	
chunk0052_297_1	chr12	124608981	124609472	+	0	NA	Intergenic	Intergenic	-41762	NM_001206654	9612	Hs.137510	NM_006312	ENSG00000196498	NCOR2	CTG26|N-CoR2|SMAP270|SMRT|SMRTE|SMRTE-tau|TNRC14|TRAC|TRAC-1|TRAC1	nuclear receptor corepressor 2	protein-coding	0.040733	0.581301	244(GGGAACAGGTTGGCCC,-,0.00)
chunk0056_254_1	chr13	89688931	89689544	+	0	NA	Intergenic	L1M1|LINE|L1	-124824	NR_046991	100874139	Hs.742173	NR_046991		LINC00353	-	long intergenic non-protein coding RNA 353	ncRNA	0.008157	0.495114	304(AAGAACACTTTGTCTT,-,0.00)
chunk0037_109_1	chr11	72271812	72272388	+	0	NA	Intergenic	L1MC2|LINE|L1	-27924	NM_005169	401	Hs.731115	NM_005169	ENSG00000165462	PHOX2A	ARIX|CFEOM2|FEOM2|NCAM2|PMX2A	paired like homeobox 2A	protein-coding	0.003472	0.343154	
chunk0120_347_1	chr3	11476112	11476499	+	0	NA	intron (NM_001136031, intron 17 of 17)	intron (NM_001136031, intron 17 of 17)	92619	NM_001128221	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.005168	0.399485	
chunk0169_330_1	chr6	106379044	106379324	+	0	NA	Intergenic	Intergenic	-53364	NM_001286111	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.017857	0.402135	
chunk0056_409_1	chr13	94178568	94178845	+	0	NA	intron (NR_046535, intron 3 of 3)	intron (NR_046535, intron 3 of 3)	9285	NR_046535	100873972	Hs.670344	NR_046535	ENSG00000236520	GPC6-AS1	-	GPC6 antisense RNA 1	ncRNA	0.000000	0.356115	
chunk0099_301_1	chr2	99102691	99103573	+	0	NA	intron (NM_182911, intron 9 of 19)	Alu|SINE|Alu	38442	NM_182911	80705	Hs.120267	NM_025244	ENSG00000135951	TSGA10	CEP4L|CT79|SPGF26	testis specific 10	protein-coding	0.011338	0.345413	
chunk0185_129_1	chr7	126772782	126773472	+	0	NA	intron (NR_028041, intron 5 of 10)	intron (NR_028041, intron 5 of 10)	285057	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.002899	0.397974	
chunk0138_59_1	chr4	31982062	31982599	+	0	NA	Intergenic	Intergenic	-15049	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.003724	0.304833	
chunk0085_112_1	chr18	2806322	2807034	+	0	NA	Intergenic	L1PA16|LINE|L1	-40352	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.004213	0.364656	
chunk0136_272_1	chr3	194494194	194494630	+	0	NA	Intergenic	Intergenic	7272	NR_033929	401106	Hs.407087	NR_033929		LINC00884	-	long intergenic non-protein coding RNA 884	ncRNA	0.006881	0.425629	
chunk0205_221_1	chr9	109843739	109843938	+	0	NA	intron (NM_053016, intron 1 of 6)	intron (NM_053016, intron 1 of 6)	63541	NM_053016	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.035176	0.565000	
chunk0108_184_1	chr2	232235070	232235964	+	0	NA	intron (NR_046476, intron 10 of 20)	intron (NR_046476, intron 10 of 20)	62864	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.006711	0.381006	535(AAGGACAGAAAGTTCA,-,0.00),536(AGGACAGAAAGTTCAT,+,0.00)
chunk0201_337_1	chr9	64061202	64061598	+	0	NA	non-coding (NR_033856, exon 7 of 7)	non-coding (NR_033856, exon 7 of 7)	44450	NR_033856	644316	Hs.632789	NR_033856		FLJ43315	-	asparagine synthetase pseudogene	pseudo	0.010101	0.352645	
chunk0123_70_1	chr3	41375599	41376138	+	0	NA	intron (NM_017886, intron 35 of 36)	L1PA7|LINE|L1	176417	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.005566	0.355556	
chunk0035_124_1	chr11	42614830	42615404	+	0	NA	Intergenic	MIR3|SINE|MIR	-361427	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.005226	0.368696	
chunk0212_212_1	chrX	135602968	135603476	+	0	NA	Intergenic	Intergenic	-82548	NR_046740	100874118	Hs.602150	NR_046740	ENSG00000225235	INTS6L-AS1	DDX26B-AS1	INTS6L antisense RNA 1	ncRNA	0.003937	0.353635	
chunk0184_387_1	chr7	121581926	121582851	+	0	NA	Intergenic	Intergenic	-186020	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.005405	0.367171	
chunk0020_303_1	chr1	237375444	237375802	+	0	NA	intron (NM_001035, intron 7 of 104)	intron (NM_001035, intron 7 of 104)	-95496	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.002793	0.317549	
chunk0114_408_1	chr20	63864945	63865248	+	0	NA	promoter-TSS (NR_045090)	promoter-TSS (NR_045090)	-132	NM_001243891	7165	Hs.473296	NM_003288	ENSG00000101150	TPD52L2	D54|TPD54	TPD52 like 2	protein-coding	0.079208	0.625000	
chunk0141_23_1	chr4	76780142	76780521	+	0	NA	3' UTR (NM_020859, exon 11 of 11)	3' UTR (NM_020859, exon 11 of 11)	117518	NM_001029870	345079	Hs.257292	NM_001029870	ENSG00000186212	SOWAHB	ANKRD56	sosondowah ankyrin repeat domain family member B	protein-coding	0.005277	0.405263	
chunk0183_130_1	chr7	105661664	105661924	+	0	NA	intron (NM_138495, intron 2 of 9)	intron (NM_138495, intron 2 of 9)	17368	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.019231	0.517241	
chunk0108_55_1	chr2	227053091	227053290	+	0	NA	intron (NM_000092, intron 31 of 47)	intron (NM_000092, intron 31 of 47)	111369	NM_000092	1286	Hs.591645	NM_000092	ENSG00000081052	COL4A4	ATS2|BFH|CA44	collagen type IV alpha 4 chain	protein-coding	0.005025	0.300000	
chunk0164_123_1	chr6	20820989	20821233	+	0	NA	intron (NM_017774, intron 8 of 15)	L2a|LINE|L2	286654	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.008197	0.502041	
chunk0057_320_1	chr13	106746381	106746605	+	0	NA	Intergenic	Intergenic	92613	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.008929	0.435556	
chunk0150_230_1	chr5	35773616	35774122	+	0	NA	intron (NM_024867, intron 27 of 36)	intron (NM_024867, intron 27 of 36)	-83006	NR_120485	3575	Hs.591742	NM_002185	ENSG00000168685	IL7R	CD127|CDW127|IL-7R-alpha|IL7RA|ILRA	interleukin 7 receptor	protein-coding	0.007905	0.390533	
chunk0110_115_1	chr20	12724424	12724778	+	0	NA	Intergenic	Intergenic	212362	NR_109872	102606466	Hs.602196	NR_109872		LOC102606466	-	uncharacterized LOC102606466	ncRNA	0.008475	0.357746	
chunk0030_350_1	chr10	118570972	118571410	+	0	NA	Intergenic	Intergenic	24457	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.006849	0.487472	237(CAGAACACAGTGTCCT,-,0.00),238(AGAACACAGTGTCCTC,+,0.00)
chunk0012_145_1	chr1	157606160	157606494	+	0	NA	Intergenic	Intergenic	-8247	NM_031282	83417	Hs.120260	NM_031282	ENSG00000163518	FCRL4	CD307d|FCRH4|IGFP2|IRTA1	Fc receptor like 4	protein-coding	0.000000	0.501493	
chunk0164_285_1	chr6	24558408	24559226	+	0	NA	intron (NM_001252328, intron 13 of 16)	intron (NM_001252328, intron 13 of 16)	24410	NM_001252328	9856	Hs.26441	NM_014809	ENSG00000137261	KIAA0319	AAVR|DYLX2|DYX2|NMIG	KIAA0319	protein-coding	0.006112	0.402930	
chunk0106_443_1	chr2	208999917	209000116	+	0	NA	Intergenic	Intergenic	-424031	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.010050	0.375000	163(GTGGACTGTCTGTTCC,-,0.00),164(TGGACTGTCTGTTCCT,+,0.00)
chunk0081_191_1	chr17	42096410	42096637	+	0	NA	Intergenic	Intergenic	16210	NM_024119	79132	Hs.55918	NM_024119	ENSG00000108771	DHX58	D11LGP2|D11lgp2e|LGP2|RLR-3	DExH-box helicase 58	protein-coding	0.004405	0.543860	
chunk0092_302_1	chr19	34305217	34305546	+	0	NA	intron (NM_014686, intron 2 of 13)	intron (NM_014686, intron 2 of 13)	50830	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.009119	0.415152	158(AGGAACACTTTGTCCT,-,0.00),159(GGAACACTTTGTCCTC,+,0.00)
chunk0090_248_1	chr18	73912110	73912309	+	0	NA	Intergenic	Intergenic	235555	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.015075	0.565000	
chunk0149_100_1	chr5	18872030	18872273	+	0	NA	Intergenic	Intergenic	1014121	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004115	0.262295	
chunk0088_115_1	chr18	45627089	45627578	+	0	NA	intron (NM_001242692, intron 5 of 20)	intron (NM_001242692, intron 5 of 20)	12532	NM_007163	8170	Hs.710927	NM_007163	ENSG00000132874	SLC14A2	HUT2|UT-A2|UT2|UTA|UTR|hUT-A6	solute carrier family 14 member 2	protein-coding	0.004090	0.467347	
chunk0033_412_1	chr11	24767262	24767855	+	0	NA	intron (NM_001252010, intron 5 of 9)	MER57F|LTR|ERV1	270588	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.006745	0.328283	
chunk0115_291_1	chr21	28252916	28253328	+	0	NA	Intergenic	Intergenic	-24455	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.004854	0.346247	
chunk0023_95_1	chr10	22615692	22616295	+	0	NA	intron (NM_005028, intron 1 of 9)	intron (NM_005028, intron 1 of 9)	98581	NM_005028	5305	Hs.57079	NM_005028	ENSG00000150867	PIP4K2A	PI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK	phosphatidylinositol-5-phosphate 4-kinase type 2 alpha	protein-coding	0.014925	0.509934	
chunk0032_259_1	chr11	8809553	8809828	+	0	NA	intron (NR_120590, intron 4 of 4)	intron (NR_120590, intron 4 of 4)	987	NM_213618	6764	Hs.117715	NM_005418	ENSG00000166444	ST5	DENND2B|HTS1|p126	suppression of tumorigenicity 5	protein-coding	0.010909	0.496377	
chunk0093_314_1	chr19	53700796	53700995	+	0	NA	promoter-TSS (NR_030195)	promoter-TSS (NR_030195)	-332	NR_030195	574473		NR_030195	ENSG00000207722	MIR520B	MIRN520B	microRNA 520b	ncRNA	0.005025	0.425000	66(GGGGACTGTGTGTCCC,-,0.00),67(GGGACTGTGTGTCCCT,+,0.00)
chunk0032_404_1	chr11	11815214	11815737	+	0	NA	Intergenic	Intergenic	-25948	NM_001282659	55031	Hs.577256	NM_017944	ENSG00000170242	USP47	TRFP	ubiquitin specific peptidase 47	protein-coding	0.005736	0.349237	
chunk0167_311_1	chr6	71910477	71910718	+	0	NA	intron (NM_014989, intron 1 of 33)	intron (NM_014989, intron 1 of 33)	23894	NM_014989	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.004149	0.392562	
chunk0057_242_1	chr13	104565844	104566397	+	0	NA	Intergenic	Intergenic	-899747	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.010850	0.333935	
chunk0179_397_1	chr7	51456820	51457029	+	0	NA	Intergenic	Intergenic	-140106	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.004785	0.357143	
chunk0161_186_1	chr5	169933582	169934645	+	0	NA	intron (NM_001129891, intron 1 of 3)	intron (NM_001129891, intron 1 of 3)	46627	NM_001129891	100131897	Hs.721917	NM_001129891	ENSG00000204767	INSYN2B	C5orf57|FAM196B	inhibitory synaptic factor family member 2B	protein-coding	0.013170	0.489662	281(ATGAACAGAGCGTGCT,-,0.00),282(TGAACAGAGCGTGCTC,+,0.00),845(AAGGGCAGGGTGTCCC,-,0.00),846(AGGGCAGGGTGTCCCC,+,0.00)
chunk0198_226_1	chr8	134023956	134024438	+	0	NA	Intergenic	Intergenic	137701	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.000000	0.370600	218(TAAGACATGCTGTTCC,-,0.00),219(AAGACATGCTGTTCCA,+,0.00)
chunk0199_53_1	chr9	1891659	1892051	+	0	NA	Intergenic	Intergenic	-123364	NM_001289397	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.005102	0.394402	
chunk0121_162_1	chr3	19521144	19521711	+	0	NA	intron (NM_144633, intron 15 of 15)	MIR|SINE|MIR	-206496	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.001764	0.357394	
chunk0086_339_1	chr18	24861542	24862526	+	0	NA	Intergenic	Intergenic	233852	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.021341	0.433503	
chunk0133_429_1	chr3	174873934	174874251	+	0	NA	intron (NM_207015, intron 1 of 13)	intron (NM_207015, intron 1 of 13)	14771	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.006309	0.386792	
chunk0102_337_1	chr2	152171725	152172039	+	0	NA	intron (NM_005843, intron 1 of 13)	intron (NM_005843, intron 1 of 13)	4110	NM_005843	10254	Hs.17200	NM_005843	ENSG00000115145	STAM2	Hbp|STAM2A|STAM2B	signal transducing adaptor molecule 2	protein-coding	0.012739	0.415873	
chunk0130_311_1	chr3	137059644	137059920	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	101917	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.000000	0.342960	
chunk0147_308_1	chr4	184898740	184899189	+	0	NA	intron (NR_039975, intron 1 of 2)	intron (NR_039975, intron 1 of 2)	497	NR_039975	100506229	Hs.378150	NR_039975		LINC01093	-	long intergenic non-protein coding RNA 1093	ncRNA	0.013363	0.475556	193(CAAGACACTGTGTTCT,-,0.00),194(AAGACACTGTGTTCTT,+,0.00)
chunk0110_465_1	chr20	21565830	21566065	+	0	NA	Intergenic	L1ME3B|LINE|L1	-4077	NR_109880	101929625	Hs.542413	NR_109880		LINC01727	-	long intergenic non-protein coding RNA 1727	ncRNA	0.008511	0.385593	
chunk0047_212_1	chr12	71605000	71605520	+	0	NA	Intergenic	Intergenic	-58637	NM_031435	83591	Hs.245798	NM_031435	ENSG00000173451	THAP2	-	THAP domain containing 2	protein-coding	0.007692	0.380038	
chunk0200_39_1	chr9	15155873	15156183	+	0	NA	Intergenic	Intergenic	94172	NM_001168342	158219	Hs.563630	NM_152574	ENSG00000155158	TTC39B	C9orf52	tetratricopeptide repeat domain 39B	protein-coding	0.012903	0.366559	
chunk0083_196_1	chr17	66580772	66581415	+	0	NA	intron (NM_002737, intron 3 of 16)	intron (NM_002737, intron 3 of 16)	-164239	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.009331	0.409938	
chunk0176_281_1	chr7	16640331	16640578	+	0	NA	intron (NM_020319, intron 1 of 9)	intron (NM_020319, intron 1 of 9)	5363	NM_020319	57037	Hs.157378	NM_020319	ENSG00000106524	ANKMY2	ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding	0.020243	0.366935	
chunk0098_41_1	chr2	66431294	66431643	+	0	NA	intron (NR_046438, intron 3 of 3)	intron (NR_046438, intron 3 of 3)	2002	NR_046438	730198	Hs.526753	NR_046438		MEIS1-AS3	-	MEIS1 antisense RNA 3	ncRNA	0.000000	0.357143	
chunk0050_296_1	chr12	106766348	106766755	+	0	NA	intron (NR_040246, intron 1 of 3)	intron (NR_040246, intron 1 of 3)	-8070	NM_018157	55188	Hs.131306	NM_018157	ENSG00000111785	RIC8B	RIC8|hSyn	RIC8 guanine nucleotide exchange factor B	protein-coding	0.017199	0.561275	
chunk0094_307_1	chr2	8784428	8784872	+	0	NA	intron (NM_020738, intron 17 of 29)	L1MC1|LINE|L1	52975	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.002252	0.375281	
chunk0165_172_1	chr6	34276910	34277146	+	0	NA	Intergenic	L2|LINE|L2	-27920	NM_001287396	221491	Hs.381300	NM_178508	ENSG00000186577	SMIM29	C6orf1|LBH	small integral membrane protein 29	protein-coding	0.008475	0.527426	178(CTGAACACAGTGCTCT,-,0.00),179(TGAACACAGTGCTCTG,+,0.00)
chunk0147_229_1	chr4	181956919	181957484	+	0	NA	Intergenic	Intergenic	187314	NR_027107	90768	Hs.175465	NR_027107		TENM3-AS1	-	TENM3 antisense RNA 1	ncRNA	0.015929	0.397527	
chunk0199_174_1	chr9	4584474	4585130	+	0	NA	intron (NM_004170, intron 11 of 11)	intron (NM_004170, intron 11 of 11)	-77492	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.003049	0.468798	
chunk0121_412_1	chr3	25664343	25664542	+	0	NA	promoter-TSS (NM_001068)	promoter-TSS (NM_001068)	-70	NM_001068	7155	Hs.475733	NM_001068	ENSG00000077097	TOP2B	TOPIIB|top2beta	DNA topoisomerase II beta	protein-coding	0.180905	0.805000	
chunk0097_184_1	chr2	50350330	50350806	+	0	NA	intron (NM_001135659, intron 18 of 23)	intron (NM_001135659, intron 18 of 23)	-2812	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.014706	0.421384	
chunk0059_128_1	chr14	31803028	31803286	+	0	NA	intron (NM_001201573, intron 5 of 8)	intron (NM_001201573, intron 5 of 8)	88588	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.000000	0.335907	
chunk0177_259_1	chr7	25334112	25334474	+	0	NA	Intergenic	Intergenic	-105807	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.005525	0.325069	
chunk0056_382_1	chr13	93200548	93201012	+	0	NA	Intergenic	L1PB4|LINE|L1	-26045	NM_005708	10082	Hs.444329	NM_005708	ENSG00000183098	GPC6	OMIMD1	glypican 6	protein-coding	0.000000	0.344086	
chunk0182_382_1	chr7	100108498	100108810	+	0	NA	intron (NR_033792, intron 12 of 14)	intron (NR_033792, intron 12 of 14)	-6714	NM_001278595	4176	Hs.438720	NM_005916	ENSG00000166508	MCM7	CDC47|MCM2|P1.1-MCM3|P1CDC47|P85MCM|PNAS146|PPP1R104	minichromosome maintenance complex component 7	protein-coding	0.009615	0.523962	216(CAGAACACTGTGGGCT,-,0.00),217(AGAACACTGTGGGCTT,+,0.00)
chunk0033_162_1	chr11	15618307	15619236	+	0	NA	Intergenic	Intergenic	-25114	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.005382	0.408602	
chunk0038_353_1	chr11	93197184	93197454	+	0	NA	5' UTR (NM_001286139, exon 1 of 11)	5' UTR (NM_001286139, exon 1 of 11)	136	NM_001286139	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.025926	0.424354	
chunk0025_82_1	chr10	50379582	50380130	+	0	NA	intron (NM_147156, intron 6 of 10)	intron (NM_147156, intron 6 of 10)	-131246	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.003650	0.413479	
chunk0042_230_1	chr12	6264675	6265209	+	0	NA	Intergenic	L2c|LINE|L2	-45494	NM_018173	55200	Hs.631660	NM_018173	ENSG00000008323	PLEKHG6	MyoGEF	pleckstrin homology and RhoGEF domain containing G6	protein-coding	0.013109	0.491589	
chunk0021_429_1	chr1	247515904	247516958	+	0	NA	intron (NM_001281834, intron 1 of 6)	intron (NM_001281834, intron 1 of 6)	-2021	NM_001281837	148823	Hs.732113	NM_145278	ENSG00000169224	GCSAML	C1orf150	germinal center associated signaling and motility like	protein-coding	0.009488	0.384834	
chunk0174_391_1	chr6	165359649	165359885	+	0	NA	intron (NM_006661, intron 19 of 22)	MER58C|DNA|hAT-Charlie	-49834	NR_106988									0.004237	0.388186	
chunk0168_175_1	chr6	84225110	84226067	+	0	NA	intron (NM_001286206, intron 1 of 26)	L2a|LINE|L2	2047	NM_001286206	22832	Hs.485865	NM_014895	ENSG00000135315	CEP162	C6orf84|KIAA1009|QN1	centrosomal protein 162	protein-coding	0.004180	0.362213	765(GGGAACAGTGAGTGCA,-,0.00),766(GGAACAGTGAGTGCAA,+,0.00)
chunk0101_99_1	chr2	124823429	124823908	+	0	NA	intron (NM_130773, intron 19 of 23)	MIRb|SINE|MIR	798381	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.004175	0.452083	
chunk0017_23_1	chr1	204506523	204506764	+	0	NA	Intergenic	Intergenic	-9736	NM_001278518	4194	Hs.497492	NM_002393	ENSG00000198625	MDM4	HDMX|MDMX|MRP1	MDM4 regulator of p53	protein-coding	0.037344	0.425620	
chunk0094_86_1	chr2	3823724	3824333	+	0	NA	intron (NM_001287444, intron 10 of 10)	MER58A|DNA|hAT-Charlie	120436	NM_001287444	728597	Hs.304233	NM_001287444	ENSG00000214866	DCDC2C	-	doublecortin domain containing 2C	protein-coding	0.001642	0.378689	
chunk0099_444_1	chr2	103267934	103268148	+	0	NA	Intergenic	Intergenic	506010	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.018692	0.427907	
chunk0145_459_1	chr4	154330988	154331205	+	0	NA	intron (NM_001142552, intron 5 of 7)	intron (NM_001142552, intron 5 of 7)	60201	NM_017639	54798	Hs.655664	NM_017639	ENSG00000197410	DCHS2	CDH27|CDHJ|CDHR7|PCDH23|PCDHJ	dachsous cadherin-related 2	protein-coding	0.009217	0.536697	167(AAGCACGTAGTGTTCC,-,0.00),168(AGCACGTAGTGTTCCA,+,0.00)
chunk0039_342_1	chr11	105438489	105439275	+	0	NA	Intergenic	Intergenic	-171191	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.001272	0.343075	399(TTGAACAACATGTACC,-,0.00),400(TGAACAACATGTACCA,+,0.00)
chunk0065_442_1	chr14	106531480	106532047	+	0	NA	Intergenic	Intergenic	49324	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.007055	0.452465	288(TGGGACTGGATGTTCA,-,0.00),289(GGGACTGGATGTTCAG,+,0.00)
chunk0145_204_1	chr4	147928650	147928849	+	0	NA	intron (NM_024605, intron 13 of 22)	intron (NM_024605, intron 13 of 22)	146154	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.010050	0.315000	
chunk0073_124_1	chr16	4870413	4870612	+	0	NA	intron (NM_001288656, intron 9 of 16)	intron (NM_001288656, intron 9 of 16)	22132	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.045226	0.590000	
chunk0191_407_1	chr8	57583592	57584107	+	0	NA	Intergenic	L2a|LINE|L2	240062	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.003883	0.343023	
chunk0008_393_1	chr1	97252592	97252957	+	0	NA	intron (NM_000110, intron 18 of 22)	intron (NM_000110, intron 18 of 22)	156851	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.005479	0.330601	
chunk0107_16_1	chr2	210203379	210203582	+	0	NA	intron (NM_001608, intron 7 of 10)	intron (NM_001608, intron 7 of 10)	22011	NM_001608	33	Hs.471277	NM_001608	ENSG00000115361	ACADL	ACAD4|LCAD	acyl-CoA dehydrogenase long chain	protein-coding	0.004926	0.274510	
chunk0191_173_1	chr8	50895409	50895627	+	0	NA	Intergenic	Intergenic	913927	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.004587	0.351598	
chunk0071_187_1	chr15	83592742	83593212	+	0	NA	intron (NM_001301109, intron 11 of 11)	intron (NM_001301109, intron 11 of 11)	-61109	NM_207517	57188	Hs.459162	NM_207517	ENSG00000156218	ADAMTSL3	ADAMTSL-3	ADAMTS like 3	protein-coding	0.004255	0.350318	
chunk0172_109_1	chr6	135027272	135027505	+	0	NA	intron (NM_001145158, intron 3 of 16)	L1MC4|LINE|L1	27510	NM_001145158	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.004292	0.320513	
chunk0069_396_1	chr15	67768685	67768941	+	0	NA	intron (NM_001206804, intron 19 of 21)	intron (NM_001206804, intron 19 of 21)	-50891	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.007812	0.400778	
chunk0097_55_1	chr2	43478517	43479002	+	0	NA	intron (NM_001083953, intron 26 of 37)	intron (NM_001083953, intron 26 of 37)	117215	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.004124	0.327160	
chunk0007_226_1	chr1	81772573	81773082	+	0	NA	intron (NM_001297704, intron 2 of 20)	intron (NM_001297704, intron 2 of 20)	-27570	NM_012302	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.009823	0.364706	
chunk0054_292_1	chr13	48018150	48019049	+	0	NA	Intergenic	L1MB3|LINE|L1	-17273	NM_003850	8803	Hs.743361	NM_003850	ENSG00000136143	SUCLA2	A-BETA|A-SCS|MTDPS5|SCS-betaA	succinate-CoA ligase ADP-forming beta subunit	protein-coding	0.005562	0.387778	
chunk0119_83_1	chr22	41446631	41447075	+	0	NA	5' UTR (NM_016272, exon 1 of 2)	5' UTR (NM_016272, exon 1 of 2)	170	NM_016272	10766	Hs.474978	NM_016272	ENSG00000183864	TOB2	APRO5|TOB4|TOBL|TROB2	transducer of ERBB2, 2	protein-coding	0.110360	0.687640	
chunk0068_65_1	chr15	51846261	51846685	+	0	NA	intron (NM_014547, intron 1 of 9)	intron (NM_014547, intron 1 of 9)	16845	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.002358	0.374118	
chunk0003_305_1	chr1	37683954	37684451	+	0	NA	intron (NM_017850, intron 3 of 4)	intron (NM_017850, intron 3 of 4)	6393	NM_001303030	54955	Hs.272673	NM_017850	ENSG00000116922	C1orf109	-	chromosome 1 open reading frame 109	protein-coding	0.012072	0.461847	
chunk0039_220_1	chr11	101470502	101470745	+	0	NA	intron (NM_004621, intron 9 of 12)	intron (NM_004621, intron 9 of 12)	49282	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.004115	0.397541	
chunk0124_208_1	chr3	56006149	56006821	+	0	NA	intron (NR_132749, intron 10 of 17)	intron (NR_132749, intron 10 of 17)	-153891	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.002976	0.317979	
chunk0171_82_1	chr6	121826230	121826444	+	0	NA	Intergenic	LTR16|LTR|ERVL	390760	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.009346	0.502326	
chunk0060_109_1	chr14	43449371	43449751	+	0	NA	Intergenic	AluJb|SINE|Alu	1057735	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.010526	0.372703	
chunk0175_429_1	chr6	169461557	169461805	+	0	NA	intron (NM_001202550, intron 21 of 21)	L1MB3|LINE|L1	-207567	NM_003247	7058	Hs.371147	NM_003247	ENSG00000186340	THBS2	TSP2	thrombospondin 2	protein-coding	0.000000	0.317269	
chunk0100_336_1	chr2	116762759	116763405	+	0	NA	Intergenic	Intergenic	-1051597	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.006192	0.374034	
chunk0124_329_1	chr3	58181225	58181681	+	0	NA	Intergenic	L2a|LINE|L2	29550	NM_001256560	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.004386	0.461707	
chunk0190_69_1	chr8	29784696	29785521	+	0	NA	intron (NR_125814, intron 1 of 3)	intron (NR_125814, intron 1 of 3)	36799	NR_125815	101929450	Hs.512440	NR_125814	ENSG00000253490	LINC02099	-	long intergenic non-protein coding RNA 2099	ncRNA	0.003636	0.375303	
chunk0206_302_1	chr9	124771274	124771710	+	0	NA	promoter-TSS (NM_033334)	promoter-TSS (NM_033334)	-182	NM_001278546	2649	Hs.20131	NM_001489	ENSG00000148200	NR6A1	CT150|GCNF|GCNF1|NR61|RTR|hGCNF|hRTR	nuclear receptor subfamily 6 group A member 1	protein-coding	0.075688	0.615561	
chunk0031_70_1	chr10	123019818	123020726	+	0	NA	intron (NM_001609, intron 1 of 10)	intron (NM_001609, intron 1 of 10)	11359	NM_001609	36	Hs.81934	NM_001609	ENSG00000196177	ACADSB	2-MEBCAD|ACAD7|SBCAD	acyl-CoA dehydrogenase short/branched chain	protein-coding	0.003304	0.381738	
chunk0196_361_1	chr8	114977549	114977785	+	0	NA	Intergenic	Intergenic	690345	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.000000	0.400844	217(AGAAACTGAATGTTCT,-,0.00),218(GAAACTGAATGTTCTC,+,0.00)
chunk0095_154_1	chr2	17102295	17102568	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	416008	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.000000	0.295620	122(GAGGACAAGGTGTACC,-,0.00),123(AGGACAAGGTGTACCT,+,0.00)
chunk0197_230_1	chr8	123024265	123025101	+	0	NA	intron (NM_001134671, intron 3 of 7)	intron (NM_001134671, intron 3 of 7)	17740	NM_001134671	79139	Hs.241576	NM_024295	ENSG00000136986	DERL1	DER-1|DER1|derlin-1	derlin 1	protein-coding	0.007177	0.419355	
chunk0003_366_1	chr1	39395254	39395453	+	0	NA	intron (NM_012090, intron 52 of 92)	intron (NM_012090, intron 52 of 92)	-14151	NM_015038	643314	Hs.658760	NM_015038	ENSG00000127603	KIAA0754	-	KIAA0754	protein-coding	0.000000	0.385000	
chunk0076_89_1	chr16	64782412	64782985	+	0	NA	Intergenic	L1MC1|LINE|L1	339439	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.006981	0.336237	
chunk0149_149_1	chr5	20202787	20203121	+	0	NA	intron (NM_001291956, intron 2 of 14)	L1MA4|LINE|L1	-214710	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002994	0.379104	
chunk0175_289_1	chr7	7779805	7780311	+	0	NA	intron (NM_001302350, intron 3 of 4)	intron (NM_001302350, intron 3 of 4)	-61451	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.007905	0.433925	
chunk0131_235_1	chr3	149371228	149371718	+	0	NA	intron (NM_014220, intron 4 of 4)	intron (NM_014220, intron 4 of 4)	-6305	NR_109810	100874091	Hs.549633	NR_046650	ENSG00000240541	TM4SF1-AS1	-	TM4SF1 antisense RNA 1	ncRNA	0.010204	0.407332	213(ATGGGCAGCATGTTCT,-,0.00),214(TGGGCAGCATGTTCTT,+,0.00)
chunk0171_47_1	chr6	120984195	120984461	+	0	NA	Intergenic	MIR3|SINE|MIR	350172	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.007519	0.352060	
chunk0120_213_1	chr3	7429359	7429846	+	0	NA	intron (NM_000844, intron 5 of 9)	MIRc|SINE|MIR	105682	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.008214	0.329918	
chunk0161_294_1	chr5	173011462	173012077	+	0	NA	intron (NM_003945, intron 2 of 3)	intron (NM_003945, intron 2 of 3)	-8957	NR_002988	677841	Hs.692720	NR_002988	ENSG00000212402	SNORA74B	U19-2	small nucleolar RNA, H/ACA box 74B	snoRNA	0.009756	0.420455	326(AGGTACATTTAGTTCC,-,0.00),327(GGTACATTTAGTTCCT,+,0.00)
chunk0065_380_1	chr14	104344740	104345200	+	0	NA	Intergenic	L2a|LINE|L2	206247	NM_015656	26153	Hs.134970	NM_015656	ENSG00000066735	KIF26A	-	kinesin family member 26A	protein-coding	0.019565	0.453362	
chunk0212_218_1	chrX	136012072	136012436	+	0	NA	intron (NM_006359, intron 7 of 15)	intron (NM_006359, intron 7 of 15)	26827	NM_001042537	10479	Hs.62185	NM_006359	ENSG00000198689	SLC9A6	MRSA|NHE6	solute carrier family 9 member A6	protein-coding	0.010989	0.383562	
chunk0022_243_1	chr10	14413586	14413797	+	0	NA	Intergenic	L1MA9|LINE|L1	-22885	NR_031668	100302116		NR_031668	ENSG00000221371	MIR1265	MIRN1265|hsa-mir-1265	microRNA 1265	ncRNA	0.018957	0.457547	
chunk0051_355_1	chr12	120677812	120678706	+	0	NA	Intergenic	Intergenic	-8865	NM_014730	9761	Hs.744910	NM_014730	ENSG00000110917	MLEC	KIAA0152	malectin	protein-coding	0.011186	0.494972	442(AGTACGCTTTGTTCTT,+,0.00)
chunk0090_320_1	chr18	75683461	75683742	+	0	NA	Intergenic	Intergenic	-255898	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.017794	0.517730	
chunk0142_184_1	chr4	96093212	96093411	+	0	NA	Intergenic	Intergenic	253223	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.010050	0.435000	
chunk0114_402_1	chr20	63658322	63658581	+	0	NA	non-coding (NR_037882, exon 1 of 38)	non-coding (NR_037882, exon 1 of 38)	641	NM_016434	51750	Hs.745057	NM_016434	ENSG00000258366	RTEL1	C20orf41|DKCA4|DKCB5|NHL|PFBMFT3|RTEL	regulator of telomere elongation helicase 1	protein-coding	0.104247	0.657692	
chunk0024_131_1	chr10	34999182	34999467	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	75006	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.000000	0.468531	
chunk0204_15_1	chr9	91778171	91778511	+	0	NA	intron (NM_004560, intron 1 of 8)	intron (NM_004560, intron 1 of 8)	-141996	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.032353	0.533724	
chunk0168_107_1	chr6	80256036	80256399	+	0	NA	intron (NM_000056, intron 8 of 10)	Tigger3a|DNA|TcMar-Tigger	149590	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.008264	0.346154	
chunk0092_229_1	chr19	32373636	32374339	+	0	NA	intron (NM_001136156, intron 5 of 6)	Tigger6a|DNA|TcMar-Tigger	28379	NM_001136156	22847	Hs.205392	NM_014910	ENSG00000168813	ZNF507	-	zinc finger protein 507	protein-coding	0.014225	0.399148	
chunk0192_212_1	chr8	65148689	65149137	+	0	NA	Intergenic	Intergenic	31427	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.002232	0.371938	
chunk0036_7_1	chr11	58142930	58143177	+	0	NA	intron (NM_001005212, intron 2 of 2)	intron (NM_001005212, intron 2 of 2)	-23609	NM_001005211	219954	Hs.632122	NM_001005211	ENSG00000172377	OR9I1	OR11-228	olfactory receptor family 9 subfamily I member 1	protein-coding	0.004049	0.435484	
chunk0127_157_1	chr3	94586520	94587371	+	0	NA	Intergenic	L2c|LINE|L2	-351318	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.002350	0.319249	
chunk0082_170_1	chr17	55842599	55843243	+	0	NA	Intergenic	Intergenic	91816	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.006211	0.344186	
chunk0057_248_1	chr13	104749779	104750014	+	0	NA	Intergenic	Intergenic	-715971	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.000000	0.266949	
chunk0092_308_1	chr19	34391803	34392091	+	0	NA	intron (NM_001184722, intron 9 of 17)	intron (NM_001184722, intron 9 of 17)	-12451	NM_032346	84306	Hs.515344	NM_032346	ENSG00000126249	PDCD2L	-	programmed cell death 2 like	protein-coding	0.000000	0.467128	
chunk0033_418_1	chr11	24821131	24821518	+	0	NA	intron (NM_001252010, intron 5 of 9)	L2a|LINE|L2	324354	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.010336	0.311856	224(AAGTACATTCCGTTCT,-,0.00),225(AGTACATTCCGTTCTC,+,0.00)
chunk0162_460_1	chr5	180929104	180929303	+	0	NA	intron (NM_001159708, intron 3 of 6)	L1PA7|LINE|L1	19639	NM_001159710	79908	Hs.189109	NM_024850	ENSG00000113303	BTNL8	BTN9.2	butyrophilin like 8	protein-coding	0.005025	0.375000	168(AAAGACACAATGTACC,-,0.00)
chunk0122_207_1	chr3	33202804	33203550	+	0	NA	intron (NM_015551, intron 3 of 4)	intron (NM_015551, intron 3 of 4)	16038	NM_015551	26032	Hs.196647	NM_015551	ENSG00000173705	SUSD5	-	sushi domain containing 5	protein-coding	0.010724	0.508701	278(CAGCACAGCCTGTTCT,-,0.00),279(AGCACAGCCTGTTCTC,+,0.00)
chunk0021_289_1	chr1	244436705	244437113	+	0	NA	intron (NM_001126, intron 2 of 12)	intron (NM_001126, intron 2 of 12)	15225	NM_001126	159	Hs.498313	NM_001126	ENSG00000035687	ADSS	ADEH|ADSS 2|ADSS2	adenylosuccinate synthase	protein-coding	0.012255	0.315403	
chunk0130_132_1	chr3	132029376	132030043	+	0	NA	intron (NM_153429, intron 2 of 16)	intron (NM_153429, intron 2 of 16)	5733	NM_130808	131034	Hs.199877	NM_130808	ENSG00000196353	CPNE4	COPN4|CPN4	copine 4	protein-coding	0.011994	0.414671	
chunk0146_451_1	chr4	170082902	170083439	+	0	NA	intron (NM_182662, intron 4 of 13)	L1MA4|LINE|L1	6862	NM_016228	51166	Hs.529735	NM_016228	ENSG00000109576	AADAT	KAT2|KATII|KYAT2	aminoadipate aminotransferase	protein-coding	0.007449	0.308550	
chunk0062_151_1	chr14	69153026	69153332	+	0	NA	promoter-TSS (NM_001284207)	promoter-TSS (NM_001284207)	18	NM_003861	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.127451	0.745928	
chunk0071_14_1	chr15	78930859	78931277	+	0	NA	intron (NM_004390, intron 7 of 11)	intron (NM_004390, intron 7 of 11)	14010	NM_004390	1512	Hs.148641	NM_004390	ENSG00000103811	CTSH	ACC-4|ACC-5|ACC4|ACC5|CPSB	cathepsin H	protein-coding	0.009569	0.536993	
chunk0135_3_1	chr3	184017825	184018035	+	0	NA	promoter-TSS (NM_005688)	promoter-TSS (NM_005688)	9	NM_001023587	10057	Hs.368563	NM_005688	ENSG00000114770	ABCC5	ABC33|EST277145|MOAT-C|MOATC|MRP5|SMRP|pABC11	ATP binding cassette subfamily C member 5	protein-coding	0.085714	0.635071	
chunk0108_296_1	chr2	235008634	235009016	+	0	NA	intron (NM_014521, intron 2 of 5)	intron (NM_014521, intron 2 of 5)	56841	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.015707	0.503916	
chunk0078_113_1	chr17	2602573	2602947	+	0	NA	intron (NM_000430, intron 1 of 10)	MIR|SINE|MIR	9131	NM_000430	5048	Hs.77318	NM_000430	ENSG00000007168	PAFAH1B1	LIS1|LIS2|MDCR|MDS|NudF|PAFAH	platelet activating factor acetylhydrolase 1b regulatory subunit 1	protein-coding	0.016043	0.416000	
chunk0148_337_1	chr5	14324191	14324652	+	0	NA	intron (NM_007118, intron 9 of 56)	intron (NM_007118, intron 9 of 56)	180701	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.002169	0.309524	
chunk0074_37_1	chr16	20675093	20675364	+	0	NA	intron (NM_052956, intron 3 of 12)	HERV15-int|LTR|ERV1	16028	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.033210	0.558824	
chunk0088_163_1	chr18	46789813	46790329	+	0	NA	Intergenic	MER77|LTR|ERVL	-32902	NM_013305	29906	Hs.465025	NM_013305	ENSG00000101638	ST8SIA5	SIAT8-E|SIAT8E|ST8SiaV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	protein-coding	0.005814	0.489362	
chunk0169_293_1	chr6	105929940	105930311	+	0	NA	Intergenic	LTR33|LTR|ERVL	-156195	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.013477	0.459677	131(CAGCACACTGTGTTAT,-,0.00),132(AGCACACTGTGTTATT,+,0.00)
chunk0140_121_1	chr4	68924865	68925066	+	0	NA	Intergenic	MER30|DNA|hAT-Charlie	26826	NM_024743	79799	Hs.122583	NM_024743	ENSG00000135220	UGT2A3	-	UDP glucuronosyltransferase family 2 member A3	protein-coding	0.014925	0.366337	
chunk0187_39_1	chr8	1345088	1345727	+	0	NA	Intergenic	Intergenic	-42800	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.012520	0.421875	
chunk0083_352_1	chr17	70375627	70375843	+	0	NA	Intergenic	Intergenic	206200	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.000000	0.387097	
chunk0088_406_1	chr18	54635837	54636245	+	0	NA	Intergenic	Intergenic	44882	NM_173629	284254	Hs.376146	NM_173629	ENSG00000178690	DYNAP	C18orf26	dynactin associated protein	protein-coding	0.000000	0.305623	
chunk0107_323_1	chr2	220219308	220219689	+	0	NA	Intergenic	Intergenic	-312933	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.002625	0.458115	
chunk0170_151_1	chr6	111427005	111427634	+	0	NA	intron (NM_002912, intron 2 of 32)	L1M4|LINE|L1	-56153	NR_034109	643749	Hs.486228	NR_034108	ENSG00000231889	TRAF3IP2-AS1	C6UAS|C6orf3|NCRNA00248|TRAF3IP2-AS2	TRAF3IP2 antisense RNA 1	ncRNA	0.004769	0.317460	
chunk0142_55_1	chr4	91989193	91989900	+	0	NA	Intergenic	Intergenic	287756	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.002829	0.327684	368(AGAAACATGCTGTTCA,-,0.00),369(GAAACATGCTGTTCAT,+,0.00)
chunk0091_145_1	chr19	7266071	7266270	+	0	NA	intron (NM_001079817, intron 2 of 20)	L1ME4a|LINE|L1	28132	NM_001079817	3643	Hs.465744	NM_000208	ENSG00000171105	INSR	CD220|HHF5	insulin receptor	protein-coding	0.025126	0.450000	
chunk0110_163_1	chr20	14064894	14065306	+	0	NA	intron (NM_080676, intron 2 of 16)	intron (NM_080676, intron 2 of 16)	69600	NM_080676	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.012136	0.397094	163(AAGAACAAATAGTTCC,-,0.00),164(AGAACAAATAGTTCCT,+,0.00)
chunk0182_440_1	chr7	101662240	101663228	+	0	NA	Intergenic	Intergenic	-33438	NM_138403	93408	Hs.247831	NM_138403	ENSG00000106436	MYL10	MYLC2PL|PLRLC	myosin light chain 10	protein-coding	0.011134	0.400404	
chunk0110_406_1	chr20	20490226	20490586	+	0	NA	intron (NM_020343, intron 36 of 39)	intron (NM_020343, intron 36 of 39)	122285	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.000000	0.277008	
chunk0019_74_1	chr1	224311857	224312340	+	0	NA	intron (NM_206840, intron 3 of 21)	MIR|SINE|MIR	18091	NM_001243147	4931	Hs.497867	NM_002533	ENSG00000143748	NVL	NVL2	nuclear VCP like	protein-coding	0.004141	0.326446	
chunk0143_369_1	chr4	122252548	122252903	+	0	NA	intron (NM_015312, intron 35 of 83)	L1M1|LINE|L1	82122	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.011268	0.536517	
chunk0056_440_1	chr13	95137664	95138092	+	0	NA	intron (NM_001105515, intron 19 of 20)	intron (NM_001105515, intron 19 of 20)	163568	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.009346	0.407925	
chunk0028_6_1	chr10	82087343	82087551	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	145473	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.009615	0.421053	
chunk0199_211_1	chr9	5038250	5038517	+	0	NA	intron (NM_004972, intron 4 of 24)	L1MB7|LINE|L1	53138	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.000000	0.313433	
chunk0068_143_1	chr15	53565209	53565884	+	0	NA	intron (NR_102334, intron 18 of 19)	L1ME4b|LINE|L1	-24443	NR_102335	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.004444	0.341716	
chunk0095_58_1	chr2	14123838	14124240	+	0	NA	Intergenic	Intergenic	276919	NR_103814	100499171	Hs.565606	NR_103814	ENSG00000230448	LINC00276	NCRNA00276	long intergenic non-protein coding RNA 276	ncRNA	0.000000	0.349876	
chunk0164_97_1	chr6	20353290	20353489	+	0	NA	Intergenic	MLT1G3|LTR|ERVL-MaLR	-48517	NM_001949	1871	Hs.269408	NM_001949	ENSG00000112242	E2F3	E2F-3	E2F transcription factor 3	protein-coding	0.020101	0.540000	
chunk0055_344_1	chr13	70068877	70069270	+	0	NA	intron (NM_020866, intron 1 of 10)	L1MCa|LINE|L1	-38140	NR_002717	6315	Hs.676453	NR_002717		ATXN8OS	KLHL1AS|NCRNA00003|SCA8	ATXN8 opposite strand lncRNA	ncRNA	0.005089	0.398477	114(AGGAGCACTCTGTTCT,-,0.00),115(GGAGCACTCTGTTCTC,+,0.00)
chunk0013_435_1	chr1	173475017	173475646	+	0	NA	intron (NR_037845, intron 1 of 2)	LTR5B|LTR|ERVK	1824	NR_037845	100506023	Hs.731284	NR_037845		LOC100506023	-	uncharacterized LOC100506023	ncRNA	0.015898	0.428571	
chunk0133_289_1	chr3	172134943	172135336	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	94585	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.005089	0.355330	178(TAGTACATAATGTCCC,-,0.00),179(AGTACATAATGTCCCT,+,0.00)
chunk0088_413_1	chr18	54777244	54777661	+	0	NA	Intergenic	Intergenic	-51025	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.002398	0.418660	66(GAGAACTTGCAGTTCT,-,0.00),67(AGAACTTGCAGTTCTC,+,0.00)
chunk0065_448_1	chr14	106549034	106549634	+	0	NA	Intergenic	L1MA9|LINE|L1	66895	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.001667	0.301165	
chunk0016_337_1	chr1	201843805	201844117	+	0	NA	intron (NM_018085, intron 1 of 23)	L1MC4a|LINE|L1	-14402	NR_046696	100873949	Hs.604842	NR_046696	ENSG00000231871	IPO9-AS1	-	IPO9 antisense RNA 1	ncRNA	0.003205	0.316294	
chunk0008_230_1	chr1	94034771	94035297	+	0	NA	intron (NM_000350, intron 26 of 49)	MIR|SINE|MIR	86115	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.005703	0.381404	331(TGGAACATCCTGTTCT,-,0.00),332(GGAACATCCTGTTCTA,+,0.00)
chunk0046_410_1	chr12	64413915	64414376	+	0	NA	intron (NM_007235, intron 2 of 24)	intron (NM_007235, intron 2 of 24)	9772	NM_007235	11260	Hs.85951	NM_007235	ENSG00000184575	XPOT	XPO3	exportin for tRNA	protein-coding	0.006508	0.374459	
chunk0001_438_1	chr1	11569561	11570089	+	0	NA	Intergenic	Intergenic	-39706	NR_104624	101929181	Hs.568616	NR_104624	ENSG00000235643	LINC01647	-	long intergenic non-protein coding RNA 1647	ncRNA	0.028409	0.578450	267(CGGAACACACTGTACC,-,0.00),268(GGAACACACTGTACCT,+,0.00)
chunk0081_44_1	chr17	37717058	37717371	+	0	NA	intron (NM_001304286, intron 4 of 6)	intron (NM_001304286, intron 4 of 6)	27864	NM_000458	6928	Hs.191144	NM_000458	ENSG00000275410	HNF1B	FJHN|HNF-1-beta|HNF-1B|HNF1beta|HNF2|HPC11|LF-B3|LFB3|MODY5|TCF-2|TCF2|VHNF1	HNF1 homeobox B	protein-coding	0.009585	0.509554	
chunk0055_401_1	chr13	74187577	74187869	+	0	NA	Intergenic	Intergenic	-53794	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.003425	0.430034	
chunk0060_140_1	chr14	44961301	44962436	+	0	NA	promoter-TSS (NM_001308112)	promoter-TSS (NM_001308112)	108	NM_017658	54813	Hs.550906	NM_017658	ENSG00000179454	KLHL28	BTBD5	kelch like family member 28	protein-coding	0.043172	0.539613	
chunk0029_137_1	chr10	99080062	99080789	+	0	NA	intron (NM_001166246, intron 3 of 12)	intron (NM_001166246, intron 3 of 12)	155450	NM_001166246	60495	Hs.500750	NM_021828	ENSG00000172987	HPSE2	HPA2|HPR2|UFS|UFS1	heparanase 2 (inactive)	protein-coding	0.001376	0.365385	
chunk0045_314_1	chr12	50713159	50713876	+	0	NA	intron (NM_173602, intron 22 of 37)	intron (NM_173602, intron 22 of 37)	-50489	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.005579	0.409471	
chunk0004_150_1	chr1	45281860	45282212	+	0	NA	Intergenic	Intergenic	-21874	NR_024270	400752	Hs.334348	NR_024270	ENSG00000281912	LINC01144	-	long intergenic non-protein coding RNA 1144	ncRNA	0.019886	0.470255	
chunk0167_132_1	chr6	62050613	62051169	+	0	NA	intron (NM_152688, intron 2 of 8)	L1ME2|LINE|L1	235304	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.005396	0.355476	
chunk0164_425_1	chr6	27339039	27339398	+	0	NA	Intergenic	Intergenic	14457	NR_045612	387316	Hs.326753	NM_032030		VN1R10P	FKSG83|VNR6I1P|b24o18.2|hs6V1-1p	vomeronasal 1 receptor 10 pseudogene	pseudo	0.005571	0.411111	
chunk0211_407_1	chrX	128836026	128836480	+	0	NA	Intergenic	(TATT)n|Simple_repeat|Simple_repeat	687252	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.000000	0.287912	
chunk0206_308_1	chr9	124947492	124947778	+	0	NA	3' UTR (NM_173690, exon 19 of 19)	3' UTR (NM_173690, exon 19 of 19)	-6528	NM_002077	2800	Hs.59504	NM_002077	ENSG00000136935	GOLGA1	golgin-97	golgin A1	protein-coding	0.000000	0.320557	
chunk0211_173_1	chrX	115413250	115413683	+	0	NA	Intergenic	Intergenic	123749	NM_016383	51213	Hs.242183	NM_016383	ENSG00000102021	LUZP4	CT-28|CT-8|CT28|HOM-TES-85	leucine zipper protein 4	protein-coding	0.006928	0.380184	
chunk0200_104_1	chr9	16746900	16747552	+	0	NA	intron (NM_017637, intron 1 of 6)	intron (NM_017637, intron 1 of 6)	123562	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.006135	0.335375	
chunk0185_50_1	chr7	124701934	124702541	+	0	NA	Intergenic	Intergenic	63788	NM_005302	2861	Hs.406094	NM_005302	ENSG00000170775	GPR37	EDNRBL|PAELR|hET(B)R-LP	G protein-coupled receptor 37	protein-coding	0.004942	0.386513	
chunk0186_121_1	chr7	138094016	138094273	+	0	NA	intron (NM_001190906, intron 3 of 7)	intron (NM_001190906, intron 3 of 7)	17712	NM_001190907	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.007782	0.348837	
chunk0053_260_1	chr13	33080903	33081371	+	0	NA	Intergenic	L1MC3|LINE|L1	64704	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.006410	0.315565	
chunk0099_250_1	chr2	97849078	97849463	+	0	NA	intron (NM_015348, intron 5 of 40)	L1MC3|LINE|L1	114864	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.005195	0.354922	
chunk0157_69_1	chr5	116293626	116294141	+	0	NA	TTS (NM_016144)	TTS (NM_016144)	80687	NR_104675	101927190	Hs.639849	NR_104675		LOC101927190	-	uncharacterized LOC101927190	ncRNA	0.005825	0.310078	
chunk0114_389_1	chr20	63207698	63208576	+	0	NA	intron (NM_017798, intron 3 of 4)	intron (NM_017798, intron 3 of 4)	8049	NM_017798	54915	Hs.744852	NM_017798	ENSG00000149658	YTHDF1	C20orf21	YTH N6-methyladenosine RNA binding protein 1	protein-coding	0.013667	0.442548	
chunk0206_229_1	chr9	123466819	123467423	+	0	NA	intron (NM_024820, intron 13 of 20)	MER45B|DNA|hAT-Tip100	18501	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.018212	0.492562	
chunk0012_443_1	chr1	165054757	165055408	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-280441	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.007680	0.357362	
chunk0075_418_1	chr16	57367103	57367588	+	0	NA	Intergenic	Intergenic	-5116	NM_002996	6376	Hs.531668	NM_002996	ENSG00000006210	CX3CL1	ABCD-3|C3Xkine|CXC3|CXC3C|NTN|NTT|SCYD1|fractalkine|neurotactin	C-X3-C motif chemokine ligand 1	protein-coding	0.010309	0.477366	
chunk0106_145_1	chr2	200239248	200239698	+	0	NA	Intergenic	Intergenic	-66408	NM_001282743	26010	Hs.120323	NM_015535	ENSG00000196141	SPATS2L	DNAPTP6|SGNP	spermatogenesis associated serine rich 2 like	protein-coding	0.004444	0.421286	
chunk0052_121_1	chr13	23347607	23348009	+	0	NA	intron (NM_001278055, intron 7 of 7)	intron (NM_001278055, intron 7 of 7)	27735	NM_001278055	26278	Hs.159492	NM_014363	ENSG00000151835	SACS	ARSACS|DNAJC29|PPP1R138|SPAX6	sacsin molecular chaperone	protein-coding	0.002488	0.426799	215(CAGAACATGCTGTCCT,-,0.00),216(AGAACATGCTGTCCTC,+,0.00)
chunk0124_202_1	chr3	55782204	55783003	+	0	NA	intron (NR_132749, intron 13 of 17)	L2a|LINE|L2	69991	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.006258	0.427500	
chunk0080_160_1	chr17	28100913	28101296	+	0	NA	intron (NM_016231, intron 1 of 10)	L1ME1|LINE|L1	58442	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.002611	0.312500	196(TTGGACTTTGTGTTCT,-,0.00),197(TGGACTTTGTGTTCTG,+,0.00)
chunk0180_451_1	chr7	77477218	77477848	+	0	NA	Intergenic	Intergenic	-59923	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.009524	0.396197	
chunk0061_46_1	chr14	56181711	56182141	+	0	NA	intron (NM_021255, intron 2 of 5)	intron (NM_021255, intron 2 of 5)	63551	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.006977	0.394432	
chunk0054_298_1	chr13	48232566	48232822	+	0	NA	promoter-TSS (NM_021999)	promoter-TSS (NM_021999)	-444	NM_021999	9445	Hs.643683	NM_021999	ENSG00000136156	ITM2B	ABRI|BRI|BRI2|BRICD2B|E25B|E3-16|FBD|RDGCA|imBRI2	integral membrane protein 2B	protein-coding	0.019531	0.474708	
chunk0097_296_1	chr2	55646939	55647634	+	0	NA	intron (NM_033109, intron 19 of 27)	(TTAT)n|Simple_repeat|Simple_repeat	-29561	NM_020463	57223	Hs.516182	NM_020463	ENSG00000275052	PPP4R3B	FLFL2|PP4R3B|PSY2|SMEK2|smk1	protein phosphatase 4 regulatory subunit 3B	protein-coding	0.008633	0.390805	
chunk0144_61_1	chr4	127007720	127008255	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-624945	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.013084	0.410448	74(TAGGACTTGCTGTTCA,-,0.00),75(AGGACTTGCTGTTCAC,+,0.00)
chunk0194_217_1	chr8	86146872	86147421	+	0	NA	intron (NM_152565, intron 5 of 7)	intron (NM_152565, intron 5 of 7)	48236	NM_152565	245972	Hs.436360	NM_152565	ENSG00000147614	ATP6V0D2	ATP6D2|VMA6	ATPase H+ transporting V0 subunit d2	protein-coding	0.005464	0.370909	
chunk0028_349_1	chr10	92267045	92267557	+	0	NA	intron (NM_014912, intron 1 of 9)	MER58C|DNA|hAT-Charlie	23817	NM_014912	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.001953	0.397661	
chunk0143_270_1	chr4	116626168	116626836	+	0	NA	Intergenic	Intergenic	326777	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.007485	0.357250	
chunk0115_127_1	chr21	23230426	23230793	+	0	NA	Intergenic	Intergenic	151325	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.013624	0.320652	
chunk0184_34_1	chr7	112099733	112100106	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	106488	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.002681	0.259358	
chunk0023_235_1	chr10	26818900	26819484	+	0	NA	intron (NM_001178116, intron 3 of 11)	intron (NM_001178116, intron 3 of 11)	41895	NM_001178123	10006	Hs.508148	NM_005470	ENSG00000136754	ABI1	ABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1	abl interactor 1	protein-coding	0.010274	0.382906	283(CAGAACAAAGTGTTAC,-,0.00)
chunk0001_361_1	chr1	10033098	10033584	+	0	NA	5' UTR (NM_006048, exon 1 of 27)	5' UTR (NM_006048, exon 1 of 27)	358	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.055556	0.601643	
chunk0147_302_1	chr4	184749529	184749922	+	0	NA	Intergenic	MIRb|SINE|MIR	-15593	NR_104593	79682	Hs.575032	NM_024629	ENSG00000151725	CENPU	CENP50|CENPU50|KLIP1|MLF1IP|PBIP1	centromere protein U	protein-coding	0.020356	0.484772	
chunk0084_91_1	chr17	75301507	75301808	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-12208	NM_001126122	60386	Hs.514470	NM_021734	ENSG00000125454	SLC25A19	DNC|MCPHA|MUP1|THMD3|THMD4|TPC	solute carrier family 25 member 19	protein-coding	0.039867	0.582781	
chunk0173_3_1	chr6	141134629	141135193	+	0	NA	Intergenic	Intergenic	451097	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.001773	0.334513	
chunk0061_325_1	chr14	63049899	63050098	+	0	NA	Intergenic	Intergenic	-4760	NM_172375	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.000000	0.445000	
chunk0182_388_1	chr7	100348753	100349467	+	0	NA	intron (NR_036569, intron 4 of 17)	intron (NR_036569, intron 4 of 17)	-3208	NR_103728	101752334	Hs.521075	NR_103728		PVRIG2P	-	poliovirus receptor related immunoglobulin domain containing 2, pseudogene	pseudo	0.008403	0.409790	263(GAGAACTTTGTGTTCT,-,0.00),264(AGAACTTTGTGTTCTA,+,0.00)
chunk0112_407_1	chr20	47079893	47080355	+	0	NA	intron (NM_172110, intron 7 of 13)	L1ME1|LINE|L1	-86843	NR_037410	100500814		NR_037410	ENSG00000264901	MIR3616	mir-3616	microRNA 3616	ncRNA	0.000000	0.332613	
chunk0015_88_1	chr1	184929718	184930482	+	0	NA	intron (NM_052966, intron 1 of 13)	intron (NM_052966, intron 1 of 13)	44486	NM_052966	116496	Hs.518662	NM_052966	ENSG00000135842	NIBAN1	C1orf24|FAM129A|GIG39|NIBAN	niban apoptosis regulator 1	protein-coding	0.009162	0.407843	
chunk0015_27_1	chr1	184402677	184403007	+	0	NA	intron (NM_030806, intron 1 of 5)	L1M5|LINE|L1	15826	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.009091	0.386707	
chunk0059_122_1	chr14	31456964	31457215	+	0	NA	intron (NM_080664, intron 1 of 2)	CpG	385	NM_080664	112487	Hs.116014	NM_080664	ENSG00000129480	DTD2	ATD|C14orf126	D-aminoacyl-tRNA deacylase 2	protein-coding	0.071713	0.619048	
chunk0098_323_1	chr2	76762009	76762457	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-223732	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.006696	0.409800	
chunk0063_9_1	chr14	76153785	76154327	+	0	NA	promoter-TSS (NR_110314)	promoter-TSS (NR_110314)	-298	NM_017972	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.003690	0.379374	
chunk0056_388_1	chr13	93713194	93713724	+	0	NA	intron (NM_005708, intron 2 of 8)	L1M5|LINE|L1	145014	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.001887	0.290019	
chunk0050_184_1	chr12	103880430	103880900	+	0	NA	intron (NR_027249, intron 9 of 15)	intron (NR_027249, intron 9 of 15)	-39468	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.010638	0.452229	
chunk0034_190_1	chr11	31653395	31653748	+	0	NA	intron (NM_019040, intron 9 of 9)	intron (NM_019040, intron 9 of 9)	143842	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.005666	0.279661	
chunk0121_418_1	chr3	25809995	25810556	+	0	NA	Intergenic	Intergenic	20203	NM_017897	54995	Hs.55781	NM_017897	ENSG00000151093	OXSM	CEM1|FASN2D|KASI|KS	3-oxoacyl-ACP synthase, mitochondrial	protein-coding	0.001783	0.407473	265(AAGAACACGATGAACT,-,0.00),266(AGAACACGATGAACTA,+,0.00)
chunk0042_393_1	chr12	10964311	10964988	+	0	NA	intron (NR_133575, intron 3 of 3)	intron (NR_133575, intron 3 of 3)	22263	NM_176890	259296	Hs.688194	NM_176890	ENSG00000212126	TAS2R50	T2R50|T2R51|TAS2R51	taste 2 receptor member 50	protein-coding	0.011817	0.386431	83(AGACACACGATGTCCC,-,0.00)
chunk0164_36_1	chr6	18422136	18422705	+	0	NA	intron (NM_182757, intron 2 of 7)	intron (NM_182757, intron 2 of 7)	35070	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.001757	0.426316	
chunk0081_227_1	chr17	42803035	42803383	+	0	NA	intron (NM_173478, intron 1 of 6)	intron (NM_173478, intron 1 of 6)	4373	NM_173478	124817	Hs.12272	NM_173478	ENSG00000176563	CNTD1	CNTD|COSA1	cyclin N-terminal domain containing 1	protein-coding	0.000000	0.472779	155(GGGATCTTTCTGTTCC,-,0.00),156(GGATCTTTCTGTTCCT,+,0.00)
chunk0158_390_1	chr5	134554298	134554728	+	0	NA	intron (NM_001308143, intron 4 of 11)	intron (NM_001308143, intron 4 of 11)	28405	NM_015288	23338	Hs.732155	NM_015288	ENSG00000043143	JADE2	JADE-2|PHF15	jade family PHD finger 2	protein-coding	0.018605	0.552204	
chunk0033_111_1	chr11	14412530	14413395	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-48456	NM_001177314	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.003468	0.370670	
chunk0019_65_1	chr1	224245190	224245389	+	0	NA	intron (NM_206840, intron 18 of 21)	intron (NM_206840, intron 18 of 21)	11852	NR_031574	100313769		NR_031574	ENSG00000221406	MIR320B2	MIR320B-2|MIRN320B2|mir-320b-2	microRNA 320b-2	ncRNA	0.000000	0.390000	
chunk0031_103_1	chr10	124186887	124187089	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	-93381	NM_001270764	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.014851	0.507389	
chunk0172_381_1	chr6	139403363	139403972	+	0	NA	Intergenic	Intergenic	-29017	NM_006079	10370	Hs.82071	NM_006079	ENSG00000164442	CITED2	ASD8|MRG-1|MRG1|P35SRJ|VSD2	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2	protein-coding	0.008210	0.470492	
chunk0207_152_1	chr9	129836368	129836567	+	0	NA	intron (NM_001008563, intron 1 of 25)	intron (NM_001008563, intron 1 of 25)	1050	NM_001110303	10868	Hs.5452	NM_006676	ENSG00000136878	USP20	LSFR3A|VDU2|hVDU2	ubiquitin specific peptidase 20	protein-coding	0.040201	0.565000	
chunk0017_223_1	chr1	207992761	207993194	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	-81639	NM_001025109	947	Hs.374990	NM_001773	ENSG00000174059	CD34	-	CD34 molecule	protein-coding	0.009238	0.387097	171(CAGTACAGGCAGTTCC,-,0.00),172(AGTACAGGCAGTTCCT,+,0.00)
chunk0180_396_1	chr7	74714901	74715350	+	0	NA	intron (NM_033001, intron 10 of 33)	intron (NM_033001, intron 10 of 33)	13793	NR_110044	101926943	Hs.654772	NR_110044	ENSG00000232729	LOC101926943	-	uncharacterized LOC101926943	ncRNA	0.006682	0.313333	75(TGCACAGACTGTGTTT,+,0.00)
chunk0110_333_1	chr20	19126862	19127247	+	0	NA	Intergenic	L1MA9|LINE|L1	-85592	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.002597	0.341969	
chunk0024_438_1	chr10	46356259	46356696	+	0	NA	Intergenic	Intergenic	-12610	NR_104039	100132929	Hs.645212	NM_001137556		FAM25BP	FAM25A|FAM25B|FAM25C|FAM25G	protein FAM25	pseudo	0.011442	0.369863	
chunk0121_461_1	chr3	27069262	27069938	+	0	NA	Intergenic	Intergenic	146923	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.010355	0.395864	
chunk0075_338_1	chr16	54927280	54927663	+	0	NA	intron (NR_110453, intron 1 of 5)	intron (NR_110453, intron 1 of 5)	1307	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.013055	0.382812	
chunk0119_175_1	chr22	43446114	43446872	+	0	NA	intron (NM_001044370, intron 3 of 6)	intron (NM_001044370, intron 3 of 6)	34479	NM_001044370	758	Hs.159538	NM_001044370	ENSG00000186732	MPPED1	239AB|C22orf1|FAM1A	metallophosphoesterase domain containing 1	protein-coding	0.010554	0.524374	
chunk0088_333_1	chr18	51045192	51045738	+	0	NA	intron (NM_005359, intron 1 of 11)	intron (NM_005359, intron 1 of 11)	15252	NM_005359	4089	Hs.75862	NM_005359	ENSG00000141646	SMAD4	DPC4|JIP|MADH4|MYHRS	SMAD family member 4	protein-coding	0.000000	0.323583	
chunk0060_381_1	chr14	52663986	52664478	+	0	NA	intron (NM_014584, intron 7 of 15)	A-rich|Low_complexity|Low_complexity	31699	NM_014584	30001	Hs.525339	NM_014584	ENSG00000197930	ERO1A	ERO1-L|ERO1-L-alpha|ERO1-alpha|ERO1L|ERO1LA|Ero1alpha	endoplasmic reticulum oxidoreductase 1 alpha	protein-coding	0.008130	0.308316	200(TGGCACAAAGTGTACC,-,0.00),201(GGCACAAAGTGTACCC,+,0.00)
chunk0189_109_1	chr8	22104192	22104715	+	0	NA	TTS (NM_022749)	TTS (NM_022749)	4966	NM_024815	79873	Hs.527101	NM_024815	ENSG00000275074	NUDT18	MTH3	nudix hydrolase 18	protein-coding	0.036329	0.564885	
chunk0052_282_1	chr12	124352994	124353193	+	0	NA	intron (NM_006312, intron 29 of 48)	LTR82A|LTR|ERVL	-15851	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.025126	0.540000	
chunk0148_167_1	chr5	7068421	7068682	+	0	NA	Intergenic	Intergenic	200803	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.019157	0.538168	214(CAGCACACCCTGTCCT,-,0.00),215(AGCACACCCTGTCCTA,+,0.00)
chunk0191_77_1	chr8	47460003	47460345	+	0	NA	intron (NR_104581, intron 6 of 16)	L1PB1|LINE|L1	199296	NM_001080394	23514	Hs.381058	NM_001080394	ENSG00000164808	SPIDR	KIAA0146	scaffold protein involved in DNA repair	protein-coding	0.002924	0.329446	
chunk0095_321_1	chr2	20536438	20536939	+	0	NA	Intergenic	L1MD3|LINE|L1	55860	NR_046836	100874343	Hs.591546	NR_046836	ENSG00000231948	HS1BP3-IT1	-	HS1BP3 intronic transcript 1	ncRNA	0.019960	0.480080	
chunk0041_63_1	chr11	123408045	123408517	+	0	NA	Intergenic	Intergenic	-26769	NR_039714	100616319		NR_039714	ENSG00000265357	MIR4493	-	microRNA 4493	ncRNA	0.012712	0.420719	
chunk0091_237_1	chr19	10653641	10653935	+	0	NA	promoter-TSS (NM_004516)	promoter-TSS (NM_004516)	84	NR_024333	147727	Hs.631616	NR_024333	ENSG00000267100	ILF3-DT	ILF3-AS1	ILF3 divergent transcript	ncRNA	0.088435	0.620339	
chunk0045_434_1	chr12	53538145	53538665	+	0	NA	intron (NM_006856, intron 4 of 11)	intron (NM_006856, intron 4 of 11)	24421	NR_046221	100652999	Hs.633602	NR_046221	ENSG00000257550	LOC100652999	-	uncharacterized LOC100652999	ncRNA	0.001923	0.414587	
chunk0049_395_1	chr12	96472393	96472592	+	0	NA	Intergenic	Intergenic	-17079	NM_001306084	144535	Hs.382121	NM_198520	ENSG00000188596	CFAP54	C12orf55|C12orf63	cilia and flagella associated protein 54	protein-coding	0.005025	0.390000	
chunk0181_93_1	chr7	80428526	80429041	+	0	NA	Intergenic	Intergenic	-54344	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.011650	0.331395	
chunk0117_40_1	chr22	12174973	12175200	+	0	NA	Intergenic	Intergenic	277680	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.017621	0.526316	
chunk0001_318_1	chr1	9435168	9435421	+	0	NA	Intergenic	CR1-3_Croc|LINE|CR1	-6298	NR_104622	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.003953	0.429134	
chunk0209_201_1	chrX	44024184	44024816	+	0	NA	Intergenic	Intergenic	-50825	NM_000266	4693	Hs.522615	NM_000266	ENSG00000124479	NDP	EVR2|FEVR|ND	norrin cystine knot growth factor NDP	protein-coding	0.004747	0.385466	
chunk0047_261_1	chr12	72773743	72774021	+	0	NA	Intergenic	Intergenic	-385308	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.000000	0.322581	
chunk0058_177_1	chr14	23913998	23914223	+	0	NA	Intergenic	LTR33|LTR|ERVL	-39625	NM_001282990	10901	Hs.528385	NM_021004	ENSG00000157326	DHRS4	CR|NRDR|PHCR|PSCD|SCAD-SRL|SDR-SRL|SDR25C1|SDR25C2	dehydrogenase/reductase 4	protein-coding	0.004444	0.500000	
chunk0058_166_1	chr14	23380009	23380229	+	0	NA	TTS (NM_001037288)	TTS (NM_001037288)	3311	NM_001288745	116173	Hs.99272	NM_138460	ENSG00000166091	CMTM5	CKLFSF5	CKLF like MARVEL transmembrane domain containing 5	protein-coding	0.031818	0.615385	
chunk0066_100_1	chr15	29829008	29829434	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1MD3|LINE|L1	-6718	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.014085	0.398126	140(TAGTACAGAGAGTTCC,-,0.00),141(AGTACAGAGAGTTCCT,+,0.00)
chunk0142_400_1	chr4	102706864	102707088	+	0	NA	intron (NM_005908, intron 5 of 16)	L1MA6|LINE|L1	54018	NM_005908	4126	Hs.480415	NM_005908	ENSG00000109323	MANBA	MANB1	mannosidase beta	protein-coding	0.000000	0.284444	
chunk0204_98_1	chr9	94572387	94572857	+	0	NA	intron (NM_003837, intron 3 of 6)	L2b|LINE|L2	17577	NR_121568	101928099	Hs.674409	NR_121566		PCAT7	PCAN-R2	prostate cancer associated transcript 7	ncRNA	0.012766	0.420382	
chunk0134_366_1	chr3	182697415	182697614	+	0	NA	Intergenic	Intergenic	-95989	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.030151	0.505000	
chunk0134_377_1	chr3	182807978	182808471	+	0	NA	intron (NM_014616, intron 1 of 29)	intron (NM_014616, intron 1 of 29)	14721	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.008114	0.350202	
chunk0058_403_1	chr13	111633856	111634208	+	0	NA	Intergenic	Intergenic	-259346	NR_046992	101928616	Hs.528450	NR_046992		LINC00354	-	long intergenic non-protein coding RNA 354	ncRNA	0.028409	0.450425	
chunk0176_128_1	chr7	12583895	12584350	+	0	NA	intron (NM_001112706, intron 3 of 15)	intron (NM_001112706, intron 3 of 15)	-5401	NM_033128	85477	Hs.633359	NM_033128	ENSG00000006747	SCIN	-	scinderin	protein-coding	0.004396	0.364035	
chunk0154_75_1	chr5	77486893	77487484	+	0	NA	intron (NM_018268, intron 2 of 12)	intron (NM_018268, intron 2 of 12)	5319	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.001692	0.334459	
chunk0170_324_1	chr6	116130363	116131095	+	0	NA	intron (NM_152729, intron 6 of 11)	L1MC5|LINE|L1	-4596	NM_000493	1300	Hs.520339	NM_000493	ENSG00000123500	COL10A1	-	collagen type X alpha 1 chain	protein-coding	0.005464	0.356071	283(ATGCACAGGGTGTTCA,-,0.00),284(TGCACAGGGTGTTCAT,+,0.00)
chunk0039_104_1	chr11	97583155	97583364	+	0	NA	Intergenic	Intergenic	-1076382	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.000000	0.423810	
chunk0179_382_1	chr7	51269478	51269734	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	47212	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.027344	0.568093	
chunk0085_411_1	chr18	10432755	10433081	+	0	NA	Intergenic	Intergenic	-18548	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.018405	0.498471	
chunk0024_361_1	chr10	44091502	44091928	+	0	NA	Intergenic	L1PA6|LINE|L1	182411	NR_033846	283033	Hs.178244	NR_033846		LINC00841	-	long intergenic non-protein coding RNA 841	ncRNA	0.007042	0.491803	
chunk0175_150_1	chr7	3695670	3696554	+	0	NA	intron (NM_152744, intron 4 of 44)	intron (NM_152744, intron 4 of 44)	394664	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.015837	0.445198	
chunk0077_234_1	chr16	80613920	80614444	+	0	NA	intron (NM_152342, intron 4 of 6)	MLT1J1|LTR|ERVL-MaLR	-41374	NR_104666	101928276	Hs.149769	NR_104665	ENSG00000260737	LINC01227	-	long intergenic non-protein coding RNA 1227	ncRNA	0.011450	0.502857	
chunk0157_271_1	chr5	120120226	120120776	+	0	NA	Intergenic	L1ME1|LINE|L1	-343777	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.007273	0.323049	
chunk0121_338_1	chr3	24513514	24513883	+	0	NA	Intergenic	Intergenic	7737	NR_039955									0.002710	0.335135	
chunk0015_453_1	chr1	192424504	192425190	+	0	NA	Intergenic	L1MA4A|LINE|L1	107855	NM_001039152	431704	Hs.558673	NM_001039152	ENSG00000253148	RGS21	-	regulator of G protein signaling 21	protein-coding	0.005831	0.535662	
chunk0013_12_1	chr1	165810870	165811291	+	0	NA	Intergenic	Intergenic	-16415	NM_012474	7371	Hs.458360	NM_012474	ENSG00000143179	UCK2	TSA903|UK|UMPK	uridine-cytidine kinase 2	protein-coding	0.007126	0.329384	
chunk0131_147_1	chr3	146019523	146019815	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	141826	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.013699	0.406143	
chunk0155_51_1	chr5	91219077	91219778	+	0	NA	Intergenic	Intergenic	94975	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.007133	0.415954	
chunk0163_228_1	chr6	12255675	12256134	+	0	NA	Intergenic	Intergenic	-34392	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.004357	0.378261	
chunk0073_200_1	chr16	9365080	9365961	+	0	NA	Intergenic	LTR83|LTR|ERVL	79465	NR_126397	104355218	Hs.564967	NR_126397	ENSG00000261397	LINC01177	-	long intergenic non-protein coding RNA 1177	ncRNA	0.004540	0.443311	
chunk0113_266_1	chr20	56398346	56398955	+	0	NA	intron (NM_001033521, intron 4 of 5)	intron (NM_001033521, intron 4 of 5)	5999	NM_001033522	1477	Hs.172865	NM_001324	ENSG00000101138	CSTF1	CstF-50|CstFp50	cleavage stimulation factor subunit 1	protein-coding	0.009852	0.381967	294(AGGTACAAGTTGTACT,-,0.00),295(GGTACAAGTTGTACTT,+,0.00)
chunk0059_281_1	chr14	35535026	35535242	+	0	NA	exon (NM_032594, exon 1 of 1)	exon (NM_032594, exon 1 of 1)	1092	NM_032594	84684	Hs.62813	NM_032594	ENSG00000168348	INSM2	IA-6|IA6|mlt1	INSM transcriptional repressor 2	protein-coding	0.097222	0.672811	
chunk0113_277_1	chr20	56713695	56713932	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	84511	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.016878	0.504202	188(AAGATCACAATGTGCT,-,0.00),189(AGATCACAATGTGCTT,+,0.00)
chunk0145_120_1	chr4	146336088	146336834	+	0	NA	intron (NM_001029998, intron 5 of 11)	L3|LINE|CR1	-72122	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.002681	0.376171	276(ATCACACCATGTTCCT,+,0.00)
chunk0048_446_1	chr12	88635636	88635912	+	0	NA	Intergenic	L1MC1|LINE|L1	-55301	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.003623	0.357401	
chunk0210_271_1	chrX	84266730	84267631	+	0	NA	Intergenic	L1P2|LINE|L1	-41352	NR_031690	100302191		NR_031690	ENSG00000221494	MIR548I4	MIR548I-4|MIRN548I4|hsa-mir-548i-4	microRNA 548i-4	ncRNA	0.013319	0.492239	
chunk0203_214_1	chr9	86683971	86684962	+	0	NA	Intergenic	Intergenic	262723	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.003027	0.385081	
chunk0077_372_1	chr16	84527047	84527658	+	0	NA	Intergenic	Intergenic	-22670	NM_020947	57707	Hs.288274	NM_020947	ENSG00000140950	MEAK7	KIAA1609|TLDC1|mEAK-7	MTOR associated protein, eak-7 homolog	protein-coding	0.036007	0.553922	130(AGGACTTAGAGTTCCC,+,0.00)
chunk0163_309_1	chr6	14622140	14622616	+	0	NA	Intergenic	Intergenic	-336924	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.023109	0.490566	
chunk0062_458_1	chr14	75815895	75816094	+	0	NA	intron (NM_015072, intron 27 of 31)	MIRb|SINE|MIR	154786	NM_015072	23093	Hs.709609	NM_015072	ENSG00000119685	TTLL5	CORD19|KIAA0998|STAMP	tubulin tyrosine ligase like 5	protein-coding	0.015075	0.450000	108(AACACTCTCTGTTCTG,+,0.00)
chunk0146_158_1	chr4	159940968	159941395	+	0	NA	Intergenic	Intergenic	673335	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.007026	0.378505	
chunk0158_22_1	chr5	125409428	125409921	+	0	NA	Intergenic	Intergenic	-83587	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.010142	0.364372	
chunk0140_354_1	chr4	74117153	74117527	+	0	NA	Intergenic	Intergenic	-18060	NM_002089	2920	Hs.75765	NM_002089	ENSG00000081041	CXCL2	CINC-2a|GRO2|GROb|MGSA-b|MIP-2a|MIP2|MIP2A|SCYB2	C-X-C motif chemokine ligand 2	protein-coding	0.005348	0.442667	
chunk0202_202_1	chr9	75490126	75490325	+	0	NA	Intergenic	Intergenic	-400419	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.000000	0.355000	0(CAGCACATACTGTTTT,-,0.00),1(AGCACATACTGTTTTT,+,0.00)
chunk0200_348_1	chr9	24701562	24702046	+	0	NA	Intergenic	Intergenic	-156128	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.002066	0.315464	
chunk0003_136_1	chr1	32763255	32763745	+	0	NA	intron (NM_020888, intron 1 of 6)	L2a|LINE|L2	-2134	NM_001198973	57648	Hs.591502	NM_020888	ENSG00000162522	KIAA1522	-	KIAA1522	protein-coding	0.022449	0.503055	
chunk0206_144_1	chr9	121356949	121357429	+	0	NA	intron (NM_001270527, intron 1 of 5)	L1M5|LINE|L1	13115	NM_001270526	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.006250	0.330561	
chunk0186_354_1	chr7	143512386	143512980	+	0	NA	intron (NR_033897, intron 3 of 4)	intron (NR_033897, intron 3 of 4)	34810	NM_176883	259287	Hs.650648	NM_176883	ENSG00000221855	TAS2R41	T2R41|T2R59	taste 2 receptor member 41	protein-coding	0.010101	0.428571	327(AGGAACAATATGTCCC,-,0.00),328(GGAACAATATGTCCCT,+,0.00)
chunk0180_158_1	chr7	64626668	64626933	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-39283	NR_104149	51427	Hs.50216	NM_016220	ENSG00000196247	ZNF107	Y8|ZFD25|ZNF588|smap-7	zinc finger protein 107	protein-coding	0.007547	0.413534	
chunk0085_161_1	chr18	3692206	3692701	+	0	NA	intron (NM_001308390, intron 4 of 10)	intron (NM_001308390, intron 4 of 10)	88716	NR_119377	84777	Hs.659053	NM_032691		DLGAP1-AS2	-	DLGAP1 antisense RNA 2	ncRNA	0.002020	0.395161	
chunk0145_54_1	chr4	145098137	145098476	+	0	NA	promoter-TSS (NM_001256710)	promoter-TSS (NM_001256710)	-87	NM_001256711	10393	Hs.480876	NM_014885	ENSG00000164162	ANAPC10	APC10|DOC1	anaphase promoting complex subunit 10	protein-coding	0.082596	0.600000	
chunk0185_450_1	chr7	135054471	135054734	+	0	NA	intron (NM_178563, intron 11 of 16)	intron (NM_178563, intron 11 of 16)	68094	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.000000	0.223485	
chunk0006_399_1	chr1	75450588	75451075	+	0	NA	intron (NM_001130058, intron 2 of 23)	L1PA16|LINE|L1	160283	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.004107	0.551230	
chunk0052_428_1	chr12	131737374	131737896	+	0	NA	intron (NM_004592, intron 7 of 17)	intron (NM_004592, intron 7 of 17)	26548	NM_001261411	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.022989	0.372849	
chunk0204_207_1	chr9	96777809	96778113	+	0	NA	5' UTR (NM_001314059, exon 1 of 6)	5' UTR (NM_001314059, exon 1 of 6)	105	NM_001314059	22869	Hs.75264	NM_014930	ENSG00000081386	ZNF510	-	zinc finger protein 510	protein-coding	0.085526	0.681967	
chunk0182_397_1	chr7	100607242	100607629	+	0	NA	intron (NM_002593, intron 6 of 8)	intron (NM_002593, intron 6 of 8)	-3397	NR_038910	100129845	Hs.714123	NR_038910	ENSG00000224729	PCOLCE-AS1	-	PCOLCE antisense RNA 1	ncRNA	0.012920	0.546392	
chunk0168_25_1	chr6	77298249	77298536	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	165011	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.003484	0.298611	
chunk0056_397_1	chr13	93941215	93941756	+	0	NA	intron (NM_005708, intron 3 of 8)	intron (NM_005708, intron 3 of 8)	-83012	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.003697	0.343173	
chunk0127_20_1	chr3	88298304	88298503	+	0	NA	Intergenic	Intergenic	-148537	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.010050	0.445000	60(TTGAACTTGGTGTCCC,-,0.00),61(TGAACTTGGTGTCCCA,+,0.00)
chunk0132_234_1	chr3	158468516	158468774	+	0	NA	intron (NM_001271834, intron 6 of 8)	MIR|SINE|MIR	102421	NR_104147	100996447	Hs.369810	NR_104147	ENSG00000243150	LOC100996447	-	uncharacterized LOC100996447	ncRNA	0.000000	0.328185	
chunk0058_416_1	chr13	112658544	112659050	+	0	NA	intron (NM_207440, intron 1 of 2)	intron (NM_207440, intron 1 of 2)	11753	NM_207440	400165	Hs.591213	NM_207440		ATP11AUN	C13orf35|SMABLO1	ATP11A upstream neighbor	protein-coding	0.005929	0.451677	
chunk0162_295_1	chr6	6422698	6423555	+	0	NA	intron (NR_026970, intron 4 of 7)	L1ME5|LINE|L1	-102435	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.000000	0.386946	
chunk0023_147_1	chr10	24168319	24168673	+	0	NA	intron (NM_001098500, intron 2 of 18)	intron (NM_001098500, intron 2 of 18)	-40295	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.005650	0.428169	
chunk0199_268_1	chr9	6342270	6342471	+	0	NA	Intergenic	L1MA4|LINE|L1	14021	NM_001001875	89882	Hs.351815	NM_033516	ENSG00000170777	TPD52L3	D55|NYDSP25|hD55	TPD52 like 3	protein-coding	0.004975	0.539604	
chunk0141_185_1	chr4	83048070	83048550	+	0	NA	intron (NM_016129, intron 2 of 9)	intron (NM_016129, intron 2 of 9)	13224	NM_016129	51138	Hs.190384	NM_016129	ENSG00000138663	COPS4	CSN4|SGN4	COP9 signalosome subunit 4	protein-coding	0.002083	0.301455	
chunk0055_108_1	chr13	56706496	56706700	+	0	NA	Intergenic	L1MC4|LINE|L1	-434320	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.004902	0.287805	
chunk0027_423_1	chr10	80850297	80850969	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	309814	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.004464	0.261516	
chunk0065_141_1	chr15	25281939	25282147	+	0	NA	Intergenic	Intergenic	3700	NR_001289	338429		NR_001289	ENSG00000239169	SNORD109B	HBII-438B	small nucleolar RNA, C/D box 109B	snoRNA	0.009615	0.315789	
chunk0001_131_1	chr1	5376959	5377158	+	0	NA	Intergenic	Intergenic	-187013	NR_039612									0.020101	0.575000	102(GGGTCTCACTGTCCTT,+,0.00),171(CAGGACAGAGAGTTTT,-,0.00),172(AGGACAGAGAGTTTTT,+,0.00)
chunk0125_192_1	chr3	66822085	66822425	+	0	NA	Intergenic	Intergenic	-176048	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.014706	0.486804	
chunk0117_63_1	chr22	16812075	16812360	+	0	NA	intron (NM_175878, intron 1 of 3)	intron (NM_175878, intron 1 of 3)	9477	NM_175878	150165	Hs.356069	NM_175878	ENSG00000172967	XKR3	XRG3|XTES	XK related 3	protein-coding	0.003509	0.388112	168(GGGCACATTCAGTACT,-,0.00),169(GGCACATTCAGTACTT,+,0.00)
chunk0164_72_1	chr6	19595372	19595887	+	0	NA	Intergenic	Intergenic	-241741	NM_001546	3400	Hs.519601	NM_001546	ENSG00000172201	ID4	IDB4|bHLHb27	inhibitor of DNA binding 4, HLH protein	protein-coding	0.001942	0.327519	
chunk0018_158_1	chr1	218833132	218833522	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	340461	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.007692	0.317136	
chunk0132_372_1	chr3	162868398	162868858	+	0	NA	Intergenic	L1P2|LINE|L1	434673	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.004348	0.494577	
chunk0144_286_1	chr4	138235544	138236100	+	0	NA	intron (NM_014331, intron 2 of 11)	intron (NM_014331, intron 2 of 11)	6527	NM_014331	23657	Hs.390594	NM_014331	ENSG00000151012	SLC7A11	CCBR1|xCT	solute carrier family 7 member 11	protein-coding	0.001799	0.335727	
chunk0171_253_1	chr6	127245931	127246364	+	0	NA	Intergenic	L1M5|LINE|L1	-20535	NM_001242851	81847	Hs.267120	NM_030963	ENSG00000118518	RNF146	-	ring finger protein 146	protein-coding	0.002309	0.274194	
chunk0014_238_1	chr1	179930219	179931171	+	0	NA	Intergenic	Intergenic	-24078	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.005252	0.352571	
chunk0070_295_1	chr15	74778958	74779625	+	0	NA	Intergenic	MER83|LTR|ERV1	-2793	NM_001127190	1445	Hs.77793	NM_004383	ENSG00000103653	CSK	-	C-terminal Src kinase	protein-coding	0.011994	0.426647	
chunk0103_190_1	chr2	163563681	163564107	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	172109	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.007042	0.362998	263(ATCACAGCGTGTACTT,+,0.00)
chunk0121_111_1	chr3	17301208	17301786	+	0	NA	intron (NM_014744, intron 14 of 21)	intron (NM_014744, intron 14 of 21)	368301	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.003460	0.347150	
chunk0123_103_1	chr3	42231031	42231230	+	0	NA	Intergenic	Intergenic	32817	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.010050	0.505000	
chunk0140_282_1	chr4	72280731	72281201	+	0	NA	TTS (NM_014243)	TTS (NM_014243)	241834	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.004255	0.339703	
chunk0149_224_1	chr5	22594529	22594776	+	0	NA	intron (NM_004061, intron 1 of 14)	intron (NM_004061, intron 1 of 14)	258970	NM_004061	1010	Hs.113684	NM_004061	ENSG00000154162	CDH12	CDHB	cadherin 12	protein-coding	0.008097	0.342742	
chunk0197_179_1	chr8	121244541	121245142	+	0	NA	Intergenic	Intergenic	-394505	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.009983	0.363787	
chunk0037_381_1	chr11	78537054	78537575	+	0	NA	intron (NR_120566, intron 1 of 3)	intron (NR_120566, intron 1 of 3)	4138	NR_120566	101928896	Hs.659055	NR_120566	ENSG00000255084	LOC101928896	-	uncharacterized LOC101928896	ncRNA	0.011516	0.415709	289(GAGTACAGATAGTACC,-,0.00)
chunk0013_315_1	chr1	171393796	171394139	+	0	NA	Intergenic	Intergenic	55071	NR_002719	7151	Hs.661092	NR_002719		TOP1P1	-	DNA topoisomerase I pseudogene 1	pseudo	0.000000	0.398256	
chunk0029_245_1	chr10	102769285	102769792	+	0	NA	intron (NM_001083913, intron 1 of 3)	intron (NM_001083913, intron 1 of 3)	-6593	NM_017787	54838	Hs.500897	NM_017787	ENSG00000166272	WBP1L	C10orf26|OPA1L|OPAL1	WW domain binding protein 1 like	protein-coding	0.009862	0.411417	
chunk0167_362_1	chr6	73198454	73198953	+	0	NA	3' UTR (NM_001160130, exon 13 of 13)	3' UTR (NM_001160130, exon 13 of 13)	26749	NM_001126063	100129128	Hs.663639	NM_001126063	ENSG00000256980	KHDC1L	-	KH domain containing 1 like	protein-coding	0.004008	0.328000	
chunk0133_150_1	chr3	169324244	169324960	+	0	NA	intron (NM_001205194, intron 1 of 15)	MIRc|SINE|MIR	-176868	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.013966	0.433752	315(AGGAACAAACTGACCT,-,0.00),316(GGAACAAACTGACCTT,+,0.00)
chunk0127_386_1	chr3	102130084	102130686	+	0	NA	Intergenic	Intergenic	189526	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003322	0.407960	90(GGGAACTTCCTGTTCC,-,0.00),91(GGAACTTCCTGTTCCA,+,0.00),342(AGAGACATCTTGTTCT,-,0.00),343(GAGACATCTTGTTCTT,+,0.00)
chunk0156_239_1	chr5	108587254	108587502	+	0	NA	Intergenic	Intergenic	140883	NR_046368	100652853	Hs.133009	NR_046368	ENSG00000272523	LINC01023	HP07349	long intergenic non-protein coding RNA 1023	ncRNA	0.004032	0.297189	
chunk0035_200_1	chr11	44589231	44589807	+	0	NA	intron (NM_001024844, intron 2 of 8)	intron (NM_001024844, intron 2 of 8)	23928	NM_002231	3732	Hs.527778	NM_002231	ENSG00000085117	CD82	4F9|C33|GR15|IA4|KAI1|R2|SAR2|ST6|TSPAN27	CD82 molecule	protein-coding	0.006944	0.483536	
chunk0122_15_1	chr3	27449977	27450177	+	0	NA	intron (NM_003615, intron 2 of 24)	Tigger17c|DNA|TcMar-Tigger	6677	NM_001258380	9497	Hs.250072	NM_003615	ENSG00000033867	SLC4A7	NBC2|NBC3|NBCN1|SBC2|SLC4A6	solute carrier family 4 member 7	protein-coding	0.005000	0.353234	
chunk0029_376_1	chr10	108661440	108662080	+	0	NA	Intergenic	Intergenic	-592467	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.007812	0.374415	
chunk0071_192_1	chr15	83892477	83893355	+	0	NA	intron (NM_207517, intron 13 of 29)	intron (NM_207517, intron 13 of 29)	-187271	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.007973	0.385666	222(TTGGACTGCATGTTCC,-,0.00),223(TGGACTGCATGTTCCG,+,0.00)
chunk0016_167_1	chr1	197853188	197853448	+	0	NA	Intergenic	Intergenic	-49234	NM_001024594	388722	Hs.61329	NM_001024594	ENSG00000203724	C1orf53	-	chromosome 1 open reading frame 53	protein-coding	0.003846	0.302682	
chunk0036_359_1	chr11	66953472	66953926	+	0	NA	intron (NM_000920, intron 1 of 21)	intron (NM_000920, intron 1 of 21)	4677	NM_001040716	5091	Hs.89890	NM_000920	ENSG00000173599	PC	PCB	pyruvate carboxylase	protein-coding	0.015419	0.448352	222(AGGAACTGTATGTACA,-,0.00),223(GGAACTGTATGTACAC,+,0.00)
chunk0190_114_1	chr8	30490747	30491075	+	0	NA	intron (NM_006867, intron 4 of 9)	intron (NM_006867, intron 4 of 9)	-105510	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.003049	0.416413	153(CAGCACAGGAAGTACT,-,0.00),154(AGCACAGGAAGTACTT,+,0.00)
chunk0212_261_1	chrX	139634107	139634456	+	0	NA	intron (NM_001171876, intron 4 of 28)	intron (NM_001171876, intron 4 of 28)	8560	NM_001171879	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.000000	0.325714	212(GGGAACTCTCTGTACT,-,0.00),213(GGAACTCTCTGTACTT,+,0.00)
chunk0187_342_1	chr7	156931821	156932474	+	0	NA	Intergenic	Intergenic	-17576	NM_138400	64434	Hs.15825	NM_138400	ENSG00000146909	NOM1	C7orf3|PPP1R113|SGD1	nucleolar protein with MIF4G domain 1	protein-coding	0.016845	0.434251	
chunk0148_417_1	chr5	15009341	15009978	+	0	NA	Intergenic	Intergenic	-137881	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.006279	0.332288	
chunk0034_215_1	chr11	32830345	32830764	+	0	NA	exon (NM_024081, exon 2 of 6)	exon (NM_024081, exon 2 of 6)	619	NM_024081	79056	Hs.471695	NM_024081	ENSG00000135378	PRRG4	PRGP4|TMG4	proline rich and Gla domain 4	protein-coding	0.045346	0.473810	
chunk0179_254_1	chr7	48632034	48632233	+	0	NA	intron (NM_152701, intron 59 of 61)	L1PA15|LINE|L1	-292428	NR_003595									0.000000	0.375000	
chunk0006_77_1	chr1	64950778	64951386	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	15422	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.004934	0.359606	
chunk0128_195_1	chr3	107604109	107604308	+	0	NA	intron (NM_001276286, intron 2 of 16)	intron (NM_001276286, intron 2 of 16)	81272	NM_001142568	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.015075	0.440000	
chunk0146_396_1	chr4	168764645	168765618	+	0	NA	intron (NM_016081, intron 10 of 20)	MIRb|SINE|MIR	-66874	NM_001166110	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.010277	0.414784	
chunk0179_409_1	chr7	51633766	51634365	+	0	NA	Intergenic	MER41D|LTR|ERV1	-317247	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.010017	0.440000	
chunk0025_253_1	chr10	54857192	54857391	+	0	NA	Intergenic	Intergenic	-56000	NM_001142773	65217	Hs.280209	NM_033056	ENSG00000150275	PCDH15	CDHR15|DFNB23|USH1F	protocadherin related 15	protein-coding	0.005025	0.265000	
chunk0082_239_1	chr17	57357335	57357707	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	100508	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.032258	0.563003	
chunk0073_249_1	chr16	11752860	11753292	+	0	NA	intron (NM_014153, intron 21 of 22)	intron (NM_014153, intron 21 of 22)	-10198	NM_001303447	51061	Hs.313847	NM_015914	ENSG00000153066	TXNDC11	EFP1	thioredoxin domain containing 11	protein-coding	0.006944	0.496536	
chunk0170_452_1	chr6	119280137	119280562	+	0	NA	intron (NM_005907, intron 5 of 12)	MIR|SINE|MIR	69417	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.002353	0.396714	189(AATAACACTCTGTGCC,-,0.00),190(ATAACACTCTGTGCCT,+,0.00)
chunk0041_326_1	chr11	130239301	130239607	+	0	NA	intron (NM_014155, intron 3 of 5)	MER58A|DNA|hAT-Charlie	75258	NM_001301099	29068	Hs.721470	NM_014155	ENSG00000196323	ZBTB44	BTBD15|HSPC063|ZNF851	zinc finger and BTB domain containing 44	protein-coding	0.006536	0.410423	
chunk0121_332_1	chr3	24416979	24417602	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-76797	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.011236	0.354167	
chunk0005_391_1	chr1	62241598	62242087	+	0	NA	intron (NM_181712, intron 9 of 9)	intron (NM_181712, intron 9 of 9)	47040	NM_001164835	54596	Hs.685462	NM_019079	ENSG00000240563	L1TD1	ECAT11	LINE1 type transposase domain containing 1	protein-coding	0.010225	0.504082	
chunk0076_119_1	chr16	66638866	66639293	+	0	NA	intron (NM_181521, intron 1 of 3)	intron (NM_181521, intron 1 of 3)	34348	NR_037619	123920	Hs.298198	NM_144601	ENSG00000140931	CMTM3	BNAS2|CKLFSF3	CKLF like MARVEL transmembrane domain containing 3	protein-coding	0.002342	0.329439	399(AATAACACACTGTACT,-,0.00),400(ATAACACACTGTACTG,+,0.00)
chunk0078_335_1	chr17	8794106	8794345	+	0	NA	Intergenic	MIR|SINE|MIR	5124	NM_152599	162387	Hs.213603	NM_152599	ENSG00000185156	MFSD6L	-	major facilitator superfamily domain containing 6 like	protein-coding	0.025105	0.458333	
chunk0176_122_1	chr7	12211494	12211778	+	0	NA	intron (NM_001134232, intron 1 of 7)	intron (NM_001134232, intron 1 of 7)	414	NM_018374	54664	Hs.396358	NM_018374	ENSG00000106460	TMEM106B	HLD16	transmembrane protein 106B	protein-coding	0.045775	0.600000	
chunk0012_237_1	chr1	160640453	160640692	+	0	NA	intron (NR_104400, intron 1 of 4)	intron (NR_104400, intron 1 of 4)	6739	NR_104401	6504	Hs.523660	NM_003037	ENSG00000117090	SLAMF1	CD150|CDw150|SLAM	signaling lymphocytic activation molecule family member 1	protein-coding	0.004184	0.408333	
chunk0112_77_1	chr20	37854166	37854370	+	0	NA	intron (NM_030877, intron 13 of 15)	intron (NM_030877, intron 13 of 15)	-48829	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.000000	0.375610	55(AGGTGCAGTGTGTACC,-,0.00),56(GGTGCAGTGTGTACCT,+,0.00)
chunk0128_2_1	chr3	103427954	103428697	+	0	NA	Intergenic	MER92B|LTR|ERV1	95791	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.005384	0.405914	
chunk0152_169_1	chr5	59548958	59549472	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	37283	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.009728	0.378641	
chunk0163_340_1	chr6	15422103	15422599	+	0	NA	intron (NM_001267040, intron 3 of 17)	intron (NM_001267040, intron 3 of 17)	173496	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.016129	0.494970	
chunk0040_419_1	chr11	121195197	121195727	+	0	NA	Intergenic	Intergenic	92796	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.007547	0.352166	
chunk0054_427_1	chr13	51081638	51081985	+	0	NA	Intergenic	Intergenic	-15654	NR_003923	2974	Hs.411573	NM_004129	ENSG00000123201	GUCY1B2	GC-SB2	guanylate cyclase 1 soluble subunit beta 2 (pseudogene)	pseudo	0.014409	0.459770	95(AGGAACACAGTGTCCT,-,0.00),96(GGAACACAGTGTCCTG,+,0.00)
chunk0063_219_1	chr14	81517477	81517676	+	0	NA	intron (NM_001244984, intron 3 of 7)	MER68-int|LTR|ERVL	16285	NM_005065	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.000000	0.425000	
chunk0202_208_1	chr9	75820753	75821264	+	0	NA	Intergenic	L1PA7|LINE|L1	-69636	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.007828	0.505859	
chunk0104_412_1	chr2	180731205	180731404	+	0	NA	intron (NR_104324, intron 3 of 4)	MLT1A1|LTR|ERVL-MaLR	39200	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.005025	0.465000	
chunk0200_342_1	chr9	24374174	24374803	+	0	NA	Intergenic	Intergenic	171188	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.006359	0.366667	
chunk0123_405_1	chr3	49092631	49092962	+	0	NA	intron (NM_017730, intron 1 of 10)	intron (NM_017730, intron 1 of 10)	1275	NM_017730	54870	Hs.297389	NM_017730	ENSG00000198218	QRICH1	AB-DIP|VERBRAS	glutamine rich 1	protein-coding	0.006042	0.379518	
chunk0121_274_1	chr3	23331135	23331721	+	0	NA	intron (NM_152653, intron 3 of 5)	L2a|LINE|L2	128135	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.000000	0.410562	459(GGGGACAAGGTGTGCT,-,0.00),460(GGGACAAGGTGTGCTA,+,0.00)
chunk0066_149_1	chr15	31500041	31500555	+	0	NA	intron (NM_130901, intron 8 of 10)	intron (NM_130901, intron 8 of 10)	155041	NM_130901	161725	Hs.355236	NM_130901	ENSG00000169918	OTUD7A	C15orf16|C16ORF15|CEZANNE2|OTUD7	OTU deubiquitinase 7A	protein-coding	0.033074	0.576699	
chunk0211_399_1	chrX	128633738	128634193	+	0	NA	Intergenic	Intergenic	-581562	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.000000	0.399123	263(AAGCACATAATGTTAC,-,0.00)
chunk0130_431_1	chr3	140917732	140918166	+	0	NA	Intergenic	Intergenic	-23871	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.013825	0.503448	
chunk0146_152_1	chr4	159787687	159788196	+	0	NA	Intergenic	Intergenic	520095	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.001965	0.374510	
chunk0032_180_1	chr11	6023383	6023622	+	0	NA	Intergenic	Intergenic	4239	NM_001001917	120796	Hs.553543	NM_001001917	ENSG00000180934	OR56A1	OR11-75	olfactory receptor family 56 subfamily A member 1	protein-coding	0.000000	0.429167	
chunk0071_356_1	chr15	88714815	88715218	+	0	NA	Intergenic	Intergenic	76273	NM_002201	3669	Hs.459265	NM_002201	ENSG00000172183	ISG20	CD25|HEM45	interferon stimulated exonuclease gene 20	protein-coding	0.019851	0.554455	104(TGGAACACGGTGTCCC,-,0.00),105(GGAACACGGTGTCCCT,+,0.00)
chunk0020_436_1	chr1	241881264	241881630	+	0	NA	intron (NM_003686, intron 11 of 13)	intron (NM_003686, intron 11 of 13)	32716	NM_006027	9156	Hs.498248	NM_003686	ENSG00000174371	EXO1	HEX1|hExoI	exonuclease 1	protein-coding	0.019126	0.422343	
chunk0163_222_1	chr6	12171621	12171899	+	0	NA	Intergenic	Intergenic	-118536	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.007194	0.405018	
chunk0173_310_1	chr6	148521038	148521645	+	0	NA	intron (NM_015278, intron 10 of 19)	intron (NM_015278, intron 10 of 19)	178748	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.009885	0.401316	320(ATGAACAGGATGTTCT,-,0.00),321(TGAACAGGATGTTCTT,+,0.00)
chunk0140_422_1	chr4	76007210	76007503	+	0	NA	intron (NM_002416, intron 1 of 3)	intron (NM_002416, intron 1 of 3)	167	NM_002416	4283	Hs.77367	NM_002416	ENSG00000138755	CXCL9	CMK|Humig|MIG|SCYB9|crg-10	C-X-C motif chemokine ligand 9	protein-coding	0.003413	0.397959	
chunk0210_464_1	chrX	107464390	107464948	+	0	NA	Intergenic	Intergenic	-57781	NM_032428	84443	Hs.496546	NM_032428	ENSG00000147234	FRMPD3	-	FERM and PDZ domain containing 3	protein-coding	0.003584	0.452594	322(GAGAACTTCCTGTTCT,-,0.00),323(AGAACTTCCTGTTCTT,+,0.00)
chunk0027_125_1	chr10	74223369	74223813	+	0	NA	intron (NM_001202449, intron 2 of 9)	Charlie2a|DNA|hAT-Charlie	47102	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.004505	0.382022	
chunk0024_432_1	chr10	46075902	46076154	+	0	NA	Intergenic	Intergenic	-29759	NM_002443	4477	Hs.255462	NM_002443	ENSG00000263639	MSMB	HPC13|IGBF|MSP|MSPB|PN44|PRPS|PSP|PSP-94|PSP57|PSP94	microseminoprotein beta	protein-coding	0.011905	0.450593	
chunk0189_140_1	chr8	22840479	22841117	+	0	NA	intron (NM_144962, intron 3 of 6)	L2b|LINE|L2	-37174	NR_125433	101929237	Hs.677838	NR_125433	ENSG00000248738	LOC101929237	-	uncharacterized LOC101929237	ncRNA	0.007837	0.449139	
chunk0144_426_1	chr4	140702235	140702503	+	0	NA	intron (NM_015130, intron 1 of 20)	MamRep605|LTR?|LTR?	53948	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.000000	0.427509	144(AAGAACAGGCTGTACC,-,0.00),145(AGAACAGGCTGTACCT,+,0.00)
chunk0201_176_1	chr9	36251462	36251933	+	0	NA	intron (NM_001128227, intron 1 of 11)	intron (NM_001128227, intron 1 of 11)	6802	NM_001190383	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.006369	0.425847	
chunk0207_158_1	chr9	130051952	130052180	+	0	NA	Intergenic	Intergenic	-1640	NM_001136558	57720	Hs.512461	NM_020960	ENSG00000148358	GPR107	GCDRP|LUSTR1|bA138E2.2	G protein-coupled receptor 107	protein-coding	0.000000	0.349345	
chunk0110_290_1	chr20	17733011	17733210	+	0	NA	intron (NM_178477, intron 3 of 3)	intron (NM_178477, intron 3 of 3)	33162	NM_178477	140836	Hs.115366	NM_178477	ENSG00000125888	BANF2	BAF-L|BAF2|BAFL|C20orf179	barrier to autointegration factor 2	protein-coding	0.010050	0.575000	
chunk0204_346_1	chr9	101509660	101510050	+	0	NA	Intergenic	Charlie3|DNA|hAT-Charlie	-22634	NM_032342	84302	Hs.388742	NM_032342	ENSG00000165152	TMEM246	C9orf125	transmembrane protein 246	protein-coding	0.012821	0.427110	
chunk0100_416_1	chr2	119814174	119814387	+	0	NA	intron (NM_002830, intron 2 of 26)	intron (NM_002830, intron 2 of 26)	54649	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.000000	0.406542	
chunk0002_446_1	chr1	28437945	28438597	+	0	NA	5' UTR (NM_023923, exon 1 of 13)	5' UTR (NM_023923, exon 1 of 13)	121	NM_023923	65979	Hs.225641	NM_023923	ENSG00000204138	PHACTR4	PPP1R124	phosphatase and actin regulator 4	protein-coding	0.013804	0.442573	244(AAGAACTGCAAGTGCT,-,0.00),245(AGAACTGCAAGTGCTC,+,0.00)
chunk0027_283_1	chr10	77507202	77507944	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	130246	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.008086	0.464334	82(AGGTACTGTTTGTTCC,-,0.00),83(GGTACTGTTTGTTCCT,+,0.00),310(ATGAACTGACTGTTCT,-,0.00),311(TGAACTGACTGTTCTT,+,0.00)
chunk0065_49_1	chr15	22301361	22301870	+	0	NA	Intergenic	L2c|LINE|L2	43001	NR_033735	646396	Hs.451294	NR_033735		REREP3	-	arginine-glutamic acid dipeptide repeats pseudogene 3	pseudo	0.005894	0.282353	
chunk0001_312_1	chr1	9331623	9332142	+	0	NA	intron (NM_025106, intron 1 of 2)	L1M5|LINE|L1	39000	NM_025106	80176	Hs.8261	NM_025106	ENSG00000171621	SPSB1	SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding	0.019268	0.451923	
chunk0129_273_1	chr3	122777159	122777523	+	0	NA	intron (NM_024610, intron 2 of 7)	MamRTE1|LINE|RTE-BovB	16478	NM_024610	79663	Hs.29169	NM_024610	ENSG00000169087	HSPBAP1	PASS1	HSPB1 associated protein 1	protein-coding	0.008242	0.304110	
chunk0151_327_1	chr5	53750941	53751336	+	0	NA	Intergenic	L1PA6|LINE|L1	190503	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.015190	0.537879	
chunk0101_208_1	chr2	130241140	130241339	+	0	NA	Intergenic	L2c|LINE|L2	-42778	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.000000	0.430000	
chunk0035_351_1	chr11	48103874	48104166	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	7238	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.020548	0.546075	
chunk0108_400_1	chr2	237421719	237421918	+	0	NA	Intergenic	HAL1|LINE|L1	-7611	NM_004369	1293	Hs.233240	NM_004369	ENSG00000163359	COL6A3	BTHLM1|DYT27|UCMD1	collagen type VI alpha 3 chain	protein-coding	0.030151	0.560000	
chunk0136_164_1	chr4	6165519	6166049	+	0	NA	intron (NM_001099433, intron 1 of 20)	Tigger1|DNA|TcMar-Tigger	28835	NM_001306133	152789	Hs.479066	NM_144720	ENSG00000152969	JAKMIP1	Gababrbp|JAMIP1|MARLIN1	janus kinase and microtubule interacting protein 1	protein-coding	0.016981	0.465160	270(AAGGTCAGCCTGTACC,-,0.00),271(AGGTCAGCCTGTACCA,+,0.00)
chunk0193_54_1	chr8	72193638	72194167	+	0	NA	Intergenic	Intergenic	57732	NR_033867	392232	Hs.454043	NR_033867		LOC392232	-	transient receptor potential cation channel subfamily A member 1 pseudogene	pseudo	0.015123	0.418868	
chunk0052_288_1	chr12	124381836	124382035	+	0	NA	intron (NM_006312, intron 19 of 48)	intron (NM_006312, intron 19 of 48)	-44693	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.065327	0.630000	
chunk0153_384_1	chr5	75042615	75042872	+	0	NA	Intergenic	Intergenic	9900	NR_126375	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.000000	0.422481	
chunk0162_1_1	chr6	158453	158813	+	0	NA	Intergenic	Intergenic	-10474	NR_109817	441123		NR_109817		LINC00266-3	C6orf88|NCRNA00266-3|NCRNA00266C|dJ24O22.2	long intergenic non-protein coding RNA 266-3	ncRNA	0.002778	0.454294	
chunk0046_4_1	chr12	53999169	53999370	+	0	NA	promoter-TSS (NM_006897)	promoter-TSS (NM_006897)	741	NR_047504	100874363	Hs.555036	NR_047504	ENSG00000250451	HOXC-AS1	-	HOXC cluster antisense RNA 1	ncRNA	0.019900	0.450495	
chunk0114_101_1	chr21	9364727	9364997	+	0	NA	Intergenic	Intergenic	-235101	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.000000	0.523985	
chunk0101_329_1	chr2	136019602	136020178	+	0	NA	Intergenic	Intergenic	-34206	NM_001293312	1615	Hs.503787	NM_001349	ENSG00000115866	DARS	HBSL|aspRS	aspartyl-tRNA synthetase	protein-coding	0.017361	0.473137	484(GGAACTAGTTGTCCCT,+,0.00)
chunk0125_356_1	chr3	71308442	71308786	+	0	NA	intron (NM_032682, intron 4 of 20)	intron (NM_032682, intron 4 of 20)	-3854	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.014535	0.397101	
chunk0100_177_1	chr2	110219387	110220118	+	0	NA	non-coding (NR_027063, exon 2 of 8)	non-coding (NR_027063, exon 2 of 8)	3188	NR_027063	205251	Hs.128499	NM_001355251	ENSG00000175701	MTLN	LINC00116|MOXI|NCRNA00116|SMIM37	mitoregulin	protein-coding	0.001368	0.435792	
chunk0167_368_1	chr6	73528796	73529461	+	0	NA	Intergenic	MIRb|SINE|MIR	-8096	NM_001402	1915	Hs.535192	NM_001402	ENSG00000156508	EEF1A1	CCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|HNGC:16303|LENG7|PTI1|eEF1A-1	eukaryotic translation elongation factor 1 alpha 1	protein-coding	0.010526	0.415916	
chunk0100_166_1	chr2	109324710	109324986	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	-11223	NR_036224	100423027		NR_036224	ENSG00000265965	MIR4266	-	microRNA 4266	ncRNA	0.025362	0.476534	
chunk0181_255_1	chr7	85765666	85766135	+	0	NA	Intergenic	LTR22B2|LTR|ERVK	-643969	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.012793	0.436170	
chunk0192_261_1	chr8	66006826	66007419	+	0	NA	Intergenic	Intergenic	-14434	NM_033105	85479	Hs.491885	NM_033105	ENSG00000147570	DNAJC5B	CSP-beta	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding	0.003373	0.318182	
chunk0100_403_1	chr2	119337595	119338382	+	0	NA	intron (NM_001017927, intron 3 of 6)	intron (NM_001017927, intron 3 of 6)	28694	NM_001017927	130355	Hs.99488	NM_001017927	ENSG00000186132	C2orf76	AIM29	chromosome 2 open reading frame 76	protein-coding	0.005083	0.426396	272(AAGAACACCGTGACCC,-,0.00),273(AGAACACCGTGACCCT,+,0.00)
chunk0158_48_1	chr5	125950326	125950549	+	0	NA	Intergenic	Intergenic	-229140	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.004484	0.401786	
chunk0117_326_1	chr22	24969831	24970452	+	0	NA	Intergenic	Intergenic	-30794	NM_001001663	255349	Hs.329040	NM_001001663	ENSG00000206069	TMEM211	bA9F11.1	transmembrane protein 211	protein-coding	0.012882	0.551447	
chunk0080_293_1	chr17	31488758	31489016	+	0	NA	intron (NM_001303542, intron 1 of 12)	intron (NM_001303542, intron 1 of 12)	886	NM_001303542	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.054264	0.656371	
chunk0068_74_1	chr15	51933095	51933460	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-9157	NR_109775	100422556	Hs.664788	NR_109775		LOC100422556	-	LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene	pseudo	0.013699	0.442623	
chunk0035_249_1	chr11	46267774	46268388	+	0	NA	Intergenic	L1ME4b|LINE|L1	-9557	NM_052854	90993	Hs.405961	NM_052854	ENSG00000157613	CREB3L1	OASIS|OI16	cAMP responsive element binding protein 3 like 1	protein-coding	0.004886	0.382114	425(CAGAACAGTGTGTATA,-,0.00)
chunk0179_440_1	chr7	52346271	52346499	+	0	NA	Intergenic	Intergenic	-689271	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.013158	0.493450	
chunk0010_236_1	chr1	116423554	116424269	+	0	NA	non-coding (NR_125972, exon 4 of 4)	non-coding (NR_125972, exon 4 of 4)	-5289	NR_027646	84852	Hs.664752	NM_032766	ENSG00000203865	ATP1A1-AS1	ATP1A1OS|C1orf203	ATP1A1 antisense RNA 1	ncRNA	0.002797	0.364525	580(CAGAACATAATGAACT,-,0.00),581(AGAACATAATGAACTG,+,0.00)
chunk0019_143_1	chr1	225736292	225736861	+	0	NA	Intergenic	Intergenic	-41237	NM_003133	6726	Hs.511425	NM_003133	ENSG00000143742	SRP9	ALURBP	signal recognition particle 9	protein-coding	0.010545	0.480702	185(AGGTTCACCATGTTCT,-,0.00),186(GGTTCACCATGTTCTC,+,0.00)
chunk0193_120_1	chr8	74234664	74235026	+	0	NA	3' UTR (NM_020647, exon 6 of 6)	3' UTR (NM_020647, exon 6 of 6)	86482	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.000000	0.300275	
chunk0115_67_1	chr21	21697862	21698162	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	39307	NR_038872	378828	Hs.551009	NR_038872	ENSG00000238265	LINC00317	C21orf117|NCRNA00317|PRED89	long intergenic non-protein coding RNA 317	ncRNA	0.003333	0.292359	
chunk0201_417_1	chr9	69604202	69604553	+	0	NA	intron (NM_001163, intron 1 of 12)	intron (NM_001163, intron 1 of 12)	67982	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.014245	0.548295	
chunk0140_288_1	chr4	72351572	72352187	+	0	NA	intron (NM_014243, intron 4 of 21)	intron (NM_014243, intron 4 of 21)	216920	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.008130	0.316558	
chunk0026_343_1	chr10	68596601	68597043	+	0	NA	intron (NM_030625, intron 2 of 11)	intron (NM_030625, intron 2 of 11)	36462	NM_030625	80312	Hs.258855	NM_030625	ENSG00000138336	TET1	CXXC6|LCX|bA119F7.1	tet methylcytosine dioxygenase 1	protein-coding	0.006787	0.361174	
chunk0203_171_1	chr9	86054594	86055232	+	0	NA	intron (NM_177937, intron 3 of 9)	MER112|DNA|hAT-Charlie	44682	NM_016548	51280	Hs.494337	NM_016548	ENSG00000135052	GOLM1	C9orf155|GOLPH2|GP73|HEL46|PSEC0257|bA379P1.3	golgi membrane protein 1	protein-coding	0.009404	0.450704	
chunk0161_357_1	chr5	175107034	175107356	+	0	NA	Intergenic	MER21-int|LTR|ERVL	-111464	NR_046113	441116	Hs.533036	NM_001004348	ENSG00000204754	LINC01951	-	long intergenic non-protein coding RNA 1951	ncRNA	0.000000	0.433437	
chunk0088_76_1	chr18	44696747	44697445	+	0	NA	intron (NM_015559, intron 1 of 5)	intron (NM_015559, intron 1 of 5)	16198	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.012894	0.469242	308(AAGTACAGAGTGTCCA,-,0.00),309(AGTACAGAGTGTCCAT,+,0.00)
chunk0096_329_1	chr2	34353790	34354304	+	0	NA	Intergenic	Intergenic	286821	NR_132381	106144585	Hs.580486	NR_132381	ENSG00000237790	LINC01318	-	long intergenic non-protein coding RNA 1318	ncRNA	0.003891	0.320388	
chunk0134_305_1	chr3	180747897	180748407	+	0	NA	intron (NR_109986, intron 6 of 13)	intron (NR_109986, intron 6 of 13)	-68657	NM_181426	339829	Hs.712820	NM_181426	ENSG00000284862	CCDC39	CILD14|FAP59	coiled-coil domain containing 39	protein-coding	0.001961	0.452055	
chunk0078_71_1	chr17	1569265	1569584	+	0	NA	3' UTR (NM_152346, exon 14 of 14)	3' UTR (NM_152346, exon 14 of 14)	-6608	NM_006224	5306	Hs.429819	NM_006224	ENSG00000174238	PITPNA	HEL-S-36|PI-TPalpha|PITPN|VIB1A	phosphatidylinositol transfer protein alpha	protein-coding	0.034483	0.556250	
chunk0107_33_1	chr2	211020000	211020354	+	0	NA	Intergenic	L1PB1|LINE|L1	402606	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.000000	0.343662	
chunk0118_4_1	chr22	25544898	25545842	+	0	NA	Intergenic	Intergenic	-19524	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.010593	0.449735	
chunk0135_310_1	chr3	189982204	189982690	+	0	NA	intron (NM_001134418, intron 8 of 14)	intron (NM_001134418, intron 8 of 14)	-138517	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.008230	0.367556	276(AGGCACATAATGTTCC,-,0.00),277(GGCACATAATGTTCCG,+,0.00)
chunk0169_410_1	chr6	108536818	108537053	+	0	NA	Intergenic	Intergenic	-22888	NM_201559	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.004255	0.305085	
chunk0209_350_1	chrX	53071480	53072174	+	0	NA	intron (NM_018969, intron 1 of 1)	intron (NM_018969, intron 1 of 1)	-10533	NM_022117	64061	Hs.136164	NM_022117	ENSG00000184205	TSPYL2	CDA1|CINAP|CTCL|DENTT|HRIHFB2216|NP79|SE204|TSPX	TSPY like 2	protein-coding	0.038905	0.517986	276(GGGTACACTGTGTACC,-,0.00),277(GGTACACTGTGTACCT,+,0.00),307(GAGTACAAGATGTACC,-,0.00),308(AGTACAAGATGTACCT,+,0.00)
chunk0196_312_1	chr8	110641645	110642105	+	0	NA	Intergenic	Intergenic	385558	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.002174	0.357918	299(ATGAACACTGTGTGCA,-,0.00),300(TGAACACTGTGTGCAG,+,0.00)
chunk0118_293_1	chr22	34236609	34236925	+	0	NA	Intergenic	Intergenic	-316339	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.006329	0.476341	15(GTGATCAGCGTGTTCC,-,0.00),16(TGATCAGCGTGTTCCT,+,0.00)
chunk0015_155_1	chr1	186492346	186493126	+	0	NA	Intergenic	Intergenic	-31628	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.008974	0.335467	
chunk0096_208_1	chr2	30444572	30444947	+	0	NA	Intergenic	Intergenic	-2467	NM_182551	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.005333	0.409574	
chunk0022_437_1	chr10	19561803	19562043	+	0	NA	intron (NM_001142308, intron 32 of 39)	L1MC2|LINE|L1	166627	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.008333	0.435685	112(AAGAACAGAATGTTCT,-,0.00),113(AGAACAGAATGTTCTT,+,0.00)
chunk0157_114_1	chr5	116882109	116883074	+	0	NA	Intergenic	Intergenic	-120382	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.004145	0.409938	
chunk0027_31_1	chr10	72308334	72308705	+	0	NA	Intergenic	Intergenic	34600	NM_019058	54541	Hs.744875	NM_019058	ENSG00000168209	DDIT4	Dig2|REDD-1|REDD1	DNA damage inducible transcript 4	protein-coding	0.005391	0.569892	
chunk0199_262_1	chr9	6198409	6198670	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-16610	NM_001314047	90865	Hs.731660	NM_033439	ENSG00000137033	IL33	C9orf26|DVS27|IL1F11|NF-HEV|NFEHEV	interleukin 33	protein-coding	0.015326	0.427481	
chunk0167_431_1	chr6	75747174	75747807	+	0	NA	Intergenic	L2c|LINE|L2	-1686	NM_001300899	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.011058	0.403785	
chunk0057_29_1	chr13	95659369	95660124	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-15040	NM_198968	22873	Hs.656580	NM_014934	ENSG00000134874	DZIP1	DZIP|DZIPt1	DAZ interacting zinc finger protein 1	protein-coding	0.000000	0.346561	
chunk0153_252_1	chr5	72613542	72613833	+	0	NA	intron (NR_105007, intron 1 of 2)	L1MA8|LINE|L1	46982	NR_105007	102477328	Hs.254516	NR_105007	ENSG00000248371	LINC02056	-	long intergenic non-protein coding RNA 2056	ncRNA	0.006873	0.390411	
chunk0126_307_1	chr3	81042955	81043551	+	0	NA	intron (NR_132411, intron 1 of 1)	intron (NR_132411, intron 1 of 1)	49385	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.006711	0.336683	
chunk0050_449_1	chr12	110543422	110544025	+	0	NA	intron (NM_139283, intron 3 of 5)	intron (NM_139283, intron 3 of 5)	39536	NM_139283	160760	Hs.13854	NM_139283	ENSG00000196850	PPTC7	TA-PP2C|TAPP2C	PTC7 protein phosphatase homolog	protein-coding	0.011609	0.470199	323(TTGAACATACTGTGCT,-,0.00),324(TGAACATACTGTGCTG,+,0.00)
chunk0152_419_1	chr5	65685677	65685876	+	0	NA	intron (NM_019072, intron 5 of 10)	intron (NM_019072, intron 5 of 10)	36338	NM_019072	54557	Hs.482301	NM_019072	ENSG00000197860	SGTB	SGT2	small glutamine rich tetratricopeptide repeat containing beta	protein-coding	0.000000	0.385000	
chunk0127_94_1	chr3	89914677	89914954	+	0	NA	Intergenic	LTR1E|LTR|ERV1	807291	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.003610	0.503597	
chunk0165_264_1	chr6	35782278	35782866	+	0	NA	intron (NM_001010886, intron 1 of 2)	L2a|LINE|L2	1518	NM_001010886	340204	Hs.131296	NM_001010886	ENSG00000204140	CLPSL1	C6orf127|ESP32|dJ510O8.6	colipase like 1	protein-coding	0.010204	0.502547	326(CAGGACAGGGTGCTCT,-,0.00),327(AGGACAGGGTGCTCTG,+,0.00)
chunk0102_417_1	chr2	156818763	156819251	+	0	NA	Intergenic	Intergenic	382619	NM_000408	2820	Hs.512382	NM_000408	ENSG00000115159	GPD2	GDH2|GPDM|mGPDH	glycerol-3-phosphate dehydrogenase 2	protein-coding	0.006148	0.445808	
chunk0052_422_1	chr12	131576808	131577022	+	0	NA	Intergenic	Intergenic	-134172	NM_004592	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.037383	0.576744	
chunk0086_419_1	chr18	27018926	27019237	+	0	NA	intron (NM_031422, intron 4 of 5)	intron (NM_031422, intron 4 of 5)	-153329	NM_001650	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.019293	0.496795	
chunk0144_194_1	chr4	133666288	133666560	+	0	NA	Intergenic	L2a|LINE|L2	517134	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.003676	0.293040	
chunk0043_321_1	chr12	22408581	22408813	+	0	NA	Intergenic	Intergenic	-73983	NM_003034	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.008621	0.459227	
chunk0180_152_1	chr7	64480472	64480868	+	0	NA	Intergenic	PRIMA4-int|LTR|ERV1	46977	NR_029404	649395	Hs.728871	NR_029404		YWHAEP1	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon pseudogene 1	pseudo	0.007576	0.418136	101(AGGCACTTTGTGTTCC,-,0.00),102(GGCACTTTGTGTTCCT,+,0.00)
chunk0011_144_1	chr1	147388716	147389187	+	0	NA	intron (NR_038423, intron 3 of 3)	L1P4d|LINE|L1	128924	NR_038423	100289211	Hs.323484	NR_038423	ENSG00000278811	LINC00624	-	long intergenic non-protein coding RNA 624	ncRNA	0.008493	0.552966	
chunk0207_396_1	chr9	136695418	136695790	+	0	NA	Intergenic	Intergenic	-8145	NM_001012727	10555	Hs.320151	NM_006412	ENSG00000169692	AGPAT2	1-AGPAT2|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2	protein-coding	0.021505	0.568365	
chunk0014_232_1	chr1	179882511	179882985	+	0	NA	exon (NM_015602, exon 1 of 10)	exon (NM_015602, exon 1 of 10)	706	NM_015602	26092	Hs.496459	NM_015602	ENSG00000143337	TOR1AIP1	LAP1|LAP1B|LGMD2Y	torsin 1A interacting protein 1	protein-coding	0.092827	0.642105	
chunk0185_244_1	chr7	130008824	130009079	+	0	NA	Intergenic	Intergenic	42500	NM_001282191	51530	Hs.194157	NM_016478	ENSG00000091732	ZC3HC1	HSPC216|NIPA	zinc finger C3HC-type containing 1	protein-coding	0.019608	0.574219	
chunk0159_89_1	chr5	137880337	137880651	+	0	NA	intron (NM_001300911, intron 5 of 10)	intron (NM_001300911, intron 5 of 10)	-8942	NM_001258448	27039	Hs.716884	NM_014386	ENSG00000078795	PKD2L2	TRPP5	polycystin 2 like 2, transient receptor potential cation channel	protein-coding	0.003185	0.387302	133(AAGGACAATCTGTACT,-,0.00),134(AGGACAATCTGTACTC,+,0.00)
chunk0073_351_1	chr16	14963341	14963689	+	0	NA	Intergenic	LTR41|LTR|ERVL	-11220	NM_001285447	23042	Hs.370781	NM_015027	ENSG00000179889	PDXDC1	LP8165	pyridoxal dependent decarboxylase domain containing 1	protein-coding	0.005747	0.498567	
chunk0113_84_1	chr20	50763028	50763304	+	0	NA	Intergenic	Intergenic	31622	NM_032521	84612	Hs.589848	NM_032521	ENSG00000124171	PARD6B	PAR6B	par-6 family cell polarity regulator beta	protein-coding	0.032609	0.581227	
chunk0132_378_1	chr3	163138093	163138856	+	0	NA	Intergenic	L1MA3|LINE|L1	164827	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.002621	0.301047	
chunk0208_223_1	chrX	19097614	19098129	+	0	NA	intron (NM_001184837, intron 1 of 26)	L2a|LINE|L2	24766	NM_001079859	10149	Hs.146978	NM_005756	ENSG00000173698	ADGRG2	CBAVDX|EDDM6|GPR64|HE6|TM7LN2	adhesion G protein-coupled receptor G2	protein-coding	0.021359	0.451550	
chunk0013_363_1	chr1	172398965	172399798	+	0	NA	intron (NM_001136127, intron 19 of 19)	intron (NM_001136127, intron 19 of 19)	-21307	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.010804	0.389688	
chunk0031_405_1	chr10	131877615	131878319	+	0	NA	Intergenic	L1MC|LINE|L1	-22677	NR_033191	55844	Hs.380372	NM_018461	ENSG00000175470	PPP2R2D	B55D|B55delta|MDS026	protein phosphatase 2 regulatory subunit Bdelta	protein-coding	0.011364	0.357447	
chunk0177_180_1	chr7	23347999	23348198	+	0	NA	intron (NM_006547, intron 6 of 14)	intron (NM_006547, intron 6 of 14)	48777	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.000000	0.425000	
chunk0104_162_1	chr2	174155700	174156528	+	0	NA	intron (NM_001011708, intron 3 of 9)	MIR|SINE|MIR	92523	NM_013341	29789	Hs.157351	NM_013341	ENSG00000138430	OLA1	DOC45|GBP45|GTBP9|GTPBP9|PTD004	Obg like ATPase 1	protein-coding	0.006039	0.382388	
chunk0040_169_1	chr11	113951944	113952143	+	0	NA	Intergenic	Intergenic	-23032	NR_046363	3359	Hs.413899	NM_000869	ENSG00000166736	HTR3A	5-HT-3|5-HT3A|5-HT3R|5HT3R|HTR3	5-hydroxytryptamine receptor 3A	protein-coding	0.030151	0.580000	
chunk0125_198_1	chr3	66998934	66999256	+	0	NA	exon (NM_032505, exon 2 of 4)	exon (NM_032505, exon 2 of 4)	792	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.021739	0.455108	
chunk0055_102_1	chr13	56352105	56352677	+	0	NA	Intergenic	Intergenic	-788527	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.010490	0.368237	
chunk0195_139_1	chr8	95112480	95113105	+	0	NA	Intergenic	Intergenic	-20929	NM_024613	79666	Hs.29724	NM_024613	ENSG00000175895	PLEKHF2	EAPF|PHAFIN2|ZFYVE18	pleckstrin homology and FYVE domain containing 2	protein-coding	0.011200	0.476038	95(GTGACAATCTGTTCTG,+,0.00)
chunk0085_83_1	chr18	2281390	2281780	+	0	NA	Intergenic	Intergenic	289918	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.007692	0.365729	
chunk0079_287_1	chr17	16584380	16584616	+	0	NA	Intergenic	CpG	-15292	NM_020653	57336	Hs.99724	NM_020653	ENSG00000141040	ZNF287	ZKSCAN13|ZSCAN45	zinc finger protein 287	protein-coding	0.080508	0.654008	
chunk0013_234_1	chr1	169574355	169574814	+	0	NA	intron (NM_000130, intron 2 of 24)	intron (NM_000130, intron 2 of 24)	11947	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.010893	0.400000	272(AAGCACTGTAAGTCCC,-,0.00),273(AGCACTGTAAGTCCCT,+,0.00)
chunk0199_273_1	chr9	6408839	6409196	+	0	NA	Intergenic	Intergenic	-4134	NR_046386	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.000000	0.385475	
chunk0015_381_1	chr1	190570726	190571138	+	0	NA	Intergenic	L1MA9|LINE|L1	-53958	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.002427	0.292978	
chunk0195_356_1	chr8	99711117	99711596	+	0	NA	intron (NM_152564, intron 36 of 61)	intron (NM_152564, intron 36 of 61)	-174495	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.002088	0.383333	
chunk0203_71_1	chr9	83667340	83667836	+	0	NA	intron (NM_013438, intron 7 of 10)	intron (NM_013438, intron 7 of 10)	40665	NM_013438	29979	Hs.9589	NM_013438	ENSG00000135018	UBQLN1	DA41|DSK2|PLIC-1|UBQN|XDRP1	ubiquilin 1	protein-coding	0.008065	0.317907	
chunk0123_54_1	chr3	41152844	41153347	+	0	NA	Intergenic	Intergenic	-46356	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.009940	0.392857	
chunk0097_125_1	chr2	46725153	46725721	+	0	NA	intron (NM_144949, intron 1 of 1)	L1MEf|LINE|L1	26227	NM_144949	9655	Hs.468426	NM_014011	ENSG00000171150	SOCS5	CIS6|CISH6|Cish5|SOCS-5	suppressor of cytokine signaling 5	protein-coding	0.001761	0.286467	
chunk0154_254_1	chr5	81451010	81451329	+	0	NA	intron (NM_001256733, intron 9 of 15)	MER63B|DNA|hAT-Blackjack	-57000	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.006270	0.356250	
chunk0094_432_1	chr2	10846137	10846603	+	0	NA	Intergenic	Intergenic	-8393	NM_001282705	10130	Hs.212102	NM_005742	ENSG00000143870	PDIA6	ERP5|P5|TXNDC7	protein disulfide isomerase family A member 6	protein-coding	0.021459	0.447537	248(GAGAACATAATGTTCT,-,0.00),249(AGAACATAATGTTCTA,+,0.00)
chunk0165_333_1	chr6	37366871	37367130	+	0	NA	intron (NM_003958, intron 2 of 7)	intron (NM_003958, intron 2 of 7)	13028	NR_046399	9025	Hs.485278	NM_003958	ENSG00000112130	RNF8	hRNF8	ring finger protein 8	protein-coding	0.003861	0.392308	
chunk0154_409_1	chr5	88831783	88832304	+	0	NA	intron (NM_001131005, intron 2 of 10)	intron (NM_001131005, intron 2 of 10)	-8116	NM_001308002	4208	Hs.649965	NM_002397	ENSG00000081189	MEF2C	C5DELq14.3|DEL5q14.3	myocyte enhancer factor 2C	protein-coding	0.005758	0.362069	
chunk0013_372_1	chr1	172469951	172470623	+	0	NA	Intergenic	Intergenic	17394	NM_001300760	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.002976	0.402675	
chunk0194_99_1	chr8	83317227	83317865	+	0	NA	Intergenic	Intergenic	-86212	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.001567	0.317684	
chunk0158_134_1	chr5	127236193	127236778	+	0	NA	Intergenic	Intergenic	-54279	NM_001308119	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.003419	0.438567	318(ATGTACAGTGTGTTCA,-,0.00),319(TGTACAGTGTGTTCAT,+,0.00)
chunk0001_86_1	chr1	2655546	2655950	+	0	NA	intron (NM_001242672, intron 4 of 6)	intron (NM_001242672, intron 4 of 6)	-22706	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.019802	0.617284	
chunk0143_192_1	chr4	112426429	112426909	+	0	NA	intron (NM_025144, intron 8 of 15)	intron (NM_025144, intron 8 of 15)	89503	NM_024019	63973	Hs.744415	NM_024019	ENSG00000178403	NEUROG2	Atoh4|Math4A|NGN2|bHLHa8|ngn-2	neurogenin 2	protein-coding	0.006250	0.376299	
chunk0084_297_1	chr17	79979271	79979918	+	0	NA	intron (NM_019020, intron 3 of 11)	intron (NM_019020, intron 3 of 11)	-28737	NM_001271845	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.041731	0.587963	
chunk0201_389_1	chr9	69044640	69045153	+	0	NA	intron (NM_000144, intron 1 of 4)	intron (NM_000144, intron 1 of 4)	9333	NM_000144	2395	Hs.20685	NM_000144	ENSG00000165060	FXN	CyaY|FA|FARR|FRDA|X25	frataxin	protein-coding	0.005848	0.527237	211(GTCACATTCTGTCCTG,+,0.00)
chunk0008_94_1	chr1	90946638	90947018	+	0	NA	intron (NM_201269, intron 2 of 5)	intron (NM_201269, intron 2 of 5)	74680	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.002632	0.351706	191(TTGAACAGCTTGTTCC,-,0.00),192(TGAACAGCTTGTTCCT,+,0.00)
chunk0187_216_1	chr7	152012018	152012310	+	0	NA	intron (NR_033169, intron 8 of 9)	MLT1H|LTR|ERVL-MaLR	-13510	NM_001304514	63917	Hs.647109	NM_022087	ENSG00000178234	GALNT11	GALNAC-T11|GALNACT11	polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0.010274	0.443686	188(GGAAACACGCTGTTCT,-,0.00),189(GAAACACGCTGTTCTG,+,0.00)
chunk0031_120_1	chr10	124721749	124721948	+	0	NA	intron (NM_014661, intron 1 of 4)	intron (NM_014661, intron 1 of 4)	17820	NR_120631	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.030151	0.490000	
chunk0097_283_1	chr2	55100049	55100307	+	0	NA	Intergenic	Intergenic	-49580	NM_020532	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.007752	0.413127	
chunk0077_73_1	chr16	77130422	77130793	+	0	NA	Intergenic	MIRb|SINE|MIR	-60312	NM_001286640	22879	Hs.513743	NM_014940	ENSG00000103111	MON1B	HSRG1|SAND2|SRG1	MON1 homolog B, secretory trafficking associated	protein-coding	0.008086	0.400538	
chunk0108_31_1	chr2	226572112	226572674	+	0	NA	Intergenic	Intergenic	86400	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.003559	0.428064	297(CTGCACATTGTGTTCT,-,0.00),298(TGCACATTGTGTTCTT,+,0.00)
chunk0177_266_1	chr7	25405636	25406276	+	0	NA	Intergenic	Intergenic	-177470	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.012500	0.482059	
chunk0017_200_1	chr1	207628801	207629145	+	0	NA	intron (NM_000651, intron 45 of 46)	CR1_Mam|LINE|CR1	-16140	NM_175710	1379	Hs.628568	NM_175710	ENSG00000197721	CR1L	-	complement C3b/C4b receptor 1 like	protein-coding	0.011628	0.339130	
chunk0177_277_1	chr7	25568652	25568851	+	0	NA	Intergenic	Intergenic	-340265	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.050251	0.470000	
chunk0104_173_1	chr2	174569640	174570286	+	0	NA	intron (NM_003387, intron 5 of 7)	L1ME4a|LINE|L1	-11891	NR_004394	26827		NR_004394	ENSG00000206625	RNU6-1	RNU6|RNU6A|U6|U6-1	RNA, U6 small nuclear 1	snRNA	0.001548	0.369397	
chunk0042_20_1	chr12	1318432	1318726	+	0	NA	intron (NM_178040, intron 15 of 18)	intron (NM_178040, intron 15 of 18)	-181912	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.006803	0.393220	
chunk0112_461_1	chr20	49105587	49106057	+	0	NA	Intergenic	Intergenic	59576	NM_001256135	1434	Hs.90073	NM_001316	ENSG00000124207	CSE1L	CAS|CSE1|XPO2	chromosome segregation 1 like	protein-coding	0.004255	0.384289	177(ATGCACATGCTGTCCT,-,0.00),178(TGCACATGCTGTCCTT,+,0.00)
chunk0132_315_1	chr3	160709423	160709938	+	0	NA	Intergenic	Intergenic	32520	NM_025047	80117	Hs.287702	NM_025047	ENSG00000179674	ARL14	ARF7	ADP ribosylation factor like GTPase 14	protein-coding	0.005825	0.393411	
chunk0206_437_1	chr9	127913843	127914060	+	0	NA	intron (NM_175040, intron 2 of 4)	intron (NM_175040, intron 2 of 4)	3075	NM_175040	27090	Hs.3972	NM_014403	ENSG00000136840	ST6GALNAC4	IV|SIAT3-C|SIAT3C|SIAT7-D|SIAT7D|ST6GALNACIV|ST6GalNAc	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	protein-coding	0.036866	0.591743	
chunk0073_185_1	chr16	8987218	8988028	+	0	NA	Intergenic	MIRc|SINE|MIR	-24139	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.017284	0.489519	
chunk0211_338_1	chrX	124294045	124294244	+	0	NA	Intergenic	AluJb|SINE|Alu	-52138	NM_001114937	4068	Hs.349094	NM_002351	ENSG00000183918	SH2D1A	DSHP|EBVS|IMD5|LYP|MTCP1|SAP|SAP/SH2D1A|XLP|XLPD|XLPD1	SH2 domain containing 1A	protein-coding	0.000000	0.435000	
chunk0090_436_1	chr18	79528877	79529223	+	0	NA	3' UTR (NM_001278672, exon 9 of 9)	3' UTR (NM_001278672, exon 9 of 9)	128776	NM_001278672	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.069364	0.561960	172(AGGAACGGCCTGTACC,-,0.00),173(GGAACGGCCTGTACCG,+,0.00)
chunk0208_351_1	chrX	25394683	25395105	+	0	NA	Intergenic	L1MEc|LINE|L1	-378946	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.007109	0.347518	
chunk0028_33_1	chr10	82871102	82871718	+	0	NA	intron (NM_001010848, intron 4 of 8)	L1MC1|LINE|L1	-638490	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.003247	0.298217	
chunk0168_411_1	chr6	95094633	95095059	+	0	NA	Intergenic	Intergenic	482605	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.004695	0.323185	
chunk0073_223_1	chr16	10947036	10947566	+	0	NA	intron (NM_015226, intron 1 of 22)	L2c|LINE|L2	2813	NM_015226	23274	Hs.35490	NM_015226	ENSG00000038532	CLEC16A	Gop-1|KIAA0350	C-type lectin domain containing 16A	protein-coding	0.018868	0.532957	286(CAGAACAGCTCGTTCC,-,0.00),287(AGAACAGCTCGTTCCC,+,0.00)
chunk0051_309_1	chr12	119415818	119416036	+	0	NA	intron (NM_178499, intron 1 of 13)	L2|LINE|L2	81215	NM_178499	160777	Hs.98188	NM_178499	ENSG00000183273	CCDC60	-	coiled-coil domain containing 60	protein-coding	0.000000	0.452055	
chunk0152_387_1	chr5	64619509	64620234	+	0	NA	Intergenic	Intergenic	44221	NR_073511	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.006897	0.384298	80(AGGCTCAGACTGTGCT,-,0.00),81(GGCTCAGACTGTGCTG,+,0.00),218(GAAAACATAGTGTGCT,-,0.00),219(AAAACATAGTGTGCTG,+,0.00),349(GAGAACATAGAGTGCT,-,0.00),350(AGAACATAGAGTGCTT,+,0.00)
chunk0043_253_1	chr12	20631699	20632001	+	0	NA	intron (NM_000921, intron 6 of 15)	intron (NM_000921, intron 6 of 15)	59986	NM_001244683	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.003311	0.363036	
chunk0131_434_1	chr3	153719712	153720377	+	0	NA	Intergenic	Intergenic	235549	NM_001101337									0.003008	0.376877	
chunk0116_56_1	chr21	33801619	33802142	+	0	NA	intron (NM_001001132, intron 19 of 29)	intron (NM_001001132, intron 19 of 29)	113974	NM_001697	539	Hs.409140	NM_001697	ENSG00000241837	ATP5PO	ATP5O|ATPO|HMC08D05|OSCP	ATP synthase peripheral stalk subunit OSCP	protein-coding	0.003824	0.375954	
chunk0109_344_1	chr2	238768295	238768502	+	0	NA	Intergenic	Intergenic	-79634	NM_001271893	117581	Hs.422585	NM_057179	ENSG00000233608	TWIST2	AMS|BBRSAY|DERMO1|FFDD3|SETLSS|bHLHa39	twist family bHLH transcription factor 2	protein-coding	0.004831	0.389423	
chunk0173_40_1	chr6	142276141	142276797	+	0	NA	Intergenic	MIRb|SINE|MIR	-25450	NM_001032395	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.001524	0.321157	
chunk0142_423_1	chr4	103754804	103755312	+	0	NA	Intergenic	LTR18A|LTR|ERVL	-35242	NM_001059	6870	Hs.942	NM_001059	ENSG00000169836	TACR3	HH11|NK-3R|NK3|NK3R|NKR|TAC3R|TAC3RL	tachykinin receptor 3	protein-coding	0.005906	0.453831	
chunk0066_123_1	chr15	31020637	31020854	+	0	NA	intron (NM_001252020, intron 26 of 26).2	intron (NM_001252020, intron 26 of 26).2	-29141	NM_017762	54893	Hs.30141	NM_017762	ENSG00000166912	MTMR10	-	myotubularin related protein 10	protein-coding	0.013825	0.454128	
chunk0198_2_1	chr9	247135	247655	+	0	NA	intron (NM_203447, intron 1 of 47)	intron (NM_203447, intron 1 of 47)	-25653	NM_001190458	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.019231	0.358925	343(AAGTACACTTAGTGCC,-,0.00),344(AGTACACTTAGTGCCT,+,0.00)
chunk0058_420_1	chr13	112804835	112805206	+	0	NA	exon (NM_015205, exon 3 of 30)	exon (NM_015205, exon 3 of 30)	-50289	NR_046661	100874205	Hs.658692	NR_046661	ENSG00000232684	ATP11A-AS1	-	ATP11A antisense RNA 1	ncRNA	0.005391	0.338710	306(AAGGACATGGTGCCCC,-,0.00),307(AGGACATGGTGCCCCT,+,0.00)
chunk0001_307_1	chr1	9225353	9225756	+	0	NA	Intergenic	Intergenic	-9250	NM_004285	9563	Hs.463511	NM_004285	ENSG00000049239	H6PD	CORTRD1|G6PDH|GDH	hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase	protein-coding	0.009926	0.549505	
chunk0030_276_1	chr10	116553155	116553896	+	0	NA	intron (NM_000936, intron 5 of 12)	Tigger3b|DNA|TcMar-Tigger	7609	NM_000936	5406	Hs.501135	NM_000936	ENSG00000175535	PNLIP	PL|PNLIPD|PTL	pancreatic lipase	protein-coding	0.025641	0.482480	
chunk0016_408_1	chr1	203291430	203291668	+	0	NA	Intergenic	Intergenic	3849	NR_117098	100506775	Hs.443859	NR_117097	ENSG00000231507	LINC01353	-	long intergenic non-protein coding RNA 1353	ncRNA	0.029412	0.518828	
chunk0168_161_1	chr6	83721387	83721832	+	0	NA	Intergenic	Intergenic	-12201	NM_001242793	9892	Hs.368046	NM_014841	ENSG00000065609	SNAP91	AP180|CALM	synaptosome associated protein 91	protein-coding	0.000000	0.282511	
chunk0201_402_1	chr9	69235721	69236074	+	0	NA	intron (NM_201629, intron 12 of 20)	intron (NM_201629, intron 12 of 20)	30735	NM_001170416	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.011331	0.423729	
chunk0087_365_1	chr18	41377758	41378337	+	0	NA	Intergenic	Intergenic	142550	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.006908	0.350000	
chunk0040_387_1	chr11	119615562	119615922	+	0	NA	Intergenic	Intergenic	112983	NM_203286	5818	Hs.334846	NM_002855	ENSG00000110400	NECTIN1	CD111|CLPED1|ED4|HIgR|HV1S|HVEC|OFC7|PRR|PRR1|PVRL1|PVRR|PVRR1|SK-12|nectin-1	nectin cell adhesion molecule 1	protein-coding	0.008333	0.479224	
chunk0056_153_1	chr13	84198010	84198387	+	0	NA	intron (NR_046871, intron 1 of 6)	intron (NR_046871, intron 1 of 6)	57596	NR_046871	100874128	Hs.578060	NR_046871		LINC00333	NCRNA00333	long intergenic non-protein coding RNA 333	ncRNA	0.000000	0.272487	
chunk0068_450_1	chr15	59786029	59786414	+	0	NA	Intergenic	L1PB|LINE|L1	-96778	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.002597	0.360104	
chunk0061_258_1	chr14	61355987	61356301	+	0	NA	intron (NM_006255, intron 1 of 13)	intron (NM_006255, intron 1 of 13)	34701	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.015924	0.520635	
chunk0145_116_1	chr4	146276161	146276700	+	0	NA	intron (NM_001029998, intron 10 of 11)	intron (NM_001029998, intron 10 of 11)	100747	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.000000	0.322222	
chunk0027_400_1	chr10	80385831	80386442	+	0	NA	Intergenic	L1MCb|LINE|L1	-21693	NM_001243779	84293	Hs.500333	NM_032333	ENSG00000122378	PRXL2A	Adrx|C10orf58|FAM213A|PAMM	peroxiredoxin like 2A	protein-coding	0.001637	0.294118	
chunk0112_111_1	chr20	38427632	38428184	+	0	NA	promoter-TSS (NR_002911)	promoter-TSS (NR_002911)	-465	NR_002911	26777	Hs.681779	NR_002911	ENSG00000225091	SNORA71A	RNU71A|U71a	small nucleolar RNA, H/ACA box 71A	snoRNA	0.010870	0.479204	
chunk0179_75_1	chr7	44259456	44260017	+	0	NA	intron (NM_172084, intron 3 of 15)	intron (NM_172084, intron 3 of 15)	58757	NM_006555	10652	Hs.520794	NM_006555	ENSG00000106636	YKT6	-	YKT6 v-SNARE homolog	protein-coding	0.021390	0.514235	
chunk0006_274_1	chr1	70352942	70353309	+	0	NA	intron (NM_030816, intron 1 of 12)	intron (NM_030816, intron 1 of 12)	1609	NM_030816	81573	Hs.744989	NM_030816	ENSG00000118454	ANKRD13C	dJ677H15.3	ankyrin repeat domain 13C	protein-coding	0.010899	0.290761	92(TGGTTCAGTGTGTTCT,-,0.00),93(GGTTCAGTGTGTTCTA,+,0.00)
chunk0038_182_1	chr11	85828366	85828603	+	0	NA	Intergenic	Intergenic	-17325	NM_001289608	54843	Hs.369520	NM_032379	ENSG00000137501	SYTL2	CHR11SYT|EXO4|PPP1R151|SGA72M|SLP2|SLP2A	synaptotagmin like 2	protein-coding	0.004219	0.327731	
chunk0178_304_1	chr7	37926725	37927201	+	0	NA	intron (NM_001242948, intron 1 of 2)	L1MC4|LINE|L1	5644	NM_001242948	54749	Hs.563491	NM_017549	ENSG00000086289	EPDR1	EPDR|MERP-1|MERP1|UCC1	ependymin related 1	protein-coding	0.004202	0.383648	
chunk0125_139_1	chr3	66037086	66037664	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	1459	NM_015520	9223	Hs.476636	NM_004742	ENSG00000151276	MAGI1	AIP-3|AIP3|BAIAP1|BAP-1|BAP1|MAGI-1|MAGI-1b|Magi1d|TNRC19|WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.031142	0.511226	101(AAGAACAACTCGTTCT,-,0.00),102(AGAACAACTCGTTCTT,+,0.00)
chunk0182_153_1	chr7	95323291	95323690	+	0	NA	intron (NM_000446, intron 1 of 8)	intron (NM_000446, intron 1 of 8)	1082	NM_000446	5444	Hs.370995	NM_000446	ENSG00000005421	PON1	ESA|MVCD5|PON	paraoxonase 1	protein-coding	0.000000	0.297500	
chunk0149_13_1	chr5	15892207	15892553	+	0	NA	intron (NM_012304, intron 2 of 3)	L2a|LINE|L2	-42802	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.011561	0.515850	
chunk0050_423_1	chr12	109972023	109972491	+	0	NA	intron (NM_001135214, intron 7 of 18)	L1MEf|LINE|L1	24132	NM_057169	9815	Hs.434996	NM_014776	ENSG00000139436	GIT2	CAT-2|CAT2|PKL	GIT ArfGAP 2	protein-coding	0.002137	0.328358	
chunk0195_198_1	chr8	96857538	96857873	+	0	NA	intron (NM_016134, intron 3 of 7)	intron (NM_016134, intron 3 of 7)	212478	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.000000	0.383929	
chunk0010_141_1	chr1	114829361	114829977	+	0	NA	Intergenic	Intergenic	-25134	NM_003176	6847	Hs.112743	NM_003176	ENSG00000198765	SYCP1	CT8|HOM-TES-14|SCP-1|SCP1	synaptonemal complex protein 1	protein-coding	0.001623	0.397083	
chunk0203_335_1	chr9	89770441	89770859	+	0	NA	Intergenic	Intergenic	130867	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.009569	0.434368	
chunk0197_94_1	chr8	119425800	119425999	+	0	NA	Intergenic	L2a|LINE|L2	9587	NM_002514	4856	Hs.235935	NM_002514	ENSG00000136999	CCN3	IBP-9|IGFBP-9|IGFBP9|NOV|NOVh	cellular communication network factor 3	protein-coding	0.010050	0.350000	
chunk0129_262_1	chr3	122444521	122444919	+	0	NA	intron (NR_026698, intron 10 of 14)	L1PA6|LINE|L1	28514	NR_125405	102723582	Hs.675056	NR_125405	ENSG00000272758	LOC102723582	-	uncharacterized LOC102723582	ncRNA	0.015075	0.483709	
chunk0150_20_1	chr5	30601101	30601364	+	0	NA	Intergenic	Intergenic	-592423	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.007605	0.340909	
chunk0149_72_1	chr5	17124596	17124795	+	0	NA	Intergenic	Intergenic	-92128	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.010050	0.435000	
chunk0188_141_1	chr8	9581922	9582129	+	0	NA	intron (NM_003747, intron 2 of 26)	intron (NM_003747, intron 2 of 26)	26090	NM_003747	8658	Hs.370267	NM_003747	ENSG00000173273	TNKS	ARTD5|PARP-5a|PARP5A|PARPL|TIN1|TINF1|TNKS1|pART5	tankyrase	protein-coding	0.000000	0.365385	
chunk0048_56_1	chr12	78314942	78315369	+	0	NA	Intergenic	MIR|SINE|MIR	483866	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.004684	0.380841	
chunk0169_286_1	chr6	105798993	105799480	+	0	NA	Intergenic	Intergenic	-287084	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.006160	0.450820	272(AGGCTCAGGCTGTCCC,-,0.00),273(GGCTCAGGCTGTCCCA,+,0.00)
chunk0196_307_1	chr8	109949818	109950065	+	0	NA	Intergenic	Intergenic	24789	NM_014379	27012	Hs.13285	NM_014379	ENSG00000164794	KCNV1	HNKA|KCNB3|KV2.3|KV8.1	potassium voltage-gated channel modifier subfamily V member 1	protein-coding	0.008097	0.375000	
chunk0006_332_1	chr1	71937615	71937838	+	0	NA	intron (NM_173808, intron 1 of 6)	intron (NM_173808, intron 1 of 6)	-100714	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.000000	0.316964	
chunk0111_15_1	chr20	21942754	21943217	+	0	NA	Intergenic	Intergenic	-111105	NR_038394	100270679	Hs.385748	NR_038394	ENSG00000234435	LINC01432	-	long intergenic non-protein coding RNA 1432	ncRNA	0.004320	0.437500	
chunk0183_10_1	chr7	102879089	102879312	+	0	NA	intron (NM_145032, intron 14 of 19)	L1M6|LINE|L1	-33697	NM_005824	10234	Hs.567412	NM_005824	ENSG00000128606	LRRC17	P37NB	leucine rich repeat containing 17	protein-coding	0.013453	0.441964	
chunk0074_281_1	chr16	28923348	28923741	+	0	NA	intron (NM_024816, intron 2 of 12)	MER113|DNA|hAT-Charlie	1667	NM_024816	79874	Hs.555978	NM_024816	ENSG00000177548	RABEP2	FRA	rabaptin, RAB GTPase binding effector protein 2	protein-coding	0.010178	0.401015	
chunk0141_200_1	chr4	84260281	84260565	+	0	NA	intron (NR_125909, intron 4 of 8)	L1PB4|LINE|L1	38746	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.000000	0.350877	
chunk0087_247_1	chr18	36833683	36834112	+	0	NA	intron (NM_020776, intron 1 of 9)	intron (NM_020776, intron 1 of 9)	-4681	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.000000	0.316279	
chunk0158_57_1	chr5	126004505	126005078	+	0	NA	Intergenic	Intergenic	-174786	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.003490	0.376307	
chunk0026_329_1	chr10	68321568	68321960	+	0	NA	intron (NM_022129, intron 1 of 9)	L1MC3|LINE|L1	-10247	NM_021644	3189	Hs.643472	NM_012207	ENSG00000096746	HNRNPH3	2H9|HNRPH3	heterogeneous nuclear ribonucleoprotein H3	protein-coding	0.002551	0.356234	
chunk0103_414_1	chr2	169507644	169508111	+	0	NA	Intergenic	Intergenic	-1825	NM_006063	10324	Hs.50550	NM_006063	ENSG00000239474	KLHL41	KBTBD10|Krp1|SARCOSIN	kelch like family member 41	protein-coding	0.004283	0.324786	
chunk0035_185_1	chr11	44151757	44152365	+	0	NA	intron (NM_001178083, intron 8 of 14)	L1MC1|LINE|L1	55864	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.004934	0.348112	
chunk0082_292_1	chr17	58401230	58401494	+	0	NA	intron (NM_001305544, intron 2 of 9)	intron (NM_001305544, intron 2 of 9)	1359	NM_001305545	54894	Hs.584916	NM_017763	ENSG00000108375	RNF43	RNF124|SSPCS|URCC	ring finger protein 43	protein-coding	0.011364	0.407547	
chunk0102_402_1	chr2	155393516	155393764	+	0	NA	Intergenic	Intergenic	695059	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.000000	0.313253	
chunk0132_12_1	chr3	154338603	154338996	+	0	NA	intron (NM_001038705, intron 3 of 3)	intron (NM_001038705, intron 3 of 3)	-14302	NM_020865	170506	Hs.446270	NM_020865	ENSG00000174953	DHX36	DDX36|G4R1|MLEL1|RHAU	DEAH-box helicase 36	protein-coding	0.010178	0.314721	
chunk0204_218_1	chr9	97357093	97357352	+	0	NA	intron (NR_036527, intron 35 of 48)	intron (NR_036527, intron 35 of 48)	6459	NR_031637	100302223		NR_031637	ENSG00000221269	MIR1302-8	MIRN1302-8|hsa-mir-1302-8	microRNA 1302-8	ncRNA	0.019305	0.557692	
chunk0026_208_1	chr10	63840945	63841267	+	0	NA	Intergenic	Intergenic	319743	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.003106	0.464396	
chunk0087_42_1	chr18	31300770	31301199	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-17105	NM_001942	1828	Hs.2633	NM_001942	ENSG00000134760	DSG1	CDHF4|DG1|DSG|EPKHE|EPKHIA|PPKS1|SPPK1	desmoglein 1	protein-coding	0.002331	0.390698	
chunk0092_437_1	chr19	38315821	38316244	+	0	NA	promoter-TSS (NM_001039673)	promoter-TSS (NM_001039673)	-66	NM_001039673	90522	Hs.280741	NM_033557	ENSG00000167645	YIF1B	FinGER8	Yip1 interacting factor homolog B, membrane trafficking protein	protein-coding	0.106383	0.709906	
chunk0156_292_1	chr5	110058026	110058575	+	0	NA	Intergenic	Intergenic	175118	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.009107	0.429091	
chunk0126_312_1	chr3	81199980	81200448	+	0	NA	Intergenic	Intergenic	206346	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.004274	0.345416	
chunk0135_40_1	chr3	185371366	185371698	+	0	NA	intron (NM_004721, intron 1 of 13)	intron (NM_004721, intron 1 of 13)	8484	NM_004721	9175	Hs.591306	NM_004721	ENSG00000073803	MAP3K13	LZK|MEKK13|MLK	mitogen-activated protein kinase kinase kinase 13	protein-coding	0.003012	0.387387	
chunk0055_117_1	chr13	57327737	57328104	+	0	NA	Intergenic	Intergenic	160723	NM_001130405	729240	Hs.525056	NM_001130405	ENSG00000229665	PRR20C	PRR20|PRR20A|PRR20B|PRR20D|PRR20E	proline rich 20C	protein-coding	0.002725	0.336957	
chunk0105_122_1	chr2	185337350	185337721	+	0	NA	Intergenic	L1MA3|LINE|L1	-401093	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.002695	0.475806	
chunk0187_203_1	chr7	151797662	151797964	+	0	NA	intron (NM_016203, intron 1 of 15)	intron (NM_016203, intron 1 of 15)	17058	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.013245	0.471947	26(AGGTACAGGGAGTTCA,-,0.00),27(GGTACAGGGAGTTCAG,+,0.00)
chunk0122_261_1	chr3	35096431	35096884	+	0	NA	intron (NR_110817, intron 2 of 3)	L1M1|LINE|L1	297366	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.000000	0.363436	
chunk0032_266_1	chr11	9047808	9048320	+	0	NA	exon (NM_020974, exon 15 of 22)	exon (NM_020974, exon 15 of 22)	42315	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.013672	0.423002	
chunk0132_73_1	chr3	155211183	155212426	+	0	NA	Intergenic	MIR|SINE|MIR	-29141	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.002414	0.360932	
chunk0076_391_1	chr16	72481460	72481757	+	0	NA	intron (NR_126330, intron 6 of 13)	L1MD1|LINE|L1	183401	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.000000	0.332215	
chunk0032_277_1	chr11	9107078	9107541	+	0	NA	Intergenic	L1ME4b|LINE|L1	12946	NR_027713	283102	Hs.689472	NR_027713	ENSG00000213538	KRT8P41	-	keratin 8 pseudogene 41	pseudo	0.012959	0.342672	
chunk0196_86_1	chr8	102839721	102840104	+	0	NA	intron (NM_001301668, intron 3 of 11)	intron (NM_001301668, intron 3 of 11)	24288	NM_148174	51582	Hs.459106	NM_015878	ENSG00000155096	AZIN1	AZI|AZI1|AZIA1|OAZI|OAZIN|ODC1L	antizyme inhibitor 1	protein-coding	0.000000	0.302083	
chunk0007_195_1	chr1	81097849	81098281	+	0	NA	Intergenic	Intergenic	456778	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.006944	0.344111	
chunk0036_136_1	chr11	61961354	61961926	+	0	NA	intron (NM_004183, intron 9 of 10)	intron (NM_004183, intron 9 of 10)	6020	NM_002032	2495	Hs.524910	NM_002032	ENSG00000167996	FTH1	FHC|FTH|FTHL6|HFE5|PIG15|PLIF	ferritin heavy chain 1	protein-coding	0.006993	0.502618	262(AAGTACTGGATGTCCA,-,0.00),263(AGTACTGGATGTCCAG,+,0.00)
chunk0070_66_1	chr15	69692104	69692898	+	0	NA	intron (NR_126437, intron 5 of 5)	intron (NR_126437, intron 5 of 5)	100301	NR_126437	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.007557	0.449057	
chunk0189_88_1	chr8	21291325	21291543	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-6805	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.004587	0.328767	
chunk0134_7_1	chr3	175352057	175352619	+	0	NA	intron (NM_207015, intron 5 of 13)	LTR52|LTR|ERVL	-17202	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.001779	0.412078	
chunk0104_92_1	chr2	172155192	172156047	+	0	NA	Intergenic	Intergenic	52613	NR_126376	104326193	Hs.600690	NR_126376	ENSG00000236651	DLX2-DT	DLX2-AS1|TCONS_00003049	DLX2 divergent transcript	ncRNA	0.017544	0.453271	
chunk0075_77_1	chr16	48165216	48165847	+	0	NA	Intergenic	L2b|LINE|L2	-18761	NM_033226	94160	Hs.410111	NM_033226	ENSG00000140798	ABCC12	MRP9	ATP binding cassette subfamily C member 12	protein-coding	0.012678	0.481013	
chunk0171_321_1	chr6	129709270	129710064	+	0	NA	intron (NM_033515, intron 1 of 14)	intron (NM_033515, intron 1 of 14)	558	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.012594	0.452830	
chunk0175_237_1	chr7	6470293	6470849	+	0	NA	intron (NM_006854, intron 2 of 4)	MER6|DNA|TcMar-Tigger	13647	NM_006854	11014	Hs.654552	NM_006854	ENSG00000136240	KDELR2	ELP-1|ERD2.2	KDEL endoplasmic reticulum protein retention receptor 2	protein-coding	0.012590	0.409336	
chunk0140_91_1	chr4	68176518	68177125	+	0	NA	Intergenic	Intergenic	-5471	NR_015446	100130017	Hs.582037	NR_015446	ENSG00000250426	FTLP10	-	ferritin light chain pseudogene 10	pseudo	0.003295	0.398026	
chunk0126_131_1	chr3	75944309	75944718	+	0	NA	Intergenic	Intergenic	-158930	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.000000	0.348780	241(CTGTACACAGTGTTCA,-,0.00),242(TGTACACAGTGTTCAT,+,0.00)
chunk0167_373_1	chr6	73752801	73753369	+	0	NA	intron (NM_133493, intron 5 of 32)	MER58A|DNA|hAT-Charlie	-56954	NR_110889	101928489	Hs.660059	NR_110889	ENSG00000231652	LOC101928489	-	uncharacterized LOC101928489	ncRNA	0.007042	0.323374	
chunk0142_31_1	chr4	90613642	90613857	+	0	NA	intron (NM_001145065, intron 5 of 10)	intron (NM_001145065, intron 5 of 10)	378718	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.009302	0.407407	
chunk0189_27_1	chr8	19693972	19694734	+	0	NA	Intergenic	Intergenic	-11603	NR_024040	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.005249	0.346003	273(GAGAACACAGTGTTCC,-,0.00),274(AGAACACAGTGTTCCA,+,0.00)
chunk0032_205_1	chr11	7349088	7349503	+	0	NA	intron (NM_175733, intron 3 of 6)	L1MB4|LINE|L1	97345	NM_175733	143425	Hs.177193	NM_175733	ENSG00000170743	SYT9	-	synaptotagmin 9	protein-coding	0.007229	0.439904	
chunk0056_64_1	chr13	78593483	78593720	+	0	NA	intron (NR_047001, intron 3 of 5)	intron (NR_047001, intron 3 of 5)	9959	NM_006237	5457	Hs.654522	NM_006237	ENSG00000152192	POU4F1	BRN3A|Oct-T1|RDC-1|brn-3A	POU class 4 homeobox 1	protein-coding	0.021097	0.357143	
chunk0042_94_1	chr12	2764261	2764744	+	0	NA	intron (NR_033958, intron 4 of 4)	intron (NR_033958, intron 4 of 4)	7167	NR_033958	283440	Hs.448720	NR_033958	ENSG00000256150	ITFG2-AS1	-	ITFG2 antisense RNA 1	ncRNA	0.002070	0.407025	
chunk0040_34_1	chr11	110356041	110356329	+	0	NA	Intergenic	MIRb|SINE|MIR	-59473	NM_001260493	5962	Hs.263671	NM_002906	ENSG00000137710	RDX	DFNB24	radixin	protein-coding	0.006944	0.352941	139(TAAACACTGTGTTCTT,+,0.00)
chunk0089_127_1	chr18	58753022	58753318	+	0	NA	Intergenic	Intergenic	-81297	NM_001289967	101927322	Hs.644875	NM_001289967		LOC101927322	-	uncharacterized LOC101927322	protein-coding	0.020270	0.444444	
chunk0209_5_1	chrX	34932083	34932560	+	0	NA	Intergenic	L1PA13|LINE|L1	-10475	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.006289	0.541841	336(GGGCACACATAGTGCC,-,0.00),337(GGCACACATAGTGCCC,+,0.00)
chunk0016_402_1	chr1	203239270	203239804	+	0	NA	Intergenic	L1MB1|LINE|L1	-9805	NM_001270509	1118	Hs.201688	NM_003465	ENSG00000133063	CHIT1	CHI3|CHIT|CHITD	chitinase 1	protein-coding	0.007491	0.409346	186(TGGACCACACTGTCCC,-,0.00),187(GGACCACACTGTCCCT,+,0.00)
chunk0162_66_1	chr6	1678894	1679378	+	0	NA	intron (NM_001253846, intron 9 of 10)	intron (NM_001253846, intron 9 of 10)	68690	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.014463	0.412371	
chunk0051_222_1	chr12	116736301	116736790	+	0	NA	intron (NM_024738, intron 1 of 4)	intron (NM_024738, intron 1 of 4)	1525	NM_024738	79794	Hs.120170	NM_024738	ENSG00000111412	C12orf49	-	chromosome 12 open reading frame 49	protein-coding	0.010225	0.455102	
chunk0069_383_1	chr15	67521255	67521651	+	0	NA	promoter-TSS (NR_040056)	promoter-TSS (NR_040056)	269	NM_001143936	145853	Hs.438385	NM_001143936	ENSG00000189227	C15orf61	-	chromosome 15 open reading frame 61	protein-coding	0.113636	0.715365	
chunk0151_219_1	chr5	50889775	50890318	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	80141	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.003683	0.352941	316(TAGTACAGTATGTACT,-,0.00),317(AGTACAGTATGTACTA,+,0.00)
chunk0141_351_1	chr4	87745159	87745358	+	0	NA	Intergenic	MER52D|LTR|ERV1	-54292	NM_004967	3381	Hs.518726	NM_004967	ENSG00000029559	IBSP	BNSP|BSP|BSP-II|SP-II	integrin binding sialoprotein	protein-coding	0.015075	0.570000	
chunk0211_274_1	chrX	121689291	121689813	+	0	NA	Intergenic	L1MB1|LINE|L1	318580	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.005747	0.328872	
chunk0200_203_1	chr9	20395680	20396050	+	0	NA	intron (NM_001286691, intron 5 of 10)	intron (NM_001286691, intron 5 of 10)	15373	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.005405	0.396226	
chunk0087_87_1	chr18	32360711	32360988	+	0	NA	intron (NM_001242409, intron 2 of 5)	intron (NM_001242409, intron 2 of 5)	109635	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.007220	0.356115	
chunk0121_399_1	chr3	25471093	25471830	+	0	NA	intron (NM_001290216, intron 2 of 7)	intron (NM_001290216, intron 2 of 7)	13151	NM_001290217	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.012212	0.355014	
chunk0094_361_1	chr2	9629394	9629708	+	0	NA	intron (NM_006826, intron 2 of 5)	intron (NM_006826, intron 2 of 5)	1504	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.009554	0.438095	178(CAGGACATTGTGTTCT,-,0.00),179(AGGACATTGTGTTCTT,+,0.00)
chunk0118_61_1	chr22	28322353	28322627	+	0	NA	intron (NM_001145418, intron 2 of 22)	Tigger15a|DNA|TcMar-Tigger	-137379	NR_106713	102466081		NR_106713	ENSG00000276162	MIR5739	hsa-mir-5739	microRNA 5739	ncRNA	0.010949	0.330909	
chunk0191_338_1	chr8	56019281	56020042	+	0	NA	Intergenic	Intergenic	54240	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.015769	0.539370	
chunk0066_97_1	chr15	29812099	29812607	+	0	NA	intron (NM_001301025, intron 2 of 28).2	L1ME3B|LINE|L1	9195	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.005906	0.404715	
chunk0137_67_1	chr4	11903984	11904501	+	0	NA	Intergenic	MIRc|SINE|MIR	-319209	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.009671	0.428571	
chunk0021_237_1	chr1	242431336	242431748	+	0	NA	intron (NM_152666, intron 2 of 10)	intron (NM_152666, intron 2 of 10)	17940	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.012136	0.368039	196(GGTACACCATGATCCT,+,0.00)
chunk0074_421_1	chr16	46383255	46383460	+	0	NA	Intergenic	Intergenic	185740	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.034146	0.378641	
chunk0019_50_1	chr1	224139077	224139647	+	0	NA	intron (NM_001136115, intron 3 of 3)	L1MC4|LINE|L1	25275	NM_001136115	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.012281	0.395797	
chunk0120_464_1	chr22	50620744	50621193	+	0	NA	Intergenic	Intergenic	7205	NM_001085428	410	Hs.88251	NM_000487	ENSG00000100299	ARSA	ASA|MLD	arylsulfatase A	protein-coding	0.037862	0.493333	
chunk0148_389_1	chr5	14778031	14778293	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	47850	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.011450	0.555133	
chunk0169_426_1	chr6	108661251	108661657	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	-90200	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.007389	0.388206	
chunk0017_249_1	chr1	208515561	208515928	+	0	NA	Intergenic	Intergenic	-271424	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.005450	0.407609	
chunk0034_278_1	chr11	34637449	34637872	+	0	NA	intron (NM_001206616, intron 1 of 8)	intron (NM_001206616, intron 1 of 8)	5196	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.007092	0.448113	
chunk0010_49_1	chr1	112896202	112896401	+	0	NA	Intergenic	LTR17|LTR|ERV1	-27049	NR_002796	246182	Hs.647691	NR_002796		AKR7A2P1	AFARP1	aldo-keto reductase family 7 member A2 pseudogene 1	pseudo	0.025126	0.510000	
chunk0112_332_1	chr20	44985657	44986147	+	0	NA	intron (NM_006282, intron 4 of 10)	intron (NM_006282, intron 4 of 10)	19423	NM_006282	6789	Hs.472838	NM_006282	ENSG00000101109	STK4	KRS2|MST1|YSK3	serine/threonine kinase 4	protein-coding	0.002041	0.352342	
chunk0061_384_1	chr14	64337097	64337380	+	0	NA	intron (NM_001291712, intron 1 of 13)	MIRc|SINE|MIR	1312	NM_001291723	2100	Hs.660607	NM_001437	ENSG00000140009	ESR2	ER-BETA|ESR-BETA|ESRB|ESTRB|Erb|NR3A2|ODG8	estrogen receptor 2	protein-coding	0.003534	0.408451	
chunk0202_217_1	chr9	76271777	76272295	+	0	NA	intron (NM_001190482, intron 24 of 36)	MLT1C|LTR|ERVL-MaLR	122492	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.003861	0.393064	
chunk0165_290_1	chr6	36349229	36349871	+	0	NA	Intergenic	L1MC4a|LINE|L1	-12665	NM_001010903	389384	Hs.162104	NM_001010903	ENSG00000189325	BNIP5	C6orf222	BCL2 interacting protein 5	protein-coding	0.012461	0.443235	
chunk0056_455_1	chr13	95246265	95246693	+	0	NA	intron (NM_001105515, intron 3 of 20)	intron (NM_001105515, intron 3 of 20)	54967	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.016355	0.522145	
chunk0188_49_1	chr8	6817273	6818056	+	0	NA	intron (NM_207411, intron 5 of 6)	MER67B|LTR|ERV1	-17890	NR_045217	100652791	Hs.369771	NR_045217	ENSG00000245857	GS1-24F4.2	-	uncharacterized LOC100652791	ncRNA	0.016603	0.494898	354(AGGTACTGTTTGTTCC,-,0.00),355(GGTACTGTTTGTTCCA,+,0.00)
chunk0037_155_1	chr11	73598485	73598853	+	0	NA	promoter-TSS (NM_015159)	promoter-TSS (NM_015159)	-480	NM_001286050	23201	Hs.475334	NM_015159	ENSG00000054965	FAM168A	KIAA0280|TCRP1	family with sequence similarity 168 member A	protein-coding	0.029891	0.555556	
chunk0143_198_1	chr4	112894424	112894881	+	0	NA	intron (NM_001127493, intron 1 of 46)	intron (NM_001127493, intron 1 of 46)	76569	NM_001127493	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.006565	0.344978	
chunk0083_225_1	chr17	67369626	67370213	+	0	NA	Intergenic	Intergenic	-3292	NM_174871	5718	Hs.4295	NM_002816	ENSG00000197170	PSMD12	Rpn5|STISS|p55	proteasome 26S subunit, non-ATPase 12	protein-coding	0.003407	0.357143	
chunk0003_241_1	chr1	36089209	36089408	+	0	NA	intron (NM_017825, intron 1 of 5)	CpG	456	NM_017825	54936	Hs.18021	NM_017825	ENSG00000116863	ADPRHL2	ARH3|CONDSIAS	ADP-ribosylhydrolase like 2	protein-coding	0.080402	0.620000	
chunk0032_84_1	chr11	2901855	2902054	+	0	NA	promoter-TSS (NM_001315502)	promoter-TSS (NM_001315502)	-328	NM_001315502	5002	Hs.50868	NM_002555	ENSG00000110628	SLC22A18	BWR1A|BWSCR1A|HET|IMPT1|ITM|ORCTL2|SLC22A1L|TSSC5|p45-BWR1A	solute carrier family 22 member 18	protein-coding	0.030151	0.650000	151(AGGGTCAGAGTGTCCA,-,0.00),152(GGGTCAGAGTGTCCAC,+,0.00)
chunk0050_125_1	chr12	102091822	102092330	+	0	NA	intron (NM_024057, intron 4 of 8)	intron (NM_024057, intron 4 of 8)	26507	NM_024057	79023	Hs.444276	NM_024057	ENSG00000075188	NUP37	MCPH24|p37	nucleoporin 37	protein-coding	0.005906	0.328094	
chunk0044_451_1	chr12	42683965	42684436	+	0	NA	Intergenic	Intergenic	-37702	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.004246	0.355932	
chunk0094_438_1	chr2	11086160	11086448	+	0	NA	Intergenic	Intergenic	45872	NR_040080	285150	Hs.329841	NM_182586	ENSG00000145063	FLJ33534	-	uncharacterized LOC285150	ncRNA	0.003472	0.366782	
chunk0083_183_1	chr17	66461966	66462438	+	0	NA	intron (NM_002737, intron 2 of 16)	intron (NM_002737, intron 2 of 16)	-45348	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.010593	0.418605	
chunk0013_378_1	chr1	172529900	172530387	+	0	NA	Intergenic	Intergenic	-2206	NM_016227	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.004107	0.383197	
chunk0182_455_1	chr7	102086301	102086568	+	0	NA	intron (NM_001202545, intron 4 of 21)	L1M5|LINE|L1	-198628	NM_020979	10603	Hs.489448	NM_020979	ENSG00000160999	SH2B2	APS	SH2B adaptor protein 2	protein-coding	0.003745	0.324627	
chunk0112_274_1	chr20	43398117	43398349	+	0	NA	Intergenic	AluJo|SINE|Alu	-59631	NR_034009	6431	Hs.684950	NM_006275	ENSG00000124193	SRSF6	B52|HEL-S-91|SFRS6|SRP55	serine and arginine rich splicing factor 6	protein-coding	0.017241	0.515021	
chunk0039_68_1	chr11	96383970	96384594	+	0	NA	exon (NM_024725, exon 4 of 10)	exon (NM_024725, exon 4 of 10)	5637	NM_024725	79780	Hs.525088	NM_014148	ENSG00000149231	CCDC82	HSPC048	coiled-coil domain containing 82	protein-coding	0.014423	0.368000	
chunk0130_81_1	chr3	130685044	130685611	+	0	NA	intron (NM_014602, intron 15 of 19)	L1MA7|LINE|L1	61525	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.005291	0.336268	
chunk0133_237_1	chr3	171365857	171366564	+	0	NA	intron (NR_027767, intron 2 of 2)	intron (NR_027767, intron 2 of 2)	94198	NM_001161566	23043	Hs.34024	NM_015028	ENSG00000154310	TNIK	MRT54	TRAF2 and NCK interacting kinase	protein-coding	0.002829	0.300847	
chunk0156_298_1	chr5	110159802	110160423	+	0	NA	Intergenic	Intergenic	276930	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.001610	0.297428	
chunk0033_77_1	chr11	13873119	13873380	+	0	NA	Intergenic	Intergenic	-89388	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.019157	0.442748	109(AGAGACATTATGTTCC,-,0.00),110(GAGACATTATGTTCCA,+,0.00)
chunk0072_67_1	chr15	90422097	90422652	+	0	NA	intron (NM_003870, intron 2 of 37)	L1ME4c|LINE|L1	34133	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.003604	0.312950	
chunk0161_193_1	chr5	170250860	170251215	+	0	NA	intron (NM_005565, intron 19 of 20)	intron (NM_005565, intron 19 of 20)	18030	NM_001305394	133874	Hs.519749	NM_001102609	ENSG00000234511	C5orf58	-	chromosome 5 open reading frame 58	protein-coding	0.008451	0.376404	
chunk0120_114_1	chr3	4687220	4687595	+	0	NA	intron (NM_002222, intron 29 of 57)	MIR|SINE|MIR	64183	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.010667	0.446809	
chunk0002_56_1	chr1	13665774	13665973	+	0	NA	Intergenic	Intergenic	-34367	NM_001135610	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.010050	0.460000	
chunk0126_318_1	chr3	81561895	81562359	+	0	NA	intron (NM_000158, intron 12 of 15)	L2b|LINE|L2	199672	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.010776	0.382796	
chunk0185_74_1	chr7	125203257	125203704	+	0	NA	intron (NR_110188, intron 3 of 8)	L1ME1|LINE|L1	18911	NR_110188	101928283	Hs.566650	NR_110188	ENSG00000224897	LOC101928283	-	uncharacterized LOC101928283	ncRNA	0.000000	0.296875	
chunk0192_15_1	chr8	58404017	58404315	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-7098	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.000000	0.408027	
chunk0099_376_1	chr2	101110492	101110829	+	0	NA	intron (NM_001102426, intron 1 of 19)	intron (NM_001102426, intron 1 of 19)	40724	NM_001102426	11138	Hs.442657	NM_007063	ENSG00000204634	TBC1D8	AD3|GRAMD8|HBLP1|TBC1D8A|VRP	TBC1 domain family member 8	protein-coding	0.020772	0.464497	
chunk0022_144_1	chr10	12246667	12247724	+	0	NA	intron (NM_006023, intron 11 of 12)	intron (NM_006023, intron 11 of 12)	-51051	NM_014142	11164	Hs.555956	NM_014142	ENSG00000165609	NUDT5	YSA1|YSA1H|YSAH1|hNUDT5	nudix hydrolase 5	protein-coding	0.012299	0.567108	211(CTGGACACTGTGTCCT,-,0.00),212(TGGACACTGTGTCCTC,+,0.00),246(CAGTACACTGTGTCTT,-,0.00),247(AGTACACTGTGTCTTC,+,0.00),280(CAGGACACTGTGTCCT,-,0.00),281(AGGACACTGTGTCCTC,+,0.00),348(CTGGACACTGTGTCCT,-,0.00),349(TGGACACTGTGTCCTC,+,0.00),486(CAGGGCACCGTGTCCC,-,0.00),487(AGGGCACCGTGTCCCC,+,0.00),552(CTGGACACTGTGTCCT,-,0.00),553(TGGACACTGTGTCCTC,+,0.00),654(CAGGACACTGTGTCCT,-,0.00),655(AGGACACTGTGTCCTC,+,0.00),720(CTGGACACTGTGTCCT,-,0.00),721(TGGACACTGTGTCCTC,+,0.00),788(CAGGACACCGTGTCCC,-,0.00),789(AGGACACCGTGTCCCC,+,0.00),822(CAGGACACTGTGTCCT,-,0.00),823(AGGACACTGTGTCCTC,+,0.00),856(CAGGACACTGTGTCCT,-,0.00),857(AGGACACTGTGTCCTC,+,0.00)
chunk0058_280_1	chr14	26415797	26416053	+	0	NA	Intergenic	Intergenic	181829	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.019531	0.431907	
chunk0053_357_1	chr13	35106673	35107287	+	0	NA	intron (NM_015678, intron 11 of 57)	intron (NM_015678, intron 11 of 57)	164693	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.004886	0.299187	
chunk0142_283_1	chr4	99996256	99997115	+	0	NA	intron (NR_125923, intron 1 of 3)	MLT1B|LTR|ERVL-MaLR	46191	NR_125923	256880	Hs.448554	NR_002799	ENSG00000245322	LOC256880	-	uncharacterized LOC256880	ncRNA	0.002328	0.363953	612(TGGGACACAATGTACC,-,0.00),613(GGGACACAATGTACCC,+,0.00)
chunk0119_118_1	chr22	42655774	42656244	+	0	NA	Intergenic	Intergenic	-6610	NM_000398	1727	Hs.561064	NM_000398	ENSG00000100243	CYB5R3	B5R|DIA1	cytochrome b5 reductase 3	protein-coding	0.017021	0.537155	220(AGGATCATGATGTTCT,-,0.00),221(GGATCATGATGTTCTC,+,0.00)
chunk0004_145_1	chr1	45141270	45141653	+	0	NA	intron (NM_020883, intron 1 of 13)	L1MD2|LINE|L1	65117	NM_020883	57643	Hs.656613	NM_020883	ENSG00000162415	ZSWIM5	-	zinc finger SWIM-type containing 5	protein-coding	0.002611	0.419271	
chunk0084_121_1	chr17	76051123	76051359	+	0	NA	intron (NM_001260502, intron 7 of 14)	intron (NM_001260502, intron 7 of 14)	2415	NM_001260503	6730	Hs.514495	NM_014230	ENSG00000167881	SRP68	-	signal recognition particle 68	protein-coding	0.021186	0.451477	
chunk0167_81_1	chr6	56550207	56550602	+	0	NA	intron (NM_183380, intron 52 of 93)	intron (NM_183380, intron 52 of 93)	92492	NM_001723	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.002532	0.340909	
chunk0198_195_1	chr8	133545648	133546401	+	0	NA	intron (NM_003033, intron 1 of 8)	intron (NM_003033, intron 1 of 8)	25916	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.011952	0.446950	
chunk0102_408_1	chr2	156200279	156200894	+	0	NA	intron (NR_110250, intron 1 of 3)	intron (NR_110250, intron 1 of 3)	54345	NR_110250	101929378	Hs.171192	NR_110249	ENSG00000226383	LINC01876	-	long intergenic non-protein coding RNA 1876	ncRNA	0.006504	0.345779	
chunk0045_18_1	chr12	43447479	43447828	+	0	NA	intron (NM_025003, intron 14 of 38)	L1PREC2|LINE|L1	104268	NM_025003	80070	Hs.287554	NM_025003	ENSG00000173157	ADAMTS20	ADAM-TS20|ADAMTS-20|GON-1	ADAM metallopeptidase with thrombospondin type 1 motif 20	protein-coding	0.005731	0.388571	
chunk0001_375_1	chr1	10299537	10299736	+	0	NA	TTS (NR_104084)	TTS (NR_104084)	670	NR_104080	101954271		NR_104080	ENSG00000207507	RNU6-9	U6-9	RNA, U6 small nuclear 9	snRNA	0.000000	0.315000	
chunk0016_389_1	chr1	202919453	202919921	+	0	NA	intron (NM_001303109, intron 3 of 9)	intron (NM_001303109, intron 3 of 9)	7585	NM_021633	59349	Hs.706793	NM_021633	ENSG00000117153	KLHL12	C3IP1|DKIR	kelch like family member 12	protein-coding	0.000000	0.362473	
chunk0142_125_1	chr4	94650162	94650514	+	0	NA	intron (NM_001256425, intron 8 of 11)	intron (NM_001256425, intron 8 of 11)	107195	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.014205	0.348442	
chunk0029_189_1	chr10	101111561	101111943	+	0	NA	intron (NR_130722, intron 2 of 2)	intron (NR_130722, intron 2 of 2)	19394	NR_130722	100038246	Hs.368784	NM_001085398	ENSG00000236311	TLX1NB	APT-B7|TD1|TDI	TLX1 neighbor	ncRNA	0.020942	0.509138	
chunk0183_394_1	chr7	110209707	110210096	+	0	NA	Intergenic	Intergenic	-249688	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.010283	0.382051	171(AGAAACTGTATGTTCC,-,0.00),195(AGGCACATGTTGTCCA,-,0.00),196(GGCACATGTTGTCCAG,+,0.00)
chunk0001_246_1	chr1	8364296	8364923	+	0	NA	intron (NM_001042682, intron 4 of 12)	intron (NM_001042682, intron 4 of 12)	46524	NM_001080397	50651	Hs.463036	NM_001080397	ENSG00000162426	SLC45A1	DNB5|IDDNPF	solute carrier family 45 member 1	protein-coding	0.019139	0.589172	
chunk0127_179_1	chr3	95366187	95366520	+	0	NA	Intergenic	MER77|LTR|ERVL	316840	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.009009	0.446108	
chunk0065_236_1	chr14	101053024	101053498	+	0	NA	TTS (NR_030162)	TTS (NR_030162)	815	NR_030162	619555		NR_030162	ENSG00000207742	MIR487A	MIRN487|MIRN487A|hsa-mir-487|mir-487a	microRNA 487a	ncRNA	0.010549	0.429474	241(GTGCACACTGTGTTCT,-,0.00),242(TGCACACTGTGTTCTA,+,0.00)
chunk0106_150_1	chr2	200367142	200367571	+	0	NA	intron (NM_001282743, intron 2 of 11)	intron (NM_001282743, intron 2 of 11)	58406	NM_001282744	26010	Hs.120323	NM_015535	ENSG00000196141	SPATS2L	DNAPTP6|SGNP	spermatogenesis associated serine rich 2 like	protein-coding	0.006993	0.369767	232(CAGAACACAGTCTTCT,-,0.00),233(AGAACACAGTCTTCTA,+,0.00)
chunk0138_269_1	chr4	40331568	40331885	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	-3603	NM_017581	55584	Hs.272278	NM_017581	ENSG00000174343	CHRNA9	HSA243342|NACHRA9	cholinergic receptor nicotinic alpha 9 subunit	protein-coding	0.006309	0.383648	
chunk0159_456_1	chr5	148904597	148904796	+	0	NA	Intergenic	Intergenic	78103	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.000000	0.515000	
chunk0114_337_1	chr21	17607758	17608102	+	0	NA	intron (NM_006806, intron 2 of 4)	intron (NM_006806, intron 2 of 4)	5020	NM_006806	10950	Hs.473420	NM_006806	ENSG00000154640	BTG3	ANA|ANA/BTG3|APRO4|TOB5|TOB55|TOFA	BTG anti-proliferation factor 3	protein-coding	0.005814	0.443478	
chunk0193_103_1	chr8	73747486	73747685	+	0	NA	promoter-TSS (NM_001164383)	promoter-TSS (NM_001164383)	123	NM_001164384	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.050251	0.535000	
chunk0144_410_1	chr4	140373916	140374183	+	0	NA	promoter-TSS (NR_033939)	promoter-TSS (NR_033939)	539	NM_001153552	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.059925	0.623134	
chunk0069_21_1	chr15	60392642	60393482	+	0	NA	intron (NM_001136015, intron 1 of 13)	intron (NM_001136015, intron 1 of 13)	4924	NM_001136015	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.008333	0.448276	
chunk0177_84_1	chr7	21639213	21639966	+	0	NA	intron (NM_001277115, intron 28 of 81)	intron (NM_001277115, intron 28 of 81)	96374	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.003984	0.387268	450(AGGGACAAACTGTACA,-,0.00),451(GGGACAAACTGTACAA,+,0.00)
chunk0087_313_1	chr18	39606930	39607432	+	0	NA	intron (NR_024391, intron 2 of 3)	intron (NR_024391, intron 2 of 3)	14994	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.013944	0.395626	
chunk0099_245_1	chr2	97750304	97750503	+	0	NA	Intergenic	MER90a|LTR|ERV1	15997	NM_207519	7535	Hs.234569	NM_001079	ENSG00000115085	ZAP70	ADMIO2|IMD48|SRK|STCD|STD|TZK|ZAP-70	zeta chain of T cell receptor associated protein kinase 70	protein-coding	0.010050	0.470000	
chunk0136_190_1	chr4	6780874	6781760	+	0	NA	Intergenic	Intergenic	-1415	NM_014743	9778	Hs.79276	NM_014743	ENSG00000170871	KIAA0232	-	KIAA0232	protein-coding	0.018059	0.456595	354(AGGGACTGTGCGTTCC,-,0.00),355(GGGACTGTGCGTTCCC,+,0.00)
chunk0066_36_1	chr15	27672519	27672943	+	0	NA	Intergenic	(GCACAT)n|Simple_repeat|Simple_repeat	426581	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.018868	0.501176	
chunk0195_192_1	chr8	96814262	96814748	+	0	NA	intron (NM_016134, intron 2 of 7)	intron (NM_016134, intron 2 of 7)	169278	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.004115	0.386037	
chunk0169_194_1	chr6	102648082	102648350	+	0	NA	Intergenic	L1M1|LINE|L1	1249231	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.007463	0.486989	
chunk0139_135_1	chr4	53455686	53456165	+	0	NA	intron (NM_030917, intron 16 of 17)	intron (NM_030917, intron 16 of 17)	-44152	NR_046622	100873939	Hs.662372	NR_046622	ENSG00000250930	LNX1-AS1	-	LNX1 antisense RNA 1	ncRNA	0.010438	0.347917	
chunk0141_249_1	chr4	85037890	85038212	+	0	NA	Intergenic	Intergenic	71233	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.006211	0.380805	
chunk0061_252_1	chr14	61285212	61286008	+	0	NA	Intergenic	MIRb|SINE|MIR	-3798	NM_001017970	161291	Hs.146180	NM_001017970	ENSG00000182107	TMEM30B	CDC50B	transmembrane protein 30B	protein-coding	0.006281	0.376412	
chunk0099_80_1	chr2	85354668	85354867	+	0	NA	promoter-TSS (NM_017750)	promoter-TSS (NM_017750)	47	NM_001135021	84173	Hs.269990	NM_032213	ENSG00000115459	ELMOD3	DFNB88|LST3|RBED1|RBM29	ELMO domain containing 3	protein-coding	0.065327	0.585000	
chunk0201_408_1	chr9	69385569	69385768	+	0	NA	intron (NM_004816, intron 8 of 10)	intron (NM_004816, intron 8 of 10)	56343	NM_004816	9413	Hs.118003	NM_004816	ENSG00000135063	FAM189A2	C9orf61|X123	family with sequence similarity 189 member A2	protein-coding	0.005025	0.450000	
chunk0014_299_1	chr1	180839069	180839273	+	0	NA	intron (NM_004736, intron 11 of 14)	Charlie2a|DNA|hAT-Charlie	-74006	NM_020950	57710	Hs.734816	NM_020950	ENSG00000135835	KIAA1614	-	KIAA1614	protein-coding	0.004902	0.297561	
chunk0173_326_1	chr6	148746243	148746563	+	0	NA	promoter-TSS (NM_005715)	promoter-TSS (NM_005715)	-732	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.040625	0.573209	199(AAGAACAGAGCGTCCT,-,0.00),200(AGAACAGAGCGTCCTC,+,0.00)
chunk0186_91_1	chr7	137351961	137352318	+	0	NA	Intergenic	Intergenic	-8339	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.002801	0.377095	174(CAGGACAGCATGTGCT,-,0.00),175(AGGACAGCATGTGCTC,+,0.00)
chunk0200_216_1	chr9	20606696	20607584	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	14847	NM_001286691	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.003378	0.344207	285(GAGAACACCTTGTCCT,-,0.00),286(AGAACACCTTGTCCTC,+,0.00)
chunk0176_96_1	chr7	11625135	11625599	+	0	NA	intron (NM_015204, intron 2 of 26)	intron (NM_015204, intron 2 of 26)	206831	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.000000	0.277419	
chunk0041_310_1	chr11	130002410	130002980	+	0	NA	promoter-TSS (NR_024233)	promoter-TSS (NR_024233)	71	NR_024233	440072	Hs.630600	NM_001007543		LINC00167	C11orf37|NCRNA00167	long intergenic non-protein coding RNA 167	ncRNA	0.054386	0.602452	
chunk0093_147_1	chr19	46874073	46874489	+	0	NA	Intergenic	Intergenic	-23286	NM_001301078	1175	Hs.119591	NM_004069	ENSG00000042753	AP2S1	AP17|CLAPS2|FBH3|FBHOk|HHC3	adaptor related protein complex 2 subunit sigma 1	protein-coding	0.007212	0.340528	227(AGGAACACACTGTTTC,-,0.00),228(GGAACACACTGTTTCT,+,0.00)
chunk0033_399_1	chr11	24565179	24565574	+	0	NA	intron (NM_001252008, intron 1 of 11)	intron (NM_001252008, intron 1 of 11)	68406	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.005063	0.378788	
chunk0129_268_1	chr3	122651313	122652226	+	0	NA	Intergenic	L1PA6|LINE|L1	-29056	NM_017554	54625	Hs.518203	NM_017554	ENSG00000173193	PARP14	ARTD8|BAL2|PARP-14|pART8	poly(ADP-ribose) polymerase family member 14	protein-coding	0.015334	0.495624	
chunk0150_94_1	chr5	32424430	32424945	+	0	NA	intron (NM_016107, intron 2 of 19)	HAL1ME|LINE|L1	20051	NM_016107	51663	Hs.435231	NM_016107	ENSG00000056097	ZFR	SPG71|ZFR1	zinc finger RNA binding protein	protein-coding	0.019417	0.356589	
chunk0050_31_1	chr12	100141739	100142337	+	0	NA	intron (NM_001006947, intron 1 of 12)	intron (NM_001006947, intron 1 of 12)	826	NM_015054	23074	Hs.572154	NM_015054	ENSG00000111647	UHRF1BP1L	SHIP164	UHRF1 binding protein 1 like	protein-coding	0.045151	0.514190	
chunk0110_264_1	chr20	16796716	16797351	+	0	NA	Intergenic	L1PA12|LINE|L1	48680	NM_020157	56914	Hs.41119	NM_020157	ENSG00000125879	OTOR	FDP|MIAL1	otoraplin	protein-coding	0.006299	0.342767	
chunk0052_91_1	chr13	22198007	22198468	+	0	NA	Intergenic	Intergenic	-12048	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.013015	0.426407	
chunk0079_427_1	chr17	19843212	19843804	+	0	NA	intron (NM_001142610, intron 7 of 27)	intron (NM_001142610, intron 7 of 27)	24418	NM_001142610	9706	Hs.168762	NM_014683	ENSG00000083290	ULK2	ATG1B|Unc51.2	unc-51 like autophagy activating kinase 2	protein-coding	0.011824	0.389545	
chunk0130_373_1	chr3	139411216	139411557	+	0	NA	intron (NR_121608, intron 1 of 3)	L1PB2|LINE|L1	21583	NR_121609	100507291	Hs.97661	NR_121608	ENSG00000248932	LOC100507291	-	uncharacterized LOC100507291	ncRNA	0.002933	0.321637	
chunk0020_29_1	chr1	232004073	232004272	+	0	NA	intron (NM_001012957, intron 10 of 12)	L1MDa|LINE|L1	78338	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.000000	0.235000	
chunk0013_141_1	chr1	168391645	168392271	+	0	NA	Intergenic	Intergenic	16434	NR_030284	693142		NR_030284	ENSG00000207974	MIR557	MIRN557|hsa-mir-557	microRNA 557	ncRNA	0.007987	0.397129	
chunk0059_191_1	chr14	32994032	32994353	+	0	NA	intron (NM_022123, intron 1 of 10)	intron (NM_022123, intron 1 of 10)	54939	NM_001164749	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.000000	0.341615	
chunk0041_324_1	chr11	130217402	130218009	+	0	NA	Intergenic	Intergenic	57918	NM_021978	6768	Hs.504315	NM_021978	ENSG00000149418	ST14	ARCI11|HAI|MT-SP1|MTSP1|PRSS14|SNC19|TADG15|TMPRSS14	suppression of tumorigenicity 14	protein-coding	0.019769	0.574013	335(TAGAACAACATGTTCT,-,0.00),336(AGAACAACATGTTCTG,+,0.00)
chunk0053_423_1	chr13	37404156	37404632	+	0	NA	Intergenic	Intergenic	80390	NR_125762	103695431	Hs.550637	NR_125762	ENSG00000230390	LINC01048	-	long intergenic non-protein coding RNA 1048	ncRNA	0.004202	0.400419	
chunk0124_175_1	chr3	55380438	55381113	+	0	NA	Intergenic	L1ME3E|LINE|L1	100623	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.001481	0.286982	
chunk0209_173_1	chrX	43654588	43655078	+	0	NA	promoter-TSS (NM_001270458)	promoter-TSS (NM_001270458)	-74	NM_001270458	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.065306	0.641548	
chunk0086_253_1	chr18	23342622	23342821	+	0	NA	intron (NM_032933, intron 13 of 14)	L1MB8|LINE|L1	95240	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.005025	0.345000	105(TGGCACTGTCTGTACC,-,0.00),106(GGCACTGTCTGTACCT,+,0.00)
chunk0016_211_1	chr1	198970882	198971081	+	0	NA	Intergenic	Intergenic	-33552	NR_040073	100131234	Hs.711077	NR_040073		MIR181A1HG	-	MIR181A1 host gene	ncRNA	0.000000	0.420000	
chunk0094_50_1	chr2	2984188	2984451	+	0	NA	intron (NR_110228, intron 3 of 6)	L1PA16|LINE|L1	141707	NR_110228	101927554	Hs.638446	NR_110228	ENSG00000234423	LINC01250	-	long intergenic non-protein coding RNA 1250	ncRNA	0.000000	0.333333	
chunk0212_117_1	chrX	130590693	130590922	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	95866	NR_027141	55855	Hs.567120	NM_018472		DENND10P1	FAM45B|FAM45BP|HT011	DENND10 pseudogene 1	pseudo	0.004367	0.439130	
chunk0121_345_1	chr3	24640501	24640707	+	0	NA	Intergenic	Intergenic	-119169	NR_039955									0.014563	0.362319	
chunk0043_387_1	chr12	25238790	25239353	+	0	NA	intron (NM_033360, intron 2 of 5)	L1ME4b|LINE|L1	11860	NM_033360	3845	Hs.505033	NM_004985	ENSG00000133703	KRAS	C-K-RAS|CFC2|K-RAS2A|K-RAS2B|K-RAS4A|K-RAS4B|K-Ras|KI-RAS|KRAS1|KRAS2|NS|NS3|RALD|RASK2|c-Ki-ras2	KRAS proto-oncogene, GTPase	protein-coding	0.001776	0.312057	
chunk0032_333_1	chr11	10222580	10223429	+	0	NA	intron (NM_030962, intron 1 of 39)	intron (NM_030962, intron 1 of 39)	71203	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.008245	0.330588	
chunk0044_130_1	chr12	29333168	29333483	+	0	NA	intron (NM_001271784, intron 10 of 10)	intron (NM_001271784, intron 10 of 10)	-15477	NR_103860	100506606	Hs.298851	NR_103860	ENSG00000257176	LOC100506606	-	uncharacterized LOC100506606	ncRNA	0.003175	0.367089	
chunk0121_276_1	chr3	23389117	23389457	+	0	NA	intron (NM_152653, intron 3 of 5)	intron (NM_152653, intron 3 of 5)	185994	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.011765	0.448680	
chunk0168_208_1	chr6	85798786	85799498	+	0	NA	Intergenic	Intergenic	-120409	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.004213	0.385694	
chunk0161_400_1	chr5	177246784	177247346	+	0	NA	intron (NM_022455, intron 10 of 22)	intron (NM_022455, intron 10 of 22)	56679	NR_109789	53917	Hs.16258	NM_130781	ENSG00000169228	RAB24	-	RAB24, member RAS oncogene family	protein-coding	0.017794	0.431616	
chunk0078_220_1	chr17	6377215	6377522	+	0	NA	Intergenic	Intergenic	57764	NM_001285402	23746	Hs.279887	NM_014336	ENSG00000129221	AIPL1	AIPL2|LCA4	aryl hydrocarbon receptor interacting protein like 1	protein-coding	0.019544	0.506494	
chunk0068_312_1	chr15	57307618	57307959	+	0	NA	TTS (NR_024433)	TTS (NR_024433)	7423	NR_024433	283663	Hs.181297	NR_024433	ENSG00000247982	LINC00926	-	long intergenic non-protein coding RNA 926	ncRNA	0.014663	0.461988	
chunk0158_241_1	chr5	129129171	129129656	+	0	NA	Intergenic	Intergenic	31725	NR_039776	100616175		NR_039776	ENSG00000264563	MIR4633	-	microRNA 4633	ncRNA	0.004124	0.393004	
chunk0020_434_1	chr1	241818702	241818901	+	0	NA	Intergenic	MIRb|SINE|MIR	-29390	NM_130398	9156	Hs.498248	NM_003686	ENSG00000174371	EXO1	HEX1|hExoI	exonuclease 1	protein-coding	0.010050	0.425000	129(AGGTACATACAGTGCC,-,0.00),130(GGTACATACAGTGCCT,+,0.00)
chunk0031_271_1	chr10	127967975	127968668	+	0	NA	intron (NM_001316676, intron 2 of 21)	intron (NM_001316676, intron 2 of 21)	-18959	NM_001316677	5791	Hs.127022	NM_006504	ENSG00000132334	PTPRE	HPTPE|PTPE|R-PTP-EPSILON	protein tyrosine phosphatase receptor type E	protein-coding	0.008658	0.495677	
chunk0168_329_1	chr6	92587206	92587572	+	0	NA	Intergenic	Intergenic	832193	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.002732	0.297003	
chunk0153_20_1	chr5	66994955	66995186	+	0	NA	intron (NM_001290226, intron 1 of 26)	intron (NM_001290226, intron 1 of 26)	9084	NR_111908	101928794	Hs.672435	NR_111908		MAST4-AS1	-	MAST4 antisense RNA 1	ncRNA	0.008658	0.336207	
chunk0200_335_1	chr9	24141629	24141849	+	0	NA	Intergenic	LTR32|LTR|ERVL	-315674	NM_004432	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.004545	0.443439	
chunk0036_447_1	chr11	68551063	68551404	+	0	NA	intron (NM_018312, intron 7 of 22)	intron (NM_018312, intron 7 of 22)	90515	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.005865	0.353801	
chunk0127_258_1	chr3	97230427	97230955	+	0	NA	intron (NM_001080448, intron 4 of 17)	MER34C_|LTR|ERV1	-208902	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.005682	0.368620	
chunk0019_438_1	chr1	231075137	231075411	+	0	NA	Intergenic	Intergenic	-35025	NM_198552	375061	Hs.38516	NM_198552	ENSG00000182118	FAM89A	C1orf153	family with sequence similarity 89 member A	protein-coding	0.021898	0.541818	
chunk0097_357_1	chr2	60331047	60331740	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	51643	NR_132991	106660609	Hs.565545	NR_132991	ENSG00000228590	MIR4432HG	-	MIR4432 host gene	ncRNA	0.010101	0.345821	178(CAGTACATACTGTACT,-,0.00),179(AGTACATACTGTACTA,+,0.00)
chunk0201_174_1	chr9	36238663	36238896	+	0	NA	intron (NM_001190383, intron 3 of 10)	L1PA17|LINE|L1	19720	NM_001190383	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.004292	0.363248	
chunk0144_424_1	chr4	140691241	140691760	+	0	NA	intron (NM_015130, intron 2 of 20)	intron (NM_015130, intron 2 of 20)	-48420	NR_077215	644962	Hs.676500	NR_077215		TNRC18P1	-	trinucleotide repeat containing 18 pseudogene 1	pseudo	0.005780	0.390385	
chunk0052_192_1	chr13	24790257	24790871	+	0	NA	intron (NM_031277, intron 9 of 35)	MLT1A1|LTR|ERVL-MaLR	26401	NM_031277	56163	Hs.97464	NM_031277	ENSG00000132972	RNF17	Mmip-2|SPATA23|TDRD4	ring finger protein 17	protein-coding	0.003257	0.383740	
chunk0210_103_1	chrX	71642953	71643282	+	0	NA	Intergenic	L1PB3|LINE|L1	-24600	NM_001504	2833	Hs.198252	NM_001504	ENSG00000186810	CXCR3	CD182|CD183|CKR-L2|CMKAR3|GPR9|IP10-R|Mig-R|MigR	C-X-C motif chemokine receptor 3	protein-coding	0.012158	0.387879	
chunk0122_108_1	chr3	30648009	30648273	+	0	NA	intron (NM_001024847, intron 3 of 7)	intron (NM_001024847, intron 3 of 7)	41639	NM_003242	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.007576	0.415094	
chunk0147_146_1	chr4	175077142	175077510	+	0	NA	Intergenic	Intergenic	158968	NM_001130704	11086	Hs.126838	NM_014269	ENSG00000168594	ADAM29	CT73|svph1	ADAM metallopeptidase domain 29	protein-coding	0.002717	0.317073	
chunk0002_444_1	chr1	28313951	28314271	+	0	NA	Intergenic	Intergenic	-14891	NM_001127350	54797	Hs.479911	NM_017638	ENSG00000130772	MED18	SRB5|p28b	mediator complex subunit 18	protein-coding	0.012500	0.551402	
chunk0144_358_1	chr4	139744173	139744513	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	78575	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.000000	0.410557	
chunk0186_192_1	chr7	139724913	139725560	+	0	NA	intron (NM_001113239, intron 1 of 14)	L2c|LINE|L2	52658	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.009274	0.408951	
chunk0111_117_1	chr20	24003041	24003306	+	0	NA	Intergenic	(ACACAC)n|Simple_repeat|Simple_repeat	-14394	NM_178311	92086	Hs.355394	NM_080920	ENSG00000149435	GGTLC1	GGTL6|GGTLA3|GGTLA4|dJ831C21.1|dJ831C21.2	gamma-glutamyltransferase light chain 1	protein-coding	0.037736	0.496241	
chunk0100_414_1	chr2	119766937	119767360	+	0	NA	intron (NM_002830, intron 1 of 26)	intron (NM_002830, intron 1 of 26)	7517	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.011820	0.386792	193(GGAACACCTCGTGCTT,+,0.00)
chunk0204_344_1	chr9	101421552	101422176	+	0	NA	exon (NM_000035, exon 9 of 9)	exon (NM_000035, exon 9 of 9)	13916	NM_000035	229	Hs.530274	NM_000035	ENSG00000136872	ALDOB	ALDB|ALDO2	aldolase, fructose-bisphosphate B	protein-coding	0.008013	0.444800	317(GTGAACATACTGTCCT,-,0.00),318(TGAACATACTGTCCTT,+,0.00)
chunk0085_217_1	chr18	6769811	6770491	+	0	NA	Intergenic	Intergenic	-64282	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.007353	0.349486	
chunk0157_466_1	chr5	125065084	125066137	+	0	NA	intron (NR_109882, intron 2 of 5)	intron (NR_109882, intron 2 of 5)	28779	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.008547	0.402277	
chunk0064_300_1	chr14	95500924	95501451	+	0	NA	Intergenic	Intergenic	-25351	NM_152592	161176	Hs.41502	NM_024633	ENSG00000176438	SYNE3	C14orf139|C14orf49|KASH3|LINC00341|NCRNA00341|NET53|Nesp3	spectrin repeat containing nuclear envelope family member 3	protein-coding	0.018975	0.486742	
chunk0157_103_1	chr5	116789424	116789996	+	0	NA	Intergenic	Intergenic	-27501	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.003497	0.336824	281(CTGTACAGCATGTTCT,-,0.00),282(TGTACAGCATGTTCTT,+,0.00)
chunk0170_63_1	chr6	109535282	109535556	+	0	NA	intron (NM_001145128, intron 27 of 40)	L1PA5|LINE|L1	-52182	NM_001164313	9841	Hs.409876	NM_014797	ENSG00000112365	ZBTB24	BIF1|ICF2|PATZ2|ZNF450	zinc finger and BTB domain containing 24	protein-coding	0.014599	0.374545	
chunk0125_428_1	chr3	72441231	72441797	+	0	NA	intron (NM_012234, intron 1 of 3)	intron (NM_012234, intron 1 of 3)	5109	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.007067	0.370370	
chunk0136_177_1	chr4	6561130	6561329	+	0	NA	intron (NM_001206994, intron 1 of 9)	MER45C|DNA|hAT-Tip100	2371	NM_001206994	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.020101	0.555000	169(AGGAACACGATGTTAC,-,0.00)
chunk0174_328_1	chr6	163547917	163548348	+	0	NA	intron (NM_206853, intron 4 of 6)	intron (NM_206853, intron 4 of 6)	133489	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.006961	0.356481	
chunk0079_353_1	chr17	17823821	17824233	+	0	NA	intron (NM_001005291, intron 1 of 19)	intron (NM_001005291, intron 1 of 19)	-10096	NR_030361	693120		NR_030361	ENSG00000207839	MIR33B	MIRN33B|hsa-mir-33b|mir-33b	microRNA 33b	ncRNA	0.067961	0.595642	
chunk0026_161_1	chr10	62845373	62845572	+	0	NA	Intergenic	Intergenic	-26305	NM_001136178	1959	Hs.1395	NM_000399	ENSG00000122877	EGR2	AT591|CHN1|CMT1D|CMT4E|KROX20	early growth response 2	protein-coding	0.015075	0.505000	118(CAGGTCAGTGTGTTCT,-,0.00),119(AGGTCAGTGTGTTCTG,+,0.00)
chunk0208_1_1	chrX	10036384	10036598	+	0	NA	intron (NM_015691, intron 1 of 22)	L1MB5|LINE|L1	20736	NM_015691	55841	Hs.527524	NM_015691	ENSG00000047644	WWC3	BM042	WWC family member 3	protein-coding	0.009346	0.460465	
chunk0125_354_1	chr3	71208490	71209183	+	0	NA	intron (NM_032682, intron 5 of 20)	intron (NM_032682, intron 5 of 20)	36329	NM_001244814	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.008658	0.407781	
chunk0095_34_1	chr2	13413119	13413508	+	0	NA	Intergenic	MIRb|SINE|MIR	-406300	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.002571	0.358974	
chunk0019_361_1	chr1	229715042	229715316	+	0	NA	Intergenic	MER66C|LTR|ERV1	88963	NM_014777	9816	Hs.533628	NM_014777	ENSG00000135763	URB2	KIAA0133|NET10|NPA2	URB2 ribosome biogenesis homolog	protein-coding	0.010949	0.469091	
chunk0153_386_1	chr5	75049784	75050199	+	0	NA	intron (NR_126375, intron 1 of 1)	MIR|SINE|MIR	2652	NR_126375	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.014458	0.485577	159(GAGCACTTTATGTGCT,-,0.00),160(AGCACTTTATGTGCTT,+,0.00)
chunk0195_91_1	chr8	94272024	94272431	+	0	NA	Intergenic	Intergenic	-9908	NM_181702	2669	Hs.654463	NM_005261	ENSG00000164949	GEM	KIR	GTP binding protein overexpressed in skeletal muscle	protein-coding	0.014742	0.477941	183(AGGAACTCAAAGTTCC,-,0.00),184(GGAACTCAAAGTTCCA,+,0.00)
chunk0039_415_1	chr11	107582202	107582765	+	0	NA	Intergenic	Intergenic	-8608	NM_001130037	55531	Hs.495779	NM_018712	ENSG00000110675	ELMOD1	-	ELMO domain containing 1	protein-coding	0.003552	0.402482	
chunk0065_315_1	chr14	103051257	103051786	+	0	NA	intron (NM_006035, intron 1 of 36)	intron (NM_006035, intron 1 of 36)	5884	NM_006035	9578	Hs.654634	NM_006035	ENSG00000198752	CDC42BPB	MRCKB	CDC42 binding protein kinase beta	protein-coding	0.009452	0.388679	
chunk0126_450_1	chr3	87185576	87186029	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	40475	NR_039958	100616161		NR_039958	ENSG00000264119	MIR4795	-	microRNA 4795	ncRNA	0.004415	0.350220	
chunk0128_123_1	chr3	106446068	106446358	+	0	NA	Intergenic	L1ME2|LINE|L1	-577170	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.010345	0.381443	
chunk0120_54_1	chr3	3103368	3103634	+	0	NA	intron (NM_000564, intron 4 of 12)	MER112|DNA|hAT-Charlie	6873	NM_000564	3568	Hs.68876	NM_000564	ENSG00000091181	IL5RA	CD125|CDw125|HSIL5R3|IL5R	interleukin 5 receptor subunit alpha	protein-coding	0.003759	0.318352	
chunk0200_71_1	chr9	15967869	15968229	+	0	NA	intron (NM_173550, intron 25 of 25)	intron (NM_173550, intron 25 of 25)	285058	NM_001271829	100129385	Hs.586441	NM_001271829	ENSG00000205549	C9orf92	Em:AL513424.1	chromosome 9 open reading frame 92	protein-coding	0.005556	0.277008	
chunk0100_164_1	chr2	109244792	109245234	+	0	NA	intron (NM_001099289, intron 1 of 9)	intron (NM_001099289, intron 1 of 9)	68612	NR_036224	100423027		NR_036224	ENSG00000265965	MIR4266	-	microRNA 4266	ncRNA	0.006787	0.537246	288(CTGAGCAGAGTGTGCC,-,0.00),289(TGAGCAGAGTGTGCCC,+,0.00)
chunk0106_368_1	chr2	207188656	207188983	+	0	NA	intron (NR_110283, intron 3 of 3)	intron (NR_110283, intron 3 of 3)	-21573	NM_001270943	8609	Hs.59908	NM_003709	ENSG00000118263	KLF7	UKLF	Kruppel like factor 7	protein-coding	0.000000	0.381098	
chunk0022_51_1	chr10	8158844	8159390	+	0	NA	Intergenic	Intergenic	104413	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.005495	0.378428	
chunk0099_299_1	chr2	98968686	98968950	+	0	NA	Intergenic	MER57A1|LTR|ERV1	-32597	NM_207362	343990	Hs.469398	NM_207362	ENSG00000196872	KIAA1211L	C2orf55	KIAA1211 like	protein-coding	0.000000	0.418868	184(CTGTACATCATGTTCC,-,0.00),185(TGTACATCATGTTCCT,+,0.00)
chunk0014_80_1	chr1	176510130	176510539	+	0	NA	intron (NM_020318, intron 1 of 22)	L1ME1|LINE|L1	47163	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.002445	0.300000	
chunk0205_298_1	chr9	112065815	112066014	+	0	NA	intron (NM_022486, intron 12 of 16)	intron (NM_022486, intron 12 of 16)	109383	NM_001282643	64420	Hs.494827	NM_022486	ENSG00000106868	SUSD1	-	sushi domain containing 1	protein-coding	0.015075	0.410000	
chunk0184_154_1	chr7	116218054	116218448	+	0	NA	intron (NM_015641, intron 1 of 6)	intron (NM_015641, intron 1 of 6)	-4700	NM_152829	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.005076	0.407595	
chunk0166_33_1	chr6	42117121	42117521	+	0	NA	intron (NM_001164446, intron 2 of 4)	MIR|SINE|MIR	25656	NM_001164446	647024	Hs.444277	NM_001164446	ENSG00000188112	C6orf132	bA7K24.2	chromosome 6 open reading frame 132	protein-coding	0.000000	0.443890	
chunk0026_411_1	chr10	70345314	70345902	+	0	NA	intron (NR_103468, intron 1 of 2)	L1MC|LINE|L1	31171	NM_001278213	55222	Hs.7778	NM_018205	ENSG00000172731	LRRC20	-	leucine rich repeat containing 20	protein-coding	0.003401	0.305603	
chunk0004_199_1	chr1	46539288	46539582	+	0	NA	intron (NR_038403, intron 1 of 7)	intron (NR_038403, intron 1 of 7)	739	NR_038403	100507423	Hs.601863	NR_038403	ENSG00000269956	MKNK1-AS1	-	MKNK1 antisense RNA 1	ncRNA	0.006803	0.437288	
chunk0188_234_1	chr8	13230058	13230507	+	0	NA	intron (NM_182643, intron 5 of 17)	intron (NM_182643, intron 5 of 17)	46266	NM_001316668	10395	Hs.134296	NM_006094	ENSG00000164741	DLC1	ARHGAP7|HP|STARD12|p122-RhoGAP	DLC1 Rho GTPase activating protein	protein-coding	0.006682	0.380000	
chunk0140_192_1	chr4	70068858	70069436	+	0	NA	intron (NR_003720, intron 2 of 12)	intron (NR_003720, intron 2 of 12)	1761	NR_003720	286828	Hs.631945	NR_003720	ENSG00000234124	CSN1S2AP	CSN1S2A	casein alpha s2 like A, pseudogene	pseudo	0.001730	0.300518	
chunk0201_53_1	chr9	33871327	33871733	+	0	NA	intron (NM_017811, intron 1 of 4)	intron (NM_017811, intron 1 of 4)	54346	NM_017811	54926	Hs.643648	NM_017811	ENSG00000107341	UBE2R2	CDC34B|E2-CDC34B|UBC3B	ubiquitin conjugating enzyme E2 R2	protein-coding	0.014778	0.321867	
chunk0039_165_1	chr11	99240550	99240933	+	0	NA	intron (NM_001243270, intron 1 of 23)	intron (NM_001243270, intron 1 of 23)	219765	NM_014361	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.010444	0.351562	
chunk0002_301_1	chr1	23576194	23576735	+	0	NA	Intergenic	MIR|SINE|MIR	-16670	NM_002167	3399	Hs.76884	NM_002167	ENSG00000117318	ID3	HEIR-1|bHLHb25	inhibitor of DNA binding 3, HLH protein	protein-coding	0.012939	0.457565	
chunk0136_416_1	chr3	197416505	197416861	+	0	NA	Intergenic	Intergenic	-117411	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.011236	0.467787	
chunk0198_149_1	chr8	132926875	132927346	+	0	NA	intron (NM_003235, intron 22 of 47)	intron (NM_003235, intron 22 of 47)	60150	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.004246	0.423729	
chunk0010_372_1	chr1	119101484	119102087	+	0	NA	intron (NM_015836, intron 1 of 5)	intron (NM_015836, intron 1 of 5)	-38611	NR_125977	101929147	Hs.697821	NR_125974	ENSG00000231365	WARS2-AS1	-	WARS2 antisense RNA 1	ncRNA	0.004975	0.395695	347(CAGAACAATGTGTGCT,-,0.00),348(AGAACAATGTGTGCTA,+,0.00)
chunk0204_401_1	chr9	102570896	102571409	+	0	NA	intron (NR_103830, intron 1 of 4)	L1M1|LINE|L1	51515	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.001949	0.321012	
chunk0070_223_1	chr15	72733819	72734655	+	0	NA	intron (NR_045565, intron 13 of 16)	intron (NR_045565, intron 13 of 16)	48058	NM_001252678	585	Hs.208681	NM_033028	ENSG00000140463	BBS4	-	Bardet-Biedl syndrome 4	protein-coding	0.002392	0.401434	
chunk0001_74_1	chr1	2494328	2494646	+	0	NA	intron (NM_001303013, intron 11 of 21)	intron (NM_001303013, intron 11 of 21)	18172	NM_001303013	9651	Hs.170156	NM_014638	ENSG00000149527	PLCH2	PLC-L4|PLC-eta2|PLCL4|PLCeta2	phospholipase C eta 2	protein-coding	0.053459	0.564263	
chunk0125_282_1	chr3	69633972	69634227	+	0	NA	Intergenic	L1PA6|LINE|L1	-105336	NM_198159	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.000000	0.378906	
chunk0165_266_1	chr6	35796010	35796216	+	0	NA	intron (NM_001832, intron 1 of 2)	MIR3|SINE|MIR	1231	NM_001832	1208	Hs.1340	NM_001832	ENSG00000137392	CLPS	-	colipase	protein-coding	0.014563	0.565217	
chunk0038_239_1	chr11	87128261	87128865	+	0	NA	intron (NM_001168724, intron 4 of 13)	intron (NM_001168724, intron 4 of 13)	90719	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.008278	0.327273	
chunk0165_277_1	chr6	36076638	36077312	+	0	NA	intron (NM_001315, intron 8 of 11)	intron (NM_001315, intron 8 of 11)	49298	NM_139013	1432	Hs.485233	NM_001315	ENSG00000112062	MAPK14	CSBP|CSBP1|CSBP2|CSPB1|EXIP|Mxi2|PRKM14|PRKM15|RK|SAPK2A|p38|p38ALPHA	mitogen-activated protein kinase 14	protein-coding	0.001484	0.365926	
chunk0106_431_1	chr2	208428159	208428526	+	0	NA	intron (NM_001309516, intron 2 of 12)	intron (NM_001309516, intron 2 of 12)	21512	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.002725	0.415761	70(AGGAGCAGATTGTCCT,-,0.00),71(GGAGCAGATTGTCCTT,+,0.00)
chunk0014_367_1	chr1	182578838	182579340	+	0	NA	intron (NM_021133, intron 5 of 6)	L1PB4|LINE|L1	10170	NM_021133	6041	Hs.518545	NM_021133	ENSG00000135828	RNASEL	PRCA1|RNS4	ribonuclease L	protein-coding	0.003984	0.389662	
chunk0158_359_1	chr5	133759564	133760244	+	0	NA	Intergenic	(CAAA)n|Simple_repeat|Simple_repeat	-147372	NM_015082	23105	Hs.483390	NM_015082	ENSG00000053108	FSTL4	-	follistatin like 4	protein-coding	0.005882	0.433186	540(AAGGACAGGCTGGTCC,-,0.00),541(AGGACAGGCTGGTCCT,+,0.00)
chunk0194_118_1	chr8	83956911	83957355	+	0	NA	Intergenic	MER94|DNA|hAT-Blackjack	-226085	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002252	0.337079	239(AGGCACAGACTGTCCC,-,0.00),240(GGCACAGACTGTCCCA,+,0.00)
chunk0093_436_1	chr19	58314705	58315268	+	0	NA	Intergenic	LTR3|LTR|ERVK	-12033	NM_181846	342945	Hs.388162	NM_181846	ENSG00000182318	ZSCAN22	HKR2|ZNF50	zinc finger and SCAN domain containing 22	protein-coding	0.024867	0.464539	
chunk0115_228_1	chr21	27174027	27174540	+	0	NA	Intergenic	Intergenic	-207163	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.007797	0.282101	
chunk0207_394_1	chr9	136679599	136680046	+	0	NA	intron (NM_006412, intron 1 of 5)	L1ME3G|LINE|L1	7637	NM_006412	10555	Hs.320151	NM_006412	ENSG00000169692	AGPAT2	1-AGPAT2|BSCL|BSCL1|LPAAB|LPAAT-beta	1-acylglycerol-3-phosphate O-acyltransferase 2	protein-coding	0.031320	0.544643	
chunk0011_146_1	chr1	147452064	147453192	+	0	NA	intron (NR_038423, intron 3 of 3)	intron (NR_038423, intron 3 of 3)	65247	NR_038423	100289211	Hs.323484	NR_038423	ENSG00000278811	LINC00624	-	long intergenic non-protein coding RNA 624	ncRNA	0.006206	0.378211	308(AAGCACTGAGTGTTCT,-,0.00),309(AGCACTGAGTGTTCTA,+,0.00),961(GGGAACACACTGGCCT,-,0.00),962(GGAACACACTGGCCTG,+,0.00)
chunk0103_280_1	chr2	165948673	165949616	+	0	NA	TTS (NR_038984)	TTS (NR_038984)	4694	NM_024753	79809	Hs.310672	NM_024753	ENSG00000123607	TTC21B	ATD4|IFT139|IFT139B|JBTS11|NPHP12|Nbla10696|SRTD4|THM1	tetratricopeptide repeat domain 21B	protein-coding	0.006363	0.344280	
chunk0070_185_1	chr15	71839241	71839444	+	0	NA	intron (NM_006901, intron 39 of 41)	intron (NM_006901, intron 39 of 41)	28794	NM_016346	10002	Hs.187354	NM_014249	ENSG00000278570	NR2E3	ESCS|PNR|RNR|RP37|rd7	nuclear receptor subfamily 2 group E member 3	protein-coding	0.000000	0.397059	
chunk0177_333_1	chr7	26413197	26414010	+	0	NA	intron (NR_015364, intron 1 of 4)	intron (NR_015364, intron 1 of 4)	10115	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.004920	0.486486	368(GGGCACACAATGGCCT,-,0.00)
chunk0047_117_1	chr12	68942484	68942698	+	0	NA	intron (NM_001874, intron 1 of 8)	L2a|LINE|L2	-9392	NM_001005502	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.004673	0.376744	
chunk0115_309_1	chr21	28543934	28544405	+	0	NA	Intergenic	Intergenic	4851	NR_026553	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.002123	0.328390	
chunk0146_10_1	chr4	154973664	154973952	+	0	NA	Intergenic	Intergenic	192303	NM_001277173	166863	Hs.133095	NM_144979	ENSG00000151962	RBM46	CT68	RNA binding motif protein 46	protein-coding	0.010417	0.404844	138(AAGTACACAGTGTCCT,-,0.00),139(AGTACACAGTGTCCTG,+,0.00)
chunk0184_58_1	chr7	112420171	112420772	+	0	NA	Intergenic	L2a|LINE|L2	-2673	NM_001197080	3475	Hs.7879	NM_001550	ENSG00000006652	IFRD1	PC4|TIS7	interferon related developmental regulator 1	protein-coding	0.013311	0.421927	
chunk0062_40_1	chr14	67241559	67241963	+	0	NA	intron (NM_022474, intron 1 of 14)	CpG	466	NM_001256550	64398	Hs.652312	NM_022474	ENSG00000072415	MPP5	PALS1	membrane palmitoylated protein 5	protein-coding	0.103960	0.703704	
chunk0144_196_1	chr4	133695832	133696661	+	0	NA	Intergenic	L1PA15|LINE|L1	505502	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.004825	0.366265	
chunk0185_375_1	chr7	133029373	133029934	+	0	NA	intron (NM_017812, intron 2 of 7)	intron (NM_017812, intron 2 of 7)	5262	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.008913	0.464413	
chunk0033_267_1	chr11	19028124	19028639	+	0	NA	Intergenic	MER54A|LTR|ERVL	31636	NM_001303615	117194	Hs.350566	NM_054030	ENSG00000183695	MRGPRX2	MGRG3|MRGX2	MAS related GPR family member X2	protein-coding	0.005825	0.437984	
chunk0179_59_1	chr7	43764145	43764409	+	0	NA	intron (NM_001253823, intron 2 of 8)	intron (NM_001253823, intron 2 of 8)	5604	NM_000712	644	Hs.488143	NM_000712	ENSG00000106605	BLVRA	BLVR|BVR|BVRA	biliverdin reductase A	protein-coding	0.022727	0.467925	
chunk0199_337_1	chr9	10977160	10977938	+	0	NA	Intergenic	L1PBa|LINE|L1	364343	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.005141	0.353017	
chunk0162_223_1	chr6	4460718	4461284	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	32999	NR_106988									0.033569	0.530864	243(GGAAACAGTTTGTCCC,-,0.00),244(GAAACAGTTTGTCCCC,+,0.00)
chunk0065_12_1	chr15	20276811	20277250	+	0	NA	Intergenic	Intergenic	-5714	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.025057	0.547727	
chunk0204_8_1	chr9	91659954	91660529	+	0	NA	Intergenic	Intergenic	-23896	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.008696	0.428819	
chunk0009_302_1	chr1	108034298	108034933	+	0	NA	Intergenic	Intergenic	-69692	NM_006113	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.001575	0.386792	
chunk0123_271_1	chr3	46167187	46167396	+	0	NA	Intergenic	L1PREC2|LINE|L1	41050	NM_001295	1230	Hs.301921	NM_001295	ENSG00000163823	CCR1	CD191|CKR-1|CKR1|CMKBR1|HM145|MIP1aR|SCYAR1	C-C motif chemokine receptor 1	protein-coding	0.000000	0.304762	
chunk0162_185_1	chr6	3803808	3804283	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-45353	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.006316	0.434874	
chunk0090_18_1	chr19	871868	872940	+	0	NA	intron (NM_005481, intron 11 of 15)	intron (NM_005481, intron 11 of 15)	12739	NM_001928	1675	Hs.155597	NM_001928	ENSG00000197766	CFD	ADIPSIN|ADN|DF|PFD	complement factor D	protein-coding	0.045709	0.660764	93(AGGGACATGCTGTCCT,-,0.00),94(GGGACATGCTGTCCTG,+,0.00),766(CAGGACAGAGTGTACC,-,0.00),767(AGGACAGAGTGTACCG,+,0.00)
chunk0040_253_1	chr11	115502567	115502766	+	0	NA	intron (NM_001301043, intron 1 of 11)	intron (NM_001301043, intron 1 of 11)	1857	NM_014333	23705	Hs.370510	NM_014333	ENSG00000182985	CADM1	BL2|IGSF4|IGSF4A|NECL2|Necl-2|RA175|ST17|SYNCAM|TSLC1|sTSLC-1|sgIGSF|synCAM1	cell adhesion molecule 1	protein-coding	0.035176	0.520000	
chunk0063_453_1	chr14	89053095	89053873	+	0	NA	Intergenic	L1MC1|LINE|L1	229331	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.011568	0.382542	
chunk0180_394_1	chr7	74664036	74664516	+	0	NA	intron (NM_001280800, intron 1 of 9)	intron (NM_001280800, intron 1 of 9)	6611	NM_001280800	2969	Hs.647041	NM_001518	ENSG00000263001	GTF2I	BAP135|BTKAP1|DIWS|GTFII-I|IB291|SPIN|TFII-I|WBS|WBSCR6	general transcription factor IIi	protein-coding	0.020833	0.461538	
chunk0202_83_1	chr9	71928309	71928784	+	0	NA	intron (NM_182505, intron 1 of 3)	intron (NM_182505, intron 1 of 3)	17039	NM_182505	138241	Hs.534190	NM_182505	ENSG00000155621	C9orf85	-	chromosome 9 open reading frame 85	protein-coding	0.002105	0.329832	209(GATACAGACTGTACTT,+,0.00)
chunk0037_327_1	chr11	77036259	77036955	+	0	NA	intron (NM_138706, intron 1 of 1)	MIR|SINE|MIR	2266	NM_138706	192134	Hs.352622	NM_138706	ENSG00000198488	B3GNT6	B3Gn-T6|BGnT-6|beta-1,3-Gn-T6|beta3Gn-T6	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6	protein-coding	0.008621	0.413199	
chunk0046_225_1	chr12	59895374	59896084	+	0	NA	Intergenic	Intergenic	206392	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001408	0.336146	
chunk0091_362_1	chr19	15445725	15446225	+	0	NA	intron (NM_021241, intron 2 of 7)	intron (NM_021241, intron 2 of 7)	-3573	NR_031716	100302127		NR_031716	ENSG00000269782	MIR1470	MIRN1470|hsa-mir-1470	microRNA 1470	ncRNA	0.016000	0.600798	
chunk0088_180_1	chr18	47370023	47370506	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	-10232	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.004141	0.322314	245(TGGTACAGTATGTACT,-,0.00),246(GGTACAGTATGTACTA,+,0.00)
chunk0064_349_1	chr14	96739829	96740255	+	0	NA	Intergenic	Intergenic	-57305	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.011737	0.402810	
chunk0046_183_1	chr12	58765937	58766495	+	0	NA	intron (NR_120452, intron 1 of 7)	L2a|LINE|L2	15500	NR_120452	101927653	Hs.130744	NR_120452	ENSG00000257259	LINC02388	-	long intergenic non-protein coding RNA 2388	ncRNA	0.003584	0.379249	
chunk0050_357_1	chr12	107773498	107774116	+	0	NA	promoter-TSS (NM_203436)	promoter-TSS (NM_203436)	-578	NM_203436	121549	Hs.149910	NM_203436	ENSG00000187855	ASCL4	HASH4|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding	0.008091	0.389338	
chunk0141_1_1	chr4	76540924	76541123	+	0	NA	intron (NM_020859, intron 1 of 10)	intron (NM_020859, intron 1 of 10)	-32545	NR_039654	100616299		NR_039654	ENSG00000263445	MIR4450	mir-4450	microRNA 4450	ncRNA	0.005025	0.310000	
chunk0054_221_1	chr13	45440401	45441010	+	0	NA	Intergenic	Intergenic	-22250	NM_001010875	253512	Hs.591230	NM_001010875	ENSG00000174032	SLC25A30	KMCP1	solute carrier family 25 member 30	protein-coding	0.004926	0.424590	253(AAGGACATGCAGTCCT,-,0.00),254(AGGACATGCAGTCCTC,+,0.00)
chunk0063_155_1	chr14	80016642	80017156	+	0	NA	Intergenic	Intergenic	-194520	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.005837	0.312621	
chunk0096_25_1	chr2	26533994	26534535	+	0	NA	intron (NM_194248, intron 2 of 46)	intron (NM_194248, intron 2 of 46)	24434	NM_001287489	9381	Hs.91608	NM_004802	ENSG00000115155	OTOF	AUNB1|DFNB6|DFNB9|FER1L2|NSRD9	otoferlin	protein-coding	0.003697	0.501845	
chunk0126_244_1	chr3	79351596	79352093	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-59883	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.004024	0.329317	244(GGGCACAGTGTGTCCT,-,0.00),245(GGCACAGTGTGTCCTT,+,0.00)
chunk0030_77_1	chr10	112258323	112258865	+	0	NA	Intergenic	Intergenic	-25062	NM_058222	6975	Hs.345485	NM_058222	ENSG00000119913	TECTB	-	tectorin beta	protein-coding	0.001845	0.401473	
chunk0052_198_1	chr13	24916321	24916934	+	0	NA	intron (NR_047594, intron 1 of 17)	intron (NR_047594, intron 1 of 17)	6262	NR_047595	55835	Hs.513379	NM_018451	ENSG00000151849	CENPJ	BM032|CENP-J|CPAP|LAP|LIP1|MCPH6|SASS4|SCKL4|Sas-4	centromere protein J	protein-coding	0.004894	0.337134	
chunk0084_369_1	chr17	81595854	81596322	+	0	NA	intron (NM_017921, intron 11 of 16)	intron (NM_017921, intron 11 of 16)	-18655	NR_130139	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.006410	0.377399	238(CAGTACATACTGTCCC,-,0.00),239(AGTACATACTGTCCCT,+,0.00)
chunk0025_419_1	chr10	59719766	59720149	+	0	NA	Intergenic	L2b|LINE|L2	-10066	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.000000	0.317708	88(AAGTACACAGTGTTCC,-,0.00),89(AGTACACAGTGTTCCT,+,0.00)
chunk0148_174_1	chr5	7626033	7626415	+	0	NA	exon (NM_020546, exon 4 of 25)	exon (NM_020546, exon 4 of 25)	225266	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.015707	0.389034	
chunk0012_431_1	chr1	164748615	164748844	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	25912	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.004367	0.443478	
chunk0021_81_1	chr10	1687273	1687668	+	0	NA	intron (NM_018702, intron 1 of 9)	Charlie15b|DNA|hAT-Charlie	50006	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.012658	0.371212	
chunk0165_205_1	chr6	34658869	34659332	+	0	NA	intron (NM_022758, intron 1 of 3)	L2b|LINE|L2	37750	NM_024294	64771	Hs.643498	NM_022758	ENSG00000196821	ILRUN	C6orf106|FP852|dJ391O22.4	inflammation and lipid regulator with UBA-like and NBR1-like domains	protein-coding	0.008639	0.437500	
chunk0103_420_1	chr2	169715269	169715789	+	0	NA	intron (NM_001199290, intron 3 of 5)	HERVL18-int|LTR|ERVL	-18317	NM_144711	151230	Hs.655150	NM_144711	ENSG00000213160	KLHL23	DITHP	kelch like family member 23	protein-coding	0.017308	0.504798	
chunk0049_41_1	chr12	89834374	89834921	+	0	NA	Intergenic	Intergenic	125692	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.003656	0.321168	254(AGAACTACTTGTACTT,+,0.00)
chunk0163_67_1	chr6	9115710	9116467	+	0	NA	Intergenic	Intergenic	463879	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.011889	0.476253	406(AAGCACACACTGTCTA,-,0.00),407(AGCACACACTGTCTAT,+,0.00)
chunk0185_307_1	chr7	131305102	131305632	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	22412	NR_125364	100506881	Hs.660830	NR_125364	ENSG00000236753	MKLN1-AS	MKLN1-AS2	MKLN1 antisense RNA	ncRNA	0.000000	0.376648	
chunk0027_193_1	chr10	75649330	75649883	+	0	NA	intron (NR_131178, intron 1 of 7)	L1MB3|LINE|L1	2097	NR_131178	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.001808	0.371841	
chunk0164_210_1	chr6	22657919	22658635	+	0	NA	Intergenic	Intergenic	88828	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.006983	0.414226	
chunk0174_322_1	chr6	163427930	163428267	+	0	NA	intron (NM_206853, intron 1 of 6)	intron (NM_206853, intron 1 of 6)	13455	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.000000	0.325444	
chunk0018_394_1	chr1	222551519	222552097	+	0	NA	Intergenic	Intergenic	-3706	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.010381	0.421416	
chunk0128_36_1	chr3	104503120	104503440	+	0	NA	Intergenic	Intergenic	-863433	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.040625	0.554517	
chunk0045_436_1	chr12	53557742	53557966	+	0	NA	intron (NM_006856, intron 2 of 11)	MER33|DNA|hAT-Charlie	43870	NR_046221	100652999	Hs.633602	NR_046221	ENSG00000257550	LOC100652999	-	uncharacterized LOC100652999	ncRNA	0.004464	0.288889	
chunk0039_106_1	chr11	97609668	97610296	+	0	NA	Intergenic	HUERS-P2-int|LTR|ERV1	-1103105	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.004777	0.443561	
chunk0089_355_1	chr18	66724641	66724946	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-120655	NR_073130	28513	Hs.42771	NM_021153	ENSG00000071991	CDH19	CDH7|CDH7L2	cadherin 19	protein-coding	0.013115	0.408497	
chunk0065_363_1	chr14	103888539	103888814	+	0	NA	Intergenic	Intergenic	32890	NM_004894	9556	Hs.109052	NM_004894	ENSG00000156411	ATP5MPL	6.8PL|C14orf2|MLQ|MP68|PLPM	ATP synthase membrane subunit 6.8PL	protein-coding	0.029091	0.583333	
chunk0007_100_1	chr1	78745324	78745748	+	0	NA	Intergenic	Intergenic	95744	NM_006417	10561	Hs.82316	NM_006417	ENSG00000137965	IFI44	MTAP44|TLDC5|p44	interferon induced protein 44	protein-coding	0.007075	0.369412	238(AAGAACAGGCTGTCCA,-,0.00),239(AGAACAGGCTGTCCAT,+,0.00)
chunk0161_449_1	chr5	178825646	178826205	+	0	NA	Intergenic	Intergenic	-34028	NM_058230	117608	Hs.724051	NM_058230	ENSG00000178338	ZNF354B	KID2	zinc finger protein 354B	protein-coding	0.010733	0.385714	
chunk0114_273_1	chr21	16290747	16291215	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	96602	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002137	0.339019	
chunk0105_439_1	chr2	194198490	194198902	+	0	NA	Intergenic	Intergenic	-145573	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.002427	0.338983	
chunk0165_84_1	chr6	31424082	31424523	+	0	NA	Intergenic	L1PB2|LINE|L1	20735	NM_000247	100507436	Hs.130838	NM_000247	ENSG00000204520	MICA	MIC-A|PERB11.1	MHC class I polypeptide-related sequence A	protein-coding	0.006803	0.402715	23(AAGCACATACTGTTCT,-,0.00),24(AGCACATACTGTTCTG,+,0.00)
chunk0078_348_1	chr16	86424111	86424491	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-78622	NR_024406	732275	Hs.558087	NR_024406	ENSG00000168367	LINC00917	-	long intergenic non-protein coding RNA 917	ncRNA	0.026316	0.417323	
chunk0155_437_1	chr5	100859227	100859726	+	0	NA	intron (NM_005668, intron 3 of 4)	intron (NM_005668, intron 3 of 4)	-42911	NR_031686	100302288		NR_031686	ENSG00000221263	MIR548P	MIRN548P|hsa-mir-548p	microRNA 548p	ncRNA	0.000000	0.284000	
chunk0077_236_1	chr16	80654109	80654511	+	0	NA	intron (NM_152342, intron 2 of 6)	intron (NM_152342, intron 2 of 6)	-81502	NR_104666	101928276	Hs.149769	NR_104665	ENSG00000260737	LINC01227	-	long intergenic non-protein coding RNA 1227	ncRNA	0.017413	0.498759	
chunk0069_257_1	chr15	64524784	64525019	+	0	NA	intron (NM_015042, intron 1 of 8)	L1MB7|LINE|L1	25481	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.004255	0.355932	
chunk0116_301_1	chr21	40453358	40454032	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	70611	NR_038899	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.005935	0.416296	405(AAGTACAAACAGTCCC,-,0.00),406(AGTACAAACAGTCCCT,+,0.00)
chunk0127_252_1	chr3	97131335	97132061	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	-307895	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.002755	0.324622	40(AGATCAAGGTGTACTT,+,0.00),367(AGGATCAGAAAGTTCC,-,0.00),368(GGATCAGAAAGTTCCC,+,0.00)
chunk0019_432_1	chr1	230950314	230950963	+	0	NA	intron (NM_024525, intron 4 of 22)	intron (NM_024525, intron 4 of 22)	28234	NM_024525	79573	Hs.424788	NM_024525	ENSG00000143643	TTC13	-	tetratricopeptide repeat domain 13	protein-coding	0.004622	0.327692	
chunk0185_86_1	chr7	125400877	125401121	+	0	NA	Intergenic	Intergenic	-136708	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.004098	0.428571	
chunk0133_373_1	chr3	173781231	173781482	+	0	NA	intron (NM_014932, intron 3 of 6)	L1ME4b|LINE|L1	139440	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.000000	0.277778	
chunk0113_264_1	chr20	56380291	56380835	+	0	NA	intron (NM_003600, intron 6 of 8)	L1MC3|LINE|L1	11732	NM_198436	6790	Hs.250822	NM_003600	ENSG00000087586	AURKA	AIK|ARK1|AURA|BTAK|PPP1R47|STK15|STK6|STK7	aurora kinase A	protein-coding	0.007353	0.370642	
chunk0012_368_1	chr1	162935922	162936491	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	-67391	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.007030	0.366667	
chunk0153_94_1	chr5	68240268	68240553	+	0	NA	intron (NM_181523, intron 2 of 15)	intron (NM_181523, intron 2 of 15)	24654	NM_181523	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.000000	0.384615	
chunk0128_425_1	chr3	114893187	114893818	+	0	NA	intron (NM_001164343, intron 3 of 11)	intron (NM_001164343, intron 3 of 11)	7120	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.000000	0.381329	323(AGGTACACAATGTGCC,-,0.00),324(GGTACACAATGTGCCT,+,0.00)
chunk0119_99_1	chr22	41998031	41998506	+	0	NA	promoter-TSS (NM_152613)	promoter-TSS (NM_152613)	-457	NM_152613	164684	Hs.655541	NM_152613	ENSG00000183066	WBP2NL	GRAMD7|PAWP	WBP2 N-terminal like	protein-coding	0.010526	0.447479	
chunk0030_399_1	chr10	119914354	119914730	+	0	NA	intron (NM_007190, intron 6 of 18)	intron (NM_007190, intron 6 of 18)	21969	NM_007190	11196	Hs.435004	NM_007190	ENSG00000107651	SEC23IP	MSTP053|P125|P125A	SEC23 interacting protein	protein-coding	0.007979	0.397878	144(AGGAACAGAGAGAGCC,-,0.00),203(AGGGACAAATTGTTCC,-,0.00),204(GGGACAAATTGTTCCT,+,0.00)
chunk0090_147_1	chr18	72261777	72262229	+	0	NA	Intergenic	MLT2D|LTR|ERVL	282485	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.002212	0.373068	
chunk0175_81_1	chr7	2354130	2354958	+	0	NA	promoter-TSS (NM_003751)	promoter-TSS (NM_003751)	-295	NM_003751	8662	Hs.371001	NM_003751	ENSG00000106263	EIF3B	EIF3-ETA|EIF3-P110|EIF3-P116|EIF3S9|PRT1	eukaryotic translation initiation factor 3 subunit B	protein-coding	0.074879	0.576598	
chunk0206_146_1	chr9	121363482	121363968	+	0	NA	intron (NM_001270527, intron 1 of 5)	MER58B|DNA|hAT-Charlie	6579	NM_001270526	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.002058	0.349076	249(GTTACACGCTGTTCCT,+,0.00)
chunk0071_422_1	chr15	89772855	89773441	+	0	NA	Intergenic	L1ME3G|LINE|L1	-3210	NM_001039958	145873	Hs.37311	NM_001039958	ENSG00000188095	MESP2	SCDO2|bHLHc6	mesoderm posterior bHLH transcription factor 2	protein-coding	0.005119	0.379898	
chunk0003_134_1	chr1	32746329	32746591	+	0	NA	intron (NM_020888, intron 1 of 6)	intron (NM_020888, intron 1 of 6)	4549	NM_020888	57648	Hs.591502	NM_020888	ENSG00000162522	KIAA1522	-	KIAA1522	protein-coding	0.007634	0.509506	
chunk0068_318_1	chr15	57451755	57451994	+	0	NA	intron (NM_001252335, intron 6 of 19)	intron (NM_001252335, intron 6 of 19)	75369	NM_001252335	84952	Hs.148989	NM_032866	ENSG00000128849	CGNL1	JACOP|PCING	cingulin like 1	protein-coding	0.000000	0.316667	
chunk0203_216_1	chr9	86692822	86693778	+	0	NA	Intergenic	AluSq2|SINE|Alu	253889	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.011506	0.367816	
chunk0140_356_1	chr4	74123137	74123546	+	0	NA	Intergenic	Intergenic	-24061	NM_002089	2920	Hs.75765	NM_002089	ENSG00000081041	CXCL2	CINC-2a|GRO2|GROb|MGSA-b|MIP-2a|MIP2|MIP2A|SCYB2	C-X-C motif chemokine ligand 2	protein-coding	0.002445	0.402439	132(CAGCACAACAAGTCCC,-,0.00),133(AGCACAACAAGTCCCC,+,0.00)
chunk0168_202_1	chr6	85593638	85593837	+	0	NA	5' UTR (NM_153816, exon 1 of 29)	5' UTR (NM_153816, exon 1 of 29)	419	NM_153816	57231	Hs.485871	NM_020468	ENSG00000135317	SNX14	RGS-PX2|SCAR20	sorting nexin 14	protein-coding	0.110553	0.695000	
chunk0043_34_1	chr12	13193155	13193640	+	0	NA	Intergenic	Intergenic	-3271	NM_001423	2012	Hs.719042	NM_001423	ENSG00000134531	EMP1	CL-20|EMP-1|TMP	epithelial membrane protein 1	protein-coding	0.012371	0.382716	
chunk0094_129_1	chr2	4701737	4702040	+	0	NA	Intergenic	HAL1ME|LINE|L1	-45666	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009901	0.338816	
chunk0015_219_1	chr1	187586997	187587313	+	0	NA	Intergenic	MIR|SINE|MIR	143527	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.009494	0.365931	
chunk0202_25_1	chr9	70514840	70515066	+	0	NA	Intergenic	Intergenic	-100296	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.004425	0.436123	
chunk0186_356_1	chr7	143816692	143817060	+	0	NA	intron (NR_015421, intron 2 of 2)	intron (NR_015421, intron 2 of 2)	6886	NR_110549	653691	Hs.632030	NR_110549		TCAF2P1	FAM115D|FAM139B|TCAF2BP	TRPM8 channel associated factor 2 pseudogene 1	pseudo	0.010870	0.409214	
chunk0143_91_1	chr4	108353020	108353368	+	0	NA	Intergenic	Intergenic	181074	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.005747	0.395415	
chunk0157_405_1	chr5	124352931	124353600	+	0	NA	intron (NR_125774, intron 4 of 5)	MIRb|SINE|MIR	85255	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.008969	0.386567	
chunk0039_113_1	chr11	97739757	97740328	+	0	NA	Intergenic	L1M4b|LINE|L1	-1233165	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.007005	0.367133	
chunk0017_1_1	chr1	204286699	204287401	+	0	NA	intron (NM_014935, intron 1 of 22)	intron (NM_014935, intron 1 of 22)	72879	NM_014935	22874	Hs.253146	NM_014935	ENSG00000143850	PLEKHA6	PEPP-3|PEPP3	pleckstrin homology domain containing A6	protein-coding	0.012821	0.513514	351(GGGAGCACCCTGTTCC,-,0.00),352(GGAGCACCCTGTTCCC,+,0.00)
chunk0208_295_1	chrX	22367217	22367778	+	0	NA	intron (NR_073010, intron 5 of 5)	intron (NR_073010, intron 5 of 5)	94584	NM_152577	158506	Hs.132485	NM_152577	ENSG00000175809	CBLL2	CT138|HAKAIL|ZNF645	Cbl proto-oncogene like 2	protein-coding	0.003565	0.373665	
chunk0084_270_1	chr17	79629464	79630022	+	0	NA	Intergenic	L1ME4a|LINE|L1	77506	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.014337	0.398927	
chunk0159_17_1	chr5	136320890	136321317	+	0	NA	intron (NM_020389, intron 2 of 11)	MIRb|SINE|MIR	-19247	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.002342	0.387850	
chunk0052_356_1	chr12	127162004	127162203	+	0	NA	Intergenic	Intergenic	-101706	NR_104646	101927592	Hs.385663	NR_104646	ENSG00000249345	LINC02405	-	long intergenic non-protein coding RNA 2405	ncRNA	0.005025	0.360000	
chunk0115_222_1	chr21	27061716	27062070	+	0	NA	Intergenic	Intergenic	-94773	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.000000	0.405634	
chunk0132_236_1	chr3	158647756	158648065	+	0	NA	intron (NM_001308164, intron 4 of 18)	L1MEh|LINE|L1	3382	NM_001308166	85476	Hs.518355	NM_024996	ENSG00000168827	GFM1	COXPD1|EFG|EFG1|EFGM|EGF1|GFM|hEFG1|mtEF-G1	G elongation factor mitochondrial 1	protein-coding	0.000000	0.351613	
chunk0048_301_1	chr12	82804850	82805554	+	0	NA	intron (NM_152588, intron 1 of 11)	LTR10C|LTR|ERV1	118047	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004261	0.385816	456(AAGAACATAAAGTACT,-,0.00),457(AGAACATAAAGTACTT,+,0.00)
chunk0125_288_1	chr3	69833683	69833932	+	0	NA	intron (NM_006722, intron 1 of 9)	intron (NM_006722, intron 1 of 9)	-32417	NM_198177	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.000000	0.392000	
chunk0032_76_1	chr11	2695310	2695776	+	0	NA	non-coding (NR_002728, exon 1 of 1)	non-coding (NR_002728, exon 1 of 1)	4455	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.015021	0.492505	
chunk0058_414_1	chr13	112594528	112594931	+	0	NA	Intergenic	L1MDa|LINE|L1	-6544	NM_006322	10426	Hs.224152	NM_006322	ENSG00000126216	TUBGCP3	104p|ALP6|GCP3|Grip104|SPBC98|Spc98|Spc98p	tubulin gamma complex associated protein 3	protein-coding	0.002481	0.309406	
chunk0096_83_1	chr2	27966276	27967098	+	0	NA	intron (NM_199191, intron 3 of 11)	intron (NM_199191, intron 3 of 11)	-29680	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.003650	0.383961	
chunk0003_57_1	chr1	30964257	30964769	+	0	NA	intron (NM_001020658, intron 14 of 21)	intron (NM_001020658, intron 14 of 21)	3724	NR_003066	692200		NR_003066		SNORD103C	HBII-251|SNORD85	small nucleolar RNA, C/D box 103C	snoRNA	0.005859	0.401559	
chunk0059_227_1	chr14	34225988	34226628	+	0	NA	Intergenic	HAL1b|LINE|L1	235954	NM_138288	171546	Hs.740577	NM_138288	ENSG00000165389	SPTSSA	C14orf147|SSSPTA	serine palmitoyltransferase small subunit A	protein-coding	0.001563	0.343214	
chunk0109_212_1	chr20	5642330	5642922	+	0	NA	Intergenic	Intergenic	-31600	NM_019593	56261	Hs.636359	NM_019593	ENSG00000125772	GPCPD1	EDI3|GDE5|GDPD6|PREI4	glycerophosphocholine phosphodiesterase 1	protein-coding	0.003378	0.396290	
chunk0201_211_1	chr9	37201974	37202696	+	0	NA	intron (NM_032226, intron 2 of 8)	L4_C_Mam|LINE|RTE-X	81737	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.000000	0.352697	
chunk0057_18_1	chr13	95576337	95577222	+	0	NA	intron (NM_006984, intron 3 of 4)	L2b|LINE|L2	24086	NM_006984	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.011299	0.393905	
chunk0081_122_1	chr17	40124283	40124636	+	0	NA	intron (NM_001012241, intron 2 of 9)	intron (NM_001012241, intron 2 of 9)	1922	NM_001012241	339287	Hs.532786	NM_001012241	ENSG00000188895	MSL1	MSL-1	MSL complex subunit 1	protein-coding	0.019830	0.508475	
chunk0210_405_1	chrX	100102820	100103447	+	0	NA	Intergenic	Intergenic	-163290	NR_024608	442459	Hs.706599	NM_001127438		XRCC6P5	-	X-ray repair cross complementing 6 pseudogene 5	pseudo	0.003190	0.332803	
chunk0128_97_1	chr3	105867948	105868469	+	0	NA	intron (NM_170662, intron 1 of 18)	intron (NM_170662, intron 1 of 18)	835	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.038388	0.498084	469(GGGGACAAAGTGTCCC,-,0.00),470(GGGACAAAGTGTCCCT,+,0.00)
chunk0181_119_1	chr7	80769934	80770451	+	0	NA	intron (NM_006379, intron 12 of 17)	intron (NM_006379, intron 12 of 17)	123539	NM_001289908	948	Hs.120949	NM_000072	ENSG00000135218	CD36	BDPLT10|CHDS7|FAT|GP3B|GP4|GPIV|PASIV|SCARB3	CD36 molecule	protein-coding	0.003868	0.364865	
chunk0115_340_1	chr21	29175360	29175881	+	0	NA	3' UTR (NM_001286634, exon 8 of 8)	3' UTR (NM_001286634, exon 8 of 8)	-17874	NR_027072	193629	Hs.720711	NM_138968	ENSG00000215533	LINC00189	C21orf109|NCRNA00189	long intergenic non-protein coding RNA 189	ncRNA	0.001919	0.342912	
chunk0144_284_1	chr4	138211095	138211294	+	0	NA	intron (NM_014331, intron 6 of 11)	L1PA16|LINE|L1	31155	NM_014331	23657	Hs.390594	NM_014331	ENSG00000151012	SLC7A11	CCBR1|xCT	solute carrier family 7 member 11	protein-coding	0.010050	0.420000	
chunk0009_229_1	chr1	106686010	106686209	+	0	NA	Intergenic	L1M5|LINE|L1	-370536	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.000000	0.270000	
chunk0171_169_1	chr6	124992998	124993210	+	0	NA	intron (NM_152553, intron 1 of 8)	intron (NM_152553, intron 1 of 8)	9740	NR_104440	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.004717	0.314554	
chunk0101_25_1	chr2	121634515	121635211	+	0	NA	intron (NM_015282, intron 1 of 38)	intron (NM_015282, intron 1 of 38)	14613	NM_001142274	23332	Hs.469840	NM_015282	ENSG00000074054	CLASP1	MAST1	cytoplasmic linker associated protein 1	protein-coding	0.008621	0.424677	
chunk0172_327_1	chr6	138400977	138401651	+	0	NA	Intergenic	L1MB8|LINE|L1	-2885	NM_014320	23593	Hs.486589	NM_014320	ENSG00000051620	HEBP2	C6ORF34B|C6orf34|PP23|SOUL	heme binding protein 2	protein-coding	0.005935	0.386667	
chunk0117_452_1	chr21	46621732	46622471	+	0	NA	Intergenic	Intergenic	-13494	NM_001242864	3275	Hs.154163	NM_001535	ENSG00000160310	PRMT2	HRMT1L1	protein arginine methyltransferase 2	protein-coding	0.009472	0.472973	
chunk0029_232_1	chr10	102505786	102506019	+	0	NA	intron (NM_016169, intron 1 of 11)	intron (NM_016169, intron 1 of 11)	1940	NM_001178133	51684	Hs.404089	NM_016169	ENSG00000107882	SUFU	JBTS32|PRO1280|SUFUH|SUFUXL	SUFU negative regulator of hedgehog signaling	protein-coding	0.012876	0.504274	
chunk0059_44_1	chr14	29965088	29965417	+	0	NA	Intergenic	Intergenic	-37559	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.281818	
chunk0149_226_1	chr5	22625851	22626245	+	0	NA	intron (NM_004061, intron 1 of 14)	L1PA15|LINE|L1	227574	NM_004061	1010	Hs.113684	NM_004061	ENSG00000154162	CDH12	CDHB	cadherin 12	protein-coding	0.007614	0.582278	
chunk0169_78_1	chr6	99416634	99417237	+	0	NA	intron (NM_032870, intron 1 of 11)	intron (NM_032870, intron 1 of 11)	-7936	NR_125843	101927365	Hs.535847	NR_125843		LOC101927365	-	uncharacterized LOC101927365	ncRNA	0.001658	0.289735	211(GAGAACAGTTTGTTCC,-,0.00),212(AGAACAGTTTGTTCCT,+,0.00)
chunk0148_53_1	chr5	1630112	1630312	+	0	NA	intron (NR_003713, intron 2 of 3)	intron (NR_003713, intron 2 of 3)	3793	NR_003713	728613	Hs.720393	NR_003713		LOC728613	-	programmed cell death 6 pseudogene	pseudo	0.015000	0.492537	
chunk0188_378_1	chr8	18314493	18314824	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-76587	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.012085	0.430723	
chunk0127_384_1	chr3	102125256	102125956	+	0	NA	Intergenic	THE1-int|LTR|ERVL-MaLR	184747	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.007143	0.363766	
chunk0118_183_1	chr22	31179451	31179846	+	0	NA	intron (NR_024212, intron 1 of 5)	intron (NR_024212, intron 1 of 5)	19496	NR_024210	91445	Hs.517553	NM_152267	ENSG00000138942	RNF185	-	ring finger protein 185	protein-coding	0.005063	0.532828	
chunk0198_100_1	chr8	130692355	130692604	+	0	NA	Intergenic	L1P4d|LINE|L1	-248819	NM_001247996	50807	Hs.655552	NM_018482	ENSG00000153317	ASAP1	AMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14P	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	protein-coding	0.004016	0.476000	
chunk0031_114_1	chr10	124596633	124596867	+	0	NA	intron (NM_022126, intron 6 of 6)	intron (NM_022126, intron 6 of 6)	-107278	NR_120630	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.008547	0.557447	
chunk0068_131_1	chr15	52679230	52679630	+	0	NA	promoter-TSS (NR_104457)	promoter-TSS (NR_104457)	-796	NR_104457	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.100000	0.710723	
chunk0102_211_1	chr2	148430761	148431885	+	0	NA	intron (NM_018328, intron 5 of 14)	Tigger13a|DNA|TcMar-Tigger	-213668	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.003559	0.345778	240(GAGTACAGTCTGTCTT,-,0.00),241(AGTACAGTCTGTCTTT,+,0.00)
chunk0010_378_1	chr1	119216310	119216617	+	0	NA	intron (NR_125975, intron 4 of 6)	L1ME3|LINE|L1	-75791	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.000000	0.373377	
chunk0133_81_1	chr3	167289474	167289676	+	0	NA	intron (NM_001199201, intron 18 of 21)	L1PA7|LINE|L1	90708	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.024752	0.566502	
chunk0190_116_1	chr8	30491487	30492033	+	0	NA	intron (NM_006867, intron 4 of 9)	intron (NM_006867, intron 4 of 9)	-106359	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.014652	0.431444	
chunk0080_183_1	chr17	28903068	28903393	+	0	NA	promoter-TSS (NM_144683)	promoter-TSS (NM_144683)	-159	NM_144683	147015	Hs.631760	NM_144683	ENSG00000167536	DHRS13	SDR7C5	dehydrogenase/reductase 13	protein-coding	0.064615	0.641104	
chunk0124_107_1	chr3	53841210	53841657	+	0	NA	intron (NM_018397, intron 1 of 8)	intron (NM_018397, intron 1 of 8)	4960	NM_018397	55349	Hs.126688	NM_018397	ENSG00000016391	CHDH	-	choline dehydrogenase	protein-coding	0.011186	0.540179	
chunk0187_335_1	chr7	156747664	156748112	+	0	NA	intron (NM_022458, intron 9 of 16)	intron (NM_022458, intron 9 of 16)	104087	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.002232	0.318486	
chunk0092_146_1	chr19	28490626	28491012	+	0	NA	intron (NR_110759, intron 5 of 9)	intron (NR_110759, intron 5 of 9)	236875	NR_110759	100420587	Hs.569956	NR_110759	ENSG00000283403	LOC100420587	-	SHC binding and spindle associated 1 pseudogene	pseudo	0.015544	0.472868	
chunk0060_327_1	chr14	51439868	51440384	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-48995	NM_001042481	122786	Hs.434914	NM_152330	ENSG00000139926	FRMD6	C14orf31|EX1|Willin|c14_5320	FERM domain containing 6	protein-coding	0.007752	0.334623	
chunk0175_373_1	chr6	167965095	167965377	+	0	NA	TTS (NM_001040000)	TTS (NM_001040000)	11703	NM_001129895	100128124	Hs.448059	NM_001129895		HGC6.3	-	uncharacterized LOC100128124	protein-coding	0.000000	0.392226	
chunk0053_125_1	chr13	29772535	29773037	+	0	NA	intron (NM_007106, intron 2 of 4)	intron (NM_007106, intron 2 of 4)	77897	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.000000	0.292247	
chunk0067_77_1	chr15	41417638	41417837	+	0	NA	intron (NM_015138, intron 1 of 17)	CpG	633	NM_015138	23168	Hs.511096	NM_015138	ENSG00000137815	RTF1	GTL7|KIAA0252	RTF1 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.050251	0.580000	
chunk0179_256_1	chr7	48637432	48638065	+	0	NA	intron (NM_152701, intron 59 of 61)	intron (NM_152701, intron 59 of 61)	-286813	NR_003595									0.001580	0.395899	
chunk0080_225_1	chr17	29766726	29766925	+	0	NA	intron (NM_001282129, intron 3 of 15)	intron (NM_001282129, intron 3 of 15)	-5393	NM_001282131	85464	Hs.654754	NM_033389	ENSG00000141298	SSH2	SSH-2|SSH-2L	slingshot protein phosphatase 2	protein-coding	0.005025	0.330000	
chunk0167_237_1	chr6	67551736	67551935	+	0	NA	Intergenic	L1M1|LINE|L1	-503516	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.000000	0.300000	
chunk0140_198_1	chr4	70313416	70314016	+	0	NA	Intergenic	Intergenic	-21238	NM_033122	85438	Hs.120316	NM_033122	ENSG00000145309	CABS1	C4orf35|CLPH|NYD-SP26	calcium binding protein, spermatid associated 1	protein-coding	0.001667	0.344426	409(AGGTTCACTCTGTACC,-,0.00),410(GGTTCACTCTGTACCT,+,0.00)
chunk0025_169_1	chr10	52797202	52797789	+	0	NA	Intergenic	L1PB1|LINE|L1	-25795	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.005111	0.404762	
chunk0146_394_1	chr4	168699332	168699733	+	0	NA	intron (NM_016081, intron 8 of 20)	intron (NM_016081, intron 8 of 20)	67915	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.002494	0.390547	
chunk0049_16_1	chr12	89376591	89377409	+	0	NA	Intergenic	Intergenic	-24141	NM_022652	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.007335	0.444444	
chunk0142_357_1	chr4	101885510	101885952	+	0	NA	intron (NM_017935, intron 5 of 16)	Tigger3a|DNA|TcMar-Tigger	71905	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.004525	0.383747	
chunk0198_425_1	chr8	143117313	143117980	+	0	NA	Intergenic	L1MEf|LINE|L1	42394	NM_002347	4062	Hs.159590	NM_002347	ENSG00000176956	LY6H	NMLY6	lymphocyte antigen 6 family member H	protein-coding	0.008996	0.488024	328(GAGGACATTGTGTGCA,-,0.00),329(AGGACATTGTGTGCAT,+,0.00)
chunk0150_258_1	chr5	36373344	36373961	+	0	NA	Intergenic	L2c|LINE|L2	-71743	NM_001161429	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.016207	0.438511	
chunk0034_62_1	chr11	27145665	27146273	+	0	NA	intron (NR_125766, intron 3 of 4)	L1ME1|LINE|L1	72799	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.003289	0.328407	
chunk0020_147_1	chr1	233735883	233736338	+	0	NA	Intergenic	Intergenic	111958	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.010989	0.379386	
chunk0069_130_1	chr15	62036372	62036947	+	0	NA	intron (NM_017684, intron 3 of 82)	intron (NM_017684, intron 3 of 82)	23806	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.006957	0.352431	331(AGGGACTGTCTGTTCC,-,0.00),332(GGGACTGTCTGTTCCC,+,0.00)
chunk0122_117_1	chr3	31247796	31248239	+	0	NA	Intergenic	Intergenic	-86230	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.004515	0.407658	
chunk0211_345_1	chrX	125176234	125176488	+	0	NA	Intergenic	Intergenic	-143759	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.003937	0.352941	105(CAGAACTCTGTGTTCC,-,0.00),106(AGAACTCTGTGTTCCC,+,0.00)
chunk0197_252_1	chr8	123415297	123415507	+	0	NA	Intergenic	Intergenic	-1323	NM_001283027	55093	Hs.18029	NM_018024	ENSG00000156795	WDYHV1	C8orf32	WDYHV motif containing 1	protein-coding	0.000000	0.383886	
chunk0093_29_1	chr19	39187277	39187790	+	0	NA	Intergenic	Intergenic	-9431	NM_001001414	342897	Hs.726934	NM_001001414	ENSG00000188505	NCCRP1	FBXO50|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding	0.015595	0.624514	
chunk0030_338_1	chr10	118410326	118410527	+	0	NA	Intergenic	Intergenic	53318	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.024876	0.549505	45(GGGCACATGGTGTGTC,-,0.00)
chunk0161_423_1	chr5	178331443	178332198	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	-98998	NM_001278346	85007	Hs.248746	NM_153373	ENSG00000175309	PHYKPL	AGXT2L2|PHLU	5-phosphohydroxy-L-lysine phospho-lyase	protein-coding	0.025166	0.603175	364(GAGAACAAAGAGTTCC,-,0.00),365(AGAACAAAGAGTTCCG,+,0.00)
chunk0137_228_1	chr4	20060534	20061114	+	0	NA	Intergenic	Intergenic	-191081	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.005172	0.388985	
chunk0106_373_1	chr2	207258442	207259025	+	0	NA	Intergenic	Intergenic	-4417	NR_110283	101927865	Hs.574609	NR_110283		MYOSLID-AS1	-	MYOSLID antisense RNA 1	ncRNA	0.005146	0.505137	
chunk0085_208_1	chr18	6687763	6688085	+	0	NA	Intergenic	Intergenic	-146509	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.000000	0.343653	
chunk0073_295_1	chr16	14082106	14082541	+	0	NA	intron (NM_001308142, intron 2 of 16)	L1MA8|LINE|L1	11009	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.009195	0.366972	178(TAGAAGAGACTGTCCT,-,0.00),179(AGAAGAGACTGTCCTT,+,0.00)
chunk0061_20_1	chr14	55739782	55740345	+	0	NA	Intergenic	Intergenic	-26182	NR_004844	645683	Hs.663461	NR_004844	ENSG00000177350	RPL13AP3	RPL13A_11_1370	ribosomal protein L13a pseudogene 3	pseudo	0.005329	0.505319	413(GAGTACAAAATGTTCC,-,0.00),414(AGTACAAAATGTTCCC,+,0.00)
chunk0175_362_1	chr6	167826282	167826614	+	0	NA	promoter-TSS (NM_001040000)	promoter-TSS (NM_001040000)	348	NR_027906	653483	Hs.520556	NM_001042508	ENSG00000198221	AFDN-DT	AFDN-AS1|C6orf124|HGC6.4|MLLT4-AS1|dJ431P23.3	AFDN divergent transcript	ncRNA	0.108434	0.684685	
chunk0185_312_1	chr7	131363463	131364200	+	0	NA	intron (NM_013255, intron 1 of 17)	L2a|LINE|L2	35995	NM_013255	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.002714	0.341463	
chunk0008_384_1	chr1	97145535	97145952	+	0	NA	intron (NM_000110, intron 20 of 22)	intron (NM_000110, intron 20 of 22)	49820	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.007194	0.392344	
chunk0178_42_1	chr7	29571758	29572217	+	0	NA	Intergenic	Intergenic	8176	NM_175887	222171	Hs.91109	NM_175887	ENSG00000176532	PRR15	-	proline rich 15	protein-coding	0.008715	0.373913	
chunk0154_59_1	chr5	77301518	77301792	+	0	NA	intron (NM_001029853, intron 1 of 20)	intron (NM_001029853, intron 1 of 20)	90774	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.007299	0.418182	
chunk0053_400_1	chr13	36357657	36358268	+	0	NA	intron (NR_045181, intron 1 of 4)	intron (NR_045181, intron 1 of 4)	-11165	NM_001142295	23111	Hs.440414	NM_015087	ENSG00000133104	SPART	SPG20|TAHCCP1	spartin	protein-coding	0.008183	0.352941	318(CAGGACTCTCAGTTCT,-,0.00),319(AGGACTCTCAGTTCTT,+,0.00)
chunk0085_329_1	chr18	8475099	8475343	+	0	NA	Intergenic	Intergenic	-108187	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.008197	0.477551	
chunk0211_267_1	chrX	121465101	121465596	+	0	NA	Intergenic	L1MA2|LINE|L1	94376	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.002020	0.316532	
chunk0199_101_1	chr9	2954277	2954814	+	0	NA	Intergenic	HAL1b|LINE|L1	-110415	NM_014878	9933	Hs.493309	NM_014878	ENSG00000080608	PUM3	HA-8|HLA-HA8|KIAA0020|PEN|PUF-A|PUF6|XTP5	pumilio RNA binding family member 3	protein-coding	0.001862	0.299257	
chunk0130_150_1	chr3	132303980	132304291	+	0	NA	Intergenic	Harlequin-int|LTR|ERV1	-13232	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.000000	0.368590	
chunk0112_345_1	chr20	45131219	45131900	+	0	NA	Intergenic	L2b|LINE|L2	-7094	NM_080869	128488	Hs.352180	NM_080869	ENSG00000168703	WFDC12	C20orf122|SWAM2|WAP2|dJ211D12.4	WAP four-disulfide core domain 12	protein-coding	0.005874	0.379765	314(TGGGACTCTCTGTCCT,-,0.00),315(GGGACTCTCTGTCCTA,+,0.00)
chunk0095_419_1	chr2	24667605	24667838	+	0	NA	intron (NM_147223, intron 4 of 21)	L2a|LINE|L2	83244	NM_147223	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.004292	0.397436	121(AGGCACACTCTGCCCC,-,0.00),122(GGCACACTCTGCCCCT,+,0.00)
chunk0209_418_1	chrX	57046168	57046494	+	0	NA	Intergenic	L1PA7|LINE|L1	-50776	NM_001010862	169981	Hs.522672	NM_001010862	ENSG00000204271	SPIN3	SPIN-3|TDRD27|bA445O16.1	spindlin family member 3	protein-coding	0.006135	0.376147	154(CAGAACAACCTGCTCC,-,0.00),155(AGAACAACCTGCTCCT,+,0.00),238(AAAGACACAATGTACC,-,0.00)
chunk0064_323_1	chr14	96029228	96029681	+	0	NA	Intergenic	Intergenic	-9870	NM_001282464	56967	Hs.6434	NM_020215	ENSG00000227051	C14orf132	C14orf88	chromosome 14 open reading frame 132	protein-coding	0.006623	0.436123	268(AGGCACACAGTGTTCA,-,0.00),269(GGCACACAGTGTTCAG,+,0.00)
chunk0212_108_1	chrY	17107606	17108206	+	0	NA	Intergenic	Intergenic	-393052	NR_028084	100302526	Hs.434364	NR_028084		FAM41AY2	-	family with sequence similarity 41 member A, Y-linked 2	ncRNA	0.005000	0.326123	
chunk0136_420_1	chr3	197468894	197469456	+	0	NA	Intergenic	Intergenic	86812	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.008897	0.483126	253(AGAGACAGCGTGTCCT,-,0.00),254(GAGACAGCGTGTCCTT,+,0.00)
chunk0077_141_1	chr16	78692802	78693212	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	593594	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.004878	0.362530	
chunk0195_422_1	chr8	100776636	100777165	+	0	NA	Intergenic	Intergenic	-54813	NM_002568	26986	Hs.387804	NM_002568	ENSG00000070756	PABPC1	PAB1|PABP|PABP1|PABPC2|PABPL1	poly(A) binding protein cytoplasmic 1	protein-coding	0.017013	0.460377	
chunk0157_120_1	chr5	117045896	117046156	+	0	NA	Intergenic	Intergenic	-283817	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.011538	0.482759	
chunk0097_193_1	chr2	50597573	50597865	+	0	NA	intron (NM_001135659, intron 9 of 23)	L2b|LINE|L2	98543	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.006849	0.423208	
chunk0147_51_1	chr4	172453811	172454108	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	234958	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.006734	0.369128	
chunk0169_424_1	chr6	108653916	108654479	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	93331	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.007105	0.455674	
chunk0135_324_1	chr3	190070844	190071474	+	0	NA	intron (NM_001134418, intron 1 of 14)	intron (NM_001134418, intron 1 of 14)	-49805	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.006349	0.302694	
chunk0120_466_1	chr22	50675404	50675864	+	0	NA	intron (NM_033517, intron 2 of 21)	(CAGTGTG)n|Simple_repeat|Simple_repeat	992	NM_033517	85358	Hs.149035	NM_033517	ENSG00000251322	SHANK3	DEL22q13.3|PROSAP2|PSAP2|SCZD15|SPANK-2	SH3 and multiple ankyrin repeat domains 3	protein-coding	0.028261	0.559653	168(AGGCACAGTGTGTGCA,-,0.00),169(GGCACAGTGTGTGCAG,+,0.00),197(GTGCACAGCATGTACA,-,0.00),198(TGCACAGCATGTACAG,+,0.00),436(GTGCACAGTGTGTGCA,-,0.00),437(TGCACAGTGTGTGCAG,+,0.00)
chunk0120_103_1	chr3	4496087	4496638	+	0	NA	intron (NM_002222, intron 2 of 57)	intron (NM_002222, intron 2 of 57)	3014	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.005445	0.367754	267(AAGTACAATCTGCTCT,-,0.00),268(AGTACAATCTGCTCTT,+,0.00)
chunk0143_282_1	chr4	117203137	117203737	+	0	NA	Intergenic	L1MA2|LINE|L1	-117857	NM_152402	133022	Hs.570737	NM_152402	ENSG00000174599	TRAM1L1	-	translocation associated membrane protein 1 like 1	protein-coding	0.001667	0.361065	
chunk0084_187_1	chr17	77828852	77829375	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	54974	NR_028337	400624	Hs.514521	NM_001001685	ENSG00000204283	LINC01973	-	long intergenic non-protein coding RNA 1973	ncRNA	0.028681	0.505725	
chunk0186_139_1	chr7	138595101	138595673	+	0	NA	intron (NM_174959, intron 11 of 11)	intron (NM_174959, intron 11 of 11)	68837	NM_174959	136306	Hs.99414	NM_174959	ENSG00000157703	SVOPL	-	SVOP like	protein-coding	0.005245	0.376963	
chunk0002_137_1	chr1	16914062	16914285	+	0	NA	Intergenic	CpG	-7777	NM_014675	9696	Hs.309403	NM_014675	ENSG00000058453	CROCC	ROLT|TAX1BP2	ciliary rootlet coiled-coil, rootletin	protein-coding	0.183857	0.834821	
chunk0079_197_1	chr17	14349295	14349590	+	0	NA	TTS (NM_006041)	TTS (NM_006041)	45702	NR_026880	84815	Hs.597458	NM_032729	ENSG00000266709	MGC12916	-	uncharacterized protein MGC12916	ncRNA	0.006780	0.351351	
chunk0021_362_1	chr1	246336446	246336987	+	0	NA	intron (NM_001167740, intron 2 of 11)	MIRb|SINE|MIR	80696	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.009242	0.337638	
chunk0087_304_1	chr18	39314773	39314972	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	307303	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.010050	0.350000	
chunk0178_365_1	chr7	39649292	39649491	+	0	NA	intron (NM_005402, intron 1 of 4)	MLT1A1|LTR|ERVL-MaLR	25838	NM_005402	5898	Hs.6906	NM_005402	ENSG00000006451	RALA	RAL	RAS like proto-oncogene A	protein-coding	0.010050	0.360000	
chunk0210_120_1	chrX	72620446	72621630	+	0	NA	intron (NM_001122670, intron 18 of 30)	intron (NM_001122670, intron 18 of 30)	-47935	NM_001166420	55869	Hs.310536	NM_018486	ENSG00000147099	HDAC8	CDA07|CDLS5|HD8|HDACL1|KDAC8|MRXS6|RPD3|WTS	histone deacetylase 8	protein-coding	0.009291	0.435443	280(CTGTACATGCAGTTCC,-,0.00),281(TGTACATGCAGTTCCT,+,0.00)
chunk0109_98_1	chr20	2264668	2265445	+	0	NA	Intergenic	L1PA6|LINE|L1	-30911	NM_003245	7053	Hs.2022	NM_003245	ENSG00000125780	TGM3	TGE|UHS2	transglutaminase 3	protein-coding	0.015444	0.529563	
chunk0184_82_1	chr7	112957748	112958446	+	0	NA	intron (NR_110162, intron 4 of 5)	L2a|LINE|L2	-18220	NM_152556	154743	Hs.489734	NM_152556	ENSG00000164603	BMT2	C7orf60|SAMTOR	base methyltransferase of 25S rRNA 2 homolog	protein-coding	0.002865	0.376252	
chunk0067_111_1	chr15	42458034	42458431	+	0	NA	promoter-TSS (NM_022473)	promoter-TSS (NM_022473)	-665	NM_022473	64397	Hs.511143	NM_022473	ENSG00000103994	ZNF106	SH3BP3|ZFP106|ZNF474	zinc finger protein 106	protein-coding	0.007557	0.389447	
chunk0112_276_1	chr20	43460154	43460604	+	0	NA	intron (NM_006275, intron 4 of 5)	intron (NM_006275, intron 4 of 5)	2515	NM_006275	6431	Hs.684950	NM_006275	ENSG00000124193	SRSF6	B52|HEL-S-91|SFRS6|SRP55	serine and arginine rich splicing factor 6	protein-coding	0.028889	0.394678	
chunk0206_231_1	chr9	123549102	123549301	+	0	NA	intron (NM_024820, intron 13 of 20)	intron (NM_024820, intron 13 of 20)	-63579	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.010050	0.535000	
chunk0052_139_1	chr13	23739748	23739988	+	0	NA	intron (NM_005932, intron 18 of 18)	L2b|LINE|L2	-149021	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.004167	0.423237	
chunk0207_360_1	chr9	135326360	135326593	+	0	NA	Intergenic	Intergenic	-16773	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.025751	0.649573	
chunk0049_300_1	chr12	94305282	94305695	+	0	NA	non-coding (NR_037687, exon 12 of 12)	non-coding (NR_037687, exon 12 of 12)	42967	NR_037687	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.009685	0.437198	
chunk0188_315_1	chr8	17255722	17255921	+	0	NA	intron (NM_001145152, intron 1 of 10)	L1MA4|LINE|L1	8929	NM_152415	137492	Hs.343873	NM_152415	ENSG00000155975	VPS37A	HCRP1|PQBP2|SPG53	VPS37A subunit of ESCRT-I	protein-coding	0.010050	0.355000	
chunk0026_25_1	chr10	60662602	60663072	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	70689	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.010638	0.348195	
chunk0114_262_1	chr21	16175312	16175684	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	-18881	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002688	0.369973	
chunk0022_146_1	chr10	12274012	12274375	+	0	NA	Intergenic	Intergenic	-75350	NM_020397	57118	Hs.600547	NM_020397	ENSG00000183049	CAMK1D	CKLiK|CaM-K1|CaMKID	calcium/calmodulin dependent protein kinase ID	protein-coding	0.008264	0.409341	
chunk0025_387_1	chr10	59315111	59315436	+	0	NA	intron (NM_001001971, intron 4 of 11)	L1ME4a|LINE|L1	47321	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.003077	0.300613	
chunk0113_333_1	chr20	58651000	58651487	+	0	NA	promoter-TSS (NM_001134772)	promoter-TSS (NM_001134772)	-10	NM_001001433	8675	Hs.307913	NM_003763	ENSG00000124222	STX16	SYN16	syntaxin 16	protein-coding	0.067762	0.702869	
chunk0065_372_1	chr14	104030889	104031369	+	0	NA	exon (NM_153046, exon 29 of 36)	exon (NM_153046, exon 29 of 36)	-54557	NM_001080464	374569	Hs.146239	NM_001080464	ENSG00000166183	ASPG	C14orf76|GPA/WT|LYSOLP	asparaginase	protein-coding	0.006250	0.347193	
chunk0194_107_1	chr8	83570249	83570566	+	0	NA	Intergenic	L2a|LINE|L2	166649	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.000000	0.402516	
chunk0007_425_1	chr1	86536952	86537411	+	0	NA	Intergenic	L1MC1|LINE|L1	-9895	NM_012128	22802	Hs.567422	NM_012128	ENSG00000016602	CLCA4	CaCC|CaCC2	chloride channel accessory 4	protein-coding	0.006536	0.450000	165(AAGAACAGAGTGCTCT,-,0.00),166(AGAACAGAGTGCTCTG,+,0.00)
chunk0004_132_1	chr1	44775434	44775633	+	0	NA	promoter-TSS (NM_001012)	promoter-TSS (NM_001012)	-41	NM_001012	6202	Hs.512675	NM_001012	ENSG00000142937	RPS8	S8	ribosomal protein S8	protein-coding	0.105528	0.590000	
chunk0132_141_1	chr3	156374237	156374695	+	0	NA	intron (NM_001308222, intron 1 of 12)	intron (NM_001308222, intron 1 of 12)	72470	NR_046618	100874084	Hs.131282	NR_046618	ENSG00000242370	KCNAB1-AS1	-	KCNAB1 antisense RNA 1	ncRNA	0.006550	0.409586	
chunk0183_396_1	chr7	110233443	110234052	+	0	NA	Intergenic	Intergenic	-273534	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.003284	0.349180	238(CTGAACTGCTTGTCCT,-,0.00),239(TGAACTGCTTGTCCTT,+,0.00)
chunk0140_139_1	chr4	69214671	69215233	+	0	NA	promoter-TSS (NM_001073)	promoter-TSS (NM_001073)	-221	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.007117	0.332149	
chunk0047_108_1	chr12	68884270	68884655	+	0	NA	intron (NM_001005502, intron 3 of 8)	intron (NM_001005502, intron 3 of 8)	48737	NM_198320	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.010390	0.461140	
chunk0008_252_1	chr1	94466394	94466734	+	0	NA	intron (NM_001122674, intron 3 of 8)	intron (NM_001122674, intron 3 of 8)	48187	NM_001122674	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.005882	0.343109	
chunk0106_81_1	chr2	197057991	197058197	+	0	NA	intron (NM_001195144, intron 16 of 27)	intron (NM_001195144, intron 16 of 27)	-131364	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.004854	0.333333	
chunk0095_169_1	chr2	17502737	17503160	+	0	NA	Intergenic	L1MC2|LINE|L1	15491	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.002364	0.252358	
chunk0210_54_1	chrX	68959602	68960130	+	0	NA	Intergenic	L1MD2|LINE|L1	130869	NM_004429	1947	Hs.144700	NM_004429	ENSG00000090776	EFNB1	CFND|CFNS|EFB1|EFL3|EPLG2|Elk-L|LERK2	ephrin B1	protein-coding	0.003788	0.383743	
chunk0159_454_1	chr5	148850720	148851235	+	0	NA	Intergenic	Intergenic	24384	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.003883	0.381783	
chunk0099_232_1	chr2	96432035	96432305	+	0	NA	Intergenic	MER4-int|LTR|ERV1	73215	NM_001285486	93082	Hs.149219	NM_001080535	ENSG00000163121	NEURL3	LINCR|RNF132	neuralized E3 ubiquitin protein ligase 3	protein-coding	0.011111	0.332103	
chunk0067_461_1	chr15	50424066	50424371	+	0	NA	promoter-TSS (NM_001128610)	promoter-TSS (NM_001128610)	-159	NM_001128610	9101	Hs.443731	NM_005154	ENSG00000138592	USP8	HumORF8|PITA4|SPG59|UBPY	ubiquitin specific peptidase 8	protein-coding	0.091803	0.643791	
chunk0159_209_1	chr5	140619016	140619487	+	0	NA	Intergenic	LTR19B|LTR|ERV1	14199	NM_000591	929	Hs.163867	NM_000591	ENSG00000170458	CD14	-	CD14 molecule	protein-coding	0.002123	0.383475	
chunk0054_353_1	chr13	49587434	49587830	+	0	NA	Intergenic	Intergenic	-2049	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.000000	0.418136	
chunk0035_295_1	chr11	46977815	46978356	+	0	NA	intron (NM_001278222, intron 1 of 7)	L2c|LINE|L2	41396	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.005545	0.374539	
chunk0082_182_1	chr17	56172514	56173115	+	0	NA	intron (NM_153228, intron 1 of 16)	intron (NM_153228, intron 1 of 16)	19339	NM_153228	162282	Hs.673040	NM_153228	ENSG00000153930	ANKFN1	-	ankyrin repeat and fibronectin type III domain containing 1	protein-coding	0.008319	0.519934	355(AGGGACACACTGATCC,-,0.00),356(GGGACACACTGATCCC,+,0.00)
chunk0065_234_1	chr14	101040659	101041374	+	0	NA	promoter-TSS (NR_030582)	promoter-TSS (NR_030582)	234	NR_029868	494325		NR_029868	ENSG00000283588	MIR376A1	MIR376A-1|MIRN376A|MIRN376A-1|MIRN376A1|mir-376a-1	microRNA 376a-1	ncRNA	0.016783	0.456704	
chunk0167_150_1	chr6	62481789	62482462	+	0	NA	Intergenic	Intergenic	-195930	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.007429	0.372404	
chunk0138_153_1	chr4	37422026	37422545	+	0	NA	intron (NM_001144990, intron 3 of 6)	intron (NM_001144990, intron 3 of 6)	-31645	NM_001104629	55286	Hs.107527	NM_018302	ENSG00000154274	C4orf19	-	chromosome 4 open reading frame 19	protein-coding	0.003854	0.384615	261(AAGTACTGCCTGTTCT,-,0.00),262(AGTACTGCCTGTTCTC,+,0.00)
chunk0159_328_1	chr5	143659843	143660094	+	0	NA	Intergenic	MIRb|SINE|MIR	-19892	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.007968	0.392857	
chunk0128_100_1	chr3	105967057	105967582	+	0	NA	Intergenic	Intergenic	-98276	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.007619	0.410646	
chunk0156_182_1	chr5	107738614	107739100	+	0	NA	Intergenic	Intergenic	-67962	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004115	0.386037	
chunk0176_439_1	chr7	19986803	19987504	+	0	NA	intron (NR_110114, intron 3 of 5)	L1MB1|LINE|L1	153273	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.005706	0.324786	
chunk0063_381_1	chr14	86310372	86311098	+	0	NA	Intergenic	L1M5|LINE|L1	376057	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.004132	0.354883	
chunk0197_384_1	chr8	127014746	127015094	+	0	NA	intron (NR_045262, intron 1 of 1)	L1ME4c|LINE|L1	1766	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.002874	0.283668	
chunk0109_207_1	chr20	5268014	5268274	+	0	NA	Intergenic	Intergenic	46225	NM_144773	128674	Hs.375029	NM_144773	ENSG00000101292	PROKR2	GPR73L1|GPR73b|GPRg2|HH3|KAL3|PKR2|dJ680N4.3	prokineticin receptor 2	protein-coding	0.007692	0.517241	
chunk0157_54_1	chr5	116062374	116062755	+	0	NA	Intergenic	MER91C|DNA|hAT-Tip100	11098	NM_001195581	644100	Hs.98288	NM_001195581	ENSG00000268223	ARL14EPL	-	ADP ribosylation factor like GTPase 14 effector protein like	protein-coding	0.005249	0.361257	
chunk0188_73_1	chr8	8384142	8384615	+	0	NA	Intergenic	Intergenic	-2544	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.019027	0.464135	
chunk0169_196_1	chr6	102745218	102745512	+	0	NA	Intergenic	Intergenic	1346380	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003401	0.240678	
chunk0072_309_1	chr15	98788797	98789598	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	4771	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.012484	0.365337	458(AGGGACACATTGTTCT,-,0.00),459(GGGACACATTGTTCTA,+,0.00)
chunk0171_387_1	chr6	131116512	131117123	+	0	NA	Intergenic	MER53|DNA|hAT	-18869	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.008183	0.341503	
chunk0088_266_1	chr18	49169106	49169656	+	0	NA	intron (NM_017653, intron 13 of 16)	L2c|LINE|L2	-119613	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.010909	0.495463	
chunk0088_277_1	chr18	49435723	49436217	+	0	NA	intron (NM_017653, intron 1 of 16)	intron (NM_017653, intron 1 of 16)	24739	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.012146	0.379798	248(ATTACAGAATGTTCTT,+,0.00)
chunk0010_12_1	chr1	111990085	111990284	+	0	NA	promoter-TSS (NM_001270945)	promoter-TSS (NM_001270945)	-384	NM_001270945									0.095477	0.700000	
chunk0091_373_1	chr19	15610429	15611031	+	0	NA	Intergenic	LTR44|LTR|ERV1	-4488	NM_007253	11283	Hs.268554	NM_007253	ENSG00000186526	CYP4F8	CPF8|CYPIVF8	cytochrome P450 family 4 subfamily F member 8	protein-coding	0.008306	0.409619	375(AGGAACAGGATGTAAC,-,0.00)
chunk0007_36_1	chr1	77674278	77674710	+	0	NA	intron (NM_001308237, intron 1 of 13)	L1ME3A|LINE|L1	8164	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.011574	0.378753	
chunk0139_142_1	chr4	53536319	53536905	+	0	NA	intron (NM_001126328, intron 2 of 10)	intron (NM_001126328, intron 2 of 10)	21657	NM_032622	84708	Hs.518760	NM_032622	ENSG00000072201	LNX1	LNX|MPDZ|PDZRN2	ligand of numb-protein X 1	protein-coding	0.003413	0.376491	184(TAGAACACACTGTGTT,-,0.00),185(AGAACACACTGTGTTC,+,0.00),186(GAACACACTGTGTTCT,-,0.00),187(AACACACTGTGTTCTA,+,0.00)
chunk0173_324_1	chr6	148709648	148710045	+	0	NA	Intergenic	L2c|LINE|L2	-37289	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.002519	0.394472	181(AGAAACAGGCTGTTCC,-,0.00),182(GAAACAGGCTGTTCCC,+,0.00)
chunk0072_228_1	chr15	95772798	95773440	+	0	NA	Intergenic	Intergenic	340026	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.007788	0.331260	
chunk0016_45_1	chr1	193165746	193166106	+	0	NA	intron (NM_024529, intron 10 of 16)	intron (NM_024529, intron 10 of 16)	20687	NM_003783	8707	Hs.518834	NM_003783	ENSG00000162630	B3GALT2	BETA3GALT2|GLCT2|beta3Gal-T2	beta-1,3-galactosyltransferase 2	protein-coding	0.000000	0.321330	
chunk0094_143_1	chr2	5070226	5070433	+	0	NA	Intergenic	L1MD1|LINE|L1	-414107	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009662	0.355769	
chunk0074_191_1	chr16	24851549	24851967	+	0	NA	intron (NM_001258413, intron 2 of 15)	MIR|SINE|MIR	5527	NM_052944	115584	Hs.164118	NM_052944	ENSG00000158865	SLC5A11	KST1|RKST1|SGLT6|SMIT2	solute carrier family 5 member 11	protein-coding	0.016746	0.400955	
chunk0198_97_1	chr8	130529362	130529874	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	-85958	NM_001247996	50807	Hs.655552	NM_018482	ENSG00000153317	ASAP1	AMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14P	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	protein-coding	0.005859	0.395712	
chunk0011_51_1	chr1	143263371	143263570	+	0	NA	Intergenic	Intergenic	159122	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.065327	0.380000	
chunk0122_467_1	chr3	39991519	39991776	+	0	NA	intron (NM_015460, intron 2 of 16)	L2a|LINE|L2	-108364	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.007782	0.445736	
chunk0067_338_1	chr15	48415267	48415476	+	0	NA	intron (NM_000138, intron 64 of 65)	Tigger19b|DNA|TcMar-Tigger	83203	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.009569	0.333333	
chunk0203_348_1	chr9	89850383	89850915	+	0	NA	Intergenic	Intergenic	-118767	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.013158	0.452158	
chunk0092_231_1	chr19	32394903	32395415	+	0	NA	intron (NR_046201, intron 2 of 2)	MER106B|DNA|hAT-Charlie	10380	NR_046201	400684	Hs.438766	NR_046201	ENSG00000267213	LOC400684	-	uncharacterized LOC400684	ncRNA	0.009766	0.440546	
chunk0143_354_1	chr4	121989642	121989922	+	0	NA	Intergenic	Intergenic	-38028	NM_001130698	7222	Hs.150981	NM_003305	ENSG00000138741	TRPC3	SCA41|TRP3	transient receptor potential cation channel subfamily C member 3	protein-coding	0.025000	0.459075	
chunk0042_258_1	chr12	6653292	6653746	+	0	NA	intron (NM_001127585, intron 1 of 6)	intron (NM_001127585, intron 1 of 6)	-6105	NM_032489	84519	Hs.123239	NM_032489	ENSG00000111644	ACRBP	CT23|OY-TES-1|SP32	acrosin binding protein	protein-coding	0.004405	0.415385	219(AAGTACTGAATGTTCA,-,0.00),220(AGTACTGAATGTTCAG,+,0.00)
chunk0200_214_1	chr9	20569437	20569951	+	0	NA	intron (NM_001286691, intron 2 of 10)	MIRb|SINE|MIR	52293	NM_001286691	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.011673	0.411650	236(TAGAACACCCAGTTCT,-,0.00),237(AGAACACCCAGTTCTA,+,0.00)
chunk0089_181_1	chr18	59792426	59792795	+	0	NA	Intergenic	Intergenic	-95198	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.010840	0.408108	
chunk0110_277_1	chr20	17515066	17515411	+	0	NA	intron (NM_001195, intron 2 of 7)	MER20|DNA|hAT-Charlie	16131	NM_001195	631	Hs.129702	NM_001195	ENSG00000125864	BFSP1	CP115|CP94|CTRCT33|LIFL-H	beaded filament structural protein 1	protein-coding	0.008696	0.395954	
chunk0110_266_1	chr20	16924631	16924830	+	0	NA	Intergenic	Intergenic	176377	NM_020157	56914	Hs.41119	NM_020157	ENSG00000125879	OTOR	FDP|MIAL1	otoraplin	protein-coding	0.025126	0.515000	
chunk0195_288_1	chr8	98556233	98556433	+	0	NA	intron (NM_006281, intron 8 of 10)	L1MEd|LINE|L1	129311	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.010000	0.407960	
chunk0070_200_1	chr15	72153291	72153688	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	35199	NM_001172111	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.002519	0.396985	
chunk0010_73_1	chr1	113217543	113217782	+	0	NA	Intergenic	Intergenic	-11409	NR_038846	643441	Hs.124895	NR_038846		LOC643441	-	uncharacterized LOC643441	ncRNA	0.020921	0.562500	
chunk0188_12_1	chr8	6338368	6339353	+	0	NA	Intergenic	Intergenic	67688	NR_040040	100287015	Hs.156928	NR_040040	ENSG00000246089	LOC100287015	-	uncharacterized LOC100287015	ncRNA	0.004061	0.436105	179(CAGAACAGAGTGGTCT,-,0.00),180(AGAACAGAGTGGTCTC,+,0.00)
chunk0026_83_1	chr10	61352461	61352760	+	0	NA	Intergenic	Intergenic	-100029	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.003344	0.346667	
chunk0160_228_1	chr5	155274528	155274910	+	0	NA	Intergenic	Intergenic	261019	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.015707	0.488251	
chunk0143_428_1	chr4	123838547	123839118	+	0	NA	intron (NR_027105, intron 3 of 4)	intron (NR_027105, intron 3 of 4)	64568	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.005254	0.351399	
chunk0038_292_1	chr11	90251518	90252020	+	0	NA	intron (NR_104190, intron 1 of 6)	MER51E|LTR|ERV1	537	NR_104190	101929222	Hs.616763	NR_104190	ENSG00000261645	DISC1FP1	Boymaw	DISC1 fusion partner 1	ncRNA	0.005976	0.427435	
chunk0042_384_1	chr12	10673643	10673967	+	0	NA	intron (NM_018423, intron 1 of 10)	intron (NM_018423, intron 1 of 10)	487	NM_018423	55359	Hs.24979	NM_018423	ENSG00000060140	STYK1	NOK|SuRTK106	serine/threonine/tyrosine kinase 1	protein-coding	0.030864	0.532308	
chunk0190_120_1	chr8	30532894	30533136	+	0	NA	intron (NM_006867, intron 5 of 9)	L2b|LINE|L2	-105585	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.000000	0.382716	
chunk0050_193_1	chr12	103994585	103994784	+	0	NA	intron (NM_031302, intron 9 of 11)	L2b|LINE|L2	28869	NM_003211	6996	Hs.584809	NM_003211	ENSG00000139372	TDG	hTDG	thymine DNA glycosylase	protein-coding	0.000000	0.445000	
chunk0212_102_1	chrY	14755216	14755415	+	0	NA	intron (NR_046355, intron 4 of 6)	intron (NR_046355, intron 4 of 6)	48718	NR_046504	100874056	Hs.743197	NR_046504	ENSG00000228787	NLGN4Y-AS1	NLGN4Y-AS|NLGN4YAS	NLGN4Y antisense RNA 1	ncRNA	0.005025	0.320000	
chunk0013_236_1	chr1	169585454	169586025	+	0	NA	intron (NM_000130, intron 1 of 24)	intron (NM_000130, intron 1 of 24)	792	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.000000	0.309441	307(AAGCACAAGGTGTTCA,-,0.00),308(AGCACAAGGTGTTCAT,+,0.00)
chunk0195_428_1	chr8	100883708	100884206	+	0	NA	Intergenic	Intergenic	66614	NM_001135702	7534	Hs.492407	NM_003406	ENSG00000164924	YWHAZ	14-3-3-zeta|HEL-S-3|HEL-S-93|HEL4|KCIP-1|POPCHAS|YWHAD	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	protein-coding	0.008032	0.442886	
chunk0113_76_1	chr20	50584286	50584562	+	0	NA	3' UTR (NM_002827, exon 10 of 10)	3' UTR (NM_002827, exon 10 of 10)	-1362	NR_030375	693230		NR_030375	ENSG00000208018	MIR645	MIRN645|hsa-mir-645	microRNA 645	ncRNA	0.007246	0.386282	
chunk0165_180_1	chr6	34350224	34350798	+	0	NA	intron (NM_001202470, intron 5 of 8)	intron (NM_001202470, intron 5 of 8)	42169	NM_006703	11165	Hs.188882	NM_006703	ENSG00000272325	NUDT3	DIPP|DIPP-1|DIPP1	nudix hydrolase 3	protein-coding	0.001742	0.347826	
chunk0074_44_1	chr16	20704117	20704715	+	0	NA	Intergenic	MIR|SINE|MIR	-13160	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.005017	0.345576	
chunk0125_91_1	chr3	65107137	65107617	+	0	NA	Intergenic	Intergenic	-419688	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.010417	0.382536	
chunk0209_412_1	chrX	56763383	56763831	+	0	NA	intron (NR_015367, intron 2 of 2)	intron (NR_015367, intron 2 of 2)	-26023	NR_002308	442454	Hs.663220	NR_002308		UQCRBP1	-	ubiquinol-cytochrome c reductase binding protein pseudogene 1	pseudo	0.008929	0.523385	
chunk0196_450_1	chr8	116642433	116642685	+	0	NA	Intergenic	Intergenic	113264	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.007937	0.284585	
chunk0101_411_1	chr2	139157711	139158328	+	0	NA	Intergenic	MIR|SINE|MIR	260695	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.004862	0.378641	
chunk0180_279_1	chr7	69848229	69848652	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	249521	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.009456	0.441038	
chunk0110_205_1	chr20	15076885	15077151	+	0	NA	intron (NM_080676, intron 5 of 16)	intron (NM_080676, intron 5 of 16)	-119840	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.000000	0.318352	
chunk0103_177_1	chr2	163168126	163168471	+	0	NA	Intergenic	Intergenic	-329551	NM_173162	90134	Hs.657413	NM_033272	ENSG00000184611	KCNH7	ERG3|HERG3|Kv11.3	potassium voltage-gated channel subfamily H member 7	protein-coding	0.002899	0.315029	
chunk0083_4_1	chr17	62538393	62538780	+	0	NA	intron (NM_001284363, intron 5 of 19)	intron (NM_001284363, intron 5 of 19)	57473	NM_001284363	11011	Hs.445078	NM_006852	ENSG00000146872	TLK2	HsHPK|MRD57|PKU-ALPHA	tousled like kinase 2	protein-coding	0.012920	0.402062	
chunk0034_336_1	chr11	35632542	35632746	+	0	NA	Intergenic	Intergenic	14457	NM_014344	24147	Hs.39384	NM_014344	ENSG00000179431	FJX1	-	four-jointed box kinase 1	protein-coding	0.000000	0.434146	
chunk0182_370_1	chr7	99983625	99983919	+	0	NA	non-coding (NR_036679, exon 2 of 2)	non-coding (NR_036679, exon 2 of 2)	3010	NR_036679	646282	Hs.721816	NR_036679	ENSG00000214313	AZGP1P1	-	AZGP1 pseudogene 1	pseudo	0.003401	0.508475	
chunk0027_357_1	chr10	78965266	78965465	+	0	NA	intron (NR_015429, intron 3 of 7)	intron (NR_015429, intron 3 of 7)	102083	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.025126	0.725000	
chunk0018_279_1	chr1	220604981	220605372	+	0	NA	intron (NM_001286128, intron 5 of 15)	MER103C|DNA|hAT-Charlie	76993	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.005115	0.318878	
chunk0003_22_1	chr1	29181696	29182175	+	0	NA	5' UTR (NM_005626, exon 1 of 6)	5' UTR (NM_005626, exon 1 of 6)	190	NM_005626	6429	Hs.469970	NM_005626	ENSG00000116350	SRSF4	SFRS4|SRP75	serine and arginine rich splicing factor 4	protein-coding	0.150313	0.747917	
chunk0088_205_1	chr18	48000138	48000756	+	0	NA	Intergenic	Charlie4a|DNA|hAT-Charlie	-69301	NM_001003652	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.004854	0.353796	
chunk0064_41_1	chr14	89665238	89665746	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-46342	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.009843	0.449902	
chunk0124_331_1	chr3	58217474	58217700	+	0	NA	Intergenic	Intergenic	-6584	NM_004944	1776	Hs.476453	NM_004944	ENSG00000163687	DNASE1L3	DHP2|DNAS1L3|LSD|SLEB16	deoxyribonuclease 1 like 3	protein-coding	0.026549	0.555066	
chunk0177_264_1	chr7	25360663	25360902	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	-132296	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.004184	0.408333	173(AAGAACTCCAAGTGCT,-,0.00),174(AGAACTCCAAGTGCTG,+,0.00)
chunk0021_368_1	chr1	246373911	246374659	+	0	NA	intron (NM_001167740, intron 1 of 11)	Tigger17a|DNA|TcMar-Tigger	43127	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.008021	0.409880	
chunk0056_370_1	chr13	92951453	92952021	+	0	NA	Intergenic	Intergenic	-93604	NR_126360	104326053	Hs.578064	NR_126360		LINC00363	TCONS_00021586	long intergenic non-protein coding RNA 363	ncRNA	0.005282	0.369069	
chunk0094_445_1	chr2	11498105	11498842	+	0	NA	Intergenic	Intergenic	-32296	NM_001278276	1876	Hs.603093	NM_198256	ENSG00000169016	E2F6	E2F-6	E2F transcription factor 6	protein-coding	0.012212	0.432249	
chunk0138_64_1	chr4	33263163	33263667	+	0	NA	Intergenic	Intergenic	776478	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.003968	0.308911	
chunk0003_447_1	chr1	41369035	41369749	+	0	NA	intron (NM_001291281, intron 1 of 1)	MER5A|DNA|hAT-Charlie	7461	NM_001291281	100132074	Hs.559677	NM_001291281		FOXO6	-	forkhead box O6	protein-coding	0.009804	0.562238	
chunk0188_363_1	chr8	18077972	18078454	+	0	NA	intron (NM_004315, intron 1 of 13)	intron (NM_004315, intron 1 of 13)	6157	NM_177924	427	Hs.527412	NM_004315	ENSG00000104763	ASAH1	AC|ACDase|ASAH|PHP|PHP32|SMAPME	N-acylsphingosine amidohydrolase 1	protein-coding	0.014523	0.405797	
chunk0087_19_1	chr18	30987453	30987797	+	0	NA	Intergenic	Intergenic	55190	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.011628	0.455072	
chunk0183_152_1	chr7	105896465	105896803	+	0	NA	Intergenic	Intergenic	-20049	NM_020725	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.000000	0.392330	
chunk0040_321_1	chr11	118044238	118044539	+	0	NA	intron (NR_038318, intron 2 of 3)	intron (NR_038318, intron 2 of 3)	-32624	NM_001173551	56649	Hs.161985	NM_019894	ENSG00000137648	TMPRSS4	CAPH2|MT-SP2|TMPRSS3	transmembrane serine protease 4	protein-coding	0.013289	0.420530	
chunk0088_84_1	chr18	44803090	44803634	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	122464	NM_015559	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.009191	0.445872	355(CAGGACAGAATGTGCT,-,0.00),356(AGGACAGAATGTGCTT,+,0.00)
chunk0048_137_1	chr12	79983974	79984231	+	0	NA	Intergenic	L2a|LINE|L2	-48647	NM_001244990	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.011673	0.437984	166(GAGAACAGCATGTGCC,-,0.00),167(AGAACAGCATGTGCCA,+,0.00)
chunk0174_17_1	chr6	153002747	153003013	+	0	NA	promoter-TSS (NM_001301047)	promoter-TSS (NM_001301047)	-65	NM_001301871	54516	Hs.225836	NM_019041	ENSG00000112031	MTRF1L	HMRF1L|MRF1L|mtRF1a	mitochondrial translational release factor 1 like	protein-coding	0.063910	0.595506	
chunk0178_313_1	chr7	38104953	38105370	+	0	NA	Intergenic	Intergenic	-73045	NM_032016	83930	Hs.309753	NM_032016	ENSG00000010270	STARD3NL	MENTHO	STARD3 N-terminal like	protein-coding	0.011990	0.356459	
chunk0141_66_1	chr4	77862478	77862906	+	0	NA	promoter-TSS (NM_020236)	promoter-TSS (NM_020236)	41	NM_020236	65008	Hs.532019	NM_020236	ENSG00000169288	MRPL1	BM022|L1MT|MRP-L1	mitochondrial ribosomal protein L1	protein-coding	0.053738	0.482517	
chunk0197_258_1	chr8	123477151	123477366	+	0	NA	Intergenic	Intergenic	54885	NM_148177	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.004651	0.435185	
chunk0171_34_1	chr6	120528324	120528784	+	0	NA	Intergenic	Intergenic	513375	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.002174	0.297180	
chunk0081_96_1	chr17	39703259	39703789	+	0	NA	intron (NR_110535, intron 1 of 26)	intron (NR_110535, intron 1 of 26)	3546	NM_001289937	2064	Hs.446352	NM_004448	ENSG00000141736	ERBB2	CD340|HER-2|HER-2/neu|HER2|MLN 19|NEU|NGL|TKR1	erb-b2 receptor tyrosine kinase 2	protein-coding	0.009434	0.512241	
chunk0162_351_1	chr6	7115473	7115839	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	7803	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.019126	0.485014	
chunk0053_449_1	chr13	39913903	39914414	+	0	NA	Intergenic	L2b|LINE|L2	-250023	NR_036190	100422940		NR_036190	ENSG00000264171	MIR4305	-	microRNA 4305	ncRNA	0.003914	0.406250	256(TTGAACACGCTGTTCT,-,0.00),257(TGAACACGCTGTTCTC,+,0.00)
chunk0071_91_1	chr15	80906387	80906876	+	0	NA	intron (NM_001293304, intron 12 of 29)	intron (NM_001293304, intron 12 of 29)	-64558	NR_030393	693132		NR_030393	ENSG00000208003	MIR549A	MIR549|MIRN549|hsa-mir-549|hsa-mir-549a|mir-549a	microRNA 549a	ncRNA	0.020450	0.526531	
chunk0090_434_1	chr18	79507906	79508168	+	0	NA	intron (NM_172387, intron 9 of 9)	intron (NM_172387, intron 9 of 9)	107763	NM_001278672	4772	Hs.534074	NM_006162	ENSG00000131196	NFATC1	NF-ATC|NF-ATc1.2|NFAT2|NFATc	nuclear factor of activated T cells 1	protein-coding	0.041985	0.448669	
chunk0146_360_1	chr4	168209032	168209290	+	0	NA	Intergenic	Intergenic	109646	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.007752	0.494208	
chunk0004_311_1	chr1	49339117	49339324	+	0	NA	intron (NM_032785, intron 3 of 13)	intron (NM_032785, intron 3 of 13)	81809	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.004831	0.326923	
chunk0132_49_1	chr3	154968640	154969077	+	0	NA	Intergenic	Intergenic	-110789	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.000000	0.301370	
chunk0131_436_1	chr3	153752740	153752981	+	0	NA	Intergenic	Intergenic	268365	NM_001101337									0.012448	0.479339	
chunk0155_144_1	chr5	93716560	93716943	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	24852	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.000000	0.304688	187(GGAAACATGATGTTCT,-,0.00),188(GAAACATGATGTTCTC,+,0.00)
chunk0194_175_1	chr8	84988993	84989421	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-117881	NM_033402	85444	Hs.193115	NM_033402	ENSG00000133739	LRRCC1	CLERC|CLERK|SAP2|VFL1	leucine rich repeat and coiled-coil centrosomal protein 1	protein-coding	0.009346	0.386946	
chunk0109_346_1	chr2	238841862	238842066	+	0	NA	Intergenic	Intergenic	-6068	NM_001271893	117581	Hs.422585	NM_057179	ENSG00000233608	TWIST2	AMS|BBRSAY|DERMO1|FFDD3|SETLSS|bHLHa39	twist family bHLH transcription factor 2	protein-coding	0.029412	0.580488	
chunk0024_50_1	chr10	33748907	33749616	+	0	NA	Intergenic	Intergenic	23419	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.007052	0.400000	
chunk0043_169_1	chr12	17062303	17062925	+	0	NA	Intergenic	Intergenic	73867	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.006431	0.393258	
chunk0137_340_1	chr4	25043562	25043890	+	0	NA	Intergenic	Intergenic	-12934	NM_018176	55203	Hs.12488	NM_018176	ENSG00000153012	LGI2	LGIL2	leucine rich repeat LGI family member 2	protein-coding	0.006098	0.489362	166(CAGCACATTCTGTACT,-,0.00),167(AGCACATTCTGTACTG,+,0.00)
chunk0007_285_1	chr1	83891375	83892008	+	0	NA	intron (NM_024686, intron 18 of 20)	L1ME3F|LINE|L1	-30695	NR_119375	101927587	Hs.621230	NR_119375	ENSG00000233008	LINC01725	-	long intergenic non-protein coding RNA 1725	ncRNA	0.009479	0.400631	
chunk0185_318_1	chr7	131452879	131453487	+	0	NA	intron (NM_001145354, intron 13 of 18)	intron (NM_001145354, intron 13 of 18)	103434	NM_001018111	5420	Hs.744213	NM_005397	ENSG00000128567	PODXL	Gp200|PC|PCLP|PCLP-1	podocalyxin like	protein-coding	0.001645	0.321839	
chunk0201_45_1	chr9	33717920	33718406	+	0	NA	Intergenic	HAL1b|LINE|L1	20253	NR_109755	101929688	Hs.372465	NR_109755	ENSG00000233776	LINC01251	-	long intergenic non-protein coding RNA 1251	ncRNA	0.010288	0.359343	
chunk0010_363_1	chr1	118899423	118899936	+	0	NA	intron (NM_152380, intron 6 of 7)	intron (NM_152380, intron 6 of 7)	89877	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.007797	0.394942	
chunk0021_431_1	chr1	247632918	247633152	+	0	NA	Intergenic	L1P2|LINE|L1	27449	NM_001001914	81469	Hs.653227	NM_001001914	ENSG00000177476	OR2G3	OR1-33	olfactory receptor family 2 subfamily G member 3	protein-coding	0.008547	0.365957	49(AGGCACAGGTTGTTCA,-,0.00),50(GGCACAGGTTGTTCAG,+,0.00)
chunk0161_31_1	chr5	165801677	165801991	+	0	NA	Intergenic	L1MB3|LINE|L1	1124536	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.009554	0.352381	
chunk0012_81_1	chr1	155925567	155925967	+	0	NA	TTS (NR_003005)	TTS (NR_003005)	319	NR_003005	677771	Hs.678903	NR_003005	ENSG00000281394	SCARNA4	ACA26	small Cajal body-specific RNA 4	ncRNA	0.005000	0.408978	226(GGGTACAGCATGTTCT,-,0.00),227(GGTACAGCATGTTCTA,+,0.00)
chunk0030_274_1	chr10	116474517	116474926	+	0	NA	intron (NM_001011709, intron 10 of 11)	L1PA13|LINE|L1	46809	NM_001011709	119548	Hs.276724	NM_001011709	ENSG00000203837	PNLIPRP3	-	pancreatic lipase related protein 3	protein-coding	0.007335	0.368293	
chunk0110_84_1	chr20	11225278	11225603	+	0	NA	Intergenic	LTR78|LTR|ERV1	47943	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.009231	0.472393	
chunk0085_202_1	chr18	6592129	6592700	+	0	NA	Intergenic	Intergenic	80998	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.007005	0.438811	312(AAGCACAGGGTGTACA,-,0.00),313(AGCACAGGGTGTACAT,+,0.00)
chunk0074_227_1	chr16	27103921	27104147	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	37136	NM_001145545	162083	Hs.120831	NM_182831		C16orf82	TNT	chromosome 16 open reading frame 82	protein-coding	0.004425	0.488987	
chunk0070_351_1	chr15	75982721	75983439	+	0	NA	intron (NM_138573, intron 3 of 5)	L1MEa|LINE|L1	29364	NM_138573	145957	Hs.732438	NM_138573	ENSG00000169752	NRG4	HRG4	neuregulin 4	protein-coding	0.004178	0.356050	
chunk0061_94_1	chr14	57415699	57416035	+	0	NA	Intergenic	Intergenic	25314	NM_001011713	122830	Hs.165465	NM_001011713	ENSG00000139977	NAA30	C14orf35|MAK3|Mak3p|NAT12|NAT12P	N(alpha)-acetyltransferase 30, NatC catalytic subunit	protein-coding	0.008929	0.364985	
chunk0007_123_1	chr1	79018698	79019117	+	0	NA	Intergenic	LTR105_Mam|LTR|ERVL	-12097	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.014320	0.459524	
chunk0175_368_1	chr6	167883166	167883433	+	0	NA	intron (NM_001207008, intron 6 of 31)	HAL1|LINE|L1	55664	NM_001291964	4301	Hs.614974	NM_005936	ENSG00000130396	AFDN	AF6|MLL-AF6|MLLT4|l-afadin	afadin, adherens junction formation factor	protein-coding	0.003745	0.384328	
chunk0206_51_1	chr9	117747680	117748053	+	0	NA	Intergenic	Intergenic	43691	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.010724	0.457219	
chunk0005_93_1	chr1	56397882	56398306	+	0	NA	Intergenic	Intergenic	181490	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.002358	0.374118	239(GGGAACACAGTGTCTT,-,0.00),240(GGAACACAGTGTCTTA,+,0.00)
chunk0160_340_1	chr5	160039867	160040238	+	0	NA	intron (NM_003314, intron 4 of 7)	Tigger3b|DNA|TcMar-Tigger	30952	NM_001282500	7265	Hs.519718	NM_003314	ENSG00000113312	TTC1	TPR1	tetratricopeptide repeat domain 1	protein-coding	0.002695	0.346774	
chunk0129_337_1	chr3	124761821	124762321	+	0	NA	3' UTR (NM_002213, exon 15 of 15)	3' UTR (NM_002213, exon 15 of 15)	29632	NR_036088	100422864		NR_036088	ENSG00000265981	MIR544B	-	microRNA 544b	ncRNA	0.004000	0.357285	
chunk0104_350_1	chr2	179921520	179921827	+	0	NA	Intergenic	Intergenic	-60168	NM_152520	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.003257	0.266234	
chunk0202_161_1	chr9	73742367	73742919	+	0	NA	Intergenic	Intergenic	590912	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.005435	0.323689	
chunk0145_114_1	chr4	146252979	146253613	+	0	NA	TTS (NM_001300842)	TTS (NM_001300842)	77613	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.007886	0.374803	
chunk0139_148_1	chr4	53636700	53636899	+	0	NA	Intergenic	Intergenic	43843	NR_046827	100873955	Hs.351074	NR_046827		LNX1-AS2	-	LNX1 antisense RNA 2	ncRNA	0.000000	0.395000	
chunk0020_18_1	chr1	231728023	231728411	+	0	NA	intron (NM_001012957, intron 3 of 12)	intron (NM_001012957, intron 3 of 12)	90300	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.015464	0.388175	
chunk0184_47_1	chr7	112263497	112263760	+	0	NA	intron (NM_021994, intron 1 of 11)	intron (NM_021994, intron 1 of 11)	57040	NM_021994	11179	Hs.655904	NM_021994	ENSG00000198839	ZNF277	NRIF4|ZNF277P	zinc finger protein 277	protein-coding	0.000000	0.416667	139(CAGTACATGCTGTTCA,-,0.00),140(AGTACATGCTGTTCAT,+,0.00)
chunk0006_267_1	chr1	70305708	70306137	+	0	NA	intron (NM_030816, intron 6 of 12)	intron (NM_030816, intron 6 of 12)	48812	NM_030816	81573	Hs.744989	NM_030816	ENSG00000118454	ANKRD13C	dJ677H15.3	ankyrin repeat domain 13C	protein-coding	0.009324	0.320930	
chunk0067_274_1	chr15	46855623	46855822	+	0	NA	Intergenic	Intergenic	-328484	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.000000	0.395000	
chunk0006_276_1	chr1	70411073	70411280	+	0	NA	promoter-TSS (NM_001902)	promoter-TSS (NM_001902)	-42	NM_153742	1491	Hs.19904	NM_001902	ENSG00000116761	CTH	-	cystathionine gamma-lyase	protein-coding	0.086957	0.625000	
chunk0203_220_1	chr9	86812308	86812968	+	0	NA	Intergenic	Intergenic	134551	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.003030	0.458396	
chunk0077_49_1	chr16	76291403	76291907	+	0	NA	intron (NM_033401, intron 1 of 23)	intron (NM_033401, intron 1 of 23)	14377	NM_033401	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.005952	0.374257	
chunk0173_452_1	chr6	151763995	151764264	+	0	NA	intron (NM_001122742, intron 2 of 9)	MER81|DNA|hAT-Blackjack	-41544	NM_001122741	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.029740	0.562963	22(GGAAACAGGCAGTTCC,-,0.00),23(GAAACAGGCAGTTCCC,+,0.00)
chunk0193_271_1	chr8	77213975	77214425	+	0	NA	Intergenic	Intergenic	-213156	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.002222	0.374723	
chunk0178_306_1	chr7	37970599	37970832	+	0	NA	Intergenic	MIRb|SINE|MIR	49396	NM_001242948	54749	Hs.563491	NM_017549	ENSG00000086289	EPDR1	EPDR|MERP-1|MERP1|UCC1	ependymin related 1	protein-coding	0.004292	0.346154	
chunk0070_249_1	chr15	73529598	73530196	+	0	NA	intron (NM_001042367, intron 2 of 5)	L2b|LINE|L2	39646	NR_103844	101241892	Hs.656678	NR_103844	ENSG00000281183	NPTN-IT1	lncRNA-LET	NPTN intronic transcript 1	ncRNA	0.003344	0.332220	
chunk0182_269_1	chr7	98086166	98086853	+	0	NA	Intergenic	Intergenic	-20376	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.021834	0.542151	
chunk0143_422_1	chr4	123744544	123744941	+	0	NA	intron (NR_027105, intron 2 of 4)	intron (NR_027105, intron 2 of 4)	-29522	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.002519	0.336683	163(GTGAACTGTTTGTTCT,-,0.00),164(TGAACTGTTTGTTCTG,+,0.00)
chunk0169_284_1	chr6	105796037	105796628	+	0	NA	Intergenic	Intergenic	-289988	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.015228	0.515203	
chunk0023_436_1	chr10	31865126	31865600	+	0	NA	intron (NM_001270696, intron 3 of 17)	L2|LINE|L2	43563	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.004219	0.366316	265(AAGTACAGTTTGTTTT,-,0.00)
chunk0049_6_1	chr12	89205659	89205915	+	0	NA	Intergenic	Intergenic	147072	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.003906	0.334630	
chunk0124_118_1	chr3	54139775	54140526	+	0	NA	intron (NM_018398, intron 2 of 37)	MIRb|SINE|MIR	17484	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.007989	0.490691	
chunk0038_298_1	chr11	90458569	90459311	+	0	NA	intron (NR_104190, intron 1 of 6)	intron (NR_104190, intron 1 of 6)	96917	NR_039711	100616186		NR_039711	ENSG00000266703	MIR4490	-	microRNA 4490	ncRNA	0.001348	0.293405	
chunk0195_282_1	chr8	98400358	98400567	+	0	NA	Intergenic	Intergenic	-26560	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.033493	0.600000	
chunk0136_280_1	chr3	194772812	194773039	+	0	NA	intron (NR_037891, intron 3 of 3)	intron (NR_037891, intron 3 of 3)	64504	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.039648	0.539474	
chunk0180_360_1	chr7	73801779	73802002	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	-28973	NM_001305	1364	Hs.647036	NM_001305	ENSG00000189143	CLDN4	CPE-R|CPER|CPETR|CPETR1|WBSCR8|hCPE-R	claudin 4	protein-coding	0.004484	0.276786	
chunk0152_321_1	chr5	62034833	62035204	+	0	NA	Intergenic	L1PA7|LINE|L1	-271144	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.013477	0.395161	18(TGGTACACTGTGTCTT,-,0.00),19(GGTACACTGTGTCTTC,+,0.00),102(AGGAGCAGGTTGTCCT,-,0.00),103(GGAGCAGGTTGTCCTG,+,0.00)
chunk0006_345_1	chr1	72487522	72487951	+	0	NA	Intergenic	Intergenic	-205142	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.002331	0.325581	
chunk0086_321_1	chr18	24305231	24305569	+	0	NA	intron (NM_080597, intron 13 of 27)	intron (NM_080597, intron 13 of 27)	6106	NM_001242508	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.008876	0.297935	
chunk0162_249_1	chr6	5059256	5059672	+	0	NA	intron (NR_126015, intron 2 of 3)	L1ME4b|LINE|L1	-26022	NM_001145115	648791	Hs.653089	NM_001145115	ENSG00000219607	PPP1R3G	-	protein phosphatase 1 regulatory subunit 3G	protein-coding	0.019231	0.462830	
chunk0042_252_1	chr12	6496965	6497550	+	0	NA	intron (NM_014865, intron 2 of 31)	intron (NM_014865, intron 2 of 31)	3125	NM_014865	9918	Hs.5719	NM_014865	ENSG00000010292	NCAPD2	CAP-D2|CNAP1|MCPH21|hCAP-D2	non-SMC condensin I complex subunit D2	protein-coding	0.005128	0.419795	
chunk0014_189_1	chr1	178752865	178753339	+	0	NA	intron (NM_001286247, intron 1 of 18)	MIRc|SINE|MIR	27955	NM_152663	55103	Hs.632485	NM_018037	ENSG00000116191	RALGPS2	dJ595C2.1	Ral GEF with PH domain and SH3 binding motif 2	protein-coding	0.004219	0.378947	241(AGGCACTGAATGTGCC,-,0.00),242(GGCACTGAATGTGCCA,+,0.00)
chunk0120_405_1	chr3	12638142	12638369	+	0	NA	intron (NM_002880, intron 1 of 16)	intron (NM_002880, intron 1 of 16)	25946	NM_002880	5894	Hs.159130	NM_002880	ENSG00000132155	RAF1	CMD1NN|CRAF|NS5|Raf-1|c-Raf	Raf-1 proto-oncogene, serine/threonine kinase	protein-coding	0.004405	0.403509	
chunk0067_332_1	chr15	48320681	48320946	+	0	NA	Intergenic	Intergenic	-10611	NM_001025248	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.000000	0.409774	
chunk0060_219_1	chr14	48970789	48971060	+	0	NA	Intergenic	Intergenic	615492	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.000000	0.360294	
chunk0189_9_1	chr8	19482061	19482291	+	0	NA	intron (NM_001130518, intron 4 of 9)	MER3|DNA|hAT-Charlie	120369	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.021739	0.415584	
chunk0043_419_1	chr12	25858502	25858876	+	0	NA	Intergenic	Intergenic	15390	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.008021	0.338667	
chunk0047_102_1	chr12	68807690	68808078	+	0	NA	promoter-TSS (NM_002392)	promoter-TSS (NM_002392)	-288	NM_002392	4193	Hs.484551	NM_002392	ENSG00000135679	MDM2	ACTFS|HDMX|hdm2	MDM2 proto-oncogene	protein-coding	0.069588	0.544987	
chunk0073_1_1	chr16	1680124	1680405	+	0	NA	intron (NM_144570, intron 1 of 4)	intron (NM_144570, intron 1 of 4)	1987	NM_144570	90861	Hs.513261	NM_144570	ENSG00000206053	JPT2	C16orf34|HN1L|L11	Jupiter microtubule associated homolog 2	protein-coding	0.032028	0.514184	
chunk0103_416_1	chr2	169641647	169641846	+	0	NA	Intergenic	Intergenic	52675	NM_001085447	129881	Hs.370111	NM_001085447	ENSG00000154479	CCDC173	C2orf77	coiled-coil domain containing 173	protein-coding	0.010050	0.360000	
chunk0113_290_1	chr20	57449755	57450271	+	0	NA	Intergenic	Intergenic	58615	NM_001291780	55544	Hs.236361	NM_017495	ENSG00000132819	RBM38	HSRNASEB|RNPC1|SEB4B|SEB4D|dJ800J21.2	RNA binding motif protein 38	protein-coding	0.015504	0.512573	
chunk0079_221_1	chr17	14950758	14951075	+	0	NA	Intergenic	Intergenic	-80059	NR_033371	94150	Hs.147654	NR_033371	ENSG00000259944	CDRT7	LINC00025|NCRNA00025	CMT1A duplicated region transcript 7	ncRNA	0.006309	0.471698	
chunk0096_411_1	chr2	38138768	38139511	+	0	NA	intron (NR_027252, intron 2 of 2)	intron (NR_027252, intron 2 of 2)	8034	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.010767	0.432796	
chunk0178_28_1	chr7	29377444	29378173	+	0	NA	intron (NM_001293069, intron 4 of 13)	Plat_L3|LINE|CR1	-101904	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.009602	0.413699	340(AAGTACACCATGTCTC,-,0.00),341(AGTACACCATGTCTCT,+,0.00)
chunk0164_226_1	chr6	22956305	22956900	+	0	NA	Intergenic	Intergenic	387153	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.008403	0.417785	
chunk0144_78_1	chr4	127975380	127975797	+	0	NA	intron (NM_001039717, intron 1 of 10)	L1MB3|LINE|L1	-9604	NM_152778	256471	Hs.480701	NM_152778	ENSG00000164073	MFSD8	CCMD|CLN7	major facilitator superfamily domain containing 8	protein-coding	0.002398	0.313397	
chunk0065_378_1	chr14	104141755	104142233	+	0	NA	intron (NM_015656, intron 2 of 14)	intron (NM_015656, intron 2 of 14)	3271	NM_015656	26153	Hs.134970	NM_015656	ENSG00000066735	KIF26A	-	kinesin family member 26A	protein-coding	0.020921	0.609603	232(AGGGACTCCGAGTCCC,-,0.00),233(GGGACTCCGAGTCCCT,+,0.00)
chunk0114_268_1	chr21	16212240	16212439	+	0	NA	intron (NR_027791, intron 1 of 5)	intron (NR_027791, intron 1 of 5)	17960	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.010050	0.365000	
chunk0015_327_1	chr1	189615079	189615400	+	0	NA	Intergenic	Intergenic	862390	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.006231	0.338509	
chunk0092_51_1	chr19	19776289	19776727	+	0	NA	promoter-TSS (NR_026956)	promoter-TSS (NR_026956)	-95	NR_026956	284440	Hs.665307	NR_026956		LINC00663	-	long intergenic non-protein coding RNA 663	ncRNA	0.050228	0.605923	
chunk0142_193_1	chr4	96638123	96638666	+	0	NA	Intergenic	Intergenic	-728532	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.003683	0.378676	
chunk0058_190_1	chr14	24271523	24271773	+	0	NA	promoter-TSS (NM_182836)	promoter-TSS (NM_182836)	-21	NM_182836	5875	Hs.377992	NM_004581	ENSG00000100949	RABGGTA	PTAR3	Rab geranylgeranyltransferase subunit alpha	protein-coding	0.116000	0.685259	
chunk0161_283_1	chr5	172869002	172869518	+	0	NA	intron (NM_001031711, intron 1 of 9)	intron (NM_001031711, intron 1 of 9)	35040	NM_001031711	57222	Hs.509163	NM_020462	ENSG00000113719	ERGIC1	AMCN|ERGIC-32|ERGIC32|NET24	endoplasmic reticulum-golgi intermediate compartment 1	protein-coding	0.011628	0.580271	250(CAGGACAGCGTGTGCT,-,0.00),251(AGGACAGCGTGTGCTC,+,0.00)
chunk0198_123_1	chr8	131932139	131932617	+	0	NA	intron (NM_015137, intron 1 of 22)	intron (NM_015137, intron 1 of 22)	28269	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.000000	0.304802	
chunk0159_322_1	chr5	143589210	143589543	+	0	NA	Intergenic	Intergenic	-90484	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.012012	0.422156	
chunk0066_2_1	chr15	26785932	26786390	+	0	NA	Intergenic	L1MEf|LINE|L1	-12373	NM_021912	2562	Hs.302352	NM_000814	ENSG00000166206	GABRB3	ECA5|EIEE43	gamma-aminobutyric acid type A receptor beta3 subunit	protein-coding	0.006550	0.374728	
chunk0146_279_1	chr4	163558739	163559168	+	0	NA	intron (NM_001166373, intron 6 of 7)	intron (NM_001166373, intron 6 of 7)	54671	NM_017923	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.006993	0.390698	249(GAGGACAAAATGTTCC,-,0.00),250(AGGACAAAATGTTCCC,+,0.00)
chunk0150_384_1	chr5	39605902	39606448	+	0	NA	Intergenic	Intergenic	85744	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.001832	0.340037	
chunk0190_54_1	chr8	29680009	29680260	+	0	NA	Intergenic	L1MC4|LINE|L1	67975	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.000000	0.404762	103(GAGTACAAGATGTGCC,-,0.00),104(AGTACAAGATGTGCCC,+,0.00)
chunk0029_299_1	chr10	104018303	104018989	+	0	NA	intron (NM_001304743, intron 13 of 17)	intron (NM_001304743, intron 13 of 17)	29540	NR_030760	100126326		NR_030760	ENSG00000283788	MIR936	MIRN936|hsa-mir-936	microRNA 936	ncRNA	0.014577	0.328967	
chunk0032_264_1	chr11	8958992	8959288	+	0	NA	intron (NM_001286094, intron 1 of 3)	intron (NM_001286094, intron 1 of 3)	-5535	NR_073431	493900	Hs.591981	NR_073431	ENSG00000254860	TMEM9B-AS1	C11orf18	TMEM9B antisense RNA 1	ncRNA	0.006757	0.451178	
chunk0133_368_1	chr3	173705178	173705504	+	0	NA	intron (NM_014932, intron 3 of 6)	intron (NM_014932, intron 3 of 6)	215455	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.000000	0.348624	
chunk0012_373_1	chr1	163161647	163162090	+	0	NA	intron (NR_110699, intron 1 of 3)	intron (NR_110699, intron 1 of 3)	193	NR_110699	101928404	Hs.683933	NR_110699	ENSG00000232892	LOC101928404	-	uncharacterized LOC101928404	ncRNA	0.009029	0.418919	
chunk0099_238_1	chr2	96800595	96800794	+	0	NA	intron (NM_020184, intron 5 of 6)	intron (NM_020184, intron 5 of 6)	2416	NR_036074	100422928		NR_036074	ENSG00000264157	MIR3127	mir-3127	microRNA 3127	ncRNA	0.020101	0.600000	
chunk0045_29_1	chr12	43857897	43858527	+	0	NA	intron (NM_001286213, intron 2 of 6)	MIR3|SINE|MIR	22351	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.017460	0.480190	
chunk0161_125_1	chr5	168076520	168076888	+	0	NA	intron (NM_001080428, intron 4 of 24)	intron (NM_001080428, intron 4 of 24)	155668	NR_109894	101927862	Hs.659376	NR_109894	ENSG00000253978	CTB-178M22.2	-	uncharacterized LOC101927862	ncRNA	0.002717	0.468835	
chunk0205_239_1	chr9	110078457	110079105	+	0	NA	intron (NM_001004065, intron 1 of 3)	intron (NM_001004065, intron 1 of 3)	30183	NM_001198656	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.009259	0.351310	
chunk0048_245_1	chr12	81601452	81601887	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-3298	NM_001220477	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.362385	
chunk0134_447_1	chr3	183772823	183773158	+	0	NA	intron (NM_018023, intron 16 of 30)	MER2|DNA|TcMar-Tigger	52615	NM_024871	79929	Hs.478465	NM_024871	ENSG00000180834	MAP6D1	MAPO6D1|SL21	MAP6 domain containing 1	protein-coding	0.002985	0.351190	
chunk0121_350_1	chr3	24678110	24678381	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-156810	NR_039955									0.007380	0.415441	
chunk0175_138_1	chr7	3507030	3507243	+	0	NA	intron (NM_152744, intron 1 of 44)	L1MEf|LINE|L1	205688	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.014085	0.439252	
chunk0038_90_1	chr11	83388787	83389583	+	0	NA	Intergenic	Intergenic	-102778	NM_001286119	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.008794	0.383940	
chunk0053_296_1	chr13	33745213	33746097	+	0	NA	Intergenic	Intergenic	-68820	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.005656	0.415819	580(GGGAACATGGTGACCT,-,0.00),581(GGAACATGGTGACCTG,+,0.00)
chunk0170_430_1	chr6	118781935	118782339	+	0	NA	promoter-TSS (NR_037662)	promoter-TSS (NR_037662)	-571	NR_037662	100287632	Hs.334026	NR_037662		SELENOKP3	-	selenoprotein K pseudogene 3	pseudo	0.004950	0.412346	
chunk0019_246_1	chr1	227550440	227550639	+	0	NA	Intergenic	L1PA4|LINE|L1	-12980	NR_102302	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.010050	0.545000	
chunk0043_339_1	chr12	22763656	22764156	+	0	NA	Intergenic	L2c|LINE|L2	138764	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.014000	0.461078	251(GTGTACATTGTGTACT,-,0.00),252(TGTACATTGTGTACTT,+,0.00)
chunk0040_58_1	chr11	111193808	111194477	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-61840	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.002990	0.395522	
chunk0080_196_1	chr17	29137565	29138175	+	0	NA	intron (NM_203318, intron 2 of 40)	intron (NM_203318, intron 2 of 40)	42519	NM_078471	399687	Hs.462590	NM_078471	ENSG00000196535	MYO18A	MAJN|MYSPDZ|SP-R210|SPR210	myosin XVIIIA	protein-coding	0.006557	0.410802	
chunk0203_39_1	chr9	83062736	83063120	+	0	NA	5' UTR (NM_152573, exon 1 of 17)	5' UTR (NM_152573, exon 1 of 17)	200	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.138021	0.768831	
chunk0126_65_1	chr3	74448294	74448932	+	0	NA	intron (NM_020872, intron 3 of 21)	MIR|SINE|MIR	72527	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.001567	0.323944	
chunk0100_263_1	chr2	113680815	113681270	+	0	NA	Intergenic	L1M4a1|LINE|L1	40326	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.006593	0.339912	
chunk0192_401_1	chr8	68903399	68904128	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	200427	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.002743	0.376712	414(GAGCACAGTATGTTCT,-,0.00),415(AGCACAGTATGTTCTA,+,0.00)
chunk0131_303_1	chr3	150703829	150704604	+	0	NA	promoter-TSS (NM_001308234)	promoter-TSS (NM_001308234)	241	NR_121674	101928085	Hs.561114	NR_121674	ENSG00000240137	ERICH6-AS1	-	ERICH6 antisense RNA 1	ncRNA	0.052903	0.516753	
chunk0062_430_1	chr14	75283071	75283596	+	0	NA	Intergenic	Intergenic	4555	NM_005252	2353	Hs.25647	NM_005252	ENSG00000170345	FOS	AP-1|C-FOS|p55	Fos proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.020952	0.416350	
chunk0101_118_1	chr2	126482886	126483135	+	0	NA	Intergenic	LTR28C|LTR|ERV1	-172925	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.020080	0.524000	
chunk0118_196_1	chr22	31579766	31580351	+	0	NA	intron (NM_014775, intron 11 of 31)	L2a|LINE|L2	41473	NR_106959	102465666		NR_106959	ENSG00000284082	MIR7109	hsa-mir-7109	microRNA 7109	ncRNA	0.003419	0.452218	
chunk0030_162_1	chr10	114044490	114044722	+	0	NA	exon (NM_000684, exon 1 of 1)	exon (NM_000684, exon 1 of 1)	559	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.090517	0.673820	
chunk0149_195_1	chr5	21495381	21495598	+	0	NA	intron (NR_027028, intron 5 of 5)	intron (NR_027028, intron 5 of 5)	36009	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.023041	0.500000	
chunk0205_170_1	chr9	108760831	108761221	+	0	NA	Intergenic	Intergenic	94969	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.005128	0.447570	202(CAGAACAGCTTGTTCC,-,0.00),203(AGAACAGCTTGTTCCA,+,0.00)
chunk0048_376_1	chr12	86352458	86352732	+	0	NA	intron (NM_013244, intron 2 of 6)	L1ME4b|LINE|L1	478300	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.000000	0.290909	96(CAGTACAAATTGTACT,-,0.00),97(AGTACAAATTGTACTT,+,0.00)
chunk0195_121_1	chr8	94927386	94928383	+	0	NA	3' UTR (NM_033285, exon 4 of 4)	3' UTR (NM_033285, exon 4 of 4)	21503	NM_033285	94241	Hs.492261	NM_033285	ENSG00000164938	TP53INP1	SIP|TP53DINP1|TP53INP1A|TP53INP1B|Teap|p53DINP1	tumor protein p53 inducible nuclear protein 1	protein-coding	0.009027	0.344689	
chunk0114_211_1	chr21	15484788	15485195	+	0	NA	Intergenic	LTR53|LTR|ERVL	-245034	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.007371	0.480392	190(CAGGACATCATGCCCT,-,0.00),191(AGGACATCATGCCCTC,+,0.00),242(TGTTCACTCTGTTCCT,+,0.00)
chunk0019_375_1	chr1	229893722	229894022	+	0	NA	Intergenic	Intergenic	-163917	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.010000	0.568106	
chunk0089_309_1	chr18	63848267	63848872	+	0	NA	Intergenic	L1ME1|LINE|L1	-39136	NM_002575	5055	Hs.594481	NM_002575	ENSG00000197632	SERPINB2	HsT1201|PAI|PAI-2|PAI2|PLANH2	serpin family B member 2	protein-coding	0.004959	0.379538	
chunk0076_454_1	chr16	74199148	74199359	+	0	NA	intron (NR_104657, intron 3 of 3)	intron (NR_104657, intron 3 of 3)	16268	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.014218	0.391509	
chunk0113_32_1	chr20	49818914	49819113	+	0	NA	intron (NM_015266, intron 2 of 15)	intron (NM_015266, intron 2 of 15)	6300	NR_048538	23315	Hs.444202	NM_015266	ENSG00000197818	SLC9A8	NHE-8|NHE8	solute carrier family 9 member A8	protein-coding	0.005025	0.355000	93(ATTACAGTGTGTTCCT,+,0.00)
chunk0108_379_1	chr2	236947470	236947669	+	0	NA	Intergenic	Intergenic	-137872	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.005025	0.440000	
chunk0009_437_1	chr1	111360295	111360646	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	13910	NM_001300831	128344	Hs.172510	NM_181643	ENSG00000173947	PIFO	C1orf88|pitchfork	primary cilia formation	protein-coding	0.005698	0.440341	
chunk0031_347_1	chr10	129607208	129607814	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	140327	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.009901	0.401977	
chunk0091_199_1	chr19	8638164	8638831	+	0	NA	Intergenic	Intergenic	-27762	NM_030957	81794	Hs.657508	NM_030957	ENSG00000142303	ADAMTS10	ADAM-TS10|ADAMTS-10|WMS|WMS1	ADAM metallopeptidase with thrombospondin type 1 motif 10	protein-coding	0.034483	0.547904	
chunk0076_209_1	chr16	68216074	68216652	+	0	NA	intron (NM_004555, intron 10 of 10)	intron (NM_004555, intron 10 of 10)	17136	NR_106831	102466194		NR_106831	ENSG00000284259	MIR6773	hsa-mir-6773	microRNA 6773	ncRNA	0.006920	0.386874	
chunk0124_161_1	chr3	55022649	55022875	+	0	NA	intron (NM_018398, intron 35 of 37)	L1MEd|LINE|L1	-55674	NM_001304389	57408	Hs.591668	NM_020678	ENSG00000144771	LRTM1	HT017	leucine rich repeats and transmembrane domains 1	protein-coding	0.008850	0.348018	
chunk0161_60_1	chr5	166369874	166370132	+	0	NA	Intergenic	Intergenic	556367	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.007752	0.409266	190(TAGAACTGTGTGTGCA,-,0.00),191(AGAACTGTGTGTGCAT,+,0.00)
chunk0021_138_1	chr10	3909508	3909723	+	0	NA	Intergenic	Intergenic	-81545	NR_106726	102464829		NR_106726	ENSG00000274809	MIR6078	hsa-mir-6078	microRNA 6078	ncRNA	0.037209	0.504630	
chunk0165_404_1	chr6	38885641	38885910	+	0	NA	intron (NM_001206927, intron 56 of 92)	L2a|LINE|L2	67332	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.007435	0.437037	
chunk0139_304_1	chr4	57658663	57659036	+	0	NA	Intergenic	Intergenic	232977	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.000000	0.390374	219(AAAACAAAATGTGCTG,+,0.00)
chunk0070_124_1	chr15	70741009	70741501	+	0	NA	intron (NM_018003, intron 1 of 18)	intron (NM_018003, intron 1 of 18)	22256	NM_018003	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.002033	0.446247	
chunk0076_328_1	chr16	70777517	70778280	+	0	NA	intron (NM_018052, intron 9 of 18)	intron (NM_018052, intron 9 of 18)	22838	NR_034083	100130894	Hs.678899	NR_034083	ENSG00000214353	VAC14-AS1	-	VAC14 antisense RNA 1	ncRNA	0.020970	0.541885	
chunk0192_8_1	chr8	58285925	58286677	+	0	NA	Intergenic	Intergenic	-14200	NR_105005	101929528	Hs.563551	NR_105005	ENSG00000253281	LOC101929528	-	uncharacterized LOC101929528	ncRNA	0.003989	0.456839	379(GAGCACAGAATGATCC,-,0.00),380(AGCACAGAATGATCCA,+,0.00)
chunk0138_75_1	chr4	34863534	34863866	+	0	NA	Intergenic	Intergenic	-823807	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.003012	0.303303	246(TAGCACACCCAGTGCA,-,0.00),247(AGCACACCCAGTGCAC,+,0.00)
chunk0079_182_1	chr17	14097613	14098119	+	0	NA	intron (NM_001303, intron 3 of 6)	intron (NM_001303, intron 3 of 6)	-28408	NR_049718	100874058	Hs.720411	NR_049718	ENSG00000236088	COX10-AS1	COX10-AS|COX10AS	COX10 antisense RNA 1	ncRNA	0.005929	0.323471	
chunk0165_259_1	chr6	35727850	35728399	+	0	NA	intron (NR_027117, intron 9 of 9)	CpG	459	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.098361	0.703636	262(TGGAACACAATGTCCC,-,0.00),263(GGAACACAATGTCCCG,+,0.00)
chunk0045_242_1	chr12	48931626	48931968	+	0	NA	Intergenic	Intergenic	-6250	NM_016594	51303	Hs.655103	NM_016594	ENSG00000134285	FKBP11	FKBP19	FKBP prolyl isomerase 11	protein-coding	0.005848	0.425656	
chunk0166_300_1	chr6	49345153	49345552	+	0	NA	Intergenic	Intergenic	117976	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.005013	0.402500	
chunk0158_366_1	chr5	133917162	133917534	+	0	NA	TTS (NR_131252)	TTS (NR_131252)	3671	NR_131252	105664404	Hs.582536	NR_131252	ENSG00000249073	WSPAR	LncTCF7|TCONS_00009511	WNT signaling pathway activating non-coding RNA	ncRNA	0.008065	0.474531	
chunk0034_403_1	chr11	37950553	37951138	+	0	NA	Intergenic	Intergenic	695511	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.001709	0.320819	
chunk0158_377_1	chr5	134246897	134247280	+	0	NA	Intergenic	Intergenic	-20829	NM_002715	5515	Hs.105818	NM_002715	ENSG00000113575	PPP2CA	NEDLBA|PP2Ac|PP2CA|PP2Calpha|RP-C	protein phosphatase 2 catalytic subunit alpha	protein-coding	0.005222	0.489583	
chunk0059_439_1	chr14	38598974	38599274	+	0	NA	Intergenic	L1PA7|LINE|L1	317758	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.003333	0.365449	36(GGTACATTGTGTCTTT,+,0.00)
chunk0199_402_1	chr9	13447980	13448342	+	0	NA	Intergenic	Intergenic	-16832	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.008287	0.413223	
chunk0034_177_1	chr11	31246465	31246978	+	0	NA	Intergenic	Intergenic	123089	NM_181807	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.003899	0.373541	256(GAGAACACACTGTCTC,-,0.00),257(AGAACACACTGTCTCC,+,0.00)
chunk0034_166_1	chr11	30795533	30796044	+	0	NA	Intergenic	Intergenic	196898	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.003914	0.382812	
chunk0193_69_1	chr8	73126154	73126903	+	0	NA	Intergenic	Intergenic	-33256	NM_153225	157869	Hs.439040	NM_153225	ENSG00000164764	SBSPON	C8orf84|RPESP	somatomedin B and thrombospondin type 1 domain containing	protein-coding	0.008011	0.417333	
chunk0143_297_1	chr4	118733725	118734257	+	0	NA	intron (NM_014822, intron 19 of 22)	intron (NM_014822, intron 19 of 22)	48621	NM_020961	57721	Hs.596872	NM_020961	ENSG00000145388	METTL14	hMETTL14	methyltransferase like 14	protein-coding	0.003759	0.335835	
chunk0084_192_1	chr17	77981740	77982032	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-22351	NM_001142640	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.017123	0.443686	
chunk0097_260_1	chr2	54406062	54406333	+	0	NA	Intergenic	Intergenic	-50120	NM_003128	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.014760	0.518382	188(AAGAACAGATTGTTTC,-,0.00),189(AGAACAGATTGTTTCT,+,0.00)
chunk0048_80_1	chr12	79015549	79016073	+	0	NA	intron (NM_001291901, intron 2 of 9)	intron (NM_001291901, intron 2 of 9)	-29842	NM_001135806	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.007634	0.339048	
chunk0103_336_1	chr2	167826943	167827236	+	0	NA	intron (NM_020981, intron 1 of 1)	intron (NM_020981, intron 1 of 1)	8417	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.006826	0.445578	157(TGGGACAGAATGTACA,-,0.00),158(GGGACAGAATGTACAA,+,0.00)
chunk0202_118_1	chr9	72983011	72983668	+	0	NA	Intergenic	Intergenic	-30022	NM_000689	216	Hs.76392	NM_000689	ENSG00000165092	ALDH1A1	ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1	aldehyde dehydrogenase 1 family member A1	protein-coding	0.001522	0.360182	
chunk0134_22_1	chr3	175490959	175491870	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	121874	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.002195	0.299342	
chunk0040_154_1	chr11	113761800	113762446	+	0	NA	intron (NM_004724, intron 2 of 15)	Tigger3|DNA|TcMar-Tigger	11640	NM_004724	9183	Hs.503886	NM_004724	ENSG00000086827	ZW10	HZW10|KNTC1AP	zw10 kinetochore protein	protein-coding	0.003096	0.377125	311(ATCACAGAGTGTACTT,+,0.00)
chunk0126_445_1	chr3	87154964	87155394	+	0	NA	intron (NR_104153, intron 2 of 2)	intron (NR_104153, intron 2 of 2)	65899	NR_047469	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.006977	0.348028	
chunk0046_358_1	chr12	63038271	63039039	+	0	NA	Intergenic	Intergenic	-103770	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.014323	0.430429	
chunk0031_265_1	chr10	127639419	127639978	+	0	NA	Intergenic	Intergenic	90349	NM_001030013	594857	Hs.643423	NM_001030013	ENSG00000214285	NPS	-	neuropeptide S	protein-coding	0.010733	0.366071	
chunk0208_126_1	chrX	15463863	15464132	+	0	NA	intron (NR_037859, intron 2 of 14)	L1ME3G|LINE|L1	27312	NR_037859	100532742	Hs.495728	NR_037859		PIR-FIGF	-	PIR-FIGF readthrough	ncRNA	0.007435	0.288889	
chunk0045_320_1	chr12	50762191	50762624	+	0	NA	Intergenic	Intergenic	-1599	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.016166	0.440092	
chunk0098_457_1	chr2	82487077	82487800	+	0	NA	Intergenic	MER57D|LTR|ERV1	-369365	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.004149	0.348066	
chunk0046_424_1	chr12	64625440	64625976	+	0	NA	intron (NR_040718, intron 1 of 3)	intron (NR_040718, intron 1 of 3)	-3103	NR_037515	100500856		NR_037515	ENSG00000266016	MIR548Z	-	microRNA 548z	ncRNA	0.024254	0.472998	
chunk0162_124_1	chr6	2887821	2888469	+	0	NA	3' UTR (NM_004155, exon 7 of 7)	3' UTR (NM_004155, exon 7 of 7)	4157	NR_110841	101927730	Hs.104879	NR_110841		LOC101927730	-	uncharacterized LOC101927730	ncRNA	0.001543	0.354391	217(AGGGACTGGATGTCCC,-,0.00),218(GGGACTGGATGTCCCA,+,0.00)
chunk0005_17_1	chr1	54277998	54278437	+	0	NA	intron (NM_018070, intron 5 of 16)	intron (NM_018070, intron 5 of 16)	41774	NR_103541	619518	Hs.591438	NM_001034847	ENSG00000198711	SSBP3-AS1	C1orf191|MST128|MSTP128	SSBP3 antisense RNA 1	ncRNA	0.004556	0.509091	
chunk0123_347_1	chr3	47985310	47985896	+	0	NA	intron (NM_030885, intron 2 of 3)	L1MC4|LINE|L1	103676	NM_002375	4134	Hs.517949	NM_002375	ENSG00000047849	MAP4	-	microtubule associated protein 4	protein-coding	0.003413	0.391823	
chunk0041_385_1	chr11	132393706	132393948	+	0	NA	Intergenic	Intergenic	109525	NR_046820	100874281		NR_046820		NTM-IT	NTM-IT3	NTM intronic transcript	ncRNA	0.004132	0.411523	155(AAGTACATTCTGCTCT,-,0.00),156(AGTACATTCTGCTCTC,+,0.00)
chunk0119_217_1	chr22	45118359	45119122	+	0	NA	Intergenic	L1M4|LINE|L1	33844	NR_038957	100506714	Hs.189902	NR_038956		NUP50-DT	NUP50-AS1	NUP50 divergent transcript	ncRNA	0.002621	0.361257	
chunk0156_197_1	chr5	107956022	107956635	+	0	NA	intron (NM_001163315, intron 7 of 8)	MER5A|DNA|hAT-Charlie	-285433	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.006525	0.350163	
chunk0080_424_1	chr17	35806834	35807808	+	0	NA	Intergenic	L1PA14|LINE|L1	-2134	NM_003487	8148	Hs.402752	NM_003487	ENSG00000270647	TAF15	Npl3|RBP56|TAF2N|TAFII68	TATA-box binding protein associated factor 15	protein-coding	0.005133	0.418462	593(AGGTTCACACTGTTCC,-,0.00),594(GGTTCACACTGTTCCT,+,0.00)
chunk0034_416_1	chr11	38380723	38381185	+	0	NA	Intergenic	Intergenic	265402	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.002165	0.367171	
chunk0106_199_1	chr2	202086962	202087287	+	0	NA	intron (NM_001277372, intron 2 of 21)	MER58A|DNA|hAT-Charlie	13869	NM_001277372	100652824	Hs.686898	NM_001080445	ENSG00000182329	KIAA2012	-	KIAA2012	protein-coding	0.003077	0.435583	
chunk0080_358_1	chr17	32925001	32925364	+	0	NA	Intergenic	MER51-int|LTR|ERV1	-2728	NM_001301746	26022	Hs.3447	NM_015544	ENSG00000006042	TMEM98	TADA1	transmembrane protein 98	protein-coding	0.000000	0.417582	
chunk0086_154_1	chr18	21457357	21457556	+	0	NA	intron (NM_001142966, intron 15 of 32)	intron (NM_001142966, intron 15 of 32)	143276	NM_052911	114799	Hs.464733	NM_052911	ENSG00000141446	ESCO1	A930014I12Rik|CTF|ECO1|EFO1|ESO1	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.000000	0.255000	
chunk0102_273_1	chr2	150130220	150130776	+	0	NA	Intergenic	Intergenic	357197	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.003597	0.378815	
chunk0185_361_1	chr7	132627261	132627632	+	0	NA	intron (NM_181775, intron 2 of 4)	HAL1|LINE|L1	21242	NM_181775	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.002695	0.330645	
chunk0124_411_1	chr3	60598739	60599075	+	0	NA	intron (NM_001166243, intron 4 of 9)	intron (NM_001166243, intron 4 of 9)	18963	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.002976	0.376855	
chunk0116_80_1	chr21	34728454	34728925	+	0	NA	intron (NR_024351, intron 4 of 5)	intron (NR_024351, intron 4 of 5)	8493	NR_024351	54064	Hs.436868	NR_024351	ENSG00000230978	LINC00160	C21orf52|NCRNA00160	long intergenic non-protein coding RNA 160	ncRNA	0.006369	0.476695	
chunk0097_79_1	chr2	44577792	44578312	+	0	NA	intron (NM_024766, intron 3 of 10)	MER34D|LTR|ERV1	216148	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.011538	0.362764	
chunk0120_70_1	chr3	3413372	3413824	+	0	NA	Intergenic	L1PB1|LINE|L1	-233881	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.008850	0.357616	
chunk0029_446_1	chr10	110424367	110424616	+	0	NA	Intergenic	Intergenic	-73376	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.000000	0.352000	160(AAGTACAGTGTGATCT,-,0.00),161(AGTACAGTGTGATCTT,+,0.00)
chunk0032_172_1	chr11	5610501	5610983	+	0	NA	intron (NM_001003819, intron 7 of 13)	intron (NM_001003819, intron 7 of 13)	-9202	NM_001003827	53840	Hs.729048	NM_021616	ENSG00000258659	TRIM34	IFP1|RNF21	tripartite motif containing 34	protein-coding	0.010373	0.486542	89(TGGCACATTCTGATCT,-,0.00),90(GGCACATTCTGATCTC,+,0.00)
chunk0118_358_1	chr22	36337530	36337784	+	0	NA	intron (NM_002473, intron 3 of 40)	intron (NM_002473, intron 3 of 40)	50410	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.007874	0.462745	
chunk0055_212_1	chr13	62102986	62103600	+	0	NA	Intergenic	L1MA8|LINE|L1	-73745	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.008143	0.349593	312(CAGAACATAATGCTCT,-,0.00),313(AGAACATAATGCTCTC,+,0.00)
chunk0174_93_1	chr6	156802802	156803016	+	0	NA	intron (NM_017519, intron 1 of 18)	intron (NM_017519, intron 1 of 18)	-23178	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.004673	0.293023	
chunk0165_341_1	chr6	37845486	37845826	+	0	NA	intron (NM_021943, intron 1 of 5)	intron (NM_021943, intron 1 of 5)	26125	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.008824	0.392962	
chunk0025_392_1	chr10	59342607	59343252	+	0	NA	intron (NM_001001971, intron 3 of 11)	intron (NM_001001971, intron 3 of 11)	19665	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.004651	0.360681	290(AAGAACACCCTGCTCT,-,0.00),291(AGAACACCCTGCTCTT,+,0.00)
chunk0105_227_1	chr2	188292954	188293288	+	0	NA	non-coding (NR_045563, exon 1 of 13)	non-coding (NR_045563, exon 1 of 13)	458	NR_045562	51454	Hs.470887	NM_016315	ENSG00000144366	GULP1	CED-6|CED6|GULP	GULP PTB domain containing engulfment adaptor 1	protein-coding	0.029940	0.531343	
chunk0101_331_1	chr2	136072526	136073267	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	43347	NM_001008540	7852	Hs.593413	NM_003467	ENSG00000121966	CXCR4	CD184|D2S201E|FB22|HM89|HSY3RR|LAP-3|LAP3|LCR1|LESTR|NPY3R|NPYR|NPYRL|NPYY3R|WHIM|WHIMS	C-X-C motif chemokine receptor 4	protein-coding	0.005398	0.396226	
chunk0038_287_1	chr11	90115541	90115951	+	0	NA	Intergenic	L1MA5A|LINE|L1	-18904	NM_005467	10003	Hs.112482	NM_005467	ENSG00000077616	NAALAD2	GCPIII|GPCIII|NAADALASE2|NAALADASE2	N-acetylated alpha-linked acidic dipeptidase 2	protein-coding	0.000000	0.364964	
chunk0067_162_1	chr15	44046255	44046821	+	0	NA	intron (NM_001286491, intron 1 of 14)	intron (NM_001286491, intron 1 of 14)	147908	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.003534	0.345679	
chunk0116_245_1	chr21	38612977	38613605	+	0	NA	intron (NR_111949, intron 1 of 4)	intron (NR_111949, intron 1 of 4)	-28346	NM_001243429	2078	Hs.473819	NM_004449	ENSG00000157554	ERG	erg-3|p55	ETS transcription factor ERG	protein-coding	0.022293	0.408585	
chunk0027_186_1	chr10	75507445	75508092	+	0	NA	intron (NM_001305581, intron 2 of 6)	intron (NM_001305581, intron 2 of 6)	-44690	NR_030337	693191		NR_030337	ENSG00000207583	MIR606	MIRN606|hsa-mir-606	microRNA 606	ncRNA	0.009274	0.402778	
chunk0113_115_1	chr20	51386559	51387047	+	0	NA	TTS (NM_012340)	TTS (NM_012340)	66174	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.010246	0.427403	
chunk0131_316_1	chr3	150877239	150877734	+	0	NA	Intergenic	Intergenic	66750	NM_052995	7401	Hs.745448	NM_052995	ENSG00000163646	CLRN1	RP61|USH3|USH3A	clarin 1	protein-coding	0.006061	0.421371	211(AAGCACATCATGTTCT,-,0.00),212(AGCACATCATGTTCTT,+,0.00)
chunk0210_459_1	chrX	106992805	106993134	+	0	NA	intron (NM_024657, intron 3 of 16)	L2b|LINE|L2	7275	NM_024657	79710	Hs.496544	NM_024657	ENSG00000133131	MORC4	ZCW4|ZCWCC2|dJ75H8.2	MORC family CW-type zinc finger 4	protein-coding	0.000000	0.381818	
chunk0137_181_1	chr4	17516360	17516836	+	0	NA	intron (NM_001079827, intron 1 of 2)	intron (NM_001079827, intron 1 of 2)	1433	NM_001079827	645104	Hs.631526	NM_001079827	ENSG00000249581	CLRN2	-	clarin 2	protein-coding	0.012605	0.312369	
chunk0097_379_1	chr2	61367339	61367613	+	0	NA	intron (NM_014709, intron 10 of 79)	FRAM|SINE|Alu	49901	NR_003707	100124537	Hs.675825	NR_003707	ENSG00000206937	SNORA70B	-	small nucleolar RNA, H/ACA box 70B	snoRNA	0.007299	0.410909	
chunk0201_273_1	chr9	38639103	38639548	+	0	NA	Intergenic	Intergenic	18237	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.000000	0.381166	
chunk0023_303_1	chr10	28833346	28833896	+	0	NA	Intergenic	Intergenic	-12787	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.010909	0.357532	
chunk0161_43_1	chr5	165920393	165920843	+	0	NA	Intergenic	L1M7|LINE|L1	1005752	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004444	0.328160	
chunk0105_44_1	chr2	182916188	182916931	+	0	NA	Intergenic	L2c|LINE|L2	-49789	NM_001463	2487	Hs.128453	NM_001463	ENSG00000162998	FRZB	FRE|FRITZ|FRP-3|FRZB-1|FRZB-PEN|FRZB1|FZRB|OS1|SFRP3|SRFP3|hFIZ	frizzled related protein	protein-coding	0.005384	0.369624	
chunk0028_395_1	chr10	92997248	92997815	+	0	NA	exon (NM_001013848, exon 19 of 22)	exon (NM_001013848, exon 19 of 22)	-63733	NM_183374	340665	Hs.369993	NM_183374	ENSG00000187553	CYP26C1	FFDD4	cytochrome P450 family 26 subfamily C member 1	protein-coding	0.000000	0.350352	
chunk0046_196_1	chr12	58915145	58916066	+	0	NA	intron (NM_153377, intron 1 of 18)	intron (NM_153377, intron 1 of 18)	3941	NM_001136051	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.006515	0.377440	
chunk0044_10_1	chr12	27012378	27012727	+	0	NA	intron (NM_016551, intron 1 of 11)	intron (NM_016551, intron 1 of 11)	1854	NM_016551	51768	Hs.438641	NM_016551	ENSG00000064115	TM7SF3	-	transmembrane 7 superfamily member 3	protein-coding	0.008596	0.391429	155(CAAAACAGAATGTGCT,-,0.00),156(AAAACAGAATGTGCTT,+,0.00),184(AAGCACATGATGATCT,-,0.00),185(AGCACATGATGATCTG,+,0.00)
chunk0130_429_1	chr3	140911965	140912169	+	0	NA	Intergenic	Intergenic	-29753	NM_001104647	55186	Hs.144130	NM_018155	ENSG00000114120	SLC25A36	PNC2	solute carrier family 25 member 36	protein-coding	0.004902	0.439024	
chunk0107_457_1	chr2	225793147	225793407	+	0	NA	Intergenic	L1MEc|LINE|L1	-349517	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003846	0.272031	
chunk0039_171_1	chr11	99693964	99694225	+	0	NA	intron (NM_175566, intron 1 of 21)	L2c|LINE|L2	137949	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.022989	0.381679	
chunk0199_389_1	chr9	13208768	13209189	+	0	NA	intron (NM_003829, intron 10 of 45)	L1M6B|LINE|L1	70586	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.002375	0.412322	
chunk0014_250_1	chr1	180073600	180074622	+	0	NA	intron (NM_014810, intron 27 of 37)	intron (NM_014810, intron 27 of 37)	-80722	NM_002826	5768	Hs.719176	NM_002826	ENSG00000116260	QSOX1	Q6|QSCN6	quiescin sulfhydryl oxidase 1	protein-coding	0.004892	0.356794	815(TGGTACTCAGTGTTCT,-,0.00),816(GGTACTCAGTGTTCTC,+,0.00)
chunk0004_431_1	chr1	52880155	52880478	+	0	NA	intron (NM_001004339, intron 10 of 13)	intron (NM_001004339, intron 10 of 13)	37805	NM_001004339	440590	Hs.658458	NM_001004339	ENSG00000203995	ZYG11A	ZYG11	zyg-11 family member A, cell cycle regulator	protein-coding	0.006192	0.425926	
chunk0157_459_1	chr5	125012788	125013069	+	0	NA	Intergenic	Intergenic	-23903	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.014235	0.446809	
chunk0116_367_1	chr21	41783433	41784346	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-16800	NM_020639	54101	Hs.517310	NM_020639	ENSG00000183421	RIPK4	ANKK2|ANKRD3|CHANDS|DIK|NKRD3|PKK|PPS2|RIP4	receptor interacting serine/threonine kinase 4	protein-coding	0.019715	0.500000	
chunk0090_314_1	chr18	75475201	75475759	+	0	NA	Intergenic	Intergenic	-47777	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.005376	0.361360	
chunk0101_468_1	chr2	140880752	140881029	+	0	NA	intron (NM_018557, intron 25 of 90)	intron (NM_018557, intron 25 of 90)	-294205	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.284173	
chunk0157_204_1	chr5	119080836	119081408	+	0	NA	intron (NM_001290321, intron 1 of 43)	intron (NM_001290321, intron 1 of 43)	10035	NM_001290322	1657	Hs.181042	NM_005509	ENSG00000172869	DMXL1	-	Dmx like 1	protein-coding	0.006993	0.418848	
chunk0136_159_1	chr4	5703240	5703624	+	0	NA	intron (NM_001166136, intron 1 of 21)	L2b|LINE|L2	5135	NM_147127	132884	Hs.87306	NM_147127	ENSG00000173040	EVC2	LBN|WAD	EvC ciliary complex subunit 2	protein-coding	0.010417	0.433766	
chunk0022_35_1	chr10	7980097	7980685	+	0	NA	intron (NM_031923, intron 4 of 6)	intron (NM_031923, intron 4 of 6)	72100	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.001701	0.383701	
chunk0129_176_1	chr3	120892826	120893622	+	0	NA	Intergenic	Intergenic	-14979	NM_014980	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.001256	0.299875	585(AAGGCCACAGTGTTCC,-,0.00),586(AGGCCACAGTGTTCCT,+,0.00)
chunk0020_95_1	chr1	232827776	232828111	+	0	NA	Intergenic	L1PB1|LINE|L1	23051	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.000000	0.369048	
chunk0030_412_1	chr10	120195819	120196018	+	0	NA	Intergenic	L1MA4A|LINE|L1	159305	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.000000	0.575000	
chunk0192_344_1	chr8	67729192	67729966	+	0	NA	intron (NM_020361, intron 1 of 10)	L2c|LINE|L2	16806	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.009044	0.362581	
chunk0039_214_1	chr11	101119335	101119920	+	0	NA	intron (NM_000926, intron 2 of 7)	intron (NM_000926, intron 2 of 7)	9436	NR_073143	5241	Hs.32405	NM_000926	ENSG00000082175	PGR	NR3C3|PR	progesterone receptor	protein-coding	0.005128	0.346416	
chunk0174_255_1	chr6	161068214	161068744	+	0	NA	intron (NM_001291958, intron 4 of 27)	intron (NM_001291958, intron 4 of 27)	76752	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.005660	0.416196	
chunk0063_140_1	chr14	79525481	79526001	+	0	NA	intron (NR_073547, intron 15 of 20)	intron (NR_073547, intron 15 of 20)	246402	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.003846	0.403071	
chunk0199_408_1	chr9	13547214	13547485	+	0	NA	Intergenic	MIRb|SINE|MIR	-116020	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.003690	0.301471	
chunk0076_322_1	chr16	70645450	70645649	+	0	NA	intron (NM_001172772, intron 1 of 6)	intron (NM_001172772, intron 1 of 6)	21557	NM_001172772	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.025126	0.550000	
chunk0066_210_1	chr15	33848567	33848818	+	0	NA	intron (NM_001036, intron 94 of 103)	intron (NM_001036, intron 94 of 103)	-120196	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.007968	0.400794	
chunk0178_135_1	chr7	32668433	32668905	+	0	NA	intron (NR_036680, intron 5 of 16)	HAL1|LINE|L1	50499	NR_036680	100129460	Hs.633705	NR_036680		DPY19L1P1	-	DPY19L1 pseudogene 1	pseudo	0.006356	0.412262	
chunk0127_46_1	chr3	88960009	88960470	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-147285	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.008677	0.404762	
chunk0045_248_1	chr12	49054974	49055490	+	0	NA	promoter-TSS (NM_003482)	promoter-TSS (NM_003482)	92	NM_003482	8085	Hs.731384	NM_003482	ENSG00000167548	KMT2D	AAD10|ALR|CAGL114|KABUK1|KMS|MLL2|MLL4|TNRC21	lysine methyltransferase 2D	protein-coding	0.007752	0.468085	
chunk0123_38_1	chr3	40773865	40774284	+	0	NA	Intergenic	Intergenic	249196	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.009547	0.452381	
chunk0053_55_1	chr13	27671357	27671626	+	0	NA	Intergenic	Intergenic	49712	NM_152705	51082	Hs.507584	NM_015972	ENSG00000186184	POLR1D	AC19|POLR1C|RPA16|RPA9|RPAC2|RPC16|RPO1-3|TCS2	RNA polymerase I and III subunit D	protein-coding	0.000000	0.300000	
chunk0176_319_1	chr7	17032215	17032724	+	0	NA	Intergenic	Intergenic	-150480	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.000000	0.345098	
chunk0105_191_1	chr2	187577177	187577376	+	0	NA	Intergenic	Intergenic	-22784	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.365000	
chunk0186_369_1	chr7	143967411	143967910	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	7733	NM_012369	26211	Hs.553595	NM_012369	ENSG00000213215	OR2F1	7M1-2|OLF3|OR14-60|OR2F3|OR2F3P|OR2F4|OR2F5|OR7-139|OR7-140	olfactory receptor family 2 subfamily F member 1 (gene/pseudogene)	protein-coding	0.010020	0.360000	
chunk0130_289_1	chr3	136567616	136567905	+	0	NA	intron (NM_005862, intron 5 of 33)	MIR|SINE|MIR	184643	NM_005862	10274	Hs.412586	NM_005862	ENSG00000118007	STAG1	MRD47|SA1|SCC3A	stromal antigen 1	protein-coding	0.000000	0.375862	
chunk0142_79_1	chr4	93890869	93891112	+	0	NA	Intergenic	Intergenic	62063	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.028807	0.459016	
chunk0002_376_1	chr1	26552849	26553339	+	0	NA	intron (NM_001006665, intron 5 of 20)	L1MC5a|LINE|L1	-1448	NR_031740	100302190		NR_031740	ENSG00000238705	MIR1976	hsa-mir-1976	microRNA 1976	ncRNA	0.006122	0.452138	
chunk0111_401_1	chr20	34270100	34270805	+	0	NA	Intergenic	Intergenic	10087	NM_001672	434	Hs.659995	NM_001672	ENSG00000101440	ASIP	AGSW|AGTI|AGTIL|ASP|SHEP9	agouti signaling protein	protein-coding	0.008511	0.473088	
chunk0113_413_1	chr20	61723557	61723842	+	0	NA	intron (NM_001252339, intron 1 of 14)	intron (NM_001252339, intron 1 of 14)	123938	NM_001252339	1002	Hs.473231	NM_001794	ENSG00000179242	CDH4	CAD4|R-CAD|RCAD	cadherin 4	protein-coding	0.010526	0.486014	
chunk0212_8_1	chrY	7110774	7111119	+	0	NA	Intergenic	Intergenic	-163026	NR_028062	5616	Hs.584730	NM_002760	ENSG00000099725	PRKY	PRKXP3|PRKYP	protein kinase Y-linked (pseudogene)	pseudo	0.011594	0.456647	
chunk0073_110_1	chr16	4624205	4624760	+	0	NA	promoter-TSS (NM_001142289)	promoter-TSS (NM_001142289)	-342	NM_001142291	23295	Hs.526494	NM_015246	ENSG00000102858	MGRN1	RNF156	mahogunin ring finger 1	protein-coding	0.041441	0.573741	
chunk0002_245_1	chr1	20834809	20835008	+	0	NA	intron (NM_001198801, intron 28 of 34)	L1M1|LINE|L1	-48220	NM_016287	50809	Hs.142442	NM_016287	ENSG00000127483	HP1BP3	HP1-BP74|HP1BP74	heterochromatin protein 1 binding protein 3	protein-coding	0.000000	0.310000	
chunk0076_240_1	chr16	69173494	69174026	+	0	NA	Intergenic	Intergenic	-13387	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.007519	0.407129	
chunk0024_244_1	chr10	38590295	38590494	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	-106202	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.025126	0.355000	
chunk0006_5_1	chr1	63788873	63789296	+	0	NA	intron (NM_001083592, intron 1 of 6)	intron (NM_001083592, intron 1 of 6)	15065	NM_001083592	4919	Hs.128753	NM_005012	ENSG00000185483	ROR1	NTRKR1|dJ537F10.1	receptor tyrosine kinase like orphan receptor 1	protein-coding	0.021277	0.511792	58(AGGTACAGGCTGTGAT,-,0.00)
chunk0171_156_1	chr6	124036480	124036719	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	232753	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.008368	0.362500	
chunk0114_53_1	chr21	8465268	8465524	+	0	NA	Intergenic	(CTCT)n|Simple_repeat|Simple_repeat	24250	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.023438	0.474708	
chunk0202_112_1	chr9	72577147	72577819	+	0	NA	intron (NM_138691, intron 1 of 23)	intron (NM_138691, intron 1 of 23)	55682	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.007440	0.427935	
chunk0046_352_1	chr12	62969581	62970015	+	0	NA	Intergenic	L2a|LINE|L2	-34913	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.009217	0.413793	
chunk0166_349_1	chr6	51152937	51153353	+	0	NA	Intergenic	Intergenic	334419	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.007212	0.386091	
chunk0050_260_1	chr12	105907849	105908363	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	201332	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.003891	0.372816	
chunk0082_221_1	chr17	57175150	57175349	+	0	NA	Intergenic	Intergenic	-81321	NM_138962	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.025126	0.570000	
chunk0203_104_1	chr9	84485413	84486006	+	0	NA	Intergenic	Intergenic	-117211	NM_022127	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.005059	0.446128	
chunk0144_225_1	chr4	134628848	134629567	+	0	NA	Intergenic	Intergenic	-427459	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.002782	0.306944	
chunk0038_427_1	chr11	94543448	94543862	+	0	NA	promoter-TSS (NM_002033)	promoter-TSS (NM_002033)	-196	NM_002033	2526	Hs.390420	NM_002033	ENSG00000196371	FUT4	CD15|ELFT|FCT3A|FUC-TIV|FUTIV|LeX|SSEA-1	fucosyltransferase 4	protein-coding	0.043478	0.522892	168(GAAAACATTTTGTTCT,-,0.00),169(AAAACATTTTGTTCTC,+,0.00)
chunk0170_3_1	chr6	109002094	109002941	+	0	NA	intron (NM_014454, intron 1 of 9)	intron (NM_014454, intron 1 of 9)	6471	NM_001199934	27244	Hs.591336	NM_014454	ENSG00000080546	SESN1	PA26|SEST1	sestrin 1	protein-coding	0.005903	0.363208	508(TAGAACAGAAAGTTCA,-,0.00),509(AGAACAGAAAGTTCAG,+,0.00)
chunk0047_344_1	chr12	74792123	74792459	+	0	NA	Intergenic	Intergenic	254520	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.005952	0.258160	
chunk0118_284_1	chr22	33832337	33832953	+	0	NA	intron (NM_133642, intron 1 of 14)	intron (NM_133642, intron 1 of 14)	87783	NM_004737	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.012987	0.542950	
chunk0020_235_1	chr1	235785374	235785599	+	0	NA	intron (NM_001301365, intron 14 of 52)	intron (NM_001301365, intron 14 of 52)	67574	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.000000	0.331858	
chunk0151_27_1	chr5	41761558	41762252	+	0	NA	intron (NM_000436, intron 14 of 16)	intron (NM_000436, intron 14 of 16)	-108125	NR_046635	100874002	Hs.375537	NR_046635	ENSG00000248668	OXCT1-AS1	-	OXCT1 antisense RNA 1	ncRNA	0.004323	0.352518	
chunk0002_80_1	chr1	14313295	14313635	+	0	NA	Intergenic	Intergenic	-285252	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.005882	0.354839	
chunk0033_201_1	chr11	16804504	16805001	+	0	NA	intron (NM_175058, intron 13 of 22)	intron (NM_175058, intron 13 of 22)	66151	NM_014267	10944	Hs.368226	NM_014267	ENSG00000110696	C11orf58	IMAGE145052|SMAP	chromosome 11 open reading frame 58	protein-coding	0.012072	0.483936	
chunk0067_418_1	chr15	49691251	49691886	+	0	NA	Intergenic	L2a|LINE|L2	70539	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.004724	0.413522	
chunk0089_340_1	chr18	65771832	65772105	+	0	NA	intron (NM_004361, intron 2 of 11)	intron (NM_004361, intron 2 of 11)	21047	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.007326	0.361314	
chunk0127_325_1	chr3	100153643	100153873	+	0	NA	intron (NM_032359, intron 2 of 9)	MLT1B|LTR|ERVL-MaLR	-32066	NR_028357	644444	Hs.652353	NR_028357	ENSG00000235156	TMEM30CP	CDC50C|TMEM30C	transmembrane protein 30C, pseudogene	pseudo	0.000000	0.324675	
chunk0151_88_1	chr5	42853663	42854236	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	-42027	NM_001093726	6414	Hs.275775	NM_005410	ENSG00000250722	SELENOP	SELP|SEPP|SEPP1|SeP	selenoprotein P	protein-coding	0.000000	0.381533	
chunk0038_24_1	chr11	81119289	81119903	+	0	NA	Intergenic	Intergenic	-356793	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.008143	0.320325	
chunk0175_132_1	chr7	3449455	3449961	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	148260	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.007905	0.374753	
chunk0179_269_1	chr7	49319811	49320010	+	0	NA	Intergenic	L1MD2|LINE|L1	395349	NR_003595									0.000000	0.330000	
chunk0025_156_1	chr10	52421645	52422250	+	0	NA	Intergenic	L2a|LINE|L2	33325	NR_120642	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.000000	0.341584	
chunk0001_129_1	chr1	4754227	4754480	+	0	NA	intron (NM_001042478, intron 2 of 5)	MER58B|DNA|hAT-Charlie	99308	NM_018836	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.000000	0.460630	
chunk0014_301_1	chr1	181022603	181023324	+	0	NA	5' UTR (NM_001286210, exon 1 of 6)	5' UTR (NM_001286210, exon 1 of 6)	158	NM_005819	10228	Hs.518417	NM_005819	ENSG00000135823	STX6	-	syntaxin 6	protein-coding	0.076283	0.670360	
chunk0053_184_1	chr13	31074208	31074687	+	0	NA	Intergenic	Intergenic	87574	NM_001286503	10808	Hs.743267	NM_006644	ENSG00000120694	HSPH1	HSP105|HSP105A|HSP105B|NY-CO-25	heat shock protein family H (Hsp110) member 1	protein-coding	0.008351	0.464583	
chunk0142_379_1	chr4	102282101	102282699	+	0	NA	intron (NM_022154, intron 5 of 7)	Tigger10|DNA|TcMar-Tigger	41912	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.003344	0.367279	435(CAGGACAAGATGTTTT,-,0.00),436(AGGACAAGATGTTTTT,+,0.00)
chunk0212_401_1	chrX	151384840	151385320	+	0	NA	Intergenic	Intergenic	-12105	NM_001017980	203547	Hs.58633	NM_001017980	ENSG00000160131	VMA21	MEAX|XMEA	vacuolar ATPase assembly factor VMA21	protein-coding	0.016667	0.534304	
chunk0189_219_1	chr8	24354765	24355378	+	0	NA	non-coding (NR_130710, exon 23 of 23)	non-coding (NR_130710, exon 23 of 23)	-29214	NM_001145272	27299	Hs.521459	NM_014479	ENSG00000134028	ADAMDEC1	M12.219	ADAM like decysin 1	protein-coding	0.004894	0.311075	
chunk0077_448_1	chr16	85777838	85778307	+	0	NA	TTS (NM_001142288)	TTS (NM_001142288)	21470	NM_006067	10328	Hs.173162	NM_006067	ENSG00000131148	EMC8	C16orf2|C16orf4|COX4NB|FAM158B|NOC4	ER membrane protein complex subunit 8	protein-coding	0.008529	0.482979	
chunk0111_8_1	chr20	21804789	21805121	+	0	NA	Intergenic	Intergenic	99296	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.018072	0.447447	
chunk0016_273_1	chr1	200570876	200571192	+	0	NA	intron (NM_001305792, intron 20 of 27)	intron (NM_001305792, intron 20 of 27)	47804	NM_001305792	9928	Hs.3104	NM_014875	ENSG00000118193	KIF14	MCPH20|MKS12	kinesin family member 14	protein-coding	0.006329	0.406940	
chunk0135_151_1	chr3	187730643	187731027	+	0	NA	intron (NM_001130845, intron 4 of 9)	L3|LINE|CR1	4072	NM_001134738	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.007812	0.457143	274(GGGAACACTGAGTTCC,-,0.00),275(GGAACACTGAGTTCCT,+,0.00)
chunk0089_222_1	chr18	61412480	61412749	+	0	NA	Intergenic	Intergenic	-77928	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.000000	0.292593	
chunk0036_364_1	chr11	67119224	67119497	+	0	NA	promoter-TSS (NM_012308)	promoter-TSS (NM_012308)	91	NM_012308	22992	Hs.124147	NM_012308	ENSG00000173120	KDM2A	CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA	lysine demethylase 2A	protein-coding	0.087912	0.700730	
chunk0030_168_1	chr10	114081897	114082262	+	0	NA	Intergenic	Intergenic	38032	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.005479	0.352459	
chunk0209_111_1	chrX	40468046	40468613	+	0	NA	Intergenic	MIRb|SINE|MIR	-112635	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.007055	0.491197	467(CAGAACACAGTGGCCC,-,0.00),468(AGAACACAGTGGCCCT,+,0.00)
chunk0096_462_1	chr2	40192944	40193193	+	0	NA	intron (NM_021097, intron 1 of 9)	intron (NM_021097, intron 1 of 9)	237236	NM_001252624	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.016064	0.400000	
chunk0101_112_1	chr2	125805583	125805924	+	0	NA	Intergenic	Intergenic	-850182	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.008798	0.380117	
chunk0139_19_1	chr4	48254943	48255142	+	0	NA	intron (NM_003215, intron 1 of 17)	intron (NM_003215, intron 1 of 17)	14755	NM_003215	7006	Hs.479670	NM_003215	ENSG00000135605	TEC	PSCTK4	tec protein tyrosine kinase	protein-coding	0.015075	0.420000	
chunk0051_127_1	chr12	115421900	115422329	+	0	NA	Intergenic	L2a|LINE|L2	726540	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.011655	0.458140	
chunk0069_360_1	chr15	67135550	67135846	+	0	NA	intron (NM_001145102, intron 1 of 8)	intron (NM_001145102, intron 1 of 8)	-2323	NM_001145103	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.010135	0.383838	
chunk0012_199_1	chr1	159949031	159949537	+	0	NA	Intergenic	L2b|LINE|L2	-3688	NM_001135050	57549	Hs.591472	NM_020789	ENSG00000085552	IGSF9	FP18798|IGSF9A|Nrt1	immunoglobulin superfamily member 9	protein-coding	0.011858	0.475345	
chunk0037_9_1	chr11	68903732	68903989	+	0	NA	promoter-TSS (NM_002180)	promoter-TSS (NM_002180)	9	NM_002180	3508	Hs.503048	NM_002180	ENSG00000132740	IGHMBP2	CATF1|CMT2S|HCSA|HMN6|SMARD1|SMUBP2|ZFAND7	immunoglobulin mu DNA binding protein 2	protein-coding	0.132296	0.705426	
chunk0007_72_1	chr1	78351490	78352348	+	0	NA	intron (NR_027310, intron 4 of 5)	intron (NR_027310, intron 4 of 5)	122320	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.002331	0.377183	
chunk0050_379_1	chr12	108704687	108704938	+	0	NA	intron (NM_014325, intron 1 of 10)	MIR|SINE|MIR	-1814	NM_001105237	23603	Hs.330384	NM_014325	ENSG00000110880	CORO1C	HCRNN4	coronin 1C	protein-coding	0.011952	0.440476	
chunk0166_6_1	chr6	41456685	41457135	+	0	NA	Intergenic	Intergenic	-45534	NR_120347	103106903	Hs.563396	NR_120347	ENSG00000226917	LINC01276	-	long intergenic non-protein coding RNA 1276	ncRNA	0.011111	0.567627	
chunk0093_320_1	chr19	53869555	53869863	+	0	NA	5' UTR (NM_001020818, exon 1 of 2)	5' UTR (NM_001020818, exon 1 of 2)	318	NM_001020818	91663	Hs.380906	NM_138373	ENSG00000179820	MYADM	SB135	myeloid associated differentiation marker	protein-coding	0.068182	0.637540	
chunk0014_444_1	chr1	183804936	183805135	+	0	NA	promoter-TSS (NM_001297671)	promoter-TSS (NM_001297671)	-46	NM_001297672	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.060302	0.545000	
chunk0019_86_1	chr1	224528937	224529301	+	0	NA	Intergenic	Intergenic	-87358	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.008242	0.501370	
chunk0212_344_1	chrX	146940057	146940612	+	0	NA	Intergenic	L1MA2|LINE|L1	-125603	NM_001144064	100129239	Hs.592233	NM_001144064	ENSG00000224440	CXorf51A	CXorf51|CXorf51B	chromosome X open reading frame 51A	protein-coding	0.005405	0.314748	
chunk0123_213_1	chr3	45126876	45127454	+	0	NA	intron (NM_022842, intron 1 of 8)	intron (NM_022842, intron 1 of 8)	19257	NM_178181	64866	Hs.476093	NM_022842	ENSG00000163814	CDCP1	CD318|SIMA135|TRASK	CUB domain containing protein 1	protein-coding	0.012111	0.428325	
chunk0085_99_1	chr18	2695734	2696196	+	0	NA	intron (NM_015295, intron 8 of 47)	intron (NM_015295, intron 8 of 47)	40078	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.008658	0.267819	232(AGGAACTCAGTGTACA,-,0.00),233(GGAACTCAGTGTACAT,+,0.00)
chunk0119_343_1	chr22	47069360	47070689	+	0	NA	intron (NM_014346, intron 11 of 12)	intron (NM_014346, intron 11 of 12)	-153982	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.039880	0.578947	
chunk0017_126_1	chr1	206478183	206478598	+	0	NA	intron (NM_001193322, intron 9 of 20)	intron (NM_001193322, intron 9 of 20)	3587	NR_106919	102466202		NR_106919	ENSG00000278465	MIR6769B	hsa-mir-6769b	microRNA 6769b	ncRNA	0.026506	0.504808	
chunk0134_48_1	chr3	175803136	175803622	+	0	NA	3' UTR (NM_207015, exon 14 of 14)	3' UTR (NM_207015, exon 14 of 14)	-27046	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.297741	
chunk0145_69_1	chr4	145621419	145621981	+	0	NA	intron (NM_172250, intron 1 of 6)	intron (NM_172250, intron 1 of 6)	2312	NM_172250	166785	Hs.452864	NM_172250	ENSG00000151611	MMAA	cblA	metabolism of cobalamin associated A	protein-coding	0.001779	0.321492	
chunk0195_297_1	chr8	98690497	98690781	+	0	NA	intron (NM_001256313, intron 4 of 8)	L1PA17|LINE|L1	135032	NM_001256313	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.007042	0.350877	
chunk0030_418_1	chr10	120259565	120259998	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	95442	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.011547	0.391705	
chunk0190_459_1	chr8	42280608	42280817	+	0	NA	intron (NM_001242778, intron 2 of 20)	intron (NM_001242778, intron 2 of 20)	9410	NM_001190720	3551	Hs.597664	NM_001556	ENSG00000104365	IKBKB	IKK-beta|IKK2|IKKB|IMD15|IMD15A|IMD15B|NFKBIKB	inhibitor of nuclear factor kappa B kinase subunit beta	protein-coding	0.019139	0.571429	
chunk0057_314_1	chr13	106704720	106704990	+	0	NA	Intergenic	L2a|LINE|L2	50975	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.014815	0.435424	
chunk0117_26_1	chr22	11818926	11819150	+	0	NA	Intergenic	ACRO1|Satellite|acro	-78368	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.017857	0.608889	
chunk0190_204_1	chr8	35178278	35178560	+	0	NA	Intergenic	L1PB3|LINE|L1	-57038	NM_080872	137970	Hs.238889	NM_080872	ENSG00000156687	UNC5D	PRO34692|Unc5h4	unc-5 netrin receptor D	protein-coding	0.007092	0.321555	62(CAGGACTAGCTGTTCT,-,0.00),63(AGGACTAGCTGTTCTT,+,0.00)
chunk0194_83_1	chr8	82892452	82893184	+	0	NA	Intergenic	Intergenic	-510940	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.001366	0.305593	
chunk0171_398_1	chr6	131225815	131226448	+	0	NA	intron (NM_016377, intron 7 of 7)	MER102c|DNA|hAT-Charlie	-24028	NM_138633	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.006319	0.392744	
chunk0115_355_1	chr21	29409742	29410315	+	0	NA	Intergenic	Intergenic	37527	NR_046564	100874322	Hs.326404	NR_046564		BACH1-IT2	-	BACH1 intronic transcript 2	ncRNA	0.003490	0.388502	
chunk0186_270_1	chr7	141681715	141682003	+	0	NA	intron (NM_001080392, intron 3 of 8)	MLT1J-int|LTR|ERVL-MaLR	20294	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.000000	0.422145	
chunk0101_462_1	chr2	140370698	140370897	+	0	NA	exon (NM_018557, exon 71 of 91)	exon (NM_018557, exon 71 of 91)	215888	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.005025	0.375000	
chunk0052_270_1	chr12	124136768	124137377	+	0	NA	intron (NM_001204299, intron 2 of 4)	MLT1K|LTR|ERVL-MaLR	-152092	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.001642	0.424590	
chunk0034_105_1	chr11	27710352	27711209	+	0	NA	intron (NM_170731, intron 1 of 1)	intron (NM_170731, intron 1 of 1)	8967	NM_001143807	627	Hs.502182	NM_001709	ENSG00000176697	BDNF	ANON2|BULN2	brain derived neurotrophic factor	protein-coding	0.003501	0.372960	
chunk0084_356_1	chr17	81365783	81366270	+	0	NA	Intergenic	Intergenic	19334	NM_001272086	100130370	Hs.646594	NM_001272086		LOC100130370	-	uncharacterized LOC100130370	protein-coding	0.030801	0.590164	
chunk0148_273_1	chr5	10538652	10539426	+	0	NA	Intergenic	Intergenic	-25284	NM_001164440	651746	Hs.26039	NM_001164440	ENSG00000164236	ANKRD33B	-	ankyrin repeat domain 33B	protein-coding	0.024548	0.521290	192(AAGAACATGCTGTGCA,-,0.00),193(AGAACATGCTGTGCAA,+,0.00)
chunk0087_148_1	chr18	34082166	34082733	+	0	NA	intron (NM_003787, intron 5 of 10)	MIR|SINE|MIR	-33837	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.008818	0.376761	
chunk0078_68_1	chr17	1560354	1561018	+	0	NA	intron (NM_006224, intron 1 of 11)	intron (NM_006224, intron 1 of 11)	2130	NM_006224	5306	Hs.429819	NM_006224	ENSG00000174238	PITPNA	HEL-S-36|PI-TPalpha|PITPN|VIB1A	phosphatidylinositol transfer protein alpha	protein-coding	0.022590	0.529323	
chunk0111_344_1	chr20	33209899	33210129	+	0	NA	intron (NR_026760, intron 8 of 8)	intron (NR_026760, intron 8 of 8)	-7296	NM_001042439	128861	Hs.360989	NM_178466	ENSG00000131059	BPIFA3	C20orf71|SPLUNC3	BPI fold containing family A member 3	protein-coding	0.039130	0.523810	
chunk0080_352_1	chr17	32854177	32854767	+	0	NA	intron (NM_015194, intron 1 of 21)	Tigger19a|DNA|TcMar-Tigger	22701	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.001695	0.345178	
chunk0143_121_1	chr4	109434933	109435835	+	0	NA	intron (NM_001042734, intron 1 of 22)	intron (NM_001042734, intron 1 of 22)	-1567	NR_039978	100533182	Hs.518927	NR_039978	ENSG00000247950	SEC24B-AS1	1/2-SBSRNA4	SEC24B antisense RNA 1	ncRNA	0.004435	0.347730	
chunk0204_117_1	chr9	95032621	95033115	+	0	NA	intron (NM_032823, intron 11 of 14)	intron (NM_032823, intron 11 of 14)	-32482	NR_106729	102466518		NR_106729	ENSG00000274115	MIR6081	hsa-mir-6081	microRNA 6081	ncRNA	0.006073	0.458586	
chunk0149_2_1	chr5	15450653	15450978	+	0	NA	Intergenic	Intergenic	-49381	NM_012304	23194	Hs.433057	NM_012304	ENSG00000183580	FBXL7	FBL6|FBL7	F-box and leucine rich repeat protein 7	protein-coding	0.033846	0.582822	
chunk0188_435_1	chr8	19159159	19159845	+	0	NA	Intergenic	Intergenic	86020	NR_038919	100128993	Hs.697742	NR_038919		LOC100128993	-	uncharacterized LOC100128993	ncRNA	0.007289	0.320233	
chunk0166_251_1	chr6	47478967	47479264	+	0	NA	intron (NM_012120, intron 1 of 17)	intron (NM_012120, intron 1 of 17)	1326	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.010101	0.375839	
chunk0031_38_1	chr10	122124520	122124835	+	0	NA	intron (NM_001291879, intron 1 of 16)	intron (NM_001291879, intron 1 of 16)	11638	NM_001291879	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.025397	0.518987	
chunk0179_370_1	chr7	51161397	51161793	+	0	NA	intron (NM_001287436, intron 5 of 13)	intron (NM_001287436, intron 5 of 13)	155223	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.007576	0.370277	
chunk0142_260_1	chr4	99167907	99168226	+	0	NA	intron (NR_037884, intron 3 of 9)	L1PB3|LINE|L1	-6419	NR_028270	359806	Hs.537400	NR_028270		PCNAP1	p1PCNA	proliferating cell nuclear antigen pseudogene 1	pseudo	0.000000	0.315625	
chunk0026_107_1	chr10	61838029	61838401	+	0	NA	Intergenic	Intergenic	-63039	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.005376	0.378016	
chunk0209_338_1	chrX	51505677	51506139	+	0	NA	non-coding (NR_110654, exon 2 of 5)	non-coding (NR_110654, exon 2 of 5)	1533	NR_110654	102723426	Hs.584513	NR_110654		LINC01496	-	long intergenic non-protein coding RNA 1496	ncRNA	0.008658	0.444924	102(ATGCACAGCTAGTCCC,-,0.00),206(ATAACACTGTGTACCC,+,0.00)
chunk0010_435_1	chr1	119882722	119882948	+	0	NA	Intergenic	Intergenic	13689	NM_021794	11085	Hs.283011	NM_021794	ENSG00000134249	ADAM30	svph4	ADAM metallopeptidase domain 30	protein-coding	0.008850	0.427313	
chunk0095_339_1	chr2	20845382	20845972	+	0	NA	Intergenic	Intergenic	-22547	NM_001282722	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.005085	0.323181	245(TGGAACAAGGTGTACT,-,0.00),246(GGAACAAGGTGTACTT,+,0.00)
chunk0055_218_1	chr13	62405464	62405735	+	0	NA	Intergenic	Intergenic	193317	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.011070	0.419118	
chunk0077_380_1	chr16	84672458	84672884	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	24160	NM_024731	79786	Hs.222731	NM_024731	ENSG00000135686	KLHL36	C16orf44	kelch like family member 36	protein-coding	0.037559	0.557377	
chunk0025_398_1	chr10	59406550	59406971	+	0	NA	Intergenic	Intergenic	-43857	NM_001143773	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.011876	0.246445	
chunk0063_52_1	chr14	77033169	77033599	+	0	NA	Intergenic	CpG	-4685	NM_024496	64207	Hs.179260	NM_024496	ENSG00000119669	IRF2BPL	C14orf4|EAP1|NEDAMSS	interferon regulatory factor 2 binding protein like	protein-coding	0.051163	0.563805	
chunk0047_8_1	chr12	65082098	65082622	+	0	NA	intron (NM_007191, intron 2 of 9)	intron (NM_007191, intron 2 of 9)	39206	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.001908	0.329524	38(AGGACTTTCTGTTTTT,+,0.00),280(AAGTACATTTTGTTCC,-,0.00),281(AGTACATTTTGTTCCA,+,0.00)
chunk0140_369_1	chr4	74638427	74638626	+	0	NA	Intergenic	Intergenic	156160	NM_001316963	685	Hs.591704	NM_001729	ENSG00000174808	BTC	-	betacellulin	protein-coding	0.000000	0.270000	
chunk0050_79_1	chr12	101615890	101616587	+	0	NA	intron (NM_206819, intron 2 of 30)	intron (NM_206819, intron 2 of 30)	21307	NM_001254719	4604	Hs.654589	NM_002465	ENSG00000196091	MYBPC1	LCCS4|MYBPCC|MYBPCS	myosin binding protein C, slow type	protein-coding	0.011478	0.395415	350(AGGATCTTCCTGTTCC,-,0.00),351(GGATCTTCCTGTTCCT,+,0.00)
chunk0113_406_1	chr20	61141098	61141328	+	0	NA	Intergenic	Intergenic	62149	NR_109919	100506470	Hs.125674	NR_109919	ENSG00000229606	LINC01718	-	long intergenic non-protein coding RNA 1718	ncRNA	0.017391	0.363636	
chunk0167_289_1	chr6	70666237	70666671	+	0	NA	Intergenic	Intergenic	-1317	NM_021940	60682	Hs.485717	NM_021940	ENSG00000112305	SMAP1	SMAP-1	small ArfGAP 1	protein-coding	0.011521	0.439080	
chunk0113_163_1	chr20	52895781	52895985	+	0	NA	Intergenic	Intergenic	-76524	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.019608	0.424390	
chunk0173_151_1	chr6	144171231	144171727	+	0	NA	intron (NM_003764, intron 1 of 1)	intron (NM_003764, intron 1 of 1)	20962	NM_003764	8676	Hs.118958	NM_003764	ENSG00000135604	STX11	FHL4|HLH4|HPLH4	syntaxin 11	protein-coding	0.002016	0.396378	
chunk0056_59_1	chr13	78372558	78373186	+	0	NA	intron (NR_047001, intron 3 of 5)	LTR26|LTR|ERV1	230688	NM_006237	5457	Hs.654522	NM_006237	ENSG00000152192	POU4F1	BRN3A|Oct-T1|RDC-1|brn-3A	POU class 4 homeobox 1	protein-coding	0.004777	0.411765	
chunk0003_364_1	chr1	39383965	39384495	+	0	NA	intron (NM_012090, intron 50 of 92)	intron (NM_012090, intron 50 of 92)	-25274	NM_015038	643314	Hs.658760	NM_015038	ENSG00000127603	KIAA0754	-	KIAA0754	protein-coding	0.011321	0.369115	
chunk0058_272_1	chr14	26138631	26138959	+	0	NA	Intergenic	Intergenic	458959	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.003049	0.319149	
chunk0182_59_1	chr7	92042172	92042752	+	0	NA	intron (NM_147185, intron 19 of 49)	intron (NM_147185, intron 19 of 49)	92064	NM_000786	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.005172	0.347676	
chunk0142_186_1	chr4	96183931	96184130	+	0	NA	Intergenic	Intergenic	343942	NM_005390	5161	Hs.131361	NM_005390	ENSG00000163114	PDHA2	PDHAL	pyruvate dehydrogenase E1 alpha 2 subunit	protein-coding	0.005025	0.300000	
chunk0161_296_1	chr5	173042423	173043127	+	0	NA	Intergenic	Intergenic	-13577	NM_001168394	153222	Hs.484195	NM_153607	ENSG00000164463	CREBRF	C5orf41|LRF	CREB3 regulatory factor	protein-coding	0.004261	0.468085	
chunk0145_347_1	chr4	151022557	151023052	+	0	NA	Intergenic	L1M5|LINE|L1	-7307	NM_006726	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.004040	0.338710	
chunk0008_11_1	chr1	87347867	87348187	+	0	NA	3' UTR (NM_006769, exon 5 of 5)	3' UTR (NM_006769, exon 5 of 5)	19559	NM_006769	8543	Hs.436792	NM_006769	ENSG00000143013	LMO4	-	LIM domain only 4	protein-coding	0.006250	0.308411	
chunk0202_107_1	chr9	72535406	72535688	+	0	NA	intron (NM_138691, intron 1 of 23)	intron (NM_138691, intron 1 of 23)	13746	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.000000	0.371025	
chunk0043_392_1	chr12	25336459	25337113	+	0	NA	Intergenic	Intergenic	-85855	NM_004985	3845	Hs.505033	NM_004985	ENSG00000133703	KRAS	C-K-RAS|CFC2|K-RAS2A|K-RAS2B|K-RAS4A|K-RAS4B|K-Ras|KI-RAS|KRAS1|KRAS2|NS|NS3|RALD|RASK2|c-Ki-ras2	KRAS proto-oncogene, GTPase	protein-coding	0.010703	0.375573	
chunk0131_320_1	chr3	150898786	150899167	+	0	NA	Intergenic	Intergenic	45260	NM_052995	7401	Hs.745448	NM_052995	ENSG00000163646	CLRN1	RP61|USH3|USH3A	clarin 1	protein-coding	0.002625	0.405759	
chunk0193_206_1	chr8	76083329	76083531	+	0	NA	Intergenic	MLT1A1-int|LTR|ERVL-MaLR	-323224	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.000000	0.522167	
chunk0081_281_1	chr17	44144978	44145606	+	0	NA	intron (NM_024032, intron 2 of 9)	intron (NM_024032, intron 2 of 9)	3386	NM_024032	78995	Hs.437059	NM_024032	ENSG00000125319	C17orf53	-	chromosome 17 open reading frame 53	protein-coding	0.009554	0.416534	164(GAGGACAGAATGTGCT,-,0.00),165(AGGACAGAATGTGCTT,+,0.00)
chunk0134_134_1	chr3	177478500	177478734	+	0	NA	intron (NR_047568, intron 1 of 3)	intron (NR_047568, intron 1 of 3)	36696	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.008547	0.391489	
chunk0136_62_1	chr4	1718219	1718584	+	0	NA	exon (NM_001127266, exon 2 of 4)	exon (NM_001127266, exon 2 of 4)	2956	NM_138385	92305	Hs.518562	NM_138385	ENSG00000168936	TMEM129	D4S2561E	transmembrane protein 129	protein-coding	0.057534	0.642077	
chunk0197_325_1	chr8	125119176	125119375	+	0	NA	intron (NM_173685, intron 3 of 7)	intron (NM_173685, intron 3 of 7)	27434	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.010050	0.410000	
chunk0067_92_1	chr15	41997311	41997942	+	0	NA	non-coding (NR_120334, exon 4 of 4)	non-coding (NR_120334, exon 4 of 4)	24863	NR_120334	101928388	Hs.738043	NR_120334	ENSG00000246740	PLA2G4E-AS1	-	PLA2G4E antisense RNA 1	ncRNA	0.014263	0.496835	
chunk0001_143_1	chr1	5949352	5949836	+	0	NA	intron (NM_001291593, intron 6 of 26)	intron (NM_001291593, intron 6 of 26)	-42704	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.024793	0.540206	
chunk0065_133_1	chr15	24943071	24943441	+	0	NA	intron (NM_022808, intron 3 of 11)	ERVL-B4-int|LTR|ERVL	-11667	NM_022804	8926	Hs.564847	NM_005678	ENSG00000273173	SNURF	-	SNRPN upstream reading frame	protein-coding	0.002703	0.458221	
chunk0201_268_1	chr9	38579730	38580020	+	0	NA	intron (NM_147195, intron 12 of 15)	L1MA5|LINE|L1	-34503	NR_047651	100289137	Hs.644630	NR_047651	ENSG00000283486	FAM95C	-	family with sequence similarity 95 member C	ncRNA	0.003448	0.350515	
chunk0055_275_1	chr13	64256610	64257249	+	0	NA	Intergenic	Intergenic	-412804	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.007825	0.367188	336(AGGAACAAAGTGTTTC,-,0.00),337(GGAACAAAGTGTTTCC,+,0.00)
chunk0208_460_1	chrX	34490979	34491366	+	0	NA	Intergenic	L1PA15|LINE|L1	166116	NM_031442	83604	Hs.8769	NM_031442	ENSG00000147027	TMEM47	BCMP1|TM4SF10|VAB-9	transmembrane protein 47	protein-coding	0.002584	0.376289	173(TAGAACAATTTGTACT,-,0.00),174(AGAACAATTTGTACTC,+,0.00)
chunk0124_25_1	chr3	52012593	52013103	+	0	NA	Intergenic	Intergenic	-16906	NM_000992	6159	Hs.425125	NM_000992	ENSG00000162244	RPL29	HIP|HUMRPL29|L29|RPL29P10|RPL29_3_370	ribosomal protein L29	protein-coding	0.019608	0.549902	241(AGGAACAGCCTGTACT,-,0.00),242(GGAACAGCCTGTACTT,+,0.00)
chunk0187_415_1	chr7	158301075	158301620	+	0	NA	intron (NM_001308267, intron 2 of 21)	intron (NM_001308267, intron 2 of 21)	231466	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.020183	0.437729	
chunk0094_244_1	chr2	7107378	7107611	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-29614	NR_110252	101929452		NR_110252	ENSG00000223884	LOC101929452	-	uncharacterized LOC101929452	ncRNA	0.008584	0.444444	
chunk0177_465_1	chr7	28778047	28778426	+	0	NA	intron (NM_182899, intron 6 of 9)	intron (NM_182899, intron 6 of 9)	92255	NM_001011666	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.007916	0.355263	
chunk0086_82_1	chr18	13540072	13540550	+	0	NA	intron (NM_181481, intron 3 of 5)	intron (NM_181481, intron 3 of 5)	-70803	NR_039752	100616130		NR_039752	ENSG00000263527	MIR4526	mir-4526	microRNA 4526	ncRNA	0.004184	0.369520	
chunk0128_13_1	chr3	103721467	103721808	+	0	NA	Intergenic	Intergenic	-197521	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.005865	0.491228	
chunk0173_385_1	chr6	150004991	150005283	+	0	NA	promoter-TSS (NR_024045)	promoter-TSS (NR_024045)	7	NR_024045	646024	Hs.560537	NR_024045	ENSG00000218358	RAET1K	-	retinoic acid early transcript 1K pseudogene	pseudo	0.082192	0.682594	
chunk0088_259_1	chr18	49072682	49072885	+	0	NA	intron (NM_017653, intron 16 of 16)	intron (NM_017653, intron 16 of 16)	-23015	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.024631	0.480392	
chunk0033_5_1	chr11	12301253	12301765	+	0	NA	intron (NM_032867, intron 3 of 8)	L1ME3|LINE|L1	14609	NM_032867	84953	Hs.60371	NM_032867	ENSG00000133816	MICALCL	Ebitein1	MICAL C-terminal like	protein-coding	0.005859	0.407407	
chunk0084_139_1	chr17	76292394	76292636	+	0	NA	exon (NM_032134, exon 4 of 19)	exon (NM_032134, exon 4 of 19)	15165	NR_130649	84074	Hs.252739	NM_032134	ENSG00000129646	QRICH2	SPGF35	glutamine rich 2	protein-coding	0.016529	0.526749	
chunk0108_294_1	chr2	234978697	234979054	+	0	NA	intron (NM_014521, intron 1 of 5)	intron (NM_014521, intron 1 of 5)	26891	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.039216	0.583799	163(AGGAACATGCTGAACC,-,0.00),164(GGAACATGCTGAACCT,+,0.00)
chunk0053_60_1	chr13	27965611	27966550	+	0	NA	intron (NM_001265, intron 1 of 2)	intron (NM_001265, intron 1 of 2)	3288	NM_001265	1045	Hs.127383	NM_001265	ENSG00000165556	CDX2	CDX-3|CDX2/AS|CDX3	caudal type homeobox 2	protein-coding	0.041534	0.542553	
chunk0110_259_1	chr20	16740471	16741225	+	0	NA	exon (NM_003092, exon 7 of 7)	exon (NM_003092, exon 7 of 7)	-7505	NM_020157	56914	Hs.41119	NM_020157	ENSG00000125879	OTOR	FDP|MIAL1	otoraplin	protein-coding	0.009284	0.347020	
chunk0101_107_1	chr2	125357616	125358102	+	0	NA	Intergenic	Intergenic	-1298076	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.008230	0.406571	
chunk0002_189_1	chr1	19424777	19425179	+	0	NA	intron (NM_001313932, intron 1 of 4)	L2b|LINE|L2	59729	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.009950	0.493797	
chunk0013_442_1	chr1	173590574	173590845	+	0	NA	intron (NM_178527, intron 4 of 27)	MER44B|DNA|TcMar-Tigger	12385	NM_178527	284525	Hs.494981	NM_178527	ENSG00000162753	SLC9C2	SLC9A11	solute carrier family 9 member C2 (putative)	protein-coding	0.003690	0.382353	
chunk0186_187_1	chr7	139679764	139680741	+	0	NA	intron (NM_001113239, intron 2 of 14)	intron (NM_001113239, intron 2 of 14)	97642	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.015353	0.462168	787(GGGTACTGAATGTCCC,-,0.00),788(GGTACTGAATGTCCCC,+,0.00)
chunk0110_404_1	chr20	20457360	20457865	+	0	NA	intron (NM_020343, intron 37 of 39)	intron (NM_020343, intron 37 of 39)	89491	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.021782	0.464427	
chunk0197_46_1	chr8	118405825	118406062	+	0	NA	intron (NR_109794, intron 3 of 4)	intron (NR_109794, intron 3 of 4)	-215058	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.000000	0.331933	
chunk0034_420_1	chr11	38460831	38461318	+	0	NA	Intergenic	Intergenic	185282	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.008214	0.409836	
chunk0159_93_1	chr5	137994409	137994986	+	0	NA	intron (NM_016603, intron 7 of 22)	intron (NM_016603, intron 7 of 22)	38416	NM_001101800	51306	Hs.567453	NM_016603	ENSG00000031003	FAM13B	ARHGAP49|C5orf5|FAM13B1|KHCHP|N61	family with sequence similarity 13 member B	protein-coding	0.003466	0.325260	
chunk0166_323_1	chr6	49820495	49820824	+	0	NA	TTS (NR_125839)	TTS (NR_125839)	4107	NR_110843	101927048	Hs.742154	NR_110843		LOC101927048	-	uncharacterized LOC101927048	ncRNA	0.006079	0.436364	
chunk0129_408_1	chr3	126942445	126942939	+	0	NA	intron (NM_032343, intron 6 of 7)	L1MC4|LINE|L1	-45902	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.008097	0.450505	
chunk0205_24_1	chr9	105308426	105309012	+	0	NA	intron (NM_001286730, intron 2 of 15)	intron (NM_001286730, intron 2 of 15)	64106	NM_001286730	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.008532	0.373083	
chunk0009_144_1	chr1	104825900	104826178	+	0	NA	Intergenic	Intergenic	753016	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.000000	0.351254	172(AAGTACAACCTGTTCA,-,0.00),173(AGTACAACCTGTTCAA,+,0.00)
chunk0128_72_1	chr3	105233001	105233251	+	0	NA	Intergenic	Intergenic	-133587	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.004000	0.374502	
chunk0151_109_1	chr5	43432516	43433106	+	0	NA	Intergenic	Intergenic	-20420	NM_148672	56477	Hs.656904	NM_019846	ENSG00000151882	CCL28	CCK1|MEC|SCYA28	C-C motif chemokine ligand 28	protein-coding	0.001695	0.443316	
chunk0200_113_1	chr9	16963588	16963831	+	0	NA	Intergenic	Intergenic	-92921	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.000000	0.352459	
chunk0091_132_1	chr19	6744617	6745354	+	0	NA	exon (NM_004240, exon 9 of 14)	exon (NM_004240, exon 9 of 14)	5303	NM_004240	9322	Hs.515094	NM_004240	ENSG00000125733	TRIP10	CIP4|HSTP|STOT|STP|TRIP-10	thyroid hormone receptor interactor 10	protein-coding	0.047490	0.642276	
chunk0193_38_1	chr8	71370214	71370541	+	0	NA	Intergenic	L2a|LINE|L2	-8145	NM_001288575	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.006116	0.378049	
chunk0148_262_1	chr5	10354196	10354583	+	0	NA	intron (NM_001270661, intron 1 of 22)	CpG	750	NM_001270661	10299	Hs.432862	NM_005885	ENSG00000145495	MARCH6	DOA10|MARCH-VI|RNF176|TEB4	membrane associated ring-CH-type finger 6	protein-coding	0.067183	0.538660	
chunk0209_399_1	chrX	55189064	55189325	+	0	NA	Intergenic	Intergenic	-5587	NR_132964	106635544		NR_132964		SNORA109	-	small nucleolar RNA, H/ACA box 109	snoRNA	0.011494	0.396947	
chunk0110_341_1	chr20	19341257	19341784	+	0	NA	intron (NM_020689, intron 2 of 16)	intron (NM_020689, intron 2 of 16)	-56924	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.007590	0.473485	
chunk0095_398_1	chr2	24242866	24243434	+	0	NA	intron (NM_019595, intron 28 of 38)	L2c|LINE|L2	68107	NM_001040710	653140	Hs.741736	NM_001040710	ENSG00000186453	FAM228A	C2orf84	family with sequence similarity 228 member A	protein-coding	0.005282	0.347979	
chunk0100_278_1	chr2	113959047	113959713	+	0	NA	non-coding (NR_102318, exon 11 of 11)	non-coding (NR_102318, exon 11 of 11)	-20189	NR_034128	440900	Hs.662205	NR_034128	ENSG00000234199	LINC01191	VIN|lnc-ACTR3	long intergenic non-protein coding RNA 1191	ncRNA	0.006006	0.329835	
chunk0138_382_1	chr4	42597126	42597661	+	0	NA	intron (NM_001105529, intron 6 of 35)	intron (NM_001105529, intron 6 of 35)	59712	NM_001105529	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.007477	0.347015	
chunk0012_311_1	chr1	162273852	162274229	+	0	NA	intron (NM_001164757, intron 2 of 9)	L1ME1|LINE|L1	-68506	NR_030283	693141		NR_030283	ENSG00000207729	MIR556	MIRN556|hsa-mir-556|mir-556	microRNA 556	ncRNA	0.013263	0.380952	
chunk0025_339_1	chr10	58070755	58071390	+	0	NA	Intergenic	L2b|LINE|L2	196862	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.011024	0.443396	
chunk0082_353_1	chr17	60060408	60061047	+	0	NA	intron (NM_022070, intron 9 of 19)	intron (NM_022070, intron 9 of 19)	-17622	NR_039890	100616210		NR_039890	ENSG00000264049	MIR4737	-	microRNA 4737	ncRNA	0.000000	0.357812	317(AGGAACTTTGTGTACA,-,0.00),318(GGAACTTTGTGTACAT,+,0.00)
chunk0078_104_1	chr17	2338512	2338711	+	0	NA	intron (NM_001098509, intron 1 of 22)	L2a|LINE|L2	1097	NM_001098509	9905	Hs.513861	NM_014853	ENSG00000141258	SGSM2	RUTBC1	small G protein signaling modulator 2	protein-coding	0.010050	0.515000	
chunk0054_182_1	chr13	44516764	44517378	+	0	NA	intron (NM_183422, intron 1 of 2)	intron (NM_183422, intron 1 of 2)	-42770	NM_001243798	8848	Hs.436383	NM_006022	ENSG00000102804	TSC22D1	Ptg-2|TGFB1I4|TSC22	TSC22 domain family member 1	protein-coding	0.008143	0.380488	484(TTGTACACAATGTGCT,-,0.00),485(TGTACACAATGTGCTC,+,0.00)
chunk0156_353_1	chr5	112230621	112230877	+	0	NA	intron (NR_110559, intron 1 of 3)	L1PB1|LINE|L1	2466	NR_110559	101927023	Hs.571002	NR_110559	ENSG00000251076	LOC101927023	-	uncharacterized LOC101927023	ncRNA	0.007812	0.361868	
chunk0121_5_1	chr3	14419950	14420208	+	0	NA	intron (NM_001134367, intron 2 of 14)	intron (NM_001134367, intron 2 of 14)	17503	NM_003043	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.019380	0.467181	
chunk0140_187_1	chr4	69920772	69920971	+	0	NA	Intergenic	L1MA5A|LINE|L1	-10210	NM_001890	1446	Hs.3155	NM_001890	ENSG00000126545	CSN1S1	CASA|CSN1	casein alpha s1	protein-coding	0.000000	0.345000	
chunk0045_316_1	chr12	50724948	50725273	+	0	NA	intron (NM_173602, intron 28 of 37)	intron (NM_173602, intron 28 of 37)	-38896	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.009231	0.426380	
chunk0068_361_1	chr15	57994321	57994658	+	0	NA	intron (NM_170697, intron 3 of 10)	intron (NM_170697, intron 3 of 10)	19608	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.005935	0.375740	
chunk0177_115_1	chr7	22223375	22223921	+	0	NA	intron (NM_012294, intron 8 of 25)	L2a|LINE|L2	133266	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.007326	0.376600	
chunk0157_70_1	chr5	116300669	116300918	+	0	NA	Intergenic	Intergenic	73777	NR_104675	101927190	Hs.639849	NR_104675		LOC101927190	-	uncharacterized LOC101927190	ncRNA	0.000000	0.380000	81(TGGCACAGATTGTTCC,-,0.00),82(GGCACAGATTGTTCCA,+,0.00)
chunk0008_325_1	chr1	95311488	95311897	+	0	NA	Intergenic	Intergenic	77537	NR_103484	25950	Hs.483512	NM_015485	ENSG00000122481	RWDD3	RSUME	RWD domain containing 3	protein-coding	0.000000	0.358537	
chunk0011_35_1	chr1	143231836	143232305	+	0	NA	Intergenic	Intergenic	190522	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.053305	0.361702	
chunk0162_85_1	chr6	1940336	1940784	+	0	NA	intron (NM_001253846, intron 6 of 10)	intron (NM_001253846, intron 6 of 10)	235431	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.004464	0.423163	
chunk0106_132_1	chr2	199815225	199815637	+	0	NA	intron (NR_034096, intron 3 of 3)	intron (NR_034096, intron 3 of 3)	35742	NR_034096									0.004854	0.326877	
chunk0200_106_1	chr9	16821389	16821588	+	0	NA	intron (NM_017637, intron 1 of 6)	intron (NM_017637, intron 1 of 6)	49300	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.000000	0.335000	
chunk0083_30_1	chr17	63235886	63236150	+	0	NA	intron (NM_025185, intron 5 of 24)	intron (NM_025185, intron 5 of 24)	204828	NM_001017917	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.000000	0.290566	
chunk0197_11_1	chr8	117025807	117026372	+	0	NA	intron (NM_001172813, intron 2 of 10)	intron (NM_001172813, intron 2 of 10)	75138	NM_001172815	169026	Hs.532270	NM_173851	ENSG00000164756	SLC30A8	ZNT8|ZnT-8	solute carrier family 30 member 8	protein-coding	0.008850	0.408127	271(GAGAACTGCCTGTCCC,-,0.00),272(AGAACTGCCTGTCCCT,+,0.00),296(AAGAACAAAGTGTTCC,-,0.00),297(AGAACAAAGTGTTCCT,+,0.00)
chunk0088_341_1	chr18	51284939	51285430	+	0	NA	Intergenic	Intergenic	-87503	NM_016626	51320	Hs.465144	NM_016626	ENSG00000176624	MEX3C	BM-013|MEX-3C|RKHD2|RNF194	mex-3 RNA binding family member C	protein-coding	0.010183	0.349593	
chunk0040_82_1	chr11	111419721	111420122	+	0	NA	Intergenic	Intergenic	-1735	NR_046085	100132078	Hs.672662	NR_046085	ENSG00000255428	LOC100132078	-	uncharacterized LOC100132078	ncRNA	0.007481	0.522388	290(AAGGACAGGCAGGTCC,-,0.00)
chunk0016_262_1	chr1	200260671	200260954	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	112980	NR_040064	554279	Hs.434694	NR_040064	ENSG00000203721	LINC00862	C1orf98|SMIM16	long intergenic non-protein coding RNA 862	ncRNA	0.003534	0.482394	
chunk0210_70_1	chrX	69959348	69959753	+	0	NA	intron (NM_001005612, intron 2 of 7)	intron (NM_001005612, intron 2 of 7)	-63307	NR_037494	100500887		NR_037494	ENSG00000211991	MIR676	hsa-mir-676|mir-676	microRNA 676	ncRNA	0.002469	0.334975	
chunk0167_145_1	chr6	62429645	62430346	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-143800	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.007133	0.343305	362(TGGAACAAACTGCTCT,-,0.00),363(GGAACAAACTGCTCTA,+,0.00)
chunk0119_208_1	chr22	44890210	44890512	+	0	NA	intron (NM_001135862, intron 9 of 13)	intron (NM_001135862, intron 9 of 13)	118632	NM_001284296	112885	Hs.254097	NM_138415	ENSG00000056487	PHF21B	BHC80L|PHF4	PHD finger protein 21B	protein-coding	0.019868	0.468647	
chunk0026_112_1	chr10	61923168	61923852	+	0	NA	intron (NM_032199, intron 2 of 9)	L2b|LINE|L2	22256	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.011696	0.478832	
chunk0171_339_1	chr6	129979866	129980162	+	0	NA	Intergenic	L1MC4|LINE|L1	-38569	NM_032438	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.000000	0.350168	213(TGGGACTATGTGTTCC,-,0.00),214(GGGACTATGTGTTCCT,+,0.00)
chunk0053_43_1	chr13	27426793	27427077	+	0	NA	intron (NM_002097, intron 1 of 8)	intron (NM_002097, intron 1 of 8)	2391	NM_002097	2971	Hs.445977	NM_002097	ENSG00000122034	GTF3A	AP2|TFIIIA	general transcription factor IIIA	protein-coding	0.007042	0.431579	
chunk0120_459_1	chr3	14312745	14313021	+	0	NA	Intergenic	Intergenic	39685	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.010870	0.353791	
chunk0124_83_1	chr3	53302089	53302737	+	0	NA	intron (NM_001290204, intron 5 of 8)	L2a|LINE|L2	45214	NM_001290205	55802	Hs.476353	NM_018403	ENSG00000272886	DCP1A	HSA275986|Nbla00360|SMAD4IP1|SMIF	decapping mRNA 1A	protein-coding	0.010802	0.357473	
chunk0019_312_1	chr1	229059682	229060078	+	0	NA	Intergenic	Intergenic	114921	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.020202	0.531486	
chunk0120_204_1	chr3	7289105	7289444	+	0	NA	intron (NM_000844, intron 2 of 9)	intron (NM_000844, intron 2 of 9)	246010	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.002950	0.388235	
chunk0163_291_1	chr6	14055363	14055682	+	0	NA	Intergenic	Intergenic	-61734	NM_001251901	9308	Hs.595133	NM_004233	ENSG00000112149	CD83	BL11|HB15	CD83 molecule	protein-coding	0.000000	0.396875	
chunk0030_92_1	chr10	112389351	112389552	+	0	NA	intron (NM_016234, intron 1 of 20)	intron (NM_016234, intron 1 of 20)	13253	NM_016234	51703	Hs.11638	NM_016234	ENSG00000197142	ACSL5	ACS2|ACS5|FACL5	acyl-CoA synthetase long chain family member 5	protein-coding	0.009950	0.485149	
chunk0032_32_1	chr11	1016799	1017109	+	0	NA	exon (NM_005961, exon 31 of 33)	exon (NM_005961, exon 31 of 33)	19752	NM_005961	4588	Hs.528432	NM_005961	ENSG00000184956	MUC6	MUC-6	mucin 6, oligomeric mucus/gel-forming	protein-coding	0.006452	0.562701	
chunk0061_230_1	chr14	60630168	60630367	+	0	NA	Intergenic	Intergenic	-8949	NR_126480	104548971		NR_126480		SALRNA1	SAL-RNA1|XLOC_023166	senescence associated long non-coding RNA 1	ncRNA	0.000000	0.390000	
chunk0075_5_1	chr16	46690815	46691014	+	0	NA	intron (NR_037620, intron 1 of 6)	intron (NR_037620, intron 1 of 6)	1268	NR_037620	23594	Hs.49760	NM_014321	ENSG00000091651	ORC6	ORC6L	origin recognition complex subunit 6	protein-coding	0.020101	0.475000	
chunk0126_129_1	chr3	75841764	75842247	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	-56422	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.004141	0.328512	
chunk0068_438_1	chr15	59636104	59636473	+	0	NA	Intergenic	L1PA10|LINE|L1	21250	NM_004492	2958	Hs.512934	NM_004492	ENSG00000140307	GTF2A2	HsT18745|T18745|TF2A2|TFIIA|TFIIA-12|TFIIA-gamma|TFIIAS	general transcription factor IIA subunit 2	protein-coding	0.008130	0.427027	
chunk0204_102_1	chr9	94630833	94631286	+	0	NA	intron (NM_001127628, intron 2 of 7)	intron (NM_001127628, intron 2 of 7)	8582	NM_000507	2203	Hs.494496	NM_000507	ENSG00000165140	FBP1	FBP	fructose-bisphosphatase 1	protein-coding	0.011038	0.460352	
chunk0135_385_1	chr3	191247450	191248013	+	0	NA	intron (NM_198184, intron 2 of 2)	L2b|LINE|L2	35198	NM_198184	344901	Hs.526794	NM_198184	ENSG00000188729	OSTN	MUSCLIN	osteocrin	protein-coding	0.021314	0.374113	
chunk0105_319_1	chr2	190655100	190655419	+	0	NA	intron (NM_005966, intron 2 of 9)	Charlie23a|DNA|hAT-Charlie	6137	NM_005966	4664	Hs.107474	NM_005966	ENSG00000138386	NAB1	-	NGFI-A binding protein 1	protein-coding	0.003135	0.350000	
chunk0193_213_1	chr8	76344443	76344738	+	0	NA	Intergenic	Intergenic	-62064	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.006780	0.358108	
chunk0191_201_1	chr8	51973611	51973952	+	0	NA	Intergenic	L1M4|LINE|L1	-74595	NM_001286782	115294	Hs.671268	NM_052937	ENSG00000168300	PCMTD1	-	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding	0.011730	0.450292	
chunk0114_45_1	chr21	8435712	8435926	+	0	NA	non-coding (NR_046235, exon 1 of 1)	non-coding (NR_046235, exon 1 of 1)	-1057	NR_003286	100008588		NR_003286		RNA18SN5	RN18S1|RNA18S5	RNA, 18S ribosomal N5	rRNA	0.191589	0.827907	
chunk0196_143_1	chr8	104503710	104503968	+	0	NA	intron (NM_001135703, intron 2 of 5)	L1M5|LINE|L1	-19374	NR_030330	693127		NR_030330	ENSG00000208032	MIR548A3	MIRN548A3	microRNA 548a-3	ncRNA	0.000000	0.301158	
chunk0209_77_1	chrX	38111154	38111624	+	0	NA	intron (NM_138780, intron 13 of 16)	MIR|SINE|MIR	77855	NM_001163334	94122	Hs.662334	NM_138780	ENSG00000147041	SYTL5	slp5	synaptotagmin like 5	protein-coding	0.010638	0.386412	
chunk0008_46_1	chr1	89166758	89167169	+	0	NA	intron (NM_207398, intron 2 of 10)	MER65A|LTR|ERV1	9077	NM_207398	388646	Hs.591450	NM_207398	ENSG00000213512	GBP7	GBP4L	guanylate binding protein 7	protein-coding	0.002433	0.407767	
chunk0155_317_1	chr5	96629690	96630153	+	0	NA	intron (NR_130776, intron 4 of 4)	intron (NR_130776, intron 4 of 4)	-32116	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.002160	0.418103	
chunk0069_10_1	chr15	60154275	60154804	+	0	NA	Intergenic	Intergenic	150317	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.003781	0.320755	323(AAGAACTTATTGTTCT,-,0.00),324(AGAACTTATTGTTCTG,+,0.00)
chunk0050_186_1	chr12	103900227	103900674	+	0	NA	intron (NR_027249, intron 4 of 15)	L2b|LINE|L2	29761	NR_027249	253724	Hs.506549	NR_027249	ENSG00000214198	TTC41P	GNN|GNNP	tetratricopeptide repeat domain 41, pseudogene	pseudo	0.004474	0.390625	106(AAGAACAATCTGTCTC,-,0.00),107(AGAACAATCTGTCTCT,+,0.00)
chunk0005_322_1	chr1	60931234	60931433	+	0	NA	Intergenic	Intergenic	39443	NR_110618	100996570	Hs.46616	NR_110617	ENSG00000237928	NFIA-AS2	-	NFIA antisense RNA 2	ncRNA	0.010050	0.470000	
chunk0019_131_1	chr1	225629622	225630230	+	0	NA	intron (NM_001008493, intron 1 of 14)	Tigger19a|DNA|TcMar-Tigger	23217	NM_001008493	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.001645	0.313629	
chunk0140_14_1	chr4	65470735	65471029	+	0	NA	intron (NM_001281765, intron 5 of 17)	MER57A1|LTR|ERV1	-199079	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.003401	0.372881	
chunk0196_445_1	chr8	116583113	116583792	+	0	NA	Intergenic	Intergenic	172371	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.011782	0.527941	144(AGGAACATCGTGTTCC,-,0.00),145(GGAACATCGTGTTCCA,+,0.00),316(AGGAGCTCCCTGTCCT,-,0.00)
chunk0123_69_1	chr3	41327768	41328083	+	0	NA	intron (NM_017886, intron 35 of 36)	intron (NM_017886, intron 35 of 36)	128474	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.009524	0.420886	130(CGGAACAGGCTGTTCC,-,0.00),131(GGAACAGGCTGTTCCA,+,0.00)
chunk0038_170_1	chr11	85086861	85087445	+	0	NA	intron (NM_001142699, intron 6 of 27)	L2a|LINE|L2	-163732	NM_001300983	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.001712	0.338462	
chunk0067_173_1	chr15	44193877	44194232	+	0	NA	intron (NM_001286490, intron 1 of 15)	intron (NM_001286490, intron 1 of 15)	392	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.022535	0.480337	
chunk0213_38_1	chrY	56873405	56873938	+	0	NA	Intergenic	Intergenic	-80584	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.016886	0.408240	
chunk0067_407_1	chr15	49461301	49461918	+	0	NA	intron (NM_002009, intron 2 of 3)	intron (NM_002009, intron 2 of 3)	38431	NM_002009	2252	Hs.567268	NM_002009	ENSG00000140285	FGF7	HBGF-7|KGF	fibroblast growth factor 7	protein-coding	0.001621	0.331715	349(AGGTACAATATGTACA,-,0.00),350(GGTACAATATGTACAT,+,0.00)
chunk0182_256_1	chr7	97253627	97254089	+	0	NA	Intergenic	L1MA8|LINE|L1	137265	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.002165	0.343413	
chunk0028_457_1	chr10	95133192	95133391	+	0	NA	Intergenic	HUERS-P3-int|LTR|ERV1	-60909	NM_207321	142827	Hs.134229	NM_207321	ENSG00000173124	ACSM6	C10orf129|bA310E22.3	acyl-CoA synthetase medium chain family member 6	protein-coding	0.005025	0.470000	
chunk0056_256_1	chr13	89700365	89700716	+	0	NA	Intergenic	Intergenic	-136127	NR_046991	100874139	Hs.742173	NR_046991		LINC00353	-	long intergenic non-protein coding RNA 353	ncRNA	0.002849	0.323864	
chunk0109_261_1	chr20	8001863	8002463	+	0	NA	intron (NM_021156, intron 2 of 7)	L2b|LINE|L2	17666	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.001667	0.312812	
chunk0151_140_1	chr5	45247090	45247377	+	0	NA	Intergenic	L1PA13|LINE|L1	438308	NM_016640	10884	Hs.124165	NM_016640	ENSG00000112996	MRPS30	MRP-S30|PAP|PDCD9|S30mt	mitochondrial ribosomal protein S30	protein-coding	0.024390	0.569444	
chunk0145_213_1	chr4	148007335	148007815	+	0	NA	intron (NM_024605, intron 18 of 22)	L3|LINE|CR1	224980	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.014583	0.446985	290(CAGAACTCGCTGTCTC,-,0.00)
chunk0201_262_1	chr9	38442823	38443024	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-18476	NM_001007563	347252	Hs.349705	NM_001007563	ENSG00000137142	IGFBPL1	IGFBP-RP4|IGFBPRP4|bA113O24.1	insulin like growth factor binding protein like 1	protein-coding	0.009950	0.549505	115(AAGTACACACAGTGCA,-,0.00),116(AGTACACACAGTGCAG,+,0.00)
chunk0083_426_1	chr17	72434588	72434966	+	0	NA	intron (NR_036488, intron 1 of 3)	L1ME4a|LINE|L1	158027	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.000000	0.287599	
chunk0194_161_1	chr8	84830265	84830972	+	0	NA	intron (NM_001100393, intron 4 of 8)	HAL1|LINE|L1	124691	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.001414	0.320621	330(TTGCACAGTATGTTCC,-,0.00),331(TGCACAGTATGTTCCT,+,0.00)
chunk0141_460_1	chr4	89467440	89467821	+	0	NA	Intergenic	LTR81C|LTR|Gypsy	-159620	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.002625	0.421466	
chunk0148_268_1	chr5	10481164	10481466	+	0	NA	Intergenic	MER74A|LTR|ERVL	3278	NR_106747	102465138		NR_106747	ENSG00000277073	MIR6131	hsa-mir-6131	microRNA 6131	ncRNA	0.016556	0.488449	101(AAGGACAGTTTGTTAC,-,0.00)
chunk0041_151_1	chr11	125655063	125655726	+	0	NA	non-coding (NR_045205, exon 13 of 13)	non-coding (NR_045205, exon 13 of 13)	25504	NM_020069	56	Hs.169222	NM_001612	ENSG00000134940	ACRV1	D11S4365|SP-10|SPACA2	acrosomal vesicle protein 1	protein-coding	0.007541	0.343373	
chunk0176_44_1	chr7	10761348	10761725	+	0	NA	Intergenic	Intergenic	178650	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.000000	0.304233	
chunk0205_90_1	chr9	107383969	107384251	+	0	NA	Intergenic	L2a|LINE|L2	82475	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.007092	0.378092	
chunk0150_46_1	chr5	31674226	31674664	+	0	NA	Intergenic	Charlie18a|DNA|hAT-Charlie	-124479	NM_178140	23037	Hs.481819	NM_015022	ENSG00000133401	PDZD2	AIPC|PAPIN|PDZK3|PIN1	PDZ domain containing 2	protein-coding	0.011416	0.403189	
chunk0129_402_1	chr3	126732390	126732703	+	0	NA	intron (NM_032343, intron 3 of 7)	L1ME4a|LINE|L1	28326	NM_032343	84303	Hs.518119	NM_032343	ENSG00000159685	CHCHD6	CHCM1|MICOS25|Mic25|PPP1R23	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.312102	
chunk0013_448_1	chr1	173868129	173869246	+	0	NA	promoter-TSS (NR_002579)	promoter-TSS (NR_002579)	332	NM_032522	84614	Hs.668497	NM_032522	ENSG00000185278	ZBTB37	D430004I08Rik|ZNF908	zinc finger and BTB domain containing 37	protein-coding	0.059087	0.613596	
chunk0189_327_1	chr8	26352169	26352532	+	0	NA	intron (NM_001177591, intron 3 of 9)	intron (NM_001177591, intron 3 of 9)	-30657	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.002755	0.387363	
chunk0108_186_1	chr2	232238473	232238857	+	0	NA	intron (NR_046476, intron 11 of 20)	(TTTC)n|Simple_repeat|Simple_repeat	66012	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.018229	0.457143	229(GGAAGAGTGTGTGCTC,+,0.00)
chunk0122_8_1	chr3	27346649	27346848	+	0	NA	intron (NM_199347, intron 4 of 24)	L2c|LINE|L2	22712	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.000000	0.320000	
chunk0199_417_1	chr9	13646428	13646931	+	0	NA	Intergenic	Intergenic	-215350	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.001988	0.355159	
chunk0063_88_1	chr14	78206446	78206648	+	0	NA	intron (NR_073547, intron 1 of 20)	intron (NR_073547, intron 1 of 20)	36174	NR_073547	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004950	0.512315	
chunk0012_132_1	chr1	157198186	157198554	+	0	NA	Intergenic	Intergenic	-59779	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.008152	0.523035	
chunk0024_74_1	chr10	34216392	34216697	+	0	NA	intron (NM_019619, intron 22 of 24)	intron (NM_019619, intron 22 of 24)	-443864	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.006557	0.437908	94(CAGGACACTGTGTTAT,-,0.00),95(AGGACACTGTGTTATT,+,0.00)
chunk0048_189_1	chr12	81112452	81112817	+	0	NA	intron (NM_024560, intron 2 of 15)	intron (NM_024560, intron 2 of 15)	34604	NM_024560	79611	Hs.259559	NM_024560	ENSG00000111058	ACSS3	-	acyl-CoA synthetase short chain family member 3	protein-coding	0.005479	0.385246	
chunk0035_126_1	chr11	42713542	42713920	+	0	NA	Intergenic	Intergenic	-460041	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.007937	0.358839	182(AAGAACTAATTGTTCT,-,0.00),183(AGAACTAATTGTTCTC,+,0.00)
chunk0167_443_1	chr6	75879117	75879411	+	0	NA	intron (NM_001300899, intron 20 of 32)	AluJb|SINE|Alu	130072	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.000000	0.447458	
chunk0138_440_1	chr4	45729156	45729589	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	394693	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.006928	0.331797	202(TAGTACATATTGTACT,-,0.00),203(AGTACATATTGTACTA,+,0.00)
chunk0131_248_1	chr3	149532998	149533251	+	0	NA	intron (NM_015472, intron 4 of 6)	intron (NM_015472, intron 4 of 6)	58543	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.007905	0.500000	
chunk0102_262_1	chr2	149556392	149557002	+	0	NA	Intergenic	Intergenic	-30661	NR_110240	101929231	Hs.5324	NR_110240	ENSG00000231969	LOC101929231	-	uncharacterized LOC101929231	ncRNA	0.001639	0.342062	
chunk0040_47_1	chr11	110815959	110816381	+	0	NA	Intergenic	Intergenic	-102981	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.002370	0.385343	
chunk0126_50_1	chr3	74118959	74119158	+	0	NA	Intergenic	MER102c|DNA|hAT-Charlie	402082	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.325000	
chunk0125_121_1	chr3	65817624	65818240	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-75884	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.003247	0.351702	
chunk0183_383_1	chr7	109892085	109892474	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	67934	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.007712	0.289744	140(CAGAACATTCTGTACA,-,0.00),141(AGAACATTCTGTACAC,+,0.00)
chunk0032_163_1	chr11	5228127	5228433	+	0	NA	Intergenic	Intergenic	-1209	NM_000518	3043	Hs.523443	NM_000518	ENSG00000244734	HBB	CD113t-C|ECYT6|beta-globin	hemoglobin subunit beta	protein-coding	0.013072	0.436482	
chunk0175_199_1	chr7	5702367	5703027	+	0	NA	intron (NM_207111, intron 13 of 16)	intron (NM_207111, intron 13 of 16)	9213	NR_106934	102466203		NR_106934	ENSG00000283419	MIR6874	hsa-mir-6874	microRNA 6874	ncRNA	0.015152	0.423601	
chunk0106_311_1	chr2	205175874	205176306	+	0	NA	intron (NM_205863, intron 12 of 21)	intron (NM_205863, intron 12 of 21)	-506410	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.009259	0.443418	
chunk0032_406_1	chr11	11902951	11903491	+	0	NA	intron (NM_017944, intron 5 of 26)	intron (NM_017944, intron 5 of 26)	61798	NM_017944	55031	Hs.577256	NM_017944	ENSG00000170242	USP47	TRFP	ubiquitin specific peptidase 47	protein-coding	0.001852	0.303142	
chunk0150_325_1	chr5	38283840	38284052	+	0	NA	non-coding (NR_046219, exon 3 of 4)	non-coding (NR_046219, exon 3 of 4)	7040	NR_046219	100852408	Hs.570954	NR_046219	ENSG00000248730	EGFLAM-AS4	-	EGFLAM antisense RNA 4	ncRNA	0.009434	0.511737	
chunk0191_350_1	chr8	56400205	56400404	+	0	NA	Intergenic	L1MC1|LINE|L1	-9594	NR_103832	442388	Hs.632065	NM_001145251	ENSG00000253542	SDR16C6P	SDR16C6	short chain dehydrogenase/reductase family 16C member 6, pseudogene	pseudo	0.000000	0.345000	
chunk0163_127_1	chr6	10406349	10406945	+	0	NA	intron (NM_001032280, intron 3 of 6)	intron (NM_001032280, intron 3 of 6)	-5671	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.001678	0.345059	
chunk0057_235_1	chr13	104426742	104427156	+	0	NA	Intergenic	L1MB7|LINE|L1	1001749	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.014493	0.380723	
chunk0043_398_1	chr12	25434010	25434517	+	0	NA	Intergenic	Intergenic	119020	NM_001256266	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.001972	0.311024	
chunk0142_294_1	chr4	100237762	100238585	+	0	NA	Intergenic	Intergenic	-47675	NM_145244	115265	Hs.480378	NM_145244	ENSG00000145358	DDIT4L	REDD2|Rtp801L	DNA damage inducible transcript 4 like	protein-coding	0.001215	0.322816	
chunk0122_401_1	chr3	38069218	38069728	+	0	NA	intron (NM_007335, intron 6 of 36)	L1M5|LINE|L1	30268	NM_007335	9940	Hs.714499	NM_007335	ENSG00000008226	DLEC1	CFAP81|DLC-1|DLC1|F56	DLEC1 cilia and flagella associated protein	protein-coding	0.005882	0.409002	
chunk0076_17_1	chr16	58756863	58757592	+	0	NA	Intergenic	Intergenic	-22870	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.015089	0.426027	
chunk0177_413_1	chr7	27609266	27609465	+	0	NA	intron (NM_152740, intron 4 of 7)	intron (NM_152740, intron 4 of 7)	-6609	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.000000	0.350000	
chunk0198_224_1	chr8	134017162	134017689	+	0	NA	Intergenic	Intergenic	130929	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.000000	0.333333	
chunk0196_65_1	chr8	102366264	102366719	+	0	NA	intron (NM_015902, intron 1 of 58)	intron (NM_015902, intron 1 of 58)	46198	NM_015902	51366	Hs.492445	NM_015902	ENSG00000104517	UBR5	DD5|EDD|EDD1|HYD	ubiquitin protein ligase E3 component n-recognin 5	protein-coding	0.010989	0.379386	
chunk0187_106_1	chr8	5346379	5347076	+	0	NA	Intergenic	Intergenic	-351921	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.005739	0.365330	
chunk0137_355_1	chr4	25723724	25724077	+	0	NA	Intergenic	Intergenic	67436	NM_001177999	10568	Hs.479372	NM_006424	ENSG00000157765	SLC34A2	NAPI-3B|NAPI-IIb|NPTIIb	solute carrier family 34 member 2	protein-coding	0.011331	0.454802	
chunk0146_257_1	chr4	162716890	162717324	+	0	NA	Intergenic	Intergenic	376521	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.002304	0.291954	
chunk0135_26_1	chr3	184566362	184566773	+	0	NA	intron (NM_004443, intron 1 of 15)	intron (NM_004443, intron 1 of 15)	4768	NM_004443	2049	Hs.2913	NM_004443	ENSG00000182580	EPHB3	EK2|ETK2|HEK2|TYRO6	EPH receptor B3	protein-coding	0.019465	0.614078	
chunk0042_325_1	chr12	9635158	9635386	+	0	NA	intron (NR_046448, intron 1 of 4)	MER67D|LTR|ERV1	1853	NR_046448	374443	Hs.569124	NR_002814	ENSG00000256594	LOC374443	-	C-type lectin domain family 2 member D pseudogene	pseudo	0.000000	0.406114	
chunk0068_432_1	chr15	59553879	59554610	+	0	NA	Intergenic	Intergenic	-57539	NM_004751	9245	Hs.194710	NM_004751	ENSG00000140297	GCNT3	C2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding	0.013680	0.446721	
chunk0204_108_1	chr9	94779661	94780115	+	0	NA	intron (NM_032823, intron 3 of 14)	Charlie29a|DNA|hAT-Charlie	20239	NM_001193329	84909	Hs.434253	NM_032823	ENSG00000148120	AOPEP	AP-O|APO|C90RF3|C9orf3|ONPEP	aminopeptidase O (putative)	protein-coding	0.008811	0.360440	
chunk0083_194_1	chr17	66548283	66548552	+	0	NA	intron (NM_002737, intron 3 of 16)	intron (NM_002737, intron 3 of 16)	-131563	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.011152	0.481481	
chunk0168_99_1	chr6	80090153	80090662	+	0	NA	Intergenic	Intergenic	-16220	NM_183050	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.005894	0.372549	
chunk0145_38_1	chr4	144381273	144381551	+	0	NA	Intergenic	Eulor5A|DNA?|DNA?	-240626	NM_002099	2993	Hs.434973	NM_002099	ENSG00000170180	GYPA	CD235a|GPA|GPErik|GPSAT|HGpMiV|HGpMiXI|HGpSta(C)|MN|MNS|PAS-2	glycophorin A (MNS blood group)	protein-coding	0.007194	0.358423	
chunk0098_395_1	chr2	79741446	79742068	+	0	NA	intron (NM_004389, intron 2 of 17)	L1M5|LINE|L1	-92398	NR_036231	100422888		NR_036231	ENSG00000266436	MIR4264	-	microRNA 4264	ncRNA	0.003215	0.325843	
chunk0180_257_1	chr7	69411643	69411994	+	0	NA	Intergenic	Intergenic	185677	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.011396	0.494318	139(AAGAACAATGTGTATC,-,0.00)
chunk0101_175_1	chr2	129261244	129261522	+	0	NA	intron (NR_122040, intron 1 of 4)	L1ME4a|LINE|L1	12508	NR_122041	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.000000	0.354839	
chunk0103_159_1	chr2	162549672	162550194	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	205860	NM_012198	25801	Hs.377894	NM_012198	ENSG00000115271	GCA	GCL	grancalcin	protein-coding	0.007663	0.340344	
chunk0023_248_1	chr10	27243233	27243475	+	0	NA	Intergenic	Intergenic	-1215	NM_001301251	91452	Hs.530597	NM_145698	ENSG00000107897	ACBD5	-	acyl-CoA binding domain containing 5	protein-coding	0.024793	0.530864	
chunk0122_344_1	chr3	37279187	37279523	+	0	NA	intron (NM_001172713, intron 3 of 22)	Tigger4|DNA|TcMar-Tigger	36164	NM_001172713	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.014881	0.462908	
chunk0160_355_1	chr5	160419393	160419755	+	0	NA	promoter-TSS (NM_006425)	promoter-TSS (NM_006425)	-413	NM_006425	10569	Hs.435342	NM_006425	ENSG00000164609	SLU7	9G8|hSlu7	SLU7 homolog, splicing factor	protein-coding	0.013812	0.355372	
chunk0199_176_1	chr9	4586880	4587141	+	0	NA	3' UTR (NM_004170, exon 12 of 12)	3' UTR (NM_004170, exon 12 of 12)	-75284	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.003831	0.343511	
chunk0092_35_1	chr19	19138188	19138675	+	0	NA	promoter-TSS (NM_001256766)	promoter-TSS (NM_001256766)	70	NM_001256766	54929	Hs.631629	NM_017814	ENSG00000064545	TMEM161A	AROS-29	transmembrane protein 161A	protein-coding	0.078029	0.620902	
chunk0019_318_1	chr1	229091903	229092230	+	0	NA	Intergenic	Intergenic	82735	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.012232	0.506098	
chunk0153_157_1	chr5	69519264	69519786	+	0	NA	intron (NM_002538, intron 4 of 8)	intron (NM_002538, intron 4 of 8)	15348	NM_001205255	100506658	Hs.592605	NM_002538	ENSG00000197822	OCLN	BLCPMG|PPP1R115|PTORCH1	occludin	protein-coding	0.005747	0.374761	
chunk0050_294_1	chr12	106758938	106759174	+	0	NA	intron (NM_032491, intron 13 of 13)	L2b|LINE|L2	-15565	NM_018157	55188	Hs.131306	NM_018157	ENSG00000111785	RIC8B	RIC8|hSyn	RIC8 guanine nucleotide exchange factor B	protein-coding	0.012712	0.485232	
chunk0061_393_1	chr14	64594449	64594691	+	0	NA	Intergenic	L1MC3|LINE|L1	44668	NM_172365	145376	Hs.144696	NM_172365	ENSG00000165807	PPP1R36	C14orf50	protein phosphatase 1 regulatory subunit 36	protein-coding	0.004132	0.370370	
chunk0005_328_1	chr1	61081838	61082444	+	0	NA	promoter-TSS (NM_005595)	promoter-TSS (NM_005595)	-167	NM_005595	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.099010	0.667216	
chunk0055_207_1	chr13	62005527	62006073	+	0	NA	intron (NR_046995, intron 1 of 1)	L1MEi|LINE|L1	23748	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.001832	0.367459	
chunk0117_151_1	chr22	19844411	19844634	+	0	NA	intron (NM_053004, intron 2 of 7)	intron (NM_053004, intron 2 of 7)	10326	NM_024627	79680	Hs.105642	NM_024627	ENSG00000215012	RTL10	BOP|C22orf29	retrotransposon Gag like 10	protein-coding	0.022422	0.629464	
chunk0187_113_1	chr7	148447569	148448324	+	0	NA	Intergenic	Intergenic	-142619	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.007947	0.345238	
chunk0086_47_1	chr18	12810693	12811572	+	0	NA	intron (NM_001207013, intron 8 of 10)	MIR|SINE|MIR	29830	NM_001308287	5771	Hs.654527	NM_002828	ENSG00000175354	PTPN2	PTN2|PTPT|TC-PTP|TCELLPTP|TCPTP	protein tyrosine phosphatase non-receptor type 2	protein-coding	0.009101	0.389773	
chunk0091_311_1	chr19	12945791	12946283	+	0	NA	intron (NR_072976, intron 1 of 7)	CpG	223	NM_001270362	5886	Hs.643267	NM_005053	ENSG00000179262	RAD23A	HHR23A|HR23A	RAD23 homolog A, nucleotide excision repair protein	protein-coding	0.126016	0.744422	
chunk0093_303_1	chr19	53425011	53425361	+	0	NA	Intergenic	Intergenic	-6788	NM_001289951	388561	Hs.433293	NM_001008401	ENSG00000160336	ZNF761	ZNF468	zinc finger protein 761	protein-coding	0.020000	0.507123	68(AAGGACAAGGAGTCCC,-,0.00),69(AGGACAAGGAGTCCCC,+,0.00)
chunk0014_137_1	chr1	177701365	177702037	+	0	NA	intron (NR_110722, intron 2 of 3)	L2a|LINE|L2	1177	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.004464	0.375929	382(TGGAACAACATGTGCA,-,0.00),383(GGAACAACATGTGCAA,+,0.00)
chunk0152_47_1	chr5	57268961	57269444	+	0	NA	Intergenic	Intergenic	55128	NM_001127236	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.012422	0.388430	226(TGGACTTAATGTCCTG,+,0.00)
chunk0005_454_1	chr1	63547635	63548108	+	0	NA	intron (NM_032437, intron 7 of 13)	MLT1H|LTR|ERVL-MaLR	-1109	NR_002771	79469	Hs.659291	NR_002771		DLEU2L	BCMSUNL	deleted in lymphocytic leukemia 2 like	ncRNA	0.004228	0.453586	
chunk0181_89_1	chr7	80373469	80373668	+	0	NA	intron (NR_110075, intron 2 of 3)	intron (NR_110075, intron 2 of 3)	871	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.010050	0.330000	
chunk0154_269_1	chr5	82023684	82024069	+	0	NA	intron (NM_031482, intron 2 of 7)	intron (NM_031482, intron 2 of 7)	51851	NM_001131028	83734	Hs.713698	NM_031482	ENSG00000152348	ATG10	APG10|APG10L|pp12616	autophagy related 10	protein-coding	0.007792	0.383420	
chunk0072_355_1	chr15	99759570	99759810	+	0	NA	Intergenic	Intergenic	-26246	NM_001284421	145748	Hs.562568	NM_152449	ENSG00000183060	LYSMD4	-	LysM domain containing 4	protein-coding	0.004167	0.340249	6(AAGAACACAGTGTAAC,-,0.00)
chunk0006_350_1	chr1	72635729	72635944	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-353242	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.004651	0.421296	
chunk0073_126_1	chr16	4887175	4887616	+	0	NA	intron (NM_002705, intron 20 of 21)	MIRc|SINE|MIR	39015	NM_001288656	29855	Hs.440219	NM_016936	ENSG00000118900	UBN1	VT|VT4	ubinuclein 1	protein-coding	0.013605	0.493213	
chunk0202_175_1	chr9	74041705	74041904	+	0	NA	Intergenic	Intergenic	-329727	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.000000	0.370000	179(TGGAACAAGTTGTACC,-,0.00),180(GGAACAAGTTGTACCC,+,0.00)
chunk0027_79_1	chr10	73413323	73413567	+	0	NA	intron (NM_004034, intron 1 of 13)	intron (NM_004034, intron 1 of 13)	638	NM_001156	310	Hs.631827	NM_001156	ENSG00000138279	ANXA7	ANX7|SNX|SYNEXIN	annexin A7	protein-coding	0.040984	0.481633	
chunk0099_446_1	chr2	103386822	103387345	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	625052	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.007648	0.364504	
chunk0081_421_1	chr17	48760611	48760934	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	-32023	NM_006361	10481	Hs.66731	NM_006361	ENSG00000159184	HOXB13	HPC9|PSGD	homeobox B13	protein-coding	0.006192	0.475309	
chunk0190_70_1	chr8	29809851	29810081	+	0	NA	Intergenic	Intergenic	18538	NR_125817	101929470	Hs.204721	NR_125817	ENSG00000248964	LOC101929470	-	uncharacterized LOC101929470	ncRNA	0.000000	0.454545	
chunk0069_394_1	chr15	67761304	67761903	+	0	NA	intron (NM_001206804, intron 19 of 21)	intron (NM_001206804, intron 19 of 21)	-58101	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.006678	0.376667	
chunk0164_2_1	chr6	17629395	17629822	+	0	NA	intron (NM_005124, intron 17 of 21)	intron (NM_005124, intron 17 of 21)	29321	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.007026	0.385514	
chunk0054_188_1	chr13	44854293	44855176	+	0	NA	Intergenic	Intergenic	-45104	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.009060	0.451357	499(TAGGACAGTGTGTGCT,-,0.00),500(AGGACAGTGTGTGCTC,+,0.00)
chunk0039_335_1	chr11	104369893	104370106	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	117408	NR_106987									0.009390	0.420561	154(GGAAACATGCTGTTCA,-,0.00),155(GAAACATGCTGTTCAG,+,0.00)
chunk0065_435_1	chr14	106350209	106350615	+	0	NA	Intergenic	Intergenic	62738	NR_033375	338004	Hs.569411	NR_033375		LINC00226	C14orf97|NCRNA00226	long intergenic non-protein coding RNA 226	ncRNA	0.012315	0.390663	
chunk0036_390_1	chr11	67677423	67677723	+	0	NA	intron (NM_001031615, intron 1 of 9)	L1PB1|LINE|L1	-2942	NM_000695	222	Hs.87539	NM_000695	ENSG00000132746	ALDH3B2	ALDH8	aldehyde dehydrogenase 3 family member B2	protein-coding	0.013333	0.418605	
chunk0159_255_1	chr5	142023719	142024202	+	0	NA	Intergenic	Intergenic	-10905	NM_005471	10007	Hs.633853	NM_005471	ENSG00000113552	GNPDA1	GNP1|GNPDA|GNPI|GPI|HLN	glucosamine-6-phosphate deaminase 1	protein-coding	0.014493	0.351240	
chunk0112_201_1	chr20	40415033	40415693	+	0	NA	Intergenic	Intergenic	273877	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.006061	0.373676	
chunk0095_392_1	chr2	24007636	24007973	+	0	NA	Intergenic	L1MB8|LINE|L1	-2279	NM_001080473	388931	Hs.407482	NM_001080473	ENSG00000205639	MFSD2B	-	major facilitator superfamily domain containing 2B	protein-coding	0.000000	0.357988	
chunk0193_265_1	chr8	77038371	77038595	+	0	NA	Intergenic	Intergenic	-37439	NM_001172086	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.008929	0.311111	
chunk0166_16_1	chr6	41705078	41705277	+	0	NA	intron (NM_001167827, intron 1 of 8)	intron (NM_001167827, intron 1 of 8)	29224	NM_001271945	7942	Hs.485360	NM_007162	ENSG00000112561	TFEB	ALPHATFEB|BHLHE35|TCFEB	transcription factor EB	protein-coding	0.010050	0.620000	76(TGGGACAGTGTGTGCC,-,0.00),77(GGGACAGTGTGTGCCT,+,0.00)
chunk0042_46_1	chr12	1732554	1733555	+	0	NA	intron (NM_024551, intron 1 of 7)	intron (NM_024551, intron 1 of 7)	41973	NM_024551	79602	Hs.371642	NM_024551	ENSG00000006831	ADIPOR2	ACDCR2|PAQR2	adiponectin receptor 2	protein-coding	0.001998	0.312375	
chunk0016_268_1	chr1	200405248	200405774	+	0	NA	3' UTR (NM_001281294, exon 3 of 3)	3' UTR (NM_001281294, exon 3 of 3)	4547	NM_001281294	23528	Hs.59757	NM_012482	ENSG00000162702	ZNF281	ZBP-99|ZNP-99	zinc finger protein 281	protein-coding	0.005703	0.337761	
chunk0046_78_1	chr12	56189442	56189862	+	0	NA	promoter-TSS (NM_001130420)	promoter-TSS (NM_001130420)	-85	NM_001130420	6601	Hs.236030	NM_003075	ENSG00000139613	SMARCC2	BAF170|CRACC2|CSS8|Rsc8	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2	protein-coding	0.126190	0.760095	
chunk0133_199_1	chr3	170806539	170806863	+	0	NA	Intergenic	Intergenic	63555	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.006173	0.409231	209(GAGGACAGTGTGCTCC,-,0.00),210(AGGACAGTGTGCTCCA,+,0.00)
chunk0193_347_1	chr8	79726152	79726453	+	0	NA	Intergenic	Intergenic	40173	NM_001282851	23462	Hs.234434	NM_012258	ENSG00000164683	HEY1	BHLHb31|CHF2|HERP2|HESR1|HRT-1|NERP2|OAF1|hHRT1	hes related family bHLH transcription factor with YRPW motif 1	protein-coding	0.003322	0.397351	
chunk0066_226_1	chr15	34038154	34038589	+	0	NA	intron (NM_020371, intron 1 of 5)	CpG	731	NM_020371	57099	Hs.555966	NM_020371	ENSG00000169857	AVEN	PDCD12	apoptosis and caspase activation inhibitor	protein-coding	0.055172	0.561927	
chunk0052_14_1	chr13	20057355	20057807	+	0	NA	intron (NM_001190964, intron 15 of 25)	Tigger17|DNA|TcMar-Tigger	-45120	NR_126380	104355137	Hs.578016	NR_126380	ENSG00000236076	LINC01072	-	long intergenic non-protein coding RNA 1072	ncRNA	0.015487	0.373068	
chunk0173_26_1	chr6	141833802	141834327	+	0	NA	Intergenic	Intergenic	254735	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.001905	0.277567	
chunk0106_138_1	chr2	200003524	200003833	+	0	NA	Intergenic	Intergenic	-47942	NR_109906	129450	Hs.204619	NM_152382	ENSG00000162971	TYW5	C2orf60|hTYW5	tRNA-yW synthesizing protein 5	protein-coding	0.000000	0.422581	
chunk0141_110_1	chr4	79633852	79634428	+	0	NA	Intergenic	Intergenic	141547	NR_038826	100506035	Hs.507664	NR_038826	ENSG00000250334	LINC00989	-	long intergenic non-protein coding RNA 989	ncRNA	0.015625	0.372617	
chunk0100_334_1	chr2	116706298	116706959	+	0	NA	Intergenic	Intergenic	-1108051	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.012103	0.415408	
chunk0194_411_1	chr8	91398013	91398212	+	0	NA	TTS (NM_052832)	TTS (NM_052832)	148824	NM_134266	115111	Hs.354013	NM_052832	ENSG00000147606	SLC26A7	SUT2	solute carrier family 26 member 7	protein-coding	0.010050	0.250000	
chunk0183_21_1	chr7	103373861	103374240	+	0	NA	TTS (NM_198999)	TTS (NM_198999)	26526	NM_001204453	5701	Hs.437366	NM_002803	ENSG00000161057	PSMC2	MSS1|Nbla10058|S7	proteasome 26S subunit, ATPase 2	protein-coding	0.002639	0.289474	
chunk0155_419_1	chr5	99879074	99879315	+	0	NA	Intergenic	L1PREC2|LINE|L1	345204	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.012448	0.549587	
chunk0087_279_1	chr18	38555180	38555746	+	0	NA	Intergenic	L2c|LINE|L2	898328	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.005300	0.380952	202(ATCACACTGTGTTCTA,+,0.00),263(AAGCACAGCCTGTGTC,-,0.00),264(AGCACAGCCTGTGTCT,+,0.00)
chunk0162_264_1	chr6	5366940	5367371	+	0	NA	intron (NM_006567, intron 1 of 6)	intron (NM_006567, intron 1 of 6)	90920	NR_125848	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.006961	0.391204	234(AGGGACAGACTGTGCT,-,0.00),235(GGGACAGACTGTGCTT,+,0.00)
chunk0174_299_1	chr6	162656723	162657015	+	0	NA	intron (NM_013988, intron 1 of 8)	L2a|LINE|L2	-70263	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.006849	0.474403	
chunk0031_125_1	chr10	124798783	124799069	+	0	NA	Intergenic	L2a|LINE|L2	-2859	NM_032182	23172	Hs.280695	NM_032182	ENSG00000165660	ABRAXAS2	ABRO1|FAM175B|KIAA0157	abraxas 2, BRISC complex subunit	protein-coding	0.013986	0.439024	
chunk0208_277_1	chrX	21800346	21801032	+	0	NA	Intergenic	Intergenic	-38849	NM_015884	51360	Hs.443490	NM_015884	ENSG00000012174	MBTPS2	BRESEK|IFAP|KFSD|KFSDX|OI19|OLMSX|S2P	membrane bound transcription factor peptidase, site 2	protein-coding	0.002915	0.433770	
chunk0013_326_1	chr1	171572399	171572874	+	0	NA	intron (NM_015172, intron 24 of 33)	intron (NM_015172, intron 24 of 33)	79997	NM_000261	4653	Hs.436037	NM_000261	ENSG00000034971	MYOC	GLC1A|GPOA|JOAG|JOAG1|TIGR	myocilin	protein-coding	0.000000	0.329832	
chunk0157_193_1	chr5	118923510	118923709	+	0	NA	intron (NM_173666, intron 4 of 5)	MER50B|LTR|ERV1	-50977	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.020101	0.455000	
chunk0134_16_1	chr3	175478961	175479675	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	109778	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.005602	0.276923	
chunk0058_36_1	chr14	20166833	20167568	+	0	NA	Intergenic	L1ME1|LINE|L1	23464	NM_001004724	390437	Hs.553766	NM_001004724	ENSG00000184394	OR4N5	-	olfactory receptor family 4 subfamily N member 5	protein-coding	0.000000	0.279891	289(AAGAACACTATGAACC,-,0.00)
chunk0064_390_1	chr14	99146505	99146704	+	0	NA	Intergenic	Intergenic	125109	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.020101	0.415000	
chunk0118_214_1	chr22	31889111	31889525	+	0	NA	intron (NR_110988, intron 34 of 38)	intron (NR_110988, intron 34 of 38)	49136	NM_001302820	25775	Hs.627602	NM_015372	ENSG00000128254	C22orf24	HSN44A4A	chromosome 22 open reading frame 24	protein-coding	0.009662	0.443373	279(CAGGCCAGCATGTTCT,-,0.00),280(AGGCCAGCATGTTCTG,+,0.00)
chunk0211_67_1	chrX	109926145	109926480	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	55911	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.011940	0.425595	153(CGGTACTCTCTGTGCC,-,0.00),154(GGTACTCTCTGTGCCC,+,0.00)
chunk0097_120_1	chr2	46575083	46575345	+	0	NA	intron (NR_104182, intron 1 of 1)	L1ME3G|LINE|L1	5024	NR_104182	100506142	Hs.658541	NR_104182	ENSG00000250116	LOC100506142	-	uncharacterized LOC100506142	ncRNA	0.003817	0.342205	130(CAGAACAACAAGTACT,-,0.00),131(AGAACAACAAGTACTG,+,0.00)
chunk0055_422_1	chr13	75191777	75192221	+	0	NA	Intergenic	Intergenic	48382	NR_027466	647288	Hs.567920	NR_027466	ENSG00000214249	CTAGE11P	-	CTAGE family member 11, pseudogene	pseudo	0.002252	0.294382	
chunk0031_283_1	chr10	128222388	128223192	+	0	NA	Intergenic	Intergenic	-63160	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.017413	0.490683	
chunk0136_2_1	chr4	27835	28232	+	0	NA	Intergenic	Intergenic	-25252	NM_001286054	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.007557	0.515075	
chunk0080_214_1	chr17	29615699	29615898	+	0	NA	exon (NM_032854, exon 10 of 10)	exon (NM_032854, exon 10 of 10)	5625	NM_032854	84940	Hs.143046	NM_032854	ENSG00000167549	CORO6	-	coronin 6	protein-coding	0.095477	0.705000	
chunk0034_226_1	chr11	33291412	33291683	+	0	NA	intron (NM_001278163, intron 2 of 15)	intron (NM_001278163, intron 2 of 15)	33216	NM_001278162	10114	Hs.201918	NM_005734	ENSG00000110422	HIPK3	DYRK6|FIST3|PKY|YAK1	homeodomain interacting protein kinase 3	protein-coding	0.014760	0.422794	171(AAGGTCAGCATGTTCT,-,0.00),172(AGGTCAGCATGTTCTA,+,0.00)
chunk0209_181_1	chrX	43698201	43698455	+	0	NA	intron (NM_000240, intron 3 of 14)	intron (NM_000240, intron 3 of 14)	43421	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.007874	0.403922	
chunk0119_427_1	chr22	50006292	50006566	+	0	NA	intron (NM_001001694, intron 3 of 14)	intron (NM_001001694, intron 3 of 14)	6197	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.025547	0.574545	
chunk0003_33_1	chr1	29912875	29913135	+	0	NA	Intergenic	L1ME4a|LINE|L1	124607	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.000000	0.333333	
chunk0101_182_1	chr2	129365242	129365479	+	0	NA	Intergenic	Intergenic	-91469	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.004219	0.327731	
chunk0182_244_1	chr7	97042324	97042595	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-17628	NM_005221	1749	Hs.99348	NM_005221	ENSG00000105880	DLX5	SHFM1D	distal-less homeobox 5	protein-coding	0.007380	0.389706	
chunk0070_264_1	chr15	73983355	73983784	+	0	NA	3' UTR (NM_001256677, exon 8 of 8)	3' UTR (NM_001256677, exon 8 of 8)	8779	NM_001256673	9399	Hs.194816	NM_004809	ENSG00000067221	STOML1	SLP-1|STORP|hUNC-24	stomatin like 1	protein-coding	0.023310	0.630233	
chunk0083_348_1	chr17	70302219	70302566	+	0	NA	Intergenic	L1MC1|LINE|L1	132857	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.002882	0.336207	159(AAGTACAGACAGTTCC,-,0.00),160(AGTACAGACAGTTCCC,+,0.00)
chunk0186_102_1	chr7	137695892	137696434	+	0	NA	intron (NM_004717, intron 1 of 33)	L2a|LINE|L2	150700	NM_004717	9162	Hs.242947	NM_004717	ENSG00000157680	DGKI	DGK-IOTA	diacylglycerol kinase iota	protein-coding	0.014760	0.390424	
chunk0120_357_1	chr3	11601389	11601838	+	0	NA	intron (NM_001128219, intron 2 of 4)	intron (NM_001128219, intron 2 of 4)	2968	NM_001284391	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.017817	0.404444	
chunk0124_221_1	chr3	56285272	56285850	+	0	NA	intron (NR_132749, intron 3 of 17)	intron (NR_132749, intron 3 of 17)	182802	NR_132749	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.005190	0.459413	357(GGGAACTGGCTGTCCT,-,0.00),358(GGAACTGGCTGTCCTC,+,0.00)
chunk0052_102_1	chr13	22468829	22469441	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	258850	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.011438	0.437194	
chunk0210_193_1	chrX	80136341	80136788	+	0	NA	Intergenic	Intergenic	113504	NM_001303475	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.000000	0.348214	
chunk0192_139_1	chr8	61984118	61984580	+	0	NA	Intergenic	Intergenic	-264593	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.006494	0.373650	
chunk0056_244_1	chr13	89153436	89153956	+	0	NA	Intergenic	Intergenic	-81595	NR_047025	100874172	Hs.569291	NR_047025		LINC00440	-	long intergenic non-protein coding RNA 440	ncRNA	0.001923	0.339731	
chunk0053_114_1	chr13	29453902	29454147	+	0	NA	intron (NM_015233, intron 2 of 8)	intron (NM_015233, intron 2 of 8)	25384	NM_015233	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.008163	0.345528	
chunk0189_289_1	chr8	25584535	25585357	+	0	NA	Intergenic	Intergenic	125949	NM_152562	157313	Hs.33366	NM_152562	ENSG00000184661	CDCA2	PPP1R81|Repo-Man	cell division cycle associated 2	protein-coding	0.014599	0.432564	
chunk0122_198_1	chr3	33058638	33059136	+	0	NA	intron (NM_000404, intron 5 of 15)	intron (NM_000404, intron 5 of 15)	37914	NM_001136238	643853	Hs.443031	NM_001039770	ENSG00000188167	TMPPE	-	transmembrane protein with metallophosphoesterase domain	protein-coding	0.010040	0.456914	
chunk0171_437_1	chr6	131717713	131718095	+	0	NA	intron (NR_133007, intron 15 of 23)	Tigger3a|DNA|TcMar-Tigger	-6887	NM_001145659	643854	Hs.632613	NM_001145659	ENSG00000236761	CTAGE9	-	CTAGE family member 9	protein-coding	0.002618	0.365535	
chunk0119_24_1	chr22	40258474	40258883	+	0	NA	intron (NM_001024843, intron 6 of 23)	intron (NM_001024843, intron 6 of 23)	80753	NM_015088	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.004890	0.397561	147(TTGTACATGATGTCCT,-,0.00),148(TGTACATGATGTCCTG,+,0.00)
chunk0197_434_1	chr8	127508003	127508332	+	0	NA	Intergenic	MER124|DNA?|DNA?	-26028	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.006079	0.351515	
chunk0153_29_1	chr5	67102692	67103058	+	0	NA	intron (NM_001290226, intron 7 of 26)	intron (NM_001290226, intron 7 of 26)	93914	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.010929	0.444142	102(GAGAACTAGCTGTGCT,-,0.00),103(AGAACTAGCTGTGCTC,+,0.00)
chunk0057_252_1	chr13	105172778	105173034	+	0	NA	Intergenic	L1MA9|LINE|L1	-292961	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.000000	0.319066	
chunk0176_389_1	chr7	18818473	18818939	+	0	NA	intron (NM_178425, intron 16 of 24)	intron (NM_178425, intron 16 of 24)	298966	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.006438	0.342612	
chunk0207_441_1	chr9	137590238	137590437	+	0	NA	5' UTR (NM_138462, exon 1 of 6)	5' UTR (NM_138462, exon 1 of 6)	148	NM_138462	116225	Hs.128096	NM_138462	ENSG00000165724	ZMYND19	MIZIP	zinc finger MYND-type containing 19	protein-coding	0.160804	0.800000	
chunk0032_249_1	chr11	8528256	8529133	+	0	NA	intron (NM_001289061, intron 1 of 12)	intron (NM_001289061, intron 1 of 12)	65314	NM_030906	65975	Hs.501833	NM_030906	ENSG00000130413	STK33	-	serine/threonine kinase 33	protein-coding	0.009122	0.359909	
chunk0040_231_1	chr11	114449104	114449303	+	0	NA	intron (NM_015523, intron 6 of 6)	intron (NM_015523, intron 6 of 6)	9817	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.000000	0.390000	
chunk0090_258_1	chr18	74282352	74283137	+	0	NA	intron (NM_001190807, intron 1 of 3)	L2b|LINE|L2	9272	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.011465	0.479644	407(GAGGACACAGTGTTAT,-,0.00),408(AGGACACAGTGTTATT,+,0.00),542(AAGGACAATCTGTTTC,-,0.00),543(AGGACAATCTGTTTCC,+,0.00)
chunk0058_425_1	chr13	112926015	112926616	+	0	NA	Intergenic	Intergenic	42323	NR_034002	100289410	Hs.667436	NR_034002		MCF2L-AS1	-	MCF2L antisense RNA 1	ncRNA	0.039933	0.531561	
chunk0130_219_1	chr3	134104055	134104459	+	0	NA	Intergenic	Intergenic	-74181	NM_005630	6578	Hs.518270	NM_005630	ENSG00000174640	SLCO2A1	MATR1|OATP2A1|PGT|PHOAR2|SLC21A2	solute carrier organic anion transporter family member 2A1	protein-coding	0.007426	0.387654	
chunk0023_94_1	chr10	22552825	22553338	+	0	NA	intron (NM_005028, intron 6 of 9)	intron (NM_005028, intron 6 of 9)	-115152	NR_036533	100499489	Hs.7444	NR_036533		LOC100499489	-	uncharacterized LOC100499489	ncRNA	0.009747	0.447471	248(CTGGACACCATGTACT,-,0.00),249(TGGACACCATGTACTC,+,0.00)
chunk0137_332_1	chr4	24840475	24840770	+	0	NA	intron (NM_001130726, intron 4 of 11)	Tigger17a|DNA|TcMar-Tigger	45159	NM_003102	6649	Hs.2420	NM_003102	ENSG00000109610	SOD3	EC-SOD	superoxide dismutase 3	protein-coding	0.016949	0.462838	
chunk0039_284_1	chr11	102629744	102630259	+	0	NA	Intergenic	Intergenic	-4669	NM_004771	9313	Hs.591946	NM_004771	ENSG00000137674	MMP20	AI2A2|MMP-20	matrix metallopeptidase 20	protein-coding	0.001942	0.331395	
chunk0089_168_1	chr18	59148338	59148549	+	0	NA	intron (NM_033280, intron 1 of 5)	intron (NM_033280, intron 1 of 5)	8586	NM_033280	90701	Hs.45107	NM_033280	ENSG00000166562	SEC11C	SEC11L3|SPC21|SPCS4C	SEC11 homolog C, signal peptidase complex subunit	protein-coding	0.018957	0.580189	115(AGGAAGAGCCTGTGCT,-,0.00),116(GGAAGAGCCTGTGCTT,+,0.00)
chunk0168_298_1	chr6	91464180	91464714	+	0	NA	Intergenic	Intergenic	-57213	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.005618	0.321495	
chunk0030_222_1	chr10	114762371	114762592	+	0	NA	Intergenic	Intergenic	-2307	NR_120628	101927692	Hs.576909	NR_120628	ENSG00000228484	LOC101927692	-	uncharacterized LOC101927692	ncRNA	0.000000	0.328829	23(GGGTACATACTGAGCC,-,0.00),24(GGTACATACTGAGCCC,+,0.00)
chunk0066_280_1	chr15	35134159	35134745	+	0	NA	Intergenic	L2c|LINE|L2	-102874	NR_003144	723972	Hs.631698	NR_003144	ENSG00000259516	ANP32AP1	-	acidic nuclear phosphoprotein 32 family member A pseudogene 1	pseudo	0.003413	0.373083	298(TAGAGCACAGTGTACT,-,0.00),299(AGAGCACAGTGTACTA,+,0.00)
chunk0079_118_1	chr17	12433744	12434154	+	0	NA	Intergenic	Intergenic	-116019	NR_034145	284034	Hs.376614	NR_034144	ENSG00000179136	LINC00670	-	long intergenic non-protein coding RNA 670	ncRNA	0.007317	0.469586	
chunk0017_84_1	chr1	205710135	205710907	+	0	NA	Intergenic	Intergenic	-30019	NM_033102	85414	Hs.278695	NM_033102	ENSG00000158715	SLC45A3	IPCA-2|IPCA-6|IPCA-8|IPCA6|PCANAP2|PCANAP6|PCANAP8|PRST	solute carrier family 45 member 3	protein-coding	0.000000	0.360931	
chunk0177_351_1	chr7	26606358	26606735	+	0	NA	Intergenic	L1MC2|LINE|L1	-31325	NM_001145531									0.005305	0.407407	119(TGGAACAGTGAGTACT,-,0.00),120(GGAACAGTGAGTACTC,+,0.00)
chunk0100_123_1	chr2	108613142	108613746	+	0	NA	intron (NM_001193482, intron 1 of 9)	intron (NM_001193482, intron 1 of 9)	6283	NM_001193482	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.013245	0.474380	8(AACACATAATGTGCTG,+,0.00)
chunk0117_363_1	chr21	44795620	44796128	+	0	NA	intron (NM_003343, intron 1 of 5)	MLT1C|LTR|ERVL-MaLR	5962	NM_001202489	7327	Hs.529420	NM_003343	ENSG00000184787	UBE2G2	UBC7	ubiquitin conjugating enzyme E2 G2	protein-coding	0.013780	0.426326	
chunk0018_19_1	chr1	215458328	215458609	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-108924	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.010676	0.411348	
chunk0137_274_1	chr4	22606526	22606771	+	0	NA	Intergenic	Intergenic	-86266	NR_102356	57733	Hs.653107	NM_020973	ENSG00000249948	GBA3	CBG|CBGL1|GLUC|KLRP	glucosylceramidase beta 3 (gene/pseudogene)	protein-coding	0.004082	0.512195	
chunk0106_453_1	chr2	209368839	209369257	+	0	NA	Intergenic	Intergenic	-54999	NM_001039538	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.011962	0.393795	
chunk0012_155_1	chr1	158117913	158118284	+	0	NA	Intergenic	Intergenic	22542	NR_033946	646268	Hs.506902	NR_033946	ENSG00000231666	LINC01704	-	long intergenic non-protein coding RNA 1704	ncRNA	0.026954	0.607527	
chunk0030_340_1	chr10	118431125	118431574	+	0	NA	Intergenic	L1M5|LINE|L1	74241	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.000000	0.277778	
chunk0025_437_1	chr10	60095131	60095330	+	0	NA	intron (NM_001204403, intron 29 of 43)	intron (NM_001204403, intron 29 of 43)	45786	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005025	0.340000	
chunk0073_180_1	chr16	8920804	8921236	+	0	NA	intron (NM_003470, intron 4 of 30)	intron (NM_003470, intron 4 of 30)	15709	NM_001286458	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.013889	0.367206	
chunk0100_285_1	chr2	114093134	114093476	+	0	NA	Intergenic	L1MC1|LINE|L1	-113321	NR_034130	100499194	Hs.662336	NR_034130		LOC100499194	-	uncharacterized LOC100499194	ncRNA	0.000000	0.355685	
chunk0144_113_1	chr4	128660120	128660932	+	0	NA	Intergenic	Intergenic	-149097	NM_024900	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.002463	0.375154	362(AGGAACAGTCTGTGCC,-,0.00),363(GGAACAGTCTGTGCCT,+,0.00),748(TAGAACAGAGTGTTTA,-,0.00),749(AGAACAGAGTGTTTAT,+,0.00)
chunk0148_37_1	chr5	1129761	1130034	+	0	NA	Intergenic	Intergenic	-17840	NM_006598	10723	Hs.172613	NM_006598	ENSG00000113504	SLC12A7	KCC4	solute carrier family 12 member 7	protein-coding	0.032967	0.572993	127(AGCCCATTGTGTCCTG,+,0.00)
chunk0132_310_1	chr3	160517264	160517706	+	0	NA	intron (NM_002268, intron 11 of 16)	L1MB7|LINE|L1	-2249	NR_003001	677767	Hs.675953	NR_003001	ENSG00000238741	SCARNA7	U90	small Cajal body-specific RNA 7	ncRNA	0.011312	0.345372	
chunk0069_148_1	chr15	62472781	62473143	+	0	NA	Intergenic	Intergenic	129933	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.013812	0.545455	
chunk0129_227_1	chr3	121942597	121942887	+	0	NA	3' UTR (NM_001145998, exon 21 of 21)	3' UTR (NM_001145998, exon 21 of 21)	48418	NM_021082	6565	Hs.518089	NM_021082	ENSG00000163406	SLC15A2	PEPT2	solute carrier family 15 member 2	protein-coding	0.003448	0.347079	44(GAAGACAGCCTGTTCA,-,0.00),45(AAGACAGCCTGTTCAT,+,0.00)
chunk0031_31_1	chr10	122034971	122035418	+	0	NA	intron (NM_001291877, intron 2 of 19)	intron (NM_001291877, intron 2 of 19)	46020	NM_206862	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.013423	0.484375	
chunk0160_274_1	chr5	157731400	157731824	+	0	NA	exon (NM_017872, exon 1 of 6)	exon (NM_017872, exon 1 of 6)	297	NM_017872	54974	Hs.353090	NM_017872	ENSG00000113272	THG1L	ICF45|IHG-1|hTHG1	tRNA-histidine guanylyltransferase 1 like	protein-coding	0.082547	0.609412	
chunk0151_373_1	chr5	55004600	55005191	+	0	NA	Intergenic	Intergenic	19274	NR_104662	102467081		NR_104662		LOC102467081	-	uncharacterized LOC102467081	ncRNA	0.001692	0.332770	
chunk0089_418_1	chr18	69322508	69323288	+	0	NA	Intergenic	L1ME2|LINE|L1	-78150	NM_152721	220164	Hs.278285	NM_152721	ENSG00000206052	DOK6	DOK5L|HsT3226	docking protein 6	protein-coding	0.005128	0.348271	
chunk0127_18_1	chr3	88182620	88182971	+	0	NA	Intergenic	L1PA6|LINE|L1	-32929	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.011396	0.482955	
chunk0131_94_1	chr3	143601785	143602442	+	0	NA	intron (NM_173653, intron 6 of 15)	intron (NM_173653, intron 6 of 15)	246418	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.009132	0.468085	
chunk0072_332_1	chr15	99210430	99210677	+	0	NA	intron (NR_109947, intron 7 of 12)	intron (NR_109947, intron 7 of 12)	39066	NM_001288615	64927	Hs.513195	NM_022905	ENSG00000103852	TTC23	HCC-8	tetratricopeptide repeat domain 23	protein-coding	0.000000	0.447581	61(AGGCACATAGTGTCCC,-,0.00),62(GGCACATAGTGTCCCA,+,0.00),114(AAGAGCAGGATGTTCT,-,0.00),115(AGAGCAGGATGTTCTC,+,0.00)
chunk0108_120_1	chr2	229829707	229830296	+	0	NA	intron (NM_004238, intron 6 of 40)	intron (NM_004238, intron 6 of 40)	50127	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.013582	0.396610	
chunk0058_97_1	chr14	21607249	21607550	+	0	NA	Intergenic	Intergenic	27541	NM_001005466	26534	Hs.554580	NM_001005466	ENSG00000255582	OR10G2	OR14-41	olfactory receptor family 10 subfamily G member 2	protein-coding	0.009967	0.470199	
chunk0061_436_1	chr14	65594148	65594725	+	0	NA	intron (NR_038170, intron 3 of 10)	LTR28B|LTR|ERV1	123334	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.019064	0.541522	336(CAGCTCAGTGTGTCCT,-,0.00),337(AGCTCAGTGTGTCCTT,+,0.00)
chunk0204_187_1	chr9	96405879	96406306	+	0	NA	intron (NM_153695, intron 1 of 4)	L1MB5|LINE|L1	12295	NM_153695	195828	Hs.494557	NM_153695	ENSG00000165244	ZNF367	AFF29|CDC14B|ZFF29	zinc finger protein 367	protein-coding	0.000000	0.303738	200(GGGAACTCTCTGTACT,-,0.00),201(GGAACTCTCTGTACTA,+,0.00)
chunk0038_343_1	chr11	92908722	92909462	+	0	NA	Intergenic	Intergenic	-60531	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.014865	0.479082	
chunk0114_421_1	chr20	64151837	64152195	+	0	NA	Intergenic	Intergenic	-12458	NM_004535	4661	Hs.279562	NM_004535	ENSG00000196132	MYT1	C20orf36|MTF1|MYTI|NZF2|PLPB1|ZC2H2C1|ZC2HC4A	myelin transcription factor 1	protein-coding	0.036313	0.562674	
chunk0067_340_1	chr15	48463295	48464019	+	0	NA	intron (NM_000138, intron 41 of 65)	Tigger19b|DNA|TcMar-Tigger	131489	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.006906	0.393103	
chunk0203_330_1	chr9	89730238	89730437	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	90554	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.015075	0.495000	
chunk0160_332_1	chr5	159862700	159862950	+	0	NA	intron (NR_109891, intron 2 of 2)	intron (NR_109891, intron 2 of 2)	8559	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.008000	0.402390	
chunk0167_219_1	chr6	66506711	66507398	+	0	NA	Intergenic	L2b|LINE|L2	719175	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.007278	0.343023	
chunk0207_304_1	chr9	133462158	133462357	+	0	NA	intron (NM_017586, intron 1 of 4)	intron (NM_017586, intron 1 of 4)	2292	NM_001135775	11094	Hs.62003	NM_017586	ENSG00000160325	CACFD1	C9orf7|D9S2135|FLOWER	calcium channel flower domain containing 1	protein-coding	0.010050	0.605000	
chunk0144_106_1	chr4	128589455	128590010	+	0	NA	Intergenic	Intergenic	161716	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.010811	0.440647	
chunk0146_19_1	chr4	155066272	155066820	+	0	NA	Intergenic	L1ME3|LINE|L1	-142083	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.007299	0.309654	
chunk0062_49_1	chr14	67345622	67346057	+	0	NA	exon (NM_015994, exon 6 of 9)	exon (NM_015994, exon 6 of 9)	14164	NM_015994	51382	Hs.272630	NM_015994	ENSG00000100554	ATP6V1D	ATP6M|VATD|VMA8	ATPase H+ transporting V1 subunit D	protein-coding	0.000000	0.373853	
chunk0027_405_1	chr10	80460726	80460997	+	0	NA	intron (NM_030927, intron 1 of 8)	intron (NM_030927, intron 1 of 8)	6579	NM_001128309	81619	Hs.308615	NM_030927	ENSG00000108219	TSPAN14	DC-TM4F2|TM4SF14|tspan-14	tetraspanin 14	protein-coding	0.011070	0.566176	
chunk0144_463_1	chr4	142498852	142499539	+	0	NA	intron (NM_003866, intron 2 of 26)	intron (NM_003866, intron 2 of 26)	347256	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.002911	0.309593	
chunk0173_378_1	chr6	149789524	149789756	+	0	NA	intron (NM_001252050, intron 3 of 6)	L1ME4b|LINE|L1	39945	NM_001252051	5110	Hs.279257	NM_005389	ENSG00000120265	PCMT1	PIMT	protein-L-isoaspartate (D-aspartate) O-methyltransferase	protein-coding	0.000000	0.291845	
chunk0068_455_1	chr15	59895295	59895698	+	0	NA	Intergenic	Intergenic	-108726	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.002481	0.418317	
chunk0086_231_1	chr18	22780875	22781311	+	0	NA	intron (NR_110782, intron 1 of 1)	intron (NR_110782, intron 1 of 1)	5744	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.002294	0.258581	
chunk0087_360_1	chr18	41170033	41170232	+	0	NA	Intergenic	Intergenic	350465	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.000000	0.340000	
chunk0029_17_1	chr10	95524598	95525051	+	0	NA	intron (NM_001290294, intron 1 of 31)	L2c|LINE|L2	36596	NM_001290294	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.008830	0.436123	345(AGGCACACACTGTCCA,-,0.00),346(GGCACACACTGTCCAC,+,0.00)
chunk0055_288_1	chr13	64764066	64764465	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-920140	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.002506	0.442500	
chunk0067_222_1	chr15	45345008	45345333	+	0	NA	Intergenic	MLT2C2|LTR|ERVL	33612	NM_001482	2628	Hs.75335	NM_001482	ENSG00000171766	GATM	AGAT|AT|CCDS3	glycine amidinotransferase	protein-coding	0.003077	0.447853	
chunk0077_310_1	chr16	82016215	82016601	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-4920	NM_145168	93517	Hs.87779	NM_145168	ENSG00000184860	SDR42E1	HSPC105	short chain dehydrogenase/reductase family 42E, member 1	protein-coding	0.015544	0.439276	
chunk0128_414_1	chr3	114766468	114766720	+	0	NA	intron (NM_001164343, intron 4 of 11)	intron (NM_001164343, intron 4 of 11)	-7317	NM_001164345	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.003968	0.363636	
chunk0165_1_1	chr6	28487470	28487711	+	0	NA	Intergenic	MER83|LTR|ERV1	28203	NM_182701	257202	Hs.448570	NM_182701	ENSG00000198704	GPX6	GPX5p|GPXP3|GPx-6|GSHPx-6|dJ1186N24|dJ1186N24.1	glutathione peroxidase 6	protein-coding	0.004149	0.450413	
chunk0016_37_1	chr1	193108461	193109170	+	0	NA	Intergenic	Intergenic	-2701	NM_016066	51022	Hs.458283	NM_016066	ENSG00000023572	GLRX2	CGI-133|GRX2	glutaredoxin 2	protein-coding	0.005642	0.408451	
chunk0134_41_1	chr3	175730725	175731111	+	0	NA	intron (NM_207015, intron 11 of 13)	intron (NM_207015, intron 11 of 13)	45415	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.000000	0.330749	
chunk0002_391_1	chr1	26939689	26939899	+	0	NA	intron (NM_006600, intron 2 of 8)	MER5A|DNA|hAT-Charlie	18072	NM_006600	10726	Hs.263812	NM_006600	ENSG00000090273	NUDC	HNUDC|MNUDC|NPD011	nuclear distribution C, dynein complex regulator	protein-coding	0.004762	0.469194	
chunk0054_107_1	chr13	42859813	42860250	+	0	NA	intron (NR_126388, intron 2 of 2)	intron (NR_126388, intron 2 of 2)	12713	NR_126388	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.004577	0.340183	216(AAGTGCATACTGTACC,-,0.00)
chunk0159_374_1	chr5	145983969	145984404	+	0	NA	intron (NM_152550, intron 2 of 9)	L2a|LINE|L2	47623	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.002299	0.380734	
chunk0068_64_1	chr15	51816467	51816767	+	0	NA	TTS (NM_001142885)	TTS (NM_001142885)	-13011	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.000000	0.315615	
chunk0105_167_1	chr2	187005631	187005962	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-156626	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.000000	0.286145	123(GAGGTCAGCATGTTCC,-,0.00),124(AGGTCAGCATGTTCCT,+,0.00)
chunk0164_336_1	chr6	25302410	25302672	+	0	NA	intron (NM_017640, intron 2 of 36)	intron (NM_017640, intron 2 of 36)	23113	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.007634	0.433460	
chunk0046_214_1	chr12	59370124	59370727	+	0	NA	Intergenic	Intergenic	-225615	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.006633	0.339404	
chunk0008_434_1	chr1	99456645	99456941	+	0	NA	Intergenic	Intergenic	31011	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.013514	0.468013	
chunk0155_169_1	chr5	94367082	94367321	+	0	NA	intron (NM_001145678, intron 20 of 20)	LTR10C|LTR|ERV1	251403	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.012552	0.433333	
chunk0123_283_1	chr3	46358352	46358717	+	0	NA	exon (NM_001123396, exon 2 of 2)	exon (NM_001123396, exon 2 of 2)	4790	NM_001123041	729230	Hs.511794	NM_001123041	ENSG00000121807	CCR2	CC-CKR-2|CCR-2|CCR2A|CCR2B|CD192|CKR2|CKR2A|CKR2B|CMKBR2|MCP-1-R	C-C motif chemokine receptor 2	protein-coding	0.021918	0.459016	
chunk0140_102_1	chr4	68447255	68448055	+	0	NA	intron (NM_014058, intron 1 of 9)	intron (NM_014058, intron 1 of 9)	206	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.002500	0.312110	
chunk0141_84_1	chr4	78610123	78610574	+	0	NA	3' UTR (NM_005139, exon 13 of 13)	3' UTR (NM_005139, exon 13 of 13)	-35646	NR_038303	100505702	Hs.235795	NR_038303		LINC01094	-	long intergenic non-protein coding RNA 1094	ncRNA	0.004435	0.314159	
chunk0145_449_1	chr4	153612904	153613357	+	0	NA	intron (NM_001131007, intron 26 of 34)	HAL1b|LINE|L1	-71159	NM_003264	7097	Hs.519033	NM_003264	ENSG00000137462	TLR2	CD282|TIL4	toll like receptor 2	protein-coding	0.004415	0.321586	
chunk0039_352_1	chr11	105530663	105530983	+	0	NA	Intergenic	Intergenic	-79250	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.000000	0.317757	
chunk0088_66_1	chr18	44430448	44430862	+	0	NA	intron (NR_110792, intron 2 of 4)	L1MC1|LINE|L1	101042	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.000000	0.298795	
chunk0041_363_1	chr11	131106878	131107077	+	0	NA	Intergenic	Intergenic	-190490	NM_001301089	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.010050	0.470000	
chunk0129_44_1	chr3	117428474	117428782	+	0	NA	Intergenic	Intergenic	507197	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.009740	0.330097	
chunk0205_208_1	chr9	109304418	109304763	+	0	NA	intron (NM_018424, intron 1 of 15)	MIR|SINE|MIR	16374	NM_018424	54566	Hs.591901	NM_018424	ENSG00000095203	EPB41L4B	CG1|EHM2	erythrocyte membrane protein band 4.1 like 4B	protein-coding	0.005797	0.459538	176(AGGCACTGTGTGTTCT,-,0.00),177(GGCACTGTGTGTTCTC,+,0.00)
chunk0159_232_1	chr5	141524747	141524946	+	0	NA	intron (NM_001314007, intron 26 of 28)	intron (NM_001314007, intron 26 of 28)	-33465	NR_038333	100505658	Hs.655458	NR_038333	ENSG00000246422	LOC100505658	-	uncharacterized LOC100505658	ncRNA	0.010050	0.500000	
chunk0099_209_1	chr2	94979675	94980076	+	0	NA	Intergenic	L2b|LINE|L2	-32533	NR_037597	442028	Hs.611545	NR_037597	ENSG00000259848	LOC442028	-	uncharacterized LOC442028	ncRNA	0.007481	0.462687	
chunk0014_89_1	chr1	176586955	176587241	+	0	NA	intron (NM_020318, intron 2 of 22)	L1PA6|LINE|L1	123927	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.337979	
chunk0057_384_1	chr13	109396100	109396682	+	0	NA	Intergenic	Intergenic	-4305	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.017182	0.427101	
chunk0097_54_1	chr2	43463065	43463740	+	0	NA	intron (NM_001083953, intron 26 of 37)	intron (NM_001083953, intron 26 of 37)	132572	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.007407	0.362426	
chunk0099_328_1	chr2	99873372	99873825	+	0	NA	intron (NM_001025108, intron 6 of 23)	MIRb|SINE|MIR	231985	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.002208	0.383260	
chunk0096_182_1	chr2	29795320	29796044	+	0	NA	intron (NM_004304, intron 1 of 28)	L1ME4c|LINE|L1	125929	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.006906	0.302069	
chunk0205_329_1	chr9	112878531	112879291	+	0	NA	TTS (NM_033051)	TTS (NM_033051)	12002	NM_033051	57864	Hs.512668	NM_033051	ENSG00000119457	SLC46A2	Ly110|TSCOT	solute carrier family 46 member 2	protein-coding	0.005263	0.417871	
chunk0204_14_1	chr9	91777119	91777356	+	0	NA	intron (NM_004560, intron 1 of 8)	intron (NM_004560, intron 1 of 8)	-140892	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.008439	0.382353	
chunk0089_162_1	chr18	59096350	59096927	+	0	NA	Intergenic	Intergenic	-43219	NM_001307941	90701	Hs.45107	NM_033280	ENSG00000166562	SEC11C	SEC11L3|SPC21|SPCS4C	SEC11 homolog C, signal peptidase complex subunit	protein-coding	0.006932	0.448097	
chunk0168_292_1	chr6	91299453	91299890	+	0	NA	Intergenic	Intergenic	-221989	NR_039786	100616174		NR_039786	ENSG00000263734	MIR4643	-	microRNA 4643	ncRNA	0.004577	0.431507	253(TGCACAGATAGTTCTT,+,0.00)
chunk0028_241_1	chr10	90073922	90074171	+	0	NA	Intergenic	L1MA3|LINE|L1	-116673	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.000000	0.296000	
chunk0030_228_1	chr10	114833369	114833719	+	0	NA	intron (NM_020940, intron 3 of 16)	intron (NM_020940, intron 3 of 16)	11800	NM_001135051	57700	Hs.192619	NM_020940	ENSG00000151553	FAM160B1	KIAA1600|bA106M7.3	family with sequence similarity 160 member B1	protein-coding	0.005714	0.333333	
chunk0111_139_1	chr20	24987828	24988371	+	0	NA	intron (NM_020531, intron 1 of 8)	intron (NM_020531, intron 1 of 8)	4690	NM_020531	57136	Hs.472330	NM_020531	ENSG00000101474	APMAP	BSCv|C20orf3	adipocyte plasma membrane associated protein	protein-coding	0.003683	0.446691	326(AGGTACATTGTGTTTT,-,0.00),327(GGTACATTGTGTTTTC,+,0.00)
chunk0090_252_1	chr18	74255385	74255696	+	0	NA	intron (NM_001190807, intron 3 of 3)	intron (NM_001190807, intron 3 of 3)	36476	NM_001914	1528	Hs.465413	NM_001914	ENSG00000166347	CYB5A	CYB5|MCB5|METAG	cytochrome b5 type A	protein-coding	0.012862	0.544872	211(CTGAACAGTCTGGCCT,-,0.00),212(TGAACAGTCTGGCCTT,+,0.00)
chunk0137_338_1	chr4	25021151	25021596	+	0	NA	intron (NM_018176, intron 4 of 7)	intron (NM_018176, intron 4 of 7)	9419	NM_018176	55203	Hs.12488	NM_018176	ENSG00000153012	LGI2	LGIL2	leucine rich repeat LGI family member 2	protein-coding	0.004494	0.369955	
chunk0138_246_1	chr4	39548515	39548890	+	0	NA	intron (NR_047679, intron 2 of 4)	intron (NR_047679, intron 2 of 4)	20863	NR_047679	100885776	Hs.640769	NR_047679	ENSG00000249348	UGDH-AS1	-	UGDH antisense RNA 1	ncRNA	0.000000	0.308511	
chunk0201_37_1	chr9	33437289	33437682	+	0	NA	Intergenic	Intergenic	10148	NM_004925	360	Hs.234642	NM_004925	ENSG00000165272	AQP3	AQP-3|GIL	aquaporin 3 (Gill blood group)	protein-coding	0.005089	0.530457	
chunk0001_269_1	chr1	8603090	8603511	+	0	NA	intron (NM_001042681, intron 4 of 22)	Charlie29a|DNA|hAT-Charlie	-108387	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.009501	0.381517	
chunk0119_90_1	chr22	41687521	41688045	+	0	NA	intron (NM_005008, intron 1 of 3)	MIRb|SINE|MIR	1126	NM_001003796	4809	Hs.182255	NM_005008	ENSG00000100138	SNU13	15.5K|FA-1|FA1|NHP2L1|NHPX|OTK27|SNRNP15-5|SPAG12|SSFA1	small nuclear ribonucleoprotein 13	protein-coding	0.019084	0.426667	
chunk0127_147_1	chr3	94416541	94416740	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-353417	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.010050	0.335000	
chunk0149_159_1	chr5	20360279	20360490	+	0	NA	intron (NM_001291956, intron 1 of 14)	MER130|DNA|DNA	215489	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.009479	0.405660	
chunk0123_423_1	chr3	49769631	49770234	+	0	NA	intron (NM_153273, intron 1 of 5)	MLT1F1|LTR|ERVL-MaLR	16262	NM_001242829	9807	Hs.386168	NM_153273	ENSG00000176095	IP6K1	IHPK1|PiUS	inositol hexakisphosphate kinase 1	protein-coding	0.001658	0.442053	
chunk0069_142_1	chr15	62428135	62428518	+	0	NA	Intergenic	Intergenic	85297	NR_106733	102464834		NR_106733	ENSG00000275451	MIR6085	hsa-mir-6085	microRNA 6085	ncRNA	0.015666	0.406250	
chunk0116_391_1	chr21	42352909	42353237	+	0	NA	Intergenic	L2|LINE|L2	-1974	NM_005423	7032	Hs.2979	NM_005423	ENSG00000160181	TFF2	SML1|SP	trefoil factor 2	protein-coding	0.024390	0.516717	189(GAGTTCACTGTGTTCC,-,0.00),190(AGTTCACTGTGTTCCT,+,0.00)
chunk0054_175_1	chr13	44389164	44389623	+	0	NA	intron (NM_001010897, intron 2 of 2)	MIR|SINE|MIR	15551	NM_001010897	387923	Hs.377972	NM_001010897	ENSG00000151778	SERP2	C13orf21|bA269C23.1	stress associated endoplasmic reticulum protein family member 2	protein-coding	0.006536	0.417391	
chunk0125_15_1	chr3	61939073	61939571	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	377753	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.012048	0.396794	
chunk0013_63_1	chr1	167360360	167360612	+	0	NA	intron (NR_037163, intron 3 of 16)	L1PA17|LINE|L1	31442	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.011905	0.399209	
chunk0138_375_1	chr4	42467659	42467985	+	0	NA	intron (NM_006095, intron 25 of 36)	L1PB1|LINE|L1	69983	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.006135	0.394495	
chunk0051_345_1	chr12	120350907	120351240	+	0	NA	intron (NM_002442, intron 11 of 14)	L2b|LINE|L2	18107	NM_002442	4440	Hs.158311	NM_002442	ENSG00000135097	MSI1	-	musashi RNA binding protein 1	protein-coding	0.027027	0.592814	
chunk0022_253_1	chr10	14623058	14623317	+	0	NA	intron (NM_001282695, intron 2 of 5)	Tigger13a|DNA|TcMar-Tigger	-18769	NM_001282697	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.007722	0.334615	
chunk0202_188_1	chr9	74827622	74827914	+	0	NA	intron (NM_001177310, intron 7 of 38)	intron (NM_001177310, intron 7 of 38)	59579	NM_001177311	140803	Hs.272225	NM_017662	ENSG00000119121	TRPM6	CHAK2|HMGX|HOMG|HOMG1|HSH	transient receptor potential cation channel subfamily M member 6	protein-coding	0.010274	0.532423	
chunk0190_193_1	chr8	33560068	33560584	+	0	NA	intron (NM_024787, intron 1 of 5)	MLT1L|LTR|ERVL-MaLR	6802	NM_024787	79845	Hs.151237	NM_024787	ENSG00000133874	RNF122	-	ring finger protein 122	protein-coding	0.009690	0.510638	
chunk0040_51_1	chr11	111021250	111021567	+	0	NA	Intergenic	Intergenic	-234574	NM_198498	341032	Hs.298685	NM_198498	ENSG00000150750	C11orf53	-	chromosome 11 open reading frame 53	protein-coding	0.006309	0.503145	
chunk0072_111_1	chr15	91472329	91472977	+	0	NA	intron (NR_110106, intron 1 of 3)	L1MB8|LINE|L1	9314	NR_110106	101926928	Hs.638788	NR_110106	ENSG00000258551	CRAT37	-	cervical cancer-associated transcript 37	ncRNA	0.007716	0.380586	
chunk0055_428_1	chr13	75419926	75420125	+	0	NA	intron (NM_001286659, intron 1 of 18)	L2b|LINE|L2	62143	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.020101	0.475000	
chunk0185_397_1	chr7	133728177	133728594	+	0	NA	intron (NM_021807, intron 10 of 17)	intron (NM_021807, intron 10 of 17)	96503	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.002398	0.351675	
chunk0212_139_1	chrX	131791856	131792334	+	0	NA	intron (NR_026975, intron 5 of 12)	intron (NR_026975, intron 5 of 12)	38548	NR_026975	286467	Hs.720385	NR_026975	ENSG00000213468	FIRRE	LINC01200	firre intergenic repeating RNA element	ncRNA	0.016736	0.419624	
chunk0144_165_1	chr4	131712615	131712833	+	0	NA	Intergenic	L2a|LINE|L2	-52114	NR_125884	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.013761	0.365297	
chunk0027_103_1	chr10	73872094	73872350	+	0	NA	intron (NM_172173, intron 2 of 19)	intron (NM_172173, intron 2 of 19)	2369	NM_172173	818	Hs.523045	NM_001222	ENSG00000148660	CAMK2G	CAMK|CAMK-II|CAMKG	calcium/calmodulin dependent protein kinase II gamma	protein-coding	0.011719	0.540856	
chunk0082_161_1	chr17	55730614	55731373	+	0	NA	intron (NM_001099640, intron 1 of 3)	intron (NM_001099640, intron 1 of 3)	1128	NM_001099640	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.007905	0.360526	393(GAGAACACGATGTTTC,-,0.00),394(AGAACACGATGTTTCT,+,0.00)
chunk0170_141_1	chr6	111166752	111167477	+	0	NA	intron (NM_018593, intron 1 of 5)	L2c|LINE|L2	79536	NM_018593	117247	Hs.591327	NM_018593	ENSG00000112394	SLC16A10	MCT10|PRO0813|TAT1	solute carrier family 16 member 10	protein-coding	0.001379	0.395317	
chunk0142_54_1	chr4	91852401	91852852	+	0	NA	Intergenic	L1PA16|LINE|L1	424676	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.008869	0.340708	
chunk0093_179_1	chr19	48571396	48572027	+	0	NA	intron (NM_177973, intron 1 of 6)	L2a|LINE|L2	-4025	NM_004605	6820	Hs.369331	NM_004605	ENSG00000088002	SULT2B1	ARCI14|HSST2	sulfotransferase family 2B member 1	protein-coding	0.006339	0.493671	
chunk0064_233_1	chr14	94176708	94177343	+	0	NA	intron (NM_058237, intron 2 of 24).2	intron (NM_058237, intron 2 of 24).2	2713	NM_058237	57718	Hs.259599	NM_020958	ENSG00000119698	PPP4R4	CFAP14|KIAA1622|PP4R4	protein phosphatase 4 regulatory subunit 4	protein-coding	0.004724	0.320755	
chunk0009_156_1	chr1	105005359	105005843	+	0	NA	Intergenic	MER52A|LTR|ERV1	613334	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.006198	0.552577	
chunk0083_220_1	chr17	67110551	67110857	+	0	NA	intron (NM_014877, intron 28 of 32)	MER58A|DNA|hAT-Charlie	66168	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.006536	0.456026	
chunk0100_97_1	chr2	108211111	108211641	+	0	NA	intron (NR_131251, intron 1 of 4)	L1M2|LINE|L1	6465	NR_131251	102724774	Hs.626744	NR_131251	ENSG00000225328	LINC01594	TCONS_l2_00015893	long intergenic non-protein coding RNA 1594	ncRNA	0.000000	0.291902	
chunk0117_315_1	chr22	24807546	24808082	+	0	NA	intron (NM_001039948, intron 2 of 25)	intron (NM_001039948, intron 2 of 25)	1593	NM_001098498	129049	Hs.474397	NM_133454	ENSG00000167037	SGSM1	RUTBC2	small G protein signaling modulator 1	protein-coding	0.016791	0.528864	
chunk0055_354_1	chr13	70391763	70391981	+	0	NA	Intergenic	LTR22B1|LTR|ERVK	-283379	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.004587	0.433790	
chunk0004_52_1	chr1	43031645	43032101	+	0	NA	Intergenic	Intergenic	-72697	NM_006516	6513	Hs.473721	NM_006516	ENSG00000117394	SLC2A1	CSE|DYT17|DYT18|DYT9|EIG12|GLUT|GLUT-1|GLUT1|GLUT1DS|HTLVR|PED|SDCHCN	solute carrier family 2 member 1	protein-coding	0.019737	0.514223	234(TGGGACTTGGTGTGCC,-,0.00),235(GGGACTTGGTGTGCCT,+,0.00)
chunk0023_386_1	chr10	30717147	30717646	+	0	NA	TTS (NR_036438)	TTS (NR_036438)	25122	NR_036438	645954	Hs.408581	NR_036438		SVIL2P	SVILP1	supervillin family member 2, pseudogene	pseudo	0.018036	0.408000	
chunk0135_234_1	chr3	188640893	188641583	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-47543	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.005797	0.364689	363(AAGTACAGTGTGTTCT,-,0.00),364(AGTACAGTGTGTTCTC,+,0.00)
chunk0068_153_1	chr15	53866997	53867616	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-104428	NR_102334	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.008078	0.356452	
chunk0056_450_1	chr13	95217951	95218736	+	0	NA	intron (NM_001301830, intron 3 of 19)	intron (NM_001301830, intron 3 of 19)	83103	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.006369	0.391858	
chunk0165_295_1	chr6	36515802	36516193	+	0	NA	intron (NM_001305102, intron 6 of 13)	intron (NM_001305102, intron 6 of 13)	31519	NM_001305102	11329	Hs.409578	NM_007271	ENSG00000112079	STK38	NDR|NDR1	serine/threonine kinase 38	protein-coding	0.007673	0.364796	
chunk0122_192_1	chr3	32745256	32745840	+	0	NA	intron (NM_001256742, intron 13 of 18)	L1ME2z|LINE|L1	50007	NM_001256742	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.006849	0.352137	218(ATAAACATTCTGTGCC,-,0.00)
chunk0114_281_1	chr21	16370128	16370460	+	0	NA	intron (NR_027790, intron 4 of 7)	intron (NR_027790, intron 4 of 7)	-168795	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.021084	0.438438	
chunk0052_108_1	chr13	22731970	22732170	+	0	NA	Intergenic	Intergenic	166111	NR_033774	646201	Hs.729338	NR_033774		BASP1P1	-	BASP1 pseudogene 1	pseudo	0.020000	0.442786	
chunk0141_266_1	chr4	86338372	86338969	+	0	NA	intron (NM_138980, intron 2 of 13)	intron (NM_138980, intron 2 of 13)	21552	NM_138982	5602	Hs.13438	NM_002753	ENSG00000109339	MAPK10	JNK3|JNK3A|PRKM10|SAPK1b|p493F12|p54bSAPK	mitogen-activated protein kinase 10	protein-coding	0.005025	0.396321	
chunk0098_136_1	chr2	69483623	69484269	+	0	NA	intron (NM_014911, intron 17 of 21)	intron (NM_014911, intron 17 of 21)	36225	NR_003705	100124535	Hs.693447	NR_003705	ENSG00000207016	SNORA36C	-	small nucleolar RNA, H/ACA box 36C	snoRNA	0.009288	0.343122	
chunk0141_277_1	chr4	86582978	86583262	+	0	NA	Intergenic	Intergenic	-11195	NM_006264	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.007042	0.361404	
chunk0160_111_1	chr5	150801301	150801554	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	23481	NM_032947	85027	Hs.29444	NM_032947	ENSG00000256235	SMIM3	C5orf62|MST150|NID67	small integral membrane protein 3	protein-coding	0.015810	0.460630	
chunk0083_342_1	chr17	70209098	70209439	+	0	NA	Intergenic	Intergenic	39733	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.005865	0.415205	189(CAGAACACCCTGTTCT,-,0.00),190(AGAACACCCTGTTCTC,+,0.00)
chunk0101_188_1	chr2	129507703	129507926	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-233923	NR_122040	151121	Hs.531687	NM_001033657	ENSG00000204460	LINC01854	-	long intergenic non-protein coding RNA 1854	ncRNA	0.000000	0.343750	
chunk0154_445_1	chr5	90381480	90381833	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	28130	NM_004365	1070	Hs.591767	NM_004365	ENSG00000153140	CETN3	CDC31|CEN3	centrin 3	protein-coding	0.016997	0.440678	
chunk0180_304_1	chr7	70579221	70579881	+	0	NA	intron (NM_015570, intron 5 of 18)	intron (NM_015570, intron 5 of 18)	-552986	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.003030	0.382753	
chunk0186_108_1	chr7	137948171	137948869	+	0	NA	intron (NM_194071, intron 1 of 11)	intron (NM_194071, intron 1 of 11)	-4828	NM_001243523									0.005731	0.386266	
chunk0206_321_1	chr9	125272771	125273299	+	0	NA	intron (NM_001282679, intron 2 of 27)	intron (NM_001282679, intron 2 of 27)	11241	NM_015635	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.003788	0.366730	
chunk0135_372_1	chr3	190807613	190808250	+	0	NA	Intergenic	Intergenic	54745	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.004710	0.435737	294(GGGAACACTTTGTGCC,-,0.00),295(GGAACACTTTGTGCCT,+,0.00)
chunk0196_370_1	chr8	115256905	115257566	+	0	NA	Intergenic	Intergenic	410777	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004539	0.332326	
chunk0140_108_1	chr4	68478739	68479331	+	0	NA	intron (NM_014058, intron 9 of 9)	L1MC4a|LINE|L1	31586	NM_014058	28983	Hs.201877	NM_014058	ENSG00000087128	TMPRSS11E	DESC1|TMPRSS11E2	transmembrane serine protease 11E	protein-coding	0.008446	0.360877	
chunk0146_304_1	chr4	165182509	165183193	+	0	NA	Intergenic	L1ME3G|LINE|L1	-24767	NM_007246	11275	Hs.388668	NM_007246	ENSG00000109466	KLHL2	ABP-KELCH|MAV|MAYVEN	kelch like family member 2	protein-coding	0.005848	0.373723	202(CAGAACAGCAAGTGCA,-,0.00),203(AGAACAGCAAGTGCAG,+,0.00),536(AAGCACACTTAGTCCT,-,0.00),537(AGCACACTTAGTCCTA,+,0.00)
chunk0208_84_1	chrX	13101813	13102041	+	0	NA	Intergenic	Intergenic	-57129	NM_174901	171484	Hs.667546	NM_174901	ENSG00000187268	FAM9C	TEX39C	family with sequence similarity 9 member C	protein-coding	0.026316	0.497817	
chunk0156_411_1	chr5	114265424	114266093	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-96561	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.002990	0.401493	
chunk0100_425_1	chr2	120118277	120118713	+	0	NA	intron (NM_020909, intron 16 of 24)	L1PA11|LINE|L1	104913	NM_024121	79134	Hs.376722	NM_024121	ENSG00000226479	TMEM185B	FAM11B	transmembrane protein 185B	protein-coding	0.013761	0.418764	
chunk0145_400_1	chr4	152640453	152641054	+	0	NA	intron (NM_152680, intron 6 of 6)	intron (NM_152680, intron 6 of 6)	39412	NM_152680	201799	Hs.518900	NM_152680	ENSG00000170006	TMEM154	-	transmembrane protein 154	protein-coding	0.014975	0.383721	
chunk0113_223_1	chr20	53867385	53867842	+	0	NA	Intergenic	Intergenic	8096	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.015317	0.358079	
chunk0047_139_1	chr12	69580813	69581071	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-3781	NR_037476	100500868		NR_037476	ENSG00000283677	MIR3913-2	mir-3913-2	microRNA 3913-2	ncRNA	0.003876	0.478764	
chunk0207_19_1	chrM	13635	14142	+	0	NA	NA	Intergenic	NA	NA									0.019724	0.450787	
chunk0144_415_1	chr4	140427900	140428167	+	0	NA	promoter-TSS (NM_004362)	promoter-TSS (NM_004362)	-372	NM_004362	1047	Hs.86368	NM_004362	ENSG00000153132	CLGN	-	calmegin	protein-coding	0.011236	0.335821	201(TAAAACAATATGTTCT,-,0.00),202(AAAACAATATGTTCTT,+,0.00)
chunk0027_116_1	chr10	74126919	74127397	+	0	NA	intron (NM_207012, intron 7 of 9)	MER2|DNA|TcMar-Tigger	23910	NM_012095	26985	Hs.500104	NM_012095	ENSG00000185009	AP3M1	-	adaptor related protein complex 3 subunit mu 1	protein-coding	0.008368	0.379958	
chunk0180_441_1	chr7	77199022	77199395	+	0	NA	exon (NM_006682, exon 1 of 2)	exon (NM_006682, exon 1 of 2)	625	NM_006682	10875	Hs.520989	NM_006682	ENSG00000127951	FGL2	T49|pT49	fibrinogen like 2	protein-coding	0.005362	0.339572	
chunk0082_411_1	chr17	61024380	61024671	+	0	NA	intron (NM_017679, intron 16 of 23)	intron (NM_017679, intron 16 of 23)	346714	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.006873	0.349315	
chunk0113_185_1	chr20	53262819	53263184	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	77718	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.005479	0.396175	
chunk0106_155_1	chr2	200538354	200538835	+	0	NA	intron (NM_152524, intron 4 of 8)	L2a|LINE|L2	12452	NM_001160033	151246	Hs.655182	NM_152524	ENSG00000163535	SGO2	SGOL2|TRIPIN	shugoshin 2	protein-coding	0.002079	0.331950	
chunk0172_150_1	chr6	135668048	135668393	+	0	NA	intron (NR_026805, intron 2 of 3)	intron (NR_026805, intron 2 of 3)	170419	NR_026805	100131814	Hs.734007	NR_026805	ENSG00000231028	LINC00271	C6orf217|NCRNA00271	long intergenic non-protein coding RNA 271	ncRNA	0.017391	0.479769	
chunk0012_453_1	chr1	165174509	165174870	+	0	NA	Intergenic	Intergenic	181552	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.011080	0.530387	167(GAGAACAGAGCGTGCT,-,0.00),168(AGAACAGAGCGTGCTC,+,0.00)
chunk0201_96_1	chr9	34741620	34742127	+	0	NA	Intergenic	Intergenic	-12335	NM_001141917	259308	Hs.522093	NM_001141917	ENSG00000205108	FAM205A	C9orf144B	family with sequence similarity 205 member A	protein-coding	0.011834	0.417323	292(GAGAACAGGAAGTGCT,-,0.00),293(AGAACAGGAAGTGCTC,+,0.00)
chunk0099_322_1	chr2	99825707	99825973	+	0	NA	intron (NM_001025108, intron 7 of 23)	intron (NM_001025108, intron 7 of 23)	279743	NM_001025108	3899	Hs.444414	NM_002285	ENSG00000144218	AFF3	LAF4|MLLT2-like	AF4/FMR2 family member 3	protein-coding	0.000000	0.449438	128(TTGTACAATGTGTTCT,-,0.00),129(TGTACAATGTGTTCTA,+,0.00)
chunk0018_441_1	chr1	222946324	222947067	+	0	NA	intron (NM_032890, intron 4 of 9)	L2c|LINE|L2	131606	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.004038	0.370968	462(GGGAACAGTTTGTGCA,-,0.00),463(GGAACAGTTTGTGCAA,+,0.00)
chunk0096_188_1	chr2	29956503	29956902	+	0	NA	Intergenic	L1M4a1|LINE|L1	-35091	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.007519	0.442500	199(GGGTACAGGCTGTTCT,-,0.00),200(GGTACAGGCTGTTCTC,+,0.00)
chunk0050_54_1	chr12	101078220	101078456	+	0	NA	intron (NM_001286616, intron 13 of 26)	(GT)n|Simple_repeat|Simple_repeat	131900	NM_145913	160728	Hs.444536	NM_145913	ENSG00000256870	SLC5A8	AIT|SMCT|SMCT1	solute carrier family 5 member 8	protein-coding	0.000000	0.413502	
chunk0142_120_1	chr4	94596043	94596333	+	0	NA	intron (NM_001256425, intron 6 of 11)	intron (NM_001256425, intron 6 of 11)	144331	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.010345	0.319588	
chunk0001_370_1	chr1	10117071	10117612	+	0	NA	intron (NM_001105562, intron 7 of 27)	intron (NM_001105562, intron 7 of 27)	84358	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.007394	0.428044	
chunk0152_51_1	chr5	57452848	57453438	+	0	NA	Intergenic	Intergenic	29666	NM_001017992	345651	Hs.482167	NM_001017992	ENSG00000169067	ACTBL2	ACT	actin beta like 2	protein-coding	0.001695	0.384095	299(AGGAACAAAATGTTCT,-,0.00),300(GGAACAAAATGTTCTT,+,0.00)
chunk0176_408_1	chr7	19311608	19312320	+	0	NA	Intergenic	Intergenic	-166543	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.004213	0.311360	
chunk0198_190_1	chr8	133508261	133508517	+	0	NA	intron (NM_003033, intron 2 of 8)	LTR16A1|LTR|ERVL	63551	NM_003033	6482	Hs.374257	NM_003033	ENSG00000008513	ST3GAL1	Gal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	protein-coding	0.019531	0.556420	98(TGGTACAGTTTGTGCT,-,0.00),99(GGTACAGTTTGTGCTC,+,0.00)
chunk0065_324_1	chr14	103208814	103209061	+	0	NA	Intergenic	Intergenic	-19909	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.008097	0.330645	
chunk0159_238_1	chr5	141791463	141791860	+	0	NA	Intergenic	L2a|LINE|L2	74541	NM_001278615	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.007557	0.447236	
chunk0004_140_1	chr1	44962720	44963023	+	0	NA	intron (NM_001166588, intron 3 of 9)	intron (NM_001166588, intron 3 of 9)	23851	NM_001166588	8891	Hs.533549	NM_020365	ENSG00000070785	EIF2B3	EIF-2B|EIF2Bgamma	eukaryotic translation initiation factor 2B subunit gamma	protein-coding	0.006601	0.404605	
chunk0058_285_1	chr14	26600109	26600529	+	0	NA	Intergenic	Intergenic	-2565	NM_002515	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.011905	0.356295	
chunk0086_51_1	chr18	12913671	12913905	+	0	NA	Intergenic	Intergenic	-29453	NM_080423	5771	Hs.654527	NM_002828	ENSG00000175354	PTPN2	PTN2|PTPT|TC-PTP|TCELLPTP|TCPTP	protein tyrosine phosphatase non-receptor type 2	protein-coding	0.000000	0.412766	
chunk0076_56_1	chr16	61354034	61354337	+	0	NA	Intergenic	L1MC1|LINE|L1	-298419	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.006601	0.371711	
chunk0081_45_1	chr17	37751773	37752299	+	0	NA	Intergenic	MIRc|SINE|MIR	-6958	NM_001165923	6928	Hs.191144	NM_000458	ENSG00000275410	HNF1B	FJHN|HNF-1-beta|HNF-1B|HNF1beta|HNF2|HPC11|LF-B3|LFB3|MODY5|TCF-2|TCF2|VHNF1	HNF1 homeobox B	protein-coding	0.020913	0.499051	
chunk0160_461_1	chr5	165170078	165170857	+	0	NA	Intergenic	Intergenic	700188	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.005135	0.332051	
chunk0199_319_1	chr9	7328402	7328799	+	0	NA	Intergenic	LTR40a|LTR|ERVL	471199	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.000000	0.439698	
chunk0013_40_1	chr1	166919278	166919584	+	0	NA	intron (NM_199351, intron 9 of 9)	intron (NM_199351, intron 9 of 9)	-43014	NM_053053	117143	Hs.435967	NM_053053	ENSG00000152382	TADA1	ADA1|HFI1|STAF42|TADA1L|hADA1	transcriptional adaptor 1	protein-coding	0.009804	0.452769	
chunk0039_358_1	chr11	105899312	105899980	+	0	NA	intron (NM_001112812, intron 6 of 9)	Tigger17a|DNA|TcMar-Tigger	122581	NM_032424	84437	Hs.266782	NM_032424	ENSG00000170903	MSANTD4	KIAA1826	Myb/SANT DNA binding domain containing 4 with coiled-coils	protein-coding	0.004491	0.357250	278(AGTACAATTAGTTCTT,+,0.00)
chunk0006_67_1	chr1	64822395	64823012	+	0	NA	intron (NM_018211, intron 11 of 11)	L1MB7|LINE|L1	77608	NM_018211	55225	Hs.591443	NM_018211	ENSG00000162437	RAVER2	-	ribonucleoprotein, PTB binding 2	protein-coding	0.001621	0.370550	
chunk0189_429_1	chr8	27999335	27999534	+	0	NA	Intergenic	Intergenic	-6582	NM_173833	286133	Hs.591833	NM_173833	ENSG00000168079	SCARA5	NET33|Tesr	scavenger receptor class A member 5	protein-coding	0.000000	0.620000	
chunk0080_171_1	chr17	28599569	28599768	+	0	NA	promoter-TSS (NM_006461)	promoter-TSS (NM_006461)	535	NR_040012	100506436	Hs.743630	NR_040012		SPAG5-AS1	-	SPAG5 antisense RNA 1	ncRNA	0.050251	0.470000	
chunk0196_269_1	chr8	108945793	108946396	+	0	NA	Intergenic	L1ME3G|LINE|L1	-141330	NM_003301	7201	Hs.3022	NM_003301	ENSG00000174417	TRHR	TRH-R	thyrotropin releasing hormone receptor	protein-coding	0.003317	0.359272	312(GGGAACATGCTGTATT,-,0.00),313(GGAACATGCTGTATTA,+,0.00)
chunk0131_20_1	chr3	142128206	142128532	+	0	NA	intron (NM_001178138, intron 1 of 13)	HAL1|LINE|L1	21175	NM_001178138	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.009202	0.422018	
chunk0173_234_1	chr6	146626516	146626817	+	0	NA	intron (NM_024694, intron 1 of 35)	L1MEc|LINE|L1	27666	NM_024694	79747	Hs.720870	NM_024694	ENSG00000118492	ADGB	C6orf103|CAPN16	androglobin	protein-coding	0.003322	0.271523	
chunk0072_338_1	chr15	99294259	99294607	+	0	NA	intron (NM_001284400, intron 5 of 8)	L1MEf|LINE|L1	36908	NR_073383	7190	Hs.656611	NR_073383	ENSG00000259706	HSP90B2P	GRP94P1|GRP94b|HSP|HSPCP2|TRA1P1|TRAP1	heat shock protein 90 beta family member 2, pseudogene	pseudo	0.002874	0.375358	
chunk0102_96_1	chr2	144217686	144218442	+	0	NA	intron (NM_001164629, intron 2 of 11)	L2b|LINE|L2	-6485	NM_001284233	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.009259	0.367239	283(CTGGACATTAAGTTCC,-,0.00)
chunk0041_315_1	chr11	130054884	130055482	+	0	NA	Intergenic	Intergenic	-14638	NM_001142276	334	Hs.370247	NM_001642	ENSG00000084234	APLP2	APLP-2|APPH|APPL2|CDEBP	amyloid beta precursor like protein 2	protein-coding	0.005017	0.362270	
chunk0203_4_1	chr9	82597490	82598527	+	0	NA	Intergenic	Intergenic	465120	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.010608	0.401734	
chunk0119_287_1	chr22	46162699	46163209	+	0	NA	intron (NM_001001928, intron 2 of 7)	L2a|LINE|L2	12358	NM_005036	5465	Hs.103110	NM_005036	ENSG00000186951	PPARA	NR1C1|PPAR|PPARalpha|hPPAR	peroxisome proliferator activated receptor alpha	protein-coding	0.027451	0.516634	
chunk0009_398_1	chr1	110235903	110236459	+	0	NA	Intergenic	Intergenic	25467	NM_004978	3749	Hs.153521	NM_004978	ENSG00000116396	KCNC4	C1orf30|HKSHIIIC|KSHIIIC|KV3.4	potassium voltage-gated channel subfamily C member 4	protein-coding	0.012590	0.439856	
chunk0089_412_1	chr18	68666202	68666675	+	0	NA	Intergenic	Intergenic	48678	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.002114	0.421941	
chunk0117_12_1	chr22	11067101	11067736	+	0	NA	Intergenic	REP522|Satellite|telo	-105889	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.026772	0.610063	
chunk0055_282_1	chr13	64457757	64458191	+	0	NA	Intergenic	MIR|SINE|MIR	-613849	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.004608	0.319540	
chunk0092_321_1	chr19	34669280	34669645	+	0	NA	Intergenic	Intergenic	-8177	NM_001289186	55900	Hs.436350	NM_018443	ENSG00000089335	ZNF302	HSD16|MST154|MSTP154|ZNF135L|ZNF140L|ZNF327	zinc finger protein 302	protein-coding	0.016438	0.491803	
chunk0208_205_1	chrX	17831096	17831650	+	0	NA	intron (NM_001172732, intron 1 of 2)	A-rich|Low_complexity|Low_complexity	29454	NR_033349	10742	Hs.446680	NM_021785	ENSG00000131831	RAI2	-	retinoic acid induced 2	protein-coding	0.007220	0.378378	347(AAGTACATGCTGTTCT,-,0.00),348(AGTACATGCTGTTCTG,+,0.00)
chunk0017_277_1	chr1	209785488	209785997	+	0	NA	3' UTR (NM_006147, exon 9 of 9)	3' UTR (NM_006147, exon 9 of 9)	-1012	NM_152485	148304	Hs.497642	NM_152485	ENSG00000162757	C1orf74	URLC4	chromosome 1 open reading frame 74	protein-coding	0.007859	0.429412	238(GAGAACACACTGTGTC,-,0.00),239(AGAACACACTGTGTCC,+,0.00),240(GAACACACTGTGTCCC,-,0.00),241(AACACACTGTGTCCCA,+,0.00)
chunk0028_359_1	chr10	92663245	92663882	+	0	NA	Intergenic	Intergenic	-26361	NM_002729	3087	Hs.118651	NM_002729	ENSG00000152804	HHEX	HEX|HMPH|HOX11L-PEN|PRH|PRHX	hematopoietically expressed homeobox	protein-coding	0.001570	0.326019	
chunk0017_266_1	chr1	209610753	209611443	+	0	NA	intron (NM_020439, intron 9 of 12)	MER58A|DNA|hAT-Charlie	12412	NR_036213	100422894		NR_036213	ENSG00000283876	MIR4260	-	microRNA 4260	ncRNA	0.007246	0.490593	169(AGGGGCAGCCTGTACC,-,0.00),170(GGGGCAGCCTGTACCA,+,0.00)
chunk0117_73_1	chr22	17081091	17081712	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-3558	NM_001289905	23765	Hs.48353	NM_014339	ENSG00000177663	IL17RA	CANDF5|CD217|CDw217|IL-17RA|IL17R|IMD51|hIL-17R	interleukin 17 receptor A	protein-coding	0.004831	0.416399	
chunk0139_130_1	chr4	53233502	53233960	+	0	NA	intron (NM_152540, intron 4 of 8)	intron (NM_152540, intron 4 of 8)	132344	NM_152540	152579	Hs.302287	NM_152540	ENSG00000184178	SCFD2	STXBP1L1	sec1 family domain containing 2	protein-coding	0.004367	0.333333	
chunk0173_372_1	chr6	149499093	149499493	+	0	NA	Intergenic	L1MD1|LINE|L1	-14281	NM_207360	340152	Hs.632618	NM_207360	ENSG00000178199	ZC3H12D	C6orf95|MCPIP4|TFL|dJ281H8.1|p34	zinc finger CCCH-type containing 12D	protein-coding	0.007500	0.401496	
chunk0107_136_1	chr2	214810867	214811203	+	0	NA	intron (NR_110292, intron 1 of 3)	L2b|LINE|L2	806	NR_110292	101928103	Hs.665619	NR_110292	ENSG00000229267	SNHG31	-	small nucleolar RNA host gene 31	ncRNA	0.017857	0.480712	
chunk0166_134_1	chr6	44809315	44809722	+	0	NA	Intergenic	UCON4|Unknown|Unknown	373877	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.004914	0.348039	
chunk0042_434_1	chr12	12208463	12208992	+	0	NA	intron (NM_002336, intron 2 of 22)	intron (NM_002336, intron 2 of 22)	58150	NM_002336	4040	Hs.584775	NM_002336	ENSG00000070018	LRP6	ADCAD2|STHAG7	LDL receptor related protein 6	protein-coding	0.001890	0.356604	
chunk0136_195_1	chr4	6858859	6859587	+	0	NA	intron (NM_014743, intron 6 of 9)	intron (NM_014743, intron 6 of 9)	-50221	NM_001113361	57533	Hs.518611	NM_020773	ENSG00000132405	TBC1D14	-	TBC1 domain family member 14	protein-coding	0.009615	0.389575	302(AAGAACACTGAGTTCC,-,0.00),303(AGAACACTGAGTTCCC,+,0.00)
chunk0028_136_1	chr10	86180995	86181260	+	0	NA	intron (NM_017551, intron 3 of 15)	intron (NM_017551, intron 3 of 15)	83661	NR_029907	442911		NR_029907	ENSG00000199104	MIR346	MIRN346|hsa-mir-346|miR-346|miRNA346	microRNA 346	ncRNA	0.011321	0.567669	
chunk0137_77_1	chr4	12947913	12948199	+	0	NA	Intergenic	Intergenic	536309	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.024476	0.445993	
chunk0046_335_1	chr12	62841586	62842094	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	93045	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.007874	0.357564	
chunk0037_237_1	chr11	75330006	75330370	+	0	NA	intron (NM_004041, intron 1 of 15)	MIRb|SINE|MIR	4998	NR_029891	442900		NR_029891	ENSG00000199090	MIR326	MIRN326|hsa-mir-326|mir-326	microRNA 326	ncRNA	0.008242	0.449315	
chunk0171_144_1	chr6	123685350	123685869	+	0	NA	Intergenic	Arthur1A|DNA|hAT-Tip100	-48516	NM_001251987	10345	Hs.144744	NM_006073	ENSG00000186439	TRDN	CPVT5|TDN|TRISK	triadin	protein-coding	0.003854	0.373077	
chunk0049_390_1	chr12	96387913	96388465	+	0	NA	intron (NM_002595, intron 1 of 16)	intron (NM_002595, intron 1 of 16)	12399	NM_001170464	5128	Hs.506415	NM_002595	ENSG00000059758	CDK17	PCTAIRE2|PCTK2	cyclin dependent kinase 17	protein-coding	0.001812	0.379747	
chunk0192_192_1	chr8	63639476	63639675	+	0	NA	Intergenic	Intergenic	-129855	NR_038875	286184	Hs.586402	NR_038875	ENSG00000253734	LINC01289	-	long intergenic non-protein coding RNA 1289	ncRNA	0.000000	0.320000	
chunk0107_359_1	chr2	222706498	222706836	+	0	NA	intron (NM_058165, intron 5 of 5)	intron (NM_058165, intron 5 of 5)	34929	NM_058165	116255	Hs.344090	NM_058165	ENSG00000124003	MOGAT1	DGAT2L|DGAT2L1|MGAT1	monoacylglycerol O-acyltransferase 1	protein-coding	0.002959	0.359882	
chunk0138_131_1	chr4	36722741	36723003	+	0	NA	Intergenic	Intergenic	-296444	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.000000	0.258555	
chunk0126_370_1	chr3	83880860	83881616	+	0	NA	Intergenic	L1MD|LINE|L1	988337	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.006614	0.291942	423(AAACACACTATGTTCC,-,0.00),424(AACACACTATGTTCCT,+,0.00)
chunk0087_394_1	chr18	41861484	41862137	+	0	NA	Intergenic	Intergenic	-93388	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.010720	0.382263	
chunk0048_119_1	chr12	79778843	79779321	+	0	NA	intron (NM_001244990, intron 23 of 24)	intron (NM_001244990, intron 23 of 24)	-88072	NM_002583	5074	Hs.643130	NM_002583	ENSG00000177425	PAWR	PAR4|Par-4	pro-apoptotic WT1 regulator	protein-coding	0.002092	0.350731	
chunk0119_170_1	chr22	43396937	43397331	+	0	NA	Intergenic	Intergenic	-14880	NM_001044370	758	Hs.159538	NM_001044370	ENSG00000186732	MPPED1	239AB|C22orf1|FAM1A	metallophosphoesterase domain containing 1	protein-coding	0.050761	0.658228	
chunk0134_251_1	chr3	179365251	179365763	+	0	NA	intron (NM_033540, intron 7 of 17)	AluJb|SINE|Alu	17815	NM_033540	55669	Hs.478383	NM_017927	ENSG00000171109	MFN1	hfzo1|hfzo2	mitofusin 1	protein-coding	0.001953	0.348928	
chunk0130_327_1	chr3	138208952	138209429	+	0	NA	intron (NM_015396, intron 2 of 22)	intron (NM_015396, intron 2 of 22)	21942	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.004193	0.364017	
chunk0017_180_1	chr1	207152933	207153392	+	0	NA	Intergenic	L1M1|LINE|L1	48900	NM_000715	722	Hs.1012	NM_000715	ENSG00000123838	C4BPA	C4BP|PRP	complement component 4 binding protein alpha	protein-coding	0.008715	0.517391	
chunk0023_179_1	chr10	24494112	24494669	+	0	NA	intron (NM_001282769, intron 2 of 13)	intron (NM_001282769, intron 2 of 13)	27885	NM_001282770	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.016158	0.435484	
chunk0021_155_1	chr10	4736706	4737052	+	0	NA	Intergenic	Intergenic	-58809	NR_024475	100216001	Hs.634869	NR_024475	ENSG00000231298	MANCR	LINC00704	mitotically associated long non coding RNA	ncRNA	0.017341	0.391931	59(AGTTACAGACTGTCCT,-,0.00),60(GTTACAGACTGTCCTT,+,0.00)
chunk0212_198_1	chrX	134388182	134388643	+	0	NA	intron (NM_032335, intron 3 of 7)	intron (NM_032335, intron 3 of 7)	15100	NM_032458	84295	Hs.356501	NM_032335	ENSG00000156531	PHF6	BFLS|BORJ|CENP-31	PHD finger protein 6	protein-coding	0.008677	0.406926	
chunk0210_357_1	chrX	96410849	96411365	+	0	NA	Intergenic	Intergenic	-73205	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.005814	0.348162	
chunk0120_193_1	chr3	7038418	7038953	+	0	NA	intron (NM_000844, intron 1 of 9)	MIR|SINE|MIR	-144668	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.011215	0.395522	
chunk0093_386_1	chr19	56392134	56392635	+	0	NA	intron (NM_144690, intron 1 of 4)	intron (NM_144690, intron 1 of 4)	1136	NM_144690	147948	Hs.244391	NM_144690	ENSG00000018869	ZNF582	-	zinc finger protein 582	protein-coding	0.005988	0.440239	
chunk0073_84_1	chr16	4042544	4042958	+	0	NA	intron (NM_001116, intron 2 of 10)	intron (NM_001116, intron 2 of 10)	73434	NM_001116	115	Hs.391860	NM_001116	ENSG00000162104	ADCY9	AC9|ACIX	adenylate cyclase 9	protein-coding	0.024155	0.385542	
chunk0106_381_1	chr2	207416089	207416435	+	0	NA	Intergenic	Intergenic	-113630	NM_004379	1385	Hs.516646	NM_004379	ENSG00000118260	CREB1	CREB|CREB-1	cAMP responsive element binding protein 1	protein-coding	0.005780	0.406340	
chunk0039_78_1	chr11	97060419	97060636	+	0	NA	Intergenic	L1MA4A|LINE|L1	-553650	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.009217	0.564220	
chunk0070_76_1	chr15	70024725	70025192	+	0	NA	Intergenic	Intergenic	54510	NR_030714	693214		NR_030714	ENSG00000207965	MIR629	MIRN629|hsa-mir-629|mir-629	microRNA 629	ncRNA	0.036403	0.581197	
chunk0182_74_1	chr7	92286165	92286538	+	0	NA	intron (NM_019004, intron 1 of 19)	intron (NM_019004, intron 1 of 19)	40117	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.010724	0.398396	
chunk0195_15_1	chr8	93050963	93051606	+	0	NA	Intergenic	AluJr|SINE|Alu	21533	NR_107051	102467005		NR_107051	ENSG00000277063	MIR8084	hsa-mir-8084	microRNA 8084	ncRNA	0.003110	0.392857	
chunk0170_236_1	chr6	113490251	113490875	+	0	NA	Intergenic	Intergenic	159512	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.001603	0.372800	
chunk0179_143_1	chr7	46150059	46150672	+	0	NA	Intergenic	L1MC3|LINE|L1	-229093	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.004894	0.421824	
chunk0199_191_1	chr9	4740434	4741271	+	0	NA	intron (NM_001199853, intron 1 of 4)	CpG	457	NM_001199852	50808	Hs.732022	NM_016282	ENSG00000147853	AK3	AK3L1|AK6|AKL3L|AKL3L1|FIX	adenylate kinase 3	protein-coding	0.086022	0.656325	
chunk0075_67_1	chr16	47970348	47970688	+	0	NA	Intergenic	Intergenic	-83388	NR_110649	100507534	Hs.407601	NR_110649	ENSG00000261325	LINC02192	-	long intergenic non-protein coding RNA 2192	ncRNA	0.005882	0.451613	
chunk0134_6_1	chr3	175346931	175347130	+	0	NA	intron (NM_207015, intron 5 of 13)	MIRb|SINE|MIR	-22510	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.010050	0.425000	
chunk0080_71_1	chr17	22065812	22066484	+	0	NA	Intergenic	Intergenic	-232616	NR_028336	284123	Hs.348578	NM_203392	ENSG00000178130	FAM27E5	FAM27L	family with sequence similarity E5	ncRNA	0.010417	0.332838	
chunk0005_56_1	chr1	55231218	55231674	+	0	NA	Intergenic	Intergenic	5805	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.002193	0.369803	
chunk0193_423_1	chr8	80787188	80787415	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	87480	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.013216	0.394737	
chunk0061_29_1	chr14	55832067	55832837	+	0	NA	Intergenic	L2a|LINE|L2	-35778	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.003896	0.407263	468(CTGCACATCCTGTCCC,-,0.00),469(TGCACATCCTGTCCCA,+,0.00)
chunk0073_205_1	chr16	9745094	9745519	+	0	NA	Intergenic	Intergenic	-289801	NR_126349	104266959	Hs.578888	NR_126349	ENSG00000261075	LINC01195	-	long intergenic non-protein coding RNA 1195	ncRNA	0.004706	0.446009	203(CAGCACTGTCTGTTCT,-,0.00),204(AGCACTGTCTGTTCTT,+,0.00)
chunk0145_125_1	chr4	146370435	146371072	+	0	NA	intron (NM_001029998, intron 5 of 11)	intron (NM_001029998, intron 5 of 11)	-37830	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.009419	0.376176	
chunk0085_298_1	chr18	8053829	8054206	+	0	NA	intron (NM_001105244, intron 7 of 32)	L1ME3F|LINE|L1	313017	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.002653	0.320106	
chunk0151_431_1	chr5	55866574	55866807	+	0	NA	5' UTR (NM_001242639, exon 3 of 16)	5' UTR (NM_001242639, exon 3 of 16)	13368	NM_001242636	133396	Hs.55378	NM_139017	ENSG00000164509	IL31RA	CRL|CRL3|GLM-R|GLMR|GPL|IL-31RA|PLCA2|PRO21384|hGLM-R	interleukin 31 receptor A	protein-coding	0.025751	0.551282	
chunk0166_48_1	chr6	42569846	42570107	+	0	NA	intron (NM_015255, intron 1 of 46)	intron (NM_015255, intron 1 of 46)	5954	NM_001184801	23304	Hs.529925	NM_015255	ENSG00000024048	UBR2	C6orf133|bA49A4.1|dJ242G1.1|dJ392M17.3	ubiquitin protein ligase E3 component n-recognin 2	protein-coding	0.000000	0.347328	
chunk0042_18_1	chr12	1262212	1262469	+	0	NA	intron (NR_027946, intron 13 of 18)	intron (NR_027946, intron 13 of 18)	234592	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.011673	0.406977	
chunk0213_31_1	chrY	56763400	56763611	+	0	NA	Intergenic	(AATGGAATGG)n|Simple_repeat|Simple_repeat	-190750	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.028436	0.367925	
chunk0056_74_1	chr13	79492685	79493304	+	0	NA	intron (NM_019080, intron 1 of 7)	L2c|LINE|L2	-11763	NR_046685	100874208	Hs.602801	NR_046685	ENSG00000232132	NDFIP2-AS1	-	NDFIP2 antisense RNA 1	ncRNA	0.004847	0.348387	
chunk0078_4_1	chr17	194335	194879	+	0	NA	Intergenic	Intergenic	-7356	NR_104420	100506371		NR_104420		LINC02091	-	long intergenic non-protein coding RNA 2091	ncRNA	0.033088	0.631193	
chunk0047_356_1	chr12	75028590	75028936	+	0	NA	Intergenic	Intergenic	180985	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.014451	0.414986	
chunk0169_113_1	chr6	100751635	100751834	+	0	NA	intron (NM_006828, intron 10 of 41)	Tigger6b|DNA|TcMar-Tigger	129638	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.015075	0.400000	
chunk0081_53_1	chr17	38328711	38329172	+	0	NA	exon (NM_001004334, exon 11 of 11)	exon (NM_001004334, exon 11 of 11)	14869	NM_001004334	440435	Hs.462915	NM_001004334	ENSG00000277399	GPR179	CSNB1E|GPR158L|GPR158L1	G protein-coupled receptor 179	protein-coding	0.008677	0.506494	
chunk0078_293_1	chr17	8068059	8068442	+	0	NA	Intergenic	MamRep564|Unknown|Unknown	19453	NM_001139	242	Hs.136574	NM_001139	ENSG00000179477	ALOX12B	12R-LOX|ARCI2	arachidonate 12-lipoxygenase, 12R type	protein-coding	0.018277	0.489583	
chunk0062_236_1	chr14	71214278	71214559	+	0	NA	Intergenic	L2c|LINE|L2	-183919	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.007117	0.329787	
chunk0108_116_1	chr2	229805541	229805986	+	0	NA	exon (NM_001284215, exon 16 of 40)	exon (NM_001284215, exon 16 of 40)	74365	NM_001284215	9320	Hs.572642	NM_004238	ENSG00000153827	TRIP12	MRD49|TRIP-12|ULF	thyroid hormone receptor interactor 12	protein-coding	0.013483	0.347534	228(TGGCACGTGCTGTTCC,-,0.00),229(GGCACGTGCTGTTCCC,+,0.00)
chunk0111_198_1	chr20	25992943	25993184	+	0	NA	Intergenic	Intergenic	-16736	NR_004846	100134868	Hs.516956	NR_004846		LOC100134868	-	uncharacterized LOC100134868	ncRNA	0.008299	0.309917	
chunk0197_147_1	chr8	120397432	120397643	+	0	NA	intron (NM_014078, intron 6 of 6)	L1PA11|LINE|L1	-47861	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.009479	0.561321	
chunk0102_128_1	chr2	145158318	145158567	+	0	NA	Intergenic	Intergenic	490475	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.004016	0.464000	
chunk0041_378_1	chr11	131897290	131897635	+	0	NA	intron (NM_001048209, intron 1 of 7)	MIR1_Amn|SINE|MIR	-13356	NM_016522	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.002899	0.410405	
chunk0020_252_1	chr1	236147741	236148218	+	0	NA	intron (NM_003272, intron 1 of 6)	intron (NM_003272, intron 1 of 6)	5447	NM_003272	7107	Hs.498160	NM_003272	ENSG00000077585	GPR137B	TM7SF1	G protein-coupled receptor 137B	protein-coding	0.012579	0.550209	220(TGGAACATGGAGTGCT,-,0.00),221(GGAACATGGAGTGCTG,+,0.00)
chunk0104_291_1	chr2	178438364	178438750	+	0	NA	intron (NM_003690, intron 6 of 7)	L1M5|LINE|L1	12071	NM_001139518	8575	Hs.570274	NM_003690	ENSG00000180228	PRKRA	DYT16|HSD14|PACT|RAX	protein activator of interferon induced protein kinase EIF2AK2	protein-coding	0.018135	0.421189	
chunk0123_449_1	chr3	50720794	50721183	+	0	NA	intron (NM_004947, intron 1 of 52)	L1PA14|LINE|L1	45747	NM_004947	1795	Hs.476284	NM_004947	ENSG00000088538	DOCK3	MOCA|NEDIDHA|PBP	dedicator of cytokinesis 3	protein-coding	0.002571	0.325641	
chunk0118_71_1	chr22	28807741	28808206	+	0	NA	Intergenic	Intergenic	-7401	NM_005080	7494	Hs.437638	NM_005080	ENSG00000100219	XBP1	TREB-5|TREB5|XBP-1|XBP2	X-box binding protein 1	protein-coding	0.017204	0.452790	
chunk0066_105_1	chr15	29862330	29862546	+	0	NA	intron (NM_001301025, intron 2 of 28).2	intron (NM_001301025, intron 2 of 28).2	-39935	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.004630	0.405530	
chunk0142_405_1	chr4	102827594	102827900	+	0	NA	promoter-TSS (NM_181887)	promoter-TSS (NM_181887)	-194	NM_181887	7323	Hs.518773	NM_003340	ENSG00000109332	UBE2D3	E2(17)KB3|UBC4/5|UBCH5C	ubiquitin conjugating enzyme E2 D3	protein-coding	0.081699	0.605863	
chunk0138_318_1	chr4	41418437	41418950	+	0	NA	intron (NM_001112717, intron 1 of 25)	intron (NM_001112717, intron 1 of 25)	57908	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.015595	0.463035	
chunk0098_359_1	chr2	77465436	77466046	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	56627	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.009836	0.379705	
chunk0054_118_1	chr13	43005447	43005757	+	0	NA	Intergenic	Intergenic	-13331	NM_033255	94240	Hs.546467	NM_033255	ENSG00000133106	EPSTI1	BRESI1	epithelial stromal interaction 1	protein-coding	0.003226	0.344051	
chunk0103_195_1	chr2	163659113	163659605	+	0	NA	intron (NM_018086, intron 2 of 2)	intron (NM_018086, intron 2 of 2)	76644	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.004065	0.350913	257(TAGAACAATCTGTCCT,-,0.00),258(AGAACAATCTGTCCTA,+,0.00)
chunk0153_436_1	chr5	76291599	76292015	+	0	NA	exon (NM_001297716, exon 8 of 13)	exon (NM_001297716, exon 8 of 13)	-111448	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.004808	0.362110	238(TGGTTCACCCTGTCCT,-,0.00),239(GGTTCACCCTGTCCTT,+,0.00)
chunk0110_1_1	chr20	9545001	9545527	+	0	NA	intron (NM_020341, intron 8 of 10)	Charlie29a|DNA|hAT-Charlie	-30266	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.001901	0.396584	269(AAGAACATACTGCACC,-,0.00),270(AGAACATACTGCACCC,+,0.00)
chunk0081_174_1	chr17	41539193	41539666	+	0	NA	Intergenic	Intergenic	-11040	NM_002276	3880	Hs.654568	NM_002276	ENSG00000171345	KRT19	CK19|K19|K1CS	keratin 19	protein-coding	0.010571	0.548523	
chunk0115_332_1	chr21	28986770	28986969	+	0	NA	exon (NM_015565, exon 2 of 30)	exon (NM_015565, exon 2 of 30)	6087	NM_015565	26046	Hs.288773	NM_015565	ENSG00000198862	LTN1	C21orf10|C21orf98|RNF160|ZNF294	listerin E3 ubiquitin protein ligase 1	protein-coding	0.015075	0.440000	
chunk0084_344_1	chr17	81239695	81240100	+	0	NA	promoter-TSS (NM_144679)	promoter-TSS (NM_144679)	586	NM_001086521	284184	Hs.356545	NM_001086521	ENSG00000224877	NDUFAF8	C17orf89	NADH:ubiquinone oxidoreductase complex assembly factor 8	protein-coding	0.061728	0.603448	
chunk0050_405_1	chr12	109482810	109483015	+	0	NA	intron (NM_183415, intron 2 of 27)	Charlie18a|DNA|hAT-Charlie	5289	NM_130466	89910	Hs.374067	NM_130466	ENSG00000151148	UBE3B	BPIDS|KOS	ubiquitin protein ligase E3B	protein-coding	0.000000	0.378641	
chunk0063_373_1	chr14	86039982	86040727	+	0	NA	intron (NR_110155, intron 1 of 3)	L1MC4|LINE|L1	105676	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.002685	0.276139	
chunk0160_399_1	chr5	163504436	163504754	+	0	NA	promoter-TSS (NM_013283)	promoter-TSS (NM_013283)	-933	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.031447	0.467085	
chunk0189_443_1	chr8	28245119	28245534	+	0	NA	Intergenic	MER51E|LTR|ERV1	-71806	NM_006228	5368	Hs.88218	NM_006228	ENSG00000168081	PNOC	N/OFQ|NOP|OFQ|PPNOC|ppN/OFQ	prepronociceptin	protein-coding	0.012048	0.495192	
chunk0141_180_1	chr4	82909282	82909596	+	0	NA	intron (NM_024672, intron 4 of 4)	L1ME4a|LINE|L1	-8523	NR_034077	100499177	Hs.728916	NR_034075	ENSG00000251022	THAP9-AS1	-	THAP9 antisense RNA 1	ncRNA	0.003185	0.301587	
chunk0014_456_1	chr1	184002051	184002281	+	0	NA	intron (NM_001303421, intron 1 of 11)	intron (NM_001303421, intron 1 of 11)	35604	NM_001303420	23127	Hs.387995	NM_015101	ENSG00000198756	COLGALT2	C1orf17|ColGalT 2|GLT25D2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0.004348	0.502165	
chunk0205_217_1	chr9	109475678	109475881	+	0	NA	intron (NM_002829, intron 1 of 25)	intron (NM_002829, intron 1 of 25)	22534	NM_002829	5774	Hs.436429	NM_002829	ENSG00000070159	PTPN3	PTP-H1|PTPH1	protein tyrosine phosphatase non-receptor type 3	protein-coding	0.014778	0.495098	
chunk0074_101_1	chr16	22207468	22207678	+	0	NA	intron (NM_013302, intron 1 of 17)	MIR|SINE|MIR	1302	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.019048	0.492891	
chunk0139_257_1	chr4	56387113	56387351	+	0	NA	intron (NM_001286669, intron 1 of 13)	intron (NM_001286669, intron 1 of 13)	276	NM_001286671	132949	Hs.104347	NM_181806	ENSG00000157426	AASDH	ACSF4|LYS2|NRPS1098|NRPS998	aminoadipate-semialdehyde dehydrogenase	protein-coding	0.054622	0.598326	
chunk0135_363_1	chr3	190693880	190694285	+	0	NA	Intergenic	MER4D1|LTR|ERV1	168594	NM_001146686	647309	Hs.518490	NM_001146686	ENSG00000205835	GMNC	GEMC1	geminin coiled-coil domain containing	protein-coding	0.000000	0.396552	182(GATACATCATGTTCTC,+,0.00)
chunk0183_87_1	chr7	104978444	104978940	+	0	NA	Intergenic	Tigger19b|DNA|TcMar-Tigger	12473	NR_039981	100216546	Hs.369356	NR_039981		LINC01004	-	long intergenic non-protein coding RNA 1004	ncRNA	0.004032	0.360161	
chunk0115_274_1	chr21	28113158	28113467	+	0	NA	intron (NR_126010, intron 2 of 4)	(GT)n|Simple_repeat|Simple_repeat	22909	NR_126011	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.016181	0.332258	212(AAGAACACGGTGTAAC,-,0.00)
chunk0185_455_1	chr7	135170143	135170758	+	0	NA	promoter-TSS (NM_001243753)	promoter-TSS (NM_001243753)	74	NM_001243752	78996	Hs.643113	NM_024033	ENSG00000122783	CYREN	C7orf49|MRI|MRI-2	cell cycle regulator of NHEJ	protein-coding	0.107317	0.724026	182(GGGAACGCGATGTGCT,-,0.00),183(GGAACGCGATGTGCTG,+,0.00)
chunk0072_399_1	chr15	100721686	100722083	+	0	NA	Intergenic	Intergenic	119334	NM_198243	140460	Hs.31845	NM_024708	ENSG00000183475	ASB7	-	ankyrin repeat and SOCS box containing 7	protein-coding	0.020151	0.474874	
chunk0169_106_1	chr6	100678895	100679459	+	0	NA	intron (NM_006828, intron 14 of 41)	Charlie1b|DNA|hAT-Charlie	202195	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.005319	0.318584	
chunk0046_71_1	chr12	56005415	56005729	+	0	NA	TTS (NM_000456)	TTS (NM_000456)	8313	NM_001032386	6821	Hs.558403	NM_000456	ENSG00000139531	SUOX	-	sulfite oxidase	protein-coding	0.012739	0.476190	
chunk0035_84_1	chr11	42000422	42000970	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	252994	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.005474	0.335155	
chunk0064_364_1	chr14	97839222	97839488	+	0	NA	Intergenic	Intergenic	138769	NR_015430	388011	Hs.651477	NR_015430	ENSG00000246223	LINC01550	C14orf64	long intergenic non-protein coding RNA 1550	ncRNA	0.022556	0.460674	
chunk0088_1_1	chr18	42998596	42998795	+	0	NA	intron (NM_001272077, intron 2 of 5)	intron (NM_001272077, intron 2 of 5)	116997	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.375000	
chunk0108_103_1	chr2	229455422	229455946	+	0	NA	intron (NM_139072, intron 7 of 12)	intron (NM_139072, intron 7 of 12)	-184343	NM_001100818	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.011450	0.443810	
chunk0031_449_1	chr10	132642841	132643058	+	0	NA	intron (NM_005539, intron 2 of 15)	intron (NM_005539, intron 2 of 15)	105100	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.027650	0.435780	
chunk0016_122_1	chr1	196896447	196896646	+	0	NA	intron (NM_001201551, intron 1 of 9)	L1M4c|LINE|L1	8532	NM_001201551	10877	Hs.710100	NM_006684	ENSG00000134365	CFHR4	CFHL4|FHR-4|FHR4	complement factor H related 4	protein-coding	0.030151	0.465000	
chunk0206_253_1	chr9	123778593	123778792	+	0	NA	intron (NM_024820, intron 3 of 20)	MER58C|DNA|hAT-Charlie	151446	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.020101	0.465000	
chunk0089_173_1	chr18	59549786	59550185	+	0	NA	intron (NM_133459, intron 2 of 10)	MamRTE1|LINE|RTE-BovB	147427	NM_133459	147372	Hs.34333	NM_133459	ENSG00000183287	CCBE1	HKLLS1	collagen and calcium binding EGF domains 1	protein-coding	0.005013	0.462500	
chunk0118_335_1	chr22	35538400	35538878	+	0	NA	Intergenic	Intergenic	-2666	NM_014310	23551	Hs.474711	NM_014310	ENSG00000100302	RASD2	Rhes|TEM2	RASD family member 2	protein-coding	0.012552	0.561587	
chunk0019_388_1	chr1	230193047	230193328	+	0	NA	intron (NM_001291866, intron 2 of 15)	intron (NM_001291866, intron 2 of 15)	125992	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.010676	0.446809	
chunk0033_67_1	chr11	13629614	13630264	+	0	NA	Intergenic	L1ME3G|LINE|L1	-38720	NM_032228	84188	Hs.501991	NM_032228	ENSG00000197601	FAR1	MLSTD2|PFCRD|SDR10E1	fatty acyl-CoA reductase 1	protein-coding	0.003077	0.314900	
chunk0072_77_1	chr15	90547564	90547955	+	0	NA	intron (NM_001042574, intron 2 of 14)	intron (NM_001042574, intron 2 of 14)	17873	NM_001042574	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.007673	0.484694	
chunk0089_407_1	chr18	68457035	68457234	+	0	NA	Intergenic	Intergenic	257982	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.005025	0.310000	
chunk0172_237_1	chr6	137122288	137123067	+	0	NA	Intergenic	FRAM|SINE|Alu	50971	NM_181310	116379	Hs.126891	NM_052962	ENSG00000164485	IL22RA2	CRF2-10|CRF2-S1|CRF2X|IL-22BP|IL-22R-alpha-2|IL-22RA2|ZCYTOR16	interleukin 22 receptor subunit alpha 2	protein-coding	0.007702	0.366667	
chunk0029_322_1	chr10	104397195	104397721	+	0	NA	intron (NM_001008723, intron 11 of 17)	intron (NM_001008723, intron 11 of 17)	43694	NM_001008723	159686	Hs.253576	NM_001008723	ENSG00000120051	CFAP58	C10orf80|CCDC147|bA127L20.4|bA127L20.5|bA554P13.1	cilia and flagella associated protein 58	protein-coding	0.005703	0.364326	
chunk0026_188_1	chr10	63572494	63573309	+	0	NA	intron (NM_001001330, intron 2 of 7)	intron (NM_001001330, intron 2 of 7)	51538	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.002454	0.340686	
chunk0149_336_1	chr5	26879449	26879741	+	0	NA	Intergenic	Intergenic	158987	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.003425	0.310580	
chunk0020_384_1	chr1	240085769	240085971	+	0	NA	Intergenic	L2a|LINE|L2	-6015	NM_001305424	56776	Hs.24889	NM_020066	ENSG00000155816	FMN2	-	formin 2	protein-coding	0.009901	0.403941	
chunk0159_299_1	chr5	142874631	142875148	+	0	NA	intron (NM_015071, intron 2 of 22)	intron (NM_015071, intron 2 of 22)	-5979	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.009671	0.490347	230(AGGAACAGGCAGATCT,-,0.00),231(GGAACAGGCAGATCTT,+,0.00)
chunk0010_452_1	chr1	121546959	121547817	+	0	NA	intron (NR_003955, intron 1 of 7)	intron (NR_003955, intron 1 of 7)	28276	NR_003955	647121	Hs.697682	NR_003955	ENSG00000231752	EMBP1	-	embigin pseudogene 1	pseudo	0.001166	0.417928	
chunk0181_444_1	chr7	90700366	90700565	+	0	NA	intron (NM_001287135, intron 2 of 14)	intron (NM_001287135, intron 2 of 14)	-8933	NM_012395	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.015075	0.435000	
chunk0113_249_1	chr20	54984898	54985567	+	0	NA	Intergenic	Intergenic	-437811	NR_110629	102723578	Hs.446269	NR_110629	ENSG00000235166	LINC01440	-	long intergenic non-protein coding RNA 1440	ncRNA	0.011958	0.395522	333(TAGAACACACTGTTCC,-,0.00),334(AGAACACACTGTTCCT,+,0.00)
chunk0116_119_1	chr21	35953586	35953916	+	0	NA	TTS (NR_110418)	TTS (NR_110418)	50916	NR_110418	101928269	Hs.589909	NR_110418		LOC101928269	-	uncharacterized LOC101928269	ncRNA	0.009091	0.419940	
chunk0183_306_1	chr7	107870363	107870669	+	0	NA	Intergenic	Intergenic	-20591	NM_001289752	1738	Hs.131711	NM_000108	ENSG00000091140	DLD	DLDD|DLDH|E3|GCSL|LAD|PHE3	dihydrolipoamide dehydrogenase	protein-coding	0.009804	0.436482	
chunk0133_155_1	chr3	169657229	169657676	+	0	NA	intron (NM_004991, intron 1 of 16)	intron (NM_004991, intron 1 of 16)	6323	NM_004991	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.006711	0.366071	
chunk0091_381_1	chr19	15869286	15869735	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-4606	NM_001302493	102724279	Hs.164360	NM_001302493		LINC01835	-	long intergenic non-protein coding RNA 1835	protein-coding	0.008909	0.422222	
chunk0165_66_1	chr6	31072800	31072999	+	0	NA	Intergenic	L1ME4a|LINE|L1	19449	NR_003948	285834	Hs.207528	NM_001348249	ENSG00000228789	HCG22	PBMUCL2	HLA complex group 22 (gene/pseudogene)	protein-coding	0.000000	0.320000	
chunk0111_356_1	chr20	33562134	33562650	+	0	NA	promoter-TSS (NM_001039709)	promoter-TSS (NM_001039709)	27	NM_001039709	9139	Hs.153934	NM_005093	ENSG00000078699	CBFA2T2	EHT|MTGR1|ZMYND3|p85	CBFA2/RUNX1 partner transcriptional co-repressor 2	protein-coding	0.007752	0.462282	
chunk0160_77_1	chr5	149932713	149933249	+	0	NA	promoter-TSS (NR_110534)	promoter-TSS (NR_110534)	-4	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.031716	0.538175	
chunk0043_437_1	chr12	26179811	26180528	+	0	NA	Intergenic	Intergenic	-15167	NM_001135823	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.012552	0.419220	555(ATGAACAGAGTGTCCT,-,0.00),556(TGAACAGAGTGTCCTG,+,0.00)
chunk0029_240_1	chr10	102644914	102645274	+	0	NA	exon (NM_030912, exon 1 of 6)	exon (NM_030912, exon 1 of 6)	599	NM_030912	81603	Hs.336810	NM_030912	ENSG00000171206	TRIM8	GERP|RNF27	tripartite motif containing 8	protein-coding	0.105556	0.689751	
chunk0013_310_1	chr1	171343889	171344649	+	0	NA	Intergenic	Intergenic	5373	NR_002719	7151	Hs.661092	NR_002719		TOP1P1	-	DNA topoisomerase I pseudogene 1	pseudo	0.010526	0.421813	
chunk0080_335_1	chr17	32621136	32621611	+	0	NA	intron (NM_015194, intron 20 of 21)	L2c|LINE|L2	134286	NM_003885	8851	Hs.500015	NM_003885	ENSG00000176749	CDK5R1	CDK5P35|CDK5R|NCK5A|p23|p25|p35|p35nck5a	cyclin dependent kinase 5 regulatory subunit 1	protein-coding	0.012632	0.413866	
chunk0167_327_1	chr6	72305865	72306271	+	0	NA	intron (NM_001168409, intron 17 of 21)	intron (NM_001168409, intron 17 of 21)	-60662	NM_001168411	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.004926	0.329238	
chunk0107_241_1	chr2	217212569	217213041	+	0	NA	Intergenic	(TGTGTGTGTA)n|Simple_repeat|Simple_repeat	-69928	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.002119	0.342495	
chunk0117_378_1	chr21	45120808	45121345	+	0	NA	intron (NM_015834, intron 1 of 12)	L1MEd|LINE|L1	46498	NM_001160230	104	Hs.474018	NM_001112	ENSG00000197381	ADARB1	ADAR2|DRABA2|DRADA2|RED1	adenosine deaminase RNA specific B1	protein-coding	0.018622	0.379182	
chunk0198_164_1	chr8	133204966	133205527	+	0	NA	intron (NM_001204870, intron 1 of 1)	intron (NM_001204870, intron 1 of 1)	14207	NM_003882	8840	Hs.492974	NM_003882	ENSG00000104415	CCN4	WISP1|WISP1-OT1|WISP1-UT1|WISP1c|WISP1i|WISP1tc	cellular communication network factor 4	protein-coding	0.005348	0.483986	191(AGGACCAGGCTGTGCC,-,0.00),192(GGACCAGGCTGTGCCT,+,0.00)
chunk0041_234_1	chr11	128453533	128454283	+	0	NA	Intergenic	Intergenic	68402	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.006667	0.462051	
chunk0135_12_1	chr3	184174241	184174918	+	0	NA	promoter-TSS (NM_004068)	promoter-TSS (NM_004068)	-267	NM_004068	1173	Hs.518460	NM_004068	ENSG00000161203	AP2M1	AP50|CLAPM1|mu2	adaptor related protein complex 2 subunit mu 1	protein-coding	0.053176	0.523599	184(GAGGACAGCCAGTCCT,-,0.00),185(AGGACAGCCAGTCCTG,+,0.00)
chunk0133_453_1	chr3	175179018	175179508	+	0	NA	intron (NM_207015, intron 2 of 13)	L2c|LINE|L2	-64021	NR_046390	100862679	Hs.148810	NR_046390	ENSG00000230292	NAALADL2-AS3	-	NAALADL2 antisense RNA 3	ncRNA	0.002041	0.331976	
chunk0085_292_1	chr18	7955153	7955567	+	0	NA	exon (NM_002845, exon 7 of 31)	exon (NM_002845, exon 7 of 31)	388044	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.016908	0.525301	245(AAGAACAAAGTGTGCT,-,0.00),246(AGAACAAAGTGTGCTG,+,0.00)
chunk0032_185_1	chr11	6251017	6251542	+	0	NA	Intergenic	Intergenic	-8395	NM_176875	887	Hs.203	NM_176875	ENSG00000110148	CCKBR	CCK-B|CCK2R|GASR	cholecystokinin B receptor	protein-coding	0.009524	0.444867	223(GGGCACAGGTTGTCCT,-,0.00),224(GGCACAGGTTGTCCTG,+,0.00)
chunk0183_365_1	chr7	109082454	109082800	+	0	NA	Intergenic	L1PA7|LINE|L1	-198040	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.002890	0.334294	
chunk0024_59_1	chr10	33928990	33929378	+	0	NA	Intergenic	Intergenic	-156504	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.018041	0.370180	
chunk0163_267_1	chr6	13203302	13203501	+	0	NA	intron (NM_030948, intron 7 of 14)	MIR|SINE|MIR	92185	NM_001242698	100130357	Hs.484678	NM_001242698		LOC100130357	-	uncharacterized LOC100130357	ncRNA	0.010050	0.400000	
chunk0123_400_1	chr3	48919743	48919942	+	0	NA	promoter-TSS (NM_001123040)	promoter-TSS (NM_001123040)	-457	NM_001123040	646450	Hs.720727	NM_001123040	ENSG00000221883	ARIH2OS	C3orf71	ariadne RBR E3 ubiquitin protein ligase 2 opposite strand	ncRNA	0.035176	0.425000	
chunk0163_276_1	chr6	13505034	13505717	+	0	NA	Intergenic	Intergenic	-17738	NM_001242629	54438	Hs.484686	NM_018988	ENSG00000145990	GFOD1	ADG-90|C6orf114	glucose-fructose oxidoreductase domain containing 1	protein-coding	0.016105	0.461988	
chunk0093_94_1	chr19	42453960	42454172	+	0	NA	intron (NR_073179, intron 1 of 1)	intron (NR_073179, intron 1 of 1)	-11082	NM_198477	284340	Hs.445586	NM_198477	ENSG00000189377	CXCL17	DMC|Dcip1|UNQ473|VCC-1|VCC1	C-X-C motif chemokine ligand 17	protein-coding	0.004717	0.417840	35(TGGAACTGGATGTTCT,-,0.00),36(GGAACTGGATGTTCTT,+,0.00)
chunk0020_258_1	chr1	236292423	236292865	+	0	NA	Intergenic	L1MC1|LINE|L1	-10605	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.009050	0.395034	174(AAGTACAGAGAGTTCT,-,0.00),175(AGTACAGAGAGTTCTC,+,0.00)
chunk0041_372_1	chr11	131504589	131504870	+	0	NA	intron (NM_001048209, intron 1 of 7)	intron (NM_001048209, intron 1 of 7)	36138	NR_110140	101929653	Hs.559159	NR_110140	ENSG00000237654	LOC101929653	-	uncharacterized LOC101929653	ncRNA	0.021352	0.556738	
chunk0163_345_1	chr6	15448062	15448604	+	0	NA	intron (NM_001267040, intron 3 of 17)	intron (NM_001267040, intron 3 of 17)	199478	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.012915	0.373849	
chunk0125_261_1	chr3	69186632	69187291	+	0	NA	intron (NM_015123, intron 19 of 22)	intron (NM_015123, intron 19 of 22)	-64366	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.006070	0.409091	
chunk0132_40_1	chr3	154792594	154793206	+	0	NA	Intergenic	Intergenic	-286747	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.003268	0.309951	
chunk0127_434_1	chr3	103042453	103042765	+	0	NA	Intergenic	Intergenic	481507	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.376997	
chunk0019_254_1	chr1	227767344	227767553	+	0	NA	intron (NM_053052, intron 4 of 4)	(GT)n|Simple_repeat|Simple_repeat	-32037	NM_001161465	65094	Hs.555974	NM_023007	ENSG00000081692	JMJD4	-	jumonji domain containing 4	protein-coding	0.009569	0.438095	
chunk0052_117_1	chr13	23193089	23193380	+	0	NA	intron (NM_000231, intron 1 of 7)	L2b|LINE|L2	12313	NM_000231	6445	Hs.37167	NM_000231	ENSG00000102683	SGCG	35DAG|A4|DAGA4|DMDA|DMDA1|LGMD2C|LGMDR5|MAM|SCARMD2|SCG3|gamma-SG	sarcoglycan gamma	protein-coding	0.017182	0.523973	61(GGGAACAACGTGTCCA,-,0.00),62(GGAACAACGTGTCCAA,+,0.00)
chunk0200_183_1	chr9	19381319	19381624	+	0	NA	Intergenic	L1MB5|LINE|L1	-1234	NM_001010	6194	Hs.408073	NM_001010	ENSG00000137154	RPS6	S6	ribosomal protein S6	protein-coding	0.003279	0.323529	
chunk0193_31_1	chr8	71093286	71093701	+	0	NA	Intergenic	Intergenic	263018	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.009639	0.317308	
chunk0019_409_1	chr1	230680403	230681117	+	0	NA	intron (NM_001145036, intron 10 of 17)	intron (NM_001145036, intron 10 of 17)	33830	NM_000029	183	Hs.19383	NM_000029	ENSG00000135744	AGT	ANHU|SERPINA8|hFLT1	angiotensinogen	protein-coding	0.005602	0.418182	
chunk0035_266_1	chr11	46519401	46519698	+	0	NA	intron (NM_001267782, intron 8 of 19)	intron (NM_001267782, intron 8 of 19)	-67660	NR_036117	100422827		NR_036117	ENSG00000265014	MIR3160-1	mir-3160-1	microRNA 3160-1	ncRNA	0.010101	0.429530	
chunk0135_73_1	chr3	185915158	185915615	+	0	NA	3' UTR (NM_004593, exon 9 of 9)	3' UTR (NM_004593, exon 9 of 9)	22750	NM_001243879	6434	Hs.533122	NM_004593	ENSG00000136527	TRA2B	Htra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B	transformer 2 beta homolog	protein-coding	0.004376	0.410480	
chunk0168_239_1	chr6	87806752	87807138	+	0	NA	intron (NR_110869, intron 2 of 4)	L2a|LINE|L2	22085	NR_110869	101928911	Hs.571178	NR_110869		LOC101928911	-	uncharacterized LOC101928911	ncRNA	0.012953	0.343669	
chunk0035_277_1	chr11	46649205	46649622	+	0	NA	intron (NM_014741, intron 6 of 16)	intron (NM_014741, intron 6 of 16)	32137	NM_014741	9776	Hs.127403	NM_014741	ENSG00000175224	ATG13	KIAA0652|PARATARG8	autophagy related 13	protein-coding	0.002398	0.440191	247(GAGTACAGCTAGTTCT,-,0.00),248(AGTACAGCTAGTTCTC,+,0.00)
chunk0002_119_1	chr1	16175925	16176392	+	0	NA	Intergenic	Intergenic	-20071	NM_004431	1969	Hs.171596	NM_004431	ENSG00000142627	EPHA2	ARCC2|CTPA|CTPP1|CTRCT6|ECK	EPH receptor A2	protein-coding	0.019272	0.514957	
chunk0111_192_1	chr20	25534452	25534692	+	0	NA	intron (NM_025176, intron 1 of 23)	Tigger3a|DNA|TcMar-Tigger	50945	NM_025176	22981	Hs.631508	NM_025176	ENSG00000101004	NINL	NLP	ninein like	protein-coding	0.004167	0.385892	29(ATCACAGAGTGTACTT,+,0.00)
chunk0176_176_1	chr7	13719670	13720137	+	0	NA	Intergenic	Intergenic	266611	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.000000	0.344017	
chunk0200_225_1	chr9	20662886	20663229	+	0	NA	intron (NM_017794, intron 2 of 45)	intron (NM_017794, intron 2 of 45)	4748	NM_017794	54914	Hs.136247	NM_017794	ENSG00000188352	FOCAD	KIAA1797	focadhesin	protein-coding	0.000000	0.328488	
chunk0164_159_1	chr6	21588745	21589011	+	0	NA	Intergenic	CpG	-4863	NM_003107	6659	Hs.643910	NM_003107	ENSG00000124766	SOX4	EVI16	SRY-box transcription factor 4	protein-coding	0.060150	0.498127	
chunk0183_247_1	chr7	107144950	107145439	+	0	NA	intron (NM_002736, intron 5 of 10)	MER58A|DNA|hAT-Charlie	-23767	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.004090	0.353061	
chunk0044_142_1	chr12	29563495	29564041	+	0	NA	intron (NM_001193451, intron 9 of 17)	L2a|LINE|L2	-66082	NM_183378	341350	Hs.674588	NM_183378	ENSG00000187950	OVCH1	OVCH	ovochymase 1	protein-coding	0.018315	0.478976	
chunk0176_167_1	chr7	13483503	13483971	+	0	NA	Intergenic	Intergenic	502777	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.004274	0.351812	
chunk0100_149_1	chr2	109009598	109010414	+	0	NA	Intergenic	L1ME4a|LINE|L1	-20634	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.009804	0.427173	514(TGGGCATTGTGTTCTT,+,0.00)
chunk0068_397_1	chr15	58644479	58644838	+	0	NA	intron (NM_001110, intron 6 of 15)	L2b|LINE|L2	48949	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.008357	0.405556	
chunk0082_25_1	chr17	50694165	50694613	+	0	NA	3' UTR (NM_052855, exon 5 of 5)	3' UTR (NM_052855, exon 5 of 5)	13520	NM_052855	91369	Hs.463426	NM_052855	ENSG00000154945	ANKRD40	-	ankyrin repeat domain 40	protein-coding	0.004464	0.405345	
chunk0066_416_1	chr15	39454842	39455184	+	0	NA	Intergenic	Intergenic	-126066	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.005848	0.361516	
chunk0142_116_1	chr4	94515899	94516550	+	0	NA	intron (NM_001256428, intron 2 of 11)	intron (NM_001256428, intron 2 of 11)	64367	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.004608	0.354294	252(TAGAACAGACCGTGCT,-,0.00),253(AGAACAGACCGTGCTG,+,0.00)
chunk0007_414_1	chr1	86104891	86105533	+	0	NA	intron (NM_152890, intron 5 of 59)	L1PA13|LINE|L1	51226	NM_152890	255631	Hs.659516	NM_152890	ENSG00000171502	COL24A1	-	collagen type XXIV alpha 1 chain	protein-coding	0.015576	0.589425	121(CAGGACTGTGTGTGCC,-,0.00),122(AGGACTGTGTGTGCCC,+,0.00)
chunk0049_233_1	chr12	93468038	93468368	+	0	NA	intron (NR_038160, intron 1 of 6)	intron (NR_038160, intron 1 of 6)	713	NR_038160	28977	Hs.199579	NM_014050	ENSG00000198015	MRPL42	HSPC204|L31MT|L42MT|MRP-L31|MRP-L42|MRP-S32|MRPL31|MRPS32|PTD007|RPML31|S32MT	mitochondrial ribosomal protein L42	protein-coding	0.015152	0.404834	
chunk0036_33_1	chr11	58675697	58675923	+	0	NA	Intergenic	Intergenic	53137	NM_000614	1270	Hs.524920	NM_000614	ENSG00000242689	CNTF	HCNTF	ciliary neurotrophic factor	protein-coding	0.022124	0.533040	101(AGGCACACTTTGTCCT,-,0.00),102(GGCACACTTTGTCCTG,+,0.00)
chunk0183_42_1	chr7	103867035	103867278	+	0	NA	intron (NM_005045, intron 2 of 64)	intron (NM_005045, intron 2 of 64)	122360	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.012346	0.344262	
chunk0192_198_1	chr8	64310668	64311233	+	0	NA	intron (NR_125826, intron 1 of 4)	L1PB4|LINE|L1	57608	NR_125826	102724623	Hs.586375	NR_125826	ENSG00000253554	LINC01414	-	long intergenic non-protein coding RNA 1414	ncRNA	0.003540	0.340989	
chunk0115_111_1	chr21	22850573	22851112	+	0	NA	Intergenic	Intergenic	-228442	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.001855	0.300000	
chunk0088_295_1	chr18	49834940	49835306	+	0	NA	intron (NM_001080467, intron 39 of 39)	intron (NM_001080467, intron 39 of 39)	21100	NR_003003	677769		NR_003003	ENSG00000267322	SCARNA17	U91	small Cajal body-specific RNA 17	ncRNA	0.005464	0.326975	
chunk0194_221_1	chr8	86175816	86176565	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	54185	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.004005	0.356000	
chunk0169_165_1	chr6	102033992	102034344	+	0	NA	intron (NM_001166247, intron 13 of 16)	intron (NM_001166247, intron 13 of 16)	635183	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.002841	0.373938	191(GAGCACTCATTGTACC,-,0.00),192(AGCACTCATTGTACCT,+,0.00)
chunk0156_25_1	chr5	102283041	102283467	+	0	NA	intron (NM_180991, intron 2 of 12)	MIRb|SINE|MIR	13295	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.002347	0.323185	
chunk0204_270_1	chr9	98332140	98332868	+	0	NA	intron (NM_005458, intron 13 of 18)	MIRb|SINE|MIR	-76783	NM_018421	55357	Hs.371016	NM_018421	ENSG00000095383	TBC1D2	PARIS-1|PARIS1|TBC1D2A	TBC1 domain family member 2	protein-coding	0.015110	0.488340	
chunk0185_153_1	chr7	127699063	127699497	+	0	NA	intron (NM_014390, intron 4 of 23)	L2a|LINE|L2	47132	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.004608	0.386207	
chunk0083_203_1	chr17	66691713	66692027	+	0	NA	intron (NM_002737, intron 8 of 16)	intron (NM_002737, intron 8 of 16)	-95202	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.025478	0.473016	
chunk0081_211_1	chr17	42540959	42541703	+	0	NA	intron (NM_000263, intron 5 of 5)	MIRc|SINE|MIR	5398	NM_000263	4669	Hs.50727	NM_000263	ENSG00000108784	NAGLU	CMT2V|MPS-IIIB|MPS3B|NAG|UFHSD	N-acetyl-alpha-glucosaminidase	protein-coding	0.022849	0.532886	
chunk0178_158_1	chr7	33781734	33782227	+	0	NA	Intergenic	L1MC|LINE|L1	-122931	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.008114	0.394737	295(AAGAACATTGCGTGCC,-,0.00),296(AGAACATTGCGTGCCT,+,0.00)
chunk0201_122_1	chr9	35350704	35351446	+	0	NA	intron (NM_006377, intron 10 of 38)	intron (NM_006377, intron 10 of 38)	-55680	NR_003581	158381	Hs.575661	NR_003581	ENSG00000179766	ATP8B5P	FetA	ATPase phospholipid transporting 8B5, pseudogene	pseudo	0.005391	0.413190	
chunk0011_253_1	chr1	150810989	150811255	+	0	NA	3' UTR (NM_001197325, exon 21 of 21)	3' UTR (NM_001197325, exon 21 of 21)	-2681	NM_000396	1513	Hs.632466	NM_000396	ENSG00000143387	CTSK	CTS02|CTSO|CTSO1|CTSO2|PKND|PYCD	cathepsin K	protein-coding	0.015038	0.397004	
chunk0144_472_1	chr4	142600914	142601432	+	0	NA	intron (NM_003866, intron 2 of 26)	L1PA11|LINE|L1	245278	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.001931	0.298651	
chunk0109_121_1	chr20	2800024	2800223	+	0	NA	intron (NM_019609, intron 1 of 13)	(GT)n|Simple_repeat|Simple_repeat	523	NM_019609	56265	Hs.659346	NM_019609	ENSG00000088882	CPXM1	CPX1|CPXM	carboxypeptidase X, M14 family member 1	protein-coding	0.090452	0.610000	
chunk0071_261_1	chr15	85520680	85521287	+	0	NA	intron (NM_007200, intron 2 of 36)	intron (NM_007200, intron 2 of 36)	-98967	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.006590	0.388158	
chunk0008_18_1	chr1	87530070	87530399	+	0	NA	Intergenic	Intergenic	-158579	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.012158	0.487879	
chunk0027_120_1	chr10	74163326	74163692	+	0	NA	intron (NM_006721, intron 1 of 10)	intron (NM_006721, intron 1 of 10)	12324	NM_001202450	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.005464	0.343324	
chunk0050_103_1	chr12	101945454	101945775	+	0	NA	Intergenic	Intergenic	68287	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.021807	0.462733	
chunk0212_192_1	chrX	134162008	134162596	+	0	NA	Intergenic	Intergenic	7150	NR_029852	574031		NR_029852	ENSG00000284499	MIR363	MIR-363|MIRN363|hsa-mir-363	microRNA 363	ncRNA	0.000000	0.334465	
chunk0077_63_1	chr16	76794330	76794787	+	0	NA	Intergenic	AluSc8|SINE|Alu	-74378	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.024070	0.427948	
chunk0117_234_1	chr22	22959144	22959343	+	0	NA	Intergenic	Intergenic	71463	NM_001178126	100423062	Hs.449574	NM_001178126	ENSG00000254709	IGLL5	IGL|IGLV|VL-MAR	immunoglobulin lambda like polypeptide 5	protein-coding	0.015075	0.440000	
chunk0029_454_1	chr10	110483670	110484110	+	0	NA	Intergenic	MIR|SINE|MIR	-13977	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.002273	0.405896	
chunk0015_150_1	chr1	186404496	186404907	+	0	NA	intron (NM_017847, intron 11 of 13)	intron (NM_017847, intron 11 of 13)	4129	NM_022375	10896	Hs.679230	NM_022375	ENSG00000262180	OCLM	TISR	oculomedin	protein-coding	0.009732	0.337379	
chunk0045_20_1	chr12	43760512	43760755	+	0	NA	intron (NM_001145258, intron 1 of 9)	L2a|LINE|L2	1689	NM_016123	51135	Hs.138499	NM_016123	ENSG00000198001	IRAK4	IPD1|IRAK-4|NY-REN-64|REN64	interleukin 1 receptor associated kinase 4	protein-coding	0.004115	0.454918	
chunk0209_355_1	chrX	53230275	53230482	+	0	NA	Intergenic	MER3|DNA|hAT-Charlie	-4956	NM_001146702	8242	Hs.631768	NM_004187	ENSG00000126012	KDM5C	DXS1272E|JARID1C|MRX13|MRXJ|MRXSCJ|MRXSJ|SMCX|XE169	lysine demethylase 5C	protein-coding	0.014493	0.427885	
chunk0124_353_1	chr3	58628920	58629529	+	0	NA	Intergenic	Intergenic	-1614	NM_001282714	11170	Hs.506357	NM_007177	ENSG00000168309	FAM107A	DRR1|TU3A	family with sequence similarity 107 member A	protein-coding	0.016420	0.508197	
chunk0173_12_1	chr6	141253117	141253772	+	0	NA	Intergenic	Intergenic	569630	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.003053	0.329268	368(TGGAACACAATGTTCT,-,0.00),369(GGAACACAATGTTCTA,+,0.00)
chunk0169_415_1	chr6	108589194	108589704	+	0	NA	intron (NM_201559, intron 2 of 3)	intron (NM_201559, intron 2 of 3)	28583	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.011765	0.510763	216(GGGGACATTCAGTACT,-,0.00),217(GGGACATTCAGTACTA,+,0.00)
chunk0135_315_1	chr3	190009504	190010017	+	0	NA	intron (NM_001134418, intron 1 of 14)	intron (NM_001134418, intron 1 of 14)	-111204	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.005848	0.394942	
chunk0007_164_1	chr1	79967325	79967649	+	0	NA	Intergenic	Intergenic	-568268	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.015432	0.310769	
chunk0066_166_1	chr15	32700443	32700811	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-17377	NM_001191323	26585	Hs.40098	NM_013372	ENSG00000166923	GREM1	C15DUPq|CKTSF1B1|CRAC1|CRCS4|DAND2|DRM|DUP15q|GREMLIN|HMPS|HMPS1|IHG-2|MPSH|PIG2	gremlin 1, DAN family BMP antagonist	protein-coding	0.016304	0.436314	
chunk0029_328_1	chr10	104492433	104492709	+	0	NA	Intergenic	Intergenic	-12296	NR_120624	101927523	Hs.407539	NR_120624	ENSG00000225768	LINC02620	-	long intergenic non-protein coding RNA 2620	ncRNA	0.003623	0.447653	
chunk0066_403_1	chr15	39273775	39274566	+	0	NA	Intergenic	Intergenic	23501	NM_207445	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.007585	0.386364	
chunk0134_300_1	chr3	180617120	180617566	+	0	NA	intron (NM_181426, intron 16 of 19)	Tigger3b|DNA|TcMar-Tigger	15213	NM_001042601	151613	Hs.43213	NM_133462	ENSG00000163728	TTC14	DRDL5813|PRO19630	tetratricopeptide repeat domain 14	protein-coding	0.004484	0.364653	
chunk0010_324_1	chr1	118142564	118142843	+	0	NA	intron (NM_206996, intron 3 of 48)	MIR|SINE|MIR	42522	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.010753	0.357143	
chunk0016_128_1	chr1	196979239	196979723	+	0	NA	intron (NM_030787, intron 1 of 9)	Tigger3b|DNA|TcMar-Tigger	1944	NM_030787	81494	Hs.282594	NM_030787	ENSG00000134389	CFHR5	CFHL5|CFHR5D|FHR-5|FHR5	complement factor H related 5	protein-coding	0.008264	0.379381	
chunk0027_54_1	chr10	72876142	72876672	+	0	NA	intron (NR_073062, intron 8 of 9)	L2|LINE|L2	-17149	NR_130125	170392	Hs.8366	NM_152635	ENSG00000138315	OIT3	LZP	oncoprotein induced transcript 3	protein-coding	0.001887	0.365348	
chunk0019_382_1	chr1	230111097	230111333	+	0	NA	intron (NM_004481, intron 1 of 15)	intron (NM_004481, intron 1 of 15)	44020	NR_120373	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.021186	0.464135	
chunk0205_343_1	chr9	113328045	113328510	+	0	NA	intron (NM_001012361, intron 5 of 10)	intron (NM_001012361, intron 5 of 10)	12063	NM_145241	114987	Hs.133331	NM_145241	ENSG00000148225	WDR31	-	WD repeat domain 31	protein-coding	0.004301	0.375536	220(CAGAACACAATGTATC,-,0.00),221(AGAACACAATGTATCT,+,0.00)
chunk0166_22_1	chr6	41787285	41787739	+	0	NA	promoter-TSS (NM_001134493)	promoter-TSS (NM_001134493)	69	NM_001134493	100188893	Hs.731633	NM_001134493	ENSG00000214736	TOMM6	OBTP|TOM6	translocase of outer mitochondrial membrane 6	protein-coding	0.079295	0.635165	
chunk0193_125_1	chr8	74280676	74281426	+	0	NA	intron (NM_020647, intron 2 of 5)	MIRb|SINE|MIR	40276	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.005333	0.338216	
chunk0155_387_1	chr5	98529794	98530280	+	0	NA	Intergenic	Intergenic	-239258	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.002058	0.283368	252(AAGAACAGCATGTCTT,-,0.00),253(AGAACAGCATGTCTTC,+,0.00)
chunk0188_324_1	chr8	17515702	17516224	+	0	NA	intron (NM_001008539, intron 1 of 11)	L3|LINE|CR1	18875	NM_001008539	6542	Hs.448520	NM_003046	ENSG00000003989	SLC7A2	ATRC2|CAT2|HCAT2	solute carrier family 7 member 2	protein-coding	0.003831	0.317400	
chunk0179_445_1	chr7	52656099	52656596	+	0	NA	Intergenic	LTR80B|LTR|ERVL	-379309	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.006036	0.361446	
chunk0105_389_1	chr2	192450503	192451232	+	0	NA	Intergenic	Intergenic	-255934	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.000000	0.339726	324(CAGGACAGGCTGCACT,-,0.00),325(AGGACAGGCTGCACTG,+,0.00)
chunk0181_250_1	chr7	85555553	85555984	+	0	NA	Intergenic	Intergenic	-433837	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.006961	0.296296	
chunk0086_146_1	chr18	21330062	21330698	+	0	NA	intron (NM_001142966, intron 1 of 32)	intron (NM_001142966, intron 1 of 32)	88138	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.009434	0.492936	
chunk0173_73_1	chr6	142629228	142629683	+	0	NA	intron (NR_027311, intron 1 of 2)	L2c|LINE|L2	8381	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.008791	0.401316	
chunk0113_200_1	chr20	53639591	53640338	+	0	NA	Intergenic	Intergenic	-56867	NM_006526	7764	Hs.155040	NM_006526	ENSG00000171940	ZNF217	ZABC1	zinc finger protein 217	protein-coding	0.008032	0.439840	
chunk0208_180_1	chrX	16996962	16997161	+	0	NA	intron (NM_004726, intron 1 of 17)	intron (NM_004726, intron 1 of 17)	50370	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.005025	0.360000	
chunk0070_333_1	chr15	75596852	75597195	+	0	NA	Intergenic	Intergenic	-17732	NM_002833	5780	Hs.445775	NM_002833	ENSG00000169410	PTPN9	MEG2|PTPMEG2	protein tyrosine phosphatase non-receptor type 9	protein-coding	0.005831	0.436047	192(AGGAACACAATGTTCC,-,0.00),193(GGAACACAATGTTCCT,+,0.00)
chunk0154_129_1	chr5	79035301	79035838	+	0	NA	intron (NR_104003, intron 2 of 9)	Chap1_Mam|DNA|hAT-Charlie	34105	NM_013391	29958	Hs.655653	NM_013391	ENSG00000132837	DMGDH	DMGDHD|ME2GLYDH	dimethylglycine dehydrogenase	protein-coding	0.007449	0.410781	
chunk0045_386_1	chr12	52417688	52418080	+	0	NA	Intergenic	L2a|LINE|L2	-11492	NM_033033	3888	Hs.134640	NM_033033	ENSG00000161850	KRT82	HB2|Hb-2|KRTHB2	keratin 82	protein-coding	0.005102	0.458015	
chunk0161_271_1	chr5	172559174	172559481	+	0	NA	Intergenic	Intergenic	-81939	NM_001308177	54492	Hs.91521	NM_001142651	ENSG00000214357	NEURL1B	NEURL3|RNF67B|hNeur2|neur2	neuralized E3 ubiquitin protein ligase 1B	protein-coding	0.026059	0.561688	
chunk0082_83_1	chr17	52085448	52086227	+	0	NA	intron (NM_001082534, intron 2 of 9)	intron (NM_001082534, intron 2 of 9)	72935	NM_020178	56934	Hs.463466	NM_020178	ENSG00000154975	CA10	CA-RPX|CARPX|HUCEP-15	carbonic anhydrase 10	protein-coding	0.003851	0.332051	
chunk0177_185_1	chr7	23507887	23508477	+	0	NA	intron (NM_001282757, intron 5 of 8)	intron (NM_001282757, intron 5 of 8)	17794	NR_026676	256355	Hs.367935	NR_026676	ENSG00000232818	RPS2P32	RPS2_14_794	ribosomal protein S2 pseudogene 32	pseudo	0.008475	0.370558	
chunk0021_453_1	chr1	248873953	248874215	+	0	NA	Intergenic	Intergenic	-14968	NM_017865	55657	Hs.377705	NM_017865	ENSG00000171163	ZNF692	AREBP|Zfp692	zinc finger protein 692	protein-coding	0.034351	0.448669	
chunk0038_208_1	chr11	86377849	86378226	+	0	NA	intron (NM_001156474, intron 1 of 14)	L1MC1|LINE|L1	3301	NM_021827	60494	Hs.144913	NM_021827	ENSG00000149201	CCDC81	-	coiled-coil domain containing 81	protein-coding	0.000000	0.349206	
chunk0031_400_1	chr10	131557077	131557373	+	0	NA	Intergenic	Intergenic	232974	NR_038365	399827	Hs.523353	NM_001001677	ENSG00000189275	LINC01164	-	long intergenic non-protein coding RNA 1164	ncRNA	0.016892	0.407407	
chunk0104_127_1	chr2	173088189	173088430	+	0	NA	intron (NM_133646, intron 1 of 11)	HAL1|LINE|L1	12472	NM_133646	51776	Hs.444451	NM_016653	ENSG00000091436	MAP3K20	AZK|CNM6|MLK7|MLT|MLTK|MLTKalpha|MLTKbeta|MRK|SFMMP|ZAK|mlklak|pk	mitogen-activated protein kinase kinase kinase 20	protein-coding	0.008299	0.388430	
chunk0138_312_1	chr4	41358676	41358974	+	0	NA	promoter-TSS (NM_001289124)	promoter-TSS (NM_001289124)	-782	NM_001289124	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.010067	0.478261	
chunk0012_381_1	chr1	163365666	163366000	+	0	NA	Intergenic	L1ME3C|LINE|L1	43900	NM_145697	83540	Hs.651950	NM_031423	ENSG00000143228	NUF2	CDCA1|CT106|NUF2R	NUF2 component of NDC80 kinetochore complex	protein-coding	0.002994	0.343284	
chunk0192_356_1	chr8	68148501	68149142	+	0	NA	intron (NM_024870, intron 34 of 39)	intron (NM_024870, intron 34 of 39)	-181901	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.001560	0.309969	285(GAAAACATTCTGTACC,-,0.00),286(AAAACATTCTGTACCA,+,0.00)
chunk0099_17_1	chr2	82912528	82912990	+	0	NA	Intergenic	L1M1|LINE|L1	55956	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.004329	0.317495	
chunk0054_112_1	chr13	42906185	42906709	+	0	NA	intron (NM_001002264, intron 9 of 12)	intron (NM_001002264, intron 9 of 12)	-33703	NR_126389	104355147	Hs.633967	NR_126388		LINC00428	-	long intergenic non-protein coding RNA 428	ncRNA	0.007634	0.438095	306(CAGGAGAGCCTGTTCT,-,0.00),307(AGGAGAGCCTGTTCTC,+,0.00)
chunk0197_18_1	chr8	117281272	117281492	+	0	NA	Intergenic	L2c|LINE|L2	146284	NM_001172814	169026	Hs.532270	NM_173851	ENSG00000164756	SLC30A8	ZNT8|ZnT-8	solute carrier family 30 member 8	protein-coding	0.000000	0.416290	
chunk0077_40_1	chr16	75553035	75553327	+	0	NA	intron (NR_074083, intron 2 of 6)	intron (NR_074083, intron 2 of 6)	3105	NR_074083	79583	Hs.156784	NM_001077416	ENSG00000205084	TMEM231	ALYE870|JBTS20|MKS11|PRO1886	transmembrane protein 231	protein-coding	0.006849	0.440273	
chunk0204_369_1	chr9	101960908	101961500	+	0	NA	Intergenic	Intergenic	-222624	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.001689	0.278246	
chunk0149_62_1	chr5	16931313	16931651	+	0	NA	intron (NM_012334, intron 1 of 40)	intron (NM_012334, intron 1 of 40)	4794	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.005917	0.522124	
chunk0004_88_1	chr1	43757587	43758270	+	0	NA	intron (NM_001270465, intron 2 of 7)	L1MB7|LINE|L1	-30585	NR_125986	101929592		NR_125986	ENSG00000229444	LOC101929592	-	uncharacterized LOC101929592	ncRNA	0.002928	0.311404	
chunk0079_175_1	chr17	13989870	13990584	+	0	NA	Intergenic	LTR16|LTR|ERVL	-34271	NR_003261	94158	Hs.633073	NR_003261		CDRT15P1	CDRT15P	CMT1A duplicated region transcript 15 pseudogene 1	pseudo	0.007003	0.409790	350(TGGCACACAGTGTCCT,-,0.00),351(GGCACACAGTGTCCTG,+,0.00)
chunk0114_96_1	chr21	9327779	9327989	+	0	NA	Intergenic	Intergenic	-198123	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.009524	0.431280	
chunk0187_78_1	chr8	2817456	2817655	+	0	NA	Intergenic	Intergenic	-89104	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.025126	0.490000	162(GAGAACACAGTGAACT,-,0.00),163(AGAACACAGTGAACTC,+,0.00)
chunk0026_221_1	chr10	64867190	64868248	+	0	NA	Intergenic	MER61E|LTR|ERV1	42191	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.004726	0.387158	142(TAGGACATAGAGTTCT,-,0.00),143(AGGACATAGAGTTCTT,+,0.00)
chunk0101_353_1	chr2	137892924	137893772	+	0	NA	intron (NR_120402, intron 2 of 2)	intron (NR_120402, intron 2 of 2)	34584	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.003538	0.321555	477(CAGTACAGAATGTACA,-,0.00),478(AGTACAGAATGTACAT,+,0.00)
chunk0195_275_1	chr8	98117534	98118313	+	0	NA	promoter-TSS (NM_005836)	promoter-TSS (NM_005836)	83	NM_015029	10940	Hs.252828	NM_015029	ENSG00000104356	POP1	ANXD2	POP1 homolog, ribonuclease P/MRP subunit	protein-coding	0.020539	0.475641	
chunk0160_173_1	chr5	153571158	153571646	+	0	NA	intron (NM_001258020, intron 3 of 16)	MER58B|DNA|hAT-Charlie	79230	NM_001258021	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.006148	0.413088	219(AGGCACTGTCTGTCCC,-,0.00),220(GGCACTGTCTGTCCCA,+,0.00)
chunk0075_127_1	chr16	50002353	50002552	+	0	NA	Intergenic	L2a|LINE|L2	-22754	NR_104043	255919	Hs.59134	NM_153261	ENSG00000205423	CNEP1R1	C16orf69|NEP1-R1|NEP1R1|TMEM188|TMP125	CTD nuclear envelope phosphatase 1 regulatory subunit 1	protein-coding	0.005025	0.440000	88(GAGAACAGGGTGTTCC,-,0.00),89(AGAACAGGGTGTTCCT,+,0.00)
chunk0143_207_1	chr4	113499229	113499462	+	0	NA	intron (NM_172114, intron 15 of 17)	intron (NM_172114, intron 15 of 17)	262582	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.000000	0.363248	
chunk0120_260_1	chr3	9124027	9124436	+	0	NA	intron (NM_001033117, intron 2 of 21)	intron (NM_001033117, intron 2 of 21)	-68262	NR_121663	101927416	Hs.475364	NR_121663	ENSG00000228723	SRGAP3-AS2	-	SRGAP3 antisense RNA 2	ncRNA	0.009780	0.492683	326(CGGGACAGGATGTCCT,-,0.00),327(GGGACAGGATGTCCTG,+,0.00)
chunk0092_82_1	chr19	21110019	21110799	+	0	NA	intron (NR_117086, intron 5 of 6)	L1PA10|LINE|L1	28262	NR_117086	148206	Hs.729186	NM_182515	ENSG00000160352	ZNF714	-	zinc finger protein 714	protein-coding	0.005128	0.339309	
chunk0047_14_1	chr12	65319541	65320113	+	0	NA	intron (NM_001031679, intron 2 of 6)	intron (NM_001031679, intron 2 of 6)	40840	NM_001193461	253827	Hs.339024	NM_198080	ENSG00000174099	MSRB3	DFNB74	methionine sulfoxide reductase B3	protein-coding	0.003497	0.322862	
chunk0136_226_1	chr4	8331039	8331269	+	0	NA	Intergenic	Intergenic	61389	NM_053044	94031	Hs.479119	NM_053044	ENSG00000170801	HTRA3	Prsp|Tasp	HtrA serine peptidase 3	protein-coding	0.021739	0.580087	79(GAGAACATCATGTTCA,-,0.00),80(AGAACATCATGTTCAC,+,0.00)
chunk0169_335_1	chr6	106419797	106420406	+	0	NA	Intergenic	Intergenic	-91754	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.003284	0.385246	
chunk0135_435_1	chr3	193863816	193864466	+	0	NA	Intergenic	Intergenic	130097	NR_027764	100128023	Hs.730112	NR_027764		DPPA2P3	-	developmental pluripotency associated 2 pseudogene 3	pseudo	0.012308	0.513057	340(CAGCACGCTCTGTTCA,-,0.00),341(AGCACGCTCTGTTCAG,+,0.00)
chunk0139_394_1	chr4	62484308	62484507	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-322642	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.005025	0.440000	
chunk0034_2_1	chr11	25766624	25767009	+	0	NA	Intergenic	Intergenic	-422307	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.007792	0.344560	
chunk0068_388_1	chr15	58604396	58604827	+	0	NA	intron (NM_001110, intron 14 of 15)	intron (NM_001110, intron 14 of 15)	88996	NR_073415	664618	Hs.670224	NR_002927		HSP90AB4P	HSP90Bd	heat shock protein 90 alpha family class B member 4, pseudogene	pseudo	0.004640	0.381944	
chunk0045_157_1	chr12	46579608	46579901	+	0	NA	intron (NR_125377, intron 3 of 3)	intron (NR_125377, intron 3 of 3)	195647	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.000000	0.401361	
chunk0203_286_1	chr9	88899503	88899962	+	0	NA	Intergenic	L1MCa|LINE|L1	-91131	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.000000	0.302174	243(ATGAACATGGAGTACC,-,0.00),244(TGAACATGGAGTACCT,+,0.00)
chunk0036_16_1	chr11	58296543	58296742	+	0	NA	Intergenic	MIR|SINE|MIR	-28382	NM_207374	81341	Hs.531507	NM_207374	ENSG00000172772	OR10W1	OR10W1P|OR10W1Q|OR11-236|UNQ6469	olfactory receptor family 10 subfamily W member 1	protein-coding	0.000000	0.320000	
chunk0166_390_1	chr6	51843283	51844070	+	0	NA	intron (NM_138694, intron 50 of 66)	intron (NM_138694, intron 50 of 66)	221806	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.008895	0.393401	
chunk0057_46_1	chr13	96397394	96398116	+	0	NA	intron (NM_153456, intron 1 of 1)	intron (NM_153456, intron 1 of 1)	-29474	NR_039723	100616137		NR_039723	ENSG00000283487	MIR4501	-	microRNA 4501	ncRNA	0.002770	0.347165	
chunk0076_299_1	chr16	69941861	69942060	+	0	NA	TTS (NM_001270454)	TTS (NM_001270454)	-8745	NM_001136214	348174	Hs.592064	NM_182619	ENSG00000157322	CLEC18A	MRCL|MRCL1|MRLP2	C-type lectin domain family 18 member A	protein-coding	0.035176	0.645000	
chunk0091_109_1	chr19	5962085	5962331	+	0	NA	intron (NM_007320, intron 1 of 15)	intron (NM_007320, intron 1 of 15)	16101	NM_001300865	8498	Hs.531752	NM_003624	ENSG00000031823	RANBP3	-	RAN binding protein 3	protein-coding	0.028455	0.522267	
chunk0053_38_1	chr13	27360499	27360986	+	0	NA	Intergenic	L2a|LINE|L2	-63802	NM_002097	2971	Hs.445977	NM_002097	ENSG00000122034	GTF3A	AP2|TFIIIA	general transcription factor IIIA	protein-coding	0.018480	0.479508	
chunk0123_55_1	chr3	41163423	41164155	+	0	NA	Intergenic	Intergenic	-35662	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.008197	0.407913	
chunk0089_77_1	chr18	58234811	58235527	+	0	NA	intron (NM_001144971, intron 3 of 30)	intron (NM_001144971, intron 3 of 30)	13647	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.018156	0.495119	245(AAGCCCAGAATGTTCC,-,0.00),246(AGCCCAGAATGTTCCC,+,0.00)
chunk0072_407_1	chr15	100890238	100890895	+	0	NA	intron (NM_001293815, intron 3 of 9)	intron (NM_001293815, intron 3 of 9)	10874	NM_000693	220	Hs.459538	NM_000693	ENSG00000184254	ALDH1A3	ALDH1A6|ALDH6|MCOP8|RALDH3	aldehyde dehydrogenase 1 family member A3	protein-coding	0.009132	0.417933	
chunk0195_346_1	chr8	99500403	99501076	+	0	NA	intron (NM_152564, intron 25 of 61)	intron (NM_152564, intron 25 of 61)	35991	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.007429	0.320475	
chunk0161_69_1	chr5	166625522	166625901	+	0	NA	Intergenic	Intergenic	300659	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.010554	0.352632	
chunk0189_237_1	chr8	24567971	24568179	+	0	NA	Intergenic	L1MEg|LINE|L1	-19457	NR_125808	101929294	Hs.637673	NR_125808		LOC101929294	-	uncharacterized LOC101929294	ncRNA	0.004808	0.411483	
chunk0175_88_1	chr7	2670845	2671247	+	0	NA	Intergenic	Intergenic	-8476	NM_133463	155185	Hs.42221	NM_133463	ENSG00000174945	AMZ1	-	archaelysin family metallopeptidase 1	protein-coding	0.037313	0.602978	
chunk0176_337_1	chr7	17512394	17512607	+	0	NA	intron (NR_110013, intron 1 of 3)	intron (NR_110013, intron 1 of 3)	46409	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.009390	0.327103	
chunk0196_59_1	chr8	102242428	102242954	+	0	NA	intron (NR_125415, intron 1 of 2)	LTR102_Mam|LTR|ERVL	3240	NR_125415	101927221	Hs.492445	NR_125415	ENSG00000246263	UBR5-AS1	-	UBR5 antisense RNA 1	ncRNA	0.007605	0.466793	
chunk0147_47_1	chr4	172364464	172364905	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	324233	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.000000	0.337104	
chunk0046_113_1	chr12	57276868	57277325	+	0	NA	intron (NM_014925, intron 12 of 21)	intron (NM_014925, intron 12 of 21)	-25903	NR_104422	246329	Hs.417595	NM_145064	ENSG00000185482	STAC3	MYPBB|NAM	SH3 and cysteine rich domain 3	protein-coding	0.010941	0.438865	185(AAGTACTGCCTGTACT,-,0.00),186(AGTACTGCCTGTACTC,+,0.00)
chunk0109_354_1	chr2	238900500	238901174	+	0	NA	intron (NM_001271893, intron 1 of 1)	L1MEj|LINE|L1	25432	NR_034162	401039	Hs.516791	NM_001001698	ENSG00000227744	LINC01940	-	long intergenic non-protein coding RNA 1940	ncRNA	0.016320	0.511111	357(TGGAACTTGGTGTTCC,-,0.00),358(GGAACTTGGTGTTCCC,+,0.00)
chunk0155_156_1	chr5	94109140	94109749	+	0	NA	intron (NR_028080, intron 1 of 8)	intron (NR_028080, intron 1 of 8)	2255	NM_001163417	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.006568	0.383607	
chunk0108_70_1	chr2	227474521	227474720	+	0	NA	intron (NM_001135189, intron 1 of 11)	intron (NM_001135189, intron 1 of 11)	2448	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.010050	0.360000	
chunk0004_453_1	chr1	53480651	53480935	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	21394	NM_033067	63948	Hs.131654	NM_033067	ENSG00000143006	DMRTB1	-	DMRT like family B with proline rich C-terminal 1	protein-coding	0.017606	0.477193	140(TAGAACTGACTGTCCC,-,0.00),141(AGAACTGACTGTCCCA,+,0.00)
chunk0043_243_1	chr12	20274779	20275342	+	0	NA	Intergenic	L1MB8|LINE|L1	-94185	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.003552	0.319149	
chunk0109_428_1	chr2	241321150	241321461	+	0	NA	intron (NM_001008492, intron 2 of 13)	L1MEj|LINE|L1	5444	NM_004404	4735	Hs.721234	NM_004404	ENSG00000168385	SEPTIN2	DIFF6|NEDD-5|NEDD5|Pnutl3|SEPT2|hNedd5	septin 2	protein-coding	0.003215	0.317308	
chunk0078_160_1	chr17	4233802	4234303	+	0	NA	intron (NR_047571, intron 2 of 23)	Tigger3a|DNA|TcMar-Tigger	29795	NM_001257999	51479	Hs.696087	NM_016376	ENSG00000185722	ANKFY1	ANKHZN|BTBD23|ZFYVE14	ankyrin repeat and FYVE domain containing 1	protein-coding	0.009980	0.390438	307(CAGAACATGCTGTACA,-,0.00),308(AGAACATGCTGTACAG,+,0.00)
chunk0118_106_1	chr22	29306189	29306863	+	0	NA	promoter-TSS (NM_152236)	promoter-TSS (NM_152236)	-469	NM_152236	10634	Hs.322852	NM_006478	ENSG00000185340	GAS2L1	GAR22	growth arrest specific 2 like 1	protein-coding	0.062315	0.654815	485(GGGAACAGGCCGTGCT,-,0.00),486(GGAACAGGCCGTGCTG,+,0.00)
chunk0149_105_1	chr5	19001116	19001427	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	885001	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003215	0.381410	
chunk0088_110_1	chr18	45396900	45397127	+	0	NA	intron (NM_001242692, intron 1 of 20)	L1PA14|LINE|L1	110023	NR_110899	101927980	Hs.591058	NR_110899		SLC14A2-AS1	-	SLC14A2 antisense RNA 1	ncRNA	0.004405	0.368421	
chunk0178_451_1	chr7	42053478	42053872	+	0	NA	intron (NM_000168, intron 4 of 14)	intron (NM_000168, intron 4 of 14)	183344	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.007614	0.400000	
chunk0198_272_1	chr8	135291364	135291563	+	0	NA	intron (NR_120395, intron 3 of 5)	MLT2B3|LTR|ERVL	57332	NR_120396	286094	Hs.440978	NR_026706	ENSG00000254083	LINC01591	-	long intergenic non-protein coding RNA 1591	ncRNA	0.000000	0.510000	
chunk0172_443_1	chr6	140880496	140880744	+	0	NA	Intergenic	Intergenic	196806	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.004032	0.349398	
chunk0115_418_1	chr21	31273875	31274576	+	0	NA	intron (NM_003253, intron 4 of 28)	intron (NM_003253, intron 4 of 28)	-235749	NM_001099219	728299	Hs.580875	NM_001099219	ENSG00000206102	KRTAP19-8	-	keratin associated protein 19-8	protein-coding	0.008559	0.440171	
chunk0164_280_1	chr6	24149936	24150180	+	0	NA	Intergenic	HAL1ME|LINE|L1	23872	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.008197	0.424490	
chunk0080_106_1	chr17	26940308	26940581	+	0	NA	Intergenic	AluYj4|SINE|Alu	353552	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.007326	0.437956	
chunk0030_355_1	chr10	118621048	118621866	+	0	NA	Intergenic	(CAGACAC)n|Simple_repeat|Simple_repeat	-25809	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.013447	0.489621	528(AAGAACAGTCCGTTCC,-,0.00),529(AGAACAGTCCGTTCCT,+,0.00)
chunk0012_140_1	chr1	157283998	157284902	+	0	NA	Intergenic	Intergenic	-145859	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.004425	0.479558	171(GAGAACAGTATGTCCT,-,0.00),172(AGAACAGTATGTCCTC,+,0.00),202(GGGAACACCATGTCCT,-,0.00),203(GGAACACCATGTCCTT,+,0.00),294(AGGAACACCGTGTCCT,-,0.00),295(GGAACACCGTGTCCTC,+,0.00),355(GGGAACACTGTGTCCT,-,0.00),356(GGAACACTGTGTCCTC,+,0.00),446(GGGAACACTATGTCCT,-,0.00),447(GGAACACTATGTCCTT,+,0.00),476(AGAAACACCATGTCCT,-,0.00),477(GAAACACCATGTCCTC,+,0.00),507(GGGAACACCATGTCCT,-,0.00),508(GGAACACCATGTCCTC,+,0.00),600(AGGAACATCATGTCCT,-,0.00),601(GGAACATCATGTCCTT,+,0.00),662(AGGAACACTGTGTCCT,-,0.00),663(GGAACACTGTGTCCTC,+,0.00),723(AGGAACACTGTGCCCT,-,0.00),724(GGAACACTGTGCCCTC,+,0.00)
chunk0203_30_1	chr9	82943825	82944084	+	0	NA	Intergenic	L1ME1|LINE|L1	119174	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.007722	0.346154	
chunk0148_421_1	chr5	15037565	15037899	+	0	NA	Intergenic	Intergenic	-165954	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.005988	0.331343	
chunk0021_27_1	chr10	625063	625319	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	16587	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.050781	0.544747	115(TTGAACTCACTGTCCC,-,0.00),116(TGAACTCACTGTCCCA,+,0.00)
chunk0110_110_1	chr20	12040696	12041114	+	0	NA	Intergenic	Intergenic	123040	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.009569	0.355609	
chunk0057_325_1	chr13	106899240	106899940	+	0	NA	Intergenic	Intergenic	245710	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.002857	0.358060	
chunk0183_135_1	chr7	105691402	105692307	+	0	NA	intron (NM_020725, intron 3 of 11)	intron (NM_020725, intron 3 of 11)	-12692	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.027624	0.434879	
chunk0021_88_1	chr10	2295353	2295552	+	0	NA	Intergenic	Intergenic	19622	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.010050	0.480000	
chunk0138_432_1	chr4	45346443	45346778	+	0	NA	Intergenic	MIRb|SINE|MIR	-619976	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.002985	0.336310	
chunk0053_206_1	chr13	32016915	32017429	+	0	NA	Intergenic	L2b|LINE|L2	-14128	NM_023037	10129	Hs.507669	NM_023037	ENSG00000073910	FRY	13CDNA73|214K23.2|C13orf14|CG003|bA207N4.2|bA37E23.1	FRY microtubule binding protein	protein-coding	0.009728	0.448544	
chunk0074_389_1	chr16	35306950	35307208	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-56337	NR_027080	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.003876	0.413127	
chunk0038_99_1	chr11	83520755	83521418	+	0	NA	intron (NM_001142699, intron 21 of 27)	intron (NM_001142699, intron 21 of 27)	161339	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.006033	0.396084	
chunk0208_341_1	chrX	25012842	25013396	+	0	NA	exon (NM_139058, exon 2 of 5)	exon (NM_139058, exon 2 of 5)	2829	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.102888	0.706306	215(AGGCACACGCTGTCCT,-,0.00),216(GGCACACGCTGTCCTC,+,0.00)
chunk0157_294_1	chr5	120938650	120939054	+	0	NA	Intergenic	Intergenic	-383698	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.002475	0.358025	
chunk0193_43_1	chr8	71616657	71616856	+	0	NA	Intergenic	Intergenic	-226367	NR_033652	100132891	Hs.137674	NR_033651	ENSG00000235531	MSC-AS1	-	MSC antisense RNA 1	ncRNA	0.015075	0.505000	
chunk0071_218_1	chr15	84779100	84779755	+	0	NA	intron (NM_014630, intron 3 of 10)	intron (NM_014630, intron 3 of 10)	30840	NM_014630	9640	Hs.79347	NM_014630	ENSG00000166716	ZNF592	CAMOS|SCAR5	zinc finger protein 592	protein-coding	0.004580	0.332317	
chunk0078_410_1	chr16	89124319	89124622	+	0	NA	intron (NM_001127214, intron 6 of 9)	intron (NM_001127214, intron 6 of 9)	-12078	NR_045667	197322	Hs.461727	NM_174917	ENSG00000176715	ACSF3	-	acyl-CoA synthetase family member 3	protein-coding	0.033003	0.509868	
chunk0206_82_1	chr9	120413394	120413593	+	0	NA	intron (NR_073556, intron 29 of 38)	intron (NR_073556, intron 29 of 38)	166677	NR_073557	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.015075	0.445000	
chunk0114_37_1	chr21	8234305	8234644	+	0	NA	intron (NR_003287, intron 1 of 2)	(TCTC)n|Simple_repeat|Simple_repeat	-15031	NR_106782	102465433		NR_106782	ENSG00000275950	MIR6724-1	MIR6724|hsa-mir-6724|hsa-mir-6724-1	microRNA 6724-1	ncRNA	0.002950	0.470588	
chunk0127_314_1	chr3	99817480	99817803	+	0	NA	promoter-TSS (NM_032359)	promoter-TSS (NM_032359)	-193	NM_032359	84319	Hs.581320	NM_032359	ENSG00000184220	CMSS1	C3orf26	cms1 ribosomal small subunit homolog	protein-coding	0.055728	0.432099	
chunk0118_113_1	chr22	29344178	29344454	+	0	NA	intron (NM_145730, intron 11 of 20)	intron (NM_145730, intron 11 of 20)	-11049	NR_037426									0.014493	0.534296	
chunk0171_302_1	chr6	128761926	128762156	+	0	NA	Intergenic	L1PA15|LINE|L1	-121100	NM_000426	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.034783	0.567100	
chunk0065_26_1	chr15	20642384	20642658	+	0	NA	Intergenic	MER49|LTR|ERV1	80172	NR_027411	729786	Hs.592025	NR_027411	ENSG00000181984	GOLGA8CP	GOLGA8C	golgin A8 family member C, pseudogene	pseudo	0.000000	0.400000	
chunk0197_95_1	chr8	119614368	119614567	+	0	NA	intron (NM_001040092, intron 8 of 24)	intron (NM_001040092, intron 8 of 24)	-21459	NR_045555	5168	Hs.190977	NM_006209	ENSG00000136960	ENPP2	ATX|ATX-X|AUTOTAXIN|LysoPLD|NPP2|PD-IALPHA|PDNP2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.005025	0.450000	
chunk0184_231_1	chr7	117522535	117523239	+	0	NA	intron (NM_000492, intron 3 of 26)	intron (NM_000492, intron 3 of 26)	42924	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.005682	0.358865	
chunk0081_268_1	chr17	43616218	43616627	+	0	NA	Intergenic	Intergenic	45141	NM_004527	4222	Hs.438	NM_004527	ENSG00000005102	MEOX1	KFS2|MOX1	mesenchyme homeobox 1	protein-coding	0.009780	0.526829	
chunk0031_184_1	chr10	125667091	125667770	+	0	NA	intron (NM_001128202, intron 1 of 3)	intron (NM_001128202, intron 1 of 3)	15714	NM_001128202	387718	Hs.148259	NM_001128202	ENSG00000175018	TEX36	C10orf122|bA383C5.1	testis expressed 36	protein-coding	0.022091	0.564706	
chunk0204_139_1	chr9	95485993	95486776	+	0	NA	intron (NM_001083606, intron 2 of 23)	intron (NM_001083606, intron 2 of 23)	20815	NM_001083607	5727	Hs.494538	NM_000264	ENSG00000185920	PTCH1	BCNS|NBCCS|PTC|PTC1|PTCH	patched 1	protein-coding	0.010217	0.469388	444(AGGAACAAACTGTATC,-,0.00)
chunk0087_257_1	chr18	37003130	37003723	+	0	NA	intron (NM_020776, intron 6 of 9)	L1MA4A|LINE|L1	-174210	NM_001271955	25941	Hs.436636	NM_015476	ENSG00000134779	TPGS2	C18orf10|HMFN0601|L17|PGs2	tubulin polyglutamylase complex subunit 2	protein-coding	0.008432	0.353535	
chunk0162_406_1	chr5	179827690	179828042	+	0	NA	intron (NM_003900, intron 5 of 7)	intron (NM_003900, intron 5 of 7)	7024	NM_003900	8878	Hs.587290	NM_003900	ENSG00000161011	SQSTM1	A170|DMRV|FTDALS3|NADGP|OSIL|PDB3|ZIP3|p60|p62|p62B	sequestosome 1	protein-coding	0.019886	0.563739	
chunk0044_19_1	chr12	27161583	27161985	+	0	NA	Intergenic	Intergenic	-79262	NM_001080406	728858	Hs.334003	NM_001080406	ENSG00000214700	C12orf71	-	chromosome 12 open reading frame 71	protein-coding	0.014925	0.429280	
chunk0046_106_1	chr12	57217621	57217984	+	0	NA	intron (NM_007224, intron 1 of 1)	intron (NM_007224, intron 1 of 1)	1007	NM_007224	11247	Hs.745023	NM_007224	ENSG00000182379	NXPH4	NPH4	neurexophilin 4	protein-coding	0.016529	0.596154	
chunk0001_59_1	chr1	2121191	2121497	+	0	NA	intron (NM_001033582, intron 1 of 14)	MLT1A|LTR|ERVL-MaLR	16628	NM_001033582	5590	Hs.496255	NM_002744	ENSG00000067606	PRKCZ	PKC-ZETA|PKC2	protein kinase C zeta	protein-coding	0.026144	0.550489	
chunk0028_305_1	chr10	91671917	91672456	+	0	NA	Intergenic	Intergenic	-39085	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.009276	0.501852	
chunk0162_163_1	chr6	3506589	3507205	+	0	NA	Intergenic	MIRb|SINE|MIR	-50338	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.009740	0.395462	309(AAGGACATACAGTACC,-,0.00),310(AGGACATACAGTACCT,+,0.00)
chunk0208_259_1	chrX	20853504	20853894	+	0	NA	Intergenic	Intergenic	-520719	NM_014927	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.007692	0.383632	
chunk0120_379_1	chr3	12257738	12258037	+	0	NA	Intergenic	Intergenic	-29963	NM_005037	5468	Hs.162646	NM_005037	ENSG00000132170	PPARG	CIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma	peroxisome proliferator activated receptor gamma	protein-coding	0.013378	0.523333	157(CAGGACATGAAGTCCT,-,0.00),158(AGGACATGAAGTCCTT,+,0.00)
chunk0037_443_1	chr11	80383595	80383941	+	0	NA	Intergenic	Intergenic	379035	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.008671	0.475504	
chunk0061_248_1	chr14	61102014	61102595	+	0	NA	Intergenic	Intergenic	121057	NR_033344	145389	Hs.200738	NM_153811	ENSG00000139974	SLC38A6	NAT-1|SNAT6	solute carrier family 38 member 6	protein-coding	0.005164	0.419244	
chunk0210_294_1	chrX	86929989	86930454	+	0	NA	Intergenic	Intergenic	-587491	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.006452	0.291845	154(AAGATCACATTGTACC,-,0.00),155(AGATCACATTGTACCT,+,0.00)
chunk0056_143_1	chr13	83655927	83656402	+	0	NA	Intergenic	Intergenic	226229	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.279412	
chunk0005_238_1	chr1	59487940	59488389	+	0	NA	intron (NM_001244714, intron 4 of 13)	L1ME4a|LINE|L1	-27465	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.006682	0.302222	
chunk0133_27_1	chr3	165800978	165801287	+	0	NA	intron (NM_000055, intron 2 of 3)	intron (NM_000055, intron 2 of 3)	36333	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.006472	0.412903	
chunk0173_435_1	chr6	151326365	151326841	+	0	NA	intron (NM_144497, intron 1 of 2)	intron (NM_144497, intron 1 of 2)	1072	NM_144497	9590	Hs.371240	NM_005100	ENSG00000131016	AKAP12	AKAP250|SSeCKS	A-kinase anchoring protein 12	protein-coding	0.010504	0.314465	
chunk0133_88_1	chr3	167724321	167724724	+	0	NA	intron (NM_145860, intron 1 of 7)	intron (NM_145860, intron 1 of 7)	10284	NM_007217	11235	Hs.478150	NM_007217	ENSG00000114209	PDCD10	CCM3|TFAR15	programmed cell death 10	protein-coding	0.002481	0.351485	
chunk0190_186_1	chr8	33422000	33422281	+	0	NA	intron (NM_032664, intron 3 of 4)	intron (NM_032664, intron 3 of 4)	51006	NM_032664	84750	Hs.458713	NM_032664	ENSG00000172728	FUT10	FUCTX	fucosyltransferase 10	protein-coding	0.017794	0.379433	
chunk0080_113_1	chr17	27076378	27076719	+	0	NA	Intergenic	Intergenic	217448	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.005865	0.350877	
chunk0115_168_1	chr21	25069223	25069713	+	0	NA	Intergenic	Intergenic	228918	NR_046198	339622	Hs.616316	NR_046198	ENSG00000226983	LINC01692	-	long intergenic non-protein coding RNA 1692	ncRNA	0.002041	0.289206	
chunk0070_163_1	chr15	71390220	71390420	+	0	NA	intron (NM_024817, intron 5 of 16)	intron (NM_024817, intron 5 of 16)	-156882	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.010000	0.383085	
chunk0110_460_1	chr20	21336330	21336854	+	0	NA	intron (NM_012255, intron 13 of 29)	L2a|LINE|L2	33288	NM_012255	22803	Hs.255932	NM_012255	ENSG00000088930	XRN2	-	5'-3' exoribonuclease 2	protein-coding	0.007634	0.434286	
chunk0165_126_1	chr6	33128517	33128735	+	0	NA	intron (NR_001435, intron 3 of 4).6	intron (NR_001435, intron 3 of 4).6	16110	NR_001435	3116	Hs.665450	NR_001435	ENSG00000224557	HLA-DPB2	DP2B|DPB2|DPbeta2|HLA-DP2B	major histocompatibility complex, class II, DP beta 2 (pseudogene)	pseudo	0.013761	0.552511	
chunk0039_183_1	chr11	100672597	100673305	+	0	NA	Intergenic	Intergenic	-14725	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.005650	0.390691	
chunk0025_302_1	chr10	57468790	57469418	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-164545	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.006369	0.395866	
chunk0194_182_1	chr8	85177907	85178267	+	0	NA	intron (NM_001083588, intron 1 of 7)	intron (NM_001083588, intron 1 of 7)	703	NM_001951	1875	Hs.445758	NM_001951	ENSG00000133740	E2F5	E2F-5	E2F transcription factor 5	protein-coding	0.050000	0.495845	
chunk0125_218_1	chr3	67687176	67687485	+	0	NA	intron (NR_109992, intron 3 of 6)	MER58A|DNA|hAT-Charlie	32633	NR_109992	101927111	Hs.518057	NR_109992	ENSG00000241316	SUCLG2-AS1	-	SUCLG2 antisense RNA 1 (head to head)	ncRNA	0.006472	0.341935	
chunk0074_402_1	chr16	35463428	35463901	+	0	NA	Intergenic	L1MB2|LINE|L1	16932	NR_026980	146481	Hs.316564	NR_026980		FRG2DP	-	FSHD region gene 2 family member D, pseudogene	pseudo	0.004228	0.331224	176(ATCACACAGTGTCCTT,+,0.00)
chunk0155_398_1	chr5	98786410	98787097	+	0	NA	intron (NM_001012761, intron 4 of 4)	intron (NM_001012761, intron 4 of 4)	-13669	NR_033932	503569	Hs.586188	NR_033932	ENSG00000246763	RGMB-AS1	-	RGMB antisense RNA 1	ncRNA	0.004367	0.392442	
chunk0085_427_1	chr18	10721243	10721732	+	0	NA	intron (NM_022068, intron 33 of 51)	intron (NM_022068, intron 33 of 51)	38162	NR_106846	102466735		NR_106846	ENSG00000274838	MIR6788	hsa-mir-6788	microRNA 6788	ncRNA	0.014315	0.387755	
chunk0120_79_1	chr3	3636787	3637092	+	0	NA	Intergenic	Intergenic	-162498	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.003279	0.460784	
chunk0039_225_1	chr11	101521764	101521963	+	0	NA	intron (NM_004621, intron 1 of 12)	MSTA-int|LTR|ERVL-MaLR	-1958	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.010050	0.405000	
chunk0003_300_1	chr1	37553898	37554224	+	0	NA	exon (NM_024700, exon 1 of 4)	exon (NM_024700, exon 1 of 4)	283	NM_024700	79753	Hs.47232	NM_024700	ENSG00000163877	SNIP1	PML1|PMRED	Smad nuclear interacting protein 1	protein-coding	0.107362	0.694190	
chunk0097_70_1	chr2	44286741	44287336	+	0	NA	intron (NM_000341, intron 4 of 9)	MIR|SINE|MIR	11580	NM_000341	6519	Hs.112916	NM_000341	ENSG00000138079	SLC3A1	ATR1|CSNU1|D2H|NBAT|RBAT	solute carrier family 3 member 1	protein-coding	0.018487	0.481544	
chunk0212_14_1	chrY	8213162	8213627	+	0	NA	Intergenic	Intergenic	408470	NR_001551	83867	Hs.667616	NR_001551	ENSG00000237048	TTTY12	NCRNA00135|TTY11|TTY12	testis-specific transcript, Y-linked 12	ncRNA	0.000000	0.300429	
chunk0015_289_1	chr1	188736557	188737106	+	0	NA	Intergenic	L1M5|LINE|L1	1293203	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.005464	0.272727	
chunk0096_353_1	chr2	36291676	36292178	+	0	NA	Intergenic	Intergenic	63643	NR_037631	100288911	Hs.432924	NR_037631		CRIM1-DT	-	CRIM1 divergent transcript	ncRNA	0.001992	0.401590	
chunk0143_98_1	chr4	108478367	108478576	+	0	NA	Intergenic	Intergenic	141986	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.009569	0.433333	15(AGGGTCATTGTGTACT,-,0.00),16(GGGTCATTGTGTACTG,+,0.00)
chunk0066_336_1	chr15	36802148	36802387	+	0	NA	intron (NR_027320, intron 3 of 3)	MIR|SINE|MIR	16239	NR_027320	161635	Hs.659822	NR_027320		CSNK1A1P1	CSNK1A1P	casein kinase 1 alpha 1 pseudogene 1	pseudo	0.004184	0.379167	
chunk0031_55_1	chr10	122701292	122701607	+	0	NA	Intergenic	L2c|LINE|L2	-1627	NM_001010912	399814	Hs.363649	NM_001010912	ENSG00000183559	C10orf120	bA318C4.1	chromosome 10 open reading frame 120	protein-coding	0.006349	0.392405	
chunk0109_282_1	chr20	8132035	8132262	+	0	NA	promoter-TSS (NM_182734)	promoter-TSS (NM_182734)	-117	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.083700	0.723684	
chunk0201_281_1	chr9	38756949	38757391	+	0	NA	Intergenic	Intergenic	136082	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.002262	0.361174	
chunk0137_407_1	chr4	27815774	27815973	+	0	NA	Intergenic	L1MEc|LINE|L1	598394	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.000000	0.325000	
chunk0057_11_1	chr13	95551541	95552202	+	0	NA	promoter-TSS (NM_006984)	promoter-TSS (NM_006984)	-822	NM_006984	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.013616	0.432024	245(AAGTACACCTTGATCT,-,0.00),246(AGTACACCTTGATCTT,+,0.00)
chunk0128_263_1	chr3	109900549	109900864	+	0	NA	Intergenic	Intergenic	297878	NR_039647	100616129		NR_039647	ENSG00000265956	MIR4445	-	microRNA 4445	ncRNA	0.000000	0.376582	
chunk0156_107_1	chr5	105484515	105484838	+	0	NA	Intergenic	Intergenic	385202	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.000000	0.293210	
chunk0168_170_1	chr6	83883204	83883518	+	0	NA	intron (NM_016230, intron 2 of 15)	L1MEf|LINE|L1	23710	NM_016230	51167	Hs.5741	NM_016230	ENSG00000065615	CYB5R4	NCB5OR|cb5/cb5R|dJ676J13.1	cytochrome b5 reductase 4	protein-coding	0.003185	0.323810	
chunk0036_41_1	chr11	58936022	58936291	+	0	NA	intron (NR_033853, intron 5 of 5)	intron (NR_033853, intron 5 of 5)	-7093	NM_080661	92292	Hs.38085	NM_080661	ENSG00000166840	GLYATL1	GATF-C|GNAT	glycine-N-acyltransferase like 1	protein-coding	0.000000	0.325926	
chunk0198_278_1	chr8	135515422	135515851	+	0	NA	intron (NM_006558, intron 1 of 8)	LTR33|LTR|ERVL	58171	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.004662	0.425581	
chunk0144_171_1	chr4	132910520	132910801	+	0	NA	Intergenic	Intergenic	238456	NR_125885	101927359	Hs.649960	NR_125885	ENSG00000250241	LOC101927359	-	uncharacterized LOC101927359	ncRNA	0.000000	0.329787	
chunk0201_421_1	chr9	69653352	69653646	+	0	NA	intron (NM_001163, intron 1 of 12)	L1M1|LINE|L1	18860	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.003401	0.355932	
chunk0111_187_1	chr20	25384270	25385028	+	0	NA	intron (NM_001042472, intron 1 of 12)	AluJb|SINE|Alu	6333	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.006596	0.430830	
chunk0059_417_1	chr14	38019583	38020185	+	0	NA	Intergenic	Intergenic	-188115	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.004983	0.328358	
chunk0139_10_1	chr4	47885955	47886369	+	0	NA	intron (NR_103795, intron 12 of 23)	L1ME3|LINE|L1	-28065	NR_125879	101927157	Hs.134190	NR_125879		LOC101927157	-	uncharacterized LOC101927157	ncRNA	0.002415	0.322892	
chunk0003_6_1	chr1	28581880	28582079	+	0	NA	promoter-TSS (NR_003035)	promoter-TSS (NR_003035)	-125	NR_024127	85028	Hs.632377	NR_024127	ENSG00000197989	SNHG12	ASLNC04080|C1orf79|LINC00100|NCRNA00100|PNAS-123	small nucleolar RNA host gene 12	ncRNA	0.130653	0.680000	
chunk0072_92_1	chr15	90873988	90874428	+	0	NA	intron (NM_001289824, intron 1 of 15)	intron (NM_001289824, intron 1 of 15)	1330	NM_001289824	5045	Hs.513153	NM_002569	ENSG00000140564	FURIN	FUR|PACE|PCSK3|SPC1	furin, paired basic amino acid cleaving enzyme	protein-coding	0.025000	0.634921	
chunk0113_124_1	chr20	51562727	51563072	+	0	NA	promoter-TSS (NM_001258295)	promoter-TSS (NM_001258295)	-68	NM_001258295	4773	Hs.744148	NM_012340	ENSG00000101096	NFATC2	NFAT1|NFATP	nuclear factor of activated T cells 2	protein-coding	0.092754	0.624277	
chunk0090_325_1	chr18	75869445	75869764	+	0	NA	Intergenic	Intergenic	-253394	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.012539	0.403125	198(TGGAACAGTGTGCTCC,-,0.00),199(GGAACAGTGTGCTCCT,+,0.00)
chunk0051_350_1	chr12	120469432	120469681	+	0	NA	promoter-TSS (NM_001037494)	promoter-TSS (NM_001037494)	199	NM_003769	8683	Hs.706889	NM_003769	ENSG00000111786	SRSF9	SFRS9|SRp30c	serine and arginine rich splicing factor 9	protein-coding	0.172691	0.728000	
chunk0160_92_1	chr5	150137147	150137459	+	0	NA	intron (NM_002609, intron 1 of 22)	MIR3|SINE|MIR	18556	NM_002609	5159	Hs.509067	NM_002609	ENSG00000113721	PDGFRB	CD140B|IBGC4|IMF1|JTK12|KOGS|PDGFR|PDGFR-1|PDGFR1|PENTT	platelet derived growth factor receptor beta	protein-coding	0.022436	0.584665	
chunk0162_32_1	chr6	1024821	1025026	+	0	NA	intron (NR_027115, intron 1 of 4)	intron (NR_027115, intron 1 of 4)	76409	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.009756	0.402913	
chunk0015_429_1	chr1	191602345	191602899	+	0	NA	Intergenic	Intergenic	-555840	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.001805	0.374775	
chunk0153_316_1	chr5	73672757	73673467	+	0	NA	intron (NM_001080479, intron 1 of 36)	intron (NM_001080479, intron 1 of 36)	46954	NM_001177693	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.004225	0.378340	
chunk0064_57_1	chr14	89924886	89925115	+	0	NA	intron (NM_001284266, intron 5 of 5)	intron (NM_001284266, intron 5 of 5)	29557	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.008734	0.321739	
chunk0182_65_1	chr7	92065705	92065962	+	0	NA	intron (NM_147185, intron 25 of 49)	intron (NM_147185, intron 25 of 49)	68693	NM_000786	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.003891	0.375969	
chunk0138_438_1	chr4	45647960	45648251	+	0	NA	Intergenic	Intergenic	475960	NM_173536	2565	Hs.375051	NM_173536	ENSG00000163285	GABRG1	-	gamma-aminobutyric acid type A receptor gamma1 subunit	protein-coding	0.003436	0.366438	
chunk0123_296_1	chr3	46608887	46609102	+	0	NA	Intergenic	Intergenic	-3441	NM_001195442	100132146	Hs.679623	NM_001195442	ENSG00000283473	FAM240A	-	family with sequence similarity 240 member A	protein-coding	0.000000	0.291667	
chunk0085_287_1	chr18	7941530	7942010	+	0	NA	intron (NM_001105244, intron 5 of 32)	L3|LINE|CR1	374454	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.012500	0.426195	
chunk0042_95_1	chr12	2764955	2765283	+	0	NA	intron (NR_033958, intron 4 of 4)	MLT1C|LTR|ERVL-MaLR	6550	NR_033958	283440	Hs.448720	NR_033958	ENSG00000256150	ITFG2-AS1	-	ITFG2 antisense RNA 1	ncRNA	0.009146	0.498480	
chunk0040_35_1	chr11	110445513	110445865	+	0	NA	intron (NM_004109, intron 2 of 3)	MIR|SINE|MIR	15752	NM_004109	2230	Hs.744	NM_004109	ENSG00000137714	FDX1	ADX|FDX|LOH11CR1D	ferredoxin 1	protein-coding	0.002841	0.334278	
chunk0079_83_1	chr17	11867386	11868093	+	0	NA	intron (NM_001372, intron 50 of 68)	HAL1|LINE|L1	-15163	NM_004662	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.004243	0.382768	107(AATAACATCCTGTTCT,-,0.00),108(ATAACATCCTGTTCTT,+,0.00)
chunk0002_89_1	chr1	14625537	14626104	+	0	NA	intron (NM_015209, intron 1 of 7)	intron (NM_015209, intron 1 of 7)	27103	NM_015209	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.024691	0.429577	
chunk0115_412_1	chr21	31110592	31110814	+	0	NA	Intergenic	MIRb|SINE|MIR	-72227	NM_001099219	728299	Hs.580875	NM_001099219	ENSG00000206102	KRTAP19-8	-	keratin associated protein 19-8	protein-coding	0.009009	0.515695	
chunk0013_430_1	chr1	173458454	173458860	+	0	NA	intron (NR_125960, intron 1 of 1)	intron (NR_125960, intron 1 of 1)	2705	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.000000	0.319410	
chunk0212_187_1	chrX	133760134	133760395	+	0	NA	intron (NM_001164619, intron 1 of 6)	L1MC2|LINE|L1	225382	NM_004484	2719	Hs.644108	NM_004484	ENSG00000147257	GPC3	DGSX|GTR2-2|MXR7|OCI-5|SDYS|SGB|SGBS|SGBS1	glypican 3	protein-coding	0.000000	0.393130	
chunk0094_370_1	chr2	9759458	9759810	+	0	NA	Intergenic	MIRc|SINE|MIR	-83808	NM_005680	9014	Hs.584833	NM_005680	ENSG00000115750	TAF1B	MGC:9349|RAF1B|RAFI63|SL1|TAFI63	TATA-box binding protein associated factor, RNA polymerase I subunit B	protein-coding	0.002841	0.467422	196(GAGCACAATGTGACCT,-,0.00),197(AGCACAATGTGACCTC,+,0.00)
chunk0037_145_1	chr11	73342283	73342787	+	0	NA	intron (NM_014786, intron 1 of 20)	intron (NM_014786, intron 1 of 20)	-33825	NM_152222	84957	Hs.533720	NM_032871	ENSG00000054967	RELT	AI3C|TNFRSF19L|TRLT	RELT TNF receptor	protein-coding	0.049603	0.576238	
chunk0102_421_1	chr2	156999701	157000018	+	0	NA	Intergenic	Intergenic	-257969	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.012618	0.399371	
chunk0182_445_1	chr7	101870382	101870591	+	0	NA	intron (NM_181552, intron 1 of 23)	intron (NM_181552, intron 1 of 23)	52884	NM_181552	1523	Hs.191482	NM_001913	ENSG00000257923	CUX1	CASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75	cut like homeobox 1	protein-coding	0.019139	0.461905	
chunk0196_256_1	chr8	108729700	108729979	+	0	NA	Intergenic	L2c|LINE|L2	57702	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.000000	0.396429	
chunk0044_441_1	chr12	42323885	42324119	+	0	NA	promoter-TSS (NR_107005)	promoter-TSS (NR_107005)	-143	NR_107005	102467003		NR_107005	ENSG00000278520	MIR7851	hsa-mir-7851	microRNA 7851	ncRNA	0.012821	0.370213	
chunk0003_251_1	chr1	36230985	36231607	+	0	NA	intron (NM_005119, intron 1 of 11)	intron (NM_005119, intron 1 of 11)	6880	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.003215	0.373997	
chunk0032_85_1	chr11	2913133	2913485	+	0	NA	intron (NM_002555, intron 5 of 10).2	intron (NM_002555, intron 5 of 10).2	-9364	NM_001302862	5003	Hs.300076	NM_007105	ENSG00000254827	SLC22A18AS	BWR1B|BWSCR1B|ORCTL2S|SLC22A1LS|p27-BWR1B	solute carrier family 22 member 18 antisense	protein-coding	0.031250	0.643059	
chunk0091_140_1	chr19	7153168	7153443	+	0	NA	intron (NM_001079817, intron 9 of 20)	(AC)n|Simple_repeat|Simple_repeat	83845	NM_001044387	79230	Hs.591380	NM_024341	ENSG00000130544	ZNF557	-	zinc finger protein 557	protein-coding	0.018182	0.539855	
chunk0118_415_1	chr22	38202483	38202815	+	0	NA	promoter-TSS (NM_001161573)	promoter-TSS (NM_001161573)	-371	NM_001161573	23764	Hs.517617	NM_012323	ENSG00000185022	MAFF	U-MAF|hMafF	MAF bZIP transcription factor F	protein-coding	0.138554	0.729730	
chunk0138_361_1	chr4	42143091	42143397	+	0	NA	intron (NM_001159547, intron 3 of 5)	intron (NM_001159547, intron 3 of 5)	9634	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.006536	0.397394	
chunk0151_138_1	chr5	45027015	45027314	+	0	NA	Intergenic	MER57F|LTR|ERV1	218239	NM_016640	10884	Hs.124165	NM_016640	ENSG00000112996	MRPS30	MRP-S30|PAP|PDCD9|S30mt	mitochondrial ribosomal protein S30	protein-coding	0.003344	0.313333	
chunk0129_439_1	chr3	128026264	128026840	+	0	NA	Intergenic	HAL1|LINE|L1	-25817	NM_013336	29927	Hs.518236	NM_013336	ENSG00000058262	SEC61A1	HNFJ4|HSEC61|SEC61|SEC61A	SEC61 translocon alpha 1 subunit	protein-coding	0.006944	0.400347	
chunk0028_377_1	chr10	92879534	92880106	+	0	NA	intron (NM_019053, intron 1 of 21)	intron (NM_019053, intron 1 of 21)	31352	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.001748	0.279232	
chunk0046_165_1	chr12	58499557	58500338	+	0	NA	Intergenic	Intergenic	-91755	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.007682	0.439898	
chunk0162_465_1	chr5	181053154	181053840	+	0	NA	exon (NM_152547, exon 6 of 11)	exon (NM_152547, exon 6 of 11)	-10013	NR_107056	102465882		NR_107056	ENSG00000277912	MIR8089	hsa-mir-8089	microRNA 8089	ncRNA	0.106414	0.675400	354(GGGGACAGGGCGTTCT,-,0.00),355(GGGACAGGGCGTTCTG,+,0.00)
chunk0090_46_1	chr19	1582056	1582753	+	0	NA	intron (NM_001281453, intron 4 of 6)	intron (NM_001281453, intron 4 of 6)	10357	NM_001281453	53615	Hs.178728	NM_003926	ENSG00000071655	MBD3	-	methyl-CpG binding domain protein 3	protein-coding	0.020086	0.577364	
chunk0017_404_1	chr1	212680947	212681194	+	0	NA	Intergenic	Intergenic	18915	NM_018664	55509	Hs.62919	NM_018664	ENSG00000123685	BATF3	JDP1|JUNDM1|SNFT	basic leucine zipper ATF-like transcription factor 3	protein-coding	0.008097	0.342742	
chunk0049_22_1	chr12	89525984	89526223	+	0	NA	promoter-TSS (NM_001199777)	promoter-TSS (NM_001199777)	159	NM_172240	282809	Hs.25130	NM_172240	ENSG00000139323	POC1B	CORD20|PIX1|TUWD12|WDR51B	POC1 centriolar protein B	protein-coding	0.071130	0.620833	
chunk0174_56_1	chr6	155016014	155016483	+	0	NA	Intergenic	L1ME3G|LINE|L1	-74041	NM_012454	26230	Hs.586279	NM_012454	ENSG00000146426	TIAM2	STEF|TIAM-2	T cell lymphoma invasion and metastasis 2	protein-coding	0.006397	0.389362	
chunk0103_210_1	chr2	163867176	163867710	+	0	NA	Intergenic	L1PA13|LINE|L1	-131440	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.003745	0.325234	
chunk0159_446_1	chr5	148775895	148776284	+	0	NA	Intergenic	L2c|LINE|L2	-50504	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.005141	0.369231	
chunk0104_67_1	chr2	171762608	171763406	+	0	NA	Intergenic	Intergenic	75335	NM_001271787	1781	Hs.546250	NM_001378	ENSG00000077380	DYNC1I2	DIC74|DNCI2|IC2	dynein cytoplasmic 1 intermediate chain 2	protein-coding	0.003759	0.396746	
chunk0106_140_1	chr2	200041008	200041207	+	0	NA	Intergenic	Intergenic	-85371	NR_109906	129450	Hs.204619	NM_152382	ENSG00000162971	TYW5	C2orf60|hTYW5	tRNA-yW synthesizing protein 5	protein-coding	0.005025	0.360000	107(GAGAACATGATGAACT,-,0.00),108(AGAACATGATGAACTT,+,0.00)
chunk0047_187_1	chr12	70785687	70785981	+	0	NA	intron (NM_002849, intron 2 of 13)	intron (NM_002849, intron 2 of 13)	3096	NM_001207015	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.006803	0.308475	
chunk0172_145_1	chr6	135556602	135556956	+	0	NA	intron (NR_026805, intron 1 of 3)	intron (NR_026805, intron 1 of 3)	58978	NR_026805	100131814	Hs.734007	NR_026805	ENSG00000231028	LINC00271	C6orf217|NCRNA00271	long intergenic non-protein coding RNA 271	ncRNA	0.005650	0.292958	278(AAGAACACAGTGTGAC,-,0.00),279(AGAACACAGTGTGACT,+,0.00)
chunk0080_165_1	chr17	28346639	28347149	+	0	NA	3' UTR (NM_021137, exon 7 of 7)	3' UTR (NM_021137, exon 7 of 7)	-10687	NM_152464	147007	Hs.594696	NM_152464	ENSG00000244045	TMEM199	C17orf32|CDG2P|VMA12|VPH2	transmembrane protein 199	protein-coding	0.011765	0.438356	
chunk0001_256_1	chr1	8439066	8439363	+	0	NA	intron (NM_001042681, intron 11 of 22)	intron (NM_001042681, intron 11 of 22)	14569	NR_125999	102724552	Hs.568612	NR_125999		RERE-AS1	-	RERE antisense RNA 1	ncRNA	0.006734	0.446309	
chunk0025_229_1	chr10	54044678	54044939	+	0	NA	intron (NM_001142769, intron 20 of 35)	intron (NM_001142769, intron 20 of 35)	563149	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.007663	0.362595	
chunk0053_265_1	chr13	33113716	33114584	+	0	NA	intron (NM_001243476, intron 12 of 17)	Charlie7a|DNA|hAT-Charlie	71929	NM_178007	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.011521	0.471807	509(CAGAGCTGGCTGTTCC,-,0.00)
chunk0074_408_1	chr16	35523866	35524537	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-17031	NR_034018	100130700	Hs.97712	NR_034018		TP53TG3HP	-	TP53 target 3 family member H, pseudogene	pseudo	0.004471	0.404762	
chunk0164_420_1	chr6	27168198	27168421	+	0	NA	Intergenic	MER92-int|LTR|ERV1	20683	NR_036096	100422934		NR_036096	ENSG00000265565	MIR3143	mir-3143	microRNA 3143	ncRNA	0.004484	0.357143	
chunk0017_341_1	chr1	211703676	211703960	+	0	NA	Intergenic	Intergenic	-28188	NM_001204182	4751	Hs.153704	NM_002497	ENSG00000117650	NEK2	HsPK21|NEK2A|NLK1|PPP1R111|RP67	NIMA related kinase 2	protein-coding	0.017606	0.498246	
chunk0036_323_1	chr11	66258358	66258647	+	0	NA	intron (NM_001134774, intron 1 of 14)	CpG	799	NM_022822	64837	Hs.280792	NM_022822	ENSG00000174996	KLC2	-	kinesin light chain 2	protein-coding	0.096886	0.700000	
chunk0147_82_1	chr4	173159685	173160115	+	0	NA	Intergenic	L2a|LINE|L2	-8853	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.002326	0.431555	
chunk0019_397_1	chr1	230492594	230493235	+	0	NA	Intergenic	Intergenic	-66986	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.003120	0.311526	
chunk0004_155_1	chr1	45375277	45375834	+	0	NA	intron (NM_007170, intron 4 of 10)	L2a|LINE|L2	-35085	NM_001293192	4595	Hs.271353	NM_012222	ENSG00000132781	MUTYH	MYH	mutY DNA glycosylase	protein-coding	0.005386	0.421147	
chunk0185_75_1	chr7	125238408	125238616	+	0	NA	intron (NR_110183, intron 3 of 3)	L1MEf|LINE|L1	25779	NR_110183	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.004808	0.287081	
chunk0192_14_1	chr8	58396719	58396935	+	0	NA	Intergenic	Intergenic	-14437	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.046296	0.511521	
chunk0060_145_1	chr14	45006683	45007018	+	0	NA	intron (NR_131765, intron 5 of 19)	L1ME4a|LINE|L1	44660	NM_001308120	23116	Hs.371078	NM_015091	ENSG00000198718	TOGARAM1	FAM179B|KIAA0423	TOG array regulator of axonemal microtubules 1	protein-coding	0.005970	0.294643	
chunk0162_115_1	chr6	2791265	2791820	+	0	NA	Intergenic	L1ME4a|LINE|L1	26110	NM_130395	56897	Hs.236828	NM_020135	ENSG00000124535	WRNIP1	WHIP|bA420G6.2	WRN helicase interacting protein 1	protein-coding	0.007207	0.381295	
chunk0008_235_1	chr1	94176342	94176753	+	0	NA	intron (NM_004815, intron 22 of 22)	MIRb|SINE|MIR	-55398	NM_000350	24	Hs.416707	NM_000350	ENSG00000198691	ABCA4	ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1	ATP binding cassette subfamily A member 4	protein-coding	0.014599	0.410194	
chunk0026_197_1	chr10	63682023	63682784	+	0	NA	Intergenic	Intergenic	161040	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.005256	0.367454	
chunk0090_11_1	chr19	534937	535284	+	0	NA	intron (NM_004359, intron 1 of 4)	intron (NM_004359, intron 1 of 4)	3377	NM_004359	997	Hs.514997	NM_004359	ENSG00000099804	CDC34	E2-CDC34|UBC3|UBCH3|UBE2R1	cell division cycle 34	protein-coding	0.020173	0.646552	
chunk0109_288_1	chr20	8219293	8219940	+	0	NA	intron (NM_015192, intron 2 of 31)	intron (NM_015192, intron 2 of 31)	87351	NM_182734	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.007728	0.362654	
chunk0075_291_1	chr16	54041738	54041973	+	0	NA	intron (NM_001080432, intron 8 of 8)	intron (NM_001080432, intron 8 of 8)	2462	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.034043	0.474576	
chunk0149_177_1	chr5	21006220	21007028	+	0	NA	Intergenic	Intergenic	-430751	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.003713	0.262052	
chunk0091_52_1	chr19	4715786	4716211	+	0	NA	intron (NM_139159, intron 3 of 21)	intron (NM_139159, intron 3 of 21)	7845	NM_139159	91039	Hs.515081	NM_139159	ENSG00000142002	DPP9	DP9|DPLP9|DPP IX|DPRP-2|DPRP2	dipeptidyl peptidase 9	protein-coding	0.042353	0.603286	
chunk0118_165_1	chr22	30694094	30694588	+	0	NA	promoter-TSS (NM_001282739)	promoter-TSS (NM_001282739)	-465	NM_030758	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.068826	0.628283	
chunk0003_349_1	chr1	39098238	39098608	+	0	NA	intron (NM_012090, intron 1 of 92)	MIRb|SINE|MIR	14256	NM_012090	23499	Hs.472475	NM_012090	ENSG00000127603	MACF1	ABP620|ACF7|LIS9|MACF|OFC4	microtubule actin crosslinking factor 1	protein-coding	0.013514	0.520216	
chunk0054_411_1	chr13	50644064	50644753	+	0	NA	Intergenic	L2a|LINE|L2	-116959	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.004354	0.405797	
chunk0079_25_1	chr17	9842286	9842797	+	0	NA	exon (NM_004246, exon 4 of 13)	exon (NM_004246, exon 4 of 13)	16990	NM_004246	9340	Hs.248202	NM_004246	ENSG00000065325	GLP2R	-	glucagon like peptide 2 receptor	protein-coding	0.023483	0.533203	
chunk0064_134_1	chr14	91415837	91416244	+	0	NA	intron (NM_001080414, intron 2 of 29)	intron (NM_001080414, intron 2 of 29)	1804	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.019656	0.458333	
chunk0086_35_1	chr18	12599555	12599924	+	0	NA	intron (NM_001128627, intron 2 of 15)	L1MC4|LINE|L1	56993	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.000000	0.451351	
chunk0210_186_1	chrX	79785454	79785932	+	0	NA	Intergenic	Intergenic	-229063	NM_001109878	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.004184	0.367432	
chunk0171_229_1	chr6	126311185	126311677	+	0	NA	Intergenic	Intergenic	-28358	NR_104462	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.010163	0.326572	230(GAGCACAAGGTGTCTT,-,0.00)
chunk0068_254_1	chr15	56191575	56192061	+	0	NA	intron (NM_022841, intron 1 of 8)	intron (NM_022841, intron 1 of 8)	51467	NM_022841	64864	Hs.745089	NM_022841	ENSG00000181827	RFX7	RFXDC2	regulatory factor X7	protein-coding	0.004115	0.404517	305(AGGGGCAAAATGTTCT,-,0.00),306(GGGGCAAAATGTTCTC,+,0.00)
chunk0135_133_1	chr3	187287644	187288321	+	0	NA	intron (NM_001031849, intron 1 of 8)	L1ME4a|LINE|L1	4040	NM_001879	5648	Hs.89983	NM_001879	ENSG00000127241	MASP1	3MC1|CRARF|CRARF1|MAP1|MASP|MASP3|MAp44|PRSS5|RaRF	mannan binding lectin serine peptidase 1	protein-coding	0.001477	0.342183	
chunk0066_62_1	chr15	28892504	28892787	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-28992	NM_005503	321	Hs.618112	NM_005503	ENSG00000034053	APBA2	D15S1518E|HsT16821|LIN-10|MGC:14091|MINT2|X11-BETA|X11L	amyloid beta precursor protein binding family A member 2	protein-coding	0.010601	0.362676	
chunk0068_409_1	chr15	59011705	59012172	+	0	NA	intron (NM_001270530, intron 1 of 13)	intron (NM_001270530, intron 1 of 13)	23792	NM_001270530	54778	Hs.404423	NM_017610	ENSG00000157450	RNF111	ARK|hRNF111	ring finger protein 111	protein-coding	0.012848	0.386752	
chunk0107_7_1	chr2	209954421	209954620	+	0	NA	intron (NM_032504, intron 47 of 63)	intron (NM_032504, intron 47 of 63)	-48045	NM_006916	6120	Hs.282260	NM_006916	ENSG00000197713	RPE	RPE2-1	ribulose-5-phosphate-3-epimerase	protein-coding	0.005025	0.315000	
chunk0143_346_1	chr4	121721633	121721934	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	-24791	NM_001154	308	Hs.480653	NM_001154	ENSG00000164111	ANXA5	ANX5|ENX2|HEL-S-7|PP4|RPRGL3	annexin A5	protein-coding	0.003322	0.380795	
chunk0190_294_1	chr8	38016145	38016431	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-14214	NM_004095	1978	Hs.411641	NM_004095	ENSG00000187840	EIF4EBP1	4E-BP1|4EBP1|BP-1|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding	0.000000	0.250871	
chunk0171_308_1	chr6	129244285	129244855	+	0	NA	intron (NM_001079823, intron 12 of 63)	intron (NM_001079823, intron 12 of 63)	361429	NM_001079823	3908	Hs.200841	NM_000426	ENSG00000196569	LAMA2	LAMM|MDC1A	laminin subunit alpha 2	protein-coding	0.005263	0.355517	
chunk0200_78_1	chr9	16267535	16268385	+	0	NA	intron (NR_073471, intron 1 of 3)	(TGC)n|Simple_repeat|Simple_repeat	8353	NR_073471									0.012941	0.434783	
chunk0081_262_1	chr17	43483564	43483970	+	0	NA	promoter-TSS (NM_001302623)	promoter-TSS (NM_001302623)	-150	NM_001302623	1659	Hs.463105	NM_004941	ENSG00000067596	DHX8	DDX8|Dhr2|HRH1|PRP22|PRPF22	DEAH-box helicase 8	protein-coding	0.068966	0.542998	
chunk0027_204_1	chr10	75788406	75788977	+	0	NA	intron (NM_032024, intron 1 of 5)	MLT1J|LTR|ERVL-MaLR	5930	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.007005	0.400350	
chunk0203_426_1	chr9	91097640	91098031	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-22703	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.007673	0.369898	
chunk0032_23_1	chr11	819535	819871	+	0	NA	5' UTR (NM_020376, exon 2 of 10)	5' UTR (NM_020376, exon 2 of 10)	802	NM_020376	57104	Hs.654697	NM_020376	ENSG00000177666	PNPLA2	1110001C14Rik|ATGL|FP17548|PEDF-R|TTS-2.2|TTS2|iPLA2zeta	patatin like phospholipase domain containing 2	protein-coding	0.154762	0.744807	
chunk0061_320_1	chr14	62800312	62801181	+	0	NA	intron (NM_139318, intron 9 of 10)	intron (NM_139318, intron 9 of 10)	244492	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.004603	0.333333	
chunk0071_212_1	chr15	84668285	84668564	+	0	NA	Intergenic	Intergenic	-9853	NM_205858	4828	Hs.386470	NM_021077	ENSG00000197696	NMB	-	neuromedin B	protein-coding	0.000000	0.439286	
chunk0059_167_1	chr14	32395469	32395856	+	0	NA	intron (NM_004274, intron 1 of 13)	intron (NM_004274, intron 1 of 13)	66389	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.002584	0.373711	119(AAGAACATCCTGCTCT,-,0.00),120(AGAACATCCTGCTCTG,+,0.00)
chunk0152_35_1	chr5	56975225	56975947	+	0	NA	Intergenic	Intergenic	-23456	NM_001297599	166968	Hs.657594	NM_152622	ENSG00000155545	MIER3	-	MIER family member 3	protein-coding	0.015235	0.408022	209(TGGCTCACCGTGTCCT,-,0.00),210(GGCTCACCGTGTCCTT,+,0.00),400(GGGACAAAGTGACCTT,+,0.00)
chunk0022_58_1	chr10	8380086	8380661	+	0	NA	Intergenic	Intergenic	-112068	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.006957	0.440972	
chunk0150_95_1	chr5	32428563	32428775	+	0	NA	intron (NM_016107, intron 2 of 19)	MER5C1|DNA|hAT-Charlie	16069	NM_016107	51663	Hs.435231	NM_016107	ENSG00000056097	ZFR	SPG71|ZFR1	zinc finger RNA binding protein	protein-coding	0.009434	0.436620	
chunk0195_207_1	chr8	96928367	96928846	+	0	NA	intron (NM_016134, intron 4 of 7)	intron (NM_016134, intron 4 of 7)	283379	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.008351	0.452083	
chunk0157_186_1	chr5	118755234	118755566	+	0	NA	Intergenic	Intergenic	159212	NR_104998	102467225	Hs.582523	NR_104998	ENSG00000249128	LINC02215	-	long intergenic non-protein coding RNA 2215	ncRNA	0.003012	0.330330	
chunk0023_230_1	chr10	26796222	26796703	+	0	NA	intron (NM_001178116, intron 3 of 11)	Tigger3a|DNA|TcMar-Tigger	64625	NM_001178123	10006	Hs.508148	NM_005470	ENSG00000136754	ABI1	ABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1	abl interactor 1	protein-coding	0.004158	0.360996	
chunk0031_296_1	chr10	128660393	128660645	+	0	NA	Intergenic	Intergenic	374569	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.011905	0.529644	
chunk0085_90_1	chr18	2560158	2560546	+	0	NA	intron (NM_001308401, intron 3 of 7)	intron (NM_001308401, intron 3 of 7)	11151	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.012887	0.326478	
chunk0153_303_1	chr5	73498202	73498529	+	0	NA	promoter-TSS (NM_001207)	promoter-TSS (NM_001207)	-60	NM_001037637	689	Hs.591768	NM_001207	ENSG00000145741	BTF3	BETA-NAC|BTF3a|BTF3b|NACB	basic transcription factor 3	protein-coding	0.073394	0.631098	
chunk0151_311_1	chr5	53351086	53351326	+	0	NA	Intergenic	Intergenic	-129228	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.008333	0.406639	
chunk0143_275_1	chr4	116674766	116675583	+	0	NA	Intergenic	Intergenic	375449	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.004896	0.300733	
chunk0141_259_1	chr4	85778848	85779606	+	0	NA	intron (NM_001042669, intron 1 of 7)	(GTTT)n|Simple_repeat|Simple_repeat	529	NM_001042669	83478	Hs.444229	NM_031305	ENSG00000138639	ARHGAP24	FILGAP|RC-GAP72|RCGAP72|p73|p73RhoGAP	Rho GTPase activating protein 24	protein-coding	0.003958	0.350461	462(ATGTACAGAATGTTCT,-,0.00),463(TGTACAGAATGTTCTT,+,0.00)
chunk0061_242_1	chr14	60862435	60862720	+	0	NA	intron (NM_002431, intron 6 of 7)	intron (NM_002431, intron 6 of 7)	118502	NM_020810	57570	Hs.380159	NM_020810	ENSG00000126814	TRMT5	COXPD26|KIAA1393|TRM5	tRNA methyltransferase 5	protein-coding	0.003509	0.370629	
chunk0186_8_1	chr7	135579895	135580504	+	0	NA	intron (NM_015135, intron 7 of 42)	intron (NM_015135, intron 7 of 42)	22285	NM_015135	23165	Hs.743250	NM_015135	ENSG00000155561	NUP205	C7orf14|NPHS13	nucleoporin 205	protein-coding	0.013136	0.345902	303(CAGAACATTTTGTTTT,-,0.00),304(AGAACATTTTGTTTTC,+,0.00)
chunk0162_178_1	chr6	3710284	3710824	+	0	NA	Intergenic	Intergenic	41458	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.012963	0.500924	
chunk0076_232_1	chr16	68884948	68885303	+	0	NA	intron (NM_024562, intron 7 of 17)	intron (NM_024562, intron 7 of 17)	41519	NM_024562	79613	Hs.13526	NM_024562	ENSG00000103047	TANGO6	TMCO7	transport and golgi organization 6 homolog	protein-coding	0.005634	0.365169	
chunk0071_98_1	chr15	81005801	81006271	+	0	NA	Intergenic	Intergenic	5082	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.002128	0.394904	
chunk0004_381_1	chr1	51837227	51837602	+	0	NA	intron (NM_002525, intron 3 of 32)	intron (NM_002525, intron 3 of 32)	-1012	NR_031580	100313892		NR_031580	ENSG00000283899	MIR761	hsa-mir-761	microRNA 761	ncRNA	0.002667	0.372340	
chunk0151_199_1	chr5	50655897	50656114	+	0	NA	Intergenic	Intergenic	-9894	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.009217	0.449541	
chunk0112_127_1	chr20	38501934	38502629	+	0	NA	intron (NM_020336, intron 5 of 29)	Tigger2b_Pri|DNA|TcMar-Tigger	-14282	NR_039605	100616190		NR_039605	ENSG00000275453	MIR548O2	-	microRNA 548o-2	ncRNA	0.002878	0.326149	188(TGGTACATACTGTACT,-,0.00),189(GGTACATACTGTACTA,+,0.00)
chunk0098_366_1	chr2	78295715	78296037	+	0	NA	Intergenic	Intergenic	-5145	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.000000	0.300310	
chunk0199_439_1	chr9	13970540	13970904	+	0	NA	Intergenic	MER70A|LTR|ERVL	42751	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.010989	0.479452	66(TAGAACATGATGTCCT,-,0.00),67(AGAACATGATGTCCTA,+,0.00)
chunk0059_402_1	chr14	37645560	37645806	+	0	NA	intron (NM_001310135, intron 3 of 32)	L2a|LINE|L2	50484	NM_001310135	319089	Hs.659936	NM_001007795	ENSG00000139865	TTC6	C14orf25|NCRNA00291	tetratricopeptide repeat domain 6	protein-coding	0.000000	0.457490	
chunk0101_197_1	chr2	129945530	129946026	+	0	NA	non-coding (NR_110285, exon 4 of 4)	non-coding (NR_110285, exon 4 of 4)	-11461	NR_026740	389033	Hs.380682	NR_026740	ENSG00000214100	PLAC9P1	-	placenta associated 9 pseudogene 1	pseudo	0.002016	0.414487	
chunk0133_52_1	chr3	166543184	166543804	+	0	NA	Intergenic	Intergenic	-706029	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.006452	0.392915	
chunk0081_273_1	chr17	43839740	43840120	+	0	NA	Intergenic	Intergenic	-6751	NR_003562	4356	Hs.396566	NM_001932	ENSG00000161647	MPP3	DLG3	membrane palmitoylated protein 3	protein-coding	0.013158	0.509186	
chunk0052_8_1	chr13	19071057	19071440	+	0	NA	Intergenic	Intergenic	62989	NR_026852	348021	Hs.314114	NR_026852	ENSG00000232685	LINC00442	-	long intergenic non-protein coding RNA 442	ncRNA	0.007833	0.604167	234(TGGCACAGCCTGTCCA,-,0.00),235(GGCACAGCCTGTCCAC,+,0.00)
chunk0178_383_1	chr7	40244357	40244933	+	0	NA	intron (NM_001193312, intron 7 of 12)	intron (NM_001193312, intron 7 of 12)	109669	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.012153	0.381282	
chunk0115_173_1	chr21	25574861	25575557	+	0	NA	TTS (NR_001458)	TTS (NR_001458)	1229	NR_030784	406947		NR_030784	ENSG00000283904	MIR155	MIRN155|miRNA155|mir-155	microRNA 155	ncRNA	0.005747	0.360115	
chunk0036_251_1	chr11	64553026	64553354	+	0	NA	Intergenic	Intergenic	-2411	NM_001307985	55867	Hs.220844	NM_018484	ENSG00000168065	SLC22A11	OAT4|hOAT4	solute carrier family 22 member 11	protein-coding	0.006098	0.455927	
chunk0161_38_1	chr5	165855894	165856597	+	0	NA	Intergenic	Intergenic	1070125	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004267	0.319602	
chunk0207_142_1	chr9	129460368	129460723	+	0	NA	Intergenic	CpG	-28115	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.087324	0.693820	
chunk0063_132_1	chr14	79419553	79420157	+	0	NA	intron (NM_138970, intron 1 of 5)	MIRb|SINE|MIR	140516	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.001656	0.429752	
chunk0019_64_1	chr1	224222405	224222700	+	0	NA	intron (NR_110668, intron 1 of 2)	intron (NR_110668, intron 1 of 2)	2939	NR_110668	101927164	Hs.710128	NR_110668	ENSG00000237101	LOC101927164	-	uncharacterized LOC101927164	ncRNA	0.006780	0.479730	
chunk0053_69_1	chr13	28186310	28186908	+	0	NA	intron (NM_175854, intron 4 of 18)	intron (NM_175854, intron 4 of 18)	-47435	NR_029383	100288730	Hs.123191	NR_029383		PAN3-AS1	-	PAN3 antisense RNA 1	ncRNA	0.005017	0.327212	470(CGGGCCACTGTGTTCC,-,0.00),471(GGGCCACTGTGTTCCA,+,0.00)
chunk0070_178_1	chr15	71669015	71669214	+	0	NA	intron (NM_001286429, intron 2 of 11)	L1ME4b|LINE|L1	22425	NR_120346	101929173	Hs.680593	NR_120346		THSD4-AS2	-	THSD4 antisense RNA 2	ncRNA	0.010050	0.320000	
chunk0108_459_1	chr2	238418263	238418620	+	0	NA	Intergenic	L2a|LINE|L2	-8544	NM_001040445	51665	Hs.516788	NM_016114	ENSG00000065802	ASB1	ASB-1	ankyrin repeat and SOCS box containing 1	protein-coding	0.011204	0.519553	73(TGGCACTCCCTGTGCC,-,0.00),74(GGCACTCCCTGTGCCT,+,0.00)
chunk0108_204_1	chr2	232745049	232745323	+	0	NA	intron (NM_001103146, intron 3 of 28)	intron (NM_001103146, intron 3 of 28)	10769	NR_103492	26058	Hs.565319	NM_015575	ENSG00000204120	GIGYF2	GYF2|PARK11|PERQ2|PERQ3|TNRC15	GRB10 interacting GYF protein 2	protein-coding	0.000000	0.414545	
chunk0157_260_1	chr5	119999497	119999742	+	0	NA	Intergenic	Intergenic	370060	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.004082	0.313008	
chunk0206_58_1	chr9	118246734	118247008	+	0	NA	Intergenic	Intergenic	542696	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.000000	0.436364	
chunk0024_370_1	chr10	44326415	44327046	+	0	NA	Intergenic	L2b|LINE|L2	33980	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.001585	0.455696	
chunk0045_393_1	chr12	52648403	52648602	+	0	NA	intron (NM_000423, intron 4 of 8)	intron (NM_000423, intron 4 of 8)	3673	NM_000423	3849	Hs.707	NM_000423	ENSG00000172867	KRT2	CK-2e|K2e|KRT2A|KRT2E|KRTE	keratin 2	protein-coding	0.010050	0.490000	
chunk0021_140_1	chr10	4058555	4059233	+	0	NA	intron (NR_120632, intron 1 of 3)	intron (NR_120632, intron 1 of 3)	7168	NR_120632	101927964	Hs.737041	NR_120632	ENSG00000236990	LOC101927964	-	uncharacterized LOC101927964	ncRNA	0.011799	0.375552	392(AGGAACAGTTTGTTTT,-,0.00),393(GGAACAGTTTGTTTTG,+,0.00)
chunk0082_331_1	chr17	59693471	59693727	+	0	NA	intron (NM_004859, intron 31 of 31)	intron (NM_004859, intron 31 of 31)	-13903	NM_030938	81671	Hs.444569	NM_030938	ENSG00000062716	VMP1	EPG3|TANGO5|TMEM49	vacuole membrane protein 1	protein-coding	0.003906	0.451362	
chunk0012_27_1	chr1	155001276	155001475	+	0	NA	Intergenic	CpG	-1255	NR_045515	51043	Hs.729279	NM_001252406	ENSG00000160685	ZBTB7B	CKROX|THPOK|ZBTB15|ZFP-67|ZFP67|ZNF857B|c-KROX|hcKROX	zinc finger and BTB domain containing 7B	protein-coding	0.050251	0.635000	
chunk0212_369_1	chrX	149863457	149863774	+	0	NA	intron (NR_109813, intron 2 of 2)	L1PA15|LINE|L1	-17526	NM_005364	4107	Hs.522803	NM_005364	ENSG00000156009	MAGEA8	CT1.8|MAGE8	MAGE family member A8	protein-coding	0.000000	0.317610	
chunk0139_279_1	chr4	57028898	57029097	+	0	NA	intron (NM_000938, intron 23 of 24)	L1MC5|LINE|L1	50357	NM_000938	5431	Hs.602757	NM_000938	ENSG00000047315	POLR2B	POL2RB|RPB2|hRPB140	RNA polymerase II subunit B	protein-coding	0.000000	0.365000	
chunk0007_215_1	chr1	81559647	81560596	+	0	NA	Intergenic	Intergenic	-2419	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.005269	0.352632	
chunk0047_270_1	chr12	73046773	73047174	+	0	NA	Intergenic	MIR|SINE|MIR	-112217	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.009975	0.308458	
chunk0200_424_1	chr9	28755664	28755863	+	0	NA	intron (NM_001258282, intron 2 of 6)	intron (NM_001258282, intron 2 of 6)	-36458	NM_152570	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.020101	0.395000	
chunk0164_105_1	chr6	20581644	20582208	+	0	NA	intron (NM_017774, intron 4 of 15)	intron (NM_017774, intron 4 of 15)	47469	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.001773	0.307965	
chunk0020_325_1	chr1	237864331	237864894	+	0	NA	intron (NR_027247, intron 2 of 11)	intron (NR_027247, intron 2 of 11)	2437	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.039076	0.576241	176(AAGGCCACTGTGTACT,-,0.00),177(AGGCCACTGTGTACTG,+,0.00)
chunk0206_154_1	chr9	121450201	121450726	+	0	NA	Intergenic	Intergenic	49564	NR_045211	2681	Hs.97469	NR_003191	ENSG00000204136	GGTA1P	GGTA|GGTA1|GLYT2|a1/3GTP	glycoprotein alpha-galactosyltransferase 1, pseudogene	pseudo	0.007619	0.446768	291(GAGTACAAACAGTCCT,-,0.00),292(AGTACAAACAGTCCTC,+,0.00)
chunk0019_455_1	chr1	231383142	231383675	+	0	NA	intron (NM_022051, intron 1 of 4)	intron (NM_022051, intron 1 of 4)	41636	NM_022051	54583	Hs.444450	NM_022051	ENSG00000135766	EGLN1	C1orf12|ECYT3|HALAH|HIF-PH2|HIFPH2|HPH-2|HPH2|PHD2|SM20|ZMYND6	egl-9 family hypoxia inducible factor 1	protein-coding	0.007505	0.387640	405(TAGAAGATTCTGTTCT,-,0.00),406(AGAAGATTCTGTTCTG,+,0.00)
chunk0143_218_1	chr4	113761580	113761931	+	0	NA	5' UTR (NM_001221, exon 1 of 19)	5' UTR (NM_001221, exon 1 of 19)	172	NM_001221	817	Hs.144114	NM_001221	ENSG00000145349	CAMK2D	CAMKD	calcium/calmodulin dependent protein kinase II delta	protein-coding	0.128205	0.735795	
chunk0042_314_1	chr12	8482129	8482718	+	0	NA	Intergenic	L1P2|LINE|L1	26428	NM_001007033	93978	Hs.591147	NM_001007033	ENSG00000205846	CLEC6A	CLEC4N|CLECSF10|dectin-2	C-type lectin domain containing 6A	protein-coding	0.005093	0.488136	
chunk0077_3_1	chr16	74485941	74486194	+	0	NA	intron (NR_027264, intron 8 of 26)	intron (NR_027264, intron 8 of 26)	-64597	NM_001011880	497190	Hs.454670	NM_001011880	ENSG00000140839	CLEC18B	MRCL2	C-type lectin domain family 18 member B	protein-coding	0.000000	0.401575	
chunk0146_148_1	chr4	159638358	159638894	+	0	NA	Intergenic	MIR|SINE|MIR	370780	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.003731	0.426443	
chunk0140_344_1	chr4	73930301	73930540	+	0	NA	Intergenic	Intergenic	51704	NM_002619	5196	Hs.81564	NM_002619	ENSG00000163737	PF4	CXCL4|PF-4|SCYB4	platelet factor 4	protein-coding	0.000000	0.425000	
chunk0048_456_1	chr12	88866217	88866573	+	0	NA	Intergenic	Intergenic	153297	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.005618	0.310924	
chunk0165_110_1	chr6	32554944	32555476	+	0	NA	intron (NR_001298, intron 2 of 5)	intron (NR_001298, intron 2 of 5)	4792	NR_001298	3128	Hs.723344	NR_001298	ENSG00000229391	HLA-DRB6	-	major histocompatibility complex, class II, DR beta 6 (pseudogene)	pseudo	0.015038	0.388368	291(AAGTACAGTGTGTATT,-,0.00)
chunk0043_302_1	chr12	22123499	22123827	+	0	NA	Intergenic	L3|LINE|CR1	77487	NM_018686	55907	Hs.311346	NM_018686	ENSG00000111726	CMAS	CSS	cytidine monophosphate N-acetylneuraminic acid synthetase	protein-coding	0.006098	0.419453	
chunk0202_197_1	chr9	75229851	75230339	+	0	NA	Intergenic	LTR18C|LTR|ERVL	141613	NM_012383	26578	Hs.494192	NM_012383	ENSG00000134996	OSTF1	OSF|SH3P2|bA235O14.1	osteoclast stimulating factor 1	protein-coding	0.006148	0.478528	
chunk0064_48_1	chr14	89750535	89750818	+	0	NA	Intergenic	Intergenic	-131526	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.014134	0.422535	
chunk0154_74_1	chr5	77485295	77485559	+	0	NA	intron (NM_018268, intron 2 of 12)	intron (NM_018268, intron 2 of 12)	7080	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.000000	0.366038	154(AGGCACATTTTGTTCT,-,0.00),155(GGCACATTTTGTTCTC,+,0.00)
chunk0187_284_1	chr7	155647595	155648196	+	0	NA	intron (NM_053043, intron 1 of 17)	intron (NM_053043, intron 1 of 17)	3386	NM_053043	155435	Hs.591815	NM_053043	ENSG00000184863	RBM33	PRR8	RNA binding motif protein 33	protein-coding	0.008319	0.378738	
chunk0131_157_1	chr3	146406221	146406623	+	0	NA	Intergenic	HERVS71-int|LTR|ERV1	62879	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.012438	0.454094	
chunk0089_332_1	chr18	65494330	65494759	+	0	NA	Intergenic	Intergenic	-255708	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.004662	0.302326	
chunk0111_369_1	chr20	33796577	33796915	+	0	NA	intron (NR_110623, intron 2 of 3)	intron (NR_110623, intron 2 of 3)	14353	NR_110623	101929746	Hs.504633	NR_110623	ENSG00000230753	ZNF341-AS1	-	ZNF341 antisense RNA 1	ncRNA	0.008876	0.542773	
chunk0036_6_1	chr11	58030576	58031156	+	0	NA	promoter-TSS (NM_001005186)	promoter-TSS (NM_001005186)	-87	NM_001005186	219952	Hs.690432	NM_001005186	ENSG00000279051	OR6Q1	OR11-226	olfactory receptor family 6 subfamily Q member 1 (gene/pseudogene)	protein-coding	0.003448	0.419966	
chunk0072_418_1	chr15	100967911	100968554	+	0	NA	intron (NM_024652, intron 2 of 33)	L1ME2z|LINE|L1	49017	NM_024652	79705	Hs.407918	NM_024652	ENSG00000154237	LRRK1	RIPK6|Roco1	leucine rich repeat kinase 1	protein-coding	0.004666	0.378882	
chunk0055_121_1	chr13	57401731	57402112	+	0	NA	Intergenic	Intergenic	-229734	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.002625	0.303665	
chunk0175_140_1	chr7	3519978	3520650	+	0	NA	intron (NM_152744, intron 1 of 44)	CR1_Mam|LINE|CR1	218866	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.002976	0.367013	353(AAGAACATCCTGTGCA,-,0.00),354(AGAACATCCTGTGCAG,+,0.00)
chunk0166_364_1	chr6	51473897	51474591	+	0	NA	Intergenic	Intergenic	-147626	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.011527	0.412950	
chunk0160_168_1	chr5	152638551	152639178	+	0	NA	intron (NR_109877, intron 4 of 4)	intron (NR_109877, intron 4 of 4)	-233585	NM_020167	56923	Hs.731911	NM_020167	ENSG00000132911	NMUR2	FM-4|FM4|NMU-R2|NMU2R|TGR-1|TGR1	neuromedin U receptor 2	protein-coding	0.003190	0.382166	269(TAGCACAGGATGCTCC,-,0.00),270(AGCACAGGATGCTCCA,+,0.00)
chunk0093_230_1	chr19	50511175	50511547	+	0	NA	promoter-TSS (NM_138334)	promoter-TSS (NM_138334)	-6	NM_001270639	126119	Hs.467151	NM_138334	ENSG00000161677	JOSD2	SBBI54	Josephin domain containing 2	protein-coding	0.123656	0.694370	
chunk0165_460_1	chr6	41091115	41091669	+	0	NA	intron (NM_021705, intron 5 of 8)	intron (NM_021705, intron 5 of 8)	-9642	NR_026938	221442	Hs.374076	NM_001010871	ENSG00000161912	ADCY10P1	-	ADCY10 pseudogene 1	pseudo	0.001805	0.405405	464(GAGCACAGATTGTTCA,-,0.00),465(AGCACAGATTGTTCAA,+,0.00)
chunk0212_270_1	chrX	139701711	139702190	+	0	NA	intron (NM_001171876, intron 1 of 28)	L2a|LINE|L2	6272	NM_001099855	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.008351	0.420833	258(TGGAACACAGAGTGCT,-,0.00),259(GGAACACAGAGTGCTT,+,0.00)
chunk0125_207_1	chr3	67374088	67374514	+	0	NA	TTS (NM_003848)	TTS (NM_003848)	148837	NR_036234	100422941		NR_036234	ENSG00000283298	MIR4272	-	microRNA 4272	ncRNA	0.004695	0.339578	
chunk0069_19_1	chr15	60386897	60387228	+	0	NA	intron (NM_004039, intron 1 of 12)	intron (NM_004039, intron 1 of 12)	10924	NM_001136015	302	Hs.511605	NM_004039	ENSG00000182718	ANXA2	ANX2|ANX2L4|CAL1H|HEL-S-270|LIP2|LPC2|LPC2D|P36|PAP-IV	annexin A2	protein-coding	0.012085	0.385542	
chunk0022_47_1	chr10	8137593	8138224	+	0	NA	Intergenic	Intergenic	83204	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.019017	0.482595	
chunk0176_101_1	chr7	11673670	11673869	+	0	NA	intron (NM_015204, intron 1 of 26)	L1PA17|LINE|L1	158429	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005025	0.540000	
chunk0175_52_1	chr7	1559142	1559363	+	0	NA	Intergenic	Intergenic	-2822	NM_001097620	202915	Hs.592174	NM_152689	ENSG00000164855	TMEM184A	SDMG1	transmembrane protein 184A	protein-coding	0.031674	0.657658	
chunk0132_3_1	chr3	154218573	154219189	+	0	NA	intron (NM_015595, intron 10 of 14)	MIR3|SINE|MIR	97521	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.004870	0.353323	
chunk0116_456_1	chr21	43880050	43880638	+	0	NA	intron (NM_020132, intron 1 of 9)	intron (NM_020132, intron 1 of 9)	15109	NM_020132	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.015306	0.558574	316(CTGGTCAGCCTGTTCT,-,0.00),317(TGGTCAGCCTGTTCTT,+,0.00)
chunk0130_9_1	chr3	128362247	128362553	+	0	NA	intron (NM_021937, intron 6 of 6)	intron (NM_021937, intron 6 of 6)	-101194	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.006536	0.485342	
chunk0100_72_1	chr2	106641924	106642220	+	0	NA	Intergenic	Intergenic	-173727	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.010135	0.474747	124(GGGTACTTTTTGTCCT,-,0.00),125(GGTACTTTTTGTCCTT,+,0.00)
chunk0082_118_1	chr17	55110575	55110905	+	0	NA	intron (NM_178509, intron 16 of 17)	MER58A|DNA|hAT-Charlie	141975	NM_178509	252983	Hs.35199	NM_178509	ENSG00000166263	STXBP4	Synip	syntaxin binding protein 4	protein-coding	0.006061	0.338369	
chunk0059_389_1	chr14	37517457	37517899	+	0	NA	intron (NM_001195296, intron 14 of 14)	L1MC5a|LINE|L1	77442	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.006787	0.349887	
chunk0145_55_1	chr4	145135825	145136240	+	0	NA	3' UTR (NM_001102653, exon 21 of 21)	3' UTR (NM_001102653, exon 21 of 21)	-37491	NM_001256708	10393	Hs.480876	NM_014885	ENSG00000164162	ANAPC10	APC10|DOC1	anaphase promoting complex subunit 10	protein-coding	0.004819	0.338942	
chunk0204_192_1	chr9	96582033	96582688	+	0	NA	intron (NM_003671, intron 1 of 12)	LTR10C|LTR|ERV1	-15439	NM_001077181	8555	Hs.40582	NM_003671	ENSG00000081377	CDC14B	CDC14B3|Cdc14B1|Cdc14B2|hCDC14B	cell division cycle 14B	protein-coding	0.010687	0.399390	
chunk0100_13_1	chr2	105040483	105041117	+	0	NA	intron (NM_182640, intron 1 of 10)	intron (NM_182640, intron 1 of 10)	-2304	NR_110603	102724691	Hs.606390	NR_110603	ENSG00000224509	LOC102724691	-	uncharacterized LOC102724691	ncRNA	0.003155	0.388976	
chunk0186_344_1	chr7	143395501	143395979	+	0	NA	intron (NM_005232, intron 11 of 17)	L2b|LINE|L2	-12073	NR_033897	285965	Hs.642649	NR_033897	ENSG00000229153	EPHA1-AS1	-	EPHA1 antisense RNA 1	ncRNA	0.025105	0.584551	
chunk0198_215_1	chr8	133882253	133882717	+	0	NA	Intergenic	Intergenic	-4011	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006466	0.421505	
chunk0180_148_1	chr7	58434497	58434697	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	984420	NM_001159279	441234	Hs.533121	NM_001159279	ENSG00000182111	ZNF716	-	zinc finger protein 716	protein-coding	0.015000	0.393035	
chunk0072_168_1	chr15	93201738	93202271	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-112790	NM_020211	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.011257	0.455056	
chunk0119_298_1	chr22	46443583	46444247	+	0	NA	intron (NM_014246, intron 2 of 34)	intron (NM_014246, intron 2 of 34)	93255	NM_014246	9620	Hs.252387	NM_014246	ENSG00000075275	CELSR1	ADGRC1|CDHF9|FMI2|HFMI2|ME2	cadherin EGF LAG seven-pass G-type receptor 1	protein-coding	0.027108	0.535338	
chunk0052_344_1	chr12	126529883	126530183	+	0	NA	Intergenic	L2c|LINE|L2	87552	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.003333	0.325581	
chunk0153_248_1	chr5	72586924	72587511	+	0	NA	intron (NR_105007, intron 1 of 2)	intron (NR_105007, intron 1 of 2)	30140	NR_105008	102503427	Hs.429280	NR_105008		LOC102503427	-	uncharacterized LOC102503427	ncRNA	0.000000	0.365646	
chunk0023_157_1	chr10	24263122	24263770	+	0	NA	intron (NM_019590, intron 2 of 20)	intron (NM_019590, intron 2 of 20)	-12239	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.013889	0.436055	
chunk0140_401_1	chr4	75514587	75515106	+	0	NA	promoter-TSS (NM_001278538)	promoter-TSS (NM_001278538)	402	NM_144721	152815	Hs.479971	NM_144721	ENSG00000174796	THAP6	-	THAP domain containing 6	protein-coding	0.050096	0.553846	
chunk0163_201_1	chr6	11849295	11849501	+	0	NA	Intergenic	Intergenic	-70351	NM_001143948	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.009709	0.463768	
chunk0161_213_1	chr5	170849320	170849715	+	0	NA	Intergenic	L1MC5a|LINE|L1	-12365	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.002532	0.416667	
chunk0088_126_1	chr18	45748763	45749148	+	0	NA	intron (NM_001308278, intron 8 of 8)	intron (NM_001308278, intron 8 of 8)	22002	NM_001146037	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.002597	0.474093	
chunk0120_294_1	chr3	9893159	9893375	+	0	NA	exon (NM_032492, exon 2 of 2)	exon (NM_032492, exon 2 of 2)	2680	NM_032492	84522	Hs.24054	NM_032492	ENSG00000171135	JAGN1	GL009|SCN6	jagunal homolog 1	protein-coding	0.018519	0.506912	
chunk0137_418_1	chr4	28119090	28119519	+	0	NA	Intergenic	Intergenic	-700278	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.006993	0.337209	163(CAGAACATTATGCTCT,-,0.00),164(AGAACATTATGCTCTG,+,0.00)
chunk0097_204_1	chr2	51079861	51080383	+	0	NA	Intergenic	Intergenic	-47586	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.007663	0.313576	
chunk0009_387_1	chr1	110000261	110000484	+	0	NA	promoter-TSS (NM_001242674)	promoter-TSS (NM_001242674)	-555	NM_001242674	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.000000	0.397321	
chunk0010_26_1	chr1	112449342	112449984	+	0	NA	intron (NM_018704, intron 4 of 5)	intron (NM_018704, intron 4 of 5)	12170	NR_036210	100422976		NR_036210	ENSG00000283296	MIR4256	-	microRNA 4256	ncRNA	0.004673	0.359253	
chunk0071_207_1	chr15	84022558	84022943	+	0	NA	intron (NM_207517, intron 26 of 29)	L2b|LINE|L2	-57437	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.002597	0.404145	
chunk0096_197_1	chr2	30184996	30185558	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	38393	NM_016061	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.007117	0.385435	280(GGGAACATTCCGTCCA,-,0.00),281(GGAACATTCCGTCCAG,+,0.00)
chunk0172_289_1	chr6	137823042	137823509	+	0	NA	TTS (NR_049793)	TTS (NR_049793)	-43913	NM_001270508	7128	Hs.211600	NM_006290	ENSG00000118503	TNFAIP3	A20|AISBL|OTUD7C|TNFA1P2	TNF alpha induced protein 3	protein-coding	0.006424	0.282051	
chunk0036_349_1	chr11	66843151	66843388	+	0	NA	promoter-TSS (NM_005133)	promoter-TSS (NM_005133)	-143	NM_001032279	9986	Hs.654972	NM_005133	ENSG00000173653	RCE1	FACE2|RCE1A|RCE1B	Ras converting CAAX endopeptidase 1	protein-coding	0.105485	0.710084	
chunk0210_79_1	chrX	70174710	70175297	+	0	NA	Intergenic	Intergenic	-2480	NM_198512	347516	Hs.454355	NM_198512	ENSG00000184210	DGAT2L6	DC3	diacylglycerol O-acyltransferase 2 like 6	protein-coding	0.006814	0.506803	
chunk0168_427_1	chr6	95543774	95544253	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	33438	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.004175	0.404167	243(CAGGACAATTTGTTCT,-,0.00),244(AGGACAATTTGTTCTT,+,0.00)
chunk0092_154_1	chr19	29515012	29515211	+	0	NA	intron (NR_040029, intron 1 of 9)	intron (NR_040029, intron 1 of 9)	10641	NR_040029	284395	Hs.631601	NR_040029	ENSG00000264515	LOC284395	-	uncharacterized LOC284395	ncRNA	0.020101	0.525000	
chunk0122_14_1	chr3	27366140	27366611	+	0	NA	intron (NM_199347, intron 2 of 24)	intron (NM_199347, intron 2 of 24)	3085	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.002123	0.451271	
chunk0025_243_1	chr10	54487635	54488085	+	0	NA	intron (NM_001142773, intron 2 of 31)	intron (NM_001142773, intron 2 of 31)	120097	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.004444	0.274945	
chunk0179_244_1	chr7	48173084	48173765	+	0	NA	intron (NM_152701, intron 1 of 61)	intron (NM_152701, intron 1 of 61)	1964	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.001468	0.368035	
chunk0200_196_1	chr9	20071764	20072267	+	0	NA	Intergenic	MER21A|LTR|ERVL	-284996	NM_001193288	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.011928	0.464286	
chunk0083_39_1	chr17	63447239	63447498	+	0	NA	Intergenic	Intergenic	-1007	NM_001915	1534	Hs.355264	NM_001915	ENSG00000008283	CYB561	CYB561A1|FRRS2|ORTHYP2	cytochrome b561	protein-coding	0.046332	0.615385	
chunk0062_380_1	chr14	74396502	74396852	+	0	NA	Intergenic	MIR|SINE|MIR	29425	NM_001105579	646658	Hs.12400	NM_001105579	ENSG00000183379	SYNDIG1L	CAPUCIN|DSPC1|IFITMD4|TMEM90A	synapse differentiation inducing 1 like	protein-coding	0.005714	0.415954	
chunk0014_119_1	chr1	177419858	177420532	+	0	NA	Intergenic	Intergenic	68609	NR_126001	102724661	Hs.146628	NR_126001		LINC01645	-	long intergenic non-protein coding RNA 1645	ncRNA	0.002967	0.339259	
chunk0003_323_1	chr1	38289116	38289635	+	0	NA	Intergenic	Intergenic	-74608	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.003854	0.457692	
chunk0095_229_1	chr2	18980699	18981096	+	0	NA	Intergenic	Intergenic	-367532	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.012594	0.404523	
chunk0157_79_1	chr5	116471808	116472525	+	0	NA	TTS (NR_109879)	TTS (NR_109879)	24668	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.004184	0.344011	
chunk0060_289_1	chr14	50554474	50554920	+	0	NA	intron (NM_001127713, intron 1 of 13)	LTR57|LTR|ERVL	-5328	NM_015915	51062	Hs.584905	NM_015915	ENSG00000198513	ATL1	AD-FSP|FSP1|GBP3|HSN1D|SPG3|SPG3A|atlastin1	atlastin GTPase 1	protein-coding	0.006726	0.465324	
chunk0133_140_1	chr3	169268297	169268844	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-120836	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.007313	0.366788	
chunk0095_308_1	chr2	20394997	20395366	+	0	NA	Intergenic	Intergenic	-44331	NM_015317	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.013550	0.429730	127(TGGAACAGCTTGTACT,-,0.00),128(GGAACAGCTTGTACTG,+,0.00)
chunk0169_214_1	chr6	103180658	103181280	+	0	NA	Intergenic	L1MD3|LINE|L1	1678950	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.004823	0.272873	
chunk0209_309_1	chrX	49824739	49825601	+	0	NA	Intergenic	L1MEf|LINE|L1	-4133	NM_007003	9506	Hs.441038	NM_007003	ENSG00000101951	PAGE4	CT16.7|GAGE-9|GAGEC1|JM-27|JM27|PAGE-1|PAGE-4	PAGE family member 4	protein-coding	0.003480	0.366165	489(CAGCACAGAGAGTCCA,-,0.00),490(AGCACAGAGAGTCCAA,+,0.00),836(AAGGACAGAATCTTCC,-,0.00),837(AGGACAGAATCTTCCT,+,0.00)
chunk0047_369_1	chr12	75128991	75129842	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	80332	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.008226	0.389671	441(AAGTACACATTGTGCT,-,0.00),442(AGTACACATTGTGCTT,+,0.00)
chunk0114_122_1	chr21	9676293	9676759	+	0	NA	Intergenic	Intergenic	144535	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.023605	0.413276	
chunk0085_170_1	chr18	4129854	4130536	+	0	NA	intron (NM_004746, intron 2 of 12)	intron (NM_004746, intron 2 of 12)	-134407	NR_036489	284215	Hs.647594	NR_036489	ENSG00000261520	DLGAP1-AS5	-	DLGAP1 antisense RNA 5	ncRNA	0.004399	0.338214	
chunk0078_194_1	chr17	5211404	5211877	+	0	NA	intron (NM_207103, intron 4 of 4)	intron (NM_207103, intron 4 of 4)	19556	NR_034082	100130950	Hs.668646	NR_034082		LOC100130950	-	uncharacterized LOC100130950	ncRNA	0.014799	0.464135	
chunk0117_435_1	chr21	46284005	46284316	+	0	NA	exon (NM_003906, exon 1 of 28)	exon (NM_003906, exon 1 of 28)	1234	NM_003906	8888	Hs.389037	NM_003906	ENSG00000160294	MCM3AP	GANP|MAP80|PNRIID|SAC3	minichromosome maintenance complex component 3 associated protein	protein-coding	0.028939	0.471154	
chunk0136_210_1	chr4	7279514	7280067	+	0	NA	intron (NM_020777, intron 1 of 26)	intron (NM_020777, intron 1 of 26)	-30660	NR_039961	100616471		NR_039961	ENSG00000264658	MIR4798	-	microRNA 4798	ncRNA	0.023508	0.478339	245(GGGAACATTTTGTACC,-,0.00),246(GGAACATTTTGTACCT,+,0.00)
chunk0074_167_1	chr16	23473987	23474479	+	0	NA	intron (NM_015044, intron 14 of 16)	intron (NM_015044, intron 14 of 16)	-21042	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.012195	0.450304	
chunk0066_159_1	chr15	32109334	32109575	+	0	NA	intron (NR_046324, intron 3 of 7)	MER41A|LTR|ERV1	78971	NR_046324	1139	Hs.511772	NM_000746	ENSG00000175344	CHRNA7	CHRNA7-2|NACHRA7	cholinergic receptor nicotinic alpha 7 subunit	protein-coding	0.004149	0.487603	
chunk0146_142_1	chr4	159541860	159542059	+	0	NA	Intergenic	Intergenic	274113	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.000000	0.340000	
chunk0142_204_1	chr4	97405239	97405438	+	0	NA	intron (NR_102713, intron 1 of 5)	intron (NR_102713, intron 1 of 5)	38412	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.015075	0.370000	
chunk0187_196_1	chr7	151754199	151754406	+	0	NA	intron (NM_001040633, intron 3 of 15)	intron (NM_001040633, intron 3 of 15)	-17988	NM_001304527	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.028986	0.557692	
chunk0200_352_1	chr9	25452661	25453258	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	225899	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.008375	0.374582	
chunk0043_229_1	chr12	19983157	19983356	+	0	NA	Intergenic	Intergenic	-31429	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.005025	0.360000	
chunk0128_334_1	chr3	112064097	112064403	+	0	NA	intron (NR_026734, intron 11 of 16)	intron (NR_026734, intron 11 of 16)	-22085	NM_024616	79669	Hs.434247	NM_024616	ENSG00000114529	C3orf52	TTMP	chromosome 3 open reading frame 52	protein-coding	0.013072	0.410423	
chunk0117_133_1	chr22	19277035	19277381	+	0	NA	intron (NM_001835, intron 1 of 31)	MIRb|SINE|MIR	14508	NM_001835	8218	Hs.368266	NM_001835	ENSG00000070371	CLTCL1	CHC22|CLH22|CLTCL|CLTD	clathrin heavy chain like 1	protein-coding	0.005780	0.429395	
chunk0060_429_1	chr14	54285032	54285283	+	0	NA	Intergenic	MIR|SINE|MIR	-111798	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.019920	0.496032	
chunk0175_109_1	chr7	3218642	3219076	+	0	NA	Intergenic	Intergenic	-60286	NR_126024	100129603	Hs.652997	NR_126024		LOC100129603	-	uncharacterized LOC100129603	ncRNA	0.013825	0.395402	
chunk0077_430_1	chr16	85524367	85524924	+	0	NA	Intergenic	Intergenic	-86778	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.026930	0.629032	
chunk0169_171_1	chr6	102095347	102096021	+	0	NA	Intergenic	Intergenic	696699	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.002967	0.311111	
chunk0010_385_1	chr1	119347062	119347411	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-21540	NM_001005783	51179	Hs.659767	NM_016527	ENSG00000116882	HAO2	GIG16|HAOX2	hydroxyacid oxidase 2	protein-coding	0.005731	0.288571	
chunk0193_184_1	chr8	75178995	75179209	+	0	NA	Intergenic	L1PA16|LINE|L1	99379	NR_103848	101805492	Hs.571424	NR_103848		CASC9	ESCCAL-1|ESSCAL1|LINC00981|linc-JPH1	cancer susceptibility 9	ncRNA	0.004673	0.516279	
chunk0109_91_1	chr20	2105460	2105791	+	0	NA	intron (NM_080836, intron 2 of 3)	MIR|SINE|MIR	3743	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.000000	0.439759	
chunk0067_181_1	chr15	44448076	44448275	+	0	NA	intron (NM_016396, intron 1 of 12)	intron (NM_016396, intron 1 of 12)	20794	NM_016396	51496	Hs.497967	NM_016396	ENSG00000137770	CTDSPL2	HSPC058|HSPC129	CTD small phosphatase like 2	protein-coding	0.020101	0.615000	
chunk0126_59_1	chr3	74343879	74344097	+	0	NA	intron (NM_020872, intron 10 of 21)	intron (NM_020872, intron 10 of 21)	177152	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.000000	0.365297	
chunk0009_34_1	chr1	100322830	100323350	+	0	NA	Intergenic	Intergenic	-29377	NM_033313	8556	Hs.127411	NM_003672	ENSG00000079335	CDC14A	DFNB105|DFNB32|DFNB35|cdc14|hCDC14	cell division cycle 14A	protein-coding	0.001923	0.316699	
chunk0073_404_1	chr16	17247421	17247642	+	0	NA	intron (NM_022166, intron 3 of 11)	intron (NM_022166, intron 3 of 11)	223350	NM_022166	64131	Hs.22907	NM_022166	ENSG00000103489	XYLT1	DBQD2|PXYLT1|XT-I|XT1|XTI|XYLTI|xylT-I	xylosyltransferase 1	protein-coding	0.018100	0.481982	
chunk0071_275_1	chr15	85705242	85705441	+	0	NA	intron (NM_007200, intron 17 of 36)	intron (NM_007200, intron 17 of 36)	53384	NR_120366	101929679	Hs.513112	NR_120366		LOC101929679	-	uncharacterized LOC101929679	ncRNA	0.000000	0.400000	
chunk0170_442_1	chr6	119201342	119202037	+	0	NA	intron (NM_005907, intron 7 of 12)	Tigger3b|DNA|TcMar-Tigger	-52496	NM_001288576	79632	Hs.443789	NM_024581	ENSG00000111879	FAM184A	C6orf60	family with sequence similarity 184 member A	protein-coding	0.005755	0.354885	
chunk0188_385_1	chr8	18445153	18445427	+	0	NA	Intergenic	L1MC1|LINE|L1	54045	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.007299	0.363636	119(CGGAACATACTGTTAC,-,0.00),120(GGAACATACTGTTACT,+,0.00)
chunk0031_43_1	chr10	122374223	122374696	+	0	NA	promoter-TSS (NM_001001974)	promoter-TSS (NM_001001974)	-119	NM_001001974	59338	Hs.643512	NM_021622	ENSG00000107679	PLEKHA1	TAPP1	pleckstrin homology domain containing A1	protein-coding	0.093023	0.611814	
chunk0163_350_1	chr6	15462798	15463154	+	0	NA	intron (NM_001267040, intron 4 of 17)	intron (NM_001267040, intron 4 of 17)	200082	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.008427	0.358543	
chunk0137_162_1	chr4	16054852	16055221	+	0	NA	intron (NM_001145847, intron 2 of 26)	intron (NM_001145847, intron 2 of 26)	21082	NM_001145851	8842	Hs.614734	NM_006017	ENSG00000007062	PROM1	AC133|CD133|CORD12|MCDR2|MSTP061|PROML1|RP41|STGD4	prominin 1	protein-coding	0.005420	0.410811	
chunk0203_410_1	chr9	90842212	90842511	+	0	NA	intron (NM_001174167, intron 1 of 13)	(TG)n|Simple_repeat|Simple_repeat	14941	NM_001174167	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.020067	0.466667	
chunk0061_316_1	chr14	62683890	62684461	+	0	NA	Intergenic	Intergenic	361063	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.008757	0.330420	
chunk0113_23_1	chr20	49625598	49626120	+	0	NA	Intergenic	Intergenic	-57689	NM_000961	5740	Hs.302085	NM_000961	ENSG00000124212	PTGIS	CYP8|CYP8A1|PGIS|PTGI	prostaglandin I2 synthase	protein-coding	0.024904	0.474187	
chunk0205_99_1	chr9	107455389	107456228	+	0	NA	intron (NR_121581, intron 1 of 7)	intron (NR_121581, intron 1 of 7)	10777	NR_121581	101928720	Hs.125496	NR_121581		LINC01509	PRCAT37	long intergenic non-protein coding RNA 1509	ncRNA	0.008343	0.402381	520(CGGAACTCAGTGTTTT,-,0.00)
chunk0069_441_1	chr15	68488135	68488760	+	0	NA	Intergenic	Intergenic	-56294	NM_001004439	22801	Hs.436416	NM_012211	ENSG00000137809	ITGA11	HsT18964	integrin subunit alpha 11	protein-coding	0.008000	0.431310	
chunk0192_369_1	chr8	68311960	68312211	+	0	NA	intron (NR_038877, intron 1 of 2)	MER58A|DNA|hAT-Charlie	-18637	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.000000	0.404762	
chunk0003_16_1	chr1	28901835	28902127	+	0	NA	intron (NM_001166007, intron 1 of 17)	L2a|LINE|L2	-12595	NM_001166006	2035	Hs.175437	NM_004437	ENSG00000159023	EPB41	4.1R|EL1|HE	erythrocyte membrane protein band 4.1	protein-coding	0.010274	0.368601	
chunk0125_346_1	chr3	71141308	71141779	+	0	NA	intron (NM_032682, intron 6 of 20)	intron (NM_032682, intron 6 of 20)	-10602	NM_001244815	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.010616	0.423729	
chunk0076_238_1	chr16	69087077	69087539	+	0	NA	Intergenic	Intergenic	-18256	NM_001199280	3038	Hs.592069	NM_005329	ENSG00000103044	HAS3	-	hyaluronan synthase 3	protein-coding	0.010823	0.524838	
chunk0058_72_1	chr14	21073088	21073287	+	0	NA	exon (NM_018071, exon 2 of 24)	exon (NM_018071, exon 2 of 24)	-2315	NM_001282211	57447	Hs.525205	NM_016250	ENSG00000165795	NDRG2	SYLD	NDRG family member 2	protein-coding	0.020101	0.595000	
chunk0122_187_1	chr3	32722015	32722528	+	0	NA	intron (NM_001256741, intron 8 of 17)	intron (NM_001256741, intron 8 of 17)	26730	NM_001256742	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.003899	0.326848	
chunk0174_446_1	chr6	166309182	166309592	+	0	NA	Intergenic	Intergenic	-1004	NM_175922	285800	Hs.731862	NM_175922	ENSG00000176381	PRR18	-	proline rich 18	protein-coding	0.014634	0.540146	175(CAGGACAGCATGGCCC,-,0.00),176(AGGACAGCATGGCCCT,+,0.00)
chunk0096_221_1	chr2	30589311	30589989	+	0	NA	intron (NM_001304446, intron 5 of 5)	intron (NM_001304446, intron 5 of 5)	142424	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.004425	0.350515	329(GTGAACTGAATGTACT,-,0.00),330(TGAACTGAATGTACTT,+,0.00)
chunk0054_25_1	chr13	40770927	40771466	+	0	NA	promoter-TSS (NM_005830)	promoter-TSS (NM_005830)	15	NM_005830	10240	Hs.596607	NM_005830	ENSG00000102738	MRPS31	IMOGN38|MRP-S31|S31mt	mitochondrial ribosomal protein S31	protein-coding	0.089054	0.631481	
chunk0125_275_1	chr3	69424811	69425339	+	0	NA	Intergenic	Intergenic	-38771	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.005682	0.353497	
chunk0134_33_1	chr3	175608308	175608533	+	0	NA	intron (NM_207015, intron 10 of 13)	UCON1|Unknown|Unknown	167913	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.008889	0.331858	106(CTGCACAATATGTTCC,-,0.00),107(TGCACAATATGTTCCG,+,0.00)
chunk0107_305_1	chr2	219160054	219160378	+	0	NA	intron (NM_024782, intron 1 of 7)	CpG	649	NM_024782	79840	Hs.225988	NM_024782	ENSG00000187736	NHEJ1	XLF	non-homologous end joining factor 1	protein-coding	0.058642	0.618462	
chunk0070_172_1	chr15	71609839	71610574	+	0	NA	intron (NM_001286429, intron 1 of 11)	intron (NM_001286429, intron 1 of 11)	63004	NM_001286429	79875	Hs.387057	NM_024817	ENSG00000187720	THSD4	ADAMTSL-6|ADAMTSL6|FVSY9334|PRO34005	thrombospondin type 1 domain containing 4	protein-coding	0.008163	0.437500	678(AGAAACAGTCTGTCCT,-,0.00),679(GAAACAGTCTGTCCTG,+,0.00)
chunk0022_82_1	chr10	8951326	8951992	+	0	NA	Intergenic	Intergenic	53670	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.009009	0.326837	461(GAGTACATACTGTACA,-,0.00),462(AGTACATACTGTACAG,+,0.00)
chunk0045_230_1	chr12	48193513	48194052	+	0	NA	Intergenic	L2c|LINE|L2	9510	NM_001004134	121275	Hs.446790	NM_001004134	ENSG00000172640	OR10AD1	OR10AD1P|OR12-1	olfactory receptor family 10 subfamily AD member 1	protein-coding	0.003711	0.392593	343(TGGGACTGAGTGTTCT,-,0.00),344(GGGACTGAGTGTTCTT,+,0.00)
chunk0185_382_1	chr7	133254610	133254809	+	0	NA	intron (NM_001037126, intron 1 of 9)	intron (NM_001037126, intron 1 of 9)	1642	NM_001037126	60412	Hs.321273	NM_021807	ENSG00000131558	EXOC4	SEC8|SEC8L1|Sec8p	exocyst complex component 4	protein-coding	0.005025	0.370000	
chunk0204_356_1	chr9	101663445	101664053	+	0	NA	intron (NM_133445, intron 3 of 8)	intron (NM_133445, intron 3 of 8)	-68748	NM_147180	5535	Hs.151167	NM_147180	ENSG00000188386	PPP3R2	PPP3RL	protein phosphatase 3 regulatory subunit B, beta	protein-coding	0.003289	0.357964	586(GTGAACTTTATGTTCT,-,0.00),587(TGAACTTTATGTTCTG,+,0.00)
chunk0063_138_1	chr14	79481440	79481787	+	0	NA	intron (NR_073547, intron 15 of 20)	Tigger3a|DNA|TcMar-Tigger	202274	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.005764	0.399425	54(CTGCACAGCGTGTTCC,-,0.00),55(TGCACAGCGTGTTCCT,+,0.00)
chunk0008_314_1	chr1	95179344	95179596	+	0	NA	intron (NM_001199691, intron 6 of 7)	MER58A|DNA|hAT-Charlie	54512	NR_125949	101928118	Hs.656443	NR_125948	ENSG00000226026	LOC101928118	-	uncharacterized LOC101928118	ncRNA	0.003968	0.446640	
chunk0123_60_1	chr3	41215367	41215657	+	0	NA	intron (NM_001098209, intron 1 of 15)	L2b|LINE|L2	16061	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.006897	0.323024	135(TAGCACATTCAGTTCA,-,0.00),136(AGCACATTCAGTTCAT,+,0.00)
chunk0164_416_1	chr6	27076049	27076544	+	0	NA	Intergenic	L1MEd|LINE|L1	-55990	NR_026776	100270746	Hs.590428	NR_026776		LOC100270746	-	uncharacterized LOC100270746	ncRNA	0.004040	0.316532	
chunk0149_420_1	chr5	29509031	29509620	+	0	NA	Intergenic	Intergenic	-113349	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.005093	0.362712	303(CTGCACTTAGTGTTCC,-,0.00),304(TGCACTTAGTGTTCCC,+,0.00)
chunk0184_146_1	chr7	115987570	115987914	+	0	NA	intron (NM_012252, intron 1 of 7)	L2b|LINE|L2	-19429	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.000000	0.350725	
chunk0011_58_1	chr1	143269292	143269491	+	0	NA	Intergenic	Intergenic	153201	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.050251	0.375000	
chunk0015_145_1	chr1	186230172	186230438	+	0	NA	Intergenic	Intergenic	-65968	NM_005807	10216	Hs.647723	NM_005807	ENSG00000116690	PRG4	CACP|HAPO|JCAP|MSF|SZP	proteoglycan 4	protein-coding	0.007519	0.419476	
chunk0187_424_1	chr7	158601522	158602179	+	0	NA	Intergenic	MIR|SINE|MIR	10234	NR_049893	100847032		NR_049893	ENSG00000265598	MIR5707	-	microRNA 5707	ncRNA	0.016743	0.465046	
chunk0209_340_1	chrX	51523167	51523863	+	0	NA	Intergenic	L1MC4|LINE|L1	-16074	NR_110654	102723426	Hs.584513	NR_110654		LINC01496	-	long intergenic non-protein coding RNA 1496	ncRNA	0.005747	0.394548	
chunk0181_376_1	chr7	88868661	88868860	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	-73043	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.000000	0.355000	
chunk0133_109_1	chr3	168040038	168040326	+	0	NA	intron (NM_001308155, intron 6 of 14)	intron (NM_001308155, intron 6 of 14)	55743	NM_014498	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.003472	0.370242	
chunk0064_22_1	chr14	89355508	89355886	+	0	NA	intron (NM_005197, intron 2 of 5)	MER112|DNA|hAT-Charlie	61413	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.010582	0.403694	
chunk0181_367_1	chr7	88746154	88746416	+	0	NA	Intergenic	Intergenic	-13083	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.007634	0.319392	
chunk0114_128_1	chr21	9818995	9819275	+	0	NA	intron (NR_038377, intron 1 of 5)	SST1|Satellite|centr	1926	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.035714	0.533808	
chunk0068_75_1	chr15	51939578	51939924	+	0	NA	intron (NM_138792, intron 11 of 11)	intron (NM_138792, intron 11 of 11)	-15631	NR_109775	100422556	Hs.664788	NR_109775		LOC100422556	-	LEO1 homolog, Paf1/RNA polymerase II complex component pseudogene	pseudo	0.005780	0.426513	249(TGGTACAGCCTGTCCT,-,0.00),250(GGTACAGCCTGTCCTA,+,0.00)
chunk0195_218_1	chr8	97064818	97065283	+	0	NA	intron (NM_016134, intron 6 of 7)	MIRc|SINE|MIR	212898	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.008602	0.422747	
chunk0069_304_1	chr15	65551249	65551495	+	0	NA	intron (NM_016395, intron 1 of 10)	intron (NM_016395, intron 1 of 10)	20883	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.004065	0.437247	
chunk0181_245_1	chr7	85342631	85343404	+	0	NA	Intergenic	Intergenic	-221086	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.000000	0.348837	477(TAGGACACTGTGTTCT,-,0.00),478(AGGACACTGTGTTCTG,+,0.00)
chunk0095_302_1	chr2	20333020	20333495	+	0	NA	intron (NM_001282752, intron 1 of 19)	AluJr|SINE|Alu	-5871	NM_001282790	23369	Hs.467824	NM_015317	ENSG00000055917	PUM2	PUMH2|PUML2	pumilio RNA binding family member 2	protein-coding	0.006316	0.392857	
chunk0164_166_1	chr6	21808223	21808926	+	0	NA	intron (NR_015410, intron 4 of 11)	intron (NR_015410, intron 4 of 11)	142130	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.019915	0.455966	
chunk0036_300_1	chr11	65890826	65891145	+	0	NA	exon (NM_006848, exon 1 of 1)	exon (NM_006848, exon 1 of 1)	581	NM_006848	11007	Hs.66713	NM_006848	ENSG00000175602	CCDC85B	DIPA	coiled-coil domain containing 85B	protein-coding	0.115987	0.718750	
chunk0164_403_1	chr6	26537396	26537876	+	0	NA	promoter-TSS (NM_006353)	promoter-TSS (NM_006353)	-708	NM_006353	10473	Hs.236774	NM_006353	ENSG00000182952	HMGN4	HMG17L3|NHC	high mobility group nucleosomal binding domain 4	protein-coding	0.056250	0.507277	
chunk0112_291_1	chr20	43968941	43969328	+	0	NA	intron (NM_032883, intron 2 of 9)	intron (NM_032883, intron 2 of 9)	23238	NM_001098798	84969	Hs.26608	NM_032883	ENSG00000124191	TOX2	C20orf100|GCX-1|GCX1|dJ1108D11.2|dJ495O3.1	TOX high mobility group box family member 2	protein-coding	0.015504	0.458763	361(GTGCACACGGTGTACA,-,0.00),362(TGCACACGGTGTACAT,+,0.00)
chunk0155_339_1	chr5	96958326	96958900	+	0	NA	5' UTR (NM_175920, exon 1 of 18)	5' UTR (NM_175920, exon 1 of 18)	161	NM_175920	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.013937	0.420870	327(AGGGCTGTGTGTTCCT,+,0.00)
chunk0026_353_1	chr10	68837610	68838174	+	0	NA	intron (NM_001130159, intron 1 of 3)	MIRc|SINE|MIR	10355	NM_001130159	219736	Hs.37636	NM_152709	ENSG00000165730	STOX1	C10orf24	storkhead box 1	protein-coding	0.008865	0.447788	
chunk0051_5_1	chr12	111219111	111219541	+	0	NA	intron (NM_015267, intron 3 of 21)	intron (NM_015267, intron 3 of 21)	-84816	NR_106818	102465455		NR_106818	ENSG00000273700	MIR6760	hsa-mir-6760	microRNA 6760	ncRNA	0.002326	0.385151	232(AGGAACTTTGTGTTCC,-,0.00),233(GGAACTTTGTGTTCCT,+,0.00)
chunk0101_221_1	chr2	130852144	130852361	+	0	NA	Intergenic	L2b|LINE|L2	-64399	NM_015320	50649	Hs.469935	NM_015320	ENSG00000136002	ARHGEF4	ASEF|ASEF1|GEF4|SMIM39|STM6	Rho guanine nucleotide exchange factor 4	protein-coding	0.023041	0.623853	
chunk0031_60_1	chr10	122827495	122827840	+	0	NA	Intergenic	Intergenic	18508	NM_022034	50624	Hs.647182	NM_022034	ENSG00000138161	CUZD1	ERG-1|ERG1|ITMAP1|UO-44	CUB and zona pellucida like domains 1	protein-coding	0.005797	0.433526	
chunk0190_79_1	chr8	29976776	29976975	+	0	NA	Intergenic	Intergenic	-19527	NR_036104	100422876		NR_036104	ENSG00000264788	MIR3148	mir-3148	microRNA 3148	ncRNA	0.015075	0.445000	
chunk0027_70_1	chr10	73175606	73175966	+	0	NA	intron (NM_173348, intron 2 of 13)	MIRb|SINE|MIR	7667	NM_173348	317662	Hs.408577	NM_173348	ENSG00000138286	FAM149B1	KIAA0974	family with sequence similarity 149 member B1	protein-coding	0.002778	0.365651	
chunk0005_299_1	chr1	60350411	60351043	+	0	NA	Intergenic	L2a|LINE|L2	-276957	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.001582	0.314376	
chunk0093_393_1	chr19	56725013	56725232	+	0	NA	Intergenic	LTR8A|LTR|ERV1	-40200	NR_110744	101929059	Hs.607132	NR_110744	ENSG00000286125	ZIM2-AS1	ZIM2as	ZIM2 antisense RNA 1	ncRNA	0.004566	0.404545	
chunk0185_409_1	chr7	134078909	134079366	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-48215	NM_144648	136332	Hs.149774	NM_144648	ENSG00000155530	LRGUK	CFAP246	leucine rich repeats and guanylate kinase domain containing	protein-coding	0.006565	0.475983	305(AAGCACTCTCTGTCCC,-,0.00),306(AGCACTCTCTGTCCCT,+,0.00)
chunk0113_85_1	chr20	50790389	50790713	+	0	NA	Intergenic	Intergenic	-4343	NM_198799	55653	Hs.381178	NM_017843	ENSG00000124243	BCAS4	CNOL	breast carcinoma amplified sequence 4	protein-coding	0.018519	0.553846	122(GGGAACTGTCTGGTCT,-,0.00),137(TAGAACTTTGTGTGCC,-,0.00),138(AGAACTTTGTGTGCCT,+,0.00)
chunk0190_379_1	chr8	40023944	40024444	+	0	NA	Intergenic	Intergenic	89239	NM_194294	169355	Hs.676257	NM_194294	ENSG00000188676	IDO2	INDOL1	indoleamine 2,3-dioxygenase 2	protein-coding	0.010000	0.405190	
chunk0106_88_1	chr2	197164943	197165464	+	0	NA	intron (NM_001195144, intron 2 of 27)	intron (NM_001195144, intron 2 of 27)	137316	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.017274	0.459770	
chunk0185_254_1	chr7	130133380	130133777	+	0	NA	3' UTR (NM_014997, exon 10 of 10)	3' UTR (NM_014997, exon 10 of 10)	63069	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.005038	0.351759	
chunk0087_130_1	chr18	33729163	33729547	+	0	NA	intron (NM_030632, intron 8 of 11)	LTR16E2|LTR|ERVL	150778	NM_030632	80816	Hs.464876	NM_030632	ENSG00000141431	ASXL3	BRPS|KIAA1713	ASXL transcriptional regulator 3	protein-coding	0.005208	0.444156	
chunk0055_297_1	chr13	65612340	65612709	+	0	NA	Intergenic	L1MB8|LINE|L1	-253523	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.005420	0.278378	
chunk0049_134_1	chr12	91659078	91659569	+	0	NA	Intergenic	L2a|LINE|L2	-476199	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.006110	0.432927	
chunk0120_186_1	chr3	6824791	6825879	+	0	NA	Intergenic	Intergenic	-19886	NR_110123	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.001838	0.370064	
chunk0156_112_1	chr5	105616539	105617044	+	0	NA	Intergenic	Intergenic	517317	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.003960	0.320158	
chunk0182_129_1	chr7	94498247	94498689	+	0	NA	Intergenic	Intergenic	-11390	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.000000	0.331828	
chunk0211_291_1	chrX	122565923	122566483	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-618040	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.001786	0.383244	
chunk0153_242_1	chr5	72291966	72292193	+	0	NA	intron (NM_001286748, intron 4 of 11)	intron (NM_001286748, intron 4 of 11)	28178	NM_001286751	23107	Hs.482491	NM_015084	ENSG00000113048	MRPS27	MRP-S27|S27mt	mitochondrial ribosomal protein S27	protein-coding	0.008811	0.289474	
chunk0061_303_1	chr14	61828485	61828932	+	0	NA	Intergenic	Intergenic	66351	NM_003082	6617	Hs.179312	NM_003082	ENSG00000023608	SNAPC1	PTFgamma|SNAP43	small nuclear RNA activating complex polypeptide 1	protein-coding	0.000000	0.370536	285(GTGACAGTTTGTCCTT,+,0.00)
chunk0197_314_1	chr8	124772293	124772492	+	0	NA	Intergenic	Intergenic	-43885	NM_001282971	9788	Hs.336994	NM_014751	ENSG00000170873	MTSS1	MIM|MIMA|MIMB	MTSS I-BAR domain containing 1	protein-coding	0.015075	0.500000	
chunk0054_83_1	chr13	42490821	42491020	+	0	NA	Intergenic	Intergenic	-71816	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.010050	0.535000	
chunk0204_198_1	chr9	96612124	96612525	+	0	NA	intron (NM_003671, intron 1 of 12)	intron (NM_003671, intron 1 of 12)	7506	NM_003671	8555	Hs.40582	NM_003671	ENSG00000081377	CDC14B	CDC14B3|Cdc14B1|Cdc14B2|hCDC14B	cell division cycle 14B	protein-coding	0.022444	0.504975	
chunk0083_104_1	chr17	64618832	64619200	+	0	NA	intron (NM_022739, intron 1 of 18)	MIR|SINE|MIR	43252	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.002717	0.360434	
chunk0180_142_1	chr7	56503538	56503898	+	0	NA	Intergenic	L1MB3|LINE|L1	7495	NR_026929	222029	Hs.568108	NR_026929		DKFZp434L192	-	uncharacterized protein DKFZp434L192	ncRNA	0.002778	0.340720	
chunk0072_162_1	chr15	93020818	93021450	+	0	NA	intron (NM_001271, intron 38 of 38)	L1MEc|LINE|L1	52026	NM_001166286	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.011076	0.379147	
chunk0011_154_1	chr1	147585447	147586037	+	0	NA	intron (NM_004326, intron 1 of 9)	intron (NM_004326, intron 1 of 9)	44241	NM_004326	607	Hs.415209	NM_004326	ENSG00000116128	BCL9	LGS	BCL9 transcription coactivator	protein-coding	0.011864	0.423012	289(TAGCACACTTTGTTCT,-,0.00),290(AGCACACTTTGTTCTT,+,0.00)
chunk0192_270_1	chr8	66049591	66050049	+	0	NA	intron (NM_033105, intron 2 of 5)	intron (NM_033105, intron 2 of 5)	28264	NM_033105	85479	Hs.491885	NM_033105	ENSG00000147570	DNAJC5B	CSP-beta	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding	0.015284	0.359477	
chunk0056_129_1	chr13	83161684	83161993	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	720555	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.006472	0.335484	149(AAGTACACTCTGTGAT,-,0.00)
chunk0168_90_1	chr6	79964078	79964587	+	0	NA	Intergenic	Intergenic	-16734	NM_022726	6785	Hs.101915	NM_022726	ENSG00000118402	ELOVL4	ADMD|CT118|ISQMR|SCA34|STGD2|STGD3	ELOVL fatty acid elongase 4	protein-coding	0.005894	0.398039	
chunk0202_221_1	chr9	76293563	76294009	+	0	NA	intron (NM_001190482, intron 25 of 36)	intron (NM_001190482, intron 25 of 36)	100742	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.017937	0.456376	
chunk0098_305_1	chr2	76320304	76320558	+	0	NA	Intergenic	Intergenic	-609446	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.007874	0.333333	
chunk0197_320_1	chr8	125063716	125064513	+	0	NA	intron (NM_014846, intron 10 of 28)	intron (NM_014846, intron 10 of 28)	27705	NM_014846	9897	Hs.270043	NM_014846	ENSG00000164961	WASHC5	KIAA0196|RTSC|RTSC1|SPG8	WASH complex subunit 5	protein-coding	0.006274	0.409774	
chunk0103_72_1	chr2	160220379	160220895	+	0	NA	Intergenic	LTR50|LTR|ERVL	-20324	NM_001282388	3694	Hs.470399	NM_000888	ENSG00000115221	ITGB6	AI1H	integrin subunit beta 6	protein-coding	0.007752	0.462282	
chunk0133_9_1	chr3	165322677	165322876	+	0	NA	intron (NR_125764, intron 1 of 5)	L1MA3|LINE|L1	115816	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.005025	0.510000	
chunk0072_201_1	chr15	94789352	94789773	+	0	NA	Intergenic	MIRb|SINE|MIR	-65801	NR_077061	440311	Hs.745156	NR_077061	ENSG00000277654	LOC440311	-	NOP53 ribosome biogenesis factor pseudogene	pseudo	0.007126	0.324645	
chunk0145_260_1	chr4	148952367	148952974	+	0	NA	Intergenic	L2b|LINE|L2	-201625	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.016474	0.383224	
chunk0113_126_1	chr20	51593625	51594305	+	0	NA	Intergenic	Intergenic	-31134	NM_001258295	4773	Hs.744148	NM_012340	ENSG00000101096	NFATC2	NFAT1|NFATP	nuclear factor of activated T cells 2	protein-coding	0.005882	0.430250	402(TAGAACACCAAGTTCT,-,0.00),403(AGAACACCAAGTTCTT,+,0.00)
chunk0090_230_1	chr18	73710891	73711435	+	0	NA	Intergenic	Intergenic	386222	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.007353	0.308257	13(CAAAACACAATGTTCT,-,0.00),14(AAAACACAATGTTCTT,+,0.00),365(TGGGACATCATGTCCA,-,0.00),366(GGGACATCATGTCCAC,+,0.00)
chunk0052_218_1	chr13	25494329	25494528	+	0	NA	intron (NM_001313741, intron 2 of 35)	intron (NM_001313741, intron 2 of 35)	25654	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.010050	0.465000	
chunk0013_26_1	chr1	166554146	166554572	+	0	NA	Intergenic	MER51-int|LTR|ERV1	-49557	NR_002925	116123	Hs.348539	NM_138784	ENSG00000215834	FMO9P	-	flavin containing dimethylaniline monoxygenase 9, pseudogene	pseudo	0.000000	0.377049	
chunk0160_201_1	chr5	154724016	154724419	+	0	NA	intron (NM_015315, intron 1 of 18)	MIR|SINE|MIR	11315	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.002481	0.428218	
chunk0123_294_1	chr3	46593878	46594465	+	0	NA	Intergenic	Intergenic	16585	NM_003212	6997	Hs.385870	NM_003212	ENSG00000241186	TDGF1	CR|CR-1|CRGF|CRIPTO	teratocarcinoma-derived growth factor 1	protein-coding	0.000000	0.336735	
chunk0022_398_1	chr10	18022058	18022656	+	0	NA	intron (NM_001282733, intron 12 of 12)	L1PA15|LINE|L1	-11795	NR_038419	100129213	Hs.568816	NR_038419	ENSG00000226083	SLC39A12-AS1	-	SLC39A12 antisense RNA 1	ncRNA	0.005017	0.335559	
chunk0211_355_1	chrX	125497065	125497709	+	0	NA	Intergenic	Intergenic	177267	NM_001195272	100129520		NM_001195272	ENSG00000282815	TEX13C	-	TEX13 family member C	protein-coding	0.006211	0.375194	343(TGGCACATACTGACCC,-,0.00),344(GGCACATACTGACCCA,+,0.00)
chunk0197_242_1	chr8	123277102	123277402	+	0	NA	Intergenic	Intergenic	-1711	NR_037873	11244	Hs.521800	NM_007222	ENSG00000165156	ZHX1	-	zinc fingers and homeoboxes 1	protein-coding	0.003333	0.325581	
chunk0143_401_1	chr4	123299254	123299616	+	0	NA	intron (NM_145207, intron 15 of 15)	intron (NM_145207, intron 15 of 15)	-97360	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.000000	0.355372	
chunk0129_96_1	chr3	119498476	119498688	+	0	NA	promoter-TSS (NM_016589)	promoter-TSS (NM_016589)	61	NM_016589	51300	Hs.477287	NM_016589	ENSG00000113845	TIMMDC1	C3orf1|MC1DN31	translocase of inner mitochondrial membrane domain containing 1	protein-coding	0.094340	0.638498	
chunk0152_302_1	chr5	61670552	61670948	+	0	NA	intron (NR_109910, intron 6 of 7)	intron (NR_109910, intron 6 of 7)	27682	NR_109910	101928651	Hs.662309	NR_109910	ENSG00000248529	LOC101928651	-	uncharacterized LOC101928651	ncRNA	0.002525	0.365239	
chunk0020_157_1	chr1	234107553	234108191	+	0	NA	intron (NM_173508, intron 2 of 7)	intron (NM_173508, intron 2 of 7)	-106339	NM_001300845	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.004702	0.384977	
chunk0150_248_1	chr5	36285750	36286526	+	0	NA	intron (NM_145000, intron 1 of 13)	LTR82A|LTR|ERVL	15771	NM_145000	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.003866	0.391248	
chunk0092_339_1	chr19	35130801	35131424	+	0	NA	intron (NM_139284, intron 6 of 8)	intron (NM_139284, intron 6 of 8)	4162	NM_139284	163175	Hs.65256	NM_139284	ENSG00000153902	LGI4	AMCNMY|LGIL3	leucine rich repeat LGI family member 4	protein-coding	0.024077	0.536859	
chunk0001_382_1	chr1	10510667	10510968	+	0	NA	intron (NM_004565, intron 2 of 8)	intron (NM_004565, intron 2 of 8)	35871	NM_004565	5195	Hs.149983	NM_004565	ENSG00000142655	PEX14	NAPP2|PBD13A|Pex14p|dJ734G22.2	peroxisomal biogenesis factor 14	protein-coding	0.013289	0.447020	
chunk0103_13_1	chr2	158954430	158954785	+	0	NA	Intergenic	Intergenic	-14027	NM_033394	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.008451	0.418539	
chunk0176_268_1	chr7	16436872	16437393	+	0	NA	Intergenic	Intergenic	-15810	NM_001101426	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.001919	0.369732	274(AGGCACTTTTTGTGCT,-,0.00),275(GGCACTTTTTGTGCTT,+,0.00)
chunk0086_302_1	chr18	23982805	23983004	+	0	NA	Intergenic	Intergenic	-9869	NM_153211	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.015075	0.430000	
chunk0058_226_1	chr14	25193521	25194025	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-143476	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.001984	0.368317	
chunk0059_53_1	chr14	30142237	30142530	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-214690	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.003413	0.452381	
chunk0026_427_1	chr10	70889073	70889434	+	0	NA	promoter-TSS (NM_000281)	promoter-TSS (NM_000281)	-467	NM_000281	5092	Hs.3192	NM_000281	ENSG00000166228	PCBD1	DCOH|PCBD|PCD|PHS	pterin-4 alpha-carbinolamine dehydratase 1	protein-coding	0.013850	0.342541	
chunk0035_178_1	chr11	43945045	43945346	+	0	NA	Intergenic	Intergenic	2639	NM_001145033	387763	Hs.530443	NM_001145033	ENSG00000187479	C11orf96	AG2	chromosome 11 open reading frame 96	protein-coding	0.023256	0.566225	110(GAGAACACGCTGGCCC,-,0.00),111(AGAACACGCTGGCCCA,+,0.00)
chunk0186_218_1	chr7	140049175	140049836	+	0	NA	intron (NR_130117, intron 4 of 10)	intron (NR_130117, intron 4 of 10)	14216	NM_022750	64761	Hs.12646	NM_022750	ENSG00000059378	PARP12	ARTD12|MST109|MSTP109|ZC3H1|ZC3HDC1	poly(ADP-ribose) polymerase family member 12	protein-coding	0.003026	0.536254	555(AGACCACACTGTTCAC,+,0.00)
chunk0148_44_1	chr5	1315619	1316850	+	0	NA	Intergenic	Intergenic	-6857	NR_039662	100616235		NR_039662	ENSG00000263670	MIR4457	mir-4457	microRNA 4457	ncRNA	0.037368	0.551136	907(AAAACTTCCTGTTCCC,+,0.00)
chunk0047_121_1	chr12	69101558	69101926	+	0	NA	Intergenic	HSMAR2|DNA|TcMar-Mariner	-137795	NM_007007	11052	Hs.369606	NM_007007	ENSG00000111605	CPSF6	CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding	0.010870	0.441734	
chunk0082_99_1	chr17	54554258	54554589	+	0	NA	Intergenic	L1MA5|LINE|L1	-346268	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.006042	0.500000	
chunk0189_368_1	chr8	27282306	27283035	+	0	NA	Intergenic	L1ME4b|LINE|L1	-24231	NM_001283054	81551	Hs.201058	NM_030795	ENSG00000015592	STMN4	RB3	stathmin 4	protein-coding	0.006859	0.354795	324(GGAGACAGACTGTTCT,-,0.00),325(GAGACAGACTGTTCTA,+,0.00),339(TAGTACATTTTGTACC,-,0.00),340(AGTACATTTTGTACCT,+,0.00)
chunk0182_432_1	chr7	101441027	101441473	+	0	NA	intron (NM_133457, intron 2 of 12)	intron (NM_133457, intron 2 of 12)	78430	NM_133457	136227	Hs.654854	NM_133457	ENSG00000160963	COL26A1	EMI6|EMID2|EMU2|SH2B	collagen type XXVI alpha 1 chain	protein-coding	0.011211	0.472036	
chunk0196_254_1	chr8	108659949	108660382	+	0	NA	Intergenic	Intergenic	127376	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.002309	0.440092	
chunk0037_132_1	chr11	73069571	73070053	+	0	NA	intron (NM_014824, intron 3 of 19)	L1MEi|LINE|L1	72286	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.002075	0.304348	
chunk0198_62_1	chr8	129359177	129359376	+	0	NA	intron (NR_130917, intron 3 of 3)	MIR3|SINE|MIR	-118036	NR_033916	728724	Hs.49902	NR_033916	ENSG00000229140	LINC00977	-	long intergenic non-protein coding RNA 977	ncRNA	0.000000	0.315000	
chunk0148_227_1	chr5	9329226	9329972	+	0	NA	intron (NM_003966, intron 4 of 22)	intron (NM_003966, intron 4 of 22)	-181734	NR_109935	101929338	Hs.675861	NR_109935	ENSG00000251370	SEMA5A-AS1	CTD-2201E9.1	SEMA5A antisense RNA 1	ncRNA	0.009383	0.409639	
chunk0156_99_1	chr5	104824871	104825385	+	0	NA	Intergenic	Intergenic	-274346	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.001946	0.330097	256(AAGCACAGATTGTGCA,-,0.00),257(AGCACAGATTGTGCAA,+,0.00)
chunk0192_297_1	chr8	66665321	66665805	+	0	NA	exon (NM_025054, exon 1 of 3)	exon (NM_025054, exon 1 of 3)	1654	NM_025054	80124	Hs.632066	NM_025054	ENSG00000175073	VCPIP1	DUBA3|VCIP135	valosin containing protein interacting protein 1	protein-coding	0.002066	0.416495	195(AGGAACATGAAGTTCA,-,0.00),196(GGAACATGAAGTTCAG,+,0.00)
chunk0142_69_1	chr4	93607044	93607462	+	0	NA	intron (NM_001286838, intron 12 of 14)	L1ME3G|LINE|L1	-221674	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.004785	0.305489	
chunk0076_189_1	chr16	67760016	67760679	+	0	NA	intron (NM_020850, intron 3 of 13)	intron (NM_020850, intron 3 of 13)	-40977	NM_001243650	81577	Hs.307084	NM_030819	ENSG00000141098	GFOD2	-	glucose-fructose oxidoreductase domain containing 2	protein-coding	0.010558	0.503012	
chunk0107_233_1	chr2	217092527	217093218	+	0	NA	Intergenic	Intergenic	-189861	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.021708	0.500000	
chunk0032_110_1	chr11	3793956	3794580	+	0	NA	intron (NM_016320, intron 1 of 32)	intron (NM_016320, intron 1 of 32)	-3456	NM_001256235	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.020833	0.433600	
chunk0174_137_1	chr6	157513017	157513232	+	0	NA	intron (NM_024630, intron 1 of 8)	intron (NM_024630, intron 1 of 8)	-16008	NR_037463	100500899		NR_037463	ENSG00000266617	MIR3692	-	microRNA 3692	ncRNA	0.023256	0.407407	
chunk0048_17_1	chr12	77149848	77150488	+	0	NA	Intergenic	Intergenic	-84588	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.003125	0.429017	
chunk0169_348_1	chr6	106572421	106572888	+	0	NA	intron (NM_032730, intron 8 of 8)	intron (NM_032730, intron 8 of 8)	56844	NM_032730	84816	Hs.155839	NM_032730	ENSG00000130347	RTN4IP1	NIMP|OPA10	reticulon 4 interacting protein 1	protein-coding	0.010707	0.455128	
chunk0135_448_1	chr3	194221550	194221751	+	0	NA	intron (NR_125403, intron 1 of 2)	intron (NR_125403, intron 1 of 2)	-15343	NR_125404	100505920	Hs.436654	NR_125403	ENSG00000225742	LINC02036	-	long intergenic non-protein coding RNA 2036	ncRNA	0.004975	0.524752	
chunk0149_414_1	chr5	29469579	29469912	+	0	NA	Intergenic	Intergenic	-73769	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.003003	0.356287	
chunk0178_257_1	chr7	36295128	36295628	+	0	NA	intron (NM_030636, intron 6 of 7)	L1MC3|LINE|L1	71795	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.006000	0.397206	
chunk0143_8_1	chr4	105714407	105714768	+	0	NA	intron (NM_001031720, intron 1 of 11)	(AATATTT)n|Simple_repeat|Simple_repeat	3774	NM_001031720	79807	Hs.161429	NM_024751	ENSG00000138780	GSTCD	-	glutathione S-transferase C-terminal domain containing	protein-coding	0.005540	0.292818	
chunk0112_355_1	chr20	45340334	45340734	+	0	NA	intron (NM_002999, intron 1 of 4)	intron (NM_002999, intron 1 of 4)	7890	NM_002999	6385	Hs.632267	NM_002999	ENSG00000124145	SDC4	SYND4	syndecan 4	protein-coding	0.012500	0.533666	
chunk0063_289_1	chr14	84355803	84356110	+	0	NA	Intergenic	L1MA3|LINE|L1	-1037923	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.006515	0.298701	
chunk0017_406_1	chr1	212763818	212764142	+	0	NA	intron (NM_015471, intron 4 of 5)	L1PB2|LINE|L1	27817	NM_001297739	25936	Hs.497692	NM_015471	ENSG00000117697	NSL1	C1orf48|DC8|MIS14	NSL1 component of MIS12 kinetochore complex	protein-coding	0.000000	0.344615	
chunk0177_460_1	chr7	28586595	28587121	+	0	NA	intron (NM_182899, intron 4 of 9)	intron (NM_182899, intron 4 of 9)	-99123	NM_001011666	9586	Hs.437075	NM_004904	ENSG00000146592	CREB5	CRE-BPA|CREB-5|CREBPA	cAMP responsive element binding protein 5	protein-coding	0.009506	0.426945	321(CGGACCAGAGTGTCCT,-,0.00),322(GGACCAGAGTGTCCTG,+,0.00)
chunk0208_465_1	chrX	34874164	34875096	+	0	NA	Intergenic	Intergenic	-68166	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.007511	0.334405	
chunk0055_270_1	chr13	64072757	64073204	+	0	NA	Intergenic	Intergenic	-228855	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.002237	0.238839	
chunk0187_410_1	chr7	158147463	158147819	+	0	NA	intron (NM_001308268, intron 6 of 22)	intron (NM_001308268, intron 6 of 22)	293056	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.047753	0.585434	
chunk0138_143_1	chr4	36984301	36984802	+	0	NA	Intergenic	L1MB3|LINE|L1	257440	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.005988	0.328685	
chunk0167_140_1	chr6	62332786	62333056	+	0	NA	Intergenic	L1MB8|LINE|L1	-46726	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.007407	0.306273	
chunk0054_343_1	chr13	49476444	49477134	+	0	NA	exon (NM_031915, exon 7 of 15)	exon (NM_031915, exon 7 of 15)	-18876	NM_001040443	51131	Hs.369039	NM_001040443	ENSG00000136147	PHF11	APY|BCAP|IGEL|IGER|IGHER|NY-REN-34|NYREN34	PHD finger protein 11	protein-coding	0.014493	0.377713	
chunk0005_80_1	chr1	56036179	56036595	+	0	NA	Intergenic	Intergenic	543197	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.007212	0.424460	380(AAGTTCAGGCTGTGCT,-,0.00),381(AGTTCAGGCTGTGCTA,+,0.00)
chunk0001_254_1	chr1	8424506	8425140	+	0	NA	intron (NR_125999, intron 1 of 3)	intron (NR_125999, intron 1 of 3)	178	NR_125999	102724552	Hs.568612	NR_125999		RERE-AS1	-	RERE antisense RNA 1	ncRNA	0.014196	0.524409	406(GAGGACAGGGTGTGCA,-,0.00),407(AGGACAGGGTGTGCAG,+,0.00)
chunk0175_9_1	chr7	142294	142943	+	0	NA	Intergenic	Intergenic	-7100	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.016949	0.495385	
chunk0023_46_1	chr10	21350225	21350460	+	0	NA	Intergenic	Intergenic	146299	NR_031736	100302129		NR_031736	ENSG00000222071	MIR1915	MIRN1915|hsa-mir-1915	microRNA 1915	ncRNA	0.021277	0.457627	
chunk0181_299_1	chr7	87016551	87017013	+	0	NA	intron (NM_001142749, intron 1 of 21)	intron (NM_001142749, intron 1 of 21)	23452	NM_001291991	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.008658	0.334773	
chunk0034_97_1	chr11	27514429	27515110	+	0	NA	TTS (NR_107054)	TTS (NR_107054)	278	NR_107054	102465881		NR_107054	ENSG00000278483	MIR8087	hsa-mir-8087	microRNA 8087	ncRNA	0.007342	0.407625	
chunk0027_38_1	chr10	72435715	72436272	+	0	NA	intron (NM_006077, intron 8 of 11)	L1PA6|LINE|L1	-80844	NM_017626	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.026930	0.560932	32(TGGCTCAGCATGTCCC,-,0.00),33(GGCTCAGCATGTCCCA,+,0.00)
chunk0157_55_1	chr5	116084929	116085272	+	0	NA	promoter-TSS (NM_001308080)	promoter-TSS (NM_001308080)	124	NM_016144	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.116618	0.706395	
chunk0008_320_1	chr1	95257793	95257992	+	0	NA	Intergenic	Intergenic	23737	NR_103484	25950	Hs.483512	NM_015485	ENSG00000122481	RWDD3	RSUME	RWD domain containing 3	protein-coding	0.005025	0.390000	
chunk0109_192_1	chr20	5033271	5033562	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	-23123	NM_203327	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.013746	0.424658	205(AGTACATTATGTTTCT,+,0.00)
chunk0017_413_1	chr1	212980591	212981379	+	0	NA	intron (NM_001136474, intron 8 of 8)	intron (NM_001136474, intron 8 of 8)	30465	NM_001136474	79805	Hs.96885	NM_024749	ENSG00000143494	VASH2	-	vasohibin 2	protein-coding	0.011421	0.508238	
chunk0065_3_1	chr15	17083221	17083491	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-3199388	NR_038836	646096	Hs.448789	NR_038836	ENSG00000259156	CHEK2P2	-	checkpoint kinase 2 pseudogene 2	pseudo	0.018519	0.483395	
chunk0039_4_1	chr11	95012069	95012503	+	0	NA	Intergenic	Intergenic	-12972	NM_001161630	390245	Hs.714692	NM_001161630	ENSG00000235268	KDM4E	JMJD2E|KDM4DL|KDM5E	lysine demethylase 4E	protein-coding	0.023041	0.579310	
chunk0194_292_1	chr8	87589408	87589967	+	0	NA	Intergenic	Intergenic	284381	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.000000	0.333929	
chunk0129_37_1	chr3	117345637	117346358	+	0	NA	Intergenic	L2c|LINE|L2	424566	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.005548	0.401662	202(CAGAACACTCTGCTCC,-,0.00),203(AGAACACTCTGCTCCC,+,0.00)
chunk0208_115_1	chrX	14073512	14074037	+	0	NA	Intergenic	Intergenic	-43858	NM_001042479	54960	Hs.592237	NM_017856	ENSG00000046647	GEMIN8	FAM51A1	gem nuclear organelle associated protein 8	protein-coding	0.001905	0.380228	246(AAAAACATACTGTTCA,-,0.00),247(AAAACATACTGTTCAC,+,0.00)
chunk0187_160_1	chr7	150406410	150406719	+	0	NA	intron (NR_027237, intron 1 of 2)	MIRc|SINE|MIR	812	NR_027237	728743	Hs.650365	NM_001080852		LOC728743	-	zinc finger protein pseudogene	pseudo	0.006472	0.509677	267(AGGAACACAGTGTCCT,-,0.00),268(GGAACACAGTGTCCTG,+,0.00)
chunk0039_293_1	chr11	102793724	102794247	+	0	NA	intron (NR_038390, intron 2 of 7)	MIR3|SINE|MIR	4250	NM_001145938	4312	Hs.83169	NM_002421	ENSG00000196611	MMP1	CLG|CLGN	matrix metallopeptidase 1	protein-coding	0.007648	0.442748	
chunk0210_55_1	chrX	68983496	68983780	+	0	NA	Intergenic	Intergenic	154641	NM_004429	1947	Hs.144700	NM_004429	ENSG00000090776	EFNB1	CFND|CFNS|EFB1|EFL3|EPLG2|Elk-L|LERK2	ephrin B1	protein-coding	0.003521	0.610526	
chunk0044_306_1	chr12	33302850	33303053	+	0	NA	Intergenic	Intergenic	136868	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.000000	0.333333	
chunk0032_460_1	chr10	133689312	133689648	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	-62685	NM_001080998	441581	Hs.690471	NM_001080998	ENSG00000225899	FRG2B	-	FSHD region gene 2 family member B	protein-coding	0.005952	0.489614	
chunk0050_69_1	chr12	101475837	101476481	+	0	NA	promoter-TSS (NM_152323)	promoter-TSS (NM_152323)	-720	NM_152323	121599	Hs.577097	NM_152323	ENSG00000166211	SPIC	SPI-C	Spi-C transcription factor	protein-coding	0.007764	0.314729	
chunk0073_178_1	chr16	8866216	8866956	+	0	NA	intron (NM_001278260, intron 1 of 4)	intron (NM_001278260, intron 1 of 4)	842	NM_001278264	23589	Hs.632184	NM_014316	ENSG00000153048	CARHSP1	CRHSP-24|CRHSP24|CSDC1	calcium regulated heat stable protein 1	protein-coding	0.040541	0.634278	
chunk0008_242_1	chr1	94252219	94252724	+	0	NA	Intergenic	Intergenic	-14720	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.009901	0.430830	244(AAGATCACCCTGTGCC,-,0.00),245(AGATCACCCTGTGCCG,+,0.00)
chunk0060_132_1	chr14	44639584	44640206	+	0	NA	Intergenic	Intergenic	-132599	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.004823	0.351525	
chunk0184_437_1	chr7	123062988	123063214	+	0	NA	Intergenic	L1PA15|LINE|L1	-67401	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.000000	0.370044	
chunk0040_302_1	chr11	117183698	117184098	+	0	NA	intron (NM_001040455, intron 7 of 25)	intron (NM_001040455, intron 7 of 25)	4675	NM_001040455	51092	Hs.712144	NM_015996	ENSG00000149577	SIDT2	CGI-40	SID1 transmembrane family member 2	protein-coding	0.020000	0.508728	179(AGGTACATTTTGTGCC,-,0.00),180(GGTACATTTTGTGCCC,+,0.00)
chunk0021_9_1	chr10	329541	329872	+	0	NA	intron (NM_014974, intron 29 of 36)	intron (NM_014974, intron 29 of 36)	-47620	NR_106988									0.024169	0.533133	164(TGGAACAGCCCGTGCT,-,0.00),165(GGAACAGCCCGTGCTG,+,0.00)
chunk0104_309_1	chr2	179104591	179105184	+	0	NA	3' UTR (NM_178123, exon 18 of 18)	3' UTR (NM_178123, exon 18 of 18)	-54828	NM_001316745	285025	Hs.324341	NM_173648	ENSG00000163492	CCDC141	CAMDI	coiled-coil domain containing 141	protein-coding	0.003373	0.372054	
chunk0166_7_1	chr6	41505720	41506232	+	0	NA	intron (NR_120347, intron 2 of 2)	L2b|LINE|L2	3532	NR_120347	103106903	Hs.563396	NR_120347	ENSG00000226917	LINC01276	-	long intergenic non-protein coding RNA 1276	ncRNA	0.013672	0.452242	232(TAGCACACTGTGTGCC,-,0.00),233(AGCACACTGTGTGCCC,+,0.00)
chunk0042_248_1	chr12	6417131	6417330	+	0	NA	Intergenic	Intergenic	-27655	NM_001242	939	Hs.355307	NM_001242	ENSG00000139193	CD27	S152|S152. LPFS2|T14|TNFRSF7|Tp55	CD27 molecule	protein-coding	0.000000	0.435000	
chunk0143_344_1	chr4	121618898	121619351	+	0	NA	Intergenic	L1PA6|LINE|L1	77868	NM_001154	308	Hs.480653	NM_001154	ENSG00000164111	ANXA5	ANX5|ENX2|HEL-S-7|PP4|RPRGL3	annexin A5	protein-coding	0.006623	0.389868	284(AAAGACACAATGTACC,-,0.00)
chunk0007_62_1	chr1	78194541	78195084	+	0	NA	Intergenic	L1ME1|LINE|L1	-34787	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.009208	0.299632	
chunk0064_136_1	chr14	91469269	91469548	+	0	NA	intron (NM_001284280, intron 10 of 14)	intron (NM_001284280, intron 10 of 14)	41072	NM_001284280	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.000000	0.296429	
chunk0210_184_1	chrX	79694268	79694956	+	0	NA	Intergenic	L1PA7|LINE|L1	-320144	NM_001109878	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.005814	0.374456	202(GGTACATTGTGTCTTT,+,0.00)
chunk0055_369_1	chr13	72175753	72176121	+	0	NA	Intergenic	Intergenic	-308745	NM_004392	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.002717	0.317073	
chunk0104_228_1	chr2	176461657	176462117	+	0	NA	Intergenic	Intergenic	139165	NR_031648	100302142		NR_031648	ENSG00000283203	MIR1246	MIRN1246|hsa-mir-1246	microRNA 1246	ncRNA	0.008696	0.357918	
chunk0059_174_1	chr14	32509463	32510034	+	0	NA	intron (NM_004274, intron 2 of 13)	intron (NM_004274, intron 2 of 13)	180475	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.014011	0.426573	268(GGCACTGTCTGCCCTT,+,0.00)
chunk0145_79_1	chr4	145761885	145762335	+	0	NA	intron (NM_178835, intron 14 of 14)	intron (NM_178835, intron 14 of 14)	81906	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.024444	0.527716	
chunk0005_376_1	chr1	61700136	61700950	+	0	NA	intron (NM_032027, intron 4 of 6)	intron (NM_032027, intron 4 of 6)	24880	NM_032027	83941	Hs.656790	NM_032027	ENSG00000162604	TM2D1	BBP	TM2 domain containing 1	protein-coding	0.004914	0.366871	
chunk0005_367_1	chr1	61568519	61569211	+	0	NA	Intergenic	Intergenic	-85377	NR_073400	414927	Hs.123471	NR_073400		MGC34796	-	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) pseudogene	pseudo	0.005780	0.392496	131(AAGAAGAGTTTGTTCT,-,0.00),197(CAGTACAGACTGTGCT,-,0.00),198(AGTACAGACTGTGCTG,+,0.00)
chunk0158_41_1	chr5	125662345	125662580	+	0	NA	Intergenic	L1PA16|LINE|L1	169201	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.000000	0.330508	
chunk0190_296_1	chr8	38034420	38034996	+	0	NA	intron (NM_004095, intron 1 of 2)	intron (NM_004095, intron 1 of 2)	4206	NM_004095	1978	Hs.411641	NM_004095	ENSG00000187840	EIF4EBP1	4E-BP1|4EBP1|BP-1|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding	0.012153	0.478336	353(GAAACAGGCAGTGCTG,+,0.00)
chunk0027_206_1	chr10	75866263	75866553	+	0	NA	intron (NM_032024, intron 1 of 5)	intron (NM_032024, intron 1 of 5)	83647	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.000000	0.505155	
chunk0203_424_1	chr9	91043064	91043409	+	0	NA	Intergenic	Intergenic	31896	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.028986	0.514451	131(GAGAACGTTCTGTTCT,-,0.00),132(AGAACGTTCTGTTCTA,+,0.00)
chunk0154_307_1	chr5	83589785	83590215	+	0	NA	Intergenic	L2a|LINE|L2	118326	NM_001126336	1462	Hs.643801	NM_004385	ENSG00000038427	VCAN	CSPG2|ERVR|GHAP|PG-M|WGN|WGN1	versican	protein-coding	0.004651	0.406032	
chunk0005_245_1	chr1	59631481	59632172	+	0	NA	intron (NM_001244714, intron 8 of 13)	intron (NM_001244714, intron 8 of 13)	101470	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.002894	0.382948	317(AAGAACTGGATGTGCC,-,0.00),318(AGAACTGGATGTGCCC,+,0.00)
chunk0135_380_1	chr3	191021576	191022006	+	0	NA	Intergenic	Intergenic	143861	NR_024343	100170222	Hs.717310	NR_024343		SNAR-I	snaR-3	small NF90 (ILF3) associated RNA I	snRNA	0.002326	0.331787	
chunk0199_128_1	chr9	3763510	3763826	+	0	NA	Intergenic	L1MC|LINE|L1	95582	NR_121586	101929302	Hs.122828	NR_121586	ENSG00000232104	RFX3-AS1	CVAT7	RFX3 antisense RNA 1	ncRNA	0.003165	0.337539	
chunk0196_382_1	chr8	115537032	115537497	+	0	NA	intron (NM_001282903, intron 5 of 6)	intron (NM_001282903, intron 5 of 6)	130748	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.002151	0.296137	
chunk0157_184_1	chr5	118698960	118699571	+	0	NA	Intergenic	MIRb|SINE|MIR	103077	NR_104998	102467225	Hs.582523	NR_104998	ENSG00000249128	LINC02215	-	long intergenic non-protein coding RNA 2215	ncRNA	0.006547	0.472222	
chunk0098_233_1	chr2	74089141	74089394	+	0	NA	intron (NM_001287491, intron 6 of 10)	L1ME1|LINE|L1	58645	NM_001035505	388962	Hs.61472	NM_212552	ENSG00000163170	BOLA3	MMDS2	bolA family member 3	protein-coding	0.015810	0.448819	144(TGAACATAGTGTTTTC,+,0.00)
chunk0141_163_1	chr4	82354162	82354361	+	0	NA	intron (NM_001003810, intron 6 of 6)	intron (NM_001003810, intron 6 of 6)	19735	NM_002138	3184	Hs.480073	NM_002138	ENSG00000138668	HNRNPD	AUF1|AUF1A|HNRPD|P37|hnRNPD0	heterogeneous nuclear ribonucleoprotein D	protein-coding	0.000000	0.325000	
chunk0141_406_1	chr4	88588228	88588892	+	0	NA	Intergenic	Intergenic	-3863	NM_014606	8916	Hs.35804	NM_014606	ENSG00000138641	HERC3	-	HECT and RLD domain containing E3 ubiquitin protein ligase 3	protein-coding	0.001506	0.342857	358(AGAGACAGAATGTCCT,-,0.00),359(GAGACAGAATGTCCTG,+,0.00)
chunk0094_153_1	chr2	5205181	5205542	+	0	NA	Intergenic	Intergenic	485757	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.011080	0.350829	
chunk0044_28_1	chr12	27286202	27286583	+	0	NA	intron (NM_015000, intron 1 of 13)	L1ME4a|LINE|L1	42247	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.000000	0.319372	
chunk0139_152_1	chr4	53653297	53653888	+	0	NA	Intergenic	Intergenic	-42309	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.010152	0.442568	
chunk0078_78_1	chr17	1779527	1780048	+	0	NA	3' UTR (NM_052928, exon 11 of 11)	3' UTR (NM_052928, exon 11 of 11)	17822	NM_002615	5176	Hs.532768	NM_002615	ENSG00000132386	SERPINF1	EPC-1|OI12|OI6|PEDF|PIG35	serpin family F member 1	protein-coding	0.013436	0.419540	
chunk0081_337_1	chr17	46794148	46794846	+	0	NA	intron (NM_030753, intron 1 of 4)	intron (NM_030753, intron 1 of 4)	24263	NM_030753	7473	Hs.445884	NM_030753	ENSG00000108379	WNT3	INT4|TETAMS	Wnt family member 3	protein-coding	0.008596	0.499285	408(CAGAACACACTGTACC,-,0.00),409(AGAACACACTGTACCA,+,0.00)
chunk0044_42_1	chr12	27539011	27539622	+	0	NA	intron (NM_003622, intron 1 of 29)	intron (NM_003622, intron 1 of 29)	15204	NM_001198916	8496	Hs.172445	NM_003622	ENSG00000110841	PPFIBP1	L2|SGT2|hSGT2|hSgt2p	PPFIA binding protein 1	protein-coding	0.006547	0.400327	
chunk0079_329_1	chr17	17491537	17492307	+	0	NA	3' UTR (NM_018019, exon 2 of 2)	3' UTR (NM_018019, exon 2 of 2)	4473	NM_001199989	51655	Hs.25829	NM_016084	ENSG00000108551	RASD1	AGS1|DEXRAS1|MGC:26290	ras related dexamethasone induced 1	protein-coding	0.029870	0.578470	372(AGGATCAGTGTGTACC,-,0.00),373(GGATCAGTGTGTACCA,+,0.00),388(AGGTACACATTGTTCC,-,0.00),389(GGTACACATTGTTCCT,+,0.00)
chunk0154_246_1	chr5	81355186	81355562	+	0	NA	intron (NM_130767, intron 5 of 14)	L1MA2|LINE|L1	38795	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.005319	0.368700	203(AAGGACATCCTGTCAT,-,0.00),204(AGGACATCCTGTCATT,+,0.00)
chunk0161_70_1	chr5	166633803	166634462	+	0	NA	Intergenic	Intergenic	292238	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.004552	0.362121	
chunk0056_438_1	chr13	95127898	95128433	+	0	NA	intron (NM_001105515, intron 19 of 20)	intron (NM_001105515, intron 19 of 20)	168124	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.003738	0.371269	259(GAATACACACTGTTCT,-,0.00),260(AATACACACTGTTCTT,+,0.00)
chunk0115_5_1	chr21	20343560	20344041	+	0	NA	Intergenic	Intergenic	459308	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.010395	0.396266	328(CAGAACAGAATGTACA,-,0.00),329(AGAACAGAATGTACAA,+,0.00)
chunk0026_90_1	chr10	61562571	61563119	+	0	NA	Intergenic	L1MC2|LINE|L1	82804	NR_120644	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.003650	0.375228	
chunk0037_138_1	chr11	73150727	73151143	+	0	NA	Intergenic	Intergenic	-8837	NM_014824	9873	Hs.744959	NM_014824	ENSG00000137478	FCHSD2	NWK|NWK1|SH3MD3	FCH and double SH3 domains 2	protein-coding	0.002404	0.489209	
chunk0138_65_1	chr4	33300435	33300861	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	739245	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.004695	0.353630	
chunk0189_362_1	chr8	27063892	27064241	+	0	NA	Intergenic	Intergenic	-15103	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.008596	0.371429	133(CAGCACATGCAGTTCT,-,0.00),134(AGCACATGCAGTTCTA,+,0.00)
chunk0204_91_1	chr9	94293890	94294248	+	0	NA	intron (NM_194320, intron 4 of 4)	L1M5|LINE|L1	34575	NM_017561	54754	Hs.648183	NM_017561	ENSG00000130950	NUTM2F	FAM22F|NUTMF	NUT family member 2F	protein-coding	0.016760	0.440111	
chunk0136_224_1	chr4	8183194	8183815	+	0	NA	Intergenic	Intergenic	-15829	NM_018986	54436	Hs.479116	NM_018986	ENSG00000125089	SH3TC1	-	SH3 domain and tetratricopeptide repeats 1	protein-coding	0.030596	0.545016	
chunk0102_44_1	chr2	142384199	142384724	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-252760	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.005714	0.317490	
chunk0179_312_1	chr7	50482921	50483432	+	0	NA	intron (NM_001082971, intron 9 of 14)	L1M5|LINE|L1	-32786	NM_001287494	63979	Hs.137516	NM_022116	ENSG00000132436	FIGNL1	-	fidgetin like 1	protein-coding	0.001957	0.296875	
chunk0203_284_1	chr9	88829270	88829573	+	0	NA	Intergenic	Intergenic	-83516	NR_036252	100423015		NR_036252	ENSG00000265873	MIR4289	-	microRNA 4289	ncRNA	0.009901	0.470395	
chunk0193_79_1	chr8	73319568	73320163	+	0	NA	intron (NM_172037, intron 3 of 5)	intron (NM_172037, intron 3 of 5)	25263	NM_172037	157506	Hs.244940	NM_172037	ENSG00000121039	RDH10	SDR16C4	retinol dehydrogenase 10	protein-coding	0.010084	0.390940	
chunk0146_371_1	chr4	168339695	168340187	+	0	NA	Intergenic	L1MC1|LINE|L1	-21134	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.006098	0.310345	
chunk0151_145_1	chr5	45861166	45861586	+	0	NA	Intergenic	L1MEh|LINE|L1	-165258	NM_021072	348980	Hs.353176	NM_021072	ENSG00000164588	HCN1	BCNG-1|BCNG1|EIEE24|HAC-2	hyperpolarization activated cyclic nucleotide gated potassium channel 1	protein-coding	0.002381	0.289786	
chunk0139_396_1	chr4	62709734	62710171	+	0	NA	Intergenic	Intergenic	-548187	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.004577	0.305936	
chunk0025_35_1	chr10	48798576	48798899	+	0	NA	intron (NM_020945, intron 24 of 61)	L1M4|LINE|L1	113264	NM_020945	57705	Hs.287379	NM_020945	ENSG00000128815	WDFY4	C10orf64	WDFY family member 4	protein-coding	0.006192	0.395062	
chunk0155_58_1	chr5	91423070	91423269	+	0	NA	Intergenic	Intergenic	-39837	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.010050	0.350000	
chunk0144_203_1	chr4	133887621	133888105	+	0	NA	Intergenic	Intergenic	313885	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.014463	0.402062	
chunk0195_344_1	chr8	99492037	99492577	+	0	NA	intron (NM_152564, intron 25 of 61)	L1P2|LINE|L1	44423	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.012963	0.512015	
chunk0016_191_1	chr1	198295949	198296466	+	0	NA	intron (NM_133494, intron 8 of 9)	intron (NM_133494, intron 8 of 9)	139229	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.013540	0.401544	240(ATGTACACATTGTCCT,-,0.00),241(TGTACACATTGTCCTT,+,0.00)
chunk0038_175_1	chr11	85625288	85625659	+	0	NA	intron (NM_001142699, intron 2 of 27)	intron (NM_001142699, intron 2 of 27)	1797	NM_001142699	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.381720	
chunk0201_227_1	chr9	37485838	37486080	+	0	NA	promoter-TSS (NM_001282766)	promoter-TSS (NM_001282766)	24	NM_001282766	64425	Hs.591087	NM_022490	ENSG00000137054	POLR1E	PAF53|PRAF1	RNA polymerase I subunit E	protein-coding	0.115702	0.703704	
chunk0196_440_1	chr8	116551997	116552749	+	0	NA	Intergenic	MIR3|SINE|MIR	203450	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.007979	0.399734	
chunk0049_359_1	chr12	95497073	95497442	+	0	NA	intron (NM_006838, intron 7 of 10)	L1MB3|LINE|L1	23211	NM_006838	10988	Hs.444986	NM_006838	ENSG00000111142	METAP2	MAP2|MNPEP|p67eIF2	methionyl aminopeptidase 2	protein-coding	0.008130	0.378378	
chunk0074_45_1	chr16	20707571	20707831	+	0	NA	Intergenic	L1M3a|LINE|L1	-16445	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.003846	0.455939	
chunk0123_186_1	chr3	44301337	44301825	+	0	NA	intron (NM_001145030, intron 12 of 19)	L1MC4|LINE|L1	-36538	NM_001282915	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.002049	0.294479	
chunk0163_162_1	chr6	11093627	11094101	+	0	NA	promoter-TSS (NM_001135575)	promoter-TSS (NM_001135575)	-169	NM_001135575	221710	Hs.656600	NM_001135575	ENSG00000224531	SMIM13	C6orf228	small integral membrane protein 13	protein-coding	0.103376	0.698947	
chunk0208_413_1	chrX	29536773	29537137	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-37323	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.000000	0.257534	
chunk0141_32_1	chr4	76954545	76955021	+	0	NA	intron (NM_018243, intron 1 of 9)	intron (NM_018243, intron 1 of 9)	5069	NM_018243	55752	Hs.128199	NM_018243	ENSG00000138758	SEPTIN11	SEPT11	septin 11	protein-coding	0.008403	0.419287	234(GGCACAGGAAGTCCAG,+,0.00)
chunk0002_17_1	chr1	12310275	12310622	+	0	NA	intron (NM_018156, intron 27 of 68)	intron (NM_018156, intron 27 of 68)	80409	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.005764	0.410920	
chunk0056_361_1	chr13	92341559	92342024	+	0	NA	intron (NR_120382, intron 2 of 2)	intron (NR_120382, intron 2 of 2)	10416	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.010753	0.315451	
chunk0155_154_1	chr5	94015128	94015427	+	0	NA	intron (NR_028080, intron 3 of 8)	L1M3f|LINE|L1	96422	NM_001163417	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.003344	0.363333	
chunk0017_115_1	chr1	206050042	206050635	+	0	NA	Intergenic	L1ME4b|LINE|L1	-2385	NM_001007544	440712	Hs.662248	NM_001007544	ENSG00000263961	RHEX	C1orf186	regulator of hemoglobinization and erythroid cell expansion	protein-coding	0.005059	0.358586	
chunk0193_379_1	chr8	80146694	80146893	+	0	NA	intron (NR_105035, intron 1 of 6)	L1ME3G|LINE|L1	24407	NR_105036	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.000000	0.345000	97(TAGCACAGAAAGTGCT,-,0.00),98(AGCACAGAAAGTGCTC,+,0.00)
chunk0110_85_1	chr20	11245846	11246401	+	0	NA	Intergenic	Intergenic	27260	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.003604	0.338129	540(AGGGGCAAAATGTTCC,-,0.00)
chunk0191_355_1	chr8	56453568	56454121	+	0	NA	intron (NR_125813, intron 1 of 3)	L1MCa|LINE|L1	-7110	NM_001135690	5179	Hs.339831	NM_006211	ENSG00000181195	PENK	PE|PENK-A	proenkephalin	protein-coding	0.003617	0.335740	
chunk0182_361_1	chr7	99839612	99840117	+	0	NA	intron (NM_001278921, intron 4 of 9)	LTR9A1|LTR|ERV1	11851	NM_057095	64816	Hs.306220	NM_022820	ENSG00000021461	CYP3A43	-	cytochrome P450 family 3 subfamily A member 43	protein-coding	0.009901	0.466403	242(AGGACTAGGTGTACTG,+,0.00)
chunk0070_341_1	chr15	75831661	75832316	+	0	NA	Intergenic	Intergenic	-11298	NM_001284382	92912	Hs.23033	NM_173469	ENSG00000140367	UBE2Q2	-	ubiquitin conjugating enzyme E2 Q2	protein-coding	0.003053	0.402439	367(GGGCACAAGGAGTCCT,-,0.00),368(GGCACAAGGAGTCCTG,+,0.00)
chunk0061_95_1	chr14	57481305	57481902	+	0	NA	exon (NM_001283060, exon 4 of 6)	exon (NM_001283060, exon 4 of 6)	12260	NM_001283058	55195	Hs.659706	NM_018168	ENSG00000100557	CCDC198	C14orf105	coiled-coil domain containing 198	protein-coding	0.008375	0.357860	
chunk0090_393_1	chr18	77702618	77702817	+	0	NA	Intergenic	Intergenic	291010	NR_104127	101927715	Hs.385670	NR_104127		LINC01029	-	long intergenic non-protein coding RNA 1029	ncRNA	0.005025	0.310000	
chunk0127_303_1	chr3	98647046	98647417	+	0	NA	Intergenic	Intergenic	-53620	NM_000097	1371	Hs.476982	NM_000097	ENSG00000080819	CPOX	COX|CPO|CPX|HCP	coproporphyrinogen oxidase	protein-coding	0.008086	0.365591	
chunk0044_365_1	chr12	39319163	39319774	+	0	NA	intron (NM_017641, intron 27 of 36)	Charlie7|DNA|hAT-Charlie	123922	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.006547	0.359477	
chunk0118_104_1	chr22	29290380	29290923	+	0	NA	TTS (NM_001163287)	TTS (NM_001163287)	-16344	NM_152236	10634	Hs.322852	NM_006478	ENSG00000185340	GAS2L1	GAR22	growth arrest specific 2 like 1	protein-coding	0.007366	0.343750	
chunk0201_44_1	chr9	33699440	33700172	+	0	NA	Intergenic	Intergenic	-22386	NR_023917	11191	Hs.493716	NR_023917	ENSG00000237984	PTENP1	PTEN-rs|PTEN2|PTENpg1|PTH2|psiPTEN	phosphatase and tensin homolog pseudogene 1	pseudo	0.004098	0.343793	
chunk0085_197_1	chr18	6544249	6544465	+	0	NA	intron (NR_120518, intron 2 of 5)	intron (NR_120518, intron 2 of 5)	32941	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.000000	0.474654	
chunk0035_172_1	chr11	43880424	43881037	+	0	NA	promoter-TSS (NM_139178)	promoter-TSS (NM_139178)	-77	NM_139178	221120	Hs.720708	NM_139178	ENSG00000166199	ALKBH3	ABH3|DEPC-1|DEPC1|PCA1|hABH3	alkB homolog 3, alpha-ketoglutaratedependent dioxygenase	protein-coding	0.061990	0.597720	
chunk0111_297_1	chr20	31798533	31798824	+	0	NA	intron (NM_012112, intron 17 of 17)	intron (NM_012112, intron 17 of 17)	-20697	NM_033118	85366	Hs.86092	NM_033118	ENSG00000101306	MYLK2	KMLC|MLCK|MLCK2|skMLCK	myosin light chain kinase 2	protein-coding	0.017182	0.452055	
chunk0088_85_1	chr18	44830693	44831055	+	0	NA	intron (NM_015559, intron 2 of 5)	intron (NM_015559, intron 2 of 5)	139292	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.002762	0.391185	179(CAGTACATTGTGTTTT,-,0.00),180(AGTACATTGTGTTTTC,+,0.00)
chunk0186_212_1	chr7	139916099	139916598	+	0	NA	intron (NM_001314028, intron 4 of 12)	intron (NM_001314028, intron 4 of 12)	87195	NM_001061	6916	Hs.520757	NM_001061	ENSG00000059377	TBXAS1	BDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS	thromboxane A synthase 1	protein-coding	0.014028	0.520000	114(CAGAACTTCTTGTTCT,-,0.00),115(AGAACTTCTTGTTCTT,+,0.00)
chunk0176_262_1	chr7	16317050	16317488	+	0	NA	intron (NM_001101417, intron 2 of 8)	MIR|SINE|MIR	104053	NM_001101417	729920	Hs.636502	NM_001101417	ENSG00000214960	CRPPA	ISPD|LGMDR20|MDDGA7|MDDGC7|Nip|hISPD	CDP-L-ribitol pyrophosphorylase A	protein-coding	0.000000	0.359909	
chunk0138_445_1	chr4	46388318	46388527	+	0	NA	intron (NM_001286827, intron 2 of 9)	intron (NM_001286827, intron 2 of 9)	957	NM_001114175	2555	Hs.48372	NM_000807	ENSG00000151834	GABRA2	-	gamma-aminobutyric acid type A receptor alpha2 subunit	protein-coding	0.009569	0.352381	
chunk0044_247_1	chr12	31785720	31786128	+	0	NA	Intergenic	Intergenic	6317	NM_001013699	440093	Hs.448697	NM_001013699	ENSG00000188375	H3F3C	H3.5	H3 histone family member 3C	protein-coding	0.009804	0.386308	
chunk0001_388_1	chr1	10635803	10636492	+	0	NA	TTS (NM_001079843)	TTS (NM_001079843)	160529	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.039187	0.656522	
chunk0003_457_1	chr1	41616737	41616990	+	0	NA	intron (NM_001127714, intron 2 of 7)	MIR|SINE|MIR	-132180	NR_126098	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.003953	0.440945	
chunk0086_308_1	chr18	24068739	24068938	+	0	NA	intron (NM_153211, intron 3 of 13)	intron (NM_153211, intron 3 of 13)	-44515	NM_001292030	125488	Hs.128576	NM_153211	ENSG00000168234	TTC39C	C18orf17|HsT2697	tetratricopeptide repeat domain 39C	protein-coding	0.010050	0.320000	
chunk0080_104_1	chr17	26939212	26939579	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	354601	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.016349	0.461957	
chunk0198_336_1	chr8	140090128	140090398	+	0	NA	intron (NM_001160372, intron 17 of 22)	intron (NM_001160372, intron 17 of 22)	367499	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.022222	0.476015	150(GGAAACACACTGTTCA,-,0.00),151(GAAACACACTGTTCAC,+,0.00)
chunk0060_311_1	chr14	50995160	50995567	+	0	NA	TTS (NM_052978)	TTS (NM_052978)	-50833	NM_001163940	5836	Hs.282417	NM_002863	ENSG00000100504	PYGL	GSD6	glycogen phosphorylase L	protein-coding	0.007371	0.330882	
chunk0108_69_1	chr2	227462622	227463170	+	0	NA	Intergenic	Intergenic	-9236	NR_049888	100847081		NR_049888	ENSG00000284092	MIR5703	mir-5703	microRNA 5703	ncRNA	0.012774	0.449909	
chunk0150_242_1	chr5	36111136	36111599	+	0	NA	intron (NM_001007527, intron 13 of 17)	intron (NM_001007527, intron 13 of 17)	36621	NR_030306	693165		NR_030306	ENSG00000207756	MIR580	MIRN580|hsa-mir-580	microRNA 580	ncRNA	0.004320	0.323276	
chunk0171_35_1	chr6	120539973	120540172	+	0	NA	Intergenic	Intergenic	524893	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.000000	0.345000	
chunk0162_341_1	chr6	6923081	6923460	+	0	NA	Intergenic	Intergenic	-184327	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.013193	0.421053	
chunk0197_248_1	chr8	123396356	123396838	+	0	NA	promoter-TSS (NM_014109)	promoter-TSS (NM_014109)	-132	NM_014109	29028	Hs.370834	NM_014109	ENSG00000156802	ATAD2	ANCCA|CT137|PRO2000	ATPase family AAA domain containing 2	protein-coding	0.099585	0.652174	
chunk0200_160_1	chr9	18569038	18569442	+	0	NA	intron (NM_052866, intron 3 of 12)	intron (NM_052866, intron 3 of 12)	-4066	NR_036107	100422869		NR_036107	ENSG00000264638	MIR3152	-	microRNA 3152	ncRNA	0.012376	0.375309	
chunk0022_392_1	chr10	17794469	17794715	+	0	NA	intron (NM_001098844, intron 3 of 3)	intron (NM_001098844, intron 3 of 3)	-14751	NM_002438	4360	Hs.75182	NM_002438	ENSG00000260314	MRC1	CD206|CLEC13D|CLEC13DL|MMR|MRC1L1|bA541I19.1|hMR	mannose receptor C-type 1	protein-coding	0.012195	0.417004	
chunk0102_227_1	chr2	148705303	148705905	+	0	NA	intron (NM_015630, intron 2 of 13)	L1PA5|LINE|L1	60613	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.008306	0.477612	
chunk0006_355_1	chr1	72766568	72766767	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-484073	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.010050	0.330000	
chunk0013_385_1	chr1	172611113	172611574	+	0	NA	3' UTR (NM_016227, exon 23 of 23)	3' UTR (NM_016227, exon 23 of 23)	-47665	NM_000639	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.004338	0.305195	
chunk0031_186_1	chr10	125683639	125684410	+	0	NA	promoter-TSS (NM_001128202)	promoter-TSS (NM_001128202)	781	NR_033848	283038	Hs.144911	NR_033848	ENSG00000228021	LOC283038	-	uncharacterized LOC283038	ncRNA	0.010376	0.488342	380(CAGGACAACCTGTCCA,-,0.00),381(AGGACAACCTGTCCAG,+,0.00)
chunk0104_222_1	chr2	176388001	176388200	+	0	NA	Intergenic	Intergenic	118705	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.000000	0.410000	
chunk0024_397_1	chr10	45063416	45064119	+	0	NA	Intergenic	Intergenic	-62857	NM_001039380	220979	Hs.707791	NM_001039380		C10orf25	-	chromosome 10 open reading frame 25	protein-coding	0.008535	0.399148	
chunk0157_296_1	chr5	120975793	120976222	+	0	NA	Intergenic	Intergenic	-346543	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.002331	0.355814	
chunk0054_217_1	chr13	45414880	45415079	+	0	NA	intron (NM_001286807, intron 1 of 9)	intron (NM_001286807, intron 1 of 9)	-3183	NR_047031	100874259	Hs.658038	NR_047031	ENSG00000251015	SLC25A30-AS1	-	SLC25A30 antisense RNA 1	ncRNA	0.010050	0.455000	
chunk0127_316_1	chr3	99857002	99857761	+	0	NA	intron (NM_001042459, intron 4 of 4)	intron (NM_001042459, intron 4 of 4)	18822	NM_014890	11259	Hs.104672	NM_014890	ENSG00000168386	FILIP1L	DOC-1|DOC1|GIP130|GIP90	filamin A interacting protein 1 like	protein-coding	0.002635	0.363158	363(TAGAACTGTATGTGCT,-,0.00),364(AGAACTGTATGTGCTT,+,0.00)
chunk0040_229_1	chr11	114433505	114433734	+	0	NA	Intergenic	Intergenic	-5767	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.004367	0.343478	
chunk0121_181_1	chr3	20081137	20081513	+	0	NA	intron (NM_003884, intron 2 of 17)	intron (NM_003884, intron 2 of 17)	41293	NM_003884	8850	Hs.533055	NM_003884	ENSG00000114166	KAT2B	CAF|P/CAF|PCAF	lysine acetyltransferase 2B	protein-coding	0.015957	0.522546	
chunk0140_212_1	chr4	70709559	70709847	+	0	NA	intron (NM_001130709, intron 1 of 11)	intron (NM_001130709, intron 1 of 11)	4766	NM_001130709	22902	Hs.740904	NM_014961	ENSG00000018189	RUFY3	RIPX|SINGAR1|ZFYVE30	RUN and FYVE domain containing 3	protein-coding	0.010417	0.432526	
chunk0208_163_1	chrX	16454683	16455106	+	0	NA	Intergenic	Intergenic	172191	NR_039762	100616428		NR_039762	ENSG00000265144	MIR548AM	-	microRNA 548am	ncRNA	0.004728	0.375000	
chunk0163_412_1	chr6	16947677	16947876	+	0	NA	Intergenic	Intergenic	-154482	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.005025	0.445000	
chunk0147_339_1	chr4	185464289	185464488	+	0	NA	intron (NM_152775, intron 2 of 6)	LTR84b|LTR|ERVL	7371	NM_152775	256309	Hs.41101	NM_152775	ENSG00000168491	CCDC110	CT52|KM-HN-1|KMHN1	coiled-coil domain containing 110	protein-coding	0.015075	0.535000	
chunk0208_406_1	chrX	29382400	29382599	+	0	NA	intron (NM_014271, intron 3 of 10)	intron (NM_014271, intron 3 of 10)	-191779	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.005025	0.375000	
chunk0046_104_1	chr12	57130932	57131299	+	0	NA	intron (NM_002332, intron 1 of 88)	intron (NM_002332, intron 1 of 88)	2616	NM_002332	4035	Hs.162757	NM_002332	ENSG00000123384	LRP1	A2MR|APOER|APR|CD91|IGFBP-3R|IGFBP3R|IGFBP3R1|KPA|LRP|LRP1A|TGFBR5	LDL receptor related protein 1	protein-coding	0.002725	0.502717	
chunk0037_311_1	chr11	76788460	76789119	+	0	NA	intron (NM_015516, intron 1 of 1)	intron (NM_015516, intron 1 of 1)	5548	NM_015516	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.016692	0.566667	
chunk0040_308_1	chr11	117668023	117668621	+	0	NA	intron (NM_020693, intron 3 of 32)	intron (NM_020693, intron 3 of 32)	128939	NM_020693	57453	Hs.659513	NM_020693	ENSG00000177103	DSCAML1	DSCAM2	DS cell adhesion molecule like 1	protein-coding	0.010033	0.490818	444(AAGCACAGTGTGCCCA,-,0.00),445(AGCACAGTGTGCCCAT,+,0.00)
chunk0017_465_1	chr1	214583111	214583400	+	0	NA	Intergenic	Intergenic	-19934	NM_016343	1063	Hs.497741	NM_016343	ENSG00000117724	CENPF	CENF|CILD31|PRO1779|STROMS|hcp-1	centromere protein F	protein-coding	0.017301	0.386207	
chunk0195_8_1	chr8	92954152	92954574	+	0	NA	intron (NM_001171798, intron 1 of 4)	A-rich|Low_complexity|Low_complexity	11226	NM_001191036	286144	Hs.440643	NM_001171795	ENSG00000205133	TRIQK	C8orf83|PRO0845|UPF0599	triple QxxK/R motif containing	protein-coding	0.002370	0.326241	
chunk0162_259_1	chr6	5192208	5192493	+	0	NA	intron (NM_001164840, intron 2 of 2)	intron (NM_001164840, intron 2 of 2)	-44028	NR_037462	100500900		NR_037462	ENSG00000265083	MIR3691	mir-3691	microRNA 3691	ncRNA	0.010526	0.510490	115(CAGTACATAATGTCCT,-,0.00),116(AGTACATAATGTCCTC,+,0.00)
chunk0042_242_1	chr12	6363822	6364312	+	0	NA	intron (NM_001159576, intron 1 of 11)	CpG-5265	11157	NM_001159576	6337	Hs.591047	NM_001038	ENSG00000111319	SCNN1A	BESC2|ENaCa|ENaCalpha|LIDLS3|SCNEA|SCNN1	sodium channel epithelial 1 alpha subunit	protein-coding	0.069388	0.610998	
chunk0205_118_1	chr9	107825785	107826463	+	0	NA	Intergenic	Intergenic	-336404	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.005900	0.432990	
chunk0099_119_1	chr2	85999333	85999532	+	0	NA	Intergenic	Intergenic	24436	NR_026984									0.010050	0.515000	
chunk0104_340_1	chr2	179682187	179682429	+	0	NA	intron (NM_152520, intron 3 of 9)	intron (NM_152520, intron 3 of 9)	63734	NM_001113397	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.000000	0.370370	
chunk0210_296_1	chrX	87417141	87417393	+	0	NA	Intergenic	L1PA16|LINE|L1	-100445	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.000000	0.387352	9(TTGAACAGGGAGTCCT,-,0.00),10(TGAACAGGGAGTCCTT,+,0.00)
chunk0051_92_1	chr12	114611476	114611911	+	0	NA	Intergenic	Intergenic	72471	NM_005996	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.006897	0.422018	
chunk0173_442_1	chr6	151549876	151550202	+	0	NA	intron (NM_025059, intron 5 of 10)	intron (NM_025059, intron 5 of 10)	55999	NM_025059	80129	Hs.660044	NM_025059	ENSG00000120262	CCDC170	C6orf97|bA282P11.1	coiled-coil domain containing 170	protein-coding	0.003067	0.308869	
chunk0101_170_1	chr2	129059026	129059452	+	0	NA	Intergenic	Intergenic	194639	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.011737	0.489461	
chunk0070_259_1	chr15	73710063	73710452	+	0	NA	intron (NM_001024736, intron 8 of 9)	MIRc|SINE|MIR	25976	NM_025240	80381	Hs.744915	NM_025240	ENSG00000103855	CD276	4Ig-B7-H3|B7-H3|B7H3|B7RP-2	CD276 molecule	protein-coding	0.002571	0.451282	
chunk0165_124_1	chr6	32964778	32965436	+	0	NA	Intergenic	MIR|SINE|MIR	-3553	NM_005104	6046	Hs.75243	NM_005104	ENSG00000204256	BRD2	BRD2-IT1|D6S113E|FSH|FSRG1|NAT|O27.1.1|RING3|RNF3	bromodomain containing 2	protein-coding	0.010638	0.403642	
chunk0070_404_1	chr15	77425069	77425448	+	0	NA	intron (NM_001304504, intron 1 of 9)	L2b|LINE|L2	4607	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.010554	0.405263	123(CAGCACTTACTGTCCA,-,0.00),124(AGCACTTACTGTCCAG,+,0.00)
chunk0098_390_1	chr2	79523282	79523838	+	0	NA	intron (NM_001282598, intron 1 of 17)	L1ME3G|LINE|L1	377	NM_001282598	1496	Hs.167368	NM_004389	ENSG00000066032	CTNNA2	CAP-R|CAPR|CDCBM9|CT114|CTNR	catenin alpha 2	protein-coding	0.001799	0.296230	
chunk0158_323_1	chr5	132853259	132853914	+	0	NA	Intergenic	Intergenic	10947	NM_005260	2661	Hs.25022	NM_005260	ENSG00000164404	GDF9	POF14	growth differentiation factor 9	protein-coding	0.006107	0.367378	
chunk0042_320_1	chr12	9050738	9050937	+	0	NA	Intergenic	MER52C|LTR|ERV1	14233	NR_034140	253128	Hs.408739	NM_001039381	ENSG00000214851	LINC00612	C12orf33	long intergenic non-protein coding RNA 612	ncRNA	0.015075	0.625000	
chunk0196_388_1	chr8	115716512	115716803	+	0	NA	Intergenic	Intergenic	-47629	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.000000	0.311644	
chunk0109_198_1	chr20	5098669	5099168	+	0	NA	TTS (NM_014145)	TTS (NM_014145)	14169	NM_001009923	29058	Hs.472024	NM_014145	ENSG00000089063	TMEM230	C20orf30|HSPC274|dJ1116H23.2.1	transmembrane protein 230	protein-coding	0.000000	0.392000	
chunk0066_272_1	chr15	35036869	35037363	+	0	NA	Intergenic	Intergenic	-48820	NM_014106	54989	Hs.744990	NM_014106	ENSG00000198146	ZNF770	PRO1914	zinc finger protein 770	protein-coding	0.000000	0.325253	
chunk0026_287_1	chr10	67547383	67547949	+	0	NA	intron (NM_001291133, intron 4 of 8)	intron (NM_001291133, intron 4 of 8)	118019	NM_001291133	29119	Hs.21375	NM_013266	ENSG00000183230	CTNNA3	ARVD13|VR22	catenin alpha 3	protein-coding	0.000000	0.333333	
chunk0141_115_1	chr4	79685263	79685578	+	0	NA	Intergenic	Intergenic	-142051	NR_026555	118425	Hs.104215	NR_026555	ENSG00000251321	PCAT4	GDEP|PCA4|PCAN1	prostate cancer associated transcript 4	ncRNA	0.012698	0.436709	
chunk0172_138_1	chr6	135333358	135333564	+	0	NA	intron (NM_017651, intron 23 of 27)	intron (NM_017651, intron 23 of 27)	94301	NR_030317	693126		NR_030317	ENSG00000207689	MIR548A2	MIRN548A2	microRNA 548a-2	ncRNA	0.000000	0.280193	59(GAAACATACAGTCCCT,+,0.00)
chunk0195_401_1	chr8	100417345	100417622	+	0	NA	Intergenic	Intergenic	34720	NR_039681	100616451		NR_039681	ENSG00000265599	MIR4471	-	microRNA 4471	ncRNA	0.010830	0.528777	
chunk0180_371_1	chr7	74043080	74043467	+	0	NA	intron (NM_001278912, intron 8 of 31)	intron (NM_001278912, intron 8 of 31)	15484	NM_001278917	2006	Hs.647061	NM_000501	ENSG00000049540	ELN	ADCL1|SVAS|WBS|WS	elastin	protein-coding	0.031008	0.649485	
chunk0068_59_1	chr15	51793418	51793871	+	0	NA	intron (NM_014548, intron 7 of 9)	intron (NM_014548, intron 7 of 9)	-35984	NM_014547	29766	Hs.4998	NM_014547	ENSG00000138594	TMOD3	UTMOD	tropomodulin 3	protein-coding	0.004415	0.383260	
chunk0110_23_1	chr20	10420680	10421067	+	0	NA	intron (NR_072977, intron 1 of 4)	intron (NR_072977, intron 1 of 4)	11052	NM_018848	8195	Hs.472119	NM_018848	ENSG00000125863	MKKS	BBS6|HMCS|KMS|MKS	McKusick-Kaufman syndrome	protein-coding	0.002584	0.371134	
chunk0066_334_1	chr15	36694287	36694583	+	0	NA	intron (NM_032499, intron 8 of 11)	intron (NM_032499, intron 8 of 11)	99566	NM_001290232	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.000000	0.289562	
chunk0018_371_1	chr1	222006493	222007151	+	0	NA	Intergenic	Intergenic	-166156	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.000000	0.329287	
chunk0060_138_1	chr14	44952600	44953214	+	0	NA	intron (NM_017658, intron 1 of 4)	intron (NM_017658, intron 1 of 4)	8225	NM_001308112	54813	Hs.550906	NM_017658	ENSG00000179454	KLHL28	BTBD5	kelch like family member 28	protein-coding	0.009772	0.356098	
chunk0084_15_1	chr17	73372843	73373372	+	0	NA	intron (NM_001144952, intron 36 of 44)	L1MA9|LINE|L1	-61103	NM_012121	23580	Hs.3903	NM_012121	ENSG00000179604	CDC42EP4	BORG4|CEP4|KAIA1777	CDC42 effector protein 4	protein-coding	0.015123	0.409434	
chunk0036_395_1	chr11	67703915	67704167	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-22827	NM_001031615	222	Hs.87539	NM_000695	ENSG00000132746	ALDH3B2	ALDH8	aldehyde dehydrogenase 3 family member B2	protein-coding	0.019841	0.498024	
chunk0097_69_1	chr2	44198353	44198789	+	0	NA	intron (NM_177969, intron 1 of 4)	intron (NM_177969, intron 1 of 4)	29768	NM_177969	5495	Hs.416769	NM_002706	ENSG00000138032	PPM1B	PP2C-beta|PP2C-beta-X|PP2CB|PP2CBETA|PPC2BETAX	protein phosphatase, Mg2+/Mn2+ dependent 1B	protein-coding	0.016055	0.425629	285(GTAACATAATGTGCCT,+,0.00)
chunk0039_330_1	chr11	104323705	104324377	+	0	NA	Intergenic	Intergenic	71450	NR_106987									0.004464	0.401189	
chunk0001_440_1	chr1	11586015	11586537	+	0	NA	Intergenic	MIRb|SINE|MIR	-23255	NR_104624	101929181	Hs.568616	NR_104624	ENSG00000235643	LINC01647	-	long intergenic non-protein coding RNA 1647	ncRNA	0.011494	0.495220	402(TGCACAGCCTGCCCTG,+,0.00)
chunk0008_248_1	chr1	94407975	94408334	+	0	NA	Intergenic	L2c|LINE|L2	-10223	NM_002858	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.019499	0.416667	
chunk0088_23_1	chr18	43578881	43579245	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	-301413	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.005495	0.427397	
chunk0073_172_1	chr16	8718866	8719414	+	0	NA	intron (NM_000663, intron 1 of 15)	L2b|LINE|L2	-1576	NM_001127448	18	Hs.336768	NM_000663	ENSG00000183044	ABAT	GABA-AT|GABAT|NPD009	4-aminobutyrate aminotransferase	protein-coding	0.027372	0.471767	
chunk0128_159_1	chr3	107194283	107194834	+	0	NA	intron (NR_028303, intron 1 of 3)	intron (NR_028303, intron 1 of 3)	46080	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.000000	0.251812	
chunk0194_298_1	chr8	87899337	87899706	+	0	NA	Intergenic	Intergenic	-25453	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.002710	0.291892	
chunk0148_191_1	chr5	8165994	8166244	+	0	NA	Intergenic	L1PA13|LINE|L1	291445	NR_039984	729506	Hs.566412	NR_039984	ENSG00000245729	LINC02226	-	long intergenic non-protein coding RNA 2226	ncRNA	0.012000	0.553785	
chunk0124_239_1	chr3	56720735	56721287	+	0	NA	Intergenic	L1MEc|LINE|L1	-37904	NM_001112736	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.000000	0.367089	
chunk0100_226_1	chr2	112074006	112074228	+	0	NA	intron (NM_032824, intron 4 of 18)	L1PREC2|LINE|L1	18894	NM_032824	84910	Hs.656298	NM_032824	ENSG00000153214	TMEM87B	-	transmembrane protein 87B	protein-coding	0.009009	0.394619	
chunk0202_170_1	chr9	73838695	73839937	+	0	NA	Intergenic	Intergenic	-532215	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.004026	0.353178	
chunk0192_121_1	chr8	61759539	61759821	+	0	NA	Intergenic	Intergenic	44892	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.010638	0.466431	
chunk0148_319_1	chr5	13938801	13939436	+	0	NA	intron (NM_001369, intron 1 of 78)	L2a|LINE|L2	5362	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.012598	0.391509	
chunk0024_64_1	chr10	34100564	34101218	+	0	NA	Intergenic	AluJb|SINE|Alu	-328211	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.012232	0.480916	
chunk0179_307_1	chr7	50181620	50181825	+	0	NA	Intergenic	Intergenic	85636	NM_001161834	100130988	Hs.99248	NM_001161834	ENSG00000164500	SPATA48	C7orf72	spermatogenesis associated 48	protein-coding	0.000000	0.339806	35(TGGCACATTCTGTCCT,-,0.00),36(GGCACATTCTGTCCTT,+,0.00)
chunk0030_127_1	chr10	113307095	113307576	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-243496	NM_001177660	3026	Hs.422542	NM_004132	ENSG00000148702	HABP2	FSAP|HABP|HGFAL|NMTC5|PHBP	hyaluronan binding protein 2	protein-coding	0.006237	0.383817	
chunk0154_131_1	chr5	79145406	79145662	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	33753	NM_001713	635	Hs.80756	NM_001713	ENSG00000145692	BHMT	BHMT1|HEL-S-61p	betaine--homocysteine S-methyltransferase	protein-coding	0.007812	0.459144	
chunk0074_174_1	chr16	23564640	23565401	+	0	NA	intron (NM_019116, intron 5 of 6)	intron (NM_019116, intron 5 of 6)	7479	NM_019116	56061	Hs.3459	NM_019116	ENSG00000103353	UBFD1	UBPH	ubiquitin family domain containing 1	protein-coding	0.013141	0.500000	179(AAGAACTTCCTGACCC,-,0.00),481(GAGGACAGCTTGTTCT,-,0.00),482(AGGACAGCTTGTTCTG,+,0.00)
chunk0066_263_1	chr15	34910407	34911107	+	0	NA	intron (NM_014691, intron 16 of 34)	L1MA9|LINE|L1	59037	NM_014691	9716	Hs.510958	NM_014691	ENSG00000021776	AQR	IBP160|fSAP164	aquarius intron-binding spliceosomal factor	protein-coding	0.001429	0.319544	
chunk0026_170_1	chr10	63266955	63267302	+	0	NA	intron (NM_032776, intron 2 of 25)	intron (NM_032776, intron 2 of 25)	2095	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.002882	0.272989	
chunk0142_206_1	chr4	97412127	97412668	+	0	NA	intron (NR_102713, intron 1 of 5)	intron (NR_102713, intron 1 of 5)	45471	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.003697	0.380074	
chunk0038_331_1	chr11	92675418	92675939	+	0	NA	intron (NM_001008781, intron 2 of 24)	intron (NM_001008781, intron 2 of 24)	-293945	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.007678	0.377395	
chunk0149_190_1	chr5	21370869	21371075	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-88508	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.004854	0.396135	
chunk0071_344_1	chr15	88148165	88148364	+	0	NA	intron (NM_002530, intron 5 of 18)	intron (NM_002530, intron 5 of 18)	-104466	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.015075	0.400000	
chunk0092_392_1	chr19	36668453	36668701	+	0	NA	Intergenic	Intergenic	-1724	NM_153257	92283	Hs.590972	NM_153257	ENSG00000197808	ZNF461	GIOT-1|GIOT1|HZF28	zinc finger protein 461	protein-coding	0.024194	0.530120	
chunk0045_46_1	chr12	45131630	45131861	+	0	NA	Intergenic	Intergenic	-66334	NR_026583	83956	Hs.650500	NM_032032		RACGAP1P	FKSG42	Rac GTPase activating protein 1 pseudogene	pseudo	0.000000	0.504310	
chunk0128_336_1	chr3	112121755	112121957	+	0	NA	3' UTR (NM_152785, exon 6 of 6)	3' UTR (NM_152785, exon 6 of 6)	9055	NR_030292	693152		NR_030292	ENSG00000207940	MIR567	MIRN567|hsa-mir-567	microRNA 567	ncRNA	0.004950	0.413793	
chunk0146_135_1	chr4	159204413	159204807	+	0	NA	Intergenic	Intergenic	-63236	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.010152	0.415190	104(GGGATCATACAGTTCT,-,0.00),105(GGATCATACAGTTCTG,+,0.00)
chunk0062_435_1	chr14	75352596	75352923	+	0	NA	Intergenic	L2b|LINE|L2	58355	NR_038421	731223	Hs.534624	NR_038421		LINC01220	-	long intergenic non-protein coding RNA 1220	ncRNA	0.009174	0.487805	
chunk0190_43_1	chr8	29375673	29376146	+	0	NA	Intergenic	L1ME2|LINE|L1	-25159	NM_001394	1846	Hs.417962	NM_001394	ENSG00000120875	DUSP4	HVH2|MKP-2|MKP2|TYP	dual specificity phosphatase 4	protein-coding	0.010571	0.358650	
chunk0048_322_1	chr12	83476086	83476318	+	0	NA	Intergenic	Intergenic	789047	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.004310	0.364807	
chunk0073_406_1	chr16	17384901	17385698	+	0	NA	intron (NM_022166, intron 1 of 11)	(AC)n|Simple_repeat|Simple_repeat	85582	NM_022166	64131	Hs.22907	NM_022166	ENSG00000103489	XYLT1	DBQD2|PXYLT1|XT-I|XT1|XTI|XYLTI|xylT-I	xylosyltransferase 1	protein-coding	0.016311	0.449875	
chunk0078_352_1	chr16	86657904	86658197	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	79541	NM_005250	2300	Hs.533830	NM_005250	ENSG00000176678	FOXL1	FKH6|FKHL11|FREAC7	forkhead box L1	protein-coding	0.013652	0.489796	
chunk0073_163_1	chr16	8172332	8172945	+	0	NA	Intergenic	Intergenic	417200	NR_110736	283953	Hs.150849	NM_001146336	ENSG00000232258	TMEM114	-	transmembrane protein 114	protein-coding	0.016313	0.420195	
chunk0130_88_1	chr3	130777995	130778244	+	0	NA	Intergenic	Intergenic	-31267	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.000000	0.316000	
chunk0039_61_1	chr11	96256378	96256826	+	0	NA	intron (NM_032427, intron 1 of 4)	L2c|LINE|L2	-84836	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.008929	0.396437	
chunk0006_181_1	chr1	67224284	67224551	+	0	NA	intron (NM_144701, intron 7 of 10)	intron (NM_144701, intron 7 of 10)	57931	NM_144701	149233	Hs.677426	NM_144701	ENSG00000162594	IL23R	-	interleukin 23 receptor	protein-coding	0.000000	0.384328	
chunk0170_435_1	chr6	118875624	118876312	+	0	NA	intron (NM_017696, intron 6 of 11)	L1MC1|LINE|L1	-18109	NM_014034	25842	Hs.292316	NM_014034	ENSG00000111875	ASF1A	CGI-98|CIA|HSPC146	anti-silencing function 1A histone chaperone	protein-coding	0.004360	0.358491	
chunk0202_287_1	chr9	77466598	77466973	+	0	NA	intron (NR_121184, intron 2 of 4)	L1M4a2|LINE|L1	19136	NR_121184	101927422	Hs.434324	NR_121184	ENSG00000231373	GNA14-AS1	-	GNA14 antisense RNA 1	ncRNA	0.008000	0.454787	
chunk0020_393_1	chr1	240522645	240522845	+	0	NA	intron (NM_022469, intron 1 of 1)	intron (NM_022469, intron 1 of 1)	89417	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.010000	0.378109	
chunk0061_314_1	chr14	62649142	62649823	+	0	NA	Intergenic	Intergenic	395756	NM_139318	27133	Hs.27043	NM_139318	ENSG00000140015	KCNH5	EAG2|H-EAG2|Kv10.2|hEAG2	potassium voltage-gated channel subfamily H member 5	protein-coding	0.008811	0.414956	
chunk0130_27_1	chr3	128794075	128794333	+	0	NA	intron (NM_004637, intron 1 of 5)	(CTGTATT)n|Simple_repeat|Simple_repeat	68068	NM_004637	7879	Hs.684374	NM_004637	ENSG00000075785	RAB7A	PRO2706|RAB7	RAB7A, member RAS oncogene family	protein-coding	0.003876	0.428571	120(CTGGACTCTGTGTTCT,-,0.00),121(TGGACTCTGTGTTCTG,+,0.00)
chunk0050_213_1	chr12	104343020	104343222	+	0	NA	intron (NM_003330, intron 14 of 14)	MIR|SINE|MIR	39389	NM_001008394	493861	Hs.659857	NM_001008394	ENSG00000255150	EID3	NS4EB|NSE4B|NSMCE4B	EP300 interacting inhibitor of differentiation 3	protein-coding	0.034653	0.522167	
chunk0196_75_1	chr8	102545223	102545836	+	0	NA	Intergenic	Intergenic	-6091	NM_024410	4956	Hs.159274	NM_024410	ENSG00000155087	ODF1	CT133|HSPB10|ODF|ODF2|ODF27|ODFP|ODFPG|ODFPGA|ODFPGB|RT7|SODF	outer dense fiber of sperm tails 1	protein-coding	0.011419	0.423453	
chunk0041_448_1	chr11	134849917	134850116	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	413534	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.015075	0.475000	
chunk0121_355_1	chr3	24772602	24772955	+	0	NA	Intergenic	L1ME5|LINE|L1	-251343	NR_039955									0.008499	0.406780	
chunk0123_379_1	chr3	48663578	48663821	+	0	NA	promoter-TSS (NM_001407)	promoter-TSS (NM_001407)	-69	NR_111921	102724368	Hs.663571	NR_111921	ENSG00000228350	LINC02585	CELSR3-AS1	long intergenic non-protein coding RNA 2585	ncRNA	0.090535	0.655738	
chunk0142_38_1	chr4	90851414	90851841	+	0	NA	intron (NM_001145065, intron 8 of 10)	intron (NM_001145065, intron 8 of 10)	616596	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.004684	0.364486	238(GTGTACAGAATGTGCT,-,0.00),239(TGTACAGAATGTGCTA,+,0.00)
chunk0177_126_1	chr7	22357763	22357962	+	0	NA	promoter-TSS (NM_012294)	promoter-TSS (NM_012294)	-948	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.015075	0.490000	
chunk0045_325_1	chr12	50924589	50925199	+	0	NA	5' UTR (NM_014033, exon 1 of 2)	5' UTR (NM_014033, exon 1 of 2)	143	NM_014033	25840	Hs.711113	NM_014033	ENSG00000185432	METTL7A	AAM-B|AAMB	methyltransferase like 7A	protein-coding	0.011475	0.459902	326(CAGCACAGCCAGTTCT,-,0.00),327(AGCACAGCCAGTTCTT,+,0.00)
chunk0031_260_1	chr10	127277960	127278464	+	0	NA	intron (NM_001290223, intron 29 of 51)	intron (NM_001290223, intron 29 of 51)	-82054	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.009921	0.429703	
chunk0158_6_1	chr5	125190044	125190794	+	0	NA	intron (NR_109882, intron 4 of 5)	intron (NR_109882, intron 4 of 5)	153588	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.009333	0.378162	277(GAGAACTGGCTGTTCA,-,0.00),278(AGAACTGGCTGTTCAA,+,0.00)
chunk0179_86_1	chr7	44571463	44571695	+	0	NA	exon (NM_001257189, exon 6 of 13)	exon (NM_001257189, exon 6 of 13)	2959	NM_001257189	54606	Hs.654762	NM_019082	ENSG00000136271	DDX56	DDX21|DDX26|NOH61	DEAD-box helicase 56	protein-coding	0.021552	0.519313	
chunk0174_444_1	chr6	166204675	166205328	+	0	NA	Intergenic	(CCAGCT)n|Simple_repeat|Simple_repeat	-31968	NR_125862	101929297	Hs.434661	NR_125862	ENSG00000233365	LOC101929297	-	uncharacterized LOC101929297	ncRNA	0.013783	0.467890	
chunk0189_81_1	chr8	21227444	21227643	+	0	NA	Intergenic	Intergenic	-70696	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.010050	0.450000	78(TAGAACATACTGAACC,-,0.00),79(AGAACATACTGAACCC,+,0.00)
chunk0208_172_1	chrX	16700878	16701077	+	0	NA	intron (NM_019857, intron 2 of 18)	MER81|DNA|hAT-Blackjack	11240	NM_001144002	56474	Hs.227049	NM_019857	ENSG00000047230	CTPS2	-	CTP synthase 2	protein-coding	0.005025	0.435000	
chunk0097_265_1	chr2	54555715	54556191	+	0	NA	intron (NM_003128, intron 2 of 35)	intron (NM_003128, intron 2 of 35)	-2441	NM_178313	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.002101	0.469602	
chunk0125_344_1	chr3	71130133	71131117	+	0	NA	exon (NM_001244815, exon 1 of 16)	exon (NM_001244815, exon 1 of 16)	316	NM_001244815	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.020325	0.423350	
chunk0080_68_1	chr17	21987617	21987862	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	295216	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.012245	0.382114	
chunk0079_343_1	chr17	17732462	17732818	+	0	NA	intron (NM_030665, intron 2 of 5)	MIR|SINE|MIR	33662	NR_130894	100861516	Hs.624874	NR_130894	ENSG00000237328	RAI1-AS1	-	RAI1 antisense RNA 1	ncRNA	0.011236	0.551821	
chunk0151_289_1	chr5	52864832	52865279	+	0	NA	exon (NM_181501, exon 5 of 29)	exon (NM_181501, exon 5 of 29)	76753	NM_181501	3672	Hs.644352	NM_181501	ENSG00000213949	ITGA1	CD49a|VLA1	integrin subunit alpha 1	protein-coding	0.006711	0.332589	
chunk0141_178_1	chr4	82786877	82787279	+	0	NA	intron (NM_001037582, intron 1 of 4)	intron (NM_001037582, intron 1 of 4)	11779	NM_024906	79966	Hs.379191	NM_024906	ENSG00000145284	SCD5	ACOD4|FADS4|HSCD5|SCD2|SCD4	stearoyl-CoA desaturase 5	protein-coding	0.009950	0.419355	
chunk0166_305_1	chr6	49607138	49607425	+	0	NA	intron (NM_000324, intron 7 of 9)	intron (NM_000324, intron 7 of 9)	29593	NM_000324	6005	Hs.120950	NM_000324	ENSG00000112077	RHAG	CD241|OHS|OHST|RH2|RH50A|RHNR|Rh50|Rh50GP|SLC42A1	Rh associated glycoprotein	protein-coding	0.003484	0.416667	
chunk0096_90_1	chr2	28009744	28010113	+	0	NA	intron (NM_199191, intron 4 of 11)	intron (NM_199191, intron 4 of 11)	13561	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.000000	0.445946	167(CAGGACAGCTTGTACA,-,0.00),168(AGGACAGCTTGTACAT,+,0.00)
chunk0103_224_1	chr2	164514663	164515006	+	0	NA	intron (NM_004490, intron 6 of 13)	L1PB1|LINE|L1	53716	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.008746	0.529070	
chunk0097_347_1	chr2	58614016	58614812	+	0	NA	intron (NR_033873, intron 1 of 13)	intron (NR_033873, intron 1 of 13)	93661	NR_033873	400955	Hs.503210	NR_033873	ENSG00000233723	LINC01122	-	long intergenic non-protein coding RNA 1122	ncRNA	0.005025	0.308657	215(TAGTTCATACTGTTCC,-,0.00),216(AGTTCATACTGTTCCT,+,0.00)
chunk0204_354_1	chr9	101567600	101567907	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	27248	NM_147180	5535	Hs.151167	NM_147180	ENSG00000188386	PPP3R2	PPP3RL	protein phosphatase 3 regulatory subunit B, beta	protein-coding	0.003257	0.396104	
chunk0075_355_1	chr16	55963791	55964482	+	0	NA	Intergenic	Intergenic	-8105	NM_001190158	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.007236	0.352601	
chunk0164_414_1	chr6	27053620	27053904	+	0	NA	Intergenic	Intergenic	-33456	NR_026776	100270746	Hs.590428	NR_026776		LOC100270746	-	uncharacterized LOC100270746	ncRNA	0.000000	0.392982	
chunk0011_398_1	chr1	154142170	154142698	+	0	NA	intron (NM_207308, intron 3 of 39)	intron (NM_207308, intron 3 of 39)	12682	NM_001159484	91181	Hs.67639	NM_207308	ENSG00000143552	NUP210L	-	nucleoporin 210 like	protein-coding	0.013258	0.376181	
chunk0008_316_1	chr1	95204630	95204857	+	0	NA	intron (NR_125948, intron 3 of 4)	L2a|LINE|L2	29239	NR_125949	101928118	Hs.656443	NR_125948	ENSG00000226026	LOC101928118	-	uncharacterized LOC101928118	ncRNA	0.004405	0.478070	98(AAGAACAATCTGTGCA,-,0.00),99(AGAACAATCTGTGCAG,+,0.00)
chunk0077_26_1	chr16	75120169	75120719	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-3672	NM_194436	197257	Hs.380929	NM_153486	ENSG00000166816	LDHD	DLACD|DLD	lactate dehydrogenase D	protein-coding	0.018182	0.397459	
chunk0101_287_1	chr2	134284207	134284878	+	0	NA	intron (NM_002410, intron 2 of 15)	intron (NM_002410, intron 2 of 15)	30283	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.004471	0.404762	
chunk0002_209_1	chr1	19615004	19615441	+	0	NA	intron (NM_001204088, intron 2 of 4)	intron (NM_001204088, intron 2 of 4)	7415	NR_077246	644068	Hs.660760	NR_077246		RPS14P3	RPS14_1_16	ribosomal protein S14 pseudogene 3	pseudo	0.002288	0.417808	
chunk0155_47_1	chr5	91165227	91165650	+	0	NA	Intergenic	Intergenic	148964	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.007092	0.367925	
chunk0035_413_1	chr11	56974871	56975193	+	0	NA	Intergenic	L1PA16|LINE|L1	-13882	NM_001005323	390181	Hs.554520	NM_001005323	ENSG00000181273	OR5AK2	-	olfactory receptor family 5 subfamily AK member 2	protein-coding	0.006211	0.371517	
chunk0069_313_1	chr15	65665225	65665434	+	0	NA	intron (NM_001144823, intron 30 of 32)	intron (NM_001144823, intron 30 of 32)	22424	NM_001254740	9187	Hs.173092	NM_004727	ENSG00000074621	SLC24A1	CSNB1D|HsT17412|NCKX|NCKX1|RODX	solute carrier family 24 member 1	protein-coding	0.004785	0.347619	
chunk0147_156_1	chr4	175708654	175709229	+	0	NA	intron (NM_201592, intron 1 of 6)	L1MEd|LINE|L1	78735	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.008696	0.321181	
chunk0190_60_1	chr8	29724329	29724784	+	0	NA	intron (NR_026765, intron 3 of 3)	intron (NR_026765, intron 3 of 3)	23553	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.017582	0.414474	
chunk0140_207_1	chr4	70566189	70566526	+	0	NA	Intergenic	L1PA14|LINE|L1	-25901	NM_016519	258	Hs.272396	NM_016519	ENSG00000178522	AMBN	AI1F	ameloblastin	protein-coding	0.002967	0.328402	
chunk0184_144_1	chr7	115775883	115776517	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	192113	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.001577	0.348031	
chunk0027_69_1	chr10	73167715	73167914	+	0	NA	promoter-TSS (NM_173348)	promoter-TSS (NM_173348)	281	NR_024203	11319	Hs.631822	NM_007265	ENSG00000122882	ECD	GCR2|HSGT1|SGT1	ecdysoneless cell cycle regulator	protein-coding	0.020101	0.500000	
chunk0010_3_1	chr1	111783515	111784093	+	0	NA	intron (NM_172198, intron 3 of 6)	L1MD2|LINE|L1	-28007	NM_198926	55924	Hs.193406	NM_019099	ENSG00000197852	INKA2	C1orf183|FAM212B	inka box actin regulator 2	protein-coding	0.003460	0.395509	
chunk0194_239_1	chr8	86354476	86354675	+	0	NA	intron (NM_007013, intron 1 of 24)	intron (NM_007013, intron 1 of 24)	11810	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.280000	
chunk0122_121_1	chr3	31272178	31272822	+	0	NA	Intergenic	Intergenic	-110713	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.009317	0.482171	222(TGGGACAAGGTGTTCA,-,0.00),223(GGGACAAGGTGTTCAC,+,0.00),317(AAGTACACACAGTGCC,-,0.00),318(AGTACACACAGTGCCC,+,0.00),423(GGGTTCACGGTGTCCT,-,0.00),424(GGTTCACGGTGTCCTT,+,0.00)
chunk0181_374_1	chr7	88864644	88865157	+	0	NA	intron (NM_181646, intron 1 of 3)	intron (NM_181646, intron 1 of 3)	-69183	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.009747	0.492218	
chunk0187_426_1	chr7	158644285	158644638	+	0	NA	intron (NR_104054, intron 29 of 30)	intron (NR_104054, intron 29 of 30)	52845	NR_049893	100847032		NR_049893	ENSG00000265598	MIR5707	-	microRNA 5707	ncRNA	0.008499	0.403955	
chunk0003_395_1	chr1	39893210	39893583	+	0	NA	Intergenic	MIRb|SINE|MIR	8619	NM_001033081	4610	Hs.437922	NM_005376	ENSG00000116990	MYCL	L-Myc|LMYC|MYCL1|bHLHe38	MYCL proto-oncogene, bHLH transcription factor	protein-coding	0.002681	0.433155	
chunk0105_262_1	chr2	189210721	189211041	+	0	NA	Intergenic	Intergenic	-31002	NM_000393	1290	Hs.445827	NM_000393	ENSG00000204262	COL5A2	EDSC|EDSCL2	collagen type V alpha 2 chain	protein-coding	0.006250	0.389408	
chunk0154_318_1	chr5	84006150	84006726	+	0	NA	intron (NM_001278642, intron 8 of 9)	L1PA15|LINE|L1	-285361	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.001736	0.358752	308(AGGAACATACTGTGTA,-,0.00)
chunk0109_139_1	chr20	3377991	3378232	+	0	NA	intron (NM_001009984, intron 3 of 36)	intron (NM_001009984, intron 3 of 36)	29551	NM_001009984	25943	Hs.516853	NM_001009984	ENSG00000088854	C20orf194	-	chromosome 20 open reading frame 194	protein-coding	0.004149	0.495868	
chunk0164_164_1	chr6	21749652	21750003	+	0	NA	intron (NR_015410, intron 2 of 11)	intron (NR_015410, intron 2 of 11)	83383	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.011396	0.443182	4(AGGTACATACTGTTAT,-,0.00)
chunk0176_273_1	chr7	16584731	16584940	+	0	NA	Intergenic	Intergenic	57955	NM_001195280	100506049	Hs.278036	NM_001195280	ENSG00000205858	LRRC72	-	leucine rich repeat containing 72	protein-coding	0.009569	0.514286	
chunk0050_38_1	chr12	100554667	100554883	+	0	NA	intron (NM_001206993, intron 7 of 8)	intron (NM_001206993, intron 7 of 8)	-18886	NM_001303130	283431	Hs.20575	NM_174942	ENSG00000139354	GAS2L3	G2L3	growth arrest specific 2 like 3	protein-coding	0.004630	0.405530	
chunk0052_98_1	chr13	22405314	22405934	+	0	NA	Intergenic	Intergenic	195339	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.009677	0.415459	
chunk0120_55_1	chr3	3117638	3118542	+	0	NA	Intergenic	Intergenic	-7716	NM_175725	3568	Hs.68876	NM_000564	ENSG00000091181	IL5RA	CD125|CDw125|HSIL5R3|IL5R	interleukin 5 receptor subunit alpha	protein-coding	0.005531	0.381215	
chunk0035_163_1	chr11	43587795	43587994	+	0	NA	Intergenic	Intergenic	6500	NR_029697	406918		NR_029697	ENSG00000199077	MIR129-2	MIR-129b|MIRN129-2|mir-129-2	microRNA 129-2	ncRNA	0.005025	0.495000	
chunk0096_287_1	chr2	32365102	32365341	+	0	NA	intron (NM_016252, intron 1 of 73)	MIR|SINE|MIR	8193	NM_016252	57448	Hs.150107	NM_016252	ENSG00000115760	BIRC6	APOLLON|BRUCE	baculoviral IAP repeat containing 6	protein-coding	0.000000	0.333333	
chunk0046_68_1	chr12	55966686	55967244	+	0	NA	promoter-TSS (NM_001200054)	promoter-TSS (NM_001200054)	196	NM_001798	1017	Hs.19192	NM_001798	ENSG00000123374	CDK2	CDKN2|p33(CDK2)	cyclin dependent kinase 2	protein-coding	0.068100	0.633274	
chunk0035_406_1	chr11	56747911	56748178	+	0	NA	Intergenic	Intergenic	4171	NR_106743	102465135		NR_106743	ENSG00000274770	MIR6128	hsa-mir-6128	microRNA 6128	ncRNA	0.011236	0.425373	
chunk0019_269_1	chr1	228381412	228381758	+	0	NA	Intergenic	L1MD1|LINE|L1	15524	NR_106800	102465444		NR_106800	ENSG00000284311	MIR6742	hsa-mir-6742	microRNA 6742	ncRNA	0.005780	0.403458	
chunk0174_301_1	chr6	162678370	162678684	+	0	NA	intron (NM_013988, intron 1 of 8)	L1ME1|LINE|L1	-48605	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.003185	0.352381	
chunk0181_232_1	chr7	85237870	85238374	+	0	NA	Intergenic	L1MC1|LINE|L1	-116191	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.001984	0.312871	
chunk0186_98_1	chr7	137581468	137582090	+	0	NA	intron (NM_004717, intron 15 of 33)	MIRc|SINE|MIR	-237979	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.004823	0.422151	
chunk0132_26_1	chr3	154688105	154688404	+	0	NA	Intergenic	Intergenic	-258539	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.006689	0.370000	
chunk0041_380_1	chr11	131938478	131938933	+	0	NA	intron (NM_001144058, intron 1 of 7)	L2a|LINE|L2	27887	NM_001144059	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.013187	0.484649	281(GAAACAGCGTGTACAT,+,0.00)
chunk0125_401_1	chr3	72027783	72028199	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	72464	NR_104116	285286	Hs.559386	NR_104116	ENSG00000241163	LINC00877	-	long intergenic non-protein coding RNA 877	ncRNA	0.004808	0.448441	
chunk0117_448_1	chr21	46514581	46515158	+	0	NA	intron (NM_206889, intron 8 of 21)	L1ME3A|LINE|L1	52398	NR_046400	100862692	Hs.737163	NR_046400	ENSG00000223692	DIP2A-IT1	-	DIP2A intronic transcript 1	ncRNA	0.005199	0.325260	
chunk0167_88_1	chr6	56732483	56732838	+	0	NA	intron (NM_183380, intron 2 of 93)	intron (NM_183380, intron 2 of 93)	-89764	NM_015548	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.005634	0.325843	
chunk0185_256_1	chr7	130296175	130296618	+	0	NA	intron (NM_001163446, intron 1 of 9)	MamSINE1|SINE|tRNA-RTE	3262	NM_001163446	51200	Hs.93764	NM_016352	ENSG00000128510	CPA4	CPA3	carboxypeptidase A4	protein-coding	0.024831	0.472973	219(AGAGACACGGTGTCCC,-,0.00),220(GAGACACGGTGTCCCA,+,0.00)
chunk0204_282_1	chr9	98848301	98848852	+	0	NA	intron (NM_024642, intron 9 of 9)	intron (NM_024642, intron 9 of 9)	40877	NM_024642	79695	Hs.47099	NM_024642	ENSG00000119514	GALNT12	CRCS1|GalNAc-T12	polypeptide N-acetylgalactosaminyltransferase 12	protein-coding	0.014519	0.494565	
chunk0029_119_1	chr10	98399479	98399938	+	0	NA	intron (NM_032709, intron 5 of 15)	intron (NM_032709, intron 5 of 15)	-4401	NR_031619	100302133		NR_031619	ENSG00000284415	MIR1287	MIRN1287|hsa-mir-1287|mir-1287	microRNA 1287	ncRNA	0.013072	0.504348	
chunk0120_184_1	chr3	6770025	6770555	+	0	NA	intron (NR_110125, intron 2 of 3)	intron (NR_110125, intron 2 of 3)	35159	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.015094	0.384181	237(TAGGACACATTGTTCT,-,0.00),238(AGGACACATTGTTCTG,+,0.00)
chunk0049_136_1	chr12	91693232	91693596	+	0	NA	Intergenic	L2a|LINE|L2	448299	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.000000	0.276712	
chunk0126_388_1	chr3	84880059	84880706	+	0	NA	Intergenic	Intergenic	-10807	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.004637	0.314815	
chunk0018_135_1	chr1	218613178	218613453	+	0	NA	intron (NR_031644, intron 3 of 6)	intron (NR_031644, intron 3 of 6)	170689	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.000000	0.394928	
chunk0189_373_1	chr8	27311384	27311655	+	0	NA	promoter-TSS (NM_173174)	promoter-TSS (NM_173174)	37	NM_173174	2185	Hs.491322	NM_004103	ENSG00000120899	PTK2B	CADTK|CAKB|FADK2|FAK2|PKB|PTK|PYK2|RAFTK	protein tyrosine kinase 2 beta	protein-coding	0.073801	0.672794	
chunk0051_418_1	chr12	122412859	122413526	+	0	NA	intron (NM_001247997, intron 1 of 25)	intron (NM_001247997, intron 1 of 25)	9377	NM_001247997	6249	Hs.524809	NM_002956	ENSG00000130779	CLIP1	CLIP|CLIP-170|CLIP170|CYLN1|RSN	CAP-Gly domain containing linker protein 1	protein-coding	0.007496	0.357784	276(TAGAACATAATGTCTC,-,0.00),277(AGAACATAATGTCTCT,+,0.00)
chunk0028_390_1	chr10	92957185	92957469	+	0	NA	intron (NM_019053, intron 17 of 21)	intron (NM_019053, intron 17 of 21)	-103937	NM_183374	340665	Hs.369993	NM_183374	ENSG00000187553	CYP26C1	FFDD4	cytochrome P450 family 26 subfamily C member 1	protein-coding	0.003521	0.378947	210(TGGAACACAATGTTCT,-,0.00),211(GGAACACAATGTTCTT,+,0.00)
chunk0167_27_1	chr6	53811084	53811686	+	0	NA	intron (NM_018214, intron 1 of 13)	intron (NM_018214, intron 1 of 13)	16405	NM_018214	55227	Hs.606493	NM_018214	ENSG00000137269	LRRC1	LANO|dJ523E19.1	leucine rich repeat containing 1	protein-coding	0.006645	0.441128	
chunk0142_213_1	chr4	97630468	97631109	+	0	NA	intron (NM_174952, intron 10 of 10)	intron (NM_174952, intron 10 of 10)	263862	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.000000	0.258567	
chunk0119_188_1	chr22	44233956	44234806	+	0	NA	Intergenic	AluSx3|SINE|Alu	53491	NM_022141	64098	Hs.658995	NM_022141	ENSG00000138964	PARVG	-	parvin gamma	protein-coding	0.015294	0.391304	
chunk0034_149_1	chr11	30141658	30142491	+	0	NA	Intergenic	Intergenic	-88942	NM_001018080	2488	Hs.36975	NM_000510	ENSG00000131808	FSHB	HH24	follicle stimulating hormone subunit beta	protein-coding	0.001200	0.336930	
chunk0094_397_1	chr2	10348878	10349261	+	0	NA	intron (NM_001258357, intron 1 of 4)	intron (NM_001258357, intron 1 of 4)	18906	NM_001258357	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.018277	0.398438	
chunk0017_178_1	chr1	207067737	207068108	+	0	NA	intron (NM_001018053, intron 9 of 14)	intron (NM_001018053, intron 9 of 14)	14647	NM_006212	5208	Hs.282702	NM_006212	ENSG00000123836	PFKFB2	PFK-2/FBPase-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	protein-coding	0.008086	0.413978	
chunk0074_53_1	chr16	20891352	20891608	+	0	NA	intron (NM_173475, intron 1 of 2)	intron (NM_173475, intron 1 of 2)	-8388	NM_020424	57149	Hs.745012	NM_020424	ENSG00000102897	LYRM1	A211C6.1	LYR motif containing 1	protein-coding	0.023438	0.451362	
chunk0197_316_1	chr8	124853231	124854100	+	0	NA	Intergenic	Intergenic	-31607	NR_039809	100616255		NR_039809	ENSG00000263735	MIR4662B	-	microRNA 4662b	ncRNA	0.008055	0.439080	184(CAGAACACTATGTATC,-,0.00)
chunk0158_349_1	chr5	133434356	133434870	+	0	NA	intron (NM_015082, intron 3 of 15)	L1ME4a|LINE|L1	-6907	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.000000	0.314563	
chunk0067_127_1	chr15	42863886	42864301	+	0	NA	intron (NM_173500, intron 3 of 14)	L1P4|LINE|L1	56716	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.004819	0.329327	
chunk0001_75_1	chr1	2522812	2523035	+	0	NA	intron (NM_018216, intron 1 of 18).2	intron (NM_018216, intron 1 of 18).2	3705	NM_018216	55229	Hs.26156	NM_018216	ENSG00000157881	PANK4	-	pantothenate kinase 4	protein-coding	0.026906	0.482143	63(GAGCACTGTGTGTGCT,-,0.00),64(AGCACTGTGTGTGCTA,+,0.00)
chunk0073_413_1	chr16	18790261	18790474	+	0	NA	promoter-TSS (NM_001030009)	promoter-TSS (NM_001030009)	-33	NM_001030009	6210	Hs.370504	NM_001019	ENSG00000134419	RPS15A	DBA20|S15a	ribosomal protein S15a	protein-coding	0.079812	0.602804	
chunk0071_401_1	chr15	89498222	89498777	+	0	NA	Intergenic	Intergenic	-1886	NM_016321	51458	Hs.459284	NM_016321	ENSG00000140519	RHCG	C15orf6|PDRC2|RHGK|SLC42A3	Rh family C glycoprotein	protein-coding	0.005405	0.458633	
chunk0113_110_1	chr20	51245466	51245918	+	0	NA	Intergenic	Intergenic	207285	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.013274	0.454746	
chunk0125_8_1	chr3	61757483	61758199	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	196272	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.008380	0.348675	
chunk0116_240_1	chr21	38390106	38390459	+	0	NA	intron (NM_004449, intron 10 of 10)	intron (NM_004449, intron 10 of 10)	-44206	NR_110545	102724678	Hs.635675	NR_110545		LINC01423	-	long intergenic non-protein coding RNA 1423	ncRNA	0.008499	0.381356	
chunk0200_30_1	chr9	14983343	14984186	+	0	NA	Intergenic	L1ME4a|LINE|L1	-9563	NR_003920	389705	Hs.431257	NR_003920		LOC389705	-	histone PARylation factor 1 pseudogene	pseudo	0.004745	0.293839	
chunk0191_181_1	chr8	51302979	51303316	+	0	NA	Intergenic	Intergenic	506298	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.002967	0.511834	
chunk0168_221_1	chr6	86326093	86326685	+	0	NA	Intergenic	L1MA2|LINE|L1	-610917	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.000000	0.365936	255(AATGACATTCTGTCCT,-,0.00),256(ATGACATTCTGTCCTT,+,0.00)
chunk0108_347_1	chr2	236055438	236055834	+	0	NA	intron (NM_001037131, intron 16 of 17)	intron (NM_001037131, intron 16 of 17)	112373	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.035354	0.528967	
chunk0180_433_1	chr7	76392686	76393146	+	0	NA	intron (NM_080744, intron 9 of 10)	intron (NM_080744, intron 9 of 10)	-4608	NM_007155	7784	Hs.656137	NM_007155	ENSG00000188372	ZP3	OOMD3|ZP3A|ZP3B|ZPC|Zp-3	zona pellucida glycoprotein 3	protein-coding	0.023913	0.505423	
chunk0144_220_1	chr4	134450683	134451367	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-249277	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.002924	0.322628	
chunk0208_178_1	chrX	16978157	16978732	+	0	NA	intron (NM_004726, intron 1 of 17)	intron (NM_004726, intron 1 of 17)	31753	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.001739	0.380208	
chunk0072_5_1	chr16	239871	240070	+	0	NA	intron (NM_032039, intron 1 of 12)	intron (NM_032039, intron 1 of 12)	5424	NR_104317	83986	Hs.513225	NM_032039	ENSG00000167930	FAM234A	C16orf9|ITFG3|gs19	family with sequence similarity 234 member A	protein-coding	0.000000	0.430000	
chunk0002_240_1	chr1	20538813	20539066	+	0	NA	Intergenic	MIRb|SINE|MIR	-13500	NM_207334	163933	Hs.429179	NM_207334	ENSG00000183114	FAM43B	-	family with sequence similarity 43 member B	protein-coding	0.000000	0.334646	
chunk0132_385_1	chr3	163413579	163414097	+	0	NA	Intergenic	Intergenic	-110537	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.001931	0.304432	
chunk0076_245_1	chr16	69217322	69217753	+	0	NA	intron (NM_006750, intron 1 of 6)	intron (NM_006750, intron 1 of 6)	30390	NM_006750	6645	Hs.461117	NM_006750	ENSG00000168807	SNTB2	D16S2531E|EST25263|SNT2B2|SNT3|SNTL	syntrophin beta 2	protein-coding	0.004640	0.398148	
chunk0053_70_1	chr13	28209936	28210312	+	0	NA	intron (NM_175854, intron 5 of 18)	intron (NM_175854, intron 5 of 18)	-70950	NR_029383	100288730	Hs.123191	NR_029383		PAN3-AS1	-	PAN3 antisense RNA 1	ncRNA	0.005319	0.368700	
chunk0098_364_1	chr2	78034461	78034897	+	0	NA	intron (NR_110288, intron 1 of 3)	intron (NR_110288, intron 1 of 3)	-54051	NR_110287	101927948	Hs.639404	NR_110287	ENSG00000229494	LOC101927948	-	uncharacterized LOC101927948	ncRNA	0.006881	0.338673	
chunk0073_115_1	chr16	4695849	4696166	+	0	NA	TTS (NM_133450)	TTS (NM_133450)	2314	NM_032349	84309	Hs.513315	NM_032349	ENSG00000168101	NUDT16L1	SDOS|TIRR	nudix hydrolase 16 like 1	protein-coding	0.009464	0.610063	
chunk0069_42_1	chr15	60615464	60615749	+	0	NA	intron (NM_002943, intron 1 of 10)	intron (NM_002943, intron 1 of 10)	11924	NM_002943	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.024561	0.510490	
chunk0035_32_1	chr11	40716231	40716927	+	0	NA	intron (NM_020929, intron 1 of 4)	intron (NM_020929, intron 1 of 4)	-423449	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001437	0.368723	
chunk0144_342_1	chr4	139496667	139497300	+	0	NA	intron (NM_001306199, intron 7 of 7)	intron (NM_001306199, intron 7 of 7)	43176	NM_031296	83452	Hs.591679	NM_031296	ENSG00000172007	RAB33B	SMC2	RAB33B, member RAS oncogene family	protein-coding	0.015798	0.440063	
chunk0076_376_1	chr16	72194471	72195262	+	0	NA	Intergenic	Intergenic	-22416	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.008850	0.458333	
chunk0064_359_1	chr14	96983748	96984096	+	0	NA	Intergenic	Intergenic	40343	NR_104113	145249	Hs.592323	NR_104113	ENSG00000225163	LINC00618	C14orf63	long intergenic non-protein coding RNA 618	ncRNA	0.028736	0.504298	
chunk0102_319_1	chr2	151639716	151640244	+	0	NA	exon (NM_001164508, exon 62 of 182)	exon (NM_001164508, exon 62 of 182)	94507	NM_001164507	4703	Hs.588655	NM_004543	ENSG00000183091	NEB	NEB177D|NEM2	nebulin	protein-coding	0.007576	0.379962	
chunk0187_30_1	chr8	815160	815449	+	0	NA	intron (NR_073397, intron 1 of 3)	MLT1A1|LTR|ERVL-MaLR	77699	NR_073397	9228	Hs.113287	NM_004745	ENSG00000198010	DLGAP2	C8orf68|DAP2|ERICH1-AS1|SAPAP2	DLG associated protein 2	protein-coding	0.006920	0.520690	123(AGGAGCACTGTGTCCT,-,0.00),124(GGAGCACTGTGTCCTC,+,0.00),154(CAGAACACCCTGTTCC,-,0.00),155(AGAACACCCTGTTCCC,+,0.00)
chunk0086_317_1	chr18	24231656	24232522	+	0	NA	intron (NM_001242508, intron 4 of 15)	intron (NM_001242508, intron 4 of 15)	40143	NM_018030	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.009238	0.386390	
chunk0066_215_1	chr15	33903641	33904068	+	0	NA	intron (NM_020371, intron 2 of 5)	Tigger3a|DNA|TcMar-Tigger	-65034	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.004684	0.320093	
chunk0093_11_1	chr2	124065	124409	+	0	NA	Intergenic	Intergenic	-77649	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.005814	0.382609	
chunk0122_297_1	chr3	36254574	36254989	+	0	NA	Intergenic	L1PA10|LINE|L1	-125706	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.002410	0.350962	
chunk0002_322_1	chr1	24206303	24206989	+	0	NA	intron (NR_027087, intron 2 of 2)	intron (NR_027087, intron 2 of 2)	6406	NR_027087	284632	Hs.638906	NR_027087	ENSG00000230023	LINC02800	-	long intergenic non-protein coding RNA 2800	ncRNA	0.010204	0.601164	116(AGGCACAGGCAGTTCC,-,0.00),117(GGCACAGGCAGTTCCT,+,0.00),217(TTGCACTCTCTGTTCC,-,0.00),218(TGCACTCTCTGTTCCT,+,0.00)
chunk0063_145_1	chr14	79632764	79633305	+	0	NA	intron (NR_073547, intron 15 of 20)	MIRb|SINE|MIR	353695	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.007394	0.361624	
chunk0141_172_1	chr4	82525240	82525918	+	0	NA	intron (NM_001080506, intron 1 of 7)	intron (NM_001080506, intron 1 of 7)	36394	NM_001080506	441027	Hs.507676	NM_001080506	ENSG00000249242	TMEM150C	TTN3	transmembrane protein 150C	protein-coding	0.005900	0.391753	
chunk0096_24_1	chr2	26380126	26380932	+	0	NA	intron (NM_033505, intron 6 of 9)	L1MC5|LINE|L1	-21383	NM_145038	92749	Hs.393714	NM_145038	ENSG00000157856	DRC1	C2orf39|CCDC164|CILD21	dynein regulatory complex subunit 1	protein-coding	0.004963	0.354399	
chunk0204_422_1	chr9	103038733	103038981	+	0	NA	Intergenic	L1PBa|LINE|L1	43546	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.008065	0.514056	
chunk0207_135_1	chr9	129327910	129328303	+	0	NA	Intergenic	Intergenic	7090	NM_001012715									0.012723	0.586294	
chunk0126_254_1	chr3	79437554	79437982	+	0	NA	intron (NM_002941, intron 2 of 30)	L1ME3A|LINE|L1	26041	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.002336	0.333333	
chunk0174_250_1	chr6	161010188	161010420	+	0	NA	intron (NM_006724, intron 1 of 25)	intron (NM_006724, intron 1 of 25)	18577	NM_001291958	4216	Hs.390428	NM_005922	ENSG00000085511	MAP3K4	MAPKKK4|MEKK 4|MEKK4|MTK1|PRO0412	mitogen-activated protein kinase kinase kinase 4	protein-coding	0.004310	0.287554	
chunk0126_409_1	chr3	85367159	85367632	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	-18315	NR_049870	100847077		NR_049870	ENSG00000264084	MIR5688	-	microRNA 5688	ncRNA	0.004228	0.305907	
chunk0160_5_1	chr5	148949896	148950433	+	0	NA	Intergenic	Intergenic	112245	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.007449	0.459108	244(AGGAGCAGAGTGTGCT,-,0.00),245(GGAGCAGAGTGTGCTG,+,0.00),375(GAGAACTGGCTGCCCT,-,0.00),376(AGAACTGGCTGCCCTG,+,0.00)
chunk0090_157_1	chr18	72409212	72409746	+	0	NA	Intergenic	Intergenic	135009	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.001873	0.442991	
chunk0069_365_1	chr15	67174960	67175205	+	0	NA	intron (NM_001145102, intron 5 of 8)	intron (NM_001145102, intron 5 of 8)	8927	NM_001145104	4088	Hs.727986	NM_005902	ENSG00000166949	SMAD3	HSPC193|HsT17436|JV15-2|LDS1C|LDS3|MADH3	SMAD family member 3	protein-coding	0.020408	0.540650	
chunk0015_311_1	chr1	189141274	189141497	+	0	NA	Intergenic	Intergenic	1336244	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004484	0.522321	
chunk0085_353_1	chr18	9104616	9104815	+	0	NA	intron (NM_021074, intron 1 of 7)	(TCCC)n|Simple_repeat|Simple_repeat	2085	NM_021074	4729	Hs.464572	NM_021074	ENSG00000178127	NDUFV2	CI-24k|MC1DN7	NADH:ubiquinone oxidoreductase core subunit V2	protein-coding	0.005025	0.415000	
chunk0153_95_1	chr5	68282973	68283172	+	0	NA	intron (NM_181523, intron 7 of 15)	intron (NM_181523, intron 7 of 15)	-5352	NM_181524	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.010050	0.440000	0(AGGAACAAAACGTCCC,-,0.00),1(GGAACAAAACGTCCCC,+,0.00)
chunk0203_78_1	chr9	83840067	83840575	+	0	NA	intron (NM_017576, intron 17 of 17)	intron (NM_017576, intron 17 of 17)	-22484	NM_001135953	80318	Hs.522255	NM_025211	ENSG00000165113	GKAP1	FKSG21|GKAP42	G kinase anchoring protein 1	protein-coding	0.003937	0.308448	
chunk0136_13_1	chr4	61874	62643	+	0	NA	intron (NM_182524, intron 3 of 3)	L1MA9|LINE|L1	8973	NM_001286053	152687	Hs.709469	NM_182524	ENSG00000272602	ZNF595	-	zinc finger protein 595	protein-coding	0.002601	0.312987	393(GAGAACATGCAGTTTC,-,0.00),394(AGAACATGCAGTTTCT,+,0.00)
chunk0127_242_1	chr3	96963519	96963843	+	0	NA	intron (NM_001080448, intron 2 of 17)	intron (NM_001080448, intron 2 of 17)	149100	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.003086	0.338462	
chunk0193_294_1	chr8	77663551	77663920	+	0	NA	Intergenic	L1MCb|LINE|L1	213038	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.008130	0.359459	
chunk0092_398_1	chr19	37247259	37247591	+	0	NA	Intergenic	L1MB7|LINE|L1	-4460	NR_110720	101927667	Hs.633102	NR_110718	ENSG00000226686	LINC01535	-	long intergenic non-protein coding RNA 1535	ncRNA	0.000000	0.336336	
chunk0096_427_1	chr2	38383796	38384134	+	0	NA	Intergenic	Intergenic	-6675	NR_024191									0.017751	0.439528	
chunk0048_209_1	chr12	81387936	81388689	+	0	NA	intron (NM_001220474, intron 6 of 30)	L1ME1|LINE|L1	-18898	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003984	0.336870	
chunk0051_162_1	chr12	115915267	115915726	+	0	NA	Intergenic	Intergenic	233158	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.008715	0.436957	
chunk0206_156_1	chr9	121537237	121537612	+	0	NA	Intergenic	AluJb|SINE|Alu	-29678	NM_032552	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.013333	0.510638	136(TTGCACAGTCTGTTCT,-,0.00),137(TGCACAGTCTGTTCTT,+,0.00)
chunk0089_276_1	chr18	62846283	62846607	+	0	NA	intron (NM_194449, intron 3 of 16)	L2c|LINE|L2	131006	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.000000	0.366154	
chunk0089_267_1	chr18	62716049	62716343	+	0	NA	exon (NM_194449, exon 1 of 17)	exon (NM_194449, exon 1 of 17)	757	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.129252	0.728814	
chunk0168_197_1	chr6	85502436	85502787	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	53027	NM_002526	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.008547	0.375000	
chunk0042_316_1	chr12	8637639	8638036	+	0	NA	Intergenic	Intergenic	-24991	NM_020661	57379	Hs.149342	NM_020661	ENSG00000111732	AICDA	AID|ARP2|CDA2|HEL-S-284|HIGM2	activation induced cytidine deaminase	protein-coding	0.010076	0.522613	
chunk0161_204_1	chr5	170572384	170572796	+	0	NA	intron (NM_001278339, intron 1 of 7)	intron (NM_001278339, intron 1 of 7)	68554	NM_001278340	30820	Hs.484111	NM_014592	ENSG00000182132	KCNIP1	KCHIP1|VABP	potassium voltage-gated channel interacting protein 1	protein-coding	0.024272	0.469734	
chunk0014_93_1	chr1	176595576	176595894	+	0	NA	intron (NM_020318, intron 3 of 22)	L2b|LINE|L2	132564	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.003145	0.457680	
chunk0201_319_1	chr9	62807729	62808397	+	0	NA	intron (NR_121647, intron 2 of 4)	L2a|LINE|L2	6598	NR_121647	103352539	Hs.351215	NR_121647	ENSG00000238113	LINC01410	-	long intergenic non-protein coding RNA 1410	ncRNA	0.007485	0.439462	
chunk0165_85_1	chr6	31540446	31541114	+	0	NA	TTS (NR_003065).7	TTS (NR_003065).7	398	NR_003065	692199		NR_003065	ENSG00000265236	SNORD84	U84	small nucleolar RNA, C/D box 84	snoRNA	0.013473	0.433483	
chunk0150_303_1	chr5	37667846	37668045	+	0	NA	intron (NM_018034, intron 10 of 17)	MER103C|DNA|hAT-Charlie	166877	NM_001278098	2668	Hs.248114	NM_000514	ENSG00000168621	GDNF	ATF|ATF1|ATF2|HFB1-GDNF|HSCR3	glial cell derived neurotrophic factor	protein-coding	0.005025	0.310000	
chunk0187_286_1	chr7	155684597	155684846	+	0	NA	intron (NM_053043, intron 5 of 17)	intron (NM_053043, intron 5 of 17)	40212	NM_053043	155435	Hs.591815	NM_053043	ENSG00000184863	RBM33	PRR8	RNA binding motif protein 33	protein-coding	0.012048	0.480000	
chunk0097_213_1	chr2	51380731	51381129	+	0	NA	Intergenic	L1ME3G|LINE|L1	-348394	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.283208	
chunk0041_442_1	chr11	134592319	134592518	+	0	NA	Intergenic	LTR53B|LTR|ERVL	155936	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.000000	0.350000	
chunk0108_38_1	chr2	226658644	226658966	+	0	NA	promoter-TSS (NR_049887)	promoter-TSS (NR_049887)	-12	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.006211	0.421053	
chunk0078_424_1	chr16	89374946	89375196	+	0	NA	intron (NM_001256182, intron 3 of 13)	Tigger2b_Pri|DNA|TcMar-Tigger	53938	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.040000	0.406375	
chunk0210_43_1	chrX	68354783	68355293	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	78419	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.001961	0.391389	
chunk0089_345_1	chr18	65918620	65919136	+	0	NA	Intergenic	Intergenic	167957	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.003876	0.323017	
chunk0127_320_1	chr3	99945469	99945727	+	0	NA	intron (NM_001042459, intron 1 of 4)	intron (NM_001042459, intron 1 of 4)	18800	NR_037486	100500859		NR_037486	ENSG00000264897	MIR3921	-	microRNA 3921	ncRNA	0.000000	0.401544	
chunk0076_80_1	chr16	63631728	63632051	+	0	NA	Intergenic	L1MD1|LINE|L1	1490248	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.000000	0.302469	
chunk0020_230_1	chr1	235686756	235687120	+	0	NA	intron (NM_001301365, intron 48 of 52)	intron (NM_001301365, intron 48 of 52)	-36184	NM_001098721	2786	Hs.159711	NM_004485	ENSG00000168243	GNG4	-	G protein subunit gamma 4	protein-coding	0.005495	0.350685	
chunk0069_247_1	chr15	64387579	64387922	+	0	NA	promoter-TSS (NM_016213)	promoter-TSS (NM_016213)	-54	NM_016213	9325	Hs.500340	NM_016213	ENSG00000103671	TRIP4	ASC-1|ASC1|HsT17391|MDCDC|SMABF1|ZC2HC5	thyroid hormone receptor interactor 4	protein-coding	0.064140	0.610465	
chunk0078_358_1	chr16	87326169	87326822	+	0	NA	TTS (NM_001282683)	TTS (NM_001282683)	-9075	NM_001256917	100506581	Hs.729380	NM_001195124	ENSG00000260456	C16orf95	-	chromosome 16 open reading frame 95	protein-coding	0.019908	0.515291	
chunk0106_9_1	chr2	195366695	195366894	+	0	NA	Intergenic	Intergenic	-290014	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.000000	0.285000	
chunk0136_72_1	chr4	2068399	2068598	+	0	NA	3' UTR (NM_178557, exon 3 of 3)	3' UTR (NM_178557, exon 3 of 3)	8986	NM_178557	339983	Hs.318529	NM_178557	ENSG00000185818	NAT8L	CML3|NACED|NAT8-LIKE	N-acetyltransferase 8 like	protein-coding	0.020101	0.460000	
chunk0119_182_1	chr22	43987969	43988168	+	0	NA	intron (NM_015380, intron 12 of 14)	L1ME4a|LINE|L1	-11143	NM_001003828	29780	Hs.475074	NM_013327	ENSG00000188677	PARVB	CGI-56	parvin beta	protein-coding	0.000000	0.290000	
chunk0129_128_1	chr3	119941331	119941964	+	0	NA	intron (NM_001146156, intron 3 of 10)	MIR|SINE|MIR	152770	NM_002093	2932	Hs.445733	NM_002093	ENSG00000082701	GSK3B	-	glycogen synthase kinase 3 beta	protein-coding	0.009479	0.342271	
chunk0158_300_1	chr5	132301703	132302655	+	0	NA	intron (NM_003059, intron 1 of 9)	intron (NM_003059, intron 1 of 9)	7727	NM_003059	6583	Hs.310591	NM_003059	ENSG00000197208	SLC22A4	DFNB60|OCTN1	solute carrier family 22 member 4	protein-coding	0.009454	0.520462	867(AAGCACAGACAGTCCA,-,0.00),868(AGCACAGACAGTCCAA,+,0.00)
chunk0166_366_1	chr6	51479216	51479940	+	0	NA	Intergenic	Intergenic	-142292	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.001381	0.344828	
chunk0126_382_1	chr3	84161656	84162144	+	0	NA	Intergenic	L1MB3|LINE|L1	707675	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.010246	0.343558	
chunk0034_100_1	chr11	27557524	27558083	+	0	NA	intron (NR_033315, intron 2 of 6)	MLT1M|LTR|ERVL-MaLR	-42756	NR_107054	102465881		NR_107054	ENSG00000278483	MIR8087	hsa-mir-8087	microRNA 8087	ncRNA	0.007156	0.371429	
chunk0116_209_1	chr21	37458520	37459138	+	0	NA	intron (NM_130436, intron 1 of 10)	intron (NM_130436, intron 1 of 10)	38529	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.014563	0.468498	
chunk0035_115_1	chr11	42560764	42561275	+	0	NA	Intergenic	Intergenic	-307329	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.001957	0.359375	
chunk0115_350_1	chr21	29293935	29294481	+	0	NA	Intergenic	Intergenic	-4587	NM_001186	571	Hs.154276	NM_001186	ENSG00000156273	BACH1	BACH-1|BTBD24	BTB domain and CNC homolog 1	protein-coding	0.000000	0.420475	
chunk0155_82_1	chr5	92040952	92041631	+	0	NA	Intergenic	Intergenic	-657959	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.002946	0.351471	
chunk0028_233_1	chr10	89895156	89895526	+	0	NA	Intergenic	L1PBb|LINE|L1	62032	NR_110655	101926924	Hs.500498	NR_110655	ENSG00000226159	LINC01375	-	long intergenic non-protein coding RNA 1375	ncRNA	0.000000	0.328841	
chunk0204_288_1	chr9	99141836	99142706	+	0	NA	intron (NM_001306210, intron 4 of 8)	MIRc|SINE|MIR	37182	NM_004612	7046	Hs.494622	NM_004612	ENSG00000106799	TGFBR1	AAT5|ACVRLK4|ALK-5|ALK5|ESS1|LDS1|LDS1A|LDS2A|MSSE|SKR4|TBR-i|TBRI|TGFR-1|tbetaR-I	transforming growth factor beta receptor 1	protein-coding	0.010345	0.408726	
chunk0202_24_1	chr9	70480552	70481275	+	0	NA	Intergenic	Intergenic	-66256	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.030429	0.469613	354(CAGTACAGAATGTTCT,-,0.00),355(AGTACAGAATGTTCTC,+,0.00)
chunk0091_9_1	chr19	2819634	2819897	+	0	NA	promoter-TSS (NM_001102651)	promoter-TSS (NM_001102651)	-109	NM_001102651	115196	Hs.307043	NM_152303	ENSG00000172006	ZNF554	-	zinc finger protein 554	protein-coding	0.114068	0.696970	
chunk0005_189_1	chr1	58903991	58904382	+	0	NA	Intergenic	CpG	-116290	NR_110626	101926925		NR_110626		LINC01358	-	long intergenic non-protein coding RNA 1358	ncRNA	0.069054	0.653061	
chunk0120_296_1	chr3	9933715	9933948	+	0	NA	promoter-TSS (NM_001077415)	promoter-TSS (NM_001077415)	-9	NM_015513	78987	Hs.9383	NM_015513	ENSG00000163703	CRELD1	AVSD2|CIRRIN	cysteine rich with EGF like domains 1	protein-coding	0.111588	0.705128	
chunk0088_124_1	chr18	45747624	45747955	+	0	NA	intron (NM_001308278, intron 7 of 8)	intron (NM_001308278, intron 7 of 8)	20836	NM_001146037	6563	Hs.101307	NM_015865	ENSG00000141469	SLC14A1	HUT11|HsT1341|JK|RACH1|RACH2|UT-B1|UT1|UTE	solute carrier family 14 member 1 (Kidd blood group)	protein-coding	0.012085	0.382530	
chunk0209_67_1	chrX	37697368	37697700	+	0	NA	intron (NM_021083, intron 2 of 2)	MamRep605|LTR?|LTR?	11654	NM_021083	7504	Hs.78919	NM_021083	ENSG00000047597	XK	KX|NA|NAC|X1k|XKR1	X-linked Kx blood group	protein-coding	0.000000	0.399399	111(AAGGACATAGAGTCCA,-,0.00),112(AGGACATAGAGTCCAT,+,0.00)
chunk0097_206_1	chr2	51158127	51158867	+	0	NA	Intergenic	Intergenic	-125961	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.002703	0.348178	
chunk0052_346_1	chr12	126549860	126550559	+	0	NA	Intergenic	Intergenic	107728	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.007153	0.401429	193(AAGACCAATGTGTCCT,-,0.00),194(AGACCAATGTGTCCTT,+,0.00)
chunk0017_172_1	chr1	207031646	207032337	+	0	NA	intron (NM_023938, intron 1 of 3)	intron (NM_023938, intron 1 of 3)	765	NM_001083924	79098	Hs.32417	NM_023938	ENSG00000182795	C1orf116	SARG	chromosome 1 open reading frame 116	protein-coding	0.008683	0.432081	
chunk0112_181_1	chr20	40004049	40005245	+	0	NA	intron (NR_109936, intron 1 of 2)	intron (NR_109936, intron 1 of 2)	186	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.004181	0.314119	
chunk0083_415_1	chr17	72159118	72159397	+	0	NA	Intergenic	Intergenic	38237	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.021505	0.535714	
chunk0004_327_1	chr1	50130583	50130782	+	0	NA	intron (NM_001294348, intron 1 of 6)	(TACT)n|Simple_repeat|Simple_repeat	21066	NM_001294348	1996	Hs.213050	NM_021952	ENSG00000162374	ELAVL4	HUD|PNEM	ELAV like RNA binding protein 4	protein-coding	0.005025	0.350000	
chunk0124_292_1	chr3	57742621	57742962	+	0	NA	Intergenic	L1ME4a|LINE|L1	-14465	NM_007159	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.000000	0.295322	
chunk0154_312_1	chr5	83683668	83684237	+	0	NA	intron (NM_001884, intron 1 of 4)	intron (NM_001884, intron 1 of 4)	37125	NM_001884	1404	Hs.2799	NM_001884	ENSG00000145681	HAPLN1	CRT1|CRTL1	hyaluronan and proteoglycan link protein 1	protein-coding	0.003515	0.424561	
chunk0105_268_1	chr2	189411853	189412457	+	0	NA	Intergenic	Intergenic	-29278	NM_032168	84128	Hs.399984	NM_032168	ENSG00000115368	WDR75	NET16|UTP17	WD repeat domain 75	protein-coding	0.008278	0.357025	277(AAGAACAACGTGTACT,-,0.00),278(AGAACAACGTGTACTA,+,0.00)
chunk0199_37_1	chr9	956510	956801	+	0	NA	intron (NM_021951, intron 4 of 4)	intron (NM_021951, intron 4 of 4)	-20313	NM_021240	58524	Hs.189174	NM_021240	ENSG00000064218	DMRT3	DMRTA3	doublesex and mab-3 related transcription factor 3	protein-coding	0.003436	0.335616	
chunk0092_156_1	chr19	29649628	29650291	+	0	NA	Intergenic	Intergenic	-15461	NM_024310	79156	Hs.466383	NM_024310	ENSG00000166289	PLEKHF1	APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology and FYVE domain containing 1	protein-coding	0.010558	0.375000	
chunk0202_427_1	chr9	81814298	81815118	+	0	NA	Intergenic	Intergenic	-98729	NR_026851	347127	Hs.215235	NM_198509	ENSG00000240632	SPATA31D5P	FAM75D5|FAM75D5P	SPATA31 subfamily D member 5, pseudogene	pseudo	0.002439	0.409257	159(AAGCACAGCCAGCTCT,-,0.00),160(AGCACAGCCAGCTCTG,+,0.00),291(AAGCACAGTGTGTTCC,-,0.00),292(AGCACAGTGTGTTCCC,+,0.00)
chunk0137_5_1	chr4	10497521	10498006	+	0	NA	intron (NM_052964, intron 18 of 18)	intron (NM_052964, intron 18 of 18)	-40355	NM_053042	85460	Hs.455089	NM_053042	ENSG00000178163	ZNF518B	-	zinc finger protein 518B	protein-coding	0.012371	0.467078	309(AGGCACACCATGTCCA,-,0.00),310(GGCACACCATGTCCAC,+,0.00)
chunk0206_398_1	chr9	127109440	127109668	+	0	NA	intron (NM_012098, intron 1 of 4)	intron (NM_012098, intron 1 of 4)	13211	NM_012098	23452	Hs.653262	NM_012098	ENSG00000136859	ANGPTL2	ARP2|HARP	angiopoietin like 2	protein-coding	0.008772	0.441048	
chunk0200_194_1	chr9	19923979	19924448	+	0	NA	Intergenic	Intergenic	-137194	NM_001193288	25769	Hs.283014	NM_020344	ENSG00000155886	SLC24A2	NCKX2	solute carrier family 24 member 2	protein-coding	0.008529	0.463830	
chunk0015_138_1	chr1	185705544	185706337	+	0	NA	Intergenic	Intergenic	-28611	NM_031935	83872	Hs.58877	NM_031935	ENSG00000143341	HMCN1	ARMD1|FBLN6|FIBL-6|FIBL6	hemicentin 1	protein-coding	0.002522	0.332494	
chunk0142_347_1	chr4	101602303	101602657	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-188127	NM_001127507	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.002825	0.383099	
chunk0077_385_1	chr16	84721955	84722407	+	0	NA	intron (NM_001272075, intron 2 of 14)	L1ME1|LINE|L1	22232	NR_073577	9100	Hs.136778	NM_005153	ENSG00000103194	USP10	UBPO	ubiquitin specific peptidase 10	protein-coding	0.002212	0.428256	
chunk0040_317_1	chr11	117970352	117970551	+	0	NA	Intergenic	Intergenic	-15940	NM_001558	3587	Hs.504035	NM_001558	ENSG00000110324	IL10RA	CD210|CD210a|CDW210A|HIL-10R|IL-10R1|IL10R	interleukin 10 receptor subunit alpha	protein-coding	0.005025	0.515000	
chunk0157_60_1	chr5	116193096	116193909	+	0	NA	intron (NM_001308080, intron 5 of 6)	L1PB1|LINE|L1	108040	NM_001308080	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.004920	0.371007	
chunk0170_133_1	chr6	110952143	110952829	+	0	NA	Intergenic	LTR44|LTR|ERV1	-6074	NM_138408	112495	Hs.418520	NM_138408	ENSG00000155115	GTF3C6	C6orf51|TFIIIC35|bA397G5.3	general transcription factor IIIC subunit 6	protein-coding	0.007289	0.417758	
chunk0185_59_1	chr7	124796529	124797006	+	0	NA	Intergenic	Intergenic	-5957	NM_001024603	154872	Hs.444163	NM_001024603	ENSG00000275356	C7orf77	-	chromosome 7 open reading frame 77	protein-coding	0.004193	0.366109	
chunk0138_129_1	chr4	36640874	36641075	+	0	NA	Intergenic	Intergenic	-214546	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.000000	0.420792	
chunk0145_186_1	chr4	147790429	147790666	+	0	NA	intron (NM_024605, intron 1 of 22)	intron (NM_024605, intron 1 of 22)	7952	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.004219	0.336134	
chunk0010_430_1	chr1	119779814	119780411	+	0	NA	Intergenic	Intergenic	-11180	NM_005518	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.011725	0.478261	
chunk0093_46_1	chr19	39951751	39951969	+	0	NA	Intergenic	Intergenic	-17234	NM_003890	8857	Hs.111732	NM_003890		FCGBP	FC(GAMMA)BP	Fc fragment of IgG binding protein	protein-coding	0.009174	0.525114	
chunk0205_107_1	chr9	107541376	107541977	+	0	NA	Intergenic	Intergenic	-51956	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.008319	0.463455	267(CAGAACTACTTGTTCC,-,0.00),268(AGAACTACTTGTTCCT,+,0.00)
chunk0117_442_1	chr21	46472789	46473436	+	0	NA	intron (NM_206889, intron 1 of 21)	intron (NM_206889, intron 1 of 21)	10641	NR_046400	100862692	Hs.737163	NR_046400	ENSG00000223692	DIP2A-IT1	-	DIP2A intronic transcript 1	ncRNA	0.007728	0.439815	193(GGGAACTGATTGTTCA,-,0.00),194(GGAACTGATTGTTCAA,+,0.00)
chunk0179_375_1	chr7	51230999	51231500	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	85569	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.001996	0.480080	
chunk0165_23_1	chr6	29516122	29516815	+	0	NA	Intergenic	L1M5|LINE|L1	-12938	NR_037181	100507362	Hs.99161	NR_037179	ENSG00000224582	LINC01015	-	long intergenic non-protein coding RNA 1015	ncRNA	0.014430	0.393372	
chunk0084_261_1	chr17	79132371	79132603	+	0	NA	intron (NM_001082575, intron 4 of 14)	intron (NM_001082575, intron 4 of 14)	57550	NM_001042573	64772	Hs.29288	NM_022759	ENSG00000167280	ENGASE	-	endo-beta-N-acetylglucosaminidase	protein-coding	0.056034	0.648069	
chunk0181_238_1	chr7	85281928	85282271	+	0	NA	Intergenic	Intergenic	-160168	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.002915	0.351744	
chunk0188_430_1	chr8	19041461	19041933	+	0	NA	Intergenic	Intergenic	-28011	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.010593	0.367865	
chunk0108_213_1	chr2	233370476	233370678	+	0	NA	intron (NM_152879, intron 1 of 29)	L1MB4|LINE|L1	16070	NM_152879	8527	Hs.471675	NM_003648	ENSG00000077044	DGKD	DGKdelta|dgkd-2	diacylglycerol kinase delta	protein-coding	0.029703	0.394089	
chunk0146_433_1	chr4	169484702	169484901	+	0	NA	intron (NM_001199399, intron 20 of 32)	MIRb|SINE|MIR	127826	NM_001199400	4750	Hs.481181	NM_012224	ENSG00000137601	NEK1	ALS24|NY-REN-55|SRPS2|SRPS2A|SRTD6	NIMA related kinase 1	protein-coding	0.010050	0.370000	
chunk0097_38_1	chr2	42876097	42876786	+	0	NA	Intergenic	Intergenic	-83830	NM_012205	23498	Hs.368805	NM_012205	ENSG00000162882	HAAO	3-HAO|HAO|VCRL1|h3HAO	3-hydroxyanthranilate 3,4-dioxygenase	protein-coding	0.018868	0.505797	
chunk0210_60_1	chrX	69327448	69327761	+	0	NA	Intergenic	Intergenic	148047	NR_103715	100996279		NR_103715	ENSG00000215162	LINC00269	CXorf62|NCRNA00269	long intergenic non-protein coding RNA 269	ncRNA	0.003195	0.296178	
chunk0169_216_1	chr6	103599432	103599631	+	0	NA	Intergenic	LTR41B|LTR|ERVL	1260388	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.485000	
chunk0163_399_1	chr6	16563966	16564188	+	0	NA	intron (NM_001128164, intron 4 of 7)	MIRb|SINE|MIR	197413	NM_000332	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.009009	0.466368	
chunk0084_218_1	chr17	78265778	78265997	+	0	NA	intron (NR_073178, intron 5 of 6)	intron (NR_073178, intron 5 of 6)	12605	NR_073178	100996291	Hs.744493	NR_073178	ENSG00000204277	LINC01993	-	long intergenic non-protein coding RNA 1993	ncRNA	0.036530	0.577273	
chunk0147_34_1	chr4	171840038	171840421	+	0	NA	intron (NM_001034845, intron 2 of 12)	intron (NM_001034845, intron 2 of 12)	26805	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.015666	0.388021	
chunk0047_91_1	chr12	68600677	68601187	+	0	NA	Intergenic	L1MC5a|LINE|L1	-9907	NM_001010942	5908	Hs.369920	NM_015646	ENSG00000127314	RAP1B	K-REV|RAL1B	RAP1B, member of RAS oncogene family	protein-coding	0.013725	0.387476	
chunk0053_405_1	chr13	36530005	36530502	+	0	NA	Intergenic	Intergenic	97981	NM_001111045	8900	Hs.417050	NM_003914	ENSG00000133101	CCNA1	CT146	cyclin A1	protein-coding	0.004024	0.493976	84(GAGCACAGACTCTCCT,-,0.00),85(AGCACAGACTCTCCTC,+,0.00)
chunk0074_268_1	chr16	28175602	28176147	+	0	NA	intron (NM_001270940, intron 5 of 24)	intron (NM_001270940, intron 5 of 24)	36044	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.009174	0.379121	
chunk0202_292_1	chr9	77663884	77664347	+	0	NA	Intergenic	Intergenic	-15799	NM_004297	9630	Hs.657795	NM_004297	ENSG00000156049	GNA14	-	G protein subunit alpha 14	protein-coding	0.008639	0.478448	336(TGGAACTTCCAGTCCT,-,0.00),337(GGAACTTCCAGTCCTG,+,0.00)
chunk0051_274_1	chr12	118063434	118064048	+	0	NA	3' UTR (NM_019086, exon 9 of 9)	3' UTR (NM_019086, exon 9 of 9)	-1567	NM_001278557	55884	Hs.506985	NM_018639	ENSG00000176871	WSB2	SBA2	WD repeat and SOCS box containing 2	protein-coding	0.006515	0.373984	
chunk0187_61_1	chr8	1972853	1973217	+	0	NA	promoter-TSS (NM_014867)	promoter-TSS (NM_014867)	-843	NM_014867	9920	Hs.5333	NM_014867	ENSG00000176595	KBTBD11	KLHDC7C	kelch repeat and BTB domain containing 11	protein-coding	0.024725	0.446575	
chunk0211_222_1	chrX	118584851	118585378	+	0	NA	exon (NM_144658, exon 16 of 53)	exon (NM_144658, exon 16 of 53)	89205	NM_144658	139818	Hs.368203	NM_144658	ENSG00000147251	DOCK11	ACG|ZIZ2|bB128O4.1	dedicator of cytokinesis 11	protein-coding	0.001898	0.354167	
chunk0001_153_1	chr1	6235932	6236131	+	0	NA	promoter-TSS (NR_103534)	promoter-TSS (NR_103534)	-47	NM_012405	23463	Hs.515688	NM_012405	ENSG00000116237	ICMT	HSTE14|MST098|MSTP098|PCCMT|PCMT|PPMT	isoprenylcysteine carboxyl methyltransferase	protein-coding	0.155779	0.785000	
chunk0100_195_1	chr2	111098865	111099153	+	0	NA	non-coding (NR_122074, exon 4 of 4)	non-coding (NR_122074, exon 4 of 4)	16579	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.006944	0.394464	
chunk0073_290_1	chr16	14015674	14016079	+	0	NA	non-coding (NR_110909, exon 1 of 3)	non-coding (NR_110909, exon 1 of 3)	142	NR_110909	101927311		NR_110909	ENSG00000262097	LINC02185	-	long intergenic non-protein coding RNA 2185	ncRNA	0.012346	0.465517	210(AGAACAGTCTGCTTTT,+,0.00)
chunk0150_436_1	chr5	40471743	40472296	+	0	NA	Intergenic	L1PA3|LINE|L1	-207911	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.014467	0.382671	354(AGAGACAGTTTGTTCT,-,0.00),355(GAGACAGTTTGTTCTG,+,0.00)
chunk0107_57_1	chr2	211432236	211432659	+	0	NA	intron (NM_001042599, intron 20 of 26)	intron (NM_001042599, intron 20 of 26)	814876	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.007092	0.339623	
chunk0177_66_1	chr7	21251395	21251861	+	0	NA	Intergenic	Intergenic	-176443	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.004292	0.368308	
chunk0131_252_1	chr3	149542556	149543335	+	0	NA	intron (NM_015472, intron 3 of 6)	intron (NM_015472, intron 3 of 6)	68364	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.008986	0.379487	258(TAGAACATAGTGGTCT,-,0.00),259(AGAACATAGTGGTCTA,+,0.00)
chunk0172_373_1	chr6	139298855	139299544	+	0	NA	Intergenic	Intergenic	-7128	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.004354	0.472464	
chunk0009_58_1	chr1	100704187	100704686	+	0	NA	Intergenic	Intergenic	-15204	NM_080682	7412	Hs.109225	NM_001078	ENSG00000162692	VCAM1	CD106|INCAM-100	vascular cell adhesion molecule 1	protein-coding	0.000000	0.368000	
chunk0191_309_1	chr8	55217429	55218202	+	0	NA	intron (NM_052898, intron 1 of 2)	L1ME3F|LINE|L1	115358	NM_052898	114786	Hs.130197	NM_052898	ENSG00000206579	XKR4	XRG4	XK related 4	protein-coding	0.002587	0.348837	
chunk0105_211_1	chr2	187946998	187947257	+	0	NA	Intergenic	Intergenic	340564	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.000000	0.334615	
chunk0092_387_1	chr19	36488981	36489444	+	0	NA	promoter-TSS (NR_036504)	promoter-TSS (NR_036504)	223	NM_032838	84924	Hs.533939	NM_032838	ENSG00000186017	ZNF566	-	zinc finger protein 566	protein-coding	0.058315	0.573276	
chunk0153_18_1	chr5	66981663	66982038	+	0	NA	intron (NM_001290226, intron 1 of 26)	intron (NM_001290226, intron 1 of 26)	22304	NR_111908	101928794	Hs.672435	NR_111908		MAST4-AS1	-	MAST4 antisense RNA 1	ncRNA	0.000000	0.375000	
chunk0051_332_1	chr12	120245198	120245499	+	0	NA	intron (NM_001243756, intron 1 of 10)	intron (NM_001243756, intron 1 of 10)	4813	NM_025157	5829	Hs.446336	NM_002859	ENSG00000089159	PXN	-	paxillin	protein-coding	0.023256	0.447020	
chunk0180_87_1	chr7	55044678	55045111	+	0	NA	intron (NM_201283, intron 1 of 9)	intron (NM_201283, intron 1 of 9)	25862	NM_005228	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.023095	0.451613	
chunk0136_36_1	chr4	1115561	1115822	+	0	NA	intron (NR_033768, intron 3 of 3)	intron (NR_033768, intron 3 of 3)	-2127	NM_001193318	285498	Hs.248290	NM_194439	ENSG00000178222	RNF212	ZHP3	ring finger protein 212	protein-coding	0.007663	0.370229	
chunk0180_28_1	chr7	53853995	53854194	+	0	NA	Intergenic	MER73|LTR|ERVL	-42163	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.020101	0.540000	
chunk0066_190_1	chr15	33152550	33152749	+	0	NA	intron (NM_001277314, intron 4 of 4)	intron (NM_001277314, intron 4 of 4)	42084	NM_001277314	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.005025	0.430000	
chunk0058_2_1	chr14	16095897	16096330	+	0	NA	Intergenic	SAR|Satellite|Satellite	-2505004	NM_001013354	440153	Hs.534880	NM_001013354	ENSG00000257115	OR11H12	-	olfactory receptor family 11 subfamily H member 12	protein-coding	0.000000	0.216590	
chunk0069_135_1	chr15	62112803	62113397	+	0	NA	Intergenic	MIRb|SINE|MIR	46123	NM_207322	145741	Hs.202656	NM_207322	ENSG00000198535	C2CD4A	FAM148A|NLF1	C2 calcium dependent domain containing 4A	protein-coding	0.015152	0.502521	319(AGGCACTGCTTGTACT,-,0.00),320(GGCACTGCTTGTACTC,+,0.00)
chunk0168_188_1	chr6	85298594	85299291	+	0	NA	Intergenic	Intergenic	-150642	NM_001204813	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.007174	0.434097	
chunk0198_420_1	chr8	142912014	142912271	+	0	NA	intron (NM_000498, intron 8 of 8)	intron (NM_000498, intron 8 of 8)	5701	NM_000498	1585	Hs.632054	NM_000498	ENSG00000179142	CYP11B2	ALDOS|CPN2|CYP11B|CYP11BL|CYPXIB2|P-450C18|P450C18|P450aldo	cytochrome P450 family 11 subfamily B member 2	protein-coding	0.007782	0.573643	
chunk0022_169_1	chr10	12689715	12690336	+	0	NA	intron (NM_020397, intron 3 of 9)	intron (NM_020397, intron 3 of 9)	35328	NR_031752	100313841		NR_031752	ENSG00000221331	MIR548Q	-	microRNA 548q	ncRNA	0.016103	0.424437	504(GAGTACTTCCTGTGCC,-,0.00),505(AGTACTTCCTGTGCCA,+,0.00)
chunk0039_194_1	chr11	100880931	100881390	+	0	NA	intron (NM_152432, intron 4 of 23)	L1PB1|LINE|L1	-110920	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.000000	0.354348	
chunk0207_365_1	chr9	135798028	135798457	+	0	NA	Intergenic	Intergenic	96057	NM_001272003	57582	Hs.104950	NM_020822	ENSG00000107147	KCNT1	EIEE14|ENFL5|KCa4.1|SLACK|Slo2.2|bA100C15.2	potassium sodium-activated channel subfamily T member 1	protein-coding	0.032634	0.625581	183(GGGAACAGCCTGACCC,-,0.00),184(GGAACAGCCTGACCCT,+,0.00)
chunk0205_25_1	chr9	105319237	105319436	+	0	NA	intron (NM_001286730, intron 3 of 15)	MER77B|LTR|ERVL	74723	NM_001286730	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.015075	0.450000	
chunk0012_219_1	chr1	160182027	160182318	+	0	NA	intron (NM_001001734, intron 3 of 4)	intron (NM_001001734, intron 3 of 4)	4761	NM_001001734	480	Hs.662219	NM_144699	ENSG00000132681	ATP1A4	ATP1A1|ATP1AL2	ATPase Na+/K+ transporting subunit alpha 4	protein-coding	0.006873	0.458904	
chunk0049_305_1	chr12	94555631	94556173	+	0	NA	Intergenic	L1MC4|LINE|L1	-5887	NR_049885	100847031		NR_049885	ENSG00000266099	MIR5700	-	microRNA 5700	ncRNA	0.005535	0.381215	213(AAGAACGGTCAGTTCT,-,0.00),214(AGAACGGTCAGTTCTA,+,0.00)
chunk0101_292_1	chr2	134457720	134458328	+	0	NA	intron (NM_030923, intron 7 of 7)	intron (NM_030923, intron 7 of 7)	203765	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.021382	0.536946	
chunk0021_327_1	chr1	245645462	245645765	+	0	NA	intron (NM_018012, intron 9 of 14)	intron (NM_018012, intron 9 of 14)	490628	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.009901	0.401316	
chunk0027_464_1	chr10	81879654	81880183	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	2231	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.003781	0.332075	
chunk0209_291_1	chrX	48346342	48346739	+	0	NA	3' UTR (NM_021014, exon 8 of 8)	3' UTR (NM_021014, exon 8 of 8)	10213	NM_021014	10214	Hs.558445	NM_021014	ENSG00000165584	SSX3	CT5.3	SSX family member 3	protein-coding	0.012594	0.464824	
chunk0210_125_1	chrX	73968223	73968597	+	0	NA	intron (NR_024582, intron 2 of 4)	L1MD3|LINE|L1	24086	NR_024582	554203	Hs.648316	NR_024582	ENSG00000225470	JPX	DCBALD06|ENOX|LINC00183|NCRNA00183	JPX transcript, XIST activator	ncRNA	0.005348	0.354667	
chunk0110_249_1	chr20	16573626	16573825	+	0	NA	promoter-TSS (NM_024704)	promoter-TSS (NM_024704)	-291	NM_001199865	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.025126	0.495000	
chunk0013_452_1	chr1	173925305	173926174	+	0	NA	Intergenic	Intergenic	-8361	NM_000488	462	Hs.75599	NM_000488	ENSG00000117601	SERPINC1	AT3|AT3D|ATIII|ATIII-R2|ATIII-T1|ATIII-T2|THPH7	serpin family C member 1	protein-coding	0.005754	0.412644	
chunk0117_49_1	chr22	12628163	12628362	+	0	NA	Intergenic	Intergenic	730856	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.015075	0.485000	
chunk0023_384_1	chr10	30583611	30584413	+	0	NA	Intergenic	Intergenic	45706	NM_183058	119180	Hs.522610	NM_183058	ENSG00000151033	LYZL2	LYZD2	lysozyme like 2	protein-coding	0.021197	0.479452	
chunk0135_236_1	chr3	188646831	188647130	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-41801	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.000000	0.413333	
chunk0122_288_1	chr3	36155241	36156042	+	0	NA	Intergenic	L1MCb|LINE|L1	-224846	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.001248	0.355362	337(AAGTACATCATGTTCA,-,0.00),338(AGTACATCATGTTCAG,+,0.00)
chunk0035_76_1	chr11	41864890	41865396	+	0	NA	Intergenic	Intergenic	150575	NR_120584	102723644	Hs.564283	NR_120584	ENSG00000255171	LINC01499	-	long intergenic non-protein coding RNA 1499	ncRNA	0.005929	0.287968	
chunk0146_313_1	chr4	165369529	165370115	+	0	NA	Intergenic	L1MB1|LINE|L1	-9123	NM_001873	1363	Hs.75360	NM_001873	ENSG00000109472	CPE	CPH	carboxypeptidase E	protein-coding	0.008532	0.391823	
chunk0055_356_1	chr13	70405266	70405787	+	0	NA	Intergenic	AluJo|SINE|Alu	-297033	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.007678	0.379310	
chunk0098_134_1	chr2	69349635	69350130	+	0	NA	intron (NM_002056, intron 9 of 18)	intron (NM_002056, intron 9 of 18)	37372	NM_002056	2673	Hs.580300	NM_002056	ENSG00000198380	GFPT1	CMS12|CMSTA1|GFA|GFAT|GFAT 1|GFAT1|GFAT1m|GFPT|GFPT1L|MSLG	glutamine--fructose-6-phosphate transaminase 1	protein-coding	0.002020	0.342742	
chunk0037_81_1	chr11	71364028	71364815	+	0	NA	Intergenic	Intergenic	58933	NR_038862	399923	Hs.128191	NM_001001680	ENSG00000172900	FLJ42102	-	uncharacterized LOC399923	ncRNA	0.008895	0.583756	
chunk0154_432_1	chr5	89852355	89852692	+	0	NA	Intergenic	Intergenic	164197	NR_037433	100500825		NR_037433	ENSG00000264342	MIR3660	mir-3660	microRNA 3660	ncRNA	0.008902	0.322485	
chunk0094_409_1	chr2	10457665	10458518	+	0	NA	Intergenic	MER97a|DNA|hAT-Tip100	8363	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.011723	0.415691	
chunk0136_425_1	chr3	197587227	197587738	+	0	NA	Intergenic	L1MEc|LINE|L1	-14159	NM_203315	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.007828	0.355469	
chunk0083_335_1	chr17	70192788	70193121	+	0	NA	Intergenic	L1M5|LINE|L1	23419	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.000000	0.254491	
chunk0010_310_1	chr1	118047794	118048165	+	0	NA	intron (NM_206996, intron 20 of 48)	L1MA8|LINE|L1	118230	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.005391	0.612903	
chunk0031_193_1	chr10	125740994	125741284	+	0	NA	non-coding (NR_110857, exon 17 of 25)	non-coding (NR_110857, exon 17 of 25)	10921	NR_120633	101927983	Hs.634269	NR_120633	ENSG00000236991	EDRF1-AS1	-	EDRF1 antisense RNA 1	ncRNA	0.006897	0.446735	
chunk0063_237_1	chr14	82043226	82043460	+	0	NA	Intergenic	Intergenic	-420282	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.000000	0.336170	
chunk0163_77_1	chr6	9399829	9400369	+	0	NA	Intergenic	Intergenic	747890	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.009259	0.349353	
chunk0040_437_1	chr11	121476223	121476837	+	0	NA	intron (NM_003105, intron 2 of 47)	intron (NM_003105, intron 2 of 47)	24327	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.008143	0.479675	
chunk0130_155_1	chr3	132537156	132537637	+	0	NA	intron (NM_015268, intron 55 of 55)	intron (NM_015268, intron 55 of 55)	-59841	NM_016557	51554	Hs.310512	NM_016557	ENSG00000129048	ACKR4	CC-CKR-11|CCBP2|CCR-11|CCR10|CCR11|CCRL1|CCX CKR|CCX-CKR|CKR-11|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding	0.008316	0.410788	
chunk0180_306_1	chr7	70598971	70599513	+	0	NA	intron (NM_015570, intron 5 of 18)	UCON55|DNA|TcMar-Tigger	-533295	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.005535	0.471455	
chunk0112_340_1	chr20	45069237	45069733	+	0	NA	intron (NM_006282, intron 10 of 10)	intron (NM_006282, intron 10 of 10)	31627	NM_002251	3787	Hs.117780	NM_002251	ENSG00000124134	KCNS1	Kv9.1	potassium voltage-gated channel modifier subfamily S member 1	protein-coding	0.002016	0.392354	
chunk0157_283_1	chr5	120661127	120661517	+	0	NA	intron (NM_001308088, intron 3 of 3)	HAL1b|LINE|L1	129858	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.002564	0.375959	
chunk0086_437_1	chr18	28728332	28728723	+	0	NA	Intergenic	Intergenic	-551081	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.007673	0.295918	
chunk0011_34_1	chr1	143230763	143231000	+	0	NA	Intergenic	Intergenic	191711	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.059072	0.365546	
chunk0162_84_1	chr6	1936098	1936575	+	0	NA	intron (NM_001253846, intron 6 of 10)	intron (NM_001253846, intron 6 of 10)	239655	NM_001253846	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.002096	0.456067	
chunk0102_439_1	chr2	157833433	157833632	+	0	NA	intron (NM_001111067, intron 1 of 10)	intron (NM_001111067, intron 1 of 10)	41579	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.005025	0.370000	
chunk0144_39_1	chr4	125658415	125658961	+	0	NA	Intergenic	Intergenic	151429	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.005495	0.318099	
chunk0169_68_1	chr6	99005814	99006013	+	0	NA	Intergenic	L2c|LINE|L2	-57907	NM_001278716	26235	Hs.536850	NM_012160	ENSG00000112234	FBXL4	FBL4|FBL5|MTDPS13	F-box and leucine rich repeat protein 4	protein-coding	0.035176	0.450000	
chunk0146_306_1	chr4	165199914	165200113	+	0	NA	Intergenic	Intergenic	-7605	NM_007246	11275	Hs.388668	NM_007246	ENSG00000109466	KLHL2	ABP-KELCH|MAV|MAYVEN	kelch like family member 2	protein-coding	0.005025	0.400000	
chunk0098_57_1	chr2	66696774	66697354	+	0	NA	TTS (NR_110265)	TTS (NR_110265)	6163	NR_110265	101927577	Hs.380543	NR_110264	ENSG00000237179	LINC01797	-	long intergenic non-protein coding RNA 1797	ncRNA	0.006897	0.349398	270(TGAACAGACTGTATTT,+,0.00)
chunk0111_91_1	chr20	23449112	23449378	+	0	NA	Intergenic	LTR16C|LTR|ERVL	3600	NM_080830	140880	Hs.128100	NM_080830	ENSG00000125831	CST11	CST8L|CTES2|SC13|dJ322G13.6	cystatin 11	protein-coding	0.015038	0.520599	
chunk0062_363_1	chr14	73901012	73901278	+	0	NA	intron (NR_040251, intron 5 of 11)	intron (NR_040251, intron 5 of 11)	14530	NM_001242924	57862	Hs.270869	NM_021188	ENSG00000119725	ZNF410	APA-1|APA1	zinc finger protein 410	protein-coding	0.003759	0.352060	
chunk0071_102_1	chr15	81032705	81032904	+	0	NA	Intergenic	AluJr4|SINE|Alu	31850	NM_022566	59274	Hs.513071	NM_022566	ENSG00000140406	TLNRD1	MESDC1	talin rod domain containing 1	protein-coding	0.000000	0.430000	
chunk0167_155_1	chr6	62623895	62624096	+	0	NA	Intergenic	Intergenic	-337800	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.000000	0.336634	
chunk0131_384_1	chr3	152405958	152406238	+	0	NA	intron (NM_001314057, intron 3 of 11)	intron (NM_001314057, intron 3 of 11)	-65108	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.000000	0.412811	
chunk0035_290_1	chr11	46837419	46837811	+	0	NA	intron (NM_001008938, intron 1 of 43)	L1MC3|LINE|L1	8693	NM_001008938	9793	Hs.201253	NM_014756	ENSG00000175216	CKAP5	CHTOG|MSPS|TOG|TOGp|ch-TOG	cytoskeleton associated protein 5	protein-coding	0.005102	0.381679	88(GAGAACACTCAGTACC,-,0.00),89(AGAACACTCAGTACCC,+,0.00)
chunk0088_351_1	chr18	52196507	52196717	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-143560	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.004762	0.308057	
chunk0014_17_1	chr1	174458284	174458534	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	10335	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.004000	0.298805	
chunk0152_437_1	chr5	66120687	66121124	+	0	NA	Intergenic	Intergenic	-23313	NM_001077199	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.004577	0.335616	
chunk0164_278_1	chr6	24016413	24016681	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-109639	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.007463	0.460967	
chunk0170_363_1	chr6	116801868	116802397	+	0	NA	intron (NM_001286354, intron 3 of 5)	intron (NM_001286354, intron 3 of 5)	26925	NM_001286355	222545	Hs.266745	NM_148963	ENSG00000173612	GPRC6A	GPCR|bA86F4.3	G protein-coupled receptor class C group 6 member A	protein-coding	0.000000	0.313208	
chunk0065_326_1	chr14	103214556	103214775	+	0	NA	Intergenic	MER90|LTR|ERV1	-25637	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.022831	0.477273	77(TAGGCCACGGTGTTCT,-,0.00),78(AGGCCACGGTGTTCTC,+,0.00)
chunk0172_81_1	chr6	134472504	134473264	+	0	NA	intron (NR_038219, intron 4 of 4)	intron (NR_038219, intron 4 of 4)	6013	NR_125852	101928231	Hs.634168	NR_125852		CT69	-	cancer/testis associated transcript 69	ncRNA	0.001316	0.329829	
chunk0039_426_1	chr11	107831612	107831918	+	0	NA	intron (NM_017515, intron 1 of 7)	intron (NM_017515, intron 1 of 7)	27423	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.000000	0.381107	
chunk0110_351_1	chr20	19676212	19676536	+	0	NA	intron (NM_020689, intron 9 of 16)	intron (NM_020689, intron 9 of 16)	-210147	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.012346	0.424615	
chunk0114_227_1	chr21	15874389	15875002	+	0	NA	intron (NM_013396, intron 22 of 23)	intron (NM_013396, intron 22 of 23)	144670	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.008157	0.372964	288(AAGTACACTCAGTACT,-,0.00),289(AGTACACTCAGTACTT,+,0.00)
chunk0195_117_1	chr8	94823122	94823321	+	0	NA	promoter-TSS (NM_017864)	promoter-TSS (NM_017864)	-69	NM_017864	55656	Hs.727669	NM_017864	ENSG00000164941	INTS8	C8orf52|INT8	integrator complex subunit 8	protein-coding	0.130653	0.665000	
chunk0182_86_1	chr7	92760324	92760598	+	0	NA	intron (NM_001145306, intron 3 of 7)	intron (NM_001145306, intron 3 of 7)	73456	NM_001259	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.000000	0.312727	
chunk0070_84_1	chr15	70159587	70159998	+	0	NA	Intergenic	Intergenic	-61875	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.014599	0.533981	188(GGGGACACCCTGTGCC,-,0.00),189(GGGACACCCTGTGCCC,+,0.00)
chunk0007_420_1	chr1	86194723	86194962	+	0	NA	Intergenic	Intergenic	-38404	NM_152890	255631	Hs.659516	NM_152890	ENSG00000171502	COL24A1	-	collagen type XXIV alpha 1 chain	protein-coding	0.016736	0.433333	
chunk0090_386_1	chr18	77377837	77378148	+	0	NA	Intergenic	Intergenic	127940	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.016077	0.528846	73(CGGCACACGCAGTGCA,-,0.00),74(GGCACACGCAGTGCAC,+,0.00),93(CAGCACACGAAGTTCA,-,0.00),94(AGCACACGAAGTTCAC,+,0.00),134(GGCACACTCAGTGCAC,+,0.00),173(CAGCACACCGTGCACT,-,0.00),174(AGCACACCGTGCACTC,+,0.00)
chunk0180_313_1	chr7	70856858	70857278	+	0	NA	Intergenic	Intergenic	-275469	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.009524	0.472684	
chunk0129_421_1	chr3	127164274	127164752	+	0	NA	Intergenic	Intergenic	-28618	NM_001007534	285311	Hs.591284	NM_001007534	ENSG00000214324	C3orf56	-	chromosome 3 open reading frame 56	protein-coding	0.004184	0.538622	
chunk0123_193_1	chr3	44357871	44358186	+	0	NA	intron (NM_001282915, intron 3 of 10)	intron (NM_001282915, intron 3 of 10)	19576	NM_173826	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.000000	0.281646	
chunk0056_86_1	chr13	79961103	79961666	+	0	NA	Intergenic	L1PA7|LINE|L1	-49693	NR_104138	101515984	Hs.569290	NR_104138		LINC01080	TCONS_00021856	long intergenic non-protein coding RNA 1080	ncRNA	0.003552	0.351064	286(AAAGACACAATGTACC,-,0.00)
chunk0136_97_1	chr4	2873733	2873932	+	0	NA	intron (NM_001286645, intron 2 of 17)	intron (NM_001286645, intron 2 of 17)	29682	NM_001286645	118	Hs.183706	NM_001119	ENSG00000087274	ADD1	ADDA	adducin 1	protein-coding	0.005025	0.290000	
chunk0067_67_1	chr15	41235664	41235863	+	0	NA	intron (NM_007236, intron 1 of 6)	intron (NM_007236, intron 1 of 6)	4524	NM_007236	11261	Hs.406234	NM_007236	ENSG00000187446	CHP1	CHP|SLC9A1BP|SPAX9|Sid470p|p22|p24	calcineurin like EF-hand protein 1	protein-coding	0.005025	0.425000	
chunk0206_387_1	chr9	126809593	126809792	+	0	NA	intron (NM_014007, intron 2 of 2)	intron (NM_014007, intron 2 of 2)	4686	NM_014007	23099	Hs.355581	NM_014007	ENSG00000169155	ZBTB43	ZBTB22B|ZNF-X|ZNF297B	zinc finger and BTB domain containing 43	protein-coding	0.015075	0.390000	
chunk0020_179_1	chr1	234603826	234604241	+	0	NA	TTS (NM_182972)	TTS (NM_182972)	5492	NM_182972	359948	Hs.350268	NM_182972	ENSG00000168264	IRF2BP2	CVID14	interferon regulatory factor 2 binding protein 2	protein-coding	0.012048	0.406250	
chunk0156_343_1	chr5	111896488	111896867	+	0	NA	intron (NM_001142474, intron 2 of 3)	intron (NM_001142474, intron 2 of 3)	-15831	NR_046678	100873948	Hs.147716	NR_046678	ENSG00000250095	NREP-AS1	-	NREP antisense RNA 1	ncRNA	0.010554	0.365789	
chunk0114_44_1	chr21	8434793	8435288	+	0	NA	non-coding (NR_046235, exon 1 of 1)	non-coding (NR_046235, exon 1 of 1)	1818	NR_046235	100861532		NR_046235		RNA45SN5	RNA45S5	RNA, 45S pre-ribosomal N5	rRNA	0.171717	0.794355	
chunk0196_153_1	chr8	104617118	104617833	+	0	NA	Intergenic	Intergenic	-28451	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.001399	0.407821	
chunk0212_91_1	chrY	12688430	12688985	+	0	NA	non-coding (NR_001545, exon 4 of 4)	non-coding (NR_001545, exon 4 of 4)	-12524	NM_004654	8287	Hs.598540	NM_004654	ENSG00000114374	USP9Y	DFFRY|SPGFY2	ubiquitin specific peptidase 9 Y-linked	protein-coding	0.005405	0.383094	
chunk0146_28_1	chr4	155379423	155380137	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-2810	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.007003	0.377622	
chunk0029_89_1	chr10	97170401	97170600	+	0	NA	intron (NR_037909, intron 11 of 14)	intron (NR_037909, intron 11 of 14)	15426	NM_003061	6585	Hs.632082	NM_003061	ENSG00000187122	SLIT1	MEGF4|SLIL1|SLIT-1|SLIT3	slit guidance ligand 1	protein-coding	0.020101	0.575000	
chunk0205_83_1	chr9	107068571	107069075	+	0	NA	intron (NR_126029, intron 3 of 4)	intron (NR_126029, intron 3 of 4)	34165	NR_126029	340512	Hs.432529	NR_126029	ENSG00000230782	LOC340512	-	uncharacterized LOC340512	ncRNA	0.005952	0.441584	169(AGGGACACTGTGTTAT,-,0.00),170(GGGACACTGTGTTATC,+,0.00),429(AGGTACATAATGTTTT,-,0.00),430(GGTACATAATGTTTTC,+,0.00)
chunk0041_49_1	chr11	123202323	123202609	+	0	NA	Intergenic	Intergenic	-7161	NM_024769	79827	Hs.591949	NM_024769	ENSG00000166250	CLMP	ACAM|ASAM|CSBM|CSBS	CXADR like membrane protein	protein-coding	0.003497	0.484321	
chunk0070_205_1	chr15	72168601	72168939	+	0	NA	intron (NM_001012642, intron 3 of 11)	intron (NM_001012642, intron 3 of 11)	29025	NM_001012642	196996	Hs.596332	NM_001012642	ENSG00000175318	GRAMD2A	GRAMD2	GRAM domain containing 2A	protein-coding	0.008876	0.584071	125(AAGCACAGCTTGTCTC,-,0.00)
chunk0083_71_1	chr17	64105453	64105727	+	0	NA	intron (NM_001433, intron 1 of 21)	(GTTT)n|Simple_repeat|Simple_repeat	24552	NM_001433	2081	Hs.133982	NM_001433	ENSG00000178607	ERN1	IRE1|IRE1P|IRE1a|hIRE1p	endoplasmic reticulum to nucleus signaling 1	protein-coding	0.007299	0.367273	
chunk0055_198_1	chr13	61883148	61883632	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	146158	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.006198	0.367010	
chunk0125_102_1	chr3	65534463	65534826	+	0	NA	intron (NM_015520, intron 2 of 24)	intron (NM_015520, intron 2 of 24)	-359172	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.008264	0.442308	
chunk0146_87_1	chr4	158112742	158113026	+	0	NA	Intergenic	Intergenic	59682	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.354386	
chunk0073_76_1	chr16	3829493	3829851	+	0	NA	intron (NM_001079846, intron 2 of 29)	L1MD3|LINE|L1	50448	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.002793	0.401114	
chunk0032_66_1	chr11	2256818	2257257	+	0	NA	Intergenic	Intergenic	13915	NM_005170	430	Hs.152475	NM_005170	ENSG00000183734	ASCL2	ASH2|HASH2|MASH2|bHLHa45	achaete-scute family bHLH transcription factor 2	protein-coding	0.029613	0.575000	
chunk0157_31_1	chr5	115626214	115626488	+	0	NA	promoter-TSS (NM_001164469)	promoter-TSS (NM_001164469)	-172	NM_181836	51014	Hs.642817	NM_181836	ENSG00000134970	TMED7	CGI-109|p24g3|p24gamma3|p27	transmembrane p24 trafficking protein 7	protein-coding	0.062044	0.538182	
chunk0090_20_1	chr19	925678	926008	+	0	NA	promoter-TSS (NM_005224)	promoter-TSS (NM_005224)	-194	NM_005224	1820	Hs.501296	NM_005224	ENSG00000116017	ARID3A	BRIGHT|DRIL1|DRIL3|E2FBP1	AT-rich interaction domain 3A	protein-coding	0.121212	0.719033	
chunk0017_264_1	chr1	209530776	209531471	+	0	NA	Intergenic	Intergenic	-52577	NM_020439	57172	Hs.199068	NM_020439	ENSG00000008118	CAMK1G	CLICK3|CLICKIII|VWS1|dJ272L16.1	calcium/calmodulin dependent protein kinase IG	protein-coding	0.007194	0.409483	351(CTGTACACCCTGTTCC,-,0.00),352(TGTACACCCTGTTCCC,+,0.00)
chunk0162_205_1	chr6	4066451	4067066	+	0	NA	Intergenic	Intergenic	-12448	NR_104464	404220	Hs.716731	NM_206834	ENSG00000185689	C6orf201	dJ1013A10.5	chromosome 6 open reading frame 201	protein-coding	0.008130	0.392857	
chunk0127_29_1	chr3	88611786	88612301	+	0	NA	Intergenic	Intergenic	-462177	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.003883	0.319767	
chunk0023_252_1	chr10	27485267	27485880	+	0	NA	Intergenic	L1ME3A|LINE|L1	-18601	NM_001256410	22931	Hs.406799	NM_021252	ENSG00000099246	RAB18	RAB18LI1|WARBM3	RAB18, member RAS oncogene family	protein-coding	0.003263	0.381107	
chunk0056_307_1	chr13	90894712	90894983	+	0	NA	intron (NR_027039, intron 4 of 5)	intron (NR_027039, intron 4 of 5)	31750	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.007380	0.345588	118(AAGAACTCTTTGTTCC,-,0.00),119(AGAACTCTTTGTTCCC,+,0.00)
chunk0006_228_1	chr1	68575968	68576415	+	0	NA	Intergenic	L1PA17|LINE|L1	-78970	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.004474	0.546875	
chunk0022_419_1	chr10	18677054	18677304	+	0	NA	3' UTR (NM_178815, exon 6 of 6)	3' UTR (NM_178815, exon 6 of 6)	17795	NM_178815	221079	Hs.25362	NM_178815	ENSG00000165997	ARL5B	ARL8	ADP ribosylation factor like GTPase 5B	protein-coding	0.004000	0.338645	
chunk0015_431_1	chr1	191608869	191609157	+	0	NA	Intergenic	HERVL18-int|LTR|ERVL	-549449	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.027778	0.550173	
chunk0057_94_1	chr13	98853566	98853948	+	0	NA	intron (NM_001130048, intron 34 of 55)	intron (NM_001130048, intron 34 of 55)	21673	NR_046663	100874096	Hs.578066	NR_046663	ENSG00000229918	DOCK9-AS1	-	DOCK9 antisense RNA 1	ncRNA	0.010471	0.462141	
chunk0166_136_1	chr6	44825564	44825763	+	0	NA	Intergenic	MIR|SINE|MIR	372107	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.005025	0.380000	87(TAGCACATGGTGTGCT,-,0.00),88(AGCACATGGTGTGCTG,+,0.00)
chunk0107_134_1	chr2	214796702	214797200	+	0	NA	intron (NM_001282543, intron 1 of 9)	MIRc|SINE|MIR	12760	NR_104212	580	Hs.591642	NM_000465	ENSG00000138376	BARD1	-	BRCA1 associated RING domain 1	protein-coding	0.002008	0.302605	
chunk0005_250_1	chr1	59686185	59686801	+	0	NA	intron (NM_001244714, intron 12 of 13)	intron (NM_001244714, intron 12 of 13)	46803	NR_039861	100616409		NR_039861	ENSG00000266150	MIR4711	-	microRNA 4711	ncRNA	0.008117	0.390600	
chunk0042_436_1	chr12	12266988	12267382	+	0	NA	promoter-TSS (NM_002336)	promoter-TSS (NM_002336)	-308	NM_002336	4040	Hs.584775	NM_002336	ENSG00000070018	LRP6	ADCAD2|STHAG7	LDL receptor related protein 6	protein-coding	0.109137	0.696203	
chunk0122_422_1	chr3	39095348	39095651	+	0	NA	3' UTR (NM_020839, exon 19 of 19)	3' UTR (NM_020839, exon 19 of 19)	-12162	NM_145755	199223	Hs.443935	NM_145755	ENSG00000168026	TTC21A	IFT139A|SPGF37|STI2	tetratricopeptide repeat domain 21A	protein-coding	0.009901	0.460526	
chunk0182_307_1	chr7	98523218	98523478	+	0	NA	Intergenic	Intergenic	-93937	NM_002523	4885	Hs.3281	NM_002523	ENSG00000106236	NPTX2	NARP|NP-II|NP2	neuronal pentraxin 2	protein-coding	0.000000	0.375479	
chunk0064_7_1	chr14	89213736	89214665	+	0	NA	intron (NM_001085471, intron 4 of 6)	MIR3|SINE|MIR	202910	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.012917	0.431183	
chunk0094_440_1	chr2	11194845	11195287	+	0	NA	intron (NM_004850, intron 27 of 32)	intron (NM_004850, intron 27 of 32)	39694	NR_104231	130814	Hs.274415	NM_152391	ENSG00000162976	SLC66A3	C2orf22|PQLC3	solute carrier family 66 member 3	protein-coding	0.002262	0.284424	
chunk0041_141_1	chr11	125329269	125329763	+	0	NA	intron (NM_022062, intron 2 of 12)	L2c|LINE|L2	164853	NM_022062	63876	Hs.278564	NM_022062	ENSG00000165495	PKNOX2	PREP2	PBX/knotted 1 homeobox 2	protein-coding	0.002024	0.339394	
chunk0176_45_1	chr7	10838203	10838529	+	0	NA	Intergenic	Intergenic	101820	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.003067	0.345566	
chunk0181_56_1	chr7	80158910	80159201	+	0	NA	intron (NM_001256414, intron 1 of 7)	intron (NM_001256414, intron 1 of 7)	23300	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.006873	0.486301	
chunk0112_228_1	chr20	41047169	41047436	+	0	NA	intron (NM_003286, intron 2 of 20)	Tigger3a|DNA|TcMar-Tigger	18480	NM_003286	7150	Hs.472737	NM_003286	ENSG00000198900	TOP1	TOPI	DNA topoisomerase I	protein-coding	0.007491	0.380597	
chunk0013_324_1	chr1	171541392	171541639	+	0	NA	exon (NM_015172, exon 16 of 34)	exon (NM_015172, exon 16 of 34)	55988	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.028340	0.483871	
chunk0046_203_1	chr12	59030245	59030915	+	0	NA	Intergenic	Intergenic	-110042	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.008955	0.427720	
chunk0114_191_1	chr21	15076705	15077160	+	0	NA	Intergenic	MIRc|SINE|MIR	-12127	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.004396	0.350877	216(AAGTACTGGATGTCCT,-,0.00),217(AGTACTGGATGTCCTC,+,0.00)
chunk0122_282_1	chr3	35947015	35947348	+	0	NA	Intergenic	Intergenic	202705	NR_029824	406916		NR_029824	ENSG00000207625	MIR128-2	MIR128B|MIRN128-2|MIRN128B|mir-128-2|mir-128b	microRNA 128-2	ncRNA	0.003003	0.461078	
chunk0162_266_1	chr6	5414445	5414749	+	0	NA	intron (NM_006567, intron 3 of 6)	L1ME1|LINE|L1	43478	NR_125848	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.003289	0.327869	
chunk0062_73_1	chr14	67698587	67699050	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-3025	NM_016026	51109	Hs.719925	NM_016026	ENSG00000072042	RDH11	ARSDR1|CGI82|HCBP12|MDT1|PSDR1|RALR1|RDJCSS|SCALD|SDR7C1	retinol dehydrogenase 11	protein-coding	0.004320	0.383621	
chunk0011_387_1	chr1	153881834	153882138	+	0	NA	intron (NM_020699, intron 1 of 10)	intron (NM_020699, intron 1 of 10)	40989	NM_020699	57459	Hs.4779	NM_020699	ENSG00000143614	GATAD2B	MRD18|P66beta|p68	GATA zinc finger domain containing 2B	protein-coding	0.023026	0.468852	
chunk0081_408_1	chr17	48456567	48456787	+	0	NA	intron (NR_110804, intron 5 of 5)	intron (NR_110804, intron 5 of 5)	11844	NR_110804	101927166	Hs.149244	NR_110804		LOC101927166	-	uncharacterized LOC101927166	ncRNA	0.013636	0.506787	
chunk0065_40_1	chr15	21272158	21272872	+	0	NA	Intergenic	Intergenic	25314	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.004202	0.376224	
chunk0182_375_1	chr7	100023639	100023983	+	0	NA	exon (NM_001287054, exon 4 of 8)	exon (NM_001287054, exon 4 of 8)	8239	NM_001287055	7586	Hs.615360	NM_003439	ENSG00000106261	ZKSCAN1	KOX18|PHZ-37|ZNF139|ZNF36|ZSCAN33	zinc finger with KRAB and SCAN domains 1	protein-coding	0.031977	0.530435	
chunk0039_30_1	chr11	95742021	95742323	+	0	NA	Intergenic	L1ME1|LINE|L1	47618	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.000000	0.287129	
chunk0118_216_1	chr22	31894160	31894643	+	0	NA	intron (NR_110988, intron 35 of 38)	(ATTGTT)n|Simple_repeat|Simple_repeat	44053	NM_001302820	25775	Hs.627602	NM_015372	ENSG00000128254	C22orf24	HSN44A4A	chromosome 22 open reading frame 24	protein-coding	0.014493	0.400826	
chunk0044_371_1	chr12	39606663	39606972	+	0	NA	intron (NM_005164, intron 3 of 9)	intron (NM_005164, intron 3 of 9)	13224	NM_005164	225	Hs.117852	NM_005164	ENSG00000173208	ABCD2	ABC39|ALDL1|ALDR|ALDRP|hALDR	ATP binding cassette subfamily D member 2	protein-coding	0.000000	0.312903	
chunk0206_34_1	chr9	116469496	116469990	+	0	NA	intron (NM_198186, intron 5 of 7)	intron (NM_198186, intron 5 of 7)	-34540	NR_033973	100128505	Hs.675821	NR_033973	ENSG00000229105	ASTN2-AS1	-	ASTN2 antisense RNA 1	ncRNA	0.012146	0.408081	
chunk0110_200_1	chr20	14851728	14851997	+	0	NA	intron (NM_080676, intron 5 of 16)	MIR|SINE|MIR	77656	NR_037841	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.003717	0.418519	
chunk0070_277_1	chr15	74359503	74360427	+	0	NA	intron (NM_000781, intron 1 of 8)	MER41-int|LTR|ERV1	-1587	NR_045207	729739	Hs.742028	NR_045207	ENSG00000260266	PPIAP46	-	peptidylprolyl isomerase A pseudogene 46	pseudo	0.012987	0.423784	582(GTGTACATTATGTTCA,-,0.00)
chunk0165_223_1	chr6	35304408	35304626	+	0	NA	intron (NM_022047, intron 1 of 10)	L2a|LINE|L2	6699	NM_022047	50619	Hs.15476	NM_022047	ENSG00000023892	DEF6	IBP|SLAT|SWAP70L	DEF6 guanine nucleotide exchange factor	protein-coding	0.004587	0.529680	50(AGGAACAGTAAGTGCA,-,0.00),51(GGAACAGTAAGTGCAA,+,0.00)
chunk0140_15_1	chr4	65502124	65502730	+	0	NA	intron (NM_001281765, intron 3 of 17)	L1PA16|LINE|L1	-167534	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.003300	0.327842	
chunk0105_53_1	chr2	183094584	183095380	+	0	NA	intron (NM_080876, intron 3 of 3)	intron (NM_080876, intron 3 of 3)	16423	NM_001142314	142679	Hs.132237	NM_080876	ENSG00000162999	DUSP19	DUSP17|LMWDSP3|SKRP1|TS-DSP1	dual specificity phosphatase 19	protein-coding	0.001256	0.291092	
chunk0034_224_1	chr11	33155934	33156433	+	0	NA	intron (NM_001033505, intron 1 of 2)	intron (NM_001033505, intron 1 of 2)	5308	NM_001033505	1479	Hs.44402	NM_001326	ENSG00000176102	CSTF3	CSTF-77	cleavage stimulation factor subunit 3	protein-coding	0.004008	0.372000	
chunk0080_216_1	chr17	29627844	29628605	+	0	NA	3' UTR (NM_033389, exon 15 of 15)	3' UTR (NM_033389, exon 15 of 15)	-6801	NM_032854	84940	Hs.143046	NM_032854	ENSG00000167549	CORO6	-	coronin 6	protein-coding	0.002628	0.426509	
chunk0154_438_1	chr5	90297308	90297741	+	0	NA	Intergenic	Intergenic	-7453	NR_120601	101929495	Hs.346679	NR_120601		LINC01339	-	long intergenic non-protein coding RNA 1339	ncRNA	0.011547	0.428571	
chunk0053_116_1	chr13	29464170	29464579	+	0	NA	intron (NM_015233, intron 2 of 8)	intron (NM_015233, intron 2 of 8)	23376	NR_046378	100874107	Hs.577987	NR_046378		MTUS2-AS1	-	MTUS2 antisense RNA 1	ncRNA	0.007335	0.531707	165(GTGAACAAACAGTTCT,-,0.00),166(TGAACAAACAGTTCTA,+,0.00),213(GAGAACAGGAAGATCT,-,0.00)
chunk0146_42_1	chr4	155505871	155506338	+	0	NA	Intergenic	MER4A|LTR|ERV1	-129134	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.008565	0.386752	
chunk0190_125_1	chr8	30603353	30604074	+	0	NA	intron (NM_002095, intron 6 of 7)	L1M5|LINE|L1	-34887	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.006935	0.300554	
chunk0028_447_1	chr10	94129279	94129554	+	0	NA	intron (NM_001165979, intron 1 of 31)	MER103C|DNA|hAT-Charlie	-20622	NR_120615	101927049	Hs.144492	NR_120615	ENSG00000232913	PLCE1-AS2	-	PLCE1 antisense RNA 2	ncRNA	0.007273	0.326087	
chunk0184_229_1	chr7	117496095	117496324	+	0	NA	intron (NM_000492, intron 1 of 26)	AluJr|SINE|Alu	16246	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.013100	0.404348	19(TAGAACAAAGTGTTCT,-,0.00),20(AGAACAAAGTGTTCTT,+,0.00)
chunk0025_51_1	chr10	49436209	49436677	+	0	NA	Intergenic	L1ME3F|LINE|L1	-40427	NM_001276451	644168	Hs.534530	NM_001080520	ENSG00000165606	DRGX	DRG11|PRRXL1	dorsal root ganglia homeobox	protein-coding	0.000000	0.275053	
chunk0197_436_1	chr8	127519017	127519810	+	0	NA	Intergenic	L1MD1|LINE|L1	-37274	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.005044	0.267003	
chunk0211_228_1	chrX	118841963	118842654	+	0	NA	intron (NR_110393, intron 2 of 6)	intron (NR_110393, intron 2 of 6)	2752	NR_110393	101928287	Hs.496647	NR_110393	ENSG00000203650	LINC01285	-	long intergenic non-protein coding RNA 1285	ncRNA	0.011577	0.437861	192(GAGGACAAGATGCTCT,-,0.00),193(AGGACAAGATGCTCTG,+,0.00),347(GAGGACTTAATGTGCC,-,0.00),348(AGGACTTAATGTGCCT,+,0.00)
chunk0129_281_1	chr3	123161168	123161413	+	0	NA	promoter-TSS (NR_106960)	promoter-TSS (NR_106960)	-504	NR_106960	102465667		NR_106960	ENSG00000284421	MIR7110	hsa-mir-7110	microRNA 7110	ncRNA	0.012245	0.556911	113(GGGGACACCCTGTGCC,-,0.00),114(GGGACACCCTGTGCCA,+,0.00)
chunk0196_64_1	chr8	102290306	102290871	+	0	NA	intron (NM_015902, intron 34 of 58)	intron (NM_015902, intron 34 of 58)	51137	NR_125415	101927221	Hs.492445	NR_125415	ENSG00000246263	UBR5-AS1	-	UBR5 antisense RNA 1	ncRNA	0.008850	0.363958	
chunk0146_247_1	chr4	162456930	162457296	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-293079	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.008197	0.400545	
chunk0007_280_1	chr1	83765134	83765629	+	0	NA	intron (NR_119375, intron 1 of 2)	intron (NR_119375, intron 1 of 2)	95165	NR_119374	101927560	Hs.559661	NR_119374	ENSG00000233008	LOC101927560	-	uncharacterized LOC101927560	ncRNA	0.006061	0.314516	221(AAGAACAAACTGTCCT,-,0.00),222(AGAACAAACTGTCCTC,+,0.00)
chunk0028_22_1	chr10	82517961	82518504	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-285312	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.007366	0.380515	
chunk0202_298_1	chr9	77867984	77868431	+	0	NA	intron (NM_002072, intron 2 of 6)	intron (NM_002072, intron 2 of 6)	163242	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.000000	0.339286	
chunk0204_121_1	chr9	95121207	95121775	+	0	NA	intron (NM_001243744, intron 10 of 13)	L1ME3F|LINE|L1	-35397	NR_036109	100422842		NR_036109	ENSG00000207617	MIR3074	mir-3074	microRNA 3074	ncRNA	0.003521	0.434095	
chunk0211_309_1	chrX	123611017	123611217	+	0	NA	intron (NM_001081550, intron 37 of 38)	intron (NM_001081550, intron 37 of 38)	121937	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.000000	0.482587	132(AGGGACTCTCTGTTCC,-,0.00),133(GGGACTCTCTGTTCCC,+,0.00)
chunk0039_286_1	chr11	102653830	102654195	+	0	NA	Intergenic	Intergenic	-28680	NM_004771	9313	Hs.591946	NM_004771	ENSG00000137674	MMP20	AI2A2|MMP-20	matrix metallopeptidase 20	protein-coding	0.019178	0.508197	
chunk0194_170_1	chr8	84874840	84875358	+	0	NA	intron (NM_001100393, intron 7 of 8)	intron (NM_001100393, intron 7 of 8)	169172	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.003861	0.314066	
chunk0128_166_1	chr3	107264747	107265349	+	0	NA	intron (NR_028302, intron 1 of 3)	intron (NR_028302, intron 1 of 3)	24356	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.016611	0.416252	
chunk0128_177_1	chr3	107361084	107361283	+	0	NA	Intergenic	AluJr|SINE|Alu	-16158	NM_032600	84692	Hs.164799	NM_032600	ENSG00000138483	CCDC54	NYD-SP17|SP17	coiled-coil domain containing 54	protein-coding	0.005025	0.470000	
chunk0128_403_1	chr3	114145117	114145699	+	0	NA	intron (NM_001282563, intron 5 of 7)	intron (NM_001282563, intron 5 of 7)	33368	NM_001290809	1814	Hs.121478	NM_000796	ENSG00000151577	DRD3	D3DR|ETM1|FET1	dopamine receptor D3	protein-coding	0.006873	0.377358	
chunk0191_222_1	chr8	52707016	52707215	+	0	NA	intron (NM_014781, intron 1 of 23)	MIRc|SINE|MIR	7351	NM_014781	9821	Hs.196102	NM_014781	ENSG00000023287	RB1CC1	ATG17|CC1|FIP200|PPP1R131	RB1 inducible coiled-coil 1	protein-coding	0.005025	0.325000	
chunk0168_182_1	chr6	84910713	84910912	+	0	NA	Intergenic	Intergenic	-146576	NM_001080508	9096	Hs.251830	NM_001080508	ENSG00000112837	TBX18	CAKUT2	T-box transcription factor 18	protein-coding	0.000000	0.340000	
chunk0137_267_1	chr4	22445468	22445766	+	0	NA	intron (NM_145290, intron 5 of 18)	L2c|LINE|L2	70437	NM_145290	166647	Hs.99195	NM_145290	ENSG00000152990	ADGRA3	GPR125|PGR21|TEM5L	adhesion G protein-coupled receptor A3	protein-coding	0.000000	0.394649	
chunk0024_75_1	chr10	34289581	34290019	+	0	NA	intron (NM_019619, intron 20 of 24)	intron (NM_019619, intron 20 of 24)	-517120	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.004566	0.369021	
chunk0109_270_1	chr20	8060867	8061354	+	0	NA	Intergenic	Intergenic	-41281	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.000000	0.342213	369(AAGGACAGTGAGTCCT,-,0.00),370(AGGACAGTGAGTCCTT,+,0.00)
chunk0027_271_1	chr10	77398612	77398811	+	0	NA	intron (NM_001271518, intron 1 of 27)	MER58A|DNA|hAT-Charlie	47839	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.005025	0.410000	
chunk0154_361_1	chr5	87551845	87552294	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-139036	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.002227	0.395556	
chunk0051_338_1	chr12	120262643	120263191	+	0	NA	intron (NM_001243756, intron 1 of 10)	intron (NM_001243756, intron 1 of 10)	2854	NM_002859	5829	Hs.446336	NM_002859	ENSG00000089159	PXN	-	paxillin	protein-coding	0.012774	0.475410	251(CAGAACACGCTGTGTT,-,0.00),252(AGAACACGCTGTGTTG,+,0.00)
chunk0038_161_1	chr11	84864034	84864533	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	59138	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.002004	0.380000	
chunk0167_453_1	chr6	76416648	76417417	+	0	NA	Intergenic	Intergenic	-344354	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.003901	0.370130	
chunk0138_450_1	chr4	47064641	47064934	+	0	NA	intron (NM_000812, intron 3 of 8)	L2a|LINE|L2	33509	NM_000812	2560	Hs.27283	NM_000812	ENSG00000163288	GABRB1	EIEE45	gamma-aminobutyric acid type A receptor beta1 subunit	protein-coding	0.003413	0.302721	
chunk0131_258_1	chr3	149752359	149752867	+	0	NA	promoter-TSS (NM_016094)	promoter-TSS (NM_016094)	-114	NM_016094	51122	Hs.432729	NM_016094	ENSG00000114744	COMMD2	HSPC042	COMM domain containing 2	protein-coding	0.068898	0.536346	
chunk0091_219_1	chr19	10003814	10004056	+	0	NA	intron (NM_015719, intron 5 of 66)	intron (NM_015719, intron 5 of 66)	6536	NM_015719	50509	Hs.235368	NM_015719	ENSG00000080573	COL5A3	-	collagen type V alpha 3 chain	protein-coding	0.012397	0.534979	
chunk0157_423_1	chr5	124677204	124677663	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	67679	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.008715	0.410870	
chunk0065_63_1	chr15	23033681	23034393	+	0	NA	intron (NM_001102610, intron 3 of 21)	MER77|LTR|ERVL	5636	NM_052903	114791	Hs.533898	NM_052903	ENSG00000275835	TUBGCP5	GCP5	tubulin gamma complex associated protein 5	protein-coding	0.005618	0.398317	
chunk0136_123_1	chr4	3714481	3714749	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-36760	NR_034136	100133461	Hs.554274	NR_034136	ENSG00000250632	LINC02171	-	long intergenic non-protein coding RNA 2171	ncRNA	0.007463	0.479554	
chunk0117_141_1	chr22	19535106	19535389	+	0	NA	Intergenic	L1MA5A|LINE|L1	-9910	NM_001130861	7122	Hs.505337	NM_003277	ENSG00000184113	CLDN5	AWAL|BEC1|CPETRL1|TMDVCF|TMVCF	claudin 5	protein-coding	0.010601	0.401408	
chunk0094_388_1	chr2	9981863	9982229	+	0	NA	intron (NM_198182, intron 8 of 15)	intron (NM_198182, intron 8 of 15)	30383	NM_198182	29841	Hs.418493	NM_198182	ENSG00000134317	GRHL1	LBP32|MGR|NH32|TFCP2L2	grainyhead like transcription factor 1	protein-coding	0.002732	0.316076	
chunk0001_64_1	chr1	2357964	2358203	+	0	NA	intron (NM_001301060, intron 9 of 10)	intron (NM_001301060, intron 9 of 10)	-5422	NR_024489	100129534	Hs.655313	NM_001127577	ENSG00000269896	LOC100129534	-	small nuclear ribonucleoprotein polypeptide N pseudogene	pseudo	0.029289	0.587500	174(GGTCCAGCGTGTTCCT,+,0.00)
chunk0160_276_1	chr5	157744859	157745686	+	0	NA	intron (NM_173491, intron 1 of 3)	intron (NM_173491, intron 1 of 3)	1577	NM_173491	134353	Hs.23648	NM_173491	ENSG00000155858	LSM11	-	LSM11, U7 small nuclear RNA associated	protein-coding	0.006046	0.423913	
chunk0160_267_1	chr5	157278292	157278841	+	0	NA	intron (NM_014376, intron 1 of 30)	MIRc|SINE|MIR	9224	NM_014376	26999	Hs.519702	NM_014376	ENSG00000055163	CYFIP2	EIEE65|PIR121	cytoplasmic FMR1 interacting protein 2	protein-coding	0.003643	0.381818	260(CATAACACAGTGTCCT,-,0.00),261(ATAACACAGTGTCCTC,+,0.00)
chunk0055_192_1	chr13	61738087	61738772	+	0	NA	Intergenic	Intergenic	291119	NR_046995	100874143	Hs.552684	NR_046995	ENSG00000229578	LINC00358	-	long intergenic non-protein coding RNA 358	ncRNA	0.004380	0.330904	
chunk0147_387_1	chr4	186603393	186603805	+	0	NA	exon (NM_005245, exon 19 of 27)	exon (NM_005245, exon 19 of 27)	-48216	NM_005958	4543	Hs.243467	NM_005958	ENSG00000168412	MTNR1A	MEL-1A-R|MT1	melatonin receptor 1A	protein-coding	0.036408	0.484262	361(GAGAACAGGTTGTCCA,-,0.00),362(AGAACAGGTTGTCCAT,+,0.00)
chunk0180_365_1	chr7	73954929	73955279	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-72685	NM_000501	2006	Hs.647061	NM_000501	ENSG00000049540	ELN	ADCL1|SVAS|WBS|WS	elastin	protein-coding	0.002857	0.378917	164(AAGTACATACTGTCTC,-,0.00),165(AGTACATACTGTCTCT,+,0.00)
chunk0159_80_1	chr5	137624801	137625453	+	0	NA	intron (NM_001257194, intron 14 of 14)	MIRb|SINE|MIR	22522	NR_030588	100126343		NR_030588	ENSG00000216009	MIR874	MIRN874|hsa-mir-874|mir-874	microRNA 874	ncRNA	0.010736	0.468606	329(ATGCACACTCTGTTCC,-,0.00),330(TGCACACTCTGTTCCT,+,0.00)
chunk0006_340_1	chr1	72284301	72284500	+	0	NA	Intergenic	Intergenic	-1806	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.025126	0.475000	
chunk0018_247_1	chr1	220151605	220151816	+	0	NA	exon (NM_012414, exon 34 of 35)	exon (NM_012414, exon 34 of 35)	-33469	NR_029711	406969		NR_029711	ENSG00000207624	MIR194-1	MIRN194-1|mir-194-1	microRNA 194-1	ncRNA	0.009479	0.500000	
chunk0130_453_1	chr3	141402830	141403277	+	0	NA	intron (NM_001080412, intron 6 of 7)	intron (NM_001080412, intron 6 of 7)	78840	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.029083	0.479911	
chunk0170_315_1	chr6	116105195	116105665	+	0	NA	intron (NM_152729, intron 1 of 11)	intron (NM_152729, intron 1 of 11)	4594	NM_152729	221294	Hs.520341	NM_152729	ENSG00000178425	NT5DC1	C6orf200|LP2642|NT5C2L1	5'-nucleotidase domain containing 1	protein-coding	0.006383	0.443737	
chunk0038_411_1	chr11	94128589	94128905	+	0	NA	promoter-TSS (NM_015368)	promoter-TSS (NM_015368)	-181	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.079114	0.624606	
chunk0144_104_1	chr4	128571595	128572102	+	0	NA	Intergenic	Intergenic	143832	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.003945	0.374016	311(CAGAACATGCTGTGCA,-,0.00),312(AGAACATGCTGTGCAT,+,0.00)
chunk0103_149_1	chr2	162175736	162176173	+	0	NA	intron (NM_001291807, intron 20 of 24)	intron (NM_001291807, intron 20 of 24)	-23550	NM_002054	2641	Hs.516494	NM_002054	ENSG00000115263	GCG	GLP-1|GLP1|GLP2|GRPP	glucagon	protein-coding	0.006865	0.426941	
chunk0210_423_1	chrX	102507253	102507908	+	0	NA	Intergenic	L1M4|LINE|L1	9191	NM_021992	11013	Hs.56145	NM_021992	ENSG00000158164	TMSB15A	TMSB15|TMSB15B|TMSL8|TMSNB|Tb15|TbNB	thymosin beta 15a	protein-coding	0.001527	0.365854	
chunk0072_276_1	chr15	97960299	97960524	+	0	NA	promoter-TSS (NM_183376)	promoter-TSS (NM_183376)	-292	NM_183376	91947	Hs.6093	NM_183376	ENSG00000140450	ARRDC4	-	arrestin domain containing 4	protein-coding	0.066667	0.619469	
chunk0180_247_1	chr7	68730868	68731469	+	0	NA	Intergenic	L2b|LINE|L2	710915	NR_120514	102723427	Hs.583491	NR_120514	ENSG00000225209	LOC102723427	-	uncharacterized LOC102723427	ncRNA	0.001664	0.461794	
chunk0082_217_1	chr17	57110096	57110421	+	0	NA	intron (NM_001242902, intron 4 of 11)	intron (NM_001242902, intron 4 of 11)	24484	NM_001242902	8165	Hs.463506	NM_003488	ENSG00000121057	AKAP1	AKAP|AKAP121|AKAP149|AKAP84|D-AKAP1|PPP1R43|PRKA1|SAKAP84|TDRD17	A-kinase anchoring protein 1	protein-coding	0.018462	0.588957	
chunk0049_366_1	chr12	95626888	95627434	+	0	NA	Intergenic	L3|LINE|CR1	-22094	NR_077225	100132594	Hs.676211	NR_077225	ENSG00000257150	PGAM1P5	-	phosphoglycerate mutase 1 pseudogene 5	pseudo	0.010989	0.387569	305(AGTACATTATGTCTTT,+,0.00)
chunk0122_428_1	chr3	39140824	39142194	+	0	NA	TTS (NM_033027)	TTS (NM_033027)	3303	NR_106880	102466743		NR_106880	ENSG00000284158	MIR6822	hsa-mir-6822	microRNA 6822	ncRNA	0.006569	0.527352	1067(AGGTACAAGGTGTTCC,-,0.00),1068(GGTACAAGGTGTTCCC,+,0.00)
chunk0207_306_1	chr9	133572880	133573262	+	0	NA	intron (NM_001145320, intron 17 of 18)	intron (NM_001145320, intron 17 of 18)	7175	NM_001080515	642968	Hs.173134	NM_001080515	ENSG00000196990	FAM163B	C9orf166	family with sequence similarity 163 member B	protein-coding	0.028796	0.647520	
chunk0148_439_1	chr4	189272714	189272976	+	0	NA	Intergenic	Intergenic	-386761	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.007634	0.463878	
chunk0106_219_1	chr2	202556063	202556657	+	0	NA	exon (NM_001204, exon 12 of 13)	exon (NM_001204, exon 12 of 13)	-78818	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.008418	0.447059	334(CAGAACAAGATGTTCT,-,0.00),335(AGAACAAGATGTTCTT,+,0.00),349(TTGCACAGGGTGTTCC,-,0.00),350(TGCACAGGGTGTTCCA,+,0.00)
chunk0006_222_1	chr1	68413935	68414278	+	0	NA	Intergenic	L1MC5a|LINE|L1	35853	NM_000329	6121	Hs.2133	NM_000329	ENSG00000116745	RPE65	BCO3|LCA2|RP20|mRPE65|p63|rd12|sRPE65	retinoid isomerohydrolase RPE65	protein-coding	0.002915	0.311047	236(TGGAACAGCAAGTCCT,-,0.00),237(GGAACAGCAAGTCCTC,+,0.00)
chunk0126_397_1	chr3	84969650	84970279	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	10982	NM_001167675	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.004769	0.312698	
chunk0192_91_1	chr8	61145371	61145745	+	0	NA	Intergenic	Intergenic	-142408	NM_173519	157807	Hs.591874	NM_173519	ENSG00000177182	CLVS1	C6orf212L|CRALBPL|RLBP1L1	clavesin 1	protein-coding	0.010695	0.453333	
chunk0057_20_1	chr13	95593566	95593991	+	0	NA	intron (NM_198968, intron 16 of 22)	MIR|SINE|MIR	41085	NM_006984	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.002353	0.352113	
chunk0203_183_1	chr9	86354160	86354733	+	0	NA	promoter-TSS (NM_001185074)	promoter-TSS (NM_001185074)	41	NM_024617	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.113438	0.700348	
chunk0062_315_1	chr14	73170811	73171131	+	0	NA	exon (NM_000021, exon 4 of 12)	exon (NM_000021, exon 4 of 12)	34536	NM_007318	5663	Hs.3260	NM_000021	ENSG00000080815	PSEN1	ACNINV3|AD3|FAD|PS-1|PS1|S182	presenilin 1	protein-coding	0.028125	0.504673	
chunk0128_416_1	chr3	114789548	114790228	+	0	NA	intron (NM_001164343, intron 4 of 11)	intron (NM_001164343, intron 4 of 11)	-30611	NM_001164345	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.004412	0.325991	
chunk0156_217_1	chr5	108124592	108125648	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	256978	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.006629	0.306528	
chunk0104_355_1	chr2	179939095	179939793	+	0	NA	Intergenic	Intergenic	67609	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.011461	0.387697	
chunk0119_197_1	chr22	44666212	44667040	+	0	NA	Intergenic	L1MD1|LINE|L1	-1921	NM_001017528	55615	Hs.102336	NM_015366	ENSG00000186654	PRR5	FLJ20185k|PP610|PROTOR-1|PROTOR1	proline rich 5	protein-coding	0.007246	0.422195	
chunk0153_147_1	chr5	69164889	69165373	+	0	NA	Intergenic	L1MC1|LINE|L1	-1879	NM_031966	891	Hs.23960	NM_031966	ENSG00000134057	CCNB1	CCNB	cyclin B1	protein-coding	0.018595	0.375258	
chunk0122_354_1	chr3	37487052	37487367	+	0	NA	intron (NM_002207, intron 4 of 27)	MIRc|SINE|MIR	34887	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.000000	0.360759	
chunk0160_345_1	chr5	160107504	160107820	+	0	NA	intron (NM_052927, intron 1 of 3)	intron (NM_052927, intron 1 of 3)	11783	NM_001130864	114825	Hs.744960	NM_052927	ENSG00000170234	PWWP2A	MST101	PWWP domain containing 2A	protein-coding	0.012658	0.400631	
chunk0092_34_1	chr19	19086622	19087204	+	0	NA	intron (NM_178526, intron 1 of 7)	L1MA9|LINE|L1	22919	NM_178526	284439	Hs.303669	NM_178526	ENSG00000181035	SLC25A42	MECREN	solute carrier family 25 member 42	protein-coding	0.006873	0.409949	
chunk0090_94_1	chr18	70775462	70775911	+	0	NA	Intergenic	MIR3|SINE|MIR	-124829	NM_001278515									0.011136	0.380000	
chunk0200_61_1	chr9	15714580	15715107	+	0	NA	intron (NM_173550, intron 11 of 25)	ERVL-E-int|LTR|ERVL	161744	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.005693	0.403409	299(AGGAACACCATGATCA,-,0.00),300(GGAACACCATGATCAG,+,0.00)
chunk0052_15_1	chr13	20110464	20110930	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	7996	NR_126380	104355137	Hs.578016	NR_126380	ENSG00000236076	LINC01072	-	long intergenic non-protein coding RNA 1072	ncRNA	0.015021	0.490364	
chunk0159_376_1	chr5	146008926	146009270	+	0	NA	intron (NM_152550, intron 4 of 9)	L1ME1|LINE|L1	72535	NM_152550	153769	Hs.443728	NM_152550	ENSG00000156463	SH3RF2	HEPP1|POSHER|PPP1R39|RNF158	SH3 domain containing ring finger 2	protein-coding	0.002907	0.379710	
chunk0026_239_1	chr10	66119163	66119610	+	0	NA	intron (NM_001127384, intron 13 of 17)	intron (NM_001127384, intron 13 of 17)	547961	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.000000	0.330357	
chunk0198_280_1	chr8	135525459	135525820	+	0	NA	intron (NM_006558, intron 2 of 8)	intron (NM_006558, intron 2 of 8)	68174	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.005540	0.359116	
chunk0105_174_1	chr2	187185169	187185765	+	0	NA	Intergenic	Intergenic	262827	NM_001271751	10203	Hs.470882	NM_005795	ENSG00000064989	CALCRL	CGRPR|CRLR	calcitonin receptor like receptor	protein-coding	0.008389	0.365159	
chunk0193_357_1	chr8	79912725	79913392	+	0	NA	Intergenic	L1MB4|LINE|L1	-41321	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.001499	0.354790	
chunk0071_108_1	chr15	81127115	81127353	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-7069	NM_173528	161502	Hs.130979	NM_173528	ENSG00000156206	CFAP161	C15orf26	cilia and flagella associated protein 161	protein-coding	0.004202	0.372385	
chunk0096_298_1	chr2	32702154	32702561	+	0	NA	intron (NM_017735, intron 9 of 19)	intron (NM_017735, intron 9 of 19)	67102	NR_039922	100616219		NR_039922	ENSG00000265057	MIR4765	-	microRNA 4765	ncRNA	0.002457	0.370098	217(TAGTACATTTTGTCCC,-,0.00),218(AGTACATTTTGTCCCT,+,0.00)
chunk0118_203_1	chr22	31648823	31649377	+	0	NA	Intergenic	FRAM|SINE|Alu	-18276	NM_014338	23761	Hs.420559	NM_014338	ENSG00000241878	PISD	DJ858B16|PSD|PSDC|PSSC|dJ858B16.2	phosphatidylserine decarboxylase	protein-coding	0.009025	0.430631	
chunk0180_42_1	chr7	54540515	54541182	+	0	NA	Intergenic	Intergenic	-1477	NM_001301009	222008	Hs.335933	NM_182546	ENSG00000170419	VSTM2A	VSTM2	V-set and transmembrane domain containing 2A	protein-coding	0.005997	0.308383	
chunk0035_333_1	chr11	47938374	47938573	+	0	NA	Intergenic	L2a|LINE|L2	-42085	NM_001098503	5795	Hs.318547	NM_002843	ENSG00000149177	PTPRJ	CD148|DEP1|HPTPeta|R-PTP-ETA|SCC1	protein tyrosine phosphatase receptor type J	protein-coding	0.015075	0.465000	
chunk0069_433_1	chr15	68340717	68341502	+	0	NA	intron (NM_001004439, intron 10 of 29)	intron (NM_001004439, intron 10 of 29)	63306	NM_015322	10116	Hs.362733	NM_015322	ENSG00000169018	FEM1B	F1A-ALPHA|F1AA|FEM1-beta	fem-1 homolog B	protein-coding	0.017834	0.516539	395(TAGAACTGACTGTTCA,-,0.00),396(AGAACTGACTGTTCAG,+,0.00)
chunk0008_436_1	chr1	99542568	99543005	+	0	NA	intron (NR_031666, intron 3 of 4)	intron (NR_031666, intron 3 of 4)	-54982	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.006865	0.385845	221(AGGGACACTTTGTCCA,-,0.00),222(GGGACACTTTGTCCAA,+,0.00)
chunk0046_216_1	chr12	59388188	59388608	+	0	NA	Intergenic	Intergenic	-207642	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.004762	0.365796	
chunk0164_334_1	chr6	25283922	25284527	+	0	NA	intron (NM_017640, intron 1 of 36)	intron (NM_017640, intron 1 of 36)	4796	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.021488	0.458746	
chunk0155_253_1	chr5	95756155	95756702	+	0	NA	intron (NM_014899, intron 6 of 11)	L1MB3|LINE|L1	25282	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.003656	0.366788	306(GTGAACATAGTGTACA,-,0.00)
chunk0186_15_1	chr7	135730424	135730743	+	0	NA	intron (NM_205855, intron 3 of 3)	intron (NM_205855, intron 3 of 3)	-2398	NM_012450	26266	Hs.490241	NM_012450	ENSG00000164707	SLC13A4	NAS2|SUT-1|SUT1	solute carrier family 13 member 4	protein-coding	0.012539	0.431250	
chunk0207_28_1	chrX	3539914	3540453	+	0	NA	Intergenic	Intergenic	-119304	NR_046643	100873944		NR_046643	ENSG00000236188	PRKX-AS1	-	PRKX antisense RNA 1	ncRNA	0.009276	0.375926	
chunk0051_111_1	chr12	115004300	115005157	+	0	NA	Intergenic	Intergenic	-320564	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.009335	0.459207	111(GGGAACAAGATGACCT,-,0.00),112(GGAACAAGATGACCTT,+,0.00)
chunk0209_127_1	chrX	40943253	40943791	+	0	NA	Intergenic	Intergenic	-110326	NR_027761	100132831	Hs.729923	NR_027761		LOC100132831	-	A20-binding inhibitor of NF-kappaB activation 2 pseudogene	pseudo	0.000000	0.397032	
chunk0159_245_1	chr5	141876563	141877486	+	0	NA	intron (NM_032420, intron 1 of 4)	CpG	1386	NM_032420	5097	Hs.79769	NM_002587	ENSG00000156453	PCDH1	PC42|PCDH42	protocadherin 1	protein-coding	0.046587	0.588745	
chunk0015_362_1	chr1	190379274	190379473	+	0	NA	intron (NM_199051, intron 2 of 7)	L2a|LINE|L2	98256	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.310000	
chunk0113_295_1	chr20	57685339	57686019	+	0	NA	intron (NM_199171, intron 1 of 3)	intron (NM_199171, intron 1 of 3)	4945	NM_001255976	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.026471	0.488987	
chunk0100_2_1	chr2	103899050	103899370	+	0	NA	Intergenic	Intergenic	509122	NR_037885	100287010	Hs.694603	NR_037885		LOC100287010	-	uncharacterized LOC100287010	ncRNA	0.006250	0.401869	
chunk0080_203_1	chr17	29331824	29332527	+	0	NA	Intergenic	Intergenic	-38027	NM_020772	57532	Hs.462598	NM_020772	ENSG00000108256	NUFIP2	182-FIP|82-FIP|FIP-82|PIG1	nuclear FMR1 interacting protein 2	protein-coding	0.007112	0.423295	
chunk0124_287_1	chr3	57692279	57692669	+	0	NA	intron (NM_152678, intron 1 of 19)	intron (NM_152678, intron 1 of 19)	615	NM_152678	201627	Hs.91085	NM_152678	ENSG00000174839	DENND6A	AFI1A|FAM116A	DENN domain containing 6A	protein-coding	0.038462	0.480818	
chunk0057_386_1	chr13	109461940	109462231	+	0	NA	Intergenic	L1MA7|LINE|L1	61389	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.000000	0.297945	
chunk0094_75_1	chr2	3523946	3524343	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-4565	NM_018269	55256	Hs.502773	NM_018269	ENSG00000182551	ADI1	APL1|ARD|Fe-ARD|HMFT1638|MTCBP1|Ni-ARD|SIPL|mtnD	acireductone dioxygenase 1	protein-coding	0.007557	0.422111	210(TGGTACAGTGTGTACC,-,0.00),211(GGTACAGTGTGTACCA,+,0.00)
chunk0111_288_1	chr20	31679746	31680554	+	0	NA	intron (NM_001191, intron 2 of 2)	MIRb|SINE|MIR	-41357	NR_131907	103021294		NR_131907	ENSG00000281376	ABALON	INXS	apoptotic BCL2L1-antisense long non-coding RNA	ncRNA	0.007426	0.442522	
chunk0200_330_1	chr9	23752918	23753194	+	0	NA	intron (NM_001171195, intron 2 of 5)	intron (NM_001171195, intron 2 of 5)	68424	NM_001171197	1993	Hs.166109	NM_004432	ENSG00000107105	ELAVL2	HEL-N1|HELN1|HUB	ELAV like RNA binding protein 2	protein-coding	0.007246	0.339350	
chunk0141_76_1	chr4	78121398	78121718	+	0	NA	intron (NM_025074, intron 2 of 73)	intron (NM_025074, intron 2 of 73)	63988	NM_025074	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.009375	0.473520	113(AAGCACACTCTGTCTA,-,0.00),114(AGCACACTCTGTCTAT,+,0.00)
chunk0198_177_1	chr8	133326595	133327429	+	0	NA	Intergenic	Intergenic	-29708	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.008393	0.447904	
chunk0198_166_1	chr8	133216138	133216942	+	0	NA	intron (NM_001204869, intron 2 of 2)	MER102a|DNA|hAT-Charlie	25501	NM_003882	8840	Hs.492974	NM_003882	ENSG00000104415	CCN4	WISP1|WISP1-OT1|WISP1-UT1|WISP1c|WISP1i|WISP1tc	cellular communication network factor 4	protein-coding	0.004975	0.423602	
chunk0121_222_1	chr3	21836311	21837034	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-85348	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.008299	0.368785	
chunk0001_397_1	chr1	10724084	10724533	+	0	NA	intron (NM_001079843, intron 2 of 20)	intron (NM_001079843, intron 2 of 20)	72368	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.024499	0.506667	
chunk0198_403_1	chr8	141851569	141851784	+	0	NA	Intergenic	Intergenic	-65363	NR_031636	100302147		NR_031636	ENSG00000221768	MIR1302-7	MIRN1302-7|hsa-mir-1302-7	microRNA 1302-7	ncRNA	0.037209	0.388889	
chunk0078_225_1	chr17	6512142	6513078	+	0	NA	intron (NM_001165966, intron 2 of 18)	MER5A|DNA|hAT-Charlie	43947	NM_031220	83394	Hs.183983	NM_031220	ENSG00000091622	PITPNM3	ACKR6|CORD5|NIR1|RDGBA3	PITPNM family member 3	protein-coding	0.007479	0.401281	
chunk0021_219_1	chr10	6191925	6192479	+	0	NA	intron (NM_001282630, intron 1 of 14)	intron (NM_001282630, intron 1 of 14)	-10675	NM_001314063	5209	Hs.195471	NM_004566	ENSG00000170525	PFKFB3	IPFK2|PFK2|iPFK-2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	protein-coding	0.012635	0.441441	
chunk0051_399_1	chr12	122023438	122023701	+	0	NA	intron (NM_001024808, intron 1 of 5)	intron (NM_001024808, intron 1 of 5)	1683	NM_020993	605	Hs.530970	NM_020993	ENSG00000110987	BCL7A	BCL7	BAF chromatin remodeling complex subunit BCL7A	protein-coding	0.049430	0.568182	
chunk0077_452_1	chr16	85891481	85891978	+	0	NA	Intergenic	Intergenic	-7439	NM_002163	3394	Hs.137427	NM_002163	ENSG00000140968	IRF8	H-ICSBP|ICSBP|ICSBP1|IMD32A|IMD32B|IRF-8	interferon regulatory factor 8	protein-coding	0.006036	0.483936	
chunk0161_405_1	chr5	177382533	177382916	+	0	NA	Intergenic	L2|LINE|L2	-1707	NM_003052	6569	Hs.936	NM_003052	ENSG00000131183	SLC34A1	FRTS2|HCINF2|NAPI-3|NPHLOP1|NPT2|NPTIIa|SLC11|SLC17A2	solute carrier family 34 member 1	protein-coding	0.026110	0.575521	203(AAGCACAGTGCGTGCT,-,0.00),204(AGCACAGTGCGTGCTT,+,0.00)
chunk0062_378_1	chr14	74350742	74351069	+	0	NA	intron (NM_018228, intron 1 of 1)	intron (NM_018228, intron 1 of 1)	2442	NM_018228	55237	Hs.578167	NM_018228	ENSG00000133980	VRTN	C14orf115|vertnin	vertebrae development associated	protein-coding	0.009174	0.384146	143(GGGAACATCATGCTCT,-,0.00),144(GGAACATCATGCTCTC,+,0.00)
chunk0163_274_1	chr6	13434815	13435443	+	0	NA	intron (NM_018988, intron 1 of 1)	intron (NM_018988, intron 1 of 1)	-26992	NM_001242630	54438	Hs.484686	NM_018988	ENSG00000145990	GFOD1	ADG-90|C6orf114	glucose-fructose oxidoreductase domain containing 1	protein-coding	0.012739	0.462639	227(AAGCACATTCTGTGCT,-,0.00),228(AGCACATTCTGTGCTA,+,0.00),483(TTGCACATGCTGTACC,-,0.00),484(TGCACATGCTGTACCC,+,0.00)
chunk0127_436_1	chr3	103138862	103139525	+	0	NA	Intergenic	Intergenic	384923	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.004525	0.344880	
chunk0199_281_1	chr9	6502225	6502943	+	0	NA	intron (NM_152896, intron 14 of 15)	intron (NM_152896, intron 14 of 15)	89433	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.006964	0.379694	
chunk0182_131_1	chr7	94507480	94507967	+	0	NA	Intergenic	L2|LINE|L2	-2135	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.002053	0.405738	
chunk0164_263_1	chr6	23646658	23646925	+	0	NA	Intergenic	L2b|LINE|L2	-479395	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.003745	0.354478	
chunk0170_378_1	chr6	116936665	116937271	+	0	NA	Intergenic	Intergenic	59755	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.004950	0.322900	240(CAGGACATTTTGTTCT,-,0.00),241(AGGACATTTTGTTCTT,+,0.00),523(AAGGTCTCTGTGTTCT,-,0.00),524(AGGTCTCTGTGTTCTT,+,0.00)
chunk0056_131_1	chr13	83201300	83201964	+	0	NA	Intergenic	Intergenic	680761	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.004518	0.362406	
chunk0124_170_1	chr3	55328985	55329612	+	0	NA	Intergenic	Intergenic	152100	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.004785	0.455414	
chunk0042_29_1	chr12	1439141	1439754	+	0	NA	intron (NR_027946, intron 17 of 18)	intron (NR_027946, intron 17 of 18)	-61044	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.006525	0.369707	
chunk0202_239_1	chr9	76634374	76634777	+	0	NA	intron (NM_001308050, intron 7 of 10)	MER57C2|LTR|ERV1	57840	NM_001308051	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.000000	0.381188	
chunk0126_64_1	chr3	74408890	74409617	+	0	NA	intron (NM_020872, intron 4 of 21)	MER57D|LTR|ERV1	111887	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.001376	0.361264	
chunk0061_18_1	chr14	55731449	55731804	+	0	NA	Intergenic	Intergenic	-34619	NR_004844	645683	Hs.663461	NR_004844	ENSG00000177350	RPL13AP3	RPL13A_11_1370	ribosomal protein L13a pseudogene 3	pseudo	0.011268	0.415730	118(CAAAACATTATGTACC,-,0.00)
chunk0015_373_1	chr1	190485868	190486297	+	0	NA	Intergenic	Intergenic	7531	NR_110717	101929120	Hs.602301	NR_110716		LINC01351	-	long intergenic non-protein coding RNA 1351	ncRNA	0.002331	0.288372	
chunk0040_144_1	chr11	113339653	113340538	+	0	NA	intron (NM_017868, intron 10 of 21)	intron (NM_017868, intron 10 of 21)	25566	NM_017868	54970	Hs.288772	NM_017868	ENSG00000149292	TTC12	TPARM	tetratricopeptide repeat domain 12	protein-coding	0.011299	0.450339	447(AGGGCCATACTGTTCT,-,0.00),448(GGGCCATACTGTTCTC,+,0.00)
chunk0126_455_1	chr3	87348848	87349631	+	0	NA	Intergenic	L2c|LINE|L2	-72652	NM_001122757	5449	Hs.591654	NM_000306	ENSG00000064835	POU1F1	CPHD1|GHF-1|PIT1|POU1F1a|Pit-1	POU class 1 homeobox 1	protein-coding	0.008940	0.360969	
chunk0046_348_1	chr12	62966022	62966323	+	0	NA	Intergenic	Intergenic	-31287	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.006645	0.281457	
chunk0177_1_1	chr7	20175704	20175988	+	0	NA	intron (NM_182762, intron 1 of 6)	intron (NM_182762, intron 1 of 6)	33930	NR_046756	100874041	Hs.145104	NR_046756	ENSG00000228598	MACC1-AS1	-	MACC1 antisense RNA 1	ncRNA	0.007042	0.357895	
chunk0120_283_1	chr3	9670190	9670554	+	0	NA	intron (NM_022485, intron 5 of 16)	intron (NM_022485, intron 5 of 16)	20939	NM_001077525	64419	Hs.475382	NM_022485	ENSG00000163719	MTMR14	C3orf29	myotubularin related protein 14	protein-coding	0.008242	0.446575	
chunk0143_102_1	chr4	108502367	108502814	+	0	NA	Intergenic	Intergenic	117867	NR_026968	285456	Hs.683863	NM_182591	ENSG00000234492	RPL34-AS1	-	RPL34 antisense RNA 1 (head to head)	ncRNA	0.004474	0.404018	
chunk0075_222_1	chr16	52845119	52845440	+	0	NA	Intergenic	L1P3|LINE|L1	-209754	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.003115	0.375776	
chunk0065_310_1	chr14	102993712	102994102	+	0	NA	intron (NM_006035, intron 5 of 36)	intron (NM_006035, intron 5 of 36)	63498	NM_006035	9578	Hs.654634	NM_006035	ENSG00000198752	CDC42BPB	MRCKB	CDC42 binding protein kinase beta	protein-coding	0.012821	0.401535	
chunk0039_410_1	chr11	107500833	107501060	+	0	NA	Intergenic	L1ME1|LINE|L1	-43100	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.004405	0.350877	
chunk0205_161_1	chr9	108603240	108603439	+	0	NA	Intergenic	Intergenic	252656	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.015075	0.535000	122(CAGAGCTGCGTGTTCT,-,0.00),123(AGAGCTGCGTGTTCTC,+,0.00)
chunk0120_125_1	chr3	4883980	4885209	+	0	NA	Intergenic	Intergenic	21907	NR_125914	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.004882	0.333333	941(TGCACAAGATGTACCT,+,0.00)
chunk0098_447_1	chr2	82274754	82274953	+	0	NA	Intergenic	Intergenic	-581950	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.005025	0.370000	
chunk0175_219_1	chr7	6196011	6196453	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	76379	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.020362	0.419865	
chunk0194_90_1	chr8	82982100	82982856	+	0	NA	Intergenic	L1MC4a|LINE|L1	-421280	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.005291	0.326288	
chunk0192_282_1	chr8	66393465	66393712	+	0	NA	Intergenic	Intergenic	35389	NR_040434	100505676	Hs.121613	NM_001242759	ENSG00000246145	RRS1-AS1	-	RRS1 antisense RNA 1 (head to head)	ncRNA	0.004049	0.459677	
chunk0051_77_1	chr12	113698158	113698406	+	0	NA	Intergenic	Intergenic	75401	NR_110025	100506465	Hs.211461	NR_110025	ENSG00000249550	LINC01234	LCAL84|onco-lncRNA-32	long intergenic non-protein coding RNA 1234	ncRNA	0.020161	0.538153	
chunk0075_340_1	chr16	55207786	55208038	+	0	NA	Intergenic	Intergenic	-116647	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.011905	0.529644	
chunk0155_321_1	chr5	96685300	96685942	+	0	NA	intron (NM_001042440, intron 2 of 29)	intron (NM_001042440, intron 2 of 29)	-17168	NM_173060	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.003115	0.334370	
chunk0189_132_1	chr8	22452908	22453202	+	0	NA	intron (NM_001243974, intron 1 of 14)	MIR|SINE|MIR	12085	NM_001243974	5533	Hs.731683	NM_005605	ENSG00000120910	PPP3CC	CALNA3|CNA3|PP2Bgamma	protein phosphatase 3 catalytic subunit gamma	protein-coding	0.006803	0.379661	
chunk0031_357_1	chr10	130063134	130063386	+	0	NA	TTS (NR_034125)	TTS (NR_034125)	-42749	NR_044994	119437	Hs.620802	NR_044994	ENSG00000233122	CTAGE7P	CTAGE7|CTAGEP|bA500G10.2|rcCTAGE5	CTAGE family member 7, pseudogene	pseudo	0.035714	0.434783	132(AAGAACATGCTGTCCA,-,0.00),133(AGAACATGCTGTCCAT,+,0.00)
chunk0024_440_1	chr10	46516715	46516914	+	0	NA	Intergenic	L2c|LINE|L2	39257	NM_014696	9721	Hs.523375	NM_014696	ENSG00000204175	GPRIN2	GRIN2|KIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding	0.020101	0.480000	
chunk0076_444_1	chr16	73846008	73846232	+	0	NA	Intergenic	Intergenic	369401	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.004464	0.444444	
chunk0011_169_1	chr1	147680346	147680839	+	0	NA	Intergenic	LTR12C|LTR|ERV1	-10080	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.020284	0.538462	
chunk0138_74_1	chr4	34776160	34776676	+	0	NA	Intergenic	Intergenic	-736525	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.003876	0.264990	
chunk0045_252_1	chr12	49188045	49188313	+	0	NA	intron (NM_006009, intron 1 of 3)	intron (NM_006009, intron 1 of 3)	1145	NM_001270400	7846	Hs.654422	NM_006009	ENSG00000167552	TUBA1A	B-ALPHA-1|LIS3|TUBA3	tubulin alpha 1a	protein-coding	0.018657	0.449814	
chunk0101_239_1	chr2	131478903	131479520	+	0	NA	intron (NM_080386, intron 2 of 4)	intron (NM_080386, intron 2 of 4)	3204	NM_080386	113457	Hs.503749	NM_080386	ENSG00000075886	TUBA3D	H2-ALPHA|KTCN9|TUBA2	tubulin alpha 3d	protein-coding	0.014587	0.474110	160(GGGAACTGGTTGTGCT,-,0.00),161(GGAACTGGTTGTGCTG,+,0.00),304(TTGAACAGCATGTGCT,-,0.00),305(TGAACAGCATGTGCTC,+,0.00),381(CAGCACACACTGTCTC,-,0.00),382(AGCACACACTGTCTCT,+,0.00)
chunk0057_179_1	chr13	102503207	102503905	+	0	NA	Intergenic	MIRb|SINE|MIR	-93380	NM_003291	7174	Hs.432424	NM_003291	ENSG00000134900	TPP2	TPP-2|TPP-II|TPPII	tripeptidyl peptidase 2	protein-coding	0.004298	0.391989	
chunk0032_1_1	chr11	236176	236392	+	0	NA	promoter-TSS (NM_012239)	promoter-TSS (NM_012239)	78	NM_012239	23410	Hs.716456	NM_012239	ENSG00000142082	SIRT3	SIR2L3	sirtuin 3	protein-coding	0.125000	0.751152	142(CAGAACGCCATGTTCC,-,0.00),143(AGAACGCCATGTTCCG,+,0.00)
chunk0118_348_1	chr22	35949337	35949616	+	0	NA	intron (NM_001082579, intron 1 of 13)	L1MB3|LINE|L1	79061	NM_001082579	23543	Hs.282998	NM_014309	ENSG00000100320	RBFOX2	FOX2|Fox-2|HNRBP2|HRNBP2|RBM9|RTA|dJ106I20.3|fxh	RNA binding fox-1 homolog 2	protein-coding	0.007168	0.371429	
chunk0029_456_1	chr10	110567211	110567740	+	0	NA	promoter-TSS (NM_005445)	promoter-TSS (NM_005445)	-216	NM_005445	9126	Hs.24485	NM_005445	ENSG00000108055	SMC3	BAM|BMH|CDLS3|CSPG6|HCAP|SMC3L1	structural maintenance of chromosomes 3	protein-coding	0.077505	0.564151	
chunk0108_271_1	chr2	234406244	234406500	+	0	NA	Intergenic	Intergenic	90677	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.031250	0.435798	
chunk0017_76_1	chr1	205677177	205677641	+	0	NA	intron (NM_033102, intron 1 of 4)	MIRb|SINE|MIR	3093	NM_033102	85414	Hs.278695	NM_033102	ENSG00000158715	SLC45A3	IPCA-2|IPCA-6|IPCA-8|IPCA6|PCANAP2|PCANAP6|PCANAP8|PRST	solute carrier family 45 member 3	protein-coding	0.012931	0.427957	
chunk0084_98_1	chr17	75577721	75578021	+	0	NA	Intergenic	Intergenic	-10187	NM_001309242	80022	Hs.390817	NM_001080847	ENSG00000266714	MYO15B	MYO15BP	myosin XVB	protein-coding	0.013333	0.514950	
chunk0009_82_1	chr1	101073742	101074231	+	0	NA	intron (NR_109849, intron 1 of 4)	intron (NR_109849, intron 1 of 4)	48140	NR_109849	102606465	Hs.593669	NR_109849		LOC102606465	-	uncharacterized LOC102606465	ncRNA	0.004090	0.330612	
chunk0039_160_1	chr11	98964219	98964699	+	0	NA	Intergenic	Intergenic	-56517	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.008333	0.318087	
chunk0010_326_1	chr1	118196417	118196903	+	0	NA	Intergenic	L1MC3|LINE|L1	-11435	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.008230	0.383984	
chunk0187_293_1	chr7	155917293	155917638	+	0	NA	Intergenic	Intergenic	-45167	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.020290	0.497110	
chunk0169_39_1	chr6	97405970	97406585	+	0	NA	intron (NR_110757, intron 1 of 4)	MER57D|LTR|ERV1	100691	NR_110757	101927314	Hs.520283	NR_110757	ENSG00000271860	LOC101927314	-	uncharacterized LOC101927314	ncRNA	0.003252	0.363636	
chunk0144_68_1	chr4	127546477	127546702	+	0	NA	Intergenic	L2c|LINE|L2	-86343	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.004444	0.464602	
chunk0135_49_1	chr3	185643570	185643915	+	0	NA	TTS (NM_001291875)	TTS (NM_001291875)	57499	NM_021627	59343	Hs.401388	NM_021627	ENSG00000163904	SENP2	AXAM2|SMT3IP2	SUMO specific peptidase 2	protein-coding	0.011594	0.436416	
chunk0007_177_1	chr1	80403271	80403730	+	0	NA	Intergenic	Intergenic	-132255	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.006536	0.341304	
chunk0205_411_1	chr9	114907976	114908577	+	0	NA	intron (NM_001252290, intron 2 of 4)	intron (NM_001252290, intron 2 of 4)	22319	NM_001244	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.004992	0.485050	478(AAGAACAGGCTCTGCT,-,0.00),479(AGAACAGGCTCTGCTC,+,0.00)
chunk0187_4_1	chr8	425515	426250	+	0	NA	intron (NM_012173, intron 2 of 8)	intron (NM_012173, intron 2 of 8)	19074	NM_012173	26260	Hs.438454	NM_012173	ENSG00000147364	FBXO25	FBX25	F-box protein 25	protein-coding	0.004082	0.384511	
chunk0074_273_1	chr16	28203432	28204090	+	0	NA	intron (NM_015171, intron 1 of 23)	intron (NM_015171, intron 1 of 23)	8157	NM_015171	23214	Hs.460468	NM_015171	ENSG00000169180	XPO6	EXP6|RANBP20	exportin 6	protein-coding	0.006079	0.440061	372(AAGAACAGGCAGGCCC,-,0.00)
chunk0060_368_1	chr14	52423446	52423867	+	0	NA	Intergenic	L1MEg|LINE|L1	109358	NM_000956	5732	Hs.2090	NM_000956	ENSG00000125384	PTGER2	EP2	prostaglandin E receptor 2	protein-coding	0.000000	0.348341	5(ATGGACAGGAAGTGCT,-,0.00),6(TGGACAGGAAGTGCTT,+,0.00),204(GAGAACATGTTGTGCA,-,0.00),205(AGAACATGTTGTGCAT,+,0.00)
chunk0066_164_1	chr15	32659567	32659869	+	0	NA	intron (NM_001144757, intron 2 of 5)	intron (NM_001144757, intron 2 of 5)	18049	NM_001144757	6447	Hs.156540	NM_003020	ENSG00000166922	SCG5	7B2|P7B2|SGNE1|SgV	secretogranin V	protein-coding	0.009934	0.534653	
chunk0007_166_1	chr1	80083840	80084308	+	0	NA	Intergenic	Intergenic	-451681	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.002137	0.362473	
chunk0165_351_1	chr6	38063033	38063462	+	0	NA	intron (NM_021943, intron 3 of 5)	intron (NM_021943, intron 3 of 5)	243716	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.004662	0.362791	
chunk0188_326_1	chr8	17537482	17538018	+	0	NA	intron (NM_001008539, intron 1 of 11)	intron (NM_001008539, intron 1 of 11)	-1027	NM_001164771	6542	Hs.448520	NM_003046	ENSG00000003989	SLC7A2	ATRC2|CAT2|HCAT2	solute carrier family 7 member 2	protein-coding	0.009328	0.495345	217(GGGAACAGGTTGTACC,-,0.00),218(GGAACAGGTTGTACCC,+,0.00),329(GGGAACGCAGTGTGCT,-,0.00),330(GGAACGCAGTGTGCTG,+,0.00)
chunk0026_298_1	chr10	67901622	67901935	+	0	NA	intron (NM_012238, intron 4 of 8)	MER58C|DNA|hAT-Charlie	10376	NM_001314049	23411	Hs.369779	NM_012238	ENSG00000096717	SIRT1	SIR2|SIR2L1|SIR2alpha	sirtuin 1	protein-coding	0.009585	0.340764	
chunk0111_422_1	chr20	34861690	34862187	+	0	NA	intron (NM_178026, intron 3 of 14)	intron (NM_178026, intron 3 of 14)	10920	NM_178026	2686	Hs.433738	NM_178026	ENSG00000131067	GGT7	D20S101|GGT4|GGTL3|GGTL5	gamma-glutamyltransferase 7	protein-coding	0.006036	0.510040	148(CAGAACAGGATGTTCT,-,0.00),149(AGAACAGGATGTTCTG,+,0.00)
chunk0056_318_1	chr13	91077166	91077836	+	0	NA	Intergenic	MIRb|SINE|MIR	12116	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.007463	0.348733	
chunk0128_280_1	chr3	110865534	110866533	+	0	NA	Intergenic	Intergenic	203926	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.008008	0.414000	
chunk0156_202_1	chr5	107977412	107978066	+	0	NA	intron (NM_001163315, intron 7 of 8)	Charlie4z|DNA|hAT-Charlie	-306844	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.006116	0.415267	
chunk0123_357_1	chr3	48215841	48216149	+	0	NA	Intergenic	Intergenic	-7352	NM_004345	820	Hs.51120	NM_004345	ENSG00000164047	CAMP	CAP-18|CAP18|CRAMP|FALL-39|FALL39|HSD26|LL37	cathelicidin antimicrobial peptide	protein-coding	0.019481	0.514563	
chunk0082_202_1	chr17	56853205	56853596	+	0	NA	intron (NM_003647, intron 7 of 11)	L1MA7|LINE|L1	19301	NM_003647	8526	Hs.239514	NM_003647	ENSG00000153933	DGKE	AHUS7|DAGK5|DAGK6|DGK|NPHS7	diacylglycerol kinase epsilon	protein-coding	0.000000	0.341837	
chunk0179_432_1	chr7	52150299	52150712	+	0	NA	Intergenic	Intergenic	-833687	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.004843	0.379227	
chunk0080_348_1	chr17	32831426	32832025	+	0	NA	intron (NM_015194, intron 1 of 21)	intron (NM_015194, intron 1 of 21)	45448	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.000000	0.361667	
chunk0172_368_1	chr6	139265465	139266091	+	0	NA	intron (NM_153235, intron 4 of 9)	L1MEf|LINE|L1	26293	NM_153235	167838	Hs.535820	NM_153235	ENSG00000164440	TXLNB	C6orf198|LST001|MDP77|dJ522B19.2	taxilin beta	protein-coding	0.004792	0.381180	
chunk0002_93_1	chr1	14738043	14738769	+	0	NA	intron (NM_015209, intron 1 of 7)	intron (NM_015209, intron 1 of 7)	139689	NM_015209	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.016529	0.482806	
chunk0086_144_1	chr18	21300189	21300551	+	0	NA	intron (NM_001142966, intron 1 of 32)	intron (NM_001142966, intron 1 of 32)	58128	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.005525	0.369146	
chunk0079_99_1	chr17	12100052	12100420	+	0	NA	intron (NM_001281435, intron 5 of 11)	L1ME1|LINE|L1	18337	NR_030613	100126313		NR_030613	ENSG00000266297	MIR744	MIRN744|hsa-mir-744|mir-744	microRNA 744	ncRNA	0.010870	0.341463	
chunk0182_318_1	chr7	98968442	98968841	+	0	NA	intron (NM_003496, intron 49 of 70)	intron (NM_003496, intron 49 of 70)	-44524	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.025063	0.500000	
chunk0011_419_1	chr1	154435908	154436128	+	0	NA	exon (NM_000565, exon 6 of 10)	exon (NM_000565, exon 6 of 10)	30825	NM_000565	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.059091	0.665158	
chunk0149_278_1	chr5	24823631	24823987	+	0	NA	Intergenic	L1PA16|LINE|L1	16774	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.002809	0.509804	184(CAGTGCACAGTGTTCT,-,0.00),185(AGTGCACAGTGTTCTG,+,0.00)
chunk0015_81_1	chr1	184836647	184837361	+	0	NA	intron (NM_052966, intron 5 of 13)	intron (NM_052966, intron 5 of 13)	-82097	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.005602	0.362238	
chunk0183_19_1	chr7	103307469	103308244	+	0	NA	intron (NM_004279, intron 7 of 12)	intron (NM_004279, intron 7 of 12)	10430	NM_004279	9512	Hs.184211	NM_004279	ENSG00000105819	PMPCB	Beta-MPP|MPP11|MPPB|MPPP52|P-52	peptidase, mitochondrial processing beta subunit	protein-coding	0.003871	0.365979	
chunk0014_240_1	chr1	179954355	179954583	+	0	NA	promoter-TSS (NM_014810)	promoter-TSS (NM_014810)	-304	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.043860	0.515284	
chunk0162_180_1	chr6	3731246	3731445	+	0	NA	intron (NM_183373, intron 3 of 4)	intron (NM_183373, intron 3 of 4)	20667	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.010050	0.360000	
chunk0033_222_1	chr11	17329506	17330054	+	0	NA	intron (NM_005013, intron 11 of 13)	L1MA2|LINE|L1	-2262	NR_132751	4925	Hs.654599	NM_005013	ENSG00000070081	NUCB2	HEL-S-109|NEFA	nucleobindin 2	protein-coding	0.007299	0.446266	234(AGGTACTGTGAGTGCT,-,0.00)
chunk0141_290_1	chr4	86837669	86838627	+	0	NA	intron (NM_197965, intron 1 of 5)	L1MC5a|LINE|L1	11115	NM_197965	345274	Hs.452996	NM_197965	ENSG00000145283	SLC10A6	SOAT	solute carrier family 10 member 6	protein-coding	0.007307	0.398332	
chunk0059_268_1	chr14	35331531	35331889	+	0	NA	Intergenic	Intergenic	39393	NM_001282232	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.016760	0.537604	
chunk0022_34_1	chr10	7973241	7973949	+	0	NA	intron (NM_031923, intron 3 of 6)	MIRb|SINE|MIR	78896	NR_104329	399717	Hs.158992	NM_207423	ENSG00000197308	GATA3-AS1	-	GATA3 antisense RNA 1	ncRNA	0.008475	0.352609	
chunk0133_219_1	chr3	171145757	171146061	+	0	NA	intron (NM_001161560, intron 12 of 31)	L4_A_Mam|LINE|RTE-X	-39150	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.003289	0.360656	
chunk0176_53_1	chr7	11130739	11131496	+	0	NA	intron (NR_033436, intron 16 of 16)	L1MC2|LINE|L1	157245	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.005284	0.374670	
chunk0120_31_1	chr3	2513476	2514035	+	0	NA	intron (NM_001206955, intron 2 of 23)	intron (NM_001206955, intron 2 of 23)	274926	NM_001206955	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.010733	0.344643	271(GGGACACTGTCTTCCT,+,0.00)
chunk0136_149_1	chr4	4643634	4644318	+	0	NA	intron (NR_037888, intron 2 of 5)	LTR10C|LTR|ERV1	101845	NR_037888	100507266	Hs.276795	NR_037888	ENSG00000247708	STX18-AS1	-	STX18 antisense RNA 1 (head to head)	ncRNA	0.011696	0.404380	431(AAGAACATAAAGTACA,-,0.00),432(AGAACATAAAGTACAT,+,0.00)
chunk0060_431_1	chr14	54332455	54332834	+	0	NA	Intergenic	Intergenic	-64311	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.013193	0.421053	247(CAGCACATCTTGTCCT,-,0.00),248(AGCACATCTTGTCCTC,+,0.00)
chunk0150_29_1	chr5	30907108	30907781	+	0	NA	Intergenic	Tigger9a|DNA|TcMar-Tigger	-286211	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.001486	0.391691	
chunk0157_449_1	chr5	124953619	124954141	+	0	NA	Intergenic	L1MC5|LINE|L1	-82951	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.003831	0.336520	255(ATGTACACTATGTACC,-,0.00),256(TGTACACTATGTACCA,+,0.00)
chunk0198_416_1	chr8	142684647	142685216	+	0	NA	Intergenic	Intergenic	4475	NM_005672	8000	Hs.652235	NM_005672	ENSG00000167653	PSCA	PRO232	prostate stem cell antigen	protein-coding	0.014060	0.514035	
chunk0014_322_1	chr1	181421845	181422044	+	0	NA	Intergenic	L2a|LINE|L2	-61606	NM_000721	777	Hs.437444	NM_000721	ENSG00000198216	CACNA1E	BII|CACH6|CACNL1A6|Cav2.3|EIEE69|gm139	calcium voltage-gated channel subunit alpha1 E	protein-coding	0.010050	0.450000	
chunk0185_370_1	chr7	132939418	132940026	+	0	NA	intron (NM_017812, intron 4 of 7)	intron (NM_017812, intron 4 of 7)	95193	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.011513	0.371100	
chunk0190_400_1	chr8	40243059	40243796	+	0	NA	Intergenic	L1PB1|LINE|L1	89959	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.001357	0.344173	
chunk0049_7_1	chr12	89212368	89212708	+	0	NA	Intergenic	Intergenic	140321	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.008824	0.425220	127(TAGAACAGGATGTCCT,-,0.00),128(AGAACAGGATGTCCTC,+,0.00)
chunk0195_108_1	chr8	94679373	94679574	+	0	NA	intron (NM_001122825, intron 13 of 13)	intron (NM_001122825, intron 13 of 13)	38337	NM_001122826	54845	Hs.487471	NM_017697	ENSG00000104413	ESRP1	DFNB109|RBM35A|RMB35A	epithelial splicing regulatory protein 1	protein-coding	0.000000	0.460396	
chunk0033_340_1	chr11	22794499	22794698	+	0	NA	intron (NM_177553, intron 7 of 7)	HAL1|LINE|L1	35238	NM_148893	258010	Hs.349096	NM_148893	ENSG00000198168	SVIP	-	small VCP interacting protein	protein-coding	0.000000	0.340000	
chunk0212_422_1	chrX	152953207	152953422	+	0	NA	intron (NM_001178109, intron 15 of 21)	intron (NM_001178109, intron 15 of 21)	11643	NM_001178115	7739	Hs.16622	NM_007150	ENSG00000147394	ZNF185	SCELL	zinc finger protein 185 with LIM domain	protein-coding	0.009302	0.416667	
chunk0024_388_1	chr10	44864843	44865114	+	0	NA	intron (NR_033842, intron 2 of 7)	CpG	-46338	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.084871	0.625000	
chunk0147_169_1	chr4	176244817	176245324	+	0	NA	intron (NM_080874, intron 1 of 6)	intron (NM_080874, intron 1 of 6)	24152	NM_080874	140458	Hs.591712	NM_080874	ENSG00000164122	ASB5	ASB-5	ankyrin repeat and SOCS box containing 5	protein-coding	0.003945	0.421260	
chunk0089_201_1	chr18	60027509	60027751	+	0	NA	Intergenic	Intergenic	127670	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.004132	0.415638	
chunk0172_431_1	chr6	140766592	140766960	+	0	NA	Intergenic	Intergenic	82962	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.000000	0.352304	
chunk0210_449_1	chrX	106160771	106161240	+	0	NA	Intergenic	Intergenic	-7300	NM_152423	139221	Hs.592221	NM_152423	ENSG00000157502	PWWP3B	MUM1L1	PWWP domain containing 3B	protein-coding	0.002132	0.342553	185(AAAGACATAATGTCCT,-,0.00),186(AAGACATAATGTCCTT,+,0.00)
chunk0114_319_1	chr21	17372016	17372620	+	0	NA	Intergenic	Intergenic	-66572	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.003311	0.302479	
chunk0024_254_1	chr10	38911589	38912946	+	0	NA	Intergenic	(GAGTG)n|Simple_repeat|Simple_repeat	215671	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.013265	0.457290	
chunk0171_146_1	chr6	123697632	123697837	+	0	NA	Intergenic	Intergenic	-60641	NM_001251987	10345	Hs.144744	NM_006073	ENSG00000186439	TRDN	CPVT5|TDN|TRISK	triadin	protein-coding	0.004878	0.349515	
chunk0069_371_1	chr15	67254423	67254985	+	0	NA	promoter-TSS (NM_001271886)	promoter-TSS (NM_001271886)	32	NM_024666	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.087189	0.680284	
chunk0194_24_1	chr8	81643731	81644363	+	0	NA	Intergenic	Intergenic	42307	NM_005536	3612	Hs.656694	NM_005536	ENSG00000133731	IMPA1	IMP|IMPA|MRT59	inositol monophosphatase 1	protein-coding	0.006329	0.366509	
chunk0002_255_1	chr1	21276316	21276781	+	0	NA	intron (NM_001113348, intron 3 of 18)	intron (NM_001113348, intron 3 of 18)	3142	NM_001113347	1889	Hs.195080	NM_001397	ENSG00000117298	ECE1	ECE	endothelin converting enzyme 1	protein-coding	0.021505	0.448498	
chunk0110_185_1	chr20	14597685	14597937	+	0	NA	intron (NR_104193, intron 1 of 4)	intron (NR_104193, intron 1 of 4)	43427	NR_104193	140848	Hs.570367	NR_104193	ENSG00000227927	MACROD2-IT1	C20orf68|NCRNA00227|bA467D7.4	MACROD2 intronic transcript 1	ncRNA	0.000000	0.252964	
chunk0076_250_1	chr16	69252117	69252816	+	0	NA	intron (NM_006750, intron 2 of 6)	intron (NM_006750, intron 2 of 6)	-58918	NM_013245	27183	Hs.128420	NM_013245	ENSG00000132612	VPS4A	SKD1|SKD1A|SKD2|VPS4|VPS4-1	vacuolar protein sorting 4 homolog A	protein-coding	0.007153	0.365714	328(AAGAACAAGGTGTTCT,-,0.00),329(AGAACAAGGTGTTCTT,+,0.00)
chunk0024_409_1	chr10	45357038	45357376	+	0	NA	Intergenic	L1M4b|LINE|L1	-16969	NM_001256153	240	Hs.89499	NM_000698	ENSG00000012779	ALOX5	5-LO|5-LOX|5LPG|LOG5	arachidonate 5-lipoxygenase	protein-coding	0.000000	0.300885	
chunk0075_309_1	chr16	54426047	54426419	+	0	NA	Intergenic	Intergenic	-139767	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.016129	0.522788	
chunk0028_134_1	chr10	86171619	86171986	+	0	NA	intron (NM_017551, intron 3 of 15)	intron (NM_017551, intron 3 of 15)	92986	NR_029907	442911		NR_029907	ENSG00000199104	MIR346	MIRN346|hsa-mir-346|miR-346|miRNA346	microRNA 346	ncRNA	0.019074	0.385870	232(AGGAACACGCTCTTCC,-,0.00),233(GGAACACGCTCTTCCC,+,0.00)
chunk0110_223_1	chr20	15523758	15524286	+	0	NA	intron (NM_001033087, intron 4 of 13)	intron (NM_001033087, intron 4 of 13)	327164	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.011364	0.455577	
chunk0212_282_1	chrX	140459563	140460032	+	0	NA	Intergenic	Intergenic	45263	NM_005634	6658	Hs.157429	NM_005634	ENSG00000134595	SOX3	GHDX|MRGH|PHP|PHPX|SOXB	SRY-box transcription factor 3	protein-coding	0.004264	0.472340	
chunk0087_396_1	chr18	41863911	41864779	+	0	NA	Intergenic	Intergenic	-90853	NM_001308020	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.006912	0.417722	
chunk0184_317_1	chr7	120243878	120244077	+	0	NA	Intergenic	MIR3|SINE|MIR	-29691	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.320000	
chunk0165_200_1	chr6	34601164	34601419	+	0	NA	intron (NM_022758, intron 3 of 3)	intron (NM_022758, intron 3 of 3)	-44958	NM_012391	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.011765	0.375000	
chunk0046_342_1	chr12	62919871	62920348	+	0	NA	intron (NM_020700, intron 1 of 9)	intron (NM_020700, intron 1 of 9)	14776	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.004193	0.414226	
chunk0174_376_1	chr6	164925743	164926132	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-103874	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.007712	0.435897	
chunk0174_367_1	chr6	164738152	164738575	+	0	NA	Intergenic	Intergenic	83700	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.014184	0.370283	
chunk0075_228_1	chr16	52897893	52898765	+	0	NA	Intergenic	L1M7|LINE|L1	-156704	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.003440	0.426117	
chunk0008_29_1	chr1	87983177	87983516	+	0	NA	Intergenic	Intergenic	-611691	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.014749	0.361765	
chunk0045_258_1	chr12	49451541	49451953	+	0	NA	intron (NM_001293285, intron 3 of 14)	L1M4a2|LINE|L1	62573	NR_033267	100335030	Hs.687044	NR_033267		LOC100335030	-	FGFR1 oncogene partner 2 pseudogene	pseudo	0.007282	0.382567	
chunk0088_223_1	chr18	48280166	48280404	+	0	NA	Intergenic	Intergenic	-142976	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.012605	0.539749	
chunk0010_40_1	chr1	112700169	112700625	+	0	NA	TTS (NM_001042678)	TTS (NM_001042678)	6659	NM_001042679	389	Hs.502659	NM_175744	ENSG00000155366	RHOC	ARH9|ARHC|H9|RHOH9	ras homolog family member C	protein-coding	0.010965	0.584245	217(GAAGACACAGTGTACT,-,0.00),218(AAGACACAGTGTACTT,+,0.00)
chunk0140_261_1	chr4	71567040	71567263	+	0	NA	intron (NM_001098484, intron 25 of 25)	intron (NM_001098484, intron 25 of 25)	217211	NM_000583	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.008969	0.370536	122(CAGAACTTCTTGTTCT,-,0.00),123(AGAACTTCTTGTTCTC,+,0.00)
chunk0063_150_1	chr14	79947639	79947838	+	0	NA	Intergenic	Intergenic	-263681	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.000000	0.400000	
chunk0095_231_1	chr2	18991934	18992178	+	0	NA	Intergenic	Intergenic	-356373	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.000000	0.473469	
chunk0037_362_1	chr11	78098813	78099426	+	0	NA	Intergenic	Intergenic	-18900	NM_001204054	4718	Hs.407860	NM_004549	ENSG00000151366	NDUFC2	B14.5b|CI-B14.5b|HLC-1|NADHDH2	NADH:ubiquinone oxidoreductase subunit C2	protein-coding	0.003263	0.412052	
chunk0091_327_1	chr19	13765521	13765956	+	0	NA	intron (NM_032285, intron 2 of 5)	L2a|LINE|L2	1215	NM_001031727	84245	Hs.439370	NM_032285	ENSG00000037757	MRI1	M1Pi|MRDI|MTNA|Ypr118w	methylthioribose-1-phosphate isomerase 1	protein-coding	0.029885	0.559633	
chunk0109_14_1	chr20	349235	349625	+	0	NA	intron (NM_024958, intron 2 of 3)	MIRb|SINE|MIR	2704	NM_024958	80023	Hs.416024	NM_024958	ENSG00000125841	NRSN2	C20orf98|dJ1103G7.6	neurensin 2	protein-coding	0.017949	0.547315	257(AAGGCCAGACTGTGCT,-,0.00),258(AGGCCAGACTGTGCTA,+,0.00)
chunk0189_138_1	chr8	22684134	22684431	+	0	NA	Intergenic	Intergenic	8107	NM_001199880	1960	Hs.534313	NM_004430	ENSG00000179388	EGR3	EGR-3|PILOT	early growth response 3	protein-coding	0.006734	0.496644	
chunk0053_54_1	chr13	27617587	27618271	+	0	NA	intron (NM_153371, intron 1 of 9)	MIRb|SINE|MIR	2654	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.005848	0.407299	
chunk0046_220_1	chr12	59549789	59550353	+	0	NA	Intergenic	SATR1|Satellite|Satellite	-45969	NM_001270622	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.005319	0.373451	416(ATGTACACTCTGTGCT,-,0.00),417(TGTACACTCTGTGCTA,+,0.00)
chunk0167_381_1	chr6	73885455	73885654	+	0	NA	Intergenic	Intergenic	-183897	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.005025	0.300000	
chunk0022_387_1	chr10	17644057	17644754	+	0	NA	promoter-TSS (NR_110370)	promoter-TSS (NR_110370)	280	NM_003473	8027	Hs.335391	NM_003473	ENSG00000136738	STAM	STAM-1|STAM1	signal transducing adaptor molecule	protein-coding	0.047346	0.591691	
chunk0062_372_1	chr14	74249589	74250027	+	0	NA	intron (NM_182894, intron 3 of 4)	intron (NM_182894, intron 3 of 4)	10336	NM_182894	338917	Hs.449771	NM_182894	ENSG00000119614	VSX2	CHX10|HOX10|MCOP2|MCOPCB3|RET1	visual system homeobox 2	protein-coding	0.015982	0.446469	339(GGCACACCGTCTTCTT,+,0.00)
chunk0200_4_1	chr9	14453177	14453686	+	0	NA	Intergenic	Intergenic	-54448	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.000000	0.343137	
chunk0103_36_1	chr2	159124466	159124665	+	0	NA	intron (NM_001145909, intron 4 of 26)	intron (NM_001145909, intron 4 of 26)	-62270	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.005025	0.460000	
chunk0174_80_1	chr6	156399502	156399794	+	0	NA	Intergenic	Intergenic	-378282	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.003425	0.317406	
chunk0170_234_1	chr6	113470306	113470505	+	0	NA	Intergenic	Intergenic	179670	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.000000	0.310000	
chunk0050_271_1	chr12	106195650	106196017	+	0	NA	Intergenic	Intergenic	52102	NM_006825	10970	Hs.74368	NM_006825	ENSG00000136026	CKAP4	CLIMP-63|ERGIC-63|p63	cytoskeleton associated protein 4	protein-coding	0.013624	0.494565	
chunk0107_48_1	chr2	211378534	211379123	+	0	NA	3' UTR (NM_005235, exon 28 of 28)	3' UTR (NM_005235, exon 28 of 28)	761257	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.006791	0.357627	
chunk0081_417_1	chr17	48728601	48729167	+	0	NA	promoter-TSS (NM_006361)	promoter-TSS (NM_006361)	-135	NM_006361	10481	Hs.66731	NM_006361	ENSG00000159184	HOXB13	HPC9|PSGD	homeobox B13	protein-coding	0.051237	0.573192	
chunk0121_228_1	chr3	21879121	21879502	+	0	NA	Intergenic	Intergenic	-77828	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.005249	0.350785	
chunk0083_171_1	chr17	66176956	66177410	+	0	NA	intron (NM_001302891, intron 2 of 24)	MER58A|DNA|hAT-Charlie	14686	NM_001302891	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.004405	0.369231	
chunk0116_93_1	chr21	34965574	34965773	+	0	NA	intron (NM_001754, intron 2 of 8)	intron (NM_001754, intron 2 of 8)	73753	NR_026812	80215	Hs.672131	NM_025143		RUNX1-IT1	C21orf96	RUNX1 intronic transcript 1	ncRNA	0.005025	0.475000	37(AAGAACTGCATGTCCT,-,0.00),38(AGAACTGCATGTCCTT,+,0.00)
chunk0111_282_1	chr20	31622886	31623184	+	0	NA	Intergenic	L1MEf|LINE|L1	-14853	NM_032609	84701	Hs.277101	NM_032609	ENSG00000131055	COX4I2	COX4|COX4-2|COX4B|COX4L2|COXIV-2|dJ857M17.2	cytochrome c oxidase subunit 4I2	protein-coding	0.003356	0.391304	
chunk0135_141_1	chr3	187397026	187397332	+	0	NA	Intergenic	MIRb|SINE|MIR	28799	NM_022147	64108	Hs.43388	NM_022147	ENSG00000136514	RTP4	IFRG28|Z3CXXC4	receptor transporter protein 4	protein-coding	0.006536	0.374593	
chunk0085_182_1	chr18	5868220	5868419	+	0	NA	Intergenic	Intergenic	23785	NM_001080209	645369		NM_001080209	ENSG00000206432	TMEM200C	TTMA	transmembrane protein 200C	protein-coding	0.020101	0.350000	
chunk0108_114_1	chr2	229700882	229701202	+	0	NA	intron (NM_139072, intron 1 of 12)	intron (NM_139072, intron 1 of 12)	13528	NM_139072	92737	Hs.234074	NM_139072	ENSG00000187957	DNER	UNQ26|bet	delta/notch like EGF repeat containing	protein-coding	0.012500	0.355140	
chunk0062_234_1	chr14	71162996	71163553	+	0	NA	Intergenic	LTR37B|LTR|ERV1	-235063	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.005386	0.392473	
chunk0208_76_1	chrX	12877171	12877853	+	0	NA	intron (NM_016562, intron 2 of 2)	intron (NM_016562, intron 2 of 2)	10429	NM_016562	51284	Hs.659215	NM_016562	ENSG00000196664	TLR7	TLR7-like	toll like receptor 7	protein-coding	0.011730	0.456808	
chunk0009_47_1	chr1	100485692	100486492	+	0	NA	TTS (NM_033313)	TTS (NM_033313)	-52080	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.006250	0.368290	
chunk0047_354_1	chr12	74986059	74986593	+	0	NA	Intergenic	Intergenic	223422	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.011236	0.484112	258(AGGAACATGAAGTTCT,-,0.00),259(GGAACATGAAGTTCTT,+,0.00)
chunk0034_13_1	chr11	26018039	26018766	+	0	NA	Intergenic	Intergenic	-170721	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.001376	0.353022	
chunk0038_25_1	chr11	81141548	81142306	+	0	NA	Intergenic	Intergenic	-379124	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.002639	0.266140	
chunk0047_428_1	chr12	76261386	76261725	+	0	NA	Intergenic	Intergenic	86887	NM_024685	79738	Hs.96322	NM_024685	ENSG00000179941	BBS10	C12orf58	Bardet-Biedl syndrome 10	protein-coding	0.002950	0.408824	
chunk0188_63_1	chr8	8228899	8229314	+	0	NA	intron (NR_024362, intron 1 of 7)	intron (NR_024362, intron 1 of 7)	536	NR_024363	286042	Hs.656318	NR_024361	ENSG00000173295	FAM86B3P	-	family with sequence similarity 86, member A pseudogene	pseudo	0.043373	0.572115	
chunk0141_333_1	chr4	87409197	87409922	+	0	NA	Intergenic	Intergenic	-13017	NM_001248011	53343	Hs.149500	NM_024047	ENSG00000170502	NUDT9	NUDT10	nudix hydrolase 9	protein-coding	0.005517	0.411846	322(CAGAACACTTTGTCCT,-,0.00),323(AGAACACTTTGTCCTA,+,0.00)
chunk0115_345_1	chr21	29206101	29206403	+	0	NA	intron (NR_027072, intron 1 of 1)	MamRTE1|LINE|RTE-BovB	12758	NR_027072	193629	Hs.720711	NM_138968	ENSG00000215533	LINC00189	C21orf109|NCRNA00189	long intergenic non-protein coding RNA 189	ncRNA	0.009934	0.415842	14(CAGGACACTATGGGCT,-,0.00)
chunk0020_20_1	chr1	231729370	231729781	+	0	NA	intron (NM_001012957, intron 3 of 12)	intron (NM_001012957, intron 3 of 12)	88942	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.004866	0.359223	75(AGGTTCACAGTGTGCT,-,0.00)
chunk0093_252_1	chr19	50889421	50890333	+	0	NA	intron (NR_002948, intron 3 of 4)	LTR40a|LTR|ERVL	6521	NR_002948	606293	Hs.643424	NR_002948	ENSG00000197588	KLKP1	KARMA|KLK31P|KRSP1|PsiKLK1|YKLK1	kallikrein pseudogene 1	pseudo	0.007675	0.453450	
chunk0190_449_1	chr8	42023219	42023484	+	0	NA	intron (NM_001305878, intron 2 of 13)	Tigger3b|DNA|TcMar-Tigger	28675	NM_001305878	7994	Hs.491577	NM_006766	ENSG00000083168	KAT6A	MOZ|MRD32|MYST-3|MYST3|RUNXBP2|ZC2HC6A|ZNF220	lysine acetyltransferase 6A	protein-coding	0.000000	0.308271	
chunk0210_400_1	chrX	98740164	98740643	+	0	NA	Intergenic	Intergenic	-1175868	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.004175	0.260417	
chunk0033_228_1	chr11	17410967	17411441	+	0	NA	intron (NM_001287174, intron 21 of 38)	L2c|LINE|L2	-21873	NM_001166290	3767	Hs.248141	NM_000525	ENSG00000187486	KCNJ11	BIR|HHF2|IKATP|KIR6.2|MODY13|PHHI|TNDM3	potassium voltage-gated channel subfamily J member 11	protein-coding	0.025316	0.509474	
chunk0132_324_1	chr3	161064452	161064896	+	0	NA	intron (NM_139245, intron 2 of 3)	intron (NM_139245, intron 2 of 3)	40221	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.011261	0.456180	
chunk0084_346_1	chr17	81254987	81255335	+	0	NA	intron (NM_138570, intron 11 of 13)	intron (NM_138570, intron 11 of 13)	15850	NM_001086521	284184	Hs.356545	NM_001086521	ENSG00000224877	NDUFAF8	C17orf89	NADH:ubiquinone oxidoreductase complex assembly factor 8	protein-coding	0.051724	0.638968	
chunk0192_422_1	chr8	69536100	69536494	+	0	NA	intron (NM_015170, intron 3 of 22)	intron (NM_015170, intron 3 of 22)	43504	NM_001128206	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.007614	0.359494	
chunk0048_93_1	chr12	79283985	79284604	+	0	NA	intron (NM_001291901, intron 3 of 9)	intron (NM_001291901, intron 3 of 9)	-134963	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.004847	0.333871	
chunk0119_353_1	chr22	47333657	47333856	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	153355	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.000000	0.555000	
chunk0212_354_1	chrX	148659142	148659497	+	0	NA	intron (NM_002025, intron 2 of 20)	intron (NM_002025, intron 2 of 20)	-59772	NM_001170628	2334	Hs.496911	NM_002025	ENSG00000155966	AFF2	FMR2|FMR2P|FRAXE|MRX2|OX19	AF4/FMR2 family member 2	protein-coding	0.000000	0.373596	
chunk0014_454_1	chr1	183952986	183953671	+	0	NA	intron (NM_001303420, intron 7 of 11)	intron (NM_001303420, intron 7 of 11)	84442	NM_001303420	23127	Hs.387995	NM_015101	ENSG00000198756	COLGALT2	C1orf17|ColGalT 2|GLT25D2	collagen beta(1-O)galactosyltransferase 2	protein-coding	0.010219	0.453353	
chunk0084_275_1	chr17	79698166	79698691	+	0	NA	Intergenic	Intergenic	8821	NR_039893	100616170		NR_039893	ENSG00000266665	MIR4739	mir-4739	microRNA 4739	ncRNA	0.026667	0.549430	
chunk0179_361_1	chr7	51034594	51034902	+	0	NA	intron (NM_001287436, intron 9 of 13)	intron (NM_001287436, intron 9 of 13)	-241286	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.006494	0.449838	
chunk0126_153_1	chr3	76936949	76937723	+	0	NA	Intergenic	Intergenic	-102807	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.003876	0.307097	
chunk0099_89_1	chr2	85498093	85498628	+	0	NA	Intergenic	MER57A-int|LTR|ERV1	40526	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.005607	0.326493	150(TAAAACACAGTGTTCC,-,0.00),151(AAAACACAGTGTTCCA,+,0.00)
chunk0005_137_1	chr1	57301193	57301751	+	0	NA	intron (NM_021080, intron 3 of 16)	intron (NM_021080, intron 3 of 16)	-335332	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.016129	0.461538	
chunk0014_209_1	chr1	179255759	179256062	+	0	NA	Intergenic	Intergenic	-26226	NM_007314	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.013201	0.529605	
chunk0208_290_1	chrX	21966593	21966986	+	0	NA	intron (NM_004595, intron 1 of 10)	intron (NM_004595, intron 1 of 10)	26216	NM_004595	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.015267	0.383249	
chunk0064_366_1	chr14	97888168	97888663	+	0	NA	Intergenic	Intergenic	89709	NR_015430	388011	Hs.651477	NR_015430	ENSG00000246223	LINC01550	C14orf64	long intergenic non-protein coding RNA 1550	ncRNA	0.012121	0.552419	
chunk0195_102_1	chr8	94502566	94502833	+	0	NA	intron (NM_015496, intron 16 of 23)	L1MC4a|LINE|L1	-27584	NM_001205262	25788	Hs.30561	NM_006550	ENSG00000197275	RAD54B	RDH54	RAD54 homolog B	protein-coding	0.007491	0.417910	
chunk0064_377_1	chr14	98775849	98776323	+	0	NA	Intergenic	Intergenic	64473	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.004219	0.362105	243(CTGGACATTCAGTACT,-,0.00),244(TGGACATTCAGTACTC,+,0.00)
chunk0157_400_1	chr5	124246107	124246494	+	0	NA	intron (NR_125774, intron 4 of 5)	L1PB3|LINE|L1	192220	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.010336	0.332474	
chunk0108_464_1	chr2	238597071	238597614	+	0	NA	Intergenic	Intergenic	-41843	NR_037809	151171	Hs.652076	NR_037809	ENSG00000225493	LINC01107	-	long intergenic non-protein coding RNA 1107	ncRNA	0.023941	0.505515	
chunk0055_139_1	chr13	59541115	59541695	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-471313	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.005172	0.361446	318(CTGTACAGCATGTACT,-,0.00),319(TGTACAGCATGTACTG,+,0.00)
chunk0212_428_1	chrX	153373191	153373762	+	0	NA	Intergenic	HAL1M8|LINE|L1	39321	NM_001080485	10838	Hs.348963	NM_020636	ENSG00000063587	ZNF275	-	zinc finger protein 275	protein-coding	0.005254	0.330420	
chunk0024_382_1	chr10	44696909	44697689	+	0	NA	Intergenic	Intergenic	-214017	NM_001123376	643236	Hs.292788	NM_001123376	ENSG00000187783	TMEM72	C10orf127|KSP37	transmembrane protein 72	protein-coding	0.006410	0.412292	
chunk0136_100_1	chr4	2896378	2896893	+	0	NA	intron (NM_014190, intron 6 of 15)	intron (NM_014190, intron 6 of 15)	37602	NM_001120	10227	Hs.632581	NM_001120	ENSG00000109736	MFSD10	TETRAN|TETTRAN	major facilitator superfamily domain containing 10	protein-coding	0.015534	0.430233	
chunk0014_328_1	chr1	182048628	182048902	+	0	NA	Intergenic	Intergenic	12947	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.003650	0.480000	
chunk0115_267_1	chr21	27966733	27967358	+	0	NA	Intergenic	(AATGA)n|Simple_repeat|Simple_repeat	-46318	NR_027246	246705	Hs.505079	NM_145180	ENSG00000178457	LINC00314	C21orf94|NCRNA00314	long intergenic non-protein coding RNA 314	ncRNA	0.000000	0.322684	316(GAAACTGAATGTTCTG,+,0.00)
chunk0169_104_1	chr6	100666391	100667030	+	0	NA	intron (NM_006828, intron 14 of 41)	intron (NM_006828, intron 14 of 41)	-203035	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.003130	0.314063	
chunk0125_117_1	chr3	65793693	65793892	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-100024	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.000000	0.410000	31(CAGGACAGTCTGTCCA,-,0.00),32(AGGACAGTCTGTCCAC,+,0.00)
chunk0020_386_1	chr1	240240041	240240240	+	0	NA	intron (NM_020066, intron 6 of 17)	intron (NM_020066, intron 6 of 17)	148255	NM_020066	56776	Hs.24889	NM_020066	ENSG00000155816	FMN2	-	formin 2	protein-coding	0.015075	0.445000	
chunk0149_334_1	chr5	26868124	26868745	+	0	NA	Intergenic	Intergenic	170148	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.004831	0.355305	197(AAAACATTGTGTTCAC,+,0.00)
chunk0178_10_1	chr7	29071231	29072065	+	0	NA	intron (NM_019029, intron 9 of 12)	intron (NM_019029, intron 9 of 12)	-53385	NR_120523	101928168	Hs.666750	NR_120523	ENSG00000285412	LOC101928168	-	uncharacterized LOC101928168	ncRNA	0.005995	0.421557	360(AACACAGACAGTCCTT,+,0.00)
chunk0206_169_1	chr9	122274687	122275067	+	0	NA	intron (NM_001173512, intron 2 of 5)	L1MEi|LINE|L1	4013	NM_199177	92399	Hs.368011	NM_138777	ENSG00000148187	MRRF	MRFF|MTRRF|RRF	mitochondrial ribosome recycling factor	protein-coding	0.000000	0.251969	
chunk0080_220_1	chr17	29672317	29673141	+	0	NA	intron (NM_001282129, intron 8 of 15)	AluSz6|SINE|Alu	-51306	NM_032854	84940	Hs.143046	NM_032854	ENSG00000167549	CORO6	-	coronin 6	protein-coding	0.009709	0.435152	192(CAGCACAGGATGTTAC,-,0.00)
chunk0053_120_1	chr13	29574877	29575566	+	0	NA	intron (NM_003045, intron 1 of 12)	intron (NM_003045, intron 1 of 12)	20467	NM_003045	6541	Hs.14846	NM_003045	ENSG00000139514	SLC7A1	ATRC1|CAT-1|ERR|HCAT1|REC1L	solute carrier family 7 member 1	protein-coding	0.011611	0.382609	
chunk0186_261_1	chr7	141393769	141394028	+	0	NA	intron (NM_001195278, intron 2 of 3)	intron (NM_001195278, intron 2 of 3)	-157380	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.003861	0.369231	
chunk0090_179_1	chr18	72813989	72814305	+	0	NA	intron (NM_138966, intron 4 of 10)	L1MEd|LINE|L1	39235	NR_049858	100847083		NR_049858	ENSG00000263750	MIR548AV	-	microRNA 548av	ncRNA	0.000000	0.343849	
chunk0187_330_1	chr7	156714300	156715025	+	0	NA	intron (NM_022458, intron 15 of 16)	intron (NM_022458, intron 15 of 16)	70861	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.016552	0.428375	
chunk0181_446_1	chr7	90706101	90706932	+	0	NA	intron (NM_001287135, intron 2 of 14)	L2b|LINE|L2	-2882	NM_012395	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.003610	0.429087	
chunk0047_282_1	chr12	73221012	73221879	+	0	NA	Intergenic	Intergenic	62255	NR_110130	101928137	Hs.694666	NR_110130	ENSG00000258123	LINC02444	-	long intergenic non-protein coding RNA 2444	ncRNA	0.002307	0.341014	
chunk0043_51_1	chr12	13718797	13719076	+	0	NA	intron (NM_000834, intron 3 of 12)	intron (NM_000834, intron 3 of 12)	261152	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.007168	0.464286	
chunk0193_193_1	chr8	75681658	75681936	+	0	NA	Intergenic	Intergenic	141829	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.000000	0.236559	
chunk0182_312_1	chr7	98745523	98746015	+	0	NA	Intergenic	Intergenic	124281	NM_152913	222865	Hs.270753	NM_152913	ENSG00000166448	TMEM130	-	transmembrane protein 130	protein-coding	0.018293	0.454361	
chunk0028_57_1	chr10	83234455	83234725	+	0	NA	Intergenic	Intergenic	-904839	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.007407	0.361624	
chunk0156_329_1	chr5	111563063	111563379	+	0	NA	intron (NR_040093, intron 1 of 6)	intron (NR_040093, intron 1 of 6)	-50624	NM_001308057	134429	Hs.93842	NM_139164	ENSG00000164211	STARD4	-	StAR related lipid transfer domain containing 4	protein-coding	0.003165	0.451104	
chunk0149_272_1	chr5	24529017	24529360	+	0	NA	intron (NM_006727, intron 5 of 11)	intron (NM_006727, intron 5 of 11)	115788	NM_006727	1008	Hs.92489	NM_006727	ENSG00000040731	CDH10	-	cadherin 10	protein-coding	0.002915	0.302326	
chunk0179_438_1	chr7	52259931	52260356	+	0	NA	Intergenic	Intergenic	-775513	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.011765	0.420188	
chunk0082_208_1	chr17	57016562	57016779	+	0	NA	Intergenic	HERV35I-int|LTR|ERV1	-28808	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.009217	0.481651	
chunk0183_304_1	chr7	107857055	107857652	+	0	NA	Intergenic	Intergenic	-33754	NM_001289752	1738	Hs.131711	NM_000108	ENSG00000091140	DLD	DLDD|DLDH|E3|GCSL|LAD|PHE3	dihydrolipoamide dehydrogenase	protein-coding	0.005025	0.421405	
chunk0080_342_1	chr17	32709505	32710034	+	0	NA	intron (NM_015194, intron 16 of 21)	L1M5|LINE|L1	167404	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.000000	0.271698	
chunk0161_103_1	chr5	167383452	167383920	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	98848	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.010684	0.358209	
chunk0038_83_1	chr11	83282386	83282648	+	0	NA	intron (NM_001286116, intron 1 of 8)	L2b|LINE|L2	3890	NM_001286117	60492	Hs.368866	NM_021825	ENSG00000137500	CCDC90B	MDS011|MDS025	coiled-coil domain containing 90B	protein-coding	0.003817	0.429658	
chunk0156_208_1	chr5	108101119	108101663	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	280707	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.001838	0.394495	
chunk0097_114_1	chr2	46315207	46315739	+	0	NA	intron (NM_001430, intron 1 of 15)	intron (NM_001430, intron 1 of 15)	18071	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.016917	0.555347	248(AGGTACATCAAGTTCT,-,0.00),249(GGTACATCAAGTTCTG,+,0.00)
chunk0106_327_1	chr2	205771255	205772174	+	0	NA	intron (NM_201266, intron 15 of 16)	intron (NM_201266, intron 15 of 16)	89214	NM_201264	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.006529	0.442391	
chunk0166_241_1	chr6	47242375	47242710	+	0	NA	intron (NM_014452, intron 4 of 5)	intron (NM_014452, intron 4 of 5)	67405	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.020896	0.491071	
chunk0118_220_1	chr22	32112333	32112878	+	0	NA	3' UTR (NM_001256314, exon 14 of 14)	3' UTR (NM_001256314, exon 14 of 14)	-9372	NR_040114	23782	Hs.581098	NR_040114	ENSG00000234479	AP1B1P1	ADTB1L1|dJ127L4.2	AP1B1 pseudogene 1	pseudo	0.003670	0.404762	
chunk0082_329_1	chr17	59678917	59679431	+	0	NA	intron (NM_004859, intron 17 of 31)	intron (NM_004859, intron 17 of 31)	-28328	NM_030938	81671	Hs.444569	NM_030938	ENSG00000062716	VMP1	EPG3|TANGO5|TMEM49	vacuole membrane protein 1	protein-coding	0.003891	0.337864	
chunk0074_74_1	chr16	21326380	21326842	+	0	NA	Intergenic	Intergenic	-22752	NR_045011	100652781	Hs.443656	NM_001012391		SNX29P1	RUNDC2B|RUNDC2L	sorting nexin 29 pseudogene 1	pseudo	0.004329	0.416847	
chunk0117_38_1	chr22	12118243	12118525	+	0	NA	Intergenic	Intergenic	220978	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.007092	0.494700	
chunk0006_392_1	chr1	75300033	75300366	+	0	NA	intron (NM_001130058, intron 5 of 23)	intron (NM_001130058, intron 5 of 23)	165317	NM_001256114	431707	Hs.403934	NM_001001933	ENSG00000162624	LHX8	LHX7	LIM homeobox 8	protein-coding	0.003003	0.257485	
chunk0158_426_1	chr5	135289742	135289977	+	0	NA	intron (NM_001277348, intron 3 of 5)	L1ME2|LINE|L1	-41682	NR_037895	340073	Hs.434422	NR_037895	ENSG00000249647	C5orf66-AS2	-	C5orf66 antisense RNA 2	ncRNA	0.004255	0.305085	
chunk0065_55_1	chr15	22860746	22861495	+	0	NA	intron (NM_001008892, intron 5 of 5)	HAL1|LINE|L1	22479	NM_001008892	81614	Hs.591003	NM_030922	ENSG00000140157	NIPA2	SLC57A2	NIPA magnesium transporter 2	protein-coding	0.006676	0.364000	
chunk0083_7_1	chr17	62725622	62726330	+	0	NA	intron (NM_001100875, intron 6 of 10)	intron (NM_001100875, intron 6 of 10)	80677	NM_001100875	162333	Hs.665663	NM_152598	ENSG00000173838	MARCH10	MARCH-X|RNF190	membrane associated ring-CH-type finger 10	protein-coding	0.009887	0.459803	
chunk0130_270_1	chr3	136282815	136283418	+	0	NA	intron (NM_000532, intron 5 of 14)	intron (NM_000532, intron 5 of 14)	32791	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.004975	0.451987	
chunk0203_395_1	chr9	90566402	90566683	+	0	NA	intron (NR_034157, intron 1 of 5)	intron (NR_034157, intron 1 of 5)	16204	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.003559	0.468085	
chunk0043_201_1	chr12	19320084	19320283	+	0	NA	intron (NM_001256470, intron 17 of 31)	intron (NM_001256470, intron 17 of 31)	114858	NM_001256787	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.010050	0.295000	
chunk0055_140_1	chr13	59686169	59686977	+	0	NA	intron (NM_001258366, intron 26 of 26)	intron (NM_001258366, intron 26 of 26)	-326145	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.008663	0.364648	
chunk0175_121_1	chr7	3350567	3350986	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	49328	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.004773	0.383333	
chunk0060_401_1	chr14	53010039	53010632	+	0	NA	Intergenic	L1ME4b|LINE|L1	-59238	NM_001135000	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.011804	0.355219	
chunk0210_3_1	chrX	66745015	66745716	+	0	NA	Intergenic	L1PB1|LINE|L1	-106067	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.007133	0.376068	
chunk0212_9_1	chrY	7210829	7211231	+	0	NA	Intergenic	Intergenic	-62942	NR_028062	5616	Hs.584730	NM_002760	ENSG00000099725	PRKY	PRKXP3|PRKYP	protein kinase Y-linked (pseudogene)	pseudo	0.007463	0.454094	
chunk0040_168_1	chr11	113905980	113906330	+	0	NA	intron (NM_006028, intron 1 of 8)	intron (NM_006028, intron 1 of 8)	1359	NM_006028	9177	Hs.241377	NM_006028	ENSG00000149305	HTR3B	5-HT3B	5-hydroxytryptamine receptor 3B	protein-coding	0.011429	0.333333	
chunk0190_430_1	chr8	41588461	41588660	+	0	NA	intron (NM_178819, intron 1 of 12)	(TTCTT)n|Simple_repeat|Simple_repeat	-10192	NR_125824	102723729	Hs.586384	NR_125824		LOC102723729	-	uncharacterized LOC102723729	ncRNA	0.010050	0.350000	
chunk0149_19_1	chr5	15993460	15993899	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	58497	NR_030616	100126347		NR_030616	ENSG00000216077	MIR887	MIRN887|hsa-mir-887	microRNA 887	ncRNA	0.004556	0.372727	
chunk0127_413_1	chr3	102576170	102576402	+	0	NA	Intergenic	Intergenic	141271	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.369099	
chunk0089_231_1	chr18	61784770	61785066	+	0	NA	Intergenic	Intergenic	36742	NR_103449	100996669	Hs.586981	NR_103449		LINC01544	-	long intergenic non-protein coding RNA 1544	ncRNA	0.013514	0.457912	186(TTGAACACACTGTGCA,-,0.00),187(TGAACACACTGTGCAC,+,0.00)
chunk0019_37_1	chr1	224012513	224012913	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	-20069	NR_132119	441124	Hs.520589	NR_132119		GTF2IP20	-	general transcription factor IIi pseudogene 20	pseudo	0.057500	0.453865	
chunk0112_156_1	chr20	39176730	39177008	+	0	NA	Intergenic	MER96|DNA|hAT-Tip100	47879	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.003597	0.519713	
chunk0132_379_1	chr3	163171190	163171866	+	0	NA	Intergenic	L1P2|LINE|L1	131773	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.007396	0.357459	
chunk0157_3_1	chr5	115144953	115145470	+	0	NA	intron (NM_001300759, intron 3 of 9)	intron (NM_001300759, intron 3 of 9)	24752	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.005803	0.305019	
chunk0113_325_1	chr20	58424581	58424929	+	0	NA	intron (NM_001195677, intron 2 of 2)	intron (NM_001195677, intron 2 of 2)	35636	NM_001195677	9217	Hs.182625	NM_004738	ENSG00000124164	VAPB	ALS8|VAMP-B|VAP-B	VAMP associated protein B and C	protein-coding	0.002874	0.329513	
chunk0131_126_1	chr3	144291183	144291534	+	0	NA	Intergenic	L1PA11|LINE|L1	318033	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.011396	0.360795	
chunk0087_210_1	chr18	36021239	36021511	+	0	NA	intron (NM_018170, intron 6 of 6)	Tigger1|DNA|TcMar-Tigger	46219	NM_001303411	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.003676	0.417582	
chunk0117_206_1	chr22	21853308	21853808	+	0	NA	intron (NM_138957, intron 1 of 7)	L1MD|LINE|L1	14122	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.010000	0.393214	
chunk0004_282_1	chr1	48469645	48470159	+	0	NA	intron (NM_019073, intron 1 of 12)	intron (NM_019073, intron 1 of 12)	2306	NM_001286238	54558	Hs.538103	NM_019073	ENSG00000132122	SPATA6	HASH|SRF-1|SRF1	spermatogenesis associated 6	protein-coding	0.013619	0.349515	
chunk0132_79_1	chr3	155239817	155240075	+	0	NA	promoter-TSS (NR_125399)	promoter-TSS (NR_125399)	-999	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.011628	0.583012	
chunk0173_69_1	chr6	142571381	142571605	+	0	NA	intron (NR_027312, intron 1 of 2)	intron (NR_027312, intron 1 of 2)	66343	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.004464	0.271111	
chunk0076_331_1	chr16	70801274	70801592	+	0	NA	promoter-TSS (NM_018052)	promoter-TSS (NM_018052)	-275	NM_018052	55697	Hs.445061	NM_018052	ENSG00000103043	VAC14	ArPIKfyve|TAX1BP2|TRX	VAC14 component of PIKFYVE complex	protein-coding	0.037736	0.438871	
chunk0156_374_1	chr5	112820282	112820865	+	0	NA	intron (NM_001127511, intron 8 of 13)	intron (NM_001127511, intron 8 of 13)	-40615	NM_001204196	6728	Hs.637001	NM_003135	ENSG00000153037	SRP19	-	signal recognition particle 19	protein-coding	0.005146	0.352740	
chunk0183_278_1	chr7	107595184	107595720	+	0	NA	intron (NM_001008405, intron 3 of 7)	intron (NM_001008405, intron 3 of 7)	14693	NM_001008405	55973	Hs.303787	NM_018844	ENSG00000075790	BCAP29	BAP29	B cell receptor associated protein 29	protein-coding	0.007463	0.391061	
chunk0021_121_1	chr10	3702660	3702859	+	0	NA	intron (NR_131187, intron 1 of 1)	intron (NR_131187, intron 1 of 1)	82522	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.005025	0.390000	
chunk0111_9_1	chr20	21812399	21812890	+	0	NA	Intergenic	Intergenic	106985	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.000000	0.481707	
chunk0167_369_1	chr6	73534794	73535102	+	0	NA	Intergenic	L1ME1|LINE|L1	-13916	NM_001402	1915	Hs.535192	NM_001402	ENSG00000156508	EEF1A1	CCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|HNGC:16303|LENG7|PTI1|eEF1A-1	eukaryotic translation elongation factor 1 alpha 1	protein-coding	0.012987	0.339806	
chunk0060_8_1	chr14	39229258	39229457	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-4564	NM_054024	4253	Hs.287694	NM_005930	ENSG00000150527	MIA2	CTAGE5|MEA6|MGEA|MGEA11|MGEA6|TALI	MIA SH3 domain ER export factor 2	protein-coding	0.005025	0.480000	
chunk0049_214_1	chr12	93226180	93226453	+	0	NA	intron (NR_040096, intron 2 of 4)	L1ME3Cz|LINE|L1	51950	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.000000	0.357664	
chunk0007_433_1	chr1	86755777	86756475	+	0	NA	Intergenic	Intergenic	51556	NM_016009	51100	Hs.136309	NM_016009	ENSG00000097033	SH3GLB1	Bif-1|CGI-61|PPP1R70|dJ612B15.2	SH3 domain containing GRB2 like, endophilin B1	protein-coding	0.004298	0.443491	
chunk0201_75_1	chr9	34258203	34258882	+	0	NA	intron (NM_194313, intron 10 of 12)	intron (NM_194313, intron 10 of 12)	70658	NM_194313	347240	Hs.710246	NM_194313	ENSG00000186638	KIF24	C9orf48|bA571F15.4	kinesin family member 24	protein-coding	0.007364	0.486765	283(AAGAACAGTGTCTTCT,-,0.00),284(AGAACAGTGTCTTCTC,+,0.00)
chunk0036_352_1	chr11	66915165	66915445	+	0	NA	intron (NM_000920, intron 2 of 21)	intron (NM_000920, intron 2 of 21)	-7436	NM_022172	5091	Hs.89890	NM_000920	ENSG00000173599	PC	PCB	pyruvate carboxylase	protein-coding	0.014286	0.580071	
chunk0095_350_1	chr2	21452624	21453072	+	0	NA	Intergenic	Intergenic	257804	NR_038837	645949	Hs.456782	NR_038837	ENSG00000229621	LINC01822	-	long intergenic non-protein coding RNA 1822	ncRNA	0.011161	0.472160	210(CAAAACACTTTGTGCT,-,0.00),211(AAAACACTTTGTGCTT,+,0.00)
chunk0071_199_1	chr15	83930588	83931309	+	0	NA	intron (NM_207517, intron 17 of 29)	intron (NM_207517, intron 17 of 29)	-149239	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.000000	0.383657	
chunk0048_427_1	chr12	88413722	88414070	+	0	NA	Intergenic	Intergenic	166577	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.005747	0.361032	
chunk0134_225_1	chr3	178820577	178821186	+	0	NA	intron (NM_001278911, intron 2 of 4)	intron (NM_001278911, intron 2 of 4)	39524	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.001642	0.362295	274(TTGAACAGAATGTTCC,-,0.00),275(TGAACAGAATGTTCCC,+,0.00)
chunk0096_454_1	chr2	39875786	39876233	+	0	NA	Intergenic	MER92A|LTR|ERV1	-41625	NR_038441	100128590	Hs.744988	NR_038441	ENSG00000227028	SLC8A1-AS1	-	SLC8A1 antisense RNA 1	ncRNA	0.002237	0.433036	
chunk0151_98_1	chr5	43138057	43138313	+	0	NA	intron (NR_123720, intron 3 of 5)	L1MB1|LINE|L1	16677	NM_001297548	7690	Hs.535804	NM_003432	ENSG00000172262	ZNF131	ZBTB35|pHZ-10	zinc finger protein 131	protein-coding	0.007812	0.404669	
chunk0031_26_1	chr10	121942687	121943183	+	0	NA	intron (NR_120495, intron 1 of 1)	intron (NR_120495, intron 1 of 1)	-14134	NM_001288736	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.000000	0.426559	
chunk0082_232_1	chr17	57296356	57296682	+	0	NA	intron (NM_138962, intron 5 of 13)	intron (NM_138962, intron 5 of 13)	39506	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.006135	0.363914	
chunk0211_156_1	chrX	114214085	114214669	+	0	NA	Intergenic	L1MC|LINE|L1	-276159	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.003425	0.350427	
chunk0002_90_1	chr1	14692396	14692716	+	0	NA	intron (NM_015209, intron 1 of 7)	intron (NM_015209, intron 1 of 7)	93839	NM_015209	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.015625	0.482866	
chunk0187_349_1	chr7	157124710	157125211	+	0	NA	Intergenic	Intergenic	-14001	NM_014671	9690	Hs.118351	NM_014671	ENSG00000009335	UBE3C	HECTH2	ubiquitin protein ligase E3C	protein-coding	0.033932	0.496016	
chunk0099_182_1	chr2	90381581	90381900	+	0	NA	Intergenic	Intergenic	1278209	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.056426	0.384375	
chunk0172_8_1	chr6	132459159	132460021	+	0	NA	3' UTR (NM_003569, exon 10 of 10)	3' UTR (NM_003569, exon 10 of 10)	53608	NM_003569	8417	Hs.593148	NM_003569	ENSG00000079950	STX7	-	syntaxin 7	protein-coding	0.005800	0.380070	
chunk0096_328_1	chr2	34109568	34109785	+	0	NA	intron (NR_126403, intron 4 of 5)	L1M8|LINE|L1	42450	NR_132381	106144585	Hs.580486	NR_132381	ENSG00000237790	LINC01318	-	long intergenic non-protein coding RNA 1318	ncRNA	0.009217	0.321101	
chunk0142_380_1	chr4	102295229	102296047	+	0	NA	intron (NM_022154, intron 5 of 7)	FLAM_C|SINE|Alu	28674	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.002445	0.374847	197(AGAAACTGACTGTTCT,-,0.00),198(GAAACTGACTGTTCTC,+,0.00)
chunk0134_183_1	chr3	178157231	178157430	+	0	NA	Intergenic	L1MEg|LINE|L1	-261871	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.000000	0.275000	
chunk0023_126_1	chr10	23821205	23821418	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	126565	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.000000	0.434579	
chunk0041_38_1	chr12	854716	855071	+	0	NA	intron (NM_213655, intron 4 of 27)	MER2|DNA|TcMar-Tigger	78183	NM_001297420	5893	Hs.410355	NM_134422	ENSG00000002016	RAD52	-	RAD52 homolog, DNA repair protein	protein-coding	0.008451	0.365169	
chunk0184_77_1	chr7	112820267	112820761	+	0	NA	3' UTR (NM_152556, exon 5 of 5)	3' UTR (NM_152556, exon 5 of 5)	-30091	NR_109840	64418	Hs.606345	NM_022484	ENSG00000146802	TMEM168	-	transmembrane protein 168	protein-coding	0.004049	0.315152	279(TGGACTAAATGTTCTT,+,0.00)
chunk0108_442_1	chr2	238141920	238142125	+	0	NA	intron (NM_198582, intron 2 of 7)	L2b|LINE|L2	3300	NM_198582	377007	Hs.591595	NM_198582	ENSG00000168427	KLHL30	-	kelch like family member 30	protein-coding	0.004878	0.577670	
chunk0077_79_1	chr16	77188106	77188681	+	0	NA	Intergenic	Intergenic	-2526	NM_001286640	22879	Hs.513743	NM_014940	ENSG00000103111	MON1B	HSRG1|SAND2|SRG1	MON1 homolog B, secretory trafficking associated	protein-coding	0.008696	0.375000	
chunk0165_393_1	chr6	38792409	38792705	+	0	NA	intron (NM_001206927, intron 21 of 92)	intron (NM_001206927, intron 21 of 92)	77216	NM_001206927	1769	Hs.520106	NM_001371	ENSG00000124721	DNAH8	ATPase|hdhc9	dynein axonemal heavy chain 8	protein-coding	0.006757	0.417508	
chunk0050_380_1	chr12	108716741	108717175	+	0	NA	intron (NM_014325, intron 1 of 10)	L2b|LINE|L2	13885	NM_001276471	23603	Hs.330384	NM_014325	ENSG00000110880	CORO1C	HCRNN4	coronin 1C	protein-coding	0.016129	0.448276	
chunk0133_121_1	chr3	168462336	168463081	+	0	NA	intron (NR_021485, intron 3 of 15)	L1M4c|LINE|L1	-89146	NR_030294	693136		NR_030294	ENSG00000207717	MIR551B	MIRN551B|mir-551b	microRNA 551b	ncRNA	0.002685	0.395442	667(GAGGACAGGATGTTTT,-,0.00),668(AGGACAGGATGTTTTG,+,0.00)
chunk0034_394_1	chr11	36736708	36737278	+	0	NA	Intergenic	L1M3f|LINE|L1	-138714	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.001754	0.415061	373(GAGCACTGCCTGTCCT,-,0.00),374(AGCACTGCCTGTCCTG,+,0.00)
chunk0158_194_1	chr5	127980724	127981019	+	0	NA	Intergenic	Intergenic	102203	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.003390	0.347973	
chunk0064_335_1	chr14	96562428	96562686	+	0	NA	intron (NM_001293628, intron 20 of 21)	intron (NM_001293628, intron 20 of 21)	59692	NM_001293628	10914	Hs.253726	NM_032632	ENSG00000090060	PAPOLA	PAP|PAP-alpha	poly(A) polymerase alpha	protein-coding	0.000000	0.335907	
chunk0206_181_1	chr9	122810475	122810748	+	0	NA	Intergenic	Intergenic	10488	NM_080859	392392	Hs.632681	NM_080859	ENSG00000165204	OR1K1	hg99	olfactory receptor family 1 subfamily K member 1	protein-coding	0.014652	0.419708	
chunk0042_178_1	chr12	4743486	4743775	+	0	NA	intron (NM_017417, intron 3 of 10)	MIR|SINE|MIR	23044	NM_017417	26290	Hs.511985	NM_017417	ENSG00000130035	GALNT8	GALNAC-T8	polypeptide N-acetylgalactosaminyltransferase 8	protein-coding	0.013841	0.441379	114(TGAGACACGGTGTTCT,-,0.00),115(GAGACACGGTGTTCTG,+,0.00)
chunk0052_289_1	chr12	124406004	124406572	+	0	NA	intron (NM_006312, intron 15 of 48)	intron (NM_006312, intron 15 of 48)	-69046	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.026408	0.530756	
chunk0151_207_1	chr5	50752801	50753346	+	0	NA	intron (NM_024615, intron 3 of 25)	intron (NM_024615, intron 3 of 25)	86135	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.000000	0.318681	
chunk0189_102_1	chr8	21937347	21937695	+	0	NA	intron (NM_015024, intron 1 of 27)	intron (NM_015024, intron 1 of 27)	17852	NM_015024	23039	Hs.172685	NM_015024	ENSG00000130227	XPO7	EXP7|RANBP16	exportin 7	protein-coding	0.008621	0.398281	
chunk0116_427_1	chr21	42955814	42956070	+	0	NA	Intergenic	Intergenic	-4928	NR_049889	100847013		NR_049889	ENSG00000264580	MIR5692B	-	microRNA 5692b	ncRNA	0.027344	0.385214	
chunk0013_294_1	chr1	171142675	171143004	+	0	NA	intron (NR_002601, intron 1 of 6)	intron (NR_002601, intron 1 of 6)	5099	NR_002601	388714	Hs.448988	NR_002601	ENSG00000117507	FMO6P	FMO6	flavin containing dimethylaniline monoxygenase 6, pseudogene	pseudo	0.012158	0.421212	
chunk0112_398_1	chr20	46976784	46977498	+	0	NA	intron (NM_172110, intron 1 of 13)	L1ME3G|LINE|L1	82517	NM_172110	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.008403	0.408392	300(TGGAACAAGATGTACA,-,0.00),301(GGAACAAGATGTACAA,+,0.00)
chunk0123_26_1	chr3	40481545	40481807	+	0	NA	intron (NM_001145083, intron 2 of 3)	intron (NM_001145083, intron 2 of 3)	4534	NM_001145083	285267	Hs.407159	NM_173656	ENSG00000177873	ZNF619	-	zinc finger protein 619	protein-coding	0.011450	0.524715	
chunk0101_454_1	chr2	140127520	140127769	+	0	NA	Intergenic	L1MEd|LINE|L1	459041	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.300000	
chunk0130_369_1	chr3	139316942	139317681	+	0	NA	Intergenic	Intergenic	-26708	NM_020191	56945	Hs.745001	NM_020191	ENSG00000175110	MRPS22	C3orf5|COXPD5|GIBT|GK002|MRP-S22|ODG7|RPMS22	mitochondrial ribosomal protein S22	protein-coding	0.009472	0.500000	
chunk0186_289_1	chr7	142588097	142588311	+	0	NA	Intergenic	Intergenic	-78095	NM_001190487	100463482		NM_001190487	ENSG00000270672	MTRNR2L6	HN6	MT-RNR2 like 6	protein-coding	0.028037	0.423256	
chunk0037_8_1	chr11	68898299	68898721	+	0	NA	intron (NM_181514, intron 2 of 6)	intron (NM_181514, intron 2 of 6)	5325	NM_181514	219927	Hs.503047	NM_181512	ENSG00000197345	MRPL21	L21mt|MRP-L21	mitochondrial ribosomal protein L21	protein-coding	0.014218	0.574468	
chunk0110_157_1	chr20	13946889	13947088	+	0	NA	intron (NR_073206, intron 2 of 20)	MER52A|LTR|ERV1	43631	NR_073206	80343	Hs.590879	NM_025229	ENSG00000101251	SEL1L2	C20orf50|sel-1L2	SEL1L2 adaptor subunit of ERAD E3 ligase	protein-coding	0.010050	0.630000	
chunk0019_96_1	chr1	224739590	224739974	+	0	NA	3' UTR (NM_152495, exon 6 of 6)	3' UTR (NM_152495, exon 6 of 6)	123305	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.007812	0.527273	168(AGGAACAGAATGACCC,-,0.00),169(GGAACAGAATGACCCA,+,0.00)
chunk0101_209_1	chr2	130246766	130247062	+	0	NA	Intergenic	Intergenic	-48453	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.000000	0.528620	
chunk0195_311_1	chr8	98876795	98877094	+	0	NA	intron (NM_001256312, intron 3 of 12)	intron (NM_001256312, intron 3 of 12)	-51263	NM_006281	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.003344	0.356667	
chunk0002_287_1	chr1	22826583	22827158	+	0	NA	intron (NM_001309192, intron 3 of 13)	L2b|LINE|L2	36356	NR_036214	100422914		NR_036214	ENSG00000264014	MIR4253	-	microRNA 4253	ncRNA	0.015652	0.534722	73(AGGACAGTGAGCTCTT,+,0.00),246(AGGACAGCAAGCTCTT,+,0.00),283(TGGCTCACTGTGTCCC,-,0.00),284(GGCTCACTGTGTCCCC,+,0.00)
chunk0135_69_1	chr3	185899957	185900548	+	0	NA	Intergenic	Intergenic	37884	NM_001243879	6434	Hs.533122	NM_004593	ENSG00000136527	TRA2B	Htra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B	transformer 2 beta homolog	protein-coding	0.003384	0.435811	275(TTGAACTCACTGTACT,-,0.00),276(TGAACTCACTGTACTT,+,0.00)
chunk0116_24_1	chr21	33016888	33017350	+	0	NA	Intergenic	L1ME4b|LINE|L1	-8789	NM_005806	10215	Hs.176977	NM_005806	ENSG00000205927	OLIG2	BHLHB1|OLIGO2|PRKCBP2|RACK17|bHLHe19	oligodendrocyte transcription factor 2	protein-coding	0.002165	0.349892	
chunk0113_11_1	chr20	49381546	49382266	+	0	NA	intron (NM_004975, intron 1 of 1)	intron (NM_004975, intron 1 of 1)	100738	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.013889	0.561720	535(AGGCACAGACTGTCCA,-,0.00),536(GGCACAGACTGTCCAT,+,0.00)
chunk0198_433_1	chr8	143366655	143366916	+	0	NA	non-coding (NR_026785, exon 1 of 1)	non-coding (NR_026785, exon 1 of 1)	1850	NR_026785	78998	Hs.245886	NM_024035	ENSG00000254389	RHPN1-AS1	C8orf51	RHPN1 antisense RNA 1 (head to head)	ncRNA	0.003831	0.480916	
chunk0187_6_1	chr8	450084	450364	+	0	NA	intron (NM_012173, intron 5 of 8)	intron (NM_012173, intron 5 of 8)	43416	NM_012173	26260	Hs.438454	NM_012173	ENSG00000147364	FBXO25	FBX25	F-box protein 25	protein-coding	0.003571	0.298932	
chunk0172_344_1	chr6	138852573	138852772	+	0	NA	intron (NM_001195037, intron 8 of 20)	intron (NM_001195037, intron 8 of 20)	56561	NM_001195037	345930	Hs.660603	NM_001077706	ENSG00000203734	ECT2L	ARHGEF32|C6orf91|FBXO49|LFDH|dJ509I19.2|dJ509I19.3|dJ509I19.5	epithelial cell transforming 2 like	protein-coding	0.015075	0.410000	16(TGGGACTTCGTGTACT,-,0.00),17(GGGACTTCGTGTACTT,+,0.00)
chunk0036_284_1	chr11	65418595	65418989	+	0	NA	Intergenic	Intergenic	-4006	NR_028272	283131	Hs.523789	NR_002802	ENSG00000245532	NEAT1	LINC00084|NCRNA00084|TncRNA|VINC	nuclear paraspeckle assembly transcript 1	ncRNA	0.020305	0.584810	
chunk0008_172_1	chr1	92874813	92875370	+	0	NA	intron (NM_001252269, intron 1 of 3)	intron (NM_001252269, intron 1 of 3)	2059	NM_001252271	388650	Hs.180946	NM_001006605	ENSG00000154511	DIPK1A	FAM69A	divergent protein kinase domain 1A	protein-coding	0.003591	0.372760	
chunk0086_168_1	chr18	21751684	21752337	+	0	NA	intron (NM_020774, intron 1 of 20)	intron (NM_020774, intron 1 of 20)	10681	NM_020774	57534	Hs.140903	NM_020774	ENSG00000101752	MIB1	DIP-1|DIP1|LVNC7|MIB|ZZANK2|ZZZ6	mindbomb E3 ubiquitin protein ligase 1	protein-coding	0.001531	0.356269	
chunk0076_118_1	chr16	66632561	66632864	+	0	NA	intron (NM_181521, intron 2 of 3)	intron (NM_181521, intron 2 of 3)	27981	NR_037619	123920	Hs.298198	NM_144601	ENSG00000140931	CMTM3	BNAS2|CKLFSF3	CKLF like MARVEL transmembrane domain containing 3	protein-coding	0.023102	0.582237	
chunk0161_435_1	chr5	178488820	178489124	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	101583	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.016447	0.580328	
chunk0070_314_1	chr15	75368354	75368740	+	0	NA	promoter-TSS (NM_001256496)	promoter-TSS (NM_001256496)	80	NM_001256494	4123	Hs.26232	NM_006715	ENSG00000140400	MAN2C1	MAN6A8|MANA|MANA1	mannosidase alpha class 2C member 1	protein-coding	0.103627	0.687339	
chunk0105_445_1	chr2	195018432	195018985	+	0	NA	Intergenic	L2c|LINE|L2	288113	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.003617	0.353791	
chunk0028_39_1	chr10	82930807	82931156	+	0	NA	intron (NM_001010848, intron 4 of 8)	intron (NM_001010848, intron 4 of 8)	-698061	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.005731	0.482857	145(AGGAACAAAATGTACT,-,0.00),146(GGAACAAAATGTACTG,+,0.00)
chunk0167_270_1	chr6	70241025	70241515	+	0	NA	intron (NM_001851, intron 31 of 37)	intron (NM_001851, intron 31 of 37)	41938	NM_078485	1297	Hs.590892	NM_001851	ENSG00000112280	COL9A1	DJ149L1.1.2|EDM6|MED|STL4	collagen type IX alpha 1 chain	protein-coding	0.010204	0.391039	
chunk0138_273_1	chr4	40453968	40454167	+	0	NA	intron (NM_019027, intron 2 of 4)	MER58A|DNA|hAT-Charlie	48052	NR_039966	100616274		NR_039966	ENSG00000263642	MIR4802	-	microRNA 4802	ncRNA	0.020101	0.445000	
chunk0202_328_1	chr9	78509845	78510619	+	0	NA	Intergenic	Intergenic	213157	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.007752	0.372903	
chunk0127_406_1	chr3	102465933	102466142	+	0	NA	intron (NM_175056, intron 7 of 10)	intron (NM_175056, intron 7 of 10)	31022	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.004785	0.476190	
chunk0118_364_1	chr22	36395090	36395540	+	0	NA	Intergenic	Intergenic	-7248	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.008889	0.509978	
chunk0127_163_1	chr3	94806099	94806453	+	0	NA	Intergenic	Intergenic	-131987	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.005650	0.307042	
chunk0044_105_1	chr12	28708840	28709039	+	0	NA	Intergenic	Intergenic	-440064	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.005025	0.490000	
chunk0058_21_1	chr14	19864684	19865002	+	0	NA	Intergenic	Intergenic	-11425	NM_001005501	390431	Hs.551345	NM_001005501	ENSG00000165762	OR4K2	OR14-15	olfactory receptor family 4 subfamily K member 2	protein-coding	0.009434	0.310345	
chunk0004_428_1	chr1	52766492	52766729	+	0	NA	intron (NM_024646, intron 2 of 13)	L1MDa|LINE|L1	40151	NM_024646	79699	Hs.476280	NM_024646	ENSG00000162378	ZYG11B	ZYG11	zyg-11 family member B, cell cycle regulator	protein-coding	0.004219	0.352941	
chunk0055_52_1	chr13	52459051	52459282	+	0	NA	intron (NM_018204, intron 2 of 8)	intron (NM_018204, intron 2 of 8)	3194	NM_001286686	26586	Hs.444028	NM_018204	ENSG00000136108	CKAP2	LB1|TMAP|se20-10	cytoskeleton associated protein 2	protein-coding	0.000000	0.383621	105(GGCACATTTTGATCTT,+,0.00)
chunk0109_453_1	chr2	241657598	241658098	+	0	NA	intron (NM_178326, intron 6 of 12)	L2a|LINE|L2	20236	NM_013325	23192	Hs.283610	NM_013325	ENSG00000168397	ATG4B	APG4B|AUTL1	autophagy related 4B cysteine peptidase	protein-coding	0.018000	0.530938	
chunk0063_218_1	chr14	81509684	81509917	+	0	NA	intron (NM_001244984, intron 3 of 7)	L1ME3G|LINE|L1	24061	NM_005065	6400	Hs.181300	NM_005065	ENSG00000071537	SEL1L	Hrd3|PRO1063|SEL1-LIKE|SEL1L1	SEL1L adaptor subunit of ERAD E3 ubiquitin ligase	protein-coding	0.000000	0.337607	
chunk0184_399_1	chr7	122054381	122054772	+	0	NA	intron (NM_001206839, intron 25 of 28)	intron (NM_001206839, intron 25 of 28)	89714	NM_005763	10157	Hs.156738	NM_005763	ENSG00000008311	AASS	LKR/SDH|LKRSDH|LORSDH	aminoadipate-semialdehyde synthase	protein-coding	0.002558	0.313776	
chunk0208_316_1	chrX	24002777	24003358	+	0	NA	intron (NM_030624, intron 3 of 3)	intron (NM_030624, intron 3 of 3)	24119	NM_030624	80311	Hs.495854	NM_030624	ENSG00000174010	KLHL15	HEL-S-305	kelch like family member 15	protein-coding	0.012048	0.463918	
chunk0060_344_1	chr14	52025172	52025772	+	0	NA	intron (NM_007361, intron 12 of 21)	intron (NM_007361, intron 12 of 21)	35962	NM_016039	51637	Hs.534457	NM_016039	ENSG00000087302	RTRAF	C14orf166|CGI-99|CGI99|CLE|CLE7|LCRP369|RLLM1|hCLE|hCLE1	RNA transcription, translation and transport factor	protein-coding	0.000000	0.420965	
chunk0022_355_1	chr10	17177584	17178275	+	0	NA	intron (NM_004412, intron 1 of 10)	intron (NM_004412, intron 1 of 10)	24142	NM_004412	1787	Hs.351665	NM_004412	ENSG00000107614	TRDMT1	DMNT2|DNMT2|MHSAIIP|PUMET|RNMT1	tRNA aspartic acid methyltransferase 1	protein-coding	0.002894	0.304913	
chunk0142_448_1	chr4	105473970	105474196	+	0	NA	promoter-TSS (NM_176866)	promoter-TSS (NM_176866)	-13	NM_176867	27068	Hs.654957	NM_006903	ENSG00000138777	PPA2	HSPC124|SCFAI|SCFI|SID6-306	pyrophosphatase (inorganic) 2	protein-coding	0.115044	0.735683	
chunk0211_398_1	chrX	128599872	128600430	+	0	NA	Intergenic	Intergenic	-547748	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.001792	0.366726	
chunk0163_302_1	chr6	14394219	14394664	+	0	NA	Intergenic	Intergenic	-108987	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.011236	0.468610	
chunk0004_354_1	chr1	51466885	51467427	+	0	NA	intron (NM_001981, intron 5 of 24)	L1ME4b|LINE|L1	-45035	NM_001159969	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.001845	0.313076	
chunk0077_379_1	chr16	84649336	84650056	+	0	NA	intron (NM_024731, intron 1 of 4)	intron (NM_024731, intron 1 of 4)	1185	NM_024731	79786	Hs.222731	NM_024731	ENSG00000135686	KLHL36	C16orf44	kelch like family member 36	protein-coding	0.029167	0.539528	267(GGGAACAGCTTGTCAT,-,0.00),348(CGGGACGGACTGTGCC,-,0.00),349(GGGACGGACTGTGCCC,+,0.00)
chunk0045_110_1	chr12	46216800	46217020	+	0	NA	intron (NM_001077484, intron 5 of 16)	intron (NM_001077484, intron 5 of 16)	49585	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.004545	0.380090	127(AGGGACAAGGTGTTCT,-,0.00),128(GGGACAAGGTGTTCTG,+,0.00)
chunk0051_243_1	chr12	117079556	117079944	+	0	NA	intron (NM_001168325, intron 1 of 6)	L1MB8|LINE|L1	19696	NM_001168325	54997	Hs.525709	NM_017899	ENSG00000088992	TESC	CHP3|TSC	tescalcin	protein-coding	0.002577	0.398458	119(AGGAACAGAAAGTACA,-,0.00),120(GGAACAGAAAGTACAC,+,0.00)
chunk0174_25_1	chr6	153267725	153267938	+	0	NA	Intergenic	Intergenic	-136577	NM_012419	26575	Hs.166313	NM_012419	ENSG00000091844	RGS17	RGS-17|RGSZ2|hRGS17	regulator of G protein signaling 17	protein-coding	0.014085	0.327103	
chunk0159_411_1	chr5	147835347	147835817	+	0	NA	intron (NM_003122, intron 1 of 4)	intron (NM_003122, intron 1 of 4)	3649	NM_003122	6690	Hs.407856	NM_003122	ENSG00000164266	SPINK1	PCTT|PSTI|Spink3|TATI|TCP	serine peptidase inhibitor, Kazal type 1	protein-coding	0.004255	0.365180	
chunk0096_240_1	chr2	30999673	31000418	+	0	NA	intron (NM_024572, intron 1 of 14)	intron (NM_024572, intron 1 of 14)	129595	NM_001253827	79623	Hs.468058	NM_024572	ENSG00000158089	GALNT14	GALNT15|GalNac-T10|GalNac-T14	polypeptide N-acetylgalactosaminyltransferase 14	protein-coding	0.008054	0.463807	166(TGGCACAGTCAGTGCA,-,0.00),167(GGCACAGTCAGTGCAG,+,0.00),385(TGGAACAGGTTGTCCT,-,0.00),386(GGAACAGGTTGTCCTG,+,0.00)
chunk0149_304_1	chr5	25744213	25744785	+	0	NA	Intergenic	Intergenic	-903916	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.000000	0.235602	
chunk0011_181_1	chr1	148424156	148424746	+	0	NA	intron (NR_111930, intron 4 of 8)	intron (NR_111930, intron 4 of 8)	21736	NR_104081	101954272		NR_104081	ENSG00000201183	RNVU1-3	RNU1-113|RNU1-151|RNVU1-12|vU1.12|vU1.3	RNA, variant U1 small nuclear 3	snRNA	0.001695	0.473773	264(AGGAACACCCTGTCCA,-,0.00),265(GGAACACCCTGTCCAG,+,0.00)
chunk0093_110_1	chr19	44258870	44259244	+	0	NA	promoter-TSS (NM_001207005)	promoter-TSS (NM_001207005)	-823	NM_001207005	353355	Hs.466891	NM_181756	ENSG00000159915	ZNF233	-	zinc finger protein 233	protein-coding	0.005348	0.298667	170(TAGTACATGCTGTGCT,-,0.00),171(AGTACATGCTGTGCTA,+,0.00)
chunk0183_272_1	chr7	107545708	107546144	+	0	NA	intron (NM_006348, intron 5 of 21)	L1M3e|LINE|L1	-18031	NR_073003	11062	Hs.97627	NM_181581	ENSG00000105865	DUS4L	DUS4|PP35	dihydrouridine synthase 4 like	protein-coding	0.006881	0.334096	179(CAGAACACTCCGTCCA,-,0.00),180(AGAACACTCCGTCCAA,+,0.00)
chunk0044_177_1	chr12	30142346	30142778	+	0	NA	Intergenic	Intergenic	-357803	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.004630	0.367206	
chunk0178_13_1	chr7	29147433	29147731	+	0	NA	intron (NM_001293069, intron 2 of 13)	MIR|SINE|MIR	1035	NM_001293069	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.010067	0.384615	
chunk0044_403_1	chr12	41026207	41026482	+	0	NA	intron (NM_175038, intron 19 of 21)	L2a|LINE|L2	117987	NM_175038	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.003636	0.376812	
chunk0065_296_1	chr14	102717258	102717823	+	0	NA	intron (NM_015156, intron 8 of 11)	MIRc|SINE|MIR	-59939	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.010619	0.452297	
chunk0187_300_1	chr7	156201020	156201569	+	0	NA	Intergenic	Intergenic	238662	NM_001291913	389602	Hs.583071	NM_001291913		LOC389602	-	uncharacterized LOC389602	protein-coding	0.003643	0.374545	
chunk0150_172_1	chr5	34444809	34445404	+	0	NA	Intergenic	L1PA7|LINE|L1	-211222	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.005042	0.359060	253(AGGAACAGGTTGTTCA,-,0.00),254(GGAACAGGTTGTTCAG,+,0.00)
chunk0017_316_1	chr1	211258911	211259569	+	0	NA	promoter-TSS (NM_001136225)	promoter-TSS (NM_001136225)	-126	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.113982	0.728376	
chunk0114_397_1	chr20	63538802	63539001	+	0	NA	Intergenic	Intergenic	-1531	NM_005975	5753	Hs.51133	NM_005975	ENSG00000101213	PTK6	BRK	protein tyrosine kinase 6	protein-coding	0.030151	0.595000	
chunk0035_320_1	chr11	47416040	47416354	+	0	NA	3' UTR (NM_001128225, exon 10 of 10)	3' UTR (NM_001128225, exon 10 of 10)	7702	NM_152264	91252	Hs.523664	NM_152264	ENSG00000165915	SLC39A13	EDSSPD3|LZT-Hs9|SCDEDS|ZIP13	solute carrier family 39 member 13	protein-coding	0.025478	0.660317	115(AGGCACATAGTGAGCC,-,0.00),116(GGCACATAGTGAGCCC,+,0.00)
chunk0099_188_1	chr2	90385972	90386234	+	0	NA	Intergenic	Intergenic	1273846	NR_027238	654342	Hs.469287	NR_027238		LSP1P4	-	LSP1 pseudogene 4	pseudo	0.057252	0.384030	
chunk0198_135_1	chr8	132712049	132712536	+	0	NA	intron (NM_001145153, intron 8 of 8)	intron (NM_001145153, intron 8 of 8)	-36675	NR_073525	23639	Hs.591865	NM_012472	ENSG00000129295	LRRC6	CILD19|LRTP|TSLRP	leucine rich repeat containing 6	protein-coding	0.002053	0.393443	
chunk0205_189_1	chr9	109062555	109062786	+	0	NA	intron (NM_032012, intron 10 of 17)	intron (NM_032012, intron 10 of 17)	-16372	NR_029506	407036		NR_029506	ENSG00000207698	MIR32	MIRN32|hsa-mir-32|miR-32|miRNA32	microRNA 32	ncRNA	0.017316	0.400862	
chunk0096_322_1	chr2	33552943	33553171	+	0	NA	intron (NM_170672, intron 15 of 18)	intron (NM_170672, intron 15 of 18)	39182	NM_015376	25780	Hs.143674	NM_015376	ENSG00000152689	RASGRP3	GRP3	RAS guanyl releasing protein 3	protein-coding	0.000000	0.454148	
chunk0041_265_1	chr11	129090948	129091297	+	0	NA	intron (NM_001142685, intron 5 of 21)	intron (NM_001142685, intron 5 of 21)	-66929	NM_014715	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.008596	0.391429	
chunk0100_21_1	chr2	105141344	105141941	+	0	NA	Intergenic	Intergenic	-38698	NR_110227	101927492	Hs.469537	NR_110227	ENSG00000231851	UTAT33	-	uncharacterized LOC101927492	ncRNA	0.011725	0.530100	472(GGGAACATTATGTTCC,-,0.00),473(GGAACATTATGTTCCA,+,0.00)
chunk0002_24_1	chr1	12376034	12376913	+	0	NA	intron (NM_018156, intron 54 of 68)	MIR|SINE|MIR	-130773	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.006826	0.429545	
chunk0179_408_1	chr7	51622082	51622309	+	0	NA	Intergenic	MER41C|LTR|ERV1	-305377	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.004405	0.438596	
chunk0082_238_1	chr17	57350328	57351113	+	0	NA	intron (NM_138962, intron 5 of 13)	(CCT)n|Simple_repeat|Simple_repeat	93707	NM_170721	124540	Hs.658922	NM_138962	ENSG00000153944	MSI2	MSI2H	musashi RNA binding protein 2	protein-coding	0.012739	0.538168	
chunk0036_424_1	chr11	68380346	68380747	+	0	NA	intron (NM_001291902, intron 5 of 22)	L1ME4a|LINE|L1	67937	NM_002335	4041	Hs.6347	NM_002335	ENSG00000162337	LRP5	BMND1|EVR1|EVR4|HBM|LR3|LRP-5|LRP-7|LRP7|OPPG|OPS|OPTA1|PCLD4|VBCH2	LDL receptor related protein 5	protein-coding	0.052369	0.609453	
chunk0194_255_1	chr8	86649669	86649870	+	0	NA	intron (NM_019098, intron 7 of 17)	L1PB|LINE|L1	93906	NM_019098	54714	Hs.154433	NM_019098	ENSG00000170289	CNGB3	ACHM1	cyclic nucleotide gated channel beta 3	protein-coding	0.000000	0.297030	
chunk0057_124_1	chr13	99411767	99412113	+	0	NA	Intergenic	L1ME3A|LINE|L1	55809	NR_030353	693208		NR_030353	ENSG00000207719	MIR623	MIRN623|hsa-mir-623	microRNA 623	ncRNA	0.011561	0.466859	
chunk0038_80_1	chr11	83195307	83195754	+	0	NA	intron (NM_001300975, intron 1 of 10)	L2c|LINE|L2	1791	NM_001300977	338699	Hs.503438	NM_182603	ENSG00000137494	ANKRD42	PPP1R79|SARP	ankyrin repeat domain 42	protein-coding	0.008949	0.388393	239(AAGAGCAGCATGTCCA,-,0.00)
chunk0089_51_1	chr18	58102889	58103196	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	-46291	NM_001144969	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.009772	0.418831	
chunk0105_143_1	chr2	186383662	186384075	+	0	NA	Intergenic	Intergenic	-102290	NM_018471	55854	Hs.741180	NM_018471	ENSG00000065548	ZC3H15	HT010|LEREPO4|MSTP012	zinc finger CCCH-type containing 15	protein-coding	0.014528	0.371981	
chunk0156_238_1	chr5	108378592	108378927	+	0	NA	intron (NM_001163315, intron 1 of 8)	L2b|LINE|L2	3339	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.029851	0.464286	
chunk0009_67_1	chr1	100883986	100884379	+	0	NA	intron (NR_048570, intron 2 of 5)	intron (NR_048570, intron 2 of 5)	10997	NM_001261440	2135	Hs.357637	NM_001439	ENSG00000162694	EXTL2	EXTR2	exostosin like glycosyltransferase 2	protein-coding	0.010178	0.398477	
chunk0196_319_1	chr8	110763208	110763619	+	0	NA	Intergenic	L1PREC2|LINE|L1	264020	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.009732	0.376214	
chunk0030_154_1	chr10	113921831	113922450	+	0	NA	Intergenic	Intergenic	67508	NM_198514	374354	Hs.369924	NM_198514	ENSG00000196865	NHLRC2	FINCA	NHL repeat containing 2	protein-coding	0.006462	0.387097	
chunk0079_56_1	chr17	10843826	10844460	+	0	NA	Intergenic	Intergenic	-6042	NM_001101387	644139	Hs.553909	NM_001101387	ENSG00000233670	PIRT	-	phosphoinositide interacting regulator of transient receptor potential channels	protein-coding	0.014196	0.533858	
chunk0097_448_1	chr2	64403879	64404534	+	0	NA	Intergenic	Intergenic	-49987	NM_014181	29094	Hs.372208	NM_014181	ENSG00000119862	LGALSL	GRP|HSPC159	galectin like	protein-coding	0.010687	0.506098	361(AGGAACTTGCTGTTCC,-,0.00),362(GGAACTTGCTGTTCCT,+,0.00)
chunk0188_60_1	chr8	7120703	7121388	+	0	NA	Intergenic	Intergenic	-64306	NM_021010	1670	Hs.655233	NM_021010	ENSG00000164816	DEFA5	DEF5|HD-5	defensin alpha 5	protein-coding	0.011679	0.424198	
chunk0186_429_1	chr7	146682046	146682747	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	415213	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.005706	0.329060	
chunk0033_339_1	chr11	22689227	22689558	+	0	NA	intron (NM_177553, intron 3 of 7)	intron (NM_177553, intron 3 of 7)	14619	NM_005256	2620	Hs.711297	NM_005256	ENSG00000148935	GAS2	GAS-2	growth arrest specific 2	protein-coding	0.009063	0.343373	
chunk0152_412_1	chr5	65329304	65329701	+	0	NA	intron (NM_197941, intron 8 of 24)	intron (NM_197941, intron 8 of 24)	152375	NM_197941	11174	Hs.482291	NM_197941	ENSG00000049192	ADAMTS6	ADAM-TS 6|ADAM-TS6|ADAMTS-6	ADAM metallopeptidase with thrombospondin type 1 motif 6	protein-coding	0.005038	0.399497	
chunk0141_303_1	chr4	87055210	87055766	+	0	NA	intron (NM_001313959, intron 3 of 19)	intron (NM_001313959, intron 3 of 19)	48487	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.003597	0.384201	
chunk0050_442_1	chr12	110466608	110467173	+	0	NA	intron (NM_001164372, intron 1 of 7)	intron (NM_001164372, intron 1 of 7)	1394	NM_001164373	51184	Hs.634680	NM_016301	ENSG00000111231	GPN3	ATPBD1C	GPN-loop GTPase 3	protein-coding	0.010619	0.487633	
chunk0153_259_1	chr5	72767484	72767861	+	0	NA	Intergenic	Intergenic	-48919	NM_002270	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.007958	0.486772	
chunk0020_23_1	chr1	231800104	231800626	+	0	NA	intron (NM_001012957, intron 8 of 12)	intron (NM_001012957, intron 8 of 12)	18152	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.011494	0.391969	162(CAGCACATCGTGTTTT,-,0.00),163(AGCACATCGTGTTTTG,+,0.00),337(ATGTACTCTGTGTGCC,-,0.00)
chunk0153_404_1	chr5	75361102	75361713	+	0	NA	3' UTR (NM_001130996, exon 19 of 19)	3' UTR (NM_001130996, exon 19 of 19)	24239	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.006547	0.369281	338(AGAAGATAATGTTCTT,+,0.00)
chunk0199_269_1	chr9	6371188	6371394	+	0	NA	Intergenic	THE1-int|LTR|ERVL-MaLR	-41860	NR_046386	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.004854	0.516908	
chunk0200_251_1	chr9	21334902	21335178	+	0	NA	5' UTR (NM_018847, exon 1 of 1)	5' UTR (NM_018847, exon 1 of 1)	390	NM_018847	55958	Hs.701778	NM_018847	ENSG00000198642	KLHL9	-	kelch like family member 9	protein-coding	0.047101	0.519856	
chunk0210_430_1	chrX	103341041	103341569	+	0	NA	Intergenic	L1MB4|LINE|L1	11119	NM_152278	56849	Hs.21861	NM_152278	ENSG00000182916	TCEAL7	WEX5	transcription elongation factor A like 7	protein-coding	0.001894	0.325142	
chunk0116_287_1	chr21	39935938	39936331	+	0	NA	Intergenic	Intergenic	68713	NM_006198	5121	Hs.80296	NM_006198	ENSG00000183036	PCP4	PEP-19	Purkinje cell protein 4	protein-coding	0.010178	0.444162	
chunk0103_257_1	chr2	165371035	165371507	+	0	NA	intron (NM_021007, intron 20 of 26)	intron (NM_021007, intron 20 of 26)	75498	NM_001040143	6326	Hs.93485	NM_021007	ENSG00000136531	SCN2A	BFIC3|BFIS3|BFNIS|EIEE11|HBA|HBSCI|HBSCII|NAC2|Na(v)1.2|Nav1.2|SCN2A1|SCN2A2	sodium voltage-gated channel alpha subunit 2	protein-coding	0.004237	0.315011	
chunk0108_380_1	chr2	236995121	236995519	+	0	NA	Intergenic	L1M6|LINE|L1	-90121	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.002513	0.305764	
chunk0038_245_1	chr11	87194148	87194815	+	0	NA	intron (NM_022918, intron 5 of 14)	intron (NM_022918, intron 5 of 14)	156637	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.004498	0.329341	
chunk0180_159_1	chr7	64744825	64745154	+	0	NA	Intergenic	Intergenic	-49399	NM_001271639	7697	Hs.184080	NM_006524	ENSG00000197008	ZNF138	pHZ-32	zinc finger protein 138	protein-coding	0.000000	0.433333	
chunk0052_429_1	chr12	131832945	131833209	+	0	NA	intron (NM_016155, intron 1 of 9)	MIR|SINE|MIR	4681	NM_016155	4326	Hs.709245	NM_016155	ENSG00000198598	MMP17	MMP-17|MT4-MMP|MT4MMP|MTMMP4	matrix metallopeptidase 17	protein-coding	0.015152	0.584906	
chunk0086_412_1	chr18	26920453	26921029	+	0	NA	intron (NM_001256316, intron 4 of 4)	intron (NM_001256316, intron 4 of 4)	-54989	NM_001650	361	Hs.315369	NM_001650	ENSG00000171885	AQP4	MIWC|WCH4	aquaporin 4	protein-coding	0.008681	0.389948	
chunk0048_90_1	chr12	79277827	79278485	+	0	NA	intron (NM_001291901, intron 3 of 9)	L1PB3|LINE|L1	-141101	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.000000	0.329287	
chunk0038_367_1	chr11	93356359	93357061	+	0	NA	intron (NM_181645, intron 3 of 13)	intron (NM_181645, intron 3 of 13)	25993	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.002849	0.311522	
chunk0154_167_1	chr5	79612075	79612383	+	0	NA	promoter-TSS (NM_173797)	promoter-TSS (NM_173797)	-191	NM_001114393	167153	Hs.418198	NM_173797	ENSG00000164329	TENT2	APD4|GLD2|PAPD4|TUT2	terminal nucleotidyltransferase 2	protein-coding	0.038961	0.598706	
chunk0190_3_1	chr8	28652130	28652440	+	0	NA	Intergenic	L1MB4|LINE|L1	49179	NR_126027	101929402	Hs.667366	NR_126027	ENSG00000246339	EXTL3-AS1	C8orf50	EXTL3 antisense RNA 1	ncRNA	0.006452	0.421222	
chunk0014_239_1	chr1	179953899	179954136	+	0	NA	promoter-TSS (NM_014810)	promoter-TSS (NM_014810)	-756	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.021097	0.445378	
chunk0157_430_1	chr5	124758784	124759105	+	0	NA	Intergenic	Intergenic	-13832	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.018692	0.397516	
chunk0195_132_1	chr8	95020439	95020825	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-4354	NM_152416	137682	Hs.435500	NM_152416	ENSG00000156170	NDUFAF6	C8orf38|MC1DN17	NADH:ubiquinone oxidoreductase complex assembly factor 6	protein-coding	0.005181	0.511628	
chunk0055_109_1	chr13	56769189	56769876	+	0	NA	Intergenic	L1MC|LINE|L1	-371386	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.007278	0.345930	
chunk0010_60_1	chr1	113021420	113022152	+	0	NA	intron (NR_103777, intron 2 of 2)	L2b|LINE|L2	51316	NR_103777	100996251	Hs.382067	NR_103777	ENSG00000238198	LRIG2-DT	-	LRIG2 divergent transcript	ncRNA	0.009563	0.399727	
chunk0136_130_1	chr4	3767637	3767870	+	0	NA	exon (NM_000683, exon 1 of 1)	exon (NM_000683, exon 1 of 1)	1184	NM_000683	152	Hs.123022	NM_000683	ENSG00000184160	ADRA2C	ADRA2L2|ADRA2RL2|ADRARL2|ALPHA2CAR	adrenoceptor alpha 2C	protein-coding	0.120172	0.683761	
chunk0139_195_1	chr4	54658669	54659156	+	0	NA	intron (NM_001093772, intron 1 of 20)	CpG	984	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.092402	0.653689	
chunk0040_162_1	chr11	113849444	113849643	+	0	NA	intron (NM_001301029, intron 1 of 21)	MER21-int|LTR|ERVL	26027	NM_001301029	57646	Hs.503891	NM_020886	ENSG00000048028	USP28	-	ubiquitin specific peptidase 28	protein-coding	0.020101	0.465000	
chunk0169_134_1	chr6	101212616	101213081	+	0	NA	Intergenic	Intergenic	-186137	NM_001166247	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.008602	0.347639	
chunk0076_112_1	chr16	66508194	66508473	+	0	NA	non-coding (NR_073520, exon 9 of 9)	non-coding (NR_073520, exon 9 of 9)	-31931	NR_109960	101927726	Hs.739193	NR_109960	ENSG00000261656	BEAN1-AS1	CTD-2258A20.5	BEAN1 antisense RNA 1	ncRNA	0.007168	0.439286	
chunk0147_181_1	chr4	176892771	176893284	+	0	NA	Intergenic	Intergenic	-100282	NM_005429	7424	Hs.435215	NM_005429	ENSG00000150630	VEGFC	Flt4-L|LMPH1D|LMPHM4|VRP	vascular endothelial growth factor C	protein-coding	0.000000	0.301556	281(AAGTACTCTCAGTTCT,-,0.00),282(AGTACTCTCAGTTCTT,+,0.00)
chunk0174_83_1	chr6	156437359	156438067	+	0	NA	Intergenic	Intergenic	-340217	NM_017519	57492	Hs.291587	NM_017519	ENSG00000049618	ARID1B	6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250R	AT-rich interaction domain 1B	protein-coding	0.011299	0.400564	
chunk0170_204_1	chr6	112470973	112471262	+	0	NA	Intergenic	Intergenic	123787	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.003460	0.403448	
chunk0008_178_1	chr1	92984910	92985285	+	0	NA	Intergenic	L1ME1|LINE|L1	-23575	NM_001006605	388650	Hs.180946	NM_001006605	ENSG00000154511	DIPK1A	FAM69A	divergent protein kinase domain 1A	protein-coding	0.000000	0.300532	
chunk0043_350_1	chr12	23060034	23060668	+	0	NA	Intergenic	Intergenic	-115285	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.007886	0.352756	
chunk0117_347_1	chr21	44054570	44055074	+	0	NA	intron (NM_003274, intron 4 of 22)	intron (NM_003274, intron 4 of 22)	42497	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.011905	0.455446	
chunk0169_57_1	chr6	98458797	98459185	+	0	NA	Intergenic	Intergenic	-375713	NM_005604	5454	Hs.182505	NM_005604	ENSG00000184486	POU3F2	BRN2|N-Oct3|OCT7|OTF-7|OTF7|POUF3|brn-2|oct-7	POU class 3 homeobox 2	protein-coding	0.002577	0.385604	208(TTGAACAGTTTGTTCC,-,0.00),209(TGAACAGTTTGTTCCA,+,0.00)
chunk0098_68_1	chr2	66971910	66972563	+	0	NA	TTS (NR_110169)	TTS (NR_110169)	-49746	NR_110600	102724321	Hs.146803	NR_110600	ENSG00000232688	LINC01628	-	long intergenic non-protein coding RNA 1628	ncRNA	0.004594	0.295107	
chunk0048_287_1	chr12	82714361	82714994	+	0	NA	intron (NM_152588, intron 1 of 11)	intron (NM_152588, intron 1 of 11)	27522	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.006319	0.356467	
chunk0141_316_1	chr4	87213319	87213587	+	0	NA	intron (NR_120447, intron 1 of 7)	intron (NR_120447, intron 1 of 7)	6815	NM_001292003	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.007463	0.375465	
chunk0116_90_1	chr21	34845684	34846143	+	0	NA	intron (NM_001001890, intron 3 of 5)	intron (NM_001001890, intron 3 of 5)	42777	NM_001122607	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.008715	0.460870	
chunk0176_129_1	chr7	12605884	12606376	+	0	NA	intron (NM_033128, intron 2 of 13)	L2a|LINE|L2	16607	NM_033128	85477	Hs.633359	NM_033128	ENSG00000006747	SCIN	-	scinderin	protein-coding	0.014228	0.330629	
chunk0025_5_1	chr10	47067185	47067862	+	0	NA	Intergenic	L1PA12|LINE|L1	135146	NM_001042357	26095	Hs.440733	NM_015605	ENSG00000204179	PTPN20	CT126|PTPN20A|PTPN20B|bA142I17.1|bA42B19.1	protein tyrosine phosphatase non-receptor type 20	protein-coding	0.007386	0.408555	
chunk0146_159_1	chr4	159946989	159947225	+	0	NA	Intergenic	Intergenic	679261	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.008475	0.333333	
chunk0062_459_1	chr14	75831703	75832414	+	0	NA	intron (NM_015072, intron 28 of 31)	intron (NM_015072, intron 28 of 31)	149964	NM_003239	7043	Hs.592317	NM_003239	ENSG00000119699	TGFB3	ARVD|ARVD1|LDS5|RNHF|TGF-beta3	transforming growth factor beta 3	protein-coding	0.007032	0.448034	
chunk0117_265_1	chr22	23895248	23895631	+	0	NA	TTS (NM_002415)	TTS (NM_002415)	1061	NM_002415	4282	Hs.407995	NM_002415	ENSG00000240972	MIF	GIF|GLIF|MMIF	macrophage migration inhibitory factor	protein-coding	0.054830	0.625000	
chunk0126_191_1	chr3	78426565	78427136	+	0	NA	Intergenic	L2b|LINE|L2	592609	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003503	0.293706	
chunk0200_349_1	chr9	24711867	24712431	+	0	NA	Intergenic	Intergenic	-166473	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.001773	0.307965	
chunk0104_419_1	chr2	180799094	180799599	+	0	NA	intron (NR_104324, intron 3 of 4)	intron (NR_104324, intron 3 of 4)	107242	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.001980	0.284585	299(TGGAACAATGTGTTCT,-,0.00),300(GGAACAATGTGTTCTG,+,0.00)
chunk0067_58_1	chr15	40937911	40938178	+	0	NA	3' UTR (NM_019074, exon 11 of 11)	3' UTR (NM_019074, exon 11 of 11)	8711	NM_019074	54567	Hs.511076	NM_019074	ENSG00000128917	DLL4	AOS6|delta4|hdelta2	delta like canonical Notch ligand 4	protein-coding	0.029963	0.611940	
chunk0063_212_1	chr14	81400588	81401243	+	0	NA	intron (NM_033104, intron 1 of 5)	MIRb|SINE|MIR	26297	NM_033104	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.018321	0.417683	
chunk0073_320_1	chr16	14305012	14305297	+	0	NA	intron (NR_132983, intron 1 of 1)	intron (NR_132983, intron 1 of 1)	1187	NR_030177	574455		NR_030177	ENSG00000207639	MIR193B	MIRN193B|mir-193b	microRNA 193b	ncRNA	0.017544	0.391608	107(TTGAACACAGCGTTCT,-,0.00),108(TGAACACAGCGTTCTT,+,0.00)
chunk0119_391_1	chr22	48835864	48836068	+	0	NA	Intergenic	Intergenic	-30804	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.039216	0.639024	139(CAGCACAGCGTGTTCT,-,0.00),140(AGCACAGCGTGTTCTC,+,0.00)
chunk0040_412_1	chr11	121089465	121089950	+	0	NA	TTS (NM_001130047)	TTS (NM_001130047)	-12959	NM_005422	7007	Hs.248162	NM_005422	ENSG00000109927	TECTA	DFNA12|DFNA8|DFNB21	tectorin alpha	protein-coding	0.002062	0.337449	
chunk0153_341_1	chr5	74167941	74168156	+	0	NA	Intergenic	Intergenic	140277	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.013953	0.375000	
chunk0140_429_1	chr4	76127803	76128036	+	0	NA	intron (NR_103782, intron 8 of 11)	L1MD2|LINE|L1	20596	NM_001278603	53371	Hs.430435	NM_017426	ENSG00000138750	NUP54	-	nucleoporin 54	protein-coding	0.008584	0.410256	
chunk0036_196_1	chr11	63240614	63241244	+	0	NA	Intergenic	Intergenic	-11277	NM_199352	387601	Hs.332119	NM_199352	ENSG00000196600	SLC22A25	HIMTP|UST6	solute carrier family 22 member 25	protein-coding	0.000000	0.358162	
chunk0163_229_1	chr6	12278952	12279634	+	0	NA	Intergenic	Intergenic	-11003	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.004399	0.414348	
chunk0007_135_1	chr1	79250866	79251301	+	0	NA	Intergenic	Intergenic	-244273	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.004598	0.357798	
chunk0004_422_1	chr1	52574631	52574858	+	0	NA	Intergenic	L2c|LINE|L2	-21654	NM_001009881	23318	Hs.655407	NM_015269	ENSG00000134744	TUT4	PAPD3|TENT3A|ZCCHC11	terminal uridylyl transferase 4	protein-coding	0.008811	0.416667	
chunk0202_322_1	chr9	78312080	78312412	+	0	NA	intron (NM_021154, intron 6 of 7)	intron (NM_021154, intron 6 of 7)	15171	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.009036	0.378378	
chunk0175_297_1	chr7	7843098	7843667	+	0	NA	intron (NM_001302349, intron 3 of 3)	intron (NM_001302349, intron 3 of 3)	-124775	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.008787	0.357895	
chunk0049_171_1	chr12	92312362	92312642	+	0	NA	Intergenic	Intergenic	-109029	NR_027933	574028	Hs.730377	NM_001025233	ENSG00000257127	CLLU1	-	chronic lymphocytic leukemia up-regulated 1	ncRNA	0.003571	0.455516	
chunk0097_380_1	chr2	61419750	61420148	+	0	NA	intron (NM_014709, intron 2 of 79)	intron (NM_014709, intron 2 of 79)	-2572	NR_003707	100124537	Hs.675825	NR_003707	ENSG00000206937	SNORA70B	-	small nucleolar RNA, H/ACA box 70B	snoRNA	0.000000	0.325815	
chunk0003_78_1	chr1	31422415	31422770	+	0	NA	intron (NM_001199039, intron 2 of 10)	L2c|LINE|L2	8779	NM_001199039	347735	Hs.270655	NM_018565	ENSG00000168528	SERINC2	FKSG84|PRO0899|TDE2|TDE2L	serine incorporator 2	protein-coding	0.008451	0.502809	
chunk0016_75_1	chr1	193767857	193768483	+	0	NA	Intergenic	AluSz|SINE|Alu	463425	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.009585	0.401914	
chunk0024_439_1	chr10	46417273	46417484	+	0	NA	TTS (NR_003277)	TTS (NR_003277)	1463	NR_003277	728643	Hs.711067	NR_003277	ENSG00000213412	HNRNPA1P33	-	heterogeneous nuclear ribonucleoprotein A1 pseudogene 33	pseudo	0.000000	0.443396	
chunk0075_339_1	chr16	55149690	55149889	+	0	NA	Intergenic	Intergenic	-174770	NM_024335	79190	Hs.369907	NM_024335	ENSG00000159387	IRX6	IRX-3|IRX7|IRXB3	iroquois homeobox 6	protein-coding	0.015075	0.440000	
chunk0028_104_1	chr10	84340077	84340614	+	0	NA	intron (NM_001284240, intron 1 of 9)	L2a|LINE|L2	11756	NM_018999	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.007449	0.356877	
chunk0031_385_1	chr10	130974410	130974925	+	0	NA	Intergenic	Intergenic	-11999	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.003883	0.339147	
chunk0101_240_1	chr2	131492735	131492936	+	0	NA	promoter-TSS (NM_001085365)	promoter-TSS (NM_001085365)	22	NR_026922	150776	Hs.535622	NR_026922	ENSG00000152117	LOC150776	-	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3) pseudogene	pseudo	0.069652	0.643564	
chunk0067_154_1	chr15	43805016	43805295	+	0	NA	exon (NM_005926, exon 9 of 9)	exon (NM_005926, exon 9 of 9)	4734	NM_016400	25764	Hs.730672	NM_016400	ENSG00000242028	HYPK	C15orf63|HSPC136	huntingtin interacting protein K	protein-coding	0.017921	0.485714	148(AAGAACTTTGTGTTCT,-,0.00),149(AGAACTTTGTGTTCTG,+,0.00)
chunk0165_230_1	chr6	35415128	35415553	+	0	NA	intron (NM_001171820, intron 3 of 5)	intron (NM_001171820, intron 3 of 5)	-37021	NM_021922	2178	Hs.302003	NM_021922	ENSG00000112039	FANCE	FACE|FAE	FA complementation group E	protein-coding	0.007059	0.523474	
chunk0159_161_1	chr5	139452295	139452518	+	0	NA	intron (NR_121659, intron 9 of 10)	(TG)n|Simple_repeat|Simple_repeat	10337	NR_121659	641700	Hs.483538	NM_001077693	ENSG00000249751	ECSCR	ARIA|ECSM2	endothelial cell surface expressed chemotaxis and apoptosis regulator	protein-coding	0.004484	0.522321	
chunk0044_416_1	chr12	41573102	41573628	+	0	NA	exon (NM_013377, exon 8 of 8)	exon (NM_013377, exon 8 of 8)	135626	NM_013377	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.034221	0.504744	
chunk0143_138_1	chr4	109786664	109787157	+	0	NA	intron (NM_000204, intron 1 of 12)	intron (NM_000204, intron 1 of 12)	15269	NM_000204	3426	Hs.312485	NM_000204	ENSG00000205403	CFI	AHUS3|ARMD13|C3BINA|C3b-INA|FI|IF|KAF	complement factor I	protein-coding	0.002028	0.386640	254(GGGCACAGGGTGTATT,-,0.00)
chunk0010_43_1	chr1	112804210	112804481	+	0	NA	Intergenic	Intergenic	46298	NR_103746	100996702	Hs.632431	NR_103746	ENSG00000215866	LINC01356	-	long intergenic non-protein coding RNA 1356	ncRNA	0.018450	0.566176	
chunk0149_441_1	chr5	29803543	29804840	+	0	NA	Intergenic	L1MC2|LINE|L1	-408215	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.006168	0.313559	859(GAGAACTCTCTGTACT,-,0.00),860(AGAACTCTCTGTACTA,+,0.00)
chunk0112_392_1	chr20	46782257	46782845	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	72911	NM_030777	81031	Hs.305971	NM_030777	ENSG00000197496	SLC2A10	ATORS|ATS|GLUT10	solute carrier family 2 member 10	protein-coding	0.008503	0.451613	
chunk0095_201_1	chr2	18345830	18346600	+	0	NA	Intergenic	L2c|LINE|L2	214478	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.009091	0.452659	
chunk0101_322_1	chr2	135965092	135965644	+	0	NA	intron (NM_001293312, intron 2 of 14)	L1ME4c|LINE|L1	-19808	NR_110199	101928243	Hs.602178	NR_110199	ENSG00000231890	DARS-AS1	-	DARS antisense RNA 1	ncRNA	0.016304	0.294756	274(AAGAACACTGAGATCC,-,0.00),275(AGAACACTGAGATCCC,+,0.00)
chunk0021_297_1	chr1	244703227	244703528	+	0	NA	intron (NR_123736, intron 3 of 3)	AluJb|SINE|Alu	50329	NR_123736	51029	Hs.498317	NM_016076	ENSG00000121644	DESI2	C1orf121|CGI-146|DESI|DESI1|DeSI-2|FAM152A|PNAS-4|PPPDE1	desumoylating isopeptidase 2	protein-coding	0.003322	0.503311	
chunk0189_108_1	chr8	22010308	22010614	+	0	NA	Intergenic	CpG	-13649	NM_001286680	10361	Hs.131055	NM_182795	ENSG00000158806	NPM2	-	nucleophosmin/nucleoplasmin 2	protein-coding	0.091503	0.671010	
chunk0199_370_1	chr9	12834306	12834519	+	0	NA	Intergenic	Intergenic	-20023	NR_125775	101929467	Hs.586443	NR_125775	ENSG00000235448	LURAP1L-AS1	-	LURAP1L antisense RNA 1	ncRNA	0.014085	0.369159	
chunk0042_172_1	chr12	4641512	4641809	+	0	NA	intron (NM_006422, intron 3 of 5)	intron (NM_006422, intron 3 of 5)	7387	NM_001278309	10566	Hs.98397	NM_006422	ENSG00000111254	AKAP3	AKAP 110|AKAP110|CT82|FSP95|HEL159|PRKA3|SOB1	A-kinase anchoring protein 3	protein-coding	0.003367	0.318792	
chunk0012_121_1	chr1	156979695	156979899	+	0	NA	intron (NM_198236, intron 4 of 40)	L2c|LINE|L2	-43553	NR_030527	768220		NR_030527	ENSG00000211581	MIR765	MIRN765|hsa-mir-765|mir-765	microRNA 765	ncRNA	0.000000	0.370732	
chunk0141_248_1	chr4	85036853	85037180	+	0	NA	Intergenic	Intergenic	70198	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.003058	0.326220	
chunk0148_440_1	chr4	189492040	189492477	+	0	NA	Intergenic	Intergenic	-167348	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.013730	0.438356	
chunk0052_443_1	chr12	132446738	132446977	+	0	NA	Intergenic	Intergenic	-43714	NM_001142641	57666	Hs.411138	NM_001142641	ENSG00000112787	FBRSL1	-	fibrosin like 1	protein-coding	0.020921	0.479167	
chunk0150_413_1	chr5	40238546	40238747	+	0	NA	Intergenic	Intergenic	186355	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.004975	0.430693	
chunk0201_254_1	chr9	38047734	38048055	+	0	NA	intron (NM_003028, intron 1 of 5)	intron (NM_003028, intron 1 of 5)	21319	NM_003028	6461	Hs.521482	NM_003028	ENSG00000107338	SHB	bA3J10.2	SH2 domain containing adaptor protein B	protein-coding	0.028037	0.515528	
chunk0188_55_1	chr8	6909894	6910096	+	0	NA	Intergenic	Intergenic	16081	NM_001926	1671	Hs.711	NM_001926	ENSG00000164822	DEFA6	DEF6|HD-6	defensin alpha 6	protein-coding	0.000000	0.423645	
chunk0030_47_1	chr10	111763800	111764306	+	0	NA	Intergenic	Intergenic	419726	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.003953	0.420118	166(AGGTACATTCTGAGCC,-,0.00),167(GGTACATTCTGAGCCC,+,0.00)
chunk0014_298_1	chr1	180827226	180827642	+	0	NA	intron (NM_001135669, intron 9 of 13)	intron (NM_001135669, intron 9 of 13)	-85743	NM_020950	57710	Hs.734816	NM_020950	ENSG00000135835	KIAA1614	-	KIAA1614	protein-coding	0.004808	0.362110	154(GTGTACATTGTGTGCT,-,0.00),155(TGTACATTGTGTGCTA,+,0.00)
chunk0201_409_1	chr9	69472766	69472965	+	0	NA	intron (NM_001163, intron 3 of 12)	intron (NM_001163, intron 3 of 12)	143540	NM_004816	9413	Hs.118003	NM_004816	ENSG00000135063	FAM189A2	C9orf61|X123	family with sequence similarity 189 member A2	protein-coding	0.000000	0.420000	
chunk0070_235_1	chr15	73000850	73001174	+	0	NA	Intergenic	L1ME4b|LINE|L1	-51472	NM_001172624	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.006173	0.326154	
chunk0117_69_1	chr22	17063324	17063924	+	0	NA	Intergenic	L1M5|LINE|L1	-21335	NM_001289905	23765	Hs.48353	NM_014339	ENSG00000177663	IL17RA	CANDF5|CD217|CDw217|IL-17RA|IL17R|IMD51|hIL-17R	interleukin 17 receptor A	protein-coding	0.011667	0.444260	
chunk0001_191_1	chr1	7510654	7510930	+	0	NA	intron (NM_015215, intron 6 of 22)	intron (NM_015215, intron 6 of 22)	-260477	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.010870	0.501805	
chunk0154_389_1	chr5	88077933	88078252	+	0	NA	Intergenic	L1PA14|LINE|L1	190787	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.000000	0.362500	
chunk0045_126_1	chr12	46349097	46349763	+	0	NA	Intergenic	L2c|LINE|L2	23432	NM_001307936	54407	Hs.221847	NM_018976	ENSG00000134294	SLC38A2	ATA2|PRO1068|SAT2|SNAT2	solute carrier family 38 member 2	protein-coding	0.006006	0.470765	
chunk0198_371_1	chr8	141114867	141115412	+	0	NA	Intergenic	Charlie5|DNA|hAT-Charlie	-13482	NM_014957	22898	Hs.18166	NM_014957	ENSG00000105339	DENND3	-	DENN domain containing 3	protein-coding	0.009174	0.489011	267(AGGTACTTTCTGTTCT,-,0.00),268(GGTACTTTCTGTTCTT,+,0.00)
chunk0038_189_1	chr11	86062603	86063190	+	0	NA	intron (NM_001206947, intron 1 of 18)	intron (NM_001206947, intron 1 of 18)	6201	NM_001206946	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.006814	0.311224	
chunk0013_260_1	chr1	170087418	170087617	+	0	NA	Intergenic	Intergenic	-12779	NM_014970	22920	Hs.433442	NM_014970	ENSG00000075945	KIFAP3	FLA3|KAP-1|KAP-3|KAP3|SMAP|Smg-GDS|dJ190I16.1	kinesin associated protein 3	protein-coding	0.005025	0.305000	
chunk0173_206_1	chr6	145390222	145390852	+	0	NA	Intergenic	Intergenic	-344332	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.006349	0.378764	
chunk0075_156_1	chr16	51585957	51586156	+	0	NA	Intergenic	L2a|LINE|L2	-176463	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.020101	0.460000	
chunk0090_23_1	chr19	940855	941395	+	0	NA	intron (NM_005224, intron 3 of 8)	CpG	15088	NM_005224	1820	Hs.501296	NM_005224	ENSG00000116017	ARID3A	BRIGHT|DRIL1|DRIL3|E2FBP1	AT-rich interaction domain 3A	protein-coding	0.098148	0.735675	
chunk0132_294_1	chr3	160171136	160171644	+	0	NA	intron (NR_108088, intron 3 of 9)	L2a|LINE|L2	35702	NR_108088	101928376	Hs.565865	NR_108088	ENSG00000244040	IL12A-AS1	ILAS1-AS1	IL12A antisense RNA 1	ncRNA	0.003937	0.445972	
chunk0129_269_1	chr3	122721813	122722256	+	0	NA	intron (NM_017554, intron 15 of 16)	L4_A_Mam|LINE|RTE-X	41209	NM_017554	54625	Hs.518203	NM_017554	ENSG00000173193	PARP14	ARTD8|BAL2|PARP-14|pART8	poly(ADP-ribose) polymerase family member 14	protein-coding	0.009029	0.326577	
chunk0056_337_1	chr13	91338594	91338954	+	0	NA	Intergenic	L1MA9|LINE|L1	-9046	NR_027349	407975	Hs.24115	NR_027349	ENSG00000215417	MIR17HG	C13orf25|FGLDS2|LINC00048|MIHG1|MIRH1|MIRHG1|NCRNA00048|miR-17-92	miR-17-92a-1 cluster host gene	ncRNA	0.000000	0.351801	210(CTGAACTTCCTGTACC,-,0.00),211(TGAACTTCCTGTACCT,+,0.00)
chunk0145_26_1	chr4	143513546	143514048	+	0	NA	non-coding (NR_104027, exon 2 of 2)	non-coding (NR_104027, exon 2 of 2)	334	NM_003601	8467	Hs.558422	NM_003601	ENSG00000153147	SMARCA5	ISWI|SNF2H|WCRF135|hISWI|hSNF2H	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding	0.111554	0.679920	
chunk0147_355_1	chr4	185709771	185710091	+	0	NA	intron (NM_001145672, intron 1 of 20)	HY1|scRNA|scRNA	-52962	NM_001145675	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.006250	0.404984	143(GGAACAAGGAGTTCAG,+,0.00)
chunk0015_401_1	chr1	191020501	191020896	+	0	NA	Intergenic	L1MA10|LINE|L1	395808	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.007595	0.305556	
chunk0042_163_1	chr12	4346959	4347514	+	0	NA	intron (NM_020375, intron 3 of 5)	L1MA2|LINE|L1	26043	NM_020375	57103	Hs.504545	NM_020375	ENSG00000078237	TIGAR	C12orf5|FR2BP	TP53 induced glycolysis regulatory phosphatase	protein-coding	0.001802	0.392086	
chunk0034_360_1	chr11	36036888	36037459	+	0	NA	intron (NM_174902, intron 2 of 5)	intron (NM_174902, intron 2 of 5)	27075	NR_039769	100616311		NR_039769	ENSG00000263389	MIR3973	-	microRNA 3973	ncRNA	0.021016	0.543706	346(GAGAACTATGTGTCCT,-,0.00),347(AGAACTATGTGTCCTG,+,0.00)
chunk0182_337_1	chr7	99210172	99210640	+	0	NA	Intergenic	Intergenic	-2940	NM_001145715	402569	Hs.253050	NM_001145715	ENSG00000185467	KPNA7	IPOA8	karyopherin subunit alpha 7	protein-coding	0.006410	0.445629	
chunk0208_242_1	chrX	20007935	20008490	+	0	NA	3' UTR (NM_001168465, exon 17 of 17)	3' UTR (NM_001168465, exon 17 of 17)	8975	NR_037414	100500809		NR_037414	ENSG00000264566	MIR23C	hsa-mir-23c|mir-23c	microRNA 23c	ncRNA	0.012613	0.397482	
chunk0058_451_1	chr13	113869659	113870170	+	0	NA	Intergenic	L1ME1|LINE|L1	5737	NR_044993	100506394	Hs.132168	NR_044993	ENSG00000272695	GAS6-DT	GAS6-AS2	GAS6 divergent transcript	ncRNA	0.000000	0.296875	244(GGAGACAGTGTGTACC,-,0.00),245(GAGACAGTGTGTACCC,+,0.00)
chunk0006_339_1	chr1	72101476	72101971	+	0	NA	intron (NM_173808, intron 1 of 6)	intron (NM_173808, intron 1 of 6)	180871	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.000000	0.320565	
chunk0010_55_1	chr1	112934551	112935047	+	0	NA	intron (NM_003051, intron 1 of 4)	intron (NM_003051, intron 1 of 4)	11449	NR_002796	246182	Hs.647691	NR_002796		AKR7A2P1	AFARP1	aldo-keto reductase family 7 member A2 pseudogene 1	pseudo	0.006048	0.380282	
chunk0102_254_1	chr2	149272581	149273018	+	0	NA	Intergenic	L2a|LINE|L2	-57186	NM_001195685	130574	Hs.21929	NM_194317	ENSG00000187123	LYPD6	-	LY6/PLAUR domain containing 6	protein-coding	0.004577	0.360731	
chunk0135_213_1	chr3	188417225	188417707	+	0	NA	intron (NM_001167671, intron 3 of 10)	intron (NM_001167671, intron 3 of 10)	151200	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.006224	0.438923	211(GGGAACAGCATGTGCA,-,0.00),212(GGAACAGCATGTGCAA,+,0.00)
chunk0016_388_1	chr1	202904402	202904705	+	0	NA	intron (NM_001303051, intron 6 of 11)	intron (NM_001303051, intron 6 of 11)	-15296	NM_002871	5877	Hs.90875	NM_002871	ENSG00000183155	RABIF	MSS4|RASGFR3|RASGRF3	RAB interacting factor	protein-coding	0.003300	0.365132	
chunk0010_184_1	chr1	115897053	115897683	+	0	NA	Intergenic	Intergenic	-22008	NR_125969	101928995	Hs.559119	NR_125969	ENSG00000228127	LINC01649	-	long intergenic non-protein coding RNA 1649	ncRNA	0.007937	0.377179	
chunk0124_255_1	chr3	56930013	56930445	+	0	NA	intron (NM_001128615, intron 3 of 12)	intron (NM_001128615, intron 3 of 12)	-9811	NR_046572	100874200	Hs.549631	NR_046572	ENSG00000240198	ARHGEF3-AS1	-	ARHGEF3 antisense RNA 1	ncRNA	0.011574	0.457275	
chunk0055_27_1	chr13	51953911	51954279	+	0	NA	intron (NM_001005918, intron 6 of 16)	L2c|LINE|L2	57399	NM_000053	540	Hs.492280	NM_000053	ENSG00000123191	ATP7B	PWD|WC1|WD|WND	ATPase copper transporting beta	protein-coding	0.005435	0.542005	121(AGGCACAGAGTGTTCT,-,0.00),122(GGCACAGAGTGTTCTG,+,0.00)
chunk0019_122_1	chr1	225453971	225454641	+	0	NA	Intergenic	L2a|LINE|L2	-25451	NM_194442	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.005970	0.433681	
chunk0187_41_1	chr8	1368108	1368326	+	0	NA	Intergenic	(TGTA)n|Simple_repeat|Simple_repeat	-65610	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.022936	0.447489	
chunk0209_253_1	chrX	46093872	46094352	+	0	NA	Intergenic	L1ME1|LINE|L1	233562	NR_110388	101927574	Hs.350952	NR_110388	ENSG00000236751	LINC01186	ZNF674-1	long intergenic non-protein coding RNA 1186	ncRNA	0.002083	0.343035	
chunk0146_336_1	chr4	165904197	165904549	+	0	NA	intron (NM_012464, intron 1 of 20)	intron (NM_012464, intron 1 of 20)	31115	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.005682	0.379603	
chunk0118_390_1	chr22	37529711	37529910	+	0	NA	Intergenic	Intergenic	-10607	NM_014550	29775	Hs.57973	NM_014550	ENSG00000100065	CARD10	BIMP1|CARMA3	caspase recruitment domain family member 10	protein-coding	0.005025	0.525000	
chunk0064_214_1	chr14	93262553	93262767	+	0	NA	intron (NM_001002860, intron 4 of 10)	intron (NM_001002860, intron 4 of 10)	-55546	NM_032490	84520	Hs.20142	NM_032490	ENSG00000170270	GON7	C14orf142|PNAS-127	GON7 subunit of KEOPS complex	protein-coding	0.000000	0.358140	
chunk0106_297_1	chr2	204533621	204534170	+	0	NA	Intergenic	AluJo|SINE|Alu	-11898	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.005464	0.449091	
chunk0026_322_1	chr10	68153742	68154020	+	0	NA	intron (NM_001256268, intron 10 of 23)	intron (NM_001256268, intron 10 of 23)	44448	NM_001256268	84665	Hs.55205	NM_032578	ENSG00000138347	MYPN	CMD1DD|CMH22|MYOP|NEM11|RCM4	myopalladin	protein-coding	0.014388	0.401434	
chunk0128_135_1	chr3	106678532	106679499	+	0	NA	Intergenic	LTR3B_|LTR|ERVK	561623	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.015512	0.410124	
chunk0003_424_1	chr1	40868221	40868814	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-6171	NM_133467	163732	Hs.355820	NM_133467	ENSG00000179862	CITED4	-	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4	protein-coding	0.003373	0.407407	
chunk0071_132_1	chr15	81856538	81857173	+	0	NA	Intergenic	Intergenic	189288	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.006299	0.386792	
chunk0130_14_1	chr3	128382145	128382548	+	0	NA	intron (NM_021937, intron 6 of 6)	intron (NM_021937, intron 6 of 6)	-81248	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.027295	0.579208	
chunk0205_376_1	chr9	113994144	113994454	+	0	NA	intron (NM_133374, intron 3 of 13)	intron (NM_133374, intron 3 of 13)	84173	NM_001633	259	Hs.436911	NM_001633	ENSG00000106927	AMBP	A1M|EDC1|HCP|HI30|IATIL|ITI|ITIL|ITILC|UTI	alpha-1-microglobulin/bikunin precursor	protein-coding	0.025806	0.575563	
chunk0032_11_1	chr11	604055	604599	+	0	NA	intron (NM_020901, intron 10 of 17)	intron (NM_020901, intron 10 of 17)	11401	NM_004031	3665	Hs.166120	NM_001572	ENSG00000185507	IRF7	IMD39|IRF-7|IRF-7H|IRF7A|IRF7B|IRF7C|IRF7H	interferon regulatory factor 7	protein-coding	0.023897	0.526606	
chunk0048_170_1	chr12	80840323	80840623	+	0	NA	intron (NM_004664, intron 4 of 5)	(GT)n|Simple_repeat|Simple_repeat	-7844	NR_030348	693202		NR_030348	ENSG00000207763	MIR617	MIRN617|hsa-mir-617	microRNA 617	ncRNA	0.010000	0.382060	
chunk0015_8_1	chr1	184080427	184081032	+	0	NA	Intergenic	Intergenic	29078	NM_001300766	116461	Hs.548197	NM_052965	ENSG00000198860	TSEN15	C1orf19|PCH2F|sen15	tRNA splicing endonuclease subunit 15	protein-coding	0.001653	0.333333	
chunk0023_110_1	chr10	22991683	22992189	+	0	NA	intron (NM_173081, intron 10 of 18)	intron (NM_173081, intron 10 of 18)	63912	NM_001282746	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.005929	0.388560	
chunk0074_244_1	chr16	27566054	27566327	+	0	NA	intron (NM_015202, intron 1 of 27)	intron (NM_015202, intron 1 of 27)	16043	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.010989	0.536496	94(TAGGACACCTTGTCCC,-,0.00),95(AGGACACCTTGTCCCC,+,0.00)
chunk0121_156_1	chr3	19347101	19347563	+	0	NA	intron (NM_144633, intron 4 of 15)	intron (NM_144633, intron 4 of 15)	-32401	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.004329	0.323974	
chunk0188_184_1	chr8	11474130	11474639	+	0	NA	Intergenic	Intergenic	-7617	NM_053279	83648	Hs.124299	NM_053279	ENSG00000154319	FAM167A	C8orf13|D8S265|DIORA-1	family with sequence similarity 167 member A	protein-coding	0.021611	0.523529	
chunk0138_268_1	chr4	40256196	40256598	+	0	NA	Intergenic	Intergenic	-50788	NR_121641	101060498	Hs.351492	NR_121640	ENSG00000249241	LINC02265	-	long intergenic non-protein coding RNA 2265	ncRNA	0.004975	0.444169	
chunk0131_460_1	chr3	154135482	154136015	+	0	NA	intron (NM_015595, intron 4 of 14)	intron (NM_015595, intron 4 of 14)	14388	NM_001251963	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.009381	0.419476	222(TGGAACACTGTGTACT,-,0.00),223(GGAACACTGTGTACTT,+,0.00)
chunk0155_127_1	chr5	93112449	93112919	+	0	NA	Intergenic	L2b|LINE|L2	458659	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.002128	0.384289	
chunk0005_112_1	chr1	56631844	56632293	+	0	NA	Intergenic	Intergenic	-13249	NM_006252	5563	Hs.437039	NM_006252	ENSG00000162409	PRKAA2	AMPK|AMPK2|AMPKa2|PRKAA	protein kinase AMP-activated catalytic subunit alpha 2	protein-coding	0.004454	0.357778	
chunk0080_390_1	chr17	34990856	34991120	+	0	NA	exon (NM_002311, exon 5 of 20)	exon (NM_002311, exon 5 of 20)	10490	NM_002311	3980	Hs.100299	NM_002311	ENSG00000005156	LIG3	LIG2|LIG3alpha	DNA ligase 3	protein-coding	0.015152	0.437736	
chunk0193_385_1	chr8	80246618	80247329	+	0	NA	Intergenic	Intergenic	5584	NR_049894	100847056		NR_049894	ENSG00000265588	MIR5708	-	microRNA 5708	ncRNA	0.008439	0.412921	278(GGGAACATTCAGTTCT,-,0.00),279(GGAACATTCAGTTCTG,+,0.00)
chunk0031_151_1	chr10	125129384	125129724	+	0	NA	intron (NM_001083914, intron 1 of 10)	intron (NM_001083914, intron 1 of 10)	29261	NM_001290215	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.014706	0.480938	170(GGGCACAGTGTGTCCT,-,0.00),171(GGCACAGTGTGTCCTG,+,0.00)
chunk0034_279_1	chr11	34639558	34640623	+	0	NA	intron (NM_001206616, intron 1 of 8)	MIRb|SINE|MIR	7626	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.006573	0.516886	
chunk0181_99_1	chr7	80485993	80486258	+	0	NA	intron (NM_001102386, intron 3 of 7)	intron (NM_001102386, intron 3 of 7)	25801	NM_001102386	346562	Hs.335049	NM_001102386	ENSG00000214415	GNAT3	GDCA	G protein subunit alpha transducin 3	protein-coding	0.003774	0.323308	
chunk0025_201_1	chr10	53533903	53534217	+	0	NA	Intergenic	LTR16E1|LTR|ERVL	-762360	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.003185	0.428571	
chunk0148_388_1	chr5	14777088	14777709	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	48614	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.014493	0.437299	295(AGGTTCACTGTGTTCT,-,0.00),296(GGTTCACTGTGTTCTG,+,0.00)
chunk0032_46_1	chr11	1514652	1514950	+	0	NA	Intergenic	Intergenic	-28022	NM_001172223	81532	Hs.370360	NM_053005	ENSG00000182208	MOB2	HCCA2	MOB kinase activator 2	protein-coding	0.053691	0.632107	136(CAGCACAGAGTGTGCT,-,0.00),137(AGCACAGAGTGTGCTG,+,0.00)
chunk0081_432_1	chr17	48841322	48841796	+	0	NA	intron (NM_001261395, intron 1 of 11)	intron (NM_001261395, intron 1 of 11)	10571	NM_001261391	10241	Hs.514920	NM_005831	ENSG00000136436	CALCOCO2	NDP52	calcium binding and coiled-coil domain 2	protein-coding	0.004219	0.423158	283(TTGCACAGAATGTTCC,-,0.00),284(TGCACAGAATGTTCCC,+,0.00)
chunk0165_157_1	chr6	33758935	33759250	+	0	NA	Intergenic	HAL1|LINE|L1	-12107	NM_054111	117283	Hs.17253	NM_054111	ENSG00000161896	IP6K3	IHPK3|INSP6K3	inositol hexakisphosphate kinase 3	protein-coding	0.019048	0.417722	
chunk0129_370_1	chr3	125498576	125498952	+	0	NA	intron (NR_073435, intron 1 of 12)	intron (NR_073435, intron 1 of 12)	21450	NR_073435	8723	Hs.507243	NM_003794	ENSG00000114520	SNX4	ATG24B	sorting nexin 4	protein-coding	0.000000	0.331565	
chunk0135_206_1	chr3	188305192	188305582	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	79982	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.002564	0.360614	
chunk0187_16_1	chr8	599649	600110	+	0	NA	Intergenic	L2c|LINE|L2	-54098	NM_175075	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.017354	0.515152	
chunk0114_64_1	chr21	9042846	9043102	+	0	NA	Intergenic	GSATII|Satellite|centr	55604	NR_037458									0.058594	0.607004	
chunk0116_170_1	chr21	36774603	36774802	+	0	NA	intron (NM_001242785, intron 7 of 11)	intron (NM_001242785, intron 7 of 11)	75569	NM_009586	6493	Hs.146186	NM_005069	ENSG00000159263	SIM2	HMC13F06|HMC29C01|SIM|bHLHe15	SIM bHLH transcription factor 2	protein-coding	0.010050	0.450000	
chunk0091_297_1	chr19	12610689	12610987	+	0	NA	promoter-TSS (NM_153358)	promoter-TSS (NM_153358)	-29	NM_020714	57474	Hs.655860	NM_020714	ENSG00000188033	ZNF490	-	zinc finger protein 490	protein-coding	0.080537	0.585284	
chunk0076_107_1	chr16	66410776	66411227	+	0	NA	TTS (NR_046242)	TTS (NR_046242)	2477	NR_046242	100505865	Hs.314372	NR_046242		LINC00920	-	long intergenic non-protein coding RNA 920	ncRNA	0.002217	0.287611	
chunk0177_11_1	chr7	20392968	20393393	+	0	NA	intron (NM_002214, intron 7 of 13)	Tigger15a|DNA|TcMar-Tigger	-61418	NR_110120	101927811	Hs.285724	NR_110119	ENSG00000271133	LOC101927811	-	uncharacterized LOC101927811	ncRNA	0.002353	0.368545	
chunk0098_104_1	chr2	68109192	68109611	+	0	NA	Intergenic	Intergenic	-46374	NM_001190263	10438	Hs.602900	NM_006333	ENSG00000197223	C1D	LRP1|Rrp47|SUN-CoR|SUNCOR|hC1D	C1D nuclear receptor corepressor	protein-coding	0.009547	0.404762	
chunk0110_393_1	chr20	20277909	20278474	+	0	NA	intron (NM_015585, intron 22 of 26)	intron (NM_015585, intron 22 of 26)	-89930	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.007080	0.524735	
chunk0008_32_1	chr1	88678356	88678836	+	0	NA	intron (NR_110682, intron 1 of 3)	intron (NR_110682, intron 1 of 3)	-5643	NM_006256	5586	Hs.440833	NM_006256	ENSG00000065243	PKN2	PAK2|PRK2|PRKCL2|PRO2042|Pak-2|STK7	protein kinase N2	protein-coding	0.008333	0.413721	
chunk0011_355_1	chr1	152544104	152544334	+	0	NA	Intergenic	Intergenic	22534	NM_178435	353145	Hs.490208	NM_178435	ENSG00000185966	LCE3E	LEP17	late cornified envelope 3E	protein-coding	0.004348	0.484848	2(TGGCACACTCTGTGCT,-,0.00),3(GGCACACTCTGTGCTG,+,0.00)
chunk0013_379_1	chr1	172544383	172544934	+	0	NA	intron (NM_014283, intron 1 of 23)	L2c|LINE|L2	11540	NM_001282751	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.005445	0.403986	238(GGGAACAGCATGAGCC,-,0.00),239(GGAACAGCATGAGCCA,+,0.00),266(CAGCACAGTCTGTGTT,-,0.00),267(AGCACAGTCTGTGTTC,+,0.00)
chunk0075_398_1	chr16	56915676	56916056	+	0	NA	TTS (NM_000339)	TTS (NM_000339)	11602	NR_106923	102466752		NR_106923	ENSG00000283471	MIR6863	hsa-mir-6863	microRNA 6863	ncRNA	0.018421	0.359580	186(TGGAACACACTGTTTT,-,0.00),187(GGAACACACTGTTTTT,+,0.00)
chunk0154_402_1	chr5	88603475	88604047	+	0	NA	intron (NR_015436, intron 3 of 4)	intron (NR_015436, intron 3 of 4)	63178	NR_030741	407047		NR_030741	ENSG00000284447	MIR9-2	MIRN9-2|hsa-mir-9-2|miRNA9-2|mir-9-2	microRNA 9-2	ncRNA	0.003497	0.373473	
chunk0094_439_1	chr2	11133061	11133511	+	0	NA	5' UTR (NM_182500, exon 1 of 4)	5' UTR (NM_182500, exon 1 of 4)	233	NM_182500	130813	Hs.406894	NM_182500	ENSG00000150873	C2orf50	-	chromosome 2 open reading frame 50	protein-coding	0.028889	0.638581	173(AGGGACAGAGTGTTCC,-,0.00),174(GGGACAGAGTGTTCCA,+,0.00)
chunk0213_26_1	chrY	26670359	26671790	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	942584	NR_001524	114760	Hs.511777	NR_001524	ENSG00000231141	TTTY3	LINC00121|NCRNA00121|TTTY3A|TTY3	testis-specific transcript, Y-linked 3	ncRNA	0.023061	0.439944	
chunk0083_305_1	chr17	69390839	69391230	+	0	NA	Intergenic	Intergenic	-23663	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.023018	0.441327	
chunk0027_380_1	chr10	79555815	79556295	+	0	NA	3' UTR (NM_001098668, exon 6 of 6)	3' UTR (NM_001098668, exon 6 of 6)	4352	NM_001098668	729238	Hs.523084	NM_001098668	ENSG00000185303	SFTPA2	COLEC5|PSAP|PSP-A|PSPA|SFTP1|SFTPA2B|SP-2A|SP-A|SPA2|SPAII	surfactant protein A2	protein-coding	0.008333	0.384615	
chunk0040_173_1	chr11	114001471	114002024	+	0	NA	Intergenic	LTR16B2|LTR|ERVL	24247	NM_001161772	3359	Hs.413899	NM_000869	ENSG00000166736	HTR3A	5-HT-3|5-HT3A|5-HT3R|5HT3R|HTR3	5-hydroxytryptamine receptor 3A	protein-coding	0.009042	0.476534	
chunk0197_115_1	chr8	119911548	119911879	+	0	NA	intron (NM_001283012, intron 1 of 6)	intron (NM_001283012, intron 1 of 6)	38058	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.006042	0.460843	
chunk0109_381_1	chr2	239819325	239819611	+	0	NA	Intergenic	Intergenic	56608	NR_037808	150935	Hs.555582	NR_037808		LOC150935	-	uncharacterized LOC150935	ncRNA	0.024476	0.592334	
chunk0168_89_1	chr6	79921862	79922061	+	0	NA	intron (NM_022726, intron 3 of 5)	intron (NM_022726, intron 3 of 5)	25637	NM_022726	6785	Hs.101915	NM_022726	ENSG00000118402	ELOVL4	ADMD|CT118|ISQMR|SCA34|STGD2|STGD3	ELOVL fatty acid elongase 4	protein-coding	0.000000	0.335000	
chunk0023_460_1	chr10	32360416	32360615	+	0	NA	intron (NR_104163, intron 1 of 1)	intron (NR_104163, intron 1 of 1)	13151	NR_104163	102031319	Hs.128132	NR_104163	ENSG00000229327	LOC102031319	-	uncharacterized LOC102031319	ncRNA	0.005025	0.430000	
chunk0040_407_1	chr11	121042421	121042671	+	0	NA	intron (NM_152715, intron 1 of 7)	intron (NM_152715, intron 1 of 7)	18442	NM_152715	219899	Hs.504136	NM_152715	ENSG00000154114	TBCEL	El|LRRC35	tubulin folding cofactor E like	protein-coding	0.004000	0.374502	102(AAGAACAAAGTGTCTT,-,0.00),103(AGAACAAAGTGTCTTG,+,0.00)
chunk0123_151_1	chr3	42960071	42960620	+	0	NA	Intergenic	L1M5|LINE|L1	-18922	NM_001129908	729085	Hs.729533	NM_001129908	ENSG00000144649	GASK1A	C3orf41|FAM198A	golgi associated kinase 1A	protein-coding	0.010929	0.374545	
chunk0180_336_1	chr7	73308697	73309003	+	0	NA	promoter-TSS (NM_001168348)	promoter-TSS (NM_001168348)	17	NM_001168347	55695	Hs.510927	NM_018044	ENSG00000130305	NSUN5	NOL1|NOL1R|NSUN5A|WBSCR20|WBSCR20A|p120|p120(NOL1)	NOP2/Sun RNA methyltransferase 5	protein-coding	0.094771	0.631922	
chunk0143_199_1	chr4	112902229	112902484	+	0	NA	intron (NM_001127493, intron 1 of 46)	intron (NM_001127493, intron 1 of 46)	84273	NM_001127493	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.003922	0.398438	
chunk0201_382_1	chr9	68912993	68913579	+	0	NA	intron (NM_003558, intron 8 of 15)	intron (NM_003558, intron 8 of 15)	62555	NR_110647	101927069	Hs.663405	NR_110647		LOC101927069	-	uncharacterized LOC101927069	ncRNA	0.005119	0.369676	
chunk0036_78_1	chr11	60382474	60382746	+	0	NA	intron (NM_021201, intron 1 of 6)	intron (NM_021201, intron 1 of 6)	4125	NM_206938	58475	Hs.530735	NM_021201	ENSG00000166927	MS4A7	4SPAN2|CD20L4|CFFM4|MS4A8	membrane spanning 4-domains A7	protein-coding	0.014706	0.399267	
chunk0183_263_1	chr7	107306957	107307184	+	0	NA	intron (NM_006348, intron 11 of 21)	intron (NM_006348, intron 11 of 21)	138055	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.004405	0.429825	
chunk0044_280_1	chr12	32573652	32573975	+	0	NA	intron (NM_001304480, intron 2 of 16)	intron (NM_001304480, intron 2 of 16)	39520	NM_001304480	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.000000	0.314815	
chunk0176_143_1	chr7	12859233	12859507	+	0	NA	Intergenic	Intergenic	172084	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.000000	0.294545	
chunk0068_421_1	chr15	59191727	59191961	+	0	NA	intron (NM_004998, intron 17 of 27)	intron (NM_004998, intron 17 of 27)	-14972	NM_033195	92483	Hs.307052	NM_033195	ENSG00000171989	LDHAL6B	LDH6B|LDHAL6|LDHL	lactate dehydrogenase A like 6B	protein-coding	0.012821	0.493617	
chunk0016_440_1	chr1	204073670	204073951	+	0	NA	intron (NM_005686, intron 1 of 13)	CpG	692	NM_005686	9580	Hs.201671	NM_005686	ENSG00000143842	SOX13	ICA12|Sox-13	SRY-box transcription factor 13	protein-coding	0.074733	0.645390	
chunk0003_196_1	chr1	34736057	34736330	+	0	NA	Intergenic	L2c|LINE|L2	-18854	NM_005268	2709	Hs.198249	NM_005268	ENSG00000189280	GJB5	CX31.1	gap junction protein beta 5	protein-coding	0.029304	0.456204	
chunk0053_435_1	chr13	38943120	38943633	+	0	NA	Intergenic	MER68|LTR|ERVL	47483	NM_145286	161003	Hs.327794	NM_145286	ENSG00000133115	STOML3	Epb7.2l|SRO	stomatin like 3	protein-coding	0.005848	0.418288	273(GGTTCACTGTGTCCTA,+,0.00)
chunk0184_332_1	chr7	120555375	120555920	+	0	NA	intron (NM_012281, intron 1 of 5)	intron (NM_012281, intron 1 of 5)	281979	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.335165	
chunk0171_201_1	chr6	125742417	125742894	+	0	NA	Intergenic	Intergenic	-6931	NM_012259	23493	Hs.144287	NM_012259	ENSG00000135547	HEY2	CHF1|GRIDLOCK|GRL|HERP1|HESR2|HRT2|bHLHb32	hes related family bHLH transcription factor with YRPW motif 2	protein-coding	0.008386	0.395397	
chunk0173_213_1	chr6	145584035	145584352	+	0	NA	Intergenic	L1PA15|LINE|L1	-150676	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.006309	0.540881	
chunk0015_344_1	chr1	189950702	189951118	+	0	NA	Intergenic	MIRb|SINE|MIR	526719	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004808	0.393285	310(GAGACCACTCTGTTCA,-,0.00),311(AGACCACTCTGTTCAT,+,0.00)
chunk0013_79_1	chr1	167634631	167634939	+	0	NA	intron (NM_052862, intron 1 of 6)	intron (NM_052862, intron 1 of 6)	4548	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.003247	0.336570	
chunk0150_406_1	chr5	39905195	39905810	+	0	NA	Intergenic	Intergenic	-146789	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.006504	0.352273	
chunk0059_74_1	chr14	30496213	30496454	+	0	NA	Intergenic	HAL1|LINE|L1	-62790	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.004149	0.376033	
chunk0150_163_1	chr5	34007990	34008588	+	0	NA	promoter-TSS (NM_001167595)	promoter-TSS (NM_001167595)	-174	NM_014324	23600	Hs.508343	NM_014324	ENSG00000242110	AMACR	AMACRD|CBAS4|P504S|RACE|RM	alpha-methylacyl-CoA racemase	protein-coding	0.060201	0.577629	
chunk0169_48_1	chr6	97690575	97691361	+	0	NA	intron (NR_110757, intron 3 of 4)	L1MEg|LINE|L1	-333563	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.001272	0.339263	
chunk0166_113_1	chr6	44339266	44339690	+	0	NA	Intergenic	Intergenic	-3182	NM_145026	221409	Hs.135283	NM_145026	ENSG00000249481	SPATS1	DDIP|SPATA8|SRSP1	spermatogenesis associated serine rich 1	protein-coding	0.009434	0.501176	
chunk0042_413_1	chr12	11696041	11696486	+	0	NA	intron (NM_001987, intron 1 of 7)	L2a|LINE|L2	46409	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.008989	0.352018	
chunk0121_398_1	chr3	25427153	25427450	+	0	NA	promoter-TSS (NR_110893)	promoter-TSS (NR_110893)	-962	NM_001290266	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.006734	0.449664	
chunk0158_410_1	chr5	134854121	134854506	+	0	NA	intron (NM_001300894, intron 1 of 2)	intron (NM_001300894, intron 1 of 2)	8345	NM_001300894	134553	Hs.708536	NM_152409	ENSG00000181904	C5orf24	-	chromosome 5 open reading frame 24	protein-coding	0.002597	0.375648	212(TGGCACATGCTGTCTT,-,0.00),213(GGCACATGCTGTCTTT,+,0.00)
chunk0077_294_1	chr16	81386177	81386643	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	1392	NR_039871	100616150		NR_039871	ENSG00000284473	MIR4720	-	microRNA 4720	ncRNA	0.004292	0.338330	
chunk0191_339_1	chr8	56027882	56028386	+	0	NA	Intergenic	L1MC3|LINE|L1	45767	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.007937	0.392079	
chunk0184_274_1	chr7	118583366	118583584	+	0	NA	Intergenic	Intergenic	358817	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.004587	0.319635	
chunk0163_243_1	chr6	12369976	12370308	+	0	NA	Intergenic	Intergenic	79846	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.030120	0.504505	134(ATGACACCCTGTACTC,+,0.00),196(AGGGACATTCTGTTCT,-,0.00),197(GGGACATTCTGTTCTG,+,0.00)
chunk0140_443_1	chr4	76252940	76253266	+	0	NA	intron (NM_001242939, intron 1 of 6)	L1MD2|LINE|L1	1403	NM_001136570	100129583	Hs.720509	NM_001136570	ENSG00000189157	FAM47E	-	family with sequence similarity 47 member E	protein-coding	0.006135	0.388379	
chunk0200_323_1	chr9	23638051	23638369	+	0	NA	intron (NR_121602, intron 9 of 27)	L2c|LINE|L2	34189	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.009434	0.398119	235(AGATCAAGCTGTACCT,+,0.00)
chunk0102_382_1	chr2	154447231	154448059	+	0	NA	intron (NM_001301627, intron 11 of 11)	intron (NM_001301627, intron 11 of 11)	9793	NM_001256368									0.002415	0.341375	
chunk0095_5_1	chr2	11744168	11744449	+	0	NA	intron (NM_001261427, intron 2 of 20)	intron (NM_001261427, intron 2 of 20)	-2288	NM_145693	23175	Hs.467740	NM_145693	ENSG00000134324	LPIN1	PAP1	lipin 1	protein-coding	0.021352	0.556738	
chunk0085_456_1	chr18	11587851	11588316	+	0	NA	Intergenic	MER75|DNA|PiggyBac	-21475	NM_001282300	646000		NM_001282300	ENSG00000236396	SLC35G4	AMAC1L1|SLC35G4P	solute carrier family 35 member G4	protein-coding	0.006452	0.371245	
chunk0069_105_1	chr15	61607733	61608042	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-378584	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.009709	0.390323	
chunk0028_68_1	chr10	83652875	83653411	+	0	NA	Intergenic	L1MDa|LINE|L1	-486286	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.001866	0.363128	
chunk0043_5_1	chr12	12779509	12779986	+	0	NA	intron (NM_001130415, intron 1 of 1)	L1ME4c|LINE|L1	-5860	NM_030817	81575	Hs.23388	NM_030817	ENSG00000178878	APOLD1	VERGE	apolipoprotein L domain containing 1	protein-coding	0.006289	0.355649	
chunk0067_82_1	chr15	41714314	41714513	+	0	NA	intron (NM_001080541, intron 9 of 22)	intron (NM_001080541, intron 9 of 22)	22828	NR_030356	693211		NR_030356	ENSG00000207766	MIR626	MIRN626|hsa-mir-626	microRNA 626	ncRNA	0.010050	0.385000	
chunk0026_209_1	chr10	63934918	63935377	+	0	NA	Intergenic	Intergenic	413784	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.004357	0.373913	
chunk0026_454_1	chr10	71631448	71632076	+	0	NA	intron (NM_001171931, intron 11 of 24)	intron (NM_001171931, intron 11 of 24)	88059	NM_001164375	414152	Hs.568788	NM_001164375	ENSG00000214688	C10orf105	-	chromosome 10 open reading frame 105	protein-coding	0.006369	0.478537	354(AGGGACAGACTGTGCT,-,0.00),355(GGGACAGACTGTGCTT,+,0.00)
chunk0140_145_1	chr4	69286983	69287844	+	0	NA	intron (NM_001207004, intron 3 of 3)	intron (NM_001207004, intron 3 of 3)	6914	NM_001207004	54490	Hs.653154	NM_053039	ENSG00000135226	UGT2B28	-	UDP glucuronosyltransferase family 2 member B28	protein-coding	0.001161	0.379350	
chunk0196_44_1	chr8	101800157	101800545	+	0	NA	intron (NM_001040629, intron 3 of 6)	L1MEg|LINE|L1	-9140	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.000000	0.246787	
chunk0114_153_1	chr21	10427354	10427767	+	0	NA	intron (NM_001187, intron 3 of 4)	intron (NM_001187, intron 3 of 4)	14028	NM_182484	85316	Hs.545789	NM_182484		BAGE5	CT2.5	BAGE family member 5	protein-coding	0.019370	0.442029	
chunk0071_138_1	chr15	82263386	82263690	+	0	NA	promoter-TSS (NM_024580)	promoter-TSS (NM_024580)	727	NM_001008226	283726	Hs.459117	NM_001008226	ENSG00000188659	SAXO2	FAM154B	stabilizer of axonemal microtubules 2	protein-coding	0.009868	0.403279	
chunk0206_355_1	chr9	125694982	125695625	+	0	NA	intron (NM_001006618, intron 1 of 7)	intron (NM_001006618, intron 1 of 7)	11931	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.009331	0.333851	
chunk0025_350_1	chr10	58269096	58269308	+	0	NA	promoter-TSS (NM_018464)	promoter-TSS (NM_018464)	100	NM_018464	55847	Hs.370102	NM_018464	ENSG00000122873	CISD1	C10orf70|MDS029|ZCD1|mitoNEET	CDGSH iron sulfur domain 1	protein-coding	0.127358	0.638498	
chunk0118_233_1	chr22	32420674	32421258	+	0	NA	intron (NM_174932, intron 11 of 14)	MIRb|SINE|MIR	-8679	NM_014306	51493	Hs.474643	NM_014306	ENSG00000100220	RTCB	C22orf28|DJ149A16.6|FAAP|HSPC117	RNA 2',3'-cyclic phosphate and 5'-OH ligase	protein-coding	0.008562	0.372650	332(CAGCACATAATGTCCT,-,0.00),333(AGCACATAATGTCCTT,+,0.00),443(AGTGACAGCGTGTCCT,-,0.00),444(GTGACAGCGTGTCCTG,+,0.00)
chunk0035_303_1	chr11	47099393	47099592	+	0	NA	intron (NM_024113, intron 3 of 8)	intron (NM_024113, intron 3 of 8)	77633	NM_032389	84364	Hs.436204	NM_032389	ENSG00000149182	ARFGAP2	IRZ|NBLA10535|ZFP289|ZNF289	ADP ribosylation factor GTPase activating protein 2	protein-coding	0.005025	0.450000	
chunk0029_182_1	chr10	100909856	100910203	+	0	NA	Intergenic	Intergenic	-2540	NM_001136123	55719	Hs.447458	NM_018121	ENSG00000119906	SLF2	C10orf6|FAM178A	SMC5-SMC6 complex localization factor 2	protein-coding	0.002882	0.416667	
chunk0069_177_1	chr15	63053031	63053667	+	0	NA	intron (NM_001301289, intron 1 of 7)	intron (NM_001301289, intron 1 of 7)	4912	NM_001301289	7168	Hs.133892	NM_000366	ENSG00000140416	TPM1	C15orf13|CMD1Y|CMH3|HEL-S-265|HTM-alpha|LVNC9|TMSA	tropomyosin 1	protein-coding	0.011006	0.491366	329(GAGAACTGCCAGTTCC,-,0.00),330(AGAACTGCCAGTTCCA,+,0.00)
chunk0026_328_1	chr10	68297159	68297654	+	0	NA	intron (NM_022129, intron 2 of 9)	L2b|LINE|L2	-34605	NM_021644	3189	Hs.643472	NM_012207	ENSG00000096746	HNRNPH3	2H9|HNRPH3	heterogeneous nuclear ribonucleoprotein H3	protein-coding	0.006061	0.510081	
chunk0164_304_1	chr6	24925835	24926541	+	0	NA	intron (NM_001286446, intron 1 of 13)	intron (NM_001286446, intron 1 of 13)	9864	NM_001286445	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.004249	0.357850	
chunk0107_39_1	chr2	211174608	211175083	+	0	NA	Intergenic	Intergenic	557274	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.008421	0.392857	
chunk0204_219_1	chr9	97395064	97395335	+	0	NA	intron (NR_026847, intron 2 of 5)	MLT1B|LTR|ERVL-MaLR	1492	NR_026847	286359	Hs.132262	NM_182600		LOC286359	-	uncharacterized LOC286359	ncRNA	0.011070	0.481618	
chunk0016_382_1	chr1	202713128	202713507	+	0	NA	Intergenic	Intergenic	-2894	NM_177402	127833	Hs.25422	NM_177402	ENSG00000143858	SYT2	CMS7|MYSPC|SytII	synaptotagmin 2	protein-coding	0.010554	0.460526	
chunk0008_163_1	chr1	92784769	92785201	+	0	NA	intron (NM_001308248, intron 1 of 18)	CpG	7419	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.111111	0.713626	
chunk0019_128_1	chr1	225602520	225603386	+	0	NA	intron (NM_001008493, intron 1 of 14)	L1ME3A|LINE|L1	50190	NM_001008493	55740	Hs.497893	NM_018212	ENSG00000154380	ENAH	ENA|MENA|NDPP1	ENAH actin regulator	protein-coding	0.003464	0.305652	
chunk0169_22_1	chr6	96784700	96785314	+	0	NA	Intergenic	Intergenic	52470	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.006515	0.471545	
chunk0053_133_1	chr13	29868725	29868960	+	0	NA	Intergenic	Intergenic	-18159	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.021277	0.402542	175(TGGAACAGATTGTCTT,-,0.00),176(GGAACAGATTGTCTTT,+,0.00)
chunk0187_323_1	chr7	156614440	156615345	+	0	NA	Intergenic	Intergenic	-11697	NR_103858	100506380	Hs.647014	NM_032625	ENSG00000182648	LINC01006	C7orf13|MY040	long intergenic non-protein coding RNA 1006	ncRNA	0.020994	0.409492	
chunk0010_296_1	chr1	117627183	117627889	+	0	NA	3' UTR (NM_017709, exon 2 of 2)	3' UTR (NM_017709, exon 2 of 2)	21554	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.011331	0.425743	
chunk0167_187_1	chr6	64231789	64232390	+	0	NA	intron (NM_001142800, intron 30 of 42)	intron (NM_001142800, intron 30 of 42)	585563	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.006656	0.290698	
chunk0176_445_1	chr7	20019187	20019874	+	0	NA	intron (NR_110114, intron 3 of 5)	HAL1|LINE|L1	120896	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.004367	0.337209	
chunk0102_440_1	chr2	157849443	157849878	+	0	NA	intron (NM_001111067, intron 1 of 10)	MER99|DNA|hAT?	25451	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.006897	0.362385	
chunk0005_118_1	chr1	56780452	56780813	+	0	NA	intron (NM_001004303, intron 4 of 19)	intron (NM_001004303, intron 4 of 19)	39064	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.002770	0.439227	150(AAGCACTTACTGTACT,-,0.00),151(AGCACTTACTGTACTT,+,0.00)
chunk0089_146_1	chr18	59053187	59053879	+	0	NA	TTS (NR_024021)	TTS (NR_024021)	17854	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.007225	0.395382	
chunk0044_420_1	chr12	41924341	41924736	+	0	NA	Intergenic	Intergenic	220333	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.005063	0.401515	
chunk0080_233_1	chr17	30090029	30090333	+	0	NA	intron (NM_198529, intron 19 of 22)	L2a|LINE|L2	-26626	NM_032141	84081	Hs.462663	NM_032141	ENSG00000126653	NSRP1	CCDC55|HSPC095|NSrp70	nuclear speckle splicing regulatory protein 1	protein-coding	0.016447	0.495082	
chunk0125_138_1	chr3	66010737	66011060	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	27936	NM_015520	9223	Hs.476636	NM_004742	ENSG00000151276	MAGI1	AIP-3|AIP3|BAIAP1|BAP-1|BAP1|MAGI-1|MAGI-1b|Magi1d|TNRC19|WWP3	membrane associated guanylate kinase, WW and PDZ domain containing 1	protein-coding	0.006192	0.469136	
chunk0132_186_1	chr3	157089248	157089523	+	0	NA	promoter-TSS (NR_034008)	promoter-TSS (NR_034008)	-496	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.043636	0.568841	
chunk0065_60_1	chr15	22944819	22945100	+	0	NA	intron (NM_001287810, intron 4 of 31)	intron (NM_001287810, intron 4 of 31)	-27646	NM_001033028	23191	Hs.26704	NM_014608	ENSG00000273749	CYFIP1	P140SRA-1|SHYC|SRA-1|SRA1	cytoplasmic FMR1 interacting protein 1	protein-coding	0.028470	0.578014	
chunk0083_377_1	chr17	71192882	71193228	+	0	NA	intron (NR_104152, intron 1 of 3)	intron (NR_104152, intron 1 of 3)	9124	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.005780	0.423631	
chunk0171_350_1	chr6	130230583	130231065	+	0	NA	intron (NM_001258275, intron 2 of 13)	L3|LINE|CR1	-7870	NM_001017373	154075	Hs.440508	NM_152552	ENSG00000164483	SAMD3	-	sterile alpha motif domain containing 3	protein-coding	0.010373	0.416149	
chunk0120_430_1	chr3	13373944	13374303	+	0	NA	intron (NM_024923, intron 11 of 39)	(ACTCAC)n|Simple_repeat|Simple_repeat	46196	NM_024923	23225	Hs.475525	NM_024923	ENSG00000132182	NUP210	GP210|POM210	nucleoporin 210	protein-coding	0.022284	0.491667	
chunk0073_316_1	chr16	14202889	14203088	+	0	NA	intron (NM_001308142, intron 3 of 16)	intron (NM_001308142, intron 3 of 16)	-99300	NR_132983	100129781	Hs.190748	NR_132983		MIR193BHG	-	MIR193B host gene	ncRNA	0.000000	0.325000	
chunk0176_65_1	chr7	11229403	11229863	+	0	NA	Intergenic	L1ME4a|LINE|L1	255761	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.000000	0.281996	
chunk0014_292_1	chr1	180666144	180666429	+	0	NA	intron (NM_001135669, intron 1 of 13)	L1M4c|LINE|L1	34276	NM_001135669	9213	Hs.227656	NM_004736	ENSG00000143324	XPR1	IBGC6|SLC53A1|SYG1|X3	xenotropic and polytropic retrovirus receptor 1	protein-coding	0.014035	0.367133	
chunk0022_181_1	chr10	13185086	13185504	+	0	NA	intron (NM_182751, intron 8 of 19)	MER70B|LTR|ERVL	23741	NM_018518	55388	Hs.198363	NM_018518	ENSG00000065328	MCM10	CNA43|DNA43|PRO2249	minichromosome maintenance 10 replication initiation factor	protein-coding	0.007177	0.520286	255(TGGTACAGTCTGTCCA,-,0.00),256(GGTACAGTCTGTCCAA,+,0.00)
chunk0141_242_1	chr4	84998627	84999022	+	0	NA	intron (NR_015359, intron 2 of 3)	L2c|LINE|L2	32006	NR_015359	404201	Hs.46730	NM_205857	ENSG00000180769	WDFY3-AS2	C4orf12|FBI4|NCRNA00247	WDFY3 antisense RNA 2	ncRNA	0.000000	0.335859	
chunk0197_413_1	chr8	127321156	127321847	+	0	NA	intron (NR_117100, intron 5 of 5)	L1MEf|LINE|L1	76864	NR_117099	103021164	Hs.571531	NR_117099		CASC21	CARLO2|CARLo-2|LINC01244	cancer susceptibility 21	ncRNA	0.002894	0.413295	
chunk0096_17_1	chr2	26141749	26142018	+	0	NA	Intergenic	L1MC5|LINE|L1	-31208	NM_001168241	150946	Hs.187912	NM_001168241	ENSG00000157833	GAREM2	FAM59B|GAREML	GRB2 associated regulator of MAPK1 subtype 2	protein-coding	0.011152	0.377778	
chunk0063_275_1	chr14	84179990	84180359	+	0	NA	Intergenic	Intergenic	-1213705	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005420	0.335135	
chunk0061_259_1	chr14	61357206	61357405	+	0	NA	intron (NM_006255, intron 1 of 13)	intron (NM_006255, intron 1 of 13)	35862	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.015075	0.425000	
chunk0061_404_1	chr14	64749773	64750498	+	0	NA	exon (NM_001024858, exon 33 of 35)	exon (NM_001024858, exon 33 of 35)	35551	NR_107009	102465841		NR_107009	ENSG00000284269	MIR7855	hsa-mir-7855	microRNA 7855	ncRNA	0.006897	0.431129	361(CAGTACAGGTTGTTCC,-,0.00),362(AGTACAGGTTGTTCCA,+,0.00)
chunk0144_134_1	chr4	129697539	129697903	+	0	NA	Intergenic	Intergenic	73757	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.005495	0.419178	81(AGGAACATTCTGTGTT,-,0.00),82(GGAACATTCTGTGTTT,+,0.00)
chunk0208_248_1	chrX	20245266	20245623	+	0	NA	intron (NM_004586, intron 1 of 21)	intron (NM_004586, intron 1 of 21)	21188	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.008403	0.296089	
chunk0148_254_1	chr5	10250244	10250493	+	0	NA	promoter-TSS (NM_199133)	promoter-TSS (NM_199133)	-169	NM_001306156	22948	Hs.1600	NM_012073	ENSG00000150753	CCT5	CCT-epsilon|CCTE|HEL-S-69|PNAS-102|TCP-1-epsilon	chaperonin containing TCP1 subunit 5	protein-coding	0.068273	0.600000	
chunk0152_92_1	chr5	58234733	58235282	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-112666	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.001821	0.325455	
chunk0148_409_1	chr5	14929196	14929953	+	0	NA	Intergenic	MER21A|LTR|ERVL	-57796	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.006605	0.476253	
chunk0196_227_1	chr8	107608093	107608577	+	0	NA	Intergenic	L1MA7|LINE|L1	-110280	NM_001146	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.004132	0.325773	
chunk0146_62_1	chr4	155914779	155915359	+	0	NA	intron (NM_005651, intron 8 of 11)	intron (NM_005651, intron 8 of 11)	11376	NM_005651	6999	Hs.183671	NM_005651	ENSG00000151790	TDO2	HYPTRP|TDO|TO|TPH2|TRPO	tryptophan 2,3-dioxygenase	protein-coding	0.013793	0.337349	
chunk0027_442_1	chr10	81189816	81190242	+	0	NA	Intergenic	L1M5|LINE|L1	649210	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.004695	0.302108	
chunk0135_265_1	chr3	189123377	189124101	+	0	NA	Intergenic	Intergenic	-48235	NM_198485	285386	Hs.729544	NM_198485	ENSG00000188001	TPRG1	FAM79B	tumor protein p63 regulated 1	protein-coding	0.013812	0.409655	293(AGGAACATGTTGTCTT,-,0.00)
chunk0042_32_1	chr12	1519204	1519506	+	0	NA	Intergenic	Intergenic	18864	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.019868	0.537954	
chunk0040_92_1	chr11	111653601	111654081	+	0	NA	intron (NM_015191, intron 3 of 14)	intron (NM_015191, intron 3 of 14)	51450	NM_015191	23235	Hs.269128	NM_015191	ENSG00000170145	SIK2	LOH11CR1I|QIK|SIK-2|SNF1LK2	salt inducible kinase 2	protein-coding	0.006250	0.370062	
chunk0197_406_1	chr8	127215126	127215721	+	0	NA	intron (NR_108049, intron 1 of 1)	intron (NR_108049, intron 1 of 1)	3845	NR_108049	100507056	Hs.343864	NR_108049		CCAT1	CARLO5|CARLo-5|onco-lncRNA-40	colon cancer associated transcript 1	ncRNA	0.003361	0.347315	102(AAATACAGGATGTCCC,-,0.00),103(AATACAGGATGTCCCC,+,0.00)
chunk0098_39_1	chr2	66212834	66213058	+	0	NA	Intergenic	Intergenic	145382	NR_039938	100616464		NR_039938	ENSG00000264525	MIR4778	-	microRNA 4778	ncRNA	0.000000	0.364444	
chunk0197_163_1	chr8	120538365	120538851	+	0	NA	3' UTR (NM_021021, exon 7 of 7)	3' UTR (NM_021021, exon 7 of 7)	-93201	NM_014078	28998	Hs.333823	NM_014078	ENSG00000172172	MRPL13	L13|L13A|L13mt|RPL13|RPML13	mitochondrial ribosomal protein L13	protein-coding	0.016461	0.435318	189(CTGCACATGCTGTTCT,-,0.00),190(TGCACATGCTGTTCTA,+,0.00)
chunk0101_17_1	chr2	121502338	121502614	+	0	NA	intron (NM_015282, intron 8 of 38)	L2a|LINE|L2	-28404	NR_023343	100151683	Hs.689638	NR_023343	ENSG00000264229	RNU4ATAC	MOPD1|RFMN|RNU4ATAC1|TALS|U4ATAC	RNA, U4atac small nuclear (U12-dependent splicing)	snRNA	0.007246	0.458484	35(GGGCACAGAGCGTTCC,-,0.00),36(GGCACAGAGCGTTCCC,+,0.00)
chunk0160_35_1	chr5	149471473	149472308	+	0	NA	Intergenic	Intergenic	41244	NR_029686	406937		NR_029686	ENSG00000276365	MIR145	MIRN145|miR-145|miRNA145	microRNA 145	ncRNA	0.014371	0.549043	
chunk0092_355_1	chr19	35485572	35485771	+	0	NA	Intergenic	MER102b|DNA|hAT-Charlie	4860	NM_001244847	388533	Hs.112457	NM_207392	ENSG00000188508	KRTDAP	KDAP|UNQ467	keratinocyte differentiation associated protein	protein-coding	0.015075	0.445000	
chunk0104_34_1	chr2	170949502	170949891	+	0	NA	exon (NM_015530, exon 3 of 10)	exon (NM_015530, exon 3 of 10)	21170	NM_015530	26003	Hs.431317	NM_015530	ENSG00000115806	GORASP2	GOLPH6|GRASP55|GRS2|p59	golgi reassembly stacking protein 2	protein-coding	0.015424	0.392308	
chunk0184_338_1	chr7	120708550	120709181	+	0	NA	intron (NM_012281, intron 1 of 5)	L2a|LINE|L2	149258	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.003170	0.335443	
chunk0180_62_1	chr7	54823984	54824643	+	0	NA	Intergenic	L1ME2|LINE|L1	65000	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.003035	0.395455	
chunk0004_91_1	chr1	43792417	43792927	+	0	NA	intron (NM_174963, intron 3 of 12)	intron (NM_174963, intron 3 of 12)	-45950	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.001961	0.502935	
chunk0211_339_1	chrX	124307321	124307707	+	0	NA	Intergenic	L2c|LINE|L2	-38768	NM_001114937	4068	Hs.349094	NM_002351	ENSG00000183918	SH2D1A	DSHP|EBVS|IMD5|LYP|MTCP1|SAP|SAP/SH2D1A|XLP|XLPD|XLPD1	SH2 domain containing 1A	protein-coding	0.000000	0.408269	320(GGGAACAGCATGTACA,-,0.00),321(GGAACAGCATGTACAA,+,0.00)
chunk0073_303_1	chr16	14109316	14109762	+	0	NA	intron (NM_001308142, intron 2 of 16)	intron (NM_001308142, intron 2 of 16)	38225	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.013453	0.348993	
chunk0071_311_1	chr15	86199889	86200130	+	0	NA	intron (NM_152336, intron 4 of 23)	intron (NM_152336, intron 4 of 23)	57998	NM_152336	123624	Hs.31795	NM_152336	ENSG00000273540	AGBL1	CCP4|FECD8	ATP/GTP binding protein like 1	protein-coding	0.008299	0.388430	
chunk0012_297_1	chr1	162165469	162165793	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	8524	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.009259	0.458462	
chunk0078_395_1	chr16	88453817	88454204	+	0	NA	intron (NM_153813, intron 1 of 9)	CpG-10141	404	NM_153813	161882	Hs.632218	NM_153813	ENSG00000179588	ZFPM1	FOG|FOG1|ZC2HC11A|ZNF408|ZNF89A	zinc finger protein, FOG family member 1	protein-coding	0.093023	0.654639	
chunk0064_171_1	chr14	92347983	92348494	+	0	NA	intron (NM_153646, intron 2 of 16)	MIRb|SINE|MIR	24430	NM_153646	123041	Hs.385530	NM_153646	ENSG00000140090	SLC24A4	AI2A5|NCKX4|SHEP6|SLC24A2	solute carrier family 24 member 4	protein-coding	0.011742	0.431641	
chunk0018_62_1	chr1	216816289	216816488	+	0	NA	intron (NM_001243513, intron 1 of 7)	L1MA8|LINE|L1	-11021	NM_001243514	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.000000	0.285000	
chunk0016_409_1	chr1	203297391	203297590	+	0	NA	Intergenic	Intergenic	7835	NR_034150	730227	Hs.293928	NR_034150	ENSG00000233791	LINC01136	-	long intergenic non-protein coding RNA 1136	ncRNA	0.020101	0.485000	
chunk0003_284_1	chr1	37461475	37462034	+	0	NA	intron (NR_038842, intron 1 of 2)	MLT1C|LTR|ERVL-MaLR	12689	NR_038842	728431	Hs.380738	NR_038842	ENSG00000233621	LINC01137	-	long intergenic non-protein coding RNA 1137	ncRNA	0.012522	0.423214	
chunk0102_388_1	chr2	154708849	154709580	+	0	NA	intron (NM_001260508, intron 1 of 1)	intron (NM_001260508, intron 1 of 1)	10633	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.004104	0.336066	448(ATGCACACTCAGTTCC,-,0.00),449(TGCACACTCAGTTCCA,+,0.00)
chunk0051_308_1	chr12	119354282	119354582	+	0	NA	intron (NM_178499, intron 1 of 13)	intron (NM_178499, intron 1 of 13)	19720	NM_178499	160777	Hs.98188	NM_178499	ENSG00000183273	CCDC60	-	coiled-coil domain containing 60	protein-coding	0.013333	0.395349	
chunk0005_331_1	chr1	61120906	61121360	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	38825	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.004405	0.323077	204(GAGGACAGCGTGTGAC,-,0.00),205(AGGACAGCGTGTGACT,+,0.00)
chunk0001_227_1	chr1	8083939	8084700	+	0	NA	Intergenic	Intergenic	-57986	NM_018948	54206	Hs.605445	NM_018948	ENSG00000116285	ERRFI1	GENE-33|MIG-6|MIG6|RALT	ERBB receptor feedback inhibitor 1	protein-coding	0.010512	0.392388	
chunk0061_341_1	chr14	63467850	63468101	+	0	NA	intron (NM_001282180, intron 2 of 13)	MIR|SINE|MIR	40263	NM_001282182	5529	Hs.334868	NM_006246	ENSG00000154001	PPP2R5E	B56E|B56epsilon	protein phosphatase 2 regulatory subunit B'epsilon	protein-coding	0.003984	0.396825	
chunk0179_176_1	chr7	46927228	46927690	+	0	NA	Intergenic	Intergenic	654685	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.004329	0.382289	
chunk0072_35_1	chr16	751781	751990	+	0	NA	Intergenic	Intergenic	-8880	NM_005823	10232	Hs.408488	NM_005823	ENSG00000102854	MSLN	MPF|SMRP	mesothelin	protein-coding	0.081340	0.685714	
chunk0151_212_1	chr5	50796360	50796641	+	0	NA	intron (NM_024615, intron 12 of 25)	intron (NM_024615, intron 12 of 25)	129562	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.003559	0.340426	
chunk0069_416_1	chr15	68028372	68028980	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-25558	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.008224	0.418719	
chunk0035_316_1	chr11	47355424	47355623	+	0	NA	exon (NM_003120, exon 5 of 5)	exon (NM_003120, exon 5 of 5)	-2821	NM_000256	4607	Hs.524906	NM_000256	ENSG00000134571	MYBPC3	CMD1MM|CMH4|FHC|LVNC10|MYBP-C	myosin binding protein C, cardiac	protein-coding	0.060302	0.665000	
chunk0130_187_1	chr3	133526972	133527641	+	0	NA	Intergenic	Intergenic	-46284	NM_017548	55573	Hs.518265	NM_017548	ENSG00000091527	CDV3	H41	CDV3 homolog	protein-coding	0.007474	0.438806	
chunk0202_17_1	chr9	70438522	70438927	+	0	NA	Intergenic	L2b|LINE|L2	-24067	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.004938	0.490148	224(GGGAACAGCAAGTACA,-,0.00)
chunk0046_233_1	chr12	60189727	60190126	+	0	NA	Intergenic	L1MEg|LINE|L1	500589	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.005013	0.372500	
chunk0008_413_1	chr1	98344227	98344942	+	0	NA	Intergenic	MER127|DNA|TcMar-Tigger	133873	NR_046088	729987	Hs.683961	NR_046088	ENSG00000226053	LINC01776	-	long intergenic non-protein coding RNA 1776	ncRNA	0.002797	0.321229	320(AAGTACAAAATGTACT,-,0.00),321(AGTACAAAATGTACTC,+,0.00)
chunk0062_70_1	chr14	67600123	67600322	+	0	NA	promoter-TSS (NM_004569)	promoter-TSS (NM_004569)	78	NM_004569	5283	Hs.553497	NM_004569	ENSG00000100564	PIGH	GPI-H	phosphatidylinositol glycan anchor biosynthesis class H	protein-coding	0.150754	0.750000	
chunk0001_44_1	chr1	1833571	1833791	+	0	NA	intron (NM_001282539, intron 1 of 10)	intron (NM_001282539, intron 1 of 10)	-53612	NM_001198994	65220	Hs.654792	NM_023018	ENSG00000008130	NADK	dJ283E3.1	NAD kinase	protein-coding	0.022727	0.506787	
chunk0088_230_1	chr18	48418450	48419074	+	0	NA	Intergenic	Intergenic	-120294	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.009615	0.560000	403(TGGAACACCGTGAGCT,-,0.00),404(GGAACACCGTGAGCTC,+,0.00)
chunk0112_339_1	chr20	45057048	45057284	+	0	NA	intron (NM_006282, intron 10 of 10)	LTR41B|LTR|ERVL	43946	NM_002251	3787	Hs.117780	NM_002251	ENSG00000124134	KCNS1	Kv9.1	potassium voltage-gated channel modifier subfamily S member 1	protein-coding	0.016949	0.544304	186(TAGGACAGCCTCTTCC,-,0.00),187(AGGACAGCCTCTTCCT,+,0.00)
chunk0155_291_1	chr5	96222099	96222470	+	0	NA	intron (NR_130776, intron 1 of 4)	L1MA4A|LINE|L1	143146	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.002695	0.319892	
chunk0081_438_1	chr17	49001207	49001406	+	0	NA	intron (NM_001160423, intron 2 of 12)	intron (NM_001160423, intron 2 of 12)	3894	NM_001160423	10642	Hs.144936	NM_006546	ENSG00000159217	IGF2BP1	CRD-BP|CRDBP|IMP-1|IMP1|VICKZ1|ZBP1	insulin like growth factor 2 mRNA binding protein 1	protein-coding	0.005025	0.305000	
chunk0184_461_1	chr7	123622648	123622858	+	0	NA	intron (NR_111922, intron 2 of 4)	intron (NR_111922, intron 2 of 4)	2204	NR_111922	102724555	Hs.83916	NR_111922	ENSG00000230442	LOC102724555	-	uncharacterized LOC102724555	ncRNA	0.000000	0.364929	
chunk0039_33_1	chr11	95795556	95796052	+	0	NA	intron (NM_001243776, intron 2 of 11)	intron (NM_001243776, intron 2 of 11)	5343	NM_014679	9702	Hs.101014	NM_014679	ENSG00000166037	CEP57	MVA2|PIG8|TSP57	centrosomal protein 57	protein-coding	0.006048	0.329980	229(CTGTACATCATGTTCC,-,0.00),230(TGTACATCATGTTCCT,+,0.00)
chunk0159_25_1	chr5	136606898	136607253	+	0	NA	Intergenic	L1MA6|LINE|L1	-241599	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.002817	0.511236	
chunk0174_411_1	chr6	165647688	165648077	+	0	NA	intron (NM_006661, intron 1 of 22)	MIR|SINE|MIR	14218	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.025707	0.451282	
chunk0042_465_1	chr12	12611476	12612288	+	0	NA	promoter-TSS (NM_001310)	promoter-TSS (NM_001310)	49	NM_001310	1389	Hs.591156	NM_001310	ENSG00000111269	CREBL2	-	cAMP responsive element binding protein like 2	protein-coding	0.064039	0.603936	
chunk0193_26_1	chr8	70951120	70951873	+	0	NA	Intergenic	Intergenic	282049	NM_001287260	389668	Hs.458938	NM_001011720	ENSG00000221947	XKR9	XRG9	XK related 9	protein-coding	0.002656	0.469496	
chunk0170_70_1	chr6	109796644	109796981	+	0	NA	exon (NM_014845, exon 22 of 23)	exon (NM_014845, exon 22 of 23)	-43596	NR_106988									0.000000	0.355030	
chunk0110_230_1	chr20	15987755	15988197	+	0	NA	intron (NM_001033087, intron 11 of 13)	intron (NM_001033087, intron 11 of 13)	-2094	NR_130924	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.000000	0.282167	222(TAGAACACAGTGATCA,-,0.00),223(AGAACACAGTGATCAA,+,0.00)
chunk0079_446_1	chr17	20201890	20202543	+	0	NA	intron (NM_001033554, intron 1 of 5)	Tigger2b_Pri|DNA|TcMar-Tigger	46222	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.004594	0.370031	276(TAGTACATACAGTACT,-,0.00),277(AGTACATACAGTACTC,+,0.00)
chunk0163_317_1	chr6	14758400	14758948	+	0	NA	Intergenic	Intergenic	-473220	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.010949	0.469945	
chunk0201_388_1	chr9	69023131	69023680	+	0	NA	Intergenic	Intergenic	-9282	NM_002732	5568	Hs.158029	NM_002732	ENSG00000165059	PRKACG	BDPLT19|KAPG|PKACg	protein kinase cAMP-activated catalytic subunit gamma	protein-coding	0.010929	0.423636	
chunk0054_56_1	chr13	41720410	41721307	+	0	NA	intron (NM_015058, intron 25 of 44)	intron (NM_015058, intron 25 of 44)	-152463	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.003344	0.345212	458(GAGTACACATTGTACA,-,0.00),459(AGTACACATTGTACAT,+,0.00)
chunk0093_126_1	chr19	45524883	45525140	+	0	NA	intron (NM_003370, intron 11 of 12)	intron (NM_003370, intron 11 of 12)	17581	NM_003370	7408	Hs.515469	NM_003370	ENSG00000125753	VASP	-	vasodilator stimulated phosphoprotein	protein-coding	0.023346	0.523256	83(TGGTACTGGATGTTCT,-,0.00),84(GGTACTGGATGTTCTC,+,0.00)
chunk0030_82_1	chr10	112330671	112330909	+	0	NA	intron (NR_028134, intron 10 of 18)	MER41E|LTR|ERV1	25805	NR_028134	390003	Hs.534691	NR_028134	ENSG00000243316	GUCY2GP	GUCY2G	guanylate cyclase 2G, pseudogene	pseudo	0.000000	0.364017	
chunk0105_50_1	chr2	183024793	183025003	+	0	NA	intron (NM_013436, intron 1 of 30)	intron (NM_013436, intron 1 of 30)	13960	NM_205842	10787	Hs.603732	NM_013436	ENSG00000061676	NCKAP1	HEM2|NAP1|NAP125|p125Nap1	NCK associated protein 1	protein-coding	0.009524	0.417062	
chunk0075_392_1	chr16	56808897	56809139	+	0	NA	intron (NM_014669, intron 5 of 21)	L1ME4b|LINE|L1	25517	NM_001242796	9688	Hs.276878	NM_014669	ENSG00000102900	NUP93	NIC96	nucleoporin 93	protein-coding	0.008264	0.399177	100(GAGACTGTATGTTCTT,+,0.00)
chunk0124_93_1	chr3	53523346	53523810	+	0	NA	intron (NM_000720, intron 3 of 48)	intron (NM_000720, intron 3 of 48)	28529	NM_001128840	776	Hs.476358	NM_000720	ENSG00000157388	CACNA1D	CACH3|CACN4|CACNL1A2|CCHL1A2|Cav1.3|PASNA|SANDD	calcium voltage-gated channel subunit alpha1 D	protein-coding	0.008621	0.425806	
chunk0057_85_1	chr13	98621198	98621662	+	0	NA	Intergenic	Intergenic	-44279	NM_001032296	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.008621	0.406452	
chunk0100_451_1	chr2	121000876	121001521	+	0	NA	Intergenic	MIR|SINE|MIR	203907	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.009302	0.472136	
chunk0183_215_1	chr7	106571030	106571229	+	0	NA	Intergenic	Intergenic	90059	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.015075	0.540000	30(GAACACAGCCTGTCCT,-,0.00),31(AACACAGCCTGTCCTC,+,0.00),54(AGGAACTCAGTGTCTT,-,0.00)
chunk0209_82_1	chrX	38602413	38602673	+	0	NA	intron (NM_004615, intron 1 of 7)	L1M|LINE|L1	41065	NM_004615	7102	Hs.441664	NM_004615	ENSG00000156298	TSPAN7	A15|CCG-B7|CD231|DXS1692E|MRX58|MXS1|TALLA-1|TM4SF2|TM4SF2b	tetraspanin 7	protein-coding	0.000000	0.287356	
chunk0098_220_1	chr2	73712988	73713213	+	0	NA	Intergenic	L1ME4a|LINE|L1	-11760	NR_132338	51471	Hs.278983	NM_016347	ENSG00000204872	NAT8B	CML2|Hcml2|NAT8BP	N-acetyltransferase 8B (putative, gene/pseudogene)	protein-coding	0.004444	0.402655	
chunk0128_313_1	chr3	111726483	111727349	+	0	NA	intron (NM_153268, intron 3 of 3)	intron (NM_153268, intron 3 of 3)	-5564	NM_001134437	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.004619	0.328720	
chunk0158_293_1	chr5	132215240	132215646	+	0	NA	intron (NM_001017973, intron 4 of 14)	intron (NM_001017973, intron 4 of 14)	2475	NR_106888	102465498		NR_106888	ENSG00000283678	MIR6830	hsa-mir-6830	microRNA 6830	ncRNA	0.014778	0.567568	196(CAGAACAGCCTGTCCC,-,0.00),197(AGAACAGCCTGTCCCG,+,0.00)
chunk0091_354_1	chr19	15280101	15280359	+	0	NA	intron (NM_014299, intron 1 of 11)	intron (NM_014299, intron 1 of 11)	221	NM_014299	23476	Hs.187763	NM_014299	ENSG00000141867	BRD4	CAP|HUNK1|HUNKI|MCAP	bromodomain containing 4	protein-coding	0.011628	0.536680	113(TGGAACAGTGTGTGCT,-,0.00),114(GGAACAGTGTGTGCTT,+,0.00)
chunk0207_403_1	chr9	136943415	136943614	+	0	NA	intron (NM_018998, intron 2 of 8)	CpG-29168	1240	NM_018998	54461	Hs.522507	NM_018998	ENSG00000159069	FBXW5	Fbw5	F-box and WD repeat domain containing 5	protein-coding	0.065327	0.680000	
chunk0121_34_1	chr3	15223725	15223924	+	0	NA	intron (NM_014296, intron 6 of 20)	L2b|LINE|L2	17598	NM_014296	23473	Hs.595234	NM_014296	ENSG00000131375	CAPN7	CALPAIN7|PALBH	calpain 7	protein-coding	0.005025	0.365000	
chunk0207_166_1	chr9	130200064	130200263	+	0	NA	promoter-TSS (NM_001128826)	promoter-TSS (NM_001128826)	-430	NM_001128826	23413	Hs.642946	NM_014286	ENSG00000107130	NCS1	FLUP|FREQ	neuronal calcium sensor 1	protein-coding	0.025126	0.545000	
chunk0207_177_1	chr9	130538928	130539127	+	0	NA	Intergenic	MIRb|SINE|MIR	40467	NR_027440	100272217	Hs.601255	NR_027440		LOC100272217	-	uncharacterized LOC100272217	ncRNA	0.020101	0.510000	
chunk0005_411_1	chr1	62600613	62601302	+	0	NA	intron (NM_014495, intron 2 of 6)	intron (NM_014495, intron 2 of 6)	3470	NM_014495	27329	Hs.209153	NM_014495	ENSG00000132855	ANGPTL3	ANG-5|ANGPT5|ANL3|FHBL2	angiopoietin like 3	protein-coding	0.002903	0.301449	375(AAAGACAAACTGTACT,-,0.00),376(AAGACAAACTGTACTT,+,0.00)
chunk0049_106_1	chr12	91001209	91001777	+	0	NA	intron (NM_004950, intron 2 of 6)	intron (NM_004950, intron 2 of 6)	3533	NM_004950	1833	Hs.435680	NM_004950	ENSG00000083782	EPYC	DSPG3|PGLB|Pg-Lb|SLRR3B	epiphycan	protein-coding	0.005282	0.302285	
chunk0018_105_1	chr1	218164009	218164534	+	0	NA	Intergenic	Intergenic	120766	NR_110794	101929631	Hs.407614	NR_110794	ENSG00000232100	LINC01653	-	long intergenic non-protein coding RNA 1653	ncRNA	0.051429	0.496198	
chunk0166_71_1	chr6	43053260	43053459	+	0	NA	TTS (NM_015950)	TTS (NM_015950)	586	NM_001168370	9820	Hs.520136	NM_014780	ENSG00000044090	CUL7	3M1|CUL-7|KIAA0076|dJ20C7.5	cullin 7	protein-coding	0.050251	0.645000	
chunk0098_342_1	chr2	77238204	77238944	+	0	NA	intron (NM_001282924, intron 3 of 3)	L1MB3|LINE|L1	252609	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.005405	0.334683	
chunk0074_50_1	chr16	20826252	20826578	+	0	NA	intron (NM_001199053, intron 8 of 19)	intron (NM_001199053, intron 8 of 19)	-19942	NM_001142725	112479	Hs.248437	NM_080663	ENSG00000196678	ERI2	EXOD1|ZGRF5	ERI1 exoribonuclease family member 2	protein-coding	0.009202	0.385321	
chunk0019_421_1	chr1	230840133	230840815	+	0	NA	intron (NM_001136495, intron 3 of 3)	AluJb|SINE|Alu	15562	NM_001136495	84886	Hs.520494	NM_032800	ENSG00000119280	C1orf198	-	chromosome 1 open reading frame 198	protein-coding	0.013196	0.450952	
chunk0130_356_1	chr3	138853854	138854153	+	0	NA	Intergenic	L2a|LINE|L2	90017	NR_121649	103344930	Hs.195033	NR_121649	ENSG00000244578	LINC01391	-	long intergenic non-protein coding RNA 1391	ncRNA	0.006689	0.413333	
chunk0180_105_1	chr7	55325357	55325752	+	0	NA	Intergenic	Intergenic	-39894	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.010127	0.489899	
chunk0038_444_1	chr11	94746571	94747113	+	0	NA	Intergenic	L2b|LINE|L2	-21500	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.005535	0.419890	
chunk0155_67_1	chr5	91609074	91609806	+	0	NA	Intergenic	Intergenic	-226108	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.004098	0.336971	
chunk0211_419_1	chrX	128977442	128977884	+	0	NA	Intergenic	Intergenic	545842	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.000000	0.401806	253(TGGGACATGATGTACC,-,0.00),254(GGGACATGATGTACCC,+,0.00)
chunk0143_373_1	chr4	122558306	122558683	+	0	NA	Intergenic	Intergenic	-60489	NR_104126	100996941	Hs.439487	NR_104126	ENSG00000227145	IL21-AS1	-	IL21 antisense RNA 1	ncRNA	0.007958	0.386243	171(TGCACACCAAGTTCTC,+,0.00)
chunk0153_205_1	chr5	71862601	71863071	+	0	NA	Intergenic	Intergenic	143673	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.002128	0.471338	
chunk0184_418_1	chr7	122708608	122709269	+	0	NA	intron (NM_017954, intron 2 of 29)	intron (NM_017954, intron 2 of 29)	-5971	NM_198085	378925	Hs.675191	NM_198085	ENSG00000235631	RNF148	-	ring finger protein 148	protein-coding	0.006051	0.345921	
chunk0202_93_1	chr9	72297317	72297909	+	0	NA	Intergenic	Intergenic	-7823	NR_110952	100507540	Hs.54957	NR_110952	ENSG00000225434	LINC01504	-	long intergenic non-protein coding RNA 1504	ncRNA	0.006757	0.386172	
chunk0176_74_1	chr7	11295026	11295305	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	321293	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.010753	0.464286	
chunk0200_33_1	chr9	15060133	15060595	+	0	NA	Intergenic	Intergenic	67037	NR_003920	389705	Hs.431257	NR_003920		LOC389705	-	histone PARylation factor 1 pseudogene	pseudo	0.004329	0.321814	
chunk0083_136_1	chr17	65609773	65610243	+	0	NA	Intergenic	Intergenic	-48386	NM_004655	8313	Hs.156527	NM_004655	ENSG00000168646	AXIN2	AXIL|ODCRCS	axin 2	protein-coding	0.004255	0.456476	272(AAACACACACTGTTCC,-,0.00),273(AACACACACTGTTCCC,+,0.00)
chunk0040_399_1	chr11	120467675	120468078	+	0	NA	intron (NM_001198665, intron 28 of 39)	MER58A|DNA|hAT-Charlie	-43870	NM_014619	2900	Hs.538738	NM_014619	ENSG00000149403	GRIK4	EAA1|GRIK|GluK4|KA1	glutamate ionotropic receptor kainate type subunit 4	protein-coding	0.014888	0.403465	
chunk0020_351_1	chr1	239434285	239434641	+	0	NA	Intergenic	L2c|LINE|L2	-194610	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.011236	0.403361	
chunk0104_392_1	chr2	180374586	180375693	+	0	NA	Intergenic	Charlie16a|DNA|hAT-Charlie	-316965	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.003613	0.346570	
chunk0024_227_1	chr10	38028809	38029292	+	0	NA	intron (NM_001278175, intron 5 of 5)	L1MB7|LINE|L1	18400	NM_006954	7581	Hs.435774	NM_006954	ENSG00000189180	ZNF33A	KOX2|KOX31|KOX5|NF11A|ZNF11|ZNF11A|ZNF33|ZZAPK	zinc finger protein 33A	protein-coding	0.008282	0.320248	
chunk0045_66_1	chr12	45617158	45617561	+	0	NA	Intergenic	Intergenic	110562	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.000000	0.376238	267(GGAACAGAGAGTTTCT,+,0.00)
chunk0188_449_1	chr8	19355230	19355653	+	0	NA	intron (NM_001174159, intron 4 of 9)	intron (NM_001174159, intron 4 of 9)	41465	NM_001174159	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.009456	0.386792	138(CAGTTCACTCTGTTCC,-,0.00),139(AGTTCACTCTGTTCCC,+,0.00)
chunk0131_1_1	chr3	141623328	141623614	+	0	NA	Intergenic	MER53|DNA|hAT	-114738	NM_014245	9616	Hs.134623	NM_014245	ENSG00000114125	RNF7	CKBBP1|ROC2|SAG|rbx2	ring finger protein 7	protein-coding	0.017483	0.501742	
chunk0036_183_1	chr11	62805237	62805514	+	0	NA	5' UTR (NM_001081491, exon 1 of 20)	5' UTR (NM_001081491, exon 1 of 20)	117	NM_001081491	10482	Hs.523739	NM_006362	ENSG00000162231	NXF1	MEX67|TAP	nuclear RNA export factor 1	protein-coding	0.119134	0.687050	
chunk0194_328_1	chr8	88871382	88872000	+	0	NA	Intergenic	L1MD2|LINE|L1	-544203	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.003236	0.347334	
chunk0140_237_1	chr4	71247830	71248095	+	0	NA	intron (NM_001098484, intron 2 of 25)	intron (NM_001098484, intron 2 of 25)	60676	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.003774	0.503759	
chunk0100_396_1	chr2	119266304	119266882	+	0	NA	TTS (NM_182915)	TTS (NM_182915)	-17522	NR_046721	100874111	Hs.704682	NR_046721	ENSG00000229867	STEAP3-AS1	-	STEAP3 antisense RNA 1	ncRNA	0.008651	0.442142	
chunk0015_102_1	chr1	185137340	185137777	+	0	NA	intron (NM_030934, intron 10 of 14)	intron (NM_030934, intron 10 of 14)	19426	NM_030934	81627	Hs.107149	NM_030934	ENSG00000121486	TRMT1L	C1orf25|MST070|MSTP070|TRM1L|bG120K12.3	tRNA methyltransferase 1 like	protein-coding	0.006865	0.347032	
chunk0167_198_1	chr6	64542133	64542411	+	0	NA	intron (NM_001142800, intron 26 of 42)	intron (NM_001142800, intron 26 of 42)	-759146	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.000000	0.297491	
chunk0036_225_1	chr11	63869314	63869647	+	0	NA	intron (NM_001039469, intron 1 of 18)	intron (NM_001039469, intron 1 of 18)	-19035	NM_017490	2011	Hs.567261	NM_004954	ENSG00000072518	MARK2	EMK-1|EMK1|PAR-1|Par-1b|Par1b	microtubule affinity regulating kinase 2	protein-coding	0.015015	0.550898	74(AGGAACTAGGTGTGCC,-,0.00),75(GGAACTAGGTGTGCCA,+,0.00)
chunk0047_327_1	chr12	74364785	74364984	+	0	NA	Intergenic	L1PA17|LINE|L1	-72253	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.005025	0.515000	
chunk0194_209_1	chr8	85876018	85876590	+	0	NA	Intergenic	Intergenic	-48362	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.001748	0.363002	
chunk0054_232_1	chr13	45610431	45610788	+	0	NA	intron (NM_182542, intron 1 of 14)	Tigger3a|DNA|TcMar-Tigger	5130	NM_182542	220081	Hs.668747	NM_182542	ENSG00000165837	ERICH6B	FAM194B	glutamate rich 6B	protein-coding	0.005602	0.405028	152(ATCACAGCGTGTGCTC,+,0.00)
chunk0194_454_1	chr8	92693091	92693765	+	0	NA	Intergenic	Intergenic	-37934	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.002967	0.306667	295(ATACACAGACTGTTCT,-,0.00),296(TACACAGACTGTTCTT,+,0.00)
chunk0024_44_1	chr10	33632358	33632823	+	0	NA	Intergenic	Intergenic	140090	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.002151	0.396996	253(GAGAAGAGACTGTTCC,-,0.00),254(AGAAGAGACTGTTCCC,+,0.00)
chunk0175_91_1	chr7	2717364	2717804	+	0	NA	Intergenic	Intergenic	29382	NM_001284355	155185	Hs.42221	NM_133463	ENSG00000174945	AMZ1	-	archaelysin family metallopeptidase 1	protein-coding	0.040909	0.555556	
chunk0185_96_1	chr7	125527597	125528275	+	0	NA	Intergenic	Intergenic	-263645	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.007375	0.259205	
chunk0053_363_1	chr13	35270614	35270813	+	0	NA	intron (NM_015678, intron 34 of 57)	L1P2|LINE|L1	205982	NM_005584	4081	Hs.584776	NM_005584	ENSG00000180660	MAB21L1	CAGR1|Nbla00126	mab-21 like 1	protein-coding	0.010050	0.575000	
chunk0134_352_1	chr3	182605773	182606109	+	0	NA	Intergenic	L1MC3|LINE|L1	-119579	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.005952	0.370920	
chunk0058_152_1	chr14	23168639	23168893	+	0	NA	intron (NM_012244, intron 1 of 10)	intron (NM_012244, intron 1 of 10)	-13308	NM_001267036	23428	Hs.596643	NM_012244	ENSG00000092068	SLC7A8	LAT2|LPI-PC1	solute carrier family 7 member 8	protein-coding	0.007874	0.454902	
chunk0012_422_1	chr1	164601745	164602700	+	0	NA	intron (NM_002585, intron 2 of 8)	intron (NM_002585, intron 2 of 8)	42862	NM_001204963	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.006283	0.464435	
chunk0077_357_1	chr16	84048352	84048740	+	0	NA	Intergenic	L1MB7|LINE|L1	-6389	NM_001080442	146167		NM_001080442	ENSG00000166558	SLC38A8	FVH2	solute carrier family 38 member 8	protein-coding	0.012887	0.501285	
chunk0051_144_1	chr12	115752206	115752499	+	0	NA	Intergenic	Intergenic	396302	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.006826	0.404762	
chunk0035_436_1	chr11	57438712	57439123	+	0	NA	Intergenic	Intergenic	-11337	NM_017611	29015	Hs.99962	NM_014096	ENSG00000134802	SLC43A3	EEG1|ENBT1|FOAP-13|PRO1659|SEEEG-1	solute carrier family 43 member 3	protein-coding	0.019465	0.529126	
chunk0113_252_1	chr20	54999004	54999617	+	0	NA	Intergenic	Intergenic	-423733	NR_110629	102723578	Hs.446269	NR_110629	ENSG00000235166	LINC01440	-	long intergenic non-protein coding RNA 1440	ncRNA	0.009788	0.377850	
chunk0017_29_1	chr1	204769722	204770229	+	0	NA	Intergenic	Intergenic	-58679	NM_001005389	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.011834	0.454724	
chunk0138_174_1	chr4	37891731	37891958	+	0	NA	intron (NM_015173, intron 1 of 19)	intron (NM_015173, intron 1 of 19)	760	NM_015173	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.022026	0.434211	77(GGGTACATCCTGTACC,-,0.00),78(GGTACATCCTGTACCA,+,0.00)
chunk0010_449_1	chr1	121442809	121443512	+	0	NA	Intergenic	Intergenic	-45255	NR_104189	100873165	Hs.568525	NR_104189	ENSG00000230806	SRGAP2-AS1	-	SRGAP2 antisense RNA 1	ncRNA	0.007112	0.345170	
chunk0054_374_1	chr13	49985069	49985634	+	0	NA	intron (NR_002612, intron 10 of 10)	intron (NR_002612, intron 10 of 10)	11150	NR_037407	100500908		NR_037407	ENSG00000264864	MIR3613	-	microRNA 3613	ncRNA	0.007080	0.438163	
chunk0165_94_1	chr6	32110521	32110951	+	0	NA	Intergenic	Intergenic	-1362	NM_019105	7148	Hs.485104	NM_019105	ENSG00000168477	TNXB	EDS3|EDSCLL|EDSCLL1|HXBL|TENX|TN-X|TNX|TNXB1|TNXB2|TNXBS|VUR8|XB|XBS	tenascin XB	protein-coding	0.018605	0.584687	
chunk0181_202_1	chr7	84371735	84372323	+	0	NA	Intergenic	Intergenic	-160447	NR_110080	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.010204	0.390492	
chunk0127_264_1	chr3	97432835	97433483	+	0	NA	intron (NM_001080448, intron 6 of 17)	intron (NM_001080448, intron 6 of 17)	-6434	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.004630	0.357473	
chunk0065_31_1	chr15	20659311	20659510	+	0	NA	Intergenic	AluSx3|SINE|Alu	96741	NR_027992	606	Hs.657985	NR_027992		NBEAP1	BCL8|BCL8A	neurobeachin pseudogene 1	pseudo	0.025126	0.535000	
chunk0039_41_1	chr11	95919421	95920088	+	0	NA	intron (NM_201278, intron 1 of 16)	intron (NM_201278, intron 1 of 16)	4453	NM_001243571	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.004498	0.344311	
chunk0125_431_1	chr3	72582478	72582829	+	0	NA	Intergenic	MER90a|LTR|ERV1	-136030	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.008547	0.403409	246(CAGAACACCATGGCCC,-,0.00),247(AGAACACCATGGCCCT,+,0.00)
chunk0112_419_1	chr20	47329112	47329319	+	0	NA	intron (NM_001281769, intron 2 of 3)	intron (NM_001281769, intron 2 of 3)	10713	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.019324	0.437500	134(CGGAACAGTGTGATCC,-,0.00),135(GGAACAGTGTGATCCA,+,0.00)
chunk0081_318_1	chr17	46039746	46040104	+	0	NA	intron (NM_001193465, intron 8 of 15)	intron (NM_001193465, intron 8 of 15)	40675	NM_001007532	246744	Hs.661831	NM_001007532	ENSG00000256762	STH	MAPTIT	saitohin	protein-coding	0.011173	0.456825	
chunk0084_289_1	chr17	79909204	79909622	+	0	NA	Intergenic	MER45R|DNA|hAT-Tip100	-9944	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.009569	0.448687	
chunk0041_114_1	chr11	124939489	124939778	+	0	NA	Intergenic	(AAAC)n|Simple_repeat|Simple_repeat	-3221	NM_152722	220296	Hs.745294	NM_152722	ENSG00000165478	HEPACAM	GlialCAM|HEPN1|MLC2A|MLC2B	hepatic and glial cell adhesion molecule	protein-coding	0.006920	0.420690	
chunk0128_87_1	chr3	105654092	105654367	+	0	NA	Intergenic	LTR78B|LTR|ERV1	214814	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.007273	0.471014	
chunk0128_28_1	chr3	104231613	104232229	+	0	NA	Intergenic	Intergenic	-707805	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.307942	
chunk0138_53_1	chr4	31748235	31748523	+	0	NA	Intergenic	MER52A|LTR|ERV1	-249000	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.013889	0.636678	
chunk0212_327_1	chrX	144006311	144006544	+	0	NA	Intergenic	MER41C|LTR|ERV1	122356	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.004292	0.393162	
chunk0178_149_1	chr7	33461780	33462101	+	0	NA	intron (NM_014451, intron 17 of 20)	intron (NM_014451, intron 17 of 20)	332400	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.003115	0.301242	
chunk0052_237_1	chr13	25866968	25867435	+	0	NA	intron (NM_001313741, intron 32 of 35)	intron (NM_001313741, intron 32 of 35)	183859	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.002141	0.410256	
chunk0136_394_1	chr3	196970494	196971233	+	0	NA	Intergenic	MER54A|LTR|ERVL	-1992	NM_025163	80235	Hs.518403	NM_025163	ENSG00000119227	PIGZ	GPI-MT-IV|PIG-Z|SMP3	phosphatidylinositol glycan anchor biosynthesis class Z	protein-coding	0.025710	0.545946	
chunk0152_77_1	chr5	58078468	58078858	+	0	NA	Intergenic	Intergenic	43678	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.005128	0.301790	
chunk0130_198_1	chr3	133711228	133711637	+	0	NA	Intergenic	L2b|LINE|L2	-34701	NM_001063	7018	Hs.518267	NM_001063	ENSG00000091513	TF	HEL-S-71p|PRO1557|PRO2086|TFQTL1	transferrin	protein-coding	0.004890	0.478049	190(AAGCTCATCCTGTTCA,-,0.00)
chunk0166_335_1	chr6	50393789	50394145	+	0	NA	Intergenic	Intergenic	-319577	NM_172238	83741	Hs.434107	NM_172238	ENSG00000008197	TFAP2D	TFAP2BL1	transcription factor AP-2 delta	protein-coding	0.002809	0.316527	
chunk0091_282_1	chr19	11729483	11729847	+	0	NA	intron (NM_001080493, intron 1 of 3)	MER54A|LTR|ERVL	9344	NM_017507	55552	Hs.142167	NM_017507	ENSG00000197933	ZNF823	HSZFP36	zinc finger protein 823	protein-coding	0.005495	0.391781	
chunk0096_93_1	chr2	28071041	28071714	+	0	NA	intron (NM_199191, intron 6 of 11)	L1MC5|LINE|L1	75010	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.011887	0.390208	338(CAGTTCAGCATGTTCC,-,0.00),339(AGTTCAGCATGTTCCT,+,0.00)
chunk0039_16_1	chr11	95512603	95513130	+	0	NA	Intergenic	Intergenic	276924	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.007590	0.359848	
chunk0107_342_1	chr2	221529929	221530504	+	0	NA	intron (NM_001304536, intron 4 of 18)	intron (NM_001304536, intron 4 of 18)	42142	NM_004438	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.017391	0.385417	
chunk0143_81_1	chr4	108235837	108236214	+	0	NA	Intergenic	L2c|LINE|L2	63905	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.002653	0.420635	
chunk0168_119_1	chr6	82013459	82014170	+	0	NA	Intergenic	Intergenic	-199622	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.002813	0.384831	
chunk0002_239_1	chr1	20431241	20431564	+	0	NA	Intergenic	Intergenic	-2608	NR_033887	339505	Hs.633269	NR_033887		LINC01141	-	long intergenic non-protein coding RNA 1141	ncRNA	0.015480	0.493827	
chunk0086_77_1	chr18	13261126	13261619	+	0	NA	intron (NM_181482, intron 1 of 5)	intron (NM_181482, intron 1 of 5)	-16733	NM_181481	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.012170	0.473684	
chunk0186_237_1	chr7	140811259	140811510	+	0	NA	intron (NM_004333, intron 3 of 17)	LTR55|LTR|ERVL?	113380	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.003984	0.531746	
chunk0207_416_1	chr9	137056974	137057492	+	0	NA	Intergenic	L1ME3D|LINE|L1	-3182	NM_203468	954	Hs.123036	NM_001246	ENSG00000054179	ENTPD2	CD39L1|NTPDase-2	ectonucleoside triphosphate diphosphohydrolase 2	protein-coding	0.028958	0.545279	218(CTGGACGTGCTGTTCT,-,0.00),219(TGGACGTGCTGTTCTG,+,0.00)
chunk0164_148_1	chr6	21403455	21403699	+	0	NA	Intergenic	Intergenic	108315	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.024590	0.395918	150(CAGTACGGGATGTCCC,-,0.00),151(AGTACGGGATGTCCCG,+,0.00)
chunk0005_161_1	chr1	58403852	58404249	+	0	NA	Intergenic	L3|LINE|CR1	142749	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.002519	0.429648	189(TACACAGTGTGTTCTC,+,0.00)
chunk0179_337_1	chr7	50710829	50711074	+	0	NA	intron (NM_001001555, intron 2 of 16)	L3|LINE|CR1	-5650	NM_001001550	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.024490	0.516260	
chunk0012_288_1	chr1	162054859	162055289	+	0	NA	Intergenic	Intergenic	-14717	NM_001164757	9722	Hs.731942	NM_014697	ENSG00000198929	NOS1AP	6330408P19Rik|CAPON	nitric oxide synthase 1 adaptor protein	protein-coding	0.006977	0.468677	
chunk0049_113_1	chr12	91327978	91328373	+	0	NA	Intergenic	Intergenic	-145051	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.007595	0.388889	
chunk0167_356_1	chr6	72947528	72948542	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	19718	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.002959	0.322167	820(GAGAACAACTTGTTCT,-,0.00),821(AGAACAACTTGTTCTG,+,0.00)
chunk0154_101_1	chr5	78207945	78208449	+	0	NA	intron (NM_003664, intron 7 of 26)	HAL1b|LINE|L1	86558	NM_001271769	8546	Hs.532091	NM_003664	ENSG00000132842	AP3B1	ADTB3|ADTB3A|HPS|HPS2|PE	adaptor related protein complex 3 subunit beta 1	protein-coding	0.000000	0.390099	
chunk0022_222_1	chr10	13990351	13991946	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-83136	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.016301	0.481830	1045(CAGGACAGTGTGCACC,-,0.00),1046(AGGACAGTGTGCACCT,+,0.00),1251(CAGAGCACAATGTTCC,-,0.00),1252(AGAGCACAATGTTCCC,+,0.00),1308(GGGACAATGCGTTCTG,+,0.00)
chunk0102_397_1	chr2	154833712	154834314	+	0	NA	intron (NM_002239, intron 2 of 2)	L1MC2|LINE|L1	135432	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.001661	0.334992	
chunk0086_399_1	chr18	26706901	26707502	+	0	NA	Intergenic	Intergenic	-3563	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.019967	0.456811	
chunk0105_450_1	chr2	195038095	195038704	+	0	NA	Intergenic	Intergenic	307804	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.003284	0.327869	259(AGGAACACGATGTCCT,-,0.00),260(GGAACACGATGTCCTT,+,0.00)
chunk0142_236_1	chr4	98584253	98584583	+	0	NA	intron (NM_005723, intron 1 of 7)	intron (NM_005723, intron 1 of 7)	74243	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.003030	0.332326	
chunk0152_399_1	chr5	64820003	64820397	+	0	NA	intron (NM_001297644, intron 10 of 12)	intron (NM_001297644, intron 10 of 12)	51282	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.002538	0.329114	
chunk0111_327_1	chr20	32634114	32634660	+	0	NA	intron (NM_182584, intron 4 of 4)	L2c|LINE|L2	17594	NM_182584	284805	Hs.353262	NM_182584	ENSG00000198547	C20orf203	-	chromosome 20 open reading frame 203	protein-coding	0.029304	0.528336	
chunk0070_18_1	chr15	69035204	69035852	+	0	NA	intron (NM_001184780, intron 6 of 15)	intron (NM_001184780, intron 6 of 15)	20833	NM_024505	79400	Hs.657932	NM_024505	ENSG00000255346	NOX5	-	NADPH oxidase 5	protein-coding	0.020062	0.599384	219(CAGAACATCCAGTTCC,-,0.00),220(AGAACATCCAGTTCCA,+,0.00)
chunk0027_49_1	chr10	72800360	72800853	+	0	NA	intron (NR_073062, intron 3 of 9)	intron (NR_073062, intron 3 of 9)	79577	NR_039823	100616286		NR_039823	ENSG00000266719	MIR4676	-	microRNA 4676	ncRNA	0.006085	0.336032	
chunk0123_452_1	chr3	51057216	51057557	+	0	NA	intron (NM_004947, intron 5 of 52)	intron (NM_004947, intron 5 of 52)	-327851	NM_006010	7873	Hs.436446	NM_006010	ENSG00000145050	MANF	ARMET|ARP	mesencephalic astrocyte derived neurotrophic factor	protein-coding	0.002933	0.374269	
chunk0020_249_1	chr1	236112556	236113051	+	0	NA	Intergenic	Intergenic	-29729	NM_003272	7107	Hs.498160	NM_003272	ENSG00000077585	GPR137B	TM7SF1	G protein-coupled receptor 137B	protein-coding	0.008081	0.451613	
chunk0161_378_1	chr5	176781962	176782182	+	0	NA	Intergenic	Intergenic	-28487	NM_133369	90249	Hs.33191	NM_133369	ENSG00000113763	UNC5A	UNC5H1	unc-5 netrin receptor A	protein-coding	0.018182	0.542986	
chunk0062_405_1	chr14	74999226	74999598	+	0	NA	Intergenic	L1ME3F|LINE|L1	-3497	NM_014239	8892	Hs.409137	NM_014239	ENSG00000119718	EIF2B2	EIF-2Bbeta|EIF2B	eukaryotic translation initiation factor 2B subunit beta	protein-coding	0.002688	0.308311	171(AGAACTACAAGTTCTT,+,0.00)
chunk0146_105_1	chr4	158789547	158789746	+	0	NA	intron (NM_020840, intron 1 of 16)	L2c|LINE|L2	20616	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.010050	0.375000	
chunk0073_436_1	chr16	19183282	19183559	+	0	NA	intron (NM_001308157, intron 4 of 7)	intron (NM_001308157, intron 4 of 7)	11063	NM_001308157	51760	Hs.258326	NM_016524	ENSG00000103528	SYT17	sytXVII	synaptotagmin 17	protein-coding	0.010830	0.482014	
chunk0211_169_1	chrX	115258527	115258927	+	0	NA	Intergenic	L2c|LINE|L2	-24655	NM_001243963	57631	Hs.65366	NM_020871	ENSG00000130224	LRCH2	dA204F4.4	leucine rich repeats and calponin homology domain containing 2	protein-coding	0.000000	0.366584	209(CAGTTCACTGTGTTCT,-,0.00),210(AGTTCACTGTGTTCTC,+,0.00),225(CAAAACATCCTGTGCT,-,0.00),226(AAAACATCCTGTGCTT,+,0.00)
chunk0174_118_1	chr6	157187627	157187876	+	0	NA	intron (NM_017519, intron 12 of 18)	intron (NM_017519, intron 12 of 18)	136508	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.000000	0.348000	
chunk0065_283_1	chr14	102481559	102482238	+	0	NA	intron (NM_014844, intron 17 of 19)	intron (NM_014844, intron 17 of 19)	27893	NM_152326	122416	Hs.432945	NM_152326	ENSG00000156381	ANKRD9	-	ankyrin repeat domain 9	protein-coding	0.016200	0.507353	
chunk0120_310_1	chr3	10202555	10202882	+	0	NA	intron (NM_001570, intron 3 of 12)	AluJo|SINE|Alu	37839	NM_001570	3656	Hs.449207	NM_001570	ENSG00000134070	IRAK2	IRAK-2	interleukin 1 receptor associated kinase 2	protein-coding	0.015291	0.451220	
chunk0022_340_1	chr10	16771471	16772233	+	0	NA	intron (NM_152724, intron 2 of 7)	intron (NM_152724, intron 2 of 7)	45602	NM_152724	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.011811	0.340760	
chunk0081_131_1	chr17	40510135	40510731	+	0	NA	Intergenic	Intergenic	-8831	NM_032865	84951	Hs.438292	NM_032865	ENSG00000131746	TNS4	CTEN|PP14434	tensin 4	protein-coding	0.021812	0.525963	314(GAGGACATGCTGTGCT,-,0.00),315(AGGACATGCTGTGCTC,+,0.00)
chunk0090_223_1	chr18	73597995	73598194	+	0	NA	Intergenic	Intergenic	273153	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.005025	0.525000	
chunk0170_405_1	chr6	117795481	117795686	+	0	NA	Intergenic	Intergenic	-111943	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.000000	0.456311	
chunk0141_29_1	chr4	76880643	76881226	+	0	NA	Intergenic	Intergenic	16915	NM_001029870	345079	Hs.257292	NM_001029870	ENSG00000186212	SOWAHB	ANKRD56	sosondowah ankyrin repeat domain family member B	protein-coding	0.003431	0.297945	
chunk0197_333_1	chr8	125174196	125174506	+	0	NA	intron (NM_173685, intron 4 of 7)	intron (NM_173685, intron 4 of 7)	82510	NM_173685	286053	Hs.388297	NM_173685	ENSG00000156831	NSMCE2	C8orf36|MMS21|NSE2|ZMIZ7	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase	protein-coding	0.012903	0.376206	
chunk0046_48_1	chr12	54934282	54934691	+	0	NA	Intergenic	MER41B|LTR|ERV1	39246	NM_014796	9840	Hs.33187	NM_014796	ENSG00000135426	TESPA1	HSPC257|ITPRID3|KIAA0748	thymocyte expressed, positive selection associated 1	protein-coding	0.002445	0.370732	
chunk0162_18_1	chr6	704824	705043	+	0	NA	Intergenic	Intergenic	-11792	NM_018303	55770	Hs.484412	NM_018303	ENSG00000112685	EXOC2	SEC5|SEC5L1|Sec5p	exocyst complex component 2	protein-coding	0.009132	0.309091	
chunk0090_185_1	chr18	72935618	72935950	+	0	NA	Intergenic	Intergenic	-68209	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.006024	0.462462	
chunk0014_24_1	chr1	174568364	174569225	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	120720	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.002323	0.345708	
chunk0128_247_1	chr3	108693540	108693802	+	0	NA	3' UTR (NM_014648, exon 33 of 33)	3' UTR (NM_014648, exon 33 of 33)	63612	NM_032579	84666	Hs.307047	NM_032579	ENSG00000163515	RETNLB	FIZZ1|FIZZ2|HXCP2|RELM-beta|RELMb|RELMbeta|XCP2	resistin like beta	protein-coding	0.003817	0.353612	
chunk0134_358_1	chr3	182642581	182643025	+	0	NA	Intergenic	Intergenic	-150700	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.015766	0.485393	
chunk0137_146_1	chr4	15661236	15661625	+	0	NA	Intergenic	MIR|SINE|MIR	-6018	NM_001193534	26234	Hs.643433	NM_012161	ENSG00000118564	FBXL5	FBL4|FBL5|FLR1	F-box and leucine rich repeat protein 5	protein-coding	0.000000	0.371795	
chunk0058_158_1	chr14	23254431	23254862	+	0	NA	intron (NM_001282322, intron 4 of 14)	AluSz6|SINE|Alu	16728	NM_001282322	100507650		NM_001282322	ENSG00000215277	RNF212B	C14orf164	ring finger protein 212B	protein-coding	0.004640	0.377315	167(TGCCCAGGCTGTTCTC,+,0.00)
chunk0151_261_1	chr5	52460148	52460502	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	-327615	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.000000	0.383099	
chunk0027_141_1	chr10	74585828	74586397	+	0	NA	intron (NM_001123, intron 7 of 10)	intron (NM_001123, intron 7 of 10)	-56788	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.003515	0.417544	246(TGGGTCAAACTGTTCC,-,0.00),247(GGGTCAAACTGTTCCC,+,0.00)
chunk0180_416_1	chr7	76077453	76077983	+	0	NA	Intergenic	Intergenic	29699	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.009434	0.380414	
chunk0015_108_1	chr1	185164373	185164690	+	0	NA	intron (NM_017673, intron 2 of 18)	Tigger1|DNA|TcMar-Tigger	7372	NM_017673	54823	Hs.134183	NM_017673	ENSG00000116668	SWT1	C1orf26|HsSwt1	SWT1 RNA endoribonuclease homolog	protein-coding	0.003155	0.402516	
chunk0063_15_1	chr14	76329378	76329700	+	0	NA	Intergenic	Intergenic	-41808	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.034161	0.541796	
chunk0167_192_1	chr6	64460887	64461239	+	0	NA	intron (NM_001142800, intron 26 of 42)	intron (NM_001142800, intron 26 of 42)	814537	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.000000	0.362606	
chunk0157_63_1	chr5	116198761	116199355	+	0	NA	intron (NM_001308080, intron 5 of 6)	L1MC1|LINE|L1	113596	NM_001308080	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.005051	0.337815	
chunk0039_323_1	chr11	104085109	104085659	+	0	NA	intron (NM_025208, intron 1 of 6)	L1MD2|LINE|L1	48804	NM_001001711	414301	Hs.591941	NM_001001711	ENSG00000170967	DDI1	-	DNA damage inducible 1 homolog 1	protein-coding	0.007273	0.326679	
chunk0170_103_1	chr6	110543006	110543407	+	0	NA	Intergenic	LTR33|LTR|ERVL	-66565	NM_033125	85413	Hs.520319	NM_033125	ENSG00000004809	SLC22A16	CT2|FLIPT2|HEL-S-18|OAT6|OCT6|OKB1|dJ261K5.1	solute carrier family 22 member 16	protein-coding	0.014963	0.614428	
chunk0065_423_1	chr14	105991584	105992078	+	0	NA	Intergenic	MER70B|LTR|ERVL	-19562	NR_002224	8755	Hs.662288	NR_002224	ENSG00000271968	ADAM6	C14orf96|tMDCIV	ADAM metallopeptidase domain 6 (pseudogene)	pseudo	0.012146	0.440404	201(AAGCCCAGGGTGTCCC,-,0.00),202(AGCCCAGGGTGTCCCT,+,0.00)
chunk0194_322_1	chr8	88474644	88474870	+	0	NA	Intergenic	L1PA11|LINE|L1	-147269	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.004425	0.563877	
chunk0082_446_1	chr17	62106500	62107181	+	0	NA	Intergenic	Intergenic	-41558	NM_005121	9969	Hs.282678	NM_005121	ENSG00000108510	MED13	ARC250|DRIP250|HSPC221|THRAP1|TRAP240	mediator complex subunit 13	protein-coding	0.004405	0.385630	
chunk0010_400_1	chr1	119542419	119543033	+	0	NA	Intergenic	Intergenic	-21154	NR_033781	128102	Hs.681806	NR_033781		HSD3BP4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 4	pseudo	0.003257	0.414634	
chunk0008_290_1	chr1	94912719	94913144	+	0	NA	intron (NM_001286055, intron 1 of 5)	intron (NM_001286055, intron 1 of 5)	12877	NM_001286056	1266	Hs.483454	NM_001839	ENSG00000117519	CNN3	-	calponin 3	protein-coding	0.011765	0.401408	
chunk0018_416_1	chr1	222684591	222685273	+	0	NA	intron (NM_022831, intron 6 of 9)	intron (NM_022831, intron 6 of 9)	27590	NM_022831	64853	Hs.156625	NM_022831	ENSG00000186063	AIDA	C1orf80	axin interactor, dorsalization associated	protein-coding	0.004399	0.342606	
chunk0081_312_1	chr17	45790524	45790727	+	0	NA	intron (NM_001303018, intron 1 of 10).3	intron (NM_001303018, intron 1 of 10).3	6345	NM_004382	1394	Hs.417628	NM_004382	ENSG00000120088	CRHR1	CRF-R|CRF-R-1|CRF-R1|CRF1|CRFR-1|CRFR1|CRH-R-1|CRH-R1|CRHR|CRHR1L	corticotropin releasing hormone receptor 1	protein-coding	0.024631	0.578431	
chunk0012_354_1	chr1	162732551	162733163	+	0	NA	intron (NM_001014796, intron 4 of 18)	intron (NM_001014796, intron 4 of 18)	-57845	NM_001304512	51478	Hs.492925	NM_016371	ENSG00000132196	HSD17B7	PRAP|SDR37C1	hydroxysteroid 17-beta dehydrogenase 7	protein-coding	0.013072	0.528548	
chunk0106_288_1	chr2	204235283	204235675	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	298731	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.005102	0.427481	
chunk0165_20_1	chr6	29222666	29222877	+	0	NA	Intergenic	Intergenic	49237	NM_030905	26707	Hs.163518	NM_030905	ENSG00000204700	OR2J2	OR6-19|OR6-8|OR6.3.8|ORL684|dJ80I19.4|hs6M1-6	olfactory receptor family 2 subfamily J member 2	protein-coding	0.009479	0.386792	
chunk0181_208_1	chr7	84536104	84536571	+	0	NA	intron (NR_110079, intron 1 of 2)	Charlie17a|DNA|hAT-Charlie	3861	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.004283	0.391026	
chunk0029_197_1	chr10	101524481	101524721	+	0	NA	intron (NM_033637, intron 5 of 14)	intron (NM_033637, intron 5 of 14)	63669	NM_001308382	27343	Hs.523230	NM_013274	ENSG00000166169	POLL	BETAN|POLKAPPA	DNA polymerase lambda	protein-coding	0.000000	0.323651	
chunk0146_166_1	chr4	160223671	160224314	+	0	NA	Intergenic	L1PA16|LINE|L1	956146	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.001555	0.541925	
chunk0128_365_1	chr3	113223957	113224228	+	0	NA	intron (NM_001301861, intron 2 of 19)	intron (NM_001301861, intron 2 of 19)	11595	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.036900	0.558824	
chunk0146_403_1	chr4	168925758	168926238	+	0	NA	intron (NM_016081, intron 20 of 20)	intron (NM_016081, intron 20 of 20)	84319	NM_032783	84869	Hs.659311	NM_032783	ENSG00000145439	CBR4	SDR45C1	carbonyl reductase 4	protein-coding	0.002083	0.359667	
chunk0062_103_1	chr14	68192503	68192741	+	0	NA	intron (NM_133509, intron 7 of 10)	MamRTE1|LINE|RTE-BovB	372843	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.000000	0.376569	
chunk0181_329_1	chr7	87956884	87957398	+	0	NA	intron (NM_021721, intron 2 of 27)	L3|LINE|CR1	22890	NM_021721	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.001946	0.341748	
chunk0210_63_1	chrX	69641318	69642009	+	0	NA	intron (NM_001005612, intron 1 of 7)	intron (NM_001005612, intron 1 of 7)	25596	NM_001399	1896	Hs.105407	NM_001399	ENSG00000158813	EDA	ECTD1|ED1|ED1-A1|ED1-A2|EDA-A1|EDA-A2|EDA1|EDA2|HED|HED1|ODT1|STHAGX1|TNLG7C|XHED|XLHED	ectodysplasin A	protein-coding	0.002894	0.358382	
chunk0089_35_1	chr18	57923215	57923432	+	0	NA	Intergenic	Intergenic	-120228	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.004608	0.435780	118(AAGCACACTTTGTTCA,-,0.00),119(AGCACACTTTGTTCAG,+,0.00)
chunk0182_176_1	chr7	95608751	95609313	+	0	NA	Intergenic	Intergenic	-12419	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.012456	0.467140	412(TAGATCACCCTGTACT,-,0.00),413(AGATCACCCTGTACTG,+,0.00)
chunk0033_387_1	chr11	24226559	24226937	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-270222	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002646	0.369393	
chunk0195_81_1	chr8	94147391	94147934	+	0	NA	intron (NM_004063, intron 14 of 17)	Charlie19a|DNA|hAT-Charlie	60925	NM_004063	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.005525	0.375000	
chunk0191_419_1	chr8	57750672	57751309	+	0	NA	Intergenic	Intergenic	-227368	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.007849	0.451411	
chunk0069_62_1	chr15	60839513	60840154	+	0	NA	intron (NM_134261, intron 1 of 10)	(TATGTA)n|Simple_repeat|Simple_repeat	158264	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.007800	0.467290	
chunk0158_330_1	chr5	132942956	132943194	+	0	NA	intron (NM_014423, intron 1 of 20)	intron (NM_014423, intron 1 of 20)	20587	NM_014423	27125	Hs.519313	NM_014423	ENSG00000072364	AFF4	AF5Q31|CHOPS|MCEF	AF4/FMR2 family member 4	protein-coding	0.008403	0.456067	
chunk0034_130_1	chr11	28526936	28527370	+	0	NA	Intergenic	Intergenic	-49605	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.002304	0.328736	
chunk0042_333_1	chr12	9770533	9771000	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-9865	NM_001781	969	Hs.208854	NM_001781	ENSG00000110848	CD69	AIM|BL-AC/P26|CLEC2C|EA1|GP32/28|MLR-3	CD69 molecule	protein-coding	0.004283	0.367521	
chunk0116_239_1	chr21	38367200	38367399	+	0	NA	TTS (NM_001243432)	TTS (NM_001243432)	-21223	NR_110545	102724678	Hs.635675	NR_110545		LINC01423	-	long intergenic non-protein coding RNA 1423	ncRNA	0.010050	0.425000	
chunk0091_422_1	chr19	16862401	16863096	+	0	NA	promoter-TSS (NM_001297597)	promoter-TSS (NM_001297597)	-526	NM_001297597	23309	Hs.13999	NM_015260	ENSG00000127511	SIN3B	-	SIN3 transcription regulator family member B	protein-coding	0.030216	0.530172	
chunk0028_203_1	chr10	89131159	89131707	+	0	NA	Intergenic	L1MC1|LINE|L1	-68022	NR_039827	100616192		NR_039827	ENSG00000265375	MIR4679-2	-	microRNA 4679-2	ncRNA	0.005474	0.311475	
chunk0056_167_1	chr13	85009636	85010033	+	0	NA	Intergenic	Intergenic	138223	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.005038	0.296482	278(TTGTACATTTTGTTCT,-,0.00),279(TGTACATTTTGTTCTT,+,0.00)
chunk0060_117_1	chr14	43778583	43778830	+	0	NA	Intergenic	Intergenic	728590	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.004049	0.322581	
chunk0184_412_1	chr7	122577232	122577929	+	0	NA	intron (NM_017954, intron 7 of 29)	L1MD3|LINE|L1	121574	NM_139175	168433	Hs.126730	NM_139175	ENSG00000188050	RNF133	-	ring finger protein 133	protein-coding	0.010043	0.366762	
chunk0104_398_1	chr2	180618156	180618459	+	0	NA	Intergenic	Intergenic	-73797	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.003300	0.421053	
chunk0165_386_1	chr6	38548420	38548996	+	0	NA	intron (NM_001172418, intron 5 of 10)	intron (NM_001172418, intron 5 of 10)	47359	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.005208	0.337955	
chunk0128_42_1	chr3	104610878	104611825	+	0	NA	Intergenic	L2b|LINE|L2	-755362	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.004224	0.350211	569(AGGTACAACTTGTTCC,-,0.00),570(GGTACAACTTGTTCCT,+,0.00)
chunk0190_326_1	chr8	38889984	38890460	+	0	NA	Intergenic	L1MD1|LINE|L1	-11013	NM_021623	59339	Hs.369123	NM_021623	ENSG00000169499	PLEKHA2	TAPP2	pleckstrin homology domain containing A2	protein-coding	0.000000	0.383648	
chunk0046_447_1	chr12	64883148	64883400	+	0	NA	promoter-TSS (NR_033988)	promoter-TSS (NR_033988)	-500	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.003968	0.458498	
chunk0103_360_1	chr2	168246326	168246799	+	0	NA	intron (NM_013233, intron 1 of 17)	CpG	1033	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.090909	0.672996	
chunk0097_236_1	chr2	53498258	53498573	+	0	NA	Intergenic	Intergenic	-269377	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.000000	0.401899	
chunk0197_76_1	chr8	119010378	119010725	+	0	NA	Intergenic	L1MC1|LINE|L1	-56634	NM_006438	10584	Hs.176615	NM_006438	ENSG00000184374	COLEC10	3MC3|CL-34|CLL1	collectin subfamily member 10	protein-coding	0.000000	0.330460	
chunk0084_429_1	chr17	82593212	82593684	+	0	NA	intron (NM_004514, intron 8 of 8)	intron (NM_004514, intron 8 of 8)	55087	NM_019613	56270	Hs.132161	NM_019613	ENSG00000141580	WDR45B	NEDSBAS|WDR45L|WIPI-3|WIPI3	WD repeat domain 45B	protein-coding	0.036017	0.615222	
chunk0043_345_1	chr12	22923924	22924124	+	0	NA	Intergenic	Intergenic	-251612	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.005000	0.402985	
chunk0161_372_1	chr5	176336968	176337316	+	0	NA	exon (NM_001308196, exon 11 of 12)	exon (NM_001308196, exon 11 of 12)	23997	NM_001308200	375484	Hs.719847	NM_198567	ENSG00000170085	SIMC1	C5orf25|OOMA1|PLEIAD	SUMO interacting motifs containing 1	protein-coding	0.005747	0.375358	
chunk0121_387_1	chr3	25230802	25231254	+	0	NA	intron (NM_001290216, intron 1 of 7)	intron (NM_001290216, intron 1 of 7)	56696	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.002212	0.315673	238(AAATACAGAATGTGCT,-,0.00),239(AATACAGAATGTGCTT,+,0.00)
chunk0056_417_1	chr13	94400956	94401290	+	0	NA	intron (NM_005708, intron 8 of 8)	MIRb|SINE|MIR	78559	NM_001129889	1638	Hs.301865	NM_001922	ENSG00000080166	DCT	TRP-2|TYRP2	dopachrome tautomerase	protein-coding	0.005988	0.417910	
chunk0028_216_1	chr10	89502795	89502995	+	0	NA	intron (NM_213606, intron 2 of 7)	intron (NM_213606, intron 2 of 7)	32661	NM_213606	387700	Hs.530338	NM_213606	ENSG00000152779	SLC16A12	CJMG|CRT2|CTRCT47|MCT12	solute carrier family 16 member 12	protein-coding	0.010000	0.427861	
chunk0202_255_1	chr9	76829370	76829816	+	0	NA	intron (NM_015225, intron 4 of 18)	MER58A|DNA|hAT-Charlie	65157	NR_132313	50652	Hs.663766	NR_015342	ENSG00000225937	PCA3	DD3|NCRNA00019|PCAT3|PRUNE2-AS1	prostate cancer associated 3	ncRNA	0.006726	0.382550	
chunk0134_196_1	chr3	178385235	178385513	+	0	NA	Intergenic	Intergenic	-33827	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.000000	0.347670	
chunk0058_396_1	chr13	111302393	111302592	+	0	NA	intron (NM_001113513, intron 19 of 19)	intron (NM_001113513, intron 19 of 19)	-13693	NM_001303133	121793	Hs.210677	NM_152324	ENSG00000153495	TEX29	C13orf16|bA474D23.1	testis expressed 29	protein-coding	0.025126	0.575000	
chunk0037_117_1	chr11	72565791	72565996	+	0	NA	Intergenic	L1M5|LINE|L1	-4763	NR_126364	101928555	Hs.376950	NR_126364	ENSG00000227467	LINC01537	-	long intergenic non-protein coding RNA 1537	ncRNA	0.004878	0.310680	
chunk0157_40_1	chr5	115812002	115812788	+	0	NA	intron (NM_001801, intron 2 of 4)	intron (NM_001801, intron 2 of 4)	4313	NM_001801	1036	Hs.442378	NM_001801	ENSG00000129596	CDO1	CDO-I	cysteine dioxygenase type 1	protein-coding	0.003817	0.325286	141(CTGGACATAATGTGCT,-,0.00),142(TGGACATAATGTGCTT,+,0.00)
chunk0106_422_1	chr2	208142804	208143031	+	0	NA	intron (NM_005210, intron 2 of 2)	intron (NM_005210, intron 2 of 2)	3236	NM_005210	1419	Hs.248102	NM_005210	ENSG00000182187	CRYGB	CRYG2|CTRCT39	crystallin gamma B	protein-coding	0.022026	0.495614	
chunk0022_228_1	chr10	14041825	14042515	+	0	NA	intron (NM_018027, intron 2 of 24)	LTR10C|LTR|ERV1	-32114	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.014493	0.412446	322(ATGTACTTTATGTTCT,-,0.00),323(TGTACTTTATGTTCTT,+,0.00)
chunk0048_239_1	chr12	81571442	81571725	+	0	NA	intron (NM_001220474, intron 2 of 30)	MIR|SINE|MIR	26788	NM_001220478	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.355634	
chunk0123_324_1	chr3	47442851	47444264	+	0	NA	intron (NM_012235, intron 1 of 22)	intron (NM_012235, intron 1 of 22)	32398	NM_012235	22937	Hs.531789	NM_012235	ENSG00000114650	SCAP	-	SREBF chaperone	protein-coding	0.012031	0.475248	220(AAGAACAACATGTGCA,-,0.00),221(AGAACAACATGTGCAG,+,0.00),821(AGAACTCTCTGCTCTT,+,0.00)
chunk0208_29_1	chrX	11191186	11191530	+	0	NA	intron (NR_109776, intron 4 of 14)	MER58A|DNA|hAT-Charlie	74617	NM_013423	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.014535	0.446377	
chunk0191_169_1	chr8	50617000	50617271	+	0	NA	intron (NM_018967, intron 13 of 18)	L2a|LINE|L2	705356	NM_001287814	54212	Hs.584914	NM_018967	ENSG00000147481	SNTG1	G1SYN|SYN4	syntrophin gamma 1	protein-coding	0.003690	0.378676	
chunk0159_175_1	chr5	140114525	140114836	+	0	NA	exon (NM_005859, exon 1 of 1)	exon (NM_005859, exon 1 of 1)	557	NM_005859	5813	Hs.443121	NM_005859	ENSG00000185129	PURA	MRD31|PUR-ALPHA|PUR1|PURALPHA	purine rich element binding protein A	protein-coding	0.112540	0.689103	
chunk0080_447_1	chr17	36772945	36773183	+	0	NA	Intergenic	L1MC2|LINE|L1	-164411	NM_005568	3975	Hs.443727	NM_005568	ENSG00000273706	LHX1	LIM-1|LIM1	LIM homeobox 1	protein-coding	0.000000	0.384937	
chunk0164_142_1	chr6	21324941	21325814	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	186515	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.006873	0.332952	
chunk0044_159_1	chr12	29858474	29859079	+	0	NA	Intergenic	L2c|LINE|L2	-74017	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.003306	0.417492	
chunk0012_282_1	chr1	161948574	161949326	+	0	NA	intron (NM_007348, intron 15 of 15)	intron (NM_007348, intron 15 of 15)	75515	NM_015441	25903	Hs.507515	NM_015441	ENSG00000162745	OLFML2B	-	olfactomedin like 2B	protein-coding	0.007979	0.393094	504(TAGGACAACCTGTCTC,-,0.00),505(AGGACAACCTGTCTCT,+,0.00)
chunk0138_211_1	chr4	38841540	38842009	+	0	NA	intron (NM_006068, intron 1 of 1)	Ricksha_0|DNA|MULE-MuDR	15043	NM_006068	10333	Hs.575090	NM_006068	ENSG00000174130	TLR6	CD286	toll like receptor 6	protein-coding	0.014925	0.344681	
chunk0100_152_1	chr2	109018511	109019132	+	0	NA	Intergenic	L2b|LINE|L2	-29449	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.019324	0.501608	
chunk0161_234_1	chr5	171387681	171387919	+	0	NA	promoter-TSS (NM_001037738)	promoter-TSS (NM_001037738)	96	NM_002520	4869	Hs.557550	NM_002520	ENSG00000181163	NPM1	B23|NPM	nucleophosmin 1	protein-coding	0.100840	0.623431	
chunk0131_295_1	chr3	150583258	150583682	+	0	NA	intron (NM_032025, intron 13 of 13)	intron (NM_032025, intron 13 of 13)	-19809	NM_016275	51714	Hs.369052	NM_016275	ENSG00000198843	SELENOT	SELT	selenoprotein T	protein-coding	0.004717	0.334118	
chunk0150_333_1	chr5	38521621	38522165	+	0	NA	intron (NM_002310, intron 5 of 19)	L1MA4A|LINE|L1	34753	NM_001127671	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.011029	0.563303	
chunk0057_185_1	chr13	102745764	102745980	+	0	NA	exon (NM_001146197, exon 4 of 4)	exon (NM_001146197, exon 4 of 4)	13200	NM_001146197	643677	Hs.368382	NM_001146197	ENSG00000175820	CCDC168	C13orf40	coiled-coil domain containing 168	protein-coding	0.000000	0.377880	
chunk0118_447_1	chr22	39255825	39256147	+	0	NA	Intergenic	MIR3|SINE|MIR	-10931	NM_002608	5155	Hs.1976	NM_002608	ENSG00000100311	PDGFB	IBGC5|PDGF-2|PDGF2|SIS|SSV|c-sis	platelet derived growth factor subunit B	protein-coding	0.027950	0.526316	
chunk0197_290_1	chr8	124343053	124343309	+	0	NA	intron (NM_194291, intron 1 of 6)	MER57A-int|LTR|ERV1	29518	NM_194291	157378	Hs.100691	NM_194291	ENSG00000164983	TMEM65	-	transmembrane protein 65	protein-coding	0.000000	0.346304	
chunk0076_83_1	chr16	64634602	64634931	+	0	NA	Intergenic	Intergenic	487371	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.006079	0.360606	
chunk0043_276_1	chr12	20968426	20969378	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-46794	NM_001009562	338821	Hs.729117	NM_001009562	ENSG00000205754	SLCO1B7	LST-3|LST-3TM12|LST3|SLC21A21	solute carrier organic anion transporter family member 1B7 (putative)	protein-coding	0.000000	0.345226	776(GGGACAATATGTTTCT,+,0.00)
chunk0060_467_1	chr14	55317653	55318249	+	0	NA	intron (NM_152231, intron 1 of 1)	HAL1|LINE|L1	45797	NM_152231	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.005034	0.402010	
chunk0043_267_1	chr12	20746658	20747175	+	0	NA	intron (NM_017435, intron 13 of 14)	L1MC5|LINE|L1	51451	NM_017435	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.003868	0.303089	
chunk0184_162_1	chr7	116271864	116272323	+	0	NA	Intergenic	Intergenic	14571	NR_130923	102724434	Hs.667624	NR_130921	ENSG00000237870	LOC102724434	-	uncharacterized LOC102724434	ncRNA	0.006536	0.417391	241(ATGCACACTCTGTCCC,-,0.00),242(TGCACACTCTGTCCCT,+,0.00)
chunk0174_112_1	chr6	157004574	157004898	+	0	NA	intron (NM_017519, intron 4 of 18)	intron (NM_017519, intron 4 of 18)	-225005	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.012346	0.381538	
chunk0057_223_1	chr13	104143799	104144396	+	0	NA	Intergenic	Intergenic	718897	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.015075	0.436455	
chunk0180_403_1	chr7	75718450	75718767	+	0	NA	intron (NM_005338, intron 1 of 30)	intron (NM_005338, intron 1 of 30)	20364	NM_001243198	3092	Hs.329266	NM_005338	ENSG00000127946	HIP1	HIP-I|ILWEQ|SHON|SHONbeta|SHONgamma	huntingtin interacting protein 1	protein-coding	0.015773	0.430818	
chunk0103_279_1	chr2	165901532	165901929	+	0	NA	exon (NM_024753, exon 20 of 29)	exon (NM_024753, exon 20 of 29)	-29789	NR_045375	100506124	Hs.709870	NR_045375		LOC100506124	-	uncharacterized LOC100506124	ncRNA	0.012594	0.399497	
chunk0180_166_1	chr7	65070794	65071295	+	0	NA	intron (NR_033416, intron 9 of 10)	intron (NR_033416, intron 9 of 10)	32690	NR_033416	643180	Hs.510847	NR_033416	ENSG00000234585	CCT6P3	CCT6-3P	chaperonin containing TCP1 subunit 6 pseudogene 3	pseudo	0.009980	0.392430	
chunk0180_177_1	chr7	65590764	65590993	+	0	NA	Intergenic	Intergenic	-56976	NR_027392	644619	Hs.676517	NR_027392	ENSG00000273024	INTS4P2	INTS4L2	integrator complex subunit 4 pseudogene 2	pseudo	0.013100	0.426087	
chunk0059_445_1	chr14	38868861	38869060	+	0	NA	intron (NR_039982, intron 2 of 4)	intron (NR_039982, intron 2 of 4)	47922	NR_039982	283547	Hs.675941	NR_039982	ENSG00000259070	LINC00639	-	long intergenic non-protein coding RNA 639	ncRNA	0.000000	0.410000	
chunk0204_9_1	chr9	91677862	91678324	+	0	NA	Intergenic	Intergenic	-41748	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.006494	0.384449	233(GAGTACATTGTGTGCA,-,0.00),234(AGTACATTGTGTGCAC,+,0.00)
chunk0153_266_1	chr5	72848413	72848612	+	0	NA	intron (NM_153188, intron 2 of 24)	CpG-22173	409	NM_153188	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.085427	0.695000	
chunk0019_281_1	chr1	228721330	228721771	+	0	NA	intron (NR_037962, intron 1 of 2)	intron (NR_037962, intron 1 of 2)	-13527	NM_021205	58480	Hs.647774	NM_021205	ENSG00000116574	RHOU	ARHU|CDC42L1|G28K|WRCH1|hG28K	ras homolog family member U	protein-coding	0.024943	0.445701	
chunk0199_256_1	chr9	6015678	6015877	+	0	NA	promoter-TSS (NM_012416)	promoter-TSS (NM_012416)	-137	NM_001243202	26953	Hs.167496	NM_012416	ENSG00000137040	RANBP6	-	RAN binding protein 6	protein-coding	0.045226	0.550000	
chunk0148_397_1	chr5	14833754	14834061	+	0	NA	intron (NM_054027, intron 1 of 11)	intron (NM_054027, intron 1 of 11)	-7895	NR_039780	100616271		NR_039780	ENSG00000264792	MIR4637	-	microRNA 4637	ncRNA	0.019544	0.480519	
chunk0062_116_1	chr14	68423570	68424166	+	0	NA	intron (NM_133509, intron 9 of 10)	intron (NM_133509, intron 9 of 10)	370046	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.003356	0.432161	
chunk0008_76_1	chr1	89877208	89878002	+	0	NA	intron (NM_001134479, intron 2 of 2)	intron (NM_001134479, intron 2 of 2)	55684	NM_018103	55144	Hs.482087	NM_018103	ENSG00000171492	LRRC8D	LRRC5	leucine rich repeat containing 8 VRAC subunit D	protein-coding	0.008816	0.363522	
chunk0117_271_1	chr22	24044541	24044989	+	0	NA	intron (NM_012295, intron 6 of 36)	MLT1A-int|LTR|ERVL-MaLR	33395	NM_001199281	23523	Hs.517478	NM_012295	ENSG00000099991	CABIN1	CAIN|KB-318B8.7|PPP3IN	calcineurin binding protein 1	protein-coding	0.008929	0.383073	
chunk0187_33_1	chr8	1049763	1049962	+	0	NA	intron (NR_073397, intron 3 of 3)	intron (NR_073397, intron 3 of 3)	252745	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.015075	0.465000	
chunk0053_12_1	chr13	26236555	26236924	+	0	NA	Intergenic	Intergenic	-14368	NM_005977	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.008130	0.443243	159(AGGAACACCATGTACA,-,0.00),160(GGAACACCATGTACAG,+,0.00)
chunk0104_156_1	chr2	174057908	174058450	+	0	NA	Intergenic	MIR|SINE|MIR	-92477	NM_003111	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.007380	0.423573	
chunk0080_22_1	chr17	21000026	21000563	+	0	NA	3' UTR (NM_015276, exon 13 of 13)	3' UTR (NM_015276, exon 13 of 13)	42745	NM_015276	23326	Hs.462492	NM_015276	ENSG00000124422	USP22	USP3L	ubiquitin specific peptidase 22	protein-coding	0.014898	0.496283	
chunk0018_177_1	chr1	219161144	219161903	+	0	NA	intron (NR_038845, intron 1 of 4)	intron (NR_038845, intron 1 of 4)	12265	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.005270	0.371053	377(AGGAACATCATGTCCA,-,0.00),378(GGAACATCATGTCCAA,+,0.00)
chunk0178_100_1	chr7	30748173	30748450	+	0	NA	Intergenic	L1ME4a|LINE|L1	-3824	NM_006774	11185	Hs.632629	NM_006774	ENSG00000241644	INMT	TEMT	indolethylamine N-methyltransferase	protein-coding	0.007220	0.478417	
chunk0130_192_1	chr3	133617806	133618632	+	0	NA	exon (NM_007027, exon 21 of 28)	exon (NM_007027, exon 21 of 28)	43674	NM_007027	11073	Hs.593379	NM_007027	ENSG00000163781	TOPBP1	Dpb11|TOP2BP1	DNA topoisomerase II binding protein 1	protein-coding	0.003632	0.343410	
chunk0207_105_1	chr9	128656688	128656887	+	0	NA	promoter-TSS (NM_052844)	promoter-TSS (NM_052844)	63	NM_052844	89891	Hs.495240	NM_052844	ENSG00000119333	WDR34	DIC5|FAP133|SRTD11|bA216B9.3	WD repeat domain 34	protein-coding	0.110553	0.635000	
chunk0114_75_1	chr21	9154453	9154690	+	0	NA	Intergenic	HERVK14-int|LTR|ERVK	-24810	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.021097	0.445378	
chunk0091_288_1	chr19	12065253	12065578	+	0	NA	intron (NM_001136501, intron 1 of 3)	intron (NM_001136501, intron 1 of 3)	684	NM_001136501	284391	Hs.646391	NM_001136501	ENSG00000223547	ZNF844	-	zinc finger protein 844	protein-coding	0.040000	0.500000	
chunk0126_439_1	chr3	87119585	87119883	+	0	NA	intron (NR_104153, intron 1 of 2)	intron (NR_104153, intron 1 of 2)	30454	NR_047469	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.000000	0.354515	132(GTGTACATGATGTTCT,-,0.00),133(TGTACATGATGTTCTG,+,0.00)
chunk0040_332_1	chr11	118307268	118307838	+	0	NA	intron (NM_000733, intron 3 of 8)	intron (NM_000733, intron 3 of 8)	2973	NM_000733	916	Hs.3003	NM_000733	ENSG00000198851	CD3E	IMD18|T3E|TCRE	CD3e molecule	protein-coding	0.007018	0.411559	
chunk0198_42_1	chr8	128330087	128330597	+	0	NA	Intergenic	Intergenic	180226	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.011765	0.422701	
chunk0120_326_1	chr3	10672516	10672815	+	0	NA	Intergenic	Intergenic	-45858	NR_046766	100874325	Hs.143004	NR_046766	ENSG00000224771	ATP2B2-IT2	-	ATP2B2 intronic transcript 2	ncRNA	0.016722	0.433333	
chunk0104_339_1	chr2	179677157	179677797	+	0	NA	intron (NM_152520, intron 3 of 9)	intron (NM_152520, intron 3 of 9)	68565	NM_001113397	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.006250	0.354134	
chunk0057_351_1	chr13	108340364	108340913	+	0	NA	Intergenic	MER67C|LTR|ERV1	71009	NM_001145645	10673	Hs.525157	NM_006573	ENSG00000102524	TNFSF13B	BAFF|BLYS|CD257|DTL|TALL-1|TALL1|THANK|TNFSF20|TNLG7A|ZTNF4	TNF superfamily member 13b	protein-coding	0.012750	0.400000	
chunk0169_364_1	chr6	106939198	106939472	+	0	NA	Intergenic	Intergenic	34704	NM_001291739	100133941	Hs.644105	NM_013230	ENSG00000272398	CD24	CD24A	CD24 molecule	protein-coding	0.007299	0.472727	
chunk0047_219_1	chr12	71721801	71722323	+	0	NA	Intergenic	MER72B|LTR|ERV1	-32816	NM_014999	23011	Hs.524590	NM_014999	ENSG00000080371	RAB21	-	RAB21, member RAS oncogene family	protein-coding	0.007663	0.455067	
chunk0137_231_1	chr4	20266354	20266612	+	0	NA	intron (NM_001289135, intron 3 of 35)	intron (NM_001289135, intron 3 of 35)	14578	NM_001289135	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.000000	0.424710	191(GAGAACAATCTGTTCT,-,0.00),192(AGAACAATCTGTTCTC,+,0.00)
chunk0195_362_1	chr8	99869652	99870172	+	0	NA	intron (NM_152564, intron 59 of 61)	intron (NM_152564, intron 59 of 61)	24102	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.017308	0.418426	
chunk0064_106_1	chr14	91109218	91109602	+	0	NA	Intergenic	Intergenic	-4603	NM_001286472	80017	Hs.309849	NM_024952	ENSG00000133943	DGLUCY	C14orf159	D-glutamate cyclase	protein-coding	0.010417	0.537662	
chunk0066_19_1	chr15	27326408	27326970	+	0	NA	intron (NM_033223, intron 3 of 9)	intron (NM_033223, intron 3 of 9)	-165370	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.008897	0.415631	
chunk0142_49_1	chr4	91368094	91368573	+	0	NA	intron (NM_001145065, intron 10 of 10)	intron (NM_001145065, intron 10 of 10)	908969	NR_125920	101929194	Hs.626389	NR_125920		LNCPRESS2	-	lncRNA p53 regulated and ESC associated 2	ncRNA	0.000000	0.291667	
chunk0211_34_1	chrX	108343393	108343701	+	0	NA	intron (NM_001287760, intron 2 of 42)	intron (NM_001287760, intron 2 of 42)	94883	NM_001287760	1288	Hs.145586	NM_001847	ENSG00000197565	COL4A6	CXDELq22.3|DELXq22.3|DFNX6	collagen type IV alpha 6 chain	protein-coding	0.000000	0.307443	
chunk0093_295_1	chr19	52527292	52527580	+	0	NA	promoter-TSS (NM_001039886)	promoter-TSS (NM_001039886)	-220	NM_001039886	388558	Hs.729294	NM_001039886	ENSG00000198482	ZNF808	-	zinc finger protein 808	protein-coding	0.065972	0.581315	
chunk0180_280_1	chr7	69860424	69860982	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	261784	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.007168	0.432916	
chunk0034_257_1	chr11	34406503	34406760	+	0	NA	Intergenic	Intergenic	-32294	NM_001752	847	Hs.502302	NM_001752	ENSG00000121691	CAT	-	catalase	protein-coding	0.011673	0.399225	
chunk0179_101_1	chr7	44787361	44787560	+	0	NA	Intergenic	Intergenic	-9176	NM_021130	5478	Hs.356331	NM_021130	ENSG00000196262	PPIA	CYPA|CYPH|HEL-S-69p	peptidylprolyl isomerase A	protein-coding	0.005025	0.530000	
chunk0153_180_1	chr5	71583047	71583747	+	0	NA	Intergenic	Intergenic	-3891	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.004286	0.459344	
chunk0131_66_1	chr3	142939855	142940505	+	0	NA	intron (NR_038455, intron 4 of 4)	intron (NR_038455, intron 4 of 4)	13505	NR_038455	100507389	Hs.38715	NR_038455	ENSG00000243818	LOC100507389	-	uncharacterized LOC100507389	ncRNA	0.001538	0.330261	
chunk0038_137_1	chr11	84173690	84174201	+	0	NA	intron (NM_001142700, intron 1 of 19)	intron (NM_001142700, intron 1 of 19)	99335	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.007828	0.386719	
chunk0027_236_1	chr10	76703302	76703568	+	0	NA	Intergenic	L1M1|LINE|L1	-184609	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.000000	0.475655	
chunk0045_1_1	chr12	42759718	42760212	+	0	NA	Intergenic	Intergenic	-113467	NR_110042	101927058	Hs.434238	NR_110042	ENSG00000257510	LINC02402	-	long intergenic non-protein coding RNA 2402	ncRNA	0.006073	0.464646	
chunk0127_76_1	chr3	89496586	89497194	+	0	NA	Intergenic	L2a|LINE|L2	389366	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004934	0.297209	
chunk0154_337_1	chr5	85633318	85633592	+	0	NA	Intergenic	LTR50|LTR|ERVL	-648989	NR_003719	285622	Hs.449272	NR_003719		NBPF22P	-	NBPF member 22, pseudogene	pseudo	0.003650	0.410909	
chunk0056_389_1	chr13	93729183	93729741	+	0	NA	intron (NM_005708, intron 2 of 8)	L1ME3A|LINE|L1	129011	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.003584	0.379249	
chunk0207_420_1	chr9	137173069	137173797	+	0	NA	Intergenic	Intergenic	-1387	NM_001282477	100505993	Hs.512463	NM_001282477	ENSG00000185863	TMEM210	-	transmembrane protein 210	protein-coding	0.026099	0.626886	32(GGGCACAGTCTGGCCC,-,0.00),33(GGCACAGTCTGGCCCC,+,0.00),529(GGGCACAGGCTGTGCA,-,0.00),530(GGCACAGGCTGTGCAT,+,0.00)
chunk0084_443_1	chr17	82876781	82877273	+	0	NA	intron (NM_005993, intron 14 of 38)	intron (NM_005993, intron 14 of 38)	-36972	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.018293	0.438134	
chunk0177_252_1	chr7	25144373	25144572	+	0	NA	intron (NM_138811, intron 7 of 9)	MER115|DNA|hAT-Tip100	-19111	NM_018947	54205	Hs.437060	NM_018947	ENSG00000172115	CYCS	CYC|HCS|THC4	cytochrome c, somatic	protein-coding	0.010050	0.545000	
chunk0061_205_1	chr14	60288160	60288653	+	0	NA	3' UTR (NM_177951, exon 4 of 4)	3' UTR (NM_177951, exon 4 of 4)	39158	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.002028	0.269231	
chunk0073_29_1	chr16	2476037	2476358	+	0	NA	intron (NM_001199107, intron 1 of 7)	intron (NM_001199107, intron 1 of 7)	1051	NM_001199107	57465	Hs.353087	NM_020705	ENSG00000162065	TBC1D24	DFNA65|DFNB86|DOORS|EIEE16|FIME|TLDC6	TBC1 domain family member 24	protein-coding	0.040498	0.568323	
chunk0189_344_1	chr8	26661277	26661769	+	0	NA	Intergenic	Intergenic	83118	NM_001244604	1808	Hs.593187	NM_001386	ENSG00000092964	DPYSL2	CRMP-2|CRMP2|DHPRP2|DRP-2|DRP2|N2A3|ULIP-2|ULIP2	dihydropyrimidinase like 2	protein-coding	0.018293	0.545639	
chunk0125_81_1	chr3	64764439	64765027	+	0	NA	intron (NR_038264, intron 1 of 5)	intron (NR_038264, intron 1 of 5)	-77044	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.008503	0.404075	
chunk0098_203_1	chr2	72633370	72633694	+	0	NA	intron (NM_015189, intron 6 of 21)	MIR|SINE|MIR	192516	NM_015189	23233	Hs.303454	NM_015189	ENSG00000144036	EXOC6B	SEC15B|SEC15L2|SEMDJL3	exocyst complex component 6B	protein-coding	0.000000	0.369231	
chunk0021_422_1	chr1	247034807	247035196	+	0	NA	3' UTR (NM_033213, exon 4 of 4)	3' UTR (NM_033213, exon 4 of 4)	-26908	NM_001204221	57116	Hs.669893	NM_020394	ENSG00000197472	ZNF695	SBZF3	zinc finger protein 695	protein-coding	0.005141	0.446154	
chunk0116_298_1	chr21	40380191	40380429	+	0	NA	intron (NR_073202, intron 3 of 32)	intron (NR_073202, intron 3 of 32)	-2773	NR_038896	100506492	Hs.667053	NR_038896	ENSG00000235123	DSCAM-AS1	M41	DSCAM antisense RNA 1	ncRNA	0.008403	0.251046	
chunk0141_436_1	chr4	88976642	88977109	+	0	NA	intron (NM_014883, intron 4 of 23)	Tigger3c|DNA|TcMar-Tigger	80320	NM_014883	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.002141	0.356838	
chunk0006_387_1	chr1	74733073	74733289	+	0	NA	promoter-TSS (NM_138467)	promoter-TSS (NM_138467)	3	NR_027962	127253	Hs.348411	NM_138467	ENSG00000162623	TYW3	C1orf171	tRNA-yW synthesizing protein 3 homolog	protein-coding	0.064815	0.571429	
chunk0147_340_1	chr4	185513844	185514219	+	0	NA	intron (NM_014476, intron 4 of 7)	intron (NM_014476, intron 4 of 7)	21527	NM_014476	27295	Hs.701364	NM_014476	ENSG00000154553	PDLIM3	ALP	PDZ and LIM domain 3	protein-coding	0.016000	0.449468	132(AAGGTCACAGTGTTCT,-,0.00),133(AGGTCACAGTGTTCTG,+,0.00)
chunk0159_118_1	chr5	138725143	138725459	+	0	NA	Intergenic	Intergenic	-28095	NM_001290309	1495	Hs.445981	NM_001903	ENSG00000044115	CTNNA1	CAP102|MDPT2	catenin alpha 1	protein-coding	0.012658	0.526814	
chunk0033_169_1	chr11	15668525	15669211	+	0	NA	intron (NM_001293172, intron 1 of 2)	L2c|LINE|L2	24983	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.005831	0.413392	298(ATCACACTCTGTACTT,+,0.00)
chunk0182_389_1	chr7	100391656	100392023	+	0	NA	intron (NM_013439, intron 3 of 6)	L2b|LINE|L2	18394	NM_178273	29992	Hs.444407	NM_013439	ENSG00000085514	PILRA	FDF03	paired immunoglobin like type 2 receptor alpha	protein-coding	0.005450	0.442935	
chunk0081_307_1	chr17	45579090	45579503	+	0	NA	Intergenic	Intergenic	22566	NR_026901	644172	Hs.448859	NR_026901		MAPK8IP1P2	-	mitogen-activated protein kinase 8 interacting protein 1 pseudogene 2	pseudo	0.004843	0.417874	
chunk0061_84_1	chr14	56918972	56919427	+	0	NA	intron (NR_029385, intron 3 of 3)	intron (NR_029385, intron 3 of 3)	106016	NR_029385	100309464	Hs.637962	NR_029385	ENSG00000248550	OTX2-AS1	OTX2OS1	OTX2 antisense RNA 1 (head to head)	ncRNA	0.000000	0.410088	
chunk0145_452_1	chr4	153786404	153786940	+	0	NA	intron (NM_003013, intron 1 of 2)	intron (NM_003013, intron 1 of 2)	2404	NM_003013	6423	Hs.481022	NM_003013	ENSG00000145423	SFRP2	FRP-2|SARP1|SDF-5	secreted frizzled related protein 2	protein-coding	0.005597	0.404097	
chunk0039_349_1	chr11	105499487	105500068	+	0	NA	Intergenic	L1MC3|LINE|L1	-110296	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.000000	0.312715	281(CTGTACAGTTTGTCCC,-,0.00),282(TGTACAGTTTGTCCCT,+,0.00)
chunk0005_83_1	chr1	56101775	56102049	+	0	NA	Intergenic	MLT1B-int|LTR|ERVL-MaLR	477672	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.003650	0.363636	
chunk0161_363_1	chr5	175597526	175598261	+	0	NA	Intergenic	Intergenic	-60144	NM_001131055	3274	Hs.247885	NM_022304	ENSG00000113749	HRH2	H2R|HH2R	histamine receptor H2	protein-coding	0.009524	0.493207	
chunk0010_31_1	chr1	112515320	112515833	+	0	NA	intron (NM_004185, intron 3 of 5)	intron (NM_004185, intron 3 of 5)	6828	NM_024494	7482	Hs.258575	NM_004185	ENSG00000134245	WNT2B	WNT13	Wnt family member 2B	protein-coding	0.003899	0.507782	
chunk0012_91_1	chr1	156282745	156282954	+	0	NA	promoter-TSS (NM_015327)	promoter-TSS (NM_015327)	-20	NM_015327	23381	Hs.516837	NM_015327	ENSG00000198952	SMG5	EST1B|LPTS-RP1|LPTSRP1|SMG-5	SMG5 nonsense mediated mRNA decay factor	protein-coding	0.110048	0.676190	
chunk0150_264_1	chr5	36603059	36603536	+	0	NA	Intergenic	Intergenic	-3058	NM_001166695	6507	Hs.481918	NM_004172	ENSG00000079215	SLC1A3	EA6|EAAT1|GLAST|GLAST1	solute carrier family 1 member 3	protein-coding	0.012579	0.447699	
chunk0183_164_1	chr7	106058523	106058872	+	0	NA	Intergenic	Intergenic	53648	NM_182715	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.022923	0.605714	
chunk0124_240_1	chr3	56737427	56737801	+	0	NA	intron (NM_001128615, intron 10 of 12)	(ATTTAT)n|Simple_repeat|Simple_repeat	38103	NM_001128616	50650	Hs.476402	NM_019555	ENSG00000163947	ARHGEF3	GEF3|STA3|XPLN	Rho guanine nucleotide exchange factor 3	protein-coding	0.008021	0.328000	
chunk0172_102_1	chr6	134863656	134864328	+	0	NA	Intergenic	Intergenic	86130	NM_170771	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.010417	0.408618	
chunk0051_437_1	chr12	123083985	123084571	+	0	NA	non-coding (NR_038290, exon 3 of 3)	non-coding (NR_038290, exon 3 of 3)	2894	NR_038290	100507091	Hs.683912	NR_038290	ENSG00000251497	PITPNM2-AS1	-	PITPNM2 antisense RNA 1	ncRNA	0.013652	0.570698	
chunk0068_96_1	chr15	52250489	52251173	+	0	NA	intron (NM_018728, intron 13 of 40)	intron (NM_018728, intron 13 of 40)	26369	NR_031670	100302202		NR_031670	ENSG00000221052	MIR1266	MIRN1266|hsa-mir-1266|mir-1266	microRNA 1266	ncRNA	0.010234	0.397080	
chunk0173_114_1	chr6	143575603	143575803	+	0	NA	Intergenic	Intergenic	-6364	NR_027113	285740	Hs.432656	NR_027113	ENSG00000235740	PHACTR2-AS1	-	PHACTR2 antisense RNA 1	ncRNA	0.010000	0.288557	
chunk0198_365_1	chr8	140946606	140946938	+	0	NA	intron (NM_153831, intron 1 of 31)	L2a|LINE|L2	54541	NM_005607	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.006024	0.348348	
chunk0071_81_1	chr15	80758052	80758597	+	0	NA	Intergenic	Intergenic	-21019	NM_001293298	57214	Hs.459088	NM_018689	ENSG00000103888	CEMIP	CCSP1|HYBID|KIAA1199|TMEM2L	cell migration inducing hyaluronidase 1	protein-coding	0.007339	0.369963	
chunk0181_343_1	chr7	88260517	88260872	+	0	NA	Intergenic	Intergenic	-33701	NM_001256892	6717	Hs.489040	NM_003130	ENSG00000075142	SRI	CP-22|CP22|SCN|V19	sorcin	protein-coding	0.000000	0.320225	
chunk0198_247_1	chr8	134553455	134554169	+	0	NA	intron (NM_020863, intron 11 of 15)	MIR|SINE|MIR	-44259	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.007003	0.465734	
chunk0148_64_1	chr5	2093933	2094198	+	0	NA	Intergenic	Intergenic	206734	NR_109912	101929081	Hs.519180	NR_109912	ENSG00000249326	CTD-2194D22.4	-	uncharacterized LOC101929081	ncRNA	0.037736	0.492481	37(ATGCACACTGTGTTCC,-,0.00),38(TGCACACTGTGTTCCA,+,0.00)
chunk0024_319_1	chr10	42833772	42834502	+	0	NA	3' UTR (NM_014753, exon 23 of 23)	3' UTR (NM_014753, exon 23 of 23)	51631	NM_014753	9790	Hs.10848	NM_014753	ENSG00000165733	BMS1	ACC|BMS1L	BMS1 ribosome biogenesis factor	protein-coding	0.008219	0.372093	
chunk0081_86_1	chr17	39461183	39461657	+	0	NA	promoter-TSS (NM_015083)	promoter-TSS (NM_015083)	-91	NM_015083	51755	Hs.345028	NM_015083	ENSG00000167258	CDK12	CRK7|CRKR|CRKRS	cyclin dependent kinase 12	protein-coding	0.061181	0.515789	
chunk0054_299_1	chr13	48274874	48275214	+	0	NA	Intergenic	Intergenic	28617	NR_046414	100862704	Hs.374221	NR_046414	ENSG00000231473	RB1-DT	LINC00441|ncRNA-RB1	RB1 divergent transcript	ncRNA	0.000000	0.392962	
chunk0206_309_1	chr9	124950149	124950724	+	0	NA	3' UTR (NM_173690, exon 19 of 19)	3' UTR (NM_173690, exon 19 of 19)	-9329	NM_002077	2800	Hs.59504	NM_002077	ENSG00000136935	GOLGA1	golgin-97	golgin A1	protein-coding	0.005217	0.388889	
chunk0088_94_1	chr18	44938897	44939716	+	0	NA	intron (NM_015559, intron 3 of 5)	L1ME2z|LINE|L1	30860	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.004884	0.409756	
chunk0178_36_1	chr7	29455991	29456504	+	0	NA	intron (NM_001293069, intron 7 of 13)	L2c|LINE|L2	-23465	NM_001293075	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.005848	0.455253	
chunk0166_214_1	chr6	46833358	46833654	+	0	NA	exon (NM_005588, exon 11 of 14)	exon (NM_005588, exon 11 of 14)	40149	NM_005588	4224	Hs.179704	NM_005588	ENSG00000112818	MEP1A	PPHA	meprin A subunit alpha	protein-coding	0.023649	0.498316	123(CGGAACAGGATGTCCT,-,0.00),124(GGAACAGGATGTCCTC,+,0.00)
chunk0107_216_1	chr2	216750789	216751348	+	0	NA	Intergenic	L1PB1|LINE|L1	-55519	NM_000599	3488	Hs.607212	NM_000599	ENSG00000115461	IGFBP5	IBP5	insulin like growth factor binding protein 5	protein-coding	0.001789	0.364286	
chunk0077_193_1	chr16	79776235	79776685	+	0	NA	intron (NR_104660, intron 1 of 3)	intron (NR_104660, intron 1 of 3)	-5928	NR_104663	102467146	Hs.657587	NR_104663	ENSG00000261390	MAFTRR	linc-MAF-4|lincMAF4	MAF transcriptional regulator RNA	ncRNA	0.004444	0.434590	
chunk0060_102_1	chr14	43378486	43378770	+	0	NA	Intergenic	Intergenic	1128668	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.000000	0.308772	
chunk0139_210_1	chr4	54938006	54938235	+	0	NA	Intergenic	Intergenic	187475	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.017467	0.465217	
chunk0184_407_1	chr7	122442961	122443181	+	0	NA	intron (NM_017954, intron 15 of 29)	intron (NM_017954, intron 15 of 29)	-138560	NM_001024613	389549	Hs.553970	NM_001024613	ENSG00000128610	FEZF1	FEZ|HH22|ZNF312B	FEZ family zinc finger 1	protein-coding	0.004545	0.352941	
chunk0163_144_1	chr6	10822581	10823120	+	0	NA	intron (NM_001242385, intron 2 of 12)	intron (NM_001242385, intron 2 of 12)	15705	NM_005906	4117	Hs.446125	NM_005906	ENSG00000111837	MAK	RP62	male germ cell associated kinase	protein-coding	0.003711	0.355556	
chunk0184_173_1	chr7	116453853	116454317	+	0	NA	Intergenic	L2a|LINE|L2	-45516	NM_001233	858	Hs.212332	NM_001233	ENSG00000105971	CAV2	CAV	caveolin 2	protein-coding	0.006466	0.352688	
chunk0205_250_1	chr9	110346383	110346668	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-8641	NM_001286947	255220	Hs.147064	NM_001003936	ENSG00000204193	TXNDC8	SPTRX-3|SPTRX3|TRX6|bA427L11.2	thioredoxin domain containing 8	protein-coding	0.007018	0.412587	
chunk0026_255_1	chr10	66626030	66626610	+	0	NA	intron (NM_001127384, intron 9 of 17)	intron (NM_001127384, intron 9 of 17)	-299714	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.005172	0.358003	
chunk0002_292_1	chr1	22969293	22969661	+	0	NA	Intergenic	Intergenic	-4047	NM_001289974	646262		NM_001289974	ENSG00000215906	LACTBL1	-	lactamase beta like 1	protein-coding	0.013587	0.498645	
chunk0134_78_1	chr3	176445249	176445598	+	0	NA	Intergenic	Intergenic	-69680	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.005731	0.337143	
chunk0189_8_1	chr8	19458246	19458587	+	0	NA	intron (NR_024040, intron 4 of 9)	intron (NR_024040, intron 4 of 9)	144129	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.038123	0.429825	
chunk0079_232_1	chr17	15650753	15651114	+	0	NA	intron (NM_006470, intron 4 of 8)	intron (NM_006470, intron 4 of 8)	-31229	NM_001282540	374286	Hs.548021	NM_006382	ENSG00000241322	CDRT1	C170RF1|C17ORF1|C17ORF1A|FBXW10B|FBXW10P1|HREP|SM25H2	CMT1A duplicated region transcript 1	protein-coding	0.016620	0.541436	
chunk0182_402_1	chr7	100679354	100679791	+	0	NA	TTS (NM_005273)	TTS (NM_005273)	5832	NM_005273	2783	Hs.185172	NM_005273	ENSG00000172354	GNB2	-	G protein subunit beta 2	protein-coding	0.022883	0.616438	270(GGGAACACGGTGACCC,-,0.00),271(GGAACACGGTGACCCC,+,0.00)
chunk0158_61_1	chr5	126055907	126056806	+	0	NA	Intergenic	Intergenic	-123221	NR_105042	102546228	Hs.582529	NR_105042	ENSG00000248107	LINC02039	-	long intergenic non-protein coding RNA 2039	ncRNA	0.005562	0.341111	
chunk0007_42_1	chr1	77750412	77751425	+	0	NA	intron (NM_015017, intron 1 of 24)	intron (NM_015017, intron 1 of 24)	8961	NM_015017	23032	Hs.480597	NM_015017	ENSG00000077254	USP33	VDU1	ubiquitin specific peptidase 33	protein-coding	0.007897	0.392505	
chunk0056_402_1	chr13	93967277	93967647	+	0	NA	intron (NM_005708, intron 3 of 8)	intron (NM_005708, intron 3 of 8)	-108989	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.005405	0.355795	
chunk0177_384_1	chr7	26948199	26948398	+	0	NA	Intergenic	Intergenic	-83555	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.000000	0.390000	
chunk0037_102_1	chr11	72092714	72092949	+	0	NA	intron (NR_026886, intron 4 of 6)	L2c|LINE|L2	10556	NM_017907	55004	Hs.731528	NM_017907	ENSG00000149357	LAMTOR1	C11orf59|PDRO|Ragulator1|p18|p27RF-Rho	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	protein-coding	0.000000	0.478814	
chunk0196_439_1	chr8	116536582	116537233	+	0	NA	Intergenic	Intergenic	-211848	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.007680	0.397239	127(AAGAACACTCTGCTCC,-,0.00),128(AGAACACTCTGCTCCG,+,0.00)
chunk0201_153_1	chr9	35966955	35967431	+	0	NA	Intergenic	L1MD2|LINE|L1	-9039	NM_019897	56656	Hs.553540	NM_019897	ENSG00000278889	OR2S2	OR37A|OST715	olfactory receptor family 2 subfamily S member 2 (gene/pseudogene)	protein-coding	0.004202	0.341719	247(AGGAACTGCCTGTTTT,-,0.00),248(GGAACTGCCTGTTTTC,+,0.00)
chunk0107_203_1	chr2	216551203	216551500	+	0	NA	Intergenic	Intergenic	52554	NM_000998	6168	Hs.433701	NM_000998	ENSG00000197756	RPL37A	L37A	ribosomal protein L37a	protein-coding	0.006734	0.426174	
chunk0174_107_1	chr6	156933272	156933682	+	0	NA	intron (NM_017519, intron 3 of 18)	intron (NM_017519, intron 3 of 18)	-153746	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.009756	0.491484	
chunk0039_251_1	chr11	102177865	102178584	+	0	NA	intron (NM_001282098, intron 3 of 6)	intron (NM_001282098, intron 3 of 6)	65784	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.005563	0.384722	
chunk0035_29_1	chr11	40592726	40593533	+	0	NA	intron (NM_020929, intron 2 of 4)	intron (NM_020929, intron 2 of 4)	-299999	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001239	0.371287	
chunk0209_58_1	chrX	36961804	36962212	+	0	NA	Intergenic	Intergenic	-46351	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.014706	0.371638	
chunk0079_374_1	chr17	18087647	18088137	+	0	NA	promoter-TSS (NM_001388)	promoter-TSS (NM_001388)	25	NM_001388	1819	Hs.78582	NM_001388	ENSG00000108591	DRG2	-	developmentally regulated GTP binding protein 2	protein-coding	0.077551	0.643585	
chunk0016_64_1	chr1	193494550	193495316	+	0	NA	Intergenic	Intergenic	190188	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.007833	0.375489	
chunk0075_169_1	chr16	51953107	51953682	+	0	NA	Intergenic	MIR|SINE|MIR	120541	NM_001242473	388276	Hs.534669	NM_001242473		C16orf97	-	chromosome 16 open reading frame 97	protein-coding	0.006957	0.423611	
chunk0017_436_1	chr1	213741396	213741951	+	0	NA	Intergenic	HAL1ME|LINE|L1	-183076	NR_046189	100861504	Hs.742586	NR_046189		LINC00538	PROX1UT|Yiya	long intergenic non-protein coding RNA 538	ncRNA	0.021622	0.433453	211(CAGAACAAACTGTTCC,-,0.00),212(AGAACAAACTGTTCCT,+,0.00)
chunk0129_256_1	chr3	122387383	122387916	+	0	NA	intron (NM_014367, intron 1 of 4)	intron (NM_014367, intron 1 of 4)	3473	NM_014367	26355	Hs.584881	NM_014367	ENSG00000114023	FAM162A	C3orf28|E2IG5|HGTD-P	family with sequence similarity 162 member A	protein-coding	0.005629	0.413858	
chunk0132_193_1	chr3	157160324	157160529	+	0	NA	5' UTR (NM_020307, exon 1 of 11)	5' UTR (NM_020307, exon 1 of 11)	334	NM_020307	57018	Hs.4859	NM_020307	ENSG00000163660	CCNL1	ANIA6A|BM-001|PRO1073|ania-6a	cyclin L1	protein-coding	0.053659	0.558252	
chunk0011_340_1	chr1	152193071	152193533	+	0	NA	Intergenic	Intergenic	30894	NM_001009931	388697	Hs.490162	NM_001009931	ENSG00000197915	HRNR	FLG3|S100A16|S100a18	hornerin	protein-coding	0.002165	0.390929	
chunk0136_279_1	chr3	194749277	194749907	+	0	NA	intron (NR_037891, intron 3 of 3)	intron (NR_037891, intron 3 of 3)	41171	NR_037891	100507391	Hs.590099	NR_037891	ENSG00000237222	LINC01968	-	long intergenic non-protein coding RNA 1968	ncRNA	0.020635	0.467512	
chunk0010_125_1	chr1	114514763	114515223	+	0	NA	Intergenic	Intergenic	-3833	NM_033020	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.006522	0.455531	175(GAGAACACGATGTGTC,-,0.00),176(AGAACACGATGTGTCC,+,0.00)
chunk0009_291_1	chr1	107767202	107767665	+	0	NA	intron (NM_006113, intron 7 of 26)	intron (NM_006113, intron 7 of 26)	-78929	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.006479	0.400862	
chunk0053_378_1	chr13	35964567	35965347	+	0	NA	intron (NM_004734, intron 3 of 17)	MER58B|DNA|hAT-Charlie	-109096	NM_001195430	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.010256	0.370038	524(TAGAAGACACTGTTCT,-,0.00),525(AGAAGACACTGTTCTG,+,0.00)
chunk0072_231_1	chr15	95802913	95803492	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	370109	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.003454	0.331034	
chunk0189_401_1	chr8	27583403	27583982	+	0	NA	Intergenic	Intergenic	27059	NR_106902	102465508		NR_106902	ENSG00000284280	MIR6843	hsa-mir-6843	microRNA 6843	ncRNA	0.017271	0.570690	
chunk0005_25_1	chr1	54385356	54385616	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	20909	NM_145716	23648	Hs.476706	NM_018070	ENSG00000157216	SSBP3	CSDP|SSDP|SSDP1	single stranded DNA binding protein 3	protein-coding	0.000000	0.429119	
chunk0007_365_1	chr1	85125861	85126428	+	0	NA	intron (NM_001288563, intron 18 of 21)	intron (NM_001288563, intron 18 of 21)	-7650	NR_039619	100616481		NR_039619	ENSG00000266110	MIR4423	mir-4423	microRNA 4423	ncRNA	0.001764	0.350352	
chunk0102_153_1	chr2	147174798	147175331	+	0	NA	Intergenic	Intergenic	588007	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.005629	0.406367	
chunk0135_114_1	chr3	186969758	186970013	+	0	NA	intron (NM_173216, intron 2 of 7)	intron (NM_173216, intron 2 of 7)	39359	NM_173217	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.023529	0.410156	101(TGGTACACACAGTACT,-,0.00),102(GGTACACACAGTACTA,+,0.00)
chunk0010_283_1	chr1	117541193	117541643	+	0	NA	Intergenic	Intergenic	64352	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.008889	0.483370	
chunk0086_274_1	chr18	23651452	23651759	+	0	NA	intron (NM_001308238, intron 1 of 8)	intron (NM_001308238, intron 1 of 8)	11280	NM_173505	147463	Hs.355689	NM_173505	ENSG00000154065	ANKRD29	-	ankyrin repeat domain 29	protein-coding	0.003257	0.431818	
chunk0209_154_1	chrX	42707672	42708642	+	0	NA	Intergenic	L1MCa|LINE|L1	70078	NR_002191									0.002062	0.331617	
chunk0016_455_1	chr1	204213829	204214182	+	0	NA	promoter-TSS (NM_198447)	promoter-TSS (NM_198447)	87	NM_198447	127845	Hs.532401	NM_198447	ENSG00000174567	GOLT1A	CGI-141|GOT1|HMFN1187|YMR292W|hGOT1b	golgi transport 1A	protein-coding	0.059490	0.649718	
chunk0157_310_1	chr5	121727123	121727466	+	0	NA	Intergenic	Intergenic	-124661	NM_177478	94033	Hs.105324	NM_177478	ENSG00000181867	FTMT	MTF	ferritin mitochondrial	protein-coding	0.017493	0.401163	
chunk0175_288_1	chr7	7773380	7773836	+	0	NA	intron (NM_001302350, intron 3 of 4)	intron (NM_001302350, intron 3 of 4)	-55001	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.000000	0.350109	
chunk0023_66_1	chr10	22086599	22088020	+	0	NA	Intergenic	Intergenic	-83588	NM_022365	64215	Hs.499000	NM_022365	ENSG00000136770	DNAJC1	DNAJL1|ERdj1|HTJ1|MTJ1	DnaJ heat shock protein family (Hsp40) member C1	protein-coding	0.007037	0.355837	
chunk0098_216_1	chr2	73546198	73546851	+	0	NA	intron (NM_015120, intron 12 of 22)	L2c|LINE|L2	89421	NR_046762	100874291	Hs.668279	NR_046762	ENSG00000230002	ALMS1-IT1	-	ALMS1 intronic transcript 1	ncRNA	0.012251	0.350153	
chunk0057_249_1	chr13	104993837	104994056	+	0	NA	Intergenic	LTR16|LTR|ERVL	-471921	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.004566	0.509091	111(AGGCACAGGGTGTGCC,-,0.00),112(GGCACAGGGTGTGCCT,+,0.00)
chunk0160_231_1	chr5	155618319	155618584	+	0	NA	Intergenic	Intergenic	604751	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.007547	0.409774	
chunk0193_458_1	chr8	81322157	81322946	+	0	NA	Intergenic	MER67C|LTR|ERV1	42068	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.002535	0.387342	
chunk0108_141_1	chr2	230755936	230756537	+	0	NA	intron (NM_001130849, intron 1 of 8)	Tigger3a|DNA|TcMar-Tigger	42688	NM_001130849	51719	Hs.603930	NM_016289	ENSG00000135932	CAB39	CGI-66|MO25	calcium binding protein 39	protein-coding	0.003328	0.416944	
chunk0191_387_1	chr8	57205659	57206160	+	0	NA	Intergenic	Intergenic	-12367	NR_038235	100507651	Hs.371831	NR_038235	ENSG00000253301	LINC01606	-	long intergenic non-protein coding RNA 1606	ncRNA	0.049900	0.569721	
chunk0048_298_1	chr12	82789506	82790187	+	0	NA	intron (NM_152588, intron 1 of 11)	MIRc|SINE|MIR	102691	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.001468	0.382698	
chunk0103_10_1	chr2	158917610	158918007	+	0	NA	Intergenic	L1MD2|LINE|L1	-50826	NM_033394	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.010076	0.389447	170(TAGAACAGCCTGTATC,-,0.00),171(AGAACAGCCTGTATCT,+,0.00),315(GAGAACAGCCTGGGCA,-,0.00),335(AGGGAGACCCTGTCCC,-,0.00),336(GGGAGACCCTGTCCCT,+,0.00)
chunk0094_191_1	chr2	6194970	6195169	+	0	NA	Intergenic	LTR10C|LTR|ERV1	180353	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.020101	0.435000	
chunk0133_422_1	chr3	174675254	174675922	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-183733	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.002994	0.346786	316(CAGAACAGACTGTTCT,-,0.00),317(AGAACAGACTGTTCTG,+,0.00)
chunk0007_247_1	chr1	82651866	82652256	+	0	NA	Intergenic	Intergenic	332861	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.007692	0.301790	
chunk0121_169_1	chr3	19901900	19902361	+	0	NA	intron (NM_144715, intron 6 of 12)	intron (NM_144715, intron 6 of 12)	32084	NM_144715	151651	Hs.733920	NM_144715	ENSG00000163576	EFHB	CFAP21	EF-hand domain family member B	protein-coding	0.010846	0.396104	
chunk0146_280_1	chr4	163641352	163641876	+	0	NA	intron (NM_001166373, intron 4 of 7)	intron (NM_001166373, intron 4 of 7)	-27990	NM_017923	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.003817	0.321905	258(AGGAACAGAATGTTCC,-,0.00),259(GGAACAGAATGTTCCT,+,0.00)
chunk0059_50_1	chr14	30014037	30014378	+	0	NA	Intergenic	LTR16A1|LTR|ERVL	-86514	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005865	0.447368	
chunk0193_324_1	chr8	78860466	78860667	+	0	NA	Intergenic	Intergenic	-55043	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.000000	0.336634	
chunk0092_228_1	chr19	32362946	32363375	+	0	NA	intron (NM_001136156, intron 5 of 6)	intron (NM_001136156, intron 5 of 6)	17552	NM_001136156	22847	Hs.205392	NM_014910	ENSG00000168813	ZNF507	-	zinc finger protein 507	protein-coding	0.013986	0.409302	
chunk0210_310_1	chrX	90267978	90268186	+	0	NA	Intergenic	L1M5|LINE|L1	346141	NM_138960	90316	Hs.592220	NM_138960	ENSG00000153779	TGIF2LX	TGIFLX	TGFB induced factor homeobox 2 like X-linked	protein-coding	0.009615	0.330144	
chunk0151_15_1	chr5	41297531	41297803	+	0	NA	Intergenic	LTR41|LTR|ERVL	-36229	NM_001115131	729	Hs.481992	NM_000065	ENSG00000039537	C6	-	complement C6	protein-coding	0.000000	0.505495	
chunk0133_282_1	chr3	172115788	172116466	+	0	NA	intron (NM_022763, intron 2 of 25)	intron (NM_022763, intron 2 of 25)	75573	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.007375	0.365243	
chunk0201_64_1	chr9	33996137	33996542	+	0	NA	intron (NM_018449, intron 3 of 28)	intron (NM_018449, intron 3 of 28)	-43485	NR_003685	100113379		NR_003685	ENSG00000238886	SNORD121A	-	small nucleolar RNA, C/D box 121A	snoRNA	0.002469	0.359606	
chunk0172_108_1	chr6	135010276	135011041	+	0	NA	intron (NM_001145158, intron 3 of 16)	intron (NM_001145158, intron 3 of 16)	-31226	NR_037435	100500880		NR_037435	ENSG00000283409	MIR3662	mir-3662	microRNA 3662	ncRNA	0.000000	0.285901	
chunk0137_51_1	chr4	11598712	11598911	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	-169898	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.005025	0.425000	
chunk0195_431_1	chr8	100942038	100942334	+	0	NA	intron (NM_001135700, intron 2 of 5)	intron (NM_001135700, intron 2 of 5)	8385	NM_001135702	7534	Hs.492407	NM_003406	ENSG00000164924	YWHAZ	14-3-3-zeta|HEL-S-3|HEL-S-93|HEL4|KCIP-1|POPCHAS|YWHAD	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta	protein-coding	0.000000	0.353535	
chunk0140_150_1	chr4	69342753	69343762	+	0	NA	Intergenic	LTR10C|LTR|ERV1	62758	NM_001207004	54490	Hs.653154	NM_053039	ENSG00000135226	UGT2B28	-	UDP glucuronosyltransferase family 2 member B28	protein-coding	0.006938	0.376238	602(AAGAACATAAAGTACA,-,0.00),603(AGAACATAAAGTACAT,+,0.00)
chunk0205_444_1	chr9	115441974	115442228	+	0	NA	Intergenic	Intergenic	300283	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.007874	0.419608	
chunk0063_261_1	chr14	83434798	83435020	+	0	NA	Intergenic	L1PB1|LINE|L1	-1811848	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.004505	0.336323	
chunk0206_340_1	chr9	125541078	125541385	+	0	NA	intron (NM_001006618, intron 7 of 7)	intron (NM_001006618, intron 7 of 7)	166003	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.019544	0.386364	
chunk0188_423_1	chr8	19007429	19007927	+	0	NA	intron (NM_015310, intron 1 of 15)	intron (NM_015310, intron 1 of 15)	6008	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.010040	0.390782	
chunk0145_458_1	chr4	154229463	154229693	+	0	NA	Intergenic	Intergenic	161719	NM_017639	54798	Hs.655664	NM_017639	ENSG00000197410	DCHS2	CDH27|CDHJ|CDHR7|PCDH23|PCDHJ	dachsous cadherin-related 2	protein-coding	0.004348	0.337662	
chunk0007_306_1	chr1	84256989	84257428	+	0	NA	Intergenic	Intergenic	-41158	NM_001010971	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.006834	0.368182	237(TGAACTTTTTGTCCTT,+,0.00)
chunk0066_304_1	chr15	35673478	35673721	+	0	NA	intron (NR_038251, intron 1 of 2)	intron (NR_038251, intron 1 of 2)	-127396	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.004115	0.413934	
chunk0114_382_1	chr20	63083840	63084160	+	0	NA	non-coding (NR_033370, exon 4 of 5)	non-coding (NR_033370, exon 4 of 5)	-17292	NR_003244	768096	Hs.549606	NR_003244		HAR1A	HAR1F|LINC00064|NCRNA00064	highly accelerated region 1A	ncRNA	0.053125	0.647975	234(GTGGTCACTGTGTTCC,-,0.00),235(TGGTCACTGTGTTCCC,+,0.00)
chunk0108_49_1	chr2	226909679	226910260	+	0	NA	intron (NM_032276, intron 5 of 6)	MER58A|DNA|hAT-Charlie	74014	NM_001167608	84236	Hs.471514	NM_032276	ENSG00000144468	RHBDD1	RHBDL4|RRP4	rhomboid domain containing 1	protein-coding	0.006885	0.414089	
chunk0120_63_1	chr3	3179538	3179831	+	0	NA	promoter-TSS (NM_001173482)	promoter-TSS (NM_001173482)	33	NM_016302	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.102389	0.717687	
chunk0175_428_1	chr6	169038790	169038989	+	0	NA	Intergenic	L1PB4|LINE|L1	123412	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.000000	0.340000	
chunk0003_225_1	chr1	35554518	35554737	+	0	NA	intron (NM_024874, intron 1 of 20)	intron (NM_024874, intron 1 of 20)	2809	NM_024874	79932	Hs.456507	NM_024874	ENSG00000142687	KIAA0319L	AAVR|AAVRL	KIAA0319 like	protein-coding	0.009132	0.350000	
chunk0065_400_1	chr14	105162389	105162737	+	0	NA	intron (NM_002226, intron 2 of 25)	intron (NM_002226, intron 2 of 25)	6261	NM_145159	3714	Hs.433445	NM_002226	ENSG00000184916	JAG2	HJ2|SER2	jagged canonical Notch ligand 2	protein-coding	0.000000	0.627507	
chunk0039_300_1	chr11	102990137	102990521	+	0	NA	Intergenic	Intergenic	-34595	NM_002427	4322	Hs.2936	NM_002427	ENSG00000137745	MMP13	CLG3|MANDP1|MDST|MMP-13	matrix metallopeptidase 13	protein-coding	0.007812	0.392208	
chunk0025_276_1	chr10	56213073	56213375	+	0	NA	Intergenic	L1PA13|LINE|L1	148049	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.013245	0.534653	
chunk0025_267_1	chr10	55650973	55651172	+	0	NA	Intergenic	Intergenic	52082	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.010050	0.255000	
chunk0010_423_1	chr1	119747109	119747308	+	0	NA	TTS (NM_005518)	TTS (NM_005518)	21724	NM_001166107	3158	Hs.59889	NM_005518	ENSG00000134240	HMGCS2	-	3-hydroxy-3-methylglutaryl-CoA synthase 2	protein-coding	0.010050	0.520000	
chunk0167_139_1	chr6	62269492	62270215	+	0	NA	intron (NM_152688, intron 1 of 8)	L1ME2|LINE|L1	16342	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.004149	0.354972	
chunk0175_354_1	chr6	167728337	167729517	+	0	NA	Intergenic	L1MC2|LINE|L1	-45140	NR_117092	441178	Hs.628956	NM_001025489	ENSG00000203688	LINC02487	-	long intergenic non-protein coding RNA 2487	ncRNA	0.011017	0.348010	
chunk0076_161_1	chr16	67346280	67346759	+	0	NA	promoter-TSS (NM_001161575)	promoter-TSS (NM_001161575)	-836	NM_001161575	55282	Hs.125139	NM_018296	ENSG00000159708	LRRC36	RORBP70|XLHSRF2	leucine rich repeat containing 36	protein-coding	0.008351	0.381250	
chunk0029_353_1	chr10	107239704	107239963	+	0	NA	Intergenic	Intergenic	-75125	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.007722	0.326923	
chunk0083_241_1	chr17	67639617	67640244	+	0	NA	intron (NM_181671, intron 6 of 9)	intron (NM_181671, intron 6 of 9)	-77903	NM_001303272	25926	Hs.463936	NM_015462	ENSG00000130935	NOL11	-	nucleolar protein 11	protein-coding	0.012759	0.442675	
chunk0176_450_1	chr7	20104376	20105070	+	0	NA	intron (NR_110114, intron 1 of 5)	(TATAT)n|Simple_repeat|Simple_repeat	35703	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.002882	0.369784	
chunk0086_111_1	chr18	14907541	14907915	+	0	NA	Intergenic	Intergenic	-38539	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.016043	0.530667	122(TGGATCAGCATGTCCC,-,0.00),123(GGATCAGCATGTCCCG,+,0.00)
chunk0094_44_1	chr2	2401771	2402111	+	0	NA	Intergenic	Intergenic	-70628	NM_015025	23040	Hs.434418	NM_015025	ENSG00000186487	MYT1L	MRD39|NZF1|ZC2H2C2|ZC2HC4B|myT1-L	myelin transcription factor 1 like	protein-coding	0.005882	0.381232	
chunk0003_183_1	chr1	33688052	33688251	+	0	NA	intron (NM_052896, intron 25 of 69)	L1ME3G|LINE|L1	-172324	NM_145205	127540	Hs.568628	NM_145205	ENSG00000176256	HMGB4	dJ1007G16.5	high mobility group box 4	protein-coding	0.005025	0.335000	
chunk0124_454_1	chr3	61610253	61610829	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	48972	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.006944	0.407279	
chunk0102_64_1	chr2	142874300	142874824	+	0	NA	Intergenic	MamGypLTR1b|LTR|Gypsy	-3064	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.003817	0.401905	
chunk0138_45_1	chr4	31411500	31412198	+	0	NA	Intergenic	Intergenic	240705	NR_125935	102723778	Hs.210739	NR_125935	ENSG00000251182	LINC02497	-	long intergenic non-protein coding RNA 2497	ncRNA	0.002865	0.316166	
chunk0087_195_1	chr18	35755191	35755652	+	0	NA	Intergenic	L2b|LINE|L2	100852	NM_020474	2589	Hs.514806	NM_020474	ENSG00000141429	GALNT1	GALNAC-T1	polypeptide N-acetylgalactosaminyltransferase 1	protein-coding	0.015184	0.497835	290(CAGAACAAAGAGTTCC,-,0.00),291(AGAACAAAGAGTTCCA,+,0.00)
chunk0028_342_1	chr10	92151693	92152015	+	0	NA	intron (NM_001178137, intron 4 of 9)	L2a|LINE|L2	91425	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.003106	0.396285	
chunk0168_391_1	chr6	94267955	94268214	+	0	NA	Intergenic	Intergenic	561001	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.003861	0.288462	
chunk0109_27_1	chr20	479546	479898	+	0	NA	Intergenic	Intergenic	-17169	NM_144628	128637	Hs.590876	NM_144628	ENSG00000125875	TBC1D20	C20orf140|WARBM4	TBC1 domain family member 20	protein-coding	0.005682	0.325779	
chunk0195_368_1	chr8	99931753	99932304	+	0	NA	Intergenic	L1M3|LINE|L1	-38014	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.001815	0.364130	
chunk0110_386_1	chr20	20102581	20103162	+	0	NA	intron (NM_015585, intron 8 of 26)	intron (NM_015585, intron 8 of 26)	46225	NM_001167816	26074	Hs.729168	NM_015585	ENSG00000089101	CFAP61	C20orf26|CaM-IP3|dJ1002M8.3|dJ1178H5.4	cilia and flagella associated protein 61	protein-coding	0.000000	0.453608	
chunk0094_227_1	chr2	6848168	6848552	+	0	NA	TTS (NM_207315)	TTS (NM_207315)	-7896	NR_126359	104326052	Hs.7155	NR_126359		NRIR	lncRNA-CMPK2	negative regulator of interferon response	ncRNA	0.000000	0.327273	
chunk0090_351_1	chr18	76606528	76606785	+	0	NA	Intergenic	Intergenic	-13121	NR_120419	400660	Hs.131718	NR_120419	ENSG00000266256	LINC00683	-	long intergenic non-protein coding RNA 683	ncRNA	0.000000	0.441860	91(ATGGACATACTGACCC,-,0.00),92(TGGACATACTGACCCT,+,0.00)
chunk0015_117_1	chr1	185339032	185339262	+	0	NA	Intergenic	Intergenic	-4108	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.004348	0.437229	
chunk0208_436_1	chrX	30457574	30457935	+	0	NA	Intergenic	MIR|SINE|MIR	120162	NM_025159	80231	Hs.665009	NM_025159	ENSG00000120280	CXorf21	-	chromosome X open reading frame 21	protein-coding	0.005540	0.367403	
chunk0171_345_1	chr6	130065851	130066074	+	0	NA	intron (NM_001007102, intron 9 of 21)	intron (NM_001007102, intron 9 of 21)	47379	NM_001007102	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.004484	0.513393	109(CAGGGCAGACTGTCCA,-,0.00),110(AGGGCAGACTGTCCAC,+,0.00)
chunk0162_434_1	chr5	180440068	180440475	+	0	NA	Intergenic	Intergenic	-54128	NM_001303241	57472	Hs.608380	NM_015455	ENSG00000113300	CNOT6	CCR4|Ccr4a	CCR4-NOT transcription complex subunit 6	protein-coding	0.017199	0.492647	
chunk0046_134_1	chr12	57772183	57772481	+	0	NA	promoter-TSS (NM_005371)	promoter-TSS (NM_005371)	-201	NM_023033	4234	Hs.42957	NM_005371	ENSG00000037897	METTL1	C12orf1|TRM8|TRMT8|YDL201w	methyltransferase like 1	protein-coding	0.030201	0.615385	
chunk0088_386_1	chr18	54303503	54303768	+	0	NA	Intergenic	L1MEd|LINE|L1	34156	NM_007195	11201	Hs.438533	NM_007195	ENSG00000101751	POLI	RAD30B|RAD3OB|eta2	DNA polymerase iota	protein-coding	0.000000	0.409774	
chunk0171_267_1	chr6	127574419	127574989	+	0	NA	Intergenic	Intergenic	-2470	NM_001010905	352999	Hs.226268	NM_001010905	ENSG00000184530	C6orf58	LEG1	chromosome 6 open reading frame 58	protein-coding	0.005263	0.345009	
chunk0159_112_1	chr5	138609435	138610157	+	0	NA	Intergenic	Intergenic	-34167	NM_004134	3313	Hs.184233	NM_004134	ENSG00000113013	HSPA9	CRP40|CSA|EVPLS|GRP-75|GRP75|HEL-S-124m|HSPA9B|MOT|MOT2|MTHSP75|PBP74|SAAN|SIDBA4	heat shock protein family A (Hsp70) member 9	protein-coding	0.018006	0.517289	
chunk0194_17_1	chr8	81573682	81574117	+	0	NA	Intergenic	L1PB1|LINE|L1	-42584	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.006897	0.380734	
chunk0009_127_1	chr1	103445704	103446129	+	0	NA	intron (NM_001286997, intron 1 of 3)	L1PA11|LINE|L1	79567	NM_001286997	101928436	Hs.558999	NM_001286997		LOC101928436	-	uncharacterized LOC101928436	protein-coding	0.004706	0.356808	
chunk0074_65_1	chr16	21222513	21222876	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-8184	NM_003460	7783	Hs.73982	NM_003460	ENSG00000103310	ZP2	OOMD6|ZPA|Zp-2	zona pellucida glycoprotein 2	protein-coding	0.002755	0.414835	
chunk0028_220_1	chr10	89589085	89589450	+	0	NA	intron (NM_148977, intron 5 of 6)	L2b|LINE|L2	3560	NR_029524	406901		NR_029524	ENSG00000198997	MIR107	MIRN107|miR-107	microRNA 107	ncRNA	0.008219	0.363388	
chunk0021_428_1	chr1	247514517	247514951	+	0	NA	intron (NM_001281834, intron 1 of 6)	L1PB|LINE|L1	-3718	NM_001281837	148823	Hs.732113	NM_145278	ENSG00000169224	GCSAML	C1orf150	germinal center associated signaling and motility like	protein-coding	0.009217	0.370115	196(TTGAACAGGGTGTCCT,-,0.00),197(TGAACAGGGTGTCCTT,+,0.00)
chunk0007_87_1	chr1	78504288	78504790	+	0	NA	intron (NM_001039585, intron 3 of 3)	intron (NM_001039585, intron 3 of 3)	13496	NM_000959	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.000000	0.270378	
chunk0161_315_1	chr5	173489540	173489769	+	0	NA	Intergenic	Intergenic	-89980	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.000000	0.347826	
chunk0070_434_1	chr15	78127947	78128203	+	0	NA	intron (NM_001301224, intron 1 of 4)	intron (NM_001301224, intron 1 of 4)	3460	NM_001301224	10518	Hs.129867	NM_006383	ENSG00000136425	CIB2	DFNB48|KIP2|USH1J	calcium and integrin binding family member 2	protein-coding	0.003906	0.463035	
chunk0191_34_1	chr8	43065658	43065872	+	0	NA	intron (NR_033698, intron 2 of 7)	HAL1|LINE|L1	9466	NR_033698	2339	Hs.370312	NM_002027	ENSG00000168522	FNTA	FPTA|PGGT1A|PTAR2	farnesyltransferase, CAAX box, alpha	protein-coding	0.004673	0.330233	
chunk0021_354_1	chr1	246245877	246246331	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	171308	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.006608	0.316484	
chunk0177_258_1	chr7	25294633	25295041	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-66351	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.009804	0.403423	
chunk0092_340_1	chr19	35146867	35147484	+	0	NA	intron (NM_022006, intron 1 of 5)	MLT1I|LTR|ERVL-MaLR	3925	NM_022006	53822	Hs.134729	NM_022006	ENSG00000221946	FXYD7	-	FXYD domain containing ion transport regulator 7	protein-coding	0.011345	0.501618	
chunk0020_223_1	chr1	235408754	235409663	+	0	NA	intron (NM_001287801, intron 3 of 17)	intron (NM_001287801, intron 3 of 17)	41848	NM_001079515	6905	Hs.744998	NM_003193	ENSG00000284770	TBCE	HRD|KCS|KCS1|PEAMO|pac2	tubulin folding cofactor E	protein-coding	0.003300	0.390110	424(GAGCACATGCTGTTTC,-,0.00),425(AGCACATGCTGTTTCC,+,0.00)
chunk0149_142_1	chr5	20036115	20036340	+	0	NA	intron (NM_001291956, intron 2 of 14)	intron (NM_001291956, intron 2 of 14)	-47983	NM_001167667	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004444	0.362832	
chunk0069_159_1	chr15	62541926	62542178	+	0	NA	Intergenic	MIRb|SINE|MIR	103129	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.007937	0.332016	
chunk0175_282_1	chr7	7640697	7641054	+	0	NA	5' UTR (NM_002947, exon 5 of 8)	5' UTR (NM_002947, exon 5 of 8)	239	NM_001302348	729852	Hs.652371	NM_001302348	ENSG00000219545	UMAD1	RPA3-AS1|RPA3OS	UBAP1-MVB12-associated (UMA) domain containing 1	protein-coding	0.084034	0.634078	
chunk0190_310_1	chr8	38494920	38495119	+	0	NA	Intergenic	Intergenic	-26185	NM_023105	2260	Hs.264887	NM_015850	ENSG00000077782	FGFR1	BFGFR|CD331|CEK|ECCL|FGFBR|FGFR-1|FLG|FLT-2|FLT2|HBGFR|HH2|HRTFDS|KAL2|N-SAM|OGD|bFGF-R-1	fibroblast growth factor receptor 1	protein-coding	0.025126	0.580000	
chunk0114_409_1	chr20	63889679	63889878	+	0	NA	intron (NM_001243891, intron 6 of 6)	intron (NM_001243891, intron 6 of 6)	-5324	NM_025219	80331	Hs.164419	NM_025219	ENSG00000101152	DNAJC5	CLN4|CLN4B|CSP|DNAJC5A|NCL|mir-941-2|mir-941-3|mir-941-4|mir-941-5	DnaJ heat shock protein family (Hsp40) member C5	protein-coding	0.020101	0.515000	
chunk0053_372_1	chr13	35719168	35719449	+	0	NA	Intergenic	Intergenic	21581	NR_132115	100507114	Hs.236298	NR_132115	ENSG00000236036	LINC00445	-	long intergenic non-protein coding RNA 445	ncRNA	0.014235	0.507092	
chunk0114_254_1	chr21	16094859	16095424	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	24027	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.005310	0.411661	
chunk0211_387_1	chrX	128048490	128048883	+	0	NA	Intergenic	L1M4b|LINE|L1	3717	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.000000	0.291878	
chunk0166_171_1	chr6	45964797	45965673	+	0	NA	intron (NM_001114086, intron 1 of 5)	intron (NM_001114086, intron 1 of 5)	-27638	NR_045673	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.004566	0.379704	
chunk0092_222_1	chr19	31990708	31991120	+	0	NA	Intergenic	Intergenic	-34948	NR_110674	100996665	Hs.443685	NR_110673	ENSG00000267779	LINC01533	CTC-360P9.3	long intergenic non-protein coding RNA 1533	ncRNA	0.009709	0.421308	
chunk0055_381_1	chr13	73258967	73259506	+	0	NA	Intergenic	Intergenic	200444	NM_001730	688	Hs.508234	NM_001730	ENSG00000102554	KLF5	BTEB2|CKLF|IKLF	Kruppel like factor 5	protein-coding	0.012987	0.457407	
chunk0086_338_1	chr18	24809742	24809960	+	0	NA	Intergenic	Intergenic	181669	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.004587	0.461187	
chunk0133_428_1	chr3	174862206	174862419	+	0	NA	intron (NM_207015, intron 1 of 13)	intron (NM_207015, intron 1 of 13)	2991	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.004695	0.485981	
chunk0080_134_1	chr17	27414717	27415613	+	0	NA	Intergenic	L2c|LINE|L2	-2840	NR_033892	440419	Hs.385755	NR_033892	ENSG00000266433	TBC1D3P5	-	TBC1 domain family member 3 pseudogene 5	pseudo	0.010045	0.464883	
chunk0006_34_1	chr1	64172385	64172931	+	0	NA	intron (NM_005012, intron 8 of 8)	intron (NM_005012, intron 8 of 8)	-31149	NM_152489	148581	Hs.388746	NM_152489	ENSG00000177414	UBE2U	-	ubiquitin conjugating enzyme E2 U	protein-coding	0.003663	0.334552	
chunk0090_249_1	chr18	74148141	74148416	+	0	NA	promoter-TSS (NM_152676)	promoter-TSS (NM_152676)	-233	NM_014177	29090	Hs.532835	NM_014177	ENSG00000075336	TIMM21	C18orf55|HSPC154|TIM21	translocase of inner mitochondrial membrane 21	protein-coding	0.072727	0.586957	
chunk0173_271_1	chr6	147433623	147433944	+	0	NA	Intergenic	Intergenic	-74909	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.003115	0.394410	
chunk0053_234_1	chr13	32507254	32507789	+	0	NA	non-coding (NR_026928, exon 1 of 1)	non-coding (NR_026928, exon 1 of 1)	1874	NR_026928	116828	Hs.658751	NR_026928	ENSG00000281026	N4BP2L2-IT2	CG030	N4BPL2 intronic transcript 2	ncRNA	0.005607	0.386194	
chunk0193_452_1	chr8	81216720	81217049	+	0	NA	Intergenic	Intergenic	-63599	NM_001444	2171	Hs.408061	NM_001444	ENSG00000164687	FABP5	E-FABP|EFABP|KFABP|PA-FABP|PAFABP	fatty acid binding protein 5	protein-coding	0.009119	0.387879	
chunk0152_338_1	chr5	62432650	62433268	+	0	NA	intron (NM_001134779, intron 1 of 29)	L1MC4|LINE|L1	14075	NM_001134779	51194	Hs.482269	NM_016338	ENSG00000086200	IPO11	RanBP11	importin 11	protein-coding	0.009709	0.355412	346(GGGAACATTCTGTTCC,-,0.00),347(GGAACATTCTGTTCCC,+,0.00)
chunk0046_57_1	chr12	55703251	55703709	+	0	NA	intron (NM_001144996, intron 1 of 24)	intron (NM_001144996, intron 1 of 24)	4422	NM_001144996	3679	Hs.524484	NM_002206	ENSG00000135424	ITGA7	-	integrin subunit alpha 7	protein-coding	0.006550	0.525054	234(AAGAACTGCCTGTTCC,-,0.00),235(AGAACTGCCTGTTCCC,+,0.00)
chunk0120_40_1	chr3	2769824	2770024	+	0	NA	intron (NM_001206955, intron 5 of 23)	intron (NM_001206955, intron 5 of 23)	-122291	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.000000	0.437811	
chunk0192_219_1	chr8	65246509	65246746	+	0	NA	Intergenic	HAL1b|LINE|L1	-66287	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.012658	0.491597	
chunk0032_258_1	chr11	8739321	8739738	+	0	NA	intron (NM_005418, intron 5 of 22)	intron (NM_005418, intron 5 of 22)	-29249	NR_120590	102724784	Hs.613276	NR_120590		LOC102724784	-	uncharacterized LOC102724784	ncRNA	0.004796	0.454545	
chunk0082_56_1	chr17	51242742	51243009	+	0	NA	intron (NM_017643, intron 2 of 16)	L1MC5a|LINE|L1	17191	NM_017643	54799	Hs.656803	NM_017643	ENSG00000011258	MBTD1	SA49P01	mbt domain containing 1	protein-coding	0.007491	0.328358	
chunk0018_420_1	chr1	222713184	222713552	+	0	NA	promoter-TSS (NM_022831)	promoter-TSS (NM_022831)	47	NM_001288581	148362	Hs.534965	NM_144695	ENSG00000162819	BROX	C1orf58	BRO1 domain and CAAX motif containing	protein-coding	0.065217	0.590786	
chunk0130_139_1	chr3	132232215	132232708	+	0	NA	Intergenic	Intergenic	-84906	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.002028	0.360324	
chunk0142_141_1	chr4	94855792	94855991	+	0	NA	intron (NM_001203, intron 1 of 12)	L1MA6|LINE|L1	97914	NM_001203	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.005025	0.280000	
chunk0066_441_1	chr15	39828774	39829056	+	0	NA	intron (NM_001271854, intron 1 of 3)	intron (NM_001271854, intron 1 of 3)	361	NM_001271855	11245	Hs.37196	NM_007223	ENSG00000166073	GPR176	HB-954	G protein-coupled receptor 176	protein-coding	0.010638	0.388693	100(GGAACGGTATGTCCAT,+,0.00)
chunk0178_123_1	chr7	31493187	31493426	+	0	NA	Intergenic	Intergenic	-20765	NM_001257967	223075	Hs.224269	NM_194300	ENSG00000180347	ITPRID1	CCDC129	ITPR interacting domain containing 1	protein-coding	0.004184	0.525000	
chunk0061_277_1	chr14	61537575	61537994	+	0	NA	intron (NM_006255, intron 12 of 13)	intron (NM_006255, intron 12 of 13)	32410	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.011933	0.480952	
chunk0084_145_1	chr17	76524644	76525122	+	0	NA	Intergenic	Intergenic	-2703	NR_033357	768206	Hs.634380	NM_001077620	ENSG00000214140	PRCD	RP36	photoreceptor disc component	protein-coding	0.025105	0.559499	
chunk0161_73_1	chr5	166788289	166788574	+	0	NA	Intergenic	Intergenic	137939	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.003509	0.384615	
chunk0061_266_1	chr14	61435738	61436316	+	0	NA	intron (NM_006255, intron 2 of 13)	intron (NM_006255, intron 2 of 13)	114584	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.006920	0.452504	
chunk0026_93_1	chr10	61595573	61596157	+	0	NA	Intergenic	Intergenic	-67096	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.000000	0.331624	
chunk0021_282_1	chr1	244348794	244349165	+	0	NA	Intergenic	Intergenic	-3656	NM_001012970	200159	Hs.442703	NM_001012970	ENSG00000173728	C1orf100	-	chromosome 1 open reading frame 100	protein-coding	0.024259	0.518817	154(AAGCACATGGTGTACC,-,0.00),155(AGCACATGGTGTACCT,+,0.00)
chunk0040_111_1	chr11	111983071	111983270	+	0	NA	intron (NM_001037954, intron 7 of 19)	intron (NM_001037954, intron 7 of 19)	5861	NM_033425	85458	Hs.655626	NM_033425	ENSG00000150764	DIXDC1	CCD1	DIX domain containing 1	protein-coding	0.010050	0.450000	
chunk0037_108_1	chr11	72265964	72266271	+	0	NA	Intergenic	HAL1|LINE|L1	-21941	NM_005169	401	Hs.731115	NM_005169	ENSG00000165462	PHOX2A	ARIX|CFEOM2|FEOM2|NCAM2|PMX2A	paired like homeobox 2A	protein-coding	0.000000	0.457792	
chunk0072_51_1	chr16	1331652	1332175	+	0	NA	Intergenic	Intergenic	-1692	NM_001199097	8938	Hs.458427	NM_003933	ENSG00000007516	BAIAP3	BAP3	BAI1 associated protein 3	protein-coding	0.032505	0.627863	
chunk0178_285_1	chr7	37332906	37333570	+	0	NA	intron (NM_001206482, intron 2 of 21)	intron (NM_001206482, intron 2 of 21)	20430	NM_001206482	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.006024	0.428571	
chunk0083_359_1	chr17	70581536	70581735	+	0	NA	Intergenic	Intergenic	412100	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.010050	0.395000	
chunk0182_408_1	chr7	100889925	100890437	+	0	NA	promoter-TSS (NM_001015072)	promoter-TSS (NM_001015072)	-463	NM_001015072	402682	Hs.534845	NM_001015072	ENSG00000176125	UFSP1	UFSP	UFM1 specific peptidase 1 (inactive)	protein-coding	0.074219	0.654971	
chunk0011_309_1	chr1	151832753	151832963	+	0	NA	promoter-TSS (NM_005060)	promoter-TSS (NM_005060)	-986	NM_005060	6097	Hs.256022	NM_005060	ENSG00000143365	RORC	IMD42|NR1F3|RORG|RZR-GAMMA|RZRG|TOR	RAR related orphan receptor C	protein-coding	0.033333	0.625592	
chunk0112_387_1	chr20	46450445	46451154	+	0	NA	Intergenic	Intergenic	6844	NR_045983	100130934	Hs.712133	NM_173643		ZNF663P	ZNF663	zinc finger protein 663, pseudogene	pseudo	0.002821	0.418310	
chunk0079_238_1	chr17	15934851	15935531	+	0	NA	Intergenic	L1M4|LINE|L1	-9726	NM_000676	136	Hs.167046	NM_000676	ENSG00000170425	ADORA2B	ADORA2	adenosine A2b receptor	protein-coding	0.007353	0.408223	
chunk0103_394_1	chr2	169010573	169010907	+	0	NA	intron (NM_003742, intron 5 of 27)	intron (NM_003742, intron 5 of 27)	20583	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.014970	0.340299	
chunk0002_298_1	chr1	23278994	23279298	+	0	NA	Intergenic	Intergenic	6372	NR_110616	100996511	Hs.99836	NR_110616		LINC01355	-	long intergenic non-protein coding RNA 1355	ncRNA	0.006579	0.357377	
chunk0207_280_1	chr9	132678674	132679254	+	0	NA	exon (NM_012204, exon 2 of 5)	exon (NM_012204, exon 2 of 5)	-8563	NM_138620	64794	Hs.660767	NM_022779	ENSG00000125485	DDX31	PPP1R25	DEAD-box helicase 31	protein-coding	0.008621	0.456110	
chunk0115_146_1	chr21	23524311	23525026	+	0	NA	Intergenic	Intergenic	-139833	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.012587	0.439944	
chunk0156_56_1	chr5	103240743	103241102	+	0	NA	Intergenic	Intergenic	-17780	NM_033211	90355	Hs.482976	NM_033211	ENSG00000181751	C5orf30	-	chromosome 5 open reading frame 30	protein-coding	0.000000	0.255556	160(GACACAAAGTGTTCTT,+,0.00)
chunk0198_87_1	chr8	130221781	130222236	+	0	NA	intron (NM_001247996, intron 5 of 30)	intron (NM_001247996, intron 5 of 30)	74525	NR_002765	29065	Hs.639318	NR_002765		ASAP1-IT1	ASAP1-IT|ASAP1IT|ASAP1IT1|DDEF1IT1|HSPC054|NCRNA00050	ASAP1 intronic transcript 1	ncRNA	0.010989	0.394737	
chunk0064_165_1	chr14	92121504	92122099	+	0	NA	promoter-TSS (NM_004545)	promoter-TSS (NM_004545)	8	NM_004545	4707	Hs.183435	NM_004545	ENSG00000183648	NDUFB1	CI-MNLL|CI-SGDH|MNLL	NADH:ubiquinone oxidoreductase subunit B1	protein-coding	0.078992	0.619128	
chunk0081_246_1	chr17	43010976	43011194	+	0	NA	intron (NM_005533, intron 1 of 6)	intron (NM_005533, intron 1 of 6)	4360	NM_005533	3430	Hs.632258	NM_005533	ENSG00000068079	IFI35	IFP35	interferon induced protein 35	protein-coding	0.000000	0.488584	
chunk0093_1_1	chr2	20262	20488	+	0	NA	Intergenic	Intergenic	26213	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.008850	0.414097	
chunk0062_54_1	chr14	67411233	67411432	+	0	NA	intron (NM_016445, intron 1 of 8)	MIRb|SINE|MIR	779	NM_016445	26499	Hs.170473	NM_016445	ENSG00000100558	PLEK2	-	pleckstrin 2	protein-coding	0.015075	0.545000	79(CAGAACATGCAGTTCC,-,0.00),80(AGAACATGCAGTTCCT,+,0.00)
chunk0007_313_1	chr1	84407550	84408395	+	0	NA	promoter-TSS (NM_058248)	promoter-TSS (NM_058248)	-379	NM_058248	58511	Hs.129142	NM_021233	ENSG00000137976	DNASE2B	DLAD	deoxyribonuclease 2 beta	protein-coding	0.003550	0.372340	423(AAGCACAAAGTGTGCA,-,0.00),424(AGCACAAAGTGTGCAG,+,0.00)
chunk0152_461_1	chr5	66633185	66633741	+	0	NA	intron (NM_198828, intron 1 of 5)	L4_A_Mam|LINE|RTE-X	37115	NM_001290228	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.003597	0.375224	
chunk0144_233_1	chr4	134883989	134884303	+	0	NA	Intergenic	Intergenic	-682398	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.003185	0.355556	
chunk0205_301_1	chr9	112173316	112173691	+	0	NA	intron (NM_022486, intron 1 of 16)	intron (NM_022486, intron 1 of 16)	1794	NM_001282643	64420	Hs.494827	NM_022486	ENSG00000106868	SUSD1	-	sushi domain containing 1	protein-coding	0.018667	0.526596	315(TGGCACAGCCTGAGCC,-,0.00),316(GGCACAGCCTGAGCCC,+,0.00)
chunk0148_153_1	chr5	6521348	6521598	+	0	NA	Intergenic	Intergenic	-60663	NR_024423	255167	Hs.435515	NR_024423	ENSG00000250056	LINC01018	SRHC	long intergenic non-protein coding RNA 1018	ncRNA	0.016000	0.466135	
chunk0185_128_1	chr7	126739756	126740113	+	0	NA	intron (NR_028041, intron 6 of 10)	Tigger3a|DNA|TcMar-Tigger	318250	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.005602	0.346369	
chunk0045_295_1	chr12	50324690	50325067	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-41308	NM_016357	51474	Hs.525419	NM_016357	ENSG00000050405	LIMA1	EPLIN|LDLCQ8|SREBP3	LIM domain and actin binding 1	protein-coding	0.010610	0.473545	
chunk0052_150_1	chr13	23796567	23796954	+	0	NA	intron (NM_005932, intron 16 of 18)	intron (NM_005932, intron 16 of 18)	-92129	NM_001014442	542767	Hs.642624	NM_001014442		PCOTH	C1QTNF9B-AS1	Pro-X-Gly collagen triple helix like repeat containing	protein-coding	0.005168	0.371134	
chunk0143_362_1	chr4	122149872	122150301	+	0	NA	Intergenic	L1MD1|LINE|L1	-20517	NM_015312	84162	Hs.408142	NM_015312	ENSG00000138688	KIAA1109	ALKKUCS|FSA|Tweek	KIAA1109	protein-coding	0.000000	0.341860	
chunk0198_28_1	chr8	128165637	128166182	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	15793	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.003670	0.402930	
chunk0071_237_1	chr15	85165816	85166200	+	0	NA	Intergenic	L1MB4|LINE|L1	39279	NR_049748									0.002604	0.335065	
chunk0075_321_1	chr16	54564034	54564421	+	0	NA	Intergenic	LTR81C|LTR|Gypsy	-277761	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.007752	0.384021	
chunk0171_77_1	chr6	121630577	121630977	+	0	NA	Intergenic	Intergenic	195200	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.000000	0.336658	
chunk0156_444_1	chr5	114787395	114787594	+	0	NA	Intergenic	Intergenic	-14081	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.005025	0.400000	
chunk0024_421_1	chr10	45823011	45823224	+	0	NA	Intergenic	L2a|LINE|L2	24356	NM_133446	119016	Hs.314437	NM_133446	ENSG00000188234	AGAP4	AGAP-4|AGAP-8|AGAP8|CTGLF1|CTGLF5|MRIP2	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	protein-coding	0.004695	0.439252	
chunk0082_444_1	chr17	61927368	61928037	+	0	NA	non-coding (NR_026641, exon 1 of 25)	non-coding (NR_026641, exon 1 of 25)	314	NM_020748	57508	Hs.279646	NM_020748	ENSG00000108506	INTS2	INT2|KIAA1287	integrator complex subunit 2	protein-coding	0.071749	0.597015	
chunk0019_227_1	chr1	227324743	227325406	+	0	NA	Intergenic	Plat_L3|LINE|CR1	-6949	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.006033	0.382530	579(TAGAACAGACTGTGAC,-,0.00),580(AGAACAGACTGTGACC,+,0.00)
chunk0180_414_1	chr7	76069225	76069799	+	0	NA	Intergenic	Intergenic	21493	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.020906	0.560000	319(AGGAACAGGGCGTCCC,-,0.00),320(GGAACAGGGCGTCCCA,+,0.00)
chunk0106_192_1	chr2	201571971	201572170	+	0	NA	intron (NM_152525, intron 7 of 14)	intron (NM_152525, intron 7 of 14)	47112	NM_001168221	151254	Hs.335788	NM_152525	ENSG00000155754	C2CD6	ALS2CR11	C2 calcium dependent domain containing 6	protein-coding	0.000000	0.310000	
chunk0069_278_1	chr15	64984937	64985522	+	0	NA	intron (NM_001127890, intron 1 of 7)	intron (NM_001127890, intron 1 of 7)	4277	NM_001127889	51324	Hs.242458	NM_016630	ENSG00000090487	SPG21	ABHD21|ACP33|BM-019|GL010|MAST	SPG21 abhydrolase domain containing, maspardin	protein-coding	0.010256	0.438567	
chunk0167_288_1	chr6	70664751	70665307	+	0	NA	Intergenic	L2c|LINE|L2	-2742	NM_021940	60682	Hs.485717	NM_021940	ENSG00000112305	SMAP1	SMAP-1	small ArfGAP 1	protein-coding	0.007194	0.382406	
chunk0036_4_1	chr11	57935888	57936432	+	0	NA	Intergenic	Intergenic	-87721	NM_001005212	219956	Hs.689841	NM_001005212	ENSG00000186509	OR9Q1	-	olfactory receptor family 9 subfamily Q member 1	protein-coding	0.001838	0.370642	
chunk0155_222_1	chr5	95336087	95336782	+	0	NA	Intergenic	Intergenic	-51859	NM_024717	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.005755	0.350575	
chunk0012_356_1	chr1	162796498	162796811	+	0	NA	exon (NM_001304512, exon 3 of 4)	exon (NM_001304512, exon 3 of 4)	5952	NM_001304513	51478	Hs.492925	NM_016371	ENSG00000132196	HSD17B7	PRAP|SDR37C1	hydroxysteroid 17-beta dehydrogenase 7	protein-coding	0.003195	0.369427	
chunk0057_1_1	chr13	95403254	95403638	+	0	NA	Intergenic	Intergenic	-30153	NM_182848	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.007812	0.436364	
chunk0005_217_1	chr1	59232258	59232518	+	0	NA	Intergenic	Intergenic	-64565	NM_018291	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.015385	0.448276	
chunk0032_179_1	chr11	5938229	5938659	+	0	NA	Intergenic	Intergenic	-8903	NM_001003443	390083	Hs.553741	NM_001003443	ENSG00000184478	OR56A3	OR56A2P|OR56A3P|OR56A6	olfactory receptor family 56 subfamily A member 3	protein-coding	0.046512	0.554524	265(TGGCACTCCGTGTTCC,-,0.00),266(GGCACTCCGTGTTCCT,+,0.00)
chunk0018_414_1	chr1	222671915	222672448	+	0	NA	intron (NM_022831, intron 8 of 9)	intron (NM_022831, intron 8 of 9)	27878	NM_001300867	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.005629	0.308989	315(AAGAACACAGTGTAAT,-,0.00)
chunk0036_293_1	chr11	65560048	65560347	+	0	NA	Intergenic	L2c|LINE|L2	-1969	NM_001164266	4054	Hs.289019	NM_021070	ENSG00000168056	LTBP3	DASS|GPHYSD3|LTBP-3|LTBP2|STHAG6|pp6425	latent transforming growth factor beta binding protein 3	protein-coding	0.013378	0.583333	
chunk0064_68_1	chr14	90129677	90130031	+	0	NA	intron (NM_022054, intron 1 of 1)	intron (NM_022054, intron 1 of 1)	68089	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.011299	0.400000	
chunk0049_39_1	chr12	89781834	89782419	+	0	NA	Intergenic	Intergenic	73171	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.005128	0.315700	
chunk0025_399_1	chr10	59454221	59454809	+	0	NA	Intergenic	L1M5|LINE|L1	-91612	NM_001143773	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.008503	0.370119	213(AGAACTGCTTGTCCAG,+,0.00)
chunk0117_405_1	chr21	45612243	45612444	+	0	NA	Intergenic	Intergenic	-69872	NM_001205206	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.054726	0.638614	
chunk0045_351_1	chr12	51590085	51590344	+	0	NA	Intergenic	MIRb|SINE|MIR	-1022	NM_001177984	6334	Hs.436550	NM_014191	ENSG00000196876	SCN8A	BFIS5|CERIII|CIAT|EIEE13|MED|MYOCL2|NaCh6|Nav1.6|PN4	sodium voltage-gated channel alpha subunit 8	protein-coding	0.011583	0.392308	
chunk0055_219_1	chr13	62431512	62431875	+	0	NA	Intergenic	L3|LINE|CR1	219411	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.000000	0.291209	
chunk0169_7_1	chr6	96296065	96296526	+	0	NA	Intergenic	L1PB3|LINE|L1	-225531	NM_015323	23376	Hs.149367	NM_015323	ENSG00000014123	UFL1	KIAA0776|Maxer|NLBP|RCAD	UFM1 specific ligase 1	protein-coding	0.002169	0.320346	
chunk0093_200_1	chr19	49409864	49410329	+	0	NA	intron (NM_144688, intron 15 of 19)	L2c|LINE|L2	13345	NM_178449	113091	Hs.339845	NM_178449	ENSG00000142538	PTH2	TIP39	parathyroid hormone 2	protein-coding	0.006452	0.452790	138(GGGCCCAGTGTGTGCT,-,0.00),139(GGCCCAGTGTGTGCTG,+,0.00)
chunk0020_66_1	chr1	232622795	232623119	+	0	NA	Intergenic	L2a|LINE|L2	-107349	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.009259	0.396923	
chunk0025_77_1	chr10	50326710	50327343	+	0	NA	intron (NM_147156, intron 8 of 10)	intron (NM_147156, intron 8 of 10)	-78416	NM_001143974	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.014218	0.419558	
chunk0182_174_1	chr7	95590449	95590893	+	0	NA	intron (NM_002612, intron 6 of 10)	intron (NM_002612, intron 6 of 10)	5942	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.009009	0.341573	
chunk0006_253_1	chr1	69418761	69419026	+	0	NA	Intergenic	L1PA7|LINE|L1	-341282	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.003774	0.353383	
chunk0056_174_1	chr13	85247732	85248415	+	0	NA	Intergenic	Intergenic	-100016	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.008785	0.372807	294(GAGAACTCTGTGTTCT,-,0.00),295(AGAACTCTGTGTTCTT,+,0.00)
chunk0176_131_1	chr7	12630411	12630924	+	0	NA	intron (NM_033128, intron 7 of 13)	intron (NM_033128, intron 7 of 13)	41144	NM_033128	85477	Hs.633359	NM_033128	ENSG00000006747	SCIN	-	scinderin	protein-coding	0.011696	0.385214	
chunk0050_378_1	chr12	108665642	108665914	+	0	NA	intron (NM_014325, intron 3 of 10)	MIR|SINE|MIR	29968	NR_039717	100616240		NR_039717	ENSG00000284388	MIR4496	-	microRNA 4496	ncRNA	0.007353	0.461538	
chunk0013_125_1	chr1	168035474	168035674	+	0	NA	intron (NM_018442, intron 11 of 19)	intron (NM_018442, intron 11 of 19)	36914	NR_031702	100313835		NR_031702	ENSG00000221545	MIR1255B2	MIR1255B-2|MIRN1255B2|hsa-mir-1255b-2	microRNA 1255b-2	ncRNA	0.005000	0.358209	
chunk0097_372_1	chr2	61187936	61188178	+	0	NA	TTS (NM_152392)	TTS (NM_152392)	10637	NM_152392	130872	Hs.655602	NM_152392	ENSG00000173209	AHSA2P	AHA1|AHSA2|Hch1	activator of HSP90 ATPase homolog 2, pseudogene	pseudo	0.004132	0.427984	
chunk0199_382_1	chr9	13141613	13142066	+	0	NA	intron (NM_001261406, intron 26 of 45)	intron (NM_001261406, intron 26 of 45)	137725	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.011038	0.325991	
chunk0087_149_1	chr18	34101808	34102075	+	0	NA	intron (NM_003787, intron 4 of 10)	L2a|LINE|L2	-53329	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.000000	0.373134	155(TTGAACATTCTGTTCC,-,0.00),156(TGAACATTCTGTTCCA,+,0.00)
chunk0158_183_1	chr5	127864523	127864850	+	0	NA	Intergenic	Intergenic	211671	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.000000	0.338415	
chunk0190_324_1	chr8	38882031	38882233	+	0	NA	Intergenic	Intergenic	-19103	NM_021623	59339	Hs.369123	NM_021623	ENSG00000169499	PLEKHA2	TAPP2	pleckstrin homology domain containing A2	protein-coding	0.004950	0.339901	
chunk0042_180_1	chr12	4845072	4845949	+	0	NA	intron (NM_002235, intron 1 of 1)	HAL1|LINE|L1	36334	NM_002235	3742	Hs.306190	NM_002235	ENSG00000130035	KCNA6	HBK2|KV1.6|PPP1R96	potassium voltage-gated channel subfamily A member 6	protein-coding	0.010262	0.394077	
chunk0196_128_1	chr8	103926564	103926812	+	0	NA	intron (NM_001282881, intron 8 of 20)	intron (NM_001282881, intron 8 of 20)	107500	NM_014677	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.004032	0.373494	
chunk0208_147_1	chrX	16100569	16101098	+	0	NA	Intergenic	Intergenic	-22468	NM_005314	2925	Hs.567282	NM_005314	ENSG00000126010	GRPR	BB2|BB2R	gastrin releasing peptide receptor	protein-coding	0.009452	0.392453	257(CAGGACTCCTTGTGCT,-,0.00),258(AGGACTCCTTGTGCTC,+,0.00)
chunk0061_290_1	chr14	61630946	61631432	+	0	NA	intron (NR_039985, intron 1 of 2)	intron (NR_039985, intron 1 of 2)	-60536	NR_110416	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.006173	0.351129	
chunk0165_384_1	chr6	38461016	38461338	+	0	NA	intron (NM_001172418, intron 5 of 10)	L1ME1|LINE|L1	134890	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.009317	0.383901	
chunk0158_225_1	chr5	128749715	128750006	+	0	NA	Intergenic	Intergenic	-211818	NM_001999	2201	Hs.519294	NM_001999	ENSG00000138829	FBN2	CCA|DA9|EOMD	fibrillin 2	protein-coding	0.020619	0.482877	
chunk0190_458_1	chr8	42245432	42245774	+	0	NA	Intergenic	LTR84b|LTR|ERVL	25358	NR_125823	101929897	Hs.60288	NR_125823	ENSG00000253408	LOC101929897	-	uncharacterized LOC101929897	ncRNA	0.014620	0.466472	
chunk0195_150_1	chr8	95305991	95306292	+	0	NA	intron (NR_038208, intron 2 of 3)	intron (NR_038208, intron 2 of 3)	-36907	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.009967	0.350993	66(AGGGACAAACAGTTCT,-,0.00),67(GGGACAAACAGTTCTT,+,0.00)
chunk0053_49_1	chr13	27576673	27577247	+	0	NA	intron (NM_153371, intron 2 of 9)	L1M4|LINE|L1	43623	NM_153371	222484	Hs.132359	NM_153371	ENSG00000139517	LNX2	PDZRN1	ligand of numb-protein X 2	protein-coding	0.003484	0.309565	
chunk0019_44_1	chr1	224063762	224064052	+	0	NA	Intergenic	Intergenic	-50180	NM_015176	23219	Hs.64691	NM_015176	ENSG00000143756	FBXO28	CENP-30|Fbx28	F-box protein 28	protein-coding	0.003448	0.422680	
chunk0134_194_1	chr3	178332391	178332825	+	0	NA	Intergenic	L1PA15|LINE|L1	-86593	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.004608	0.381609	
chunk0028_214_1	chr10	89470317	89470609	+	0	NA	intron (NM_213606, intron 2 of 7)	intron (NM_213606, intron 2 of 7)	14472	NR_120614	101926906	Hs.568874	NR_120614	ENSG00000234452	SLC16A12-AS1	-	SLC16A12 antisense RNA 1	ncRNA	0.000000	0.501706	
chunk0164_135_1	chr6	21142129	21143116	+	0	NA	intron (NM_017774, intron 13 of 15)	intron (NM_017774, intron 13 of 15)	369270	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.004053	0.406883	
chunk0081_74_1	chr17	39123817	39124094	+	0	NA	intron (NM_020405, intron 2 of 13)	MamGypsy2-I|LTR|Gypsy	27694	NM_020405	57125	Hs.125036	NM_020405	ENSG00000161381	PLXDC1	TEM3|TEM7	plexin domain containing 1	protein-coding	0.018051	0.589928	
chunk0186_431_1	chr7	146683503	146683786	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	413965	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.003534	0.345070	
chunk0168_255_1	chr6	89022546	89023219	+	0	NA	Intergenic	Intergenic	-57828	NM_006813	10957	Hs.75969	NM_006813	ENSG00000146278	PNRC1	B4-2|PNAS-145|PROL2|PRR2	proline rich nuclear receptor coactivator 1	protein-coding	0.001486	0.363501	270(CAGAACATAGAGTACT,-,0.00),271(AGAACATAGAGTACTT,+,0.00)
chunk0033_321_1	chr11	20862018	20862321	+	0	NA	intron (NM_006157, intron 4 of 19)	intron (NM_006157, intron 4 of 19)	192618	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.006601	0.391447	
chunk0150_180_1	chr5	34510644	34511548	+	0	NA	Intergenic	Intergenic	-145232	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.009956	0.393370	
chunk0044_263_1	chr12	32267890	32268566	+	0	NA	intron (NM_001003398, intron 2 of 8)	intron (NM_001003398, intron 2 of 8)	160977	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.014793	0.443131	
chunk0127_205_1	chr3	96347166	96347532	+	0	NA	Intergenic	L1ME1|LINE|L1	-12615	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.002732	0.307902	
chunk0188_357_1	chr8	18066550	18067289	+	0	NA	intron (NM_004315, intron 5 of 13)	L1ME3|LINE|L1	17451	NM_177924	427	Hs.527412	NM_004315	ENSG00000104763	ASAH1	AC|ACDase|ASAH|PHP|PHP32|SMAPME	N-acylsphingosine amidohydrolase 1	protein-coding	0.006766	0.377027	
chunk0162_29_1	chr6	935446	935652	+	0	NA	Intergenic	Intergenic	67051	NR_110853	101927691	Hs.552556	NR_110853		LOC101927691	-	uncharacterized LOC101927691	ncRNA	0.014563	0.541063	
chunk0104_58_1	chr2	171492746	171493238	+	0	NA	Intergenic	Intergenic	-29255	NM_001256909	79901	Hs.221941	NM_024843	ENSG00000071967	CYBRD1	CYB561A2|DCYTB|FRRS3	cytochrome b reductase 1	protein-coding	0.010163	0.385396	214(AAGTACTCAGTGTTCC,-,0.00),215(AGTACTCAGTGTTCCT,+,0.00)
chunk0191_253_1	chr8	53227787	53228454	+	0	NA	3' UTR (NM_001282904, exon 5 of 5)	3' UTR (NM_001282904, exon 5 of 5)	23514	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.007496	0.407186	317(AGGGACATCATGTCCT,-,0.00),318(GGGACATCATGTCCTC,+,0.00)
chunk0105_375_1	chr2	192126918	192127117	+	0	NA	intron (NM_016192, intron 4 of 9)	intron (NM_016192, intron 4 of 9)	67916	NM_001305134	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.000000	0.320000	
chunk0067_419_1	chr15	49724090	49724519	+	0	NA	Intergenic	Intergenic	103275	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.002331	0.323256	
chunk0043_332_1	chr12	22727210	22727523	+	0	NA	Intergenic	L1ME1|LINE|L1	102224	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.000000	0.305732	
chunk0182_53_1	chr7	91918462	91919436	+	0	NA	Intergenic	Intergenic	-21926	NM_005751	10142	Hs.651221	NM_005751	ENSG00000127914	AKAP9	AKAP-9|AKAP350|AKAP450|CG-NAP|HYPERION|LQT11|MU-RMS-40.16A|PPP1R45|PRKA9|YOTIAO	A-kinase anchoring protein 9	protein-coding	0.002053	0.329231	366(ATAACATCTTGTTCTT,+,0.00)
chunk0095_111_1	chr2	15571794	15572206	+	0	NA	Intergenic	MER67B|LTR|ERV1	-10652	NM_015909	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.007282	0.426150	
chunk0010_357_1	chr1	118820912	118821352	+	0	NA	Intergenic	Intergenic	168424	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.002273	0.324263	146(GAGCACAGAATGTTCT,-,0.00),147(AGCACAGAATGTTCTT,+,0.00)
chunk0012_198_1	chr1	159945936	159946211	+	0	NA	promoter-TSS (NM_001135050)	promoter-TSS (NM_001135050)	-477	NM_001135050	57549	Hs.591472	NM_020789	ENSG00000085552	IGSF9	FP18798|IGSF9A|Nrt1	immunoglobulin superfamily member 9	protein-coding	0.061818	0.641304	
chunk0161_236_1	chr5	171439433	171439679	+	0	NA	intron (NM_003862, intron 3 of 4)	MIRc|SINE|MIR	19893	NM_003862	8817	Hs.87191	NM_003862	ENSG00000156427	FGF18	FGF-18|ZFGF5	fibroblast growth factor 18	protein-coding	0.004065	0.587045	69(CTGGACACTCTGTCCT,-,0.00),70(TGGACACTCTGTCCTG,+,0.00),127(CAGGACACTGAGTTCC,-,0.00),128(AGGACACTGAGTTCCA,+,0.00)
chunk0001_128_1	chr1	4729930	4730559	+	0	NA	intron (NM_001042478, intron 2 of 5)	intron (NM_001042478, intron 2 of 5)	75199	NM_018836	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.027027	0.496825	
chunk0089_302_1	chr18	63683076	63683530	+	0	NA	Intergenic	Intergenic	-19001	NM_080475	89778	Hs.350958	NM_080475	ENSG00000206072	SERPINB11	EPIPIN|SERPIN11	serpin family B member 11 (gene/pseudogene)	protein-coding	0.004405	0.410989	
chunk0179_268_1	chr7	49273880	49274166	+	0	NA	Intergenic	Intergenic	349462	NR_003595									0.000000	0.393728	
chunk0077_449_1	chr16	85819236	85819460	+	0	NA	Intergenic	Intergenic	19781	NM_001861	1327	Hs.433419	NM_001861	ENSG00000131143	COX4I1	COX IV-1|COX4|COX4-1|COXIV|COXIV-1	cytochrome c oxidase subunit 4I1	protein-coding	0.040179	0.555556	
chunk0041_405_1	chr11	133821628	133822223	+	0	NA	Intergenic	Intergenic	-11549	NR_120444	646522	Hs.560000	NR_120444	ENSG00000255258	LINC02743	-	long intergenic non-protein coding RNA 2743	ncRNA	0.023529	0.562081	
chunk0056_53_1	chr13	77642322	77642581	+	0	NA	intron (NM_003843, intron 30 of 31)	intron (NM_003843, intron 30 of 31)	20352	NM_001310140	100129307		NM_001310140		LOC100129307	-	putative UPF0607 protein ENSP00000383144	protein-coding	0.003861	0.396154	
chunk0043_274_1	chr12	20967697	20968263	+	0	NA	Intergenic	LTR57-int|LTR|ERVL	-47716	NM_001009562	338821	Hs.729117	NM_001009562	ENSG00000205754	SLCO1B7	LST-3|LST-3TM12|LST3|SLC21A21	solute carrier organic anion transporter family member 1B7 (putative)	protein-coding	0.001767	0.266314	
chunk0205_56_1	chr9	106536298	106536607	+	0	NA	Intergenic	Intergenic	-64476	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.009709	0.400000	
chunk0022_67_1	chr10	8584512	8585050	+	0	NA	Intergenic	Intergenic	-313208	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.005576	0.432282	246(TGGAACAGGAAGTCCT,-,0.00),247(GGAACAGGAAGTCCTG,+,0.00)
chunk0091_192_1	chr19	8435308	8435639	+	0	NA	intron (NM_001005415, intron 4 of 4)	L1MC1|LINE|L1	-9355	NM_001297418	4670	Hs.465808	NM_005968	ENSG00000099783	HNRNPM	CEAR|HNRNPM4|HNRPM|HNRPM4|HTGR1|NAGR1|hnRNP M	heterogeneous nuclear ribonucleoprotein M	protein-coding	0.012085	0.412651	75(AAGTACAGAGAGTTCC,-,0.00),76(AGTACAGAGAGTTCCT,+,0.00)
chunk0076_202_1	chr16	68093456	68093691	+	0	NA	intron (NM_173163, intron 1 of 10)	intron (NM_173163, intron 1 of 10)	8207	NM_004555	4775	Hs.436585	NM_004555	ENSG00000072736	NFATC3	NF-AT4c|NFAT4|NFATX	nuclear factor of activated T cells 3	protein-coding	0.004255	0.296610	
chunk0108_372_1	chr2	236753357	236753556	+	0	NA	Intergenic	Intergenic	183719	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.015075	0.545000	
chunk0072_144_1	chr15	92708947	92709619	+	0	NA	Intergenic	Intergenic	-53482	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.017857	0.505201	
chunk0180_164_1	chr7	65048548	65049411	+	0	NA	intron (NR_033416, intron 1 of 10)	Charlie15b|DNA|hAT-Charlie	10625	NR_033416	643180	Hs.510847	NR_033416	ENSG00000234585	CCT6P3	CCT6-3P	chaperonin containing TCP1 subunit 6 pseudogene 3	pseudo	0.005794	0.312500	249(AAGCACATTCAGTACT,-,0.00),250(AGCACATTCAGTACTA,+,0.00)
chunk0013_31_1	chr1	166691404	166692206	+	0	NA	Intergenic	Intergenic	87889	NR_002925	116123	Hs.348539	NM_138784	ENSG00000215834	FMO9P	-	flavin containing dimethylaniline monoxygenase 9, pseudogene	pseudo	0.004988	0.397260	
chunk0052_368_1	chr12	128669209	128669494	+	0	NA	intron (NM_001136103, intron 4 of 8)	intron (NM_001136103, intron 4 of 8)	154645	NM_145648	121260	Hs.507260	NM_145648	ENSG00000139370	SLC15A4	FP12591|PHT1|PTR4	solute carrier family 15 member 4	protein-coding	0.007018	0.437063	79(TGGTACAGTGTGTCTT,-,0.00),80(GGTACAGTGTGTCTTG,+,0.00)
chunk0153_264_1	chr5	72830537	72830773	+	0	NA	intron (NM_002270, intron 1 of 24)	intron (NM_002270, intron 1 of 24)	14064	NM_002270	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.004237	0.312236	
chunk0199_254_1	chr9	5997783	5998113	+	0	NA	intron (NM_001017969, intron 1 of 7)	intron (NM_001017969, intron 1 of 7)	-9878	NR_039811	100616288		NR_039811	ENSG00000263575	MIR4665	mir-4665	microRNA 4665	ncRNA	0.003030	0.323263	
chunk0059_432_1	chr14	38315767	38315966	+	0	NA	Intergenic	Intergenic	-59496	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.005025	0.350000	
chunk0029_24_1	chr10	95656520	95657103	+	0	NA	promoter-TSS (NM_002860)	promoter-TSS (NM_002860)	-1	NM_002860	5832	Hs.500645	NM_002860	ENSG00000059573	ALDH18A1	ADCL3|ARCL3A|GSAS|P5CS|PYCS|SPG9|SPG9A|SPG9B	aldehyde dehydrogenase 18 family member A1	protein-coding	0.096055	0.648973	
chunk0165_252_1	chr6	35715511	35715802	+	0	NA	intron (NM_001145775, intron 2 of 11)	L2c|LINE|L2	12927	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.017182	0.551370	
chunk0079_189_1	chr17	14205881	14206512	+	0	NA	intron (NM_001303, intron 6 of 6)	intron (NM_001303, intron 6 of 6)	30637	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.023772	0.553797	
chunk0166_348_1	chr6	51118797	51119299	+	0	NA	Intergenic	Intergenic	300322	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.005976	0.407555	
chunk0115_437_1	chr21	31987205	31987441	+	0	NA	intron (NM_014586, intron 8 of 10)	intron (NM_014586, intron 8 of 10)	98972	NR_038033	100551499	Hs.224449	NR_038033		LINC00159	C21orf44|NCRNA00159	long intergenic non-protein coding RNA 159	ncRNA	0.016949	0.523207	
chunk0145_310_1	chr4	150398143	150398683	+	0	NA	intron (NM_001199282, intron 47 of 56)	intron (NM_001199282, intron 47 of 56)	-183512	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.005556	0.310536	
chunk0063_102_1	chr14	78767930	78768579	+	0	NA	intron (NR_073547, intron 8 of 20)	intron (NR_073547, intron 8 of 20)	364523	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.001541	0.315385	384(AAGAACACCTTGTGCC,-,0.00),385(AGAACACCTTGTGCCT,+,0.00)
chunk0177_179_1	chr7	23346143	23346508	+	0	NA	intron (NM_006547, intron 7 of 14)	intron (NM_006547, intron 7 of 14)	47004	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.002740	0.371585	
chunk0156_301_1	chr5	110365659	110366192	+	0	NA	Intergenic	Intergenic	147990	NR_031644	100302159		NR_031644	ENSG00000221436	MIR548F3	MIR548F-3|MIRN548F3|hsa-mir-548f-3	microRNA 548f-3	ncRNA	0.005629	0.400749	
chunk0084_199_1	chr17	78105525	78106217	+	0	NA	3' UTR (NM_001142640, exon 22 of 22)	3' UTR (NM_001142640, exon 22 of 22)	5928	NR_040071	100131096	Hs.635442	NR_040071	ENSG00000204282	TNRC6C-AS1	TMC6|lnc	TNRC6C antisense RNA 1	ncRNA	0.021676	0.411255	278(TTGCACTGAGTGTCCT,-,0.00),279(TGCACTGAGTGTCCTC,+,0.00)
chunk0108_234_1	chr2	233710432	233710689	+	0	NA	intron (NM_205862, intron 2 of 5)	L1ME1|LINE|L1	-2432	NM_019078	54579	Hs.554822	NM_019078	ENSG00000240224	UGT1A5	UDPGT|UDPGT 1-5|UGT1E	UDP glucuronosyltransferase family 1 member A5	protein-coding	0.003891	0.333333	
chunk0062_114_1	chr14	68365144	68365343	+	0	NA	intron (NM_133509, intron 8 of 10)	intron (NM_133509, intron 8 of 10)	428671	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.025126	0.485000	
chunk0127_84_1	chr3	89665823	89666131	+	0	NA	Intergenic	L1MEc|LINE|L1	558453	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.000000	0.265372	
chunk0128_19_1	chr3	104144195	104144461	+	0	NA	Intergenic	L1M5|LINE|L1	-620212	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.003759	0.254682	
chunk0034_21_1	chr11	26144612	26145133	+	0	NA	Intergenic	Intergenic	-44251	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.007678	0.394636	
chunk0027_363_1	chr10	79071245	79071481	+	0	NA	intron (NM_020338, intron 1 of 24)	intron (NM_020338, intron 1 of 24)	2328	NM_020338	57178	Hs.193118	NM_020338	ENSG00000108175	ZMIZ1	MIZ|RAI17|TRAFIP10|ZIMP10	zinc finger MIZ-type containing 1	protein-coding	0.033898	0.611814	
chunk0154_273_1	chr5	82135420	82135637	+	0	NA	intron (NM_031482, intron 3 of 7)	L1PA7|LINE|L1	142888	NM_001025	6228	Hs.527193	NM_001025	ENSG00000186468	RPS23	BTDD|MABAS|MCINS|PAMAS|S23|uS12	ribosomal protein S23	protein-coding	0.004608	0.330275	
chunk0117_116_1	chr22	18064710	18064912	+	0	NA	Intergenic	Intergenic	-13109	NM_017929	55670	Hs.517400	NM_017929	ENSG00000215193	PEX26	PBD7A|PBD7B|PEX26M1T|Pex26pM1T	peroxisomal biogenesis factor 26	protein-coding	0.019802	0.507389	
chunk0210_458_1	chrX	106809075	106809665	+	0	NA	intron (NM_198881, intron 1 of 11)	L2a|LINE|L2	6681	NM_198881	54885	Hs.351798	NM_017752	ENSG00000133138	TBC1D8B	GRAMD8B	TBC1 domain family member 8B	protein-coding	0.006780	0.402707	
chunk0097_378_1	chr2	61282206	61282635	+	0	NA	intron (NM_014709, intron 37 of 79)	intron (NM_014709, intron 37 of 79)	105000	NM_152392	130872	Hs.655602	NM_152392	ENSG00000173209	AHSA2P	AHA1|AHSA2|Hch1	activator of HSP90 ATPase homolog 2, pseudogene	pseudo	0.016317	0.420930	
chunk0009_355_1	chr1	109602370	109602573	+	0	NA	TTS (NM_005272)	TTS (NM_005272)	3578	NR_029583	406974		NR_029583	ENSG00000284443	MIR197	MIRN197|miR-197|miRNA197	microRNA 197	ncRNA	0.009852	0.372549	
chunk0185_439_1	chr7	134943063	134943269	+	0	NA	intron (NM_033157, intron 7 of 14)	intron (NM_033157, intron 7 of 14)	-43342	NM_178563	340351	Hs.648616	NM_178563	ENSG00000146856	AGBL3	CCP3	ATP/GTP binding protein like 3	protein-coding	0.014563	0.381643	
chunk0050_372_1	chr12	108558496	108558705	+	0	NA	intron (NM_014706, intron 1 of 18)	intron (NM_014706, intron 1 of 18)	2789	NM_014706	9733	Hs.584842	NM_014706	ENSG00000075856	SART3	DSAP1|P100|RP11-13G14|TIP110|p110|p110(nrb)	spliceosome associated factor 3, U4/U6 recycling protein	protein-coding	0.009569	0.514286	
chunk0023_185_1	chr10	24762273	24762563	+	0	NA	Intergenic	Intergenic	-38750	NM_020824	57584	Hs.524195	NM_020824	ENSG00000107863	ARHGAP21	ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.006897	0.381443	
chunk0087_100_1	chr18	32438025	32438503	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	32220	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.012552	0.465553	
chunk0078_33_1	chr17	910718	911319	+	0	NA	intron (NM_022463, intron 1 of 7)	intron (NM_022463, intron 1 of 7)	-46907	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.011647	0.415282	337(AAGGACTCCAAGTTCC,-,0.00),338(AGGACTCCAAGTTCCC,+,0.00),584(AGGAACAGTCTGTTTC,-,0.00),585(GGAACAGTCTGTTTCT,+,0.00)
chunk0132_400_1	chr3	164031609	164032373	+	0	NA	Intergenic	AluSx1|SINE|Alu	139565	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.006545	0.403922	
chunk0210_324_1	chrX	93657285	93657968	+	0	NA	Intergenic	MIR|SINE|MIR	16057	NM_004538	4675	Hs.21365	NM_004538	ENSG00000186310	NAP1L3	MB20|NPL3	nucleosome assembly protein 1 like 3	protein-coding	0.001464	0.384503	
chunk0023_223_1	chr10	26697135	26697594	+	0	NA	promoter-TSS (NM_014317)	promoter-TSS (NM_014317)	-302	NM_014317	23590	Hs.558468	NM_014317	ENSG00000148459	PDSS1	COQ1|COQ10D2|COQ1A|DPS|SPS|TPRT|TPT|TPT 1|hDPS1	decaprenyl diphosphate synthase subunit 1	protein-coding	0.078431	0.623913	
chunk0111_381_1	chr20	34027249	34027985	+	0	NA	intron (NM_016732, intron 1 of 9)	intron (NM_016732, intron 1 of 9)	-21502	NR_039911	100616434		NR_039911	ENSG00000264616	MIR4755	mir-4755	microRNA 4755	ncRNA	0.001359	0.417910	
chunk0049_104_1	chr12	90945788	90946368	+	0	NA	intron (NR_038868, intron 3 of 4)	intron (NR_038868, intron 3 of 4)	9069	NR_130711	196477	Hs.128574	NM_152638	ENSG00000197651	CCER1	C12orf12	coiled-coil glutamate rich protein 1	protein-coding	0.000000	0.306368	366(AGAAACACAGTGTCCA,-,0.00),367(GAAACACAGTGTCCAG,+,0.00)
chunk0101_469_1	chr2	140889816	140890695	+	0	NA	intron (NM_018557, intron 23 of 90)	L1ME3Cz|LINE|L1	-303570	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.001138	0.288636	
chunk0136_158_1	chr4	5680281	5680524	+	0	NA	intron (NM_147127, intron 7 of 21)	Tigger3b|DNA|TcMar-Tigger	28165	NM_147127	132884	Hs.87306	NM_147127	ENSG00000173040	EVC2	LBN|WAD	EvC ciliary complex subunit 2	protein-coding	0.020576	0.413934	
chunk0105_86_1	chr2	183998243	183998448	+	0	NA	Intergenic	L2a|LINE|L2	-380630	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.417476	
chunk0038_446_1	chr11	94758462	94759083	+	0	NA	Intergenic	Intergenic	-9570	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.006441	0.353698	
chunk0170_271_1	chr6	114051056	114051753	+	0	NA	intron (NR_125845, intron 4 of 9)	Tigger3b|DNA|TcMar-Tigger	11473	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.001435	0.339542	
chunk0190_452_1	chr8	42051859	42052405	+	0	NA	promoter-TSS (NM_006766)	promoter-TSS (NM_006766)	-106	NM_006766	7994	Hs.491577	NM_006766	ENSG00000083168	KAT6A	MOZ|MRD32|MYST-3|MYST3|RUNXBP2|ZC2HC6A|ZNF220	lysine acetyltransferase 6A	protein-coding	0.097070	0.740402	
chunk0093_249_1	chr19	50873049	50873431	+	0	NA	promoter-TSS (NM_005551)	promoter-TSS (NM_005551)	-193	NM_001256080	3817	Hs.515560	NM_005551	ENSG00000167751	KLK2	KLK2A2|hGK-1|hK2	kallikrein related peptidase 2	protein-coding	0.013089	0.561358	213(TGGAACAGCAAGTGCT,-,0.00),214(GGAACAGCAAGTGCTG,+,0.00)
chunk0083_134_1	chr17	65498368	65498653	+	0	NA	Intergenic	Intergenic	40969	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.010526	0.363636	
chunk0128_441_1	chr3	115018500	115019207	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	52561	NM_001164343	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.004243	0.346045	329(AATACATAATGTTCTT,+,0.00),426(GAGAACATTTTGTTCT,-,0.00),427(AGAACATTTTGTTCTG,+,0.00)
chunk0157_324_1	chr5	122003942	122004725	+	0	NA	intron (NM_152546, intron 4 of 7)	L1M3e|LINE|L1	42372	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.010217	0.397959	429(TTGAACAGACTGTCCT,-,0.00),430(TGAACAGACTGTCCTT,+,0.00)
chunk0135_120_1	chr3	187014410	187015122	+	0	NA	intron (NM_173216, intron 2 of 7)	intron (NM_173216, intron 2 of 7)	-7111	NM_003032	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.005618	0.448808	
chunk0098_335_1	chr2	77059232	77059821	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	73561	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.003396	0.340678	
chunk0029_287_1	chr10	103793526	103793725	+	0	NA	intron (NM_014631, intron 2 of 13)	intron (NM_014631, intron 2 of 13)	46846	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.000000	0.505000	
chunk0069_272_1	chr15	64825717	64826064	+	0	NA	promoter-TSS (NM_025049)	promoter-TSS (NM_025049)	-222	NM_001286499	80119	Hs.112160	NM_025049	ENSG00000140451	PIF1	C15orf20|PIF	PIF1 5'-to-3' DNA helicase	protein-coding	0.048991	0.583333	
chunk0100_394_1	chr2	119233539	119233891	+	0	NA	intron (NM_182915, intron 2 of 5)	intron (NM_182915, intron 2 of 5)	9907	NM_018234	55240	Hs.647822	NM_018234	ENSG00000115107	STEAP3	AHMIO2|STMP3|TSAP6|dudlin-2|dudulin-2|pHyde	STEAP3 metalloreductase	protein-coding	0.011364	0.495751	
chunk0095_274_1	chr2	19874757	19875031	+	0	NA	intron (NR_033875, intron 5 of 9)	intron (NR_033875, intron 5 of 9)	6040	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.010949	0.487273	
chunk0080_359_1	chr17	32928600	32929059	+	0	NA	intron (NM_001033504, intron 1 of 6)	intron (NM_001033504, intron 1 of 6)	919	NM_015544	26022	Hs.3447	NM_015544	ENSG00000006042	TMEM98	TADA1	transmembrane protein 98	protein-coding	0.026144	0.463043	
chunk0008_180_1	chr1	93078882	93079410	+	0	NA	promoter-TSS (NM_001164391)	promoter-TSS (NM_001164391)	-89	NM_001164393	22823	Hs.31016	NM_007358	ENSG00000143033	MTF2	M96|PCL2|TDRD19A|dJ976O13.2	metal response element binding transcription factor 2	protein-coding	0.073864	0.582231	
chunk0041_103_1	chr11	124763170	124763764	+	0	NA	intron (NR_120579, intron 1 of 1)	intron (NR_120579, intron 1 of 1)	1036	NR_120579	101929340	Hs.173840	NR_120577	ENSG00000250073	LOC101929340	-	uncharacterized LOC101929340	ncRNA	0.033670	0.499160	
chunk0212_381_1	chrX	150205024	150205401	+	0	NA	Intergenic	Intergenic	-22792	NR_031748	100313839		NR_031748	ENSG00000252454	MIR2114	-	microRNA 2114	ncRNA	0.005305	0.558201	164(GGGTACATTTTGTTCT,-,0.00),165(GGTACATTTTGTTCTC,+,0.00)
chunk0133_139_1	chr3	169214127	169214641	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-66650	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.003891	0.306796	
chunk0173_54_1	chr6	142367796	142367995	+	0	NA	exon (NM_198569, exon 3 of 25)	exon (NM_198569, exon 3 of 25)	65976	NM_020455	57211	Hs.743302	NM_020455	ENSG00000112414	ADGRG6	APG1|DREG|GPR126|LCCS9|PR126|PS1TP2|VIGR	adhesion G protein-coupled receptor G6	protein-coding	0.010050	0.420000	
chunk0046_241_1	chr12	60402855	60403374	+	0	NA	Intergenic	L2|LINE|L2	713777	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.005780	0.334615	
chunk0194_456_1	chr8	92736659	92737278	+	0	NA	intron (NR_046114, intron 1 of 2)	intron (NR_046114, intron 1 of 2)	49092	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.001616	0.414516	
chunk0140_362_1	chr4	74322417	74322830	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	14153	NM_001270990	255324	Hs.401237	NM_001013442	ENSG00000182585	EPGN	ALGV3072|EPG|PRO9904	epithelial mitogen	protein-coding	0.004843	0.371981	305(CAGAACTGACTGTACC,-,0.00),306(AGAACTGACTGTACCT,+,0.00)
chunk0156_250_1	chr5	108876290	108876537	+	0	NA	intron (NM_001308028, intron 6 of 17)	Cheshire|DNA|hAT-Charlie	-48193	NM_001308031	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.000000	0.407258	
chunk0039_395_1	chr11	107224750	107225383	+	0	NA	Intergenic	Intergenic	-206621	NM_001256424	2977	Hs.24321	NM_000855	ENSG00000152402	GUCY1A2	GC-SA2|GUC1A2	guanylate cyclase 1 soluble subunit alpha 2	protein-coding	0.000000	0.384858	
chunk0004_369_1	chr1	51581325	51581973	+	0	NA	Intergenic	L1MC3|LINE|L1	-35225	NM_024586	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.007716	0.416025	
chunk0035_434_1	chr11	57345351	57345551	+	0	NA	intron (NM_002559, intron 1 of 11)	intron (NM_002559, intron 1 of 11)	7084	NM_002559	5024	Hs.146738	NM_002559	ENSG00000109991	P2RX3	P2X3	purinergic receptor P2X 3	protein-coding	0.020000	0.432836	
chunk0069_334_1	chr15	66399118	66399642	+	0	NA	intron (NM_002755, intron 1 of 10)	intron (NM_002755, intron 1 of 10)	12507	NM_002755	5604	Hs.145442	NM_002755	ENSG00000169032	MAP2K1	CFC3|MAPKK1|MEK1|MKK1|PRKMK1	mitogen-activated protein kinase kinase 1	protein-coding	0.015267	0.409524	89(GGAACGGAATGTTCAC,+,0.00)
chunk0051_146_1	chr12	115764087	115764314	+	0	NA	Intergenic	Intergenic	384454	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.008811	0.447368	
chunk0095_332_1	chr2	20795641	20796332	+	0	NA	intron (NM_001282721, intron 1 of 5)	intron (NM_001282721, intron 1 of 5)	27144	NM_001282724	60526	Hs.187823	NM_021925	ENSG00000118961	LDAH	C2orf43|hLDAH	lipid droplet associated hydrolase	protein-coding	0.002894	0.362717	
chunk0036_330_1	chr11	66480426	66480854	+	0	NA	promoter-TSS (NR_120586)	promoter-TSS (NR_120586)	-391	NR_120586	101928069	Hs.523816	NR_120586	ENSG00000255517	LOC101928069	-	uncharacterized LOC101928069	ncRNA	0.058411	0.610723	277(CTGGACACTCTGTCCC,-,0.00),278(TGGACACTCTGTCCCA,+,0.00)
chunk0028_171_1	chr10	87647825	87648440	+	0	NA	Intergenic	L1MC4a|LINE|L1	-11587	NM_001015880	9060	Hs.524491	NM_004670	ENSG00000198682	PAPSS2	ATPSK2|BCYM4|SK2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	protein-coding	0.003252	0.363636	333(AGGTACATGATGTGCA,-,0.00),334(GGTACATGATGTGCAT,+,0.00)
chunk0164_433_1	chr6	27534224	27534946	+	0	NA	Intergenic	L1MA6|LINE|L1	-61467	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.002770	0.331950	605(GAGAACAAACAGTACC,-,0.00),606(AGAACAAACAGTACCG,+,0.00)
chunk0155_309_1	chr5	96538844	96539235	+	0	NA	intron (NR_130776, intron 4 of 4)	intron (NR_130776, intron 4 of 4)	-105758	NM_000439	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.002558	0.329082	
chunk0090_1_1	chr19	267125	267534	+	0	NA	Intergenic	CpG	23840	NM_177543	8612	Hs.465506	NM_003712	ENSG00000141934	PLPP2	LPP2|PAP-2c|PAP2-g|PPAP2C	phospholipid phosphatase 2	protein-coding	0.139364	0.712195	129(CAGGACGCGCAGTTCC,-,0.00),130(AGGACGCGCAGTTCCC,+,0.00)
chunk0105_307_1	chr2	190279428	190279674	+	0	NA	intron (NM_198047, intron 6 of 12)	LTR10C|LTR|ERV1	40494	NM_198047	26275	Hs.656685	NM_014362	ENSG00000198130	HIBCH	HIBYLCOAH	3-hydroxyisobutyryl-CoA hydrolase	protein-coding	0.004065	0.360324	
chunk0031_63_1	chr10	122864727	122865286	+	0	NA	intron (NM_152644, intron 1 of 3)	L1MC2|LINE|L1	-14627	NR_027282	399815	Hs.113871	NR_027282		LOC399815	-	chromosome 10 open reading frame 88 pseudogene	pseudo	0.001789	0.364286	
chunk0138_176_1	chr4	37904201	37904564	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	13298	NM_015173	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.016529	0.370879	205(CTGAACAGCCTGTACC,-,0.00),206(TGAACAGCCTGTACCT,+,0.00)
chunk0167_282_1	chr6	70450269	70450747	+	0	NA	intron (NM_020819, intron 3 of 20)	L1MA7|LINE|L1	24069	NM_001162529	57579	Hs.211700	NM_020819	ENSG00000082269	FAM135A	KIAA1411	family with sequence similarity 135 member A	protein-coding	0.002092	0.331942	
chunk0138_167_1	chr4	37873247	37873864	+	0	NA	Intergenic	L1ME4b|LINE|L1	-17529	NM_001253912	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.001621	0.331715	304(CTGTACACACTGTTCT,-,0.00),305(TGTACACACTGTTCTT,+,0.00)
chunk0127_266_1	chr3	97484750	97485593	+	0	NA	intron (NM_001080448, intron 10 of 17)	intron (NM_001080448, intron 10 of 17)	45578	NM_173655	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.005931	0.432464	
chunk0163_51_1	chr6	8767149	8767429	+	0	NA	intron (NR_038980, intron 3 of 4)	intron (NR_038980, intron 3 of 4)	115080	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.000000	0.341637	
chunk0082_250_1	chr17	57521031	57521358	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	2403	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.015291	0.521341	
chunk0118_359_1	chr22	36343571	36343770	+	0	NA	intron (NM_002473, intron 2 of 40)	intron (NM_002473, intron 2 of 40)	44397	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.015075	0.485000	
chunk0098_71_1	chr2	67172103	67172302	+	0	NA	intron (NR_038844, intron 3 of 7)	intron (NR_038844, intron 3 of 7)	-41206	NR_110568	101927661	Hs.580508	NR_110568	ENSG00000235885	LOC101927661	-	uncharacterized LOC101927661	ncRNA	0.000000	0.360000	43(AAATACAATGTGTTCT,-,0.00),44(AATACAATGTGTTCTG,+,0.00),128(AAGGACATGTTGTCCC,-,0.00),129(AGGACATGTTGTCCCA,+,0.00)
chunk0165_258_1	chr6	35726792	35727218	+	0	NA	non-coding (NR_027117, exon 10 of 10)	non-coding (NR_027117, exon 10 of 10)	1578	NM_001145775	2289	Hs.407190	NM_004117	ENSG00000096060	FKBP5	AIG6|FKBP51|FKBP54|P54|PPIase|Ptg-10	FKBP prolyl isomerase 5	protein-coding	0.014085	0.515222	
chunk0113_20_1	chr20	49583539	49584220	+	0	NA	Intergenic	Intergenic	-15709	NM_000961	5740	Hs.302085	NM_000961	ENSG00000124212	PTGIS	CYP8|CYP8A1|PGIS|PTGI	prostaglandin I2 synthase	protein-coding	0.013216	0.543988	
chunk0060_261_1	chr14	50225292	50226572	+	0	NA	intron (NM_006939, intron 1 of 22)	intron (NM_006939, intron 1 of 22)	5449	NM_006939	6655	Hs.291533	NM_006939	ENSG00000100485	SOS2	NS9|SOS-2	SOS Ras/Rho guanine nucleotide exchange factor 2	protein-coding	0.009375	0.379391	1072(CAGATCACCCTGTACT,-,0.00),1073(AGATCACCCTGTACTT,+,0.00)
chunk0181_25_1	chr7	77934962	77935208	+	0	NA	intron (NM_020432, intron 9 of 16)	intron (NM_020432, intron 9 of 16)	94955	NM_001127357	57157	Hs.203965	NM_020432	ENSG00000006576	PHTF2	-	putative homeodomain transcription factor 2	protein-coding	0.000000	0.319838	
chunk0029_90_1	chr10	97197148	97197512	+	0	NA	intron (NR_037909, intron 11 of 14)	intron (NR_037909, intron 11 of 14)	-11404	NM_003061	6585	Hs.632082	NM_003061	ENSG00000187122	SLIT1	MEGF4|SLIL1|SLIT-1|SLIT3	slit guidance ligand 1	protein-coding	0.008242	0.383562	
chunk0052_362_1	chr12	127414306	127414505	+	0	NA	Intergenic	Intergenic	-74333	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.020101	0.605000	
chunk0059_438_1	chr14	38451831	38452324	+	0	NA	Intergenic	L1PA10|LINE|L1	-195707	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.004057	0.360324	
chunk0091_198_1	chr19	8595785	8596039	+	0	NA	intron (NM_030957, intron 11 of 25)	intron (NM_030957, intron 11 of 25)	-3716	NM_001282352	81794	Hs.657508	NM_030957	ENSG00000142303	ADAMTS10	ADAM-TS10|ADAMTS-10|WMS|WMS1	ADAM metallopeptidase with thrombospondin type 1 motif 10	protein-coding	0.035433	0.592157	62(GGGTACACAAAGTCCT,-,0.00),63(GGTACACAAAGTCCTG,+,0.00)
chunk0186_362_1	chr7	143901197	143901629	+	0	NA	intron (NM_001206938, intron 1 of 8)	intron (NM_001206938, intron 1 of 8)	666	NM_014719	9747	Hs.735149	NM_014719	ENSG00000198420	TCAF1	FAM115A	TRPM8 channel associated factor 1	protein-coding	0.032407	0.517321	76(AGACACATTCTGTCCT,-,0.00),77(GACACATTCTGTCCTT,+,0.00)
chunk0130_282_1	chr3	136461218	136461417	+	0	NA	intron (NM_005862, intron 13 of 33)	L1MA4|LINE|L1	210992	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.000000	0.345000	
chunk0108_378_1	chr2	236916373	236916615	+	0	NA	Intergenic	Intergenic	-168947	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.008264	0.444444	52(CTGCACACACTGTCCA,-,0.00),53(TGCACACACTGTCCAG,+,0.00)
chunk0176_312_1	chr7	16928044	16928356	+	0	NA	Intergenic	Intergenic	-46211	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.003205	0.335463	
chunk0021_139_1	chr10	3935882	3936577	+	0	NA	Intergenic	MER131|DNA?|DNA?	-54931	NR_106726	102464829		NR_106726	ENSG00000274809	MIR6078	hsa-mir-6078	microRNA 6078	ncRNA	0.015827	0.389368	
chunk0118_241_1	chr22	32575349	32576008	+	0	NA	intron (NM_003490, intron 6 of 12)	intron (NM_003490, intron 6 of 12)	100441	NM_001257990	25793	Hs.5912	NM_012179	ENSG00000100225	FBXO7	FBX|FBX07|FBX7|PARK15|PKPS	F-box protein 7	protein-coding	0.021244	0.460606	
chunk0112_253_1	chr20	42001544	42001947	+	0	NA	Intergenic	L1M2|LINE|L1	-383251	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.009926	0.571782	
chunk0080_241_1	chr17	30177085	30177578	+	0	NA	intron (NM_001261467, intron 2 of 5)	AluJb|SINE|Alu	58637	NM_001045	6532	Hs.29792	NM_001045	ENSG00000108576	SLC6A4	5-HTT|5-HTTLPR|5HTT|HTT|OCD1|SERT|SERT1|hSERT	solute carrier family 6 member 4	protein-coding	0.014199	0.477733	
chunk0136_396_1	chr3	197031421	197031732	+	0	NA	Intergenic	Intergenic	-1760	NM_005929	4241	Hs.184727	NM_005929	ENSG00000163975	MELTF	CD228|MAP97|MFI2|MTF1|MTf	melanotransferrin	protein-coding	0.019293	0.483974	
chunk0134_30_1	chr3	175554703	175554944	+	0	NA	intron (NM_207015, intron 9 of 13)	intron (NM_207015, intron 9 of 13)	185283	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.000000	0.256198	
chunk0138_417_1	chr4	45054883	45055487	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-328551	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.006623	0.295868	251(CAGAACATTCAGTTCT,-,0.00),252(AGAACATTCAGTTCTA,+,0.00)
chunk0013_423_1	chr1	173384897	173385442	+	0	NA	intron (NR_037845, intron 2 of 2)	Charlie25|DNA|hAT-Charlie	76193	NR_125960	101928673	Hs.674889	NR_125960	ENSG00000203739	LOC101928673	-	uncharacterized LOC101928673	ncRNA	0.001835	0.324176	
chunk0053_141_1	chr13	30027454	30027783	+	0	NA	Intergenic	MER34B|LTR|ERV1	81257	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.003040	0.390909	
chunk0045_200_1	chr12	47718529	47718728	+	0	NA	intron (NM_006025, intron 1 of 8)	intron (NM_006025, intron 1 of 8)	6944	NM_006025	8909	Hs.997	NM_006025	ENSG00000111405	ENDOU	P11|PP11|PRSS26	endonuclease, poly(U) specific	protein-coding	0.005025	0.460000	17(AGGAACATCCTGTACC,-,0.00),18(GGAACATCCTGTACCT,+,0.00)
chunk0019_191_1	chr1	226703515	226703714	+	0	NA	intron (NM_002221, intron 2 of 7)	CpG	-28546	NR_103784	100506443	Hs.664293	NR_103784		ITPKB-IT1	-	ITPKB intronic transcript 1	ncRNA	0.145729	0.770000	
chunk0173_120_1	chr6	143634110	143634641	+	0	NA	intron (NM_001100166, intron 1 of 11)	intron (NM_001100166, intron 1 of 11)	26195	NM_014721	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.001883	0.347744	243(AGGAACACTTAGTCCT,-,0.00),244(GGAACACTTAGTCCTT,+,0.00)
chunk0166_342_1	chr6	51029518	51029938	+	0	NA	Intergenic	L1ME4c|LINE|L1	211002	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.002381	0.311164	
chunk0015_15_1	chr1	184276409	184277027	+	0	NA	Intergenic	L1MA3|LINE|L1	-110298	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.004854	0.373183	
chunk0202_119_1	chr9	72985070	72985302	+	0	NA	Intergenic	Intergenic	-31869	NM_000689	216	Hs.76392	NM_000689	ENSG00000165092	ALDH1A1	ALDC|ALDH-E1|ALDH1|ALDH11|HEL-9|HEL-S-53e|HEL12|PUMB1|RALDH1	aldehyde dehydrogenase 1 family member A1	protein-coding	0.012931	0.420601	
chunk0123_63_1	chr3	41234768	41235194	+	0	NA	intron (NM_001098209, intron 10 of 15)	intron (NM_001098209, intron 10 of 15)	35530	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.002347	0.344262	
chunk0199_440_1	chr9	13979653	13979974	+	0	NA	Intergenic	Intergenic	51842	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.003115	0.394410	
chunk0027_315_1	chr10	78048889	78049165	+	0	NA	intron (NM_001142285, intron 4 of 4)	intron (NM_001142285, intron 4 of 4)	15267	NM_001142284	6229	Hs.280130	NM_001026	ENSG00000138326	RPS24	DBA3|S24|eS24	ribosomal protein S24	protein-coding	0.014493	0.494585	
chunk0057_295_1	chr13	106303022	106303221	+	0	NA	Intergenic	Intergenic	-73442	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.000000	0.320000	
chunk0207_414_1	chr9	137046334	137046853	+	0	NA	promoter-TSS (NM_015392)	promoter-TSS (NM_015392)	-369	NM_015392	56654	Hs.719906	NM_015392	ENSG00000107281	NPDC1	CAB|CAB-|CAB-1|CAB1|NPDC-1	neural proliferation, differentiation and control 1	protein-coding	0.067437	0.651923	
chunk0131_185_1	chr3	147895214	147895468	+	0	NA	Intergenic	MER49|LTR|ERV1	474014	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.003937	0.439216	
chunk0093_351_1	chr19	55166764	55167055	+	0	NA	promoter-TSS (NM_001256715)	promoter-TSS (NM_001256715)	-187	NM_001256716	352909	Hs.351582	NM_178837	ENSG00000167646	DNAAF3	C19orf51|CILD2|DAB1|PCD|PF22	dynein axonemal assembly factor 3	protein-coding	0.054983	0.506849	
chunk0113_386_1	chr20	59970916	59971517	+	0	NA	intron (NM_177980, intron 3 of 17)	intron (NM_177980, intron 3 of 17)	12800	NM_177980	60437	Hs.729046	NM_021810	ENSG00000124215	CDH26	VR20	cadherin 26	protein-coding	0.006656	0.403654	
chunk0128_304_1	chr3	111498237	111498436	+	0	NA	Intergenic	MER54B|LTR|ERVL	-43743	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.005025	0.440000	
chunk0135_54_1	chr3	185695482	185695850	+	0	NA	intron (NM_001291869, intron 4 of 15)	intron (NM_001291869, intron 4 of 15)	-17586	NR_126326	646600	Hs.647949	NR_027317	ENSG00000163915	IGF2BP2-AS1	C3orf65	IGF2BP2 antisense RNA 1	ncRNA	0.002717	0.379404	
chunk0004_270_1	chr1	48309623	48310084	+	0	NA	intron (NM_001286238, intron 11 of 12)	L1M4|LINE|L1	87168	NM_001135181	200010	Hs.37890	NM_001011547	ENSG00000117834	SLC5A9	SGLT4	solute carrier family 5 member 9	protein-coding	0.004338	0.389610	
chunk0083_57_1	chr17	63741428	63741695	+	0	NA	intron (NM_001003787, intron 1 of 12)	CpG	409	NM_001165969	92335	Hs.514402	NM_153335	ENSG00000266173	STRADA	LYK5|NY-BR-96|PMSE|STRAD|STRAD alpha|Stlk	STE20 related adaptor alpha	protein-coding	0.074906	0.686567	
chunk0167_428_1	chr6	75661131	75661650	+	0	NA	intron (NM_001304792, intron 7 of 14)	intron (NM_001304792, intron 7 of 14)	59881	NM_015571	26054	Hs.485784	NM_015571	ENSG00000112701	SENP6	SSP1|SUSP1	SUMO specific peptidase 6	protein-coding	0.005780	0.394231	340(ATGTACAGGATGTGCA,-,0.00),341(TGTACAGGATGTGCAG,+,0.00)
chunk0131_223_1	chr3	149223818	149224082	+	0	NA	Intergenic	(ACCA)n|Simple_repeat|Simple_repeat	-1905	NM_000096	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.007576	0.430189	
chunk0211_253_1	chrX	120659508	120660053	+	0	NA	Intergenic	L2a|LINE|L2	-29630	NM_152692	29071	Hs.643920	NM_152692	ENSG00000171155	C1GALT1C1	C1GALT2|C38H2-L1|COSMC|HSPC067|MST143|TNPS	C1GALT1 specific chaperone 1	protein-coding	0.009174	0.368132	
chunk0001_122_1	chr1	4614313	4614717	+	0	NA	Intergenic	Intergenic	-40530	NM_001042478	55966	Hs.12473	NM_018836	ENSG00000196581	AJAP1	MOT8|SHREW-1|SHREW1	adherens junctions associated protein 1	protein-coding	0.022277	0.553086	
chunk0073_434_1	chr16	19172924	19173550	+	0	NA	intron (NM_001308157, intron 2 of 7)	intron (NM_001308157, intron 2 of 7)	880	NM_001308157	51760	Hs.258326	NM_016524	ENSG00000103528	SYT17	sytXVII	synaptotagmin 17	protein-coding	0.022364	0.454545	334(GAAAACATTTTGTTCT,-,0.00),335(AAAACATTTTGTTCTA,+,0.00)
chunk0179_262_1	chr7	49172618	49173123	+	0	NA	Intergenic	Intergenic	248309	NR_003595									0.001980	0.377470	
chunk0151_117_1	chr5	43627042	43627356	+	0	NA	intron (NM_182977, intron 6 of 21)	MLT1L|LTR|ERVL-MaLR	-23969	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.006369	0.488889	213(ATGGACTGTATGTCCT,-,0.00),214(TGGACTGTATGTCCTA,+,0.00)
chunk0024_281_1	chr10	41889355	41889643	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	478546	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.013889	0.401384	
chunk0012_192_1	chr1	159779417	159780009	+	0	NA	Intergenic	MIR|SINE|MIR	-1256	NM_017823	54935	Hs.425801	NM_017823	ENSG00000158716	DUSP23	DUSP25|LDP-3|LDP3|MOSP|VHZ	dual specificity phosphatase 23	protein-coding	0.006757	0.445194	279(TGGATCACTGTGTCCT,-,0.00),280(GGATCACTGTGTCCTT,+,0.00)
chunk0101_119_1	chr2	126495170	126495648	+	0	NA	Intergenic	L1M4|LINE|L1	-160526	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.008368	0.425887	
chunk0208_18_1	chrX	10939266	10939861	+	0	NA	Intergenic	L2b|LINE|L2	-105873	NM_033290	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.005042	0.397651	259(GAGATCAGGTTGTTCC,-,0.00),260(AGATCAGGTTGTTCCT,+,0.00)
chunk0089_229_1	chr18	61714137	61715039	+	0	NA	Intergenic	PRIMA41-int|LTR|ERV1	-33588	NR_103449	100996669	Hs.586981	NR_103449		LINC01544	-	long intergenic non-protein coding RNA 1544	ncRNA	0.012195	0.433001	
chunk0054_189_1	chr13	44870398	44870985	+	0	NA	Intergenic	Intergenic	-61061	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.013629	0.542517	291(CAGCACAGCCAGTTCC,-,0.00),292(AGCACAGCCAGTTCCA,+,0.00),325(GAGGACAGAATGTCCA,-,0.00),326(AGGACAGAATGTCCAC,+,0.00)
chunk0025_332_1	chr10	57953202	57953530	+	0	NA	Intergenic	Intergenic	314568	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.006098	0.322188	
chunk0145_326_1	chr4	150713931	150715309	+	0	NA	intron (NM_001199282, intron 36 of 56)	L1MA8|LINE|L1	132695	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.003628	0.311095	
chunk0174_99_1	chr6	156827416	156827825	+	0	NA	intron (NM_017519, intron 1 of 18)	intron (NM_017519, intron 1 of 18)	-47889	NR_039676	100616154		NR_039676	ENSG00000271899	MIR4466	mir-4466	microRNA 4466	ncRNA	0.009780	0.504878	281(CTGTACATGCTGTTCC,-,0.00),282(TGTACATGCTGTTCCC,+,0.00)
chunk0098_171_1	chr2	70993052	70993766	+	0	NA	intron (NM_144582, intron 2 of 5)	intron (NM_144582, intron 2 of 5)	1462	NM_144582	113419	Hs.516087	NM_144582	ENSG00000144043	TEX261	TEG-261	testis expressed 261	protein-coding	0.015406	0.513287	
chunk0138_389_1	chr4	42717872	42718385	+	0	NA	Intergenic	Intergenic	-61023	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.003899	0.332685	
chunk0074_432_1	chr16	46399753	46400223	+	0	NA	Intergenic	Intergenic	169109	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.029787	0.352442	
chunk0087_97_1	chr18	32413334	32413860	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	56887	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.000000	0.303605	
chunk0209_392_1	chrX	54990339	54990930	+	0	NA	intron (NR_073450, intron 1 of 12)	L1ME3A|LINE|L1	3444	NM_002625	5207	Hs.444304	NM_002625	ENSG00000158571	PFKFB1	F6PK|HL2K|PFRX	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	protein-coding	0.000000	0.307432	
chunk0003_330_1	chr1	38724877	38725621	+	0	NA	Intergenic	Intergenic	134574	NM_001271851	64121	Hs.532461	NM_022157	ENSG00000116954	RRAGC	GTR2|RAGC|TIB929	Ras related GTP binding C	protein-coding	0.005376	0.416107	
chunk0147_67_1	chr4	172819101	172819512	+	0	NA	intron (NM_001034845, intron 7 of 12)	intron (NM_001034845, intron 7 of 12)	-92428	NR_125894	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.002433	0.359223	
chunk0097_73_1	chr2	44377427	44377941	+	0	NA	intron (NM_024766, intron 2 of 10)	intron (NM_024766, intron 2 of 10)	15780	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.003891	0.349515	
chunk0077_283_1	chr16	81237308	81237718	+	0	NA	Intergenic	Intergenic	-1178	NM_017429	53630	Hs.212172	NM_017429	ENSG00000135697	BCO1	BCDO|BCDO1|BCMO|BCMO1|BCO	beta-carotene oxygenase 1	protein-coding	0.019512	0.476886	
chunk0004_187_1	chr1	46171939	46172211	+	0	NA	intron (NM_001303427, intron 1 of 9)	intron (NM_001303427, intron 1 of 9)	-3002	NM_005727	10103	Hs.38972	NM_005727	ENSG00000117472	TSPAN1	NET1|TM4C|TM4SF	tetraspanin 1	protein-coding	0.018382	0.641026	
chunk0020_1_1	chr1	231577131	231577630	+	0	NA	intron (NR_028397, intron 5 of 12)	L2a|LINE|L2	34710	NR_034037	100287814	Hs.25555	NR_034037	ENSG00000229228	LINC00582	-	long intergenic non-protein coding RNA 582	ncRNA	0.018036	0.382000	
chunk0034_451_1	chr11	39707694	39708126	+	0	NA	Intergenic	Intergenic	585220	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.000000	0.288684	
chunk0097_12_1	chr2	41613306	41613645	+	0	NA	Intergenic	Intergenic	-264080	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.002950	0.320588	
chunk0025_274_1	chr10	56156569	56156859	+	0	NA	Intergenic	Intergenic	204559	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.000000	0.240550	
chunk0106_139_1	chr2	200034713	200034974	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-79107	NR_109906	129450	Hs.204619	NM_152382	ENSG00000162971	TYW5	C2orf60|hTYW5	tRNA-yW synthesizing protein 5	protein-coding	0.000000	0.301527	
chunk0058_360_1	chr14	28965411	28965758	+	0	NA	Intergenic	Intergenic	192880	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.008646	0.313218	
chunk0099_287_1	chr2	98704812	98705071	+	0	NA	intron (NM_012214, intron 2 of 15)	intron (NM_012214, intron 2 of 15)	26185	NM_012214	11320	Hs.177576	NM_012214	ENSG00000071073	MGAT4A	GNT-IV|GNT-IVA|GnT-4a	alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A	protein-coding	0.007722	0.430769	
chunk0007_304_1	chr1	84247376	84247661	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-50848	NM_001010971	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.017544	0.409091	
chunk0064_39_1	chr14	89654945	89655387	+	0	NA	Intergenic	Intergenic	-36016	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.002262	0.417607	
chunk0049_68_1	chr12	90179824	90180295	+	0	NA	Intergenic	L1ME3F|LINE|L1	471104	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.006369	0.288136	
chunk0134_160_1	chr3	177849820	177850019	+	0	NA	intron (NR_110826, intron 1 of 2)	intron (NR_110826, intron 1 of 2)	33054	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.005025	0.470000	
chunk0104_82_1	chr2	171945977	171946447	+	0	NA	intron (NR_027862, intron 2 of 9)	L1MC|LINE|L1	23787	NM_003642	8520	Hs.632532	NM_003642	ENSG00000128708	HAT1	KAT1	histone acetyltransferase 1	protein-coding	0.002128	0.380042	
chunk0047_155_1	chr12	69751270	69751469	+	0	NA	intron (NM_175623, intron 1 of 10)	L1MC5a|LINE|L1	11979	NR_103520	117177	Hs.258209	NM_022456	ENSG00000127328	RAB3IP	RABIN3|RABIN8	RAB3A interacting protein	protein-coding	0.015075	0.470000	
chunk0189_98_1	chr8	21834081	21834283	+	0	NA	Intergenic	Intergenic	-45348	NM_001495	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.004950	0.512315	
chunk0016_269_1	chr1	200416431	200416630	+	0	NA	Intergenic	MIRc|SINE|MIR	-6472	NM_001281293	23528	Hs.59757	NM_012482	ENSG00000162702	ZNF281	ZBP-99|ZNP-99	zinc finger protein 281	protein-coding	0.000000	0.385000	
chunk0175_356_1	chr6	167738006	167738280	+	0	NA	Intergenic	L2b|LINE|L2	-54356	NR_117092	441178	Hs.628956	NM_001025489	ENSG00000203688	LINC02487	-	long intergenic non-protein coding RNA 2487	ncRNA	0.021898	0.480000	
chunk0156_137_1	chr5	106965746	106966331	+	0	NA	intron (NR_104671, intron 2 of 3)	intron (NR_104671, intron 2 of 3)	44976	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.001709	0.349829	289(TAGGTCACAATGTGCC,-,0.00)
chunk0193_40_1	chr8	71562944	71563409	+	0	NA	Intergenic	Intergenic	-200944	NM_001288575	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.002151	0.354077	
chunk0019_319_1	chr1	229114241	229114589	+	0	NA	Intergenic	L2c|LINE|L2	60386	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.011494	0.441261	
chunk0042_205_1	chr12	5964691	5965183	+	0	NA	intron (NM_000552, intron 47 of 51)	intron (NM_000552, intron 47 of 51)	-18705	NM_001278597	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.014228	0.553753	265(GGGAACAGCCTGCTCT,-,0.00),266(GGAACAGCCTGCTCTG,+,0.00)
chunk0052_373_1	chr12	128823894	128824267	+	0	NA	promoter-TSS (NM_145648)	promoter-TSS (NM_145648)	-84	NM_145648	121260	Hs.507260	NM_145648	ENSG00000139370	SLC15A4	FP12591|PHT1|PTR4	solute carrier family 15 member 4	protein-coding	0.101877	0.700535	
chunk0148_370_1	chr5	14627768	14628356	+	0	NA	Intergenic	Intergenic	24320	NR_132980	106635683		NR_132980		SNORD141A	-	small nucleolar RNA, C/D box 141A	snoRNA	0.010204	0.341256	238(TAGAACATGTTGTACC,-,0.00),239(AGAACATGTTGTACCC,+,0.00),367(GTAACAGGATGTTCTG,+,0.00)
chunk0132_31_1	chr3	154713603	154713802	+	0	NA	Intergenic	Intergenic	-283987	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.005025	0.350000	
chunk0130_91_1	chr3	130800714	130801261	+	0	NA	Intergenic	Intergenic	-49538	NM_001199182	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.016453	0.374088	
chunk0120_452_1	chr3	14265553	14265889	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	86847	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.023810	0.459941	
chunk0026_119_1	chr10	61981513	61981959	+	0	NA	intron (NM_032199, intron 3 of 9)	intron (NM_032199, intron 3 of 9)	-67475	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.004484	0.445190	
chunk0030_34_1	chr10	111390425	111390907	+	0	NA	Intergenic	Intergenic	313634	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.004149	0.376812	
chunk0171_332_1	chr6	129920069	129920579	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-59053	NM_001010876	253582		NM_001010876	ENSG00000203756	TMEM244	C6orf191|bA174C7.4	transmembrane protein 244	protein-coding	0.003922	0.360078	
chunk0073_18_1	chr16	2226415	2226933	+	0	NA	intron (NM_001288776, intron 1 of 13)	intron (NM_001288776, intron 1 of 13)	3186	NM_001288778	1877	Hs.513268	NM_004424	ENSG00000167967	E4F1	E4F	E4F transcription factor 1	protein-coding	0.021236	0.545279	
chunk0202_391_1	chr9	81165557	81166050	+	0	NA	Intergenic	L1PA7|LINE|L1	523732	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002028	0.366397	
chunk0184_201_1	chr7	117054085	117054543	+	0	NA	intron (NM_021908, intron 1 of 15)	intron (NM_021908, intron 1 of 15)	34103	NR_106748	102466616		NR_106748	ENSG00000283923	MIR6132	hsa-mir-6132	microRNA 6132	ncRNA	0.017467	0.461874	
chunk0018_190_1	chr1	219279211	219279950	+	0	NA	Intergenic	Intergenic	104611	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.004060	0.375676	
chunk0204_109_1	chr9	94867295	94867494	+	0	NA	intron (NM_032823, intron 5 of 14)	intron (NM_032823, intron 5 of 14)	57432	NR_031755	100313780		NR_031755	ENSG00000252153	MIR2278	mir-2278	microRNA 2278	ncRNA	0.030151	0.505000	
chunk0129_388_1	chr3	126338195	126338394	+	0	NA	Intergenic	Intergenic	19099	NM_014079	28999	Hs.272215	NM_014079	ENSG00000163884	KLF15	KKLF	Kruppel like factor 15	protein-coding	0.015075	0.600000	
chunk0046_136_1	chr12	57888452	57888920	+	0	NA	Intergenic	Intergenic	-41722	NM_005730	10106	Hs.524530	NM_005730	ENSG00000175215	CTDSP2	OS4|PSR2|SCP2	CTD small phosphatase 2	protein-coding	0.025641	0.535181	
chunk0211_321_1	chrX	123860067	123860332	+	0	NA	promoter-TSS (NM_001167)	promoter-TSS (NM_001167)	32	NR_037916	331	Hs.356076	NM_001167	ENSG00000101966	XIAP	API3|BIRC4|IAP-3|ILP1|MIHA|XLP2|hIAP-3|hIAP3	X-linked inhibitor of apoptosis	protein-coding	0.094340	0.672932	
chunk0126_122_1	chr3	75717461	75718387	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-20356	NR_036235	100422955		NR_036235	ENSG00000266396	MIR4273	-	microRNA 4273	ncRNA	0.012959	0.485437	
chunk0110_384_1	chr20	20085651	20086249	+	0	NA	intron (NM_015585, intron 6 of 26)	intron (NM_015585, intron 6 of 26)	29304	NM_001167816	26074	Hs.729168	NM_015585	ENSG00000089101	CFAP61	C20orf26|CaM-IP3|dJ1002M8.3|dJ1178H5.4	cilia and flagella associated protein 61	protein-coding	0.006689	0.362270	370(AAGGACTTAGTGTGCC,-,0.00),371(AGGACTTAGTGTGCCC,+,0.00)
chunk0198_441_1	chr8	143840775	143840974	+	0	NA	promoter-TSS (NM_178564)	promoter-TSS (NM_178564)	100	NM_178564	340371	Hs.521926	NM_178564	ENSG00000185189	NRBP2	TRG16|pp9320	nuclear receptor binding protein 2	protein-coding	0.130653	0.795000	
chunk0116_188_1	chr21	36987595	36988311	+	0	NA	intron (NM_000411, intron 1 of 11)	L1MC4a|LINE|L1	2292	NM_000411	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.002793	0.334728	
chunk0186_373_1	chr7	144097364	144097630	+	0	NA	Intergenic	L1M5|LINE|L1	2389	NM_001004135	346525	Hs.553708	NM_001004135	ENSG00000221858	OR2A12	OR2A12P|OR2A16P	olfactory receptor family 2 subfamily A member 12	protein-coding	0.007519	0.348315	
chunk0144_7_1	chr4	124504687	124504977	+	0	NA	intron (NR_110838, intron 7 of 8)	L3|LINE|CR1	53602	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.006897	0.323024	
chunk0208_434_1	chrX	30299750	30300372	+	0	NA	Intergenic	MER68B|LTR|ERVL	9317	NM_000475	190	Hs.268490	NM_000475	ENSG00000169297	NR0B1	AHC|AHCH|AHX|DAX-1|DAX1|DSS|GTD|HHG|NROB1|SRXY2	nuclear receptor subfamily 0 group B member 1	protein-coding	0.012862	0.425361	310(CTGGACAGTTTGTGCA,-,0.00)
chunk0180_190_1	chr7	66122321	66122892	+	0	NA	intron (NM_001040648, intron 1 of 2)	intron (NM_001040648, intron 1 of 2)	7788	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.008757	0.400350	132(GAGATCATTTTGTTCT,-,0.00),133(AGATCATTTTGTTCTG,+,0.00)
chunk0093_185_1	chr19	48819380	48820097	+	0	NA	intron (NM_016246, intron 5 of 8)	intron (NM_016246, intron 5 of 8)	-8675	NM_001164773	587	Hs.512670	NM_001190	ENSG00000105552	BCAT2	BCAM|BCATM|BCT2|PP18	branched chain amino acid transaminase 2	protein-coding	0.011158	0.533426	
chunk0066_28_1	chr15	27564594	27565059	+	0	NA	Intergenic	Intergenic	-403507	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.004301	0.508584	
chunk0005_208_1	chr1	59104275	59104724	+	0	NA	Intergenic	Intergenic	42308	NR_027120	729467	Hs.662291	NR_027120	ENSG00000224609	HSD52	-	uncharacterized LOC729467	ncRNA	0.004454	0.448889	
chunk0051_231_1	chr12	116931304	116931940	+	0	NA	intron (NM_012174, intron 2 of 10)	L1MA8|LINE|L1	20666	NM_153348	26259	Hs.624537	NM_012174	ENSG00000174989	FBXW8	FBW6|FBW8|FBX29|FBXO29|FBXW6	F-box and WD repeat domain containing 8	protein-coding	0.001572	0.324961	
chunk0027_378_1	chr10	79448979	79449618	+	0	NA	Intergenic	Intergenic	-3671	NM_153367	219654	Hs.523080	NM_153367	ENSG00000165424	ZCCHC24	C10orf56|Z3CXXC8	zinc finger CCHC-type containing 24	protein-coding	0.006260	0.492188	
chunk0161_49_1	chr5	166057689	166057931	+	0	NA	Intergenic	Intergenic	868560	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.008264	0.374486	
chunk0173_405_1	chr6	150745962	150746623	+	0	NA	intron (NM_001029884, intron 3 of 16)	Tigger9b|DNA|TcMar-Tigger	-119387	NM_015440	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.012103	0.386707	371(CAGAACTGACTGTACC,-,0.00),372(AGAACTGACTGTACCT,+,0.00)
chunk0093_223_1	chr19	50061716	50062164	+	0	NA	non-coding (NR_027257, exon 2 of 3)	non-coding (NR_027257, exon 2 of 3)	11260	NR_027257	400710	Hs.628968	NR_027257	ENSG00000204666	LOC400710	-	uncharacterized LOC400710	ncRNA	0.008929	0.494432	
chunk0021_356_1	chr1	246281103	246282126	+	0	NA	intron (NM_001167740, intron 5 of 11)	L2c|LINE|L2	135798	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.005865	0.393555	173(CAGGACAATGTGTTCT,-,0.00),174(AGGACAATGTGTTCTC,+,0.00),200(GTGAACTCACTGTGCT,-,0.00),201(TGAACTCACTGTGCTT,+,0.00)
chunk0057_66_1	chr13	98111823	98112179	+	0	NA	Intergenic	MER68|LTR|ERVL	-30561	NM_001286839	10160	Hs.403917	NM_005766	ENSG00000152767	FARP1	CDEP|FARP1-IT1|PLEKHC2|PPP1R75	FERM, ARH/RhoGEF and pleckstrin domain protein 1	protein-coding	0.014045	0.512605	59(AAGGTCACACTGTTCA,-,0.00),60(AGGTCACACTGTTCAC,+,0.00)
chunk0066_87_1	chr15	29726570	29726798	+	0	NA	intron (NM_175610, intron 17 of 26)	intron (NM_175610, intron 17 of 26)	94864	NM_001301026	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.004386	0.340611	
chunk0119_240_1	chr22	45597572	45598208	+	0	NA	intron (NM_006486, intron 16 of 16)	intron (NM_006486, intron 16 of 16)	7757	NR_131244	100506737	Hs.517692	NR_131244	ENSG00000238120	LINC01589	TCONS_00029353	long intergenic non-protein coding RNA 1589	ncRNA	0.025157	0.557300	356(GTGAACTTGATGTTCC,-,0.00),357(TGAACTTGATGTTCCT,+,0.00)
chunk0153_290_1	chr5	73338118	73339013	+	0	NA	Intergenic	Intergenic	109962	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.021229	0.483259	173(CGGCACAAATTGTTCT,-,0.00),174(GGCACAAATTGTTCTG,+,0.00)
chunk0070_436_1	chr15	78157940	78158232	+	0	NA	intron (NM_005530, intron 3 of 10)	intron (NM_005530, intron 3 of 10)	8709	NM_005530	3419	Hs.591110	NM_005530	ENSG00000166411	IDH3A	-	isocitrate dehydrogenase (NAD(+)) 3 alpha	protein-coding	0.010274	0.358362	
chunk0176_307_1	chr7	16857124	16857801	+	0	NA	Intergenic	Intergenic	24527	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.001477	0.262537	
chunk0131_249_1	chr3	149534908	149535255	+	0	NA	intron (NM_015472, intron 4 of 6)	intron (NM_015472, intron 4 of 6)	60500	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.005764	0.471264	
chunk0008_277_1	chr1	94743784	94744494	+	0	NA	intron (NR_104131, intron 1 of 4)	intron (NR_104131, intron 1 of 4)	1761	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.002817	0.438819	332(GAGGACAGACTGTGCT,-,0.00),333(AGGACAGACTGTGCTT,+,0.00)
chunk0108_73_1	chr2	227511073	227511397	+	0	NA	intron (NM_001135189, intron 2 of 11)	intron (NM_001135189, intron 2 of 11)	39063	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.000000	0.372308	
chunk0008_266_1	chr1	94595754	94596438	+	0	NA	Intergenic	LTR78|LTR|ERV1	-54239	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.007310	0.486131	
chunk0177_94_1	chr7	21889838	21890405	+	0	NA	intron (NM_001277115, intron 76 of 81)	MIRb|SINE|MIR	55803	NM_018719	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.005291	0.392606	
chunk0087_36_1	chr18	31205231	31205740	+	0	NA	Intergenic	Intergenic	-42629	NM_004948	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.003929	0.403922	196(AAGGACAATGAGTTCC,-,0.00),197(AGGACAATGAGTTCCA,+,0.00)
chunk0085_255_1	chr18	7616669	7617009	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	49523	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.008824	0.557185	142(GAGATCTGCCTGTTCT,-,0.00),143(AGATCTGCCTGTTCTC,+,0.00)
chunk0188_193_1	chr8	11750924	11751135	+	0	NA	intron (NM_001308093, intron 3 of 5)	L1M5|LINE|L1	-10227	NR_103552									0.000000	0.259434	
chunk0083_48_1	chr17	63555787	63556297	+	0	NA	intron (NR_073585, intron 1 of 7)	intron (NR_073585, intron 1 of 7)	5607	NR_073585	10238	Hs.410596	NM_005828	ENSG00000136485	DCAF7	AN11|HAN11|SWAN-1|WDR68	DDB1 and CUL4 associated factor 7	protein-coding	0.007843	0.414873	
chunk0065_357_1	chr14	103773494	103773875	+	0	NA	intron (NM_015316, intron 4 of 16)	HAL1|LINE|L1	57940	NM_024071	79038	Hs.592322	NM_024071	ENSG00000100711	ZFYVE21	HCVP7TP1|ZF21	zinc finger FYVE-type containing 21	protein-coding	0.005249	0.403141	
chunk0118_136_1	chr22	29856494	29857103	+	0	NA	Intergenic	L2b|LINE|L2	-18494	NM_032204	84164	Hs.731754	NM_032204	ENSG00000100325	ASCC2	ASC1p100|p100	activating signal cointegrator 1 complex subunit 2	protein-coding	0.006568	0.450820	
chunk0107_171_1	chr2	215529319	215529558	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	75731	NR_110607	102724849	Hs.116161	NR_110607	ENSG00000225166	LOC102724849	-	uncharacterized LOC102724849	ncRNA	0.004184	0.395833	
chunk0011_67_1	chr1	143635121	143635665	+	0	NA	Intergenic	L2a|LINE|L2	64226	NR_104078	101954269		NR_104078	ENSG00000207349	RNVU1-17	RNU1-127|vU1.17	RNA, variant U1 small nuclear 17	snRNA	0.007353	0.504587	
chunk0149_135_1	chr5	19880692	19881194	+	0	NA	intron (NM_001291957, intron 1 of 12)	Tigger19b|DNA|TcMar-Tigger	5329	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.001992	0.332008	
chunk0094_281_1	chr2	8246989	8247344	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	81253	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.005634	0.497191	132(CAGAACACGGTGTTCT,-,0.00),133(AGAACACGGTGTTCTC,+,0.00)
chunk0114_256_1	chr21	16117678	16118223	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	46836	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.007339	0.340659	
chunk0058_279_1	chr14	26410617	26411143	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	186874	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.001901	0.360531	
chunk0048_188_1	chr12	81088397	81088613	+	0	NA	intron (NM_024560, intron 1 of 15)	MIR|SINE|MIR	10475	NM_024560	79611	Hs.259559	NM_024560	ENSG00000111058	ACSS3	-	acyl-CoA synthetase short chain family member 3	protein-coding	0.004630	0.281106	
chunk0023_351_1	chr10	29713391	29713864	+	0	NA	intron (NM_003174, intron 1 of 35)	MER58A|DNA|hAT-Charlie	22174	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.004228	0.371308	
chunk0089_243_1	chr18	62089205	62089404	+	0	NA	intron (NM_176787, intron 24 of 30)	intron (NM_176787, intron 24 of 30)	97752	NM_012327	23556	Hs.157031	NM_012327	ENSG00000197563	PIGN	MCAHS|MCAHS1|MCD4|MDC4|PIG-N	phosphatidylinositol glycan anchor biosynthesis class N	protein-coding	0.000000	0.335000	
chunk0067_34_1	chr15	40420795	40421159	+	0	NA	3' UTR (NM_001159508, exon 11 of 11)	3' UTR (NM_001159508, exon 11 of 11)	15492	NM_001159508	3712	Hs.513646	NM_002225	ENSG00000128928	IVD	ACAD2	isovaleryl-CoA dehydrogenase	protein-coding	0.008242	0.542466	
chunk0043_399_1	chr12	25437541	25437855	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	115585	NM_001256266	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.009554	0.482540	
chunk0080_136_1	chr17	27449644	27449843	+	0	NA	Intergenic	Intergenic	-22267	NM_014238	8844	Hs.133534	NM_014238	ENSG00000141068	KSR1	KSR|RSU2	kinase suppressor of ras 1	protein-coding	0.000000	0.500000	156(GAGCACAGGGTGTACC,-,0.00),157(AGCACAGGGTGTACCC,+,0.00)
chunk0203_33_1	chr9	83002994	83003278	+	0	NA	intron (NM_152573, intron 9 of 16)	intron (NM_152573, intron 9 of 16)	59992	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.007042	0.294737	
chunk0009_181_1	chr1	105695059	105695300	+	0	NA	Intergenic	L1MEc|LINE|L1	-76244	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004149	0.392562	
chunk0150_205_1	chr5	35094977	35095305	+	0	NA	intron (NM_000949, intron 2 of 9)	intron (NM_000949, intron 2 of 9)	22981	NM_001204316	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.006098	0.449848	206(AAGGACATAATGTGCT,-,0.00),207(AGGACATAATGTGCTC,+,0.00)
chunk0036_61_1	chr11	59560981	59561230	+	0	NA	Intergenic	Intergenic	34053	NR_036120	100422880		NR_036120	ENSG00000264559	MIR3162	mir-3162	microRNA 3162	ncRNA	0.052209	0.528000	108(AAGAACTTTCAGTCCT,-,0.00),109(AGAACTTTCAGTCCTC,+,0.00)
chunk0097_315_1	chr2	56312919	56313345	+	0	NA	intron (NM_001080433, intron 2 of 5)	intron (NM_001080433, intron 2 of 5)	-127362	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.002347	0.304450	
chunk0167_91_1	chr6	56899687	56900069	+	0	NA	intron (NM_001144769, intron 3 of 96)	intron (NM_001144769, intron 3 of 96)	-47962	NM_001144770	667	Hs.604915	NM_001723	ENSG00000151914	DST	BP240|BPA|BPAG1|CATX-15|CATX15|D6S1101|DMH|DT|EBSB2|HSAN6|MACF2	dystonin	protein-coding	0.005236	0.514360	
chunk0175_198_1	chr7	5693000	5693431	+	0	NA	intron (NM_207111, intron 13 of 16)	MER58A|DNA|hAT-Charlie	-12754	NR_046834	100874342	Hs.665728	NR_046834	ENSG00000237738	RNF216-IT1	-	RNF216 intronic transcript 1	ncRNA	0.018561	0.428241	
chunk0111_155_1	chr20	25100819	25101280	+	0	NA	Intergenic	Intergenic	-18670	NR_045948	30813	Hs.274264	NM_014588	ENSG00000100987	VSX1	CAASDS|KTCN|KTCN1|PPCD|PPCD1|PPD|RINX	visual system homeobox 1	protein-coding	0.008677	0.487013	
chunk0108_12_1	chr2	226115682	226116172	+	0	NA	Intergenic	Intergenic	-26867	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.002041	0.348269	
chunk0113_179_1	chr20	53171052	53171251	+	0	NA	intron (NM_173485, intron 1 of 2)	intron (NM_173485, intron 1 of 2)	-14132	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.025126	0.395000	
chunk0127_180_1	chr3	95388615	95388909	+	0	NA	Intergenic	L1MEc|LINE|L1	294431	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.003401	0.342373	
chunk0183_105_1	chr7	105261860	105262248	+	0	NA	intron (NM_182692, intron 2 of 15)	L2|LINE|L2	7023	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.002577	0.424165	
chunk0133_356_1	chr3	173410099	173410549	+	0	NA	intron (NM_014932, intron 1 of 6)	intron (NM_014932, intron 1 of 6)	11876	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.008889	0.394678	
chunk0198_304_1	chr8	138289962	138290208	+	0	NA	intron (NM_015912, intron 3 of 19)	intron (NM_015912, intron 3 of 19)	206737	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.008130	0.497976	
chunk0010_193_1	chr1	116001145	116001579	+	0	NA	intron (NM_018420, intron 2 of 11)	L1M1|LINE|L1	-24086	NR_125970	101928977	Hs.627914	NR_125970		LOC101928977	-	uncharacterized LOC101928977	ncRNA	0.002304	0.319540	
chunk0199_75_1	chr9	2436775	2437100	+	0	NA	Intergenic	L1PB1|LINE|L1	-184856	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.000000	0.303681	
chunk0052_81_1	chr13	21752527	21753584	+	0	NA	Intergenic	MIR|SINE|MIR	81979	NM_002010	2254	Hs.111	NM_002010	ENSG00000102678	FGF9	FGF-9|GAF|HBFG-9|HBGF-9|SYNS3	fibroblast growth factor 9	protein-coding	0.004730	0.361059	
chunk0035_18_1	chr11	40252928	40253328	+	0	NA	intron (NM_001258419, intron 4 of 6)	intron (NM_001258419, intron 4 of 6)	40002	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005000	0.316708	195(AGAAACACTCTGTGCT,-,0.00),196(GAAACACTCTGTGCTT,+,0.00)
chunk0007_441_1	chr1	86870908	86871740	+	0	NA	intron (NM_004261, intron 3 of 4)	intron (NM_004261, intron 3 of 4)	43100	NM_004261	9403	Hs.362728	NM_004261	ENSG00000183291	SELENOF	SEP15	selenoprotein F	protein-coding	0.004808	0.300120	
chunk0132_125_1	chr3	156037294	156037638	+	0	NA	Intergenic	Intergenic	-83082	NM_172160	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.002907	0.414493	
chunk0103_396_1	chr2	169013243	169013554	+	0	NA	exon (NM_003742, exon 5 of 28)	exon (NM_003742, exon 5 of 28)	17925	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.016077	0.400641	
chunk0176_86_1	chr7	11506484	11507289	+	0	NA	intron (NM_015204, intron 6 of 26)	L2a|LINE|L2	325312	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.002484	0.382134	506(GGGTACTGTCTGTTCA,-,0.00),507(GGTACTGTCTGTTCAT,+,0.00)
chunk0087_425_1	chr18	42274614	42275142	+	0	NA	intron (NR_046454, intron 3 of 6)	intron (NR_046454, intron 3 of 6)	88210	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.001894	0.434783	
chunk0193_63_1	chr8	72822222	72822540	+	0	NA	intron (NM_004770, intron 2 of 2)	intron (NM_004770, intron 2 of 2)	90336	NR_110656	101926908	Hs.680588	NR_110656	ENSG00000253726	LOC101926908	-	uncharacterized LOC101926908	ncRNA	0.009434	0.460815	
chunk0084_132_1	chr17	76196498	76197202	+	0	NA	intron (NM_052916, intron 2 of 18)	LTR16A1|LTR|ERVL	43459	NM_052916	114804	Hs.500643	NM_052916	ENSG00000141576	RNF157	-	ring finger protein 157	protein-coding	0.008523	0.492199	371(TGGTACAAGCTGTACT,-,0.00),372(GGTACAAGCTGTACTC,+,0.00)
chunk0088_252_1	chr18	48892399	48893035	+	0	NA	Intergenic	Intergenic	50090	NM_001190823	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.026730	0.546311	
chunk0135_405_1	chr3	192614907	192615487	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	112402	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.005172	0.323580	
chunk0099_90_1	chr2	85514415	85514616	+	0	NA	Intergenic	X6B_LINE|LINE|CR1	24371	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.024876	0.326733	
chunk0028_71_1	chr10	83695121	83695377	+	0	NA	Intergenic	Intergenic	-444180	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.003906	0.509728	
chunk0013_449_1	chr1	173876774	173877139	+	0	NA	intron (NM_001122770, intron 4 of 4)	Tigger3a|DNA|TcMar-Tigger	8601	NM_032522	84614	Hs.668497	NM_032522	ENSG00000185278	ZBTB37	D430004I08Rik|ZNF908	zinc finger and BTB domain containing 37	protein-coding	0.013699	0.330601	
chunk0110_252_1	chr20	16606926	16607205	+	0	NA	Intergenic	Intergenic	-33631	NM_001199865	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.007168	0.425000	122(GGAACAAGGAGTCCAC,+,0.00)
chunk0148_269_1	chr5	10511819	10512502	+	0	NA	Intergenic	L2b|LINE|L2	-9432	NR_104606	101929412	Hs.508287	NR_104606	ENSG00000249396	LINC02212	-	long intergenic non-protein coding RNA 2212	ncRNA	0.010249	0.444444	
chunk0091_139_1	chr19	6903415	6903614	+	0	NA	intron (NM_001256253, intron 6 of 19)	intron (NM_001256253, intron 6 of 19)	15965	NM_001256255	2015	Hs.2375	NM_001974	ENSG00000174837	ADGRE1	EMR1|TM7LN3	adhesion G protein-coupled receptor E1	protein-coding	0.000000	0.455000	
chunk0151_102_1	chr5	43314621	43315293	+	0	NA	Intergenic	Intergenic	-1445	NM_002130	3157	Hs.397729	NM_002130	ENSG00000112972	HMGCS1	HMGCS	3-hydroxy-3-methylglutaryl-CoA synthase 1	protein-coding	0.010417	0.369985	
chunk0021_198_1	chr10	5780350	5780778	+	0	NA	intron (NM_001494, intron 6 of 10)	L1ME2|LINE|L1	32985	NM_001115156	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.011682	0.337995	
chunk0189_207_1	chr8	24218647	24219107	+	0	NA	Intergenic	Intergenic	-75163	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.004348	0.455531	
chunk0212_155_1	chrX	132117572	132118236	+	0	NA	intron (NM_194277, intron 1 of 11)	L1ME4c|LINE|L1	10116	NM_001306193	90167	Hs.170776	NM_194277	ENSG00000165694	FRMD7	NYS|NYS1|XIPAN	FERM domain containing 7	protein-coding	0.004518	0.330827	
chunk0116_182_1	chr21	36858504	36858764	+	0	NA	intron (NM_001242785, intron 7 of 11)	L2a|LINE|L2	108022	NM_001242784	3141	Hs.371350	NM_000411	ENSG00000159267	HLCS	HCS	holocarboxylase synthetase	protein-coding	0.011538	0.521073	
chunk0007_19_1	chr1	77405475	77405689	+	0	NA	intron (NM_012093, intron 6 of 13)	LTR16D|LTR|ERVL	122980	NM_012093	26289	Hs.559718	NM_012093	ENSG00000154027	AK5	AK6	adenylate kinase 5	protein-coding	0.000000	0.576744	
chunk0103_152_1	chr2	162251707	162252371	+	0	NA	Intergenic	Intergenic	-8504	NM_004460	2191	Hs.654370	NM_004460	ENSG00000078098	FAP	DPPIV|FAPA|FAPalpha|SIMP	fibroblast activation protein alpha	protein-coding	0.007530	0.386466	309(CTGGACTCCGTGTCCT,-,0.00),310(TGGACTCCGTGTCCTC,+,0.00)
chunk0119_328_1	chr22	46845362	46845709	+	0	NA	intron (NM_014346, intron 4 of 12)	intron (NM_014346, intron 4 of 12)	70507	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.014409	0.339080	
chunk0083_447_1	chr17	72915934	72916173	+	0	NA	intron (NM_139177, intron 5 of 9)	intron (NM_139177, intron 5 of 9)	176661	NM_139177	201266	Hs.221127	NM_139177	ENSG00000133195	SLC39A11	C17orf26|ZIP-11|ZIP11	solute carrier family 39 member 11	protein-coding	0.016736	0.454167	
chunk0129_382_1	chr3	126226471	126227144	+	0	NA	Intergenic	Intergenic	-45621	NM_001270364	10840	Hs.434435	NM_012190	ENSG00000144908	ALDH1L1	10-FTHFDH|10-fTHF|FDH|FTHFD	aldehyde dehydrogenase 1 family member L1	protein-coding	0.004458	0.342730	
chunk0117_54_1	chr22	12693380	12694120	+	0	NA	Intergenic	CpG	796344	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.060811	0.690958	452(GGGCCCAGGCTGTCCC,-,0.00),453(GGCCCAGGCTGTCCCA,+,0.00)
chunk0135_103_1	chr3	186644708	186645055	+	0	NA	exon (NM_014375, exon 4 of 7)	exon (NM_014375, exon 4 of 7)	4521	NM_001308077	26998	Hs.81073	NM_014375	ENSG00000090512	FETUB	16G2|Gugu|IRL685	fetuin B	protein-coding	0.008646	0.422414	
chunk0068_439_1	chr15	59637561	59637797	+	0	NA	TTS (NM_004492)	TTS (NM_004492)	19859	NM_004492	2958	Hs.512934	NM_004492	ENSG00000140307	GTF2A2	HsT18745|T18745|TF2A2|TFIIA|TFIIA-12|TFIIA-gamma|TFIIAS	general transcription factor IIA subunit 2	protein-coding	0.004237	0.358650	
chunk0169_377_1	chr6	107272315	107272574	+	0	NA	intron (NM_020381, intron 3 of 7)	MLT1J|LTR|ERVL-MaLR	-158012	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.007722	0.438462	
chunk0169_366_1	chr6	107080790	107081128	+	0	NA	intron (NM_001080450, intron 4 of 4)	intron (NM_001080450, intron 4 of 4)	33473	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.005917	0.454277	
chunk0120_324_1	chr3	10440379	10440639	+	0	NA	intron (NM_001001331, intron 2 of 22)	L2b|LINE|L2	-45947	NR_030614	100126334		NR_030614	ENSG00000216135	MIR885	MIRN885|hsa-mir-885|mir-885	microRNA 885	ncRNA	0.015385	0.475096	
chunk0142_315_1	chr4	100722190	100722618	+	0	NA	Intergenic	MIRb|SINE|MIR	-47291	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.007009	0.389277	209(AGGAACAGTGTGTTCT,-,0.00),210(GGAACAGTGTGTTCTT,+,0.00)
chunk0119_209_1	chr22	44903625	44903968	+	0	NA	intron (NM_001135862, intron 6 of 13)	L1MEi|LINE|L1	105197	NM_001284296	112885	Hs.254097	NM_138415	ENSG00000056487	PHF21B	BHC80L|PHF4	PHD finger protein 21B	protein-coding	0.005831	0.334302	
chunk0001_96_1	chr1	3181676	3181941	+	0	NA	intron (NM_022114, intron 1 of 16)	intron (NM_022114, intron 1 of 16)	53833	NR_036215	100422968		NR_036215	ENSG00000283572	MIR4251	-	microRNA 4251	ncRNA	0.056604	0.481203	
chunk0171_338_1	chr6	129958198	129958482	+	0	NA	Intergenic	MER52D|LTR|ERV1	-60243	NM_032438	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.014085	0.642105	
chunk0194_89_1	chr8	82976491	82977135	+	0	NA	Intergenic	L1MC2|LINE|L1	-426945	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.001553	0.331783	
chunk0074_361_1	chr16	34574151	34574404	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	-414241	NR_038368									0.027668	0.338583	
chunk0125_150_1	chr3	66415834	66416131	+	0	NA	intron (NM_015541, intron 4 of 18)	intron (NM_015541, intron 4 of 18)	84439	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.000000	0.469799	189(CTGGACTGTTTGTTCT,-,0.00),190(TGGACTGTTTGTTCTC,+,0.00)
chunk0032_20_1	chr11	755586	756009	+	0	NA	intron (NM_006755, intron 1 of 7)	intron (NM_006755, intron 1 of 7)	8365	NM_006755	6888	Hs.438678	NM_006755	ENSG00000177156	TALDO1	TAL|TAL-H|TALDOR|TALH	transaldolase 1	protein-coding	0.037825	0.544811	
chunk0027_234_1	chr10	76491090	76491579	+	0	NA	intron (NR_131178, intron 7 of 7)	L1M1|LINE|L1	-396710	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.002045	0.324490	
chunk0084_311_1	chr17	80278783	80279168	+	0	NA	intron (NM_001256071, intron 3 of 67)	intron (NM_001256071, intron 3 of 67)	18114	NM_001256071	57674	Hs.195642	NM_020914	ENSG00000173821	RNF213	ALO17|C17orf27|KIAA1618|MYMY2|MYSTR|NET57	ring finger protein 213	protein-coding	0.031169	0.567358	
chunk0014_353_1	chr1	182338249	182338456	+	0	NA	Intergenic	Intergenic	-24291	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.019324	0.471154	142(CAGAACACTTAGTCCA,-,0.00),143(AGAACACTTAGTCCAC,+,0.00)
chunk0120_458_1	chr3	14303775	14304945	+	0	NA	Intergenic	Intergenic	48208	NR_110135	101927565	Hs.306905	NR_110135	ENSG00000251576	LINC01267	-	long intergenic non-protein coding RNA 1267	ncRNA	0.010256	0.558497	
chunk0040_345_1	chr11	118530253	118530522	+	0	NA	promoter-TSS (NM_032780)	promoter-TSS (NM_032780)	388	NR_120574	101929089	Hs.666633	NR_120572	ENSG00000255435	LOC101929089	-	uncharacterized LOC101929089	ncRNA	0.033457	0.485185	
chunk0195_237_1	chr8	97520327	97520777	+	0	NA	Intergenic	L1PREC2|LINE|L1	-74055	NR_125390	101927066	Hs.732112	NR_125390		LOC101927066	-	uncharacterized LOC101927066	ncRNA	0.006667	0.345898	
chunk0145_63_1	chr4	145436075	145436452	+	0	NA	Intergenic	Intergenic	-45536	NM_005900	4086	Hs.604588	NM_005900	ENSG00000170365	SMAD1	BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1	SMAD family member 1	protein-coding	0.010610	0.391534	235(AATGACACAATGTTCC,-,0.00),236(ATGACACAATGTTCCT,+,0.00),269(TAGAACATGAAGTACC,-,0.00),270(AGAACATGAAGTACCT,+,0.00)
chunk0191_321_1	chr8	55798169	55798368	+	0	NA	intron (NM_024831, intron 7 of 12)	intron (NM_024831, intron 7 of 12)	-24861	NM_001286661	137695	Hs.420076	NM_152417	ENSG00000167904	TMEM68	-	transmembrane protein 68	protein-coding	0.000000	0.375000	
chunk0095_77_1	chr2	14577775	14578139	+	0	NA	Intergenic	Intergenic	-54729	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.010989	0.457534	
chunk0189_346_1	chr8	26734222	26734543	+	0	NA	Intergenic	Intergenic	131023	NM_033302	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.006231	0.428571	
chunk0132_423_1	chr3	164608915	164609215	+	0	NA	Intergenic	MER57C1|LTR|ERV1	222415	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.010000	0.395349	
chunk0040_267_1	chr11	116373639	116373838	+	0	NA	Intergenic	Intergenic	399260	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.010050	0.575000	105(TGGTACACCATGTTCT,-,0.00),106(GGTACACCATGTTCTC,+,0.00)
chunk0040_276_1	chr11	116808057	116809176	+	0	NA	Intergenic	Intergenic	14679	NM_000482	337	Hs.1247	NM_000482	ENSG00000110244	APOA4	-	apolipoprotein A4	protein-coding	0.014298	0.503571	
chunk0213_40_1	chrY	56878091	56878449	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-75985	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.005587	0.431755	
chunk0105_318_1	chr2	190520606	190520805	+	0	NA	intron (NM_001142645, intron 2 of 8)	L2a|LINE|L2	14037	NM_001142645	100131211	Hs.659824	NM_001142645	ENSG00000189362	NEMP2	TMEM194B	nuclear envelope integral membrane protein 2	protein-coding	0.000000	0.475000	
chunk0033_253_1	chr11	18317954	18318189	+	0	NA	intron (NM_181507, intron 1 of 22)	intron (NM_181507, intron 1 of 22)	4103	NM_007216	11234	Hs.437599	NM_007216	ENSG00000110756	HPS5	AIBP63|BLOC2S2	HPS5 biogenesis of lysosomal organelles complex 2 subunit 2	protein-coding	0.008511	0.415254	
chunk0027_372_1	chr10	79329554	79329935	+	0	NA	Intergenic	L2c|LINE|L2	-17720	NM_005729	10105	Hs.381072	NM_005729	ENSG00000108179	PPIF	CYP3|CyP-M|Cyp-D|CypD	peptidylprolyl isomerase F	protein-coding	0.023622	0.534031	204(AGGAACAGGACGTGCA,-,0.00)
chunk0085_93_1	chr18	2612795	2613336	+	0	NA	intron (NM_006101, intron 16 of 16)	intron (NM_006101, intron 16 of 16)	41554	NM_006101	10403	Hs.414407	NM_006101	ENSG00000080986	NDC80	HEC|HEC1|HsHec1|KNTC2|TID3|hsNDC80	NDC80 kinetochore complex component	protein-coding	0.005545	0.374539	
chunk0141_434_1	chr4	88865532	88865731	+	0	NA	intron (NM_014883, intron 6 of 23)	MER58A|DNA|hAT-Charlie	-42270	NM_001015045	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.010050	0.390000	
chunk0196_37_1	chr8	101633614	101634024	+	0	NA	intron (NM_024915, intron 11 of 15)	intron (NM_024915, intron 11 of 15)	141379	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.002439	0.401460	156(CTGCACTGTCTGTGCC,-,0.00),157(TGCACTGTCTGTGCCC,+,0.00)
chunk0150_266_1	chr5	36703793	36704537	+	0	NA	Intergenic	Intergenic	97810	NM_001289939	6507	Hs.481918	NM_004172	ENSG00000079215	SLC1A3	EA6|EAAT1|GLAST|GLAST1	solute carrier family 1 member 3	protein-coding	0.002688	0.393289	
chunk0050_73_1	chr12	101532818	101533017	+	0	NA	Intergenic	Intergenic	56038	NM_152323	121599	Hs.577097	NM_152323	ENSG00000166211	SPIC	SPI-C	Spi-C transcription factor	protein-coding	0.000000	0.260000	
chunk0122_381_1	chr3	37795922	37796389	+	0	NA	intron (NR_110532, intron 4 of 5)	L2b|LINE|L2	65625	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.002141	0.450855	220(TTGCACATCATGTTCC,-,0.00),221(TGCACATCATGTTCCC,+,0.00)
chunk0035_147_1	chr11	42980845	42981251	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	288321	NR_033868	399881	Hs.446761	NR_033868	ENSG00000251557	HNRNPKP3	-	heterogeneous nuclear ribonucleoprotein K pseudogene 3	pseudo	0.004926	0.348894	
chunk0209_398_1	chrX	55161001	55161200	+	0	NA	promoter-TSS (NM_001166704)	promoter-TSS (NM_001166704)	2	NM_001166703	90736	Hs.415414	NM_138362	ENSG00000182518	FAM104B	CXorf44	family with sequence similarity 104 member B	protein-coding	0.080402	0.605000	
chunk0044_272_1	chr12	32457195	32458010	+	0	NA	Intergenic	Intergenic	-28370	NM_001304481	121512	Hs.117835	NM_139241	ENSG00000139132	FGD4	CMT4H|FRABP|ZFYVE6	FYVE, RhoGEF and PH domain containing 4	protein-coding	0.001227	0.321078	350(AAAGACAGTTTGTCCT,-,0.00),351(AAGACAGTTTGTCCTT,+,0.00)
chunk0183_177_1	chr7	106183049	106183443	+	0	NA	Intergenic	L1ME1|LINE|L1	-70599	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.005076	0.346835	
chunk0176_246_1	chr7	16130363	16131106	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-79752	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.000000	0.392473	
chunk0032_386_1	chr11	11477597	11478320	+	0	NA	intron (NM_198516, intron 1 of 10)	MamTip2|DNA|hAT-Tip100	-124601	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.004149	0.381215	
chunk0003_4_1	chr1	28552673	28553037	+	0	NA	promoter-TSS (NR_003109)	promoter-TSS (NR_003109)	-162	NM_017846	54952	Hs.533626	NM_017846	ENSG00000180098	TRNAU1AP	PRO1902|SECP43|TRSPAP1	tRNA selenocysteine 1 associated protein 1	protein-coding	0.063187	0.547945	
chunk0183_166_1	chr7	106071914	106072381	+	0	NA	Intergenic	Intergenic	40198	NM_182715	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.008565	0.438034	
chunk0181_411_1	chr7	90211708	90211911	+	0	NA	promoter-TSS (NR_110029)	promoter-TSS (NR_110029)	-51	NM_001040665	261729	Hs.489051	NM_152999	ENSG00000157214	STEAP2	IPCA1|PCANAP1|PUMPCn|STAMP1|STMP	STEAP2 metalloreductase	protein-coding	0.128079	0.735294	
chunk0183_403_1	chr7	110381169	110381459	+	0	NA	Intergenic	Intergenic	-421101	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.000000	0.298969	
chunk0041_120_1	chr11	124988019	124988441	+	0	NA	intron (NM_025004, intron 8 of 15)	Tigger1|DNA|TcMar-Tigger	34109	NM_025004	80071	Hs.287555	NM_025004	ENSG00000149548	CCDC15	-	coiled-coil domain containing 15	protein-coding	0.009479	0.354610	
chunk0094_421_1	chr2	10584210	10584788	+	0	NA	intron (NR_048552, intron 18 of 19)	intron (NR_048552, intron 18 of 19)	105488	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.015571	0.390328	
chunk0037_15_1	chr11	68982634	68983190	+	0	NA	Intergenic	L1ME2z|LINE|L1	-1926	NM_198923	116512	Hs.527802	NM_198923	ENSG00000172938	MRGPRD	MRGD|TGR7	MAS related GPR family member D	protein-coding	0.000000	0.307002	276(CTAAACAGTCTGTCCT,-,0.00),277(TAAACAGTCTGTCCTT,+,0.00)
chunk0133_192_1	chr3	170670079	170670333	+	0	NA	Intergenic	Intergenic	-84132	NM_020949	57709	Hs.596660	NM_020949	ENSG00000013293	SLC7A14	PPP1R142	solute carrier family 7 member 14	protein-coding	0.011811	0.478431	
chunk0051_51_1	chr12	112364896	112365145	+	0	NA	intron (NM_001109662, intron 1 of 75)	MER58A|DNA|hAT-Charlie	17072	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.004016	0.356000	
chunk0149_433_1	chr5	29706925	29707338	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-311155	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.326087	
chunk0163_146_1	chr6	10834097	10834603	+	0	NA	intron (NM_001242957, intron 1 of 14)	intron (NM_001242957, intron 1 of 14)	4205	NM_005906	4117	Hs.446125	NM_005906	ENSG00000111837	MAK	RP62	male germ cell associated kinase	protein-coding	0.003953	0.366864	179(AAGGCCATCATGTTCC,-,0.00),180(AGGCCATCATGTTCCT,+,0.00)
chunk0044_334_1	chr12	38316494	38316854	+	0	NA	promoter-TSS (NM_001013620)	promoter-TSS (NM_001013620)	-81	NM_001013620	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.077778	0.551247	
chunk0107_214_1	chr2	216644401	216644705	+	0	NA	intron (NM_000597, intron 1 of 3)	intron (NM_000597, intron 1 of 3)	11149	NM_000597	3485	Hs.438102	NM_000597	ENSG00000115457	IGFBP2	IBP2|IGF-BP53	insulin like growth factor binding protein 2	protein-coding	0.003289	0.495082	
chunk0166_216_1	chr6	46912533	46912907	+	0	NA	intron (NM_015234, intron 1 of 20)	MER83|LTR|ERV1	9249	NR_110658	101926962	Hs.680113	NR_110658		LOC101926962	-	uncharacterized LOC101926962	ncRNA	0.002674	0.416000	
chunk0013_400_1	chr1	172964951	172965584	+	0	NA	Intergenic	Intergenic	85696	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.001580	0.370662	
chunk0114_59_1	chr21	8883556	8883767	+	0	NA	Intergenic	L1MB8|LINE|L1	-103338	NR_128711	103504731		NR_128711	ENSG00000264462	MIR3648-2	hsa-mir-3648-2	microRNA 3648-2	ncRNA	0.018957	0.344340	
chunk0171_111_1	chr6	122399436	122399635	+	0	NA	promoter-TSS (NM_001243094)	promoter-TSS (NM_001243094)	-16	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.110553	0.700000	
chunk0081_450_1	chr17	49333813	49334230	+	0	NA	intron (NM_014897, intron 1 of 5)	L1MB7|LINE|L1	-27144	NR_110884	102724596	Hs.559253	NR_110882	ENSG00000248714	LOC102724596	-	uncharacterized LOC102724596	ncRNA	0.002398	0.342105	
chunk0088_258_1	chr18	48996950	48997969	+	0	NA	Intergenic	MIR3|SINE|MIR	-46748	NM_001190821	4092	Hs.465087	NM_005904	ENSG00000101665	SMAD7	CRCS3|MADH7|MADH8	SMAD family member 7	protein-coding	0.015702	0.502941	
chunk0192_155_1	chr8	62172290	62172817	+	0	NA	Intergenic	L1PA17|LINE|L1	-76389	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.009488	0.344697	
chunk0181_161_1	chr7	82198795	82199473	+	0	NA	intron (NM_001302890, intron 3 of 10)	intron (NM_001302890, intron 3 of 10)	189957	NR_110077	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.007375	0.312224	
chunk0198_19_1	chr8	128025084	128025355	+	0	NA	intron (NR_003367, intron 5 of 8)	intron (NR_003367, intron 5 of 8)	16321	NR_031611	100302170		NR_031611	ENSG00000283200	MIR1206	MIRN1206|hsa-mir-1206	microRNA 1206	ncRNA	0.033210	0.628676	
chunk0079_245_1	chr17	16085309	16085837	+	0	NA	intron (NM_006311, intron 23 of 45)	L1ME2z|LINE|L1	-85881	NM_001042697	125150	Hs.593985	NM_001042697	ENSG00000214941	ZSWIM7	SWS1	zinc finger SWIM-type containing 7	protein-coding	0.000000	0.378072	
chunk0001_37_1	chr1	1504727	1505115	+	0	NA	Intergenic	Intergenic	-7222	NM_018188	55210	Hs.23413	NM_018188	ENSG00000197785	ATAD3A	HAYOS	ATPase family AAA domain containing 3A	protein-coding	0.025773	0.557841	
chunk0097_363_1	chr2	60540939	60541486	+	0	NA	intron (NM_138559, intron 2 of 4)	intron (NM_138559, intron 2 of 4)	12286	NM_138559	53335	Hs.370549	NM_018014	ENSG00000119866	BCL11A	BCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856	BAF chromatin remodeling complex subunit BCL11A	protein-coding	0.007313	0.374088	
chunk0177_386_1	chr7	26994244	26995036	+	0	NA	Intergenic	L2c|LINE|L2	101366	NM_005522	3198	Hs.67397	NM_005522	ENSG00000105991	HOXA1	BSAS|HOX1|HOX1F	homeobox A1	protein-coding	0.005051	0.426230	102(AAGCACAGCATGTTTC,-,0.00),103(AGCACAGCATGTTTCT,+,0.00)
chunk0142_12_1	chr4	89898166	89898392	+	0	NA	intron (NM_007351, intron 1 of 7)	MIR|SINE|MIR	3378	NM_007351	22915	Hs.268107	NM_007351	ENSG00000138722	MMRN1	ECM|EMILIN4|GPIa*|MMRN	multimerin 1	protein-coding	0.004425	0.321586	
chunk0066_42_1	chr15	27805947	27806146	+	0	NA	intron (NM_001300984, intron 22 of 22)	intron (NM_001300984, intron 22 of 22)	293266	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.030151	0.470000	
chunk0197_84_1	chr8	119143967	119144509	+	0	NA	Intergenic	Intergenic	-64133	NM_052886	114569	Hs.201083	NM_052886	ENSG00000147676	MAL2	-	mal, T cell differentiation protein 2 (gene/pseudogene)	protein-coding	0.000000	0.302026	
chunk0172_15_1	chr6	132856479	132856765	+	0	NA	Intergenic	L2c|LINE|L2	39403	NR_002436	594839	Hs.671378	NR_002436	ENSG00000200534	SNORA33	ACA33	small nucleolar RNA, H/ACA box 33	snoRNA	0.003497	0.449477	
chunk0079_376_1	chr17	18129196	18129497	+	0	NA	intron (NM_016239, intron 7 of 64)	intron (NM_016239, intron 7 of 64)	20640	NM_016239	51168	Hs.462390	NM_016239	ENSG00000091536	MYO15A	DFNB3|MYO15	myosin XVA	protein-coding	0.009967	0.546358	
chunk0161_141_1	chr5	168491884	168492619	+	0	NA	intron (NM_002887, intron 2 of 14)	intron (NM_002887, intron 2 of 14)	5793	NM_002887	5917	Hs.654907	NM_002887	ENSG00000113643	RARS	ArgRS|DALRD1|HLD9	arginyl-tRNA synthetase	protein-coding	0.002721	0.366848	149(AAGCACTTTGTGTGCA,-,0.00),150(AGCACTTTGTGTGCAT,+,0.00)
chunk0089_317_1	chr18	64803592	64803845	+	0	NA	Intergenic	L1PA15|LINE|L1	-543663	NR_033983	400654	Hs.434235	NR_033983	ENSG00000266952	LINC01538	-	long intergenic non-protein coding RNA 1538	ncRNA	0.000000	0.389764	
chunk0166_203_1	chr6	46649241	46649440	+	0	NA	intron (NM_016593, intron 1 of 11)	MLT1F2|LTR|ERVL-MaLR	3490	NM_001278739	51302	Hs.387367	NM_016593	ENSG00000146233	CYP39A1	-	cytochrome P450 family 39 subfamily A member 1	protein-coding	0.005025	0.405000	
chunk0092_67_1	chr19	20357529	20358313	+	0	NA	Intergenic	LTR10C|LTR|ERV1	41433	NR_036053	100302179		NR_036053	ENSG00000238517	MIR1270	MIR1270-1|MIR1270-2|MIRN1270|hsa-mir-1270|hsa-mir-1270-1|mir-1270	microRNA 1270	ncRNA	0.011480	0.421656	304(AAGAACATAAAGTACA,-,0.00),305(AGAACATAAAGTACAT,+,0.00)
chunk0042_277_1	chr12	7009870	7010448	+	0	NA	intron (NM_005768, intron 1 of 12)	intron (NM_005768, intron 1 of 12)	8379	NM_005768	10162	Hs.655248	NM_005768	ENSG00000111684	LPCAT3	C3F|LPCAT|LPLAT 5|LPSAT|MBOAT5|OACT5|nessy	lysophosphatidylcholine acyltransferase 3	protein-coding	0.003460	0.362694	
chunk0142_73_1	chr4	93842596	93843042	+	0	NA	Intergenic	Intergenic	13892	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.004484	0.409396	
chunk0145_40_1	chr4	144424997	144425410	+	0	NA	Intergenic	Intergenic	-220793	NM_022475	64399	Hs.507991	NM_022475	ENSG00000164161	HHIP	HIP	hedgehog interacting protein	protein-coding	0.002421	0.405797	
chunk0075_253_1	chr16	53435374	53436076	+	0	NA	intron (NM_005611, intron 1 of 21)	intron (NM_005611, intron 1 of 21)	1286	NM_005611	5934	Hs.513609	NM_005611	ENSG00000103479	RBL2	P130|Rb2	RB transcriptional corepressor like 2	protein-coding	0.019943	0.421053	
chunk0099_24_1	chr2	83121672	83122085	+	0	NA	Intergenic	L1MD2|LINE|L1	265075	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007264	0.301932	
chunk0164_371_1	chr6	25844469	25844903	+	0	NA	TTS (NM_006632)	TTS (NM_006632)	-12627	NM_005074	6568	Hs.205816	NM_005074	ENSG00000124568	SLC17A1	NAPI-1|NPT-1|NPT1	solute carrier family 17 member 1	protein-coding	0.004608	0.445977	
chunk0178_195_1	chr7	34405406	34405623	+	0	NA	intron (NR_033664, intron 4 of 4)	intron (NR_033664, intron 4 of 4)	-252725	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.013825	0.481651	
chunk0017_434_1	chr1	213705861	213706176	+	0	NA	Intergenic	L1MA2|LINE|L1	-218731	NR_046189	100861504	Hs.742586	NR_046189		LINC00538	PROX1UT|Yiya	long intergenic non-protein coding RNA 538	ncRNA	0.000000	0.490506	
chunk0129_254_1	chr3	122338167	122338722	+	0	NA	intron (NM_005213, intron 2 of 2)	intron (NM_005213, intron 2 of 2)	13280	NM_005213	1475	Hs.518198	NM_005213	ENSG00000121552	CSTA	AREI|PSS4|STF1|STFA	cystatin A	protein-coding	0.005405	0.339928	
chunk0184_350_1	chr7	120793147	120793785	+	0	NA	intron (NM_012338, intron 7 of 7)	L4_B_Mam|LINE|RTE-X	64657	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.003135	0.345853	238(TGGGACTTGGTGTCCT,-,0.00),239(GGGACTTGGTGTCCTT,+,0.00),551(CAGTACTGTATGTCCA,-,0.00),552(AGTACTGTATGTCCAT,+,0.00)
chunk0152_276_1	chr5	61304972	61305287	+	0	NA	Intergenic	Intergenic	-27144	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.012698	0.433544	
chunk0048_182_1	chr12	80937417	80937700	+	0	NA	intron (NM_004664, intron 1 of 5)	CpG	357	NM_004664	8825	Hs.144333	NM_004664	ENSG00000111052	LIN7A	LIN-7A|LIN7|MALS-1|MALS1|TIP-33|VELI1	lin-7 homolog A, crumbs cell polarity complex component	protein-coding	0.088339	0.665493	
chunk0066_365_1	chr15	38397819	38398569	+	0	NA	Intergenic	Intergenic	-55933	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.002667	0.398136	391(AAGCACACCATGTTCC,-,0.00),392(AGCACACCATGTTCCC,+,0.00)
chunk0196_96_1	chr8	103021012	103021349	+	0	NA	5' UTR (NM_001695, exon 1 of 13)	5' UTR (NM_001695, exon 1 of 13)	160	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.091988	0.662722	
chunk0025_111_1	chr10	51207446	51207854	+	0	NA	intron (NM_006258, intron 2 of 17)	intron (NM_006258, intron 2 of 17)	-91923	NR_030336	693190		NR_030336	ENSG00000207813	MIR605	MIRN605|hsa-mir-605|mir-605	microRNA 605	ncRNA	0.009804	0.396088	
chunk0076_217_1	chr16	68351865	68352207	+	0	NA	intron (NM_019023, intron 14 of 18)	intron (NM_019023, intron 14 of 18)	40922	NM_001290018	54496	Hs.640229	NM_019023	ENSG00000132600	PRMT7	SBIDDS	protein arginine methyltransferase 7	protein-coding	0.014620	0.556851	
chunk0204_52_1	chr9	93201447	93202217	+	0	NA	intron (NM_001282394, intron 1 of 29)	intron (NM_001282394, intron 1 of 29)	16902	NM_001282394	65268	Hs.654856	NM_006648	ENSG00000165238	WNK2	NY-CO-43|P/OKcl.13|PRKWNK2|SDCCAG43	WNK lysine deficient protein kinase 2	protein-coding	0.016883	0.590143	
chunk0099_427_1	chr2	102726251	102726598	+	0	NA	intron (NM_032718, intron 4 of 5)	intron (NM_032718, intron 4 of 5)	10454	NM_032718	84804	Hs.590898	NM_032718	ENSG00000135953	MFSD9	-	major facilitator superfamily domain containing 9	protein-coding	0.005764	0.456897	
chunk0102_269_1	chr2	150099766	150100253	+	0	NA	Intergenic	Intergenic	387686	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.002053	0.329918	
chunk0135_116_1	chr3	186971477	186972098	+	0	NA	intron (NM_173216, intron 2 of 7)	intron (NM_173216, intron 2 of 7)	41261	NM_173217	6480	Hs.207459	NM_003032	ENSG00000073849	ST6GAL1	SIAT1|ST6GalI|ST6N	ST6 beta-galactoside alpha-2,6-sialyltransferase 1	protein-coding	0.003221	0.456592	
chunk0047_453_1	chr12	76629061	76629460	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	-69451	NM_020841	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.002506	0.360000	
chunk0030_387_1	chr10	119565778	119566393	+	0	NA	Intergenic	AluJo|SINE|Alu	-23375	NM_001005339	6001	Hs.501200	NM_002925	ENSG00000148908	RGS10	-	regulator of G protein signaling 10	protein-coding	0.003252	0.400974	
chunk0086_267_1	chr18	23557684	23557905	+	0	NA	intron (NM_000271, intron 6 of 24)	L1MC4a|LINE|L1	28823	NM_000271	4864	Hs.464779	NM_000271	ENSG00000141458	NPC1	NPC|POGZ|SLC65A1	NPC intracellular cholesterol transporter 1	protein-coding	0.013575	0.468468	
chunk0117_120_1	chr22	18890834	18891188	+	0	NA	Intergenic	HSATI|Satellite|Satellite	-15212	NM_005675	8214	Hs.474185	NM_005675	ENSG00000183628	DGCR6	-	DiGeorge syndrome critical region gene 6	protein-coding	0.005650	0.442254	
chunk0175_192_1	chr7	5513769	5514463	+	0	NA	promoter-TSS (NM_024963)	promoter-TSS (NM_024963)	262	NR_126168	221946	Hs.385633	NR_126168		LOC221946	-	uncharacterized LOC221946	ncRNA	0.064841	0.565468	
chunk0100_360_1	chr2	117743127	117743735	+	0	NA	Intergenic	Intergenic	-71248	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.006579	0.405583	
chunk0098_214_1	chr2	73090293	73090636	+	0	NA	intron (NM_015470, intron 1 of 4)	L1MC2|LINE|L1	-18628	NM_144579	94097	Hs.368171	NM_144579	ENSG00000144040	SFXN5	BBG-TCC|SLC56A5	sideroflexin 5	protein-coding	0.008746	0.430233	
chunk0138_408_1	chr4	43718194	43718804	+	0	NA	Intergenic	Intergenic	-298362	NR_131959	100506827	Hs.156197	NR_131958	ENSG00000251350	LINC02475	LVCAT1	long intergenic non-protein coding RNA 2475	ncRNA	0.003279	0.369885	
chunk0193_326_1	chr8	78917868	78918305	+	0	NA	Intergenic	L1MA2|LINE|L1	-112563	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.006865	0.390411	
chunk0121_253_1	chr3	23020173	23020390	+	0	NA	Intergenic	L1PB1|LINE|L1	-183012	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.000000	0.559633	
chunk0066_247_1	chr15	34613019	34613574	+	0	NA	Intergenic	Intergenic	-29726	NR_027410	440270	Hs.720151	NM_001023567	ENSG00000215252	GOLGA8B	GOLGA5	golgin A8 family member B	protein-coding	0.003604	0.352518	
chunk0079_80_1	chr17	11667044	11667620	+	0	NA	intron (NM_001372, intron 15 of 68)	intron (NM_001372, intron 15 of 68)	68901	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.005208	0.329289	
chunk0152_345_1	chr5	62603729	62603985	+	0	NA	intron (NM_016338, intron 29 of 29)	Tigger3a|DNA|TcMar-Tigger	25122	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.015625	0.400778	
chunk0006_321_1	chr1	71638970	71639291	+	0	NA	intron (NM_173808, intron 4 of 6)	intron (NM_173808, intron 4 of 6)	197882	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.000000	0.363354	
chunk0197_205_1	chr8	122575339	122575538	+	0	NA	Intergenic	Intergenic	-6794	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.010050	0.480000	
chunk0050_315_1	chr12	107058091	107058453	+	0	NA	intron (NM_004075, intron 1 of 12)	L3|LINE|CR1	35585	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.005525	0.347107	
chunk0038_56_1	chr11	82876037	82876698	+	0	NA	intron (NM_005040, intron 1 of 8)	intron (NM_005040, intron 1 of 8)	24148	NM_005040	5547	Hs.523936	NM_005040	ENSG00000137509	PRCP	HUMPCP|PCP	prolylcarboxypeptidase	protein-coding	0.012103	0.450151	
chunk0109_9_1	chr20	250763	251150	+	0	NA	Intergenic	L1ME1|LINE|L1	-6780	NM_207469	400830	Hs.516819	NM_207469	ENSG00000186458	DEFB132	BD-32|DEFB-32|DEFB32|HEL-75|KFLL827|UNQ827	defensin beta 132	protein-coding	0.010336	0.337629	
chunk0139_72_1	chr4	49108288	49108807	+	0	NA	Intergenic	(CATTC)n|Satellite|Satellite	121905	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.021195	0.413462	
chunk0020_295_1	chr1	237190409	237190887	+	0	NA	intron (NM_001035, intron 1 of 104)	MER2|DNA|TcMar-Tigger	148246	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.006276	0.350731	
chunk0044_164_1	chr12	29927742	29928238	+	0	NA	Intergenic	L2c|LINE|L2	-143231	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.000000	0.370221	
chunk0118_305_1	chr22	35050881	35051161	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-15115	NM_001303508	91464	Hs.567637	NM_001008494	ENSG00000175329	ISX	Pix-1|RAXLX	intestine specific homeobox	protein-coding	0.017857	0.430605	
chunk0188_379_1	chr8	18317036	18317553	+	0	NA	Intergenic	L2a|LINE|L2	-73951	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.007737	0.393822	227(TGGAACACTCTGTCTT,-,0.00),228(GGAACACTCTGTCTTC,+,0.00)
chunk0071_289_1	chr15	85837080	85837591	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	11700	NR_049805	100847084		NR_049805	ENSG00000264406	MIR548AP	-	microRNA 548ap	ncRNA	0.015656	0.488281	
chunk0172_207_1	chr6	136710800	136711395	+	0	NA	intron (NM_005923, intron 2 of 29)	intron (NM_005923, intron 2 of 29)	81421	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.011765	0.407718	
chunk0021_14_1	chr10	422592	422938	+	0	NA	intron (NM_014974, intron 5 of 36)	intron (NM_014974, intron 5 of 36)	-140679	NR_106988									0.040462	0.596542	
chunk0191_154_1	chr8	49026688	49026911	+	0	NA	Intergenic	Intergenic	-27537	NM_001256596	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.013453	0.424107	
chunk0149_306_1	chr5	25849258	25849583	+	0	NA	Intergenic	AluJr|SINE|Alu	-1008837	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.006154	0.383436	
chunk0037_98_1	chr11	72041828	72042079	+	0	NA	intron (NM_006185, intron 2 of 26)	intron (NM_006185, intron 2 of 26)	27662	NR_104178	100128494	Hs.713607	NR_104178	ENSG00000251143	LOC100128494	-	uncharacterized LOC100128494	ncRNA	0.047809	0.638889	
chunk0017_314_1	chr1	211257978	211258421	+	0	NA	Intergenic	Intergenic	-1167	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.018059	0.430180	
chunk0028_113_1	chr10	84441135	84441711	+	0	NA	intron (NM_001284243, intron 3 of 7)	HAL1|LINE|L1	16241	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.003472	0.315425	
chunk0157_26_1	chr5	115542144	115542529	+	0	NA	intron (NM_020177, intron 2 of 2)	intron (NM_020177, intron 2 of 2)	2558	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.002597	0.341969	
chunk0155_355_1	chr5	97192945	97193173	+	0	NA	Intergenic	L1PB1|LINE|L1	-9758	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.008772	0.524017	
chunk0161_380_1	chr5	176799629	176800313	+	0	NA	Intergenic	Intergenic	-10588	NM_133369	90249	Hs.33191	NM_133369	ENSG00000113763	UNC5A	UNC5H1	unc-5 netrin receptor A	protein-coding	0.019006	0.472993	385(AAAAACATGGTGTCCT,-,0.00),386(AAAACATGGTGTCCTG,+,0.00)
chunk0122_52_1	chr3	28621126	28621799	+	0	NA	intron (NR_038840, intron 2 of 4)	L1PA6|LINE|L1	46184	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.000000	0.372404	418(AAGGACACAATGTACC,-,0.00),419(AGGACACAATGTACCA,+,0.00)
chunk0134_4_1	chr3	175338888	175339769	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	-30212	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.007946	0.400227	547(AAATACAATCTGTTCT,-,0.00),548(AATACAATCTGTTCTG,+,0.00)
chunk0065_294_1	chr14	102697043	102697420	+	0	NA	intron (NM_015156, intron 3 of 11)	intron (NM_015156, intron 3 of 11)	-80248	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.005305	0.431217	
chunk0075_47_1	chr16	47445301	47445634	+	0	NA	intron (NM_030790, intron 5 of 17)	Charlie2a|DNA|hAT-Charlie	15807	NM_030790	81533	Hs.42217	NM_030790	ENSG00000129636	ITFG1	2310047C21Rik|CDA08|LNKN-1|TIP	integrin alpha FG-GAP repeat containing 1	protein-coding	0.003003	0.365269	232(TAGCACATTGTGTTTT,-,0.00),233(AGCACATTGTGTTTTC,+,0.00)
chunk0140_199_1	chr4	70386986	70387185	+	0	NA	intron (NM_006685, intron 2 of 2)	L2|LINE|L2	4007	NM_006685	10879	Hs.650650	NM_006685	ENSG00000171201	SMR3B	P-B|PBII|PRL3|PROL3|SMR1B	submaxillary gland androgen regulated protein 3B	protein-coding	0.010050	0.380000	
chunk0036_426_1	chr11	68398005	68398461	+	0	NA	intron (NM_002335, intron 7 of 22)	intron (NM_002335, intron 7 of 22)	-62485	NM_001164164	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.030702	0.562363	
chunk0025_168_1	chr10	52768299	52768569	+	0	NA	exon (NM_000242, exon 4 of 4)	exon (NM_000242, exon 4 of 4)	3266	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.000000	0.472325	
chunk0004_192_1	chr1	46340523	46341033	+	0	NA	promoter-TSS (NM_001256128)	promoter-TSS (NM_001256128)	-400	NM_001256128	387338	Hs.163424	NM_199044	ENSG00000117481	NSUN4	SHTAP	NOP2/Sun RNA methyltransferase 4	protein-coding	0.076471	0.608611	
chunk0120_151_1	chr3	5344270	5344469	+	0	NA	Intergenic	L1ME3B|LINE|L1	-94114	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.005025	0.430000	
chunk0043_407_1	chr12	25707674	25707873	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	-59211	NM_001145727	160492	Hs.44647	NM_152590	ENSG00000152936	LMNTD1	IFLTD1|LMNARS1|PAS1C1	lamin tail domain containing 1	protein-coding	0.000000	0.475000	
chunk0054_444_1	chr13	51401049	51401565	+	0	NA	intron (NM_012141, intron 4 of 17)	L2a|LINE|L2	51832	NM_012141	26512	Hs.439440	NM_012141	ENSG00000102786	INTS6	DBI-1|DDX26|DDX26A|DICE1|HDB|INT6|Notchl2	integrator complex subunit 6	protein-coding	0.000000	0.326886	
chunk0080_305_1	chr17	31744604	31744952	+	0	NA	Intergenic	Intergenic	114529	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.005747	0.461318	
chunk0059_86_1	chr14	30771628	30771827	+	0	NA	Intergenic	Intergenic	-102808	NM_004086	1690	Hs.21016	NM_004086	ENSG00000100473	COCH	COCH-5B2|COCH5B2|DFNA9|DFNB110	cochlin	protein-coding	0.015075	0.410000	
chunk0209_387_1	chrX	54794990	54795791	+	0	NA	intron (NM_198510, intron 2 of 12)	Charlie7a|DNA|hAT-Charlie	2850	NM_198510	347365	Hs.454272	NM_198510	ENSG00000102313	ITIH6	ITIH5L|UNQ6369|dJ14O9.1	inter-alpha-trypsin inhibitor heavy chain family member 6	protein-coding	0.004994	0.443890	609(AAGTACTTGCAGTTCC,-,0.00)
chunk0210_26_1	chrX	67604734	67604966	+	0	NA	intron (NM_001011645, intron 1 of 7)	intron (NM_001011645, intron 1 of 7)	36009	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.000000	0.347639	73(GGTACAGAATGTATTT,+,0.00)
chunk0093_85_1	chr19	40920830	40921864	+	0	NA	Intergenic	Intergenic	-2918	NR_001278	1556	Hs.529117	NR_001278	ENSG00000256612	CYP2B7P	CYP2B|CYP2B7|CYP2B7P1	cytochrome P450 family 2 subfamily B member 7, pseudogene	pseudo	0.008704	0.498551	
chunk0010_379_1	chr1	119238516	119238727	+	0	NA	intron (NR_125975, intron 4 of 6)	MER5A|DNA|hAT-Charlie	-97949	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.004739	0.377358	
chunk0078_6_1	chr17	315437	316028	+	0	NA	intron (NM_001190411, intron 4 of 8)	intron (NM_001190411, intron 4 of 8)	-15473	NR_040011	100506388	Hs.627744	NM_001242780	ENSG00000262061	LOC100506388	-	uncharacterized LOC100506388	protein-coding	0.005076	0.581081	
chunk0159_343_1	chr5	144156334	144156583	+	0	NA	Intergenic	Intergenic	14256	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.000000	0.336000	
chunk0175_14_1	chr7	235307	236127	+	0	NA	intron (NM_020223, intron 3 of 9)	intron (NM_020223, intron 3 of 9)	42748	NM_020223	56975	Hs.134742	NM_020223	ENSG00000177706	FAM20C	DMP-4|DMP4|G-CK|GEF-CK|RNS	FAM20C golgi associated secretory pathway kinase	protein-coding	0.040244	0.595615	
chunk0026_89_1	chr10	61529279	61529500	+	0	NA	Intergenic	Intergenic	49348	NR_120644	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.004525	0.337838	
chunk0149_28_1	chr5	16272047	16272301	+	0	NA	Intergenic	MER110|LTR|ERV1	-92386	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.015748	0.427451	
chunk0158_352_1	chr5	133514586	133514787	+	0	NA	intron (NM_015082, intron 3 of 15)	L1M6|LINE|L1	-86980	NR_031621	100302134		NR_031621	ENSG00000221287	MIR1289-2	MIRN1289-2|hsa-mir-1289-2	microRNA 1289-2	ncRNA	0.004975	0.326733	
chunk0153_406_1	chr5	75381735	75381969	+	0	NA	intron (NM_031361, intron 14 of 16)	intron (NM_031361, intron 14 of 16)	44684	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.008547	0.374468	
chunk0125_289_1	chr3	69877820	69878160	+	0	NA	intron (NM_198177, intron 1 of 9)	intron (NM_198177, intron 1 of 9)	11766	NM_198177	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.008824	0.334311	
chunk0170_213_1	chr6	113073909	113074419	+	0	NA	Intergenic	L1ME2|LINE|L1	575911	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.005882	0.326810	
chunk0092_291_1	chr19	34161659	34161858	+	0	NA	Intergenic	Intergenic	-10689	NM_015578	26065	Hs.744009	NM_015578	ENSG00000257103	LSM14A	C19orf13|FAM61A|RAP55|RAP55A	LSM14A mRNA processing body assembly factor	protein-coding	0.010050	0.350000	
chunk0067_398_1	chr15	49183776	49184260	+	0	NA	intron (NM_002044, intron 1 of 9)	L1MA3|LINE|L1	14002	NM_002044	2585	Hs.122006	NM_002044	ENSG00000156958	GALK2	GK2	galactokinase 2	protein-coding	0.004132	0.352577	
chunk0115_302_1	chr21	28435616	28436253	+	0	NA	Intergenic	Intergenic	-103384	NR_026552	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.003140	0.369906	
chunk0121_47_1	chr3	15529762	15530159	+	0	NA	Intergenic	L2a|LINE|L2	-8209	NM_005677	8292	Hs.146735	NM_005677	ENSG00000206561	COLQ	CMS5|EAD	collagen like tail subunit of asymmetric acetylcholinesterase	protein-coding	0.012594	0.457286	109(ATGCACAGAGTGTACA,-,0.00),110(TGCACAGAGTGTACAA,+,0.00)
chunk0048_221_1	chr12	81431055	81431620	+	0	NA	intron (NM_001220478, intron 3 of 28)	intron (NM_001220478, intron 3 of 28)	-61923	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003540	0.302120	
chunk0149_87_1	chr5	17401620	17402051	+	0	NA	Intergenic	LTR23|LTR|ERV1	-14525	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.011601	0.402778	
chunk0094_128_1	chr2	4687416	4687919	+	0	NA	Intergenic	Intergenic	-31445	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.003976	0.335317	
chunk0072_243_1	chr15	96003282	96003776	+	0	NA	Intergenic	Intergenic	-322399	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.004049	0.327273	
chunk0136_383_1	chr3	196739742	196739943	+	0	NA	promoter-TSS (NM_002577)	promoter-TSS (NM_002577)	-15	NM_002577	5062	Hs.518530	NM_002577	ENSG00000180370	PAK2	PAK65|PAKgamma	p21 (RAC1) activated kinase 2	protein-coding	0.134328	0.787129	
chunk0165_11_1	chr6	28742593	28743044	+	0	NA	Intergenic	Intergenic	120859	NR_033379	401242	Hs.448285	NR_033379	ENSG00000225595	LINC01623	-	long intergenic non-protein coding RNA 1623	ncRNA	0.035477	0.393805	
chunk0047_88_1	chr12	68445849	68446121	+	0	NA	intron (NR_120458, intron 1 of 3)	L1MA5A|LINE|L1	5499	NR_120458	100507195	Hs.450772	NR_120458	ENSG00000251301	LINC02384	-	long intergenic non-protein coding RNA 2384	ncRNA	0.003676	0.351648	
chunk0078_251_1	chr17	7227946	7228619	+	0	NA	intron (NM_004422, intron 9 of 14)	L1ME3B|LINE|L1	-4903	NR_029896	442898		NR_029896	ENSG00000199053	MIR324	MIRN324|hsa-mir-324|mir-324	microRNA 324	ncRNA	0.014859	0.482196	312(GAGTACACGCTGTACA,-,0.00),313(AGTACACGCTGTACAG,+,0.00)
chunk0203_323_1	chr9	89621341	89622179	+	0	NA	Intergenic	Intergenic	16748	NM_006705	10912	Hs.9701	NM_006705	ENSG00000130222	GADD45G	CR6|DDIT2|GADD45gamma|GRP17	growth arrest and DNA damage inducible gamma	protein-coding	0.005967	0.488677	412(GTGCACAGTATGTTCT,-,0.00),413(TGCACAGTATGTTCTG,+,0.00)
chunk0171_168_1	chr6	124868905	124869737	+	0	NA	Intergenic	L1MC1|LINE|L1	-93224	NM_001286398	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.002404	0.363745	
chunk0018_263_1	chr1	220438344	220438943	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-89540	NM_018650	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.006678	0.418333	
chunk0074_131_1	chr16	22719984	22720465	+	0	NA	Intergenic	Intergenic	-94315	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.012474	0.336100	
chunk0143_443_1	chr4	124116903	124117433	+	0	NA	Intergenic	Intergenic	342904	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.007547	0.357815	
chunk0160_243_1	chr5	156561908	156562200	+	0	NA	intron (NM_000337, intron 4 of 8)	L2a|LINE|L2	235297	NM_000337	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.003425	0.324232	
chunk0188_79_1	chr8	8408285	8408634	+	0	NA	Intergenic	Intergenic	-26625	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.002865	0.434286	
chunk0169_136_1	chr6	101241425	101241624	+	0	NA	Intergenic	LTR33B|LTR|ERVL	-157461	NM_001166247	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.355000	
chunk0191_58_1	chr8	46671355	46671748	+	0	NA	Intergenic	Intergenic	-169335	NR_027013	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.010178	0.403553	
chunk0177_157_1	chr7	23086160	23086706	+	0	NA	Intergenic	Intergenic	19270	NR_046220	100775104		NR_046220	ENSG00000230658	KLHL7-DT	KLHL7-AS1|PLATAK	KLHL7 divergent transcript	ncRNA	0.005495	0.376600	
chunk0108_133_1	chr2	230347012	230347653	+	0	NA	intron (NM_138402, intron 2 of 18)	L1M2|LINE|L1	20152	NM_001308163	93349	Hs.589661	NM_138402	ENSG00000185404	SP140L	-	SP140 nuclear body protein like	protein-coding	0.003120	0.518692	
chunk0062_213_1	chr14	70842448	70843047	+	0	NA	Intergenic	Intergenic	-33576	NM_001284230	4293	Hs.445496	NM_033141	ENSG00000006432	MAP3K9	MEKK9|MLK1|PRKE1	mitogen-activated protein kinase kinase kinase 9	protein-coding	0.001669	0.415000	264(GAAAACACACAGTTCC,-,0.00)
chunk0204_381_1	chr9	102165193	102165683	+	0	NA	Intergenic	MER57F|LTR|ERV1	-354199	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.000000	0.309572	
chunk0100_130_1	chr2	108670113	108670583	+	0	NA	intron (NM_001193482, intron 2 of 9)	Charlie2b|DNA|hAT-Charlie	15536	NM_001193485	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.004255	0.401274	
chunk0141_314_1	chr4	87154137	87154587	+	0	NA	Intergenic	L1MA4A|LINE|L1	65906	NM_001292003	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.006667	0.352550	
chunk0033_47_1	chr11	13294953	13295304	+	0	NA	intron (NM_001030272, intron 1 of 18)	intron (NM_001030272, intron 1 of 18)	17401	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.002849	0.556818	
chunk0151_401_1	chr5	55534426	55535179	+	0	NA	promoter-TSS (NR_001575)	promoter-TSS (NR_001575)	-260	NR_001575	379013	Hs.745164	NR_001575		RNF138P1	-	ring finger protein 138 pseudogene 1	pseudo	0.119522	0.738727	
chunk0153_413_1	chr5	75505738	75506238	+	0	NA	exon (NM_005713, exon 2 of 18)	exon (NM_005713, exon 2 of 18)	5641	NM_031361	10087	Hs.270437	NM_005713	ENSG00000113163	CERT1	CERT|CERTL|COL4A3BP|GPBP|MRD34|STARD11	ceramide transporter 1	protein-coding	0.008000	0.357285	
chunk0185_44_1	chr7	124525559	124526325	+	0	NA	Intergenic	Intergenic	-173846	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.001305	0.406780	
chunk0123_3_1	chr3	40065930	40066263	+	0	NA	intron (NM_001284425, intron 3 of 15)	intron (NM_001284425, intron 3 of 15)	-33915	NM_001284426	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.006006	0.488024	
chunk0105_438_1	chr2	194025823	194026022	+	0	NA	Intergenic	L1MEg|LINE|L1	-318347	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.000000	0.235000	
chunk0116_221_1	chr21	37900926	37901472	+	0	NA	intron (NM_002240, intron 1 of 3)	intron (NM_002240, intron 1 of 3)	15239	NM_002240	3763	Hs.626242	NM_002240	ENSG00000157542	KCNJ6	BIR1|GIRK-2|GIRK2|KATP-2|KATP2|KCNJ7|KIR3.2|KPLBS|hiGIRK2	potassium voltage-gated channel subfamily J member 6	protein-coding	0.001832	0.371115	
chunk0161_448_1	chr5	178787918	178788226	+	0	NA	Intergenic	Intergenic	-11796	NR_024035	729522	Hs.382790	NR_024035	ENSG00000250420	AACSP1	AACSL	acetoacetyl-CoA synthetase pseudogene 1	pseudo	0.025974	0.521036	179(TGGCACAGAATGTCCT,-,0.00),180(GGCACAGAATGTCCTG,+,0.00)
chunk0137_243_1	chr4	20563425	20564034	+	0	NA	intron (NM_001289135, intron 25 of 35)	intron (NM_001289135, intron 25 of 35)	35454	NR_029631	407000		NR_029631	ENSG00000207732	MIR218-1	MIRN218-1|mir-218-1	microRNA 218-1	ncRNA	0.003284	0.385246	
chunk0006_58_1	chr1	64564178	64564621	+	0	NA	intron (NM_020925, intron 2 of 26)	MER34C2|LTR|ERV1	-15448	NR_039957	100616338		NR_039957	ENSG00000264470	MIR4794	-	microRNA 4794	ncRNA	0.006772	0.457207	
chunk0013_55_1	chr1	167191307	167191918	+	0	NA	intron (NR_110811, intron 2 of 3)	L1ME4b|LINE|L1	4193	NR_110811	101928484	Hs.568496	NR_110811		LINC01363	RBSG4	long intergenic non-protein coding RNA 1363	ncRNA	0.001637	0.330065	
chunk0081_50_1	chr17	38257272	38257471	+	0	NA	promoter-TSS (NR_036750).3	promoter-TSS (NR_036750).3	-122	NR_036750	440434	Hs.443837	NR_036750	ENSG00000274487	LOC440434	-	aminopeptidase puromycin sensitive pseudogene	pseudo	0.140704	0.810000	
chunk0146_263_1	chr4	162830911	162831314	+	0	NA	Intergenic	Intergenic	262516	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.007444	0.336634	
chunk0212_88_1	chrY	12268743	12269393	+	0	NA	Intergenic	AluSz|SINE|Alu	152522	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.006154	0.417819	
chunk0007_142_1	chr1	79346821	79347136	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-340168	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.006349	0.360759	
chunk0062_206_1	chr14	70183568	70184043	+	0	NA	intron (NR_104122, intron 1 of 5)	MER83|LTR|ERV1	5265	NR_104122	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.002105	0.443277	
chunk0069_190_1	chr15	63212048	63212504	+	0	NA	intron (NM_016530, intron 1 of 7)	intron (NM_016530, intron 1 of 7)	22747	NM_016530	51762	Hs.389733	NM_016530	ENSG00000166128	RAB8B	-	RAB8B, member RAS oncogene family	protein-coding	0.013158	0.422319	
chunk0012_369_1	chr1	162993114	162993385	+	0	NA	Intergenic	L2c|LINE|L2	-75357	NM_001102445	5999	Hs.386726	NM_005613	ENSG00000117152	RGS4	RGP4|SCZD9	regulator of G protein signaling 4	protein-coding	0.003690	0.352941	
chunk0084_431_1	chr17	82636582	82636983	+	0	NA	intron (NM_019613, intron 2 of 9)	LTR10G|LTR|ERV1	11753	NM_019613	56270	Hs.132161	NM_019613	ENSG00000141580	WDR45B	NEDSBAS|WDR45L|WIPI-3|WIPI3	WD repeat domain 45B	protein-coding	0.019950	0.435323	239(CTGTACACATTGTTCC,-,0.00),240(TGTACACATTGTTCCC,+,0.00)
chunk0165_46_1	chr6	30206719	30207082	+	0	NA	intron (NM_003449, intron 1 of 9).8	MIR3|SINE|MIR	6594	NM_001242783	7726	Hs.485041	NM_003449	ENSG00000234127	TRIM26	AFP|RNF95|ZNF173	tripartite motif containing 26	protein-coding	0.011019	0.530220	132(GAGGACAGTGAGTGCC,-,0.00),133(AGGACAGTGAGTGCCA,+,0.00)
chunk0139_36_1	chr4	48479747	48480259	+	0	NA	Intergenic	Intergenic	-3340	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.000000	0.380117	
chunk0030_398_1	chr10	119896894	119897490	+	0	NA	intron (NR_037771, intron 1 of 17)	L2|LINE|L2	4619	NM_007190	11196	Hs.435004	NM_007190	ENSG00000107651	SEC23IP	MSTP053|P125|P125A	SEC23 interacting protein	protein-coding	0.008389	0.428811	
chunk0036_194_1	chr11	63183140	63183514	+	0	NA	intron (NM_199352, intron 5 of 8)	intron (NM_199352, intron 5 of 8)	-39106	NM_173586	283238	Hs.375139	NM_173586	ENSG00000197658	SLC22A24	NET46	solute carrier family 22 member 24	protein-coding	0.000000	0.362667	
chunk0178_210_1	chr7	35025239	35025790	+	0	NA	intron (NM_015283, intron 1 of 21)	intron (NM_015283, intron 1 of 21)	12527	NM_015283	23333	Hs.408623	NM_015283	ENSG00000173852	DPY19L1	-	dpy-19 like C-mannosyltransferase 1	protein-coding	0.003630	0.378623	
chunk0168_322_1	chr6	92431130	92431623	+	0	NA	Intergenic	Intergenic	-740948	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.004057	0.242915	
chunk0171_418_1	chr6	131478234	131478554	+	0	NA	Intergenic	Intergenic	-94810	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.000000	0.267913	
chunk0066_135_1	chr15	31254508	31254818	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-23816	NM_001243538	283710	Hs.591097	NM_001243538		LOC283710	-	uncharacterized LOC283710	protein-coding	0.009677	0.485531	
chunk0142_435_1	chr4	105143960	105144422	+	0	NA	Intergenic	Intergenic	-1684	NM_017628	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.004329	0.332613	214(AAGAACACCCTGTTAC,-,0.00),215(AGAACACCCTGTTACA,+,0.00)
chunk0061_178_1	chr14	59969167	59969885	+	0	NA	intron (NR_075071, intron 12 of 32)	intron (NR_075071, intron 12 of 32)	49813	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.009749	0.376912	
chunk0028_106_1	chr10	84345175	84345926	+	0	NA	intron (NM_001284240, intron 1 of 9)	intron (NM_001284240, intron 1 of 9)	16961	NM_018999	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.005326	0.317819	
chunk0136_21_1	chr4	491498	491873	+	0	NA	intron (NM_133474, intron 1 of 2)	intron (NM_133474, intron 1 of 2)	7486	NM_133474	170960	Hs.428360	NM_133474	ENSG00000182903	ZNF721	-	zinc finger protein 721	protein-coding	0.008000	0.353723	230(AGGAACATTGTGTTTA,-,0.00),254(CAGGACTTGGTGTCCT,-,0.00),255(AGGACTTGGTGTCCTT,+,0.00)
chunk0056_273_1	chr13	90295971	90296242	+	0	NA	Intergenic	Intergenic	64924	NR_030754	693207		NR_030754	ENSG00000283783	MIR622	MIRN622|hsa-mir-622	microRNA 622	ncRNA	0.000000	0.272059	
chunk0046_305_1	chr12	62273087	62273521	+	0	NA	intron (NM_006313, intron 1 of 20)	L2c|LINE|L2	12945	NR_106740	102465133		NR_106740	ENSG00000284360	MIR6125	hsa-mir-6125|mir-6125	microRNA 6125	ncRNA	0.004608	0.354023	
chunk0037_207_1	chr11	74532559	74532758	+	0	NA	Intergenic	L1MEc|LINE|L1	-38948	NM_001144869	387787	Hs.591971	NM_001144869	ENSG00000175536	LIPT2	-	lipoyl(octanoyl) transferase 2	protein-coding	0.010050	0.460000	
chunk0085_17_1	chr18	329833	330325	+	0	NA	intron (NM_130386, intron 8 of 9)	AluJr|SINE|Alu	-62020	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.014228	0.488844	
chunk0052_199_1	chr13	24922938	24923233	+	0	NA	promoter-TSS (NM_018451)	promoter-TSS (NM_018451)	-196	NR_047594	55835	Hs.513379	NM_018451	ENSG00000151849	CENPJ	BM032|CENP-J|CPAP|LAP|LIP1|MCPH6|SASS4|SCKL4|Sas-4	centromere protein J	protein-coding	0.101695	0.628378	
chunk0206_291_1	chr9	124450726	124451322	+	0	NA	Intergenic	Intergenic	-35551	NM_002799	5695	Hs.213470	NM_002799	ENSG00000136930	PSMB7	Z	proteasome subunit beta 7	protein-coding	0.028523	0.599665	142(CAGGACACCGTGTTTT,-,0.00),143(AGGACACCGTGTTTTC,+,0.00)
chunk0133_14_1	chr3	165640848	165641047	+	0	NA	Intergenic	Intergenic	196518	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.350000	
chunk0172_98_1	chr6	134764840	134765039	+	0	NA	Intergenic	Intergenic	185183	NM_170771	64577	Hs.486520	NM_022568	ENSG00000118514	ALDH8A1	ALDH12|DJ352A20.2	aldehyde dehydrogenase 8 family member A1	protein-coding	0.005025	0.330000	96(AGGAACAATGTGTGCT,-,0.00),97(GGAACAATGTGTGCTC,+,0.00)
chunk0170_38_1	chr6	109351683	109352110	+	0	NA	Intergenic	L2|LINE|L2	30663	NM_001142404	8763	Hs.520313	NM_006016	ENSG00000135535	CD164	DFNA66|MGC-24|MGC-24v|MUC-24|endolyn	CD164 molecule	protein-coding	0.002342	0.441589	198(AAGGACACTGAGTTCT,-,0.00),199(AGGACACTGAGTTCTC,+,0.00)
chunk0002_197_1	chr1	19452142	19452712	+	0	NA	intron (NM_001206541, intron 1 of 8)	L2b|LINE|L2	32280	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.022807	0.572680	221(AGGAAGAGGCTGTTCT,-,0.00),222(GGAAGAGGCTGTTCTT,+,0.00)
chunk0138_101_1	chr4	36055242	36055509	+	0	NA	Intergenic	Intergenic	-188741	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.007491	0.317164	
chunk0186_199_1	chr7	139772128	139772667	+	0	NA	intron (NM_001113239, intron 1 of 14)	intron (NM_001113239, intron 1 of 14)	5497	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.016698	0.416667	
chunk0044_414_1	chr12	41510554	41510803	+	0	NA	intron (NM_001164595, intron 5 of 9)	intron (NM_001164595, intron 5 of 9)	72939	NM_013377	29951	Hs.380044	NM_013377	ENSG00000165966	PDZRN4	LNX4|SAMCAP3L	PDZ domain containing ring finger 4	protein-coding	0.004016	0.392000	
chunk0105_361_1	chr2	191877828	191878470	+	0	NA	Intergenic	Intergenic	-30869	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.006231	0.354588	421(CAAGACACTATGTTCC,-,0.00),422(AAGACACTATGTTCCT,+,0.00)
chunk0182_273_1	chr7	98123071	98123371	+	0	NA	intron (NM_014916, intron 1 of 13)	HAL1|LINE|L1	16336	NM_014916	22853	Hs.444179	NM_014916	ENSG00000164715	LMTK2	AATYK2|BREK|KPI-2|KPI2|LMR2|PPP1R100|cprk|hBREK	lemur tyrosine kinase 2	protein-coding	0.010000	0.411960	
chunk0064_348_1	chr14	96715167	96715648	+	0	NA	Intergenic	Intergenic	-81940	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.010395	0.412863	
chunk0151_8_1	chr5	40835104	40835542	+	0	NA	promoter-TSS (NM_000997)	promoter-TSS (NM_000997)	-38	NM_000997	6167	Hs.80545	NM_000997	ENSG00000145592	RPL37	L37	ribosomal protein L37	protein-coding	0.082192	0.585421	
chunk0149_313_1	chr5	26336084	26336501	+	0	NA	Intergenic	Intergenic	702290	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.002398	0.358852	
chunk0006_154_1	chr1	66344072	66344542	+	0	NA	intron (NM_001037339, intron 1 of 9)	intron (NM_001037339, intron 1 of 9)	-10071	NM_001297442	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.000000	0.329087	7(AAGGACACAGTGCCCC,-,0.00),8(AGGACACAGTGCCCCC,+,0.00),212(AGGAACTGGTTGTGCA,-,0.00)
chunk0067_156_1	chr15	43859188	43860087	+	0	NA	intron (NM_001167941, intron 11 of 12)	intron (NM_001167941, intron 11 of 12)	18534	NR_003571	728758	Hs.658099	NR_003571		PIN4P1	-	peptidylprolyl cis/trans isomerase, NIMA-interacting 4 pseudogene 1	pseudo	0.008899	0.416667	
chunk0013_184_1	chr1	169059243	169059666	+	0	NA	intron (NR_104091, intron 2 of 4)	intron (NR_104091, intron 2 of 4)	27551	NR_104091	101978719	Hs.517849	NR_104091	ENSG00000203601	LINC00970	-	long intergenic non-protein coding RNA 970	ncRNA	0.000000	0.360849	
chunk0079_137_1	chr17	12821317	12821923	+	0	NA	intron (NM_014859, intron 1 of 20)	intron (NM_014859, intron 1 of 20)	-31336	NR_104607	100128006	Hs.567641	NR_104607	ENSG00000265489	LOC100128006	-	uncharacterized LOC100128006	ncRNA	0.006601	0.362438	
chunk0111_88_1	chr20	23358547	23358936	+	0	NA	promoter-TSS (NR_109884)	promoter-TSS (NR_109884)	-614	NR_109884	100505683	Hs.140295	NR_109884	ENSG00000232645	LINC01431	-	long intergenic non-protein coding RNA 1431	ncRNA	0.015424	0.343590	
chunk0062_38_1	chr14	67187688	67188125	+	0	NA	Intergenic	L2c|LINE|L2	-1487	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.002288	0.442922	
chunk0060_98_1	chr14	43087593	43088026	+	0	NA	Intergenic	Intergenic	1419487	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.004619	0.345622	
chunk0083_390_1	chr17	71584267	71584478	+	0	NA	Intergenic	L1ME4a|LINE|L1	-382193	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.009479	0.254717	
chunk0095_92_1	chr2	15191551	15191836	+	0	NA	intron (NR_052013, intron 47 of 50)	intron (NR_052013, intron 47 of 50)	369655	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.007018	0.395105	134(CAGATCAGGATGTTCT,-,0.00),135(AGATCAGGATGTTCTG,+,0.00)
chunk0165_325_1	chr6	37178307	37178572	+	0	NA	Intergenic	L1ME3C|LINE|L1	8293	NM_001243186	5292	Hs.81170	NM_002648	ENSG00000137193	PIM1	PIM	Pim-1 proto-oncogene, serine/threonine kinase	protein-coding	0.007547	0.417293	
chunk0139_425_1	chr4	64193062	64193747	+	0	NA	Intergenic	L1P4d|LINE|L1	216056	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.001460	0.390671	
chunk0097_133_1	chr2	47174995	47175212	+	0	NA	promoter-TSS (NM_001305626)	promoter-TSS (NM_001305626)	-896	NM_001305626	805	Hs.468442	NM_001743	ENSG00000143933	CALM2	CALM|CALML2|CAM1|CAM3|CAMC|CAMII|CAMIII|LQT15|PHKD|PHKD2|caM	calmodulin 2	protein-coding	0.018433	0.444954	
chunk0181_331_1	chr7	87986392	87986975	+	0	NA	intron (NM_021721, intron 3 of 27)	intron (NM_021721, intron 3 of 27)	52432	NM_021721	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.001715	0.344178	
chunk0174_202_1	chr6	160141150	160141732	+	0	NA	intron (NM_153187, intron 7 of 9)	intron (NM_153187, intron 7 of 9)	19610	NM_003057	6580	Hs.117367	NM_003057	ENSG00000175003	SLC22A1	HOCT1|OCT1|oct1_cds	solute carrier family 22 member 1	protein-coding	0.006873	0.403087	
chunk0122_140_1	chr3	31831577	31831909	+	0	NA	intron (NM_017784, intron 3 of 11)	L1ME4b|LINE|L1	127530	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.006024	0.408408	
chunk0158_284_1	chr5	131768977	131769247	+	0	NA	intron (NM_001008738, intron 1 of 16)	intron (NM_001008738, intron 1 of 16)	27951	NM_133372	96459	Hs.591273	NM_133372	ENSG00000217128	FNIP1	-	folliculin interacting protein 1	protein-coding	0.003704	0.273063	
chunk0025_418_1	chr10	59710206	59710431	+	0	NA	promoter-TSS (NM_194298)	promoter-TSS (NM_194298)	-427	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.048889	0.619469	
chunk0020_110_1	chr1	233121791	233122089	+	0	NA	intron (NM_014801, intron 21 of 33)	L1MC3|LINE|L1	171316	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.003356	0.377926	
chunk0070_303_1	chr15	74905830	74906108	+	0	NA	intron (NM_020447, intron 2 of 4)	intron (NM_020447, intron 2 of 4)	1152	NM_020447	57184	Hs.367690	NM_020447	ENSG00000178761	FAM219B	C15orf17	family with sequence similarity 219 member B	protein-coding	0.014388	0.451613	
chunk0139_123_1	chr4	53055544	53055970	+	0	NA	intron (NM_152540, intron 5 of 8)	intron (NM_152540, intron 5 of 8)	193429	NM_023940	65997	Hs.8035	NM_023940	ENSG00000128045	RASL11B	-	RAS like family 11 member B	protein-coding	0.007042	0.477752	
chunk0015_212_1	chr1	187523404	187523713	+	0	NA	Intergenic	Intergenic	79930	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006472	0.335484	
chunk0183_62_1	chr7	104146145	104146452	+	0	NA	intron (NM_002553, intron 12 of 13)	L1MD2|LINE|L1	61749	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.009772	0.357143	179(GAGAACTGCATGTTCA,-,0.00),180(AGAACTGCATGTTCAC,+,0.00)
chunk0082_80_1	chr17	51771522	51771946	+	0	NA	intron (NM_001082534, intron 4 of 9)	intron (NM_001082534, intron 4 of 9)	387038	NM_020178	56934	Hs.463466	NM_020178	ENSG00000154975	CA10	CA-RPX|CARPX|HUCEP-15	carbonic anhydrase 10	protein-coding	0.004717	0.477647	
chunk0127_341_1	chr3	100603460	100603670	+	0	NA	Intergenic	Intergenic	-6024	NM_032787	84873	Hs.334511	NM_032787	ENSG00000144820	ADGRG7	GPR128	adhesion G protein-coupled receptor G7	protein-coding	0.014286	0.492891	
chunk0158_424_1	chr5	135188456	135189321	+	0	NA	intron (NM_001277348, intron 3 of 5)	intron (NM_001277348, intron 3 of 5)	59289	NR_037895	340073	Hs.434422	NR_037895	ENSG00000249647	C5orf66-AS2	-	C5orf66 antisense RNA 2	ncRNA	0.017341	0.363741	
chunk0163_35_1	chr6	8259159	8259723	+	0	NA	Intergenic	L2c|LINE|L2	-156846	NM_001135650	9521	Hs.602353	NM_004280	ENSG00000124802	EEF1E1	AIMP3|P18	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.010638	0.382301	
chunk0031_430_1	chr10	132444966	132445515	+	0	NA	promoter-TSS (NM_173541)	promoter-TSS (NM_173541)	30	NM_173541									0.010929	0.580000	
chunk0156_80_1	chr5	104044078	104044693	+	0	NA	Intergenic	Intergenic	-481584	NM_031438	83594	Hs.434289	NM_031438	ENSG00000112874	NUDT12	-	nudix hydrolase 12	protein-coding	0.003252	0.323052	322(ATGAACATCAAGTACT,-,0.00)
chunk0139_285_1	chr4	57233164	57233994	+	0	NA	Intergenic	Intergenic	-123194	NM_001553	3490	Hs.479808	NM_001553	ENSG00000163453	IGFBP7	AGM|FSTL2|IBP-7|IGFBP-7|IGFBP-7v|IGFBPRP1|MAC25|PSF|RAMSVPS|TAF	insulin like growth factor binding protein 7	protein-coding	0.006024	0.421179	
chunk0009_340_1	chr1	109168089	109168785	+	0	NA	intron (NM_001267048, intron 3 of 19)	L2b|LINE|L2	-18112	NM_001284353	57535	Hs.708190	NM_020775	ENSG00000116299	KIAA1324	EIG121	KIAA1324	protein-coding	0.005747	0.441894	
chunk0194_119_1	chr8	83958355	83958967	+	0	NA	Intergenic	L1M1|LINE|L1	-224557	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004902	0.300163	
chunk0034_158_1	chr11	30369996	30370649	+	0	NA	Intergenic	L1MC4a|LINE|L1	47223	NM_152316	120534	Hs.502208	NM_152316	ENSG00000152219	ARL14EP	ARF7EP|C11orf46|dJ299F11.1	ADP ribosylation factor like GTPase 14 effector protein	protein-coding	0.001531	0.313456	369(AGGCACTAAGTGTGCT,-,0.00),370(GGCACTAAGTGTGCTC,+,0.00)
chunk0037_346_1	chr11	77424708	77424934	+	0	NA	intron (NM_001128620, intron 1 of 15)	L2a|LINE|L2	49242	NM_001128620	5058	Hs.435714	NM_002576	ENSG00000149269	PAK1	IDDMSSD|PAKalpha	p21 (RAC1) activated kinase 1	protein-coding	0.008850	0.431718	
chunk0043_92_1	chr12	14753317	14753711	+	0	NA	Intergenic	Intergenic	17617	NM_175054	121504	Hs.745457	NM_175054	ENSG00000197837	HIST4H4	H4/p	histone cluster 4 H4	protein-coding	0.012690	0.382278	
chunk0046_366_1	chr12	63221111	63221680	+	0	NA	Intergenic	MIR|SINE|MIR	-68585	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.003515	0.359649	
chunk0077_43_1	chr16	75784040	75784510	+	0	NA	Intergenic	L1MA7|LINE|L1	136538	NM_018975	54386	Hs.301419	NM_018975	ENSG00000166848	TERF2IP	DRIP5|RAP1	TERF2 interacting protein	protein-coding	0.004255	0.341826	
chunk0109_219_1	chr20	5765969	5766645	+	0	NA	intron (NM_001303477, intron 2 of 3)	intron (NM_001303477, intron 2 of 3)	15920	NM_152504	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.010355	0.447563	299(AAAGACAGGATGTTCT,-,0.00),300(AAGACAGGATGTTCTT,+,0.00)
chunk0046_377_1	chr12	63461219	63461689	+	0	NA	Intergenic	L1PB1|LINE|L1	207120	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.002128	0.343949	
chunk0162_303_1	chr6	6531314	6531519	+	0	NA	intron (NR_026970, intron 3 of 7)	intron (NR_026970, intron 3 of 7)	-57285	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.004878	0.417476	17(AGGTACAGTGTGTTCC,-,0.00),18(GGTACAGTGTGTTCCA,+,0.00)
chunk0028_165_1	chr10	87163156	87163355	+	0	NA	intron (NM_019054, intron 4 of 8)	L1MC4a|LINE|L1	-62193	NM_001099338	728118	Hs.710565	NM_001099338	ENSG00000184923	NUTM2A	FAM22A	NUT family member 2A	protein-coding	0.010050	0.415000	20(CAGGACATACTGTTAT,-,0.00),21(AGGACATACTGTTATG,+,0.00)
chunk0112_154_1	chr20	39005595	39005839	+	0	NA	intron (NR_033905, intron 11 of 21)	L2a|LINE|L2	43379	NM_021931	60625	Hs.444520	NM_021931	ENSG00000101452	DHX35	C20orf15|DDX35|KAIA0875	DEAH-box helicase 35	protein-coding	0.004098	0.412245	
chunk0171_162_1	chr6	124311500	124312269	+	0	NA	intron (NM_001300740, intron 1 of 5)	intron (NM_001300740, intron 1 of 5)	28879	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.010403	0.355844	
chunk0159_217_1	chr5	140725959	140726435	+	0	NA	promoter-TSS (NR_026705)	promoter-TSS (NR_026705)	38	NR_026705	56662		NR_026705	ENSG00000202515	VTRNA1-3	HVG3|VAULTRC3|VR3|hvg-3	vault RNA 1-3	ncRNA	0.031513	0.475891	
chunk0009_222_1	chr1	106602327	106602526	+	0	NA	Intergenic	Intergenic	-454219	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.010050	0.315000	
chunk0129_397_1	chr3	126501748	126502035	+	0	NA	exon (NM_001165974, exon 10 of 21)	exon (NM_001165974, exon 10 of 21)	15882	NM_144639	131669	Hs.331148	NM_144639	ENSG00000159650	UROC1	HMFN0320|UROCD	urocanate hydratase 1	protein-coding	0.020906	0.611111	128(AAGGACACACAGTCCC,-,0.00),129(AGGACACACAGTCCCA,+,0.00)
chunk0091_270_1	chr19	11485636	11485851	+	0	NA	exon (NM_138783, exon 7 of 9)	exon (NM_138783, exon 7 of 9)	-4755	NM_001420	1995	Hs.1701	NM_001420	ENSG00000196361	ELAVL3	HUC|HUCL|PLE21	ELAV like RNA binding protein 3	protein-coding	0.023256	0.574074	
chunk0117_204_1	chr22	21843568	21843929	+	0	NA	intron (NM_138957, intron 1 of 7)	intron (NM_138957, intron 1 of 7)	23932	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.002770	0.337017	
chunk0062_265_1	chr14	71765130	71765578	+	0	NA	Intergenic	Intergenic	-166746	NM_001204423	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.004464	0.336303	
chunk0029_239_1	chr10	102621461	102622012	+	0	NA	intron (NM_016169, intron 10 of 11)	intron (NM_016169, intron 10 of 11)	-22759	NM_030912	81603	Hs.336810	NM_030912	ENSG00000171206	TRIM8	GERP|RNF27	tripartite motif containing 8	protein-coding	0.018149	0.556159	
chunk0045_23_1	chr12	43798096	43798637	+	0	NA	intron (NM_002822, intron 5 of 8)	intron (NM_002822, intron 5 of 8)	8009	NR_073472	5756	Hs.189075	NM_002822	ENSG00000151239	TWF1	A6|PTK9	twinfilin actin binding protein 1	protein-coding	0.005545	0.317343	243(AAGAACATGGTGTGCA,-,0.00),244(AGAACATGGTGTGCAT,+,0.00)
chunk0099_298_1	chr2	98940232	98940650	+	0	NA	Intergenic	MER85|DNA|PiggyBac	-4220	NM_207362	343990	Hs.469398	NM_207362	ENSG00000196872	KIAA1211L	C2orf55	KIAA1211 like	protein-coding	0.002392	0.393795	
chunk0131_124_1	chr3	144161988	144162487	+	0	NA	Intergenic	Intergenic	188912	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.002004	0.342000	
chunk0185_191_1	chr7	128342064	128342457	+	0	NA	intron (NM_018077, intron 1 of 18)	intron (NM_018077, intron 1 of 18)	1648	NM_001166135	55131	Hs.274263	NM_018077	ENSG00000106344	RBM28	ANES	RNA binding motif protein 28	protein-coding	0.012723	0.428934	
chunk0058_130_1	chr14	22510429	22510831	+	0	NA	Intergenic	Intergenic	78607	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.004975	0.382134	
chunk0072_317_1	chr15	98875098	98875383	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	90814	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.017544	0.370629	
chunk0134_330_1	chr3	181892968	181893676	+	0	NA	Intergenic	Intergenic	-59042	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.005650	0.431594	
chunk0082_367_1	chr17	60342099	60342507	+	0	NA	intron (NM_032582, intron 2 of 33)	L1P2|LINE|L1	49922	NM_032582	84669	Hs.132868	NM_032582	ENSG00000170832	USP32	NY-REN-60|USP10	ubiquitin specific peptidase 32	protein-coding	0.012255	0.496333	
chunk0170_347_1	chr6	116384252	116384952	+	0	NA	intron (NM_013352, intron 1 of 5)	intron (NM_013352, intron 1 of 5)	13655	NM_013352	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.008571	0.386591	
chunk0133_187_1	chr3	170466868	170467260	+	0	NA	exon (NM_020949, exon 8 of 8)	exon (NM_020949, exon 8 of 8)	43961	NR_106886	102465497		NR_106886	ENSG00000283474	MIR6828	hsa-mir-6828	microRNA 6828	ncRNA	0.017857	0.470738	
chunk0054_250_1	chr13	46182701	46182900	+	0	NA	promoter-TSS (NM_002298)	promoter-TSS (NM_002298)	-476	NM_002298	3936	Hs.381099	NM_002298	ENSG00000136167	LCP1	CP64|HEL-S-37|L-PLASTIN|LC64P|LPL|PLS2	lymphocyte cytosolic protein 1	protein-coding	0.010050	0.340000	
chunk0189_15_1	chr8	19510937	19511285	+	0	NA	intron (NR_024040, intron 2 of 9)	intron (NR_024040, intron 2 of 9)	91434	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.011494	0.469914	
chunk0082_376_1	chr17	60466943	60467499	+	0	NA	intron (NM_006380, intron 4 of 12)	intron (NM_006380, intron 4 of 12)	44717	NM_181707	124773	Hs.129312	NM_181707	ENSG00000141371	C17orf64	-	chromosome 17 open reading frame 64	protein-coding	0.000000	0.296230	240(TAGAACATTATGTTCA,-,0.00),241(AGAACATTATGTTCAT,+,0.00)
chunk0106_369_1	chr2	207220297	207220496	+	0	NA	intron (NR_110283, intron 3 of 3)	intron (NR_110283, intron 3 of 3)	33920	NR_110283	101927865	Hs.574609	NR_110283		MYOSLID-AS1	-	MYOSLID antisense RNA 1	ncRNA	0.025126	0.430000	
chunk0198_148_1	chr8	132920014	132920756	+	0	NA	intron (NM_003235, intron 21 of 47)	intron (NM_003235, intron 21 of 47)	53425	NM_003235	7038	Hs.654591	NM_003235	ENSG00000042832	TG	AITD3|TGN	thyroglobulin	protein-coding	0.002695	0.388964	
chunk0180_215_1	chr7	66920827	66921323	+	0	NA	promoter-TSS (NM_017994)	promoter-TSS (NM_017994)	-141	NM_017994	55069	Hs.488478	NM_017994	ENSG00000106609	TMEM248	C7orf42	transmembrane protein 248	protein-coding	0.106855	0.619718	
chunk0103_451_1	chr2	170255010	170255640	+	0	NA	intron (NR_045684, intron 7 of 34)	L1PA16|LINE|L1	77180	NM_001083615	140469	Hs.671900	NM_138995	ENSG00000071909	MYO3B	-	myosin IIIB	protein-coding	0.009524	0.513471	
chunk0144_241_1	chr4	135175595	135175794	+	0	NA	Intergenic	HERV35I-int|LTR|ERV1	712399	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.000000	0.305000	
chunk0011_291_1	chr1	151498616	151498815	+	0	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-12671	NM_020770	57530	Hs.591464	NM_020770	ENSG00000143375	CGN	-	cingulin	protein-coding	0.010050	0.480000	157(CTGAACAGAAAGTTCT,-,0.00),158(TGAACAGAAAGTTCTT,+,0.00)
chunk0206_127_1	chr9	120982769	120983284	+	0	NA	intron (NM_001735, intron 25 of 40)	intron (NM_001735, intron 25 of 40)	-53853	NM_001190945	7185	Hs.531251	NM_005658	ENSG00000056558	TRAF1	EBI6|MGC:10353	TNF receptor associated factor 1	protein-coding	0.005825	0.321705	
chunk0003_160_1	chr1	33348924	33349260	+	0	NA	intron (NM_198040, intron 8 of 13)	intron (NM_198040, intron 8 of 13)	806	NM_004427	1912	Hs.524271	NM_004427	ENSG00000134686	PHC2	EDR2|HPH2|PH2	polyhomeotic homolog 2	protein-coding	0.032738	0.445104	185(CAGAACAGCTTGTCCC,-,0.00),186(AGAACAGCTTGTCCCT,+,0.00)
chunk0170_265_1	chr6	113886438	113886858	+	0	NA	Intergenic	Intergenic	-13301	NR_038863	285758	Hs.359399	NR_038863	ENSG00000227502	LINC01268	ROCKI	long intergenic non-protein coding RNA 1268	ncRNA	0.002381	0.358670	
chunk0082_245_1	chr17	57428613	57429173	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	94704	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.005357	0.431373	214(AAACACACCCAGTTCT,-,0.00),215(AACACACCCAGTTCTT,+,0.00),501(GGATCTGCGTGTCCTC,+,0.00)
chunk0002_221_1	chr1	19798023	19798482	+	0	NA	intron (NM_181719, intron 1 of 15)	intron (NM_181719, intron 1 of 15)	1665	NM_181719	255104	Hs.466729	NM_181719	ENSG00000162542	TMCO4	-	transmembrane and coiled-coil domains 4	protein-coding	0.015251	0.497826	
chunk0090_126_1	chr18	71810247	71810804	+	0	NA	Intergenic	MER70B|LTR|ERVL	-28299	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.005386	0.448029	
chunk0152_5_1	chr5	56185861	56186094	+	0	NA	intron (NM_024669, intron 2 of 11)	intron (NM_024669, intron 2 of 11)	47382	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.008584	0.431624	
chunk0211_154_1	chrX	113875457	113876021	+	0	NA	intron (NR_131204, intron 1 of 2)	intron (NR_131204, intron 1 of 2)	62479	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.001773	0.357522	
chunk0025_162_1	chr10	52615418	52615956	+	0	NA	Intergenic	L2a|LINE|L2	-145154	NR_120641	101928687	Hs.380362	NR_120641	ENSG00000231131	LNCAROD	A-ROD|LINC01468|lnc-MBL2-4	lncRNA activating regulator of DKK1	ncRNA	0.005576	0.398887	289(GAGAACAGACTGTTTT,-,0.00),290(AGAACAGACTGTTTTA,+,0.00)
chunk0160_317_1	chr5	159329335	159329656	+	0	NA	intron (NM_002187, intron 1 of 7)	intron (NM_002187, intron 1 of 7)	978	NM_002187	3593	Hs.674	NM_002187	ENSG00000113302	IL12B	CLMF|CLMF2|IL-12B|IMD28|IMD29|NKSF|NKSF2	interleukin 12B	protein-coding	0.006231	0.434783	
chunk0153_115_1	chr5	68565346	68565568	+	0	NA	Intergenic	L1PB1|LINE|L1	272889	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.018018	0.551570	
chunk0173_70_1	chr6	142592235	142593270	+	0	NA	intron (NR_027312, intron 1 of 2)	L1ME2z|LINE|L1	45084	NR_027311	153910	Hs.350819	NR_027311	ENSG00000236366	LOC153910	-	uncharacterized LOC153910	ncRNA	0.001932	0.315637	
chunk0065_186_1	chr15	26629089	26629785	+	0	NA	promoter-TSS (NM_001191321)	promoter-TSS (NM_001191321)	-259	NR_103801	2562	Hs.302352	NM_000814	ENSG00000166206	GABRB3	ECA5|EIEE43	gamma-aminobutyric acid type A receptor beta3 subunit	protein-coding	0.047414	0.604017	
chunk0004_198_1	chr1	46522636	46522871	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	15757	NM_147192	127343	Hs.375623	NM_147192	ENSG00000197587	DMBX1	MBX|OTX3|PAXB	diencephalon/mesencephalon homeobox 1	protein-coding	0.034043	0.572034	
chunk0113_230_1	chr20	53994615	53995100	+	0	NA	intron (NM_003657, intron 6 of 11)	intron (NM_003657, intron 6 of 11)	73628	NR_039913	100616225		NR_039913	ENSG00000265595	MIR4756	-	microRNA 4756	ncRNA	0.008247	0.318930	
chunk0132_60_1	chr3	155142216	155142563	+	0	NA	intron (NM_000902, intron 12 of 22)	intron (NM_000902, intron 12 of 22)	62099	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.014409	0.393678	195(AGGACATGGTGAACTT,+,0.00)
chunk0179_45_1	chr7	43421597	43422278	+	0	NA	intron (NM_015052, intron 8 of 29)	intron (NM_015052, intron 8 of 29)	100605	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.007342	0.423754	
chunk0144_359_1	chr4	139774058	139774399	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	108460	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.005865	0.464912	
chunk0154_211_1	chr5	80425004	80425947	+	0	NA	intron (NM_001105251, intron 2 of 18)	L1ME5|LINE|L1	17462	NM_001284236	9765	Hs.482660	NM_014733	ENSG00000039319	ZFYVE16	PPP1R69	zinc finger FYVE-type containing 16	protein-coding	0.006363	0.336864	
chunk0195_443_1	chr8	101277883	101278626	+	0	NA	Intergenic	Intergenic	-72190	NM_001267709	51123	Hs.374485	NM_016096	ENSG00000120963	ZNF706	HSPC038|PNAS-106|PNAS-113	zinc finger protein 706	protein-coding	0.005384	0.415323	336(AGGAACAAATAGTCCT,-,0.00),337(GGAACAAATAGTCCTG,+,0.00)
chunk0023_124_1	chr10	23775842	23776141	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	81245	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.003344	0.293333	
chunk0049_203_1	chr12	93135002	93135788	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-38971	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.006361	0.397713	
chunk0036_30_1	chr11	58626956	58627253	+	0	NA	Intergenic	Intergenic	4431	NM_000614	1270	Hs.524920	NM_000614	ENSG00000242689	CNTF	HCNTF	ciliary neurotrophic factor	protein-coding	0.006734	0.395973	
chunk0210_385_1	chrX	97584972	97585655	+	0	NA	intron (NM_006729, intron 26 of 26)	intron (NM_006729, intron 26 of 26)	-20778	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.002928	0.358187	
chunk0108_435_1	chr2	237995911	237996239	+	0	NA	intron (NR_037904, intron 4 of 18)	Tigger15a|DNA|TcMar-Tigger	27282	NM_001278305	140739	Hs.471785	NM_080678	ENSG00000184182	UBE2F	NCE2	ubiquitin conjugating enzyme E2 F (putative)	protein-coding	0.006098	0.349544	
chunk0158_196_1	chr5	127994365	127994591	+	0	NA	Intergenic	Intergenic	88596	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.004425	0.409692	43(CAGGACATGCTGTCAT,-,0.00)
chunk0137_317_1	chr4	24551864	24552262	+	0	NA	intron (NM_001358, intron 5 of 13)	intron (NM_001358, intron 5 of 13)	-31773	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.002513	0.348371	
chunk0146_215_1	chr4	161762695	161763257	+	0	NA	intron (NM_001128427, intron 5 of 15)	intron (NM_001128427, intron 5 of 15)	-259757	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.003559	0.369449	240(TGGAACAGGGAGTACA,-,0.00),241(GGAACAGGGAGTACAT,+,0.00)
chunk0061_172_1	chr14	59931046	59931480	+	0	NA	intron (NR_075071, intron 4 of 32)	MIRc|SINE|MIR	11550	NR_075071	341883	Hs.666245	NM_198499	ENSG00000131951	LRRC9	-	leucine rich repeat containing 9	protein-coding	0.002304	0.331034	
chunk0122_109_1	chr3	30689190	30689618	+	0	NA	intron (NM_001024847, intron 7 of 7)	intron (NM_001024847, intron 7 of 7)	82902	NM_003242	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.011682	0.461538	160(GAGAACAGTGTGGCCC,-,0.00),161(AGAACAGTGTGGCCCT,+,0.00)
chunk0083_233_1	chr17	67432486	67433144	+	0	NA	intron (NM_181671, intron 1 of 9)	intron (NM_181671, intron 1 of 9)	-38674	NR_037517	100500895		NR_037517	ENSG00000207688	MIR548AA2	-	microRNA 548aa-2	ncRNA	0.010638	0.391502	
chunk0074_312_1	chr16	30488815	30489273	+	0	NA	intron (NM_001114380, intron 7 of 28)	intron (NM_001114380, intron 7 of 28)	-14875	NR_039743	100616405		NR_039743	ENSG00000266305	MIR4518	mir-4518	microRNA 4518	ncRNA	0.017467	0.553377	
chunk0064_220_1	chr14	93619874	93620424	+	0	NA	intron (NM_020818, intron 29 of 49)	intron (NM_020818, intron 29 of 49)	168271	NM_178013	145270	Hs.432401	NM_178004	ENSG00000175785	PRIMA1	PRIMA	proline rich membrane anchor 1	protein-coding	0.018182	0.377495	
chunk0174_208_1	chr6	160298949	160299179	+	0	NA	Intergenic	Intergenic	-40133	NM_003058	6582	Hs.436385	NM_003058	ENSG00000112499	SLC22A2	OCT2	solute carrier family 22 member 2	protein-coding	0.013043	0.424242	125(AAGGACAGCATGATCC,-,0.00),126(AGGACAGCATGATCCG,+,0.00)
chunk0084_362_1	chr17	81427566	81427770	+	0	NA	intron (NM_001291324, intron 2 of 27)	intron (NM_001291324, intron 2 of 27)	23520	NR_036152	100422944		NR_036152	ENSG00000266189	MIR3186	mir-3186	microRNA 3186	ncRNA	0.044118	0.678049	
chunk0035_95_1	chr11	42176641	42177172	+	0	NA	Intergenic	Intergenic	76784	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.001883	0.357143	
chunk0199_455_1	chr9	14179297	14179948	+	0	NA	intron (NM_001190737, intron 3 of 10)	intron (NM_001190737, intron 3 of 10)	1180	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.006144	0.340491	
chunk0157_385_1	chr5	124020048	124020666	+	0	NA	Intergenic	L1MEg|LINE|L1	418163	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004854	0.310178	
chunk0101_456_1	chr2	140189771	140190116	+	0	NA	Intergenic	(TAA)n|Simple_repeat|Simple_repeat	396742	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.008696	0.280347	
chunk0121_82_1	chr3	16060329	16060674	+	0	NA	Intergenic	Intergenic	-114176	NM_054110	117248	Hs.411308	NM_054110	ENSG00000131386	GALNT15	GALNACT15|GALNT13|GALNT7|GALNTL2|PIH5|pp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.011594	0.468208	
chunk0013_296_1	chr1	171153091	171153792	+	0	NA	intron (NR_002601, intron 5 of 6)	L2a|LINE|L2	15701	NR_002601	388714	Hs.448988	NR_002601	ENSG00000117507	FMO6P	FMO6	flavin containing dimethylaniline monoxygenase 6, pseudogene	pseudo	0.004280	0.351852	
chunk0059_246_1	chr14	34895714	34896433	+	0	NA	Intergenic	Intergenic	-20426	NM_013448	11177	Hs.509140	NM_013448	ENSG00000198604	BAZ1A	ACF1|WALp1|WCRF180|hACF1	bromodomain adjacent to zinc finger domain 1A	protein-coding	0.019471	0.401389	379(AAGGACAGTGTCTTCC,-,0.00),380(AGGACAGTGTCTTCCT,+,0.00)
chunk0003_410_1	chr1	40257571	40258326	+	0	NA	promoter-TSS (NM_005857)	promoter-TSS (NM_005857)	-102	NM_005857	10269	Hs.132642	NM_005857	ENSG00000084073	ZMPSTE24	FACE-1|FACE1|HGPS|PRO1|STE24|Ste24p	zinc metallopeptidase STE24	protein-coding	0.062252	0.609788	
chunk0174_329_1	chr6	163549680	163550112	+	0	NA	intron (NM_206853, intron 4 of 6)	intron (NM_206853, intron 4 of 6)	135253	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.002315	0.314088	
chunk0050_133_1	chr12	102389763	102390213	+	0	NA	Intergenic	Intergenic	88663	NM_001111284	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.000000	0.312639	
chunk0077_60_1	chr16	76719349	76719852	+	0	NA	Intergenic	L1PB1|LINE|L1	84602	NR_110934	101928203	Hs.737035	NR_110934	ENSG00000250514	LINC02125	-	long intergenic non-protein coding RNA 2125	ncRNA	0.003976	0.347222	
chunk0105_432_1	chr2	193676672	193677175	+	0	NA	Intergenic	Intergenic	-667346	NR_110222	101927406	Hs.385793	NR_110222	ENSG00000225539	LINC01821	-	long intergenic non-protein coding RNA 1821	ncRNA	0.000000	0.416667	204(AAGAACTATCTGTGCT,-,0.00),205(AGAACTATCTGTGCTC,+,0.00)
chunk0041_204_1	chr11	126655621	126656124	+	0	NA	promoter-TSS (NR_120533)	promoter-TSS (NR_120533)	-214	NR_120533	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.009940	0.480159	19(GGGAGCAGTGTGTGCC,-,0.00),20(GGAGCAGTGTGTGCCC,+,0.00)
chunk0192_27_1	chr8	58506004	58506302	+	0	NA	Intergenic	MIRb|SINE|MIR	-5992	NM_000780	1581	Hs.1644	NM_000780	ENSG00000167910	CYP7A1	CP7A|CYP7|CYPVII	cytochrome P450 family 7 subfamily A member 1	protein-coding	0.006711	0.364548	
chunk0161_442_1	chr5	178587654	178588091	+	0	NA	intron (NM_173465, intron 1 of 28)	intron (NM_173465, intron 1 of 28)	2683	NM_173465	91522	Hs.660026	NM_173465	ENSG00000050767	COL23A1	-	collagen type XXIII alpha 1 chain	protein-coding	0.018307	0.486301	
chunk0060_275_1	chr14	50358892	50360046	+	0	NA	intron (NM_001282236, intron 2 of 8)	L2c|LINE|L2	36455	NM_004196	8814	Hs.280881	NM_004196	ENSG00000100490	CDKL1	KKIALRE|P42	cyclin dependent kinase like 1	protein-coding	0.006932	0.388745	
chunk0087_72_1	chr18	31983052	31983368	+	0	NA	Intergenic	Intergenic	-35272	NM_017831	54941	Hs.633703	NM_017831	ENSG00000101695	RNF125	TNORS|TRAC-1|TRAC1	ring finger protein 125	protein-coding	0.009494	0.473186	82(CAAAACACCCTGTGCC,-,0.00),83(AAAACACCCTGTGCCT,+,0.00),114(AGAACTACTTGTACTT,+,0.00)
chunk0126_281_1	chr3	80098378	80098870	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-330715	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.316430	268(AGGGACACTGTGTTCC,-,0.00),269(GGGACACTGTGTTCCA,+,0.00)
chunk0199_64_1	chr9	2297989	2298441	+	0	NA	Intergenic	L2a|LINE|L2	139759	NM_001289400	6595	Hs.298990	NM_003070	ENSG00000080503	SMARCA2	BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	protein-coding	0.004425	0.432671	
chunk0175_187_1	chr7	5419110	5419329	+	0	NA	intron (NM_001080495, intron 2 of 29)	intron (NM_001080495, intron 2 of 29)	4327	NM_001080495	84629	Hs.520638	NM_001013722	ENSG00000182095	TNRC18	CAGL79|TNRC18A	trinucleotide repeat containing 18	protein-coding	0.059361	0.618182	
chunk0123_430_1	chr3	50184258	50184775	+	0	NA	intron (NM_004186, intron 12 of 18)	L2|LINE|L2	-7094	NM_000172	2779	Hs.517978	NM_000172	ENSG00000114349	GNAT1	CSNB1G|CSNBAD3|GBT1|GNATR	G protein subunit alpha transducin 1	protein-coding	0.027079	0.610039	240(GGGGACAGACAGTGCA,-,0.00),241(GGGACAGACAGTGCAG,+,0.00)
chunk0192_88_1	chr8	61013518	61014180	+	0	NA	Intergenic	Intergenic	-46101	NR_034003	100130298	Hs.636194	NR_034003		LOC100130298	-	hCG1816373-like	ncRNA	0.013595	0.450980	177(AGGCACTGTGTGTGCC,-,0.00),178(GGCACTGTGTGTGCCG,+,0.00)
chunk0203_16_1	chr9	82721536	82722250	+	0	NA	Intergenic	Intergenic	341235	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.004202	0.374825	
chunk0080_377_1	chr17	33615818	33616051	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-82174	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.008584	0.487179	
chunk0172_346_1	chr6	138956240	138956701	+	0	NA	intron (NM_001128617, intron 1 of 18)	intron (NM_001128617, intron 1 of 18)	31791	NM_001128617	85021	Hs.334603	NM_031922	ENSG00000135597	REPS1	NBIA7|RALBP1	RALBP1 associated Eps domain containing 1	protein-coding	0.006508	0.415584	
chunk0080_366_1	chr17	33086730	33087499	+	0	NA	intron (NM_183377, intron 3 of 9)	intron (NM_183377, intron 3 of 9)	95250	NM_173847	124912	Hs.434112	NM_173847	ENSG00000141316	SPACA3	ALLP17|CT54|LYC3|LYZC|LYZL3|SLLP1	sperm acrosome associated 3	protein-coding	0.001300	0.484416	
chunk0095_407_1	chr2	24482145	24482399	+	0	NA	Intergenic	L2a|LINE|L2	-102205	NM_003743	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.011811	0.352941	
chunk0030_392_1	chr10	119714243	119714599	+	0	NA	Intergenic	Intergenic	-11626	NM_014937	22876	Hs.369755	NM_014937	ENSG00000198825	INPP5F	MSTP007|MSTPO47|SAC2|hSAC2	inositol polyphosphate-5-phosphatase F	protein-coding	0.008427	0.450980	
chunk0149_365_1	chr5	28059415	28059776	+	0	NA	Intergenic	Intergenic	587303	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.002770	0.306630	
chunk0168_328_1	chr6	92569651	92570047	+	0	NA	Intergenic	Intergenic	849733	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.000000	0.254408	
chunk0132_43_1	chr3	154850763	154851933	+	0	NA	Intergenic	Intergenic	-228299	NM_000902	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.005128	0.376601	
chunk0106_270_1	chr2	203813011	203813310	+	0	NA	Intergenic	L1MB4|LINE|L1	-54628	NM_001037631	1493	Hs.247824	NM_005214	ENSG00000163599	CTLA4	ALPS5|CD|CD152|CELIAC3|CTLA-4|GRD4|GSE|IDDM12	cytotoxic T-lymphocyte associated protein 4	protein-coding	0.013378	0.393333	
chunk0172_275_1	chr6	137593293	137593556	+	0	NA	Intergenic	THE1B-int|LTR|ERVL-MaLR	-72222	NR_125867	102723649	Hs.129235	NR_125867		LOC102723649	-	uncharacterized LOC102723649	ncRNA	0.007605	0.553030	
chunk0147_291_1	chr4	184358524	184358942	+	0	NA	Intergenic	Intergenic	-4756	NR_040108	728175	Hs.590107	NR_040108	ENSG00000180712	LINC02363	-	long intergenic non-protein coding RNA 2363	ncRNA	0.004785	0.463007	178(GGGAACACAGTGTTCC,-,0.00),179(GGAACACAGTGTTCCA,+,0.00)
chunk0118_366_1	chr22	36434598	36435242	+	0	NA	Intergenic	Intergenic	46720	NM_012473	25828	Hs.211929	NM_012473	ENSG00000100348	TXN2	COXPD29|MT-TRX|MTRX|TRX2|TXN	thioredoxin 2	protein-coding	0.026398	0.562791	
chunk0127_259_1	chr3	97257869	97258437	+	0	NA	intron (NM_001080448, intron 5 of 17)	L2a|LINE|L2	-181440	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.001761	0.325132	
chunk0019_439_1	chr1	231235966	231236563	+	0	NA	intron (NM_152379, intron 2 of 6)	intron (NM_152379, intron 2 of 6)	-4909	NM_001316350	8443	Hs.498028	NM_014236	ENSG00000116906	GNPAT	DAP-AT|DAPAT|DHAPAT|RCDP2	glyceronephosphate O-acyltransferase	protein-coding	0.006700	0.399666	
chunk0007_148_1	chr1	79580413	79580612	+	0	NA	Intergenic	L1MA7|LINE|L1	-573702	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.000000	0.305000	
chunk0087_13_1	chr18	30959068	30959500	+	0	NA	Intergenic	Intergenic	83531	NM_024423	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.011574	0.351039	68(AGGGTCAGTGAGTTCT,-,0.00),69(GGGTCAGTGAGTTCTT,+,0.00)
chunk0168_209_1	chr6	85826447	85826917	+	0	NA	Intergenic	L1M2|LINE|L1	-147949	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.010638	0.569002	
chunk0208_314_1	chrX	23902638	23902919	+	0	NA	intron (NR_026545, intron 1 of 7)	intron (NR_026545, intron 1 of 7)	5162	NM_024122	79135	Hs.495851	NM_024122	ENSG00000184831	APOO	FAM121B|MIC26|MICOS26|Mic23|My025	apolipoprotein O	protein-coding	0.010676	0.418440	61(AAGTACAATGTGTACT,-,0.00),62(AGTACAATGTGTACTT,+,0.00)
chunk0004_356_1	chr1	51495523	51496061	+	0	NA	intron (NM_001981, intron 1 of 24)	intron (NM_001981, intron 1 of 24)	23531	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.000000	0.300557	
chunk0153_32_1	chr5	67131610	67132054	+	0	NA	exon (NM_001290227, exon 14 of 26)	exon (NM_001290227, exon 14 of 26)	64957	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.004505	0.341573	
chunk0071_429_1	chr15	89827872	89828509	+	0	NA	Intergenic	Intergenic	-13350	NM_001150	290	Hs.1239	NM_001150	ENSG00000166825	ANPEP	APN|CD13|GP150|LAP1|P150|PEPN	alanyl aminopeptidase, membrane	protein-coding	0.020408	0.592476	
chunk0028_415_1	chr10	93435070	93435522	+	0	NA	intron (NM_013451, intron 3 of 53)	intron (NM_013451, intron 3 of 53)	47021	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.011062	0.419426	
chunk0075_82_1	chr16	48244312	48244660	+	0	NA	exon (NM_001300948, exon 1 of 14)	exon (NM_001300948, exon 1 of 14)	319	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.091954	0.707736	
chunk0162_316_1	chr6	6696644	6697051	+	0	NA	Intergenic	Intergenic	-74021	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.004914	0.433824	
chunk0065_379_1	chr14	104215292	104215491	+	0	NA	Intergenic	Intergenic	76668	NM_015656	26153	Hs.134970	NM_015656	ENSG00000066735	KIF26A	-	kinesin family member 26A	protein-coding	0.000000	0.545000	
chunk0107_415_1	chr2	224331612	224332089	+	0	NA	Intergenic	Intergenic	70144	NM_024785	79843	Hs.147585	NM_024785	ENSG00000124019	FAM124B	-	family with sequence similarity 124 member B	protein-coding	0.016771	0.464435	109(CAGGACAGCTTGTGCA,-,0.00),110(AGGACAGCTTGTGCAC,+,0.00)
chunk0138_337_1	chr4	41606538	41606737	+	0	NA	intron (NM_001112717, intron 6 of 25)	intron (NM_001112717, intron 6 of 25)	-6135	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.370000	
chunk0212_52_1	chrY	11314072	11314464	+	0	NA	Intergenic	Intergenic	1107322	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.033163	0.557252	
chunk0054_137_1	chr13	43567768	43567973	+	0	NA	intron (NM_001242863, intron 2 of 16)	intron (NM_001242863, intron 2 of 16)	61607	NM_001127615	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.000000	0.339806	
chunk0128_148_1	chr3	106963432	106963966	+	0	NA	Intergenic	Intergenic	276939	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.003745	0.338318	
chunk0006_82_1	chr1	64956552	64957071	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	9693	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.003854	0.434615	
chunk0053_380_1	chr13	36006230	36006633	+	0	NA	intron (NM_004734, intron 3 of 17)	intron (NM_004734, intron 3 of 17)	124946	NM_004734	9201	Hs.507755	NM_004734	ENSG00000133083	DCLK1	CL1|CLICK1|DCAMKL1|DCDC3A|DCLK	doublecortin like kinase 1	protein-coding	0.012407	0.460396	
chunk0130_121_1	chr3	131488438	131488789	+	0	NA	intron (NM_007208, intron 5 of 9)	L2c|LINE|L2	-9380	NR_002985	677836	Hs.735762	NR_002985		SNORA58	ACA58|SNORA58B	small nucleolar RNA, H/ACA box 58	snoRNA	0.000000	0.306818	
chunk0079_301_1	chr17	17032275	17032743	+	0	NA	Intergenic	Intergenic	-10251	NM_201274	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.021368	0.573561	
chunk0114_269_1	chr21	16228635	16228966	+	0	NA	intron (NR_027791, intron 1 of 5)	L1PA7|LINE|L1	34421	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.006042	0.385542	
chunk0095_162_1	chr2	17244527	17245180	+	0	NA	Intergenic	Intergenic	273586	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.009188	0.429664	
chunk0008_404_1	chr1	97820350	97821055	+	0	NA	intron (NM_001160301, intron 3 of 5)	intron (NM_001160301, intron 3 of 5)	23781	NR_046591	100873933	Hs.568669	NR_046591	ENSG00000235777	DPYD-AS2	-	DPYD antisense RNA 2	ncRNA	0.007092	0.313031	350(AGAGACATTCTGTACT,-,0.00),351(GAGACATTCTGTACTG,+,0.00)
chunk0008_259_1	chr1	94543247	94543835	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-1684	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.008503	0.337861	192(GATACACAATGTGCCT,+,0.00)
chunk0036_160_1	chr11	62468761	62469225	+	0	NA	intron (NM_024060, intron 5 of 5)	intron (NM_024060, intron 5 of 5)	49958	NM_003357	7356	Hs.523732	NM_003357	ENSG00000149021	SCGB1A1	CC10|CC16|CCPBP|CCSP|UGB|UP-1|UP1	secretoglobin family 1A member 1	protein-coding	0.010776	0.440860	
chunk0201_59_1	chr9	33905176	33905646	+	0	NA	intron (NM_017811, intron 3 of 4)	intron (NM_017811, intron 3 of 4)	28953	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.002128	0.403397	
chunk0140_132_1	chr4	69178072	69178893	+	0	NA	Intergenic	LTR10C|LTR|ERV1	36249	NM_001073	10720	Hs.339811	NM_001073	ENSG00000213759	UGT2B11	-	UDP glucuronosyltransferase family 2 member B11	protein-coding	0.006090	0.361314	349(AAGAACATAAAGTACA,-,0.00),350(AGAACATAAAGTACAT,+,0.00)
chunk0136_451_1	chr3	198080971	198081260	+	0	NA	promoter-TSS (NR_003291)	promoter-TSS (NR_003291)	-444	NR_003291	348840	Hs.512227	NM_182631	ENSG00000226435	ANKRD18DP	-	ankyrin repeat domain 18D, pseudogene	pseudo	0.086505	0.751724	
chunk0015_207_1	chr1	187517408	187518063	+	0	NA	Intergenic	Intergenic	74107	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003053	0.378049	
chunk0157_151_1	chr5	117731381	117731886	+	0	NA	intron (NR_104997, intron 1 of 2)	intron (NR_104997, intron 1 of 2)	1272	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.005941	0.373518	
chunk0069_164_1	chr15	62570076	62570641	+	0	NA	Intergenic	Intergenic	74823	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.008850	0.434629	
chunk0020_126_1	chr1	233520741	233520996	+	0	NA	Intergenic	MLT2B3|LTR|ERVL	-93136	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.007843	0.539062	
chunk0175_270_1	chr7	7501434	7501894	+	0	NA	intron (NM_001037763, intron 11 of 34)	intron (NM_001037763, intron 11 of 34)	34165	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.008696	0.440347	
chunk0004_139_1	chr1	44899052	44899512	+	0	NA	intron (NM_001166588, intron 5 of 9)	L1ME1|LINE|L1	-56338	NM_001166292	8643	Hs.591497	NM_003738	ENSG00000117425	PTCH2	PTC2	patched 2	protein-coding	0.002174	0.340564	
chunk0047_140_1	chr12	69586853	69587079	+	0	NA	intron (NM_006431, intron 3 of 15)	intron (NM_006431, intron 3 of 15)	1284	NM_001198842	10576	Hs.189772	NM_006431	ENSG00000166226	CCT2	99D8.1|CCT-beta|CCTB|HEL-S-100n|PRO1633|TCP-1-beta	chaperonin containing TCP1 subunit 2	protein-coding	0.017699	0.339207	
chunk0059_318_1	chr14	36470750	36471219	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	42801	NM_001101341	253970	Hs.509165	NM_001101341	ENSG00000229415	SFTA3	NANCI|SFTPH|SP-H|SPH	surfactant associated 3	ncRNA	0.006397	0.410638	
chunk0113_157_1	chr20	52800836	52801128	+	0	NA	Intergenic	Intergenic	-171425	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.003425	0.412969	
chunk0106_187_1	chr2	201406663	201407169	+	0	NA	intron (NM_015049, intron 3 of 15)	intron (NM_015049, intron 3 of 15)	44680	NM_015049	66008	Hs.152774	NM_015049	ENSG00000115993	TRAK2	ALS2CR3|CALS-C|GRIF-1|GRIF1|MILT2|OIP98	trafficking kinesin protein 2	protein-coding	0.003953	0.297830	
chunk0082_189_1	chr17	56489820	56490596	+	0	NA	Intergenic	L2c|LINE|L2	-103491	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.002577	0.406692	
chunk0029_298_1	chr10	103991911	103992217	+	0	NA	intron (NM_001304743, intron 2 of 17)	L2b|LINE|L2	24879	NM_014720	9748	Hs.591922	NM_014720	ENSG00000065613	SLK	LOSK|STK2|bA16H23.1|se20-9	STE20 like kinase	protein-coding	0.003268	0.306189	
chunk0133_369_1	chr3	173741738	173742080	+	0	NA	intron (NM_014932, intron 3 of 6)	intron (NM_014932, intron 3 of 6)	178887	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.014620	0.437318	
chunk0205_238_1	chr9	110073171	110073815	+	0	NA	intron (NM_001004065, intron 1 of 3)	intron (NM_001004065, intron 1 of 3)	24895	NM_001198656	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.003106	0.398450	
chunk0159_202_1	chr5	140431517	140432115	+	0	NA	intron (NM_024668, intron 1 of 10)	intron (NM_024668, intron 1 of 10)	30002	NM_017978	54882	Hs.594084	NM_017747	ENSG00000131503	ANKHD1	MASK|MASK1|PP2500|VBARP	ankyrin repeat and KH domain containing 1	protein-coding	0.003344	0.355593	464(ATGAACAGTCTGTCAC,-,0.00)
chunk0010_294_1	chr1	117602835	117603441	+	0	NA	intron (NR_121626, intron 2 of 2)	intron (NR_121626, intron 2 of 2)	2632	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.008251	0.380560	298(AAGAACACAGTGTATT,-,0.00),299(AGAACACAGTGTATTT,+,0.00)
chunk0099_239_1	chr2	96888457	96888942	+	0	NA	intron (NM_016490, intron 2 of 4)	intron (NM_016490, intron 2 of 4)	6463	NM_001172667	51252	Hs.107922	NM_016490	ENSG00000168754	FAM178B	-	family with sequence similarity 178 member B	protein-coding	0.018557	0.563786	
chunk0089_144_1	chr18	58967802	58968163	+	0	NA	intron (NM_018181, intron 8 of 10)	intron (NM_018181, intron 8 of 10)	-67697	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.011080	0.444751	
chunk0146_278_1	chr4	163494398	163494766	+	0	NA	promoter-TSS (NM_018352)	promoter-TSS (NM_018352)	61	NM_018352	55319	Hs.267446	NM_018352	ENSG00000198498	TMA16	C4orf43	translation machinery associated 16 homolog	protein-coding	0.086957	0.639566	
chunk0156_189_1	chr5	107906054	107906823	+	0	NA	intron (NM_001163315, intron 7 of 8)	MIRb|SINE|MIR	-235543	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.002601	0.328571	
chunk0076_99_1	chr16	65773101	65773568	+	0	NA	Intergenic	MIRb|SINE|MIR	-197034	NR_027755	283867	Hs.444774	NM_001101346	ENSG00000261742	LINC00922	-	long intergenic non-protein coding RNA 922	ncRNA	0.008565	0.470085	
chunk0098_165_1	chr2	70603196	70603432	+	0	NA	Intergenic	L1MD1|LINE|L1	-49299	NM_003236	7039	Hs.170009	NM_003236	ENSG00000163235	TGFA	TFGA	transforming growth factor alpha	protein-coding	0.000000	0.291139	
chunk0172_218_1	chr6	136883266	136883828	+	0	NA	intron (NM_000288, intron 8 of 9)	L2|LINE|L2	-38694	NM_001008783	340146	Hs.369703	NM_001008783	ENSG00000182747	SLC35D3	FRCL1	solute carrier family 35 member D3	protein-coding	0.008897	0.415631	
chunk0115_243_1	chr21	27491244	27491549	+	0	NA	Intergenic	Intergenic	-230983	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.006557	0.343137	
chunk0141_235_1	chr4	84892323	84893133	+	0	NA	intron (NM_014991, intron 3 of 67)	L2a|LINE|L2	73663	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.001235	0.346486	
chunk0132_184_1	chr3	157082326	157082879	+	0	NA	non-coding (NR_034007, exon 4 of 4)	non-coding (NR_034007, exon 4 of 4)	-7279	NR_034008	100498859	Hs.633655	NR_034008	ENSG00000241135	LINC00881	-	long intergenic non-protein coding RNA 881	ncRNA	0.018083	0.525271	
chunk0083_364_1	chr17	70913054	70913537	+	0	NA	Intergenic	MER53|DNA|hAT	288884	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.004141	0.314050	
chunk0182_268_1	chr7	97896956	97897253	+	0	NA	Intergenic	L1M2|LINE|L1	-24562	NM_001178076	440	Hs.489207	NM_001673	ENSG00000070669	ASNS	ASNSD|TS11	asparagine synthetase (glutamine-hydrolyzing)	protein-coding	0.006734	0.315436	
chunk0111_52_1	chr20	22594119	22594343	+	0	NA	intron (NR_109883, intron 1 of 2)	intron (NR_109883, intron 1 of 2)	-8768	NM_153675	3170	Hs.155651	NM_021784	ENSG00000125798	FOXA2	HNF3B|TCF3B	forkhead box A2	protein-coding	0.004464	0.377778	
chunk0211_47_1	chrX	108609579	108610016	+	0	NA	intron (NM_033380, intron 29 of 50)	L1ME2z|LINE|L1	126580	NM_003604	8471	Hs.407141	NM_003604	ENSG00000133124	IRS4	IRS-4|PY160	insulin receptor substrate 4	protein-coding	0.002288	0.287671	
chunk0102_59_1	chr2	142846254	142846494	+	0	NA	Intergenic	Helitron1Nb_Mam|RC|Helitron	-31252	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.012500	0.315353	
chunk0056_268_1	chr13	90083864	90084425	+	0	NA	intron (NR_047489, intron 3 of 5)	L1ME1|LINE|L1	35573	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.007130	0.318505	
chunk0061_406_1	chr14	64908730	64908929	+	0	NA	Intergenic	Intergenic	-5532	NM_145165	91612	Hs.731537	NM_145165	ENSG00000258289	CHURC1	C14orf52|My015|chch	churchill domain containing 1	protein-coding	0.015075	0.380000	
chunk0110_11_1	chr20	9972496	9973088	+	0	NA	Intergenic	L1MB7|LINE|L1	-13541	NR_109861	101929371	Hs.619265	NR_109861		PARAL1	-	PPARG activating RBM14 associated lncRNA 1	ncRNA	0.020270	0.399663	
chunk0012_14_1	chr1	154842623	154842969	+	0	NA	intron (NM_001204087, intron 1 of 8)	intron (NM_001204087, intron 1 of 8)	17066	NM_170782	3782	Hs.490765	NM_002249	ENSG00000143603	KCNN3	KCa2.3|SK3|SKCA3|hSK3	potassium calcium-activated channel subfamily N member 3	protein-coding	0.017341	0.521614	
chunk0203_300_1	chr9	89260602	89260845	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-50472	NM_001827	1164	Hs.83758	NM_001827	ENSG00000123975	CKS2	CKSHS2	CDC28 protein kinase regulatory subunit 2	protein-coding	0.008230	0.495902	
chunk0179_53_1	chr7	43570876	43571254	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	-12028	NM_004760	9263	Hs.709489	NM_004760	ENSG00000164543	STK17A	DRAK1	serine/threonine kinase 17a	protein-coding	0.000000	0.427441	
chunk0178_226_1	chr7	35688352	35688958	+	0	NA	intron (NM_022373, intron 2 of 8)	intron (NM_022373, intron 2 of 8)	6507	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.003300	0.357496	
chunk0160_302_1	chr5	158992359	158992843	+	0	NA	intron (NM_182708, intron 5 of 14)	intron (NM_182708, intron 5 of 14)	107179	NM_182708	1879	Hs.573143	NM_024007	ENSG00000164330	EBF1	COE1|EBF|O/E-1|OLF1	EBF transcription factor 1	protein-coding	0.002066	0.336082	252(TGGATCAGAATGTTCT,-,0.00),253(GGATCAGAATGTTCTT,+,0.00)
chunk0207_334_1	chr9	134369754	134370162	+	0	NA	intron (NM_002957, intron 1 of 9)	intron (NM_002957, intron 1 of 9)	-9337	NM_001291920	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.024510	0.599022	215(ATGAGCAGGGTGTACT,-,0.00)
chunk0162_248_1	chr6	5034724	5035206	+	0	NA	intron (NR_126018, intron 1 of 1)	Tigger17b|DNA|TcMar-Tigger	4993	NR_126018	100129461	Hs.131700	NR_126015	ENSG00000272142	LYRM4-AS1	-	LYRM4 antisense RNA 1	ncRNA	0.016598	0.436853	
chunk0084_373_1	chr17	81713899	81714130	+	0	NA	intron (NM_012140, intron 1 of 10)	intron (NM_012140, intron 1 of 10)	1778	NM_001270953	1468	Hs.548187	NM_012140	ENSG00000183048	SLC25A10	DIC	solute carrier family 25 member 10	protein-coding	0.038961	0.612069	
chunk0060_218_1	chr14	48905050	48905690	+	0	NA	Intergenic	L2a|LINE|L2	681046	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.001563	0.343214	
chunk0078_16_1	chr17	691068	691590	+	0	NA	intron (NM_001128159, intron 4 of 21)	L3|LINE|CR1	23527	NM_001128159	55275	Hs.461819	NM_018289	ENSG00000141252	VPS53	HCCS1|PCH2E|hVps53L|pp13624	VPS53 subunit of GARP complex	protein-coding	0.003831	0.399618	
chunk0027_435_1	chr10	81011697	81012313	+	0	NA	Intergenic	Intergenic	471186	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.006494	0.374392	
chunk0152_201_1	chr5	60010072	60010678	+	0	NA	intron (NM_001165899, intron 2 of 16)	intron (NM_001165899, intron 2 of 16)	-116581	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.004950	0.369028	386(CAGCACATTATGTTTT,-,0.00),387(AGCACATTATGTTTTC,+,0.00)
chunk0124_119_1	chr3	54175941	54176447	+	0	NA	intron (NM_018398, intron 2 of 37)	intron (NM_018398, intron 2 of 37)	53528	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.005929	0.408284	
chunk0038_299_1	chr11	90709435	90710073	+	0	NA	intron (NR_104190, intron 3 of 6)	intron (NR_104190, intron 3 of 6)	-153897	NR_039711	100616186		NR_039711	ENSG00000266703	MIR4490	-	microRNA 4490	ncRNA	0.001567	0.309859	
chunk0001_281_1	chr1	8725797	8726084	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	91700	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.003484	0.302083	
chunk0081_143_1	chr17	40687042	40687241	+	0	NA	Intergenic	Intergenic	16609	NM_019016	192666	Hs.87383	NM_019016	ENSG00000167916	KRT24	K24|KA24	keratin 24	protein-coding	0.020101	0.410000	
chunk0197_404_1	chr8	127197755	127198461	+	0	NA	promoter-TSS (NR_120364)	promoter-TSS (NR_120364)	-481	NR_120364	103021165	Hs.573407	NR_120364		CASC19	CARLO6|CARLo-6|LINC01245	cancer susceptibility 19	ncRNA	0.001416	0.390382	
chunk0213_3_1	chrY	19563443	19563768	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-3753	NR_045128	246126	Hs.522863	NM_001005852	ENSG00000131002	TXLNGY	CYorf15A|CYorf15B|TXLNG2P	taxilin gamma pseudogene, Y-linked	pseudo	0.000000	0.371166	
chunk0110_46_1	chr20	10591402	10591650	+	0	NA	intron (NM_001009608, intron 4 of 7)	intron (NM_001009608, intron 4 of 7)	58169	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.000000	0.389558	
chunk0197_259_1	chr8	123534477	123534916	+	0	NA	intron (NM_058229, intron 2 of 8)	intron (NM_058229, intron 2 of 8)	-2553	NM_148177	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.000000	0.372727	
chunk0063_401_1	chr14	88024223	88024700	+	0	NA	promoter-TSS (NR_046094)	promoter-TSS (NR_046094)	-89	NR_046094	283587	Hs.525513	NR_046094	ENSG00000258867	LINC01146	-	long intergenic non-protein coding RNA 1146	ncRNA	0.008386	0.399582	
chunk0200_395_1	chr9	27065423	27065728	+	0	NA	Intergenic	Intergenic	-43566	NM_000459	7010	Hs.89640	NM_000459	ENSG00000120156	TEK	CD202B|GLC3E|TIE-2|TIE2|VMCM|VMCM1	TEK receptor tyrosine kinase	protein-coding	0.003279	0.388889	
chunk0137_302_1	chr4	24076670	24077052	+	0	NA	Intergenic	HAL1|LINE|L1	-186784	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.005236	0.328982	
chunk0133_270_1	chr3	171943784	171944214	+	0	NA	Intergenic	MIRb|SINE|MIR	-43259	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.016279	0.375870	
chunk0098_415_1	chr2	80108854	80109145	+	0	NA	intron (NM_004389, intron 7 of 17)	intron (NM_004389, intron 7 of 17)	195363	NM_178839	347730	Hs.591580	NM_178839	ENSG00000162951	LRRTM1	-	leucine rich repeat transmembrane neuronal 1	protein-coding	0.003436	0.397260	
chunk0134_61_1	chr3	176154814	176155385	+	0	NA	Intergenic	Intergenic	-360004	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.010508	0.381119	
chunk0208_95_1	chrX	13538327	13538813	+	0	NA	Intergenic	Intergenic	-31005	NM_001167890	25975	Hs.12844	NM_015507	ENSG00000198759	EGFL6	MAEG|W80	EGF like domain multiple 6	protein-coding	0.006173	0.400411	
chunk0158_78_1	chr5	126365552	126366315	+	0	NA	intron (NM_001146319, intron 1 of 13)	intron (NM_001146319, intron 1 of 13)	5837	NM_001146319	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.005242	0.379581	
chunk0196_281_1	chr8	109312430	109312922	+	0	NA	intron (NM_001128211, intron 2 of 9)	L1ME3G|LINE|L1	17257	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.010163	0.361055	
chunk0118_7_1	chr22	25554403	25554745	+	0	NA	Intergenic	Intergenic	-10320	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.000000	0.486880	206(TAGCACACACTGTTCC,-,0.00),207(AGCACACACTGTTCCC,+,0.00)
chunk0071_443_1	chr15	90071263	90071561	+	0	NA	intron (NM_198526, intron 2 of 4)	intron (NM_198526, intron 2 of 4)	29209	NM_001289910	3418	Hs.596461	NM_002168	ENSG00000182054	IDH2	D2HGA2|ICD-M|IDH|IDHM|IDP|IDPM|mNADP-IDH	isocitrate dehydrogenase (NADP(+)) 2, mitochondrial	protein-coding	0.006711	0.387960	
chunk0003_286_1	chr1	37464214	37464476	+	0	NA	intron (NR_038842, intron 1 of 2)	Charlie21a|DNA|hAT-Charlie	10098	NR_038842	728431	Hs.380738	NR_038842	ENSG00000233621	LINC01137	-	long intergenic non-protein coding RNA 1137	ncRNA	0.003817	0.281369	
chunk0044_190_1	chr12	30438742	30439268	+	0	NA	Intergenic	Intergenic	238239	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.005703	0.337761	
chunk0122_88_1	chr3	30013184	30013776	+	0	NA	Intergenic	Intergenic	-79324	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.000000	0.391231	
chunk0088_46_1	chr18	43956183	43956934	+	0	NA	Intergenic	Intergenic	575139	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.002663	0.325798	
chunk0025_173_1	chr10	52809082	52809655	+	0	NA	Intergenic	Intergenic	-37668	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.005236	0.357143	
chunk0025_407_1	chr10	59586356	59586966	+	0	NA	Intergenic	Intergenic	123230	NM_194298	220963	Hs.499709	NM_194298	ENSG00000165449	SLC16A9	C10orf36|MCT9	solute carrier family 16 member 9	protein-coding	0.003279	0.445172	298(GAGAACAGTCTGCACT,-,0.00),299(AGAACAGTCTGCACTT,+,0.00)
chunk0065_260_1	chr14	101764514	101764729	+	0	NA	intron (NM_001161725, intron 2 of 15)	intron (NM_001161725, intron 2 of 15)	2823	NM_001161726	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.000000	0.430556	
chunk0059_131_1	chr14	31827328	31828027	+	0	NA	intron (NM_001201573, intron 6 of 8)	L4_A_Mam|LINE|RTE-X	113108	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.002861	0.390000	
chunk0074_307_1	chr16	30418033	30418242	+	0	NA	exon (NM_001142305, exon 3 of 3)	exon (NM_001142305, exon 3 of 3)	10723	NM_016643	51333	Hs.148584	NM_016643	ENSG00000179965	ZNF771	DSC43	zinc finger protein 771	protein-coding	0.157895	0.728571	
chunk0078_41_1	chr17	1096189	1096454	+	0	NA	intron (NM_001092, intron 2 of 21)	intron (NM_001092, intron 2 of 21)	12779	NM_001092	29	Hs.159306	NM_001092	ENSG00000159842	ABR	MDB	ABR activator of RhoGEF and GTPase	protein-coding	0.030189	0.571429	
chunk0164_313_1	chr6	25013939	25014138	+	0	NA	intron (NM_001286446, intron 1 of 13)	intron (NM_001286446, intron 1 of 13)	28130	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.010050	0.420000	
chunk0168_17_1	chr6	76865901	76866656	+	0	NA	Intergenic	LTR80B|LTR|ERVL	597125	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.007947	0.346561	
chunk0036_410_1	chr11	68138164	68138764	+	0	NA	Intergenic	L1ME3|LINE|L1	-17073	NM_212469	1119	Hs.77221	NM_001277	ENSG00000110721	CHKA	CHK|CK|CKI|EK	choline kinase alpha	protein-coding	0.010000	0.435940	294(AAGAACAGTGAGTGCC,-,0.00),295(AGAACAGTGAGTGCCC,+,0.00)
chunk0017_235_1	chr1	208114309	208114536	+	0	NA	intron (NM_025179, intron 4 of 31)	intron (NM_025179, intron 4 of 31)	129898	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.013216	0.500000	
chunk0129_455_1	chr3	128276925	128277213	+	0	NA	intron (NM_021937, intron 4 of 6)	intron (NM_021937, intron 4 of 6)	123612	NM_021937	60678	Hs.477498	NM_021937	ENSG00000132394	EEFSEC	EFSEC|SELB	eukaryotic elongation factor, selenocysteine-tRNA specific	protein-coding	0.010417	0.598616	46(AAGCACAGCAAGTACT,-,0.00),47(AGCACAGCAAGTACTG,+,0.00)
chunk0049_348_1	chr12	95259216	95259859	+	0	NA	intron (NM_017599, intron 3 of 11)	MIR|SINE|MIR	41791	NM_017599	55591	Hs.24135	NM_017599	ENSG00000028203	VEZT	VEZATIN	vezatin, adherens junctions transmembrane protein	protein-coding	0.004666	0.369565	
chunk0204_453_1	chr9	104418491	104418690	+	0	NA	Intergenic	Intergenic	-85673	NM_001004485	138805	Hs.553602	NM_001004485	ENSG00000186881	OR13F1	OR9-6	olfactory receptor family 13 subfamily F member 1	protein-coding	0.010050	0.355000	
chunk0095_412_1	chr2	24545120	24545759	+	0	NA	Intergenic	L1MC3|LINE|L1	-39038	NM_003743	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.003130	0.407813	
chunk0063_8_1	chr14	76143461	76143712	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-8299	NM_017926	55668	Hs.410231	NM_017926	ENSG00000089916	GPATCH2L	C14orf118	G-patch domain containing 2 like	protein-coding	0.015936	0.404762	
chunk0047_52_1	chr12	67299505	67300017	+	0	NA	intron (NM_018448, intron 7 of 14)	intron (NM_018448, intron 7 of 14)	30480	NM_018448	55832	Hs.546407	NM_018448	ENSG00000111530	CAND1	TIP120|TIP120A	cullin associated and neddylation dissociated 1	protein-coding	0.003906	0.331384	
chunk0035_314_1	chr11	47269034	47269272	+	0	NA	promoter-TSS (NM_130476)	promoter-TSS (NM_130476)	-223	NM_130470	8567	Hs.82548	NM_003682	ENSG00000110514	MADD	DENN|IG20|RAB3GEP	MAP kinase activating death domain	protein-coding	0.025210	0.518828	
chunk0069_414_1	chr15	68021929	68022646	+	0	NA	Intergenic	Intergenic	-31947	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.019526	0.506964	260(AAGAACTTGTTGTACT,-,0.00),261(AGAACTTGTTGTACTT,+,0.00)
chunk0002_353_1	chr1	25681770	25682585	+	0	NA	intron (NM_001289010, intron 1 of 11)	L3|LINE|CR1	64709	NM_020379	57134	Hs.197043	NM_020379	ENSG00000117643	MAN1C1	HMIC|MAN1A3|MAN1C|pp6318	mannosidase alpha class 1C member 1	protein-coding	0.007362	0.432598	743(AAGAACACTATGTCAT,-,0.00)
chunk0143_289_1	chr4	118276479	118277160	+	0	NA	Intergenic	Intergenic	-1943	NR_003584	100093630	Hs.535762	NR_003584	ENSG00000269893	SNHG8	LINC00060|NCRNA00060	small nucleolar RNA host gene 8	ncRNA	0.004405	0.322581	317(CTGAACAAGATGTTCA,-,0.00),318(TGAACAAGATGTTCAG,+,0.00)
chunk0153_178_1	chr5	71565506	71565730	+	0	NA	3' UTR (NM_018429, exon 39 of 39)	3' UTR (NM_018429, exon 39 of 39)	-21670	NM_022132	64087	Hs.604789	NM_022132	ENSG00000131844	MCCC2	MCCB	methylcrotonoyl-CoA carboxylase 2	protein-coding	0.017857	0.413333	
chunk0015_98_1	chr1	185068450	185068685	+	0	NA	intron (NM_007212, intron 1 of 6)	MLT1D|LTR|ERVL-MaLR	23148	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.000000	0.478814	
chunk0107_165_1	chr2	215417387	215417823	+	0	NA	intron (NM_001306131, intron 12 of 44)	intron (NM_001306131, intron 12 of 44)	18463	NM_212476	2335	Hs.203717	NM_002026	ENSG00000115414	FN1	CIG|ED-B|FINC|FN|FNZ|GFND|GFND2|LETS|MSF|SMDCF	fibronectin 1	protein-coding	0.006881	0.400458	337(GGGATCTTGCTGTTCT,-,0.00),338(GGATCTTGCTGTTCTC,+,0.00)
chunk0191_82_1	chr8	47604752	47605040	+	0	NA	intron (NM_001080394, intron 10 of 19)	L2c|LINE|L2	133268	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.017361	0.453287	
chunk0110_325_1	chr20	19106500	19106754	+	0	NA	Intergenic	MIRb|SINE|MIR	-106019	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.011811	0.435294	
chunk0093_124_1	chr19	45175731	45176030	+	0	NA	intron (NM_001270891, intron 1 of 5)	L2a|LINE|L2	2363	NM_024108	79090	Hs.466929	NM_024108	ENSG00000007255	TRAPPC6A	TRS33	trafficking protein particle complex 6A	protein-coding	0.003344	0.483333	
chunk0167_121_1	chr6	60869924	60870217	+	0	NA	Intergenic	L2a|LINE|L2	-704033	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.003413	0.435374	242(CAAAACATTATGTACC,-,0.00),243(AAAACATTATGTACCC,+,0.00)
chunk0074_86_1	chr16	21952916	21953471	+	0	NA	5' UTR (NM_003366, exon 1 of 14)	5' UTR (NM_003366, exon 1 of 14)	129	NM_003366	7385	Hs.528803	NM_003366	ENSG00000140740	UQCRC2	MC3DN5|QCR2|UQCR2	ubiquinol-cytochrome c reductase core protein 2	protein-coding	0.048649	0.535971	
chunk0125_443_1	chr3	72812250	72812672	+	0	NA	intron (NM_018130, intron 9 of 10)	intron (NM_018130, intron 9 of 10)	35986	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.004739	0.340426	
chunk0186_132_1	chr7	138460376	138460592	+	0	NA	5' UTR (NM_003852, exon 1 of 19)	5' UTR (NM_003852, exon 1 of 19)	150	NM_015905	8805	Hs.490287	NM_003852	ENSG00000122779	TRIM24	PTC6|RNF82|TF1A|TIF1|TIF1A|TIF1ALPHA|hTIF1	tripartite motif containing 24	protein-coding	0.125000	0.755760	
chunk0052_132_1	chr13	23580501	23580700	+	0	NA	intron (NM_018647, intron 1 of 8)	intron (NM_018647, intron 1 of 8)	1240	NM_018647	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.010050	0.395000	
chunk0077_55_1	chr16	76432230	76432500	+	0	NA	intron (NM_138994, intron 4 of 22)	intron (NM_138994, intron 4 of 22)	122527	NM_138994	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.003704	0.365314	
chunk0192_109_1	chr8	61674291	61674644	+	0	NA	TTS (NM_001164756)	TTS (NM_001164756)	15382	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.000000	0.336158	
chunk0068_227_1	chr15	55318898	55319437	+	0	NA	promoter-TSS (NM_001308423)	promoter-TSS (NM_001308423)	27	NM_001308421	101928527	Hs.493512	NM_001308421	ENSG00000225973	PIGBOS1	HP06981	PIGB opposite strand 1	protein-coding	0.076067	0.598148	
chunk0062_69_1	chr14	67589347	67589770	+	0	NA	TTS (NM_020715)	TTS (NM_020715)	10742	NM_004569	5283	Hs.553497	NM_004569	ENSG00000100564	PIGH	GPI-H	phosphatidylinositol glycan anchor biosynthesis class H	protein-coding	0.004728	0.365566	
chunk0171_407_1	chr6	131264349	131264742	+	0	NA	intron (NM_138633, intron 2 of 2)	intron (NM_138633, intron 2 of 2)	14386	NM_004842	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.000000	0.335025	
chunk0201_256_1	chr9	38178326	38178678	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-109289	NM_003028	6461	Hs.521482	NM_003028	ENSG00000107338	SHB	bA3J10.2	SH2 domain containing adaptor protein B	protein-coding	0.002841	0.430595	
chunk0125_145_1	chr3	66220162	66220701	+	0	NA	promoter-TSS (NM_001164796)	promoter-TSS (NM_001164796)	-311	NM_001164796	115286	Hs.379386	NM_173471	ENSG00000144741	SLC25A26	COXPD28|SAMC	solute carrier family 25 member 26	protein-coding	0.020408	0.355556	
chunk0056_262_1	chr13	90012118	90012515	+	0	NA	Intergenic	Intergenic	107401	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.005038	0.321608	
chunk0131_23_1	chr3	142147502	142148022	+	0	NA	intron (NM_001178138, intron 1 of 13)	intron (NM_001178138, intron 1 of 13)	1782	NM_001178138	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.001923	0.358925	246(AGGCACAAGATGTTCT,-,0.00),247(GGCACAAGATGTTCTA,+,0.00)
chunk0070_242_1	chr15	73150677	73151094	+	0	NA	intron (NM_002499, intron 5 of 28)	L1ME2z|LINE|L1	98401	NM_002499	4756	Hs.388613	NM_002499	ENSG00000067141	NEO1	IGDCC2|NGN|NTN1R2	neogenin 1	protein-coding	0.002398	0.368421	
chunk0072_308_1	chr15	98778886	98779455	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	-5256	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.007030	0.347368	
chunk0173_204_1	chr6	145362789	145363335	+	0	NA	Intergenic	L1ME4b|LINE|L1	-371807	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.003663	0.319927	300(GAAAACACTGTGTTCT,-,0.00),301(AAAACACTGTGTTCTC,+,0.00)
chunk0121_58_1	chr3	15673377	15674115	+	0	NA	intron (NM_015199, intron 27 of 27)	L2a|LINE|L2	23625	NR_036085	100422990		NR_036085	ENSG00000264354	MIR3134	-	microRNA 3134	ncRNA	0.002710	0.420839	346(GGGGACAGAGTGTTCA,-,0.00),347(GGGACAGAGTGTTCAG,+,0.00)
chunk0207_278_1	chr9	132643295	132643770	+	0	NA	intron (NM_022779, intron 13 of 19)	MIR|SINE|MIR	-26809	NM_012204	9329	Hs.22302	NM_012204	ENSG00000125484	GTF3C4	KAT12|TF3C-delta|TFIII90|TFIIIC290|TFIIIC90|TFIIICDELTA	general transcription factor IIIC subunit 4	protein-coding	0.018947	0.466387	
chunk0172_212_1	chr6	136726699	136727415	+	0	NA	intron (NM_005923, intron 1 of 29)	intron (NM_005923, intron 1 of 29)	65461	NM_005923	4217	Hs.186486	NM_005923	ENSG00000197442	MAP3K5	ASK1|MAPKKK5|MEKK5	mitogen-activated protein kinase kinase kinase 5	protein-coding	0.004190	0.298466	
chunk0186_311_1	chr7	142969366	142969670	+	0	NA	Intergenic	Intergenic	-7102	NM_000420	3792	Hs.368588	NM_000420	ENSG00000197993	KEL	CD238|ECE3	Kell metallo-endopeptidase (Kell blood group)	protein-coding	0.013158	0.422951	121(GGGAACACGCAGTACT,-,0.00),122(GGAACACGCAGTACTG,+,0.00)
chunk0116_353_1	chr21	41568702	41569155	+	0	NA	Intergenic	MIR|SINE|MIR	-60770	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.026490	0.502203	24(CTGCACAGATTGTCCA,-,0.00),25(TGCACAGATTGTCCAG,+,0.00)
chunk0195_289_1	chr8	98568306	98569082	+	0	NA	intron (NM_006281, intron 8 of 10)	HAL1|LINE|L1	141672	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.003866	0.341055	
chunk0208_235_1	chrX	19670291	19670703	+	0	NA	intron (NM_031892, intron 6 of 17)	intron (NM_031892, intron 6 of 17)	504	NM_001184960	30011	Hs.726365	NM_031892	ENSG00000147010	SH3KBP1	AGMX2|CD2BP3|CIN85|GIG10|HSB-1|HSB1|IMD61|MIG18	SH3 domain containing kinase binding protein 1	protein-coding	0.012136	0.433414	
chunk0103_383_1	chr2	168678374	168678943	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	95715	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.007030	0.422807	
chunk0075_154_1	chr16	51507693	51508289	+	0	NA	Intergenic	Intergenic	-254528	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.006711	0.371859	
chunk0204_155_1	chr9	95807306	95807714	+	0	NA	non-coding (NR_023390, exon 3 of 3)	non-coding (NR_023390, exon 3 of 3)	-68108	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.012255	0.449878	
chunk0132_296_1	chr3	160179640	160180395	+	0	NA	intron (NR_108088, intron 3 of 9)	intron (NR_108088, intron 3 of 9)	27075	NR_108088	101928376	Hs.565865	NR_108088	ENSG00000244040	IL12A-AS1	ILAS1-AS1	IL12A antisense RNA 1	ncRNA	0.006623	0.351852	
chunk0160_229_1	chr5	155546022	155546590	+	0	NA	Intergenic	MER54A|LTR|ERVL	532606	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.000000	0.400703	
chunk0176_361_1	chr7	18319302	18319555	+	0	NA	intron (NM_001204144, intron 2 of 12)	intron (NM_001204144, intron 2 of 12)	-176318	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.003953	0.287402	
chunk0143_429_1	chr4	123849415	123849989	+	0	NA	intron (NR_027105, intron 3 of 4)	intron (NR_027105, intron 3 of 4)	75438	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.005226	0.351304	
chunk0043_412_1	chr12	25824588	25825147	+	0	NA	Intergenic	Intergenic	49212	NR_036188	100422897		NR_036188	ENSG00000283603	MIR4302	-	microRNA 4302	ncRNA	0.007156	0.446429	410(AGCACACACTCTCCCT,+,0.00)
chunk0150_341_1	chr5	38582850	38583121	+	0	NA	intron (NR_103553, intron 1 of 2)	intron (NR_103553, intron 1 of 2)	12420	NM_002310	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.025830	0.422794	
chunk0024_128_1	chr10	34954011	34954540	+	0	NA	Intergenic	Intergenic	120055	NM_001198778	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.011342	0.473585	
chunk0022_291_1	chr10	15472097	15472365	+	0	NA	Intergenic	Intergenic	-101172	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.011194	0.446097	21(GAGGACAGTGTGTATC,-,0.00),22(AGGACAGTGTGTATCA,+,0.00)
chunk0160_308_1	chr5	159148733	159149014	+	0	NA	Intergenic	Intergenic	48390	NR_109890	101927740	Hs.738721	NR_109890	ENSG00000245812	LINC02202	-	long intergenic non-protein coding RNA 2202	ncRNA	0.000000	0.343972	85(AAGGACATAGTGTTTC,-,0.00),86(AGGACATAGTGTTTCT,+,0.00)
chunk0014_182_1	chr1	178690370	178691098	+	0	NA	Intergenic	Intergenic	12985	NR_039622	100616328		NR_039622	ENSG00000266417	MIR4424	-	microRNA 4424	ncRNA	0.010989	0.412894	
chunk0107_106_1	chr2	214147383	214147963	+	0	NA	intron (NR_047659, intron 16 of 17)	intron (NR_047659, intron 16 of 17)	-264064	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.003448	0.328744	37(AAGAACATCAAGTCCA,-,0.00),38(AGAACATCAAGTCCAT,+,0.00)
chunk0191_47_1	chr8	43305110	43305724	+	0	NA	intron (NM_001002920, intron 5 of 12)	Zaphod2|DNA|hAT-Tip100	12975	NM_001005365	340441	Hs.531579	NM_001002920	ENSG00000188877	POTEA	A26A1|CT104.3|POTE-8|POTE8	POTE ankyrin domain family member A	protein-coding	0.006515	0.409756	
chunk0162_242_1	chr6	4910111	4910452	+	0	NA	intron (NR_026590, intron 4 of 8)	intron (NR_026590, intron 4 of 8)	20289	NM_001143971	9425	Hs.269092	NM_004824	ENSG00000153046	CDYL	CDYL1	chromodomain Y like	protein-coding	0.011730	0.423977	
chunk0052_311_1	chr12	124940479	124940799	+	0	NA	Intergenic	L2a|LINE|L2	25092	NR_049820	100847004		NR_049820	ENSG00000265345	MIR5188	mir-5188	microRNA 5188	ncRNA	0.031250	0.523364	
chunk0064_216_1	chr14	93298034	93298339	+	0	NA	intron (NM_001002860, intron 1 of 10)	intron (NM_001002860, intron 1 of 10)	34906	NM_001289133	55727	Hs.525549	NM_018167	ENSG00000011114	BTBD7	FUP1	BTB domain containing 7	protein-coding	0.019672	0.352941	
chunk0090_460_1	chr18	80182068	80182557	+	0	NA	intron (NM_032510, intron 2 of 2)	intron (NM_032510, intron 2 of 2)	34388	NR_028339	100130522	Hs.352602	NM_001145731	ENSG00000267270	PARD6G-AS1	-	PARD6G antisense RNA 1	ncRNA	0.006135	0.534694	
chunk0146_334_1	chr4	165867015	165867433	+	0	NA	Intergenic	Intergenic	-6034	NM_001204760	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.002392	0.295943	211(CAGCACACTGTGTTTT,-,0.00),212(AGCACACTGTGTTTTT,+,0.00)
chunk0167_297_1	chr6	71209593	71210119	+	0	NA	Intergenic	Intergenic	-78918	NM_024576	79627	Hs.648434	NM_024576	ENSG00000119900	OGFRL1	dJ331H24.1	opioid growth factor receptor like 1	protein-coding	0.000000	0.341556	
chunk0145_430_1	chr4	153121538	153121802	+	0	NA	Intergenic	Intergenic	-31448	NM_001130067	23321	Hs.435711	NM_015271	ENSG00000109654	TRIM2	CMT2R|RNF86	tripartite motif containing 2	protein-coding	0.011364	0.418868	
chunk0071_145_1	chr15	82750234	82750456	+	0	NA	promoter-TSS (NR_110100)	promoter-TSS (NR_110100)	-219	NR_110099	100505616	Hs.513091	NR_110096	ENSG00000250988	SNHG21	FSD2-AS1|SCARNA15HG	small nucleolar RNA host gene 21	ncRNA	0.063063	0.578475	
chunk0115_317_1	chr21	28737793	28738042	+	0	NA	Intergenic	Intergenic	147456	NM_013240	29104	Hs.163846	NM_013240	ENSG00000156239	N6AMT1	C21orf127|HEMK2|MTQ2|N6AMT|PRED28|m.HsaHemK2P	N-6 adenine-specific DNA methyltransferase 1	protein-coding	0.004016	0.472000	
chunk0209_169_1	chrX	43615436	43616080	+	0	NA	Intergenic	L2|LINE|L2	-39149	NM_001270458	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.012422	0.437209	378(GAGAACATTGAGTGCT,-,0.00),379(AGAACATTGAGTGCTC,+,0.00)
chunk0128_142_1	chr3	106829045	106829369	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	411431	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.009259	0.396923	
chunk0205_374_1	chr9	113979476	113980154	+	0	NA	intron (NM_133374, intron 2 of 13)	L2a|LINE|L2	98657	NM_001633	259	Hs.436911	NM_001633	ENSG00000106927	AMBP	A1M|EDC1|HCP|HI30|IATIL|ITI|ITIL|ITILC|UTI	alpha-1-microglobulin/bikunin precursor	protein-coding	0.008850	0.472754	
chunk0189_261_1	chr8	25250544	25250925	+	0	NA	intron (NM_024940, intron 2 of 51)	L2a|LINE|L2	65962	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.010499	0.437173	
chunk0154_45_1	chr5	77168336	77169491	+	0	NA	Intergenic	Intergenic	-41968	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.013853	0.525087	114(CAGAACTGCCTGTGCA,-,0.00),115(AGAACTGCCTGTGCAG,+,0.00)
chunk0003_426_1	chr1	40930067	40930574	+	0	NA	Intergenic	Intergenic	-48979	NM_001905	1503	Hs.473087	NM_001905	ENSG00000171793	CTPS1	CTPS|GATD5|IMD24	CTP synthase 1	protein-coding	0.005917	0.505906	
chunk0179_211_1	chr7	47598304	47598557	+	0	NA	Intergenic	HUERS-P2-int|LTR|ERV1	-16286	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.003953	0.488189	
chunk0023_85_1	chr10	22325025	22325274	+	0	NA	intron (NM_005180, intron 1 of 9)	intron (NM_005180, intron 1 of 9)	3939	NM_005180	648	Hs.380403	NM_005180	ENSG00000168283	BMI1	FLVI2/BMI1|PCGF4|RNF51|flvi-2/bmi-1	BMI1 proto-oncogene, polycomb ring finger	protein-coding	0.024096	0.400000	
chunk0187_395_1	chr7	157839910	157840273	+	0	NA	intron (NM_001308268, intron 12 of 22)	intron (NM_001308268, intron 12 of 22)	-14494	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.038567	0.543956	
chunk0121_154_1	chr3	19194160	19194473	+	0	NA	intron (NM_144633, intron 1 of 15)	intron (NM_144633, intron 1 of 15)	45791	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.000000	0.312102	
chunk0146_272_1	chr4	163109730	163110407	+	0	NA	Intergenic	Intergenic	-16440	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.002954	0.371681	365(CAGAACATACAGTACT,-,0.00),366(AGAACATACAGTACTT,+,0.00)
chunk0176_438_1	chr7	19970158	19970903	+	0	NA	intron (NR_110114, intron 3 of 5)	L2a|LINE|L2	169896	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.002685	0.355228	
chunk0192_52_1	chr8	59394795	59395139	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-275759	NM_014729	9760	Hs.491805	NM_014729	ENSG00000198846	TOX	TOX1	thymocyte selection associated high mobility group box	protein-coding	0.002907	0.394203	
chunk0205_232_1	chr9	109963130	109963454	+	0	NA	intron (NM_147150, intron 6 of 9)	intron (NM_147150, intron 6 of 9)	-85306	NM_001004065	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.003086	0.433846	
chunk0159_208_1	chr5	140548159	140548422	+	0	NA	intron (NM_003732, intron 1 of 2)	intron (NM_003732, intron 1 of 2)	624	NM_003732	8637	Hs.594084	NM_003732	ENSG00000243056	EIF4EBP3	4E-BP3|4EBP3	eukaryotic translation initiation factor 4E binding protein 3	protein-coding	0.041825	0.590909	
chunk0017_95_1	chr1	205823665	205824402	+	0	NA	Intergenic	L1MA8|LINE|L1	-10837	NM_173854	254428	Hs.20274	NM_173854	ENSG00000133065	SLC41A1	MgtE	solute carrier family 41 member 1	protein-coding	0.004071	0.383469	
chunk0094_37_1	chr2	1835302	1836003	+	0	NA	intron (NM_015025, intron 21 of 24)	intron (NM_015025, intron 21 of 24)	-91105	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.017118	0.492877	
chunk0059_312_1	chr14	36401161	36401576	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	-80692	NM_001308110	51562	Hs.368647	NM_016586	ENSG00000151332	MBIP	-	MAP3K12 binding inhibitory protein 1	protein-coding	0.000000	0.362981	
chunk0098_113_1	chr2	68440613	68440912	+	0	NA	Intergenic	Intergenic	26496	NM_001024680	554251	Hs.164117	NM_001024680	ENSG00000204923	FBXO48	-	F-box protein 48	protein-coding	0.010033	0.426667	
chunk0013_43_1	chr1	166978404	166978787	+	0	NA	intron (NM_001286378, intron 1 of 12)	MER5A|DNA|hAT-Charlie	3013	NM_001286378	84944	Hs.651245	NM_032858	ENSG00000143194	MAEL	CT128|SPATA35	maelstrom spermatogenic transposon silencer	protein-coding	0.000000	0.424479	
chunk0029_292_1	chr10	103923927	103924693	+	0	NA	Intergenic	Intergenic	-6023	NM_024928	79991	Hs.62314	NM_024928	ENSG00000107960	STN1	AAF-44|AAF44|OBFC1|RPA-32|bA541N10.2	STN1 subunit of CST complex	protein-coding	0.000000	0.372881	
chunk0203_6_1	chr9	82604966	82605499	+	0	NA	Intergenic	Intergenic	457896	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.005629	0.398876	
chunk0079_250_1	chr17	16121954	16122161	+	0	NA	intron (NM_006311, intron 15 of 45)	MIR|SINE|MIR	72582	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.004831	0.394231	
chunk0212_109_1	chrY	17387478	17388018	+	0	NA	Intergenic	Intergenic	-113210	NR_028084	100302526	Hs.434364	NR_028084		FAM41AY2	-	family with sequence similarity 41 member A, Y-linked 2	ncRNA	0.003704	0.336414	254(TAAGACATGATGTTCT,-,0.00),255(AAGACATGATGTTCTT,+,0.00)
chunk0027_133_1	chr10	74384590	74385098	+	0	NA	intron (NM_001123, intron 4 of 10)	intron (NM_001123, intron 4 of 10)	144480	NR_120673	102723439		NR_120673		LOC102723439	-	uncharacterized LOC102723439	ncRNA	0.007874	0.390963	
chunk0153_172_1	chr5	71483982	71484273	+	0	NA	intron (NM_018429, intron 8 of 38)	intron (NM_018429, intron 8 of 38)	28512	NM_018429	55814	Hs.258272	NM_018429	ENSG00000145734	BDP1	DFNB112|HSA238520|TAF3B1|TFC5|TFIIIB''|TFIIIB150|TFIIIB90|TFNR	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	protein-coding	0.000000	0.376712	
chunk0064_203_1	chr14	92972885	92973551	+	0	NA	intron (NM_001142594, intron 5 of 10)	intron (NM_001142594, intron 5 of 10)	50118	NM_001301690	1113	Hs.150793	NM_001275	ENSG00000100604	CHGA	CGA	chromogranin A	protein-coding	0.019520	0.530735	168(AAGAACACGCTGTCCC,-,0.00),169(AGAACACGCTGTCCCA,+,0.00)
chunk0180_272_1	chr7	69687872	69688691	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	89362	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.007326	0.360976	553(GAGTACAGGCTGTGCA,-,0.00),554(AGTACAGGCTGTGCAT,+,0.00)
chunk0081_445_1	chr17	49108247	49108446	+	0	NA	Intergenic	Intergenic	-24114	NM_001159388	124872	Hs.374679	NM_153446	ENSG00000167080	B4GALNT2	B4GALT|GALGT2	beta-1,4-N-acetyl-galactosaminyltransferase 2	protein-coding	0.020101	0.460000	
chunk0131_85_1	chr3	143306429	143306738	+	0	NA	intron (NM_173653, intron 14 of 15)	L2a|LINE|L2	-35663	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.003236	0.429032	
chunk0135_204_1	chr3	188294425	188295048	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	69331	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.008026	0.386218	223(GGGTACTGACAGTCCT,-,0.00),224(GGTACTGACAGTCCTG,+,0.00)
chunk0209_419_1	chrX	57074327	57075018	+	0	NA	Intergenic	L1MD3|LINE|L1	46874	NM_001006681	474343	Hs.460717	NM_001006681	ENSG00000186787	SPIN2B	SPIN-2|SPIN-2B|SPIN2_duplicate|TDRD26|dJ323P24.2	spindlin family member 2B	protein-coding	0.008683	0.390173	
chunk0169_359_1	chr6	106764522	106764989	+	0	NA	intron (NR_033557, intron 1 of 6)	L2-3_Crp|LINE|L2	-19370	NR_030314	693172		NR_030314	ENSG00000207577	MIR587	MIRN587|hsa-mir-587	microRNA 587	ncRNA	0.002141	0.431624	
chunk0095_418_1	chr2	24644789	24645310	+	0	NA	intron (NM_147223, intron 2 of 21)	intron (NM_147223, intron 2 of 21)	60572	NM_147223	8648	Hs.596314	NM_003743	ENSG00000084676	NCOA1	F-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74	nuclear receptor coactivator 1	protein-coding	0.009597	0.398467	
chunk0018_272_1	chr1	220552883	220553643	+	0	NA	intron (NM_001286128, intron 1 of 15)	ERVL-int|LTR|ERVL	25080	NM_001286129	4139	Hs.497806	NM_018650	ENSG00000116141	MARK1	MARK|Par-1c|Par1c	microtubule affinity regulating kinase 1	protein-coding	0.002632	0.429698	
chunk0052_138_1	chr13	23733601	23734064	+	0	NA	intron (NM_005932, intron 18 of 18)	intron (NM_005932, intron 18 of 18)	154472	NM_018647	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.002160	0.381466	291(CAAAACACAGTGTTCT,-,0.00),292(AAAACACAGTGTTCTT,+,0.00)
chunk0041_70_1	chr11	123678012	123678211	+	0	NA	Intergenic	LTR33C|LTR|ERVL	-23504	NM_018400	55800	Hs.4865	NM_018400	ENSG00000166257	SCN3B	ATFB16|BRGDA7|HSA243396|SCNB3	sodium voltage-gated channel beta subunit 3	protein-coding	0.005025	0.425000	
chunk0098_106_1	chr2	68187226	68187723	+	0	NA	intron (NM_000945, intron 3 of 5)	intron (NM_000945, intron 3 of 5)	29601	NM_020143	56902	Hs.262858	NM_020143	ENSG00000115946	PNO1	KHRBP1|RRP20	partner of NOB1 homolog	protein-coding	0.004024	0.313253	
chunk0130_297_1	chr3	136943600	136944012	+	0	NA	intron (NM_001190796, intron 1 of 2)	L2c|LINE|L2	13331	NM_001190796	4690	Hs.126889	NM_006153	ENSG00000158092	NCK1	NCK|NCKalpha|nck-1	NCK adaptor protein 1	protein-coding	0.009709	0.375303	
chunk0087_224_1	chr18	36188175	36188518	+	0	NA	intron (NM_017947, intron 1 of 14)	intron (NM_017947, intron 1 of 14)	829	NM_017947	55034	Hs.405028	NM_017947	ENSG00000075643	MOCOS	HMCS|MCS|MOS	molybdenum cofactor sulfurase	protein-coding	0.023324	0.514535	
chunk0211_82_1	chrX	110103806	110104624	+	0	NA	intron (NM_032227, intron 3 of 6)	Tigger2b_Pri|DNA|TcMar-Tigger	22097	NR_039774	100616491		NR_039774	ENSG00000265584	MIR3978	-	microRNA 3978	ncRNA	0.007335	0.365079	439(TAGTACATACTGTACT,-,0.00),440(AGTACATACTGTACTC,+,0.00)
chunk0106_14_1	chr2	195457297	195457496	+	0	NA	Intergenic	Intergenic	-199412	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.000000	0.285000	
chunk0180_334_1	chr7	72783999	72784386	+	0	NA	intron (NM_001145440, intron 6 of 13)	intron (NM_001145440, intron 6 of 13)	44042	NM_001145440	441250	Hs.488614	NM_001145440	ENSG00000277149	TYW1B	LINC00069|NCRNA00069|RSAFD2	tRNA-yW synthesizing protein 1 homolog B	protein-coding	0.000000	0.394330	
chunk0202_89_1	chr9	72041735	72042190	+	0	NA	Intergenic	Intergenic	18643	NM_001128618	138240	Hs.371235	NM_001128618	ENSG00000204669	C9orf57	-	chromosome 9 open reading frame 57	protein-coding	0.015385	0.427632	166(AAGAACACGCTGCACT,-,0.00),167(AGAACACGCTGCACTC,+,0.00)
chunk0186_138_1	chr7	138569596	138570086	+	0	NA	intron (NM_015905, intron 10 of 18)	L1ME2z|LINE|L1	94383	NM_174959	136306	Hs.99414	NM_174959	ENSG00000157703	SVOPL	-	SVOP like	protein-coding	0.002041	0.386965	283(GGGAACATTTTGTTCT,-,0.00),284(GGAACATTTTGTTCTA,+,0.00)
chunk0103_21_1	chr2	159041052	159041510	+	0	NA	intron (NM_001145909, intron 2 of 26)	L1PA6|LINE|L1	72647	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.010917	0.544662	
chunk0155_181_1	chr5	94433315	94433922	+	0	NA	intron (NM_001145678, intron 14 of 20)	MIR|SINE|MIR	184986	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.008237	0.360197	
chunk0016_59_1	chr1	193333770	193334001	+	0	NA	intron (NR_125789, intron 1 of 3)	intron (NR_125789, intron 1 of 3)	29140	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.004329	0.491379	
chunk0049_220_1	chr12	93409781	93410307	+	0	NA	exon (NM_003348, exon 4 of 4)	exon (NM_003348, exon 4 of 4)	31494	NM_001301022	11163	Hs.506325	NM_019094	ENSG00000173598	NUDT4	DIPP-2B|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P|NUDT4B	nudix hydrolase 4	protein-coding	0.007605	0.347249	
chunk0137_229_1	chr4	20074518	20074892	+	0	NA	Intergenic	Intergenic	-177200	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.005348	0.378667	
chunk0003_194_1	chr1	34406630	34406835	+	0	NA	Intergenic	Intergenic	229780	NM_001134734	84970	Hs.194610	NM_032884	ENSG00000142698	C1orf94	-	chromosome 1 open reading frame 94	protein-coding	0.009756	0.480583	
chunk0015_346_1	chr1	190022139	190022691	+	0	NA	Intergenic	L1MC1|LINE|L1	455214	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.001812	0.323689	
chunk0171_92_1	chr6	121940596	121941188	+	0	NA	Intergenic	L1M4|LINE|L1	-458659	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.003378	0.313659	
chunk0181_175_1	chr7	82965291	82965564	+	0	NA	intron (NM_014510, intron 4 of 19)	intron (NM_014510, intron 4 of 19)	197454	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.003663	0.266423	
chunk0183_159_1	chr7	105962760	105963452	+	0	NA	promoter-TSS (NM_152750)	promoter-TSS (NM_152750)	-105	NM_001301161	222256	Hs.150120	NM_152750	ENSG00000128536	CDHR3	CDH28	cadherin related family member 3	protein-coding	0.015896	0.494949	373(AAGAACAAACAGTCCT,-,0.00),374(AGAACAAACAGTCCTG,+,0.00)
chunk0100_257_1	chr2	113206366	113206877	+	0	NA	Intergenic	MIR|SINE|MIR	-28906	NR_047570	654433	Hs.656660	NR_015377	ENSG00000189223	PAX8-AS1	-	PAX8 antisense RNA 1	ncRNA	0.011742	0.507812	
chunk0111_109_1	chr20	23756029	23756609	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-5382	NM_001898	1469	Hs.123114	NM_001898	ENSG00000170373	CST1	-	cystatin SN	protein-coding	0.015517	0.454389	
chunk0203_251_1	chr9	87450803	87451688	+	0	NA	Intergenic	Intergenic	-45983	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.010169	0.379233	231(GAGCACACTCTGTTTA,-,0.00)
chunk0150_259_1	chr5	36390148	36390825	+	0	NA	Intergenic	Intergenic	-88577	NM_001161429	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.011817	0.463127	
chunk0023_23_1	chr10	21021908	21022107	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	-124405	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.020101	0.505000	
chunk0137_308_1	chr4	24472814	24473329	+	0	NA	Intergenic	CpG	47219	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.122330	0.711240	239(GGGGACAGCCTGTACT,-,0.00),240(GGGACAGCCTGTACTA,+,0.00)
chunk0140_311_1	chr4	73088575	73088774	+	0	NA	intron (NM_032217, intron 29 of 33)	intron (NM_032217, intron 29 of 33)	-18915	NM_001297733	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.005025	0.230000	28(GGCACATAATGATCTA,+,0.00)
chunk0053_442_1	chr13	39700061	39700260	+	0	NA	intron (NM_020751, intron 13 of 18)	L5|LINE|RTE-X	-36025	NR_036190	100422940		NR_036190	ENSG00000264171	MIR4305	-	microRNA 4305	ncRNA	0.000000	0.335000	
chunk0042_341_1	chr12	9936766	9937416	+	0	NA	intron (NR_104634, intron 4 of 4)	intron (NR_104634, intron 4 of 4)	-4710	NM_207375	387836	Hs.527665	NM_207375	ENSG00000188393	CLEC2A	INPE5792|KACL|PILAR|UNQ5792	C-type lectin domain family 2 member A	protein-coding	0.015385	0.360983	323(AAGGACACTATGTGAC,-,0.00)
chunk0033_58_1	chr11	13420506	13420914	+	0	NA	intron (NM_032320, intron 3 of 8)	intron (NM_032320, intron 3 of 8)	19569	NM_001297742	84280	Hs.332382	NM_032320	ENSG00000148925	BTBD10	GMRP-1|GMRP1	BTB domain containing 10	protein-coding	0.000000	0.325183	146(TAGAACACTCTGTACA,-,0.00),147(AGAACACTCTGTACAG,+,0.00)
chunk0030_339_1	chr10	118428963	118429482	+	0	NA	Intergenic	Intergenic	72114	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.019268	0.409615	
chunk0119_93_1	chr22	41844483	41844842	+	0	NA	intron (NM_004599, intron 1 of 18)	intron (NM_004599, intron 1 of 18)	11583	NM_004599	6721	Hs.443258	NM_004599	ENSG00000198911	SREBF2	SREBP-2|SREBP2|bHLHd2	sterol regulatory element binding transcription factor 2	protein-coding	0.008357	0.452778	
chunk0037_212_1	chr11	74663441	74663911	+	0	NA	Intergenic	L1MEc|LINE|L1	47691	NM_001304417	25884	Hs.432379	NM_015424	ENSG00000054938	CHRDL2	BNF1|CHL2	chordin like 2	protein-coding	0.002128	0.316348	
chunk0048_353_1	chr12	85280967	85281212	+	0	NA	intron (NM_006982, intron 1 of 3)	intron (NM_006982, intron 1 of 3)	831	NM_006982	8092	Hs.41683	NM_006982	ENSG00000180318	ALX1	CART1|FND3|HEL23	ALX homeobox 1	protein-coding	0.036735	0.369919	
chunk0085_328_1	chr18	8406009	8406421	+	0	NA	3' UTR (NM_002845, exon 31 of 31)	3' UTR (NM_002845, exon 31 of 31)	-39181	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.014563	0.443099	
chunk0184_267_1	chr7	118378558	118378921	+	0	NA	Intergenic	Intergenic	154081	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.002755	0.447802	
chunk0043_162_1	chr12	16900336	16901025	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-88067	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.002903	0.320290	
chunk0152_350_1	chr5	62931622	62931992	+	0	NA	Intergenic	Intergenic	353072	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.002703	0.323450	
chunk0184_276_1	chr7	118611090	118611704	+	0	NA	Intergenic	Intergenic	386739	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.001629	0.334959	
chunk0107_113_1	chr2	214378474	214379199	+	0	NA	intron (NR_047659, intron 17 of 17)	intron (NR_047659, intron 17 of 17)	-32901	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.004138	0.438017	329(AGGGACACTGTGCCCT,-,0.00),330(GGGACACTGTGCCCTC,+,0.00)
chunk0174_217_1	chr6	160400371	160400871	+	0	NA	intron (NM_021977, intron 2 of 10)	L1MC1|LINE|L1	52248	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.004000	0.417166	230(CAGTACACCATGTCCA,-,0.00),231(AGTACACCATGTCCAC,+,0.00)
chunk0032_230_1	chr11	7612838	7613037	+	0	NA	intron (NM_003621, intron 6 of 23)	intron (NM_003621, intron 6 of 23)	7203	NM_001256569	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.005025	0.425000	
chunk0013_60_1	chr1	167305789	167306189	+	0	NA	intron (NR_037163, intron 2 of 16)	intron (NR_037163, intron 2 of 16)	-23055	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.005000	0.408978	
chunk0077_296_1	chr16	81437918	81438344	+	0	NA	Intergenic	Intergenic	-7039	NM_198390	80790	Hs.594095	NM_030629	ENSG00000153815	CMIP	TCMIP	c-Maf inducing protein	protein-coding	0.021127	0.494145	
chunk0081_65_1	chr17	38825200	38825523	+	0	NA	promoter-TSS (NR_039880)	promoter-TSS (NR_039880)	-11	NM_017748	54883	Hs.406223	NM_017748	ENSG00000273559	CWC25	CCDC49	CWC25 spliceosome associated protein homolog	protein-coding	0.095975	0.580247	
chunk0193_3_1	chr8	70456218	70456702	+	0	NA	Intergenic	Intergenic	-14674	NR_110653	101926892	Hs.367827	NR_110653	ENSG00000253967	LOC101926892	-	uncharacterized LOC101926892	ncRNA	0.016529	0.410309	
chunk0085_454_1	chr18	11513507	11514119	+	0	NA	Intergenic	Intergenic	23765	NR_110778	101927433	Hs.331210	NR_110778	ENSG00000267252	LINC01255	-	long intergenic non-protein coding RNA 1255	ncRNA	0.001634	0.309951	
chunk0015_275_1	chr1	188542102	188542885	+	0	NA	Intergenic	L1MEc|LINE|L1	1098865	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.005109	0.304847	
chunk0141_95_1	chr4	79115322	79115576	+	0	NA	intron (NR_038342, intron 3 of 5)	intron (NR_038342, intron 3 of 5)	143701	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.000000	0.329412	
chunk0085_209_1	chr18	6688717	6689333	+	0	NA	Intergenic	L1MC1|LINE|L1	-145408	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.006494	0.358185	
chunk0101_89_1	chr2	124183193	124183907	+	0	NA	intron (NM_130773, intron 1 of 23)	intron (NM_130773, intron 1 of 23)	158263	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.008403	0.330070	
chunk0164_365_1	chr6	25642087	25642823	+	0	NA	Intergenic	Intergenic	-9746	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.004076	0.405699	
chunk0130_402_1	chr3	140331807	140332567	+	0	NA	intron (NM_022131, intron 2 of 16)	L2c|LINE|L2	176602	NR_108084	101927808	Hs.581236	NR_108084	ENSG00000250433	CLSTN2-AS1	-	CLSTN2 antisense RNA 1	ncRNA	0.005263	0.431012	
chunk0093_342_1	chr19	54847302	54847555	+	0	NA	intron (NM_001083539, intron 7 of 10).20	intron (NM_001083539, intron 7 of 10).20	-3015	NM_006737	3812	Hs.645228	NM_006737	ENSG00000240403	KIR3DL2	3DL2|CD158K|KIR-3DL2|NKAT-4|NKAT4|NKAT4B|p140	killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2	protein-coding	0.011858	0.574803	
chunk0027_394_1	chr10	80168149	80168397	+	0	NA	intron (NM_145868, intron 5 of 15)	intron (NM_145868, intron 5 of 15)	35771	NM_001012973	219348	Hs.204947	NM_001012973	ENSG00000189129	PLAC9	-	placenta associated 9	protein-coding	0.020161	0.522088	
chunk0018_193_1	chr1	219297555	219297800	+	0	NA	Intergenic	Intergenic	122708	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.004082	0.345528	
chunk0057_214_1	chr13	104009071	104009439	+	0	NA	Intergenic	Intergenic	584055	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.008152	0.276423	
chunk0190_304_1	chr8	38266770	38267642	+	0	NA	exon (NM_001102560, exon 5 of 5)	exon (NM_001102560, exon 5 of 5)	2014	NM_032483	84513	Hs.567619	NM_032483	ENSG00000147535	PLPP5	DPPL1|HTPAP|PPAPDC1B	phospholipid phosphatase 5	protein-coding	0.009174	0.382589	
chunk0117_36_1	chr22	11931116	11932576	+	0	NA	intron (NR_110761, intron 2 of 2)	intron (NR_110761, intron 2 of 2)	34440	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.010274	0.541410	317(GAGGACTTTATGTTCA,-,0.00),318(AGGACTTTATGTTCAA,+,0.00),1045(GAGGACTTTATGTTCA,-,0.00),1046(AGGACTTTATGTTCAA,+,0.00)
chunk0115_255_1	chr21	27678425	27678964	+	0	NA	Intergenic	Intergenic	-43685	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.005566	0.381481	
chunk0196_108_1	chr8	103135950	103136402	+	0	NA	intron (NR_027071, intron 1 of 1)	intron (NR_027071, intron 1 of 1)	-4517	NM_024812	79870	Hs.533446	NM_024812	ENSG00000164929	BAALC	-	BAALC binder of MAP3K1 and KLF4	protein-coding	0.004425	0.350993	
chunk0069_79_1	chr15	61038615	61039040	+	0	NA	intron (NM_134261, intron 1 of 10)	MIR3|SINE|MIR	190476	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.011765	0.443662	
chunk0113_48_1	chr20	50071609	50071885	+	0	NA	Intergenic	MIRb|SINE|MIR	-30118	NR_051976	100887755	Hs.195705	NR_051976		TRERNA1	LINC00651|treRNA	translation regulatory long non-coding RNA 1	ncRNA	0.047101	0.555957	
chunk0052_370_1	chr12	128680426	128680994	+	0	NA	intron (NM_001136103, intron 5 of 8)	intron (NM_001136103, intron 5 of 8)	143286	NM_145648	121260	Hs.507260	NM_145648	ENSG00000139370	SLC15A4	FP12591|PHT1|PTR4	solute carrier family 15 member 4	protein-coding	0.007042	0.414763	316(AAGATCAGGTTGTTCT,-,0.00),317(AGATCAGGTTGTTCTG,+,0.00)
chunk0158_205_1	chr5	128141472	128141671	+	0	NA	intron (NR_046207, intron 9 of 26)	intron (NR_046207, intron 9 of 26)	57780	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.000000	0.315000	
chunk0212_244_1	chrX	137847251	137847646	+	0	NA	Intergenic	Intergenic	281261	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.005063	0.401515	
chunk0123_313_1	chr3	47163334	47163786	+	0	NA	promoter-TSS (NR_033373)	promoter-TSS (NR_033373)	417	NM_014159	29072	Hs.517941	NM_012271	ENSG00000181555	SETD2	HBP231|HIF-1|HIP-1|HSPC069|HYPB|KMT3A|LLS|SET2|p231HBP	SET domain containing 2, histone lysine methyltransferase	protein-coding	0.159292	0.783664	
chunk0121_301_1	chr3	23959171	23959905	+	0	NA	intron (NR_110524, intron 3 of 8)	intron (NR_110524, intron 3 of 8)	13417	NM_001145425	9975	Hs.37288	NM_005126	ENSG00000174738	NR1D2	BD73|EAR-1R|REVERBB|REVERBbeta|RVR	nuclear receptor subfamily 1 group D member 2	protein-coding	0.008174	0.393197	534(AGTACAAGAAGTGCCT,+,0.00)
chunk0153_293_1	chr5	73365996	73366482	+	0	NA	Intergenic	Intergenic	82288	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.016461	0.552361	118(GGGCACAGCCAGTGCC,-,0.00),119(GGCACAGCCAGTGCCT,+,0.00),360(AGGAACAGAGTGTCCA,-,0.00),361(GGAACAGAGTGTCCAA,+,0.00)
chunk0119_243_1	chr22	45690289	45690919	+	0	NA	intron (NM_013236, intron 2 of 11)	intron (NM_013236, intron 2 of 11)	18806	NM_013236	25814	Hs.475125	NM_013236	ENSG00000130638	ATXN10	E46L|HUMEEP|SCA10	ataxin 10	protein-coding	0.006349	0.372425	
chunk0040_188_1	chr11	114098924	114099323	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	38557	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.007519	0.410000	
chunk0046_384_1	chr12	63689038	63689571	+	0	NA	Intergenic	Intergenic	-20730	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.001876	0.320225	
chunk0050_279_1	chr12	106309094	106309293	+	0	NA	intron (NM_001286262, intron 1 of 6)	intron (NM_001286262, intron 1 of 6)	6402	NM_001286262	255394	Hs.696047	NM_152772	ENSG00000166046	TCP11L2	-	t-complex 11 like 2	protein-coding	0.005025	0.465000	
chunk0024_8_1	chr10	32693229	32694016	+	0	NA	intron (NM_024688, intron 5 of 22)	MER6|DNA|TcMar-Tigger	125899	NM_024688	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.005083	0.357868	
chunk0153_4_1	chr5	66732310	66732764	+	0	NA	intron (NM_198828, intron 1 of 5)	L2c|LINE|L2	-96239	NM_015183	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.004405	0.448352	
chunk0100_73_1	chr2	106642712	106642934	+	0	NA	Intergenic	L2a|LINE|L2	-174478	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.000000	0.394619	
chunk0013_105_1	chr1	167796965	167797405	+	0	NA	Intergenic	Intergenic	75235	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.004545	0.471655	129(TGGAACACACAGTTCC,-,0.00),130(GGAACACACAGTTCCC,+,0.00)
chunk0092_161_1	chr19	29685279	29685809	+	0	NA	Intergenic	Intergenic	20124	NM_024310	79156	Hs.466383	NM_024310	ENSG00000166289	PLEKHF1	APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology and FYVE domain containing 1	protein-coding	0.018868	0.500942	
chunk0031_306_1	chr10	128851784	128852032	+	0	NA	Intergenic	Intergenic	565958	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.020161	0.481928	139(CTGGACACAGAGTACC,-,0.00),140(TGGACACAGAGTACCT,+,0.00)
chunk0081_155_1	chr17	40892360	40892649	+	0	NA	Intergenic	Intergenic	-7261	NM_019010	54474	Hs.84905	NM_019010	ENSG00000171431	KRT20	CD20|CK-20|CK20|K20|KRT21	keratin 20	protein-coding	0.000000	0.455172	
chunk0083_179_1	chr17	66365912	66366414	+	0	NA	intron (NM_002737, intron 2 of 16)	intron (NM_002737, intron 2 of 16)	50691	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.005976	0.347913	
chunk0180_193_1	chr7	66159519	66159933	+	0	NA	Intergenic	L1MB4|LINE|L1	44908	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.004831	0.375904	250(AAGAACAAACAGTCCA,-,0.00),251(AGAACAAACAGTCCAG,+,0.00)
chunk0192_450_1	chr8	70152541	70152757	+	0	NA	intron (NM_006540, intron 11 of 22)	intron (NM_006540, intron 11 of 22)	-81322	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.013889	0.368664	
chunk0195_397_1	chr8	100309846	100310504	+	0	NA	promoter-TSS (NM_183419)	promoter-TSS (NM_183419)	-9	NM_183419	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.118541	0.737481	
chunk0175_53_1	chr7	1648144	1648720	+	0	NA	Intergenic	Intergenic	33962	NR_001288	260341	Hs.534596	NR_001288		TFAMP1	MTTF1|TCF6L1	transcription factor A, mitochondrial pseudogene 1	pseudo	0.046875	0.634315	302(GGCCCAGCCTGTCCCG,+,0.00)
chunk0055_318_1	chr13	68461126	68461350	+	0	NA	Intergenic	Intergenic	424087	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.004464	0.395556	123(TAGCACACGCTGACCT,-,0.00),124(AGCACACGCTGACCTG,+,0.00)
chunk0077_280_1	chr16	81114368	81114567	+	0	NA	intron (NR_126532, intron 39 of 42)	intron (NR_126532, intron 39 of 42)	-18092	NM_004483	2653	Hs.546256	NM_004483	ENSG00000140905	GCSH	GCE|NKH	glycine cleavage system protein H	protein-coding	0.000000	0.395000	
chunk0140_269_1	chr4	72070858	72071225	+	0	NA	intron (NM_001144756, intron 2 of 4)	intron (NM_001144756, intron 2 of 4)	31909	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.002725	0.342391	
chunk0003_333_1	chr1	38858682	38858980	+	0	NA	intron (NM_022157, intron 1 of 6)	intron (NM_022157, intron 1 of 6)	992	NM_001271851	64121	Hs.532461	NM_022157	ENSG00000116954	RRAGC	GTR2|RAGC|TIB929	Ras related GTP binding C	protein-coding	0.020134	0.434783	
chunk0085_144_1	chr18	3262086	3262302	+	0	NA	promoter-TSS (NM_001144944)	promoter-TSS (NM_001144944)	81	NM_033546	103910	Hs.190086	NM_033546	ENSG00000118680	MYL12B	MLC-B|MRLC2	myosin light chain 12B	protein-coding	0.143519	0.718894	
chunk0122_74_1	chr3	29585302	29585813	+	0	NA	intron (NM_001003793, intron 3 of 14)	MIRb|SINE|MIR	304245	NM_014483	27303	Hs.221436	NM_014483	ENSG00000144642	RBMS3	-	RNA binding motif single stranded interacting protein 3	protein-coding	0.005871	0.384766	
chunk0117_425_1	chr21	46110564	46110763	+	0	NA	intron (NM_001849, intron 1 of 27)	intron (NM_001849, intron 1 of 27)	12544	NM_058175	1292	Hs.420269	NM_001849	ENSG00000142173	COL6A2	BTHLM1|PP3610|UCMD1	collagen type VI alpha 2 chain	protein-coding	0.045226	0.655000	
chunk0114_132_1	chr21	9951893	9952103	+	0	NA	Intergenic	LTR68|LTR|ERV1	-130937	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.000000	0.398104	
chunk0210_19_1	chrX	67044001	67044685	+	0	NA	Intergenic	Intergenic	-405045	NM_001199687	60401	Hs.302017	NM_021783	ENSG00000131080	EDA2R	EDA-A2R|EDAA2R|TNFRSF27|XEDAR	ectodysplasin A2 receptor	protein-coding	0.005848	0.389781	277(AAGTACACTCTGTTCC,-,0.00),278(AGTACACTCTGTTCCA,+,0.00)
chunk0118_252_1	chr22	32946755	32947175	+	0	NA	intron (NM_003490, intron 2 of 12)	intron (NM_003490, intron 2 of 12)	59856	NM_003490	8224	Hs.608750	NM_003490	ENSG00000185666	SYN3	-	synapsin III	protein-coding	0.004762	0.384798	
chunk0016_81_1	chr1	194114426	194114633	+	0	NA	Intergenic	Intergenic	809784	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.009662	0.533654	
chunk0133_174_1	chr3	170033604	170033829	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-4231	NM_014373	26996	Hs.231320	NM_014373	ENSG00000173890	GPR160	GPCR1|GPCR150	G protein-coupled receptor 160	protein-coding	0.026667	0.526549	
chunk0167_389_1	chr6	74698481	74698824	+	0	NA	Intergenic	L2b|LINE|L2	507255	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.002915	0.377907	
chunk0020_71_1	chr1	232667125	232667488	+	0	NA	Intergenic	Intergenic	75409	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.002755	0.425824	
chunk0168_437_1	chr6	95684261	95684460	+	0	NA	Intergenic	Intergenic	106863	NM_024641	79694	Hs.734632	NM_024641	ENSG00000172469	MANEA	ENDO|hEndo	mannosidase endo-alpha	protein-coding	0.010050	0.295000	
chunk0044_294_1	chr12	32801533	32802211	+	0	NA	intron (NM_001005242, intron 10 of 12)	intron (NM_001005242, intron 10 of 12)	-45919	NM_001040436	51067	Hs.505231	NM_015936	ENSG00000139131	YARS2	CGI-04|MLASA2|MT-TYRRS|TYRRS	tyrosyl-tRNA synthetase 2	protein-coding	0.005900	0.296024	
chunk0149_3_1	chr5	15612491	15612948	+	0	NA	intron (NR_109945, intron 1 of 2)	Charlie29a|DNA|hAT-Charlie	2283	NR_109945	101929472	Hs.662664	NR_109945		CTD-2350J17.1	-	uncharacterized LOC101929472	ncRNA	0.015317	0.399563	
chunk0024_401_1	chr10	45151521	45151738	+	0	NA	intron (NR_024472, intron 2 of 8)	intron (NR_024472, intron 2 of 8)	2967	NR_024472	100133308	Hs.434365	NR_024472		RSU1P2	-	Ras suppressor protein 1 pseudogene 2	pseudo	0.013825	0.573394	
chunk0151_96_1	chr5	43105702	43105901	+	0	NA	Intergenic	Intergenic	-15100	NR_123719									0.030151	0.570000	
chunk0111_244_1	chr20	29868387	29868717	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-11832	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.000000	0.410876	
chunk0080_252_1	chr17	30412102	30412424	+	0	NA	intron (NM_001304, intron 2 of 20)	L1PA6|LINE|L1	31785	NM_001199775	1362	Hs.446079	NM_001304	ENSG00000108582	CPD	GP180	carboxypeptidase D	protein-coding	0.006211	0.547988	
chunk0099_162_1	chr2	88425413	88425988	+	0	NA	Intergenic	L1MEd|LINE|L1	26835	NM_001135649	344167	Hs.131262	NM_001135649	ENSG00000214336	FOXI3	-	forkhead box I3	protein-coding	0.000000	0.329861	
chunk0058_363_1	chr14	28982141	28982825	+	0	NA	Intergenic	L1PREC2|LINE|L1	209779	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.002924	0.373723	
chunk0136_49_1	chr4	1245169	1245444	+	0	NA	intron (NM_001012614, intron 1 of 9)	intron (NM_001012614, intron 1 of 9)	3814	NM_001012614	1487	Hs.208597	NM_001328	ENSG00000159692	CTBP1	BARS|HADDTS	C-terminal binding protein 1	protein-coding	0.032727	0.601449	
chunk0021_53_1	chr10	1057880	1058394	+	0	NA	intron (NM_014023, intron 1 of 13)	L3|LINE|CR1	1301	NM_014023	22884	Hs.188495	NM_014023	ENSG00000047056	WDR37	-	WD repeat domain 37	protein-coding	0.017510	0.438835	
chunk0134_163_1	chr3	177877131	177877528	+	0	NA	intron (NR_110826, intron 1 of 2)	intron (NR_110826, intron 1 of 2)	60464	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.002519	0.422111	
chunk0053_152_1	chr13	30247538	30248212	+	0	NA	intron (NM_001014380, intron 4 of 10)	intron (NM_001014380, intron 4 of 10)	59179	NM_001014380	84056	Hs.243596	NM_032116	ENSG00000102781	KATNAL1	-	katanin catalytic subunit A1 like 1	protein-coding	0.001484	0.360000	38(CAGAACAGCAAGTTCA,-,0.00),39(AGAACAGCAAGTTCAA,+,0.00),306(AGGGACAGTGTGTTCT,-,0.00),307(GGGACAGTGTGTTCTC,+,0.00)
chunk0166_351_1	chr6	51164046	51164273	+	0	NA	Intergenic	Intergenic	345433	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.000000	0.298246	
chunk0031_28_1	chr10	122019091	122019392	+	0	NA	intron (NM_001291877, intron 1 of 19)	intron (NM_001291877, intron 1 of 19)	30067	NM_206862	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.046512	0.539735	
chunk0158_84_1	chr5	126508916	126509473	+	0	NA	Intergenic	Intergenic	44099	NM_001146322	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.000000	0.349462	225(GGGGACACAATGTTCC,-,0.00),226(GGGACACAATGTTCCC,+,0.00)
chunk0065_164_1	chr15	25780511	25780924	+	0	NA	intron (NM_024490, intron 2 of 20)	intron (NM_024490, intron 2 of 20)	68108	NR_039865	100616474		NR_039865	ENSG00000266517	MIR4715	-	microRNA 4715	ncRNA	0.024213	0.519324	
chunk0019_207_1	chr1	226988169	226988627	+	0	NA	TTS (NM_020247)	TTS (NM_020247)	48161	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.017467	0.553377	
chunk0206_411_1	chr9	127452765	127452969	+	0	NA	intron (NM_001005374, intron 1 of 24)	intron (NM_001005374, intron 1 of 24)	612	NM_001005374	90678	Hs.495188	NM_138361	ENSG00000148356	LRSAM1	CMT2P|RIFLE|TAL	leucine rich repeat and sterile alpha motif containing 1	protein-coding	0.004902	0.531707	
chunk0156_321_1	chr5	111402041	111402314	+	0	NA	intron (NM_001744, intron 5 of 10)	LTR50|LTR|ERVL	-110049	NR_040093	100505678	Hs.745061	NR_040093	ENSG00000246859	STARD4-AS1	-	STARD4 antisense RNA 1	ncRNA	0.007326	0.445255	
chunk0002_345_1	chr1	25252808	25253309	+	0	NA	Intergenic	LTR66|LTR|ERVL	-5564	NM_020317	57035	Hs.259412	NM_020317	ENSG00000117616	RSRP1	C1orf63|NPD014	arginine and serine rich protein 1	protein-coding	0.015968	0.428287	
chunk0076_340_1	chr16	71472549	71472866	+	0	NA	Intergenic	Intergenic	-10455	NM_001304492	7571	Hs.656643	NM_145911	ENSG00000167377	ZNF23	KOX16|ZNF359|ZNF612|Zfp612	zinc finger protein 23	protein-coding	0.009464	0.484277	179(TGGGACAGTTTGTACT,-,0.00),180(GGGACAGTTTGTACTG,+,0.00)
chunk0132_280_1	chr3	159807765	159808300	+	0	NA	intron (NM_014575, intron 2 of 7)	intron (NM_014575, intron 2 of 7)	-31829	NM_001197109	29970	Hs.134665	NM_014575	ENSG00000151967	SCHIP1	SCHIP-1	schwannomin interacting protein 1	protein-coding	0.000000	0.391791	
chunk0024_344_1	chr10	43396717	43396916	+	0	NA	promoter-TSS (NM_001098208)	promoter-TSS (NM_001098208)	15	NM_001098208	3185	Hs.808	NM_004966	ENSG00000169813	HNRNPF	HNRPF|OK/SW-cl.23|mcs94-1	heterogeneous nuclear ribonucleoprotein F	protein-coding	0.110553	0.805000	
chunk0194_35_1	chr8	81813026	81814381	+	0	NA	intron (NM_022133, intron 6 of 8)	L1MB7|LINE|L1	28583	NM_022133	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.003690	0.300885	
chunk0117_97_1	chr22	17600897	17601096	+	0	NA	intron (NM_001039367, intron 4 of 7)	A-rich|Low_complexity|Low_complexity	-11804	NM_001288707	101929372	Hs.629929	NM_001288707		LOC101929372	-	uncharacterized LOC101929372	protein-coding	0.000000	0.350000	
chunk0075_444_1	chr16	58022715	58023376	+	0	NA	Intergenic	Intergenic	-2333	NM_002428	4324	Hs.80343	NM_002428	ENSG00000102996	MMP15	MMP-15|MT2-MMP|MT2MMP|MTMMP2|SMCP-2	matrix metallopeptidase 15	protein-coding	0.027231	0.584592	
chunk0204_445_1	chr9	104098164	104098607	+	0	NA	intron (NM_001042550, intron 3 of 24)	intron (NM_001042550, intron 3 of 24)	3835	NM_001042550	10592	Hs.119023	NM_006444	ENSG00000136824	SMC2	CAP-E|CAPE|SMC-2|SMC2L1	structural maintenance of chromosomes 2	protein-coding	0.011287	0.364865	229(TAGCACAAGGTGTGCA,-,0.00),230(AGCACAAGGTGTGCAT,+,0.00)
chunk0059_9_1	chr14	29736620	29736957	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	190905	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.002967	0.405325	
chunk0129_443_1	chr3	128084324	128085208	+	0	NA	intron (NM_003707, intron 9 of 10)	intron (NM_003707, intron 9 of 10)	8956	NR_046645	100874089	Hs.581603	NR_046645	ENSG00000239608	RUVBL1-AS1	-	RUVBL1 antisense RNA 1	ncRNA	0.016968	0.503955	257(AGGGACACTCTGCTCT,-,0.00),258(GGGACACTCTGCTCTC,+,0.00)
chunk0100_315_1	chr2	116117336	116117554	+	0	NA	Intergenic	L2c|LINE|L2	955338	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.009174	0.392694	162(TAGCACACACTGTTCT,-,0.00),163(AGCACACACTGTTCTC,+,0.00)
chunk0041_36_1	chr12	852477	852770	+	0	NA	intron (NM_213655, intron 4 of 27)	intron (NM_213655, intron 4 of 27)	80453	NM_001297420	5893	Hs.410355	NM_134422	ENSG00000002016	RAD52	-	RAD52 homolog, DNA repair protein	protein-coding	0.006826	0.323129	
chunk0163_119_1	chr6	10261477	10261993	+	0	NA	Intergenic	MIR|SINE|MIR	-150583	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.007752	0.353965	217(AAAAACAGTATGTACC,-,0.00),218(AAAACAGTATGTACCA,+,0.00)
chunk0144_325_1	chr4	139028355	139028611	+	0	NA	intron (NM_012118, intron 1 of 2)	intron (NM_012118, intron 1 of 2)	12724	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.031250	0.513619	122(TTGTACACTCTGTGCT,-,0.00),123(TGTACACTCTGTGCTG,+,0.00)
chunk0071_64_1	chr15	80504089	80504406	+	0	NA	intron (NM_014862, intron 5 of 18)	intron (NM_014862, intron 5 of 18)	58697	NR_120363	101929586	Hs.569426	NR_120363	ENSG00000259175	LOC101929586	-	uncharacterized LOC101929586	ncRNA	0.015773	0.443396	176(GTAACAATCTGTTCTG,+,0.00)
chunk0046_252_1	chr12	60534845	60535792	+	0	NA	Intergenic	Intergenic	845981	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001056	0.343882	428(CAGTACAAACTGTCCT,-,0.00),429(AGTACAAACTGTCCTA,+,0.00),705(ATGGACTTAGTGTGCT,-,0.00),706(TGGACTTAGTGTGCTT,+,0.00)
chunk0148_81_1	chr5	2715859	2716187	+	0	NA	Intergenic	Intergenic	35632	NM_033267	153572	Hs.282089	NM_033267	ENSG00000170561	IRX2	IRXA2	iroquois homeobox 2	protein-coding	0.018293	0.574468	102(CAGAACAGACTGTCCC,-,0.00),103(AGAACAGACTGTCCCT,+,0.00)
chunk0166_249_1	chr6	47464125	47464575	+	0	NA	Intergenic	Intergenic	-13439	NM_012120	23607	Hs.485518	NM_012120	ENSG00000198087	CD2AP	CMS	CD2 associated protein	protein-coding	0.002222	0.337029	
chunk0050_360_1	chr12	107833121	107833377	+	0	NA	Intergenic	Intergenic	58864	NM_203436	121549	Hs.149910	NM_203436	ENSG00000187855	ASCL4	HASH4|bHLHa44	achaete-scute family bHLH transcription factor 4	protein-coding	0.007812	0.338521	
chunk0082_321_1	chr17	59366838	59367467	+	0	NA	TTS (NR_039882)	TTS (NR_039882)	1069	NR_039882	100616204		NR_039882	ENSG00000263857	MIR4729	-	microRNA 4729	ncRNA	0.011129	0.469841	484(AGGGGCAGCCAGTCCC,-,0.00)
chunk0066_310_1	chr15	35728029	35728691	+	0	NA	intron (NR_038251, intron 2 of 2)	intron (NR_038251, intron 2 of 2)	-182157	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.003021	0.416290	
chunk0076_222_1	chr16	68637161	68637612	+	0	NA	Intergenic	MIR|SINE|MIR	-6862	NM_001793	1001	Hs.191842	NM_001793	ENSG00000062038	CDH3	CDHP|HJMD|PCAD	cadherin 3	protein-coding	0.006652	0.407080	260(TAGAACACTGAGTTCC,-,0.00),261(AGAACACTGAGTTCCA,+,0.00)
chunk0123_87_1	chr3	42035823	42036158	+	0	NA	Intergenic	L2a|LINE|L2	-55264	NM_001042646	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.008955	0.529762	90(CTGCACAGCCTGTTCT,-,0.00),91(TGCACAGCCTGTTCTG,+,0.00)
chunk0134_413_1	chr3	183249491	183249699	+	0	NA	intron (NM_015078, intron 15 of 29)	intron (NM_015078, intron 15 of 29)	-3649	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.014423	0.555024	
chunk0099_412_1	chr2	102240517	102240817	+	0	NA	Intergenic	Intergenic	53694	NM_003854	8808	Hs.659863	NM_003854	ENSG00000115598	IL1RL2	IL-1Rrp2|IL-36R|IL1R-rp2|IL1RRP2	interleukin 1 receptor like 2	protein-coding	0.010000	0.401993	
chunk0045_348_1	chr12	51485760	51485968	+	0	NA	exon (NM_001258401, exon 17 of 25)	exon (NM_001258401, exon 17 of 25)	60747	NM_001258403	9498	Hs.4749	NM_004858	ENSG00000050438	SLC4A8	NBC3|NDCBE	solute carrier family 4 member 8	protein-coding	0.004808	0.406699	
chunk0054_47_1	chr13	41648357	41648695	+	0	NA	intron (NM_015058, intron 37 of 44)	intron (NM_015058, intron 37 of 44)	-80131	NR_049803	100847026		NR_049803	ENSG00000284584	MIR5006	-	microRNA 5006	ncRNA	0.008876	0.353982	
chunk0125_455_1	chr3	73069114	73069651	+	0	NA	Intergenic	Intergenic	7723	NM_018029	55096	Hs.658858	NM_018029	ENSG00000255423	EBLN2	EBLN-2	endogenous Bornavirus like nucleoprotein 2	protein-coding	0.013035	0.423792	
chunk0112_137_1	chr20	38585354	38585970	+	0	NA	intron (NM_001018082, intron 1 of 2)	intron (NM_001018082, intron 1 of 2)	4467	NR_130907	149685	Hs.368028	NM_174906	ENSG00000182035	ADIG	SMAF1	adipogenin	protein-coding	0.012987	0.478120	
chunk0039_314_1	chr11	103413016	103413297	+	0	NA	intron (NM_001377, intron 84 of 88)	intron (NM_001377, intron 84 of 88)	303725	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.003559	0.382979	
chunk0028_1_1	chr10	81924436	81924724	+	0	NA	intron (NM_001165973, intron 1 of 10)	intron (NM_001165973, intron 1 of 10)	46893	NM_001165973	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.013889	0.432526	
chunk0065_414_1	chr14	105761631	105762164	+	0	NA	Intergenic	(CACAT)n|Simple_repeat|Simple_repeat	-89090	NR_046211	2003	Hs.744419	NR_046211		ELK2AP	ELK2|ELK2.1|ELK2P1	ETS transcription factor ELK2A, pseudogene	pseudo	0.018762	0.513109	
chunk0206_161_1	chr9	121676181	121676380	+	0	NA	intron (NM_032552, intron 1 of 16)	intron (NM_032552, intron 1 of 16)	-66505	NM_138709	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.010050	0.570000	83(AAGCACACAGTGCCCC,-,0.00),84(AGCACACAGTGCCCCA,+,0.00)
chunk0186_269_1	chr7	141663197	141663524	+	0	NA	intron (NM_001080392, intron 8 of 8)	intron (NM_001080392, intron 8 of 8)	38793	NM_001080392	57189	Hs.521240	NM_001080392	ENSG00000257093	DENND11	KIAA1147|LCHN|PRO2561	DENN domain containing 11	protein-coding	0.012232	0.469512	
chunk0130_389_1	chr3	140023555	140023814	+	0	NA	intron (NM_022131, intron 1 of 16)	intron (NM_022131, intron 1 of 16)	88499	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.023166	0.588462	
chunk0173_149_1	chr6	144150208	144150480	+	0	NA	promoter-TSS (NM_003764)	promoter-TSS (NM_003764)	-173	NM_003764	8676	Hs.118958	NM_003764	ENSG00000135604	STX11	FHL4|HLH4|HPLH4	syntaxin 11	protein-coding	0.117647	0.761905	
chunk0002_276_1	chr1	22052274	22052575	+	0	NA	promoter-TSS (NM_001791)	promoter-TSS (NM_001791)	-203	NM_044472	998	Hs.467637	NM_001791	ENSG00000070831	CDC42	CDC42Hs|G25K|TKS	cell division cycle 42	protein-coding	0.063123	0.559603	
chunk0002_267_1	chr1	21625359	21626070	+	0	NA	intron (NM_001145657, intron 4 of 26)	intron (NM_001145657, intron 4 of 26)	26141	NM_001145658	5909	Hs.148178	NM_002885	ENSG00000076864	RAP1GAP	RAP1GA1|RAP1GAP1|RAP1GAPII|RAPGAP	RAP1 GTPase activating protein	protein-coding	0.014065	0.467697	
chunk0019_98_1	chr1	224785024	224785422	+	0	NA	Intergenic	Intergenic	-144431	NM_001145154	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.005025	0.375940	
chunk0199_429_1	chr9	13735042	13735310	+	0	NA	Intergenic	Intergenic	-192795	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.007463	0.327138	
chunk0123_28_1	chr3	40631094	40631766	+	0	NA	Intergenic	L1PB1|LINE|L1	106552	NM_198484	285268	Hs.19977	NM_198484	ENSG00000172888	ZNF621	-	zinc finger protein 621	protein-coding	0.008929	0.505201	370(AGGGACATGGTGAACC,-,0.00)
chunk0176_219_1	chr7	14939002	14939465	+	0	NA	Intergenic	Intergenic	-97783	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.006479	0.338362	
chunk0091_45_1	chr19	4338030	4338413	+	0	NA	intron (NM_001013841, intron 1 of 12)	intron (NM_001013841, intron 1 of 12)	629	NM_001013841	55620	Hs.194385	NM_017720	ENSG00000178078	STAP2	BKS	signal transducing adaptor family member 2	protein-coding	0.028721	0.531250	
chunk0142_279_1	chr4	99701797	99702180	+	0	NA	Intergenic	L1PA7|LINE|L1	-114836	NM_014395	27071	Hs.436271	NM_014395	ENSG00000070190	DAPP1	BAM32	dual adaptor of phosphotyrosine and 3-phosphoinositides 1	protein-coding	0.005222	0.356771	140(CTGAACAGCCTGCTCC,-,0.00),141(TGAACAGCCTGCTCCC,+,0.00),225(AAAGACACAATGTACC,-,0.00)
chunk0144_46_1	chr4	126539867	126540205	+	0	NA	Intergenic	Intergenic	1032777	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.008876	0.356932	
chunk0096_51_1	chr2	27154579	27154920	+	0	NA	Intergenic	Intergenic	5672	NM_175769	150921	Hs.591583	NM_175769	ENSG00000163792	TCF23	OUT|TCF-23|bHLHa24	transcription factor 23	protein-coding	0.011730	0.532164	172(ATGAGCACAGTGTTCT,-,0.00),173(TGAGCACAGTGTTCTT,+,0.00)
chunk0146_193_1	chr4	161246058	161246549	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-776430	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.282520	238(AAGAACTTCTTGTTCT,-,0.00),239(AGAACTTCTTGTTCTG,+,0.00)
chunk0014_201_1	chr1	179081374	179081730	+	0	NA	promoter-TSS (NM_022371)	promoter-TSS (NM_022371)	-425	NM_022371	64222	Hs.584957	NM_022371	ENSG00000186283	TOR3A	ADIR|ADIR2	torsin family 3 member A	protein-coding	0.036517	0.537815	
chunk0029_173_1	chr10	100420589	100420838	+	0	NA	Intergenic	L2a|LINE|L2	-42342	NM_003393	7479	Hs.421281	NM_003393	ENSG00000075290	WNT8B	-	Wnt family member 8B	protein-coding	0.020080	0.432000	
chunk0175_174_1	chr7	4888089	4888443	+	0	NA	Intergenic	L2a|LINE|L2	-4562	NM_018059	55698	Hs.667336	NM_018059	ENSG00000157927	RADIL	RASIP2	Rap associating with DIL domain	protein-coding	0.008475	0.430986	
chunk0188_190_1	chr8	11738531	11738730	+	0	NA	intron (NM_002052, intron 2 of 6)	L1ME4b|LINE|L1	-22626	NR_103552									0.010050	0.390000	
chunk0069_260_1	chr15	64571982	64572363	+	0	NA	intron (NM_015042, intron 1 of 8)	L2a|LINE|L2	72752	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.007874	0.421466	127(AAGTACAGCAAGTGCA,-,0.00)
chunk0055_131_1	chr13	58728097	58728446	+	0	NA	Intergenic	Intergenic	-495154	NR_132367	106144531	Hs.736640	NR_132367	ENSG00000232954	LINC00374	-	long intergenic non-protein coding RNA 374	ncRNA	0.011461	0.305714	118(CAGAACAGAATGTACC,-,0.00),119(AGAACAGAATGTACCT,+,0.00)
chunk0016_373_1	chr1	202553538	202554088	+	0	NA	intron (NM_001197131, intron 1 of 6)	intron (NM_001197131, intron 1 of 6)	13699	NM_001197131	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.005455	0.446461	
chunk0001_108_1	chr1	3529275	3529901	+	0	NA	intron (NM_001409, intron 4 of 36)	intron (NM_001409, intron 4 of 36)	31202	NR_030277	693135		NR_030277	ENSG00000207776	MIR551A	MIRN551A|mir-551a	microRNA 551a	ncRNA	0.031949	0.636364	
chunk0089_322_1	chr18	64969544	64969935	+	0	NA	Intergenic	Intergenic	-709684	NR_033983	400654	Hs.434235	NR_033983	ENSG00000266952	LINC01538	-	long intergenic non-protein coding RNA 1538	ncRNA	0.005115	0.336735	
chunk0036_264_1	chr11	65104280	65104482	+	0	NA	intron (NM_013265, intron 2 of 9)	L1M4|LINE|L1	-7473	NM_001277233	7108	Hs.31130	NM_003273	ENSG00000149809	TM7SF2	ANG1|C14SR|DHCR14A|NET47	transmembrane 7 superfamily member 2	protein-coding	0.009901	0.399015	
chunk0086_188_1	chr18	22047483	22047919	+	0	NA	Intergenic	Intergenic	121267	NR_102763	100128893	Hs.514745	NR_102763	ENSG00000266010	GATA6-AS1	BM742401|locus5689	GATA6 antisense RNA 1 (head to head)	ncRNA	0.006881	0.475973	
chunk0092_411_1	chr19	37923412	37923754	+	0	NA	intron (NM_015073, intron 1 of 21)	Tigger3b|DNA|TcMar-Tigger	16362	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.008772	0.373178	
chunk0151_37_1	chr5	41986820	41987121	+	0	NA	Intergenic	Intergenic	61716	NM_033484	26272	Hs.165575	NM_012176	ENSG00000151876	FBXO4	FBX4	F-box protein 4	protein-coding	0.000000	0.288079	140(GAGAACAAAATGTCCT,-,0.00),141(AGAACAAAATGTCCTC,+,0.00)
chunk0031_313_1	chr10	128901396	128901890	+	0	NA	Intergenic	Intergenic	-565541	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.000000	0.319192	
chunk0033_301_1	chr11	20068435	20068888	+	0	NA	intron (NM_001244963, intron 24 of 39)	intron (NM_001244963, intron 24 of 39)	-19358	NR_046672	100874014	Hs.557916	NR_046672	ENSG00000254453	NAV2-AS2	-	NAV2 antisense RNA 2	ncRNA	0.008830	0.403084	
chunk0200_434_1	chr9	29813552	29813971	+	0	NA	Intergenic	Intergenic	594693	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.002387	0.328571	
chunk0211_137_1	chrX	112842216	112842950	+	0	NA	Intergenic	Intergenic	-1768	NM_133265	154796	Hs.528051	NM_133265	ENSG00000126016	AMOT	-	angiomotin	protein-coding	0.005450	0.398639	
chunk0118_384_1	chr22	36999574	36999842	+	0	NA	intron (NM_178552, intron 4 of 5)	intron (NM_178552, intron 4 of 5)	8128	NM_178552	339669	Hs.124502	NM_178552	ENSG00000185264	TEX33	C22orf33|EAN57|cE81G9.2	testis expressed 33	protein-coding	0.007463	0.583643	81(GGGGACTGGATGTTCC,-,0.00),82(GGGACTGGATGTTCCC,+,0.00)
chunk0128_452_1	chr3	115680837	115681237	+	0	NA	intron (NM_002045, intron 2 of 2)	intron (NM_002045, intron 2 of 2)	57733	NM_002045	2596	Hs.134974	NM_002045	ENSG00000172020	GAP43	B-50|PP46	growth associated protein 43	protein-coding	0.005000	0.354115	
chunk0138_91_1	chr4	35601704	35602112	+	0	NA	Intergenic	Intergenic	-642208	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.000000	0.290954	
chunk0204_65_1	chr9	93527157	93527562	+	0	NA	intron (NM_001286723, intron 8 of 9)	intron (NM_001286723, intron 8 of 9)	-49268	NM_005392	5253	Hs.211441	NM_005392	ENSG00000197724	PHF2	CENP-35|GRC5|JHDM1E|KDM7C	PHD finger protein 2	protein-coding	0.017284	0.440887	
chunk0154_14_1	chr5	76637527	76637992	+	0	NA	intron (NM_001285461, intron 5 of 23)	Tigger19b|DNA|TcMar-Tigger	-14325	NM_004101	2151	Hs.42502	NM_004101	ENSG00000164220	F2RL2	PAR-3|PAR3	coagulation factor II thrombin receptor like 2	protein-coding	0.004301	0.381974	
chunk0127_225_1	chr3	96712498	96713282	+	0	NA	Intergenic	Intergenic	-101691	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.005102	0.286624	
chunk0044_186_1	chr12	30361179	30361578	+	0	NA	Intergenic	MER4CL34|LTR|ERV1	315866	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.002506	0.387500	
chunk0071_153_1	chr15	82900301	82901015	+	0	NA	intron (NM_199330, intron 1 of 8)	intron (NM_199330, intron 1 of 8)	52066	NM_004839	9455	Hs.578443	NM_004839	ENSG00000103942	HOMER2	ACPD|CPD|DFNA68|HOMER-2|VESL-2	homer scaffold protein 2	protein-coding	0.001401	0.374825	
chunk0155_329_1	chr5	96876009	96876783	+	0	NA	5' UTR (NM_022350, exon 1 of 19)	5' UTR (NM_022350, exon 1 of 19)	456	NM_022350	64167	Hs.482910	NM_022350	ENSG00000164308	ERAP2	L-RAP|LRAP	endoplasmic reticulum aminopeptidase 2	protein-coding	0.011628	0.419355	412(TAGTACTTACTGTACT,-,0.00),413(AGTACTTACTGTACTC,+,0.00)
chunk0003_290_1	chr1	37499061	37499772	+	0	NA	intron (NR_073090, intron 5 of 8)	intron (NR_073090, intron 5 of 8)	1578	NR_049844	100847010		NR_049844	ENSG00000263675	MIR5581	-	microRNA 5581	ncRNA	0.005626	0.426966	
chunk0114_138_1	chr21	10077901	10078455	+	0	NA	Intergenic	Intergenic	-257117	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.001805	0.356757	
chunk0170_195_1	chr6	112259429	112259700	+	0	NA	intron (NR_121193, intron 2 of 2)	intron (NR_121193, intron 2 of 2)	-4849	NM_001105208	3910	Hs.654572	NM_002290	ENSG00000112769	LAMA4	CMD1JJ|LAMA3|LAMA4*-1	laminin subunit alpha 4	protein-coding	0.003690	0.437500	
chunk0177_57_1	chr7	21093401	21093671	+	0	NA	Intergenic	Intergenic	258105	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.007407	0.380074	
chunk0107_66_1	chr2	212096839	212097246	+	0	NA	intron (NM_001042599, intron 2 of 26)	intron (NM_001042599, intron 2 of 26)	329318	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.004914	0.348039	
chunk0209_232_1	chrX	45211957	45212156	+	0	NA	Intergenic	Intergenic	-11155	NM_024689	79742	Hs.98321	NM_024689	ENSG00000147113	DIPK2B	4930578C19Rik|CXorf36|DIA1R|EPQL1862|PRO3743|bA435K1.1	divergent protein kinase domain 2B	protein-coding	0.000000	0.400000	
chunk0155_208_1	chr5	94998344	94999036	+	0	NA	intron (NM_024717, intron 2 of 22)	LTR51|LTR|ERV1	83176	NM_001002796	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.011561	0.441558	
chunk0055_312_1	chr13	67187061	67187270	+	0	NA	intron (NM_203487, intron 2 of 4)	intron (NM_203487, intron 2 of 4)	43171	NM_020403	5101	Hs.654709	NM_020403	ENSG00000184226	PCDH9	-	protocadherin 9	protein-coding	0.009569	0.433333	75(ATGGTCATGCTGTTCC,-,0.00)
chunk0004_268_1	chr1	48292300	48292622	+	0	NA	Intergenic	Intergenic	69776	NM_001135181	200010	Hs.37890	NM_001011547	ENSG00000117834	SLC5A9	SGLT4	solute carrier family 5 member 9	protein-coding	0.003106	0.551084	
chunk0123_365_1	chr3	48300964	48301275	+	0	NA	intron (NM_001308426, intron 1 of 5)	CpG	292	NM_005793	10201	Hs.465558	NM_005793	ENSG00000172113	NME6	IPIA-ALPHA|NDK 6|NM23-H6	NME/NM23 nucleoside diphosphate kinase 6	protein-coding	0.077170	0.676282	
chunk0105_327_1	chr2	191013738	191014207	+	0	NA	intron (NM_007315, intron 1 of 24)	CpG	278	NM_139266	6772	Hs.642990	NM_007315	ENSG00000115415	STAT1	CANDF7|IMD31A|IMD31B|IMD31C|ISGF-3|STAT91	signal transducer and activator of transcription 1	protein-coding	0.091684	0.651064	
chunk0025_292_1	chr10	56958055	56959002	+	0	NA	Intergenic	Intergenic	346031	NR_037490	100500834		NR_037490	ENSG00000264747	MIR3924	-	microRNA 3924	ncRNA	0.005280	0.382911	318(GAGGACTCACTGTACC,-,0.00),319(AGGACTCACTGTACCT,+,0.00)
chunk0027_10_1	chr10	72096218	72096815	+	0	NA	non-coding (NR_045564, exon 10 of 10)	non-coding (NR_045564, exon 10 of 10)	-7484	NM_001134434	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.008375	0.463211	
chunk0062_195_1	chr14	69937552	69937751	+	0	NA	intron (NM_022137, intron 1 of 11)	intron (NM_022137, intron 1 of 11)	58254	NM_022137	64093	Hs.497349	NM_022137	ENSG00000198732	SMOC1	OAS	SPARC related modular calcium binding 1	protein-coding	0.045226	0.555000	
chunk0099_168_1	chr2	88627435	88627654	+	0	NA	promoter-TSS (NM_004836)	promoter-TSS (NM_004836)	32	NM_004836	9451	Hs.591589	NM_004836	ENSG00000172071	EIF2AK3	PEK|PERK|WRS	eukaryotic translation initiation factor 2 alpha kinase 3	protein-coding	0.073059	0.577273	
chunk0123_247_1	chr3	45751727	45752281	+	0	NA	Intergenic	Intergenic	44539	NM_020208	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.012635	0.477477	
chunk0205_169_1	chr9	108709919	108710724	+	0	NA	Intergenic	Intergenic	145674	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.003727	0.460298	
chunk0053_158_1	chr13	30389674	30390291	+	0	NA	Intergenic	Intergenic	-16068	NR_024464	100188949	Hs.439791	NR_024464	ENSG00000238121	LINC00426	-	long intergenic non-protein coding RNA 426	ncRNA	0.011345	0.461165	
chunk0119_317_1	chr22	46714437	46715006	+	0	NA	intron (NM_022766, intron 3 of 12)	L1ME3A|LINE|L1	23534	NM_022766	64781	Hs.200668	NM_022766	ENSG00000100422	CERK	LK4|dA59H18.2|dA59H18.3|hCERK	ceramide kinase	protein-coding	0.008787	0.342105	
chunk0041_285_1	chr11	129410417	129410709	+	0	NA	intron (NM_003658, intron 1 of 3)	HAL1|LINE|L1	34577	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.006849	0.488055	
chunk0080_258_1	chr17	30502993	30503322	+	0	NA	intron (NM_001007024, intron 6 of 8)	intron (NM_001007024, intron 6 of 8)	25749	NM_001007025	9527	Hs.462680	NM_004871	ENSG00000108587	GOSR1	GOLIM2|GOS-28|GOS28|GOS28/P28|GS28|P28	golgi SNAP receptor complex member 1	protein-coding	0.000000	0.278788	
chunk0102_373_1	chr2	153456298	153457026	+	0	NA	Intergenic	MIR|SINE|MIR	22146	NM_019845	56475	Hs.100890	NM_019845	ENSG00000177519	RPRM	REPRIMO	reprimo, TP53 dependent G2 arrest mediator homolog	protein-coding	0.005495	0.404664	274(AAGAACACCTAGTACC,-,0.00),275(AGAACACCTAGTACCT,+,0.00)
chunk0185_261_1	chr7	130410943	130411545	+	0	NA	intron (NM_018718, intron 4 of 10)	intron (NM_018718, intron 4 of 10)	29966	NM_001257158	95681	Hs.368315	NM_018718	ENSG00000106477	CEP41	JBTS15|TSGA14	centrosomal protein 41	protein-coding	0.006645	0.371476	
chunk0064_23_1	chr14	89401693	89402362	+	0	NA	intron (NM_005197, intron 2 of 5)	intron (NM_005197, intron 2 of 5)	15083	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.010463	0.410448	
chunk0175_211_1	chr7	6037214	6037534	+	0	NA	TTS (NM_001271700)	TTS (NM_001271700)	5998	NM_001271700	100310846	Hs.744468	NM_001271700	ENSG00000157999	ANKRD61	-	ankyrin repeat domain 61	protein-coding	0.018750	0.364486	
chunk0187_434_1	chr7	158740975	158741346	+	0	NA	intron (NM_020728, intron 17 of 21)	intron (NM_020728, intron 17 of 21)	-36329	NM_017760	54892	Hs.18616	NM_017760	ENSG00000146918	NCAPG2	3KS|CAP-G2|CAPG2|LUZP5|MTB|hCAP-G2	non-SMC condensin II complex subunit G2	protein-coding	0.037736	0.508065	
chunk0041_123_1	chr11	125026243	125026485	+	0	NA	intron (NM_025004, intron 13 of 15)	L1M1|LINE|L1	-36753	NM_001145290	219855	Hs.352661	NM_198277	ENSG00000134955	SLC37A2	pp11662	solute carrier family 37 member 2	protein-coding	0.004132	0.518519	
chunk0068_15_1	chr15	50671529	50672208	+	0	NA	intron (NM_001301212, intron 1 of 38)	Tigger3b|DNA|TcMar-Tigger	14947	NM_001301212	54822	Hs.512894	NM_017672	ENSG00000092439	TRPM7	ALSPDC|CHAK|CHAK1|LTRPC7|LTrpC-7|TRP-PLIK	transient receptor potential cation channel subfamily M member 7	protein-coding	0.014728	0.452941	
chunk0123_42_1	chr3	40924859	40925256	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	-274394	NM_001098210	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.007557	0.437186	
chunk0054_82_1	chr13	42421908	42422258	+	0	NA	Intergenic	MER53|DNA|hAT	-140653	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.008571	0.393162	139(GAGAACACAAAGTCCC,-,0.00),140(AGAACACAAAGTCCCT,+,0.00)
chunk0014_350_1	chr1	182279287	182280055	+	0	NA	intron (NR_104175, intron 2 of 2)	intron (NR_104175, intron 2 of 2)	34390	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.015625	0.498049	
chunk0079_154_1	chr17	13258625	13258922	+	0	NA	Intergenic	Intergenic	-240709	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.000000	0.422819	
chunk0028_295_1	chr10	91527650	91527896	+	0	NA	intron (NR_024467, intron 2 of 4)	L1ME3G|LINE|L1	83687	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.004065	0.392713	
chunk0134_115_1	chr3	177154731	177155059	+	0	NA	intron (NM_024665, intron 1 of 15)	L1ME1|LINE|L1	42365	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.006098	0.282675	
chunk0182_139_1	chr7	94721008	94721685	+	0	NA	Intergenic	Intergenic	65021	NM_001172438	23089	Hs.147492	NM_015068	ENSG00000242265	PEG10	EDR|HB-1|MEF3L|Mar2|Mart2|RGAG3|RTL2|SIRH1	paternally expressed 10	protein-coding	0.000000	0.272861	
chunk0030_56_1	chr10	111916200	111916449	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	267455	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.008032	0.392000	
chunk0058_315_1	chr14	27542850	27543617	+	0	NA	Intergenic	Intergenic	-69355	NR_039992	100505967	Hs.668484	NR_039992	ENSG00000258548	LINC00645	-	long intergenic non-protein coding RNA 645	ncRNA	0.007823	0.305990	
chunk0022_25_1	chr10	7817036	7817508	+	0	NA	Intergenic	Intergenic	-1232	NM_031923	83860	Hs.527688	NM_031923	ENSG00000165632	TAF3	TAF140|TAFII-140|TAFII140	TATA-box binding protein associated factor 3	protein-coding	0.021186	0.403805	235(GGGGACAGAGTGTCCA,-,0.00),236(GGGACAGAGTGTCCAG,+,0.00)
chunk0135_100_1	chr3	186605655	186605979	+	0	NA	Intergenic	Intergenic	-7244	NM_001622	197	Hs.324746	NM_001622	ENSG00000145192	AHSG	A2HS|AHS|APMR1|FETUA|HSGA	alpha 2-HS glycoprotein	protein-coding	0.006173	0.504615	
chunk0093_348_1	chr19	55026131	55026517	+	0	NA	intron (NM_001083899, intron 4 of 7).10	L1MB2|LINE|L1	11940	NM_001083899	51206	Hs.661752	NM_016363	ENSG00000088053	GP6	BDPLT11|GPIV|GPVI	glycoprotein VI platelet	protein-coding	0.002591	0.366925	
chunk0192_244_1	chr8	65652838	65653308	+	0	NA	intron (NM_001145839, intron 1 of 6)	MER113A|DNA|hAT-Charlie	8420	NM_001145839	9650	Hs.584788	NM_014637	ENSG00000066855	MTFR1	CHPPR|FAM54A2	mitochondrial fission regulator 1	protein-coding	0.008511	0.392781	
chunk0056_139_1	chr13	83420116	83420500	+	0	NA	Intergenic	L1PA16|LINE|L1	462085	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.010417	0.381818	
chunk0171_292_1	chr6	128339629	128340146	+	0	NA	intron (NM_001291981, intron 2 of 32).2	intron (NM_001291981, intron 2 of 32).2	180787	NM_001291982	5796	Hs.155919	NM_002844	ENSG00000152894	PTPRK	R-PTP-kappa	protein tyrosine phosphatase receptor type K	protein-coding	0.003868	0.393822	
chunk0202_231_1	chr9	76497555	76498116	+	0	NA	intron (NM_001097635, intron 1 of 2)	intron (NM_001097635, intron 1 of 2)	-2798	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.008913	0.343416	
chunk0116_267_1	chr21	39183426	39183670	+	0	NA	promoter-TSS (NM_203433)	promoter-TSS (NM_203433)	-34	NM_003720	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.131148	0.738776	155(AGGCACACCCTGAGCT,-,0.00),156(GGCACACCCTGAGCTC,+,0.00)
chunk0108_360_1	chr2	236548509	236549039	+	0	NA	Intergenic	Intergenic	-20963	NM_020311	57007	Hs.471751	NM_020311	ENSG00000144476	ACKR3	CMKOR1|CXC-R7|CXCR-7|CXCR7|GPR159|RDC-1|RDC1	atypical chemokine receptor 3	protein-coding	0.013208	0.414313	
chunk0090_214_1	chr18	73461832	73462432	+	0	NA	Intergenic	Intergenic	137191	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.005000	0.377704	
chunk0157_304_1	chr5	121392769	121393013	+	0	NA	Intergenic	Intergenic	70341	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.004098	0.322449	
chunk0153_330_1	chr5	74103467	74104027	+	0	NA	Intergenic	LTR83|LTR|ERVL	204578	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.016071	0.459893	
chunk0129_145_1	chr3	120484701	120484900	+	0	NA	Intergenic	Intergenic	-33729	NM_007085	11167	Hs.269512	NM_007085	ENSG00000163430	FSTL1	FRP|FSL1|MIR198|OCC-1|OCC1|tsc36	follistatin like 1	protein-coding	0.005025	0.400000	
chunk0087_120_1	chr18	33014033	33014439	+	0	NA	intron (NM_001308126, intron 20 of 22)	L1MB7|LINE|L1	-241225	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.009852	0.393120	
chunk0131_216_1	chr3	149157482	149157791	+	0	NA	intron (NM_001308258, intron 8 of 15)	intron (NM_001308258, intron 8 of 15)	28052	NM_001308258	84343	Hs.558314	NM_032383	ENSG00000163755	HPS3	BLOC2S1|SUTAL	HPS3 biogenesis of lysosomal organelles complex 2 subunit 1	protein-coding	0.000000	0.425806	
chunk0116_345_1	chr21	41521506	41522067	+	0	NA	Intergenic	Intergenic	-13628	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.007130	0.435943	
chunk0154_187_1	chr5	80181403	80182299	+	0	NA	intron (NM_178276, intron 2 of 12)	LTR62|LTR|ERVL	74231	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.008929	0.422520	
chunk0040_182_1	chr11	114078298	114078731	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	17948	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.006928	0.447005	
chunk0023_203_1	chr10	25280516	25280849	+	0	NA	intron (NM_020752, intron 2 of 10)	L1MEd|LINE|L1	-104406	NR_027333	100128811	Hs.700407	NR_027333	ENSG00000233642	GPR158-AS1	-	GPR158 antisense RNA 1	ncRNA	0.015015	0.332335	
chunk0049_124_1	chr12	91529856	91530277	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-346942	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.002375	0.379147	
chunk0104_189_1	chr2	175096344	175096751	+	0	NA	intron (NR_045768, intron 12 of 16)	intron (NR_045768, intron 12 of 16)	71162	NR_030630	100126350		NR_030630	ENSG00000215973	MIR933	MIRN933|hsa-mir-933|mir-933	microRNA 933	ncRNA	0.002457	0.289216	
chunk0201_373_1	chr9	68719560	68720121	+	0	NA	intron (NM_001278253, intron 1 of 13)	intron (NM_001278253, intron 1 of 13)	14426	NM_001278253	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.003565	0.361210	
chunk0132_420_1	chr3	164597872	164598235	+	0	NA	Intergenic	LTR40a|LTR|ERVL	233427	NR_126405	104355289	Hs.574909	NR_126405	ENSG00000241767	LINC01324	-	long intergenic non-protein coding RNA 1324	ncRNA	0.011019	0.414835	91(GAGAACATGACGTTCC,-,0.00),92(AGAACATGACGTTCCC,+,0.00)
chunk0210_304_1	chrX	88857032	88857913	+	0	NA	Intergenic	L1PA15|LINE|L1	110247	NM_001184771	53336	Hs.458292	NM_033048	ENSG00000147183	CPXCR1	CT77	CPX chromosome region candidate 1	protein-coding	0.006810	0.353741	
chunk0047_450_1	chr12	76611661	76611875	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-51959	NM_020841	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.009346	0.427907	116(CAAAACAGAGTGTTCC,-,0.00),117(AAAACAGAGTGTTCCA,+,0.00)
chunk0089_328_1	chr18	65446434	65447108	+	0	NA	Intergenic	Intergenic	-303481	NM_033646	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.005935	0.357037	
chunk0113_447_1	chr20	62831069	62831672	+	0	NA	intron (NM_001853, intron 24 of 31)	intron (NM_001853, intron 24 of 31)	-13196	NM_080750	100132911		NM_080750		DPH3P1	C20orf143|DPH3B|ZCSL1	diphthamide biosynthesis 3 pseudogene 1	protein-coding	0.036484	0.624172	79(TTGAACACCATGTCCC,-,0.00),80(TGAACACCATGTCCCA,+,0.00)
chunk0001_102_1	chr1	3392959	3393185	+	0	NA	intron (NM_022114, intron 4 of 16)	intron (NM_022114, intron 4 of 16)	-61511	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.017699	0.427313	
chunk0086_182_1	chr18	21980017	21980334	+	0	NA	Intergenic	Intergenic	-148769	NR_110369	102723167	Hs.658808	NR_110369	ENSG00000265142	MIR133A1HG	MIR1-2HG	MIR133A1 host gene	ncRNA	0.006309	0.440252	
chunk0147_161_1	chr4	175891875	175892320	+	0	NA	intron (NR_048571, intron 1 of 5)	intron (NR_048571, intron 1 of 5)	-78983	NM_201591	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.006742	0.345291	
chunk0019_275_1	chr1	228501165	228501626	+	0	NA	Intergenic	MER77B|LTR|ERVL	10893	NM_001287262	100129094	Hs.730208	NM_001287262		BTNL10	BTN4|BUTR1	butyrophilin like 10	protein-coding	0.030369	0.564935	
chunk0172_439_1	chr6	140833388	140834088	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	149924	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.001429	0.389444	
chunk0184_353_1	chr7	120842018	120842571	+	0	NA	intron (NM_012338, intron 2 of 7)	L2a|LINE|L2	15829	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.009042	0.391697	
chunk0152_182_1	chr5	59755492	59755870	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	12931	NM_001197218	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.002646	0.316623	
chunk0191_137_1	chr8	48783348	48784115	+	0	NA	Intergenic	Intergenic	-48420	NR_024605	79645	Hs.23245	NM_024593	ENSG00000034239	EFCAB1	-	EF-hand calcium binding domain 1	protein-coding	0.009126	0.442708	
chunk0210_441_1	chrX	103801742	103802136	+	0	NA	Intergenic	Intergenic	25086	NM_001305004	5354	Hs.1787	NM_000533	ENSG00000123560	PLP1	GPM6C|HLD1|MMPL|PLP|PLP/DM20|PMD|SPG2	proteolipid protein 1	protein-coding	0.005076	0.384810	
chunk0048_276_1	chr12	82426017	82426599	+	0	NA	intron (NM_032230, intron 5 of 11)	intron (NM_032230, intron 5 of 11)	-67503	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.008591	0.401372	
chunk0098_66_1	chr2	66919403	66919849	+	0	NA	intron (NR_110169, intron 1 of 4)	intron (NR_110169, intron 1 of 4)	2864	NR_110600	102724321	Hs.146803	NR_110600	ENSG00000232688	LINC01628	-	long intergenic non-protein coding RNA 1628	ncRNA	0.006726	0.337808	
chunk0114_311_1	chr21	17160495	17161000	+	0	NA	Intergenic	Intergenic	-278143	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.005941	0.330040	203(TGGAACTGTCTGTGCT,-,0.00),204(GGAACTGTCTGTGCTC,+,0.00)
chunk0048_267_1	chr12	82119459	82119756	+	0	NA	Intergenic	L1PA16|LINE|L1	165888	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.013468	0.419463	151(AAGAACATGCAGTACT,-,0.00),152(AGAACATGCAGTACTT,+,0.00)
chunk0067_56_1	chr15	40937268	40937611	+	0	NA	exon (NM_019074, exon 10 of 11)	exon (NM_019074, exon 10 of 11)	8106	NM_019074	54567	Hs.511076	NM_019074	ENSG00000128917	DLL4	AOS6|delta4|hdelta2	delta like canonical Notch ligand 4	protein-coding	0.020408	0.587209	190(AGGGACTCCATGTACC,-,0.00),191(GGGACTCCATGTACCA,+,0.00)
chunk0023_216_1	chr10	25651369	25652009	+	0	NA	promoter-TSS (NR_108069)	promoter-TSS (NR_108069)	-23	NR_108067	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.004687	0.346334	323(CAGAACAGAGTGTGAT,-,0.00),324(AGAACAGAGTGTGATC,+,0.00)
chunk0019_346_1	chr1	229426019	229426344	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	7915	NM_001100	58	Hs.1288	NM_001100	ENSG00000143632	ACTA1	ACTA|ASMA|CFTD|CFTD1|CFTDM|MPFD|NEM1|NEM2|NEM3|SHPM	actin alpha 1, skeletal muscle	protein-coding	0.006154	0.503067	
chunk0048_345_1	chr12	84330968	84331429	+	0	NA	Intergenic	Intergenic	581631	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.004338	0.333333	
chunk0026_146_1	chr10	62306905	62307104	+	0	NA	Intergenic	LTR1D1|LTR|ERV1	-38141	NM_145307	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.020101	0.585000	
chunk0100_363_1	chr2	117832262	117832799	+	0	NA	TTS (NM_006773)	TTS (NM_006773)	17851	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.001862	0.358736	
chunk0167_408_1	chr6	75306087	75306440	+	0	NA	intron (NM_001300866, intron 6 of 6)	intron (NM_001300866, intron 6 of 6)	21249	NR_040081	100506804	Hs.743708	NR_040081		LOC100506804	-	uncharacterized LOC100506804	ncRNA	0.008499	0.387006	
chunk0117_123_1	chr22	19045146	19045617	+	0	NA	TTS (NR_024157)	TTS (NR_024157)	2994	NR_024157	25786	Hs.720269	NR_024157	ENSG00000273311	DGCR11	DGS-D	DiGeorge syndrome critical region gene 11	ncRNA	0.014862	0.408898	
chunk0136_141_1	chr4	4493978	4494312	+	0	NA	intron (NM_016930, intron 1 of 10)	intron (NM_016930, intron 1 of 10)	-12445	NR_126434	104472519	Hs.691848	NR_126434	ENSG00000248221	STX18-IT1	-	STX18 intronic transcript 1	ncRNA	0.002994	0.364179	269(GGGCTCACAGTGTACC,-,0.00),270(GGCTCACAGTGTACCC,+,0.00)
chunk0115_93_1	chr21	22399925	22400538	+	0	NA	Intergenic	MER51-int|LTR|ERV1	301614	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.001631	0.333876	
chunk0134_32_1	chr3	175601615	175601814	+	0	NA	intron (NM_207015, intron 10 of 13)	LFSINE_Vert|SINE|tRNA	174619	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.005025	0.335000	
chunk0058_12_1	chr14	18980643	18980877	+	0	NA	promoter-TSS (NR_110505)	promoter-TSS (NR_110505)	33	NR_110505	100508046	Hs.433218	NR_110505	ENSG00000275563	LOC100508046	-	uncharacterized LOC100508046	ncRNA	0.004274	0.408511	
chunk0046_258_1	chr12	60678281	60679039	+	0	NA	Intergenic	L1MA5A|LINE|L1	989323	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.001319	0.429513	
chunk0143_397_1	chr4	123250958	123251274	+	0	NA	intron (NM_145207, intron 14 of 15)	intron (NM_145207, intron 14 of 15)	-145679	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.000000	0.350158	
chunk0032_57_1	chr11	2001143	2001425	+	0	NA	non-coding (NR_131224, exon 1 of 5)	non-coding (NR_131224, exon 1 of 5)	182	NR_131224	283120	Hs.533566	NR_002196	ENSG00000130600	H19	ASM|ASM1|BWS|D11S813E|LINC00008|MIR675HG|NCRNA00008|WT2	H19 imprinted maternally expressed transcript	ncRNA	0.031915	0.583039	113(AGGAACACTGTGCGCT,-,0.00),114(GGAACACTGTGCGCTC,+,0.00)
chunk0097_360_1	chr2	60506774	60507132	+	0	NA	intron (NM_138559, intron 2 of 4)	intron (NM_138559, intron 2 of 4)	46545	NM_138559	53335	Hs.370549	NM_018014	ENSG00000119866	BCL11A	BCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856	BAF chromatin remodeling complex subunit BCL11A	protein-coding	0.008380	0.311978	
chunk0003_76_1	chr1	31405059	31405564	+	0	NA	Intergenic	L1MB3|LINE|L1	-4254	NM_001199038	347735	Hs.270655	NM_018565	ENSG00000168528	SERINC2	FKSG84|PRO0899|TDE2|TDE2L	serine incorporator 2	protein-coding	0.005941	0.456522	
chunk0063_128_1	chr14	79381517	79381967	+	0	NA	intron (NM_138970, intron 1 of 5)	intron (NM_138970, intron 1 of 5)	102403	NM_001105250	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.006667	0.376940	
chunk0031_365_1	chr10	130306597	130306796	+	0	NA	Intergenic	Intergenic	170321	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.000000	0.415000	
chunk0013_403_1	chr1	172976374	172976882	+	0	NA	Intergenic	Intergenic	74335	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.003937	0.402750	
chunk0011_411_1	chr1	154351247	154351777	+	0	NA	TTS (NM_020452)	TTS (NM_020452)	23712	NM_020452	57198	Hs.435700	NM_020452	ENSG00000143515	ATP8B2	ATPID	ATPase phospholipid transporting 8B2	protein-coding	0.015094	0.431262	
chunk0045_220_1	chr12	48021763	48022356	+	0	NA	Intergenic	Intergenic	-17557	NM_001844	1280	Hs.408182	NM_001844	ENSG00000139219	COL2A1	ANFH|AOM|COL11A3|SEDC|STL1	collagen type II alpha 1 chain	protein-coding	0.011804	0.474747	458(AAAAACAATGTGTTCT,-,0.00),459(AAAACAATGTGTTCTA,+,0.00)
chunk0081_453_1	chr17	49351882	49352586	+	0	NA	intron (NM_014897, intron 1 of 5)	intron (NM_014897, intron 1 of 5)	-8931	NR_110884	102724596	Hs.559253	NR_110882	ENSG00000248714	LOC102724596	-	uncharacterized LOC102724596	ncRNA	0.002841	0.357447	
chunk0159_181_1	chr5	140174603	140174805	+	0	NA	promoter-TSS (NM_032412)	promoter-TSS (NM_032412)	-364	NM_032412	84418	Hs.529798	NM_032412	ENSG00000120306	CYSTM1	C5orf32|ORF1-FL49	cysteine rich transmembrane module containing 1	protein-coding	0.019802	0.536946	
chunk0173_100_1	chr6	143158169	143158547	+	0	NA	intron (NM_001286587, intron 3 of 6)	intron (NM_001286587, intron 3 of 6)	97516	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.007937	0.461741	210(AAGACCTCTCTGTTCT,-,0.00)
chunk0177_134_1	chr7	22586794	22586993	+	0	NA	Intergenic	MER21C|LTR|ERVL	23556	NR_038393	100506178	Hs.668122	NR_038393	ENSG00000232759	LOC100506178	-	uncharacterized LOC100506178	ncRNA	0.000000	0.460000	
chunk0075_250_1	chr16	53291974	53292259	+	0	NA	intron (NM_001308319, intron 27 of 37)	intron (NM_001308319, intron 27 of 37)	79013	NM_001207030	643802	Hs.451336	NM_001207030		LOC643802	-	u3 small nucleolar ribonucleoprotein protein MPP10-like	protein-coding	0.000000	0.370629	
chunk0207_193_1	chr9	130872982	130873843	+	0	NA	intron (NM_007313, intron 6 of 10)	intron (NM_007313, intron 6 of 10)	23400	NM_198180	347148	Hs.660704	NM_198180	ENSG00000188710	QRFP	26RFa|P518	pyroglutamylated RFamide peptide	protein-coding	0.017422	0.481439	400(GAGTACTCATTGTTCC,-,0.00),401(AGTACTCATTGTTCCT,+,0.00)
chunk0108_279_1	chr2	234633706	234634226	+	0	NA	Intergenic	Intergenic	-48702	NR_132376	106144537	Hs.580616	NR_132376	ENSG00000280744	LINC01173	-	long intergenic non-protein coding RNA 1173	ncRNA	0.015385	0.428023	
chunk0113_22_1	chr20	49604446	49604817	+	0	NA	Intergenic	L2c|LINE|L2	-36461	NM_000961	5740	Hs.302085	NM_000961	ENSG00000124212	PTGIS	CYP8|CYP8A1|PGIS|PTGI	prostaglandin I2 synthase	protein-coding	0.013477	0.529570	193(GAGGACAGGATGTCTC,-,0.00),194(AGGACAGGATGTCTCT,+,0.00)
chunk0058_73_1	chr14	21085352	21085575	+	0	NA	intron (NM_001278529, intron 18 of 23)	MIR3|SINE|MIR	13186	NM_016423	51222	Hs.250493	NM_016423	ENSG00000165804	ZNF219	ZFP219	zinc finger protein 219	protein-coding	0.017937	0.446429	
chunk0012_45_1	chr1	155288717	155289052	+	0	NA	TTS (NM_000298)	TTS (NM_000298)	11457	NM_020897	57657	Hs.706960	NM_020897	ENSG00000143630	HCN3	-	hyperpolarization activated cyclic nucleotide gated potassium channel 3	protein-coding	0.008955	0.541667	
chunk0205_419_1	chr9	114996122	114996800	+	0	NA	Intergenic	MIRc|SINE|MIR	-65866	NM_001252290	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.007375	0.422680	
chunk0076_228_1	chr16	68744767	68745097	+	0	NA	intron (NM_004360, intron 2 of 15)	intron (NM_004360, intron 2 of 15)	2416	NR_106988									0.021212	0.495468	
chunk0201_81_1	chr9	34512623	34513111	+	0	NA	intron (NM_001281428, intron 15 of 19)	intron (NM_001281428, intron 15 of 19)	10172	NM_198573	375704	Hs.522085	NM_198573	ENSG00000168913	ENHO	C9orf165|UNQ470	energy homeostasis associated	protein-coding	0.008197	0.562372	359(TAGTTCAGTCTGTCCT,-,0.00),360(AGTTCAGTCTGTCCTG,+,0.00)
chunk0165_359_1	chr6	38123152	38123705	+	0	NA	intron (NM_021943, intron 5 of 5)	intron (NM_021943, intron 5 of 5)	303897	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.005425	0.420578	
chunk0099_418_1	chr2	102450975	102451543	+	0	NA	intron (NM_003853, intron 11 of 11)	intron (NM_003853, intron 11 of 11)	18970	NR_039930	100616157		NR_039930	ENSG00000264764	MIR4772	mir-4772	microRNA 4772	ncRNA	0.007042	0.492091	
chunk0055_307_1	chr13	66331591	66332055	+	0	NA	intron (NM_203487, intron 4 of 4)	intron (NM_203487, intron 4 of 4)	113573	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.002155	0.372043	200(AGGAACAACAAGTTCC,-,0.00),201(GGAACAACAAGTTCCT,+,0.00)
chunk0104_376_1	chr2	180242080	180242656	+	0	NA	Intergenic	Intergenic	-235315	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.001736	0.386482	215(CAGTACTTCATGTTCC,-,0.00),216(AGTACTTCATGTTCCA,+,0.00)
chunk0016_431_1	chr1	203812212	203812539	+	0	NA	intron (NM_014827, intron 4 of 19)	L1PA12|LINE|L1	14852	NM_001174108	100381270		NM_001174108	ENSG00000257315	ZBED6	MGR	zinc finger BED-type containing 6	protein-coding	0.000000	0.417683	150(GAGAACATGCTGTATT,-,0.00),151(AGAACATGCTGTATTT,+,0.00)
chunk0104_367_1	chr2	180125724	180125983	+	0	NA	Intergenic	Intergenic	-118800	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.023166	0.461538	
chunk0078_29_1	chr17	866498	866996	+	0	NA	intron (NM_022463, intron 1 of 7)	intron (NM_022463, intron 1 of 7)	-2636	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.018072	0.460922	
chunk0005_228_1	chr1	59422791	59423542	+	0	NA	intron (NM_001244714, intron 3 of 13)	intron (NM_001244714, intron 3 of 13)	-92463	NM_001278224	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.006658	0.422872	
chunk0199_145_1	chr9	4137886	4138099	+	0	NA	intron (NM_001042413, intron 2 of 10)	intron (NM_001042413, intron 2 of 10)	14191	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.004695	0.392523	
chunk0044_79_1	chr12	28117839	28118414	+	0	NA	Intergenic	MER91C|DNA|hAT-Tip100	-139074	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.006957	0.366319	
chunk0018_357_1	chr1	221708985	221709436	+	0	NA	intron (NR_111940, intron 1 of 2)	intron (NR_111940, intron 1 of 2)	27690	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.006652	0.440265	
chunk0027_279_1	chr10	77498106	77499299	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	139117	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.005029	0.472362	324(AAGCACAGTTTGTACC,-,0.00),325(AGCACAGTTTGTACCT,+,0.00),928(ATGCACACAAAGTGCT,-,0.00),929(TGCACACAAAGTGCTT,+,0.00),958(GAGGACAGTCTGTGCT,-,0.00),959(AGGACAGTCTGTGCTC,+,0.00)
chunk0154_369_1	chr5	87658632	87659004	+	0	NA	Intergenic	Intergenic	-245785	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.005376	0.319035	
chunk0013_280_1	chr1	170775122	170775515	+	0	NA	Intergenic	MIRc|SINE|MIR	111146	NM_022716	5396	Hs.283416	NM_006902	ENSG00000116132	PRRX1	AGOTC|PHOX1|PMX1|PRX-1|PRX1	paired related homeobox 1	protein-coding	0.007634	0.362944	
chunk0165_136_1	chr6	33429583	33429984	+	0	NA	intron (NM_006772, intron 3 of 18)	intron (NM_006772, intron 3 of 18)	-8548	NR_049800	100847012		NR_049800	ENSG00000284256	MIR5004	mir-5004	microRNA 5004	ncRNA	0.012469	0.480100	279(AATAACAGGATGTTCT,-,0.00),280(ATAACAGGATGTTCTG,+,0.00)
chunk0093_203_1	chr19	49553413	49553784	+	0	NA	Intergenic	AluSz|SINE|Alu	25980	NM_020650	57333	Hs.567550	NM_020650	ENSG00000142552	RCN3	RLP49	reticulocalbin 3	protein-coding	0.008086	0.451613	
chunk0091_211_1	chr19	9700601	9701168	+	0	NA	promoter-TSS (NM_001199814)	promoter-TSS (NM_001199814)	-67	NM_001199814	729648	Hs.626848	NM_001199814		ZNF812P	ZNF812	zinc finger protein 812, pseudogene	pseudo	0.010582	0.404930	372(AAGAACATAAAGTACA,-,0.00),373(AGAACATAAAGTACAT,+,0.00)
chunk0005_309_1	chr1	60576066	60576339	+	0	NA	Intergenic	Intergenic	249382	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.007326	0.354015	
chunk0179_14_1	chr7	42561004	42561235	+	0	NA	Intergenic	Intergenic	145328	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.000000	0.379310	
chunk0098_295_1	chr2	76007888	76008324	+	0	NA	Intergenic	LTR9|LTR|ERV1	-297121	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.013761	0.475973	
chunk0180_357_1	chr7	73749460	73750373	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-11049	NM_001301058	83451	Hs.647045	NM_148912	ENSG00000106077	ABHD11	PP1226|WBSCR21	abhydrolase domain containing 11	protein-coding	0.019715	0.477024	822(GGGGACGGTCAGTTCT,-,0.00),823(GGGACGGTCAGTTCTT,+,0.00)
chunk0012_53_1	chr1	155475636	155476068	+	0	NA	intron (NM_018489, intron 3 of 27)	L2b|LINE|L2	42672	NR_034180	645682	Hs.632482	NR_034180	ENSG00000237872	POU5F1P4	OCT3|OCT4|OTF-3|OTF3|Oct-3|Oct-4|Oct4-pg4|POU5F1|POU5FLC1	POU class 5 homeobox 1 pseudogene 4	pseudo	0.002315	0.360277	
chunk0195_153_1	chr8	95423066	95423265	+	0	NA	intron (NR_038209, intron 2 of 3)	intron (NR_038209, intron 2 of 3)	-153931	NM_177965	157657	Hs.548157	NM_177965	ENSG00000156172	C8orf37	BBS21|CORD16|RP64|smalltalk	chromosome 8 open reading frame 37	protein-coding	0.015075	0.570000	
chunk0206_83_1	chr9	120486537	120486872	+	0	NA	intron (NR_073556, intron 15 of 38)	L2c|LINE|L2	93466	NR_073557	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.011940	0.500000	
chunk0129_289_1	chr3	123338403	123338604	+	0	NA	intron (NM_001199642, intron 3 of 20)	intron (NM_001199642, intron 3 of 20)	77839	NM_001199642	111	Hs.593292	NM_183357	ENSG00000173175	ADCY5	AC5|FDFM	adenylate cyclase 5	protein-coding	0.014925	0.514851	
chunk0056_198_1	chr13	85719189	85719607	+	0	NA	Intergenic	Intergenic	79950	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.009569	0.355609	
chunk0033_137_1	chr11	15342403	15342602	+	0	NA	Intergenic	L2a|LINE|L2	193400	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.000000	0.455000	
chunk0119_302_1	chr22	46494929	46495671	+	0	NA	intron (NM_014246, intron 1 of 34)	Tigger3b|DNA|TcMar-Tigger	41870	NM_014246	9620	Hs.252387	NM_014246	ENSG00000075275	CELSR1	ADGRC1|CDHF9|FMI2|HFMI2|ME2	cadherin EGF LAG seven-pass G-type receptor 1	protein-coding	0.010782	0.448183	103(ATCACAGAGTGTCCTT,+,0.00)
chunk0122_244_1	chr3	34315558	34315757	+	0	NA	Intergenic	L1MD|LINE|L1	517086	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.000000	0.305000	
chunk0160_255_1	chr5	156824868	156825348	+	0	NA	Intergenic	Intergenic	-25430	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.004167	0.357588	
chunk0092_25_1	chr19	18834273	18834620	+	0	NA	intron (NM_001297549, intron 1 of 23)	intron (NM_001297549, intron 1 of 23)	2511	NM_001297549	5976	Hs.515266	NM_002911	ENSG00000005007	UPF1	HUPF1|NORF1|RENT1|pNORF1|smg-2	UPF1 RNA helicase and ATPase	protein-coding	0.020173	0.462644	
chunk0211_301_1	chrX	123264195	123264477	+	0	NA	intron (NM_007325, intron 3 of 15)	MER67A|LTR|ERV1	80093	NM_007325	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.003546	0.420495	
chunk0061_4_1	chr14	55427575	55427774	+	0	NA	intron (NM_199047, intron 5 of 6)	intron (NM_199047, intron 5 of 6)	12871	NM_199047	387332	Hs.528278	NM_199047	ENSG00000182521	TBPL2	TBP2|TRF3	TATA-box binding protein like 2	protein-coding	0.015075	0.570000	
chunk0019_218_1	chr1	227269102	227269301	+	0	NA	intron (NM_014826, intron 1 of 34)	MER58A|DNA|hAT-Charlie	48924	NM_003607	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.000000	0.390000	
chunk0126_102_1	chr3	74954419	74954799	+	0	NA	Intergenic	Intergenic	-259867	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.002632	0.401575	
chunk0145_87_1	chr4	145909892	145910150	+	0	NA	intron (NM_178835, intron 1 of 14)	intron (NM_178835, intron 1 of 14)	28939	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.034884	0.525097	
chunk0034_380_1	chr11	36435940	36436238	+	0	NA	intron (NM_001160167, intron 5 of 8)	intron (NM_001160167, intron 5 of 8)	35092	NM_001160169	79899	Hs.19987	NM_024841	ENSG00000135362	PRR5L	PROTOR2	proline rich 5 like	protein-coding	0.016779	0.461538	
chunk0029_168_1	chr10	99945313	99945674	+	0	NA	intron (NR_024130, intron 2 of 4)	MER99|DNA|hAT?	18284	NR_024130	100188954	Hs.656104	NR_024130		DNMBP-AS1	NCRNA00093	DNMBP antisense RNA 1	ncRNA	0.008310	0.383978	136(AGAAGAGTGTGTGCTC,+,0.00)
chunk0177_48_1	chr7	20958853	20959805	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	123898	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.008403	0.398741	
chunk0193_247_1	chr8	76889796	76890253	+	0	NA	Intergenic	Intergenic	76826	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004376	0.351528	
chunk0143_64_1	chr4	108044853	108045285	+	0	NA	Intergenic	Intergenic	55355	NM_001184705	3033	Hs.438289	NM_005327	ENSG00000138796	HADH	HAD|HADH1|HADHSC|HCDH|HHF4|MSCHAD|SCHAD	hydroxyacyl-CoA dehydrogenase	protein-coding	0.006944	0.327945	
chunk0007_324_1	chr1	84541491	84541996	+	0	NA	intron (NM_001310156, intron 8 of 13)	L1MC4|LINE|L1	32737	NM_004388	1486	Hs.513557	NM_004388	ENSG00000117151	CTBS	CTB	chitobiase	protein-coding	0.003960	0.314229	353(AGGAACAGGGAGTGTT,-,0.00)
chunk0066_326_1	chr15	36492762	36493332	+	0	NA	Intergenic	Intergenic	-86556	NM_001130010	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.003509	0.323993	
chunk0016_368_1	chr1	202478821	202479070	+	0	NA	intron (NM_032103, intron 1 of 11)	intron (NM_032103, intron 1 of 11)	16202	NM_032104	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.004016	0.376000	
chunk0010_164_1	chr1	115558127	115558735	+	0	NA	Intergenic	MER70B|LTR|ERVL	-83522	NM_138959	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.004934	0.412151	333(TAGAACAGGGTGTTCT,-,0.00),334(AGAACAGGGTGTTCTG,+,0.00)
chunk0196_117_1	chr8	103437486	103437978	+	0	NA	intron (NM_015420, intron 8 of 10)	intron (NM_015420, intron 8 of 10)	-22397	NR_102338	81034	Hs.532265	NM_030780	ENSG00000164933	SLC25A32	MFT|MFTC|RREI	solute carrier family 25 member 32	protein-coding	0.002033	0.279919	
chunk0135_97_1	chr3	186493836	186494284	+	0	NA	promoter-TSS (NR_033844)	promoter-TSS (NR_033844)	-399	NR_033844	253573	Hs.97386	NR_033844	ENSG00000224406	LINC02052	-	long intergenic non-protein coding RNA 2052	ncRNA	0.031250	0.534521	
chunk0168_144_1	chr6	83078469	83078668	+	0	NA	intron (NM_001199942, intron 1 of 39)	intron (NM_001199942, intron 1 of 39)	10902	NM_015018	23033	Hs.520246	NM_015018	ENSG00000083097	DOP1A	DOP1|DOPEY1|KIAA1117|dJ202D23.2	DOP1 leucine zipper like protein A	protein-coding	0.005025	0.335000	
chunk0074_9_1	chr16	19720481	19720681	+	0	NA	intron (NM_001305121, intron 2 of 8)	MIR|SINE|MIR	-2411	NM_001012991	400506	Hs.585209	NM_001012991	ENSG00000103550	KNOP1	101F10.1|C16orf88|FAM191A|TSG118	lysine rich nucleolar protein 1	protein-coding	0.005000	0.393035	
chunk0183_31_1	chr7	103523403	103523648	+	0	NA	exon (NM_173054, exon 47 of 64)	exon (NM_173054, exon 47 of 64)	-77348	NM_001167962	375611	Hs.585146	NM_198999	ENSG00000170615	SLC26A5	DFNB61|PRES	solute carrier family 26 member 5	protein-coding	0.012245	0.434959	
chunk0104_80_1	chr2	171875910	171876264	+	0	NA	intron (NR_047549, intron 2 of 16)	intron (NR_047549, intron 2 of 16)	18219	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.005650	0.343662	
chunk0173_36_1	chr6	142196047	142196292	+	0	NA	intron (NM_016485, intron 5 of 7)	L1MEc|LINE|L1	49007	NM_001286372	51534	Hs.431367	NM_016485	ENSG00000009844	VTA1	C6orf55|DRG-1|DRG1|HSPC228|LIP5|My012|SBP1	vesicle trafficking 1	protein-coding	0.012245	0.333333	
chunk0083_94_1	chr17	64385635	64385987	+	0	NA	intron (NM_000442, intron 2 of 15)	L2c|LINE|L2	5067	NM_000442	5175	Hs.376675	NM_000442	ENSG00000261371	PECAM1	CD31|CD31/EndoCAM|GPIIA'|PECA1|PECAM-1|endoCAM	platelet and endothelial cell adhesion molecule 1	protein-coding	0.011364	0.592068	170(GAGAACAGCGTGTCCC,-,0.00),171(AGAACAGCGTGTCCCA,+,0.00)
chunk0202_146_1	chr9	73515217	73515722	+	0	NA	Intergenic	CR1-16_AMi|LINE|CR1	363738	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.007921	0.320158	
chunk0100_234_1	chr2	112529912	112530319	+	0	NA	3' UTR (NM_153712, exon 7 of 7)	3' UTR (NM_153712, exon 7 of 7)	-11800	NM_019014	84172	Hs.745127	NM_019014	ENSG00000125630	POLR1B	RPA135|RPA2|Rpo1-2	RNA polymerase I subunit B	protein-coding	0.007371	0.409314	
chunk0077_105_1	chr16	78184417	78184940	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	85265	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.015296	0.358779	
chunk0161_152_1	chr5	168989637	168990268	+	0	NA	intron (NM_003062, intron 4 of 35)	intron (NM_003062, intron 4 of 35)	-23275	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.009509	0.469937	
chunk0041_149_1	chr11	125592086	125592460	+	0	NA	promoter-TSS (NM_152713)	promoter-TSS (NM_152713)	295	NR_132372	105369550	Hs.732083	NR_132372	ENSG00000149557	STT3A-AS1	-	STT3A antisense RNA 1	ncRNA	0.045455	0.520000	
chunk0057_71_1	chr13	98257068	98257464	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	48742	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.012626	0.352645	
chunk0085_437_1	chr18	10973947	10974206	+	0	NA	intron (NM_022068, intron 3 of 51)	intron (NM_022068, intron 3 of 51)	174686	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.023166	0.519231	
chunk0114_199_1	chr21	15299662	15300050	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	-235051	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.010309	0.403599	
chunk0145_306_1	chr4	150244646	150244903	+	0	NA	intron (NR_036614, intron 12 of 16)	intron (NR_036614, intron 12 of 16)	166500	NM_001040261	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.011673	0.434109	
chunk0159_355_1	chr5	144549589	144549929	+	0	NA	Intergenic	Intergenic	378886	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.008824	0.431085	
chunk0036_290_1	chr11	65487882	65488175	+	0	NA	Intergenic	Intergenic	-9734	NR_002819	378938	Hs.621695	NR_002819	ENSG00000251562	MALAT1	HCN|LINC00047|NCRNA00047|NEAT2|PRO2853	metastasis associated lung adenocarcinoma transcript 1	ncRNA	0.030717	0.581633	
chunk0112_301_1	chr20	44310677	44311293	+	0	NA	exon (NM_001080472, exon 1 of 2)	exon (NM_001080472, exon 1 of 2)	264	NM_001080472	128486	Hs.632269	NM_001080472	ENSG00000197296	FITM2	C20orf142|Fit2|dJ881L22.2	fat storage inducing transmembrane protein 2	protein-coding	0.081169	0.664506	
chunk0063_96_1	chr14	78541698	78542356	+	0	NA	intron (NM_004796, intron 1 of 16)	L1PA6|LINE|L1	138296	NM_004796	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.004559	0.493171	
chunk0095_292_1	chr2	20196190	20197024	+	0	NA	Intergenic	(ATGA)n|Simple_repeat|Simple_repeat	28559	NM_002997	6382	Hs.224607	NM_002997	ENSG00000115884	SDC1	CD138|SDC|SYND1|syndecan	syndecan 1	protein-coding	0.021583	0.586826	
chunk0193_365_1	chr8	80049327	80049624	+	0	NA	intron (NM_001287142, intron 4 of 6)	intron (NM_001287142, intron 4 of 6)	-19204	NM_014018	28957	Hs.521124	NM_014018	ENSG00000147586	MRPS28	HSPC007|MRP-S28|MRP-S35|MRPS35	mitochondrial ribosomal protein S28	protein-coding	0.003367	0.352349	
chunk0069_294_1	chr15	65326096	65326675	+	0	NA	TTS (NM_004884)	TTS (NM_004884)	21708	NR_002757	26832		NR_002757	ENSG00000200156	RNU5B-1	RNU5B|RNU5B-1P|U5B1	RNA, U5B small nuclear 1	snRNA	0.025907	0.563793	
chunk0164_3_1	chr6	17630047	17630253	+	0	NA	intron (NM_005124, intron 17 of 21)	intron (NM_005124, intron 17 of 21)	29863	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.004854	0.386473	
chunk0100_372_1	chr2	117996683	117996921	+	0	NA	intron (NM_019044, intron 4 of 23)	intron (NM_019044, intron 4 of 23)	17361	NM_019044	54520	Hs.107845	NM_019044	ENSG00000125633	CCDC93	-	coiled-coil domain containing 93	protein-coding	0.008403	0.414226	
chunk0138_288_1	chr4	40806867	40807567	+	0	NA	intron (NM_024677, intron 11 of 11)	intron (NM_024677, intron 11 of 11)	49938	NM_001166051	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.010000	0.395150	
chunk0039_235_1	chr11	101944951	101945633	+	0	NA	intron (NM_020802, intron 3 of 10)	L2c|LINE|L2	-28770	NM_178127	253935	Hs.318370	NM_178127	ENSG00000187151	ANGPTL5	-	angiopoietin like 5	protein-coding	0.007331	0.354319	345(AAGAACAGCTTGTACA,-,0.00),346(AGAACAGCTTGTACAA,+,0.00)
chunk0044_379_1	chr12	39892196	39892481	+	0	NA	intron (NM_052885, intron 4 of 9)	intron (NM_052885, intron 4 of 9)	213521	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.003509	0.461538	
chunk0032_48_1	chr11	1639862	1640184	+	0	NA	Intergenic	Intergenic	10220	NM_001001480	439915	Hs.653467	NM_001001480	ENSG00000185940	KRTAP5-5	KRTAP5-11|KRTAP5.5	keratin associated protein 5-5	protein-coding	0.031056	0.517028	
chunk0047_74_1	chr12	67710599	67710976	+	0	NA	intron (NR_110063, intron 4 of 4)	intron (NR_110063, intron 4 of 4)	18688	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.007958	0.478836	
chunk0051_119_1	chr12	115268953	115269678	+	0	NA	Intergenic	Intergenic	-585151	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.001379	0.446281	
chunk0135_425_1	chr3	193710183	193710781	+	0	NA	Intergenic	Intergenic	-83150	NR_046634	100873941	Hs.679364	NR_046634	ENSG00000224855	OPA1-AS1	-	OPA1 antisense RNA 1	ncRNA	0.020067	0.449082	
chunk0099_92_1	chr2	85524594	85525191	+	0	NA	Intergenic	Intergenic	13994	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.015075	0.501672	
chunk0112_444_1	chr20	47924915	47925499	+	0	NA	Intergenic	Intergenic	-58019	NR_109942	101060004	Hs.129970	NR_109942		LINC01523	-	long intergenic non-protein coding RNA 1523	ncRNA	0.008562	0.441026	383(AGGTACTCACTGTTCC,-,0.00),384(GGTACTCACTGTTCCT,+,0.00)
chunk0029_418_1	chr10	109967617	109967989	+	0	NA	intron (NR_038943, intron 2 of 4)	intron (NR_038943, intron 2 of 4)	-38165	NM_019903	120	Hs.501012	NM_001121	ENSG00000148700	ADD3	ADDL|CPSQ3	adducin 3	protein-coding	0.005376	0.436997	
chunk0187_18_1	chr8	624309	624509	+	0	NA	intron (NM_001303100, intron 5 of 5)	L1MB7|LINE|L1	-78628	NM_175075	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.015000	0.457711	162(CAGCACAGTCTGTATC,-,0.00),163(AGCACAGTCTGTATCA,+,0.00)
chunk0151_122_1	chr5	43785169	43785672	+	0	NA	Intergenic	MIR3|SINE|MIR	-182190	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.005964	0.426587	
chunk0010_414_1	chr1	119637497	119638212	+	0	NA	intron (NM_001080470, intron 1 of 2)	intron (NM_001080470, intron 1 of 2)	9913	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.002797	0.353352	
chunk0026_231_1	chr10	65334936	65335900	+	0	NA	Intergenic	Intergenic	-236007	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.002075	0.336788	
chunk0182_356_1	chr7	99827086	99827854	+	0	NA	promoter-TSS (NM_022820)	promoter-TSS (NM_022820)	-543	NR_103869	64816	Hs.306220	NM_022820	ENSG00000021461	CYP3A43	-	cytochrome P450 family 3 subfamily A member 43	protein-coding	0.002604	0.391417	357(AGGCACAGGGAGTCCT,-,0.00),358(GGCACAGGGAGTCCTT,+,0.00)
chunk0132_105_1	chr3	155724007	155724363	+	0	NA	Intergenic	L1PB1|LINE|L1	-19977	NM_014996	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.000000	0.344538	
chunk0153_61_1	chr5	67792869	67793215	+	0	NA	promoter-TSS (NR_130779)	promoter-TSS (NR_130779)	-171	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.008671	0.423631	133(AAGTACAGAGAGTTCC,-,0.00),134(AGTACAGAGAGTTCCA,+,0.00)
chunk0027_360_1	chr10	78995292	78995924	+	0	NA	intron (NR_015429, intron 3 of 7)	intron (NR_015429, intron 3 of 7)	71840	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.011076	0.519747	
chunk0188_414_1	chr8	18899402	18900101	+	0	NA	intron (NM_015310, intron 2 of 15)	Tigger2|DNA|TcMar-Tigger	-90856	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.004292	0.400000	
chunk0092_83_1	chr19	21236651	21237560	+	0	NA	Intergenic	LTR10C|LTR|ERV1	92305	NM_021269	7562	Hs.466296	NM_021269	ENSG00000182141	ZNF708	KOX8|ZNF15|ZNF15L1	zinc finger protein 708	protein-coding	0.007701	0.403297	251(ATGTACTTTATGTTCT,-,0.00),252(TGTACTTTATGTTCTT,+,0.00)
chunk0107_295_1	chr2	218747185	218747384	+	0	NA	intron (NM_014640, intron 9 of 19)	intron (NM_014640, intron 9 of 19)	-34465	NM_000784	1593	Hs.516700	NM_000784	ENSG00000135929	CYP27A1	CP27|CTX|CYP27	cytochrome P450 family 27 subfamily A member 1	protein-coding	0.010050	0.535000	
chunk0136_236_1	chr4	8746466	8746665	+	0	NA	Intergenic	Intergenic	125252	NM_001306142	3166	Hs.104134	NM_018942	ENSG00000215612	HMX1	H6|NKX5-3	H6 family homeobox 1	protein-coding	0.025126	0.475000	
chunk0109_361_1	chr2	239240451	239240947	+	0	NA	intron (NM_006037, intron 2 of 26)	intron (NM_006037, intron 2 of 26)	-45242	NR_026664	85009	Hs.744565	NM_032923		MGC16025	-	uncharacterized LOC85009	ncRNA	0.032258	0.527163	277(CAGCACATGATGTGCC,-,0.00),278(AGCACATGATGTGCCC,+,0.00),430(AAGACAGACAGTGCTT,+,0.00)
chunk0056_356_1	chr13	92223557	92223977	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	128440	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.002381	0.296912	
chunk0087_405_1	chr18	42018404	42019015	+	0	NA	intron (NM_001308020, intron 11 of 23)	L2a|LINE|L2	63511	NM_002647	5289	Hs.464971	NM_002647	ENSG00000078142	PIK3C3	VPS34|Vps34|hVps34	phosphatidylinositol 3-kinase catalytic subunit type 3	protein-coding	0.004910	0.366013	
chunk0198_458_1	chr8	144409091	144409290	+	0	NA	intron (NM_013291, intron 1 of 37)	CpG-27806	159	NM_013291	29894	Hs.493202	NM_013291	ENSG00000071894	CPSF1	CPSF160|HSU37012|P/cl.18	cleavage and polyadenylation specific factor 1	protein-coding	0.125628	0.735000	
chunk0150_225_1	chr5	35540016	35540379	+	0	NA	Intergenic	Intergenic	-77690	NM_144722	79925	Hs.298863	NM_024867	ENSG00000152582	SPEF2	CT122|KPL2	sperm flagellar 2	protein-coding	0.008264	0.398352	342(CGGGGCATTGTGTTCT,-,0.00),343(GGGGCATTGTGTTCTG,+,0.00)
chunk0103_141_1	chr2	162112110	162112768	+	0	NA	Intergenic	Intergenic	-2002	NR_110255	101929532	Hs.639883	NR_110255	ENSG00000236841	LOC101929532	-	uncharacterized LOC101929532	ncRNA	0.006079	0.374810	
chunk0096_146_1	chr2	29112437	29112636	+	0	NA	intron (NM_001287528, intron 1 of 14)	L1ME3Cz|LINE|L1	-2342	NR_109844	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.000000	0.325000	
chunk0183_283_1	chr7	107605170	107605674	+	0	NA	intron (NM_001008405, intron 5 of 7)	intron (NM_001008405, intron 5 of 7)	24663	NM_001008405	55973	Hs.303787	NM_018844	ENSG00000075790	BCAP29	BAP29	B cell receptor associated protein 29	protein-coding	0.003968	0.388119	162(GAAAACAGTTTGTTCT,-,0.00),163(AAAACAGTTTGTTCTC,+,0.00)
chunk0044_260_1	chr12	32181886	32182115	+	0	NA	intron (NM_001003398, intron 1 of 8)	intron (NM_001003398, intron 1 of 8)	74749	NM_001714	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.004367	0.373913	
chunk0093_216_1	chr19	49877288	49877771	+	0	NA	promoter-TSS (NM_032375)	promoter-TSS (NM_032375)	104	NM_024682	79735	Hs.631587	NM_024682	ENSG00000104946	TBC1D17	-	TBC1 domain family member 17	protein-coding	0.066253	0.588843	
chunk0106_211_1	chr2	202417944	202418495	+	0	NA	intron (NM_001204, intron 1 of 12)	intron (NM_001204, intron 1 of 12)	41892	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.005445	0.391304	
chunk0148_431_1	chr4	189111501	189112242	+	0	NA	Intergenic	Intergenic	-547735	NR_121679	101928971	Hs.519164	NR_121679	ENSG00000250739	LINC01262	TCONS_l2_00021807	long intergenic non-protein coding RNA 1262	ncRNA	0.005398	0.358491	
chunk0065_190_1	chr14	100011876	100012274	+	0	NA	Intergenic	MIRc|SINE|MIR	-53339	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.002513	0.375940	
chunk0198_324_1	chr8	139855915	139856325	+	0	NA	intron (NM_001160372, intron 21 of 22)	intron (NM_001160372, intron 21 of 22)	-153064	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.012195	0.547445	203(GAGCACAGACTGAGCC,-,0.00),204(AGCACAGACTGAGCCA,+,0.00)
chunk0150_183_1	chr5	34526441	34526979	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-129618	NM_015577	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.005576	0.419295	
chunk0146_357_1	chr4	167379313	167379946	+	0	NA	Intergenic	Intergenic	-145039	NM_001204358	50859	Hs.481133	NM_016950	ENSG00000196104	SPOCK3	HSAJ1454|TES-3|TICN3	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3	protein-coding	0.007899	0.395899	
chunk0135_36_1	chr3	185253177	185253408	+	0	NA	promoter-TSS (NR_106712)	promoter-TSS (NR_106712)	-20	NR_106712	100847054		NR_106712	ENSG00000264614	MIR5588	-	microRNA 5588	ncRNA	0.008658	0.422414	133(AAGGACAGCCTGGACT,-,0.00),134(AGGACAGCCTGGACTC,+,0.00)
chunk0057_335_1	chr13	107064416	107064775	+	0	NA	Intergenic	Intergenic	410715	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.011142	0.363889	
chunk0211_444_1	chrX	129652257	129652747	+	0	NA	intron (NM_017413, intron 1 of 2)	intron (NM_017413, intron 1 of 2)	2454	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.022449	0.568228	
chunk0043_298_1	chr12	21984630	21984978	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-48110	NM_020297	10060	Hs.732701	NM_005691	ENSG00000069431	ABCC9	ABC37|ATFB12|CANTU|CMD1O|SUR2	ATP binding cassette subfamily C member 9	protein-coding	0.002874	0.349570	
chunk0108_10_1	chr2	226028420	226029000	+	0	NA	Intergenic	Intergenic	-114084	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003448	0.332186	
chunk0173_97_1	chr6	143078889	143079248	+	0	NA	intron (NM_001286587, intron 2 of 6)	L1MD1|LINE|L1	18226	NM_001286589	51390	Hs.567501	NM_016108	ENSG00000146416	AIG1	AIG-1|dJ95L4.1	androgen induced 1	protein-coding	0.008357	0.400000	
chunk0183_125_1	chr7	105489383	105489776	+	0	NA	intron (NM_019042, intron 7 of 15)	intron (NM_019042, intron 7 of 15)	32659	NM_019042	54517	Hs.520619	NM_019042	ENSG00000091127	PUS7	IDDABS	pseudouridine synthase 7	protein-coding	0.007634	0.428934	
chunk0138_422_1	chr4	45086801	45087322	+	0	NA	Intergenic	Intergenic	-360427	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.001919	0.323755	308(CAGAACAATCTGTACT,-,0.00),309(AGAACAATCTGTACTA,+,0.00)
chunk0058_378_1	chr14	29346422	29346734	+	0	NA	Intergenic	Intergenic	573874	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.003205	0.300319	
chunk0134_178_1	chr3	178087567	178087767	+	0	NA	Intergenic	Intergenic	270802	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.000000	0.358209	
chunk0117_149_1	chr22	19690399	19690642	+	0	NA	Intergenic	L1MC4|LINE|L1	-23944	NM_002688	5413	Hs.728762	NM_002688	ENSG00000184702	SEPTIN5	CDCREL|CDCREL-1|CDCREL1|H5|HCDCREL-1|PNUTL1|SEPT5	septin 5	protein-coding	0.032922	0.590164	
chunk0176_327_1	chr7	17213405	17213704	+	0	NA	Intergenic	Intergenic	-85098	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.003344	0.336667	
chunk0063_37_1	chr14	76799694	76800464	+	0	NA	intron (NM_015305, intron 7 of 9)	intron (NM_015305, intron 7 of 9)	12861	NM_015305	23357	Hs.497448	NM_015305	ENSG00000013523	ANGEL1	Ccr4e|KIAA0759	angel homolog 1	protein-coding	0.006494	0.391699	
chunk0028_66_1	chr10	83580181	83580488	+	0	NA	Intergenic	L1PA16|LINE|L1	-559095	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.009772	0.548701	167(GAAGACAGCTTGTCCT,-,0.00),168(AAGACAGCTTGTCCTC,+,0.00)
chunk0109_438_1	chr2	241383412	241383661	+	0	NA	intron (NM_014808, intron 2 of 26)	intron (NM_014808, intron 2 of 26)	27287	NM_001282983	9855	Hs.726316	NM_014808	ENSG00000006607	FARP2	FIR|FRG|PLEKHC3	FERM, ARH/RhoGEF and pleckstrin domain protein 2	protein-coding	0.012048	0.560000	
chunk0189_44_1	chr8	19928371	19928958	+	0	NA	Intergenic	AluJo|SINE|Alu	-10407	NM_000237	4023	Hs.180878	NM_000237	ENSG00000175445	LPL	HDLCQ11|LIPD	lipoprotein lipase	protein-coding	0.008518	0.447279	340(GAGAACAGCCTGGGCA,-,0.00)
chunk0102_362_1	chr2	152649356	152650138	+	0	NA	TTS (NM_052905)	TTS (NM_052905)	67714	NM_017892	55660	Hs.643580	NM_017892	ENSG00000196504	PRPF40A	FBP-11|FBP11|FLAF1|FNBP3|HIP-10|HIP10|HYPA|NY-REN-6|Prp40	pre-mRNA processing factor 40 homolog A	protein-coding	0.008951	0.332056	
chunk0008_225_1	chr1	93983661	93984171	+	0	NA	Intergenic	MER68B|LTR|ERVL	-74318	NM_001308253	2730	Hs.315562	NM_002061	ENSG00000023909	GCLM	GLCLR	glutamate-cysteine ligase modifier subunit	protein-coding	0.001961	0.454012	
chunk0011_25_1	chr1	143210838	143211037	+	0	NA	Intergenic	Intergenic	211655	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.040201	0.375000	
chunk0083_20_1	chr17	63039329	63039901	+	0	NA	intron (NM_025185, intron 1 of 24)	intron (NM_025185, intron 1 of 24)	30078	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.006993	0.389180	
chunk0041_100_1	chr11	124705033	124705235	+	0	NA	Intergenic	SVA_D|Retroposon|SVA	-28831	NM_001199922	54414	Hs.10056	NM_018978	ENSG00000110013	SIAE	AIS6|CSE-C|CSEC|LSE|YSG2	sialic acid acetylesterase	protein-coding	0.024752	0.502463	
chunk0147_83_1	chr4	173169363	173169562	+	0	NA	intron (NM_017423, intron 1 of 11)	CpG	709	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.105528	0.770000	
chunk0187_147_1	chr7	149720387	149721011	+	0	NA	intron (NM_032534, intron 3 of 16)	intron (NM_032534, intron 3 of 16)	5688	NM_001290187	84626	Hs.299560	NM_032534	ENSG00000133619	KRBA1	-	KRAB-A domain containing 1	protein-coding	0.030449	0.625600	310(TGGGACATGGTGTCTC,-,0.00),311(GGGACATGGTGTCTCC,+,0.00),459(CGGCACAGCCTGCACC,-,0.00),460(GGCACAGCCTGCACCT,+,0.00)
chunk0016_362_1	chr1	202374061	202374532	+	0	NA	intron (NM_002481, intron 1 of 23)	L2c|LINE|L2	25594	NM_001167858	4660	Hs.444403	NM_002481	ENSG00000077157	PPP1R12B	MYPT2|PP1bp55	protein phosphatase 1 regulatory subunit 12B	protein-coding	0.002123	0.370763	
chunk0069_186_1	chr15	63157200	63157556	+	0	NA	intron (NM_015920, intron 1 of 3)	CpG	164	NM_015920	51065	Hs.108957	NM_015920	ENSG00000185088	RPS27L	-	ribosomal protein S27 like	protein-coding	0.081461	0.635854	
chunk0071_397_1	chr15	89378311	89378919	+	0	NA	intron (NR_133002, intron 2 of 5)	CpG	573	NR_015411	254559	Hs.136313	NR_015411	ENSG00000255571	MIR9-3HG	LINC00925	MIR9-3 host gene	ncRNA	0.078947	0.643678	
chunk0088_241_1	chr18	48608522	48608950	+	0	NA	intron (NM_001142397, intron 2 of 12)	intron (NM_001142397, intron 2 of 12)	-61864	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.014019	0.573427	202(GTGCACAGCCTGTTCT,-,0.00),203(TGCACAGCCTGTTCTG,+,0.00)
chunk0100_378_1	chr2	118077599	118078255	+	0	NA	Intergenic	Intergenic	-10547	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.013720	0.403349	410(GAGGACACAGTGTTTT,-,0.00),411(AGGACACAGTGTTTTA,+,0.00)
chunk0167_167_1	chr6	63111532	63112203	+	0	NA	Intergenic	L1MA3|LINE|L1	208110	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.004471	0.462798	
chunk0106_174_1	chr2	200810346	200810623	+	0	NA	intron (NR_110275, intron 1 of 3)	intron (NR_110275, intron 1 of 3)	-1062	NM_001207067	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.000000	0.431655	
chunk0012_211_1	chr1	160109598	160110180	+	0	NA	Intergenic	Intergenic	-5841	NM_000702	477	Hs.34114	NM_000702	ENSG00000018625	ATP1A2	FHM2|MHP2	ATPase Na+/K+ transporting subunit alpha 2	protein-coding	0.012027	0.499142	
chunk0082_253_1	chr17	57534918	57535133	+	0	NA	intron (NM_138962, intron 7 of 13)	intron (NM_138962, intron 7 of 13)	-11428	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.009302	0.550926	
chunk0209_299_1	chrX	48761854	48762491	+	0	NA	intron (NM_001080489, intron 1 of 3)	intron (NM_001080489, intron 1 of 3)	422	NM_001080489	392465	Hs.437539	NM_001080489	ENSG00000171433	GLOD5	-	glyoxalase domain containing 5	protein-coding	0.014129	0.531348	450(AAGGACATGGTGTTCC,-,0.00),451(AGGACATGGTGTTCCG,+,0.00)
chunk0049_23_1	chr12	89533969	89534168	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-7806	NM_001199782	100528030	Hs.25130	NM_001199781	ENSG00000259075	POC1B-GALNT4	GALNT4|GalNAc-T4	POC1B-GALNT4 readthrough	protein-coding	0.010050	0.480000	
chunk0110_241_1	chr20	16423618	16423945	+	0	NA	intron (NM_001199865, intron 15 of 24)	intron (NM_001199865, intron 15 of 24)	149653	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.009174	0.496951	
chunk0068_261_1	chr15	56393271	56393470	+	0	NA	intron (NM_198524, intron 7 of 12)	intron (NM_198524, intron 7 of 12)	27946	NM_198524	374618	Hs.511476	NM_198524	ENSG00000151575	TEX9	-	testis expressed 9	protein-coding	0.005025	0.445000	
chunk0164_430_1	chr6	27503868	27504286	+	0	NA	Intergenic	Intergenic	-30959	NM_007149	7738	Hs.158174	NM_007149	ENSG00000096654	ZNF184	kr-ZNF3	zinc finger protein 184	protein-coding	0.016746	0.453461	
chunk0036_333_1	chr11	66618754	66618953	+	0	NA	intron (NM_001198846, intron 1 of 1)	intron (NM_001198846, intron 1 of 1)	2271	NM_001198836	10432	Hs.533712	NM_006328	ENSG00000239306	RBM14	COAA|PSP2|SIP|SYTIP1|TMEM137	RNA binding motif protein 14	protein-coding	0.015075	0.465000	
chunk0183_423_1	chr7	110962586	110963236	+	0	NA	intron (NM_032549, intron 4 of 5)	intron (NM_032549, intron 4 of 5)	-128095	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.006154	0.342550	
chunk0185_15_1	chr7	123956695	123957541	+	0	NA	intron (NM_153189, intron 4 of 4)	L2b|LINE|L2	31263	NM_001174046	6677	Hs.121494	NM_003117	ENSG00000106304	SPAM1	HEL-S-96n|HYA1|HYAL1|HYAL3|HYAL5|PH-20|PH20|SPAG15	sperm adhesion molecule 1	protein-coding	0.002364	0.354191	
chunk0045_216_1	chr12	48012119	48012520	+	0	NA	Intergenic	Intergenic	-7817	NM_001844	1280	Hs.408182	NM_001844	ENSG00000139219	COL2A1	ANFH|AOM|COL11A3|SEDC|STL1	collagen type II alpha 1 chain	protein-coding	0.014963	0.330846	
chunk0161_158_1	chr5	169032790	169032989	+	0	NA	intron (NR_109897, intron 3 of 4)	L1MA9|LINE|L1	19662	NR_109897	728095	Hs.145601	NR_109897		LOC728095	-	uncharacterized LOC728095	ncRNA	0.000000	0.285000	
chunk0094_8_1	chr2	883538	883751	+	0	NA	Intergenic	Intergenic	-15218	NR_033880	339822	Hs.651879	NR_033880	ENSG00000237667	LINC01115	-	long intergenic non-protein coding RNA 1115	ncRNA	0.032864	0.514019	
chunk0023_220_1	chr10	26462039	26462246	+	0	NA	intron (NM_019043, intron 2 of 14)	MER58C|DNA|hAT-Charlie	23805	NM_019043	54518	Hs.310421	NM_019043	ENSG00000077420	APBB1IP	INAG1|PREL1|RARP1|RIAM	amyloid beta precursor protein binding family B member 1 interacting protein	protein-coding	0.009662	0.384615	
chunk0132_177_1	chr3	156926420	156927014	+	0	NA	intron (NM_001004316, intron 4 of 12)	L2b|LINE|L2	100358	NM_001193283	389170	Hs.478048	NM_001004316	ENSG00000197980	LEKR1	-	leucine, glutamate and lysine rich 1	protein-coding	0.000000	0.346218	
chunk0191_301_1	chr8	54763685	54763953	+	0	NA	Intergenic	Intergenic	147752	NM_006269	6101	Hs.732820	NM_006269	ENSG00000104237	RP1	DCDC4A|ORP1	RP1 axonemal microtubule associated	protein-coding	0.011194	0.386617	130(AAGGACATAATGCTCC,-,0.00),131(AGGACATAATGCTCCA,+,0.00)
chunk0193_313_1	chr8	78290557	78290859	+	0	NA	Intergenic	Intergenic	-225393	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.000000	0.240924	
chunk0200_18_1	chr9	14650382	14651021	+	0	NA	intron (NM_178566, intron 7 of 9)	intron (NM_178566, intron 7 of 9)	42781	NM_178566	340481	Hs.649522	NM_178566	ENSG00000175893	ZDHHC21	DHHC-21|DHHC21|DNZ1|HSPC097	zinc finger DHHC-type containing 21	protein-coding	0.003130	0.315625	
chunk0132_166_1	chr3	156706169	156706712	+	0	NA	3' UTR (NM_001184718, exon 6 of 6)	3' UTR (NM_001184718, exon 6 of 6)	29776	NM_001184718	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.003683	0.365809	
chunk0155_217_1	chr5	95207201	95207880	+	0	NA	intron (NM_024717, intron 1 of 22)	intron (NM_024717, intron 1 of 22)	77035	NM_024717	79772	Hs.591248	NM_024717	ENSG00000175471	MCTP1	-	multiple C2 and transmembrane domain containing 1	protein-coding	0.001473	0.364706	
chunk0107_1_1	chr2	209566151	209566394	+	0	NA	intron (NM_001039538, intron 2 of 14)	intron (NM_001039538, intron 2 of 14)	-13407	NM_002374	4133	Hs.368281	NM_002374	ENSG00000078018	MAP2	MAP-2|MAP2A|MAP2B|MAP2C	microtubule associated protein 2	protein-coding	0.016461	0.401639	
chunk0122_450_1	chr3	39744586	39745104	+	0	NA	Intergenic	Intergenic	-64069	NM_001284423	25924	Hs.594535	NM_015460	ENSG00000170011	MYRIP	SLAC2-C|SLAC2C	myosin VIIA and Rab interacting protein	protein-coding	0.005792	0.360308	
chunk0087_103_1	chr18	32454582	32455043	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	15672	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.004338	0.396104	
chunk0125_397_1	chr3	71983588	71984164	+	0	NA	Intergenic	Intergenic	116579	NR_104116	285286	Hs.559386	NR_104116	ENSG00000241163	LINC00877	-	long intergenic non-protein coding RNA 877	ncRNA	0.008681	0.467938	273(GAGCGCACACTGTCCT,-,0.00),274(AGCGCACACTGTCCTA,+,0.00)
chunk0005_222_1	chr1	59286417	59286876	+	0	NA	Intergenic	L1M2|LINE|L1	-10307	NM_018291	55277	Hs.444301	NM_018291	ENSG00000172456	FGGY	-	FGGY carbohydrate kinase domain containing	protein-coding	0.006536	0.310870	
chunk0022_161_1	chr10	12605589	12606034	+	0	NA	intron (NM_020397, intron 2 of 9)	intron (NM_020397, intron 2 of 9)	27058	NR_039700	100616151		NR_039700	ENSG00000263584	MIR4480	-	microRNA 4480	ncRNA	0.020225	0.589686	1(CAGTACAGTTTGTGCC,-,0.00),2(AGTACAGTTTGTGCCC,+,0.00)
chunk0097_394_1	chr2	62013822	62014497	+	0	NA	intron (NM_152516, intron 2 of 2)	intron (NM_152516, intron 2 of 2)	108491	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.002963	0.406805	
chunk0066_63_1	chr15	28969774	28969973	+	0	NA	intron (NM_001130414, intron 1 of 12)	intron (NM_001130414, intron 1 of 12)	48236	NM_001130414	321	Hs.618112	NM_005503	ENSG00000034053	APBA2	D15S1518E|HsT16821|LIN-10|MGC:14091|MINT2|X11-BETA|X11L	amyloid beta precursor protein binding family A member 2	protein-coding	0.040201	0.595000	
chunk0137_93_1	chr4	13385886	13386685	+	0	NA	intron (NM_001017979, intron 4 of 6)	L1PA13|LINE|L1	98080	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.000000	0.338750	
chunk0019_212_1	chr1	227085425	227085916	+	0	NA	intron (NM_014826, intron 15 of 34)	L1M7|LINE|L1	145433	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.000000	0.367886	
chunk0119_308_1	chr22	46638822	46639427	+	0	NA	intron (NM_015124, intron 2 of 17)	intron (NM_015124, intron 2 of 17)	12363	NM_015124	23151	Hs.475150	NM_015124	ENSG00000075240	GRAMD4	DIP	GRAM domain containing 4	protein-coding	0.028099	0.526403	279(ATGAACTCTGTGTGCT,-,0.00),280(TGAACTCTGTGTGCTC,+,0.00)
chunk0005_340_1	chr1	61152724	61152923	+	0	NA	intron (NM_001145511, intron 2 of 10)	intron (NM_001145511, intron 2 of 10)	70515	NM_001134673	4774	Hs.740757	NM_005595	ENSG00000162599	NFIA	BRMUTD|CTF|NF-I/A|NF1-A|NFI-A|NFI-L	nuclear factor I A	protein-coding	0.000000	0.410000	
chunk0135_285_1	chr3	189430765	189430964	+	0	NA	Intergenic	L1PBa|LINE|L1	-190270	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.005025	0.505000	
chunk0182_192_1	chr7	95855199	95855735	+	0	NA	intron (NM_001135556, intron 5 of 16)	L1MA8|LINE|L1	82961	NM_001278422	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.005597	0.361266	
chunk0119_229_1	chr22	45280592	45281034	+	0	NA	Intergenic	Intergenic	-4174	NM_001167574	7380	Hs.632787	NM_006953	ENSG00000100373	UPK3A	UP3A|UPIII|UPIIIA|UPK3	uroplakin 3A	protein-coding	0.006787	0.424379	
chunk0067_446_1	chr15	50224808	50225331	+	0	NA	intron (NM_003645, intron 5 of 9)	intron (NM_003645, intron 5 of 9)	40896	NM_001306146	3067	Hs.1481	NM_002112	ENSG00000140287	HDC	-	histidine decarboxylase	protein-coding	0.003824	0.322519	
chunk0006_444_1	chr1	76753036	76753288	+	0	NA	Intergenic	U6|snRNA|snRNA	-114339	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.007937	0.343874	
chunk0203_436_1	chr9	91261918	91262418	+	0	NA	intron (NM_001306190, intron 5 of 8)	intron (NM_001306190, intron 5 of 8)	99756	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.006000	0.317365	
chunk0145_365_1	chr4	151427258	151427709	+	0	NA	intron (NM_001109977, intron 1 of 13)	intron (NM_001109977, intron 1 of 13)	18237	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.002217	0.305310	223(TGGTACAAATTGTTCT,-,0.00),224(GGTACAAATTGTTCTC,+,0.00)
chunk0184_197_1	chr7	116971478	116971761	+	0	NA	intron (NM_021908, intron 1 of 15)	intron (NM_021908, intron 1 of 15)	-17285	NR_002330	93653	Hs.597516	NR_002330	ENSG00000227199	ST7-AS1	ST7AS1|ST7OT1	ST7 antisense RNA 1	ncRNA	0.003534	0.380282	
chunk0043_292_1	chr12	21689088	21689579	+	0	NA	Intergenic	L1PA15|LINE|L1	-31478	NM_001315537	3945	Hs.446149	NM_002300	ENSG00000111716	LDHB	HEL-S-281|LDH-B|LDH-H|LDHBD|TRG-5	lactate dehydrogenase B	protein-coding	0.004073	0.414634	244(TGAACATATTGTCCAC,+,0.00)
chunk0131_220_1	chr3	149191278	149191814	+	0	NA	intron (NR_046371, intron 9 of 17)	L1MD|LINE|L1	30499	NR_046371	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.001866	0.310987	147(TAGCACAGGATGTTTT,-,0.00),148(AGCACAGGATGTTTTT,+,0.00)
chunk0087_116_1	chr18	32769961	32770172	+	0	NA	exon (NM_020805, exon 2 of 9)	exon (NM_020805, exon 2 of 9)	2945	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.052133	0.603774	
chunk0120_441_1	chr3	13724517	13724769	+	0	NA	intron (NR_027103, intron 4 of 5)	L1MDa|LINE|L1	73922	NR_027103	285375	Hs.319969	NR_027103	ENSG00000224514	LINC00620	-	long intergenic non-protein coding RNA 620	ncRNA	0.000000	0.355731	
chunk0138_428_1	chr4	45148960	45149683	+	0	NA	Intergenic	Intergenic	-422687	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.005533	0.343923	
chunk0011_83_1	chr1	145208983	145209182	+	0	NA	intron (NR_111954, intron 1 of 3)	intron (NR_111954, intron 1 of 3)	6989	NR_111956	103091866	Hs.271249	NR_111954	ENSG00000272419	LINC01145	-	long intergenic non-protein coding RNA 1145	ncRNA	0.005025	0.450000	
chunk0077_177_1	chr16	79639929	79640128	+	0	NA	Intergenic	Intergenic	-39303	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.000000	0.405000	
chunk0160_93_1	chr5	150161468	150161774	+	0	NA	Intergenic	Intergenic	-5160	NM_001804	1044	Hs.1545	NM_001804	ENSG00000113722	CDX1	-	caudal type homeobox 1	protein-coding	0.013072	0.557003	
chunk0077_166_1	chr16	79390287	79390818	+	0	NA	Intergenic	Intergenic	210173	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.009416	0.402256	274(AGGAACAGACTGCTCT,-,0.00),275(GGAACAGACTGCTCTG,+,0.00)
chunk0162_33_1	chr6	1035335	1036132	+	0	NA	intron (NR_027115, intron 1 of 4)	L2a|LINE|L2	65599	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.031368	0.525063	
chunk0077_403_1	chr16	84946996	84947396	+	0	NA	Intergenic	Intergenic	64339	NM_001145548	55625	Hs.461610	NM_017740	ENSG00000153786	ZDHHC7	DHHC7|SERZ-B|SERZ1|ZNF370	zinc finger DHHC-type containing 7	protein-coding	0.022500	0.511222	
chunk0197_225_1	chr8	123011945	123012849	+	0	NA	TTS (NM_024295)	TTS (NM_024295)	30026	NM_001134671	79139	Hs.241576	NM_024295	ENSG00000136986	DERL1	DER-1|DER1|derlin-1	derlin 1	protein-coding	0.015487	0.470718	
chunk0138_354_1	chr4	42048170	42048873	+	0	NA	intron (NM_006345, intron 8 of 17)	intron (NM_006345, intron 8 of 17)	58015	NM_006345	10463	Hs.479634	NM_006345	ENSG00000014824	SLC30A9	BILAPES|C4orf1|GAC63|HUEL|ZNT9	solute carrier family 30 member 9	protein-coding	0.001422	0.340909	268(GGGGACATACAGTTCT,-,0.00),269(GGGACATACAGTTCTC,+,0.00)
chunk0079_82_1	chr17	11704898	11705169	+	0	NA	exon (NM_001372, exon 26 of 69)	exon (NM_001372, exon 26 of 69)	106602	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.014760	0.518382	
chunk0132_416_1	chr3	164479371	164479570	+	0	NA	Intergenic	Intergenic	-307914	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.000000	0.300000	
chunk0006_301_1	chr1	71311679	71311963	+	0	NA	Intergenic	Intergenic	230497	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.014085	0.336842	
chunk0109_432_1	chr2	241334819	241335227	+	0	NA	intron (NM_001008491, intron 4 of 13)	MIRb|SINE|MIR	19162	NM_004404	4735	Hs.721234	NM_004404	ENSG00000168385	SEPTIN2	DIFF6|NEDD-5|NEDD5|Pnutl3|SEPT2|hNedd5	septin 2	protein-coding	0.004902	0.378973	
chunk0049_85_1	chr12	90770793	90771228	+	0	NA	Intergenic	Intergenic	-147013	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.004598	0.327982	
chunk0026_51_1	chr10	60967060	60967818	+	0	NA	intron (NR_024554, intron 2 of 11)	AluSz6|SINE|Alu	-23164	NM_001242359	9886	Hs.737374	NM_014836	ENSG00000072422	RHOBTB1	-	Rho related BTB domain containing 1	protein-coding	0.013193	0.421607	419(AGGAACACATTGTTCC,-,0.00),420(GGAACACATTGTTCCC,+,0.00)
chunk0070_33_1	chr15	69366833	69367188	+	0	NA	intron (NM_001104554, intron 3 of 8)	L1MEd|LINE|L1	-47236	NM_001281301	9493	Hs.270845	NM_004856	ENSG00000137807	KIF23	CHO1|KNSL5|MKLP-1|MKLP1	kinesin family member 23	protein-coding	0.008451	0.303371	
chunk0009_99_1	chr1	102191544	102192091	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-194583	NM_001288823	118427	Hs.484475	NM_058170	ENSG00000118733	OLFM3	NOE3|NOELIN3|OPTIMEDIN	olfactomedin 3	protein-coding	0.005484	0.394161	
chunk0191_444_1	chr8	57988488	57988704	+	0	NA	Intergenic	LTR33A|LTR|ERVL	-5958	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.004630	0.442396	
chunk0201_431_1	chr9	69996770	69997362	+	0	NA	Intergenic	MIR3|SINE|MIR	-46515	NM_153267	256691	Hs.547172	NM_153267	ENSG00000165072	MAMDC2	-	MAM domain containing 2	protein-coding	0.003378	0.376054	269(AAGGACAGAATGTTCC,-,0.00),270(AGGACAGAATGTTCCC,+,0.00)
chunk0211_250_1	chrX	120550568	120551104	+	0	NA	intron (NM_003588, intron 4 of 21)	L1ME4b|LINE|L1	10126	NM_001079872	8450	Hs.102914	NM_003588	ENSG00000158290	CUL4B	CUL-4B|MRXHF2|MRXS15|MRXSC|SFM2	cullin 4B	protein-coding	0.014925	0.389199	138(GGGAACATTCTGTTTT,-,0.00),139(GGAACATTCTGTTTTT,+,0.00)
chunk0113_134_1	chr20	51842374	51842573	+	0	NA	intron (NR_110016, intron 2 of 2)	intron (NR_110016, intron 2 of 2)	20440	NR_110016	101927678	Hs.683840	NR_110016	ENSG00000227964	LINC01429	-	long intergenic non-protein coding RNA 1429	ncRNA	0.000000	0.495000	
chunk0195_64_1	chr8	93819405	93820093	+	0	NA	TTS (NR_024522)	TTS (NR_024522)	64905	NM_001142301	91147	Hs.116240	NM_153704	ENSG00000164953	TMEM67	JBTS6|MECKELIN|MKS3|NPHP11|TNEM67	transmembrane protein 67	protein-coding	0.008721	0.433962	299(TGGAACAGTATGTGCT,-,0.00),300(GGAACAGTATGTGCTC,+,0.00)
chunk0145_247_1	chr4	148779023	148779568	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-336775	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.009174	0.364469	
chunk0161_396_1	chr5	177157890	177158101	+	0	NA	intron (NM_022455, intron 2 of 22)	L1MB7|LINE|L1	24163	NM_022455	64324	Hs.106861	NM_022455	ENSG00000165671	NSD1	ARA267|KMT3B|SOTOS|SOTOS1|STO	nuclear receptor binding SET domain protein 1	protein-coding	0.009479	0.339623	
chunk0179_187_1	chr7	47122505	47122704	+	0	NA	Intergenic	Intergenic	459540	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.010050	0.525000	
chunk0099_173_1	chr2	88857134	88857676	+	0	NA	Intergenic	Intergenic	45035	NR_039635	100616399		NR_039635	ENSG00000265510	MIR4436A	mir-4436a	microRNA 4436a	ncRNA	0.018450	0.523020	
chunk0058_372_1	chr14	29199776	29200354	+	0	NA	Intergenic	L1P4|LINE|L1	427361	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.001730	0.338515	
chunk0134_172_1	chr3	178063450	178063806	+	0	NA	Intergenic	Intergenic	246763	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.002809	0.425770	239(AGGAACTGACAGTGCA,-,0.00)
chunk0099_407_1	chr2	102120212	102121178	+	0	NA	intron (NM_001288706, intron 1 of 11)	intron (NM_001288706, intron 1 of 11)	-22081	NM_000877	3554	Hs.701982	NM_000877	ENSG00000115594	IL1R1	CD121A|D2S1473|IL-1R-alpha|IL1R|IL1RA|P80	interleukin 1 receptor type 1	protein-coding	0.012422	0.458118	
chunk0204_50_1	chr9	93194318	93195039	+	0	NA	intron (NM_001282394, intron 1 of 29)	L1MC2|LINE|L1	9748	NM_001282394	65268	Hs.654856	NM_006648	ENSG00000165238	WNK2	NY-CO-43|P/OKcl.13|PRKWNK2|SDCCAG43	WNK lysine deficient protein kinase 2	protein-coding	0.005548	0.369806	
chunk0177_22_1	chr7	20593754	20594495	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	-21498	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.014845	0.439353	383(GAGAACAGCATGTGCT,-,0.00),384(AGAACAGCATGTGCTC,+,0.00)
chunk0098_1_1	chr2	64906794	64907318	+	0	NA	intron (NR_036586, intron 1 of 2)	7SLRNA|srpRNA|srpRNA	25391	NR_036586	400958	Hs.591565	NR_036586		LINC02245	-	long intergenic non-protein coding RNA 2245	ncRNA	0.007634	0.440000	
chunk0166_223_1	chr6	46950020	46950354	+	0	NA	intron (NM_015234, intron 1 of 20)	L3|LINE|CR1	4751	NM_015234	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.020958	0.498507	
chunk0205_34_1	chr9	105679474	105679938	+	0	NA	Intergenic	Intergenic	-14819	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.010776	0.438710	
chunk0151_128_1	chr5	43982529	43982761	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-379415	NR_073113	100652772	Hs.482043	NR_073113		NNT-AS1	-	NNT antisense RNA 1	ncRNA	0.004310	0.351931	
chunk0110_359_1	chr20	19783919	19784157	+	0	NA	Intergenic	Intergenic	-102483	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.037815	0.602510	
chunk0193_87_1	chr8	73606221	73606420	+	0	NA	intron (NM_001164384, intron 7 of 10)	L1ME1|LINE|L1	140607	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.000000	0.205000	
chunk0130_167_1	chr3	133017110	133017356	+	0	NA	Intergenic	Intergenic	-21055	NM_001136469	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.004065	0.437247	
chunk0029_412_1	chr10	109926418	109926797	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-3054	NR_030724									0.018470	0.444737	
chunk0039_95_1	chr11	97293198	97293889	+	0	NA	Intergenic	Intergenic	-786666	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.005789	0.427746	
chunk0129_429_1	chr3	127553852	127554052	+	0	NA	Intergenic	L1ME4b|LINE|L1	-16172	NR_125397	101927149	Hs.407798	NR_125397	ENSG00000239921	LINC01471	-	long intergenic non-protein coding RNA 1471	ncRNA	0.015000	0.437811	
chunk0143_153_1	chr4	110073391	110073867	+	0	NA	intron (NM_001130721, intron 3 of 4)	intron (NM_001130721, intron 3 of 4)	124986	NM_001130721	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.010504	0.436059	
chunk0193_28_1	chr8	71053785	71054123	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	302557	NM_172059	2138	Hs.444971	NM_000503	ENSG00000104313	EYA1	BOP|BOR|BOS1|OFC1	EYA transcriptional coactivator and phosphatase 1	protein-coding	0.002959	0.460177	
chunk0014_5_1	chr1	174200343	174200912	+	0	NA	intron (NM_014857, intron 1 of 20)	intron (NM_014857, intron 1 of 20)	41213	NM_014857	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.003515	0.301754	
chunk0148_362_1	chr5	14588798	14589591	+	0	NA	intron (NM_019018, intron 1 of 7)	L2c|LINE|L2	7412	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.012610	0.498741	317(GAAAACAGTCAGTCCC,-,0.00),421(AAGGACACCGTGTGCT,-,0.00),422(AGGACACCGTGTGCTA,+,0.00)
chunk0055_246_1	chr13	63058793	63059329	+	0	NA	Intergenic	Intergenic	-251702	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.007463	0.283054	
chunk0145_42_1	chr4	144582901	144583391	+	0	NA	Intergenic	Intergenic	-62850	NM_022475	64399	Hs.507991	NM_022475	ENSG00000164161	HHIP	HIP	hedgehog interacting protein	protein-coding	0.008163	0.393075	
chunk0034_442_1	chr11	39444834	39445899	+	0	NA	Intergenic	Intergenic	796508	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.007512	0.403377	
chunk0013_420_1	chr1	173300697	173301115	+	0	NA	intron (NR_037845, intron 2 of 2)	MIRb|SINE|MIR	-93593	NM_003326	7292	Hs.181097	NM_003326	ENSG00000117586	TNFSF4	CD134L|CD252|GP34|OX-40L|OX4OL|TNLG2B|TXGP1	TNF superfamily member 4	protein-coding	0.007177	0.303103	
chunk0173_123_1	chr6	143642502	143642884	+	0	NA	intron (NM_001100166, intron 1 of 11)	MLT1C|LTR|ERVL-MaLR	34513	NM_014721	9749	Hs.102471	NM_014721	ENSG00000112419	PHACTR2	C6orf56	phosphatase and actin regulator 2	protein-coding	0.005236	0.441253	
chunk0201_368_1	chr9	68648963	68649360	+	0	NA	Intergenic	Intergenic	-56253	NM_003558	8395	Hs.534371	NM_003558	ENSG00000107242	PIP5K1B	MSS4|STM7	phosphatidylinositol-4-phosphate 5-kinase type 1 beta	protein-coding	0.002519	0.467337	
chunk0054_58_1	chr13	41781175	41781875	+	0	NA	intron (NM_015058, intron 19 of 44)	intron (NM_015058, intron 19 of 44)	179560	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.004286	0.375178	
chunk0124_35_1	chr3	52238419	52238785	+	0	NA	intron (NM_007284, intron 1 of 8)	intron (NM_007284, intron 1 of 8)	565	NM_007284	11344	Hs.436439	NM_007284	ENSG00000247596	TWF2	A6RP|A6r|MSTP011|PTK9L	twinfilin actin binding protein 2	protein-coding	0.024590	0.501362	
chunk0094_344_1	chr2	9336829	9337329	+	0	NA	intron (NM_003887, intron 9 of 27)	intron (NM_003887, intron 9 of 27)	86435	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.014000	0.463074	
chunk0045_203_1	chr12	47737272	47737878	+	0	NA	exon (NM_001098532, exon 27 of 27)	exon (NM_001098532, exon 27 of 27)	-12003	NM_001172440	8909	Hs.997	NM_006025	ENSG00000111405	ENDOU	P11|PP11|PRSS26	endonuclease, poly(U) specific	protein-coding	0.028053	0.622735	
chunk0108_394_1	chr2	237235407	237235754	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	150139	NM_198189	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.008646	0.479885	
chunk0142_10_1	chr4	89855803	89856284	+	0	NA	Intergenic	Intergenic	-17747	NM_001146055	6622	Hs.21374	NM_000345	ENSG00000145335	SNCA	NACP|PARK1|PARK4|PD1	synuclein alpha	protein-coding	0.008316	0.367220	
chunk0066_40_1	chr15	27768279	27768487	+	0	NA	intron (NM_001300984, intron 22 of 22)	LTR23|LTR|ERV1	330929	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.024038	0.468900	132(AAAGACACTGTGTTCC,-,0.00),133(AAGACACTGTGTTCCC,+,0.00)
chunk0167_417_1	chr6	75436576	75437137	+	0	NA	intron (NR_125859, intron 4 of 8)	MER63A|DNA|hAT-Blackjack	8449	NR_039670	100616389		NR_039670	ENSG00000263533	MIR4463	-	microRNA 4463	ncRNA	0.010695	0.435943	375(GAGCACAATCAGTTCC,-,0.00),376(AGCACAATCAGTTCCT,+,0.00)
chunk0173_285_1	chr6	148027083	148027585	+	0	NA	Intergenic	Intergenic	-315259	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.005976	0.397614	
chunk0112_250_1	chr20	41693316	41693742	+	0	NA	Intergenic	LTR91|LTR|ERVL	-75035	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.037559	0.461358	
chunk0088_359_1	chr18	52901627	52901826	+	0	NA	intron (NM_005215, intron 2 of 28)	intron (NM_005215, intron 2 of 28)	-335375	NR_130465	100616232		NR_130465	ENSG00000263872	MIR4528	-	microRNA 4528	ncRNA	0.005025	0.355000	
chunk0201_311_1	chr9	43071050	43071257	+	0	NA	Intergenic	Intergenic	282753	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.000000	0.336538	
chunk0172_44_1	chr6	134020014	134020605	+	0	NA	intron (NM_145176, intron 2 of 4)	intron (NM_145176, intron 2 of 4)	32342	NM_145176	154091	Hs.486508	NM_145176	ENSG00000146411	SLC2A12	GLUT12|GLUT8	solute carrier family 2 member 12	protein-coding	0.001692	0.324324	281(TAGAACAGCAAGTACT,-,0.00),282(AGAACAGCAAGTACTT,+,0.00)
chunk0080_46_1	chr17	21602168	21602510	+	0	NA	Intergenic	Intergenic	-50661	NM_001113434	339263	Hs.514016	NM_001113434	ENSG00000212719	LINC02693	C17orf51	long intergenic non-protein coding RNA 2693	ncRNA	0.011696	0.591837	
chunk0161_451_1	chr5	178833974	178834517	+	0	NA	Intergenic	L1M4|LINE|L1	-25708	NM_058230	117608	Hs.724051	NM_058230	ENSG00000178338	ZNF354B	KID2	zinc finger protein 354B	protein-coding	0.001842	0.305147	
chunk0009_208_1	chr1	106134532	106135002	+	0	NA	Intergenic	L2|LINE|L2	-515832	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.006383	0.333333	
chunk0070_41_1	chr15	69468533	69469130	+	0	NA	Intergenic	Intergenic	16011	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.018425	0.530100	
chunk0059_327_1	chr14	36797715	36798089	+	0	NA	intron (NM_030631, intron 3 of 9)	intron (NM_030631, intron 3 of 9)	140334	NM_006194	5083	Hs.132576	NM_006194	ENSG00000198807	PAX9	STHAG3	paired box 9	protein-coding	0.002674	0.309333	
chunk0061_160_1	chr14	59787315	59787682	+	0	NA	intron (NM_021136, intron 1 of 8)	MIRb|SINE|MIR	83341	NM_021136	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.002725	0.434783	
chunk0109_312_1	chr20	8981439	8981912	+	0	NA	Intergenic	Intergenic	-87379	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.012685	0.455696	
chunk0021_273_1	chr1	243991749	243992037	+	0	NA	intron (NR_033883, intron 2 of 11)	L4_C_Mam|LINE|RTE-X	-57046	NM_001278196	10472	Hs.69997	NM_006352	ENSG00000179456	ZBTB18	C2H2-171|MRD22|RP58|TAZ-1|ZNF238	zinc finger and BTB domain containing 18	protein-coding	0.006944	0.460208	
chunk0144_384_1	chr4	140085675	140086537	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	67973	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.013921	0.383546	
chunk0009_329_1	chr1	109058376	109058612	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-16266	NM_001142550	22911	Hs.570055	NM_014969	ENSG00000085433	WDR47	-	WD repeat domain 47	protein-coding	0.000000	0.426160	
chunk0110_7_1	chr20	9582681	9583061	+	0	NA	intron (NM_020341, intron 4 of 10)	L1MC3|LINE|L1	-67873	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.002632	0.401575	
chunk0207_186_1	chr9	130795023	130795651	+	0	NA	intron (NM_007313, intron 1 of 10)	intron (NM_007313, intron 1 of 10)	-39918	NM_005157	25	Hs.431048	NM_005157	ENSG00000097007	ABL1	ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-abl	ABL proto-oncogene 1, non-receptor tyrosine kinase	protein-coding	0.009554	0.410175	
chunk0186_256_1	chr7	141276655	141276879	+	0	NA	intron (NM_001195278, intron 2 of 3)	Tigger3b|DNA|TcMar-Tigger	202535	NM_001195278	100507421	Hs.283851	NM_001195278	ENSG00000261115	TMEM178B	-	transmembrane protein 178B	protein-coding	0.004464	0.426667	
chunk0147_107_1	chr4	173683520	173684348	+	0	NA	Intergenic	Intergenic	153476	NR_003679	79804	Hs.61435	NR_003679	ENSG00000237125	HAND2-AS1	DEIN|NBLA00301|UPH	HAND2 antisense RNA 1	ncRNA	0.002415	0.310012	
chunk0015_319_1	chr1	189369106	189369305	+	0	NA	Intergenic	Intergenic	1108424	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.005025	0.390000	
chunk0200_95_1	chr9	16604699	16605182	+	0	NA	intron (NM_017637, intron 3 of 6)	intron (NM_017637, intron 3 of 6)	265848	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.010352	0.371901	
chunk0046_11_1	chr12	54136217	54136437	+	0	NA	Intergenic	Intergenic	10256	NR_026656	400043	Hs.19193	NR_026656	ENSG00000250742	LINC02381	-	long intergenic non-protein coding RNA 2381	ncRNA	0.013636	0.542986	
chunk0162_41_1	chr6	1118105	1118486	+	0	NA	Intergenic	Intergenic	-16963	NR_027115	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.013123	0.434555	271(ATGGACAGGATGTTCT,-,0.00),272(TGGACAGGATGTTCTA,+,0.00)
chunk0090_415_1	chr18	79011274	79011958	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	31341	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.027778	0.505109	
chunk0081_140_1	chr17	40637702	40638279	+	0	NA	intron (NM_003079, intron 4 of 10)	intron (NM_003079, intron 4 of 10)	9861	NM_003079	6605	Hs.743978	NM_003079	ENSG00000073584	SMARCE1	BAF57|CSS5	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	protein-coding	0.001733	0.366782	
chunk0088_7_1	chr18	43138949	43139221	+	0	NA	Intergenic	L3|LINE|CR1	-23393	NM_001272077	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.362637	
chunk0192_445_1	chr8	69951334	69951597	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-116401	NM_030958	81796	Hs.152460	NM_030958	ENSG00000137571	SLCO5A1	OATP-J|OATP-RP4|OATP5A1|OATPJ|OATPRP4|SLC21A15	solute carrier organic anion transporter family member 5A1	protein-coding	0.011407	0.412879	
chunk0060_44_1	chr14	41084105	41084501	+	0	NA	intron (NR_109758, intron 3 of 3)	intron (NR_109758, intron 3 of 3)	129592	NR_109757	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.000000	0.337531	212(CAGTACATACTGTCTC,-,0.00),213(AGTACATACTGTCTCT,+,0.00)
chunk0153_426_1	chr5	75856069	75856376	+	0	NA	Intergenic	L1MA2|LINE|L1	-138734	NM_001099271	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.000000	0.370130	
chunk0125_388_1	chr3	71693852	71694733	+	0	NA	intron (NM_173359, intron 5 of 7)	intron (NM_173359, intron 5 of 7)	31083	NM_001134651	317649	Hs.581355	NM_173359	ENSG00000163412	EIF4E3	eIF-4E3|eIF4E-3	eukaryotic translation initiation factor 4E family member 3	protein-coding	0.009081	0.383220	190(ATGCACTTTCTGTGCC,-,0.00),191(TGCACTTTCTGTGCCC,+,0.00)
chunk0094_108_1	chr2	4246122	4246988	+	0	NA	Intergenic	Intergenic	-272523	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.013857	0.419839	
chunk0208_395_1	chrX	29023455	29023683	+	0	NA	intron (NM_014271, intron 2 of 10)	intron (NM_014271, intron 2 of 10)	436005	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.000000	0.292576	
chunk0084_370_1	chr17	81600649	81600856	+	0	NA	intron (NM_017921, intron 8 of 16)	intron (NM_017921, intron 8 of 16)	-23319	NR_130139	55666	Hs.464333	NM_017921	ENSG00000182446	NPLOC4	NPL4	NPL4 homolog, ubiquitin recognition factor	protein-coding	0.000000	0.456731	
chunk0052_256_1	chr12	123633630	123633915	+	0	NA	promoter-TSS (NM_001516)	promoter-TSS (NM_001516)	4	NM_001414	1967	Hs.741273	NM_001414	ENSG00000111361	EIF2B1	EIF2B|EIF2BA	eukaryotic translation initiation factor 2B subunit alpha	protein-coding	0.094737	0.674825	
chunk0187_235_1	chr7	152615958	152616388	+	0	NA	Intergenic	Intergenic	59992	NM_005431	7516	Hs.647093	NM_005431	ENSG00000196584	XRCC2	FANCU	X-ray repair cross complementing 2	protein-coding	0.004651	0.338747	227(AGGAACAAAAAGTCCC,-,0.00),228(GGAACAAAAAGTCCCT,+,0.00)
chunk0043_427_1	chr12	25968584	25969616	+	0	NA	intron (NM_001164748, intron 1 of 4)	L2a|LINE|L2	-4655	NM_001164747	11228	Hs.696433	NM_007211	ENSG00000123094	RASSF8	C12orf2|HOJ1	Ras association domain family member 8	protein-coding	0.009690	0.458858	163(GAGAGCACACTGTACT,-,0.00),164(AGAGCACACTGTACTA,+,0.00)
chunk0064_351_1	chr14	96827523	96828074	+	0	NA	intron (NM_003384, intron 1 of 12)	LTR41|LTR|ERVL	30451	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.001815	0.360507	
chunk0034_49_1	chr11	26929501	26930156	+	0	NA	Intergenic	Intergenic	-64253	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.000000	0.368902	
chunk0036_406_1	chr11	68090526	68091188	+	0	NA	intron (NM_001277, intron 2 of 11)	intron (NM_001277, intron 2 of 11)	30534	NM_001277	1119	Hs.77221	NM_001277	ENSG00000110721	CHKA	CHK|CK|CKI|EK	choline kinase alpha	protein-coding	0.012085	0.363499	
chunk0095_287_1	chr2	20133592	20134095	+	0	NA	Intergenic	Intergenic	-81815	NM_014713	9741	Hs.467807	NM_014713	ENSG00000068697	LAPTM4A	HUMORF13|LAPTM4|MBNT|Mtrp	lysosomal protein transmembrane 4 alpha	protein-coding	0.013917	0.402778	234(GGGCACACGGTGTTCC,-,0.00),235(GGCACACGGTGTTCCT,+,0.00)
chunk0045_68_1	chr12	45622413	45622896	+	0	NA	Intergenic	L2a|LINE|L2	105267	NR_028408	400027	Hs.597122	NR_028408		LINC00938	-	long intergenic non-protein coding RNA 938	ncRNA	0.006211	0.440083	
chunk0102_311_1	chr2	151120072	151120649	+	0	NA	Intergenic	Intergenic	141515	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.005199	0.356401	
chunk0010_278_1	chr1	117366594	117366825	+	0	NA	promoter-TSS (NM_006699)	promoter-TSS (NM_006699)	-754	NM_006699	10905	Hs.435938	NM_006699	ENSG00000198162	MAN1A2	MAN1B	mannosidase alpha class 1A member 2	protein-coding	0.125541	0.728448	
chunk0057_106_1	chr13	99065753	99066023	+	0	NA	intron (NM_001130049, intron 1 of 32)	L2c|LINE|L2	20518	NM_001130049	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.007407	0.365314	
chunk0185_98_1	chr7	125563035	125563628	+	0	NA	Intergenic	L1M7|LINE|L1	-299040	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.011804	0.368687	
chunk0192_65_1	chr8	60403745	60403982	+	0	NA	non-coding (NR_103854, exon 3 of 3)	non-coding (NR_103854, exon 3 of 3)	9955	NR_103854	100505532	Hs.720321	NR_103854		LINC01301	-	long intergenic non-protein coding RNA 1301	ncRNA	0.029536	0.491597	
chunk0142_257_1	chr4	99143984	99144410	+	0	NA	5' UTR (NM_001306171, exon 1 of 10)	5' UTR (NM_001306171, exon 1 of 10)	101	NM_001306172	127	Hs.1219	NM_000670	ENSG00000198099	ADH4	ADH-2|HEL-S-4	alcohol dehydrogenase 4 (class II), pi polypeptide	protein-coding	0.004695	0.388759	
chunk0179_356_1	chr7	50911990	50912440	+	0	NA	Intergenic	L1MC1|LINE|L1	-118753	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.004444	0.356984	
chunk0072_17_1	chr16	456771	458177	+	0	NA	intron (NM_014700, intron 1 of 13)	intron (NM_014700, intron 1 of 13)	-17376	NM_001142272	9727	Hs.531642	NM_014700	ENSG00000090565	RAB11FIP3	CART1|FIP3-Rab11|Rab11-FIP3	RAB11 family interacting protein 3	protein-coding	0.016358	0.438522	
chunk0126_401_1	chr3	85006018	85006223	+	0	NA	intron (NM_001167674, intron 1 of 9)	MamRTE1|LINE|RTE-BovB	47138	NM_001167675	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.000000	0.441748	
chunk0146_294_1	chr4	164846707	164846926	+	0	NA	Intergenic	Intergenic	-30172	NM_001297550	100506013	Hs.105196	NM_001297550	ENSG00000248329	APELA	ELA|Ende|tdl	apelin receptor early endogenous ligand	protein-coding	0.009132	0.390909	
chunk0029_332_1	chr10	104821936	104822657	+	0	NA	intron (NM_014978, intron 1 of 26)	intron (NM_014978, intron 1 of 26)	-156080	NR_104028	100505890	Hs.348526	NR_104028	ENSG00000226387	SORCS3-AS1	-	SORCS3 antisense RNA 1	ncRNA	0.005548	0.423823	
chunk0114_81_1	chr21	9246253	9248286	+	0	NA	Intergenic	Intergenic	-117508	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.003443	0.465093	
chunk0149_326_1	chr5	26619888	26620287	+	0	NA	Intergenic	MIRc|SINE|MIR	418495	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.000000	0.265000	
chunk0101_35_1	chr2	122366290	122366954	+	0	NA	Intergenic	L2a|LINE|L2	611077	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.004518	0.419549	
chunk0118_325_1	chr22	35364302	35364548	+	0	NA	Intergenic	Intergenic	-16642	NM_002133	3162	Hs.517581	NM_002133	ENSG00000100292	HMOX1	HMOX1D|HO-1|HSP32|bK286B10	heme oxygenase 1	protein-coding	0.012195	0.453441	
chunk0122_50_1	chr3	28553474	28553692	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-21695	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.000000	0.456621	
chunk0160_17_1	chr5	149019009	149019796	+	0	NA	intron (NM_024577, intron 12 of 16)	intron (NM_024577, intron 12 of 16)	43007	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.006353	0.355330	342(ATTACAGCATGTTCTC,+,0.00)
chunk0092_175_1	chr19	29964827	29965076	+	0	NA	intron (NR_045557, intron 1 of 9)	intron (NR_045557, intron 1 of 9)	22712	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.000000	0.360000	
chunk0106_262_1	chr2	203693283	203693869	+	0	NA	Intergenic	Intergenic	-12899	NM_001243077	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.005119	0.379898	
chunk0071_388_1	chr15	89241931	89242330	+	0	NA	Intergenic	Intergenic	-1833	NM_001113378	55215	Hs.513126	NM_018193	ENSG00000140525	FANCI	KIAA1794	FA complementation group I	protein-coding	0.005013	0.395000	180(AAGAACATTTAGTTCC,-,0.00),181(AGAACATTTAGTTCCA,+,0.00)
chunk0047_143_1	chr12	69610451	69610650	+	0	NA	exon (NM_201550, exon 1 of 1)	exon (NM_201550, exon 1 of 1)	612	NM_201550	376132	Hs.448708	NM_201550	ENSG00000198812	LRRC10	HRLRRP|LRRC10A	leucine rich repeat containing 10	protein-coding	0.015075	0.575000	
chunk0082_47_1	chr17	50970516	50970887	+	0	NA	intron (NM_001130528, intron 29 of 29)	intron (NM_001130528, intron 29 of 29)	76267	NM_001251971	9043	Hs.463439	NM_003971	ENSG00000008294	SPAG9	CT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6	sperm associated antigen 9	protein-coding	0.016173	0.408602	
chunk0051_89_1	chr12	114535887	114536120	+	0	NA	Intergenic	Intergenic	-127561	NM_000192	6910	Hs.381715	NM_000192	ENSG00000089225	TBX5	HOS	T-box transcription factor 5	protein-coding	0.017167	0.324786	
chunk0002_350_1	chr1	25500868	25501599	+	0	NA	Intergenic	Intergenic	-42352	NM_015627	26119	Hs.590911	NM_015627	ENSG00000157978	LDLRAP1	ARH|ARH1|ARH2|FHCB1|FHCB2	low density lipoprotein receptor adaptor protein 1	protein-coding	0.004104	0.435792	
chunk0076_355_1	chr16	71758123	71758909	+	0	NA	promoter-TSS (NR_003059)	promoter-TSS (NR_003059)	-29	NR_003059	692111		NR_003059	ENSG00000223224	SNORD71	HBII-239|MIRN768|hsa-mir-768	small nucleolar RNA, C/D box 71	snoRNA	0.007634	0.395172	
chunk0185_207_1	chr7	128698216	128698475	+	0	NA	Intergenic	Intergenic	-10716	NM_001282789	84691	Hs.732440	NM_032599	ENSG00000135248	FAM71F1	FAM137A|NYD-SP18	family with sequence similarity 71 member F1	protein-coding	0.011583	0.603846	
chunk0036_413_1	chr11	68146115	68146673	+	0	NA	Intergenic	Intergenic	-25003	NM_212469	1119	Hs.77221	NM_001277	ENSG00000110721	CHKA	CHK|CK|CKI|EK	choline kinase alpha	protein-coding	0.026882	0.613596	
chunk0137_17_1	chr4	10814263	10814815	+	0	NA	Intergenic	Intergenic	-129777	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.001812	0.347197	283(AAGAACAAAATGTTCC,-,0.00),284(AGAACAAAATGTTCCT,+,0.00)
chunk0174_222_1	chr6	160424908	160425426	+	0	NA	intron (NM_021977, intron 5 of 10)	UCON40|Unknown|Unknown	76794	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.001931	0.356455	
chunk0128_26_1	chr3	104228314	104228802	+	0	NA	Intergenic	Intergenic	-704442	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.002049	0.353783	226(CAGGACACATTGTACC,-,0.00),227(AGGACACATTGTACCT,+,0.00)
chunk0057_113_1	chr13	99198528	99198928	+	0	NA	intron (NR_036532, intron 1 of 1)	Charlie1a|DNA|hAT-Charlie	-1697	NM_001144072	337867	Hs.508545	NM_177967	ENSG00000134882	UBAC2	PHGDHL1	UBA domain containing 2	protein-coding	0.010000	0.359102	
chunk0011_107_1	chr1	145997179	145997411	+	0	NA	promoter-TSS (NM_006472)	promoter-TSS (NM_006472)	-664	NM_006472	10628	Hs.533977	NM_006472	ENSG00000265972	TXNIP	ARRDC6|EST01027|HHCPA78|THIF|VDUP1	thioredoxin interacting protein	protein-coding	0.030172	0.523605	
chunk0112_189_1	chr20	40197748	40198248	+	0	NA	Intergenic	Intergenic	193537	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.006000	0.435130	
chunk0171_170_1	chr6	124999624	124999823	+	0	NA	intron (NR_104440, intron 2 of 6)	Charlie29a|DNA|hAT-Charlie	16359	NR_104440	154214	Hs.12876	NM_152553	ENSG00000146373	RNF217	C6orf172|IBRDC1|OSTL|dJ84N20.1	ring finger protein 217	protein-coding	0.005025	0.355000	
chunk0144_252_1	chr4	136370976	136371306	+	0	NA	Intergenic	Intergenic	-457461	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.000000	0.256798	
chunk0083_157_1	chr17	65944056	65944359	+	0	NA	intron (NM_001302891, intron 16 of 24)	L1PA10|LINE|L1	-117664	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.404605	
chunk0064_249_1	chr14	94519535	94519734	+	0	NA	Intergenic	(GGT)n|Simple_repeat|Simple_repeat	-1790	NM_173850	145264	Hs.99476	NM_173850	ENSG00000165953	SERPINA12	OL-64	serpin family A member 12	protein-coding	0.000000	0.525000	
chunk0039_18_1	chr11	95585086	95585420	+	0	NA	Intergenic	L1PREC2|LINE|L1	204537	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.005988	0.397015	34(GGTACATATTGTACAT,+,0.00)
chunk0180_294_1	chr7	70163009	70163328	+	0	NA	intron (NM_015570, intron 4 of 18)	intron (NM_015570, intron 4 of 18)	564249	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.006270	0.459375	205(CAGGACGAGATGTTCC,-,0.00),206(AGGACGAGATGTTCCC,+,0.00)
chunk0148_132_1	chr5	5579790	5580234	+	0	NA	Intergenic	Intergenic	157339	NM_015325	23379	Hs.449296	NM_015325	ENSG00000164151	ICE1	KIAA0947	interactor of little elongation complex ELL subunit 1	protein-coding	0.002252	0.370787	
chunk0037_227_1	chr11	74964046	74964320	+	0	NA	intron (NM_014752, intron 1 of 4)	L1MC|LINE|L1	14936	NM_014752	9789	Hs.282700	NM_014752	ENSG00000118363	SPCS2	-	signal peptidase complex subunit 2	protein-coding	0.014599	0.403636	
chunk0046_325_1	chr12	62621156	62621574	+	0	NA	Intergenic	L2b|LINE|L2	17679	NR_029661	406891		NR_029661	ENSG00000199179	MIRLET7I	LET7I|MIRNLET7I|hsa-let-7i|let-7i	microRNA let-7i	ncRNA	0.014354	0.463007	
chunk0091_262_1	chr19	11152683	11153021	+	0	NA	intron (NM_001317033, intron 1 of 4)	intron (NM_001317033, intron 1 of 4)	2960	NM_182513	147841	Hs.381225	NM_182513	ENSG00000161888	SPC24	SPBC24	SPC24 component of NDC80 kinetochore complex	protein-coding	0.014793	0.551622	
chunk0022_118_1	chr10	11512579	11512834	+	0	NA	intron (NM_001080491, intron 4 of 13)	L2c|LINE|L2	19574	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.007843	0.441406	
chunk0130_337_1	chr3	138609116	138609895	+	0	NA	intron (NM_018147, intron 1 of 4)	intron (NM_018147, intron 1 of 4)	428	NM_018147	55179	Hs.173438	NM_018147	ENSG00000158234	FAIM	FAIM1	Fas apoptotic inhibitory molecule	protein-coding	0.064185	0.546154	
chunk0174_340_1	chr6	164098713	164099319	+	0	NA	Intergenic	Intergenic	684373	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.018152	0.439868	493(GAGCACAAGATGTACA,-,0.00),494(AGCACAAGATGTACAT,+,0.00)
chunk0138_121_1	chr4	36394761	36395116	+	0	NA	Intergenic	Intergenic	31490	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.005634	0.325843	
chunk0120_148_1	chr3	5246218	5246417	+	0	NA	Intergenic	Intergenic	3938	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.005025	0.455000	
chunk0126_344_1	chr3	82585715	82586059	+	0	NA	Intergenic	Intergenic	-824088	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.002907	0.382609	
chunk0030_299_1	chr10	117367823	117368217	+	0	NA	intron (NM_173791, intron 1 of 4)	intron (NM_173791, intron 1 of 4)	7447	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.015228	0.402532	
chunk0062_226_1	chr14	71041949	71042264	+	0	NA	intron (NM_001308160, intron 17 of 33)	L1M2|LINE|L1	134701	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.006349	0.322785	184(GAGGACAGTGTGTATT,-,0.00),185(AGGACAGTGTGTATTT,+,0.00)
chunk0042_78_1	chr12	2194538	2195128	+	0	NA	intron (NM_001129846, intron 3 of 45)	intron (NM_001129846, intron 3 of 45)	28648	NR_046578	100874234	Hs.372570	NR_046578	ENSG00000256025	CACNA1C-AS4	-	CACNA1C antisense RNA 4	ncRNA	0.008475	0.445008	275(AGGAGCACAGTGTTCC,-,0.00),276(GGAGCACAGTGTTCCC,+,0.00)
chunk0037_44_1	chr11	70371268	70371591	+	0	NA	intron (NM_003626, intron 21 of 27)	L1MD|LINE|L1	-27077	NM_005231	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.015480	0.395062	
chunk0023_39_1	chr10	21231490	21232006	+	0	NA	Intergenic	Intergenic	57446	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.015504	0.446809	
chunk0005_181_1	chr1	58753078	58753559	+	0	NA	Intergenic	Intergenic	30795	NM_002228	3725	Hs.696684	NM_002228	ENSG00000177606	JUN	AP-1|AP1|c-Jun|p39	Jun proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.018711	0.460581	
chunk0133_273_1	chr3	172002611	172002965	+	0	NA	Intergenic	L1ME1|LINE|L1	-36840	NM_022763	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.005650	0.307042	
chunk0053_21_1	chr13	26584994	26585477	+	0	NA	intron (NM_006646, intron 1 of 9)	intron (NM_006646, intron 1 of 9)	27532	NM_001291965	10810	Hs.618732	NM_006646	ENSG00000132970	WASF3	Brush-1|SCAR3|WAVE3	WASP family member 3	protein-coding	0.002070	0.336777	
chunk0012_268_1	chr1	161765864	161766543	+	0	NA	promoter-TSS (NM_007348)	promoter-TSS (NM_007348)	-41	NM_007348	22926	Hs.492740	NM_007348	ENSG00000118217	ATF6	ACHM7|ATF6A	activating transcription factor 6	protein-coding	0.042710	0.442647	271(CGGGACAGAAAGTCCT,-,0.00),272(GGGACAGAAAGTCCTG,+,0.00)
chunk0179_198_1	chr7	47292780	47293148	+	0	NA	intron (NM_022748, intron 25 of 30)	intron (NM_022748, intron 25 of 30)	289180	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.010870	0.449864	
chunk0203_316_1	chr9	89503480	89503798	+	0	NA	Intergenic	Intergenic	-23943	NM_001142287	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.006289	0.454545	
chunk0140_256_1	chr4	71486747	71487658	+	0	NA	intron (NM_001098484, intron 15 of 25)	intron (NM_001098484, intron 15 of 25)	148149	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.005488	0.350877	715(TAGAACGGACTGTGCC,-,0.00),716(AGAACGGACTGTGCCT,+,0.00)
chunk0195_75_1	chr8	93986179	93986447	+	0	NA	Intergenic	Intergenic	69262	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.003731	0.442379	
chunk0070_16_1	chr15	68995316	68995875	+	0	NA	intron (NR_033672, intron 2 of 16)	(TG)n|Simple_repeat|Simple_repeat	-19100	NM_001184779	79400	Hs.657932	NM_024505	ENSG00000255346	NOX5	-	NADPH oxidase 5	protein-coding	0.008945	0.412500	
chunk0068_218_1	chr15	55234301	55234998	+	0	NA	intron (NM_183236, intron 3 of 6)	intron (NM_183236, intron 3 of 6)	35637	NM_183234	5873	Hs.654978	NM_004580	ENSG00000069974	RAB27A	GS2|HsT18676|RAB27|RAM	RAB27A, member RAS oncogene family	protein-coding	0.002869	0.383954	
chunk0118_11_1	chr22	25614652	25615196	+	0	NA	intron (NM_005160, intron 2 of 20)	intron (NM_005160, intron 2 of 20)	50030	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.005515	0.411009	
chunk0134_264_1	chr3	179505586	179505946	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-54183	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.013889	0.404432	
chunk0193_433_1	chr8	80964955	80965799	+	0	NA	Intergenic	Intergenic	-90596	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.010664	0.442604	
chunk0211_189_1	chrX	117507997	117508420	+	0	NA	Intergenic	Intergenic	465530	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.004728	0.363208	
chunk0089_255_1	chr18	62483086	62483644	+	0	NA	Intergenic	L1PREC2|LINE|L1	-40060	NM_017742	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.005376	0.327370	
chunk0170_226_1	chr6	113352244	113352464	+	0	NA	Intergenic	LTR33|LTR|ERVL	297721	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.000000	0.443439	
chunk0065_263_1	chr14	101834812	101835344	+	0	NA	intron (NM_001161725, intron 3 of 15)	L4_C_Mam|LINE|RTE-X	25275	NM_002719	5527	Hs.368264	NM_002719	ENSG00000078304	PPP2R5C	B56G|B56gamma|PR61G	protein phosphatase 2 regulatory subunit B'gamma	protein-coding	0.009398	0.515947	
chunk0162_16_1	chr6	689003	689501	+	0	NA	intron (NR_073064, intron 1 of 29)	intron (NR_073064, intron 1 of 29)	3889	NR_073064	55770	Hs.484412	NM_018303	ENSG00000112685	EXOC2	SEC5|SEC5L1|Sec5p	exocyst complex component 2	protein-coding	0.006024	0.438878	
chunk0046_46_1	chr12	54891888	54892691	+	0	NA	Intergenic	Intergenic	37774	NM_058173	118430	Hs.348419	NM_058173	ENSG00000172551	MUCL1	SBEM	mucin like 1	protein-coding	0.003736	0.384328	
chunk0077_336_1	chr16	82524831	82525325	+	0	NA	Intergenic	Intergenic	-101716	NM_001220489	1012	Hs.654386	NM_001257	ENSG00000140945	CDH13	CDHH|P105	cadherin 13	protein-coding	0.002024	0.410101	
chunk0044_193_1	chr12	30542313	30542787	+	0	NA	Intergenic	L1PB2|LINE|L1	134694	NM_001190995	10526	Hs.505136	NM_006390	ENSG00000133704	IPO8	RANBP8	importin 8	protein-coding	0.000000	0.305263	
chunk0116_201_1	chr21	37391720	37391984	+	0	NA	intron (NM_101395, intron 1 of 12)	intron (NM_101395, intron 1 of 12)	24295	NM_101395	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.011364	0.433962	110(TGGAGCATACTGTGCT,-,0.00),111(GGAGCATACTGTGCTT,+,0.00)
chunk0032_390_1	chr11	11590691	11591052	+	0	NA	intron (NM_198516, intron 1 of 10)	Tigger3b|DNA|TcMar-Tigger	31143	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.008310	0.334254	
chunk0111_143_1	chr20	25011649	25012196	+	0	NA	intron (NM_032501, intron 12 of 13)	intron (NM_032501, intron 12 of 13)	-19133	NM_020531	57136	Hs.472330	NM_020531	ENSG00000101474	APMAP	BSCv|C20orf3	adipocyte plasma membrane associated protein	protein-coding	0.021938	0.558394	
chunk0145_135_1	chr4	146491760	146491973	+	0	NA	intron (NM_001029998, intron 4 of 11)	intron (NM_001029998, intron 4 of 11)	30105	NM_001029998	84068	Hs.659209	NM_032128	ENSG00000120519	SLC10A7	C4orf13|P7|SSASKS	solute carrier family 10 member 7	protein-coding	0.018779	0.471963	132(CTAAACAGGATGTTCT,-,0.00),133(TAAACAGGATGTTCTC,+,0.00)
chunk0071_440_1	chr15	89998952	89999336	+	0	NA	Intergenic	L2c|LINE|L2	-2347	NM_198526	374655	Hs.459311	NM_198526	ENSG00000140548	ZNF710	-	zinc finger protein 710	protein-coding	0.015625	0.509091	150(TTGGACAGACTGTTCT,-,0.00),151(TGGACAGACTGTTCTC,+,0.00)
chunk0151_421_1	chr5	55682148	55682567	+	0	NA	intron (NM_173514, intron 3 of 15)	intron (NM_173514, intron 3 of 15)	10696	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.002387	0.404762	
chunk0151_281_1	chr5	52780204	52780574	+	0	NA	Intergenic	Intergenic	-7551	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.013514	0.401617	
chunk0188_334_1	chr8	17674930	17676000	+	0	NA	intron (NM_001001924, intron 7 of 14)	intron (NM_001001924, intron 7 of 14)	6192	NR_036103	100422850		NR_036103	ENSG00000265520	MIR548V	-	microRNA 548v	ncRNA	0.012150	0.377218	
chunk0206_107_1	chr9	120778659	120779136	+	0	NA	intron (NM_012164, intron 3 of 7)	intron (NM_012164, intron 3 of 7)	14565	NM_012164	26190	Hs.494985	NM_012164	ENSG00000119402	FBXW2	FBW2|Fwd2|Md6	F-box and WD repeat domain containing 2	protein-coding	0.008386	0.397490	
chunk0193_135_1	chr8	74418179	74418964	+	0	NA	Intergenic	L1ME1|LINE|L1	68188	NM_018972	54332	Hs.168950	NM_018972	ENSG00000104381	GDAP1	CMT4|CMT4A|CMTRIA	ganglioside induced differentiation associated protein 1	protein-coding	0.000000	0.310433	
chunk0037_191_1	chr11	74270500	74270881	+	0	NA	intron (NM_001288748, intron 10 of 12)	MIR|SINE|MIR	-40672	NR_120556	101928580	Hs.569025	NR_120556	ENSG00000246211	P4HA3-AS1	-	P4HA3 antisense RNA 1	ncRNA	0.002625	0.342932	
chunk0010_272_1	chr1	117225115	117225418	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-14306	NM_024626	79679	Hs.546434	NM_024626	ENSG00000134258	VTCN1	B7-H4|B7H4|B7S1|B7X|B7h.5|PRO1291|VCTN1	V-set domain containing T cell activation inhibitor 1	protein-coding	0.009901	0.496711	
chunk0111_445_1	chr20	35327088	35327704	+	0	NA	intron (NM_018244, intron 7 of 9)	MIRc|SINE|MIR	-34974	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.001623	0.448947	
chunk0132_62_1	chr3	155157484	155157944	+	0	NA	intron (NM_000902, intron 16 of 22)	intron (NM_000902, intron 16 of 22)	77424	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.000000	0.336226	218(AGGGACAAAATGTCCT,-,0.00),219(GGGACAAAATGTCCTG,+,0.00)
chunk0002_201_1	chr1	19466232	19466557	+	0	NA	intron (NM_001206541, intron 1 of 8)	intron (NM_001206541, intron 1 of 8)	18313	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.018462	0.506135	152(GAAGACAAAATGTTCC,-,0.00),153(AAGACAAAATGTTCCT,+,0.00)
chunk0090_463_1	chr18	80249318	80249660	+	0	NA	Intergenic	Intergenic	-1975	NM_032510	84552	Hs.654920	NM_032510	ENSG00000178184	PARD6G	PAR-6G|PAR6gamma	par-6 family cell polarity regulator gamma	protein-coding	0.008772	0.448980	
chunk0127_196_1	chr3	96100976	96101769	+	0	NA	Intergenic	L1PA17|LINE|L1	-258592	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.003783	0.343829	
chunk0033_80_1	chr11	13952659	13953237	+	0	NA	Intergenic	L2a|LINE|L2	-9689	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.006920	0.354059	
chunk0138_297_1	chr4	41077533	41078226	+	0	NA	intron (NM_004307, intron 3 of 17)	HAL1|LINE|L1	136739	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.002886	0.358790	
chunk0024_117_1	chr10	34781586	34782354	+	0	NA	intron (NM_019619, intron 1 of 24)	intron (NM_019619, intron 1 of 24)	33355	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.005208	0.396619	189(TAGAACACACAGTTCT,-,0.00),190(AGAACACACAGTTCTG,+,0.00),239(CAGAACACTGTGCTCT,-,0.00),240(AGAACACTGTGCTCTA,+,0.00),616(AAGGACAGCATGTAAC,-,0.00)
chunk0090_106_1	chr18	71052203	71052477	+	0	NA	Intergenic	L2a|LINE|L2	-401483	NM_001278515									0.014599	0.501818	
chunk0106_268_1	chr2	203737138	203737968	+	0	NA	3' UTR (NM_006139, exon 4 of 4)	3' UTR (NM_006139, exon 4 of 4)	31078	NM_001243078	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.004819	0.345367	196(GGGCACACAGAGTTCT,-,0.00),197(GGCACACAGAGTTCTT,+,0.00),649(ATGTACATTATGTTCT,-,0.00),650(TGTACATTATGTTCTA,+,0.00)
chunk0173_13_1	chr6	141301886	141302085	+	0	NA	Intergenic	Intergenic	618171	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.005025	0.305000	102(AAGTACAACTTGTTCA,-,0.00),103(AGTACAACTTGTTCAT,+,0.00)
chunk0188_272_1	chr8	15185225	15185639	+	0	NA	intron (NM_139167, intron 1 of 7)	intron (NM_139167, intron 1 of 7)	52851	NM_139167	137868	Hs.545526	NM_139167	ENSG00000185053	SGCZ	ZSG1	sarcoglycan zeta	protein-coding	0.004831	0.344578	
chunk0052_59_1	chr13	21095718	21096260	+	0	NA	Intergenic	AluJb|SINE|Alu	-34406	NM_014572	26524	Hs.78960	NM_014572	ENSG00000150457	LATS2	KPM	large tumor suppressor kinase 2	protein-coding	0.005535	0.421731	
chunk0131_104_1	chr3	143827308	143827749	+	0	NA	intron (NM_173653, intron 2 of 15)	intron (NM_173653, intron 2 of 15)	21003	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.006803	0.350679	
chunk0143_75_1	chr4	108135351	108135732	+	0	NA	intron (NM_016269, intron 3 of 11)	intron (NM_016269, intron 3 of 11)	31256	NM_001166119	51176	Hs.743478	NM_016269	ENSG00000138795	LEF1	LEF-1|TCF10|TCF1ALPHA|TCF7L3	lymphoid enhancer binding factor 1	protein-coding	0.015748	0.539267	
chunk0099_399_1	chr2	101831881	101832393	+	0	NA	intron (NM_145686, intron 7 of 30)	intron (NM_145686, intron 7 of 30)	134061	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.001953	0.345029	225(TAGAACTTTTTGTTCC,-,0.00),226(AGAACTTTTTGTTCCT,+,0.00)
chunk0016_138_1	chr1	197196743	197197291	+	0	NA	intron (NM_194314, intron 1 of 9)	L2c|LINE|L2	3525	NM_194314	360023	Hs.529439	NM_194314	ENSG00000177888	ZBTB41	FRBZ1|ZNF924	zinc finger and BTB domain containing 41	protein-coding	0.000000	0.351548	
chunk0146_186_1	chr4	160959798	160960092	+	0	NA	Intergenic	Intergenic	-1062788	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.010204	0.308475	
chunk0186_59_1	chr7	136666066	136666477	+	0	NA	Intergenic	MIR|SINE|MIR	-202381	NM_001006627	1129	Hs.535891	NM_000739	ENSG00000181072	CHRM2	HM2	cholinergic receptor muscarinic 2	protein-coding	0.012165	0.364078	
chunk0022_462_1	chr10	20205968	20206281	+	0	NA	intron (NM_032812, intron 9 of 13)	L1MA7|LINE|L1	-345846	NR_039822	100616383		NR_039822	ENSG00000265372	MIR4675	-	microRNA 4675	ncRNA	0.006390	0.277070	
chunk0128_385_1	chr3	113738045	113738353	+	0	NA	intron (NM_025146, intron 1 of 4)	intron (NM_025146, intron 1 of 4)	8100	NM_001308445	80218	Hs.372378	NM_025146	ENSG00000121579	NAA50	MAK3|NAT13|NAT13P|NAT5|NAT5P|SAN|hNaa50p	N(alpha)-acetyltransferase 50, NatE catalytic subunit	protein-coding	0.006494	0.368932	
chunk0185_346_1	chr7	132225239	132225666	+	0	NA	intron (NM_020911, intron 8 of 31)	intron (NM_020911, intron 8 of 31)	315232	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.016393	0.570093	
chunk0199_237_1	chr9	5407036	5407666	+	0	NA	intron (NM_018465, intron 3 of 5)	intron (NM_018465, intron 3 of 5)	30586	NM_018465	55848	Hs.584242	NM_018465	ENSG00000107020	PLGRKT	AD025|C9orf46|MDS030|PLG-RKT|Plg-R(KT)	plasminogen receptor with a C-terminal lysine	protein-coding	0.000000	0.272583	
chunk0033_367_1	chr11	23153256	23153467	+	0	NA	Intergenic	L2b|LINE|L2	265829	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.004739	0.410377	
chunk0182_187_1	chr7	95691283	95691902	+	0	NA	Intergenic	Intergenic	-80914	NM_001278421	1780	Hs.440364	NM_004411	ENSG00000158560	DYNC1I1	DNCI1|DNCIC1	dynein cytoplasmic 1 intermediate chain 1	protein-coding	0.008078	0.446774	
chunk0033_376_1	chr11	23525795	23526213	+	0	NA	Intergenic	Intergenic	-106814	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.002392	0.272076	
chunk0081_109_1	chr17	39953663	39953948	+	0	NA	Intergenic	Intergenic	-9168	NM_178171	284110	Hs.448873	NM_178171	ENSG00000167914	GSDMA	FKSG9|GSDM|GSDM1	gasdermin A	protein-coding	0.010526	0.552448	147(AGGAACATTCTGTACC,-,0.00),148(GGAACATTCTGTACCT,+,0.00)
chunk0006_189_1	chr1	67449226	67449470	+	0	NA	Intergenic	Intergenic	-18908	NM_015640	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.000000	0.465306	
chunk0013_159_1	chr1	168693052	168693897	+	0	NA	Intergenic	Intergenic	35730	NM_001937	1805	Hs.80552	NM_001937	ENSG00000143196	DPT	TRAMP	dermatopontin	protein-coding	0.009467	0.399527	
chunk0040_353_1	chr11	118733484	118733746	+	0	NA	Intergenic	LTR39|LTR|ERV1	-53943	NM_007180	11181	Hs.129712	NM_007180	ENSG00000118094	TREH	TRE|TREA|TREHD	trehalase	protein-coding	0.007634	0.475285	
chunk0056_187_1	chr13	85589568	85589767	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	209681	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.005025	0.395000	
chunk0109_318_1	chr20	9129284	9129588	+	0	NA	intron (NM_001172646, intron 1 of 37)	LTR16C|LTR|ERVL	60382	NM_001172646	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.006579	0.426230	
chunk0014_345_1	chr1	182263661	182264173	+	0	NA	intron (NR_104175, intron 2 of 2)	intron (NR_104175, intron 2 of 2)	50144	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.003906	0.389864	
chunk0009_202_1	chr1	106044538	106045246	+	0	NA	Intergenic	L1MC1|LINE|L1	-425957	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001412	0.311707	
chunk0123_371_1	chr3	48465269	48465692	+	0	NA	promoter-TSS (NM_016381)	promoter-TSS (NM_016381)	-40	NM_007248	11277	Hs.707026	NM_007248	ENSG00000213689	TREX1	AGS1|CRV|DRN3|HERNS	three prime repair exonuclease 1	protein-coding	0.021277	0.568396	
chunk0148_311_1	chr5	13081108	13081376	+	0	NA	Intergenic	LTR2752|LTR|ERV1	413383	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.014925	0.572491	32(GGGGCCACCATGTTCC,-,0.00),33(GGGCCACCATGTTCCT,+,0.00)
chunk0014_276_1	chr1	180502191	180502796	+	0	NA	5' UTR (NM_032360, exon 1 of 8)	5' UTR (NM_032360, exon 1 of 8)	394	NM_032360	84320	Hs.200051	NM_032360	ENSG00000230124	ACBD6	-	acyl-CoA binding domain containing 6	protein-coding	0.102479	0.688119	
chunk0115_328_1	chr21	28942533	28942732	+	0	NA	intron (NM_015565, intron 24 of 29)	L2c|LINE|L2	50324	NM_015565	26046	Hs.288773	NM_015565	ENSG00000198862	LTN1	C21orf10|C21orf98|RNF160|ZNF294	listerin E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.360000	106(TTGTACATGATGTTCT,-,0.00),107(TGTACATGATGTTCTC,+,0.00)
chunk0111_65_1	chr20	22972129	22972545	+	0	NA	Intergenic	L1PB1|LINE|L1	-63083	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.002404	0.350120	
chunk0125_382_1	chr3	71614760	71615279	+	0	NA	Intergenic	Intergenic	-31030	NM_032682	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.007707	0.400000	
chunk0038_339_1	chr11	92837478	92837810	+	0	NA	intron (NM_001008781, intron 15 of 24)	intron (NM_001008781, intron 15 of 24)	-131979	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.012048	0.468468	
chunk0165_377_1	chr6	38358176	38358703	+	0	NA	intron (NM_001099272, intron 6 of 10)	intron (NM_001099272, intron 6 of 10)	237628	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.007590	0.477273	278(AAGTACATACTGTACA,-,0.00),279(AGTACATACTGTACAT,+,0.00)
chunk0104_137_1	chr2	173399147	173399647	+	0	NA	Intergenic	Intergenic	44564	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.008000	0.447106	261(GAGAACAAGCTGCCCC,-,0.00),262(AGAACAAGCTGCCCCT,+,0.00)
chunk0177_233_1	chr7	24580415	24580947	+	0	NA	intron (NM_001303037, intron 1 of 11)	intron (NM_001303037, intron 1 of 11)	7335	NM_001303037	51678	Hs.533355	NM_016447	ENSG00000105926	MPP6	PALS2|VAM-1|VAM1|p55T	membrane palmitoylated protein 6	protein-coding	0.003759	0.358349	
chunk0115_209_1	chr21	26845197	26845487	+	0	NA	promoter-TSS (NM_006988)	promoter-TSS (NM_006988)	67	NM_006988	9510	Hs.643357	NM_006988	ENSG00000154734	ADAMTS1	C3-C5|METH1	ADAM metallopeptidase with thrombospondin type 1 motif 1	protein-coding	0.065517	0.666667	
chunk0129_150_1	chr3	120554336	120554720	+	0	NA	Intergenic	L2c|LINE|L2	-41753	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.002604	0.350649	
chunk0185_275_1	chr7	130905748	130905947	+	0	NA	intron (NR_110472, intron 2 of 3)	intron (NR_110472, intron 2 of 3)	7463	NR_110473	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.000000	0.495000	
chunk0115_454_1	chr21	32579173	32579617	+	0	NA	intron (NM_144659, intron 3 of 4)	intron (NM_144659, intron 3 of 4)	6140	NM_144659	140290	Hs.728804	NM_018277	ENSG00000242220	TCP10L	C21orf77|PRED77|TCP10A-1|TCP10A-2	t-complex 10 like	protein-coding	0.022523	0.458427	91(TGGAACAGGGTGATCC,-,0.00),92(GGAACAGGGTGATCCT,+,0.00)
chunk0207_294_1	chr9	133149230	133149599	+	0	NA	promoter-TSS (NM_001042368)	promoter-TSS (NM_001042368)	-194	NM_001042368	5900	Hs.106185	NM_006266	ENSG00000160271	RALGDS	RGDS|RGF|RalGEF	ral guanine nucleotide dissociation stimulator	protein-coding	0.154472	0.800000	
chunk0103_380_1	chr2	168653736	168653998	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	70924	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.000000	0.361217	
chunk0197_78_1	chr8	119099638	119100178	+	0	NA	intron (NM_006438, intron 3 of 5)	intron (NM_006438, intron 3 of 5)	32723	NM_006438	10584	Hs.176615	NM_006438	ENSG00000184374	COLEC10	3MC3|CL-34|CLL1	collectin subfamily member 10	protein-coding	0.003704	0.334566	
chunk0033_245_1	chr11	18093868	18094478	+	0	NA	intron (NM_138421, intron 3 of 11)	intron (NM_138421, intron 3 of 11)	11918	NM_138421	113174	Hs.591998	NM_138421	ENSG00000166788	SAAL1	SPACIA1	serum amyloid A like 1	protein-coding	0.003279	0.417349	
chunk0034_141_1	chr11	29344212	29344558	+	0	NA	Intergenic	Intergenic	638008	NR_132652	106456574	Hs.128812	NR_132652	ENSG00000261340	LINC01616	n341006	long intergenic non-protein coding RNA 1616	ncRNA	0.002890	0.291066	
chunk0068_212_1	chr15	55201872	55202118	+	0	NA	TTS (NM_004580)	TTS (NM_004580)	-4962	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.008130	0.384615	
chunk0179_192_1	chr7	47219756	47219955	+	0	NA	Intergenic	Intergenic	362289	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.005025	0.270000	
chunk0121_367_1	chr3	24877971	24878229	+	0	NA	Intergenic	L1MEd|LINE|L1	-296232	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.011628	0.343629	
chunk0121_376_1	chr3	25056410	25056684	+	0	NA	Intergenic	Intergenic	-117785	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.000000	0.316364	
chunk0071_409_1	chr15	89690404	89690785	+	0	NA	promoter-TSS (NM_001284395)	promoter-TSS (NM_001284395)	190	NM_003847	8800	Hs.31034	NM_003847	ENSG00000166821	PEX11A	PEX11-ALPHA|PMP28|hsPEX11p	peroxisomal biogenesis factor 11 alpha	protein-coding	0.060367	0.630890	300(GGGAACGGTCAGTCCC,-,0.00)
chunk0047_445_1	chr12	76457062	76457453	+	0	NA	intron (NM_020841, intron 3 of 23)	Tigger2b_Pri|DNA|TcMar-Tigger	102552	NM_001003712	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.012788	0.295918	
chunk0075_80_1	chr16	48210901	48211329	+	0	NA	exon (NM_032583, exon 11 of 30)	exon (NM_032583, exon 11 of 30)	21156	NM_033151	85320	Hs.652267	NM_032583	ENSG00000121270	ABCC11	EWWD|MRP8|WW	ATP binding cassette subfamily C member 11	protein-coding	0.011682	0.515152	81(GGGCCCAGGCTGTTCC,-,0.00),82(GGCCCAGGCTGTTCCC,+,0.00)
chunk0124_146_1	chr3	54736312	54736963	+	0	NA	intron (NM_018398, intron 11 of 37)	L1ME4a|LINE|L1	-96780	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.006144	0.365031	343(TTGAACATCTTGTTCT,-,0.00),344(TGAACATCTTGTTCTC,+,0.00)
chunk0012_262_1	chr1	161703187	161703418	+	0	NA	Intergenic	L1ME1|LINE|L1	-3670	NM_001184871	84824	Hs.266331	NM_032738	ENSG00000132185	FCRLA	FCRL|FCRL1|FCRLM1|FCRLX|FCRLb|FCRLc1|FCRLc2|FCRLd|FCRLe|FCRX|FREB	Fc receptor like A	protein-coding	0.004329	0.331897	
chunk0071_254_1	chr15	85427840	85428200	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	47404	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.000000	0.407202	202(AGGTACTCACTGTACC,-,0.00),203(GGTACTCACTGTACCT,+,0.00)
chunk0135_72_1	chr3	185901263	185901622	+	0	NA	Intergenic	Intergenic	36694	NM_001243879	6434	Hs.533122	NM_004593	ENSG00000136527	TRA2B	Htra2-beta|PPP1R156|SFRS10|SRFS10|TRA2-BETA|TRAN2B	transformer 2 beta homolog	protein-coding	0.005571	0.347222	
chunk0031_371_1	chr10	130463990	130464536	+	0	NA	Intergenic	LTR18B|LTR|ERVL	327888	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.009158	0.502742	
chunk0191_189_1	chr8	51664629	51665003	+	0	NA	intron (NM_144651, intron 1 of 22)	intron (NM_144651, intron 1 of 22)	144629	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.010695	0.570667	
chunk0168_229_1	chr6	87219289	87219792	+	0	NA	intron (NM_015021, intron 4 of 7)	intron (NM_015021, intron 4 of 7)	63989	NM_015021	23036	Hs.444800	NM_015021	ENSG00000188994	ZNF292	Nbla00365|ZFP292|ZN-16|Zn-15|bA393I2.3	zinc finger protein 292	protein-coding	0.005964	0.353175	
chunk0092_107_1	chr19	23439035	23439361	+	0	NA	Intergenic	Intergenic	-23124	NR_126449	104472717	Hs.162105	NR_126448	ENSG00000269416	LINC01224	-	long intergenic non-protein coding RNA 1224	ncRNA	0.015337	0.443425	
chunk0057_165_1	chr13	101590459	101590894	+	0	NA	intron (NM_001271754, intron 5 of 10)	intron (NM_001271754, intron 5 of 10)	100724	NM_001271756	9358	Hs.696554	NM_004791	ENSG00000198542	ITGBL1	OSCP|TIED	integrin subunit beta like 1	protein-coding	0.009195	0.380734	
chunk0016_311_1	chr1	201468264	201468573	+	0	NA	exon (NM_012396, exon 1 of 2)	exon (NM_012396, exon 1 of 2)	753	NM_012396	23612	Hs.153944	NM_012396	ENSG00000174307	PHLDA3	TIH1	pleckstrin homology like domain family A member 3	protein-coding	0.051780	0.625806	
chunk0003_178_1	chr1	33643005	33643684	+	0	NA	intron (NM_052896, intron 29 of 69)	intron (NM_052896, intron 29 of 69)	170713	NM_145238	7579	Hs.442705	NM_145238	ENSG00000121903	ZSCAN20	KOX29|ZFP-31|ZNF31|ZNF360	zinc finger and SCAN domain containing 20	protein-coding	0.005891	0.463235	
chunk0135_13_1	chr3	184211664	184212102	+	0	NA	Intergenic	L1M5|LINE|L1	-18646	NM_138345	90113	Hs.584997	NM_138345	ENSG00000145198	VWA5B2	-	von Willebrand factor A domain containing 5B2	protein-coding	0.013699	0.343964	222(TGAAACAGTCTGTCCT,-,0.00),223(GAAACAGTCTGTCCTC,+,0.00)
chunk0029_111_1	chr10	97916656	97916855	+	0	NA	intron (NM_018058, intron 5 of 14)	intron (NM_018058, intron 5 of 14)	66517	NM_001010917	401647	Hs.567524	NM_001010917	ENSG00000155265	GOLGA7B	C10orf132|C10orf133|bA451M19.3|bA459F3.4	golgin A7 family member B	protein-coding	0.005025	0.480000	34(AGGATCTCTCTGTCCC,-,0.00)
chunk0087_70_1	chr18	31943360	31944138	+	0	NA	promoter-TSS (NM_014939)	promoter-TSS (NM_014939)	-621	NM_014939	22878	Hs.202001	NM_014939	ENSG00000153339	TRAPPC8	GSG1|HsT2706|KIAA1012|TRS85	trafficking protein particle complex 8	protein-coding	0.039846	0.496791	
chunk0032_233_1	chr11	7633533	7634015	+	0	NA	intron (NM_003621, intron 12 of 23)	intron (NM_003621, intron 12 of 23)	28040	NM_001256569	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.004149	0.465839	
chunk0107_110_1	chr2	214359475	214359899	+	0	NA	intron (NR_047659, intron 17 of 17)	intron (NR_047659, intron 17 of 17)	-52050	NM_001080500	402117	Hs.534834	NM_001080500	ENSG00000174453	VWC2L	-	von Willebrand factor C domain containing 2 like	protein-coding	0.000000	0.301176	
chunk0095_427_1	chr2	24871758	24872436	+	0	NA	intron (NM_004036, intron 2 of 20)	intron (NM_004036, intron 2 of 20)	47089	NM_004036	109	Hs.467898	NM_004036	ENSG00000138031	ADCY3	AC-III|AC3|BMIQ19	adenylate cyclase 3	protein-coding	0.017699	0.536082	
chunk0139_116_1	chr4	52643970	52644246	+	0	NA	intron (NM_022832, intron 1 of 8)	intron (NM_022832, intron 1 of 8)	12484	NM_001134223	64854	Hs.7966	NM_022832	ENSG00000109189	USP46	-	ubiquitin specific peptidase 46	protein-coding	0.010870	0.487365	
chunk0121_245_1	chr3	22836367	22836566	+	0	NA	Intergenic	MER50|LTR|ERV1	-366827	NM_152653	7325	Hs.475688	NM_152653	ENSG00000182247	UBE2E2	UBCH8	ubiquitin conjugating enzyme E2 E2	protein-coding	0.005025	0.445000	
chunk0152_353_1	chr5	63146093	63146882	+	0	NA	Intergenic	L1ME3A|LINE|L1	567752	NR_073584	101180901	Hs.482269	NR_073584	ENSG00000086200	IPO11-LRRC70	-	IPO11-LRRC70 readthrough	ncRNA	0.002535	0.312658	
chunk0184_182_1	chr7	116700426	116700977	+	0	NA	intron (NM_000245, intron 2 of 20)	intron (NM_000245, intron 2 of 20)	28296	NM_000245	4233	Hs.132966	NM_000245	ENSG00000105976	MET	AUTS9|DFNB97|HGFR|RCCP2|c-Met	MET proto-oncogene, receptor tyrosine kinase	protein-coding	0.003630	0.284420	
chunk0205_156_1	chr9	108552800	108553070	+	0	NA	Intergenic	Intergenic	303060	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.014815	0.453875	
chunk0174_228_1	chr6	160518252	160518514	+	0	NA	Intergenic	MER50|LTR|ERV1	-7259	NR_028092	80350	Hs.654503	NM_024492	ENSG00000213071	LPAL2	APOA2|APOAL|APOARGC|apo(a)rg-C	lipoprotein(a) like 2, pseudogene	pseudo	0.003817	0.418251	
chunk0109_131_1	chr20	3058297	3058496	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	12367	NM_030811	64949	Hs.18946	NM_030811	ENSG00000125901	MRPS26	C20orf193|GI008|MRP-S13|MRP-S26|MRPS13|NY-BR-87|RPMS13|dJ534B8.3	mitochondrial ribosomal protein S26	protein-coding	0.005025	0.480000	113(CAGGCCACTCTGTACT,-,0.00),114(AGGCCACTCTGTACTT,+,0.00)
chunk0192_143_1	chr8	62018167	62018550	+	0	NA	Intergenic	Intergenic	-230584	NR_130764	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.002611	0.393229	
chunk0064_200_1	chr14	92946196	92946398	+	0	NA	intron (NM_001142593, intron 10 of 10)	intron (NM_001142593, intron 10 of 10)	23197	NM_001301690	1113	Hs.150793	NM_001275	ENSG00000100604	CHGA	CGA	chromogranin A	protein-coding	0.044554	0.630542	
chunk0140_59_1	chr4	67035380	67035941	+	0	NA	Intergenic	MER54A|LTR|ERVL	386340	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.003565	0.435943	
chunk0180_186_1	chr7	66013976	66014230	+	0	NA	Intergenic	Intergenic	-31789	NM_001284290	2990	Hs.255230	NM_000181	ENSG00000169919	GUSB	BG|MPS7	glucuronidase beta	protein-coding	0.007874	0.521569	
chunk0147_175_1	chr4	176579155	176579853	+	0	NA	Intergenic	Intergenic	213241	NM_005429	7424	Hs.435215	NM_005429	ENSG00000150630	VEGFC	Flt4-L|LMPH1D|LMPHM4|VRP	vascular endothelial growth factor C	protein-coding	0.008596	0.389127	
chunk0153_286_1	chr5	73281382	73281743	+	0	NA	Intergenic	UCON62|DNA?|DNA?	108366	NM_153217	134288	Hs.508588	NM_153217	ENSG00000164325	TMEM174	-	transmembrane protein 174	protein-coding	0.013850	0.461326	
chunk0065_215_1	chr14	100246958	100247594	+	0	NA	intron (NM_003403, intron 1 of 4)	intron (NM_003403, intron 1 of 4)	8511	NM_003403	7528	Hs.388927	NM_003403	ENSG00000100811	YY1	DELTA|GADEVS|INO80S|NF-E1|UCRBP|YIN-YANG-1	YY1 transcription factor	protein-coding	0.007862	0.412873	
chunk0174_309_1	chr6	162727712	162728026	+	0	NA	promoter-TSS (NM_004562)	promoter-TSS (NM_004562)	-67	NM_013988	5071	Hs.132954	NM_004562	ENSG00000185345	PRKN	AR-JP|LPRS2|PARK2|PDJ	parkin RBR E3 ubiquitin protein ligase	protein-coding	0.101911	0.695238	
chunk0079_253_1	chr17	16131524	16132114	+	0	NA	intron (NM_006311, intron 14 of 45)	MIRb|SINE|MIR	62820	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.006780	0.360406	302(GGGCACTCTCTGTGCC,-,0.00),303(GGCACTCTCTGTGCCT,+,0.00)
chunk0125_409_1	chr3	72279299	72279500	+	0	NA	Intergenic	Intergenic	128142	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.009950	0.470297	
chunk0027_130_1	chr10	74254571	74255056	+	0	NA	intron (NM_001123, intron 3 of 10)	intron (NM_001123, intron 3 of 10)	78324	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.000000	0.288066	
chunk0125_254_1	chr3	69093170	69093460	+	0	NA	intron (NM_006407, intron 1 of 2)	intron (NM_006407, intron 1 of 2)	8376	NM_006407	10550	Hs.518060	NM_006407	ENSG00000144746	ARL6IP5	DERP11|GTRAP3-18|HSPC127|JWA|PRAF3|Yip6b|addicsin|hp22|jmx	ADP ribosylation factor like GTPase 6 interacting protein 5	protein-coding	0.003448	0.378007	265(AAGGAGACACTGTTCT,-,0.00),266(AGGAGACACTGTTCTC,+,0.00)
chunk0121_80_1	chr3	15989412	15989672	+	0	NA	Intergenic	L1MC1|LINE|L1	115771	NR_030289	693148		NR_030289	ENSG00000207815	MIR563	MIRN563|hsa-mir-563	microRNA 563	ncRNA	0.003846	0.379310	
chunk0095_24_1	chr2	12686763	12687201	+	0	NA	Intergenic	Intergenic	-29890	NM_021643	28951	Hs.467751	NM_021643	ENSG00000071575	TRIB2	C5FW|GS3955|TRB2	tribbles pseudokinase 2	protein-coding	0.011416	0.441913	
chunk0060_191_1	chr14	47566097	47566448	+	0	NA	intron (NM_001113498, intron 1 of 16)	L1PA15|LINE|L1	108682	NM_001113498	161357	Hs.436380	NM_182830	ENSG00000139915	MDGA2	MAMDC1|c14_5286	MAM domain containing glycosylphosphatidylinositol anchor 2	protein-coding	0.002849	0.525568	
chunk0049_223_1	chr12	93412925	93413191	+	0	NA	intron (NM_003348, intron 1 of 3)	L2a|LINE|L2	29192	NM_003348	7334	Hs.524630	NM_003348	ENSG00000177889	UBE2N	HEL-S-71|UBC13|UBCHBEN; UBC13|UbcH-ben|UbcH13	ubiquitin conjugating enzyme E2 N	protein-coding	0.011278	0.363296	
chunk0022_112_1	chr10	10623904	10624338	+	0	NA	Intergenic	Intergenic	-161772	NR_120637	101928322	Hs.576789	NR_120637	ENSG00000270111	CELF2-DT	-	CELF2 divergent transript	ncRNA	0.009217	0.448276	190(AAGAACAGGATGTACC,-,0.00),191(AGAACAGGATGTACCA,+,0.00)
chunk0047_65_1	chr12	67540264	67541146	+	0	NA	intron (NR_103861, intron 1 of 2)	intron (NR_103861, intron 1 of 2)	20623	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.006803	0.394111	
chunk0008_78_1	chr1	89929473	89929878	+	0	NA	intron (NM_001134479, intron 2 of 2)	Tigger3d|DNA|TcMar-Tigger	65291	NR_002830	492303	Hs.550796	NR_002830		GEMIN8P4	-	gem nuclear organelle associated protein 8 pseudogene 4	pseudo	0.007407	0.428571	
chunk0075_245_1	chr16	53147228	53148036	+	0	NA	intron (NM_025134, intron 1 of 38)	L1MB4|LINE|L1	-8294	NM_001308319	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.004950	0.385661	410(CTGAACATAGTGTTCT,-,0.00),411(TGAACATAGTGTTCTC,+,0.00)
chunk0049_185_1	chr12	92722923	92723341	+	0	NA	Intergenic	L2b|LINE|L2	-13357	NM_001004330	440107	Hs.591013	NM_001004330	ENSG00000187510	PLEKHG7	-	pleckstrin homology and RhoGEF domain containing G7	protein-coding	0.004785	0.422434	
chunk0187_95_1	chr8	4317014	4317362	+	0	NA	intron (NM_033225, intron 3 of 69)	MIRc|SINE|MIR	677618	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.008621	0.366762	
chunk0194_231_1	chr8	86289834	86290501	+	0	NA	Intergenic	L2c|LINE|L2	-52598	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.005997	0.396707	295(CTACACAGTCTGTTCT,-,0.00),296(TACACAGTCTGTTCTT,+,0.00),647(CAGAACTTTCTGTTTT,-,0.00),648(AGAACTTTCTGTTTTT,+,0.00)
chunk0091_268_1	chr19	11375693	11375988	+	0	NA	exon (NM_175871, exon 2 of 2)	exon (NM_175871, exon 2 of 2)	1133	NM_175871	126074	Hs.631619	NM_175871	ENSG00000173928	SWSAP1	C19orf39|SWS1AP1|ZSWIM7AP1	SWIM-type zinc finger 7 associated protein 1	protein-coding	0.033898	0.652027	
chunk0098_460_1	chr2	82488658	82489101	+	0	NA	Intergenic	Intergenic	-367924	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.006772	0.351351	
chunk0122_129_1	chr3	31533492	31533848	+	0	NA	intron (NM_178862, intron 1 of 15)	CpG	1169	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.098315	0.677871	
chunk0148_138_1	chr5	5983312	5983642	+	0	NA	Intergenic	Intergenic	353815	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.015152	0.483384	
chunk0204_244_1	chr9	98062158	98062867	+	0	NA	intron (NM_018946, intron 2 of 5)	L1ME4c|LINE|L1	5835	NM_018946	54187	Hs.522310	NM_018946	ENSG00000095380	NANS	HEL-S-100|SAS|SEMDCG|SEMDG	N-acetylneuraminate synthase	protein-coding	0.008463	0.390141	455(GTGAACATCGAGTTCT,-,0.00),456(TGAACATCGAGTTCTG,+,0.00)
chunk0183_43_1	chr7	103906525	103906819	+	0	NA	intron (NM_005045, intron 2 of 64)	intron (NM_005045, intron 2 of 64)	82844	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.003401	0.433898	
chunk0036_32_1	chr11	58657904	58658467	+	0	NA	Intergenic	Intergenic	35512	NM_000614	1270	Hs.524920	NM_000614	ENSG00000242689	CNTF	HCNTF	ciliary neurotrophic factor	protein-coding	0.012433	0.446809	
chunk0144_258_1	chr4	136681660	136682173	+	0	NA	Intergenic	Intergenic	-768236	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.007797	0.321012	
chunk0018_186_1	chr1	219254631	219255177	+	0	NA	Intergenic	L1PA14|LINE|L1	79935	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.009158	0.352834	
chunk0195_382_1	chr8	100125335	100125544	+	0	NA	Intergenic	L2|LINE|L2	-19323	NM_001286692	26166	Hs.120021	NM_015668	ENSG00000132554	RGS22	CT145|PRTD-NY2	regulator of G protein signaling 22	protein-coding	0.014354	0.395238	57(TAGAACAAAGTGTACA,-,0.00),58(AGAACAAAGTGTACAG,+,0.00)
chunk0136_380_1	chr3	196603750	196603949	+	0	NA	Intergenic	LTR57|LTR|ERVL	28738	NR_132101	101929769	Hs.518527	NR_132101	ENSG00000232065	LINC01063	-	long intergenic non-protein coding RNA 1063	ncRNA	0.010050	0.520000	
chunk0024_102_1	chr10	34584287	34584545	+	0	NA	intron (NM_019619, intron 2 of 24)	MIRc|SINE|MIR	230909	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.382239	73(TAGGACTTTCAGTTCC,-,0.00),74(AGGACTTTCAGTTCCA,+,0.00)
chunk0072_240_1	chr15	95958468	95958697	+	0	NA	Intergenic	Intergenic	-367346	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.021834	0.430435	
chunk0006_245_1	chr1	69122846	69123057	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-625730	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.000000	0.481132	
chunk0152_221_1	chr5	60374524	60374728	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-113087	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.009804	0.404878	
chunk0003_115_1	chr1	32369014	32369335	+	0	NA	intron (NM_001143888, intron 9 of 10)	L1ME4a|LINE|L1	6913	NM_052841	81629	Hs.512763	NM_052841	ENSG00000162526	TSSK3	SPOGA3|STK22C|STK22D|TSK3	testis specific serine kinase 3	protein-coding	0.006231	0.434783	
chunk0170_210_1	chr6	112806982	112807301	+	0	NA	Intergenic	Intergenic	459811	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.006270	0.418750	
chunk0169_384_1	chr6	107727971	107728403	+	0	NA	intron (NM_198081, intron 5 of 7)	intron (NM_198081, intron 5 of 7)	4209	NM_001286409	256380	Hs.486109	NM_198081	ENSG00000146285	SCML4	dJ47M23.1	Scm polycomb group protein like 4	protein-coding	0.016204	0.390300	
chunk0203_242_1	chr9	87335128	87335706	+	0	NA	Intergenic	Intergenic	-161811	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.001730	0.336788	
chunk0127_78_1	chr3	89503549	89504494	+	0	NA	Intergenic	Intergenic	396497	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.007407	0.378436	
chunk0053_451_1	chr13	40016846	40017379	+	0	NA	Intergenic	Intergenic	-164697	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.007505	0.370787	
chunk0153_160_1	chr5	69528102	69528364	+	0	NA	intron (NM_002538, intron 4 of 8)	intron (NM_002538, intron 4 of 8)	24056	NM_001205255	100506658	Hs.592605	NM_002538	ENSG00000197822	OCLN	BLCPMG|PPP1R115|PTORCH1	occludin	protein-coding	0.007634	0.429658	
chunk0086_221_1	chr18	22585647	22586110	+	0	NA	Intergenic	Intergenic	-167963	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.002160	0.366379	229(AGAGACAGTTTGTCCT,-,0.00),230(GAGACAGTTTGTCCTT,+,0.00)
chunk0162_349_1	chr6	7046811	7047163	+	0	NA	Intergenic	Charlie23a|DNA|hAT-Charlie	-60610	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.005682	0.390935	
chunk0015_44_1	chr1	184527462	184527848	+	0	NA	intron (NM_030806, intron 3 of 5)	MIRb|SINE|MIR	140639	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.010363	0.465116	186(TGGGACACGCTGTCCT,-,0.00),187(GGGACACGCTGTCCTA,+,0.00)
chunk0199_150_1	chr9	4235863	4236290	+	0	NA	intron (NM_001042413, intron 2 of 10)	intron (NM_001042413, intron 2 of 10)	63959	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.011710	0.392523	
chunk0111_50_1	chr20	22452614	22453388	+	0	NA	Intergenic	Intergenic	-32358	NR_027089	284788	Hs.651993	NR_027089	ENSG00000204684	LOC284788	-	uncharacterized LOC284788	ncRNA	0.005168	0.361290	
chunk0183_55_1	chr7	104089162	104089828	+	0	NA	Intergenic	Intergenic	-99979	NM_173054	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.004505	0.391304	
chunk0062_210_1	chr14	70672849	70673176	+	0	NA	3' UTR (NM_015351, exon 3 of 3)	3' UTR (NM_015351, exon 3 of 3)	-25686	NR_125769	103695436	Hs.572296	NR_125769	ENSG00000258689	LINC01269	-	long intergenic non-protein coding RNA 1269	ncRNA	0.000000	0.429878	
chunk0108_130_1	chr2	230097562	230098348	+	0	NA	Intergenic	L1ME1|LINE|L1	-28956	NM_152527	151473	Hs.504317	NM_152527	ENSG00000163053	SLC16A14	MCT14	solute carrier family 16 member 14	protein-coding	0.005089	0.346887	
chunk0056_369_1	chr13	92903126	92903481	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	-142038	NR_126360	104326053	Hs.578064	NR_126360		LINC00363	TCONS_00021586	long intergenic non-protein coding RNA 363	ncRNA	0.000000	0.221910	
chunk0160_240_1	chr5	155983956	155984369	+	0	NA	Intergenic	MIRc|SINE|MIR	-342595	NM_172244	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.007264	0.355072	
chunk0017_457_1	chr1	214482010	214482209	+	0	NA	intron (NM_005401, intron 1 of 18)	intron (NM_005401, intron 1 of 18)	69572	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.000000	0.345000	
chunk0143_440_1	chr4	124013806	124014144	+	0	NA	Intergenic	L1PA6|LINE|L1	239711	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.011834	0.545723	
chunk0029_77_1	chr10	96719128	96719876	+	0	NA	intron (NM_152309, intron 1 of 16)	L2c|LINE|L2	1020	NM_152309	118788	Hs.310456	NM_152309	ENSG00000155629	PIK3AP1	BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.009358	0.469960	
chunk0104_250_1	chr2	177394254	177394507	+	0	NA	intron (NM_003659, intron 1 of 19)	L2c|LINE|L2	1637	NM_003659	8540	Hs.516543	NM_003659	ENSG00000018510	AGPS	ADAP-S|ADAS|ADHAPS|ADPS|ALDHPSY|RCDP3	alkylglycerone phosphate synthase	protein-coding	0.000000	0.389764	
chunk0006_367_1	chr1	73148218	73148546	+	0	NA	Intergenic	Intergenic	-157788	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.015244	0.462006	
chunk0203_320_1	chr9	89609004	89609350	+	0	NA	Intergenic	Intergenic	4165	NM_006705	10912	Hs.9701	NM_006705	ENSG00000130222	GADD45G	CR6|DDIT2|GADD45gamma|GRP17	growth arrest and DNA damage inducible gamma	protein-coding	0.002890	0.368876	210(AGGACAAAATGATCTC,+,0.00)
chunk0146_79_1	chr4	157996755	157997092	+	0	NA	Intergenic	Intergenic	175643	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.002967	0.334320	
chunk0193_371_1	chr8	80080623	80081022	+	0	NA	promoter-TSS (NM_001287143)	promoter-TSS (NM_001287143)	9	NM_001025252	7163	Hs.368433	NM_005079	ENSG00000076554	TPD52	D52|N8L|PC-1|PrLZ|hD52	tumor protein D52	protein-coding	0.007519	0.420000	
chunk0018_260_1	chr1	220365290	220365605	+	0	NA	Intergenic	Intergenic	-92946	NM_012414	25782	Hs.654849	NM_012414	ENSG00000118873	RAB3GAP2	RAB3-GAP150|RAB3GAP150|SPG69|WARBM2|p150	RAB3 GTPase activating non-catalytic protein subunit 2	protein-coding	0.003175	0.465190	
chunk0070_349_1	chr15	75965154	75965626	+	0	NA	intron (NM_138573, intron 3 of 5)	intron (NM_138573, intron 3 of 5)	-32260	NR_003136									0.008475	0.365751	
chunk0182_369_1	chr7	99971268	99971470	+	0	NA	intron (NM_001185, intron 2 of 3)	MIRb|SINE|MIR	4743	NM_001185	563	Hs.546239	NM_001185	ENSG00000160862	AZGP1	ZA2G|ZAG	alpha-2-glycoprotein 1, zinc-binding	protein-coding	0.014851	0.546798	
chunk0172_319_1	chr6	138287276	138287514	+	0	NA	intron (NM_020340, intron 17 of 33)	intron (NM_020340, intron 17 of 33)	-68905	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.008403	0.527197	
chunk0161_383_1	chr5	176862403	176862878	+	0	NA	exon (NM_133369, exon 2 of 15)	exon (NM_133369, exon 2 of 15)	36692	NM_002115	3101	Hs.411695	NM_002115	ENSG00000160883	HK3	HKIII|HXK3	hexokinase 3	protein-coding	0.042105	0.647059	
chunk0159_222_1	chr5	140992547	140992959	+	0	NA	intron (NM_018906, intron 3 of 3)	intron (NM_018906, intron 3 of 3)	25986	NM_031883	56134	Hs.199343	NM_018899	ENSG00000243232	PCDHAC2	PCDH-ALPHA-C2	protocadherin alpha subfamily C, 2	protein-coding	0.004854	0.443099	
chunk0066_3_1	chr15	26870675	26870882	+	0	NA	intron (NM_001165037, intron 3 of 10)	intron (NM_001165037, intron 3 of 10)	3652	NM_001165037	2558	Hs.24969	NM_000810	ENSG00000186297	GABRA5	-	gamma-aminobutyric acid type A receptor alpha5 subunit	protein-coding	0.009662	0.350962	
chunk0150_284_1	chr5	37046472	37046958	+	0	NA	intron (NM_015384, intron 38 of 45)	intron (NM_015384, intron 38 of 45)	169956	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.000000	0.328542	384(AAGAACAGTCTGTCCA,-,0.00),385(AGAACAGTCTGTCCAG,+,0.00)
chunk0009_217_1	chr1	106480707	106481027	+	0	NA	Intergenic	L1PB2|LINE|L1	-575778	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.006250	0.364486	
chunk0016_199_1	chr1	198682270	198682784	+	0	NA	intron (NR_052021, intron 2 of 2)	intron (NR_052021, intron 2 of 2)	43559	NM_080921	5788	Hs.654514	NM_002838	ENSG00000081237	PTPRC	B220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200	protein tyrosine phosphatase receptor type C	protein-coding	0.001946	0.349515	
chunk0045_39_1	chr12	44519776	44520293	+	0	NA	exon (NM_001145110, exon 20 of 21)	exon (NM_001145110, exon 20 of 21)	355627	NM_001145109	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.015474	0.484556	243(GAGTACACTCAGTGCC,-,0.00),244(AGTACACTCAGTGCCA,+,0.00)
chunk0092_462_1	chr19	39167610	39167809	+	0	NA	intron (NM_001014834, intron 1 of 7)	intron (NM_001014834, intron 1 of 7)	-29255	NM_001001414	342897	Hs.726934	NM_001001414	ENSG00000188505	NCCRP1	FBXO50|NCCRP-1	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	protein-coding	0.035176	0.705000	
chunk0198_385_1	chr8	141272664	141273390	+	0	NA	Intergenic	Intergenic	-18398	NM_001286646	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.023416	0.471802	438(AAGGACACACTGCCCC,-,0.00),439(AGGACACACTGCCCCC,+,0.00)
chunk0183_184_1	chr7	106206767	106207345	+	0	NA	Intergenic	LTR16A|LTR|ERVL	78136	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.006920	0.516408	183(GAGATCAGGCTGTCCT,-,0.00),184(AGATCAGGCTGTCCTG,+,0.00)
chunk0133_268_1	chr3	171915349	171915553	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-14711	NR_046852	100874219	Hs.730556	NR_046852	ENSG00000234717	TMEM212-AS1	-	TMEM212 antisense RNA 1	ncRNA	0.004902	0.243902	
chunk0059_219_1	chr14	33990830	33991153	+	0	NA	Intergenic	Intergenic	-39913	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.000000	0.354938	
chunk0049_351_1	chr12	95318073	95318637	+	0	NA	Intergenic	Intergenic	8432	NR_037456	100500802		NR_037456	ENSG00000265917	MIR3685	-	microRNA 3685	ncRNA	0.005319	0.380531	
chunk0159_340_1	chr5	144124981	144125461	+	0	NA	Intergenic	Intergenic	45493	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.002083	0.380457	147(AAGTACAAATTGTTCC,-,0.00),148(AGTACAAATTGTTCCC,+,0.00)
chunk0006_80_1	chr1	64955053	64955594	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	11181	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.014787	0.429889	222(CAGAACACGACGTACT,-,0.00),223(AGAACACGACGTACTG,+,0.00)
chunk0113_390_1	chr20	60044430	60044955	+	0	NA	Intergenic	L1M2|LINE|L1	-11233	NM_173644									0.003810	0.365019	
chunk0081_88_1	chr17	39573637	39573854	+	0	NA	Intergenic	CpG	34177	NM_006160	4761	Hs.322431	NM_006160	ENSG00000171532	NEUROD2	EIEE72|NDRF|bHLHa1	neuronal differentiation 2	protein-coding	0.105991	0.743119	
chunk0008_358_1	chr1	96538342	96538685	+	0	NA	Intergenic	Intergenic	-164388	NR_110693	101928241	Hs.514137	NR_110693	ENSG00000231987	LINC01787	-	long intergenic non-protein coding RNA 1787	ncRNA	0.005831	0.459302	215(TAGAACATCCTGTGCT,-,0.00),216(AGAACATCCTGTGCTC,+,0.00)
chunk0176_9_1	chr7	8199770	8200033	+	0	NA	intron (NM_001136020, intron 6 of 13)	L1MA2|LINE|L1	62151	NM_022307	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.003802	0.397727	
chunk0197_196_1	chr8	121732456	121732706	+	0	NA	Intergenic	L1PB3|LINE|L1	-91191	NM_005328	3037	Hs.159226	NM_005328	ENSG00000170961	HAS2	-	hyaluronan synthase 2	protein-coding	0.000000	0.302789	
chunk0043_170_1	chr12	17076189	17076810	+	0	NA	Intergenic	Intergenic	87752	NR_036619	728622	Hs.741380	NR_036619		SKP1P2	SKP1B|p19B	S-phase kinase associated protein 1 pseudogene 2	pseudo	0.001610	0.353698	
chunk0011_331_1	chr1	152111655	152111878	+	0	NA	exon (NM_007113, exon 3 of 3)	exon (NM_007113, exon 3 of 3)	3688	NM_007113	7062	Hs.432416	NM_007113	ENSG00000159450	TCHH	THH|THL|TRHY|UHS3	trichohyalin	protein-coding	0.107623	0.669643	
chunk0094_117_1	chr2	4462903	4463192	+	0	NA	Intergenic	(TATATT)n|Simple_repeat|Simple_repeat	193175	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.003460	0.303448	199(AAGTACAGTAAGTCCT,-,0.00),200(AGTACAGTAAGTCCTC,+,0.00)
chunk0178_38_1	chr7	29497293	29497500	+	0	NA	intron (NM_001293078, intron 2 of 4)	intron (NM_001293078, intron 2 of 4)	13580	NM_001293081	1124	Hs.654611	NM_004067	ENSG00000106069	CHN2	ARHGAP3|BCH|CHN2-3|RHOGAP3	chimerin 2	protein-coding	0.004831	0.350962	
chunk0164_326_1	chr6	25174819	25175096	+	0	NA	Intergenic	Intergenic	-36565	NR_027626	8418	Hs.484918	NR_002174	ENSG00000168405	CMAHP	CMAH|CSAH	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	pseudo	0.021661	0.428058	
chunk0081_27_1	chr17	37352818	37353392	+	0	NA	intron (NM_198839, intron 4 of 59)	intron (NM_198839, intron 4 of 59)	6011	NM_198836	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.006969	0.349565	264(CAGTACTAAATGTTCT,-,0.00),265(AGTACTAAATGTTCTA,+,0.00)
chunk0008_424_1	chr1	98874800	98875219	+	0	NA	Intergenic	L1MC3|LINE|L1	-129267	NR_033940	100129620	Hs.588631	NR_033940	ENSG00000232825	LOC100129620	-	uncharacterized LOC100129620	ncRNA	0.004773	0.409524	317(AGGCACTGGGTGTGCT,-,0.00),318(GGCACTGGGTGTGCTC,+,0.00)
chunk0065_278_1	chr14	102305166	102305365	+	0	NA	promoter-TSS (NM_014226)	promoter-TSS (NM_014226)	-65	NM_001272011	5891	Hs.36859	NM_014226	ENSG00000080823	MOK	RAGE|RAGE-1|RAGE1|STK30	MOK protein kinase	protein-coding	0.085427	0.615000	
chunk0154_356_1	chr5	87340580	87340886	+	0	NA	intron (NM_022650, intron 5 of 24)	intron (NM_022650, intron 5 of 24)	-17105	NR_130929	644285	Hs.709256	NR_130929		LOC644285	-	uncharacterized LOC644285	ncRNA	0.003268	0.342020	
chunk0003_32_1	chr1	29870804	29871037	+	0	NA	Intergenic	Intergenic	166692	NR_110790	101929406	Hs.639413	NR_110790	ENSG00000233399	LINC01648	-	long intergenic non-protein coding RNA 1648	ncRNA	0.012876	0.581197	
chunk0027_257_1	chr10	77240055	77240445	+	0	NA	intron (NM_001014797, intron 3 of 28)	intron (NM_001014797, intron 3 of 28)	99419	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.010256	0.398977	
chunk0018_379_1	chr1	222274073	222274594	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	273769	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.003839	0.438697	
chunk0070_6_1	chr15	68812953	68813353	+	0	NA	intron (NM_006305, intron 1 of 6)	intron (NM_006305, intron 1 of 6)	-6052	NR_026808	80035	Hs.662150	NM_024970		ANP32A-IT1	C15orf28|HsT18971|NCRNA00321	ANP32A intronic transcript 1	ncRNA	0.002500	0.441397	347(CAGGACAACTAGTTCT,-,0.00)
chunk0119_437_1	chr22	50115846	50116045	+	0	NA	intron (NM_001164105, intron 8 of 25)	intron (NM_001164105, intron 8 of 25)	25689	NM_001164105	54456	Hs.62880	NM_018995	ENSG00000073146	MOV10L1	CHAMP|DJ402G11.8	Mov10 like RISC complex RNA helicase 1	protein-coding	0.020101	0.620000	
chunk0149_310_1	chr5	26273063	26273407	+	0	NA	Intergenic	L1MEc|LINE|L1	765347	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.008721	0.431884	
chunk0088_305_1	chr18	50281210	50281424	+	0	NA	intron (NM_001204143, intron 1 of 13)	intron (NM_001204143, intron 1 of 13)	450	NM_001204143	4152	Hs.405610	NM_002384	ENSG00000141644	MBD1	CXXC3|PCM1|RFT	methyl-CpG binding domain protein 1	protein-coding	0.065421	0.632558	
chunk0038_156_1	chr11	84804017	84804545	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	119140	NM_001364	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.001894	0.357278	
chunk0134_76_1	chr3	176437999	176438642	+	0	NA	Intergenic	Intergenic	-76783	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.001555	0.335404	361(GGGCACACACTGTCTT,-,0.00),362(GGCACACACTGTCTTG,+,0.00)
chunk0190_142_1	chr8	30804477	30805011	+	0	NA	intron (NM_001009552, intron 1 of 6)	intron (NM_001009552, intron 1 of 6)	8092	NM_001009552	5516	Hs.491440	NM_004156	ENSG00000104695	PPP2CB	PP2Abeta|PP2CB	protein phosphatase 2 catalytic subunit beta	protein-coding	0.005618	0.396262	
chunk0034_236_1	chr11	33796589	33797123	+	0	NA	Intergenic	L1MA2|LINE|L1	22157	NR_120550	101928440	Hs.202343	NR_120550	ENSG00000254508	FBXO3-DT	FBXO3-AS1	FBXO3 divergent transcript	ncRNA	0.009363	0.394393	
chunk0128_151_1	chr3	106972335	106972904	+	0	NA	Intergenic	MIR|SINE|MIR	268019	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.005272	0.326316	247(TGGACTCCCAGTTCTT,+,0.00)
chunk0187_314_1	chr7	156480836	156481260	+	0	NA	intron (NR_103858, intron 1 of 1)	LTR78|LTR|ERV1	-35460	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.030660	0.517647	
chunk0171_427_1	chr6	131574079	131574777	+	0	NA	intron (NM_001270521, intron 29 of 29)	intron (NM_001270521, intron 29 of 29)	1224	NM_001244438	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.002865	0.396280	
chunk0177_364_1	chr7	26700811	26701350	+	0	NA	intron (NM_001303468, intron 9 of 12)	intron (NM_001303468, intron 9 of 12)	61995	NM_001302625									0.000000	0.403704	
chunk0163_89_1	chr6	9540195	9540670	+	0	NA	Intergenic	Intergenic	-871886	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.000000	0.321429	
chunk0068_207_1	chr15	55055700	55056138	+	0	NA	Intergenic	L2b|LINE|L2	141114	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004566	0.378132	
chunk0056_270_1	chr13	90156200	90156844	+	0	NA	Intergenic	Intergenic	-36805	NR_047489	100874187	Hs.564526	NR_047489	ENSG00000261446	LINC00559	-	long intergenic non-protein coding RNA 559	ncRNA	0.003106	0.379845	
chunk0028_460_1	chr10	95181674	95182096	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-12315	NM_207321	142827	Hs.134229	NM_207321	ENSG00000173124	ACSM6	C10orf129|bA310E22.3	acyl-CoA synthetase medium chain family member 6	protein-coding	0.004739	0.373522	
chunk0047_50_1	chr12	67242611	67242961	+	0	NA	Intergenic	Intergenic	-26495	NM_018448	55832	Hs.546407	NM_018448	ENSG00000111530	CAND1	TIP120|TIP120A	cullin associated and neddylation dissociated 1	protein-coding	0.008571	0.367521	
chunk0209_56_1	chrX	36921575	36921774	+	0	NA	Intergenic	L1MA3|LINE|L1	-86685	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.000000	0.295000	
chunk0031_135_1	chr10	124942664	124942863	+	0	NA	exon (NM_017580, exon 1 of 9)	exon (NM_017580, exon 1 of 9)	640	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.015075	0.460000	
chunk0210_148_1	chrX	75627830	75628372	+	0	NA	Intergenic	L1PB1|LINE|L1	-104599	NM_144969	158866	Hs.253211	NM_144969	ENSG00000102383	ZDHHC15	DHHC15|MRX91	zinc finger DHHC-type containing 15	protein-coding	0.001845	0.370166	174(AGGGACAGTTTGTCTT,-,0.00),175(GGGACAGTTTGTCTTC,+,0.00)
chunk0020_113_1	chr1	233287019	233287277	+	0	NA	intron (NM_014801, intron 1 of 33)	intron (NM_014801, intron 1 of 33)	8565	NM_014801	80003	Hs.370605	NM_014801	ENSG00000135749	PCNX2	PCNXL2	pecanex 2	protein-coding	0.003876	0.374517	
chunk0061_194_1	chr14	60233782	60234091	+	0	NA	Intergenic	L1M4|LINE|L1	-11816	NM_177952	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.000000	0.458065	
chunk0122_143_1	chr3	31919649	31919941	+	0	NA	intron (NM_017784, intron 1 of 11)	intron (NM_017784, intron 1 of 11)	-61979	NM_001137674	344787	Hs.585139	NM_001137674	ENSG00000197385	ZNF860	-	zinc finger protein 860	protein-coding	0.003425	0.409556	
chunk0141_457_1	chr4	89425554	89425825	+	0	NA	Intergenic	Intergenic	-117679	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.003690	0.345588	
chunk0162_6_1	chr6	313117	313424	+	0	NA	intron (NR_104473, intron 3 of 5)	intron (NR_104473, intron 3 of 5)	21213	NR_104474	56940	Hs.29106	NM_020185	ENSG00000112679	DUSP22	JKAP|JSP-1|JSP1|LMW-DSP2|LMWDSP2|MKP-x|MKPX|VHX	dual specificity phosphatase 22	protein-coding	0.003257	0.444805	175(TGGAACACACTGTCAT,-,0.00),176(GGAACACACTGTCATG,+,0.00)
chunk0042_284_1	chr12	7329614	7329829	+	0	NA	Intergenic	Intergenic	25389	NM_001080454	341392	Hs.450804	NM_001080454	ENSG00000215009	ACSM4	-	acyl-CoA synthetase medium chain family member 4	protein-coding	0.000000	0.305556	
chunk0143_388_1	chr4	122842937	122843397	+	0	NA	intron (NM_002006, intron 1 of 2)	L2c|LINE|L2	16459	NM_002006	2247	Hs.284244	NM_002006	ENSG00000138685	FGF2	BFGF|FGF-2|FGFB|HBGF-2	fibroblast growth factor 2	protein-coding	0.004348	0.422993	
chunk0195_409_1	chr8	100559319	100559813	+	0	NA	5' UTR (NM_001270378, exon 1 of 5)	5' UTR (NM_001270378, exon 1 of 5)	145	NM_001270378	157567	Hs.530199	NM_198401	ENSG00000186106	ANKRD46	ANK-S|GENX-115279	ankyrin repeat domain 46	protein-coding	0.101215	0.709091	
chunk0180_379_1	chr7	74199327	74199943	+	0	NA	Intergenic	Intergenic	8437	NR_030321	693175		NR_030321	ENSG00000207741	MIR590	MIRN590|hsa-mir-590|mir-590	microRNA 590	ncRNA	0.032468	0.473258	
chunk0191_80_1	chr8	47525806	47526655	+	0	NA	intron (NR_104581, intron 6 of 16)	intron (NR_104581, intron 6 of 16)	211934	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.004711	0.450588	
chunk0055_432_1	chr13	75454452	75454867	+	0	NA	intron (NM_001286659, intron 1 of 18)	intron (NM_001286659, intron 1 of 18)	27509	NM_001286659	9882	Hs.210891	NM_014832	ENSG00000136111	TBC1D4	AS160|NIDDM5	TBC1 domain family member 4	protein-coding	0.004819	0.326923	
chunk0195_254_1	chr8	97912254	97912694	+	0	NA	intron (NM_030583, intron 2 of 18)	intron (NM_030583, intron 2 of 18)	43391	NM_030583	4147	Hs.189445	NM_002380	ENSG00000132561	MATN2	-	matrilin 2	protein-coding	0.020455	0.473923	
chunk0169_252_1	chr6	105288021	105288357	+	0	NA	intron (NM_002726, intron 11 of 14)	intron (NM_002726, intron 11 of 14)	-108206	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.011905	0.388724	
chunk0075_189_1	chr16	52264334	52264586	+	0	NA	Intergenic	Intergenic	179179	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.000000	0.351779	159(GAGAACTTCTTGTTCT,-,0.00),160(AGAACTTCTTGTTCTT,+,0.00)
chunk0049_249_1	chr12	93688956	93689462	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	11834	NM_003805	8738	Hs.38533	NM_003805	ENSG00000169372	CRADD	MRT34|RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.003953	0.424063	
chunk0155_99_1	chr5	92382988	92383235	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	-999779	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.012146	0.342742	132(TAGAACAAAATGTTTC,-,0.00)
chunk0180_79_1	chr7	54988373	54988994	+	0	NA	Intergenic	Intergenic	-30349	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.003221	0.340836	
chunk0137_240_1	chr4	20536972	20537475	+	0	NA	intron (NM_001289135, intron 17 of 35)	Tigger3b|DNA|TcMar-Tigger	8948	NR_029631	407000		NR_029631	ENSG00000207732	MIR218-1	MIRN218-1|mir-218-1	microRNA 218-1	ncRNA	0.009940	0.388889	
chunk0099_111_1	chr2	85907761	85908016	+	0	NA	Intergenic	Intergenic	18608	NR_110569	101928113	Hs.625888	NR_110569		ST3GAL5-AS1	-	ST3GAL5 antisense RNA 1 (head to head)	ncRNA	0.019608	0.488281	
chunk0100_133_1	chr2	108691288	108692002	+	0	NA	Intergenic	AluSx3|SINE|Alu	-27836	NM_006267	5903	Hs.199561	NM_006267	ENSG00000153201	RANBP2	ADANE|ANE1|IIAE3|NUP358|TRP1|TRP2	RAN binding protein 2	protein-coding	0.015406	0.381818	289(TAGAACATCCAGTACA,-,0.00),290(AGAACATCCAGTACAG,+,0.00)
chunk0109_246_1	chr20	6134588	6134787	+	0	NA	Intergenic	MER54B|LTR|ERVL	-11143	NM_017671	55612	Hs.472054	NM_017671	ENSG00000101311	FERMT1	C20orf42|DTGCU2|KIND1|UNC112A|URP1	fermitin family member 1	protein-coding	0.025126	0.505000	
chunk0191_245_1	chr8	53103036	53103630	+	0	NA	Intergenic	Intergenic	148301	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.001684	0.352941	313(AGGTACAGACTGTGAT,-,0.00)
chunk0085_302_1	chr18	8119987	8120662	+	0	NA	intron (NM_001105244, intron 13 of 32)	intron (NM_001105244, intron 13 of 32)	246710	NR_024419	100192426	Hs.666655	NR_024419	ENSG00000266149	LOC100192426	-	uncharacterized LOC100192426	ncRNA	0.008889	0.377219	
chunk0074_327_1	chr16	30951692	30952157	+	0	NA	intron (NM_152288, intron 1 of 1)	MER102b|DNA|hAT-Charlie	2840	NM_152288	93129	Hs.745104	NM_152288	ENSG00000175938	ORAI3	TMEM142C	ORAI calcium release-activated calcium modulator 3	protein-coding	0.006452	0.412017	
chunk0175_268_1	chr7	7454686	7455207	+	0	NA	intron (NM_001037763, intron 16 of 34)	intron (NM_001037763, intron 16 of 34)	80883	NM_001037763	340267	Hs.491104	NM_001037763	ENSG00000215018	COL28A1	COL28	collagen type XXVIII alpha 1 chain	protein-coding	0.005758	0.360153	
chunk0010_263_1	chr1	116885311	116885881	+	0	NA	Intergenic	L2a|LINE|L2	-24327	NM_020440	5738	Hs.418093	NM_020440	ENSG00000134247	PTGFRN	CD315|CD9P-1|EWI-F|FPRP|SMAP-6	prostaglandin F2 receptor inhibitor	protein-coding	0.005263	0.436077	
chunk0185_218_1	chr7	128989874	128990330	+	0	NA	intron (NR_034053, intron 11 of 23)	intron (NR_034053, intron 11 of 23)	49432	NM_001098627	3663	Hs.521181	NM_032643	ENSG00000128604	IRF5	SLEB10	interferon regulatory factor 5	protein-coding	0.019737	0.396061	
chunk0025_427_1	chr10	59906881	59907331	+	0	NA	promoter-TSS (NM_005436)	promoter-TSS (NM_005436)	-450	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.042222	0.494457	
chunk0161_21_1	chr5	165753900	165754250	+	0	NA	Intergenic	MIRc|SINE|MIR	1172295	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005714	0.284900	
chunk0003_465_1	chr1	41849314	41849695	+	0	NA	intron (NR_038260, intron 1 of 2)	intron (NR_038260, intron 1 of 2)	69203	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.000000	0.460733	
chunk0058_435_1	chr13	113208519	113208851	+	0	NA	promoter-TSS (NM_001258212)	promoter-TSS (NM_001258212)	-9	NM_001278514	8451	Hs.339735	NM_003589	ENSG00000139842	CUL4A	-	cullin 4A	protein-coding	0.114458	0.732733	
chunk0008_196_1	chr1	93362190	93362488	+	0	NA	3' UTR (NM_001938, exon 3 of 3)	3' UTR (NM_001938, exon 3 of 3)	16418	NM_001938	1810	Hs.348418	NM_001938	ENSG00000117505	DR1	NC2|NC2-BETA|NC2B|NCB2	down-regulator of transcription 1	protein-coding	0.006711	0.294314	
chunk0011_118_1	chr1	146943580	146943869	+	0	NA	intron (NM_001278141, intron 2 of 36)	intron (NM_001278141, intron 2 of 36)	5179	NM_001278141	149013	Hs.666981	NM_001278141	ENSG00000268043	NBPF12	COAS1|KIAA1245	NBPF member 12	protein-coding	0.010381	0.458621	
chunk0191_376_1	chr8	56994068	56994336	+	0	NA	promoter-TSS (NM_017813)	promoter-TSS (NM_017813)	-331	NM_017813	54928	Hs.438689	NM_017813	ENSG00000104331	IMPAD1	GPAPP|IMP 3|IMP-3|IMPA3	inositol monophosphatase domain containing 1	protein-coding	0.029851	0.460967	180(TAGACAGCCTGTACCT,+,0.00)
chunk0178_213_1	chr7	35442666	35442890	+	0	NA	Intergenic	Intergenic	128923	NR_038864	401324	Hs.377034	NR_038864		LOC401324	-	uncharacterized LOC401324	ncRNA	0.022321	0.480000	85(TGGGACATGCTGTTCC,-,0.00),86(GGGACATGCTGTTCCT,+,0.00)
chunk0069_193_1	chr15	63332679	63333112	+	0	NA	intron (NM_001218, intron 8 of 10)	L2c|LINE|L2	49215	NM_206925	771	Hs.210995	NM_001218	ENSG00000074410	CA12	CA-XII|CAXII|HsT18816|T18816	carbonic anhydrase 12	protein-coding	0.013857	0.426267	
chunk0197_424_1	chr8	127408273	127409003	+	0	NA	intron (NR_117100, intron 5 of 5)	intron (NR_117100, intron 5 of 5)	-6974	NM_001159542	5462	Hs.450254	NM_001159542	ENSG00000212993	POU5F1B	OCT4-PG1|OCT4PG1|OTF3C|OTF3P1|POU5F1P1|POU5F1P4|POU5FLC20|POU5FLC8	POU class 5 homeobox 1B	protein-coding	0.006849	0.450068	551(GGTGCATCCTGTCCCT,+,0.00)
chunk0040_221_1	chr11	114308786	114309311	+	0	NA	intron (NM_006169, intron 2 of 2)	intron (NM_006169, intron 2 of 2)	13235	NM_006169	4837	Hs.503911	NM_006169	ENSG00000166741	NNMT	-	nicotinamide N-methyltransferase	protein-coding	0.009524	0.391635	
chunk0022_107_1	chr10	10104996	10105364	+	0	NA	Intergenic	Intergenic	46458	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.005435	0.330623	
chunk0018_79_1	chr1	217275790	217276108	+	0	NA	Intergenic	Intergenic	-138194	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.009434	0.366771	187(GTGAACATTCTGTACT,-,0.00),188(TGAACATTCTGTACTT,+,0.00)
chunk0146_260_1	chr4	162775722	162776213	+	0	NA	Intergenic	Intergenic	317661	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.006110	0.302846	
chunk0004_211_1	chr1	46681516	46682429	+	0	NA	intron (NM_014774, intron 10 of 10)	intron (NM_014774, intron 10 of 10)	7936	NR_038827	100130197	Hs.568643	NR_038827	ENSG00000228237	EFCAB14-AS1	KIAA0494-AS1	EFCAB14 antisense RNA 1	ncRNA	0.002191	0.409190	
chunk0197_358_1	chr8	125654990	125655192	+	0	NA	Intergenic	MIRb|SINE|MIR	222882	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.000000	0.349754	
chunk0037_319_1	chr11	76855523	76855833	+	0	NA	Intergenic	L1ME4a|LINE|L1	-5195	NM_001300954	55331	Hs.23862	NM_018367	ENSG00000078124	ACER3	APHC|PHCA|PLDECO	alkaline ceramidase 3	protein-coding	0.003226	0.289389	
chunk0109_375_1	chr2	239396662	239397313	+	0	NA	intron (NM_006037, intron 1 of 26)	intron (NM_006037, intron 1 of 26)	3962	NM_006037	9759	Hs.20516	NM_006037	ENSG00000068024	HDAC4	AHO3|BDMR|HA6116|HD4|HDAC-4|HDAC-A|HDACA	histone deacetylase 4	protein-coding	0.024578	0.478528	295(AAGAACATGATGTCTT,-,0.00),296(AGAACATGATGTCTTC,+,0.00)
chunk0194_146_1	chr8	84506904	84507198	+	0	NA	intron (NM_001100392, intron 2 of 9)	intron (NM_001100392, intron 2 of 9)	-198876	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.003401	0.352542	
chunk0162_251_1	chr6	5108175	5108483	+	0	NA	TTS (NR_104418)	TTS (NR_104418)	22843	NM_001145115	648791	Hs.653089	NM_001145115	ENSG00000219607	PPP1R3G	-	protein phosphatase 1 regulatory subunit 3G	protein-coding	0.016234	0.436893	
chunk0054_253_1	chr13	46246595	46247101	+	0	NA	intron (NM_001282460, intron 6 of 9)	intron (NM_001282460, intron 6 of 9)	34905	NM_001282460	220416	Hs.267765	NM_001024609	ENSG00000173988	LRRC63	-	leucine rich repeat containing 63	protein-coding	0.005929	0.268245	177(AAGCACAAAATGTACA,-,0.00),178(AGCACAAAATGTACAG,+,0.00)
chunk0133_262_1	chr3	171774354	171774553	+	0	NA	intron (NM_001130081, intron 1 of 25)	intron (NM_001130081, intron 1 of 25)	36041	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.015075	0.535000	
chunk0039_434_1	chr11	108008808	108009414	+	0	NA	5' UTR (NM_003478, exon 1 of 19)	5' UTR (NM_003478, exon 1 of 19)	429	NM_003478	8065	Hs.440320	NM_003478	ENSG00000166266	CUL5	CUL-5|VACM-1|VACM1	cullin 5	protein-coding	0.100660	0.657331	
chunk0065_334_1	chr14	103293989	103294541	+	0	NA	Intergenic	Intergenic	-39737	NM_001969	1983	Hs.433702	NM_001969	ENSG00000100664	EIF5	EIF-5|EIF-5A	eukaryotic translation initiation factor 5	protein-coding	0.034420	0.593128	471(CAGAACTTTTTGTTCA,-,0.00),472(AGAACTTTTTGTTCAG,+,0.00)
chunk0058_133_1	chr14	22574859	22575162	+	0	NA	intron (NM_001344, intron 2 of 2)	intron (NM_001344, intron 2 of 2)	14227	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.000000	0.391447	
chunk0159_309_1	chr5	143108333	143109091	+	0	NA	intron (NM_015071, intron 17 of 22)	intron (NM_015071, intron 17 of 22)	-83788	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.006596	0.401845	
chunk0134_333_1	chr3	181947640	181948061	+	0	NA	Intergenic	L2c|LINE|L2	-4514	NR_104146	100996490	Hs.606987	NR_104146	ENSG00000242512	LINC01206	-	long intergenic non-protein coding RNA 1206	ncRNA	0.002375	0.450237	
chunk0142_130_1	chr4	94679951	94680809	+	0	NA	Intergenic	Intergenic	77153	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.015152	0.448196	
chunk0066_430_1	chr15	39639499	39639957	+	0	NA	intron (NM_152597, intron 10 of 11)	intron (NM_152597, intron 10 of 11)	58649	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.002183	0.333333	
chunk0197_284_1	chr8	124160722	124160921	+	0	NA	intron (NR_103547, intron 1 of 4)	L2c|LINE|L2	10701	NR_103547	157376	Hs.662360	NM_182525	ENSG00000253868	FER1L6-AS2	C8orf78	FER1L6 antisense RNA 2	ncRNA	0.000000	0.490000	94(GGGCACAGCCTCTTCC,-,0.00),95(GGCACAGCCTCTTCCT,+,0.00)
chunk0077_159_1	chr16	79165478	79165865	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	435054	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.020672	0.461340	
chunk0022_175_1	chr10	12873194	12873393	+	0	NA	Intergenic	Intergenic	128411	NM_031455	83643	Hs.498720	NM_031455	ENSG00000151468	CCDC3	-	coiled-coil domain containing 3	protein-coding	0.020101	0.445000	
chunk0150_196_1	chr5	34838603	34839297	+	0	NA	promoter-TSS (NM_144725)	promoter-TSS (NM_144725)	-214	NM_144725	153657	Hs.435742	NM_144725	ENSG00000205838	TTC23L	MC25-1	tetratricopeptide repeat domain 23 like	protein-coding	0.070605	0.585612	
chunk0100_435_1	chr2	120526814	120527172	+	0	NA	Intergenic	Intergenic	-60644	NR_027181	84931	Hs.334519	NM_032845	ENSG00000280409	LINC01101	-	long intergenic non-protein coding RNA 1101	ncRNA	0.027933	0.495822	
chunk0113_233_1	chr20	54070484	54070838	+	0	NA	5' UTR (NM_001316361, exon 1 of 10)	5' UTR (NM_001316361, exon 1 of 10)	104	NM_001316361	8537	Hs.400556	NM_003657	ENSG00000064787	BCAS1	AIBC1|NABC1	breast carcinoma amplified sequence 1	protein-coding	0.016949	0.591549	
chunk0047_129_1	chr12	69345634	69346417	+	0	NA	Intergenic	LTR83|LTR|ERVL	-2329	NM_000239	4069	Hs.524579	NM_000239	ENSG00000090382	LYZ	LYZF1|LZM	lysozyme	protein-coding	0.006386	0.394133	28(AAGAACATGCAGTACA,-,0.00),29(AGAACATGCAGTACAT,+,0.00),389(ATAACTGGCTGTTCTT,+,0.00)
chunk0065_272_1	chr14	101947732	101948353	+	0	NA	Intergenic	CpG	-16486	NM_001376	1778	Hs.614080	NM_001376	ENSG00000197102	DYNC1H1	CMT2O|DHC1|DHC1a|DNCH1|DNCL|DNECL|DYHC|Dnchc1|HL-3|SMALED1|p22	dynein cytoplasmic 1 heavy chain 1	protein-coding	0.064412	0.599678	
chunk0114_362_1	chr21	19810761	19811264	+	0	NA	Intergenic	Intergenic	992096	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.009940	0.386905	267(CGGGACTGAGTGTACT,-,0.00),268(GGGACTGAGTGTACTC,+,0.00)
chunk0099_274_1	chr2	98274792	98275620	+	0	NA	intron (NM_144992, intron 22 of 27)	L2a|LINE|L2	-70949	NM_001298	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.010870	0.492159	
chunk0003_406_1	chr1	40052169	40052622	+	0	NA	intron (NM_006367, intron 1 of 12)	intron (NM_006367, intron 1 of 12)	11812	NM_001105530	10487	Hs.370581	NM_006367	ENSG00000131236	CAP1	CAP|CAP1-PEN	cyclase associated actin cytoskeleton regulatory protein 1	protein-coding	0.006623	0.361233	
chunk0003_163_1	chr1	33414101	33414721	+	0	NA	Intergenic	Intergenic	-38818	NM_198040	1912	Hs.524271	NM_004427	ENSG00000134686	PHC2	EDR2|HPH2|PH2	polyhomeotic homolog 2	protein-coding	0.000000	0.381643	
chunk0196_401_1	chr8	115939215	115939417	+	0	NA	Intergenic	Intergenic	-270288	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.000000	0.275862	
chunk0122_65_1	chr3	28940563	28941039	+	0	NA	Intergenic	Intergenic	340138	NR_109804	100873979	Hs.99391	NR_109804		RBMS3-AS3	-	RBMS3 antisense RNA 3	ncRNA	0.000000	0.436059	
chunk0147_112_1	chr4	174226880	174227404	+	0	NA	Intergenic	Intergenic	-6744	NR_125896	101928509	Hs.147719	NR_125896	ENSG00000248174	LINC02268	-	long intergenic non-protein coding RNA 2268	ncRNA	0.005725	0.356190	
chunk0076_181_1	chr16	67594827	67595197	+	0	NA	intron (NM_001191022, intron 2 of 9)	intron (NM_001191022, intron 2 of 9)	32605	NM_006565	10664	Hs.368367	NM_006565	ENSG00000102974	CTCF	MRD21	CCCTC-binding factor	protein-coding	0.002703	0.425876	203(GGGAACAAACTGTACA,-,0.00),204(GGAACAAACTGTACAG,+,0.00)
chunk0143_254_1	chr4	115671410	115672093	+	0	NA	Intergenic	Intergenic	-557875	NM_022569	64579	Hs.591700	NM_022569	ENSG00000138653	NDST4	N-HSST|N-HSST 4|NDST-4|NHSST4	N-deacetylase and N-sulfotransferase 4	protein-coding	0.008785	0.327485	
chunk0122_445_1	chr3	39419699	39420443	+	0	NA	Intergenic	L2a|LINE|L2	9017	NR_002324	6044	Hs.449909	NR_002324	ENSG00000202363	SNORA62	E2|E2-1|RNE2|RNU108	small nucleolar RNA, H/ACA box 62	snoRNA	0.004032	0.405369	
chunk0160_454_1	chr5	165108532	165109364	+	0	NA	Intergenic	AluSz6|SINE|Alu	638669	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.003606	0.415366	664(GAGAACAGTCAGTACA,-,0.00),665(AGAACAGTCAGTACAG,+,0.00)
chunk0068_346_1	chr15	57758960	57759412	+	0	NA	Intergenic	MIR|SINE|MIR	52665	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.006637	0.399558	
chunk0200_314_1	chr9	23271021	23271406	+	0	NA	Intergenic	L1P2|LINE|L1	401186	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.002597	0.362694	320(AGGAACAGATTGTTCA,-,0.00),321(GGAACAGATTGTTCAG,+,0.00)
chunk0143_409_1	chr4	123350398	123350690	+	0	NA	Intergenic	Intergenic	-46251	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.003425	0.399317	
chunk0031_433_1	chr10	132479711	132479991	+	0	NA	Intergenic	Intergenic	34641	NM_173541									0.028571	0.601423	196(GGGAACAGGCAGTGCC,-,0.00),197(GGAACAGGCAGTGCCC,+,0.00)
chunk0203_248_1	chr9	87397990	87398588	+	0	NA	Intergenic	L1ME4a|LINE|L1	-98939	NM_001288731	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.001672	0.328881	
chunk0020_415_1	chr1	241566793	241567186	+	0	NA	intron (NM_003679, intron 9 of 14)	intron (NM_003679, intron 9 of 14)	34855	NM_003679	8564	Hs.731056	NM_003679	ENSG00000117009	KMO	dJ317G22.1	kynurenine 3-monooxygenase	protein-coding	0.025445	0.474619	
chunk0009_343_1	chr1	109323008	109323483	+	0	NA	intron (NM_002959, intron 14 of 19)	intron (NM_002959, intron 14 of 19)	-16204	NM_001265613	343263	Hs.443402	NM_001010985	ENSG00000221986	MYBPHL	-	myosin binding protein H like	protein-coding	0.012632	0.462185	121(AGAGACACACTGTTCA,-,0.00),122(GAGACACACTGTTCAG,+,0.00)
chunk0040_197_1	chr11	114129737	114130571	+	0	NA	intron (NM_006006, intron 2 of 6)	intron (NM_006006, intron 2 of 6)	69588	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.017986	0.486228	
chunk0160_328_1	chr5	159712772	159713058	+	0	NA	Intergenic	L2c|LINE|L2	158469	NR_109891	101927766	Hs.638568	NR_109891	ENSG00000253311	LINC01847	-	long intergenic non-protein coding RNA 1847	ncRNA	0.010490	0.411150	
chunk0042_424_1	chr12	11885535	11886188	+	0	NA	intron (NM_001987, intron 6 of 7)	intron (NM_001987, intron 6 of 7)	-185083	NM_138723	79370	Hs.210343	NM_030766	ENSG00000121380	BCL2L14	BCLG	BCL2 like 14	protein-coding	0.013783	0.466361	
chunk0107_126_1	chr2	214654215	214654708	+	0	NA	Intergenic	L1MEg|LINE|L1	144279	NR_047698	100885780	Hs.665982	NR_047698	ENSG00000224257	VWC2L-IT1	-	VWC2L intronic transcript 1	ncRNA	0.002028	0.380567	
chunk0038_392_1	chr11	93623707	93624083	+	0	NA	Intergenic	Intergenic	-37755	NM_033395	85459	Hs.458418	NM_033395	ENSG00000166004	CEP295	KIAA1731	centrosomal protein 295	protein-coding	0.002660	0.437666	
chunk0110_366_1	chr20	19890516	19891415	+	0	NA	intron (NM_018993, intron 1 of 10)	MER110|LTR|ERV1	1399	NM_018993	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.005562	0.395556	
chunk0024_108_1	chr10	34690452	34691054	+	0	NA	intron (NM_019619, intron 2 of 24)	intron (NM_019619, intron 2 of 24)	124572	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.021595	0.484245	360(GAGTACAGAGAGTGCC,-,0.00),361(AGTACAGAGAGTGCCA,+,0.00)
chunk0207_379_1	chr9	136051889	136052088	+	0	NA	intron (NM_144653, intron 1 of 5)	CpG	43297	NM_144653	138151	Hs.112895	NM_144653	ENSG00000148411	NACC2	BEND9|BTBD14|BTBD14A|BTBD31|NAC-2|RBB	NACC family member 2	protein-coding	0.080402	0.680000	
chunk0005_355_1	chr1	61338419	61338844	+	0	NA	intron (NM_001145511, intron 4 of 10)	intron (NM_001145511, intron 4 of 10)	-85113	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.011765	0.359155	274(AATACAAAATGTTCTT,+,0.00)
chunk0078_316_1	chr17	8448178	8448658	+	0	NA	intron (NM_001025579, intron 4 of 9)	intron (NM_001025579, intron 4 of 9)	12566	NM_030808	81565	Hs.372123	NM_030808	ENSG00000166579	NDEL1	EOPA|MITAP1|NDE1L1|NDE2|NUDEL	nudE neurodevelopment protein 1 like 1	protein-coding	0.006250	0.349272	
chunk0171_287_1	chr6	128144293	128144598	+	0	NA	intron (NM_001291981, intron 7 of 32).2	L2a|LINE|L2	116580	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.003279	0.375817	
chunk0088_377_1	chr18	54212221	54212521	+	0	NA	intron (NM_003927, intron 1 of 6)	intron (NM_003927, intron 1 of 6)	10041	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.003333	0.372093	179(GAAACACTGAGTTCTG,+,0.00)
chunk0189_439_1	chr8	28176160	28176555	+	0	NA	intron (NM_018091, intron 14 of 14)	L1MB4|LINE|L1	83290	NM_001284224	55140	Hs.491336	NM_018091	ENSG00000134014	ELP3	KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.005063	0.436869	
chunk0072_454_1	chr15	101825606	101825840	+	0	NA	Intergenic	Intergenic	7536	NM_001001674	390649	Hs.554589	NM_001001674	ENSG00000182854	OR4F15	-	olfactory receptor family 4 subfamily F member 15	protein-coding	0.004274	0.382979	147(CTGAACATGTTGTTCT,-,0.00),148(TGAACATGTTGTTCTC,+,0.00)
chunk0068_275_1	chr15	56687262	56687540	+	0	NA	intron (NM_001002843, intron 8 of 20)	L1ME4b|LINE|L1	46685	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.000000	0.297491	
chunk0117_13_1	chr22	11211102	11211467	+	0	NA	Intergenic	SAR|Satellite|Satellite	-249755	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.008219	0.193989	
chunk0162_300_1	chr6	6506117	6506412	+	0	NA	intron (NR_026970, intron 3 of 7)	intron (NR_026970, intron 3 of 7)	-82437	NM_004271	9450	Hs.653138	NM_004271	ENSG00000112799	LY86	MD-1|MD1|MMD-1|dJ80N2.1	lymphocyte antigen 86	protein-coding	0.010169	0.449324	101(GTTACAGGCTGTGCCT,+,0.00),132(TTGAACTGATTGTTCT,-,0.00),133(TGAACTGATTGTTCTT,+,0.00)
chunk0072_328_1	chr15	99143379	99144003	+	0	NA	intron (NR_109947, intron 11 of 12)	intron (NR_109947, intron 11 of 12)	38611	NM_145728	23336	Hs.207106	NM_015286	ENSG00000182253	SYNM	DMN|SYN	synemin	protein-coding	0.006410	0.438400	
chunk0045_104_1	chr12	46187153	46187406	+	0	NA	3' UTR (NM_001278387, exon 18 of 18)	3' UTR (NM_001278387, exon 18 of 18)	79216	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.007905	0.452756	
chunk0185_212_1	chr7	128771487	128772121	+	0	NA	TTS (NM_001708)	TTS (NM_001708)	3986	NM_001708	611	Hs.656404	NM_001708	ENSG00000128617	OPN1SW	BCP|BOP|CBT	opsin 1, short wave sensitive	protein-coding	0.011041	0.359055	
chunk0095_170_1	chr2	17580801	17581145	+	0	NA	intron (NM_003385, intron 1 of 3)	L1ME4a|LINE|L1	40433	NM_003385	7447	Hs.444212	NM_003385	ENSG00000163032	VSNL1	HLP3|HPCAL3|HUVISL1|VILIP|VILIP-1	visinin like 1	protein-coding	0.000000	0.307246	
chunk0013_62_1	chr1	167344846	167345541	+	0	NA	intron (NR_037163, intron 3 of 16)	intron (NR_037163, intron 3 of 16)	16149	NM_001198783	5451	Hs.283402	NM_002697	ENSG00000143190	POU2F1	OCT1|OTF1|oct-1B	POU class 2 homeobox 1	protein-coding	0.011511	0.420977	
chunk0008_284_1	chr1	94850505	94851006	+	0	NA	intron (NM_001258342, intron 8 of 13)	intron (NM_001258342, intron 8 of 13)	30211	NM_001301079	126969	Hs.483423	NM_152369	ENSG00000143036	SLC44A3	CTL3	solute carrier family 44 member 3	protein-coding	0.003992	0.418327	280(AGGAACATCTAGTACC,-,0.00),281(GGAACATCTAGTACCT,+,0.00)
chunk0036_172_1	chr11	62554771	62555202	+	0	NA	Intergenic	Intergenic	5320	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.013921	0.574074	
chunk0123_433_1	chr3	50260053	50260322	+	0	NA	TTS (NM_001282617)	TTS (NM_001282617)	7184	NR_110702	101928931	Hs.587216	NR_110702	ENSG00000232352	SEMA3B-AS1	-	SEMA3B antisense RNA 1 (head to head)	ncRNA	0.130112	0.774074	
chunk0211_367_1	chrX	126052573	126052819	+	0	NA	Intergenic	Intergenic	-57066	NR_110409	101928495	Hs.545998	NR_110409	ENSG00000237208	LOC101928495	-	uncharacterized LOC101928495	ncRNA	0.004065	0.327935	168(AGAACTTTGTGATCTT,+,0.00)
chunk0211_376_1	chrX	126655026	126655367	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-102337	NM_178470	139170	Hs.120403	NM_178470	ENSG00000198889	DCAF12L1	KIAA1892L|WDR40B	DDB1 and CUL4 associated factor 12 like 1	protein-coding	0.002933	0.406433	
chunk0020_165_1	chr1	234394465	234394690	+	0	NA	intron (NM_005646, intron 26 of 29)	intron (NM_005646, intron 26 of 29)	20876	NM_001301733	388753	Hs.23198	NM_001012985	ENSG00000168275	COA6	C1orf31|CEMCOX4	cytochrome c oxidase assembly factor 6	protein-coding	0.013333	0.455752	
chunk0204_74_1	chr9	93811905	93812250	+	0	NA	Intergenic	L2a|LINE|L2	-7280	NR_036254	100422927		NR_036254	ENSG00000265347	MIR4291	-	microRNA 4291	ncRNA	0.005797	0.508671	
chunk0124_51_1	chr3	52742416	52742642	+	0	NA	intron (NM_001193533, intron 11 of 14)	intron (NM_001193533, intron 11 of 14)	28420	NM_003157	6787	Hs.631921	NM_003157	ENSG00000114904	NEK4	NRK2|STK2|pp12301	NIMA related kinase 4	protein-coding	0.000000	0.356828	
chunk0171_90_1	chr6	121885319	121885994	+	0	NA	Intergenic	Intergenic	450079	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.005926	0.430473	442(AGGGACTGACTGAGCT,-,0.00)
chunk0211_245_1	chrX	120428339	120428622	+	0	NA	3' UTR (NM_001122606, exon 9 of 9)	3' UTR (NM_001122606, exon 9 of 9)	40869	NM_013995	3920	Hs.496684	NM_002294	ENSG00000005893	LAMP2	CD107b|LAMP-2|LAMPB|LGP-96|LGP110	lysosomal associated membrane protein 2	protein-coding	0.007067	0.383803	64(TTGCACAGCATGTCCT,-,0.00),65(TGCACAGCATGTCCTG,+,0.00)
chunk0197_352_1	chr8	125557029	125557330	+	0	NA	Intergenic	MER5A1|DNA|hAT-Charlie	124970	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.009967	0.516556	
chunk0093_39_1	chr19	39463238	39463936	+	0	NA	intron (NM_001111020, intron 10 of 29)	L1M4|LINE|L1	-16825	NM_001001563	92609	Hs.590956	NM_001001563	ENSG00000105197	TIMM50	MGCA9|TIM50|TIM50L	translocase of inner mitochondrial membrane 50	protein-coding	0.007163	0.366237	
chunk0030_238_1	chr10	115030788	115031333	+	0	NA	Intergenic	L2b|LINE|L2	36403	NR_120677	102724589		NR_120677	ENSG00000236799	LINC02626	-	long intergenic non-protein coding RNA 2626	ncRNA	0.005505	0.441392	
chunk0152_197_1	chr5	59955269	59955753	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	-61717	NM_001104631	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.006198	0.457732	162(AGGAACATGCTGCCCC,-,0.00),163(GGAACATGCTGCCCCA,+,0.00)
chunk0111_129_1	chr20	24620956	24621637	+	0	NA	intron (NM_024893, intron 3 of 3)	intron (NM_024893, intron 3 of 3)	152097	NM_024893	79953	Hs.124638	NM_024893	ENSG00000101463	SYNDIG1	C20orf39|DSPC2|IFITMD5|TMEM90B	synapse differentiation inducing 1	protein-coding	0.001468	0.357771	
chunk0150_358_1	chr5	38782959	38783989	+	0	NA	intron (NR_109951, intron 2 of 3)	MIR3|SINE|MIR	62355	NR_109951	101929768	Hs.546623	NR_109951		OSMR-AS1	CTD-2127H9.1	OSMR antisense RNA 1 (head to head)	ncRNA	0.005825	0.432590	739(AAGGACAGAGTCTTCT,-,0.00),740(AGGACAGAGTCTTCTT,+,0.00)
chunk0001_8_1	chr1	877568	878151	+	0	NA	Intergenic	Intergenic	-1057	NR_027055	284593	Hs.449006	NR_027055	ENSG00000230368	FAM41C	-	family with sequence similarity 41 member C	ncRNA	0.003431	0.513699	
chunk0055_361_1	chr13	70732530	70732828	+	0	NA	Intergenic	Intergenic	-282462	NR_047699	100885781	Hs.372660	NR_047699	ENSG00000226846	LINC00348	-	long intergenic non-protein coding RNA 348	ncRNA	0.006711	0.408027	
chunk0137_454_1	chr4	29276150	29276690	+	0	NA	Intergenic	Intergenic	456838	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.001852	0.351201	
chunk0106_273_1	chr2	204011875	204012371	+	0	NA	Intergenic	MLT1K-int|LTR|ERVL-MaLR	75375	NM_012092	29851	Hs.56247	NM_012092	ENSG00000163600	ICOS	AILIM|CD278|CVID1	inducible T cell costimulator	protein-coding	0.004032	0.402414	
chunk0082_154_1	chr17	55607527	55608215	+	0	NA	Intergenic	Intergenic	114993	NM_018286	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.005814	0.404935	284(GAGGACACAGTCTTCT,-,0.00),285(AGGACACAGTCTTCTG,+,0.00)
chunk0125_75_1	chr3	64522042	64522474	+	0	NA	exon (NM_182920, exon 39 of 40)	exon (NM_182920, exon 39 of 40)	-39088	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.011574	0.473441	
chunk0078_303_1	chr17	8262159	8262526	+	0	NA	intron (NM_012393, intron 11 of 27)	L1ME4b|LINE|L1	13064	NM_012393	5198	Hs.573976	NM_012393	ENSG00000178921	PFAS	FGAMS|FGAR-AT|FGARAT|GATD8|PURL	phosphoribosylformylglycinamidine synthase	protein-coding	0.010899	0.366848	
chunk0011_112_1	chr1	146012727	146013175	+	0	NA	Intergenic	HAL1|LINE|L1	8871	NM_213652	148738	Hs.632436	NM_145277	ENSG00000168509	HJV	HFE2|HFE2A|JH|RGMC	hemojuvelin BMP co-receptor	protein-coding	0.002232	0.296214	
chunk0086_197_1	chr18	22242032	22242271	+	0	NA	Intergenic	Intergenic	72714	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.025105	0.479167	
chunk0150_424_1	chr5	40376143	40376661	+	0	NA	Intergenic	Intergenic	-303528	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.003861	0.339114	248(AAGTACAGCAAGTTCT,-,0.00),249(AGTACAGCAAGTTCTT,+,0.00)
chunk0102_199_1	chr2	147909859	147910322	+	0	NA	intron (NM_001616, intron 4 of 10)	intron (NM_001616, intron 4 of 10)	65095	NM_001616	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.006479	0.351293	
chunk0041_72_1	chr11	123833164	123834070	+	0	NA	Intergenic	L1MA9|LINE|L1	-27268	NM_001005325	390261	Hs.557924	NM_001005325	ENSG00000196099	OR6M1	OR11-271	olfactory receptor family 6 subfamily M member 1	protein-coding	0.004415	0.352811	
chunk0098_126_1	chr2	68945881	68946703	+	0	NA	intron (NM_182536, intron 5 of 5)	intron (NM_182536, intron 5 of 5)	6678	NM_182536	200504	Hs.16757	NM_182536	ENSG00000183607	GKN2	BRICD1B|GDDR|PRO813|TFIZ1|VLTI465	gastrokine 2	protein-coding	0.006083	0.375456	560(GAGAACATGTTGTCCA,-,0.00),561(AGAACATGTTGTCCAG,+,0.00)
chunk0061_286_1	chr14	61567158	61567737	+	0	NA	intron (NR_110417, intron 1 of 3)	L1MA5A|LINE|L1	2747	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.003454	0.341379	349(AAGAACATACAGTGTT,-,0.00)
chunk0087_204_1	chr18	35936927	35937440	+	0	NA	Intergenic	Intergenic	-3041	NR_037497	100500864		NR_037497	ENSG00000265641	MIR3929	-	microRNA 3929	ncRNA	0.003899	0.476654	253(AAGTACAATGTGATCC,-,0.00)
chunk0211_80_1	chrX	110086098	110086526	+	0	NA	intron (NM_032227, intron 3 of 6)	MER58A|DNA|hAT-Charlie	4194	NR_039774	100616491		NR_039774	ENSG00000265584	MIR3978	-	microRNA 3978	ncRNA	0.000000	0.351981	
chunk0164_40_1	chr6	18441201	18441872	+	0	NA	intron (NM_182757, intron 4 of 7)	intron (NM_182757, intron 4 of 7)	54186	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.002981	0.407738	
chunk0042_196_1	chr12	5347926	5348681	+	0	NA	Intergenic	Intergenic	-83811	NM_001102654	4908	Hs.99171	NM_002527	ENSG00000185652	NTF3	HDNF|NGF-2|NGF2|NT-3|NT3	neurotrophin 3	protein-coding	0.006623	0.419312	
chunk0082_58_1	chr17	51305282	51306118	+	0	NA	Intergenic	L1PA6|LINE|L1	29462	NR_110751	101927274	Hs.591168	NR_110751	ENSG00000249383	LINC02071	-	long intergenic non-protein coding RNA 2071	ncRNA	0.015550	0.502987	485(TTGTACAGCCTGTGCT,-,0.00),486(TGTACAGCCTGTGCTG,+,0.00)
chunk0206_331_1	chr9	125343625	125344020	+	0	NA	intron (NM_001282679, intron 19 of 27)	intron (NM_001282679, intron 19 of 27)	44932	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.005063	0.358586	
chunk0015_191_1	chr1	187306879	187307408	+	0	NA	intron (NR_126347, intron 2 of 3)	intron (NR_126347, intron 2 of 3)	-136485	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007561	0.420755	
chunk0207_260_1	chr9	132249154	132249353	+	0	NA	Intergenic	Intergenic	87306	NM_032536	84628	Hs.163642	NM_032536	ENSG00000196358	NTNG2	LHLL9381|Lmnt2|NTNG1|bA479K20.1	netrin G2	protein-coding	0.015075	0.660000	
chunk0156_58_1	chr5	103327722	103328256	+	0	NA	Intergenic	Intergenic	68632	NM_001316968	90355	Hs.482976	NM_033211	ENSG00000181751	C5orf30	-	chromosome 5 open reading frame 30	protein-coding	0.000000	0.424299	
chunk0190_148_1	chr8	30980769	30981498	+	0	NA	Intergenic	L1ME1|LINE|L1	51668	NM_013357	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.006859	0.327397	
chunk0136_442_1	chr3	197926564	197926890	+	0	NA	intron (NM_032263, intron 6 of 11)	LTR16B2|LTR|ERVL	23198	NM_001134435	84223	Hs.591675	NM_032263	ENSG00000114473	IQCG	CFAP122|DRC9	IQ motif containing G	protein-coding	0.018405	0.544343	
chunk0178_265_1	chr7	36663813	36664339	+	0	NA	intron (NM_001637, intron 3 of 20)	L1MCa|LINE|L1	60473	NM_001177507	313	Hs.488007	NM_001637	ENSG00000136250	AOAH	-	acyloxyacyl hydrolase	protein-coding	0.005703	0.292220	
chunk0092_118_1	chr19	27707075	27707300	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-86280	NR_110689	101927151	Hs.567934	NR_110687	ENSG00000267575	LOC101927151	-	uncharacterized LOC101927151	ncRNA	0.000000	0.415929	11(AGGGACATTGTGTCTT,-,0.00),12(GGGACATTGTGTCTTT,+,0.00)
chunk0132_159_1	chr3	156667884	156668548	+	0	NA	Intergenic	Intergenic	-6200	NM_015508	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.007530	0.413534	
chunk0112_367_1	chr20	45539962	45540161	+	0	NA	promoter-TSS (NM_080827)	promoter-TSS (NM_080827)	-566	NM_080827	140870	Hs.673237	NM_080827	ENSG00000243543	WFDC6	C20orf171|HEL-S-295|WAP6|dJ461P17.11	WAP four-disulfide core domain 6	protein-coding	0.020101	0.380000	
chunk0195_440_1	chr8	101201684	101202220	+	0	NA	intron (NM_001267709, intron 1 of 3)	L1ME3|LINE|L1	3780	NM_001042510	51123	Hs.374485	NM_016096	ENSG00000120963	ZNF706	HSPC038|PNAS-106|PNAS-113	zinc finger protein 706	protein-coding	0.014925	0.372439	335(ATGTACAAAATGTTCT,-,0.00),336(TGTACAAAATGTTCTG,+,0.00)
chunk0112_376_1	chr20	46088364	46088941	+	0	NA	intron (NM_020967, intron 1 of 7)	intron (NM_020967, intron 1 of 7)	1289	NM_020967	57727	Hs.654991	NM_020967	ENSG00000124160	NCOA5	CIA|bA465L10.6	nuclear receptor coactivator 5	protein-coding	0.012132	0.399654	
chunk0001_401_1	chr1	10791783	10792020	+	0	NA	intron (NM_001079843, intron 1 of 20)	intron (NM_001079843, intron 1 of 20)	4775	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.012658	0.378151	
chunk0003_413_1	chr1	40301894	40302405	+	0	NA	intron (NM_001852, intron 30 of 31)	MIR|SINE|MIR	15118	NM_001852	1298	Hs.418012	NM_001852	ENSG00000049089	COL9A2	DJ39G22.4|EDM2|MED|STL5	collagen type IX alpha 2 chain	protein-coding	0.011742	0.414062	
chunk0010_215_1	chr1	116189370	116189881	+	0	NA	Intergenic	L1MA3|LINE|L1	77870	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.005871	0.308594	
chunk0050_130_1	chr12	102232233	102232619	+	0	NA	Intergenic	Intergenic	-34581	NM_002674	5367	Hs.707990	NM_002674	ENSG00000183395	PMCH	MCH|ppMCH	pro-melanin concentrating hormone	protein-coding	0.002591	0.405685	
chunk0025_90_1	chr10	50511848	50512189	+	0	NA	intron (NM_147156, intron 3 of 10)	L2c|LINE|L2	111959	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.008798	0.415205	
chunk0112_245_1	chr20	41533573	41533912	+	0	NA	intron (NM_032221, intron 2 of 36)	L2b|LINE|L2	84752	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.005900	0.400000	
chunk0116_5_1	chr21	32701069	32701598	+	0	NA	intron (NM_001160302, intron 3 of 31)	Charlie10a|DNA|hAT-Charlie	26606	NM_001160302	8867	Hs.473632	NM_003895	ENSG00000159082	SYNJ1	EIEE53|INPP5G|PARK20	synaptojanin 1	protein-coding	0.009452	0.360377	395(AAGAACACTTTGAGCT,-,0.00),396(AGAACACTTTGAGCTG,+,0.00)
chunk0004_53_1	chr1	43039250	43039927	+	0	NA	Intergenic	Intergenic	-80412	NM_006516	6513	Hs.473721	NM_006516	ENSG00000117394	SLC2A1	CSE|DYT17|DYT18|DYT9|EIG12|GLUT|GLUT-1|GLUT1|GLUT1DS|HTLVR|PED|SDCHCN	solute carrier family 2 member 1	protein-coding	0.017725	0.464602	255(GTTACAGTCTGTCCTT,+,0.00)
chunk0135_224_1	chr3	188571355	188572034	+	0	NA	intron (NM_001167671, intron 5 of 10)	MIR|SINE|MIR	-3028	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.010309	0.376471	362(TGGAACACTCTGTATC,-,0.00),363(GGAACACTCTGTATCC,+,0.00)
chunk0041_13_1	chr12	389240	389483	+	0	NA	promoter-TSS (NM_001042603)	promoter-TSS (NM_001042603)	11	NM_001130148	84318	Hs.631656	NM_032358	ENSG00000120647	CCDC77	-	coiled-coil domain containing 77	protein-coding	0.053498	0.565574	
chunk0201_199_1	chr9	36755876	36756080	+	0	NA	Intergenic	MER53|DNA|hAT	67621	NR_039686	100616289		NR_039686	ENSG00000266255	MIR4475	-	microRNA 4475	ncRNA	0.009804	0.365854	
chunk0083_230_1	chr17	67415197	67415820	+	0	NA	intron (NM_181671, intron 1 of 9)	intron (NM_181671, intron 1 of 9)	38227	NM_181671	26207	Hs.591185	NM_012417	ENSG00000154217	PITPNC1	M-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1	phosphatidylinositol transfer protein cytoplasmic 1	protein-coding	0.012841	0.407051	282(CTGGACTGACTGTTCA,-,0.00),283(TGGACTGACTGTTCAG,+,0.00)
chunk0210_142_1	chrX	74696255	74696562	+	0	NA	Intergenic	L1PA6|LINE|L1	-81782	NM_016120	51132	Hs.653288	NM_016120	ENSG00000131263	RLIM	MRX61|NY-REN-43|RNF12|TOKAS	ring finger protein, LIM domain interacting	protein-coding	0.003257	0.503247	
chunk0048_407_1	chr12	88172828	88173464	+	0	NA	intron (NM_181783, intron 8 of 13)	intron (NM_181783, intron 8 of 13)	30850	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.000000	0.326531	
chunk0134_205_1	chr3	178478419	178479163	+	0	NA	Intergenic	Intergenic	-57507	NM_181361	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.002688	0.389262	199(TAGAGCATAGTGTACT,-,0.00),200(AGAGCATAGTGTACTT,+,0.00)
chunk0152_170_1	chr5	59583754	59584086	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	2578	NM_006203	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.012048	0.441441	
chunk0187_248_1	chr7	153127503	153127830	+	0	NA	Intergenic	Intergenic	284568	NR_125776	103724390	Hs.614280	NR_125776	ENSG00000234722	LINC01287	TCONS_l2_00027522	long intergenic non-protein coding RNA 1287	ncRNA	0.021407	0.481707	
chunk0160_89_1	chr5	150038673	150039153	+	0	NA	intron (NM_014983, intron 13 of 19)	L1ME1|LINE|L1	-37746	NM_030953	81789	Hs.169333	NM_030953	ENSG00000164296	TIGD6	-	tigger transposable element derived 6	protein-coding	0.006250	0.384615	
chunk0079_419_1	chr17	19753035	19753584	+	0	NA	Intergenic	Intergenic	-4876	NM_000691	218	Hs.531682	NM_000691	ENSG00000108602	ALDH3A1	ALDH3|ALDHIII	aldehyde dehydrogenase 3 family member A1	protein-coding	0.025501	0.530909	
chunk0044_31_1	chr12	27330848	27331200	+	0	NA	Intergenic	Intergenic	-1830	NM_001248004	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.002841	0.388102	
chunk0107_23_1	chr2	210233417	210234079	+	0	NA	Intergenic	LTR57|LTR|ERVL	-8257	NM_001608	33	Hs.471277	NM_001608	ENSG00000115361	ACADL	ACAD4|LCAD	acyl-CoA dehydrogenase long chain	protein-coding	0.004532	0.447964	330(AGGAACACCATGTGCT,-,0.00),331(GGAACACCATGTGCTG,+,0.00)
chunk0188_336_1	chr8	17728440	17728740	+	0	NA	intron (NM_001001924, intron 3 of 14)	intron (NM_001001924, intron 3 of 14)	-6015	NM_001166393	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.003333	0.392027	
chunk0118_393_1	chr22	37777131	37777555	+	0	NA	TTS (NM_007032)	TTS (NM_007032)	-27764	NM_005318	3005	Hs.745024	NM_005318	ENSG00000189060	H1F0	H10|H1FV	H1 histone family member 0	protein-coding	0.018868	0.494118	
chunk0127_194_1	chr3	96044748	96044947	+	0	NA	Intergenic	THE1C-int|LTR|ERVL-MaLR	-315117	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.535000	
chunk0084_64_1	chr17	74744653	74745271	+	0	NA	intron (NM_001006638, intron 7 of 8)	intron (NM_001006638, intron 7 of 8)	-3650	NM_004252	9368	Hs.724482	NM_004252	ENSG00000109062	SLC9A3R1	EBP50|NHERF|NHERF-1|NHERF1|NPHLOP2	SLC9A3 regulator 1	protein-coding	0.029126	0.628433	333(GAGGACACTCTCTCCC,-,0.00)
chunk0193_142_1	chr8	74534277	74534786	+	0	NA	Intergenic	Intergenic	-14012	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.003929	0.350980	
chunk0096_308_1	chr2	32990178	32990979	+	0	NA	intron (NM_206943, intron 2 of 33)	intron (NM_206943, intron 2 of 33)	43276	NM_206943	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.008739	0.372818	
chunk0135_210_1	chr3	188362473	188362929	+	0	NA	intron (NM_001167671, intron 2 of 10)	intron (NM_001167671, intron 2 of 10)	137296	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.019737	0.400438	
chunk0086_170_1	chr18	21798684	21799151	+	0	NA	intron (NM_020774, intron 8 of 20)	intron (NM_020774, intron 8 of 20)	26868	NR_029675	406922		NR_029675	ENSG00000283927	MIR133A1	MIRN133A1|mir-133a-1	microRNA 133a-1	ncRNA	0.002141	0.350427	
chunk0209_250_1	chrX	45906550	45907061	+	0	NA	Intergenic	Intergenic	-55315	NR_125365	401585	Hs.633348	NR_125365	ENSG00000231566	LINC02595	-	long intergenic non-protein coding RNA 2595	ncRNA	0.005871	0.410156	
chunk0032_7_1	chr11	429319	429552	+	0	NA	intron (NM_001012302, intron 11 of 22)	intron (NM_001012302, intron 11 of 22)	-12038	NM_021805	59307	Hs.501624	NM_021805	ENSG00000185187	SIGIRR	IL-1R8|TIR8	single Ig and TIR domain containing	protein-coding	0.068670	0.662393	
chunk0196_212_1	chr8	106755033	106755624	+	0	NA	Intergenic	L1M5|LINE|L1	14916	NM_139166	137735	Hs.374668	NM_139166	ENSG00000174429	ABRA	STARS	actin binding Rho activating protein	protein-coding	0.001692	0.354730	
chunk0073_6_1	chr16	1935297	1935787	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	7751	NM_016332	51734	Hs.655346	NM_016332	ENSG00000198736	MSRB1	HSPC270|SELR|SELX|SEPX1|SepR	methionine sulfoxide reductase B1	protein-coding	0.024490	0.531568	144(GGGAACACCATGATCC,-,0.00),145(GGAACACCATGATCCA,+,0.00)
chunk0098_85_1	chr2	67561387	67562177	+	0	NA	Intergenic	Intergenic	164472	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.013924	0.414665	351(GAGAACACTGTGTCAC,-,0.00),352(AGAACACTGTGTCACG,+,0.00)
chunk0117_226_1	chr22	22568435	22568974	+	0	NA	Intergenic	Intergenic	-9343	NM_206956	23532	Hs.30743	NM_006115	ENSG00000185686	PRAME	CT130|MAPE|OIP-4|OIP4	preferentially expressed antigen in melanoma	protein-coding	0.003711	0.388889	
chunk0035_349_1	chr11	48086530	48086761	+	0	NA	intron (NM_002843, intron 1 of 24)	intron (NM_002843, intron 1 of 24)	-10137	NR_036119	100423000		NR_036119	ENSG00000263693	MIR3161	-	microRNA 3161	ncRNA	0.012987	0.512931	
chunk0069_449_1	chr15	68691801	68692008	+	0	NA	intron (NM_001190456, intron 2 of 11)	intron (NM_001190456, intron 2 of 11)	59916	NM_001190457	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.019324	0.543269	
chunk0167_268_1	chr6	70222425	70222703	+	0	NA	intron (NM_001851, intron 37 of 37)	intron (NM_001851, intron 37 of 37)	60644	NM_078485	1297	Hs.590892	NM_001851	ENSG00000112280	COL9A1	DJ149L1.1.2|EDM6|MED|STL4	collagen type IX alpha 1 chain	protein-coding	0.007194	0.362007	
chunk0183_379_1	chr7	109584686	109584956	+	0	NA	Intergenic	L1PA16|LINE|L1	375392	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.003704	0.335793	
chunk0181_355_1	chr7	88391211	88391721	+	0	NA	Intergenic	Intergenic	-84553	NM_024636	79689	Hs.521008	NM_024636	ENSG00000127954	STEAP4	STAMP2|SchLAH|TIARP|TNFAIP9	STEAP4 metalloreductase	protein-coding	0.000000	0.358121	
chunk0131_106_1	chr3	143864276	143864776	+	0	NA	Intergenic	Intergenic	-15995	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.006000	0.371257	
chunk0146_184_1	chr4	160839981	160840180	+	0	NA	Intergenic	Intergenic	-1182653	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.000000	0.235000	
chunk0140_388_1	chr4	74972570	74972912	+	0	NA	intron (NM_015393, intron 1 of 3)	intron (NM_015393, intron 1 of 3)	-2379	NR_121617	100507388	Hs.570765	NR_121617	ENSG00000249717	LOC100507388	-	uncharacterized LOC100507388	ncRNA	0.008772	0.387755	
chunk0161_257_1	chr5	171997095	171997524	+	0	NA	intron (NM_012300, intron 1 of 12)	intron (NM_012300, intron 1 of 12)	9564	NM_033644	23291	Hs.484138	NM_012300	ENSG00000072803	FBXW11	BTRC2|BTRCP2|FBW1B|FBXW1B|Fbw11|Hos	F-box and WD repeat domain containing 11	protein-coding	0.009324	0.386047	
chunk0021_101_1	chr10	3015113	3015312	+	0	NA	Intergenic	Intergenic	-52308	NM_002627	5214	Hs.26010	NM_002627	ENSG00000067057	PFKP	ATP-PFK|PFK-C|PFK-P|PFKF	phosphofructokinase, platelet	protein-coding	0.040201	0.485000	
chunk0010_336_1	chr1	118432758	118433005	+	0	NA	Intergenic	Intergenic	-247656	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.000000	0.383065	
chunk0033_374_1	chr11	23494705	23495522	+	0	NA	Intergenic	L1MEf|LINE|L1	-75923	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.003672	0.328851	
chunk0132_278_1	chr3	159770598	159770990	+	0	NA	intron (NM_014575, intron 2 of 7)	intron (NM_014575, intron 2 of 7)	-2182	NR_121669	100874433	Hs.601476	NR_121669		IQCJ-SCHIP1-AS1	uaz98	IQCJ-SCHIP1 readthrough antisense RNA 1	ncRNA	0.005102	0.412214	
chunk0141_41_1	chr4	77104661	77105358	+	0	NA	Intergenic	Intergenic	-29037	NM_006835	10983	Hs.518827	NM_006835	ENSG00000118816	CCNI	CCNI1|CYC1|CYI	cyclin I	protein-coding	0.011478	0.452722	191(AAGGACACAGAGTTCT,-,0.00),192(AGGACACAGAGTTCTT,+,0.00)
chunk0208_323_1	chrX	24476645	24476904	+	0	NA	intron (NM_005391, intron 1 of 10)	MER58A|DNA|hAT-Charlie	11547	NM_005391	5165	Hs.296031	NM_005391	ENSG00000067992	PDK3	CMTX6|GS1-358P8.4	pyruvate dehydrogenase kinase 3	protein-coding	0.003861	0.388462	
chunk0212_432_1	chrX	153985025	153985224	+	0	NA	Intergenic	Intergenic	-3948	NR_036175	100422877		NR_036175	ENSG00000283694	MIR3202-2	mir-3202-2	microRNA 3202-2	ncRNA	0.020101	0.525000	
chunk0067_189_1	chr15	44712042	44712566	+	0	NA	intron (NM_004048, intron 1 of 3)	MIR|SINE|MIR	817	NM_004048	567	Hs.534255	NM_004048	ENSG00000166710	B2M	IMD43	beta-2-microglobulin	protein-coding	0.043893	0.459048	288(AAGGACTTTATGTGCT,-,0.00),289(AGGACTTTATGTGCTT,+,0.00)
chunk0014_332_1	chr1	182139269	182139532	+	0	NA	Intergenic	L2c|LINE|L2	-77688	NM_001009992	127665	Hs.684328	NM_001009992	ENSG00000179930	ZNF648	-	zinc finger protein 648	protein-coding	0.007605	0.401515	116(AGGAACAGTACGTGCA,-,0.00)
chunk0185_344_1	chr7	132158333	132158762	+	0	NA	intron (NM_020911, intron 25 of 31)	MIR|SINE|MIR	248327	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.006993	0.460465	
chunk0020_68_1	chr1	232634155	232634444	+	0	NA	Intergenic	Intergenic	108416	NR_110683	101927683	Hs.520568	NR_110683	ENSG00000236497	LINC01744	-	long intergenic non-protein coding RNA 1744	ncRNA	0.013841	0.537931	
chunk0146_55_1	chr4	155679380	155679738	+	0	NA	intron (NM_000856, intron 3 of 10)	MSTB1|LTR|ERVL-MaLR	11896	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.013966	0.484680	
chunk0150_410_1	chr5	40040727	40041152	+	0	NA	Intergenic	Intergenic	-11352	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.014118	0.455399	
chunk0103_133_1	chr2	162065727	162066101	+	0	NA	intron (NM_001935, intron 2 of 25)	L2c|LINE|L2	8628	NM_001935	1803	Hs.368912	NM_001935	ENSG00000197635	DPP4	ADABP|ADCP2|CD26|DPPIV|TP103	dipeptidyl peptidase 4	protein-coding	0.000000	0.408000	
chunk0183_79_1	chr7	104760424	104760624	+	0	NA	intron (NM_199000, intron 2 of 2)	intron (NM_199000, intron 2 of 2)	43568	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.005000	0.348259	
chunk0172_421_1	chr6	140413978	140414438	+	0	NA	Intergenic	(TGAATT)n|Simple_repeat|Simple_repeat	208956	NR_037441	100500879		NR_037441	ENSG00000263514	MIR3668	-	microRNA 3668	ncRNA	0.000000	0.366594	
chunk0033_232_1	chr11	17711865	17712168	+	0	NA	Intergenic	Intergenic	-7547	NM_002478	4654	Hs.181768	NM_002478	ENSG00000129152	MYOD1	MYF3|MYOD|PUM|bHLHc1	myogenic differentiation 1	protein-coding	0.009901	0.500000	88(GAGGACAAACTGTCCT,-,0.00),89(AGGACAAACTGTCCTT,+,0.00)
chunk0066_151_1	chr15	31504423	31504876	+	0	NA	intron (NM_130901, intron 6 of 10)	intron (NM_130901, intron 6 of 10)	150690	NM_130901	161725	Hs.355236	NM_130901	ENSG00000169918	OTUD7A	C15orf16|C16ORF15|CEZANNE2|OTUD7	OTU deubiquitinase 7A	protein-coding	0.017660	0.557269	
chunk0165_364_1	chr6	38169901	38170621	+	0	NA	3' UTR (NM_152733, exon 10 of 10)	3' UTR (NM_152733, exon 10 of 10)	350730	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.034722	0.595007	428(GTGAGCACGCTGTCCC,-,0.00),429(TGAGCACGCTGTCCCT,+,0.00)
chunk0014_274_1	chr1	180458680	180459466	+	0	NA	intron (NM_032360, intron 3 of 7)	intron (NM_032360, intron 3 of 7)	-20683	NR_036067	100423032		NR_036067	ENSG00000265435	MIR3121	mir-3121	microRNA 3121	ncRNA	0.003817	0.297332	
chunk0158_163_1	chr5	127652654	127653049	+	0	NA	promoter-TSS (NM_001127385)	promoter-TSS (NM_001127385)	-164	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.005063	0.446970	
chunk0057_39_1	chr13	96115155	96115407	+	0	NA	intron (NM_153456, intron 1 of 1)	L1PA8A|LINE|L1	24442	NM_153456	266722	Hs.171001	NM_153456	ENSG00000185352	HS6ST3	HS6ST-3	heparan sulfate 6-O-sulfotransferase 3	protein-coding	0.011905	0.387352	
chunk0126_207_1	chr3	78728681	78729040	+	0	NA	intron (NM_133631, intron 3 of 28)	intron (NM_133631, intron 3 of 28)	290599	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.008357	0.394444	
chunk0034_363_1	chr11	36051924	36052514	+	0	NA	intron (NM_174902, intron 2 of 5)	intron (NM_174902, intron 2 of 5)	42121	NR_039769	100616311		NR_039769	ENSG00000263389	MIR3973	-	microRNA 3973	ncRNA	0.003390	0.414552	308(TTGAACAGGGAGTGCT,-,0.00),309(TGAACAGGGAGTGCTA,+,0.00)
chunk0158_406_1	chr5	134744585	134745096	+	0	NA	intron (NM_001745, intron 3 of 3)	intron (NM_001745, intron 3 of 3)	6360	NM_001745	819	Hs.529846	NM_001745	ENSG00000164615	CAMLG	CAML|GET2	calcium modulating ligand	protein-coding	0.005871	0.320312	
chunk0166_460_1	chr6	53309115	53309396	+	0	NA	intron (NM_001242828, intron 1 of 8)	L2b|LINE|L2	28362	NR_046241	647190	Hs.520189	NR_046241		RPS16P5	RPS16_3_702	ribosomal protein S16 pseudogene 5	pseudo	0.003559	0.453901	
chunk0042_160_1	chr12	4057002	4057639	+	0	NA	Intergenic	Intergenic	-183872	NM_001286521	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.004710	0.463950	
chunk0043_221_1	chr12	19912939	19913387	+	0	NA	Intergenic	L2b|LINE|L2	-101522	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.011161	0.449889	
chunk0175_101_1	chr7	2847193	2847458	+	0	NA	Intergenic	AluJr|SINE|Alu	-3000	NM_007353	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.000000	0.387218	
chunk0207_296_1	chr9	133264256	133264726	+	0	NA	intron (NM_020469, intron 1 of 6)	L1ME2|LINE|L1	10723	NM_020469	28	Hs.654423	NM_020469	ENSG00000175164	ABO	A3GALNT|A3GALT1|GTB|NAGAT	ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase	protein-coding	0.017021	0.409766	
chunk0169_179_1	chr6	102297912	102298423	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	899182	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.320312	
chunk0115_456_1	chr21	32628589	32629325	+	0	NA	3' UTR (NM_203446, exon 33 of 33)	3' UTR (NM_203446, exon 33 of 33)	-16349	NM_021254	56683	Hs.5811	NM_017835	ENSG00000159079	CFAP298	C21orf48|C21orf59|CILD26|FBB18|Kur	cilia and flagella associated protein 298	protein-coding	0.004076	0.318860	341(GAGAACACAGAGTTCA,-,0.00),342(AGAACACAGAGTTCAC,+,0.00)
chunk0049_1_1	chr12	89158459	89158998	+	0	NA	Intergenic	Tigger18a|DNA|TcMar-Tigger	-139036	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.003711	0.405556	
chunk0077_278_1	chr16	81076754	81076988	+	0	NA	intron (NM_152337, intron 1 of 3)	intron (NM_152337, intron 1 of 3)	396	NM_152337	123775	Hs.658684	NM_152337	ENSG00000166455	C16orf46	-	chromosome 16 open reading frame 46	protein-coding	0.051282	0.570213	
chunk0147_99_1	chr4	173425237	173425467	+	0	NA	Intergenic	Intergenic	-25886	NM_007281	11341	Hs.7122	NM_007281	ENSG00000164106	SCRG1	SCRG-1	stimulator of chondrogenesis 1	protein-coding	0.004348	0.372294	
chunk0121_374_1	chr3	25047395	25047752	+	0	NA	Intergenic	Intergenic	-126759	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.002801	0.365922	
chunk0004_408_1	chr1	52306978	52307214	+	0	NA	intron (NM_007324, intron 12 of 17)	intron (NM_007324, intron 12 of 17)	59109	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.012712	0.472574	
chunk0018_55_1	chr1	216528590	216529274	+	0	NA	intron (NM_206595, intron 6 of 7)	intron (NM_206595, intron 6 of 7)	-105536	NM_007123	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.002924	0.375182	
chunk0063_319_1	chr14	85159707	85160199	+	0	NA	Intergenic	Intergenic	-233926	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.290061	
chunk0050_451_1	chr12	110681323	110681705	+	0	NA	intron (NM_001256413, intron 2 of 6)	L1ME4c|LINE|L1	7643	NM_032369	84329	Hs.211511	NM_032369	ENSG00000122986	HVCN1	HV1|VSOP	hydrogen voltage gated channel 1	protein-coding	0.007853	0.412533	
chunk0202_308_1	chr9	78035016	78035414	+	0	NA	Intergenic	Intergenic	-3766	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.005025	0.416040	
chunk0184_298_1	chr7	119888274	119888566	+	0	NA	intron (NR_131960, intron 1 of 4)	intron (NR_131960, intron 1 of 4)	18955	NR_131960	105375475	Hs.566654	NR_131960	ENSG00000225546	LINC02476	LVCAT5	long intergenic non-protein coding RNA 2476	ncRNA	0.003425	0.406143	
chunk0200_242_1	chr9	20833843	20834458	+	0	NA	intron (NM_017794, intron 17 of 45)	L1PA11|LINE|L1	118045	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.011382	0.391234	
chunk0107_85_1	chr2	212940098	212940490	+	0	NA	Intergenic	Intergenic	-13958	NR_039936	100616472		NR_039936	ENSG00000283637	MIR4776-2	mir-4776-2	microRNA 4776-2	ncRNA	0.010204	0.399491	
chunk0044_125_1	chr12	29260334	29260630	+	0	NA	intron (NM_001271784, intron 1 of 10)	intron (NM_001271784, intron 1 of 10)	36859	NM_018099	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.000000	0.457912	122(AAGCACTCAGTGTACT,-,0.00),123(AGCACTCAGTGTACTC,+,0.00)
chunk0035_6_1	chr11	39845056	39845610	+	0	NA	Intergenic	Intergenic	447797	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001805	0.317117	
chunk0104_56_1	chr2	171417361	171417672	+	0	NA	intron (NM_024770, intron 1 of 9)	MIR|SINE|MIR	-16735	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.003215	0.365385	
chunk0163_322_1	chr6	14841933	14842310	+	0	NA	Intergenic	L1ME5|LINE|L1	-403854	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.021220	0.428571	
chunk0055_50_1	chr13	52392919	52393524	+	0	NA	intron (NM_018676, intron 3 of 4)	MIR|SINE|MIR	13273	NM_018676	55901	Hs.325667	NM_018676	ENSG00000136114	THSD1	TMTSP|UNQ3010	thrombospondin type 1 domain containing 1	protein-coding	0.004959	0.348185	
chunk0176_140_1	chr7	12756635	12756938	+	0	NA	Intergenic	Intergenic	69500	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.009901	0.404605	
chunk0102_145_1	chr2	146687192	146687649	+	0	NA	Intergenic	Intergenic	100363	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.010941	0.318777	225(CAGCACAACATGTACT,-,0.00),226(AGCACAACATGTACTT,+,0.00)
chunk0044_283_1	chr12	32680047	32680898	+	0	NA	intron (NM_001278464, intron 1 of 20)	intron (NM_001278464, intron 1 of 20)	1272	NM_012062	10059	Hs.556296	NM_005690	ENSG00000087470	DNM1L	DLP1|DRP1|DVLP|DYMPLE|EMPF|EMPF1|HDYNIV|OPA5	dynamin 1 like	protein-coding	0.014101	0.334507	402(AGGAACTTACTGTTCA,-,0.00),403(GGAACTTACTGTTCAA,+,0.00)
chunk0094_15_1	chr2	1058925	1059139	+	0	NA	intron (NM_018968, intron 1 of 16)	intron (NM_018968, intron 1 of 16)	108164	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.009346	0.516279	
chunk0071_256_1	chr15	85484948	85485251	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	104483	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.000000	0.388158	
chunk0016_443_1	chr1	204084241	204084741	+	0	NA	intron (NM_005686, intron 1 of 13)	intron (NM_005686, intron 1 of 13)	11373	NM_005686	9580	Hs.201671	NM_005686	ENSG00000143842	SOX13	ICA12|Sox-13	SRY-box transcription factor 13	protein-coding	0.008000	0.622754	
chunk0124_144_1	chr3	54645624	54645838	+	0	NA	intron (NM_018398, intron 11 of 37)	intron (NM_018398, intron 11 of 37)	-5874	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.009346	0.474419	4(AGGTACTTGCTGTTCC,-,0.00),5(GGTACTTGCTGTTCCC,+,0.00)
chunk0037_421_1	chr11	80021474	80021812	+	0	NA	Intergenic	Intergenic	-580992	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.002959	0.327434	
chunk0126_98_1	chr3	74890125	74890841	+	0	NA	Intergenic	Intergenic	-323993	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.000000	0.312413	275(AAGGACACACTGTTCA,-,0.00),276(AGGACACACTGTTCAT,+,0.00)
chunk0151_44_1	chr5	42215811	42216139	+	0	NA	Intergenic	L1MA1|LINE|L1	-40630	NR_104636	101926960	Hs.365692	NR_104635		LOC101926960	-	uncharacterized LOC101926960	ncRNA	0.000000	0.492401	
chunk0185_401_1	chr7	133888267	133888620	+	0	NA	intron (NM_021807, intron 11 of 17)	intron (NM_021807, intron 11 of 17)	-63555	NR_120513	101928861	Hs.675747	NR_120513		LOC101928861	-	uncharacterized LOC101928861	ncRNA	0.008499	0.327684	
chunk0030_189_1	chr10	114245156	114245496	+	0	NA	intron (NM_001272046, intron 1 of 13)	MIRb|SINE|MIR	6072	NM_001272046	340706	Hs.197741	NM_198496	ENSG00000165816	VWA2	AMACO|CCSP-2|CCSP2|NET42	von Willebrand factor A domain containing 2	protein-coding	0.014706	0.492669	
chunk0139_114_1	chr4	52602148	52602460	+	0	NA	intron (NM_022832, intron 6 of 8)	intron (NM_022832, intron 6 of 8)	54288	NM_001134223	64854	Hs.7966	NM_022832	ENSG00000109189	USP46	-	ubiquitin specific peptidase 46	protein-coding	0.003205	0.431310	
chunk0140_440_1	chr4	76208394	76208794	+	0	NA	intron (NM_005506, intron 1 of 11)	intron (NM_005506, intron 1 of 11)	5305	NM_005506	950	Hs.349656	NM_005506	ENSG00000138760	SCARB2	AMRF|CD36L2|EPM4|HLGP85|LGP85|LIMP-2|LIMPII|SR-BII	scavenger receptor class B member 2	protein-coding	0.015000	0.483791	
chunk0163_240_1	chr6	12337742	12338285	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	47717	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.029466	0.439338	231(CAACACAGAATGTACC,-,0.00),232(AACACAGAATGTACCT,+,0.00)
chunk0078_235_1	chr17	6683062	6683716	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	25670	NR_045985	100652883	Hs.549540	NR_045985		ALOX15P1	ALOX15P	arachidonate 15-lipoxygenase pseudogene 1	pseudo	0.004587	0.479389	
chunk0166_110_1	chr6	44156308	44156782	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-2266	NM_007058	11131	Hs.225953	NM_007058	ENSG00000137225	CAPN11	calpain11	calpain 11	protein-coding	0.008439	0.541053	
chunk0180_55_1	chr7	54795936	54796508	+	0	NA	intron (NR_110040, intron 2 of 2)	LTR91|LTR|ERVL	36909	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.012238	0.380454	
chunk0145_148_1	chr4	147050600	147050804	+	0	NA	Intergenic	Intergenic	-104820	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.004902	0.414634	
chunk0189_122_1	chr8	22171178	22171878	+	0	NA	intron (NR_033403, intron 1 of 19)	intron (NR_033403, intron 1 of 19)	6388	NR_033404	649	Hs.1274	NM_001199	ENSG00000168487	BMP1	OI13|PCOLC|PCP|PCP2|TLD	bone morphogenetic protein 1	protein-coding	0.010000	0.446505	
chunk0130_268_1	chr3	136255370	136255592	+	0	NA	intron (NM_000532, intron 1 of 14)	intron (NM_000532, intron 1 of 14)	5156	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.009009	0.484305	
chunk0180_184_1	chr7	65946968	65947317	+	0	NA	intron (NM_001284342, intron 1 of 1)	AluJb|SINE|Alu	35172	NM_001293104	2990	Hs.255230	NM_000181	ENSG00000169919	GUSB	BG|MPS7	glucuronidase beta	protein-coding	0.011461	0.385714	152(AGGAACATCCTGTCTC,-,0.00),153(GGAACATCCTGTCTCA,+,0.00)
chunk0204_375_1	chr9	102064206	102064423	+	0	NA	Intergenic	L1PA6|LINE|L1	-325734	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.000000	0.371560	161(GGTACATTGTGTCTTT,+,0.00)
chunk0039_29_1	chr11	95732425	95732720	+	0	NA	Intergenic	L1ME3|LINE|L1	57218	NM_144664	143684	Hs.288304	NM_144664	ENSG00000077458	FAM76B	-	family with sequence similarity 76 member B	protein-coding	0.010169	0.368243	81(ATGAACATAGTGTACA,-,0.00)
chunk0205_58_1	chr9	106585987	106586234	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-14818	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.000000	0.334677	
chunk0129_373_1	chr3	125622404	125622738	+	0	NA	Intergenic	Tigger16b|DNA|TcMar-Tigger	-27034	NM_022776	114885	Hs.477440	NM_022776	ENSG00000144909	OSBPL11	ORP-11|ORP11|OSBP12|TCCCIA00292	oxysterol binding protein like 11	protein-coding	0.014970	0.537313	165(GGGTACTTTGTGTTCC,-,0.00),166(GGTACTTTGTGTTCCA,+,0.00)
chunk0112_299_1	chr20	44204083	44204434	+	0	NA	intron (NM_016470, intron 2 of 3)	intron (NM_016470, intron 2 of 3)	6648	NM_016470	51526	Hs.75798	NM_016470	ENSG00000132823	OSER1	C20orf111|HSPC207|Osr1|Perit1|dJ1183I21.1	oxidative stress responsive serine rich 1	protein-coding	0.002849	0.309659	
chunk0151_227_1	chr5	50943517	50943716	+	0	NA	Intergenic	L1PB2|LINE|L1	26571	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.005025	0.355000	0(AAGACACCCTGTTCAA,+,0.00)
chunk0079_169_1	chr17	13771625	13772493	+	0	NA	Intergenic	Intergenic	-170117	NM_006042	9955	Hs.462270	NM_006042	ENSG00000153976	HS3ST3A1	3-OST-3A|3OST3A1	heparan sulfate-glucosamine 3-sulfotransferase 3A1	protein-coding	0.003456	0.376295	
chunk0201_145_1	chr9	35833799	35834035	+	0	NA	intron (NM_001042589, intron 2 of 13)	intron (NM_001042589, intron 2 of 13)	4419	NM_001042590	51754	Hs.9187	NM_016446	ENSG00000137103	TMEM8B	C9orf127|FP588|LINC00950|NAG-5|NAG5|NGX6	transmembrane protein 8B	protein-coding	0.012712	0.556962	
chunk0046_393_1	chr12	63875085	63875555	+	0	NA	intron (NM_020762, intron 1 of 21)	intron (NM_020762, intron 1 of 21)	30559	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.004255	0.354565	
chunk0101_229_1	chr2	131120676	131121358	+	0	NA	intron (NM_001100623, intron 2 of 7)	intron (NM_001100623, intron 2 of 7)	16170	NM_001267067	55041	Hs.469944	NM_017958	ENSG00000115762	PLEKHB2	EVT2	pleckstrin homology domain containing B2	protein-coding	0.026393	0.491947	
chunk0125_256_1	chr3	69122791	69123381	+	0	NA	promoter-TSS (NM_001304418)	promoter-TSS (NM_001304418)	-491	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.001695	0.372250	
chunk0153_284_1	chr5	73193697	73194003	+	0	NA	Intergenic	Intergenic	20654	NM_153217	134288	Hs.508588	NM_153217	ENSG00000164325	TMEM174	-	transmembrane protein 174	protein-coding	0.013072	0.439739	101(AGACCAACATGTTCCT,+,0.00)
chunk0052_388_1	chr12	130030881	130031123	+	0	NA	Intergenic	MER50|LTR|ERV1	11340	NR_024457	100190940	Hs.625993	NR_024457	ENSG00000214039	LINC02418	-	long intergenic non-protein coding RNA 2418	ncRNA	0.008264	0.481481	
chunk0177_7_1	chr7	20351709	20352354	+	0	NA	intron (NM_002214, intron 1 of 13)	intron (NM_002214, intron 1 of 13)	-20269	NR_110120	101927811	Hs.285724	NR_110119	ENSG00000271133	LOC101927811	-	uncharacterized LOC101927811	ncRNA	0.003101	0.377709	
chunk0138_14_1	chr4	30406850	30407428	+	0	NA	Intergenic	L1M2|LINE|L1	-313269	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.005190	0.538860	
chunk0040_170_1	chr11	113992280	113992690	+	0	NA	Intergenic	Intergenic	14985	NM_001161772	3359	Hs.413899	NM_000869	ENSG00000166736	HTR3A	5-HT-3|5-HT3A|5-HT3R|5HT3R|HTR3	5-hydroxytryptamine receptor 3A	protein-coding	0.009756	0.506083	101(AAGTACACTCAGTTCT,-,0.00),102(AGTACACTCAGTTCTC,+,0.00)
chunk0154_91_1	chr5	78050698	78051378	+	0	NA	intron (NM_003664, intron 22 of 26)	intron (NM_003664, intron 22 of 26)	92791	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.008824	0.312775	
chunk0023_463_1	chr10	32477529	32477908	+	0	NA	intron (NR_109826, intron 9 of 16)	L1MC2|LINE|L1	31636	NR_109826	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.002639	0.339474	
chunk0018_184_1	chr1	219232663	219232911	+	0	NA	Intergenic	L1MB2|LINE|L1	57818	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.004032	0.321285	
chunk0027_383_1	chr10	79605006	79605265	+	0	NA	Intergenic	MER52-int|LTR|ERV1	-5804	NM_001164647	653509	Hs.535295	NM_005411	ENSG00000122852	SFTPA1	COLEC4|PSAP|PSP-A|PSPA|SFTP1|SFTPA1B|SP-A|SP-A1|SPA|SPA1	surfactant protein A1	protein-coding	0.000000	0.426923	184(GAGAACAATCTGAGCC,-,0.00)
chunk0051_17_1	chr12	111758084	111758586	+	0	NA	Intergenic	Intergenic	-8552	NM_001204889	217	Hs.604551	NM_000690	ENSG00000111275	ALDH2	ALDH-E2|ALDHI|ALDM	aldehyde dehydrogenase 2 family member	protein-coding	0.019920	0.592445	
chunk0120_135_1	chr3	4992584	4992841	+	0	NA	Intergenic	Intergenic	-12751	NR_037903	100507582	Hs.434505	NR_037903	ENSG00000235831	BHLHE40-AS1	-	BHLHE40 antisense RNA 1	ncRNA	0.007782	0.445736	
chunk0131_113_1	chr3	144031890	144032299	+	0	NA	Intergenic	Intergenic	58769	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.009780	0.431707	
chunk0133_101_1	chr3	167915054	167915527	+	0	NA	intron (NR_033843, intron 5 of 7)	intron (NR_033843, intron 5 of 7)	19342	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.004228	0.354430	
chunk0197_410_1	chr8	127243549	127244202	+	0	NA	promoter-TSS (NR_117099)	promoter-TSS (NR_117099)	-762	NR_117099	103021164	Hs.571531	NR_117099		CASC21	CARLO2|CARLo-2|LINC01244	cancer susceptibility 21	ncRNA	0.004594	0.360856	
chunk0155_112_1	chr5	92937261	92937501	+	0	NA	Intergenic	Intergenic	633962	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.265560	
chunk0005_127_1	chr1	57006195	57006394	+	0	NA	intron (NM_021080, intron 16 of 16)	L2|LINE|L2	-40154	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.000000	0.465000	
chunk0023_165_1	chr10	24349322	24349678	+	0	NA	intron (NM_019590, intron 2 of 20)	MIRb|SINE|MIR	73815	NR_030334	693188		NR_030334	ENSG00000207930	MIR603	MIRN603|hsa-mir-603	microRNA 603	ncRNA	0.000000	0.453782	230(TAGGACAGCCTGTTTC,-,0.00),231(AGGACAGCCTGTTTCC,+,0.00)
chunk0078_95_1	chr17	2090652	2091143	+	0	NA	intron (NM_001256827, intron 6 of 11)	intron (NM_001256827, intron 6 of 11)	-2136	NM_001282326	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.002037	0.388211	
chunk0014_338_1	chr1	182203066	182203861	+	0	NA	TTS (NR_104175)	TTS (NR_104175)	110598	NR_104175	400799	Hs.634884	NR_104175	ENSG00000228918	LINC01344	GS1-122H1.2	long intergenic non-protein coding RNA 1344	ncRNA	0.003774	0.316583	
chunk0207_184_1	chr9	130732815	130733472	+	0	NA	intron (NM_007313, intron 1 of 10)	intron (NM_007313, intron 1 of 10)	19262	NM_007313	25	Hs.431048	NM_005157	ENSG00000097007	ABL1	ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-abl	ABL proto-oncogene 1, non-receptor tyrosine kinase	protein-coding	0.006088	0.370821	
chunk0131_415_1	chr3	152969756	152970395	+	0	NA	Intergenic	L2a|LINE|L2	135382	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.000000	0.346875	
chunk0144_386_1	chr4	140116419	140116708	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	37516	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.013841	0.475862	
chunk0055_129_1	chr13	57720917	57721294	+	0	NA	intron (NM_001040429, intron 3 of 3)	intron (NM_001040429, intron 3 of 3)	89450	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.000000	0.328042	
chunk0171_353_1	chr6	130307926	130308202	+	0	NA	intron (NM_001258275, intron 2 of 13)	intron (NM_001258275, intron 2 of 13)	57361	NM_001258275	154075	Hs.440508	NM_152552	ENSG00000164483	SAMD3	-	sterile alpha motif domain containing 3	protein-coding	0.000000	0.371841	
chunk0212_438_1	chrX	154512343	154512818	+	0	NA	intron (NM_001282311, intron 2 of 9)	intron (NM_001282311, intron 2 of 9)	3662	NM_001282312	60343	Hs.289108	NM_021806	ENSG00000071889	FAM3A	2.19|DLD|DXS560S|XAP-7	family with sequence similarity 3 member A	protein-coding	0.010526	0.548319	
chunk0204_307_1	chr9	100208579	100209128	+	0	NA	intron (NM_014425, intron 3 of 16)	intron (NM_014425, intron 3 of 16)	109633	NM_014425	27130	Hs.558477	NM_014425	ENSG00000119509	INVS	INV|NPH2|NPHP2	inversin	protein-coding	0.005464	0.372727	344(GAGTACTCGCTGTGCA,-,0.00),345(AGTACTCGCTGTGCAC,+,0.00)
chunk0186_254_1	chr7	141072426	141072706	+	0	NA	Intergenic	CpG	-1666	NM_001195278	100507421	Hs.283851	NM_001195278	ENSG00000261115	TMEM178B	-	transmembrane protein 178B	protein-coding	0.064286	0.540925	
chunk0002_407_1	chr1	27444518	27444881	+	0	NA	intron (NM_001201404, intron 1 of 7)	LFSINE_Vert|SINE|tRNA	45488	NM_006990	10163	Hs.469244	NM_006990	ENSG00000158195	WASF2	IMD2|SCAR2|WASF4|WAVE2|dJ393P12.2	WASP family member 2	protein-coding	0.000000	0.365385	
chunk0188_62_1	chr8	7768098	7768471	+	0	NA	Intergenic	Intergenic	-1300	NR_046351	441328	Hs.694406	NM_001164447		FAM90A10P	FAM90A10	putative protein FAM90A10	pseudo	0.032172	0.435829	
chunk0002_173_1	chr1	18944827	18945295	+	0	NA	intron (NM_001136265, intron 1 of 8)	L2c|LINE|L2	11271	NM_001136265	126917	Hs.466625	NM_001136265	ENSG00000169991	IFFO2	-	intermediate filament family orphan 2	protein-coding	0.008547	0.533049	233(TTGTACACGCTGTCCT,-,0.00),234(TGTACACGCTGTCCTC,+,0.00)
chunk0186_409_1	chr7	145566189	145566944	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-549795	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.001325	0.359788	
chunk0052_409_1	chr12	131035161	131035482	+	0	NA	intron (NM_198827, intron 13 of 24)	intron (NM_198827, intron 13 of 24)	-41345	NR_131951	105755954	Hs.677534	NR_131950		ADGRD1-AS1	LACAT8	ADGRD1 antisense RNA 1	ncRNA	0.049844	0.639752	
chunk0019_117_1	chr1	225397245	225397588	+	0	NA	intron (NM_001373, intron 82 of 83)	intron (NM_001373, intron 82 of 83)	30697	NM_002296	3930	Hs.435166	NM_002296	ENSG00000143815	LBR	C14SR|DHCR14B|LMN2R|PHA|PHASK|TDRD18	lamin B receptor	protein-coding	0.011662	0.572674	142(CAGCACAGGCTGTTCC,-,0.00),143(AGCACAGGCTGTTCCA,+,0.00)
chunk0153_358_1	chr5	74489159	74489733	+	0	NA	intron (NR_126354, intron 1 of 2)	Tigger3a|DNA|TcMar-Tigger	47530	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.001742	0.398261	171(TGGAACAAACAGTGCT,-,0.00),172(GGAACAAACAGTGCTC,+,0.00)
chunk0192_432_1	chr8	69663822	69664238	+	0	NA	Intergenic	Intergenic	71130	NR_132437	23213	Hs.409602	NM_015170	ENSG00000137573	SULF1	SULF-1	sulfatase 1	protein-coding	0.019231	0.434053	232(TAGAACAGCTTGATCC,-,0.00),233(AGAACAGCTTGATCCT,+,0.00)
chunk0052_254_1	chr12	123601533	123601746	+	0	NA	promoter-TSS (NM_020936)	promoter-TSS (NM_020936)	-486	NM_020936	57696	Hs.286173	NM_020936	ENSG00000111364	DDX55	-	DEAD-box helicase 55	protein-coding	0.037559	0.509346	
chunk0056_297_1	chr13	90659070	90659322	+	0	NA	Intergenic	L1PA12|LINE|L1	165908	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.011905	0.513834	
chunk0033_238_1	chr11	17934030	17934577	+	0	NA	intron (NR_104040, intron 9 of 11)	intron (NR_104040, intron 9 of 11)	78859	NR_104041	26297	Hs.32470	NM_012139	ENSG00000129158	SERGEF	DELGEF|Gnefr	secretion regulating guanine nucleotide exchange factor	protein-coding	0.001828	0.326642	
chunk0132_334_1	chr3	161224758	161225332	+	0	NA	exon (NM_015938, exon 3 of 16)	exon (NM_015938, exon 3 of 16)	3734	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.015679	0.349565	
chunk0090_39_1	chr19	1407195	1407412	+	0	NA	promoter-TSS (NM_170711)	promoter-TSS (NM_170711)	-266	NM_170711	26528	Hs.222510	NM_018959	ENSG00000071626	DAZAP1	-	DAZ associated protein 1	protein-coding	0.156682	0.733945	
chunk0026_317_1	chr10	68083709	68084570	+	0	NA	Intergenic	Intergenic	-8793	NM_001278187	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.002323	0.321346	390(AAGGACAGAGTGTTCC,-,0.00),391(AGGACAGAGTGTTCCT,+,0.00)
chunk0092_99_1	chr19	23131284	23131754	+	0	NA	intron (NM_001277403, intron 1 of 3)	intron (NM_001277403, intron 1 of 3)	14544	NM_001277403	100129543	Hs.427120	NM_001277403	ENSG00000183850	ZNF730	-	zinc finger protein 730	protein-coding	0.002128	0.335456	
chunk0179_428_1	chr7	51995749	51996380	+	0	NA	Intergenic	L1PA16|LINE|L1	-679246	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.006339	0.563291	290(AAGCACTGGCTGTACT,-,0.00),291(AGCACTGGCTGTACTG,+,0.00),300(TGTACTGGCTGTACTG,+,0.00),323(AGGGACAAAGTGTTCT,-,0.00),324(GGGACAAAGTGTTCTC,+,0.00)
chunk0196_218_1	chr8	107338650	107339224	+	0	NA	intron (NM_001146, intron 2 of 8)	intron (NM_001146, intron 2 of 8)	-2422	NM_001314051	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.003484	0.342609	
chunk0008_160_1	chr1	92718126	92718475	+	0	NA	intron (NM_001308248, intron 2 of 18)	L1PA6|LINE|L1	74104	NM_005665	7813	Hs.594434	NM_005665	ENSG00000067208	EVI5	EVI-5|NB4S	ecotropic viral integration site 5	protein-coding	0.014327	0.388571	
chunk0029_267_1	chr10	103187460	103188141	+	0	NA	intron (NM_012229, intron 1 of 18)	intron (NM_012229, intron 1 of 18)	5506	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.010279	0.346041	
chunk0193_148_1	chr8	74569487	74570098	+	0	NA	Intergenic	LTR24C|LTR|ERV1	-21183	NR_049871	100847091		NR_049871	ENSG00000283505	MIR5681B	-	microRNA 5681b	ncRNA	0.001637	0.392157	
chunk0069_400_1	chr15	67885773	67886306	+	0	NA	Intergenic	Intergenic	-45994	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.001876	0.346442	
chunk0108_451_1	chr2	238286523	238286884	+	0	NA	intron (NM_022817, intron 1 of 22)	intron (NM_022817, intron 1 of 22)	1863	NM_022817	8864	Hs.58756	NM_003894	ENSG00000132326	PER2	FASPS|FASPS1	period circadian regulator 2	protein-coding	0.016620	0.494475	
chunk0035_300_1	chr11	47012144	47012873	+	0	NA	intron (NR_103472, intron 2 of 7)	intron (NR_103472, intron 2 of 7)	75819	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.004115	0.397260	
chunk0029_276_1	chr10	103502604	103502824	+	0	NA	intron (NR_120675, intron 2 of 3)	intron (NR_120675, intron 2 of 3)	8736	NM_004210	9148	Hs.594708	NM_004210	ENSG00000107954	NEURL1	NEUR1|NEURL|RNF67|bA416N2.1|neu|neu-1	neuralized E3 ubiquitin protein ligase 1	protein-coding	0.013636	0.529412	
chunk0179_354_1	chr7	50885839	50886711	+	0	NA	Intergenic	L1MC4a|LINE|L1	-92813	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.000000	0.325315	677(GAGCACACCTAGTGCC,-,0.00)
chunk0144_20_1	chr4	124879185	124879697	+	0	NA	Intergenic	Intergenic	-166709	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.005859	0.346979	
chunk0146_296_1	chr4	164872464	164872849	+	0	NA	Intergenic	L2b|LINE|L2	-4332	NM_001297550	100506013	Hs.105196	NM_001297550	ENSG00000248329	APELA	ELA|Ende|tdl	apelin receptor early endogenous ligand	protein-coding	0.007792	0.352332	
chunk0118_230_1	chr22	32337963	32338453	+	0	NA	Intergenic	Intergenic	-16677	NM_006604	10738	Hs.558455	NM_006604	ENSG00000128276	RFPL3	RNF120	ret finger protein like 3	protein-coding	0.016327	0.413442	
chunk0082_339_1	chr17	59829634	59829928	+	0	NA	intron (NM_030938, intron 10 of 11)	intron (NM_030938, intron 10 of 11)	-11485	NR_029493	406991	Hs.444569	NR_029493	ENSG00000284190	MIR21	MIRN21|hsa-mir-21|miR-21|miRNA21	microRNA 21	ncRNA	0.006803	0.393220	
chunk0178_70_1	chr7	30275224	30275676	+	0	NA	Intergenic	Intergenic	-8857	NM_147128	223082	Hs.263912	NM_147128	ENSG00000180233	ZNRF2	RNF202	zinc and ring finger 2	protein-coding	0.008850	0.331126	
chunk0111_438_1	chr20	35263644	35263843	+	0	NA	intron (NM_006690, intron 4 of 8)	intron (NM_006690, intron 4 of 8)	14414	NR_102706									0.035176	0.615000	
chunk0212_361_1	chrX	149399374	149399762	+	0	NA	Intergenic	L1MB7|LINE|L1	105786	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.000000	0.293059	
chunk0114_150_1	chr21	10417743	10417987	+	0	NA	intron (NM_181704, intron 2 of 8)	intron (NM_181704, intron 2 of 8)	4333	NM_182484	85316	Hs.545789	NM_182484		BAGE5	CT2.5	BAGE family member 5	protein-coding	0.016393	0.481633	
chunk0037_281_1	chr11	75831940	75832286	+	0	NA	intron (NM_003369, intron 1 of 14)	intron (NM_003369, intron 1 of 14)	16946	NM_003369	7405	Hs.202470	NM_003369	ENSG00000198382	UVRAG	DHTX|VPS38|p63	UV radiation resistance associated	protein-coding	0.008671	0.412104	157(AGGGACTGTCTGTACC,-,0.00),158(GGGACTGTCTGTACCT,+,0.00),173(TAGGACAGTCTGTGCT,-,0.00),174(AGGACAGTCTGTGCTG,+,0.00)
chunk0080_230_1	chr17	29906532	29906731	+	0	NA	intron (NM_001282129, intron 1 of 15)	L1PA11|LINE|L1	-23225	NM_001145053	374786	Hs.662411	NM_198529	ENSG00000176927	EFCAB5	-	EF-hand calcium binding domain 5	protein-coding	0.000000	0.320000	
chunk0004_389_1	chr1	51948287	51949292	+	0	NA	intron (NM_002867, intron 2 of 4)	L2a|LINE|L2	41975	NM_002867	5865	Hs.123072	NM_002867	ENSG00000169213	RAB3B	-	RAB3B, member RAS oncogene family	protein-coding	0.005970	0.448310	618(AGGGCCAGAGTGTTCC,-,0.00),619(GGGCCAGAGTGTTCCA,+,0.00)
chunk0151_191_1	chr5	50562340	50563255	+	0	NA	Intergenic	Intergenic	-103102	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.003279	0.347162	105(TGGTACAGCCTGCTCT,-,0.00),106(GGTACAGCCTGCTCTC,+,0.00)
chunk0138_187_1	chr4	37988039	37988404	+	0	NA	intron (NM_015173, intron 2 of 19)	MIR3|SINE|MIR	27786	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.010959	0.445355	
chunk0167_262_1	chr6	69620532	69620991	+	0	NA	Intergenic	MER53|DNA|hAT	176396	NM_018368	55788	Hs.271643	NM_018368	ENSG00000168216	LMBRD1	C6orf209|LMBD1|MAHCF|NESI	LMBR1 domain containing 1	protein-coding	0.002179	0.358696	
chunk0127_286_1	chr3	97893412	97893863	+	0	NA	intron (NM_153605, intron 11 of 21)	intron (NM_153605, intron 11 of 21)	71597	NM_153605	131544	Hs.733378	NM_153605	ENSG00000080200	CRYBG3	DKFZp667G2110|vlAKAP	crystallin beta-gamma domain containing 3	protein-coding	0.008869	0.393805	
chunk0016_145_1	chr1	197383533	197383917	+	0	NA	intron (NM_201253, intron 5 of 11)	intron (NM_201253, intron 5 of 11)	115521	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.005208	0.348052	
chunk0053_130_1	chr13	29810308	29810799	+	0	NA	intron (NM_007106, intron 1 of 4)	L2c|LINE|L2	40130	NM_007106	5412	Hs.145575	NM_007106	ENSG00000122042	UBL3	HCG-1|PNSC1	ubiquitin like 3	protein-coding	0.002037	0.349593	56(GAGCACAGACTGAGCT,-,0.00),57(AGCACAGACTGAGCTC,+,0.00)
chunk0013_215_1	chr1	169492088	169492294	+	0	NA	Intergenic	Intergenic	-6221	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.009709	0.550725	
chunk0126_275_1	chr3	80017914	80018257	+	0	NA	Intergenic	Intergenic	-250176	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.241279	
chunk0052_382_1	chr12	129244352	129244713	+	0	NA	intron (NM_133448, intron 4 of 8)	intron (NM_133448, intron 4 of 8)	35931	NR_110058	101927735	Hs.569212	NR_110058	ENSG00000256699	TMEM132D-AS2	-	TMEM132D antisense RNA 2	ncRNA	0.013850	0.367403	
chunk0014_111_1	chr1	176858552	176858935	+	0	NA	intron (NM_001286164, intron 22 of 22)	MamSINE1|SINE|tRNA-RTE	170702	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.010444	0.416667	
chunk0071_59_1	chr15	80326591	80326828	+	0	NA	intron (NR_033833, intron 1 of 2)	MamGypLTR1c|LTR|Gypsy	15096	NR_033833	283688	Hs.525933	NR_033833	ENSG00000259361	LINC00927	-	long intergenic non-protein coding RNA 927	ncRNA	0.016878	0.500000	
chunk0095_221_1	chr2	18800222	18801005	+	0	NA	Intergenic	Intergenic	-211033	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.007663	0.447704	
chunk0091_337_1	chr19	14201656	14201999	+	0	NA	intron (NM_001008701, intron 1 of 23)	L2a|LINE|L2	4358	NM_001008701	22859	Hs.94229	NM_014921	ENSG00000072071	ADGRL1	CIRL1|CL1|LEC2|LPHN1	adhesion G protein-coupled receptor L1	protein-coding	0.026239	0.511628	
chunk0088_233_1	chr18	48445603	48446245	+	0	NA	Intergenic	Intergenic	-93132	NM_001142397	9811	Hs.145230	NM_014772	ENSG00000134030	CTIF	Gm672|KIAA0427	cap binding complex dependent translation initiation factor	protein-coding	0.006231	0.449456	
chunk0008_410_1	chr1	98333277	98333890	+	0	NA	Intergenic	Intergenic	122872	NR_046088	729987	Hs.683961	NR_046088	ENSG00000226053	LINC01776	-	long intergenic non-protein coding RNA 1776	ncRNA	0.009788	0.486971	296(AGGTACAGGCTGTGCT,-,0.00),297(GGTACAGGCTGTGCTT,+,0.00),378(AGGTACACACTGTGCT,-,0.00),379(GGTACACACTGTGCTT,+,0.00)
chunk0046_230_1	chr12	60168522	60168777	+	0	NA	Intergenic	MER49|LTR|ERV1	479312	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.015686	0.394531	
chunk0209_301_1	chrX	48811976	48812464	+	0	NA	intron (NM_006044, intron 10 of 28)	intron (NM_006044, intron 10 of 28)	10140	NM_006044	10013	Hs.6764	NM_006044	ENSG00000094631	HDAC6	CPBHM|HD6|JM21|PPP1R90	histone deacetylase 6	protein-coding	0.002049	0.343558	
chunk0101_302_1	chr2	134839494	134840106	+	0	NA	intron (NM_138326, intron 1 of 9)	intron (NM_138326, intron 1 of 9)	1184	NM_001307983	130013	Hs.655728	NM_138326	ENSG00000153086	ACMSD	-	aminocarboxymuconate semialdehyde decarboxylase	protein-coding	0.004902	0.376835	334(AGGAACATGCTGTTCT,-,0.00),335(GGAACATGCTGTTCTG,+,0.00)
chunk0049_295_1	chr12	94152521	94153215	+	0	NA	intron (NM_005761, intron 1 of 30)	intron (NM_005761, intron 1 of 30)	4145	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.008646	0.428777	
chunk0130_262_1	chr3	136019532	136019839	+	0	NA	intron (NM_002718, intron 2 of 13)	intron (NM_002718, intron 2 of 13)	-3050	NM_181897	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.003257	0.347403	
chunk0172_281_1	chr6	137726041	137726767	+	0	NA	Intergenic	MIRb|SINE|MIR	12633	NR_121619	100507406	Hs.556703	NR_121618	ENSG00000234956	LINC02539	-	long intergenic non-protein coding RNA 2539	ncRNA	0.000000	0.401651	
chunk0206_99_1	chr9	120741679	120742165	+	0	NA	Intergenic	Intergenic	-27435	NM_001080497	1955	Hs.744903	NM_001080497	ENSG00000106780	MEGF9	EGFL5	multiple EGF like domains 9	protein-coding	0.002058	0.326489	192(TGGTACATCCAGTGCT,-,0.00),193(GGTACATCCAGTGCTT,+,0.00)
chunk0017_323_1	chr1	211461693	211461917	+	0	NA	Intergenic	L1MA1|LINE|L1	31112	NM_001164688	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.008929	0.408889	
chunk0180_296_1	chr7	70189771	70190344	+	0	NA	intron (NM_015570, intron 4 of 18)	intron (NM_015570, intron 4 of 18)	591138	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.008726	0.385017	
chunk0028_124_1	chr10	84710883	84711563	+	0	NA	Intergenic	HAL1|LINE|L1	286041	NM_001284242	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.001471	0.411160	
chunk0109_74_1	chr20	1798829	1799435	+	0	NA	Intergenic	L1MC3|LINE|L1	-19386	NR_037142	100289473	Hs.641525	NR_037142	ENSG00000232528	LOC100289473	-	cytoskeleton associated protein 2-like pseudogene	pseudo	0.006601	0.329489	
chunk0148_145_1	chr5	6283452	6283786	+	0	NA	Intergenic	L1MEd|LINE|L1	53673	NR_028351	401172	Hs.376760	NM_001001702	ENSG00000250490	LINC02145	-	long intergenic non-protein coding RNA 2145	ncRNA	0.005988	0.328358	
chunk0126_346_1	chr3	82684549	82684782	+	0	NA	Intergenic	L1MA7|LINE|L1	-922866	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.341880	
chunk0075_238_1	chr16	53090985	53091337	+	0	NA	intron (NM_025134, intron 1 of 38)	intron (NM_025134, intron 1 of 38)	36128	NM_025134	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.022727	0.592068	176(GGGTTCAGAGTGTTCT,-,0.00),177(GGTTCAGAGTGTTCTT,+,0.00)
chunk0110_233_1	chr20	16192997	16193342	+	0	NA	Intergenic	Intergenic	-207287	NR_130924	613266	Hs.309149	NR_130924		LOC613266	-	uncharacterized LOC613266	ncRNA	0.000000	0.375723	
chunk0119_146_1	chr22	42990830	42991401	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	24063	NM_001184970	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.005254	0.494755	276(CAGAACACACTGCCCC,-,0.00),277(AGAACACACTGCCCCC,+,0.00)
chunk0103_435_1	chr2	169951345	169951745	+	0	NA	intron (NM_172070, intron 23 of 38)	L2c|LINE|L2	124037	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.010000	0.401496	
chunk0131_165_1	chr3	146499711	146500121	+	0	NA	Intergenic	Intergenic	-3925	NM_020359	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.002439	0.350365	176(TAGAACATATTGTTTT,-,0.00),177(AGAACATATTGTTTTA,+,0.00)
chunk0194_437_1	chr8	92503401	92504050	+	0	NA	Intergenic	Intergenic	151769	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.007704	0.358462	
chunk0113_366_1	chr20	59224812	59225520	+	0	NA	intron (NM_178457, intron 3 of 4)	intron (NM_178457, intron 3 of 4)	34146	NM_178457	128611	Hs.473204	NM_178457	ENSG00000124203	ZNF831	C20orf174	zinc finger protein 831	protein-coding	0.005650	0.322990	
chunk0059_381_1	chr14	37417745	37418379	+	0	NA	intron (NM_001195296, intron 12 of 14)	intron (NM_001195296, intron 12 of 14)	177058	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.003155	0.321260	526(GTGAACAGTGTGGTCT,-,0.00),527(TGAACAGTGTGGTCTT,+,0.00)
chunk0163_328_1	chr6	15171730	15171955	+	0	NA	Intergenic	Intergenic	-74133	NM_004973	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.008889	0.508850	
chunk0202_302_1	chr9	77917973	77918325	+	0	NA	intron (NM_002072, intron 2 of 6)	intron (NM_002072, intron 2 of 6)	113300	NM_002072	2776	Hs.269782	NM_002072	ENSG00000156052	GNAQ	CMC1|G-ALPHA-q|GAQ|SWS	G protein subunit alpha q	protein-coding	0.005682	0.433428	
chunk0043_197_1	chr12	19222983	19223425	+	0	NA	intron (NM_001256787, intron 1 of 25)	Kanga1b|DNA|TcMar-Tc2	17879	NM_001256787	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.006787	0.365688	
chunk0184_292_1	chr7	118872580	118872779	+	0	NA	Intergenic	Intergenic	648021	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.000000	0.380000	
chunk0023_415_1	chr10	31262611	31263453	+	0	NA	Intergenic	Intergenic	56063	NR_024284	220930	Hs.372654	NR_024284	ENSG00000237036	ZEB1-AS1	-	ZEB1 antisense RNA 1	ncRNA	0.010689	0.411625	460(AAGCTCAGCGTGTCCC,-,0.00),461(AGCTCAGCGTGTCCCA,+,0.00)
chunk0200_248_1	chr9	21315866	21316625	+	0	NA	Intergenic	Intergenic	-10932	NM_002169	3442	Hs.37113	NM_002169	ENSG00000147873	IFNA5	IFN-alpha-5|IFN-alphaG|INA5|INFA5|leIF G	interferon alpha 5	protein-coding	0.009223	0.378947	
chunk0197_160_1	chr8	120490316	120490629	+	0	NA	exon (NM_022045, exon 13 of 22)	exon (NM_022045, exon 13 of 22)	-45065	NM_014078	28998	Hs.333823	NM_014078	ENSG00000172172	MRPL13	L13|L13A|L13mt|RPL13|RPML13	mitochondrial ribosomal protein L13	protein-coding	0.003195	0.334395	
chunk0140_409_1	chr4	75672230	75673132	+	0	NA	intron (NM_203505, intron 1 of 11)	CpG	478	NM_012297	9908	Hs.303676	NM_012297	ENSG00000138757	G3BP2	-	G3BP stress granule assembly factor 2	protein-coding	0.065410	0.565891	
chunk0210_371_1	chrX	97068788	97069051	+	0	NA	intron (NM_006729, intron 17 of 26)	intron (NM_006729, intron 17 of 26)	185011	NM_013347	29935	Hs.659349	NM_013347	ENSG00000204086	RPA4	HSU24186	replication protein A4	protein-coding	0.015209	0.344697	
chunk0203_314_1	chr9	89484547	89484746	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-4950	NM_001142287	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.015075	0.480000	
chunk0097_451_1	chr2	64516464	64517153	+	0	NA	Intergenic	L1MC5a|LINE|L1	-7497	NM_203437	54812	Hs.655167	NM_017657	ENSG00000119844	AFTPH	Nbla10388	aftiphilin	protein-coding	0.002903	0.424638	
chunk0163_454_1	chr6	17600705	17601081	+	0	NA	exon (NM_016255, exon 1 of 5)	exon (NM_016255, exon 1 of 5)	606	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.098404	0.726790	
chunk0004_402_1	chr1	52241391	52241614	+	0	NA	intron (NM_007324, intron 4 of 17)	intron (NM_007324, intron 4 of 17)	99408	NM_007324	9372	Hs.532345	NM_004799	ENSG00000157077	ZFYVE9	MADHIP|NSP|PPP1R173|SARA|SMADIP	zinc finger FYVE-type containing 9	protein-coding	0.000000	0.312500	
chunk0140_254_1	chr4	71476755	71477036	+	0	NA	intron (NM_001098484, intron 14 of 25)	intron (NM_001098484, intron 14 of 25)	137842	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.007117	0.333333	
chunk0170_224_1	chr6	113329953	113331060	+	0	NA	Intergenic	MamGypsy2-LTR|LTR|Gypsy	319569	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.004517	0.359206	
chunk0065_159_1	chr15	25542484	25542683	+	0	NA	Intergenic	Intergenic	-103555	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.000000	0.325000	
chunk0134_266_1	chr3	179533187	179533796	+	0	NA	Intergenic	L1MC1|LINE|L1	-29389	NM_004301	86	Hs.435326	NM_004301	ENSG00000136518	ACTL6A	ACTL6|ARPN-BETA|Arp4|BAF53A|INO80K	actin like 6A	protein-coding	0.006568	0.368852	
chunk0116_92_1	chr21	34877504	34877849	+	0	NA	intron (NM_001001890, intron 2 of 5)	intron (NM_001001890, intron 2 of 5)	11014	NM_001122607	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.017391	0.476879	
chunk0191_299_1	chr8	54558683	54559295	+	0	NA	Intergenic	Intergenic	-57078	NM_006269	6101	Hs.732820	NM_006269	ENSG00000104237	RP1	DCDC4A|ORP1	RP1 axonemal microtubule associated	protein-coding	0.011438	0.414356	
chunk0077_334_1	chr16	82515487	82515822	+	0	NA	Intergenic	Charlie15a|DNA|hAT-Charlie	-111140	NM_001220489	1012	Hs.654386	NM_001257	ENSG00000140945	CDH13	CDHH|P105	cadherin 13	protein-coding	0.008955	0.410714	
chunk0157_371_1	chr5	123557192	123557692	+	0	NA	intron (NM_001031812, intron 3 of 12)	intron (NM_001031812, intron 3 of 12)	12025	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.002000	0.309381	
chunk0121_238_1	chr3	22111773	22111998	+	0	NA	Intergenic	Intergenic	154746	NR_046876	100874221	Hs.160616	NR_046876	ENSG00000223351	ZNF385D-AS2	-	ZNF385D antisense RNA 2	ncRNA	0.008889	0.398230	
chunk0128_430_1	chr3	114941490	114942126	+	0	NA	intron (NM_001164343, intron 2 of 11)	intron (NM_001164343, intron 2 of 11)	-41186	NR_121662	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.004717	0.321821	
chunk0105_109_1	chr2	184744455	184744978	+	0	NA	intron (NM_194250, intron 1 of 3)	intron (NM_194250, intron 1 of 3)	146350	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.003824	0.349237	
chunk0001_346_1	chr1	9815073	9815595	+	0	NA	intron (NM_001009566, intron 1 of 18)	L3|LINE|CR1	9192	NM_014944	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.005747	0.395793	
chunk0054_169_1	chr13	44317687	44318170	+	0	NA	Intergenic	Intergenic	-55914	NM_001010897	387923	Hs.377972	NM_001010897	ENSG00000151778	SERP2	C13orf21|bA269C23.1	stress associated endoplasmic reticulum protein family member 2	protein-coding	0.012422	0.473140	192(AAGAACAGAGTGTAAT,-,0.00)
chunk0039_436_1	chr11	108016665	108016878	+	0	NA	intron (NM_003478, intron 1 of 18)	AluJr|SINE|Alu	8089	NM_003478	8065	Hs.440320	NM_003478	ENSG00000166266	CUL5	CUL-5|VACM-1|VACM1	cullin 5	protein-coding	0.000000	0.467290	
chunk0138_369_1	chr4	42320959	42321415	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-76652	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.010965	0.459519	
chunk0004_167_1	chr1	45669872	45670108	+	0	NA	intron (NM_021639, intron 2 of 12)	L2a|LINE|L2	16640	NM_021639	60313	Hs.238432	NM_021639	ENSG00000159592	GPBP1L1	SP192	GC-rich promoter binding protein 1 like 1	protein-coding	0.004237	0.358650	
chunk0077_263_1	chr16	80956575	80956975	+	0	NA	Intergenic	L1PA13|LINE|L1	-49723	NM_001100624	55839	Hs.726537	NM_018455	ENSG00000166451	CENPN	BM039|C16orf60|CENP-N|ICEN32	centromere protein N	protein-coding	0.002500	0.381546	
chunk0004_176_1	chr1	45864579	45865133	+	0	NA	intron (NM_015112, intron 3 of 28)	intron (NM_015112, intron 3 of 28)	61243	NM_015112	23139	Hs.319481	NM_015112	ENSG00000086015	MAST2	MAST205|MTSSK	microtubule associated serine/threonine kinase 2	protein-coding	0.012635	0.380180	
chunk0169_94_1	chr6	100147024	100147226	+	0	NA	Intergenic	Intergenic	-152887	NM_032503	84539	Hs.591342	NM_032503	ENSG00000152034	MCHR2	GPR145|GPRv17|MCH-2R|MCH-R2|MCH2|MCH2R|MCHR-2|SLT	melanin concentrating hormone receptor 2	protein-coding	0.000000	0.320197	
chunk0069_31_1	chr15	60479334	60479680	+	0	NA	promoter-TSS (NM_001018089)	promoter-TSS (NM_001018089)	329	NR_120340	101928784	Hs.655155	NR_120339	ENSG00000245534	RORA-AS1	-	RORA antisense RNA 1	ncRNA	0.023121	0.449568	
chunk0035_41_1	chr11	40960477	40960897	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	498949	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.002381	0.380048	44(GAGAACATAGTGTGAC,-,0.00)
chunk0017_251_1	chr1	208624431	208624632	+	0	NA	Intergenic	(CTG)n|Simple_repeat|Simple_repeat	-380211	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.000000	0.465347	
chunk0129_431_1	chr3	127590993	127591249	+	0	NA	promoter-TSS (NM_001136053)	promoter-TSS (NM_001136053)	-362	NM_001142646	131601	Hs.6418	NM_016372	ENSG00000163870	TPRA1	GPR175|TMEM227|TPRA40	transmembrane protein adipocyte associated 1	protein-coding	0.136719	0.785992	
chunk0155_107_1	chr5	92750178	92750430	+	0	NA	Intergenic	Intergenic	821039	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.003968	0.316206	
chunk0087_213_1	chr18	36044567	36045063	+	0	NA	intron (NM_001303412, intron 1 of 8)	L1MC5a|LINE|L1	22779	NM_001303411	55197	Hs.464912	NM_018170	ENSG00000141425	RPRD1A	HsT3101|P15RS	regulation of nuclear pre-mRNA domain containing 1A	protein-coding	0.010081	0.418511	191(ATGCACAAAATGTACC,-,0.00)
chunk0207_60_1	chrX	8844217	8844616	+	0	NA	Intergenic	ORSL-2b|DNA|hAT-Tip100	-43033	NM_174951	171482	Hs.382062	NM_174951	ENSG00000183304	FAM9A	TEX39A	family with sequence similarity 9 member A	protein-coding	0.010025	0.390000	
chunk0099_276_1	chr2	98299618	98300359	+	0	NA	intron (NM_144992, intron 24 of 27)	intron (NM_144992, intron 24 of 27)	-46167	NM_001298	1261	Hs.234785	NM_001298	ENSG00000144191	CNGA3	ACHM2|CCNC1|CCNCa|CCNCalpha|CNCG3|CNG3	cyclic nucleotide gated channel alpha 3	protein-coding	0.005398	0.440701	
chunk0099_267_1	chr2	98107833	98108566	+	0	NA	intron (NM_144992, intron 2 of 27)	L1MDa|LINE|L1	21067	NM_144992	200403	Hs.269977	NM_144992	ENSG00000168658	VWA3B	SCAR22	von Willebrand factor A domain containing 3B	protein-coding	0.002729	0.291553	
chunk0058_380_1	chr14	29385169	29385829	+	0	NA	Intergenic	Intergenic	542194	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.003030	0.394856	
chunk0123_148_1	chr3	42923763	42924009	+	0	NA	Intergenic	LTR25-int|LTR|ERV1	-12456	NM_001205272	100506243	Hs.720172	NM_015673	ENSG00000240747	KRBOX1	-	KRAB box domain containing 1	protein-coding	0.000000	0.425101	
chunk0134_180_1	chr3	178131289	178131779	+	0	NA	Intergenic	Intergenic	-287667	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.004082	0.338086	103(TGGGACAGTTTGTTTT,-,0.00),104(GGGACAGTTTGTTTTA,+,0.00)
chunk0053_257_1	chr13	33046121	33046956	+	0	NA	intron (NM_004795, intron 1 of 4)	L1MEc|LINE|L1	30105	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.003593	0.303828	
chunk0142_383_1	chr4	102318660	102318936	+	0	NA	intron (NM_022154, intron 1 of 7)	intron (NM_022154, intron 1 of 7)	5514	NM_001135148	64116	Hs.288034	NM_022154	ENSG00000138821	SLC39A8	BIGM103|CDG2N|LZT-Hs6|PP3105|ZIP8	solute carrier family 39 member 8	protein-coding	0.010870	0.425993	
chunk0133_337_1	chr3	172711003	172711319	+	0	NA	promoter-TSS (NM_020792)	promoter-TSS (NM_020792)	57	NM_001146278	57552	Hs.444099	NM_020792	ENSG00000144959	NCEH1	AADACL1|NCEH	neutral cholesterol ester hydrolase 1	protein-coding	0.056962	0.580442	
chunk0156_398_1	chr5	113747142	113747837	+	0	NA	Intergenic	LTR37B|LTR|ERV1	233795	NM_022828	64848	Hs.231942	NM_022828	ENSG00000047188	YTHDC2	CAHL|hYTHDC2	YTH domain containing 2	protein-coding	0.002878	0.334770	
chunk0150_194_1	chr5	34831329	34831703	+	0	NA	3' UTR (NM_001145525, exon 20 of 20)	3' UTR (NM_001145525, exon 20 of 20)	-7648	NM_144725	153657	Hs.435742	NM_144725	ENSG00000205838	TTC23L	MC25-1	tetratricopeptide repeat domain 23 like	protein-coding	0.000000	0.301333	
chunk0102_429_1	chr2	157291138	157291596	+	0	NA	intron (NM_014568, intron 3 of 9)	MamRTE1|LINE|RTE-BovB	33539	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.004367	0.403050	
chunk0002_412_1	chr1	27542397	27542805	+	0	NA	intron (NM_001029882, intron 6 of 6)	MIRb|SINE|MIR	-52414	NM_001201404	10163	Hs.469244	NM_006990	ENSG00000158195	WASF2	IMD2|SCAR2|WASF4|WAVE2|dJ393P12.2	WASP family member 2	protein-coding	0.031863	0.567237	
chunk0115_89_1	chr21	22341834	22342421	+	0	NA	Intergenic	Intergenic	243510	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.000000	0.411565	
chunk0082_398_1	chr17	60801394	60801672	+	0	NA	intron (NM_017679, intron 6 of 23)	L1MD2|LINE|L1	123722	NM_001099432	54828	Hs.655028	NM_017679	ENSG00000141376	BCAS3	GAOB1|MAAB	BCAS3 microtubule associated cell migration factor	protein-coding	0.007194	0.347670	115(AGAACTTCCAGTACTC,+,0.00)
chunk0152_427_1	chr5	65947983	65948440	+	0	NA	intron (NM_018695, intron 1 of 24)	AluJb|SINE|Alu	-2638	NR_028474	100303749	Hs.608060	NR_028474		LOC100303749	-	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) pseudogene	pseudo	0.008753	0.410480	
chunk0080_157_1	chr17	28084350	28084578	+	0	NA	intron (NM_016231, intron 1 of 10)	MIRc|SINE|MIR	41802	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.004386	0.406114	193(CTGTACATTCTGTCCC,-,0.00),194(TGTACATTCTGTCCCA,+,0.00)
chunk0164_452_1	chr6	28355660	28355859	+	0	NA	intron (NM_001242894, intron 2 of 6)	HERVL18-int|LTR|ERVL	5845	NM_001242894	80317	Hs.380930	NM_024493	ENSG00000189298	ZKSCAN3	ZF47|ZFP306|ZNF306|ZNF309|ZSCAN13|ZSCAN35|Zfp47|dJ874C20.1|dJ874C20.1.|zfp-47	zinc finger with KRAB and SCAN domains 3	protein-coding	0.010050	0.435000	
chunk0079_34_1	chr17	10147022	10147382	+	0	NA	intron (NM_201433, intron 1 of 13)	intron (NM_201433, intron 1 of 13)	51349	NM_201433	8522	Hs.462214	NM_003644	ENSG00000007237	GAS7	-	growth arrest specific 7	protein-coding	0.011111	0.396122	
chunk0001_275_1	chr1	8630051	8630588	+	0	NA	intron (NM_001042681, intron 2 of 22)	intron (NM_001042681, intron 2 of 22)	-135406	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.007449	0.381041	
chunk0016_289_1	chr1	200993074	200993376	+	0	NA	intron (NM_017596, intron 15 of 33)	intron (NM_017596, intron 15 of 33)	30475	NM_001252102	23046	Hs.169182	NM_017596	ENSG00000116852	KIF21B	-	kinesin family member 21B	protein-coding	0.016556	0.544554	
chunk0204_312_1	chr9	100295294	100295514	+	0	NA	intron (NR_051962, intron 15 of 17)	intron (NR_051962, intron 15 of 17)	57167	NM_001161584	54881	Hs.494648	NM_017746	ENSG00000136891	TEX10	Ipi1|bA208F1.2	testis expressed 10	protein-coding	0.009091	0.429864	
chunk0041_210_1	chr11	126943138	126943808	+	0	NA	intron (NR_046986, intron 1 of 2)	intron (NR_046986, intron 1 of 2)	2727	NR_046986	100874251	Hs.319053	NR_046986	ENSG00000254960	KIRREL3-AS2	-	KIRREL3 antisense RNA 2	ncRNA	0.011940	0.481371	
chunk0006_238_1	chr1	68955248	68955855	+	0	NA	Intergenic	Intergenic	-458330	NM_001114120	55635	Hs.445098	NM_017779	ENSG00000024526	DEPDC1	DEP.8|DEPDC1-V2|DEPDC1A|SDP35	DEP domain containing 1	protein-coding	0.009885	0.401316	
chunk0073_16_1	chr16	2205431	2205768	+	0	NA	promoter-TSS (NM_001199174)	promoter-TSS (NM_001199174)	-132	NM_001199174	64223	Hs.29203	NM_022372	ENSG00000167965	MLST8	GBL|GbetaL|LST8|POP3|WAT1	MTOR associated protein, LST8 homolog	protein-coding	0.118694	0.733728	
chunk0048_418_1	chr12	88291518	88291972	+	0	NA	Intergenic	Intergenic	149449	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.006608	0.371429	
chunk0143_256_1	chr4	115760952	115761382	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	-538558	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.000000	0.354988	
chunk0104_446_1	chr2	181517600	181518238	+	0	NA	intron (NM_000885, intron 17 of 27)	intron (NM_000885, intron 17 of 27)	61027	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.001567	0.402191	186(GTGAACATTGTGTTTC,-,0.00),187(TGAACATTGTGTTTCT,+,0.00)
chunk0159_67_1	chr5	137315813	137316431	+	0	NA	intron (NM_004598, intron 2 of 10)	MLT1A0|LTR|ERVL-MaLR	183207	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.009709	0.463651	340(AGGAACACTGTGTGCT,-,0.00),341(GGAACACTGTGTGCTC,+,0.00)
chunk0200_316_1	chr9	23431571	23431770	+	0	NA	Intergenic	Intergenic	240729	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.015075	0.470000	
chunk0050_21_1	chr12	99796929	99797233	+	0	NA	intron (NM_152788, intron 4 of 25)	intron (NM_152788, intron 4 of 25)	149331	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.000000	0.288525	
chunk0197_30_1	chr8	118039725	118040221	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	71846	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.004032	0.364185	261(AAAAACATACAGTCCT,-,0.00)
chunk0110_364_1	chr20	19831940	19832139	+	0	NA	Intergenic	MIR|SINE|MIR	-54482	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.020101	0.430000	
chunk0130_273_1	chr3	136292289	136292961	+	0	NA	intron (NM_000532, intron 6 of 14)	intron (NM_000532, intron 6 of 14)	42300	NM_001178014	5096	Hs.63788	NM_000532	ENSG00000114054	PCCB	-	propionyl-CoA carboxylase subunit beta	protein-coding	0.001488	0.350669	332(GAGAACAGTGTGTATT,-,0.00),333(AGAACAGTGTGTATTG,+,0.00)
chunk0022_99_1	chr10	9847348	9847547	+	0	NA	Intergenic	Intergenic	-211275	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.000000	0.245000	
chunk0033_299_1	chr11	19939585	19939979	+	0	NA	intron (NM_001244963, intron 9 of 39)	intron (NM_001244963, intron 9 of 39)	-82774	NM_001111019	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.015228	0.460759	159(CTGGACAGCCTGCTCT,-,0.00),160(TGGACAGCCTGCTCTG,+,0.00),251(TGGAACAGCATGAACC,-,0.00),252(GGAACAGCATGAACCC,+,0.00)
chunk0129_368_1	chr3	125375836	125376502	+	0	NA	promoter-TSS (NM_021964)	promoter-TSS (NM_021964)	-815	NM_021964	7707	Hs.592591	NM_021964	ENSG00000163848	ZNF148	BERF-1|BFCOL1|GDACCF|HT-BETA|ZBP-89|ZFP148|pHZ-52	zinc finger protein 148	protein-coding	0.016517	0.446777	
chunk0122_432_1	chr3	39180482	39181088	+	0	NA	Intergenic	Intergenic	11801	NM_194293	165904	Hs.447868	NM_194293	ENSG00000168334	XIRP1	CMYA1|Xin	xin actin binding repeat containing 1	protein-coding	0.075908	0.665568	
chunk0152_24_1	chr5	56640961	56641515	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	-35006	NM_001287053	101928448	Hs.208052	NM_001287053	ENSG00000225940	C5orf67	-	chromosome 5 open reading frame 67	ncRNA	0.003610	0.472072	
chunk0088_364_1	chr18	53422880	53423371	+	0	NA	intron (NM_005215, intron 21 of 28)	MamTip2|DNA|hAT-Tip100	-145322	NR_110798	102724651	Hs.123442	NR_110798	ENSG00000263438	LINC01919	-	long intergenic non-protein coding RNA 1919	ncRNA	0.008147	0.388211	
chunk0144_179_1	chr4	133270548	133271401	+	0	NA	Intergenic	Intergenic	121684	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.001172	0.270492	
chunk0154_288_1	chr5	82751745	82752329	+	0	NA	Intergenic	Intergenic	-88118	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.001712	0.290598	
chunk0201_429_1	chr9	69942509	69943033	+	0	NA	Intergenic	L1MB8|LINE|L1	-100810	NM_153267	256691	Hs.547172	NM_153267	ENSG00000165072	MAMDC2	-	MAM domain containing 2	protein-coding	0.005725	0.348571	
chunk0012_101_1	chr1	156500922	156501121	+	0	NA	promoter-TSS (NM_005920)	promoter-TSS (NM_005920)	-179	NM_005920	4209	Hs.314327	NM_005920	ENSG00000116604	MEF2D	-	myocyte enhancer factor 2D	protein-coding	0.095477	0.745000	
chunk0127_410_1	chr3	102529340	102530034	+	0	NA	Intergenic	Intergenic	94672	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.008646	0.437410	384(TGGAACAATCAGTTCC,-,0.00),385(GGAACAATCAGTTCCT,+,0.00)
chunk0078_314_1	chr17	8379471	8379774	+	0	NA	intron (NM_001315530, intron 3 of 3)	intron (NM_001315530, intron 3 of 3)	-2911	NM_001304947	124751	Hs.304604	NM_213597	ENSG00000184619	KRBA2	-	KRAB-A domain containing 2	protein-coding	0.016502	0.401316	
chunk0093_165_1	chr19	48246157	48246477	+	0	NA	intron (NM_001184903, intron 1 of 10)	L1MC4a|LINE|L1	3316	NR_033678	22900	Hs.68846	NM_014959	ENSG00000105483	CARD8	CARDINAL|DACAR|DAKAR|NDPP|NDPP1|TUCAN	caspase recruitment domain family member 8	protein-coding	0.009375	0.389408	
chunk0057_68_1	chr13	98174522	98174764	+	0	NA	intron (NM_001001715, intron 1 of 2)	intron (NM_001001715, intron 1 of 2)	2624	NM_178861	140432	Hs.296045	NM_178861	ENSG00000139797	RNF113B	RNF161|ZNF183L1|bA10G5.1	ring finger protein 113B	protein-coding	0.016529	0.419753	
chunk0045_463_1	chr12	53825212	53825892	+	0	NA	Intergenic	Intergenic	-68518	NR_104332	102216268	Hs.742074	NR_104332	ENSG00000260492	CISTR	CISTR-ACT|CISTRACT|re52431	chondrogenesis-associated transcript	ncRNA	0.004412	0.449339	
chunk0014_399_1	chr1	182911346	182911728	+	0	NA	intron (NM_030933, intron 6 of 9)	L1MB5|LINE|L1	41881	NM_030933	81626	Hs.497034	NM_030933	ENSG00000157060	SHCBP1L	C1orf14|GE36	SHC binding and spindle associated 1 like	protein-coding	0.002618	0.326371	
chunk0045_106_1	chr12	46197738	46198309	+	0	NA	exon (NM_001278387, exon 16 of 18)	exon (NM_001278387, exon 16 of 18)	68472	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.008757	0.358392	
chunk0173_226_1	chr6	146169137	146169640	+	0	NA	intron (NM_001278064, intron 2 of 7)	intron (NM_001278064, intron 2 of 7)	140190	NM_001278067	2911	Hs.32945	NM_000838	ENSG00000152822	GRM1	GPRC1A|MGLU1|MGLUR1|PPP1R85|SCA44|SCAR13	glutamate metabotropic receptor 1	protein-coding	0.003976	0.359127	
chunk0190_433_1	chr8	41598132	41598699	+	0	NA	5' UTR (NM_178819, exon 2 of 13)	5' UTR (NM_178819, exon 2 of 13)	-20047	NR_125824	102723729	Hs.586384	NR_125824		LOC102723729	-	uncharacterized LOC102723729	ncRNA	0.007055	0.473592	291(GAGACATTGTGTGCCA,+,0.00)
chunk0141_349_1	chr4	87717116	87717373	+	0	NA	Intergenic	Intergenic	66942	NM_001079911	1758	Hs.652366	NM_004407	ENSG00000152592	DMP1	ARHP|ARHR|DMP-1	dentin matrix acidic phosphoprotein 1	protein-coding	0.000000	0.325581	
chunk0061_352_1	chr14	63677889	63678382	+	0	NA	Intergenic	LTR47A2|LTR|ERVL	-36212	NM_001258272	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.006085	0.408907	
chunk0101_317_1	chr2	135555361	135555850	+	0	NA	intron (NM_001282799, intron 1 of 22)	L1MB8|LINE|L1	24150	NM_015361	23518	Hs.412462	NM_015361	ENSG00000048991	R3HDM1	R3HDM	R3H domain containing 1	protein-coding	0.012270	0.389796	
chunk0116_418_1	chr21	42715972	42716607	+	0	NA	intron (NM_001001576, intron 2 of 14)	L1MC2|LINE|L1	62537	NM_001001576	5152	Hs.473927	NM_002606	ENSG00000160191	PDE9A	HSPDE9A2	phosphodiesterase 9A	protein-coding	0.006299	0.386792	
chunk0051_322_1	chr12	119959558	119959934	+	0	NA	Intergenic	Intergenic	-30098	NM_207311	92558	Hs.369763	NM_207311	ENSG00000135127	BICDL1	BICDR-1|BICDR1|CCDC64|CCDC64A|H_267D11.1	BICD family like cargo adaptor 1	protein-coding	0.005319	0.384615	
chunk0113_7_1	chr20	49330420	49330829	+	0	NA	Intergenic	Intergenic	49941	NR_003030	692057		NR_003030	ENSG00000212304	SNORD12	HBII-99|MIR1259|MIRN1259	small nucleolar RNA, C/D box 12	snoRNA	0.002445	0.417073	
chunk0008_286_1	chr1	94864817	94865093	+	0	NA	intron (NM_001258340, intron 11 of 14)	intron (NM_001258340, intron 11 of 14)	44411	NM_001301079	126969	Hs.483423	NM_152369	ENSG00000143036	SLC44A3	CTL3	solute carrier family 44 member 3	protein-coding	0.021739	0.476534	
chunk0191_238_1	chr8	52986835	52987425	+	0	NA	Intergenic	Intergenic	47222	NM_005285	2831	Hs.248117	NM_005285	ENSG00000183729	NPBWR1	GPR7	neuropeptides B and W receptor 1	protein-coding	0.005085	0.348562	
chunk0198_430_1	chr8	143281714	143282077	+	0	NA	promoter-TSS (NR_120683)	promoter-TSS (NR_120683)	-195	NR_120683	100507316	Hs.446671	NR_120682	ENSG00000253716	MINCR	LINC01604	MYC-induced long non-coding RNA	ncRNA	0.046832	0.585165	
chunk0083_46_1	chr17	63550358	63550584	+	0	NA	promoter-TSS (NM_005828)	promoter-TSS (NM_005828)	36	NR_073585	10238	Hs.410596	NM_005828	ENSG00000136485	DCAF7	AN11|HAN11|SWAN-1|WDR68	DDB1 and CUL4 associated factor 7	protein-coding	0.119469	0.651982	
chunk0151_319_1	chr5	53483039	53483238	+	0	NA	intron (NM_006350, intron 2 of 5)	intron (NM_006350, intron 2 of 5)	2704	NM_013409	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.020101	0.575000	
chunk0211_374_1	chrX	126536039	126536484	+	0	NA	Intergenic	Intergenic	16598	NM_178470	139170	Hs.120403	NM_178470	ENSG00000198889	DCAF12L1	KIAA1892L|WDR40B	DDB1 and CUL4 associated factor 12 like 1	protein-coding	0.004494	0.327354	
chunk0200_303_1	chr9	22956832	22957073	+	0	NA	Intergenic	L1M4|LINE|L1	310752	NR_038977	441389		NR_038977	ENSG00000234840	LINC01239	-	long intergenic non-protein coding RNA 1239	ncRNA	0.008299	0.404959	
chunk0121_299_1	chr3	23843033	23843679	+	0	NA	intron (NM_001202476, intron 2 of 4)	intron (NM_001202476, intron 2 of 4)	32913	NM_001202476	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.003096	0.366306	240(CAGGACATACAGTTCC,-,0.00),241(AGGACATACAGTTCCT,+,0.00)
chunk0009_161_1	chr1	105260171	105260420	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	358640	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.016064	0.384000	
chunk0156_156_1	chr5	107404886	107405336	+	0	NA	intron (NM_001962, intron 2 of 4)	intron (NM_001962, intron 2 of 4)	265784	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.017778	0.447894	
chunk0058_448_1	chr13	113856564	113857094	+	0	NA	intron (NM_000820, intron 2 of 14)	intron (NM_000820, intron 2 of 14)	7274	NM_000820	2621	Hs.646346	NM_000820	ENSG00000183087	GAS6	AXLLG|AXSF	growth arrest specific 6	protein-coding	0.024528	0.536723	
chunk0051_240_1	chr12	117038205	117038845	+	0	NA	TTS (NR_031766)	TTS (NR_031766)	-51188	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.020313	0.528861	
chunk0195_59_1	chr8	93717854	93718282	+	0	NA	intron (NM_001283034, intron 5 of 6)	intron (NM_001283034, intron 5 of 6)	17561	NR_104267	137392	Hs.125038	NM_145269	ENSG00000188343	FAM92A	FAM92A1|PAPA9	family with sequence similarity 92 member A	protein-coding	0.009346	0.391608	
chunk0171_221_1	chr6	126170203	126170860	+	0	NA	Intergenic	Intergenic	-169258	NR_104462	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.009132	0.379939	
chunk0175_337_1	chr6	167238040	167238267	+	0	NA	Intergenic	LTR1C3|LTR|ERV1	-53162	NM_018974	54346	Hs.567508	NM_018974	ENSG00000112494	UNC93A	Unc-93A|dJ366N23.1|dJ366N23.2	unc-93 homolog A	protein-coding	0.008811	0.513158	
chunk0124_437_1	chr3	61288018	61288226	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	-36663	NM_001166243	2272	Hs.655995	NM_002012	ENSG00000189283	FHIT	AP3Aase|FRA3B	fragile histidine triad diadenosine triphosphatase	protein-coding	0.024038	0.507177	
chunk0068_401_1	chr15	58771862	58772284	+	0	NA	exon (NM_001040453, exon 1 of 9)	exon (NM_001040453, exon 1 of 9)	879	NM_001040450	54629	Hs.591122	NM_019092	ENSG00000128923	MINDY2	FAM63B	MINDY lysine 48 deubiquitinase 2	protein-coding	0.035545	0.581560	
chunk0109_450_1	chr2	241619315	241619594	+	0	NA	intron (NM_015963, intron 2 of 5)	Tigger3c|DNA|TcMar-Tigger	-1953	NM_001164356	51078	Hs.435759	NM_015963	ENSG00000176946	THAP4	CGI-36|Nb(III)|PP238	THAP domain containing 4	protein-coding	0.021505	0.453571	132(TGGCACAGCCTGTGCT,-,0.00),133(GGCACAGCCTGTGCTC,+,0.00)
chunk0027_451_1	chr10	81286340	81286833	+	0	NA	Intergenic	L1PA15|LINE|L1	-588728	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.004057	0.528340	
chunk0150_426_1	chr5	40381934	40382612	+	0	NA	Intergenic	Intergenic	-297657	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.002950	0.331370	
chunk0063_44_1	chr14	76904887	76905501	+	0	NA	Intergenic	MIRb|SINE|MIR	78812	NM_194287	145497	Hs.147276	NM_194287	ENSG00000100565	LRRC74A	C14orf166B|LRRC74	leucine rich repeat containing 74A	protein-coding	0.019544	0.468293	
chunk0207_43_1	chrX	6228866	6229314	+	0	NA	promoter-TSS (NM_001282145)	promoter-TSS (NM_001282145)	-208	NM_001282145	57502	Hs.21107	NM_020742	ENSG00000146938	NLGN4X	ASPGX2|AUTSX2|HLNX|HNL4X|NLGN4	neuroligin 4 X-linked	protein-coding	0.026786	0.469933	
chunk0138_270_1	chr4	40395708	40396130	+	0	NA	Intergenic	Intergenic	60590	NM_017581	55584	Hs.272278	NM_017581	ENSG00000174343	CHRNA9	HSA243342|NACHRA9	cholinergic receptor nicotinic alpha 9 subunit	protein-coding	0.011848	0.491726	
chunk0167_273_1	chr6	70291358	70291796	+	0	NA	intron (NM_001851, intron 5 of 37)	L2c|LINE|L2	-8369	NM_078485	1297	Hs.590892	NM_001851	ENSG00000112280	COL9A1	DJ149L1.1.2|EDM6|MED|STL4	collagen type IX alpha 1 chain	protein-coding	0.002283	0.346241	
chunk0142_21_1	chr4	90442508	90442976	+	0	NA	intron (NM_001145065, intron 4 of 10)	intron (NM_001145065, intron 4 of 10)	207711	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.004274	0.377399	
chunk0211_232_1	chrX	118855583	118856102	+	0	NA	intron (NR_110393, intron 6 of 6)	intron (NR_110393, intron 6 of 6)	16286	NR_110393	101928287	Hs.496647	NR_110393	ENSG00000203650	LINC01285	-	long intergenic non-protein coding RNA 1285	ncRNA	0.007707	0.438462	259(CAGCACAGGCAGTACT,-,0.00),260(AGCACAGGCAGTACTC,+,0.00),329(AAACACACATTGTCCC,-,0.00),330(AACACACATTGTCCCT,+,0.00)
chunk0127_160_1	chr3	94735582	94735799	+	0	NA	Intergenic	L2|LINE|L2	-202573	NR_015400	255025	Hs.130994	NR_015400	ENSG00000239589	LINC00879	-	long intergenic non-protein coding RNA 879	ncRNA	0.004608	0.325688	
chunk0032_305_1	chr11	9820968	9821269	+	0	NA	intron (NM_030962, intron 28 of 39)	MER4C|LTR|ERV1	-18024	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.009967	0.400662	
chunk0189_37_1	chr8	19767228	19767932	+	0	NA	Intergenic	Intergenic	-49827	NM_018142	55174	Hs.512627	NM_018142	ENSG00000104613	INTS10	C8orf35|INT10	integrator complex subunit 10	protein-coding	0.002841	0.391489	430(AAAGACAGACTGTTCC,-,0.00),431(AAGACAGACTGTTCCC,+,0.00)
chunk0117_210_1	chr22	22010767	22010977	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	-28029	NM_001282112	8940	Hs.436401	NM_003935	ENSG00000100038	TOP3B	TOP3B1	DNA topoisomerase III beta	protein-coding	0.014286	0.450237	93(TGGGACTGTCAGTGCT,-,0.00),94(GGGACTGTCAGTGCTA,+,0.00)
chunk0008_30_1	chr1	88216791	88216990	+	0	NA	Intergenic	Intergenic	-467349	NM_006256	5586	Hs.440833	NM_006256	ENSG00000065243	PKN2	PAK2|PRK2|PRKCL2|PRO2042|Pak-2|STK7	protein kinase N2	protein-coding	0.000000	0.520000	
chunk0042_194_1	chr12	5328363	5328621	+	0	NA	Intergenic	L3|LINE|CR1	-85341	NR_120477	101929584	Hs.436529	NR_120476	ENSG00000256115	LINC02443	-	long intergenic non-protein coding RNA 2443	ncRNA	0.003876	0.351351	
chunk0157_135_1	chr5	117417372	117417726	+	0	NA	intron (NR_046089, intron 1 of 5)	intron (NR_046089, intron 1 of 5)	2037	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.000000	0.309859	
chunk0004_417_1	chr1	52383613	52383893	+	0	NA	intron (NM_001190818, intron 12 of 16)	intron (NM_001190818, intron 12 of 16)	-17548	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.014286	0.526690	
chunk0083_325_1	chr17	69713912	69714316	+	0	NA	intron (NR_109972, intron 3 of 4)	intron (NR_109972, intron 3 of 4)	120127	NR_109972	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.007426	0.375309	
chunk0136_435_1	chr3	197816738	197817240	+	0	NA	intron (NM_032773, intron 2 of 18)	MIRc|SINE|MIR	25763	NM_032773	84859	Hs.518414	NM_032773	ENSG00000186001	LRCH3	-	leucine rich repeats and calponin homology domain containing 3	protein-coding	0.007968	0.337972	
chunk0202_317_1	chr9	78247841	78248279	+	0	NA	intron (NM_032171, intron 6 of 14)	intron (NM_032171, intron 6 of 14)	11985	NM_001098802	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.002283	0.348519	
chunk0098_124_1	chr2	68828871	68829544	+	0	NA	Intergenic	(TTG)n|Simple_repeat|Simple_repeat	42310	NM_014482	27302	Hs.158317	NM_014482	ENSG00000163217	BMP10	-	bone morphogenetic protein 10	protein-coding	0.014859	0.488131	199(TAGGACAATTTGTACT,-,0.00),200(AGGACAATTTGTACTA,+,0.00)
chunk0061_284_1	chr14	61560217	61560561	+	0	NA	intron (NR_110417, intron 3 of 3)	intron (NR_110417, intron 3 of 3)	9805	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.000000	0.420290	
chunk0035_16_1	chr11	40230817	40231246	+	0	NA	intron (NM_020929, intron 3 of 4)	intron (NM_020929, intron 3 of 4)	62099	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.009324	0.388372	
chunk0162_457_1	chr5	180869691	180870055	+	0	NA	Intergenic	Intergenic	-8587	NM_001172638	643836	Hs.509227	NM_152283	ENSG00000196670	ZFP62	ZET|ZNF755	ZFP62 zinc finger protein	protein-coding	0.002747	0.449315	147(GAGAACTGGATGTCCT,-,0.00),148(AGAACTGGATGTCCTC,+,0.00)
chunk0046_157_1	chr12	58309166	58310227	+	0	NA	Intergenic	L1MA9|LINE|L1	-282006	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.004713	0.384181	749(AAGAACACTGAGTCCA,-,0.00),750(AGAACACTGAGTCCAA,+,0.00)
chunk0081_9_1	chr17	37177229	37177543	+	0	NA	intron (NM_198836, intron 41 of 55).2	intron (NM_198836, intron 41 of 55).2	-67415	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.009554	0.431746	
chunk0132_263_1	chr3	159169708	159170223	+	0	NA	intron (NM_001042706, intron 1 of 3)	intron (NM_001042706, intron 1 of 3)	100713	NM_001197114	100505385	Hs.134665	NM_001197113	ENSG00000283154	IQCJ-SCHIP1	-	IQCJ-SCHIP1 readthrough	protein-coding	0.000000	0.434109	
chunk0013_278_1	chr1	170597392	170597696	+	0	NA	Intergenic	L1M4a1|LINE|L1	-64935	NR_125958	101928650	Hs.676662	NR_125958		GORAB-AS1	-	GORAB antisense RNA 1	ncRNA	0.000000	0.321311	
chunk0075_299_1	chr16	54292847	54293391	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-6653	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.005515	0.425688	139(TAGTACAGGATGTTCA,-,0.00),140(AGTACAGGATGTTCAT,+,0.00)
chunk0003_341_1	chr1	39008623	39008822	+	0	NA	Intergenic	Intergenic	17478	NM_001136275	79647	Hs.293563	NM_024595	ENSG00000174574	AKIRIN1	C1orf108|STRF2	akirin 1	protein-coding	0.005025	0.385000	41(AGGAACAGAGTGTAAT,-,0.00)
chunk0176_88_1	chr7	11573640	11574021	+	0	NA	intron (NM_015204, intron 4 of 26)	L2b|LINE|L2	258368	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.007874	0.306283	
chunk0054_419_1	chr13	50914654	50914875	+	0	NA	intron (NM_001142279, intron 1 of 9)	intron (NM_001142279, intron 1 of 9)	-4052	NR_046552	100874255	Hs.741501	NR_046552		RNASEH2B-AS1	-	RNASEH2B antisense RNA 1	ncRNA	0.000000	0.378378	
chunk0196_346_1	chr8	114390624	114391292	+	0	NA	Intergenic	L1M5|LINE|L1	-953945	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.002994	0.298954	
chunk0210_135_1	chrX	74262538	74262802	+	0	NA	intron (NR_028379, intron 5 of 6)	intron (NR_028379, intron 5 of 6)	24539	NR_030258	664614		NR_030258	ENSG00000207820	MIR545	MIRN545|hsa-mir-545|mir-545	microRNA 545	ncRNA	0.003788	0.388679	
chunk0070_457_1	chr15	78461597	78461868	+	0	NA	intron (NM_004136, intron 2 of 21)	intron (NM_004136, intron 2 of 21)	23556	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.007380	0.408088	
chunk0002_162_1	chr1	18298645	18299136	+	0	NA	intron (NM_032880, intron 3 of 9)	L2a|LINE|L2	-182040	NM_152375	127707	Hs.406913	NM_152375	ENSG00000179023	KLHDC7A	-	kelch domain containing 7A	protein-coding	0.018330	0.439024	
chunk0031_148_1	chr10	125060801	125061391	+	0	NA	intron (NM_001290214, intron 2 of 10)	intron (NM_001290214, intron 2 of 10)	-28226	NR_036178	100423041		NR_036178	ENSG00000264572	MIR4296	-	microRNA 4296	ncRNA	0.035593	0.568528	
chunk0025_221_1	chr10	53886553	53887245	+	0	NA	intron (NM_001142769, intron 28 of 35)	intron (NM_001142769, intron 28 of 35)	721058	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.008671	0.393939	
chunk0148_289_1	chr5	11785794	11786028	+	0	NA	intron (NR_109988, intron 1 of 21)	intron (NR_109988, intron 1 of 21)	118132	NM_001332	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.012821	0.582979	109(GGAACAGACTCTTCAT,+,0.00),141(CTGGACAGCCAGTGCC,-,0.00),142(TGGACAGCCAGTGCCC,+,0.00)
chunk0158_178_1	chr5	127802068	127802311	+	0	NA	Intergenic	L2c|LINE|L2	149174	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.004115	0.405738	
chunk0034_378_1	chr11	36396524	36396846	+	0	NA	intron (NM_024841, intron 2 of 9)	MIR|SINE|MIR	-4312	NM_001160169	79899	Hs.19987	NM_024841	ENSG00000135362	PRR5L	PROTOR2	proline rich 5 like	protein-coding	0.006211	0.417957	
chunk0097_21_1	chr2	42249854	42250116	+	0	NA	intron (NM_019063, intron 2 of 22)	MER130|DNA|DNA	-79754	NR_110584	102723824	Hs.639826	NR_110584		LOC102723824	-	uncharacterized LOC102723824	ncRNA	0.007634	0.422053	
chunk0129_362_1	chr3	125348564	125349222	+	0	NA	intron (NM_021964, intron 1 of 8)	L1M3|LINE|L1	26461	NM_021964	7707	Hs.592591	NM_021964	ENSG00000163848	ZNF148	BERF-1|BFCOL1|GDACCF|HT-BETA|ZBP-89|ZFP148|pHZ-52	zinc finger protein 148	protein-coding	0.007599	0.368741	422(AAGAACAGTCTCTTCA,-,0.00)
chunk0171_197_1	chr6	125612433	125612831	+	0	NA	Intergenic	Intergenic	-61721	NR_038906	643623	Hs.520367	NR_038906	ENSG00000224506	LINC02523	-	long intergenic non-protein coding RNA 2523	ncRNA	0.005025	0.350877	
chunk0122_438_1	chr3	39291284	39291812	+	0	NA	Intergenic	MER4C|LTR|ERV1	-9813	NM_001171174	1524	Hs.78913	NM_001337	ENSG00000168329	CX3CR1	CCRL1|CMKBRL1|CMKDR1|GPR13|GPRV28|V28	C-X3-C motif chemokine receptor 1	protein-coding	0.009470	0.446125	232(ATCACAGGTTGTTCTT,+,0.00)
chunk0148_429_1	chr4	188631471	188631691	+	0	NA	Intergenic	CpG	176003	NR_033869	401164	Hs.435756	NR_033869	ENSG00000249378	LINC01060	-	long intergenic non-protein coding RNA 1060	ncRNA	0.063636	0.547511	
chunk0196_207_1	chr8	106582801	106583563	+	0	NA	intron (NM_001198532, intron 2 of 15)	MamRep1151|LTR?|LTR?	-74626	NM_181354	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.003937	0.319790	
chunk0146_60_1	chr4	155778284	155778851	+	0	NA	intron (NM_001291952, intron 5 of 14)	UCON2|DNA?|DNA?	19594	NM_001291955	2983	Hs.77890	NM_000857	ENSG00000061918	GUCY1B1	GC-S-beta-1|GC-SB3|GUC1B3|GUCB3|GUCSB3|GUCY1B3	guanylate cyclase 1 soluble subunit beta 1	protein-coding	0.001764	0.322183	
chunk0210_433_1	chrX	103491569	103492066	+	0	NA	Intergenic	Intergenic	27672	NM_080879	142684	Hs.706904	NM_080879	ENSG00000172476	RAB40A	RAR2|RAR2A	RAB40A, member RAS oncogene family	protein-coding	0.006036	0.407631	
chunk0067_245_1	chr15	45522998	45523635	+	0	NA	promoter-TSS (NM_013309)	promoter-TSS (NM_013309)	-512	NM_013309	7782	Hs.162989	NM_013309	ENSG00000104154	SLC30A4	ZNT4|znT-4	solute carrier family 30 member 4	protein-coding	0.031397	0.467085	
chunk0108_383_1	chr2	237000136	237000379	+	0	NA	Intergenic	MIRb|SINE|MIR	-85184	NM_006710	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.012346	0.528689	126(CAGCACTCACTGTTCC,-,0.00),127(AGCACTCACTGTTCCC,+,0.00)
chunk0203_235_1	chr9	87120520	87121064	+	0	NA	Intergenic	Intergenic	-27852	NM_001001709									0.014706	0.433028	
chunk0141_300_1	chr4	87025687	87025896	+	0	NA	intron (NM_001313960, intron 1 of 17)	intron (NM_001313960, intron 1 of 17)	18790	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.023923	0.504762	
chunk0087_347_1	chr18	40817640	40818213	+	0	NA	Intergenic	Intergenic	702671	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.008726	0.325784	
chunk0001_98_1	chr1	3333824	3334474	+	0	NA	intron (NM_022114, intron 3 of 16)	MIRc|SINE|MIR	-120434	NM_014448	27237	Hs.87435	NM_014448	ENSG00000130762	ARHGEF16	GEF16|NBR	Rho guanine nucleotide exchange factor 16	protein-coding	0.018462	0.560676	277(GGGCACAGCCTGTGAT,-,0.00),278(GGCACAGCCTGTGATT,+,0.00)
chunk0048_412_1	chr12	88238662	88238861	+	0	NA	Intergenic	L1M1|LINE|L1	96465	NM_181783	160418	Hs.331268	NM_181783	ENSG00000139324	TMTC3	LIS8|SMILE	transmembrane O-mannosyltransferase targeting cadherins 3	protein-coding	0.005025	0.565000	
chunk0074_381_1	chr16	34725881	34726122	+	0	NA	Intergenic	Intergenic	444390	NR_002837	606551	Hs.646441	NR_002837		UBE2MP1	-	ubiquitin conjugating enzyme E2 M pseudogene 1	pseudo	0.041494	0.359504	
chunk0086_90_1	chr18	13679048	13679436	+	0	NA	intron (NM_001098801, intron 3 of 4)	intron (NM_001098801, intron 3 of 4)	37484	NM_001276251	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.010309	0.341902	
chunk0208_349_1	chrX	25371660	25372114	+	0	NA	Intergenic	Intergenic	-355939	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.015419	0.437363	
chunk0199_81_1	chr9	2486600	2487289	+	0	NA	Intergenic	L3|LINE|CR1	-134849	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.000000	0.375362	519(CAAGACAAACTGTTCC,-,0.00),520(AAGACAAACTGTTCCA,+,0.00)
chunk0087_265_1	chr18	37261626	37262248	+	0	NA	intron (NM_001025088, intron 10 of 12)	intron (NM_001025088, intron 10 of 12)	204567	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.020900	0.579454	
chunk0090_68_1	chr19	2309741	2309943	+	0	NA	Intergenic	Intergenic	-1685	NM_001101391	645191		NM_001101391	ENSG00000220008	LINGO3	LERN2|LRRN6B	leucine rich repeat and Ig domain containing 3	protein-coding	0.029703	0.635468	
chunk0085_35_1	chr18	567011	567482	+	0	NA	Intergenic	Intergenic	-13097	NM_004066	1068	Hs.122511	NM_004066	ENSG00000177143	CETN1	CEN1|CETN	centrin 1	protein-coding	0.006369	0.394068	
chunk0061_358_1	chr14	63727840	63728398	+	0	NA	promoter-TSS (NM_030791)	promoter-TSS (NM_030791)	-24	NM_030791	81537	Hs.24678	NM_030791	ENSG00000126821	SGPP1	SPP-1|SPPase1	sphingosine-1-phosphate phosphatase 1	protein-coding	0.129032	0.738819	
chunk0089_391_1	chr18	67952897	67953314	+	0	NA	Intergenic	Intergenic	-436375	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.009592	0.461722	
chunk0157_433_1	chr5	124824559	124825189	+	0	NA	Intergenic	Intergenic	-79762	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.007937	0.350238	463(GAAAACAATCTGTTCC,-,0.00),464(AAAACAATCTGTTCCC,+,0.00)
chunk0065_62_1	chr15	22979689	22979939	+	0	NA	intron (NM_001287810, intron 1 of 31)	CpG	605	NM_001287810	23191	Hs.26704	NM_014608	ENSG00000273749	CYFIP1	P140SRA-1|SHYC|SRA-1|SRA1	cytoplasmic FMR1 interacting protein 1	protein-coding	0.060000	0.529880	
chunk0136_133_1	chr4	3911510	3911788	+	0	NA	Intergenic	Intergenic	43779	NR_130741	348926	Hs.591720	NR_024253	ENSG00000251669	FAM86EP	-	family with sequence similarity 86, member A pseudogene	pseudo	0.035971	0.483871	
chunk0077_215_1	chr16	80147938	80148137	+	0	NA	Intergenic	L2a|LINE|L2	352788	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.010050	0.360000	
chunk0061_424_1	chr14	65214872	65215283	+	0	NA	intron (NR_103769, intron 3 of 3)	intron (NR_103769, intron 3 of 3)	7270	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.002433	0.497573	
chunk0006_374_1	chr1	73765655	73765882	+	0	NA	Intergenic	L2c|LINE|L2	432419	NM_001105659	127255	Hs.644625	NM_145258	ENSG00000162620	LRRIQ3	LRRC44	leucine rich repeats and IQ motif containing 3	protein-coding	0.000000	0.368421	
chunk0067_376_1	chr15	48959330	48959605	+	0	NA	intron (NM_203349, intron 1 of 11)	L2a|LINE|L2	3977	NM_203349	399694	Hs.642615	NM_203349	ENSG00000185634	SHC4	RaLP|SHCD	SHC adaptor protein 4	protein-coding	0.000000	0.380435	
chunk0067_367_1	chr15	48781389	48782138	+	0	NA	intron (NM_001194998, intron 11 of 26)	intron (NM_001194998, intron 11 of 26)	29383	NM_014985	22995	Hs.443005	NM_014985	ENSG00000103995	CEP152	MCPH4|MCPH9|SCKL5	centrosomal protein 152	protein-coding	0.006676	0.422667	311(AAGAACAGGTTGTACT,-,0.00),312(AGAACAGGTTGTACTT,+,0.00)
chunk0178_459_1	chr7	42089883	42090611	+	0	NA	intron (NM_000168, intron 3 of 14)	Tigger3c|DNA|TcMar-Tigger	146772	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.009615	0.401920	
chunk0154_282_1	chr5	82573997	82574594	+	0	NA	Intergenic	Intergenic	-265860	NR_039773	100616297		NR_039773	ENSG00000283359	MIR3977	-	microRNA 3977	ncRNA	0.006700	0.321070	
chunk0209_137_1	chrX	41614059	41614586	+	0	NA	intron (NM_001126055, intron 10 of 24)	MER66B|LTR|ERV1	-74651	NM_001097579	2857	Hs.495989	NM_005300	ENSG00000171659	GPR34	LYPSR1	G protein-coupled receptor 34	protein-coding	0.005693	0.382576	
chunk0007_3_1	chr1	77160266	77160877	+	0	NA	intron (NM_005482, intron 8 of 10)	intron (NM_005482, intron 8 of 10)	58876	NM_005482	10026	Hs.178305	NM_005482	ENSG00000142892	PIGK	GPI8	phosphatidylinositol glycan anchor biosynthesis class K	protein-coding	0.001637	0.346405	271(AGGAACAGCCTGTGCT,-,0.00),272(GGAACAGCCTGTGCTT,+,0.00)
chunk0187_303_1	chr7	156258209	156258408	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	187280	NR_038232	285889	Hs.407095	NR_038232	ENSG00000182648	LOC285889	-	uncharacterized LOC285889	ncRNA	0.005025	0.485000	
chunk0150_286_1	chr5	37073956	37074182	+	0	NA	Intergenic	HAL1|LINE|L1	175359	NM_023073	65250	Hs.586199	NM_023073	ENSG00000197603	CPLANE1	C5orf42|Hug|JBTS17|OFD6	ciliogenesis and planar polarity effector 1	protein-coding	0.004425	0.308370	
chunk0045_415_1	chr12	53157675	53158349	+	0	NA	3' UTR (NM_001244705, exon 17 of 17)	3' UTR (NM_001244705, exon 17 of 17)	6481	NM_001244706	51380	Hs.279815	NM_015989	ENSG00000139631	CSAD	CSD|PCAP	cysteine sulfinic acid decarboxylase	protein-coding	0.005935	0.336296	
chunk0032_366_1	chr11	10808820	10809329	+	0	NA	promoter-TSS (NM_001418)	promoter-TSS (NM_001418)	-39	NM_001042559	1982	Hs.183684	NM_001418	ENSG00000110321	EIF4G2	AAG1|DAP5|NAT1|P97	eukaryotic translation initiation factor 4 gamma 2	protein-coding	0.080550	0.623529	
chunk0091_101_1	chr19	5805567	5806307	+	0	NA	Intergenic	CpG	-14699	NM_020175	56931	Hs.284297	NM_020175	ENSG00000141994	DUS3L	DUS3	dihydrouridine synthase 3 like	protein-coding	0.059459	0.643725	390(GGGGACACGGTGTCCT,-,0.00),391(GGGACACGGTGTCCTC,+,0.00)
chunk0143_59_1	chr4	107751712	107751911	+	0	NA	Intergenic	Intergenic	-31548	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.010050	0.360000	86(AAGAACAGAAAGTTTC,-,0.00),87(AGAACAGAAAGTTTCT,+,0.00)
chunk0093_113_1	chr19	44547820	44548383	+	0	NA	intron (NR_027754, intron 2 of 7)	intron (NR_027754, intron 2 of 7)	8816	NR_027754	388550	Hs.446909	NR_027754	ENSG00000230666	CEACAM22P	-	carcinoembryonic antigen related cell adhesion molecule 22, pseudogene	pseudo	0.005329	0.379433	390(AAGCACTTAGTGTGCA,-,0.00)
chunk0018_43_1	chr1	215728843	215729342	+	0	NA	intron (NM_206933, intron 60 of 71)	MLT1H2|LTR|ERVL-MaLR	161700	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.006012	0.398000	
chunk0052_75_1	chr13	21683704	21683903	+	0	NA	intron (NM_002010, intron 2 of 2)	intron (NM_002010, intron 2 of 2)	12727	NM_002010	2254	Hs.111	NM_002010	ENSG00000102678	FGF9	FGF-9|GAF|HBFG-9|HBGF-9|SYNS3	fibroblast growth factor 9	protein-coding	0.015075	0.475000	
chunk0100_448_1	chr2	120955352	120956013	+	0	NA	intron (NM_005270, intron 4 of 12)	L2a|LINE|L2	158391	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.022693	0.580060	
chunk0204_318_1	chr9	100465900	100466518	+	0	NA	intron (NM_001198812, intron 1 of 9)	intron (NM_001198812, intron 1 of 9)	-7029	NM_003692	8577	Hs.598100	NM_003692	ENSG00000241697	TMEFF1	C9orf2|CT120.1|H7365|TR-1	transmembrane protein with EGF like and two follistatin like domains 1	protein-coding	0.000000	0.431341	345(GAAACATCTTGTCCTT,+,0.00)
chunk0026_229_1	chr10	65237798	65237997	+	0	NA	Intergenic	L1M5|LINE|L1	-333528	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.000000	0.260000	167(AAATACACCATGTTCC,-,0.00),168(AATACACCATGTTCCC,+,0.00)
chunk0002_418_1	chr1	27755784	27756306	+	0	NA	intron (NM_152660, intron 7 of 8)	MamRep605|LTR?|LTR?	-17138	NM_177424	23673	Hs.523855	NM_177424	ENSG00000117758	STX12	STX13|STX14	syntaxin 12	protein-coding	0.007663	0.428298	
chunk0105_140_1	chr2	186140966	186141438	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-54885	NR_110218	101927217	Hs.130011	NR_110218	ENSG00000237877	LINC01473	-	long intergenic non-protein coding RNA 1473	ncRNA	0.004237	0.386892	
chunk0008_426_1	chr1	99306539	99306754	+	0	NA	exon (NM_014839, exon 7 of 7)	exon (NM_014839, exon 7 of 7)	42354	NM_001166252	9890	Hs.13245	NM_014839	ENSG00000117600	PLPPR4	LPPR4|LPR4|PHP1|PRG-1|PRG1	phospholipid phosphatase related 4	protein-coding	0.023256	0.532407	
chunk0156_392_1	chr5	113215426	113215671	+	0	NA	intron (NM_001085377, intron 3 of 18)	MLT1A1|LTR|ERVL-MaLR	79367	NM_002387	4163	Hs.593171	NM_002387	ENSG00000171444	MCC	MCC1	MCC regulator of WNT signaling pathway	protein-coding	0.016327	0.508130	190(GAGGACACAGTGTTCT,-,0.00),191(AGGACACAGTGTTCTT,+,0.00)
chunk0126_212_1	chr3	78774472	78775093	+	0	NA	intron (NM_133631, intron 2 of 28)	intron (NM_133631, intron 2 of 28)	244677	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004831	0.300643	
chunk0019_108_1	chr1	225065311	225066042	+	0	NA	intron (NM_001373, intron 17 of 83)	L1MA7|LINE|L1	136015	NM_144989	127602	Hs.133977	NM_001373	ENSG00000185842	DNAH14	C1orf67|Dnahc14|HL-18|HL18	dynein axonemal heavy chain 14	protein-coding	0.000000	0.337432	
chunk0035_323_1	chr11	47517269	47517647	+	0	NA	intron (NM_001172639, intron 1 of 15)	L1MC4a|LINE|L1	6530	NM_001172639	10658	Hs.595333	NM_006560	ENSG00000149187	CELF1	BRUNOL2|CUG-BP|CUGBP|CUGBP1|EDEN-BP|NAB50|NAPOR|hNab50	CUGBP Elav-like family member 1	protein-coding	0.005291	0.324538	
chunk0123_142_1	chr3	42825559	42826266	+	0	NA	intron (NM_001296, intron 2 of 2)	L1MB7|LINE|L1	16440	NM_001296	1238	Hs.146346	NM_001296	ENSG00000144648	ACKR2	CCBP2|CCR10|CCR9|CMKBR9|D6|hD6	atypical chemokine receptor 2	protein-coding	0.005658	0.358757	
chunk0197_194_1	chr8	121506985	121507184	+	0	NA	Intergenic	Intergenic	-132262	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.005025	0.445000	
chunk0020_104_1	chr1	233006652	233007089	+	0	NA	intron (NM_014801, intron 28 of 33)	intron (NM_014801, intron 28 of 33)	56246	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.009153	0.458904	
chunk0026_308_1	chr10	68046310	68046598	+	0	NA	intron (NM_022079, intron 3 of 25)	intron (NM_022079, intron 3 of 25)	28892	NM_015601	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.006944	0.363322	
chunk0093_106_1	chr19	43786802	43787039	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	-5663	NM_002250	3783	Hs.10082	NM_002250	ENSG00000104783	KCNN4	DHS2|IK|IK1|IKCA1|KCA4|KCa3.1|SK4|hIKCa1|hKCa4|hSK4	potassium calcium-activated channel subfamily N member 4	protein-coding	0.004219	0.466387	78(AGGAACAGTATGTTCC,-,0.00),79(GGAACAGTATGTTCCT,+,0.00)
chunk0205_47_1	chr9	105965512	105965941	+	0	NA	Intergenic	Intergenic	271201	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.004662	0.376744	
chunk0181_181_1	chr7	83109202	83109499	+	0	NA	intron (NM_014510, intron 3 of 19)	intron (NM_014510, intron 3 of 19)	53531	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.003367	0.359060	
chunk0105_52_1	chr2	183035386	183035787	+	0	NA	intron (NM_205842, intron 1 of 31)	intron (NM_205842, intron 1 of 31)	3272	NM_205842	10787	Hs.603732	NM_013436	ENSG00000061676	NCKAP1	HEM2|NAP1|NAP125|p125Nap1	NCK associated protein 1	protein-coding	0.000000	0.340796	
chunk0034_234_1	chr11	33743706	33743984	+	0	NA	intron (NM_012175, intron 10 of 10)	L2a|LINE|L2	-7366	NM_203330	966	Hs.278573	NM_000611	ENSG00000085063	CD59	16.3A5|1F5|EJ16|EJ30|EL32|G344|HRF-20|HRF20|MAC-IP|MACIF|MEM43|MIC11|MIN1|MIN2|MIN3|MIRL|MSK21|p18-20	CD59 molecule (CD59 blood group)	protein-coding	0.014388	0.372760	171(AAGGACATAGTGTTTA,-,0.00),172(AGGACATAGTGTTTAT,+,0.00)
chunk0170_72_1	chr6	109804498	109805171	+	0	NA	intron (NM_014845, intron 22 of 22)	intron (NM_014845, intron 22 of 22)	-51618	NR_106988									0.001486	0.313056	289(GGGAACAGAAAGTCCT,-,0.00),290(GGAACAGAAAGTCCTT,+,0.00)
chunk0101_243_1	chr2	131556269	131556620	+	0	NA	Intergenic	L1PA16|LINE|L1	28610	NM_001258306	90557	Hs.351461	NM_138770	ENSG00000163040	CCDC74A	-	coiled-coil domain containing 74A	protein-coding	0.008547	0.400568	
chunk0154_354_1	chr5	87245316	87245799	+	0	NA	intron (NR_105018, intron 3 of 3)	intron (NR_105018, intron 3 of 3)	-6356	NR_130914	55338	Hs.677194	NM_018382		LINC01949	-	long intergenic non-protein coding RNA 1949	ncRNA	0.006211	0.376033	
chunk0013_272_1	chr1	170225569	170226134	+	0	NA	Intergenic	Intergenic	58357	NR_026957	284688	Hs.135668	NR_026957	ENSG00000224286	LINC01142	-	long intergenic non-protein coding RNA 1142	ncRNA	0.001770	0.397527	339(AGGCACACACTGTTTA,-,0.00),340(GGCACACACTGTTTAG,+,0.00)
chunk0177_366_1	chr7	26716484	26716941	+	0	NA	intron (NM_001303468, intron 9 of 12)	L1MEi|LINE|L1	77627	NM_001302625									0.006565	0.305677	
chunk0108_21_1	chr2	226378753	226379364	+	0	NA	Intergenic	Intergenic	236264	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.003273	0.356209	
chunk0017_300_1	chr1	211095192	211095540	+	0	NA	intron (NM_002238, intron 3 of 10)	intron (NM_002238, intron 3 of 10)	38749	NM_172362	3756	Hs.553187	NM_002238	ENSG00000143473	KCNH1	EAG|EAG1|Kv10.1|TMBTS|ZLS1|h-eag|hEAG1	potassium voltage-gated channel subfamily H member 1	protein-coding	0.002874	0.455587	
chunk0084_397_1	chr17	82133946	82134575	+	0	NA	intron (NM_198082, intron 14 of 16)	intron (NM_198082, intron 14 of 16)	-36030	NM_004104	2194	Hs.83190	NM_004104	ENSG00000169710	FASN	FAS|OA-519|SDR27X1	fatty acid synthase	protein-coding	0.022258	0.504762	328(AAGAACAGCATGTTCC,-,0.00),329(AGAACAGCATGTTCCT,+,0.00)
chunk0201_289_1	chr9	40991778	40992505	+	0	NA	promoter-TSS (NR_034006)	promoter-TSS (NR_034006)	-196	NR_034006	100132352	Hs.231861	NR_034006		FRG1HP	-	FSHD region gene 1 family member H, pseudogene	pseudo	0.074278	0.638736	
chunk0097_383_1	chr2	61630793	61631416	+	0	NA	Intergenic	Intergenic	-92821	NM_003400	7514	Hs.370770	NM_003400	ENSG00000082898	XPO1	CRM-1|CRM1|emb|exp1	exportin 1	protein-coding	0.016051	0.455128	162(TAGCACAGTGTGTATC,-,0.00),163(AGCACAGTGTGTATCT,+,0.00)
chunk0187_316_1	chr7	156595164	156595373	+	0	NA	intron (NR_103858, intron 1 of 1)	intron (NR_103858, intron 1 of 1)	7927	NR_103858	100506380	Hs.647014	NM_032625	ENSG00000182648	LINC01006	C7orf13|MY040	long intergenic non-protein coding RNA 1006	ncRNA	0.009569	0.538095	
chunk0158_172_1	chr5	127700214	127700986	+	0	NA	Intergenic	Intergenic	47585	NM_001127385	613212	Hs.66194	NM_001048252	ENSG00000205279	CTXN3	KABE	cortexin 3	protein-coding	0.015544	0.416559	
chunk0199_373_1	chr9	12888162	12888650	+	0	NA	Intergenic	L1MA2|LINE|L1	-74017	NR_125775	101929467	Hs.586443	NR_125775	ENSG00000235448	LURAP1L-AS1	-	LURAP1L antisense RNA 1	ncRNA	0.004098	0.503067	
chunk0062_72_1	chr14	67696887	67697370	+	0	NA	Intergenic	L2b|LINE|L2	-1335	NM_016026	51109	Hs.719925	NM_016026	ENSG00000072042	RDH11	ARSDR1|CGI82|HCBP12|MDT1|PSDR1|RALR1|RDJCSS|SCALD|SDR7C1	retinol dehydrogenase 11	protein-coding	0.008282	0.382231	
chunk0042_286_1	chr12	7398175	7398406	+	0	NA	exon (NM_001297650, exon 7 of 20)	exon (NM_001297650, exon 7 of 20)	45895	NM_001297650	283316	Hs.631727	NM_174941	ENSG00000177675	CD163L1	CD163B|M160|SCARI2|WC1	CD163 molecule like 1	protein-coding	0.004329	0.396552	
chunk0055_445_1	chr13	75643125	75643795	+	0	NA	intron (NM_001306080, intron 1 of 30)	L2a|LINE|L2	7172	NM_001306080	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.004478	0.380030	
chunk0079_387_1	chr17	18855797	18856123	+	0	NA	promoter-TSS (NM_001243942)	promoter-TSS (NM_001243942)	-339	NM_001243936	5636	Hs.632236	NM_002767	ENSG00000141127	PRPSAP2	PAP41	phosphoribosyl pyrophosphate synthetase associated protein 2	protein-coding	0.030675	0.559633	63(AGGAACAGCATGTGTC,-,0.00),64(GGAACAGCATGTGTCC,+,0.00)
chunk0013_334_1	chr1	171753908	171754608	+	0	NA	Intergenic	Intergenic	-12019	NR_033704	8674	Hs.6651	NM_003762	ENSG00000117533	VAMP4	VAMP-4|VAMP24	vesicle associated membrane protein 4	protein-coding	0.004286	0.452211	280(TGTACTGTTTGTTCCT,+,0.00)
chunk0112_238_1	chr20	41248630	41249196	+	0	NA	intron (NM_015035, intron 2 of 3)	intron (NM_015035, intron 2 of 3)	51186	NM_015035	23051	Hs.380133	NM_015035	ENSG00000174306	ZHX3	TIX1	zinc fingers and homeoboxes 3	protein-coding	0.005300	0.368607	173(GAGAACAAACTGTTCT,-,0.00),174(AGAACAAACTGTTCTC,+,0.00)
chunk0119_51_1	chr22	40751254	40751530	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	62566	NR_039923	100616283		NR_039923	ENSG00000266594	MIR4766	mir-4766	microRNA 4766	ncRNA	0.007246	0.339350	145(TAGAAGAGAATGTTCT,-,0.00),146(AGAAGAGAATGTTCTC,+,0.00)
chunk0015_281_1	chr1	188579433	188579671	+	0	NA	Intergenic	Intergenic	1135924	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004202	0.284519	
chunk0031_142_1	chr10	125008337	125009127	+	0	NA	intron (NM_001290215, intron 3 of 10)	LTR10C|LTR|ERV1	19152	NM_022802	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.020253	0.475348	
chunk0170_13_1	chr6	109094791	109095473	+	0	NA	promoter-TSS (NM_014454)	promoter-TSS (NM_014454)	-21	NM_001271852	285753	Hs.632616	NM_173830	ENSG00000183137	CEP57L1	C6orf182|bA487F23.2|cep57R	centrosomal protein 57 like 1	protein-coding	0.086510	0.636896	
chunk0195_256_1	chr8	97931334	97931935	+	0	NA	intron (NM_030583, intron 3 of 18)	L2a|LINE|L2	62551	NM_030583	4147	Hs.189445	NM_002380	ENSG00000132561	MATN2	-	matrilin 2	protein-coding	0.014975	0.485050	
chunk0002_168_1	chr1	18670200	18670516	+	0	NA	intron (NM_002584, intron 4 of 7)	intron (NM_002584, intron 4 of 7)	39352	NM_001135254	5081	Hs.113253	NM_002584	ENSG00000009709	PAX7	HUP1|PAX7B|RMS2	paired box 7	protein-coding	0.006329	0.529968	
chunk0202_243_1	chr9	76662608	76663347	+	0	NA	intron (NM_015225, intron 9 of 18)	intron (NM_015225, intron 9 of 18)	29438	NM_001308051	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.006766	0.429730	
chunk0120_371_1	chr3	11846476	11847112	+	0	NA	non-coding (NR_104314, exon 1 of 10)	non-coding (NR_104314, exon 1 of 10)	125	NR_104314	132001	Hs.475472	NM_138807	ENSG00000144559	TAMM41	C3orf31|RAM41|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding	0.084906	0.643642	
chunk0016_429_1	chr1	203721342	203721725	+	0	NA	intron (NM_001001396, intron 17 of 21)	intron (NM_001001396, intron 17 of 21)	-8048	NR_003019	677843	Hs.676135	NR_003019	ENSG00000221643	SNORA77	ACA63|SNORA77A	small nucleolar RNA, H/ACA box 77	snoRNA	0.018277	0.473958	248(GAGTACAGTGTGTACT,-,0.00),249(AGTACAGTGTGTACTG,+,0.00)
chunk0109_244_1	chr20	6031872	6032314	+	0	NA	intron (NM_001127458, intron 5 of 6)	intron (NM_001127458, intron 5 of 6)	21987	NM_152611	164312	Hs.149133	NM_152611	ENSG00000125872	LRRN4	C20orf75|NLRR-4|NLRR4|dJ1056H1.1	leucine rich repeat neuronal 4	protein-coding	0.006787	0.322799	
chunk0051_209_1	chr12	116509320	116509891	+	0	NA	Intergenic	MER96B|DNA|hAT-Tip100	-23817	NR_027345	100287569	Hs.441601	NM_207436	ENSG00000196668	LINC00173	NCRNA00173	long intergenic non-protein coding RNA 173	ncRNA	0.010508	0.389860	
chunk0152_287_1	chr5	61538959	61539600	+	0	NA	intron (NM_020928, intron 11 of 13)	intron (NM_020928, intron 11 of 13)	-98502	NM_173667									0.004680	0.373832	
chunk0043_353_1	chr12	23169529	23169735	+	0	NA	Intergenic	Intergenic	-6004	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.004854	0.439614	
chunk0066_385_1	chr15	38895072	38895752	+	0	NA	Intergenic	L2a|LINE|L2	198814	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.002941	0.336270	
chunk0048_162_1	chr12	80691299	80691818	+	0	NA	Intergenic	Intergenic	-16071	NM_002469	4618	Hs.35937	NM_002469	ENSG00000111046	MYF6	CNM3|MRF4|bHLHc4|myf-6	myogenic factor 6	protein-coding	0.003854	0.332692	
chunk0196_98_1	chr8	103038078	103038277	+	0	NA	intron (NM_001695, intron 1 of 12)	MLT1H2|LTR|ERVL-MaLR	17157	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.005025	0.485000	
chunk0030_367_1	chr10	118851518	118851717	+	0	NA	Intergenic	Intergenic	-96371	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.000000	0.525000	
chunk0086_287_1	chr18	23742077	23742322	+	0	NA	intron (NR_130106, intron 2 of 12)	L1MC4|LINE|L1	52756	NR_130106	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.008163	0.426829	
chunk0198_3_1	chr9	261436	261866	+	0	NA	intron (NM_203447, intron 1 of 47)	L1MEg|LINE|L1	-11397	NM_001190458	81704	Hs.132599	NM_203447	ENSG00000107099	DOCK8	HEL-205|MRD2|ZIR8	dedicator of cytokinesis 8	protein-coding	0.004651	0.336427	
chunk0051_328_1	chr12	120117991	120118612	+	0	NA	Intergenic	L1ME4b|LINE|L1	-1462	NM_006861	11021	Hs.524788	NM_006861	ENSG00000111737	RAB35	H-ray|RAB1C|RAY	RAB35, member RAS oncogene family	protein-coding	0.017713	0.413183	
chunk0188_159_1	chr8	10520421	10520662	+	0	NA	Intergenic	Intergenic	-5005	NM_198464	203074	Hs.591394	NM_198464	ENSG00000184647	PRSS55	CT153|T-SP1|TSP1|UNQ9391	serine protease 55	protein-coding	0.016598	0.479339	165(AGGAACACCAAGTGCC,-,0.00),166(GGAACACCAAGTGCCC,+,0.00)
chunk0030_245_1	chr10	115248385	115248746	+	0	NA	intron (NM_207303, intron 10 of 28)	intron (NM_207303, intron 10 of 28)	155200	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.008310	0.279006	
chunk0100_380_1	chr2	118114677	118115323	+	0	NA	Intergenic	Intergenic	26526	NM_016133	51141	Hs.7089	NM_016133	ENSG00000125629	INSIG2	INSIG-2	insulin induced gene 2	protein-coding	0.006192	0.397218	
chunk0042_30_1	chr12	1457907	1458122	+	0	NA	intron (NM_178040, intron 18 of 18)	intron (NM_178040, intron 18 of 18)	-42477	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.000000	0.490741	
chunk0040_90_1	chr11	111640051	111640688	+	0	NA	intron (NM_015191, intron 3 of 14)	intron (NM_015191, intron 3 of 14)	37978	NM_015191	23235	Hs.269128	NM_015191	ENSG00000170145	SIK2	LOH11CR1I|QIK|SIK-2|SNF1LK2	salt inducible kinase 2	protein-coding	0.001570	0.343260	
chunk0008_194_1	chr1	93324488	93325133	+	0	NA	intron (NR_034089, intron 7 of 8)	L3b|LINE|CR1	21001	NR_034089	100131564	Hs.732666	NR_034089		CCDC18-AS1	-	CCDC18 antisense RNA 1	ncRNA	0.004651	0.368421	
chunk0184_239_1	chr7	117665342	117665796	+	0	NA	intron (NM_000492, intron 26 of 26)	intron (NM_000492, intron 26 of 26)	185606	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.000000	0.314286	
chunk0132_215_1	chr3	157626819	157627358	+	0	NA	Intergenic	Intergenic	83744	NR_024016	152078	Hs.259046	NM_001099777	ENSG00000174899	SLC66A1L	C3orf55|PQLC2L|SLC66A2L	solute carrier family 66 member 1 like	protein-coding	0.005566	0.425926	
chunk0204_131_1	chr9	95284016	95284469	+	0	NA	intron (NM_001243744, intron 1 of 13)	intron (NM_001243744, intron 1 of 13)	33012	NM_001243743	2176	Hs.494529	NM_000136	ENSG00000158169	FANCC	FA3|FAC|FACC	FA complementation group C	protein-coding	0.008830	0.374449	
chunk0038_58_1	chr11	82902477	82902986	+	0	NA	intron (NM_145018, intron 1 of 5)	L2c|LINE|L2	1036	NM_145018	220042	Hs.165607	NM_145018	ENSG00000165490	DDIAS	C11orf82|noxin	DNA damage induced apoptosis suppressor	protein-coding	0.009823	0.427451	
chunk0180_60_1	chr7	54822076	54822403	+	0	NA	Intergenic	Intergenic	62926	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.003058	0.240854	
chunk0194_144_1	chr8	84492159	84492801	+	0	NA	intron (NM_001100392, intron 2 of 9)	intron (NM_001100392, intron 2 of 9)	-213447	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.001558	0.300156	
chunk0208_251_1	chrX	20261266	20261882	+	0	NA	intron (NM_004586, intron 1 of 21)	intron (NM_004586, intron 1 of 21)	5058	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.003247	0.294976	
chunk0028_23_1	chr10	82548877	82549223	+	0	NA	intron (NM_001010848, intron 2 of 8)	MIRb|SINE|MIR	-316130	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.002890	0.406340	
chunk0058_442_1	chr13	113449729	113449975	+	0	NA	promoter-TSS (NM_199162)	promoter-TSS (NM_199162)	-710	NM_199162	113622	Hs.98669	NM_138430	ENSG00000153531	ADPRHL1	ARH2	ADP-ribosylhydrolase like 1	protein-coding	0.024390	0.522267	
chunk0019_8_1	chr1	223286654	223286961	+	0	NA	intron (NM_001037175, intron 3 of 5)	intron (NM_001037175, intron 3 of 5)	77395	NM_017982	55061	Hs.497841	NM_017982	ENSG00000143502	SUSD4	PRO222	sushi domain containing 4	protein-coding	0.013029	0.474026	
chunk0166_66_1	chr6	42960633	42961374	+	0	NA	intron (NM_018960, intron 1 of 5)	CpG	241	NM_018960	27232	Hs.144914	NM_018960	ENSG00000124713	GNMT	HEL-S-182mP	glycine N-methyltransferase	protein-coding	0.075574	0.665768	138(GTGGACAGCGTGTACC,-,0.00),139(TGGACAGCGTGTACCG,+,0.00),504(AGGCACTGCGAGTGCC,-,0.00)
chunk0037_96_1	chr11	72040604	72040947	+	0	NA	intron (NM_006185, intron 2 of 26)	intron (NM_006185, intron 2 of 26)	26484	NR_104178	100128494	Hs.713607	NR_104178	ENSG00000251143	LOC100128494	-	uncharacterized LOC100128494	ncRNA	0.034985	0.540698	
chunk0157_87_1	chr5	116571481	116571932	+	0	NA	intron (NM_001300780, intron 1 of 19)	intron (NM_001300780, intron 1 of 19)	3220	NM_020796	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.008869	0.327434	
chunk0109_129_1	chr20	2996334	2996854	+	0	NA	intron (NM_080840, intron 8 of 22)	L1ME3G|LINE|L1	-47028	NM_001501	2797	Hs.129715	NM_001501	ENSG00000125787	GNRH2	GnRH-II|LH-RHII	gonadotropin releasing hormone 2	protein-coding	0.001923	0.353167	
chunk0012_402_1	chr1	163917074	163917402	+	0	NA	Intergenic	L1M2c|LINE|L1	-494047	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.006098	0.510638	
chunk0209_245_1	chrX	45748078	45748307	+	0	NA	Intergenic	L2a|LINE|L2	-1068	NR_029636	407007		NR_029636	ENSG00000207725	MIR222	MIRN222|miRNA222|mir-222	microRNA 222	ncRNA	0.004367	0.417391	116(TTGGACAAGGTGTTCT,-,0.00),117(TGGACAAGGTGTTCTT,+,0.00)
chunk0071_269_1	chr15	85607489	85608154	+	0	NA	intron (NM_007200, intron 8 of 36)	intron (NM_007200, intron 8 of 36)	-12129	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.004511	0.361862	
chunk0161_360_1	chr5	175493430	175493632	+	0	NA	intron (NM_022754, intron 2 of 10)	intron (NM_022754, intron 2 of 10)	15020	NM_022754	94081	Hs.369440	NM_022754	ENSG00000164466	SFXN1	SLC56A1|TCC	sideroflexin 1	protein-coding	0.029703	0.438424	
chunk0159_127_1	chr5	138983800	138984317	+	0	NA	intron (NM_001037633, intron 8 of 10)	intron (NM_001037633, intron 8 of 10)	-108690	NM_015564	26045	Hs.656653	NM_015564	ENSG00000146006	LRRTM2	-	leucine rich repeat transmembrane neuronal 2	protein-coding	0.001934	0.490347	
chunk0009_112_1	chr1	102736482	102736824	+	0	NA	Intergenic	Intergenic	371843	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.011696	0.338192	
chunk0157_28_1	chr5	115558143	115559127	+	0	NA	Intergenic	Intergenic	-13741	NM_020177	56929	Hs.47367	NM_020177	ENSG00000145780	FEM1C	EUROIMAGE686608|EUROIMAGE783647|FEM1A	fem-1 homolog C	protein-coding	0.006098	0.383756	640(GAGAACATTCTGTGCT,-,0.00),641(AGAACATTCTGTGCTG,+,0.00),689(AAGAACAAAATGTCCA,-,0.00),690(AGAACAAAATGTCCAC,+,0.00)
chunk0117_2_1	chr22	10694180	10694736	+	0	NA	Intergenic	L1MB4|LINE|L1	267071	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.008993	0.362657	
chunk0094_212_1	chr2	6611408	6612037	+	0	NA	Intergenic	L1PA7|LINE|L1	22065	NR_110500	102800315	Hs.729713	NR_110498	ENSG00000236172	LINC01246	-	long intergenic non-protein coding RNA 1246	ncRNA	0.006359	0.366667	
chunk0059_27_1	chr14	29845717	29846282	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	81694	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.001770	0.298587	
chunk0184_170_1	chr7	116339562	116340102	+	0	NA	Intergenic	Intergenic	-53105	NR_130922	102724434	Hs.667624	NR_130921	ENSG00000237870	LOC102724434	-	uncharacterized LOC102724434	ncRNA	0.005556	0.369686	266(CAGGTCACCTTGTTCT,-,0.00),267(AGGTCACCTTGTTCTA,+,0.00)
chunk0015_122_1	chr1	185404722	185404921	+	0	NA	Intergenic	Intergenic	-69782	NR_038424	100288079	Hs.131220	NR_038424	ENSG00000261024	GS1-279B7.1	-	microtubule associated protein 1 light chain 3 beta pseudogene	pseudo	0.005025	0.300000	
chunk0186_64_1	chr7	136999560	137000022	+	0	NA	intron (NM_001006626, intron 4 of 4)	intron (NM_001006626, intron 4 of 4)	96624	NR_030165	574443		NR_030165	ENSG00000207597	MIR490	MIRN490|hsa-mir-490|miR-490	microRNA 490	ncRNA	0.006494	0.360691	
chunk0032_136_1	chr11	4606176	4606941	+	0	NA	intron (NM_018073, intron 1 of 6)	intron (NM_018073, intron 1 of 6)	1701	NM_001304496	55128	Hs.523438	NM_018073	ENSG00000167333	TRIM68	GC109|RNF137|SS-56|SS56	tripartite motif containing 68	protein-coding	0.001307	0.406005	257(AGGGACATGTTGATCC,-,0.00),258(GGGACATGTTGATCCT,+,0.00)
chunk0025_188_1	chr10	53237043	53237367	+	0	NA	Intergenic	Intergenic	-465505	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.003086	0.381538	
chunk0194_308_1	chr8	88110571	88111488	+	0	NA	intron (NM_005941, intron 6 of 9)	L2a|LINE|L2	216459	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.007634	0.336601	
chunk0187_436_1	chr7	158796630	158796829	+	0	NA	intron (NM_020728, intron 3 of 21)	intron (NM_020728, intron 3 of 21)	32899	NM_020728	57488	Hs.490795	NM_020728	ENSG00000117868	ESYT2	CHR2SYT|E-Syt2|FAM62B	extended synaptotagmin 2	protein-coding	0.060302	0.645000	
chunk0046_94_1	chr12	56695811	56696012	+	0	NA	Intergenic	Intergenic	-7503	NM_001282604	10728	Hs.50425	NM_006601	ENSG00000110958	PTGES3	P23|TEBP|cPGES	prostaglandin E synthase 3	protein-coding	0.004975	0.391089	
chunk0052_64_1	chr13	21202911	21203570	+	0	NA	Intergenic	Intergenic	-26638	NM_001166017	221150	Hs.88523	NM_145061	ENSG00000165480	SKA3	C13orf3|RAMA1	spindle and kinetochore associated complex subunit 3	protein-coding	0.003035	0.483333	
chunk0150_61_1	chr5	32017373	32018003	+	0	NA	intron (NM_178140, intron 5 of 23)	intron (NM_178140, intron 5 of 23)	-81529	NR_036241	100422874		NR_036241	ENSG00000266243	MIR4279	-	microRNA 4279	ncRNA	0.006349	0.424723	239(GAGAACACAGTGTCCC,-,0.00),240(AGAACACAGTGTCCCT,+,0.00)
chunk0059_88_1	chr14	30779241	30779553	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-95138	NM_004086	1690	Hs.21016	NM_004086	ENSG00000100473	COCH	COCH-5B2|COCH5B2|DFNA9|DFNB110	cochlin	protein-coding	0.000000	0.354633	
chunk0115_119_1	chr21	23008061	23008827	+	0	NA	Intergenic	Intergenic	-70840	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.005222	0.409387	
chunk0209_367_1	chrX	54011071	54012068	+	0	NA	intron (NM_001184897, intron 7 of 21)	intron (NM_001184897, intron 7 of 21)	31625	NM_001184898	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.006018	0.370741	
chunk0210_28_1	chrX	67612312	67612655	+	0	NA	intron (NM_001011645, intron 1 of 7)	intron (NM_001011645, intron 1 of 7)	43642	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.008746	0.459302	
chunk0194_229_1	chr8	86263230	86263714	+	0	NA	Intergenic	MER21C|LTR|ERVL	-33097	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.004132	0.426804	
chunk0181_340_1	chr7	88226851	88227373	+	0	NA	promoter-TSS (NM_001256892)	promoter-TSS (NM_001256892)	-119	NM_001256892	6717	Hs.489040	NM_003130	ENSG00000075142	SRI	CP-22|CP22|SCN|V19	sorcin	protein-coding	0.001916	0.378585	
chunk0146_31_1	chr4	155400472	155401040	+	0	NA	Intergenic	Intergenic	-23786	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.008803	0.404218	
chunk0122_131_1	chr3	31614646	31614845	+	0	NA	intron (NM_178862, intron 5 of 15)	intron (NM_178862, intron 5 of 15)	82244	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.010050	0.350000	
chunk0180_125_1	chr7	55645025	55645453	+	0	NA	Intergenic	Intergenic	42793	NR_027340	360132	Hs.446691	NM_182827	ENSG00000176826	FKBP9P1	FKBP9L	FKBP prolyl isomerase 9 pseudogene 1	pseudo	0.014019	0.393939	
chunk0079_156_1	chr17	13311304	13311611	+	0	NA	Intergenic	HAL1ME|LINE|L1	232189	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.003257	0.412338	
chunk0172_37_1	chr6	133990954	133991531	+	0	NA	exon (NM_145176, exon 5 of 5)	exon (NM_145176, exon 5 of 5)	38079	NM_004865	9519	Hs.486507	NM_004865	ENSG00000028839	TBPL1	MGC:8389|MGC:9620|STUD|TLF|TLP|TRF2	TATA-box binding protein like 1	protein-coding	0.005199	0.418685	
chunk0149_26_1	chr5	16171792	16172287	+	0	NA	intron (NM_001102562, intron 2 of 3)	intron (NM_001102562, intron 2 of 3)	7749	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.008081	0.383065	223(GGGTACATGTTGTCCC,-,0.00),224(GGTACATGTTGTCCCC,+,0.00)
chunk0052_455_1	chr12	132700521	132700875	+	0	NA	intron (NM_018663, intron 3 of 4)	L1PB4|LINE|L1	-10109	NM_138575	192111	Hs.102558	NM_138575	ENSG00000247077	PGAM5	BXLBV68	PGAM family member 5, mitochondrial serine/threonine protein phosphatase	protein-coding	0.005650	0.374648	
chunk0019_401_1	chr1	230517810	230518038	+	0	NA	Intergenic	Intergenic	-91996	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.004386	0.572052	
chunk0002_111_1	chr1	15820615	15821246	+	0	NA	Intergenic	AluJr|SINE|Alu	-13231	NM_001089591	440567	Hs.568229	NM_001089591	ENSG00000233954	UQCRHL	-	ubiquinol-cytochrome c reductase hinge protein like	protein-coding	0.009509	0.473101	
chunk0116_274_1	chr21	39341553	39341855	+	0	NA	TTS (NM_004965)	TTS (NM_004965)	7417	NM_004965	3150	Hs.356285	NM_004965	ENSG00000205581	HMGN1	HMG14	high mobility group nucleosome binding domain 1	protein-coding	0.006623	0.339934	
chunk0168_231_1	chr6	87418497	87418907	+	0	NA	intron (NM_001031743, intron 7 of 12)	intron (NM_001031743, intron 7 of 12)	10730	NM_001031743	154313	Hs.82921	NM_178823	ENSG00000272514	CFAP206	C6orf165|dJ382I10.1	cilia and flagella associated protein 206	protein-coding	0.004878	0.333333	
chunk0058_49_1	chr14	20455067	20455418	+	0	NA	promoter-TSS (NM_017807)	promoter-TSS (NM_017807)	111	NM_001244249	328	Hs.73722	NM_001641	ENSG00000100823	APEX1	APE|APE1|APEN|APEX|APX|HAP1|REF1	apurinic/apyrimidinic endodeoxyribonuclease 1	protein-coding	0.062678	0.568182	
chunk0157_306_1	chr5	121479480	121479986	+	0	NA	Intergenic	Intergenic	157183	NR_104999	102467226		NR_104999		LOC102467226	-	uncharacterized LOC102467226	ncRNA	0.001976	0.355030	
chunk0090_216_1	chr18	73485093	73485292	+	0	NA	Intergenic	Intergenic	160251	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.000000	0.325000	
chunk0180_283_1	chr7	69861139	69861690	+	0	NA	intron (NM_015570, intron 1 of 18)	intron (NM_015570, intron 1 of 18)	262495	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.005445	0.411232	220(AGGGACATGGTGCTCC,-,0.00),221(GGGACATGGTGCTCCC,+,0.00),286(ATGCACACACTGTACC,-,0.00),287(TGCACACACTGTACCA,+,0.00)
chunk0136_363_1	chr3	196021521	196022346	+	0	NA	Intergenic	LTR13|LTR|ERVK	-31654	NR_003264	255812	Hs.566872	NR_003264	ENSG00000185485	SDHAP1	SDHAL1|SDHALP1	succinate dehydrogenase complex flavoprotein subunit A pseudogene 1	pseudo	0.019394	0.423729	451(GGGCACGAGCTGTTCC,-,0.00)
chunk0192_246_1	chr8	65717339	65717544	+	0	NA	3' UTR (NM_001242318, exon 13 of 13)	3' UTR (NM_001242318, exon 13 of 13)	47568	NM_001145838	9650	Hs.584788	NM_014637	ENSG00000066855	MTFR1	CHPPR|FAM54A2	mitochondrial fission regulator 1	protein-coding	0.000000	0.427184	
chunk0036_84_1	chr11	60744698	60745420	+	0	NA	TTS (NM_001310141)	TTS (NM_001310141)	-11808	NR_103481	219995	Hs.207465	NM_152717	ENSG00000166961	MS4A15	-	membrane spanning 4-domains A15	protein-coding	0.005540	0.359613	
chunk0147_343_1	chr4	185573854	185574053	+	0	NA	Intergenic	Intergenic	-38395	NM_001114107	27295	Hs.701364	NM_014476	ENSG00000154553	PDLIM3	ALP	PDZ and LIM domain 3	protein-coding	0.025126	0.595000	
chunk0171_188_1	chr6	125224318	125224588	+	0	NA	intron (NM_001003395, intron 2 of 6)	intron (NM_001003395, intron 2 of 6)	70179	NM_001292026	7164	Hs.591347	NM_003287	ENSG00000111907	TPD52L1	D53	TPD52 like 1	protein-coding	0.003704	0.450185	86(AAGAACACACAGTGCT,-,0.00),87(AGAACACACAGTGCTC,+,0.00)
chunk0018_283_1	chr1	220690274	220690552	+	0	NA	exon (NM_024709, exon 1 of 2)	exon (NM_024709, exon 1 of 2)	127	NM_024709	79762	Hs.519839	NM_024709	ENSG00000162817	C1orf115	-	chromosome 1 open reading frame 115	protein-coding	0.118705	0.759857	
chunk0209_80_1	chrX	38305939	38306358	+	0	NA	intron (NM_001034853, intron 7 of 14)	intron (NM_001034853, intron 7 of 14)	21387	NM_001034853	6103	Hs.61438	NM_000328	ENSG00000156313	RPGR	COD1|CORDX1|CRD|PCDX|RP15|RP3|XLRP3|orf15	retinitis pigmentosa GTPase regulator	protein-coding	0.007160	0.369048	
chunk0047_86_1	chr12	68335206	68335609	+	0	NA	Intergenic	Intergenic	-3026	NM_020128	56890	Hs.655702	NM_017440	ENSG00000111554	MDM1	-	Mdm1 nuclear protein	protein-coding	0.009926	0.502475	
chunk0091_408_1	chr19	16629504	16629753	+	0	NA	Intergenic	Intergenic	-1424	NM_004831	9441	Hs.715040	NM_004831	ENSG00000105085	MED26	CRSP7|CRSP70	mediator complex subunit 26	protein-coding	0.020080	0.444000	
chunk0131_214_1	chr3	149038261	149038679	+	0	NA	intron (NM_003071, intron 23 of 24)	MIR|SINE|MIR	47062	NM_004130	2992	Hs.477892	NM_004130	ENSG00000163754	GYG1	GSD15|GYG	glycogenin 1	protein-coding	0.007177	0.396181	
chunk0192_375_1	chr8	68466478	68467145	+	0	NA	intron (NM_052958, intron 3 of 13)	L1ME3Cz|LINE|L1	-135320	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.005997	0.287425	
chunk0060_37_1	chr14	40677380	40677579	+	0	NA	Intergenic	Intergenic	-277232	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.000000	0.260000	
chunk0062_97_1	chr14	68172785	68173536	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	353381	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.001332	0.371011	592(GGGAACACTCTGGCCT,-,0.00),593(GGAACACTCTGGCCTT,+,0.00)
chunk0018_125_1	chr1	218490279	218490883	+	0	NA	intron (NR_031644, intron 2 of 6)	L2a|LINE|L2	47955	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.003311	0.409917	
chunk0001_15_1	chr1	1079453	1079816	+	0	NA	Intergenic	Intergenic	-5327	NM_001205252	401934	Hs.568137	NM_001205252	ENSG00000237330	RNF223	-	ring finger protein 223	protein-coding	0.049587	0.667582	
chunk0116_332_1	chr21	41322188	41322520	+	0	NA	intron (NM_206964, intron 1 of 6)	intron (NM_206964, intron 1 of 6)	5620	NM_058186	54097	Hs.473877	NM_058186	ENSG00000183844	FAM3B	2-21|C21orf11|C21orf76|ORF9|PANDER|PRED44	family with sequence similarity 3 member B	protein-coding	0.018072	0.498498	
chunk0210_306_1	chrX	88950990	88951678	+	0	NA	Intergenic	L1MDb|LINE|L1	204109	NM_001184771	53336	Hs.458292	NM_033048	ENSG00000147183	CPXCR1	CT77	CPX chromosome region candidate 1	protein-coding	0.001453	0.368650	
chunk0044_55_1	chr12	27710204	27710952	+	0	NA	promoter-TSS (NM_001190864)	promoter-TSS (NM_001190864)	-195	NM_001190864	60488	Hs.714076	NM_021821	ENSG00000061794	MRPS35	HDCMD11P|MDS023|MRP-S28|MRPS28	mitochondrial ribosomal protein S35	protein-coding	0.049465	0.508678	
chunk0084_440_1	chr17	82858435	82858737	+	0	NA	intron (NM_005993, intron 13 of 38)	intron (NM_005993, intron 13 of 38)	-18531	NM_024702	79755	Hs.464391	NM_024702	ENSG00000141579	ZNF750	ZFP750	zinc finger protein 750	protein-coding	0.016556	0.488449	
chunk0207_423_1	chr9	137227002	137227459	+	0	NA	promoter-TSS (NM_001190228)	promoter-TSS (NM_001190228)	-336	NM_001190228	643596	Hs.730186	NM_001190228	ENSG00000233198	RNF224	-	ring finger protein 224	protein-coding	0.039387	0.668122	
chunk0127_293_1	chr3	97948277	97948618	+	0	NA	intron (NM_153182, intron 7 of 9)	MER90a|LTR|ERV1	24004	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.008798	0.423977	
chunk0037_37_1	chr11	70255494	70256029	+	0	NA	Intergenic	Intergenic	-14939	NR_045286	8500	Hs.530749	NM_003626	ENSG00000131626	PPFIA1	LIP.1|LIP1|LIPRIN	PTPRF interacting protein alpha 1	protein-coding	0.018692	0.458955	
chunk0090_203_1	chr18	73244456	73244771	+	0	NA	intron (NR_034133, intron 2 of 5)	intron (NR_034133, intron 2 of 5)	19885	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.003175	0.344937	
chunk0176_155_1	chr7	13288741	13289115	+	0	NA	Intergenic	Intergenic	601642	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.000000	0.376000	
chunk0010_280_1	chr1	117466749	117466949	+	0	NA	intron (NM_006699, intron 8 of 12)	L2b|LINE|L2	99386	NM_006699	10905	Hs.435938	NM_006699	ENSG00000198162	MAN1A2	MAN1B	mannosidase alpha class 1A member 2	protein-coding	0.000000	0.432836	
chunk0204_361_1	chr9	101730098	101730662	+	0	NA	intron (NM_133445, intron 1 of 8)	intron (NM_133445, intron 1 of 8)	8200	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.005319	0.352212	318(AAGAACACACTGCTCT,-,0.00),319(AGAACACACTGCTCTA,+,0.00)
chunk0102_150_1	chr2	147031147	147031447	+	0	NA	Intergenic	Intergenic	444240	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.010000	0.431894	
chunk0099_5_1	chr2	82674792	82675429	+	0	NA	Intergenic	Intergenic	-181693	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007849	0.340125	
chunk0048_274_1	chr12	82414086	82414454	+	0	NA	intron (NM_032230, intron 5 of 11)	intron (NM_032230, intron 5 of 11)	-55465	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.002717	0.368564	
chunk0170_425_1	chr6	118538979	118539650	+	0	NA	intron (NM_206921, intron 3 of 5)	Tigger3a|DNA|TcMar-Tigger	-8965	NM_002667	5350	Hs.170839	NM_002667	ENSG00000198523	PLN	CMD1P|CMH18|PLB	phospholamban	protein-coding	0.005961	0.303571	
chunk0065_105_1	chr15	24103265	24103556	+	0	NA	Intergenic	L1MCa|LINE|L1	66496	NR_026647	791115	Hs.560378	NR_026647	ENSG00000260551	PWRN2	NCRNA00199	Prader-Willi region non-protein coding RNA 2	ncRNA	0.010309	0.315068	
chunk0024_98_1	chr10	34532837	34533107	+	0	NA	intron (NM_019619, intron 2 of 24)	Tigger3a|DNA|TcMar-Tigger	282353	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.003704	0.350554	
chunk0041_2_1	chr12	55051	55441	+	0	NA	Intergenic	Intergenic	-11637	NM_001170738	440073	Hs.536319	NM_015232	ENSG00000120645	IQSEC3	-	IQ motif and Sec7 domain 3	protein-coding	0.020513	0.508951	
chunk0212_86_1	chrY	11749002	11749232	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	672473	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.026087	0.415584	
chunk0146_283_1	chr4	163805360	163805887	+	0	NA	intron (NM_001166373, intron 3 of 7)	intron (NM_001166373, intron 3 of 7)	-191999	NM_017923	55016	Hs.592804	NM_017923	ENSG00000145416	MARCH1	MARCH-I|RNF171	membrane associated ring-CH-type finger 1	protein-coding	0.005693	0.350379	
chunk0022_202_1	chr10	13627776	13628298	+	0	NA	intron (NM_003675, intron 9 of 9)	UCON78|DNA|DNA	41098	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.009579	0.428298	
chunk0074_140_1	chr16	23092627	23093260	+	0	NA	intron (NM_020718, intron 6 of 15)	L1MB5|LINE|L1	56327	NM_020718	57478	Hs.183817	NM_020718	ENSG00000103404	USP31	-	ubiquitin specific peptidase 31	protein-coding	0.007899	0.354890	
chunk0026_144_1	chr10	62295506	62295953	+	0	NA	Intergenic	L1ME1|LINE|L1	-26866	NM_145307	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.004474	0.350446	
chunk0140_455_1	chr4	76458501	76459020	+	0	NA	intron (NM_020859, intron 1 of 10)	(TTTG)n|Simple_repeat|Simple_repeat	23660	NM_020859	57619	Hs.683808	NM_020859	ENSG00000138771	SHROOM3	APXL3|MSTP013|SHRM|ShrmL	shroom family member 3	protein-coding	0.005780	0.365385	
chunk0210_313_1	chrX	91331216	91331937	+	0	NA	Intergenic	L1PB1|LINE|L1	-103022	NM_080832	140886	Hs.246590	NM_080832	ENSG00000174740	PABPC5	PABP5	poly(A) binding protein cytoplasmic 5	protein-coding	0.005548	0.516620	
chunk0020_348_1	chr1	239322449	239322804	+	0	NA	Intergenic	Intergenic	-306447	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.011268	0.396067	
chunk0196_15_1	chr8	101474308	101474517	+	0	NA	Intergenic	Intergenic	-18028	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.014354	0.533333	7(AGGGACAGGCTGTCTT,-,0.00),8(GGGACAGGCTGTCTTC,+,0.00)
chunk0161_279_1	chr5	172782705	172782911	+	0	NA	Intergenic	L1MB7|LINE|L1	-11608	NM_004417	1843	Hs.171695	NM_004417	ENSG00000120129	DUSP1	CL100|HVH1|MKP-1|MKP1|PTPN10	dual specificity phosphatase 1	protein-coding	0.009709	0.405797	
chunk0038_321_1	chr11	91713315	91713690	+	0	NA	Intergenic	Intergenic	-638594	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.005333	0.332447	
chunk0023_214_1	chr10	25602435	25602699	+	0	NA	TTS (NM_020752)	TTS (NM_020752)	-49145	NR_108067	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.003788	0.426415	
chunk0019_344_1	chr1	229396520	229396781	+	0	NA	Intergenic	MER74A|LTR|ERVL	37446	NM_001100	58	Hs.1288	NM_001100	ENSG00000143632	ACTA1	ACTA|ASMA|CFTD|CFTD1|CFTDM|MPFD|NEM1|NEM2|NEM3|SHPM	actin alpha 1, skeletal muscle	protein-coding	0.007663	0.469466	
chunk0030_137_1	chr10	113612179	113612466	+	0	NA	exon (NM_006175, exon 29 of 41)	exon (NM_006175, exon 29 of 41)	51748	NM_198060	4892	Hs.268788	NM_006175	ENSG00000197893	NRAP	N-RAP	nebulin related anchoring protein	protein-coding	0.010453	0.534722	
chunk0152_298_1	chr5	61620525	61621199	+	0	NA	Intergenic	MIR3|SINE|MIR	-16919	NM_173667									0.007418	0.456296	
chunk0086_298_1	chr18	23884114	23884925	+	0	NA	intron (NM_001127718, intron 3 of 36)	intron (NM_001127718, intron 3 of 36)	11499	NM_000227	3909	Hs.436367	NM_000227	ENSG00000053747	LAMA3	BM600|E170|LAMNA|LOCS	laminin subunit alpha 3	protein-coding	0.012330	0.449507	288(CAGAACTCTCTGTTCT,-,0.00),289(AGAACTCTCTGTTCTT,+,0.00)
chunk0128_326_1	chr3	111924184	111924622	+	0	NA	intron (NM_145753, intron 5 of 16)	L2b|LINE|L2	-54473	NM_018394	55347	Hs.477115	NM_018394	ENSG00000144827	ABHD10	-	abhydrolase domain containing 10	protein-coding	0.015982	0.482916	
chunk0062_425_1	chr14	75254292	75254972	+	0	NA	Intergenic	Intergenic	-24146	NM_005252	2353	Hs.25647	NM_005252	ENSG00000170345	FOS	AP-1|C-FOS|p55	Fos proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.014706	0.537445	
chunk0146_125_1	chr4	159106513	159106909	+	0	NA	Intergenic	Intergenic	-22094	NR_039963	100616303		NR_039963	ENSG00000283379	MIR3688-2	mir-3688-2	microRNA 3688-2	ncRNA	0.010101	0.365239	
chunk0071_370_1	chr15	89098271	89098705	+	0	NA	intron (NM_007011, intron 2 of 14)	intron (NM_007011, intron 2 of 14)	10338	NM_007011	11057	Hs.122337	NM_007011	ENSG00000140526	ABHD2	HS1-2|LABH2|PHPS1-2	abhydrolase domain containing 2	protein-coding	0.004608	0.455172	175(CTGAACACCCTGTGCC,-,0.00),176(TGAACACCCTGTGCCC,+,0.00)
chunk0055_74_1	chr13	53197118	53197930	+	0	NA	Intergenic	Intergenic	-45624	NR_125788	102723875	Hs.149083	NR_125788		LINC01065	-	long intergenic non-protein coding RNA 1065	ncRNA	0.006158	0.354244	
chunk0188_280_1	chr8	15543166	15543365	+	0	NA	intron (NM_006765, intron 1 of 10)	MamRep605|LTR?|LTR?	3178	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.000000	0.350000	
chunk0139_38_1	chr4	48546083	48546673	+	0	NA	intron (NM_015030, intron 41 of 63)	intron (NM_015030, intron 41 of 63)	56126	NM_175619	326340	Hs.276457	NM_175619	ENSG00000182223	ZAR1	Z3CXXC6	zygote arrest 1	protein-coding	0.006780	0.395939	
chunk0183_357_1	chr7	108650605	108651260	+	0	NA	Intergenic	L1ME4a|LINE|L1	-81164	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.003053	0.339939	
chunk0009_462_1	chr1	111651057	111651341	+	0	NA	intron (NM_001010935, intron 2 of 8)	intron (NM_001010935, intron 2 of 8)	31052	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.007042	0.354386	
chunk0201_150_1	chr9	35918997	35920112	+	0	NA	Intergenic	Intergenic	10071	NR_024283									0.004484	0.373656	
chunk0002_338_1	chr1	24853664	24854170	+	0	NA	Intergenic	Intergenic	65499	NR_106789	102465437		NR_106789	ENSG00000278034	MIR6731	hsa-mir-6731	microRNA 6731	ncRNA	0.013834	0.382643	
chunk0103_234_1	chr2	164694590	164694847	+	0	NA	exon (NM_001278458, exon 15 of 17)	exon (NM_001278458, exon 15 of 17)	-6941	NR_033309	100337591	Hs.664357	NR_033309	ENSG00000206869	SNORA70F	U70F	small nucleolar RNA, H/ACA box 70F	snoRNA	0.011673	0.453488	
chunk0082_34_1	chr17	50786050	50786307	+	0	NA	Intergenic	Intergenic	17528	NR_107026	102466918		NR_107026	ENSG00000278672	MIR8059	hsa-mir-8059	microRNA 8059	ncRNA	0.011673	0.507752	
chunk0170_36_1	chr6	109349540	109349988	+	0	NA	Intergenic	Intergenic	32795	NM_001142404	8763	Hs.520313	NM_006016	ENSG00000135535	CD164	DFNA66|MGC-24|MGC-24v|MUC-24|endolyn	CD164 molecule	protein-coding	0.004464	0.489978	
chunk0080_94_1	chr17	26802472	26802672	+	0	NA	Intergenic	Intergenic	491424	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.025000	0.398010	
chunk0180_31_1	chr7	54074778	54075016	+	0	NA	Intergenic	LTR102_Mam|LTR|ERVL	127524	NR_004422									0.021008	0.468619	
chunk0204_438_1	chr9	103964608	103964973	+	0	NA	Intergenic	Intergenic	-34919	NR_109803	101928523		NR_109803	ENSG00000285483	LOC101928523	-	uncharacterized LOC101928523	ncRNA	0.000000	0.346995	
chunk0092_217_1	chr19	31667030	31667241	+	0	NA	Intergenic	Intergenic	74854	NM_001205273	100507527	Hs.432564	NM_001205273		THEG5	-	testis highly expressed protein 5	protein-coding	0.014218	0.481132	
chunk0042_61_1	chr12	1993710	1993942	+	0	NA	intron (NM_152640, intron 2 of 8)	intron (NM_152640, intron 2 of 8)	10685	NM_152640	196513	Hs.130934	NM_152640	ENSG00000151065	DCP1B	DCP1	decapping mRNA 1B	protein-coding	0.000000	0.261803	
chunk0123_19_1	chr3	40371534	40372270	+	0	NA	Intergenic	Intergenic	-15254	NM_001291961	956	Hs.441145	NM_001248	ENSG00000168032	ENTPD3	CD39L3|HB6|NTPDase-3	ectonucleoside triphosphate diphosphohydrolase 3	protein-coding	0.005435	0.415197	
chunk0013_164_1	chr1	168751069	168751500	+	0	NA	Intergenic	Intergenic	-22080	NM_001937	1805	Hs.80552	NM_001937	ENSG00000143196	DPT	TRAMP	dermatopontin	protein-coding	0.006961	0.405093	
chunk0056_91_1	chr13	81873943	81874721	+	0	NA	Intergenic	L1PB4|LINE|L1	-647349	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.008997	0.319641	
chunk0156_34_1	chr5	102522025	102522478	+	0	NA	Intergenic	Intergenic	-23235	NM_001289004	133482	Hs.388874	NM_173488	ENSG00000205359	SLCO6A1	CT48|GST|OATP-I|OATP6A1|OATPY	solute carrier organic anion transporter family member 6A1	protein-coding	0.004415	0.334802	
chunk0140_64_1	chr4	67086751	67087044	+	0	NA	Intergenic	Intergenic	335103	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.000000	0.299320	
chunk0011_343_1	chr1	152208825	152209279	+	0	NA	Intergenic	L1ME3C|LINE|L1	15144	NM_001009931	388697	Hs.490162	NM_001009931	ENSG00000197915	HRNR	FLG3|S100A16|S100a18	hornerin	protein-coding	0.004405	0.327473	225(AGGTACACACTGTCTT,-,0.00),226(GGTACACACTGTCTTG,+,0.00)
chunk0103_372_1	chr2	168526692	168527251	+	0	NA	intron (NM_001256126, intron 1 of 10)	LTR50|LTR|ERVL	-55972	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.007156	0.416071	259(AAGAACACTCTGTGCT,-,0.00),260(AGAACACTCTGTGCTG,+,0.00)
chunk0029_201_1	chr10	101631875	101632142	+	0	NA	intron (NM_022039, intron 5 of 8)	intron (NM_022039, intron 5 of 8)	-30511	NR_036115	100423033		NR_036115	ENSG00000283558	MIR3158-2	mir-3158-2	microRNA 3158-2	ncRNA	0.011236	0.526119	
chunk0169_157_1	chr6	101878887	101879409	+	0	NA	intron (NM_001166247, intron 10 of 16)	MLT1I|LTR|ERVL-MaLR	480163	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.005747	0.365201	191(GAGAACATGGTGAACT,-,0.00),192(AGAACATGGTGAACTG,+,0.00)
chunk0190_365_1	chr8	39852735	39853072	+	0	NA	Intergenic	LTR10G|LTR|ERV1	-14614	NM_001278113	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.020772	0.449704	
chunk0111_86_1	chr20	23337784	23338590	+	0	NA	Intergenic	L1MEd|LINE|L1	-12549	NM_013248	29107	Hs.516933	NM_013248	ENSG00000132661	NXT1	MTR2|P15	nuclear transport factor 2 like export factor 1	protein-coding	0.003722	0.411400	
chunk0060_96_1	chr14	42961684	42961961	+	0	NA	Intergenic	Intergenic	1354261	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.007220	0.374101	45(GAGAACACCATGTTCT,-,0.00),46(AGAACACCATGTTCTA,+,0.00)
chunk0177_136_1	chr7	22593994	22594537	+	0	NA	Intergenic	Intergenic	30928	NR_038393	100506178	Hs.668122	NR_038393	ENSG00000232759	LOC100506178	-	uncharacterized LOC100506178	ncRNA	0.003683	0.408088	527(GGGTACAACCTGTGCA,-,0.00),528(GGTACAACCTGTGCAC,+,0.00)
chunk0144_393_1	chr4	140158101	140158352	+	0	NA	Intergenic	Intergenic	-4147	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.011952	0.420635	
chunk0139_206_1	chr4	54842224	54842975	+	0	NA	Intergenic	Intergenic	184671	NM_001093772	3815	Hs.479754	NM_000222	ENSG00000157404	KIT	C-Kit|CD117|MASTC|PBT|SCFR	KIT proto-oncogene, receptor tyrosine kinase	protein-coding	0.009321	0.442819	
chunk0212_307_1	chrX	142484106	142484305	+	0	NA	Intergenic	LTR101_Mam|LTR|ERVL	-278915	NM_016249	51438	Hs.123536	NM_016249	ENSG00000046774	MAGEC2	CT10|HCA587|MAGEE1	MAGE family member C2	protein-coding	0.005025	0.420000	
chunk0118_94_1	chr22	29129524	29130315	+	0	NA	intron (NM_001039570, intron 5 of 8)	intron (NM_001039570, intron 5 of 8)	56841	NM_032045	83999	Hs.229335	NM_032045	ENSG00000183762	KREMEN1	ECTD13|KREMEN|KRM1	kringle containing transmembrane protein 1	protein-coding	0.008850	0.483586	
chunk0014_173_1	chr1	178394314	178394920	+	0	NA	intron (NM_170692, intron 4 of 17)	intron (NM_170692, intron 4 of 17)	53146	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.001650	0.339374	
chunk0018_31_1	chr1	215606783	215607186	+	0	NA	intron (NM_016121, intron 13 of 17)	intron (NM_016121, intron 13 of 17)	39592	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.004963	0.269802	198(TAGAACAAAATGTCCC,-,0.00),199(AGAACAAAATGTCCCC,+,0.00)
chunk0107_200_1	chr2	216416515	216417150	+	0	NA	intron (NM_014140, intron 4 of 17)	intron (NM_014140, intron 4 of 17)	4082	NM_001127207	50485	Hs.516674	NM_014140	ENSG00000138375	SMARCAL1	HARP|HHARP	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1	protein-coding	0.007874	0.468553	292(GAGTACTCTCTGTGCA,-,0.00),293(AGTACTCTCTGTGCAG,+,0.00)
chunk0014_407_1	chr1	183030171	183030402	+	0	NA	intron (NM_002293, intron 1 of 27)	MER58B|DNA|hAT-Charlie	6826	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.004329	0.452586	
chunk0084_388_1	chr17	82061352	82062004	+	0	NA	exon (NM_022156, exon 7 of 14)	exon (NM_022156, exon 7 of 14)	4143	NM_022156	64118	Hs.514599	NM_022156	ENSG00000169718	DUS1L	DUS1|PP3111	dihydrouridine synthase 1 like	protein-coding	0.041411	0.649311	322(AGGCACTGGATGTTCC,-,0.00),323(GGCACTGGATGTTCCC,+,0.00)
chunk0027_396_1	chr10	80212788	80213131	+	0	NA	intron (NR_038464, intron 1 of 1)	intron (NR_038464, intron 1 of 1)	5249	NR_038464	439990	Hs.365566	NR_038464	ENSG00000237523	LINC00857	-	long intergenic non-protein coding RNA 857	ncRNA	0.005831	0.328488	273(ATGAACAATGTGTTCA,-,0.00),274(TGAACAATGTGTTCAT,+,0.00)
chunk0124_317_1	chr3	58072683	58072920	+	0	NA	intron (NM_001164317, intron 1 of 46)	intron (NM_001164317, intron 1 of 46)	64401	NM_001457	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.008439	0.399160	
chunk0190_306_1	chr8	38313888	38314870	+	0	NA	intron (NM_023034, intron 12 of 23)	intron (NM_023034, intron 12 of 23)	-45159	NM_001102559	84513	Hs.567619	NM_032483	ENSG00000147535	PLPP5	DPPL1|HTPAP|PPAPDC1B	phospholipid phosphatase 5	protein-coding	0.004073	0.361139	668(GGGAACAAGATGTCCT,-,0.00),669(GGAACAAGATGTCCTA,+,0.00)
chunk0098_249_1	chr2	75028448	75028958	+	0	NA	Intergenic	L2a|LINE|L2	-62109	NR_049796	100846995		NR_049796	ENSG00000263909	MIR5000	-	microRNA 5000	ncRNA	0.007843	0.420744	
chunk0057_216_1	chr13	104023677	104023915	+	0	NA	Intergenic	MSTB|LTR|ERVL-MaLR	598596	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.004202	0.351464	
chunk0175_417_1	chr6	168858714	168859429	+	0	NA	Intergenic	Intergenic	303230	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.006993	0.386872	
chunk0033_446_1	chr11	25435100	25435554	+	0	NA	Intergenic	MIRb|SINE|MIR	-753796	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.002203	0.347253	
chunk0084_254_1	chr17	79025464	79025847	+	0	NA	promoter-TSS (NR_049769)	promoter-TSS (NR_049769)	-8	NR_049769	114897	Hs.201398	NM_030968	ENSG00000173918	C1QTNF1	CTRP1|GIP|ZSIG37	C1q and TNF related 1	protein-coding	0.026110	0.593750	
chunk0163_93_1	chr6	9560806	9561313	+	0	NA	Intergenic	Intergenic	-851259	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.009862	0.336614	
chunk0084_409_1	chr17	82267524	82267796	+	0	NA	intron (NR_110578, intron 1 of 8)	intron (NR_110578, intron 1 of 8)	6058	NM_001893	1453	Hs.631725	NM_001893	ENSG00000141551	CSNK1D	ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID	casein kinase 1 delta	protein-coding	0.022059	0.461538	
chunk0093_335_1	chr19	54552687	54552928	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	20115	NR_104097	90011	Hs.288520	NM_033206	ENSG00000104970	KIR3DX1	KIR3DL0|LENG12	killer cell immunoglobulin like receptor, three Ig domains X1 (pseudogene)	pseudo	0.033195	0.491736	
chunk0207_31_1	chrX	3697847	3698295	+	0	NA	intron (NM_005044, intron 1 of 8)	intron (NM_005044, intron 1 of 8)	15563	NM_005044	5613	Hs.390788	NM_005044	ENSG00000183943	PRKX	PKX1	protein kinase X-linked	protein-coding	0.017857	0.487751	139(GGGCACTCTCTGTTCT,-,0.00),140(GGCACTCTCTGTTCTG,+,0.00)
chunk0088_134_1	chr18	45821055	45821360	+	0	NA	Intergenic	Intergenic	-4373	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.006557	0.385621	141(ATGGACTTTATGTTCT,-,0.00),142(TGGACTTTATGTTCTC,+,0.00)
chunk0104_299_1	chr2	178764806	178765498	+	0	NA	intron (NM_133378, intron 41 of 311)	intron (NM_133378, intron 41 of 311)	-11774	NR_120594	101927055	Hs.570275	NR_120594	ENSG00000237298	LOC101927055	-	uncharacterized LOC101927055	ncRNA	0.004335	0.369408	
chunk0123_441_1	chr3	50569258	50569457	+	0	NA	promoter-TSS (NM_016173)	promoter-TSS (NM_016173)	-121	NM_016173	51409	Hs.517987	NM_016173	ENSG00000114735	HEMK1	HEMK|MTQ1	HemK methyltransferase family member 1	protein-coding	0.055276	0.620000	
chunk0167_45_1	chr6	55487003	55487347	+	0	NA	intron (NR_109869, intron 3 of 4)	intron (NR_109869, intron 3 of 4)	92039	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.000000	0.359420	
chunk0129_138_1	chr3	120298482	120298967	+	0	NA	Intergenic	Intergenic	50615	NM_001099678	116064	Hs.518084	NM_001099678	ENSG00000163428	LRRC58	-	leucine rich repeat containing 58	protein-coding	0.004124	0.320988	46(AAGGACTTTTTGTTCT,-,0.00),47(AGGACTTTTTGTTCTG,+,0.00)
chunk0069_60_1	chr15	60807639	60807951	+	0	NA	intron (NM_134261, intron 1 of 10)	L1PB|LINE|L1	126226	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.003205	0.383387	187(AAGTACACCCTGTTCA,-,0.00),188(AGTACACCCTGTTCAA,+,0.00)
chunk0046_386_1	chr12	63805134	63805586	+	0	NA	exon (NM_001278237, exon 5 of 6)	exon (NM_001278237, exon 5 of 6)	16796	NR_126167	104169670	Hs.735874	NR_126167	ENSG00000255850	RXYLT1-AS1	TMEM5-AS1	RXYLT1 antisense RNA 1	ncRNA	0.004425	0.344371	264(GAGAACAGTAAGTTCT,-,0.00),265(AGAACAGTAAGTTCTA,+,0.00)
chunk0116_338_1	chr21	41432986	41434149	+	0	NA	intron (NM_001178046, intron 3 of 14)	L1ME3D|LINE|L1	1517	NM_001282920	4599	Hs.517307	NM_002462	ENSG00000157601	MX1	IFI-78K|IFI78|MX|MxA	MX dynamin like GTPase 1	protein-coding	0.006019	0.451031	102(GAGAACAGAGTGTGTC,-,0.00),103(AGAACAGAGTGTGTCT,+,0.00)
chunk0165_447_1	chr6	40617783	40618380	+	0	NA	Intergenic	L1ME2z|LINE|L1	-30617	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.006700	0.364548	
chunk0110_134_1	chr20	13524268	13524985	+	0	NA	intron (NM_017714, intron 10 of 13)	intron (NM_017714, intron 10 of 13)	114310	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.009763	0.364903	
chunk0212_246_1	chrX	138011444	138011803	+	0	NA	Intergenic	Intergenic	445436	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.002786	0.458333	
chunk0139_347_1	chr4	59881588	59882042	+	0	NA	Intergenic	LTR22A|LTR|ERVK	-1040804	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.004405	0.490110	
chunk0101_437_1	chr2	139402767	139403088	+	0	NA	Intergenic	Intergenic	505603	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.012461	0.322981	
chunk0091_402_1	chr19	16461632	16462164	+	0	NA	intron (NR_047665, intron 1 of 22)	intron (NR_047665, intron 1 of 22)	10114	NM_021235	58513	Hs.654639	NM_021235	ENSG00000127527	EPS15L1	EPS15R	epidermal growth factor receptor pathway substrate 15 like 1	protein-coding	0.018797	0.549719	
chunk0028_223_1	chr10	89627875	89628429	+	0	NA	intron (NM_148977, intron 1 of 6)	L1MB8|LINE|L1	15739	NM_138316	53354	Hs.163555	NM_138316	ENSG00000152782	PANK1	PANK	pantothenate kinase 1	protein-coding	0.005415	0.347748	
chunk0151_439_1	chr5	56050795	56051001	+	0	NA	Intergenic	Intergenic	55731	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.000000	0.386473	70(GTGAACAGAGTGTCTC,-,0.00)
chunk0073_33_1	chr16	2682226	2682654	+	0	NA	promoter-TSS (NM_018992)	promoter-TSS (NM_018992)	-54	NM_018992	54442	Hs.61960	NM_018992	ENSG00000167977	KCTD5	-	potassium channel tetramerization domain containing 5	protein-coding	0.100467	0.694639	
chunk0198_310_1	chr8	139429614	139430094	+	0	NA	Intergenic	L2b|LINE|L2	273202	NM_001282534	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.012500	0.440748	290(TTGCACATCTTGTTCC,-,0.00),291(TGCACATCTTGTTCCA,+,0.00)
chunk0031_304_1	chr10	128812031	128812256	+	0	NA	Intergenic	Intergenic	526193	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.044444	0.561947	
chunk0041_195_1	chr11	126484248	126484601	+	0	NA	intron (NM_032531, intron 4 of 16)	MIR|SINE|MIR	78242	NM_001254759	6484	Hs.591947	NM_006278	ENSG00000110080	ST3GAL4	CGS23|NANTA3|SAT3|SIAT4|SIAT4C|ST-4|ST3GalA.2|ST3GalIV|STZ|gal-NAc6S	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	protein-coding	0.005666	0.412429	
chunk0165_22_1	chr6	29323525	29324209	+	0	NA	Intergenic	L1PB1|LINE|L1	17177	NM_030946	442191	Hs.632004	NM_030946	ENSG00000204695	OR14J1	OR5U1|OR6-25|bA150A6.4|hs6M1-28	olfactory receptor family 14 subfamily J member 1	protein-coding	0.001462	0.325547	
chunk0021_417_1	chr1	246865429	246865656	+	0	NA	intron (NM_015446, intron 26 of 35)	intron (NM_015446, intron 26 of 35)	65882	NM_015446	25909	Hs.300887	NM_015446	ENSG00000153207	AHCTF1	ELYS|MST108|MSTP108|TMBS62	AT-hook containing transcription factor 1	protein-coding	0.004405	0.337719	
chunk0181_228_1	chr7	85230314	85230518	+	0	NA	Intergenic	Intergenic	-108485	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.004902	0.370732	
chunk0206_343_1	chr9	125549585	125549891	+	0	NA	intron (NM_001006618, intron 6 of 7)	intron (NM_001006618, intron 6 of 7)	157496	NM_001006618	79109	Hs.495138	NM_024117	ENSG00000119487	MAPKAP1	JC310|MIP1|SIN1|SIN1b|SIN1g	MAPK associated protein 1	protein-coding	0.016340	0.459283	
chunk0190_28_1	chr8	29209892	29210609	+	0	NA	intron (NM_015254, intron 2 of 39)	intron (NM_015254, intron 2 of 39)	52843	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.004184	0.423398	489(AAGAACTGATTGTCCA,-,0.00),490(AGAACTGATTGTCCAG,+,0.00)
chunk0009_118_1	chr1	102839898	102840437	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	268329	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.007421	0.385185	
chunk0114_145_1	chr21	10330646	10331496	+	0	NA	Intergenic	Intergenic	-82449	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.017647	0.519389	350(CAGAGCACTCTGTGCT,-,0.00),351(AGAGCACTCTGTGCTG,+,0.00)
chunk0140_153_1	chr4	69396030	69396445	+	0	NA	Intergenic	Intergenic	99671	NM_001297615	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.002410	0.343750	
chunk0181_309_1	chr7	87316912	87317294	+	0	NA	Intergenic	Intergenic	28389	NR_015381	11257	Hs.274329	NM_007233	ENSG00000182165	TP53TG1	LINC00096|NCRNA00096|P53TG1|P53TG1-D|TP53AP1	TP53 target 1	ncRNA	0.000000	0.407311	
chunk0133_176_1	chr3	170045624	170046027	+	0	NA	intron (NM_014373, intron 2 of 3)	MIR|SINE|MIR	7878	NM_014373	26996	Hs.231320	NM_014373	ENSG00000173890	GPR160	GPCR1|GPCR150	G protein-coupled receptor 160	protein-coding	0.009926	0.467822	
chunk0082_387_1	chr17	60600021	60600294	+	0	NA	promoter-TSS (NM_003620)	promoter-TSS (NM_003620)	-26	NM_003620	8493	Hs.286073	NM_003620	ENSG00000170836	PPM1D	IDDGIP|PP2C-DELTA|WIP1	protein phosphatase, Mg2+/Mn2+ dependent 1D	protein-coding	0.135531	0.733577	
chunk0133_167_1	chr3	169871588	169871875	+	0	NA	Intergenic	Intergenic	-1796	NM_001277128	79782	Hs.411295	NM_024727	ENSG00000114248	LRRC31	HEL-S-293	leucine rich repeat containing 31	protein-coding	0.000000	0.496528	
chunk0168_51_1	chr6	78673386	78673833	+	0	NA	Intergenic	L1PB4|LINE|L1	-193935	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.002237	0.377232	
chunk0111_375_1	chr20	33826551	33827320	+	0	NA	intron (NM_176812, intron 1 of 4)	intron (NM_176812, intron 1 of 4)	15631	NM_176812	128866	Hs.472471	NM_176812	ENSG00000101421	CHMP4B	C20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4	charged multivesicular body protein 4B	protein-coding	0.002601	0.453247	
chunk0113_359_1	chr20	59032236	59032553	+	0	NA	promoter-TSS (NM_006886)	promoter-TSS (NM_006886)	-27	NM_006886	514	Hs.177530	NM_006886	ENSG00000124172	ATP5F1E	ATP5E|ATPE|MC5DN3	ATP synthase F1 subunit epsilon	protein-coding	0.119874	0.726415	
chunk0106_389_1	chr2	207583904	207584446	+	0	NA	intron (NM_001308021, intron 3 of 4)	L1MD3|LINE|L1	40797	NM_145280	151194	Hs.664764	NM_145280	ENSG00000144401	METTL21A	FAM119A|HCA557b|HSPA-KMT	methyltransferase like 21A	protein-coding	0.001845	0.325967	
chunk0085_146_1	chr18	3328505	3329058	+	0	NA	Intergenic	Intergenic	66062	NM_001144945	103910	Hs.190086	NM_033546	ENSG00000118680	MYL12B	MLC-B|MRLC2	myosin light chain 12B	protein-coding	0.001808	0.359206	
chunk0146_423_1	chr4	169177152	169177807	+	0	NA	intron (NM_020870, intron 2 of 11)	intron (NM_020870, intron 2 of 11)	93619	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.001527	0.303354	
chunk0111_246_1	chr20	29883834	29884083	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-3495	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.016064	0.500000	
chunk0176_453_1	chr7	20129184	20129574	+	0	NA	intron (NR_110114, intron 1 of 5)	intron (NR_110114, intron 1 of 5)	11047	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.005128	0.358056	202(AGAAACACTTTGTCCT,-,0.00),203(GAAACACTTTGTCCTT,+,0.00)
chunk0016_150_1	chr1	197527540	197527739	+	0	NA	intron (NR_125340, intron 17 of 19)	intron (NR_125340, intron 17 of 19)	247854	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.020101	0.325000	
chunk0202_437_1	chr9	82039151	82039661	+	0	NA	Intergenic	Intergenic	50634	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.007843	0.369863	
chunk0197_61_1	chr8	118620777	118621123	+	0	NA	promoter-TSS (NR_038210)	promoter-TSS (NR_038210)	-51	NR_038210	552860	Hs.571527	NR_038210	ENSG00000281641	SAMD12-AS1	C8orf26|NCRNA00252	SAMD12 antisense RNA 1	ncRNA	0.017341	0.475504	138(AGGCACAGCTTGACCT,-,0.00),139(GGCACAGCTTGACCTC,+,0.00)
chunk0136_315_1	chr3	195274541	195275085	+	0	NA	TTS (NM_012287)	TTS (NM_012287)	-3647	NM_152531	152002	Hs.478741	NM_152531	ENSG00000173950	XXYLT1	C3orf21	xyloside xylosyltransferase 1	protein-coding	0.000000	0.291743	
chunk0029_350_1	chr10	106969835	106970034	+	0	NA	intron (NM_052918, intron 1 of 25)	intron (NM_052918, intron 1 of 25)	194774	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.005025	0.420000	
chunk0044_296_1	chr12	32863014	32863312	+	0	NA	intron (NM_001005242, intron 4 of 12)	intron (NM_001005242, intron 4 of 12)	33683	NM_001005242	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.026846	0.424749	
chunk0046_20_1	chr12	54278025	54278224	+	0	NA	intron (NM_012117, intron 1 of 4)	MER20|DNA|hAT-Charlie	2007	NM_012117	23468	Hs.349283	NM_012117	ENSG00000094916	CBX5	HEL25|HP1|HP1A	chromobox 5	protein-coding	0.020101	0.460000	
chunk0025_182_1	chr10	53157570	53158293	+	0	NA	Intergenic	L1MC4a|LINE|L1	-386231	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.004149	0.312155	
chunk0039_303_1	chr11	103029397	103029815	+	0	NA	Intergenic	L2a|LINE|L2	62609	NM_032299	84259	Hs.503716	NM_032299	ENSG00000137692	DCUN1D5	SCCRO5	defective in cullin neddylation 1 domain containing 5	protein-coding	0.004785	0.374702	
chunk0170_123_1	chr6	110681582	110681963	+	0	NA	intron (NM_015076, intron 2 of 12)	intron (NM_015076, intron 2 of 12)	-132849	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.005249	0.350785	
chunk0054_339_1	chr13	49417422	49417739	+	0	NA	intron (NM_001287337, intron 3 of 11)	MERX|DNA|TcMar-Tigger	-3829	NM_001287338	81617	Hs.87159	NM_030925	ENSG00000102547	CAB39L	MO25-BETA|MO2L|bA103J18.3	calcium binding protein 39 like	protein-coding	0.006309	0.333333	
chunk0107_351_1	chr2	221817041	221817449	+	0	NA	Intergenic	Intergenic	-243043	NM_001304536	2043	Hs.371218	NM_004438	ENSG00000116106	EPHA4	EK8|HEK8|SEK|TYRO1	EPH receptor A4	protein-coding	0.009804	0.476773	
chunk0065_403_1	chr14	105300584	105300995	+	0	NA	promoter-TSS (NM_001243127)	promoter-TSS (NM_001243127)	-22	NM_001243127	23241	Hs.525626	NM_015197	ENSG00000179364	PACS2	EIEE66|PACS-2|PACS1L	phosphofurin acidic cluster sorting protein 2	protein-coding	0.170316	0.793689	
chunk0194_302_1	chr8	88038022	88038431	+	0	NA	3' UTR (NM_005941, exon 10 of 10)	3' UTR (NM_005941, exon 10 of 10)	-164158	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.000000	0.351220	
chunk0010_420_1	chr1	119675814	119676130	+	0	NA	Intergenic	Intergenic	-28205	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.009494	0.466877	
chunk0178_54_1	chr7	30012736	30013244	+	0	NA	non-coding (NR_046479, exon 3 of 3)	non-coding (NR_046479, exon 3 of 3)	13811	NR_046478	55033	Hs.390838	NM_017946	ENSG00000106080	FKBP14	EDSKMH|EDSKSCL2|FKBP22|IPBP12	FKBP prolyl isomerase 14	protein-coding	0.005906	0.337917	
chunk0134_404_1	chr3	183116071	183116805	+	0	NA	Intergenic	Intergenic	-16851	NM_001293273	56922	Hs.47649	NM_020166	ENSG00000078070	MCCC1	MCC-B|MCCA	methylcrotonoyl-CoA carboxylase 1	protein-coding	0.036785	0.604082	
chunk0048_111_1	chr12	79547872	79548374	+	0	NA	Intergenic	Intergenic	128866	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.009960	0.435388	
chunk0015_128_1	chr1	185516197	185516907	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	111936	NR_110793	101929093	Hs.535227	NR_110793	ENSG00000228309	LINC01350	GS1-204I12.1	long intergenic non-protein coding RNA 1350	ncRNA	0.002817	0.292546	
chunk0091_389_1	chr19	16079082	16079349	+	0	NA	intron (NM_003290, intron 1 of 7)	intron (NM_003290, intron 1 of 7)	2890	NM_003290	7171	Hs.631618	NM_003290	ENSG00000167460	TPM4	HEL-S-108	tropomyosin 4	protein-coding	0.018727	0.376866	
chunk0131_171_1	chr3	147335167	147335522	+	0	NA	Intergenic	Intergenic	57086	NR_040762	84107	Hs.415766	NM_032153	ENSG00000174963	ZIC4	-	Zic family member 4	protein-coding	0.002817	0.320225	
chunk0075_446_1	chr16	58087399	58087834	+	0	NA	Intergenic	(CACATA)n|Simple_repeat|Simple_repeat	41776	NM_013242	29105	Hs.532755	NM_013242	ENSG00000070761	CFAP20	BUG22|C16orf80|EVORF|GTL3|fSAP23	cilia and flagella associated protein 20	protein-coding	0.036782	0.465596	
chunk0053_10_1	chr13	26210891	26211257	+	0	NA	intron (NM_183045, intron 5 of 5)	intron (NM_183045, intron 5 of 5)	10683	NM_183044	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.002732	0.348774	
chunk0207_283_1	chr9	132798218	132798555	+	0	NA	intron (NM_152572, intron 10 of 12)	intron (NM_152572, intron 10 of 12)	-79934	NR_133631	11092	Hs.62595	NM_018956	ENSG00000165698	SPACA9	C9orf9|Mast	sperm acrosome associated 9	protein-coding	0.011869	0.500000	168(GAGAACAAGCTGCTCC,-,0.00),169(AGAACAAGCTGCTCCT,+,0.00)
chunk0027_158_1	chr10	74823808	74824120	+	0	NA	Intergenic	MER131|DNA?|DNA?	-2449	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.009615	0.402556	
chunk0109_50_1	chr20	891124	891821	+	0	NA	intron (NM_015985, intron 1 of 8)	intron (NM_015985, intron 1 of 8)	24845	NM_015985	51378	Hs.278973	NM_015985	ENSG00000101280	ANGPT4	ANG3|ANG4	angiopoietin 4	protein-coding	0.007174	0.557307	335(GTGAACAGTGTGTTCT,-,0.00),336(TGAACAGTGTGTTCTC,+,0.00)
chunk0024_346_1	chr10	43436457	43436773	+	0	NA	promoter-TSS (NR_026693)	promoter-TSS (NR_026693)	-511	NR_026693									0.063291	0.627760	
chunk0079_392_1	chr17	19248023	19248648	+	0	NA	intron (NM_001102664, intron 1 of 7)	intron (NM_001102664, intron 1 of 7)	10958	NM_014964	22905	Hs.743983	NM_014964	ENSG00000072134	EPN2	EHB21	epsin 2	protein-coding	0.003200	0.415335	
chunk0204_432_1	chr9	103625149	103625348	+	0	NA	Intergenic	L2|LINE|L2	-300215	NR_121578	101928496	Hs.410860	NR_121578	ENSG00000225564	LINC01492	-	long intergenic non-protein coding RNA 1492	ncRNA	0.000000	0.375000	
chunk0207_125_1	chr9	129026999	129027379	+	0	NA	intron (NM_020145, intron 1 of 10)	MIRb|SINE|MIR	1164	NM_001287045	56904	Hs.460238	NM_020145	ENSG00000148341	SH3GLB2	PP6569|PP9455|RRIG1	SH3 domain containing GRB2 like, endophilin B2	protein-coding	0.021053	0.524934	
chunk0128_63_1	chr3	105017794	105018128	+	0	NA	Intergenic	MIRb|SINE|MIR	-348752	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.008982	0.316418	175(ATGCACATTATGTGCT,-,0.00),176(TGCACATTATGTGCTT,+,0.00)
chunk0100_49_1	chr2	106030641	106030840	+	0	NA	Intergenic	Intergenic	-34917	NM_032411	84417	Hs.43125	NM_032411	ENSG00000119147	ECRG4	C2orf40	ECRG4 augurin precursor	protein-coding	0.005025	0.495000	
chunk0021_176_1	chr10	5492023	5492667	+	0	NA	Intergenic	Intergenic	7225	NM_017422	51806	Hs.180142	NM_017422	ENSG00000178372	CALML5	CLSP	calmodulin like 5	protein-coding	0.007764	0.472868	
chunk0021_167_1	chr10	5268237	5268676	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	71621	NM_001818	1109	Hs.567245	NM_001818	ENSG00000198610	AKR1C4	3-alpha-HSD|C11|CDR|CHDR|DD-4|DD4|HAKRA	aldo-keto reductase family 1 member C4	protein-coding	0.000000	0.325000	167(GAGTGCAGCATGTTCC,-,0.00),168(AGTGCAGCATGTTCCT,+,0.00)
chunk0107_249_1	chr2	217293826	217294499	+	0	NA	intron (NR_026597, intron 12 of 12)	L4_B_Mam|LINE|RTE-X	11429	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.002972	0.318991	
chunk0009_468_1	chr1	111745539	111745970	+	0	NA	non-coding (NR_125963, exon 3 of 3)	non-coding (NR_125963, exon 3 of 3)	5913	NR_038951	100506343	Hs.485810	NR_038951	ENSG00000227811	INKA2-AS1	FAM212B-AS1	INKA2 antisense RNA 1	ncRNA	0.011601	0.500000	
chunk0018_423_1	chr1	222777457	222778097	+	0	NA	Intergenic	Intergenic	-37312	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.001563	0.341654	231(ATCACAGAGTGTACTT,+,0.00)
chunk0210_365_1	chrX	96609660	96610244	+	0	NA	Intergenic	Intergenic	-74711	NM_006729	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.003425	0.370940	
chunk0134_341_1	chr3	182284671	182285328	+	0	NA	Intergenic	Intergenic	201363	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.010654	0.457447	
chunk0058_141_1	chr14	22978028	22978405	+	0	NA	promoter-TSS (NM_198086)	promoter-TSS (NM_198086)	-993	NM_198086	84962	Hs.655832	NM_032876	ENSG00000129474	AJUBA	JUB	ajuba LIM protein	protein-coding	0.007958	0.584656	
chunk0002_332_1	chr1	24541029	24541366	+	0	NA	intron (NR_109781, intron 2 of 2)	intron (NR_109781, intron 2 of 2)	14827	NR_109781	100506985	Hs.607088	NR_109781		NCMAP-DT	-	NCMAP divergent transcript	ncRNA	0.011869	0.366864	
chunk0039_316_1	chr11	103444341	103444610	+	0	NA	intron (NM_001377, intron 85 of 88)	intron (NM_001377, intron 85 of 88)	335044	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.003717	0.288889	
chunk0093_71_1	chr19	40634245	40634826	+	0	NA	Intergenic	Intergenic	33164	NM_001042545	8425	Hs.466766	NM_003573	ENSG00000090006	LTBP4	ARCL1C|LTBP-4|LTBP4L|LTBP4S	latent transforming growth factor beta binding protein 4	protein-coding	0.058520	0.579038	
chunk0144_230_1	chr4	134780249	134780513	+	0	NA	Intergenic	L1MEg|LINE|L1	-578633	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.003788	0.426415	222(GAGCACAGTCTGACCC,-,0.00),223(AGCACAGTCTGACCCA,+,0.00)
chunk0180_423_1	chr7	76128974	76129353	+	0	NA	Intergenic	L2c|LINE|L2	-72730	NM_001110199	222183	Hs.511025	NM_001039212	ENSG00000177679	SRRM3	-	serine/arginine repetitive matrix 3	protein-coding	0.005277	0.405263	
chunk0007_310_1	chr1	84319659	84319886	+	0	NA	intron (NM_001010971, intron 2 of 3)	intron (NM_001010971, intron 2 of 3)	17121	NM_001134664	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.004405	0.407895	
chunk0118_20_1	chr22	25701571	25701863	+	0	NA	intron (NM_005160, intron 13 of 20)	intron (NM_005160, intron 13 of 20)	-40436	NM_032608	84700	Hs.417959	NM_032608	ENSG00000133454	MYO18B	KFS4	myosin XVIIIB	protein-coding	0.023973	0.470990	
chunk0210_247_1	chrX	82917769	82918213	+	0	NA	Intergenic	MER31-int|LTR|ERV1	-590270	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.002252	0.350562	
chunk0048_461_1	chr12	88958184	88958541	+	0	NA	Intergenic	Tigger19b|DNA|TcMar-Tigger	61330	NR_038385	728084	Hs.132563	NR_038385	ENSG00000246363	LINC02458	-	long intergenic non-protein coding RNA 2458	ncRNA	0.000000	0.371508	
chunk0113_241_1	chr20	54148960	54149437	+	0	NA	Intergenic	Intergenic	24779	NM_001128915	1591	Hs.89663	NM_000782	ENSG00000019186	CYP24A1	CP24|CYP24|HCAI|HCINF1|P450-CC24	cytochrome P450 family 24 subfamily A member 1	protein-coding	0.010482	0.424686	
chunk0069_43_1	chr15	60674741	60675076	+	0	NA	intron (NM_134261, intron 2 of 10)	intron (NM_134261, intron 2 of 10)	-6661	NR_120318	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.002985	0.467262	
chunk0129_311_1	chr3	123874730	123874961	+	0	NA	intron (NM_053025, intron 2 of 33)	L1ME1|LINE|L1	9457	NM_053028	4638	Hs.477375	NM_005965	ENSG00000065534	MYLK	AAT7|KRP|MLCK|MLCK1|MLCK108|MLCK210|MSTP083|MYLK1|smMLCK	myosin light chain kinase	protein-coding	0.004329	0.284483	
chunk0157_365_1	chr5	123453203	123453510	+	0	NA	Intergenic	Intergenic	-29764	NM_153223	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.009772	0.363636	
chunk0002_274_1	chr1	21944253	21944777	+	0	NA	Intergenic	Intergenic	-7218	NM_001291860	3339	Hs.562227	NM_005529	ENSG00000142798	HSPG2	HSPG|PLC|PRCAN|SJA|SJS|SJS1	heparan sulfate proteoglycan 2	protein-coding	0.022901	0.540952	
chunk0103_378_1	chr2	168639496	168639731	+	0	NA	intron (NM_001256126, intron 4 of 10)	intron (NM_001256126, intron 4 of 10)	56670	NR_039933	100616356		NR_039933	ENSG00000265694	MIR4774	-	microRNA 4774	ncRNA	0.000000	0.444915	
chunk0117_195_1	chr22	21653948	21654249	+	0	NA	TTS (NR_029845)	TTS (NR_029845)	794	NR_029845	406920		NR_029845	ENSG00000283871	MIR130B	MIRN130B|mir-130b	microRNA 130b	ncRNA	0.009967	0.513245	
chunk0126_261_1	chr3	79865969	79866533	+	0	NA	Intergenic	Intergenic	-98342	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.003546	0.297345	
chunk0210_42_1	chrX	68331997	68332354	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	101282	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.005602	0.368715	
chunk0127_330_1	chr3	100416207	100416447	+	0	NA	intron (NM_001085451, intron 1 of 3)	L1MC5|LINE|L1	-14929	NM_014820	9868	Hs.227253	NM_014820	ENSG00000154174	TOMM70	TOMM70A|Tom70	translocase of outer mitochondrial membrane 70	protein-coding	0.000000	0.315353	
chunk0014_92_1	chr1	176594747	176594946	+	0	NA	exon (NM_021936, exon 3 of 5)	exon (NM_021936, exon 3 of 5)	131675	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.020101	0.575000	
chunk0121_446_1	chr3	26439433	26439989	+	0	NA	Intergenic	Intergenic	-183098	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.005396	0.394973	
chunk0074_109_1	chr16	22240153	22240688	+	0	NA	intron (NM_013302, intron 2 of 17)	L1ME4b|LINE|L1	34149	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.001869	0.356343	182(ATGTACTGTCTGTGCC,-,0.00),377(CAGCACTGTTTGTACT,-,0.00),378(AGCACTGTTTGTACTA,+,0.00)
chunk0192_86_1	chr8	60949930	60950288	+	0	NA	Intergenic	Intergenic	17639	NR_034003	100130298	Hs.636194	NR_034003		LOC100130298	-	hCG1816373-like	ncRNA	0.016760	0.490251	
chunk0072_391_1	chr15	100526114	100526681	+	0	NA	intron (NM_001290341, intron 2 of 13)	intron (NM_001290341, intron 2 of 13)	17889	NM_001290342	204219	Hs.662371	NM_178842	ENSG00000154227	CERS3	ARCI9|LASS3	ceramide synthase 3	protein-coding	0.010582	0.466549	
chunk0203_18_1	chr9	82722593	82722934	+	0	NA	Intergenic	L2c|LINE|L2	340365	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.005865	0.350877	
chunk0136_73_1	chr4	2101738	2102061	+	0	NA	intron (NM_181808, intron 19 of 25)	L1M2|LINE|L1	42387	NM_178557	339983	Hs.318529	NM_178557	ENSG00000185818	NAT8L	CML3|NACED|NAT8-LIKE	N-acetyltransferase 8 like	protein-coding	0.006192	0.570988	
chunk0057_203_1	chr13	103798803	103799432	+	0	NA	Intergenic	Intergenic	373917	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.011129	0.361905	
chunk0036_266_1	chr11	65104575	65104886	+	0	NA	intron (NM_013265, intron 2 of 9)	L1M4|LINE|L1	-7124	NM_001277233	7108	Hs.31130	NM_003273	ENSG00000149809	TM7SF2	ANG1|C14SR|DHCR14A|NET47	transmembrane 7 superfamily member 2	protein-coding	0.012862	0.397436	
chunk0009_331_1	chr1	109080033	109080258	+	0	NA	Intergenic	Intergenic	-4143	NM_005645	6884	Hs.632426	NM_005645	ENSG00000197780	TAF13	MRT60|TAF(II)18|TAF2K|TAFII-18|TAFII18	TATA-box binding protein associated factor 13	protein-coding	0.008889	0.424779	
chunk0175_167_1	chr7	4610889	4611210	+	0	NA	Intergenic	Zaphod2|DNA|hAT-Tip100	-71250	NM_001037165	221937	Hs.487393	NM_001037165	ENSG00000164916	FOXK1	FOXK1L	forkhead box K1	protein-coding	0.009346	0.478261	
chunk0175_176_1	chr7	5083455	5083654	+	0	NA	Intergenic	Intergenic	11494	NR_015343	389458	Hs.733005	NM_203393	ENSG00000273313	RBAKDN	-	RBAK downstream neighbor	ncRNA	0.050251	0.500000	
chunk0020_220_1	chr1	235331237	235331866	+	0	NA	intron (NR_036605, intron 1 of 2)	intron (NR_036605, intron 1 of 2)	2997	NR_036605	9453	Hs.730768	NM_004837	ENSG00000152904	GGPS1	GGPPS|GGPPS1	geranylgeranyl diphosphate synthase 1	protein-coding	0.006359	0.336508	
chunk0031_441_1	chr10	132556762	132557244	+	0	NA	intron (NM_005539, intron 1 of 15)	intron (NM_005539, intron 1 of 15)	19154	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.018672	0.469979	
chunk0200_436_1	chr9	30061083	30061285	+	0	NA	Intergenic	Intergenic	347270	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.000000	0.359606	
chunk0098_351_1	chr2	77375291	77375661	+	0	NA	intron (NM_001282924, intron 3 of 3)	L1MA10|LINE|L1	146892	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.002703	0.328841	
chunk0118_386_1	chr22	37147198	37147526	+	0	NA	intron (NM_000878, intron 1 of 9)	intron (NM_000878, intron 1 of 9)	2560	NM_000878	3560	Hs.474787	NM_000878	ENSG00000100385	IL2RB	CD122|IL15RB|P70-75	interleukin 2 receptor subunit beta	protein-coding	0.024390	0.534954	
chunk0157_42_1	chr5	115842466	115842850	+	0	NA	promoter-TSS (NR_073603)	promoter-TSS (NR_073603)	736	NM_001284	1176	Hs.406191	NM_001284	ENSG00000177879	AP3S1	CLAPS3|Sigma3A	adaptor related protein complex 3 subunit sigma 1	protein-coding	0.057292	0.519481	
chunk0106_402_1	chr2	207844991	207845690	+	0	NA	intron (NM_001080475, intron 7 of 7)	intron (NM_001080475, intron 7 of 7)	-75921	NM_003468	7855	Hs.17631	NM_003468	ENSG00000163251	FZD5	C2orf31|HFZ5	frizzled class receptor 5	protein-coding	0.002861	0.332857	347(CAGAACATACTGCTCA,-,0.00),348(AGAACATACTGCTCAG,+,0.00)
chunk0149_385_1	chr5	28650252	28650461	+	0	NA	Intergenic	Intergenic	-276514	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.004785	0.395238	
chunk0011_217_1	chr1	150191996	150192262	+	0	NA	Intergenic	Intergenic	41543	NM_001304723	51177	Hs.438824	NM_016274	ENSG00000023902	PLEKHO1	CKIP-1|CKIP1|JBP|OC120	pleckstrin homology domain containing O1	protein-coding	0.000000	0.359551	
chunk0022_329_1	chr10	16544107	16544569	+	0	NA	Intergenic	Intergenic	-22333	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.006494	0.388769	302(GGGAACAGCCTGTCTC,-,0.00),303(GGAACAGCCTGTCTCC,+,0.00)
chunk0122_312_1	chr3	36933522	36933772	+	0	NA	intron (NM_014831, intron 1 of 22)	intron (NM_014831, intron 1 of 22)	11410	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.000000	0.482072	
chunk0088_57_1	chr18	44182277	44182791	+	0	NA	Intergenic	Intergenic	349163	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.005837	0.374757	
chunk0096_437_1	chr2	38767024	38767311	+	0	NA	Intergenic	MIR|SINE|MIR	-11018	NM_024775	79833	Hs.143818	NM_024775	ENSG00000152147	GEMIN6	-	gem nuclear organelle associated protein 6	protein-coding	0.006969	0.333333	
chunk0160_391_1	chr5	162939903	162940290	+	0	NA	Intergenic	Intergenic	-497475	NM_199246	900	Hs.79101	NM_004060	ENSG00000113328	CCNG1	CCNG	cyclin G1	protein-coding	0.010336	0.407216	122(AAGAACAGCCAGTGCA,-,0.00),123(AGAACAGCCAGTGCAG,+,0.00)
chunk0008_61_1	chr1	89545396	89545668	+	0	NA	intron (NM_001134476, intron 2 of 7)	intron (NM_001134476, intron 2 of 7)	-13181	NM_015350	23507	Hs.482017	NM_015350	ENSG00000197147	LRRC8B	TA-LRRP|TALRRP	leucine rich repeat containing 8 VRAC subunit B	protein-coding	0.003676	0.380952	
chunk0123_304_1	chr3	47020213	47020693	+	0	NA	intron (NM_014159, intron 18 of 20)	intron (NM_014159, intron 18 of 20)	8911	NR_024046	100129354	Hs.201522	NR_024046		NRADDP	-	neurotrophin receptor associated death domain, pseudogene	pseudo	0.010417	0.471933	
chunk0022_208_1	chr10	13816490	13817121	+	0	NA	intron (NM_018027, intron 3 of 24)	intron (NM_018027, intron 3 of 24)	229866	NM_003675	8559	Hs.660649	NM_003675	ENSG00000165630	PRPF18	PRP18|hPrp18	pre-mRNA processing factor 18	protein-coding	0.009509	0.427215	
chunk0020_342_1	chr1	239084450	239085200	+	0	NA	Intergenic	L1PB1|LINE|L1	-544248	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.005333	0.555260	
chunk0053_360_1	chr13	35209708	35210617	+	0	NA	intron (NM_015678, intron 32 of 57)	intron (NM_015678, intron 32 of 57)	266533	NM_005584	4081	Hs.584776	NM_005584	ENSG00000180660	MAB21L1	CAGR1|Nbla00126	mab-21 like 1	protein-coding	0.002200	0.291209	
chunk0099_350_1	chr2	100230526	100231096	+	0	NA	intron (NR_103730, intron 1 of 2)	L2a|LINE|L2	22557	NR_103730	150577	Hs.434127	NM_001102655	ENSG00000232084	LINC01104	-	long intergenic non-protein coding RNA 1104	ncRNA	0.003509	0.462347	
chunk0131_71_1	chr3	142973584	142973962	+	0	NA	intron (NR_125393, intron 2 of 4)	intron (NR_125393, intron 2 of 4)	9715	NR_125393	101927832	Hs.710007	NR_125393	ENSG00000241570	PAQR9-AS1	-	PAQR9 antisense RNA 1	ncRNA	0.018519	0.554090	
chunk0114_289_1	chr21	16530046	16530337	+	0	NA	intron (NR_111004, intron 5 of 5)	L1MD1|LINE|L1	-8898	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.003436	0.263699	
chunk0184_427_1	chr7	122854316	122854805	+	0	NA	intron (NM_017954, intron 1 of 29)	intron (NM_017954, intron 1 of 29)	32199	NM_001009571	93664	Hs.649459	NM_017954	ENSG00000081803	CADPS2	CAPS2	calcium dependent secretion activator 2	protein-coding	0.010225	0.428571	261(CAGAACAAGGTGTGCT,-,0.00),262(AGAACAAGGTGTGCTG,+,0.00)
chunk0054_398_1	chr13	50427946	50428765	+	0	NA	intron (NR_109974, intron 3 of 6)	intron (NR_109974, intron 3 of 6)	99094	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.007326	0.410976	371(AGGGACATTCTGTATT,-,0.00),372(GGGACATTCTGTATTT,+,0.00)
chunk0138_198_1	chr4	38205991	38206613	+	0	NA	Intergenic	Intergenic	86348	NM_001253915	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.001608	0.362761	
chunk0024_218_1	chr10	37789406	37789967	+	0	NA	intron (NM_001267607, intron 6 of 6)	intron (NM_001267607, intron 6 of 6)	5489	NR_051997	100419868	Hs.741719	NR_051997		ZNF33BP1	-	zinc finger protein 33B pseudogene 1	pseudo	0.000000	0.364769	
chunk0069_184_1	chr15	63121482	63121952	+	0	NA	promoter-TSS (NM_001288585)	promoter-TSS (NM_001288585)	-83	NM_032857	114294	Hs.410388	NM_032857	ENSG00000103642	LACTB	G24|MRPL56	lactamase beta	protein-coding	0.065957	0.592357	
chunk0095_182_1	chr2	17799740	17800394	+	0	NA	Intergenic	Intergenic	-16452	NM_001105569	343930		NM_001105569	ENSG00000151379	MSGN1	MSOG|pMsgn1	mesogenin 1	protein-coding	0.012232	0.462595	464(AAGAACATCGTGTCCA,-,0.00),465(AGAACATCGTGTCCAT,+,0.00)
chunk0124_302_1	chr3	57907610	57908279	+	0	NA	exon (NM_007159, exon 15 of 21)	exon (NM_007159, exon 15 of 21)	18030	NM_001304422	7871	Hs.476432	NM_007159	ENSG00000163681	SLMAP	SLAP	sarcolemma associated protein	protein-coding	0.004484	0.334328	
chunk0036_180_1	chr11	62718642	62718921	+	0	NA	intron (NR_037946, intron 10 of 23)	intron (NR_037946, intron 10 of 23)	8603	NR_037946	100534595	Hs.533709	NR_037946	ENSG00000234857	HNRNPUL2-BSCL2	-	HNRNPUL2-BSCL2 readthrough (NMD candidate)	ncRNA	0.021505	0.421429	
chunk0120_28_1	chr3	2038825	2039271	+	0	NA	Intergenic	MIR|SINE|MIR	-59818	NM_175607	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.008969	0.382550	
chunk0072_119_1	chr15	92457362	92457752	+	0	NA	intron (NM_006011, intron 5 of 5)	intron (NM_006011, intron 5 of 5)	13989	NR_126501	104613533	Hs.97584	NR_126501	ENSG00000259170	LOC104613533	-	uncharacterized LOC104613533	ncRNA	0.020513	0.406650	
chunk0212_131_1	chrX	131206342	131206862	+	0	NA	Intergenic	Intergenic	82459	NM_001170963	3547	Hs.22111	NM_001555	ENSG00000147255	IGSF1	CHTE|IGCD1|IGDC1|INHBP|PGSF2|p120	immunoglobulin superfamily member 1	protein-coding	0.003846	0.351248	
chunk0106_176_1	chr2	200819041	200819759	+	0	NA	intron (NM_001207067, intron 9 of 11)	intron (NM_001207067, intron 9 of 11)	7067	NM_001207068	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.009749	0.449235	
chunk0091_417_1	chr19	16733765	16734353	+	0	NA	intron (NM_001007525, intron 3 of 18)	intron (NM_001007525, intron 3 of 18)	14083	NM_001007525	284434	Hs.406014	NM_001007525	ENSG00000188039	NWD1	-	NACHT and WD repeat domain containing 1	protein-coding	0.023810	0.528014	
chunk0106_167_1	chr2	200777200	200777631	+	0	NA	intron (NR_001557, intron 25 of 30)	intron (NR_001557, intron 25 of 30)	-34131	NM_001207067	9689	Hs.355983	NM_014670	ENSG00000082153	BZW1	BZAP45|Nbla10236	basic leucine zipper and W2 domains 1	protein-coding	0.000000	0.409722	
chunk0170_149_1	chr6	111334752	111334974	+	0	NA	intron (NM_001286431, intron 25 of 34)	intron (NM_001286431, intron 25 of 34)	75584	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.018018	0.300448	
chunk0130_53_1	chr3	129509708	129510123	+	0	NA	intron (NM_018262, intron 22 of 28)	MIR|SINE|MIR	-18724	NM_000539	6010	Hs.247565	NM_000539	ENSG00000163914	RHO	CSNBAD1|OPN2|RP4	rhodopsin	protein-coding	0.009639	0.475962	259(TAGCACAGAGTGACCC,-,0.00),260(AGCACAGAGTGACCCT,+,0.00)
chunk0133_389_1	chr3	174198005	174198758	+	0	NA	intron (NM_014932, intron 4 of 6)	intron (NM_014932, intron 4 of 6)	-277585	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.005312	0.299735	
chunk0156_169_1	chr5	107598968	107599405	+	0	NA	intron (NM_001962, intron 1 of 4)	L1MC5a|LINE|L1	71709	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.009153	0.372146	
chunk0045_214_1	chr12	47995871	47996207	+	0	NA	intron (NM_033150, intron 7 of 52)	intron (NM_033150, intron 7 of 52)	8463	NM_033150	1280	Hs.408182	NM_001844	ENSG00000139219	COL2A1	ANFH|AOM|COL11A3|SEDC|STL1	collagen type II alpha 1 chain	protein-coding	0.014881	0.537092	
chunk0116_77_1	chr21	34700663	34700943	+	0	NA	intron (NM_053277, intron 1 of 5)	intron (NM_053277, intron 1 of 5)	31640	NM_053277	54102	Hs.473695	NM_053277	ENSG00000159212	CLIC6	CLIC1L	chloride intracellular channel 6	protein-coding	0.032143	0.544484	
chunk0016_237_1	chr1	199821074	199821809	+	0	NA	Intergenic	Intergenic	-206161	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005442	0.385870	
chunk0008_330_1	chr1	95406186	95406385	+	0	NA	Intergenic	MER50|LTR|ERV1	-68452	NR_033966	440594	Hs.514123	NR_033966	ENSG00000233907	LINC01761	-	long intergenic non-protein coding RNA 1761	ncRNA	0.005025	0.470000	
chunk0120_87_1	chr3	3928733	3929239	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	129549	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.000000	0.333333	
chunk0172_122_1	chr6	135146412	135147079	+	0	NA	Intergenic	Intergenic	-34570	NM_001161660	4602	Hs.606320	NM_005375	ENSG00000118513	MYB	Cmyb|c-myb|c-myb_CDS|efg	MYB proto-oncogene, transcription factor	protein-coding	0.010495	0.441617	
chunk0129_199_1	chr3	121438912	121439181	+	0	NA	intron (NM_199420, intron 27 of 29)	intron (NM_199420, intron 27 of 29)	106960	NM_199420	10721	Hs.241517	NM_199420	ENSG00000051341	POLQ	PRO0327	DNA polymerase theta	protein-coding	0.007435	0.318519	
chunk0178_405_1	chr7	40947608	40947969	+	0	NA	Intergenic	L1M4|LINE|L1	32151	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.000000	0.364641	
chunk0116_399_1	chr21	42485769	42486661	+	0	NA	intron (NM_080860, intron 4 of 8)	intron (NM_080860, intron 4 of 8)	10139	NM_001286506	89765	Hs.661069	NM_080860	ENSG00000160188	RSPH1	CT79|RSP44|RSPH10A|TSA2|TSGA2	radial spoke head component 1	protein-coding	0.014574	0.506159	
chunk0207_400_1	chr9	136797123	136797360	+	0	NA	intron (NM_001039374, intron 1 of 13)	LTR5B|LTR|ERVK	903	NM_001039374	84960	Hs.728796	NM_032874	ENSG00000213213	CCDC183	KIAA1984|PARF|bA216L13.7	coiled-coil domain containing 183	protein-coding	0.012658	0.432773	
chunk0199_138_1	chr9	3962411	3962926	+	0	NA	intron (NM_001042413, intron 4 of 10)	intron (NM_001042413, intron 4 of 10)	64022	NR_026663	84850	Hs.676113	NM_032764	ENSG00000237009	GLIS3-AS1	C9orf70	GLIS3 antisense RNA 1	ncRNA	0.005825	0.406977	
chunk0061_225_1	chr14	60618335	60618603	+	0	NA	Intergenic	Intergenic	-20747	NR_126480	104548971		NR_126480		SALRNA1	SAL-RNA1|XLOC_023166	senescence associated long non-coding RNA 1	ncRNA	0.003731	0.408922	
chunk0145_19_1	chr4	143408352	143408551	+	0	NA	intron (NM_002039, intron 1 of 9)	L1ME3G|LINE|L1	64991	NR_036091	100423017		NR_036091	ENSG00000265623	MIR3139	-	microRNA 3139	ncRNA	0.005025	0.355000	
chunk0128_310_1	chr3	111702527	111702819	+	0	NA	intron (NM_153268, intron 1 of 3)	intron (NM_153268, intron 1 of 3)	-25240	NR_046733	100874115	Hs.626740	NR_046733		PLCXD2-AS1	-	PLCXD2 antisense RNA 1	ncRNA	0.003425	0.399317	
chunk0164_26_1	chr6	18186004	18186303	+	0	NA	intron (NM_153042, intron 8 of 17)	intron (NM_153042, intron 8 of 17)	30765	NM_153042	221656	Hs.709336	NM_153042	ENSG00000165097	KDM1B	AOF1|C6orf193|LSD2	lysine demethylase 1B	protein-coding	0.003344	0.450000	
chunk0081_327_1	chr17	46168014	46168322	+	0	NA	intron (NM_001193465, intron 3 of 15)	intron (NM_001193465, intron 3 of 15)	24632	NM_001193466	284058	Hs.648744	NM_015443	ENSG00000120071	KANSL1	CENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1	KAT8 regulatory NSL complex subunit 1	protein-coding	0.003247	0.385113	
chunk0166_1_1	chr6	41322623	41322976	+	0	NA	Intergenic	L1M5|LINE|L1	-12991	NM_001199509	9436	Hs.194721	NM_004828	ENSG00000096264	NCR2	CD336|LY95|NK-p44|NKP44|dJ149M18.1	natural cytotoxicity triggering receptor 2	protein-coding	0.008499	0.381356	
chunk0015_37_1	chr1	184458086	184458533	+	0	NA	intron (NM_030806, intron 1 of 5)	intron (NM_030806, intron 1 of 5)	71293	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.011186	0.421875	
chunk0098_223_1	chr2	73730622	73731276	+	0	NA	intron (NM_016058, intron 3 of 4)	intron (NM_016058, intron 3 of 4)	6441	NM_016058	51002	Hs.157401	NM_016058	ENSG00000144034	TPRKB	CGI-121|CGI121|GAMOS5	TP53RK binding protein	protein-coding	0.007645	0.442748	
chunk0061_183_1	chr14	60091677	60092070	+	0	NA	promoter-TSS (NM_022495)	promoter-TSS (NM_022495)	-38	NM_022495	64430	Hs.509499	NM_022495	ENSG00000126773	PCNX4	C14orf135|FBP2|PCNXL4	pecanex 4	protein-coding	0.083969	0.586294	
chunk0087_464_1	chr18	42835157	42835771	+	0	NA	intron (NM_002930, intron 4 of 4)	intron (NM_002930, intron 4 of 4)	280228	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.292683	
chunk0021_402_1	chr1	246661815	246662072	+	0	NA	intron (NM_152609, intron 10 of 10)	intron (NM_152609, intron 10 of 10)	-62133	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.007782	0.410853	
chunk0056_288_1	chr13	90476844	90477633	+	0	NA	Intergenic	Intergenic	-16050	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.001267	0.327848	
chunk0046_179_1	chr12	58680228	58680467	+	0	NA	intron (NR_120452, intron 1 of 7)	L1MA4A|LINE|L1	88645	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.004184	0.520833	
chunk0078_18_1	chr17	703284	703786	+	0	NA	intron (NM_001128159, intron 2 of 21)	intron (NM_001128159, intron 2 of 21)	11321	NM_001128159	55275	Hs.461819	NM_018289	ENSG00000141252	VPS53	HCCS1|PCH2E|hVps53L|pp13624	VPS53 subunit of GARP complex	protein-coding	0.013944	0.429423	
chunk0198_40_1	chr8	128317129	128317408	+	0	NA	Intergenic	MIR3|SINE|MIR	167152	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.014337	0.492857	
chunk0069_55_1	chr15	60752246	60753148	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	71128	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.018847	0.426357	593(AGAAACAAACTGTACC,-,0.00),594(GAAACAAACTGTACCT,+,0.00)
chunk0097_396_1	chr2	62036727	62037338	+	0	NA	intron (NM_152516, intron 2 of 2)	intron (NM_152516, intron 2 of 2)	131364	NM_152516	150684	Hs.468702	NM_152516	ENSG00000173163	COMMD1	C2orf5|MURR1	copper metabolism domain containing 1	protein-coding	0.004910	0.356209	
chunk0120_306_1	chr3	9986666	9986903	+	0	NA	promoter-TSS (NM_018447)	promoter-TSS (NM_018447)	54	NM_018447	55831	Hs.475392	NM_018447	ENSG00000125037	EMC3	POB|TMEM111	ER membrane protein complex subunit 3	protein-coding	0.084388	0.630252	
chunk0028_249_1	chr10	90480904	90481213	+	0	NA	intron (NR_110657, intron 2 of 6)	intron (NR_110657, intron 2 of 6)	59747	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.003236	0.380645	
chunk0007_63_1	chr1	78222139	78222669	+	0	NA	Intergenic	Intergenic	-7195	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.007547	0.327684	259(CAGAACATTTTGTGTT,-,0.00)
chunk0147_202_1	chr4	178116372	178116719	+	0	NA	Intergenic	LTR54|LTR|ERV1	-208609	NR_108093	101928656	Hs.508131	NR_108092	ENSG00000251504	LINC01099	-	long intergenic non-protein coding RNA 1099	ncRNA	0.005764	0.307471	109(TAATACACTCTGTTCT,-,0.00),110(AATACACTCTGTTCTT,+,0.00)
chunk0193_441_1	chr8	81099617	81099918	+	0	NA	intron (NM_018440, intron 1 of 8)	L1MB8|LINE|L1	12301	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.006645	0.397351	
chunk0203_434_1	chr9	91239895	91240269	+	0	NA	intron (NM_001306190, intron 5 of 8)	intron (NM_001306190, intron 5 of 8)	121842	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.005348	0.330667	
chunk0067_444_1	chr15	50195562	50195782	+	0	NA	intron (NM_003645, intron 1 of 9)	intron (NM_003645, intron 1 of 9)	13476	NM_003645	11001	Hs.11729	NM_003645	ENSG00000140284	SLC27A2	ACSVL1|FACVL1|FATP2|HsT17226|VLACS|VLCS|hFACVL1	solute carrier family 27 member 2	protein-coding	0.004545	0.334842	
chunk0030_301_1	chr10	117373258	117373514	+	0	NA	intron (NM_173791, intron 1 of 4)	intron (NM_173791, intron 1 of 4)	2081	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.015625	0.428016	160(AAGTACACTATGTACA,-,0.00),161(AGTACACTATGTACAG,+,0.00)
chunk0104_238_1	chr2	176638529	176638758	+	0	NA	intron (NR_110599, intron 1 of 3)	intron (NR_110599, intron 1 of 3)	889	NR_110599	102724224	Hs.663125	NR_110599	ENSG00000224577	LINC01117	-	long intergenic non-protein coding RNA 1117	ncRNA	0.000000	0.313043	
chunk0013_190_1	chr1	169134457	169134656	+	0	NA	intron (NR_104229, intron 12 of 12)	intron (NR_104229, intron 12 of 12)	27847	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.010050	0.395000	
chunk0047_318_1	chr12	74168942	74169279	+	0	NA	intron (NR_038300, intron 4 of 6)	intron (NR_038300, intron 4 of 6)	123521	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.002967	0.352071	
chunk0184_24_1	chr7	111957587	111958060	+	0	NA	intron (NM_014705, intron 8 of 51)	intron (NM_014705, intron 8 of 51)	149318	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.006342	0.345992	208(AAGAACAGTGTGAACT,-,0.00),209(AGAACAGTGTGAACTT,+,0.00)
chunk0059_140_1	chr14	32022850	32023724	+	0	NA	Intergenic	Intergenic	53412	NR_027263	84837	Hs.496755	NM_032751		ARHGAP5-AS1	C14orf128	ARHGAP5 antisense RNA 1 (head to head)	ncRNA	0.008009	0.418286	416(AGGGACATTTTGTTCC,-,0.00),417(GGGACATTTTGTTCCA,+,0.00)
chunk0001_261_1	chr1	8482940	8483154	+	0	NA	intron (NM_001042681, intron 10 of 22)	intron (NM_001042681, intron 10 of 22)	11866	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.004673	0.353488	
chunk0077_164_1	chr16	79327601	79328151	+	0	NA	Intergenic	Intergenic	272849	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.012727	0.408348	
chunk0092_329_1	chr19	35006360	35007144	+	0	NA	intron (NM_020895, intron 1 of 19)	L2b|LINE|L2	6410	NM_001136199	57655	Hs.515351	NM_020895	ENSG00000089351	GRAMD1A	KIAA1533	GRAM domain containing 1A	protein-coding	0.017857	0.527389	
chunk0028_351_1	chr10	92333438	92333812	+	0	NA	intron (NM_017824, intron 2 of 5)	intron (NM_017824, intron 2 of 5)	42462	NM_017824	54708	Hs.573490	NM_017824	ENSG00000198060	MARCH5	MARCH-V|MITOL|RNF153	membrane associated ring-CH-type finger 5	protein-coding	0.005348	0.410667	150(AAGAACATAAAGTACT,-,0.00),151(AGAACATAAAGTACTA,+,0.00)
chunk0208_33_1	chrX	11257394	11258024	+	0	NA	intron (NM_006125, intron 1 of 10)	L2b|LINE|L2	8266	NM_013423	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.006349	0.415214	181(AGGGACATTTTGTTCT,-,0.00),182(GGGACATTTTGTTCTT,+,0.00)
chunk0087_114_1	chr18	32679788	32680326	+	0	NA	intron (NM_020805, intron 7 of 8)	intron (NM_020805, intron 7 of 8)	92954	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.009294	0.330241	
chunk0158_76_1	chr5	126360055	126360471	+	0	NA	5' UTR (NM_001146319, exon 1 of 14)	5' UTR (NM_001146319, exon 1 of 14)	167	NM_001146319	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.016827	0.467626	
chunk0058_236_1	chr14	25508839	25509196	+	0	NA	Intergenic	Intergenic	-458720	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.005602	0.346369	
chunk0059_52_1	chr14	30137030	30137229	+	0	NA	Intergenic	Intergenic	-209436	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.010050	0.360000	
chunk0092_208_1	chr19	31274095	31274637	+	0	NA	TTS (NM_020856)	TTS (NM_020856)	74918	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.011070	0.434622	
chunk0105_453_1	chr2	195125336	195125536	+	0	NA	Intergenic	MER52A|LTR|ERV1	394841	NR_110223	101927431	Hs.558215	NR_110223	ENSG00000230173	LINC01790	-	long intergenic non-protein coding RNA 1790	ncRNA	0.005000	0.532338	
chunk0132_414_1	chr3	164418335	164419032	+	0	NA	Intergenic	L1M6|LINE|L1	-247127	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.001435	0.363897	
chunk0090_342_1	chr18	76422999	76423595	+	0	NA	intron (NM_014643, intron 3 of 6)	intron (NM_014643, intron 3 of 6)	71893	NM_014643	9658	Hs.436973	NM_014643	ENSG00000101493	ZNF516	HsT287	zinc finger protein 516	protein-coding	0.026846	0.489112	
chunk0192_312_1	chr8	66967747	66968454	+	0	NA	Intergenic	Intergenic	-5510	NM_001193502	100129654	Hs.120040	NM_001193502	ENSG00000261787	TCF24	TCF-24|bHLHa25	transcription factor 24	protein-coding	0.004243	0.353107	
chunk0118_179_1	chr22	31055553	31055972	+	0	NA	Intergenic	Intergenic	-25534	NM_134269	6525	Hs.149098	NM_006932	ENSG00000183963	SMTN	-	smoothelin	protein-coding	0.028640	0.557143	
chunk0103_12_1	chr2	158919208	158919813	+	0	NA	Intergenic	LTR37A|LTR|ERV1	-49124	NM_033394	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.000000	0.311881	282(TAGAACACACTGTTTA,-,0.00),283(AGAACACACTGTTTAT,+,0.00)
chunk0030_444_1	chr10	120940677	120941308	+	0	NA	Intergenic	Intergenic	-89813	NR_033850	283089	Hs.568750	NR_033850	ENSG00000227165	WDR11-AS1	-	WDR11 antisense RNA 1	ncRNA	0.012678	0.438291	
chunk0054_156_1	chr13	44123397	44123634	+	0	NA	intron (NR_104065, intron 1 of 4)	L1M5|LINE|L1	12966	NR_104065	101929212	Hs.534877	NR_104064	ENSG00000227258	SMIM2-AS1	C13orf44-AS1|C3orf81-AS1	SMIM2 antisense RNA 1	ncRNA	0.004219	0.420168	113(CAGTACAGATTGTGCT,-,0.00),114(AGTACAGATTGTGCTT,+,0.00)
chunk0138_356_1	chr4	42130917	42131560	+	0	NA	intron (NM_001159547, intron 3 of 5)	L1PA10|LINE|L1	21640	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.010886	0.388199	
chunk0049_110_1	chr12	91299442	91299867	+	0	NA	Intergenic	L1PA10|LINE|L1	-116530	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.000000	0.328638	
chunk0133_402_1	chr3	174340666	174341497	+	0	NA	Intergenic	Intergenic	-420285	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.003610	0.361779	
chunk0175_389_1	chr6	168369847	168370298	+	0	NA	Intergenic	Intergenic	-50318	NM_001286351	168002	Hs.673059	NM_214462	ENSG00000164488	DACT2	C6orf116|DAPPER2|DPR2|bA503C24.7	dishevelled binding antagonist of beta catenin 2	protein-coding	0.028825	0.449115	
chunk0189_421_1	chr8	27885382	27885607	+	0	NA	TTS (NR_036249)	TTS (NR_036249)	622	NR_036249	100422828		NR_036249	ENSG00000265847	MIR4287	-	microRNA 4287	ncRNA	0.008889	0.526549	58(TAGGACACTGTGAGCC,-,0.00),59(AGGACACTGTGAGCCT,+,0.00)
chunk0183_193_1	chr7	106309373	106309853	+	0	NA	Intergenic	Intergenic	-24421	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.000000	0.403326	
chunk0080_179_1	chr17	28760973	28761663	+	0	NA	intron (NM_001077498, intron 2 of 2)	intron (NM_001077498, intron 2 of 2)	17313	NM_004295	9618	Hs.8375	NM_004295	ENSG00000076604	TRAF4	CART1|MLN62|RNF83	TNF receptor associated factor 4	protein-coding	0.010145	0.493488	
chunk0003_277_1	chr1	36771609	36772066	+	0	NA	Intergenic	Intergenic	262406	NM_000831	2899	Hs.128848	NM_000831	ENSG00000163873	GRIK3	EAA5|GLR7|GLUR7|GluK3|GluR7a	glutamate ionotropic receptor kainate type subunit 3	protein-coding	0.032823	0.561135	
chunk0010_105_1	chr1	114099311	114099588	+	0	NA	intron (NM_205848, intron 4 of 7)	intron (NM_205848, intron 4 of 7)	52991	NM_205848	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.010830	0.453237	126(GAGGACACTCTGTGCT,-,0.00),127(AGGACACTCTGTGCTT,+,0.00)
chunk0103_73_1	chr2	160433699	160434077	+	0	NA	intron (NM_002897, intron 1 of 13)	intron (NM_002897, intron 1 of 13)	-26006	NR_039946	100616364		NR_039946	ENSG00000283734	MIR4785	mir-4785	microRNA 4785	ncRNA	0.005291	0.332454	
chunk0212_318_1	chrX	143710529	143711012	+	0	NA	Intergenic	Intergenic	9898	NM_001009615	494119		NM_001009615	ENSG00000268988	SPANXN2	CT11.7|SPANX-N2	SPANX family member N2	protein-coding	0.004141	0.307851	
chunk0150_4_1	chr5	30227820	30228611	+	0	NA	Intergenic	Intergenic	-832239	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.339646	
chunk0022_343_1	chr10	16893586	16893934	+	0	NA	intron (NM_001081, intron 54 of 66)	L1MD1|LINE|L1	-76306	NM_012425	6251	Hs.524161	NM_012425	ENSG00000148484	RSU1	RSP-1	Ras suppressor protein 1	protein-coding	0.011494	0.329513	
chunk0051_255_1	chr12	117518657	117519399	+	0	NA	intron (NM_173598, intron 14 of 19)	L2a|LINE|L2	-157226	NM_000620	4842	Hs.654410	NM_000620	ENSG00000089250	NOS1	IHPS1|N-NOS|NC-NOS|NOS|bNOS|nNOS	nitric oxide synthase 1	protein-coding	0.014825	0.491252	392(GTAGACACTGTGTTCT,-,0.00),393(TAGACACTGTGTTCTG,+,0.00)
chunk0090_220_1	chr18	73531444	73531964	+	0	NA	Intergenic	(AG)n|Simple_repeat|Simple_repeat	206763	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.003846	0.395393	
chunk0043_188_1	chr12	18879228	18879738	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	141372	NM_033328	93661	Hs.131288	NM_033328	ENSG00000177938	CAPZA3	CAPPA3|Gsg3|HEL-S-86	capping actin protein of muscle Z-line subunit alpha 3	protein-coding	0.001961	0.422701	
chunk0088_48_1	chr18	43984254	43985110	+	0	NA	Intergenic	L1PA6|LINE|L1	547015	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.009346	0.498250	
chunk0131_335_1	chr3	151186433	151186798	+	0	NA	intron (NM_053002, intron 11 of 42)	L2a|LINE|L2	16586	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.008219	0.486339	
chunk0014_418_1	chr1	183155547	183156089	+	0	NA	Intergenic	Tigger2b_Pri|DNA|TcMar-Tigger	-30221	NM_005562	3918	Hs.591484	NM_005562	ENSG00000058085	LAMC2	B2T|BM600|CSF|EBR2|EBR2A|LAMB2T|LAMNB2	laminin subunit gamma 2	protein-coding	0.007380	0.397790	249(CAGTACATACTGTACT,-,0.00),250(AGTACATACTGTACTA,+,0.00)
chunk0161_394_1	chr5	177013797	177013996	+	0	NA	Intergenic	MER68|LTR|ERVL	-7102	NM_001199298	51720	Hs.232721	NM_016290	ENSG00000087206	UIMC1	RAP80|X2HRIP110	ubiquitin interaction motif containing 1	protein-coding	0.000000	0.465000	
chunk0065_280_1	chr14	102461851	102462227	+	0	NA	intron (NM_001172631, intron 16 of 16)	intron (NM_001172631, intron 16 of 16)	47752	NM_152326	122416	Hs.432945	NM_152326	ENSG00000156381	ANKRD9	-	ankyrin repeat domain 9	protein-coding	0.013298	0.472149	241(GTGAACTCCGTGTTCT,-,0.00),242(TGAACTCCGTGTTCTG,+,0.00)
chunk0113_136_1	chr20	51910614	51911297	+	0	NA	Intergenic	Intergenic	-48042	NR_110016	101927678	Hs.683840	NR_110016	ENSG00000227964	LINC01429	-	long intergenic non-protein coding RNA 1429	ncRNA	0.008785	0.396199	
chunk0130_174_1	chr3	133343458	133343657	+	0	NA	intron (NM_001282865, intron 2 of 3)	L1MD3|LINE|L1	-56438	NM_003571	8419	Hs.659862	NM_003571	ENSG00000170819	BFSP2	CP47|CP49|CTRCT12|LIFL-L|PHAKOSIN	beaded filament structural protein 2	protein-coding	0.000000	0.350000	
chunk0136_378_1	chr3	196423161	196423501	+	0	NA	intron (NM_015562, intron 1 of 10)	intron (NM_015562, intron 1 of 10)	9143	NM_015562	26043	Hs.518524	NM_015562	ENSG00000163960	UBXN7	UBXD7	UBX domain protein 7	protein-coding	0.020588	0.580645	
chunk0107_223_1	chr2	216934825	216935318	+	0	NA	Intergenic	Intergenic	64299	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.004057	0.514170	
chunk0174_127_1	chr6	157314606	157314998	+	0	NA	intron (NM_018452, intron 3 of 3)	intron (NM_018452, intron 3 of 3)	9457	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.010204	0.348601	
chunk0185_102_1	chr7	125601490	125601715	+	0	NA	Intergenic	MIRb|SINE|MIR	-337311	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.000000	0.292035	
chunk0213_19_1	chrY	21641967	21642263	+	0	NA	Intergenic	L1M4c|LINE|L1	-47449	NR_001537	83868	Hs.615432	NR_001537	ENSG00000184991	TTTY13	NCRNA00136|TTY13	testis-specific transcript, Y-linked 13	ncRNA	0.013514	0.407407	
chunk0094_275_1	chr2	8134522	8135124	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	-158009	NR_015405	339788	Hs.46864	NR_015405	ENSG00000235665	LINC00298	-	long intergenic non-protein coding RNA 298	ncRNA	0.013289	0.489221	
chunk0089_89_1	chr18	58311929	58312195	+	0	NA	intron (NM_001144970, intron 4 of 28)	intron (NM_001144970, intron 4 of 28)	90540	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.015038	0.404494	126(AAGGACACAGTGTTTT,-,0.00),127(AGGACACAGTGTTTTA,+,0.00)
chunk0143_269_1	chr4	116552980	116553375	+	0	NA	Intergenic	L1PA13|LINE|L1	253452	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.010127	0.525253	
chunk0015_96_1	chr1	185057232	185057777	+	0	NA	intron (NM_007212, intron 1 of 6)	intron (NM_007212, intron 1 of 6)	12085	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.011009	0.364469	
chunk0107_185_1	chr2	216088735	216089369	+	0	NA	intron (NM_001142310, intron 2 of 3)	intron (NM_001142310, intron 2 of 3)	7186	NM_138390	92691	Hs.334916	NM_138390	ENSG00000163449	TMEM169	-	transmembrane protein 169	protein-coding	0.007886	0.396850	296(AGGAACAGAGTGTGCT,-,0.00),297(GGAACAGAGTGTGCTG,+,0.00)
chunk0199_311_1	chr9	7147164	7147416	+	0	NA	intron (NM_015061, intron 19 of 21)	intron (NM_015061, intron 19 of 21)	389649	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.011905	0.486166	111(AGGTCAAGCTGTGCTC,+,0.00)
chunk0074_88_1	chr16	22007369	22007585	+	0	NA	promoter-TSS (NM_001164579)	promoter-TSS (NM_001164579)	-658	NM_001164579	730094	Hs.498890	NM_173501	ENSG00000185716	MOSMO	ATTHOG|BC030336|C16orf52	modulator of smoothened	protein-coding	0.041667	0.483871	
chunk0009_175_1	chr1	105533080	105533770	+	0	NA	Intergenic	L1PB2|LINE|L1	85510	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001449	0.321274	
chunk0097_158_1	chr2	48482840	48483100	+	0	NA	intron (NM_001135629, intron 13 of 21)	L1PA11|LINE|L1	42201	NM_152994	129285	Hs.654619	NM_152994	ENSG00000162869	PPP1R21	CCDC128|KLRAQ1	protein phosphatase 1 regulatory subunit 21	protein-coding	0.007692	0.467433	
chunk0137_119_1	chr4	14428620	14428819	+	0	NA	Intergenic	Intergenic	316751	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.005025	0.460000	
chunk0094_346_1	chr2	9337773	9338217	+	0	NA	intron (NM_003887, intron 9 of 27)	intron (NM_003887, intron 9 of 27)	85519	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.018018	0.462921	
chunk0122_307_1	chr3	36887765	36888311	+	0	NA	intron (NM_014831, intron 7 of 22)	L1MB8|LINE|L1	57019	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.007326	0.361974	
chunk0047_131_1	chr12	69440074	69440547	+	0	NA	Intergenic	Intergenic	-30039	NM_001278354	10818	Hs.593446	NM_006654	ENSG00000166225	FRS2	FRS1A|FRS2A|FRS2alpha|SNT|SNT-1|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.006342	0.453586	
chunk0169_393_1	chr6	108063824	108064107	+	0	NA	intron (NM_014028, intron 2 of 5)	MIR|SINE|MIR	10772	NM_014028	28962	Hs.226780	NM_014028	ENSG00000081087	OSTM1	GIPN|GL|HSPC019|OPTB5	osteoclastogenesis associated transmembrane protein 1	protein-coding	0.007067	0.376761	
chunk0187_29_1	chr8	801955	802232	+	0	NA	intron (NR_073397, intron 1 of 3)	intron (NR_073397, intron 1 of 3)	64488	NR_073397	9228	Hs.113287	NM_004745	ENSG00000198010	DLGAP2	C8orf68|DAP2|ERICH1-AS1|SAPAP2	DLG associated protein 2	protein-coding	0.028881	0.679856	95(GGGAACAGTCTGCACC,-,0.00),96(GGAACAGTCTGCACCC,+,0.00)
chunk0083_252_1	chr17	68019760	68020133	+	0	NA	Intergenic	tRNA-Arg-AGG|tRNA|tRNA	-15786	NM_002266	3838	Hs.594238	NM_002266	ENSG00000182481	KPNA2	IPOA1|QIP2|RCH1|SRP1-alpha|SRP1alpha	karyopherin subunit alpha 2	protein-coding	0.080429	0.572193	
chunk0144_157_1	chr4	130751730	130751957	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-980365	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.004405	0.394737	
chunk0180_449_1	chr7	77453650	77453922	+	0	NA	Intergenic	Intergenic	-37386	NM_017439	54103	Hs.186649	NM_017439	ENSG00000186088	GSAP	PION	gamma-secretase activating protein	protein-coding	0.007353	0.439560	
chunk0007_40_1	chr1	77742220	77742456	+	0	NA	intron (NM_201624, intron 1 of 23)	MER20|DNA|hAT-Charlie	17541	NM_015017	23032	Hs.480597	NM_015017	ENSG00000077254	USP33	VDU1	ubiquitin specific peptidase 33	protein-coding	0.012712	0.451477	
chunk0135_2_1	chr3	184012283	184012590	+	0	NA	intron (NM_001023587, intron 2 of 6)	MIR|SINE|MIR	5503	NM_001023587	10057	Hs.368563	NM_005688	ENSG00000114770	ABCC5	ABC33|EST277145|MOAT-C|MOATC|MRP5|SMRP|pABC11	ATP binding cassette subfamily C member 5	protein-coding	0.013029	0.399351	
chunk0056_422_1	chr13	94548788	94549136	+	0	NA	Intergenic	MER5A|DNA|hAT-Charlie	47313	NM_014305	23483	Hs.12393	NM_014305	ENSG00000088451	TGDS	CATMANS|SDR2E1|TDPGD	TDP-glucose 4,6-dehydratase	protein-coding	0.043103	0.567335	
chunk0082_419_1	chr17	61314511	61314729	+	0	NA	intron (NM_017679, intron 22 of 23)	intron (NM_017679, intron 22 of 23)	84986	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.004587	0.465753	
chunk0111_318_1	chr20	32309888	32310091	+	0	NA	exon (NM_004798, exon 2 of 9)	exon (NM_004798, exon 2 of 9)	32338	NM_004798	9371	Hs.369670	NM_004798	ENSG00000101350	KIF3B	FLA8|HH0048|KLP-11	kinesin family member 3B	protein-coding	0.024631	0.500000	
chunk0108_396_1	chr2	237242013	237242487	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	156809	NM_198189	10920	Hs.531713	NM_006710	ENSG00000198612	COPS8	COP9|CSN8|SGN8	COP9 signalosome subunit 8	protein-coding	0.006329	0.418947	
chunk0091_167_1	chr19	7664820	7665447	+	0	NA	Intergenic	AluJr|SINE|Alu	-3953	NM_020415	56729	Hs.283091	NM_020415	ENSG00000104918	RETN	ADSF|FIZZ3|RETN1|RSTN|XCP1	resistin	protein-coding	0.007974	0.442675	
chunk0037_122_1	chr11	72833819	72834324	+	0	NA	Intergenic	Intergenic	19665	NM_033388	89849	Hs.653186	NM_033388	ENSG00000168010	ATG16L2	ATG16B|WDR80	autophagy related 16 like 2	protein-coding	0.013861	0.438735	214(AGGAACAAGATGCTCT,-,0.00),215(GGAACAAGATGCTCTT,+,0.00)
chunk0074_27_1	chr16	20439741	20440225	+	0	NA	intron (NM_017888, intron 13 of 13)	L2b|LINE|L2	-11478	NM_001308954	123876	Hs.298252	NM_001010845	ENSG00000183747	ACSM2A	A-923A4.1|ACSM2	acyl-CoA synthetase medium chain family member 2A	protein-coding	0.008264	0.490722	350(AAGCACATTTTGTTCC,-,0.00),351(AGCACATTTTGTTCCT,+,0.00),372(AAGAACAGCCTGATCC,-,0.00),373(AGAACAGCCTGATCCC,+,0.00)
chunk0148_237_1	chr5	9538437	9538897	+	0	NA	intron (NM_003966, intron 1 of 22)	intron (NM_003966, intron 1 of 22)	7454	NM_003966	9037	Hs.27621	NM_003966	ENSG00000112902	SEMA5A	SEMAF|semF	semaphorin 5A	protein-coding	0.015217	0.446855	
chunk0106_417_1	chr2	208031531	208031867	+	0	NA	Intergenic	Intergenic	-6139	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.014881	0.456973	
chunk0091_176_1	chr19	8115508	8115909	+	0	NA	intron (NM_032447, intron 28 of 62)	intron (NM_032447, intron 28 of 62)	31793	NM_032447	84467	Hs.370362	NM_032447	ENSG00000142449	FBN3	-	fibrillin 3	protein-coding	0.014963	0.544776	
chunk0028_200_1	chr10	88952323	88952554	+	0	NA	intron (NM_001141945, intron 1 of 8)	intron (NM_001141945, intron 1 of 8)	385	NM_001613	59	Hs.500483	NM_001613	ENSG00000107796	ACTA2	ACTSA	actin alpha 2, smooth muscle	protein-coding	0.000000	0.362069	
chunk0021_408_1	chr1	246755312	246755919	+	0	NA	intron (NM_016002, intron 5 of 11)	intron (NM_016002, intron 5 of 11)	31539	NM_016002	51097	Hs.498397	NM_016002	ENSG00000143653	SCCPDH	CGI-49|NET11	saccharopine dehydrogenase (putative)	protein-coding	0.016474	0.440789	273(AGGCACACATTGTGCC,-,0.00),274(GGCACACATTGTGCCA,+,0.00)
chunk0177_359_1	chr7	26673091	26673384	+	0	NA	intron (NM_001303468, intron 11 of 12)	intron (NM_001303468, intron 11 of 12)	34152	NM_001302625									0.000000	0.357143	
chunk0104_374_1	chr2	180211726	180212387	+	0	NA	Intergenic	Intergenic	-205003	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.003026	0.370091	463(TAGAACACTGAGTTCC,-,0.00),464(AGAACACTGAGTTCCT,+,0.00)
chunk0122_375_1	chr3	37707092	37707722	+	0	NA	intron (NM_002207, intron 18 of 27)	(TTATTT)n|Simple_repeat|Simple_repeat	154373	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.004762	0.348653	
chunk0009_107_1	chr1	102588473	102588922	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	519799	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.004454	0.368889	
chunk0158_333_1	chr5	133065503	133065780	+	0	NA	intron (NM_002154, intron 2 of 18)	intron (NM_002154, intron 2 of 18)	13671	NM_002154	3308	Hs.90093	NM_002154	ENSG00000170606	HSPA4	APG-2|HEL-S-5a|HS24/P52|HSPH2|RY|hsp70|hsp70RY	heat shock protein family A (Hsp70) member 4	protein-coding	0.000000	0.377698	
chunk0012_417_1	chr1	164479711	164479995	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-79507	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.003521	0.301754	
chunk0042_330_1	chr12	9742606	9743061	+	0	NA	Intergenic	L1M4|LINE|L1	-9534	NM_001267701	160365	Hs.560087	NM_172004	ENSG00000184293	CLECL1	DCAL-1|DCAL1	C-type lectin like 1	protein-coding	0.010989	0.469298	204(TGCACAGGCTGAGCTT,+,0.00),297(TGCACAGGCTGAGCTT,+,0.00)
chunk0121_56_1	chr3	15669950	15670178	+	0	NA	3' UTR (NM_001195098, exon 28 of 28)	3' UTR (NM_001195098, exon 28 of 28)	27307	NR_036085	100422990		NR_036085	ENSG00000264354	MIR3134	-	microRNA 3134	ncRNA	0.000000	0.393013	25(GAGTGCACAGTGTCCC,-,0.00),26(AGTGCACAGTGTCCCC,+,0.00)
chunk0059_109_1	chr14	31090973	31092047	+	0	NA	intron (NM_001128126, intron 5 of 5)	intron (NM_001128126, intron 5 of 5)	64867	NM_001254728	11154	Hs.293411	NM_007077	ENSG00000100478	AP4S1	AP47B|CLA20|CLAPS4|CPSQ6|SPG52	adaptor related protein complex 4 subunit sigma 1	protein-coding	0.005587	0.388837	
chunk0034_133_1	chr11	28537582	28538193	+	0	NA	Intergenic	L1M5|LINE|L1	-60339	NR_107035	102466876		NR_107035	ENSG00000273912	MIR8068	hsa-mir-8068	microRNA 8068	ncRNA	0.003273	0.303922	
chunk0101_144_1	chr2	127618603	127618844	+	0	NA	intron (NM_001080527, intron 25 of 46)	intron (NM_001080527, intron 25 of 46)	-27141	NM_001161416	2840	Hs.46453	NM_005291	ENSG00000144230	GPR17	-	G protein-coupled receptor 17	protein-coding	0.012448	0.504132	
chunk0182_282_1	chr7	98174245	98175098	+	0	NA	intron (NM_014916, intron 7 of 13)	intron (NM_014916, intron 7 of 13)	-37583	NM_177455	168620	Hs.511979	NM_177455	ENSG00000180535	BHLHA15	BHLHB8|MIST1	basic helix-loop-helix family member a15	protein-coding	0.018757	0.504684	267(CAGGACTTCCTGTCCC,-,0.00),268(AGGACTTCCTGTCCCC,+,0.00)
chunk0135_195_1	chr3	188241180	188241419	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	15894	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.025105	0.516667	
chunk0165_134_1	chr6	33348809	33349174	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	-25975	NM_001254717	1616	Hs.336916	NM_001350	ENSG00000204209	DAXX	BING2|DAP6|EAP1|SMIM40	death domain associated protein	protein-coding	0.016438	0.461749	
chunk0038_253_1	chr11	88362735	88362934	+	0	NA	Intergenic	Intergenic	-25047	NM_148170	1075	Hs.128065	NM_001814	ENSG00000109861	CTSC	CPPI|DPP-I|DPP1|DPPI|HMS|JP|JPD|PALS|PDON1|PLS	cathepsin C	protein-coding	0.000000	0.345000	
chunk0110_447_1	chr20	21127765	21128090	+	0	NA	intron (NM_001276389, intron 1 of 10)	intron (NM_001276389, intron 1 of 10)	1944	NM_001163022	55857	Hs.187635	NM_018474	ENSG00000088970	KIZ	C20orf19|HT013|Kizuna|NCRNA00153|PLK1S1|RP69	kizuna centrosomal protein	protein-coding	0.003077	0.386503	
chunk0047_312_1	chr12	73974889	73975176	+	0	NA	Intergenic	L1MEb|LINE|L1	317599	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.003484	0.354167	
chunk0003_84_1	chr1	31657152	31657504	+	0	NA	intron (NM_001856, intron 64 of 70)	L2b|LINE|L2	-12091	NM_012392	553115	Hs.470417	NM_012392	ENSG00000162517	PEF1	ABP32|PEF1A	penta-EF-hand domain containing 1	protein-coding	0.019886	0.586402	156(AAGAACAGACCGTGCC,-,0.00),157(AGAACAGACCGTGCCT,+,0.00),253(ATGAACAGCCTGAGCC,-,0.00),254(TGAACAGCCTGAGCCG,+,0.00)
chunk0200_29_1	chr9	14927093	14927292	+	0	NA	Intergenic	Intergenic	-16197	NM_144966	158326	Hs.50850	NM_144966	ENSG00000164946	FREM1	BNAR|C9orf143|C9orf145|C9orf154|MOTA|TILRR|TRIGNO2	FRAS1 related extracellular matrix 1	protein-coding	0.010050	0.450000	
chunk0063_439_1	chr14	88792638	88792837	+	0	NA	promoter-TSS (NM_183387)	promoter-TSS (NM_183387)	15	NM_183387	161436	Hs.325846	NM_183387	ENSG00000165521	EML5	EMAP-2|EMAP-5	EMAP like 5	protein-coding	0.115578	0.725000	
chunk0184_90_1	chr7	113268614	113268861	+	0	NA	Intergenic	L1PA17|LINE|L1	-150155	NR_015442									0.004049	0.491935	
chunk0040_239_1	chr11	114554141	114554342	+	0	NA	intron (NM_152315, intron 1 of 5)	MLT1J1|LTR|ERVL-MaLR	5654	NM_152315	120400	Hs.550126	NM_152315	ENSG00000095110	NXPE1	FAM55A	neurexophilin and PC-esterase domain family member 1	protein-coding	0.009950	0.460396	124(CAGGACACTGAGTTCT,-,0.00),125(AGGACACTGAGTTCTC,+,0.00)
chunk0176_381_1	chr7	18629613	18629922	+	0	NA	intron (NM_178425, intron 6 of 24)	intron (NM_178425, intron 6 of 24)	120490	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.000000	0.367742	133(AGGAACAGGCAGTCCA,-,0.00),134(GGAACAGGCAGTCCAT,+,0.00)
chunk0207_449_1	chr9	137698247	137698596	+	0	NA	intron (NM_001145527, intron 1 of 15)	intron (NM_001145527, intron 1 of 15)	-64601	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.005731	0.451429	
chunk0032_241_1	chr11	8018461	8018683	+	0	NA	Intergenic	Intergenic	-2063	NR_125366	103581031	Hs.249366	NR_125366	ENSG00000255420	CASC23	LINC01464	cancer susceptibility 23	ncRNA	0.018018	0.497758	
chunk0147_208_1	chr4	179733562	179733761	+	0	NA	Intergenic	Intergenic	1425488	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.010050	0.350000	
chunk0195_269_1	chr8	98091280	98091866	+	0	NA	intron (NM_173549, intron 2 of 2)	MER102c|DNA|hAT-Charlie	25617	NM_005836	10247	Hs.18426	NM_005836	ENSG00000132541	RIDA	HRSP12|P14.5|PSP|UK114|hp14.5	reactive intermediate imine deaminase A homolog	protein-coding	0.005119	0.453152	
chunk0014_162_1	chr1	178288012	178288245	+	0	NA	intron (NM_170692, intron 2 of 17)	MER5C|DNA|hAT-Charlie	-53343	NM_004841	9462	Hs.496139	NM_004841	ENSG00000075391	RASAL2	NGAP	RAS protein activator like 2	protein-coding	0.004292	0.346154	
chunk0122_246_1	chr3	34589651	34590279	+	0	NA	Intergenic	L1PA15|LINE|L1	791394	NM_001256192	10015	Hs.475896	NM_013374	ENSG00000170248	PDCD6IP	AIP1|ALIX|DRIP4|HP95	programmed cell death 6 interacting protein	protein-coding	0.000000	0.344992	
chunk0050_396_1	chr12	109278105	109278492	+	0	NA	3' UTR (NM_213596, exon 10 of 10)	3' UTR (NM_213596, exon 10 of 10)	30922	NM_213596	121643	Hs.528316	NM_213596	ENSG00000139445	FOXN4	-	forkhead box N4	protein-coding	0.018088	0.507732	
chunk0044_60_1	chr12	27751744	27752025	+	0	NA	intron (NM_021821, intron 7 of 7)	LTR18B|LTR|ERVL	19392	NM_001146221	100287284		NM_001146221	ENSG00000205693	MANSC4	-	MANSC domain containing 4	protein-coding	0.021352	0.500000	
chunk0094_207_1	chr2	6493698	6494316	+	0	NA	Intergenic	(TTC)n|Simple_repeat|Simple_repeat	-118585	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.016181	0.445880	
chunk0020_216_1	chr1	235295949	235296386	+	0	NA	intron (NM_031371, intron 2 of 22)	intron (NM_031371, intron 2 of 22)	31320	NM_001206794	51742	Hs.575782	NM_016374	ENSG00000054267	ARID4B	BCAA|BRCAA1|RBBP1L1|RBP1L1|SAP180	AT-rich interaction domain 4B	protein-coding	0.009153	0.456621	
chunk0147_329_1	chr4	185211362	185211568	+	0	NA	intron (NM_031953, intron 1 of 18)	intron (NM_031953, intron 1 of 18)	1335	NM_031953	83891	Hs.369091	NM_031953	ENSG00000109762	SNX25	MSTP043|SBBI31	sorting nexin 25	protein-coding	0.009709	0.352657	
chunk0003_205_1	chr1	35080134	35080423	+	0	NA	intron (NM_024772, intron 1 of 9)	intron (NM_024772, intron 1 of 9)	915	NM_001289091	79830	Hs.471243	NM_024772	ENSG00000197056	ZMYM1	MYM	zinc finger MYM-type containing 1	protein-coding	0.020761	0.437931	
chunk0039_320_1	chr11	103547560	103547868	+	0	NA	Intergenic	(TGTG)n|Simple_repeat|Simple_repeat	-302192	NR_039842	100616457		NR_039842	ENSG00000264200	MIR4693	-	microRNA 4693	ncRNA	0.006494	0.482201	208(AGGGACAGTGTGTGCA,-,0.00),209(GGGACAGTGTGTGCAA,+,0.00)
chunk0010_166_1	chr1	115566733	115567066	+	0	NA	Intergenic	Intergenic	-75054	NM_138959	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.000000	0.272455	
chunk0095_188_1	chr2	17930720	17931241	+	0	NA	5' UTR (NM_002252, exon 3 of 3)	5' UTR (NM_002252, exon 3 of 3)	52323	NM_002252	3790	Hs.414489	NM_002252	ENSG00000170745	KCNS3	KV9.3	potassium voltage-gated channel modifier subfamily S member 3	protein-coding	0.011516	0.450192	
chunk0010_177_1	chr1	115810957	115811605	+	0	NA	Intergenic	MER77|LTR|ERVL	29431	NM_001111061	4808	Hs.46296	NM_005599	ENSG00000177551	NHLH2	HEN2|NSCL2|bHLHa34	nescient helix-loop-helix 2	protein-coding	0.003086	0.468413	351(TAGCACAATCTGATCC,-,0.00),352(AGCACAATCTGATCCA,+,0.00)
chunk0124_308_1	chr3	57992446	57992821	+	0	NA	Intergenic	Intergenic	-15767	NM_001164317	2317	Hs.476448	NM_001457	ENSG00000136068	FLNB	ABP-278|ABP-280|AOI|FH1|FLN-B|FLN1L|LRS1|SCT|TABP|TAP	filamin B	protein-coding	0.000000	0.486702	
chunk0010_403_1	chr1	119549888	119550087	+	0	NA	Intergenic	Intergenic	-13893	NR_033781	128102	Hs.681806	NR_033781		HSD3BP4	-	hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 4	pseudo	0.015075	0.545000	131(CGGTGCATGGTGTTCC,-,0.00),132(GGTGCATGGTGTTCCT,+,0.00)
chunk0088_22_1	chr18	43555151	43555351	+	0	NA	Intergenic	L1PA15|LINE|L1	-277601	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.005000	0.333333	
chunk0209_189_1	chrX	43805470	43806575	+	0	NA	intron (NM_000898, intron 3 of 14)	L1MC3|LINE|L1	76453	NM_000898	4129	Hs.654473	NM_000898	ENSG00000069535	MAOB	-	monoamine oxidase B	protein-coding	0.005430	0.354430	598(TAGTACAGAAAGTTCC,-,0.00),599(AGTACAGAAAGTTCCC,+,0.00),696(TAGATCACTATGTACT,-,0.00),697(AGATCACTATGTACTA,+,0.00)
chunk0007_326_1	chr1	84573805	84574077	+	0	NA	intron (NM_004388, intron 1 of 6)	intron (NM_004388, intron 1 of 6)	539	NM_004388	1486	Hs.513557	NM_004388	ENSG00000117151	CTBS	CTB	chitobiase	protein-coding	0.022059	0.465201	
chunk0054_392_1	chr13	50357714	50357977	+	0	NA	intron (NR_109974, intron 2 of 6)	intron (NR_109974, intron 2 of 6)	169604	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.019011	0.454545	
chunk0060_128_1	chr14	44052765	44053168	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	454330	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.002481	0.309406	
chunk0100_236_1	chr2	112588283	112589087	+	0	NA	intron (NM_001304353, intron 3 of 3)	intron (NM_001304353, intron 3 of 3)	3813	NM_001304354	84269	Hs.375707	NM_032309	ENSG00000125611	CHCHD5	C2orf9|CHTM1|MIC14|MIX14	coiled-coil-helix-coiled-coil-helix domain containing 5	protein-coding	0.013682	0.508075	
chunk0085_51_1	chr18	824235	824870	+	0	NA	Intergenic	Intergenic	-12226	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.003150	0.374214	
chunk0202_144_1	chr9	73492885	73493176	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	341299	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.428082	
chunk0140_397_1	chr4	75408401	75408988	+	0	NA	Intergenic	L1MA5A|LINE|L1	54618	NR_033964	441025	Hs.407667	NR_033964	ENSG00000251383	LINC02483	-	long intergenic non-protein coding RNA 2483	ncRNA	0.005111	0.324830	297(GAGAACATACAGTTTT,-,0.00)
chunk0192_131_1	chr8	61835988	61836343	+	0	NA	Intergenic	L1M2|LINE|L1	121377	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.002817	0.452247	
chunk0109_143_1	chr20	3471075	3471274	+	0	NA	exon (NM_139321, exon 1 of 29)	exon (NM_139321, exon 1 of 29)	156	NM_139321	8455	Hs.276252	NM_012070	ENSG00000088812	ATRN	DPPT-L|MGCA	attractin	protein-coding	0.115578	0.765000	
chunk0206_202_1	chr9	123049696	123050305	+	0	NA	intron (NM_012197, intron 13 of 25)	MIRb|SINE|MIR	16357	NM_005294	2844	Hs.722039	NM_005294	ENSG00000011454	GPR21	-	G protein-coupled receptor 21	protein-coding	0.004926	0.408197	304(CAGAACAGCCTGGCCC,-,0.00),305(AGAACAGCCTGGCCCT,+,0.00)
chunk0142_158_1	chr4	95108950	95109688	+	0	NA	intron (NM_001256792, intron 2 of 10)	intron (NM_001256792, intron 2 of 10)	17828	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.006775	0.370771	
chunk0005_67_1	chr1	55694380	55694926	+	0	NA	Intergenic	Intergenic	469012	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.005495	0.477148	
chunk0075_56_1	chr16	47660022	47660518	+	0	NA	intron (NM_001031835, intron 21 of 31)	intron (NM_001031835, intron 21 of 31)	-198311	NR_110650	101927132	Hs.589404	NR_110650	ENSG00000261231	LINC02133	-	long intergenic non-protein coding RNA 2133	ncRNA	0.010081	0.346076	219(AAGAACAGAGAGTCCA,-,0.00),220(AGAACAGAGAGTCCAT,+,0.00)
chunk0039_242_1	chr11	102085604	102086271	+	0	NA	Intergenic	Intergenic	-24524	NM_001282100	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.007496	0.399701	
chunk0145_304_1	chr4	150199071	150199948	+	0	NA	intron (NM_001040261, intron 5 of 16)	intron (NM_001040261, intron 5 of 16)	121235	NM_001040261	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.003421	0.386105	
chunk0146_400_1	chr4	168839951	168840477	+	0	NA	intron (NM_001166110, intron 1 of 11)	intron (NM_001166110, intron 1 of 11)	8209	NM_001166110	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.003802	0.358634	266(GAGTACATACTGTCCA,-,0.00),267(AGTACATACTGTCCAC,+,0.00)
chunk0062_100_1	chr14	68184820	68185212	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	365237	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.000000	0.346056	
chunk0017_33_1	chr1	204896214	204896600	+	0	NA	intron (NM_001005389, intron 1 of 15)	intron (NM_001005389, intron 1 of 15)	-47819	NM_001160331	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.005181	0.441860	
chunk0008_4_1	chr1	87105029	87105299	+	0	NA	3' UTR (NM_012262, exon 7 of 7)	3' UTR (NM_012262, exon 7 of 7)	-24601	NR_026988	339524	Hs.306423	NM_207357	ENSG00000267272	LINC01140	-	long intergenic non-protein coding RNA 1140	ncRNA	0.000000	0.317343	
chunk0110_22_1	chr20	10337500	10337895	+	0	NA	Intergenic	L1MB7|LINE|L1	94228	NM_018848	8195	Hs.472119	NM_018848	ENSG00000125863	MKKS	BBS6|HMCS|KMS|MKS	McKusick-Kaufman syndrome	protein-coding	0.005063	0.388889	
chunk0084_75_1	chr17	74971944	74972450	+	0	NA	intron (NR_110878, intron 1 of 2)	CpG	608	NM_030630	283987	Hs.11067	NM_030630	ENSG00000167861	HID1	17orf28|C17orf28|DMC1|HID-1	HID1 domain containing	protein-coding	0.069170	0.708087	
chunk0008_293_1	chr1	94935680	94935879	+	0	NA	intron (NR_033998, intron 2 of 3)	intron (NR_033998, intron 2 of 3)	7751	NR_033998	729970	Hs.297988	NR_033998	ENSG00000235501	LOC729970	-	hCG2028352-like	ncRNA	0.005025	0.390000	
chunk0105_155_1	chr2	186623844	186624807	+	0	NA	intron (NM_001144999, intron 3 of 29)	intron (NM_001144999, intron 3 of 29)	24120	NM_001144999	3685	Hs.436873	NM_002210	ENSG00000138448	ITGAV	CD51|MSK8|VNRA|VTNR	integrin subunit alpha V	protein-coding	0.006231	0.383817	
chunk0120_365_1	chr3	11770415	11771451	+	0	NA	Intergenic	Intergenic	-50165	NM_001284390	9686	Hs.740389	NM_014667	ENSG00000144560	VGLL4	VGL-4	vestigial like family member 4	protein-coding	0.021236	0.536162	
chunk0099_201_1	chr2	94601002	94601499	+	0	NA	Intergenic	MIR|SINE|MIR	-14067	NR_024443	100133920	Hs.645503	NR_024443	ENSG00000261522	LOC100133920	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like pseudogene	pseudo	0.018109	0.491968	
chunk0185_108_1	chr7	125660069	125660320	+	0	NA	Intergenic	LTR9|LTR|ERV1	-395903	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.007968	0.519841	
chunk0010_416_1	chr1	119647927	119648500	+	0	NA	promoter-TSS (NM_001080470)	promoter-TSS (NM_001080470)	-446	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.094241	0.712544	
chunk0161_10_1	chr5	165459029	165459228	+	0	NA	Intergenic	Intergenic	988849	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.030151	0.305000	
chunk0180_400_1	chr7	75611538	75612205	+	0	NA	intron (NM_005338, intron 1 of 30)	intron (NM_005338, intron 1 of 30)	-83748	NR_028059	5387	Hs.659871	NM_005395	ENSG00000127957	PMS2P3	PMS2L3|PMS2L9|PMS5|PMSR3	PMS1 homolog 2, mismatch repair system component pseudogene 3	pseudo	0.025487	0.645210	163(GAGAACAGGCTGTTCT,-,0.00),164(AGAACAGGCTGTTCTC,+,0.00)
chunk0112_446_1	chr20	48316452	48316873	+	0	NA	Intergenic	L1ME3G|LINE|L1	-43249	NR_026958	284749	Hs.299080	NR_026958	ENSG00000235621	LINC00494	-	long intergenic non-protein coding RNA 494	ncRNA	0.007126	0.343602	
chunk0136_372_1	chr3	196218228	196218671	+	0	NA	intron (NM_152672, intron 2 of 8)	intron (NM_152672, intron 2 of 8)	1937	NM_152672	200931	Hs.630585	NM_152672	ENSG00000163959	SLC51A	OSTA|OSTalpha	solute carrier family 51 alpha subunit	protein-coding	0.020316	0.500000	
chunk0186_397_1	chr7	144631731	144632198	+	0	NA	intron (NM_001042482, intron 5 of 7)	intron (NM_001042482, intron 5 of 7)	204089	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.010707	0.386752	
chunk0111_312_1	chr20	32235696	32236109	+	0	NA	3' UTR (NM_015352, exon 7 of 7)	3' UTR (NM_015352, exon 7 of 7)	-1893	NR_031726	100302183		NR_031726	ENSG00000284125	MIR1825	MIRN1825|hsa-mir-1825	microRNA 1825	ncRNA	0.000000	0.468599	
chunk0056_428_1	chr13	94892163	94892420	+	0	NA	intron (NR_110754, intron 2 of 4)	MER57B2|LTR|ERV1	-67750	NR_047487	100861544	Hs.48706	NR_047487	ENSG00000260962	LINC00557	-	long intergenic non-protein coding RNA 557	ncRNA	0.015564	0.422481	
chunk0002_399_1	chr1	27278000	27278535	+	0	NA	intron (NM_015023, intron 3 of 15)	MER58A|DNA|hAT-Charlie	43751	NM_001276252	23038	Hs.469154	NM_015023	ENSG00000142784	WDTC1	ADP|DCAF9	WD and tetratricopeptide repeats 1	protein-coding	0.001869	0.399254	
chunk0188_416_1	chr8	18922427	18923072	+	0	NA	intron (NM_015310, intron 2 of 15)	MER21B|LTR|ERVL	90937	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.015504	0.478328	
chunk0011_208_1	chr1	150064968	150065194	+	0	NA	Intergenic	Intergenic	-2212	NM_007259	11311	Hs.443750	NM_007259	ENSG00000136631	VPS45	H1|H1VPS45|SCN5|VPS45A|VPS45B|VPS54A|VSP45|VSP45A	vacuolar protein sorting 45 homolog	protein-coding	0.000000	0.378855	
chunk0018_400_1	chr1	222615498	222615837	+	0	NA	Intergenic	L2a|LINE|L2	-2435	NM_198551	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.005900	0.417647	
chunk0079_339_1	chr17	17685957	17686175	+	0	NA	intron (NM_030665, intron 1 of 5)	L2b|LINE|L2	4593	NM_030665	10743	Hs.655395	NM_030665	ENSG00000108557	RAI1	SMCR|SMS	retinoic acid induced 1	protein-coding	0.045872	0.552511	
chunk0178_103_1	chr7	30772233	30772466	+	0	NA	intron (NM_032222, intron 1 of 17)	intron (NM_032222, intron 1 of 17)	932	NM_032222	84182	Hs.660192	NM_032222	ENSG00000106125	MINDY4	AQP-1|AQP1|C7orf67|CHIP28|FAM188B	MINDY lysine 48 deubiquitinase 4	protein-coding	0.017167	0.427350	
chunk0056_354_1	chr13	92054460	92055047	+	0	NA	intron (NM_004466, intron 6 of 7)	intron (NM_004466, intron 6 of 7)	297454	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.000000	0.324830	
chunk0120_247_1	chr3	8744035	8744338	+	0	NA	intron (NM_001234, intron 1 of 2)	intron (NM_001234, intron 1 of 2)	10386	NM_033337	859	Hs.98303	NM_001234	ENSG00000182533	CAV3	LGMD1C|LQT9|MPDT|RMD2|VIP-21|VIP21	caveolin 3	protein-coding	0.006601	0.480263	
chunk0169_230_1	chr6	104780048	104780445	+	0	NA	intron (NM_020771, intron 14 of 23)	intron (NM_020771, intron 14 of 23)	79673	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.304020	
chunk0166_295_1	chr6	48933876	48934570	+	0	NA	Intergenic	L1MA3|LINE|L1	529105	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.000000	0.279137	
chunk0193_19_1	chr8	70631172	70631464	+	0	NA	intron (NR_038881, intron 1 of 3)	L1PA6|LINE|L1	22741	NR_038881	286190	Hs.662204	NR_038881	ENSG00000246366	LACTB2-AS1	-	LACTB2 antisense RNA 1	ncRNA	0.017123	0.529010	
chunk0055_450_1	chr13	75763482	75763960	+	0	NA	intron (NM_001306080, intron 4 of 30)	intron (NM_001306080, intron 4 of 30)	3060	NM_015842	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.006276	0.367432	
chunk0022_217_1	chr10	13917586	13917789	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	-156597	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.009852	0.450980	
chunk0182_428_1	chr7	101382667	101383439	+	0	NA	intron (NM_001278563, intron 1 of 12)	AluSz|SINE|Alu	20233	NM_133457	136227	Hs.654854	NM_133457	ENSG00000160963	COL26A1	EMI6|EMID2|EMU2|SH2B	collagen type XXVI alpha 1 chain	protein-coding	0.009067	0.391979	
chunk0136_234_1	chr4	8439145	8439585	+	0	NA	intron (NM_003501, intron 1 of 17)	HERV3-int|LTR|ERV1	1360	NM_001101667	8310	Hs.479122	NM_003501	ENSG00000087008	ACOX3	-	acyl-CoA oxidase 3, pristanoyl	protein-coding	0.006818	0.392290	
chunk0052_397_1	chr12	130754525	130754724	+	0	NA	Intergenic	(AGCAGG)n|Simple_repeat|Simple_repeat	84650	NM_001980	2054	Hs.437585	NM_001980	ENSG00000111450	STX2	EPIM|EPM|STX2A|STX2B|STX2C	syntaxin 2	protein-coding	0.000000	0.505000	
chunk0004_101_1	chr1	43991543	43991862	+	0	NA	promoter-TSS (NM_152499)	promoter-TSS (NM_152499)	94	NM_152499	149473	Hs.632394	NM_152499	ENSG00000159214	CCDC24	-	coiled-coil domain containing 24	protein-coding	0.094044	0.718750	145(AAGGACTGGCAGTTCC,-,0.00),146(AGGACTGGCAGTTCCG,+,0.00)
chunk0093_214_1	chr19	49791017	49791333	+	0	NA	promoter-TSS (NR_106857)	promoter-TSS (NR_106857)	-691	NR_106857	102465479		NR_106857	ENSG00000276270	MIR6799	hsa-mir-6799	microRNA 6799	ncRNA	0.018987	0.536278	120(TGGCACAGGCTGTTCC,-,0.00),121(GGCACAGGCTGTTCCC,+,0.00)
chunk0192_318_1	chr8	67064297	67064556	+	0	NA	promoter-TSS (NM_024790)	promoter-TSS (NM_024790)	58	NM_024790	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.108108	0.723077	
chunk0119_35_1	chr22	40437741	40438031	+	0	NA	intron (NM_001282660, intron 1 of 11)	L2a|LINE|L2	25554	NM_001282660	57591	Hs.654688	NM_020831	ENSG00000196588	MRTFA	BSAC|MAL|MKL|MKL1|MRTF-A	myocardin related transcription factor A	protein-coding	0.020690	0.419244	
chunk0012_176_1	chr1	159161047	159161247	+	0	NA	Intergenic	Intergenic	-10440	NM_021189	57863	Hs.365689	NM_021189	ENSG00000162706	CADM3	BIgR|IGSF4B|NECL1|Necl-1|TSLL1|synCAM3	cell adhesion molecule 3	protein-coding	0.010000	0.487562	
chunk0133_408_1	chr3	174394717	174395111	+	0	NA	Intergenic	Intergenic	-464407	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.002538	0.336709	
chunk0167_211_1	chr6	65638960	65639229	+	0	NA	intron (NM_001142801, intron 2 of 11)	intron (NM_001142801, intron 2 of 11)	-59290	NM_198283	346007	Hs.25067	NM_198283	ENSG00000188107	EYS	C6orf178|C6orf179|C6orf180|EGFL10|EGFL11|RP25|SPAM|bA166P24.2|bA307F22.3|bA74E24.1|dJ1018A4.2|dJ22I17.2|dJ303F19.1	eyes shut homolog	protein-coding	0.000000	0.307407	
chunk0057_342_1	chr13	107711758	107712328	+	0	NA	intron (NM_001080396, intron 1 of 2)	intron (NM_001080396, intron 1 of 2)	123415	NR_046848	100874375	Hs.653972	NR_046848		FAM155A-IT1	-	FAM155A intronic transcript 1	ncRNA	0.001754	0.323993	
chunk0012_167_1	chr1	158275086	158275622	+	0	NA	Intergenic	LTR16|LTR|ERVL	-14419	NM_001765	911	Hs.132448	NM_001765	ENSG00000158481	CD1C	BDCA1|CD1|CD1A|R7	CD1c molecule	protein-coding	0.003731	0.445065	
chunk0092_202_1	chr19	31023110	31023361	+	0	NA	Intergenic	MER70A|LTR|ERVL	326049	NM_020856	57616	Hs.278436	NM_020856	ENSG00000121297	TSHZ3	TSH3|ZNF537	teashirt zinc finger homeobox 3	protein-coding	0.031873	0.503968	146(TAGAACACGATGTCCT,-,0.00),147(AGAACACGATGTCCTT,+,0.00)
chunk0126_15_1	chr3	73516687	73517007	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-4475	NR_121660	101927296	Hs.662049	NR_121660		LOC101927296	-	uncharacterized LOC101927296	ncRNA	0.012500	0.454829	109(CAGGACACGGAGTCCT,-,0.00),110(AGGACACGGAGTCCTG,+,0.00)
chunk0090_348_1	chr18	76528713	76529237	+	0	NA	intron (NR_015417, intron 1 of 2)	intron (NR_015417, intron 1 of 2)	320	NR_015417	284276	Hs.390287	NR_015417	ENSG00000266256	LINC00908	-	long intergenic non-protein coding RNA 908	ncRNA	0.036260	0.571429	
chunk0115_391_1	chr21	30477676	30478481	+	0	NA	Intergenic	Intergenic	2239	NM_181607	337882	Hs.61552	NM_181607	ENSG00000184351	KRTAP19-1	KAP19.1	keratin associated protein 19-1	protein-coding	0.004969	0.348635	
chunk0152_239_1	chr5	60544044	60544582	+	0	NA	intron (NR_024617, intron 3 of 3)	L2c|LINE|L2	-56215	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005576	0.365492	
chunk0086_239_1	chr18	22848580	22848855	+	0	NA	Intergenic	Intergenic	-61880	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.000000	0.369565	128(GGGAACAAGCTGCCCC,-,0.00)
chunk0142_396_1	chr4	102631682	102631942	+	0	NA	3' UTR (NM_005908, exon 17 of 17)	3' UTR (NM_005908, exon 17 of 17)	129182	NM_005908	4126	Hs.480415	NM_005908	ENSG00000109323	MANBA	MANB1	mannosidase beta	protein-coding	0.011538	0.494253	
chunk0211_446_1	chrX	129692414	129692850	+	0	NA	Intergenic	Intergenic	-37676	NM_017413	8862	Hs.303084	NM_017413	ENSG00000171388	APLN	APEL|XNPEP2	apelin	protein-coding	0.004587	0.400458	
chunk0002_77_1	chr1	14258995	14259623	+	0	NA	Intergenic	Intergenic	-339408	NM_201628	23254	Hs.368823	NM_015209	ENSG00000189337	KAZN	KAZ	kazrin, periplakin interacting protein	protein-coding	0.033439	0.559618	248(TGGGACAGTTTGTTCC,-,0.00),249(GGGACAGTTTGTTCCA,+,0.00)
chunk0102_237_1	chr2	148877183	148877797	+	0	NA	intron (NM_004522, intron 1 of 25)	intron (NM_004522, intron 1 of 25)	2267	NM_004522	3800	Hs.435557	NM_004522	ENSG00000168280	KIF5C	CDCBM2|KINN|NKHC|NKHC-2|NKHC2	kinesin family member 5C	protein-coding	0.011401	0.479675	409(GGGGACATCTAGTCCC,-,0.00),410(GGGACATCTAGTCCCT,+,0.00)
chunk0068_117_1	chr15	52466366	52466766	+	0	NA	intron (NM_001142495, intron 1 of 39)	L1M2|LINE|L1	62484	NM_000259	4644	Hs.21213	NM_000259	ENSG00000197535	MYO5A	GS1|MYH12|MYO5|MYR12	myosin VA	protein-coding	0.002500	0.536160	
chunk0179_297_1	chr7	50036480	50036945	+	0	NA	intron (NM_001159878, intron 4 of 7)	L1MEd|LINE|L1	56552	NM_007009	11055	Hs.388841	NM_007009	ENSG00000042813	ZPBP	ZPBP1	zona pellucida binding protein	protein-coding	0.000000	0.266094	
chunk0198_326_1	chr8	139897064	139897270	+	0	NA	intron (NM_001160372, intron 20 of 22)	intron (NM_001160372, intron 20 of 22)	-194111	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.014563	0.526570	
chunk0045_171_1	chr12	46873056	46873396	+	0	NA	Intergenic	MIRb|SINE|MIR	-47229	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.000000	0.337243	
chunk0120_42_1	chr3	2844756	2845173	+	0	NA	intron (NM_001206955, intron 6 of 23)	Tigger13a|DNA|TcMar-Tigger	-47251	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.009592	0.368421	181(TGGAGCACTCTGTTCC,-,0.00),182(GGAGCACTCTGTTCCT,+,0.00)
chunk0057_220_1	chr13	104064713	104064960	+	0	NA	Intergenic	Intergenic	639636	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.004049	0.395161	
chunk0177_241_1	chr7	24951580	24952061	+	0	NA	intron (NM_015550, intron 1 of 22)	intron (NM_015550, intron 1 of 22)	28392	NM_015550	26031	Hs.520259	NM_015550	ENSG00000070882	OSBPL3	ORP-3|ORP3|OSBP3	oxysterol binding protein like 3	protein-coding	0.006237	0.367220	
chunk0014_412_1	chr1	183069768	183070187	+	0	NA	intron (NM_002293, intron 1 of 27)	L2c|LINE|L2	46517	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.007160	0.442857	
chunk0212_312_1	chrX	143597470	143597901	+	0	NA	Intergenic	Intergenic	36818	NM_001184750	139065	Hs.272284	NM_173078	ENSG00000179542	SLITRK4	-	SLIT and NTRK like family member 4	protein-coding	0.004640	0.351852	196(TAGAACATGTTGTCCA,-,0.00),197(AGAACATGTTGTCCAA,+,0.00)
chunk0020_203_1	chr1	234987554	234987824	+	0	NA	Intergenic	Intergenic	-23690	NR_125945	101927851	Hs.520684	NR_125945	ENSG00000238005	LOC101927851	-	uncharacterized LOC101927851	ncRNA	0.022222	0.538745	
chunk0043_182_1	chr12	17949857	17950056	+	0	NA	Intergenic	L1MA9|LINE|L1	140237	NM_001286201	79785	Hs.732831	NM_024730	ENSG00000111404	RERGL	-	RERG like	protein-coding	0.000000	0.560000	
chunk0030_250_1	chr10	115566782	115567312	+	0	NA	intron (NM_207303, intron 26 of 28)	intron (NM_207303, intron 26 of 28)	473682	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.003774	0.342750	
chunk0094_98_1	chr2	4139465	4140195	+	0	NA	Intergenic	Intergenic	-165798	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.006849	0.389877	
chunk0164_385_1	chr6	26112929	26113296	+	0	NA	Intergenic	Intergenic	-4976	NM_005323	3010	Hs.533293	NM_005323	ENSG00000187475	HIST1H1T	H1.6|H1FT|H1t|dJ221C16.2	histone cluster 1 H1 family member t	protein-coding	0.008174	0.385870	
chunk0165_57_1	chr6	30672599	30673110	+	0	NA	5' UTR (NM_003587, exon 1 of 20).3	5' UTR (NM_003587, exon 1 of 20).3	199	NM_001164239	8449	Hs.485060	NM_003587	ENSG00000204560	DHX16	DBP2|DDX16|PRO2014|PRP8|PRPF2|Prp2	DEAH-box helicase 16	protein-coding	0.086106	0.634766	
chunk0150_330_1	chr5	38441791	38442430	+	0	NA	intron (NM_152403, intron 17 of 21)	intron (NM_152403, intron 17 of 21)	-3366	NM_182801	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.006260	0.317188	
chunk0029_5_1	chr10	95300280	95300627	+	0	NA	Intergenic	L1MC4|LINE|L1	-9305	NM_020992	9124	Hs.368525	NM_020992	ENSG00000107438	PDLIM1	CLIM1|CLP-36|CLP36|HEL-S-112|hCLIM1	PDZ and LIM domain 1	protein-coding	0.008646	0.402299	187(AAGAACATCGTGTAAC,-,0.00)
chunk0208_286_1	chrX	21914312	21915060	+	0	NA	Intergenic	Intergenic	-25887	NM_001258423	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.002674	0.361816	
chunk0159_321_1	chr5	143561126	143561833	+	0	NA	Intergenic	Intergenic	-118381	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.009901	0.409605	333(GAGCACACATTGTTCT,-,0.00),334(AGCACACATTGTTCTC,+,0.00)
chunk0079_340_1	chr17	17697232	17697486	+	0	NA	intron (NM_030665, intron 1 of 5)	intron (NM_030665, intron 1 of 5)	15886	NM_030665	10743	Hs.655395	NM_030665	ENSG00000108557	RAI1	SMCR|SMS	retinoic acid induced 1	protein-coding	0.027559	0.541176	
chunk0014_144_1	chr1	177956408	177956973	+	0	NA	intron (NM_033127, intron 10 of 25)	intron (NM_033127, intron 10 of 25)	13225	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.003540	0.302120	275(AAGTACAGACAGTCCC,-,0.00),276(AGTACAGACAGTCCCT,+,0.00)
chunk0056_9_1	chr13	77090736	77091632	+	0	NA	intron (NM_015057, intron 59 of 82)	intron (NM_015057, intron 59 of 82)	15670	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.003348	0.343367	
chunk0185_132_1	chr7	126846894	126847315	+	0	NA	intron (NR_028041, intron 5 of 10)	intron (NR_028041, intron 5 of 10)	211080	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.000000	0.310427	
chunk0126_443_1	chr3	87153671	87154113	+	0	NA	intron (NR_104153, intron 1 of 2)	intron (NR_104153, intron 1 of 2)	64612	NR_047469	100846978	Hs.570649	NR_047469	ENSG00000281392	LINC00506	-	long intergenic non-protein coding RNA 506	ncRNA	0.004525	0.358916	
chunk0162_284_1	chr6	6178830	6179038	+	0	NA	intron (NM_000129, intron 11 of 14)	L2|LINE|L2	-9499	NR_107007	102466866		NR_107007	ENSG00000263572	MIR7853	hsa-mir-7853	microRNA 7853	ncRNA	0.024038	0.521531	
chunk0063_388_1	chr14	86919277	86919583	+	0	NA	intron (NR_038445, intron 3 of 4)	Charlie29a|DNA|hAT-Charlie	13652	NR_038445	283585	Hs.381998	NR_038445	ENSG00000258804	LINC01148	-	long intergenic non-protein coding RNA 1148	ncRNA	0.009804	0.270358	
chunk0042_6_1	chr12	1076909	1077482	+	0	NA	intron (NR_027949, intron 2 of 15)	intron (NR_027949, intron 2 of 15)	49447	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.008726	0.322300	
chunk0011_374_1	chr1	153649701	153650147	+	0	NA	Intergenic	Intergenic	-8730	NM_012437	23557	Hs.32018	NM_012437	ENSG00000143553	SNAPIN	BLOC1S7|BLOS7|BORCS3|SNAPAP	SNAP associated protein	protein-coding	0.004484	0.548098	
chunk0182_9_1	chr7	91037786	91038497	+	0	NA	intron (NM_001287136, intron 9 of 13)	intron (NM_001287136, intron 9 of 13)	-226327	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.005626	0.360955	
chunk0031_263_1	chr10	127371331	127371782	+	0	NA	intron (NM_001290223, intron 33 of 51)	intron (NM_001290223, intron 33 of 51)	-175398	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.002217	0.393805	
chunk0169_249_1	chr6	105268133	105268662	+	0	NA	Intergenic	L1MC1|LINE|L1	-88414	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.011342	0.396226	
chunk0049_252_1	chr12	93704083	93704749	+	0	NA	intron (NM_003805, intron 2 of 2)	L2a|LINE|L2	27041	NM_003805	8738	Hs.38533	NM_003805	ENSG00000169372	CRADD	MRT34|RAIDD	CASP2 and RIPK1 domain containing adaptor with death domain	protein-coding	0.004505	0.391304	216(TGGTACATCATGTACT,-,0.00),217(GGTACATCATGTACTC,+,0.00),646(AGGGACACCGTGACCT,-,0.00),647(GGGACACCGTGACCTG,+,0.00)
chunk0128_55_1	chr3	104826349	104826668	+	0	NA	Intergenic	Intergenic	-540205	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.003135	0.400000	
chunk0132_148_1	chr3	156537395	156537927	+	0	NA	3' UTR (NM_003471, exon 14 of 14)	3' UTR (NM_003471, exon 14 of 14)	16464	NM_001308205	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.000000	0.333959	
chunk0101_162_1	chr2	128579015	128579579	+	0	NA	Intergenic	LTR24|LTR|ERV1	-260700	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.012411	0.428319	
chunk0079_222_1	chr17	15099531	15100083	+	0	NA	Intergenic	L2|LINE|L2	6380	NR_103559	94151	Hs.98684	NR_103559		CDRT8	-	CMT1A duplicated region transcript 8	ncRNA	0.009058	0.424955	
chunk0069_310_1	chr15	65569797	65570309	+	0	NA	intron (NM_016395, intron 7 of 10)	intron (NM_016395, intron 7 of 10)	39564	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.003906	0.356725	
chunk0035_410_1	chr11	56890675	56891320	+	0	NA	Intergenic	Intergenic	42519	NR_110136	101927120	Hs.472675	NR_110136	ENSG00000255433	LINC02735	-	long intergenic non-protein coding RNA 2735	ncRNA	0.010853	0.461300	
chunk0036_314_1	chr11	66135452	66135702	+	0	NA	intron (NM_018026, intron 1 of 23)	intron (NM_018026, intron 1 of 23)	65224	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.008000	0.438247	
chunk0030_118_1	chr10	112906642	112907228	+	0	NA	Intergenic	Intergenic	-43315	NM_001198529	6934	Hs.593995	NM_030756	ENSG00000148737	TCF7L2	TCF-4|TCF4	transcription factor 7 like 2	protein-coding	0.022184	0.538330	468(GGGGACATGCTGTCCT,-,0.00),469(GGGACATGCTGTCCTC,+,0.00)
chunk0209_161_1	chrX	43143750	43144149	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-33045	NR_110387	101927501	Hs.495998	NR_110387	ENSG00000224294	PINCR	-	p53-induced noncoding RNA	ncRNA	0.002506	0.377500	
chunk0190_159_1	chr8	31351964	31352247	+	0	NA	Intergenic	LTR39|LTR|ERV1	-287647	NM_013962	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.003534	0.415493	
chunk0011_232_1	chr1	150407683	150408089	+	0	NA	intron (NM_001297673, intron 1 of 10)	intron (NM_001297673, intron 1 of 10)	43775	NM_015203	23248	Hs.213666	NM_015203	ENSG00000163125	RPRD2	HSPC099|KIAA0460	regulation of nuclear pre-mRNA domain containing 2	protein-coding	0.007389	0.380835	125(TGTACTGAGTGTCCTT,+,0.00)
chunk0016_98_1	chr1	195237605	195237804	+	0	NA	Intergenic	MER52A|LTR|ERV1	1344777	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.000000	0.580000	
chunk0003_95_1	chr1	31910977	31911268	+	0	NA	intron (NM_080391, intron 4 of 5)	intron (NM_080391, intron 4 of 5)	8536	NM_001195100	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.006873	0.397260	93(ATGAACAAACAGTACC,-,0.00)
chunk0189_269_1	chr8	25319758	25320243	+	0	NA	intron (NM_024940, intron 15 of 51)	intron (NM_024940, intron 15 of 51)	-25402	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.006186	0.386831	
chunk0043_89_1	chr12	14710872	14711429	+	0	NA	Intergenic	Intergenic	-14565	NM_004963	2984	Hs.524278	NM_004963	ENSG00000070019	GUCY2C	DIAR6|GC-C|GUC2C|MECIL|MUCIL|STAR	guanylate cyclase 2C	protein-coding	0.005386	0.379928	
chunk0087_448_1	chr18	42644847	42645170	+	0	NA	intron (NR_046174, intron 7 of 9)	MER89|LTR|ERV1	458340	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.009288	0.447531	
chunk0034_405_1	chr11	38009971	38010349	+	0	NA	Intergenic	Intergenic	636196	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.002646	0.356201	
chunk0196_429_1	chr8	116324733	116325238	+	0	NA	promoter-TSS (NR_046215)	promoter-TSS (NR_046215)	74	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.015842	0.498024	
chunk0152_322_1	chr5	62087872	62088231	+	0	NA	Intergenic	Intergenic	-218111	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.008357	0.355556	
chunk0186_319_1	chr7	143069900	143070099	+	0	NA	Intergenic	Intergenic	-6214	NR_002140	89883	Hs.339818	NR_002140		OR6W1P	OR6W1|sdolf	olfactory receptor family 6 subfamily W member 1 pseudogene	pseudo	0.015075	0.555000	
chunk0015_256_1	chr1	188073353	188073867	+	0	NA	Intergenic	L1PA15|LINE|L1	629982	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001946	0.374757	
chunk0195_281_1	chr8	98374291	98374803	+	0	NA	Intergenic	Intergenic	-52475	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.003906	0.428850	
chunk0099_51_1	chr2	84502919	84503215	+	0	NA	Intergenic	L1M1|LINE|L1	-13388	NM_001370	1768	Hs.249972	NM_001370	ENSG00000115423	DNAH6	DNHL1|Dnahc6|HL-2|HL2	dynein axonemal heavy chain 6	protein-coding	0.003378	0.346801	
chunk0164_357_1	chr6	25548501	25548700	+	0	NA	intron (NM_017640, intron 26 of 36)	intron (NM_017640, intron 26 of 36)	-103601	NM_006998	10590	Hs.116428	NM_006998	ENSG00000079689	SCGN	CALBL|DJ501N12.8|SECRET|SEGN|setagin	secretagogin, EF-hand calcium binding protein	protein-coding	0.005025	0.470000	
chunk0160_221_1	chr5	155027940	155028537	+	0	NA	Intergenic	L1M1|LINE|L1	14538	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.001675	0.424749	
chunk0150_349_1	chr5	38666806	38667488	+	0	NA	intron (NR_103554, intron 8 of 8)	intron (NR_103554, intron 8 of 8)	53126	NR_104631	101926904	Hs.634191	NR_104631	ENSG00000249740	LINC01265	-	long intergenic non-protein coding RNA 1265	ncRNA	0.007331	0.496340	321(AAGCACAGCGTGTTCC,-,0.00),322(AGCACAGCGTGTTCCT,+,0.00),342(ATGAACATACTGTTAT,-,0.00)
chunk0066_260_1	chr15	34850087	34850432	+	0	NA	Intergenic	Intergenic	-54533	NM_005159	70	Hs.118127	NM_005159	ENSG00000159251	ACTC1	ACTC|ASD5|CMD1R|CMH11|LVNC4	actin alpha cardiac muscle 1	protein-coding	0.026087	0.537572	
chunk0058_206_1	chr14	24908401	24908625	+	0	NA	intron (NM_014178, intron 2 of 5)	L2|LINE|L2	140487	NM_001304477	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.004464	0.444444	
chunk0026_407_1	chr10	70227876	70228451	+	0	NA	intron (NM_021129, intron 2 of 10)	intron (NM_021129, intron 2 of 10)	5271	NM_021129	5464	Hs.437403	NM_021129	ENSG00000180817	PPA1	HEL-S-66p|IOPPP|PP|PP1|SID6-8061	pyrophosphatase (inorganic) 1	protein-coding	0.001739	0.378472	267(TGGGACAGGGCGTGCC,-,0.00),268(GGGACAGGGCGTGCCA,+,0.00)
chunk0193_334_1	chr8	79310870	79311265	+	0	NA	Intergenic	L2c|LINE|L2	-299747	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.005063	0.363636	
chunk0092_238_1	chr19	32702497	32702886	+	0	NA	intron (NM_001105570, intron 1 of 2)	L1MEc|LINE|L1	10730	NM_001105570	390916	Hs.203961	NM_001105570	ENSG00000213965	NUDT19	RP2	nudix hydrolase 19	protein-coding	0.007712	0.356410	
chunk0067_331_1	chr15	48308358	48308751	+	0	NA	Intergenic	MIRb|SINE|MIR	-22870	NM_001025248	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.007634	0.365482	
chunk0026_173_1	chr10	63289348	63289637	+	0	NA	intron (NM_032776, intron 2 of 25)	intron (NM_032776, intron 2 of 25)	-20269	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.000000	0.289655	
chunk0127_41_1	chr3	88802038	88802237	+	0	NA	Intergenic	L1PA13|LINE|L1	-305387	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.005025	0.325000	
chunk0033_99_1	chr11	14235830	14236168	+	0	NA	intron (NM_006108, intron 6 of 15)	L2a|LINE|L2	122486	NM_001177315	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.005917	0.519174	87(GGGAACAGCAAGTGCA,-,0.00),88(GGAACAGCAAGTGCAA,+,0.00)
chunk0203_341_1	chr9	89794595	89795185	+	0	NA	Intergenic	Intergenic	155107	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.023729	0.522843	177(GTTACAGAGTGTGCTT,+,0.00)
chunk0022_299_1	chr10	15601764	15602313	+	0	NA	intron (NM_001291494, intron 19 of 28)	intron (NM_001291494, intron 19 of 28)	118297	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.005464	0.345455	
chunk0039_264_1	chr11	102344902	102345116	+	0	NA	Intergenic	L1MC5a|LINE|L1	-2173	NM_001256166	329	Hs.696238	NM_001166	ENSG00000110330	BIRC2	API1|HIAP2|Hiap-2|MIHB|RNF48|c-IAP1|cIAP1	baculoviral IAP repeat containing 2	protein-coding	0.004673	0.386047	
chunk0089_188_1	chr18	59901365	59901564	+	0	NA	intron (NM_021127, intron 1 of 1)	intron (NM_021127, intron 1 of 1)	1504	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.010050	0.340000	
chunk0042_251_1	chr12	6470560	6470759	+	0	NA	non-coding (NR_123717, exon 1 of 4)	non-coding (NR_123717, exon 1 of 4)	240	NM_016830	6843	Hs.20021	NM_014231	ENSG00000139190	VAMP1	CMS25|SPAX1|SYB1|VAMP-1	vesicle associated membrane protein 1	protein-coding	0.115578	0.670000	
chunk0019_373_1	chr1	229893133	229893555	+	0	NA	Intergenic	Intergenic	-164445	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.007109	0.401891	198(CTAAACAGGGTGTTCT,-,0.00),199(TAAACAGGGTGTTCTC,+,0.00)
chunk0086_322_1	chr18	24362879	24363196	+	0	NA	intron (NM_080597, intron 4 of 27)	L1M4a1|LINE|L1	34832	NM_080597	114876	Hs.370725	NM_018030	ENSG00000141447	OSBPL1A	ORP-1|ORP1|OSBPL1B	oxysterol binding protein like 1A	protein-coding	0.006309	0.452830	
chunk0152_240_1	chr5	60699697	60700109	+	0	NA	intron (NM_018369, intron 1 of 10)	CpG	263	NM_001145208	55789	Hs.482233	NM_018369	ENSG00000035499	DEPDC1B	BRCC3|XTP1	DEP domain containing 1B	protein-coding	0.065534	0.634383	54(GGGAACAGCCTGGTCT,-,0.00),55(GGAACAGCCTGGTCTT,+,0.00)
chunk0128_184_1	chr3	107438542	107439256	+	0	NA	intron (NR_110039, intron 1 of 2)	intron (NR_110039, intron 1 of 2)	7969	NR_110039	101929607	Hs.252565	NR_110039	ENSG00000273125	LINC01990	-	long intergenic non-protein coding RNA 1990	ncRNA	0.005602	0.404196	343(TGGAACACGGTGTTCC,-,0.00),344(GGAACACGGTGTTCCT,+,0.00)
chunk0117_383_1	chr21	45212300	45212589	+	0	NA	intron (NM_015834, intron 10 of 12)	intron (NM_015834, intron 10 of 12)	75452	NM_133635	23275	Hs.592164	NM_015227	ENSG00000186866	POFUT2	C21orf80|FUT13	protein O-fucosyltransferase 2	protein-coding	0.006920	0.558621	
chunk0187_178_1	chr7	150928836	150929399	+	0	NA	Intergenic	L1MC5|LINE|L1	26712	NM_001204798	3757	Hs.647099	NM_000238	ENSG00000055118	KCNH2	ERG-1|ERG1|H-ERG|HERG|HERG1|Kv11.1|LQT2|SQT1	potassium voltage-gated channel subfamily H member 2	protein-coding	0.007105	0.381206	
chunk0048_243_1	chr12	81594921	81595254	+	0	NA	intron (NM_001220474, intron 2 of 30)	UCON132b|DNA|hAT-Tip100	3284	NM_001220478	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003003	0.341317	
chunk0020_390_1	chr1	240459190	240459460	+	0	NA	intron (NM_020066, intron 16 of 17)	L4_C_Mam|LINE|RTE-X	152837	NM_022469	64388	Hs.98206	NM_022469	ENSG00000180875	GREM2	CKTSF1B2|DAND3|PRDC|STHAG9	gremlin 2, DAN family BMP antagonist	protein-coding	0.007407	0.420664	
chunk0202_162_1	chr9	73751652	73751851	+	0	NA	Intergenic	L1PA16|LINE|L1	600020	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.560000	
chunk0050_210_1	chr12	104285803	104286238	+	0	NA	promoter-TSS (NM_001261446)	promoter-TSS (NM_001261446)	-662	NM_001261446	7296	Hs.654922	NM_003330	ENSG00000198431	TXNRD1	GRIM-12|TR|TR1|TRXR1|TXNR	thioredoxin reductase 1	protein-coding	0.006897	0.440367	
chunk0197_300_1	chr8	124490571	124491702	+	0	NA	intron (NR_027427, intron 12 of 12)	L2a|LINE|L2	16369	NM_007218	11236	Hs.744151	NM_007218	ENSG00000170881	RNF139	HRCA1|RCA1|TRC8	ring finger protein 139	protein-coding	0.005305	0.452297	
chunk0074_198_1	chr16	24986836	24987406	+	0	NA	intron (NM_018054, intron 1 of 18)	MER58B|DNA|hAT-Charlie	28257	NM_018054	55114	Hs.373793	NM_018054	ENSG00000140750	ARHGAP17	MST066|MST110|MSTP038|MSTP066|MSTP110|NADRIN|PP367|PP4534|RICH-1|RICH1|WBP15	Rho GTPase activating protein 17	protein-coding	0.012281	0.441331	
chunk0083_110_1	chr17	64708739	64709199	+	0	NA	Intergenic	Intergenic	-46701	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.013043	0.431670	
chunk0131_305_1	chr3	150727756	150728250	+	0	NA	Intergenic	Intergenic	10982	NR_121657	101928105		NR_121657		LOC101928105	-	uncharacterized LOC101928105	ncRNA	0.016194	0.533333	250(GGGAACAGTGTGTGCT,-,0.00),251(GGAACAGTGTGTGCTG,+,0.00)
chunk0041_21_1	chr12	510140	510936	+	0	NA	intron (NM_173593, intron 1 of 19)	intron (NM_173593, intron 1 of 19)	50161	NM_173593	283358	Hs.504416	NM_173593	ENSG00000139044	B4GALNT3	-	beta-1,4-N-acetyl-galactosaminyltransferase 3	protein-coding	0.012563	0.535759	
chunk0100_265_1	chr2	113708929	113709499	+	0	NA	Intergenic	Intergenic	12154	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.008772	0.397548	
chunk0073_160_1	chr16	8055600	8056292	+	0	NA	Intergenic	Intergenic	533892	NR_110736	283953	Hs.150849	NM_001146336	ENSG00000232258	TMEM114	-	transmembrane protein 114	protein-coding	0.011561	0.401154	379(AAGAACACGGTGTCCT,-,0.00),380(AGAACACGGTGTCCTA,+,0.00)
chunk0127_16_1	chr3	88149503	88150291	+	0	NA	promoter-TSS (NM_001195308)	promoter-TSS (NM_001195308)	-31	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.065990	0.594423	
chunk0142_210_1	chr4	97554963	97555714	+	0	NA	Intergenic	MER34C_|LTR|ERV1	188412	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.001332	0.333777	
chunk0201_346_1	chr9	66608258	66608462	+	0	NA	Intergenic	L1MEg|LINE|L1	-292369	NM_033160	26149	Hs.522147	NM_033160	ENSG00000274349	ZNF658	-	zinc finger protein 658	protein-coding	0.000000	0.331707	
chunk0178_435_1	chr7	41233063	41233363	+	0	NA	Intergenic	Intergenic	131609	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.006667	0.435216	
chunk0017_194_1	chr1	207393442	207393879	+	0	NA	Intergenic	L1MC1|LINE|L1	-60640	NM_001877	1380	Hs.445757	NM_001877	ENSG00000117322	CR2	C3DR|CD21|CR|CVID7|SLEB9	complement C3d receptor 2	protein-coding	0.016018	0.422374	
chunk0063_440_1	chr14	88829198	88829575	+	0	NA	intron (NM_198309, intron 2 of 14)	intron (NM_198309, intron 2 of 14)	5233	NM_198310	123016	Hs.303055	NM_144596	ENSG00000165533	TTC8	BBS8|RP51	tetratricopeptide repeat domain 8	protein-coding	0.007958	0.322751	
chunk0199_108_1	chr9	3346596	3346982	+	0	NA	intron (NM_001282116, intron 2 of 16)	intron (NM_001282116, intron 2 of 16)	48807	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.007772	0.377261	145(CTGCACAGTCTGTACC,-,0.00),146(TGCACAGTCTGTACCT,+,0.00)
chunk0040_240_1	chr11	114662452	114662828	+	0	NA	Intergenic	L1M1|LINE|L1	-15838	NM_182495	120406	Hs.446760	NM_182495	ENSG00000204361	NXPE2	FAM55B	neurexophilin and PC-esterase domain family member 2	protein-coding	0.010638	0.541114	
chunk0147_374_1	chr4	185993578	185993796	+	0	NA	Intergenic	MIRb|SINE|MIR	-36971	NM_001270771	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.009174	0.442922	
chunk0109_45_1	chr20	812511	812736	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-21074	NM_001289146	83541	Hs.574822	NM_031424	ENSG00000125898	FAM110A	C20orf55|F10|bA371L19.3	family with sequence similarity 110 member A	protein-coding	0.004444	0.420354	20(CAGTGCATTGTGTCCT,-,0.00),21(AGTGCATTGTGTCCTT,+,0.00)
chunk0085_201_1	chr18	6585416	6585686	+	0	NA	intron (NR_120518, intron 3 of 5)	L1PA16|LINE|L1	74135	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.000000	0.313653	
chunk0066_79_1	chr15	29438266	29438735	+	0	NA	intron (NM_015307, intron 1 of 10)	MER101B|LTR|ERV1	132223	NM_015307	23359	Hs.383564	NM_015307	ENSG00000104059	FAM189A1	TMEM228	family with sequence similarity 189 member A1	protein-coding	0.012793	0.485106	
chunk0051_24_1	chr12	111841786	111842197	+	0	NA	promoter-TSS (NM_139078)	promoter-TSS (NM_139078)	-237	NM_139078	8550	Hs.333120	NM_003668	ENSG00000089022	MAPKAPK5	MAPKAP-K5|MK-5|MK5|PRAK	MAPK activated protein kinase 5	protein-coding	0.094891	0.648058	
chunk0138_88_1	chr4	35520151	35520581	+	0	NA	Intergenic	MER61C|LTR|ERV1	-723750	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.004651	0.392111	
chunk0204_176_1	chr9	96068392	96069001	+	0	NA	intron (NR_033838, intron 1 of 8)	intron (NR_033838, intron 1 of 8)	2857	NR_033838	158435	Hs.652615	NR_033838		LOC158435	-	uncharacterized LOC158435	ncRNA	0.019704	0.485246	
chunk0204_167_1	chr9	95915891	95916140	+	0	NA	intron (NM_001010895, intron 5 of 13)	intron (NM_001010895, intron 5 of 13)	-40038	NR_023390	100128782	Hs.494549	NR_023389	ENSG00000175611	LINC00476	C9orf130|NAG11|NAG12	long intergenic non-protein coding RNA 476	ncRNA	0.012048	0.348000	202(AAGAACATTCTGTTTT,-,0.00),203(AGAACATTCTGTTTTC,+,0.00)
chunk0141_426_1	chr4	88803557	88803879	+	0	NA	intron (NM_001265578, intron 1 of 16)	intron (NM_001265578, intron 1 of 16)	19643	NM_001265580	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.009317	0.383901	
chunk0171_456_1	chr6	132270972	132271496	+	0	NA	Intergenic	Intergenic	130300	NM_015529	26002	Hs.6909	NM_015529	ENSG00000079931	MOXD1	MOX|PRO5780|dJ248E1.1	monooxygenase DBH like 1	protein-coding	0.003817	0.430476	
chunk0183_151_1	chr7	105876454	105876821	+	0	NA	promoter-TSS (NM_152749)	promoter-TSS (NM_152749)	-52	NM_020725	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.122616	0.714674	
chunk0040_322_1	chr11	118127369	118127789	+	0	NA	Intergenic	L1ME1|LINE|L1	17890	NR_024527	6330	Hs.65239	NM_174934	ENSG00000177098	SCN4B	ATFB17|LQT10|Navbeta4	sodium voltage-gated channel beta subunit 4	protein-coding	0.009524	0.377672	
chunk0198_43_1	chr8	128362002	128362226	+	0	NA	Intergenic	Intergenic	202565	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.004464	0.466667	
chunk0073_410_1	chr16	17606111	17606905	+	0	NA	Intergenic	MIR|SINE|MIR	-135627	NM_022166	64131	Hs.22907	NM_022166	ENSG00000103489	XYLT1	DBQD2|PXYLT1|XT-I|XT1|XTI|XYLTI|xylT-I	xylosyltransferase 1	protein-coding	0.002519	0.366038	
chunk0104_329_1	chr2	179486919	179487383	+	0	NA	intron (NM_001282725, intron 5 of 9)	intron (NM_001282725, intron 5 of 9)	75437	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.010776	0.369892	
chunk0120_336_1	chr3	10902718	10903231	+	0	NA	intron (NM_014229, intron 6 of 13)	MIR|SINE|MIR	86742	NM_014229	6538	Hs.655078	NM_014229	ENSG00000132164	SLC6A11	GAT-3|GAT3|GAT4	solute carrier family 6 member 11	protein-coding	0.013645	0.439689	
chunk0113_113_1	chr20	51383009	51383383	+	0	NA	Intergenic	Intergenic	69781	NR_036162	100422889		NR_036162	ENSG00000266761	MIR3194	mir-3194	microRNA 3194	ncRNA	0.034759	0.570667	
chunk0111_101_1	chr20	23602109	23602958	+	0	NA	3' UTR (NM_001008693, exon 2 of 2)	3' UTR (NM_001008693, exon 2 of 2)	3440	NM_001008693	128822	Hs.698020	NM_001008693	ENSG00000173335	CST9	CLM|CTES7A	cystatin 9	protein-coding	0.010601	0.537647	
chunk0007_60_1	chr1	78146233	78146897	+	0	NA	Intergenic	Helitron3Na_Mam|RC|Helitron	-83034	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.004518	0.383459	
chunk0049_384_1	chr12	96048397	96048793	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-5075	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.012626	0.400504	
chunk0147_232_1	chr4	181964623	181964853	+	0	NA	Intergenic	Intergenic	179777	NR_027107	90768	Hs.175465	NR_027107		TENM3-AS1	-	TENM3 antisense RNA 1	ncRNA	0.026087	0.385281	
chunk0201_275_1	chr9	38672094	38672639	+	0	NA	Intergenic	Intergenic	51278	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.034862	0.489011	205(CGGGACAAGCAGTTCC,-,0.00),206(GGGACAAGCAGTTCCA,+,0.00)
chunk0038_127_1	chr11	83987876	83988146	+	0	NA	intron (NM_001142699, intron 11 of 27)	L1PA11|LINE|L1	285269	NM_001142700	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.335793	
chunk0055_268_1	chr13	63855463	63855849	+	0	NA	Intergenic	MER70B|LTR|ERVL	-11531	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.010363	0.431525	89(CAGAACAGGATGTTCT,-,0.00),90(AGAACAGGATGTTCTG,+,0.00)
chunk0150_251_1	chr5	36287944	36288277	+	0	NA	intron (NM_145000, intron 1 of 13)	L1ME2|LINE|L1	13799	NM_145000	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.000000	0.389222	
chunk0154_327_1	chr5	84905978	84906504	+	0	NA	Intergenic	L1MC3|LINE|L1	-521374	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.001901	0.387097	85(AGAACATTTTGTGTTT,+,0.00)
chunk0140_319_1	chr4	73375394	73375956	+	0	NA	Intergenic	Intergenic	-28580	NM_000477	213	Hs.418167	NM_000477	ENSG00000163631	ALB	HSA|PRO0883|PRO0903|PRO1341	albumin	protein-coding	0.001779	0.388988	242(CAGAACACTATGTTCT,-,0.00),243(AGAACACTATGTTCTT,+,0.00)
chunk0162_352_1	chr6	7124869	7125284	+	0	NA	intron (NM_001003698, intron 1 of 11)	intron (NM_001003698, intron 1 of 11)	17223	NM_001003700	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.002410	0.463942	
chunk0030_331_1	chr10	118309882	118310394	+	0	NA	3' UTR (NM_001134672, exon 8 of 8)	3' UTR (NM_001134672, exon 8 of 8)	32189	NM_022063	63877	Hs.105575	NM_022063	ENSG00000165669	FAM204A	C10orf84|bA319I23.1	family with sequence similarity 204 member A	protein-coding	0.007812	0.366472	
chunk0104_208_1	chr2	175929876	175930463	+	0	NA	exon (NM_001305011, exon 11 of 11)	exon (NM_001305011, exon 11 of 11)	72176	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.008518	0.362245	301(AAGAACATCGTGTTCT,-,0.00),302(AGAACATCGTGTTCTA,+,0.00)
chunk0087_380_1	chr18	41612469	41612668	+	0	NA	Intergenic	L2a|LINE|L2	-91971	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.000000	0.320000	
chunk0023_305_1	chr10	28839694	28840252	+	0	NA	Intergenic	Intergenic	-6435	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.016129	0.422182	
chunk0202_412_1	chr9	81558553	81558814	+	0	NA	Intergenic	Intergenic	130852	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.015326	0.435115	
chunk0067_118_1	chr15	42528968	42529540	+	0	NA	intron (NM_003825, intron 6 of 7)	MER58A|DNA|hAT-Charlie	19550	NM_153260	255252	Hs.234681	NM_153260	ENSG00000180979	LRRC57	-	leucine rich repeat containing 57	protein-coding	0.005245	0.382199	
chunk0105_187_1	chr2	187552413	187552872	+	0	NA	intron (NM_001032281, intron 1 of 6)	intron (NM_001032281, intron 1 of 6)	1850	NM_006287	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.273913	
chunk0206_238_1	chr9	123633121	123633546	+	0	NA	intron (NM_024820, intron 9 of 20)	L2b|LINE|L2	-147711	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.011765	0.464789	151(AGGAAGATCCTGTCCT,-,0.00)
chunk0102_346_1	chr2	152402178	152402430	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	67067	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.027778	0.498024	
chunk0175_432_1	chr6	169473132	169473368	+	0	NA	intron (NM_001202550, intron 21 of 21)	intron (NM_001202550, intron 21 of 21)	-219136	NM_003247	7058	Hs.371147	NM_003247	ENSG00000186340	THBS2	TSP2	thrombospondin 2	protein-coding	0.012712	0.455696	
chunk0123_263_1	chr3	46003779	46004807	+	0	NA	Intergenic	MER50-int|LTR|ERV1	-8469	NM_024513	79443	Hs.200227	NM_024513	ENSG00000163820	FYCO1	CATC2|CTRCT18|RUFY3|ZFYVE7	FYVE and coiled-coil domain containing 1	protein-coding	0.003891	0.463557	165(GGGCACAAGGTGTCCA,-,0.00),166(GGCACAAGGTGTCCAA,+,0.00)
chunk0163_170_1	chr6	11188236	11188486	+	0	NA	intron (NM_001142393, intron 6 of 7)	intron (NM_001142393, intron 6 of 7)	44321	NM_182966	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.008000	0.390438	
chunk0075_99_1	chr16	48457800	48458033	+	0	NA	Intergenic	L1ME3A|LINE|L1	-72598	NM_003031	6477	Hs.706828	NM_003031	ENSG00000196470	SIAH1	SIAH1A	siah E3 ubiquitin protein ligase 1	protein-coding	0.008584	0.333333	
chunk0044_326_1	chr12	34253704	34254343	+	0	NA	Intergenic	L1MB2|LINE|L1	231742	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.007825	0.348438	
chunk0019_81_1	chr1	224362703	224362941	+	0	NA	intron (NM_014184, intron 2 of 4)	HAL1|LINE|L1	6011	NM_001277197	29097	Hs.445890	NM_014184	ENSG00000143771	CNIH4	CNIH-4|CNIH2|HSPC163	cornichon family AMPA receptor auxiliary protein 4	protein-coding	0.004202	0.426778	
chunk0145_278_1	chr4	149618418	149618708	+	0	NA	Intergenic	L1PB4|LINE|L1	-459711	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.000000	0.333333	
chunk0146_3_1	chr4	154660043	154660525	+	0	NA	Intergenic	Intergenic	-47476	NM_000509	2266	Hs.727584	NM_000509	ENSG00000171557	FGG	-	fibrinogen gamma chain	protein-coding	0.006224	0.383023	
chunk0041_383_1	chr11	131972793	131973200	+	0	NA	intron (NM_001144058, intron 1 of 7)	intron (NM_001144058, intron 1 of 7)	62178	NM_001144059	50863	Hs.504352	NM_016522	ENSG00000182667	NTM	CEPU-1|HNT|IGLON2|NTRI	neurotrimin	protein-coding	0.009828	0.370098	
chunk0150_6_1	chr5	30239783	30240314	+	0	NA	Intergenic	LTR28C|LTR|ERV1	-844072	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.009416	0.486842	
chunk0212_101_1	chrY	14580795	14581444	+	0	NA	intron (NR_028319, intron 1 of 5)	intron (NR_028319, intron 1 of 5)	-40902	NM_001164238	22829	Hs.439199	NM_014893	ENSG00000165246	NLGN4Y	HNL4Y	neuroligin 4 Y-linked	protein-coding	0.001541	0.364615	489(AGTCACAGAATGTTCT,-,0.00),490(GTCACAGAATGTTCTC,+,0.00)
chunk0074_356_1	chr16	34045587	34045961	+	0	NA	Intergenic	L1MB4|LINE|L1	114262	NR_038368									0.002674	0.314667	
chunk0001_429_1	chr1	11404046	11404582	+	0	NA	Intergenic	MIR|SINE|MIR	-74924	NM_020780	57540	Hs.202355	NM_020780	ENSG00000204624	DISP3	PTCHD2	dispatched RND transporter family member 3	protein-coding	0.013060	0.452514	
chunk0005_82_1	chr1	56039179	56039505	+	0	NA	Intergenic	Intergenic	540242	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.000000	0.376147	
chunk0200_172_1	chr9	19182441	19182966	+	0	NA	Intergenic	Intergenic	-48062	NM_017925	55667	Hs.249591	NM_017925	ENSG00000137145	DENND4C	C9orf55|C9orf55B|RAB10GEF|bA513M16.3	DENN domain containing 4C	protein-coding	0.007619	0.442966	364(AGGGACAGGGAGTACA,-,0.00),365(GGGACAGGGAGTACAG,+,0.00)
chunk0088_68_1	chr18	44518099	44518427	+	0	NA	non-coding (NR_110792, exon 2 of 5)	non-coding (NR_110792, exon 2 of 5)	13434	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.012195	0.410334	230(ATGAACAAGTTGTACT,-,0.00),231(TGAACAAGTTGTACTG,+,0.00)
chunk0051_427_1	chr12	122870820	122871215	+	0	NA	exon (NM_024667, exon 2 of 4)	exon (NM_024667, exon 2 of 4)	25148	NM_024667	79720	Hs.507162	NM_024667	ENSG00000139722	VPS37B	-	VPS37B subunit of ESCRT-I	protein-coding	0.015190	0.492424	
chunk0181_398_1	chr7	89798147	89798414	+	0	NA	Intergenic	L1PA13|LINE|L1	-321120	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.003745	0.563433	
chunk0096_162_1	chr2	29430576	29431546	+	0	NA	intron (NM_004304, intron 4 of 28)	intron (NM_004304, intron 4 of 28)	315635	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.005155	0.398558	
chunk0139_49_1	chr4	48687030	48687485	+	0	NA	intron (NM_015030, intron 2 of 63)	intron (NM_015030, intron 2 of 63)	93042	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.004396	0.375000	
chunk0148_98_1	chr5	3851613	3851955	+	0	NA	Intergenic	L1MB8|LINE|L1	255730	NM_024337	79192	Hs.424156	NM_024337	ENSG00000170549	IRX1	IRX-5|IRXA1	iroquois homeobox 1	protein-coding	0.002924	0.390671	
chunk0176_270_1	chr7	16464013	16464212	+	0	NA	intron (NM_015464, intron 1 of 1)	intron (NM_015464, intron 1 of 1)	1737	NM_015464	25928	Hs.648106	NM_015464	ENSG00000171243	SOSTDC1	CDA019|DAND7|ECTODIN|USAG1	sclerostin domain containing 1	protein-coding	0.015075	0.355000	
chunk0209_411_1	chrX	56750562	56751243	+	0	NA	intron (NR_015367, intron 2 of 2)	L2|LINE|L2	-13318	NR_002308	442454	Hs.663220	NR_002308		UQCRBP1	-	ubiquinol-cytochrome c reductase binding protein pseudogene 1	pseudo	0.001468	0.357771	
chunk0016_207_1	chr1	198837392	198838078	+	0	NA	intron (NR_040073, intron 2 of 2)	intron (NR_040073, intron 2 of 2)	21247	NR_029612	406955		NR_029612	ENSG00000207975	MIR181B1	MIRN181B1|mir-181b-1	microRNA 181b-1	ncRNA	0.007289	0.397380	294(AGAGACTCACTGTTCC,-,0.00),295(GAGACTCACTGTTCCT,+,0.00)
chunk0008_300_1	chr1	95014018	95014379	+	0	NA	intron (NR_131032, intron 2 of 2)	intron (NR_131032, intron 2 of 2)	-47398	NR_132786	101928098	Hs.730090	NR_132786	ENSG00000230427	LOC101928098	-	uncharacterized LOC101928098	ncRNA	0.005540	0.400552	
chunk0117_21_1	chr22	11312803	11313056	+	0	NA	Intergenic	L1PA12|LINE|L1	-351400	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.015810	0.527559	
chunk0057_364_1	chr13	108957318	108957830	+	0	NA	intron (NM_001198950, intron 16 of 34)	intron (NM_001198950, intron 16 of 34)	209729	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.017578	0.432749	248(GGGGACACCATGTCCA,-,0.00),249(GGGACACCATGTCCAG,+,0.00)
chunk0169_351_1	chr6	106642328	106643008	+	0	NA	intron (NM_018292, intron 3 of 10)	intron (NM_018292, intron 3 of 10)	13102	NM_018292	55278	Hs.406917	NM_018292	ENSG00000130348	QRSL1	GatA	glutaminyl-tRNA amidotransferase subunit QRSL1	protein-coding	0.014706	0.430250	310(GAGTACACAGTGTTCC,-,0.00),311(AGTACACAGTGTTCCC,+,0.00),397(GAGCACAGTAAGTACT,-,0.00),398(AGCACAGTAAGTACTG,+,0.00)
chunk0124_274_1	chr3	57530035	57530797	+	0	NA	intron (NM_198564, intron 2 of 11)	intron (NM_198564, intron 2 of 11)	13928	NM_001291661	201625	Hs.201378	NM_178504	ENSG00000174844	DNAH12	DHC3|DLP12|DLP3|DNAH12L|DNAH7L|DNAHC12|DNAHC3|DNHD2|HDHC3|HL-19|HL19	dynein axonemal heavy chain 12	protein-coding	0.002625	0.391874	
chunk0197_349_1	chr8	125434073	125434800	+	0	NA	intron (NM_025195, intron 2 of 2)	intron (NM_025195, intron 2 of 2)	2227	NM_001282985	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.009629	0.424451	154(AAGAACAAGATGAGCT,-,0.00),155(AGAACAAGATGAGCTT,+,0.00)
chunk0137_197_1	chr4	17958496	17958752	+	0	NA	intron (NM_001166139, intron 4 of 6)	intron (NM_001166139, intron 4 of 6)	63236	NM_153686	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.011719	0.295720	
chunk0133_438_1	chr3	174973328	174973897	+	0	NA	intron (NM_207015, intron 1 of 13)	Tigger3a|DNA|TcMar-Tigger	114291	NM_207015	254827	Hs.565848	NM_207015	ENSG00000177694	NAALADL2	-	N-acetylated alpha-linked acidic dipeptidase like 2	protein-coding	0.010545	0.314035	
chunk0086_328_1	chr18	24557477	24558251	+	0	NA	Intergenic	L2a|LINE|L2	-70318	NR_040033	729950	Hs.585850	NR_040033	ENSG00000265485	LINC01915	-	long intergenic non-protein coding RNA 1915	ncRNA	0.009044	0.430968	
chunk0128_296_1	chr3	111124473	111124991	+	0	NA	intron (NM_015480, intron 4 of 5)	intron (NM_015480, intron 4 of 5)	52564	NM_001243288	25945	Hs.293917	NM_015480	ENSG00000177707	NECTIN3	CD113|CDW113|NECTIN-3|PPR3|PRR3|PVRL3|PVRR3	nectin cell adhesion molecule 3	protein-coding	0.005792	0.314066	
chunk0080_124_1	chr17	27256188	27256849	+	0	NA	Intergenic	L1ME4b|LINE|L1	37478	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.004539	0.397281	
chunk0034_116_1	chr11	28104595	28104829	+	0	NA	intron (NM_031217, intron 1 of 16)	L2a|LINE|L2	3487	NM_031217	81930	Hs.301052	NM_031217	ENSG00000121621	KIF18A	MS-KIF18A|PPP1R99	kinesin family member 18A	protein-coding	0.004274	0.340426	
chunk0005_47_1	chr1	54976919	54977158	+	0	NA	Intergenic	Intergenic	-3626	NM_182532	199964	Hs.663950	NM_182532	ENSG00000143001	TMEM61	-	transmembrane protein 61	protein-coding	0.016736	0.512500	
chunk0051_287_1	chr12	118276879	118277450	+	0	NA	intron (NM_016281, intron 1 of 20)	intron (NM_016281, intron 1 of 20)	95781	NM_016281	51347	Hs.644420	NM_016281	ENSG00000135090	TAOK3	DPK|JIK|MAP3K18|hKFC-A	TAO kinase 3	protein-coding	0.005254	0.396853	
chunk0152_209_1	chr5	60264122	60264728	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-223288	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.004950	0.401977	
chunk0124_111_1	chr3	53932353	53932655	+	0	NA	Intergenic	L1MEf|LINE|L1	-40542	NM_021237	58515	Hs.58471	NM_021237	ENSG00000113811	SELENOK	HSPC030|HSPC297|SELK	selenoprotein K	protein-coding	0.003311	0.290429	
chunk0102_207_1	chr2	148244380	148244886	+	0	NA	intron (NM_018328, intron 4 of 14)	L2a|LINE|L2	-223029	NM_181742	5000	Hs.558364	NM_002552	ENSG00000115947	ORC4	ORC4L|ORC4P	origin recognition complex subunit 4	protein-coding	0.001976	0.341223	
chunk0016_275_1	chr1	200625348	200625591	+	0	NA	Intergenic	Intergenic	-4735	NM_014875	9928	Hs.3104	NM_014875	ENSG00000118193	KIF14	MCPH20|MKS12	kinesin family member 14	protein-coding	0.008230	0.372951	
chunk0001_289_1	chr1	8794502	8794718	+	0	NA	intron (NM_012102, intron 1 of 23)	intron (NM_012102, intron 1 of 23)	23030	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.009259	0.423963	
chunk0053_224_1	chr13	32257617	32258108	+	0	NA	intron (NM_023037, intron 51 of 60)	intron (NM_023037, intron 51 of 60)	54092	NM_001136571	646799	Hs.569254	NM_001136571	ENSG00000189167	ZAR1L	Z3CXXC7|ZAR2	zygote arrest 1 like	protein-coding	0.004073	0.325203	
chunk0152_328_1	chr5	62176792	62177314	+	0	NA	Intergenic	Intergenic	-129109	NM_001243952	3796	Hs.558351	NM_004520	ENSG00000068796	KIF2A	CDCBM3|HK2|KIF2	kinesin family member 2A	protein-coding	0.005747	0.399618	255(CAGTACTTACTGTACC,-,0.00),256(AGTACTTACTGTACCA,+,0.00),347(AGGTACAGGCTGATCT,-,0.00),348(GGTACAGGCTGATCTC,+,0.00)
chunk0085_350_1	chr18	9055183	9055657	+	0	NA	Intergenic	Intergenic	-47210	NM_021074	4729	Hs.464572	NM_021074	ENSG00000178127	NDUFV2	CI-24k|MC1DN7	NADH:ubiquinone oxidoreductase core subunit V2	protein-coding	0.002110	0.324211	191(AAGAACAAAATGACCT,-,0.00),192(AGAACAAAATGACCTT,+,0.00)
chunk0016_346_1	chr1	202018444	202019189	+	0	NA	Intergenic	L2b|LINE|L2	8254	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.026846	0.587131	
chunk0092_374_1	chr19	36201729	36201979	+	0	NA	intron (NM_001042474, intron 2 of 4)	intron (NM_001042474, intron 2 of 4)	-12748	NM_001099638	7705	Hs.643436	NM_007145	ENSG00000167635	ZNF146	OZF	zinc finger protein 146	protein-coding	0.016000	0.494024	178(AAGAACACAGTGTCCA,-,0.00),179(AGAACACAGTGTCCAT,+,0.00)
chunk0193_278_1	chr8	77396156	77396799	+	0	NA	Intergenic	Intergenic	-54220	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.009331	0.360248	259(AGGTACACTATGTTAT,-,0.00)
chunk0029_146_1	chr10	99389671	99390273	+	0	NA	intron (NM_020348, intron 9 of 10)	intron (NM_020348, intron 9 of 10)	40801	NM_002079	2805	Hs.500756	NM_002079	ENSG00000120053	GOT1	AST1|ASTQTL1|GIG18|cAspAT|cCAT	glutamic-oxaloacetic transaminase 1	protein-coding	0.011628	0.484245	318(GAGAACACATTGTTCT,-,0.00),319(AGAACACATTGTTCTC,+,0.00),468(ATGACACCCTGTACTT,+,0.00)
chunk0020_233_1	chr1	235769090	235769348	+	0	NA	intron (NM_001301365, intron 20 of 52)	L2b|LINE|L2	83841	NR_031718	100302139		NR_031718	ENSG00000222831	MIR1537	MIRN1537|hsa-mir-1537|mir-1537	microRNA 1537	ncRNA	0.003876	0.370656	
chunk0141_30_1	chr4	76923809	76924134	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-25743	NM_001306147	55752	Hs.128199	NM_018243	ENSG00000138758	SEPTIN11	SEPT11	septin 11	protein-coding	0.012308	0.374233	
chunk0202_168_1	chr9	73832508	73833349	+	0	NA	Intergenic	Intergenic	-538603	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.002378	0.339667	
chunk0127_323_1	chr3	100103785	100104247	+	0	NA	intron (NM_001042459, intron 1 of 4)	intron (NM_001042459, intron 1 of 4)	10497	NM_001042459	11259	Hs.104672	NM_014890	ENSG00000168386	FILIP1L	DOC-1|DOC1|GIP130|GIP90	filamin A interacting protein 1 like	protein-coding	0.006494	0.440605	
chunk0074_192_1	chr16	24892270	24892470	+	0	NA	intron (NM_052944, intron 9 of 15)	L2a|LINE|L2	46139	NM_052944	115584	Hs.164118	NM_052944	ENSG00000158865	SLC5A11	KST1|RKST1|SGLT6|SMIT2	solute carrier family 5 member 11	protein-coding	0.010000	0.383085	
chunk0118_124_1	chr22	29563541	29564065	+	0	NA	intron (NM_003634, intron 4 of 9)	MLT1C|LTR|ERVL-MaLR	-10056	NM_003678	8563	Hs.75361	NM_003678	ENSG00000100296	THOC5	C22orf19|Fmip|PK1.3|fSAP79	THO complex 5	protein-coding	0.005725	0.434286	238(GAGAACAGCATGTGAC,-,0.00)
chunk0097_210_1	chr2	51287034	51287702	+	0	NA	Intergenic	Intergenic	-254832	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.333333	264(GTGAACATTATGTTTT,-,0.00),265(TGAACATTATGTTTTT,+,0.00)
chunk0100_213_1	chr2	111920074	111920274	+	0	NA	intron (NM_006343, intron 1 of 18)	MER53|DNA|hAT	21560	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.020000	0.432836	
chunk0113_415_1	chr20	61755396	61755602	+	0	NA	intron (NM_001252339, intron 2 of 14)	(AC)n|Simple_repeat|Simple_repeat	155738	NM_001252339	1002	Hs.473231	NM_001794	ENSG00000179242	CDH4	CAD4|R-CAD|RCAD	cadherin 4	protein-coding	0.009709	0.526570	
chunk0133_361_1	chr3	173540676	173541522	+	0	NA	intron (NM_014932, intron 2 of 6)	intron (NM_014932, intron 2 of 6)	142651	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.002364	0.349469	
chunk0099_231_1	chr2	96374160	96374511	+	0	NA	3' UTR (NM_001281710, exon 18 of 18)	3' UTR (NM_001281710, exon 18 of 18)	38594	NM_015341	23397	Hs.308045	NM_015341	ENSG00000121152	NCAPH	BRRN1|CAP-H|CAPH|MCPH23	non-SMC condensin I complex subunit H	protein-coding	0.011396	0.494318	
chunk0067_462_1	chr15	50446463	50446684	+	0	NA	intron (NM_005154, intron 3 of 19)	intron (NM_005154, intron 3 of 19)	22196	NM_005154	9101	Hs.443731	NM_005154	ENSG00000138592	USP8	HumORF8|PITA4|SPG59|UBPY	ubiquitin specific peptidase 8	protein-coding	0.004525	0.292793	125(CAGGACATGGTGTGCT,-,0.00),126(AGGACATGGTGTGCTA,+,0.00),177(TGAACAAACTGTACAC,+,0.00)
chunk0144_185_1	chr4	133457362	133458100	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	308441	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.002710	0.365359	
chunk0002_243_1	chr1	20680127	20680501	+	0	NA	intron (NM_001287212, intron 11 of 14)	L1MC4|LINE|L1	-18770	NM_005216	1650	Hs.523145	NM_005216	ENSG00000244038	DDOST	AGER1|CDG1R|GATD6|OKSWcl45|OST|OST48|WBP1	dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit	protein-coding	0.013369	0.416000	
chunk0185_138_1	chr7	127119566	127119977	+	0	NA	intron (NR_028041, intron 1 of 10)	L2a|LINE|L2	-61587	NR_030323	693177		NR_030323	ENSG00000207692	MIR592	MIRN592|hsa-mir-592|mir-592	microRNA 592	ncRNA	0.004866	0.400485	
chunk0023_377_1	chr10	30387108	30387350	+	0	NA	Intergenic	Intergenic	-15322	NR_120609	729668	Hs.652158	NR_003524		GOLGA2P6	-	GOLGA2 pseudogene 6	pseudo	0.024793	0.555556	
chunk0023_366_1	chr10	30057468	30057784	+	0	NA	intron (NM_020848, intron 1 of 3)	intron (NM_020848, intron 1 of 3)	1933	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.012658	0.498423	
chunk0105_14_1	chr2	181987655	181988209	+	0	NA	intron (NM_001080545, intron 2 of 4)	intron (NM_001080545, intron 2 of 4)	2108	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.005415	0.380180	
chunk0063_382_1	chr14	86390137	86390379	+	0	NA	Intergenic	MER52A|LTR|ERV1	455580	NR_110155	101928767	Hs.536380	NR_110155		LINC02328	-	long intergenic non-protein coding RNA 2328	ncRNA	0.012397	0.609053	
chunk0180_430_1	chr7	76349397	76349793	+	0	NA	intron (NM_012479, intron 1 of 1)	intron (NM_012479, intron 1 of 1)	9430	NM_012479	7532	Hs.744840	NM_012479	ENSG00000170027	YWHAG	14-3-3GAMMA|EIEE56|PPP1R170	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma	protein-coding	0.005051	0.370277	
chunk0144_223_1	chr4	134611383	134611874	+	0	NA	Intergenic	Intergenic	-409880	NM_001114734	132430	Hs.49889	NM_001114734	ENSG00000254535	PABPC4L	-	poly(A) binding protein cytoplasmic 4 like	protein-coding	0.006110	0.331301	189(AAAACAGGCTGCTCTT,+,0.00)
chunk0156_181_1	chr5	107711935	107712425	+	0	NA	Intergenic	Intergenic	-41285	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004082	0.315682	
chunk0201_207_1	chr9	37155531	37156126	+	0	NA	intron (NM_032226, intron 2 of 8)	intron (NM_032226, intron 2 of 8)	35230	NM_001289121	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.005042	0.360738	285(AGGAACATTCTGTTTT,-,0.00),286(GGAACATTCTGTTTTG,+,0.00)
chunk0087_442_1	chr18	42609279	42609527	+	0	NA	intron (NR_046174, intron 7 of 9)	MLT1D|LTR|ERVL-MaLR	422735	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.008065	0.441767	
chunk0141_286_1	chr4	86693191	86693724	+	0	NA	intron (NM_006264, intron 5 of 46)	intron (NM_006264, intron 5 of 46)	99142	NM_080685	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.007505	0.333333	
chunk0161_72_1	chr5	166785884	166786248	+	0	NA	Intergenic	Intergenic	140304	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.008242	0.438356	
chunk0208_194_1	chrX	17466399	17466758	+	0	NA	intron (NM_001291867, intron 1 of 8)	intron (NM_001291867, intron 1 of 8)	40697	NR_039925	100616249		NR_039925	ENSG00000265465	MIR4768	-	microRNA 4768	ncRNA	0.008357	0.438889	186(AGGAACAGAAAGTTCT,-,0.00),187(GGAACAGAAAGTTCTT,+,0.00)
chunk0107_157_1	chr2	215216857	215217249	+	0	NA	Intergenic	Intergenic	-78625	NM_173076	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.005102	0.325700	
chunk0079_309_1	chr17	17201129	17201751	+	0	NA	3' UTR (NM_178836, exon 2 of 2)	3' UTR (NM_178836, exon 2 of 2)	4892	NM_178836	201164	Hs.729079	NM_178836	ENSG00000179598	PLD6	ZUC	phospholipase D family member 6	protein-coding	0.022508	0.465490	
chunk0008_251_1	chr1	94425853	94426079	+	0	NA	intron (NM_001122674, intron 1 of 8)	MIRb|SINE|MIR	7589	NM_001122674	5825	Hs.700576	NM_002858	ENSG00000117528	ABCD3	ABC43|CBAS5|PMP70|PXMP1|ZWS2	ATP binding cassette subfamily D member 3	protein-coding	0.008850	0.370044	
chunk0030_112_1	chr10	112793667	112793975	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	-29675	NR_120684	103344931	Hs.458447	NR_120684	ENSG00000260917	LOC103344931	-	uncharacterized LOC103344931	ncRNA	0.019481	0.498382	
chunk0169_200_1	chr6	102799865	102800293	+	0	NA	Intergenic	Intergenic	1401094	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.002336	0.310023	
chunk0093_7_1	chr2	35782	36121	+	0	NA	Intergenic	Intergenic	10637	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.008850	0.532353	
chunk0101_168_1	chr2	128988735	128988953	+	0	NA	Intergenic	Intergenic	124244	NR_110278	101927881	Hs.570247	NR_110278		LOC101927881	-	uncharacterized LOC101927881	ncRNA	0.018349	0.552511	
chunk0096_418_1	chr2	38215943	38216172	+	0	NA	Intergenic	L1MB8|LINE|L1	84952	NR_027252	285154	Hs.353894	NM_173652	ENSG00000232973	CYP1B1-AS1	C2orf58	CYP1B1 antisense RNA 1	ncRNA	0.000000	0.330435	
chunk0136_204_1	chr4	6991458	6991763	+	0	NA	intron (NM_001286805, intron 1 of 11)	intron (NM_001286805, intron 1 of 11)	4102	NM_001286805	57533	Hs.518611	NM_020773	ENSG00000132405	TBC1D14	-	TBC1 domain family member 14	protein-coding	0.019672	0.584967	165(AGGTACAGCGTGTCCT,-,0.00),166(GGTACAGCGTGTCCTT,+,0.00)
chunk0004_131_1	chr1	44739670	44739879	+	0	NA	promoter-TSS (NM_001297655)	promoter-TSS (NM_001297655)	-44	NM_006845	11004	Hs.720061	NM_006845	ENSG00000142945	KIF2C	CT139|KNSL6|MCAK	kinesin family member 2C	protein-coding	0.114833	0.633333	
chunk0157_159_1	chr5	117950266	117950936	+	0	NA	intron (NR_104997, intron 2 of 2)	L1MC4|LINE|L1	220240	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.002985	0.351714	
chunk0124_338_1	chr3	58306101	58306300	+	0	NA	promoter-TSS (NR_049758)	promoter-TSS (NR_049758)	-45	NR_049758	11102	Hs.446320	NM_007042	ENSG00000163684	RPP14	P14	ribonuclease P/MRP subunit p14	protein-coding	0.110553	0.630000	
chunk0145_272_1	chr4	149435194	149435695	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	281149	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.003992	0.352590	
chunk0010_433_1	chr1	119790864	119791224	+	0	NA	Intergenic	MIRb|SINE|MIR	20536	NM_001159353	83998	Hs.660883	NM_032044	ENSG00000134193	REG4	GISP|REG-IV|RELP	regenerating family member 4	protein-coding	0.008333	0.412742	154(AGAGACAGCCAGTTCT,-,0.00)
chunk0058_347_1	chr14	28876273	28876994	+	0	NA	Intergenic	Intergenic	103929	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.006935	0.383657	
chunk0168_5_1	chr6	76669744	76670288	+	0	NA	Intergenic	Intergenic	-597338	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.005515	0.361468	314(ATGAACAAAATGTACT,-,0.00),315(TGAACAAAATGTACTT,+,0.00)
chunk0120_62_1	chr3	3150626	3151226	+	0	NA	exon (NM_001173482, exon 11 of 11)	exon (NM_001173482, exon 11 of 11)	24010	NM_001302946	51095	Hs.732725	NM_016000	ENSG00000072756	TRNT1	CCA1|CGI-47|MtCCA|RPEM|SIFD	tRNA nucleotidyl transferase 1	protein-coding	0.008333	0.356073	
chunk0175_438_1	chr6	169751661	169752003	+	0	NA	promoter-TSS (NM_174910)	promoter-TSS (NM_174910)	210	NM_001278533	55780	Hs.47546	NM_018341	ENSG00000130023	ERMARD	C6orf70|PVNH6|dJ266L20.3	ER membrane associated RNA degradation	protein-coding	0.131579	0.752187	
chunk0134_147_1	chr3	177650928	177651732	+	0	NA	intron (NR_047568, intron 3 of 3)	intron (NR_047568, intron 3 of 3)	-165535	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.006219	0.361491	
chunk0113_165_1	chr20	52914771	52915215	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	-57414	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.002252	0.429213	
chunk0008_349_1	chr1	96075721	96076051	+	0	NA	Intergenic	Intergenic	83818	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.003030	0.350453	
chunk0131_377_1	chr3	152231908	152232288	+	0	NA	Intergenic	L1MA1|LINE|L1	-36370	NM_207292	4154	Hs.201858	NM_021038	ENSG00000152601	MBNL1	EXP|MBNL	muscleblind like splicing regulator 1	protein-coding	0.002632	0.356955	
chunk0201_98_1	chr9	34746541	34746767	+	0	NA	Intergenic	L1ME3A|LINE|L1	-17116	NM_001141917	259308	Hs.522093	NM_001141917	ENSG00000205108	FAM205A	C9orf144B	family with sequence similarity 205 member A	protein-coding	0.000000	0.317181	
chunk0206_232_1	chr9	123551124	123551343	+	0	NA	intron (NM_024820, intron 13 of 20)	intron (NM_024820, intron 13 of 20)	-65611	NR_106972	102465688		NR_106972	ENSG00000274932	MIR7150	hsa-mir-7150	microRNA 7150	ncRNA	0.004566	0.472727	
chunk0131_366_1	chr3	151986682	151987167	+	0	NA	Intergenic	L2c|LINE|L2	-58749	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.002062	0.345679	
chunk0067_112_1	chr15	42475609	42476263	+	0	NA	intron (NM_001284307, intron 1 of 19)	intron (NM_001284307, intron 1 of 19)	15261	NM_001284307	64397	Hs.511143	NM_022473	ENSG00000103994	ZNF106	SH3BP3|ZFP106|ZNF474	zinc finger protein 106	protein-coding	0.004587	0.302290	342(AATACAAACTGTGCTT,+,0.00)
chunk0151_75_1	chr5	42636679	42637355	+	0	NA	intron (NM_001242403, intron 3 of 9)	intron (NM_001242403, intron 3 of 9)	71153	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.002959	0.329394	
chunk0145_334_1	chr4	150778006	150778205	+	0	NA	intron (NM_001199282, intron 34 of 56)	intron (NM_001199282, intron 34 of 56)	196180	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.000000	0.300000	
chunk0116_317_1	chr21	41028899	41029473	+	0	NA	Intergenic	HAL1ME|LINE|L1	118878	NR_024100	284835	Hs.106234	NR_024100	ENSG00000226496	LINC00323	C21orf130|NCRNA00323|PRED42	long intergenic non-protein coding RNA 323	ncRNA	0.001742	0.335652	
chunk0146_430_1	chr4	169439114	169439583	+	0	NA	intron (NM_001199399, intron 24 of 32)	intron (NM_001199399, intron 24 of 32)	-168250	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.000000	0.370213	
chunk0062_130_1	chr14	68569792	68570375	+	0	NA	intron (NM_133509, intron 10 of 10)	intron (NM_133509, intron 10 of 10)	223831	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.008576	0.554795	317(CAGAACAGGCTGTGCC,-,0.00),318(AGAACAGGCTGTGCCA,+,0.00)
chunk0101_418_1	chr2	139224130	139224723	+	0	NA	Intergenic	Intergenic	327102	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.005059	0.308081	
chunk0017_30_1	chr1	204813238	204813551	+	0	NA	Intergenic	Intergenic	-15260	NM_001005389	23114	Hs.13349	NM_015090	ENSG00000163531	NFASC	NEDCPMD|NF|NRCAML	neurofascin	protein-coding	0.009585	0.538217	
chunk0108_210_1	chr2	233156648	233156931	+	0	NA	intron (NM_001017915, intron 9 of 26)	MER68|LTR|ERVL	-94782	NM_001190266	55054	Hs.529322	NM_017974	ENSG00000085978	ATG16L1	APG16L|ATG16A|ATG16L|IBD10|WDR30	autophagy related 16 like 1	protein-coding	0.007067	0.500000	
chunk0096_168_1	chr2	29599020	29599465	+	0	NA	intron (NM_004304, intron 3 of 28)	intron (NM_004304, intron 3 of 28)	322369	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.006742	0.372197	
chunk0200_178_1	chr9	19286358	19287023	+	0	NA	intron (NR_073201, intron 2 of 31)	intron (NR_073201, intron 2 of 31)	55925	NR_073201	55667	Hs.249591	NM_017925	ENSG00000137145	DENND4C	C9orf55|C9orf55B|RAB10GEF|bA513M16.3	DENN domain containing 4C	protein-coding	0.007519	0.342342	
chunk0188_433_1	chr8	19122012	19122788	+	0	NA	Intergenic	L1MC2|LINE|L1	-108714	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.006443	0.379665	340(AAGTACAGACAGTTCC,-,0.00),341(AGTACAGACAGTTCCT,+,0.00)
chunk0197_6_1	chr8	116825338	116825906	+	0	NA	Intergenic	L1M4a1|LINE|L1	-48802	NR_033886	644660	Hs.706174	NR_033886	ENSG00000253327	RAD21-AS1	C8orf81|NCRNA00255	RAD21 antisense RNA 1	ncRNA	0.003521	0.265378	
chunk0206_374_1	chr9	126204574	126205002	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	71127	NR_121584	101929116	Hs.382124	NR_121584	ENSG00000228392	LOC101929116	-	uncharacterized LOC101929116	ncRNA	0.000000	0.473193	
chunk0195_421_1	chr8	100752001	100752584	+	0	NA	Intergenic	Intergenic	-30205	NM_002568	26986	Hs.387804	NM_002568	ENSG00000070756	PABPC1	PAB1|PABP|PABP1|PABPC2|PABPL1	poly(A) binding protein cytoplasmic 1	protein-coding	0.003431	0.380137	
chunk0077_142_1	chr16	78834029	78834330	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	734766	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.013289	0.463576	
chunk0058_265_1	chr14	26011863	26012235	+	0	NA	Intergenic	L1MA3|LINE|L1	585705	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.005376	0.310992	
chunk0028_230_1	chr10	89790612	89791049	+	0	NA	Intergenic	Intergenic	-38663	NR_038382	643529	Hs.618956	NR_038382	ENSG00000232229	LINC00865	-	long intergenic non-protein coding RNA 865	ncRNA	0.004577	0.369863	
chunk0021_438_1	chr1	248022446	248022645	+	0	NA	exon (NM_001258284, exon 1 of 1)	exon (NM_001258284, exon 1 of 1)	597	NM_001258284	81466	Hs.742583	NM_001258284	ENSG00000197454	OR2L5	OR2L11|OR2L5P	olfactory receptor family 2 subfamily L member 5	protein-coding	0.010050	0.470000	84(GAGTACACAGTGTTTT,-,0.00),85(AGTACACAGTGTTTTT,+,0.00)
chunk0196_289_1	chr8	109539764	109540356	+	0	NA	promoter-TSS (NM_001278938)	promoter-TSS (NM_001278938)	-15	NM_004215	9166	Hs.409368	NM_004215	ENSG00000147654	EBAG9	EB9|PDAF	estrogen receptor binding site associated antigen 9	protein-coding	0.096284	0.676223	
chunk0072_197_1	chr15	94451660	94451948	+	0	NA	intron (NM_018349, intron 18 of 21)	intron (NM_018349, intron 18 of 21)	95869	NM_001159644	55784	Hs.33368	NM_018349	ENSG00000140563	MCTP2	-	multiple C2 and transmembrane domain containing 2	protein-coding	0.003472	0.387543	
chunk0207_3_1	chrM	1703	3868	+	0	NA	NA	Intergenic	NA	NA									0.027739	0.440185	
chunk0051_90_1	chr12	114555222	114555869	+	0	NA	Intergenic	Intergenic	128619	NM_005996	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.004637	0.439815	261(AGGAACAGAGTGGCCC,-,0.00),262(GGAACAGAGTGGCCCT,+,0.00)
chunk0024_150_1	chr10	35352121	35352420	+	0	NA	intron (NM_001282852, intron 1 of 8)	intron (NM_001282852, intron 1 of 8)	15396	NM_145012	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.003344	0.390000	
chunk0076_154_1	chr16	67246821	67247287	+	0	NA	intron (NM_013241, intron 1 of 21)	CpG	468	NM_013241	29109	Hs.95231	NM_013241	ENSG00000135723	FHOD1	FHOS	formin homology 2 domain containing 1	protein-coding	0.064378	0.663812	
chunk0095_89_1	chr2	15180807	15181693	+	0	NA	intron (NR_052013, intron 49 of 50)	intron (NR_052013, intron 49 of 50)	380098	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.009029	0.418264	168(TAGCACTCAATGTTCT,-,0.00),169(AGCACTCAATGTTCTA,+,0.00)
chunk0070_358_1	chr15	76138892	76139384	+	0	NA	intron (NM_152335, intron 3 of 10)	intron (NM_152335, intron 3 of 10)	42348	NR_120360	101929439	Hs.631721	NR_120360	ENSG00000259422	LOC101929439	-	uncharacterized LOC101929439	ncRNA	0.008130	0.462475	
chunk0009_137_1	chr1	104631831	104632372	+	0	NA	Intergenic	Intergenic	559078	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.005545	0.370849	233(TGGAACAGAGTGCTCT,-,0.00),234(GGAACAGAGTGCTCTT,+,0.00)
chunk0199_102_1	chr9	3223810	3224160	+	0	NA	3' UTR (NM_134428, exon 18 of 18)	3' UTR (NM_134428, exon 18 of 18)	42396	NR_121585	101929247	Hs.547178	NR_121585		LINC01231	-	long intergenic non-protein coding RNA 1231	ncRNA	0.011429	0.384615	
chunk0158_303_1	chr5	132339877	132340247	+	0	NA	intron (NM_003059, intron 8 of 9)	intron (NM_003059, intron 8 of 9)	25537	NR_037500	100500865		NR_037500	ENSG00000263597	MIR3936	mir-3936	microRNA 3936	ncRNA	0.000000	0.396226	
chunk0148_275_1	chr5	10556193	10556816	+	0	NA	Intergenic	Intergenic	-7819	NM_001164440	651746	Hs.26039	NM_001164440	ENSG00000164236	ANKRD33B	-	ankyrin repeat domain 33B	protein-coding	0.008026	0.491987	
chunk0042_300_1	chr12	7794554	7794783	+	0	NA	intron (NM_001297698, intron 3 of 3)	intron (NM_001297698, intron 3 of 3)	5272	NM_024865	79923	Hs.635882	NM_024865	ENSG00000111704	NANOG	-	Nanog homeobox	protein-coding	0.004367	0.491304	
chunk0070_424_1	chr15	77955209	77955426	+	0	NA	Intergenic	L1MD2|LINE|L1	-28471	NR_027024	645752	Hs.546408	NR_027024		LOC645752	-	golgin A6 family member A pseudogene	pseudo	0.009217	0.417431	
chunk0119_276_1	chr22	46055132	46055523	+	0	NA	intron (NR_027034, intron 1 of 2)	intron (NR_027034, intron 1 of 2)	-1183	NM_018280	55267	Hs.567529	NM_018280		PRR34	C22orf26	PRR34 long non-coding RNA	protein-coding	0.025575	0.545918	214(GGGACAGGTTGCTCCA,+,0.00)
chunk0100_38_1	chr2	105514797	105515316	+	0	NA	Intergenic	Intergenic	-76283	NM_201557	2274	Hs.443687	NM_001450	ENSG00000115641	FHL2	AAG11|DRAL|FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.007707	0.442308	
chunk0119_267_1	chr22	45919333	45919841	+	0	NA	TTS (NM_058238)	TTS (NM_058238)	57541	NM_058238	7477	Hs.512714	NM_058238	ENSG00000188064	WNT7B	-	Wnt family member 7B	protein-coding	0.029528	0.654224	
chunk0040_454_1	chr11	121908471	121908710	+	0	NA	Intergenic	Intergenic	191254	NR_029671	406911		NR_029671	ENSG00000207971	MIR125B1	MIRN125B1|mir-125b-1	microRNA 125b-1	ncRNA	0.012552	0.516667	
chunk0104_202_1	chr2	175827778	175828218	+	0	NA	Intergenic	Intergenic	174347	NM_001305008	80856	Hs.209561	NM_030650	ENSG00000144320	LNPK	KIAA1715|LNP|LNP1|NEDEHCC|Ul|ulnaless	lunapark, ER junction formation factor	protein-coding	0.004545	0.371882	
chunk0063_254_1	chr14	82845671	82846221	+	0	NA	Intergenic	Intergenic	-1222885	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.003636	0.295826	
chunk0017_286_1	chr1	210021105	210021664	+	0	NA	intron (NR_027459, intron 5 of 8)	intron (NR_027459, intron 5 of 8)	83210	NM_001146262	255928	Hs.658866	NM_153262	ENSG00000143469	SYT14	SCAR11|sytXIV	synaptotagmin 14	protein-coding	0.005367	0.364286	
chunk0063_409_1	chr14	88271421	88271680	+	0	NA	promoter-TSS (NM_138318)	promoter-TSS (NM_138318)	-639	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.007722	0.426923	
chunk0184_93_1	chr7	113333313	113333714	+	0	NA	Intergenic	L1PA8A|LINE|L1	-214931	NR_015442									0.002494	0.350746	194(TGAACAACCTGCTCTT,+,0.00)
chunk0202_418_1	chr9	81685798	81686693	+	0	NA	intron (NM_005077, intron 2 of 19)	intron (NM_005077, intron 2 of 19)	3290	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.004469	0.390625	
chunk0040_209_1	chr11	114162711	114163258	+	0	NA	intron (NM_006006, intron 3 of 6)	intron (NM_006006, intron 3 of 6)	102418	NM_001018011	7704	Hs.591945	NM_006006	ENSG00000109906	ZBTB16	PLZF|ZNF145	zinc finger and BTB domain containing 16	protein-coding	0.027422	0.527372	304(AAGAACACACTGTACC,-,0.00),305(AGAACACACTGTACCC,+,0.00)
chunk0148_346_1	chr5	14473896	14474350	+	0	NA	intron (NM_007118, intron 40 of 56)	intron (NM_007118, intron 40 of 56)	-107659	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.017621	0.452747	117(AAGAAGATGGTGTTCC,-,0.00),118(AGAAGATGGTGTTCCT,+,0.00)
chunk0055_262_1	chr13	63539466	63539819	+	0	NA	Intergenic	Intergenic	-197793	NR_002171	283491	Hs.363054	NR_002171		OR7E156P	-	olfactory receptor family 7 subfamily E member 156 pseudogene	pseudo	0.002833	0.302260	
chunk0004_318_1	chr1	49639271	49639760	+	0	NA	intron (NM_032785, intron 3 of 13)	MIR|SINE|MIR	-167430	NR_046839	100874313	Hs.551277	NR_046839	ENSG00000225623	AGBL4-IT1	-	AGBL4 intronic transcript 1	ncRNA	0.000000	0.344898	
chunk0147_238_1	chr4	182813251	182813519	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	104092	NM_001012732	1635	Hs.183850	NM_001921	ENSG00000129187	DCTD	-	dCMP deaminase	protein-coding	0.007463	0.535316	
chunk0153_395_1	chr5	75336032	75336813	+	0	NA	promoter-TSS (NM_001130996)	promoter-TSS (NM_001130996)	-746	NM_000859	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.030730	0.469309	
chunk0160_197_1	chr5	154700996	154701495	+	0	NA	Intergenic	Intergenic	-11657	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.010020	0.462000	
chunk0046_124_1	chr12	57388493	57388751	+	0	NA	Intergenic	MER83|LTR|ERV1	-46063	NM_005538	3626	Hs.632722	NM_005538	ENSG00000175189	INHBC	IHBC	inhibin subunit beta C	protein-coding	0.015504	0.471042	
chunk0162_424_1	chr5	180093957	180094229	+	0	NA	Intergenic	L1ME4b|LINE|L1	-21975	NM_018434	55819	Hs.484363	NM_018434	ENSG00000113269	RNF130	G1RZFP|GOLIATH|GP	ring finger protein 130	protein-coding	0.011029	0.479853	
chunk0044_63_1	chr12	27864993	27865704	+	0	NA	Intergenic	Intergenic	85094	NM_020782	57542	Hs.505104	NM_020782	ENSG00000087448	KLHL42	Ctb9|KLHDC5	kelch like family member 42	protein-coding	0.002813	0.358146	
chunk0194_77_1	chr8	82724599	82725272	+	0	NA	Intergenic	Intergenic	-678823	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.004458	0.375371	
chunk0058_69_1	chr14	20989499	20989948	+	0	NA	promoter-TSS (NM_022734)	promoter-TSS (NM_022734)	-83	NM_001029991	64745	Hs.512693	NM_022734	ENSG00000165792	METTL17	METT11D1	methyltransferase like 17	protein-coding	0.046771	0.491111	
chunk0144_249_1	chr4	136070605	136070835	+	0	NA	Intergenic	L1PA5|LINE|L1	-157040	NR_103763	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.000000	0.385281	
chunk0002_308_1	chr1	23830163	23830817	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-5031	NM_001166059	3155	Hs.533444	NM_000191	ENSG00000117305	HMGCL	HL	3-hydroxy-3-methylglutaryl-CoA lyase	protein-coding	0.006116	0.395420	126(ATGAACAAAATGTGCT,-,0.00),127(TGAACAAAATGTGCTA,+,0.00)
chunk0064_252_1	chr14	94564665	94565398	+	0	NA	intron (NM_006215, intron 2 of 4)	LTR33C|LTR|ERVL	3611	NM_001289033	5267	Hs.719893	NM_006215	ENSG00000100665	SERPINA4	KAL|KLST|KST|PI-4|PI4|kallistatin	serpin family A member 4	protein-coding	0.004093	0.423706	
chunk0103_204_1	chr2	163736557	163736756	+	0	NA	promoter-TSS (NM_018086)	promoter-TSS (NM_018086)	-653	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.115578	0.770000	
chunk0052_227_1	chr13	25608079	25608697	+	0	NA	intron (NM_001313741, intron 24 of 35)	intron (NM_001313741, intron 24 of 35)	139614	NM_001313741	51761	Hs.444957	NM_016529	ENSG00000132932	ATP8A2	ATP|ATPIB|CAMRQ4|IB|ML-1	ATPase phospholipid transporting 8A2	protein-coding	0.003236	0.392569	326(CATGACAGTATGTTCT,-,0.00),327(ATGACAGTATGTTCTC,+,0.00)
chunk0011_299_1	chr1	151563433	151563653	+	0	NA	intron (NM_001301317, intron 4 of 13)	Tigger3a|DNA|TcMar-Tigger	17747	NR_030280	693139		NR_030280	ENSG00000207606	MIR554	MIRN554|hsa-mir-554	microRNA 554	ncRNA	0.004545	0.429864	
chunk0166_325_1	chr6	49855385	49855711	+	0	NA	intron (NM_001205220, intron 2 of 7)	L2b|LINE|L2	10957	NM_170609	167	Hs.109620	NM_001131	ENSG00000124812	CRISP1	AEGL1|ARP|CRISP-1|HEL-S-57|HSCRISP1D|HSCRISP1G|HUMARP	cysteine rich secretory protein 1	protein-coding	0.006135	0.363914	
chunk0068_132_1	chr15	52698501	52699351	+	0	NA	Intergenic	Intergenic	-20292	NR_104457	56204	Hs.152385	NM_019600	ENSG00000047346	FAM214A	KIAA1370	family with sequence similarity 214 member A	protein-coding	0.005882	0.356052	
chunk0096_92_1	chr2	28036631	28037031	+	0	NA	intron (NM_199191, intron 5 of 11)	L2c|LINE|L2	40464	NR_036230	100422965		NR_036230	ENSG00000265321	MIR4263	-	microRNA 4263	ncRNA	0.007500	0.356608	162(GAAACTGAGTGTCCCG,+,0.00),337(TGGCACAGTATGTGCT,-,0.00),338(GGCACAGTATGTGCTC,+,0.00)
chunk0026_418_1	chr10	70576604	70576803	+	0	NA	Intergenic	Intergenic	26072	NM_001083116	5551	Hs.2200	NM_005041	ENSG00000180644	PRF1	HPLH2|P1|PFP	perforin 1	protein-coding	0.010050	0.550000	
chunk0002_229_1	chr1	20074029	20074408	+	0	NA	intron (NM_000929, intron 1 of 4)	intron (NM_000929, intron 1 of 4)	4010	NM_000929	5322	Hs.319438	NM_000929	ENSG00000127472	PLA2G5	FRFB|GV-PLA2|PLA2-10|hVPLA(2)	phospholipase A2 group V	protein-coding	0.013193	0.507895	
chunk0186_227_1	chr7	140425814	140426053	+	0	NA	exon (NM_001008749, exon 4 of 4)	exon (NM_001008749, exon 4 of 4)	21890	NM_001008749	401409	Hs.583545	NM_001008749	ENSG00000146955	RAB19	RAB19B	RAB19, member RAS oncogene family	protein-coding	0.041841	0.479167	
chunk0200_115_1	chr9	16989882	16990401	+	0	NA	Intergenic	L1ME1|LINE|L1	-119353	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.005780	0.348077	
chunk0153_457_1	chr5	76414775	76415298	+	0	NA	intron (NM_006633, intron 1 of 35)	intron (NM_006633, intron 1 of 35)	11781	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.005736	0.387405	
chunk0023_7_1	chr10	20885742	20886153	+	0	NA	intron (NM_006393, intron 4 of 27)	intron (NM_006393, intron 4 of 27)	11655	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.012165	0.381068	
chunk0199_467_1	chr9	14337601	14338206	+	0	NA	intron (NM_001190738, intron 1 of 8)	intron (NM_001190738, intron 1 of 8)	-23857	NM_001190737	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.018182	0.440594	
chunk0151_388_1	chr5	55355929	55356325	+	0	NA	intron (NM_015360, intron 14 of 26)	intron (NM_015360, intron 14 of 26)	48379	NM_015360	23517	Hs.274531	NM_015360	ENSG00000039123	MTREX	Dob1|KIAA0052|Mtr4|SKIV2L2|fSAP118	Mtr4 exosome RNA helicase	protein-coding	0.002525	0.531486	
chunk0086_17_1	chr18	12267065	12267579	+	0	NA	intron (NM_001279, intron 3 of 4)	intron (NM_001279, intron 3 of 4)	12961	NR_036468									0.013619	0.450485	305(CTGAACAGAATGCTCT,-,0.00),306(TGAACAGAATGCTCTT,+,0.00)
chunk0187_413_1	chr7	158234079	158234644	+	0	NA	intron (NM_001308267, intron 2 of 21)	L1M3f|LINE|L1	298452	NR_030325	693180		NR_030325	ENSG00000207637	MIR595	MIRN595|hsa-mir-595	microRNA 595	ncRNA	0.001770	0.303887	
chunk0045_305_1	chr12	50623155	50624216	+	0	NA	intron (NM_173602, intron 1 of 37)	L1ME4b|LINE|L1	118700	NM_173602	57609	Hs.505516	NM_020849	ENSG00000066084	DIP2B	-	disco interacting protein 2 homolog B	protein-coding	0.007540	0.411488	
chunk0055_273_1	chr13	64223063	64223262	+	0	NA	Intergenic	Intergenic	-379037	NR_130763	102723968	Hs.551671	NR_130763	ENSG00000219926	LOC102723968	-	uncharacterized LOC102723968	ncRNA	0.005025	0.365000	
chunk0135_21_1	chr3	184371537	184372107	+	0	NA	TTS (NM_001177598)	TTS (NM_001177598)	6386	NM_001177598	7066	Hs.1166	NM_000460	ENSG00000090534	THPO	MGDF|MKCSF|ML|MPLLG|THCYT1|TPO	thrombopoietin	protein-coding	0.008772	0.488616	
chunk0029_231_1	chr10	102493015	102493342	+	0	NA	intron (NM_005736, intron 1 of 10)	intron (NM_005736, intron 1 of 10)	9577	NM_005736	10121	Hs.153961	NM_005736	ENSG00000138107	ACTR1A	ARP1|Arp1A|CTRN1	actin related protein 1A	protein-coding	0.003058	0.500000	50(CAGGGCAGCCAGTTCT,-,0.00),51(AGGGCAGCCAGTTCTC,+,0.00)
chunk0138_52_1	chr4	31682722	31682937	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-314550	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.004651	0.398148	
chunk0185_199_1	chr7	128448726	128449311	+	0	NA	Intergenic	L2a|LINE|L2	-6812	NM_001098786	29923	Hs.706124	NM_013332	ENSG00000135245	HILPDA	C7orf68|HIG-2|HIG2	hypoxia inducible lipid droplet associated	protein-coding	0.010256	0.402730	
chunk0139_236_1	chr4	55425732	55426309	+	0	NA	non-coding (NR_073070, exon 7 of 7)	non-coding (NR_073070, exon 7 of 7)	30107	NR_073070	55858	Hs.479766	NM_018475	ENSG00000134851	TMEM165	CDG2K|FT27|GDT1|TMPT27|TPARL	transmembrane protein 165	protein-coding	0.001733	0.304498	
chunk0039_76_1	chr11	96900197	96900567	+	0	NA	Intergenic	L1MC3|LINE|L1	-393505	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.005405	0.315364	
chunk0130_143_1	chr3	132255085	132255386	+	0	NA	Intergenic	Intergenic	-62132	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.013289	0.463576	
chunk0173_383_1	chr6	149896131	149896925	+	0	NA	promoter-TSS (NM_001243328)	promoter-TSS (NM_001243328)	-469	NM_001243328	135250	Hs.511818	NM_139165	ENSG00000164520	RAET1E	LETAL|N2DL-4|NKG2DL4|RAET1E2|RL-4|ULBP4|bA350J20.7	retinoic acid early transcript 1E	protein-coding	0.008816	0.508176	
chunk0093_366_1	chr19	55676269	55676951	+	0	NA	promoter-TSS (NM_001130071)	promoter-TSS (NM_001130071)	-15	NM_001130071	29924	Hs.279953	NM_013333	ENSG00000063245	EPN1	-	epsin 1	protein-coding	0.010264	0.418741	307(AAGCACTGCATGTACC,-,0.00),308(AGCACTGCATGTACCC,+,0.00)
chunk0044_310_1	chr12	33441243	33441501	+	0	NA	Intergenic	Intergenic	-1553	NM_198992	341359	Hs.118703	NM_198992	ENSG00000110975	SYT10	-	synaptotagmin 10	protein-coding	0.003876	0.343629	
chunk0032_113_1	chr11	3815902	3816474	+	0	NA	intron (NR_045925, intron 3 of 5)	intron (NR_045925, intron 3 of 5)	7652	NR_027016	27315	Hs.133968	NM_014489	ENSG00000148985	PGAP2	CWH43-N|FRAG1|HPMRS3|MRT17|MRT21	post-GPI attachment to proteins 2	protein-coding	0.012238	0.542757	
chunk0107_230_1	chr2	217049331	217049782	+	0	NA	Intergenic	Intergenic	178784	NR_130782	101928327	Hs.350698	NR_130782	ENSG00000223874	LINC01921	-	long intergenic non-protein coding RNA 1921	ncRNA	0.013304	0.455752	249(GTGAACATTGTGTGCT,-,0.00),250(TGAACATTGTGTGCTT,+,0.00)
chunk0093_377_1	chr19	56142125	56142586	+	0	NA	intron (NM_018337, intron 1 of 4)	MIR|SINE|MIR	1189	NM_001253792	55311	Hs.24545	NM_018337	ENSG00000167685	ZNF444	EZF-2|EZF2|ZSCAN17	zinc finger protein 444	protein-coding	0.023861	0.484848	
chunk0005_154_1	chr1	58183103	58183744	+	0	NA	intron (NM_021080, intron 1 of 16)	L1MB7|LINE|L1	67116	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.004680	0.395639	
chunk0152_17_1	chr5	56378774	56379148	+	0	NA	Intergenic	L1MCa|LINE|L1	102808	NR_104664	102467147	Hs.650177	NR_104664	ENSG00000248727	LINC01948	-	long intergenic non-protein coding RNA 1948	ncRNA	0.000000	0.376000	214(TTGGACAGAATGTTCT,-,0.00),215(TGGACAGAATGTTCTC,+,0.00)
chunk0106_361_1	chr2	207060555	207060830	+	0	NA	Intergenic	L2a|LINE|L2	49381	NR_036227	100423036		NR_036227	ENSG00000253008	MIR2355	mir-2355	microRNA 2355	ncRNA	0.007273	0.518116	
chunk0059_356_1	chr14	37268179	37268737	+	0	NA	intron (NM_001195296, intron 6 of 14)	intron (NM_001195296, intron 6 of 14)	70545	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.005376	0.336315	254(CTGCACTGACTGTCCC,-,0.00),255(TGCACTGACTGTCCCA,+,0.00)
chunk0022_374_1	chr10	17542029	17542376	+	0	NA	Intergenic	Intergenic	75172	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.008646	0.359195	197(AGTGCACATTGTTCTT,+,0.00)
chunk0081_121_1	chr17	40113665	40113905	+	0	NA	Intergenic	Intergenic	-8752	NM_001012241	339287	Hs.532786	NM_001012241	ENSG00000188895	MSL1	MSL-1	MSL complex subunit 1	protein-coding	0.012500	0.535270	
chunk0123_278_1	chr3	46265262	46265602	+	0	NA	exon (NM_001837, exon 3 of 3)	exon (NM_001837, exon 3 of 3)	23051	NM_001164680	1232	Hs.506190	NM_001837	ENSG00000183625	CCR3	CC-CKR-3|CD193|CKR3|CMKBR3	C-C motif chemokine receptor 3	protein-coding	0.023529	0.516129	
chunk0004_375_1	chr1	51679588	51679937	+	0	NA	intron (NM_148908, intron 3 of 22)	MER44B|DNA|TcMar-Tigger	-50052	NM_148907	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.000000	0.337143	
chunk0090_233_1	chr18	73729055	73729348	+	0	NA	Intergenic	Intergenic	404260	NR_038340	100505817	Hs.197042	NR_038340	ENSG00000261780	LINC02582	-	long intergenic non-protein coding RNA 2582	ncRNA	0.006826	0.418367	
chunk0005_58_1	chr1	55356469	55357327	+	0	NA	Intergenic	Intergenic	131257	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.004662	0.414435	464(GAGGACAGGATGTTCC,-,0.00),465(AGGACAGGATGTTCCT,+,0.00)
chunk0073_426_1	chr16	19103605	19104336	+	0	NA	Intergenic	Intergenic	-9962	NR_028028	162073	Hs.530899	NM_001034841	ENSG00000205730	ITPRIPL2	-	ITPRIP like 2	protein-coding	0.005472	0.461749	349(GGTACACAGAGTCCAT,+,0.00)
chunk0109_211_1	chr20	5621318	5621608	+	0	NA	Intergenic	Intergenic	-10437	NM_019593	56261	Hs.636359	NM_019593	ENSG00000125772	GPCPD1	EDI3|GDE5|GDPD6|PREI4	glycerophosphocholine phosphodiesterase 1	protein-coding	0.006897	0.470790	
chunk0145_263_1	chr4	148954038	148954266	+	0	NA	Intergenic	Intergenic	-200143	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.008772	0.427948	
chunk0149_357_1	chr5	27655667	27656029	+	0	NA	Intergenic	L2|LINE|L2	183556	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.002762	0.366391	
chunk0166_46_1	chr6	42449024	42449667	+	0	NA	intron (NM_001297573, intron 2 of 17)	intron (NM_001297573, intron 2 of 17)	2706	NM_033502	55809	Hs.485392	NM_018415	ENSG00000124496	TRERF1	BCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5	transcriptional regulating factor 1	protein-coding	0.010886	0.391304	
chunk0042_16_1	chr12	1250203	1250439	+	0	NA	intron (NR_027946, intron 13 of 18)	intron (NR_027946, intron 13 of 18)	222573	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.000000	0.337553	
chunk0164_193_1	chr6	22362540	22362796	+	0	NA	Intergenic	Intergenic	-59815	NM_001163558	5617	Hs.1905	NM_000948	ENSG00000172179	PRL	GHA1	prolactin	protein-coding	0.015625	0.385214	
chunk0172_256_1	chr6	137356376	137356575	+	0	NA	Intergenic	Intergenic	-137045	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.000000	0.275000	
chunk0035_194_1	chr11	44229089	44229348	+	0	NA	intron (NM_001178083, intron 11 of 14)	intron (NM_001178083, intron 11 of 14)	80948	NM_021926	60529	Hs.436055	NM_021926	ENSG00000052850	ALX4	CRS5|FND2	ALX homeobox 4	protein-coding	0.007722	0.438462	
chunk0001_145_1	chr1	5979169	5979418	+	0	NA	intron (NR_111987, intron 2 of 32)	L2a|LINE|L2	-13005	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.016064	0.520000	
chunk0052_44_1	chr13	20843630	20844312	+	0	NA	intron (NM_022459, intron 4 of 22)	intron (NM_022459, intron 4 of 22)	58803	NM_022459	64328	Hs.507452	NM_022459	ENSG00000132953	XPO4	exp4	exportin 4	protein-coding	0.004399	0.326501	509(CAGGACACACTGTTCC,-,0.00),510(AGGACACACTGTTCCT,+,0.00)
chunk0142_226_1	chr4	98261641	98262099	+	0	NA	intron (NM_001100427, intron 1 of 14)	CpG-21364	494	NM_001100426	5910	Hs.132858	NM_021159	ENSG00000138698	RAP1GDS1	GDS1|SmgGDS	Rap1 GTPase-GDP dissociation stimulator 1	protein-coding	0.104803	0.675381	
chunk0127_349_1	chr3	100783458	100784100	+	0	NA	intron (NM_015429, intron 24 of 34)	MER58A|DNA|hAT-Charlie	74237	NM_001195478	10342	Hs.518123	NM_006070	ENSG00000114354	TFG	HMSNP|SPG57|TF6|TRKT3	trafficking from ER to golgi regulator	protein-coding	0.004673	0.416796	295(CAGTACACATTGTACA,-,0.00),296(AGTACACATTGTACAT,+,0.00)
chunk0198_296_1	chr8	137465293	137465795	+	0	NA	Intergenic	Intergenic	-51956	NR_125428	101927915	Hs.695851	NR_125428		LOC101927915	-	uncharacterized LOC101927915	ncRNA	0.003984	0.395626	
chunk0030_107_1	chr10	112717060	112717388	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	83054	NR_036177	100422909		NR_036177	ENSG00000264763	MIR4295	-	microRNA 4295	ncRNA	0.006098	0.452888	
chunk0179_327_1	chr7	50585161	50585641	+	0	NA	Intergenic	Intergenic	-19944	NM_001082971	1644	Hs.359698	NM_000790	ENSG00000132437	DDC	AADC	dopa decarboxylase	protein-coding	0.010417	0.442827	
chunk0060_256_1	chr14	50116823	50117487	+	0	NA	promoter-TSS (NM_001040662)	promoter-TSS (NM_001040662)	-576	NM_024558	79609	Hs.558541	NM_024558	ENSG00000100483	VCPKMT	C14orf138|METTL21D|VCP-KMT	valosin containing protein lysine methyltransferase	protein-coding	0.004518	0.333835	
chunk0048_302_1	chr12	82820904	82821411	+	0	NA	intron (NM_152588, intron 1 of 11)	AluJr4|SINE|Alu	134002	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.009862	0.403543	
chunk0111_337_1	chr20	33029019	33029218	+	0	NA	Intergenic	Intergenic	-2530	NM_174897	128859	Hs.375090	NM_174897	ENSG00000167104	BPIFB6	BPIL3|LPLUNC6	BPI fold containing family B member 6	protein-coding	0.010050	0.555000	108(AGGGACAGTGTGAGCA,-,0.00)
chunk0067_107_1	chr15	42308958	42309361	+	0	NA	intron (NM_001301409, intron 9 of 11)	intron (NM_001301409, intron 9 of 11)	34991	NM_198141	2595	Hs.730806	NM_198141	ENSG00000214013	GANC	-	glucosidase alpha, neutral C	protein-coding	0.007444	0.443069	
chunk0166_11_1	chr6	41577916	41578190	+	0	NA	exon (NM_138457, exon 3 of 17)	exon (NM_138457, exon 3 of 17)	-20670	NR_039784	100616178		NR_039784	ENSG00000266494	MIR4641	-	microRNA 4641	ncRNA	0.010949	0.618182	
chunk0042_41_1	chr12	1593769	1594081	+	0	NA	exon (NM_152441, exon 1 of 2)	exon (NM_152441, exon 1 of 2)	240	NM_152441	144699	Hs.367956	NM_152441	ENSG00000171823	FBXL14	Fbl14	F-box and leucine rich repeat protein 14	protein-coding	0.083333	0.693291	
chunk0031_278_1	chr10	128130264	128130465	+	0	NA	Intergenic	Intergenic	-4160	NM_002417	4288	Hs.80976	NM_002417	ENSG00000148773	MKI67	KIA|MIB-|MIB-1|PPP1R105	marker of proliferation Ki-67	protein-coding	0.004975	0.381188	
chunk0193_215_1	chr8	76372807	76373395	+	0	NA	Intergenic	Intergenic	-33553	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.003401	0.375212	
chunk0163_24_1	chr6	8064087	8064286	+	0	NA	intron (NR_037618, intron 3 of 6)	CpG	228	NM_201280	63915	Hs.719272	NM_201280	ENSG00000188428	BLOC1S5	BLOS5|MU|MUTED	biogenesis of lysosomal organelles complex 1 subunit 5	protein-coding	0.095477	0.670000	
chunk0196_145_1	chr8	104559775	104560179	+	0	NA	intron (NM_013437, intron 1 of 6)	MIRb|SINE|MIR	29047	NM_001135703	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.004950	0.274074	
chunk0050_226_1	chr12	104895405	104895685	+	0	NA	intron (NM_032148, intron 2 of 9)	Charlie13b|DNA|hAT-Charlie	33149	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.003571	0.334520	
chunk0200_32_1	chr9	15007949	15008442	+	0	NA	intron (NR_003920, intron 3 of 4)	intron (NR_003920, intron 3 of 4)	14868	NR_003920	389705	Hs.431257	NR_003920		LOC389705	-	histone PARylation factor 1 pseudogene	pseudo	0.004057	0.388664	
chunk0009_250_1	chr1	107073207	107073612	+	0	NA	Intergenic	Intergenic	16764	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.000000	0.295567	
chunk0168_201_1	chr6	85580678	85580884	+	0	NA	intron (NM_001304479, intron 1 of 28)	L1M1|LINE|L1	13375	NM_153816	57231	Hs.485871	NM_020468	ENSG00000135317	SNX14	RGS-PX2|SCAR20	sorting nexin 14	protein-coding	0.004854	0.463768	
chunk0083_126_1	chr17	65123829	65124108	+	0	NA	Intergenic	Intergenic	-13370	NM_001165933	8787	Hs.664380	NM_003835	ENSG00000108370	RGS9	PERRS|RGS9L	regulator of G protein signaling 9	protein-coding	0.017921	0.453571	
chunk0124_77_1	chr3	53164619	53165262	+	0	NA	intron (NM_001316327, intron 1 of 18)	intron (NM_001316327, intron 1 of 18)	3419	NM_001316327	5580	Hs.155342	NM_006254	ENSG00000163932	PRKCD	ALPS3|CVID9|MAY1|PKCD|nPKC-delta	protein kinase C delta	protein-coding	0.015552	0.562112	257(AGGGACACAGTGTTCC,-,0.00),258(GGGACACAGTGTTCCA,+,0.00)
chunk0157_336_1	chr5	122435103	122435613	+	0	NA	intron (NR_131761, intron 6 of 12)	intron (NR_131761, intron 6 of 12)	43729	NR_051996	153163	Hs.679757	NR_051996	ENSG00000250328	MGC32805	-	uncharacterized LOC153163	ncRNA	0.007843	0.454012	
chunk0071_421_1	chr15	89756791	89757356	+	0	NA	Intergenic	Intergenic	-5764	NM_018670	55897	Hs.447531	NM_018670	ENSG00000166823	MESP1	bHLHc5	mesoderm posterior bHLH transcription factor 1	protein-coding	0.017699	0.432862	
chunk0094_150_1	chr2	5151455	5151822	+	0	NA	Intergenic	L1MB8|LINE|L1	-495416	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.000000	0.317935	
chunk0041_451_1	chr11	135022020	135022219	+	0	NA	Intergenic	LTR53|LTR|ERVL	585637	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.005025	0.500000	
chunk0176_14_1	chr7	8278223	8278431	+	0	NA	intron (NR_125740, intron 3 of 5)	intron (NR_125740, intron 3 of 5)	-15715	NM_001276478	3382	Hs.487561	NM_004968	ENSG00000003147	ICA1	ICA69|ICAp69	islet cell autoantigen 1	protein-coding	0.000000	0.468900	
chunk0173_21_1	chr6	141552529	141553062	+	0	NA	Intergenic	L1MB7|LINE|L1	536004	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.001876	0.374532	
chunk0209_83_1	chrX	38937301	38937655	+	0	NA	Intergenic	Intergenic	-133595	NR_046706	100874211	Hs.662789	NR_046706		MID1IP1-AS1	-	MID1IP1 antisense RNA 1	ncRNA	0.002825	0.433803	
chunk0098_230_1	chr2	73983642	73984014	+	0	NA	Intergenic	Intergenic	-2389	NR_104030	100874048	Hs.600674	NR_104029	ENSG00000237883	DGUOK-AS1	-	DGUOK antisense RNA 1	ncRNA	0.040323	0.560322	
chunk0116_302_1	chr21	40521646	40522217	+	0	NA	intron (NR_073202, intron 3 of 32)	L1MA6|LINE|L1	108836	NR_046774	100874326	Hs.679746	NR_046774	ENSG00000233756	DSCAM-IT1	zag4	DSCAM intronic transcript 1	ncRNA	0.015762	0.372378	
chunk0064_384_1	chr14	98975927	98976149	+	0	NA	Intergenic	L1MEc|LINE|L1	264425	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.004505	0.286996	171(GAGAACATAATGATCC,-,0.00),172(AGAACATAATGATCCT,+,0.00)
chunk0210_336_1	chrX	95383698	95384229	+	0	NA	Intergenic	Intergenic	-320737	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.003766	0.355263	
chunk0059_198_1	chr14	33388839	33389392	+	0	NA	intron (NM_022123, intron 3 of 10)	intron (NM_022123, intron 3 of 10)	-319822	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.012658	0.357401	
chunk0016_218_1	chr1	199046581	199046884	+	0	NA	intron (NR_126351, intron 2 of 2)	L1PA16|LINE|L1	-27768	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.003300	0.483553	
chunk0135_383_1	chr3	191235597	191235858	+	0	NA	intron (NM_198184, intron 2 of 2)	LTR78|LTR|ERV1	23194	NM_198184	344901	Hs.526794	NM_198184	ENSG00000188729	OSTN	MUSCLIN	osteocrin	protein-coding	0.003831	0.496183	
chunk0150_16_1	chr5	30542246	30542611	+	0	NA	Intergenic	L1MA3|LINE|L1	-651227	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.002740	0.295082	
chunk0110_39_1	chr20	10566531	10567007	+	0	NA	intron (NM_001009608, intron 4 of 7)	ERVL-E-int|LTR|ERVL	82926	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.008403	0.454927	
chunk0112_99_1	chr20	38126095	38126446	+	0	NA	Intergenic	MIRb|SINE|MIR	39028	NM_004613	7052	Hs.517033	NM_004613	ENSG00000198959	TGM2	TG(C)|TGC	transglutaminase 2	protein-coding	0.008547	0.559659	
chunk0051_170_1	chr12	116027254	116027476	+	0	NA	intron (NM_015335, intron 4 of 30)	AluJb|SINE|Alu	121289	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.013514	0.488789	76(GAGGACAGCTTGAGCC,-,0.00),77(AGGACAGCTTGAGCCT,+,0.00)
chunk0026_168_1	chr10	63264622	63265133	+	0	NA	intron (NM_032776, intron 2 of 25)	intron (NM_032776, intron 2 of 25)	4346	NM_001282948	221037	Hs.413416	NM_004241	ENSG00000171988	JMJD1C	KDM3C|TRIP-8|TRIP8	jumonji domain containing 1C	protein-coding	0.000000	0.308594	
chunk0069_326_1	chr15	66059636	66060007	+	0	NA	intron (NM_032445, intron 5 of 22)	intron (NM_032445, intron 5 of 22)	19588	NR_036196	100422905		NR_036196	ENSG00000263512	MIR4311	-	microRNA 4311	ncRNA	0.010782	0.526882	
chunk0035_426_1	chr11	57269457	57270174	+	0	NA	Intergenic	Intergenic	-32362	NM_005161	187	Hs.438311	NM_005161	ENSG00000134817	APLNR	AGTRL1|APJ|APJR|HG11	apelin receptor	protein-coding	0.006974	0.502786	482(AGTTACAGCCTGTTCT,-,0.00),483(GTTACAGCCTGTTCTT,+,0.00)
chunk0199_117_1	chr9	3491067	3491384	+	0	NA	intron (NM_134428, intron 1 of 17)	intron (NM_134428, intron 1 of 17)	-1738	NM_001282117	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.003155	0.308176	
chunk0012_432_1	chr1	164830753	164831453	+	0	NA	intron (NM_001204963, intron 8 of 8)	L1ME2z|LINE|L1	-56462	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.011429	0.373752	
chunk0019_368_1	chr1	229843861	229845301	+	0	NA	Intergenic	MER70B|LTR|ERVL	-213208	NM_001291866	2590	Hs.743964	NM_004481	ENSG00000143641	GALNT2	GalNAc-T2	polypeptide N-acetylgalactosaminyltransferase 2	protein-coding	0.007639	0.446218	289(TGGTACACAATGTCCT,-,0.00),290(GGTACACAATGTCCTG,+,0.00),1111(AGGTACACAGTGTTCC,-,0.00),1112(GGTACACAGTGTTCCC,+,0.00)
chunk0200_465_1	chr9	31909065	31909479	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-475331	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.014493	0.455422	
chunk0073_194_1	chr16	9055759	9055996	+	0	NA	Intergenic	MIR|SINE|MIR	-35803	NM_014117	29035	Hs.221497	NM_014117	ENSG00000182831	C16orf72	PRO0149	chromosome 16 open reading frame 72	protein-coding	0.008439	0.390756	
chunk0125_421_1	chr3	72403306	72403800	+	0	NA	intron (NM_012234, intron 1 of 3)	intron (NM_012234, intron 1 of 3)	43070	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.004049	0.383838	
chunk0138_140_1	chr4	36892784	36893425	+	0	NA	Intergenic	MamTip2|DNA|hAT-Tip100	348887	NR_039965	100616435		NR_039965	ENSG00000264319	MIR4801	-	microRNA 4801	ncRNA	0.000000	0.376947	
chunk0101_92_1	chr2	124482520	124482796	+	0	NA	intron (NM_130773, intron 7 of 23)	intron (NM_130773, intron 7 of 23)	457371	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.018116	0.527076	
chunk0174_321_1	chr6	163392741	163393030	+	0	NA	Intergenic	Intergenic	21065	NR_037593	100526820	Hs.644159	NR_037593	ENSG00000270419	CAHM	LINC00468	colon adenocarcinoma hypermethylated	ncRNA	0.006920	0.413793	
chunk0127_6_1	chr3	87926207	87926430	+	0	NA	Intergenic	Intergenic	-56258	NM_000866	3355	Hs.248136	NM_000866	ENSG00000179097	HTR1F	5-HT-1F|5-HT1F|5HT6|HTR1EL|MR77	5-hydroxytryptamine receptor 1F	protein-coding	0.000000	0.330357	
chunk0054_340_1	chr13	49452879	49453408	+	0	NA	intron (NM_001160308, intron 1 of 12)	L1MC3|LINE|L1	1591	NM_001160308	83852	Hs.631789	NM_031915	ENSG00000136169	SETDB2	C13orf4|CLLD8|CLLL8|KMT1F	SET domain bifurcated histone lysine methyltransferase 2	protein-coding	0.009452	0.388679	
chunk0163_427_1	chr6	17202638	17202960	+	0	NA	Intergenic	Intergenic	-78779	NM_001143942	221662	Hs.519904	NM_153020	ENSG00000112183	RBM24	RNPC6|dJ259A10.1	RNA binding motif protein 24	protein-coding	0.012422	0.414861	
chunk0124_399_1	chr3	59773901	59774319	+	0	NA	intron (NM_001166243, intron 8 of 9)	intron (NM_001166243, intron 8 of 9)	-724121	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.009569	0.365155	
chunk0091_361_1	chr19	15421359	15421640	+	0	NA	TTS (NM_021241)	TTS (NM_021241)	-2378	NR_111971	26993	Hs.399800	NM_014371	ENSG00000011243	AKAP8L	HA95|HAP95|NAKAP|NAKAP95	A-kinase anchoring protein 8 like	protein-coding	0.024911	0.489362	
chunk0165_68_1	chr6	31125837	31126088	+	0	NA	intron (NM_014068, intron 2 of 5).4	intron (NM_014068, intron 2 of 5).4	-5487	NM_001264	1041	Hs.310958	NM_001264	ENSG00000204539	CDSN	HTSS|HTSS1|HYPT2|PSS|PSS1|S	corneodesmosin	protein-coding	0.007968	0.555556	113(AGGGACATGGTGCCCT,-,0.00),114(GGGACATGGTGCCCTC,+,0.00)
chunk0194_338_1	chr8	89036841	89037472	+	0	NA	Intergenic	Intergenic	-709668	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.001585	0.303797	
chunk0062_257_1	chr14	71638452	71639097	+	0	NA	intron (NM_001284245, intron 4 of 20)	L1MDa|LINE|L1	51203	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.001550	0.356037	183(AGTACAAGAAGTTCTA,+,0.00)
chunk0187_406_1	chr7	157995142	157995446	+	0	NA	intron (NM_001308268, intron 11 of 22)	intron (NM_001308268, intron 11 of 22)	140709	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.029605	0.465574	
chunk0088_39_1	chr18	43880060	43880405	+	0	NA	Intergenic	Intergenic	-602582	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.008696	0.459538	195(CAGAACAAAGTGTTTC,-,0.00),196(AGAACAAAGTGTTTCT,+,0.00)
chunk0156_355_1	chr5	112354093	112354669	+	0	NA	intron (NM_022140, intron 1 of 22)	intron (NM_022140, intron 1 of 22)	64932	NM_022140	64097	Hs.584954	NM_022140	ENSG00000129595	EPB41L4A	EPB41L4|NBL4	erythrocyte membrane protein band 4.1 like 4A	protein-coding	0.008681	0.386482	
chunk0039_290_1	chr11	102733379	102733929	+	0	NA	Intergenic	Intergenic	-8700	NM_001304442	4317	Hs.161839	NM_002424	ENSG00000118113	MMP8	CLG1|HNC|MMP-8|PMNL-CL	matrix metallopeptidase 8	protein-coding	0.012727	0.446461	316(TGGTCACAATGTTCCT,+,0.00)
chunk0036_235_1	chr11	64228947	64229323	+	0	NA	intron (NM_001128612, intron 3 of 5)	MIR1_Amn|SINE|MIR	-1146	NM_005528	3338	Hs.172847	NM_005528	ENSG00000110011	DNAJC4	DANJC4|HSPF2|MCG18	DnaJ heat shock protein family (Hsp40) member C4	protein-coding	0.026596	0.522546	
chunk0047_337_1	chr12	74586388	74586944	+	0	NA	Intergenic	L1MD2|LINE|L1	48895	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.003597	0.418312	
chunk0177_113_1	chr7	22175466	22175865	+	0	NA	intron (NM_012294, intron 11 of 25)	intron (NM_012294, intron 11 of 25)	181249	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.015038	0.355000	
chunk0066_294_1	chr15	35506345	35506634	+	0	NA	intron (NM_080650, intron 3 of 8)	intron (NM_080650, intron 3 of 8)	-39706	NR_038251	100507466	Hs.536420	NR_038251	ENSG00000248079	DPH6-DT	ATPBD4-AS1|DPH6-AS1	DPH6 divergent transcript	ncRNA	0.013841	0.413793	217(CTGAACTCACTGTACT,-,0.00),218(TGAACTCACTGTACTG,+,0.00)
chunk0122_101_1	chr3	30476592	30476854	+	0	NA	Intergenic	Intergenic	-129779	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.003817	0.338403	
chunk0017_410_1	chr1	212881838	212882058	+	0	NA	intron (NM_014053, intron 3 of 9)	L1ME3C|LINE|L1	23693	NM_014053	28982	Hs.7055	NM_014053	ENSG00000162769	FLVCR1	AXPC1|FLVCR|MFSD7B|PCA|PCARP|SLC49A1	feline leukemia virus subgroup C cellular receptor 1	protein-coding	0.000000	0.357466	
chunk0090_390_1	chr18	77485884	77486083	+	0	NA	Intergenic	Intergenic	235931	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.005025	0.535000	
chunk0078_404_1	chr16	88763349	88763831	+	0	NA	intron (NM_001142864, intron 1 of 50)	intron (NM_001142864, intron 1 of 50)	20823	NR_120387	339059	Hs.449817	NR_120387	ENSG00000182376	LOC339059	-	uncharacterized LOC339059	ncRNA	0.018672	0.534161	
chunk0078_259_1	chr17	7483770	7483990	+	0	NA	promoter-TSS (NM_000937)	promoter-TSS (NM_000937)	369	NM_020899	57659	Hs.35096	NM_020899	ENSG00000174282	ZBTB4	KAISO-L1|ZNF903	zinc finger and BTB domain containing 4	protein-coding	0.059091	0.588235	
chunk0127_300_1	chr3	98227146	98227456	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-36984	NM_001005479	79295	Hs.554712	NM_001005479	ENSG00000230301	OR5H6	OR3-11	olfactory receptor family 5 subfamily H member 6 (gene/pseudogene)	protein-coding	0.000000	0.353698	
chunk0183_385_1	chr7	109987302	109987579	+	0	NA	Intergenic	L1MC3|LINE|L1	-27227	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.003610	0.287770	
chunk0161_224_1	chr5	171024950	171025298	+	0	NA	intron (NM_022897, intron 14 of 27)	L2b|LINE|L2	163242	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.000000	0.363897	
chunk0198_184_1	chr8	133413373	133413572	+	0	NA	Intergenic	Intergenic	-116168	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.000000	0.345000	
chunk0034_54_1	chr11	27051832	27052042	+	0	NA	intron (NR_125768, intron 3 of 3)	L1MA9|LINE|L1	10975	NM_003986	8424	Hs.591996	NM_003986	ENSG00000129151	BBOX1	BBH|BBOX|G-BBH|gamma-BBH	gamma-butyrobetaine hydroxylase 1	protein-coding	0.000000	0.265403	
chunk0177_415_1	chr7	27662978	27663213	+	0	NA	promoter-TSS (NM_152740)	promoter-TSS (NM_152740)	-94	NM_152740	11112	Hs.406758	NM_152740	ENSG00000106049	HIBADH	NS5ATP1	3-hydroxyisobutyrate dehydrogenase	protein-coding	0.068085	0.622881	
chunk0136_70_1	chr4	1939804	1940166	+	0	NA	3' UTR (NM_007331, exon 11 of 11)	3' UTR (NM_007331, exon 11 of 11)	-34651	NR_003004	677770	Hs.676951	NR_003004	ENSG00000249784	SCARNA22	ACA11	small Cajal body-specific RNA 22	ncRNA	0.011050	0.432507	
chunk0123_272_1	chr3	46182945	46183151	+	0	NA	Intergenic	Intergenic	25293	NM_001295	1230	Hs.301921	NM_001295	ENSG00000163823	CCR1	CD191|CKR-1|CKR1|CMKBR1|HM145|MIP1aR|SCYAR1	C-C motif chemokine receptor 1	protein-coding	0.004854	0.560386	
chunk0009_301_1	chr1	107985183	107985750	+	0	NA	intron (NR_046653, intron 1 of 2)	intron (NR_046653, intron 1 of 2)	-20543	NM_006113	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.001764	0.306338	
chunk0076_82_1	chr16	64564490	64564875	+	0	NA	Intergenic	Intergenic	557455	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.010390	0.313472	
chunk0208_410_1	chrX	29491211	29492247	+	0	NA	intron (NM_014271, intron 5 of 10)	intron (NM_014271, intron 5 of 10)	-82549	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.004826	0.322083	221(GAAACAGAAAGTCCCT,+,0.00)
chunk0029_51_1	chr10	96390376	96390789	+	0	NA	intron (NM_012465, intron 13 of 20)	intron (NM_012465, intron 13 of 20)	-31217	NM_033207	93377	Hs.12449	NM_033207	ENSG00000197430	OPALIN	HTMP10|TMEM10|TMP10	oligodendrocytic myelin paranodal and inner loop protein	protein-coding	0.009685	0.567633	
chunk0200_163_1	chr9	18873294	18873493	+	0	NA	intron (NM_001040272, intron 23 of 28)	L1PB1|LINE|L1	159865	NM_153707	158297	Hs.731593	NM_153707	ENSG00000155875	SAXO1	C9orf138|FAM154A	stabilizer of axonemal microtubules 1	protein-coding	0.005025	0.345000	
chunk0046_85_1	chr12	56299572	56299861	+	0	NA	intron (NM_004077, intron 1 of 10)	intron (NM_004077, intron 1 of 10)	675	NM_004077	1431	Hs.743252	NM_004077	ENSG00000062485	CS	-	citrate synthase	protein-coding	0.024221	0.503448	
chunk0106_432_1	chr2	208468553	208469032	+	0	NA	intron (NM_001309516, intron 9 of 12)	L2a|LINE|L2	61962	NM_005048	5746	Hs.570296	NM_005048	ENSG00000144407	PTH2R	PTHR2	parathyroid hormone 2 receptor	protein-coding	0.004175	0.364583	
chunk0125_281_1	chr3	69596022	69596235	+	0	NA	Intergenic	Intergenic	-143307	NM_198159	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.004695	0.308411	
chunk0176_187_1	chr7	13879868	13880117	+	0	NA	Intergenic	Intergenic	106522	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.000000	0.376000	
chunk0167_445_1	chr6	75894231	75894805	+	0	NA	intron (NM_001300899, intron 28 of 32)	intron (NM_001300899, intron 28 of 32)	145326	NM_004999	4646	Hs.149387	NM_004999	ENSG00000196586	MYO6	DFNA22|DFNB37	myosin VI	protein-coding	0.005226	0.356522	
chunk0092_299_1	chr19	34259220	34259776	+	0	NA	intron (NM_014686, intron 1 of 13)	intron (NM_014686, intron 1 of 13)	4947	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.008993	0.414722	
chunk0096_407_1	chr2	37925322	37925726	+	0	NA	intron (NM_001170791, intron 1 of 10)	CpG	205	NM_001170791	151393	Hs.591566	NM_144713	ENSG00000115841	RMDN2	BLOCK18|FAM82A|FAM82A1|PRO34163|PYST9371|RMD-2|RMD2|RMD4	regulator of microtubule dynamics 2	protein-coding	0.091584	0.688889	
chunk0048_229_1	chr12	81540042	81540326	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-27793	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.322807	
chunk0022_238_1	chr10	14192642	14193280	+	0	NA	intron (NM_018027, intron 2 of 24)	intron (NM_018027, intron 2 of 24)	118677	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.003135	0.364632	
chunk0035_286_1	chr11	46761384	46761764	+	0	NA	TTS (NR_003056)	TTS (NR_003056)	925	NR_003056	692108	Hs.693252	NR_003056	ENSG00000212135	SNORD67	HBII-166	small nucleolar RNA, C/D box 67	snoRNA	0.015789	0.380577	
chunk0123_334_1	chr3	47617222	47618147	+	0	NA	intron (NM_003074, intron 25 of 27)	intron (NM_003074, intron 25 of 27)	-37444	NM_001206945	10675	Hs.45127	NM_006574	ENSG00000114646	CSPG5	NGC	chondroitin sulfate proteoglycan 5	protein-coding	0.005405	0.385529	
chunk0096_173_1	chr2	29723255	29723518	+	0	NA	intron (NM_004304, intron 1 of 28)	L2a|LINE|L2	198225	NM_004304	238	Hs.654469	NM_004304	ENSG00000171094	ALK	CD246|NBLST3	ALK receptor tyrosine kinase	protein-coding	0.003802	0.496212	
chunk0197_41_1	chr8	118225547	118225781	+	0	NA	intron (NR_109794, intron 4 of 4)	L2b|LINE|L2	-113845	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.008547	0.429787	
chunk0192_337_1	chr8	67542102	67542816	+	0	NA	intron (NM_020361, intron 2 of 10)	Tigger19b|DNA|TcMar-Tigger	-198782	NM_006421	10565	Hs.656902	NM_006421	ENSG00000066777	ARFGEF1	ARFGEP1|BIG1|P200	ADP ribosylation factor guanine nucleotide exchange factor 1	protein-coding	0.005602	0.402797	453(AGGTACAATCTGTTCT,-,0.00),454(GGTACAATCTGTTCTG,+,0.00),658(GAAGACAGGCAGTTCT,-,0.00),659(AAGACAGGCAGTTCTT,+,0.00)
chunk0187_32_1	chr8	907944	908143	+	0	NA	intron (NR_073397, intron 3 of 3)	intron (NR_073397, intron 3 of 3)	170438	NR_073397	9228	Hs.113287	NM_004745	ENSG00000198010	DLGAP2	C8orf68|DAP2|ERICH1-AS1|SAPAP2	DLG associated protein 2	protein-coding	0.010050	0.320000	
chunk0172_59_1	chr6	134186050	134186472	+	0	NA	intron (NM_001143676, intron 3 of 13)	ERVL-B4-int|LTR|ERVL	-8389	NM_001143677	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.004739	0.326241	
chunk0053_13_1	chr13	26238470	26238712	+	0	NA	Intergenic	Intergenic	-16028	NM_001260	1024	Hs.382306	NM_001260	ENSG00000132964	CDK8	K35	cyclin dependent kinase 8	protein-coding	0.008264	0.423868	
chunk0169_223_1	chr6	104388492	104388719	+	0	NA	Intergenic	L1MA7|LINE|L1	471314	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.004405	0.276316	
chunk0167_65_1	chr6	56235277	56235570	+	0	NA	intron (NM_030820, intron 1 of 29)	intron (NM_030820, intron 1 of 29)	12157	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.000000	0.387755	
chunk0036_95_1	chr11	60892414	60893806	+	0	NA	intron (NM_014502, intron 15 of 15)	Tigger3b|DNA|TcMar-Tigger	13479	NM_014502	27339	Hs.502705	NM_014502	ENSG00000110107	PRPF19	NMP200|PRP19|PSO4|SNEV|UBOX4|hPSO4	pre-mRNA processing factor 19	protein-coding	0.015805	0.457286	
chunk0109_53_1	chr20	1024125	1024374	+	0	NA	Intergenic	L2a|LINE|L2	-21985	NM_001029871	343637	Hs.444980	NM_001029871	ENSG00000101282	RSPO4	C20orf182|CRISTIN4	R-spondin 4	protein-coding	0.008032	0.392000	101(AGAACAGTGTGCCCAG,+,0.00)
chunk0108_226_1	chr2	233572339	233572889	+	0	NA	Intergenic	MSTB1|LTR|ERVL-MaLR	-7024	NM_018218	55230	Hs.96513	NM_018218	ENSG00000085982	USP40	-	ubiquitin specific peptidase 40	protein-coding	0.010909	0.484574	
chunk0003_314_1	chr1	37989900	37990381	+	0	NA	promoter-TSS (NM_006802)	promoter-TSS (NM_006802)	-51	NM_006802	10946	Hs.77897	NM_006802	ENSG00000183431	SF3A3	PRP9|PRPF9|SAP61|SF3a60	splicing factor 3a subunit 3	protein-coding	0.062370	0.595436	
chunk0102_218_1	chr2	148593613	148594127	+	0	NA	Intergenic	AluY|SINE|Alu	-51121	NM_015630	26122	Hs.23270	NM_015630	ENSG00000135999	EPC2	EPC-LIKE	enhancer of polycomb homolog 2	protein-coding	0.019455	0.403883	
chunk0128_60_1	chr3	104952437	104952796	+	0	NA	Intergenic	Intergenic	-414097	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.000000	0.402778	
chunk0002_302_1	chr1	23638898	23639112	+	0	NA	intron (NR_027042, intron 4 of 6)	intron (NR_027042, intron 4 of 6)	11671	NR_027042									0.009346	0.465116	
chunk0196_443_1	chr8	116567406	116567628	+	0	NA	Intergenic	L2c|LINE|L2	188306	NM_003756	8667	Hs.492599	NM_003756	ENSG00000147677	EIF3H	EIF3S3|eIF3-gamma|eIF3-p40	eukaryotic translation initiation factor 3 subunit H	protein-coding	0.000000	0.390135	
chunk0188_371_1	chr8	18208889	18209818	+	0	NA	promoter-TSS (NM_000662)	promoter-TSS (NM_000662)	-750	NM_001160171	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.009688	0.426882	
chunk0071_281_1	chr15	85800526	85800767	+	0	NA	Intergenic	Intergenic	-5688	NM_022480	64410	Hs.498371	NM_022480	ENSG00000183655	KLHL25	ENC-2|ENC2	kelch like family member 25	protein-coding	0.004149	0.557851	
chunk0067_175_1	chr15	44221589	44221882	+	0	NA	Intergenic	Intergenic	-26441	NM_032892	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.006826	0.285714	
chunk0060_59_1	chr14	41575460	41575676	+	0	NA	Intergenic	Intergenic	-31993	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.004630	0.391705	
chunk0053_72_1	chr13	28320834	28321584	+	0	NA	intron (NM_002019, intron 23 of 29)	intron (NM_002019, intron 23 of 29)	173919	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.016000	0.476698	271(GAGTCCAGGCTGTTCT,-,0.00),272(AGTCCAGGCTGTTCTT,+,0.00)
chunk0198_55_1	chr8	128535904	128536254	+	0	NA	intron (NR_121672, intron 2 of 7)	LTR16A2|LTR|ERVL	28600	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.002857	0.472934	
chunk0008_16_1	chr1	87433224	87433468	+	0	NA	Intergenic	Intergenic	-61691	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.008197	0.400000	92(TAGAACACTGAGTCCT,-,0.00),93(AGAACACTGAGTCCTT,+,0.00)
chunk0107_393_1	chr2	223836019	223836259	+	0	NA	intron (NR_110905, intron 1 of 5)	intron (NR_110905, intron 1 of 5)	1463	NR_110905	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.029167	0.560166	
chunk0030_175_1	chr10	114172707	114173101	+	0	NA	intron (NM_018017, intron 1 of 15)	intron (NM_018017, intron 1 of 15)	1275	NR_031747	100302224		NR_031747	ENSG00000284442	MIR2110	hsa-mir-2110|mir-2110	microRNA 2110	ncRNA	0.010152	0.364557	
chunk0063_75_1	chr14	77590843	77591152	+	0	NA	intron (NM_004863, intron 2 of 11)	intron (NM_004863, intron 2 of 11)	25770	NM_004863	9517	Hs.435661	NM_004863	ENSG00000100596	SPTLC2	HSN1C|LCB2|LCB2A|NSAN1C|SPT2|hLCB2a	serine palmitoyltransferase long chain base subunit 2	protein-coding	0.003236	0.390323	
chunk0205_127_1	chr9	107954222	107954596	+	0	NA	Intergenic	Intergenic	-464689	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.010695	0.440000	250(CAGTACTCACTGTCCA,-,0.00),251(AGTACTCACTGTCCAG,+,0.00)
chunk0085_5_1	chr18	167189	167645	+	0	NA	intron (NM_001037334, intron 3 of 14)	L1M5|LINE|L1	8934	NM_001037334	9097	Hs.464416	NM_005151	ENSG00000101557	USP14	TGT	ubiquitin specific peptidase 14	protein-coding	0.017544	0.428884	
chunk0181_339_1	chr7	88220009	88220491	+	0	NA	promoter-TSS (NM_001256891)	promoter-TSS (NM_001256891)	-166	NM_003130	6717	Hs.489040	NM_003130	ENSG00000075142	SRI	CP-22|CP22|SCN|V19	sorcin	protein-coding	0.082988	0.606625	
chunk0012_438_1	chr1	164943566	164943871	+	0	NA	Intergenic	L1PB3|LINE|L1	-169077	NR_038072	100505795	Hs.661039	NR_038072	ENSG00000233693	LOC100505795	-	uncharacterized LOC100505795	ncRNA	0.003279	0.392157	
chunk0210_62_1	chrX	69620985	69621233	+	0	NA	intron (NM_001005612, intron 1 of 7)	intron (NM_001005612, intron 1 of 7)	5042	NM_001399	1896	Hs.105407	NM_001399	ENSG00000158813	EDA	ECTD1|ED1|ED1-A1|ED1-A2|EDA-A1|EDA-A2|EDA1|EDA2|HED|HED1|ODT1|STHAGX1|TNLG7C|XHED|XLHED	ectodysplasin A	protein-coding	0.004032	0.325301	
chunk0019_362_1	chr1	229768237	229768455	+	0	NA	Intergenic	Intergenic	142130	NM_014777	9816	Hs.533628	NM_014777	ENSG00000135763	URB2	KIAA0133|NET10|NPA2	URB2 ribosome biogenesis homolog	protein-coding	0.013761	0.461187	
chunk0007_184_1	chr1	80729871	80730580	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	88938	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.005642	0.383099	
chunk0066_186_1	chr15	33126149	33126480	+	0	NA	intron (NM_001277313, intron 4 of 20)	intron (NM_001277313, intron 4 of 20)	-58282	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.012085	0.524096	
chunk0026_162_1	chr10	62856108	62856868	+	0	NA	Intergenic	Intergenic	-37321	NM_001136178	1959	Hs.1395	NM_000399	ENSG00000122877	EGR2	AT591|CHN1|CMT1D|CMT4E|KROX20	early growth response 2	protein-coding	0.005263	0.345598	428(TGAACTTGATGTCCTG,+,0.00)
chunk0202_173_1	chr9	73869381	73869674	+	0	NA	Intergenic	Intergenic	-502004	NR_121182	101927358	Hs.559523	NR_121182	ENSG00000227809	LOC101927358	-	uncharacterized LOC101927358	ncRNA	0.006826	0.408163	
chunk0155_367_1	chr5	97439363	97440197	+	0	NA	Intergenic	Intergenic	-64916	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.004796	0.401198	
chunk0155_376_1	chr5	97716348	97716697	+	0	NA	Intergenic	Intergenic	211826	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.000000	0.291429	
chunk0202_407_1	chr9	81509563	81509762	+	0	NA	Intergenic	HAL1M8|LINE|L1	179873	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.010050	0.485000	
chunk0109_174_1	chr20	4270049	4270660	+	0	NA	Intergenic	Intergenic	-21342	NM_000678	146	Hs.557	NM_000678	ENSG00000171873	ADRA1D	ADRA1|ADRA1A|ADRA1R|ALPHA1|DAR|dJ779E11.2	adrenoceptor alpha 1D	protein-coding	0.000000	0.349673	
chunk0004_307_1	chr1	49173770	49173969	+	0	NA	intron (NM_032785, intron 4 of 13)	L2a|LINE|L2	-83542	NR_125988	101929721	Hs.639985	NR_125988	ENSG00000230114	LOC101929721	-	uncharacterized LOC101929721	ncRNA	0.005025	0.370000	101(AAGAACATGCAGTTTC,-,0.00)
chunk0206_299_1	chr9	124730881	124731080	+	0	NA	intron (NM_033334, intron 2 of 9)	intron (NM_033334, intron 2 of 9)	37270	NR_029782	406956		NR_029782	ENSG00000207737	MIR181B2	MIRN181B2|mir-181b-2	microRNA 181b-2	ncRNA	0.000000	0.385000	80(GAGAACACTCAGTGCT,-,0.00),81(AGAACACTCAGTGCTT,+,0.00)
chunk0008_41_1	chr1	88947499	88947711	+	0	NA	intron (NM_001008661, intron 11 of 13)	MER54A|LTR|ERVL	45355	NM_019610	494115	Hs.481898	NM_019610	ENSG00000213516	RBMXL1	RBM1	RBMX like 1	protein-coding	0.000000	0.497653	
chunk0046_23_1	chr12	54387582	54388092	+	0	NA	intron (NM_001130967, intron 1 of 7)	MIR|SINE|MIR	-2048	NM_001290002	25946	Hs.505653	NM_015481	ENSG00000161642	ZNF385A	HZF|RZF|ZFP385|ZNF385	zinc finger protein 385A	protein-coding	0.001961	0.461840	
chunk0073_286_1	chr16	13496877	13497487	+	0	NA	Intergenic	L1MA7|LINE|L1	-422975	NM_005236	2072	Hs.567265	NM_005236	ENSG00000175595	ERCC4	ERCC11|FANCQ|RAD1|XFEPS|XPF	ERCC excision repair 4, endonuclease catalytic subunit	protein-coding	0.008197	0.332242	212(AGGAACATCTTGTCCT,-,0.00),213(GGAACATCTTGTCCTG,+,0.00)
chunk0193_263_1	chr8	76992182	76992507	+	0	NA	intron (NM_000318, intron 1 of 3)	intron (NM_000318, intron 1 of 3)	7944	NM_000318	5828	Hs.437966	NM_000318	ENSG00000164751	PEX2	PAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3	peroxisomal biogenesis factor 2	protein-coding	0.003077	0.432515	167(TGGTACAGGCAGTCCA,-,0.00),168(GGTACAGGCAGTCCAA,+,0.00)
chunk0134_434_1	chr3	183500833	183501115	+	0	NA	intron (NM_130446, intron 3 of 6)	intron (NM_130446, intron 3 of 6)	-47761	NR_046687	100874019		NR_046687	ENSG00000242522	KLHL6-AS1	-	KLHL6 antisense RNA 1	ncRNA	0.021277	0.487633	192(TGGTACAGTGAGTTCC,-,0.00),193(GGTACAGTGAGTTCCG,+,0.00)
chunk0158_242_1	chr5	129662149	129662374	+	0	NA	intron (NM_133638, intron 15 of 22)	intron (NM_133638, intron 15 of 22)	-85930	NM_001257308	100127206	Hs.582534	NM_001257308	ENSG00000186367	MINAR2	KIAA1024L	membrane integral NOTCH2 associated receptor 2	protein-coding	0.013333	0.358407	
chunk0068_311_1	chr15	57263621	57263845	+	0	NA	intron (NM_003205, intron 17 of 19)	Tigger3b|DNA|TcMar-Tigger	-36632	NR_024433	283663	Hs.181297	NR_024433	ENSG00000247982	LINC00926	-	long intergenic non-protein coding RNA 926	ncRNA	0.000000	0.355556	
chunk0177_165_1	chr7	23236001	23236200	+	0	NA	Intergenic	Intergenic	-10597	NM_001005340	10457	Hs.190495	NM_002510	ENSG00000136235	GPNMB	HGFIN|NMB|PLCA3	glycoprotein nmb	protein-coding	0.025126	0.535000	
chunk0208_160_1	chrX	16267201	16267822	+	0	NA	Intergenic	Intergenic	100030	NM_001277307	645864	Hs.632792	NM_001277307	ENSG00000182798	MAGEB17	-	MAGE family member B17	protein-coding	0.009662	0.356913	194(AAGAACATGATGCTCC,-,0.00),195(AGAACATGATGCTCCT,+,0.00)
chunk0187_115_1	chr7	148578813	148579276	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	-11521	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.017279	0.523707	
chunk0045_377_1	chr12	52147459	52147772	+	0	NA	Intergenic	Intergenic	44385	NM_182507	144501	Hs.140978	NM_182507	ENSG00000167767	KRT80	KB20	keratin 80	protein-coding	0.038339	0.627389	
chunk0045_366_1	chr12	52043368	52044146	+	0	NA	intron (NM_001202233, intron 2 of 7)	intron (NM_001202233, intron 2 of 7)	6042	NM_001202234	3164	Hs.524430	NM_002135	ENSG00000123358	NR4A1	GFRP1|HMR|N10|NAK-1|NGFIB|NP10|NUR77|TR3	nuclear receptor subfamily 4 group A member 1	protein-coding	0.024422	0.587933	
chunk0080_85_1	chr17	25788560	25788759	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	1505337	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.015075	0.415000	
chunk0012_361_1	chr1	162873537	162874556	+	0	NA	Intergenic	Intergenic	-5231	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.007851	0.385294	
chunk0093_305_1	chr19	53443947	53444169	+	0	NA	promoter-TSS (NM_001289952)	promoter-TSS (NM_001289952)	-943	NM_001289952	388561	Hs.433293	NM_001008401	ENSG00000160336	ZNF761	ZNF468	zinc finger protein 761	protein-coding	0.000000	0.488789	103(AGGGACACAATGCACT,-,0.00),104(GGGACACAATGCACTG,+,0.00)
chunk0088_104_1	chr18	45084235	45084543	+	0	NA	Intergenic	Intergenic	-114223	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.038961	0.527508	100(GTGACAGGATGTTCTG,+,0.00),249(GAGAACATTGTGTCTT,-,0.00),250(AGAACATTGTGTCTTT,+,0.00)
chunk0072_353_1	chr15	99669029	99669716	+	0	NA	intron (NM_005587, intron 4 of 10)	intron (NM_005587, intron 4 of 10)	36394	NM_001130928	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.001456	0.344477	
chunk0031_272_1	chr10	127989477	127990078	+	0	NA	intron (NM_001316677, intron 1 of 20)	intron (NM_001316677, intron 1 of 20)	2497	NM_001316677	5791	Hs.127022	NM_006504	ENSG00000132334	PTPRE	HPTPE|PTPE|R-PTP-EPSILON	protein tyrosine phosphatase receptor type E	protein-coding	0.013311	0.405316	
chunk0097_226_1	chr2	52414822	52415021	+	0	NA	Intergenic	Intergenic	287694	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.010050	0.400000	
chunk0130_445_1	chr3	141285662	141285894	+	0	NA	intron (NM_001037172, intron 4 of 5)	intron (NM_001037172, intron 4 of 5)	-38435	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.004310	0.407725	
chunk0129_108_1	chr3	119703502	119704126	+	0	NA	intron (NM_033364, intron 1 of 17)	L2c|LINE|L2	792	NM_033364	89876	Hs.341906	NM_033364	ENSG00000183833	MAATS1	AAT1|AAT1alpha|C3orf15|CFAP91|CaM-IP2|SPATA26	MYCBP associated and testis expressed 1	protein-coding	0.016026	0.411200	
chunk0158_320_1	chr5	132808322	132808808	+	0	NA	Intergenic	MIRc|SINE|MIR	-4759	NM_175873	134548	Hs.13308	NM_175873	ENSG00000198944	SOWAHA	ANKRD43	sosondowah ankyrin repeat domain family member A	protein-coding	0.004115	0.375770	
chunk0081_297_1	chr17	45146880	45147092	+	0	NA	promoter-TSS (NM_006460)	promoter-TSS (NM_006460)	-331	NM_006460	10614	Hs.586945	NM_006460	ENSG00000186834	HEXIM1	CLP1|EDG1|HIS1|MAQ1	HEXIM P-TEFb complex subunit 1	protein-coding	0.023585	0.478873	
chunk0016_212_1	chr1	198973893	198974346	+	0	NA	Intergenic	Tigger6a|DNA|TcMar-Tigger	-36690	NR_040073	100131234	Hs.711077	NR_040073		MIR181A1HG	-	MIR181A1 host gene	ncRNA	0.006623	0.290749	192(GAGATCACTTTGTACT,-,0.00),253(AAGGACTGCTTGTACT,-,0.00),254(AGGACTGCTTGTACTA,+,0.00)
chunk0118_85_1	chr22	29030113	29030663	+	0	NA	intron (NR_046851, intron 2 of 2)	intron (NR_046851, intron 2 of 2)	1088	NR_046851	100874123	Hs.674708	NR_046851	ENSG00000177993	ZNRF3-AS1	-	ZNRF3 antisense RNA 1	ncRNA	0.045455	0.480944	
chunk0007_55_1	chr1	77934562	77935448	+	0	NA	intron (NM_001172309, intron 9 of 11)	MIR1_Amn|SINE|MIR	44200	NM_001303433	8880	Hs.567380	NM_003902	ENSG00000162613	FUBP1	FBP|FUBP|hDH V	far upstream element binding protein 1	protein-coding	0.009029	0.472379	
chunk0034_120_1	chr11	28197922	28198570	+	0	NA	intron (NM_001113528, intron 3 of 6)	intron (NM_001113528, intron 3 of 6)	89995	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.004630	0.292758	
chunk0042_323_1	chr12	9339580	9339779	+	0	NA	Intergenic	Intergenic	-27785	NR_120479	101930452	Hs.734183	NR_120479	ENSG00000260423	LINC02367	-	long intergenic non-protein coding RNA 2367	ncRNA	0.000000	0.395000	
chunk0110_104_1	chr20	11906993	11907447	+	0	NA	intron (NM_001282550, intron 1 of 4)	intron (NM_001282550, intron 1 of 4)	-10645	NM_001282551	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.002203	0.378022	
chunk0197_16_1	chr8	117231934	117232427	+	0	NA	Intergenic	Intergenic	97082	NM_001172814	169026	Hs.532270	NM_173851	ENSG00000164756	SLC30A8	ZNT8|ZnT-8	solute carrier family 30 member 8	protein-coding	0.006085	0.419028	
chunk0098_393_1	chr2	79684369	79684890	+	0	NA	intron (NM_004389, intron 2 of 17)	intron (NM_004389, intron 2 of 17)	-35270	NR_036231	100422888		NR_036231	ENSG00000266436	MIR4264	-	microRNA 4264	ncRNA	0.005758	0.327586	
chunk0059_192_1	chr14	33218698	33219021	+	0	NA	intron (NM_173159, intron 3 of 11)	intron (NM_173159, intron 3 of 11)	279606	NM_001164749	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.000000	0.317901	
chunk0101_407_1	chr2	139066139	139066514	+	0	NA	Intergenic	Intergenic	169002	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.008000	0.348404	
chunk0151_254_1	chr5	51860444	51861031	+	0	NA	Intergenic	Intergenic	-477405	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.003407	0.331633	
chunk0091_432_1	chr19	17014272	17014585	+	0	NA	intron (NM_015692, intron 3 of 41)	intron (NM_015692, intron 3 of 41)	12387	NM_015692	27151	Hs.631644	NM_015692	ENSG00000160111	CPAMD8	ASGD8|K-CAP|VIP	C3 and PZP like alpha-2-macroglobulin domain containing 8	protein-coding	0.019169	0.461783	
chunk0104_343_1	chr2	179801164	179801738	+	0	NA	intron (NM_152520, intron 1 of 9)	intron (NM_152520, intron 1 of 9)	-55409	NM_001113397	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.003484	0.398261	
chunk0155_80_1	chr5	91883394	91883593	+	0	NA	Intergenic	Intergenic	-500161	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.330000	
chunk0160_353_1	chr5	160310457	160310656	+	0	NA	intron (NR_131769, intron 2 of 7)	intron (NR_131769, intron 2 of 7)	2044	NM_001308173	79616	Hs.14070	NM_024565	ENSG00000135083	CCNJL	-	cyclin J like	protein-coding	0.010050	0.485000	
chunk0151_409_1	chr5	55619960	55620497	+	0	NA	Intergenic	L2b|LINE|L2	72825	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.003724	0.418216	
chunk0073_30_1	chr16	2514041	2514256	+	0	NA	exon (NM_001694, exon 1 of 3)	exon (NM_001694, exon 1 of 3)	278	NM_001694	527	Hs.389107	NM_001694	ENSG00000185883	ATP6V0C	ATP6C|ATP6L|ATPL|VATL|VPPC|Vma3	ATPase H+ transporting V0 subunit c	protein-coding	0.144186	0.745370	
chunk0004_86_1	chr1	43751581	43751780	+	0	NA	intron (NM_001270465, intron 2 of 7)	intron (NM_001270465, intron 2 of 7)	-24337	NR_125986	101929592		NR_125986	ENSG00000229444	LOC101929592	-	uncharacterized LOC101929592	ncRNA	0.010050	0.385000	
chunk0116_229_1	chr21	38159065	38159429	+	0	NA	Intergenic	MIRb|SINE|MIR	37796	NR_026841	84677	Hs.733345	NM_032589	ENSG00000198054	DSCR8	C21orf65|CT25.1a|CT25.1b|MMA-1|MMA-1a|MMA-1b|MMA1|MTAG2	Down syndrome critical region 8	ncRNA	0.005495	0.487671	
chunk0008_33_1	chr1	88683809	88684244	+	0	NA	promoter-TSS (NM_006256)	promoter-TSS (NM_006256)	-213	NM_006256	5586	Hs.440833	NM_006256	ENSG00000065243	PKN2	PAK2|PRK2|PRKCL2|PRO2042|Pak-2|STK7	protein kinase N2	protein-coding	0.078161	0.584862	
chunk0177_71_1	chr7	21367159	21367437	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-60773	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.010791	0.365591	
chunk0157_105_1	chr5	116792726	116792925	+	0	NA	Intergenic	Intergenic	-30616	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.010050	0.360000	
chunk0088_348_1	chr18	51972912	51973283	+	0	NA	Intergenic	L1MCb|LINE|L1	-367075	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.005391	0.381720	
chunk0114_98_1	chr21	9330049	9330452	+	0	NA	Intergenic	Intergenic	-200489	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.019851	0.455446	
chunk0087_236_1	chr18	36487666	36487977	+	0	NA	intron (NM_001281739, intron 3 of 23)	intron (NM_001281739, intron 3 of 23)	175597	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.006431	0.432692	
chunk0187_76_1	chr8	2769763	2770349	+	0	NA	Intergenic	Intergenic	-41605	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.008532	0.432709	
chunk0058_114_1	chr14	22213149	22213494	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	375916	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.008696	0.369942	
chunk0180_326_1	chr7	72632779	72632991	+	0	NA	intron (NM_001145440, intron 11 of 13)	MIR|SINE|MIR	-65018	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.000000	0.446009	
chunk0079_355_1	chr17	17840181	17840614	+	0	NA	Intergenic	CpG	-3386	NM_001005291	6720	Hs.592123	NM_004176	ENSG00000072310	SREBF1	SREBP1|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.096998	0.714286	143(GGGGACAGGCTGGGCT,-,0.00),144(GGGACAGGCTGGGCTC,+,0.00)
chunk0134_314_1	chr3	181329089	181329390	+	0	NA	intron (NR_075092, intron 3 of 6)	intron (NR_075092, intron 3 of 6)	97502	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.006645	0.344371	
chunk0159_47_1	chr5	137209511	137210209	+	0	NA	intron (NM_004598, intron 3 of 10)	intron (NM_004598, intron 3 of 10)	289469	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.007163	0.380544	
chunk0194_412_1	chr8	91534411	91534628	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	285231	NM_134266	115111	Hs.354013	NM_052832	ENSG00000147606	SLC26A7	SUT2	solute carrier family 26 member 7	protein-coding	0.009217	0.334862	
chunk0039_413_1	chr11	107514670	107515080	+	0	NA	intron (NM_138775, intron 10 of 11)	intron (NM_138775, intron 10 of 11)	50860	NM_138775	91801	Hs.503763	NM_138775	ENSG00000137760	ALKBH8	ABH8|TRM9|TRMT9|TRMT9A	alkB homolog 8, tRNA methyltransferase	protein-coding	0.007317	0.394161	
chunk0017_4_1	chr1	204319630	204319833	+	0	NA	intron (NM_014935, intron 1 of 22)	L2c|LINE|L2	40198	NM_014935	22874	Hs.253146	NM_014935	ENSG00000143850	PLEKHA6	PEPP-3|PEPP3	pleckstrin homology domain containing A6	protein-coding	0.009852	0.475490	55(CAGCACTCTGAGTTCC,-,0.00),56(AGCACTCTGAGTTCCT,+,0.00)
chunk0065_313_1	chr14	103033729	103034260	+	0	NA	intron (NM_006035, intron 1 of 36)	intron (NM_006035, intron 1 of 36)	23411	NM_006035	9578	Hs.654634	NM_006035	ENSG00000198752	CDC42BPB	MRCKB	CDC42 binding protein kinase beta	protein-coding	0.016949	0.413534	
chunk0120_280_1	chr3	9433359	9433966	+	0	NA	intron (NM_001292043, intron 4 of 24)	intron (NM_001292043, intron 4 of 24)	35962	NM_001080517	55209	Hs.288164	NM_018187	ENSG00000168137	SETD5	-	SET domain containing 5	protein-coding	0.009885	0.445724	
chunk0203_266_1	chr9	87991295	87991954	+	0	NA	Intergenic	L1MC1|LINE|L1	-16844	NM_001039803	23552	Hs.522274	NM_012119	ENSG00000156345	CDK20	CCRK|CDCH|P42|PNQALRE	cyclin dependent kinase 20	protein-coding	0.003035	0.356061	234(AAGAACATCTTGATCT,-,0.00),235(AGAACATCTTGATCTA,+,0.00)
chunk0210_105_1	chrX	72046209	72046803	+	0	NA	intron (NM_001013627, intron 1 of 7)	MIR|SINE|MIR	2097	NR_002309	441502	Hs.449523	NR_002309		RPS26P11	RPS26L1|RPS26_22_1784|bA366E13.1	ribosomal protein S26 pseudogene 11	pseudo	0.008418	0.458824	
chunk0081_422_1	chr17	48779360	48780008	+	0	NA	intron (NM_001130918, intron 13 of 15)	L1ME2z|LINE|L1	14640	NM_173623	284076	Hs.91930	NM_173623	ENSG00000170703	TTLL6	TTL.6	tubulin tyrosine ligase like 6	protein-coding	0.007716	0.348228	
chunk0036_18_1	chr11	58337476	58338215	+	0	NA	Intergenic	L1MC|LINE|L1	21224	NM_001005489	219965		NM_001005489	ENSG00000197786	OR5B17	OR11-237|OR5B20P	olfactory receptor family 5 subfamily B member 17	protein-coding	0.002706	0.336486	
chunk0203_277_1	chr9	88697906	88698509	+	0	NA	Intergenic	Intergenic	-46047	NM_001100111									0.009950	0.473510	
chunk0057_48_1	chr13	96727903	96728410	+	0	NA	intron (NM_153456, intron 1 of 1)	intron (NM_153456, intron 1 of 1)	256016	NR_051966	100887754	Hs.617003	NR_051966		LINC00359	-	long intergenic non-protein coding RNA 359	ncRNA	0.001972	0.332677	
chunk0122_389_1	chr3	37863231	37863578	+	0	NA	intron (NM_001008392, intron 1 of 7)	intron (NM_001008392, intron 1 of 7)	1226	NM_005808	10217	Hs.475963	NM_005808	ENSG00000144677	CTDSPL	C3orf8|HYA22|PSR1|RBSP3|SCP3	CTD small phosphatase like	protein-coding	0.008646	0.531609	188(TGGAACTTTCTGTGCC,-,0.00),189(GGAACTTTCTGTGCCT,+,0.00),220(TTGGACAGACTGTTTT,-,0.00),221(TGGACAGACTGTTTTG,+,0.00)
chunk0021_307_1	chr1	244860155	244860472	+	0	NA	intron (NM_031844, intron 4 of 13)	AluSx|SINE|Alu	4212	NM_004501	3192	Hs.106212	NM_004501	ENSG00000153187	HNRNPU	EIEE54|GRIP120|HNRNPU-AS1|HNRPU|SAF-A|SAFA|U21.1|hnRNP U|pp120	heterogeneous nuclear ribonucleoprotein U	protein-coding	0.022082	0.455975	
chunk0068_368_1	chr15	58056460	58056659	+	0	NA	intron (NM_003888, intron 1 of 12)	intron (NM_003888, intron 1 of 12)	9364	NM_001206897	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.000000	0.315000	
chunk0110_348_1	chr20	19524367	19525201	+	0	NA	intron (NM_020689, intron 3 of 16)	intron (NM_020689, intron 3 of 16)	-240188	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.004796	0.384431	
chunk0024_443_1	chr10	46552933	46553254	+	0	NA	intron (NM_014696, intron 2 of 2)	MIRb|SINE|MIR	2978	NM_014696	9721	Hs.523375	NM_014696	ENSG00000204175	GPRIN2	GRIN2|KIAA0514	G protein regulated inducer of neurite outgrowth 2	protein-coding	0.018692	0.524845	
chunk0116_144_1	chr21	36402379	36402854	+	0	NA	intron (NM_005441, intron 7 of 13)	intron (NM_005441, intron 7 of 13)	17225	NM_005441	8208	Hs.75238	NM_005441	ENSG00000159259	CHAF1B	CAF-1|CAF-IP60|CAF1|CAF1A|CAF1P60|MPHOSPH7|MPP7	chromatin assembly factor 1 subunit B	protein-coding	0.018947	0.361345	
chunk0095_391_1	chr2	23934446	23934676	+	0	NA	Intergenic	Intergenic	-5945	NM_181713	165324	Hs.591576	NM_181713	ENSG00000173960	UBXN2A	UBXD4	UBX domain protein 2A	protein-coding	0.004348	0.415584	
chunk0175_86_1	chr7	2456616	2457207	+	0	NA	Intergenic	L1M4a2|LINE|L1	19148	NR_108066									0.003384	0.320946	
chunk0099_35_1	chr2	83680573	83681165	+	0	NA	Intergenic	Intergenic	-609813	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.006757	0.340641	
chunk0192_176_1	chr8	62836632	62837253	+	0	NA	intron (NR_130764, intron 4 of 6)	intron (NR_130764, intron 4 of 6)	-140919	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.001610	0.371383	
chunk0185_81_1	chr7	125357884	125359082	+	0	NA	intron (NR_110188, intron 7 of 8)	intron (NR_110188, intron 7 of 8)	-94192	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.003339	0.331943	
chunk0100_271_1	chr2	113738156	113738855	+	0	NA	intron (NM_025181, intron 7 of 15)	L1MA9|LINE|L1	-17137	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.005722	0.335714	
chunk0113_214_1	chr20	53827904	53828992	+	0	NA	Intergenic	Intergenic	47261	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.011029	0.385675	
chunk0123_164_1	chr3	43588749	43588960	+	0	NA	intron (NM_001204833, intron 2 of 10)	L1M7|LINE|L1	33214	NM_001204833	55129	Hs.656657	NM_018075	ENSG00000160746	ANO10	SCAR10|TMEM16K	anoctamin 10	protein-coding	0.004739	0.301887	
chunk0013_19_1	chr1	165887823	165888369	+	0	NA	intron (NM_012474, intron 1 of 6)	intron (NM_012474, intron 1 of 6)	-19825	NR_037431	100500832		NR_037431	ENSG00000283936	MIR3658	-	microRNA 3658	ncRNA	0.010989	0.343693	
chunk0059_14_1	chr14	29791889	29792384	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	135557	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.004040	0.292339	
chunk0035_61_1	chr11	41521997	41522662	+	0	NA	Intergenic	Intergenic	-62693	NM_001258419	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.003008	0.343844	
chunk0103_54_1	chr2	159595518	159596094	+	0	NA	intron (NM_001289975, intron 1 of 35)	MER57B1|LTR|ERV1	-19488	NR_110588	643072	Hs.632541	NR_110587		LOC643072	-	uncharacterized LOC643072	ncRNA	0.008681	0.379549	
chunk0031_414_1	chr10	132163266	132163793	+	0	NA	intron (NM_001105521, intron 19 of 23)	intron (NM_001105521, intron 19 of 23)	-23381	NM_006426	10570	Hs.100058	NM_006426	ENSG00000151640	DPYSL4	CRMP3|DRP-4|ULIP4	dihydropyrimidinase like 4	protein-coding	0.034156	0.655303	
chunk0143_37_1	chr4	107126686	107127231	+	0	NA	Intergenic	L2c|LINE|L2	-90662	NM_014421	27123	Hs.211869	NM_014421	ENSG00000155011	DKK2	DKK-2	dickkopf WNT signaling pathway inhibitor 2	protein-coding	0.011009	0.401099	
chunk0176_198_1	chr7	14095213	14095691	+	0	NA	Intergenic	L2|LINE|L2	-104027	NM_001163148	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.010460	0.371608	
chunk0170_394_1	chr6	117414968	117415426	+	0	NA	intron (NM_002944, intron 3 of 42)	intron (NM_002944, intron 3 of 42)	10658	NM_002944	6098	Hs.1041	NM_002944	ENSG00000047936	ROS1	MCF3|ROS|c-ros-1	ROS proto-oncogene 1, receptor tyrosine kinase	protein-coding	0.000000	0.350763	236(TAGCACATGCTGTACC,-,0.00),237(AGCACATGCTGTACCT,+,0.00)
chunk0078_180_1	chr17	4677309	4677831	+	0	NA	intron (NM_014389, intron 5 of 16)	Charlie4a|DNA|hAT-Charlie	-26660	NR_103482	101559451	Hs.634966	NR_103482	ENSG00000244184	LOC101559451	-	uncharacterized LOC101559451	ncRNA	0.009579	0.428298	
chunk0053_425_1	chr13	37627381	37628002	+	0	NA	Intergenic	L1MD2|LINE|L1	-28847	NM_001135935	10631	Hs.136348	NM_006475	ENSG00000133110	POSTN	OSF-2|OSF2|PDLPOSTN|PN	periostin	protein-coding	0.006441	0.342444	
chunk0028_94_1	chr10	84107873	84108354	+	0	NA	Intergenic	Intergenic	-31316	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.004158	0.431535	
chunk0015_370_1	chr1	190466158	190466476	+	0	NA	intron (NM_199051, intron 1 of 7)	intron (NM_199051, intron 1 of 7)	11312	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.326019	
chunk0184_322_1	chr7	120414778	120414977	+	0	NA	intron (NM_012281, intron 1 of 5)	L2b|LINE|L2	141209	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.000000	0.385000	
chunk0092_446_1	chr19	38837720	38838360	+	0	NA	intron (NM_001005335, intron 10 of 12)	intron (NM_001005335, intron 10 of 12)	-6183	NM_001398	1891	Hs.196176	NM_001398	ENSG00000104823	ECH1	HPXEL	enoyl-CoA hydratase 1	protein-coding	0.017188	0.503900	
chunk0175_307_1	chr6	166615093	166615531	+	0	NA	intron (NM_001006932, intron 2 of 21)	intron (NM_001006932, intron 2 of 21)	11926	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.018265	0.469248	192(AAGAACATCGTGTCTC,-,0.00),193(AGAACATCGTGTCTCA,+,0.00)
chunk0124_407_1	chr3	60363626	60363825	+	0	NA	intron (NM_001166243, intron 5 of 9)	LTR33|LTR|ERVL	254145	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.010050	0.560000	
chunk0158_29_1	chr5	125497882	125498503	+	0	NA	intron (NR_109887, intron 1 of 3)	intron (NR_109887, intron 1 of 3)	4931	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.000000	0.300643	
chunk0209_175_1	chrX	43655834	43656143	+	0	NA	5' UTR (NM_001270458, exon 1 of 16)	5' UTR (NM_001270458, exon 1 of 16)	1081	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.035599	0.580645	
chunk0068_431_1	chr15	59549663	59549919	+	0	NA	Intergenic	MER4B|LTR|ERV1	-61992	NM_004751	9245	Hs.194710	NM_004751	ENSG00000140297	GCNT3	C2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding	0.011719	0.389105	
chunk0086_255_1	chr18	23401412	23401992	+	0	NA	intron (NM_032933, intron 3 of 14)	intron (NM_032933, intron 3 of 14)	36259	NM_032933	85019	Hs.137562	NM_032933	ENSG00000134490	TMEM241	C18orf45|hVVT	transmembrane protein 241	protein-coding	0.010345	0.483649	
chunk0128_31_1	chr3	104300049	104300848	+	0	NA	Intergenic	L1MA2|LINE|L1	-776332	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.000000	0.343750	
chunk0124_173_1	chr3	55355170	55355375	+	0	NA	Intergenic	L1MB3|LINE|L1	126126	NM_001256105	7474	Hs.643085	NM_003392	ENSG00000114251	WNT5A	hWNT5A	Wnt family member 5A	protein-coding	0.019512	0.359223	
chunk0119_201_1	chr22	44754930	44755495	+	0	NA	intron (NM_181335, intron 1 of 11)	MIR|SINE|MIR	2654	NM_001017526	23779	Hs.102336	NM_181335	ENSG00000241484	ARHGAP8	BPGAP1|PP610	Rho GTPase activating protein 8	protein-coding	0.015929	0.519435	
chunk0145_190_1	chr4	147822281	147822586	+	0	NA	intron (NM_024605, intron 1 of 22)	intron (NM_024605, intron 1 of 22)	39838	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.006557	0.477124	
chunk0152_255_1	chr5	60848697	60849291	+	0	NA	Intergenic	Intergenic	-4720	NM_024930	79993	Hs.274256	NM_024930	ENSG00000164181	ELOVL7	-	ELOVL fatty acid elongase 7	protein-coding	0.000000	0.270588	
chunk0121_343_1	chr3	24592250	24593239	+	0	NA	Intergenic	MIRb|SINE|MIR	-71309	NR_039955									0.006067	0.391919	
chunk0049_46_1	chr12	89879220	89879544	+	0	NA	Intergenic	Intergenic	170427	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.003086	0.347692	
chunk0074_369_1	chr16	34586742	34587541	+	0	NA	Intergenic	Intergenic	-427105	NR_038368									0.046308	0.363750	
chunk0066_357_1	chr15	38251685	38252094	+	0	NA	promoter-TSS (NM_152594)	promoter-TSS (NM_152594)	-962	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.056235	0.563415	
chunk0207_40_1	chrX	5986618	5986817	+	0	NA	intron (NM_181332, intron 3 of 5)	L1ME3B|LINE|L1	240486	NM_001282146	57502	Hs.21107	NM_020742	ENSG00000146938	NLGN4X	ASPGX2|AUTSX2|HLNX|HNL4X|NLGN4	neuroligin 4 X-linked	protein-coding	0.010050	0.370000	
chunk0163_298_1	chr6	14261451	14261692	+	0	NA	Intergenic	L1MEg|LINE|L1	23883	NR_108097	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.004149	0.318182	
chunk0062_394_1	chr14	74804395	74804822	+	0	NA	intron (NM_019589, intron 6 of 20)	L2c|LINE|L2	41242	NM_019589	56252	Hs.531111	NM_019589	ENSG00000119596	YLPM1	C14orf170|PPP1R169|ZAP113|ZAP3	YLP motif containing 1	protein-coding	0.004684	0.380841	
chunk0084_319_1	chr17	80668498	80668924	+	0	NA	intron (NM_020761, intron 3 of 33)	intron (NM_020761, intron 3 of 33)	123886	NM_001163034	57521	Hs.133044	NM_020761	ENSG00000141564	RPTOR	KOG1|Mip1	regulatory associated protein of MTOR complex 1	protein-coding	0.023474	0.475410	
chunk0211_202_1	chrX	118022584	118023277	+	0	NA	intron (NM_001168303, intron 1 of 6)	L1MA9|LINE|L1	-37517	NM_001168299	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.002886	0.327089	
chunk0032_335_1	chr11	10242750	10243225	+	0	NA	intron (NM_030962, intron 1 of 39)	L1MA10|LINE|L1	51220	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.000000	0.302521	273(GAACACACAGTGTCCT,-,0.00),274(AACACACAGTGTCCTC,+,0.00)
chunk0021_86_1	chr10	1782656	1783246	+	0	NA	Intergenic	Intergenic	-45475	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.010169	0.407783	279(GGGAACATTATGTCAC,-,0.00)
chunk0006_208_1	chr1	67814172	67814639	+	0	NA	intron (NM_018841, intron 1 of 3)	intron (NM_018841, intron 1 of 3)	-17883	NR_040077	100289178	Hs.677603	NR_040077	ENSG00000232284	GNG12-AS1	-	GNG12, DIRAS3 and WLS antisense RNA 1	ncRNA	0.002141	0.373932	438(CTGGACTTTCTGTCCT,-,0.00),439(TGGACTTTCTGTCCTC,+,0.00)
chunk0178_378_1	chr7	40239580	40240257	+	0	NA	intron (NM_001193312, intron 7 of 12)	intron (NM_001193312, intron 7 of 12)	104942	NM_024728	79783	Hs.586313	NM_024728	ENSG00000175600	SUGCT	C7orf10|DERP13|GA3|ORF19	succinyl-CoA:glutarate-CoA transferase	protein-coding	0.005908	0.383481	
chunk0031_164_1	chr10	125314804	125315049	+	0	NA	Intergenic	Intergenic	-153871	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.012245	0.378049	
chunk0162_225_1	chr6	4499831	4500126	+	0	NA	Intergenic	Intergenic	71976	NR_106988									0.000000	0.361486	
chunk0182_327_1	chr7	99079243	99079442	+	0	NA	intron (NM_020429, intron 1 of 18)	intron (NM_020429, intron 1 of 18)	64778	NM_020429	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.025126	0.575000	
chunk0197_33_1	chr8	118087426	118088302	+	0	NA	intron (NM_000127, intron 1 of 10)	intron (NM_000127, intron 1 of 10)	23955	NM_000127	2131	Hs.492618	NM_000127	ENSG00000182197	EXT1	EXT|LGCR|LGS|TRPS2|TTV	exostosin glycosyltransferase 1	protein-coding	0.006849	0.343216	
chunk0129_8_1	chr3	116344772	116345249	+	0	NA	intron (NM_002338, intron 1 of 6)	intron (NM_002338, intron 1 of 6)	-15014	NR_109998	101926903	Hs.26479	NR_109998	ENSG00000240922	LSAMP-AS1	-	LSAMP antisense RNA 1	ncRNA	0.002096	0.338912	
chunk0141_293_1	chr4	86849157	86849628	+	0	NA	promoter-TSS (NM_197965)	promoter-TSS (NM_197965)	-129	NM_197965	345274	Hs.452996	NM_197965	ENSG00000145283	SLC10A6	SOAT	solute carrier family 10 member 6	protein-coding	0.012739	0.406780	283(ATCACATTGTGTCCCT,+,0.00)
chunk0006_329_1	chr1	71875489	71875688	+	0	NA	intron (NM_173808, intron 2 of 6)	MER91A|DNA|hAT-Tip100	-38576	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005025	0.415000	
chunk0123_414_1	chr3	49402064	49402299	+	0	NA	intron (NM_001313946, intron 1 of 2)	intron (NM_001313946, intron 1 of 2)	9916	NM_001313941	387	Hs.247077	NM_001664	ENSG00000067560	RHOA	ARH12|ARHA|RHO12|RHOH12	ras homolog family member A	protein-coding	0.008511	0.355932	
chunk0014_243_1	chr1	179978119	179978982	+	0	NA	intron (NM_014810, intron 1 of 37)	L1MA5A|LINE|L1	23777	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.005794	0.355324	502(GAGAACATGCTGTGTT,-,0.00),503(AGAACATGCTGTGTTT,+,0.00)
chunk0040_255_1	chr11	115920963	115921662	+	0	NA	Intergenic	Intergenic	-161112	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.011445	0.474286	
chunk0162_183_1	chr6	3762041	3763139	+	0	NA	Intergenic	AluSx1|SINE|Alu	-10578	NM_183373	221749	Hs.484500	NM_183373	ENSG00000168994	PXDC1	C6orf145	PX domain containing 1	protein-coding	0.030055	0.486806	
chunk0049_11_1	chr12	89301312	89301803	+	0	NA	Intergenic	L1ME3B|LINE|L1	51302	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.008147	0.298780	
chunk0103_120_1	chr2	161741457	161741665	+	0	NA	intron (NM_001178016, intron 2 of 26)	L1MA3|LINE|L1	117226	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.000000	0.406699	
chunk0189_256_1	chr8	25201498	25201994	+	0	NA	intron (NM_024940, intron 1 of 51)	intron (NM_024940, intron 1 of 51)	16974	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.012097	0.448692	
chunk0070_225_1	chr15	72814550	72814935	+	0	NA	Intergenic	L1ME5|LINE|L1	-30957	NR_023319									0.002597	0.373057	
chunk0012_131_1	chr1	157169186	157169621	+	0	NA	Intergenic	L1MC3|LINE|L1	-30812	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.011494	0.401376	324(GACACAAAGTGTGCTT,+,0.00)
chunk0025_119_1	chr10	51547986	51548261	+	0	NA	intron (NM_006258, intron 3 of 17)	intron (NM_006258, intron 3 of 17)	151472	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.007273	0.420290	101(AAGAACAAATTGTTCT,-,0.00),102(AGAACAAATTGTTCTC,+,0.00),138(AAAGACACAGTGTTCC,-,0.00),139(AAGACACAGTGTTCCA,+,0.00)
chunk0033_343_1	chr11	22916313	22916722	+	0	NA	Intergenic	Intergenic	-56091	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.007335	0.358537	154(TGGAACATATTGTTCA,-,0.00),155(GGAACATATTGTTCAT,+,0.00)
chunk0208_330_1	chrX	24643224	24643466	+	0	NA	intron (NM_001163264, intron 1 of 7)	intron (NM_001163264, intron 1 of 7)	3993	NM_001163265	9468	Hs.660708	NM_004845	ENSG00000102230	PCYT1B	CCTB|CTB	phosphate cytidylyltransferase 1, choline, beta	protein-coding	0.000000	0.399177	
chunk0070_183_1	chr15	71752911	71753316	+	0	NA	intron (NM_001286429, intron 8 of 11)	intron (NM_001286429, intron 8 of 11)	-57435	NM_014249	10002	Hs.187354	NM_014249	ENSG00000278570	NR2E3	ESCS|PNR|RNR|RP37|rd7	nuclear receptor subfamily 2 group E member 3	protein-coding	0.014815	0.369458	156(GAGTACAGAGTGTGTC,-,0.00),157(AGTACAGAGTGTGTCT,+,0.00)
chunk0045_136_1	chr12	46445328	46446042	+	0	NA	intron (NR_125381, intron 2 of 2)	intron (NR_125381, intron 2 of 2)	61578	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.007003	0.365035	355(TAGAACATTTTGTACT,-,0.00),356(AGAACATTTTGTACTT,+,0.00)
chunk0185_373_1	chr7	132944636	132945221	+	0	NA	intron (NM_017812, intron 4 of 7)	intron (NM_017812, intron 4 of 7)	89987	NR_037427	100500804		NR_037427	ENSG00000284135	MIR3654	-	microRNA 3654	ncRNA	0.006838	0.308874	
chunk0133_86_1	chr3	167534650	167535135	+	0	NA	intron (NM_178824, intron 7 of 14)	intron (NM_178824, intron 7 of 14)	-60760	NM_001012303	5276	Hs.445555	NM_006217	ENSG00000114204	SERPINI2	MEPI|PANCPIN|PI14|TSA2004	serpin family I member 2	protein-coding	0.004124	0.327160	
chunk0053_97_1	chr13	28588355	28588616	+	0	NA	Intergenic	L1M5|LINE|L1	-70519	NM_015932	51371	Hs.268742	NM_015932	ENSG00000132963	POMP	C13orf12|HSPC014|PNAS-110|PRAAS2|UMP1	proteasome maturation protein	protein-coding	0.011494	0.316794	
chunk0190_166_1	chr8	31846384	31846977	+	0	NA	intron (NM_013962, intron 1 of 4)	intron (NM_013962, intron 1 of 4)	-179056	NR_104158	100856811	Hs.97362	NR_104156		NRG1-IT1	-	NRG1 intronic transcript 1	ncRNA	0.003373	0.341751	242(TGGAACATAATGTACA,-,0.00),243(GGAACATAATGTACAA,+,0.00)
chunk0190_177_1	chr8	32958299	32958906	+	0	NA	Intergenic	L1PA16|LINE|L1	236769	NM_001159996	3084	Hs.453951	NM_004495	ENSG00000157168	NRG1	ARIA|GGF|GGF2|HGL|HRG|HRG1|HRGA|MST131|MSTP131|NDF|NRG1-IT2|SMDF	neuregulin 1	protein-coding	0.008237	0.393092	151(GAGGACATGCTGTATT,-,0.00),152(AGGACATGCTGTATTT,+,0.00)
chunk0177_335_1	chr7	26422985	26423184	+	0	NA	intron (NR_015364, intron 1 of 4)	MLT1H2|LTR|ERVL-MaLR	19596	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.015075	0.490000	
chunk0073_61_1	chr16	3479649	3479916	+	0	NA	intron (NM_001083600, intron 3 of 6)	intron (NM_001083600, intron 3 of 6)	5687	NR_106741	102465134		NR_106741	ENSG00000273776	MIR6126	hsa-mir-6126	microRNA 6126	ncRNA	0.033708	0.544776	
chunk0114_207_1	chr21	15455387	15456027	+	0	NA	Intergenic	L1PA10|LINE|L1	-274318	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.015625	0.510140	
chunk0007_400_1	chr1	85504184	85504751	+	0	NA	intron (NM_001134445, intron 1 of 6)	MamGypsy2-LTR|LTR|Gypsy	-39261	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.003527	0.397887	
chunk0041_152_1	chr11	125731865	125732064	+	0	NA	Intergenic	Intergenic	-14329	NM_138294	160065	Hs.148565	NM_138294	ENSG00000171053	PATE1	PATE	prostate and testis expressed 1	protein-coding	0.010050	0.495000	131(AAGAAGATGATGTTCT,-,0.00)
chunk0187_290_1	chr7	155756193	155756672	+	0	NA	intron (NM_053043, intron 14 of 17)	Merlin1_HS|DNA|Merlin	52640	NR_132318	6469	Hs.164537	NM_000193	ENSG00000164690	SHH	HHG1|HLP3|HPE3|MCOPCB5|SMMCI|ShhNC|TPT|TPTPS	sonic hedgehog signaling molecule	protein-coding	0.010438	0.329167	
chunk0039_163_1	chr11	99079520	99079750	+	0	NA	intron (NM_001243270, intron 1 of 23)	L2c|LINE|L2	58659	NM_014361	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.008696	0.354978	
chunk0130_74_1	chr3	130243004	130243633	+	0	NA	intron (NR_027898, intron 12 of 22)	L2a|LINE|L2	30498	NR_027898	646300	Hs.170475	NR_027898		COL6A4P2	COL6A4	collagen type VI alpha 4 pseudogene 2	pseudo	0.004769	0.412698	384(AGCACATACTCTTCCT,+,0.00)
chunk0083_66_1	chr17	64074007	64074301	+	0	NA	intron (NM_001433, intron 5 of 21)	intron (NM_001433, intron 5 of 21)	-53520	NM_001099786	3384	Hs.431460	NM_000873	ENSG00000108622	ICAM2	CD102	intercellular adhesion molecule 2	protein-coding	0.010204	0.393220	
chunk0015_269_1	chr1	188397194	188397470	+	0	NA	Intergenic	L1MA5|LINE|L1	953704	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007246	0.487365	
chunk0129_401_1	chr3	126681937	126682161	+	0	NA	Intergenic	Intergenic	19968	NR_034158	255330	Hs.145435	NM_174935	ENSG00000198284	NUP210P1	C3orf46	nucleoporin 210 pseudogene 1	pseudo	0.000000	0.435556	
chunk0149_294_1	chr5	25583003	25583442	+	0	NA	Intergenic	L1PB2|LINE|L1	-742639	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.002278	0.311364	
chunk0155_137_1	chr5	93575260	93576062	+	0	NA	intron (NR_109818, intron 1 of 6)	intron (NR_109818, intron 1 of 6)	-4318	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.006234	0.364882	
chunk0164_379_1	chr6	25928437	25929053	+	0	NA	intron (NM_005835, intron 1 of 10)	intron (NM_005835, intron 1 of 10)	1981	NM_005835	10246	Hs.591802	NM_005835	ENSG00000112337	SLC17A2	NPT3	solute carrier family 17 member 2	protein-coding	0.006494	0.314425	
chunk0176_356_1	chr7	18059333	18059690	+	0	NA	Intergenic	Intergenic	-27438	NM_001204144	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.011204	0.444134	
chunk0090_447_1	chr18	79824064	79824388	+	0	NA	Intergenic	AluJb|SINE|Alu	-39442	NM_012283	26251	Hs.247905	NM_012283	ENSG00000178342	KCNG2	KCNF2|KV6.2	potassium voltage-gated channel modifier subfamily G member 2	protein-coding	0.021605	0.489231	
chunk0207_63_1	chrX	8914688	8915274	+	0	NA	Intergenic	L1ME5|LINE|L1	-113598	NM_174951	171482	Hs.382062	NM_174951	ENSG00000183304	FAM9A	TEX39A	family with sequence similarity 9 member A	protein-coding	0.008532	0.379898	
chunk0063_64_1	chr14	77204396	77204623	+	0	NA	intron (NM_020431, intron 1 of 23)	intron (NM_020431, intron 1 of 23)	22750	NM_020431	57156	Hs.22452	NM_020431	ENSG00000165548	TMEM63C	C14orf171|CSC1|hsCSC1	transmembrane protein 63C	protein-coding	0.008811	0.482456	
chunk0026_332_1	chr10	68335813	68336418	+	0	NA	intron (NM_012207, intron 1 of 9)	intron (NM_012207, intron 1 of 9)	-3188	NM_022129	64081	Hs.198158	NM_022129	ENSG00000108187	PBLD	HEL-S-306|MAWBP|MAWDBP	phenazine biosynthesis like protein domain containing	protein-coding	0.001653	0.389439	
chunk0171_119_1	chr6	122609812	122610134	+	0	NA	promoter-TSS (NM_032471)	promoter-TSS (NM_032471)	-259	NM_032471	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.040373	0.461300	
chunk0128_125_1	chr3	106457270	106457585	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-588384	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.003175	0.446203	
chunk0133_307_1	chr3	172317445	172318077	+	0	NA	intron (NM_022763, intron 11 of 25)	intron (NM_022763, intron 11 of 25)	130695	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.017405	0.420221	
chunk0181_169_1	chr7	82758987	82759350	+	0	NA	intron (NM_033026, intron 24 of 24)	intron (NM_033026, intron 24 of 24)	-315362	NM_001302890	781	Hs.282151	NM_000722	ENSG00000153956	CACNA2D1	CACNA2|CACNL2A|CCHL2A|LINC01112|lncRNA-N3	calcium voltage-gated channel auxiliary subunit alpha2delta 1	protein-coding	0.000000	0.277473	
chunk0201_261_1	chr9	38437193	38437729	+	0	NA	Intergenic	Intergenic	-13014	NM_001007563	347252	Hs.349705	NM_001007563	ENSG00000137142	IGFBPL1	IGFBP-RP4|IGFBPRP4|bA113O24.1	insulin like growth factor binding protein like 1	protein-coding	0.014925	0.499069	
chunk0128_283_1	chr3	110881151	110881398	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	188685	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.012146	0.504032	
chunk0048_144_1	chr12	80189842	80190486	+	0	NA	Intergenic	Intergenic	-19289	NM_173591	283310	Hs.723594	NM_173591	ENSG00000165899	OTOGL	C12orf64|DFNB84B	otogelin like	protein-coding	0.009317	0.390698	367(GGGAACAGGATGTGCT,-,0.00),368(GGAACAGGATGTGCTG,+,0.00)
chunk0206_446_1	chr9	128057477	128057751	+	0	NA	Intergenic	Intergenic	9706	NM_197956	203245	Hs.373606	NM_197956	ENSG00000171169	NAIF1	C9orf90|bA379C10.2	nuclear apoptosis inducing factor 1	protein-coding	0.029197	0.487273	
chunk0071_122_1	chr15	81454234	81454547	+	0	NA	Intergenic	L1PB4|LINE|L1	-80313	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.003195	0.318471	
chunk0003_434_1	chr1	41154440	41155027	+	0	NA	intron (NM_001031694, intron 3 of 15)	intron (NM_001031694, intron 3 of 15)	5200	NM_001172222	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.003407	0.302721	
chunk0109_262_1	chr20	8021544	8021884	+	0	NA	Intergenic	Intergenic	-1885	NM_021156	56255	Hs.169358	NM_021156	ENSG00000125827	TMX4	DJ971N18.2|PDIA14|TXNDC13	thioredoxin related transmembrane protein 4	protein-coding	0.000000	0.425220	152(AAGCACATTGTGTACT,-,0.00),153(AGCACATTGTGTACTT,+,0.00)
chunk0111_167_1	chr20	25233205	25233780	+	0	NA	Intergenic	Intergenic	-14578	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.013913	0.541667	
chunk0111_176_1	chr20	25279878	25280571	+	0	NA	intron (NM_002862, intron 9 of 19)	intron (NM_002862, intron 9 of 19)	32154	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.027417	0.572046	
chunk0133_375_1	chr3	173826939	173827320	+	0	NA	intron (NM_014932, intron 4 of 6)	L2a|LINE|L2	93667	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.002625	0.376963	176(GGGGACAGAACGTTCT,-,0.00),177(GGGACAGAACGTTCTA,+,0.00)
chunk0091_318_1	chr19	13058955	13059414	+	0	NA	intron (NM_001271043, intron 2 of 10)	intron (NM_001271043, intron 2 of 10)	34603	NM_001271043	4784	Hs.257970	NM_002501	ENSG00000008441	NFIX	CTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2	nuclear factor I X	protein-coding	0.023965	0.554348	229(CAGGACATTGTGTATC,-,0.00),230(AGGACATTGTGTATCT,+,0.00)
chunk0051_239_1	chr12	117033685	117033974	+	0	NA	Intergenic	Intergenic	-46492	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.034602	0.568966	
chunk0085_345_1	chr18	8803180	8803631	+	0	NA	intron (NM_015210, intron 10 of 16)	MIRb|SINE|MIR	86034	NM_015210	23255	Hs.707920	NM_015210	ENSG00000168502	MTCL1	CCDC165|KIAA0802|SOGA2	microtubule crosslinking factor 1	protein-coding	0.015521	0.444690	
chunk0176_192_1	chr7	13937511	13938014	+	0	NA	intron (NR_120445, intron 7 of 14)	intron (NR_120445, intron 7 of 14)	48752	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.007952	0.341270	
chunk0005_321_1	chr1	60898913	60899116	+	0	NA	Intergenic	L2c|LINE|L2	71762	NR_110618	100996570	Hs.46616	NR_110617	ENSG00000237928	NFIA-AS2	-	NFIA antisense RNA 2	ncRNA	0.000000	0.421569	
chunk0101_77_1	chr2	123840619	123840935	+	0	NA	Intergenic	L1PA16|LINE|L1	-184510	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.009494	0.539432	
chunk0041_396_1	chr11	133383464	133384114	+	0	NA	intron (NM_001012393, intron 1 of 7)	intron (NM_001012393, intron 1 of 7)	148719	NM_001012393	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.012308	0.445469	
chunk0065_247_1	chr14	101477228	101477704	+	0	NA	Intergenic	Intergenic	-69544	NR_126006	338002	Hs.124848	NR_126006	ENSG00000259023	LINC00524	C14orf71	long intergenic non-protein coding RNA 524	ncRNA	0.018908	0.545073	
chunk0210_416_1	chrX	100957876	100958533	+	0	NA	Intergenic	Intergenic	-11504	NR_103709	392509	Hs.147237	NM_001162491	ENSG00000174225	ARL13A	ARL13|dJ341D10.2	ADP ribosylation factor like GTPase 13A	protein-coding	0.006088	0.373860	
chunk0117_158_1	chr22	20039979	20040357	+	0	NA	intron (NR_104275, intron 1 of 5)	intron (NR_104275, intron 1 of 5)	3408	NR_104275	128989	Hs.474233	NM_152906	ENSG00000183597	TANGO2	C22orf25|MECRCN	transport and golgi organization 2 homolog	protein-coding	0.007937	0.469657	
chunk0067_25_1	chr15	40353715	40354004	+	0	NA	intron (NM_001145643, intron 2 of 2)	intron (NM_001145643, intron 2 of 2)	2826	NM_001145643	644844	Hs.447537	NM_001145643	ENSG00000233041	PHGR1	-	proline, histidine and glycine rich 1	protein-coding	0.013841	0.586207	
chunk0019_311_1	chr1	229058729	229059227	+	0	NA	Intergenic	Intergenic	115823	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.024096	0.535070	280(GAGGACAGTCTGTGCT,-,0.00),281(AGGACAGTCTGTGCTG,+,0.00)
chunk0065_365_1	chr14	103921227	103921671	+	0	NA	intron (NM_001127393, intron 1 of 4)	CpG	117	NM_004894	9556	Hs.109052	NM_004894	ENSG00000156411	ATP5MPL	6.8PL|C14orf2|MLQ|MP68|PLPM	ATP synthase membrane subunit 6.8PL	protein-coding	0.096847	0.689888	
chunk0023_241_1	chr10	27003407	27003676	+	0	NA	TTS (NM_001256053)	TTS (NM_001256053)	-61540	NR_026795	387644	Hs.529965	NR_026795	ENSG00000283709	FAM238C	C10orf51|LINC00202|LINC00202-1|NCRNA00202|bB27G4.1	family with sequence similarity 238 member C	ncRNA	0.000000	0.348148	
chunk0089_353_1	chr18	66647737	66648088	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-43774	NR_073130	28513	Hs.42771	NM_021153	ENSG00000071991	CDH19	CDH7|CDH7L2	cadherin 19	protein-coding	0.002849	0.386364	
chunk0042_33_1	chr12	1536747	1537397	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	36581	NR_028415	100292680	Hs.391695	NR_028415	ENSG00000249628	LINC00942	-	long intergenic non-protein coding RNA 942	ncRNA	0.013846	0.471582	
chunk0040_93_1	chr11	111682715	111682998	+	0	NA	intron (NM_015191, intron 3 of 14)	intron (NM_015191, intron 3 of 14)	80465	NM_015191	23235	Hs.269128	NM_015191	ENSG00000170145	SIK2	LOH11CR1I|QIK|SIK-2|SNF1LK2	salt inducible kinase 2	protein-coding	0.000000	0.316901	
chunk0202_399_1	chr9	81350993	81351428	+	0	NA	Intergenic	L1M1|LINE|L1	338325	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002299	0.327982	
chunk0184_209_1	chr7	117168106	117168344	+	0	NA	intron (NM_021908, intron 9 of 15)	intron (NM_021908, intron 9 of 15)	-14456	NR_002332	93655	Hs.368131	NR_002332	ENSG00000004866	ST7-OT3	NCRNA00026|ST7|ST7OT3	ST7 overlapping transcript 3	ncRNA	0.008403	0.372385	
chunk0184_454_1	chr7	123407774	123408738	+	0	NA	Intergenic	Intergenic	124692	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.008299	0.397927	407(TGGAACATTCTGTGTT,-,0.00),408(GGAACATTCTGTGTTT,+,0.00),495(TGGAACATTCTGTGTT,-,0.00),496(GGAACATTCTGTGTTT,+,0.00),583(TGGAACATTCTGTGTT,-,0.00),584(GGAACATTCTGTGTTT,+,0.00)
chunk0204_101_1	chr9	94622317	94622570	+	0	NA	intron (NM_001127628, intron 2 of 7)	intron (NM_001127628, intron 2 of 7)	17198	NM_000507	2203	Hs.494496	NM_000507	ENSG00000165140	FBP1	FBP	fructose-bisphosphatase 1	protein-coding	0.035573	0.570866	
chunk0211_329_1	chrX	124015758	124016151	+	0	NA	intron (NM_001282418, intron 2 of 33)	intron (NM_001282418, intron 2 of 33)	54248	NM_001042751	10735	Hs.496710	NM_006603	ENSG00000101972	STAG2	NEDXCF|SA-2|SA2|SCC3B|bA517O1.1	stromal antigen 2	protein-coding	0.002545	0.324873	
chunk0198_449_1	chr8	144125750	144126006	+	0	NA	Intergenic	CpG	-11891	NM_016458	51236	Hs.300224	NM_016458	ENSG00000235173	HGH1	BRP16|BRP16L|C8orf30A|C8orf30B|FAM203A|FAM203B	HGH1 homolog	protein-coding	0.101562	0.610895	
chunk0085_267_1	chr18	7719467	7719954	+	0	NA	intron (NM_001105244, intron 1 of 32)	L1M4|LINE|L1	152394	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.002053	0.303279	
chunk0157_416_1	chr5	124617377	124618040	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	127404	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.007541	0.385542	
chunk0085_276_1	chr18	7840918	7841134	+	0	NA	intron (NM_001105244, intron 2 of 32)	intron (NM_001105244, intron 2 of 32)	273710	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.000000	0.341014	
chunk0136_116_1	chr4	3410370	3411029	+	0	NA	intron (NM_198227, intron 2 of 15)	intron (NM_198227, intron 2 of 15)	-31234	NM_001528	3083	Hs.104	NM_001528	ENSG00000109758	HGFAC	HGFA	HGF activator	protein-coding	0.030349	0.551515	
chunk0184_328_1	chr7	120453073	120453289	+	0	NA	intron (NM_012281, intron 1 of 5)	L1PA13|LINE|L1	179513	NM_012281	3751	Hs.654739	NM_012281	ENSG00000184408	KCND2	KV4.2|RK5	potassium voltage-gated channel subfamily D member 2	protein-coding	0.004630	0.557604	
chunk0194_418_1	chr8	92087533	92088162	+	0	NA	intron (NM_001198627, intron 2 of 13)	intron (NM_001198627, intron 2 of 13)	7415	NM_001198632	862	Hs.368431	NM_004349	ENSG00000079102	RUNX1T1	AML1-MTG8|AML1T1|CBFA2T1|CDR|ETO|MTG8|ZMYND2	RUNX1 partner transcriptional co-repressor 1	protein-coding	0.007949	0.371429	
chunk0093_136_1	chr19	46289229	46289684	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-7590	NM_152795	64344	Hs.420830	NM_022462	ENSG00000124440	HIF3A	HIF-3A|HIF3-alpha-1|IPAS|MOP7|PASD7|bHLHe17	hypoxia inducible factor 3 subunit alpha	protein-coding	0.002198	0.462719	
chunk0106_131_1	chr2	199751523	199751813	+	0	NA	Intergenic	Intergenic	99505	NR_034096									0.017241	0.484536	
chunk0034_204_1	chr11	32329227	32329946	+	0	NA	Intergenic	MER101|LTR|ERV1	101231	NM_001198552	7490	Hs.591980	NM_000378	ENSG00000184937	WT1	AWT1|GUD|NPHS4|WAGR|WIT-2|WT33	WT1 transcription factor	protein-coding	0.016690	0.406944	
chunk0212_167_1	chrX	132455290	132456079	+	0	NA	intron (NM_001170704, intron 1 of 8)	intron (NM_001170704, intron 1 of 8)	-15994	NM_133486	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.012674	0.374684	
chunk0110_220_1	chr20	15440402	15440936	+	0	NA	intron (NM_001033087, intron 3 of 13)	intron (NM_001033087, intron 3 of 13)	243811	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.005618	0.400000	
chunk0165_203_1	chr6	34602679	34603255	+	0	NA	intron (NM_022758, intron 3 of 3)	intron (NM_022758, intron 3 of 3)	-46634	NM_012391	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.013889	0.504333	
chunk0062_10_1	chr14	66238184	66238703	+	0	NA	Intergenic	Intergenic	-247928	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.005780	0.400000	
chunk0146_40_1	chr4	155468425	155468795	+	0	NA	Intergenic	Intergenic	-91640	NM_001039580	79884	Hs.61271	NM_001039580	ENSG00000164114	MAP9	ASAP	microtubule associated protein 9	protein-coding	0.000000	0.355795	266(AGGCTCACTCTGTTCT,-,0.00),267(GGCTCACTCTGTTCTC,+,0.00)
chunk0017_330_1	chr1	211529541	211529825	+	0	NA	Intergenic	Intergenic	-36766	NM_183059	343035	Hs.632495	NM_183059	ENSG00000198570	RD3	C1orf36|LCA12	retinal degeneration 3, GUCY2D regulator	protein-coding	0.031690	0.536842	
chunk0190_105_1	chr8	30369566	30370170	+	0	NA	Intergenic	L1ME3G|LINE|L1	-14633	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.003311	0.330579	
chunk0016_261_1	chr1	200184180	200184447	+	0	NA	Intergenic	Intergenic	141488	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.011236	0.447761	
chunk0020_57_1	chr1	232542665	232543005	+	0	NA	Intergenic	Intergenic	-27227	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.011765	0.457478	
chunk0088_342_1	chr18	51512343	51512727	+	0	NA	intron (NR_040074, intron 1 of 2)	L1P3|LINE|L1	120493	NR_040075	100287225	Hs.448920	NR_040074	ENSG00000227115	LINC01630	-	long intergenic non-protein coding RNA 1630	ncRNA	0.000000	0.340260	
chunk0202_77_1	chr9	71791545	71792103	+	0	NA	Intergenic	L2a|LINE|L2	-22940	NM_001135820	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.005376	0.377460	
chunk0101_399_1	chr2	138825072	138825525	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	-45057	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.006623	0.310573	
chunk0012_312_1	chr1	162285226	162285546	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	-57160	NR_030283	693141		NR_030283	ENSG00000207729	MIR556	MIRN556|hsa-mir-556|mir-556	microRNA 556	ncRNA	0.012500	0.504673	
chunk0081_354_1	chr17	47613002	47613292	+	0	NA	intron (NM_006310, intron 18 of 22)	intron (NM_006310, intron 18 of 22)	-36691	NM_002265	3837	Hs.532793	NM_002265	ENSG00000108424	KPNB1	IMB1|IPO1|IPOB|Impnb|NTF97	karyopherin subunit beta 1	protein-coding	0.006897	0.360825	
chunk0110_342_1	chr20	19411442	19411674	+	0	NA	intron (NM_020689, intron 2 of 16)	intron (NM_020689, intron 2 of 16)	-126962	NR_024564	100130264	Hs.683814	NR_024564	ENSG00000179447	LOC100130264	-	uncharacterized LOC100130264	ncRNA	0.008621	0.454936	
chunk0013_304_1	chr1	171264848	171265119	+	0	NA	intron (NM_001282694, intron 2 of 7)	MER5A1|DNA|hAT-Charlie	7060	NM_001282692	2326	Hs.1424	NM_002021	ENSG00000010932	FMO1	-	flavin containing dimethylaniline monoxygenase 1	protein-coding	0.025830	0.415441	
chunk0063_153_1	chr14	80003073	80003764	+	0	NA	Intergenic	L2c|LINE|L2	-208001	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.010130	0.381503	
chunk0068_362_1	chr15	58001630	58001964	+	0	NA	intron (NM_170697, intron 2 of 10)	intron (NM_170697, intron 2 of 10)	12300	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.000000	0.382090	
chunk0090_48_1	chr19	1871286	1871627	+	0	NA	Intergenic	Intergenic	-7891	NM_031918	83855	Hs.136280	NM_031918	ENSG00000129911	KLF16	BTEB4|DRRF|NSLP2	Kruppel like factor 16	protein-coding	0.038123	0.573099	215(CAGGACACTGTGGTCT,-,0.00),216(AGGACACTGTGGTCTG,+,0.00)
chunk0151_397_1	chr5	55452272	55452767	+	0	NA	intron (NR_103485, intron 4 of 6)	MSTB|LTR|ERVL-MaLR	56407	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.002020	0.403226	
chunk0081_428_1	chr17	48818355	48819215	+	0	NA	Intergenic	Intergenic	-1678	NM_001130918	284076	Hs.91930	NM_173623	ENSG00000170703	TTLL6	TTL.6	tubulin tyrosine ligase like 6	protein-coding	0.013953	0.493612	
chunk0065_42_1	chr15	21285108	21285652	+	0	NA	Intergenic	LTR9|LTR|ERV1	12449	NR_027053	646214	Hs.510697	NR_027053		LOC646214	-	p21 protein (Cdc42/Rac)-activated kinase 2 pseudogene	pseudo	0.012868	0.471560	
chunk0170_10_1	chr6	109023351	109023775	+	0	NA	intron (NM_014454, intron 1 of 9)	intron (NM_014454, intron 1 of 9)	-14008	NM_001199933	27244	Hs.591336	NM_014454	ENSG00000080546	SESN1	PA26|SEST1	sestrin 1	protein-coding	0.000000	0.334118	208(GAGTACATTCTGTCCC,-,0.00),209(AGTACATTCTGTCCCA,+,0.00)
chunk0047_176_1	chr12	70574285	70574751	+	0	NA	intron (NM_001109754, intron 11 of 33)	intron (NM_001109754, intron 11 of 33)	35326	NM_001206971	5787	Hs.201030	NM_002837	ENSG00000127329	PTPRB	HPTP-BETA|HPTPB|PTPB|R-PTP-BETA|VEPTP	protein tyrosine phosphatase receptor type B	protein-coding	0.004292	0.387580	
chunk0209_107_1	chrX	40149137	40149743	+	0	NA	intron (NM_001123383, intron 1 of 14)	intron (NM_001123383, intron 1 of 14)	27889	NM_001123383	54880	Hs.659681	NM_017745	ENSG00000183337	BCOR	ANOP2|MAA2|MCOPS2	BCL6 corepressor	protein-coding	0.029703	0.517298	
chunk0055_45_1	chr13	52252801	52253081	+	0	NA	Intergenic	L1MA8|LINE|L1	-58474	NR_051964	100887750	Hs.553878	NR_002816	ENSG00000243406	MRPS31P5	MRPS31P3	mitochondrial ribosomal protein S31 pseudogene 5	pseudo	0.007143	0.391459	
chunk0193_190_1	chr8	75430164	75430546	+	0	NA	Intergenic	Intergenic	-109613	NM_004133	3174	Hs.241529	NM_004133	ENSG00000164749	HNF4G	NR2A2|NR2A3	hepatocyte nuclear factor 4 gamma	protein-coding	0.002618	0.394256	
chunk0169_23_1	chr6	96789072	96789550	+	0	NA	Intergenic	Intergenic	48166	NM_030784	81491	Hs.221364	NM_030784	ENSG00000112218	GPR63	PSP24(beta)|PSP24B	G protein-coupled receptor 63	protein-coding	0.002092	0.323591	
chunk0175_375_1	chr6	168007835	168008314	+	0	NA	Intergenic	Intergenic	-9799	NM_005355	3834	Hs.150013	NM_005355	ENSG00000125337	KIF25	KNSL3	kinesin family member 25	protein-coding	0.000000	0.381250	
chunk0174_58_1	chr6	155044178	155044459	+	0	NA	Intergenic	Intergenic	-45971	NM_012454	26230	Hs.586279	NM_012454	ENSG00000146426	TIAM2	STEF|TIAM-2	T cell lymphoma invasion and metastasis 2	protein-coding	0.021352	0.464539	
chunk0053_123_1	chr13	29693798	29693997	+	0	NA	Intergenic	MIR1_Amn|SINE|MIR	-98209	NM_003045	6541	Hs.14846	NM_003045	ENSG00000139514	SLC7A1	ATRC1|CAT-1|ERR|HCAT1|REC1L	solute carrier family 7 member 1	protein-coding	0.035176	0.475000	
chunk0013_441_1	chr1	173573429	173574187	+	0	NA	intron (NM_178527, intron 8 of 27)	L2c|LINE|L2	29286	NM_178527	284525	Hs.494981	NM_178527	ENSG00000162753	SLC9C2	SLC9A11	solute carrier family 9 member C2 (putative)	protein-coding	0.006596	0.451910	
chunk0187_333_1	chr7	156738227	156738670	+	0	NA	intron (NM_022458, intron 9 of 16)	L1M1|LINE|L1	94647	NM_001308274	140545	Hs.446194	NM_030936	ENSG00000105982	RNF32	FKSG33|HSD15|LMBR2	ring finger protein 32	protein-coding	0.004515	0.529279	
chunk0148_261_1	chr5	10353286	10353888	+	0	NA	promoter-TSS (NM_005885)	promoter-TSS (NM_005885)	-52	NM_001270660	10299	Hs.432862	NM_005885	ENSG00000145495	MARCH6	DOA10|MARCH-VI|RNF176|TEB4	membrane associated ring-CH-type finger 6	protein-coding	0.109635	0.714760	
chunk0091_131_1	chr19	6550109	6550456	+	0	NA	Intergenic	Intergenic	19283	NM_003811	8744	Hs.1524	NM_003811	ENSG00000125657	TNFSF9	4-1BB-L|CD137L|TNLG5A	TNF superfamily member 9	protein-coding	0.002882	0.370690	245(AGGACAGACTGAACAT,+,0.00)
chunk0194_168_1	chr8	84863314	84863864	+	0	NA	intron (NM_001100393, intron 6 of 8)	intron (NM_001100393, intron 6 of 8)	157662	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005455	0.379310	
chunk0018_40_1	chr1	215638890	215639384	+	0	NA	intron (NM_206933, intron 69 of 71)	intron (NM_206933, intron 69 of 71)	71745	NM_016121	51133	Hs.335139	NM_016121	ENSG00000136636	KCTD3	NY-REN-45	potassium channel tetramerization domain containing 3	protein-coding	0.016194	0.375758	
chunk0044_430_1	chr12	42090165	42090509	+	0	NA	intron (NM_001099650, intron 6 of 6)	intron (NM_001099650, intron 6 of 6)	54534	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.005814	0.400000	
chunk0117_396_1	chr21	45432912	45433577	+	0	NA	intron (NM_130445, intron 2 of 42)	intron (NM_130445, intron 2 of 42)	-8174	NR_027498	378832	Hs.517353	NM_199175	ENSG00000183535	COL18A1-AS1	C21orf123|NCRNA00175|PRED80	COL18A1 antisense RNA 1	ncRNA	0.022556	0.478979	328(CAGAACATTTAGTTCA,-,0.00)
chunk0212_417_1	chrX	152527444	152527709	+	0	NA	Intergenic	Intergenic	-76217	NM_000808	2556	Hs.123024	NM_000808	ENSG00000011677	GABRA3	-	gamma-aminobutyric acid type A receptor alpha3 subunit	protein-coding	0.007547	0.443609	
chunk0041_158_1	chr11	125953048	125953377	+	0	NA	Intergenic	Intergenic	48846	NM_013264	29118	Hs.420263	NM_013264	ENSG00000109832	DDX25	GRTH	DEAD-box helicase 25	protein-coding	0.024316	0.606061	
chunk0053_285_1	chr13	33380860	33381172	+	0	NA	intron (NM_001243476, intron 5 of 17)	intron (NM_001243476, intron 5 of 17)	-95252	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.003205	0.396166	
chunk0071_128_1	chr15	81715912	81716208	+	0	NA	Intergenic	Intergenic	330083	NM_032246	84206	Hs.104744	NM_032246	ENSG00000183496	MEX3B	MEX-3B|RKHD3|RNF195	mex-3 RNA binding family member B	protein-coding	0.003378	0.400673	
chunk0195_37_1	chr8	93260161	93260360	+	0	NA	Intergenic	Intergenic	-93410	NM_001242668									0.010050	0.470000	
chunk0118_223_1	chr22	32135826	32136392	+	0	NA	Intergenic	Intergenic	14132	NR_040114	23782	Hs.581098	NR_040114	ENSG00000234479	AP1B1P1	ADTB1L1|dJ127L4.2	AP1B1 pseudogene 1	pseudo	0.010601	0.518519	
chunk0007_449_1	chr1	86970890	86971466	+	0	NA	intron (NM_012262, intron 1 of 6)	intron (NM_012262, intron 1 of 6)	56526	NM_012262	9653	Hs.743280	NM_012262	ENSG00000153936	HS2ST1	dJ604K5.2	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.005208	0.329289	
chunk0067_83_1	chr15	41771731	41772189	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-2474	NM_001128608	23005	Hs.513661	NM_014994	ENSG00000137802	MAPKBP1	JNKBP-1|JNKBP1|NPHP20	mitogen-activated protein kinase binding protein 1	protein-coding	0.006550	0.374728	
chunk0203_84_1	chr9	83981398	83982075	+	0	NA	intron (NM_024945, intron 1 of 2)	intron (NM_024945, intron 1 of 2)	1014	NM_024945	80010	Hs.726327	NM_024945	ENSG00000178966	RMI1	BLAP75|C9orf76|FAAP75	RecQ mediated genome instability 1	protein-coding	0.020679	0.414454	
chunk0057_447_1	chr13	110776511	110777103	+	0	NA	Intergenic	L1MC4|LINE|L1	61370	NM_001267728	3621	Hs.46700	NM_005537	ENSG00000153487	ING1	p24ING1c|p33|p33ING1|p33ING1b|p47|p47ING1a	inhibitor of growth family member 1	protein-coding	0.005068	0.379427	
chunk0118_185_1	chr22	31207063	31207760	+	0	NA	TTS (NM_001135825)	TTS (NM_001135825)	-4853	NM_005569	3985	Hs.474596	NM_005569	ENSG00000182541	LIMK2	-	LIM domain kinase 2	protein-coding	0.010043	0.467049	
chunk0036_147_1	chr11	62186199	62186594	+	0	NA	Intergenic	L1PA13|LINE|L1	-3842	NM_006552	10648	Hs.202686	NM_006552	ENSG00000168515	SCGB1D1	LIPA|LPHA|LPNA	secretoglobin family 1D member 1	protein-coding	0.005063	0.477273	
chunk0175_246_1	chr7	7023666	7024211	+	0	NA	Intergenic	L1PA11|LINE|L1	43107	NR_037454	100500886		NR_037454	ENSG00000266287	MIR3683	-	microRNA 3683	ncRNA	0.011009	0.368132	
chunk0189_59_1	chr8	20104163	20104710	+	0	NA	Intergenic	LTR41|LTR|ERVL	78770	NM_001142324	6570	Hs.158322	NM_003053	ENSG00000036565	SLC18A1	CGAT|VAT1|VMAT1	solute carrier family 18 member A1	protein-coding	0.003656	0.494526	
chunk0149_186_1	chr5	21219703	21220083	+	0	NA	Intergenic	MER67B|LTR|ERV1	-239587	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.010526	0.430446	
chunk0021_375_1	chr1	246420802	246421396	+	0	NA	intron (NM_001167740, intron 1 of 11)	intron (NM_001167740, intron 1 of 11)	-3687	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003367	0.312605	
chunk0023_359_1	chr10	29946761	29947328	+	0	NA	Intergenic	Intergenic	112515	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.010582	0.515845	249(CAGGACAGAATGTTCC,-,0.00),250(AGGACAGAATGTTCCA,+,0.00)
chunk0122_408_1	chr3	38284635	38285076	+	0	NA	Intergenic	Intergenic	19048	NM_004256	9390	Hs.225941	NM_004256	ENSG00000172940	SLC22A13	OAT10|OCTL1|OCTL3|ORCTL-3|ORCTL3	solute carrier family 22 member 13	protein-coding	0.018141	0.452489	
chunk0009_189_1	chr1	105855290	105855734	+	0	NA	Intergenic	L1MC4|LINE|L1	-236577	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004505	0.386517	201(GAGTACTAAGTGTTCT,-,0.00),202(AGTACTAAGTGTTCTC,+,0.00)
chunk0210_403_1	chrX	99552525	99552747	+	0	NA	intron (NR_024608, intron 10 of 10)	L1ME1|LINE|L1	387207	NR_024608	442459	Hs.706599	NM_001127438		XRCC6P5	-	X-ray repair cross complementing 6 pseudogene 5	pseudo	0.004505	0.331839	
chunk0030_25_1	chr10	111131102	111131455	+	0	NA	Intergenic	Intergenic	54246	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.011331	0.435028	
chunk0203_205_1	chr9	86555700	86556075	+	0	NA	Intergenic	L1MB5|LINE|L1	-201400	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.002667	0.396277	
chunk0059_187_1	chr14	32756626	32756976	+	0	NA	intron (NM_004274, intron 11 of 13)	L1MA8|LINE|L1	-182452	NM_173159	64067	Hs.657892	NM_022123	ENSG00000151322	NPAS3	MOP6|PASD6|bHLHe12	neuronal PAS domain protein 3	protein-coding	0.005714	0.592593	
chunk0100_114_1	chr2	108440417	108440886	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	-8470	NM_181453	9648	Hs.436505	NM_181453	ENSG00000135968	GCC2	GCC185|RANBP2L4|REN53	GRIP and coiled-coil domain containing 2	protein-coding	0.004264	0.319149	
chunk0022_56_1	chr10	8327060	8327292	+	0	NA	Intergenic	Intergenic	-58871	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.008621	0.343348	
chunk0113_171_1	chr20	53071475	53071980	+	0	NA	intron (NM_173485, intron 1 of 2)	intron (NM_173485, intron 1 of 2)	99320	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.013861	0.454545	
chunk0141_330_1	chr4	87360382	87360606	+	0	NA	intron (NM_016245, intron 4 of 6)	MLT1K|LTR|ERVL-MaLR	30809	NM_016245	51170	Hs.594923	NM_016245	ENSG00000198189	HSD17B11	17-BETA-HSD11|17-BETA-HSDXI|17BHSD11|DHRS8|PAN1B|RETSDR2|SDR16C2	hydroxysteroid 17-beta dehydrogenase 11	protein-coding	0.008929	0.413333	
chunk0106_318_1	chr2	205226329	205226941	+	0	NA	intron (NM_205863, intron 15 of 21)	L1MA2|LINE|L1	-455865	NM_201267	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.008170	0.365416	277(TGAAGAGACTGTTCTT,+,0.00),406(AGGATCATGCTGTTCT,-,0.00),407(GGATCATGCTGTTCTG,+,0.00)
chunk0205_67_1	chr9	106755872	106756093	+	0	NA	Intergenic	Intergenic	-107115	NM_021224	58499	Hs.370379	NM_021224	ENSG00000148143	ZNF462	ZFPIP|Zfp462	zinc finger protein 462	protein-coding	0.022624	0.500000	
chunk0111_417_1	chr20	34771797	34772085	+	0	NA	intron (NM_014071, intron 4 of 14)	intron (NM_014071, intron 4 of 14)	53689	NM_001242539	23054	Hs.368971	NM_014071	ENSG00000198646	NCOA6	AIB3|ASC2|NRC|PRIP|RAP250|TRBP	nuclear receptor coactivator 6	protein-coding	0.003472	0.397924	
chunk0006_202_1	chr1	67635614	67636045	+	0	NA	Intergenic	Intergenic	-49348	NM_001199741	1647	Hs.80409	NM_001924	ENSG00000116717	GADD45A	DDIT1|GADD45	growth arrest and DNA damage inducible alpha	protein-coding	0.016241	0.481481	
chunk0178_372_1	chr7	39734213	39734526	+	0	NA	intron (NR_026999, intron 1 of 11)	intron (NR_026999, intron 1 of 11)	801	NR_026999	349114	Hs.414183	NM_198284		LINC00265	NCRNA00265	long intergenic non-protein coding RNA 265	ncRNA	0.012780	0.477707	
chunk0200_76_1	chr9	16225300	16225610	+	0	NA	intron (NR_073471, intron 1 of 3)	L1PA7|LINE|L1	27652	NM_001271829	100129385	Hs.586441	NM_001271829	ENSG00000205549	C9orf92	Em:AL513424.1	chromosome 9 open reading frame 92	protein-coding	0.006452	0.405145	
chunk0147_446_1	chr4	187768994	187769214	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-96463	NR_110436	100506272	Hs.508163	NR_110436	ENSG00000250590	LINC02492	-	long intergenic non-protein coding RNA 2492	ncRNA	0.018182	0.425339	
chunk0081_282_1	chr17	44149697	44149993	+	0	NA	intron (NM_024032, intron 3 of 9)	L2c|LINE|L2	7939	NM_024032	78995	Hs.437059	NM_024032	ENSG00000125319	C17orf53	-	chromosome 17 open reading frame 53	protein-coding	0.010135	0.464646	
chunk0002_144_1	chr1	17297913	17298463	+	0	NA	Intergenic	Intergenic	-10007	NM_012387	23569	Hs.522969	NM_012387	ENSG00000159339	PADI4	PAD|PAD4|PADI5|PDI4|PDI5	peptidyl arginine deiminase 4	protein-coding	0.018182	0.491833	224(TGGGACAGCATGATCC,-,0.00),225(GGGACAGCATGATCCA,+,0.00)
chunk0086_93_1	chr18	13810972	13811401	+	0	NA	Intergenic	Intergenic	-14358	NM_005913	4161	Hs.248145	NM_005913	ENSG00000176136	MC5R	MC2	melanocortin 5 receptor	protein-coding	0.020979	0.504651	
chunk0120_420_1	chr3	13005700	13006119	+	0	NA	intron (NM_001134382, intron 1 of 13)	intron (NM_001134382, intron 1 of 13)	-38211	NM_014869	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.007160	0.514286	210(CAGCACACAGAGTGCC,-,0.00),211(AGCACACAGAGTGCCA,+,0.00)
chunk0131_241_1	chr3	149395655	149396029	+	0	NA	Intergenic	Intergenic	-18061	NM_014220	4071	Hs.351316	NM_014220	ENSG00000169908	TM4SF1	H-L6|L6|M3S1|TAAL6	transmembrane 4 L six family member 1	protein-coding	0.005348	0.400000	
chunk0115_182_1	chr21	25887563	25888166	+	0	NA	intron (NM_001136016, intron 16 of 16)	Tigger3a|DNA|TcMar-Tigger	-152210	NM_001685	522	Hs.246310	NM_001685	ENSG00000154723	ATP5PF	ATP5|ATP5A|ATP5J|ATPM|CF6|F6	ATP synthase peripheral stalk subunit F6	protein-coding	0.013267	0.405629	
chunk0157_403_1	chr5	124274445	124275459	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	163568	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005917	0.416749	
chunk0125_128_1	chr3	65854768	65855456	+	0	NA	intron (NM_015520, intron 1 of 24)	intron (NM_015520, intron 1 of 24)	-38704	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.010174	0.455733	
chunk0136_103_1	chr4	2958343	2958590	+	0	NA	intron (NM_003703, intron 1 of 18)	intron (NM_003703, intron 1 of 18)	5040	NM_001291978	8602	Hs.627133	NM_003703	ENSG00000087269	NOP14	C4orf9|NOL14|RES4-25|RES425|UTP2	NOP14 nucleolar protein	protein-coding	0.012146	0.463710	
chunk0157_166_1	chr5	118027012	118027240	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	-255448	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.004386	0.393013	
chunk0157_177_1	chr5	118489732	118489931	+	0	NA	intron (NR_104610, intron 4 of 9)	MLT1I|LTR|ERVL-MaLR	72286	NR_104610	101927280	Hs.543951	NR_104610		LINC02208	HRAT56	long intergenic non-protein coding RNA 2208	ncRNA	0.005025	0.425000	140(GAGAACAGAATGTTCC,-,0.00),141(AGAACAGAATGTTCCA,+,0.00)
chunk0126_150_1	chr3	76582651	76583328	+	0	NA	Intergenic	Intergenic	-457154	NM_001290065	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.007386	0.367257	129(GGAGACAGTGTGTTCA,-,0.00),130(GAGACAGTGTGTTCAT,+,0.00)
chunk0021_246_1	chr1	243256173	243256425	+	0	NA	promoter-TSS (NM_014812)	promoter-TSS (NM_014812)	294	NM_006642	10806	Hs.591530	NM_006642	ENSG00000054282	SDCCAG8	BBS16|CCCAP|CCCAP SLSN7|HSPC085|NPHP10|NY-CO-8|SLSN7|hCCCAP	serologically defined colon cancer antigen 8	protein-coding	0.039683	0.557312	
chunk0208_293_1	chrX	22233938	22234137	+	0	NA	intron (NM_001282754, intron 20 of 20)	L1PA7|LINE|L1	-38876	NM_152577	158506	Hs.132485	NM_152577	ENSG00000175809	CBLL2	CT138|HAKAIL|ZNF645	Cbl proto-oncogene like 2	protein-coding	0.010050	0.455000	
chunk0039_115_1	chr11	97752474	97752673	+	0	NA	Intergenic	MER52A|LTR|ERV1	-1245696	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.005025	0.575000	
chunk0107_179_1	chr2	215772201	215772400	+	0	NA	intron (NR_037195, intron 1 of 9)	intron (NR_037195, intron 1 of 9)	54257	NR_132383	105373869	Hs.152812	NR_132383		LINC01614	LCAL4	long intergenic non-protein coding RNA 1614	ncRNA	0.005025	0.375000	
chunk0174_154_1	chr6	157851956	157852286	+	0	NA	intron (NM_016224, intron 1 of 17)	L1MB4|LINE|L1	28950	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.012121	0.365559	
chunk0119_350_1	chr22	47276154	47276541	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	210764	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.010336	0.497423	
chunk0159_82_1	chr5	137754352	137754828	+	0	NA	promoter-TSS (NM_006805)	promoter-TSS (NM_006805)	-240	NM_006805	10949	Hs.96996	NM_006805	ENSG00000177733	HNRNPA0	HNRPA0	heterogeneous nuclear ribonucleoprotein A0	protein-coding	0.109244	0.672956	
chunk0058_271_1	chr14	26125040	26125261	+	0	NA	Intergenic	Intergenic	472604	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.004525	0.346847	
chunk0178_234_1	chr7	35859407	35859621	+	0	NA	intron (NM_001011553, intron 2 of 12)	L1M4|LINE|L1	58528	NM_001011553	989	Hs.191346	NM_001788	ENSG00000122545	SEPTIN7	CDC10|CDC3|NBLA02942|SEPT7|SEPT7A	septin 7	protein-coding	0.014019	0.348837	
chunk0071_96_1	chr15	80989877	80990076	+	0	NA	promoter-TSS (NM_015154)	promoter-TSS (NM_015154)	-98	NR_126328	23184	Hs.578450	NM_015154	ENSG00000117899	MESD	BOCA|MESDC2	mesoderm development LRP chaperone	protein-coding	0.085427	0.690000	
chunk0181_34_1	chr7	78495956	78496769	+	0	NA	intron (NM_001301128, intron 5 of 20)	intron (NM_001301128, intron 5 of 20)	149120	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.007380	0.334152	
chunk0146_310_1	chr4	165362522	165363226	+	0	NA	Intergenic	MIRc|SINE|MIR	-16071	NM_001873	1363	Hs.75360	NM_001873	ENSG00000109472	CPE	CPH	carboxypeptidase E	protein-coding	0.001420	0.331915	
chunk0004_361_1	chr1	51551691	51552266	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-32655	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.008696	0.418403	
chunk0210_280_1	chrX	84865063	84865615	+	0	NA	Intergenic	Intergenic	-68812	NR_024062	100131816	Hs.460809	NM_178567	ENSG00000229547	UBE2DNL	-	ubiquitin conjugating enzyme E2 D N-terminal like (pseudogene)	pseudo	0.000000	0.330922	
chunk0145_414_1	chr4	152930844	152931201	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-11961	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.000000	0.393855	
chunk0028_179_1	chr10	88346575	88346887	+	0	NA	intron (NM_001031709, intron 5 of 6)	intron (NM_001031709, intron 5 of 6)	236594	NM_018363	55328	Hs.149849	NM_018363	ENSG00000184719	RNLS	C10orf59|RENALASE	renalase, FAD dependent amine oxidase	protein-coding	0.003205	0.392971	
chunk0081_91_1	chr17	39652201	39652748	+	0	NA	intron (NM_001165937, intron 1 of 14)	L2a|LINE|L2	-12872	NM_003673	8557	Hs.77628	NM_003673	ENSG00000173991	TCAP	CMD1N|CMH25|LGMD2G|LGMDR7|T-cap|TELE|telethonin	titin-cap	protein-coding	0.007313	0.510949	
chunk0173_152_1	chr6	144185363	144185734	+	0	NA	intron (NM_003764, intron 1 of 1)	intron (NM_003764, intron 1 of 1)	35031	NM_003764	8676	Hs.118958	NM_003764	ENSG00000135604	STX11	FHL4|HLH4|HPLH4	syntaxin 11	protein-coding	0.002695	0.341398	
chunk0178_363_1	chr7	39247775	39248383	+	0	NA	intron (NM_007252, intron 5 of 10)	intron (NM_007252, intron 5 of 10)	158267	NR_046711	100861520	Hs.571292	NR_046711	ENSG00000224122	POU6F2-AS1	-	POU6F2 antisense RNA 1	ncRNA	0.004934	0.369458	
chunk0191_217_1	chr8	52340178	52340635	+	0	NA	intron (NM_014682, intron 2 of 25)	intron (NM_014682, intron 2 of 25)	69473	NM_014682	9705	Hs.655499	NM_014682	ENSG00000147488	ST18	NZF-3|NZF3|ZC2H2C3|ZC2HC10|ZNF387	ST18 C2H2C-type zinc finger transcription factor	protein-coding	0.010941	0.412664	
chunk0141_61_1	chr4	77679741	77680053	+	0	NA	Intergenic	L1ME5|LINE|L1	139493	NM_001286790	246175	Hs.592519	NM_144571	ENSG00000138767	CNOT6L	CCR4b	CCR4-NOT transcription complex subunit 6 like	protein-coding	0.009615	0.367412	
chunk0188_313_1	chr8	17155697	17155928	+	0	NA	promoter-TSS (NM_016353)	promoter-TSS (NM_016353)	-515	NM_016353	51201	Hs.728241	NM_016353	ENSG00000104219	ZDHHC2	DHHC2|ZNF372	zinc finger DHHC-type containing 2	protein-coding	0.025974	0.495690	
chunk0098_386_1	chr2	79471835	79472354	+	0	NA	Intergenic	MLT1A0-int|LTR|ERVL-MaLR	28750	NR_110289	101927987	Hs.574704	NR_110289	ENSG00000229385	LOC101927987	-	uncharacterized LOC101927987	ncRNA	0.003854	0.392308	
chunk0059_270_1	chr14	35353810	35354235	+	0	NA	Intergenic	L1ME3G|LINE|L1	50732	NM_020529	4792	Hs.81328	NM_020529	ENSG00000100906	NFKBIA	EDAID2|IKBA|MAD-3|NFKBI	NFKB inhibitor alpha	protein-coding	0.002353	0.438967	
chunk0118_351_1	chr22	36151221	36151762	+	0	NA	intron (NM_030644, intron 1 of 4)	HAL1|LINE|L1	9438	NM_030644	80833	Hs.474737	NM_014349	ENSG00000128284	APOL3	APOLIII|CG121|CG12_1|apoL-III	apolipoprotein L3	protein-coding	0.001848	0.345018	214(GAGAACATTATGTACT,-,0.00),215(AGAACATTATGTACTG,+,0.00)
chunk0112_343_1	chr20	45112339	45112950	+	0	NA	intron (NM_145652, intron 1 of 3)	intron (NM_145652, intron 1 of 3)	2528	NM_145652	149708	Hs.375031	NM_145652	ENSG00000175121	WFDC5	PRG5|WAP1|dJ211D12.5	WAP four-disulfide core domain 5	protein-coding	0.013093	0.433007	
chunk0023_136_1	chr10	23884786	23885539	+	0	NA	intron (NM_001098500, intron 1 of 18)	L1MA9|LINE|L1	190416	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.003984	0.384615	
chunk0161_36_1	chr5	165828568	165829097	+	0	NA	Intergenic	L1MEf|LINE|L1	1097538	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.001890	0.281132	403(GTGACAGAATGTGCCC,+,0.00)
chunk0084_227_1	chr17	78585294	78585493	+	0	NA	Intergenic	Intergenic	-7999	NM_173628	8632	Hs.375975	NM_003727	ENSG00000187775	DNAH17	DNAHL1|DNEL2	dynein axonemal heavy chain 17	protein-coding	0.005025	0.530000	
chunk0143_122_1	chr4	109443306	109443839	+	0	NA	intron (NM_001042734, intron 1 of 22)	intron (NM_001042734, intron 1 of 22)	-9755	NR_039978	100533182	Hs.518927	NR_039978	ENSG00000247950	SEC24B-AS1	1/2-SBSRNA4	SEC24B antisense RNA 1	ncRNA	0.003752	0.393258	
chunk0075_202_1	chr16	52501792	52502476	+	0	NA	intron (NM_001080430, intron 1 of 6)	intron (NM_001080430, intron 1 of 6)	44760	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.007310	0.414599	
chunk0012_86_1	chr1	156217945	156218491	+	0	NA	intron (NM_001199664, intron 1 of 4)	L1ME5|LINE|L1	5230	NM_001199653	11243	Hs.530479	NM_007221	ENSG00000160783	PMF1	-	polyamine modulated factor 1	protein-coding	0.003663	0.398537	
chunk0043_119_1	chr12	15596113	15596538	+	0	NA	3' UTR (NM_030668, exon 14 of 14)	3' UTR (NM_030668, exon 14 of 14)	49981	NM_030668	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.011765	0.424883	
chunk0212_389_1	chrX	150664371	150665030	+	0	NA	intron (NM_000252, intron 14 of 14)	intron (NM_000252, intron 14 of 14)	-28664	NM_001306144	8776	Hs.347187	NM_003828	ENSG00000063601	MTMR1	-	myotubularin related protein 1	protein-coding	0.003035	0.381818	
chunk0194_92_1	chr8	83100629	83100937	+	0	NA	Intergenic	Intergenic	-302975	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.012987	0.566343	
chunk0064_325_1	chr14	96063485	96064019	+	0	NA	intron (NM_001282463, intron 2 of 2)	L1PB|LINE|L1	24428	NM_001252507	56967	Hs.6434	NM_020215	ENSG00000227051	C14orf132	C14orf88	chromosome 14 open reading frame 132	protein-coding	0.007491	0.405607	
chunk0097_195_1	chr2	50643161	50643382	+	0	NA	intron (NM_001135659, intron 5 of 23)	MIR|SINE|MIR	52991	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.004525	0.360360	
chunk0046_249_1	chr12	60526573	60526947	+	0	NA	Intergenic	L1MA7|LINE|L1	837423	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.000000	0.242667	
chunk0068_81_1	chr15	51995077	51995640	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-23557	NM_001286430	123169	Hs.567662	NM_138792	ENSG00000166477	LEO1	RDL	LEO1 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.007105	0.482270	337(AGGGACAAGAAGTCCT,-,0.00),338(GGGACAAGAAGTCCTT,+,0.00)
chunk0101_461_1	chr2	140362100	140362708	+	0	NA	intron (NM_018557, intron 72 of 90)	Tigger5|DNA|TcMar-Tigger	224281	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.003289	0.384236	
chunk0073_293_1	chr16	14072535	14072934	+	0	NA	intron (NM_001308142, intron 1 of 16)	intron (NM_001308142, intron 1 of 16)	1420	NM_001308142	57496	Hs.49143	NM_014048	ENSG00000186260	MRTFB	MKL2|MRTF-B|NPD001	myocardin related transcription factor B	protein-coding	0.017544	0.460000	
chunk0096_111_1	chr2	28470173	28470492	+	0	NA	Intergenic	Intergenic	-25739	NM_001170585	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.006270	0.509375	
chunk0103_116_1	chr2	161584214	161584448	+	0	NA	Intergenic	L1ME4a|LINE|L1	-40004	NM_001178015	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.000000	0.331915	
chunk0084_44_1	chr17	74137640	74137839	+	0	NA	Intergenic	L1ME2|LINE|L1	-65917	NM_001035258	6169	Hs.380953	NM_000999	ENSG00000172809	RPL38	L38	ribosomal protein L38	protein-coding	0.000000	0.395000	
chunk0073_4_1	chr16	1827071	1827399	+	0	NA	promoter-TSS (NM_005326)	promoter-TSS (NM_005326)	11	NM_001142398	81889	Hs.513265	NM_031208	ENSG00000180185	FAHD1	C16orf36|YISKL	fumarylacetoacetate hydrolase domain containing 1	protein-coding	0.103659	0.674772	
chunk0106_246_1	chr2	203266193	203266682	+	0	NA	intron (NM_177538, intron 4 of 12)	intron (NM_177538, intron 4 of 12)	27996	NM_177538	57404	Hs.446065	NM_020674	ENSG00000119004	CYP20A1	CYP-M	cytochrome P450 family 20 subfamily A member 1	protein-coding	0.010225	0.371429	
chunk0202_338_1	chr9	79154364	79154785	+	0	NA	Intergenic	L2c|LINE|L2	-8908	NR_109771	101927450	Hs.738041	NR_109771	ENSG00000260995	LOC101927450	-	uncharacterized LOC101927450	ncRNA	0.011876	0.379147	
chunk0047_402_1	chr12	75784621	75784911	+	0	NA	Intergenic	Intergenic	247010	NM_007350	22822	Hs.602085	NM_007350	ENSG00000139289	PHLDA1	DT1P1B11|PHRIP|TDAG51	pleckstrin homology like domain family A member 1	protein-coding	0.003448	0.508591	173(GAGGAGAGGCTGTGCT,-,0.00),174(AGGAGAGGCTGTGCTG,+,0.00)
chunk0060_370_1	chr14	52445512	52445740	+	0	NA	intron (NM_001160047, intron 18 of 20)	Tigger3a|DNA|TcMar-Tigger	106957	NM_001160047	57544	Hs.532609	NM_020784	ENSG00000087301	TXNDC16	ERp90|KIAA1344	thioredoxin domain containing 16	protein-coding	0.004386	0.336245	
chunk0128_449_1	chr3	115205844	115206138	+	0	NA	Intergenic	L2c|LINE|L2	-58711	NM_015642	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.003401	0.325424	
chunk0113_71_1	chr20	50527939	50528490	+	0	NA	intron (NM_001278618, intron 1 of 8)	L2c|LINE|L2	17893	NM_001278618	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.012704	0.456522	
chunk0098_20_1	chr2	65411484	65411888	+	0	NA	intron (NM_181784, intron 1 of 5)	intron (NM_181784, intron 1 of 5)	20836	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.012376	0.419753	
chunk0055_53_1	chr13	52483900	52484334	+	0	NA	Intergenic	Intergenic	-4876	NR_002793	220115	Hs.528448	NR_002793		TPTE2P3	TPTEps1	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 3	pseudo	0.009217	0.473563	417(ATGATCACAGTGTGCT,-,0.00),418(TGATCACAGTGTGCTT,+,0.00)
chunk0039_178_1	chr11	100399457	100399821	+	0	NA	Intergenic	Intergenic	-288037	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.008242	0.397260	
chunk0062_279_1	chr14	72097111	72097632	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	164302	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.003839	0.375479	
chunk0121_202_1	chr3	21109660	21109975	+	0	NA	Intergenic	MIRb|SINE|MIR	-295909	NR_002311	391518	Hs.543226	NR_002311		VENTXP7	HPX42|VENTX1	VENT homeobox pseudogene 7	pseudo	0.003175	0.325949	
chunk0187_264_1	chr7	155069950	155070427	+	0	NA	promoter-TSS (NM_024012)	promoter-TSS (NM_024012)	-136	NM_024012	3361	Hs.65791	NM_024012	ENSG00000157219	HTR5A	5-HT5A	5-hydroxytryptamine receptor 5A	protein-coding	0.060797	0.635983	
chunk0142_2_1	chr4	89541960	89542384	+	0	NA	Intergenic	L1MA9|LINE|L1	-234162	NM_198281	285513	Hs.100912	NM_198281	ENSG00000185477	GPRIN3	GRIN3	GPRIN family member 3	protein-coding	0.000000	0.604706	
chunk0064_46_1	chr14	89702075	89702660	+	0	NA	Intergenic	Intergenic	-83217	NM_001085471	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.006838	0.414676	
chunk0177_214_1	chr7	24127760	24128437	+	0	NA	Intergenic	Intergenic	-156090	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.004431	0.302360	
chunk0211_343_1	chrX	125062836	125063234	+	0	NA	Intergenic	L3|LINE|CR1	-99218	NM_001163278	10178	Hs.23796	NM_014253	ENSG00000009694	TENM1	ODZ1|ODZ3|TEN-M1|TNM|TNM1|ten-1	teneurin transmembrane protein 1	protein-coding	0.000000	0.348371	
chunk0066_193_1	chr15	33218056	33218636	+	0	NA	Intergenic	L1PB3|LINE|L1	-23613	NM_001277313	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.003448	0.330465	
chunk0021_318_1	chr1	245258307	245258958	+	0	NA	intron (NM_018012, intron 2 of 14)	intron (NM_018012, intron 2 of 14)	103647	NM_018012	55083	Hs.143134	NM_018012	ENSG00000162849	KIF26B	-	kinesin family member 26B	protein-coding	0.019969	0.544479	
chunk0161_425_1	chr5	178372152	178372351	+	0	NA	intron (NM_173465, intron 2 of 28)	intron (NM_173465, intron 2 of 28)	-139429	NM_001278346	85007	Hs.248746	NM_153373	ENSG00000175309	PHYKPL	AGXT2L2|PHLU	5-phosphohydroxy-L-lysine phospho-lyase	protein-coding	0.045226	0.585000	
chunk0149_260_1	chr5	23958215	23958414	+	0	NA	intron (NR_131245, intron 1 of 4)	L1PA10|LINE|L1	6966	NR_131245	439936	Hs.638078	NR_131245	ENSG00000248874	C5orf17	-	chromosome 5 open reading frame 17 (putative)	ncRNA	0.005025	0.370000	
chunk0078_205_1	chr17	5359598	5359819	+	0	NA	intron (NM_001083585, intron 8 of 16)	intron (NM_001083585, intron 8 of 16)	-59933	NR_027679	84268	Hs.462086	NM_032308	ENSG00000129197	RPAIN	HRIP|RIP	RPA interacting protein	protein-coding	0.009050	0.297297	
chunk0012_307_1	chr1	162225015	162225312	+	0	NA	intron (NM_001164757, intron 2 of 9)	intron (NM_001164757, intron 2 of 9)	68056	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.006734	0.486577	
chunk0111_389_1	chr20	34135655	34135854	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-23398	NM_003908	8894	Hs.429180	NM_003908	ENSG00000125977	EIF2S2	EIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta	eukaryotic translation initiation factor 2 subunit beta	protein-coding	0.010050	0.405000	
chunk0139_380_1	chr4	61240516	61241042	+	0	NA	Intergenic	L2b|LINE|L2	-256342	NM_015236	23284	Hs.28391	NM_015236	ENSG00000150471	ADGRL3	CIRL3|CL3|LEC3|LPHN3	adhesion G protein-coupled receptor L3	protein-coding	0.001901	0.278937	
chunk0114_218_1	chr21	15659206	15659796	+	0	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	-70524	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.005085	0.306261	
chunk0071_37_1	chr15	79777857	79778883	+	0	NA	Intergenic	Intergenic	118627	NR_037654	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.005848	0.429406	725(AAGAACACAGTGAGCC,-,0.00),726(AGAACACAGTGAGCCA,+,0.00)
chunk0014_302_1	chr1	181040464	181040663	+	0	NA	intron (NM_001310213, intron 3 of 6)	intron (NM_001310213, intron 3 of 6)	7138	NM_001310213	3140	Hs.13500	NM_001531	ENSG00000153029	MR1	HLALS	major histocompatibility complex, class I-related	protein-coding	0.005025	0.525000	
chunk0107_386_1	chr2	223471318	223471745	+	0	NA	Intergenic	MER66-int|LTR|ERV1	130968	NM_003469	7857	Hs.516726	NM_003469	ENSG00000171951	SCG2	CHGC|EM66|SN|SgII	secretogranin II	protein-coding	0.004684	0.415888	
chunk0160_188_1	chr5	154296802	154297238	+	0	NA	intron (NM_198321, intron 2 of 11)	intron (NM_198321, intron 2 of 11)	-50086	NR_031626	100302181		NR_031626	ENSG00000221430	MIR1294	MIRN1294|hsa-mir-1294|mir-1294	microRNA 1294	ncRNA	0.006881	0.450801	
chunk0050_2_1	chr12	99063168	99063565	+	0	NA	intron (NM_001204066, intron 3 of 11)	MamRTE1|LINE|RTE-BovB	-29993	NR_110095	101928937	Hs.555499	NR_110095	ENSG00000258039	LOC101928937	-	uncharacterized LOC101928937	ncRNA	0.007557	0.459799	185(GAGGACAAGCAGTGCT,-,0.00),186(AGGACAAGCAGTGCTA,+,0.00)
chunk0024_289_1	chr10	42080481	42080909	+	0	NA	Intergenic	Intergenic	287350	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.056075	0.375291	
chunk0083_1_1	chr17	62308555	62308900	+	0	NA	Intergenic	Intergenic	-33072	NR_027486	440452	Hs.448884	NR_027486	ENSG00000188755	TBC1D3P2	-	TBC1 domain family member 3 pseudogene 2	pseudo	0.005797	0.338150	
chunk0017_61_1	chr1	205497265	205497865	+	0	NA	Intergenic	Intergenic	-6991	NM_002596	5129	Hs.445402	NM_002596	ENSG00000117266	CDK18	PCTAIRE|PCTAIRE3|PCTK3	cyclin dependent kinase 18	protein-coding	0.013333	0.517471	281(GTGTACACAGTGTTCC,-,0.00),282(TGTACACAGTGTTCCT,+,0.00)
chunk0103_103_1	chr2	161314506	161315267	+	0	NA	intron (NM_005805, intron 1 of 11)	L1MB5|LINE|L1	6611	NM_005805	10213	Hs.740477	NM_005805	ENSG00000115233	PSMD14	PAD1|POH1|RPN11	proteasome 26S subunit, non-ATPase 14	protein-coding	0.006570	0.367454	
chunk0101_111_1	chr2	125711030	125711446	+	0	NA	Intergenic	Intergenic	-944697	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.004808	0.386091	
chunk0096_461_1	chr2	40181874	40182253	+	0	NA	intron (NM_021097, intron 1 of 9)	intron (NM_021097, intron 1 of 9)	248241	NM_001252624	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.007916	0.439474	
chunk0188_87_1	chr8	8600702	8601290	+	0	NA	Intergenic	Intergenic	-101160	NM_194284	137075	Hs.183617	NM_194284	ENSG00000253958	CLDN23	CLDNL|hCG1646163	claudin 23	protein-coding	0.017007	0.461800	
chunk0209_112_1	chrX	40501509	40501708	+	0	NA	Intergenic	Intergenic	-79356	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.015075	0.590000	
chunk0089_221_1	chr18	61388135	61388571	+	0	NA	Intergenic	Intergenic	-102189	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.004587	0.375286	
chunk0091_246_1	chr19	10740749	10741286	+	0	NA	intron (NM_001005360, intron 1 of 20)	L1M4|LINE|L1	22613	NR_030368	693223		NR_030368	ENSG00000207972	MIR638	MIRN638|hsa-mir-638	microRNA 638	ncRNA	0.009311	0.338290	
chunk0135_152_1	chr3	187739100	187740076	+	0	NA	intron (NM_001706, intron 1 of 9)	intron (NM_001706, intron 1 of 9)	-3091	NM_001130845	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.060451	0.547595	429(GGGGACATTGTGTCCT,-,0.00),430(GGGACATTGTGTCCTG,+,0.00),803(AGGCACTAACTGTCCT,-,0.00),804(GGCACTAACTGTCCTT,+,0.00)
chunk0074_14_1	chr16	19860197	19860893	+	0	NA	intron (NM_001304771, intron 3 of 3)	intron (NM_001304771, intron 3 of 3)	24366	NM_016235	51704	Hs.148685	NM_016235	ENSG00000167191	GPRC5B	RAIG-2|RAIG2	G protein-coupled receptor class C group 5 member B	protein-coding	0.027299	0.463415	
chunk0033_202_1	chr11	16818423	16818770	+	0	NA	intron (NM_175058, intron 10 of 22)	L2c|LINE|L2	79995	NM_014267	10944	Hs.368226	NM_014267	ENSG00000110696	C11orf58	IMAGE145052|SMAP	chromosome 11 open reading frame 58	protein-coding	0.011527	0.448276	
chunk0161_97_1	chr5	167365688	167365910	+	0	NA	intron (NM_001122679, intron 1 of 28)	L1M5|LINE|L1	80961	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.000000	0.309417	
chunk0010_87_1	chr1	113488597	113488806	+	0	NA	intron (NM_152900, intron 1 of 20)	L1PA13|LINE|L1	97848	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.004785	0.566667	
chunk0032_214_1	chr11	7533052	7533758	+	0	NA	intron (NM_003621, intron 1 of 23)	L2c|LINE|L2	19640	NM_003621	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.007082	0.445545	
chunk0133_318_1	chr3	172449720	172449979	+	0	NA	Intergenic	CpG	-1393	NM_198407	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.069498	0.603846	
chunk0091_375_1	chr19	15623021	15623343	+	0	NA	exon (NM_007253, exon 7 of 13)	exon (NM_007253, exon 7 of 13)	7964	NM_007253	11283	Hs.268554	NM_007253	ENSG00000186526	CYP4F8	CPF8|CYPIVF8	cytochrome P450 family 4 subfamily F member 8	protein-coding	0.031056	0.563467	163(AAGGACTTCCTGTACT,-,0.00),164(AGGACTTCCTGTACTT,+,0.00)
chunk0059_369_1	chr14	37330433	37330938	+	0	NA	intron (NM_001195296, intron 11 of 14)	intron (NM_001195296, intron 11 of 14)	132772	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.001980	0.337945	
chunk0126_237_1	chr3	79167216	79167576	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-147937	NM_001145845	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.002778	0.335180	
chunk0158_436_1	chr5	135486593	135486894	+	0	NA	Intergenic	Intergenic	-34344	NM_001099221	497189	Hs.552091	NM_001099221	ENSG00000255833	TIFAB	-	TIFA inhibitor	protein-coding	0.023256	0.500000	
chunk0108_195_1	chr2	232310780	232311498	+	0	NA	intron (NR_046476, intron 14 of 20)	intron (NR_046476, intron 14 of 20)	-67395	NM_001632	250	Hs.284255	NM_001632	ENSG00000163283	ALPP	ALP|ALPI|IAP|PALP|PLAP|PLAP-1	alkaline phosphatase, placental	protein-coding	0.004178	0.477051	
chunk0149_79_1	chr5	17289688	17289967	+	0	NA	Intergenic	L2|LINE|L2	72266	NM_006317	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.017921	0.514286	
chunk0175_131_1	chr7	3426059	3426370	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	124766	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.016077	0.490385	
chunk0055_174_1	chr13	60855882	60856343	+	0	NA	Intergenic	MIRb|SINE|MIR	183157	NR_047003	101926930	Hs.578045	NR_047003		LINC00378	-	long intergenic non-protein coding RNA 378	ncRNA	0.002169	0.322511	
chunk0010_28_1	chr1	112462291	112462884	+	0	NA	promoter-TSS (NR_036210)	promoter-TSS (NR_036210)	-754	NR_036210	100422976		NR_036210	ENSG00000283296	MIR4256	-	microRNA 4256	ncRNA	0.010118	0.447811	
chunk0102_15_1	chr2	141492793	141493208	+	0	NA	intron (NM_018557, intron 2 of 90)	MIRb|SINE|MIR	638701	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.007229	0.312500	158(GAAAACAAACTGTCCT,-,0.00),159(AAAACAAACTGTCCTT,+,0.00),252(GAGCACATAATGTCCA,-,0.00),253(AGCACATAATGTCCAT,+,0.00)
chunk0092_56_1	chr19	20044127	20044377	+	0	NA	Intergenic	Intergenic	-4784	NM_033196	91120	Hs.306298	NM_033196	ENSG00000197124	ZNF682	BC39498_3	zinc finger protein 682	protein-coding	0.004000	0.517928	154(AGGAACAGTGTGGGCT,-,0.00),155(GGAACAGTGTGGGCTT,+,0.00)
chunk0064_11_1	chr14	89298522	89298883	+	0	NA	intron (NM_005197, intron 3 of 5)	intron (NM_005197, intron 3 of 5)	118408	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.005540	0.430939	
chunk0068_373_1	chr15	58235424	58235860	+	0	NA	Intergenic	Intergenic	97433	NM_020980	366	Hs.104624	NM_020980	ENSG00000103569	AQP9	AQP-9|HsT17287|SSC1|T17287	aquaporin 9	protein-coding	0.004587	0.370709	
chunk0037_370_1	chr11	78168318	78169047	+	0	NA	intron (NR_102281, intron 2 of 2)	intron (NR_102281, intron 2 of 2)	19947	NM_001029859	283219	Hs.528439	NM_001029859	ENSG00000188997	KCTD21	KCASH2	potassium channel tetramerization domain containing 21	protein-coding	0.019204	0.527397	
chunk0006_217_1	chr1	68307979	68308435	+	0	NA	Intergenic	Intergenic	-75606	NM_024911	79971	Hs.647659	NM_024911	ENSG00000116729	WLS	C1orf139|EVI|GPR177|MRP|mig-14	Wnt ligand secretion mediator	protein-coding	0.002193	0.376368	199(CAGAAGAGAGTGTTCT,-,0.00),200(AGAAGAGAGTGTTCTC,+,0.00)
chunk0149_379_1	chr5	28421290	28421550	+	0	NA	Intergenic	Intergenic	-505450	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.007692	0.314176	
chunk0174_47_1	chr6	154731891	154732471	+	0	NA	Intergenic	L2a|LINE|L2	-1197	NM_001286188	22828	Hs.591329	NM_014892	ENSG00000213079	SCAF8	RBM16	SR-related CTD associated factor 8	protein-coding	0.010345	0.464716	
chunk0048_437_1	chr12	88522774	88523521	+	0	NA	intron (NM_000899, intron 3 of 9)	intron (NM_000899, intron 3 of 9)	57326	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.016064	0.390374	
chunk0134_235_1	chr3	179026864	179027772	+	0	NA	intron (NM_022470, intron 5 of 5)	intron (NM_022470, intron 5 of 5)	44550	NM_022470	64393	Hs.371609	NM_022470	ENSG00000172667	ZMAT3	PAG608|WIG-1|WIG1	zinc finger matrin-type 3	protein-coding	0.007709	0.370737	516(AGGTACAGAATGTACC,-,0.00),517(GGTACAGAATGTACCC,+,0.00)
chunk0182_219_1	chr7	96370059	96370410	+	0	NA	Intergenic	L1MC1|LINE|L1	-48087	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.002849	0.355114	
chunk0069_3_1	chr15	60006477	60007089	+	0	NA	TTS (NM_012182)	TTS (NM_012182)	2561	NM_012182	27023	Hs.734475	NM_012182	ENSG00000171956	FOXB1	FKH5|HFKH-5	forkhead box B1	protein-coding	0.031046	0.460033	
chunk0035_4_1	chr11	39794305	39794558	+	0	NA	Intergenic	Intergenic	498699	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.011858	0.334646	
chunk0080_249_1	chr17	30344548	30345201	+	0	NA	Intergenic	Intergenic	-10827	NM_206832	388364	Hs.371005	NM_206832	ENSG00000182271	TMIGD1	TMIGD|UNQ9372	transmembrane and immunoglobulin domain containing 1	protein-coding	0.009188	0.464832	
chunk0138_155_1	chr4	37478775	37478974	+	0	NA	intron (NM_001104629, intron 1 of 3)	intron (NM_001104629, intron 1 of 3)	24944	NM_001104629	55286	Hs.107527	NM_018302	ENSG00000154274	C4orf19	-	chromosome 4 open reading frame 19	protein-coding	0.005025	0.355000	
chunk0188_306_1	chr8	16537779	16538010	+	0	NA	Intergenic	Intergenic	-345103	NM_138716	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.004329	0.310345	62(AAGCACATGTTGTTTT,-,0.00),63(AGCACATGTTGTTTTT,+,0.00),97(TAGAACATTGTGTTCT,-,0.00),98(AGAACATTGTGTTCTA,+,0.00)
chunk0183_452_1	chr7	111387185	111387622	+	0	NA	intron (NM_032549, intron 3 of 5)	intron (NM_032549, intron 3 of 5)	174888	NM_032549	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.002288	0.340183	185(AAGAACACTTTGTTAC,-,0.00)
chunk0087_49_1	chr18	31422197	31422578	+	0	NA	intron (NR_110788, intron 1 of 3)	intron (NR_110788, intron 1 of 3)	4601	NR_110788	101927718	Hs.625473	NR_110788	ENSG00000266729	DSG1-AS1	-	DSG1 antisense RNA 1	ncRNA	0.002625	0.293194	
chunk0035_293_1	chr11	46947310	46947859	+	0	NA	intron (NM_001278222, intron 1 of 7)	intron (NM_001278222, intron 1 of 7)	10895	NM_001003678	79096	Hs.368296	NM_024113	ENSG00000149179	C11orf49	-	chromosome 11 open reading frame 49	protein-coding	0.003643	0.354545	
chunk0125_37_1	chr3	62643858	62644288	+	0	NA	intron (NM_003716, intron 6 of 29)	intron (NM_003716, intron 6 of 29)	231316	NM_183394	8618	Hs.654933	NM_003716	ENSG00000163618	CADPS	CADPS1|CAPS|CAPS1|UNC-31	calcium dependent secretion activator	protein-coding	0.006977	0.406032	
chunk0054_355_1	chr13	49597192	49597750	+	0	NA	Intergenic	Intergenic	-11888	NM_018191	55213	Hs.508021	NM_018191	ENSG00000136144	RCBTB1	CLLD7|CLLL7|GLP|RDEOA	RCC1 and BTB domain containing protein 1	protein-coding	0.017921	0.461538	
chunk0132_19_1	chr3	154465030	154465652	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-35626	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.003215	0.373997	
chunk0096_338_1	chr2	35473184	35473580	+	0	NA	Intergenic	Intergenic	1977	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.002525	0.304786	202(AGGAACAACTAGTACT,-,0.00)
chunk0053_149_1	chr13	30240343	30240641	+	0	NA	exon (NM_032116, exon 6 of 11)	exon (NM_032116, exon 6 of 11)	66562	NM_001014380	84056	Hs.243596	NM_032116	ENSG00000102781	KATNAL1	-	katanin catalytic subunit A1 like 1	protein-coding	0.000000	0.357860	
chunk0090_134_1	chr18	71879851	71880301	+	0	NA	Intergenic	Intergenic	-97850	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.008889	0.321508	
chunk0062_360_1	chr14	73884645	73885592	+	0	NA	3' UTR (NM_152444, exon 10 of 10)	3' UTR (NM_152444, exon 10 of 10)	-1497	NM_021188	57862	Hs.270869	NM_021188	ENSG00000119725	ZNF410	APA-1|APA1	zinc finger protein 410	protein-coding	0.011616	0.415612	
chunk0019_199_1	chr1	226833193	226833596	+	0	NA	Intergenic	MER21B|LTR|ERVL	-37178	NM_012486	5664	Hs.25363	NM_000447	ENSG00000143801	PSEN2	AD3L|AD4|CMD1V|PS2|STM2	presenilin 2	protein-coding	0.009926	0.460396	
chunk0056_219_1	chr13	88189599	88190286	+	0	NA	intron (NR_131919, intron 1 of 4)	intron (NR_131919, intron 1 of 4)	47075	NR_131919	105370306	Hs.560133	NR_131919	ENSG00000231019	LINC00373	-	long intergenic non-protein coding RNA 373	ncRNA	0.002911	0.327035	
chunk0202_111_1	chr9	72573928	72574289	+	0	NA	intron (NM_138691, intron 1 of 23)	L1PA14|LINE|L1	52307	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.005540	0.406077	
chunk0026_399_1	chr10	69845732	69846142	+	0	NA	intron (NM_080798, intron 3 of 34)	L2b|LINE|L2	44049	NM_080798	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.012195	0.484185	
chunk0145_164_1	chr4	147232684	147233161	+	0	NA	Intergenic	Intergenic	111795	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.000000	0.330544	
chunk0156_340_1	chr5	111790156	111790709	+	0	NA	intron (NM_001142474, intron 2 of 3)	L1M5|LINE|L1	-32214	NM_001142476	9315	Hs.36053	NM_004772	ENSG00000134986	NREP	C5orf13|D4S114|P311|PRO1873|PTZ17|SEZ17	neuronal regeneration related protein	protein-coding	0.001808	0.324910	
chunk0076_321_1	chr16	70614550	70615114	+	0	NA	intron (NM_001172771, intron 1 of 6)	intron (NM_001172771, intron 1 of 6)	-9160	NM_001172772	146433	Hs.461214	NM_152456	ENSG00000157368	IL34	C16orf77|IL-34	interleukin 34	protein-coding	0.007092	0.403540	
chunk0009_80_1	chr1	101017252	101017496	+	0	NA	intron (NM_015958, intron 3 of 7)	intron (NM_015958, intron 3 of 7)	8432	NM_001077395	51611	Hs.440776	NM_015958	ENSG00000117543	DPH5	AD-018|CGI-30|HSPC143|NPD015	diphthamide biosynthesis 5	protein-coding	0.008197	0.334694	
chunk0179_9_1	chr7	42466801	42467090	+	0	NA	Intergenic	Intergenic	-229926	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.010381	0.510345	
chunk0131_136_1	chr3	144932008	144932349	+	0	NA	Intergenic	L1MA2|LINE|L1	958853	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.002933	0.505848	
chunk0038_67_1	chr11	83045238	83045709	+	0	NA	intron (NM_014488, intron 1 of 5)	L2c|LINE|L2	-3875	NR_033347	100379250	Hs.725115	NR_033347	ENSG00000207221	SNORA70E	U70E	small nucleolar RNA, H/ACA box 70E	snoRNA	0.008493	0.449153	
chunk0155_444_1	chr5	101603737	101604128	+	0	NA	Intergenic	L1MD1|LINE|L1	692617	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.005115	0.316327	
chunk0123_190_1	chr3	44338438	44338784	+	0	NA	5' UTR (NM_173826, exon 1 of 11)	5' UTR (NM_173826, exon 1 of 11)	159	NM_173826	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.095376	0.731988	
chunk0151_64_1	chr5	42502849	42503261	+	0	NA	intron (NM_001242401, intron 2 of 10)	intron (NM_001242401, intron 2 of 10)	-44988	NM_001242402	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.004854	0.389831	
chunk0180_310_1	chr7	70712903	70713419	+	0	NA	intron (NM_015570, intron 6 of 18)	intron (NM_015570, intron 6 of 18)	-419376	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.009690	0.431335	250(AAAGACAAACTGTTCC,-,0.00),251(AAGACAAACTGTTCCA,+,0.00)
chunk0007_423_1	chr1	86433745	86434736	+	0	NA	intron (NM_006536, intron 5 of 13)	intron (NM_006536, intron 5 of 13)	10154	NM_006536	9635	Hs.241551	NM_006536	ENSG00000137975	CLCA2	CACC|CACC3|CLCRG2|CaCC-3	chloride channel accessory 2	protein-coding	0.002018	0.371976	
chunk0021_131_1	chr10	3810082	3810627	+	0	NA	Intergenic	Intergenic	-25073	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.011009	0.461538	252(GAGAACGGTGAGTTCC,-,0.00),253(AGAACGGTGAGTTCCC,+,0.00)
chunk0105_192_1	chr2	187592157	187592639	+	0	NA	Intergenic	Intergenic	-37906	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.004149	0.312629	
chunk0118_249_1	chr22	32852844	32853090	+	0	NA	intron (NM_000362, intron 2 of 4)	intron (NM_000362, intron 2 of 4)	52151	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.016260	0.562753	128(GGGGACATTATGTCCC,-,0.00),129(GGGACATTATGTCCCA,+,0.00)
chunk0201_15_1	chr9	33061626	33061976	+	0	NA	intron (NM_018225, intron 5 of 11)	intron (NM_018225, intron 5 of 11)	14915	NM_018225	55234	Hs.655351	NM_018225	ENSG00000122692	SMU1	BWD|SMU-1|fSAP57	SMU1 DNA replication regulator and spliceosomal factor	protein-coding	0.000000	0.461538	
chunk0147_56_1	chr4	172614918	172615200	+	0	NA	intron (NM_001034845, intron 5 of 12)	intron (NM_001034845, intron 5 of 12)	73858	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.010638	0.381625	
chunk0194_407_1	chr8	91250139	91250610	+	0	NA	intron (NM_001282356, intron 3 of 19)	intron (NM_001282356, intron 3 of 19)	1086	NM_134266	115111	Hs.354013	NM_052832	ENSG00000147606	SLC26A7	SUT2	solute carrier family 26 member 7	protein-coding	0.004246	0.358051	
chunk0087_141_1	chr18	33907242	33907817	+	0	NA	intron (NM_001198548, intron 7 of 8)	intron (NM_001198548, intron 7 of 8)	141083	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.006957	0.336806	
chunk0120_416_1	chr3	12964729	12965068	+	0	NA	intron (NM_001134382, intron 1 of 13)	intron (NM_001134382, intron 1 of 13)	2800	NM_014869	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.008850	0.479412	
chunk0039_172_1	chr11	99780563	99781012	+	0	NA	intron (NM_175566, intron 1 of 21)	intron (NM_175566, intron 1 of 21)	224642	NM_175566	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.004454	0.331111	224(AGGAACACACTGTGCC,-,0.00),225(GGAACACACTGTGCCA,+,0.00)
chunk0073_330_1	chr16	14472021	14472664	+	0	NA	intron (NM_002582, intron 22 of 23)	intron (NM_002582, intron 22 of 23)	-102076	NR_131191	105447648	Hs.554151	NR_131191	ENSG00000260009	LINC02130	-	long intergenic non-protein coding RNA 2130	ncRNA	0.007776	0.386646	319(GAGAACAGGCTGATCC,-,0.00),320(AGAACAGGCTGATCCT,+,0.00)
chunk0098_94_1	chr2	67812400	67812951	+	0	NA	intron (NR_110271, intron 2 of 2)	L1PB1|LINE|L1	12887	NR_110271	101927701	Hs.348697	NR_110271	ENSG00000237013	LINC01812	-	long intergenic non-protein coding RNA 1812	ncRNA	0.000000	0.346014	
chunk0007_283_1	chr1	83872364	83872939	+	0	NA	intron (NM_024686, intron 20 of 20)	intron (NM_024686, intron 20 of 20)	-11655	NR_119375	101927587	Hs.621230	NR_119375	ENSG00000233008	LINC01725	-	long intergenic non-protein coding RNA 1725	ncRNA	0.005217	0.333333	
chunk0168_345_1	chr6	93036943	93037408	+	0	NA	Intergenic	L1PA15-16|LINE|L1	382407	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.002151	0.493562	179(GAGTACACAGTGGCCT,-,0.00)
chunk0022_446_1	chr10	19785485	19786008	+	0	NA	Intergenic	L1PREC2|LINE|L1	-30697	NM_032812	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.009560	0.360687	
chunk0188_247_1	chr8	14331397	14331596	+	0	NA	intron (NM_139167, intron 2 of 7)	intron (NM_139167, intron 2 of 7)	522014	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.000000	0.335000	
chunk0202_332_1	chr9	78548784	78548983	+	0	NA	Intergenic	Intergenic	251808	NM_021154	29968	Hs.494261	NM_021154	ENSG00000135069	PSAT1	EPIP|NLS2|PSA|PSAT|PSATD	phosphoserine aminotransferase 1	protein-coding	0.015075	0.385000	
chunk0171_391_1	chr6	131134270	131135085	+	0	NA	Intergenic	Intergenic	-1009	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.014724	0.371324	334(GGGAACTGGTTGTACT,-,0.00),335(GGAACTGGTTGTACTT,+,0.00)
chunk0091_86_1	chr19	5372613	5372924	+	0	NA	Intergenic	Intergenic	-31965	NM_130853	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.003215	0.445513	
chunk0104_99_1	chr2	172378679	172378903	+	0	NA	Intergenic	LTR90A|LTR|LTR	-48563	NM_001316306	3655	Hs.133397	NM_000210	ENSG00000091409	ITGA6	CD49f|ITGA6B|VLA-6	integrin subunit alpha 6	protein-coding	0.004464	0.395556	
chunk0030_411_1	chr10	120193331	120193734	+	0	NA	Intergenic	L1MA4A|LINE|L1	161691	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.004963	0.339109	267(TAGACCAGGGTGTTCC,-,0.00),268(AGACCAGGGTGTTCCC,+,0.00)
chunk0132_441_1	chr3	165133434	165133928	+	0	NA	Intergenic	Intergenic	-55186	NM_001041	6476	Hs.429596	NM_001041	ENSG00000090402	SI	-	sucrase-isomaltase	protein-coding	0.000000	0.296970	
chunk0140_439_1	chr4	76207366	76207774	+	0	NA	intron (NM_005506, intron 1 of 11)	intron (NM_005506, intron 1 of 11)	6329	NM_005506	950	Hs.349656	NM_005506	ENSG00000138760	SCARB2	AMRF|CD36L2|EPM4|HLGP85|LGP85|LIMP-2|LIMPII|SR-BII	scavenger receptor class B member 2	protein-coding	0.000000	0.378973	
chunk0163_239_1	chr6	12331865	12332310	+	0	NA	Intergenic	L2b|LINE|L2	41791	NM_001168319	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.006742	0.448430	
chunk0004_432_1	chr1	52913218	52913505	+	0	NA	intron (NM_018281, intron 1 of 8)	L2|LINE|L2	8413	NM_018281	55268	Hs.476319	NM_018281	ENSG00000121310	ECHDC2	-	enoyl-CoA hydratase domain containing 2	protein-coding	0.006969	0.423611	
chunk0191_343_1	chr8	56074596	56074843	+	0	NA	promoter-TSS (NM_001146227)	promoter-TSS (NM_001146227)	-138	NM_001146227	6224	Hs.8102	NM_001023	ENSG00000008988	RPS20	S20|uS10	ribosomal protein S20	protein-coding	0.076923	0.616935	
chunk0167_450_1	chr6	76127304	76127750	+	0	NA	Intergenic	Intergenic	-54849	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.008969	0.353468	
chunk0138_453_1	chr4	47462615	47462826	+	0	NA	intron (NM_017845, intron 1 of 4)	MIR3|SINE|MIR	939	NM_017845	54951	Hs.23956	NM_017845	ENSG00000169019	COMMD8	-	COMM domain containing 8	protein-coding	0.000000	0.400943	
chunk0207_310_1	chr9	133842157	133842601	+	0	NA	intron (NM_001134398, intron 3 of 29)	intron (NM_001134398, intron 3 of 29)	-102424	NM_007101	1757	Hs.198003	NM_007101	ENSG00000123453	SARDH	BPR-2|DMGDHL1|SAR|SARD|SDH	sarcosine dehydrogenase	protein-coding	0.038288	0.584270	219(GAGAACAGGCAGAGCC,-,0.00),220(AGAACAGGCAGAGCCT,+,0.00)
chunk0188_365_1	chr8	18083198	18084499	+	0	NA	intron (NM_004315, intron 1 of 13)	CpG	522	NM_177924	427	Hs.527412	NM_004315	ENSG00000104763	ASAH1	AC|ACDase|ASAH|PHP|PHP32|SMAPME	N-acylsphingosine amidohydrolase 1	protein-coding	0.071483	0.599846	679(CAGCACGAGGTGTTCC,-,0.00),680(AGCACGAGGTGTTCCT,+,0.00),1242(GGGTGCAGCCTGTCCC,-,0.00),1243(GGTGCAGCCTGTCCCG,+,0.00)
chunk0193_164_1	chr8	74741601	74742102	+	0	NA	intron (NR_033830, intron 4 of 5)	Tigger17c|DNA|TcMar-Tigger	36158	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.011976	0.396414	
chunk0121_329_1	chr3	24379881	24380876	+	0	NA	intron (NM_001128176, intron 1 of 10)	L2|LINE|L2	-113709	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.004020	0.387550	
chunk0105_356_1	chr2	191724494	191725184	+	0	NA	Intergenic	Intergenic	34658	NR_131917	105747689	Hs.104972	NR_131917		LOC105747689	-	uncharacterized LOC105747689	ncRNA	0.004348	0.286541	308(GGGCACGTCATGTTCC,-,0.00),309(GGCACGTCATGTTCCC,+,0.00)
chunk0034_70_1	chr11	27173884	27174358	+	0	NA	intron (NR_125766, intron 2 of 4)	intron (NR_125766, intron 2 of 4)	44647	NR_125768	103695435	Hs.196133	NR_125766	ENSG00000254560	BBOX1-AS1	-	BBOX1 antisense RNA 1	ncRNA	0.008439	0.427368	
chunk0112_217_1	chr20	40664231	40664475	+	0	NA	Intergenic	Intergenic	24887	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.020492	0.640816	
chunk0159_154_1	chr5	139341703	139341902	+	0	NA	promoter-TSS (NR_109830)	promoter-TSS (NR_109830)	-30	NM_016480	51247	Hs.396644	NM_016480	ENSG00000120727	PAIP2	PAIP-2|PAIP2A	poly(A) binding protein interacting protein 2	protein-coding	0.115578	0.655000	
chunk0202_274_1	chr9	77150777	77151187	+	0	NA	Intergenic	Intergenic	-26463	NM_033305	23230	Hs.459790	NM_015186	ENSG00000197969	VPS13A	CHAC|CHOREIN	vacuolar protein sorting 13 homolog A	protein-coding	0.004878	0.423358	
chunk0176_139_1	chr7	12730153	12730849	+	0	NA	Intergenic	Intergenic	43215	NM_001195396	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.002874	0.362984	
chunk0021_312_1	chr1	245016352	245017223	+	0	NA	intron (NM_001290327, intron 2 of 7)	intron (NM_001290327, intron 2 of 7)	-45918	NR_111907	101928068	Hs.134857	NR_111907		LOC101928068	-	uncharacterized LOC101928068	ncRNA	0.011481	0.389908	
chunk0109_273_1	chr20	8094243	8095036	+	0	NA	Intergenic	LTR85b|LTR|Gypsy?	-37626	NM_015192	23236	Hs.431173	NM_015192	ENSG00000182621	PLCB1	EIEE12|PI-PLC|PLC-154|PLC-I|PLC-beta-1|PLC154|PLCB1A|PLCB1B	phospholipase C beta 1	protein-coding	0.003783	0.386650	
chunk0077_304_1	chr16	81768093	81768545	+	0	NA	Intergenic	L1ME1|LINE|L1	-10939	NM_002661	5336	Hs.372303	NM_002661	ENSG00000197943	PLCG2	APLAID|FCAS3|PLC-IV|PLC-gamma-2	phospholipase C gamma 2	protein-coding	0.013274	0.423841	
chunk0089_197_1	chr18	59983496	59983730	+	0	NA	Intergenic	Intergenic	83653	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.004274	0.442553	
chunk0137_182_1	chr4	17517680	17517879	+	0	NA	intron (NM_001079827, intron 1 of 2)	intron (NM_001079827, intron 1 of 2)	2614	NM_001079827	645104	Hs.631526	NM_001079827	ENSG00000249581	CLRN2	-	clarin 2	protein-coding	0.015075	0.490000	
chunk0168_276_1	chr6	90528786	90529350	+	0	NA	intron (NM_003188, intron 12 of 15)	intron (NM_003188, intron 12 of 15)	58233	NM_003188	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.005319	0.384071	151(TGCTCATTCTGTTCTT,+,0.00),286(GAGGACATGGAGTGCC,-,0.00),287(AGGACATGGAGTGCCT,+,0.00)
chunk0128_400_1	chr3	114104456	114104774	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	47880	NM_001256837	79691	Hs.477162	NM_024638	ENSG00000151576	QTRT2	QTRTD1	queuine tRNA-ribosyltransferase accessory subunit 2	protein-coding	0.009434	0.347962	
chunk0032_171_1	chr11	5519319	5519572	+	0	NA	intron (NR_133006, intron 2 of 2)	MIRb|SINE|MIR	2340	NR_133006	101927763		NR_133006		OLFM5P	-	olfactomedin family member 5, pseudogene	pseudo	0.003953	0.307087	
chunk0091_307_1	chr19	12864763	12865150	+	0	NA	intron (NM_014975, intron 13 of 25)	intron (NM_014975, intron 13 of 25)	12696	NR_106852	102466196		NR_106852	ENSG00000276181	MIR6794	hsa-mir-6794	microRNA 6794	ncRNA	0.036176	0.564433	
chunk0010_42_1	chr1	112748180	112748467	+	0	NA	Intergenic	Intergenic	27756	NM_182759	284467	Hs.439116	NM_182759	ENSG00000184599	TAFA3	FAM19A3|TAFA-3	TAFA chemokine like family member 3	protein-coding	0.041812	0.517361	
chunk0173_158_1	chr6	144287071	144287451	+	0	NA	Intergenic	Intergenic	-4476	NM_007124	7402	Hs.133135	NM_007124	ENSG00000152818	UTRN	DMDL|DRP|DRP1	utrophin	protein-coding	0.047368	0.527559	
chunk0135_396_1	chr3	192352968	192353451	+	0	NA	intron (NM_021032, intron 2 of 4)	intron (NM_021032, intron 2 of 4)	55840	NM_021032	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.008282	0.378099	
chunk0108_2_1	chr2	225861665	225862385	+	0	NA	Intergenic	L1MC3|LINE|L1	-280769	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.004167	0.323162	
chunk0122_176_1	chr3	32458197	32458467	+	0	NA	Intergenic	Intergenic	44579	NM_017801	54918	Hs.380627	NM_017801	ENSG00000091317	CMTM6	CKLFSF6|PRO2219	CKLF like MARVEL transmembrane domain containing 6	protein-coding	0.018519	0.446494	
chunk0029_35_1	chr10	96129718	96130131	+	0	NA	promoter-TSS (NM_001278525)	promoter-TSS (NM_001278525)	-132	NM_001278525	9849	Hs.600823	NM_014803	ENSG00000177853	ZNF518A	ZNF518	zinc finger protein 518A	protein-coding	0.072639	0.601449	
chunk0046_200_1	chr12	58959654	58960275	+	0	NA	Intergenic	Intergenic	-39426	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.001610	0.339228	
chunk0016_15_1	chr1	192844288	192844864	+	0	NA	Intergenic	Intergenic	35537	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.006944	0.391681	265(AGGCACATTCTGTTCT,-,0.00),266(GGCACATTCTGTTCTA,+,0.00)
chunk0094_443_1	chr2	11483077	11483357	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-17040	NM_001278276	1876	Hs.603093	NM_198256	ENSG00000169016	E2F6	E2F-6	E2F transcription factor 6	protein-coding	0.114286	0.665480	
chunk0003_18_1	chr1	28956246	28956549	+	0	NA	intron (NM_001166006, intron 1 of 14)	Penelope1_Vert|LINE|Penelope	41821	NM_001166006	2035	Hs.175437	NM_004437	ENSG00000159023	EPB41	4.1R|EL1|HE	erythrocyte membrane protein band 4.1	protein-coding	0.000000	0.368421	
chunk0165_342_1	chr6	37883214	37883502	+	0	NA	intron (NM_021943, intron 1 of 5)	intron (NM_021943, intron 1 of 5)	63827	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.006944	0.356401	
chunk0075_329_1	chr16	54657561	54658120	+	0	NA	Intergenic	Intergenic	270938	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.005367	0.425000	
chunk0151_153_1	chr5	49601488	49602423	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	839445	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.022460	0.409188	
chunk0211_217_1	chrX	118496359	118496879	+	0	NA	intron (NM_144658, intron 1 of 52)	intron (NM_144658, intron 1 of 52)	710	NM_144658	139818	Hs.368203	NM_144658	ENSG00000147251	DOCK11	ACG|ZIZ2|bB128O4.1	dedicator of cytokinesis 11	protein-coding	0.063462	0.637236	388(AGGGAGAGTGTGTCCC,-,0.00),389(GGGAGAGTGTGTCCCT,+,0.00)
chunk0166_258_1	chr6	47622134	47622351	+	0	NA	intron (NM_012120, intron 17 of 17)	L1PB1|LINE|L1	-34348	NM_153839	222611	Hs.724860	NM_153839	ENSG00000164393	ADGRF2	GPR111|PGR20|hGPCR35	adhesion G protein-coupled receptor F2	protein-coding	0.027650	0.582569	
chunk0063_397_1	chr14	87592883	87593354	+	0	NA	Intergenic	Intergenic	400153	NM_001201401	2581	Hs.513439	NM_000153	ENSG00000054983	GALC	-	galactosylceramidase	protein-coding	0.004246	0.338983	
chunk0119_5_1	chr22	39996089	39996695	+	0	NA	intron (NM_138435, intron 1 of 4)	MER53|DNA|hAT	1443	NM_138435	113828	Hs.26192	NM_138435	ENSG00000133477	FAM83F	-	family with sequence similarity 83 member F	protein-coding	0.011551	0.479407	
chunk0024_429_1	chr10	46047957	46048639	+	0	NA	Intergenic	Intergenic	-2029	NM_002443	4477	Hs.255462	NM_002443	ENSG00000263639	MSMB	HPC13|IGBF|MSP|MSPB|PN44|PRPS|PSP|PSP-94|PSP57|PSP94	microseminoprotein beta	protein-coding	0.002933	0.480234	
chunk0185_362_1	chr7	132782858	132783258	+	0	NA	Intergenic	Intergenic	134264	NR_046323	286023	Hs.671875	NM_173682	ENSG00000183470	FLJ40288	-	uncharacterized FLJ40288	ncRNA	0.002500	0.421446	
chunk0075_208_1	chr16	52561992	52562626	+	0	NA	intron (NR_033920, intron 3 of 3)	intron (NR_033920, intron 3 of 3)	-14507	NM_001146188	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.007886	0.507087	287(TGAAACAGTGTGTACC,-,0.00),288(GAAACAGTGTGTACCC,+,0.00)
chunk0190_280_1	chr8	37737067	37737304	+	0	NA	intron (NM_001003790, intron 1 of 6)	CpG-27161	241	NR_125821	102723701	Hs.588388	NR_125821	ENSG00000183154	LOC102723701	-	uncharacterized LOC102723701	ncRNA	0.050633	0.588235	
chunk0143_128_1	chr4	109610690	109611461	+	0	NA	intron (NM_017918, intron 1 of 7)	LTR68|LTR|ERV1	50876	NM_017918	55013	Hs.234149	NM_017918	ENSG00000005059	MCUB	CCDC109B	mitochondrial calcium uniporter dominant negative beta subunit	protein-coding	0.002594	0.379534	
chunk0208_61_1	chrX	11559095	11559605	+	0	NA	intron (NR_109776, intron 1 of 14)	L2c|LINE|L2	106351	NM_013427	395	Hs.435291	NM_001174	ENSG00000047648	ARHGAP6	RHOGAP6|RHOGAPX-1	Rho GTPase activating protein 6	protein-coding	0.003922	0.424658	
chunk0188_42_1	chr8	6651208	6651644	+	0	NA	intron (NR_125386, intron 1 of 4)	MER41C|LTR|ERV1	-29206	NR_107022	102465861		NR_107022	ENSG00000276580	MIR8055	hsa-mir-8055	microRNA 8055	ncRNA	0.009174	0.400458	
chunk0110_203_1	chr20	15005241	15005695	+	0	NA	intron (NM_080676, intron 5 of 16)	Tigger14a|DNA|TcMar-Tigger	-75950	NR_110318	100379174	Hs.407533	NR_037841	ENSG00000235914	MACROD2-AS1	BA318C17.1|NCRNA00186	MACROD2 antisense RNA 1	ncRNA	0.002203	0.375824	
chunk0175_312_1	chr6	166660241	166660850	+	0	NA	intron (NM_001006932, intron 2 of 21)	L2b|LINE|L2	-33307	NM_021135	6196	Hs.655277	NM_021135	ENSG00000071242	RPS6KA2	HU-2|MAPKAPK1C|RSK|RSK3|S6K-alpha|S6K-alpha2|p90-RSK3|p90RSK2|pp90RSK3	ribosomal protein S6 kinase A2	protein-coding	0.013136	0.436066	
chunk0103_405_1	chr2	169127395	169127621	+	0	NA	3' UTR (NM_004525, exon 79 of 79)	3' UTR (NM_004525, exon 79 of 79)	46401	NM_001142271	10170	Hs.179608	NM_005771	ENSG00000073737	DHRS9	3-alpha-HSD|3ALPHA-HSD|RDH-E2|RDH-TBE|RDH15|RDHL|RDHTBE|RETSDR8|SDR9C4	dehydrogenase/reductase 9	protein-coding	0.008850	0.414097	
chunk0165_220_1	chr6	35203642	35204064	+	0	NA	Intergenic	Intergenic	-10209	NM_001303136	222663	Hs.12923	NM_152753	ENSG00000146197	SCUBE3	CEGF3	signal peptide, CUB domain and EGF like domain containing 3	protein-coding	0.004739	0.517730	
chunk0183_324_1	chr7	108103653	108103863	+	0	NA	intron (NM_007356, intron 9 of 33)	intron (NM_007356, intron 9 of 33)	26598	NM_007356	22798	Hs.62022	NM_007356	ENSG00000091128	LAMB4	-	laminin subunit beta 4	protein-coding	0.009524	0.473934	
chunk0036_434_1	chr11	68480106	68480739	+	0	NA	intron (NM_001164161, intron 1 of 23)	L2a|LINE|L2	19704	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.006319	0.365931	
chunk0122_417_1	chr3	38952652	38952905	+	0	NA	intron (NM_001287223, intron 1 of 26)	L2b|LINE|L2	873	NM_001287223	11280	Hs.591657	NM_014139	ENSG00000168356	SCN11A	FEPS3|HSAN7|NAV1.9|NaN|PN5|SCN12A|SNS-2	sodium voltage-gated channel alpha subunit 11	protein-coding	0.003953	0.464567	178(AAGAACATGATGTCCA,-,0.00),179(AGAACATGATGTCCAG,+,0.00)
chunk0057_134_1	chr13	99774609	99775106	+	0	NA	intron (NR_104592, intron 2 of 9)	intron (NR_104592, intron 2 of 9)	-45856	NR_120383	101927465	Hs.130690	NR_046525		CLYBL-AS1	-	CLYBL antisense RNA 1	ncRNA	0.002012	0.349398	
chunk0155_250_1	chr5	95735961	95736373	+	0	NA	intron (NM_014899, intron 2 of 11)	intron (NM_014899, intron 2 of 11)	5021	NM_014899	22836	Hs.445030	NM_014899	ENSG00000164292	RHOBTB3	-	Rho related BTB domain containing 3	protein-coding	0.012136	0.370460	
chunk0142_195_1	chr4	96820716	96821094	+	0	NA	Intergenic	Intergenic	-546021	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.005291	0.337731	
chunk0177_171_1	chr7	23315243	23315916	+	0	NA	intron (NM_006547, intron 12 of 14)	intron (NM_006547, intron 12 of 14)	16258	NM_138446	115416	Hs.87385	NM_138446	ENSG00000156928	MALSU1	C7orf30|mtRsfA	mitochondrial assembly of ribosomal large subunit 1	protein-coding	0.011887	0.393175	
chunk0156_309_1	chr5	110726842	110727305	+	0	NA	promoter-TSS (NM_001039763)	promoter-TSS (NM_001039763)	-324	NM_001039763	642987	Hs.729154	NM_001039763	ENSG00000186952	TMEM232	-	transmembrane protein 232	protein-coding	0.021598	0.372845	
chunk0020_447_1	chr1	242222406	242222814	+	0	NA	intron (NM_001195812, intron 3 of 8)	intron (NM_001195812, intron 3 of 8)	-223527	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.019608	0.520782	
chunk0069_430_1	chr15	68337845	68338097	+	0	NA	intron (NM_001004439, intron 11 of 29)	intron (NM_001004439, intron 11 of 29)	60168	NM_015322	10116	Hs.362733	NM_015322	ENSG00000169018	FEM1B	F1A-ALPHA|F1AA|FEM1-beta	fem-1 homolog B	protein-coding	0.019841	0.521739	
chunk0035_330_1	chr11	47578854	47579059	+	0	NA	promoter-TSS (NM_018095)	promoter-TSS (NM_018095)	13	NM_016506	55709	Hs.718483	NM_016506	ENSG00000123444	KBTBD4	BKLHD4|HSPC252	kelch repeat and BTB domain containing 4	protein-coding	0.073171	0.611650	
chunk0198_125_1	chr8	131956083	131956413	+	0	NA	intron (NM_015137, intron 7 of 22)	intron (NM_015137, intron 7 of 22)	52139	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.003030	0.350453	
chunk0084_191_1	chr17	77968748	77969127	+	0	NA	Intergenic	Intergenic	-35300	NM_001142640	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.010554	0.410526	206(GTGAACACAGCGTTCT,-,0.00),207(TGAACACAGCGTTCTT,+,0.00)
chunk0096_332_1	chr2	35223653	35224259	+	0	NA	Intergenic	Intergenic	-247449	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.006601	0.316310	
chunk0012_375_1	chr1	163290155	163290767	+	0	NA	intron (NM_001254748, intron 2 of 5)	intron (NM_001254748, intron 2 of 5)	31330	NR_045630	8490	Hs.24950	NM_003617	ENSG00000143248	RGS5	MST092|MST106|MST129|MSTP032|MSTP092|MSTP106|MSTP129	regulator of G protein signaling 5	protein-coding	0.009804	0.380098	
chunk0144_23_1	chr4	124964291	124964981	+	0	NA	Intergenic	Intergenic	-251904	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.008696	0.366136	
chunk0078_277_1	chr17	7940762	7941202	+	0	NA	intron (NM_001037144, intron 9 of 18)	MER58A|DNA|hAT-Charlie	8858	NM_053051	116840	Hs.348012	NM_053051	ENSG00000170037	CNTROB	LIP8|PP1221	centrobin, centriole duplication and spindle assembly protein	protein-coding	0.015909	0.424036	
chunk0181_387_1	chr7	89665963	89666524	+	0	NA	Intergenic	Intergenic	-453157	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.007130	0.325623	
chunk0118_200_1	chr22	31586049	31586596	+	0	NA	intron (NM_001258327, intron 12 of 30)	L2c|LINE|L2	35209	NR_106959	102465666		NR_106959	ENSG00000284082	MIR7109	hsa-mir-7109	microRNA 7109	ncRNA	0.005484	0.479927	300(GAGTACAGCCTGTCCC,-,0.00),301(AGTACAGCCTGTCCCT,+,0.00)
chunk0007_31_1	chr1	77611528	77611878	+	0	NA	intron (NM_001308237, intron 4 of 13)	L1MA9|LINE|L1	70955	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.014286	0.347578	202(AGGGACAGTCAGTTCA,-,0.00),203(GGGACAGTCAGTTCAA,+,0.00)
chunk0082_309_1	chr17	59106033	59106470	+	0	NA	intron (NM_001005207, intron 1 of 24)	intron (NM_001005207, intron 1 of 24)	654	NM_001005207	4591	Hs.579079	NM_015294	ENSG00000108395	TRIM37	MUL|POB1|TEF3	tripartite motif containing 37	protein-coding	0.043478	0.577626	
chunk0178_73_1	chr7	30330042	30330685	+	0	NA	intron (NM_147128, intron 2 of 4)	intron (NM_147128, intron 2 of 4)	-39687	NR_002186	222161	Hs.112423	NR_002186		DKFZP586I1420	-	uncharacterized protein DKFZp586I1420	pseudo	0.000000	0.346273	
chunk0161_123_1	chr5	167987932	167988349	+	0	NA	intron (NM_001080428, intron 2 of 24)	intron (NM_001080428, intron 2 of 24)	233204	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.014388	0.418660	
chunk0088_216_1	chr18	48205675	48206211	+	0	NA	Intergenic	Intergenic	-68634	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.001866	0.426443	
chunk0107_94_1	chr2	213253390	213253613	+	0	NA	Intergenic	Intergenic	30704	NM_001242575									0.004484	0.379464	
chunk0148_15_1	chr5	335346	335545	+	0	NA	intron (NM_020731, intron 1 of 11)	L1M2|LINE|L1	31269	NM_001242412	57491	Hs.50823	NM_020731	ENSG00000286169	AHRR	AHH|AHHR|bHLHe77	aryl-hydrocarbon receptor repressor	protein-coding	0.005025	0.645000	
chunk0178_12_1	chr7	29100420	29100878	+	0	NA	intron (NM_019029, intron 3 of 12)	intron (NM_019029, intron 3 of 12)	-24384	NR_120523	101928168	Hs.666750	NR_120523	ENSG00000285412	LOC101928168	-	uncharacterized LOC101928168	ncRNA	0.006550	0.485839	
chunk0105_198_1	chr2	187716406	187717329	+	0	NA	Intergenic	Intergenic	-162375	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.004334	0.298701	
chunk0164_186_1	chr6	22066641	22067413	+	0	NA	intron (NR_015410, intron 8 of 11)	intron (NR_015410, intron 8 of 11)	80166	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.006477	0.386805	
chunk0012_246_1	chr1	161020568	161020991	+	0	NA	intron (NM_016946, intron 1 of 9)	intron (NM_016946, intron 1 of 9)	564	NM_016946	50848	Hs.517293	NM_016946	ENSG00000158769	F11R	CD321|JAM|JAM1|JAMA|JCAM|KAT|PAM-1	F11 receptor	protein-coding	0.052009	0.639151	
chunk0080_200_1	chr17	29180855	29181299	+	0	NA	promoter-TSS (NM_078471)	promoter-TSS (NM_078471)	-688	NM_203318	399687	Hs.462590	NM_078471	ENSG00000196535	MYO18A	MAJN|MYSPDZ|SP-R210|SPR210	myosin XVIIIA	protein-coding	0.006757	0.525843	
chunk0110_216_1	chr20	15406970	15407294	+	0	NA	intron (NM_001033087, intron 2 of 13)	LTR16C|LTR|ERVL	210274	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.024691	0.538462	
chunk0096_274_1	chr2	31944660	31945139	+	0	NA	intron (NM_001301852, intron 1 of 7)	L1ME3Cz|LINE|L1	65765	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.000000	0.306250	
chunk0199_401_1	chr9	13440116	13440598	+	0	NA	Intergenic	MIR|SINE|MIR	-9028	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.006224	0.368530	
chunk0200_264_1	chr9	21948995	21949317	+	0	NA	Intergenic	MSTA|LTR|ERVL-MaLR	-17983	NR_024274	51198	Hs.721053	NM_016349		CDKN2A-DT	C9orf53|CDKN2A-AS1|bA149I2.3	CDKN2A divergent transcript	ncRNA	0.000000	0.337461	
chunk0045_241_1	chr12	48925417	48925715	+	0	NA	promoter-TSS (NM_001143781)	promoter-TSS (NM_001143781)	-19	NM_016594	51303	Hs.655103	NM_016594	ENSG00000134285	FKBP11	FKBP19	FKBP prolyl isomerase 11	protein-coding	0.083893	0.672241	
chunk0053_100_1	chr13	28648511	28648823	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-10337	NM_015932	51371	Hs.268742	NM_015932	ENSG00000132963	POMP	C13orf12|HSPC014|PNAS-110|PRAAS2|UMP1	proteasome maturation protein	protein-coding	0.009615	0.348243	
chunk0079_181_1	chr17	14069102	14069453	+	0	NA	promoter-TSS (NM_001303)	promoter-TSS (NM_001303)	-125	NM_001303	1352	Hs.462278	NM_001303	ENSG00000006695	COX10	-	cytochrome c oxidase assembly factor heme A:farnesyltransferase COX10	protein-coding	0.076923	0.644886	
chunk0106_86_1	chr2	197158745	197159823	+	0	NA	intron (NM_001195144, intron 2 of 27)	intron (NM_001195144, intron 2 of 27)	143235	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.005566	0.367933	
chunk0173_396_1	chr6	150320191	150320856	+	0	NA	Intergenic	Intergenic	-48369	NM_203395	389434	Hs.310225	NM_203395	ENSG00000009765	IYD	C6orf71|DEHAL1|IYD-1|TDH4	iodotyrosine deiodinase	protein-coding	0.016541	0.460961	
chunk0209_118_1	chrX	40526253	40526715	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-54480	NM_005765	10159	Hs.495960	NM_005765	ENSG00000182220	ATP6AP2	APT6M8-9|ATP6IP2|ATP6M8-9|ELDF10|HT028|M8-9|MRXE|MRXSH|MSTP009|PRR|RENR|XMRE|XPDS	ATPase H+ transporting accessory protein 2	protein-coding	0.004329	0.451404	
chunk0030_161_1	chr10	114042406	114043489	+	0	NA	Intergenic	Intergenic	-1100	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.039705	0.493542	
chunk0095_119_1	chr2	15766167	15766991	+	0	NA	Intergenic	Intergenic	75797	NR_110201	101926966	Hs.502835	NR_110201	ENSG00000231031	LINC01804	-	long intergenic non-protein coding RNA 1804	ncRNA	0.018204	0.561212	413(AAGAACAAAGTGGCCC,-,0.00)
chunk0014_229_1	chr1	179871995	179872246	+	0	NA	intron (NM_001199260, intron 2 of 6)	intron (NM_001199260, intron 2 of 6)	5686	NM_145034	163590	Hs.571797	NM_022347	ENSG00000169905	TOR1AIP2	IFRG15|LULL1|NET9	torsin 1A interacting protein 2	protein-coding	0.003984	0.404762	44(GTACACACACTGTTCC,-,0.00),45(TACACACACTGTTCCC,+,0.00)
chunk0006_343_1	chr1	72471382	72471912	+	0	NA	Intergenic	Intergenic	-189053	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.003774	0.363465	316(GAGAACAATGAGTCCA,-,0.00)
chunk0160_182_1	chr5	154092272	154092848	+	0	NA	Intergenic	Intergenic	53601	NM_001135037	4238	Hs.432818	NM_005927	ENSG00000037749	MFAP3	-	microfibril associated protein 3	protein-coding	0.006944	0.402080	
chunk0014_308_1	chr1	181095521	181096292	+	0	NA	Intergenic	Intergenic	7404	NM_016545	51278	Hs.15725	NM_016545	ENSG00000162783	IER5	SBBI48	immediate early response 5	protein-coding	0.009079	0.468912	
chunk0120_403_1	chr3	12627000	12627378	+	0	NA	intron (NM_002880, intron 1 of 16)	intron (NM_002880, intron 1 of 16)	37012	NM_002880	5894	Hs.159130	NM_002880	ENSG00000132155	RAF1	CMD1NN|CRAF|NS5|Raf-1|c-Raf	Raf-1 proto-oncogene, serine/threonine kinase	protein-coding	0.005291	0.329815	
chunk0120_166_1	chr3	5744137	5744436	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-494031	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.010033	0.416667	164(TAGGCCACAGTGTTCT,-,0.00),165(AGGCCACAGTGTTCTC,+,0.00)
chunk0077_441_1	chr16	85681090	85681671	+	0	NA	intron (NM_016095, intron 3 of 4)	(GACA)n|Simple_repeat|Simple_repeat	7602	NM_016095	51659	Hs.433180	NM_016095	ENSG00000131153	GINS2	HSPC037|PSF2|Pfs2	GINS complex subunit 2	protein-coding	0.017212	0.489691	
chunk0114_212_1	chr21	15551120	15551373	+	0	NA	Intergenic	Intergenic	-178779	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.003953	0.397638	
chunk0157_420_1	chr5	124667462	124667756	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	77503	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.006803	0.383051	
chunk0097_2_1	chr2	40737283	40737780	+	0	NA	Intergenic	Intergenic	-225096	NM_001112802	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.004024	0.323293	237(AAAGACACTCTGTTCC,-,0.00),238(AAGACACTCTGTTCCA,+,0.00)
chunk0136_120_1	chr4	3587765	3587964	+	0	NA	intron (NR_040045, intron 1 of 2)	intron (NR_040045, intron 1 of 2)	10995	NR_040045	285492	Hs.145563	NM_173661		LINC00955	-	long intergenic non-protein coding RNA 955	ncRNA	0.005025	0.555000	
chunk0020_22_1	chr1	231792770	231793207	+	0	NA	intron (NM_001164546, intron 6 of 6)	intron (NM_001164546, intron 6 of 6)	25529	NR_002227	27184	Hs.720568	NR_002227		DISC2	DISC1-AS1|DISC1OS|NCRNA00015	disrupted in schizophrenia 2	ncRNA	0.009153	0.436073	
chunk0204_337_1	chr9	101373621	101373874	+	0	NA	intron (NM_001701, intron 1 of 3)	intron (NM_001701, intron 1 of 3)	9772	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.011858	0.385827	
chunk0002_437_1	chr1	28170140	28170419	+	0	NA	intron (NM_001164722, intron 1 of 1)	intron (NM_001164722, intron 1 of 1)	6665	NM_001164723	5724	Hs.77542	NM_000952	ENSG00000169403	PTAFR	PAFR	platelet activating factor receptor	protein-coding	0.007168	0.475000	
chunk0186_439_1	chr7	147053146	147053610	+	0	NA	intron (NM_014141, intron 4 of 23)	intron (NM_014141, intron 4 of 23)	44231	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.002155	0.313978	255(GAGAACATGGTGAGCC,-,0.00),256(AGAACATGGTGAGCCT,+,0.00)
chunk0033_329_1	chr11	22221405	22221943	+	0	NA	intron (NM_001142649, intron 5 of 21)	L2a|LINE|L2	28498	NM_001142649	203859	Hs.154329	NM_213599	ENSG00000171714	ANO5	GDD1|LGMD2L|LGMDR12|TMEM16E	anoctamin 5	protein-coding	0.001859	0.283859	
chunk0133_312_1	chr3	172363321	172363536	+	0	NA	intron (NM_022763, intron 23 of 25)	intron (NM_022763, intron 23 of 25)	85028	NM_004122	2693	Hs.130212	NM_004122	ENSG00000121853	GHSR	GHDP	growth hormone secretagogue receptor	protein-coding	0.009302	0.347222	188(GGTGACAGAATGTTCT,-,0.00),189(GTGACAGAATGTTCTG,+,0.00)
chunk0210_420_1	chrX	101208993	101209360	+	0	NA	Intergenic	UCON47|Unknown|Unknown	-10768	NM_001171184	1821	Hs.159291	NM_001939	ENSG00000102385	DRP2	DRP-2	dystrophin related protein 2	protein-coding	0.002725	0.364130	
chunk0067_411_1	chr15	49496012	49496375	+	0	NA	intron (NM_152647, intron 11 of 15)	intron (NM_152647, intron 11 of 15)	73015	NM_002009	2252	Hs.567268	NM_002009	ENSG00000140285	FGF7	HBGF-7|KGF	fibroblast growth factor 7	protein-coding	0.002755	0.266484	
chunk0033_208_1	chr11	16966668	16966963	+	0	NA	intron (NM_175058, intron 3 of 22)	intron (NM_175058, intron 3 of 22)	47601	NM_175058	144100	Hs.12332	NM_175058	ENSG00000166689	PLEKHA7	-	pleckstrin homology domain containing A7	protein-coding	0.013559	0.472973	
chunk0127_33_1	chr3	88620540	88621117	+	0	NA	Intergenic	Intergenic	-470962	NM_001195308	8545	Hs.444818	NM_003663	ENSG00000163320	CGGBP1	CGGBP|p20-CGGBP	CGG triplet repeat binding protein 1	protein-coding	0.005199	0.333910	
chunk0132_304_1	chr3	160253211	160253723	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	27831	NM_001168214	401097	Hs.729755	NM_001168214	ENSG00000180044	C3orf80	-	chromosome 3 open reading frame 80	protein-coding	0.000000	0.395712	
chunk0072_182_1	chr15	94110653	94111126	+	0	NA	Intergenic	Intergenic	-2951	NR_120320	101927112	Hs.134687	NR_120320	ENSG00000259724	LINC01581	-	long intergenic non-protein coding RNA 1581	ncRNA	0.002114	0.377637	
chunk0199_8_1	chr9	489045	489774	+	0	NA	intron (NM_001256876, intron 3 of 15)	MER53|DNA|hAT	-15286	NM_015158	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.004115	0.394521	
chunk0034_38_1	chr11	26694448	26694678	+	0	NA	intron (NM_178498, intron 8 of 14)	L1M5|LINE|L1	27464	NM_178498	159963	Hs.148907	NM_178498	ENSG00000148942	SLC5A12	SMCT2	solute carrier family 5 member 12	protein-coding	0.004348	0.367965	14(AAGGACAGAGTGTGAC,-,0.00)
chunk0158_18_1	chr5	125339959	125340391	+	0	NA	intron (NR_109882, intron 5 of 5)	MIR|SINE|MIR	-153086	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.009259	0.362587	
chunk0092_250_1	chr19	32977191	32977688	+	0	NA	TTS (NM_001300978)	TTS (NM_001300978)	5222	NM_152266	91442	Hs.579899	NM_152266	ENSG00000131944	FAAP24	C19orf40	FA core complex associated protein 24	protein-coding	0.020121	0.469880	
chunk0111_174_1	chr20	25277934	25278239	+	0	NA	intron (NM_002862, intron 7 of 19)	intron (NM_002862, intron 7 of 19)	30016	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.019672	0.611111	101(AGGTACAGAATGTTCC,-,0.00),102(GGTACAGAATGTTCCA,+,0.00),177(ATGGACACTGTGTCCC,-,0.00),178(TGGACACTGTGTCCCG,+,0.00)
chunk0080_1_1	chr17	20312546	20312900	+	0	NA	intron (NM_001033553, intron 14 of 14)	intron (NM_001033553, intron 14 of 14)	-8451	NR_023380	348254	Hs.462475	NR_023380		CCDC144CP	CCDC144C	coiled-coil domain containing 144C, pseudogene	pseudo	0.005650	0.414085	
chunk0053_2_1	chr13	26033998	26034268	+	0	NA	Intergenic	Intergenic	16927	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.007407	0.428044	130(AAAGACATTCTGTGCT,-,0.00),131(AAGACATTCTGTGCTA,+,0.00)
chunk0085_332_1	chr18	8506080	8506786	+	0	NA	Intergenic	Intergenic	-103012	NM_001025300	201475	Hs.270074	NM_001025300	ENSG00000206418	RAB12	-	RAB12, member RAS oncogene family	protein-coding	0.014164	0.471004	398(TTGGACATTTTGTTCC,-,0.00),399(TGGACATTTTGTTCCT,+,0.00)
chunk0210_414_1	chrX	100890598	100890952	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-16430	NM_001271815	27035	Hs.592227	NM_007052	ENSG00000007952	NOX1	GP91-2|MOX1|NOH-1|NOH1	NADPH oxidase 1	protein-coding	0.002825	0.343662	165(CAGAACATGCTGAACT,-,0.00),166(AGAACATGCTGAACTG,+,0.00)
chunk0114_344_1	chr21	17798959	17799434	+	0	NA	intron (NM_017447, intron 2 of 4)	intron (NM_017447, intron 2 of 4)	-6687	NR_038871	246312	Hs.473425	NR_038870	ENSG00000240770	C21orf91-OT1	D21S2089E|NCRNA00285	C21orf91 overlapping transcript 1	ncRNA	0.006316	0.342437	
chunk0163_188_1	chr6	11535389	11536140	+	0	NA	Intergenic	Intergenic	-2463	NM_001100829	100113407	Hs.146317	NM_001100829	ENSG00000205269	TMEM170B	-	transmembrane protein 170B	protein-coding	0.005326	0.368351	
chunk0019_443_1	chr1	231277941	231278638	+	0	NA	TTS (NM_001316350)	TTS (NM_001316350)	-37102	NM_001300830	128061	Hs.743464	NM_152379	ENSG00000143633	C1orf131	-	chromosome 1 open reading frame 131	protein-coding	0.007174	0.441261	
chunk0179_140_1	chr7	46090504	46091135	+	0	NA	Intergenic	L1PA15|LINE|L1	-169547	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.003170	0.322785	
chunk0145_280_1	chr4	149708594	149708980	+	0	NA	Intergenic	Intergenic	-369487	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.002591	0.354005	
chunk0041_394_1	chr11	133174106	133174368	+	0	NA	intron (NM_001012393, intron 1 of 7)	intron (NM_001012393, intron 1 of 7)	-231095	NM_002545	4978	Hs.4817	NM_002545	ENSG00000183715	OPCML	IGLON1|OBCAM|OPCM	opioid binding protein/cell adhesion molecule like	protein-coding	0.022901	0.509506	
chunk0027_97_1	chr10	73730343	73730786	+	0	NA	promoter-TSS (NR_026592)	promoter-TSS (NR_026592)	-50	NR_026592	729096	Hs.709171	NR_026592	ENSG00000271816	BMS1P4	BMS1LP4	BMS1 pseudogene 4	pseudo	0.088036	0.641892	
chunk0184_456_1	chr7	123425142	123425813	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	107471	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.004471	0.363095	
chunk0194_5_1	chr8	81368086	81368606	+	0	NA	Intergenic	AluJb|SINE|Alu	79138	NM_002677	5375	Hs.571512	NM_002677	ENSG00000147588	PMP2	CMT1G|FABP8|M-FABP|MP2|P2	peripheral myelin protein 2	protein-coding	0.003846	0.399232	259(GGGCTCAAGCTGTTCT,-,0.00),260(GGCTCAAGCTGTTCTC,+,0.00)
chunk0013_28_1	chr1	166609647	166610192	+	0	NA	intron (NR_002925, intron 2 of 6)	HERVK-int|LTR|ERVK	6003	NR_002925	116123	Hs.348539	NM_138784	ENSG00000215834	FMO9P	-	flavin containing dimethylaniline monoxygenase 9, pseudogene	pseudo	0.023853	0.443223	
chunk0006_25_1	chr1	64023554	64023794	+	0	NA	intron (NM_001083592, intron 2 of 6)	L1ME4a|LINE|L1	88531	NR_110666	101927034	Hs.680824	NR_110665	ENSG00000223949	ROR1-AS1	-	ROR1 antisense RNA 1	ncRNA	0.004167	0.261411	
chunk0168_399_1	chr6	94562736	94563330	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	855950	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.005051	0.352941	
chunk0078_290_1	chr17	8056294	8057030	+	0	NA	Intergenic	Intergenic	17622	NM_001141	247	Hs.111256	NM_001141	ENSG00000179593	ALOX15B	15-LOX-2	arachidonate 15-lipoxygenase type B	protein-coding	0.023098	0.500678	
chunk0085_274_1	chr18	7761390	7761849	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	194303	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.008715	0.432609	
chunk0022_137_1	chr10	11842172	11842542	+	0	NA	intron (NM_153256, intron 1 of 3)	L1MEd|LINE|L1	18959	NM_153256	254427	Hs.435775	NM_153256	ENSG00000148426	PROSER2	C10orf47	proline and serine rich 2	protein-coding	0.005405	0.312668	
chunk0090_359_1	chr18	76889180	76889379	+	0	NA	intron (NM_001306089, intron 9 of 30)	intron (NM_001306089, intron 9 of 30)	65119	NM_007345	7776	Hs.719137	NM_007345	ENSG00000130856	ZNF236	ZNF236A|ZNF236B	zinc finger protein 236	protein-coding	0.015075	0.495000	
chunk0136_114_1	chr4	3362787	3363155	+	0	NA	intron (NM_198229, intron 3 of 17)	(GT)n|Simple_repeat|Simple_repeat	-7026	NM_198227	6002	Hs.527061	NM_002926	ENSG00000159788	RGS12	-	regulator of G protein signaling 12	protein-coding	0.032609	0.539295	
chunk0001_362_1	chr1	10034648	10034949	+	0	NA	intron (NM_001105562, intron 1 of 27)	intron (NM_001105562, intron 1 of 27)	1815	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.013289	0.390728	
chunk0032_348_1	chr11	10366818	10367173	+	0	NA	intron (NR_103765, intron 2 of 3)	intron (NR_103765, intron 2 of 3)	58682	NR_103765	100130460	Hs.501890	NR_103765		CAND1.11	-	uncharacterized LOC100130460	ncRNA	0.014085	0.528090	
chunk0118_1_1	chr22	25213177	25213534	+	0	NA	Intergenic	Intergenic	-6290	NM_000496	1415	Hs.373074	NM_000496	ENSG00000244752	CRYBB2	CCA2|CRYB2|CRYB2A|CTRCT3|D22S665	crystallin beta B2	protein-coding	0.011204	0.446927	
chunk0169_110_1	chr6	100712983	100713537	+	0	NA	intron (NM_006828, intron 13 of 41)	L1MC1|LINE|L1	168112	NM_006828	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.014440	0.383784	
chunk0189_388_1	chr8	27429989	27430371	+	0	NA	intron (NM_004103, intron 7 of 31)	intron (NM_004103, intron 7 of 31)	-3190	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.013089	0.569191	
chunk0119_407_1	chr22	49512524	49512961	+	0	NA	intron (NR_110523, intron 1 of 4)	intron (NR_110523, intron 1 of 4)	30724	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.016018	0.385845	
chunk0152_119_1	chr5	58700394	58700773	+	0	NA	intron (NM_138453, intron 2 of 4)	MIRc|SINE|MIR	117471	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.000000	0.313158	
chunk0131_48_1	chr3	142687655	142688192	+	0	NA	intron (NM_002670, intron 9 of 15)	L1MC5|LINE|L1	31026	NM_001172312	5357	Hs.203637	NM_002670	ENSG00000120756	PLS1	-	plastin 1	protein-coding	0.009311	0.371747	
chunk0119_173_1	chr22	43436158	43436867	+	0	NA	intron (NM_001044370, intron 3 of 6)	intron (NM_001044370, intron 3 of 6)	24498	NM_001044370	758	Hs.159538	NM_001044370	ENSG00000186732	MPPED1	239AB|C22orf1|FAM1A	metallophosphoesterase domain containing 1	protein-coding	0.033850	0.615493	
chunk0088_335_1	chr18	51137777	51138183	+	0	NA	Intergenic	MIR|SINE|MIR	59701	NM_016626	51320	Hs.465144	NM_016626	ENSG00000176624	MEX3C	BM-013|MEX-3C|RKHD2|RNF194	mex-3 RNA binding family member C	protein-coding	0.019704	0.520885	
chunk0093_134_1	chr19	46182542	46182775	+	0	NA	Intergenic	Intergenic	-27584	NR_027003	93429	Hs.569940	NR_027003	ENSG00000268460	LOC93429	-	uncharacterized LOC93429	ncRNA	0.034335	0.465812	
chunk0015_64_1	chr1	184675287	184675551	+	0	NA	Intergenic	L1MA5A|LINE|L1	79488	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.003788	0.332075	
chunk0050_149_1	chr12	102854765	102855080	+	0	NA	intron (NM_000277, intron 6 of 12)	intron (NM_000277, intron 6 of 12)	-30523	NR_033855	283432	Hs.382110	NR_033855	ENSG00000258169	LINC00485	-	long intergenic non-protein coding RNA 485	ncRNA	0.003175	0.439873	
chunk0036_29_1	chr11	58579666	58580309	+	0	NA	intron (NM_001197051, intron 1 of 10)	intron (NM_001197051, intron 1 of 10)	873	NM_053023	80829	Hs.524920	NM_053023	ENSG00000186660	ZFP91	DMS-8|DSM-8|FKSG11|PZF|ZFP-91|ZNF757	ZFP91 zinc finger protein	protein-coding	0.045101	0.482919	
chunk0034_206_1	chr11	32440092	32440460	+	0	NA	TTS (NR_120546)	TTS (NR_120546)	4237	NR_120546	51352	Hs.567499	NM_015855	ENSG00000183242	WT1-AS	WIT-1|WIT1|WT1-AS1|WT1AS	WT1 antisense RNA	ncRNA	0.008152	0.314363	
chunk0167_131_1	chr6	62035802	62036522	+	0	NA	intron (NM_152688, intron 3 of 8)	intron (NM_152688, intron 3 of 8)	250033	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.005556	0.377254	
chunk0049_393_1	chr12	96448223	96448569	+	0	NA	Intergenic	Intergenic	-41175	NM_001306084	144535	Hs.382121	NM_198520	ENSG00000188596	CFAP54	C12orf55|C12orf63	cilia and flagella associated protein 54	protein-coding	0.005780	0.380403	
chunk0083_249_1	chr17	67990218	67990670	+	0	NA	TTS (NM_181656)	TTS (NM_181656)	3205	NM_181655	284018	Hs.90790	NM_181655	ENSG00000186665	C17orf58	-	chromosome 17 open reading frame 58	protein-coding	0.006637	0.403974	318(AAGTACAGCCTGATCT,-,0.00),319(AGTACAGCCTGATCTT,+,0.00)
chunk0064_157_1	chr14	91872566	91872912	+	0	NA	intron (NM_006329, intron 10 of 10)	intron (NM_006329, intron 10 of 10)	-5203	NM_001128596	123036	Hs.510262	NM_152332	ENSG00000165929	TC2N	C14orf47|C2CD1|MTAC2D1|Tac2-N	tandem C2 domains, nuclear	protein-coding	0.020231	0.550432	
chunk0052_122_1	chr13	23373655	23374145	+	0	NA	intron (NM_014363, intron 3 of 9)	intron (NM_014363, intron 3 of 9)	1643	NM_001278055	26278	Hs.159492	NM_014363	ENSG00000151835	SACS	ARSACS|DNAJC29|PPP1R138|SPAX6	sacsin molecular chaperone	protein-coding	0.030612	0.513238	
chunk0102_117_1	chr2	144694223	144694488	+	0	NA	intron (NR_033870, intron 1 of 4)	intron (NR_033870, intron 1 of 4)	26388	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.007547	0.368421	
chunk0135_279_1	chr3	189383619	189384243	+	0	NA	Intergenic	L1MC1|LINE|L1	-143337	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.008013	0.436800	293(TAGAACAAAATGTTCT,-,0.00),294(AGAACAAAATGTTCTA,+,0.00)
chunk0068_237_1	chr15	55803178	55803484	+	0	NA	Intergenic	Intergenic	-60212	NM_173814	283659	Hs.130957	NM_173814	ENSG00000166450	PRTG	IGDCC5	protogenin	protein-coding	0.006536	0.537459	
chunk0168_77_1	chr6	79737001	79737550	+	0	NA	Intergenic	Intergenic	74971	NR_131786	89758	Hs.288213	NM_001243308		LINC01621	C6orf7	long intergenic non-protein coding RNA 1621	ncRNA	0.018215	0.409091	
chunk0031_105_1	chr10	124304595	124305480	+	0	NA	Intergenic	Intergenic	113939	NM_001171814	4942	Hs.523332	NM_000274	ENSG00000065154	OAT	GACR|HOGA|OATASE|OKT	ornithine aminotransferase	protein-coding	0.005650	0.436795	
chunk0173_360_1	chr6	149349544	149349898	+	0	NA	intron (NM_015093, intron 3 of 8)	Tigger9b|DNA|TcMar-Tigger	31421	NM_015093	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.002825	0.323944	
chunk0195_439_1	chr8	101186926	101187574	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	18482	NM_001042510	51123	Hs.374485	NM_016096	ENSG00000120963	ZNF706	HSPC038|PNAS-106|PNAS-113	zinc finger protein 706	protein-coding	0.009259	0.306626	
chunk0120_190_1	chr3	6902529	6903147	+	0	NA	intron (NM_000844, intron 1 of 9)	intron (NM_000844, intron 1 of 9)	-8821	NR_131906	105376946	Hs.616038	NR_131906	ENSG00000237665	GRM7-AS2	-	GRM7 antisense RNA 2	ncRNA	0.003236	0.323102	
chunk0191_83_1	chr8	47611000	47611479	+	0	NA	intron (NM_001080394, intron 10 of 19)	intron (NM_001080394, intron 10 of 19)	126925	NM_005195	1052	Hs.440829	NM_005195	ENSG00000221869	CEBPD	C/EBP-delta|CELF|CRP3|NF-IL6-beta	CCAAT enhancer binding protein delta	protein-coding	0.008351	0.489583	
chunk0174_398_1	chr6	165480844	165481342	+	0	NA	intron (NM_006661, intron 4 of 22)	intron (NM_006661, intron 4 of 22)	71492	NR_106988									0.014056	0.388778	
chunk0097_100_1	chr2	45991353	45991552	+	0	NA	intron (NM_005400, intron 6 of 14)	intron (NM_005400, intron 6 of 14)	-305950	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.005025	0.360000	
chunk0055_402_1	chr13	74228745	74229634	+	0	NA	Intergenic	Intergenic	-95260	NM_007249	11278	Hs.373857	NM_007249	ENSG00000118922	KLF12	AP-2rep|AP2REP|HSPC122	Kruppel like factor 12	protein-coding	0.004499	0.340449	
chunk0028_384_1	chr10	92902335	92902851	+	0	NA	intron (NM_019053, intron 5 of 21)	L1ME3A|LINE|L1	54125	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.000000	0.324952	
chunk0063_269_1	chr14	83960997	83961630	+	0	NA	Intergenic	Intergenic	-1432566	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003160	0.397476	
chunk0087_378_1	chr18	41594527	41594859	+	0	NA	Intergenic	Intergenic	-74096	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.006024	0.501502	108(GGGAACACCCTGTCAT,-,0.00),109(GGAACACCCTGTCATC,+,0.00)
chunk0076_419_1	chr16	72936019	72936616	+	0	NA	intron (NM_006885, intron 3 of 9)	L2a|LINE|L2	112058	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.010050	0.474916	304(GTCACACACTGTTCTA,+,0.00),553(TAGAACAGCAAGTGCA,-,0.00),554(AGAACAGCAAGTGCAA,+,0.00)
chunk0099_229_1	chr2	96356879	96357290	+	0	NA	intron (NM_015341, intron 9 of 17)	MamSINE1|SINE|tRNA-RTE	21343	NM_015341	23397	Hs.308045	NM_015341	ENSG00000121152	NCAPH	BRRN1|CAP-H|CAPH|MCPH23	non-SMC condensin I complex subunit H	protein-coding	0.014599	0.500000	
chunk0170_152_1	chr6	111456050	111456652	+	0	NA	intron (NM_002912, intron 2 of 32)	intron (NM_002912, intron 2 of 32)	-27121	NR_034109	643749	Hs.486228	NR_034108	ENSG00000231889	TRAF3IP2-AS1	C6UAS|C6orf3|NCRNA00248|TRAF3IP2-AS2	TRAF3IP2 antisense RNA 1	ncRNA	0.006645	0.361526	
chunk0099_308_1	chr2	99349482	99349967	+	0	NA	intron (NM_015904, intron 1 of 23)	L1MA6|LINE|L1	12353	NM_015904	9669	Hs.158688	NM_015904	ENSG00000158417	EIF5B	IF2	eukaryotic translation initiation factor 5B	protein-coding	0.002062	0.318930	
chunk0165_214_1	chr6	35044171	35045141	+	0	NA	intron (NM_015245, intron 11 of 23)	intron (NM_015245, intron 11 of 23)	96754	NM_001093728									0.018557	0.495366	
chunk0205_309_1	chr9	112562491	112562856	+	0	NA	intron (NM_001287036, intron 1 of 4)	LTR86C|LTR|ERVL	75705	NM_001287036	158405	Hs.656619	NM_133465	ENSG00000165185	KIAA1958	-	KIAA1958	protein-coding	0.005479	0.377049	
chunk0089_170_1	chr18	59452010	59452384	+	0	NA	intron (NM_133459, intron 6 of 10)	intron (NM_133459, intron 6 of 10)	-92921	NM_005570	3998	Hs.465295	NM_005570	ENSG00000074695	LMAN1	ERGIC-53|ERGIC53|F5F8D|FMFD1|MCFD1|MR60|gp58	lectin, mannose binding 1	protein-coding	0.018717	0.480000	
chunk0154_27_1	chr5	76976971	76977625	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	24443	NM_001882	1393	Hs.115617	NM_001882	ENSG00000145708	CRHBP	CRF-BP|CRFBP	corticotropin releasing hormone binding protein	protein-coding	0.009174	0.390840	
chunk0199_212_1	chr9	5113805	5114186	+	0	NA	intron (NM_004972, intron 22 of 24)	intron (NM_004972, intron 22 of 24)	71623	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.020997	0.578534	
chunk0027_36_1	chr10	72364380	72364584	+	0	NA	Intergenic	Intergenic	-9333	NM_017626	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.029412	0.585366	
chunk0128_193_1	chr3	107537584	107538189	+	0	NA	intron (NM_001276286, intron 2 of 16)	intron (NM_001276286, intron 2 of 16)	14950	NM_001142568	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.003306	0.377888	
chunk0176_422_1	chr7	19438269	19438720	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	266942	NR_036101	100422967		NR_036101	ENSG00000265932	MIR3146	mir-3146	microRNA 3146	ncRNA	0.000000	0.334071	
chunk0006_83_1	chr1	64959382	64959663	+	0	NA	intron (NM_002227, intron 1 of 24)	intron (NM_002227, intron 1 of 24)	6982	NM_002227	3716	Hs.207538	NM_002227	ENSG00000162434	JAK1	JAK1A|JAK1B|JTK3	Janus kinase 1	protein-coding	0.003559	0.354610	
chunk0093_57_1	chr19	40257185	40257433	+	0	NA	intron (NM_001243028, intron 1 of 12)	intron (NM_001243028, intron 1 of 12)	25332	NR_030371	693226		NR_030371	ENSG00000207631	MIR641	MIRN641|hsa-mir-641|mir-641	microRNA 641	ncRNA	0.016129	0.650602	
chunk0062_152_1	chr14	69191320	69191912	+	0	NA	promoter-TSS (NR_034165)	promoter-TSS (NR_034165)	139	NM_018199	55218	Hs.533878	NM_018199	ENSG00000081177	EXD2	C14orf114|EXDL2	exonuclease 3'-5' domain containing 2	protein-coding	0.074324	0.647555	
chunk0187_180_1	chr7	150967349	150967627	+	0	NA	intron (NM_172056, intron 2 of 8)	L1ME5|LINE|L1	10826	NM_172056	3757	Hs.647099	NM_000238	ENSG00000055118	KCNH2	ERG-1|ERG1|H-ERG|HERG|HERG1|Kv11.1|LQT2|SQT1	potassium voltage-gated channel subfamily H member 2	protein-coding	0.017986	0.408602	194(AAGAACAGACTGTTTA,-,0.00),195(AGAACAGACTGTTTAC,+,0.00)
chunk0123_105_1	chr3	42232317	42232579	+	0	NA	Intergenic	Charlie10|DNA|hAT-Charlie	31499	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.007634	0.239544	
chunk0104_112_1	chr2	172843742	172844329	+	0	NA	intron (NM_001100397, intron 1 of 27)	intron (NM_001100397, intron 1 of 27)	-16003	NM_001282899	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.013629	0.430272	
chunk0138_327_1	chr4	41505116	41505455	+	0	NA	intron (NM_001112717, intron 2 of 25)	intron (NM_001112717, intron 2 of 25)	-107487	NM_001112719	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.011799	0.435294	
chunk0040_119_1	chr11	112221114	112221733	+	0	NA	Intergenic	L2b|LINE|L2	-4942	NM_000317	5805	Hs.503860	NM_000317	ENSG00000150787	PTS	PTPS	6-pyruvoyltetrahydropterin synthase	protein-coding	0.004847	0.396774	
chunk0054_127_1	chr13	43465252	43465550	+	0	NA	intron (NM_001127615, intron 3 of 16)	L1MC3|LINE|L1	16549	NR_120399	100874130	Hs.738887	NR_120399		ENOX1-AS2	-	ENOX1 antisense RNA 2	ncRNA	0.006711	0.337793	
chunk0029_243_1	chr10	102658135	102658919	+	0	NA	TTS (NM_030912)	TTS (NM_030912)	14032	NM_030912	81603	Hs.336810	NM_030912	ENSG00000171206	TRIM8	GERP|RNF27	tripartite motif containing 8	protein-coding	0.019133	0.554140	86(GTGGACTTCCTGTTCT,-,0.00),87(TGGACTTCCTGTTCTC,+,0.00)
chunk0140_122_1	chr4	68935265	68935591	+	0	NA	intron (NM_024743, intron 2 of 5).2	L1PA6|LINE|L1	16363	NM_024743	79799	Hs.122583	NM_024743	ENSG00000135220	UGT2A3	-	UDP glucuronosyltransferase family 2 member A3	protein-coding	0.000000	0.370031	
chunk0149_184_1	chr5	21196509	21196778	+	0	NA	Intergenic	Intergenic	-262837	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.003717	0.322222	
chunk0011_301_1	chr1	151619592	151620077	+	0	NA	intron (NM_030918, intron 1 of 11)	intron (NM_030918, intron 1 of 11)	7648	NM_030918	81609	Hs.192326	NM_030918	ENSG00000143376	SNX27	MRT1|MY014	sorting nexin 27	protein-coding	0.006186	0.397119	
chunk0175_244_1	chr7	6588645	6589338	+	0	NA	TTS (NM_001134387)	TTS (NM_001134387)	-1030	NM_024067	79034	Hs.487511	NM_024067	ENSG00000146576	C7orf26	-	chromosome 7 open reading frame 26	protein-coding	0.023088	0.523055	
chunk0013_313_1	chr1	171353145	171354026	+	0	NA	Intergenic	L2a|LINE|L2	14689	NR_002719	7151	Hs.661092	NR_002719		TOP1P1	-	DNA topoisomerase I pseudogene 1	pseudo	0.007946	0.407029	
chunk0020_136_1	chr1	233665872	233666192	+	0	NA	intron (NM_002245, intron 1 of 2)	intron (NM_002245, intron 1 of 2)	41880	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.006250	0.395639	
chunk0004_129_1	chr1	44708343	44708877	+	0	NA	intron (NM_001145636, intron 6 of 11)	L2|LINE|L2	13291	NR_002753	26828		NR_002753	ENSG00000199377	RNU5F-1	RNU5F|U5F	RNA, U5F small nuclear 1	snRNA	0.011236	0.510280	
chunk0114_8_1	chr21	6370592	6371027	+	0	NA	Intergenic	Intergenic	96799	NM_000071	875	Hs.533013	NM_000071	ENSG00000160200	CBS	CBSL|HIP4	cystathionine-beta-synthase	protein-coding	0.027586	0.500000	
chunk0144_126_1	chr4	129065447	129065646	+	0	NA	intron (NM_001300898, intron 2 of 5)	MER58A|DNA|hAT-Charlie	28061	NM_144643	132320	Hs.654690	NM_144643	ENSG00000151466	SCLT1	CAP-1A|CAP1A	sodium channel and clathrin linker 1	protein-coding	0.005025	0.355000	
chunk0210_164_1	chrX	77953001	77953678	+	0	NA	intron (NR_104109, intron 1 of 9)	L1PA16|LINE|L1	16299	NM_001029891	441531	Hs.632822	NM_001029891	ENSG00000226784	PGAM4	PGAM-B|PGAM1|PGAM3|dJ1000K24.1	phosphoglycerate mutase family member 4	protein-coding	0.010340	0.376106	
chunk0149_55_1	chr5	16815404	16815981	+	0	NA	intron (NM_012334, intron 3 of 40)	intron (NM_012334, intron 3 of 40)	120584	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.006932	0.377163	
chunk0090_241_1	chr18	73826738	73826989	+	0	NA	Intergenic	Intergenic	320901	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.000000	0.543651	
chunk0115_298_1	chr21	28377911	28378480	+	0	NA	Intergenic	Intergenic	-149528	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.005272	0.343860	
chunk0173_279_1	chr6	147832361	147832562	+	0	NA	Intergenic	Intergenic	323769	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.014925	0.396040	
chunk0070_4_1	chr15	68802944	68803389	+	0	NA	TTS (NR_026808)	TTS (NR_026808)	-1241	NR_036197	100422971		NR_036197	ENSG00000265195	MIR4312	-	microRNA 4312	ncRNA	0.008989	0.493274	
chunk0100_116_1	chr2	108472181	108472843	+	0	NA	intron (NR_028063, intron 5 of 21)	intron (NR_028063, intron 5 of 21)	23391	NR_028063	9648	Hs.436505	NM_181453	ENSG00000135968	GCC2	GCC185|RANBP2L4|REN53	GRIP and coiled-coil domain containing 2	protein-coding	0.003021	0.294118	
chunk0005_387_1	chr1	61997293	61997705	+	0	NA	intron (NM_176877, intron 28 of 42)	intron (NM_176877, intron 28 of 42)	-81287	NR_036058	100422902		NR_036058	ENSG00000263908	MIR3116-1	-	microRNA 3116-1	ncRNA	0.009709	0.370460	
chunk0207_458_1	chr9	137763152	137763475	+	0	NA	non-coding (NR_024341, exon 1 of 1)	non-coding (NR_024341, exon 1 of 1)	291	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.030960	0.586420	
chunk0192_211_1	chr8	65143487	65143686	+	0	NA	Intergenic	Intergenic	36754	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.015075	0.545000	
chunk0111_53_1	chr20	22623142	22623450	+	0	NA	Intergenic	Intergenic	-15779	NR_109883	101929685	Hs.563018	NR_109883	ENSG00000237396	LNCNEF	LINC01384|lncRNA-NEF	lncRNA neighboring enhancer of FOXA2	ncRNA	0.012987	0.521036	
chunk0157_164_1	chr5	118019444	118019789	+	0	NA	intron (NR_104997, intron 2 of 2)	intron (NR_104997, intron 2 of 2)	-262958	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.002899	0.286127	
chunk0069_151_1	chr15	62506063	62506670	+	0	NA	Intergenic	Intergenic	138815	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.001647	0.450658	
chunk0108_100_1	chr2	229369515	229369855	+	0	NA	intron (NM_139072, intron 11 of 12)	intron (NM_139072, intron 11 of 12)	-98344	NM_001100818	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.005882	0.442815	79(GTCACATGCTGTTCCC,+,0.00)
chunk0196_362_1	chr8	114983818	114984132	+	0	NA	Intergenic	Intergenic	684037	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.006369	0.371429	
chunk0114_401_1	chr20	63655452	63655699	+	0	NA	Intergenic	Intergenic	-1965	NR_075070	50861	Hs.639609	NM_015894	ENSG00000197457	STMN3	SCLIP	stathmin 3	protein-coding	0.012146	0.536290	
chunk0179_52_1	chr7	43554218	43554435	+	0	NA	intron (NM_015052, intron 28 of 29)	intron (NM_015052, intron 28 of 29)	-28767	NM_004760	9263	Hs.709489	NM_004760	ENSG00000164543	STK17A	DRAK1	serine/threonine kinase 17a	protein-coding	0.000000	0.357798	140(CAGAACATAAAGTCCT,-,0.00),141(AGAACATAAAGTCCTT,+,0.00)
chunk0178_236_1	chr7	35988750	35988949	+	0	NA	Intergenic	Intergenic	-106461	NR_108089	101928618	Hs.561704	NR_108089	ENSG00000261184	LOC101928618	-	uncharacterized LOC101928618	ncRNA	0.005025	0.380000	
chunk0078_76_1	chr17	1669462	1669858	+	0	NA	intron (NM_006445, intron 24 of 42).2	L2|LINE|L2	15222	NM_006445	10594	Hs.181368	NM_006445	ENSG00000174231	PRPF8	HPRP8|PRP8|PRPC8|RP13|SNRNP220	pre-mRNA processing factor 8	protein-coding	0.007576	0.486146	
chunk0088_71_1	chr18	44570743	44571407	+	0	NA	Intergenic	Intergenic	39296	NR_131768	105667213	Hs.135737	NR_131768		LINC01601	-	long intergenic non-protein coding RNA 1601	ncRNA	0.004518	0.407519	333(GAGAACAATGTGTATC,-,0.00)
chunk0141_183_1	chr4	83012791	83013463	+	0	NA	promoter-TSS (NM_001115007)	promoter-TSS (NM_001115007)	-186	NM_001115007	132660	Hs.96952	NM_194282	ENSG00000189308	LIN54	CXCDC1|JC8.6|MIP120|TCX1	lin-54 DREAM MuvB core complex component	protein-coding	0.093750	0.612184	
chunk0046_1_1	chr12	53916948	53917194	+	0	NA	Intergenic	L1MEd|LINE|L1	-21721	NM_017410	3229	Hs.118608	NM_017410	ENSG00000123364	HOXC13	ECTD9|HOX3|HOX3G	homeobox C13	protein-coding	0.004065	0.299595	
chunk0177_348_1	chr7	26580677	26581224	+	0	NA	Intergenic	Intergenic	-42125	NR_022006	9808	Hs.69749	NM_014769	ENSG00000122548	KIAA0087	-	KIAA0087 lncRNA	ncRNA	0.009141	0.375912	
chunk0174_156_1	chr6	158113494	158113749	+	0	NA	TTS (NR_073096)	TTS (NR_073096)	54659	NR_073096	84947	Hs.154706	NM_032861	ENSG00000122335	SERAC1	-	serine active site containing 1	protein-coding	0.003922	0.355469	
chunk0191_25_1	chr8	42910323	42911129	+	0	NA	intron (NM_032410, intron 2 of 21)	L2c|LINE|L2	13836	NM_032410	84376	Hs.162852	NM_032410	ENSG00000168172	HOOK3	HK3	hook microtubule tethering protein 3	protein-coding	0.009926	0.379182	549(AAGTACACAATGTTAC,-,0.00)
chunk0052_128_1	chr13	23540802	23541474	+	0	NA	Intergenic	L1M4a1|LINE|L1	-29232	NM_148957	55504	Hs.149168	NM_018647	ENSG00000127863	TNFRSF19	TAJ|TAJ-alpha|TRADE|TROY	TNF receptor superfamily member 19	protein-coding	0.007440	0.368499	196(CAGAACAGGCTGTTTT,-,0.00),197(AGAACAGGCTGTTTTC,+,0.00)
chunk0185_150_1	chr7	127673864	127674539	+	0	NA	intron (NM_014390, intron 1 of 23)	L1MC4|LINE|L1	22053	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.004444	0.455621	356(GGTACTAGGTGTGCCC,+,0.00)
chunk0129_275_1	chr3	122959339	122959859	+	0	NA	intron (NM_001256348, intron 1 of 21)	intron (NM_001256348, intron 1 of 21)	16535	NM_001256347	54437	Hs.210870	NM_018987	ENSG00000082684	SEMA5B	SEMAG|SemG	semaphorin 5B	protein-coding	0.009615	0.439539	
chunk0204_273_1	chr9	98341322	98341769	+	0	NA	intron (NM_005458, intron 13 of 18)	L4_C_Mam|LINE|RTE-X	-85824	NM_018421	55357	Hs.371016	NM_018421	ENSG00000095383	TBC1D2	PARIS-1|PARIS1|TBC1D2A	TBC1 domain family member 2	protein-coding	0.020134	0.435268	
chunk0075_411_1	chr16	57233989	57234345	+	0	NA	intron (NM_133368, intron 13 of 14)	L2a|LINE|L2	-10959	NM_012106	23568	Hs.632873	NM_012106	ENSG00000102931	ARL2BP	BART|BART1|RP66	ADP ribosylation factor like GTPase 2 binding protein	protein-coding	0.019663	0.476190	206(GGGCACTTGCTGTTCC,-,0.00),207(GGCACTTGCTGTTCCT,+,0.00)
chunk0085_461_1	chr18	11752511	11753104	+	0	NA	intron (NM_001142339, intron 2 of 12)	intron (NM_001142339, intron 2 of 12)	1335	NM_001142339	2774	Hs.136295	NM_002071	ENSG00000141404	GNAL	DYT25	G protein subunit alpha L	protein-coding	0.064081	0.562290	
chunk0164_43_1	chr6	18446742	18447034	+	0	NA	intron (NM_182757, intron 4 of 7)	(GT)n|Simple_repeat|Simple_repeat	59538	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.006849	0.440273	
chunk0180_458_1	chr7	77516084	77516753	+	0	NA	Intergenic	Intergenic	-21038	NM_002835	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.005979	0.389552	
chunk0206_301_1	chr9	124758615	124759017	+	0	NA	intron (NM_001278546, intron 1 of 9)	intron (NM_001278546, intron 1 of 9)	12494	NM_033334	2649	Hs.20131	NM_001489	ENSG00000148200	NR6A1	CT150|GCNF|GCNF1|NR61|RTR|hGCNF|hRTR	nuclear receptor subfamily 6 group A member 1	protein-coding	0.000000	0.369727	
chunk0023_447_1	chr10	32055132	32055602	+	0	NA	intron (NM_004521, intron 1 of 25)	intron (NM_004521, intron 1 of 25)	1076	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.021277	0.401274	
chunk0189_382_1	chr8	27398621	27399084	+	0	NA	intron (NM_004103, intron 3 of 31)	intron (NM_004103, intron 3 of 31)	-34518	NR_106901	102465507		NR_106901	ENSG00000273836	MIR6842	hsa-mir-6842	microRNA 6842	ncRNA	0.006479	0.461207	229(TAGCACACGCTGTGCT,-,0.00),230(AGCACACGCTGTGCTT,+,0.00)
chunk0037_397_1	chr11	79209898	79210390	+	0	NA	intron (NM_001098816, intron 3 of 33)	intron (NM_001098816, intron 3 of 33)	191965	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.008130	0.387424	
chunk0058_116_1	chr14	22250914	22251371	+	0	NA	Intergenic	Intergenic	338095	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.000000	0.373362	
chunk0097_149_1	chr2	48221911	48222276	+	0	NA	Intergenic	Intergenic	-92563	NM_002158	3344	Hs.468478	NM_002158	ENSG00000170802	FOXN2	HTLF	forkhead box N2	protein-coding	0.002740	0.396175	
chunk0134_316_1	chr3	181660757	181660993	+	0	NA	intron (NR_075093, intron 4 of 4)	intron (NR_075093, intron 4 of 4)	50541	NR_075089	347689	Hs.654932	NR_004053		SOX2-OT	NCRNA00043|SOX2OT	SOX2 overlapping transcript	ncRNA	0.000000	0.295359	176(TGGAACACCTAGTACT,-,0.00),177(GGAACACCTAGTACTG,+,0.00)
chunk0180_324_1	chr7	72326370	72326569	+	0	NA	intron (NM_031468, intron 2 of 6)	intron (NM_031468, intron 2 of 6)	10754	NM_001017440	83698	Hs.592750	NM_031468	ENSG00000183166	CALN1	CABP8	calneuron 1	protein-coding	0.005025	0.410000	
chunk0087_372_1	chr18	41505925	41507012	+	0	NA	intron (NR_002838, intron 2 of 5)	HAL1|LINE|L1	14129	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.006440	0.315257	348(AGAGCTCTGTGTTCTC,+,0.00)
chunk0039_341_1	chr11	105146666	105146920	+	0	NA	Intergenic	Intergenic	-7059	NM_021571	59082	Hs.56279	NM_021571	ENSG00000255501	CARD18	ICEBERG|UNQ5804|pseudo-ICE	caspase recruitment domain family member 18	protein-coding	0.007874	0.262745	
chunk0209_99_1	chrX	39830299	39830882	+	0	NA	Intergenic	Intergenic	-6971	NR_039763	100616251		NR_039763	ENSG00000263972	MIR1587	-	microRNA 1587	ncRNA	0.005146	0.458904	210(CAGAACAAAGTGTTCT,-,0.00),211(AGAACAAAGTGTTCTT,+,0.00),428(TAGAACACCCTCTTCC,-,0.00),429(AGAACACCCTCTTCCT,+,0.00)
chunk0106_74_1	chr2	196988708	196989045	+	0	NA	3' UTR (NM_001195144, exon 28 of 28)	3' UTR (NM_001195144, exon 28 of 28)	-62146	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.014837	0.428994	
chunk0025_93_1	chr10	50544565	50545028	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	79181	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.008639	0.392241	
chunk0203_264_1	chr9	87909795	87910084	+	0	NA	Intergenic	Intergenic	-8023	NM_001145124	441452	Hs.652956	NM_001145124		SPATA31C1	FAM75C1|SPATA31C2	SPATA31 subfamily C member 1	protein-coding	0.027682	0.548276	
chunk0174_392_1	chr6	165419096	165419639	+	0	NA	intron (NM_006661, intron 11 of 22)	MIR|SINE|MIR	9766	NR_106988									0.005525	0.378676	
chunk0027_123_1	chr10	74206931	74207234	+	0	NA	intron (NM_001202449, intron 2 of 9)	MER52A|LTR|ERV1	30593	NM_001123	132	Hs.656586	NM_001123	ENSG00000156110	ADK	AK	adenosine kinase	protein-coding	0.026403	0.585526	
chunk0004_50_1	chr1	42966513	42966795	+	0	NA	intron (NR_033967, intron 1 of 3)	intron (NR_033967, intron 1 of 3)	-7478	NM_006516	6513	Hs.473721	NM_006516	ENSG00000117394	SLC2A1	CSE|DYT17|DYT18|DYT9|EIG12|GLUT|GLUT-1|GLUT1|GLUT1DS|HTLVR|PED|SDCHCN	solute carrier family 2 member 1	protein-coding	0.003546	0.448763	
chunk0192_174_1	chr8	62770771	62770970	+	0	NA	intron (NR_130764, intron 4 of 6)	L1M4a1|LINE|L1	-206991	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.020101	0.370000	
chunk0041_10_1	chr12	338036	338334	+	0	NA	intron (NM_001042603, intron 10 of 27)	MER68|LTR|ERVL	-51165	NM_001130147	84318	Hs.631656	NM_032358	ENSG00000120647	CCDC77	-	coiled-coil domain containing 77	protein-coding	0.003356	0.428094	
chunk0113_216_1	chr20	53845701	53846193	+	0	NA	Intergenic	L1MC1|LINE|L1	29762	NR_002189	391257	Hs.449977	NR_002189		SUMO1P1	PIC1L|UBL2|UBL6	SUMO1 pseudogene 1	pseudo	0.004065	0.356998	
chunk0155_56_1	chr5	91280439	91280638	+	0	NA	Intergenic	CpG	33864	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.085427	0.585000	
chunk0116_146_1	chr21	36408178	36408847	+	0	NA	intron (NM_005441, intron 8 of 13)	intron (NM_005441, intron 8 of 13)	23121	NM_005441	8208	Hs.75238	NM_005441	ENSG00000159259	CHAF1B	CAF-1|CAF-IP60|CAF1|CAF1A|CAF1P60|MPHOSPH7|MPP7	chromatin assembly factor 1 subunit B	protein-coding	0.011958	0.501493	305(AGGCTCACTATGTTCT,-,0.00),306(GGCTCACTATGTTCTC,+,0.00),405(GAGAACAGACAGTGCC,-,0.00),406(AGAACAGACAGTGCCG,+,0.00)
chunk0027_285_1	chr10	77541435	77542032	+	0	NA	intron (NM_001014797, intron 1 of 28)	MER5B|DNA|hAT-Charlie	96086	NM_001271521	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.003350	0.394649	
chunk0011_250_1	chr1	150623112	150623494	+	0	NA	TTS (NM_207047)	TTS (NM_207047)	5830	NM_207045	2029	Hs.632456	NM_004436	ENSG00000143420	ENSA	ARPP-19e	endosulfine alpha	protein-coding	0.000000	0.433420	
chunk0105_91_1	chr2	184296133	184296380	+	0	NA	Intergenic	Intergenic	-82719	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.000000	0.314516	
chunk0005_34_1	chr1	54834805	54835113	+	0	NA	intron (NM_001110533, intron 9 of 9)	L1ME2z|LINE|L1	28896	NM_152607	163747	Hs.376018	NM_152607	ENSG00000162398	LEXM	C1orf177|LEM	lymphocyte expansion molecule	protein-coding	0.006494	0.355987	
chunk0123_166_1	chr3	43691381	43691753	+	0	NA	intron (NM_016006, intron 1 of 6)	CpG	684	NM_016006	51099	Hs.19385	NM_016006	ENSG00000011198	ABHD5	CGI58|IECN2|NCIE2	abhydrolase domain containing 5	protein-coding	0.072581	0.621984	127(AGGTACTACCTGTGCT,-,0.00),128(GGTACTACCTGTGCTC,+,0.00)
chunk0085_338_1	chr18	8688063	8688570	+	0	NA	Intergenic	Intergenic	19305	NR_120598	100287082	Hs.439434	NR_120598	ENSG00000265962	GACAT2	MTCL1-AS1|MTCL1AS1	gastric cancer associated transcript 2	ncRNA	0.011834	0.454724	
chunk0061_33_1	chr14	55915401	55915850	+	0	NA	Intergenic	Intergenic	-118951	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.008909	0.466667	326(GAGAACATGTTGTTTT,-,0.00),327(AGAACATGTTGTTTTC,+,0.00)
chunk0163_182_1	chr6	11335258	11335747	+	0	NA	intron (NM_001142393, intron 1 of 7)	HSMAR1|DNA|TcMar-Mariner	46846	NM_001142393	4739	Hs.37982	NM_006403	ENSG00000111859	NEDD9	CAS-L|CAS2|CASL|CASS2|HEF1	neural precursor cell expressed, developmentally down-regulated 9	protein-coding	0.014315	0.442857	
chunk0031_416_1	chr10	132206088	132206471	+	0	NA	TTS (NM_006426)	TTS (NM_006426)	19369	NM_006426	10570	Hs.100058	NM_006426	ENSG00000151640	DPYSL4	CRMP3|DRP-4|ULIP4	dihydropyrimidinase like 4	protein-coding	0.049608	0.638021	206(AGGGACACCTTGTGCC,-,0.00),207(GGGACACCTTGTGCCA,+,0.00)
chunk0170_396_1	chr6	117423672	117424100	+	0	NA	intron (NM_002944, intron 1 of 42)	intron (NM_002944, intron 1 of 42)	1969	NM_002944	6098	Hs.1041	NM_002944	ENSG00000047936	ROS1	MCF3|ROS|c-ros-1	ROS proto-oncogene 1, receptor tyrosine kinase	protein-coding	0.007009	0.375291	230(GGGAACATGTAGTACT,-,0.00),231(GGAACATGTAGTACTT,+,0.00)
chunk0176_282_1	chr7	16642723	16643139	+	0	NA	intron (NM_020319, intron 1 of 9)	Charlie29a|DNA|hAT-Charlie	2886	NM_020319	57037	Hs.157378	NM_020319	ENSG00000106524	ANKMY2	ZMYND20	ankyrin repeat and MYND domain containing 2	protein-coding	0.004808	0.342926	188(AGGTACAGCCTGTTTA,-,0.00),189(GGTACAGCCTGTTTAT,+,0.00)
chunk0032_342_1	chr11	10292093	10292342	+	0	NA	intron (NM_030962, intron 1 of 39)	L1MC4|LINE|L1	1990	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.004016	0.404000	
chunk0001_368_1	chr1	10109029	10109804	+	0	NA	intron (NM_001105562, intron 7 of 27)	intron (NM_001105562, intron 7 of 27)	76433	NM_006048	10277	Hs.593974	NM_006048	ENSG00000130939	UBE4B	E4|HDNB1|UBOX3|UFD2|UFD2A	ubiquitination factor E4B	protein-coding	0.016774	0.465206	
chunk0190_414_1	chr8	40904293	40904492	+	0	NA	Intergenic	Intergenic	-6568	NM_024645	79698	Hs.591850	NM_024645	ENSG00000165061	ZMAT4	-	zinc finger matrin-type 4	protein-coding	0.005025	0.460000	
chunk0104_331_1	chr2	179558727	179558940	+	0	NA	intron (NM_152520, intron 3 of 9)	intron (NM_152520, intron 3 of 9)	3755	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.004695	0.509346	
chunk0030_208_1	chr10	114568479	114568678	+	0	NA	intron (NM_001003407, intron 4 of 21)	intron (NM_001003407, intron 4 of 21)	-41652	NM_006720	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.005025	0.345000	
chunk0137_239_1	chr4	20512557	20512775	+	0	NA	intron (NM_001289135, intron 11 of 35)	intron (NM_001289135, intron 11 of 35)	-15609	NR_029631	407000		NR_029631	ENSG00000207732	MIR218-1	MIRN218-1|mir-218-1	microRNA 218-1	ncRNA	0.000000	0.392694	
chunk0092_444_1	chr19	38745422	38745628	+	0	NA	Intergenic	Intergenic	-1051	NM_144691	147968	Hs.731775	NM_144691	ENSG00000182472	CAPN12	-	calpain 12	protein-coding	0.024272	0.642512	
chunk0130_312_1	chr3	137071221	137071582	+	0	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	113536	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.005540	0.477901	
chunk0122_45_1	chr3	28283678	28283900	+	0	NA	intron (NM_182523, intron 2 of 3)	intron (NM_182523, intron 2 of 3)	42156	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.004505	0.394619	
chunk0030_329_1	chr10	118269012	118269318	+	0	NA	Intergenic	MIRb|SINE|MIR	73162	NM_022063	63877	Hs.105575	NM_022063	ENSG00000165669	FAM204A	C10orf84|bA319I23.1	family with sequence similarity 204 member A	protein-coding	0.016340	0.439739	240(GAGAACATTTTGTTCA,-,0.00),241(AGAACATTTTGTTCAA,+,0.00)
chunk0148_117_1	chr5	5159356	5159714	+	0	NA	intron (NM_139056, intron 3 of 22)	intron (NM_139056, intron 3 of 22)	19205	NM_139056	170690	Hs.661915	NM_139056	ENSG00000145536	ADAMTS16	ADAMTS16s	ADAM metallopeptidase with thrombospondin type 1 motif 16	protein-coding	0.005587	0.398329	
chunk0078_333_1	chr17	8692816	8693418	+	0	NA	Intergenic	L1MC5a|LINE|L1	51719	NM_144681	146849	Hs.121438	NM_144681	ENSG00000161973	CCDC42	CCDC42A	coiled-coil domain containing 42	protein-coding	0.018272	0.446103	
chunk0119_92_1	chr22	41843064	41843418	+	0	NA	intron (NM_004599, intron 1 of 18)	intron (NM_004599, intron 1 of 18)	10162	NM_004599	6721	Hs.443258	NM_004599	ENSG00000198911	SREBF2	SREBP-2|SREBP2|bHLHd2	sterol regulatory element binding transcription factor 2	protein-coding	0.008475	0.397183	
chunk0023_22_1	chr10	21011188	21011395	+	0	NA	intron (NM_213569, intron 3 of 6)	LTR81B|LTR|Gypsy	-113689	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.028986	0.447115	
chunk0007_357_1	chr1	84899871	84900281	+	0	NA	Intergenic	Intergenic	-6863	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.002439	0.386861	
chunk0177_220_1	chr7	24167062	24167460	+	0	NA	Intergenic	Intergenic	-116927	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.002513	0.278195	
chunk0167_312_1	chr6	71935304	71935880	+	0	NA	intron (NM_014989, intron 1 of 33)	intron (NM_014989, intron 1 of 33)	48889	NM_014989	22999	Hs.485729	NM_014989	ENSG00000079841	RIMS1	CORD7|RAB3IP2|RIM|RIM1	regulating synaptic membrane exocytosis 1	protein-coding	0.005208	0.334489	
chunk0207_452_1	chr9	137715024	137715587	+	0	NA	intron (NM_001145527, intron 2 of 15)	intron (NM_001145527, intron 2 of 15)	-47717	NR_024341	79813	Hs.495511	NM_024757	ENSG00000181090	EHMT1	EHMT1-IT1|EUHMTASE1|Eu-HMTase1|FP13812|GLP|GLP1|KLEFS1|KMT1D	euchromatic histone lysine methyltransferase 1	protein-coding	0.014210	0.423759	136(GGGAACAGTTTGACCC,-,0.00),137(GGAACAGTTTGACCCT,+,0.00)
chunk0115_292_1	chr21	28256372	28256691	+	0	NA	Intergenic	Intergenic	-27864	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.006270	0.396875	
chunk0031_403_1	chr10	131840605	131840856	+	0	NA	Intergenic	Intergenic	-50531	NR_038365	399827	Hs.523353	NM_001001677	ENSG00000189275	LINC01164	-	long intergenic non-protein coding RNA 1164	ncRNA	0.007968	0.519841	
chunk0067_208_1	chr15	44992733	44993297	+	0	NA	Intergenic	L1PA6|LINE|L1	-30089	NM_003104	6652	Hs.878	NM_003104	ENSG00000140263	SORD	HEL-S-95n|RDH|SDH|SORD1|XDH	sorbitol dehydrogenase	protein-coding	0.003546	0.380531	346(AAAGACACAATGTACC,-,0.00)
chunk0013_365_1	chr1	172431902	172432456	+	0	NA	intron (NM_139240, intron 1 of 6)	L1PA6|LINE|L1	11491	NM_139240	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.016245	0.549550	
chunk0031_166_1	chr10	125407756	125407955	+	0	NA	Intergenic	L1MA3|LINE|L1	-166516	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.005025	0.500000	
chunk0092_301_1	chr19	34297416	34298105	+	0	NA	intron (NM_014686, intron 1 of 13)	intron (NM_014686, intron 1 of 13)	43209	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.010160	0.384058	226(GGGAACAGCCTGCCCC,-,0.00),227(GGAACAGCCTGCCCCG,+,0.00)
chunk0211_25_1	chrX	107929112	107929621	+	0	NA	3' UTR (NM_012216, exon 10 of 10)	3' UTR (NM_012216, exon 10 of 10)	6614	NR_110395	101928335	Hs.657090	NR_110395	ENSG00000236064	LOC101928335	-	uncharacterized LOC101928335	ncRNA	0.003929	0.380392	
chunk0031_177_1	chr10	125626260	125626482	+	0	NA	Intergenic	Intergenic	52000	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.009009	0.511211	
chunk0094_199_1	chr2	6349510	6350016	+	0	NA	Intergenic	Intergenic	25659	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.007905	0.386588	
chunk0034_347_1	chr11	35763227	35763930	+	0	NA	intron (NM_017583, intron 4 of 4)	MIR3|SINE|MIR	100826	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.007112	0.433239	
chunk0021_450_1	chr1	248858006	248858327	+	0	NA	exon (NM_017865, exon 2 of 12)	exon (NM_017865, exon 2 of 12)	760	NM_001136036	55657	Hs.377705	NM_017865	ENSG00000171163	ZNF692	AREBP|Zfp692	zinc finger protein 692	protein-coding	0.062305	0.673913	
chunk0121_161_1	chr3	19424561	19424903	+	0	NA	intron (NM_144633, intron 7 of 15)	L1PB2|LINE|L1	-109801	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.005848	0.309038	
chunk0208_183_1	chrX	17072653	17073204	+	0	NA	intron (NM_004726, intron 11 of 17)	intron (NM_004726, intron 11 of 17)	126237	NM_004726	9185	Hs.186810	NM_004726	ENSG00000169891	REPS2	POB1	RALBP1 associated Eps domain containing 2	protein-coding	0.009074	0.509058	305(AAGATCTCTGTGTTCT,-,0.00),306(AGATCTCTGTGTTCTC,+,0.00)
chunk0123_416_1	chr3	49513549	49514171	+	0	NA	intron (NM_001177637, intron 3 of 3)	intron (NM_001177637, intron 3 of 3)	40506	NR_038866	100132677	Hs.435651	NR_038866	ENSG00000226913	BSN-DT	BSN-AS2	BSN divergent transcript	ncRNA	0.009646	0.436597	
chunk0164_60_1	chr6	19302954	19303830	+	0	NA	Intergenic	Intergenic	-122912	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.011416	0.434436	
chunk0024_138_1	chr10	35090416	35090771	+	0	NA	promoter-TSS (NM_001198777)	promoter-TSS (NM_001198777)	49	NM_001198777	8453	Hs.82919	NM_003591	ENSG00000108094	CUL2	-	cullin 2	protein-coding	0.081690	0.615169	
chunk0034_265_1	chr11	34529605	34530262	+	0	NA	Intergenic	Intergenic	-16133	NM_001243080	2001	Hs.11713	NM_001422	ENSG00000135374	ELF5	ESE2	E74 like ETS transcription factor 5	protein-coding	0.001522	0.398176	
chunk0009_299_1	chr1	107964178	107964500	+	0	NA	promoter-TSS (NR_046653)	promoter-TSS (NR_046653)	-104	NR_046653	100873946	Hs.568676	NR_046653	ENSG00000230489	VAV3-AS1	-	VAV3 antisense RNA 1	ncRNA	0.046584	0.470588	
chunk0072_239_1	chr15	95950035	95950555	+	0	NA	Intergenic	Intergenic	-375633	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.003846	0.347409	244(AGGACAAATAGTCCCC,+,0.00)
chunk0189_409_1	chr8	27631213	27631770	+	0	NA	Intergenic	Intergenic	-2569	NM_016240	51435	Hs.128856	NM_016240	ENSG00000168077	SCARA3	APC7|CSR|CSR1|MSLR1|MSRL1	scavenger receptor class A member 3	protein-coding	0.010772	0.474910	
chunk0189_254_1	chr8	25174533	25174797	+	0	NA	Intergenic	L1MC|LINE|L1	-10107	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.018939	0.343396	
chunk0212_211_1	chrX	135473706	135474292	+	0	NA	Intergenic	Intergenic	-46631	NM_182540	203522	Hs.496829	NM_182540	ENSG00000165359	INTS6L	DDX26B	integrator complex subunit 6 like	protein-coding	0.005119	0.424191	
chunk0081_192_1	chr17	42135559	42136037	+	0	NA	intron (NM_001252039, intron 1 of 6)	intron (NM_001252039, intron 1 of 6)	13060	NM_033194	94086	Hs.620611	NM_033194	ENSG00000260325	HSPB9	CT51	heat shock protein family B (small) member 9	protein-coding	0.014644	0.521921	
chunk0016_117_1	chr1	196109473	196109672	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	472909	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005025	0.425000	
chunk0196_368_1	chr8	115194201	115195031	+	0	NA	Intergenic	Intergenic	473396	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.010843	0.369434	
chunk0190_164_1	chr8	31833419	31833902	+	0	NA	intron (NM_013962, intron 1 of 4)	intron (NM_013962, intron 1 of 4)	-192076	NR_104158	100856811	Hs.97362	NR_104156		NRG1-IT1	-	NRG1 intronic transcript 1	ncRNA	0.008282	0.378099	
chunk0117_10_1	chr22	11056792	11057015	+	0	NA	Intergenic	AluSg|SINE|Alu	-95374	NR_132320	102723780		NR_132320		FRG1FP	-	FSHD region gene 1 family member F, pseudogene	pseudo	0.013453	0.513393	
chunk0162_330_1	chr6	6788439	6788989	+	0	NA	Intergenic	LTR33|LTR|ERVL	-165888	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.007273	0.470054	
chunk0013_247_1	chr1	169741226	169741579	+	0	NA	Intergenic	MIRb|SINE|MIR	-7323	NM_000450	6401	Hs.82848	NM_000450	ENSG00000007908	SELE	CD62E|ELAM|ELAM1|ESEL|LECAM2	selectin E	protein-coding	0.014164	0.403955	
chunk0059_297_1	chr14	35929034	35929744	+	0	NA	Intergenic	L1ME1|LINE|L1	102998	NM_032352	84312	Hs.525299	NM_032352	ENSG00000100916	BRMS1L	BRMS1	BRMS1 like transcriptional repressor	protein-coding	0.008451	0.367089	
chunk0045_134_1	chr12	46428277	46428476	+	0	NA	intron (NR_125381, intron 2 of 2)	L1PA17|LINE|L1	44269	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.000000	0.340000	
chunk0199_218_1	chr9	5190090	5190554	+	0	NA	Intergenic	L1MD1|LINE|L1	-4704	NM_007179	11172	Hs.632648	NM_007179	ENSG00000120210	INSL6	RIF1	insulin like 6	protein-coding	0.002155	0.326882	
chunk0176_428_1	chr7	19708979	19709244	+	0	NA	promoter-TSS (NM_001002926)	promoter-TSS (NM_001002926)	-74	NM_001002926	221830	Hs.353035	NM_001002926	ENSG00000105849	TWISTNB	-	TWIST neighbor	protein-coding	0.101887	0.620301	
chunk0039_404_1	chr11	107467634	107468268	+	0	NA	Intergenic	Intergenic	-10105	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.003155	0.324409	
chunk0112_25_1	chr20	36122390	36122612	+	0	NA	intron (NM_001258329, intron 2 of 22)	intron (NM_001258329, intron 2 of 22)	29791	NM_001258329	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.009009	0.609865	
chunk0065_304_1	chr14	102839418	102839809	+	0	NA	intron (NM_145725, intron 2 of 11)	intron (NM_145725, intron 2 of 11)	62134	NM_003300	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.010230	0.410714	
chunk0026_267_1	chr10	66991131	66991672	+	0	NA	intron (NR_111911, intron 1 of 6)	intron (NR_111911, intron 1 of 6)	20752	NR_111911	101928961	Hs.687014	NR_111911		LOC101928961	-	uncharacterized LOC101928961	ncRNA	0.007394	0.315498	
chunk0159_339_1	chr5	144114580	144115031	+	0	NA	Intergenic	L1MB7|LINE|L1	55909	NM_001271732	81555	Hs.372050	NM_030799	ENSG00000145817	YIPF5	FinGER5|SB140|SMAP-5|SMAP5|YIP1A	Yip1 domain family member 5	protein-coding	0.002217	0.307522	
chunk0026_276_1	chr10	67211453	67212103	+	0	NA	intron (NM_001291133, intron 7 of 8)	MIRc|SINE|MIR	191632	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.003077	0.313364	
chunk0149_296_1	chr5	25606124	25607006	+	0	NA	Intergenic	Intergenic	-765982	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.005669	0.405436	532(AAGTACAAAGTGTACT,-,0.00),533(AGTACAAAGTGTACTC,+,0.00)
chunk0075_161_1	chr16	51698494	51699090	+	0	NA	Intergenic	Intergenic	-63727	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.005034	0.376884	
chunk0013_42_1	chr1	166952050	166952338	+	0	NA	intron (NM_199351, intron 3 of 9)	intron (NM_199351, intron 3 of 9)	23130	NM_199351	387597	Hs.444835	NM_199351	ENSG00000143195	ILDR2	C1orf32|dJ782G3.1	immunoglobulin like domain containing receptor 2	protein-coding	0.006944	0.449827	174(ATAAACAGCCTGTCCT,-,0.00),175(TAAACAGCCTGTCCTT,+,0.00)
chunk0170_158_1	chr6	111521613	111521935	+	0	NA	intron (NR_034109, intron 1 of 1)	intron (NR_034109, intron 1 of 1)	-38059	NM_001286432	5980	Hs.232021	NM_002912	ENSG00000009413	REV3L	POLZ|REV3	REV3 like, DNA directed polymerase zeta catalytic subunit	protein-coding	0.009317	0.331269	111(AAGAACATTCAGTTCC,-,0.00),112(AGAACATTCAGTTCCA,+,0.00)
chunk0192_53_1	chr8	59566081	59566399	+	0	NA	Intergenic	L1PB1|LINE|L1	-447032	NM_014729	9760	Hs.491805	NM_014729	ENSG00000198846	TOX	TOX1	thymocyte selection associated high mobility group box	protein-coding	0.003145	0.341693	
chunk0205_222_1	chr9	109877435	109877766	+	0	NA	intron (NM_053016, intron 2 of 6)	MIR|SINE|MIR	97303	NM_053016	445815	Hs.591908	NM_007203	ENSG00000157654	PALM2-AKAP2	AKAP-2|AKAP-KL|AKAP2|AKAPKL|MISP2|PALM2|PRKA2	PALM2-AKAP2 fusion	protein-coding	0.003021	0.430723	
chunk0172_397_1	chr6	139732505	139732739	+	0	NA	Intergenic	Intergenic	-38451	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.008547	0.476596	
chunk0175_450_1	chr6	170146217	170146418	+	0	NA	Intergenic	Intergenic	-14325	NR_125878	102724511	Hs.550045	NR_125878		LOC102724511	-	uncharacterized LOC102724511	ncRNA	0.000000	0.579208	
chunk0145_420_1	chr4	152968887	152969390	+	0	NA	intron (NM_033393, intron 9 of 10)	intron (NM_033393, intron 9 of 10)	26155	NM_033393	85462	Hs.132629	NM_033393	ENSG00000137460	FHDC1	-	FH2 domain containing 1	protein-coding	0.015905	0.430556	329(AGGAACAGTGTGCTCC,-,0.00),330(GGAACAGTGTGCTCCT,+,0.00)
chunk0111_211_1	chr20	28602539	28602936	+	0	NA	promoter-TSS (NR_132315)	promoter-TSS (NR_132315)	-72	NR_132315	100289097	Hs.529357	NR_132315	ENSG00000282826	FRG1CP	-	FSHD region gene 1 family member C, pseudogene	pseudo	0.062972	0.600503	
chunk0113_203_1	chr20	53683653	53684050	+	0	NA	Intergenic	Intergenic	-100754	NM_006526	7764	Hs.155040	NM_006526	ENSG00000171940	ZNF217	ZABC1	zinc finger protein 217	protein-coding	0.015113	0.434673	288(GGAACACAAAGATCTT,+,0.00)
chunk0140_128_1	chr4	69027259	69028009	+	0	NA	Intergenic	Intergenic	-7237	NM_001075	7365	Hs.201634	NM_001075	ENSG00000109181	UGT2B10	UDPGT2B10	UDP glucuronosyltransferase family 2 member B10	protein-coding	0.004000	0.375499	
chunk0146_324_1	chr4	165657147	165657365	+	0	NA	Intergenic	Intergenic	-27383	NR_121676	101928151	Hs.639858	NR_121676	ENSG00000249500	LINC01179	-	long intergenic non-protein coding RNA 1179	ncRNA	0.004587	0.383562	
chunk0198_357_1	chr8	140708948	140709500	+	0	NA	intron (NM_001316342, intron 23 of 32)	intron (NM_001316342, intron 23 of 32)	23429	NR_029892	442893		NR_029892	ENSG00000254324	MIR151A	MIR151|MIRN151|hsa-mir-151|hsa-mir-151a	microRNA 151a	ncRNA	0.000000	0.327306	
chunk0080_295_1	chr17	31494938	31495433	+	0	NA	intron (NM_001303542, intron 1 of 12)	intron (NM_001303542, intron 1 of 12)	7184	NM_001303542	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.010101	0.578629	260(AGGTGCAGGCTGTGCC,-,0.00),261(GGTGCAGGCTGTGCCA,+,0.00)
chunk0003_436_1	chr1	41175086	41175321	+	0	NA	intron (NM_001172219, intron 2 of 14)	MLT2B1|LTR|ERVL	-12186	NM_001172221	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.004255	0.415254	
chunk0019_145_1	chr1	225744094	225744557	+	0	NA	Intergenic	L1PA10|LINE|L1	-33488	NM_003133	6726	Hs.511425	NM_003133	ENSG00000143742	SRP9	ALURBP	signal recognition particle 9	protein-coding	0.015119	0.459052	266(TGTACATCCTGTACAT,+,0.00)
chunk0104_118_1	chr2	172943945	172944279	+	0	NA	intron (NM_001282901, intron 1 of 24)	intron (NM_001282901, intron 1 of 24)	15907	NM_001282901	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.008982	0.385075	
chunk0196_431_1	chr8	116450723	116451414	+	0	NA	Intergenic	MER126|DNA|DNA	-126009	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.002894	0.355491	346(AAGAACAGATTGTGAC,-,0.00)
chunk0060_397_1	chr14	52960836	52961420	+	0	NA	Intergenic	Intergenic	-10031	NM_001135000	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.001712	0.444444	261(GTAACACAATGTCCTC,+,0.00)
chunk0062_158_1	chr14	69310299	69310591	+	0	NA	intron (NM_001168368, intron 1 of 14)	L1M5|LINE|L1	50481	NM_001168368	57452	Hs.21035	NM_020692	ENSG00000100626	GALNT16	GALNACT16|GALNTL1|GalNAc-T16	polypeptide N-acetylgalactosaminyltransferase 16	protein-coding	0.000000	0.361775	
chunk0026_345_1	chr10	68633968	68634853	+	0	NA	intron (NM_030625, intron 3 of 11)	intron (NM_030625, intron 3 of 11)	74050	NM_030625	80312	Hs.258855	NM_030625	ENSG00000138336	TET1	CXXC6|LCX|bA119F7.1	tet methylcytosine dioxygenase 1	protein-coding	0.007910	0.397291	
chunk0205_340_1	chr9	113257881	113258798	+	0	NA	intron (NM_001859, intron 3 of 4)	intron (NM_001859, intron 3 of 4)	17250	NM_139286	246184	Hs.727648	NM_139286	ENSG00000176386	CDC26	ANAPC12|APC12|C9orf17	cell division cycle 26	protein-coding	0.007634	0.373638	
chunk0048_146_1	chr12	80320106	80320683	+	0	NA	intron (NM_173591, intron 32 of 57)	intron (NM_173591, intron 32 of 57)	110941	NM_173591	283310	Hs.723594	NM_173591	ENSG00000165899	OTOGL	C12orf64|DFNB84B	otogelin like	protein-coding	0.003466	0.344291	
chunk0091_74_1	chr19	4991447	4992537	+	0	NA	intron (NM_015015, intron 1 of 22)	L1M4|LINE|L1	22879	NM_015015	23030	Hs.654816	NM_015015	ENSG00000127663	KDM4B	JMJD2B|TDRD14B	lysine demethylase 4B	protein-coding	0.020183	0.433547	
chunk0066_283_1	chr15	35278415	35278711	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	41237	NR_003144	723972	Hs.631698	NR_003144	ENSG00000259516	ANP32AP1	-	acidic nuclear phosphoprotein 32 family member A pseudogene 1	pseudo	0.006757	0.589226	
chunk0161_2_1	chr5	165280376	165281056	+	0	NA	Intergenic	Intergenic	810437	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.004412	0.330396	193(AAGAACACCAAGTGCT,-,0.00),194(AGAACACCAAGTGCTT,+,0.00)
chunk0004_445_1	chr1	53238453	53238762	+	0	NA	promoter-TSS (NM_002370)	promoter-TSS (NM_002370)	-3	NR_038953	100507564	Hs.592502	NR_038953	ENSG00000226754	LOC100507564	-	uncharacterized LOC100507564	ncRNA	0.090615	0.632258	
chunk0119_418_1	chr22	49826160	49826489	+	0	NA	promoter-TSS (NM_001304809)	promoter-TSS (NM_001304809)	-424	NM_001304809	23774	Hs.127950	NM_014577	ENSG00000100425	BRD1	BRL|BRPF1|BRPF2	bromodomain containing 1	protein-coding	0.048632	0.606061	
chunk0041_279_1	chr11	129324469	129324961	+	0	NA	Intergenic	Intergenic	-51271	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.018293	0.513185	
chunk0192_45_1	chr8	58844895	58845595	+	0	NA	intron (NM_014729, intron 4 of 8)	intron (NM_014729, intron 4 of 8)	-185400	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.007143	0.332382	
chunk0051_188_1	chr12	116200945	116201170	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	-52403	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.000000	0.362832	
chunk0060_455_1	chr14	55064312	55064775	+	0	NA	intron (NM_144578, intron 3 of 3)	intron (NM_144578, intron 3 of 3)	12899	NM_144578	93487	Hs.594338	NM_144578	ENSG00000168175	MAPK1IP1L	C14orf32|MISS|c14_5346	mitogen-activated protein kinase 1 interacting protein 1 like	protein-coding	0.006479	0.323276	
chunk0022_444_1	chr10	19749773	19750226	+	0	NA	Intergenic	MER54B|LTR|ERVL	-21449	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.008830	0.464758	
chunk0120_414_1	chr3	12897453	12897879	+	0	NA	3' UTR (NM_001134382, exon 14 of 14)	3' UTR (NM_001134382, exon 14 of 14)	-56084	NM_000994	6161	Hs.265174	NM_000994	ENSG00000144713	RPL32	L32|PP9932	ribosomal protein L32	protein-coding	0.016432	0.491803	
chunk0202_345_1	chr9	79539394	79539696	+	0	NA	Intergenic	Intergenic	-32228	NM_001282749	7091	Hs.444213	NM_007005	ENSG00000106829	TLE4	BCE-1|BCE1|E(spI)|E(spl)|ESG|ESG4|GRG4|Grg-4	TLE family member 4, transcriptional corepressor	protein-coding	0.006623	0.415842	
chunk0142_425_1	chr4	104128423	104129246	+	0	NA	Intergenic	Intergenic	-362131	NR_125926	101929468	Hs.480435	NR_125926	ENSG00000245384	CXXC4-AS1	-	CXXC4 antisense RNA 1	ncRNA	0.000000	0.359223	
chunk0093_22_1	chr2	291507	291994	+	0	NA	Intergenic	Intergenic	-3442	NM_001002919	285016	Hs.355207	NM_001002919	ENSG00000189292	ALKAL2	AUGA|FAM150B|PRO1097|RGPG542	ALK and LTK ligand 2	protein-coding	0.006160	0.305328	
chunk0084_421_1	chr17	82494522	82494721	+	0	NA	Intergenic	Intergenic	-25097	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.010050	0.500000	
chunk0102_108_1	chr2	144433221	144433587	+	0	NA	intron (NM_014795, intron 2 of 9)	intron (NM_014795, intron 2 of 9)	-86210	NR_040248	100303491	Hs.560789	NR_040248	ENSG00000238057	ZEB2-AS1	ZEB2-AS|ZEB2AS|ZEB2NAT	ZEB2 antisense RNA 1	ncRNA	0.000000	0.329700	
chunk0105_354_1	chr2	191677864	191678611	+	0	NA	non-coding (NR_045623, exon 1 of 7)	non-coding (NR_045623, exon 1 of 7)	101	NR_045623	64859	Hs.591610	NM_022837	ENSG00000173559	NABP1	OBFC2A|SOSS-B2|SSB2	nucleic acid binding protein 1	protein-coding	0.091031	0.652406	
chunk0193_177_1	chr8	74921246	74921734	+	0	NA	Intergenic	Intergenic	-62983	NM_031461	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.010246	0.413088	
chunk0132_313_1	chr3	160684506	160684756	+	0	NA	Intergenic	Intergenic	7471	NM_025047	80117	Hs.287702	NM_025047	ENSG00000179674	ARL14	ARF7	ADP ribosylation factor like GTPase 14	protein-coding	0.008000	0.454183	
chunk0144_110_1	chr4	128638529	128638793	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-170962	NM_024900	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.007576	0.449057	
chunk0050_97_1	chr12	101891558	101892305	+	0	NA	intron (NM_018370, intron 1 of 6)	intron (NM_018370, intron 1 of 6)	14604	NM_018370	55332	Hs.525634	NM_018370	ENSG00000136048	DRAM1	DRAM	DNA damage regulated autophagy modulator 1	protein-coding	0.006693	0.406417	
chunk0193_403_1	chr8	80579447	80580077	+	0	NA	Intergenic	MIRc|SINE|MIR	93549	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.006349	0.372425	
chunk0191_411_1	chr8	57678323	57678531	+	0	NA	Intergenic	Intergenic	-299931	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.004808	0.272727	
chunk0154_52_1	chr5	77193613	77194231	+	0	NA	Intergenic	L1ME2|LINE|L1	-16959	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.000000	0.303716	
chunk0073_183_1	chr16	8958266	8958478	+	0	NA	intron (NM_003470, intron 1 of 30)	intron (NM_003470, intron 1 of 30)	5112	NM_003470	7874	Hs.386939	NM_003470	ENSG00000187555	USP7	HAUSP|TEF1	ubiquitin specific peptidase 7	protein-coding	0.014151	0.563380	145(CAGGACACCAAGTCCT,-,0.00),146(AGGACACCAAGTCCTT,+,0.00)
chunk0030_343_1	chr10	118456965	118457213	+	0	NA	Intergenic	Intergenic	99981	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.012097	0.341365	164(AAGTACATAATGTTTT,-,0.00),165(AGTACATAATGTTTTT,+,0.00)
chunk0117_360_1	chr21	44773367	44774050	+	0	NA	intron (NM_001202489, intron 2 of 3)	intron (NM_001202489, intron 2 of 3)	28128	NM_001202489	7327	Hs.529420	NM_003343	ENSG00000184787	UBE2G2	UBC7	ubiquitin conjugating enzyme E2 G2	protein-coding	0.026354	0.504386	
chunk0077_306_1	chr16	81844664	81845028	+	0	NA	intron (NM_002661, intron 2 of 32)	intron (NM_002661, intron 2 of 32)	65588	NM_002661	5336	Hs.372303	NM_002661	ENSG00000197943	PLCG2	APLAID|FCAS3|PLC-IV|PLC-gamma-2	phospholipase C gamma 2	protein-coding	0.008242	0.400000	256(TGAGACACCATGTTCT,-,0.00),257(GAGACACCATGTTCTT,+,0.00)
chunk0105_428_1	chr2	193368263	193368468	+	0	NA	Intergenic	Intergenic	618520	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.000000	0.262136	
chunk0116_231_1	chr21	38234618	38235057	+	0	NA	intron (NM_001276438, intron 1 of 2)	intron (NM_001276438, intron 1 of 2)	4922	NM_001276437	3772	Hs.411299	NM_002243	ENSG00000157551	KCNJ15	IRKK|KIR1.3|KIR4.2	potassium voltage-gated channel subfamily J member 15	protein-coding	0.006834	0.354545	
chunk0100_120_1	chr2	108533763	108534124	+	0	NA	promoter-TSS (NM_001193483)	promoter-TSS (NM_001193483)	-412	NM_001193483	3987	Hs.597715	NM_004987	ENSG00000169756	LIMS1	PINCH|PINCH-1|PINCH1	LIM zinc finger domain containing 1	protein-coding	0.069252	0.640884	
chunk0202_267_1	chr9	77038595	77039044	+	0	NA	Intergenic	Intergenic	19164	NM_001013735	442425	Hs.553843	NM_001013735	ENSG00000204612	FOXB2	bA159H20.4	forkhead box B2	protein-coding	0.000000	0.326667	
chunk0145_105_1	chr4	146134721	146135118	+	0	NA	Intergenic	MER130|DNA|DNA	-13006	NR_038331	100505545	Hs.122199	NR_038331	ENSG00000248809	LINC01095	-	long intergenic non-protein coding RNA 1095	ncRNA	0.015113	0.484925	
chunk0095_93_1	chr2	15198381	15198780	+	0	NA	intron (NR_052013, intron 47 of 50)	intron (NR_052013, intron 47 of 50)	362768	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.010025	0.415000	
chunk0179_27_1	chr7	42944724	42944997	+	0	NA	Intergenic	LTR23|LTR|ERV1	12520	NM_031903	64983	Hs.50252	NM_031903	ENSG00000106591	MRPL32	HSPC283|L32mt|MRP-L32|bMRP-59b	mitochondrial ribosomal protein L32	protein-coding	0.007326	0.397810	
chunk0165_335_1	chr6	37473104	37473914	+	0	NA	exon (NM_015050, exon 17 of 24)	exon (NM_015050, exon 17 of 24)	26415	NM_138493	154467	Hs.284207	NM_138493	ENSG00000198937	CCDC167	C6orf129|HSPC265	coiled-coil domain containing 167	protein-coding	0.009877	0.484587	124(GGGGACTCAGTGTTCT,-,0.00),125(GGGACTCAGTGTTCTT,+,0.00)
chunk0139_435_1	chr4	64581400	64581835	+	0	NA	Intergenic	L2a|LINE|L2	-172157	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.006897	0.419725	
chunk0031_280_1	chr10	128175773	128176325	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-49845	NM_002417	4288	Hs.80976	NM_002417	ENSG00000148773	MKI67	KIA|MIB-|MIB-1|PPP1R105	marker of proliferation Ki-67	protein-coding	0.001812	0.338156	
chunk0097_123_1	chr2	46644907	46645337	+	0	NA	Intergenic	Intergenic	27950	NM_014171	9419	Hs.133998	NM_014171	ENSG00000119878	CRIPT	HSPC139|SSMDF	CXXC repeat containing interactor of PDZ3 domain	protein-coding	0.009302	0.357309	
chunk0135_394_1	chr3	191801266	191801465	+	0	NA	Intergenic	L1MB3|LINE|L1	340202	NM_001083308	152138	Hs.690618	NM_001083308	ENSG00000253548	PYDC2	POP2|cPOP2	pyrin domain containing 2	protein-coding	0.010050	0.500000	
chunk0101_345_1	chr2	137645333	137645846	+	0	NA	intron (NM_001316349, intron 21 of 27)	intron (NM_001316349, intron 21 of 27)	282343	NR_120402	101928273	Hs.560928	NR_120402		LOC101928273	-	uncharacterized LOC101928273	ncRNA	0.007797	0.352140	
chunk0140_96_1	chr4	68346568	68346767	+	0	NA	intron (NM_133370, intron 1 of 15)	MER44B|DNA|TcMar-Tigger	3439	NM_133370	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.005025	0.395000	
chunk0172_64_1	chr6	134287590	134288043	+	0	NA	intron (NM_001143676, intron 1 of 13)	LTR64|LTR|ERV1	30242	NM_001143676	6446	Hs.510078	NM_005627	ENSG00000118515	SGK1	SGK	serum/glucocorticoid regulated kinase 1	protein-coding	0.000000	0.286344	
chunk0201_108_1	chr9	35096444	35096688	+	0	NA	promoter-TSS (NM_152850)	promoter-TSS (NM_152850)	-17	NM_032634	84720	Hs.522099	NM_032634	ENSG00000165282	PIGO	HPMRS2	phosphatidylinositol glycan anchor biosynthesis class O	protein-coding	0.073770	0.661224	
chunk0085_77_1	chr18	2099612	2099858	+	0	NA	Intergenic	L1MEc|LINE|L1	471768	NM_022840	64863	Hs.126888	NM_022840	ENSG00000101574	METTL4	HsT661	methyltransferase like 4	protein-coding	0.004065	0.323887	
chunk0104_175_1	chr2	174585190	174585559	+	0	NA	intron (NM_003387, intron 2 of 7)	intron (NM_003387, intron 2 of 7)	-27302	NR_004394	26827		NR_004394	ENSG00000206625	RNU6-1	RNU6|RNU6A|U6|U6-1	RNA, U6 small nuclear 1	snRNA	0.024390	0.497297	
chunk0070_61_1	chr15	69603851	69604407	+	0	NA	intron (NR_126438, intron 1 of 3)	intron (NR_126438, intron 1 of 3)	11929	NR_126437	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.007194	0.500898	
chunk0011_137_1	chr1	147238089	147238510	+	0	NA	Intergenic	Intergenic	-4342	NM_001256337	9557	Hs.191164	NM_004284	ENSG00000131778	CHD1L	ALC1|CHDL	chromodomain helicase DNA binding protein 1 like	protein-coding	0.004751	0.383886	
chunk0094_311_1	chr2	8821893	8822276	+	0	NA	intron (NM_020738, intron 2 of 29)	intron (NM_020738, intron 2 of 29)	15541	NM_020738	57498	Hs.9873	NM_020738	ENSG00000134313	KIDINS220	ARMS|SINO	kinase D interacting substrate 220	protein-coding	0.005222	0.375000	
chunk0151_269_1	chr5	52544061	52544470	+	0	NA	Intergenic	Intergenic	-243675	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.014670	0.373171	
chunk0184_89_1	chr7	113264636	113265263	+	0	NA	Intergenic	L1M1|LINE|L1	-146367	NR_015442									0.004785	0.283439	
chunk0148_102_1	chr5	4206191	4206546	+	0	NA	Intergenic	Intergenic	-567113	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.002817	0.500000	152(CAGGACAGGATGTGAT,-,0.00)
chunk0107_258_1	chr2	217384024	217384279	+	0	NA	intron (NR_026597, intron 8 of 12)	UCON38|Unknown|Unknown	101418	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.007843	0.410156	
chunk0199_275_1	chr9	6425055	6425519	+	0	NA	intron (NM_152896, intron 2 of 15)	L1MC3|LINE|L1	12136	NM_152896	115426	Hs.493401	NM_152896	ENSG00000147854	UHRF2	NIRF|RNF107|TDRD23|URF2	ubiquitin like with PHD and ring finger domains 2	protein-coding	0.006466	0.406452	
chunk0027_149_1	chr10	74687444	74688398	+	0	NA	intron (NM_001123, intron 10 of 10)	L2a|LINE|L2	-138492	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.010482	0.381152	
chunk0130_307_1	chr3	136993533	136993732	+	0	NA	intron (NM_144717, intron 5 of 6)	L1PA6|LINE|L1	35767	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.020101	0.465000	
chunk0004_65_1	chr1	43285220	43285435	+	0	NA	intron (NM_001164829, intron 1 of 2)	intron (NM_001164829, intron 1 of 2)	252	NM_182517	149466	Hs.158963	NM_182517	ENSG00000253313	C1orf210	TEMP	chromosome 1 open reading frame 210	protein-coding	0.009302	0.532407	
chunk0093_447_1	chr19	58431000	58431206	+	0	NA	Intergenic	Intergenic	9119	NM_003433	7691	Hs.156169	NM_003433	ENSG00000131849	ZNF132	pHZ-12	zinc finger protein 132	protein-coding	0.000000	0.478261	
chunk0077_28_1	chr16	75306333	75306613	+	0	NA	intron (NM_006324, intron 5 of 6)	intron (NM_006324, intron 5 of 6)	-38420	NM_001170715	9564	Hs.479747	NM_014567	ENSG00000050820	BCAR1	CAS|CAS1|CASS1|CRKAS|P130Cas	BCAR1 scaffold protein, Cas family member	protein-coding	0.017857	0.487544	192(CAGTACATGCTGAGCT,-,0.00),193(AGTACATGCTGAGCTT,+,0.00)
chunk0187_205_1	chr7	151806302	151806598	+	0	NA	intron (NM_016203, intron 1 of 15)	Charlie19a|DNA|hAT-Charlie	8421	NM_001040633	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.027027	0.441077	
chunk0134_248_1	chr3	179347910	179348472	+	0	NA	intron (NM_033540, intron 1 of 17)	CpG	499	NM_033540	55669	Hs.478383	NM_017927	ENSG00000171109	MFN1	hfzo1|hfzo2	mitofusin 1	protein-coding	0.064057	0.571936	
chunk0036_436_1	chr11	68494815	68495346	+	0	NA	intron (NM_001164161, intron 1 of 23)	intron (NM_001164161, intron 1 of 23)	34362	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.000000	0.349624	
chunk0057_136_1	chr13	99825280	99826010	+	0	NA	intron (NR_120421, intron 1 of 4)	intron (NR_120421, intron 1 of 4)	-96644	NR_120383	101927465	Hs.130690	NR_046525		CLYBL-AS1	-	CLYBL antisense RNA 1	ncRNA	0.016438	0.474692	
chunk0037_64_1	chr11	71112889	71113626	+	0	NA	intron (NM_012309, intron 4 of 24)	intron (NM_012309, intron 4 of 24)	111539	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.028494	0.514905	
chunk0096_345_1	chr2	35651029	35651491	+	0	NA	Intergenic	L1MEf|LINE|L1	179855	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.000000	0.250540	
chunk0166_94_1	chr6	43741699	43742217	+	0	NA	Intergenic	Intergenic	-28251	NM_001025367	7422	Hs.73793	NM_003376	ENSG00000112715	VEGFA	MVCD1|VEGF|VPF	vascular endothelial growth factor A	protein-coding	0.007722	0.373796	241(TTGGACATAGTGTCCA,-,0.00),242(TGGACATAGTGTCCAT,+,0.00)
chunk0088_214_1	chr18	48202479	48203062	+	0	NA	Intergenic	Intergenic	-65461	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.018868	0.623288	281(GGAACACGATGCACTG,+,0.00)
chunk0105_282_1	chr2	189798240	189798642	+	0	NA	intron (NM_001289408, intron 3 of 11)	intron (NM_001289408, intron 3 of 11)	-14070	NM_001128150	94101	Hs.700632	NM_016467	ENSG00000128699	ORMDL1	-	ORMDL sphingolipid biosynthesis regulator 1	protein-coding	0.007463	0.411911	225(TAGCACACTGTGTACT,-,0.00),226(AGCACACTGTGTACTT,+,0.00)
chunk0126_431_1	chr3	86922544	86923419	+	0	NA	Intergenic	Intergenic	68126	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.004571	0.409817	226(GGGGACTTAATGTTCC,-,0.00),227(GGGACTTAATGTTCCA,+,0.00),504(TGGACTCTTTGTTCTT,+,0.00)
chunk0066_31_1	chr15	27608473	27609025	+	0	NA	Intergenic	LTR12|LTR|ERV1	-447430	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.014493	0.461121	
chunk0132_87_1	chr3	155525329	155525528	+	0	NA	intron (NM_001130960, intron 9 of 22)	MLT1A0|LTR|ERVL-MaLR	150888	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.020101	0.485000	
chunk0110_214_1	chr20	15338717	15339054	+	0	NA	intron (NM_001033087, intron 2 of 13)	intron (NM_001033087, intron 2 of 13)	142027	NM_001033087	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.002967	0.372781	
chunk0052_96_1	chr13	22324795	22325164	+	0	NA	Intergenic	Intergenic	114694	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.005420	0.291892	
chunk0029_302_1	chr10	104197675	104198185	+	0	NA	exon (NM_025145, exon 9 of 38)	exon (NM_025145, exon 9 of 38)	20953	NR_030340	693194		NR_030340	ENSG00000208033	MIR609	MIRN609|hsa-mir-609	microRNA 609	ncRNA	0.005882	0.375734	108(AAGGACAGCCTCTGCC,-,0.00),109(AGGACAGCCTCTGCCT,+,0.00)
chunk0050_36_1	chr12	100462902	100463539	+	0	NA	Intergenic	L2c|LINE|L2	-10553	NM_001206978	9971	Hs.282735	NM_005123	ENSG00000012504	NR1H4	BAR|FXR|HRR-1|HRR1|PFIC5|RIP14	nuclear receptor subfamily 1 group H member 4	protein-coding	0.001570	0.346395	
chunk0035_183_1	chr11	44143825	44144400	+	0	NA	intron (NM_207122, intron 7 of 13)	intron (NM_207122, intron 7 of 13)	47915	NM_000401	2132	Hs.368404	NM_000401	ENSG00000151348	EXT2	SOTV|SSMS	exostosin glycosyltransferase 2	protein-coding	0.012174	0.432292	
chunk0103_271_1	chr2	165803069	165803962	+	0	NA	Intergenic	MIRb|SINE|MIR	-9222	NM_004482	2591	Hs.170986	NM_004482	ENSG00000115339	GALNT3	GalNAc-T3|HFTC|HFTC1|HHS	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.005599	0.372483	
chunk0096_276_1	chr2	31949457	31949656	+	0	NA	intron (NM_001301852, intron 1 of 7)	L1MA1|LINE|L1	61108	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.000000	0.375000	
chunk0046_66_1	chr12	55933731	55934027	+	0	NA	intron (NM_201444, intron 1 of 23)	MIRb|SINE|MIR	1851	NM_201445	1606	Hs.524488	NM_001345	ENSG00000065357	DGKA	DAGK|DAGK1|DGK-alpha	diacylglycerol kinase alpha	protein-coding	0.006757	0.387205	
chunk0096_267_1	chr2	31811347	31811973	+	0	NA	Intergenic	Intergenic	199004	NM_001137602	51072	Hs.444969	NM_015955	ENSG00000162959	MEMO1	C2orf4|CGI-27|MEMO|NS5ATP7	mediator of cell motility 1	protein-coding	0.006390	0.373206	314(GAGCACATGCTGTACT,-,0.00),315(AGCACATGCTGTACTC,+,0.00)
chunk0164_184_1	chr6	22049111	22049310	+	0	NA	intron (NR_015410, intron 7 of 11)	intron (NR_015410, intron 7 of 11)	97983	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.000000	0.345000	
chunk0016_102_1	chr1	195363954	195364216	+	0	NA	Intergenic	L1MA1|LINE|L1	1218396	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.003817	0.353612	
chunk0129_218_1	chr3	121837329	121837922	+	0	NA	intron (NM_018456, intron 1 of 5)	MIRb|SINE|MIR	2438	NM_018456	55840	Hs.477325	NM_018456	ENSG00000145088	EAF2	BM040|TRAITS|U19	ELL associated factor 2	protein-coding	0.006745	0.367003	
chunk0159_398_1	chr5	147310169	147310644	+	0	NA	intron (NM_145001, intron 4 of 6)	intron (NM_145001, intron 4 of 6)	75390	NM_145001	202374	Hs.585069	NM_145001	ENSG00000169302	STK32A	YANK1	serine/threonine kinase 32A	protein-coding	0.014737	0.483193	
chunk0089_427_1	chr18	69924970	69925289	+	0	NA	intron (NM_001303619, intron 1 of 4)	CR1_Mam|LINE|CR1	22724	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.009404	0.400000	
chunk0113_348_1	chr20	58816657	58816997	+	0	NA	TTS (NR_029844)	TTS (NR_029844)	867	NR_029844	407022		NR_029844	ENSG00000284040	MIR296	MIRN296|miRNA296|mir-296	microRNA 296	ncRNA	0.026471	0.574780	
chunk0012_244_1	chr1	160941070	160941729	+	0	NA	intron (NR_110695, intron 3 of 5)	L1P2|LINE|L1	8934	NR_110695	101928372		NR_110695	ENSG00000198358	LOC101928372	-	uncharacterized LOC101928372	ncRNA	0.010622	0.536364	299(GGGGGCAGTCTGTCCA,-,0.00),300(GGGGCAGTCTGTCCAT,+,0.00)
chunk0041_360_1	chr11	130907908	130908193	+	0	NA	exon (NM_014758, exon 5 of 11)	exon (NM_014758, exon 5 of 11)	8437	NM_014758	399979	Hs.444024	NM_014758	ENSG00000120451	SNX19	CHET8	sorting nexin 19	protein-coding	0.021053	0.569930	
chunk0035_225_1	chr11	45554561	45555118	+	0	NA	Intergenic	L2b|LINE|L2	110817	NM_003654	8534	Hs.104576	NM_003654	ENSG00000175264	CHST1	C6ST|GST-1|KS6ST|KSGal6ST|KSST	carbohydrate sulfotransferase 1	protein-coding	0.014363	0.467742	
chunk0194_350_1	chr8	89307631	89308273	+	0	NA	Intergenic	Intergenic	449759	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.007788	0.367030	301(AGGAACATAATGTGCT,-,0.00),302(GGAACATAATGTGCTA,+,0.00)
chunk0200_266_1	chr9	22005284	22005534	+	0	NA	3' UTR (NM_004936, exon 2 of 2)	3' UTR (NM_004936, exon 2 of 2)	3904	NM_004936	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.052000	0.561753	
chunk0076_34_1	chr16	59597429	59597656	+	0	NA	Intergenic	LTR33|LTR|ERVL	157649	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.017621	0.491228	44(CTGTACACCCTGTCCA,-,0.00),45(TGTACACCCTGTCCAC,+,0.00)
chunk0203_333_1	chr9	89756696	89757378	+	0	NA	Intergenic	Intergenic	117254	NR_024280	100129066	Hs.125947	NR_024280	ENSG00000237372	UNQ6494	-	uncharacterized LOC100129066	ncRNA	0.014663	0.550512	398(GAGGACAGCGTGTGTT,-,0.00),399(AGGACAGCGTGTGTTG,+,0.00),516(CAGGTCAGTCTGTGCC,-,0.00),517(AGGTCAGTCTGTGCCT,+,0.00)
chunk0108_285_1	chr2	234837335	234838003	+	0	NA	Intergenic	Intergenic	-114315	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.008982	0.405082	
chunk0038_340_1	chr11	92843567	92843878	+	0	NA	intron (NM_001008781, intron 17 of 24)	intron (NM_001008781, intron 17 of 24)	-125901	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.016077	0.429487	
chunk0067_343_1	chr15	48475421	48476181	+	0	NA	intron (NM_000138, intron 32 of 65)	intron (NM_000138, intron 32 of 65)	143633	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.001316	0.369251	47(AAGAACATAAAGTACT,-,0.00),48(AGAACATAAAGTACTA,+,0.00),439(AAGAACAGATTGCTCC,-,0.00),440(AGAACAGATTGCTCCT,+,0.00)
chunk0154_140_1	chr5	79240564	79241461	+	0	NA	intron (NM_152405, intron 1 of 10)	intron (NM_152405, intron 1 of 10)	4910	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.002230	0.334076	621(TAGAACAGACTGTACA,-,0.00),622(AGAACAGACTGTACAA,+,0.00)
chunk0089_24_1	chr18	57766892	57767227	+	0	NA	intron (NM_005603, intron 1 of 27)	L2c|LINE|L2	36036	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.008955	0.467262	99(AAGAACAGCCTGTTCT,-,0.00),100(AGAACAGCCTGTTCTT,+,0.00)
chunk0074_121_1	chr16	22659918	22660555	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	114538	NR_003676	653786	Hs.564945	NR_003676	ENSG00000257838	OTOAP1	-	OTOA pseudogene 1	pseudo	0.007849	0.438871	
chunk0009_238_1	chr1	106920633	106921153	+	0	NA	Intergenic	Intergenic	-135752	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.005769	0.345489	
chunk0173_394_1	chr6	150194209	150194989	+	0	NA	intron (NM_030949, intron 1 of 3)	intron (NM_030949, intron 1 of 3)	51547	NM_030949	81706	Hs.486798	NM_030949	ENSG00000198729	PPP1R14C	CPI17-like|KEPI|NY-BR-81	protein phosphatase 1 regulatory inhibitor subunit 14C	protein-coding	0.005128	0.341869	453(TAGCACAAACAGTTCT,-,0.00),454(AGCACAAACAGTTCTG,+,0.00)
chunk0156_67_1	chr5	103544300	103544663	+	0	NA	Intergenic	Intergenic	-2496	NR_104670	102467212	Hs.641885	NR_104670	ENSG00000248757	LINC02115	-	long intergenic non-protein coding RNA 2115	ncRNA	0.008264	0.348901	
chunk0140_37_1	chr4	66357548	66358073	+	0	NA	Intergenic	L1PA16|LINE|L1	80986	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.001905	0.336502	
chunk0100_54_1	chr2	106167120	106167592	+	0	NA	intron (NM_001253875, intron 1 of 14)	intron (NM_001253875, intron 1 of 14)	26983	NM_001253875	80146	Hs.469561	NM_025076	ENSG00000115652	UXS1	SDR6E1|UGD	UDP-glucuronate decarboxylase 1	protein-coding	0.010593	0.456660	
chunk0099_317_1	chr2	99488641	99488848	+	0	NA	intron (NM_001037872, intron 1 of 22)	intron (NM_001037872, intron 1 of 22)	1274	NM_001037872	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.014493	0.461538	
chunk0082_67_1	chr17	51423301	51423897	+	0	NA	Intergenic	Intergenic	86884	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.005034	0.457286	
chunk0164_55_1	chr6	19181070	19181463	+	0	NA	promoter-TSS (NR_110860)	promoter-TSS (NR_110860)	-786	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.000000	0.380711	
chunk0010_19_1	chr1	112309542	112309934	+	0	NA	Intergenic	Intergenic	-86440	NM_018704	55917	Hs.744100	NM_018704	ENSG00000143079	CTTNBP2NL	-	CTTNBP2 N-terminal like	protein-coding	0.012755	0.465649	
chunk0120_164_1	chr3	5644615	5645216	+	0	NA	Intergenic	L1PA10|LINE|L1	-394660	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.004992	0.428571	
chunk0169_126_1	chr6	101080012	101080484	+	0	NA	Intergenic	Intergenic	-198876	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.004237	0.395349	
chunk0126_368_1	chr3	83625421	83625694	+	0	NA	Intergenic	Intergenic	1244018	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.000000	0.299270	
chunk0002_51_1	chr1	13578551	13578863	+	0	NA	Intergenic	Intergenic	-5050	NM_198389	10630	Hs.468675	NM_006474	ENSG00000162493	PDPN	AGGRUS|GP36|GP40|Gp38|HT1A-1|OTS8|PA2.26|T1A|T1A-2|T1A2|TI1A	podoplanin	protein-coding	0.028846	0.476038	
chunk0151_370_1	chr5	54981098	54981524	+	0	NA	intron (NM_001135604, intron 1 of 1)	intron (NM_001135604, intron 1 of 1)	4275	NM_007036	11082	Hs.129944	NM_007036	ENSG00000164283	ESM1	endocan	endothelial cell specific molecule 1	protein-coding	0.007042	0.318501	
chunk0038_222_1	chr11	86820504	86820789	+	0	NA	intron (NR_120591, intron 1 of 4)	intron (NR_120591, intron 1 of 4)	20406	NR_120592	11098	Hs.25338	NM_007173	ENSG00000150687	PRSS23	SIG13|SPUVE|ZSIG13	serine protease 23	protein-coding	0.007018	0.283217	
chunk0077_313_1	chr16	82035845	82036479	+	0	NA	intron (NM_002153, intron 1 of 4)	intron (NM_002153, intron 1 of 4)	909	NM_002153	3294	Hs.162795	NM_002153	ENSG00000086696	HSD17B2	EDH17B2|HSD17|SDR9C2	hydroxysteroid 17-beta dehydrogenase 2	protein-coding	0.006309	0.420472	
chunk0147_137_1	chr4	174532760	174532972	+	0	NA	Intergenic	Intergenic	-9968	NM_001256305	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.000000	0.314554	139(GAGTACATTTTGTACT,-,0.00),140(AGTACATTTTGTACTG,+,0.00)
chunk0187_84_1	chr8	3162476	3163151	+	0	NA	intron (NM_033225, intron 37 of 69)	intron (NM_033225, intron 37 of 69)	-434362	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.001481	0.291420	319(ATGAACAGTCTGTTCT,-,0.00),320(TGAACAGTCTGTTCTT,+,0.00)
chunk0160_298_1	chr5	158594765	158595375	+	0	NA	Intergenic	MIR|SINE|MIR	-185297	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.006557	0.373159	
chunk0188_19_1	chr8	6503121	6503364	+	0	NA	exon (NM_001118888, exon 8 of 8)	exon (NM_001118888, exon 8 of 8)	60021	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.020576	0.479508	
chunk0069_26_1	chr15	60448468	60448839	+	0	NA	intron (NM_024611, intron 10 of 15)	intron (NM_024611, intron 10 of 15)	30507	NM_024611	79664	Hs.200943	NM_024611	ENSG00000128915	ICE2	BRCC1|NARG2	interactor of little elongation complex ELL subunit 2	protein-coding	0.008086	0.319892	
chunk0087_363_1	chr18	41338180	41338869	+	0	NA	Intergenic	LTR86A2|LTR|ERVL	182073	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.002903	0.379710	
chunk0056_155_1	chr13	84208368	84208929	+	0	NA	intron (NR_046871, intron 1 of 6)	intron (NR_046871, intron 1 of 6)	68046	NR_046871	100874128	Hs.578060	NR_046871		LINC00333	NCRNA00333	long intergenic non-protein coding RNA 333	ncRNA	0.008913	0.387900	
chunk0048_231_1	chr12	81543034	81543476	+	0	NA	intron (NM_001220474, intron 2 of 30)	L1MC3|LINE|L1	-30864	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.002262	0.379233	
chunk0132_306_1	chr3	160265165	160265631	+	0	NA	intron (NM_001190242, intron 18 of 18)	intron (NM_001190242, intron 18 of 18)	39762	NM_001168214	401097	Hs.729755	NM_001168214	ENSG00000180044	C3orf80	-	chromosome 3 open reading frame 80	protein-coding	0.002146	0.321199	
chunk0191_161_1	chr8	49341469	49341924	+	0	NA	Intergenic	Intergenic	269355	NM_001256597	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.004396	0.274123	
chunk0094_138_1	chr2	4950914	4951229	+	0	NA	Intergenic	Intergenic	-294849	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.009524	0.392405	
chunk0193_416_1	chr8	80727454	80727654	+	0	NA	intron (NM_001033723, intron 2 of 8)	intron (NM_001033723, intron 2 of 8)	147227	NM_001033723	619279	Hs.434957	NM_032651	ENSG00000164684	ZNF704	Gig1	zinc finger protein 704	protein-coding	0.040000	0.467662	
chunk0144_460_1	chr4	142373701	142373900	+	0	NA	intron (NM_001101669, intron 7 of 25)	intron (NM_001101669, intron 7 of 25)	472651	NM_003866	8821	Hs.176376	NM_003866	ENSG00000109452	INPP4B	-	inositol polyphosphate-4-phosphatase type II B	protein-coding	0.000000	0.265000	
chunk0165_71_1	chr6	31149874	31150294	+	0	NA	exon (NM_001105564, exon 8 of 18)	exon (NM_001105564, exon 8 of 18)	7705	NM_001105564	54535	Hs.485075	NM_019052	ENSG00000204536	CCHCR1	C6orf18|HCR|SBP|pg8	coiled-coil alpha-helical rod protein 1	protein-coding	0.009524	0.524941	
chunk0091_450_1	chr19	17515990	17516189	+	0	NA	intron (NM_012088, intron 1 of 4)	MIR|SINE|MIR	4466	NM_012088	25796	Hs.466165	NM_012088	ENSG00000130313	PGLS	6PGL|HEL-S-304	6-phosphogluconolactonase	protein-coding	0.020101	0.520000	
chunk0024_199_1	chr10	36396547	36396903	+	0	NA	Intergenic	Intergenic	618423	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.002809	0.308123	
chunk0098_258_1	chr2	75202585	75202847	+	0	NA	Intergenic	L1ME3G|LINE|L1	-3197	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.003817	0.288973	
chunk0037_153_1	chr11	73558696	73559167	+	0	NA	intron (NM_001286050, intron 1 of 8)	L1MB5|LINE|L1	39258	NM_015159	23201	Hs.475334	NM_015159	ENSG00000054965	FAM168A	KIAA0280|TCRP1	family with sequence similarity 168 member A	protein-coding	0.010616	0.343220	
chunk0050_285_1	chr12	106404463	106405245	+	0	NA	intron (NM_018082, intron 10 of 27)	L1ME2|LINE|L1	46772	NM_001160708	55703	Hs.62696	NM_018082	ENSG00000013503	POLR3B	C128|HLD8|INMAP|RPC2	RNA polymerase III subunit B	protein-coding	0.001279	0.293742	
chunk0056_453_1	chr13	95235212	95235614	+	0	NA	intron (NM_001105515, intron 3 of 20)	intron (NM_001105515, intron 3 of 20)	66033	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.004975	0.409429	
chunk0083_223_1	chr17	67245676	67245925	+	0	NA	promoter-TSS (NM_014877)	promoter-TSS (NM_014877)	-597	NM_014877	9931	Hs.370140	NM_014877	ENSG00000198265	HELZ	DHRC|DRHC|HUMORF5	helicase with zinc finger	protein-coding	0.080321	0.624000	61(GAGGACGCCGTGTCCC,-,0.00),62(AGGACGCCGTGTCCCC,+,0.00)
chunk0064_230_1	chr14	94104738	94104937	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-5896	NM_001288958	3429	Hs.532634	NM_005532	ENSG00000165949	IFI27	FAM14D|ISG12|ISG12A|P27	interferon alpha inducible protein 27	protein-coding	0.025126	0.525000	
chunk0131_57_1	chr3	142837649	142838210	+	0	NA	intron (NM_013363, intron 5 of 8)	intron (NM_013363, intron 5 of 8)	51274	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.003565	0.395018	
chunk0201_102_1	chr9	34811956	34812434	+	0	NA	Intergenic	FLAM_A|SINE|Alu	26391	NR_024481	389715	Hs.713965	NM_001126494		FAM205BP	C9orf144|C9orf144A|FAM205B	transmembrane protein C9orf144B pseudogene	pseudo	0.012552	0.398747	
chunk0058_54_1	chr14	20578479	20579429	+	0	NA	Intergenic	AluJb|SINE|Alu	-9270	NR_122043	254028	Hs.652569	NR_122043	ENSG00000258573	LOC254028	-	uncharacterized LOC254028	ncRNA	0.015789	0.497371	820(TGGAACAGCCTGAGCT,-,0.00),821(GGAACAGCCTGAGCTG,+,0.00)
chunk0010_441_1	chr1	120032118	120032580	+	0	NA	intron (NM_024408, intron 1 of 33)	intron (NM_024408, intron 1 of 33)	37354	NM_024408	4853	Hs.487360	NM_024408	ENSG00000134250	NOTCH2	AGS2|HJCYS|hN2	notch receptor 2	protein-coding	0.006494	0.462203	
chunk0174_339_1	chr6	164043223	164043529	+	0	NA	Intergenic	Intergenic	628733	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.006536	0.465798	
chunk0050_123_1	chr12	102080731	102080930	+	0	NA	intron (NM_024057, intron 5 of 8)	intron (NM_024057, intron 5 of 8)	-18706	NM_001301107	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.010050	0.415000	
chunk0125_439_1	chr3	72750541	72750790	+	0	NA	exon (NM_018130, exon 11 of 11)	exon (NM_018130, exon 11 of 11)	97782	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.012048	0.488000	6(AAGAACTGACTGTCTC,-,0.00)
chunk0182_453_1	chr7	102082580	102083078	+	0	NA	intron (NM_001202545, intron 4 of 21)	L1ME2|LINE|L1	-202233	NM_020979	10603	Hs.489448	NM_020979	ENSG00000160999	SH2B2	APS	SH2B adaptor protein 2	protein-coding	0.006024	0.380762	
chunk0190_190_1	chr8	33485763	33486161	+	0	NA	intron (NM_032509, intron 1 of 9)	L2a|LINE|L2	795	NM_032509	84549	Hs.583805	NM_032509	ENSG00000198042	MAK16	MAK16L|RBM13	MAK16 homolog	protein-coding	0.002513	0.383459	
chunk0027_100_1	chr10	73819460	73819995	+	0	NA	intron (NM_172171, intron 16 of 20)	intron (NM_172171, intron 16 of 20)	-7896	NM_003635	8509	Hs.654758	NM_003635	ENSG00000166507	NDST2	HSST2|N-HSST 2|NST2	N-deacetylase and N-sulfotransferase 2	protein-coding	0.037383	0.664179	
chunk0112_411_1	chr20	47252784	47253275	+	0	NA	intron (NM_001281781, intron 11 of 20)	MER58A|DNA|hAT-Charlie	-65473	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.012220	0.502033	
chunk0121_83_1	chr3	16071322	16071670	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-103181	NM_054110	117248	Hs.411308	NM_054110	ENSG00000131386	GALNT15	GALNACT15|GALNT13|GALNT7|GALNTL2|PIH5|pp-GalNAc-T15	polypeptide N-acetylgalactosaminyltransferase 15	protein-coding	0.011494	0.395415	
chunk0188_441_1	chr8	19291010	19291349	+	0	NA	Intergenic	Intergenic	-22391	NM_001174160	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.014749	0.335294	
chunk0196_373_1	chr8	115273237	115273484	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	394652	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004049	0.387097	58(AAGAACATCCTGCACC,-,0.00),59(AGAACATCCTGCACCG,+,0.00)
chunk0030_217_1	chr10	114682113	114682675	+	0	NA	intron (NM_001003407, intron 1 of 21)	intron (NM_001003407, intron 1 of 21)	2261	NM_001003407	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.007117	0.351687	212(AAGGACAGGATGATCT,-,0.00),213(AGGACAGGATGATCTT,+,0.00)
chunk0132_247_1	chr3	158696575	158697232	+	0	NA	TTS (NM_206963)	TTS (NM_206963)	-24210	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.004566	0.302432	
chunk0076_387_1	chr16	72415425	72415800	+	0	NA	intron (NR_126330, intron 7 of 13)	L1MC4a|LINE|L1	-243162	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.002667	0.305851	
chunk0116_51_1	chr21	33775037	33775337	+	0	NA	intron (NM_001001132, intron 14 of 29)	L2c|LINE|L2	132709	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.006667	0.385382	
chunk0194_201_1	chr8	85564974	85565173	+	0	NA	Intergenic	Intergenic	90603	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.005025	0.470000	
chunk0107_252_1	chr2	217339994	217340695	+	0	NA	intron (NR_133642, intron 5 of 5)	intron (NR_133642, intron 5 of 5)	57611	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.005706	0.401709	
chunk0148_108_1	chr5	4542239	4542976	+	0	NA	Intergenic	Intergenic	-230874	NR_104619	101929153	Hs.385526	NR_104619	ENSG00000249521	LINC02114	-	long intergenic non-protein coding RNA 2114	ncRNA	0.016282	0.462060	
chunk0183_40_1	chr7	103802204	103802926	+	0	NA	intron (NM_005045, intron 3 of 64)	intron (NM_005045, intron 3 of 64)	186951	NM_005045	5649	Hs.655654	NM_005045	ENSG00000189056	RELN	ETL7|LIS2|PRO1598|RL	reelin	protein-coding	0.002770	0.309820	
chunk0108_425_1	chr2	237860988	237861600	+	0	NA	intron (NM_005855, intron 1 of 2)	intron (NM_005855, intron 1 of 2)	1750	NM_005855	10267	Hs.471783	NM_005855	ENSG00000132329	RAMP1	-	receptor activity modifying protein 1	protein-coding	0.011438	0.371941	391(GAGCACAGGCTGTTTC,-,0.00),392(AGCACAGGCTGTTTCC,+,0.00)
chunk0124_5_1	chr3	51487231	51487516	+	0	NA	intron (NM_001171904, intron 1 of 24)	L1MD3|LINE|L1	12629	NM_014703	9730	Hs.716623	NM_014703	ENSG00000145041	DCAF1	RIP|VPRBP	DDB1 and CUL4 associated factor 1	protein-coding	0.003509	0.377622	92(TAGTACACAGTGTTCC,-,0.00),93(AGTACACAGTGTTCCC,+,0.00)
chunk0203_76_1	chr9	83827383	83827812	+	0	NA	Intergenic	L2b|LINE|L2	-9760	NM_001135953	80318	Hs.522255	NM_025211	ENSG00000165113	GKAP1	FKSG21|GKAP42	G kinase anchoring protein 1	protein-coding	0.009324	0.379070	
chunk0106_244_1	chr2	203142688	203143143	+	0	NA	intron (NM_001114132, intron 30 of 54)	L3|LINE|CR1	-95526	NM_177538	57404	Hs.446065	NM_020674	ENSG00000119004	CYP20A1	CYP-M	cytochrome P450 family 20 subfamily A member 1	protein-coding	0.006593	0.355263	
chunk0019_429_1	chr1	230877578	230878102	+	0	NA	intron (NR_110681, intron 2 of 2)	intron (NR_110681, intron 2 of 2)	2994	NR_110681	101927604	Hs.638929	NR_110681	ENSG00000223393	LOC101927604	-	uncharacterized LOC101927604	ncRNA	0.007634	0.382857	
chunk0199_98_1	chr9	2828383	2828655	+	0	NA	intron (NM_014878, intron 9 of 17)	intron (NM_014878, intron 9 of 17)	15611	NM_014878	9933	Hs.493309	NM_014878	ENSG00000080608	PUM3	HA-8|HLA-HA8|KIAA0020|PEN|PUF-A|PUF6|XTP5	pumilio RNA binding family member 3	protein-coding	0.003676	0.326007	
chunk0110_171_1	chr20	14208780	14209413	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	128571	NM_198391	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.001580	0.376972	
chunk0168_338_1	chr6	92806137	92806769	+	0	NA	Intergenic	Intergenic	613129	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.003165	0.352291	315(GAACACAGCATGTGCT,-,0.00),316(AACACAGCATGTGCTG,+,0.00)
chunk0071_439_1	chr15	89970813	89971572	+	0	NA	Intergenic	MIR|SINE|MIR	-30299	NM_198526	374655	Hs.459311	NM_198526	ENSG00000140548	ZNF710	-	zinc finger protein 710	protein-coding	0.013175	0.459211	
chunk0033_25_1	chr11	12730065	12730429	+	0	NA	intron (NM_021961, intron 2 of 12)	MIRc|SINE|MIR	55825	NM_021961	7003	Hs.655331	NM_021961	ENSG00000187079	TEAD1	AA|NTEF-1|REF1|TCF-13|TCF13|TEAD-1|TEF-1	TEA domain transcription factor 1	protein-coding	0.010989	0.369863	
chunk0137_292_1	chr4	23958742	23959071	+	0	NA	Intergenic	Intergenic	-68829	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.006079	0.296970	
chunk0089_287_1	chr18	63075117	63075317	+	0	NA	Intergenic	Intergenic	244163	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.060000	0.636816	
chunk0075_83_1	chr16	48261370	48262115	+	0	NA	intron (NM_031490, intron 5 of 14)	intron (NM_031490, intron 5 of 14)	17575	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.006711	0.343164	
chunk0211_411_1	chrX	128865168	128865516	+	0	NA	Intergenic	Intergenic	658163	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.005747	0.378223	
chunk0040_391_1	chr11	120034515	120034737	+	0	NA	Intergenic	L2b|LINE|L2	103529	NM_012101	23650	Hs.504115	NM_012101	ENSG00000137699	TRIM29	ATDC	tripartite motif containing 29	protein-coding	0.013514	0.573991	
chunk0092_137_1	chr19	28135981	28136184	+	0	NA	Intergenic	Intergenic	-342142	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.000000	0.465686	59(AAGAACAGTGTGTTCA,-,0.00),60(AGAACAGTGTGTTCAG,+,0.00)
chunk0051_182_1	chr12	116133150	116133680	+	0	NA	intron (NM_015335, intron 2 of 30)	intron (NM_015335, intron 2 of 30)	15239	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.007547	0.423729	244(GGAAACAGCCTGTGCC,-,0.00),245(GAAACAGCCTGTGCCT,+,0.00)
chunk0020_359_1	chr1	239612193	239612594	+	0	NA	Intergenic	Intergenic	-16680	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.002494	0.325871	
chunk0177_216_1	chr7	24139809	24140102	+	0	NA	Intergenic	LTR86A1|LTR|ERVL	-144233	NM_000905	4852	Hs.1832	NM_000905	ENSG00000122585	NPY	PYY4	neuropeptide Y	protein-coding	0.017065	0.448980	
chunk0007_193_1	chr1	81015117	81015788	+	0	NA	Intergenic	Intergenic	374165	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000000	0.318452	
chunk0105_422_1	chr2	193250277	193250922	+	0	NA	Intergenic	L1MB1|LINE|L1	500754	NR_002769	64002	Hs.546994	NR_002769	ENSG00000227418	PCGEM1	LINC00071|NCRNA00071|PCAT9	PCGEM1 prostate-specific transcript	ncRNA	0.000000	0.325077	
chunk0022_250_1	chr10	14577537	14578346	+	0	NA	intron (NM_001282695, intron 2 of 5)	intron (NM_001282695, intron 2 of 5)	-5568	NM_001282700	83641	Hs.446315	NM_031453	ENSG00000065809	FAM107B	C10orf45|HITS	family with sequence similarity 107 member B	protein-coding	0.013597	0.416049	
chunk0135_10_1	chr3	184144803	184145030	+	0	NA	exon (NM_003907, exon 16 of 16)	exon (NM_003907, exon 16 of 16)	9894	NM_003907	8893	Hs.283551	NM_003907	ENSG00000145191	EIF2B5	CACH|CLE|EIF-2B|EIF2Bepsilon|LVWM	eukaryotic translation initiation factor 2B subunit epsilon	protein-coding	0.008811	0.543860	
chunk0055_417_1	chr13	74891543	74892093	+	0	NA	Intergenic	Intergenic	338975	NR_034025	338864	Hs.97408	NR_034024	ENSG00000236678	LINC00347	-	long intergenic non-protein coding RNA 347	ncRNA	0.009091	0.413793	107(GGAGCAATGTGTCCTG,+,0.00)
chunk0187_266_1	chr7	155166643	155167193	+	0	NA	Intergenic	Intergenic	-95361	NR_038945	100128264	Hs.248137	NR_038945	ENSG00000220575	HTR5A-AS1	HTR5AOS	HTR5A antisense RNA 1	ncRNA	0.034545	0.568058	
chunk0087_73_1	chr18	31983785	31984057	+	0	NA	Intergenic	Intergenic	-34561	NM_017831	54941	Hs.633703	NM_017831	ENSG00000101695	RNF125	TNORS|TRAC-1|TRAC1	ring finger protein 125	protein-coding	0.011029	0.380952	168(TTGCACAGGGTGTTCT,-,0.00),169(TGCACAGGGTGTTCTT,+,0.00)
chunk0001_81_1	chr1	2630274	2631014	+	0	NA	intron (NM_033467, intron 1 of 23)	(GT)n|Simple_repeat|Simple_repeat	2398	NM_033467	79258	Hs.591453	NM_033467	ENSG00000142606	MMEL1	MMEL2|NEP2|NEPII|NL1|NL2|SEP	membrane metalloendopeptidase like 1	protein-coding	0.056757	0.527665	
chunk0097_97_1	chr2	45938748	45939010	+	0	NA	intron (NM_005400, intron 2 of 14)	intron (NM_005400, intron 2 of 14)	286975	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.022901	0.479087	
chunk0005_419_1	chr1	62707101	62707928	+	0	NA	Intergenic	L2c|LINE|L2	-19146	NM_001272001	85440	Hs.744927	NM_033407	ENSG00000116641	DOCK7	EIEE23|ZIR2	dedicator of cytokinesis 7	protein-coding	0.006046	0.421498	
chunk0167_375_1	chr6	73773460	73773779	+	0	NA	intron (NM_133493, intron 15 of 32)	intron (NM_133493, intron 15 of 32)	-77488	NR_110889	101928489	Hs.660059	NR_110889	ENSG00000231652	LOC101928489	-	uncharacterized LOC101928489	ncRNA	0.006270	0.340625	
chunk0088_171_1	chr18	47174707	47175440	+	0	NA	intron (NM_016097, intron 1 of 2)	L2c|LINE|L2	1301	NM_016097	51124	Hs.130917	NM_016097	ENSG00000134049	IER3IP1	HSPC039|MEDS|PRO2309	immediate early response 3 interacting protein 1	protein-coding	0.015007	0.412807	
chunk0211_161_1	chrX	114731785	114732077	+	0	NA	intron (NM_001256760, intron 5 of 6)	intron (NM_001256760, intron 5 of 6)	16698	NR_031578	100302153		NR_031578	ENSG00000221710	MIR1298	MIRN1298|hsa-mir-1298	microRNA 1298	ncRNA	0.003425	0.334471	
chunk0077_42_1	chr16	75640665	75641013	+	0	NA	intron (NM_001130089, intron 3 of 14)	MER58B|DNA|hAT-Charlie	6848	NM_005548	3735	Hs.3100	NM_005548	ENSG00000065427	KARS	CMTRIB|DFNB89|KARS1|KARS2|KRS	lysyl-tRNA synthetase	protein-coding	0.017241	0.481375	
chunk0107_384_1	chr2	223273949	223274476	+	0	NA	Intergenic	Intergenic	222282	NM_080671	23704	Hs.348522	NM_080671	ENSG00000152049	KCNE4	MIRP3	potassium voltage-gated channel subfamily E regulatory subunit 4	protein-coding	0.000000	0.361742	
chunk0199_207_1	chr9	4933115	4933425	+	0	NA	Intergenic	Intergenic	-51975	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.006452	0.395498	
chunk0166_386_1	chr6	51747489	51747972	+	0	NA	intron (NM_138694, intron 58 of 66)	intron (NM_138694, intron 58 of 66)	125860	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.004141	0.380165	194(AGACCACAATGTACCT,+,0.00)
chunk0149_60_1	chr5	16889635	16889974	+	0	NA	intron (NM_012334, intron 1 of 40)	intron (NM_012334, intron 1 of 40)	46472	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.002950	0.402941	
chunk0126_362_1	chr3	83250808	83251062	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-1489136	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.003937	0.392157	
chunk0203_290_1	chr9	88965402	88965670	+	0	NA	Intergenic	Intergenic	-25327	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.026119	0.513011	
chunk0045_447_1	chr12	53591923	53592405	+	0	NA	intron (NM_006856, intron 2 of 11)	intron (NM_006856, intron 2 of 11)	33832	NM_001206683	11016	Hs.12286	NM_006856	ENSG00000170653	ATF7	ATFA	activating transcription factor 7	protein-coding	0.006224	0.378882	212(GGGCACATGGTGTGCC,-,0.00),213(GGCACATGGTGTGCCA,+,0.00)
chunk0081_139_1	chr17	40579341	40579887	+	0	NA	Intergenic	L2b|LINE|L2	-14130	NM_001301714	1236	Hs.370036	NM_001838	ENSG00000126353	CCR7	BLR2|CC-CKR-7|CCR-7|CD197|CDw197|CMKBR7|EBI1	C-C motif chemokine receptor 7	protein-coding	0.007326	0.455210	200(GAGAACATCTTGCTCC,-,0.00),201(AGAACATCTTGCTCCT,+,0.00),285(GTGAACACTATGTGCC,-,0.00),286(TGAACACTATGTGCCA,+,0.00)
chunk0072_292_1	chr15	98654852	98655261	+	0	NA	intron (NM_001291858, intron 1 of 20)	intron (NM_001291858, intron 1 of 20)	-3835	NR_126453	104472848	Hs.349049	NR_126453		IRAIN	IGF1R-AS	IGF1R antisense imprinted non-protein coding RNA	ncRNA	0.004890	0.404878	
chunk0204_268_1	chr9	98229303	98229811	+	0	NA	promoter-TSS (NR_106913)	promoter-TSS (NR_106913)	-340	NR_106913	102465514		NR_106913	ENSG00000278412	MIR6854	hsa-mir-6854	microRNA 6854	ncRNA	0.001969	0.459725	
chunk0089_90_1	chr18	58315006	58315327	+	0	NA	intron (NM_001144970, intron 4 of 28)	intron (NM_001144970, intron 4 of 28)	93644	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.015576	0.506211	
chunk0130_375_1	chr3	139454468	139455030	+	0	NA	exon (NM_004164, exon 3 of 4)	exon (NM_004164, exon 3 of 4)	21761	NM_004164	5948	Hs.655516	NM_004164	ENSG00000114113	RBP2	CRABP-II|CRBP2|CRBPII|RBPC2	retinol binding protein 2	protein-coding	0.008897	0.499112	262(AGGTACAGCTTGTCCC,-,0.00),263(GGTACAGCTTGTCCCC,+,0.00)
chunk0009_232_1	chr1	106703666	106704439	+	0	NA	Intergenic	L1MC1|LINE|L1	-352593	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.005175	0.365633	
chunk0196_81_1	chr8	102647573	102647836	+	0	NA	Intergenic	Intergenic	6260	NR_103759	7071	Hs.435001	NM_005655	ENSG00000155090	KLF10	EGR-alpha|EGRA|TIEG|TIEG1	Kruppel like factor 10	protein-coding	0.003802	0.473485	
chunk0158_434_1	chr5	135393193	135393470	+	0	NA	intron (NM_004893, intron 1 of 8)	MLT1J2|LTR|ERVL-MaLR	5907	NM_138609	9555	Hs.420272	NM_004893	ENSG00000113648	H2AFY	H2A.y|H2A/y|H2AF12M|MACROH2A1.1|mH2A1|macroH2A1.2	H2A histone family member Y	protein-coding	0.003610	0.446043	
chunk0154_109_1	chr5	78547118	78547590	+	0	NA	intron (NM_005779, intron 3 of 4)	intron (NM_005779, intron 3 of 4)	101471	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.012712	0.467230	
chunk0086_391_1	chr18	26582338	26582595	+	0	NA	intron (NM_001258222, intron 1 of 4)	L1ME4b|LINE|L1	9069	NR_107024	102466874		NR_107024	ENSG00000276221	MIR8057	hsa-mir-8057	microRNA 8057	ncRNA	0.007782	0.317829	88(AAGAACACATTGTACT,-,0.00),89(AGAACACATTGTACTA,+,0.00)
chunk0038_309_1	chr11	91308007	91308319	+	0	NA	Intergenic	Intergenic	-438961	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.006410	0.428115	
chunk0094_132_1	chr2	4880342	4880541	+	0	NA	Intergenic	MIR|SINE|MIR	-224219	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.000000	0.400000	
chunk0183_63_1	chr7	104149823	104150245	+	0	NA	intron (NM_002553, intron 12 of 13)	intron (NM_002553, intron 12 of 13)	58013	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.007109	0.323877	
chunk0130_246_1	chr3	135636097	135636579	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-329335	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.008299	0.447205	234(TGGAACACAGTGTGCC,-,0.00),235(GGAACACAGTGTGCCC,+,0.00)
chunk0104_107_1	chr2	172677231	172677568	+	0	NA	Intergenic	HAL1|LINE|L1	-58398	NM_007023	11069	Hs.470646	NM_007023	ENSG00000091428	RAPGEF4	CAMP-GEFII|CGEF2|EPAC|EPAC 2|EPAC2|Nbla00496	Rap guanine nucleotide exchange factor 4	protein-coding	0.005935	0.381657	
chunk0152_391_1	chr5	64706523	64707020	+	0	NA	intron (NM_001164442, intron 2 of 2)	MER4-int|LTR|ERV1	16463	NM_001164442	100132916	Hs.591776	NM_001164442	ENSG00000145642	SHISAL2B	FAM159B	shisa like 2B	protein-coding	0.002012	0.331325	
chunk0115_239_1	chr21	27426277	27426535	+	0	NA	Intergenic	Intergenic	-295973	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.003876	0.389961	139(GAGCACATACTGTTCC,-,0.00),140(AGCACATACTGTTCCT,+,0.00)
chunk0043_93_1	chr12	14777337	14777587	+	0	NA	non-coding (NR_027716, exon 2 of 2)	non-coding (NR_027716, exon 2 of 2)	3126	NM_177925	55766	Hs.524280	NM_018267	ENSG00000246705	H2AFJ	H2AJ	H2A histone family member J	protein-coding	0.012000	0.490040	
chunk0038_228_1	chr11	86988299	86988725	+	0	NA	intron (NR_038905, intron 2 of 2)	intron (NR_038905, intron 2 of 2)	32891	NR_038905	100506368	Hs.559920	NR_038905	ENSG00000246523	FZD4-DT	-	FZD4 divergent transcript	ncRNA	0.004695	0.313817	
chunk0031_420_1	chr10	132293462	132293850	+	0	NA	intron (NM_173575, intron 1 of 11)	intron (NM_173575, intron 1 of 11)	14317	NM_173575	282974	Hs.469002	NM_173575	ENSG00000165752	STK32C	PKE|YANK3	serine/threonine kinase 32C	protein-coding	0.028351	0.663239	
chunk0047_45_1	chr12	67035176	67035725	+	0	NA	Intergenic	Intergenic	60834	NR_120490	102724421	Hs.135774	NR_120490	ENSG00000257083	LOC102724421	-	uncharacterized LOC102724421	ncRNA	0.009107	0.407273	
chunk0160_292_1	chr5	158225627	158225839	+	0	NA	Intergenic	L2a|LINE|L2	184040	NR_109888	101927697	Hs.483960	NR_109888	ENSG00000276778	LINC02227	-	long intergenic non-protein coding RNA 2227	ncRNA	0.004717	0.460094	
chunk0012_450_1	chr1	165093253	165093659	+	0	NA	Intergenic	LTR5B|LTR|ERVK	262785	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.004926	0.503686	
chunk0112_161_1	chr20	39271243	39271509	+	0	NA	Intergenic	Intergenic	-46628	NR_027124	339568	Hs.434319	NR_027124	ENSG00000230324	LINC01734	-	long intergenic non-protein coding RNA 1734	ncRNA	0.018797	0.580524	131(GGAACACTTCGTCCTG,+,0.00)
chunk0166_20_1	chr6	41747276	41748196	+	0	NA	promoter-TSS (NM_001166424)	promoter-TSS (NM_001166424)	-335	NM_001166424	5225	Hs.1867	NM_002630	ENSG00000096088	PGC	PEPC|PGII	progastricsin	protein-coding	0.017391	0.507058	500(TGGAACAAATAGTTCT,-,0.00),501(GGAACAAATAGTTCTT,+,0.00)
chunk0193_105_1	chr8	73878829	73879111	+	0	NA	promoter-TSS (NM_001271015)	promoter-TSS (NM_001271015)	-60	NM_001271015	55284	Hs.128841	NM_018299	ENSG00000104343	UBE2W	UBC-16|UBC16	ubiquitin conjugating enzyme E2 W	protein-coding	0.113475	0.706714	
chunk0145_403_1	chr4	152692004	152692214	+	0	NA	Intergenic	Intergenic	-11944	NM_152680	201799	Hs.518900	NM_152680	ENSG00000170006	TMEM154	-	transmembrane protein 154	protein-coding	0.019048	0.497630	
chunk0145_166_1	chr4	147244904	147245323	+	0	NA	Intergenic	Intergenic	99604	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.002387	0.411905	
chunk0079_291_1	chr17	16653462	16654115	+	0	NA	promoter-TSS (NM_020787)	promoter-TSS (NM_020787)	65	NM_020787	57547	Hs.128078	NM_020787	ENSG00000197566	ZNF624	-	zinc finger protein 624	protein-coding	0.076570	0.629969	287(CGGGACAACGAGTACC,-,0.00),288(GGGACAACGAGTACCT,+,0.00)
chunk0145_177_1	chr4	147524782	147525195	+	0	NA	intron (NR_045958, intron 3 of 6)	intron (NR_045958, intron 3 of 6)	44071	NM_001166055	1909	Hs.183713	NM_001957	ENSG00000151617	EDNRA	ET-A|ETA|ETA-R|ETAR|ETRA|MFDA|hET-AR	endothelin receptor type A	protein-coding	0.004843	0.287440	243(CAGGACAAAGAGTTCC,-,0.00),244(AGGACAAAGAGTTCCC,+,0.00)
chunk0002_231_1	chr1	20172167	20172416	+	0	NA	intron (NM_001316722, intron 3 of 4)	intron (NM_001316722, intron 3 of 4)	5073	NM_001316722	391013	Hs.512512	NM_001105572	ENSG00000187980	PLA2G2C	-	phospholipase A2 group IIC	protein-coding	0.024096	0.556000	
chunk0168_111_1	chr6	80892937	80893495	+	0	NA	Intergenic	L1M5|LINE|L1	786589	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.000000	0.259392	272(ATGAACTCTCTGTTCT,-,0.00),273(TGAACTCTCTGTTCTA,+,0.00)
chunk0033_83_1	chr11	13964490	13964792	+	0	NA	intron (NM_006108, intron 1 of 15)	CpG	2004	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.109272	0.689769	109(AGGAACAGTCTGACCC,-,0.00),110(GGAACAGTCTGACCCC,+,0.00)
chunk0099_243_1	chr2	97645429	97645896	+	0	NA	promoter-TSS (NM_001862)	promoter-TSS (NM_001862)	-396	NM_001862	1329	Hs.1342	NM_001862	ENSG00000135940	COX5B	COXVB	cytochrome c oxidase subunit 5B	protein-coding	0.047109	0.581197	
chunk0134_242_1	chr3	179192453	179193036	+	0	NA	intron (NM_006218, intron 1 of 20)	MER58A|DNA|hAT-Charlie	44221	NM_006218	5290	Hs.553498	NM_006218	ENSG00000121879	PIK3CA	CLAPO|CLOVE|CWS5|MCAP|MCM|MCMTC|PI3K|PI3K-alpha|p110-alpha	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha	protein-coding	0.005146	0.364726	
chunk0075_25_1	chr16	46887639	46887870	+	0	NA	intron (NM_001142466, intron 2 of 11)	intron (NM_001142466, intron 2 of 11)	2640	NM_001142466	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.012987	0.534483	
chunk0090_136_1	chr18	72024655	72025158	+	0	NA	Intergenic	Intergenic	-242680	NR_126324	102724913		NR_126324	ENSG00000265352	LINC01899	-	long intergenic non-protein coding RNA 1899	ncRNA	0.007952	0.305556	
chunk0077_365_1	chr16	84211779	84212207	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	20876	NM_001145400	161931	Hs.8977	NM_139174	ENSG00000140955	ADAD2	TENRL	adenosine deaminase domain containing 2	protein-coding	0.009346	0.426573	
chunk0045_22_1	chr12	43770334	43770837	+	0	NA	intron (NM_001145256, intron 3 of 11)	intron (NM_001145256, intron 3 of 11)	11641	NM_016123	51135	Hs.138499	NM_016123	ENSG00000198001	IRAK4	IPD1|IRAK-4|NY-REN-64|REN64	interleukin 1 receptor associated kinase 4	protein-coding	0.000000	0.375000	
chunk0173_10_1	chr6	141233666	141234006	+	0	NA	Intergenic	Intergenic	550022	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.011765	0.363636	
chunk0161_195_1	chr5	170252705	170253226	+	0	NA	TTS (NR_131092)	TTS (NR_131092)	19958	NM_001305394	133874	Hs.519749	NM_001102609	ENSG00000234511	C5orf58	-	chromosome 5 open reading frame 58	protein-coding	0.013436	0.373563	249(AAGAACATATTGTTCA,-,0.00),250(AGAACATATTGTTCAT,+,0.00)
chunk0108_97_1	chr2	229179545	229179997	+	0	NA	intron (NM_001100818, intron 1 of 2)	intron (NM_001100818, intron 1 of 2)	91570	NM_017933	55022	Hs.745038	NM_017933	ENSG00000153823	PID1	HMFN2073|NYGGF4|P-CLI1|PCLI1	phosphotyrosine interaction domain containing 1	protein-coding	0.011062	0.439294	
chunk0155_446_1	chr5	101663060	101663721	+	0	NA	Intergenic	Intergenic	633159	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.001513	0.330816	
chunk0077_247_1	chr16	80836944	80838087	+	0	NA	intron (NR_131948, intron 2 of 2)	intron (NR_131948, intron 2 of 2)	-33237	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.009624	0.365385	
chunk0093_48_1	chr19	39996971	39997170	+	0	NA	promoter-TSS (NM_001297763)	promoter-TSS (NM_001297763)	34	NM_001297763	339327	Hs.125008	NM_178544	ENSG00000187187	ZNF546	ZNF49	zinc finger protein 546	protein-coding	0.090452	0.590000	
chunk0004_143_1	chr1	45001251	45001509	+	0	NA	Intergenic	Intergenic	9975	NM_024602	79654	Hs.525084	NM_024602	ENSG00000126107	HECTD3	-	HECT domain E3 ubiquitin protein ligase 3	protein-coding	0.019380	0.555985	
chunk0060_153_1	chr14	45112885	45113624	+	0	NA	intron (NM_017922, intron 11 of 13)	intron (NM_017922, intron 11 of 13)	2379	NR_003691	100113389	Hs.712501	NR_003691	ENSG00000239043	SNORD127	-	small nucleolar RNA, C/D box 127	snoRNA	0.005413	0.358108	
chunk0029_229_1	chr10	102477536	102478107	+	0	NA	TTS (NM_024789)	TTS (NM_024789)	16408	NM_024789	79847	Hs.309069	NM_024789	ENSG00000138111	MFSD13A	C10orf77|TMEM180|bA18I14.8	major facilitator superfamily domain containing 13A	protein-coding	0.010508	0.498252	278(GGGCCAGATTGTTCTC,+,0.00)
chunk0001_373_1	chr1	10258037	10258425	+	0	NA	intron (NM_015074, intron 3 of 46)	intron (NM_015074, intron 3 of 46)	30513	NR_036176									0.002577	0.349614	
chunk0095_255_1	chr2	19428129	19428479	+	0	NA	Intergenic	Intergenic	-69693	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.005714	0.373219	
chunk0016_108_1	chr1	195979830	195980029	+	0	NA	Intergenic	LTR55|LTR|ERVL?	602552	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005025	0.455000	
chunk0159_392_1	chr5	147031780	147032170	+	0	NA	intron (NM_001271900, intron 2 of 10)	L1PB|LINE|L1	24162	NM_181674	5521	Hs.627618	NM_181674	ENSG00000156475	PPP2R2B	B55BETA|PP2AB55BETA|PP2ABBETA|PP2APR55B|PP2APR55BETA|PR2AB55BETA|PR2ABBETA|PR2APR55BETA|PR52B|PR55-BETA|PR55BETA|SCA12	protein phosphatase 2 regulatory subunit Bbeta	protein-coding	0.002564	0.363171	
chunk0048_51_1	chr12	78127008	78127425	+	0	NA	intron (NM_014903, intron 17 of 38)	intron (NM_014903, intron 17 of 38)	295927	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.004796	0.358852	
chunk0058_120_1	chr14	22265845	22266220	+	0	NA	Intergenic	Intergenic	323205	NM_001344	1603	Hs.82890	NM_001344	ENSG00000129562	DAD1	OST2	defender against cell death 1	protein-coding	0.005333	0.444149	151(TGGAACAGAATGCTCC,-,0.00),152(GGAACAGAATGCTCCT,+,0.00)
chunk0178_141_1	chr7	32931535	32931849	+	0	NA	intron (NR_003500, intron 2 of 5)	intron (NR_003500, intron 2 of 5)	11478	NR_003500	441212	Hs.648086	NM_001039754	ENSG00000205763	RP9P	-	RP9 pseudogene	pseudo	0.006369	0.425397	
chunk0029_308_1	chr10	104277601	104278199	+	0	NA	exon (NM_183239, exon 4 of 7)	exon (NM_183239, exon 4 of 7)	2771	NM_001191015	119391	Hs.107384	NM_183239	ENSG00000065621	GSTO2	GSTO 2-2|bA127L20.1	glutathione S-transferase omega 2	protein-coding	0.005017	0.392321	
chunk0142_123_1	chr4	94623121	94623917	+	0	NA	intron (NM_001256425, intron 7 of 11)	L2c|LINE|L2	134014	NR_121610	100507012	Hs.128612	NR_121610		BMPR1B-DT	BMPR1B-AS1	BMPR1B divergent transcript	ncRNA	0.005025	0.405270	304(AAGACCAGCTTGTTCC,-,0.00),305(AGACCAGCTTGTTCCC,+,0.00)
chunk0066_423_1	chr15	39586207	39586762	+	0	NA	intron (NM_003246, intron 7 of 21)	intron (NM_003246, intron 7 of 21)	5405	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.019820	0.451439	
chunk0134_320_1	chr3	181797457	181797752	+	0	NA	Intergenic	Intergenic	85680	NM_003106	6657	Hs.518438	NM_003106	ENSG00000181449	SOX2	ANOP3|MCOPS3	SRY-box transcription factor 2	protein-coding	0.003390	0.391892	
chunk0152_456_1	chr5	66517323	66517700	+	0	NA	Intergenic	Intergenic	-5907	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.005305	0.425926	
chunk0158_314_1	chr5	132556941	132557336	+	0	NA	5' UTR (NM_005732, exon 1 of 25)	5' UTR (NM_005732, exon 1 of 25)	214	NM_005732	10111	Hs.633509	NM_005732	ENSG00000113522	RAD50	NBSLD|RAD502|hRad50	RAD50 double strand break repair protein	protein-coding	0.086076	0.671717	
chunk0080_126_1	chr17	27265198	27265755	+	0	NA	Intergenic	Intergenic	28520	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.001795	0.353047	
chunk0128_294_1	chr3	110984898	110985300	+	0	NA	Intergenic	LTR3B|LTR|ERVK	84860	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.009950	0.451613	
chunk0203_32_1	chr9	82996108	82996358	+	0	NA	intron (NM_152573, intron 14 of 16)	Helitron2Na_Mam|RC?|Helitron?	66895	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.000000	0.346614	
chunk0053_226_1	chr13	32280091	32280325	+	0	NA	intron (NM_023037, intron 58 of 60)	intron (NM_023037, intron 58 of 60)	31746	NM_001136571	646799	Hs.569254	NM_001136571	ENSG00000189167	ZAR1L	Z3CXXC7|ZAR2	zygote arrest 1 like	protein-coding	0.004274	0.382979	
chunk0104_25_1	chr2	170666344	170666747	+	0	NA	Intergenic	Intergenic	48022	NR_027433	440925	Hs.668461	NM_001013712	ENSG00000222033	LINC01124	-	long intergenic non-protein coding RNA 1124	ncRNA	0.012407	0.386139	
chunk0160_24_1	chr5	149135451	149135814	+	0	NA	Intergenic	Intergenic	-5851	NM_014945	22885	Hs.49688	NM_014945	ENSG00000173210	ABLIM3	HMFN1661	actin binding LIM protein family member 3	protein-coding	0.005510	0.445055	141(AAGATCACAGTGTTCC,-,0.00),142(AGATCACAGTGTTCCA,+,0.00)
chunk0188_148_1	chr8	10030673	10031230	+	0	NA	Intergenic	L1ME1|LINE|L1	-23318	NM_012331	4482	Hs.490981	NM_012331	ENSG00000175806	MSRA	PMSR	methionine sulfoxide reductase A	protein-coding	0.008977	0.401434	
chunk0092_367_1	chr19	35931537	35931787	+	0	NA	Intergenic	CpG	-5458	NM_024509	79414	Hs.143792	NM_024509	ENSG00000126243	LRFN3	FIGLER1|SALM4	leucine rich repeat and fibronectin type III domain containing 3	protein-coding	0.116000	0.677291	
chunk0015_440_1	chr1	191879592	191879971	+	0	NA	Intergenic	Intergenic	-278681	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.000000	0.278947	
chunk0029_144_1	chr10	99357749	99357975	+	0	NA	intron (NM_020348, intron 2 of 10)	intron (NM_020348, intron 2 of 10)	28763	NM_020348	26507	Hs.274579	NM_020348	ENSG00000119946	CNNM1	ACDP1|CLP-1	cyclin and CBS domain divalent metal cation transport mediator 1	protein-coding	0.008850	0.528634	192(GGAAACACAGTGTTCC,-,0.00),193(GAAACACAGTGTTCCC,+,0.00)
chunk0092_376_1	chr19	36214492	36214927	+	0	NA	promoter-TSS (NM_152477)	promoter-TSS (NM_152477)	-36	NM_152477	147929	Hs.596338	NM_152477	ENSG00000196357	ZNF565	-	zinc finger protein 565	protein-coding	0.080460	0.607798	
chunk0153_16_1	chr5	66945586	66945969	+	0	NA	intron (NM_015183, intron 3 of 27)	intron (NM_015183, intron 3 of 27)	-13093	NM_001290226	375449	Hs.595458	NM_015183	ENSG00000069020	MAST4	-	microtubule associated serine/threonine kinase family member 4	protein-coding	0.010444	0.390625	
chunk0149_283_1	chr5	25211150	25211478	+	0	NA	Intergenic	Intergenic	-370731	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.006098	0.322188	
chunk0175_143_1	chr7	3544919	3545141	+	0	NA	intron (NM_152744, intron 1 of 44)	MLT1I|LTR|ERVL-MaLR	243582	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.009009	0.533632	
chunk0195_191_1	chr8	96670019	96670333	+	0	NA	intron (NM_016134, intron 1 of 7)	Tigger17a|DNA|TcMar-Tigger	24949	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.006369	0.349206	
chunk0016_344_1	chr1	202009347	202009884	+	0	NA	promoter-TSS (NM_001114309)	promoter-TSS (NM_001114309)	-947	NM_004433	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.014898	0.503717	
chunk0010_148_1	chr1	115284231	115284491	+	0	NA	Intergenic	Intergenic	53875	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.003846	0.475096	127(CAGCACAGAATGTTCT,-,0.00),128(AGCACAGAATGTTCTA,+,0.00)
chunk0009_56_1	chr1	100629372	100629761	+	0	NA	intron (NR_038914, intron 3 of 4)	L2c|LINE|L2	17438	NR_038914	100128787	Hs.536050	NR_038914		LINC01349	-	long intergenic non-protein coding RNA 1349	ncRNA	0.000000	0.366667	
chunk0108_72_1	chr2	227482498	227482746	+	0	NA	intron (NM_001135189, intron 1 of 11)	intron (NM_001135189, intron 1 of 11)	10450	NM_001135187	3267	Hs.352962	NM_004504	ENSG00000173744	AGFG1	HRB|RAB|RIP	ArfGAP with FG repeats 1	protein-coding	0.000000	0.301205	
chunk0138_9_1	chr4	30321912	30322256	+	0	NA	Intergenic	L1ME2|LINE|L1	-398324	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.000000	0.284058	
chunk0089_298_1	chr18	63451790	63452141	+	0	NA	Intergenic	MER50|LTR|ERV1	-24946	NM_002639	5268	Hs.55279	NM_002639	ENSG00000206075	SERPINB5	PI5|maspin	serpin family B member 5	protein-coding	0.014245	0.488636	88(AGGCACACCCAGTGCA,-,0.00),89(GGCACACCCAGTGCAG,+,0.00),163(GGGAACACATAGTGCT,-,0.00),164(GGAACACATAGTGCTG,+,0.00)
chunk0168_168_1	chr6	83870601	83871020	+	0	NA	intron (NM_016230, intron 2 of 15)	Tigger17c|DNA|TcMar-Tigger	11159	NM_016230	51167	Hs.5741	NM_016230	ENSG00000065615	CYB5R4	NCB5OR|cb5/cb5R|dJ676J13.1	cytochrome b5 reductase 4	protein-coding	0.004773	0.338095	180(AGTACTCACAGTGCTT,+,0.00)
chunk0121_107_1	chr3	17235708	17236161	+	0	NA	intron (NM_001134381, intron 18 of 23)	intron (NM_001134381, intron 18 of 23)	302738	NR_037465	100500913		NR_037465	ENSG00000283885	MIR3714	-	microRNA 3714	ncRNA	0.004415	0.381057	
chunk0022_189_1	chr10	13426565	13427152	+	0	NA	Intergenic	L1PB3|LINE|L1	76118	NM_001100912	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.001704	0.340136	
chunk0061_251_1	chr14	61269656	61270040	+	0	NA	Intergenic	Intergenic	11964	NM_001017970	161291	Hs.146180	NM_001017970	ENSG00000182107	TMEM30B	CDC50B	transmembrane protein 30B	protein-coding	0.041667	0.527273	
chunk0109_408_1	chr2	240638769	240639168	+	0	NA	Intergenic	HAL1ME|LINE|L1	13723	NM_005301	2859	Hs.112218	NM_005301	ENSG00000178623	GPR35	-	G protein-coupled receptor 35	protein-coding	0.025063	0.472500	190(GGGAACATGGTGTGCT,-,0.00),191(GGAACATGGTGTGCTC,+,0.00)
chunk0072_24_1	chr16	562406	562605	+	0	NA	intron (NM_145270, intron 1 of 2)	(AC)n|Simple_repeat|Simple_repeat	2083	NM_145270	146325	Hs.632220	NM_145270	ENSG00000161992	PRR35	C16orf11|LA16c-366D1.2	proline rich 35	protein-coding	0.045226	0.535000	
chunk0180_26_1	chr7	53799913	53800344	+	0	NA	intron (NR_038371, intron 1 of 5)	intron (NR_038371, intron 1 of 5)	11803	NR_038371	401337	Hs.531378	NM_001001707	ENSG00000205628	LINC01446	GS1-179L18.1	long intergenic non-protein coding RNA 1446	ncRNA	0.006961	0.361111	
chunk0118_126_1	chr22	29636592	29637215	+	0	NA	intron (NM_181829, intron 2 of 15)	intron (NM_181829, intron 2 of 15)	33347	NM_181830	4771	Hs.187898	NM_000268	ENSG00000186575	NF2	ACN|BANF|SCH	neurofibromin 2	protein-coding	0.012841	0.451923	249(AAGGACACAGTGGCCT,-,0.00),250(AGGACACAGTGGCCTG,+,0.00)
chunk0148_8_1	chr5	166596	167273	+	0	NA	intron (NM_052909, intron 11 of 17)	intron (NM_052909, intron 11 of 17)	-24577	NM_001080478	389257	Hs.103142	NM_001080478	ENSG00000185028	LRRC14B	-	leucine rich repeat containing 14B	protein-coding	0.023634	0.535398	262(TAGAACATTAAGTTCT,-,0.00),263(AGAACATTAAGTTCTG,+,0.00)
chunk0191_112_1	chr8	48254177	48254376	+	0	NA	Intergenic	L1PBa|LINE|L1	245841	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.010050	0.515000	
chunk0207_385_1	chr9	136409845	136410075	+	0	NA	promoter-TSS (NM_001282946)	promoter-TSS (NM_001282946)	-613	NM_015160	23203	Hs.495471	NM_015160	ENSG00000165688	PMPCA	Alpha-MPP|CLA1|CPD3|INPP5E|P-55|SCAR2	peptidase, mitochondrial processing alpha subunit	protein-coding	0.073913	0.649351	39(TGGAACTGTCTGTCTT,-,0.00),40(GGAACTGTCTGTCTTG,+,0.00)
chunk0070_194_1	chr15	72071002	72071213	+	0	NA	intron (NM_006901, intron 1 of 41)	L1P4|LINE|L1	-43151	NM_001166340	123228	Hs.513002	NM_145204	ENSG00000166192	SENP8	DEN1|NEDP1|PRSC2	SUMO peptidase family member, NEDD8 specific	protein-coding	0.000000	0.320755	
chunk0072_427_1	chr15	101192165	101192529	+	0	NA	intron (NM_014918, intron 2 of 2)	intron (NM_014918, intron 2 of 2)	59585	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.008242	0.476712	
chunk0059_91_1	chr14	30852477	30853004	+	0	NA	Intergenic	MamRep1527|LTR|LTR	-21795	NM_004086	1690	Hs.21016	NM_004086	ENSG00000100473	COCH	COCH-5B2|COCH5B2|DFNA9|DFNB110	cochlin	protein-coding	0.003795	0.395833	
chunk0210_263_1	chrX	84064800	84065350	+	0	NA	exon (NM_014496, exon 21 of 22)	exon (NM_014496, exon 21 of 22)	122860	NM_014496	27330	Hs.234478	NM_014496	ENSG00000072133	RPS6KA6	PP90RSK4|RSK-4|RSK4|S6K-alpha-6|p90RSK6	ribosomal protein S6 kinase A6	protein-coding	0.005455	0.313975	
chunk0122_268_1	chr3	35288618	35289052	+	0	NA	intron (NR_110817, intron 2 of 3)	intron (NR_110817, intron 2 of 3)	105188	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.011521	0.349425	
chunk0091_129_1	chr19	6410900	6411235	+	0	NA	Intergenic	L1ME4b|LINE|L1	5444	NR_037505	100500888		NR_037505	ENSG00000284159	MIR3940	mir-3940	microRNA 3940	ncRNA	0.014925	0.473214	
chunk0068_289_1	chr15	56974299	56974862	+	0	NA	intron (NM_003205, intron 3 of 19)	intron (NM_003205, intron 3 of 19)	55945	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.003552	0.308511	
chunk0017_352_1	chr1	211862366	211862787	+	0	NA	Intergenic	L1MC1|LINE|L1	-31804	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.002375	0.319905	
chunk0113_39_1	chr20	49889375	49889606	+	0	NA	non-coding (NR_048540, exon 12 of 12)	non-coding (NR_048540, exon 12 of 12)	24249	NM_001135773	9825	Hs.48513	NM_006038	ENSG00000158480	SPATA2	PD1|PPP1R145|tamo	spermatogenesis associated 2	protein-coding	0.008658	0.577586	
chunk0162_194_1	chr6	3906178	3906671	+	0	NA	Intergenic	Intergenic	57026	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.028398	0.556680	48(TGGGACTGTTTGTCCC,-,0.00),49(GGGACTGTTTGTCCCA,+,0.00),198(CAGCACGAACTGTCCC,-,0.00),199(AGCACGAACTGTCCCC,+,0.00)
chunk0026_201_1	chr10	63712151	63712720	+	0	NA	Intergenic	Intergenic	191072	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.008787	0.524561	
chunk0132_135_1	chr3	156269289	156269513	+	0	NA	intron (NM_003471, intron 1 of 13)	L1MA2|LINE|L1	-21586	NM_172159	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.004464	0.337778	
chunk0045_390_1	chr12	52625826	52626334	+	0	NA	Intergenic	L1MD1|LINE|L1	-7521	NM_175068	319101	Hs.55410	NM_175068	ENSG00000186049	KRT73	IRT6IRS3|K6IRS3|KRT6IRS3	keratin 73	protein-coding	0.001969	0.359528	
chunk0141_284_1	chr4	86660908	86661398	+	0	NA	intron (NM_006264, intron 2 of 46)	L1ME3|LINE|L1	66838	NM_080685	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.000000	0.315682	
chunk0211_118_1	chrX	112128808	112129179	+	0	NA	intron (NM_001004308, intron 1 of 2)	L1MEd|LINE|L1	45968	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.002695	0.306452	
chunk0166_157_1	chr6	45390190	45390527	+	0	NA	intron (NM_001024630, intron 2 of 8)	intron (NM_001024630, intron 2 of 8)	-12307	NM_001261823	8464	Hs.368325	NM_003599	ENSG00000196284	SUPT3H	SPT3|SPT3L	SPT3 homolog, SAGA and STAGA complex component	protein-coding	0.008902	0.390533	
chunk0042_457_1	chr12	12529702	12530110	+	0	NA	intron (NM_030640, intron 1 of 6)	L1MA8|LINE|L1	32608	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.004902	0.339853	
chunk0174_169_1	chr6	158706350	158706911	+	0	NA	intron (NM_001242394, intron 6 of 17)	intron (NM_001242394, intron 6 of 17)	56616	NM_001242395	94120	Hs.436977	NM_001009991	ENSG00000164674	SYTL3	SLP3	synaptotagmin like 3	protein-coding	0.010695	0.427046	277(GGGAACACTGTGTTCA,-,0.00),278(GGAACACTGTGTTCAC,+,0.00)
chunk0021_143_1	chr10	4141471	4141851	+	0	NA	Intergenic	L1MCc|LINE|L1	89935	NR_120632	101927964	Hs.737041	NR_120632	ENSG00000236990	LOC101927964	-	uncharacterized LOC101927964	ncRNA	0.010526	0.553806	
chunk0208_196_1	chrX	17495119	17495413	+	0	NA	intron (NM_001291867, intron 1 of 8)	intron (NM_001291867, intron 1 of 8)	63861	NR_046632	100873920	Hs.584577	NR_046632		NHS-AS1	-	NHS antisense RNA 1	ncRNA	0.003401	0.366102	
chunk0092_80_1	chr19	21030322	21030769	+	0	NA	intron (NM_025189, intron 2 of 4)	intron (NM_025189, intron 2 of 4)	9925	NM_001172671	80264	Hs.729202	NM_025189	ENSG00000118620	ZNF430	-	zinc finger protein 430	protein-coding	0.006711	0.375000	
chunk0024_373_1	chr10	44501163	44501524	+	0	NA	Intergenic	L1MB7|LINE|L1	-116246	NM_199168	6387	Hs.522891	NM_000609	ENSG00000107562	CXCL12	IRH|PBSF|SCYB12|SDF1|TLSF|TPAR1	C-X-C motif chemokine ligand 12	protein-coding	0.016620	0.342541	
chunk0028_11_1	chr10	82300055	82300287	+	0	NA	intron (NM_001165973, intron 2 of 10)	L1MC5a|LINE|L1	-67251	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.000000	0.266094	
chunk0157_263_1	chr5	120052981	120053706	+	0	NA	Intergenic	Intergenic	-410935	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.004138	0.366391	359(GAGTACATGGTGTACT,-,0.00),360(AGTACATGGTGTACTT,+,0.00)
chunk0136_206_1	chr4	7046659	7047070	+	0	NA	promoter-TSS (NR_033828)	promoter-TSS (NR_033828)	-633	NR_033828	100129931	Hs.707753	NR_033828	ENSG00000245748	LOC100129931	-	uncharacterized LOC100129931	ncRNA	0.012165	0.543689	
chunk0160_427_1	chr5	164473254	164473787	+	0	NA	intron (NR_105065, intron 1 of 3)	intron (NR_105065, intron 1 of 3)	3241	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.009381	0.406367	
chunk0084_122_1	chr17	76147274	76147643	+	0	NA	non-coding (NR_040017, exon 6 of 8)	non-coding (NR_040017, exon 6 of 8)	-6159	NM_001454	2302	Hs.651204	NM_001454	ENSG00000129654	FOXJ1	FKHL13|HFH-4|HFH4	forkhead box J1	protein-coding	0.024390	0.532432	
chunk0115_170_1	chr21	25297270	25297469	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	134332	NR_024027	54072	Hs.234016	NM_058184	ENSG00000185433	LINC00158	C21orf42|NCRNA00158	long intergenic non-protein coding RNA 158	ncRNA	0.005025	0.385000	
chunk0087_435_1	chr18	42413816	42414229	+	0	NA	intron (NR_046174, intron 4 of 9)	intron (NR_046174, intron 4 of 9)	227354	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.004843	0.410628	
chunk0143_227_1	chr4	114187640	114187839	+	0	NA	Intergenic	Intergenic	-208017	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.000000	0.355000	
chunk0169_66_1	chr6	98958742	98959374	+	0	NA	Intergenic	Intergenic	-11052	NM_001278716	26235	Hs.536850	NM_012160	ENSG00000112234	FBXL4	FBL4|FBL5|MTDPS13	F-box and leucine rich repeat protein 4	protein-coding	0.012658	0.390205	
chunk0020_7_1	chr1	231651363	231652200	+	0	NA	intron (NM_001164556, intron 1 of 4)	L1HS|LINE|L1	24966	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.015532	0.546539	618(AGGTACAGTCTGTCAC,-,0.00)
chunk0203_115_1	chr9	84746112	84746430	+	0	NA	intron (NM_001007097, intron 11 of 12)	MER58B|DNA|hAT-Charlie	75894	NM_001018064	4915	Hs.494312	NM_006180	ENSG00000148053	NTRK2	EIEE58|GP145-TrkB|OBHD|TRKB|trk-B	neurotrophic receptor tyrosine kinase 2	protein-coding	0.012579	0.407524	132(ATGAACAGAGTGTTAC,-,0.00)
chunk0062_383_1	chr14	74534182	74534569	+	0	NA	intron (NM_000428, intron 9 of 35)	L2b|LINE|L2	40655	NM_194279	122961	Hs.291079	NM_194279	ENSG00000165898	ISCA2	HBLD1|ISA2|MMDS4|c14_5557	iron-sulfur cluster assembly 2	protein-coding	0.010336	0.518041	211(CAGCACAAACTGTTCT,-,0.00),212(AGCACAAACTGTTCTT,+,0.00)
chunk0016_8_1	chr1	192707309	192707591	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-8878	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.003546	0.335689	
chunk0025_240_1	chr10	54277240	54277701	+	0	NA	intron (NM_001142769, intron 9 of 35)	MER53|DNA|hAT	330487	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.008677	0.326840	
chunk0097_13_1	chr2	41615465	41615874	+	0	NA	Intergenic	Intergenic	-261886	NR_033996	388942	Hs.631883	NR_033996	ENSG00000214691	LINC01913	-	long intergenic non-protein coding RNA 1913	ncRNA	0.004890	0.365854	
chunk0202_5_1	chr9	70286122	70286380	+	0	NA	exon (NM_015110, exon 8 of 25)	exon (NM_015110, exon 8 of 25)	27289	NM_015110	23137	Hs.534189	NM_015110	ENSG00000198887	SMC5	SMC5L1	structural maintenance of chromosomes 5	protein-coding	0.003876	0.366795	
chunk0006_112_1	chr1	65524638	65525186	+	0	NA	promoter-TSS (NM_001198687)	promoter-TSS (NM_001198687)	-777	NM_001198688	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.018248	0.417122	
chunk0164_449_1	chr6	28112461	28112767	+	0	NA	Intergenic	L1MEi|LINE|L1	-11995	NM_025231	80345	Hs.656641	NM_025231	ENSG00000196812	ZSCAN16	ZNF392|ZNF435|dJ265C24.3	zinc finger and SCAN domain containing 16	protein-coding	0.000000	0.371336	
chunk0111_273_1	chr20	31157642	31157932	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	-99877	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.013793	0.432990	
chunk0104_83_1	chr2	171956489	171956750	+	0	NA	intron (NR_027862, intron 3 of 9)	MLT1D-int|LTR|ERVL-MaLR	34194	NM_003642	8520	Hs.632532	NM_003642	ENSG00000128708	HAT1	KAT1	histone acetyltransferase 1	protein-coding	0.000000	0.427481	
chunk0100_459_1	chr2	121136633	121136873	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	148449	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.008333	0.477178	
chunk0003_242_1	chr1	36105402	36105630	+	0	NA	intron (NM_005202, intron 2 of 3)	intron (NM_005202, intron 2 of 3)	16664	NM_017825	54936	Hs.18021	NM_017825	ENSG00000116863	ADPRHL2	ARH3|CONDSIAS	ADP-ribosylhydrolase like 2	protein-coding	0.030702	0.567686	
chunk0085_173_1	chr18	5031034	5031233	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	166123	NM_001145194	642597	Hs.437160	NM_001145194	ENSG00000231824	AKAIN1	C18orf42	A-kinase anchor inhibitor 1	protein-coding	0.000000	0.435000	
chunk0028_46_1	chr10	83183237	83183461	+	0	NA	Intergenic	L2|LINE|L2	-950429	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.000000	0.364444	8(TAGTACTGATTGTTCC,-,0.00),9(AGTACTGATTGTTCCA,+,0.00)
chunk0090_377_1	chr18	77206232	77206496	+	0	NA	Intergenic	Intergenic	-43688	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.018939	0.403774	
chunk0136_213_1	chr4	7517753	7518224	+	0	NA	intron (NM_020777, intron 2 of 26)	intron (NM_020777, intron 2 of 26)	57960	NR_036238	100422826		NR_036238	ENSG00000266690	MIR4274	-	microRNA 4274	ncRNA	0.014862	0.436441	
chunk0015_388_1	chr1	190682796	190683377	+	0	NA	intron (NR_033922, intron 1 of 4)	L1MCb|LINE|L1	58196	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.001721	0.280069	
chunk0170_383_1	chr6	116982466	116982747	+	0	NA	Intergenic	L1MEc|LINE|L1	105393	NM_173560	222546	Hs.352276	NM_173560	ENSG00000185002	RFX6	MTCHRS|MTFS|RFXDC1|dJ955L16.1	regulatory factor X6	protein-coding	0.000000	0.262411	
chunk0105_297_1	chr2	190080389	190080824	+	0	NA	Intergenic	Intergenic	-17877	NM_005259	2660	Hs.41565	NM_005259	ENSG00000138379	MSTN	GDF8|MSLHP	myostatin	protein-coding	0.000000	0.419725	
chunk0189_64_1	chr8	20394571	20394863	+	0	NA	Intergenic	Intergenic	118944	NR_047509	100874051	Hs.385799	NR_047509	ENSG00000253733	LZTS1-AS1	-	LZTS1 antisense RNA 1	ncRNA	0.010274	0.426621	
chunk0145_336_1	chr4	150789938	150790401	+	0	NA	intron (NM_001199282, intron 34 of 56)	intron (NM_001199282, intron 34 of 56)	208244	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.002160	0.370690	
chunk0112_331_1	chr20	44979288	44979548	+	0	NA	intron (NM_006282, intron 3 of 10)	intron (NM_006282, intron 3 of 10)	12939	NM_006282	6789	Hs.472838	NM_006282	ENSG00000101109	STK4	KRS2|MST1|YSK3	serine/threonine kinase 4	protein-coding	0.007692	0.356322	
chunk0049_94_1	chr12	90836657	90837110	+	0	NA	Intergenic	Intergenic	-81140	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.015453	0.438326	
chunk0125_319_1	chr3	70850980	70851313	+	0	NA	Intergenic	Intergenic	213777	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.009009	0.422156	
chunk0174_419_1	chr6	165834682	165835012	+	0	NA	Intergenic	Intergenic	-152704	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.012121	0.586103	
chunk0149_31_1	chr5	16275461	16275902	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-95893	NM_001102562	441061	Hs.662216	NM_001102562	ENSG00000183654	MARCH11	MARCH-XI|RNF226	membrane associated ring-CH-type finger 11	protein-coding	0.006803	0.366516	206(AAGTACACTCTGTGAT,-,0.00)
chunk0182_27_1	chr7	91504131	91504770	+	0	NA	Intergenic	UCON17|Unknown|Unknown	239982	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.007825	0.390625	
chunk0003_320_1	chr1	38229655	38229854	+	0	NA	Intergenic	Intergenic	-14987	NR_038928	339442	Hs.434245	NR_038928	ENSG00000237290	LINC01343	-	long intergenic non-protein coding RNA 1343	ncRNA	0.010050	0.515000	52(TGACCAGCATGTTCCT,+,0.00)
chunk0056_88_1	chr13	81305976	81306294	+	0	NA	Intergenic	Intergenic	-79152	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.000000	0.382445	
chunk0206_367_1	chr9	125904116	125904804	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	156261	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.007267	0.404935	
chunk0055_337_1	chr13	69269318	69269517	+	0	NA	intron (NR_125752, intron 1 of 3)	intron (NR_125752, intron 1 of 3)	47071	NR_125752	103689913	Hs.585628	NR_125752	ENSG00000235221	LINC00383	LINC00401	long intergenic non-protein coding RNA 383	ncRNA	0.005025	0.300000	
chunk0144_1_1	chr4	124329181	124329552	+	0	NA	Intergenic	Intergenic	229068	NR_110838	101927087	Hs.518966	NR_110838	ENSG00000261083	LINC02516	-	long intergenic non-protein coding RNA 2516	ncRNA	0.000000	0.346774	
chunk0051_221_1	chr12	116658726	116659065	+	0	NA	Intergenic	Intergenic	79175	NM_024738	79794	Hs.120170	NM_024738	ENSG00000111412	C12orf49	-	chromosome 12 open reading frame 49	protein-coding	0.017699	0.505882	
chunk0171_240_1	chr6	127022894	127023460	+	0	NA	Intergenic	Intergenic	-95726	NM_032784	84870	Hs.135254	NM_032784	ENSG00000146374	RSPO3	CRISTIN1|PWTSR|THSD2	R-spondin 3	protein-coding	0.001767	0.388007	
chunk0178_448_1	chr7	42024969	42025244	+	0	NA	intron (NM_000168, intron 9 of 14)	intron (NM_000168, intron 9 of 14)	211913	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.021818	0.503623	
chunk0064_179_1	chr14	92644382	92644668	+	0	NA	intron (NM_024832, intron 5 of 9)	intron (NM_024832, intron 5 of 9)	104177	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.013986	0.473868	
chunk0076_156_1	chr16	67318014	67318227	+	0	NA	intron (NM_001100915, intron 2 of 15)	intron (NM_001100915, intron 2 of 15)	8638	NM_001100915	146212	Hs.299127	NM_001100915	ENSG00000168676	KCTD19	-	potassium channel tetramerization domain containing 19	protein-coding	0.000000	0.378505	
chunk0101_5_1	chr2	121260449	121261233	+	0	NA	intron (NM_014553, intron 2 of 14)	intron (NM_014553, intron 2 of 14)	24361	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.012755	0.543949	384(TGGATCACAGTGTTCC,-,0.00),385(GGATCACAGTGTTCCC,+,0.00)
chunk0146_26_1	chr4	155304519	155304718	+	0	NA	Intergenic	Intergenic	-49598	NR_125937	102724776	Hs.61271	NR_125937	ENSG00000250910	LOC102724776	-	uncharacterized LOC102724776	ncRNA	0.010050	0.490000	
chunk0212_273_1	chrX	139739139	139739430	+	0	NA	intron (NM_001010986, intron 27 of 28)	(T)n|Simple_repeat|Simple_repeat	-31062	NM_001171876	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.006873	0.414384	95(AGTCACAGAGTGTTCC,-,0.00),96(GTCACAGAGTGTTCCT,+,0.00)
chunk0139_363_1	chr4	60378014	60378662	+	0	NA	Intergenic	Intergenic	-544281	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.001543	0.349769	320(AAGCACATCCTGTCTC,-,0.00),321(AGCACATCCTGTCTCT,+,0.00),350(CAGCACTTTCTGTTCT,-,0.00),351(AGCACTTTCTGTTCTA,+,0.00)
chunk0165_463_1	chr6	41225672	41225873	+	0	NA	Intergenic	Intergenic	-2552	NM_198153	285852	Hs.434181	NM_198153	ENSG00000188056	TREML4	TLT-4|TLT4	triggering receptor expressed on myeloid cells like 4	protein-coding	0.014925	0.292079	
chunk0094_362_1	chr2	9635871	9636287	+	0	NA	Intergenic	Intergenic	-5024	NM_006826	10971	Hs.74405	NM_006826	ENSG00000134308	YWHAQ	14-3-3|1C5|HS1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta	protein-coding	0.014423	0.417266	
chunk0070_426_1	chr15	78003531	78003941	+	0	NA	intron (NM_015079, intron 10 of 12)	intron (NM_015079, intron 10 of 12)	-9511	NR_026998	91450	Hs.406766	NR_026998		LOC91450	-	uncharacterized LOC91450	ncRNA	0.026829	0.542579	
chunk0189_455_1	chr8	28499363	28499689	+	0	NA	intron (NM_145866, intron 1 of 6)	L1ME4a|LINE|L1	5321	NM_145866	7976	Hs.40735	NM_017412	ENSG00000104290	FZD3	Fz-3	frizzled class receptor 3	protein-coding	0.003067	0.293578	
chunk0073_78_1	chr16	3846546	3846821	+	0	NA	intron (NM_001079846, intron 2 of 29)	L1ME3G|LINE|L1	33437	NM_001079846	1387	Hs.459759	NM_004380	ENSG00000005339	CREBBP	CBP|KAT3A|MKHK1|RSTS|RSTS1	CREB binding protein	protein-coding	0.021818	0.445652	
chunk0093_233_1	chr19	50610618	50611198	+	0	NA	Intergenic	L1MC2|LINE|L1	5945	NR_004384	100126781	Hs.707968	NR_004384		SNAR-F	-	small NF90 (ILF3) associated RNA F	snRNA	0.018966	0.388985	
chunk0039_84_1	chr11	97140834	97141284	+	0	NA	Intergenic	L1M3b|LINE|L1	-634182	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.002222	0.330377	
chunk0141_352_1	chr4	87802763	87803341	+	0	NA	intron (NM_004967, intron 4 of 6)	intron (NM_004967, intron 4 of 6)	3502	NM_004967	3381	Hs.518726	NM_004967	ENSG00000029559	IBSP	BNSP|BSP|BSP-II|SP-II	integrin binding sialoprotein	protein-coding	0.001730	0.338515	
chunk0120_278_1	chr3	9422621	9423168	+	0	NA	intron (NM_001292043, intron 1 of 24)	intron (NM_001292043, intron 1 of 24)	25194	NM_001080517	55209	Hs.288164	NM_018187	ENSG00000168137	SETD5	-	SET domain containing 5	protein-coding	0.007313	0.414234	
chunk0168_418_1	chr6	95371108	95371388	+	0	NA	Intergenic	Intergenic	206203	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.355872	
chunk0171_322_1	chr6	129722001	129722263	+	0	NA	Intergenic	Intergenic	-11907	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.007634	0.429658	26(AGGGACATCCAGTGCT,-,0.00),27(GGGACATCCAGTGCTT,+,0.00)
chunk0161_210_1	chr5	170834913	170835295	+	0	NA	Intergenic	Intergenic	-26778	NM_022897	64901	Hs.410810	NM_022897	ENSG00000204764	RANBP17	-	RAN binding protein 17	protein-coding	0.002618	0.352480	164(CTGCACTGAATGTCCT,-,0.00),165(TGCACTGAATGTCCTG,+,0.00)
chunk0012_50_1	chr1	155473103	155473514	+	0	NA	intron (NM_018489, intron 3 of 27)	intron (NM_018489, intron 3 of 27)	40128	NR_034180	645682	Hs.632482	NR_034180	ENSG00000237872	POU5F1P4	OCT3|OCT4|OTF-3|OTF3|Oct-3|Oct-4|Oct4-pg4|POU5F1|POU5FLC1	POU class 5 homeobox 1 pseudogene 4	pseudo	0.004866	0.359223	
chunk0208_358_1	chrX	25930449	25931167	+	0	NA	Intergenic	L1MC2|LINE|L1	-207535	NM_173699	286514	Hs.350683	NM_173699	ENSG00000176774	MAGEB18	-	MAGE family member B18	protein-coding	0.001393	0.312935	
chunk0017_284_1	chr1	209900222	209900422	+	0	NA	Intergenic	LTR50|LTR|ERVL	-37852	NM_001146264	255928	Hs.658866	NM_153262	ENSG00000143469	SYT14	SCAR11|sytXIV	synaptotagmin 14	protein-coding	0.015000	0.512438	
chunk0063_256_1	chr14	82880202	82880738	+	0	NA	Intergenic	Intergenic	-1257409	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.007463	0.366853	
chunk0206_80_1	chr9	120014736	120015229	+	0	NA	Intergenic	MIR|SINE|MIR	79922	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.014199	0.491903	
chunk0081_369_1	chr17	47948607	47949202	+	0	NA	3' UTR (NM_018129, exon 7 of 7)	3' UTR (NM_018129, exon 7 of 7)	7381	NM_018129	55163	Hs.631742	NM_018129	ENSG00000108439	PNPO	HEL-S-302|PDXPO	pyridoxamine 5'-phosphate oxidase	protein-coding	0.008403	0.528523	
chunk0153_41_1	chr5	67235706	67236006	+	0	NA	Intergenic	Tigger19b|DNA|TcMar-Tigger	-39067	NM_005582	4064	Hs.87205	NM_005582	ENSG00000134061	CD180	LY64|Ly78|RP105	CD180 molecule	protein-coding	0.020000	0.441860	
chunk0033_107_1	chr11	14374115	14374621	+	0	NA	Intergenic	L2c|LINE|L2	-9862	NM_001177314	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.001976	0.416174	
chunk0119_332_1	chr22	46881375	46881685	+	0	NA	intron (NM_014346, intron 5 of 12)	intron (NM_014346, intron 5 of 12)	34512	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.025806	0.578778	197(GGGAACAGGCTGTTCT,-,0.00),198(GGAACAGGCTGTTCTT,+,0.00)
chunk0137_24_1	chr4	10935121	10935798	+	0	NA	Intergenic	Intergenic	-250697	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.005908	0.382006	
chunk0211_331_1	chrX	124079954	124080380	+	0	NA	intron (NM_001042749, intron 27 of 34)	L1MA9|LINE|L1	118461	NM_001042751	10735	Hs.496710	NM_006603	ENSG00000101972	STAG2	NEDXCF|SA-2|SA2|SCC3B|bA517O1.1	stromal antigen 2	protein-coding	0.004695	0.360656	
chunk0162_426_1	chr5	180222061	180222268	+	0	NA	Intergenic	LTR41C|LTR|ERVL	-13034	NM_175062	255426	Hs.190559	NM_175062	ENSG00000146090	RASGEF1C	-	RasGEF domain family member 1C	protein-coding	0.038647	0.548077	
chunk0046_126_1	chr12	57389237	57389832	+	0	NA	Intergenic	Intergenic	-45151	NM_005538	3626	Hs.632722	NM_005538	ENSG00000175189	INHBC	IHBC	inhibin subunit beta C	protein-coding	0.001681	0.348993	
chunk0071_319_1	chr15	86796420	86796924	+	0	NA	intron (NM_152336, intron 22 of 23)	MER58A|DNA|hAT-Charlie	-479704	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.003968	0.386139	
chunk0126_132_1	chr3	75974527	75974726	+	0	NA	Intergenic	Intergenic	-189043	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.000000	0.265000	
chunk0122_262_1	chr3	35151650	35152270	+	0	NA	intron (NR_110817, intron 2 of 3)	MLT1D|LTR|ERVL-MaLR	242063	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.001613	0.333333	
chunk0014_146_1	chr1	178033177	178033619	+	0	NA	intron (NR_037167, intron 3 of 9)	intron (NR_037167, intron 3 of 9)	4609	NR_037167	730102	Hs.733192	NR_037167	ENSG00000242193	CRYZL2P	-	crystallin zeta like 2, pseudogene	pseudo	0.002262	0.431151	
chunk0142_72_1	chr4	93831739	93832563	+	0	NA	Intergenic	Intergenic	3224	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.031553	0.446061	
chunk0105_121_1	chr2	185336950	185337149	+	0	NA	Intergenic	L1MA3|LINE|L1	-401579	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.005025	0.365000	
chunk0208_284_1	chrX	21904343	21904875	+	0	NA	Intergenic	Intergenic	-35964	NM_001258423	6611	Hs.724874	NM_004595	ENSG00000102172	SMS	MRSR|SPMSY|SRS|SpS	spermine synthase	protein-coding	0.005639	0.422139	
chunk0198_79_1	chr8	130092508	130092919	+	0	NA	intron (NM_001247996, intron 25 of 30)	intron (NM_001247996, intron 25 of 30)	-7945	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.004866	0.395631	124(AAGAAGAGTGTGTGCT,-,0.00),125(AGAAGAGTGTGTGCTT,+,0.00)
chunk0141_196_1	chr4	83874044	83874437	+	0	NA	Intergenic	MIR|SINE|MIR	337923	NM_032717	84803	Hs.99196	NM_032717	ENSG00000138678	GPAT3	AGPAT 10|AGPAT10|AGPAT8|AGPAT9|HMFN0839|LPAAT-theta|MAG1	glycerol-3-phosphate acyltransferase 3	protein-coding	0.005089	0.370558	
chunk0076_392_1	chr16	72490581	72491076	+	0	NA	intron (NR_126330, intron 6 of 13)	intron (NR_126330, intron 6 of 13)	174181	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.004040	0.322581	
chunk0185_145_1	chr7	127588794	127589126	+	0	NA	intron (NM_001662, intron 1 of 5)	CpG	608	NM_001662	381	Hs.653202	NM_001662	ENSG00000004059	ARF5	-	ADP ribosylation factor 5	protein-coding	0.063253	0.627628	
chunk0060_75_1	chr14	41985996	41986605	+	0	NA	Intergenic	Intergenic	378739	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.003284	0.326230	
chunk0017_424_1	chr1	213125549	213125980	+	0	NA	intron (NM_001287219, intron 6 of 14)	intron (NM_001287219, intron 6 of 14)	74531	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.004640	0.310185	
chunk0011_376_1	chr1	153725996	153726230	+	0	NA	Intergenic	Intergenic	-1978	NM_023015	65123	Hs.438723	NM_023015	ENSG00000143624	INTS3	C1orf193|C1orf60|INT3|SOSS-A|SOSSA	integrator complex subunit 3	protein-coding	0.000000	0.348936	
chunk0011_367_1	chr1	153390002	153390215	+	0	NA	TTS (NM_002964)	TTS (NM_002964)	1080	NM_002964	6279	Hs.416073	NM_002964	ENSG00000143546	S100A8	60B8AG|CAGA|CFAG|CGLA|CP-10|L1Ag|MA387|MIF|MRP8|NIF|P8	S100 calcium binding protein A8	protein-coding	0.004695	0.467290	
chunk0031_159_1	chr10	125246196	125246631	+	0	NA	Intergenic	Intergenic	-85358	NM_001083914	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.006897	0.456422	173(AGAGACAAACTGTTCT,-,0.00),174(GAGACAAACTGTTCTG,+,0.00)
chunk0191_118_1	chr8	48292400	48293046	+	0	NA	Intergenic	L1MD1|LINE|L1	-258844	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.007740	0.335394	
chunk0033_175_1	chr11	15750746	15751162	+	0	NA	Intergenic	Intergenic	107069	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.016827	0.522782	
chunk0144_295_1	chr4	138345803	138346255	+	0	NA	intron (NR_051987, intron 1 of 2)	intron (NR_051987, intron 1 of 2)	36318	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.006637	0.337748	288(AAGAACACCTTGTGTT,-,0.00),289(AGAACACCTTGTGTTG,+,0.00)
chunk0201_8_1	chr9	32136738	32137359	+	0	NA	Intergenic	Intergenic	-247555	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.004831	0.390675	
chunk0190_263_1	chr8	37302080	37303184	+	0	NA	Intergenic	Intergenic	191281	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.011775	0.466063	167(AGGAACAGGATGAGCC,-,0.00),168(GGAACAGGATGAGCCT,+,0.00)
chunk0102_401_1	chr2	155190140	155190745	+	0	NA	Intergenic	Intergenic	491861	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.000000	0.297030	351(AAGAACAGGCTGTTCT,-,0.00),352(AGAACAGGCTGTTCTT,+,0.00)
chunk0082_291_1	chr17	58391585	58391912	+	0	NA	intron (NM_001305544, intron 2 of 9)	intron (NM_001305544, intron 2 of 9)	10973	NM_001305545	54894	Hs.584916	NM_017763	ENSG00000108375	RNF43	RNF124|SSPCS|URCC	ring finger protein 43	protein-coding	0.018349	0.503049	
chunk0011_245_1	chr1	150578601	150578802	+	0	NA	intron (NM_001197320, intron 2 of 3)	intron (NM_001197320, intron 2 of 3)	1037	NM_021960	4170	Hs.632486	NM_021960	ENSG00000143384	MCL1	BCL2L3|EAT|MCL1-ES|MCL1L|MCL1S|Mcl-1|TM|bcl2-L-3|mcl1/EAT	MCL1 apoptosis regulator, BCL2 family member	protein-coding	0.034826	0.495050	
chunk0066_43_1	chr15	27902771	27903005	+	0	NA	intron (NM_001300984, intron 18 of 22)	CpG	196424	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.081197	0.663830	85(AGGCACAGTGCGTTCC,-,0.00),86(GGCACAGTGCGTTCCT,+,0.00)
chunk0142_13_1	chr4	90063501	90063913	+	0	NA	Intergenic	Intergenic	-63826	NM_001145065	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.004854	0.351090	
chunk0211_112_1	chrX	111682089	111682345	+	0	NA	exon (NM_001039210, exon 2 of 4)	exon (NM_001039210, exon 2 of 4)	560	NM_001257239	79868	Hs.443061	NM_018466	ENSG00000101901	ALG13	CDG1S|CXorf45|EIEE36|GLT28D1|MDS031|TDRD13|YGL047W	ALG13 UDP-N-acetylglucosaminyltransferase subunit	protein-coding	0.019531	0.404669	
chunk0165_165_1	chr6	33974057	33974310	+	0	NA	Intergenic	L1ME1|LINE|L1	25868	NR_031681	100302123		NR_031681	ENSG00000221697	MIR1275	MIRN1275|hsa-mir-1275|mir-1275	microRNA 1275	ncRNA	0.011858	0.409449	
chunk0119_111_1	chr22	42261003	42261427	+	0	NA	intron (NM_005650, intron 1 of 5)	L1ME2|LINE|L1	-8538	NR_036498	388906	Hs.730075	NR_036498		OGFRP1	-	opioid growth factor receptor pseudogene 1	pseudo	0.004717	0.355294	
chunk0133_65_1	chr3	166864738	166864950	+	0	NA	Intergenic	Intergenic	515439	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.014151	0.586854	
chunk0189_153_1	chr8	23022209	23023099	+	0	NA	non-coding (NR_027140, exon 9 of 9)	non-coding (NR_027140, exon 9 of 9)	23075	NM_015178	23221	Hs.372688	NM_015178	ENSG00000008853	RHOBTB2	DBC2|EIEE64	Rho related BTB domain containing 2	protein-coding	0.017978	0.483726	634(GTGTACAAGGTGTCCC,-,0.00),635(TGTACAAGGTGTCCCT,+,0.00)
chunk0129_261_1	chr3	122443841	122444356	+	0	NA	TTS (NR_125405)	TTS (NR_125405)	27892	NR_125405	102723582	Hs.675056	NR_125405	ENSG00000272758	LOC102723582	-	uncharacterized LOC102723582	ncRNA	0.015534	0.447674	
chunk0011_80_1	chr1	145140668	145140867	+	0	NA	Intergenic	Intergenic	44767	NM_207418	728833	Hs.535577	NM_207418	ENSG00000215784	FAM72D	GCUD2	family with sequence similarity 72 member D	protein-coding	0.005025	0.410000	71(AGGCACTGTGTGTACT,-,0.00),72(GGCACTGTGTGTACTA,+,0.00)
chunk0090_305_1	chr18	75335275	75335474	+	0	NA	Intergenic	Intergenic	92329	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.030151	0.570000	
chunk0117_130_1	chr22	19229445	19229942	+	0	NA	intron (NM_001835, intron 11 of 31)	intron (NM_001835, intron 11 of 31)	-50830	NM_005984	6576	Hs.111024	NM_005984	ENSG00000100075	SLC25A1	CMS23|CTP|D2L2AD|SEA|SLC20A3	solute carrier family 25 member 1	protein-coding	0.004024	0.421687	
chunk0160_90_1	chr5	150073289	150073795	+	0	NA	intron (NR_109969, intron 5 of 19)	intron (NR_109969, intron 5 of 19)	13098	NR_109969	1436	Hs.586219	NM_005211	ENSG00000182578	CSF1R	C-FMS|CD115|CSF-1R|CSFR|FIM2|FMS|HDLS|M-CSF-R	colony stimulating factor 1 receptor	protein-coding	0.001976	0.495069	
chunk0162_30_1	chr6	1016558	1016840	+	0	NA	intron (NR_027115, intron 1 of 4)	intron (NR_027115, intron 1 of 4)	84633	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.017730	0.399293	
chunk0077_433_1	chr16	85564112	85564342	+	0	NA	Intergenic	L2c|LINE|L2	-47196	NM_001134473	23199	Hs.461647	NM_014615	ENSG00000131149	GSE1	CRHSP24|KIAA0182	Gse1 coiled-coil protein	protein-coding	0.004348	0.510823	
chunk0083_85_1	chr17	64254717	64255371	+	0	NA	intron (NM_018469, intron 1 of 11)	AluJr|SINE|Alu	8279	NM_001288732	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.003058	0.416794	
chunk0127_395_1	chr3	102333040	102333418	+	0	NA	Intergenic	Intergenic	-101786	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.000000	0.387863	339(AAGAACTTTCTGACCC,-,0.00),340(AGAACTTTCTGACCCT,+,0.00)
chunk0039_277_1	chr11	102513596	102514418	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	16740	NM_002423	4316	Hs.2256	NM_002423	ENSG00000137673	MMP7	MMP-7|MPSL1|PUMP-1	matrix metallopeptidase 7	protein-coding	0.006083	0.397327	
chunk0139_73_1	chr4	49118652	49119602	+	0	NA	Intergenic	(TCCAT)n|Simple_repeat|Simple_repeat	132485	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.017895	0.412198	
chunk0193_336_1	chr8	79355740	79356749	+	0	NA	Intergenic	Intergenic	-254570	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.007929	0.340594	
chunk0058_204_1	chr14	24813266	24813465	+	0	NA	intron (NM_014178, intron 5 of 5)	intron (NM_014178, intron 5 of 5)	-179139	NM_004131	3002	Hs.1051	NM_004131	ENSG00000100453	GZMB	C11|CCPI|CGL-1|CGL1|CSP-B|CSPB|CTLA1|CTSGL1|HLP|SECT	granzyme B	protein-coding	0.010050	0.345000	
chunk0103_69_1	chr2	160165928	160166457	+	0	NA	intron (NM_000888, intron 7 of 14)	intron (NM_000888, intron 7 of 14)	34121	NM_001282354	3694	Hs.470399	NM_000888	ENSG00000115221	ITGB6	AI1H	integrin subunit beta 6	protein-coding	0.005671	0.347170	
chunk0109_402_1	chr2	240379060	240379593	+	0	NA	Intergenic	L2|LINE|L2	-56372	NM_002081	2817	Hs.328232	NM_002081	ENSG00000063660	GPC1	glypican	glypican 1	protein-coding	0.016886	0.498127	
chunk0070_30_1	chr15	69307268	69307688	+	0	NA	intron (NM_017705, intron 1 of 8)	(GAGGG)n|Simple_repeat|Simple_repeat	-6925	NM_001104554	54852	Hs.591096	NM_017705	ENSG00000137819	PAQR5	MPRG	progestin and adipoQ receptor family member 5	protein-coding	0.014286	0.510689	
chunk0139_12_1	chr4	48001532	48001930	+	0	NA	intron (NM_000087, intron 2 of 10)	L1MEf|LINE|L1	11213	NM_000087	1259	Hs.1323	NM_000087	ENSG00000198515	CNGA1	CNCG|CNCG1|CNG-1|CNG1|RCNC1|RCNCa|RCNCalpha|RP49	cyclic nucleotide gated channel alpha 1	protein-coding	0.000000	0.323308	
chunk0072_90_1	chr15	90866082	90866655	+	0	NA	Intergenic	Intergenic	-2224	NM_002569	5045	Hs.513153	NM_002569	ENSG00000140564	FURIN	FUR|PACE|PCSK3|SPC1	furin, paired basic amino acid cleaving enzyme	protein-coding	0.022688	0.513937	
chunk0128_186_1	chr3	107456592	107456914	+	0	NA	intron (NR_110039, intron 1 of 2)	intron (NR_110039, intron 1 of 2)	25823	NR_110039	101929607	Hs.252565	NR_110039	ENSG00000273125	LINC01990	-	long intergenic non-protein coding RNA 1990	ncRNA	0.003106	0.352941	
chunk0163_353_1	chr6	15573536	15573768	+	0	NA	intron (NM_001271667, intron 7 of 9)	intron (NM_001271667, intron 7 of 9)	89406	NM_001271668	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.008621	0.459227	
chunk0210_215_1	chrX	81301934	81302159	+	0	NA	Intergenic	L1MB7|LINE|L1	-100104	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.000000	0.371681	
chunk0201_401_1	chr9	69214914	69215328	+	0	NA	intron (NM_201629, intron 2 of 20)	L1PA17|LINE|L1	9959	NM_001170416	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.009662	0.375904	
chunk0137_287_1	chr4	23887267	23887527	+	0	NA	intron (NM_013261, intron 1 of 12)	intron (NM_013261, intron 1 of 12)	2680	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.000000	0.379310	
chunk0168_162_1	chr6	83805233	83805694	+	0	NA	Intergenic	Intergenic	-47803	NM_001009994	134701	Hs.149454	NM_001009994	ENSG00000203877	RIPPLY2	C6orf159|SCDO6|dJ237I15.1	ripply transcriptional repressor 2	protein-coding	0.004338	0.354978	
chunk0146_385_1	chr4	168587633	168587834	+	0	NA	intron (NM_016081, intron 2 of 20)	intron (NM_016081, intron 2 of 20)	-43884	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.000000	0.470297	
chunk0181_154_1	chr7	82049518	82050153	+	0	NA	TTS (NM_001302890)	TTS (NM_001302890)	40658	NR_110077	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.009449	0.388365	
chunk0113_104_1	chr20	51026125	51026511	+	0	NA	Intergenic	Intergenic	-3180	NM_002237	3755	Hs.118695	NM_002237	ENSG00000026559	KCNG1	K13|KCNG|KV6.1|kH2	potassium voltage-gated channel modifier subfamily G member 1	protein-coding	0.015544	0.470284	155(AGAACACTATGCACCT,+,0.00)
chunk0154_381_1	chr5	87774800	87775493	+	0	NA	Intergenic	Intergenic	-362113	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.004329	0.367435	
chunk0099_437_1	chr2	103026913	103027214	+	0	NA	Intergenic	Intergenic	265032	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.003322	0.360927	
chunk0198_379_1	chr8	141228380	141228900	+	0	NA	promoter-TSS (NM_001286648)	promoter-TSS (NM_001286648)	-66	NM_001080431	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.023077	0.548944	
chunk0038_181_1	chr11	85821438	85821936	+	0	NA	Intergenic	Intergenic	-10528	NM_001289608	54843	Hs.369520	NM_032379	ENSG00000137501	SYTL2	CHR11SYT|EXO4|PPP1R151|SGA72M|SLP2|SLP2A	synaptotagmin like 2	protein-coding	0.006024	0.448898	
chunk0021_445_1	chr1	248418392	248418591	+	0	NA	Intergenic	LTR1D1|LTR|ERV1	12496	NM_030904	26696	Hs.626885	NM_030904	ENSG00000175143	OR2T1	OR1-25	olfactory receptor family 2 subfamily T member 1	protein-coding	0.005025	0.455000	
chunk0120_272_1	chr3	9351689	9351916	+	0	NA	Intergenic	MER101B|LTR|ERV1	-11231	NM_015453	25917	Hs.443081	NM_015453	ENSG00000134077	THUMPD3	-	THUMP domain containing 3	protein-coding	0.004405	0.434211	
chunk0195_227_1	chr8	97320316	97320887	+	0	NA	intron (NR_125390, intron 2 of 2)	AluJr|SINE|Alu	-42653	NM_033512	85453	Hs.173094	NM_033512	ENSG00000180543	TSPYL5	-	TSPY like 5	protein-coding	0.001751	0.402098	
chunk0191_331_1	chr8	55970040	55970695	+	0	NA	intron (NM_001111097, intron 10 of 12)	intron (NM_001111097, intron 10 of 12)	90540	NM_001111097	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.010687	0.399390	
chunk0114_117_1	chr21	9625232	9625442	+	0	NA	Intergenic	Intergenic	195724	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.019048	0.488152	
chunk0201_344_1	chr9	65645231	65645463	+	0	NA	Intergenic	Intergenic	-30487	NM_001024916	220869	Hs.355950	NM_001024916	ENSG00000147996	CBWD5	CBWD3|DC36	COBW domain containing 5	protein-coding	0.012931	0.476395	131(AGGAACACACTGTGCC,-,0.00),132(GGAACACACTGTGCCT,+,0.00)
chunk0153_323_1	chr5	73867795	73867994	+	0	NA	exon (NM_001177693, exon 19 of 36)	exon (NM_001177693, exon 19 of 36)	54376	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.010050	0.475000	
chunk0141_424_1	chr4	88756043	88756242	+	0	NA	intron (NM_014883, intron 14 of 23)	intron (NM_014883, intron 14 of 23)	46353	NR_002806	285512	Hs.744957	NR_002806	ENSG00000248019	FAM13A-AS1	FAM13A1OS|FAM13AOS|NCRNA00039	FAM13A antisense RNA 1	ncRNA	0.000000	0.280000	
chunk0180_385_1	chr7	74478211	74478426	+	0	NA	intron (NM_001199207, intron 1 of 26)	intron (NM_001199207, intron 1 of 26)	24528	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.037209	0.574074	112(GGGCACTTGGTGTCCC,-,0.00),113(GGCACTTGGTGTCCCC,+,0.00)
chunk0178_442_1	chr7	41942538	41942737	+	0	NA	Intergenic	Intergenic	-239529	NM_002192	3624	Hs.28792	NM_002192	ENSG00000122641	INHBA	EDF|FRP	inhibin subunit beta A	protein-coding	0.035176	0.485000	
chunk0136_265_1	chr3	194423370	194423783	+	0	NA	intron (NM_024524, intron 29 of 31)	intron (NM_024524, intron 29 of 31)	-24310	NM_004488	2814	Hs.73734	NM_004488	ENSG00000178732	GP5	CD42d|GPV	glycoprotein V platelet	protein-coding	0.009685	0.388889	
chunk0147_367_1	chr4	185880405	185881078	+	0	NA	intron (NM_021069, intron 1 of 20)	HAL1b|LINE|L1	-68485	NM_001145670	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.004458	0.375371	
chunk0147_376_1	chr4	186083630	186084166	+	0	NA	exon (NM_003265, exon 4 of 5)	exon (NM_003265, exon 4 of 5)	14743	NM_003265	7098	Hs.657724	NM_003265	ENSG00000164342	TLR3	CD283|IIAE2	toll like receptor 3	protein-coding	0.007463	0.378026	266(CAGTACATCGAGTTCT,-,0.00),267(AGTACATCGAGTTCTT,+,0.00)
chunk0007_79_1	chr1	78379046	78379438	+	0	NA	Intergenic	Intergenic	-111801	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.002551	0.396947	
chunk0093_390_1	chr19	56508480	56508739	+	0	NA	intron (NM_020813, intron 1 of 4)	intron (NM_020813, intron 1 of 4)	766	NM_020813	57573	Hs.230188	NM_020813	ENSG00000196263	ZNF471	ERP1|Z1971	zinc finger protein 471	protein-coding	0.034749	0.530769	
chunk0049_386_1	chr12	96094489	96094738	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	-51093	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.008032	0.380000	
chunk0126_138_1	chr3	76157472	76158002	+	0	NA	Intergenic	Intergenic	-372154	NM_001290208	100131827	Hs.556877	NM_001128223	ENSG00000227124	ZNF717	OB1|X17|ZNF838	zinc finger protein 717	protein-coding	0.000000	0.354049	
chunk0068_429_1	chr15	59488092	59488751	+	0	NA	intron (NM_152450, intron 3 of 8)	L1MA3|LINE|L1	50248	NM_152450	145773	Hs.531168	NM_152450	ENSG00000157470	FAM81A	-	family with sequence similarity 81 member A	protein-coding	0.003035	0.356061	
chunk0137_90_1	chr4	13301635	13302205	+	0	NA	Intergenic	Intergenic	182445	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.005263	0.390543	
chunk0112_462_1	chr20	49140952	49141528	+	0	NA	intron (NM_001037328, intron 5 of 13)	L1ME3Cz|LINE|L1	47127	NM_017454	6780	Hs.596704	NM_004602	ENSG00000124214	STAU1	PPP1R150|STAU	staufen double-stranded RNA binding protein 1	protein-coding	0.010417	0.381282	
chunk0018_385_1	chr1	222464411	222464926	+	0	NA	Intergenic	Intergenic	83434	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.001942	0.362403	
chunk0072_287_1	chr15	98528065	98528875	+	0	NA	Intergenic	Intergenic	-14088	NM_182562	283777	Hs.668070	NM_182562	ENSG00000283597	FAM169B	-	family with sequence similarity 169 member B	protein-coding	0.011111	0.436498	
chunk0136_347_1	chr3	195760209	195760640	+	0	NA	intron (NM_018406, intron 16 of 24)	L2a|LINE|L2	39542	NM_020790	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.030162	0.590278	
chunk0171_209_1	chr6	125923298	125923497	+	0	NA	intron (NM_001122842, intron 13 of 15)	intron (NM_001122842, intron 13 of 15)	4173	NM_001199622	135112	Hs.171426	NM_181782	ENSG00000111912	NCOA7	ERAP140|ESNA1|NCOA7-AS|Nbla00052|Nbla10993|TLDC4|dJ187J11.3	nuclear receptor coactivator 7	protein-coding	0.010050	0.455000	
chunk0168_412_1	chr6	95230297	95230538	+	0	NA	Intergenic	Intergenic	347034	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.000000	0.330579	
chunk0203_163_1	chr9	85940775	85941062	+	0	NA	promoter-TSS (NM_024635)	promoter-TSS (NM_024635)	-224	NM_024635	60560	Hs.436098	NM_021929	ENSG00000135040	NAA35	EGAP|MAK10|MAK10P|bA379P1.1	N(alpha)-acetyltransferase 35, NatC auxiliary subunit	protein-coding	0.101045	0.604167	
chunk0208_352_1	chrX	25436050	25436451	+	0	NA	Intergenic	Intergenic	-420302	NM_139058	170302	Hs.300304	NM_139058	ENSG00000004848	ARX	CT121|EIEE1|ISSX|MRX29|MRX32|MRX33|MRX36|MRX38|MRX43|MRX54|MRX76|MRX87|MRXS1|PRTS	aristaless related homeobox	protein-coding	0.004988	0.330846	
chunk0027_224_1	chr10	76261402	76261915	+	0	NA	intron (NR_131178, intron 6 of 7)	intron (NR_131178, intron 6 of 7)	478897	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.003899	0.359922	
chunk0203_406_1	chr9	90799151	90799839	+	0	NA	Intergenic	L1MC1|LINE|L1	-2185	NM_001135052	6850	Hs.371720	NM_003177	ENSG00000165025	SYK	p72-Syk	spleen associated tyrosine kinase	protein-coding	0.005814	0.378810	
chunk0124_345_1	chr3	58387693	58387953	+	0	NA	intron (NM_017771, intron 4 of 17)	intron (NM_017771, intron 4 of 17)	46016	NR_033384	5162	Hs.161357	NM_000925	ENSG00000168291	PDHB	PDHBD|PDHE1-B|PDHE1B|PHE1B	pyruvate dehydrogenase E1 beta subunit	protein-coding	0.003846	0.536398	
chunk0209_343_1	chrX	51749054	51749430	+	0	NA	Intergenic	Intergenic	5857	NM_018094	23708	Hs.59523	NM_018094	ENSG00000189369	GSPT2	ERF3B|GST2	G1 to S phase transition 2	protein-coding	0.005319	0.405836	
chunk0102_344_1	chr2	152348504	152348852	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	13441	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.008621	0.383954	
chunk0003_248_1	chr1	36199848	36200629	+	0	NA	Intergenic	L2b|LINE|L2	-24178	NM_005119	9967	Hs.744057	NM_005119	ENSG00000054118	THRAP3	BCLAF2|TRAP150	thyroid hormone receptor associated protein 3	protein-coding	0.016645	0.506394	289(TTGCACAAGCTGTTCC,-,0.00),290(TGCACAAGCTGTTCCT,+,0.00)
chunk0083_23_1	chr17	63086311	63086861	+	0	NA	intron (NM_025185, intron 2 of 24)	L1MCa|LINE|L1	77049	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.005455	0.373866	
chunk0078_172_1	chr17	4350356	4350806	+	0	NA	intron (NM_003342, intron 1 of 5)	L4_A_Mam|LINE|RTE-X	16093	NM_003342	7326	Hs.741319	NM_003342	ENSG00000132388	UBE2G1	E217K|UBC7|UBE2G	ubiquitin conjugating enzyme E2 G1	protein-coding	0.011111	0.405765	
chunk0041_130_1	chr11	125133242	125133579	+	0	NA	Intergenic	Intergenic	-21647	NM_001258238	219854	Hs.7626	NM_001080546	ENSG00000150433	TMEM218	-	transmembrane protein 218	protein-coding	0.008902	0.556213	
chunk0006_118_1	chr1	65677655	65677985	+	0	NA	Intergenic	L1ME1|LINE|L1	-114690	NM_001037341	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.000000	0.329305	237(AGGTACAGGATGTATT,-,0.00)
chunk0013_371_1	chr1	172466587	172466975	+	0	NA	intron (NM_001300760, intron 4 of 4)	intron (NM_001300760, intron 4 of 4)	13888	NM_001300760	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.002577	0.419023	176(AGGAACAGCATGTTAT,-,0.00),177(GGAACAGCATGTTATG,+,0.00)
chunk0175_445_1	chr6	170014366	170014780	+	0	NA	Intergenic	Intergenic	51950	NR_027434	100131532	Hs.703417	NR_027434		LOC100131532	-	uncharacterized LOC100131532	ncRNA	0.002415	0.383133	
chunk0109_389_1	chr2	240111207	240111599	+	0	NA	Intergenic	Intergenic	24927	NM_001163424	150678	Hs.293884	NM_138336	ENSG00000172428	COPS9	CSNAP|MYEOV2	COP9 signalosome subunit 9	protein-coding	0.028061	0.521628	
chunk0050_13_1	chr12	99663484	99664193	+	0	NA	intron (NM_152788, intron 8 of 25)	intron (NM_152788, intron 8 of 25)	16088	NM_153364	196472	Hs.591011	NM_153364	ENSG00000180219	FAM71C	-	family with sequence similarity 71 member C	protein-coding	0.005642	0.307042	381(CAACACATTATGTTCC,-,0.00),382(AACACATTATGTTCCT,+,0.00)
chunk0149_423_1	chr5	29556328	29556643	+	0	NA	Intergenic	L1MA5|LINE|L1	-160509	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.009524	0.515823	
chunk0121_175_1	chr3	20023698	20024396	+	0	NA	Intergenic	Intergenic	-11774	NM_001252657	151649	Hs.733161	NM_144714	ENSG00000183977	PP2D1	C3orf48	protein phosphatase 2C like domain containing 1	protein-coding	0.001433	0.444921	32(GGTACAGGCTGTTACT,+,0.00)
chunk0123_159_1	chr3	43473347	43473578	+	0	NA	intron (NM_018075, intron 11 of 12)	intron (NM_018075, intron 11 of 12)	-121500	NR_046757	100873954	Hs.600984	NR_046757		SNRK-AS1	-	SNRK antisense RNA 1	ncRNA	0.017316	0.504310	
chunk0143_191_1	chr4	112284734	112284967	+	0	NA	intron (NM_052864, intron 1 of 1)	MIR3|SINE|MIR	1053	NM_052864	92610	Hs.310640	NM_052864	ENSG00000145365	TIFA	T2BP|T6BP|TIFAA	TRAF interacting protein with forkhead associated domain	protein-coding	0.004292	0.410256	
chunk0091_50_1	chr19	4694040	4694623	+	0	NA	intron (NM_139159, intron 13 of 21)	MER58A|DNA|hAT-Charlie	15049	NM_001242901	100131094	Hs.678135	NM_001242901		DPP9-AS1	-	DPP9 antisense RNA 1	protein-coding	0.017153	0.522260	
chunk0195_44_1	chr8	93397979	93398327	+	0	NA	intron (NR_033858, intron 7 of 10)	intron (NR_033858, intron 7 of 10)	-231303	NM_001242668									0.000000	0.461318	
chunk0019_150_1	chr1	225810330	225810544	+	0	NA	5' UTR (NM_001291163, exon 1 of 9)	5' UTR (NM_001291163, exon 1 of 9)	303	NM_001291163	2052	Hs.89649	NM_000120	ENSG00000143819	EPHX1	EPHX|EPOX|HYL1|MEH	epoxide hydrolase 1	protein-coding	0.112150	0.720930	
chunk0025_209_1	chr10	53624632	53625440	+	0	NA	Intergenic	Intergenic	-853336	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.008663	0.352287	
chunk0179_453_1	chr7	52775871	52776479	+	0	NA	Intergenic	Intergenic	-259481	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.003289	0.349754	
chunk0049_20_1	chr12	89414401	89414637	+	0	NA	Intergenic	Intergenic	-61660	NM_022652	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.004237	0.459916	131(ATTACATTGTGTTCCT,+,0.00)
chunk0026_350_1	chr10	68733955	68734609	+	0	NA	intron (NR_104262, intron 2 of 23)	intron (NR_104262, intron 2 of 23)	13138	NR_104262	55749	Hs.49853	NM_018237	ENSG00000060339	CCAR1	-	cell division cycle and apoptosis regulator 1	protein-coding	0.006116	0.357252	255(AAGCACAAATTGTTCT,-,0.00),256(AGCACAAATTGTTCTT,+,0.00)
chunk0165_415_1	chr6	39099973	39100384	+	0	NA	Intergenic	L1ME4b|LINE|L1	15008	NM_001304793	55776	Hs.58382	NM_018322	ENSG00000112167	SAYSD1	C6orf64	SAYSVFN motif domain containing 1	protein-coding	0.004866	0.342233	
chunk0074_354_1	chr16	34030565	34030996	+	0	NA	Intergenic	Intergenic	129256	NR_038368									0.011601	0.409722	
chunk0007_379_1	chr1	85297709	85298400	+	0	NA	Intergenic	Intergenic	-21150	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.015919	0.442197	
chunk0050_72_1	chr12	101526452	101526806	+	0	NA	Intergenic	Intergenic	49750	NM_152323	121599	Hs.577097	NM_152323	ENSG00000166211	SPIC	SPI-C	Spi-C transcription factor	protein-coding	0.005650	0.388732	
chunk0025_328_1	chr10	57898399	57898604	+	0	NA	Intergenic	LTR9A1|LTR|ERV1	369433	NM_152230	253430	Hs.30280	NM_152230	ENSG00000151151	IPMK	-	inositol polyphosphate multikinase	protein-coding	0.000000	0.485437	36(TGGCACACCTAGTCCT,-,0.00),37(GGCACACCTAGTCCTA,+,0.00)
chunk0057_377_1	chr13	109204240	109204851	+	0	NA	intron (NM_001198950, intron 34 of 34)	intron (NM_001198950, intron 34 of 34)	-37242	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.006547	0.439542	
chunk0057_366_1	chr13	108980183	108980877	+	0	NA	intron (NM_001198950, intron 20 of 34)	intron (NM_001198950, intron 20 of 34)	186773	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.010086	0.372662	329(GAGAGCAGAATGTCCC,-,0.00),330(AGAGCAGAATGTCCCT,+,0.00)
chunk0036_303_1	chr11	65988907	65989542	+	0	NA	Intergenic	Intergenic	-12855	NM_001143985	8815	Hs.433759	NM_003860	ENSG00000175334	BANF1	BAF|BCRP1|D14S1460|NGPS	barrier to autointegration factor 1	protein-coding	0.014173	0.471698	389(ATGAACAGCCTGGTCT,-,0.00),390(TGAACAGCCTGGTCTG,+,0.00),551(GGCACTGCTAGTTCTT,+,0.00)
chunk0124_267_1	chr3	57235439	57235902	+	0	NA	intron (NM_012096, intron 2 of 21)	intron (NM_012096, intron 2 of 21)	7933	NM_012096	26060	Hs.476415	NM_012096	ENSG00000157500	APPL1	APPL|DIP13alpha|MODY14	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1	protein-coding	0.008639	0.329741	
chunk0074_428_1	chr16	46394423	46395049	+	0	NA	Intergenic	Intergenic	174361	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.044728	0.358852	
chunk0141_78_1	chr4	78227568	78227767	+	0	NA	intron (NM_025074, intron 2 of 73)	MamRTE1|LINE|RTE-BovB	170097	NM_025074	80144	Hs.369448	NM_020875	ENSG00000138759	FRAS1	FRASRS1	Fraser extracellular matrix complex subunit 1	protein-coding	0.000000	0.435000	
chunk0084_37_1	chr17	73929975	73930834	+	0	NA	Intergenic	Intergenic	-101867	NR_027146	283982	Hs.464079	NM_182564		LINC00469	C17orf54	long intergenic non-protein coding RNA 469	ncRNA	0.012806	0.502326	
chunk0198_186_1	chr8	133424682	133425135	+	0	NA	Intergenic	L2a|LINE|L2	-127604	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.004415	0.409692	
chunk0018_151_1	chr1	218705722	218706209	+	0	NA	intron (NR_031644, intron 4 of 6)	intron (NR_031644, intron 4 of 6)	263339	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.006160	0.418033	
chunk0111_268_1	chr20	31073929	31074479	+	0	NA	Intergenic	(GGAAT)n|Simple_repeat|Simple_repeat	-183460	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.007273	0.393829	
chunk0118_460_1	chr22	39871542	39871950	+	0	NA	intron (NM_152512, intron 2 of 6)	intron (NM_152512, intron 2 of 6)	22044	NM_152512	150350	Hs.474869	NM_152512	ENSG00000176177	ENTHD1	CACNA1I|dJ370M22.3	ENTH domain containing 1	protein-coding	0.004902	0.334963	
chunk0043_240_1	chr12	20199691	20200016	+	0	NA	Intergenic	L1PB3|LINE|L1	-169392	NM_000921	5139	Hs.386791	NM_000921	ENSG00000172572	PDE3A	CGI-PDE|CGI-PDE A|CGI-PDE-A|HTNB	phosphodiesterase 3A	protein-coding	0.006154	0.343558	
chunk0029_437_1	chr10	110097539	110097826	+	0	NA	intron (NM_016824, intron 1 of 14)	L1MC4a|LINE|L1	-89301	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.006969	0.329861	
chunk0056_52_1	chr13	77623037	77624219	+	0	NA	intron (NM_003843, intron 26 of 31)	intron (NM_003843, intron 26 of 31)	-17077	NR_126413	104355296	Hs.667682	NR_126412	ENSG00000224347	SCEL-AS1	-	SCEL antisense RNA 1	ncRNA	0.005076	0.387151	178(ATGAGCAGTCTGTGCT,-,0.00),179(TGAGCAGTCTGTGCTT,+,0.00)
chunk0117_257_1	chr22	23499590	23499978	+	0	NA	Intergenic	(CACACG)n|Simple_repeat|Simple_repeat	-12804	NR_110539	388882	Hs.542766	NR_110539	ENSG00000178248	FAM230I	LINC01658	family with sequence similarity 230 member I	ncRNA	0.025773	0.537275	
chunk0128_379_1	chr3	113508495	113509089	+	0	NA	intron (NM_144718, intron 1 of 17)	L1MB7|LINE|L1	6395	NM_144718	152185	Hs.477144	NM_144718	ENSG00000163611	SPICE1	CCDC52|SPICE	spindle and centriole associated protein 1	protein-coding	0.006734	0.368067	
chunk0060_440_1	chr14	54489716	54490271	+	0	NA	promoter-TSS (NM_004124)	promoter-TSS (NM_004124)	-967	NM_004124	2764	Hs.151413	NM_004124	ENSG00000197045	GMFB	GMF	glia maturation factor beta	protein-coding	0.007207	0.437050	
chunk0046_110_1	chr12	57259595	57259840	+	0	NA	intron (NM_014925, intron 17 of 21)	L2b|LINE|L2	-8524	NR_104422	246329	Hs.417595	NM_145064	ENSG00000185482	STAC3	MYPBB|NAM	SH3 and cysteine rich domain 3	protein-coding	0.004082	0.398374	144(GGGCACTGAGTGTACA,-,0.00)
chunk0202_350_1	chr9	79748348	79748584	+	0	NA	Intergenic	L2a|LINE|L2	-76064	NR_121213	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.000000	0.341772	
chunk0197_395_1	chr8	127091674	127092193	+	0	NA	non-coding (NR_109833, exon 1 of 1)	non-coding (NR_109833, exon 1 of 1)	-9712	NR_119373	103164619	Hs.571401	NR_119373	ENSG00000254166	PCAT2	CARLO4|CARLo-4|PCA2|TCONS_00015167	prostate cancer associated transcript 2	ncRNA	0.009634	0.378846	
chunk0136_69_1	chr4	1908199	1908445	+	0	NA	intron (NM_001042424, intron 3 of 21)	intron (NM_001042424, intron 3 of 21)	7696	NM_133334	7468	Hs.113876	NM_007331	ENSG00000109685	NSD2	KMT3F|KMT3G|MMSET|REIIBP|TRX5|WHS|WHSC1	nuclear receptor binding SET domain protein 2	protein-coding	0.004065	0.473684	
chunk0033_331_1	chr11	22625195	22625478	+	0	NA	exon (NM_022725, exon 1 of 1)	exon (NM_022725, exon 1 of 1)	505	NM_022725	2188	Hs.632151	NM_022725	ENSG00000183161	FANCF	FAF	FA complementation group F	protein-coding	0.067138	0.633803	
chunk0186_421_1	chr7	146589767	146590451	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	473748	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.008772	0.382482	
chunk0067_99_1	chr15	42271016	42271699	+	0	NA	intron (NM_001286487, intron 1 of 18)	intron (NM_001286487, intron 1 of 18)	2227	NM_015497	25963	Hs.511138	NM_015497	ENSG00000103978	TMEM87A	-	transmembrane protein 87A	protein-coding	0.010249	0.353801	
chunk0143_319_1	chr4	119302139	119302401	+	0	NA	intron (NM_001170330, intron 1 of 2)	intron (NM_001170330, intron 1 of 2)	-1457	NM_001001701	401152	Hs.173705	NM_001001701	ENSG00000164096	C4orf3	ALN|HCVFTP1	chromosome 4 open reading frame 3	protein-coding	0.007634	0.376426	
chunk0200_404_1	chr9	27312408	27312654	+	0	NA	Intergenic	Intergenic	-15392	NM_001161585	54586	Hs.163070	NM_020641	ENSG00000120160	EQTN	AFAF|C9orf11|SPACA8	equatorin	protein-coding	0.020325	0.477733	
chunk0153_251_1	chr5	72604531	72604829	+	0	NA	intron (NR_105007, intron 1 of 2)	intron (NR_105007, intron 1 of 2)	47603	NR_105008	102503427	Hs.429280	NR_105008		LOC102503427	-	uncharacterized LOC102503427	ncRNA	0.013423	0.408027	80(TGGAACAAATTGTTCC,-,0.00),81(GGAACAAATTGTTCCA,+,0.00)
chunk0200_259_1	chr9	21802114	21802895	+	0	NA	promoter-TSS (NM_002451)	promoter-TSS (NM_002451)	-132	NM_002451	4507	Hs.193268	NM_002451	ENSG00000099810	MTAP	BDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fus	methylthioadenosine phosphorylase	protein-coding	0.076825	0.599744	
chunk0199_261_1	chr9	6143807	6144534	+	0	NA	Intergenic	L1MEg|LINE|L1	-70979	NM_001314047	90865	Hs.731660	NM_033439	ENSG00000137033	IL33	C9orf26|DVS27|IL1F11|NF-HEV|NFEHEV	interleukin 33	protein-coding	0.011004	0.384615	
chunk0164_125_1	chr6	20864214	20864636	+	0	NA	intron (NM_017774, intron 9 of 15)	L2c|LINE|L2	329968	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.000000	0.269504	
chunk0110_113_1	chr20	12113543	12113742	+	0	NA	Intergenic	MLT1E3|LTR|ERVL-MaLR	195777	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.010050	0.500000	
chunk0085_168_1	chr18	3973798	3974011	+	0	NA	intron (NR_102696, intron 1 of 4)	Tigger3a|DNA|TcMar-Tigger	11551	NR_102696	101410534	Hs.141055	NR_102696	ENSG00000263878	DLGAP1-AS4	-	DLGAP1 antisense RNA 4	ncRNA	0.014085	0.462617	
chunk0131_390_1	chr3	152484452	152484675	+	0	NA	Intergenic	L1PA16|LINE|L1	-143573	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.013453	0.540179	
chunk0035_284_1	chr11	46736521	46737057	+	0	NA	intron (NM_001311257, intron 12 of 13)	L1MC4|LINE|L1	16403	NR_049846	100847020		NR_049846	ENSG00000263540	MIR5582	-	microRNA 5582	ncRNA	0.013060	0.383613	
chunk0123_336_1	chr3	47656134	47656795	+	0	NA	intron (NM_003074, intron 21 of 27)	MIR3|SINE|MIR	-76224	NM_001206945	10675	Hs.45127	NM_006574	ENSG00000114646	CSPG5	NGC	chondroitin sulfate proteoglycan 5	protein-coding	0.012103	0.410876	
chunk0180_151_1	chr7	64453822	64454068	+	0	NA	Intergenic	L1MA6|LINE|L1	20252	NR_029404	649395	Hs.728871	NR_029404		YWHAEP1	-	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon pseudogene 1	pseudo	0.004065	0.291498	
chunk0061_16_1	chr14	55711183	55711924	+	0	NA	Intergenic	Intergenic	-54692	NR_004844	645683	Hs.663461	NR_004844	ENSG00000177350	RPL13AP3	RPL13A_11_1370	ribosomal protein L13a pseudogene 3	pseudo	0.004049	0.405660	341(GAAGACACAGTGTGCT,-,0.00),342(AAGACACAGTGTGCTT,+,0.00)
chunk0052_421_1	chr12	131536363	131536569	+	0	NA	Intergenic	Intergenic	-174621	NM_004592	6433	Hs.308171	NM_004592	ENSG00000061936	SFSWAP	SFRS8|SWAP	splicing factor SWAP	protein-coding	0.019417	0.536232	
chunk0172_440_1	chr6	140834361	140834668	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	150700	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.006515	0.386364	173(AAGAACTTTGAGTTCT,-,0.00),174(AGAACTTTGAGTTCTG,+,0.00),279(CTGGACATTTTGTGCT,-,0.00),280(TGGACATTTTGTGCTC,+,0.00)
chunk0012_143_1	chr1	157419691	157420555	+	0	NA	Intergenic	Intergenic	132397	NM_031281	83416	Hs.415950	NM_031281	ENSG00000143297	FCRL5	BXMAS1|CD307|CD307e|FCRH5|IRTA2|PRO820	Fc receptor like 5	protein-coding	0.008102	0.479769	147(GAGAGCACAGTGTTCC,-,0.00),148(AGAGCACAGTGTTCCT,+,0.00),177(GAGGACATGGTGTTCC,-,0.00),178(AGGACATGGTGTTCCC,+,0.00),207(CAGGACACAATGGTCC,-,0.00),208(AGGACACAATGGTCCC,+,0.00),238(GAGGACACAGTGTTCC,-,0.00),239(AGGACACAGTGTTCCT,+,0.00),298(GAAGACACAGTGTTCC,-,0.00),299(AAGACACAGTGTTCCC,+,0.00),359(GAGGACAAGGTGTTTT,-,0.00),360(AGGACAAGGTGTTTTT,+,0.00),420(GAGGACATGGTGTTTC,-,0.00),421(AGGACATGGTGTTTCT,+,0.00),450(GAGGACATGGTGTTCC,-,0.00),451(AGGACATGGTGTTCCT,+,0.00),511(GAGGACACAGTGTTCC,-,0.00),512(AGGACACAGTGTTCCT,+,0.00),603(GAGGACATGGTGTTCC,-,0.00),604(AGGACATGGTGTTCCC,+,0.00),634(AAGGGCACTGTGTTCC,-,0.00),635(AGGGCACTGTGTTCCC,+,0.00),665(GAGGACATACTGTTCT,-,0.00),666(AGGACATACTGTTCTC,+,0.00)
chunk0075_118_1	chr16	49464678	49465007	+	0	NA	Intergenic	Intergenic	91034	NM_144602	123970	Hs.125875	NM_144602	ENSG00000166152	C16orf78	-	chromosome 16 open reading frame 78	protein-coding	0.027356	0.566667	
chunk0212_268_1	chrX	139680483	139680875	+	0	NA	intron (NM_001171876, intron 1 of 28)	intron (NM_001171876, intron 1 of 28)	27543	NM_001099855	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.005102	0.353690	
chunk0113_68_1	chr20	50516332	50516739	+	0	NA	intron (NM_001278618, intron 1 of 8)	intron (NM_001278618, intron 1 of 8)	6214	NM_001278618	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.007371	0.375000	
chunk0139_378_1	chr4	60944162	60944422	+	0	NA	Intergenic	Intergenic	21673	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.000000	0.367816	
chunk0181_47_1	chr7	79915582	79915978	+	0	NA	Intergenic	L1P2|LINE|L1	-219044	NM_002069	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.012626	0.531486	
chunk0205_181_1	chr9	108972844	108973043	+	0	NA	intron (NM_003798, intron 8 of 18)	intron (NM_003798, intron 8 of 18)	38550	NM_017832	54942	Hs.29276	NM_017832	ENSG00000119328	ABITRAM	C9orf6|CG-8|FAM206A|Simiate	actin binding transcription modulator	protein-coding	0.005025	0.470000	
chunk0160_170_1	chr5	153467083	153467605	+	0	NA	Intergenic	L2a|LINE|L2	-23180	NM_001258020	2890	Hs.519693	NM_000827	ENSG00000155511	GRIA1	GLUH1|GLUR1|GLURA|GluA1|HBGR1	glutamate ionotropic receptor AMPA type subunit 1	protein-coding	0.000000	0.388145	192(AAGAACATCATGAGCC,-,0.00),193(AGAACATCATGAGCCT,+,0.00)
chunk0115_427_1	chr21	31781028	31781267	+	0	NA	Intergenic	Intergenic	-49029	NM_020706	57466	Hs.17255	NM_020706	ENSG00000156304	SCAF4	SFRS15|SRA4	SR-related CTD associated factor 4	protein-coding	0.012552	0.429167	
chunk0120_263_1	chr3	9142241	9142859	+	0	NA	intron (NM_001033117, intron 1 of 21)	intron (NM_001033117, intron 1 of 21)	-49943	NR_121663	101927416	Hs.475364	NR_121663	ENSG00000228723	SRGAP3-AS2	-	SRGAP3 antisense RNA 2	ncRNA	0.009709	0.403877	
chunk0152_89_1	chr5	58205001	58205468	+	0	NA	Intergenic	Intergenic	-82893	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.006424	0.369658	
chunk0086_89_1	chr18	13619144	13619456	+	0	NA	intron (NM_001003675, intron 1 of 2)	intron (NM_001003675, intron 1 of 2)	7536	NM_001276249	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.019231	0.543131	106(AAGGCCAGAGTGTCCC,-,0.00),107(AGGCCAGAGTGTCCCA,+,0.00)
chunk0196_311_1	chr8	110629279	110629568	+	0	NA	Intergenic	LTR75|LTR|ERVL	398010	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.006920	0.437931	144(AGGGACACTGTGTTCT,-,0.00),145(GGGACACTGTGTTCTT,+,0.00)
chunk0185_289_1	chr7	131050398	131051025	+	0	NA	intron (NR_109850, intron 3 of 5)	L2a|LINE|L2	56319	NR_024153	378805	Hs.150556	NM_001085379	ENSG00000231721	LINC-PINT	LincRNA-Pint|MKLN1-AS1|PINT	long intergenic non-protein coding RNA, p53 induced transcript	ncRNA	0.004785	0.417197	
chunk0003_316_1	chr1	38142491	38143247	+	0	NA	Intergenic	Intergenic	53638	NR_037432	100500801		NR_037432	ENSG00000265596	MIR3659	mir-3659	microRNA 3659	ncRNA	0.003968	0.438573	
chunk0159_419_1	chr5	147994732	147994969	+	0	NA	Intergenic	L1MA10|LINE|L1	-69122	NM_001127698	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.004219	0.336134	
chunk0072_170_1	chr15	93356443	93356642	+	0	NA	Intergenic	Intergenic	-267328	NM_020211	56963	Hs.271277	NM_020211	ENSG00000182175	RGMA	RGM	repulsive guidance molecule BMP co-receptor a	protein-coding	0.000000	0.430000	
chunk0011_189_1	chr1	149648594	149648833	+	0	NA	intron (NR_111950, intron 2 of 8)	intron (NR_111950, intron 2 of 8)	41701	NR_111951	57234	Hs.456578	NR_046135	ENSG00000277147	LINC00869	FAM91A2	long intergenic non-protein coding RNA 869	ncRNA	0.029289	0.462500	
chunk0112_107_1	chr20	38373300	38373850	+	0	NA	intron (NM_004139, intron 13 of 14)	intron (NM_004139, intron 13 of 14)	27164	NM_004139	3929	Hs.154078	NM_004139	ENSG00000129988	LBP	BPIFD2	lipopolysaccharide binding protein	protein-coding	0.009091	0.479129	306(TGGAACGCCCTGTTCT,-,0.00),307(GGAACGCCCTGTTCTT,+,0.00)
chunk0133_50_1	chr3	166475897	166476300	+	0	NA	Intergenic	Intergenic	-638633	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.002481	0.304455	
chunk0121_118_1	chr3	17424402	17424773	+	0	NA	intron (NM_014744, intron 4 of 21)	intron (NM_014744, intron 4 of 21)	275433	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.005391	0.311828	
chunk0166_393_1	chr6	51891758	51892415	+	0	NA	intron (NM_138694, intron 43 of 66)	intron (NM_138694, intron 43 of 66)	195539	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.009132	0.452888	
chunk0109_417_1	chr2	241102238	241102583	+	0	NA	promoter-TSS (NR_028051)	promoter-TSS (NR_028051)	-78	NR_028050	130916	Hs.159556	NM_182501	ENSG00000122085	MTERF4	MTERFD2	mitochondrial transcription termination factor 4	protein-coding	0.133333	0.708092	
chunk0037_388_1	chr11	78802064	78802544	+	0	NA	intron (NM_001098816, intron 15 of 33)	MIR|SINE|MIR	-227440	NM_001243251	79731	Hs.503389	NM_024678	ENSG00000137513	NARS2	DFNB94|SLM5|asnRS	asparaginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.014583	0.467775	
chunk0059_422_1	chr14	38170619	38170972	+	0	NA	Intergenic	Intergenic	-37204	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.000000	0.271186	
chunk0096_350_1	chr2	35822626	35822825	+	0	NA	Intergenic	MamRep1151|LTR?|LTR?	351320	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.005025	0.290000	
chunk0035_352_1	chr11	48306783	48306982	+	0	NA	exon (NM_001004725, exon 1 of 1)	exon (NM_001004725, exon 1 of 1)	659	NM_001004725	256148	Hs.553657	NM_001004725	ENSG00000176555	OR4S1	OR11-100	olfactory receptor family 4 subfamily S member 1	protein-coding	0.025126	0.465000	
chunk0149_449_1	chr5	29949487	29949733	+	0	NA	Intergenic	MER70B|LTR|ERVL	-553634	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.020325	0.473684	75(AAGCCCAGGATGTCCC,-,0.00)
chunk0084_96_1	chr17	75549307	75549663	+	0	NA	intron (NM_001015002, intron 2 of 9)	intron (NM_001015002, intron 2 of 9)	23783	NM_001031803	3993	Hs.514477	NM_004524	ENSG00000073350	LLGL2	HGL|Hugl-2|LGL2	LLGL scribble cell polarity complex component 2	protein-coding	0.028090	0.649860	209(AGGGCCAGGTTGTTCT,-,0.00),210(GGGCCAGGTTGTTCTG,+,0.00)
chunk0155_232_1	chr5	95543028	95543694	+	0	NA	intron (NM_014639, intron 4 of 42)	intron (NM_014639, intron 4 of 42)	11644	NM_014639	9652	Hs.482868	NM_014639	ENSG00000198677	TTC37	KIAA0372|Ski3|THES	tetratricopeptide repeat domain 37	protein-coding	0.004505	0.364318	
chunk0209_208_1	chrX	44348049	44348253	+	0	NA	Intergenic	L1MC4|LINE|L1	-4474	NM_025184	80258	Hs.521953	NM_025184	ENSG00000183690	EFHC2	MRX74|dJ1158H2.1	EF-hand domain containing 2	protein-coding	0.004902	0.419512	119(AGGCACATAATGTGCT,-,0.00),120(GGCACATAATGTGCTT,+,0.00)
chunk0095_454_1	chr2	25711627	25712120	+	0	NA	Intergenic	Intergenic	-38226	NM_001256303	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.020284	0.443320	217(ATGGACACAAAGTACT,-,0.00)
chunk0125_44_1	chr3	63880656	63881036	+	0	NA	intron (NM_000333, intron 1 of 12)	L2c|LINE|L2	16289	NM_000333	6314	Hs.476595	NM_000333	ENSG00000163635	ATXN7	ADCAII|OPCA3|SCA7|SGF73	ataxin 7	protein-coding	0.013158	0.425197	
chunk0003_303_1	chr1	37661976	37662175	+	0	NA	Intergenic	Intergenic	-27152	NM_001242909	284654	Hs.135015	NM_173640	ENSG00000169218	RSPO1	CRISTIN3|RSPO	R-spondin 1	protein-coding	0.015075	0.505000	62(GAGCACAGCATGTCCA,-,0.00),63(AGCACAGCATGTCCAA,+,0.00)
chunk0001_311_1	chr1	9325541	9325740	+	0	NA	intron (NM_025106, intron 1 of 2)	L2a|LINE|L2	32758	NM_025106	80176	Hs.8261	NM_025106	ENSG00000171621	SPSB1	SSB-1|SSB1	splA/ryanodine receptor domain and SOCS box containing 1	protein-coding	0.015075	0.545000	
chunk0095_209_1	chr2	18650267	18650850	+	0	NA	Intergenic	Intergenic	-60978	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.003431	0.376712	
chunk0007_186_1	chr1	80731320	80731519	+	0	NA	Intergenic	L1MA3|LINE|L1	90132	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.000000	0.505000	
chunk0114_102_1	chr21	9369076	9369347	+	0	NA	Intergenic	Intergenic	-239450	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.003690	0.275735	
chunk0039_180_1	chr11	100575831	100576346	+	0	NA	Intergenic	L2c|LINE|L2	-111588	NM_152432	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.001942	0.288760	
chunk0209_329_1	chrX	51292442	51292641	+	0	NA	Intergenic	Intergenic	-39690	NM_153183	170685	Hs.375178	NM_153183	ENSG00000122824	NUDT10	APS2|DIPP3-alpha|DIPP3a	nudix hydrolase 10	protein-coding	0.000000	0.415000	
chunk0194_267_1	chr8	87013952	87014726	+	0	NA	intron (NM_173538, intron 4 of 10)	MER4B-int|LTR|ERV1	147891	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.001292	0.249032	
chunk0194_276_1	chr8	87221223	87222114	+	0	NA	intron (NM_173538, intron 5 of 10)	intron (NM_173538, intron 5 of 10)	355220	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.004489	0.303812	
chunk0128_260_1	chr3	109833111	109833630	+	0	NA	Intergenic	Intergenic	230542	NR_039647	100616129		NR_039647	ENSG00000265956	MIR4445	-	microRNA 4445	ncRNA	0.001927	0.278846	
chunk0137_170_1	chr4	16592512	16592767	+	0	NA	intron (NM_001290, intron 3 of 7)	intron (NM_001290, intron 3 of 7)	306170	NM_001290	9079	Hs.714330	NM_001290	ENSG00000169744	LDB2	CLIM1|LDB-2|LDB1	LIM domain binding 2	protein-coding	0.000000	0.328125	
chunk0168_173_1	chr6	83976467	83976770	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-57083	NM_138409	112609	Hs.370055	NM_138409	ENSG00000135324	MRAP2	C6orf117|bA51G5.2	melanocortin 2 receptor accessory protein 2	protein-coding	0.009901	0.437500	
chunk0024_431_1	chr10	46064290	46064730	+	0	NA	Intergenic	Intergenic	-18241	NM_002443	4477	Hs.255462	NM_002443	ENSG00000263639	MSMB	HPC13|IGBF|MSP|MSPB|PN44|PRPS|PSP|PSP-94|PSP57|PSP94	microseminoprotein beta	protein-coding	0.000000	0.408163	
chunk0040_89_1	chr11	111627549	111628160	+	0	NA	intron (NM_015191, intron 3 of 14)	intron (NM_015191, intron 3 of 14)	25463	NM_015191	23235	Hs.269128	NM_015191	ENSG00000170145	SIK2	LOH11CR1I|QIK|SIK-2|SNF1LK2	salt inducible kinase 2	protein-coding	0.004910	0.343137	
chunk0164_31_1	chr6	18314313	18314837	+	0	NA	Intergenic	Intergenic	-50007	NM_001134709	7913	Hs.484813	NM_003472	ENSG00000124795	DEK	D6S231E	DEK proto-oncogene	protein-coding	0.000000	0.380952	
chunk0155_374_1	chr5	97643981	97644751	+	0	NA	intron (NR_105028, intron 2 of 3)	L1PA16|LINE|L1	139670	NR_105028	102546227	Hs.582516	NR_105028	ENSG00000250331	LINC01340	-	long intergenic non-protein coding RNA 1340	ncRNA	0.001299	0.363165	
chunk0071_227_1	chr15	84860944	84861440	+	0	NA	intron (NM_020778, intron 9 of 13)	L1MC5a|LINE|L1	-23469	NM_201651	9154	Hs.459187	NM_004213	ENSG00000156222	SLC28A1	CNT1|HCNT1	solute carrier family 28 member 1	protein-coding	0.002016	0.364185	
chunk0194_345_1	chr8	89192497	89193316	+	0	NA	Intergenic	Intergenic	564805	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.003663	0.306098	241(GAGCACATAGTGTACT,-,0.00),242(AGCACATAGTGTACTA,+,0.00)
chunk0002_35_1	chr1	12484596	12484909	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-22494	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.015974	0.455414	171(TAGCACAGAGTGTTTT,-,0.00),172(AGCACAGAGTGTTTTT,+,0.00)
chunk0109_176_1	chr20	4603723	4604239	+	0	NA	Intergenic	Intergenic	-82170	NM_001080121	5621	Hs.472010	NM_000311	ENSG00000171867	PRNP	ASCR|AltPrP|CD230|CJD|GSS|KURU|PRIP|PrP|PrP27-30|PrP33-35C|PrPc|p27-30	prion protein	protein-coding	0.023256	0.431335	247(CAGATCTTTCTGTTCT,-,0.00),248(AGATCTTTCTGTTCTT,+,0.00)
chunk0109_167_1	chr20	4064559	4064991	+	0	NA	Intergenic	Intergenic	-49206	NM_001134338	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.020833	0.547344	261(GGGAACAGCCTGGGCC,-,0.00),262(GGAACAGCCTGGGCCC,+,0.00)
chunk0033_118_1	chr11	14529603	14529911	+	0	NA	intron (NM_148976, intron 2 of 10)	intron (NM_148976, intron 2 of 10)	-9312	NM_001143937	5682	Hs.102798	NM_002786	ENSG00000129084	PSMA1	HC2|HEL-S-275|NU|PROS30	proteasome subunit alpha 1	protein-coding	0.009740	0.414239	
chunk0193_159_1	chr8	74721155	74721586	+	0	NA	intron (NR_033830, intron 4 of 5)	MLT1J|LTR|ERVL-MaLR	15677	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.002320	0.435185	
chunk0191_175_1	chr8	51019030	51019609	+	0	NA	Intergenic	Intergenic	790126	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.006908	0.365517	133(GGTACTGAAAGTTCTG,+,0.00)
chunk0134_436_1	chr3	183636638	183637039	+	0	NA	intron (NM_017644, intron 1 of 7)	CpG	1215	NM_017644	54800	Hs.407709	NM_017644	ENSG00000114796	KLHL24	DRE1|EBSSH|KRIP6	kelch like family member 24	protein-coding	0.099751	0.654229	
chunk0008_395_1	chr1	97310296	97310757	+	0	NA	intron (NR_046590, intron 4 of 4)	intron (NR_046590, intron 4 of 4)	214603	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.004338	0.339827	
chunk0021_50_1	chr10	1034577	1035055	+	0	NA	intron (NR_024629, intron 1 of 2)	intron (NR_024629, intron 1 of 2)	-8957	NM_033261	91734	Hs.9270	NM_033261	ENSG00000148377	IDI2	IPPI2	isopentenyl-diphosphate delta isomerase 2	protein-coding	0.010460	0.415449	
chunk0159_169_1	chr5	139698064	139698743	+	0	NA	Intergenic	Intergenic	47820	NR_105053	101929696	Hs.147408	NR_105052	ENSG00000249131	PSD2-AS1	-	PSD2 antisense RNA 1	ncRNA	0.016200	0.566176	
chunk0057_7_1	chr13	95513058	95513529	+	0	NA	intron (NR_046533, intron 2 of 3)	L2b|LINE|L2	20617	NR_046533	100874194	Hs.569229	NR_046533	ENSG00000223392	CLDN10-AS1	-	CLDN10 antisense RNA 1	ncRNA	0.004246	0.402542	
chunk0119_77_1	chr22	41410210	41410828	+	0	NA	Intergenic	Intergenic	28590	NM_003216	7008	Hs.181159	NM_003216	ENSG00000167074	TEF	-	TEF transcription factor, PAR bZIP family member	protein-coding	0.017799	0.576737	308(GAGCACAGGATGTCCC,-,0.00),309(AGCACAGGATGTCCCT,+,0.00)
chunk0172_388_1	chr6	139536978	139537667	+	0	NA	Intergenic	Intergenic	-62726	NR_033919	645434	Hs.666240	NR_033919	ENSG00000238099	LINC01625	-	long intergenic non-protein coding RNA 1625	ncRNA	0.010160	0.439130	435(GAGAACAGTCTCTCCT,-,0.00),436(AGAACAGTCTCTCCTG,+,0.00)
chunk0036_248_1	chr11	64448013	64448441	+	0	NA	promoter-TSS (NR_073177)	promoter-TSS (NR_073177)	-830	NR_073177	100996455	Hs.634142	NR_073177	ENSG00000181908	LINC02724	-	long intergenic non-protein coding RNA 2724	ncRNA	0.021028	0.491841	
chunk0073_284_1	chr16	12877677	12877894	+	0	NA	Intergenic	Intergenic	-23835	NM_001145205	729993	Hs.130661	NM_001145204	ENSG00000237515	SHISA9	CKAMP44	shisa family member 9	protein-coding	0.000000	0.380734	
chunk0062_451_1	chr14	75566069	75566782	+	0	NA	Intergenic	Intergenic	-12172	NM_017791	55640	Hs.509966	NM_017791	ENSG00000119686	FLVCR2	C14orf58|CCT|EPV|FLVCRL14q|MFSD7C|PVHH|SLC49A2	feline leukemia virus subgroup C cellular receptor family member 2	protein-coding	0.005610	0.466387	
chunk0146_151_1	chr4	159723295	159723494	+	0	NA	Intergenic	MER52A|LTR|ERV1	455548	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.015075	0.595000	
chunk0071_44_1	chr15	79923901	79924100	+	0	NA	promoter-TSS (NM_001199760)	promoter-TSS (NM_001199760)	-246	NR_037652	400410	Hs.729127	NM_001100879	ENSG00000180953	ST20	HCCS-1	suppressor of tumorigenicity 20	protein-coding	0.100503	0.655000	
chunk0126_199_1	chr3	78608834	78609076	+	0	NA	intron (NM_133631, intron 26 of 28)	L2|LINE|L2	410504	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004132	0.362140	
chunk0045_364_1	chr12	52026063	52026262	+	0	NA	intron (NM_001202233, intron 1 of 7)	MIRc|SINE|MIR	3330	NM_001202233	3164	Hs.524430	NM_002135	ENSG00000123358	NR4A1	GFRP1|HMR|N10|NAK-1|NGFIB|NP10|NUR77|TR3	nuclear receptor subfamily 4 group A member 1	protein-coding	0.025126	0.495000	36(ATCACACCCTGTCCCG,+,0.00)
chunk0032_39_1	chr11	1147711	1148182	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-10007	NM_001304359	4586	Hs.534332	NM_017511	ENSG00000215182	MUC5AC	MUC5|TBM|leB|mucin	mucin 5AC, oligomeric mucus/gel-forming	protein-coding	0.012739	0.491525	
chunk0104_411_1	chr2	180726234	180726512	+	0	NA	intron (NR_104324, intron 3 of 4)	MER77|LTR|ERVL	34269	NR_104324	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.000000	0.473118	
chunk0030_99_1	chr10	112446927	112447433	+	0	NA	promoter-TSS (NM_001303134)	promoter-TSS (NM_001303134)	182	NM_145206	143187	Hs.194554	NM_145206	ENSG00000151532	VTI1A	MMDS3|MVti1|VTI1RP2|Vti1-rp2	vesicle transport through interaction with t-SNAREs 1A	protein-coding	0.077075	0.577909	
chunk0119_399_1	chr22	49017671	49017930	+	0	NA	Intergenic	Intergenic	151030	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.042471	0.550000	
chunk0162_160_1	chr6	3494409	3495147	+	0	NA	Intergenic	MIR3|SINE|MIR	-38219	NM_001286456	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.010840	0.431664	
chunk0190_334_1	chr8	39031887	39032386	+	0	NA	intron (NR_027878, intron 11 of 20)	L1P2|LINE|L1	35150	NR_027638	8754	Hs.591852	NM_003816	ENSG00000168615	ADAM9	CORD9|MCMP|MDC9|Mltng	ADAM metallopeptidase domain 9	protein-coding	0.008016	0.540000	
chunk0153_349_1	chr5	74379997	74380347	+	0	NA	intron (NR_126354, intron 2 of 2)	MamRTE1|LINE|RTE-BovB	57686	NR_105010	101929082	Hs.434316	NR_105010	ENSG00000249343	LINC01333	-	long intergenic non-protein coding RNA 1333	ncRNA	0.005714	0.387464	103(AAGAACAAAATGTGCA,-,0.00),104(AGAACAAAATGTGCAG,+,0.00)
chunk0196_138_1	chr8	104297131	104297360	+	0	NA	Intergenic	Intergenic	-42551	NM_030788	81501	Hs.652230	NM_030788	ENSG00000164935	DCSTAMP	FIND|TM7SF4|hDC-STAMP	dendrocyte expressed seven transmembrane protein	protein-coding	0.017467	0.413043	
chunk0140_421_1	chr4	75967389	75967778	+	0	NA	intron (NM_018115, intron 11 of 21)	intron (NM_018115, intron 11 of 21)	-13207	NR_125906	101928809	Hs.637575	NR_125906	ENSG00000245928	LOC101928809	-	uncharacterized LOC101928809	ncRNA	0.005141	0.371795	
chunk0163_221_1	chr6	12170390	12170773	+	0	NA	Intergenic	Intergenic	-119715	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.026110	0.453125	
chunk0088_106_1	chr18	45167178	45167539	+	0	NA	Intergenic	Intergenic	-45624	NM_001242692	8170	Hs.710927	NM_007163	ENSG00000132874	SLC14A2	HUT2|UT-A2|UT2|UTA|UTR|hUT-A6	solute carrier family 14 member 2	protein-coding	0.005540	0.397790	
chunk0038_355_1	chr11	93216771	93217096	+	0	NA	Intergenic	Intergenic	-18958	NM_152313	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.009231	0.435583	
chunk0154_155_1	chr5	79495152	79495829	+	0	NA	intron (NM_001277077, intron 1 of 5)	L2c|LINE|L2	18346	NM_001277078	9456	Hs.591761	NM_004272	ENSG00000152413	HOMER1	HOMER|HOMER1A|HOMER1B|HOMER1C|SYN47|Ves-1	homer scaffold protein 1	protein-coding	0.004431	0.384956	
chunk0097_224_1	chr2	52086346	52087060	+	0	NA	Intergenic	Intergenic	615912	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.002801	0.302098	
chunk0078_413_1	chr16	89217603	89217990	+	0	NA	promoter-TSS (NM_001201407)	promoter-TSS (NM_001201407)	93	NM_182531	197320	Hs.647385	NM_182531	ENSG00000170100	ZNF778	-	zinc finger protein 778	protein-coding	0.118863	0.685567	
chunk0059_288_1	chr14	35747425	35747786	+	0	NA	intron (NM_001283043, intron 10 of 41)	intron (NM_001283043, intron 10 of 41)	61621	NM_001283044	253959	Hs.113150	NM_014990	ENSG00000174373	RALGAPA1	GARNL1|GRIPE|RalGAPalpha1|TULIP1|p240	Ral GTPase activating protein catalytic alpha subunit 1	protein-coding	0.000000	0.403315	
chunk0169_1_1	chr6	96104781	96105296	+	0	NA	intron (NM_006581, intron 1 of 2)	intron (NM_006581, intron 1 of 2)	89069	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.011650	0.343023	
chunk0158_235_1	chr5	129051280	129051841	+	0	NA	Intergenic	Intergenic	-43189	NM_016048	51015	Hs.483296	NM_016048	ENSG00000066583	ISOC1	CGI-111	isochorismatase domain containing 1	protein-coding	0.007130	0.362989	
chunk0070_160_1	chr15	71295074	71295377	+	0	NA	intron (NM_024817, intron 5 of 16)	MIRb|SINE|MIR	-106166	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.006601	0.490132	
chunk0110_106_1	chr20	11927215	11927448	+	0	NA	TTS (NM_001282554)	TTS (NM_001282554)	9466	NM_014962	22903	Hs.709366	NM_014962	ENSG00000132640	BTBD3	dJ742J24.1	BTB domain containing 3	protein-coding	0.012876	0.401709	
chunk0125_227_1	chr3	67955836	67956102	+	0	NA	Intergenic	Intergenic	-35623	NM_001252216	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.011278	0.333333	
chunk0061_41_1	chr14	56148431	56148637	+	0	NA	intron (NM_021255, intron 1 of 5)	L2c|LINE|L2	30159	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.004854	0.550725	117(TGGGACACCCTGTCCT,-,0.00),118(GGGACACCCTGTCCTC,+,0.00)
chunk0005_392_1	chr1	62267885	62268277	+	0	NA	intron (NM_181712, intron 5 of 9)	intron (NM_181712, intron 5 of 9)	51331	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.017857	0.455471	
chunk0121_331_1	chr3	24404874	24405545	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-88878	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.005961	0.339286	
chunk0147_189_1	chr4	177511626	177511825	+	0	NA	Intergenic	Intergenic	-69222	NM_000027	175	Hs.207776	NM_000027	ENSG00000038002	AGA	AGU|ASRG|GA	aspartylglucosaminidase	protein-coding	0.010050	0.455000	
chunk0024_368_1	chr10	44295175	44295389	+	0	NA	TTS (NM_001258000)	TTS (NM_001258000)	2532	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.009346	0.479070	
chunk0157_278_1	chr5	120575317	120575516	+	0	NA	intron (NM_001308088, intron 1 of 3)	L1M2|LINE|L1	43952	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.005025	0.370000	
chunk0190_272_1	chr8	37421587	37421999	+	0	NA	intron (NR_121620, intron 5 of 6)	intron (NR_121620, intron 5 of 6)	72120	NR_121620	100507420	Hs.105962	NR_121620		LINC01605	LincDUSP	long intergenic non-protein coding RNA 1605	ncRNA	0.014563	0.508475	
chunk0170_451_1	chr6	119261383	119261659	+	0	NA	intron (NM_005907, intron 5 of 12)	intron (NM_005907, intron 5 of 12)	88245	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.003623	0.332130	
chunk0080_110_1	chr17	26982547	26982746	+	0	NA	Intergenic	Intergenic	311350	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.000000	0.580000	
chunk0013_135_1	chr1	168243463	168244099	+	0	NA	TTS (NM_199344)	TTS (NM_199344)	3649	NR_026844	84832	Hs.537067	NR_026844	ENSG00000214262	ANKRD36BP1	ANKRD26L1|ANKRD36BL1	ankyrin repeat domain 36B pseudogene 1	pseudo	0.007862	0.525903	
chunk0054_67_1	chr13	42039680	42039920	+	0	NA	promoter-TSS (NM_001204504)	promoter-TSS (NM_001204504)	-236	NM_001204504	160851	Hs.630380	NM_152910	ENSG00000102780	DGKH	DGKeta	diacylglycerol kinase eta	protein-coding	0.016667	0.460581	
chunk0100_70_1	chr2	106576037	106576802	+	0	NA	Intergenic	L1MA7|LINE|L1	-108074	NM_001144013	653489	Hs.726367	NM_001144013	ENSG00000153165	RGPD3	RGP3	RANBP2 like and GRIP domain containing 3	protein-coding	0.015686	0.408616	
chunk0053_210_1	chr13	32048193	32049117	+	0	NA	intron (NM_023037, intron 1 of 60)	intron (NM_023037, intron 1 of 60)	-17016	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.002165	0.396757	
chunk0009_446_1	chr1	111513130	111513726	+	0	NA	intron (NM_001081976, intron 1 of 5)	intron (NM_001081976, intron 1 of 5)	-9307	NM_020683	57413	Hs.281342	NM_020683	ENSG00000121933	TMIGD3	AD026	transmembrane and immunoglobulin domain containing 3	protein-coding	0.010067	0.458961	
chunk0031_336_1	chr10	129507696	129508111	+	0	NA	intron (NM_002412, intron 1 of 4)	X9_LINE|LINE|L1	40719	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.012048	0.427885	
chunk0151_256_1	chr5	52177148	52177564	+	0	NA	Intergenic	Intergenic	-610584	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.002404	0.364508	
chunk0037_440_1	chr11	80361560	80362055	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	400996	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.002020	0.320565	264(TGGTACAGAATGTACT,-,0.00),265(GGTACAGAATGTACTA,+,0.00)
chunk0068_443_1	chr15	59688620	59688947	+	0	NA	intron (NM_004330, intron 1 of 9)	intron (NM_004330, intron 1 of 9)	660	NM_004330	663	Hs.592515	NM_004330	ENSG00000140299	BNIP2	BNIP-2|NIP2	BCL2 interacting protein 2	protein-coding	0.048930	0.530488	
chunk0176_121_1	chr7	12066241	12066650	+	0	NA	Intergenic	Intergenic	-144777	NM_001134232	54664	Hs.396358	NM_018374	ENSG00000106460	TMEM106B	HLD16	transmembrane protein 106B	protein-coding	0.009780	0.380488	
chunk0056_140_1	chr13	83447778	83448166	+	0	NA	Intergenic	Intergenic	434421	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002577	0.269923	
chunk0175_50_1	chr7	1504503	1504805	+	0	NA	promoter-TSS (NM_001080453)	promoter-TSS (NM_001080453)	-272	NM_001080453	26173	Hs.532188	NM_001080453	ENSG00000164880	INTS1	INT1|NET28	integrator complex subunit 1	protein-coding	0.109272	0.693069	
chunk0091_143_1	chr19	7183437	7183728	+	0	NA	intron (NM_001079817, intron 3 of 20)	intron (NM_001079817, intron 3 of 20)	110720	NM_001079817	3643	Hs.465744	NM_000208	ENSG00000171105	INSR	CD220|HHF5	insulin receptor	protein-coding	0.017182	0.452055	119(GGAGACAGTATGTTCT,-,0.00),120(GAGACAGTATGTTCTG,+,0.00)
chunk0107_325_1	chr2	220302962	220303161	+	0	NA	Intergenic	Intergenic	-396496	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.000000	0.345000	
chunk0071_191_1	chr15	83857305	83857656	+	0	NA	intron (NM_207517, intron 7 of 29)	L1ME3G|LINE|L1	203394	NM_001301110	57188	Hs.459162	NM_207517	ENSG00000156218	ADAMTSL3	ADAMTSL-3	ADAMTS like 3	protein-coding	0.005698	0.332386	
chunk0096_201_1	chr2	30217775	30218362	+	0	NA	Intergenic	Intergenic	-13463	NM_030915	81606	Hs.567598	NM_030915	ENSG00000213626	LBH	-	LBH regulator of WNT signaling pathway	protein-coding	0.017036	0.500000	
chunk0110_165_1	chr20	14069478	14069677	+	0	NA	intron (NM_080676, intron 2 of 16)	intron (NM_080676, intron 2 of 16)	74077	NM_080676	140733	Hs.661576	NM_080676	ENSG00000172264	MACROD2	C20orf133|C2orf133	mono-ADP ribosylhydrolase 2	protein-coding	0.000000	0.320000	
chunk0068_145_1	chr15	53577755	53577973	+	0	NA	intron (NR_102334, intron 18 of 19)	intron (NR_102334, intron 18 of 19)	-36761	NR_102335	256764	Hs.122125	NM_182758	ENSG00000166415	WDR72	AI2A3	WD repeat domain 72	protein-coding	0.000000	0.255708	
chunk0174_387_1	chr6	165082618	165083172	+	0	NA	Intergenic	Intergenic	226727	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.007220	0.342342	
chunk0123_62_1	chr3	41217704	41218008	+	0	NA	intron (NM_001098209, intron 1 of 15)	intron (NM_001098209, intron 1 of 15)	18405	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.003289	0.281967	
chunk0139_372_1	chr4	60743240	60743930	+	0	NA	Intergenic	Intergenic	-179034	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.007246	0.363242	
chunk0022_80_1	chr10	8873069	8873714	+	0	NA	Intergenic	Intergenic	-24598	NR_131944	105755953	Hs.564146	NR_131944	ENSG00000234752	LINC02676	-	long intergenic non-protein coding RNA 2676	ncRNA	0.006202	0.329721	
chunk0212_262_1	chrX	139635996	139636238	+	0	NA	intron (NM_001171876, intron 4 of 28)	Tigger16a|DNA|TcMar-Tigger	6724	NM_001171879	4168	Hs.387262	NM_005369	ENSG00000101977	MCF2	ARHGEF21|DBL	MCF.2 cell line derived transforming sequence	protein-coding	0.008264	0.358025	
chunk0098_11_1	chr2	65281818	65282037	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	54232	NM_001005386	10097	Hs.643727	NM_005722	ENSG00000138071	ACTR2	ARP2	actin related protein 2	protein-coding	0.009132	0.472727	
chunk0094_373_1	chr2	9851748	9852185	+	0	NA	intron (NM_005680, intron 4 of 14)	MER103C|DNA|hAT-Charlie	8524	NM_005680	9014	Hs.584833	NM_005680	ENSG00000115750	TAF1B	MGC:9349|RAF1B|RAFI63|SL1|TAFI63	TATA-box binding protein associated factor, RNA polymerase I subunit B	protein-coding	0.011442	0.365297	
chunk0177_104_1	chr7	22061722	22061956	+	0	NA	Intergenic	Intergenic	-115915	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.000000	0.327660	
chunk0059_428_1	chr14	38282279	38282539	+	0	NA	Intergenic	Intergenic	-26039	NM_175060	161198	Hs.525307	NM_175060	ENSG00000176435	CLEC14A	C14orf27|CEG1|EGFR-5	C-type lectin domain containing 14A	protein-coding	0.007692	0.340996	
chunk0203_178_1	chr9	86131580	86131779	+	0	NA	intron (NR_110996, intron 2 of 4)	MLT1J|LTR|ERVL-MaLR	4139	NR_110996	101927623	Hs.575644	NR_110996		LOC101927623	-	uncharacterized LOC101927623	ncRNA	0.000000	0.515000	
chunk0140_281_1	chr4	72243563	72243995	+	0	NA	Intergenic	Intergenic	204647	NM_001144756	10886	Hs.99231	NM_004885	ENSG00000056291	NPFFR2	GPR74|HLWAR77|NPFF2|NPGPR	neuropeptide FF receptor 2	protein-coding	0.006944	0.353349	
chunk0005_156_1	chr1	58188710	58189208	+	0	NA	intron (NM_021080, intron 1 of 16)	intron (NM_021080, intron 1 of 16)	61580	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.000000	0.376754	
chunk0021_129_1	chr10	3785261	3785555	+	0	NA	promoter-TSS (NM_001160125)	promoter-TSS (NM_001160125)	-127	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.122449	0.711864	
chunk0078_115_1	chr17	2815792	2816273	+	0	NA	intron (NM_015085, intron 2 of 24)	intron (NM_015085, intron 2 of 24)	19594	NM_015085	23108	Hs.499659	NM_015085	ENSG00000132359	RAP1GAP2	GARNL4|RAP1GA3	RAP1 GTPase activating protein 2	protein-coding	0.033264	0.535270	
chunk0192_268_1	chr8	66022063	66022633	+	0	NA	intron (NM_033105, intron 1 of 5)	intron (NM_033105, intron 1 of 5)	792	NM_033105	85479	Hs.491885	NM_033105	ENSG00000147570	DNAJC5B	CSP-beta	DnaJ heat shock protein family (Hsp40) member C5 beta	protein-coding	0.019298	0.528897	
chunk0167_361_1	chr6	73167010	73167209	+	0	NA	intron (NM_019842, intron 10 of 13)	intron (NM_019842, intron 10 of 13)	-23595	NR_046621	100873997	Hs.741819	NR_046621	ENSG00000229154	KCNQ5-AS1	-	KCNQ5 antisense RNA 1	ncRNA	0.005025	0.435000	
chunk0059_354_1	chr14	37247681	37248371	+	0	NA	intron (NM_001195296, intron 5 of 14)	intron (NM_001195296, intron 5 of 14)	50113	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.002899	0.396527	
chunk0139_234_1	chr4	55378960	55379498	+	0	NA	intron (NR_037969, intron 1 of 3)	LTR3B_|LTR|ERVK	6351	NR_037969	100506462	Hs.718667	NR_037969	ENSG00000249700	SRD5A3-AS1	-	SRD5A3 antisense RNA 1	ncRNA	0.020446	0.432282	
chunk0154_453_1	chr5	90558325	90558927	+	0	NA	promoter-TSS (NM_032119)	promoter-TSS (NM_032119)	-174	NR_003149	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.061462	0.625207	
chunk0103_38_1	chr2	159157432	159158019	+	0	NA	intron (NM_001145909, intron 7 of 26)	intron (NM_001145909, intron 7 of 26)	-29110	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.013629	0.420068	
chunk0116_35_1	chr21	33331459	33331739	+	0	NA	intron (NM_000629, intron 1 of 10)	L1M2a|LINE|L1	6690	NM_000629	3454	Hs.529400	NM_000629	ENSG00000142166	IFNAR1	AVP|IFN-alpha-REC|IFNAR|IFNBR|IFRC	interferon alpha and beta receptor subunit 1	protein-coding	0.003571	0.523132	11(TGAGACACCCTGTTCT,-,0.00),12(GAGACACCCTGTTCTA,+,0.00)
chunk0125_191_1	chr3	66763312	66763542	+	0	NA	Intergenic	Intergenic	-234876	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.008696	0.424242	
chunk0073_424_1	chr16	19086581	19086869	+	0	NA	Intergenic	CpG	18808	NM_001190983	10229	Hs.157113	NM_016138	ENSG00000167186	COQ7	CAT5|CLK-1|CLK1|COQ10D8	coenzyme Q7, hydroxylase	protein-coding	0.104167	0.664360	
chunk0001_132_1	chr1	5494438	5494836	+	0	NA	Intergenic	Intergenic	-69434	NR_039612									0.012563	0.421053	249(CAGTACACTCTGTTCT,-,0.00),250(AGTACACTCTGTTCTT,+,0.00)
chunk0145_159_1	chr4	147147545	147147873	+	0	NA	Intergenic	L1MC4|LINE|L1	197008	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.003049	0.373860	
chunk0065_142_1	chr15	25325156	25325667	+	0	NA	Intergenic	Intergenic	47068	NR_001289	338429		NR_001289	ENSG00000239169	SNORD109B	HBII-438B	small nucleolar RNA, C/D box 109B	snoRNA	0.001957	0.388672	
chunk0022_376_1	chr10	17574649	17575184	+	0	NA	Intergenic	L1ME4b|LINE|L1	42458	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.003738	0.350746	7(AGAAGAGAGTGTACTT,+,0.00)
chunk0172_254_1	chr6	137336694	137337291	+	0	NA	Intergenic	L1MC2|LINE|L1	-117562	NM_000416	3459	Hs.520414	NM_000416	ENSG00000027697	IFNGR1	CD119|IFNGR|IMD27A|IMD27B	interferon gamma receptor 1	protein-coding	0.001675	0.381271	302(AGGCACAAATTGTTCA,-,0.00),303(GGCACAAATTGTTCAG,+,0.00)
chunk0073_358_1	chr16	14982469	14983086	+	0	NA	intron (NM_015027, intron 1 of 22).2	intron (NM_015027, intron 1 of 22).2	7814	NM_001285444	23042	Hs.370781	NM_015027	ENSG00000179889	PDXDC1	LP8165	pyridoxal dependent decarboxylase domain containing 1	protein-coding	0.006483	0.411003	262(AGGAACATTATGTTCT,-,0.00),263(GGAACATTATGTTCTT,+,0.00)
chunk0089_239_1	chr18	61976779	61977199	+	0	NA	Intergenic	L1MEg|LINE|L1	-83918	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.000000	0.282660	
chunk0035_196_1	chr11	44564454	44565020	+	0	NA	promoter-TSS (NM_002231)	promoter-TSS (NM_002231)	-854	NM_001024844	3732	Hs.527778	NM_002231	ENSG00000085117	CD82	4F9|C33|GR15|IA4|KAI1|R2|SAR2|ST6|TSPAN27	CD82 molecule	protein-coding	0.017668	0.564374	276(CAGCACTGGTTGTTCT,-,0.00),277(AGCACTGGTTGTTCTG,+,0.00)
chunk0172_409_1	chr6	140053720	140054315	+	0	NA	intron (NR_121623, intron 1 of 1)	intron (NR_121623, intron 1 of 1)	-62756	NR_121624	103352541	Hs.582647	NR_121624		LOC103352541	-	uncharacterized LOC103352541	ncRNA	0.001681	0.310403	
chunk0107_46_1	chr2	211331389	211332056	+	0	NA	Intergenic	MER67D|LTR|ERV1	714151	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.008996	0.377246	
chunk0191_107_1	chr8	48140730	48141347	+	0	NA	Intergenic	L1ME3G|LINE|L1	132603	NM_003350	7336	Hs.491695	NM_003350	ENSG00000169139	UBE2V2	DDVIT1|DDVit-1|EDAF-1|EDPF-1|EDPF1|MMS2|UEV-2|UEV2	ubiquitin conjugating enzyme E2 V2	protein-coding	0.011345	0.414239	
chunk0176_297_1	chr7	16803772	16804307	+	0	NA	intron (NM_006408, intron 1 of 7)	intron (NM_006408, intron 1 of 7)	1075	NM_006408	10551	Hs.530009	NM_006408	ENSG00000106541	AGR2	AG-2|AG2|GOB-4|HAG-2|HEL-S-116|HPC8|PDIA17|XAG-2	anterior gradient 2, protein disulphide isomerase family member	protein-coding	0.003738	0.339552	
chunk0092_189_1	chr19	30437752	30438112	+	0	NA	intron (NM_014717, intron 1 of 4)	intron (NM_014717, intron 1 of 4)	65539	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.005556	0.462604	165(AGGGGCAAGCTGTTCT,-,0.00),166(GGGGCAAGCTGTTCTC,+,0.00)
chunk0132_371_1	chr3	162835397	162835596	+	0	NA	Intergenic	L1M1|LINE|L1	467805	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.005025	0.485000	
chunk0208_78_1	chrX	12965382	12966103	+	0	NA	Intergenic	MER77B|LTR|ERVL	-9365	NM_021109	7114	Hs.437277	NM_021109	ENSG00000205542	TMSB4X	FX|PTMB4|TB4X|TMSB4	thymosin beta 4 X-linked	protein-coding	0.006935	0.426593	
chunk0075_112_1	chr16	49071103	49071635	+	0	NA	Intergenic	L1MEf|LINE|L1	210462	NM_004352	869	Hs.458423	NM_004352	ENSG00000102924	CBLN1	-	cerebellin 1 precursor	protein-coding	0.007519	0.313321	
chunk0198_294_1	chr8	135931050	135931317	+	0	NA	Intergenic	Intergenic	473718	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.003745	0.537313	
chunk0142_224_1	chr4	98092938	98093137	+	0	NA	intron (NM_174952, intron 5 of 10)	intron (NM_174952, intron 5 of 10)	50203	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.010050	0.300000	
chunk0043_328_1	chr12	22625629	22625828	+	0	NA	intron (NM_001039481, intron 1 of 2)	intron (NM_001039481, intron 1 of 2)	586	NM_001039481	55500	Hs.29464	NM_018638	ENSG00000139163	ETNK1	EKI|EKI 1|EKI1|Nbla10396	ethanolamine kinase 1	protein-coding	0.040201	0.555000	
chunk0150_395_1	chr5	39716465	39717111	+	0	NA	Intergenic	Intergenic	196357	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.003096	0.426584	
chunk0131_233_1	chr3	149356120	149356532	+	0	NA	Intergenic	Intergenic	-21452	NR_109810	100874091	Hs.549633	NR_046650	ENSG00000240541	TM4SF1-AS1	-	TM4SF1 antisense RNA 1	ncRNA	0.014563	0.443099	
chunk0004_244_1	chr1	47348405	47348634	+	0	NA	intron (NM_001136140, intron 1 of 4)	intron (NM_001136140, intron 1 of 4)	14722	NM_016308	51727	Hs.731647	NM_016308	ENSG00000162368	CMPK1	CK|CMK|CMPK|UMK|UMP-CMPK|UMPK	cytidine/uridine monophosphate kinase 1	protein-coding	0.004367	0.426087	
chunk0051_353_1	chr12	120525971	120526608	+	0	NA	intron (NM_032314, intron 1 of 6)	Tigger6a|DNA|TcMar-Tigger	2872	NM_032314	84274	Hs.17250	NM_032314	ENSG00000110871	COQ5	-	coenzyme Q5, methyltransferase	protein-coding	0.003140	0.371473	
chunk0175_129_1	chr7	3404577	3404776	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	103228	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.385000	
chunk0022_245_1	chr10	14490930	14491208	+	0	NA	Intergenic	Intergenic	54493	NR_031668	100302116		NR_031668	ENSG00000221371	MIR1265	MIRN1265|hsa-mir-1265	microRNA 1265	ncRNA	0.007194	0.412186	
chunk0059_282_1	chr14	35567634	35568255	+	0	NA	intron (NM_001283043, intron 39 of 41)	intron (NM_001283043, intron 39 of 41)	33902	NM_032594	84684	Hs.62813	NM_032594	ENSG00000168348	INSM2	IA-6|IA6|mlt1	INSM transcriptional repressor 2	protein-coding	0.000000	0.344051	
chunk0048_35_1	chr12	77768357	77768630	+	0	NA	Intergenic	MER52A|LTR|ERV1	-62796	NM_014903	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.003663	0.591241	
chunk0050_224_1	chr12	104771159	104771358	+	0	NA	Intergenic	L1MEc|LINE|L1	157436	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.000000	0.285000	
chunk0006_107_1	chr1	65493669	65494485	+	0	NA	intron (NM_001003680, intron 2 of 19)	intron (NM_001003680, intron 2 of 19)	-31612	NM_001198688	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.004902	0.359853	
chunk0112_175_1	chr20	39935599	39936049	+	0	NA	Intergenic	Intergenic	-68637	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.004444	0.310421	
chunk0107_11_1	chr2	210129067	210129277	+	0	NA	exon (NM_152519, exon 3 of 15)	exon (NM_152519, exon 3 of 15)	42198	NM_001307976	151050	Hs.282260	NM_152519	ENSG00000144445	KANSL1L	C2orf67|MSL1v2	KAT8 regulatory NSL complex subunit 1 like	protein-coding	0.009524	0.398104	
chunk0081_187_1	chr17	41869470	41869727	+	0	NA	intron (NM_198830, intron 24 of 27)	intron (NM_198830, intron 24 of 27)	-4167	NM_018143	55175	Hs.13268	NM_018143	ENSG00000178502	KLHL11	-	kelch like family member 11	protein-coding	0.031128	0.488372	
chunk0037_254_1	chr11	75513386	75513851	+	0	NA	intron (NM_030792, intron 1 of 16)	intron (NM_030792, intron 1 of 16)	11936	NM_030792	81544	Hs.503297	NM_030792	ENSG00000158555	GDPD5	GDE2|PP1665	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding	0.015054	0.545064	
chunk0056_109_1	chr13	82752895	82753505	+	0	NA	Intergenic	MIR|SINE|MIR	1129193	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.292962	272(TGTACTCCATGTTCTG,+,0.00),440(TAGAACATCCAGTCCA,-,0.00),441(AGAACATCCAGTCCAC,+,0.00)
chunk0168_92_1	chr6	80012536	80012865	+	0	NA	intron (NM_001166691, intron 8 of 21)	intron (NM_001166691, intron 8 of 21)	8095	NM_001166691	7272	Hs.169840	NM_003318	ENSG00000112742	TTK	CT96|ESK|MPH1|MPS1|MPS1L1|PYT	TTK protein kinase	protein-coding	0.006079	0.272727	
chunk0196_132_1	chr8	104025674	104026170	+	0	NA	intron (NM_001282881, intron 16 of 20)	Tigger3a|DNA|TcMar-Tigger	-197413	NM_001282882	9699	Hs.655271	NM_014677	ENSG00000176406	RIMS2	OBOE|RAB3IP3|RIM2	regulating synaptic membrane exocytosis 2	protein-coding	0.006048	0.336016	
chunk0098_325_1	chr2	76787962	76788654	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	-197657	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.005780	0.324675	
chunk0130_438_1	chr3	141176874	141177329	+	0	NA	Intergenic	L1MD1|LINE|L1	-54724	NM_152282	92370	Hs.657887	NM_152282	ENSG00000155893	PXYLP1	ACPL2|HEL124|XYLP	2-phosphoxylose phosphatase 1	protein-coding	0.006593	0.372807	
chunk0042_395_1	chr12	11040651	11040978	+	0	NA	intron (NM_001316893, intron 2 of 4)	L1MA2|LINE|L1	-9407	NM_176885	259290	Hs.688197	NM_176885	ENSG00000256436	TAS2R31	T2R31|T2R44|T2R53|TAS2R44	taste 2 receptor member 31	protein-coding	0.003058	0.332317	
chunk0077_371_1	chr16	84511507	84511706	+	0	NA	Intergenic	L1MC3|LINE|L1	-6924	NM_020947	57707	Hs.288274	NM_020947	ENSG00000140950	MEAK7	KIAA1609|TLDC1|mEAK-7	MTOR associated protein, eak-7 homolog	protein-coding	0.045226	0.475000	
chunk0210_272_1	chrX	84291662	84292050	+	0	NA	Intergenic	L1M1|LINE|L1	-66028	NR_031690	100302191		NR_031690	ENSG00000221494	MIR548I4	MIR548I-4|MIRN548I4|hsa-mir-548i-4	microRNA 548i-4	ncRNA	0.002577	0.323907	
chunk0094_81_1	chr2	3689949	3690192	+	0	NA	intron (NM_018436, intron 7 of 11)	L1M1|LINE|L1	-13522	NM_001287444	728597	Hs.304233	NM_001287444	ENSG00000214866	DCDC2C	-	doublecortin domain containing 2C	protein-coding	0.000000	0.352459	216(TGGAACATTGAGTCCA,-,0.00),217(GGAACATTGAGTCCAT,+,0.00)
chunk0185_429_1	chr7	134759467	134759680	+	0	NA	Intergenic	L2c|LINE|L2	-19840	NM_033157	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.014085	0.495327	
chunk0153_300_1	chr5	73436936	73437723	+	0	NA	Intergenic	CpG	11198	NM_004472	2297	Hs.519385	NM_004472	ENSG00000251493	FOXD1	FKHL8|FREAC-4|FREAC4	forkhead box D1	protein-coding	0.100381	0.672589	
chunk0075_462_1	chr16	58426859	58427443	+	0	NA	Intergenic	Intergenic	34757	NM_001126130	64785	Hs.47125	NM_022770	ENSG00000181938	GINS3	PSF3	GINS complex subunit 3	protein-coding	0.008562	0.458120	349(AGGGACACTCTGAACC,-,0.00),350(GGGACACTCTGAACCA,+,0.00)
chunk0115_287_1	chr21	28208098	28208484	+	0	NA	intron (NR_126012, intron 3 of 5)	intron (NR_126012, intron 3 of 5)	20376	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.010363	0.369509	
chunk0190_278_1	chr8	37691837	37692050	+	0	NA	Intergenic	Intergenic	-3808	NM_025069	80139	Hs.288042	NM_025069	ENSG00000183779	ZNF703	NLZ1|ZEPPO1|ZNF503L|ZPO1	zinc finger protein 703	protein-coding	0.014085	0.411215	
chunk0064_386_1	chr14	99004160	99004819	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	267224	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.009105	0.386364	
chunk0005_398_1	chr1	62344023	62344222	+	0	NA	Intergenic	Intergenic	-24710	NM_181712	163782	Hs.283398	NM_181712	ENSG00000132854	KANK4	ANKRD38|dJ1078M7.1	KN motif and ankyrin repeat domains 4	protein-coding	0.025126	0.545000	87(GGGAACTGGCTGCTCT,-,0.00),88(GGAACTGGCTGCTCTG,+,0.00)
chunk0078_32_1	chr17	883145	883612	+	0	NA	intron (NM_022463, intron 1 of 7)	intron (NM_022463, intron 1 of 7)	-19267	NM_001205319	64359	Hs.527989	NM_022463	ENSG00000167693	NXN	NRX|TRG-4	nucleoredoxin	protein-coding	0.012848	0.523504	166(GGAAACACCCTGTTCA,-,0.00),167(GAAACACCCTGTTCAC,+,0.00)
chunk0157_272_1	chr5	120151804	120152145	+	0	NA	Intergenic	Intergenic	-312304	NM_001300783	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.000000	0.418129	
chunk0024_362_1	chr10	44112886	44113203	+	0	NA	Intergenic	Intergenic	-179706	NM_001258000	100130539	Hs.694626	NM_001258000	ENSG00000277288	C10orf142	-	chromosome 10 open reading frame 142	protein-coding	0.003155	0.371069	49(GAAAACAGTATGTGCT,-,0.00),50(AAAACAGTATGTGCTA,+,0.00)
chunk0085_412_1	chr18	10443495	10443706	+	0	NA	Intergenic	Intergenic	-11028	NM_153000	147495	Hs.293274	NM_153000	ENSG00000154856	APCDD1	B7323|DRAPC1|FP7019|HHS|HTS|HYPT1	APC down-regulated 1	protein-coding	0.000000	0.311321	
chunk0095_322_1	chr2	20580860	20581059	+	0	NA	Intergenic	Intergenic	11589	NR_046836	100874343	Hs.591546	NR_046836	ENSG00000231948	HS1BP3-IT1	-	HS1BP3 intronic transcript 1	ncRNA	0.010050	0.525000	
chunk0206_189_1	chr9	122941333	122941566	+	0	NA	intron (NM_012197, intron 1 of 25)	intron (NM_012197, intron 1 of 25)	440	NM_012197	23637	Hs.271341	NM_012197	ENSG00000011454	RABGAP1	GAPCENA|TBC1D11	RAB GTPase activating protein 1	protein-coding	0.030043	0.572650	
chunk0211_175_1	chrX	116405578	116405863	+	0	NA	Intergenic	Intergenic	-30859	NM_007231	11254	Hs.522109	NM_007231	ENSG00000268104	SLC6A14	BMIQ11	solute carrier family 6 member 14	protein-coding	0.000000	0.363636	
chunk0183_430_1	chr7	111117699	111118188	+	0	NA	intron (NM_001099658, intron 2 of 2)	intron (NM_001099658, intron 2 of 2)	26937	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.000000	0.334694	216(AGGCACACTTTGTTCT,-,0.00),217(GGCACACTTTGTTCTT,+,0.00)
chunk0164_423_1	chr6	27332493	27333375	+	0	NA	Intergenic	Intergenic	8173	NR_045612	387316	Hs.326753	NM_032030		VN1R10P	FKSG83|VNR6I1P|b24o18.2|hs6V1-1p	vomeronasal 1 receptor 10 pseudogene	pseudo	0.027211	0.412231	183(AGGAAGAGAATGTCCT,-,0.00)
chunk0052_281_1	chr12	124270434	124270731	+	0	NA	intron (NM_001204299, intron 3 of 4)	L2a|LINE|L2	-18582	NM_181709	144347	Hs.432901	NM_181709	ENSG00000178882	RFLNA	CFM2|FAM101A	refilin A	protein-coding	0.006734	0.459732	
chunk0114_108_1	chr21	9554666	9555051	+	0	NA	Intergenic	MER66C|LTR|ERV1	266203	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.007792	0.287565	
chunk0060_382_1	chr14	52690937	52691481	+	0	NA	intron (NM_014584, intron 1 of 15)	intron (NM_014584, intron 1 of 15)	4722	NM_014584	30001	Hs.525339	NM_014584	ENSG00000197930	ERO1A	ERO1-L|ERO1-L-alpha|ERO1-alpha|ERO1L|ERO1LA|Ero1alpha	endoplasmic reticulum oxidoreductase 1 alpha	protein-coding	0.009191	0.405505	
chunk0020_366_1	chr1	239737802	239738001	+	0	NA	intron (NM_000740, intron 3 of 4)	intron (NM_000740, intron 3 of 4)	-18782	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.005025	0.330000	
chunk0069_324_1	chr15	66000380	66000737	+	0	NA	intron (NM_032445, intron 5 of 22)	intron (NM_032445, intron 5 of 22)	-39675	NR_036196	100422905		NR_036196	ENSG00000263512	MIR4311	-	microRNA 4311	ncRNA	0.002801	0.441341	
chunk0020_377_1	chr1	239879266	239879566	+	0	NA	intron (NM_000740, intron 4 of 4)	intron (NM_000740, intron 4 of 4)	20456	NR_046582	100873984	Hs.199475	NR_046582	ENSG00000234601	CHRM3-AS1	-	CHRM3 antisense RNA 1	ncRNA	0.016667	0.478405	130(TAGAACGGCCTGTGCT,-,0.00),131(AGAACGGCCTGTGCTT,+,0.00)
chunk0031_62_1	chr10	122850981	122851610	+	0	NA	intron (NM_152644, intron 2 of 3)	intron (NM_152644, intron 2 of 3)	-5120	NR_037912	50624	Hs.647182	NM_022034	ENSG00000138161	CUZD1	ERG-1|ERG1|ITMAP1|UO-44	CUB and zona pellucida like domains 1	protein-coding	0.004769	0.369841	
chunk0106_143_1	chr2	200203559	200203843	+	0	NA	Intergenic	MER51B|LTR|ERV1	-102180	NM_001282743	26010	Hs.120323	NM_015535	ENSG00000196141	SPATS2L	DNAPTP6|SGNP	spermatogenesis associated serine rich 2 like	protein-coding	0.000000	0.368421	
chunk0155_238_1	chr5	95652711	95653334	+	0	NA	non-coding (NR_125328, exon 8 of 8)	non-coding (NR_125328, exon 8 of 8)	6143	NM_001131065	317671	Hs.399758	NM_173362	ENSG00000175449	RFESD	-	Rieske Fe-S domain containing	protein-coding	0.003210	0.423077	
chunk0027_72_1	chr10	73176415	73176614	+	0	NA	intron (NM_173348, intron 2 of 13)	intron (NM_173348, intron 2 of 13)	8395	NM_173348	317662	Hs.408577	NM_173348	ENSG00000138286	FAM149B1	KIAA0974	family with sequence similarity 149 member B1	protein-coding	0.015075	0.340000	
chunk0035_358_1	chr11	49151291	49151946	+	0	NA	intron (NM_001193471, intron 18 of 19)	intron (NM_001193471, intron 18 of 19)	57052	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.016794	0.341463	363(GGGAACAGAGTGTATC,-,0.00),364(GGAACAGAGTGTATCT,+,0.00)
chunk0195_319_1	chr8	98944235	98944546	+	0	NA	promoter-TSS (NM_001286841)	promoter-TSS (NM_001286841)	-13	NM_001286841	116039	Hs.253247	NM_053001	ENSG00000164920	OSR2	-	odd-skipped related transciption factor 2	protein-coding	0.093248	0.676282	
chunk0101_201_1	chr2	129982014	129982562	+	0	NA	3' UTR (NM_032144, exon 1 of 1)	3' UTR (NM_032144, exon 1 of 1)	-1816	NR_036537	100131320	Hs.535586	NR_036537	ENSG00000225449	RAB6C-AS1	-	RAB6C antisense RNA 1	ncRNA	0.009124	0.335155	
chunk0032_104_1	chr11	3725323	3725771	+	0	NA	intron (NM_016320, intron 14 of 32)	intron (NM_016320, intron 14 of 32)	-54163	NM_001303035	57053	Hs.732806	NM_020402	ENSG00000129749	CHRNA10	-	cholinergic receptor nicotinic alpha 10 subunit	protein-coding	0.006696	0.354120	
chunk0027_13_1	chr10	72102093	72102567	+	0	NA	intron (NM_001198800, intron 9 of 9)	intron (NM_001198800, intron 9 of 9)	-13298	NM_001134434	9806	Hs.523009	NM_014767	ENSG00000107742	SPOCK2	testican-2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	protein-coding	0.008439	0.397895	
chunk0151_59_1	chr5	42474483	42474813	+	0	NA	intron (NM_001242401, intron 1 of 10)	intron (NM_001242401, intron 1 of 10)	49656	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.009091	0.362538	
chunk0207_151_1	chr9	129751953	129752211	+	0	NA	intron (NM_004878, intron 1 of 2)	intron (NM_004878, intron 1 of 2)	983	NM_004878	9536	Hs.146688	NM_004878	ENSG00000148344	PTGES	MGST-IV|MGST1-L1|MGST1L1|MPGES|PGES|PIG12|PP102|PP1294|TP53I12|mPGES-1	prostaglandin E synthase	protein-coding	0.011628	0.552124	
chunk0036_242_1	chr11	64378190	64378831	+	0	NA	Intergenic	L1ME4a|LINE|L1	9908	NR_031602	100302280		NR_031602	ENSG00000221273	MIR1237	MIRN1237|hsa-mir-1237	microRNA 1237	ncRNA	0.021841	0.434579	
chunk0090_7_1	chr19	485773	486208	+	0	NA	Intergenic	Intergenic	-10500	NM_130760	8174	Hs.102598	NM_130760	ENSG00000099866	MADCAM1	MACAM1	mucosal vascular addressin cell adhesion molecule 1	protein-coding	0.034483	0.623853	
chunk0149_400_1	chr5	28917308	28917669	+	0	NA	Intergenic	Intergenic	-9382	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.002770	0.292818	
chunk0033_112_1	chr11	14435770	14436216	+	0	NA	Intergenic	Intergenic	63865	NM_016451	1315	Hs.339278	NM_016451	ENSG00000129083	COPB1	COPB	coatomer protein complex subunit beta 1	protein-coding	0.004484	0.404922	
chunk0133_129_1	chr3	168889569	168890182	+	0	NA	Intergenic	Intergenic	-12070	NR_109989	100507661	Hs.65918	NR_109989	ENSG00000242268	LINC02082	-	long intergenic non-protein coding RNA 2082	ncRNA	0.001631	0.390879	
chunk0007_294_1	chr1	84132172	84132635	+	0	NA	intron (NM_207578, intron 1 of 8)	L1MC3|LINE|L1	-11845	NM_001300916	5567	Hs.487325	NM_002731	ENSG00000142875	PRKACB	PKA C-beta|PKACB	protein kinase cAMP-activated catalytic subunit beta	protein-coding	0.002160	0.346983	
chunk0066_296_1	chr15	35530702	35531143	+	0	NA	intron (NM_001141972, intron 3 of 3)	intron (NM_001141972, intron 3 of 3)	-15273	NR_038251	100507466	Hs.536420	NR_038251	ENSG00000248079	DPH6-DT	ATPBD4-AS1|DPH6-AS1	DPH6 divergent transcript	ncRNA	0.004535	0.425339	
chunk0121_462_1	chr3	27138495	27138694	+	0	NA	intron (NM_152534, intron 34 of 38)	LTR41C|LTR|ERVL	77929	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.000000	0.385000	
chunk0153_108_1	chr5	68543198	68543619	+	0	NA	Intergenic	Intergenic	250840	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.004751	0.424171	194(GAGTACAGCTTGTCCT,-,0.00),195(AGTACAGCTTGTCCTG,+,0.00)
chunk0166_211_1	chr6	46821538	46822194	+	0	NA	intron (NM_005588, intron 7 of 13)	intron (NM_005588, intron 7 of 13)	28509	NM_005588	4224	Hs.179704	NM_005588	ENSG00000112818	MEP1A	PPHA	meprin A subunit alpha	protein-coding	0.006098	0.368341	455(AAGAAGACACTGTACT,-,0.00)
chunk0163_141_1	chr6	10711129	10711328	+	0	NA	Intergenic	L1MD1|LINE|L1	-11687	NM_016462	51522	Hs.519557	NM_016462	ENSG00000111843	TMEM14C	C6orf53|HSPC194|MSTP073|NET26|bA421M1.6	transmembrane protein 14C	protein-coding	0.000000	0.355000	
chunk0180_329_1	chr7	72670607	72671223	+	0	NA	intron (NM_001145440, intron 11 of 13)	intron (NM_001145440, intron 11 of 13)	-26988	NR_039793	100616310		NR_039793	ENSG00000266525	MIR4650-1	-	microRNA 4650-1	ncRNA	0.011364	0.359806	157(GAAACACTCAGTGCTT,+,0.00)
chunk0211_63_1	chrX	109862401	109862784	+	0	NA	Intergenic	Intergenic	-7809	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.002611	0.463542	
chunk0204_157_1	chr9	95823023	95823641	+	0	NA	intron (NR_023390, intron 2 of 2)	intron (NR_023390, intron 2 of 2)	-52286	NM_001010895	375748	Hs.432364	NM_020207	ENSG00000182150	ERCC6L2	BMFS2|C9orf102|RAD26L|SR278	ERCC excision repair 6 like 2	protein-coding	0.016181	0.504039	
chunk0080_312_1	chr17	31858292	31858791	+	0	NA	intron (NM_018405, intron 1 of 3)	L2a|LINE|L2	766	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.030060	0.514000	
chunk0182_342_1	chr7	99380530	99380731	+	0	NA	intron (NM_005720, intron 1 of 9)	intron (NM_005720, intron 1 of 9)	5955	NM_005720	10095	Hs.489284	NM_005720	ENSG00000130429	ARPC1B	ARC41|PLTEID|p40-ARC|p41-ARC	actin related protein 2/3 complex subunit 1B	protein-coding	0.014925	0.579208	
chunk0070_362_1	chr15	76163918	76164303	+	0	NA	intron (NM_152335, intron 5 of 10)	L1MB5|LINE|L1	17376	NR_120360	101929439	Hs.631721	NR_120360	ENSG00000259422	LOC101929439	-	uncharacterized LOC101929439	ncRNA	0.025974	0.487047	
chunk0208_237_1	chrX	19787454	19787810	+	0	NA	intron (NM_031892, intron 2 of 17)	intron (NM_031892, intron 2 of 17)	12167	NM_001024666	30011	Hs.726365	NM_031892	ENSG00000147010	SH3KBP1	AGMX2|CD2BP3|CIN85|GIG10|HSB-1|HSB1|IMD61|MIG18	SH3 domain containing kinase binding protein 1	protein-coding	0.002809	0.366947	
chunk0094_426_1	chr2	10664529	10665261	+	0	NA	intron (NR_048552, intron 7 of 19)	L1ME4b|LINE|L1	25092	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.015027	0.392906	
chunk0180_208_1	chr7	66493518	66493942	+	0	NA	Intergenic	CpG	-93322	NR_026873	285908	Hs.50755	NM_181722	ENSG00000179406	LINC00174	NCRNA00174	long intergenic non-protein coding RNA 174	ncRNA	0.094340	0.649412	
chunk0043_54_1	chr12	13762422	13762621	+	0	NA	intron (NM_000834, intron 2 of 12)	intron (NM_000834, intron 2 of 12)	217567	NM_000834	2904	Hs.504844	NM_000834	ENSG00000273079	GRIN2B	EIEE27|GluN2B|MRD6|NMDAR2B|NR2B|NR3|hNR3	glutamate ionotropic receptor NMDA type subunit 2B	protein-coding	0.020101	0.390000	120(AGAACATCACGTTCAT,+,0.00)
chunk0176_241_1	chr7	16075651	16076009	+	0	NA	Intergenic	Intergenic	-134656	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.000000	0.320334	
chunk0192_179_1	chr8	62985522	62986000	+	0	NA	TTS (NR_027378)	TTS (NR_027378)	7900	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.000000	0.356994	
chunk0032_381_1	chr11	11422361	11422612	+	0	NA	intron (NM_198516, intron 3 of 10)	intron (NM_198516, intron 3 of 10)	-69129	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.003984	0.496032	
chunk0083_450_1	chr17	73075759	73076652	+	0	NA	intron (NM_001159770, intron 3 of 9)	intron (NM_001159770, intron 3 of 9)	16509	NM_139177	201266	Hs.221127	NM_139177	ENSG00000133195	SLC39A11	C17orf26|ZIP-11|ZIP11	solute carrier family 39 member 11	protein-coding	0.004479	0.370246	243(CAGAACACCTTGTACA,-,0.00),244(AGAACACCTTGTACAC,+,0.00)
chunk0173_111_1	chr6	143450529	143450866	+	0	NA	promoter-TSS (NM_003630)	promoter-TSS (NM_003630)	7	NM_182503	134637	Hs.709561	NM_182503	ENSG00000189007	ADAT2	DEADC1|TAD2|dJ20N2|dJ20N2.1	adenosine deaminase tRNA specific 2	protein-coding	0.097923	0.665680	
chunk0018_208_1	chr1	219446446	219446652	+	0	NA	Intergenic	Intergenic	271580	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.014563	0.473430	
chunk0011_400_1	chr1	154155502	154156009	+	0	NA	promoter-TSS (NM_001159484)	promoter-TSS (NM_001159484)	-639	NM_207308	91181	Hs.67639	NM_207308	ENSG00000143552	NUP210L	-	nucleoporin 210 like	protein-coding	0.015779	0.401575	
chunk0003_37_1	chr1	30461681	30462014	+	0	NA	Intergenic	Intergenic	-256925	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.000000	0.520958	
chunk0182_220_1	chr7	96371609	96372045	+	0	NA	Intergenic	Intergenic	-49680	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.002294	0.281465	
chunk0203_269_1	chr9	88180088	88180679	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-45398	NM_001166137	645961	Hs.632070	NM_001166137		SPATA31C2	FAM75C2	SPATA31 subfamily C member 2	protein-coding	0.035533	0.516892	
chunk0109_325_1	chr20	9198012	9198632	+	0	NA	intron (NM_001172646, intron 1 of 37)	intron (NM_001172646, intron 1 of 37)	-19068	NM_182797	5332	Hs.472101	NM_000933	ENSG00000101333	PLCB4	ARCND2|PI-PLC	phospholipase C beta 4	protein-coding	0.000000	0.347826	
chunk0112_63_1	chr20	37721118	37721607	+	0	NA	intron (NM_030877, intron 1 of 15)	intron (NM_030877, intron 1 of 15)	27407	NM_030877	56259	Hs.472667	NM_030877	ENSG00000132792	CTNNBL1	C20orf33|NAP|P14L|PP8304|dJ633O20.1	catenin beta like 1	protein-coding	0.004090	0.400000	
chunk0133_200_1	chr3	170809481	170809742	+	0	NA	Intergenic	Intergenic	60645	NM_001099645	200916	Hs.380933	NM_001099645	ENSG00000163584	RPL22L1	-	ribosomal protein L22 like 1	protein-coding	0.015326	0.511450	
chunk0022_423_1	chr10	19169161	19169689	+	0	NA	intron (NM_001142308, intron 13 of 39)	intron (NM_001142308, intron 13 of 39)	120654	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.003788	0.332703	
chunk0061_117_1	chr14	58463220	58463532	+	0	NA	intron (NM_001244192, intron 15 of 31)	L2a|LINE|L2	23695	NM_001244193	9786	Hs.232532	NM_014749	ENSG00000100578	KIAA0586	JBTS23|SRTD14|Talpid3	KIAA0586	protein-coding	0.000000	0.316294	
chunk0040_271_1	chr11	116667394	116667728	+	0	NA	Intergenic	L1PA6|LINE|L1	105437	NM_032725	84811	Hs.437341	NM_032725	ENSG00000137656	BUD13	Cwc26|fSAP71	BUD13 homolog	protein-coding	0.002994	0.465672	
chunk0189_341_1	chr8	26630102	26630799	+	0	NA	intron (NM_001244604, intron 7 of 13)	intron (NM_001244604, intron 7 of 13)	52045	NM_001244604	1808	Hs.593187	NM_001386	ENSG00000092964	DPYSL2	CRMP-2|CRMP2|DHPRP2|DRP-2|DRP2|N2A3|ULIP-2|ULIP2	dihydropyrimidinase like 2	protein-coding	0.015782	0.521490	428(CTGGACACTGTGTTCC,-,0.00),429(TGGACACTGTGTTCCT,+,0.00)
chunk0191_326_1	chr8	55926188	55926576	+	0	NA	intron (NM_001111097, intron 1 of 12)	intron (NM_001111097, intron 1 of 12)	46555	NM_001111097	4067	Hs.491767	NM_002350	ENSG00000254087	LYN	JTK8|p53Lyn|p56Lyn	LYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.005155	0.370180	
chunk0123_253_1	chr3	45818201	45818485	+	0	NA	Intergenic	Intergenic	-21800	NM_022405	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.014085	0.424561	
chunk0025_103_1	chr10	50614576	50614808	+	0	NA	intron (NM_147156, intron 1 of 10)	intron (NM_147156, intron 1 of 10)	9285	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.017241	0.506438	
chunk0057_428_1	chr13	110094824	110095040	+	0	NA	Intergenic	Intergenic	41647	NR_126387	104355146	Hs.508690	NR_126387	ENSG00000231428	LINC00396	-	long intergenic non-protein coding RNA 396	ncRNA	0.023148	0.529954	
chunk0187_397_1	chr7	157847846	157848615	+	0	NA	intron (NM_001308268, intron 12 of 22)	intron (NM_001308268, intron 12 of 22)	-6355	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.016905	0.476623	
chunk0084_316_1	chr17	80454649	80454885	+	0	NA	Intergenic	CpG	21837	NM_002522	4884	Hs.514556	NM_002522	ENSG00000171246	NPTX1	NP1	neuronal pentraxin 1	protein-coding	0.152542	0.742616	
chunk0194_383_1	chr8	90701067	90701613	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-55435	NM_001146273	169200	Hs.567759	NM_001008495	ENSG00000180694	TMEM64	-	transmembrane protein 64	protein-coding	0.007326	0.382084	
chunk0179_104_1	chr7	44884119	44884334	+	0	NA	3' UTR (NM_033224, exon 1 of 1)	3' UTR (NM_033224, exon 1 of 1)	1159	NM_033224	5814	Hs.349150	NM_033224	ENSG00000146676	PURB	PURBETA	purine rich element binding protein B	protein-coding	0.027907	0.458333	
chunk0036_128_1	chr11	61820921	61821501	+	0	NA	intron (NM_001281502, intron 1 of 11)	intron (NM_001281502, intron 1 of 11)	-4154	NM_013402	3992	Hs.503546	NM_013402	ENSG00000149485	FADS1	D5D|FADS6|FADSD5|LLCDL1|TU12	fatty acid desaturase 1	protein-coding	0.006897	0.430293	
chunk0090_422_1	chr18	79180427	79180915	+	0	NA	intron (NM_001306085, intron 8 of 28)	L1MEf|LINE|L1	111396	NM_001306085	374868	Hs.465475	NM_198531	ENSG00000166377	ATP9B	ATPASEP|ATPIIB|HUSSY-20|NEO1L|hMMR1	ATPase phospholipid transporting 9B (putative)	protein-coding	0.010246	0.388548	
chunk0148_33_1	chr5	800993	801647	+	0	NA	intron (NM_024786, intron 11 of 12)	MIRc|SINE|MIR	49666	NM_024786	79844	Hs.654874	NM_024786	ENSG00000188818	ZDHHC11	ZNF399	zinc finger DHHC-type containing 11	protein-coding	0.006116	0.427481	401(AGAGACAAAGTGTGCT,-,0.00),402(GAGACAAAGTGTGCTT,+,0.00)
chunk0074_377_1	chr16	34594929	34595341	+	0	NA	Intergenic	Intergenic	-435099	NR_038368									0.036408	0.363196	
chunk0114_300_1	chr21	16968429	16968949	+	0	NA	Intergenic	Intergenic	378452	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.003846	0.343570	209(AAGTACAGCATGTCAC,-,0.00)
chunk0074_366_1	chr16	34584618	34584995	+	0	NA	Intergenic	Intergenic	-424770	NR_038368									0.045699	0.369973	
chunk0057_354_1	chr13	108561097	108561727	+	0	NA	Intergenic	Intergenic	-34740	NM_015011	23026	Hs.656587	NM_015011	ENSG00000041515	MYO16	MYAP3|MYR8|Myo16b|NYAP3|PPP1R107	myosin XVI	protein-coding	0.006349	0.342314	
chunk0071_147_1	chr15	82865133	82865510	+	0	NA	intron (NM_199330, intron 3 of 8)	intron (NM_199330, intron 3 of 8)	55693	NM_001080435	123720	Hs.377360	NM_001080435	ENSG00000156232	WHAMM	WHAMM1|WHDC1	WASP homolog associated with actin, golgi membranes and microtubules	protein-coding	0.005305	0.457672	
chunk0115_315_1	chr21	28699503	28700161	+	0	NA	Intergenic	Intergenic	160514	NR_026553	118421	Hs.438549	NR_026552	ENSG00000226935	LINC00161	C21orf100|Linc-USP16|NCRNA00161	long intergenic non-protein coding RNA 161	ncRNA	0.004559	0.342944	
chunk0030_458_1	chr10	121289384	121289781	+	0	NA	Intergenic	Intergenic	304385	NM_001144913	2263	Hs.533683	NM_000141	ENSG00000066468	FGFR2	BBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25	fibroblast growth factor receptor 2	protein-coding	0.005038	0.396985	42(AAGCTCAATGTGTGCT,-,0.00)
chunk0190_419_1	chr8	41225635	41225860	+	0	NA	Intergenic	L1PA6|LINE|L1	45396	NR_049801	100847068		NR_049801	ENSG00000263372	MIR548AO	-	microRNA 548ao	ncRNA	0.008889	0.530973	
chunk0167_295_1	chr6	71031988	71032313	+	0	NA	Intergenic	Intergenic	-75065	NM_080742	135152	Hs.713609	NM_080742	ENSG00000112309	B3GAT2	GLCATS	beta-1,3-glucuronyltransferase 2	protein-coding	0.012308	0.438650	
chunk0094_194_1	chr2	6273709	6274328	+	0	NA	Intergenic	HAL1|LINE|L1	101404	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.003231	0.277419	
chunk0021_200_1	chr10	5789570	5790251	+	0	NA	intron (NM_001115156, intron 3 of 9)	Tigger2b_Pri|DNA|TcMar-Tigger	23639	NM_001115156	2665	Hs.299055	NM_001494	ENSG00000057608	GDI2	HEL-S-46e|RABGDIB	GDP dissociation inhibitor 2	protein-coding	0.011747	0.366569	270(CAGTACATACTGTACT,-,0.00),271(AGTACATACTGTACTA,+,0.00)
chunk0028_408_1	chr10	93395336	93395971	+	0	NA	intron (NM_013451, intron 16 of 53)	intron (NM_013451, intron 16 of 53)	86664	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.009449	0.382075	
chunk0203_370_1	chr9	89999923	90000423	+	0	NA	Intergenic	Intergenic	23362	NR_036253	100422963		NR_036253	ENSG00000263967	MIR4290	-	microRNA 4290	ncRNA	0.016000	0.502994	
chunk0006_326_1	chr1	71761181	71761540	+	0	NA	intron (NM_173808, intron 3 of 6)	MER58A|DNA|hAT-Charlie	75652	NR_046218	100852409	Hs.681780	NR_046218	ENSG00000228853	NEGR1-IT1	-	NEGR1 intronic transcript 1	ncRNA	0.005571	0.344444	
chunk0193_321_1	chr8	78615786	78615998	+	0	NA	Intergenic	Intergenic	-50155	NM_016010	51101	Hs.271876	NM_016010	ENSG00000104427	ZC2HC1A	C8orf70|CGI-62|FAM164A	zinc finger C2HC-type containing 1A	protein-coding	0.000000	0.366197	
chunk0029_72_1	chr10	96670844	96671287	+	0	NA	intron (NM_152309, intron 2 of 16)	MamRep434|DNA|TcMar-Tigger	49457	NM_152309	118788	Hs.310456	NM_152309	ENSG00000155629	PIK3AP1	BCAP	phosphoinositide-3-kinase adaptor protein 1	protein-coding	0.009029	0.441441	
chunk0143_434_1	chr4	123860642	123861013	+	0	NA	intron (NR_027105, intron 3 of 4)	intron (NR_027105, intron 3 of 4)	86563	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.005391	0.301075	
chunk0049_262_1	chr12	93742234	93742942	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-4765	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.060734	0.582511	
chunk0130_295_1	chr3	136898487	136899114	+	0	NA	intron (NM_001291999, intron 1 of 3)	intron (NM_001291999, intron 1 of 3)	-31675	NM_001190796	4690	Hs.126889	NM_006153	ENSG00000158092	NCK1	NCK|NCKalpha|nck-1	NCK adaptor protein 1	protein-coding	0.006380	0.345541	
chunk0151_333_1	chr5	53934788	53935452	+	0	NA	intron (NM_019087, intron 4 of 4)	intron (NM_019087, intron 4 of 4)	16479	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.000000	0.372932	
chunk0207_202_1	chr9	131167270	131167762	+	0	NA	intron (NM_005085, intron 21 of 35)	L1ME3B|LINE|L1	41955	NM_005085	8021	Hs.654530	NM_005085	ENSG00000126883	NUP214	CAIN|CAN	nucleoporin 214	protein-coding	0.012195	0.365112	
chunk0031_253_1	chr10	127142393	127142739	+	0	NA	intron (NM_001039762, intron 5 of 5)	intron (NM_001039762, intron 5 of 5)	53592	NM_001039762	642938	Hs.613882	NM_001039762	ENSG00000188916	INSYN2A	C10orf141|FAM196A|INSYN2	inhibitory synaptic factor 2A	protein-coding	0.008671	0.521614	
chunk0067_458_1	chr15	50352517	50352936	+	0	NA	non-coding (NR_026891, exon 1 of 1)	non-coding (NR_026891, exon 1 of 1)	-1448	NR_024490	100129387	Hs.659360	NR_024490		GABPB1-AS1	-	GABPB1 antisense RNA 1	ncRNA	0.019093	0.421429	
chunk0072_372_1	chr15	100031575	100032001	+	0	NA	intron (NM_139057, intron 18 of 21)	L2b|LINE|L2	-224861	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.018779	0.451991	
chunk0108_144_1	chr2	230814457	230814859	+	0	NA	intron (NM_016289, intron 7 of 8)	MER58A|DNA|hAT-Charlie	-49940	NM_001287241	81618	Hs.111577	NM_030926	ENSG00000135916	ITM2C	BRI3|BRICD2C|E25|E25C|ITM3	integral membrane protein 2C	protein-coding	0.009950	0.436725	
chunk0086_271_1	chr18	23618914	23619164	+	0	NA	intron (NM_001308238, intron 7 of 8)	intron (NM_001308238, intron 7 of 8)	-32422	NM_000271	4864	Hs.464779	NM_000271	ENSG00000141458	NPC1	NPC|POGZ|SLC65A1	NPC intracellular cholesterol transporter 1	protein-coding	0.016000	0.537849	
chunk0209_151_1	chrX	42563170	42563437	+	0	NA	Intergenic	Intergenic	214932	NR_002191									0.000000	0.365672	
chunk0081_447_1	chr17	49191291	49192038	+	0	NA	Intergenic	L1ME4b|LINE|L1	17717	NM_031498	2793	Hs.181781	NM_031498	ENSG00000167083	GNGT2	G-GAMMA-8|G-GAMMA-C|GNG8|GNG9|GNGT8	G protein subunit gamma transducin 2	protein-coding	0.018742	0.330214	
chunk0205_19_1	chr9	105141331	105141692	+	0	NA	Intergenic	Intergenic	-103102	NM_080546	23446	Hs.573495	NM_022109	ENSG00000070214	SLC44A1	CD92|CDW92|CHTL1|CTL1	solute carrier family 44 member 1	protein-coding	0.005540	0.480663	
chunk0045_139_1	chr12	46446666	46446865	+	0	NA	intron (NR_125381, intron 2 of 2)	intron (NR_125381, intron 2 of 2)	62658	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.005025	0.415000	
chunk0016_33_1	chr1	193059273	193059783	+	0	NA	promoter-TSS (NM_015984)	promoter-TSS (NM_015984)	106	NM_001173524	6738	Hs.288178	NM_004600	ENSG00000116747	RO60	RORNP|SSA2|TROVE2	Ro60, Y RNA binding protein	protein-coding	0.090196	0.669276	
chunk0147_400_1	chr4	186790436	186791099	+	0	NA	Intergenic	Intergenic	-66934	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.004525	0.359940	
chunk0025_116_1	chr10	51367593	51368175	+	0	NA	intron (NM_006258, intron 2 of 17)	intron (NM_006258, intron 2 of 17)	68311	NR_030336	693190		NR_030336	ENSG00000207813	MIR605	MIRN605|hsa-mir-605|mir-605	microRNA 605	ncRNA	0.001718	0.341338	
chunk0072_234_1	chr15	95913689	95914281	+	0	NA	Intergenic	Intergenic	-411943	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.001689	0.345700	
chunk0173_338_1	chr6	148943210	148943588	+	0	NA	intron (NM_005715, intron 3 of 7)	intron (NM_005715, intron 3 of 7)	21285	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.000000	0.332454	164(AAGAACACAAAGTACA,-,0.00),165(AGAACACAAAGTACAG,+,0.00)
chunk0152_271_1	chr5	61280864	61281261	+	0	NA	Intergenic	Intergenic	-51211	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.005038	0.452261	
chunk0003_96_1	chr1	31926319	31926920	+	0	NA	intron (NM_080391, intron 1 of 5)	intron (NM_080391, intron 1 of 5)	-6961	NM_001195101	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.001664	0.337209	
chunk0189_404_1	chr8	27595628	27596433	+	0	NA	TTS (NR_045494)	TTS (NR_045494)	14721	NR_106902	102465508		NR_106902	ENSG00000284280	MIR6843	hsa-mir-6843	microRNA 6843	ncRNA	0.003727	0.514888	
chunk0081_22_1	chr17	37317872	37318354	+	0	NA	intron (NM_198836, intron 3 of 55).2	intron (NM_198836, intron 3 of 55).2	-18346	NM_198838	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.004149	0.428571	
chunk0164_376_1	chr6	25916751	25917173	+	0	NA	intron (NM_005835, intron 7 of 10)	intron (NM_005835, intron 7 of 10)	8917	NM_001286123	10246	Hs.591802	NM_005835	ENSG00000112337	SLC17A2	NPT3	solute carrier family 17 member 2	protein-coding	0.007109	0.494090	196(AGGTACAAGGTGTGCA,-,0.00),197(GGTACAAGGTGTGCAC,+,0.00),231(GAGGACAGGATGTGCT,-,0.00),232(AGGACAGGATGTGCTC,+,0.00)
chunk0057_282_1	chr13	106096462	106097044	+	0	NA	Intergenic	Intergenic	-279810	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.008591	0.403087	280(TGTACTCTCTGTACTT,+,0.00)
chunk0065_228_1	chr14	100899575	100899857	+	0	NA	intron (NR_024149, intron 2 of 3)	MIRb|SINE|MIR	1796	NR_003080	692215		NR_003080	ENSG00000275662	SNORD112	14q(0)	small nucleolar RNA, C/D box 112	snoRNA	0.017730	0.480565	
chunk0131_192_1	chr3	148533619	148533843	+	0	NA	Intergenic	Intergenic	-164140	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.000000	0.364444	
chunk0043_120_1	chr12	15597093	15597600	+	0	NA	3' UTR (NM_030668, exon 14 of 14)	3' UTR (NM_030668, exon 14 of 14)	51002	NM_030668	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.007890	0.405512	
chunk0042_261_1	chr12	6768459	6768746	+	0	NA	intron (NM_002824, intron 1 of 4)	intron (NM_002824, intron 1 of 4)	2227	NM_002824	5763	Hs.504613	NM_002824	ENSG00000159335	PTMS	ParaT	parathymosin	protein-coding	0.017422	0.552083	
chunk0039_409_1	chr11	107499226	107499656	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	-41595	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.004651	0.382831	
chunk0039_254_1	chr11	102214453	102214985	+	0	NA	intron (NM_001130145, intron 6 of 8)	intron (NM_001130145, intron 6 of 8)	102279	NM_001195045	10413	Hs.503692	NM_006106	ENSG00000137693	YAP1	COB1|YAP|YAP2|YAP65|YKI	Yes associated protein 1	protein-coding	0.003759	0.317073	
chunk0174_215_1	chr6	160391313	160391703	+	0	NA	intron (NM_021977, intron 1 of 10)	MIRb|SINE|MIR	43135	NM_021977	6581	Hs.567337	NM_021977	ENSG00000146477	SLC22A3	EMT|EMTH|OCT3	solute carrier family 22 member 3	protein-coding	0.010256	0.375959	
chunk0046_312_1	chr12	62480376	62480894	+	0	NA	intron (NM_001278472, intron 2 of 35)	intron (NM_001278472, intron 2 of 35)	13818	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.009653	0.410405	
chunk0206_449_1	chr9	128102888	128103584	+	0	NA	intron (NM_001006642, intron 4 of 9)	intron (NM_001006642, intron 4 of 9)	4754	NR_049766	114789	Hs.5476	NM_052901	ENSG00000148339	SLC25A25	MCSC|PCSCL|SCAMC-2	solute carrier family 25 member 25	protein-coding	0.033046	0.599713	
chunk0177_381_1	chr7	26895591	26896442	+	0	NA	Intergenic	L1ME4c|LINE|L1	-31273	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.000000	0.333333	368(AAGAACAGGTAGTACA,-,0.00),369(AGAACAGGTAGTACAT,+,0.00)
chunk0146_208_1	chr4	161400206	161401114	+	0	NA	intron (NM_001128427, intron 15 of 15)	intron (NM_001128427, intron 15 of 15)	-622073	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.001101	0.271727	
chunk0184_347_1	chr7	120743228	120743577	+	0	NA	intron (NM_012281, intron 4 of 5)	L2b|LINE|L2	114721	NM_012338	23554	Hs.16529	NM_012338	ENSG00000106025	TSPAN12	EVR5|NET-2|NET2|TM4SF12	tetraspanin 12	protein-coding	0.011461	0.422857	
chunk0181_403_1	chr7	90029615	90029997	+	0	NA	intron (NR_110029, intron 2 of 2)	L1MC5|LINE|L1	-89594	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.007853	0.342037	
chunk0012_185_1	chr1	159581333	159581909	+	0	NA	Intergenic	Intergenic	-6205	NM_001639	325	Hs.507080	NM_001639	ENSG00000132703	APCS	HEL-S-92n|PTX2|SAP	amyloid P component, serum	protein-coding	0.005208	0.415945	
chunk0100_255_1	chr2	113158819	113159589	+	0	NA	Intergenic	L2a|LINE|L2	-14779	NM_012455	23550	Hs.516306	NM_012455	ENSG00000125637	PSD4	EFA6B|TIC	pleckstrin and Sec7 domain containing 4	protein-coding	0.005195	0.457847	481(CAGGACAGGCTGTGCT,-,0.00),482(AGGACAGGCTGTGCTT,+,0.00),577(GGGAACAGCAAGTGCA,-,0.00),578(GGAACAGCAAGTGCAA,+,0.00)
chunk0164_245_1	chr6	23377818	23378133	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	-748211	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.000000	0.382911	
chunk0181_177_1	chr7	83036740	83037154	+	0	NA	intron (NM_014510, intron 3 of 19)	intron (NM_014510, intron 3 of 19)	125934	NM_014510	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.004831	0.342169	146(ATGGACATTGTGTCCT,-,0.00),147(TGGACATTGTGTCCTT,+,0.00)
chunk0115_12_1	chr21	20377317	20377894	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	425503	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005199	0.358131	
chunk0171_116_1	chr6	122494851	122495254	+	0	NA	intron (NM_001270393, intron 3 of 7)	L1PA15-16|LINE|L1	23135	NM_001270393	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.002481	0.547030	
chunk0166_53_1	chr6	42883912	42884165	+	0	NA	intron (NM_198486, intron 3 of 5)	intron (NM_198486, intron 3 of 5)	4105	NM_198486	285855	Hs.520133	NM_198486	ENSG00000146223	RPL7L1	dJ475N16.4	ribosomal protein L7 like 1	protein-coding	0.003953	0.468504	
chunk0114_349_1	chr21	18087219	18087563	+	0	NA	intron (NM_001204176, intron 2 of 6)	L1M2a1|LINE|L1	-157442	NM_024944	140578	Hs.283725	NM_024944	ENSG00000154645	CHODL	C21orf68|MT75|PRED12	chondrolectin	protein-coding	0.005814	0.518841	
chunk0201_33_1	chr9	33425055	33425590	+	0	NA	Intergenic	Intergenic	22311	NM_004925	360	Hs.234642	NM_004925	ENSG00000165272	AQP3	AQP-3|GIL	aquaporin 3 (Gill blood group)	protein-coding	0.014953	0.434701	
chunk0033_310_1	chr11	20510686	20511424	+	0	NA	Intergenic	Intergenic	-88345	NM_004211	9152	Hs.136557	NM_004211	ENSG00000165970	SLC6A5	GLYT-2|GLYT2|HKPX3|NET1	solute carrier family 6 member 5	protein-coding	0.004065	0.349120	
chunk0092_400_1	chr19	37362491	37362975	+	0	NA	exon (NM_181786, exon 6 of 6)	exon (NM_181786, exon 6 of 6)	-8424	NM_032453	84503	Hs.590940	NM_032453	ENSG00000189164	ZNF527	-	zinc finger protein 527	protein-coding	0.014463	0.494845	
chunk0151_76_1	chr5	42638293	42638668	+	0	NA	intron (NM_001242403, intron 3 of 9)	Tigger3a|DNA|TcMar-Tigger	72616	NM_001242462	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.005333	0.327128	
chunk0131_356_1	chr3	151838236	151838601	+	0	NA	intron (NR_110202, intron 1 of 3)	intron (NR_110202, intron 1 of 3)	24345	NM_001086	13	Hs.506908	NM_001086	ENSG00000114771	AADAC	CES5A1|DAC	arylacetamide deacetylase	protein-coding	0.010959	0.297814	
chunk0111_179_1	chr20	25321943	25322314	+	0	NA	intron (NM_001042472, intron 3 of 12)	intron (NM_001042472, intron 3 of 12)	68854	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.010782	0.400538	
chunk0172_180_1	chr6	136517019	136517462	+	0	NA	intron (NM_003980, intron 1 of 17)	intron (NM_003980, intron 1 of 17)	8973	NM_001198608	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.000000	0.387387	
chunk0090_354_1	chr18	76657256	76657760	+	0	NA	Intergenic	Intergenic	-18497	NR_110784	101927651	Hs.569848	NR_110784		LINC01927	-	long intergenic non-protein coding RNA 1927	ncRNA	0.009921	0.441584	200(GGGGCACTTTGTTCTG,+,0.00)
chunk0015_205_1	chr1	187477309	187477882	+	0	NA	TTS (NR_132374)	TTS (NR_132374)	33967	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.008726	0.350174	362(AGGAACACACTGTATC,-,0.00),363(GGAACACACTGTATCT,+,0.00)
chunk0120_34_1	chr3	2566780	2566979	+	0	NA	intron (NM_001206955, intron 2 of 23)	intron (NM_001206955, intron 2 of 23)	-325336	NM_001206956	152330	Hs.298705	NM_175607	ENSG00000144619	CNTN4	AXCAM|BIG-2	contactin 4	protein-coding	0.010050	0.385000	
chunk0136_119_1	chr4	3494947	3495217	+	0	NA	TTS (NM_173660)	TTS (NM_173660)	10538	NM_001256896	285489	Hs.122110	NM_173660	ENSG00000175920	DOK7	C4orf25|CMS10|CMS1B|FADS3	docking protein 7	protein-coding	0.025926	0.616236	
chunk0122_94_1	chr3	30354696	30355742	+	0	NA	Intergenic	Intergenic	-251283	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.009560	0.427889	849(AAGGACAAGCTGCCCC,-,0.00),850(AGGACAAGCTGCCCCT,+,0.00)
chunk0157_419_1	chr5	124661457	124661956	+	0	NA	intron (NM_020747, intron 2 of 8)	intron (NM_020747, intron 2 of 8)	83406	NM_020747	57507	Hs.266616	NM_020747	ENSG00000168916	ZNF608	NY-REN-36	zinc finger protein 608	protein-coding	0.012024	0.402000	
chunk0198_446_1	chr8	144063225	144063765	+	0	NA	Intergenic	L2a|LINE|L2	-2792	NM_017570	26873	Hs.305882	NM_017570	ENSG00000178814	OPLAH	5-Opase|OPLA|OPLAHD	5-oxoprolinase, ATP-hydrolysing	protein-coding	0.035185	0.634011	256(TGGCACAGGCTGTTCC,-,0.00),257(GGCACAGGCTGTTCCC,+,0.00)
chunk0052_29_1	chr13	20505987	20506554	+	0	NA	intron (NM_015974, intron 2 of 7)	intron (NM_015974, intron 2 of 7)	19603	NM_015974	51084	Hs.370703	NM_015974	ENSG00000165475	CRYL1	GDH|HEL30|gul3DH|lambda-CRY	crystallin lambda 1	protein-coding	0.003527	0.343310	247(AAGTACAACCAGTTCT,-,0.00),248(AGTACAACCAGTTCTG,+,0.00)
chunk0162_431_1	chr5	180316581	180316780	+	0	NA	intron (NM_005110, intron 12 of 18)	intron (NM_005110, intron 12 of 18)	-24609	NM_002752	5601	Hs.484371	NM_002752	ENSG00000050748	MAPK9	JNK-55|JNK2|JNK2A|JNK2ALPHA|JNK2B|JNK2BETA|PRKM9|SAPK|SAPK1a|p54a|p54aSAPK	mitogen-activated protein kinase 9	protein-coding	0.045226	0.540000	
chunk0020_91_1	chr1	232817618	232818107	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	12970	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.006135	0.385714	
chunk0046_131_1	chr12	57547226	57547450	+	0	NA	promoter-TSS (NM_001261413)	promoter-TSS (NM_001261413)	-7	NM_001261412	10540	Hs.289123	NM_006400	ENSG00000175203	DCTN2	DCTN50|DYNAMITIN|HEL-S-77|RBP50	dynactin subunit 2	protein-coding	0.040179	0.542222	
chunk0133_249_1	chr3	171644622	171644853	+	0	NA	intron (NM_001130081, intron 21 of 25)	intron (NM_001130081, intron 21 of 25)	165757	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.008658	0.336207	
chunk0058_255_1	chr14	25698901	25699241	+	0	NA	Intergenic	Intergenic	-648774	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.005882	0.357771	
chunk0060_180_1	chr14	46595273	46595687	+	0	NA	Intergenic	L1MA7|LINE|L1	56345	NM_080746	140801	Hs.308332	NM_080746	ENSG00000165496	RPL10L	RPL10_5_1358	ribosomal protein L10 like	protein-coding	0.000000	0.332530	
chunk0202_396_1	chr9	81237574	81237983	+	0	NA	Intergenic	Intergenic	451757	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.002445	0.365854	
chunk0184_206_1	chr7	117116253	117116452	+	0	NA	intron (NR_109981, intron 4 of 4)	intron (NR_109981, intron 4 of 4)	-25571	NR_109980	93654	Hs.628891	NR_002331	ENSG00000226367	ST7-AS2	ST7AS2|ST7OT2	ST7 antisense RNA 2	ncRNA	0.005025	0.405000	
chunk0155_193_1	chr5	94674868	94675234	+	0	NA	intron (NM_032290, intron 14 of 20)	intron (NM_032290, intron 14 of 20)	56365	NM_032290	84250	Hs.657315	NM_032290	ENSG00000133302	SLF1	ANKRD32|BRCTD1|BRCTx	SMC5-SMC6 complex localization factor 1	protein-coding	0.000000	0.362398	185(AGGCACAGTGTGTGCT,-,0.00),186(GGCACAGTGTGTGCTT,+,0.00)
chunk0095_120_1	chr2	15832713	15832991	+	0	NA	Intergenic	L1ME3|LINE|L1	-87547	NR_125783	103752554	Hs.269571	NR_125783	ENSG00000223850	MYCNUT	MYCNUN|lncUSMycN	MYCN upstream transcript	ncRNA	0.010791	0.412186	120(AAGTACACACCGTACT,-,0.00),121(AGTACACACCGTACTG,+,0.00)
chunk0014_210_1	chr1	179296633	179297249	+	0	NA	intron (NR_045530, intron 1 of 13)	intron (NR_045530, intron 1 of 13)	3227	NM_001252511	6646	Hs.445588	NM_003101	ENSG00000057252	SOAT1	ACACT|ACAT|ACAT-1|ACAT1|SOAT|STAT	sterol O-acyltransferase 1	protein-coding	0.006494	0.385737	
chunk0036_122_1	chr11	61688330	61688559	+	0	NA	intron (NM_006133, intron 1 of 19)	intron (NM_006133, intron 1 of 19)	8011	NM_006133	747	Hs.241564	NM_006133	ENSG00000134780	DAGLA	C11orf11|DAGL(ALPHA)|DAGLALPHA|NSDDR	diacylglycerol lipase alpha	protein-coding	0.013100	0.556522	
chunk0107_417_1	chr2	224360846	224361110	+	0	NA	Intergenic	Intergenic	41016	NM_024785	79843	Hs.147585	NM_024785	ENSG00000124019	FAM124B	-	family with sequence similarity 124 member B	protein-coding	0.011364	0.309434	
chunk0100_93_1	chr2	107802346	107802902	+	0	NA	intron (NR_126370, intron 2 of 4)	L1MEd|LINE|L1	24145	NR_024439	729121	Hs.386155	NR_024439	ENSG00000230651	RGPD4-AS1	-	RGPD4 antisense RNA 1 (head to head)	ncRNA	0.000000	0.402154	
chunk0102_33_1	chr2	141739051	141739636	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	392358	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.006838	0.324232	
chunk0064_273_1	chr14	95111831	95112188	+	0	NA	intron (NM_001195573, intron 12 of 24)	intron (NM_001195573, intron 12 of 24)	21494	NM_001195573	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.005602	0.321229	
chunk0070_368_1	chr15	76313918	76314354	+	0	NA	Intergenic	Intergenic	-2667	NM_000126	2108	Hs.39925	NM_000126	ENSG00000140374	ETFA	EMA|GA2|MADD	electron transfer flavoprotein subunit alpha	protein-coding	0.016055	0.482838	
chunk0175_351_1	chr6	167590407	167590620	+	0	NA	Intergenic	(CAC)n|Simple_repeat|Simple_repeat	88710	NR_117091	401286	Hs.487182	NR_117091	ENSG00000272549	LINC02538	-	long intergenic non-protein coding RNA 2538	ncRNA	0.000000	0.514019	
chunk0015_84_1	chr1	184861820	184862408	+	0	NA	intron (NM_052966, intron 5 of 13)	intron (NM_052966, intron 5 of 13)	-107207	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.011905	0.453311	
chunk0024_160_1	chr10	35495443	35495869	+	0	NA	intron (NM_145012, intron 2 of 9)	intron (NM_145012, intron 2 of 9)	-109754	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.011737	0.494145	328(GTGCACTTTGTGTCCT,-,0.00),329(TGCACTTTGTGTCCTG,+,0.00)
chunk0135_274_1	chr3	189304349	189305144	+	0	NA	intron (NM_198485, intron 4 of 5)	intron (NM_198485, intron 4 of 5)	-64152	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.012579	0.456030	489(TAGATCATGTTGTTCT,-,0.00),490(AGATCATGTTGTTCTG,+,0.00)
chunk0124_451_1	chr3	61593798	61594579	+	0	NA	intron (NM_002841, intron 1 of 29)	intron (NM_002841, intron 1 of 29)	32619	NM_002841	5793	Hs.595541	NM_002841	ENSG00000144724	PTPRG	HPTPG|PTPG|R-PTP-GAMMA|RPTPG	protein tyrosine phosphatase receptor type G	protein-coding	0.014085	0.429668	
chunk0080_318_1	chr17	32150778	32151386	+	0	NA	non-coding (NR_002222, exon 1 of 1)	non-coding (NR_002222, exon 1 of 1)	489	NR_002222	503640	Hs.631752	NR_002222		ARGFXP2	-	arginine-fifty homeobox pseudogene 2	pseudo	0.006579	0.490969	
chunk0152_114_1	chr5	58582927	58583312	+	0	NA	promoter-TSS (NM_138453)	promoter-TSS (NM_138453)	7	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.067532	0.595855	
chunk0027_437_1	chr10	81040889	81041436	+	0	NA	Intergenic	Intergenic	500343	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.003656	0.364964	
chunk0119_257_1	chr22	45817975	45818732	+	0	NA	intron (NM_001167621, intron 9 of 10)	intron (NM_001167621, intron 9 of 10)	57829	NR_039919	100616253		NR_039919	ENSG00000264160	MIR4762	-	microRNA 4762	ncRNA	0.017173	0.509235	
chunk0066_301_1	chr15	35631039	35631419	+	0	NA	intron (NR_038251, intron 1 of 2)	intron (NR_038251, intron 1 of 2)	-85026	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.005263	0.414698	
chunk0023_198_1	chr10	25170445	25171092	+	0	NA	intron (NR_027333, intron 1 of 1)	intron (NR_027333, intron 1 of 1)	-4593	NM_020752	57512	Hs.499108	NM_020752	ENSG00000151025	GPR158	-	G protein-coupled receptor 158	protein-coding	0.004637	0.334877	334(AAGAACAATGAGTTCC,-,0.00),335(AGAACAATGAGTTCCT,+,0.00)
chunk0050_144_1	chr12	102584975	102585349	+	0	NA	Intergenic	L1PA13|LINE|L1	-104517	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.000000	0.336000	
chunk0205_441_1	chr9	115342956	115343398	+	0	NA	intron (NM_017418, intron 4 of 7)	intron (NM_017418, intron 4 of 7)	201359	NM_017418	50514	Hs.148841	NM_017418	ENSG00000173077	DEC1	CTS9	deleted in esophageal cancer 1	ncRNA	0.000000	0.325056	
chunk0199_395_1	chr9	13271644	13272151	+	0	NA	intron (NM_003829, intron 1 of 45)	L1ME1|LINE|L1	7667	NM_001261406	8777	Hs.169378	NM_003829	ENSG00000107186	MPDZ	HYC2|MUPP1	multiple PDZ domain crumbs cell polarity complex component	protein-coding	0.007890	0.374016	
chunk0112_326_1	chr20	44911563	44911762	+	0	NA	intron (NM_001124756, intron 1 of 14)	intron (NM_001124756, intron 1 of 14)	1600	NM_001124756	80336	Hs.641481	NM_001124756	ENSG00000101104	PABPC1L	C20orf119|EPAB|PABPC1L1|dJ1069P2.3	poly(A) binding protein cytoplasmic 1 like	protein-coding	0.030151	0.600000	
chunk0195_434_1	chr8	101051651	101052205	+	0	NA	promoter-TSS (NR_033962)	promoter-TSS (NR_033962)	-126	NR_033962	441374	Hs.652045	NR_033962	ENSG00000248599	FLJ42969	-	uncharacterized LOC441374	ncRNA	0.019856	0.520721	
chunk0055_252_1	chr13	63297291	63297967	+	0	NA	intron (NR_126409, intron 2 of 6)	intron (NR_126409, intron 2 of 6)	30465	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.005917	0.330871	
chunk0197_261_1	chr8	123551529	123551892	+	0	NA	Intergenic	Intergenic	-10457	NM_001242463	114907	Hs.403933	NM_058229	ENSG00000156804	FBXO32	Fbx32|MAFbx	F-box protein 32	protein-coding	0.011019	0.497253	137(CAGAACTGGGAGTGCC,-,0.00),138(AGAACTGGGAGTGCCA,+,0.00)
chunk0135_332_1	chr3	190230043	190230515	+	0	NA	Intergenic	Intergenic	92167	NM_021101	9076	Hs.439060	NM_021101	ENSG00000163347	CLDN1	CLD1|ILVASC|SEMP1	claudin 1	protein-coding	0.004237	0.401691	
chunk0196_330_1	chr8	112387692	112388082	+	0	NA	intron (NM_198123, intron 36 of 70)	L2b|LINE|L2	-255606	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.005128	0.355499	
chunk0028_389_1	chr10	92945056	92945431	+	0	NA	intron (NM_019053, intron 13 of 21)	L1MA7|LINE|L1	96775	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.000000	0.345745	
chunk0063_264_1	chr14	83756278	83756686	+	0	NA	Intergenic	Intergenic	-1637397	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.300733	
chunk0162_368_1	chr6	7236563	7237140	+	0	NA	intron (NM_001003698, intron 10 of 11)	intron (NM_001003698, intron 10 of 11)	76463	NM_003144	6745	Hs.114033	NM_003144	ENSG00000124783	SSR1	TRAPA	signal sequence receptor subunit 1	protein-coding	0.001733	0.435986	
chunk0141_237_1	chr4	84915299	84915776	+	0	NA	intron (NM_014991, intron 2 of 67)	intron (NM_014991, intron 2 of 67)	50854	NM_014991	23001	Hs.480116	NM_014991	ENSG00000163625	WDFY3	ALFY|BCHS|MCPH18|ZFYVE25	WD repeat and FYVE domain containing 3	protein-coding	0.000000	0.309623	
chunk0191_63_1	chr8	46962314	46962581	+	0	NA	Intergenic	LTR57|LTR|ERVL	121561	NR_027012	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.007491	0.503731	
chunk0098_167_1	chr2	70661553	70661850	+	0	NA	TTS (NM_001617)	TTS (NM_001617)	106014	NM_001185054	119	Hs.66187	NM_001617	ENSG00000075340	ADD2	ADDB	adducin 2	protein-coding	0.010101	0.483221	144(GAGCACAGGGTGTTCC,-,0.00),145(AGCACAGGGTGTTCCC,+,0.00)
chunk0041_77_1	chr11	124111270	124111870	+	0	NA	Intergenic	MIRb|SINE|MIR	-3834	NM_001130142	4013	Hs.152944	NM_014622	ENSG00000110002	VWA5A	BCSC-1|BCSC1|LOH11CR2A	von Willebrand factor A domain containing 5A	protein-coding	0.005000	0.371048	
chunk0184_38_1	chr7	112160427	112161228	+	0	NA	intron (NM_014705, intron 1 of 51)	intron (NM_014705, intron 1 of 51)	45580	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.009988	0.411471	267(GAAAACAGAATGTTCC,-,0.00),268(AAAACAGAATGTTCCT,+,0.00)
chunk0101_396_1	chr2	138798548	138799101	+	0	NA	Intergenic	L1PA7|LINE|L1	-18583	NM_007226	11249	Hs.435019	NM_007226	ENSG00000144227	NXPH2	NPH2	neurexophilin 2	protein-coding	0.001808	0.357401	338(AAAGACACAATGTACC,-,0.00)
chunk0118_318_1	chr22	35231164	35231397	+	0	NA	promoter-TSS (NR_126356)	promoter-TSS (NR_126356)	-224	NR_126356	104310353	Hs.581009	NR_126356	ENSG00000233080	LINC01399	-	long intergenic non-protein coding RNA 1399	ncRNA	0.012876	0.508547	
chunk0138_71_1	chr4	33482556	33483153	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	557039	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.001675	0.364548	
chunk0205_304_1	chr9	112383526	112383848	+	0	NA	intron (NR_036651, intron 1 of 9)	L1M5|LINE|L1	3778	NM_032303	84263	Hs.59486	NM_032303	ENSG00000119471	HSDL2	C9orf99|SDR13C1	hydroxysteroid dehydrogenase like 2	protein-coding	0.009317	0.436533	
chunk0074_305_1	chr16	30178588	30178807	+	0	NA	Intergenic	MIRb|SINE|MIR	-4713	NM_007074	11151	Hs.415067	NM_007074	ENSG00000102879	CORO1A	CLABP|CLIPINA|HCORO1|IMD8|TACO|p57	coronin 1A	protein-coding	0.009132	0.540909	
chunk0117_399_1	chr21	45505654	45506194	+	0	NA	exon (NM_030582, exon 37 of 42)	exon (NM_030582, exon 37 of 42)	27658	NR_106873	102465489		NR_106873	ENSG00000275167	MIR6815	hsa-mir-6815	microRNA 6815	ncRNA	0.050000	0.619224	
chunk0154_68_1	chr5	77418462	77418893	+	0	NA	intron (NM_001029854, intron 17 of 20)	intron (NM_001029854, intron 17 of 20)	73830	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.016241	0.418981	268(GAGGACATCCTGTCTT,-,0.00),269(AGGACATCCTGTCTTT,+,0.00)
chunk0099_224_1	chr2	96260303	96260762	+	0	NA	intron (NM_017849, intron 2 of 3)	intron (NM_017849, intron 2 of 3)	5481	NM_001193304	55654	Hs.164303	NM_017849	ENSG00000135956	TMEM127	-	transmembrane protein 127	protein-coding	0.015251	0.510870	
chunk0024_410_1	chr10	45361257	45361902	+	0	NA	Intergenic	L1P2|LINE|L1	-12597	NM_001256153	240	Hs.89499	NM_000698	ENSG00000012779	ALOX5	5-LO|5-LOX|5LPG|LOG5	arachidonate 5-lipoxygenase	protein-coding	0.004651	0.368421	
chunk0131_198_1	chr3	148631429	148631689	+	0	NA	Intergenic	L1MA3|LINE|L1	-66312	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.003846	0.467433	
chunk0085_360_1	chr18	9336982	9337601	+	0	NA	exon (NM_020648, exon 2 of 5)	exon (NM_020648, exon 2 of 5)	2524	NM_020648	57045	Hs.514685	NM_020648	ENSG00000128791	TWSG1	TSG	twisted gastrulation BMP signaling modulator 1	protein-coding	0.000000	0.364516	
chunk0076_414_1	chr16	72914341	72914699	+	0	NA	intron (NM_006885, intron 3 of 9)	intron (NM_006885, intron 3 of 9)	133855	NM_006885	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.008380	0.420613	
chunk0057_288_1	chr13	106181829	106182377	+	0	NA	Intergenic	L1ME3G|LINE|L1	-194460	NR_034119	728192	Hs.559194	NR_034119		LINC00460	-	long intergenic non-protein coding RNA 460	ncRNA	0.010949	0.315118	
chunk0065_222_1	chr14	100664922	100665171	+	0	NA	intron (NR_024096, intron 1 of 1)	intron (NR_024096, intron 1 of 1)	7778	NR_024096	283601	Hs.379802	NM_001007560	ENSG00000196273	LINC00523	C14orf70	long intergenic non-protein coding RNA 523	ncRNA	0.020080	0.528000	
chunk0047_179_1	chr12	70643904	70644372	+	0	NA	intron (NR_073474, intron 9 of 10)	MER57F|LTR|ERV1	-6698	NM_001109754	5787	Hs.201030	NM_002837	ENSG00000127329	PTPRB	HPTP-BETA|HPTPB|PTPB|R-PTP-BETA|VEPTP	protein tyrosine phosphatase receptor type B	protein-coding	0.006410	0.347548	
chunk0149_189_1	chr5	21350396	21351000	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-108782	NR_027028	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.003311	0.338843	
chunk0022_125_1	chr10	11556383	11556582	+	0	NA	intron (NM_014688, intron 2 of 14)	L1MEg|LINE|L1	-24202	NM_001080491	9712	Hs.498661	NM_014688	ENSG00000148429	USP6NL	RNTRE|TRE2NL|USP6NL-IT1	USP6 N-terminal like	protein-coding	0.005025	0.300000	
chunk0094_30_1	chr2	1686589	1687404	+	0	NA	intron (NM_012293, intron 4 of 22)	intron (NM_012293, intron 4 of 22)	57551	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.031902	0.511029	
chunk0103_391_1	chr2	168973804	168974012	+	0	NA	intron (NM_003742, intron 12 of 27)	intron (NM_003742, intron 12 of 27)	57415	NM_003742	8647	Hs.158316	NM_003742	ENSG00000073734	ABCB11	ABC16|BRIC2|BSEP|PFIC-2|PFIC2|PGY4|SPGP	ATP binding cassette subfamily B member 11	protein-coding	0.014423	0.406699	
chunk0006_63_1	chr1	64727354	64727847	+	0	NA	Intergenic	Intergenic	-17495	NM_018211	55225	Hs.591443	NM_018211	ENSG00000162437	RAVER2	-	ribonucleoprotein, PTB binding 2	protein-coding	0.006085	0.376518	
chunk0125_18_1	chr3	62007359	62007875	+	0	NA	intron (NM_002841, intron 4 of 29)	L2c|LINE|L2	311330	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.003876	0.394584	
chunk0098_417_1	chr2	80269836	80270310	+	0	NA	intron (NM_004389, intron 7 of 17)	intron (NM_004389, intron 7 of 17)	34289	NM_178839	347730	Hs.591580	NM_178839	ENSG00000162951	LRRTM1	-	leucine rich repeat transmembrane neuronal 1	protein-coding	0.012658	0.402105	
chunk0146_202_1	chr4	161363735	161364209	+	0	NA	Intergenic	Intergenic	-658761	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004219	0.414737	
chunk0114_6_1	chr21	6369311	6369989	+	0	NA	Intergenic	Intergenic	97958	NM_000071	875	Hs.533013	NM_000071	ENSG00000160200	CBS	CBSL|HIP4	cystathionine-beta-synthase	protein-coding	0.029499	0.528719	
chunk0022_283_1	chr10	15253278	15253564	+	0	NA	intron (NM_001010924, intron 4 of 7)	intron (NM_001010924, intron 4 of 7)	-84711	NM_001308295	9397	Hs.60339	NM_004808	ENSG00000152465	NMT2	-	N-myristoyltransferase 2	protein-coding	0.010490	0.376307	
chunk0142_144_1	chr4	94920642	94921248	+	0	NA	intron (NM_001203, intron 2 of 12)	intron (NM_001203, intron 2 of 12)	-75287	NM_001256792	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.004950	0.362438	
chunk0007_446_1	chr1	86937200	86937517	+	0	NA	intron (NM_012262, intron 1 of 6)	intron (NM_012262, intron 1 of 6)	22706	NM_012262	9653	Hs.743280	NM_012262	ENSG00000153936	HS2ST1	dJ604K5.2	heparan sulfate 2-O-sulfotransferase 1	protein-coding	0.000000	0.298742	
chunk0040_114_1	chr11	112013368	112013855	+	0	NA	intron (NM_001037954, intron 17 of 19)	L2c|LINE|L2	-11203	NM_001931	1737	Hs.335551	NM_001931	ENSG00000150768	DLAT	DLTA|E2|PDC-E2|PDCE2	dihydrolipoamide S-acetyltransferase	protein-coding	0.002053	0.352459	
chunk0046_318_1	chr12	62520102	62520767	+	0	NA	intron (NM_001278469, intron 8 of 35)	Charlie1a|DNA|hAT-Charlie	53617	NM_001278471	23041	Hs.389378	NM_015026	ENSG00000061987	MON2	-	MON2 homolog, regulator of endosome-to-Golgi trafficking	protein-coding	0.010526	0.361862	
chunk0202_158_1	chr9	73701407	73701818	+	0	NA	Intergenic	L1MB8|LINE|L1	549881	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.002433	0.385922	
chunk0065_340_1	chr14	103525408	103526024	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-2857	NM_001823	1152	Hs.173724	NM_001823	ENSG00000166165	CKB	B-CK|BCK|CKBB|CPK-B|HEL-211|HEL-S-29	creatine kinase B	protein-coding	0.021104	0.523501	207(AGTGCATCGTGTCCCT,+,0.00)
chunk0039_440_1	chr11	108093150	108093875	+	0	NA	intron (NM_003478, intron 13 of 18)	Tigger6a|DNA|TcMar-Tigger	-28019	NM_000019	38	Hs.232375	NM_000019	ENSG00000075239	ACAT1	ACAT|MAT|T2|THIL	acetyl-CoA acetyltransferase 1	protein-coding	0.005517	0.365014	
chunk0140_29_1	chr4	65892995	65893343	+	0	NA	Intergenic	Intergenic	-222674	NM_004439	2044	Hs.654492	NM_004439	ENSG00000145242	EPHA5	CEK7|EHK-1|EHK1|EK7|HEK7|TYRO4	EPH receptor A5	protein-coding	0.005747	0.326648	
chunk0019_78_1	chr1	224323571	224323786	+	0	NA	intron (NM_206840, intron 1 of 21)	MLT1B-int|LTR|ERVL-MaLR	6511	NM_001243147	4931	Hs.497867	NM_002533	ENSG00000143748	NVL	NVL2	nuclear VCP like	protein-coding	0.013953	0.541667	
chunk0053_231_1	chr13	32426589	32426839	+	0	NA	intron (NM_052818, intron 1 of 4)	intron (NM_052818, intron 1 of 4)	1464	NM_001286459	90634	Hs.732118	NM_052818	ENSG00000139597	N4BP2L1	CG018	NEDD4 binding protein 2 like 1	protein-coding	0.028000	0.498008	
chunk0173_274_1	chr6	147741516	147741715	+	0	NA	Intergenic	Intergenic	232923	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.035176	0.470000	
chunk0072_378_1	chr15	100128897	100129121	+	0	NA	intron (NM_139057, intron 12 of 21)	intron (NM_139057, intron 12 of 21)	212969	NM_139057	170691	Hs.513200	NM_139057	ENSG00000140470	ADAMTS17	WMS4	ADAM metallopeptidase with thrombospondin type 1 motif 17	protein-coding	0.017857	0.480000	
chunk0133_351_1	chr3	173166131	173166425	+	0	NA	Intergenic	Intergenic	-25010	NM_031955	83893	Hs.444236	NM_031955	ENSG00000144962	SPATA16	NYD-SP12|SPGF6	spermatogenesis associated 16	protein-coding	0.000000	0.359322	
chunk0210_169_1	chrX	78202988	78203310	+	0	NA	Intergenic	Intergenic	-63467	NM_015975	51616	Hs.592248	NM_015975	ENSG00000187325	TAF9B	DN-7|DN7|TAF9L|TAFII31L|TFIID-31	TATA-box binding protein associated factor 9b	protein-coding	0.003106	0.448916	
chunk0088_327_1	chr18	51020375	51020959	+	0	NA	Intergenic	MIR|SINE|MIR	-9546	NM_005359	4089	Hs.75862	NM_005359	ENSG00000141646	SMAD4	DPC4|JIP|MADH4|MYHRS	SMAD family member 4	protein-coding	0.010274	0.381197	
chunk0055_384_1	chr13	73325514	73326207	+	0	NA	Intergenic	Intergenic	-238384	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.011544	0.396254	
chunk0009_186_1	chr1	105785202	105785457	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-166394	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.011765	0.371094	
chunk0121_310_1	chr3	24141277	24141862	+	0	NA	intron (NM_000461, intron 7 of 9)	L2a|LINE|L2	-9755	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.006838	0.395904	
chunk0207_329_1	chr9	134284299	134284610	+	0	NA	Intergenic	Intergenic	-42009	NM_002957	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.025723	0.612179	
chunk0028_402_1	chr10	93254101	93255358	+	0	NA	Intergenic	Intergenic	180839	NM_000783	1592	Hs.150595	NM_000783	ENSG00000095596	CYP26A1	CP26|CYP26|P450RAI|P450RAI1	cytochrome P450 family 26 subfamily A member 1	protein-coding	0.003978	0.424483	
chunk0023_356_1	chr10	29842090	29842316	+	0	NA	Intergenic	Intergenic	-106402	NM_003174	6840	Hs.499209	NM_003174	ENSG00000197321	SVIL	-	supervillin	protein-coding	0.013274	0.594714	
chunk0037_180_1	chr11	74079725	74080403	+	0	NA	intron (NM_001286577, intron 22 of 32)	MER46C|DNA|TcMar-Tigger	-70827	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.002950	0.340206	282(GGGCACAGTGTGTTTT,-,0.00),283(GGCACAGTGTGTTTTA,+,0.00)
chunk0139_170_1	chr4	53942094	53942357	+	0	NA	Intergenic	L1PREC2|LINE|L1	45057	NR_027153	402176	Hs.452943	NM_001011538		RPL21P44	RPL21_17_477	ribosomal protein L21 pseudogene 44	pseudo	0.003802	0.401515	
chunk0114_251_1	chr21	16079785	16080468	+	0	NA	intron (NR_027790, intron 2 of 7)	L2a|LINE|L2	9012	NR_111004	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.002928	0.350877	
chunk0184_213_1	chr7	117332350	117332549	+	0	NA	Intergenic	L1MEf|LINE|L1	-9160	NM_003391	7472	Hs.567356	NM_003391	ENSG00000105989	WNT2	INT1L1|IRP	Wnt family member 2	protein-coding	0.005025	0.305000	115(GAAGACATACTGTCCC,-,0.00),116(AAGACATACTGTCCCT,+,0.00)
chunk0071_18_1	chr15	78950073	78950466	+	0	NA	Intergenic	Intergenic	-5191	NM_004390	1512	Hs.148641	NM_004390	ENSG00000103811	CTSH	ACC-4|ACC-5|ACC4|ACC5|CPSB	cathepsin H	protein-coding	0.005089	0.492386	300(AGGCACTGTTTGTCCC,-,0.00),301(GGCACTGTTTGTCCCC,+,0.00)
chunk0107_176_1	chr2	215625309	215625517	+	0	NA	intron (NR_037195, intron 5 of 9)	intron (NR_037195, intron 5 of 9)	-92630	NR_132383	105373869	Hs.152812	NR_132383		LINC01614	LCAL4	long intergenic non-protein coding RNA 1614	ncRNA	0.004808	0.464115	
chunk0166_174_1	chr6	46024161	46024858	+	0	NA	intron (NM_001114086, intron 1 of 5)	MLT1K|LTR|ERVL-MaLR	-8620	NM_001256023	53405	Hs.485489	NM_016929	ENSG00000112782	CLIC5	DFNB102|DFNB103|MST130|MSTP130	chloride intracellular channel 5	protein-coding	0.001435	0.395415	
chunk0118_131_1	chr22	29798556	29799561	+	0	NA	intron (NM_001242906, intron 14 of 18)	intron (NM_001242906, intron 14 of 18)	31689	NM_001003684	29796	Hs.284292	NM_013387	ENSG00000184076	UQCR10	HSPC051|HSPC119|HSPC151|QCR9|UCCR7.2|UCRC	ubiquinol-cytochrome c reductase, complex III subunit X	protein-coding	0.012935	0.531809	427(AAGGGCACAGTGTTCC,-,0.00),428(AGGGCACAGTGTTCCA,+,0.00)
chunk0021_249_1	chr1	243306183	243306442	+	0	NA	intron (NM_006642, intron 7 of 17)	intron (NM_006642, intron 7 of 17)	-39864	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.003861	0.234615	
chunk0191_40_1	chr8	43139792	43140232	+	0	NA	promoter-TSS (NM_152419)	promoter-TSS (NM_152419)	-437	NM_152419	138050	Hs.600384	NM_152419	ENSG00000165102	HGSNAT	HGNAT|MPS3C|RP73|TMEM76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding	0.045455	0.575964	
chunk0157_169_1	chr5	118060439	118061023	+	0	NA	intron (NR_104997, intron 2 of 2)	L1MA8|LINE|L1	-221843	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.001712	0.336752	
chunk0101_158_1	chr2	128250108	128250395	+	0	NA	Intergenic	Intergenic	68346	NM_004807	9394	Hs.512841	NM_004807	ENSG00000136720	HS6ST1	HH15|HS6ST	heparan sulfate 6-O-sulfotransferase 1	protein-coding	0.010453	0.423611	
chunk0117_77_1	chr22	17141499	17141997	+	0	NA	intron (NM_017829, intron 5 of 7)	MIRb|SINE|MIR	17531	NM_033070	27440	Hs.26890	NM_017829	ENSG00000069998	HDHD5	CECR5	haloacid dehalogenase like hydrolase domain containing 5	protein-coding	0.010040	0.507014	
chunk0008_261_1	chr1	94545103	94545455	+	0	NA	Intergenic	Intergenic	-3422	NM_001178096	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.000000	0.334278	144(AGGAACACAGAGTTCT,-,0.00),145(GGAACACAGAGTTCTG,+,0.00)
chunk0017_237_1	chr1	208186300	208186558	+	0	NA	intron (NM_025179, intron 3 of 31)	intron (NM_025179, intron 3 of 31)	57891	NM_025179	5362	Hs.497626	NM_025179	ENSG00000076356	PLXNA2	OCT|PLXN2	plexin A2	protein-coding	0.003876	0.366795	
chunk0059_7_1	chr14	29734211	29735020	+	0	NA	intron (NM_002742, intron 1 of 17)	L1MEc|LINE|L1	193078	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.008653	0.418519	
chunk0054_371_1	chr13	49925848	49926318	+	0	NA	intron (NR_023351, intron 1 of 2)	intron (NR_023351, intron 1 of 2)	10418	NR_023351	57213	Hs.44235	NM_020456	ENSG00000123178	SPRYD7	C13orf1|CLLD6	SPRY domain containing 7	protein-coding	0.004255	0.341826	
chunk0174_334_1	chr6	163738540	163739225	+	0	NA	Intergenic	Intergenic	324239	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.001460	0.381924	
chunk0127_261_1	chr3	97287454	97287780	+	0	NA	intron (NM_001080448, intron 5 of 17)	L1MA4A|LINE|L1	-151976	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.006135	0.327217	
chunk0116_195_1	chr21	37182266	37182582	+	0	NA	intron (NM_001001894, intron 35 of 45)	intron (NM_001001894, intron 35 of 45)	-26079	NR_026719	257203	Hs.505159	NM_148675	ENSG00000230366	DSCR9	NCRNA00038	Down syndrome critical region 9	ncRNA	0.018987	0.438486	
chunk0126_330_1	chr3	82030783	82031209	+	0	NA	Intergenic	Intergenic	-269197	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.011737	0.423888	298(TGGAACGCCTTGTTCC,-,0.00),299(GGAACGCCTTGTTCCT,+,0.00)
chunk0138_171_1	chr4	37882370	37883359	+	0	NA	Intergenic	Charlie18a|DNA|hAT-Charlie	-8220	NM_001253912	23216	Hs.176503	NM_015173	ENSG00000065882	TBC1D1	TBC|TBC1	TBC1 domain family member 1	protein-coding	0.006067	0.378788	
chunk0204_393_1	chr9	102421424	102421945	+	0	NA	Intergenic	L1MD1|LINE|L1	-97953	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.000000	0.293103	
chunk0182_203_1	chr7	96042615	96042842	+	0	NA	intron (NM_001278421, intron 13 of 15)	L1MC5|LINE|L1	177028	NR_030322	693176		NR_030322	ENSG00000208025	MIR591	MIRN591|hsa-mir-591	microRNA 591	ncRNA	0.000000	0.320175	
chunk0159_215_1	chr5	140718358	140719171	+	0	NA	promoter-TSS (NR_026704)	promoter-TSS (NR_026704)	-162	NR_026704	56663		NR_026704	ENSG00000202111	VTRNA1-2	HVG2|VAULTRC2|VR2|hvg-2	vault RNA 1-2	ncRNA	0.027060	0.500000	
chunk0119_130_1	chr22	42912145	42912450	+	0	NA	intron (NM_001184970, intron 1 of 10)	intron (NM_001184970, intron 1 of 10)	34744	NM_007229	11252	Hs.162877	NM_007229	ENSG00000100266	PACSIN2	SDPII	protein kinase C and casein kinase substrate in neurons 2	protein-coding	0.013115	0.444444	
chunk0002_2_1	chr1	11907985	11908535	+	0	NA	TTS (NR_002754)	TTS (NR_002754)	106	NR_002754	26829		NR_002754	ENSG00000199347	RNU5E-1	RNU5E|U5E	RNA, U5E small nuclear 1	snRNA	0.036364	0.404719	
chunk0028_167_1	chr10	87557532	87557851	+	0	NA	Intergenic	Intergenic	49858	NM_001178118	9562	Hs.121260	NM_004897	ENSG00000107789	MINPP1	HIPER1|MINPP2|MIPP	multiple inositol-polyphosphate phosphatase 1	protein-coding	0.009404	0.359375	
chunk0121_63_1	chr3	15753046	15753748	+	0	NA	intron (NM_015199, intron 3 of 27)	intron (NM_015199, intron 3 of 27)	3154	NM_001195099	23243	Hs.335239	NM_015199	ENSG00000206560	ANKRD28	PITK|PPP1R65	ankyrin repeat domain 28	protein-coding	0.007123	0.435277	
chunk0061_108_1	chr14	57932842	57933075	+	0	NA	Intergenic	Intergenic	-67084	NM_001306087	341880	Hs.28280	NM_001080455	ENSG00000151812	SLC35F4	C14orf36|c14_5373	solute carrier family 35 member F4	protein-coding	0.004292	0.354701	
chunk0028_176_1	chr10	88114713	88115328	+	0	NA	Intergenic	L2a|LINE|L2	251582	NM_000314	5728	Hs.500466	NM_000314	ENSG00000171862	PTEN	10q23del|BZS|CWS1|DEC|GLM2|MHAM|MMAC1|PTEN1|PTENbeta|TEP1	phosphatase and tensin homolog	protein-coding	0.008130	0.459416	
chunk0037_277_1	chr11	75739592	75740332	+	0	NA	Intergenic	L1MC3|LINE|L1	22073	NM_025098	80168	Hs.288568	NM_025098	ENSG00000166391	MOGAT2	DGAT2L5|DGAT2L5.|MGAT2|hDC5	monoacylglycerol O-acyltransferase 2	protein-coding	0.002703	0.391363	
chunk0046_375_1	chr12	63458076	63458589	+	0	NA	Intergenic	Intergenic	210242	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.003899	0.324903	
chunk0037_266_1	chr11	75642298	75642987	+	0	NA	intron (NM_207577, intron 1 of 2)	intron (NM_207577, intron 1 of 2)	25792	NM_033063	4135	Hs.585540	NM_033063	ENSG00000171533	MAP6	MAP6-N|MTAP6|N-STOP|STOP	microtubule associated protein 6	protein-coding	0.002903	0.376812	348(GACACACATTGTGCTT,+,0.00)
chunk0137_73_1	chr4	12861322	12862001	+	0	NA	Intergenic	L2c|LINE|L2	622704	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.001473	0.358824	
chunk0171_120_1	chr6	122621472	122621728	+	0	NA	intron (NM_181795, intron 1 of 4)	L2c|LINE|L2	11368	NM_181795	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.000000	0.377432	
chunk0051_141_1	chr12	115714287	115714486	+	0	NA	Intergenic	Intergenic	434268	NR_030351	693205		NR_030351	ENSG00000207967	MIR620	MIRN620|hsa-mir-620	microRNA 620	ncRNA	0.000000	0.360000	158(AGGTACTTTGTGTGCC,-,0.00),159(GGTACTTTGTGTGCCT,+,0.00)
chunk0174_272_1	chr6	161473167	161473427	+	0	NA	intron (NM_013988, intron 6 of 8)	intron (NM_013988, intron 6 of 8)	-199222	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.000000	0.279693	
chunk0194_451_1	chr8	92631423	92631749	+	0	NA	intron (NR_125827, intron 2 of 4)	intron (NR_125827, intron 2 of 4)	23908	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.012270	0.376147	
chunk0137_12_1	chr4	10694547	10694746	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-9884	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.010050	0.375000	
chunk0141_150_1	chr4	81486562	81486957	+	0	NA	Intergenic	MIR3|SINE|MIR	-14831	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.002532	0.446970	
chunk0156_42_1	chr5	102738189	102738482	+	0	NA	Intergenic	L1MD1|LINE|L1	-66871	NR_103756	285708	Hs.533011	NR_103753		LINC00491	-	long intergenic non-protein coding RNA 491	ncRNA	0.010239	0.397959	
chunk0087_292_1	chr18	38963824	38964385	+	0	NA	Intergenic	Intergenic	658071	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.007130	0.405694	
chunk0212_386_1	chrX	150570590	150570915	+	0	NA	intron (NM_000252, intron 1 of 14)	intron (NM_000252, intron 1 of 14)	2155	NM_000252	4534	Hs.655056	NM_000252	ENSG00000171100	MTM1	CNM|MTMX|XLMTM	myotubularin 1	protein-coding	0.006154	0.389571	
chunk0139_287_1	chr4	57278130	57278740	+	0	NA	Intergenic	Intergenic	-147437	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.004918	0.399345	
chunk0043_116_1	chr12	15496612	15497215	+	0	NA	intron (NM_030667, intron 2 of 26)	MIRc|SINE|MIR	-49431	NM_030671	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.003317	0.312914	
chunk0094_160_1	chr2	5315925	5316490	+	0	NA	Intergenic	Intergenic	374911	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.001770	0.416961	
chunk0144_438_1	chr4	141066635	141067082	+	0	NA	intron (NM_020724, intron 1 of 6)	Tigger3a|DNA|TcMar-Tigger	66604	NM_020724	57484	Hs.659104	NM_020724	ENSG00000170153	RNF150	-	ring finger protein 150	protein-coding	0.006711	0.308036	
chunk0150_15_1	chr5	30507160	30507540	+	0	NA	Intergenic	Intergenic	-686305	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.005263	0.307087	
chunk0097_437_1	chr2	63984328	63984566	+	0	NA	intron (NM_001005739, intron 1 of 22)	MIR|SINE|MIR	34633	NM_001005739	51542	Hs.48499	NM_016516	ENSG00000143952	VPS54	HCC8|PPP1R164|SLP-8p|VPS54L|WR|hVps54L	VPS54 subunit of GARP complex	protein-coding	0.004202	0.351464	
chunk0093_198_1	chr19	49374804	49375003	+	0	NA	exon (NM_001197302, exon 5 of 5)	exon (NM_001197302, exon 5 of 5)	11118	NM_014419	27120	Hs.515855	NM_014419	ENSG00000104901	DKKL1	CT34|SGY|SGY-1|SGY1	dickkopf like acrosomal protein 1	protein-coding	0.055276	0.635000	
chunk0019_358_1	chr1	229619790	229619991	+	0	NA	intron (NM_001025247, intron 1 of 3)	intron (NM_001025247, intron 1 of 3)	6157	NM_014409	27097	Hs.270621	NM_014409	ENSG00000135801	TAF5L	PAF65B	TATA-box binding protein associated factor 5 like	protein-coding	0.009950	0.504950	
chunk0153_117_1	chr5	68573691	68574157	+	0	NA	Intergenic	L1M7|LINE|L1	281356	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.002146	0.297645	
chunk0071_434_1	chr15	89893810	89894319	+	0	NA	non-coding (NR_037582, exon 1 of 6)	non-coding (NR_037582, exon 1 of 6)	321	NM_005829	10239	Hs.632161	NM_005829	ENSG00000157823	AP3S2	AP3S3|sigma3b	adaptor related protein complex 3 subunit sigma 2	protein-coding	0.082515	0.627451	
chunk0003_122_1	chr1	32496122	32496757	+	0	NA	Intergenic	Intergenic	31382	NM_001145720	728116	Hs.647658	NM_001145720	ENSG00000273274	ZBTB8B	ZNF916B	zinc finger and BTB domain containing 8B	protein-coding	0.011024	0.349057	
chunk0160_315_1	chr5	159189199	159189515	+	0	NA	intron (NM_144726, intron 3 of 10)	L1MB7|LINE|L1	18291	NM_001199382	153830	Hs.349306	NM_144726	ENSG00000145860	RNF145	-	ring finger protein 145	protein-coding	0.006329	0.350158	
chunk0092_31_1	chr19	19040699	19040935	+	0	NA	intron (NM_001199196, intron 2 of 8)	AluSx|SINE|Alu	7239	NM_001199196	93436	Hs.77876	NM_033415	ENSG00000105676	ARMC6	R30923_1	armadillo repeat containing 6	protein-coding	0.021186	0.502110	
chunk0206_283_1	chr9	124384382	124385115	+	0	NA	intron (NM_002799, intron 5 of 7)	intron (NM_002799, intron 5 of 7)	30725	NM_002799	5695	Hs.213470	NM_002799	ENSG00000136930	PSMB7	Z	proteasome subunit beta 7	protein-coding	0.006821	0.420981	
chunk0090_91_1	chr18	70669156	70669852	+	0	NA	Intergenic	MER52D|LTR|ERV1	-18647	NM_001278515									0.005747	0.576758	326(ATGAACAGCCTGATCT,-,0.00),327(TGAACAGCCTGATCTC,+,0.00)
chunk0190_34_1	chr8	29283186	29283385	+	0	NA	Intergenic	Intergenic	-20192	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.000000	0.455000	
chunk0026_158_1	chr10	62806961	62807688	+	0	NA	3' UTR (NM_032804, exon 1 of 1)	3' UTR (NM_032804, exon 1 of 1)	2568	NM_032804	84890	Hs.99821	NM_032804	ENSG00000181915	ADO	C10orf22	2-aminoethanethiol dioxygenase	protein-coding	0.006878	0.372253	
chunk0192_94_1	chr8	61386826	61387107	+	0	NA	intron (NM_173519, intron 3 of 5)	intron (NM_173519, intron 3 of 5)	99000	NM_173519	157807	Hs.591874	NM_173519	ENSG00000177182	CLVS1	C6orf212L|CRALBPL|RLBP1L1	clavesin 1	protein-coding	0.000000	0.333333	
chunk0020_354_1	chr1	239456316	239456550	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-172640	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.021368	0.391489	
chunk0128_446_1	chr3	115097584	115097925	+	0	NA	intron (NM_015642, intron 1 of 9)	intron (NM_015642, intron 1 of 9)	-2669	NR_046877	100874131		NR_046877	ENSG00000242767	ZBTB20-AS4	-	ZBTB20 antisense RNA 4	ncRNA	0.005865	0.397661	
chunk0156_247_1	chr5	108781574	108782100	+	0	NA	intron (NM_001308028, intron 2 of 17)	L1MC1|LINE|L1	32910	NM_001308028	2241	Hs.107418	NM_005246	ENSG00000151422	FER	PPP1R74|TYK3|p94-Fer	FER tyrosine kinase	protein-coding	0.001901	0.406072	278(AAGAACAGAATGTTCT,-,0.00),279(AGAACAGAATGTTCTA,+,0.00)
chunk0082_247_1	chr17	57429997	57430297	+	0	NA	intron (NM_138962, intron 6 of 13)	intron (NM_138962, intron 6 of 13)	93450	NR_110808	101927557	Hs.639984	NR_110808	ENSG00000266100	LOC101927557	-	uncharacterized LOC101927557	ncRNA	0.010000	0.418605	
chunk0170_267_1	chr6	113971026	113971584	+	0	NA	promoter-TSS (NR_033441)	promoter-TSS (NR_033441)	-110	NM_001527	3066	Hs.3352	NM_001527	ENSG00000196591	HDAC2	HD2|KDAC2|RPD3|YAF1	histone deacetylase 2	protein-coding	0.094982	0.694097	
chunk0170_276_1	chr6	114168175	114168519	+	0	NA	intron (NR_125845, intron 6 of 9)	intron (NR_125845, intron 6 of 9)	-105470	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.020349	0.472464	
chunk0025_120_1	chr10	51610688	51610963	+	0	NA	intron (NM_006258, intron 3 of 17)	L1PA8|LINE|L1	88770	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.003636	0.460145	
chunk0106_249_1	chr2	203464769	203465053	+	0	NA	intron (NM_213589, intron 4 of 13)	L1MC1|LINE|L1	70424	NM_213589	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.000000	0.326316	
chunk0075_63_1	chr16	47860664	47861004	+	0	NA	intron (NR_110650, intron 1 of 5)	MER6|DNA|TcMar-Tigger	2253	NR_110650	101927132	Hs.589404	NR_110650	ENSG00000261231	LINC02133	-	long intergenic non-protein coding RNA 2133	ncRNA	0.011765	0.457478	
chunk0020_428_1	chr1	241682788	241683445	+	0	NA	intron (NM_144625, intron 5 of 26)	intron (NM_144625, intron 5 of 26)	30838	NM_144625	128025	Hs.97527	NM_144625	ENSG00000162843	WDR64	-	WD repeat domain 64	protein-coding	0.006088	0.352584	
chunk0038_441_1	chr11	94708495	94709279	+	0	NA	Intergenic	Intergenic	-59455	NM_130847	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.006378	0.373248	
chunk0114_323_1	chr21	17441472	17441713	+	0	NA	intron (NR_037585, intron 1 of 3)	intron (NR_037585, intron 1 of 3)	2702	NR_037586	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.004149	0.433884	
chunk0103_119_1	chr2	161710363	161710562	+	0	NA	intron (NM_001178016, intron 2 of 26)	intron (NM_001178016, intron 2 of 26)	86127	NM_001178016	57282	Hs.333958	NM_022058	ENSG00000144290	SLC4A10	NBCn2|NCBE	solute carrier family 4 member 10	protein-coding	0.005025	0.265000	
chunk0032_453_1	chr10	133304391	133304596	+	0	NA	intron (NR_046330, intron 1 of 17)	Charlie4z|DNA|hAT-Charlie	-4396	NR_130127	118472	Hs.422113	NM_145806	ENSG00000198546	ZNF511	-	zinc finger protein 511	protein-coding	0.014634	0.427184	
chunk0111_386_1	chr20	34069562	34069804	+	0	NA	intron (NM_016732, intron 2 of 9)	intron (NM_016732, intron 2 of 9)	20564	NR_039911	100616434		NR_039911	ENSG00000264616	MIR4755	mir-4755	microRNA 4755	ncRNA	0.012397	0.473251	
chunk0005_414_1	chr1	62659510	62660083	+	0	NA	intron (NM_001272001, intron 2 of 47)	L1MDa|LINE|L1	28572	NM_033407	85440	Hs.744927	NM_033407	ENSG00000116641	DOCK7	EIEE23|ZIR2	dedicator of cytokinesis 7	protein-coding	0.003490	0.304878	
chunk0133_185_1	chr3	170240694	170241061	+	0	NA	intron (NM_002740, intron 2 of 17)	intron (NM_002740, intron 2 of 17)	18445	NM_002740	5584	Hs.478199	NM_002740	ENSG00000163558	PRKCI	DXS1179E|PKCI|nPKC-iota	protein kinase C iota	protein-coding	0.000000	0.320652	
chunk0212_20_1	chrY	9168442	9168977	+	0	NA	Intergenic	L1M4c|LINE|L1	154165	NR_001547	286557	Hs.567833	NR_001547		RBMY1A3P	-	RNA binding motif protein, Y-linked, family 1, member A3 pseudogene	pseudo	0.001869	0.326493	
chunk0170_345_1	chr6	116380952	116381287	+	0	NA	intron (NM_013352, intron 1 of 5)	intron (NM_013352, intron 1 of 5)	10172	NM_013352	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.005970	0.372024	
chunk0082_365_1	chr17	60275511	60275710	+	0	NA	intron (NM_032582, intron 5 of 33)	intron (NM_032582, intron 5 of 33)	-43965	NR_002999	677681		NR_002999	ENSG00000252577	SCARNA20	ACA66	small Cajal body-specific RNA 20	ncRNA	0.000000	0.365000	
chunk0072_315_1	chr15	98856501	98856716	+	0	NA	intron (NM_001291858, intron 2 of 20)	intron (NM_001291858, intron 2 of 20)	72182	NR_039864	100616432		NR_039864	ENSG00000264480	MIR4714	-	microRNA 4714	ncRNA	0.000000	0.337963	
chunk0006_310_1	chr1	71426484	71426926	+	0	NA	intron (NM_173808, intron 6 of 6)	intron (NM_173808, intron 6 of 6)	345381	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.002262	0.316027	
chunk0041_338_1	chr11	130592616	130593201	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-73827	NR_107019	102466873		NR_107019	ENSG00000274999	MIR8052	hsa-mir-8052	microRNA 8052	ncRNA	0.003419	0.486348	305(AGGTACAGTGTGTGCC,-,0.00),306(GGTACAGTGTGTGCCC,+,0.00)
chunk0018_217_1	chr1	219531666	219532252	+	0	NA	Intergenic	Tigger2a|DNA|TcMar-Tigger	356990	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.003413	0.327087	
chunk0144_361_1	chr4	139857213	139857515	+	0	NA	intron (NM_018717, intron 3 of 5)	intron (NM_018717, intron 3 of 5)	191596	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.009934	0.445545	
chunk0156_365_1	chr5	112630321	112630972	+	0	NA	non-coding (NR_104672, exon 3 of 3)	non-coding (NR_104672, exon 3 of 3)	2210	NR_104672	102467214	Hs.124613	NR_104672		LINC02200	-	long intergenic non-protein coding RNA 2200	ncRNA	0.004608	0.403374	
chunk0062_267_1	chr14	71910720	71911383	+	0	NA	Intergenic	Intergenic	-21049	NM_001204423	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.007541	0.406627	
chunk0022_400_1	chr10	18178956	18179562	+	0	NA	intron (NM_001167945, intron 2 of 13)	intron (NM_001167945, intron 2 of 13)	38446	NM_001167945	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.004950	0.367381	
chunk0117_111_1	chr22	17944279	17944758	+	0	NA	intron (NM_015241, intron 1 of 31)	intron (NM_015241, intron 1 of 31)	36443	NR_030378	693233		NR_030378	ENSG00000207780	MIR648	MIRN648|hsa-mir-648	microRNA 648	ncRNA	0.025052	0.529167	
chunk0062_276_1	chr14	72064707	72065012	+	0	NA	intron (NM_001204418, intron 2 of 16)	intron (NM_001204418, intron 2 of 16)	131790	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.006557	0.320261	
chunk0091_249_1	chr19	10764450	10765048	+	0	NA	intron (NM_001005360, intron 2 of 20)	L2|LINE|L2	-15505	NR_039903	100616425		NR_039903	ENSG00000265879	MIR4748	mir-4748	microRNA 4748	ncRNA	0.025084	0.585977	394(TGGAACGCCCTGTTCC,-,0.00),395(GGAACGCCCTGTTCCC,+,0.00)
chunk0084_320_1	chr17	80671144	80671491	+	0	NA	intron (NM_020761, intron 3 of 33)	intron (NM_020761, intron 3 of 33)	126492	NM_001163034	57521	Hs.133044	NM_020761	ENSG00000141564	RPTOR	KOG1|Mip1	regulatory associated protein of MTOR complex 1	protein-coding	0.028818	0.502874	
chunk0207_343_1	chr9	134703066	134703265	+	0	NA	intron (NM_000093, intron 4 of 65)	intron (NM_000093, intron 4 of 65)	61360	NM_000093	1289	Hs.210283	NM_000093	ENSG00000130635	COL5A1	EDSC|EDSCL1	collagen type V alpha 1 chain	protein-coding	0.020101	0.560000	
chunk0064_262_1	chr14	94709901	94710368	+	0	NA	Intergenic	L1ME3G|LINE|L1	60028	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.008565	0.382479	
chunk0157_387_1	chr5	124022974	124023405	+	0	NA	Intergenic	Charlie7|DNA|hAT-Charlie	415331	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.004640	0.340278	
chunk0199_457_1	chr9	14198673	14198962	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	-18015	NM_001282787	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.006920	0.458621	
chunk0045_192_1	chr12	47346646	47346965	+	0	NA	Intergenic	Intergenic	17464	NR_039715	100616478		NR_039715	ENSG00000264906	MIR4494	-	microRNA 4494	ncRNA	0.003135	0.418750	
chunk0107_389_1	chr2	223771464	223771862	+	0	NA	intron (NR_110906, intron 2 of 3)	intron (NR_110906, intron 2 of 3)	65939	NR_110905	130340	Hs.632555	NM_178814	ENSG00000152056	AP1S3	PSORS15	adaptor related protein complex 1 subunit sigma 3	protein-coding	0.007538	0.343358	
chunk0134_281_1	chr3	179713119	179713941	+	0	NA	intron (NM_003940, intron 6 of 20)	intron (NM_003940, intron 6 of 20)	60385	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.009732	0.385176	
chunk0177_453_1	chr7	28195447	28195742	+	0	NA	intron (NR_034097, intron 2 of 3)	MIR|SINE|MIR	-14776	NM_175061	221895	Hs.368944	NM_175061	ENSG00000153814	JAZF1	TIP27|ZNF802	JAZF zinc finger 1	protein-coding	0.023729	0.486486	
chunk0084_242_1	chr17	78780980	78781595	+	0	NA	intron (NM_004762, intron 1 of 12)	intron (NM_004762, intron 1 of 12)	1055	NM_004762	9267	Hs.191215	NM_004762	ENSG00000108669	CYTH1	B2-1|CYTOHESIN-1|D17S811E|PSCD1|SEC7	cytohesin 1	protein-coding	0.055285	0.506494	
chunk0143_147_1	chr4	109966735	109967207	+	0	NA	intron (NM_001963, intron 10 of 23)	L1PB4|LINE|L1	54087	NM_001178130	1950	Hs.419815	NM_001963	ENSG00000138798	EGF	HOMG4|URG	epidermal growth factor	protein-coding	0.002119	0.338266	
chunk0017_150_1	chr1	206748562	206749127	+	0	NA	Intergenic	MER91C|DNA|hAT-Tip100	23650	NM_000572	3586	Hs.193717	NM_000572	ENSG00000136634	IL10	CSIF|GVHDS|IL-10|IL10A|TGIF	interleukin 10	protein-coding	0.005310	0.420495	331(CAGCACACTTTGTTCC,-,0.00),332(AGCACACTTTGTTCCT,+,0.00)
chunk0115_234_1	chr21	27329142	27329757	+	0	NA	Intergenic	L2a|LINE|L2	-362329	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.008130	0.366883	
chunk0009_379_1	chr1	109960008	109960856	+	0	NA	Intergenic	Intergenic	-24333	NM_001242673	10768	Hs.743973	NM_006621	ENSG00000168710	AHCYL1	DCAL|IRBIT|PPP1R78|PRO0233|XPVKONA	adenosylhomocysteinase like 1	protein-coding	0.009434	0.431095	
chunk0108_437_1	chr2	238030354	238030911	+	0	NA	intron (NR_103498, intron 6 of 8)	intron (NR_103498, intron 6 of 8)	-30292	NM_016510	51540	Hs.731909	NM_016510	ENSG00000132330	SCLY	SCL|hSCL	selenocysteine lyase	protein-coding	0.014363	0.505376	
chunk0137_315_1	chr4	24518237	24518830	+	0	NA	Intergenic	Intergenic	1757	NR_030299	693158		NR_030299	ENSG00000207697	MIR573	MIRN573|hsa-mir-573|mir-573	microRNA 573	ncRNA	0.001686	0.336700	262(AAGTACATAATGTCCT,-,0.00),263(AGTACATAATGTCCTG,+,0.00)
chunk0196_61_1	chr8	102253435	102253642	+	0	NA	3' UTR (NM_001282873, exon 59 of 59)	3' UTR (NM_001282873, exon 59 of 59)	14087	NR_125415	101927221	Hs.492445	NR_125415	ENSG00000246263	UBR5-AS1	-	UBR5 antisense RNA 1	ncRNA	0.000000	0.307692	
chunk0146_217_1	chr4	161799672	161800152	+	0	NA	intron (NM_001128427, intron 4 of 15)	intron (NM_001128427, intron 4 of 15)	-222821	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.006250	0.334719	
chunk0209_26_1	chrX	35777327	35777868	+	0	NA	Intergenic	MER51E|LTR|ERV1	-20745	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.005545	0.413284	
chunk0047_20_1	chr12	65630426	65630989	+	0	NA	intron (NR_120432, intron 1 of 4)	L2c|LINE|L2	11665	NR_120432	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.005329	0.347518	
chunk0113_381_1	chr20	59925902	59926272	+	0	NA	intron (NM_014258, intron 1 of 43)	intron (NM_014258, intron 1 of 43)	6067	NM_014258	10388	Hs.202676	NM_014258	ENSG00000196074	SYCP2	SCP-2|SCP2	synaptonemal complex protein 2	protein-coding	0.000000	0.393531	
chunk0093_356_1	chr19	55519759	55520060	+	0	NA	TTS (NM_001144950)	TTS (NM_001144950)	16385	NM_001101401	646643	Hs.532676	NM_001101401	ENSG00000187550	SBK2	SGK069	SH3 domain binding kinase family member 2	protein-coding	0.019934	0.456954	
chunk0005_164_1	chr1	58529192	58529457	+	0	NA	intron (NM_145243, intron 6 of 8)	intron (NM_145243, intron 6 of 8)	17475	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.000000	0.323308	112(AATAACAGATTGTTCC,-,0.00),113(ATAACAGATTGTTCCT,+,0.00)
chunk0098_402_1	chr2	79832613	79832912	+	0	NA	intron (NM_004389, intron 3 of 17)	intron (NM_004389, intron 3 of 17)	33821	NR_107047	102465877		NR_107047	ENSG00000276917	MIR8080	hsa-mir-8080	microRNA 8080	ncRNA	0.010033	0.410000	
chunk0025_54_1	chr10	49504853	49505484	+	0	NA	intron (NM_000124, intron 6 of 20)	intron (NM_000124, intron 6 of 20)	19113	NM_170753	267004	Hs.49063	NM_170753	ENSG00000225830	PGBD3	-	piggyBac transposable element derived 3	protein-coding	0.006339	0.365506	
chunk0154_104_1	chr5	78399063	78399452	+	0	NA	intron (NM_004866, intron 2 of 8)	L1MC1|LINE|L1	-38716	NR_105014	728769	Hs.586193	NR_105014	ENSG00000245556	SCAMP1-AS1	-	SCAMP1 antisense RNA 1	ncRNA	0.000000	0.343590	
chunk0191_310_1	chr8	55225697	55226044	+	0	NA	intron (NM_052898, intron 1 of 2)	intron (NM_052898, intron 1 of 2)	123413	NM_052898	114786	Hs.130197	NM_052898	ENSG00000206579	XKR4	XRG4	XK related 4	protein-coding	0.011527	0.431034	
chunk0178_182_1	chr7	34235934	34236602	+	0	NA	Intergenic	Intergenic	331357	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.002994	0.458894	
chunk0039_75_1	chr11	96877989	96878213	+	0	NA	Intergenic	MER52A|LTR|ERV1	-371224	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.000000	0.528889	
chunk0024_30_1	chr10	33216630	33216859	+	0	NA	intron (NM_001244972, intron 8 of 16)	intron (NM_001244972, intron 8 of 16)	118161	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.008734	0.452174	125(GAGCACATTTAGTTCT,-,0.00),126(AGCACATTTAGTTCTT,+,0.00)
chunk0026_396_1	chr10	69744970	69745196	+	0	NA	Intergenic	MIRc|SINE|MIR	-56805	NM_001130103	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.008850	0.405286	
chunk0188_228_1	chr8	12865806	12866327	+	0	NA	Intergenic	Intergenic	-54665	NR_015383	340357	Hs.434302	NR_015383	ENSG00000254813	LOC340357	-	uncharacterized LOC340357	ncRNA	0.003839	0.417625	485(CTGAACATCTTGTCCT,-,0.00),486(TGAACATCTTGTCCTC,+,0.00)
chunk0145_253_1	chr4	148874199	148874669	+	0	NA	Intergenic	LTR33|LTR|ERVL	-279861	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.004255	0.392781	128(AAGTTCAGCATGTTCT,-,0.00),129(AGTTCAGCATGTTCTA,+,0.00)
chunk0181_420_1	chr7	90272201	90272861	+	0	NA	intron (NM_001039706, intron 8 of 22)	intron (NM_001039706, intron 8 of 22)	27357	NM_001039706	79846	Hs.521014	NM_024788	ENSG00000105792	CFAP69	C7orf63|FAP69|SPGF24	cilia and flagella associated protein 69	protein-coding	0.006061	0.363086	
chunk0028_417_1	chr10	93444041	93444767	+	0	NA	intron (NM_013451, intron 3 of 53)	L2a|LINE|L2	37913	NM_133337	26509	Hs.602086	NM_013451	ENSG00000138119	MYOF	FER1L3	myoferlin	protein-coding	0.009642	0.441541	
chunk0195_18_1	chr8	93102486	93102806	+	0	NA	Intergenic	Intergenic	64204	NM_001242668									0.006250	0.414330	
chunk0056_216_1	chr13	87780827	87781026	+	0	NA	Intergenic	Intergenic	29594	NR_104059	101930749	Hs.539610	NR_104059	ENSG00000223404	LINC00397	-	long intergenic non-protein coding RNA 397	ncRNA	0.000000	0.280000	49(AGAGACAGAATGTTCC,-,0.00),50(GAGACAGAATGTTCCT,+,0.00)
chunk0019_196_1	chr1	226732962	226733258	+	0	NA	intron (NM_002221, intron 2 of 7)	intron (NM_002221, intron 2 of 7)	6065	NM_002221	3707	Hs.528087	NM_002221	ENSG00000143772	ITPKB	IP3-3KB|IP3K|IP3K-B|IP3KB|PIG37	inositol-trisphosphate 3-kinase B	protein-coding	0.013514	0.538721	
chunk0053_146_1	chr13	30125725	30126131	+	0	NA	Intergenic	Intergenic	-17053	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.004926	0.425061	281(TTGTACAGAATGTTCC,-,0.00),282(TGTACAGAATGTTCCC,+,0.00)
chunk0160_12_1	chr5	148996470	148996890	+	0	NA	3' UTR (NM_024577, exon 17 of 17)	3' UTR (NM_024577, exon 17 of 17)	65729	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.011905	0.399050	
chunk0075_40_1	chr16	47058688	47059353	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	85005	NM_001201477	81831	Hs.645802	NM_018092	ENSG00000171208	NETO2	BTCL2|NEOT2	neuropilin and tolloid like 2	protein-coding	0.006015	0.445946	
chunk0118_375_1	chr22	36594980	36595478	+	0	NA	intron (NM_006078, intron 1 of 3)	intron (NM_006078, intron 1 of 3)	-65999	NM_003753	8664	Hs.55682	NM_003753	ENSG00000100353	EIF3D	EIF3S7|eIF3-p66|eIF3-zeta	eukaryotic translation initiation factor 3 subunit D	protein-coding	0.018072	0.539078	245(GGGAACACACTGTCCC,-,0.00),246(GGAACACACTGTCCCT,+,0.00)
chunk0089_133_1	chr18	58813571	58813944	+	0	NA	Intergenic	Intergenic	-49072	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.002681	0.355615	
chunk0072_73_1	chr15	90489665	90490579	+	0	NA	intron (NM_003870, intron 33 of 37)	intron (NM_003870, intron 33 of 37)	-39764	NM_022769	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.007659	0.419672	
chunk0188_309_1	chr8	17064621	17064820	+	0	NA	intron (NM_181723, intron 2 of 14)	Charlie1a|DNA|hAT-Charlie	37482	NM_181723	286097	Hs.403594	NM_181723	ENSG00000155970	MICU3	EFHA2	mitochondrial calcium uptake family member 3	protein-coding	0.000000	0.275000	
chunk0012_200_1	chr1	159958010	159958321	+	0	NA	Intergenic	ERV3-16A3_LTR|LTR|ERVL	-3059	NR_038849	100505633	Hs.445045	NR_038849	ENSG00000224259	LINC01133	-	long intergenic non-protein coding RNA 1133	ncRNA	0.022508	0.554487	
chunk0172_266_1	chr6	137546145	137546877	+	0	NA	Intergenic	L1ME4b|LINE|L1	-52117	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.010929	0.356071	
chunk0080_246_1	chr17	30291126	30291374	+	0	NA	intron (NM_000386, intron 2 of 11)	intron (NM_000386, intron 2 of 11)	916	NM_000386	642	Hs.371914	NM_000386	ENSG00000108578	BLMH	BH|BMH	bleomycin hydrolase	protein-coding	0.028226	0.489960	
chunk0033_63_1	chr11	13535495	13536195	+	0	NA	Intergenic	Intergenic	-39670	NM_001316352	5741	Hs.37045	NM_000315	ENSG00000152266	PTH	PTH1	parathyroid hormone	protein-coding	0.005714	0.378031	
chunk0009_79_1	chr1	101003934	101004549	+	0	NA	intron (NM_015958, intron 4 of 7)	intron (NM_015958, intron 4 of 7)	21565	NM_001077395	51611	Hs.440776	NM_015958	ENSG00000117543	DPH5	AD-018|CGI-30|HSPC143|NPD015	diphthamide biosynthesis 5	protein-coding	0.001626	0.347403	
chunk0206_31_1	chr9	116419165	116419445	+	0	NA	Intergenic	Intergenic	-18699	NR_103711	493913	Hs.728832	NR_103711	ENSG00000256040	PAPPA-AS1	DIPAS|NCRNA00156|PAPPA-AS|PAPPAAS|PAPPAS|TAF2C2|TAF4B|TAFII105	PAPPA antisense RNA 1	ncRNA	0.003571	0.508897	
chunk0182_216_1	chr7	96349379	96350071	+	0	NA	Intergenic	MER70B|LTR|ERVL	-27578	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.005780	0.453102	344(TGGAACAGGATGTTCT,-,0.00),345(GGAACAGGATGTTCTA,+,0.00)
chunk0092_283_1	chr19	33700184	33700498	+	0	NA	intron (NM_022467, intron 2 of 3)	intron (NM_022467, intron 2 of 3)	15813	NM_022467	64377	Hs.165724	NM_022467	ENSG00000124302	CHST8	GALNAC4ST1|GalNAc4ST|PSS3	carbohydrate sulfotransferase 8	protein-coding	0.015924	0.473016	
chunk0166_45_1	chr6	42354707	42354988	+	0	NA	intron (NM_001297573, intron 3 of 17)	L1M5|LINE|L1	97204	NM_033502	55809	Hs.485392	NM_018415	ENSG00000124496	TRERF1	BCAR2|HSA277276|RAPA|TREP132|TReP-132|dJ139D8.5	transcriptional regulating factor 1	protein-coding	0.003559	0.333333	
chunk0047_386_1	chr12	75404600	75404816	+	0	NA	intron (NR_072995, intron 2 of 6)	MER31-int|LTR|ERV1	13638	NR_072995	144321	Hs.406728	NM_152436	ENSG00000180481	GLIPR1L2	-	GLIPR1 like 2	protein-coding	0.000000	0.267281	
chunk0139_90_1	chr4	49574025	49574224	+	0	NA	Intergenic	THE1D-int|LTR|ERVL-MaLR	587482	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.000000	0.520000	
chunk0072_12_1	chr16	401680	402242	+	0	NA	5' UTR (NM_020664, exon 1 of 9)	5' UTR (NM_020664, exon 1 of 9)	103	NM_020664	26063	Hs.628831	NM_020664	ENSG00000242612	DECR2	PDCR|SDR17C1	2,4-dienoyl-CoA reductase 2	protein-coding	0.122776	0.721137	
chunk0080_375_1	chr17	33579210	33579644	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-45667	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.020737	0.480460	
chunk0118_246_1	chr22	32779660	32780111	+	0	NA	intron (NM_003490, intron 5 of 12)	intron (NM_003490, intron 5 of 12)	-20931	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.017738	0.506637	
chunk0010_309_1	chr1	118027681	118028205	+	0	NA	intron (NM_206996, intron 26 of 48)	MIR|SINE|MIR	98194	NM_006784	10885	Hs.310809	NM_006784	ENSG00000065183	WDR3	DIP2|UTP12	WD repeat domain 3	protein-coding	0.001908	0.363810	
chunk0117_338_1	chr21	43958968	43959257	+	0	NA	intron (NM_001037553, intron 1 of 8)	(GT)n|Simple_repeat|Simple_repeat	33714	NM_001037553	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.020761	0.524138	
chunk0149_245_1	chr5	23564216	23564763	+	0	NA	Intergenic	L1MA10|LINE|L1	56834	NM_001310214	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.007313	0.366788	
chunk0010_228_1	chr1	116329561	116329897	+	0	NA	Intergenic	Intergenic	-43444	NM_000701	476	Hs.371889	NM_000701	ENSG00000163399	ATP1A1	CMT2DD|HOMGSMR2	ATPase Na+/K+ transporting subunit alpha 1	protein-coding	0.008929	0.519288	165(GGGCACTCGCTGTTCC,-,0.00),166(GGCACTCGCTGTTCCT,+,0.00)
chunk0060_277_1	chr14	50389939	50390191	+	0	NA	intron (NM_001282236, intron 2 of 8)	intron (NM_001282236, intron 2 of 8)	5859	NM_004196	8814	Hs.280881	NM_004196	ENSG00000100490	CDKL1	KKIALRE|P42	cyclin dependent kinase like 1	protein-coding	0.007937	0.383399	
chunk0160_73_1	chr5	149878413	149878884	+	0	NA	intron (NM_000440, intron 17 of 21)	L1ME4b|LINE|L1	54329	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.014862	0.417373	
chunk0029_224_1	chr10	102302700	102302946	+	0	NA	intron (NM_001199378, intron 3 of 39)	MER20|DNA|hAT-Charlie	57325	NM_001199379	8729	Hs.290243	NM_004193	ENSG00000107862	GBF1	ARF1GEF	golgi brefeldin A resistant guanine nucleotide exchange factor 1	protein-coding	0.008130	0.433198	213(GGTACAAAATGTACAT,+,0.00)
chunk0041_111_1	chr11	124903846	124904112	+	0	NA	Intergenic	L1M5|LINE|L1	-6044	NM_001301088	54538	Hs.524121	NM_019055	ENSG00000154133	ROBO4	ECSM4|MRB	roundabout guidance receptor 4	protein-coding	0.000000	0.277154	
chunk0020_282_1	chr1	236611800	236611999	+	0	NA	Intergenic	L1MEc|LINE|L1	-7358	NM_018072	55127	Hs.708114	NM_018072	ENSG00000119285	HEATR1	BAP28|UTP10	HEAT repeat containing 1	protein-coding	0.005025	0.495000	
chunk0043_103_1	chr12	14903771	14904130	+	0	NA	Intergenic	MIR|SINE|MIR	-18031	NM_001190839	4256	Hs.365706	NM_000900	ENSG00000111341	MGP	GIG36|MGLAP|NTI	matrix Gla protein	protein-coding	0.008357	0.388889	
chunk0175_223_1	chr7	6259020	6259635	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	13284	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.008130	0.337662	
chunk0020_422_1	chr1	241609960	241610590	+	0	NA	intron (NM_014322, intron 1 of 3)	L2c|LINE|L2	25655	NM_001821	1122	Hs.654545	NM_001821	ENSG00000203668	CHML	REP2	CHM like Rab escort protein	protein-coding	0.011111	0.391442	
chunk0015_180_1	chr1	187156832	187157162	+	0	NA	intron (NR_126347, intron 1 of 3)	L1MC1|LINE|L1	64155	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.000000	0.329305	
chunk0063_76_1	chr14	77600559	77600778	+	0	NA	intron (NM_004863, intron 1 of 11)	intron (NM_004863, intron 1 of 11)	16099	NM_004863	9517	Hs.435661	NM_004863	ENSG00000100596	SPTLC2	HSN1C|LCB2|LCB2A|NSAN1C|SPT2|hLCB2a	serine palmitoyltransferase long chain base subunit 2	protein-coding	0.009132	0.300000	
chunk0095_103_1	chr2	15360072	15360609	+	0	NA	intron (NR_052013, intron 32 of 50)	(A)n|Simple_repeat|Simple_repeat	201008	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.005587	0.382900	
chunk0209_385_1	chrX	54683537	54683736	+	0	NA	Intergenic	Intergenic	114604	NM_198510	347365	Hs.454272	NM_198510	ENSG00000102313	ITIH6	ITIH5L|UNQ6369|dJ14O9.1	inter-alpha-trypsin inhibitor heavy chain family member 6	protein-coding	0.005025	0.330000	
chunk0080_307_1	chr17	31803523	31804093	+	0	NA	Intergenic	Intergenic	55499	NM_018405	55352	Hs.462729	NM_018405	ENSG00000172301	COPRS	C17orf79|COPR5|HSA272196|TTP1	coordinator of PRMT5 and differentiation stimulator	protein-coding	0.017544	0.446585	
chunk0041_274_1	chr11	129286623	129287205	+	0	NA	Intergenic	Intergenic	-89072	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.012027	0.404803	
chunk0026_152_1	chr10	62441966	62442525	+	0	NA	intron (NM_199450, intron 3 of 4)	intron (NM_199450, intron 3 of 4)	-67118	NR_104162	283045		NR_104162		LOC283045	-	uncharacterized LOC283045	ncRNA	0.010733	0.412500	177(GGAAACAGAGTGTACT,-,0.00),178(GAAACAGAGTGTACTT,+,0.00)
chunk0022_449_1	chr10	19888004	19888728	+	0	NA	intron (NM_032812, intron 1 of 13)	intron (NM_032812, intron 1 of 13)	71923	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.006906	0.406897	
chunk0034_89_1	chr11	27416548	27417387	+	0	NA	intron (NM_018490, intron 1 of 17)	intron (NM_018490, intron 1 of 17)	-53719	NM_080654	91057	Hs.143733	NM_030771	ENSG00000109881	CCDC34	L15|NY-REN-41|RAMA3	coiled-coil domain containing 34	protein-coding	0.002384	0.345238	
chunk0057_91_1	chr13	98792372	98792588	+	0	NA	Intergenic	Intergenic	-39604	NR_046663	100874096	Hs.578066	NR_046663	ENSG00000229918	DOCK9-AS1	-	DOCK9 antisense RNA 1	ncRNA	0.023148	0.460829	
chunk0019_352_1	chr1	229553879	229554144	+	0	NA	intron (NM_012089, intron 1 of 12)	intron (NM_012089, intron 1 of 12)	4684	NM_012089	23456	Hs.17614	NM_012089	ENSG00000135776	ABCB10	EST20237|M-ABC2|MTABC2	ATP binding cassette subfamily B member 10	protein-coding	0.011321	0.421053	
chunk0120_419_1	chr3	12979275	12980030	+	0	NA	intron (NM_001134382, intron 1 of 13)	L1ME4b|LINE|L1	-11954	NM_014869	9922	Hs.475506	NM_014869	ENSG00000144711	IQSEC1	ARF-GEP100|ARFGEP100|BRAG2|GEP100	IQ motif and Sec7 domain 1	protein-coding	0.027815	0.497354	308(AGCTCACTGTGTACCC,+,0.00)
chunk0003_128_1	chr1	32650414	32650613	+	0	NA	promoter-TSS (NM_005610)	promoter-TSS (NM_005610)	77	NM_178547	339487	Hs.655921	NM_178547	ENSG00000176261	ZBTB8OS	ARCH|ARCH2	zinc finger and BTB domain containing 8 opposite strand	protein-coding	0.050251	0.510000	
chunk0035_237_1	chr11	45934661	45935087	+	0	NA	intron (NM_016621, intron 17 of 17)	intron (NM_016621, intron 17 of 17)	12198	NM_001300721	120071	Hs.86543	NM_152312	ENSG00000165905	LARGE2	GYLTL1B|PP5656	LARGE xylosyl- and glucuronyltransferase 2	protein-coding	0.007042	0.526932	
chunk0031_321_1	chr10	129203438	129203669	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-263631	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.008658	0.375000	126(GGTTCACAATGTCCCC,+,0.00)
chunk0074_7_1	chr16	19613282	19613559	+	0	NA	intron (NM_001300743, intron 12 of 27)	MLT1K|LTR|ERVL-MaLR	58005	NM_001300743	57020	Hs.654964	NM_020314	ENSG00000103544	VPS35L	C16orf62	VPS35 endosomal protein sorting factor like	protein-coding	0.000000	0.460432	
chunk0092_423_1	chr19	38060281	38060504	+	0	NA	intron (NM_015073, intron 2 of 21)	MER113B|DNA|hAT-Charlie	153171	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.013453	0.361607	
chunk0083_74_1	chr17	64128551	64129494	+	0	NA	intron (NM_001433, intron 1 of 21)	intron (NM_001433, intron 1 of 21)	1120	NM_001433	2081	Hs.133982	NM_001433	ENSG00000178607	ERN1	IRE1|IRE1P|IRE1a|hIRE1p	endoplasmic reticulum to nucleus signaling 1	protein-coding	0.018028	0.420551	
chunk0130_66_1	chr3	129881152	129881677	+	0	NA	promoter-TSS (NM_001017395)	promoter-TSS (NM_001017395)	-855	NM_001017395	23023	Hs.477547	NM_015008	ENSG00000172765	TMCC1	-	transmembrane and coiled-coil domain family 1	protein-coding	0.007619	0.336502	
chunk0155_357_1	chr5	97229439	97230060	+	0	NA	Intergenic	Intergenic	-46448	NM_001159749	55781	Hs.27021	NM_018343	ENSG00000058729	RIOK2	RIO2	RIO kinase 2	protein-coding	0.009662	0.376206	
chunk0041_332_1	chr11	130429764	130430451	+	0	NA	Intergenic	Intergenic	-1463	NM_007037	11095	Hs.271605	NM_007037	ENSG00000134917	ADAMTS8	ADAM-TS8|METH2	ADAM metallopeptidase with thrombospondin type 1 motif 8	protein-coding	0.007278	0.476744	405(TGGGACATCCTGTACA,-,0.00),406(GGGACATCCTGTACAG,+,0.00),426(TGGGACAGTCTGACCT,-,0.00),427(GGGACAGTCTGACCTG,+,0.00)
chunk0159_263_1	chr5	142221277	142221731	+	0	NA	Intergenic	L2a|LINE|L2	96818	NR_131221	100642175	Hs.684549	NR_131221		SPRY4-IT1	SPRIGHTLY	SPRY4 intronic transcript 1	ncRNA	0.015419	0.468132	426(GGGAACAGCAAGTGCA,-,0.00),427(GGAACAGCAAGTGCAA,+,0.00)
chunk0105_359_1	chr2	191866981	191867394	+	0	NA	Intergenic	Intergenic	-19907	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.004843	0.422705	
chunk0193_253_1	chr8	76935733	76936220	+	0	NA	Intergenic	Intergenic	30874	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.004107	0.348361	
chunk0172_205_1	chr6	136699541	136699743	+	0	NA	intron (NM_005923, intron 3 of 29)	intron (NM_005923, intron 3 of 29)	70528	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.014851	0.512315	
chunk0210_34_1	chrX	67746952	67747619	+	0	NA	Intergenic	Intergenic	178444	NM_001011645	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.005997	0.462575	
chunk0212_94_1	chrY	12740193	12740637	+	0	NA	intron (NM_004654, intron 12 of 45)	L1ME3B|LINE|L1	39184	NM_004654	8287	Hs.598540	NM_004654	ENSG00000114374	USP9Y	DFFRY|SPGFY2	ubiquitin specific peptidase 9 Y-linked	protein-coding	0.004505	0.337079	
chunk0181_280_1	chr7	86658803	86659419	+	0	NA	intron (NM_000840, intron 1 of 5)	intron (NM_000840, intron 1 of 5)	15197	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.008117	0.317666	
chunk0078_370_1	chr16	87438303	87438502	+	0	NA	intron (NM_015144, intron 2 of 12)	Kanga1d|DNA|TcMar-Tc2	46207	NM_022818	81631	Hs.356061	NM_022818	ENSG00000140941	MAP1LC3B	ATG8F|LC3B|MAP1A/1BLC3|MAP1LC3B-a	microtubule associated protein 1 light chain 3 beta	protein-coding	0.010050	0.370000	
chunk0126_293_1	chr3	80438488	80438937	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-555156	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.006682	0.417778	
chunk0045_356_1	chr12	51873037	51873762	+	0	NA	Intergenic	Intergenic	-14610	NM_001130015	341405	Hs.433492	NM_182608	ENSG00000167612	ANKRD33	C12orf7|PANKY	ankyrin repeat domain 33	protein-coding	0.012414	0.493113	
chunk0208_150_1	chrX	16115341	16116059	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-7601	NM_005314	2925	Hs.567282	NM_005314	ENSG00000126010	GRPR	BB2|BB2R	gastrin releasing peptide receptor	protein-coding	0.004178	0.349096	432(AGGCACACTGTGGTCC,-,0.00)
chunk0061_102_1	chr14	57611650	57612070	+	0	NA	intron (NM_001306087, intron 1 of 7)	L1MEc|LINE|L1	-117997	NM_018168	55195	Hs.659706	NM_018168	ENSG00000100557	CCDC198	C14orf105	coiled-coil domain containing 198	protein-coding	0.002381	0.446556	
chunk0126_4_1	chr3	73422721	73423013	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	11129	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.006849	0.389078	
chunk0122_179_1	chr3	32623711	32624127	+	0	NA	Intergenic	L1MB5|LINE|L1	-53045	NM_016141	51143	Hs.529495	NM_016141	ENSG00000144635	DYNC1LI1	DLC-A|DNCLI1|LIC1	dynein cytoplasmic 1 light intermediate chain 1	protein-coding	0.004808	0.333333	
chunk0204_230_1	chr9	97645744	97646283	+	0	NA	intron (NM_002486, intron 6 of 22)	MER5A|DNA|hAT-Charlie	-12333	NM_139246	158427	Hs.723236	NM_139246	ENSG00000136925	TSTD2	C9orf97	thiosulfate sulfurtransferase like domain containing 2	protein-coding	0.000000	0.351852	
chunk0195_147_1	chr8	95167044	95167390	+	0	NA	Intergenic	Intergenic	33496	NM_024613	79666	Hs.29724	NM_024613	ENSG00000175895	PLEKHF2	EAPF|PHAFIN2|ZFYVE18	pleckstrin homology and FYVE domain containing 2	protein-coding	0.011561	0.443804	
chunk0070_81_1	chr15	70094670	70095010	+	0	NA	promoter-TSS (NM_001282982)	promoter-TSS (NM_001282982)	-55	NM_001282982	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.023529	0.466276	
chunk0180_343_1	chr7	73509344	73509772	+	0	NA	intron (NM_032408, intron 2 of 19)	AluJo|SINE|Alu	12727	NM_032408	9031	Hs.743372	NM_023005	ENSG00000009954	BAZ1B	WBSCR10|WBSCR9|WSTF	bromodomain adjacent to zinc finger domain 1B	protein-coding	0.014019	0.456876	
chunk0072_363_1	chr15	99852947	99853591	+	0	NA	Intergenic	L1MC3|LINE|L1	-46342	NR_003260	196968	Hs.567763	NM_194295	ENSG00000182397	DNM1P46	C15orf51|DNM1DN14.2|DNM1DN14@	dynamin 1 pseudogene 46	pseudo	0.007764	0.325581	
chunk0192_386_1	chr8	68699233	68699708	+	0	NA	intron (NM_052958, intron 8 of 13)	intron (NM_052958, intron 8 of 13)	-367979	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.004211	0.428571	
chunk0082_313_1	chr17	59206442	59206654	+	0	NA	3' UTR (NM_018304, exon 10 of 10)	3' UTR (NM_018304, exon 10 of 10)	-3462	NM_018149	55181	Hs.7296	NM_018149	ENSG00000167447	SMG8	C17orf71	SMG8 nonsense mediated mRNA decay factor	protein-coding	0.004717	0.366197	
chunk0059_305_1	chr14	36227790	36228185	+	0	NA	Intergenic	Intergenic	-51336	NR_049735	100886964	Hs.742592	NR_049735		PTCSC3	-	papillary thyroid carcinoma susceptibility candidate 3	ncRNA	0.005063	0.373737	
chunk0172_84_1	chr6	134502796	134503097	+	0	NA	non-coding (NR_038219, exon 5 of 5)	non-coding (NR_038219, exon 5 of 5)	-24049	NR_125852	101928231	Hs.634168	NR_125852		CT69	-	cancer/testis associated transcript 69	ncRNA	0.019934	0.519868	
chunk0080_86_1	chr17	25920082	25920333	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	1373789	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.007968	0.400794	
chunk0012_351_1	chr1	162696465	162696698	+	0	NA	intron (NM_006182, intron 2 of 17)	intron (NM_006182, intron 2 of 17)	64143	NM_006182	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.012876	0.529915	
chunk0147_283_1	chr4	184306415	184306906	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	47317	NR_040108	728175	Hs.590107	NR_040108	ENSG00000180712	LINC02363	-	long intergenic non-protein coding RNA 2363	ncRNA	0.002037	0.363821	
chunk0018_343_1	chr1	221549092	221549291	+	0	NA	Intergenic	Intergenic	187709	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.015075	0.500000	
chunk0134_421_1	chr3	183302157	183302618	+	0	NA	intron (NM_015078, intron 10 of 29)	intron (NM_015078, intron 10 of 29)	49143	NM_032047	84002	Hs.718506	NM_032047	ENSG00000176597	B3GNT5	B3GN-T5|beta3Gn-T5	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	protein-coding	0.017354	0.495671	
chunk0184_69_1	chr7	112553134	112553373	+	0	NA	Intergenic	(ACAGTTTT)n|Simple_repeat|Simple_repeat	-64812	NR_110159	100996249	Hs.561749	NR_110159		LOC100996249	-	uncharacterized LOC100996249	ncRNA	0.000000	0.312500	
chunk0093_192_1	chr19	49165073	49165706	+	0	NA	intron (NM_017636, intron 2 of 24)	MER113|DNA|hAT-Charlie	7630	NM_001195227	54795	Hs.467101	NM_017636	ENSG00000130529	TRPM4	LTrpC4|PFHB1B|TRPM4B|hTRPM4	transient receptor potential cation channel subfamily M member 4	protein-coding	0.037915	0.482650	
chunk0077_67_1	chr16	76929591	76929822	+	0	NA	Intergenic	Intergenic	60770	NR_039870	100616172		NR_039870	ENSG00000266426	MIR4719	-	microRNA 4719	ncRNA	0.004329	0.370690	
chunk0060_84_1	chr14	42192851	42193389	+	0	NA	Intergenic	LTR16C|LTR|ERVL	585559	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.007435	0.382189	
chunk0024_426_1	chr10	46035152	46035579	+	0	NA	intron (NM_138634, intron 2 of 2)	L1MB4|LINE|L1	-4651	NM_001145260	8031	Hs.643658	NM_005437	ENSG00000266412	NCOA4	ARA70|ELE1|PTC3|RFG	nuclear receptor coactivator 4	protein-coding	0.002342	0.373832	
chunk0087_298_1	chr18	39011071	39011430	+	0	NA	Intergenic	Intergenic	610925	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.011142	0.477778	
chunk0111_94_1	chr20	23586121	23587013	+	0	NA	Intergenic	Intergenic	-17818	NM_080610	128821	Hs.121554	NM_080610	ENSG00000101435	CST9L	CTES7B|bA218C14.1	cystatin 9 like	protein-coding	0.010090	0.550952	
chunk0147_125_1	chr4	174317545	174317898	+	0	NA	3' UTR (NM_001040157, exon 12 of 12)	3' UTR (NM_001040157, exon 12 of 12)	-33470	NM_012180	26269	Hs.76917	NM_012180	ENSG00000164117	FBXO8	DC10|FBS|FBX8	F-box protein 8	protein-coding	0.000000	0.327684	
chunk0144_432_1	chr4	140894332	140894903	+	0	NA	intron (NM_020724, intron 6 of 6)	intron (NM_020724, intron 6 of 6)	-138300	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.008757	0.365385	
chunk0004_85_1	chr1	43741283	43741690	+	0	NA	intron (NM_001270465, intron 2 of 7)	intron (NM_001270465, intron 2 of 7)	-14143	NR_125986	101929592		NR_125986	ENSG00000229444	LOC101929592	-	uncharacterized LOC101929592	ncRNA	0.007371	0.384804	
chunk0174_278_1	chr6	161696861	161697131	+	0	NA	intron (NM_013988, intron 4 of 8)	intron (NM_013988, intron 4 of 8)	-422921	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.007407	0.435424	
chunk0160_363_1	chr5	161114508	161115043	+	0	NA	Intergenic	Intergenic	-176149	NR_027111	285629	Hs.554279	NR_027111	ENSG00000253417	LINC02159	-	long intergenic non-protein coding RNA 2159	ncRNA	0.000000	0.347015	
chunk0011_31_1	chr1	143222147	143222473	+	0	NA	Intergenic	Intergenic	200282	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.049080	0.366972	
chunk0162_81_1	chr6	1862047	1862435	+	0	NA	intron (NM_001253846, intron 7 of 10)	intron (NM_001253846, intron 7 of 10)	251795	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.010309	0.359897	
chunk0142_437_1	chr4	105182247	105182646	+	0	NA	intron (NR_126420, intron 2 of 5)	MamRep38|DNA|hAT	35761	NM_001127208	54790	Hs.367639	NM_017628	ENSG00000168769	TET2	KIAA1546|MDS	tet methylcytosine dioxygenase 2	protein-coding	0.007519	0.372500	
chunk0112_310_1	chr20	44508548	44508937	+	0	NA	intron (NM_006811, intron 5 of 9)	L1ME3E|LINE|L1	13343	NM_006811	10955	Hs.272168	NM_006811	ENSG00000132824	SERINC3	AIGP1|DIFF33|SBBI99|TDE|TDE1|TMS-1	serine incorporator 3	protein-coding	0.002571	0.358974	
chunk0032_155_1	chr11	4923692	4924021	+	0	NA	exon (NM_001005237, exon 1 of 1)	exon (NM_001005237, exon 1 of 1)	483	NM_001005237	79324	Hs.554541	NM_001005237	ENSG00000278870	OR51G1	OR11-29|OR51G3P	olfactory receptor family 51 subfamily G member 1 (gene/pseudogene)	protein-coding	0.018237	0.524242	
chunk0010_340_1	chr1	118504850	118505346	+	0	NA	Intergenic	Intergenic	-319873	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.008065	0.360161	183(GGAACAAATAGTGCTT,+,0.00)
chunk0082_306_1	chr17	58960137	58960336	+	0	NA	intron (NR_048561, intron 2 of 5)	MLT1K|LTR|ERVL-MaLR	146669	NM_001005207	4591	Hs.579079	NM_015294	ENSG00000108395	TRIM37	MUL|POB1|TEF3	tripartite motif containing 37	protein-coding	0.000000	0.430000	
chunk0078_269_1	chr17	7844078	7844277	+	0	NA	intron (NM_001080424, intron 1 of 21)	CpG	4260	NM_001080424	23135	Hs.223678	NM_001080424	ENSG00000132510	KDM6B	JMJD3	lysine demethylase 6B	protein-coding	0.110553	0.695000	
chunk0207_217_1	chr9	131617888	131618427	+	0	NA	intron (NM_198679, intron 11 of 23)	MLT1H|LTR|ERVL-MaLR	-86882	NM_001261451	83549	Hs.9597	NM_031432	ENSG00000130717	UCK1	URK1	uridine-cytidine kinase 1	protein-coding	0.009276	0.516667	
chunk0038_19_1	chr11	80939591	80939966	+	0	NA	Intergenic	Intergenic	-176975	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.327128	
chunk0124_21_1	chr3	51926833	51927146	+	0	NA	Intergenic	L1ME2|LINE|L1	14952	NM_004704	9136	Hs.153768	NM_004704	ENSG00000114767	RRP9	RNU3IP2|U3-55K	ribosomal RNA processing 9, U3 small nucleolar RNA binding protein	protein-coding	0.012780	0.366242	
chunk0187_455_1	chr7	159227114	159227665	+	0	NA	Intergenic	Intergenic	-82432	NM_003382	7434	Hs.585052	NM_003382	ENSG00000106018	VIPR2	C16DUPq36.3|DUP7q36.3|PACAP-R-3|PACAP-R3|VIP-R-2|VPAC2|VPAC2R|VPCAP2R	vasoactive intestinal peptide receptor 2	protein-coding	0.007260	0.440217	
chunk0137_363_1	chr4	26082422	26082987	+	0	NA	Intergenic	Intergenic	168512	NM_001145432	389203	Hs.479386	NM_001145432	ENSG00000250317	SMIM20	C4orf52|MITRAC7|PNX	small integral membrane protein 20	protein-coding	0.012389	0.378092	
chunk0168_360_1	chr6	93357046	93357433	+	0	NA	intron (NM_004440, intron 4 of 16)	intron (NM_004440, intron 4 of 16)	62343	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.005168	0.327320	
chunk0154_39_1	chr5	77103310	77103919	+	0	NA	intron (NR_024398, intron 2 of 3)	intron (NR_024398, intron 2 of 3)	-16409	NM_032367	84327	Hs.584988	NM_032367	ENSG00000132846	ZBED3	-	zinc finger BED-type containing 3	protein-coding	0.006568	0.426230	291(CAGAACTCTGTGTTCC,-,0.00),292(AGAACTCTGTGTTCCA,+,0.00),313(AGGCACTGTCTGTTCT,-,0.00),314(GGCACTGTCTGTTCTG,+,0.00)
chunk0156_306_1	chr5	110588526	110588995	+	0	NA	intron (NM_001039763, intron 10 of 13)	L3|LINE|CR1	-74845	NR_031644	100302159		NR_031644	ENSG00000221436	MIR548F3	MIR548F-3|MIRN548F3|hsa-mir-548f-3	microRNA 548f-3	ncRNA	0.006397	0.391489	
chunk0037_84_1	chr11	71454775	71455097	+	0	NA	intron (NM_018161, intron 1 of 20)	intron (NM_018161, intron 1 of 20)	1765	NM_018161	55191	Hs.556986	NM_018161	ENSG00000172890	NADSYN1	-	NAD synthetase 1	protein-coding	0.012422	0.464396	
chunk0020_288_1	chr1	237068384	237068583	+	0	NA	intron (NM_001035, intron 1 of 104)	intron (NM_001035, intron 1 of 104)	26081	NM_001035	6262	Hs.109514	NM_001035	ENSG00000198626	RYR2	ARVC2|ARVD2|RYR-2|RyR|VTSIP	ryanodine receptor 2	protein-coding	0.005025	0.385000	
chunk0200_153_1	chr9	18280460	18280659	+	0	NA	Intergenic	L1M4|LINE|L1	-193522	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.005025	0.345000	63(GTGAACATGGTGTGCC,-,0.00),64(TGAACATGGTGTGCCT,+,0.00)
chunk0046_86_1	chr12	56468403	56468694	+	0	NA	promoter-TSS (NM_207344)	promoter-TSS (NM_207344)	31	NM_207344	283377	Hs.128676	NM_207344	ENSG00000176422	SPRYD4	-	SPRY domain containing 4	protein-coding	0.089347	0.613014	
chunk0132_67_1	chr3	155176087	155176413	+	0	NA	intron (NM_000902, intron 22 of 22)	intron (NM_000902, intron 22 of 22)	-64695	NR_125399	101928190	Hs.121410	NR_125399	ENSG00000241336	LINC01487	-	long intergenic non-protein coding RNA 1487	ncRNA	0.000000	0.318043	
chunk0073_237_1	chr16	11497590	11497789	+	0	NA	Intergenic	Intergenic	32429	NR_110907	101927131	Hs.569654	NR_110907	ENSG00000262999	LOC101927131	-	uncharacterized LOC101927131	ncRNA	0.010050	0.600000	
chunk0206_423_1	chr9	127574450	127575042	+	0	NA	intron (NM_001035534, intron 1 of 13)	intron (NM_001035534, intron 1 of 13)	4261	NM_001035534	64855	Hs.522401	NM_022833	ENSG00000136830	NIBAN2	C9orf88|FAM129B|MEG-3|MINERVA|OC58|bA356B19.6	niban apoptosis regulator 2	protein-coding	0.013514	0.534570	
chunk0012_249_1	chr1	161132995	161133294	+	0	NA	promoter-TSS (NM_001039711)	promoter-TSS (NM_001039711)	-456	NM_032998	9191	Hs.744092	NM_004216	ENSG00000158796	DEDD	CASP8IP1|DEDD1|DEFT|FLDED1|KE05	death effector domain containing	protein-coding	0.056856	0.550000	
chunk0188_340_1	chr8	17794620	17795407	+	0	NA	intron (NM_001001924, intron 1 of 14)	intron (NM_001001924, intron 1 of 14)	5904	NM_001001925	57509	Hs.7946	NM_020749	ENSG00000129422	MTUS1	ATBP|ATIP|ATIP3|ICIS|MP44|MTSG1	microtubule associated scaffold protein 1	protein-coding	0.006353	0.329949	
chunk0164_189_1	chr6	22217081	22217362	+	0	NA	Intergenic	Intergenic	-70028	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.010676	0.361702	
chunk0063_290_1	chr14	84420071	84420903	+	0	NA	Intergenic	Intergenic	-973392	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003606	0.315726	
chunk0167_66_1	chr6	56266061	56266328	+	0	NA	Intergenic	Intergenic	-18614	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.007491	0.335821	
chunk0082_28_1	chr17	50708774	50709183	+	0	NA	Intergenic	Intergenic	-1069	NM_052855	91369	Hs.463426	NM_052855	ENSG00000154945	ANKRD40	-	ankyrin repeat domain 40	protein-coding	0.002445	0.409756	
chunk0036_96_1	chr11	60912977	60913285	+	0	NA	promoter-TSS (NM_024092)	promoter-TSS (NM_024092)	-768	NM_024092	79073	Hs.13662	NM_024092	ENSG00000110108	TMEM109	-	transmembrane protein 109	protein-coding	0.038961	0.527508	
chunk0156_87_1	chr5	104559219	104560007	+	0	NA	Intergenic	L1MC4a|LINE|L1	-539861	NR_000039	9366	Hs.158296	NR_000039	ENSG00000232159	RAB9BP1	RAB9P1	RAB9B, member RAS oncogene family pseudogene 1	pseudo	0.002538	0.306717	124(ATGTACAAATTGTTCC,-,0.00)
chunk0120_169_1	chr3	5876714	5877088	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-626646	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.008021	0.456000	171(GAGCGCACAATGTGCT,-,0.00),172(AGCGCACAATGTGCTT,+,0.00)
chunk0045_198_1	chr12	47604115	47604683	+	0	NA	Intergenic	Intergenic	101662	NM_001146076	79657	Hs.437855	NM_024604	ENSG00000005175	RPAP3	Tah1|hSpagh	RNA polymerase II associated protein 3	protein-coding	0.001761	0.444640	
chunk0099_13_1	chr2	82866556	82866829	+	0	NA	Intergenic	Intergenic	9889	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.003663	0.317518	
chunk0185_225_1	chr7	129192898	129193130	+	0	NA	intron (NM_005631, intron 1 of 11)	intron (NM_005631, intron 1 of 11)	4142	NM_005631	6608	Hs.437846	NM_005631	ENSG00000128602	SMO	CRJS|FZD11|Gx|SMOH	smoothened, frizzled class receptor	protein-coding	0.008621	0.502146	
chunk0211_310_1	chrX	123635242	123635509	+	0	NA	intron (NM_001081550, intron 19 of 38)	intron (NM_001081550, intron 19 of 38)	97679	NM_001081550	57187	Hs.149991	NM_020449	ENSG00000125676	THOC2	CXorf3|MRX12|MRX35|THO2|dJ506G2.1|hTREX120	THO complex 2	protein-coding	0.000000	0.305970	
chunk0105_241_1	chr2	188523712	188524350	+	0	NA	intron (NR_045563, intron 6 of 12)	intron (NR_045563, intron 6 of 12)	226539	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.004702	0.286385	
chunk0070_373_1	chr15	76358902	76359287	+	0	NA	intron (NM_020843, intron 28 of 30)	intron (NM_020843, intron 28 of 30)	22370	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.002597	0.502591	
chunk0051_49_1	chr12	112341044	112341430	+	0	NA	intron (NM_001109662, intron 1 of 75)	intron (NM_001109662, intron 1 of 75)	40855	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.000000	0.416021	
chunk0064_268_1	chr14	94850469	94850905	+	0	NA	Intergenic	Intergenic	-80525	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.025229	0.455378	
chunk0165_327_1	chr6	37244948	37245194	+	0	NA	intron (NM_001286401, intron 1 of 2)	MLT1H|LTR|ERVL-MaLR	12566	NM_145316	221468	Hs.520101	NM_145316	ENSG00000172738	TMEM217	C6orf128|dJ355M6.2	transmembrane protein 217	protein-coding	0.004065	0.445344	
chunk0161_231_1	chr5	171188004	171188372	+	0	NA	intron (NM_022897, intron 18 of 27)	L3|LINE|CR1	-121096	NM_021025	30012	Hs.249125	NM_021025	ENSG00000164438	TLX3	HOX11L2|RNX	T cell leukemia homeobox 3	protein-coding	0.010870	0.414634	
chunk0139_427_1	chr4	64465196	64465729	+	0	NA	Intergenic	Intergenic	-56002	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.007505	0.353933	
chunk0156_28_1	chr5	102368530	102369135	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-72283	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.004959	0.323432	
chunk0014_226_1	chr1	179737933	179738134	+	0	NA	Intergenic	L1MA5|LINE|L1	-5130	NM_173509	148753	Hs.400696	NM_173509	ENSG00000143340	FAM163A	C1orf76|NDSP	family with sequence similarity 163 member A	protein-coding	0.004975	0.410891	
chunk0095_116_1	chr2	15735518	15735962	+	0	NA	Intergenic	L2a|LINE|L2	44958	NR_110201	101926966	Hs.502835	NR_110201	ENSG00000231031	LINC01804	-	long intergenic non-protein coding RNA 1804	ncRNA	0.006757	0.483146	
chunk0011_283_1	chr1	151428116	151428315	+	0	NA	exon (NM_207171, exon 4 of 17)	exon (NM_207171, exon 4 of 17)	13990	NM_207171	23126	Hs.489873	NM_015100	ENSG00000143442	POGZ	MRD37|WHSUS|ZNF280E|ZNF635|ZNF635m	pogo transposable element derived with ZNF domain	protein-coding	0.025126	0.580000	
chunk0116_2_1	chr21	32683862	32684297	+	0	NA	exon (NM_203446, exon 10 of 33)	exon (NM_203446, exon 10 of 33)	43860	NM_001160302	8867	Hs.473632	NM_003895	ENSG00000159082	SYNJ1	EIEE53|INPP5G|PARK20	synaptojanin 1	protein-coding	0.002299	0.307339	
chunk0123_321_1	chr3	47425145	47425520	+	0	NA	intron (NM_012235, intron 8 of 22)	intron (NM_012235, intron 8 of 22)	44350	NM_001304482	25930	Hs.25524	NM_015466	ENSG00000076201	PTPN23	HD-PTP|HDPTP|PTP-TD14	protein tyrosine phosphatase non-receptor type 23	protein-coding	0.013333	0.460106	
chunk0178_188_1	chr7	34307067	34307362	+	0	NA	Intergenic	MIR3|SINE|MIR	-351025	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.006780	0.402027	
chunk0091_200_1	chr19	8731716	8731915	+	0	NA	exon (NM_001004699, exon 1 of 1)	exon (NM_001004699, exon 1 of 1)	861	NM_001004699	284383	Hs.553675	NM_001004699	ENSG00000181733	OR2Z1	OR19-4|OR2Z2	olfactory receptor family 2 subfamily Z member 1	protein-coding	0.035176	0.550000	
chunk0002_195_1	chr1	19444288	19444741	+	0	NA	intron (NM_001313932, intron 1 of 4)	intron (NM_001313932, intron 1 of 4)	40193	NM_001282162	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.006623	0.451542	
chunk0052_436_1	chr12	132327370	132327661	+	0	NA	intron (NM_001122636, intron 1 of 10)	intron (NM_001122636, intron 1 of 10)	1804	NM_001122636	50614	Hs.301062	NM_021808	ENSG00000182870	GALNT9	GALNAC-T9|GALNACT9	polypeptide N-acetylgalactosaminyltransferase 9	protein-coding	0.041237	0.544521	
chunk0047_94_1	chr12	68614091	68614548	+	0	NA	intron (NM_001251917, intron 1 of 5)	intron (NM_001251917, intron 1 of 5)	3480	NM_015646	5908	Hs.369920	NM_015646	ENSG00000127314	RAP1B	K-REV|RAL1B	RAP1B, member of RAS oncogene family	protein-coding	0.010941	0.336245	
chunk0033_326_1	chr11	21552833	21553147	+	0	NA	intron (NM_006157, intron 16 of 19)	intron (NM_006157, intron 16 of 19)	-640186	NM_213599	203859	Hs.154329	NM_213599	ENSG00000171714	ANO5	GDD1|LGMD2L|LGMDR12|TMEM16E	anoctamin 5	protein-coding	0.000000	0.371429	
chunk0008_15_1	chr1	87399722	87400015	+	0	NA	Intergenic	Intergenic	-28213	NR_038324	100505768	Hs.125247	NR_038324	ENSG00000227290	LINC01364	-	long intergenic non-protein coding RNA 1364	ncRNA	0.010239	0.452381	
chunk0011_125_1	chr1	147106139	147106452	+	0	NA	intron (NR_103466, intron 4 of 5)	LTR5_Hs|LTR|ERVK	8051	NR_103466	644861	Hs.451804	NR_103466		NBPF13P	-	NBPF member 13, pseudogene	pseudo	0.019169	0.455414	
chunk0037_205_1	chr11	74442699	74442994	+	0	NA	Intergenic	L2c|LINE|L2	24709	NM_005472	10008	Hs.523899	NM_005472	ENSG00000175538	KCNE3	BRGDA6|HOKPP|HYPP|MiRP2	potassium voltage-gated channel subfamily E regulatory subunit 3	protein-coding	0.010169	0.435811	
chunk0198_56_1	chr8	128585265	128585554	+	0	NA	Intergenic	Intergenic	-20730	NR_121673	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.003460	0.410345	189(AGGGACAATAAGTCCT,-,0.00),190(GGGACAATAAGTCCTT,+,0.00)
chunk0004_23_1	chr1	42312494	42313089	+	0	NA	intron (NM_001198850, intron 1 of 12)	intron (NM_001198850, intron 1 of 12)	22174	NM_001198851	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.008403	0.422819	267(TGGGACACAATGTACA,-,0.00),268(GGGACACAATGTACAA,+,0.00)
chunk0162_373_1	chr6	7341760	7342392	+	0	NA	intron (NM_205864, intron 8 of 10)	intron (NM_205864, intron 8 of 10)	-28762	NM_001292008	6745	Hs.114033	NM_003144	ENSG00000124783	SSR1	TRAPA	signal sequence receptor subunit 1	protein-coding	0.015823	0.522907	241(AAGCTCAAGGTGTTCT,-,0.00),242(AGCTCAAGGTGTTCTT,+,0.00)
chunk0147_31_1	chr4	171683090	171683563	+	0	NA	Intergenic	MIR|SINE|MIR	-130098	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.008457	0.318565	
chunk0084_248_1	chr17	78995620	78996291	+	0	NA	intron (NM_001159772, intron 4 of 5)	intron (NM_001159772, intron 4 of 5)	13862	NM_138793	124583	Hs.8859	NM_138793	ENSG00000171302	CANT1	DBQD|DBQD1|EDM7|SCAN-1|SCAN1|SHAPY	calcium activated nucleotidase 1	protein-coding	0.020864	0.537202	
chunk0160_133_1	chr5	151349610	151349982	+	0	NA	Intergenic	Intergenic	-2206	NM_181776	153201	Hs.483877	NM_181776	ENSG00000186335	SLC36A2	PAT2|TRAMD1	solute carrier family 36 member 2	protein-coding	0.002688	0.404826	
chunk0017_429_1	chr1	213303246	213303531	+	0	NA	Intergenic	Intergenic	252155	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.010526	0.489510	
chunk0169_246_1	chr6	105254955	105255231	+	0	NA	Intergenic	L2|LINE|L2	-75110	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.003623	0.397112	88(GTGGACAAACTGTCCA,-,0.00)
chunk0031_154_1	chr10	125133870	125134356	+	0	NA	intron (NM_001290214, intron 1 of 10)	intron (NM_001290214, intron 1 of 10)	24702	NM_001290215	1488	Hs.501345	NM_001329	ENSG00000175029	CTBP2	-	C-terminal binding protein 2	protein-coding	0.024691	0.476386	
chunk0067_385_1	chr15	49085997	49086362	+	0	NA	Intergenic	Intergenic	-39616	NM_014701	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.010959	0.330601	
chunk0108_243_1	chr2	233853189	233853443	+	0	NA	intron (NM_001282962, intron 2 of 6)	intron (NM_001282962, intron 2 of 6)	1250	NM_001282962	55355	Hs.532968	NM_018410	ENSG00000123485	HJURP	FAKTS|URLC9|hFLEG1	Holliday junction recognition protein	protein-coding	0.007874	0.388235	
chunk0197_98_1	chr8	119655214	119655473	+	0	NA	Intergenic	Intergenic	-16477	NM_001040092	5168	Hs.190977	NM_006209	ENSG00000136960	ENPP2	ATX|ATX-X|AUTOTAXIN|LysoPLD|NPP2|PD-IALPHA|PDNP2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.015444	0.411538	
chunk0094_293_1	chr2	8485924	8486420	+	0	NA	Intergenic	L1MB1|LINE|L1	97620	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.010081	0.362173	
chunk0139_292_1	chr4	57444411	57444728	+	0	NA	intron (NR_125907, intron 4 of 5)	L2c|LINE|L2	18697	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.000000	0.427673	296(TAGAACTGTAAGTTCT,-,0.00),297(AGAACTGTAAGTTCTG,+,0.00)
chunk0101_21_1	chr2	121618265	121618713	+	0	NA	intron (NM_015282, intron 1 of 38)	intron (NM_015282, intron 1 of 38)	30987	NM_001142274	23332	Hs.469840	NM_015282	ENSG00000074054	CLASP1	MAST1	cytoplasmic linker associated protein 1	protein-coding	0.004464	0.340757	
chunk0040_265_1	chr11	116177671	116178157	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-417714	NR_034148	283143	Hs.130499	NR_034148		LINC00900	-	long intergenic non-protein coding RNA 900	ncRNA	0.006173	0.521561	
chunk0087_287_1	chr18	38849248	38849720	+	0	NA	Intergenic	Intergenic	772691	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.006356	0.367865	
chunk0074_241_1	chr16	27556429	27557068	+	0	NA	intron (NM_015202, intron 1 of 27)	intron (NM_015202, intron 1 of 27)	6601	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.006260	0.353125	
chunk0117_412_1	chr21	45797443	45797707	+	0	NA	Intergenic	(TGGA)n|Simple_repeat|Simple_repeat	38844	NR_038876	100129027	Hs.689591	NR_038876	ENSG00000205424	LOC100129027	-	uncharacterized LOC100129027	ncRNA	0.011364	0.460377	
chunk0089_12_1	chr18	57577334	57578087	+	0	NA	intron (NM_000140, intron 2 of 10)	intron (NM_000140, intron 2 of 10)	9027	NM_000140	2235	Hs.365365	NM_000140	ENSG00000066926	FECH	EPP|EPP1|FCE	ferrochelatase	protein-coding	0.007968	0.351459	
chunk0154_220_1	chr5	80625046	80625755	+	0	NA	TTS (NR_110936)	TTS (NR_110936)	-2876	NR_125754	103689917	Hs.740035	NR_125754	ENSG00000251221	LINC01337	TCONS_00009713	long intergenic non-protein coding RNA 1337	ncRNA	0.012694	0.392958	358(AAGAACGTCTTGTTCT,-,0.00),359(AGAACGTCTTGTTCTT,+,0.00)
chunk0196_426_1	chr8	116313721	116314174	+	0	NA	intron (NR_046215, intron 1 of 13)	intron (NR_046215, intron 1 of 13)	11112	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.011038	0.363436	
chunk0040_347_1	chr11	118566100	118566299	+	0	NA	promoter-TSS (NM_001168618)	promoter-TSS (NM_001168618)	-123	NM_020153	56912	Hs.533738	NM_020153	ENSG00000118096	IFT46	C11orf2|C11orf60|CFAP32	intraflagellar transport 46	protein-coding	0.035176	0.510000	
chunk0179_216_1	chr7	47769358	47769594	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	8000	NR_038407	84847	Hs.488236	NR_038407	ENSG00000146666	LINC00525	-	long intergenic non-protein coding RNA 525	ncRNA	0.008475	0.388186	
chunk0003_421_1	chr1	40862712	40863151	+	0	NA	promoter-TSS (NM_133467)	promoter-TSS (NM_133467)	-585	NM_133467	163732	Hs.355820	NM_133467	ENSG00000179862	CITED4	-	Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4	protein-coding	0.013667	0.497727	
chunk0112_430_1	chr20	47501502	47501701	+	0	NA	promoter-TSS (NM_006534)	promoter-TSS (NM_006534)	-256	NM_006534	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.050251	0.495000	
chunk0189_277_1	chr8	25370366	25370684	+	0	NA	intron (NM_024940, intron 34 of 51)	AluJr|SINE|Alu	25123	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.006289	0.413793	
chunk0189_266_1	chr8	25266791	25267315	+	0	NA	intron (NM_024940, intron 2 of 51)	intron (NM_024940, intron 2 of 51)	-78349	NR_106936	102465527		NR_106936	ENSG00000274988	MIR6876	hsa-mir-6876	microRNA 6876	ncRNA	0.013359	0.411429	
chunk0068_196_1	chr15	54941397	54941928	+	0	NA	Intergenic	Intergenic	255371	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.011299	0.392857	
chunk0072_133_1	chr15	92638940	92639612	+	0	NA	intron (NM_207446, intron 1 of 2)	intron (NM_207446, intron 1 of 2)	16525	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.016369	0.481426	
chunk0201_6_1	chr9	32016936	32017568	+	0	NA	Intergenic	L1MEd|LINE|L1	-367351	NM_002197	48	Hs.567229	NM_002197	ENSG00000122729	ACO1	ACONS|HEL60|IREB1|IREBP|IREBP1|IRP1	aconitase 1	protein-coding	0.009494	0.349131	
chunk0190_156_1	chr8	31194663	31194914	+	0	NA	Intergenic	Intergenic	-161073	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.015936	0.452381	
chunk0099_97_1	chr2	85538701	85539130	+	0	NA	promoter-TSS (NR_038942)	promoter-TSS (NR_038942)	-29	NR_038942	100630918	Hs.66049	NR_038942		PARTICL	PARTICLE	promoter of MAT2A antisense radiation-induced circulating long non-coding RNA	ncRNA	0.114219	0.690698	
chunk0010_181_1	chr1	115881173	115881902	+	0	NA	Intergenic	Intergenic	-37839	NR_125969	101928995	Hs.559119	NR_125969	ENSG00000228127	LINC01649	-	long intergenic non-protein coding RNA 1649	ncRNA	0.005487	0.339726	
chunk0133_85_1	chr3	167439062	167439493	+	0	NA	Intergenic	Intergenic	34855	NM_006217	5276	Hs.445555	NM_006217	ENSG00000114204	SERPINI2	MEPI|PANCPIN|PI14|TSA2004	serpin family I member 2	protein-coding	0.004640	0.351852	
chunk0083_445_1	chr17	72802953	72803218	+	0	NA	intron (NM_001159770, intron 6 of 9)	intron (NM_001159770, intron 6 of 9)	-162613	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.030189	0.507519	
chunk0064_211_1	chr14	93043328	93043886	+	0	NA	intron (NM_001142594, intron 3 of 10)	intron (NM_001142594, intron 3 of 10)	-23845	NR_002808	319085	Hs.612888	NR_002808	ENSG00000258730	ITPK1-AS1	C14orf85|ITPK1-AS|ITPK1AS|NCRNA00203	ITPK1 antisense RNA 1	ncRNA	0.014337	0.567084	255(AAGAACAAAGTGCACC,-,0.00)
chunk0052_316_1	chr12	125079865	125080391	+	0	NA	intron (NM_023928, intron 3 of 17)	intron (NM_023928, intron 3 of 17)	14749	NM_023928	65985	Hs.656073	NM_023928	ENSG00000081760	AACS	ACSF1|SUR-5	acetoacetyl-CoA synthetase	protein-coding	0.019011	0.455408	
chunk0083_65_1	chr17	64051149	64051655	+	0	NA	intron (NM_001433, intron 17 of 21)	L1MC4|LINE|L1	-30768	NM_001099786	3384	Hs.431460	NM_000873	ENSG00000108622	ICAM2	CD102	intercellular adhesion molecule 2	protein-coding	0.005929	0.396450	
chunk0194_152_1	chr8	84654536	84655036	+	0	NA	intron (NM_001100393, intron 2 of 8)	L1MA3|LINE|L1	-51141	NM_001287244	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.004000	0.381238	
chunk0011_60_1	chr1	143270655	143271041	+	0	NA	Intergenic	Intergenic	151744	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.049223	0.364341	
chunk0039_153_1	chr11	98807617	98808193	+	0	NA	Intergenic	L1PB4|LINE|L1	-213071	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003472	0.318891	
chunk0107_101_1	chr2	213982022	213982546	+	0	NA	intron (NR_047659, intron 14 of 17)	intron (NR_047659, intron 14 of 17)	224217	NR_039640	100616375		NR_039640	ENSG00000265734	MIR4438	-	microRNA 4438	ncRNA	0.005725	0.262857	
chunk0022_296_1	chr10	15523169	15523586	+	0	NA	intron (NM_001291494, intron 27 of 28)	intron (NM_001291494, intron 27 of 28)	-152318	NM_001010924	221061	Hs.66762	NM_001010924	ENSG00000148468	FAM171A1	APCN|C10orf38	family with sequence similarity 171 member A1	protein-coding	0.007194	0.387560	
chunk0058_454_1	chr13	113904369	113904639	+	0	NA	intron (NM_001278674, intron 3 of 7)	intron (NM_001278674, intron 3 of 7)	9401	NM_001278674	643365	Hs.127655	NM_001039767		LINC00452	LINC00453	long intergenic non-protein coding RNA 452	protein-coding	0.018519	0.479705	157(GAGCACACAGTGTGCC,-,0.00),158(AGCACACAGTGTGCCG,+,0.00)
chunk0041_162_1	chr11	126058069	126058552	+	0	NA	intron (NM_016952, intron 1 of 19)	intron (NM_016952, intron 1 of 19)	4982	NM_001243597	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.010352	0.386364	210(CAGAACAAAATGTTCT,-,0.00),211(AGAACAAAATGTTCTT,+,0.00)
chunk0063_32_1	chr14	76702214	76702482	+	0	NA	Intergenic	Intergenic	-59544	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.014925	0.468401	26(CAGGACAGTGTGTACC,-,0.00),27(AGGACAGTGTGTACCA,+,0.00)
chunk0150_346_1	chr5	38651104	38651443	+	0	NA	intron (NR_103554, intron 6 of 8)	intron (NR_103554, intron 6 of 8)	-55868	NM_002310	3977	Hs.133421	NM_002310	ENSG00000113594	LIFR	CD118|LIF-R|SJS2|STWS|SWS	LIF receptor subunit alpha	protein-coding	0.008850	0.355882	
chunk0103_89_1	chr2	160813650	160813903	+	0	NA	Intergenic	Intergenic	-319969	NM_002897	5937	Hs.470412	NM_002897	ENSG00000153250	RBMS1	C2orf12|HCC-4|MSSP|MSSP-1|MSSP-2|MSSP-3|SCR2|YC1	RNA binding motif single stranded interacting protein 1	protein-coding	0.015810	0.503937	
chunk0176_366_1	chr7	18396069	18396397	+	0	NA	intron (NM_001204144, intron 2 of 12)	L2a|LINE|L2	-99513	NM_178423	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.006098	0.419453	121(AGGGACATTGTGTGCC,-,0.00),122(GGGACATTGTGTGCCA,+,0.00)
chunk0016_300_1	chr1	201281203	201282654	+	0	NA	Intergenic	Intergenic	-1524	NM_000299	5317	Hs.497350	NM_000299	ENSG00000081277	PKP1	B6P	plakophilin 1	protein-coding	0.010338	0.409780	
chunk0147_43_1	chr4	172188081	172188916	+	0	NA	intron (NM_001034845, intron 2 of 12)	L2b|LINE|L2	375074	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.008383	0.418660	
chunk0176_377_1	chr7	18552867	18553720	+	0	NA	intron (NM_001204147, intron 1 of 9)	intron (NM_001204147, intron 1 of 9)	44016	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.010551	0.357143	636(AAGAACAAACAGTACT,-,0.00),637(AGAACAAACAGTACTT,+,0.00)
chunk0132_291_1	chr3	159999921	160000371	+	0	NA	intron (NR_108088, intron 6 of 9)	intron (NR_108088, intron 6 of 9)	11310	NM_000882	3592	Hs.673	NM_000882	ENSG00000168811	IL12A	CLMF|IL-12A|NFSK|NKSF1|P35	interleukin 12A	protein-coding	0.006667	0.334812	
chunk0008_207_1	chr1	93554031	93554655	+	0	NA	3' UTR (NM_001164473, exon 17 of 17)	3' UTR (NM_001164473, exon 17 of 17)	30819	NM_001308251	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.003205	0.331200	311(AAGGACTAACTGTTCT,-,0.00),312(AGGACTAACTGTTCTT,+,0.00)
chunk0015_404_1	chr1	191093485	191093836	+	0	NA	Intergenic	L1PB4|LINE|L1	468770	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.000000	0.309659	
chunk0029_100_1	chr10	97448005	97448236	+	0	NA	intron (NR_109895, intron 1 of 8)	intron (NR_109895, intron 1 of 8)	1989	NM_198045	84287	Hs.76662	NM_032327	ENSG00000171307	ZDHHC16	APH2|DHHC-16	zinc finger DHHC-type containing 16	protein-coding	0.012987	0.409483	
chunk0058_328_1	chr14	28629334	28629627	+	0	NA	Intergenic	Intergenic	135839	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.006826	0.363946	86(AGGATCAAAATGTCCC,-,0.00),87(GGATCAAAATGTCCCC,+,0.00)
chunk0143_95_1	chr4	108389303	108389946	+	0	NA	Intergenic	L1MD1|LINE|L1	217504	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.004666	0.332298	
chunk0015_259_1	chr1	188168852	188170501	+	0	NA	Intergenic	Intergenic	726048	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004245	0.338182	
chunk0191_3_1	chr8	42351338	42351537	+	0	NA	intron (NM_002690, intron 5 of 13)	Tigger15a|DNA|TcMar-Tigger	12982	NM_002690	5423	Hs.654484	NM_002690	ENSG00000070501	POLB	-	DNA polymerase beta	protein-coding	0.010050	0.380000	
chunk0211_430_1	chrX	129403998	129404737	+	0	NA	Intergenic	Intergenic	119138	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.002706	0.393243	
chunk0181_159_1	chr7	82158329	82158762	+	0	NA	intron (NM_001302890, intron 4 of 10)	intron (NM_001302890, intron 4 of 10)	149368	NR_110077	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.000000	0.322581	
chunk0183_175_1	chr7	106175412	106175844	+	0	NA	Intergenic	L1ME3G|LINE|L1	-62981	NM_006754	6856	Hs.80919	NM_006754	ENSG00000008282	SYPL1	H-SP1|SYPL	synaptophysin like 1	protein-coding	0.002315	0.357968	
chunk0102_6_1	chr2	141075651	141076231	+	0	NA	intron (NM_018557, intron 7 of 90)	intron (NM_018557, intron 7 of 90)	-489256	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.001724	0.361446	284(TGGAACACATTGTGCA,-,0.00),285(GGAACACATTGTGCAA,+,0.00)
chunk0173_92_1	chr6	143014583	143014918	+	0	NA	intron (NR_038987, intron 2 of 2)	intron (NR_038987, intron 2 of 2)	22832	NR_038987	100507489	Hs.486645	NR_038987		LINC01277	-	long intergenic non-protein coding RNA 1277	ncRNA	0.008955	0.324405	
chunk0198_374_1	chr8	141153964	141154279	+	0	NA	intron (NM_014957, intron 7 of 22)	intron (NM_014957, intron 7 of 22)	25500	NM_014957	22898	Hs.18166	NM_014957	ENSG00000105339	DENND3	-	DENN domain containing 3	protein-coding	0.044444	0.575949	
chunk0001_194_1	chr1	7648821	7649397	+	0	NA	intron (NM_015215, intron 7 of 22)	intron (NM_015215, intron 7 of 22)	-122160	NM_004781	9341	Hs.66708	NM_004781	ENSG00000049245	VAMP3	CEB	vesicle associated membrane protein 3	protein-coding	0.024306	0.566724	236(AAGTACTGGGTGTACC,-,0.00),237(AGTACTGGGTGTACCA,+,0.00)
chunk0109_252_1	chr20	6485555	6486157	+	0	NA	intron (NR_109953, intron 3 of 3)	intron (NR_109953, intron 3 of 3)	59124	NR_109953	101929244	Hs.542488	NR_109953	ENSG00000229876	CASC20	-	cancer susceptibility 20	ncRNA	0.008306	0.381426	
chunk0012_124_1	chr1	157037315	157037832	+	0	NA	intron (NM_198236, intron 1 of 40)	L2b|LINE|L2	7797	NM_014784	9826	Hs.516954	NM_014784	ENSG00000132694	ARHGEF11	GTRAP48|PDZ-RHOGEF	Rho guanine nucleotide exchange factor 11	protein-coding	0.013540	0.415058	
chunk0150_275_1	chr5	36936190	36936736	+	0	NA	intron (NM_015384, intron 1 of 45)	Tigger3a|DNA|TcMar-Tigger	59704	NM_133433	25836	Hs.481927	NM_015384	ENSG00000164190	NIPBL	CDLS|CDLS1|IDN3|IDN3-B|Scc2	NIPBL cohesin loading factor	protein-coding	0.005495	0.360146	316(AGGTACATTCTGTTAT,-,0.00)
chunk0201_251_1	chr9	37986976	37987621	+	0	NA	intron (NM_003028, intron 2 of 5)	MIRb|SINE|MIR	81915	NM_003028	6461	Hs.521482	NM_003028	ENSG00000107338	SHB	bA3J10.2	SH2 domain containing adaptor protein B	protein-coding	0.017054	0.554180	275(AGGAACACTGCGTGCT,-,0.00),276(GGAACACTGCGTGCTG,+,0.00)
chunk0122_230_1	chr3	33724634	33725158	+	0	NA	Intergenic	Intergenic	-6683	NM_015097	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.001908	0.333333	
chunk0204_179_1	chr9	96080226	96080642	+	0	NA	intron (NR_033838, intron 1 of 8)	intron (NR_033838, intron 1 of 8)	14595	NR_033838	158435	Hs.652615	NR_033838		LOC158435	-	uncharacterized LOC158435	ncRNA	0.021635	0.467626	
chunk0187_75_1	chr8	2738390	2738887	+	0	NA	Intergenic	L1M4|LINE|L1	-10187	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.008048	0.299197	
chunk0145_82_1	chr4	145842209	145842592	+	0	NA	intron (NM_178835, intron 7 of 14)	intron (NM_178835, intron 7 of 14)	96560	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.018277	0.476562	175(GTGGACTTCGTGTTCT,-,0.00),176(TGGACTTCGTGTTCTC,+,0.00)
chunk0101_383_1	chr2	138558802	138559366	+	0	NA	exon (NM_001001664, exon 6 of 11)	exon (NM_001001664, exon 6 of 11)	57304	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.007092	0.300885	
chunk0069_217_1	chr15	63543503	63543787	+	0	NA	intron (NR_046342, intron 4 of 15)	intron (NR_046342, intron 4 of 15)	39134	NR_046341	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.007042	0.347368	
chunk0210_392_1	chrX	97921473	97922171	+	0	NA	Intergenic	L1PA6|LINE|L1	-357287	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.011461	0.489270	
chunk0052_303_1	chr12	124804360	124804559	+	0	NA	intron (NM_001082959, intron 7 of 11)	MLT1K|LTR|ERVL-MaLR	59514	NM_005505	949	Hs.731377	NM_005505	ENSG00000073060	SCARB1	CD36L1|CLA-1|CLA1|HDLQTL6|SR-BI|SRB1	scavenger receptor class B member 1	protein-coding	0.010050	0.480000	
chunk0042_275_1	chr12	6989094	6989326	+	0	NA	intron (NM_005768, intron 1 of 12)	intron (NM_005768, intron 1 of 12)	18429	NM_006331	10436	Hs.558447	NM_006331	ENSG00000126749	EMG1	C2F|Grcc2f|NEP1	EMG1 N1-specific pseudouridine methyltransferase	protein-coding	0.012931	0.373391	
chunk0193_47_1	chr8	71989827	71990148	+	0	NA	intron (NR_033652, intron 4 of 4)	intron (NR_033652, intron 4 of 4)	85597	NM_007332	8989	Hs.716816	NM_007332	ENSG00000104321	TRPA1	ANKTM1|FEPS|FEPS1	transient receptor potential cation channel subfamily A member 1	protein-coding	0.003115	0.260870	
chunk0148_300_1	chr5	12299428	12299633	+	0	NA	Intergenic	Intergenic	-275327	NR_033383	404663	Hs.552273	NR_033383		LINC01194	CT49|TAG	long intergenic non-protein coding RNA 1194	ncRNA	0.000000	0.504854	157(AAGCACTGTGTGTGCT,-,0.00),158(AGCACTGTGTGTGCTC,+,0.00)
chunk0114_33_1	chr21	8216794	8217057	+	0	NA	intron (NR_003287, intron 1 of 2)	LSU-rRNA_Hsa|rRNA|rRNA	3037	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.171103	0.871212	
chunk0184_271_1	chr7	118575251	118576016	+	0	NA	Intergenic	L2a|LINE|L2	350975	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.002614	0.372063	
chunk0201_349_1	chr9	67732997	67733212	+	0	NA	Intergenic	L1MDb|LINE|L1	-6361	NR_027422	100133121	Hs.744835	NR_027422		FAM27B	FAM27A2	family with sequence similarity 27 member B	ncRNA	0.004651	0.384259	
chunk0041_412_1	chr11	133976599	133977054	+	0	NA	Intergenic	Intergenic	-20072	NM_001277285	22997	Hs.204121	NM_014987	ENSG00000080854	IGSF9B	-	immunoglobulin superfamily member 9B	protein-coding	0.017582	0.528509	
chunk0068_358_1	chr15	57974885	57975475	+	0	NA	intron (NM_170696, intron 6 of 11)	L1ME1|LINE|L1	38917	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.003390	0.350254	
chunk0042_346_1	chr12	10060365	10060733	+	0	NA	intron (NM_207345, intron 5 of 8)	L1MD1|LINE|L1	29872	NM_207345	283420	Hs.531189	NM_207345	ENSG00000197992	CLEC9A	CD370|DNGR-1|DNGR1|UNQ9341	C-type lectin domain containing 9A	protein-coding	0.002717	0.352304	
chunk0066_80_1	chr15	29449144	29449398	+	0	NA	intron (NM_015307, intron 1 of 10)	intron (NM_015307, intron 1 of 10)	121452	NM_015307	23359	Hs.383564	NM_015307	ENSG00000104059	FAM189A1	TMEM228	family with sequence similarity 189 member A1	protein-coding	0.003937	0.525490	
chunk0027_229_1	chr10	76324238	76324744	+	0	NA	intron (NR_131178, intron 7 of 7)	intron (NR_131178, intron 7 of 7)	541730	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.013834	0.422091	
chunk0079_247_1	chr17	16098810	16099199	+	0	NA	intron (NM_006311, intron 20 of 45)	MER102b|DNA|hAT-Charlie	95635	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.010283	0.382051	
chunk0045_187_1	chr12	47247413	47247789	+	0	NA	Intergenic	Intergenic	-31158	NR_026544	100233209	Hs.657722	NR_026544	ENSG00000247774	PCED1B-AS1	-	PCED1B antisense RNA 1	ncRNA	0.002660	0.437666	
chunk0203_256_1	chr9	87580838	87581218	+	0	NA	intron (NM_001288730, intron 2 of 25)	intron (NM_001288730, intron 2 of 25)	82493	NM_001288729	1612	Hs.380277	NM_004938	ENSG00000196730	DAPK1	DAPK|ROCO3	death associated protein kinase 1	protein-coding	0.026316	0.440945	
chunk0068_424_1	chr15	59366561	59367385	+	0	NA	intron (NM_004998, intron 1 of 27)	intron (NM_004998, intron 1 of 27)	5899	NM_004998	4643	Hs.654506	NM_004998	ENSG00000157483	MYO1E	FSGS6|HuncM-IC|MYO1C	myosin IE	protein-coding	0.009709	0.360000	647(AGGTACTATATGTTCT,-,0.00),648(GGTACTATATGTTCTT,+,0.00)
chunk0157_392_1	chr5	124121778	124122167	+	0	NA	intron (NR_125774, intron 4 of 5)	LTR107_Mam|LTR|LTR	316548	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.005141	0.361538	
chunk0120_339_1	chr3	11261930	11262276	+	0	NA	3' UTR (NM_000861, exon 3 of 3)	3' UTR (NM_000861, exon 3 of 3)	9404	NM_000861	3269	Hs.1570	NM_000861	ENSG00000196639	HRH1	H1-R|H1R|HH1R|hisH1	histamine receptor H1	protein-coding	0.011561	0.374640	
chunk0104_326_1	chr2	179442487	179443091	+	0	NA	3' UTR (NM_152520, exon 10 of 10)	3' UTR (NM_152520, exon 10 of 10)	119799	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.008278	0.355372	
chunk0127_212_1	chr3	96483462	96484197	+	0	NA	Intergenic	Intergenic	123865	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.269022	
chunk0192_157_1	chr8	62249495	62249957	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	784	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.015152	0.503240	288(GAGAACAGAGTGAACC,-,0.00),289(AGAACAGAGTGAACCG,+,0.00)
chunk0190_398_1	chr8	40195363	40195798	+	0	NA	Intergenic	Intergenic	42112	NM_020130	56892	Hs.591849	NM_020130	ENSG00000176907	TCIM	C8orf4|TC-1|TC1	transcriptional and immune response regulator	protein-coding	0.009195	0.366972	
chunk0171_204_1	chr6	125780733	125781114	+	0	NA	promoter-TSS (NM_001199620)	promoter-TSS (NM_001199620)	-238	NM_001199619	135112	Hs.171426	NM_181782	ENSG00000111912	NCOA7	ERAP140|ESNA1|NCOA7-AS|Nbla00052|Nbla10993|TLDC4|dJ187J11.3	nuclear receptor coactivator 7	protein-coding	0.052493	0.492147	
chunk0015_341_1	chr1	189844859	189845415	+	0	NA	Intergenic	L2a|LINE|L2	632492	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003597	0.299820	
chunk0133_23_1	chr3	165746554	165747406	+	0	NA	Intergenic	L1MEc|LINE|L1	90485	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.005869	0.309496	
chunk0027_308_1	chr10	77892773	77893199	+	0	NA	intron (NM_004747, intron 1 of 31)	MIRc|SINE|MIR	33604	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.011737	0.484778	
chunk0063_115_1	chr14	79224624	79224968	+	0	NA	intron (NR_073547, intron 14 of 20)	MLT1C|LTR|ERVL-MaLR	-54543	NR_073546	9369	Hs.368307	NM_004796	ENSG00000021645	NRXN3	C14orf60	neurexin 3	protein-coding	0.002907	0.440580	125(GAGAACATTGTGTGCA,-,0.00),126(AGAACATTGTGTGCAG,+,0.00)
chunk0096_21_1	chr2	26347534	26347850	+	0	NA	promoter-TSS (NM_153835)	promoter-TSS (NM_153835)	-875	NM_153835	165082	Hs.631878	NM_153835	ENSG00000173567	ADGRF3	GPR113|PGR23	adhesion G protein-coupled receptor F3	protein-coding	0.003165	0.353312	
chunk0100_322_1	chr2	116477142	116477711	+	0	NA	Intergenic	Intergenic	1315319	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.005272	0.364912	
chunk0109_384_1	chr2	239973490	239973722	+	0	NA	intron (NM_004544, intron 9 of 9)	intron (NM_004544, intron 9 of 9)	-30512	NR_039949	100616417		NR_039949	ENSG00000264279	MIR4786	mir-4786	microRNA 4786	ncRNA	0.017241	0.424893	
chunk0197_207_1	chr8	122618166	122618682	+	0	NA	Intergenic	MIR|SINE|MIR	-49780	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.017442	0.439072	
chunk0147_60_1	chr4	172628878	172629462	+	0	NA	TTS (NR_125895)	TTS (NR_125895)	59747	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.006849	0.317949	337(AGGAACAAATTGTTCA,-,0.00),338(GGAACAAATTGTTCAG,+,0.00)
chunk0117_162_1	chr22	20136625	20136919	+	0	NA	intron (NM_013373, intron 1 of 10)	intron (NM_013373, intron 1 of 10)	4931	NM_001185024	29801	Hs.63128	NM_013373	ENSG00000099904	ZDHHC8	DHHC8|ZDHHCL1|ZNF378	zinc finger DHHC-type containing 8	protein-coding	0.017007	0.491525	
chunk0062_5_1	chr14	66075160	66075491	+	0	NA	Intergenic	Intergenic	-411046	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.015106	0.590361	
chunk0123_154_1	chr3	43298569	43298768	+	0	NA	intron (NM_001100594, intron 1 of 5)	intron (NM_001100594, intron 1 of 5)	12156	NM_001100594	54861	Hs.476052	NM_017719	ENSG00000163788	SNRK	HSNFRK	SNF related kinase	protein-coding	0.000000	0.405000	
chunk0044_208_1	chr12	30862465	30862880	+	0	NA	Intergenic	Intergenic	-64232	NM_001080509	441631	Hs.505141	NM_001080509	ENSG00000110900	TSPAN11	VSSW1971	tetraspanin 11	protein-coding	0.012048	0.444712	
chunk0011_43_1	chr1	143244900	143245136	+	0	NA	Intergenic	Intergenic	177574	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.025424	0.350211	
chunk0098_101_1	chr2	67983469	67983916	+	0	NA	Intergenic	Intergenic	79335	NM_006333	10438	Hs.602900	NM_006333	ENSG00000197223	C1D	LRP1|Rrp47|SUN-CoR|SUNCOR|hC1D	C1D nuclear receptor corepressor	protein-coding	0.004474	0.428571	
chunk0086_347_1	chr18	25089239	25089934	+	0	NA	intron (NM_001308225, intron 5 of 6)	intron (NM_001308225, intron 5 of 6)	262664	NM_001308225	25925	Hs.116935	NM_015461	ENSG00000198795	ZNF521	EHZF|Evi3	zinc finger protein 521	protein-coding	0.008633	0.431034	255(GTGGACATTGTGTACA,-,0.00),256(TGGACATTGTGTACAG,+,0.00)
chunk0007_232_1	chr1	81978117	81978731	+	0	NA	intron (NM_001297706, intron 15 of 18)	intron (NM_001297706, intron 15 of 18)	178027	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.003257	0.313821	356(AAGGACAGAATGTTAC,-,0.00),357(AGGACAGAATGTTACC,+,0.00)
chunk0086_265_1	chr18	23550906	23551112	+	0	NA	intron (NM_000271, intron 10 of 24)	intron (NM_000271, intron 10 of 24)	35608	NM_000271	4864	Hs.464779	NM_000271	ENSG00000141458	NPC1	NPC|POGZ|SLC65A1	NPC intracellular cholesterol transporter 1	protein-coding	0.000000	0.386473	
chunk0030_385_1	chr10	119537634	119538120	+	0	NA	intron (NM_001005339, intron 1 of 4)	L1ME4b|LINE|L1	-1344	NM_002925	6001	Hs.501200	NM_002925	ENSG00000148908	RGS10	-	regulator of G protein signaling 10	protein-coding	0.012346	0.455852	
chunk0100_240_1	chr2	112652412	112652958	+	0	NA	intron (NM_005415, intron 4 of 10)	intron (NM_005415, intron 4 of 10)	6828	NM_005415	6574	Hs.187946	NM_005415	ENSG00000144136	SLC20A1	GLVR1|Glvr-1|PIT1|PiT-1	solute carrier family 20 member 1	protein-coding	0.009158	0.385740	
chunk0164_250_1	chr6	23403919	23404564	+	0	NA	Intergenic	Intergenic	-721945	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.004651	0.359133	
chunk0105_7_1	chr2	181771270	181771746	+	0	NA	Intergenic	Intergenic	-90843	NM_002500	4760	Hs.574626	NM_002500	ENSG00000162992	NEUROD1	BETA2|BHF-1|MODY6|NEUROD|bHLHa3	neuronal differentiation 1	protein-coding	0.006303	0.373166	
chunk0099_425_1	chr2	102629960	102630459	+	0	NA	intron (NM_003048, intron 1 of 11)	L1MEd|LINE|L1	10520	NM_003048	6549	Hs.250083	NM_003048	ENSG00000115616	SLC9A2	NHE2	solute carrier family 9 member A2	protein-coding	0.004008	0.278000	
chunk0168_130_1	chr6	82739201	82739559	+	0	NA	Intergenic	Intergenic	326461	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.005587	0.367688	268(CAACACACCGTGTACT,-,0.00),269(AACACACCGTGTACTT,+,0.00)
chunk0076_215_1	chr16	68293552	68293976	+	0	NA	intron (NM_001076785, intron 8 of 11)	intron (NM_001076785, intron 8 of 11)	17201	NM_032178	84138	Hs.729520	NM_032178	ENSG00000103061	SLC7A6OS	-	solute carrier family 7 member 6 opposite strand	protein-coding	0.018868	0.501176	
chunk0025_204_1	chr10	53576545	53576830	+	0	NA	Intergenic	Intergenic	-804987	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.014035	0.388112	
chunk0021_85_1	chr10	1746884	1747102	+	0	NA	Intergenic	Intergenic	-9517	NM_018702	105	Hs.586663	NM_018702	ENSG00000185736	ADARB2	ADAR3|RED2	adenosine deaminase RNA specific B2 (inactive)	protein-coding	0.073394	0.484018	
chunk0001_426_1	chr1	11281931	11282237	+	0	NA	intron (NM_013319, intron 1 of 1)	L1ME2|LINE|L1	8886	NM_013319	29914	Hs.522933	NM_013319	ENSG00000120942	UBIAD1	SCCD|TERE1	UbiA prenyltransferase domain containing 1	protein-coding	0.006536	0.390879	
chunk0082_433_1	chr17	61511305	61512007	+	0	NA	Intergenic	Intergenic	55210	NM_018488	9496	Hs.143907	NM_018488	ENSG00000121075	TBX4	ICPPS|SPS	T-box transcription factor 4	protein-coding	0.005698	0.496444	281(TAGAACATCAAGTGCT,-,0.00),282(AGAACATCAAGTGCTG,+,0.00)
chunk0049_45_1	chr12	89873890	89874179	+	0	NA	Intergenic	Intergenic	165079	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.013841	0.520690	
chunk0007_374_1	chr1	85229003	85229496	+	0	NA	Intergenic	L1M5|LINE|L1	-28204	NM_032184	84144	Hs.533853	NM_032184	ENSG00000097096	SYDE2	-	synapse defective Rho GTPase homolog 2	protein-coding	0.002028	0.358300	182(AGGATCATATTGTTCT,-,0.00),183(GGATCATATTGTTCTA,+,0.00)
chunk0074_359_1	chr16	34078779	34078979	+	0	NA	Intergenic	Intergenic	81157	NR_038368									0.045000	0.343284	
chunk0066_376_1	chr15	38708996	38709612	+	0	NA	Intergenic	Intergenic	12706	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.004870	0.379254	
chunk0066_367_1	chr15	38430353	38430552	+	0	NA	Intergenic	MLT1G|LTR|ERVL-MaLR	-23675	NM_173611	283742	Hs.6799	NM_173611	ENSG00000171262	FAM98B	-	family with sequence similarity 98 member B	protein-coding	0.010050	0.495000	
chunk0116_210_1	chr21	37518961	37519459	+	0	NA	Intergenic	Intergenic	98910	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.014056	0.434870	
chunk0156_135_1	chr5	106923316	106923921	+	0	NA	intron (NR_104671, intron 2 of 3)	intron (NR_104671, intron 2 of 3)	87396	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.001653	0.323432	
chunk0177_27_1	chr7	20647301	20647524	+	0	NA	promoter-TSS (NM_001163993)	promoter-TSS (NM_001163993)	69	NM_001163942	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.004484	0.312500	
chunk0134_122_1	chr3	177299908	177301157	+	0	NA	intron (NR_047465, intron 1 of 1)	intron (NR_047465, intron 1 of 1)	6090	NR_047465	100820709	Hs.518409	NR_047465	ENSG00000203645	LINC00501	-	long intergenic non-protein coding RNA 501	ncRNA	0.011209	0.435200	
chunk0055_46_1	chr13	52338100	52338438	+	0	NA	intron (NR_120400, intron 1 of 2)	L1ME3A|LINE|L1	3974	NR_120400	103191607		NR_120400	ENSG00000271564	LINC02333	-	long intergenic non-protein coding RNA 2333	ncRNA	0.005917	0.395280	165(CAGTACAGTATGTACT,-,0.00),166(AGTACAGTATGTACTC,+,0.00)
chunk0113_140_1	chr20	52013317	52013577	+	0	NA	Intergenic	Intergenic	-150534	NR_110016	101927678	Hs.683840	NR_110016	ENSG00000227964	LINC01429	-	long intergenic non-protein coding RNA 1429	ncRNA	0.015385	0.501916	
chunk0086_206_1	chr18	22432838	22433178	+	0	NA	Intergenic	Intergenic	-15093	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.032353	0.454545	
chunk0159_190_1	chr5	140291864	140293127	+	0	NA	intron (NM_002622, intron 2 of 3)	intron (NM_002622, intron 2 of 3)	10609	NM_002622	5201	Hs.483564	NM_002622	ENSG00000113068	PFDN1	PDF|PFD1	prefoldin subunit 1	protein-coding	0.003167	0.340981	
chunk0047_157_1	chr12	69825939	69826280	+	0	NA	intron (NM_182530, intron 1 of 24)	intron (NM_182530, intron 1 of 24)	786	NM_182530	196446	Hs.253773	NM_182530	ENSG00000166268	MYRFL	C12orf15|C12orf28|bcm1377	myelin regulatory factor like	protein-coding	0.011730	0.391813	
chunk0152_206_1	chr5	60243746	60244045	+	0	NA	intron (NM_001165899, intron 1 of 16)	L1MA3|LINE|L1	-243818	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.003344	0.356667	
chunk0041_168_1	chr11	126083114	126083393	+	0	NA	Intergenic	Intergenic	-19961	NM_016952	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.000000	0.482143	
chunk0099_285_1	chr2	98630114	98630431	+	0	NA	intron (NM_001160154, intron 11 of 12)	L1ME3E|LINE|L1	21693	NM_014044	25972	Hs.13370	NM_014044	ENSG00000115446	UNC50	GMH1|HSD23|PDLs22|UNCL|URP	unc-50 inner nuclear membrane RNA binding protein	protein-coding	0.012618	0.380503	100(GAGAACAGATCGTGCT,-,0.00),101(AGAACAGATCGTGCTG,+,0.00)
chunk0034_119_1	chr11	28144443	28144642	+	0	NA	intron (NM_001113528, intron 3 of 6)	L4_A_Mam|LINE|RTE-X	36291	NM_001113528	196074	Hs.243326	NM_152636	ENSG00000169519	METTL15	METT5D1	methyltransferase like 15	protein-coding	0.005025	0.325000	
chunk0148_251_1	chr5	10222153	10222870	+	0	NA	Intergenic	Intergenic	27398	NM_199133	134145	Hs.481569	NM_199133	ENSG00000150756	ATPSCKMT	FAM173B|JS-2|hFAM173B	ATP synthase c subunit lysine N-methyltransferase	protein-coding	0.005579	0.494429	380(GGGTACTTCTTGTTCT,-,0.00),381(GGTACTTCTTGTTCTT,+,0.00)
chunk0197_346_1	chr8	125430002	125430490	+	0	NA	promoter-TSS (NM_025195)	promoter-TSS (NM_025195)	-75	NM_025195	10221	Hs.444947	NM_025195	ENSG00000173334	TRIB1	C8FW|GIG-2|GIG2|SKIP1|TRB-1|TRB1	tribbles pseudokinase 1	protein-coding	0.084016	0.672802	
chunk0185_78_1	chr7	125351816	125352311	+	0	NA	intron (NR_110188, intron 7 of 8)	intron (NR_110188, intron 7 of 8)	-87772	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.002020	0.322581	231(AGGAACAGAGAGTGTC,-,0.00)
chunk0178_221_1	chr7	35634052	35634597	+	0	NA	exon (NM_022373, exon 8 of 9)	exon (NM_022373, exon 8 of 9)	60838	NM_022373	64224	Hs.643051	NM_022373	ENSG00000122557	HERPUD2	-	HERPUD family member 2	protein-coding	0.005505	0.327839	
chunk0051_448_1	chr12	123278030	123278545	+	0	NA	Intergenic	L1MB7|LINE|L1	-5971	NR_073007	8099	Hs.433201	NM_004642	ENSG00000111328	CDK2AP1	DOC1|DORC1|ST19|doc-1|p12DOC-1	cyclin dependent kinase 2 associated protein 1	protein-coding	0.005825	0.368217	
chunk0058_240_1	chr14	25579676	25580073	+	0	NA	Intergenic	Intergenic	-529577	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.002519	0.278894	
chunk0079_87_1	chr17	11885202	11885401	+	0	NA	intron (NM_004662, intron 2 of 14)	intron (NM_004662, intron 2 of 14)	2399	NM_004662	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.005025	0.535000	
chunk0004_185_1	chr1	46113910	46114262	+	0	NA	intron (NM_001303427, intron 1 of 9)	intron (NM_001303427, intron 1 of 9)	18622	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.014205	0.422096	
chunk0063_413_1	chr14	88411574	88412365	+	0	NA	intron (NM_001040428, intron 3 of 10)	L1PA15-16|LINE|L1	26325	NM_018418	55812	Hs.525518	NM_018418	ENSG00000042317	SPATA7	HEL-S-296|HSD-3.1|HSD3|LCA3	spermatogenesis associated 7	protein-coding	0.006321	0.401515	409(AAGAACAGTGTGTAAT,-,0.00),410(AGAACAGTGTGTAATT,+,0.00)
chunk0061_401_1	chr14	64696399	64696881	+	0	NA	Intergenic	Intergenic	-7768	NM_001308147	26030	Hs.509637	NM_015549	ENSG00000126822	PLEKHG3	ARHGEF43|KIAA0599	pleckstrin homology and RhoGEF domain containing G3	protein-coding	0.010373	0.492754	226(TAGGACAGGATGTTCT,-,0.00),227(AGGACAGGATGTTCTT,+,0.00),309(AGGCACAAACCGTGCT,-,0.00),310(GGCACAAACCGTGCTT,+,0.00)
chunk0197_275_1	chr8	123949987	123950382	+	0	NA	intron (NM_001039112, intron 1 of 40)	intron (NM_001039112, intron 1 of 40)	90598	NR_040044	439941	Hs.683919	NM_001038706	ENSG00000181171	FER1L6-AS1	C8orf54	FER1L6 antisense RNA 1	ncRNA	0.020253	0.484848	
chunk0077_127_1	chr16	78472780	78473539	+	0	NA	intron (NM_016373, intron 8 of 8)	AluSz|SINE|Alu	373746	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.019763	0.440789	
chunk0004_223_1	chr1	46903528	46903926	+	0	NA	Intergenic	HERVK11-int|LTR|ERVK	-3252	NR_002788	163720	Hs.591431	NR_002788	ENSG00000154198	CYP4Z2P	-	cytochrome P450 family 4 subfamily Z member 2, pseudogene	pseudo	0.012563	0.463659	
chunk0016_349_1	chr1	202046230	202046594	+	0	NA	Intergenic	Intergenic	35850	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.008242	0.608219	
chunk0086_38_1	chr18	12605866	12606605	+	0	NA	intron (NM_001128627, intron 2 of 15)	L2a|LINE|L2	50497	NM_001128627	56907	Hs.515283	NM_020148	ENSG00000134278	SPIRE1	Spir-1	spire type actin nucleation factor 1	protein-coding	0.008119	0.417568	443(TGGCACATTAAGTTCT,-,0.00),444(GGCACATTAAGTTCTC,+,0.00)
chunk0139_298_1	chr4	57497633	57498597	+	0	NA	Intergenic	Intergenic	72243	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.008299	0.386528	
chunk0023_369_1	chr10	30188738	30189569	+	0	NA	Intergenic	Intergenic	-22699	NR_120653	101929279	Hs.559153	NR_120653		LOC101929279	-	uncharacterized LOC101929279	ncRNA	0.013237	0.457933	
chunk0173_407_1	chr6	150821016	150821215	+	0	NA	intron (NM_001029884, intron 13 of 16)	intron (NM_001029884, intron 13 of 16)	-44564	NM_015440	25902	Hs.591343	NM_015440	ENSG00000120254	MTHFD1L	FTHFSDC1|MTC1THFS|dJ292B18.2	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like	protein-coding	0.005025	0.370000	
chunk0094_330_1	chr2	9048941	9049682	+	0	NA	Intergenic	L1MC4|LINE|L1	-45564	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.013495	0.355795	
chunk0055_325_1	chr13	68778035	68778275	+	0	NA	Intergenic	LTR80A|LTR|ERVL	107170	NR_038878	338862		NR_038878	ENSG00000281778	LINC00550	-	long intergenic non-protein coding RNA 550	ncRNA	0.004167	0.398340	
chunk0173_173_1	chr6	144493190	144493501	+	0	NA	exon (NM_007124, exon 32 of 74)	exon (NM_007124, exon 32 of 74)	87690	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.006431	0.439103	
chunk0152_38_1	chr5	57014169	57014368	+	0	NA	Intergenic	L1MEc|LINE|L1	-62138	NM_001297599	166968	Hs.657594	NM_152622	ENSG00000155545	MIER3	-	MIER family member 3	protein-coding	0.000000	0.285000	
chunk0022_55_1	chr10	8320751	8321247	+	0	NA	Intergenic	Intergenic	-52694	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.002016	0.352113	
chunk0038_148_1	chr11	84450172	84450719	+	0	NA	intron (NM_001142699, intron 7 of 27)	L2c|LINE|L2	-133106	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.001828	0.355839	221(CAGAACAAGAAGTACT,-,0.00),222(AGAACAAGAAGTACTT,+,0.00)
chunk0020_121_1	chr1	233425760	233426399	+	0	NA	Intergenic	L1MD1|LINE|L1	98311	NM_032435	84451	Hs.547779	NM_032435	ENSG00000143674	MAP3K21	MLK4|dJ862P8.3	mitogen-activated protein kinase kinase kinase 21	protein-coding	0.003130	0.345313	
chunk0145_47_1	chr4	144995556	144996420	+	0	NA	intron (NM_001256712, intron 3 of 3)	L1M2a1|LINE|L1	-102016	NM_002940	6059	Hs.12013	NM_002940	ENSG00000164163	ABCE1	ABC38|OABP|RLI|RLI1|RNASEL1|RNASELI|RNS4I	ATP binding cassette subfamily E member 1	protein-coding	0.010417	0.398844	
chunk0112_3_1	chr20	35636103	35636471	+	0	NA	intron (NM_001198863, intron 1 of 15)	intron (NM_001198863, intron 1 of 15)	17622	NM_003915	8904	Hs.246413	NM_003915	ENSG00000214078	CPNE1	COPN1|CPN1	copine 1	protein-coding	0.005435	0.457995	
chunk0154_348_1	chr5	87020072	87020604	+	0	NA	Intergenic	L1PA15-16|LINE|L1	94616	NR_036243	100422887		NR_036243	ENSG00000265919	MIR4280	-	microRNA 4280	ncRNA	0.003759	0.529081	
chunk0028_337_1	chr10	92117667	92118100	+	0	NA	intron (NM_001178137, intron 6 of 9)	MIR|SINE|MIR	125396	NM_001178137	22849	Hs.131683	NM_014912	ENSG00000107864	CPEB3	-	cytoplasmic polyadenylation element binding protein 3	protein-coding	0.000000	0.308756	
chunk0164_301_1	chr6	24855291	24855666	+	0	NA	intron (NM_014722, intron 8 of 22)	intron (NM_014722, intron 8 of 22)	21887	NM_001286447	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.008000	0.335106	
chunk0184_114_1	chr7	113764512	113764986	+	0	NA	Intergenic	Intergenic	154278	NM_002711	5506	Hs.458309	NM_002711	ENSG00000154415	PPP1R3A	GM|PP1G|PPP1R3	protein phosphatase 1 regulatory subunit 3A	protein-coding	0.002110	0.349474	
chunk0119_360_1	chr22	47460809	47461442	+	0	NA	TTS (NR_109967)	TTS (NR_109967)	25986	NR_109967	101927722	Hs.589927	NR_109967	ENSG00000218357	LINC01644	LL22NC03-75H12.2	long intergenic non-protein coding RNA 1644	ncRNA	0.012638	0.482650	
chunk0162_199_1	chr6	3968376	3968691	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-52802	NM_003913	8899	Hs.159014	NM_003913	ENSG00000112739	PRPF4B	PR4H|PRP4|PRP4H|PRP4K|dJ1013A10.1	pre-mRNA processing factor 4B	protein-coding	0.006349	0.370253	
chunk0079_306_1	chr17	17115341	17115690	+	0	NA	intron (NM_015134, intron 3 of 22)	intron (NM_015134, intron 3 of 22)	72755	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.017192	0.528571	
chunk0166_273_1	chr6	48118195	48118669	+	0	NA	Intergenic	MIRc|SINE|MIR	-49743	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.004219	0.313684	
chunk0174_164_1	chr6	158456059	158456645	+	0	NA	intron (NM_001007466, intron 5 of 12)	MER30|DNA|hAT-Charlie	-80084	NM_020823	57583	Hs.99145	NM_020823	ENSG00000146433	TMEM181	GPR178|KIAA1423	transmembrane protein 181	protein-coding	0.011945	0.453152	
chunk0092_60_1	chr19	20127315	20127545	+	0	NA	Intergenic	Intergenic	-39784	NM_052852	90649	Hs.590991	NM_052852	ENSG00000256229	ZNF486	KRBO2	zinc finger protein 486	protein-coding	0.004348	0.372294	
chunk0042_207_1	chr12	6007158	6007386	+	0	NA	intron (NM_000552, intron 34 of 51)	L1MB1|LINE|L1	-61040	NM_001278597	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.004386	0.358079	
chunk0144_318_1	chr4	138897837	138898435	+	0	NA	Intergenic	Intergenic	-117623	NM_012118	25819	Hs.639842	NM_012118	ENSG00000151014	NOCT	CCR4L|CCRN4L|Ccr4c|NOC	nocturnin	protein-coding	0.006689	0.432387	
chunk0087_24_1	chr18	31056380	31056753	+	0	NA	Intergenic	Intergenic	-13751	NM_001941	1825	Hs.41690	NM_001941	ENSG00000134762	DSC3	CDHF3|DSC|DSC1|DSC2|DSC4|HT-CP	desmocollin 3	protein-coding	0.002681	0.363636	
chunk0007_238_1	chr1	82343331	82343565	+	0	NA	Intergenic	Intergenic	543051	NM_001297705	23266	Hs.24212	NM_012302	ENSG00000117114	ADGRL2	CIRL2|CL2|LEC1|LPHH1|LPHN2	adhesion G protein-coupled receptor L2	protein-coding	0.008547	0.400000	
chunk0035_443_1	chr11	57569380	57569729	+	0	NA	Intergenic	L2c|LINE|L2	-1224	NM_198183	9246	Hs.425777	NM_004223	ENSG00000156587	UBE2L6	RIG-B|UBCH8	ubiquitin conjugating enzyme E2 L6	protein-coding	0.022923	0.485714	
chunk0069_343_1	chr15	66530713	66531395	+	0	NA	intron (NM_017975, intron 12 of 18)	intron (NM_017975, intron 12 of 18)	25971	NM_001287821	55055	Hs.21331	NM_017975	ENSG00000174442	ZWILCH	KNTC1AP|hZwilch	zwilch kinetochore protein	protein-coding	0.004399	0.332357	
chunk0131_369_1	chr3	152012857	152013064	+	0	NA	Intergenic	Intergenic	-84785	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.000000	0.298077	
chunk0164_444_1	chr6	27897226	27897614	+	0	NA	Intergenic	Intergenic	3995	NM_003527	8348	Hs.484991	NM_003527	ENSG00000274641	HIST1H2BO	H2B.2|H2B/n|H2BFN|dJ193B12.2	histone cluster 1 H2B family member o	protein-coding	0.000000	0.331620	
chunk0008_346_1	chr1	96010120	96010656	+	0	NA	intron (NR_125991, intron 4 of 4)	intron (NR_125991, intron 4 of 4)	18320	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.005597	0.351955	381(GAGAACTGCTTGTACT,-,0.00),382(AGAACTGCTTGTACTC,+,0.00)
chunk0100_209_1	chr2	111905910	111906677	+	0	NA	intron (NM_006343, intron 1 of 18)	intron (NM_006343, intron 1 of 18)	7679	NM_006343	10461	Hs.306178	NM_006343	ENSG00000153208	MERTK	MER|RP38|Tyro12|c-Eyk|c-mer	MER proto-oncogene, tyrosine kinase	protein-coding	0.005215	0.407552	551(AAGAACAGGCTGTCTT,-,0.00),552(AGAACAGGCTGTCTTA,+,0.00)
chunk0196_30_1	chr8	101572733	101573345	+	0	NA	intron (NM_024915, intron 5 of 15)	MER58A|DNA|hAT-Charlie	80599	NM_024915	79977	Hs.661088	NM_024915	ENSG00000083307	GRHL2	BOM|DFNA28|ECTDS|PPCD4|TFCP2L3	grainyhead like transcription factor 2	protein-coding	0.008170	0.332790	
chunk0117_168_1	chr22	20338437	20338641	+	0	NA	Intergenic	Intergenic	-18434	NM_033257	85359	Hs.410965	NM_033257	ENSG00000128185	DGCR6L	DGCR6	DiGeorge syndrome critical region gene 6 like	protein-coding	0.004902	0.287805	
chunk0104_63_1	chr2	171572110	171572455	+	0	NA	Intergenic	LTR47B2|LTR|ERVL	49926	NM_001127383	79901	Hs.221941	NM_024843	ENSG00000071967	CYBRD1	CYB561A2|DCYTB|FRRS3	cytochrome b reductase 1	protein-coding	0.014493	0.424855	
chunk0150_207_1	chr5	35159316	35159738	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	-41405	NM_001204318	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.007109	0.411348	185(CGGGACAGAAAGTCCT,-,0.00),186(GGGACAGAAAGTCCTT,+,0.00)
chunk0097_317_1	chr2	56755598	56756037	+	0	NA	Intergenic	Intergenic	-570047	NR_125368	100129434	Hs.580330	NR_125368		LOC100129434	-	uncharacterized LOC100129434	ncRNA	0.002278	0.397727	
chunk0167_126_1	chr6	61758515	61758774	+	0	NA	intron (NM_152688, intron 6 of 8)	intron (NM_152688, intron 6 of 8)	184541	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.003861	0.303846	
chunk0100_328_1	chr2	116665485	116665900	+	0	NA	Intergenic	L1MB7|LINE|L1	-1148987	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.002410	0.312500	
chunk0189_84_1	chr8	21261829	21262434	+	0	NA	Intergenic	Intergenic	-36108	NR_104677	101929172	Hs.128668	NR_104677	ENSG00000254334	LOC101929172	-	uncharacterized LOC101929172	ncRNA	0.023140	0.524752	
chunk0079_313_1	chr17	17228085	17228569	+	0	NA	intron (NM_144997, intron 3 of 13)	intron (NM_144997, intron 3 of 13)	8861	NM_144606	201163	Hs.31652	NM_144606	ENSG00000154803	FLCN	BHD|DENND8B|FLCL	folliculin	protein-coding	0.018595	0.581443	
chunk0155_294_1	chr5	96267262	96267601	+	0	NA	intron (NR_130776, intron 1 of 4)	L1MA4|LINE|L1	164728	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.002950	0.350000	
chunk0149_137_1	chr5	19891718	19891945	+	0	NA	intron (NM_001167667, intron 2 of 12)	intron (NM_001167667, intron 2 of 12)	-5559	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.004405	0.372807	
chunk0126_410_1	chr3	85522359	85522655	+	0	NA	intron (NM_001256503, intron 2 of 9)	intron (NM_001256503, intron 2 of 9)	17448	NM_001256502	253559	Hs.164578	NM_153184	ENSG00000175161	CADM2	IGSF4D|NECL3|Necl-3|SynCAM 2|synCAM2	cell adhesion molecule 2	protein-coding	0.006757	0.309764	
chunk0089_363_1	chr18	66980637	66981015	+	0	NA	Intergenic	L1MC3|LINE|L1	-100758	NR_049809	100847002		NR_049809	ENSG00000263354	MIR5011	-	microRNA 5011	ncRNA	0.002646	0.364116	
chunk0195_95_1	chr8	94427296	94428013	+	0	NA	TTS (NM_001256141)	TTS (NM_001256141)	9298	NM_001256141	100861412	Hs.30561	NM_001256141	ENSG00000265817	FSBP	-	fibrinogen silencer binding protein	protein-coding	0.002789	0.246518	
chunk0039_455_1	chr11	108534412	108534913	+	0	NA	intron (NM_001308019, intron 4 of 6)	L2c|LINE|L2	3545	NM_001144764	23086	Hs.28540	NM_015065	ENSG00000110723	EXPH5	SLAC2-B|SLAC2B	exophilin 5	protein-coding	0.005988	0.468127	273(AGGAACATCATGTGTC,-,0.00)
chunk0065_355_1	chr14	103736137	103736683	+	0	NA	intron (NM_015316, intron 15 of 16)	intron (NM_015316, intron 15 of 16)	20666	NM_024071	79038	Hs.592322	NM_024071	ENSG00000100711	ZFYVE21	HCVP7TP1|ZF21	zinc finger FYVE-type containing 21	protein-coding	0.020147	0.579525	
chunk0056_68_1	chr13	79317056	79317418	+	0	NA	Intergenic	Intergenic	88984	NM_022118	64062	Hs.558528	NM_018605	ENSG00000139746	RBM26	ARRS2|C13orf10|PPP1R132|PRO1777|SE70-2|ZC3H17	RNA binding motif protein 26	protein-coding	0.002762	0.330579	
chunk0085_257_1	chr18	7618735	7619210	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	51656	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.010526	0.394958	
chunk0040_38_1	chr11	110610219	110610778	+	0	NA	intron (NM_001258418, intron 7 of 14)	intron (NM_001258418, intron 7 of 14)	101552	NM_001258415	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.008945	0.341071	
chunk0102_300_1	chr2	150817910	150818311	+	0	NA	Intergenic	Intergenic	189213	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.000000	0.300995	
chunk0176_305_1	chr7	16844404	16844723	+	0	NA	Intergenic	Intergenic	37426	NM_176813	155465	Hs.100686	NM_176813	ENSG00000173467	AGR3	AG-3|AG3|BCMP11|HAG3|PDIA18|hAG-3	anterior gradient 3, protein disulphide isomerase family member	protein-coding	0.009404	0.434375	
chunk0152_213_1	chr5	60303820	60304397	+	0	NA	intron (NM_001165899, intron 1 of 16)	U6|snRNA|snRNA	-183605	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.017331	0.411765	
chunk0119_279_1	chr22	46067561	46068314	+	0	NA	Intergenic	Intergenic	-13793	NM_018280	55267	Hs.567529	NM_018280		PRR34	C22orf26	PRR34 long non-coding RNA	protein-coding	0.015936	0.391247	
chunk0212_157_1	chrX	132260517	132260897	+	0	NA	intron (NR_110410, intron 2 of 2)	L1MA9|LINE|L1	-41227	NR_073150	57826	Hs.119889	NM_021183	ENSG00000123728	RAP2C	-	RAP2C, member of RAS oncogene family	protein-coding	0.002632	0.335958	
chunk0048_210_1	chr12	81394785	81395624	+	0	NA	intron (NM_001220474, intron 6 of 30)	L1M5|LINE|L1	-25790	NM_001220480	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.003576	0.308333	
chunk0189_205_1	chr8	24123345	24123891	+	0	NA	Intergenic	Intergenic	-170422	NR_130709	10863	Hs.174030	NM_014265	ENSG00000042980	ADAM28	ADAM 28|MDC-L|MDCL|eMDC II|eMDCII	ADAM metallopeptidase domain 28	protein-coding	0.000000	0.394881	282(TGGTACAGGCTGGTCC,-,0.00),283(GGTACAGGCTGGTCCT,+,0.00)
chunk0032_27_1	chr11	842543	842919	+	0	NA	promoter-TSS (NM_003271)	promoter-TSS (NM_003271)	-93	NM_001025239	7106	Hs.654836	NM_003271	ENSG00000214063	TSPAN4	NAG-2|NAG2|TETRASPAN|TM4SF7|TSPAN-4	tetraspanin 4	protein-coding	0.156915	0.761273	
chunk0006_430_1	chr1	76478214	76478562	+	0	NA	intron (NM_152996, intron 3 of 4)	intron (NM_152996, intron 3 of 4)	-389113	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.005747	0.404011	135(GTGGACTACCTGTCCT,-,0.00),136(TGGACTACCTGTCCTG,+,0.00)
chunk0061_344_1	chr14	63624559	63625155	+	0	NA	intron (NM_080666, intron 2 of 2)	L1ME1|LINE|L1	17066	NM_080666	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.008389	0.321608	
chunk0210_398_1	chrX	98110693	98111357	+	0	NA	Intergenic	MIRb|SINE|MIR	-546490	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.007530	0.401504	
chunk0050_243_1	chr12	105274602	105274801	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	-38471	NM_001251904	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.010050	0.545000	
chunk0076_263_1	chr16	69396605	69396985	+	0	NA	Intergenic	Intergenic	-10807	NM_005652	7014	Hs.63335	NM_005652	ENSG00000132604	TERF2	TRBF2|TRF2	telomeric repeat binding factor 2	protein-coding	0.010526	0.412073	
chunk0083_143_1	chr17	65770345	65770880	+	0	NA	intron (NM_001302891, intron 19 of 24)	L1MEc|LINE|L1	55931	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.005607	0.285448	
chunk0064_174_1	chr14	92503143	92503360	+	0	NA	Intergenic	Intergenic	-10530	NM_024832	79890	Hs.326822	NM_024832	ENSG00000100599	RIN3	-	Ras and Rab interactor 3	protein-coding	0.009217	0.518349	124(CTGAACATCCTGTCCT,-,0.00),125(TGAACATCCTGTCCTC,+,0.00)
chunk0039_64_1	chr11	96310879	96311663	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-30167	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.003827	0.383439	
chunk0016_251_1	chr1	200090701	200091454	+	0	NA	intron (NM_205860, intron 5 of 7)	intron (NM_205860, intron 5 of 7)	48252	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.005312	0.448276	
chunk0135_173_1	chr3	188039994	188040495	+	0	NA	Intergenic	L2a|LINE|L2	-113629	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.005988	0.394422	
chunk0055_11_1	chr13	51682087	51682762	+	0	NA	intron (NM_052950, intron 3 of 11)	L2b|LINE|L2	98076	NM_052950	115825	Hs.46506	NM_052950	ENSG00000139668	WDFY2	PROF|WDF2|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.004444	0.386095	306(AGGGACTGTGTGTACT,-,0.00),307(GGGACTGTGTGTACTT,+,0.00)
chunk0169_307_1	chr6	106090515	106091103	+	0	NA	intron (NM_001198, intron 2 of 6)	intron (NM_001198, intron 2 of 6)	4489	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.005102	0.331070	
chunk0135_407_1	chr3	192629401	192629925	+	0	NA	intron (NM_004113, intron 2 of 5)	intron (NM_004113, intron 2 of 5)	97936	NM_004113	2257	Hs.390250	NM_004113	ENSG00000114279	FGF12	EIEE47|FGF12B|FHF1	fibroblast growth factor 12	protein-coding	0.015267	0.401905	
chunk0206_60_1	chr9	119092061	119092542	+	0	NA	Intergenic	Intergenic	277160	NM_014618	1620	Hs.532316	NM_014618	ENSG00000078725	BRINP1	DBC1|DBCCR1|FAM5A	BMP/retinoic acid inducible neural specific 1	protein-coding	0.010395	0.410788	
chunk0208_429_1	chrX	29989568	29990199	+	0	NA	Intergenic	L1MA3|LINE|L1	-225675	NM_002364	4113	Hs.113824	NM_002364	ENSG00000099399	MAGEB2	CT3.2|DAM6|MAGE-XP-2	MAGE family member B2	protein-coding	0.004754	0.359177	
chunk0113_52_1	chr20	50142109	50142569	+	0	NA	intron (NR_027889, intron 3 of 6)	L2a|LINE|L2	11459	NM_001162505	387521	Hs.744839	NM_199129	ENSG00000240849	TMEM189	KUA	transmembrane protein 189	protein-coding	0.015217	0.483731	
chunk0027_302_1	chr10	77873661	77873971	+	0	NA	intron (NM_004747, intron 1 of 31)	intron (NM_004747, intron 1 of 31)	52774	NM_004747	9231	Hs.652690	NM_004747	ENSG00000151208	DLG5	LP-DLG|P-DLG5|PDLG	discs large MAGUK scaffold protein 5	protein-coding	0.012903	0.594855	87(CAGCACACAGAGTTCT,-,0.00),88(AGCACACAGAGTTCTC,+,0.00)
chunk0157_398_1	chr5	124207065	124207266	+	0	NA	intron (NR_125774, intron 4 of 5)	intron (NR_125774, intron 4 of 5)	231355	NR_125774	103724389	Hs.582211	NR_125774		LINC01170	-	long intergenic non-protein coding RNA 1170	ncRNA	0.000000	0.381188	
chunk0087_427_1	chr18	42342117	42342431	+	0	NA	intron (NR_046174, intron 4 of 9)	LTR48|LTR|ERV1	155606	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.006369	0.412698	156(AAAAACTTTCTGTCCT,-,0.00),157(AAAACTTTCTGTCCTT,+,0.00)
chunk0071_314_1	chr15	86402982	86403682	+	0	NA	intron (NM_152336, intron 17 of 23)	intron (NM_152336, intron 17 of 23)	-86364	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.002857	0.363766	
chunk0005_272_1	chr1	59902020	59902480	+	0	NA	intron (NM_000775, intron 7 of 8)	intron (NM_000775, intron 7 of 8)	24501	NM_000775	1573	Hs.152096	NM_000775	ENSG00000134716	CYP2J2	CPJ2|CYPIIJ2	cytochrome P450 family 2 subfamily J member 2	protein-coding	0.002174	0.379610	
chunk0148_349_1	chr5	14523405	14524115	+	0	NA	Intergenic	L1MC1|LINE|L1	-58022	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.021127	0.478200	
chunk0068_352_1	chr15	57902831	57903219	+	0	NA	Intergenic	Intergenic	111072	NM_170697	8854	Hs.643455	NM_003888	ENSG00000128918	ALDH1A2	RALDH(II)|RALDH2|RALDH2-T	aldehyde dehydrogenase 1 family member A2	protein-coding	0.002577	0.347044	
chunk0024_61_1	chr10	33963714	33964467	+	0	NA	Intergenic	Intergenic	-191410	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.006640	0.399204	
chunk0023_270_1	chr10	27938851	27939517	+	0	NA	intron (NM_001290020, intron 14 of 19)	intron (NM_001290020, intron 14 of 19)	42733	NM_001290021	55130	Hs.127530	NM_018076	ENSG00000169126	ARMC4	CILD23	armadillo repeat containing 4	protein-coding	0.010511	0.418291	
chunk0063_406_1	chr14	88212843	88213042	+	0	NA	intron (NM_021161, intron 4 of 6)	intron (NM_021161, intron 4 of 6)	57969	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.000000	0.505000	
chunk0017_289_1	chr1	210301556	210301846	+	0	NA	Intergenic	Intergenic	-26551	NM_001122834	55733	Hs.58650	NM_018194	ENSG00000054392	HHAT	MART2|SKI1|Skn	hedgehog acyltransferase	protein-coding	0.017241	0.405498	
chunk0065_181_1	chr15	26472958	26473416	+	0	NA	Intergenic	LTR23|LTR|ERV1	155991	NM_001191321	2562	Hs.302352	NM_000814	ENSG00000166206	GABRB3	ECA5|EIEE43	gamma-aminobutyric acid type A receptor beta3 subunit	protein-coding	0.013100	0.407407	
chunk0098_337_1	chr2	77180619	77180907	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	194798	NR_110284	101927907	Hs.382185	NR_110284	ENSG00000234653	LOC101927907	-	uncharacterized LOC101927907	ncRNA	0.006944	0.314879	207(CAGAACATTGTGTTCC,-,0.00),208(AGAACATTGTGTTCCA,+,0.00)
chunk0078_59_1	chr17	1456126	1456337	+	0	NA	promoter-TSS (NM_016823)	promoter-TSS (NM_016823)	36	NM_005206	1398	Hs.461896	NM_005206	ENSG00000167193	CRK	CRKII|p38	CRK proto-oncogene, adaptor protein	protein-coding	0.146919	0.783019	
chunk0002_226_1	chr1	20021499	20022046	+	0	NA	Intergenic	Intergenic	-41333	NM_001161728	5320	Hs.466804	NM_000300	ENSG00000188257	PLA2G2A	MOM1|PLA2|PLA2B|PLA2L|PLA2S|PLAS1|sPLA2	phospholipase A2 group IIA	protein-coding	0.018282	0.346715	
chunk0081_233_1	chr17	42895097	42895579	+	0	NA	intron (NR_027254, intron 1 of 5)	intron (NR_027254, intron 1 of 5)	3396	NR_027254	388387	Hs.632257	NM_207388	ENSG00000213373	LINC00671	-	long intergenic non-protein coding RNA 671	ncRNA	0.006224	0.457557	287(CAGACCAGACTGTACT,-,0.00),288(AGACCAGACTGTACTT,+,0.00)
chunk0135_162_1	chr3	187830253	187830898	+	0	NA	Intergenic	L2a|LINE|L2	-84850	NM_001706	604	Hs.478588	NM_001706	ENSG00000113916	BCL6	BCL5|BCL6A|LAZ3|ZBTB27|ZNF51	BCL6 transcription repressor	protein-coding	0.006202	0.413313	
chunk0001_410_1	chr1	11012227	11012838	+	0	NA	promoter-TSS (NM_007375)	promoter-TSS (NM_007375)	-90	NM_007375	23435	Hs.300624	NM_007375	ENSG00000120948	TARDBP	ALS10|TDP-43	TAR DNA binding protein	protein-coding	0.083470	0.658497	
chunk0008_218_1	chr1	93847568	93847798	+	0	NA	promoter-TSS (NM_001261408)	promoter-TSS (NM_001261408)	-533	NM_001261408	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.056522	0.484848	
chunk0022_60_1	chr10	8389515	8390205	+	0	NA	Intergenic	7SK|RNA|RNA	-121555	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.004348	0.384949	
chunk0011_296_1	chr1	151549062	151549261	+	0	NA	intron (NM_001126337, intron 1 of 11)	intron (NM_001126337, intron 1 of 11)	3365	NR_030280	693139		NR_030280	ENSG00000207606	MIR554	MIRN554|hsa-mir-554	microRNA 554	ncRNA	0.005025	0.485000	
chunk0196_160_1	chr8	104895814	104896453	+	0	NA	Intergenic	Intergenic	-307109	NM_013437	29967	Hs.600630	NM_013437	ENSG00000147650	LRP12	MIG13A|ST7	LDL receptor related protein 12	protein-coding	0.001565	0.431250	234(TAGGACAGACAGTTCT,-,0.00),235(AGGACAGACAGTTCTT,+,0.00),252(CAGAACAGAGTGTTTA,-,0.00),253(AGAACAGAGTGTTTAC,+,0.00),420(CAACACATCCTGTACT,-,0.00),421(AACACATCCTGTACTC,+,0.00)
chunk0096_451_1	chr2	39631175	39631446	+	0	NA	Intergenic	Intergenic	-34188	NM_001167959	130733	Hs.40808	NM_152390	ENSG00000152154	TMEM178A	TMEM178	transmembrane protein 178A	protein-coding	0.003690	0.316176	
chunk0144_246_1	chr4	135400673	135401005	+	0	NA	Intergenic	Intergenic	487254	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.000000	0.240240	
chunk0054_42_1	chr13	41136414	41136622	+	0	NA	intron (NR_120423, intron 1 of 3)	MER89-int|LTR|ERV1	3590	NR_120423	101929140	Hs.663088	NR_120423	ENSG00000278390	LOC101929140	-	uncharacterized LOC101929140	ncRNA	0.004808	0.377990	
chunk0108_302_1	chr2	235052742	235053519	+	0	NA	intron (NM_014521, intron 5 of 5)	intron (NM_014521, intron 5 of 5)	101146	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.025740	0.508997	148(CAGCACTGGGTGTGCC,-,0.00),149(AGCACTGGGTGTGCCT,+,0.00),254(CAGAACTGCCTGTCCC,-,0.00),255(AGAACTGCCTGTCCCT,+,0.00)
chunk0059_359_1	chr14	37278635	37279258	+	0	NA	intron (NM_001195296, intron 8 of 14)	intron (NM_001195296, intron 8 of 14)	81033	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.004815	0.314103	
chunk0049_211_1	chr12	93200187	93200737	+	0	NA	intron (NR_040096, intron 3 of 4)	LTR16E2|LTR|ERVL	26096	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.007273	0.480944	321(GAGCACTGGCTGTCCA,-,0.00),322(AGCACTGGCTGTCCAA,+,0.00)
chunk0021_124_1	chr10	3754811	3755135	+	0	NA	Intergenic	Intergenic	30308	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.015432	0.415385	
chunk0082_371_1	chr17	60356050	60356349	+	0	NA	intron (NM_032582, intron 1 of 33)	L1M4|LINE|L1	36026	NM_032582	84669	Hs.132868	NM_032582	ENSG00000170832	USP32	NY-REN-60|USP10	ubiquitin specific peptidase 32	protein-coding	0.000000	0.400000	
chunk0005_263_1	chr1	59775403	59775842	+	0	NA	intron (NR_110627, intron 2 of 2)	intron (NR_110627, intron 2 of 2)	2827	NR_110627	101926944	Hs.720353	NR_110627		LOC101926944	-	uncharacterized LOC101926944	ncRNA	0.009112	0.395455	
chunk0093_369_1	chr19	55683772	55684428	+	0	NA	intron (NM_001130071, intron 3 of 10)	intron (NM_001130071, intron 3 of 10)	7475	NM_001130071	29924	Hs.279953	NM_013333	ENSG00000063245	EPN1	-	epsin 1	protein-coding	0.018293	0.511416	
chunk0012_23_1	chr1	154961433	154961682	+	0	NA	TTS (NM_001130040)	TTS (NM_001130040)	225	NM_138300	90780	Hs.533597	NM_138300	ENSG00000163348	PYGO2	1190004M21Rik	pygopus family PHD finger 2	protein-coding	0.092369	0.768000	
chunk0154_203_1	chr5	80307679	80307906	+	0	NA	Intergenic	Intergenic	-7314	NR_004845	644936	Hs.627173	NR_004845		LOC644936	-	actin beta pseudogene	pseudo	0.013216	0.337719	
chunk0185_196_1	chr7	128403918	128404808	+	0	NA	intron (NM_001304521, intron 1 of 13)	intron (NM_001304521, intron 1 of 13)	1607	NM_001142574	3614	Hs.654401	NM_000883	ENSG00000106348	IMPDH1	IMPD|IMPD1|IMPDH-I|LCA11|RP10|sWSS2608	inosine monophosphate dehydrogenase 1	protein-coding	0.014607	0.528620	638(AGGAACACTATGAACT,-,0.00),639(GGAACACTATGAACTG,+,0.00)
chunk0023_187_1	chr10	24795073	24795512	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-71624	NM_020824	57584	Hs.524195	NM_020824	ENSG00000107863	ARHGAP21	ARHGAP10	Rho GTPase activating protein 21	protein-coding	0.011390	0.456818	164(GAGAACACAGTGGCCC,-,0.00),165(AGAACACAGTGGCCCT,+,0.00)
chunk0063_172_1	chr14	80385409	80385633	+	0	NA	intron (NR_038355, intron 4 of 8)	intron (NR_038355, intron 4 of 8)	-154467	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.004464	0.511111	
chunk0092_55_1	chr19	20035996	20036367	+	0	NA	intron (NM_033196, intron 1 of 3)	intron (NM_033196, intron 1 of 3)	3074	NM_001077349	91120	Hs.306298	NM_033196	ENSG00000197124	ZNF682	BC39498_3	zinc finger protein 682	protein-coding	0.013477	0.403226	133(AGGTACAGAGCGTACT,-,0.00),134(GGTACAGAGCGTACTC,+,0.00)
chunk0115_133_1	chr21	23299553	23299991	+	0	NA	Intergenic	Intergenic	85063	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.004566	0.339408	
chunk0014_195_1	chr1	178970227	178970721	+	0	NA	Intergenic	Intergenic	-55465	NM_014864	9917	Hs.5737	NM_014864	ENSG00000116199	FAM20B	gxk1	FAM20B glycosaminoglycan xylosylkinase	protein-coding	0.012146	0.557576	190(AAGCACAACCTGTGCT,-,0.00),191(AGCACAACCTGTGCTA,+,0.00)
chunk0009_357_1	chr1	109632386	109633154	+	0	NA	TTS (NM_004037)	TTS (NM_004037)	7343	NM_203404	271	Hs.82927	NM_004037	ENSG00000116337	AMPD2	PCH9|SPG63	adenosine monophosphate deaminase 2	protein-coding	0.010417	0.585176	406(TGGAACAGCATGAGCC,-,0.00),407(GGAACAGCATGAGCCT,+,0.00)
chunk0102_16_1	chr2	141497304	141497684	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	634207	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.010526	0.370079	
chunk0076_334_1	chr16	71181494	71182100	+	0	NA	intron (NM_001270974, intron 3 of 85)	L2a|LINE|L2	48925	NM_001270974	54768	Hs.351914	NM_017558	ENSG00000157423	HYDIN	CILD5|HYDIN1|HYDIN2|PPP1R31	HYDIN axonemal central pair apparatus protein	protein-coding	0.003300	0.359143	
chunk0089_234_1	chr18	61882064	61882802	+	0	NA	intron (NM_173557, intron 1 of 1)	intron (NM_173557, intron 1 of 1)	10638	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.004065	0.401894	
chunk0054_365_1	chr13	49772641	49773116	+	0	NA	intron (NM_002267, intron 1 of 16)	L1ME1|LINE|L1	20043	NM_002267	3839	Hs.527919	NM_002267	ENSG00000102753	KPNA3	IPOA4|SRP1|SRP1gamma|SRP4|hSRP1	karyopherin subunit alpha 3	protein-coding	0.006316	0.373950	
chunk0138_165_1	chr4	37851101	37851898	+	0	NA	intron (NM_018290, intron 12 of 13)	intron (NM_018290, intron 12 of 13)	24839	NM_018290	55276	Hs.23363	NM_018290	ENSG00000169299	PGM2	MSTP006	phosphoglucomutase 2	protein-coding	0.010038	0.413534	
chunk0172_259_1	chr6	137401044	137401553	+	0	NA	Intergenic	Intergenic	93096	NM_175747	167826	Hs.195398	NM_175747	ENSG00000177468	OLIG3	Bhlhb7|bHLHe20	oligodendrocyte transcription factor 3	protein-coding	0.011788	0.388235	
chunk0092_184_1	chr19	30152504	30153215	+	0	NA	Intergenic	Intergenic	210620	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.014065	0.522472	
chunk0140_320_1	chr4	73394169	73394424	+	0	NA	Intergenic	MIR|SINE|MIR	-9959	NM_000477	213	Hs.418167	NM_000477	ENSG00000163631	ALB	HSA|PRO0883|PRO0903|PRO1341	albumin	protein-coding	0.003922	0.382812	
chunk0145_154_1	chr4	147093200	147093621	+	0	NA	Intergenic	Intergenic	-147528	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.004751	0.379147	
chunk0047_230_1	chr12	71856630	71857053	+	0	NA	intron (NR_027449, intron 1 of 15)	intron (NR_027449, intron 1 of 15)	-5858	NR_024072	729633	Hs.716256	NR_024072		MRS2P2	-	MRS2 pseudogene 2	pseudo	0.007092	0.375000	
chunk0200_440_1	chr9	30482430	30482953	+	0	NA	Intergenic	L1PREC2|LINE|L1	-74237	NR_046204	401497	Hs.680131	NR_046204		LINC01242	-	long intergenic non-protein coding RNA 1242	ncRNA	0.007648	0.360687	
chunk0046_361_1	chr12	63068178	63068685	+	0	NA	Intergenic	Intergenic	84379	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.003945	0.375984	
chunk0073_429_1	chr16	19131300	19131984	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	17710	NM_001034841	162073	Hs.530899	NM_001034841	ENSG00000205730	ITPRIPL2	-	ITPRIP like 2	protein-coding	0.010234	0.452555	
chunk0151_32_1	chr5	41790293	41791013	+	0	NA	intron (NM_000436, intron 13 of 16)	intron (NM_000436, intron 13 of 16)	-79377	NR_046635	100874002	Hs.375537	NR_046635	ENSG00000248668	OXCT1-AS1	-	OXCT1 antisense RNA 1	ncRNA	0.008333	0.345354	
chunk0205_148_1	chr9	108294480	108294758	+	0	NA	Intergenic	MIRc|SINE|MIR	561376	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.010791	0.444444	
chunk0187_382_1	chr7	157662051	157662560	+	0	NA	intron (NM_001308268, intron 13 of 22)	intron (NM_001308268, intron 13 of 22)	-87883	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.031434	0.545098	
chunk0099_149_1	chr2	86703502	86704176	+	0	NA	intron (NM_001198954, intron 1 of 7)	LTR3B|LTR|ERVK	-16452	NM_022780	64795	Hs.75277	NM_022780	ENSG00000153561	RMND5A	CTLH|GID2|GID2A|RMD5|p44CTLH	required for meiotic nuclear division 5 homolog A	protein-coding	0.019288	0.404444	
chunk0039_397_1	chr11	107334079	107334602	+	0	NA	intron (NM_152434, intron 16 of 17)	intron (NM_152434, intron 16 of 17)	123506	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.003824	0.333969	
chunk0037_341_1	chr11	77374425	77375219	+	0	NA	intron (NM_001128620, intron 4 of 15)	Tigger3c|DNA|TcMar-Tigger	-87404	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.007557	0.371069	
chunk0016_323_1	chr1	201604813	201605377	+	0	NA	Intergenic	Intergenic	-43227	NM_020443	89796	Hs.585374	NM_020443	ENSG00000134369	NAV1	POMFIL3|STEERIN1|UNC53H1	neuron navigator 1	protein-coding	0.008865	0.430088	
chunk0207_99_1	chrX	9906718	9907290	+	0	NA	intron (NM_001649, intron 5 of 9)	intron (NM_001649, intron 5 of 9)	-60354	NM_001195081	100288814		NM_001195081	ENSG00000234469	CLDN34	-	claudin 34	protein-coding	0.022727	0.528796	180(AGGAACATAGTGTCCC,-,0.00),181(GGAACATAGTGTCCCT,+,0.00)
chunk0043_459_1	chr12	26739995	26740194	+	0	NA	intron (NM_002223, intron 2 of 56)	intron (NM_002223, intron 2 of 56)	93104	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.010050	0.355000	
chunk0029_123_1	chr10	98517200	98518106	+	0	NA	intron (NM_001166246, intron 9 of 12)	intron (NM_001166246, intron 9 of 12)	-70690	NM_001311345	3257	Hs.404568	NM_000195	ENSG00000107521	HPS1	BLOC3S1|HPS	HPS1 biogenesis of lysosomal organelles complex 3 subunit 1	protein-coding	0.007726	0.446527	
chunk0142_308_1	chr4	100592610	100593025	+	0	NA	Intergenic	MER53|DNA|hAT	-74724	NM_016242	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.000000	0.358173	
chunk0043_204_1	chr12	19439420	19440199	+	0	NA	promoter-TSS (NM_001267043)	promoter-TSS (NM_001267043)	135	NM_153207	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.119384	0.750000	
chunk0004_249_1	chr1	47477936	47478543	+	0	NA	Intergenic	Intergenic	-40922	NR_126355	102724077	Hs.159718	NR_126355		LINC01389	-	long intergenic non-protein coding RNA 1389	ncRNA	0.019769	0.560855	
chunk0060_404_1	chr14	53047319	53047751	+	0	NA	intron (NM_030637, intron 11 of 11)	L2a|LINE|L2	-96438	NM_001135000	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.009259	0.443418	
chunk0175_124_1	chr7	3369309	3369860	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	68136	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.005445	0.342391	
chunk0198_299_1	chr8	137975044	137975647	+	0	NA	Intergenic	Intergenic	521477	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.000000	0.382450	
chunk0127_346_1	chr3	100712404	100712753	+	0	NA	intron (NM_001195479, intron 1 of 7)	intron (NM_001195479, intron 1 of 7)	3036	NM_001195478	10342	Hs.518123	NM_006070	ENSG00000114354	TFG	HMSNP|SPG57|TF6|TRKT3	trafficking from ER to golgi regulator	protein-coding	0.008596	0.371429	
chunk0170_350_1	chr6	116416501	116416971	+	0	NA	intron (NM_001080976, intron 2 of 5)	intron (NM_001080976, intron 2 of 5)	-44634	NM_001010919	441168	Hs.381220	NM_001010919	ENSG00000188820	CALHM6	C6orf187|FAM26F|INAM|dJ93H18.5	calcium homeostasis modulator family member 6	protein-coding	0.002128	0.301486	
chunk0128_238_1	chr3	108409761	108410161	+	0	NA	intron (NM_014981, intron 32 of 41)	L1ME3G|LINE|L1	98176	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.010000	0.349127	
chunk0142_229_1	chr4	98345783	98346582	+	0	NA	intron (NM_021159, intron 3 of 14)	intron (NM_021159, intron 3 of 14)	84806	NM_001100426	5910	Hs.132858	NM_021159	ENSG00000138698	RAP1GDS1	GDS1|SmgGDS	Rap1 GTPase-GDP dissociation stimulator 1	protein-coding	0.007509	0.372500	
chunk0029_285_1	chr10	103768014	103768541	+	0	NA	intron (NM_014631, intron 2 of 13)	L2a|LINE|L2	21498	NR_038940	100505839	Hs.655149	NR_038940	ENSG00000280693	SH3PXD2A-AS1	-	SH3PXD2A antisense RNA 1	ncRNA	0.020873	0.515152	
chunk0052_242_1	chr13	25980976	25981509	+	0	NA	intron (NM_001313741, intron 34 of 35)	intron (NM_001313741, intron 34 of 35)	69818	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.005629	0.325843	
chunk0162_311_1	chr6	6678907	6679227	+	0	NA	Intergenic	Intergenic	-56241	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.028125	0.535826	129(CGGAACGAGGTGTGCC,-,0.00),130(GGAACGAGGTGTGCCT,+,0.00)
chunk0037_259_1	chr11	75592690	75593420	+	0	NA	intron (NM_033063, intron 3 of 3)	L2b|LINE|L2	30999	NM_001235	871	Hs.596449	NM_001235	ENSG00000149257	SERPINH1	AsTP3|CBP1|CBP2|HSP47|OI10|PIG14|PPROM|RA-A47|SERPINH2|gp46	serpin family H member 1	protein-coding	0.002740	0.470588	
chunk0050_308_1	chr12	106894942	106895398	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-60596	NM_152261	90488	Hs.257664	NM_152261	ENSG00000151135	TMEM263	C12orf23	transmembrane protein 263	protein-coding	0.006579	0.431072	
chunk0056_104_1	chr13	82561155	82561727	+	0	NA	Intergenic	Intergenic	1320952	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.000000	0.244328	
chunk0004_351_1	chr1	51255532	51255975	+	0	NA	intron (NM_014372, intron 1 of 2)	L1ME3A|LINE|L1	19480	NM_014372	26994	Hs.309641	NM_014372	ENSG00000123091	RNF11	CGI-123|SID1669	ring finger protein 11	protein-coding	0.004515	0.382883	
chunk0157_339_1	chr5	122493757	122494204	+	0	NA	Intergenic	L2b|LINE|L2	-14893	NR_051996	153163	Hs.679757	NR_051996	ENSG00000250328	MGC32805	-	uncharacterized LOC153163	ncRNA	0.006711	0.462054	
chunk0083_129_1	chr17	65416915	65417212	+	0	NA	Intergenic	Intergenic	-40478	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.010101	0.489933	141(GGGGACAGGATGTGCT,-,0.00),142(GGGACAGGATGTGCTG,+,0.00)
chunk0071_95_1	chr15	80961556	80962040	+	0	NA	intron (NR_126328, intron 1 of 2)	L1PA6|LINE|L1	28080	NR_126327	23184	Hs.578450	NM_015154	ENSG00000117899	MESD	BOCA|MESDC2	mesoderm development LRP chaperone	protein-coding	0.004132	0.354639	299(AGGAACAACCTGTACC,-,0.00),300(GGAACAACCTGTACCA,+,0.00)
chunk0150_212_1	chr5	35198097	35198451	+	0	NA	intron (NM_000949, intron 1 of 9)	intron (NM_000949, intron 1 of 9)	32315	NM_000949	5618	Hs.368587	NM_000949	ENSG00000113494	PRLR	HPRL|MFAB|RI-PRLR|hPRLrI	prolactin receptor	protein-coding	0.011299	0.509859	
chunk0093_270_1	chr19	51509047	51509246	+	0	NA	Intergenic	Intergenic	-7357	NM_053003	89858	Hs.249741	NM_033329	ENSG00000254521	SIGLEC12	S2V|SIGLECL1|SLG|Siglec-XII	sialic acid binding Ig like lectin 12 (gene/pseudogene)	protein-coding	0.030151	0.630000	
chunk0138_415_1	chr4	44876249	44877207	+	0	NA	Intergenic	Intergenic	-150094	NR_073094	132789	Hs.21398	NM_138335	ENSG00000163281	GNPDA2	GNP2|SB52	glucosamine-6-phosphate deaminase 2	protein-coding	0.006263	0.346194	584(GAGTACAGGTTGTTCT,-,0.00),585(AGTACAGGTTGTTCTC,+,0.00)
chunk0050_229_1	chr12	104956990	104957272	+	0	NA	Intergenic	L1MB7|LINE|L1	-28437	NM_032148	84102	Hs.577463	NM_032148	ENSG00000136052	SLC41A2	SLC41A1-L1	solute carrier family 41 member 2	protein-coding	0.014184	0.367491	
chunk0183_112_1	chr7	105339380	105339742	+	0	NA	intron (NM_182692, intron 2 of 15)	intron (NM_182692, intron 2 of 15)	-40782	NM_001278273	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.002762	0.396694	
chunk0044_217_1	chr12	31280081	31280601	+	0	NA	TTS (NM_001135812)	TTS (NM_001135812)	-43975	NR_026806	79857	Hs.534485	NM_024799	ENSG00000177340	FLJ13224	-	uncharacterized LOC79857	ncRNA	0.000000	0.357006	281(GGGAACATTTTGTTCT,-,0.00),282(GGAACATTTTGTTCTT,+,0.00)
chunk0118_361_1	chr22	36370101	36370596	+	0	NA	intron (NM_002473, intron 1 of 40)	intron (NM_002473, intron 1 of 40)	17719	NM_002473	4627	Hs.474751	NM_002473	ENSG00000100345	MYH9	BDPLT6|DFNA17|EPSTS|FTNS|MATINS|MHA|NMHC-II-A|NMMHC-IIA|NMMHCA	myosin heavy chain 9	protein-coding	0.018182	0.504032	
chunk0094_61_1	chr2	3380408	3380809	+	0	NA	intron (NM_016030, intron 1 of 11)	intron (NM_016030, intron 1 of 11)	933	NM_016030	51112	Hs.252713	NM_016030	ENSG00000171853	TRAPPC12	CGI-87|PEBAS|TTC-15|TTC15	trafficking protein particle complex 12	protein-coding	0.022444	0.390547	
chunk0147_296_1	chr4	184530597	184531070	+	0	NA	Intergenic	L1ME1|LINE|L1	-56261	NM_002199	3660	Hs.654566	NM_002199	ENSG00000168310	IRF2	IRF-2	interferon regulatory factor 2	protein-coding	0.006342	0.369198	
chunk0182_104_1	chr7	93265209	93265573	+	0	NA	intron (NM_024553, intron 9 of 11)	MER58A|DNA|hAT-Charlie	33051	NM_024553	55610	Hs.202424	NM_017667	ENSG00000004766	VPS50	CCDC132|VPS54L	VPS50 subunit of EARP/GARPII complex	protein-coding	0.010989	0.372603	
chunk0212_230_1	chrX	136291177	136291618	+	0	NA	Intergenic	Intergenic	-9566	NM_153834	139378	Hs.381354	NM_153834	ENSG00000156920	ADGRG4	GPR112|PGR17|RP1-299I16	adhesion G protein-coupled receptor G4	protein-coding	0.009070	0.454751	
chunk0025_70_1	chr10	49931990	49932396	+	0	NA	exon (NM_001303487, exon 3 of 17)	exon (NM_001303487, exon 3 of 17)	9834	NR_130169	8505	Hs.535298	NM_003631	ENSG00000227345	PARG	PARG99	poly(ADP-ribose) glycohydrolase	protein-coding	0.012315	0.398034	
chunk0186_242_1	chr7	140913219	140913439	+	0	NA	intron (NM_004333, intron 1 of 17)	L2a|LINE|L2	11435	NM_004333	673	Hs.324250	NM_004333	ENSG00000157764	BRAF	B-RAF1|B-raf|BRAF1|NS7|RAFB1	B-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.000000	0.416290	
chunk0172_341_1	chr6	138807700	138808204	+	0	NA	intron (NM_001195037, intron 1 of 20)	L1ME3B|LINE|L1	11841	NM_001195037	345930	Hs.660603	NM_001077706	ENSG00000203734	ECT2L	ARHGEF32|C6orf91|FBXO49|LFDH|dJ509I19.2|dJ509I19.3|dJ509I19.5	epithelial cell transforming 2 like	protein-coding	0.000000	0.388119	
chunk0080_361_1	chr17	33048954	33049445	+	0	NA	intron (NM_183377, intron 3 of 9)	MIRb|SINE|MIR	57335	NM_173847	124912	Hs.434112	NM_173847	ENSG00000141316	SPACA3	ALLP17|CT54|LYC3|LYZC|LYZL3|SLLP1	sperm acrosome associated 3	protein-coding	0.006110	0.449187	
chunk0036_281_1	chr11	65382281	65382943	+	0	NA	promoter-TSS (NM_001278250)	promoter-TSS (NM_001278250)	62	NM_001077241	283130	Hs.661604	NM_182556	ENSG00000162241	SLC25A45	-	solute carrier family 25 member 45	protein-coding	0.025680	0.609351	
chunk0161_35_1	chr5	165816922	165817465	+	0	NA	Intergenic	Intergenic	1109177	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.005525	0.312500	
chunk0012_85_1	chr1	156115764	156116086	+	0	NA	intron (NM_001282625, intron 4 of 12)	intron (NM_001282625, intron 4 of 12)	1255	NM_005572	4000	Hs.594444	NM_005572	ENSG00000160789	LMNA	CDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1	lamin A/C	protein-coding	0.021739	0.616099	
chunk0052_320_1	chr12	125341531	125341806	+	0	NA	intron (NM_052907, intron 1 of 8)	intron (NM_052907, intron 1 of 8)	15052	NM_052907	114795	Hs.524838	NM_052907	ENSG00000139364	TMEM132B	-	transmembrane protein 132B	protein-coding	0.003636	0.427536	
chunk0185_358_1	chr7	132411463	132412081	+	0	NA	intron (NM_001105543, intron 3 of 3)	intron (NM_001105543, intron 3 of 3)	164792	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.011327	0.474960	
chunk0148_323_1	chr5	13962848	13963048	+	0	NA	Intergenic	Intergenic	-18468	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.040000	0.577114	38(AAAGACAAACTGTCCC,-,0.00),39(AAGACAAACTGTCCCG,+,0.00)
chunk0181_62_1	chr7	80210336	80211021	+	0	NA	intron (NM_002069, intron 5 of 7)	intron (NM_002069, intron 5 of 7)	74923	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.005839	0.348397	
chunk0206_55_1	chr9	117946379	117946659	+	0	NA	Intergenic	Intergenic	242344	NM_003266	7099	Hs.174312	NM_003266	ENSG00000136869	TLR4	ARMD10|CD284|TLR-4|TOLL	toll like receptor 4	protein-coding	0.007143	0.323843	
chunk0210_339_1	chrX	95464931	95465482	+	0	NA	Intergenic	L1M4|LINE|L1	-401980	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.007260	0.297101	
chunk0192_393_1	chr8	68808727	68809074	+	0	NA	intron (NM_052958, intron 12 of 13)	intron (NM_052958, intron 12 of 13)	295290	NR_039986	100505718	Hs.122386	NR_039986	ENSG00000253658	LINC01592	-	long intergenic non-protein coding RNA 1592	ncRNA	0.002882	0.364943	
chunk0070_311_1	chr15	75181888	75182351	+	0	NA	Intergenic	Intergenic	-19761	NM_015492	56905	Hs.17936	NM_015492	ENSG00000167173	C15orf39	-	chromosome 15 open reading frame 39	protein-coding	0.008639	0.413793	
chunk0041_92_1	chr11	124625085	124625714	+	0	NA	intron (NM_032811, intron 2 of 8)	intron (NM_032811, intron 2 of 8)	2553	NR_016021	84897	Hs.436410	NM_032811	ENSG00000154144	TBRG1	NIAM|TB-5	transforming growth factor beta regulator 1	protein-coding	0.012719	0.404762	
chunk0126_286_1	chr3	80190081	80190376	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	-422319	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.010169	0.432432	
chunk0185_424_1	chr7	134646448	134646656	+	0	NA	promoter-TSS (NM_001293085)	promoter-TSS (NM_001293085)	-227	NM_199186	669	Hs.198365	NM_001724	ENSG00000172331	BPGM	DPGM|ECYT8	bisphosphoglycerate mutase	protein-coding	0.052885	0.535885	
chunk0017_145_1	chr1	206709029	206709302	+	0	NA	intron (NM_032960, intron 1 of 9)	intron (NM_032960, intron 1 of 9)	24145	NM_032960	9261	Hs.643566	NM_004759	ENSG00000162889	MAPKAPK2	MAPKAP-K2|MK-2|MK2	MAPK activated protein kinase 2	protein-coding	0.007326	0.419708	
chunk0186_320_1	chr7	143075741	143075940	+	0	NA	Intergenic	Intergenic	-12055	NR_002140	89883	Hs.339818	NR_002140		OR6W1P	OR6W1|sdolf	olfactory receptor family 6 subfamily W member 1 pseudogene	pseudo	0.010050	0.460000	
chunk0208_443_1	chrX	31315974	31316557	+	0	NA	intron (NM_004021, intron 19 of 34)	intron (NM_004021, intron 19 of 34)	-49358	NM_004015	1756	Hs.495912	NM_000109	ENSG00000198947	DMD	BMD|CMD3B|DXS142|DXS164|DXS206|DXS230|DXS239|DXS268|DXS269|DXS270|DXS272|MRX85	dystrophin	protein-coding	0.003431	0.376712	
chunk0100_17_1	chr2	105106994	105107905	+	0	NA	Intergenic	Intergenic	-4505	NR_110227	101927492	Hs.469537	NR_110227	ENSG00000231851	UTAT33	-	uncharacterized LOC101927492	ncRNA	0.013172	0.412281	
chunk0001_160_1	chr1	6343649	6343889	+	0	NA	intron (NM_181864, intron 2 of 8)	intron (NM_181864, intron 2 of 8)	15175	NM_181866	11332	Hs.126137	NM_007274	ENSG00000097021	ACOT7	ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH	acyl-CoA thioesterase 7	protein-coding	0.016667	0.535270	
chunk0209_452_1	chrX	66003667	66003866	+	0	NA	Intergenic	L2b|LINE|L2	-15104	NR_029637	407008		NR_029637	ENSG00000284567	MIR223	MIRN223|miRNA223|mir-223	microRNA 223	ncRNA	0.005025	0.340000	
chunk0059_241_1	chr14	34676872	34677128	+	0	NA	Intergenic	MIRb|SINE|MIR	36817	NM_021914	1073	Hs.180141	NM_021914	ENSG00000165410	CFL2	NEM7	cofilin 2	protein-coding	0.000000	0.431907	
chunk0179_220_1	chr7	47791560	47792248	+	0	NA	intron (NM_138295, intron 56 of 56)	intron (NM_138295, intron 56 of 56)	-3387	NM_025031	80099	Hs.287647	NM_025031		C7orf69	-	chromosome 7 open reading frame 69	ncRNA	0.007267	0.447025	189(AGGTACTTCATGTTCT,-,0.00),190(GGTACTTCATGTTCTC,+,0.00),360(GGCACATGGTGTGTCT,+,0.00)
chunk0169_312_1	chr6	106136047	106136565	+	0	NA	Intergenic	Intergenic	37444	NM_182907	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.025097	0.514451	
chunk0125_95_1	chr3	65348693	65349086	+	0	NA	Intergenic	L2a|LINE|L2	-544927	NR_046575	100873983	Hs.663889	NR_046575	ENSG00000240175	MAGI1-AS1	-	MAGI1 antisense RNA 1	ncRNA	0.005089	0.373096	
chunk0135_412_1	chr3	192851809	192852294	+	0	NA	intron (NM_178496, intron 1 of 1)	intron (NM_178496, intron 1 of 1)	66110	NM_178496	151963	Hs.151443	NM_178496	ENSG00000180611	MB21D2	C3orf59	Mab-21 domain containing 2	protein-coding	0.008247	0.442387	
chunk0013_291_1	chr1	171119275	171119560	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	-17611	NR_031627	100302178		NR_031627	ENSG00000221390	MIR1295A	MIR1295|MIRN1295|hsa-mir-1295|hsa-mir-1295a|mir-1295a	microRNA 1295a	ncRNA	0.003509	0.328671	
chunk0101_451_1	chr2	140066899	140067470	+	0	NA	Intergenic	Intergenic	519501	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.001751	0.351399	
chunk0118_438_1	chr22	38924437	38924787	+	0	NA	Intergenic	Charlie25|DNA|hAT-Charlie	-32910	NM_145699	200315	Hs.226307	NM_145699	ENSG00000128383	APOBEC3A	A3A|ARP3|PHRBN|bK150C2.1	apolipoprotein B mRNA editing enzyme catalytic subunit 3A	protein-coding	0.014286	0.435897	
chunk0151_115_1	chr5	43551299	43551560	+	0	NA	intron (NM_006451, intron 2 of 10)	intron (NM_006451, intron 2 of 10)	5664	NM_006451	10605	Hs.482038	NM_006451	ENSG00000172239	PAIP1	-	poly(A) binding protein interacting protein 1	protein-coding	0.007663	0.278626	
chunk0069_329_1	chr15	66248406	66249029	+	0	NA	intron (NM_032445, intron 1 of 22)	intron (NM_032445, intron 1 of 22)	5020	NM_032445	84465	Hs.712886	NM_032445	ENSG00000157890	MEGF11	-	multiple EGF like domains 11	protein-coding	0.004815	0.392628	
chunk0080_438_1	chr17	36146754	36147145	+	0	NA	Intergenic	L1M5|LINE|L1	29629	NM_001291462	101060321	Hs.454716	NM_001291462	ENSG00000260287	TBC1D3G	TBC1D3C|TBC1D3D	TBC1 domain family member 3G	protein-coding	0.002558	0.357143	
chunk0179_342_1	chr7	50739030	50739759	+	0	NA	intron (NM_001001555, intron 2 of 16)	Charlie9|DNA|hAT-Charlie	-7041	NM_001001549	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.016461	0.400000	
chunk0158_191_1	chr5	127956958	127957634	+	0	NA	Intergenic	MamGypLTR2c|LTR|Gypsy	125778	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.005917	0.474151	350(AGAGACAAAGTGTGCT,-,0.00)
chunk0204_94_1	chr9	94507535	94507734	+	0	NA	Intergenic	L1MA7|LINE|L1	-47411	NR_121566	101928099	Hs.674409	NR_121566		PCAT7	PCAN-R2	prostate cancer associated transcript 7	ncRNA	0.005025	0.330000	
chunk0102_41_1	chr2	141908102	141908649	+	0	NA	intron (NM_018557, intron 1 of 90)	L2b|LINE|L2	223326	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.001828	0.301095	164(ATGAACATAATGTTCA,-,0.00),165(TGAACATAATGTTCAT,+,0.00)
chunk0119_10_1	chr22	40048480	40048945	+	0	NA	intron (NM_001024843, intron 1 of 23)	L1ME1|LINE|L1	3895	NM_001024843	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.021505	0.439914	
chunk0131_187_1	chr3	148204200	148204470	+	0	NA	Intergenic	Intergenic	-493536	NM_000685	185	Hs.477887	NM_000685	ENSG00000144891	AGTR1	AG2S|AGTR1B|AT1|AT1AR|AT1B|AT1BR|AT1R|AT2R1|HAT1R	angiotensin II receptor type 1	protein-coding	0.000000	0.332103	
chunk0124_396_1	chr3	59734697	59734944	+	0	NA	Intergenic	Intergenic	-684831	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.020243	0.383065	
chunk0149_250_1	chr5	23727159	23727745	+	0	NA	Intergenic	Intergenic	219797	NM_001310214	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.011945	0.357751	
chunk0154_216_1	chr5	80622806	80623125	+	0	NA	promoter-TSS (NR_125754)	promoter-TSS (NR_125754)	-441	NR_125754	103689917	Hs.740035	NR_125754	ENSG00000251221	LINC01337	TCONS_00009713	long intergenic non-protein coding RNA 1337	ncRNA	0.006270	0.396875	
chunk0027_317_1	chr10	78166647	78167637	+	0	NA	Intergenic	Intergenic	-81483	NR_038985	100132987	Hs.55047	NR_038985	ENSG00000230417	LINC00856	-	long intergenic non-protein coding RNA 856	ncRNA	0.005051	0.402624	
chunk0004_200_1	chr1	46602427	46602649	+	0	NA	intron (NM_198973, intron 1 of 11)	intron (NM_198973, intron 1 of 11)	1756	NM_001135553	8569	Hs.371594	NM_003684	ENSG00000079277	MKNK1	MNK1	MAPK interacting serine/threonine kinase 1	protein-coding	0.013514	0.461883	81(GGGAACAAATTGTGCA,-,0.00),82(GGAACAAATTGTGCAG,+,0.00)
chunk0016_41_1	chr1	193145147	193145557	+	0	NA	intron (NM_024529, intron 7 of 16)	Charlie1|DNA|hAT-Charlie	8849	NR_031691	100302163		NR_031691	ENSG00000221680	MIR1278	MIRN1278|hsa-mir-1278|mir-1278	microRNA 1278	ncRNA	0.004878	0.335766	
chunk0128_374_1	chr3	113287069	113287557	+	0	NA	3' UTR (NM_033254, exon 20 of 20)	3' UTR (NM_033254, exon 20 of 20)	74816	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.018443	0.478528	
chunk0205_142_1	chr9	108207835	108208198	+	0	NA	Intergenic	Intergenic	647979	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.008264	0.409341	
chunk0187_388_1	chr7	157682737	157683040	+	0	NA	exon (NM_002847, exon 13 of 23)	exon (NM_002847, exon 13 of 23)	-108466	NR_029689	406945		NR_029689	ENSG00000207960	MIR153-2	MIRN153-2|mir-153-2	microRNA 153-2	ncRNA	0.029703	0.569079	
chunk0117_407_1	chr21	45645887	45646136	+	0	NA	Intergenic	Intergenic	-103540	NM_001205206	6573	Hs.84190	NM_003056	ENSG00000173638	SLC19A1	CHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1	solute carrier family 19 member 1	protein-coding	0.012048	0.488000	
chunk0083_50_1	chr17	63600708	63601115	+	0	NA	promoter-TSS (NM_016360)	promoter-TSS (NM_016360)	39	NM_016360	51204	Hs.174134	NM_016360	ENSG00000136463	TACO1	CCDC44	translational activator of cytochrome c oxidase I	protein-coding	0.078624	0.627451	293(CGGAACTGCTTGTTCC,-,0.00),294(GGAACTGCTTGTTCCG,+,0.00)
chunk0155_260_1	chr5	95811539	95811923	+	0	NA	Intergenic	LTR5B|LTR|ERVK	11142	NM_001243658	2745	Hs.28988	NM_002064	ENSG00000173221	GLRX	GRX|GRX1	glutaredoxin	protein-coding	0.031250	0.483117	147(AGGCACAGCATGTTTC,-,0.00),148(GGCACAGCATGTTTCC,+,0.00)
chunk0169_131_1	chr6	101132602	101132801	+	0	NA	Intergenic	Intergenic	-251329	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.005025	0.445000	
chunk0074_136_1	chr16	22952046	22952521	+	0	NA	Intergenic	Intergenic	137744	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.002105	0.315126	
chunk0148_16_1	chr5	343016	343347	+	0	NA	intron (NM_020731, intron 1 of 11)	intron (NM_020731, intron 1 of 11)	39005	NM_001242412	57491	Hs.50823	NM_020731	ENSG00000286169	AHRR	AHH|AHHR|bHLHe77	aryl-hydrocarbon receptor repressor	protein-coding	0.030211	0.575301	
chunk0047_393_1	chr12	75618545	75618762	+	0	NA	Intergenic	L1PA7|LINE|L1	-107015	NM_007043	11103	Hs.645517	NM_007043	ENSG00000111615	KRR1	HRB2|RIP-1	KRR1 small subunit processome component homolog	protein-coding	0.013825	0.362385	
chunk0078_256_1	chr17	7254793	7255348	+	0	NA	intron (NM_015362, intron 5 of 8)	L2c|LINE|L2	2869	NM_015362	23587	Hs.417029	NM_015362	ENSG00000170291	ELP5	C17orf81|DERP6|HSPC002|MST071|MSTP071	elongator acetyltransferase complex subunit 5	protein-coding	0.010811	0.424460	
chunk0128_232_1	chr3	108383176	108383791	+	0	NA	intron (NM_014981, intron 41 of 41)	intron (NM_014981, intron 41 of 41)	71698	NM_001282557	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.003252	0.342532	
chunk0068_78_1	chr15	51991209	51991513	+	0	NA	Intergenic	Intergenic	-19560	NM_001286430	123169	Hs.567662	NM_138792	ENSG00000166477	LEO1	RDL	LEO1 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.013158	0.318033	
chunk0048_226_1	chr12	81537250	81537767	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-25117	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.005803	0.376448	255(AAGAACTGAGTGTACT,-,0.00),256(AGAACTGAGTGTACTT,+,0.00)
chunk0035_289_1	chr11	46800696	46801076	+	0	NA	intron (NM_001008938, intron 9 of 43)	intron (NM_001008938, intron 9 of 43)	-38387	NR_003056	692108	Hs.693252	NR_003056	ENSG00000212135	SNORD67	HBII-166	small nucleolar RNA, C/D box 67	snoRNA	0.005263	0.272966	
chunk0019_225_1	chr1	227318454	227318737	+	0	NA	promoter-TSS (NM_003607)	promoter-TSS (NM_003607)	-470	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.127208	0.788732	
chunk0124_152_1	chr3	54856001	54856394	+	0	NA	intron (NM_018398, intron 17 of 37)	intron (NM_018398, intron 17 of 37)	45058	NR_046666	100874237	Hs.570583	NR_046666	ENSG00000243715	CACNA2D3-AS1	-	CACNA2D3 antisense RNA 1	ncRNA	0.012723	0.472081	
chunk0136_89_1	chr4	2598620	2598917	+	0	NA	Intergenic	Intergenic	-26664	NM_003704	8603	Hs.652364	NM_003704	ENSG00000125386	FAM193A	C4orf8|RES4-22	family with sequence similarity 193 member A	protein-coding	0.016835	0.540268	
chunk0092_296_1	chr19	34228276	34228493	+	0	NA	3' UTR (NM_001114093, exon 11 of 11)	3' UTR (NM_001114093, exon 11 of 11)	-26167	NM_014686	9710	Hs.330073	NM_014686	ENSG00000166398	KIAA0355	-	KIAA0355	protein-coding	0.004608	0.334862	
chunk0163_448_1	chr6	17557692	17558345	+	0	NA	TTS (NM_006366)	TTS (NM_006366)	-42269	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.004594	0.310398	
chunk0099_100_1	chr2	85602572	85602896	+	0	NA	promoter-TSS (NR_046347)	promoter-TSS (NR_046347)	-35	NR_033179									0.132716	0.763077	
chunk0140_248_1	chr4	71389376	71389858	+	0	NA	intron (NM_001098484, intron 6 of 25)	intron (NM_001098484, intron 6 of 25)	50564	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.004149	0.432712	
chunk0121_3_1	chr3	14388158	14388529	+	0	NA	Intergenic	L2b|LINE|L2	-14233	NM_001134368	6533	Hs.529488	NM_003043	ENSG00000131389	SLC6A6	TAUT	solute carrier family 6 member 6	protein-coding	0.013477	0.532258	185(AGGAACAGTGTGAGCA,-,0.00)
chunk0142_302_1	chr4	100555544	100556053	+	0	NA	Intergenic	Intergenic	-37705	NM_016242	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.001965	0.349020	376(CTGAGCATCCTGTCCT,-,0.00)
chunk0153_401_1	chr5	75356840	75357342	+	0	NA	intron (NM_000859, intron 15 of 19)	L1MB2|LINE|L1	19923	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.017928	0.393638	
chunk0089_378_1	chr18	67432953	67433213	+	0	NA	Intergenic	Intergenic	-83463	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.015385	0.406130	143(AAGAACAGGATGTATC,-,0.00),144(AGAACAGGATGTATCA,+,0.00)
chunk0031_47_1	chr10	122559257	122559745	+	0	NA	Intergenic	Intergenic	-1164	NM_017579	1755	Hs.279611	NM_004406	ENSG00000187908	DMBT1	GP340|SAG|SALSA|muclin	deleted in malignant brain tumors 1	protein-coding	0.004098	0.470348	
chunk0019_183_1	chr1	226553521	226554201	+	0	NA	intron (NM_001003665, intron 1 of 3)	HAL1ME|LINE|L1	5061	NM_001003665	375057	Hs.116827	NM_001003665	ENSG00000203685	STUM	C1orf95	stum, mechanosensory transduction mediator homolog	protein-coding	0.011765	0.402349	
chunk0200_409_1	chr9	27394169	27394568	+	0	NA	intron (NM_024761, intron 2 of 3)	intron (NM_024761, intron 2 of 3)	-97229	NM_001161585	54586	Hs.163070	NM_020641	ENSG00000120160	EQTN	AFAF|C9orf11|SPACA8	equatorin	protein-coding	0.007519	0.420000	
chunk0130_460_1	chr3	141505316	141505524	+	0	NA	intron (NM_006506, intron 1 of 23)	L2c|LINE|L2	18373	NM_001303245	5922	Hs.98445	NM_006506	ENSG00000155903	RASA2	GAP1M	RAS p21 protein activator 2	protein-coding	0.000000	0.387560	
chunk0108_308_1	chr2	235184031	235184264	+	0	NA	Intergenic	Intergenic	232163	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.004292	0.337607	
chunk0146_99_1	chr4	158523962	158524253	+	0	NA	intron (NR_045583, intron 1 of 16)	intron (NR_045583, intron 1 of 16)	2393	NM_001253730	59350	Hs.591686	NM_021634	ENSG00000171509	RXFP1	LGR7|RXFPR1	relaxin family peptide receptor 1	protein-coding	0.013746	0.417808	215(TAGGACATTCAGTGCC,-,0.00),216(AGGACATTCAGTGCCT,+,0.00)
chunk0135_168_1	chr3	188014781	188015042	+	0	NA	Intergenic	L1MD1|LINE|L1	-138962	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.003831	0.324427	
chunk0081_390_1	chr17	48213668	48214374	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-57510	NR_031607	100302211		NR_031607	ENSG00000221739	MIR1203	MIRN1203|hsa-mir-1203	microRNA 1203	ncRNA	0.004249	0.397454	
chunk0126_426_1	chr3	86867024	86867777	+	0	NA	Intergenic	Intergenic	123707	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.003984	0.346154	464(AAGAACATACAGTTTT,-,0.00),465(AGAACATACAGTTTTT,+,0.00)
chunk0185_284_1	chr7	130951349	130951792	+	0	NA	intron (NR_109855, intron 3 of 4)	intron (NR_109855, intron 3 of 4)	38106	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.020316	0.527027	
chunk0113_88_1	chr20	50824435	50824707	+	0	NA	intron (NM_017843, intron 2 of 5)	intron (NM_017843, intron 2 of 5)	29677	NM_001010974	55653	Hs.381178	NM_017843	ENSG00000124243	BCAS4	CNOL	breast carcinoma amplified sequence 4	protein-coding	0.007353	0.498168	
chunk0162_132_1	chr6	3042920	3043234	+	0	NA	Intergenic	L1MEf|LINE|L1	18286	NR_132750	101927759	Hs.145597	NR_132750		LOC101927759	-	uncharacterized LOC101927759	ncRNA	0.009554	0.374603	
chunk0030_151_1	chr10	113909479	113910086	+	0	NA	3' UTR (NM_198514, exon 11 of 11)	3' UTR (NM_198514, exon 11 of 11)	55150	NM_198514	374354	Hs.369924	NM_198514	ENSG00000196865	NHLRC2	FINCA	NHL repeat containing 2	protein-coding	0.001647	0.251645	
chunk0046_432_1	chr12	64734347	64734848	+	0	NA	intron (NM_002076, intron 9 of 13)	L2c|LINE|L2	24849	NM_002076	2799	Hs.334534	NM_002076	ENSG00000135677	GNS	G6S	glucosamine (N-acetyl)-6-sulfatase	protein-coding	0.017964	0.490040	
chunk0008_212_1	chr1	93638374	93638755	+	0	NA	intron (NM_003567, intron 3 of 11)	intron (NM_003567, intron 3 of 11)	-24419	NM_001261410	8412	Hs.36958	NM_003567	ENSG00000137936	BCAR3	AND-34|NSP2|SH2D3B	BCAR3 adaptor protein, NSP family member	protein-coding	0.010499	0.390052	
chunk0165_9_1	chr6	28682860	28683585	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-95887	NM_052923	114821	Hs.176980	NM_052923	ENSG00000232040	ZBED9	Buster4|SCAND3|ZFP38-L|ZNF305P2|ZNF452|dJ1186N24.3	zinc finger BED-type containing 9	protein-coding	0.023448	0.477961	
chunk0208_145_1	chrX	15908691	15909362	+	0	NA	Intergenic	Intergenic	-54012	NM_001272071	8905	Hs.121592	NM_003916	ENSG00000182287	AP1S2	DC22|MRX59|MRXS21|MRXS5|MRXSF|PGS|SIGMA1B	adaptor related protein complex 1 subunit sigma 2	protein-coding	0.004471	0.436012	
chunk0177_140_1	chr7	22672979	22673778	+	0	NA	Intergenic	HAL1|LINE|L1	-7845	NR_122075	401312	Hs.583393	NR_122075	ENSG00000105889	LOC401312	-	uncharacterized LOC401312	ncRNA	0.006258	0.430000	
chunk0120_156_1	chr3	5356025	5356283	+	0	NA	Intergenic	L1MD2|LINE|L1	-105899	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.003876	0.374517	
chunk0036_421_1	chr11	68354582	68354806	+	0	NA	intron (NM_001291902, intron 2 of 22)	MIRb|SINE|MIR	42085	NM_002335	4041	Hs.6347	NM_002335	ENSG00000162337	LRP5	BMND1|EVR1|EVR4|HBM|LR3|LRP-5|LRP-7|LRP7|OPPG|OPS|OPTA1|PCLD4|VBCH2	LDL receptor related protein 5	protein-coding	0.040179	0.622222	
chunk0183_331_1	chr7	108280071	108280742	+	0	NA	intron (NM_001193582, intron 3 of 30)	intron (NM_001193582, intron 3 of 30)	-40236	NM_001037132	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.007452	0.383929	
chunk0131_14_1	chr3	142061733	142062260	+	0	NA	intron (NM_001178138, intron 3 of 13)	Tigger2a|DNA|TcMar-Tigger	-33331	NM_006286	7029	Hs.379018	NM_006286	ENSG00000114126	TFDP2	DP2	transcription factor Dp-2	protein-coding	0.007590	0.410985	
chunk0013_127_1	chr1	168107808	168108251	+	0	NA	intron (NM_001267611, intron 1 of 5)	MSTB1|LTR|ERVL-MaLR	28407	NM_001267612	23432	Hs.271809	NM_007369	ENSG00000143147	GPR161	RE2	G protein-coupled receptor 161	protein-coding	0.000000	0.466216	
chunk0063_178_1	chr14	80523026	80523329	+	0	NA	intron (NM_152446, intron 22 of 23)	intron (NM_152446, intron 22 of 23)	-292123	NM_000793	1734	Hs.202354	NM_000793	ENSG00000211448	DIO2	5DII|D2|DIOII|SelY|TXDI2	iodothyronine deiodinase 2	protein-coding	0.000000	0.421053	
chunk0024_4_1	chr10	32665145	32665922	+	0	NA	intron (NM_024688, intron 3 of 22)	L1MA8|LINE|L1	97810	NM_024688	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.002574	0.304627	
chunk0011_184_1	chr1	148522565	148523049	+	0	NA	Intergenic	Intergenic	-39522	NM_001123068	644591	Hs.534674	NM_001123068	ENSG00000236334	PPIAL4G	COAS-2	peptidylprolyl isomerase A like 4G	protein-coding	0.049587	0.517526	
chunk0149_301_1	chr5	25713349	25713691	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	-872937	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.020468	0.492711	
chunk0125_235_1	chr3	68315380	68315909	+	0	NA	intron (NM_213609, intron 2 of 4)	intron (NM_213609, intron 2 of 4)	311428	NM_213609	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.005671	0.343396	
chunk0134_37_1	chr3	175651731	175652442	+	0	NA	intron (NM_207015, intron 11 of 13)	intron (NM_207015, intron 11 of 13)	124247	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.009845	0.353933	
chunk0024_293_1	chr10	42089826	42090100	+	0	NA	Intergenic	Intergenic	278082	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.065693	0.389091	
chunk0138_113_1	chr4	36230405	36230970	+	0	NA	intron (NM_015230, intron 1 of 32)	intron (NM_015230, intron 1 of 32)	-13429	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.005310	0.342756	
chunk0054_313_1	chr13	48655377	48655980	+	0	NA	intron (NM_001308471, intron 1 of 1)	MIRc|SINE|MIR	1967	NM_001308467	57105	Hs.253706	NM_020377	ENSG00000152207	CYSLTR2	CYSLT2|CYSLT2R|GPCR21|HG57|HPN321|KPG_011|PSEC0146|hGPCR21	cysteinyl leukotriene receptor 2	protein-coding	0.003317	0.399007	
chunk0058_17_1	chr14	19680411	19680610	+	0	NA	Intergenic	Intergenic	33822	NM_001197287	79334	Hs.554706	NM_001197287	ENSG00000258453	OR11H2	C14orf15|OR11H13|OR11H2P|OR11H8P	olfactory receptor family 11 subfamily H member 2	protein-coding	0.000000	0.260000	
chunk0075_3_1	chr16	46587903	46588394	+	0	NA	intron (NM_024745, intron 10 of 12)	L1PA5|LINE|L1	-19051	NR_026556	124149	Hs.97414	NM_001004299		ANKRD26P1	-	ankyrin repeat domain 26 pseudogene 1	pseudo	0.004073	0.376016	
chunk0018_99_1	chr1	217921796	217922044	+	0	NA	Intergenic	MER70C|LTR|ERVL	29020	NR_048550	100885798	Hs.434632	NR_048550	ENSG00000231814	LINC00210	NCRNA00210	long intergenic non-protein coding RNA 210	ncRNA	0.008065	0.506024	
chunk0041_173_1	chr11	126141352	126141551	+	0	NA	Intergenic	Intergenic	70241	NM_032795	84881	Hs.150458	NM_032795	ENSG00000165526	RPUSD4	-	RNA pseudouridine synthase D4	protein-coding	0.020101	0.555000	
chunk0187_440_1	chr7	158903746	158904349	+	0	NA	intron (NM_018051, intron 10 of 24)	intron (NM_018051, intron 10 of 24)	47469	NM_018051	55112	Hs.389945	NM_018051	ENSG00000126870	WDR60	FAP163|SRPS6|SRTD8	WD repeat domain 60	protein-coding	0.014925	0.415563	332(ATCACAGTCTGTGCTG,+,0.00)
chunk0066_189_1	chr15	33149997	33150513	+	0	NA	3' UTR (NM_001277314, exon 5 of 5)	3' UTR (NM_001277314, exon 5 of 5)	44478	NM_001277314	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.001938	0.423598	
chunk0041_407_1	chr11	133868471	133869006	+	0	NA	Intergenic	L1M4a2|LINE|L1	-23200	NM_174927	219938	Hs.97541	NM_174927	ENSG00000166118	SPATA19	CT132|SPAS1|spergen1	spermatogenesis associated 19	protein-coding	0.001869	0.330224	
chunk0209_324_1	chrX	50479607	50479838	+	0	NA	Intergenic	HAL1|LINE|L1	-8984	NM_001013742	139189	Hs.38132	NM_001013742	ENSG00000274588	DGKK	-	diacylglycerol kinase kappa	protein-coding	0.000000	0.405172	
chunk0118_432_1	chr22	38656240	38656796	+	0	NA	promoter-TSS (NM_015373)	promoter-TSS (NM_015373)	111	NM_001291030	646851	Hs.542707	NM_001013647	ENSG00000184949	FAM227A	-	family with sequence similarity 227 member A	protein-coding	0.079137	0.635548	
chunk0149_444_1	chr5	29824464	29824993	+	0	NA	Intergenic	Intergenic	-428752	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.005671	0.390566	
chunk0111_393_1	chr20	34180012	34180635	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-67967	NM_003908	8894	Hs.429180	NM_003908	ENSG00000125977	EIF2S2	EIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta	eukaryotic translation initiation factor 2 subunit beta	protein-coding	0.011236	0.395833	
chunk0069_202_1	chr15	63449755	63450052	+	0	NA	Intergenic	Intergenic	-54608	NM_001256702	9960	Hs.458499	NM_006537	ENSG00000140455	USP3	SIH003|UBP	ubiquitin specific peptidase 3	protein-coding	0.006734	0.597315	
chunk0130_110_1	chr3	131325530	131325873	+	0	NA	non-coding (NR_038976, exon 4 of 4)	non-coding (NR_038976, exon 4 of 4)	-36144	NR_002949	152195	Hs.380350	NM_194289	ENSG00000246082	NUDT16P1	NUDT16P	nudix hydrolase 16 pseudogene 1	pseudo	0.002915	0.287791	
chunk0032_140_1	chr11	4678027	4678444	+	0	NA	Intergenic	Intergenic	19611	NM_030774	81285	Hs.501758	NM_030774	ENSG00000167332	OR51E2	HPRAJ|OR51E3P|OR52A2|PSGR	olfactory receptor family 51 subfamily E member 2	protein-coding	0.007194	0.394737	
chunk0091_85_1	chr19	5345829	5346135	+	0	NA	Intergenic	MER113|DNA|hAT-Charlie	-5179	NM_130853	5802	Hs.744928	NM_002850	ENSG00000105426	PTPRS	PTPSIGMA|R-PTP-S|R-PTP-sigma	protein tyrosine phosphatase receptor type S	protein-coding	0.009804	0.517915	
chunk0095_204_1	chr2	18419385	18419641	+	0	NA	Intergenic	L1MA4|LINE|L1	141180	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.003906	0.361868	
chunk0044_343_1	chr12	38579208	38579561	+	0	NA	Intergenic	L1MA1|LINE|L1	262629	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.008499	0.384181	160(AAGAGCTGTCTGTACT,-,0.00)
chunk0095_459_1	chr2	25776202	25776908	+	0	NA	intron (NM_018263, intron 4 of 11)	L1MB7|LINE|L1	101888	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.007082	0.329562	
chunk0159_164_1	chr5	139574908	139575107	+	0	NA	intron (NM_181838, intron 2 of 7)	L1ME2|LINE|L1	13841	NM_181838	7322	Hs.108332	NM_003339	ENSG00000131508	UBE2D2	E2(17)KB2|PUBC1|UBC4|UBC4/5|UBCH4|UBCH5B	ubiquitin conjugating enzyme E2 D2	protein-coding	0.005025	0.325000	
chunk0067_151_1	chr15	43775506	43775750	+	0	NA	intron (NM_025165, intron 4 of 10)	intron (NM_025165, intron 4 of 10)	-1468	NM_001199877	10169	Hs.424126	NM_005770	ENSG00000140264	SERF2	4F5REL|FAM2C|H4F5REL|HsT17089	small EDRK-rich factor 2	protein-coding	0.000000	0.555102	
chunk0193_154_1	chr8	74687307	74687639	+	0	NA	intron (NR_033830, intron 2 of 5)	L1MA10|LINE|L1	-18220	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.003012	0.366366	
chunk0105_366_1	chr2	191946689	191946888	+	0	NA	Intergenic	Intergenic	-99508	NM_004657	8436	Hs.26530	NM_004657	ENSG00000168497	CAVIN2	PS-p68|SDPR|SDR|cavin-2	caveolae associated protein 2	protein-coding	0.005025	0.400000	
chunk0023_14_1	chr10	20901754	20902054	+	0	NA	intron (NM_213569, intron 4 of 6)	intron (NM_213569, intron 4 of 6)	-4302	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.010000	0.342193	
chunk0073_289_1	chr16	13926423	13926997	+	0	NA	exon (NM_005236, exon 3 of 11)	exon (NM_005236, exon 3 of 11)	6553	NM_005236	2072	Hs.567265	NM_005236	ENSG00000175595	ERCC4	ERCC11|FANCQ|RAD1|XFEPS|XPF	ERCC excision repair 4, endonuclease catalytic subunit	protein-coding	0.010453	0.360000	337(AAGAACATTATGTGAC,-,0.00)
chunk0188_355_1	chr8	17945209	17945778	+	0	NA	intron (NM_001315508, intron 6 of 35)	intron (NM_001315508, intron 6 of 35)	22636	NM_001315508	5108	Hs.491148	NM_006197	ENSG00000078674	PCM1	PTC4|RET/PCM-1	pericentriolar material 1	protein-coding	0.001757	0.347368	
chunk0138_106_1	chr4	36099436	36100068	+	0	NA	intron (NM_015230, intron 27 of 32)	MIR|SINE|MIR	-144364	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.007911	0.358610	
chunk0090_297_1	chr18	75161731	75161950	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	43673	NM_001306093	284273	Hs.465433	NM_175907	ENSG00000180011	ZADH2	PRG-3	zinc binding alcohol dehydrogenase domain containing 2	protein-coding	0.027397	0.568182	
chunk0026_21_1	chr10	60645923	60646257	+	0	NA	intron (NM_001204403, intron 1 of 43)	L2c|LINE|L2	-73134	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.002994	0.382090	
chunk0040_69_1	chr11	111303487	111303820	+	0	NA	intron (NM_001271457, intron 2 of 4)	intron (NM_001271457, intron 2 of 4)	1395	NM_001302644	399948	Hs.729225	NM_207429		COLCA1	C11orf92|CASC12|LOH11CR1F	colorectal cancer associated 1	protein-coding	0.006006	0.473054	
chunk0127_207_1	chr3	96394525	96394991	+	0	NA	Intergenic	Intergenic	34794	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.361884	
chunk0054_306_1	chr13	48485399	48485687	+	0	NA	Intergenic	Intergenic	-40839	NM_005767	10161	Hs.123464	NM_005767	ENSG00000139679	LPAR6	ARWH1|HYPT8|LAH3|P2RY5|P2Y5	lysophosphatidic acid receptor 6	protein-coding	0.006944	0.439446	
chunk0056_39_1	chr13	77356050	77356754	+	0	NA	Intergenic	L1MC5a|LINE|L1	-29360	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.002841	0.351773	
chunk0168_257_1	chr6	89081746	89082112	+	0	NA	intron (NM_006813, intron 1 of 1)	CpG	1219	NM_006813	10957	Hs.75969	NM_006813	ENSG00000146278	PNRC1	B4-2|PNAS-145|PROL2|PRR2	proline rich nuclear receptor coactivator 1	protein-coding	0.101093	0.694823	
chunk0177_52_1	chr7	20986383	20987173	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	151347	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.006329	0.390645	
chunk0206_296_1	chr9	124638889	124639436	+	0	NA	intron (NM_033334, intron 2 of 9)	MIR|SINE|MIR	-19274	NR_038975	100379345	Hs.660412	NR_038975	ENSG00000224020	MIR181A2HG	-	MIR181A2 host gene	ncRNA	0.010969	0.370438	
chunk0204_20_1	chr9	92319394	92319898	+	0	NA	intron (NR_046106, intron 4 of 16)	intron (NR_046106, intron 4 of 16)	-5822	NM_001012267	401541	Hs.713775	NM_001012267	ENSG00000188312	CENPP	CENP-P	centromere protein P	protein-coding	0.007937	0.346535	
chunk0180_99_1	chr7	55181292	55181577	+	0	NA	exon (NM_005228, exon 20 of 28)	exon (NM_005228, exon 20 of 28)	7515	NR_047551	100507500	Hs.720489	NR_047551	ENSG00000224057	EGFR-AS1	-	EGFR antisense RNA 1	ncRNA	0.042105	0.583916	
chunk0163_380_1	chr6	16236001	16236254	+	0	NA	Intergenic	LTR8|LTR|ERV1	-2453	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.011858	0.440945	103(GGGAACGTGCTGTTCT,-,0.00),104(GGAACGTGCTGTTCTC,+,0.00)
chunk0080_432_1	chr17	35950277	35950502	+	0	NA	Intergenic	Intergenic	-6679	NM_001199951	57151	Hs.97477	NM_020426	ENSG00000275722	LYZL6	HEL-S-6a|LYC1|LYZB|PRO1485|TKAL754|UNQ754	lysozyme like 6	protein-coding	0.008889	0.557522	
chunk0164_137_1	chr6	21148861	21149205	+	0	NA	intron (NM_017774, intron 13 of 15)	L2c|LINE|L2	362859	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.000000	0.344928	
chunk0097_229_1	chr2	52920107	52920822	+	0	NA	Intergenic	Intergenic	-217849	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.004196	0.324022	
chunk0144_307_1	chr4	138534914	138535612	+	0	NA	Intergenic	L1ME3G|LINE|L1	225552	NR_051987	100874047	Hs.570848	NR_051987	ENSG00000251372	LINC00499	-	long intergenic non-protein coding RNA 499	ncRNA	0.005731	0.356223	664(GTGCACAATCAGTTCT,-,0.00),665(TGCACAATCAGTTCTG,+,0.00)
chunk0186_248_1	chr7	140982944	140983673	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	31371	NM_016071	51650	Hs.416207	NM_016071	ENSG00000090263	MRPS33	CGI-139|MRP-S33|PTD003|S33mt	mitochondrial ribosomal protein S33	protein-coding	0.006859	0.367123	488(AAGTACACTCTGTGAT,-,0.00)
chunk0106_23_1	chr2	195818808	195819478	+	0	NA	intron (NM_018897, intron 49 of 64)	L2c|LINE|L2	162015	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.002985	0.391952	
chunk0201_323_1	chr9	63337954	63338576	+	0	NA	Intergenic	Intergenic	-3745	NR_002817	375719	Hs.658215	NR_002817		AQP7P1	bA251O17.3	aquaporin 7 pseudogene 1	pseudo	0.009646	0.422151	
chunk0173_168_1	chr6	144398004	144398341	+	0	NA	intron (NM_007124, intron 1 of 73)	intron (NM_007124, intron 1 of 73)	-7483	NR_132778	106635530		NR_132778		SNORA98	-	small nucleolar RNA, H/ACA box 98	snoRNA	0.008902	0.455621	
chunk0084_436_1	chr17	82745472	82745831	+	0	NA	intron (NM_022158, intron 4 of 5)	L1ME1|LINE|L1	-6413	NM_005993	6904	Hs.464391	NM_005993	ENSG00000141556	TBCD	PEBAT|SSD-1|tfcD	tubulin folding cofactor D	protein-coding	0.013928	0.430556	
chunk0155_79_1	chr5	91835180	91835461	+	0	NA	Intergenic	L1MA8|LINE|L1	-451988	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.003559	0.397163	78(CTGAACACAGTGTCCT,-,0.00),79(TGAACACAGTGTCCTC,+,0.00)
chunk0126_194_1	chr3	78497832	78498436	+	0	NA	Intergenic	Intergenic	521325	NM_133631	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.004967	0.371901	
chunk0045_369_1	chr12	52086312	52086540	+	0	NA	intron (NR_120439, intron 1 of 1)	intron (NR_120439, intron 1 of 1)	1680	NR_120439	26628	Hs.524431	NR_120438	ENSG00000257542	OR7E47P	OR7E141	olfactory receptor family 7 subfamily E member 47 pseudogene	pseudo	0.008772	0.462882	
chunk0097_308_1	chr2	56021163	56021446	+	0	NA	intron (NR_126406, intron 1 of 2)	intron (NR_126406, intron 1 of 2)	-20509	NR_030623	100126319		NR_030623	ENSG00000211520	MIR216B	MIRN216B|mir-216b	microRNA 216b	ncRNA	0.017668	0.366197	
chunk0174_190_1	chr6	159996652	159996904	+	0	NA	intron (NM_000876, intron 2 of 47)	L1PA17|LINE|L1	10886	NR_047511	100271873	Hs.742166	NR_047511	ENSG00000268257	AIRN	AIR|IGF2R-AS|IGF2R-AS1|IGF2RAS|NCRNA00088	antisense of IGF2R non-protein coding RNA	ncRNA	0.023810	0.533597	
chunk0119_394_1	chr22	48879488	48879997	+	0	NA	intron (NR_038944, intron 1 of 6)	L1ME1|LINE|L1	12972	NR_038944	100128946	Hs.535676	NR_038944	ENSG00000205632	LINC01310	WI2-81516E3.1	long intergenic non-protein coding RNA 1310	ncRNA	0.017682	0.362745	
chunk0190_339_1	chr8	39099470	39099784	+	0	NA	intron (NR_027878, intron 19 of 20)	L1ME4b|LINE|L1	-7902	NM_145004	203102	Hs.521545	NM_145004	ENSG00000197140	ADAM32	-	ADAM metallopeptidase domain 32	protein-coding	0.003185	0.285714	
chunk0193_58_1	chr8	72696947	72697146	+	0	NA	intron (NM_004770, intron 2 of 2)	intron (NM_004770, intron 2 of 2)	-34999	NR_110656	101926908	Hs.680588	NR_110656	ENSG00000253726	LOC101926908	-	uncharacterized LOC101926908	ncRNA	0.010050	0.345000	
chunk0052_248_1	chr12	123390782	123391195	+	0	NA	intron (NM_020382, intron 3 of 7)	intron (NM_020382, intron 3 of 7)	6831	NM_020382	387893	Hs.443735	NM_020382	ENSG00000183955	KMT5A	PR-Set7|PR/SET07|SET07|SET8|SETD8	lysine methyltransferase 5A	protein-coding	0.007264	0.454106	
chunk0153_344_1	chr5	74252261	74252460	+	0	NA	Intergenic	Intergenic	55965	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.000000	0.585000	
chunk0122_157_1	chr3	32180136	32180920	+	0	NA	Intergenic	Intergenic	-58151	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.008929	0.445860	
chunk0115_435_1	chr21	31932032	31932312	+	0	NA	intron (NM_014586, intron 2 of 10)	intron (NM_014586, intron 2 of 10)	58857	NM_014586	30811	Hs.109437	NM_014586	ENSG00000142149	HUNK	-	hormonally up-regulated Neu-associated kinase	protein-coding	0.021429	0.540925	
chunk0197_212_1	chr8	122683707	122684400	+	0	NA	intron (NR_126348, intron 2 of 3)	intron (NR_126348, intron 2 of 3)	10053	NR_126348	104266958	Hs.575540	NR_126348	ENSG00000253819	LINC01151	-	long intergenic non-protein coding RNA 1151	ncRNA	0.014430	0.373199	
chunk0141_443_1	chr4	89111008	89111492	+	0	NA	Intergenic	CpG	-1567	NM_145715	166815	Hs.58924	NM_145715	ENSG00000180346	TIGD2	HEL106	tigger transposable element derived 2	protein-coding	0.109504	0.715464	
chunk0029_36_1	chr10	96208873	96209276	+	0	NA	intron (NR_047683, intron 7 of 13)	intron (NR_047683, intron 7 of 13)	62442	NR_047681	29760	Hs.665244	NM_013314	ENSG00000095585	BLNK	AGM4|BASH|BLNK-S|LY57|SLP-65|SLP65|bca	B cell linker	protein-coding	0.014888	0.383663	
chunk0212_393_1	chrX	150789699	150790305	+	0	NA	intron (NM_001184808, intron 4 of 7)	L1MC3|LINE|L1	96638	NM_003828	8776	Hs.347187	NM_003828	ENSG00000063601	MTMR1	-	myotubularin related protein 1	protein-coding	0.003300	0.410214	
chunk0116_226_1	chr21	38139971	38140718	+	0	NA	intron (NR_026839, intron 2 of 2)	intron (NR_026839, intron 2 of 2)	18893	NR_026841	84677	Hs.733345	NM_032589	ENSG00000198054	DSCR8	C21orf65|CT25.1a|CT25.1b|MMA-1|MMA-1a|MMA-1b|MMA1|MTAG2	Down syndrome critical region 8	ncRNA	0.009371	0.427807	
chunk0054_28_1	chr13	40940820	40941147	+	0	NA	exon (NM_172373, exon 8 of 9)	exon (NM_172373, exon 8 of 9)	-19209	NR_003365	283507	Hs.442781	NR_003365	ENSG00000239827	SUGT1P3	SUGT1L1	SUGT1 pseudogene 3	pseudo	0.009174	0.423780	169(TGGGACAGCCTGTACT,-,0.00),170(GGGACAGCCTGTACTG,+,0.00)
chunk0166_268_1	chr6	48045827	48046294	+	0	NA	intron (NM_207499, intron 1 of 2)	intron (NM_207499, intron 1 of 2)	22629	NM_001013732	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.006424	0.346154	
chunk0192_230_1	chr8	65419356	65420110	+	0	NA	Intergenic	L2c|LINE|L2	142933	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.005305	0.374834	
chunk0027_243_1	chr10	77066910	77067152	+	0	NA	intron (NM_001014797, intron 14 of 28)	MLT2B4|LTR|ERVL	-73800	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.004132	0.448560	146(GGGTCACAGTGTACCC,+,0.00)
chunk0204_386_1	chr9	102205055	102205711	+	0	NA	Intergenic	Intergenic	-314254	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.004573	0.337900	242(GGGTACTTTCTGTACC,-,0.00),243(GGTACTTTCTGTACCT,+,0.00)
chunk0185_352_1	chr7	132297373	132297888	+	0	NA	intron (NM_020911, intron 4 of 31)	intron (NM_020911, intron 4 of 31)	278934	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.011650	0.459302	
chunk0134_96_1	chr3	176767332	176767732	+	0	NA	Intergenic	L1M1|LINE|L1	49469	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.005000	0.523691	
chunk0054_87_1	chr13	42549976	42550202	+	0	NA	Intergenic	Intergenic	-12647	NM_033012	8600	Hs.333791	NM_003701	ENSG00000120659	TNFSF11	CD254|ODF|OPGL|OPTB2|RANKL|TNLG6B|TRANCE|hRANKL2|sOdf	TNF superfamily member 11	protein-coding	0.004425	0.453744	119(GAGAACAGCATGTCCA,-,0.00),120(AGAACAGCATGTCCAG,+,0.00)
chunk0170_162_1	chr6	111556074	111556433	+	0	NA	3' UTR (NM_001164283, exon 4 of 4)	3' UTR (NM_001164283, exon 4 of 4)	11107	NM_001164283	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.013928	0.444444	
chunk0001_284_1	chr1	8742002	8742544	+	0	NA	intron (NM_001042681, intron 1 of 22)	intron (NM_001042681, intron 1 of 22)	75367	NM_012102	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.003690	0.372007	
chunk0086_204_1	chr18	22319092	22319291	+	0	NA	Intergenic	Intergenic	98724	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.015075	0.485000	
chunk0102_457_1	chr2	158403865	158404064	+	0	NA	intron (NM_001301685, intron 1 of 6)	MIRb|SINE|MIR	52789	NM_138803	130940	Hs.668597	NM_138803	ENSG00000153237	CCDC148	-	coiled-coil domain containing 148	protein-coding	0.005025	0.405000	
chunk0068_30_1	chr15	50924648	50924907	+	0	NA	intron (NM_007347, intron 4 of 20)	intron (NM_007347, intron 4 of 20)	16105	NM_001252127	23431	Hs.413366	NM_007347	ENSG00000081014	AP4E1	CPSQ4|SPG51|STUT1	adaptor related protein complex 4 subunit epsilon 1	protein-coding	0.003861	0.273077	
chunk0180_112_1	chr7	55410868	55411098	+	0	NA	intron (NM_018697, intron 5 of 8)	intron (NM_018697, intron 5 of 8)	45535	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.000000	0.424242	
chunk0090_270_1	chr18	74561646	74562345	+	0	NA	intron (NM_032649, intron 4 of 11)	intron (NM_032649, intron 4 of 11)	27538	NM_032649	84735	Hs.400613	NM_032649	ENSG00000150656	CNDP1	CN1|CPGL2|HsT2308	carnosine dipeptidase 1	protein-coding	0.015737	0.432857	
chunk0064_417_1	chr14	99578881	99579797	+	0	NA	intron (NM_001144995, intron 1 of 5)	intron (NM_001144995, intron 1 of 5)	25051	NM_001144995	317762	Hs.709288	NM_001144995	ENSG00000205476	CCDC85C	-	coiled-coil domain containing 85C	protein-coding	0.014192	0.633588	418(TGGACGCAGTGTCCCT,+,0.00)
chunk0053_229_1	chr13	32378594	32378923	+	0	NA	intron (NM_000059, intron 21 of 26)	intron (NM_000059, intron 21 of 26)	49420	NM_001286459	90634	Hs.732118	NM_052818	ENSG00000139597	N4BP2L1	CG018	NEDD4 binding protein 2 like 1	protein-coding	0.000000	0.336364	
chunk0153_212_1	chr5	71961046	71961331	+	0	NA	Intergenic	Intergenic	-146103	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.017544	0.447552	
chunk0207_331_1	chr9	134355079	134355459	+	0	NA	intron (NM_002957, intron 1 of 9)	intron (NM_002957, intron 1 of 9)	-24026	NM_001291920	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.018421	0.577428	
chunk0063_341_1	chr14	85360863	85361245	+	0	NA	Intergenic	Intergenic	-32825	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.000000	0.326371	
chunk0025_265_1	chr10	55552334	55552594	+	0	NA	Intergenic	Intergenic	-46526	NM_001190478	100463289		NM_001190478	ENSG00000249860	MTRNR2L5	HN5	MT-RNR2 like 5	protein-coding	0.000000	0.256705	119(AGTACTAGCTGTGCTA,+,0.00)
chunk0206_260_1	chr9	123894142	123894498	+	0	NA	intron (NM_024820, intron 1 of 20)	intron (NM_024820, intron 1 of 20)	35818	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.008427	0.355742	
chunk0027_35_1	chr10	72354668	72354910	+	0	NA	exon (NM_017626, exon 1 of 9)	exon (NM_017626, exon 1 of 9)	360	NM_001002762	54788	Hs.500013	NM_017626	ENSG00000148719	DNAJB12	DJ10	DnaJ heat shock protein family (Hsp40) member B12	protein-coding	0.078512	0.633745	
chunk0003_227_1	chr1	35660933	35661218	+	0	NA	Intergenic	Intergenic	-19231	NM_002794	5690	Hs.471441	NM_002794	ENSG00000126067	PSMB2	HC7-I	proteasome subunit beta 2	protein-coding	0.010526	0.479021	
chunk0123_392_1	chr3	48847149	48847380	+	0	NA	promoter-TSS (NR_109997)	promoter-TSS (NR_109997)	573	NM_004157	5576	Hs.631923	NM_004157	ENSG00000114302	PRKAR2A	PKR2|PRKAR2	protein kinase cAMP-dependent type II regulatory subunit alpha	protein-coding	0.077922	0.659483	
chunk0157_58_1	chr5	116137987	116138469	+	0	NA	intron (NM_001308080, intron 5 of 6)	intron (NM_001308080, intron 5 of 6)	52766	NM_001308080	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.000000	0.273292	
chunk0137_442_1	chr4	28842217	28842668	+	0	NA	Intergenic	Intergenic	22860	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.013304	0.396018	
chunk0053_308_1	chr13	34011606	34011960	+	0	NA	Intergenic	LTR1D|LTR|ERV1	193714	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.019774	0.546479	
chunk0152_204_1	chr5	60196312	60196907	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-291104	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.003361	0.412752	
chunk0156_142_1	chr5	107217641	107218223	+	0	NA	Intergenic	Intergenic	-206918	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.008591	0.466552	315(AGAAACAGTATGTACT,-,0.00),316(GAAACAGTATGTACTT,+,0.00)
chunk0118_129_1	chr22	29766275	29766474	+	0	NA	promoter-TSS (NM_013387)	promoter-TSS (NM_013387)	606	NM_001003692	55954	Hs.713647	NM_019103	ENSG00000100319	ZMAT5	SNRNP20|U11/U12-20K|ZC3H19	zinc finger matrin-type 5	protein-coding	0.020101	0.535000	
chunk0103_17_1	chr2	158998843	158999399	+	0	NA	intron (NM_001145909, intron 1 of 26)	intron (NM_001145909, intron 1 of 26)	30487	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.005396	0.441652	
chunk0030_430_1	chr10	120555992	120556641	+	0	NA	intron (NM_001030059, intron 5 of 6)	L3|LINE|CR1	-41633	NR_103717	404216	Hs.196578	NM_001012711	ENSG00000177234	LINC01561	C10orf85	long intergenic non-protein coding RNA 1561	ncRNA	0.004622	0.404615	
chunk0059_57_1	chr14	30143597	30144243	+	0	NA	Intergenic	Intergenic	-216227	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.003096	0.343122	
chunk0062_162_1	chr14	69356884	69357392	+	0	NA	Intergenic	L2c|LINE|L2	41166	NM_004450	2079	Hs.509791	NM_004450	ENSG00000100632	ERH	DROER	ERH mRNA splicing and mitosis factor	protein-coding	0.009843	0.467583	
chunk0092_379_1	chr19	36245845	36246255	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-30966	NM_001042474	147929	Hs.596338	NM_152477	ENSG00000196357	ZNF565	-	zinc finger protein 565	protein-coding	0.104878	0.652068	
chunk0018_112_1	chr1	218302435	218302972	+	0	NA	intron (NM_016052, intron 2 of 4)	intron (NM_016052, intron 2 of 4)	17416	NM_016052	51018	Hs.660109	NM_016052	ENSG00000067533	RRP15	CGI-115|KIAA0507	ribosomal RNA processing 15 homolog	protein-coding	0.007449	0.323420	
chunk0083_361_1	chr17	70736576	70736917	+	0	NA	Intergenic	L1M4|LINE|L1	465433	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.000000	0.347953	
chunk0028_262_1	chr10	90856390	90856623	+	0	NA	intron (NM_019859, intron 1 of 3)	intron (NM_019859, intron 1 of 3)	1408	NM_019859	3363	Hs.73739	NM_000872	ENSG00000148680	HTR7	5-HT7	5-hydroxytryptamine receptor 7	protein-coding	0.012876	0.487179	
chunk0091_126_1	chr19	6350537	6351107	+	0	NA	Intergenic	Intergenic	-10630	NM_006012	8192	Hs.515092	NM_006012	ENSG00000125656	CLPP	DFNB81|PRLTS3	caseinolytic mitochondrial matrix peptidase proteolytic subunit	protein-coding	0.008772	0.465849	
chunk0149_56_1	chr5	16846048	16846617	+	0	NA	intron (NM_012334, intron 2 of 40)	intron (NM_012334, intron 2 of 40)	89944	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.007030	0.419298	
chunk0074_22_1	chr16	20327446	20328197	+	0	NA	promoter-TSS (NM_001502)	promoter-TSS (NM_001502)	-201	NM_001007241	2813	Hs.53985	NM_001502	ENSG00000169347	GP2	ZAP75	glycoprotein 2	protein-coding	0.011984	0.448138	
chunk0037_172_1	chr11	73996357	73997125	+	0	NA	Intergenic	L1ME3A|LINE|L1	12496	NM_022803	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.006510	0.390117	
chunk0210_154_1	chrX	77572992	77573403	+	0	NA	intron (NM_138270, intron 27 of 33)	Tigger3a|DNA|TcMar-Tigger	125522	NM_003868	8823	Hs.666364	NM_003868	ENSG00000196468	FGF16	FGF-16|MF4	fibroblast growth factor 16	protein-coding	0.004866	0.347087	
chunk0161_317_1	chr5	173511108	173511491	+	0	NA	Intergenic	L1ME3A|LINE|L1	-68335	NR_027109	285593	Hs.409730	NR_027108	ENSG00000253955	LOC285593	-	uncharacterized LOC285593	ncRNA	0.005222	0.270833	184(TTGGACACAGTGTTCT,-,0.00),185(TGGACACAGTGTTCTG,+,0.00)
chunk0203_388_1	chr9	90464303	90464610	+	0	NA	intron (NR_034157, intron 5 of 5)	intron (NR_034157, intron 5 of 5)	-30967	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.019544	0.493506	
chunk0092_79_1	chr19	20982112	20982552	+	0	NA	Intergenic	Intergenic	-38288	NM_025189	80264	Hs.729202	NM_025189	ENSG00000118620	ZNF430	-	zinc finger protein 430	protein-coding	0.004545	0.408163	
chunk0181_215_1	chr7	84646775	84647047	+	0	NA	Intergenic	(AATAATT)n|Simple_repeat|Simple_repeat	114435	NR_110079	101927378	Hs.539042	NR_110079	ENSG00000235139	LOC101927378	-	uncharacterized LOC101927378	ncRNA	0.003676	0.271062	
chunk0010_291_1	chr1	117574348	117574864	+	0	NA	Intergenic	Intergenic	31164	NR_121626	100996263	Hs.202533	NR_121626	ENSG00000236866	LOC100996263	-	uncharacterized LOC100996263	ncRNA	0.005814	0.475822	
chunk0171_265_1	chr6	127463024	127463683	+	0	NA	intron (NM_001012279, intron 7 of 11)	intron (NM_001012279, intron 7 of 11)	-3963	NM_014702	9729	Hs.319247	NM_014702	ENSG00000189367	KIAA0408	-	KIAA0408	protein-coding	0.009105	0.390909	
chunk0196_352_1	chr8	114554576	114555050	+	0	NA	Intergenic	LTR75|LTR|ERVL	1113199	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004219	0.404211	
chunk0135_350_1	chr3	190446700	190447176	+	0	NA	intron (NM_207316, intron 2 of 4)	intron (NM_207316, intron 2 of 4)	2938	NM_207316	131920	Hs.335321	NM_207316	ENSG00000198398	TMEM207	UNQ846	transmembrane protein 207	protein-coding	0.008403	0.387841	
chunk0008_401_1	chr1	97665055	97665254	+	0	NA	intron (NM_000110, intron 8 of 22)	intron (NM_000110, intron 8 of 22)	-131767	NR_046591	100873933	Hs.568669	NR_046591	ENSG00000235777	DPYD-AS2	-	DPYD antisense RNA 2	ncRNA	0.005025	0.345000	
chunk0015_115_1	chr1	185292138	185292596	+	0	NA	TTS (NM_001105518)	TTS (NM_001105518)	24962	NM_006469	10625	Hs.497183	NM_006469	ENSG00000116679	IVNS1ABP	ARA3|FLARA3|HSPC068|KLHL39|ND1|NS-1|NS1-BP|NS1BP	influenza virus NS1A binding protein	protein-coding	0.010917	0.333333	
chunk0171_347_1	chr6	130091029	130091520	+	0	NA	intron (NM_001007102, intron 15 of 21)	L1M5|LINE|L1	72691	NM_001007102	84456	Hs.658051	NM_032438	ENSG00000198945	L3MBTL3	MBT-1|MBT1	L3MBTL histone methyl-lysine binding protein 3	protein-coding	0.004073	0.323171	
chunk0188_291_1	chr8	15677187	15677645	+	0	NA	intron (NM_006765, intron 6 of 10)	intron (NM_006765, intron 6 of 10)	137329	NM_006765	7991	Hs.426324	NM_006765	ENSG00000104723	TUSC3	D8S1992|M33|MRT22|MRT7|MagT2|N33|OST3A|SLC58A2	tumor suppressor candidate 3	protein-coding	0.004367	0.405229	
chunk0157_154_1	chr5	117830178	117830377	+	0	NA	intron (NR_104997, intron 1 of 2)	L1PA8A|LINE|L1	99916	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.005025	0.465000	
chunk0094_225_1	chr2	6827609	6827984	+	0	NA	TTS (NR_126359)	TTS (NR_126359)	12668	NR_126359	104326052	Hs.7155	NR_126359		NRIR	lncRNA-CMPK2	negative regulator of interferon response	ncRNA	0.005333	0.372340	
chunk0055_230_1	chr13	62721776	62722513	+	0	NA	intron (NR_047029, intron 5 of 7)	intron (NR_047029, intron 5 of 7)	74548	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.009498	0.368564	
chunk0191_26_1	chr8	42916483	42916742	+	0	NA	intron (NM_032410, intron 2 of 21)	LTR56|LTR|ERV1	19722	NM_032410	84376	Hs.162852	NM_032410	ENSG00000168172	HOOK3	HK3	hook microtubule tethering protein 3	protein-coding	0.003861	0.388462	
chunk0208_199_1	chrX	17710105	17710580	+	0	NA	intron (NM_001291868, intron 3 of 7)	intron (NM_001291868, intron 3 of 7)	-27107	NM_006746	6322	Hs.109655	NM_006746	ENSG00000047634	SCML1	-	Scm polycomb group protein like 1	protein-coding	0.000000	0.357143	
chunk0014_100_1	chr1	176730599	176731263	+	0	NA	intron (NM_020318, intron 12 of 22)	intron (NM_020318, intron 12 of 22)	267760	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.003012	0.293233	
chunk0174_177_1	chr6	159066365	159066755	+	0	NA	Intergenic	Intergenic	-21408	NM_054114	117289	Hs.529984	NM_054114	ENSG00000164691	TAGAP	ARHGAP47|FKSG15|IDDM21|TAGAP1	T cell activation RhoGTPase activating protein	protein-coding	0.007692	0.419437	215(AATCACAGACTGTTCT,-,0.00),216(ATCACAGACTGTTCTT,+,0.00)
chunk0048_13_1	chr12	77027073	77027272	+	0	NA	intron (NM_203394, intron 11 of 12)	intron (NM_203394, intron 11 of 12)	38408	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.005025	0.300000	
chunk0107_273_1	chr2	217923299	217923538	+	0	NA	intron (NM_022648, intron 1 of 32)	MIR|SINE|MIR	-3182	NM_001308022	7145	Hs.471381	NM_022648	ENSG00000079308	TNS1	MST091|MST122|MST127|MSTP091|MSTP122|MSTP127|MXRA6|PPP1R155|TNS	tensin 1	protein-coding	0.012552	0.429167	
chunk0174_403_1	chr6	165566890	165567335	+	0	NA	intron (NM_001130690, intron 1 of 21)	L1ME3A|LINE|L1	94988	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.004494	0.329596	
chunk0044_25_1	chr12	27239225	27239686	+	0	NA	Intergenic	L1M5|LINE|L1	-4690	NM_015000	23012	Hs.184523	NM_015000	ENSG00000211455	STK38L	NDR2	serine/threonine kinase 38 like	protein-coding	0.004338	0.283550	
chunk0139_182_1	chr4	54217670	54217945	+	0	NA	Intergenic	Intergenic	-11290	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.040000	0.579710	
chunk0078_75_1	chr17	1649706	1650379	+	0	NA	promoter-TSS (NM_031430)	promoter-TSS (NM_031430)	56	NM_031430	83547	Hs.534497	NM_031430	ENSG00000167705	RILP	PP10141	Rab interacting lysosomal protein	protein-coding	0.050520	0.637982	
chunk0125_303_1	chr3	70239753	70240168	+	0	NA	Intergenic	Intergenic	240216	NR_110000	101927152	Hs.382046	NR_110000	ENSG00000240405	SAMMSON	LINC01212	survival associated mitochondrial melanoma specific oncogenic non-coding RNA	ncRNA	0.014458	0.317308	
chunk0136_328_1	chr3	195551438	195551836	+	0	NA	Intergenic	Intergenic	-8236	NR_133014	5504	Hs.535731	NM_006241	ENSG00000184203	PPP1R2	IPP-2|IPP2|PPP1R2A	protein phosphatase 1 regulatory inhibitor subunit 2	protein-coding	0.015075	0.531328	
chunk0083_438_1	chr17	72634652	72635124	+	0	NA	intron (NR_033876, intron 2 of 4)	intron (NR_033876, intron 2 of 4)	5584	NR_033876	400619	Hs.447555	NR_033876	ENSG00000227036	LINC00511	LCAL5|onco-lncRNA-12	long intergenic non-protein coding RNA 511	ncRNA	0.019068	0.566596	315(ATGCACATTGAGTGCC,-,0.00),316(TGCACATTGAGTGCCT,+,0.00)
chunk0130_124_1	chr3	131542582	131542901	+	0	NA	exon (NM_001289112, exon 15 of 16)	exon (NM_001289112, exon 15 of 16)	-39725	NM_007208	11222	Hs.205163	NM_007208	ENSG00000114686	MRPL3	COXPD9|MRL3|RPML3	mitochondrial ribosomal protein L3	protein-coding	0.021944	0.540625	17(AAGAACAGGCTCTCCC,-,0.00),18(AGAACAGGCTCTCCCT,+,0.00)
chunk0079_304_1	chr17	17079266	17079535	+	0	NA	intron (NM_015134, intron 3 of 22)	intron (NM_015134, intron 3 of 22)	36640	NM_015134	23164	Hs.462341	NM_015134	ENSG00000133030	MPRIP	M-RIP|MRIP|RHOIP3|RIP3|p116Rip	myosin phosphatase Rho interacting protein	protein-coding	0.018587	0.500000	159(TGGACACTCCGTTCCT,+,0.00)
chunk0094_183_1	chr2	6092110	6092377	+	0	NA	Intergenic	Intergenic	110265	NR_026833	400940	Hs.378814	NM_207479		LOC400940	-	uncharacterized LOC400940	ncRNA	0.007491	0.462687	
chunk0003_44_1	chr1	30718683	30718906	+	0	NA	promoter-TSS (NR_034182)	promoter-TSS (NR_034182)	22	NR_034182	100129196	Hs.659751	NR_034182	ENSG00000186056	MATN1-AS1	-	MATN1 antisense RNA 1	ncRNA	0.116592	0.696429	
chunk0116_72_1	chr21	34636495	34636768	+	0	NA	Intergenic	LTR108d_Mam|LTR|ERVL	-21489	NM_004414	1827	Hs.282326	NM_004414	ENSG00000159200	RCAN1	ADAPT78|CSP1|DSC1|DSCR1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.018315	0.467153	
chunk0100_456_1	chr2	121109678	121109877	+	0	NA	Intergenic	L1MC4|LINE|L1	175425	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.010050	0.465000	
chunk0008_344_1	chr1	95981585	95982276	+	0	NA	Intergenic	Intergenic	-10138	NR_125991	102723661	Hs.143911	NR_125991	ENSG00000237435	LINC02790	-	long intergenic non-protein coding RNA 2790	ncRNA	0.004342	0.306358	
chunk0207_118_1	chr9	128878361	128878837	+	0	NA	intron (NM_001287390, intron 1 of 14)	intron (NM_001287390, intron 1 of 14)	3476	NM_001287390	883	Hs.495250	NM_004059	ENSG00000171097	KYAT1	CCBL1|GTK|KAT1|KATI	kynurenine aminotransferase 1	protein-coding	0.006303	0.425577	
chunk0066_238_1	chr15	34342851	34343050	+	0	NA	promoter-TSS (NM_001284292)	promoter-TSS (NM_001284292)	211	NM_018648	55505	Hs.14317	NM_018648	ENSG00000182117	NOP10	DKCB1|NOLA3|NOP10P	NOP10 ribonucleoprotein	protein-coding	0.055276	0.505000	
chunk0092_260_1	chr19	33055507	33056089	+	0	NA	intron (NM_033103, intron 1 of 14)	intron (NM_033103, intron 1 of 14)	9120	NM_033103	85415	Hs.466435	NM_033103	ENSG00000131941	RHPN2	P76RBE|RHOBP	rhophilin Rho GTPase binding protein 2	protein-coding	0.008591	0.466552	317(CAGGACACAATGAACC,-,0.00),318(AGGACACAATGAACCC,+,0.00)
chunk0167_124_1	chr6	61655830	61656139	+	0	NA	Intergenic	Intergenic	81881	NM_001190706	100463487		NM_001190706		MTRNR2L9	HN9	MT-RNR2 like 9	protein-coding	0.006472	0.354839	
chunk0106_126_1	chr2	198710471	198710964	+	0	NA	Intergenic	Intergenic	-335620	NR_110267	101927619	Hs.632942	NR_110267		LINC01923	-	long intergenic non-protein coding RNA 1923	ncRNA	0.002028	0.392713	
chunk0093_121_1	chr19	44796728	44796945	+	0	NA	intron (NM_012116, intron 9 of 10)	intron (NM_012116, intron 9 of 10)	-12223	NM_005581	4059	Hs.625725	NM_005581	ENSG00000187244	BCAM	AU|CD239|LU|MSK19	basal cell adhesion molecule (Lutheran blood group)	protein-coding	0.036866	0.555046	
chunk0034_93_1	chr11	27506108	27506558	+	0	NA	promoter-TSS (NR_033313)	promoter-TSS (NR_033313)	446	NM_018362	55327	Hs.91393	NM_018362	ENSG00000148943	LIN7C	LIN-7-C|LIN-7C|MALS-3|MALS3|VELI3	lin-7 homolog C, crumbs cell polarity complex component	protein-coding	0.053333	0.505543	
chunk0079_441_1	chr17	20182600	20183287	+	0	NA	intron (NM_001033554, intron 1 of 5)	MLT1J|LTR|ERVL-MaLR	26949	NM_001243438	92521	Hs.431045	NM_152904	ENSG00000128487	SPECC1	CYTSB|HCMOGT-1|HCMOGT1|NSP	sperm antigen with calponin homology and coiled-coil domains 1	protein-coding	0.010189	0.388081	
chunk0159_420_1	chr5	147998417	147998747	+	0	NA	Intergenic	MIR|SINE|MIR	-65390	NM_001127698	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.000000	0.341390	
chunk0211_385_1	chrX	127456357	127456747	+	0	NA	Intergenic	Intergenic	595851	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.002564	0.352941	
chunk0206_379_1	chr9	126643016	126643525	+	0	NA	intron (NM_002316, intron 2 of 7)	intron (NM_002316, intron 2 of 7)	28827	NM_001174147	4010	Hs.129133	NM_002316	ENSG00000136944	LMX1B	LMX1.2|NPS1	LIM homeobox transcription factor 1 beta	protein-coding	0.007859	0.576471	471(GAGCACAATCTGTACT,-,0.00),472(AGCACAATCTGTACTC,+,0.00)
chunk0174_416_1	chr6	165693766	165694151	+	0	NA	Intergenic	Intergenic	-31858	NM_001130690	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.005195	0.334197	
chunk0073_138_1	chr16	6565844	6566220	+	0	NA	intron (NM_018723, intron 2 of 15)	MLT1I|LTR|ERVL-MaLR	-207777	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.005319	0.397878	
chunk0004_1_1	chr1	41860506	41861288	+	0	NA	intron (NR_038260, intron 1 of 2)	intron (NR_038260, intron 1 of 2)	57810	NM_001127714	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.012788	0.466156	
chunk0060_172_1	chr14	45706060	45706315	+	0	NA	Intergenic	Intergenic	-357972	NR_102702	100506412	Hs.207545	NR_102699	ENSG00000258700	LINC00871	-	long intergenic non-protein coding RNA 871	ncRNA	0.007843	0.359375	
chunk0155_296_1	chr5	96306303	96306969	+	0	NA	intron (NR_130776, intron 1 of 4)	L1PA7|LINE|L1	125523	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.001502	0.347826	335(GGTACATTGTGTCTTT,+,0.00),418(AAGAGCAGGTTGTTCA,-,0.00)
chunk0020_187_1	chr1	234831226	234831559	+	0	NA	Intergenic	L2b|LINE|L2	107350	NR_038856	100506810	Hs.586634	NR_038856	ENSG00000227630	LINC01132	-	long intergenic non-protein coding RNA 1132	ncRNA	0.006006	0.407186	
chunk0184_103_1	chr7	113414437	113415158	+	0	NA	Intergenic	Intergenic	-296215	NR_015442									0.001387	0.342105	
chunk0090_369_1	chr18	77107276	77107537	+	0	NA	intron (NM_001025101, intron 1 of 8)	intron (NM_001025101, intron 1 of 8)	25412	NM_001025101	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.011494	0.526718	
chunk0069_411_1	chr15	67954757	67955208	+	0	NA	Intergenic	Intergenic	-99252	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.006652	0.442478	205(CAGTACACAGTGTGCT,-,0.00),206(AGTACACAGTGTGCTC,+,0.00)
chunk0061_346_1	chr14	63641671	63641997	+	0	NA	promoter-TSS (NM_001008726)	promoter-TSS (NM_001008726)	89	NM_080666	112840	Hs.655666	NM_080666	ENSG00000140006	WDR89	C14orf150|MSTP050	WD repeat domain 89	protein-coding	0.092025	0.614679	
chunk0059_134_1	chr14	31889382	31889589	+	0	NA	Intergenic	L1MC5|LINE|L1	174916	NM_001201574	80224	Hs.288981	NM_025152	ENSG00000151413	NUBPL	C14orf127|IND1|MC1DN21|huInd1	nucleotide binding protein like	protein-coding	0.004831	0.466346	
chunk0045_297_1	chr12	50326578	50327068	+	0	NA	TTS (NM_001145475)	TTS (NM_001145475)	-43253	NM_016357	51474	Hs.525419	NM_016357	ENSG00000050405	LIMA1	EPLIN|LDLCQ8|SREBP3	LIM domain and actin binding 1	protein-coding	0.008163	0.411405	
chunk0095_69_1	chr2	14520142	14520435	+	0	NA	Intergenic	Intergenic	-112398	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.013652	0.431973	
chunk0070_429_1	chr15	78032089	78032401	+	0	NA	intron (NM_015079, intron 3 of 12)	L1MEc|LINE|L1	-38020	NR_026998	91450	Hs.406766	NR_026998		LOC91450	-	uncharacterized LOC91450	ncRNA	0.019231	0.444089	256(AGGATCAAACTGTTCC,-,0.00),257(GGATCAAACTGTTCCA,+,0.00)
chunk0009_31_1	chr1	100252573	100253227	+	0	NA	Intergenic	L1ME3F|LINE|L1	-3047	NM_001918	1629	Hs.709187	NM_001918	ENSG00000137992	DBT	BCATE2|BCKAD-E2|BCKADE2|BCOADC-E2|E2|E2B	dihydrolipoamide branched chain transacylase E2	protein-coding	0.007645	0.335878	
chunk0206_79_1	chr9	120009894	120010329	+	0	NA	Intergenic	MIR|SINE|MIR	75051	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.006897	0.422018	197(GGGCACATCATGTGCC,-,0.00),198(GGCACATCATGTGCCA,+,0.00)
chunk0031_392_1	chr10	131129419	131129921	+	0	NA	intron (NM_174937, intron 8 of 11)	intron (NM_174937, intron 8 of 11)	34452	NR_120623	101927489	Hs.659317	NR_120623	ENSG00000230098	TCERG1L-AS1	-	TCERG1L antisense RNA 1	ncRNA	0.017928	0.431412	198(AAGCACACACTGGACC,-,0.00)
chunk0196_284_1	chr8	109422260	109422884	+	0	NA	intron (NM_177531, intron 23 of 77)	L1MD2|LINE|L1	60095	NM_177531	93035	Hs.170128	NM_177531	ENSG00000205038	PKHD1L1	PKHDL1	PKHD1 like 1	protein-coding	0.014423	0.361600	
chunk0170_412_1	chr6	117960033	117960498	+	0	NA	intron (NM_001029858, intron 1 of 7)	intron (NM_001029858, intron 1 of 7)	52739	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.002151	0.375536	
chunk0072_442_1	chr15	101615546	101615785	+	0	NA	Intergenic	Intergenic	36726	NM_025141	80213	Hs.288912	NM_025141	ENSG00000184277	TM2D3	BLP2	TM2 domain containing 3	protein-coding	0.020921	0.579167	170(GTGGACATAGTGTTCC,-,0.00),171(TGGACATAGTGTTCCC,+,0.00)
chunk0064_176_1	chr14	92607745	92608524	+	0	NA	intron (NM_024832, intron 3 of 9)	L1MD2|LINE|L1	94353	NM_024832	79890	Hs.326822	NM_024832	ENSG00000100599	RIN3	-	Ras and Rab interactor 3	protein-coding	0.007702	0.387179	
chunk0064_167_1	chr14	92290700	92290899	+	0	NA	Intergenic	L3|LINE|CR1	-31782	NM_153648	123041	Hs.385530	NM_153646	ENSG00000140090	SLC24A4	AI2A5|NCKX4|SHEP6|SLC24A2	solute carrier family 24 member 4	protein-coding	0.010050	0.455000	
chunk0109_94_1	chr20	2171086	2171913	+	0	NA	Intergenic	L2b|LINE|L2	-35429	NM_001287682									0.020556	0.532609	568(GAGGACTTCTTGTCCT,-,0.00),569(AGGACTTCTTGTCCTT,+,0.00)
chunk0015_32_1	chr1	184422769	184423419	+	0	NA	intron (NM_030806, intron 1 of 5)	MIRb|SINE|MIR	36078	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.007692	0.388633	
chunk0162_429_1	chr5	180282045	180282667	+	0	NA	intron (NM_002752, intron 1 of 11)	intron (NM_002752, intron 1 of 11)	-1748	NM_001308244	5601	Hs.484371	NM_002752	ENSG00000050748	MAPK9	JNK-55|JNK2|JNK2A|JNK2ALPHA|JNK2B|JNK2BETA|PRKM9|SAPK|SAPK1a|p54a|p54aSAPK	mitogen-activated protein kinase 9	protein-coding	0.016077	0.470305	
chunk0046_129_1	chr12	57488414	57488833	+	0	NA	intron (NM_004990, intron 1 of 20)	intron (NM_004990, intron 1 of 20)	670	NM_004990	4141	Hs.632707	NM_004990	ENSG00000166986	MARS	CMT2U|ILFS2|ILLD|METRS|MRS|MTRNS|SPG70	methionyl-tRNA synthetase	protein-coding	0.014320	0.490476	
chunk0173_350_1	chr6	149093643	149093947	+	0	NA	Intergenic	(T)n|Simple_repeat|Simple_repeat	-124129	NM_001292035	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.006579	0.426230	
chunk0112_385_1	chr20	46399161	46399882	+	0	NA	intron (NM_133171, intron 1 of 21)	L2c|LINE|L2	7111	NM_133171	63916	Hs.210469	NM_022086	ENSG00000062598	ELMO2	CED-12|CED12|Ced-12A|ELMO-2|VMPI	engulfment and cell motility 2	protein-coding	0.009709	0.465374	520(CAGCACTTGGTGTCCA,-,0.00),521(AGCACTTGGTGTCCAG,+,0.00)
chunk0178_287_1	chr7	37446452	37446651	+	0	NA	intron (NM_001206480, intron 1 of 21)	L2a|LINE|L2	2401	NM_014800	9844	Hs.434989	NM_014800	ENSG00000155849	ELMO1	CED-12|CED12|ELMO-1	engulfment and cell motility 1	protein-coding	0.005025	0.485000	
chunk0063_404_1	chr14	88186881	88187162	+	0	NA	intron (NM_021161, intron 6 of 6)	intron (NM_021161, intron 6 of 6)	83890	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.003559	0.436170	
chunk0160_442_1	chr5	164760709	164761110	+	0	NA	Intergenic	Intergenic	290630	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.004988	0.378109	
chunk0063_259_1	chr14	83297428	83297756	+	0	NA	Intergenic	Intergenic	-1674531	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.009146	0.334347	
chunk0061_275_1	chr14	61526418	61527094	+	0	NA	intron (NM_006255, intron 10 of 13)	intron (NM_006255, intron 10 of 13)	43438	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.011834	0.539143	
chunk0197_401_1	chr8	127117703	127118139	+	0	NA	Intergenic	AluJr|SINE|Alu	-35700	NR_119373	103164619	Hs.571401	NR_119373	ENSG00000254166	PCAT2	CARLO4|CARLo-4|PCA2|TCONS_00015167	prostate cancer associated transcript 2	ncRNA	0.006881	0.393593	
chunk0084_147_1	chr17	76579216	76579556	+	0	NA	intron (NM_006456, intron 1 of 8)	intron (NM_006456, intron 1 of 8)	6677	NM_006456	10610	Hs.592105	NM_006456	ENSG00000070731	ST6GALNAC2	SAITL1|SIAT7|SIAT7B|SIATL1|ST6GalNAII|STHM	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	protein-coding	0.005882	0.475073	
chunk0143_242_1	chr4	114652753	114653192	+	0	NA	intron (NM_003360, intron 1 of 4)	L1M6|LINE|L1	-3787	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.009112	0.379545	
chunk0062_412_1	chr14	75101543	75101918	+	0	NA	exon (NM_033116, exon 15 of 22)	exon (NM_033116, exon 15 of 22)	25345	NM_033116	91754	Hs.7200	NM_033116	ENSG00000119638	NEK9	APUG|LCCS10|NC|NERCC|NERCC1	NIMA related kinase 9	protein-coding	0.010667	0.396277	
chunk0146_112_1	chr4	158833570	158833814	+	0	NA	intron (NM_020840, intron 6 of 16)	intron (NM_020840, intron 6 of 16)	64662	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.012295	0.351020	
chunk0077_181_1	chr16	79677502	79677713	+	0	NA	Intergenic	Intergenic	-76882	NM_001031804	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.000000	0.330189	102(AGGAACAAAATGATCC,-,0.00),103(GGAACAAAATGATCCT,+,0.00)
chunk0042_8_1	chr12	1131730	1132191	+	0	NA	intron (NM_178040, intron 7 of 18)	intron (NM_178040, intron 7 of 18)	104212	NM_001301248	23085	Hs.601216	NM_178039	ENSG00000082805	ERC1	Cast2|ELKS|ERC-1|RAB6IP2	ELKS/RAB6-interacting/CAST family member 1	protein-coding	0.008677	0.419913	
chunk0072_380_1	chr15	100253666	100254282	+	0	NA	intron (NM_139057, intron 7 of 21)	intron (NM_139057, intron 7 of 21)	88004	NM_139057	170691	Hs.513200	NM_139057	ENSG00000140470	ADAMTS17	WMS4	ADAM metallopeptidase with thrombospondin type 1 motif 17	protein-coding	0.003247	0.437601	
chunk0136_240_1	chr4	8918041	8918464	+	0	NA	Intergenic	Intergenic	-31499	NM_001040071	650293	Hs.535167	NM_001040071		LOC650293	-	seven transmembrane helix receptor	pseudo	0.023641	0.509434	
chunk0006_385_1	chr1	74697865	74698297	+	0	NA	Intergenic	L2c|LINE|L2	-24343	NM_001002912	127254	Hs.531182	NM_001002912	ENSG00000178965	ERICH3	C1orf173	glutamate rich 3	protein-coding	0.004630	0.441109	210(AGGTACACAGTGTCTT,-,0.00),211(GGTACACAGTGTCTTT,+,0.00)
chunk0013_355_1	chr1	172275458	172275898	+	0	NA	intron (NM_001136127, intron 15 of 19)	intron (NM_001136127, intron 15 of 19)	-130843	NR_038397	100628315	Hs.584880	NR_038397		DNM3OS	DNM3-AS1|MIR199A2HG	DNM3 opposite strand/antisense RNA	ncRNA	0.002273	0.362812	
chunk0207_462_1	chr9	138003966	138004257	+	0	NA	intron (NM_001243812, intron 15 of 45)	L1ME3Cz|LINE|L1	40960	NR_121582	101928786	Hs.678847	NR_121582		LOC101928786	-	uncharacterized LOC101928786	ncRNA	0.020619	0.455479	
chunk0049_402_1	chr12	96849842	96850067	+	0	NA	intron (NM_001306084, intron 66 of 67)	intron (NM_001306084, intron 66 of 67)	-57269	NM_001135177	121441	Hs.270084	NM_152905	ENSG00000139350	NEDD1	GCP-WD|TUBGCP7	NEDD1 gamma-tubulin ring complex targeting factor	protein-coding	0.008889	0.415929	
chunk0169_244_1	chr6	105210916	105211242	+	0	NA	Intergenic	Intergenic	-31096	NM_022361	64208	Hs.458336	NM_022361	ENSG00000132429	POPDC3	POP3|bA355M14.1	popeye domain containing 3	protein-coding	0.000000	0.330275	
chunk0203_382_1	chr9	90358742	90359819	+	0	NA	intron (NR_109795, intron 2 of 2)	(AAAAT)n|Simple_repeat|Simple_repeat	74209	NR_109795	101927873	Hs.598482	NR_109795	ENSG00000231107	LINC01508	-	long intergenic non-protein coding RNA 1508	ncRNA	0.005571	0.348794	
chunk0141_199_1	chr4	84259006	84259557	+	0	NA	intron (NR_125909, intron 4 of 8)	L1PB4|LINE|L1	39888	NR_125909	101928978	Hs.647977	NR_125909	ENSG00000250546	LOC101928978	-	uncharacterized LOC101928978	ncRNA	0.001815	0.510870	
chunk0121_151_1	chr3	19151363	19151782	+	0	NA	intron (NM_144633, intron 1 of 15)	intron (NM_144633, intron 1 of 15)	3047	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.002387	0.261905	
chunk0162_289_1	chr6	6319163	6319385	+	0	NA	intron (NM_000129, intron 1 of 14)	L2a|LINE|L2	1417	NM_000129	2162	Hs.335513	NM_000129	ENSG00000124491	F13A1	F13A	coagulation factor XIII A chain	protein-coding	0.000000	0.443946	
chunk0014_149_1	chr1	178139828	178140027	+	0	NA	intron (NM_170692, intron 1 of 17)	intron (NM_170692, intron 1 of 17)	-45934	NR_027982	100302401	Hs.736117	NR_027982	ENSG00000224687	RASAL2-AS1	-	RASAL2 antisense RNA 1	ncRNA	0.000000	0.300000	
chunk0037_178_1	chr11	74070908	74071513	+	0	NA	intron (NM_001286577, intron 24 of 32)	intron (NM_001286577, intron 24 of 32)	-61973	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.006612	0.447195	
chunk0068_194_1	chr15	54868149	54868567	+	0	NA	Intergenic	L1MA7|LINE|L1	328675	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.004785	0.329356	
chunk0189_264_1	chr8	25253806	25254298	+	0	NA	intron (NM_024940, intron 2 of 51)	L1MC1|LINE|L1	69280	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.006098	0.344828	
chunk0195_320_1	chr8	98967380	98967668	+	0	NA	Intergenic	Intergenic	23121	NM_053001	116039	Hs.253247	NM_053001	ENSG00000164920	OSR2	-	odd-skipped related transciption factor 2	protein-coding	0.010417	0.387543	
chunk0139_188_1	chr4	54348545	54348874	+	0	NA	Intergenic	L2a|LINE|L2	119612	NM_006206	5156	Hs.74615	NM_006206	ENSG00000134853	PDGFRA	CD140A|PDGFR-2|PDGFR2	platelet derived growth factor receptor alpha	protein-coding	0.009119	0.448485	
chunk0205_371_1	chr9	113921929	113922778	+	0	NA	intron (NM_133374, intron 1 of 13)	intron (NM_133374, intron 1 of 13)	46071	NM_133374	114991	Hs.349208	NM_133374	ENSG00000157657	ZNF618	FP13169|NEDD10	zinc finger protein 618	protein-coding	0.008245	0.389412	
chunk0083_432_1	chr17	72588998	72589297	+	0	NA	intron (NR_036488, intron 1 of 3)	intron (NR_036488, intron 1 of 3)	3657	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.036789	0.516667	
chunk0160_380_1	chr5	161306306	161306505	+	0	NA	intron (NM_000813, intron 9 of 9)	intron (NM_000813, intron 9 of 9)	241719	NM_000813	2561	Hs.303527	NM_000813	ENSG00000145864	GABRB2	ICEE2	gamma-aminobutyric acid type A receptor beta2 subunit	protein-coding	0.000000	0.345000	
chunk0196_424_1	chr8	116289326	116289613	+	0	NA	intron (NR_046215, intron 1 of 13)	intron (NR_046215, intron 1 of 13)	35590	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.013937	0.447917	
chunk0183_99_1	chr7	105173664	105174370	+	0	NA	intron (NM_001278273, intron 4 of 16)	FLAM_C|SINE|Alu	95060	NM_182691	6733	Hs.285197	NM_182691	ENSG00000135250	SRPK2	SFRSK2	SRSF protein kinase 2	protein-coding	0.004249	0.381895	
chunk0055_393_1	chr13	73667349	73667987	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	103424	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.001567	0.380282	
chunk0034_255_1	chr11	34353541	34353740	+	0	NA	intron (NM_145804, intron 1 of 16)	intron (NM_145804, intron 1 of 16)	4368	NM_145804	25841	Hs.23361	NM_145804	ENSG00000166016	ABTB2	ABTB2A|BTBD22	ankyrin repeat and BTB domain containing 2	protein-coding	0.010050	0.385000	
chunk0179_214_1	chr7	47757806	47758294	+	0	NA	Intergenic	Intergenic	-3426	NR_038407	84847	Hs.488236	NR_038407	ENSG00000146666	LINC00525	-	long intergenic non-protein coding RNA 525	ncRNA	0.020492	0.468303	235(CAGAACATCTTGTTCC,-,0.00),236(AGAACATCTTGTTCCT,+,0.00)
chunk0147_260_1	chr4	183599471	183599945	+	0	NA	Intergenic	L1M4|LINE|L1	59511	NM_152682	201965	Hs.133337	NM_152682	ENSG00000182552	RWDD4	FAM28A|RWDD4A	RWD domain containing 4	protein-coding	0.000000	0.397895	
chunk0198_80_1	chr8	130094987	130095336	+	0	NA	intron (NM_001247996, intron 25 of 30)	intron (NM_001247996, intron 25 of 30)	-10393	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.008596	0.351429	
chunk0043_69_1	chr12	14272977	14273526	+	0	NA	Intergenic	Intergenic	-92381	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.010929	0.401818	
chunk0093_297_1	chr19	52601191	52601393	+	0	NA	Intergenic	Intergenic	4608	NR_023311	7696	Hs.373648	NM_003438		ZNF137P	ZNF137|pHZ-30	zinc finger protein 137, pseudogene	pseudo	0.089109	0.645320	
chunk0122_11_1	chr3	27359898	27360828	+	0	NA	intron (NM_199347, intron 2 of 24)	intron (NM_199347, intron 2 of 24)	9097	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.005376	0.392052	
chunk0196_358_1	chr8	114756331	114757072	+	0	NA	Intergenic	Intergenic	911311	NM_001282902	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.002699	0.340970	
chunk0020_14_1	chr1	231684225	231685001	+	0	NA	intron (NM_001164556, intron 1 of 4)	L1ME3D|LINE|L1	57798	NM_001164538	27185	Hs.13318	NM_018662	ENSG00000162946	DISC1	C1orf136|SCZD9	DISC1 scaffold protein	protein-coding	0.012887	0.416988	
chunk0036_319_1	chr11	66186378	66186974	+	0	NA	intron (NM_018026, intron 1 of 23)	L2a|LINE|L2	-70618	NM_001134775	64837	Hs.280792	NM_022822	ENSG00000174996	KLC2	-	kinesin light chain 2	protein-coding	0.010067	0.458961	275(CAGAACAGCATGTGCC,-,0.00),276(AGAACAGCATGTGCCT,+,0.00)
chunk0190_154_1	chr8	31183640	31184324	+	0	NA	Intergenic	MamGypLTR2b|LTR|Gypsy	-150267	NM_001015508	29942	Hs.373778	NM_013357	ENSG00000172733	PURG	PURG-A|PURG-B|PURGA|PURGB	purine rich element binding protein G	protein-coding	0.011696	0.474453	
chunk0026_257_1	chr10	66656333	66656935	+	0	NA	intron (NM_001127384, intron 9 of 17)	intron (NM_001127384, intron 9 of 17)	-269400	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.000000	0.378109	
chunk0053_302_1	chr13	33807254	33807873	+	0	NA	Intergenic	Intergenic	-10506	NM_181558	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.006462	0.324194	
chunk0137_448_1	chr4	29152761	29152999	+	0	NA	Intergenic	Intergenic	333298	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.000000	0.334728	
chunk0105_233_1	chr2	188339415	188340009	+	0	NA	intron (NR_045563, intron 2 of 12)	L1MC5|LINE|L1	42220	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.000000	0.329412	
chunk0156_148_1	chr5	107271758	107272231	+	0	NA	Intergenic	Intergenic	-260980	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.000000	0.350211	
chunk0004_295_1	chr1	48938074	48938457	+	0	NA	intron (NM_032785, intron 5 of 13)	L2a|LINE|L2	-161296	NM_024603	79656	Hs.475348	NM_024603	ENSG00000162373	BEND5	C1orf165	BEN domain containing 5	protein-coding	0.007833	0.367188	352(GGGAACACAGCGTTCT,-,0.00),353(GGAACACAGCGTTCTA,+,0.00)
chunk0153_218_1	chr5	72021967	72022420	+	0	NA	Intergenic	L1PA15|LINE|L1	-85098	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.013245	0.444934	226(AGAACACGCAGTGTTT,+,0.00)
chunk0123_398_1	chr3	48897957	48898156	+	0	NA	intron (NM_000387, intron 1 of 8)	intron (NM_000387, intron 1 of 8)	937	NM_000387	788	Hs.13845	NM_000387	ENSG00000178537	SLC25A20	CAC|CACT	solute carrier family 25 member 20	protein-coding	0.015075	0.525000	
chunk0039_269_1	chr11	102377378	102377766	+	0	NA	exon (NM_001166, exon 7 of 9)	exon (NM_001166, exon 7 of 9)	30198	NM_001256163	329	Hs.696238	NM_001166	ENSG00000110330	BIRC2	API1|HIAP2|Hiap-2|MIHB|RNF48|c-IAP1|cIAP1	baculoviral IAP repeat containing 2	protein-coding	0.007732	0.308483	
chunk0042_401_1	chr12	11434601	11435015	+	0	NA	Intergenic	Intergenic	-39244	NM_006248	653247	Hs.654486	NM_006248	ENSG00000121335	PRB2	IB-9|PRPPRB1|Ps|cP7	proline rich protein BstNI subfamily 2	protein-coding	0.002415	0.428916	190(GAGAACATTTTGTTTT,-,0.00),191(AGAACATTTTGTTTTT,+,0.00)
chunk0175_460_1	chr6	170471174	170471496	+	0	NA	Intergenic	Intergenic	81994	NM_002793	5689	Hs.352768	NM_002793	ENSG00000008018	PSMB1	HC5|PMSB1|PSC5	proteasome subunit beta 1	protein-coding	0.018634	0.458204	
chunk0015_163_1	chr1	186566344	186567018	+	0	NA	Intergenic	L2c|LINE|L2	-105573	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.004451	0.339259	
chunk0180_118_1	chr7	55438880	55439079	+	0	NA	Intergenic	L2a|LINE|L2	73531	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.030151	0.595000	
chunk0170_168_1	chr6	111657098	111657462	+	0	NA	Intergenic	Intergenic	-51006	NM_147686	10758	Hs.561514	NM_147200	ENSG00000056972	TRAF3IP2	ACT1|C6orf2|C6orf4|C6orf5|C6orf6|CANDF8|CIKS|PSORS13	TRAF3 interacting protein 2	protein-coding	0.000000	0.350685	
chunk0082_148_1	chr17	55494842	55495801	+	0	NA	Intergenic	Chap1_Mam|DNA|hAT-Charlie	-73341	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.007299	0.404167	
chunk0002_13_1	chr1	12202241	12202519	+	0	NA	intron (NM_001066, intron 9 of 9)	L2c|LINE|L2	10667	NR_039775	100616438		NR_039775	ENSG00000263676	MIR4632	-	microRNA 4632	ncRNA	0.021583	0.612903	
chunk0185_410_1	chr7	134260869	134261347	+	0	NA	intron (NM_144648, intron 19 of 19)	L1MB4|LINE|L1	55967	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.006276	0.413361	
chunk0057_270_1	chr13	105816375	105817301	+	0	NA	Intergenic	Intergenic	110008	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.002160	0.399137	382(GAGGACACTCAGTTCC,-,0.00),383(AGGACACTCAGTTCCT,+,0.00)
chunk0075_151_1	chr16	50988787	50989017	+	0	NA	intron (NR_039672, intron 2 of 6)	intron (NR_039672, intron 2 of 6)	-28856	NR_110913	101927334	Hs.555184	NR_110913	ENSG00000261637	LINC02127	-	long intergenic non-protein coding RNA 2127	ncRNA	0.008696	0.441558	
chunk0198_367_1	chr8	141000290	141000618	+	0	NA	intron (NM_005607, intron 1 of 31)	CpG	859	NM_005607	5747	Hs.395482	NM_005607	ENSG00000169398	PTK2	FADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK	protein tyrosine kinase 2	protein-coding	0.115854	0.732523	
chunk0171_213_1	chr6	126030924	126031246	+	0	NA	intron (NM_001031712, intron 12 of 12)	intron (NM_001031712, intron 12 of 12)	44655	NM_001031712	60487	Hs.404186	NM_021820	ENSG00000066651	TRMT11	C6orf75|MDS024|TRM11|TRMT11-1	tRNA methyltransferase 11 homolog	protein-coding	0.006211	0.383901	
chunk0173_201_1	chr6	145277967	145278177	+	0	NA	Intergenic	Intergenic	-456797	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.360190	28(AAAAACTGTATGTCCT,-,0.00)
chunk0198_376_1	chr8	141188157	141188747	+	0	NA	intron (NM_014957, intron 18 of 22)	Tigger17a|DNA|TcMar-Tigger	40122	NM_001286648	57210	Hs.372492	NM_001080431	ENSG00000022567	SLC45A4	-	solute carrier family 45 member 4	protein-coding	0.025424	0.460237	183(GAGCACTGCCAGTTCT,-,0.00),184(AGCACTGCCAGTTCTG,+,0.00)
chunk0018_118_1	chr1	218390711	218390914	+	0	NA	intron (NM_001135599, intron 2 of 7)	intron (NM_001135599, intron 2 of 7)	-45134	NR_046268	728463	Hs.568469	NR_046268	ENSG00000232480	TGFB2-AS1	-	TGFB2 antisense RNA 1 (head to head)	ncRNA	0.004926	0.431373	
chunk0030_3_1	chr10	110797357	110797579	+	0	NA	intron (NM_001134363, intron 5 of 13)	intron (NM_001134363, intron 5 of 13)	73436	NR_026932	282997	Hs.599931	NR_026932		PDCD4-AS1	-	PDCD4 antisense RNA 1	ncRNA	0.018018	0.421525	
chunk0181_263_1	chr7	85940918	85941361	+	0	NA	Intergenic	Intergenic	-702775	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.006772	0.333333	
chunk0032_9_1	chr11	506211	506467	+	0	NA	intron (NM_203386, intron 1 of 10)	intron (NM_203386, intron 1 of 10)	482	NM_203384	6050	Hs.530687	NM_002939	ENSG00000023191	RNH1	RAI|RNH	ribonuclease/angiogenin inhibitor 1	protein-coding	0.050781	0.583658	
chunk0062_168_1	chr14	69432813	69433389	+	0	NA	intron (NM_001252150, intron 2 of 6)	L1PA16|LINE|L1	34433	NM_001252148	55334	Hs.432690	NM_018375	ENSG00000029364	SLC39A9	ZIP-9|ZIP9	solute carrier family 39 member 9	protein-coding	0.000000	0.341421	
chunk0128_189_1	chr3	107487865	107488710	+	0	NA	Intergenic	Mam_R4|LINE|Dong-R4	-34649	NM_001276286	56987	Hs.124366	NM_020235	ENSG00000114439	BBX	ARTC1|HBP2|HSPC339|MDS001	BBX high mobility group box domain containing	protein-coding	0.001183	0.343972	601(AAGAACAGCATCTTCC,-,0.00),602(AGAACAGCATCTTCCT,+,0.00)
chunk0011_79_1	chr1	145017750	145018131	+	0	NA	intron (NM_001271870, intron 1 of 8)	intron (NM_001271870, intron 1 of 8)	75422	NM_001271870	647135	Hs.497575	NM_001271870	ENSG00000196369	SRGAP2B	SRGAP2L|SRGAP2P2	SLIT-ROBO Rho GTPase activating protein 2B	protein-coding	0.005249	0.421466	237(AAGAGCATAATGTTCT,-,0.00),238(AGAGCATAATGTTCTG,+,0.00)
chunk0096_130_1	chr2	28695224	28695584	+	0	NA	Intergenic	Intergenic	-56344	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.005556	0.518006	156(TGGAACAGCCTGTGCT,-,0.00),157(GGAACAGCCTGTGCTC,+,0.00)
chunk0178_24_1	chr7	29336860	29337601	+	0	NA	intron (NM_001293070, intron 2 of 13)	intron (NM_001293070, intron 2 of 13)	-128260	NR_120522	102724484	Hs.638665	NR_120522		LOC102724484	-	uncharacterized LOC102724484	ncRNA	0.010796	0.464960	
chunk0144_74_1	chr4	127896109	127896320	+	0	NA	intron (NM_014264, intron 14 of 15)	MIRb|SINE|MIR	14970	NM_001190801	10733	Hs.172052	NM_014264	ENSG00000142731	PLK4	MCCRP2|SAK|STK18	polo like kinase 4	protein-coding	0.004739	0.353774	
chunk0012_126_1	chr1	157075893	157076255	+	0	NA	Intergenic	MLT1J1|LTR|ERVL-MaLR	23734	NM_001004341	440695	Hs.127138	NM_001004341	ENSG00000253831	ETV3L	-	ETS variant 3 like	protein-coding	0.011050	0.435262	
chunk0015_413_1	chr1	191302634	191302927	+	0	NA	Intergenic	L1PA16|LINE|L1	677890	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.003413	0.551020	
chunk0067_3_1	chr15	39891009	39891208	+	0	NA	intron (NM_001271854, intron 1 of 3)	intron (NM_001271854, intron 1 of 3)	29784	NM_001271854	11245	Hs.37196	NM_007223	ENSG00000166073	GPR176	HB-954	G protein-coupled receptor 176	protein-coding	0.000000	0.295000	
chunk0072_448_1	chr15	101652320	101652679	+	0	NA	promoter-TSS (NM_025141)	promoter-TSS (NM_025141)	-108	NM_001307960	80213	Hs.288912	NM_025141	ENSG00000184277	TM2D3	BLP2	TM2 domain containing 3	protein-coding	0.111421	0.694444	
chunk0109_20_1	chr20	396726	397248	+	0	NA	3' UTR (NM_001301190, exon 4 of 4)	3' UTR (NM_001301190, exon 4 of 4)	-11078	NM_031229	10616	Hs.29546	NM_006462	ENSG00000125826	RBCK1	C20orf18|HOIL-1|HOIL1|PBMEI|PGBM1|RBCK2|RNF54|UBCE7IP3|XAP3|XAP4|ZRANB4	RANBP2-type and C3HC4-type zinc finger containing 1	protein-coding	0.003831	0.520076	294(GGGTACACTTTGTACC,-,0.00),295(GGTACACTTTGTACCA,+,0.00)
chunk0085_451_1	chr18	11449568	11450188	+	0	NA	Intergenic	L1PA16|LINE|L1	-38692	NR_110779	101927433	Hs.331210	NR_110778	ENSG00000267252	LINC01255	-	long intergenic non-protein coding RNA 1255	ncRNA	0.001613	0.344605	
chunk0147_379_1	chr4	186248616	186248815	+	0	NA	intron (NM_000892, intron 6 of 14)	L1MB7|LINE|L1	-17249	NM_000128	2160	Hs.1430	NM_000128	ENSG00000088926	F11	FXI|PTA	coagulation factor XI	protein-coding	0.000000	0.355000	
chunk0175_110_1	chr7	3239357	3239572	+	0	NA	Intergenic	Intergenic	-61984	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.032558	0.569444	91(CGGAACGTTCTGTTCC,-,0.00),92(GGAACGTTCTGTTCCG,+,0.00)
chunk0185_160_1	chr7	127752874	127753225	+	0	NA	intron (NM_014390, intron 10 of 23)	intron (NM_014390, intron 10 of 23)	100901	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.002849	0.423295	
chunk0031_398_1	chr10	131181613	131182246	+	0	NA	intron (NM_174937, intron 4 of 11)	intron (NM_174937, intron 4 of 11)	86711	NR_120623	101927489	Hs.659317	NR_120623	ENSG00000230098	TCERG1L-AS1	-	TCERG1L antisense RNA 1	ncRNA	0.017378	0.509464	129(AGCACACTCAGCTCCT,+,0.00)
chunk0089_49_1	chr18	58097308	58097576	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	50216	NM_001144964	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.011194	0.464684	
chunk0017_199_1	chr1	207591320	207591526	+	0	NA	intron (NM_000651, intron 35 of 46)	L1PA7|LINE|L1	-53690	NM_175710	1379	Hs.628568	NM_175710	ENSG00000197721	CR1L	-	complement C3b/C4b receptor 1 like	protein-coding	0.019417	0.396135	6(CTGAACAGCCTGCTCT,-,0.00),7(TGAACAGCCTGCTCTG,+,0.00),89(AAAGACACAATGTACC,-,0.00)
chunk0138_68_1	chr4	33453633	33454114	+	0	NA	Intergenic	L1PA15-16|LINE|L1	586020	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.000000	0.512448	151(CAGTGCAGGGTGTTCT,-,0.00),152(AGTGCAGGGTGTTCTC,+,0.00)
chunk0062_418_1	chr14	75178213	75178532	+	0	NA	Intergenic	Intergenic	-1726	NM_006827	10972	Hs.74137	NM_006827	ENSG00000170348	TMED10	P24(DELTA)|S31I125|S31III125|TMP21|Tmp-21-I|p23|p24d1	transmembrane p24 trafficking protein 10	protein-coding	0.000000	0.359375	
chunk0146_118_1	chr4	158888326	158888604	+	0	NA	intron (NM_020840, intron 14 of 16)	L2c|LINE|L2	119435	NM_020840	57600	Hs.652441	NM_020840	ENSG00000052795	FNIP2	FNIPL|MAPO1	folliculin interacting protein 2	protein-coding	0.010791	0.430108	
chunk0007_80_1	chr1	78438359	78438752	+	0	NA	Intergenic	Intergenic	-52488	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.000000	0.345178	
chunk0118_50_1	chr22	27902054	27902389	+	0	NA	intron (NM_001284277, intron 3 of 10)	L2c|LINE|L2	16993	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.011940	0.467262	
chunk0165_140_1	chr6	33597917	33598268	+	0	NA	Intergenic	Intergenic	-4754	NR_027908	401253	Hs.520075	NM_207497	ENSG00000197251	LINC00336	C6orf227|NCRNA00336	long intergenic non-protein coding RNA 336	ncRNA	0.008547	0.630682	158(CTGAACAGAGTGTCCT,-,0.00),159(TGAACAGAGTGTCCTT,+,0.00)
chunk0150_401_1	chr5	39864101	39864637	+	0	NA	Intergenic	Intergenic	-187922	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.011194	0.433892	
chunk0143_248_1	chr4	114755654	114756115	+	0	NA	Intergenic	Intergenic	99125	NR_030303	693162		NR_030303	ENSG00000207931	MIR577	MIRN577|hsa-mir-577|mir-577	microRNA 577	ncRNA	0.006508	0.335498	
chunk0042_344_1	chr12	10027664	10028239	+	0	NA	non-coding (NR_120484, exon 2 of 3)	non-coding (NR_120484, exon 2 of 3)	2655	NR_120484	102724020	Hs.737731	NR_120484	ENSG00000256803	LOC102724020	-	uncharacterized LOC102724020	ncRNA	0.010435	0.425347	
chunk0177_9_1	chr7	20369621	20369999	+	0	NA	intron (NM_002214, intron 3 of 13)	A-rich|Low_complexity|Low_complexity	-38048	NR_110120	101927811	Hs.285724	NR_110119	ENSG00000271133	LOC101927811	-	uncharacterized LOC101927811	ncRNA	0.005291	0.266491	
chunk0160_448_1	chr5	165028316	165029199	+	0	NA	Intergenic	Intergenic	558478	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.002265	0.257919	
chunk0011_260_1	chr1	150936315	150936704	+	0	NA	intron (NM_001243491, intron 3 of 8)	L1ME3E|LINE|L1	10170	NM_001145415	9869	Hs.643565	NM_012432	ENSG00000143379	SETDB1	ESET|H3-K9-HMTase4|KG1T|KMT1E|TDRD21	SET domain bifurcated histone lysine methyltransferase 1	protein-coding	0.005141	0.328205	
chunk0171_206_1	chr6	125804777	125805168	+	0	NA	intron (NR_126386, intron 1 of 2)	intron (NR_126386, intron 1 of 2)	13886	NR_126386	104355145	Hs.590370	NR_126386	ENSG00000232131	NCOA7-AS1	-	NCOA7 antisense RNA 1	ncRNA	0.017903	0.341837	
chunk0194_10_1	chr8	81501651	81501949	+	0	NA	Intergenic	Intergenic	-18562	NM_001442	2167	Hs.391561	NM_001442	ENSG00000170323	FABP4	A-FABP|AFABP|ALBP|HEL-S-104|aP2	fatty acid binding protein 4	protein-coding	0.016779	0.461538	
chunk0196_196_1	chr8	106208865	106209064	+	0	NA	Intergenic	CR1_Mam|LINE|CR1	-61214	NM_001198533	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.000000	0.385000	
chunk0009_423_1	chr1	110991621	110992235	+	0	NA	Intergenic	L1PB1|LINE|L1	-27984	NM_001006945	55791	Hs.25245	NM_018372	ENSG00000121931	LRIF1	C1orf103|HBiX1|RIF1	ligand dependent nuclear receptor interacting factor 1	protein-coding	0.008143	0.360976	
chunk0025_38_1	chr10	48999682	48999928	+	0	NA	Intergenic	Intergenic	-14218	NR_036182	100422895		NR_036182	ENSG00000264800	MIR4294	-	microRNA 4294	ncRNA	0.004065	0.534413	
chunk0155_55_1	chr5	91266348	91266598	+	0	NA	Intergenic	Intergenic	47929	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.000000	0.290837	
chunk0104_324_1	chr2	179417537	179417988	+	0	NA	Intergenic	L1MA8|LINE|L1	144826	NM_001113398	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.002217	0.373894	
chunk0068_426_1	chr15	59456174	59456476	+	0	NA	intron (NM_152450, intron 1 of 8)	L2c|LINE|L2	18152	NM_152450	145773	Hs.531168	NM_152450	ENSG00000157470	FAM81A	-	family with sequence similarity 81 member A	protein-coding	0.023179	0.544554	
chunk0049_389_1	chr12	96263227	96263985	+	0	NA	intron (NM_001303511, intron 2 of 2)	intron (NM_001303511, intron 2 of 2)	8146	NM_001303511	2004	Hs.46523	NM_005230	ENSG00000111145	ELK3	ERP|NET|SAP-2|SAP2	ETS transcription factor ELK3	protein-coding	0.018470	0.404480	
chunk0122_325_1	chr3	37082077	37082806	+	0	NA	intron (NM_017724, intron 7 of 13)	L1MC1|LINE|L1	88664	NM_001167617	4292	Hs.195364	NM_000249	ENSG00000076242	MLH1	COCA2|FCC2|HNPCC|HNPCC2|hMLH1	mutL homolog 1	protein-coding	0.004115	0.373973	
chunk0180_331_1	chr7	72743941	72744573	+	0	NA	intron (NM_001145440, intron 8 of 13)	L1M4|LINE|L1	46354	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.009494	0.357030	
chunk0007_245_1	chr1	82564018	82564740	+	0	NA	Intergenic	(TATA)n|Simple_repeat|Simple_repeat	420543	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.004155	0.282158	197(GAGAACAGTGAGTTCT,-,0.00),198(AGAACAGTGAGTTCTA,+,0.00)
chunk0155_184_1	chr5	94451489	94452123	+	0	NA	intron (NM_001145678, intron 13 of 20)	intron (NM_001145678, intron 13 of 20)	166798	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.007886	0.346457	
chunk0188_127_1	chr8	9188079	9188496	+	0	NA	promoter-TSS (NR_125431)	promoter-TSS (NR_125431)	-712	NR_125431	101929128		NR_125431	ENSG00000248538	LOC101929128	-	uncharacterized LOC101929128	ncRNA	0.011990	0.492823	230(AGGCACTCCCAGTGCT,-,0.00),231(GGCACTCCCAGTGCTG,+,0.00)
chunk0021_110_1	chr10	3260490	3261290	+	0	NA	Intergenic	Intergenic	-57805	NR_131187	105376360	Hs.212226	NR_131187		LOC105376360	-	uncharacterized LOC105376360	ncRNA	0.015000	0.456929	
chunk0109_386_1	chr2	240039386	240040098	+	0	NA	Intergenic	L1MA4|LINE|L1	3240	NM_001080835	643905	Hs.693479	NM_001080835		PRR21	-	proline rich 21	protein-coding	0.001404	0.464236	
chunk0019_61_1	chr1	224204846	224205115	+	0	NA	Intergenic	Intergenic	8299	NR_110669	101927143	Hs.638720	NR_110669	ENSG00000232628	LOC101927143	-	uncharacterized LOC101927143	ncRNA	0.029740	0.551852	
chunk0033_151_1	chr11	15532342	15533061	+	0	NA	Intergenic	L1MA6|LINE|L1	-111184	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.005563	0.325000	
chunk0066_232_1	chr15	34208668	34208919	+	0	NA	intron (NM_024713, intron 1 of 9)	intron (NM_024713, intron 1 of 9)	1303	NM_024713	79768	Hs.633566	NM_024713	ENSG00000134152	KATNBL1	C15orf29	katanin regulatory subunit B1 like 1	protein-coding	0.011952	0.376984	
chunk0061_98_1	chr14	57502750	57503044	+	0	NA	Intergenic	Intergenic	-9034	NM_018168	55195	Hs.659706	NM_018168	ENSG00000100557	CCDC198	C14orf105	coiled-coil domain containing 198	protein-coding	0.017007	0.525424	
chunk0126_78_1	chr3	74663375	74663846	+	0	NA	Intergenic	L1MD3|LINE|L1	-142470	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.002123	0.349576	
chunk0087_221_1	chr18	36114401	36114600	+	0	NA	intron (NM_001099406, intron 5 of 7)	intron (NM_001099406, intron 5 of 7)	14894	NM_012319	25800	Hs.79136	NM_012319	ENSG00000141424	SLC39A6	LIV-1|ZIP6	solute carrier family 39 member 6	protein-coding	0.005025	0.420000	
chunk0172_178_1	chr6	136434442	136435068	+	0	NA	intron (NM_003980, intron 1 of 17)	intron (NM_003980, intron 1 of 17)	32120	NM_001198615	9053	Hs.486548	NM_003980	ENSG00000135525	MAP7	E-MAP-115|EMAP115	microtubule associated protein 7	protein-coding	0.004792	0.392344	354(AGGCACAAAGTGTGCT,-,0.00),355(GGCACAAAGTGTGCTA,+,0.00)
chunk0133_460_1	chr3	175270274	175270660	+	0	NA	intron (NM_207015, intron 4 of 13)	intron (NM_207015, intron 4 of 13)	629	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.007772	0.372093	
chunk0005_62_1	chr1	55575823	55576136	+	0	NA	Intergenic	Intergenic	350338	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.006390	0.477707	188(AGGAACAGAGTGTTAC,-,0.00),189(GGAACAGAGTGTTACG,+,0.00)
chunk0122_46_1	chr3	28295545	28295744	+	0	NA	intron (NM_182523, intron 2 of 3)	L2a|LINE|L2	53483	NM_022461	64343	Hs.706676	NM_022461	ENSG00000163512	AZI2	AZ2|NAP1|TILP	5-azacytidine induced 2	protein-coding	0.000000	0.320000	
chunk0088_88_1	chr18	44870668	44871088	+	0	NA	intron (NM_015559, intron 3 of 5)	intron (NM_015559, intron 3 of 5)	99288	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.021429	0.432304	
chunk0202_130_1	chr9	73215896	73216386	+	0	NA	Intergenic	Intergenic	64410	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.004082	0.356415	182(GAAAACAGACTGTTCC,-,0.00),183(AAAACAGACTGTTCCT,+,0.00),212(AAGGACTTTCAGTCCT,-,0.00),213(AGGACTTTCAGTCCTG,+,0.00)
chunk0016_457_1	chr1	204255456	204256056	+	0	NA	intron (NM_014935, intron 9 of 22)	intron (NM_014935, intron 9 of 22)	-41664	NM_198447	127845	Hs.532401	NM_198447	ENSG00000174567	GOLT1A	CGI-141|GOT1|HMFN1187|YMR292W|hGOT1b	golgi transport 1A	protein-coding	0.013333	0.509151	
chunk0150_8_1	chr5	30326782	30327218	+	0	NA	Intergenic	Intergenic	-866655	NM_004932	1004	Hs.124776	NM_004932	ENSG00000113361	CDH6	CAD6|KCAD	cadherin 6	protein-coding	0.002294	0.290618	
chunk0124_279_1	chr3	57544771	57545057	+	0	NA	promoter-TSS (NM_001291661)	promoter-TSS (NM_001291661)	-570	NM_198564	201625	Hs.201378	NM_178504	ENSG00000174844	DNAH12	DHC3|DLP12|DLP3|DNAH12L|DNAH7L|DNAHC12|DNAHC3|DNHD2|HDHC3|HL-19|HL19	dynein axonemal heavy chain 12	protein-coding	0.010490	0.362369	
chunk0135_201_1	chr3	188266925	188267386	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	41750	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.006508	0.478355	224(TGGAACATTCTGTTCC,-,0.00),225(GGAACATTCTGTTCCC,+,0.00)
chunk0001_358_1	chr1	9950437	9950665	+	0	NA	intron (NM_001297779, intron 1 of 4)	intron (NM_001297779, intron 1 of 4)	7123	NM_022787	64802	Hs.633762	NM_022787	ENSG00000173614	NMNAT1	LCA9|NMNAT|PNAT1	nicotinamide nucleotide adenylyltransferase 1	protein-coding	0.021930	0.550218	
chunk0007_367_1	chr1	85159343	85159996	+	0	NA	intron (NM_032184, intron 6 of 6)	intron (NM_032184, intron 6 of 6)	25875	NR_039619	100616481		NR_039619	ENSG00000266110	MIR4423	mir-4423	microRNA 4423	ncRNA	0.007657	0.327217	
chunk0060_178_1	chr14	46401061	46401457	+	0	NA	intron (NR_102702, intron 3 of 3)	(TG)n|Simple_repeat|Simple_repeat	-70100	NR_102700	100506412	Hs.207545	NR_102699	ENSG00000258700	LINC00871	-	long intergenic non-protein coding RNA 871	ncRNA	0.005051	0.340050	
chunk0007_376_1	chr1	85277837	85278259	+	0	NA	TTS (NR_045484)	TTS (NR_045484)	-1144	NM_003921	8915	Hs.193516	NM_003921	ENSG00000142867	BCL10	CARMEN|CIPER|CLAP|IMD37|c-E10|mE10	BCL10 immune signaling adaptor	protein-coding	0.009479	0.352246	
chunk0066_374_1	chr15	38702707	38702914	+	0	NA	Intergenic	LTR22A|LTR|ERVK	6212	NM_207444	400359	Hs.448785	NM_207444	ENSG00000175779	LINC02694	C15orf53	long intergenic non-protein coding RNA 2694	ncRNA	0.004831	0.528846	
chunk0147_79_1	chr4	173038527	173038984	+	0	NA	intron (NM_001034845, intron 12 of 12)	intron (NM_001034845, intron 12 of 12)	-129998	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.002188	0.371179	
chunk0010_127_1	chr1	114530064	114530651	+	0	NA	Intergenic	L1MC4|LINE|L1	-19197	NM_033020	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.003407	0.425170	
chunk0039_370_1	chr11	106172430	106172780	+	0	NA	Intergenic	LTR56|LTR|ERV1	-77414	NR_120552	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.005714	0.364672	
chunk0088_27_1	chr18	43797282	43797781	+	0	NA	Intergenic	L1MEi|LINE|L1	-519881	NM_020783	6860	Hs.8059	NM_020783	ENSG00000132872	SYT4	HsT1192	synaptotagmin 4	protein-coding	0.002004	0.284000	
chunk0073_132_1	chr16	4971701	4972144	+	0	NA	intron (NM_014692, intron 2 of 15)	intron (NM_014692, intron 2 of 15)	13605	NM_014692	9717	Hs.512856	NM_014692	ENSG00000103184	SEC14L5	PRELID4B	SEC14 like lipid binding 5	protein-coding	0.013544	0.445946	
chunk0061_212_1	chr14	60443408	60443901	+	0	NA	intron (NM_174978, intron 16 of 17)	L1PA6|LINE|L1	42392	NM_174978	317761	Hs.335754	NM_174978	ENSG00000179008	C14orf39	Six6os1	chromosome 14 open reading frame 39	protein-coding	0.000000	0.520243	
chunk0071_320_1	chr15	86884621	86885209	+	0	NA	intron (NM_152336, intron 22 of 23)	intron (NM_152336, intron 22 of 23)	-567947	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.008503	0.361630	
chunk0128_376_1	chr3	113360047	113360253	+	0	NA	intron (NM_001164496, intron 21 of 34)	intron (NM_001164496, intron 21 of 34)	-43848	NR_046728	100874029	Hs.599665	NR_046728	ENSG00000243849	CFAP44-AS1	WDR52-AS1	CFAP44 antisense RNA 1	ncRNA	0.004854	0.338164	
chunk0161_308_1	chr5	173454513	173455028	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	107315	NR_107023	102465862		NR_107023	ENSG00000274994	MIR8056	hsa-mir-8056	microRNA 8056	ncRNA	0.007767	0.443798	
chunk0128_367_1	chr3	113234650	113235080	+	0	NA	intron (NM_001301861, intron 2 of 19)	intron (NM_001301861, intron 2 of 19)	22368	NM_001301861	91653	Hs.591318	NM_033254	ENSG00000144857	BOC	CDON2	BOC cell adhesion associated, oncogene regulated	protein-coding	0.013953	0.489559	259(TAATACACTGTGTTCT,-,0.00),260(AATACACTGTGTTCTT,+,0.00)
chunk0146_175_1	chr4	160555424	160555673	+	0	NA	Intergenic	Intergenic	1287702	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.000000	0.348000	133(ATGGACAGTCTGTCTC,-,0.00),134(TGGACAGTCTGTCTCT,+,0.00)
chunk0029_195_1	chr10	101462708	101462907	+	0	NA	intron (NM_033637, intron 3 of 14)	intron (NM_033637, intron 3 of 14)	108774	NM_033637	8945	Hs.643802	NM_003939	ENSG00000166167	BTRC	BETA-TRCP|FBW1A|FBXW1|FBXW1A|FWD1|bTrCP|bTrCP1|betaTrCP	beta-transducin repeat containing E3 ubiquitin protein ligase	protein-coding	0.010050	0.320000	
chunk0049_417_1	chr12	97449464	97449803	+	0	NA	Intergenic	L2c|LINE|L2	-15388	NR_024037	196475	Hs.652568	NR_024037	ENSG00000255794	RMST	LINC00054|NCRMS|NCRNA00054	rhabdomyosarcoma 2 associated transcript	ncRNA	0.000000	0.376471	
chunk0078_409_1	chr16	89037661	89037940	+	0	NA	Intergenic	Intergenic	-56009	NM_174917	197322	Hs.461727	NM_174917	ENSG00000176715	ACSF3	-	acyl-CoA synthetase family member 3	protein-coding	0.043011	0.635714	
chunk0076_62_1	chr16	61459774	61460533	+	0	NA	Intergenic	L2b|LINE|L2	-404387	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.007905	0.348684	293(CAGCACGCCATGTTCC,-,0.00),294(AGCACGCCATGTTCCA,+,0.00)
chunk0016_395_1	chr1	203128664	203128957	+	0	NA	5' UTR (NM_000674, exon 3 of 4)	5' UTR (NM_000674, exon 3 of 4)	1102	NM_001048230	134	Hs.77867	NM_000674	ENSG00000163485	ADORA1	RDC7	adenosine A1 receptor	protein-coding	0.040956	0.646259	
chunk0038_371_1	chr11	93378815	93379108	+	0	NA	intron (NM_181645, intron 7 of 13)	intron (NM_181645, intron 7 of 13)	48244	NM_181645	159989	Hs.436625	NM_181645	ENSG00000165325	DEUP1	CCDC67	deuterosome assembly protein 1	protein-coding	0.000000	0.431973	
chunk0026_130_1	chr10	62093548	62094023	+	0	NA	3' UTR (NM_001244638, exon 7 of 7)	3' UTR (NM_001244638, exon 7 of 7)	44574	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.006316	0.331933	
chunk0205_135_1	chr9	108108877	108109579	+	0	NA	Intergenic	MIRb|SINE|MIR	-619508	NM_001314052	9314	Hs.376206	NM_004235	ENSG00000136826	KLF4	EZF|GKLF	Kruppel like factor 4	protein-coding	0.002849	0.374111	
chunk0071_242_1	chr15	85331043	85331728	+	0	NA	Intergenic	Intergenic	-49211	NR_106993	102465803		NR_106993	ENSG00000284160	MIR7706	hsa-mir-7706	microRNA 7706	ncRNA	0.020438	0.553936	330(TGGAACACTCTGTTCT,-,0.00),331(GGAACACTCTGTTCTT,+,0.00)
chunk0130_23_1	chr3	128680667	128681158	+	0	NA	Intergenic	CpG	-30036	NM_002950	6184	Hs.518244	NM_002950	ENSG00000163902	RPN1	OST1|RBPH1	ribophorin I	protein-coding	0.087576	0.652439	
chunk0193_398_1	chr8	80549635	80550084	+	0	NA	Intergenic	Intergenic	63646	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.000000	0.328889	
chunk0046_65_1	chr12	55927242	55927535	+	0	NA	promoter-TSS (NM_001143853)	promoter-TSS (NM_001143853)	-263	NM_001143853	84305	Hs.505687	NM_032345	ENSG00000170473	PYM1	PYM|WIBG	PYM homolog 1, exon junction complex associated factor	protein-coding	0.030717	0.530612	
chunk0096_257_1	chr2	31390797	31391077	+	0	NA	intron (NM_000379, intron 6 of 35)	L1MC1|LINE|L1	23808	NM_000379	7498	Hs.250	NM_000379	ENSG00000158125	XDH	XAN1|XO|XOR	xanthine dehydrogenase	protein-coding	0.007143	0.334520	
chunk0050_35_1	chr12	100230082	100230281	+	0	NA	Intergenic	HAL1ME|LINE|L1	29404	NR_048568	64431	Hs.115088	NM_022496	ENSG00000075089	ACTR6	ARP6|CDA12|HSPC281|MSTP136|hARP6|hARPX	actin related protein 6	protein-coding	0.010050	0.430000	37(AAGGACTCAAAGTGCC,-,0.00)
chunk0052_95_1	chr13	22312035	22312411	+	0	NA	Intergenic	Intergenic	101938	NR_103810	100506622	Hs.255773	NR_103810	ENSG00000276476	LINC00540	-	long intergenic non-protein coding RNA 540	ncRNA	0.010638	0.538462	
chunk0048_224_1	chr12	81518578	81519158	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-6477	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.001724	0.308090	
chunk0123_339_1	chr3	47757640	47758115	+	0	NA	intron (NM_003074, intron 2 of 27)	L1MEd|LINE|L1	24038	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.021053	0.411765	
chunk0120_58_1	chr3	3126354	3126960	+	0	NA	promoter-TSS (NM_182916)	promoter-TSS (NM_182916)	-259	NM_182916	51095	Hs.732725	NM_016000	ENSG00000072756	TRNT1	CCA1|CGI-47|MtCCA|RPEM|SIFD	tRNA nucleotidyl transferase 1	protein-coding	0.085809	0.598023	
chunk0186_95_1	chr7	137551313	137551563	+	0	NA	intron (NM_004717, intron 20 of 33)	intron (NM_004717, intron 20 of 33)	-207638	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.012000	0.470120	
chunk0200_256_1	chr9	21392153	21393124	+	0	NA	Intergenic	Intergenic	-7241	NM_000605	3440	Hs.211575	NM_000605	ENSG00000188379	IFNA2	IFN-alphaA|IFNA|IFNA2B|INFA2	interferon alpha 2	protein-coding	0.013388	0.463992	
chunk0143_316_1	chr4	119212842	119213457	+	0	NA	promoter-TSS (NR_125931)	promoter-TSS (NR_125931)	-505	NR_125931	101929762	Hs.570735	NR_125931		LOC101929762	-	uncharacterized LOC101929762	ncRNA	0.052033	0.577922	
chunk0037_32_1	chr11	70169603	70170115	+	0	NA	intron (NM_018043, intron 21 of 25)	intron (NM_018043, intron 21 of 25)	-33304	NM_003824	8772	Hs.86131	NM_003824	ENSG00000168040	FADD	GIG3|MORT1	Fas associated via death domain	protein-coding	0.025391	0.629630	
chunk0128_245_1	chr3	108556136	108556810	+	0	NA	intron (NM_020890, intron 17 of 20)	Tigger4a|DNA|TcMar-Tigger	-27151	NM_014981	22989	Hs.731060	NM_014981	ENSG00000144821	MYH15	-	myosin heavy chain 15	protein-coding	0.000000	0.308148	
chunk0041_350_1	chr11	130744744	130745308	+	0	NA	Intergenic	Intergenic	72070	NM_001271983	283171	Hs.376151	NM_001271983		C11orf44	-	chromosome 11 open reading frame 44	protein-coding	0.005319	0.380531	
chunk0185_286_1	chr7	130989315	130989739	+	0	NA	intron (NR_109855, intron 2 of 4)	intron (NR_109855, intron 2 of 4)	76063	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.000000	0.414118	
chunk0204_252_1	chr9	98110197	98110396	+	0	NA	intron (NM_014788, intron 1 of 5)	intron (NM_014788, intron 1 of 5)	9057	NM_033219	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.000000	0.450000	
chunk0095_213_1	chr2	18708127	18708667	+	0	NA	Intergenic	Intergenic	-118817	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.001852	0.367837	
chunk0126_424_1	chr3	86606178	86606416	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	384810	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.008403	0.397490	
chunk0054_441_1	chr13	51397258	51397919	+	0	NA	intron (NM_012141, intron 4 of 17)	intron (NM_012141, intron 4 of 17)	-48949	NR_049878	100847003		NR_049878	ENSG00000266072	MIR5693	-	microRNA 5693	ncRNA	0.009077	0.422961	
chunk0174_420_1	chr6	165835463	165836057	+	0	NA	Intergenic	Intergenic	-151791	NR_027284	441177	Hs.708964	NM_001013720	ENSG00000281832	LINC00602	-	long intergenic non-protein coding RNA 602	ncRNA	0.026936	0.574790	249(GAGAACAGGGAGTCCC,-,0.00),250(AGAACAGGGAGTCCCT,+,0.00)
chunk0125_320_1	chr3	70941332	70941868	+	0	NA	Intergenic	Intergenic	123323	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.003731	0.350093	
chunk0064_408_1	chr14	99538188	99538391	+	0	NA	intron (NM_001144995, intron 1 of 5)	intron (NM_001144995, intron 1 of 5)	56887	NM_001099402	8812	Hs.510409	NM_003858	ENSG00000090061	CCNK	CPR4|IDDHDF	cyclin K	protein-coding	0.009852	0.598039	3(AGGAACAAAGTGTCCC,-,0.00),4(GGAACAAAGTGTCCCC,+,0.00)
chunk0046_445_1	chr12	64872290	64872574	+	0	NA	intron (NM_015279, intron 11 of 11)	MER58A|DNA|hAT-Charlie	-11342	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.003521	0.442105	
chunk0126_358_1	chr3	83023166	83023410	+	0	NA	Intergenic	Intergenic	-1261489	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004098	0.432653	61(AAGGACAGGGTGTGCT,-,0.00),62(AGGACAGGGTGTGCTG,+,0.00)
chunk0014_285_1	chr1	180589382	180589649	+	0	NA	Intergenic	Intergenic	30541	NR_125716	148756		NR_125716	ENSG00000236719	OVAAL	LINC01131|OVAL	ovarian adenocarcinoma amplified long non-coding RNA	ncRNA	0.003745	0.347015	
chunk0128_80_1	chr3	105395466	105395908	+	0	NA	intron (NM_001627, intron 1 of 15)	intron (NM_001627, intron 1 of 15)	28974	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.004525	0.349887	
chunk0053_317_1	chr13	34161975	34162404	+	0	NA	Intergenic	Intergenic	344120	NM_002915	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.004662	0.379070	
chunk0119_158_1	chr22	43150832	43151171	+	0	NA	promoter-TSS (NM_001256531)	promoter-TSS (NM_001256531)	-513	NM_000714	706	Hs.202	NM_000714	ENSG00000100300	TSPO	BPBS|BZRP|DBI|IBP|MBR|PBR|PBS|PKBS|PTBR|mDRC|pk18	translocator protein	protein-coding	0.035398	0.635294	
chunk0192_11_1	chr8	58350300	58350576	+	0	NA	Intergenic	Intergenic	-60826	NM_001077619	137886	Hs.155572	NM_001077619	ENSG00000215114	UBXN2B	p37	UBX domain protein 2B	protein-coding	0.010870	0.418773	
chunk0060_115_1	chr14	43740268	43740630	+	0	NA	Intergenic	Intergenic	766847	NM_032135	84075	Hs.307086	NM_032135	ENSG00000189139	FSCB	C14orf155	fibrous sheath CABYR binding protein	protein-coding	0.002762	0.358127	
chunk0023_297_1	chr10	28785325	28786123	+	0	NA	intron (NR_120652, intron 2 of 3)	intron (NR_120652, intron 2 of 3)	10326	NR_038376	100507605	Hs.119207	NR_038374	ENSG00000235824	LINC00837	-	long intergenic non-protein coding RNA 837	ncRNA	0.010025	0.377972	
chunk0103_322_1	chr2	167648892	167649166	+	0	NA	Intergenic	Intergenic	-169643	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.003650	0.374545	
chunk0056_165_1	chr13	84756705	84757154	+	0	NA	Intergenic	L1MCa|LINE|L1	-26725	NR_132852	106635542		NR_132852		SNORA107	-	small nucleolar RNA, H/ACA box 107	snoRNA	0.006682	0.426667	264(AAGAACAGAATGTTCT,-,0.00),265(AGAACAGAATGTTCTG,+,0.00)
chunk0087_353_1	chr18	40964028	40964774	+	0	NA	Intergenic	L1PA15|LINE|L1	556196	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.001340	0.333333	
chunk0069_25_1	chr15	60439713	60440418	+	0	NA	intron (NM_024611, intron 12 of 15)	Tigger6a|DNA|TcMar-Tigger	39095	NM_024611	79664	Hs.200943	NM_024611	ENSG00000128915	ICE2	BRCC1|NARG2	interactor of little elongation complex ELL subunit 2	protein-coding	0.004255	0.366856	
chunk0017_311_1	chr1	211216589	211217204	+	0	NA	Intergenic	Intergenic	-42470	NM_001136224	55758	Hs.356399	NM_018254	ENSG00000117625	RCOR3	-	REST corepressor 3	protein-coding	0.006504	0.339286	246(TTGTACATAATGTTCT,-,0.00),247(TGTACATAATGTTCTT,+,0.00)
chunk0001_78_1	chr1	2583833	2584057	+	0	NA	intron (NR_121638, intron 3 of 3)	LTR40c|LTR|ERVL	-2515	NR_036638	127281	Hs.462033	NM_152371	ENSG00000157870	PRXL2B	C1orf93|FAM213B	peroxiredoxin like 2B	protein-coding	0.026786	0.564444	
chunk0125_242_1	chr3	68556192	68556608	+	0	NA	Intergenic	Intergenic	376210	NM_001005527	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.004808	0.273381	
chunk0086_70_1	chr18	13191655	13192030	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-26888	NM_181482	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.010667	0.430851	
chunk0065_291_1	chr14	102678829	102679279	+	0	NA	intron (NM_015156, intron 2 of 11)	L1ME1|LINE|L1	86395	NM_015156	23186	Hs.510521	NM_015156	ENSG00000089902	RCOR1	COREST|RCOR	REST corepressor 1	protein-coding	0.006667	0.305987	
chunk0106_110_1	chr2	197515720	197516167	+	0	NA	promoter-TSS (NM_001204094)	promoter-TSS (NM_001204094)	-100	NM_015387	25843	Hs.633165	NM_015387	ENSG00000115540	MOB4	2C4D|CGI-95|MOB1|MOB3|MOBKL3|PHOCN|PREI3	MOB family member 4, phocein	protein-coding	0.107383	0.678571	
chunk0152_70_1	chr5	58040066	58040265	+	0	NA	Intergenic	Intergenic	82176	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.000000	0.345000	
chunk0091_460_1	chr19	18154015	18154278	+	0	NA	intron (NR_073517, intron 1 of 15)	intron (NR_073517, intron 1 of 15)	968	NR_073517	5296	Hs.371344	NM_005027	ENSG00000105647	PIK3R2	MPPH|MPPH1|P85B|p85|p85-BETA	phosphoinositide-3-kinase regulatory subunit 2	protein-coding	0.041825	0.583333	152(AGAACAGCACGTCCAT,+,0.00)
chunk0172_115_1	chr6	135093457	135093734	+	0	NA	Intergenic	MIRb|SINE|MIR	-38697	NM_001145207	10767	Hs.378532	NM_006620	ENSG00000112339	HBS1L	EF-1a|ERFS|HBS1|HSPC276|eRF3c	HBS1 like translational GTPase	protein-coding	0.018051	0.370504	
chunk0044_161_1	chr12	29859466	29859671	+	0	NA	Intergenic	L2c|LINE|L2	-74809	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.000000	0.373786	118(CAGAACACCTAGTCCA,-,0.00)
chunk0173_5_1	chr6	141164082	141165070	+	0	NA	Intergenic	Intergenic	480762	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.006073	0.397371	
chunk0011_186_1	chr1	149428303	149428967	+	0	NA	Intergenic	Intergenic	-155188	NM_001135789	653598	Hs.534674	NM_001135789	ENSG00000263464	PPIAL4C	COAS-2	peptidylprolyl isomerase A like 4C	protein-coding	0.009036	0.436090	281(GGGTCACTATGTACTC,+,0.00)
chunk0159_416_1	chr5	147911354	147911978	+	0	NA	Intergenic	Intergenic	-5128	NM_206966	389336	Hs.660038	NM_206966	ENSG00000178776	C5orf46	SSSP1	chromosome 5 open reading frame 46	protein-coding	0.009615	0.366400	284(AGGAACACCATGTTAC,-,0.00)
chunk0033_385_1	chr11	23990958	23991247	+	0	NA	Intergenic	L2c|LINE|L2	-505868	NM_001009909	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.003460	0.406897	
chunk0191_151_1	chr8	48925170	48925605	+	0	NA	Intergenic	Intergenic	-3947	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.004598	0.399083	
chunk0194_279_1	chr8	87305551	87306171	+	0	NA	intron (NM_173538, intron 8 of 10)	L1PB1|LINE|L1	439413	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.003226	0.359098	
chunk0181_334_1	chr7	88109596	88110224	+	0	NA	intron (NM_021721, intron 5 of 27)	intron (NM_021721, intron 5 of 27)	-106750	NR_120517	102723885	Hs.489040	NR_120517		LOC102723885	-	uncharacterized LOC102723885	ncRNA	0.004777	0.400636	
chunk0158_281_1	chr5	131672005	131672730	+	0	NA	exon (NM_133372, exon 14 of 18)	exon (NM_133372, exon 14 of 18)	-37131	NM_001164389	51735	Hs.483329	NM_016340	ENSG00000158987	RAPGEF6	KIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2	Rap guanine nucleotide exchange factor 6	protein-coding	0.002759	0.410468	
chunk0192_46_1	chr8	58877429	58877961	+	0	NA	intron (NM_014729, intron 3 of 8)	intron (NM_014729, intron 3 of 8)	-217850	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.003759	0.375235	
chunk0043_265_1	chr12	20735183	20735443	+	0	NA	intron (NM_017435, intron 10 of 14)	MIR3|SINE|MIR	39848	NM_017435	53919	Hs.47261	NM_017435	ENSG00000139155	SLCO1C1	OATP-F|OATP1|OATP14|OATP1C1|OATPF|OATPRP5|SLC21A14	solute carrier organic anion transporter family member 1C1	protein-coding	0.007692	0.413793	
chunk0060_465_1	chr14	55297698	55298114	+	0	NA	intron (NM_152231, intron 1 of 1)	intron (NM_152231, intron 1 of 1)	25752	NM_152231	55030	Hs.525348	NM_017943	ENSG00000178974	FBXO34	CGI-301|Fbx34	F-box protein 34	protein-coding	0.007212	0.374101	
chunk0007_189_1	chr1	80976970	80977564	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	335980	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.003367	0.356303	
chunk0057_187_1	chr13	102823818	102824379	+	0	NA	intron (NM_017693, intron 7 of 10)	Charlie7|DNA|hAT-Charlie	16952	NM_001204425	100533467	Hs.258429	NM_001204425	ENSG00000134899	BIVM-ERCC5	ERCC5-202	BIVM-ERCC5 readthrough	protein-coding	0.001783	0.373665	
chunk0118_445_1	chr22	39160780	39161326	+	0	NA	Intergenic	L1MEd|LINE|L1	-8520	NM_175709	23492	Hs.356416	NM_175709	ENSG00000100307	CBX7	-	chromobox 7	protein-coding	0.005495	0.369287	
chunk0040_70_1	chr11	111305292	111305952	+	0	NA	promoter-TSS (NM_001302644)	promoter-TSS (NM_001302644)	-574	NM_001302644	399948	Hs.729225	NM_207429		COLCA1	C11orf92|CASC12|LOH11CR1F	colorectal cancer associated 1	protein-coding	0.007576	0.376702	312(AAGAACACAGTGTCCT,-,0.00),313(AGAACACAGTGTCCTT,+,0.00),546(TGGTACTCTATGTTCC,-,0.00),547(GGTACTCTATGTTCCT,+,0.00)
chunk0059_22_1	chr14	29820272	29820642	+	0	NA	intron (NM_002742, intron 1 of 17)	L2c|LINE|L2	107236	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005405	0.361186	
chunk0184_120_1	chr7	114021432	114021840	+	0	NA	Intergenic	Intergenic	-64674	NR_033766	93986	Hs.282787	NM_014491	ENSG00000128573	FOXP2	CAGH44|SPCH1|TNRC10	forkhead box P2	protein-coding	0.002451	0.400978	
chunk0015_172_1	chr1	186749028	186749374	+	0	NA	Intergenic	Intergenic	68547	NR_125801	103752588	Hs.441636	NR_125801	ENSG00000273129	PACERR	PACER|PTGS2-AS1|PTGS2AS1	PTGS2 antisense NFKB1 complex-mediated expression regulator RNA	ncRNA	0.002890	0.328530	
chunk0210_82_1	chrX	70245755	70246079	+	0	NA	Intergenic	Intergenic	11262	NM_001013579	158833	Hs.407641	NM_001013579	ENSG00000204195	AWAT1	DGA2|DGAT2L3	acyl-CoA wax alcohol acyltransferase 1	protein-coding	0.012346	0.335385	
chunk0163_133_1	chr6	10602211	10602982	+	0	NA	intron (NM_145655, intron 1 of 2)	intron (NM_145655, intron 1 of 2)	16836	NM_145655	2651	Hs.519884	NM_001491	ENSG00000111846	GCNT2	CCAT|CTRCT13|GCNT2C|GCNT5|IGNT|II|NACGT1|NAGCT1|ULG3|bA360O19.2|bA421M1.1	glucosaminyl (N-acetyl) transferase 2 (I blood group)	protein-coding	0.010376	0.417098	
chunk0181_272_1	chr7	86215364	86215716	+	0	NA	Intergenic	Intergenic	-428374	NM_000840	2913	Hs.590575	NM_000840	ENSG00000198822	GRM3	GLUR3|GPRC1C|MGLUR3|mGlu3	glutamate metabotropic receptor 3	protein-coding	0.000000	0.337110	194(CTGTACATTCAGTTCT,-,0.00),195(TGTACATTCAGTTCTC,+,0.00)
chunk0078_382_1	chr16	87779205	87779497	+	0	NA	promoter-TSS (NR_120309)	promoter-TSS (NR_120309)	-203	NR_120309	102724467	Hs.587857	NR_120309		LOC102724467	-	uncharacterized LOC102724467	ncRNA	0.075342	0.655290	
chunk0080_445_1	chr17	36731038	36731599	+	0	NA	Intergenic	Intergenic	129722	NM_024864	79922	Hs.194864	NM_024864	ENSG00000278619	MRM1	-	mitochondrial rRNA methyltransferase 1	protein-coding	0.008913	0.565836	151(TGGGGCAGTGTGTCCC,-,0.00),152(GGGGCAGTGTGTCCCA,+,0.00)
chunk0054_304_1	chr13	48390894	48391698	+	0	NA	intron (NM_000321, intron 17 of 26)	L1MEc|LINE|L1	22221	NM_001162498	10161	Hs.123464	NM_005767	ENSG00000139679	LPAR6	ARWH1|HYPT8|LAH3|P2RY5|P2Y5	lysophosphatidic acid receptor 6	protein-coding	0.006219	0.337888	
chunk0091_110_1	chr19	5968671	5968917	+	0	NA	intron (NM_007320, intron 1 of 15)	L2b|LINE|L2	9515	NM_001300865	8498	Hs.531752	NM_003624	ENSG00000031823	RANBP3	-	RAN binding protein 3	protein-coding	0.024390	0.550607	
chunk0182_415_1	chr7	101085625	101086009	+	0	NA	intron (NM_030961, intron 1 of 2)	intron (NM_030961, intron 1 of 2)	378	NM_030961	81844	Hs.521092	NM_030961	ENSG00000169871	TRIM56	RNF109	tripartite motif containing 56	protein-coding	0.028646	0.610390	
chunk0130_85_1	chr3	130708106	130708876	+	0	NA	exon (NM_014602, exon 10 of 20)	exon (NM_014602, exon 10 of 20)	38361	NM_014602	30849	Hs.149032	NM_014602	ENSG00000196455	PIK3R4	VPS15|p150	phosphoinositide-3-kinase regulatory subunit 4	protein-coding	0.003896	0.335927	
chunk0006_151_1	chr1	66308858	66309559	+	0	NA	intron (NM_001037340, intron 5 of 14)	intron (NM_001037340, intron 5 of 14)	-22900	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.005706	0.353276	
chunk0159_166_1	chr5	139643792	139644096	+	0	NA	Intergenic	Intergenic	-4772	NM_016463	51523	Hs.189119	NM_016463	ENSG00000171604	CXXC5	CF5|HSPC195|RINF|WID	CXXC finger protein 5	protein-coding	0.003289	0.521311	
chunk0159_403_1	chr5	147571348	147571829	+	0	NA	intron (NR_038902, intron 1 of 3)	L1MD2|LINE|L1	11594	NR_038902	153469	Hs.184323	NR_038902	ENSG00000280780	JAKMIP2-AS1	-	JAKMIP2 antisense RNA 1	ncRNA	0.008316	0.352697	275(AGGTACACATTGTCCC,-,0.00),276(GGTACACATTGTCCCA,+,0.00)
chunk0193_156_1	chr8	74715361	74716052	+	0	NA	intron (NR_033830, intron 4 of 5)	intron (NR_033830, intron 4 of 5)	10013	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.005789	0.371387	
chunk0176_233_1	chr7	15833130	15833531	+	0	NA	Intergenic	Intergenic	144952	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.002494	0.348259	
chunk0037_115_1	chr11	72441823	72442310	+	0	NA	Intergenic	MLT1E1A|LTR|ERVL-MaLR	-7382	NM_001258392	81570	Hs.523877	NM_030813	ENSG00000162129	CLPB	ANKCLB|HSP78|MEGCANN|MGCA7|SKD3	ClpB homolog, mitochondrial AAA ATPase chaperonin	protein-coding	0.006160	0.420082	
chunk0109_179_1	chr20	4686128	4686403	+	0	NA	promoter-TSS (NM_001080123)	promoter-TSS (NM_001080123)	114	NM_000311	5621	Hs.472010	NM_000311	ENSG00000171867	PRNP	ASCR|AltPrP|CD230|CJD|GSS|KURU|PRIP|PrP|PrP27-30|PrP33-35C|PrPc|p27-30	prion protein	protein-coding	0.105455	0.615942	
chunk0202_257_1	chr9	76836122	76836846	+	0	NA	intron (NM_015225, intron 4 of 18)	intron (NM_015225, intron 4 of 18)	69603	NR_131751	158471	Hs.262857	NM_015225	ENSG00000106772	PRUNE2	BMCC1|BNIPXL|C9orf65|KIAA0367	prune homolog 2 with BCH domain	protein-coding	0.008287	0.395862	
chunk0056_415_1	chr13	94369779	94370149	+	0	NA	intron (NM_005708, intron 6 of 8)	L2b|LINE|L2	109718	NM_001129889	1638	Hs.301865	NM_001922	ENSG00000080166	DCT	TRP-2|TYRP2	dopachrome tautomerase	protein-coding	0.005405	0.388140	
chunk0117_350_1	chr21	44188544	44188746	+	0	NA	Intergenic	Intergenic	52359	NM_001283051	23308	Hs.14155	NM_015259	ENSG00000160223	ICOSLG	B7-H2|B7H2|B7RP-1|B7RP1|B7h|CD275|GL50|ICOS-L|ICOSL|LICOS	inducible T cell costimulator ligand	protein-coding	0.044554	0.546798	
chunk0043_347_1	chr12	23024286	23024485	+	0	NA	Intergenic	Intergenic	-151251	NR_120471	101928441	Hs.129111	NR_120471	ENSG00000256321	LOC101928441	-	uncharacterized LOC101928441	ncRNA	0.005025	0.250000	
chunk0084_434_1	chr17	82686911	82687338	+	0	NA	intron (NM_006822, intron 1 of 5)	intron (NM_006822, intron 1 of 5)	11598	NM_006822	10966	Hs.484068	NM_006822	ENSG00000141542	RAB40B	RAR|SEC4L	RAB40B, member RAS oncogene family	protein-coding	0.018735	0.497664	
chunk0115_442_1	chr21	32159240	32159483	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-73066	NR_038033	100551499	Hs.224449	NR_038033		LINC00159	C21orf44|NCRNA00159	long intergenic non-protein coding RNA 159	ncRNA	0.000000	0.262295	
chunk0140_95_1	chr4	68338172	68338545	+	0	NA	exon (NM_001031732, exon 2 of 17)	exon (NM_001031732, exon 2 of 17)	11748	NM_133370	91746	Hs.175955	NM_133370	ENSG00000083896	YTHDC1	YT521|YT521-B	YTH domain containing 1	protein-coding	0.002681	0.294118	193(CAGAACATTAAGTTCT,-,0.00),194(AGAACATTAAGTTCTC,+,0.00)
chunk0142_35_1	chr4	90732347	90732800	+	0	NA	intron (NM_001145065, intron 7 of 10)	MER68B|LTR|ERVL	497542	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.002208	0.365639	
chunk0207_107_1	chr9	128786930	128787129	+	0	NA	promoter-TSS (NM_001286772)	promoter-TSS (NM_001286772)	-178	NM_018201	54662	Hs.3376	NM_018201	ENSG00000107021	TBC1D13	-	TBC1 domain family member 13	protein-coding	0.090452	0.650000	
chunk0049_167_1	chr12	92208423	92208816	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-62722	NM_001731	694	Hs.255935	NM_001731	ENSG00000133639	BTG1	APRO2	BTG anti-proliferation factor 1	protein-coding	0.012723	0.393401	
chunk0189_333_1	chr8	26409803	26410464	+	0	NA	intron (NM_004331, intron 5 of 5)	intron (NM_004331, intron 5 of 5)	27126	NM_004331	665	Hs.131226	NM_004331	ENSG00000104765	BNIP3L	BNIP3a|NIX	BCL2 interacting protein 3 like	protein-coding	0.010590	0.415408	
chunk0018_175_1	chr1	219140669	219141162	+	0	NA	intron (NR_038845, intron 3 of 4)	intron (NR_038845, intron 3 of 4)	32873	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.002028	0.350202	212(GGGTACATAGAGTTCA,-,0.00),213(GGTACATAGAGTTCAG,+,0.00)
chunk0100_89_1	chr2	107738226	107738791	+	0	NA	Intergenic	Intergenic	-15604	NR_126370	104326057	Hs.585967	NR_126369	ENSG00000232991	GACAT1	LINC00876	gastric cancer associated transcript 1	ncRNA	0.008850	0.388693	219(TAGGACTTAATGTTCC,-,0.00),220(AGGACTTAATGTTCCC,+,0.00)
chunk0036_191_1	chr11	63132489	63132868	+	0	NA	intron (NM_173586, intron 2 of 3)	L1PA7|LINE|L1	11543	NM_001136506	283238	Hs.375139	NM_173586	ENSG00000197658	SLC22A24	NET46	solute carrier family 22 member 24	protein-coding	0.007916	0.513158	
chunk0153_346_1	chr5	74288667	74288949	+	0	NA	Intergenic	Intergenic	19517	NR_105009	102503429	Hs.519391	NR_105009	ENSG00000248942	LINC01335	-	long intergenic non-protein coding RNA 1335	ncRNA	0.007092	0.353357	89(AAGAACAAAGTGTACT,-,0.00),90(AGAACAAAGTGTACTG,+,0.00)
chunk0060_32_1	chr14	40390215	40390575	+	0	NA	Intergenic	Intergenic	-564316	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.005556	0.385042	
chunk0192_325_1	chr8	67110169	67110368	+	0	NA	intron (NM_001291339, intron 6 of 25)	MER61F|LTR|ERV1	26420	NM_001291339	79848	Hs.370147	NM_024790	ENSG00000104218	CSPP1	CSPP|JBTS21	centrosome and spindle pole associated protein 1	protein-coding	0.000000	0.370000	
chunk0124_10_1	chr3	51544536	51545510	+	0	NA	intron (NM_015106, intron 1 of 21)	intron (NM_015106, intron 1 of 21)	3443	NM_015106	23132	Hs.105399	NM_015106	ENSG00000164080	RAD54L2	ARIP4|HSPC325|SRISNF2L	RAD54 like 2	protein-coding	0.014374	0.470769	
chunk0080_65_1	chr17	21973046	21973252	+	0	NA	Intergenic	(ATGGA)n|Simple_repeat|Simple_repeat	280626	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.009709	0.429952	
chunk0151_404_1	chr5	55573678	55574131	+	0	NA	Intergenic	L1MC2|LINE|L1	-38826	NM_003711	8611	Hs.696231	NM_003711	ENSG00000067113	PLPP1	LLP1a|LPP1|PAP-2a|PAP2|PPAP2A	phospholipid phosphatase 1	protein-coding	0.006623	0.376652	177(GGGAACTGTCTGTACA,-,0.00),178(GGAACTGTCTGTACAA,+,0.00)
chunk0151_259_1	chr5	52415776	52416278	+	0	NA	Intergenic	Intergenic	-371913	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.003984	0.339960	
chunk0153_275_1	chr5	72915212	72915670	+	0	NA	Intergenic	Intergenic	36850	NR_039968	100616152		NR_039968	ENSG00000263593	MIR4804	-	microRNA 4804	ncRNA	0.006550	0.359477	222(TTGGACATCATGTTCT,-,0.00),223(TGGACATCATGTTCTA,+,0.00)
chunk0141_311_1	chr4	87105654	87105856	+	0	NA	intron (NM_001313959, intron 8 of 19)	intron (NM_001313959, intron 8 of 19)	98754	NM_005935	4299	Hs.480190	NM_005935	ENSG00000172493	AFF1	AF4|MLLT2|PBM1	AF4/FMR2 family member 1	protein-coding	0.004950	0.463054	
chunk0116_224_1	chr21	38121261	38121460	+	0	NA	promoter-TSS (NM_005867)	promoter-TSS (NM_005867)	0	NM_005867	10281	Hs.23251	NM_005867	ENSG00000184029	DSCR4	DCRB|DSCRB	Down syndrome critical region 4	ncRNA	0.060302	0.545000	
chunk0069_83_1	chr15	61108274	61108755	+	0	NA	intron (NM_134261, intron 1 of 10)	MER58A|DNA|hAT-Charlie	120789	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.008316	0.360996	
chunk0009_449_1	chr1	111580123	111580543	+	0	NA	Intergenic	Intergenic	-16330	NM_001302680	57413	Hs.281342	NM_020683	ENSG00000121933	TMIGD3	AD026	transmembrane and immunoglobulin domain containing 3	protein-coding	0.009524	0.382423	
chunk0118_65_1	chr22	28570600	28571435	+	0	NA	intron (NM_001145418, intron 2 of 22)	intron (NM_001145418, intron 2 of 22)	108848	NM_001145418	23331	Hs.387856	NM_015281	ENSG00000100154	TTC28	TPRBK	tetratricopeptide repeat domain 28	protein-coding	0.003593	0.302632	
chunk0074_57_1	chr16	20900438	20900925	+	0	NA	promoter-TSS (NM_001302835)	promoter-TSS (NM_001302835)	15	NR_126516	57149	Hs.745012	NM_020424	ENSG00000102897	LYRM1	A211C6.1	LYR motif containing 1	protein-coding	0.065708	0.620902	337(TGGACCAGCCTGTGCT,-,0.00),338(GGACCAGCCTGTGCTC,+,0.00)
chunk0004_66_1	chr1	43313893	43314209	+	0	NA	intron (NM_005424, intron 14 of 22)	intron (NM_005424, intron 14 of 22)	13156	NM_005424	7075	Hs.78824	NM_005424	ENSG00000066056	TIE1	JTK14|TIE	tyrosine kinase with immunoglobulin like and EGF like domains 1	protein-coding	0.022152	0.444795	
chunk0204_384_1	chr9	102185228	102185770	+	0	NA	Intergenic	Intergenic	-334138	NR_103830	414319	Hs.385790	NR_103830	ENSG00000204250	LINC00587	C9orf107|bA785H23.1	long intergenic non-protein coding RNA 587	ncRNA	0.005535	0.401473	
chunk0172_32_1	chr6	133783455	133783738	+	0	NA	intron (NR_109982, intron 2 of 8)	L1ME3E|LINE|L1	-37551	NR_027030	154089	Hs.126165	NR_027030		LINC01312	-	long intergenic non-protein coding RNA 1312	ncRNA	0.021201	0.383803	
chunk0101_257_1	chr2	133287330	133288006	+	0	NA	intron (NM_207481, intron 4 of 17)	intron (NM_207481, intron 4 of 17)	21473	NR_110294	101928161	Hs.661917	NR_110294	ENSG00000226953	NCKAP5-AS2	-	NCKAP5 antisense RNA 2	ncRNA	0.004438	0.373708	
chunk0155_60_1	chr5	91506863	91507402	+	0	NA	Intergenic	MIR|SINE|MIR	-123800	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.009276	0.388889	
chunk0024_225_1	chr10	37873227	37873658	+	0	NA	Intergenic	Intergenic	-15358	NM_001267597	57209	Hs.528423	NM_021045	ENSG00000198105	ZNF248	bA162G10.3	zinc finger protein 248	protein-coding	0.004640	0.349537	
chunk0057_14_1	chr13	95558970	95559553	+	0	NA	intron (NM_006984, intron 1 of 4)	intron (NM_006984, intron 1 of 4)	6568	NM_006984	9071	Hs.534377	NM_006984	ENSG00000134873	CLDN10	CPETRL3|HELIX|OSP-L|OSPL	claudin 10	protein-coding	0.012007	0.333904	
chunk0103_328_1	chr2	167776558	167777148	+	0	NA	Intergenic	Intergenic	-41819	NM_020981	8708	Hs.735833	NM_020981	ENSG00000172318	B3GALT1	beta3Gal-T1	beta-1,3-galactosyltransferase 1	protein-coding	0.010169	0.363790	
chunk0153_207_1	chr5	71892015	71892291	+	0	NA	Intergenic	Intergenic	172990	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.007246	0.555957	136(AGGGACAGGCTGTTCC,-,0.00),137(GGGACAGGCTGTTCCA,+,0.00)
chunk0058_89_1	chr14	21489201	21489645	+	0	NA	intron (NM_001303523, intron 4 of 7)	intron (NM_001303523, intron 4 of 7)	12247	NM_001303523	9878	Hs.555910	NM_014828	ENSG00000092203	TOX4	C14orf92|KIAA0737|LCP1|MIG7	TOX high mobility group box family member 4	protein-coding	0.009009	0.397753	
chunk0144_244_1	chr4	135329130	135329564	+	0	NA	Intergenic	L2a|LINE|L2	558746	NR_103762	100507528	Hs.518987	NR_103762	ENSG00000248330	LINC00613	-	long intergenic non-protein coding RNA 613	ncRNA	0.002304	0.317241	
chunk0208_138_1	chrX	15638087	15638295	+	0	NA	intron (NM_020665, intron 5 of 5)	intron (NM_020665, intron 5 of 5)	26840	NM_020665	57393	Hs.129614	NM_020665	ENSG00000147003	CLTRN	NX-17|NX17|TMEM27	collectrin, amino acid transport regulator	protein-coding	0.000000	0.315789	128(ATGCACATCTTGTACC,-,0.00)
chunk0103_209_1	chr2	163840219	163840619	+	0	NA	Intergenic	Intergenic	-104416	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.000000	0.306733	
chunk0180_107_1	chr7	55351263	55351966	+	0	NA	Intergenic	L1ME4a|LINE|L1	-13834	NM_018697	55915	Hs.595384	NM_018697	ENSG00000132434	LANCL2	GPR69B|TASP	LanC like 2	protein-coding	0.005690	0.409091	49(AAGCACTTCATGTCCT,-,0.00),50(AGCACTTCATGTCCTC,+,0.00)
chunk0024_183_1	chr10	36054395	36054847	+	0	NA	Intergenic	Intergenic	276319	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.011062	0.445916	
chunk0064_402_1	chr14	99385831	99386491	+	0	NA	Intergenic	Intergenic	94728	NM_032233	84193	Hs.510407	NM_032233	ENSG00000183576	SETD3	C14orf154|hSETD3	SET domain containing 3, actin histidine methyltransferase	protein-coding	0.012121	0.520424	337(TGGTACTTTGTGTTCC,-,0.00),338(GGTACTTTGTGTTCCT,+,0.00)
chunk0121_26_1	chr3	15102151	15102670	+	0	NA	Intergenic	Intergenic	-3253	NR_126155	64145	Hs.475565	NM_022340	ENSG00000131381	RBSN	Rabenosyn-5|ZFYVE20	rabenosyn, RAB effector	protein-coding	0.007707	0.536538	
chunk0204_258_1	chr9	98157544	98157924	+	0	NA	intron (NM_052820, intron 1 of 11)	intron (NM_052820, intron 1 of 11)	15158	NM_003389	7464	Hs.113094	NM_003389	ENSG00000106789	CORO2A	CLIPINB|IR10|WDR2	coronin 2A	protein-coding	0.026316	0.496063	
chunk0115_380_1	chr21	30244235	30244595	+	0	NA	Intergenic	Intergenic	-28264	NM_199328	9073	Hs.162209	NM_012132	ENSG00000156284	CLDN8	HEL-S-79	claudin 8	protein-coding	0.002778	0.401662	168(AAACACATTCTGTTCT,-,0.00),169(AACACATTCTGTTCTT,+,0.00)
chunk0178_170_1	chr7	34064669	34065042	+	0	NA	intron (NM_133468, intron 12 of 15)	intron (NM_133468, intron 12 of 15)	159944	NM_133468	168667	Hs.660998	NM_133468	ENSG00000164619	BMPER	CRIM3|CV-2|CV2	BMP binding endothelial regulator	protein-coding	0.005362	0.395722	
chunk0098_262_1	chr2	75300163	75300483	+	0	NA	Intergenic	L2a|LINE|L2	-100804	NM_015727	6869	Hs.633301	NM_001058	ENSG00000115353	TACR1	NK1R|NKIR|SPR|TAC1R	tachykinin receptor 1	protein-coding	0.006250	0.330218	
chunk0043_38_1	chr12	13362292	13362575	+	0	NA	Intergenic	LTR41C|LTR|ERVL	14312	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.007067	0.528169	
chunk0200_59_1	chr9	15700870	15701368	+	0	NA	intron (NM_173550, intron 11 of 25)	L1MA4|LINE|L1	148020	NM_173550	203238	Hs.17267	NM_173550	ENSG00000164989	CCDC171	C9orf93|bA536D16.1|bA778P13.1	coiled-coil domain containing 171	protein-coding	0.006024	0.342685	
chunk0021_126_1	chr10	3776688	3777293	+	0	NA	non-coding (NR_027653, exon 4 of 4)	non-coding (NR_027653, exon 4 of 4)	8291	NM_001160124	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.013223	0.384488	104(CTGAACAGAATGTACT,-,0.00),105(TGAACAGAATGTACTT,+,0.00)
chunk0212_11_1	chrY	7527695	7528133	+	0	NA	Intergenic	Intergenic	173333	NR_001552	252948	Hs.522848	NR_001552		TTTY16	NCRNA00139	testis-specific transcript, Y-linked 16	ncRNA	0.004566	0.394077	
chunk0005_159_1	chr1	58294855	58295240	+	0	NA	Intergenic	Intergenic	-44508	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.005195	0.455959	
chunk0125_248_1	chr3	68955582	68955998	+	0	NA	Intergenic	Intergenic	-23180	NM_182522	151647	Hs.187873	NM_182522	ENSG00000163377	TAFA4	FAM19A4|TAFA-4	TAFA chemokine like family member 4	protein-coding	0.002404	0.446043	
chunk0047_46_1	chr12	67040382	67040581	+	0	NA	Intergenic	Intergenic	55803	NR_120490	102724421	Hs.135774	NR_120490	ENSG00000257083	LOC102724421	-	uncharacterized LOC102724421	ncRNA	0.010050	0.410000	
chunk0209_40_1	chrX	36527863	36528239	+	0	NA	Intergenic	Intergenic	-87759	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.005319	0.379310	
chunk0117_201_1	chr22	21834819	21835177	+	0	NA	intron (NM_138957, intron 1 of 7)	intron (NM_138957, intron 1 of 7)	32682	NM_002745	5594	Hs.431850	NM_002745	ENSG00000100030	MAPK1	ERK|ERK-2|ERK2|ERT1|MAPK2|P42MAPK|PRKM1|PRKM2|p38|p40|p41|p41mapk|p42-MAPK	mitogen-activated protein kinase 1	protein-coding	0.008380	0.448468	
chunk0055_157_1	chr13	60157546	60157745	+	0	NA	intron (NM_001258369, intron 1 of 26)	L1MEb|LINE|L1	6340	NM_001258368	81624	Hs.283127	NM_030932	ENSG00000139734	DIAPH3	AN|AUNA1|DIA2|DRF3|NSDAN|diap3|mDia2	diaphanous related formin 3	protein-coding	0.000000	0.355000	
chunk0131_121_1	chr3	144105367	144106048	+	0	NA	Intergenic	Intergenic	132382	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.005874	0.398827	
chunk0182_113_1	chr7	93653198	93653599	+	0	NA	Intergenic	MIR|SINE|MIR	-63530	NR_039796	100616206		NR_039796	ENSG00000265423	MIR4652	-	microRNA 4652	ncRNA	0.007481	0.313433	256(GGGTACAGAATGTACT,-,0.00),257(GGTACAGAATGTACTA,+,0.00)
chunk0179_71_1	chr7	44062672	44063233	+	0	NA	intron (NM_000290, intron 2 of 2)	intron (NM_000290, intron 2 of 2)	2635	NM_000290	5224	Hs.632642	NM_000290	ENSG00000164708	PGAM2	GSD10|PGAM-M|PGAMM	phosphoglycerate mutase 2	protein-coding	0.016043	0.572954	
chunk0012_460_1	chr1	165328225	165328424	+	0	NA	intron (NM_177398, intron 3 of 8)	intron (NM_177398, intron 3 of 8)	27917	NM_001174069	4009	Hs.667312	NM_177398	ENSG00000162761	LMX1A	LMX1|LMX1.1	LIM homeobox transcription factor 1 alpha	protein-coding	0.010050	0.460000	12(GAGGTCACAGTGTTCA,-,0.00),13(AGGTCACAGTGTTCAC,+,0.00)
chunk0172_406_1	chr6	140009406	140009634	+	0	NA	intron (NR_121623, intron 1 of 1)	intron (NR_121623, intron 1 of 1)	-18259	NR_121624	103352541	Hs.582647	NR_121624		LOC103352541	-	uncharacterized LOC103352541	ncRNA	0.008772	0.358079	
chunk0095_347_1	chr2	21121811	21122298	+	0	NA	Intergenic	L1MEd|LINE|L1	-1932	NM_001306137	100129278	Hs.651096	NM_001306137	ENSG00000218819	TDRD15	-	tudor domain containing 15	protein-coding	0.002053	0.301230	
chunk0089_236_1	chr18	61887762	61888071	+	0	NA	intron (NM_173557, intron 1 of 1)	intron (NM_173557, intron 1 of 1)	5155	NM_173557	220441	Hs.165062	NM_173557	ENSG00000176641	RNF152	-	ring finger protein 152	protein-coding	0.006472	0.448387	
chunk0189_76_1	chr8	20948350	20948798	+	0	NA	Intergenic	L1ME2|LINE|L1	-5059	NR_130773	102467222	Hs.444226	NR_130773	ENSG00000253147	LOC102467222	-	uncharacterized LOC102467222	ncRNA	0.004464	0.407572	
chunk0172_163_1	chr6	135943993	135944485	+	0	NA	intron (NM_018945, intron 1 of 12)	intron (NM_018945, intron 1 of 12)	92543	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.012195	0.490872	
chunk0080_143_1	chr17	27631488	27631701	+	0	NA	intron (NM_002308, intron 1 of 9)	intron (NM_002308, intron 1 of 9)	446	NM_009587	3965	Hs.81337	NM_002308	ENSG00000168961	LGALS9	HUAT|LGALS9A	galectin 9	protein-coding	0.023474	0.560748	
chunk0075_26_1	chr16	46894040	46894239	+	0	NA	intron (NM_001142466, intron 2 of 11)	intron (NM_001142466, intron 2 of 11)	9025	NM_001142466	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.030151	0.605000	
chunk0053_243_1	chr13	32682585	32683017	+	0	NA	intron (NM_015032, intron 10 of 34)	L1ME2|LINE|L1	96374	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.002315	0.327945	
chunk0077_355_1	chr16	83813994	83814193	+	0	NA	Intergenic	Intergenic	6190	NM_001537	3281	Hs.250899	NM_001537	ENSG00000230989	HSBP1	NPC-A-13	heat shock factor binding protein 1	protein-coding	0.000000	0.370000	29(GGGAACATAGAGTCCT,-,0.00),30(GGAACATAGAGTCCTC,+,0.00)
chunk0161_302_1	chr5	173364839	173365188	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	17558	NR_107023	102465862		NR_107023	ENSG00000274994	MIR8056	hsa-mir-8056	microRNA 8056	ncRNA	0.014327	0.408571	
chunk0022_379_1	chr10	17590340	17590705	+	0	NA	intron (NM_014241, intron 6 of 6)	intron (NM_014241, intron 6 of 6)	26852	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.002740	0.341530	
chunk0145_156_1	chr4	147117232	147117872	+	0	NA	Intergenic	LFSINE_Vert|SINE|tRNA	-171670	NM_031956	83894	Hs.378893	NM_031956	ENSG00000137473	TTC29	NYD-SP14|TBPP2A	tetratricopeptide repeat domain 29	protein-coding	0.009375	0.433697	
chunk0157_47_1	chr5	115978993	115979291	+	0	NA	intron (NM_173800, intron 1 of 19)	LTR78|LTR|ERV1	16688	NM_173800	206338	Hs.98288	NM_173800	ENSG00000172901	LVRN	APQ|AQPEP|TAQPEP	laeverin	protein-coding	0.003356	0.505017	
chunk0056_113_1	chr13	82938451	82938758	+	0	NA	Intergenic	LTR2752|LTR|ERV1	943789	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.006515	0.529221	
chunk0085_21_1	chr18	370378	370843	+	0	NA	intron (NM_130386, intron 2 of 9)	intron (NM_130386, intron 2 of 9)	-102551	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.012903	0.452790	
chunk0060_163_1	chr14	45332711	45333085	+	0	NA	Intergenic	Intergenic	-79496	NM_018353	55320	Hs.732769	NM_018353	ENSG00000129534	MIS18BP1	C14orf106|HSA242977|KNL2|M18BP1	MIS18 binding protein 1	protein-coding	0.008021	0.416000	
chunk0059_48_1	chr14	29987416	29987815	+	0	NA	Intergenic	Intergenic	-59922	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.000000	0.325000	
chunk0020_270_1	chr1	236350694	236350999	+	0	NA	Intergenic	LTR23|LTR|ERV1	-43534	NM_145861	128178	Hs.352224	NM_080738	ENSG00000186197	EDARADD	ECTD11A|ECTD11B|ED3|EDA3	EDAR associated death domain	protein-coding	0.003279	0.424837	
chunk0060_406_1	chr14	53057211	53057604	+	0	NA	intron (NM_030637, intron 9 of 11)	intron (NM_030637, intron 9 of 11)	95921	NM_001160147	80821	Hs.125525	NM_030637	ENSG00000100523	DDHD1	PA-PLA1|PAPLA1|SPG28	DDHD domain containing 1	protein-coding	0.000000	0.271574	
chunk0169_74_1	chr6	99245346	99245578	+	0	NA	Intergenic	Intergenic	104193	NM_032511	84553	Hs.573245	NM_032511	ENSG00000146267	FAXC	C6orf168|dJ273F20	failed axon connections homolog, metaxin like GST domain containing	protein-coding	0.012931	0.394850	
chunk0111_11_1	chr20	21867938	21868546	+	0	NA	Intergenic	Intergenic	162583	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.006579	0.384236	
chunk0036_227_1	chr11	63874526	63874916	+	0	NA	intron (NM_001039469, intron 1 of 18)	intron (NM_001039469, intron 1 of 18)	-13794	NM_017490	2011	Hs.567261	NM_004954	ENSG00000072518	MARK2	EMK-1|EMK1|PAR-1|Par-1b|Par1b	microtubule affinity regulating kinase 2	protein-coding	0.015385	0.485934	
chunk0047_325_1	chr12	74317015	74317798	+	0	NA	Intergenic	Intergenic	-24775	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.002554	0.431122	247(GAGCACACCAAGTTCC,-,0.00),248(AGCACACCAAGTTCCT,+,0.00)
chunk0163_435_1	chr6	17385215	17385491	+	0	NA	Intergenic	Intergenic	-8152	NM_006366	10486	Hs.132902	NM_006366	ENSG00000112186	CAP2	-	cyclase associated actin cytoskeleton regulatory protein 2	protein-coding	0.003623	0.368231	
chunk0140_235_1	chr4	71233887	71234311	+	0	NA	intron (NM_001098484, intron 1 of 25)	L2a|LINE|L2	46813	NM_001134742	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.004717	0.414118	164(TGTACTTGCTGTTCCC,+,0.00)
chunk0158_421_1	chr5	135168522	135168959	+	0	NA	intron (NM_001277348, intron 2 of 5)	Tigger15a|DNA|TcMar-Tigger	79437	NR_037895	340073	Hs.434422	NR_037895	ENSG00000249647	C5orf66-AS2	-	C5orf66 antisense RNA 2	ncRNA	0.006865	0.472603	216(GTGTACAGTTTGTCCT,-,0.00),217(TGTACAGTTTGTCCTG,+,0.00)
chunk0097_35_1	chr2	42733915	42734372	+	0	NA	intron (NM_001282755, intron 17 of 17)	L1MA3|LINE|L1	30118	NM_148962	165140	Hs.168439	NM_148962	ENSG00000162881	OXER1	GPCR|GPR170|TG1019	oxoeicosanoid receptor 1	protein-coding	0.002188	0.338428	
chunk0193_392_1	chr8	80389184	80389717	+	0	NA	Intergenic	Intergenic	-96169	NM_001277145	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.005629	0.380150	
chunk0095_265_1	chr2	19706498	19706713	+	0	NA	Intergenic	MIR3|SINE|MIR	-162249	NR_033875	400946	Hs.289062	NR_033875	ENSG00000228784	LINC00954	-	long intergenic non-protein coding RNA 954	ncRNA	0.000000	0.500000	
chunk0127_344_1	chr3	100683077	100683376	+	0	NA	intron (NM_001308362, intron 9 of 9)	MER52A|LTR|ERV1	-26064	NM_001007565	10342	Hs.518123	NM_006070	ENSG00000114354	TFG	HMSNP|SPG57|TF6|TRKT3	trafficking from ER to golgi regulator	protein-coding	0.020067	0.553333	
chunk0210_47_1	chrX	68428510	68428787	+	0	NA	intron (NM_002547, intron 2 of 24)	intron (NM_002547, intron 2 of 24)	4809	NM_002547	4983	Hs.128824	NM_002547	ENSG00000079482	OPHN1	ARHGAP41|MRX60|OPN1	oligophrenin 1	protein-coding	0.007220	0.399281	
chunk0186_235_1	chr7	140696875	140697167	+	0	NA	promoter-TSS (NR_024454)	promoter-TSS (NR_024454)	56	NR_024454	100134713	Hs.534141	NR_024454	ENSG00000240889	NDUFB2-AS1	-	NDUFB2 antisense RNA 1	ncRNA	0.109589	0.709898	173(TGGGACACCGTGTGCA,-,0.00),174(GGGACACCGTGTGCAG,+,0.00)
chunk0028_273_1	chr10	90945859	90946416	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-1163	NR_131214	105378427		NR_131214		XLOC_008559	-	uncharacterized LOC105378427	ncRNA	0.008977	0.405018	412(AAGCACAACCAGTTCT,-,0.00),413(AGCACAACCAGTTCTC,+,0.00)
chunk0037_406_1	chr11	79546469	79546758	+	0	NA	Intergenic	Intergenic	-105962	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.024221	0.420690	
chunk0054_19_1	chr13	40607073	40607274	+	0	NA	intron (NM_002015, intron 1 of 2)	intron (NM_002015, intron 1 of 2)	59424	NM_002015	2308	Hs.370666	NM_002015	ENSG00000150907	FOXO1	FKH1|FKHR|FOXO1A	forkhead box O1	protein-coding	0.029851	0.534653	
chunk0189_290_1	chr8	25765640	25765928	+	0	NA	Intergenic	Intergenic	279340	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.003472	0.512111	
chunk0056_106_1	chr13	82627135	82627704	+	0	NA	Intergenic	Intergenic	1254974	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.003515	0.310526	
chunk0068_160_1	chr15	54034207	54035039	+	0	NA	intron (NM_001080534, intron 1 of 30)	intron (NM_001080534, intron 1 of 30)	21719	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.004808	0.362545	
chunk0037_163_1	chr11	73787872	73788297	+	0	NA	intron (NM_016055, intron 1 of 7)	CpG	212	NM_016055	51642	Hs.503239	NM_016055	ENSG00000175581	MRPL48	CGI-118|HSPC290|L48MT|MRP-L48	mitochondrial ribosomal protein L48	protein-coding	0.082353	0.640845	
chunk0132_355_1	chr3	161454457	161455007	+	0	NA	Intergenic	L1MEc|LINE|L1	28305	NR_102265	101243545	Hs.737526	NR_102265	ENSG00000240567	LINC02067	-	long intergenic non-protein coding RNA 2067	ncRNA	0.005455	0.346642	225(GAGAACAGGAAGTACA,-,0.00),226(AGAACAGGAAGTACAG,+,0.00)
chunk0115_448_1	chr21	32411335	32412327	+	0	NA	promoter-TSS (NR_104472)	promoter-TSS (NR_104472)	-606	NR_104472	59271	Hs.208358	NM_058187	ENSG00000166979	EVA1C	B18|B19|C21orf63|C21orf64|FAM176C|PRED34|SUE21	eva-1 homolog C	protein-coding	0.082661	0.631420	385(GGGAACACTGTGTGCC,-,0.00),386(GGAACACTGTGTGCCT,+,0.00)
chunk0166_337_1	chr6	50880540	50880797	+	0	NA	Intergenic	L2c|LINE|L2	61942	NM_003221	7021	Hs.33102	NM_003221	ENSG00000008196	TFAP2B	AP-2B|AP2-B|PDA2	transcription factor AP-2 beta	protein-coding	0.000000	0.348837	152(TAGAACATGCTGTTTT,-,0.00),153(AGAACATGCTGTTTTC,+,0.00)
chunk0127_401_1	chr3	102365961	102366525	+	0	NA	Intergenic	L1PA7|LINE|L1	-68772	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.003546	0.346903	
chunk0012_110_1	chr1	156725707	156726185	+	0	NA	intron (NM_001303095, intron 2 of 3)	intron (NM_001303095, intron 2 of 3)	2493	NM_001303095	81875	Hs.301904	NM_030980	ENSG00000143319	ISG20L2	HSD38	interferon stimulated exonuclease gene 20 like 2	protein-coding	0.033473	0.540710	195(GGGAACAGCGTGTCCA,-,0.00),196(GGAACAGCGTGTCCAG,+,0.00)
chunk0052_235_1	chr13	25798259	25798526	+	0	NA	intron (NM_001313741, intron 27 of 35)	intron (NM_001313741, intron 27 of 35)	252668	NM_001007538	387914	Hs.433791	NM_001007538	ENSG00000180730	SHISA2	C13orf13|PRO28631|TMEM46|WGAR9166|bA398O19.2|hShisa	shisa family member 2	protein-coding	0.003745	0.384328	
chunk0147_294_1	chr4	184417810	184418338	+	0	NA	intron (NM_002199, intron 5 of 8)	intron (NM_002199, intron 5 of 8)	-35768	NR_125933	102723766	Hs.432281	NR_125933	ENSG00000249096	LINC02362	-	long intergenic non-protein coding RNA 2362	ncRNA	0.007576	0.421550	
chunk0212_325_1	chrX	143974044	143974775	+	0	NA	Intergenic	Intergenic	90338	NR_121210	389898	Hs.585177	NM_001012989	ENSG00000276380	UBE2NL	Li174	ubiquitin conjugating enzyme E2 N like (gene/pseudogene)	protein-coding	0.005472	0.381148	
chunk0064_389_1	chr14	99120013	99120487	+	0	NA	Intergenic	Intergenic	151463	NM_138576	64919	Hs.709690	NM_022898	ENSG00000127152	BCL11B	ATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha	BAF chromatin remodeling complex subunit BCL11B	protein-coding	0.023207	0.416842	213(ATGAACACCAAGTCCC,-,0.00),214(TGAACACCAAGTCCCT,+,0.00)
chunk0017_132_1	chr1	206550294	206550930	+	0	NA	intron (NM_182663, intron 2 of 5)	intron (NM_182663, intron 2 of 5)	-6552	NM_182665	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.006289	0.445840	
chunk0111_46_1	chr20	22374254	22374454	+	0	NA	Intergenic	MIR|SINE|MIR	46289	NR_027090	284788	Hs.651993	NR_027089	ENSG00000204684	LOC284788	-	uncharacterized LOC284788	ncRNA	0.015000	0.388060	
chunk0060_413_1	chr14	53166968	53167328	+	0	NA	Intergenic	Intergenic	13794	NR_110062	101927620		NR_110062	ENSG00000258731	LOC101927620	-	uncharacterized LOC101927620	ncRNA	0.002778	0.371191	
chunk0041_201_1	chr11	126594717	126595020	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	-57910	NR_120532	101929427	Hs.600341	NR_120532	ENSG00000254607	LOC101929427	-	uncharacterized LOC101929427	ncRNA	0.036304	0.559211	
chunk0043_213_1	chr12	19610029	19610270	+	0	NA	Intergenic	L1PA15|LINE|L1	169568	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.000000	0.433884	
chunk0107_262_1	chr2	217419314	217420029	+	0	NA	intron (NR_026597, intron 8 of 12)	intron (NR_026597, intron 8 of 12)	136938	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.006993	0.407821	
chunk0201_395_1	chr9	69143305	69143796	+	0	NA	intron (NM_001170414, intron 1 of 21)	intron (NM_001170414, intron 1 of 21)	22286	NM_001170414	9414	Hs.50382	NM_004817	ENSG00000119139	TJP2	C9DUPq21.11|DFNA51|DUP9q21.11|PFIC4|X104|ZO2	tight junction protein 2	protein-coding	0.002037	0.363821	
chunk0185_426_1	chr7	134677880	134678364	+	0	NA	intron (NM_001724, intron 2 of 2)	(TAC)n|Simple_repeat|Simple_repeat	31343	NM_001293085	669	Hs.198365	NM_001724	ENSG00000172331	BPGM	DPGM|ECYT8	bisphosphoglycerate mutase	protein-coding	0.002066	0.381443	
chunk0085_383_1	chr18	9825605	9826076	+	0	NA	intron (NM_006868, intron 5 of 6)	L1PA16|LINE|L1	-59886	NM_001098529	84203	Hs.98712	NM_032243	ENSG00000168454	TXNDC2	SPTRX|SPTRX1	thioredoxin domain containing 2	protein-coding	0.012739	0.459746	
chunk0195_316_1	chr8	98922353	98922964	+	0	NA	intron (NM_001256312, intron 1 of 12)	intron (NM_001256312, intron 1 of 12)	19913	NM_001256312	6788	Hs.492333	NM_006281	ENSG00000104375	STK3	KRS1|MST2	serine/threonine kinase 3	protein-coding	0.004910	0.315359	
chunk0153_98_1	chr5	68396600	68396956	+	0	NA	Intergenic	Intergenic	104210	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.016854	0.470588	
chunk0090_187_1	chr18	72993109	72993839	+	0	NA	Intergenic	Intergenic	-125899	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.009589	0.314637	
chunk0170_173_1	chr6	111687313	111687580	+	0	NA	intron (NM_153048, intron 9 of 10)	intron (NM_153048, intron 9 of 10)	32616	NM_153047	2534	Hs.390567	NM_002037	ENSG00000010810	FYN	SLK|SYN|p59-FYN	FYN proto-oncogene, Src family tyrosine kinase	protein-coding	0.007491	0.376866	
chunk0203_75_1	chr9	83814497	83814871	+	0	NA	intron (NM_025211, intron 2 of 12)	intron (NM_025211, intron 2 of 12)	3153	NM_025211	80318	Hs.522255	NM_025211	ENSG00000165113	GKAP1	FKSG21|GKAP42	G kinase anchoring protein 1	protein-coding	0.005348	0.354667	
chunk0170_407_1	chr6	117920362	117920939	+	0	NA	intron (NM_001029858, intron 1 of 7)	MamRep1879|DNA|hAT-Tip100?	13124	NM_001029858	222553	Hs.654841	NM_001029858	ENSG00000196376	SLC35F1	C6orf169|dJ230I3.1	solute carrier family 35 member F1	protein-coding	0.013865	0.415225	
chunk0020_369_1	chr1	239761008	239761291	+	0	NA	intron (NM_000740, intron 3 of 4)	L1MEc|LINE|L1	-42030	NR_103776	100506915	Hs.667175	NR_103776	ENSG00000233355	CHRM3-AS2	-	CHRM3 antisense RNA 2	ncRNA	0.010601	0.299296	
chunk0199_33_1	chr9	816848	817145	+	0	NA	Intergenic	L1MD1|LINE|L1	-24694	NM_021951	1761	Hs.98586	NM_021951	ENSG00000137090	DMRT1	CT154|DMT1	doublesex and mab-3 related transcription factor 1	protein-coding	0.003367	0.352349	
chunk0206_186_1	chr9	122860844	122861145	+	0	NA	intron (NM_001100588, intron 10 of 20)	L2a|LINE|L2	19325	NR_003071	692206	Hs.693253	NR_003071	ENSG00000212447	SNORD90	HBII-295	small nucleolar RNA, C/D box 90	snoRNA	0.000000	0.350993	
chunk0022_260_1	chr10	14838068	14838330	+	0	NA	promoter-TSS (NM_016299)	promoter-TSS (NM_016299)	39	NR_103464	51182	Hs.534169	NM_016299	ENSG00000187522	HSPA14	HSP70-4|HSP70L1	heat shock protein family A (Hsp70) member 14	protein-coding	0.110687	0.650190	
chunk0171_69_1	chr6	121497784	121498441	+	0	NA	Intergenic	Intergenic	62535	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.013699	0.413374	
chunk0062_407_1	chr14	75064163	75064461	+	0	NA	promoter-TSS (NM_001302616)	promoter-TSS (NM_001302616)	-263	NM_001107	97	Hs.18573	NM_001107	ENSG00000119640	ACYP1	ACYPE	acylphosphatase 1	protein-coding	0.013423	0.478261	
chunk0187_256_1	chr7	154603761	154604035	+	0	NA	intron (NM_001290252, intron 5 of 23)	L1ME3A|LINE|L1	298686	NM_001290252	1804	Hs.490684	NM_001936	ENSG00000130226	DPP6	DPL1|DPPX|MRD33|VF2	dipeptidyl peptidase like 6	protein-coding	0.007299	0.349091	
chunk0047_11_1	chr12	65100618	65101218	+	0	NA	intron (NM_007191, intron 2 of 9)	intron (NM_007191, intron 2 of 9)	20648	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.008333	0.347754	
chunk0062_173_1	chr14	69579778	69580269	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-5140	NM_001271507	56936	Hs.458319	NM_020181	ENSG00000267909	CCDC177	C14orf162|PLPL	coiled-coil domain containing 177	protein-coding	0.008147	0.428862	
chunk0165_88_1	chr6	31875310	31875565	+	0	NA	intron (NM_025257, intron 4 of 20).4	MIR|SINE|MIR	2234	NM_001178045	80736	Hs.335355	NM_025257	ENSG00000204385	SLC44A4	C6orf29|CTL4|DFNA72|NG22|TPPT|hTPPT1	solute carrier family 44 member 4	protein-coding	0.007843	0.382812	
chunk0066_299_1	chr15	35557009	35557463	+	0	NA	intron (NR_038251, intron 1 of 2)	LTR33|LTR|ERVL	-11033	NM_001141972	89978	Hs.107196	NM_080650	ENSG00000134146	DPH6	ATPBD4	diphthamine biosynthesis 6	protein-coding	0.008811	0.410989	
chunk0108_35_1	chr2	226650030	226650586	+	0	NA	Intergenic	Intergenic	8485	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.021583	0.488330	
chunk0111_325_1	chr20	32391156	32391375	+	0	NA	intron (NM_015338, intron 3 of 11)	L1ME1|LINE|L1	32921	NM_015338	171023	Hs.374043	NM_015338	ENSG00000171456	ASXL1	BOPS|MDS	ASXL transcriptional regulator 1	protein-coding	0.004566	0.368182	
chunk0124_394_1	chr3	59678233	59678610	+	0	NA	Intergenic	Intergenic	-628432	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.007958	0.441799	
chunk0102_395_1	chr2	154789048	154789612	+	0	NA	intron (NM_002239, intron 2 of 2)	intron (NM_002239, intron 2 of 2)	90749	NM_001260509	3760	Hs.591606	NM_002239	ENSG00000162989	KCNJ3	GIRK1|KGA|KIR3.1	potassium voltage-gated channel subfamily J member 3	protein-coding	0.000000	0.316814	
chunk0014_36_1	chr1	174935965	174936379	+	0	NA	intron (NR_121196, intron 4 of 5)	Tigger12|DNA|TcMar-Tigger	18089	NR_121196	101928696	Hs.666680	NR_121196	ENSG00000229531	LOC101928696	-	uncharacterized LOC101928696	ncRNA	0.004831	0.397590	165(GAGAACACAAAGTCCA,-,0.00),166(AGAACACAAAGTCCAA,+,0.00)
chunk0154_214_1	chr5	80486485	80486914	+	0	NA	Intergenic	L1MB8|LINE|L1	-1282	NM_205548	167555	Hs.338182	NM_205548	ENSG00000152380	FAM151B	UNQ9217	family with sequence similarity 151 member B	protein-coding	0.004662	0.372093	
chunk0165_27_1	chr6	29738353	29738552	+	0	NA	intron (NR_026972, intron 3 of 5)	intron (NR_026972, intron 3 of 5)	10597	NR_026972	285830	Hs.646985	NM_001003807	ENSG00000214922	HLA-F-AS1	-	HLA-F antisense RNA 1	ncRNA	0.010050	0.385000	89(AGGGTCATCATGTCCT,-,0.00),90(GGGTCATCATGTCCTG,+,0.00)
chunk0212_46_1	chrY	11308774	11309161	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1112623	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.023256	0.481959	
chunk0023_121_1	chr10	23481492	23481983	+	0	NA	Intergenic	Tigger5|DNA|TcMar-Tigger	42468	NM_001145373	220213	Hs.499042	NM_001145373	ENSG00000165312	OTUD1	DUBA7|OTDC1	OTU deubiquitinase 1	protein-coding	0.002037	0.406504	
chunk0138_220_1	chr4	38948850	38949410	+	0	NA	Intergenic	MIRb|SINE|MIR	81098	NR_030300	693159		NR_030300	ENSG00000207944	MIR574	MIR574-3p|MIRN574|hsa-mir-574|mir-574	microRNA 574	ncRNA	0.008929	0.388592	
chunk0167_223_1	chr6	66786749	66786971	+	0	NA	Intergenic	Intergenic	998981	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.004505	0.291480	
chunk0131_428_1	chr3	153624926	153625452	+	0	NA	Intergenic	Intergenic	140694	NM_001101337									0.001901	0.311195	262(TGGTACAGGATGTTCT,-,0.00),263(GGTACAGGATGTTCTT,+,0.00)
chunk0107_53_1	chr2	211408327	211409017	+	0	NA	intron (NM_005235, intron 25 of 27)	intron (NM_005235, intron 25 of 27)	791101	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.011594	0.376266	322(AAGCACAAGTTGTTCT,-,0.00),323(AGCACAAGTTGTTCTT,+,0.00)
chunk0018_83_1	chr1	217468031	217468452	+	0	NA	intron (NM_018040, intron 8 of 9)	L1MC5a|LINE|L1	162861	NM_001297754	55105	Hs.362343	NM_018040	ENSG00000092978	GPATCH2	CT110|GPATC2|PPP1R30|Pfa1	G-patch domain containing 2	protein-coding	0.004751	0.353081	
chunk0131_354_1	chr3	151793830	151794516	+	0	NA	intron (NR_110202, intron 1 of 3)	intron (NR_110202, intron 1 of 3)	-19900	NM_001086	13	Hs.506908	NM_001086	ENSG00000114771	AADAC	CES5A1|DAC	arylacetamide deacetylase	protein-coding	0.002915	0.311499	
chunk0167_185_1	chr6	64067468	64068121	+	0	NA	intron (NM_001142800, intron 32 of 42)	intron (NM_001142800, intron 32 of 42)	421268	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.001531	0.298165	
chunk0176_447_1	chr7	20025571	20025770	+	0	NA	intron (NR_110114, intron 3 of 5)	L1PA7|LINE|L1	114756	NR_110114	101927668	Hs.715900	NR_110114		LOC101927668	-	uncharacterized LOC101927668	ncRNA	0.000000	0.335000	
chunk0060_333_1	chr14	51547036	51547615	+	0	NA	intron (NR_047477, intron 3 of 3)	intron (NR_047477, intron 3 of 3)	52627	NR_047477	100874185	Hs.578226	NR_047477	ENSG00000258537	FRMD6-AS2	-	FRMD6 antisense RNA 2	ncRNA	0.005181	0.391379	
chunk0191_452_1	chr8	58030344	58031064	+	0	NA	intron (NM_147189, intron 1 of 4)	intron (NM_147189, intron 1 of 4)	36150	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.016667	0.398058	
chunk0051_234_1	chr12	116991371	116991962	+	0	NA	intron (NM_012174, intron 7 of 10)	intron (NM_012174, intron 7 of 10)	-4329	NR_103809	100506551	Hs.657861	NR_103809	ENSG00000257279	LOC100506551	-	uncharacterized LOC100506551	ncRNA	0.008460	0.408784	
chunk0088_381_1	chr18	54254398	54254825	+	0	NA	Intergenic	Intergenic	-14868	NM_007195	11201	Hs.438533	NM_007195	ENSG00000101751	POLI	RAD30B|RAD3OB|eta2	DNA polymerase iota	protein-coding	0.023419	0.441589	
chunk0138_342_1	chr4	41670214	41670879	+	0	NA	intron (NM_001112717, intron 16 of 25)	intron (NM_001112717, intron 16 of 25)	57774	NM_001112720	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.010526	0.373874	
chunk0211_324_1	chrX	123906495	123906916	+	0	NA	intron (NR_037916, intron 5 of 5)	L2c|LINE|L2	46538	NR_037916	331	Hs.356076	NM_001167	ENSG00000101966	XIAP	API3|BIRC4|IAP-3|ILP1|MIHA|XLP2|hIAP-3|hIAP3	X-linked inhibitor of apoptosis	protein-coding	0.014252	0.473934	
chunk0054_142_1	chr13	43727069	43727725	+	0	NA	intron (NM_017993, intron 1 of 16)	intron (NM_017993, intron 1 of 16)	59583	NM_017993	55068	Hs.128258	NM_017993	ENSG00000120658	ENOX1	CNOX|PIG38|bA64J21.1|cCNOX	ecto-NOX disulfide-thiol exchanger 1	protein-coding	0.006098	0.455099	
chunk0090_356_1	chr18	76793002	76793434	+	0	NA	Intergenic	Intergenic	29077	NR_040024	100131655	Hs.385806	NR_040024	ENSG00000264278	ZNF236-DT	-	ZNF236 divergent transcript	ncRNA	0.018519	0.515012	373(AGGAACACTCTGAACT,-,0.00),374(GGAACACTCTGAACTC,+,0.00)
chunk0198_444_1	chr8	143985661	143985976	+	0	NA	exon (NM_032789, exon 3 of 11)	exon (NM_032789, exon 3 of 11)	649	NM_032789	84875	Hs.348609	NM_032789	ENSG00000178685	PARP10	ARTD10	poly(ADP-ribose) polymerase family member 10	protein-coding	0.038095	0.677215	
chunk0110_381_1	chr20	20010604	20011189	+	0	NA	Intergenic	Intergenic	-6394	NM_016100	51126	Hs.368783	NM_016100	ENSG00000173418	NAA20	NAT3|NAT3P|NAT5|NAT5P|dJ1002M8.1	N(alpha)-acetyltransferase 20, NatB catalytic subunit	protein-coding	0.005128	0.370307	155(GAGCACATGGTGTTTT,-,0.00),156(AGCACATGGTGTTTTG,+,0.00),380(AATAACAGCATGTCCT,-,0.00),381(ATAACAGCATGTCCTA,+,0.00)
chunk0028_45_1	chr10	83172775	83173005	+	0	NA	Intergenic	L1MA1|LINE|L1	-939970	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.004348	0.316017	
chunk0168_396_1	chr6	94541628	94542232	+	0	NA	Intergenic	L1PA15|LINE|L1	834847	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.006623	0.340496	
chunk0206_357_1	chr9	125749533	125750006	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	1570	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.004228	0.324895	
chunk0211_458_1	chrX	130199206	130199499	+	0	NA	Intergenic	L1M4|LINE|L1	27553	NM_004794	9363	Hs.654356	NM_004794	ENSG00000134594	RAB33A	RabS10	RAB33A, member RAS oncogene family	protein-coding	0.003413	0.387755	199(AGGACCACACTGTTCT,-,0.00),200(GGACCACACTGTTCTG,+,0.00)
chunk0042_117_1	chr12	3315228	3315659	+	0	NA	Intergenic	Intergenic	-65906	NM_001256536	56341	Hs.504530	NM_019854	ENSG00000111218	PRMT8	HRMT1L3|HRMT1L4	protein arginine methyltransferase 8	protein-coding	0.023202	0.564815	
chunk0166_417_1	chr6	52551405	52551879	+	0	NA	intron (NM_012288, intron 1 of 10)	intron (NM_012288, intron 1 of 10)	25422	NM_012288	9697	Hs.520182	NM_012288	ENSG00000065308	TRAM2	-	translocation associated membrane protein 2	protein-coding	0.010549	0.530526	
chunk0172_333_1	chr6	138481653	138482202	+	0	NA	intron (NM_020464, intron 2 of 6)	intron (NM_020464, intron 2 of 6)	17515	NM_001144060	57224	Hs.652741	NM_020464	ENSG00000135540	NHSL1	C6orf63	NHS like 1	protein-coding	0.007286	0.349091	
chunk0184_459_1	chr7	123528696	123529211	+	0	NA	intron (NR_104245, intron 1 of 11)	A-rich|Low_complexity|Low_complexity	3995	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.000000	0.286822	
chunk0140_147_1	chr4	69321088	69321778	+	0	NA	Intergenic	LTR2752|LTR|ERV1	40934	NM_001207004	54490	Hs.653154	NM_053039	ENSG00000135226	UGT2B28	-	UDP glucuronosyltransferase family 2 member B28	protein-coding	0.002899	0.515195	
chunk0051_372_1	chr12	121500468	121500765	+	0	NA	intron (NM_001005366, intron 11 of 22)	intron (NM_001005366, intron 11 of 22)	-56264	NR_106957	102465665		NR_106957	ENSG00000284402	MIR7107	hsa-mir-7107	microRNA 7107	ncRNA	0.023569	0.553691	
chunk0202_394_1	chr9	81230350	81230709	+	0	NA	Intergenic	L1ME1|LINE|L1	459006	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.000000	0.272222	
chunk0135_267_1	chr3	189212656	189213232	+	0	NA	intron (NM_198485, intron 2 of 5)	intron (NM_198485, intron 2 of 5)	27650	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.003472	0.357019	
chunk0158_128_1	chr5	127179118	127179317	+	0	NA	Intergenic	Intergenic	-105725	NM_001164479	401207	Hs.49573	NM_001164478	ENSG00000164241	C5orf63	YDR286C	chromosome 5 open reading frame 63	protein-coding	0.000000	0.360000	
chunk0146_25_1	chr4	155198830	155199310	+	0	NA	Intergenic	Intergenic	-9559	NM_000910	4887	Hs.37125	NM_000910	ENSG00000185149	NPY2R	NPY2-R	neuropeptide Y receptor Y2	protein-coding	0.000000	0.363825	267(CTGAACACCATGTTCA,-,0.00),268(TGAACACCATGTTCAT,+,0.00)
chunk0135_276_1	chr3	189324696	189325049	+	0	NA	Intergenic	Intergenic	-84278	NR_046722	100874027	Hs.616080	NR_046722	ENSG00000230115	TPRG1-AS2	-	TPRG1 antisense RNA 2	ncRNA	0.008499	0.449153	
chunk0091_1_1	chr19	2524585	2525004	+	0	NA	intron (NM_052847, intron 3 of 4)	CpG	48669	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.050119	0.533333	
chunk0086_116_1	chr18	14935431	14936190	+	0	NA	Intergenic	Intergenic	-10457	NR_104164	400644	Hs.514732	NR_104164	ENSG00000266554	LINC01443	-	long intergenic non-protein coding RNA 1443	ncRNA	0.006588	0.476316	
chunk0196_183_1	chr8	106016848	106017047	+	0	NA	intron (NR_125797, intron 1 of 4)	L1MEc|LINE|L1	43556	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.000000	0.320000	
chunk0034_328_1	chr11	35337614	35338505	+	0	NA	intron (NM_001195728, intron 1 of 11)	intron (NM_001195728, intron 1 of 11)	81499	NM_004171	6506	Hs.502338	NM_004171	ENSG00000110436	SLC1A2	EAAT2|EIEE41|GLT-1|HBGT	solute carrier family 1 member 2	protein-coding	0.004489	0.405830	
chunk0030_63_1	chr10	111972244	111972443	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	211436	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.010050	0.470000	
chunk0116_100_1	chr21	35256606	35256805	+	0	NA	Intergenic	Intergenic	-207407	NM_001754	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.020101	0.465000	13(CTGCTCAGCCTGTTCT,-,0.00),14(TGCTCAGCCTGTTCTT,+,0.00)
chunk0076_166_1	chr16	67377996	67378207	+	0	NA	intron (NM_018296, intron 11 of 13)	intron (NM_018296, intron 11 of 13)	15434	NM_015964	51673	Hs.534458	NM_015964	ENSG00000159713	TPPP3	CGI-38|TPPP/p20|p20|p25gamma	tubulin polymerization promoting protein family member 3	protein-coding	0.000000	0.320755	
chunk0196_225_1	chr8	107528981	107529259	+	0	NA	Intergenic	Intergenic	-31065	NM_001146	284	Hs.369675	NM_001146	ENSG00000154188	ANGPT1	AGP1|AGPT|ANG1	angiopoietin 1	protein-coding	0.010791	0.401434	
chunk0034_209_1	chr11	32497925	32498320	+	0	NA	Intergenic	Intergenic	62083	NR_120546	51352	Hs.567499	NM_015855	ENSG00000183242	WT1-AS	WIT-1|WIT1|WT1-AS1|WT1AS	WT1 antisense RNA	ncRNA	0.005063	0.414141	
chunk0050_146_1	chr12	102643810	102644219	+	0	NA	Intergenic	Intergenic	-163369	NM_000618	3479	Hs.160562	NM_000618	ENSG00000017427	IGF1	IGF|IGF-I|IGFI|MGF	insulin like growth factor 1	protein-coding	0.004890	0.463415	
chunk0179_415_1	chr7	51743625	51743903	+	0	NA	Intergenic	Intergenic	-426946	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.010791	0.362007	
chunk0025_271_1	chr10	56117854	56118408	+	0	NA	Intergenic	L1MDa|LINE|L1	243142	NM_007057	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.003610	0.335135	256(AGGCACATACTGTTCC,-,0.00),257(GGCACATACTGTTCCC,+,0.00)
chunk0094_352_1	chr2	9451099	9451640	+	0	NA	intron (NM_016207, intron 11 of 17)	intron (NM_016207, intron 11 of 17)	-23172	NM_001039613	285148	Hs.667226	NM_001039613	ENSG00000134330	IAH1	-	isoamyl acetate hydrolyzing esterase 1 (putative)	protein-coding	0.005545	0.387454	
chunk0205_313_1	chr9	112652223	112652661	+	0	NA	intron (NM_001287038, intron 3 of 3)	intron (NM_001287038, intron 3 of 3)	65665	NM_021218	58493	Hs.658575	NM_021218	ENSG00000148153	INIP	C9orf80|HSPC043|MISE|SOSSC|SSBIP1|hSSBIP1	INTS3 and NABP interacting protein	protein-coding	0.015982	0.366743	
chunk0152_116_1	chr5	58636397	58636841	+	0	NA	intron (NM_138453, intron 2 of 4)	intron (NM_138453, intron 2 of 4)	53507	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.009009	0.384270	268(AGGAACAAAATGTGCC,-,0.00),269(GGAACAAAATGTGCCT,+,0.00)
chunk0165_453_1	chr6	40906998	40907796	+	0	NA	intron (NR_110873, intron 1 of 5)	intron (NR_110873, intron 1 of 5)	115883	NR_110873	101929555	Hs.552555	NR_110873		LOC101929555	-	uncharacterized LOC101929555	ncRNA	0.007519	0.476846	278(CAGGACAGACTGACCC,-,0.00),279(AGGACAGACTGACCCT,+,0.00)
chunk0139_353_1	chr4	60112621	60112830	+	0	NA	Intergenic	Intergenic	-809894	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.009569	0.285714	
chunk0023_282_1	chr10	28410473	28410975	+	0	NA	Intergenic	L2c|LINE|L2	-121374	NR_107053	102465880		NR_107053	ENSG00000275036	MIR8086	hsa-mir-8086	microRNA 8086	ncRNA	0.005976	0.397614	
chunk0040_103_1	chr11	111800465	111800938	+	0	NA	intron (NM_024740, intron 14 of 14)	L2b|LINE|L2	-34256	NM_181700	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.008457	0.377637	
chunk0063_266_1	chr14	83829189	83829388	+	0	NA	Intergenic	Intergenic	-1564591	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.010050	0.320000	
chunk0208_368_1	chrX	26495343	26495542	+	0	NA	Intergenic	Intergenic	-62895	NR_001559	139538	Hs.447377	NR_001559	ENSG00000259849	VENTXP1	CT18|NA88A|VENTX2P1	VENT homeobox pseudogene 1	pseudo	0.000000	0.355000	81(ATCACACACTGTTCCA,+,0.00)
chunk0112_324_1	chr20	44885494	44885693	+	0	NA	promoter-TSS (NM_139323)	promoter-TSS (NM_139323)	-6	NM_003404	7529	Hs.643544	NM_003404	ENSG00000166913	YWHAB	GW128|HEL-S-1|HS1|KCIP-1|YWHAA	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta	protein-coding	0.085427	0.710000	
chunk0195_436_1	chr8	101086727	101087285	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	34952	NR_033962	441374	Hs.652045	NR_033962	ENSG00000248599	FLJ42969	-	uncharacterized LOC441374	ncRNA	0.003584	0.472272	
chunk0013_228_1	chr1	169555617	169555816	+	0	NA	intron (NM_000130, intron 6 of 24)	MIR|SINE|MIR	30815	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.000000	0.235000	
chunk0005_280_1	chr1	60034174	60034619	+	0	NA	intron (NM_152377, intron 6 of 11)	intron (NM_152377, intron 6 of 11)	39374	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.002247	0.369955	
chunk0199_41_1	chr9	1200690	1201214	+	0	NA	Intergenic	Intergenic	150332	NM_181872	10655	Hs.59506	NM_006557	ENSG00000173253	DMRT2	-	doublesex and mab-3 related transcription factor 2	protein-coding	0.007634	0.506667	
chunk0081_359_1	chr17	47831209	47831427	+	0	NA	promoter-TSS (NM_033413)	promoter-TSS (NM_033413)	223	NM_148887	124995	Hs.347535	NM_145255	ENSG00000159111	MRPL10	L10MT|MRP-L10|MRP-L8|MRPL8|RPML8	mitochondrial ribosomal protein L10	protein-coding	0.036697	0.520548	
chunk0112_458_1	chr20	48995283	48996093	+	0	NA	intron (NM_006420, intron 22 of 38)	intron (NM_006420, intron 22 of 38)	50368	NR_110624	102723483	Hs.209000	NR_110624	ENSG00000227431	CSE1L-AS1	-	CSE1L antisense RNA 1	ncRNA	0.006173	0.369914	
chunk0176_22_1	chr7	8408926	8409148	+	0	NA	Intergenic	Charlie23a|DNA|hAT-Charlie	-24918	NM_152745	30010	Hs.487564	NM_152745	ENSG00000122584	NXPH1	NPH1|Nbla00697	neurexophilin 1	protein-coding	0.004505	0.327354	
chunk0179_165_1	chr7	46640273	46640567	+	0	NA	Intergenic	LTR33|LTR|ERVL	-719148	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.010204	0.484746	
chunk0152_103_1	chr5	58416192	58416507	+	0	NA	Intergenic	LTR33|LTR|ERVL	43790	NM_001252226	10769	Hs.398157	NM_006622	ENSG00000145632	PLK2	SNK|hPlk2|hSNK	polo like kinase 2	protein-coding	0.000000	0.477848	
chunk0014_13_1	chr1	174417218	174417487	+	0	NA	intron (NM_014857, intron 13 of 20)	intron (NM_014857, intron 13 of 20)	-30722	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.011152	0.355556	
chunk0048_100_1	chr12	79360969	79361481	+	0	NA	intron (NM_001291901, intron 8 of 9)	MIR|SINE|MIR	-58032	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.000000	0.401559	
chunk0189_115_1	chr8	22143576	22144092	+	0	NA	Intergenic	Intergenic	-1883	NM_025232	80346	Hs.289063	NM_025232	ENSG00000168476	REEP4	C8orf20|PP432|Yip2c	receptor accessory protein 4	protein-coding	0.013566	0.580271	
chunk0086_103_1	chr18	14089648	14090306	+	0	NA	intron (NR_033354, intron 1 of 5)	intron (NR_033354, intron 1 of 5)	42513	NM_145287	162655	Hs.352635	NM_145287	ENSG00000175322	ZNF519	HsT2362	zinc finger protein 519	protein-coding	0.021277	0.433991	
chunk0055_20_1	chr13	51836187	51836739	+	0	NA	intron (NR_027047, intron 2 of 4)	L1MC4|LINE|L1	8687	NR_027047									0.005435	0.432188	
chunk0081_241_1	chr17	42964239	42964651	+	0	NA	promoter-TSS (NM_001261434)	promoter-TSS (NM_001261434)	53	NM_001261434	80755	Hs.317403	NM_001261434	ENSG00000266967	AARSD1	-	alanyl-tRNA synthetase domain containing 1	protein-coding	0.067961	0.566586	
chunk0078_397_1	chr16	88549115	88549582	+	0	NA	Intergenic	Intergenic	-21033	NM_144604	124245	Hs.93670	NM_144604	ENSG00000158545	ZC3H18	NHN1	zinc finger CCCH-type containing 18	protein-coding	0.029979	0.493590	
chunk0012_295_1	chr1	162140906	162141152	+	0	NA	intron (NM_001164757, intron 1 of 9)	L1PA16|LINE|L1	-16078	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.008130	0.315789	
chunk0115_141_1	chr21	23445300	23445828	+	0	NA	Intergenic	Intergenic	-60729	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.007576	0.374291	272(ATGGACATTCTGTACC,-,0.00),273(TGGACATTCTGTACCT,+,0.00)
chunk0009_55_1	chr1	100603298	100603830	+	0	NA	Intergenic	L1PA5|LINE|L1	43440	NR_038914	100128787	Hs.536050	NR_038914		LINC01349	-	long intergenic non-protein coding RNA 1349	ncRNA	0.005639	0.470919	
chunk0090_198_1	chr18	73169053	73169656	+	0	NA	intron (NR_034133, intron 3 of 5)	intron (NR_034133, intron 3 of 5)	95144	NR_034133	400655	Hs.579378	NR_034133	ENSG00000263711	LOC400655	-	uncharacterized LOC400655	ncRNA	0.004975	0.283113	
chunk0127_108_1	chr3	90091544	90091765	+	0	NA	Intergenic	Intergenic	984130	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.009050	0.450450	
chunk0067_63_1	chr15	40966143	40966342	+	0	NA	Intergenic	Intergenic	12804	NM_001142776	79094	Hs.155569	NM_024111	ENSG00000128965	CHAC1	-	ChaC glutathione specific gamma-glutamylcyclotransferase 1	protein-coding	0.020101	0.585000	
chunk0203_64_1	chr9	83464066	83464549	+	0	NA	intron (NM_001244959, intron 1 of 14)	intron (NM_001244959, intron 1 of 14)	3435	NM_001244960	257019	Hs.127535	NM_174938	ENSG00000172159	FRMD3	4.1O|EPB41L4O|EPB41LO|P410	FERM domain containing 3	protein-coding	0.010352	0.483471	163(AAGAACGGTGTGTTCT,-,0.00),164(AGAACGGTGTGTTCTG,+,0.00)
chunk0155_423_1	chr5	100274575	100275190	+	0	NA	Intergenic	Intergenic	113372	NR_027503	100133050	Hs.534796	NR_027503		LOC100133050	-	glucuronidase beta pseudogene	pseudo	0.000000	0.334416	
chunk0136_93_1	chr4	2660526	2661396	+	0	NA	intron (NM_001256667, intron 9 of 19)	intron (NM_001256667, intron 9 of 19)	35529	NM_001256667	8603	Hs.652364	NM_003704	ENSG00000125386	FAM193A	C4orf8|RES4-22	family with sequence similarity 193 member A	protein-coding	0.010345	0.422503	404(AGAGACACTGTGTACT,-,0.00),405(GAGACACTGTGTACTC,+,0.00)
chunk0131_282_1	chr3	150314623	150314864	+	0	NA	intron (NR_110187, intron 1 of 1)	intron (NR_110187, intron 1 of 1)	9004	NR_110186	101928022	Hs.555199	NR_110186		LINC01214	-	long intergenic non-protein coding RNA 1214	ncRNA	0.008299	0.495868	
chunk0004_126_1	chr1	44674730	44675283	+	0	NA	promoter-TSS (NM_024587)	promoter-TSS (NM_024587)	284	NM_001145636	339541	Hs.173679	NM_001004307	ENSG00000198520	ARMH1	C1orf228|NCRNA00082|p40	armadillo like helical domain containing 1	protein-coding	0.028933	0.507220	
chunk0020_139_1	chr1	233689159	233690025	+	0	NA	Intergenic	Intergenic	65440	NR_039625	100616390		NR_039625	ENSG00000265744	MIR4427	-	microRNA 4427	ncRNA	0.005774	0.434833	199(CAGATCACAGTGTCCT,-,0.00),200(AGATCACAGTGTCCTC,+,0.00)
chunk0092_357_1	chr19	35533613	35534387	+	0	NA	intron (NM_014364, intron 1 of 10)	intron (NM_014364, intron 1 of 10)	588	NM_014364	26330	Hs.248017	NM_014364	ENSG00000105679	GAPDHS	GAPD2|GAPDH-2|GAPDS|HEL-S-278|HSD-35	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic	protein-coding	0.052972	0.630968	478(AAGGCCAGAGTGTGCC,-,0.00),479(AGGCCAGAGTGTGCCC,+,0.00)
chunk0199_16_1	chr9	563599	564069	+	0	NA	intron (NM_001256877, intron 2 of 12)	intron (NM_001256877, intron 2 of 12)	59139	NM_001256877	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.012766	0.392781	
chunk0040_116_1	chr11	112025081	112025428	+	0	NA	5' UTR (NM_001931, exon 1 of 14)	5' UTR (NM_001931, exon 1 of 14)	440	NM_001931	1737	Hs.335551	NM_001931	ENSG00000150768	DLAT	DLTA|E2|PDC-E2|PDCE2	dihydrolipoamide S-acetyltransferase	protein-coding	0.083573	0.620690	
chunk0061_261_1	chr14	61409774	61410229	+	0	NA	intron (NM_006255, intron 2 of 13)	intron (NM_006255, intron 2 of 13)	88558	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.004396	0.388158	
chunk0168_158_1	chr6	83429806	83430030	+	0	NA	intron (NM_002395, intron 1 of 13)	intron (NM_002395, intron 1 of 13)	1301	NM_002395	4199	Hs.21160	NM_002395	ENSG00000065833	ME1	HUMNDME|MES	malic enzyme 1	protein-coding	0.017857	0.395556	
chunk0014_72_1	chr1	176119252	176119472	+	0	NA	intron (NM_001001740, intron 7 of 18)	intron (NM_001001740, intron 7 of 18)	87882	NM_001286644	64326	Hs.523744	NM_022457	ENSG00000143207	COP1	RFWD2|RNF200	COP1 E3 ubiquitin ligase	protein-coding	0.000000	0.280543	
chunk0044_112_1	chr12	29025578	29026515	+	0	NA	Intergenic	L2a|LINE|L2	-122957	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.002134	0.371002	
chunk0183_217_1	chr7	106618529	106618834	+	0	NA	Intergenic	Intergenic	42507	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.000000	0.356209	
chunk0205_28_1	chr9	105555230	105555503	+	0	NA	Intergenic	Intergenic	-2764	NM_001079802	2218	Hs.55777	NM_006731	ENSG00000106692	FKTN	CMD1X|FCMD|LGMD2M|LGMDR13|MDDGA4|MDDGB4|MDDGC4	fukutin	protein-coding	0.007326	0.423358	
chunk0023_428_1	chr10	31677945	31678558	+	0	NA	Intergenic	Intergenic	230675	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.026101	0.565147	
chunk0039_59_1	chr11	96237336	96237717	+	0	NA	intron (NM_032427, intron 1 of 4)	intron (NM_032427, intron 1 of 4)	-103912	NR_036125	100422991		NR_036125	ENSG00000266192	MIR1260B	mir-1260b	microRNA 1260b	ncRNA	0.007874	0.356021	
chunk0006_452_1	chr1	77034604	77034981	+	0	NA	intron (NM_030965, intron 2 of 4)	intron (NM_030965, intron 2 of 4)	-25351	NR_106978	102466995		NR_106978	ENSG00000276081	MIR7156	hsa-mir-7156	microRNA 7156	ncRNA	0.010610	0.447090	
chunk0002_149_1	chr1	17866745	17867024	+	0	NA	Intergenic	MIR3|SINE|MIR	111571	NM_030812	81569	Hs.2149	NM_030812	ENSG00000117148	ACTL8	CT57	actin like 8	protein-coding	0.010753	0.442857	
chunk0146_83_1	chr4	158039712	158039911	+	0	NA	Intergenic	L1PA16|LINE|L1	132755	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.365000	
chunk0173_276_1	chr6	147775550	147775866	+	0	NA	Intergenic	Intergenic	267016	NM_001030060	389432	Hs.567973	NM_001030060	ENSG00000203727	SAMD5	dJ875H10.1	sterile alpha motif domain containing 5	protein-coding	0.000000	0.441640	
chunk0186_147_1	chr7	138963326	138963886	+	0	NA	intron (NM_020910, intron 1 of 19)	intron (NM_020910, intron 1 of 19)	17712	NM_001164665	57670	Hs.605380	NM_020910	ENSG00000122778	KIAA1549	-	KIAA1549	protein-coding	0.012500	0.393939	
chunk0198_301_1	chr8	138206039	138206472	+	0	NA	intron (NM_015912, intron 7 of 19)	intron (NM_015912, intron 7 of 19)	290567	NM_015912	51059	Hs.126024	NM_015912	ENSG00000147724	FAM135B	C8ORFK32	family with sequence similarity 135 member B	protein-coding	0.009238	0.569124	
chunk0173_267_1	chr6	147192164	147192744	+	0	NA	intron (NR_034115, intron 1 of 10)	MER58A|DNA|hAT-Charlie	-11904	NM_139244	134957	Hs.86320	NM_139244	ENSG00000164506	STXBP5	LGL3|LLGL3|Nbla04300	syntaxin binding protein 5	protein-coding	0.006897	0.428571	
chunk0017_362_1	chr1	211940035	211940288	+	0	NA	TTS (NM_001199812)	TTS (NM_001199812)	-95392	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.007905	0.460630	
chunk0205_87_1	chr9	107336969	107337402	+	0	NA	Intergenic	Intergenic	52416	NM_001244713	5887	Hs.521640	NM_002874	ENSG00000119318	RAD23B	HHR23B|HR23B|P58	RAD23 homolog B, nucleotide excision repair protein	protein-coding	0.009238	0.493088	
chunk0055_386_1	chr13	73355062	73355399	+	0	NA	Intergenic	Intergenic	-209014	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.008902	0.369822	
chunk0163_315_1	chr6	14722084	14722730	+	0	NA	Intergenic	Intergenic	-436953	NR_108096	102216342	Hs.563409	NR_108096	ENSG00000226673	LINC01108	LncRNA-ES1	long intergenic non-protein coding RNA 1108	ncRNA	0.004644	0.372488	
chunk0009_184_1	chr1	105724226	105724975	+	0	NA	Intergenic	MIR3|SINE|MIR	-105665	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002670	0.318667	
chunk0144_129_1	chr4	129278853	129279132	+	0	NA	Intergenic	Intergenic	182865	NM_001099783	132321	Hs.567679	NM_173487	ENSG00000151470	C4orf33	-	chromosome 4 open reading frame 33	protein-coding	0.003584	0.367857	
chunk0042_467_1	chr12	12679768	12680112	+	0	NA	intron (NM_006143, intron 3 of 3)	MIR|SINE|MIR	16247	NM_006143	2842	Hs.657862	NM_006143	ENSG00000183150	GPR19	-	G protein-coupled receptor 19	protein-coding	0.000000	0.307246	
chunk0174_159_1	chr6	158152472	158152935	+	0	NA	intron (NR_073096, intron 3 of 12)	Tigger3c|DNA|TcMar-Tigger	15577	NR_073096	84947	Hs.154706	NM_032861	ENSG00000122335	SERAC1	-	serine active site containing 1	protein-coding	0.012959	0.443966	
chunk0178_239_1	chr7	36128428	36129062	+	0	NA	Intergenic	Intergenic	-24482	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.015773	0.445669	
chunk0130_223_1	chr3	134236416	134236958	+	0	NA	intron (NM_002958, intron 1 of 14)	L1M4|LINE|L1	14057	NM_002958	6259	Hs.654562	NM_002958	ENSG00000163785	RYK	D3S3195|JTK5|JTK5A|RYK1	receptor like tyrosine kinase	protein-coding	0.003690	0.364641	
chunk0094_284_1	chr2	8256053	8256618	+	0	NA	intron (NR_034135, intron 7 of 8)	intron (NR_034135, intron 7 of 8)	72084	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.010619	0.422261	
chunk0159_62_1	chr5	137292608	137292942	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	206554	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.020958	0.397015	
chunk0037_333_1	chr11	77243328	77243634	+	0	NA	intron (NM_182833, intron 12 of 15)	intron (NM_182833, intron 12 of 15)	43937	NM_182833	220032	Hs.249795	NM_182833	ENSG00000178795	GDPD4	GDE6	glycerophosphodiester phosphodiesterase domain containing 4	protein-coding	0.009804	0.413681	
chunk0173_345_1	chr6	149061057	149061556	+	0	NA	intron (NM_005715, intron 7 of 7)	intron (NM_005715, intron 7 of 7)	-96622	NR_038408	100128176	Hs.557541	NR_038408		UST-AS1	-	UST antisense RNA 1	ncRNA	0.014028	0.438000	
chunk0134_319_1	chr3	181782222	181782432	+	0	NA	Intergenic	HAL1|LINE|L1	70403	NM_003106	6657	Hs.518438	NM_003106	ENSG00000181449	SOX2	ANOP3|MCOPS3	SRY-box transcription factor 2	protein-coding	0.000000	0.398104	
chunk0182_335_1	chr7	99162387	99162587	+	0	NA	Intergenic	Intergenic	-18367	NM_181349	57154	Hs.189329	NM_020429	ENSG00000198742	SMURF1	-	SMAD specific E3 ubiquitin protein ligase 1	protein-coding	0.015000	0.477612	
chunk0141_368_1	chr4	88044127	88044336	+	0	NA	intron (NM_000297, intron 5 of 14)	L2a|LINE|L2	36584	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.004785	0.376190	
chunk0107_211_1	chr2	216621153	216622057	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-11223	NM_001313993	3485	Hs.438102	NM_000597	ENSG00000115457	IGFBP2	IBP2|IGF-BP53	insulin like growth factor binding protein 2	protein-coding	0.006637	0.493923	
chunk0094_424_1	chr2	10622150	10622360	+	0	NA	intron (NR_048552, intron 12 of 19)	L1ME3G|LINE|L1	67732	NR_048552	79954	Hs.222494	NM_024894	ENSG00000115761	NOL10	PQBP5	nucleolar protein 10	protein-coding	0.014286	0.360190	
chunk0029_210_1	chr10	101905896	101906411	+	0	NA	intron (NM_024541, intron 23 of 25)	L1ME3Cz|LINE|L1	-62233	NM_173197	30819	Hs.97044	NM_014591	ENSG00000120049	KCNIP2	KCHIP2	potassium voltage-gated channel interacting protein 2	protein-coding	0.009709	0.343023	
chunk0147_357_1	chr4	185713571	185713953	+	0	NA	intron (NM_001145672, intron 1 of 20)	intron (NM_001145672, intron 1 of 20)	-56793	NM_001145675	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.005236	0.360313	
chunk0202_10_1	chr9	70353752	70353951	+	0	NA	3' UTR (NM_015110, exon 25 of 25)	3' UTR (NM_015110, exon 25 of 25)	60806	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.010050	0.275000	
chunk0013_340_1	chr1	171962822	171963412	+	0	NA	intron (NM_001136127, intron 2 of 19)	L1MC1|LINE|L1	98925	NR_046845	100874284		NR_046845	ENSG00000233540	DNM3-IT1	-	DNM3 intronic transcript 1	ncRNA	0.005085	0.375635	
chunk0199_323_1	chr9	7676579	7676786	+	0	NA	Intergenic	Intergenic	123117	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.000000	0.360577	
chunk0062_77_1	chr14	67786191	67786506	+	0	NA	intron (NM_015346, intron 16 of 41)	intron (NM_015346, intron 16 of 41)	30241	NM_015346	23503	Hs.98041	NM_015346	ENSG00000072121	ZFYVE26	FYVE-CENT|SPG15	zinc finger FYVE-type containing 26	protein-coding	0.012698	0.417722	159(AAATACATGCTGTGCC,-,0.00)
chunk0116_149_1	chr21	36481346	36482100	+	0	NA	intron (NM_001146077, intron 2 of 2)	intron (NM_001146077, intron 2 of 2)	-1633	NM_001146079	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.013263	0.419868	
chunk0177_327_1	chr7	26379968	26380329	+	0	NA	Intergenic	MIRc|SINE|MIR	15823	NM_001199838	29887	Hs.741316	NM_013322	ENSG00000086300	SNX10	OPTB8	sorting nexin 10	protein-coding	0.008310	0.392265	205(GGATACAGAATGTCCT,-,0.00),206(GATACAGAATGTCCTA,+,0.00)
chunk0129_349_1	chr3	124860759	124861467	+	0	NA	intron (NM_002213, intron 2 of 14)	intron (NM_002213, intron 2 of 14)	26192	NM_002213	3693	Hs.13155	NM_002213	ENSG00000082781	ITGB5	-	integrin subunit beta 5	protein-coding	0.016949	0.465444	
chunk0045_91_1	chr12	45990540	45991305	+	0	NA	promoter-TSS (NM_004719)	promoter-TSS (NM_004719)	-304	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.065359	0.604439	
chunk0208_362_1	chrX	26128519	26128798	+	0	NA	Intergenic	Intergenic	-9685	NM_173699	286514	Hs.350683	NM_173699	ENSG00000176774	MAGEB18	-	MAGE family member B18	protein-coding	0.014337	0.317857	
chunk0170_77_1	chr6	109815616	109815995	+	0	NA	intron (NM_014845, intron 22 of 22)	intron (NM_014845, intron 22 of 22)	-62589	NR_106988									0.005277	0.363158	64(AGGGACATTGTGCTCC,-,0.00),65(GGGACATTGTGCTCCC,+,0.00)
chunk0185_61_1	chr7	124828618	124829244	+	0	NA	intron (NR_003103, intron 15 of 17)	CR1-L3A_Croc|LINE|CR1	-38121	NM_001024603	154872	Hs.444163	NM_001024603	ENSG00000275356	C7orf77	-	chromosome 7 open reading frame 77	protein-coding	0.003195	0.357257	
chunk0203_153_1	chr9	85661378	85661577	+	0	NA	intron (NM_001286715, intron 7 of 24)	intron (NM_001286715, intron 7 of 24)	80552	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.005025	0.320000	
chunk0205_42_1	chr9	105776371	105776931	+	0	NA	TTS (NM_018112)	TTS (NM_018112)	82126	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.003571	0.381462	
chunk0175_66_1	chr7	2029182	2029650	+	0	NA	intron (NM_003550, intron 12 of 18)	L1ME3|LINE|L1	-88866	NM_001304525	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.023504	0.420043	258(GTGACACCGTGTTCCC,+,0.00)
chunk0122_384_1	chr3	37811246	37812199	+	0	NA	intron (NM_002207, intron 27 of 27)	intron (NM_002207, intron 27 of 27)	50058	NR_110531	101928153	Hs.657314	NR_110531	ENSG00000235257	ITGA9-AS1	-	ITGA9 antisense RNA 1	ncRNA	0.001049	0.494759	
chunk0104_385_1	chr2	180364660	180365363	+	0	NA	Intergenic	Intergenic	-327093	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.004267	0.384943	
chunk0034_240_1	chr11	34084683	34085032	+	0	NA	intron (NM_005898, intron 9 of 18)	intron (NM_005898, intron 9 of 18)	-20707	NM_024662	55226	Hs.577281	NM_024662	ENSG00000135372	NAT10	ALP|Kre33|NET43	N-acetyltransferase 10	protein-coding	0.005731	0.374286	
chunk0046_74_1	chr12	56053539	56053807	+	0	NA	Intergenic	Intergenic	11771	NM_001029	6231	Hs.447562	NM_001029	ENSG00000197728	RPS26	DBA10|S26|eS26	ribosomal protein S26	protein-coding	0.003731	0.379182	
chunk0035_81_1	chr11	41983894	41984517	+	0	NA	Intergenic	L2c|LINE|L2	269485	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.003210	0.386218	
chunk0170_399_1	chr6	117497510	117497940	+	0	NA	intron (NM_173674, intron 1 of 14)	intron (NM_173674, intron 1 of 14)	15068	NM_173674	285761	Hs.658304	NM_173674	ENSG00000164465	DCBLD1	dJ94G16.1	discoidin, CUB and LCCL domain containing 1	protein-coding	0.004651	0.299304	
chunk0052_18_1	chr13	20163400	20163800	+	0	NA	Intergenic	Intergenic	-2556	NM_021954	2700	Hs.130313	NM_021954	ENSG00000121743	GJA3	CTRCT14|CX46|CZP3	gap junction protein alpha 3	protein-coding	0.017500	0.446384	
chunk0031_419_1	chr10	132268990	132269327	+	0	NA	intron (NM_173575, intron 1 of 11)	intron (NM_173575, intron 1 of 11)	38815	NM_173575	282974	Hs.469002	NM_173575	ENSG00000165752	STK32C	PKE|YANK3	serine/threonine kinase 32C	protein-coding	0.041543	0.553254	
chunk0198_250_1	chr8	134565153	134565745	+	0	NA	intron (NM_020863, intron 10 of 15)	intron (NM_020863, intron 10 of 15)	-32622	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.021959	0.537943	186(GGAGACATGCTGTTCC,-,0.00),187(GAGACATGCTGTTCCA,+,0.00),480(AGGCACAGCCAGCTCC,-,0.00)
chunk0141_431_1	chr4	88843477	88843888	+	0	NA	intron (NM_014883, intron 7 of 23)	intron (NM_014883, intron 7 of 23)	-20321	NM_001015045	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.009732	0.395631	
chunk0073_373_1	chr16	15590923	15591361	+	0	NA	Intergenic	MIR|SINE|MIR	19953	NR_106761	102465252		NR_106761	ENSG00000284184	MIR6506	hsa-mir-6506	microRNA 6506	ncRNA	0.015982	0.482916	
chunk0155_125_1	chr5	93088869	93089492	+	0	NA	Intergenic	Intergenic	482163	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.011236	0.339744	
chunk0194_130_1	chr8	84288873	84289451	+	0	NA	intron (NM_001100391, intron 1 of 8)	MER67C|LTR|ERV1	104297	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.003460	0.390328	
chunk0123_169_1	chr3	43887417	43887823	+	0	NA	Intergenic	HAL1|LINE|L1	196737	NM_016006	51099	Hs.19385	NM_016006	ENSG00000011198	ABHD5	CGI58|IECN2|NCIE2	abhydrolase domain containing 5	protein-coding	0.000000	0.348894	
chunk0155_283_1	chr5	96100137	96100486	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	21173	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.002865	0.500000	
chunk0131_422_1	chr3	153292449	153292729	+	0	NA	Intergenic	L2a|LINE|L2	130377	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.003571	0.281139	
chunk0144_50_1	chr4	126609020	126609316	+	0	NA	Intergenic	Intergenic	-1023764	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.006757	0.303030	
chunk0060_290_1	chr14	50658064	50658691	+	0	NA	intron (NM_021818, intron 2 of 4)	intron (NM_021818, intron 2 of 4)	9976	NM_021818	60485	Hs.642842	NM_021818	ENSG00000151748	SAV1	SAV|WW45|WWP4	salvador family WW domain containing protein 1	protein-coding	0.011164	0.328025	
chunk0074_364_1	chr16	34582134	34582507	+	0	NA	Intergenic	Intergenic	-422284	NR_038368									0.037534	0.342246	
chunk0152_405_1	chr5	64958226	64958425	+	0	NA	intron (NM_001297644, intron 11 of 12)	intron (NM_001297644, intron 11 of 12)	189407	NM_001297645	10283	Hs.371372	NM_005869	ENSG00000153015	CWC27	NY-CO-10|RPSKA|SDCCAG-10|SDCCAG10	CWC27 spliceosome associated cyclophilin	protein-coding	0.015075	0.375000	
chunk0119_451_1	chr22	50387450	50387745	+	0	NA	intron (NM_001242900, intron 2 of 22)	MER63B|DNA|hAT-Blackjack	44280	NM_001242899	9701	Hs.449098	NM_014678	ENSG00000100239	PPP6R2	KIAA0685|PP6R2|SAP190|SAPS2	protein phosphatase 6 regulatory subunit 2	protein-coding	0.023729	0.462838	
chunk0207_25_1	chrX	3213838	3214119	+	0	NA	Intergenic	L1ME3F|LINE|L1	-57842	NR_038428	100129464	Hs.187816	NR_038428	ENSG00000228459	LINC01546	CXorf28	long intergenic non-protein coding RNA 1546	ncRNA	0.024911	0.407801	
chunk0189_413_1	chr8	27744207	27744594	+	0	NA	intron (NM_001304529, intron 5 of 6)	intron (NM_001304529, intron 5 of 6)	28253	NR_130761	55246	Hs.445512	NM_018246	ENSG00000147419	CCDC25	-	coiled-coil domain containing 25	protein-coding	0.007752	0.386598	
chunk0051_378_1	chr12	121753685	121754146	+	0	NA	intron (NM_001080825, intron 5 of 11)	intron (NM_001080825, intron 5 of 11)	39773	NM_019034	54509	Hs.707579	NM_019034	ENSG00000139725	RHOF	ARHF|RIF	ras homolog family member F, filopodia associated	protein-coding	0.021692	0.558442	
chunk0115_49_1	chr21	21283813	21284368	+	0	NA	intron (NM_004540, intron 2 of 17)	intron (NM_004540, intron 2 of 17)	285775	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.007207	0.336331	
chunk0179_106_1	chr7	44986555	44986991	+	0	NA	promoter-TSS (NR_003697)	promoter-TSS (NR_003697)	-113	NR_003697	285958	Hs.25892	NR_003697	ENSG00000232956	SNHG15	C7orf40|Linc-Myo1g|MYO1GUT	small nucleolar RNA host gene 15	ncRNA	0.105505	0.654462	
chunk0062_399_1	chr14	74881553	74882154	+	0	NA	promoter-TSS (NM_001244883)	promoter-TSS (NM_001244883)	-38	NM_001244883	1743	Hs.525459	NM_001933	ENSG00000119689	DLST	DLTS	dihydrolipoamide S-succinyltransferase	protein-coding	0.099834	0.702658	
chunk0084_314_1	chr17	80298026	80298620	+	0	NA	exon (NM_020954, exon 11 of 17)	exon (NM_020954, exon 11 of 17)	37462	NM_001256071	57674	Hs.195642	NM_020914	ENSG00000173821	RNF213	ALO17|C17orf27|KIAA1618|MYMY2|MYSTR|NET57	ring finger protein 213	protein-coding	0.035354	0.589916	
chunk0128_137_1	chr3	106709341	106709648	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	531144	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.009772	0.370130	
chunk0106_295_1	chr2	204483616	204483815	+	0	NA	Intergenic	Intergenic	-62078	NM_057177	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.010050	0.450000	
chunk0064_101_1	chr14	91060477	91060866	+	0	NA	promoter-TSS (NM_004755)	promoter-TSS (NM_004755)	-22	NM_182398	9252	Hs.510225	NM_004755	ENSG00000100784	RPS6KA5	MSK1|MSPK1|RLPK	ribosomal protein S6 kinase A5	protein-coding	0.115681	0.697436	
chunk0037_76_1	chr11	71228877	71229494	+	0	NA	Intergenic	L1MD1|LINE|L1	-4389	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.001621	0.333333	
chunk0120_321_1	chr3	10399380	10400016	+	0	NA	intron (NM_001001331, intron 5 of 22)	L2b|LINE|L2	-5136	NR_030614	100126334		NR_030614	ENSG00000216135	MIR885	MIRN885|hsa-mir-885|mir-885	microRNA 885	ncRNA	0.004717	0.477237	
chunk0138_348_1	chr4	41763728	41764051	+	0	NA	Intergenic	L3|LINE|CR1	-14919	NM_003924	8929	Hs.87202	NM_003924	ENSG00000109132	PHOX2B	CCHS|NBLST2|NBPhox|PMX2B	paired like homeobox 2B	protein-coding	0.006192	0.435185	
chunk0086_405_1	chr18	26764041	26764831	+	0	NA	Intergenic	L3|LINE|CR1	-60798	NR_024259	728606	Hs.170599	NR_024259	ENSG00000265369	PCAT18	LINC01092	prostate cancer associated transcript 18	ncRNA	0.001266	0.438685	523(AGTACTATTTGTTCTT,+,0.00)
chunk0109_230_1	chr20	5901758	5901957	+	0	NA	Intergenic	Intergenic	-9471	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.005025	0.430000	60(TAGCACATTTTGTGCA,-,0.00),61(AGCACATTTTGTGCAA,+,0.00)
chunk0012_1_1	chr1	154643987	154644258	+	0	NA	Intergenic	L1MC1|LINE|L1	-16142	NM_001025107	103	Hs.12341	NM_001111	ENSG00000160710	ADAR	ADAR1|AGS6|DRADA|DSH|DSRAD|G1P1|IFI-4|IFI4|K88DSRBP|P136	adenosine deaminase RNA specific	protein-coding	0.000000	0.279412	
chunk0176_48_1	chr7	10940576	10940796	+	0	NA	promoter-TSS (NM_002489)	promoter-TSS (NM_002489)	-500	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.068182	0.565611	
chunk0123_419_1	chr3	49615126	49615360	+	0	NA	intron (NM_003458, intron 1 of 11)	intron (NM_003458, intron 1 of 11)	-58759	NM_001640	327	Hs.517969	NM_001640	ENSG00000164062	APEH	AARE|ACPH|APH|D3F15S2|D3S48E|DNF15S2|OPH	acylaminoacyl-peptide hydrolase	protein-coding	0.004274	0.506383	
chunk0118_74_1	chr22	28818666	28818954	+	0	NA	Intergenic	Intergenic	-18238	NM_005080	7494	Hs.437638	NM_005080	ENSG00000100219	XBP1	TREB-5|TREB5|XBP-1|XBP2	X-box binding protein 1	protein-coding	0.003472	0.467128	
chunk0071_29_1	chr15	79410076	79410427	+	0	NA	Intergenic	Intergenic	-22265	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.005698	0.329545	
chunk0005_420_1	chr1	62725741	62726131	+	0	NA	Intergenic	Intergenic	-37568	NM_001272001	85440	Hs.744927	NM_033407	ENSG00000116641	DOCK7	EIEE23|ZIR2	dedicator of cytokinesis 7	protein-coding	0.002564	0.358056	
chunk0063_205_1	chr14	81366092	81366777	+	0	NA	intron (NM_033104, intron 4 of 5)	intron (NM_033104, intron 4 of 5)	60778	NM_033104	85439	Hs.14248	NM_033104	ENSG00000140022	STON2	STN2|STNB|STNB2	stonin 2	protein-coding	0.013139	0.530612	
chunk0197_117_1	chr8	119919606	119920057	+	0	NA	intron (NM_001283012, intron 1 of 6)	intron (NM_001283012, intron 1 of 6)	46176	NM_022783	64798	Hs.112981	NM_022783	ENSG00000155792	DEPTOR	DEP.6|DEPDC6	DEP domain containing MTOR interacting protein	protein-coding	0.002217	0.418142	
chunk0122_252_1	chr3	34864325	34864993	+	0	NA	Intergenic	Intergenic	529364	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.005988	0.439462	
chunk0065_67_1	chr15	23370001	23370230	+	0	NA	Intergenic	Intergenic	15367	NR_038843	653061	Hs.528454	NM_001355465		GOLGA8S	-	golgin A8 family member S	protein-coding	0.008734	0.347826	
chunk0083_307_1	chr17	69462050	69462679	+	0	NA	intron (NM_002758, intron 1 of 11)	intron (NM_002758, intron 1 of 11)	47667	NM_002758	5608	Hs.49329	NM_002758	ENSG00000108984	MAP2K6	MAPKK6|MEK6|MKK6|PRKMK6|SAPKK-3|SAPKK3	mitogen-activated protein kinase kinase 6	protein-coding	0.022258	0.479365	289(CAGCACATGCAGTCCC,-,0.00),290(AGCACATGCAGTCCCT,+,0.00),320(GAGAACACAGTGTGCT,-,0.00),321(AGAACACAGTGTGCTA,+,0.00)
chunk0031_169_1	chr10	125495457	125495765	+	0	NA	Intergenic	Intergenic	-78760	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.009740	0.375405	
chunk0108_146_1	chr2	230879507	230880204	+	0	NA	TTS (NM_001287241)	TTS (NM_001287241)	-6691	NR_038238	151484	Hs.559309	NR_038238	ENSG00000232520	LOC151484	-	uncharacterized LOC151484	ncRNA	0.017217	0.448424	348(AGACACACCTTGTTCC,-,0.00),349(GACACACCTTGTTCCC,+,0.00)
chunk0011_357_1	chr1	152828177	152828376	+	0	NA	TTS (NM_178348)	TTS (NM_178348)	803	NM_178348	353131	Hs.534645	NM_178348	ENSG00000186844	LCE1A	LEP1	late cornified envelope 1A	protein-coding	0.010050	0.485000	
chunk0129_6_1	chr3	116269196	116269742	+	0	NA	intron (NM_002338, intron 1 of 6)	L2b|LINE|L2	-90555	NR_109998	101926903	Hs.26479	NR_109998	ENSG00000240922	LSAMP-AS1	-	LSAMP antisense RNA 1	ncRNA	0.003663	0.351005	
chunk0143_436_1	chr4	123863452	123863724	+	0	NA	non-coding (NR_027106, exon 3 of 3)	non-coding (NR_027106, exon 3 of 3)	89324	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.011029	0.450549	
chunk0160_236_1	chr5	155678246	155678871	+	0	NA	Intergenic	HUERS-P2-int|LTR|ERV1	-648199	NM_172244	6444	Hs.387207	NM_000337	ENSG00000170624	SGCD	35DAG|CMD1L|DAGD|LGMDR6|SG-delta|SGCDP|SGD	sarcoglycan delta	protein-coding	0.004800	0.450479	
chunk0023_422_1	chr10	31574391	31575081	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	253601	NM_001174094	6935	Hs.124503	NM_030751	ENSG00000148516	ZEB1	AREB6|BZP|DELTAEF1|FECD6|NIL2A|PPCD3|TCF8|ZFHEP|ZFHX1A	zinc finger E-box binding homeobox 1	protein-coding	0.005797	0.396527	
chunk0169_143_1	chr6	101499205	101499699	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	100467	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004049	0.258586	
chunk0091_295_1	chr19	12453613	12453859	+	0	NA	Intergenic	HERVK14-int|LTR|ERVK	-12624	NM_005815	10224	Hs.636894	NM_005815	ENSG00000180855	ZNF443	ZK1	zinc finger protein 443	protein-coding	0.020325	0.437247	
chunk0213_34_1	chrY	56855658	56855898	+	0	NA	Intergenic	Intergenic	-98477	NM_005840	10251	Hs.381912	NM_005840	ENSG00000168939	SPRY3	spry-3	sprouty RTK signaling antagonist 3	protein-coding	0.016667	0.414938	145(AGGAACACCCTGCTCA,-,0.00),146(GGAACACCCTGCTCAG,+,0.00)
chunk0002_100_1	chr1	15179260	15179467	+	0	NA	intron (NM_018022, intron 1 of 2)	L1ME2|LINE|L1	-7739	NM_001278502	727684	Hs.667584	NM_001278501		C1orf195	-	chromosome 1 open reading frame 195	protein-coding	0.004831	0.490385	
chunk0056_71_1	chr13	79441413	79442163	+	0	NA	Intergenic	LTR22A|LTR|ERVK	35479	NR_038991	100505538	Hs.600720	NR_038991	ENSG00000227354	RBM26-AS1	-	RBM26 antisense RNA 1	ncRNA	0.016000	0.492676	
chunk0190_253_1	chr8	36991183	36991519	+	0	NA	Intergenic	Intergenic	207027	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.002976	0.394659	
chunk0037_290_1	chr11	76056052	76056722	+	0	NA	intron (NM_003369, intron 12 of 14)	L1ME2z|LINE|L1	150143	NM_004626	7481	Hs.108219	NM_004626	ENSG00000085741	WNT11	HWNT11	Wnt family member 11	protein-coding	0.007463	0.359165	
chunk0068_293_1	chr15	57041313	57041893	+	0	NA	intron (NM_003205, intron 3 of 19)	intron (NM_003205, intron 3 of 19)	122968	NM_207038	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.001724	0.318417	
chunk0189_163_1	chr8	23246086	23246533	+	0	NA	5' UTR (NM_152272, exon 2 of 11)	5' UTR (NM_152272, exon 2 of 11)	2672	NM_152272	91782	Hs.5019	NM_152272	ENSG00000147457	CHMP7	-	charged multivesicular body protein 7	protein-coding	0.046980	0.470982	
chunk0165_155_1	chr6	33740257	33740458	+	0	NA	intron (NM_001142883, intron 1 of 6)	intron (NM_001142883, intron 1 of 6)	6628	NM_001142883	117283	Hs.17253	NM_054111	ENSG00000161896	IP6K3	IHPK3|INSP6K3	inositol hexakisphosphate kinase 3	protein-coding	0.019900	0.569307	
chunk0189_406_1	chr8	27603148	27603743	+	0	NA	intron (NM_001831, intron 6 of 8)	intron (NM_001831, intron 6 of 8)	7306	NR_106902	102465508		NR_106902	ENSG00000284280	MIR6843	hsa-mir-6843	microRNA 6843	ncRNA	0.011765	0.464765	
chunk0172_76_1	chr6	134400941	134401472	+	0	NA	Intergenic	Intergenic	-36510	NR_038217	154092	Hs.223718	NR_038216		LINC01010	-	long intergenic non-protein coding RNA 1010	ncRNA	0.005650	0.377820	250(AGTGACACAGTGTTCT,-,0.00),251(GTGACACAGTGTTCTA,+,0.00)
chunk0072_236_1	chr15	95917096	95917812	+	0	NA	Intergenic	Intergenic	-408474	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.002793	0.327755	
chunk0133_66_1	chr3	166865386	166865653	+	0	NA	Intergenic	MER52D|LTR|ERV1	514764	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.003745	0.589552	
chunk0182_71_1	chr7	92267359	92267879	+	0	NA	intron (NM_019004, intron 1 of 19)	L1ME3A|LINE|L1	21385	NM_019004	54467	Hs.83293	NM_019004	ENSG00000001629	ANKIB1	-	ankyrin repeat and IBR domain containing 1	protein-coding	0.003846	0.351248	
chunk0009_296_1	chr1	107790128	107790592	+	0	NA	intron (NM_006113, intron 2 of 26)	L2a|LINE|L2	-101856	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002155	0.483871	
chunk0068_4_1	chr15	50523630	50524513	+	0	NA	intron (NM_203494, intron 6 of 6)	L1MA7|LINE|L1	22634	NM_203494	373509	Hs.677758	NM_203494	ENSG00000170236	USP50	-	ubiquitin specific peptidase 50	protein-coding	0.006795	0.332579	275(CAAAACAGCATGTTCT,-,0.00),276(AAAACAGCATGTTCTG,+,0.00)
chunk0025_114_1	chr10	51366074	51366751	+	0	NA	intron (NM_006258, intron 2 of 17)	intron (NM_006258, intron 2 of 17)	66839	NR_030336	693190		NR_030336	ENSG00000207813	MIR605	MIRN605|hsa-mir-605|mir-605	microRNA 605	ncRNA	0.002954	0.340708	208(TAGAACATGGAGTTCA,-,0.00),209(AGAACATGGAGTTCAT,+,0.00)
chunk0019_410_1	chr1	230682307	230682747	+	0	NA	intron (NM_001145036, intron 10 of 17)	intron (NM_001145036, intron 10 of 17)	32063	NM_000029	183	Hs.19383	NM_000029	ENSG00000135744	AGT	ANHU|SERPINA8|hFLT1	angiotensinogen	protein-coding	0.006818	0.446712	367(AAGCACATTATGTACT,-,0.00),368(AGCACATTATGTACTA,+,0.00)
chunk0049_337_1	chr12	94963846	94964118	+	0	NA	Intergenic	Intergenic	39731	NM_001258338	55967	Hs.506374	NM_018838	ENSG00000184752	NDUFA12	B17.2|DAP13|MC1DN23	NADH:ubiquinone oxidoreductase subunit A12	protein-coding	0.011029	0.355311	
chunk0179_113_1	chr7	45111647	45111986	+	0	NA	promoter-TSS (NM_001261834)	promoter-TSS (NM_001261834)	-69	NM_030900	9238	Hs.231411	NM_004749	ENSG00000136270	TBRG4	CPR2|FASTKD4	transforming growth factor beta regulator 4	protein-coding	0.100295	0.623529	
chunk0125_29_1	chr3	62282907	62283110	+	0	NA	intron (NM_002841, intron 28 of 29)	intron (NM_002841, intron 28 of 29)	35939	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.000000	0.343137	
chunk0035_373_1	chr11	49372238	49372631	+	0	NA	Intergenic	Intergenic	-163764	NM_001193471	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.000000	0.335025	
chunk0083_86_1	chr17	64255806	64256007	+	0	NA	intron (NM_018469, intron 1 of 11)	intron (NM_018469, intron 1 of 11)	7417	NM_001288732	55852	Hs.175414	NM_018469	ENSG00000136478	TEX2	HT008|TMEM96	testis expressed 2	protein-coding	0.014925	0.519802	
chunk0155_31_1	chr5	91059734	91060259	+	0	NA	intron (NR_003149, intron 85 of 89)	intron (NR_003149, intron 85 of 89)	254406	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.003810	0.330798	
chunk0015_264_1	chr1	188222410	188222964	+	0	NA	Intergenic	MER63C|DNA|hAT-Blackjack	779059	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.003610	0.356757	
chunk0055_94_1	chr13	55361291	55361687	+	0	NA	Intergenic	Intergenic	187035	NR_049804	100846996		NR_049804	ENSG00000264387	MIR5007	-	microRNA 5007	ncRNA	0.000000	0.365239	
chunk0183_343_1	chr7	108497071	108497270	+	0	NA	intron (NM_001256007, intron 6 of 10)	intron (NM_001256007, intron 6 of 10)	29148	NM_001256009	50640	Hs.617340	NM_015723	ENSG00000135241	PNPLA8	IPLA2-2|IPLA2G|MMLA|PNPLA-gamma|iPLA2gamma	patatin like phospholipase domain containing 8	protein-coding	0.005025	0.295000	
chunk0017_431_1	chr1	213365678	213366104	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	314658	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.002347	0.421546	
chunk0129_251_1	chr3	122203517	122203796	+	0	NA	intron (NM_001178065, intron 1 of 6)	Tigger3c|DNA|TcMar-Tigger	19322	NM_001178065	846	Hs.435615	NM_000388	ENSG00000036828	CASR	CAR|EIG8|FHH|FIH|GPRC2A|HHC|HHC1|HYPOC1|NSHPT|PCAR1|hCasR	calcium sensing receptor	protein-coding	0.003584	0.357143	161(TAGGACTCACTGTGCA,-,0.00),162(AGGACTCACTGTGCAC,+,0.00)
chunk0149_299_1	chr5	25615153	25615509	+	0	NA	Intergenic	L1M4c|LINE|L1	-774748	NR_037896	340107	Hs.145181	NR_037896	ENSG00000248908	LINC02239	-	long intergenic non-protein coding RNA 2239	ncRNA	0.008427	0.375350	
chunk0026_279_1	chr10	67259192	67259544	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	144042	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.005682	0.348442	
chunk0161_144_1	chr5	168595869	168596098	+	0	NA	Intergenic	L1PA5|LINE|L1	-16374	NM_024594	79646	Hs.388400	NM_024594	ENSG00000120137	PANK3	-	pantothenate kinase 3	protein-coding	0.000000	0.400000	
chunk0159_336_1	chr5	143898468	143898668	+	0	NA	Intergenic	MIRb|SINE|MIR	86407	NM_021182	57824	Hs.158320	NM_021182	ENSG00000158497	HMHB1	HB-1|HB-1Y|HLA-HB1	histocompatibility minor HB-1	protein-coding	0.005000	0.422886	
chunk0007_250_1	chr1	82685624	82685925	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	299148	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.006645	0.331126	83(TAGTACATACTGTACT,-,0.00),84(AGTACATACTGTACTA,+,0.00)
chunk0039_256_1	chr11	102276329	102276571	+	0	NA	Intergenic	Tigger16a|DNA|TcMar-Tigger	-41000	NM_182962	330	Hs.127799	NM_001165	ENSG00000023445	BIRC3	AIP1|API2|CIAP2|HAIP1|HIAP1|IAP-1|MALT2|MIHC|RNF49|c-IAP2	baculoviral IAP repeat containing 3	protein-coding	0.008264	0.415638	103(CAGCACAGCCAGTTCC,-,0.00),104(AGCACAGCCAGTTCCA,+,0.00)
chunk0048_149_1	chr12	80474606	80475048	+	0	NA	intron (NM_001145026, intron 8 of 44)	intron (NM_001145026, intron 8 of 44)	30481	NM_001145026	374462	Hs.539284	NM_001145026	ENSG00000139304	PTPRQ	DFNA73|DFNB84|DFNB84A|PTPGMC1|R-PTP-Q	protein tyrosine phosphatase receptor type Q	protein-coding	0.002262	0.320542	
chunk0032_327_1	chr11	10087011	10087685	+	0	NA	intron (NM_030962, intron 2 of 39)	intron (NM_030962, intron 2 of 39)	206859	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.002967	0.336296	308(TAGAACATTGTGTTCT,-,0.00),309(AGAACATTGTGTTCTA,+,0.00)
chunk0164_232_1	chr6	23137122	23137807	+	0	NA	Intergenic	L1MA4|LINE|L1	568015	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007299	0.537901	
chunk0207_83_1	chrX	9372780	9373167	+	0	NA	Intergenic	Intergenic	-90322	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.023256	0.451031	
chunk0063_84_1	chr14	77933736	77933963	+	0	NA	3' UTR (NM_001142545, exon 10 of 10)	3' UTR (NM_001142545, exon 10 of 10)	133766	NM_020421	57143	Hs.413208	NM_020421	ENSG00000063761	ADCK1	-	aarF domain containing kinase 1	protein-coding	0.008811	0.478070	
chunk0024_78_1	chr10	34319846	34320092	+	0	NA	intron (NM_019619, intron 19 of 24)	intron (NM_019619, intron 19 of 24)	495356	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.000000	0.360324	
chunk0171_114_1	chr6	122432588	122432888	+	0	NA	3' UTR (NM_001135564, exon 12 of 12)	3' UTR (NM_001135564, exon 12 of 12)	33187	NM_001135564	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.013333	0.365449	85(GGGAACATAAAGTGCC,-,0.00),86(GGAACATAAAGTGCCT,+,0.00)
chunk0053_437_1	chr13	39065919	39066437	+	0	NA	Intergenic	L1MB2|LINE|L1	27867	NM_001012754	387921	Hs.507783	NM_001012754	ENSG00000188811	NHLRC3	-	NHL repeat containing 3	protein-coding	0.013514	0.433526	273(CTGTACTCAGTGTTCT,-,0.00),274(TGTACTCAGTGTTCTT,+,0.00)
chunk0090_192_1	chr18	73047559	73048091	+	0	NA	Intergenic	Intergenic	-180250	NM_001201465	81832	Hs.465407	NM_138966	ENSG00000166342	NETO1	BCTL1|BTCL1	neuropilin and tolloid like 1	protein-coding	0.000000	0.288931	265(GGAACAGTATGACCAT,+,0.00)
chunk0127_102_1	chr3	90018897	90019364	+	0	NA	Intergenic	Intergenic	911606	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004283	0.403846	
chunk0181_164_1	chr7	82540127	82540667	+	0	NA	Intergenic	Intergenic	-96591	NM_001302890	781	Hs.282151	NM_000722	ENSG00000153956	CACNA2D1	CACNA2|CACNL2A|CCHL2A|LINC01112|lncRNA-N3	calcium voltage-gated channel auxiliary subunit alpha2delta 1	protein-coding	0.009259	0.349353	230(AAGCACACCGTGTCTT,-,0.00),231(AGCACACCGTGTCTTC,+,0.00)
chunk0038_42_1	chr11	82234913	82235473	+	0	NA	intron (NR_120571, intron 3 of 7)	MIRb|SINE|MIR	168720	NR_120571	101928989	Hs.145117	NR_120571	ENSG00000245832	MIR4300HG	-	MIR4300 host gene	ncRNA	0.001786	0.329768	
chunk0008_102_1	chr1	91253532	91253783	+	0	NA	Intergenic	L1PREC2|LINE|L1	151212	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.003984	0.535714	
chunk0047_258_1	chr12	72590187	72590490	+	0	NA	intron (NM_013381, intron 12 of 18)	L1MEf|LINE|L1	-316829	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.003300	0.282895	
chunk0097_231_1	chr2	52934257	52934558	+	0	NA	Intergenic	Intergenic	-231792	NR_039630	100616431		NR_039630	ENSG00000264975	MIR4431	-	microRNA 4431	ncRNA	0.006645	0.360927	
chunk0084_95_1	chr17	75524996	75525351	+	0	NA	promoter-TSS (NM_004524)	promoter-TSS (NM_004524)	-529	NM_001015002	3993	Hs.514477	NM_004524	ENSG00000073350	LLGL2	HGL|Hugl-2|LGL2	LLGL scribble cell polarity complex component 2	protein-coding	0.104225	0.741573	
chunk0035_362_1	chr11	49167727	49168446	+	0	NA	intron (NM_001014986, intron 12 of 17)	intron (NM_001014986, intron 12 of 17)	40584	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.006954	0.348611	393(GATACTGTCTGTTCCT,+,0.00)
chunk0133_295_1	chr3	172195054	172195696	+	0	NA	intron (NM_022763, intron 3 of 25)	intron (NM_022763, intron 3 of 25)	154821	NM_001135095	64778	Hs.744888	NM_022763	ENSG00000075420	FNDC3B	FAD104|PRO4979|YVTM2421	fibronectin type III domain containing 3B	protein-coding	0.003115	0.351477	
chunk0096_360_1	chr2	36433323	36433682	+	0	NA	intron (NM_016441, intron 2 of 16)	intron (NM_016441, intron 2 of 16)	77275	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.011142	0.491667	
chunk0062_338_1	chr14	73451373	73451895	+	0	NA	intron (NM_001005743, intron 1 of 12)	intron (NM_001005743, intron 1 of 12)	6946	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.009579	0.395793	
chunk0194_257_1	chr8	86652638	86653239	+	0	NA	intron (NM_019098, intron 7 of 17)	Tigger3b|DNA|TcMar-Tigger	90737	NM_019098	54714	Hs.154433	NM_019098	ENSG00000170289	CNGB3	ACHM1	cyclic nucleotide gated channel beta 3	protein-coding	0.003328	0.363787	
chunk0144_65_1	chr4	127252226	127252715	+	0	NA	Intergenic	MIRb|SINE|MIR	-380462	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.004090	0.365306	
chunk0190_321_1	chr8	38793072	38793476	+	0	NA	intron (NM_001146216, intron 2 of 12)	intron (NM_001146216, intron 2 of 12)	6070	NM_001122824	6867	Hs.279245	NM_006283	ENSG00000147526	TACC1	Ga55	transforming acidic coiled-coil containing protein 1	protein-coding	0.007426	0.395062	
chunk0200_370_1	chr9	26323870	26324204	+	0	NA	Intergenic	LTR85c|LTR|Gypsy?	257362	NM_001004352	100506422	Hs.533221	NM_001004352		LOC100506422	-	putative deoxyuridine 5'-triphosphate nucleotidohydrolase-like protein FLJ16323	protein-coding	0.002994	0.355224	
chunk0041_267_1	chr11	129113052	129113990	+	0	NA	intron (NM_001142685, intron 4 of 21)	Tigger2|DNA|TcMar-Tigger	78677	NM_001142685	9743	Hs.440379	NM_014715	ENSG00000134909	ARHGAP32	GC-GAP|GRIT|PX-RICS|RICS|p200RhoGAP|p250GAP	Rho GTPase activating protein 32	protein-coding	0.005330	0.338658	280(TAGTACAGTATGTACT,-,0.00),281(AGTACAGTATGTACTA,+,0.00),799(CAAAACAAACTGTACT,-,0.00)
chunk0198_137_1	chr8	132730939	132731138	+	0	NA	intron (NM_144649, intron 5 of 9)	MIRb|SINE|MIR	29630	NM_144649	137835	Hs.293842	NM_144649	ENSG00000165071	TMEM71	-	transmembrane protein 71	protein-coding	0.000000	0.345000	
chunk0176_134_1	chr7	12686868	12687201	+	0	NA	promoter-TSS (NM_001195396)	promoter-TSS (NM_001195396)	207	NM_001037164	10124	Hs.245540	NM_005738	ENSG00000122644	ARL4A	ARL4	ADP ribosylation factor like GTPase 4A	protein-coding	0.105105	0.721557	
chunk0056_171_1	chr13	85236192	85236591	+	0	NA	Intergenic	L1MC2|LINE|L1	-88334	NR_126383	104355140		NR_126383	ENSG00000226370	LINC00375	-	long intergenic non-protein coding RNA 375	ncRNA	0.002506	0.320000	
chunk0109_157_1	chr20	3918116	3918726	+	0	NA	promoter-TSS (NR_031722)	promoter-TSS (NR_031722)	-858	NR_031722	100302282		NR_031722	ENSG00000283320	MIR103B2	MIR103-2-AS|MIR103-2AS|MIRN103-2AS|hsa-mir-103-2-as	microRNA 103b-2	ncRNA	0.009836	0.355155	
chunk0170_338_1	chr6	116308068	116308637	+	0	NA	intron (NM_001080976, intron 1 of 5)	intron (NM_001080976, intron 1 of 5)	28232	NM_001080976	29940	Hs.458358	NM_013352	ENSG00000111817	DSE	DS-epi1|DSEP|DSEPI|EDSMC2|SART-2|SART2	dermatan sulfate epimerase	protein-coding	0.005272	0.340351	
chunk0114_395_1	chr20	63387489	63387880	+	0	NA	Intergenic	(CACATG)n|Simple_repeat|Simple_repeat	-26288	NM_001256573	1137	Hs.10734	NM_000744	ENSG00000101204	CHRNA4	BFNC|EBN|EBN1|NACHR|NACHRA4|NACRA4	cholinergic receptor nicotinic alpha 4 subunit	protein-coding	0.040921	0.512755	
chunk0202_279_1	chr9	77180285	77180849	+	0	NA	intron (NM_001018038, intron 1 of 68)	L1MD|LINE|L1	-2650	NR_026668	100286938	Hs.662256	NR_026668	ENSG00000232998	VPS13A-AS1	-	VPS13A antisense RNA 1	ncRNA	0.001773	0.322124	
chunk0089_442_1	chr18	70221382	70222130	+	0	NA	Intergenic	Intergenic	-16030	NM_173630	25914	Hs.654809	NM_173630	ENSG00000176225	RTTN	MSSP	rotatin	protein-coding	0.013369	0.440587	
chunk0123_387_1	chr3	48759589	48760043	+	0	NA	intron (NM_004157, intron 8 of 10)	intron (NM_004157, intron 8 of 10)	-42538	NM_001146179	51447	Hs.595983	NM_016291	ENSG00000068745	IP6K2	IHPK2|InsP6K2|PIUS	inositol hexakisphosphate kinase 2	protein-coding	0.011013	0.397802	
chunk0015_333_1	chr1	189774735	189775211	+	0	NA	Intergenic	Intergenic	702656	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.004202	0.350105	
chunk0121_458_1	chr3	27059266	27059667	+	0	NA	Intergenic	Intergenic	157057	NM_001304384	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.002494	0.395522	384(GGGACAGTTTGAGCTT,+,0.00)
chunk0128_250_1	chr3	108795012	108795599	+	0	NA	Intergenic	L1MC3|LINE|L1	-27479	NM_016388	50852	Hs.138701	NM_016388	ENSG00000163519	TRAT1	HSPC062|TCRIM|TRIM|pp29/30	T cell receptor associated transmembrane adaptor 1	protein-coding	0.003407	0.309524	
chunk0204_46_1	chr9	92776947	92777677	+	0	NA	Intergenic	Intergenic	-12511	NM_015250	23299	Hs.436939	NM_015250	ENSG00000185963	BICD2	SMALED2|SMALED2A|SMALED2B|bA526D8.1	BICD cargo adaptor 2	protein-coding	0.002740	0.303694	
chunk0077_309_1	chr16	81901414	81901761	+	0	NA	intron (NM_002661, intron 14 of 32)	Charlie4a|DNA|hAT-Charlie	109901	NM_145168	93517	Hs.87779	NM_145168	ENSG00000184860	SDR42E1	HSPC105	short chain dehydrogenase/reductase family 42E, member 1	protein-coding	0.025937	0.451149	
chunk0163_372_1	chr6	16109115	16109336	+	0	NA	Intergenic	MER68|LTR|ERVL	-19861	NM_013262	29116	Hs.484738	NM_013262	ENSG00000007944	MYLIP	IDOL|MIR	myosin regulatory light chain interacting protein	protein-coding	0.004525	0.445946	160(AAGGACTCACTGTGCC,-,0.00),161(AGGACTCACTGTGCCT,+,0.00)
chunk0041_345_1	chr11	130705764	130706727	+	0	NA	intron (NM_001271983, intron 1 of 2)	intron (NM_001271983, intron 1 of 2)	33289	NM_001271983	283171	Hs.376151	NM_001271983		C11orf44	-	chromosome 11 open reading frame 44	protein-coding	0.008307	0.454357	421(AGGTACAGTCTGATCA,-,0.00),422(GGTACAGTCTGATCAG,+,0.00)
chunk0167_200_1	chr6	64785435	64785952	+	0	NA	intron (NM_001142800, intron 22 of 42)	intron (NM_001142800, intron 22 of 42)	-515725	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.001934	0.326255	
chunk0044_175_1	chr12	30088136	30088682	+	0	NA	Intergenic	L1ME2|LINE|L1	-303650	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.007326	0.382084	
chunk0077_228_1	chr16	80492199	80492584	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-48343	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.005195	0.435233	163(GGGAACATTGTGTTCT,-,0.00),164(GGAACATTGTGTTCTA,+,0.00)
chunk0159_159_1	chr5	139410313	139410766	+	0	NA	3' UTR (NM_152686, exon 8 of 8)	3' UTR (NM_152686, exon 8 of 8)	-6452	NM_194296	202051	Hs.373612	NM_194296	ENSG00000170469	SPATA24	CCDC161|T6441	spermatogenesis associated 24	protein-coding	0.006623	0.420705	
chunk0193_169_1	chr8	74772773	74773319	+	0	NA	Intergenic	Intergenic	-51491	NM_015886	51050	Hs.98558	NM_015886	ENSG00000137558	PI15	CRISP8|P24TI|P25TI	peptidase inhibitor 15	protein-coding	0.003663	0.365631	
chunk0182_171_1	chr7	95586870	95587476	+	0	NA	intron (NM_002612, intron 9 of 10)	intron (NM_002612, intron 9 of 10)	9440	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.008251	0.367381	
chunk0121_324_1	chr3	24354076	24354782	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-139658	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.004249	0.387553	58(AAACACTGCGTGTTCT,-,0.00)
chunk0046_450_1	chr12	64893977	64894497	+	0	NA	intron (NR_033988, intron 1 of 2)	intron (NR_033988, intron 1 of 2)	10463	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.007692	0.358925	
chunk0162_150_1	chr6	3363451	3363776	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	81400	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.018462	0.576687	
chunk0199_349_1	chr9	12091962	12092415	+	0	NA	Intergenic	L1P4b|LINE|L1	-601198	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.008830	0.541850	
chunk0087_182_1	chr18	35497536	35498105	+	0	NA	promoter-TSS (NM_001308064)	promoter-TSS (NM_001308064)	-171	NM_001308064	125476	Hs.464903	NM_194281	ENSG00000153391	INO80C	C18orf37|IES6|hIes6	INO80 complex subunit C	protein-coding	0.094903	0.628070	
chunk0045_354_1	chr12	51740583	51740890	+	0	NA	intron (NM_014191, intron 12 of 26)	L1MA2|LINE|L1	91181	NM_001013690	401720	Hs.648218	NM_001013690	ENSG00000261308	FIGNL2	-	fidgetin like 2	protein-coding	0.006515	0.428571	
chunk0004_110_1	chr1	44345351	44345773	+	0	NA	intron (NM_001301699, intron 1 of 7)	intron (NM_001301699, intron 1 of 7)	9717	NM_001301700	79033	Hs.731413	NM_024066	ENSG00000117419	ERI3	PINT1|PRNPIP	ERI1 exoribonuclease family member 3	protein-coding	0.000000	0.425532	
chunk0086_54_1	chr18	12998239	12998849	+	0	NA	intron (NM_032142, intron 1 of 44)	intron (NM_032142, intron 1 of 44)	7182	NM_032142	55125	Hs.100914	NM_018069	ENSG00000101639	CEP192	PPP1R62	centrosomal protein 192	protein-coding	0.009836	0.369885	
chunk0152_54_1	chr5	57499520	57499779	+	0	NA	Intergenic	(AAAC)n|Simple_repeat|Simple_repeat	-16840	NM_001017992	345651	Hs.482167	NM_001017992	ENSG00000169067	ACTBL2	ACT	actin beta like 2	protein-coding	0.007722	0.411538	
chunk0040_120_1	chr11	112234284	112234724	+	0	NA	TTS (NM_000317)	TTS (NM_000317)	8139	NM_000317	5805	Hs.503860	NM_000317	ENSG00000150787	PTS	PTPS	6-pyruvoyltetrahydropterin synthase	protein-coding	0.006818	0.324263	
chunk0192_384_1	chr8	68609875	68610563	+	0	NA	intron (NM_052958, intron 7 of 13)	intron (NM_052958, intron 7 of 13)	-278728	NR_038877	286189	Hs.593427	NR_038877	ENSG00000248801	C8orf34-AS1	-	C8orf34 antisense RNA 1	ncRNA	0.005814	0.362845	
chunk0093_288_1	chr19	52123381	52123819	+	0	NA	intron (NM_178523, intron 3 of 3)	AluJb|SINE|Alu	16338	NM_178523	90317	Hs.645225	NM_178523	ENSG00000204611	ZNF616	-	zinc finger protein 616	protein-coding	0.009132	0.464692	
chunk0184_70_1	chr7	112561862	112562605	+	0	NA	Intergenic	Intergenic	-55832	NR_110159	100996249	Hs.561749	NR_110159		LOC100996249	-	uncharacterized LOC100996249	ncRNA	0.005384	0.311828	
chunk0154_165_1	chr5	79564071	79564312	+	0	NA	Intergenic	Intergenic	-48229	NM_001114393	167153	Hs.418198	NM_173797	ENSG00000164329	TENT2	APD4|GLD2|PAPD4|TUT2	terminal nucleotidyltransferase 2	protein-coding	0.016598	0.433884	
chunk0088_453_1	chr18	57131697	57132616	+	0	NA	Intergenic	Intergenic	-14906	NM_001257964	284257	Hs.127882	NM_001257964	ENSG00000228075	BOD1L2	BOD1P|FAM44C	biorientation of chromosomes in cell division 1 like 2	protein-coding	0.002176	0.454348	
chunk0045_428_1	chr12	53426928	53427302	+	0	NA	intron (NM_020547, intron 6 of 10)	L2a|LINE|L2	3260	NM_001164690	269	Hs.659889	NM_020547	ENSG00000135409	AMHR2	AMHR|MISR2|MISRII|MRII	anti-Mullerian hormone receptor type 2	protein-coding	0.008021	0.418667	174(AAAAACACACAGTCCC,-,0.00),175(AAAACACACAGTCCCT,+,0.00)
chunk0050_51_1	chr12	100974571	100975223	+	0	NA	intron (NM_001286616, intron 6 of 26)	intron (NM_001286616, intron 6 of 26)	73251	NM_001286616	121601	Hs.58785	NM_178826	ENSG00000151572	ANO4	TMEM16D	anoctamin 4	protein-coding	0.016871	0.416539	324(TAGCACGCTCTGTCCT,-,0.00),325(AGCACGCTCTGTCCTG,+,0.00)
chunk0082_441_1	chr17	61875367	61875967	+	0	NA	intron (NM_020748, intron 18 of 24)	HAL1|LINE|L1	-12108	NM_032043	83990	Hs.128903	NM_032043	ENSG00000136492	BRIP1	BACH1|FANCJ|OF	BRCA1 interacting protein C-terminal helicase 1	protein-coding	0.005000	0.344426	
chunk0066_56_1	chr15	28269195	28269563	+	0	NA	exon (NM_004667, exon 11 of 93)	exon (NM_004667, exon 11 of 93)	52773	NM_004667	8924	Hs.434890	NM_004667	ENSG00000128731	HERC2	D15F37S1|MRT38|SHEP1|jdf2|p528	HECT and RLD domain containing E3 ubiquitin protein ligase 2	protein-coding	0.019022	0.449864	
chunk0038_247_1	chr11	87203291	87203982	+	0	NA	intron (NM_022918, intron 5 of 14)	L1MC1|LINE|L1	165792	NM_001168724	65084	Hs.188591	NM_022918	ENSG00000166575	TMEM135	PMP52	transmembrane protein 135	protein-coding	0.007236	0.365607	
chunk0110_453_1	chr20	21246211	21246840	+	0	NA	TTS (NM_001163023)	TTS (NM_001163023)	-28236	NR_109956	101929591	Hs.656066	NR_109956	ENSG00000232712	KIZ-AS1	-	KIZ antisense RNA 1	ncRNA	0.006359	0.366667	
chunk0024_358_1	chr10	43903311	43903664	+	0	NA	Intergenic	Intergenic	-5817	NR_033846	283033	Hs.178244	NR_033846		LINC00841	-	long intergenic non-protein coding RNA 841	ncRNA	0.014164	0.485876	
chunk0144_445_1	chr4	141327317	141327516	+	0	NA	intron (NR_121625, intron 1 of 3)	MLT1C|LTR|ERVL-MaLR	5201	NR_121625	100507639	Hs.535010	NR_121625		LINC02432	-	long intergenic non-protein coding RNA 2432	ncRNA	0.000000	0.370000	
chunk0116_285_1	chr21	39821834	39822298	+	0	NA	Intergenic	Intergenic	-45355	NM_006198	5121	Hs.80296	NM_006198	ENSG00000183036	PCP4	PEP-19	Purkinje cell protein 4	protein-coding	0.006466	0.410753	
chunk0101_279_1	chr2	133795492	133795931	+	0	NA	Intergenic	L1MC3|LINE|L1	-227251	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.002278	0.297727	172(CTGGGCACTCTGTTCT,-,0.00),173(TGGGCACTCTGTTCTC,+,0.00)
chunk0027_146_1	chr10	74683644	74684165	+	0	NA	intron (NM_001123, intron 10 of 10)	intron (NM_001123, intron 10 of 10)	-142509	NM_012330	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.013436	0.394636	
chunk0180_411_1	chr7	75950548	75950764	+	0	NA	intron (NM_000941, intron 1 of 15)	intron (NM_000941, intron 1 of 15)	6873	NR_002955	677801	Hs.689708	NR_002955	ENSG00000201643	SNORA14A	ACA14a	small nucleolar RNA, H/ACA box 14A	snoRNA	0.000000	0.382488	
chunk0129_323_1	chr3	124245053	124245519	+	0	NA	intron (NM_003947, intron 3 of 33)	L1MA4|LINE|L1	112357	NR_049798	100847021		NR_049798	ENSG00000266383	MIR5002	-	microRNA 5002	ncRNA	0.004292	0.383298	215(CTGAACATAATGTCCT,-,0.00),216(TGAACATAATGTCCTT,+,0.00)
chunk0204_325_1	chr9	100723732	100723992	+	0	NA	Intergenic	L2c|LINE|L2	145783	NM_001018116	347273	Hs.99004	NM_001018116	ENSG00000170681	CAVIN4	MURC|cavin-4	caveolae associated protein 4	protein-coding	0.007692	0.440613	
chunk0075_324_1	chr16	54639590	54640096	+	0	NA	Intergenic	Intergenic	288935	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.001976	0.364892	
chunk0051_73_1	chr12	113246197	113246781	+	0	NA	intron (NM_001301214, intron 1 of 26)	intron (NM_001301214, intron 1 of 26)	2228	NM_001301214	53373	Hs.524763	NM_017901	ENSG00000186815	TPCN1	TPC1	two pore segment channel 1	protein-coding	0.023973	0.589744	169(CAGGACAAAATGTTTC,-,0.00),170(AGGACAAAATGTTTCC,+,0.00)
chunk0151_266_1	chr5	52491417	52491942	+	0	NA	Intergenic	Intergenic	-296261	NM_015946	53918	Hs.644352	NM_015946	ENSG00000152684	PELO	CGI-17|PRO1770	pelota mRNA surveillance and ribosome rescue factor	protein-coding	0.005714	0.414449	
chunk0166_408_1	chr6	52081503	52082258	+	0	NA	intron (NM_138694, intron 4 of 66)	intron (NM_138694, intron 4 of 66)	5745	NM_170724	5314	Hs.662050	NM_138694	ENSG00000170927	PKHD1	ARPKD|FCYT|FPC|PKD4|TIGM1	PKHD1 ciliary IPT domain containing fibrocystin/polyductin	protein-coding	0.005298	0.371693	
chunk0042_108_1	chr12	3080555	3080912	+	0	NA	intron (NM_001168320, intron 1 of 7)	L1MB2|LINE|L1	3378	NM_001168320	10867	Hs.504517	NM_006675	ENSG00000011105	TSPAN9	NET-5|NET5|PP1057	tetraspanin 9	protein-coding	0.014006	0.444134	
chunk0105_48_1	chr2	182978699	182979165	+	0	NA	intron (NM_205842, intron 14 of 31)	intron (NM_205842, intron 14 of 31)	59926	NM_205842	10787	Hs.603732	NM_013436	ENSG00000061676	NCKAP1	HEM2|NAP1|NAP125|p125Nap1	NCK associated protein 1	protein-coding	0.006438	0.267666	
chunk0099_210_1	chr2	94994752	94995283	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-30638	NM_022438	4118	Hs.80395	NM_002371	ENSG00000172005	MAL	MVP17|VIP17	mal, T cell differentiation protein	protein-coding	0.007533	0.539474	
chunk0116_123_1	chr21	36126965	36127770	+	0	NA	promoter-TSS (NR_040084)	promoter-TSS (NR_040084)	-727	NR_040084	100133286	Hs.728809	NR_040084	ENSG00000230212	LOC100133286	-	uncharacterized LOC100133286	ncRNA	0.013665	0.459057	422(GTGGACATTCAGTCCT,-,0.00),423(TGGACATTCAGTCCTT,+,0.00)
chunk0024_424_1	chr10	46016748	46017327	+	0	NA	intron (NM_001145263, intron 1 of 9)	intron (NM_001145263, intron 1 of 9)	2500	NM_001145262	8031	Hs.643658	NM_005437	ENSG00000266412	NCOA4	ARA70|ELE1|PTC3|RFG	nuclear receptor coactivator 4	protein-coding	0.005181	0.355172	
chunk0156_441_1	chr5	114730531	114730913	+	0	NA	intron (NR_130785, intron 1 of 12)	L2c|LINE|L2	42691	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.000000	0.415144	
chunk0209_3_1	chrX	34920497	34920798	+	0	NA	Intergenic	Intergenic	-22149	NM_152631	170062	Hs.197801	NM_152631	ENSG00000189132	FAM47B	-	family with sequence similarity 47 member B	protein-coding	0.003322	0.337748	
chunk0183_208_1	chr7	106418073	106418694	+	0	NA	Intergenic	L2a|LINE|L2	-133191	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.003221	0.368167	273(CAGAACAGTCTGTGCT,-,0.00),274(AGAACAGTCTGTGCTC,+,0.00)
chunk0082_304_1	chr17	58813709	58813973	+	0	NA	intron (NR_048561, intron 1 of 5)	intron (NR_048561, intron 1 of 5)	57972	NM_014906	22843	Hs.245044	NM_014906	ENSG00000175175	PPM1E	CaMKP-N|POPX1|PP2CH|caMKN	protein phosphatase, Mg2+/Mn2+ dependent 1E	protein-coding	0.000000	0.407547	
chunk0175_295_1	chr7	7811880	7812253	+	0	NA	intron (NM_001302349, intron 3 of 3)	intron (NM_001302349, intron 3 of 3)	-93459	NM_002947	6119	Hs.487540	NM_002947	ENSG00000106399	RPA3	REPA3|RP-A p14	replication protein A3	protein-coding	0.005362	0.368984	280(GAAACATAATGTTCAT,+,0.00)
chunk0118_450_1	chr22	39522559	39523347	+	0	NA	TTS (NM_182810)	TTS (NM_182810)	2389	NM_182810	468	Hs.496487	NM_001675	ENSG00000128272	ATF4	CREB-2|CREB2|TAXREB67|TXREB	activating transcription factor 4	protein-coding	0.020305	0.520913	421(AGGGACAGCCTGGGCC,-,0.00),422(GGGACAGCCTGGGCCT,+,0.00)
chunk0094_78_1	chr2	3575019	3575468	+	0	NA	promoter-TSS (NM_001011)	promoter-TSS (NM_001011)	-20	NM_001011	6201	Hs.534346	NM_001011	ENSG00000171863	RPS7	DBA8|S7|eS7	ribosomal protein S7	protein-coding	0.077951	0.602222	
chunk0111_258_1	chr20	31052062	31052306	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	-205480	NM_001037730	245929	Hs.580793	NM_001037730	ENSG00000215547	DEFB115	DEFB-15	defensin beta 115	protein-coding	0.012295	0.412245	
chunk0073_362_1	chr16	15054620	15055149	+	0	NA	intron (NM_173474, intron 1 of 9)	intron (NM_173474, intron 1 of 9)	1195	NM_001270766	123803	Hs.592045	NM_173474	ENSG00000157045	NTAN1	PNAA|PNAD	N-terminal asparagine amidase	protein-coding	0.017013	0.447170	
chunk0018_161_1	chr1	218847932	218848356	+	0	NA	intron (NR_031644, intron 6 of 6)	Tigger19a|DNA|TcMar-Tigger	325644	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.004717	0.378824	
chunk0057_139_1	chr13	99871410	99871854	+	0	NA	intron (NR_104592, intron 7 of 9)	intron (NR_104592, intron 7 of 9)	85533	NR_120421	101927437	Hs.619936	NR_120421		LOC101927437	-	uncharacterized LOC101927437	ncRNA	0.013514	0.370787	
chunk0104_151_1	chr2	173985406	173985997	+	0	NA	Intergenic	Intergenic	-19999	NM_003111	6670	Hs.531587	NM_003111	ENSG00000172845	SP3	SPR2	Sp3 transcription factor	protein-coding	0.005076	0.388514	
chunk0202_360_1	chr9	80235875	80236104	+	0	NA	Intergenic	Intergenic	260966	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.004367	0.269565	
chunk0155_400_1	chr5	98927186	98927502	+	0	NA	promoter-TSS (NM_001270)	promoter-TSS (NM_001270)	-810	NM_001270	1105	Hs.643465	NM_001270	ENSG00000153922	CHD1	CHD-1|PILBOS	chromodomain helicase DNA binding protein 1	protein-coding	0.022152	0.447950	
chunk0197_102_1	chr8	119721833	119722370	+	0	NA	Intergenic	MIR3|SINE|MIR	-83235	NM_001040092	5168	Hs.190977	NM_006209	ENSG00000136960	ENPP2	ATX|ATX-X|AUTOTAXIN|LysoPLD|NPP2|PD-IALPHA|PDNP2	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding	0.003724	0.388476	
chunk0160_141_1	chr5	151413706	151415102	+	0	NA	Intergenic	L2c|LINE|L2	-22588	NM_001308151	206358	Hs.269004	NM_078483	ENSG00000123643	SLC36A1	Dct1|LYAAT1|PAT1|TRAMD3	solute carrier family 36 member 1	protein-coding	0.007163	0.413028	1048(AAGAACACAATGTCCC,-,0.00),1049(AGAACACAATGTCCCT,+,0.00)
chunk0108_231_1	chr2	233607925	233608188	+	0	NA	Intergenic	L1M5|LINE|L1	-9589	NM_019076	54576	Hs.554822	NM_019076	ENSG00000242366	UGT1A8	GNT1|UDPGT|UDPGT 1-8|UGT-1A|UGT-1H|UGT1|UGT1-01|UGT1-08|UGT1.1|UGT1.8|UGT1A|UGT1A1|UGT1A8S|UGT1H|hUG-BR1	UDP glucuronosyltransferase family 1 member A8	protein-coding	0.011407	0.424242	
chunk0117_267_1	chr22	23938620	23939258	+	0	NA	intron (NR_003082, intron 4 of 4)	MER34-int|LTR|ERV1	22242	NM_001080843	653689	Hs.654462	NM_001080843	ENSG00000133433	GSTT2B	GSTT2P	glutathione S-transferase theta 2B (gene/pseudogene)	protein-coding	0.006270	0.449139	354(AGGCACTATTTGTCCC,-,0.00)
chunk0156_304_1	chr5	110558512	110558711	+	0	NA	intron (NM_001039763, intron 11 of 13)	L1PA13|LINE|L1	-44696	NR_031644	100302159		NR_031644	ENSG00000221436	MIR548F3	MIR548F-3|MIRN548F3|hsa-mir-548f-3	microRNA 548f-3	ncRNA	0.000000	0.520000	
chunk0150_108_1	chr5	32814619	32814944	+	0	NA	Intergenic	Intergenic	103449	NM_001204375	4883	Hs.13528	NM_000908	ENSG00000113389	NPR3	ANP-C|ANPR-C|ANPRC|C5orf23|GUCY2B|NPR-C|NPRC	natriuretic peptide receptor 3	protein-coding	0.000000	0.358896	
chunk0199_251_1	chr9	5832706	5832905	+	0	NA	exon (NM_024896, exon 1 of 15)	exon (NM_024896, exon 1 of 15)	276	NM_024896	79956	Hs.591078	NM_024896	ENSG00000099219	ERMP1	FXNA|KIAA1815|bA207C16.3	endoplasmic reticulum metallopeptidase 1	protein-coding	0.155779	0.765000	
chunk0200_269_1	chr9	22068548	22068904	+	0	NA	intron (NR_003529, intron 12 of 18)	intron (NR_003529, intron 12 of 18)	-59413	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.008427	0.386555	
chunk0153_261_1	chr5	72790015	72790702	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-26233	NM_002270	3842	Hs.482497	NM_002270	ENSG00000083312	TNPO1	IPO2|KPNB2|MIP|MIP1|TRN	transportin 1	protein-coding	0.002911	0.383721	
chunk0048_285_1	chr12	82687600	82687972	+	0	NA	intron (NM_152588, intron 1 of 11)	CpG	631	NM_152588	160335	Hs.577775	NM_152588	ENSG00000179104	TMTC2	IBDBP1	transmembrane O-mannosyltransferase targeting cadherins 2	protein-coding	0.059140	0.560322	
chunk0117_345_1	chr21	44012251	44012487	+	0	NA	promoter-TSS (NM_003274)	promoter-TSS (NM_003274)	44	NM_003274	7109	Hs.126221	NM_003274	ENSG00000160218	TRAPPC10	EHOC-1|EHOC1|GT334|TMEM1|TRS130|TRS30	trafficking protein particle complex 10	protein-coding	0.169492	0.818565	
chunk0149_238_1	chr5	23491980	23492521	+	0	NA	Intergenic	L1PA15|LINE|L1	-15359	NM_020227	56979	Hs.283096	NM_020227	ENSG00000164256	PRDM9	KMT8B|MEISETZ|MSBP3|PFM6|ZNF899	PR/SET domain 9	protein-coding	0.009242	0.551661	
chunk0170_111_1	chr6	110653926	110654656	+	0	NA	intron (NM_015076, intron 4 of 12)	intron (NM_015076, intron 4 of 12)	-160330	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.002740	0.350205	580(AGGTACATACTGTGTT,-,0.00),581(GGTACATACTGTGTTT,+,0.00)
chunk0092_193_1	chr19	30578317	30578540	+	0	NA	Intergenic	Intergenic	206035	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.022422	0.522321	
chunk0080_450_1	chr17	36967203	36967478	+	0	NA	intron (NM_012138, intron 4 of 11)	HAL1|LINE|L1	18465	NM_012138	26574	Hs.195740	NM_012138	ENSG00000275700	AATF	BFR2|CHE-1|CHE1|DED	apoptosis antagonizing transcription factor	protein-coding	0.000000	0.311594	
chunk0152_120_1	chr5	58760777	58761271	+	0	NA	intron (NM_138453, intron 3 of 4)	intron (NM_138453, intron 3 of 4)	177912	NM_138453	115827	Hs.4290	NM_138453	ENSG00000152932	RAB3C	-	RAB3C, member RAS oncogene family	protein-coding	0.004049	0.349495	
chunk0180_161_1	chr7	64913270	64913857	+	0	NA	intron (NM_021148, intron 1 of 3)	intron (NM_021148, intron 1 of 3)	10321	NM_021148	10793	Hs.520889	NM_021148	ENSG00000198039	ZNF273	HZF9	zinc finger protein 273	protein-coding	0.015332	0.389456	
chunk0072_141_1	chr15	92696070	92696734	+	0	NA	Intergenic	MER112|DNA|hAT-Charlie	-40601	NM_207446	400451	Hs.27373	NM_207446	ENSG00000185442	FAM174B	-	family with sequence similarity 174 member B	protein-coding	0.010542	0.410526	
chunk0085_158_1	chr18	3599469	3599683	+	0	NA	intron (NM_001003809, intron 4 of 9)	intron (NM_001003809, intron 4 of 9)	-4161	NR_119377	84777	Hs.659053	NM_032691		DLGAP1-AS2	-	DLGAP1 antisense RNA 2	ncRNA	0.018692	0.493023	135(AAGGACAGAGAGTTTT,-,0.00),136(AGGACAGAGAGTTTTT,+,0.00)
chunk0120_253_1	chr3	8932422	8932828	+	0	NA	intron (NM_020165, intron 7 of 12)	L1ME1|LINE|L1	30850	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.002463	0.380835	
chunk0169_129_1	chr6	101092230	101092485	+	0	NA	Intergenic	L1M2|LINE|L1	-210985	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.000000	0.527344	
chunk0051_315_1	chr12	119676860	119677470	+	0	NA	intron (NM_006253, intron 5 of 6)	intron (NM_006253, intron 5 of 6)	9209	NM_006253	5564	Hs.741184	NM_006253	ENSG00000111725	PRKAB1	AMPK|HAMPKb	protein kinase AMP-activated non-catalytic subunit beta 1	protein-coding	0.014754	0.469722	280(AAGAACAGCCAGTTCT,-,0.00),281(AGAACAGCCAGTTCTG,+,0.00)
chunk0043_271_1	chr12	20902935	20903613	+	0	NA	intron (NM_019844, intron 15 of 15)	L1MC2|LINE|L1	92570	NM_019844	28234	Hs.504966	NM_019844	ENSG00000111700	SLCO1B3	HBLRR|LST-2|LST-3TM13|LST3|OATP-8|OATP1B3|OATP8|SLC21A8	solute carrier organic anion transporter family member 1B3	protein-coding	0.004425	0.412371	
chunk0106_66_1	chr2	196884226	196885208	+	0	NA	intron (NM_024989, intron 12 of 26)	intron (NM_024989, intron 12 of 26)	42013	NM_024989	80055	Hs.229988	NM_024989	ENSG00000197121	PGAP1	Bst1|ISPD3024|MRT42|SPG67	post-GPI attachment to proteins 1	protein-coding	0.003055	0.317396	664(AAGAACTTGCTGACCT,-,0.00)
chunk0095_114_1	chr2	15616326	15616857	+	0	NA	intron (NM_004939, intron 14 of 25)	MIRb|SINE|MIR	24970	NM_004939	1653	Hs.440599	NM_004939	ENSG00000079785	DDX1	DBP-RB|UKVH5d	DEAD-box helicase 1	protein-coding	0.007533	0.342105	
chunk0014_224_1	chr1	179707654	179707966	+	0	NA	Intergenic	Intergenic	-35353	NM_173509	148753	Hs.400696	NM_173509	ENSG00000143340	FAM163A	C1orf76|NDSP	family with sequence similarity 163 member A	protein-coding	0.006410	0.380192	
chunk0138_216_1	chr4	38897914	38898589	+	0	NA	intron (NR_033290, intron 2 of 12)	intron (NR_033290, intron 2 of 12)	30219	NR_030300	693159		NR_030300	ENSG00000207944	MIR574	MIR574-3p|MIRN574|hsa-mir-574|mir-574	microRNA 574	ncRNA	0.010370	0.350592	
chunk0024_196_1	chr10	36254253	36254662	+	0	NA	Intergenic	MIR|SINE|MIR	476155	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.007335	0.370732	
chunk0026_10_1	chr10	60481002	60481428	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	-91339	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.009390	0.419204	
chunk0192_252_1	chr8	65763650	65764318	+	0	NA	intron (NM_002603, intron 3 of 12)	intron (NM_002603, intron 3 of 12)	25110	NM_002603	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.008982	0.348281	293(CAGAACATTCTGTTCT,-,0.00),294(AGAACATTCTGTTCTT,+,0.00)
chunk0052_434_1	chr12	131952543	131952756	+	0	NA	intron (NM_015409, intron 1 of 52)	AluJo|SINE|Alu	2729	NM_015409	57634	Hs.723478	NM_015409	ENSG00000183495	EP400	CAGH32|P400|TNRC12	E1A binding protein p400	protein-coding	0.014085	0.476636	
chunk0127_117_1	chr3	91472096	91472583	+	0	NA	Intergenic	MIRb|SINE|MIR	2364815	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.008214	0.342213	
chunk0019_30_1	chr1	223765865	223766449	+	0	NA	intron (NM_001748, intron 15 of 20)	intron (NM_001748, intron 15 of 20)	53740	NM_001748	824	Hs.350899	NM_001748	ENSG00000162909	CAPN2	CANP2|CANPL2|CANPml|mCANP	calpain 2	protein-coding	0.010274	0.432479	
chunk0031_387_1	chr10	131022434	131022633	+	0	NA	Intergenic	Intergenic	-59865	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.030151	0.585000	
chunk0132_309_1	chr3	160446127	160446798	+	0	NA	intron (NM_173084, intron 2 of 2)	L1M6|LINE|L1	3376	NM_173084	286827	Hs.212957	NM_173084	ENSG00000213186	TRIM59	IFT80L|MRF1|RNF104|TRIM57|TSBF1	tripartite motif containing 59	protein-coding	0.010432	0.382440	
chunk0199_6_1	chr9	468639	469179	+	0	NA	Intergenic	Intergenic	-1385	NM_001256876	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.009259	0.402957	251(ATGAACAAACTGTTCT,-,0.00),252(TGAACAAACTGTTCTG,+,0.00)
chunk0185_330_1	chr7	131927841	131928223	+	0	NA	intron (NR_110836, intron 2 of 5)	(AC)n|Simple_repeat|Simple_repeat	17812	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.015707	0.522193	
chunk0028_211_1	chr10	89374117	89374651	+	0	NA	Intergenic	Intergenic	-3672	NM_001010987	439996	Hs.500491	NM_001010987	ENSG00000204010	IFIT1B	IFIT1L|bA149I23.6	interferon induced protein with tetratricopeptide repeats 1B	protein-coding	0.005618	0.405607	311(AAGGACACACTGGGCC,-,0.00)
chunk0134_191_1	chr3	178306656	178306936	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-112405	NR_046786	100874330	Hs.201902	NR_046786	ENSG00000223941	LINC01014	KCNMB2-IT1	long intergenic non-protein coding RNA 1014	ncRNA	0.000000	0.334520	
chunk0204_11_1	chr9	91711621	91711895	+	0	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-75413	NR_037489	100500902		NR_037489	ENSG00000283351	MIR3910-2	mir-3910-2	microRNA 3910-2	ncRNA	0.007299	0.490909	
chunk0208_373_1	chrX	27580211	27580977	+	0	NA	Intergenic	Intergenic	-117253	NR_002784									0.006527	0.367666	64(CAGGACTATCTGTGCC,-,0.00),65(AGGACTATCTGTGCCC,+,0.00),426(TAGAACATCATGTCTT,-,0.00),427(AGAACATCATGTCTTT,+,0.00)
chunk0132_228_1	chr3	158211994	158212325	+	0	NA	intron (NM_016625, intron 4 of 9)	L2c|LINE|L2	102107	NM_001271834	51319	Hs.591283	NM_016625	ENSG00000174891	RSRC1	BM-011|MRT70|SFRS21|SRrp53	arginine and serine rich coiled-coil 1	protein-coding	0.006042	0.298193	
chunk0033_324_1	chr11	21368508	21369205	+	0	NA	intron (NM_006157, intron 14 of 19)	MIR|SINE|MIR	699305	NM_006157	4745	Hs.657172	NM_006157	ENSG00000165973	NELL1	IDH3GL|NRP1	neural EGFL like 1	protein-coding	0.010043	0.366762	350(ATAACACTATGTGCCG,+,0.00)
chunk0045_282_1	chr12	50006995	50007228	+	0	NA	intron (NM_013277, intron 4 of 18)	intron (NM_013277, intron 4 of 18)	18413	NM_013277	29127	Hs.505469	NM_013277	ENSG00000161800	RACGAP1	CYK4|HsCYK-4|ID-GAP|MgcRacGAP	Rac GTPase activating protein 1	protein-coding	0.004292	0.337607	
chunk0045_422_1	chr12	53242439	53242702	+	0	NA	Intergenic	Intergenic	-9016	NM_001170790	84975	Hs.654660	NM_032889	ENSG00000182544	MFSD5	hsMOT2	major facilitator superfamily domain containing 5	protein-coding	0.003802	0.575758	
chunk0125_436_1	chr3	72723007	72723237	+	0	NA	Intergenic	Intergenic	125325	NM_018130	55164	Hs.606584	NM_018130	ENSG00000144736	SHQ1	GRIM-1|Shq1p	SHQ1, H/ACA ribonucleoprotein assembly factor	protein-coding	0.017391	0.506494	
chunk0093_282_1	chr19	51960265	51960945	+	0	NA	intron (NR_103847, intron 1 of 2)	LTR5B|LTR|ERVK	11471	NR_103847	101669766	Hs.637744	NR_103847	ENSG00000269235	ZNF350-AS1	HCCAT3|uc002pyc	ZNF350 antisense RNA 1	ncRNA	0.013235	0.493392	
chunk0048_36_1	chr12	77847740	77848213	+	0	NA	intron (NM_014903, intron 1 of 38)	intron (NM_014903, intron 1 of 38)	16687	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.006342	0.409283	
chunk0174_336_1	chr6	163816060	163816337	+	0	NA	Intergenic	Intergenic	401555	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.003610	0.424460	
chunk0097_51_1	chr2	43441228	43441529	+	0	NA	intron (NM_001083953, intron 26 of 37)	L4_A_Mam|LINE|RTE-X	154596	NM_001271643	63892	Hs.369592	NM_022065	ENSG00000115970	THADA	ARMC13|GITA	THADA armadillo repeat containing	protein-coding	0.003322	0.377483	
chunk0147_193_1	chr4	177570700	177570927	+	0	NA	Intergenic	Intergenic	-128310	NM_000027	175	Hs.207776	NM_000027	ENSG00000038002	AGA	AGU|ASRG|GA	aspartylglucosaminidase	protein-coding	0.013216	0.342105	
chunk0069_331_1	chr15	66261048	66261424	+	0	NA	Intergenic	L2c|LINE|L2	-7499	NM_032445	84465	Hs.712886	NM_032445	ENSG00000157890	MEGF11	-	multiple EGF like domains 11	protein-coding	0.007979	0.442971	
chunk0035_431_1	chr11	57311429	57311866	+	0	NA	intron (NM_033396, intron 5 of 11)	intron (NM_033396, intron 5 of 11)	13292	NM_033396	85456	Hs.530730	NM_033396	ENSG00000149115	TNKS1BP1	TAB182	tankyrase 1 binding protein 1	protein-coding	0.041190	0.657534	
chunk0129_41_1	chr3	117403532	117403754	+	0	NA	Intergenic	Intergenic	482212	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.004505	0.354260	
chunk0028_174_1	chr10	87854052	87854408	+	0	NA	Intergenic	MLT1H-int|LTR|ERVL-MaLR	9207	NM_001126049	100144748	Hs.559820	NM_001126049	ENSG00000227268	KLLN	CWS4|KILLIN	killin, p53 regulated DNA replication inhibitor	protein-coding	0.002809	0.392157	
chunk0017_373_1	chr1	212088538	212088859	+	0	NA	intron (NM_016448, intron 13 of 14)	L2c|LINE|L2	11085	NR_036068	100422947		NR_036068	ENSG00000264358	MIR3122	mir-3122	microRNA 3122	ncRNA	0.012461	0.462733	
chunk0087_188_1	chr18	35608251	35608777	+	0	NA	Intergenic	Intergenic	16777	NR_039771	100616257		NR_039771	ENSG00000283514	MIR3975	-	microRNA 3975	ncRNA	0.001901	0.322581	
chunk0212_384_1	chrX	150339733	150340610	+	0	NA	Intergenic	Intergenic	-23107	NM_001177465	10046	Hs.20136	NM_005491	ENSG00000013619	MAMLD1	CG1|CXorf6|F18|HYSP2	mastermind like domain containing 1	protein-coding	0.009122	0.503417	
chunk0189_178_1	chr8	23558457	23558795	+	0	NA	intron (NM_016612, intron 1 of 3)	intron (NM_016612, intron 1 of 3)	29776	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.014793	0.542773	
chunk0012_66_1	chr1	155677983	155678432	+	0	NA	TTS (NR_132762)	TTS (NR_132762)	1048	NR_132762	106633810		NR_132762		SCARNA26A	-	small Cajal body-specific RNA 26A	ncRNA	0.011136	0.353333	
chunk0043_114_1	chr12	15273968	15275131	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-47708	NM_030667	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.006879	0.397766	907(AAGTACAACCTGTACC,-,0.00),908(AGTACAACCTGTACCA,+,0.00)
chunk0119_383_1	chr22	48254463	48255017	+	0	NA	Intergenic	Intergenic	-19624	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.021661	0.488288	127(GGTACTCGGTGTGCAT,+,0.00)
chunk0199_300_1	chr9	6968237	6968654	+	0	NA	intron (NR_130707, intron 8 of 14)	intron (NR_130707, intron 8 of 14)	210804	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.004796	0.377990	206(AGGAACTTTGTGTTCT,-,0.00),207(GGAACTTTGTGTTCTG,+,0.00)
chunk0046_244_1	chr12	60438034	60438256	+	0	NA	Intergenic	LTR1E|LTR|ERV1	748808	NR_073055	9194	Hs.88156	NM_004731	ENSG00000118596	SLC16A7	MCT2	solute carrier family 16 member 7	protein-coding	0.018018	0.538117	
chunk0203_397_1	chr9	90573233	90573684	+	0	NA	intron (NR_034157, intron 1 of 5)	HAL1ME|LINE|L1	9288	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.008869	0.327434	
chunk0021_1_1	chr10	128402	128852	+	0	NA	Intergenic	Intergenic	-5838	NM_006624	10771	Hs.292265	NM_006624	ENSG00000015171	ZMYND11	BRAM1|BS69|MRD30	zinc finger MYND-type containing 11	protein-coding	0.006667	0.257206	
chunk0134_44_1	chr3	175777941	175778704	+	0	NA	intron (NM_207015, intron 13 of 13)	intron (NM_207015, intron 13 of 13)	-1989	NR_046714	100874245	Hs.614827	NR_046714		NAALADL2-AS1	-	NAALADL2 antisense RNA 1	ncRNA	0.005242	0.373037	
chunk0075_452_1	chr16	58221948	58222247	+	0	NA	Intergenic	L1ME3G|LINE|L1	-24219	NM_001896	1459	Hs.82201	NM_001896	ENSG00000070770	CSNK2A2	CK2A2|CK2alpha'|CSNK2A1	casein kinase 2 alpha 2	protein-coding	0.003344	0.390000	
chunk0157_321_1	chr5	121987693	121988006	+	0	NA	intron (NM_152546, intron 3 of 7)	intron (NM_152546, intron 3 of 7)	25888	NM_152546	153443	Hs.107622	NM_152546	ENSG00000151304	SRFBP1	BUD22|P49|Rlb1|STRAP|p49/STRAP	serum response factor binding protein 1	protein-coding	0.003195	0.356688	
chunk0077_340_1	chr16	82924630	82925128	+	0	NA	intron (NM_001220490, intron 2 of 12)	intron (NM_001220490, intron 2 of 12)	65419	NR_110937	101928417	Hs.569538	NR_110937	ENSG00000260832	LOC101928417	-	uncharacterized LOC101928417	ncRNA	0.012048	0.394790	
chunk0098_45_1	chr2	66472154	66472805	+	0	NA	intron (NM_002398, intron 7 of 12)	L2c|LINE|L2	-32149	NR_046625	100873998	Hs.734698	NR_046625	ENSG00000230749	MEIS1-AS2	MEIS1-AS1	MEIS1 antisense RNA 2	ncRNA	0.007680	0.420245	
chunk0083_131_1	chr17	65441030	65441667	+	0	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	-16193	NR_131984	105827617		NR_131984	ENSG00000263520	LINC02563	CRAT40	long intergenic non-protein coding RNA 2563	ncRNA	0.003140	0.457680	
chunk0169_50_1	chr6	97952230	97952602	+	0	NA	Intergenic	L1MC1|LINE|L1	-72115	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.000000	0.386059	211(GGGACATTCTCTTCTT,+,0.00)
chunk0116_97_1	chr21	35115042	35115241	+	0	NA	Intergenic	Intergenic	-65843	NM_001754	861	Hs.149261	NM_001754	ENSG00000159216	RUNX1	AML1|AML1-EVI-1|AMLCR1|CBF2alpha|CBFA2|EVI-1|PEBP2aB|PEBP2alpha	RUNX family transcription factor 1	protein-coding	0.005025	0.350000	
chunk0071_436_1	chr15	89910827	89911245	+	0	NA	intron (NM_001199058, intron 1 of 9)	MIRc|SINE|MIR	1651	NM_001282380	348110	Hs.6734	NM_182616	ENSG00000242498	ARPIN	C15orf38	actin related protein 2/3 complex inhibitor	protein-coding	0.007177	0.482100	
chunk0181_190_1	chr7	83420869	83421413	+	0	NA	intron (NM_001178129, intron 4 of 16)	intron (NM_001178129, intron 4 of 16)	220290	NM_001178129	9723	Hs.440730	NM_012431	ENSG00000170381	SEMA3E	M-SEMAH|M-SemaK|SEMAH|coll-5	semaphorin 3E	protein-coding	0.000000	0.280734	
chunk0035_368_1	chr11	49196253	49196551	+	0	NA	intron (NM_001193473, intron 2 of 16)	L1M5|LINE|L1	12268	NM_001193473	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.003356	0.257525	
chunk0130_351_1	chr3	138764602	138765110	+	0	NA	Intergenic	L2c|LINE|L2	-5497	NM_006219	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.005906	0.426326	300(AAGCTCACTGTGTACT,-,0.00),301(AGCTCACTGTGTACTC,+,0.00)
chunk0134_227_1	chr3	178846103	178846428	+	0	NA	intron (NR_126561, intron 2 of 5)	intron (NR_126561, intron 2 of 5)	14140	NR_126560	104797538	Hs.478363	NR_126560		KCNMB2-AS1	-	KCNMB2 antisense RNA 1	ncRNA	0.006154	0.374233	
chunk0048_425_1	chr12	88412800	88413014	+	0	NA	Intergenic	Intergenic	167566	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.000000	0.334884	
chunk0050_231_1	chr12	105003532	105004108	+	0	NA	Intergenic	MER57D|LTR|ERV1	17500	NM_152318	121053	Hs.295563	NM_152318	ENSG00000151131	C12orf45	-	chromosome 12 open reading frame 45	protein-coding	0.006944	0.383016	205(AGGTTCAGAGTGTTCC,-,0.00),206(GGTTCAGAGTGTTCCA,+,0.00)
chunk0019_426_1	chr1	230861859	230862409	+	0	NA	intron (NM_001136494, intron 3 of 5)	intron (NM_001136494, intron 3 of 5)	-6098	NM_001136495	84886	Hs.520494	NM_032800	ENSG00000119280	C1orf198	-	chromosome 1 open reading frame 198	protein-coding	0.012727	0.460980	165(CAGGACAGAAAGTCCC,-,0.00),166(AGGACAGAAAGTCCCA,+,0.00),247(TGGAACACGTTGTTCC,-,0.00),248(GGAACACGTTGTTCCT,+,0.00)
chunk0170_274_1	chr6	114159163	114160302	+	0	NA	intron (NR_125845, intron 6 of 9)	intron (NR_125845, intron 6 of 9)	-96855	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.002634	0.339474	
chunk0167_249_1	chr6	68115192	68115833	+	0	NA	Intergenic	Intergenic	60161	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.001560	0.299065	
chunk0047_252_1	chr12	72382464	72382910	+	0	NA	intron (NM_013381, intron 3 of 18)	intron (NM_013381, intron 3 of 18)	-109178	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.000000	0.369128	
chunk0008_108_1	chr1	91431771	91432005	+	0	NA	Intergenic	L2c|LINE|L2	-27019	NM_001017975	164045	Hs.454818	NM_001017975	ENSG00000162669	HFM1	MER3|POF9|SEC63D1|Si-11|Si-11-6|helicase	helicase for meiosis 1	protein-coding	0.008547	0.365957	
chunk0160_49_1	chr5	149600877	149601432	+	0	NA	exon (NM_001001669, exon 3 of 13)	exon (NM_001001669, exon 3 of 13)	19582	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.014414	0.476619	
chunk0038_313_1	chr11	91382787	91383314	+	0	NA	Intergenic	Intergenic	-513848	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.005693	0.373106	328(GGGAACATTCAGTACT,-,0.00),329(GGAACATTCAGTACTT,+,0.00)
chunk0067_310_1	chr15	47857634	47858354	+	0	NA	Intergenic	MIRb|SINE|MIR	-11758	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.004167	0.417476	
chunk0077_222_1	chr16	80204815	80205101	+	0	NA	intron (NR_120307, intron 2 of 5)	intron (NR_120307, intron 2 of 5)	-335776	NM_001305017	83657	Hs.98849	NM_130897	ENSG00000168589	DYNLRB2	DNCL2B|DNLC2B|ROBLD2	dynein light chain roadblock-type 2	protein-coding	0.006993	0.477352	
chunk0210_321_1	chrX	92754450	92754742	+	0	NA	Intergenic	L1PA13|LINE|L1	70307	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.006849	0.351536	
chunk0175_1_1	chr7	56323	56565	+	0	NA	Intergenic	Intergenic	-93274	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.024793	0.559671	77(GAGTACAGGCAGTACC,-,0.00),78(AGTACAGGCAGTACCC,+,0.00)
chunk0158_37_1	chr5	125609670	125610394	+	0	NA	Intergenic	Intergenic	116771	NR_109887	101927460	Hs.407582	NR_109887	ENSG00000260192	LINC02240	-	long intergenic non-protein coding RNA 2240	ncRNA	0.008287	0.348966	
chunk0154_113_1	chr5	78717991	78718385	+	0	NA	Intergenic	Intergenic	-69363	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.012690	0.458228	
chunk0005_416_1	chr1	62691345	62691598	+	0	NA	Intergenic	Intergenic	-3103	NM_001272001	85440	Hs.744927	NM_033407	ENSG00000116641	DOCK7	EIEE23|ZIR2	dedicator of cytokinesis 7	protein-coding	0.007905	0.389764	
chunk0111_384_1	chr20	34040299	34040670	+	0	NA	intron (NM_016732, intron 2 of 9)	intron (NM_016732, intron 2 of 9)	-8635	NR_039911	100616434		NR_039911	ENSG00000264616	MIR4755	mir-4755	microRNA 4755	ncRNA	0.018868	0.462366	
chunk0207_161_1	chr9	130102380	130102872	+	0	NA	intron (NM_001287346, intron 12 of 16)	intron (NM_001287346, intron 12 of 16)	48920	NM_020960	57720	Hs.512461	NM_020960	ENSG00000148358	GPR107	GCDRP|LUSTR1|bA138E2.2	G protein-coupled receptor 107	protein-coding	0.010163	0.456389	323(GGGAACATTCTGTCTC,-,0.00),324(GGAACATTCTGTCTCT,+,0.00)
chunk0187_269_1	chr7	155224261	155224584	+	0	NA	Intergenic	Intergenic	-73354	NM_198337	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.018576	0.438272	
chunk0163_378_1	chr6	16200325	16200532	+	0	NA	Intergenic	Intergenic	-38152	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.028986	0.533654	
chunk0062_274_1	chr14	72061765	72062339	+	0	NA	intron (NM_001204418, intron 2 of 16)	L2a|LINE|L2	128983	NM_001204421	9628	Hs.509872	NM_004296	ENSG00000182732	RGS6	GAP|HA117|S914	regulator of G protein signaling 6	protein-coding	0.001742	0.412174	
chunk0131_91_1	chr3	143586705	143586904	+	0	NA	intron (NM_173653, intron 6 of 15)	intron (NM_173653, intron 6 of 15)	244558	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.000000	0.445000	
chunk0031_34_1	chr10	122063185	122063643	+	0	NA	intron (NM_206861, intron 3 of 19)	intron (NM_206861, intron 3 of 19)	-49625	NM_001291879	10579	Hs.501252	NM_006997	ENSG00000138162	TACC2	AZU-1|ECTACC	transforming acidic coiled-coil containing protein 2	protein-coding	0.017467	0.494553	
chunk0009_43_1	chr1	100452665	100453124	+	0	NA	intron (NM_003672, intron 7 of 15)	intron (NM_003672, intron 7 of 15)	-85278	NM_022049	54112	Hs.170053	NM_022049	ENSG00000181656	GPR88	COCPMR|STRG	G protein-coupled receptor 88	protein-coding	0.002179	0.306522	
chunk0113_327_1	chr20	58550526	58551050	+	0	NA	intron (NR_034147, intron 6 of 6)	intron (NR_034147, intron 6 of 6)	35409	NR_034147	149773	Hs.685214	NR_034147	ENSG00000231290	APCDD1L-DT	APCDD1L-AS1	APCDD1L divergent transcript	ncRNA	0.020992	0.476190	
chunk0144_143_1	chr4	129849832	129850491	+	0	NA	Intergenic	L1PREC2|LINE|L1	-78683	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.006070	0.378788	
chunk0002_285_1	chr1	22717511	22717934	+	0	NA	intron (NM_001309192, intron 1 of 13)	intron (NM_001309192, intron 1 of 13)	-1795	NR_039832	100616391		NR_039832	ENSG00000265422	MIR4684	-	microRNA 4684	ncRNA	0.014184	0.509434	
chunk0076_280_1	chr16	69598211	69598760	+	0	NA	intron (NM_138713, intron 2 of 14)	intron (NM_138713, intron 2 of 14)	32519	NM_006599	10725	Hs.371987	NM_006599	ENSG00000102908	NFAT5	NF-AT5|NFATL1|NFATZ|OREBP|TONEBP	nuclear factor of activated T cells 5	protein-coding	0.010929	0.398182	
chunk0110_155_1	chr20	13857394	13857674	+	0	NA	intron (NM_001271539, intron 16 of 17)	intron (NM_001271539, intron 16 of 17)	72508	NM_024120	79133	Hs.472165	NM_024120	ENSG00000101247	NDUFAF5	C20orf7|MC1DN16|bA526K24.2|dJ842G6.1	NADH:ubiquinone oxidoreductase complex assembly factor 5	protein-coding	0.007143	0.519573	
chunk0132_340_1	chr3	161272481	161272863	+	0	NA	Intergenic	Intergenic	51361	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.002618	0.349869	
chunk0024_284_1	chr10	42067631	42067831	+	0	NA	Intergenic	Intergenic	300314	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.060000	0.368159	
chunk0178_298_1	chr7	37671313	37672152	+	0	NA	Intergenic	L2b|LINE|L2	-68662	NM_181791	353345	Hs.563492	NM_181791	ENSG00000187037	GPR141	PGR13	G protein-coupled receptor 141	protein-coding	0.007151	0.359524	
chunk0105_22_1	chr2	182062504	182063114	+	0	NA	intron (NM_001080545, intron 3 of 4)	intron (NM_001080545, intron 3 of 4)	76985	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.004918	0.327332	277(TTGTACATTATGTTCT,-,0.00),278(TGTACATTATGTTCTT,+,0.00)
chunk0030_310_1	chr10	117796308	117796791	+	0	NA	Intergenic	Intergenic	250054	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.024845	0.458678	
chunk0048_97_1	chr12	79326702	79326956	+	0	NA	intron (NM_001291901, intron 7 of 9)	intron (NM_001291901, intron 7 of 9)	-92428	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.000000	0.356863	
chunk0011_193_1	chr1	149919124	149919596	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-1478	NM_014849	9900	Hs.516153	NM_014849	ENSG00000159164	SV2A	SV2	synaptic vesicle glycoprotein 2A	protein-coding	0.004237	0.391121	
chunk0116_425_1	chr21	42844497	42845231	+	0	NA	intron (NM_033661, intron 11 of 11)	LTR41|LTR|ERVL	34411	NM_001260477	10785	Hs.248815	NM_018669	ENSG00000160193	WDR4	GAMOS6|MIGSB|TRM82|TRMT82	WD repeat domain 4	protein-coding	0.025886	0.591837	
chunk0188_67_1	chr8	8333546	8333958	+	0	NA	intron (NM_001080826, intron 3 of 4)	intron (NM_001080826, intron 3 of 4)	48082	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.007282	0.469734	
chunk0002_123_1	chr1	16248370	16249246	+	0	NA	3' UTR (NM_018994, exon 10 of 10)	3' UTR (NM_018994, exon 10 of 10)	-11644	NM_030907	79363	Hs.546430	NM_030907	ENSG00000132881	CPLANE2	C1orf89|RSG1	ciliogenesis and planar polarity effector 2	protein-coding	0.007991	0.440137	
chunk0017_81_1	chr1	205702933	205703504	+	0	NA	Intergenic	Intergenic	-22716	NM_033102	85414	Hs.278695	NM_033102	ENSG00000158715	SLC45A3	IPCA-2|IPCA-6|IPCA-8|IPCA6|PCANAP2|PCANAP6|PCANAP8|PRST	solute carrier family 45 member 3	protein-coding	0.003503	0.430070	
chunk0151_205_1	chr5	50734972	50735237	+	0	NA	intron (NM_024615, intron 2 of 25)	intron (NM_024615, intron 2 of 25)	68166	NM_024615	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.003774	0.319549	
chunk0108_51_1	chr2	226995689	226996126	+	0	NA	3' UTR (NM_001167608, exon 9 of 9)	3' UTR (NM_001167608, exon 9 of 9)	159952	NM_001167608	84236	Hs.471514	NM_032276	ENSG00000144468	RHBDD1	RHBDL4|RRP4	rhomboid domain containing 1	protein-coding	0.036613	0.575342	
chunk0079_148_1	chr17	13181561	13182090	+	0	NA	Intergenic	LTR54B|LTR|ERV1	-163761	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.003781	0.369811	181(CAGAACAGCCAGTTTT,-,0.00),182(AGAACAGCCAGTTTTG,+,0.00)
chunk0045_288_1	chr12	50187990	50188790	+	0	NA	intron (NM_001113546, intron 9 of 10)	intron (NM_001113546, intron 9 of 10)	13143	NM_001243775	51474	Hs.525419	NM_016357	ENSG00000050405	LIMA1	EPLIN|LDLCQ8|SREBP3	LIM domain and actin binding 1	protein-coding	0.006250	0.443196	
chunk0128_301_1	chr3	111428210	111428686	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	-113631	NM_198196	10225	Hs.142023	NM_005816	ENSG00000153283	CD96	TACTILE	CD96 molecule	protein-coding	0.000000	0.371069	
chunk0055_179_1	chr13	61332265	61332480	+	0	NA	Intergenic	Intergenic	83150	NM_022843	64881	Hs.391781	NM_022843	ENSG00000280165	PCDH20	PCDH13	protocadherin 20	protein-coding	0.004651	0.384259	116(ATTACATGCTGTTCTT,+,0.00)
chunk0082_19_1	chr17	50466355	50466759	+	0	NA	intron (NM_001267, intron 1 of 3)	intron (NM_001267, intron 1 of 3)	-1772	NR_110232	80221	Hs.288959	NM_025149	ENSG00000167107	ACSF2	ACSMW|AVYV493	acyl-CoA synthetase family member 2	protein-coding	0.017327	0.585185	219(GGTACACGGTGAACTT,+,0.00)
chunk0093_428_1	chr19	57840057	57840746	+	0	NA	intron (NM_001204818, intron 2 of 3)	intron (NM_001204818, intron 2 of 3)	-9412	NM_001204817	84914	Hs.642598	NM_032828	ENSG00000198466	ZNF587	ZF6	zinc finger protein 587	protein-coding	0.007257	0.401449	
chunk0015_76_1	chr1	184801519	184801782	+	0	NA	intron (NM_052966, intron 12 of 13)	L2b|LINE|L2	-46743	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.000000	0.500000	
chunk0130_249_1	chr3	135678382	135678781	+	0	NA	Intergenic	Intergenic	-287092	NM_001190447	5523	Hs.518155	NM_002718	ENSG00000073711	PPP2R3A	PPP2R3|PR130|PR72	protein phosphatase 2 regulatory subunit B''alpha	protein-coding	0.010025	0.445000	
chunk0142_231_1	chr4	98481348	98481926	+	0	NA	intron (NM_005723, intron 4 of 7)	intron (NM_005723, intron 4 of 7)	177024	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.008651	0.392055	
chunk0038_306_1	chr11	90921489	90921815	+	0	NA	Intergenic	Intergenic	-52450	NR_031663	100302228		NR_031663	ENSG00000221586	MIR1261	MIRN1261|hsa-mir-1261	microRNA 1261	ncRNA	0.003067	0.360856	
chunk0088_155_1	chr18	46632152	46632351	+	0	NA	intron (NM_144612, intron 4 of 39)	MIR|SINE|MIR	24782	NM_144612	125336	Hs.345877	NM_144612	ENSG00000167210	LOXHD1	DFNB77|LH2D1	lipoxygenase homology domains 1	protein-coding	0.005025	0.465000	
chunk0023_91_1	chr10	22495569	22496158	+	0	NA	Intergenic	L1ME1|LINE|L1	-57934	NR_036533	100499489	Hs.7444	NR_036533		LOC100499489	-	uncharacterized LOC100499489	ncRNA	0.003396	0.357627	
chunk0156_19_1	chr5	102175323	102175909	+	0	NA	Intergenic	Intergenic	120933	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.003413	0.333901	
chunk0119_21_1	chr22	40199242	40199668	+	0	NA	intron (NM_015088, intron 1 of 20)	L1MC4|LINE|L1	21530	NM_015088	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.004695	0.393443	
chunk0059_364_1	chr14	37311170	37311737	+	0	NA	intron (NM_001195296, intron 11 of 14)	intron (NM_001195296, intron 11 of 14)	113540	NM_138731	145282	Hs.660396	NM_138731	ENSG00000151338	MIPOL1	CCDC193	mirror-image polydactyly 1	protein-coding	0.003527	0.302817	
chunk0167_351_1	chr6	72850207	72850955	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	117172	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.005348	0.383178	
chunk0005_166_1	chr1	58533861	58534209	+	0	NA	exon (NM_145243, exon 5 of 9)	exon (NM_145243, exon 5 of 9)	12764	NM_145243	115209	Hs.425769	NM_145243	ENSG00000162600	OMA1	2010001O09Rik|DAB1|MPRP-1|MPRP1|YKR087C|ZMPOMA1|peptidase	OMA1 zinc metallopeptidase	protein-coding	0.008621	0.320917	101(AAGTACTGCATGTGCT,-,0.00),102(AGTACTGCATGTGCTA,+,0.00)
chunk0093_354_1	chr19	55418221	55418420	+	0	NA	Intergenic	Intergenic	-10363	NM_014501	27338	Hs.396393	NM_014501	ENSG00000108106	UBE2S	E2-EPF|E2EPF|EPF5	ubiquitin conjugating enzyme E2 S	protein-coding	0.020101	0.510000	
chunk0207_411_1	chr9	136988454	136988988	+	0	NA	Intergenic	Intergenic	-3697	NM_183241	286257	Hs.409582	NM_183241	ENSG00000148362	PAXX	C9orf142|XLS	PAXX non-homologous end joining factor	protein-coding	0.028090	0.467290	
chunk0192_258_1	chr8	65900669	65901040	+	0	NA	Intergenic	Intergenic	-59120	NM_001242318	5150	Hs.527119	NM_002603	ENSG00000205268	PDE7A	HCP1|PDE7	phosphodiesterase 7A	protein-coding	0.008086	0.389785	
chunk0005_177_1	chr1	58731865	58732153	+	0	NA	Intergenic	Intergenic	-31934	NM_001085487	114803	Hs.744921	NM_001085487	ENSG00000162601	MYSM1	2A-DUB|2ADUB|BMFS4	Myb like, SWIRM and MPN domains 1	protein-coding	0.006944	0.467128	
chunk0185_4_1	chr7	123757532	123757968	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-8679	NM_003941	8976	Hs.143728	NM_003941	ENSG00000106299	WASL	N-WASP|NWASP|WASPB	WASP like actin nucleation promoting factor	protein-coding	0.006881	0.432494	210(AAGGACATAGTGTACT,-,0.00),211(AGGACATAGTGTACTT,+,0.00)
chunk0053_144_1	chr13	30072304	30072992	+	0	NA	Intergenic	Intergenic	36227	NR_046998	100874146	Hs.574116	NR_046998	ENSG00000224511	LINC00365	-	long intergenic non-protein coding RNA 365	ncRNA	0.015988	0.439768	
chunk0019_194_1	chr1	226722265	226722464	+	0	NA	intron (NM_002221, intron 2 of 7)	intron (NM_002221, intron 2 of 7)	16811	NM_002221	3707	Hs.528087	NM_002221	ENSG00000143772	ITPKB	IP3-3KB|IP3K|IP3K-B|IP3KB|PIG37	inositol-trisphosphate 3-kinase B	protein-coding	0.020101	0.555000	
chunk0150_102_1	chr5	32615257	32615636	+	0	NA	Intergenic	L1MC4a|LINE|L1	29947	NM_006713	10923	Hs.229641	NM_006713	ENSG00000113387	SUB1	P15|PC4|p14	SUB1 regulator of transcription	protein-coding	0.007916	0.392105	
chunk0129_16_1	chr3	117046443	117047045	+	0	NA	Intergenic	Intergenic	125313	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.001661	0.321725	
chunk0022_357_1	chr10	17201491	17201848	+	0	NA	5' UTR (NM_004412, exon 1 of 11)	5' UTR (NM_004412, exon 1 of 11)	402	NM_004412	1787	Hs.351665	NM_004412	ENSG00000107614	TRDMT1	DMNT2|DNMT2|MHSAIIP|PUMET|RNMT1	tRNA aspartic acid methyltransferase 1	protein-coding	0.092437	0.681564	
chunk0026_394_1	chr10	69724092	69724441	+	0	NA	Intergenic	L2a|LINE|L2	-77622	NM_001130103	1305	Hs.695934	NM_005203	ENSG00000197467	COL13A1	CMS19|COLXIIIA1	collagen type XIII alpha 1 chain	protein-coding	0.017192	0.500000	
chunk0116_36_1	chr21	33404212	33404431	+	0	NA	intron (NM_005534, intron 1 of 6)	intron (NM_005534, intron 1 of 6)	1425	NM_005534	3460	Hs.634632	NM_005534	ENSG00000159128	IFNGR2	AF-1|IFGR2|IFNGT1|IMD28	interferon gamma receptor 2	protein-coding	0.041096	0.577273	
chunk0074_390_1	chr16	35348039	35348371	+	0	NA	Intergenic	Intergenic	-15211	NR_027080	283914	Hs.385772	NR_027079	ENSG00000259841	LINC01566	-	long intergenic non-protein coding RNA 1566	ncRNA	0.012048	0.420420	
chunk0209_430_1	chrX	62707733	62708155	+	0	NA	Intergenic	MER11D|LTR|ERVK	643395	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.004739	0.420804	
chunk0197_108_1	chr8	119777309	119778071	+	0	NA	intron (NM_003184, intron 18 of 25)	intron (NM_003184, intron 18 of 25)	55144	NM_003184	6873	Hs.122752	NM_003184	ENSG00000064313	TAF2	CIF150|MRT40|TAF2B|TAFII150	TATA-box binding protein associated factor 2	protein-coding	0.003937	0.305374	
chunk0164_299_1	chr6	24835996	24836620	+	0	NA	intron (NM_014722, intron 15 of 22)	intron (NM_014722, intron 15 of 22)	-37412	NM_001282492	101928603	Hs.635133	NM_001282492	ENSG00000260286	ARMH2	C6orf229	armadillo like helical domain containing 2	protein-coding	0.004808	0.369600	356(AGAGACATGATGTTCT,-,0.00),357(GAGACATGATGTTCTA,+,0.00)
chunk0107_45_1	chr2	211250531	211250753	+	0	NA	Intergenic	Intergenic	633071	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.004505	0.340807	
chunk0044_107_1	chr12	28807381	28807995	+	0	NA	Intergenic	Intergenic	-341315	NM_001271783	55711	Hs.684482	NM_018099	ENSG00000064763	FAR2	HEL-S-81|MLSTD1|SDR10E2	fatty acyl-CoA reductase 2	protein-coding	0.008143	0.373984	
chunk0073_368_1	chr16	15442238	15442714	+	0	NA	intron (NM_033201, intron 1 of 5)	intron (NM_033201, intron 1 of 5)	8008	NM_033201	89927	Hs.401798	NM_033201	ENSG00000166780	BMERB1	C16orf45|MINP	bMERB domain containing 1	protein-coding	0.002101	0.345912	
chunk0080_244_1	chr17	30273739	30274479	+	0	NA	exon (NM_000386, exon 7 of 12)	exon (NM_000386, exon 7 of 12)	18057	NM_000386	642	Hs.371914	NM_000386	ENSG00000108578	BLMH	BH|BMH	bleomycin hydrolase	protein-coding	0.009459	0.385965	
chunk0103_93_1	chr2	161203202	161203569	+	0	NA	intron (NM_133484, intron 2 of 3)	intron (NM_133484, intron 2 of 3)	-41354	NR_110164	100996579	Hs.660929	NR_110163	ENSG00000227403	LINC01806	-	long intergenic non-protein coding RNA 1806	ncRNA	0.005450	0.342391	
chunk0111_252_1	chr20	30519596	30519820	+	0	NA	Intergenic	ACRO1|Satellite|acro	-116246	NR_045115	140678	Hs.653099	NR_045115		MLLT10P1	MLLT10L|bA348I14.3	MLLT10 pseudogene 1	pseudo	0.008929	0.542222	
chunk0158_96_1	chr5	126631857	126632056	+	0	NA	intron (NM_207408, intron 1 of 2)	intron (NM_207408, intron 1 of 2)	234	NM_207408	389320	Hs.177983	NM_207408	ENSG00000196900	TEX43	C5orf48|Tseg7	testis expressed 43	protein-coding	0.005025	0.415000	
chunk0139_221_1	chr4	55050622	55050821	+	0	NA	Intergenic	Intergenic	74874	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.005025	0.380000	
chunk0085_152_1	chr18	3491053	3491485	+	0	NA	Intergenic	Intergenic	25019	NR_110429	100505592	Hs.635114	NR_110428	ENSG00000266835	GAPLINC	LINC01540	gastric adenocarcinoma associated, positive CD44 regulator, long intergenic non-coding RNA	ncRNA	0.000000	0.330254	
chunk0133_1_1	chr3	165196919	165197341	+	0	NA	promoter-TSS (NM_014926)	promoter-TSS (NM_014926)	-449	NM_014926	22865	Hs.101745	NM_014926	ENSG00000121871	SLITRK3	-	SLIT and NTRK like family member 3	protein-coding	0.042654	0.498818	
chunk0047_384_1	chr12	75275950	75276527	+	0	NA	TTS (NM_001286549)	TTS (NM_001286549)	53818	NM_032606	84698	Hs.733835	NM_032606	ENSG00000180881	CAPS2	UG0636c06	calcyphosine 2	protein-coding	0.006932	0.316609	
chunk0009_60_1	chr1	100726972	100727236	+	0	NA	intron (NM_080682, intron 4 of 7)	L2c|LINE|L2	7464	NM_001199834	7412	Hs.109225	NM_001078	ENSG00000162692	VCAM1	CD106|INCAM-100	vascular cell adhesion molecule 1	protein-coding	0.000000	0.339623	
chunk0118_244_1	chr22	32700298	32700610	+	0	NA	intron (NM_003490, intron 5 of 12)	intron (NM_003490, intron 5 of 12)	-100362	NM_000362	7078	Hs.644633	NM_000362	ENSG00000100234	TIMP3	HSMRK222|K222|K222TA2|SFD	TIMP metallopeptidase inhibitor 3	protein-coding	0.009615	0.460064	
chunk0060_264_1	chr14	50312757	50313287	+	0	NA	promoter-TSS (NM_024884)	promoter-TSS (NM_024884)	693	NM_015684	27109	Hs.438489	NM_015684	ENSG00000125375	DMAC2L	ATP5S|ATPW|FB|HSU79253	distal membrane arm assembly complex 2 like	protein-coding	0.035849	0.465160	499(AAGGACTTCGTGTGCC,-,0.00),500(AGGACTTCGTGTGCCT,+,0.00)
chunk0089_380_1	chr18	67497438	67497640	+	0	NA	Intergenic	L1MEd|LINE|L1	-19007	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.009901	0.310345	
chunk0155_449_1	chr5	101696169	101696606	+	0	NA	Intergenic	Intergenic	600162	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.002288	0.283105	
chunk0207_189_1	chr9	130833601	130834830	+	0	NA	intron (NM_007313, intron 1 of 10)	MIRb|SINE|MIR	-1040	NM_005157	25	Hs.431048	NM_005157	ENSG00000097007	ABL1	ABL|CHDSKM|JTK7|bcr/abl|c-ABL|c-ABL1|p150|v-abl	ABL proto-oncogene 1, non-receptor tyrosine kinase	protein-coding	0.018714	0.450407	
chunk0037_320_1	chr11	76888955	76889244	+	0	NA	intron (NM_001300953, intron 1 of 9)	L1MEd|LINE|L1	28226	NM_001300955	55331	Hs.23862	NM_018367	ENSG00000078124	ACER3	APHC|PHCA|PLDECO	alkaline ceramidase 3	protein-coding	0.003460	0.420690	
chunk0068_323_1	chr15	57505949	57506334	+	0	NA	intron (NM_001252335, intron 9 of 19)	intron (NM_001252335, intron 9 of 19)	-85763	NM_001018091	145781	Hs.437256	NM_001018090	ENSG00000137878	GCOM1	GRINL1A|Gcom2|MYZAP|MYZAP-POLR2M|gcom	GRINL1A complex locus 1	protein-coding	0.023377	0.502591	
chunk0093_9_1	chr2	69581	70206	+	0	NA	Intergenic	Intergenic	-23305	NM_001077710	642273	Hs.8379	NM_001077710	ENSG00000184731	FAM110C	-	family with sequence similarity 110 member C	protein-coding	0.011200	0.448882	
chunk0055_124_1	chr13	57583518	57583908	+	0	NA	Intergenic	Intergenic	-47942	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.002564	0.286445	
chunk0009_326_1	chr1	108828385	108828974	+	0	NA	intron (NM_152763, intron 10 of 15)	intron (NM_152763, intron 10 of 15)	28425	NM_152763	254268	Hs.729441	NM_152763	ENSG00000162641	AKNAD1	C1orf62	AKNA domain containing 1	protein-coding	0.011885	0.474576	301(AAAAACATGCTGTCCT,-,0.00),302(AAAACATGCTGTCCTC,+,0.00)
chunk0050_350_1	chr12	107729161	107729518	+	0	NA	Intergenic	Intergenic	-7216	NR_120474	101929162	Hs.667028	NR_120474	ENSG00000258136	LOC101929162	-	uncharacterized LOC101929162	ncRNA	0.011204	0.396648	
chunk0010_82_1	chr1	113419880	113420262	+	0	NA	intron (NM_152900, intron 1 of 20)	L3|LINE|CR1	29218	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.007853	0.451697	
chunk0107_143_1	chr2	214985503	214985882	+	0	NA	intron (NR_103740, intron 30 of 54)	intron (NR_103740, intron 30 of 54)	46394	NM_015657	26154	Hs.134585	NM_015657	ENSG00000144452	ABCA12	ARCI4A|ARCI4B|ICR2B|LI2	ATP binding cassette subfamily A member 12	protein-coding	0.007916	0.384211	
chunk0161_92_1	chr5	167295396	167295598	+	0	NA	intron (NM_001122679, intron 1 of 28)	intron (NM_001122679, intron 1 of 28)	10659	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.009901	0.502463	
chunk0026_72_1	chr10	61279012	61279364	+	0	NA	Intergenic	Intergenic	-173451	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.008523	0.342776	
chunk0187_281_1	chr7	155610768	155611095	+	0	NA	Intergenic	Intergenic	33475	NR_126344	100506302	Hs.87856	NR_126344	ENSG00000216895	LOC100506302	-	uncharacterized LOC100506302	ncRNA	0.024465	0.545732	
chunk0130_230_1	chr3	134445582	134446073	+	0	NA	Intergenic	L1ME1|LINE|L1	8000	NR_039951	100616281		NR_039951	ENSG00000284561	MIR4788	-	microRNA 4788	ncRNA	0.002037	0.416667	
chunk0105_68_1	chr2	183650397	183650647	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	526167	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.016000	0.398406	
chunk0188_82_1	chr8	8461330	8461593	+	0	NA	Intergenic	Intergenic	-79627	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.011407	0.515152	
chunk0052_404_1	chr12	130906098	130906383	+	0	NA	Intergenic	Intergenic	34246	NM_001300796	5901	Hs.10842	NM_006325	ENSG00000132341	RAN	ARA24|Gsp1|TC4	RAN, member RAS oncogene family	protein-coding	0.010526	0.419580	104(CTGTACTCAGTGTTCC,-,0.00),105(TGTACTCAGTGTTCCC,+,0.00)
chunk0174_365_1	chr6	164646969	164647338	+	0	NA	Intergenic	L1M2|LINE|L1	174910	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.005420	0.348649	
chunk0037_242_1	chr11	75372240	75372854	+	0	NA	Intergenic	Intergenic	-20716	NM_004041	408	Hs.503284	NM_004041	ENSG00000137486	ARRB1	ARB1|ARR1	arrestin beta 1	protein-coding	0.008143	0.439024	
chunk0206_151_1	chr9	121372902	121373526	+	0	NA	Intergenic	Intergenic	-2910	NM_004099	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.008013	0.406400	
chunk0103_427_1	chr2	169852183	169852628	+	0	NA	intron (NM_172070, intron 1 of 38)	MER58A|DNA|hAT-Charlie	24897	NM_172070	130507	Hs.379548	NM_172070	ENSG00000144357	UBR3	ZNF650	ubiquitin protein ligase E3 component n-recognin 3	protein-coding	0.013483	0.401345	
chunk0132_339_1	chr3	161246837	161247560	+	0	NA	intron (NM_015938, intron 12 of 15)	intron (NM_015938, intron 12 of 15)	25887	NM_015938	51068	Hs.598836	NM_015938	ENSG00000169251	NMD3	CGI-07	NMD3 ribosome export adaptor	protein-coding	0.000000	0.331492	
chunk0153_429_1	chr5	76134443	76135211	+	0	NA	intron (NM_014979, intron 2 of 12)	intron (NM_014979, intron 2 of 12)	51413	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.002604	0.375813	
chunk0185_300_1	chr7	131186712	131187230	+	0	NA	intron (NM_001145354, intron 2 of 18)	L2c|LINE|L2	76875	NM_001145354	4289	Hs.44693	NM_013255	ENSG00000128585	MKLN1	TWA2	muskelin 1	protein-coding	0.013514	0.435453	268(AGGAACATTGTGTGCA,-,0.00),269(GGAACATTGTGTGCAG,+,0.00)
chunk0200_421_1	chr9	27652612	27653023	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-78951	NM_145005	203228	Hs.493639	NM_018325	ENSG00000147894	C9orf72	ALSFTD|DENND9|DENNL72|FTDALS|FTDALS1	C9orf72-SMCR8 complex subunit	protein-coding	0.004866	0.349515	
chunk0110_187_1	chr20	14708193	14708546	+	0	NA	intron (NM_080676, intron 5 of 16)	MER58A|DNA|hAT-Charlie	153985	NR_104193	140848	Hs.570367	NR_104193	ENSG00000227927	MACROD2-IT1	C20orf68|NCRNA00227|bA467D7.4	MACROD2 intronic transcript 1	ncRNA	0.005666	0.367232	
chunk0195_178_1	chr8	96261563	96262020	+	0	NA	promoter-TSS (NM_014754)	promoter-TSS (NM_014754)	-95	NM_014754	9791	Hs.292579	NM_014754	ENSG00000156471	PTDSS1	LMHD|PSS1|PSSA	phosphatidylserine synthase 1	protein-coding	0.113786	0.716157	
chunk0002_257_1	chr1	21310086	21310352	+	0	NA	intron (NM_001113348, intron 1 of 18)	MLT1K|LTR|ERVL-MaLR	16929	NR_038404	100506801	Hs.663049	NR_038404	ENSG00000231105	LOC100506801	-	uncharacterized LOC100506801	ncRNA	0.007519	0.501873	
chunk0186_404_1	chr7	144776398	144776904	+	0	NA	intron (NM_001042482, intron 2 of 7)	intron (NM_001042482, intron 2 of 7)	59402	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.009881	0.370809	
chunk0186_259_1	chr7	141386225	141386806	+	0	NA	intron (NM_001195278, intron 2 of 3)	L1MA6|LINE|L1	-164763	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.012048	0.407216	
chunk0015_316_1	chr1	189258606	189259070	+	0	NA	Intergenic	Intergenic	1218791	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.008621	0.337634	
chunk0071_32_1	chr15	79656358	79656638	+	0	NA	Intergenic	MLT1J|LTR|ERVL-MaLR	223982	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.003571	0.462633	
chunk0103_24_1	chr2	159059731	159060229	+	0	NA	intron (NM_001145909, intron 2 of 26)	(TTT)n|Simple_repeat|Simple_repeat	91346	NM_001145909	85461	Hs.61590	NM_033394	ENSG00000115183	TANC1	ROLSB|TANC	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	protein-coding	0.006024	0.384770	
chunk0082_334_1	chr17	59728028	59728637	+	0	NA	intron (NM_030938, intron 1 of 11)	L2c|LINE|L2	-20734	NM_001015509	51651	Hs.12677	NM_016077	ENSG00000141378	PTRH2	BIT1|CFAP37|CGI-147|IMNEPD|PTH|PTH 2|PTH2	peptidyl-tRNA hydrolase 2	protein-coding	0.008210	0.352459	
chunk0183_238_1	chr7	107033516	107034128	+	0	NA	Intergenic	Intergenic	-10911	NM_002736	5577	Hs.433068	NM_002736	ENSG00000005249	PRKAR2B	PRKAR2|RII-BETA	protein kinase cAMP-dependent type II regulatory subunit beta	protein-coding	0.000000	0.345840	
chunk0144_45_1	chr4	126202067	126202380	+	0	NA	Intergenic	LTR2752|LTR|ERV1	694964	NR_031746	100302267		NR_031746	ENSG00000283550	MIR2054	hsa-mir-2054	microRNA 2054	ncRNA	0.019169	0.500000	
chunk0179_359_1	chr7	50946955	50947285	+	0	NA	Intergenic	L1M2a|LINE|L1	-153658	NM_001001555	2887	Hs.164060	NM_005311	ENSG00000106070	GRB10	GRB-IR|Grb-10|IRBP|MEG1|RSS	growth factor receptor bound protein 10	protein-coding	0.021212	0.570997	
chunk0074_203_1	chr16	25049672	25050209	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	18199	NR_038379	554206	Hs.552959	NR_038379	ENSG00000262587	LOC554206	-	leucine carboxyl methyltransferase 1 pseudogene	pseudo	0.009311	0.381041	
chunk0007_107_1	chr1	78887663	78888435	+	0	NA	Intergenic	Intergenic	118761	NM_022159	64123	Hs.132314	NM_022159	ENSG00000162618	ADGRL4	ELTD1|ETL|KPG_003	adhesion G protein-coupled receptor L4	protein-coding	0.003886	0.335058	
chunk0106_11_1	chr2	195370367	195370998	+	0	NA	Intergenic	Intergenic	-286126	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.004754	0.367089	
chunk0091_46_1	chr19	4455970	4456178	+	0	NA	promoter-TSS (NM_001171091)	promoter-TSS (NM_001171091)	-776	NM_001171091	80700	Hs.435255	NM_025241	ENSG00000167671	UBXN6	UBXD1|UBXDC2	UBX domain protein 6	protein-coding	0.024038	0.617225	
chunk0197_132_1	chr8	120080188	120080735	+	0	NA	Intergenic	Intergenic	-44647	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.003656	0.399635	
chunk0194_425_1	chr8	92414022	92414517	+	0	NA	Intergenic	Intergenic	241225	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.002020	0.300403	
chunk0038_62_1	chr11	83007020	83007223	+	0	NA	intron (NM_001286060, intron 1 of 4)	MIRc|SINE|MIR	27448	NM_001286059	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.004926	0.450980	
chunk0069_250_1	chr15	64423340	64423960	+	0	NA	intron (NM_016213, intron 9 of 12)	intron (NM_016213, intron 9 of 12)	35846	NM_016213	9325	Hs.500340	NM_016213	ENSG00000103671	TRIP4	ASC-1|ASC1|HsT17391|MDCDC|SMABF1|ZC2HC5	thyroid hormone receptor interactor 4	protein-coding	0.014516	0.396135	
chunk0108_201_1	chr2	232588917	232589126	+	0	NA	Intergenic	Intergenic	-17036	NM_001243252	80303	Hs.516769	NM_025202	ENSG00000115468	EFHD1	MST133|MSTP133|PP3051|SWS2	EF-hand domain family member D1	protein-coding	0.004785	0.542857	
chunk0032_297_1	chr11	9575176	9575496	+	0	NA	5' UTR (NM_001143976, exon 1 of 11)	5' UTR (NM_001143976, exon 1 of 11)	649	NM_001143976	7465	Hs.249441	NM_003390	ENSG00000166483	WEE1	WEE1A|WEE1hu	WEE1 G2 checkpoint kinase	protein-coding	0.025000	0.439252	
chunk0076_371_1	chr16	72156697	72156938	+	0	NA	intron (NM_031293, intron 3 of 20)	intron (NM_031293, intron 3 of 20)	15348	NM_031293	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.016598	0.384298	
chunk0082_272_1	chr17	57931433	57932023	+	0	NA	intron (NM_001271875, intron 1 of 10)	intron (NM_001271875, intron 1 of 10)	23595	NM_001271875	404093	Hs.46679	NM_001271875	ENSG00000180891	CUEDC1	-	CUE domain containing 1	protein-coding	0.013559	0.522843	297(AGGGACTTCATGTCCC,-,0.00),298(GGGACTTCATGTCCCA,+,0.00)
chunk0209_449_1	chrX	65838083	65838872	+	0	NA	Intergenic	Intergenic	170833	NM_002444	4478	Hs.87752	NM_002444	ENSG00000147065	MSN	HEL70|IMD50	moesin	protein-coding	0.005070	0.525316	255(GGCTCAGCTTGTTCCT,+,0.00),275(TGGTTCAGCCTGTGCC,-,0.00),276(GGTTCAGCCTGTGCCT,+,0.00),417(GGTACAGACCGTACTT,+,0.00)
chunk0049_312_1	chr12	94586726	94587357	+	0	NA	intron (NM_020698, intron 1 of 3)	intron (NM_020698, intron 1 of 3)	-15689	NR_106998	102465834		NR_106998	ENSG00000283818	MIR7844	hsa-mir-7844	microRNA 7844	ncRNA	0.012678	0.425633	508(CAGGACACTGTGTTTC,-,0.00),509(AGGACACTGTGTTTCT,+,0.00)
chunk0149_208_1	chr5	21693749	21694008	+	0	NA	Intergenic	L2a|LINE|L2	-190576	NR_132788	106635540		NR_132788		SNORA105B	-	small nucleolar RNA, H/ACA box 105B	snoRNA	0.000000	0.346154	
chunk0090_140_1	chr18	72188091	72188985	+	0	NA	Intergenic	L1MC1|LINE|L1	355950	NM_182511	147381	Hs.569851	NM_182511	ENSG00000141668	CBLN2	-	cerebellin 2 precursor	protein-coding	0.004474	0.356425	
chunk0081_415_1	chr17	48725658	48725887	+	0	NA	3' UTR (NM_006361, exon 2 of 2)	3' UTR (NM_006361, exon 2 of 2)	-1297	NR_036150	100422978		NR_036150	ENSG00000263602	MIR3185	-	microRNA 3185	ncRNA	0.039301	0.595652	
chunk0204_66_1	chr9	93532164	93532491	+	0	NA	TTS (NM_001286724)	TTS (NM_001286724)	-44300	NM_005392	5253	Hs.211441	NM_005392	ENSG00000197724	PHF2	CENP-35|GRC5|JHDM1E|KDM7C	PHD finger protein 2	protein-coding	0.024465	0.454268	
chunk0022_385_1	chr10	17624872	17625626	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	-7875	NM_014241	9200	Hs.114062	NM_014241	ENSG00000165996	HACD1	CAP|PTPLA	3-hydroxyacyl-CoA dehydratase 1	protein-coding	0.011936	0.451656	
chunk0013_392_1	chr1	172847840	172848039	+	0	NA	Intergenic	LTR19-int|LTR|ERV1	188931	NM_001302746	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.000000	0.430000	
chunk0169_211_1	chr6	103049956	103050485	+	0	NA	Intergenic	Intergenic	1651235	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.007561	0.330189	224(CAGTACAATCTGTTCT,-,0.00),225(AGTACAATCTGTTCTA,+,0.00)
chunk0059_342_1	chr14	37030884	37031711	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	-78906	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.002418	0.353865	617(GGGAACTATTTGTTCC,-,0.00),618(GGAACTATTTGTTCCA,+,0.00)
chunk0115_265_1	chr21	27840364	27840590	+	0	NA	Intergenic	Intergenic	118098	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.008850	0.370044	
chunk0090_52_1	chr19	1978551	1978799	+	0	NA	exon (NM_001319, exon 5 of 12)	exon (NM_001319, exon 5 of 12)	-24126	NR_033400	255193	Hs.374717	NM_152771	ENSG00000180846	CSNK1G2-AS1	C19orf34	CSNK1G2 antisense RNA 1	ncRNA	0.100806	0.710843	
chunk0065_58_1	chr15	22869051	22869652	+	0	NA	TTS (NM_014608).2	TTS (NM_014608).2	30710	NM_001008892	81614	Hs.591003	NM_030922	ENSG00000140157	NIPA2	SLC57A2	NIPA magnesium transporter 2	protein-coding	0.016639	0.481728	
chunk0078_191_1	chr17	4959149	4959620	+	0	NA	3' UTR (NM_004890, exon 7 of 7)	3' UTR (NM_004890, exon 7 of 7)	8295	NM_053013	2027	Hs.224171	NM_001976	ENSG00000108515	ENO3	GSD13|MSE	enolase 3	protein-coding	0.019108	0.521186	
chunk0005_135_1	chr1	57252377	57252773	+	0	NA	intron (NM_021080, intron 4 of 16)	L2c|LINE|L2	-286435	NM_000066	732	Hs.391835	NM_000066	ENSG00000021852	C8B	C82	complement C8 beta chain	protein-coding	0.002525	0.350126	
chunk0184_73_1	chr7	112604795	112605420	+	0	NA	Intergenic	Intergenic	-12958	NR_110159	100996249	Hs.561749	NR_110159		LOC100996249	-	uncharacterized LOC100996249	ncRNA	0.004800	0.359425	
chunk0084_266_1	chr17	79407291	79407924	+	0	NA	intron (NM_001082575, intron 2 of 14)	intron (NM_001082575, intron 2 of 14)	108541	NM_001082575	146713	Hs.135229	NM_001025448	ENSG00000167281	RBFOX3	FOX-3|FOX3|HRNBP3|NEUN	RNA binding fox-1 homolog 3	protein-coding	0.015798	0.479495	
chunk0084_277_1	chr17	79814881	79815193	+	0	NA	Intergenic	CpG	-17921	NM_020649	57332	Hs.387258	NM_020649	ENSG00000141570	CBX8	PC3|RC1	chromobox 8	protein-coding	0.096154	0.699681	
chunk0143_172_1	chr4	110907616	110908312	+	0	NA	Intergenic	MIRb|SINE|MIR	-47317	NR_030643	100126354		NR_030643	ENSG00000215961	MIR297	MIRN297|hsa-mir-297	microRNA 297	ncRNA	0.002874	0.341463	
chunk0106_46_1	chr2	196247157	196247726	+	0	NA	intron (NM_020760, intron 19 of 28)	intron (NM_020760, intron 19 of 28)	-12583	NR_110225	101927482	Hs.191841	NR_110225		HECW2-AS1	-	HECW2 antisense RNA 1	ncRNA	0.008787	0.357895	220(AATACAAAATGTTCTT,+,0.00)
chunk0177_297_1	chr7	25902720	25903092	+	0	NA	Intergenic	MIRb|SINE|MIR	47080	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.008065	0.353887	25(GGAACTTAGTGCTCTT,+,0.00),212(GGCACTCAAAGTTCTC,+,0.00)
chunk0104_193_1	chr2	175225962	175226548	+	0	NA	Intergenic	L1MC5|LINE|L1	-44493	NM_001190329	518	Hs.429	NM_001689	ENSG00000154518	ATP5MC3	ATP5G3|P3	ATP synthase membrane subunit c locus 3	protein-coding	0.000000	0.316865	
chunk0059_220_1	chr14	34113162	34113385	+	0	NA	Intergenic	Intergenic	-162195	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.008969	0.424107	
chunk0179_241_1	chr7	48120043	48120647	+	0	NA	Intergenic	MER34B-int|LTR|ERV1	31091	NR_109837	7378	Hs.488240	NM_003364	ENSG00000183696	UPP1	UDRPASE|UP|UPASE|UPP	uridine phosphorylase 1	protein-coding	0.008278	0.352066	
chunk0199_4_1	chr9	407989	408444	+	0	NA	intron (NM_001190458, intron 26 of 45)	intron (NM_001190458, intron 26 of 45)	-62078	NM_001256876	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.010989	0.447368	
chunk0128_112_1	chr3	106277569	106277905	+	0	NA	Intergenic	Intergenic	-408694	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.000000	0.320475	
chunk0102_78_1	chr2	143284445	143284785	+	0	NA	intron (NM_018460, intron 6 of 13)	intron (NM_018460, intron 6 of 13)	155285	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.008824	0.354839	
chunk0199_293_1	chr9	6681532	6681866	+	0	NA	Intergenic	CpG	-36007	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.083832	0.597015	
chunk0192_460_1	chr8	70307658	70307879	+	0	NA	intron (NM_006540, intron 1 of 22)	intron (NM_006540, intron 1 of 22)	96017	NM_006540	10499	Hs.446678	NM_006540	ENSG00000140396	NCOA2	GRIP1|KAT13C|NCoA-2|SRC2|TIF2|bHLHe75	nuclear receptor coactivator 2	protein-coding	0.009050	0.328829	
chunk0071_115_1	chr15	81388130	81388862	+	0	NA	intron (NR_120365, intron 6 of 6)	intron (NR_120365, intron 6 of 6)	-14419	NM_001080532	342125	Hs.253489	NM_181841	ENSG00000188869	TMC3	-	transmembrane channel like 3	protein-coding	0.006831	0.446112	366(GAGAACTGTCTGTTCC,-,0.00),367(AGAACTGTCTGTTCCT,+,0.00)
chunk0115_347_1	chr21	29215721	29216536	+	0	NA	intron (NR_027072, intron 1 of 1)	intron (NR_027072, intron 1 of 1)	22634	NR_027072	193629	Hs.720711	NM_138968	ENSG00000215533	LINC00189	C21orf109|NCRNA00189	long intergenic non-protein coding RNA 189	ncRNA	0.004908	0.376225	587(AAGAACAATCTGTTCC,-,0.00),588(AGAACAATCTGTTCCC,+,0.00)
chunk0051_70_1	chr12	113116564	113116855	+	0	NA	intron (NM_004658, intron 9 of 21)	intron (NM_004658, intron 9 of 21)	18890	NM_001301202	8437	Hs.528693	NM_004658	ENSG00000111344	RASAL1	RASAL	RAS protein activator like 1	protein-coding	0.003436	0.417808	
chunk0042_138_1	chr12	3816078	3816328	+	0	NA	intron (NR_104461, intron 6 of 8)	intron (NR_104461, intron 6 of 8)	57245	NR_104461	57097	Hs.657268	NM_020367	ENSG00000111224	PARP11	ARTD11|C12orf6|MIB006	poly(ADP-ribose) polymerase family member 11	protein-coding	0.008000	0.318725	46(CAGAACTTTATGTTCT,-,0.00),47(AGAACTTTATGTTCTC,+,0.00)
chunk0092_151_1	chr19	28861520	28861736	+	0	NA	Intergenic	Intergenic	-103503	NR_027318	148145	Hs.112651	NR_027318	ENSG00000267339	LINC00906	-	long intergenic non-protein coding RNA 906	ncRNA	0.013889	0.373272	
chunk0081_165_1	chr17	41190309	41190508	+	0	NA	exon (NM_001190460, exon 1 of 1)	exon (NM_001190460, exon 1 of 1)	521	NM_001190460	728318	Hs.727478	NM_001190460	ENSG00000240542	KRTAP9-1	KAP9.1|KRTAP9L3	keratin associated protein 9-1	protein-coding	0.000000	0.585000	
chunk0112_186_1	chr20	40175427	40175694	+	0	NA	Intergenic	Intergenic	171099	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.000000	0.440299	
chunk0162_212_1	chr6	4130345	4131010	+	0	NA	TTS (NM_001085401)	TTS (NM_001085401)	4791	NM_001166010	10455	Hs.15250	NM_006117	ENSG00000198721	ECI2	ACBD2|DRS-1|DRS1|HCA88|PECI|dJ1013A10.3	enoyl-CoA delta isomerase 2	protein-coding	0.009023	0.427928	
chunk0172_320_1	chr6	138337039	138337537	+	0	NA	3' UTR (NM_020340, exon 34 of 34)	3' UTR (NM_020340, exon 34 of 34)	-66911	NM_014320	23593	Hs.486589	NM_014320	ENSG00000051620	HEBP2	C6ORF34B|C6orf34|PP23|SOUL	heme binding protein 2	protein-coding	0.008032	0.406814	
chunk0106_325_1	chr2	205734536	205735028	+	0	NA	intron (NM_003872, intron 7 of 16)	intron (NM_003872, intron 7 of 16)	52282	NM_201264	8828	Hs.471200	NM_003872	ENSG00000118257	NRP2	NP2|NPN2|PRO2714|VEGF165R2	neuropilin 2	protein-coding	0.010163	0.466531	25(GAGGACACACAGATCT,-,0.00),26(AGGACACACAGATCTG,+,0.00)
chunk0052_341_1	chr12	126513025	126513416	+	0	NA	Intergenic	Intergenic	70739	NR_130748	100128554	Hs.408255	NR_015398	ENSG00000214043	LINC02347	-	long intergenic non-protein coding RNA 2347	ncRNA	0.002558	0.390306	
chunk0043_442_1	chr12	26416344	26417011	+	0	NA	intron (NM_002223, intron 50 of 56)	intron (NM_002223, intron 50 of 56)	221104	NM_005086	8082	Hs.183428	NM_005086	ENSG00000123096	SSPN	DAGA5|KRAG|NSPN|SPN1|SPN2	sarcospan	protein-coding	0.005997	0.345808	
chunk0097_201_1	chr2	51036764	51037300	+	0	NA	Intergenic	Intergenic	-4496	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.009328	0.411546	
chunk0060_242_1	chr14	49862869	49863336	+	0	NA	promoter-TSS (NR_027260)	promoter-TSS (NR_027260)	-253	NR_027260	378706		NR_027260	ENSG00000274012	RN7SL2	7L1C|7L30.1|7SL1c|RNSRP2	RNA component of signal recognition particle 7SL2	scRNA	0.062099	0.547009	205(CAGAACACCACGTTCC,-,0.00),206(AGAACACCACGTTCCT,+,0.00)
chunk0140_404_1	chr4	75546959	75547358	+	0	NA	Intergenic	Intergenic	-8890	NM_001257072	152816	Hs.24510	NM_178497	ENSG00000174792	ODAPH	AI2A4|C4orf26	odontogenesis associated phosphoprotein	protein-coding	0.007519	0.445000	
chunk0203_319_1	chr9	89605804	89606026	+	0	NA	intron (NM_006705, intron 3 of 3)	CpG-28470	903	NM_006705	10912	Hs.9701	NM_006705	ENSG00000130222	GADD45G	CR6|DDIT2|GADD45gamma|GRP17	growth arrest and DNA damage inducible gamma	protein-coding	0.103604	0.690583	
chunk0163_204_1	chr6	11875440	11875740	+	0	NA	Intergenic	Intergenic	-96543	NM_001143948	84830	Hs.126409	NM_032744	ENSG00000111863	ADTRP	AIG1L|C6orf105|dJ413H6.1	androgen dependent TFPI regulating protein	protein-coding	0.013333	0.411960	137(TAGTACTTTATGTTCT,-,0.00),138(AGTACTTTATGTTCTC,+,0.00)
chunk0120_291_1	chr3	9803202	9803939	+	0	NA	intron (NM_001198793, intron 4 of 11)	L3|LINE|CR1	-6390	NR_037162	26140	Hs.726435	NM_015644	ENSG00000214021	TTLL3	HOTTL	tubulin tyrosine ligase like 3	protein-coding	0.005427	0.471545	
chunk0062_308_1	chr14	73104931	73105717	+	0	NA	intron (NM_021239, intron 10 of 18)	intron (NM_021239, intron 10 of 18)	-31111	NM_000021	5663	Hs.3260	NM_000021	ENSG00000080815	PSEN1	ACNINV3|AD3|FAD|PS-1|PS1|S182	presenilin 1	protein-coding	0.003817	0.360864	415(GAGAACTTTCAGTGCT,-,0.00),416(AGAACTTTCAGTGCTG,+,0.00)
chunk0198_107_1	chr8	130762083	130762364	+	0	NA	Intergenic	L1MA8|LINE|L1	278366	NM_001115	114	Hs.591859	NM_001115	ENSG00000155897	ADCY8	AC8|ADCY3|HBAC1	adenylate cyclase 8	protein-coding	0.010676	0.361702	
chunk0062_229_1	chr14	71062664	71063395	+	0	NA	intron (NM_001308160, intron 24 of 33)	Tigger3|DNA|TcMar-Tigger	155624	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.005472	0.362022	
chunk0030_296_1	chr10	117348197	117348789	+	0	NA	intron (NM_173791, intron 1 of 4)	MLT1B|LTR|ERVL-MaLR	26974	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.010135	0.396290	
chunk0198_473_1	chr8	145001797	145002055	+	0	NA	promoter-TSS (NR_026974)	promoter-TSS (NR_026974)	-885	NR_026974	286103	Hs.359978	NM_001039382	ENSG00000255559	ZNF252P-AS1	C8orf77	ZNF252P antisense RNA 1	ncRNA	0.015504	0.509653	
chunk0176_104_1	chr7	11713479	11713965	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	118476	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.006173	0.353183	
chunk0039_128_1	chr11	98246424	98246981	+	0	NA	Intergenic	L1MA4|LINE|L1	-774274	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.005386	0.329749	
chunk0170_308_1	chr6	116016686	116017330	+	0	NA	intron (NM_002031, intron 1 of 7)	intron (NM_002031, intron 1 of 7)	-21723	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.004658	0.389147	220(CAGAGCAGCTTGTTCT,-,0.00),221(AGAGCAGCTTGTTCTC,+,0.00)
chunk0080_262_1	chr17	30713617	30714025	+	0	NA	intron (NR_024187, intron 1 of 7)	L2a|LINE|L2	4213	NR_024187	440423	Hs.628886	NR_024187		SUZ12P1	SUZ12P	SUZ12 pseudogene 1	pseudo	0.019608	0.518337	
chunk0036_382_1	chr11	67582348	67582855	+	0	NA	promoter-TSS (NM_000852)	promoter-TSS (NM_000852)	-994	NM_000852	2950	Hs.523836	NM_000852	ENSG00000084207	GSTP1	DFN7|FAEES3|GST3|GSTP|HEL-S-22|PI	glutathione S-transferase pi 1	protein-coding	0.013807	0.427165	
chunk0060_320_1	chr14	51342179	51342658	+	0	NA	intron (NR_038358, intron 1 of 4)	MLT1E1A|LTR|ERVL-MaLR	9025	NR_038358	283553	Hs.325752	NR_038358	ENSG00000258479	LINC00640	-	long intergenic non-protein coding RNA 640	ncRNA	0.008351	0.425000	
chunk0070_212_1	chr15	72474097	72474300	+	0	NA	promoter-TSS (NM_005744)	promoter-TSS (NM_005744)	-128	NM_005744	25820	Hs.268787	NM_005744	ENSG00000166233	ARIH1	ARI|HARI|HHARI|UBCH7BP	ariadne RBR E3 ubiquitin protein ligase 1	protein-coding	0.113300	0.681373	
chunk0151_95_1	chr5	43077032	43077376	+	0	NA	intron (NR_102752, intron 2 of 2)	LTR5B|LTR|ERVK	-9765	NR_104651	648987	Hs.649468	NR_034085	ENSG00000177738	LOC648987	-	uncharacterized LOC648987	ncRNA	0.005814	0.475362	
chunk0015_303_1	chr1	188944624	188944918	+	0	NA	Intergenic	MER90|LTR|ERV1	1501143	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006803	0.400000	
chunk0167_230_1	chr6	67311723	67312221	+	0	NA	Intergenic	L1PB3|LINE|L1	-743379	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.006024	0.322645	
chunk0138_233_1	chr4	39337820	39338347	+	0	NA	intron (NM_002913, intron 4 of 24)	intron (NM_002913, intron 4 of 24)	28298	NM_001204747	5981	Hs.507475	NM_002913	ENSG00000035928	RFC1	A1|CANVAS|MHCBFB|PO-GA|RECC1|RFC|RFC140	replication factor C subunit 1	protein-coding	0.009488	0.325758	
chunk0065_154_1	chr15	25441205	25441509	+	0	NA	Intergenic	L2c|LINE|L2	-2329	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.000000	0.357377	164(AAGAACTTGCAGTTCC,-,0.00),165(AGAACTTGCAGTTCCA,+,0.00)
chunk0170_229_1	chr6	113434554	113435202	+	0	NA	Intergenic	Intergenic	215197	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.007716	0.371341	
chunk0211_186_1	chrX	117310055	117310590	+	0	NA	Intergenic	Intergenic	663416	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.003738	0.360075	
chunk0142_350_1	chr4	101697203	101697532	+	0	NA	Intergenic	Intergenic	-93240	NM_001127507	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.009119	0.424242	
chunk0053_162_1	chr13	30477763	30478070	+	0	NA	intron (NM_001313893, intron 1 of 4)	intron (NM_001313893, intron 1 of 4)	-11951	NM_002128	3146	Hs.434102	NM_002128	ENSG00000189403	HMGB1	HMG-1|HMG1|HMG3|SBP-1	high mobility group box 1	protein-coding	0.009772	0.428571	
chunk0099_152_1	chr2	86802999	86803536	+	0	NA	intron (NM_001145873, intron 2 of 8)	L1MA9|LINE|L1	5129	NM_001145873	925	Hs.85258	NM_001768	ENSG00000153563	CD8A	CD8|Leu2|p32	CD8a molecule	protein-coding	0.007449	0.332714	
chunk0150_132_1	chr5	33317423	33317867	+	0	NA	Intergenic	L1ME3B|LINE|L1	-123051	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.006757	0.330337	
chunk0127_199_1	chr3	96180554	96180900	+	0	NA	Intergenic	Intergenic	-179237	NR_107027	102465864		NR_107027	ENSG00000278103	MIR8060	hsa-mir-8060	microRNA 8060	ncRNA	0.000000	0.270893	
chunk0160_69_1	chr5	149857260	149858002	+	0	NA	TTS (NM_000440)	TTS (NM_000440)	75346	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.008086	0.480485	454(CTGTACACTATGTTCT,-,0.00),455(TGTACACTATGTTCTC,+,0.00)
chunk0008_311_1	chr1	95138493	95138726	+	0	NA	intron (NM_001199691, intron 1 of 7)	Tigger3b|DNA|TcMar-Tigger	20686	NM_001199691	100527978	Hs.483512	NM_001199691	ENSG00000271092	TLCD4-RWDD3	TMEM56-RWDD3	TLCD4-RWDD3 readthrough	protein-coding	0.000000	0.371795	
chunk0047_460_1	chr12	76869521	76869730	+	0	NA	intron (NM_001300965, intron 1 of 5)	intron (NM_001300965, intron 1 of 5)	9415	NM_001300965	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.004785	0.428571	
chunk0197_138_1	chr8	120217235	120217949	+	0	NA	intron (NM_021110, intron 14 of 47)	intron (NM_021110, intron 14 of 47)	92484	NM_021110	7373	Hs.409662	NM_021110	ENSG00000187955	COL14A1	UND	collagen type XIV alpha 1 chain	protein-coding	0.002801	0.331469	
chunk0209_400_1	chrX	55262173	55262615	+	0	NA	intron (NM_001017931, intron 3 of 4)	intron (NM_001017931, intron 3 of 4)	2452	NM_001017931	139793	Hs.163473	NM_001017931	ENSG00000204279	PAGE3	CT16.6|GAGED1|PAGE-3	PAGE family member 3	protein-coding	0.002262	0.329571	248(AATCACATTCTGTTCC,-,0.00)
chunk0079_414_1	chr17	19644487	19644891	+	0	NA	Intergenic	Intergenic	-4062	NM_001031806	224	Hs.499886	NM_000382	ENSG00000072210	ALDH3A2	ALDH10|FALDH|SLS	aldehyde dehydrogenase 3 family member A2	protein-coding	0.009901	0.367901	
chunk0212_110_1	chrY	17418146	17418624	+	0	NA	Intergenic	HUERS-P1-int|LTR|ERV1	-82573	NR_028084	100302526	Hs.434364	NR_028084		FAM41AY2	-	family with sequence similarity 41 member A, Y-linked 2	ncRNA	0.002092	0.342380	
chunk0048_257_1	chr12	81983615	81984264	+	0	NA	intron (NR_110089, intron 2 of 2)	L1MC1|LINE|L1	30220	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.003082	0.321538	
chunk0073_8_1	chr16	1983885	1984258	+	0	NA	promoter-TSS (NM_005262)	promoter-TSS (NM_005262)	-78	NM_005262	2671	Hs.27184	NM_005262	ENSG00000127554	GFER	ALR|ERV1|HERV1|HPO|HPO1|HPO2|HSS	growth factor, augmenter of liver regeneration	protein-coding	0.136729	0.778075	
chunk0125_413_1	chr3	72306704	72307436	+	0	NA	Intergenic	Intergenic	139553	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.017760	0.507503	
chunk0096_224_1	chr2	30616159	30616612	+	0	NA	intron (NM_001304446, intron 5 of 5)	intron (NM_001304446, intron 5 of 5)	169159	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.002208	0.325991	
chunk0184_363_1	chr7	121046716	121047333	+	0	NA	intron (NM_001105533, intron 3 of 17)	intron (NM_001105533, intron 3 of 17)	57633	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.001621	0.325243	223(AGGAACACCCTGTATA,-,0.00)
chunk0043_380_1	chr12	24699083	24699379	+	0	NA	Intergenic	Intergenic	-115063	NR_029451	144360	Hs.350668	NM_144667	ENSG00000197503	LINC00477	C12orf67|FAM191B	long intergenic non-protein coding RNA 477	ncRNA	0.006757	0.380471	
chunk0155_3_1	chr5	90767007	90767227	+	0	NA	intron (NR_003149, intron 59 of 89)	L1M5|LINE|L1	208317	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.000000	0.389140	
chunk0044_137_1	chr12	29425303	29426140	+	0	NA	intron (NR_073172, intron 1 of 1)	MIR|SINE|MIR	36427	NR_073170	101055625	Hs.569158	NR_073170	ENSG00000257599	OVCH1-AS1	-	OVCH1 antisense RNA 1	ncRNA	0.007168	0.362768	250(AAGAACACAGAGTGCT,-,0.00),251(AGAACACAGAGTGCTT,+,0.00)
chunk0174_313_1	chr6	162874497	162874749	+	0	NA	intron (NM_152410, intron 3 of 6)	intron (NM_152410, intron 3 of 6)	146653	NM_001080379	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.011905	0.521739	
chunk0103_90_1	chr2	161100121	161100587	+	0	NA	Intergenic	Intergenic	-36601	NM_133484	10010	Hs.132257	NM_004180	ENSG00000136560	TANK	I-TRAF|ITRAF|TRAF2	TRAF family member associated NFKB activator	protein-coding	0.004292	0.308351	
chunk0084_84_1	chr17	75163127	75163852	+	0	NA	Intergenic	AluJr|SINE|Alu	-8806	NM_001002032	51155	Hs.532803	NM_016185	ENSG00000189159	JPT1	ARM2|HN1|HN1A	Jupiter microtubule associated homolog 1	protein-coding	0.019310	0.464187	
chunk0115_38_1	chr21	21135410	21136064	+	0	NA	intron (NM_004540, intron 1 of 17)	MLT1I-int|LTR|ERVL-MaLR	137422	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.012232	0.386260	
chunk0161_407_1	chr5	177446330	177446529	+	0	NA	promoter-TSS (NM_001174101)	promoter-TSS (NM_001174101)	-366	NM_001174101	80758	Hs.534492	NM_030567	ENSG00000131188	PRR7	-	proline rich 7, synaptic	protein-coding	0.070352	0.680000	
chunk0146_189_1	chr4	161111701	161112180	+	0	NA	Intergenic	L1MB1|LINE|L1	-910793	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.006263	0.368750	
chunk0012_325_1	chr1	162444475	162444783	+	0	NA	Intergenic	Intergenic	-32491	NM_053282	117157	Hs.350581	NM_053282	ENSG00000198574	SH2D1B	EAT2	SH2 domain containing 1B	protein-coding	0.006494	0.472492	92(CAGGACTTAATGTTCT,-,0.00),93(AGGACTTAATGTTCTC,+,0.00)
chunk0078_227_1	chr17	6530891	6531249	+	0	NA	intron (NM_031220, intron 2 of 19)	intron (NM_031220, intron 2 of 19)	25487	NM_031220	83394	Hs.183983	NM_031220	ENSG00000091622	PITPNM3	ACKR6|CORD5|NIR1|RDGBA3	PITPNM family member 3	protein-coding	0.005587	0.426184	
chunk0067_55_1	chr15	40908421	40908692	+	0	NA	Intergenic	Intergenic	14126	NM_020857	57617	Hs.23876	NM_020857	ENSG00000104142	VPS18	PEP3	VPS18 core subunit of CORVET and HOPS complexes	protein-coding	0.007380	0.433824	
chunk0001_395_1	chr1	10716524	10716723	+	0	NA	intron (NM_001079843, intron 2 of 20)	intron (NM_001079843, intron 2 of 20)	80053	NM_001079843	54897	Hs.439894	NM_017766	ENSG00000130940	CASZ1	CAS11|CST|SRG|ZNF693|dJ734G22.1	castor zinc finger 1	protein-coding	0.025126	0.585000	
chunk0064_86_1	chr14	90716379	90716828	+	0	NA	intron (NM_001010854, intron 5 of 19)	(TG)n|Simple_repeat|Simple_repeat	73974	NR_110134	101928909	Hs.662545	NR_110134	ENSG00000259163	LOC101928909	-	uncharacterized LOC101928909	ncRNA	0.002227	0.380000	
chunk0028_50_1	chr10	83194883	83195479	+	0	NA	Intergenic	L1MC3|LINE|L1	-944248	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.008389	0.378559	
chunk0069_444_1	chr15	68592447	68593123	+	0	NA	intron (NM_006091, intron 1 of 11)	intron (NM_006091, intron 1 of 11)	13816	NM_006091	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.007396	0.428360	
chunk0149_202_1	chr5	21649891	21650404	+	0	NA	Intergenic	Intergenic	190667	NR_027027	728411	Hs.88181	NM_207331	ENSG00000183666	GUSBP1	-	GUSB pseudogene 1	pseudo	0.007797	0.340467	206(CAGAACAGAGTGCACC,-,0.00),207(AGAACAGAGTGCACCT,+,0.00)
chunk0198_175_1	chr8	133322246	133322674	+	0	NA	Intergenic	Intergenic	-25156	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.009346	0.470862	210(GTGGACACTTTGTTCC,-,0.00),211(TGGACACTTTGTTCCT,+,0.00)
chunk0183_374_1	chr7	109501308	109501810	+	0	NA	Intergenic	L1PA13|LINE|L1	458654	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.007968	0.347913	
chunk0164_343_1	chr6	25414649	25415324	+	0	NA	intron (NM_017640, intron 2 of 36)	intron (NM_017640, intron 2 of 36)	135558	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.002963	0.417160	298(AAGGACACTGTGTACT,-,0.00),299(AGGACACTGTGTACTT,+,0.00)
chunk0082_278_1	chr17	58007567	58007848	+	0	NA	promoter-TSS (NR_034041)	promoter-TSS (NR_034041)	-361	NM_001078166	6426	Hs.68714	NM_006924	ENSG00000136450	SRSF1	ASF|SF2|SF2p33|SFRS1|SRp30a	serine and arginine rich splicing factor 1	protein-coding	0.078292	0.581560	
chunk0036_440_1	chr11	68506707	68507361	+	0	NA	intron (NM_018312, intron 2 of 22)	intron (NM_018312, intron 2 of 22)	46316	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.006116	0.378626	
chunk0100_353_1	chr2	117546546	117546981	+	0	NA	Intergenic	Intergenic	-267916	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.004598	0.307339	
chunk0057_140_1	chr13	99902630	99903545	+	0	NA	intron (NR_104592, intron 8 of 9)	intron (NR_104592, intron 8 of 9)	54078	NR_120421	101927437	Hs.619936	NR_120421		LOC101927437	-	uncharacterized LOC101927437	ncRNA	0.014208	0.415939	
chunk0095_442_1	chr2	25312133	25312332	+	0	NA	intron (NM_175629, intron 2 of 22)	intron (NM_175629, intron 2 of 22)	16489	NR_031570	100302246		NR_031570	ENSG00000221445	MIR1301	MIRN1301|hsa-mir-1301|mir-1301	microRNA 1301	ncRNA	0.030151	0.610000	184(CAGGACTATCAGTTCT,-,0.00)
chunk0097_350_1	chr2	59624922	59625159	+	0	NA	Intergenic	Intergenic	407332	NR_110219	101927285	Hs.570209	NR_110219	ENSG00000222030	LINC01793	-	long intergenic non-protein coding RNA 1793	ncRNA	0.012658	0.441176	
chunk0003_75_1	chr1	31390128	31390409	+	0	NA	Intergenic	MLT1O|LTR|ERVL-MaLR	-17192	NM_004102	2170	Hs.576372	NM_004102	ENSG00000121769	FABP3	FABP11|H-FABP|M-FABP|MDGI|O-FABP	fatty acid binding protein 3	protein-coding	0.021352	0.542553	
chunk0016_78_1	chr1	193863367	193863566	+	0	NA	Intergenic	THE1B|LTR|ERVL-MaLR	558721	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.015075	0.450000	
chunk0020_88_1	chr1	232793704	232794201	+	0	NA	Intergenic	Intergenic	-10940	NM_019090	54627	Hs.160373	NM_019090	ENSG00000212916	MAP10	KIAA1383|MTR120	microtubule associated protein 10	protein-coding	0.008048	0.421687	
chunk0129_61_1	chr3	117585993	117586839	+	0	NA	Intergenic	Intergenic	664985	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.002364	0.308146	375(CAGGACAGGGTGTCTA,-,0.00)
chunk0081_463_1	chr17	49403656	49404395	+	0	NA	TTS (NM_001281497)	TTS (NM_001281497)	10833	NM_001281496	5245	Hs.514303	NM_002634	ENSG00000167085	PHB	HEL-215|HEL-S-54e|PHB1	prohibitin	protein-coding	0.014885	0.518919	341(TAGAACACTCTGTTCT,-,0.00),342(AGAACACTCTGTTCTG,+,0.00)
chunk0006_186_1	chr1	67414576	67414907	+	0	NA	intron (NM_001018067, intron 7 of 7)	intron (NM_001018067, intron 7 of 7)	15699	NM_001018067	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.003021	0.352410	
chunk0033_379_1	chr11	23527213	23527697	+	0	NA	Intergenic	Intergenic	-108265	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.002066	0.319588	
chunk0031_355_1	chr10	129820327	129820975	+	0	NA	Intergenic	L2a|LINE|L2	22723	NR_036179	100422873		NR_036179	ENSG00000266676	MIR4297	-	microRNA 4297	ncRNA	0.004630	0.406780	
chunk0081_106_1	chr17	39864876	39865075	+	0	NA	promoter-TSS (NM_001257412)	promoter-TSS (NM_001257412)	-787	NM_001257411	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.000000	0.390000	
chunk0020_27_1	chr1	231919762	231920540	+	0	NA	intron (NM_001164541, intron 9 of 9)	MER20|DNA|hAT-Charlie	-5683	NR_126441	104472714		NR_126441	ENSG00000226758	DISC1-IT1	-	DISC1 intronic transcript 1	ncRNA	0.010283	0.414634	
chunk0151_235_1	chr5	51181428	51181650	+	0	NA	Intergenic	Intergenic	-201585	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.000000	0.381166	140(AAGAACATCATGATCT,-,0.00),141(AGAACATCATGATCTC,+,0.00)
chunk0111_110_1	chr20	23756977	23757236	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-6169	NM_001898	1469	Hs.123114	NM_001898	ENSG00000170373	CST1	-	cystatin SN	protein-coding	0.007722	0.403846	
chunk0130_393_1	chr3	140186147	140186807	+	0	NA	intron (NM_022131, intron 2 of 16)	intron (NM_022131, intron 2 of 16)	251292	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.001515	0.379728	
chunk0071_413_1	chr15	89707521	89707932	+	0	NA	intron (NM_020212, intron 4 of 16)	L1ME1|LINE|L1	16929	NM_020212	56964	Hs.177557	NM_020212	ENSG00000140527	WDR93	-	WD repeat domain 93	protein-coding	0.002433	0.364078	
chunk0185_349_1	chr7	132250822	132251734	+	0	NA	intron (NM_020911, intron 4 of 31)	intron (NM_020911, intron 4 of 31)	325286	NM_020911	91584	Hs.511454	NM_020911	ENSG00000221866	PLXNA4	FAYV2820|PLEXA4|PLXNA4A|PLXNA4B|PRO34003	plexin A4	protein-coding	0.007675	0.491785	542(AAGCACAGCCTGCTCA,-,0.00)
chunk0064_307_1	chr14	95619879	95620115	+	0	NA	Intergenic	MIR|SINE|MIR	-31181	NR_028288	27004	Hs.510368	NM_012468		TCL6	TNG1|TNG2	T cell leukemia/lymphoma 6	ncRNA	0.021186	0.430380	
chunk0195_172_1	chr8	96103994	96104199	+	0	NA	Intergenic	Intergenic	56696	NM_001001557	392255	Hs.492277	NM_001001557	ENSG00000156466	GDF6	BMP-13|BMP13|CDMP2|KFM|KFS|KFS1|KFSL|SGM1|SYNS4	growth differentiation factor 6	protein-coding	0.000000	0.368932	
chunk0136_170_1	chr4	6382770	6382969	+	0	NA	promoter-TSS (NM_181876)	promoter-TSS (NM_181876)	-999	NM_181876	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.015075	0.580000	158(AAGCACAGAGTGTTCT,-,0.00),159(AGCACAGAGTGTTCTA,+,0.00)
chunk0128_331_1	chr3	112005013	112005340	+	0	NA	intron (NM_001008272, intron 3 of 4)	MIRb|SINE|MIR	6016	NM_001008273	29114	Hs.169330	NM_013259	ENSG00000144834	TAGLN3	NP22|NP24|NP25	transgelin 3	protein-coding	0.003058	0.402439	
chunk0182_7_1	chr7	90976543	90977020	+	0	NA	intron (NM_001287136, intron 8 of 13)	L1MA5A|LINE|L1	266965	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.008386	0.376569	
chunk0098_445_1	chr2	82158265	82158812	+	0	NA	Intergenic	Intergenic	-691592	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.001828	0.295620	
chunk0134_64_1	chr3	176206967	176207441	+	0	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	-307899	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.006329	0.301053	
chunk0038_336_1	chr11	92769029	92769573	+	0	NA	intron (NM_001008781, intron 5 of 24)	intron (NM_001008781, intron 5 of 24)	-200322	NM_005959	4544	Hs.569039	NM_005959	ENSG00000134640	MTNR1B	FGQTL2|MEL-1B-R|MT2	melatonin receptor 1B	protein-coding	0.003676	0.405505	
chunk0165_369_1	chr6	38242928	38243187	+	0	NA	intron (NM_001099272, intron 9 of 10)	intron (NM_001099272, intron 9 of 10)	353010	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.000000	0.396154	
chunk0012_46_1	chr1	155308587	155308910	+	0	NA	promoter-TSS (NM_001242825)	promoter-TSS (NM_001242825)	0	NM_001242825	2224	Hs.335918	NM_002004	ENSG00000160752	FDPS	FPPS|FPS|POROK9	farnesyl diphosphate synthase	protein-coding	0.083591	0.608025	
chunk0154_136_1	chr5	79176221	79176676	+	0	NA	Intergenic	MIRb|SINE|MIR	-59654	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.002198	0.333333	
chunk0005_433_1	chr1	63051904	63052120	+	0	NA	Intergenic	Intergenic	265245	NR_038252	199899	Hs.116210	NR_038252	ENSG00000224209	LINC00466	-	long intergenic non-protein coding RNA 466	ncRNA	0.004630	0.396313	
chunk0084_205_1	chr17	78169224	78169474	+	0	NA	intron (NM_004710, intron 1 of 3)	intron (NM_004710, intron 1 of 3)	759	NM_004710	9144	Hs.464210	NM_004710	ENSG00000108639	SYNGR2	-	synaptogyrin 2	protein-coding	0.012000	0.629482	
chunk0037_248_1	chr11	75441264	75441463	+	0	NA	intron (NM_030792, intron 13 of 16)	intron (NM_030792, intron 13 of 16)	-10734	NM_001039548	283212	Hs.292451	NM_173583	ENSG00000149243	KLHL35	-	kelch like family member 35	protein-coding	0.050251	0.640000	117(AAGCACGTCCTGTTCA,-,0.00)
chunk0158_256_1	chr5	130985703	130986373	+	0	NA	Intergenic	Intergenic	179310	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.002985	0.385991	
chunk0126_457_1	chr3	87358911	87359110	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-82423	NM_001122757	5449	Hs.591654	NM_000306	ENSG00000064835	POU1F1	CPHD1|GHF-1|PIT1|POU1F1a|Pit-1	POU class 1 homeobox 1	protein-coding	0.010050	0.385000	
chunk0107_65_1	chr2	211958035	211958411	+	0	NA	intron (NM_001042599, intron 2 of 26)	intron (NM_001042599, intron 2 of 26)	468137	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.002660	0.326260	
chunk0174_28_1	chr6	153764908	153765235	+	0	NA	Intergenic	Intergenic	-245425	NM_001145280	4988	Hs.2353	NM_000914	ENSG00000112038	OPRM1	LMOR|M-OR-1|MOP|MOR|MOR1|OPRM	opioid receptor mu 1	protein-coding	0.006116	0.362805	
chunk0191_186_1	chr8	51587540	51588061	+	0	NA	intron (NM_144651, intron 3 of 22)	intron (NM_144651, intron 3 of 22)	221645	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.003839	0.323755	
chunk0168_226_1	chr6	86568362	86568638	+	0	NA	Intergenic	LTR78|LTR|ERV1	-368806	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.000000	0.509025	
chunk0081_113_1	chr17	40010550	40010749	+	0	NA	Intergenic	Intergenic	-4712	NM_000759	1440	Hs.2233	NM_000759	ENSG00000108342	CSF3	C17orf33|CSF3OS|GCSF	colony stimulating factor 3	protein-coding	0.010050	0.500000	
chunk0169_53_1	chr6	97985569	97985834	+	0	NA	Intergenic	L1MD2|LINE|L1	-38830	NR_031579	100302164		NR_031579	ENSG00000238367	MIR2113	hsa-mir-2113	microRNA 2113	ncRNA	0.003774	0.296992	
chunk0124_149_1	chr3	54738448	54738647	+	0	NA	intron (NM_018398, intron 11 of 37)	intron (NM_018398, intron 11 of 37)	-98690	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.000000	0.385000	
chunk0118_268_1	chr22	33461659	33461889	+	0	NA	intron (NM_133642, intron 6 of 14)	MLT1F|LTR|ERVL-MaLR	-25105	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.004348	0.415584	
chunk0071_406_1	chr15	89632600	89632799	+	0	NA	intron (NM_198525, intron 14 of 18)	intron (NM_198525, intron 14 of 18)	22752	NM_198525	374654	Hs.513134	NM_198525	ENSG00000166813	KIF7	ACLS|AGBK|HLS2|JBTS12|UNQ340	kinesin family member 7	protein-coding	0.005025	0.535000	
chunk0060_248_1	chr14	49950876	49951164	+	0	NA	Intergenic	Intergenic	-15379	NR_106724	102464828		NR_106724	ENSG00000278038	MIR6076	hsa-mir-6076	microRNA 6076	ncRNA	0.006944	0.519031	
chunk0123_355_1	chr3	48184736	48185281	+	0	NA	intron (NM_201567, intron 2 of 13)	intron (NM_201567, intron 2 of 13)	3303	NM_001789	993	Hs.437705	NM_001789	ENSG00000164045	CDC25A	CDC25A2	cell division cycle 25A	protein-coding	0.005505	0.362637	
chunk0121_379_1	chr3	25117077	25117634	+	0	NA	Intergenic	L2b|LINE|L2	-56977	NM_001290216	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.007181	0.421147	109(GAGAACAAACTGTTCA,-,0.00),110(AGAACAAACTGTTCAA,+,0.00)
chunk0043_448_1	chr12	26686367	26686931	+	0	NA	intron (NM_002223, intron 10 of 56)	intron (NM_002223, intron 10 of 56)	146549	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.012411	0.389381	
chunk0211_294_1	chrX	122744259	122744475	+	0	NA	Intergenic	L1MDb|LINE|L1	-439876	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.000000	0.322581	
chunk0062_302_1	chr14	72982378	72982693	+	0	NA	intron (NM_021260, intron 4 of 11)	intron (NM_021260, intron 4 of 11)	4421	NM_178441	53349	Hs.335106	NM_021260	ENSG00000165861	ZFYVE1	DFCP1|PPP1R172|SR3|TAFF1|ZNFN2A1	zinc finger FYVE-type containing 1	protein-coding	0.003175	0.370253	271(AAGCACATGCTGCTCC,-,0.00),272(AGCACATGCTGCTCCA,+,0.00)
chunk0004_258_1	chr1	47874988	47875334	+	0	NA	intron (NM_001194986, intron 2 of 6)	intron (NM_001194986, intron 2 of 6)	121729	NM_001194986	388630	Hs.61504	NM_001194986	ENSG00000269113	TRABD2B	TIKI2	TraB domain containing 2B	protein-coding	0.014451	0.472622	200(GGAAACAGTCTGTTCC,-,0.00),201(GAAACAGTCTGTTCCA,+,0.00)
chunk0109_185_1	chr20	4927164	4927508	+	0	NA	intron (NM_005116, intron 3 of 16)	intron (NM_005116, intron 3 of 16)	74163	NM_005116	9962	Hs.516866	NM_005116	ENSG00000089057	SLC23A2	NBTL1|SLC23A1|SVCT2|YSPL2	solute carrier family 23 member 2	protein-coding	0.008721	0.463768	
chunk0050_201_1	chr12	104131561	104131956	+	0	NA	intron (NM_006166, intron 2 of 7)	L2c|LINE|L2	6483	NR_106988									0.012658	0.421717	
chunk0035_8_1	chr11	39984635	39985218	+	0	NA	Intergenic	L1PA5|LINE|L1	308204	NR_047674	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.005146	0.474315	
chunk0063_314_1	chr14	85122674	85123211	+	0	NA	Intergenic	Intergenic	-270937	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.003724	0.328996	
chunk0162_218_1	chr6	4320752	4321336	+	0	NA	Intergenic	Intergenic	-106958	NR_106988									0.003425	0.353846	
chunk0007_175_1	chr1	80392089	80393070	+	0	NA	Intergenic	Intergenic	-143176	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.004077	0.320774	
chunk0099_158_1	chr2	88198083	88198355	+	0	NA	Intergenic	MIRc|SINE|MIR	25080	NM_018271	55258	Hs.739080	NM_018271	ENSG00000144115	THNSL2	SOFAT|THS2|TSH2	threonine synthase like 2	protein-coding	0.018382	0.516484	83(CAGCACTCTGTGTTCC,-,0.00),84(AGCACTCTGTGTTCCT,+,0.00)
chunk0139_119_1	chr4	52868207	52868695	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	6123	NM_023940	65997	Hs.8035	NM_023940	ENSG00000128045	RASL11B	-	RAS like family 11 member B	protein-coding	0.012295	0.494888	
chunk0049_131_1	chr12	91637629	91638340	+	0	NA	Intergenic	MER97a|DNA|hAT-Tip100	-454860	NM_001920	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.007032	0.327247	
chunk0194_285_1	chr8	87440619	87440880	+	0	NA	Intergenic	L1MA4|LINE|L1	433319	NM_152418	138009	Hs.371738	NM_152418	ENSG00000176566	DCAF4L2	WDR21C	DDB1 and CUL4 associated factor 4 like 2	protein-coding	0.007663	0.339695	
chunk0075_79_1	chr16	48182116	48182324	+	0	NA	intron (NM_033151, intron 22 of 28)	intron (NM_033151, intron 22 of 28)	-35450	NM_033226	94160	Hs.410111	NM_033226	ENSG00000140798	ABCC12	MRP9	ATP binding cassette subfamily C member 12	protein-coding	0.004808	0.483254	
chunk0068_16_1	chr15	50686094	50686557	+	0	NA	intron (NM_001301212, intron 1 of 38)	CpG	490	NM_001301212	54822	Hs.512894	NM_017672	ENSG00000092439	TRPM7	ALSPDC|CHAK|CHAK1|LTRPC7|LTrpC-7|TRP-PLIK	transient receptor potential cation channel subfamily M member 7	protein-coding	0.077754	0.646552	
chunk0070_218_1	chr15	72670837	72671113	+	0	NA	Intergenic	Intergenic	15174	NR_002780									0.010870	0.592058	
chunk0167_393_1	chr6	74774324	74775099	+	0	NA	Intergenic	Intergenic	431196	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.007742	0.365979	220(GAGAGCAGTATGTACC,-,0.00),221(AGAGCAGTATGTACCA,+,0.00),307(CAGAACATCTTGTACC,-,0.00),308(AGAACATCTTGTACCA,+,0.00)
chunk0170_302_1	chr6	115707940	115708153	+	0	NA	Intergenic	L3|LINE|CR1	-330685	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.014085	0.355140	
chunk0009_40_1	chr1	100430261	100430904	+	0	NA	intron (NM_003672, intron 5 of 15)	intron (NM_003672, intron 5 of 15)	78115	NM_003672	8556	Hs.127411	NM_003672	ENSG00000079335	CDC14A	DFNB105|DFNB32|DFNB35|cdc14|hCDC14	cell division cycle 14A	protein-coding	0.006221	0.378882	
chunk0115_213_1	chr21	26918388	26918782	+	0	NA	3' UTR (NM_007038, exon 8 of 8)	3' UTR (NM_007038, exon 8 of 8)	-35376	NR_039916	100616243		NR_039916	ENSG00000266133	MIR4759	-	microRNA 4759	ncRNA	0.010152	0.313924	
chunk0036_388_1	chr11	67674453	67674965	+	0	NA	promoter-TSS (NM_000695)	promoter-TSS (NM_000695)	-78	NM_000695	222	Hs.87539	NM_000695	ENSG00000132746	ALDH3B2	ALDH8	aldehyde dehydrogenase 3 family member B2	protein-coding	0.017578	0.596491	
chunk0073_344_1	chr16	14565219	14565975	+	0	NA	intron (NM_002582, intron 18 of 23)	intron (NM_002582, intron 18 of 23)	64674	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.005291	0.398943	
chunk0194_123_1	chr8	83998674	83999047	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-184358	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.002681	0.355615	
chunk0188_47_1	chr8	6735499	6735918	+	0	NA	intron (NM_018361, intron 4 of 7)	L1MCa|LINE|L1	-9456	NR_039803	100616348		NR_039803	ENSG00000266038	MIR4659A	mir-4659a	microRNA 4659a	ncRNA	0.009547	0.378571	315(AAGAACAGAGTGTTCC,-,0.00),316(AGAACAGAGTGTTCCT,+,0.00)
chunk0101_224_1	chr2	131048807	131049006	+	0	NA	3' UTR (NM_001009993, exon 7 of 7)	3' UTR (NM_001009993, exon 7 of 7)	44525	NM_001009993	130074	Hs.534679	NM_001009993	ENSG00000152102	FAM168B	MANI	family with sequence similarity 168 member B	protein-coding	0.025126	0.560000	
chunk0165_270_1	chr6	35926558	35927151	+	0	NA	Intergenic	Intergenic	-5674	NR_034069	6732	Hs.443861	NM_003137	ENSG00000096063	SRPK1	SFRSK1	SRSF protein kinase 1	protein-coding	0.003373	0.425926	
chunk0125_406_1	chr3	72229810	72230361	+	0	NA	Intergenic	Intergenic	78828	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.009074	0.436594	
chunk0079_164_1	chr17	13565727	13566041	+	0	NA	intron (NM_006042, intron 1 of 1)	L1MEd|LINE|L1	-22238	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.009554	0.333333	
chunk0176_39_1	chr7	10044711	10045383	+	0	NA	Intergenic	L1MC3|LINE|L1	410777	NR_002790	168741	Hs.545134	NR_002790		PER4	-	period circadian regulator 3 pseudogene	pseudo	0.001488	0.322437	224(TAGTACAGAGAGTTCA,-,0.00),225(AGTACAGAGAGTTCAC,+,0.00)
chunk0174_306_1	chr6	162715717	162716201	+	0	NA	intron (NM_013988, intron 1 of 8)	intron (NM_013988, intron 1 of 8)	-11173	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.014463	0.412371	
chunk0089_114_1	chr18	58552102	58552573	+	0	NA	intron (NM_052947, intron 4 of 12)	intron (NM_052947, intron 4 of 12)	-48283	NR_132963	106635543		NR_132963		SNORA108	-	small nucleolar RNA, H/ACA box 108	snoRNA	0.008493	0.425847	
chunk0143_178_1	chr4	111886735	111887019	+	0	NA	Intergenic	Intergenic	-258520	NM_152400	132720	Hs.23439	NM_152400	ENSG00000174749	FAM241A	C4orf32	family with sequence similarity 241 member A	protein-coding	0.003521	0.326316	
chunk0069_301_1	chr15	65534200	65534740	+	0	NA	intron (NM_016395, intron 1 of 10)	intron (NM_016395, intron 1 of 10)	3981	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.012963	0.432532	
chunk0108_350_1	chr2	236073984	236074767	+	0	NA	intron (NM_001037131, intron 16 of 17)	intron (NM_001037131, intron 16 of 17)	93634	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.008940	0.441327	467(TGGCACAGGCTGTTCT,-,0.00),468(GGCACAGGCTGTTCTT,+,0.00)
chunk0035_401_1	chr11	56700277	56700566	+	0	NA	promoter-TSS (NM_001013358)	promoter-TSS (NM_001013358)	33	NM_001013358	504191		NM_001013358		OR9G9	OR9G1	olfactory receptor family 9 subfamily G member 9	protein-coding	0.013841	0.455172	
chunk0180_189_1	chr7	66119591	66119829	+	0	NA	intron (NM_001040648, intron 1 of 2)	MER21A|LTR|ERVL	4892	NM_001142414	27297	Hs.300684	NM_014478	ENSG00000241258	CRCP	CGRP-RCP|CGRPRCP|RCP|RCP9|RPC9	CGRP receptor component	protein-coding	0.004202	0.401674	
chunk0116_257_1	chr21	38906964	38907512	+	0	NA	intron (NR_120405, intron 2 of 3)	intron (NR_120405, intron 2 of 3)	31191	NR_120405	400867	Hs.689509	NR_120405		LOC400867	-	uncharacterized LOC400867	ncRNA	0.020073	0.566485	
chunk0057_52_1	chr13	97165925	97166219	+	0	NA	Intergenic	Intergenic	13550	NR_125725	103625683	Hs.679591	NR_125725	ENSG00000233124	LINC00456	-	long intergenic non-protein coding RNA 456	ncRNA	0.000000	0.359322	
chunk0103_287_1	chr2	165989668	165989952	+	0	NA	3' UTR (NM_001165964, exon 26 of 26)	3' UTR (NM_001165964, exon 26 of 26)	32392	NR_110598	102724058	Hs.570269	NR_110598	ENSG00000236107	LOC102724058	-	uncharacterized LOC102724058	ncRNA	0.000000	0.259649	
chunk0059_348_1	chr14	37172283	37172494	+	0	NA	non-coding (NR_033240, exon 1 of 1)	non-coding (NR_033240, exon 1 of 1)	272	NM_030631	89874	Hs.730857	NM_030631	ENSG00000183032	SLC25A21	ODC|ODC1	solute carrier family 25 member 21	protein-coding	0.075829	0.646226	
chunk0112_294_1	chr20	44092534	44093209	+	0	NA	Intergenic	L1MEc|LINE|L1	94707	NM_175913	57158	Hs.441737	NM_020433	ENSG00000149596	JPH2	CMH17|JP-2|JP2	junctophilin 2	protein-coding	0.013333	0.522189	231(GAGCAGACACTGTTCC,-,0.00),232(AGCAGACACTGTTCCT,+,0.00)
chunk0013_398_1	chr1	172932091	172932348	+	0	NA	Intergenic	Intergenic	118744	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.015564	0.333333	
chunk0022_26_1	chr10	7886092	7886422	+	0	NA	intron (NM_031923, intron 2 of 6)	intron (NM_031923, intron 2 of 6)	67753	NM_031923	83860	Hs.527688	NM_031923	ENSG00000165632	TAF3	TAF140|TAFII-140|TAFII140	TATA-box binding protein associated factor 3	protein-coding	0.006061	0.462236	
chunk0018_189_1	chr1	219277238	219277661	+	0	NA	Intergenic	Intergenic	102480	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.000000	0.408019	158(TAGAACAGCCTGTGCC,-,0.00),159(AGAACAGCCTGTGCCT,+,0.00)
chunk0121_79_1	chr3	15925810	15926645	+	0	NA	Intergenic	Intergenic	52456	NR_030289	693148		NR_030289	ENSG00000207815	MIR563	MIRN563|hsa-mir-563	microRNA 563	ncRNA	0.001198	0.348086	
chunk0033_260_1	chr11	18574849	18575706	+	0	NA	intron (NM_001261382, intron 2 of 10)	intron (NM_001261382, intron 2 of 10)	4241	NM_001261385	55293	Hs.407991	NM_018314	ENSG00000151116	UEVLD	ATTP|UEV3	UEV and lactate/malate dehyrogenase domains	protein-coding	0.003501	0.372960	
chunk0196_395_1	chr8	115861419	115861621	+	0	NA	Intergenic	Intergenic	-192492	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.004950	0.384236	
chunk0137_69_1	chr4	12532169	12532708	+	0	NA	Intergenic	Intergenic	308987	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.000000	0.335185	
chunk0066_99_1	chr15	29823152	29823475	+	0	NA	promoter-TSS (NM_003257)	promoter-TSS (NM_003257)	-810	NM_175610	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.012384	0.404321	
chunk0187_421_1	chr7	158590588	158591051	+	0	NA	promoter-TSS (NR_049893)	promoter-TSS (NR_049893)	190	NR_132379	105375616	Hs.641681	NR_132379		LINC01022	-	long intergenic non-protein coding RNA 1022	ncRNA	0.028078	0.547414	
chunk0199_330_1	chr9	8854664	8855072	+	0	NA	intron (NM_002839, intron 11 of 45)	intron (NM_002839, intron 11 of 45)	-3150	NR_121600	101929407	Hs.649971	NR_121599		PTPRD-AS1	-	PTPRD antisense RNA 1	ncRNA	0.004902	0.332518	
chunk0122_126_1	chr3	31431984	31432183	+	0	NA	Intergenic	LTR33|LTR|ERVL	-100418	NM_178862	201595	Hs.475812	NM_178862	ENSG00000163527	STT3B	CDG1X|SIMP|STT3-B	STT3 oligosaccharyltransferase complex catalytic subunit B	protein-coding	0.005025	0.520000	
chunk0042_132_1	chr12	3740311	3740895	+	0	NA	intron (NM_032680, intron 1 of 10)	MIRc|SINE|MIR	12597	NM_032680	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.010274	0.396581	
chunk0128_118_1	chr3	106349953	106350813	+	0	NA	Intergenic	Intergenic	-481340	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.004651	0.344948	34(GGGCACATGCTGTTTT,-,0.00),35(GGCACATGCTGTTTTA,+,0.00),521(GAGTACATGTAGTTCT,-,0.00),522(AGTACATGTAGTTCTC,+,0.00)
chunk0034_298_1	chr11	34910849	34911595	+	0	NA	intron (NM_015957, intron 1 of 6)	L2|LINE|L2	-4908	NM_001166158	8050	Hs.502315	NM_003477	ENSG00000110435	PDHX	DLDBP|E3BP|OPDX|PDHXD|PDX1|proX	pyruvate dehydrogenase complex component X	protein-coding	0.004021	0.397590	404(AGGTACTGGATGTACT,-,0.00),405(GGTACTGGATGTACTT,+,0.00)
chunk0107_445_1	chr2	225271160	225271685	+	0	NA	Intergenic	L1MA7|LINE|L1	-129464	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.000000	0.313688	
chunk0148_358_1	chr5	14569870	14570452	+	0	NA	Intergenic	Intergenic	-11621	NM_019018	54491	Hs.155085	NM_019018	ENSG00000145569	OTULINL	FAM105A|NET20	OTU deubiquitinase with linear linkage specificity like	protein-coding	0.006873	0.449400	
chunk0053_92_1	chr13	28513748	28514364	+	0	NA	Intergenic	L1MCa|LINE|L1	-18928	NM_001160030	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.009740	0.390600	
chunk0028_445_1	chr10	94075791	94076577	+	0	NA	intron (NM_001288989, intron 2 of 32)	intron (NM_001288989, intron 2 of 32)	-12842	NM_001165979	51196	Hs.655033	NM_016341	ENSG00000138193	PLCE1	NPHS3|PLCE|PPLC	phospholipase C epsilon 1	protein-coding	0.006361	0.421855	
chunk0162_346_1	chr6	7031475	7032024	+	0	NA	Intergenic	L2b|LINE|L2	-75848	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.010929	0.461818	217(GGGTACTCAGTGTCCT,-,0.00),218(GGTACTCAGTGTCCTG,+,0.00),253(AGACCAAAGTGTCCCT,+,0.00)
chunk0146_80_1	chr4	157997366	157997780	+	0	NA	Intergenic	L2|LINE|L2	174993	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.000000	0.387952	
chunk0060_316_1	chr14	51267560	51267925	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	27574	NM_030755	81542	Hs.125221	NM_030755	ENSG00000139921	TMX1	PDIA11|TMX|TXNDC|TXNDC1	thioredoxin related transmembrane protein 1	protein-coding	0.005479	0.327869	274(CAATACAGTATGTTCC,-,0.00),275(AATACAGTATGTTCCA,+,0.00)
chunk0165_187_1	chr6	34462473	34462863	+	0	NA	Intergenic	Intergenic	-3393	NM_020804	29993	Hs.520087	NM_020804	ENSG00000124507	PACSIN1	SDPI	protein kinase C and casein kinase substrate in neurons 1	protein-coding	0.017949	0.567775	
chunk0198_331_1	chr8	140032211	140032734	+	0	NA	intron (NM_001160372, intron 17 of 22)	intron (NM_001160372, intron 17 of 22)	-329416	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.003824	0.354962	
chunk0132_392_1	chr3	163734143	163734379	+	0	NA	Intergenic	Intergenic	-430960	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.000000	0.320675	
chunk0171_442_1	chr6	131760944	131761259	+	0	NA	Intergenic	Intergenic	-31071	NR_039610	100616455		NR_039610	ENSG00000266807	MIR548H5	-	microRNA 548h-5	ncRNA	0.000000	0.376582	
chunk0061_429_1	chr14	65250114	65250481	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-27950	NR_103769	100128233	Hs.497323	NR_103769	ENSG00000255002	LINC02324	-	long intergenic non-protein coding RNA 2324	ncRNA	0.010899	0.459239	
chunk0204_1_1	chr9	91521703	91522239	+	0	NA	Intergenic	L1MB3|LINE|L1	-97345	NM_001290000	4783	Hs.79334	NM_005384	ENSG00000165030	NFIL3	E4BP4|IL3BP1|NF-IL3A|NFIL3A	nuclear factor, interleukin 3 regulated	protein-coding	0.001866	0.290503	279(ATGTACAGTATGTTCT,-,0.00),280(TGTACAGTATGTTCTC,+,0.00)
chunk0172_316_1	chr6	138258873	138259561	+	0	NA	intron (NM_020340, intron 10 of 33)	intron (NM_020340, intron 10 of 33)	-40727	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.013081	0.433962	228(GGGGCCAGGATGTTCT,-,0.00),229(GGGCCAGGATGTTCTG,+,0.00)
chunk0206_26_1	chr9	116151258	116151973	+	0	NA	Intergenic	MIRb|SINE|MIR	-2177	NM_002581	5069	Hs.643599	NM_002581	ENSG00000182752	PAPPA	ASBABP2|DIPLA1|IGFBP-4ase|PAPA|PAPP-A|PAPPA1	pappalysin 1	protein-coding	0.005594	0.379888	
chunk0070_346_1	chr15	75922223	75922460	+	0	NA	intron (NR_037623, intron 4 of 5)	intron (NR_037623, intron 4 of 5)	10789	NR_003136									0.008439	0.483193	
chunk0027_350_1	chr10	78657823	78658070	+	0	NA	Intergenic	MIR3|SINE|MIR	390618	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.000000	0.491935	
chunk0182_377_1	chr7	100088631	100088866	+	0	NA	promoter-TSS (NM_006833)	promoter-TSS (NM_006833)	-212	NM_006833	10980	Hs.15591	NM_006833	ENSG00000168090	COPS6	CSN6|MOV34-34KD	COP9 signalosome subunit 6	protein-coding	0.080851	0.563559	
chunk0011_385_1	chr1	153875366	153875970	+	0	NA	intron (NM_020699, intron 1 of 10)	intron (NM_020699, intron 1 of 10)	47307	NM_020699	57459	Hs.4779	NM_020699	ENSG00000143614	GATAD2B	MRD18|P66beta|p68	GATA zinc finger domain containing 2B	protein-coding	0.008278	0.381818	
chunk0149_217_1	chr5	22060700	22060918	+	0	NA	intron (NM_004061, intron 5 of 14)	LTR40b|LTR|ERVL	-81543	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.009174	0.388128	
chunk0090_88_1	chr18	70523032	70523466	+	0	NA	Intergenic	Intergenic	127608	NM_001278515									0.011521	0.420690	
chunk0090_27_1	chr19	1142014	1142290	+	0	NA	intron (NM_014963, intron 4 of 31)	intron (NM_014963, intron 4 of 31)	-9878	NM_001100122	22904	Hs.408708	NM_014963	ENSG00000064932	SBNO2	KIAA0963|SNO|STNO	strawberry notch homolog 2	protein-coding	0.010870	0.559567	
chunk0037_303_1	chr11	76371179	76371447	+	0	NA	intron (NR_130898, intron 1 of 5)	L2b|LINE|L2	9652	NR_130898	5612	Hs.503315	NM_004705	ENSG00000137492	THAP12	DAP4|P52rIPK|PRKRIR|THAP0	THAP domain containing 12	protein-coding	0.007463	0.416357	
chunk0056_366_1	chr13	92649311	92649857	+	0	NA	intron (NM_004466, intron 7 of 7)	Mam_R4|LINE|Dong-R4	70371	NR_049776	100873969	Hs.577863	NR_046520	ENSG00000235984	GPC5-AS1	-	GPC5 antisense RNA 1	ncRNA	0.001832	0.308958	
chunk0109_351_1	chr2	238893380	238893743	+	0	NA	intron (NM_001271893, intron 1 of 1)	intron (NM_001271893, intron 1 of 1)	32708	NR_034162	401039	Hs.516791	NM_001001698	ENSG00000227744	LINC01940	-	long intergenic non-protein coding RNA 1940	ncRNA	0.044077	0.557692	106(AAGCACAGCCTGTGCC,-,0.00),107(AGCACAGCCTGTGCCT,+,0.00)
chunk0201_352_1	chr9	68412653	68413094	+	0	NA	intron (NM_021965, intron 6 of 10)	intron (NM_021965, intron 6 of 10)	-55007	NR_121192	572558	Hs.552819	NR_015423	ENSG00000224958	PGM5-AS1	FAM233A	PGM5 antisense RNA 1	ncRNA	0.006803	0.411765	
chunk0036_75_1	chr11	60246957	60247170	+	0	NA	Intergenic	L1PA14|LINE|L1	-33478	NM_024021	51338	Hs.325960	NM_024021	ENSG00000110079	MS4A4A	4SPAN1|CD20-L1|CD20L1|HDCME31P|MS4A4|MS4A7	membrane spanning 4-domains A4A	protein-coding	0.000000	0.542056	
chunk0105_39_1	chr2	182890866	182891252	+	0	NA	Intergenic	Intergenic	-24289	NM_001463	2487	Hs.128453	NM_001463	ENSG00000162998	FRZB	FRE|FRITZ|FRP-3|FRZB-1|FRZB-PEN|FRZB1|FZRB|OS1|SFRP3|SRFP3|hFIZ	frizzled related protein	protein-coding	0.007772	0.372093	
chunk0161_412_1	chr5	177538571	177538770	+	0	NA	intron (NR_024019, intron 3 of 11)	intron (NR_024019, intron 3 of 11)	15877	NM_001190946	54540	Hs.484289	NM_019057	ENSG00000146067	FAM193B	IRIZIO	family with sequence similarity 193 member B	protein-coding	0.015075	0.550000	
chunk0178_328_1	chr7	38271132	38271331	+	0	NA	intron (NM_001003806, intron 1 of 3)	intron (NM_001003806, intron 1 of 3)	2416	NM_001003799	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.000000	0.355000	
chunk0071_172_1	chr15	83279629	83279828	+	0	NA	intron (NM_001717, intron 1 of 4)	intron (NM_001717, intron 1 of 4)	3729	NM_001301206	646	Hs.459153	NM_001717	ENSG00000169594	BNC1	BNC|BSN1|HsT19447	basonuclin 1	protein-coding	0.000000	0.455000	
chunk0059_216_1	chr14	33938328	33938803	+	0	NA	intron (NM_001308103, intron 1 of 4)	intron (NM_001308103, intron 1 of 4)	12261	NM_001308103	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.027368	0.535714	
chunk0003_440_1	chr1	41216370	41216953	+	0	NA	intron (NM_001172219, intron 1 of 14)	intron (NM_001172219, intron 1 of 14)	25482	NM_001172218	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.001715	0.414384	
chunk0205_336_1	chr9	113164233	113164851	+	0	NA	TTS (NM_015258)	TTS (NM_015258)	13584	NM_001860	1318	Hs.24030	NM_001860	ENSG00000136867	SLC31A2	COPT2|CTR2|hCTR2	solute carrier family 31 member 2	protein-coding	0.004854	0.455574	
chunk0191_260_1	chr8	53399793	53400040	+	0	NA	Intergenic	Intergenic	-148219	NM_001282904	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.004049	0.443548	
chunk0014_10_1	chr1	174290141	174290378	+	0	NA	intron (NM_014857, intron 10 of 20)	L1MA9|LINE|L1	130845	NM_014857	9910	Hs.585378	NM_014857	ENSG00000152061	RABGAP1L	HHL|TBC1D18	RAB GTPase activating protein 1 like	protein-coding	0.000000	0.500000	
chunk0198_468_1	chr8	144755419	144755900	+	0	NA	promoter-TSS (NM_138367)	promoter-TSS (NM_138367)	-74	NM_138367	90987	Hs.534516	NM_138367	ENSG00000198169	ZNF251	-	zinc finger protein 251	protein-coding	0.112266	0.695021	
chunk0048_130_1	chr12	79884585	79885013	+	0	NA	intron (NM_001244990, intron 2 of 24)	intron (NM_001244990, intron 2 of 24)	29112	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.004673	0.331002	
chunk0139_391_1	chr4	62253045	62253473	+	0	NA	Intergenic	Intergenic	-91494	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.009346	0.349650	
chunk0025_442_1	chr10	60175189	60175768	+	0	NA	intron (NM_001204403, intron 19 of 43)	intron (NM_001204403, intron 19 of 43)	-34462	NM_001149	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.012090	0.446552	
chunk0137_265_1	chr4	22201901	22202485	+	0	NA	Intergenic	Charlie24|DNA|hAT-Charlie	137473	NR_037877	100505912	Hs.270471	NR_037877		LOC100505912	-	uncharacterized LOC100505912	ncRNA	0.005137	0.338462	
chunk0146_367_1	chr4	168274740	168275375	+	0	NA	intron (NM_017631, intron 16 of 37)	intron (NM_017631, intron 16 of 37)	43750	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.003150	0.323899	
chunk0074_342_1	chr16	31544679	31545049	+	0	NA	Intergenic	LTR10C|LTR|ERV1	16982	NM_016633	51327	Hs.274309	NM_016633	ENSG00000169877	AHSP	EDRF|ERAF	alpha hemoglobin stabilizing protein	protein-coding	0.002703	0.404313	
chunk0135_35_1	chr3	185173106	185173590	+	0	NA	intron (NR_038990, intron 1 of 6)	MIRb|SINE|MIR	10447	NR_038990	339926	Hs.567848	NR_038990	ENSG00000223358	EHHADH-AS1	-	EHHADH antisense RNA 1	ncRNA	0.014463	0.391753	
chunk0146_376_1	chr4	168409067	168409469	+	0	NA	intron (NM_001291510, intron 22 of 29)	intron (NM_001291510, intron 22 of 29)	71246	NM_001012967	91351	Hs.535011	NM_001012967	ENSG00000181381	DDX60L	-	DExD/H-box 60 like	protein-coding	0.004975	0.359801	183(CAGAACACACTGTAAT,-,0.00)
chunk0169_45_1	chr6	97497630	97498083	+	0	NA	intron (NR_110757, intron 1 of 4)	intron (NR_110757, intron 1 of 4)	192270	NR_110757	101927314	Hs.520283	NR_110757	ENSG00000271860	LOC101927314	-	uncharacterized LOC101927314	ncRNA	0.004415	0.378855	217(GAGAACACAGTGTACT,-,0.00),218(AGAACACAGTGTACTG,+,0.00)
chunk0128_175_1	chr3	107293349	107294137	+	0	NA	intron (NR_028302, intron 2 of 3)	L1ME1|LINE|L1	53051	NR_028301	344595	Hs.543039	NR_028301	ENSG00000243701	DUBR	DUM|LINC00883|LINC0883	DPPA2 upstream binding RNA	ncRNA	0.000000	0.307985	
chunk0143_115_1	chr4	109362679	109363099	+	0	NA	Intergenic	MIR|SINE|MIR	-60246	NM_032518	84570	Hs.658842	NM_032518	ENSG00000188517	COL25A1	AMY|CFEOM5|CLAC|CLAC-P|CLACP	collagen type XXV alpha 1 chain	protein-coding	0.004762	0.372922	
chunk0164_329_1	chr6	25242686	25242964	+	0	NA	Intergenic	Intergenic	18582	NR_110862	101928663	Hs.561600	NR_110862		LOC101928663	-	uncharacterized LOC101928663	ncRNA	0.007194	0.412186	
chunk0020_109_1	chr1	233059435	233059857	+	0	NA	intron (NM_014801, intron 23 of 33)	L2c|LINE|L2	109022	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.000000	0.373522	
chunk0197_199_1	chr8	122436970	122437431	+	0	NA	intron (NR_131202, intron 2 of 3)	intron (NR_131202, intron 2 of 3)	131444	NR_131202	105375734	Hs.628341	NR_131202		SMILR	-	smooth muscle induced lncRNA, enhancer of proliferation	ncRNA	0.002169	0.348485	
chunk0146_245_1	chr4	162317925	162318515	+	0	NA	Intergenic	L1P4b|LINE|L1	-154186	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.010169	0.477157	
chunk0137_347_1	chr4	25312574	25312919	+	0	NA	promoter-TSS (NM_024936)	promoter-TSS (NM_024936)	-28	NM_024936	29063	Hs.278945	NM_024936	ENSG00000168228	ZCCHC4	HSPC052|ZGRF4	zinc finger CCHC-type containing 4	protein-coding	0.086957	0.687861	
chunk0102_352_1	chr2	152473604	152473977	+	0	NA	intron (NM_052905, intron 1 of 25)	intron (NM_052905, intron 1 of 25)	138553	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.013405	0.374332	
chunk0164_208_1	chr6	22640688	22641129	+	0	NA	Intergenic	Intergenic	71459	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.004535	0.309955	
chunk0074_220_1	chr16	25696155	25696592	+	0	NA	intron (NM_006040, intron 1 of 1)	intron (NM_006040, intron 1 of 1)	4347	NM_006040	9951	Hs.655275	NM_006040	ENSG00000182601	HS3ST4	3-OST-4|30ST4|3OST4|h3-OST-4	heparan sulfate-glucosamine 3-sulfotransferase 4	protein-coding	0.018307	0.488584	
chunk0064_312_1	chr14	95770633	95771028	+	0	NA	Intergenic	Intergenic	-56634	NM_021966	8115	Hs.2484	NM_021966	ENSG00000100721	TCL1A	TCL1	T cell leukemia/lymphoma 1A	protein-coding	0.007595	0.469697	
chunk0028_65_1	chr10	83374741	83375085	+	0	NA	Intergenic	Intergenic	-764516	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.000000	0.336232	
chunk0154_241_1	chr5	81245346	81245686	+	0	NA	intron (NR_034121, intron 1 of 2)	intron (NR_034121, intron 1 of 2)	12196	NM_001099735	1160	Hs.80691	NM_001825	ENSG00000131730	CKMT2	SMTCK	creatine kinase, mitochondrial 2	protein-coding	0.011765	0.475073	
chunk0026_224_1	chr10	64873486	64873767	+	0	NA	Intergenic	Intergenic	48098	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.003559	0.333333	127(AGGCACATCCAGTTCA,-,0.00),128(GGCACATCCAGTTCAA,+,0.00)
chunk0192_126_1	chr8	61791068	61791333	+	0	NA	Intergenic	Intergenic	76412	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.003774	0.436090	
chunk0160_347_1	chr5	160108185	160108535	+	0	NA	intron (NM_052927, intron 1 of 3)	intron (NM_052927, intron 1 of 3)	11085	NM_001130864	114825	Hs.744960	NM_052927	ENSG00000170234	PWWP2A	MST101	PWWP domain containing 2A	protein-coding	0.005714	0.410256	
chunk0129_330_1	chr3	124591442	124591641	+	0	NA	intron (NM_007064, intron 1 of 26)	L2b|LINE|L2	6882	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.000000	0.400000	
chunk0156_215_1	chr5	108122815	108123062	+	0	NA	intron (NM_001163315, intron 6 of 8)	intron (NM_001163315, intron 6 of 8)	259160	NM_001163315	64839	Hs.657225	NM_022824	ENSG00000145743	FBXL17	FBXO13|Fbl17|Fbx13	F-box and leucine rich repeat protein 17	protein-coding	0.012146	0.403226	40(GAAAACAACATGTTCC,-,0.00),41(AAAACAACATGTTCCT,+,0.00)
chunk0188_58_1	chr8	7027056	7027727	+	0	NA	Intergenic	MER51E|LTR|ERV1	2098	NR_073421	724068	Hs.690600	NR_073421	ENSG00000234178	DEFA11P	DEFAP3	defensin alpha 11, pseudogene	pseudo	0.017884	0.421131	
chunk0148_196_1	chr5	8333464	8333948	+	0	NA	non-coding (NR_039984, exon 6 of 6)	non-coding (NR_039984, exon 6 of 6)	123858	NR_039984	729506	Hs.566412	NR_039984	ENSG00000245729	LINC02226	-	long intergenic non-protein coding RNA 2226	ncRNA	0.010331	0.441237	
chunk0116_130_1	chr21	36183162	36183764	+	0	NA	intron (NM_005128, intron 2 of 36)	intron (NM_005128, intron 2 of 36)	18922	NM_005128	9980	Hs.204575	NM_005128	ENSG00000142197	DOP1B	21orf5|C21orf5|DOPEY2	DOP1 leucine zipper like protein B	protein-coding	0.018272	0.525705	
chunk0062_317_1	chr14	73239117	73239743	+	0	NA	intron (NM_173462, intron 1 of 25)	intron (NM_173462, intron 1 of 25)	1933	NM_173462	89932	Hs.509909	NM_173462	ENSG00000100767	PAPLN	PPN	papilin, proteoglycan like sulfated glycoprotein	protein-coding	0.038339	0.502392	407(GAAACAAGTTGTTCTT,+,0.00)
chunk0201_284_1	chr9	39036135	39036350	+	0	NA	Intergenic	Intergenic	252061	NM_033655	79937	Hs.128474	NM_033655	ENSG00000106714	CNTNAP3	CASPR3|CNTNAP3A	contactin associated protein like 3	protein-coding	0.009302	0.328704	
chunk0126_395_1	chr3	84893130	84893607	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-23793	NR_033860	440970	Hs.411049	NR_033860	ENSG00000242641	LINC00971	-	long intergenic non-protein coding RNA 971	ncRNA	0.008386	0.372385	
chunk0076_433_1	chr16	73070470	73070850	+	0	NA	Intergenic	Intergenic	-12025	NM_001164766	463	Hs.598297	NM_006885	ENSG00000140836	ZFHX3	ATBF1|ATBT|ZNF927	zinc finger homeobox 3	protein-coding	0.044737	0.553806	
chunk0049_375_1	chr12	95762191	95762574	+	0	NA	intron (NM_021229, intron 2 of 9)	intron (NM_021229, intron 2 of 9)	28376	NM_021229	59277	Hs.201034	NM_021229	ENSG00000074527	NTN4	PRO3091	netrin 4	protein-coding	0.002611	0.395833	
chunk0059_203_1	chr14	33464529	33464970	+	0	NA	intron (NM_022123, intron 3 of 10)	MamRTE1|LINE|RTE-BovB	-244188	NR_132771	106635522		NR_132771		SNORA89	-	small nucleolar RNA, H/ACA box 89	snoRNA	0.013605	0.477376	147(CAGAGCATGCTGTCCT,-,0.00),148(AGAGCATGCTGTCCTT,+,0.00),282(GAGAACTGCCTGGTCC,-,0.00),283(AGAACTGCCTGGTCCT,+,0.00)
chunk0034_239_1	chr11	34068119	34068849	+	0	NA	intron (NM_005898, intron 2 of 18)	intron (NM_005898, intron 2 of 18)	16801	NM_203364	4076	Hs.471818	NM_005898	ENSG00000135387	CAPRIN1	GPIAP1|GPIP137|GRIP137|M11S1|RNG105|p137GPI	cell cycle associated protein 1	protein-coding	0.005479	0.369357	
chunk0082_215_1	chr17	57057177	57057690	+	0	NA	Intergenic	MIR|SINE|MIR	11955	NR_002818	376412	Hs.132299	NR_002818	ENSG00000261192	RNF126P1	-	ring finger protein 126 pseudogene 1	pseudo	0.001949	0.375486	
chunk0203_227_1	chr9	87004066	87004297	+	0	NA	Intergenic	Intergenic	37945	NR_027471	440173	Hs.127361	NR_027471	ENSG00000269994	LOC440173	-	uncharacterized LOC440173	ncRNA	0.000000	0.396552	
chunk0180_245_1	chr7	68665057	68665618	+	0	NA	Intergenic	Intergenic	645084	NR_120514	102723427	Hs.583491	NR_120514	ENSG00000225209	LOC102723427	-	uncharacterized LOC102723427	ncRNA	0.012478	0.391459	
chunk0072_265_1	chr15	96641180	96641579	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	140275	NR_102754	100652749	Hs.303588	NR_102753	ENSG00000259282	SPATA8-AS1	-	SPATA8 antisense RNA 1 (head to head)	ncRNA	0.012531	0.362500	
chunk0006_260_1	chr1	69594121	69594456	+	0	NA	Intergenic	Intergenic	-165887	NM_020794	57554	Hs.479658	NM_020794	ENSG00000033122	LRRC7	DENSIN	leucine rich repeat containing 7	protein-coding	0.011940	0.300595	
chunk0018_367_1	chr1	221868874	221869073	+	0	NA	Intergenic	Intergenic	-28307	NR_125989	101929771	Hs.557001	NR_125989	ENSG00000227925	LINC01655	-	long intergenic non-protein coding RNA 1655	ncRNA	0.000000	0.325000	
chunk0018_376_1	chr1	222225401	222225824	+	0	NA	Intergenic	Intergenic	322490	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.014184	0.356132	
chunk0154_359_1	chr5	87452386	87452926	+	0	NA	Intergenic	Intergenic	-39623	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.003704	0.349353	
chunk0040_133_1	chr11	112488206	112488606	+	0	NA	TTS (NR_120560)	TTS (NR_120560)	4061	NR_120560	101928823	Hs.126118	NR_120559	ENSG00000254968	LINC02763	-	long intergenic non-protein coding RNA 2763	ncRNA	0.007500	0.374065	
chunk0159_42_1	chr5	137143407	137143802	+	0	NA	intron (NM_004598, intron 3 of 10)	MIR|SINE|MIR	355725	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.005063	0.411616	
chunk0163_70_1	chr6	9200069	9200360	+	0	NA	Intergenic	Intergenic	548005	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.003436	0.349315	
chunk0208_8_1	chrX	10176790	10177101	+	0	NA	intron (NM_001256944, intron 2 of 10)	L1ME3A|LINE|L1	20000	NM_001830	1183	Hs.495674	NM_001830	ENSG00000073464	CLCN4	CLC4|ClC-4|ClC-4A|MRX15|MRX49|MRXSRC	chloride voltage-gated channel 4	protein-coding	0.019293	0.500000	
chunk0075_186_1	chr16	52149177	52149621	+	0	NA	Intergenic	Intergenic	64118	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.004505	0.375281	
chunk0018_245_1	chr1	220046307	220046908	+	0	NA	promoter-TSS (NM_004446)	promoter-TSS (NM_004446)	51	NM_004446	2058	Hs.497788	NM_004446	ENSG00000136628	EPRS	EARS|GLUPRORS|HLD15|PARS|PIG32|QARS|QPRS	glutamyl-prolyl-tRNA synthetase	protein-coding	0.088186	0.564784	
chunk0195_163_1	chr8	95746105	95746653	+	0	NA	intron (NR_038205, intron 2 of 2)	intron (NR_038205, intron 2 of 2)	201969	NR_036611	100500773	Hs.741582	NR_036611		LOC100500773	-	serine and arginine rich splicing factor 3 pseudogene	pseudo	0.010949	0.406193	
chunk0180_376_1	chr7	74174029	74174390	+	0	NA	promoter-TSS (NM_022170)	promoter-TSS (NM_022170)	-167	NM_031992	7458	Hs.520943	NM_022170	ENSG00000106682	EIF4H	WBSCR1|WSCR1|eIF-4H	eukaryotic translation initiation factor 4H	protein-coding	0.149584	0.756906	
chunk0180_367_1	chr7	73959201	73959735	+	0	NA	Intergenic	(TTTTG)n|Simple_repeat|Simple_repeat	-68321	NM_000501	2006	Hs.647061	NM_000501	ENSG00000049540	ELN	ADCL1|SVAS|WBS|WS	elastin	protein-coding	0.005618	0.349533	
chunk0147_385_1	chr4	186547031	186547757	+	0	NA	intron (NM_005958, intron 1 of 1)	intron (NM_005958, intron 1 of 1)	7989	NM_005958	4543	Hs.243467	NM_005958	ENSG00000168412	MTNR1A	MEL-1A-R|MT1	melatonin receptor 1A	protein-coding	0.030303	0.563961	17(GGGACACACCGTCCAC,+,0.00),48(TGGGACACACCGTCCT,-,0.00),49(GGGACACACCGTCCTC,+,0.00),77(TGGGACACACCGTCCT,-,0.00),78(GGGACACACCGTCCTC,+,0.00),106(TGGGACACACCGTCCT,-,0.00),107(GGGACACACCGTCCTC,+,0.00),171(GGGACACACCGTCCAC,+,0.00),203(GGGACACACCGTCCAC,+,0.00),235(GGGACACACCGTCCAC,+,0.00),267(GGGACACACCGTCCAC,+,0.00),298(TGGGACACACCGTCCT,-,0.00),299(GGGACACACCGTCCTC,+,0.00),330(TGGGACACACTGTCCA,-,0.00),331(GGGACACACTGTCCAC,+,0.00),362(TGGGACACACTGTCCT,-,0.00),363(GGGACACACTGTCCTC,+,0.00),391(TGGGACACACTGTCCT,-,0.00),392(GGGACACACTGTCCTC,+,0.00),423(TGGGACATGCTGTACC,-,0.00),424(GGGACATGCTGTACCC,+,0.00),439(CATCACACCCTGTTCC,-,0.00),440(ATCACACCCTGTTCCT,+,0.00),502(CTGAACACCCTGTTCC,-,0.00),503(TGAACACCCTGTTCCA,+,0.00)
chunk0072_347_1	chr15	99574034	99574469	+	0	NA	intron (NM_001130927, intron 1 of 9)	intron (NM_001130927, intron 1 of 9)	8323	NM_005587	4205	Hs.268675	NM_005587	ENSG00000068305	MEF2A	ADCAD1|RSRFC4|RSRFC9|mef2	myocyte enhancer factor 2A	protein-coding	0.009195	0.344037	
chunk0195_406_1	chr8	100486489	100486825	+	0	NA	Intergenic	Intergenic	73054	NM_001270378	157567	Hs.530199	NM_198401	ENSG00000186106	ANKRD46	ANK-S|GENX-115279	ankyrin repeat domain 46	protein-coding	0.000000	0.379822	
chunk0160_265_1	chr5	157129022	157129539	+	0	NA	Intergenic	AluSq2|SINE|Alu	13495	NM_001100816	9443	Hs.279902	NM_004270	ENSG00000155868	MED7	ARC34|CRSP33|CRSP9	mediator complex subunit 7	protein-coding	0.003868	0.378378	
chunk0092_26_1	chr19	18839626	18839825	+	0	NA	intron (NM_001297549, intron 1 of 23)	intron (NM_001297549, intron 1 of 23)	7790	NM_001297549	5976	Hs.515266	NM_002911	ENSG00000005007	UPF1	HUPF1|NORF1|RENT1|pNORF1|smg-2	UPF1 RNA helicase and ATPase	protein-coding	0.025126	0.595000	
chunk0013_339_1	chr1	171920578	171920853	+	0	NA	intron (NM_001136127, intron 1 of 19)	intron (NM_001136127, intron 1 of 19)	56523	NR_046845	100874284		NR_046845	ENSG00000233540	DNM3-IT1	-	DNM3 intronic transcript 1	ncRNA	0.007273	0.286232	
chunk0124_285_1	chr3	57597461	57597833	+	0	NA	promoter-TSS (NM_001660)	promoter-TSS (NM_001660)	-142	NR_132369	106144532	Hs.667207	NR_132369	ENSG00000272146	ARF4-AS1	-	ARF4 antisense RNA 1	ncRNA	0.088710	0.613941	
chunk0209_283_1	chrX	47551644	47552150	+	0	NA	Intergenic	L1MEc|LINE|L1	-9203	NM_001654	369	Hs.446641	NM_001654	ENSG00000078061	ARAF	A-RAF|ARAF1|PKS2|RAFA1	A-Raf proto-oncogene, serine/threonine kinase	protein-coding	0.009881	0.424063	
chunk0003_388_1	chr1	39858806	39859005	+	0	NA	intron (NR_132406, intron 1 of 8)	intron (NR_132406, intron 1 of 8)	24606	NR_132407	54802	Hs.356554	NM_017646	ENSG00000043514	TRIT1	COXPD35|GRO1|IPPT|IPT|IPTase|MOD5|hGRO1	tRNA isopentenyltransferase 1	protein-coding	0.015075	0.395000	
chunk0181_142_1	chr7	81453556	81454112	+	0	NA	Intergenic	L1PB1|LINE|L1	172382	NR_126026	100128317	Hs.571267	NR_126025	ENSG00000233491	LOC100128317	-	uncharacterized LOC100128317	ncRNA	0.000000	0.357271	
chunk0016_358_1	chr1	202305110	202305624	+	0	NA	intron (NM_001017403, intron 11 of 17)	intron (NM_001017403, intron 11 of 17)	36599	NM_014176	29089	Hs.5199	NM_014176	ENSG00000077152	UBE2T	FANCT|HSPC150|PIG50	ubiquitin conjugating enzyme E2 T	protein-coding	0.007782	0.565049	
chunk0010_154_1	chr1	115376998	115377249	+	0	NA	Intergenic	MamRTE1|LINE|RTE-BovB	-38887	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.007968	0.400794	
chunk0113_297_1	chr20	57743721	57744072	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-32360	NM_199171	56937	Hs.517155	NM_020182	ENSG00000124225	PMEPA1	STAG1|TMEPAI	prostate transmembrane protein, androgen induced 1	protein-coding	0.017094	0.454545	
chunk0159_247_1	chr5	141903911	141904767	+	0	NA	Intergenic	MIRb|SINE|MIR	-7644	NR_033244	729080	Hs.730564	NR_033244		LOC729080	-	glycine cleavage system protein H (aminomethyl carrier) pseudogene	pseudo	0.007009	0.397900	673(GGCACAGTTTGTTTCC,+,0.00),697(GATCACACACTGTTCC,-,0.00),698(ATCACACACTGTTCCT,+,0.00)
chunk0029_158_1	chr10	99682076	99682607	+	0	NA	intron (NM_020354, intron 5 of 12)	intron (NM_020354, intron 5 of 12)	22835	NM_020354	57089	Hs.28326	NM_020354	ENSG00000198018	ENTPD7	LALP1	ectonucleoside triphosphate diphosphohydrolase 7	protein-coding	0.001883	0.327068	
chunk0018_80_1	chr1	217296284	217296483	+	0	NA	Intergenic	Intergenic	-158628	NM_001243510	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.005025	0.435000	
chunk0109_249_1	chr20	6311543	6311782	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-115070	NR_109953	101929244	Hs.542488	NR_109953	ENSG00000229876	CASC20	-	cancer susceptibility 20	ncRNA	0.008368	0.545833	
chunk0124_123_1	chr3	54243463	54243662	+	0	NA	intron (NM_018398, intron 2 of 37)	intron (NM_018398, intron 2 of 37)	120896	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.015075	0.355000	
chunk0077_392_1	chr16	84779591	84780172	+	0	NA	TTS (NM_005153)	TTS (NM_005153)	-40100	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.018933	0.388316	
chunk0016_424_1	chr1	203555304	203555503	+	0	NA	Intergenic	Intergenic	61260	NM_014359	26254	Hs.632468	NM_014359	ENSG00000188770	OPTC	OPT	opticin	protein-coding	0.025126	0.530000	
chunk0210_291_1	chrX	85877379	85878138	+	0	NA	intron (NM_000390, intron 13 of 14)	intron (NM_000390, intron 13 of 14)	25949	NR_029848	494323		NR_029848	ENSG00000199051	MIR361	MIRN361|hsa-mir-361|mir-361	microRNA 361	ncRNA	0.002635	0.332895	380(CAGAACAGTTTGTCTT,-,0.00),381(AGAACAGTTTGTCTTC,+,0.00)
chunk0060_303_1	chr14	50865564	50865848	+	0	NA	Intergenic	Intergenic	-6454	NM_001206673	145447	Hs.271896	NM_181533	ENSG00000131969	ABHD12B	BEM46L3|C14orf29|c14_5314	abhydrolase domain containing 12B	protein-coding	0.028169	0.480702	
chunk0055_85_1	chr13	54365011	54365314	+	0	NA	Intergenic	L1MDa|LINE|L1	-53114	NR_031628	100302187		NR_031628	ENSG00000283126	MIR1297	MIRN1297|hsa-mir-1297|mir-1297	microRNA 1297	ncRNA	0.003300	0.263158	
chunk0015_320_1	chr1	189371861	189372073	+	0	NA	Intergenic	Intergenic	1105662	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.295775	
chunk0134_397_1	chr3	183081461	183081834	+	0	NA	intron (NR_120639, intron 2 of 15)	LTR18B|LTR|ERVL	17596	NR_120640	56922	Hs.47649	NM_020166	ENSG00000078070	MCCC1	MCC-B|MCCA	methylcrotonoyl-CoA carboxylase 1	protein-coding	0.005362	0.454545	211(AGGCACATACTGCACT,-,0.00),212(GGCACATACTGCACTT,+,0.00)
chunk0058_197_1	chr14	24442098	24442511	+	0	NA	promoter-TSS (NR_110032)	promoter-TSS (NR_110032)	497	NM_020195	56948	Hs.643552	NM_020195	ENSG00000100445	SDR39U1	C14orf124|HCDI	short chain dehydrogenase/reductase family 39U member 1	protein-coding	0.062954	0.623188	173(AAGCACACAGTGCCCC,-,0.00),174(AGCACACAGTGCCCCT,+,0.00)
chunk0208_401_1	chrX	29113207	29113820	+	0	NA	intron (NM_014271, intron 2 of 10)	L1MEd|LINE|L1	-460765	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.001631	0.356678	
chunk0143_32_1	chr4	106628616	106628959	+	0	NA	Intergenic	Intergenic	-261352	NM_001195138	100507096	Hs.722750	NM_001195138	ENSG00000250298	GIMD1	-	GIMAP family P-loop NTPase domain containing 1	protein-coding	0.008746	0.366279	
chunk0009_310_1	chr1	108190678	108191148	+	0	NA	intron (NM_013386, intron 1 of 9)	intron (NM_013386, intron 1 of 9)	1896	NM_213651	29957	Hs.656870	NM_013386	ENSG00000085491	SLC25A24	APC1|SCAMC-1|SCAMC1	solute carrier family 25 member 24	protein-coding	0.008511	0.371550	161(TGAAACAGAATGTTCT,-,0.00),162(GAAACAGAATGTTCTG,+,0.00)
chunk0121_186_1	chr3	20092439	20092778	+	0	NA	intron (NM_003884, intron 2 of 17)	L1MA5|LINE|L1	-44957	NR_036086	100422901		NR_036086	ENSG00000266745	MIR3135A	MIR3135|hsa-mir-3135a	microRNA 3135a	ncRNA	0.005900	0.388235	
chunk0067_43_1	chr15	40764137	40764461	+	0	NA	intron (NM_005258, intron 1 of 2)	CpG	212	NM_005258	2644	Hs.631717	NM_005258	ENSG00000137880	GCHFR	GFRP|HsT16933|P35	GTP cyclohydrolase I feedback regulator	protein-coding	0.080247	0.707692	
chunk0157_291_1	chr5	120873067	120873367	+	0	NA	Intergenic	Intergenic	341753	NM_001308088	51334	Hs.157461	NM_016644	ENSG00000184838	PRR16	DSC54|LARGEN	proline rich 16	protein-coding	0.000000	0.362126	79(TGGCACTACATGTTCT,-,0.00),80(GGCACTACATGTTCTA,+,0.00)
chunk0172_303_1	chr6	138133154	138133725	+	0	NA	Intergenic	L1M1|LINE|L1	-25916	NM_022121	64065	Hs.201446	NM_022121	ENSG00000112378	PERP	KCP1|KRTCAP1|PIGPC1|THW|dJ496H19.1	p53 apoptosis effector related to PMP22	protein-coding	0.000000	0.300699	
chunk0193_355_1	chr8	79906669	79907423	+	0	NA	Intergenic	Intergenic	-35309	NR_110954	101927040	Hs.350876	NR_110954	ENSG00000249328	LOC101927040	-	uncharacterized LOC101927040	ncRNA	0.005305	0.377483	
chunk0015_242_1	chr1	187849526	187849943	+	0	NA	Intergenic	Intergenic	406106	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.000000	0.342105	
chunk0180_80_1	chr7	54996075	54996408	+	0	NA	Intergenic	L2|LINE|L2	-22791	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.009009	0.428144	
chunk0008_199_1	chr1	93437987	93438316	+	0	NA	Intergenic	Intergenic	-9980	NM_001024948	54874	Hs.134060	NM_017737	ENSG00000137942	FNBP1L	C1orf39|TOCA1	formin binding protein 1 like	protein-coding	0.000000	0.324242	
chunk0074_348_1	chr16	33339766	33340043	+	0	NA	Intergenic	(TGGCTTGGC)n|Simple_repeat|Simple_repeat	-20973	NM_016212	24150	Hs.592038	NM_015369	ENSG00000183632	TP53TG3	P53TG3|TP53TG3A|TP53TG3E|TP53TG3F	TP53 target 3	protein-coding	0.007220	0.669065	
chunk0069_137_1	chr15	62124468	62124712	+	0	NA	Intergenic	Intergenic	40693	NM_001007595	388125	Hs.144372	NM_001007595	ENSG00000205502	C2CD4B	FAM148B|NLF2	C2 calcium dependent domain containing 4B	protein-coding	0.008197	0.326531	
chunk0017_401_1	chr1	212598520	212598773	+	0	NA	intron (NM_001030287, intron 1 of 3)	L1MA2|LINE|L1	-9982	NM_001674	467	Hs.460	NM_001674	ENSG00000162772	ATF3	-	activating transcription factor 3	protein-coding	0.007905	0.409449	
chunk0122_110_1	chr3	30750947	30751289	+	0	NA	intron (NM_207359, intron 14 of 14)	MER51E|LTR|ERV1	143543	NM_207359	339896	Hs.657052	NM_207359	ENSG00000144644	GADL1	ADC|CSADC|HuADC|HuCSADC	glutamate decarboxylase like 1	protein-coding	0.017544	0.466472	
chunk0025_448_1	chr10	60267723	60268273	+	0	NA	intron (NM_001204403, intron 6 of 43)	AluJo|SINE|Alu	121878	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.014545	0.426497	
chunk0159_306_1	chr5	143063168	143063647	+	0	NA	intron (NM_015071, intron 17 of 22)	L2b|LINE|L2	-129093	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.012526	0.472917	26(GGGAACTCAGAGTTCT,-,0.00),27(GGAACTCAGAGTTCTA,+,0.00)
chunk0162_98_1	chr6	2264262	2264498	+	0	NA	intron (NR_046229, intron 3 of 6)	MLT1B|LTR|ERVL-MaLR	18627	NR_046229	100508120	Hs.188825	NR_046229		GMDS-DT	GMDS-AS1	GMDS divergent transcript	ncRNA	0.000000	0.468354	
chunk0105_104_1	chr2	184566679	184567241	+	0	NA	Intergenic	Intergenic	-31406	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.005338	0.357016	
chunk0092_385_1	chr19	36473326	36473789	+	0	NA	intron (NM_032838, intron 2 of 4)	intron (NM_032838, intron 2 of 4)	15878	NM_032838	84924	Hs.533939	NM_032838	ENSG00000186017	ZNF566	-	zinc finger protein 566	protein-coding	0.004320	0.383621	
chunk0138_364_1	chr4	42216756	42217493	+	0	NA	Intergenic	Intergenic	-64246	NM_207406	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.009498	0.403794	
chunk0071_178_1	chr15	83404184	83404986	+	0	NA	Intergenic	Intergenic	-42643	NM_001301109	6457	Hs.270055	NM_003027	ENSG00000140600	SH3GL3	CNSA3|EEN-B2|HsT19371|SH3D2C|SH3P13	SH3 domain containing GRB2 like 3, endophilin A3	protein-coding	0.003741	0.417186	
chunk0054_164_1	chr13	44221677	44222134	+	0	NA	Intergenic	Intergenic	-25705	NR_107046	102465876		NR_107046	ENSG00000276319	MIR8079	hsa-mir-8079	microRNA 8079	ncRNA	0.010941	0.419214	
chunk0183_299_1	chr7	107811847	107812504	+	0	NA	Intergenic	L1ME2|LINE|L1	-8942	NM_000111	1811	Hs.1650	NM_000111	ENSG00000091138	SLC26A3	CLD|DRA	solute carrier family 26 member 3	protein-coding	0.013699	0.389058	
chunk0149_343_1	chr5	27212479	27213149	+	0	NA	Intergenic	Intergenic	-174232	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.001493	0.350224	
chunk0021_46_1	chr10	947268	947615	+	0	NA	Intergenic	Intergenic	14415	NR_120629	101927762	Hs.151159	NR_120629	ENSG00000229869	LOC101927762	-	uncharacterized LOC101927762	ncRNA	0.020173	0.474138	220(CAGAACAAAATGTTCT,-,0.00),221(AGAACAAAATGTTCTG,+,0.00)
chunk0100_197_1	chr2	111154514	111155040	+	0	NA	intron (NM_138623, intron 5 of 5)	L1MC4|LINE|L1	33863	NM_001204106	10018	Hs.469658	NM_006538	ENSG00000153094	BCL2L11	BAM|BIM|BOD	BCL2 like 11	protein-coding	0.007605	0.426945	114(AAGCACATGATGTCCA,-,0.00),115(AGCACATGATGTCCAT,+,0.00)
chunk0164_202_1	chr6	22520867	22521622	+	0	NA	Intergenic	Intergenic	-48205	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.007947	0.391534	
chunk0016_284_1	chr1	200755399	200756111	+	0	NA	intron (NM_001297708, intron 1 of 16)	L2b|LINE|L2	16197	NM_001297708	23271	Hs.23585	NM_203459	ENSG00000118200	CAMSAP2	CAMSAP1L1	calmodulin regulated spectrin associated protein family member 2	protein-coding	0.007022	0.441795	
chunk0080_273_1	chr17	31094622	31094821	+	0	NA	promoter-TSS (NM_001128147)	promoter-TSS (NM_001128147)	-206	NM_000267	4763	Hs.113577	NM_000267	ENSG00000196712	NF1	NFNS|VRNF|WSS	neurofibromin 1	protein-coding	0.070352	0.675000	
chunk0049_86_1	chr12	90782286	90782824	+	0	NA	Intergenic	Intergenic	-135468	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.001859	0.294991	
chunk0003_409_1	chr1	40236527	40237076	+	0	NA	exon (NM_012421, exon 8 of 8)	exon (NM_012421, exon 8 of 8)	-11100	NM_001008740	127391	Hs.406265	NM_001008740	ENSG00000188800	TMCO2	dJ39G22.2	transmembrane and coiled-coil domains 2	protein-coding	0.016393	0.396364	197(CGGTACAGACTGTTCC,-,0.00),198(GGTACAGACTGTTCCC,+,0.00)
chunk0044_444_1	chr12	42362788	42363000	+	0	NA	intron (NM_016488, intron 4 of 12)	LTR40c|LTR|ERVL	36749	NM_201440	51535	Hs.444157	NM_016488	ENSG00000134283	PPHLN1	CR|HSPC206|HSPC232	periphilin 1	protein-coding	0.000000	0.455399	
chunk0053_173_1	chr13	30843200	30843406	+	0	NA	Intergenic	Intergenic	-39259	NR_103813	440132	Hs.729493	NR_103813	ENSG00000236094	LINC00545	-	long intergenic non-protein coding RNA 545	ncRNA	0.019417	0.478261	
chunk0175_325_1	chr6	166992624	166993213	+	0	NA	Intergenic	LTR16C|LTR|ERVL	4994	NR_037504	100500857		NR_037504	ENSG00000265828	MIR3939	mir-3939	microRNA 3939	ncRNA	0.003396	0.438983	
chunk0203_191_1	chr9	86405088	86405768	+	0	NA	Intergenic	Intergenic	-50941	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.004412	0.375918	
chunk0136_24_1	chr4	681955	682200	+	0	NA	TTS (NM_002477)	TTS (NM_002477)	4155	NM_002477	4636	Hs.410970	NM_002477	ENSG00000215375	MYL5	MYLC2	myosin light chain 5	protein-coding	0.085714	0.723577	
chunk0102_424_1	chr2	157182782	157183439	+	0	NA	Intergenic	Intergenic	-74718	NM_014568	11227	Hs.269027	NM_014568	ENSG00000136542	GALNT5	GALNAC-T5|GALNACT5	polypeptide N-acetylgalactosaminyltransferase 5	protein-coding	0.006088	0.384498	
chunk0047_126_1	chr12	69287232	69287671	+	0	NA	Intergenic	Intergenic	-14233	NR_031692	100302182		NR_031692	ENSG00000283476	MIR1279	MIRN1279|hsa-mir-1279	microRNA 1279	ncRNA	0.006834	0.436364	
chunk0209_423_1	chrX	57354671	57355217	+	0	NA	intron (NM_174912, intron 5 of 10)	L1ME4a|LINE|L1	68267	NM_174912	158584	Hs.496205	NM_174912	ENSG00000165591	FAAH2	AMDD	fatty acid amide hydrolase 2	protein-coding	0.001832	0.263254	265(CTGAACAGAGTGTACC,-,0.00),266(TGAACAGAGTGTACCA,+,0.00)
chunk0115_69_1	chr21	21775108	21775689	+	0	NA	intron (NR_109958, intron 2 of 4)	intron (NR_109958, intron 2 of 4)	28413	NR_109958	101927821	Hs.334181	NR_109958	ENSG00000233997	LINC01425	-	long intergenic non-protein coding RNA 1425	ncRNA	0.003442	0.264605	
chunk0211_260_1	chrX	120824396	120824606	+	0	NA	Intergenic	Intergenic	51424	NM_001145718	643311	Hs.729566	NM_001145718	ENSG00000236446	CT47B1	CT47.13|CT47A13	cancer/testis antigen family 47 member B1	protein-coding	0.004762	0.398104	
chunk0127_132_1	chr3	94051437	94051855	+	0	NA	intron (NM_182896, intron 9 of 10)	intron (NM_182896, intron 9 of 10)	11341	NM_176815	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.002392	0.300716	
chunk0150_199_1	chr5	34844978	34845282	+	0	NA	intron (NM_144725, intron 2 of 10)	MIRb|SINE|MIR	5966	NM_144725	153657	Hs.435742	NM_144725	ENSG00000205838	TTC23L	MC25-1	tetratricopeptide repeat domain 23 like	protein-coding	0.000000	0.370492	156(GTCACACACTGTGCTG,+,0.00)
chunk0108_5_1	chr2	225975733	225976148	+	0	NA	Intergenic	HAL1ME|LINE|L1	-166854	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.002410	0.334135	
chunk0130_157_1	chr3	132578104	132578522	+	0	NA	intron (NR_132427, intron 14 of 17)	intron (NR_132427, intron 14 of 17)	-18924	NM_016557	51554	Hs.310512	NM_016557	ENSG00000129048	ACKR4	CC-CKR-11|CCBP2|CCR-11|CCR10|CCR11|CCRL1|CCX CKR|CCX-CKR|CKR-11|PPR1|VSHK1	atypical chemokine receptor 4	protein-coding	0.009569	0.408115	
chunk0171_448_1	chr6	131915004	131915550	+	0	NA	Intergenic	Intergenic	36101	NM_001901	1490	Hs.410037	NM_001901	ENSG00000118523	CCN2	CTGF|HCS24|IGFBP8|NOV2	cellular communication network factor 2	protein-coding	0.016484	0.446069	
chunk0017_8_1	chr1	204388196	204388655	+	0	NA	Intergenic	Intergenic	-18706	NR_027022	127841	Hs.213144	NR_027022	ENSG00000280924	LINC00628	-	long intergenic non-protein coding RNA 628	ncRNA	0.004357	0.382609	
chunk0040_435_1	chr11	121460946	121461145	+	0	NA	intron (NM_003105, intron 1 of 47)	intron (NM_003105, intron 1 of 47)	8842	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.005025	0.515000	
chunk0207_245_1	chr9	132059041	132059761	+	0	NA	intron (NM_001253881, intron 2 of 6)	intron (NM_001253881, intron 2 of 6)	20486	NM_001253881	9442	Hs.374262	NM_004269	ENSG00000160563	MED27	CRAP34|CRSP34|CRSP8|MED3|TRAP37	mediator complex subunit 27	protein-coding	0.018056	0.496533	379(AAGTACAAATTGTGCT,-,0.00),380(AGTACAAATTGTGCTG,+,0.00)
chunk0063_235_1	chr14	81996884	81997458	+	0	NA	Intergenic	Intergenic	-374110	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.012195	0.356522	
chunk0107_129_1	chr2	214734316	214734583	+	0	NA	intron (NM_001282549, intron 3 of 4)	intron (NM_001282549, intron 3 of 4)	75262	NR_104212	580	Hs.591642	NM_000465	ENSG00000138376	BARD1	-	BRCA1 associated RING domain 1	protein-coding	0.000000	0.264925	
chunk0132_398_1	chr3	163951175	163951814	+	0	NA	Intergenic	Intergenic	220062	NR_031665	100302148		NR_031665	ENSG00000221251	MIR1263	MIRN1263|hsa-mir-1263	microRNA 1263	ncRNA	0.004695	0.303125	
chunk0136_427_1	chr3	197607298	197607684	+	0	NA	Intergenic	Intergenic	20390	NR_003266	220729	Hs.478854	NR_003266	ENSG00000214135	LOC220729	-	succinate dehydrogenase complex flavoprotein subunit A pseudogene	pseudo	0.015544	0.472868	
chunk0083_337_1	chr17	70193361	70193850	+	0	NA	Intergenic	Intergenic	24070	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.004090	0.320408	
chunk0125_178_1	chr3	66615757	66616331	+	0	NA	Intergenic	MIRb|SINE|MIR	-115623	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.010453	0.427826	
chunk0157_127_1	chr5	117188273	117188472	+	0	NA	Intergenic	Intergenic	-227140	NR_046089	728342	Hs.434420	NR_046089		LINC00992	-	long intergenic non-protein coding RNA 992	ncRNA	0.005025	0.365000	
chunk0160_206_1	chr5	154754895	154755139	+	0	NA	intron (NM_015315, intron 1 of 18)	CpG	42115	NM_015315	23367	Hs.292078	NM_015315	ENSG00000155506	LARP1	LARP	La ribonucleoprotein domain family member 1	protein-coding	0.073770	0.653061	
chunk0084_180_1	chr17	77551593	77552108	+	0	NA	intron (NR_040050, intron 1 of 1)	L1ME1|LINE|L1	4909	NR_040050	100507351	Hs.514518	NR_040050		LOC100507351	-	uncharacterized LOC100507351	ncRNA	0.009709	0.470930	
chunk0143_163_1	chr4	110620725	110621122	+	0	NA	intron (NM_153427, intron 4 of 4)	CpG	2175	NM_000325	5308	Hs.643588	NM_000325	ENSG00000164093	PITX2	ARP1|ASGD4|Brx1|IDG2|IGDS|IGDS2|IHG2|IRID2|Otlx2|PTX2|RGS|RIEG|RIEG1|RS	paired like homeodomain 2	protein-coding	0.055416	0.620603	137(AGGAACACAATGTCCT,-,0.00),138(GGAACACAATGTCCTG,+,0.00)
chunk0124_36_1	chr3	52261845	52262365	+	0	NA	intron (NM_025222, intron 3 of 8)	L1MB7|LINE|L1	6256	NR_029660	406890		NR_029660	ENSG00000199150	MIRLET7G	LET7G|MIRNLET7G|hsa-let-7g|let-7g	microRNA let-7g	ncRNA	0.001923	0.364683	
chunk0185_41_1	chr7	124489961	124490213	+	0	NA	Intergenic	Intergenic	-137991	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.007937	0.395257	
chunk0119_2_1	chr22	39968490	39969027	+	0	NA	intron (NM_001291825, intron 5 of 6)	intron (NM_001291825, intron 5 of 6)	21941	NM_001291825	9402	Hs.517499	NM_004810	ENSG00000100351	GRAP2	GADS|GRAP-2|GRB2L|GRBLG|GRID|GRPL|GrbX|Grf40|Mona|P38	GRB2 related adaptor protein 2	protein-coding	0.016760	0.494424	273(GGGCACACAAAGTCCT,-,0.00),274(GGCACACAAAGTCCTT,+,0.00)
chunk0137_213_1	chr4	19455220	19455717	+	0	NA	Intergenic	Intergenic	-796437	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.038229	0.500000	
chunk0168_210_1	chr6	85868917	85869383	+	0	NA	Intergenic	Intergenic	-190417	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.015021	0.456103	
chunk0014_394_1	chr1	182802316	182802847	+	0	NA	intron (NM_030769, intron 3 of 12)	intron (NM_030769, intron 3 of 12)	13132	NM_001200050	80896	Hs.496969	NM_030769	ENSG00000135838	NPL	C112|C1orf13|NAL|NPL1	N-acetylneuraminate pyruvate lyase	protein-coding	0.001883	0.387218	273(TAGCACTCTGTGTTCT,-,0.00),274(AGCACTCTGTGTTCTT,+,0.00)
chunk0079_190_1	chr17	14212746	14212945	+	0	NA	Intergenic	Intergenic	23988	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.015075	0.475000	
chunk0023_9_1	chr10	20888536	20889196	+	0	NA	intron (NM_006393, intron 3 of 27)	intron (NM_006393, intron 3 of 27)	8736	NM_006393	10529	Hs.5025	NM_006393	ENSG00000078114	NEBL	LASP2|LNEBL	nebulette	protein-coding	0.009091	0.385779	
chunk0205_62_1	chr9	106612044	106612262	+	0	NA	Intergenic	MLT2F|LTR|ERVL	-3905	NR_104145	100996590	Hs.147110	NR_104145	ENSG00000234323	LINC01505	-	long intergenic non-protein coding RNA 1505	ncRNA	0.004587	0.447489	
chunk0175_46_1	chr7	1156786	1157386	+	0	NA	intron (NM_182491, intron 3 of 4)	intron (NM_182491, intron 3 of 4)	3133	NM_182491	90637	Hs.648111	NM_182491	ENSG00000178381	ZFAND2A	AIRAP	zinc finger AN1-type containing 2A	protein-coding	0.013333	0.475874	
chunk0144_174_1	chr4	132918873	132919247	+	0	NA	Intergenic	L1ME3B|LINE|L1	230056	NR_125885	101927359	Hs.649960	NR_125885	ENSG00000250241	LOC101927359	-	uncharacterized LOC101927359	ncRNA	0.000000	0.296000	
chunk0201_424_1	chr9	69711118	69711536	+	0	NA	3' UTR (NM_001099666, exon 8 of 8)	3' UTR (NM_001099666, exon 8 of 8)	-38968	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.004785	0.343675	196(TATACACTCTGTTCCT,+,0.00)
chunk0088_369_1	chr18	53882470	53882931	+	0	NA	Intergenic	L1PA10|LINE|L1	-301641	NR_110800	101928167	Hs.382012	NR_110800	ENSG00000260433	LINC01917	-	long intergenic non-protein coding RNA 1917	ncRNA	0.008677	0.562771	
chunk0112_260_1	chr20	42513900	42514359	+	0	NA	intron (NM_133170, intron 7 of 31)	L1ME3E|LINE|L1	-171354	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.006536	0.352174	
chunk0072_206_1	chr15	95197681	95198028	+	0	NA	Intergenic	Intergenic	129246	NR_034095	400456	Hs.536404	NR_034095	ENSG00000248441	LINC01197	-	long intergenic non-protein coding RNA 1197	ncRNA	0.002882	0.261494	
chunk0078_319_1	chr17	8557393	8557655	+	0	NA	intron (NM_001256095, intron 7 of 41)	intron (NM_001256095, intron 7 of 41)	73237	NM_005964	4628	Hs.16355	NM_005964	ENSG00000133026	MYH10	NMMHC-IIB|NMMHCB	myosin heavy chain 10	protein-coding	0.015267	0.467681	13(AGGAACAAACTGTGAT,-,0.00)
chunk0057_88_1	chr13	98650359	98650730	+	0	NA	Intergenic	Intergenic	-73393	NM_001032296	8428	Hs.508514	NM_003576	ENSG00000102572	STK24	HEL-S-95|MST3|MST3B|STE20|STK3	serine/threonine kinase 24	protein-coding	0.021563	0.567204	
chunk0049_307_1	chr12	94561926	94562484	+	0	NA	TTS (NR_049885)	TTS (NR_049885)	416	NR_049885	100847031		NR_049885	ENSG00000266099	MIR5700	-	microRNA 5700	ncRNA	0.021505	0.527728	271(CAGCTCAGTCTGTCCC,-,0.00),272(AGCTCAGTCTGTCCCC,+,0.00)
chunk0207_367_1	chr9	135952314	135952745	+	0	NA	intron (NM_016172, intron 3 of 9)	intron (NM_016172, intron 3 of 9)	8851	NM_016172	10422	Hs.9194	NM_016172	ENSG00000130560	UBAC1	GBDR1|KPC2|UBADC1	UBA domain containing 1	protein-coding	0.027842	0.500000	
chunk0114_183_1	chr21	14967666	14968057	+	0	NA	exon (NM_003489, exon 4 of 4)	exon (NM_003489, exon 4 of 4)	96944	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.005115	0.451531	
chunk0025_380_1	chr10	59240642	59240841	+	0	NA	intron (NM_032439, intron 4 of 4)	intron (NM_032439, intron 4 of 4)	63274	NM_001143774	84457	Hs.499704	NM_032439	ENSG00000165443	PHYHIPL	-	phytanoyl-CoA 2-hydroxylase interacting protein like	protein-coding	0.000000	0.340000	
chunk0206_385_1	chr9	126802352	126803095	+	0	NA	Intergenic	Intergenic	-2283	NM_001135776	23099	Hs.355581	NM_014007	ENSG00000169155	ZBTB43	ZBTB22B|ZNF-X|ZNF297B	zinc finger and BTB domain containing 43	protein-coding	0.010767	0.419355	
chunk0143_413_1	chr4	123397142	123397667	+	0	NA	promoter-TSS (NM_001258039)	promoter-TSS (NM_001258039)	609	NM_199327	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.074286	0.553232	
chunk0211_379_1	chrX	126899304	126899882	+	0	NA	Intergenic	L1MC2|LINE|L1	79829	NM_001122716	100130613	Hs.130370	NM_001122716	ENSG00000183631	PRR32	CXorf64	proline rich 32	protein-coding	0.006920	0.338515	295(TAGTACATCGTGTCCA,-,0.00),296(AGTACATCGTGTCCAG,+,0.00)
chunk0141_401_1	chr4	88514598	88515473	+	0	NA	Intergenic	Intergenic	8766	NM_001042616	84992	Hs.26136	NM_001042616	ENSG00000255072	PIGY	HPMRS6|PIG-Y	phosphatidylinositol glycan anchor biosynthesis class Y	protein-coding	0.008000	0.360731	496(AAGTACACTCTGTGAT,-,0.00)
chunk0121_294_1	chr3	23740439	23740779	+	0	NA	Intergenic	OldhAT1|DNA|hAT-Ac	-65284	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.002941	0.416422	139(AGAGACACTGTGTCCC,-,0.00),140(GAGACACTGTGTCCCT,+,0.00)
chunk0194_100_1	chr8	83515021	83515564	+	0	NA	Intergenic	Intergenic	111534	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.005525	0.352941	
chunk0151_314_1	chr5	53367396	53367861	+	0	NA	Intergenic	Intergenic	-112806	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.006452	0.416309	
chunk0077_398_1	chr16	84914213	84914702	+	0	NA	Intergenic	L1MC4|LINE|L1	94476	NM_031476	83716	Hs.513779	NM_031476	ENSG00000103196	CRISPLD2	CRISP11|LCRISP2|LGL1	cysteine rich secretory protein LCCL domain containing 2	protein-coding	0.010225	0.436735	
chunk0195_115_1	chr8	94813004	94813553	+	0	NA	Intergenic	L2c|LINE|L2	-10012	NM_017864	55656	Hs.727669	NM_017864	ENSG00000164941	INTS8	C8orf52|INT8	integrator complex subunit 8	protein-coding	0.009107	0.403636	
chunk0114_225_1	chr21	15789138	15789539	+	0	NA	intron (NM_013396, intron 4 of 23)	intron (NM_013396, intron 4 of 23)	59313	NM_013396	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.009975	0.330846	
chunk0165_14_1	chr6	28751587	28751831	+	0	NA	Intergenic	Intergenic	111968	NR_033379	401242	Hs.448285	NR_033379	ENSG00000225595	LINC01623	-	long intergenic non-protein coding RNA 1623	ncRNA	0.028689	0.506122	
chunk0144_53_1	chr4	126724379	126724578	+	0	NA	Intergenic	Intergenic	-908454	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.000000	0.360000	
chunk0101_13_1	chr2	121363690	121364155	+	0	NA	intron (NM_015282, intron 35 of 38)	intron (NM_015282, intron 35 of 38)	-78720	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.008602	0.388412	
chunk0003_382_1	chr1	39793809	39794071	+	0	NA	Intergenic	Intergenic	-5079	NM_001720	656	Hs.734367	NM_001720	ENSG00000116985	BMP8B	BMP8|OP2	bone morphogenetic protein 8b	protein-coding	0.007634	0.494297	142(CAGTTCATCATGTTCC,-,0.00),143(AGTTCATCATGTTCCC,+,0.00)
chunk0016_352_1	chr1	202057036	202057254	+	0	NA	Intergenic	Intergenic	46583	NM_001114309	1999	Hs.603657	NM_004433	ENSG00000163435	ELF3	EPR-1|ERT|ESE-1|ESX	E74 like ETS transcription factor 3	protein-coding	0.036697	0.607306	
chunk0152_435_1	chr5	66048216	66048853	+	0	NA	intron (NM_018695, intron 18 of 24)	intron (NM_018695, intron 18 of 24)	-95684	NM_001077199	140890	Hs.49367	NM_139168	ENSG00000153914	SREK1	SFRS12|SRrp508|SRrp86	splicing regulatory glutamic acid and lysine rich protein 1	protein-coding	0.009419	0.326019	64(TTGAACTTAATGTTCT,-,0.00),65(TGAACTTAATGTTCTG,+,0.00)
chunk0190_291_1	chr8	37882750	37883167	+	0	NA	intron (NM_001002814, intron 1 of 5)	intron (NM_001002814, intron 1 of 5)	16539	NM_001002814	80223	Hs.191179	NM_025151	ENSG00000156675	RAB11FIP1	NOEL1A|RCP|rab11-FIP1	RAB11 family interacting protein 1	protein-coding	0.014388	0.440191	
chunk0072_213_1	chr15	95563415	95563947	+	0	NA	Intergenic	MIR|SINE|MIR	130588	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.007519	0.418386	
chunk0015_248_1	chr1	187971773	187972410	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	528463	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.006279	0.368339	
chunk0170_243_1	chr6	113649182	113649561	+	0	NA	intron (NR_125844, intron 1 of 2)	intron (NR_125844, intron 1 of 2)	704	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.018470	0.400000	
chunk0082_263_1	chr17	57839562	57839798	+	0	NA	3' UTR (NM_016070, exon 5 of 5)	3' UTR (NM_016070, exon 5 of 5)	10392	NM_016070	51649	Hs.5836	NM_016070	ENSG00000181610	MRPS23	CGI-138|HSPC329|MRP-S23	mitochondrial ribosomal protein S23	protein-coding	0.000000	0.375527	
chunk0167_157_1	chr6	62656594	62657169	+	0	NA	Intergenic	Intergenic	-370686	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.001739	0.281250	
chunk0179_136_1	chr7	45943199	45943697	+	0	NA	Intergenic	L1MEg|LINE|L1	-22176	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.004016	0.288577	
chunk0128_107_1	chr3	106183019	106183488	+	0	NA	Intergenic	Intergenic	-314210	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.010661	0.395745	
chunk0112_79_1	chr20	37956218	37956417	+	0	NA	Intergenic	L3|LINE|CR1	53220	NM_080607	128434	Hs.517029	NM_080607	ENSG00000132821	VSTM2L	C20orf102|dJ1118M15.2	V-set and transmembrane domain containing 2 like	protein-coding	0.005025	0.405000	
chunk0161_168_1	chr5	169223047	169223719	+	0	NA	intron (NM_003062, intron 3 of 35)	intron (NM_003062, intron 3 of 35)	40311	NR_030311	693170		NR_030311	ENSG00000207619	MIR585	MIRN585|hsa-mir-585|mir-585	microRNA 585	ncRNA	0.008929	0.450223	
chunk0137_206_1	chr4	18578483	18578797	+	0	NA	Intergenic	Intergenic	-556780	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.006369	0.380952	
chunk0156_263_1	chr5	109365236	109365528	+	0	NA	intron (NM_014819, intron 5 of 9)	L1ME4b|LINE|L1	44592	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.017123	0.313993	
chunk0175_11_1	chr7	206409	206616	+	0	NA	intron (NM_020223, intron 2 of 9)	CpG	13543	NM_020223	56975	Hs.134742	NM_020223	ENSG00000177706	FAM20C	DMP-4|DMP4|G-CK|GEF-CK|RNS	FAM20C golgi associated secretory pathway kinase	protein-coding	0.072464	0.663462	
chunk0133_325_1	chr3	172561816	172562177	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-38489	NM_003810	8743	Hs.478275	NM_003810	ENSG00000121858	TNFSF10	APO2L|Apo-2L|CD253|TL2|TNLG6A|TRAIL	TNF superfamily member 10	protein-coding	0.005540	0.383978	
chunk0086_435_1	chr18	28358906	28359550	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-181782	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.010870	0.367442	
chunk0068_251_1	chr15	55993401	55993600	+	0	NA	intron (NM_006154, intron 1 of 28)	CpG	246	NM_006154	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.120603	0.720000	
chunk0109_200_1	chr20	5099910	5100411	+	0	NA	3' UTR (NM_014145, exon 4 of 4)	3' UTR (NM_014145, exon 4 of 4)	12927	NM_001009923	29058	Hs.472024	NM_014145	ENSG00000089063	TMEM230	C20orf30|HSPC274|dJ1116H23.2.1	transmembrane protein 230	protein-coding	0.005988	0.350598	
chunk0088_270_1	chr18	49192348	49192866	+	0	NA	intron (NM_017653, intron 13 of 16)	L1M2|LINE|L1	-142839	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.003861	0.341040	298(CTGTACAATGTGTTCT,-,0.00),299(TGTACAATGTGTTCTA,+,0.00)
chunk0171_380_1	chr6	131014988	131015575	+	0	NA	intron (NM_001431, intron 1 of 19)	intron (NM_001431, intron 1 of 19)	-14514	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.006814	0.370748	
chunk0198_112_1	chr8	131829767	131830242	+	0	NA	Intergenic	Intergenic	-74105	NM_015137	23167	Hs.204564	NM_015137	ENSG00000132294	EFR3A	-	EFR3 homolog A	protein-coding	0.004211	0.455882	183(AAGCACAGGCTGTGCC,-,0.00),184(AGCACAGGCTGTGCCA,+,0.00)
chunk0159_313_1	chr5	143150936	143151640	+	0	NA	intron (NM_015071, intron 20 of 22)	L1MC2|LINE|L1	-41212	NR_046816	100874372	Hs.666717	NR_046816	ENSG00000230789	ARHGAP26-IT1	-	ARHGAP26 intronic transcript 1	ncRNA	0.002841	0.346099	
chunk0141_8_1	chr4	76594027	76594624	+	0	NA	intron (NM_020859, intron 2 of 10)	L2b|LINE|L2	18774	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.003350	0.391304	
chunk0129_293_1	chr3	123524993	123525193	+	0	NA	intron (NM_198402, intron 4 of 6)	intron (NM_198402, intron 4 of 6)	59984	NM_198402	201562	Hs.705480	NM_198402	ENSG00000206527	HACD2	PTPLB	3-hydroxyacyl-CoA dehydratase 2	protein-coding	0.015000	0.407960	
chunk0204_295_1	chr9	99906899	99907098	+	0	NA	promoter-TSS (NR_038853)	promoter-TSS (NR_038853)	365	NM_017919	55014	Hs.704031	NM_017919	ENSG00000136874	STX17	-	syntaxin 17	protein-coding	0.115578	0.690000	
chunk0039_37_1	chr11	95898677	95899264	+	0	NA	intron (NM_016156, intron 1 of 14)	intron (NM_016156, intron 1 of 14)	25237	NM_001243571	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.005111	0.353741	
chunk0065_47_1	chr15	22253261	22253463	+	0	NA	Intergenic	Intergenic	-5252	NR_033735	646396	Hs.451294	NR_033735		REREP3	-	arginine-glutamic acid dipeptide repeats pseudogene 3	pseudo	0.019802	0.497537	
chunk0054_414_1	chr13	50809600	50810146	+	0	NA	intron (NR_046551, intron 2 of 4)	intron (NR_046551, intron 2 of 4)	2018	NR_046551	100874074	Hs.734030	NR_046551	ENSG00000176124	DLEU7-AS1	-	DLEU7 antisense RNA 1	ncRNA	0.005495	0.405850	
chunk0044_301_1	chr12	32897008	32897701	+	0	NA	promoter-TSS (NM_004572)	promoter-TSS (NM_004572)	-508	NM_004572	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.049062	0.518732	
chunk0129_4_1	chr3	116240302	116240669	+	0	NA	intron (NM_002338, intron 1 of 6)	intron (NM_002338, intron 1 of 6)	-119539	NR_109998	101926903	Hs.26479	NR_109998	ENSG00000240922	LSAMP-AS1	-	LSAMP antisense RNA 1	ncRNA	0.002725	0.361413	
chunk0097_5_1	chr2	41074840	41075212	+	0	NA	Intergenic	L1ME1|LINE|L1	-562591	NM_001112802	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.000000	0.391421	
chunk0176_68_1	chr7	11248351	11248550	+	0	NA	Intergenic	Intergenic	274578	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.010050	0.425000	97(TACACAGTGTGTGCTT,+,0.00)
chunk0042_199_1	chr12	5733347	5733731	+	0	NA	intron (NM_001278596, intron 13 of 25)	intron (NM_001278596, intron 13 of 25)	211720	NM_001278596	57101	Hs.148970	NM_020373	ENSG00000047617	ANO2	C12orf3|TMEM16B	anoctamin 2	protein-coding	0.018229	0.477922	129(GAGGACTTCATGTTCC,-,0.00),130(AGGACTTCATGTTCCT,+,0.00)
chunk0056_305_1	chr13	90867444	90867664	+	0	NA	Intergenic	Intergenic	59043	NR_027039	144776	Hs.434120	NR_027039	ENSG00000231674	LINC00410	-	long intergenic non-protein coding RNA 410	ncRNA	0.018182	0.443439	
chunk0046_273_1	chr12	61386993	61387582	+	0	NA	Intergenic	L2c|LINE|L2	805552	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.005093	0.328814	
chunk0162_207_1	chr6	4102658	4103270	+	0	NA	intron (NR_104464, intron 2 of 5)	intron (NR_104464, intron 2 of 5)	-23741	NM_173563	222826	Hs.657342	NM_173563	ENSG00000145975	FAM217A	C6orf146	family with sequence similarity 217 member A	protein-coding	0.009804	0.425775	
chunk0087_456_1	chr18	42742699	42743229	+	0	NA	TTS (NM_002930)	TTS (NM_002930)	372728	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.000000	0.404896	
chunk0098_129_1	chr2	69065684	69066074	+	0	NA	intron (NM_053034, intron 3 of 14)	MamGypsy2-I|LTR|Gypsy	-37803	NR_036073	100423030		NR_036073	ENSG00000266649	MIR3126	mir-3126	microRNA 3126	ncRNA	0.000000	0.347826	
chunk0133_46_1	chr3	166444856	166445062	+	0	NA	Intergenic	LTR2752|LTR|ERV1	-607494	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.024272	0.613527	
chunk0202_72_1	chr9	71758788	71759214	+	0	NA	intron (NM_001135820, intron 1 of 22)	intron (NM_001135820, intron 1 of 22)	9883	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.007042	0.372365	
chunk0201_196_1	chr9	36566828	36567076	+	0	NA	Intergenic	Intergenic	-5910	NM_001256690	9833	Hs.184339	NM_014791	ENSG00000165304	MELK	HPK38	maternal embryonic leucine zipper kinase	protein-coding	0.020161	0.550201	
chunk0028_143_1	chr10	86664833	86665471	+	0	NA	intron (NM_001030015, intron 10 of 10)	intron (NM_001030015, intron 10 of 10)	-3297	NM_001171610	11155	Hs.657271	NM_007078	ENSG00000122367	LDB3	CMD1C|CMH24|CMPD3|CYPHER|LDB3Z1|LDB3Z4|LVNC3|MFM4|ORACLE|PDLIM6|ZASP	LIM domain binding 3	protein-coding	0.007837	0.585290	299(TGGAACAGGATGTCTC,-,0.00),300(GGAACAGGATGTCTCT,+,0.00)
chunk0020_52_1	chr1	232413628	232413990	+	0	NA	intron (NM_020808, intron 17 of 20)	intron (NM_020808, intron 17 of 20)	101799	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.008287	0.446281	
chunk0110_270_1	chr20	17357173	17357613	+	0	NA	intron (NM_002594, intron 2 of 11)	intron (NM_002594, intron 2 of 11)	130441	NM_001201529	5126	Hs.315186	NM_002594	ENSG00000125851	PCSK2	NEC 2|NEC-2|NEC2|PC2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding	0.002273	0.403628	
chunk0137_38_1	chr4	11407905	11408512	+	0	NA	intron (NM_005114, intron 1 of 1)	MIRb|SINE|MIR	20705	NM_005114	9957	Hs.507348	NM_005114	ENSG00000002587	HS3ST1	3OST|3OST1	heparan sulfate-glucosamine 3-sulfotransferase 1	protein-coding	0.003295	0.402961	
chunk0050_345_1	chr12	107604705	107605211	+	0	NA	intron (NM_001018072, intron 4 of 16)	L1MA8|LINE|L1	24101	NM_001017523	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.001976	0.329389	276(GAGGACATTATGTTAC,-,0.00)
chunk0207_137_1	chr9	129413182	129413405	+	0	NA	Intergenic	CpG	-75367	NR_038955	100506190	Hs.529860	NR_038955		LINC00963	MetaLnc9	long intergenic non-protein coding RNA 963	ncRNA	0.121076	0.727679	
chunk0084_259_1	chr17	79114895	79115201	+	0	NA	intron (NM_001082575, intron 5 of 14)	intron (NM_001082575, intron 5 of 14)	40111	NM_001042573	64772	Hs.29288	NM_022759	ENSG00000167280	ENGASE	-	endo-beta-N-acetylglucosaminidase	protein-coding	0.026144	0.576547	
chunk0122_295_1	chr3	36202473	36202768	+	0	NA	Intergenic	Intergenic	-177867	NM_003149	6769	Hs.56045	NM_003149	ENSG00000144681	STAC	STAC1	SH3 and cysteine rich domain	protein-coding	0.006780	0.462838	142(CAGAACACACTGTTTA,-,0.00),143(AGAACACACTGTTTAC,+,0.00)
chunk0066_217_1	chr15	33941611	33942333	+	0	NA	intron (NM_020371, intron 2 of 5)	intron (NM_020371, intron 2 of 5)	-26916	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.002770	0.322268	337(AGGGACAGCCTGCCCT,-,0.00),338(GGGACAGCCTGCCCTA,+,0.00),367(AAAAACACTCAGTCCT,-,0.00)
chunk0189_303_1	chr8	26035916	26036999	+	0	NA	intron (NM_022659, intron 5 of 15)	intron (NM_022659, intron 5 of 15)	8667	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.006464	0.376384	
chunk0088_139_1	chr18	46030742	46030941	+	0	NA	intron (NM_024430, intron 2 of 14)	HAL1b|LINE|L1	41443	NM_024430	9050	Hs.567384	NM_024430	ENSG00000152229	PSTPIP2	MAYP	proline-serine-threonine phosphatase interacting protein 2	protein-coding	0.005025	0.385000	
chunk0167_20_1	chr6	53695147	53696123	+	0	NA	Intergenic	L1MC4|LINE|L1	-29927	NM_001003760	401265	Hs.131064	NM_001003760	ENSG00000124743	KLHL31	BKLHD6|KBTBD1|KLHL|bA345L23.2	kelch like family member 31	protein-coding	0.009221	0.409417	600(CAGAACAGCCTGTGCT,-,0.00),601(AGAACAGCCTGTGCTC,+,0.00)
chunk0204_460_1	chr9	104578355	104579064	+	0	NA	Intergenic	MIRb|SINE|MIR	9541	NM_001004483	138802	Hs.553599	NM_001004483	ENSG00000186943	OR13C8	OR37H|OR9-10	olfactory receptor family 13 subfamily C member 8	protein-coding	0.011283	0.380282	284(AAGAACAGGTAGTCCA,-,0.00)
chunk0098_244_1	chr2	74845163	74845785	+	0	NA	intron (NM_000189, intron 1 of 17)	intron (NM_000189, intron 1 of 17)	12819	NM_000189	3099	Hs.406266	NM_000189	ENSG00000159399	HK2	HKII|HXK2	hexokinase 2	protein-coding	0.014469	0.547352	
chunk0124_13_1	chr3	51621397	51621820	+	0	NA	intron (NM_015106, intron 2 of 21)	intron (NM_015106, intron 2 of 21)	-49567	NR_024012	51368	Hs.517864	NM_015926	ENSG00000164081	TEX264	ZSIG11	testis expressed 264, ER-phagy receptor	protein-coding	0.002364	0.455189	
chunk0002_360_1	chr1	26004828	26005193	+	0	NA	Intergenic	L2c|LINE|L2	-6853	NM_000437	5051	Hs.477083	NM_000437	ENSG00000158006	PAFAH2	HSD-PLA2	platelet activating factor acetylhydrolase 2	protein-coding	0.005479	0.502732	120(GGGAACATAACGTTCT,-,0.00),121(GGAACATAACGTTCTC,+,0.00)
chunk0076_365_1	chr16	71966935	71967253	+	0	NA	intron (NM_181536, intron 15 of 29)	intron (NM_181536, intron 15 of 29)	32884	NM_181536	342372	Hs.675286	NM_181536	ENSG00000277481	PKD1L3	-	polycystin 1 like 3, transient receptor potential channel interacting	protein-coding	0.009434	0.438871	
chunk0135_146_1	chr3	187636548	187637020	+	0	NA	Intergenic	Intergenic	33629	NM_001048	6750	Hs.12409	NM_001048	ENSG00000157005	SST	SMST	somatostatin	protein-coding	0.000000	0.315011	
chunk0151_434_1	chr5	55928115	55928743	+	0	NA	Intergenic	LTR16A2|LTR|ERVL	66564	NM_175767	3572	Hs.532082	NM_002184	ENSG00000134352	IL6ST	CD130|CDW130|GP130|IL-6RB	interleukin 6 signal transducer	protein-coding	0.019108	0.526232	
chunk0073_117_1	chr16	4814143	4814622	+	0	NA	intron (NM_001308096, intron 11 of 15)	intron (NM_001308096, intron 11 of 15)	-11432	NR_046480	79641	Hs.459795	NM_024589	ENSG00000067836	ROGDI	KTZS	rogdi atypical leucine zipper	protein-coding	0.020877	0.497917	102(AGGCACATTCAGTTCC,-,0.00),103(GGCACATTCAGTTCCA,+,0.00)
chunk0143_333_1	chr4	120275935	120276476	+	0	NA	Intergenic	Intergenic	-209347	NM_002358	4085	Hs.591697	NM_002358	ENSG00000164109	MAD2L1	HSMAD2|MAD2	mitotic arrest deficient 2 like 1	protein-coding	0.003697	0.311808	268(GGGCACATATAGTCCC,-,0.00),269(GGCACATATAGTCCCC,+,0.00)
chunk0083_176_1	chr17	66308331	66308969	+	0	NA	intron (NM_002737, intron 2 of 16)	intron (NM_002737, intron 2 of 16)	5842	NM_002737	5578	Hs.531704	NM_002737	ENSG00000154229	PRKCA	AAG6|PKC-alpha|PKCA|PKCI+/-|PKCalpha|PRKACA	protein kinase C alpha	protein-coding	0.006270	0.339593	
chunk0200_37_1	chr9	15112769	15113135	+	0	NA	Intergenic	L2b|LINE|L2	119625	NR_003920	389705	Hs.431257	NR_003920		LOC389705	-	histone PARylation factor 1 pseudogene	pseudo	0.005464	0.346049	
chunk0144_262_1	chr4	136862592	136862820	+	0	NA	Intergenic	Intergenic	669792	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.008772	0.323144	
chunk0083_167_1	chr17	66061354	66061911	+	0	NA	intron (NM_001302891, intron 9 of 24)	L1MA6|LINE|L1	130237	NM_001302891	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.003591	0.370968	308(AAGGACATTGTGTTCA,-,0.00),309(AGGACATTGTGTTCAG,+,0.00)
chunk0069_80_1	chr15	61079447	61079813	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	149673	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.013661	0.425068	
chunk0124_72_1	chr3	53145211	53145818	+	0	NA	Intergenic	Intergenic	-15060	NM_052859	91869	Hs.631910	NM_052859	ENSG00000163933	RFT1	CDG1N	RFT1 homolog	protein-coding	0.013180	0.559211	29(GGCACTGGCTGCTCTC,+,0.00)
chunk0096_36_1	chr2	26869931	26870453	+	0	NA	intron (NM_001253724, intron 1 of 12)	L1ME3G|LINE|L1	21768	NM_001253724	56896	Hs.299315	NM_020134	ENSG00000157851	DPYSL5	CRAM|CRMP-5|CRMP5|Ulip6	dihydropyrimidinase like 5	protein-coding	0.015326	0.374761	
chunk0017_108_1	chr1	205954985	205955289	+	0	NA	intron (NR_110983, intron 2 of 3)	intron (NR_110983, intron 2 of 3)	-2788	NR_110982	103021295	Hs.741319	NR_110982		LOC103021295	-	uncharacterized LOC103021295	ncRNA	0.016447	0.537705	
chunk0165_192_1	chr6	34546571	34547288	+	0	NA	intron (NM_001252294, intron 1 of 4)	intron (NM_001252294, intron 1 of 4)	9404	NM_001252294	25803	Hs.485158	NM_012391	ENSG00000124664	SPDEF	PDEF|bA375E1.3	SAM pointed domain containing ETS transcription factor	protein-coding	0.015342	0.604457	
chunk0050_276_1	chr12	106291357	106291665	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-11280	NM_152772	255394	Hs.696047	NM_152772	ENSG00000166046	TCP11L2	-	t-complex 11 like 2	protein-coding	0.009740	0.407767	136(AAGCACACTCTGTGAT,-,0.00)
chunk0025_141_1	chr10	52206680	52207023	+	0	NA	intron (NM_006258, intron 9 of 17)	L1PA15|LINE|L1	107277	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.002915	0.546512	
chunk0067_423_1	chr15	49876274	49876877	+	0	NA	intron (NR_073596, intron 24 of 27)	intron (NR_073596, intron 24 of 27)	236741	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.009950	0.435430	221(CAGTCCACGCTGTTCT,-,0.00),222(AGTCCACGCTGTTCTG,+,0.00)
chunk0110_139_1	chr20	13563816	13564357	+	0	NA	intron (NM_017714, intron 7 of 13)	L1MB3|LINE|L1	74850	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.003697	0.322878	
chunk0076_42_1	chr16	59904262	59904759	+	0	NA	intron (NR_110917, intron 1 of 3)	intron (NR_110917, intron 1 of 3)	49157	NR_110917	101927580	Hs.552235	NR_110917	ENSG00000261807	LINC02141	-	long intergenic non-protein coding RNA 2141	ncRNA	0.012072	0.379518	
chunk0100_188_1	chr2	110955592	110955830	+	0	NA	intron (NM_001142807, intron 12 of 17)	L2a|LINE|L2	159877	NR_122074	400997	Hs.652337	NR_122074	ENSG00000204581	ACOXL-AS1	-	ACOXL antisense RNA 1	ncRNA	0.008403	0.569038	108(CTGGACATTCTGTACC,-,0.00),109(TGGACATTCTGTACCC,+,0.00),144(TGCACAGGCTGCTCTC,+,0.00)
chunk0113_354_1	chr20	58963183	58963762	+	0	NA	Intergenic	L1MCa|LINE|L1	-17736	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.012090	0.484483	182(CAGGGCATTCTGTTCT,-,0.00),183(AGGGCATTCTGTTCTT,+,0.00),559(TAGTACATCATGTCCA,-,0.00),560(AGTACATCATGTCCAG,+,0.00)
chunk0012_258_1	chr1	161399365	161399951	+	0	NA	Intergenic	CpG	-31775	NM_001013625	257177	Hs.534593	NM_001013625	ENSG00000188931	CFAP126	C1orf192|Flattop|Fltp	cilia and flagella associated protein 126	protein-coding	0.078498	0.584327	
chunk0106_384_1	chr2	207528156	207528730	+	0	NA	Intergenic	L2b|LINE|L2	-1449	NM_004379	1385	Hs.516646	NM_004379	ENSG00000118260	CREB1	CREB|CREB-1	cAMP responsive element binding protein 1	protein-coding	0.026132	0.474783	
chunk0167_386_1	chr6	74598643	74599134	+	0	NA	intron (NR_110856, intron 2 of 3)	MER63A|DNA|hAT-Blackjack	529437	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.002037	0.357724	
chunk0181_304_1	chr7	87150999	87151701	+	0	NA	Intergenic	Intergenic	-1011	NR_024549	9988	Hs.196129	NM_021145	ENSG00000135164	DMTF1	DMP1|DMTF|MRUL|hDMP1	cyclin D binding myb like transcription factor 1	protein-coding	0.012821	0.362731	
chunk0099_21_1	chr2	83079002	83079417	+	0	NA	Intergenic	L1PA15|LINE|L1	222406	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007229	0.324519	
chunk0127_362_1	chr3	101573921	101574173	+	0	NA	promoter-TSS (NM_020357)	promoter-TSS (NM_020357)	-151	NM_020357	57092	Hs.732633	NM_020357	ENSG00000081154	PCNP	-	PEST proteolytic signal containing nuclear protein	protein-coding	0.063492	0.584980	
chunk0069_245_1	chr15	64287757	64288143	+	0	NA	intron (NM_022048, intron 2 of 11)	HAL1|LINE|L1	68293	NM_022048	53944	Hs.646508	NM_022048	ENSG00000169118	CSNK1G1	CK1gamma1	casein kinase 1 gamma 1	protein-coding	0.000000	0.299742	
chunk0070_15_1	chr15	68944531	68945064	+	0	NA	intron (NM_001184780, intron 1 of 15)	MER58A|DNA|hAT-Charlie	14297	NM_145658	246777	Hs.657932	NM_145658	ENSG00000258484	SPESP1	ESP|SP-ESP	sperm equatorial segment protein 1	protein-coding	0.009381	0.397004	
chunk0095_236_1	chr2	19070840	19071561	+	0	NA	Intergenic	Intergenic	-277229	NR_039914	100616307		NR_039914	ENSG00000266738	MIR4757	-	microRNA 4757	ncRNA	0.011096	0.425208	
chunk0195_76_1	chr8	94000229	94000802	+	0	NA	Intergenic	Intergenic	83464	NM_001161781	54704	Hs.22265	NM_018444	ENSG00000164951	PDP1	PDH|PDP|PDPC|PPM2A|PPM2C	pyruvate dehyrogenase phosphatase catalytic subunit 1	protein-coding	0.005236	0.407666	
chunk0089_347_1	chr18	65934831	65935322	+	0	NA	Intergenic	MSTB2|LTR|ERVL-MaLR	184155	NM_004361	1005	Hs.541003	NM_004361	ENSG00000081138	CDH7	CDH7L1	cadherin 7	protein-coding	0.004073	0.396341	
chunk0140_266_1	chr4	71849819	71850435	+	0	NA	Intergenic	L1MA9|LINE|L1	-44607	NM_001204306	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.008117	0.338736	
chunk0190_67_1	chr8	29769712	29770812	+	0	NA	intron (NR_125814, intron 1 of 3)	MIRb|SINE|MIR	21953	NR_125815	101929450	Hs.512440	NR_125814	ENSG00000253490	LINC02099	-	long intergenic non-protein coding RNA 2099	ncRNA	0.001818	0.358765	
chunk0161_111_1	chr5	167543565	167544182	+	0	NA	intron (NM_001122679, intron 2 of 28)	MLT1C|LTR|ERVL-MaLR	-211063	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.008104	0.409385	
chunk0163_103_1	chr6	9707387	9707777	+	0	NA	Intergenic	Intergenic	-704736	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.002564	0.301790	
chunk0101_97_1	chr2	124646012	124646428	+	0	NA	intron (NM_130773, intron 12 of 23)	MIR3|SINE|MIR	620933	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.007212	0.412470	
chunk0089_265_1	chr18	62584354	62584561	+	0	NA	non-coding (NR_126534, exon 15 of 15)	non-coding (NR_126534, exon 15 of 15)	61032	NR_126534	54877	Hs.114191	NM_017742	ENSG00000141664	ZCCHC2	C18orf49	zinc finger CCHC-type containing 2	protein-coding	0.028986	0.519231	
chunk0197_81_1	chr8	119114342	119114695	+	0	NA	Intergenic	Intergenic	47333	NM_006438	10584	Hs.176615	NM_006438	ENSG00000184374	COLEC10	3MC3|CL-34|CLL1	collectin subfamily member 10	protein-coding	0.002833	0.372881	136(GTGAACAAGGTGTTCC,-,0.00),137(TGAACAAGGTGTTCCC,+,0.00)
chunk0168_195_1	chr6	85498883	85499082	+	0	NA	Intergenic	Intergenic	49398	NM_002526	4907	Hs.153952	NM_002526	ENSG00000135318	NT5E	CALJA|CD73|E5NT|NT|NT5|NTE|eN|eNT	5'-nucleotidase ecto	protein-coding	0.000000	0.425000	
chunk0054_334_1	chr13	49335882	49336636	+	0	NA	intron (NM_001079670, intron 9 of 10)	intron (NM_001079670, intron 9 of 10)	65279	NM_030925	81617	Hs.87159	NM_030925	ENSG00000102547	CAB39L	MO25-BETA|MO2L|bA103J18.3	calcium binding protein 39 like	protein-coding	0.003979	0.329801	
chunk0134_254_1	chr3	179396404	179397045	+	0	NA	3' UTR (NM_021629, exon 10 of 10)	3' UTR (NM_021629, exon 10 of 10)	49032	NM_033540	55669	Hs.478383	NM_017927	ENSG00000171109	MFN1	hfzo1|hfzo2	mitofusin 1	protein-coding	0.001560	0.299065	
chunk0040_12_1	chr11	108672318	108672517	+	0	NA	intron (NM_004398, intron 1 of 17)	intron (NM_004398, intron 1 of 17)	7392	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.010050	0.370000	93(TGGGACAGTATGTTAT,-,0.00),94(GGGACAGTATGTTATT,+,0.00)
chunk0159_433_1	chr5	148197204	148197492	+	0	NA	Intergenic	Intergenic	-5446	NM_001195290	404203	Hs.334274	NM_205841	ENSG00000178172	SPINK6	BUSI2|UNQ844	serine peptidase inhibitor, Kazal type 6	protein-coding	0.000000	0.297578	
chunk0134_409_1	chr3	183193700	183194254	+	0	NA	intron (NM_015078, intron 26 of 29)	L2c|LINE|L2	-31098	NM_014398	27074	Hs.518448	NM_014398	ENSG00000078081	LAMP3	CD208|DC LAMP|DC-LAMP|DCLAMP|LAMP|LAMP-3|TSC403	lysosomal associated membrane protein 3	protein-coding	0.007220	0.437838	
chunk0096_425_1	chr2	38313988	38314187	+	0	NA	intron (NM_022374, intron 6 of 12)	intron (NM_022374, intron 6 of 12)	62443	NM_001308076	64225	Hs.594950	NM_022374	ENSG00000119787	ATL2	ARL3IP2|ARL6IP2|aip-2|atlastin2	atlastin GTPase 2	protein-coding	0.005025	0.395000	
chunk0176_203_1	chr7	14687624	14688279	+	0	NA	intron (NM_145695, intron 8 of 23)	intron (NM_145695, intron 8 of 23)	153499	NM_004080	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.007634	0.312500	
chunk0191_193_1	chr8	51770857	51771609	+	0	NA	intron (NM_144651, intron 1 of 22)	intron (NM_144651, intron 1 of 22)	38212	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.011968	0.426295	325(AGAAACATTCTGTGCT,-,0.00),326(GAAACATTCTGTGCTC,+,0.00)
chunk0008_373_1	chr1	96827177	96827766	+	0	NA	Intergenic	L2|LINE|L2	104833	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.010187	0.394915	
chunk0183_446_1	chr7	111259976	111260398	+	0	NA	intron (NM_032549, intron 3 of 5)	Tigger3b|DNA|TcMar-Tigger	169181	NM_001099660	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.009479	0.371158	
chunk0171_141_1	chr6	123614804	123615081	+	0	NA	intron (NM_006073, intron 1 of 40)	L1MA5|LINE|L1	22151	NM_001256021	10345	Hs.144744	NM_006073	ENSG00000186439	TRDN	CPVT5|TDN|TRISK	triadin	protein-coding	0.007220	0.287770	
chunk0162_15_1	chr6	617463	617846	+	0	NA	intron (NR_073064, intron 8 of 29)	intron (NR_073064, intron 8 of 29)	39310	NM_148959	135458	Hs.669039	NM_148959	ENSG00000188996	HUS1B	-	HUS1 checkpoint clamp component B	protein-coding	0.015666	0.455729	252(GAGGGCATCCTGTGCT,-,0.00),253(AGGGCATCCTGTGCTT,+,0.00)
chunk0069_376_1	chr15	67384742	67385279	+	0	NA	exon (NM_001031715, exon 11 of 21)	exon (NM_001031715, exon 11 of 21)	-129812	NM_001271885	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.007449	0.351301	
chunk0069_367_1	chr15	67212376	67212924	+	0	NA	intron (NM_024666, intron 5 of 9)	intron (NM_024666, intron 5 of 9)	42086	NM_024666	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.007299	0.322404	248(GAGTTCATTATGTTCC,-,0.00),249(AGTTCATTATGTTCCG,+,0.00)
chunk0093_327_1	chr19	54159766	54160198	+	0	NA	promoter-TSS (NM_024316)	promoter-TSS (NM_024316)	-239	NM_024316	79165	Hs.590974	NM_024316	ENSG00000105617	LENG1	-	leukocyte receptor cluster member 1	protein-coding	0.071759	0.568129	
chunk0107_244_1	chr2	217249897	217250096	+	0	NA	Intergenic	Intergenic	-32737	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.015075	0.530000	127(TGCACGCAGTGTTCTT,+,0.00),155(CTGTACAGAGAGTTCC,-,0.00),156(TGTACAGAGAGTTCCA,+,0.00)
chunk0166_246_1	chr6	47318226	47318952	+	0	NA	Intergenic	Intergenic	-8642	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.004132	0.381018	76(TGGAACTGGTTGTTCC,-,0.00),77(GGAACTGGTTGTTCCT,+,0.00)
chunk0152_12_1	chr5	56347910	56348369	+	0	NA	Intergenic	Intergenic	-114780	NM_024669	79722	Hs.436214	NM_024669	ENSG00000164512	ANKRD55	-	ankyrin repeat domain 55	protein-coding	0.002179	0.326087	
chunk0061_150_1	chr14	59632399	59632945	+	0	NA	intron (NM_021136, intron 3 of 8)	intron (NM_021136, intron 3 of 8)	-1858	NM_206852	6252	Hs.368626	NM_021136	ENSG00000139970	RTN1	NSP	reticulon 1	protein-coding	0.012821	0.491773	250(GGAAACAGCGTGTACT,-,0.00),251(GAAACAGCGTGTACTG,+,0.00),298(GAATACACAATGTTCC,-,0.00),299(AATACACAATGTTCCC,+,0.00)
chunk0138_57_1	chr4	31896064	31896778	+	0	NA	Intergenic	Intergenic	-100958	NR_125936	102723828	Hs.575118	NR_125936	ENSG00000251129	LINC02506	-	long intergenic non-protein coding RNA 2506	ncRNA	0.001401	0.352448	
chunk0080_45_1	chr17	21566016	21566374	+	0	NA	Intergenic	Intergenic	-14517	NM_001113434	339263	Hs.514016	NM_001113434	ENSG00000212719	LINC02693	C17orf51	long intergenic non-protein coding RNA 2693	ncRNA	0.005587	0.384401	
chunk0163_116_1	chr6	10205113	10205470	+	0	NA	Intergenic	Intergenic	-207027	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.008403	0.474860	
chunk0136_292_1	chr3	194975975	194976381	+	0	NA	Intergenic	Intergenic	-118410	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.012315	0.493857	
chunk0091_384_1	chr19	15975739	15976247	+	0	NA	Intergenic	MER51D|LTR|ERV1	26985	NM_001004465	126541	Hs.553579	NM_001004465	ENSG00000176231	OR10H4	OR19-28	olfactory receptor family 10 subfamily H member 4	protein-coding	0.003937	0.440079	
chunk0051_54_1	chr12	112370774	112371367	+	0	NA	intron (NM_001109662, intron 1 of 75)	intron (NM_001109662, intron 1 of 75)	11022	NM_001109662	283450	Hs.530943	NM_173813	ENSG00000173064	HECTD4	C12ord51|C12orf51|HEEL|POTAGE	HECT domain E3 ubiquitin protein ligase 4	protein-coding	0.008432	0.409091	
chunk0128_83_1	chr3	105455326	105455867	+	0	NA	intron (NM_001627, intron 1 of 15)	MER66B|LTR|ERV1	88883	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.025878	0.470480	
chunk0086_12_1	chr18	12123273	12123772	+	0	NA	intron (NM_001277333, intron 11 of 13)	intron (NM_001277333, intron 11 of 13)	29673	NM_001277333	342850	Hs.448906	NM_001277333	ENSG00000181626	ANKRD62	DKFZp779B1634	ankyrin repeat domain 62	protein-coding	0.010020	0.352000	
chunk0176_216_1	chr7	14887162	14887541	+	0	NA	Intergenic	L2a|LINE|L2	-45901	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.005277	0.434211	303(GTGTACACTCAGTCCC,-,0.00),304(TGTACACTCAGTCCCT,+,0.00)
chunk0199_426_1	chr9	13717678	13718080	+	0	NA	Intergenic	Intergenic	-210092	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.000000	0.362283	165(CAGGACATGCAGTTCA,-,0.00),166(AGGACATGCAGTTCAC,+,0.00)
chunk0181_441_1	chr7	90676884	90677271	+	0	NA	intron (NM_001287135, intron 2 of 14)	intron (NM_001287135, intron 2 of 14)	-32321	NM_012395	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.005168	0.319588	
chunk0155_40_1	chr5	91126524	91127302	+	0	NA	intron (NR_003149, intron 87 of 89)	intron (NR_003149, intron 87 of 89)	187489	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.005141	0.440308	
chunk0186_277_1	chr7	141956130	141956329	+	0	NA	Intergenic	Charlie8|DNA|hAT-Charlie	-9222	NM_001301167	23601	Hs.446235	NM_013252	ENSG00000258227	CLEC5A	CLECSF5|MDL-1|MDL1	C-type lectin domain containing 5A	protein-coding	0.005025	0.345000	
chunk0173_146_1	chr6	144095593	144095851	+	0	NA	promoter-TSS (NM_031287)	promoter-TSS (NM_031287)	-105	NM_031287	83443	Hs.110695	NM_031287	ENSG00000169976	SF3B5	SF3b10|Ysf3	splicing factor 3b subunit 5	protein-coding	0.058140	0.567568	85(AAGCACATTCTGTCAC,-,0.00)
chunk0052_266_1	chr12	123951527	123951919	+	0	NA	intron (NM_001304958, intron 1 of 5)	intron (NM_001304958, intron 1 of 5)	20367	NM_001304959	80212	Hs.114111	NM_025140	ENSG00000119242	CCDC92	-	coiled-coil domain containing 92	protein-coding	0.010204	0.465649	190(GGGCACTTTCTGTACC,-,0.00),191(GGCACTTTCTGTACCG,+,0.00)
chunk0152_73_1	chr5	58069819	58070403	+	0	NA	Intergenic	Intergenic	52230	NR_104669	101928569	Hs.319708	NR_104669		LINC02101	-	long intergenic non-protein coding RNA 2101	ncRNA	0.008562	0.357265	
chunk0166_375_1	chr6	51608888	51609087	+	0	NA	Intergenic	Intergenic	-12883	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.000000	0.300000	
chunk0036_153_1	chr11	62325254	62325831	+	0	NA	Intergenic	Intergenic	-11760	NM_001083926	80150	Hs.535326	NM_025080	ENSG00000162174	ASRGL1	ALP|ALP1|CRASH	asparaginase like 1	protein-coding	0.003466	0.403114	
chunk0115_271_1	chr21	28063295	28063919	+	0	NA	intron (NR_126010, intron 1 of 4)	LTR40A1|LTR|ERVL	15193	NR_126010	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.006410	0.396800	
chunk0057_453_1	chr13	110819967	110820290	+	0	NA	Intergenic	Intergenic	50180	NR_027701	283487	Hs.245390	NM_178514	ENSG00000255874	LINC00346	C13orf29|NCRNA00346	long intergenic non-protein coding RNA 346	ncRNA	0.003096	0.265432	
chunk0105_348_1	chr2	191411486	191411933	+	0	NA	intron (NM_001130158, intron 27 of 30)	intron (NM_001130158, intron 27 of 30)	166181	NM_001161819	4430	Hs.439620	NM_012223	ENSG00000128641	MYO1B	MMI-alpha|MMIa|MYH-1c|myr1	myosin IB	protein-coding	0.011186	0.406250	
chunk0064_361_1	chr14	97233596	97234171	+	0	NA	Intergenic	Intergenic	-224933	NR_110166	101929241	Hs.650839	NR_110165	ENSG00000246084	LINC02325	-	long intergenic non-protein coding RNA 2325	ncRNA	0.013913	0.355903	
chunk0078_439_1	chr16	89509567	89509961	+	0	NA	intron (NM_199367, intron 1 of 9)	intron (NM_199367, intron 1 of 9)	1376	NM_199367	6687	Hs.185597	NM_003119	ENSG00000197912	SPG7	CAR|CMAR|PGN|SPG5C	SPG7 matrix AAA peptidase subunit, paraplegin	protein-coding	0.012690	0.506329	
chunk0179_377_1	chr7	51261270	51261554	+	0	NA	intron (NM_001287436, intron 1 of 13)	L2a|LINE|L2	55406	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.007042	0.424561	75(TAGAACATAATGTGTC,-,0.00)
chunk0099_383_1	chr2	101327766	101328050	+	0	NA	Intergenic	Intergenic	18458	NR_049881	100847007		NR_049881	ENSG00000264857	MIR5696	-	microRNA 5696	ncRNA	0.007042	0.456140	
chunk0189_316_1	chr8	26201925	26202392	+	0	NA	Intergenic	Intergenic	-89333	NM_002717	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.002141	0.344017	
chunk0142_276_1	chr4	99586516	99586771	+	0	NA	intron (NM_001300785, intron 3 of 17)	intron (NM_001300785, intron 3 of 17)	22565	NM_000253	4547	Hs.195799	NM_000253	ENSG00000138823	MTTP	ABL|MTP	microsomal triglyceride transfer protein	protein-coding	0.000000	0.328125	
chunk0026_100_1	chr10	61758120	61758398	+	0	NA	intron (NM_173554, intron 4 of 6)	intron (NM_173554, intron 4 of 6)	95298	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.007194	0.383513	
chunk0142_267_1	chr4	99352835	99353560	+	0	NA	promoter-TSS (NM_000669)	promoter-TSS (NM_000669)	-152	NM_000669	126	Hs.654537	NM_000669	ENSG00000248144	ADH1C	ADH3	alcohol dehydrogenase 1C (class I), gamma polypeptide	protein-coding	0.013793	0.431129	
chunk0192_66_1	chr8	60416828	60417274	+	0	NA	Intergenic	Intergenic	-3233	NR_103854	100505532	Hs.720321	NR_103854		LINC01301	-	long intergenic non-protein coding RNA 1301	ncRNA	0.013453	0.487696	
chunk0130_20_1	chr3	128623558	128624138	+	0	NA	intron (NM_002950, intron 8 of 9)	L1MC4|LINE|L1	27028	NM_002950	6184	Hs.518244	NM_002950	ENSG00000163902	RPN1	OST1|RBPH1	ribophorin I	protein-coding	0.013793	0.449225	257(CTGAACGTGCTGTTCT,-,0.00)
chunk0197_373_1	chr8	126785624	126786216	+	0	NA	Intergenic	L1ME3E|LINE|L1	-227234	NR_045262	100750225	Hs.571530	NR_045262	ENSG00000253438	PCAT1	PCA1|PCAT-1	prostate cancer associated transcript 1	ncRNA	0.006757	0.342327	
chunk0040_315_1	chr11	117814859	117815086	+	0	NA	Intergenic	Intergenic	9772	NM_001680	486	Hs.731865	NM_001680	ENSG00000137731	FXYD2	ATP1G1|HOMG2	FXYD domain containing ion transport regulator 2	protein-coding	0.030837	0.504386	
chunk0142_345_1	chr4	101468282	101468552	+	0	NA	Intergenic	L1M6|LINE|L1	120640	NR_033874	90024	Hs.534513	NR_033874	ENSG00000254531	FLJ20021	-	uncharacterized LOC90024	ncRNA	0.003704	0.332103	
chunk0022_458_1	chr10	20018604	20018842	+	0	NA	intron (NM_001282736, intron 2 of 12)	intron (NM_001282736, intron 2 of 12)	202280	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.000000	0.271967	
chunk0202_425_1	chr9	81787966	81788627	+	0	NA	Intergenic	Intergenic	98583	NR_109772	101927502	Hs.528628	NR_109772	ENSG00000233926	LOC101927502	-	uncharacterized LOC101927502	ncRNA	0.001513	0.432024	
chunk0117_51_1	chr22	12692228	12692964	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	795190	NR_110761	102723769	Hs.652926	NR_110761		LOC102723769	-	uncharacterized LOC102723769	ncRNA	0.023098	0.502035	
chunk0106_252_1	chr2	203569956	203570438	+	0	NA	Intergenic	Intergenic	-34862	NM_203365	65059	Hs.471162	NM_025252	ENSG00000173166	RAPH1	ALS2CR18|ALS2CR9|LPD|PREL-2|PREL2|RMO1|RalGDS/AF-6	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	protein-coding	0.010373	0.422360	
chunk0008_81_1	chr1	89938346	89938668	+	0	NA	Intergenic	Intergenic	56459	NR_002830	492303	Hs.550796	NR_002830		GEMIN8P4	-	gem nuclear organelle associated protein 8 pseudogene 4	pseudo	0.009317	0.396285	
chunk0081_171_1	chr17	41484134	41484817	+	0	NA	Intergenic	L3|LINE|CR1	-3335	NM_002280	3886	Hs.73082	NM_002280	ENSG00000197079	KRT35	HA5|Ha-5|K35|KRTHA5|hHa5	keratin 35	protein-coding	0.007321	0.519006	
chunk0022_324_1	chr10	16436824	16437231	+	0	NA	promoter-TSS (NM_001261838)	promoter-TSS (NM_001261838)	84	NM_030664	9317	Hs.444321	NM_030664	ENSG00000165983	PTER	HPHRP|RPR-1	phosphotriesterase related	protein-coding	0.068796	0.656863	
chunk0123_228_1	chr3	45406924	45407552	+	0	NA	intron (NM_015340, intron 4 of 21)	intron (NM_015340, intron 4 of 21)	18655	NM_015340	23395	Hs.526975	NM_015340	ENSG00000011376	LARS2	HLASA|LEURS|PRLTS4|mtLeuRS	leucyl-tRNA synthetase 2, mitochondrial	protein-coding	0.011146	0.445151	
chunk0083_417_1	chr17	72189927	72190185	+	0	NA	Intergenic	Intergenic	69036	NM_000346	6662	Hs.647409	NM_000346	ENSG00000125398	SOX9	CMD1|CMPD1|SRA1|SRXX2|SRXY10	SRY-box transcription factor 9	protein-coding	0.000000	0.490347	
chunk0134_440_1	chr3	183644263	183644997	+	0	NA	intron (NM_017644, intron 2 of 7)	intron (NM_017644, intron 2 of 7)	9007	NM_017644	54800	Hs.407709	NM_017644	ENSG00000114796	KLHL24	DRE1|EBSSH|KRIP6	kelch like family member 24	protein-coding	0.002725	0.336054	
chunk0121_357_1	chr3	24817334	24817743	+	0	NA	Intergenic	L1MEf|LINE|L1	-296103	NR_039955									0.002445	0.297561	216(ATGAACATAATGTGCC,-,0.00),217(TGAACATAATGTGCCA,+,0.00)
chunk0066_343_1	chr15	37349456	37349841	+	0	NA	Intergenic	Intergenic	-248349	NM_002399	4212	Hs.510989	NM_002399	ENSG00000134138	MEIS2	CPCMR|HsT18361|MRG1	Meis homeobox 2	protein-coding	0.015584	0.494819	
chunk0211_193_1	chrX	117543789	117544318	+	0	NA	Intergenic	Intergenic	429685	NM_033495	90293	Hs.348262	NM_033495	ENSG00000003096	KLHL13	BKLHD2	kelch like family member 13	protein-coding	0.005671	0.373585	
chunk0019_6_1	chr1	223203043	223203243	+	0	NA	Intergenic	Intergenic	-59861	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.040000	0.587065	32(CGGAACAAGCTGTGCA,-,0.00),33(GGAACAAGCTGTGCAG,+,0.00)
chunk0028_74_1	chr10	83779426	83779823	+	0	NA	Intergenic	Intergenic	-359805	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.005038	0.369347	215(ATGTACAGTATGTACA,-,0.00)
chunk0081_214_1	chr17	42554315	42554652	+	0	NA	exon (NM_000413, exon 5 of 6)	exon (NM_000413, exon 5 of 6)	2517	NM_000413	3292	Hs.654385	NM_000413	ENSG00000108786	HSD17B1	17-beta-HSD|20-alpha-HSD|E2DH|EDH17B2|EDHB17|HSD17|SDR28C1	hydroxysteroid 17-beta dehydrogenase 1	protein-coding	0.074184	0.683432	
chunk0199_30_1	chr9	745727	746245	+	0	NA	3' UTR (NM_001256877, exon 13 of 13)	3' UTR (NM_001256877, exon 13 of 13)	39180	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.021236	0.398844	242(AGAAACACAGTGTTCT,-,0.00),243(GAAACACAGTGTTCTC,+,0.00)
chunk0155_326_1	chr5	96775015	96775710	+	0	NA	TTS (NM_001284213)	TTS (NM_001284213)	31822	NR_104285	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.008633	0.386494	
chunk0012_252_1	chr1	161187544	161187743	+	0	NA	Intergenic	Intergenic	-9675	NM_001199874	8703	Hs.321231	NM_003779	ENSG00000158850	B4GALT3	beta4Gal-T3	beta-1,4-galactosyltransferase 3	protein-coding	0.000000	0.510000	
chunk0202_123_1	chr9	73107426	73107842	+	0	NA	Intergenic	Intergenic	-44097	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.002404	0.383693	
chunk0071_264_1	chr15	85532607	85533120	+	0	NA	intron (NM_007200, intron 3 of 36)	intron (NM_007200, intron 3 of 36)	-87087	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.007797	0.400778	
chunk0054_278_1	chr13	46663521	46663929	+	0	NA	intron (NM_001164213, intron 2 of 18)	intron (NM_001164213, intron 2 of 18)	110564	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.004902	0.378973	
chunk0062_437_1	chr14	75400234	75400674	+	0	NA	Intergenic	Intergenic	-27352	NM_001135047	122953	Hs.196482	NM_130469	ENSG00000140044	JDP2	JUNDM2	Jun dimerization protein 2	protein-coding	0.015909	0.553288	
chunk0146_137_1	chr4	159293239	159293495	+	0	NA	intron (NM_014247, intron 1 of 23)	L2a|LINE|L2	25521	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.011719	0.365759	
chunk0210_67_1	chrX	69947245	69947469	+	0	NA	intron (NM_001005612, intron 1 of 7)	MamRTE1|LINE|RTE-BovB	-75500	NR_037494	100500887		NR_037494	ENSG00000211991	MIR676	hsa-mir-676|mir-676	microRNA 676	ncRNA	0.000000	0.408889	
chunk0036_455_1	chr11	68683118	68683496	+	0	NA	Intergenic	Intergenic	-1168	NM_015973	51083	Hs.278959	NM_015973	ENSG00000069482	GAL	ETL8|GAL-GMAP|GALN|GLNN|GMAP	galanin and GMAP prepropeptide	protein-coding	0.018519	0.567282	
chunk0129_410_1	chr3	126948954	126949524	+	0	NA	intron (NM_032343, intron 6 of 7)	intron (NM_032343, intron 6 of 7)	-39355	NM_032242	5361	Hs.432329	NM_032242	ENSG00000114554	PLXNA1	NOV|NOVP|PLEXIN-A1|PLXN1	plexin A1	protein-coding	0.022807	0.570928	260(AGGGACAACCTGACCC,-,0.00),261(GGGACAACCTGACCCT,+,0.00)
chunk0115_114_1	chr21	22948664	22949266	+	0	NA	Intergenic	Intergenic	-130319	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.000000	0.281924	
chunk0194_224_1	chr8	86201955	86202215	+	0	NA	Intergenic	Intergenic	28290	NM_138817	157724	Hs.149095	NM_138817	ENSG00000164893	SLC7A13	AGT-1|AGT1|XAT2	solute carrier family 7 member 13	protein-coding	0.003846	0.371648	112(AGGAACACCTTGTTCT,-,0.00),113(GGAACACCTTGTTCTG,+,0.00)
chunk0057_155_1	chr13	100435565	100435764	+	0	NA	intron (NM_001127692, intron 19 of 22)	MER51A|LTR|ERV1	45351	NR_047686	100885777	Hs.662554	NR_047686		PCCA-AS1	-	PCCA antisense RNA 1	ncRNA	0.010050	0.355000	
chunk0086_363_1	chr18	25983179	25983408	+	0	NA	Intergenic	Intergenic	107354	NM_001007559	6760	Hs.129261	NM_005637	ENSG00000141380	SS18	SSXT|SYT	SS18 subunit of BAF chromatin remodeling complex	protein-coding	0.004367	0.386957	
chunk0007_411_1	chr1	85850271	85850723	+	0	NA	intron (NM_152890, intron 37 of 59)	intron (NM_152890, intron 37 of 59)	-142064	NM_017953	54680	Hs.5111	NM_017953	ENSG00000117174	ZNHIT6	BCD1|C1orf181|NY-BR-75	zinc finger HIT-type containing 6	protein-coding	0.004425	0.375276	
chunk0152_363_1	chr5	63923844	63924482	+	0	NA	Intergenic	Intergenic	38129	NM_000524	3350	Hs.247940	NM_000524	ENSG00000178394	HTR1A	5-HT-1A|5-HT1A|5HT1a|ADRB2RL1|ADRBRL1|G-21|PFMCD	5-hydroxytryptamine receptor 1A	protein-coding	0.006270	0.413146	
chunk0150_81_1	chr5	32218129	32218368	+	0	NA	Intergenic	Intergenic	-43929	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.033473	0.475000	156(TAGAACACACTGAGCC,-,0.00),157(AGAACACACTGAGCCC,+,0.00)
chunk0205_403_1	chr9	114681929	114682208	+	0	NA	promoter-TSS (NM_001199233)	promoter-TSS (NM_001199233)	21	NM_001199233	100505478	Hs.200101	NM_001199233	ENSG00000230601	TEX48	-	testis expressed 48	protein-coding	0.010753	0.535714	
chunk0052_84_1	chr13	21814366	21814854	+	0	NA	Intergenic	Intergenic	63550	NR_047040	100874182	Hs.148951	NR_047040	ENSG00000226722	LINC00424	-	long intergenic non-protein coding RNA 424	ncRNA	0.010246	0.449898	
chunk0179_305_1	chr7	50150619	50151045	+	0	NA	intron (NM_001161834, intron 7 of 8)	intron (NM_001161834, intron 7 of 8)	54746	NM_001161834	100130988	Hs.99248	NM_001161834	ENSG00000164500	SPATA48	C7orf72	spermatogenesis associated 48	protein-coding	0.007042	0.370023	
chunk0009_430_1	chr1	111142625	111143023	+	0	NA	intron (NM_006090, intron 1 of 8)	L2b|LINE|L2	-2608	NM_178454	128338	Hs.485606	NM_178454	ENSG00000156171	DRAM2	CORD21|PRO180|TMEM77|WWFQ154	DNA damage regulated autophagy modulator 2	protein-coding	0.005025	0.358396	
chunk0031_340_1	chr10	129558834	129559405	+	0	NA	intron (NM_002412, intron 2 of 4)	intron (NM_002412, intron 2 of 4)	91935	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.022767	0.414336	
chunk0101_285_1	chr2	134261797	134262246	+	0	NA	intron (NM_002410, intron 1 of 15)	intron (NM_002410, intron 1 of 15)	7762	NM_002410	4249	Hs.4988	NM_002410	ENSG00000152127	MGAT5	GNT-V|GNT-VA|MGAT5A	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase	protein-coding	0.004454	0.368889	234(GGAACACATTGTGTTC,+,0.00),235(GAACACATTGTGTTCC,-,0.00),236(AACACATTGTGTTCCT,+,0.00)
chunk0037_436_1	chr11	80258899	80259401	+	0	NA	Intergenic	L1MD1|LINE|L1	503653	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.007968	0.379722	308(AAGGACATCCAGTTTT,-,0.00)
chunk0075_357_1	chr16	56014045	56014268	+	0	NA	Intergenic	Intergenic	-58125	NM_001190158	221223	Hs.350800	NM_145024	ENSG00000159398	CES5A	CAUXIN|CES4C1|CES5|CES7|HEL126	carboxylesterase 5A	protein-coding	0.022422	0.517857	
chunk0056_136_1	chr13	83256476	83256868	+	0	NA	Intergenic	Intergenic	625721	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002551	0.277354	
chunk0097_345_1	chr2	58347550	58348207	+	0	NA	Intergenic	L1MA4A|LINE|L1	-106498	NM_018062	55120	Hs.631890	NM_018062	ENSG00000115392	FANCL	FAAP43|PHF9|POG	FA complementation group L	protein-coding	0.000000	0.325228	
chunk0101_123_1	chr2	127081095	127081512	+	0	NA	intron (NM_004305, intron 1 of 14)	intron (NM_004305, intron 1 of 14)	26024	NM_139349	274	Hs.193163	NM_004305	ENSG00000136717	BIN1	AMPH2|AMPHL|CNM2|SH3P9	bridging integrator 1	protein-coding	0.033573	0.645933	52(GGGCACAGGCAGTGCA,-,0.00),53(GGCACAGGCAGTGCAC,+,0.00)
chunk0167_94_1	chr6	56999485	56999767	+	0	NA	intron (NM_152731, intron 3 of 6)	L1PA15-16|LINE|L1	44651	NM_152731	221336	Hs.582993	NM_152731	ENSG00000151917	BEND6	C6orf65	BEN domain containing 6	protein-coding	0.003546	0.547703	190(CAGACCACTGTGTACT,-,0.00),191(AGACCACTGTGTACTC,+,0.00)
chunk0182_136_1	chr7	94573397	94573897	+	0	NA	Intergenic	L1PREC2|LINE|L1	63789	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.000000	0.373253	
chunk0079_263_1	chr17	16171620	16171930	+	0	NA	intron (NM_001190438, intron 1 of 18)	intron (NM_001190438, intron 1 of 18)	22864	NM_001190438	9611	Hs.462323	NM_006311	ENSG00000141027	NCOR1	N-CoR|N-CoR1|PPP1R109|TRAC1|hN-CoR	nuclear receptor corepressor 1	protein-coding	0.019355	0.424437	
chunk0015_29_1	chr1	184413812	184414024	+	0	NA	intron (NM_030806, intron 1 of 5)	intron (NM_030806, intron 1 of 5)	26902	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.361502	
chunk0158_370_1	chr5	133993518	133994192	+	0	NA	intron (NM_003374, intron 1 of 8)	intron (NM_003374, intron 1 of 8)	11111	NR_036624	7416	Hs.519320	NM_003374	ENSG00000213585	VDAC1	PORIN|VDAC-1	voltage dependent anion channel 1	protein-coding	0.002967	0.389630	398(CTGTACATGGTGTGCT,-,0.00),399(TGTACATGGTGTGCTC,+,0.00)
chunk0199_286_1	chr9	6595898	6596324	+	0	NA	intron (NM_000170, intron 8 of 24)	intron (NM_000170, intron 8 of 24)	49581	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.004695	0.423888	242(GTGACACACTGTGCCC,+,0.00)
chunk0166_307_1	chr6	49619282	49619876	+	0	NA	intron (NM_000324, intron 1 of 9)	intron (NM_000324, intron 1 of 9)	17295	NM_000324	6005	Hs.120950	NM_000324	ENSG00000112077	RHAG	CD241|OHS|OHST|RH2|RH50A|RHNR|Rh50|Rh50GP|SLC42A1	Rh associated glycoprotein	protein-coding	0.000000	0.376471	
chunk0089_213_1	chr18	61048332	61048848	+	0	NA	Intergenic	Intergenic	-441952	NM_031891	28316	Hs.671510	NM_031891	ENSG00000101542	CDH20	CDH7L3|Cdh7	cadherin 20	protein-coding	0.001938	0.319149	276(AGGAACAAGTTGTCCA,-,0.00),277(GGAACAAGTTGTCCAA,+,0.00)
chunk0067_31_1	chr15	40397507	40398126	+	0	NA	Intergenic	L1M5|LINE|L1	-7669	NM_002225	3712	Hs.513646	NM_002225	ENSG00000128928	IVD	ACAD2	isovaleryl-CoA dehydrogenase	protein-coding	0.011309	0.441935	
chunk0019_251_1	chr1	227669949	227670341	+	0	NA	intron (NR_102302, intron 5 of 5)	intron (NR_102302, intron 5 of 5)	27562	NR_036753	401983	Hs.681816	NR_036753		ZNF847P	gm127	zinc finger protein 847, pseudogene	pseudo	0.012755	0.366412	
chunk0127_431_1	chr3	102773901	102774298	+	0	NA	Intergenic	Intergenic	339084	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.007557	0.319095	
chunk0034_170_1	chr11	31001098	31001302	+	0	NA	Intergenic	L1MC4|LINE|L1	-8514	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.000000	0.278049	
chunk0143_290_1	chr4	118286870	118287079	+	0	NA	intron (NM_003619, intron 11 of 12)	intron (NM_003619, intron 11 of 12)	7784	NR_002963	677809	Hs.744742	NR_002963	ENSG00000275994	SNORA24	ACA24|SNORA24A	small nucleolar RNA, H/ACA box 24	snoRNA	0.009569	0.361905	
chunk0097_276_1	chr2	54952756	54953607	+	0	NA	intron (NM_001039753, intron 30 of 40)	intron (NM_001039753, intron 30 of 40)	57153	NM_007008	57142	Hs.637850	NM_007008	ENSG00000115310	RTN4	ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C	reticulon 4	protein-coding	0.015276	0.435446	220(AAGAACTCCGTGTCTT,-,0.00)
chunk0209_60_1	chrX	37367900	37368378	+	0	NA	intron (NM_001173490, intron 1 of 3)	L1MCb|LINE|L1	18809	NM_001173490	5638	Hs.190341	NM_000950	ENSG00000130962	PRRG1	PRGP1	proline rich and Gla domain 1	protein-coding	0.006276	0.336117	
chunk0047_66_1	chr12	67574554	67574782	+	0	NA	Intergenic	Intergenic	54586	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.000000	0.323144	
chunk0097_267_1	chr2	54584455	54585137	+	0	NA	intron (NM_178313, intron 1 of 30)	intron (NM_178313, intron 1 of 30)	26402	NM_178313	6711	Hs.503178	NM_003128	ENSG00000115306	SPTBN1	ELF|HEL102|SPTB2|betaSpII	spectrin beta, non-erythrocytic 1	protein-coding	0.002933	0.417277	
chunk0031_222_1	chr10	126186890	126187089	+	0	NA	intron (NM_001288973, intron 3 of 22)	MIRc|SINE|MIR	201569	NM_001288975	8038	Hs.594351	NM_003474	ENSG00000148848	ADAM12	ADAM12-OT1|CAR10|MCMP|MCMPMltna|MLTN|MLTNA	ADAM metallopeptidase domain 12	protein-coding	0.000000	0.435000	
chunk0017_102_1	chr1	205864023	205864588	+	0	NA	intron (NR_046097, intron 1 of 2)	L1PB1|LINE|L1	2226	NR_046097	284581		NR_046097		LOC284581	-	uncharacterized LOC284581	ncRNA	0.008850	0.393993	
chunk0181_19_1	chr7	77786551	77786774	+	0	NA	Intergenic	L2c|LINE|L2	11768	NM_032936	85025	Hs.19025	NM_032936	ENSG00000135211	TMEM60	C7orf35|DC32	transmembrane protein 60	protein-coding	0.000000	0.379464	135(AGGAACATATTGTACA,-,0.00),136(GGAACATATTGTACAC,+,0.00)
chunk0177_91_1	chr7	21759392	21759731	+	0	NA	intron (NM_001277115, intron 54 of 81)	intron (NM_001277115, intron 54 of 81)	186363	NM_018719	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.011799	0.370588	
chunk0198_161_1	chr8	133165624	133166044	+	0	NA	Intergenic	Intergenic	-25205	NM_001204870	8840	Hs.492974	NM_003882	ENSG00000104415	CCN4	WISP1|WISP1-OT1|WISP1-UT1|WISP1c|WISP1i|WISP1tc	cellular communication network factor 4	protein-coding	0.007143	0.484561	373(CAGCACAGATTGCTCC,-,0.00)
chunk0041_231_1	chr11	128400988	128401300	+	0	NA	Intergenic	Intergenic	121166	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.009615	0.453674	
chunk0045_327_1	chr12	50927342	50927693	+	0	NA	intron (NM_014033, intron 1 of 1)	MIRb|SINE|MIR	2766	NM_014033	25840	Hs.711113	NM_014033	ENSG00000185432	METTL7A	AAM-B|AAMB	methyltransferase like 7A	protein-coding	0.005698	0.389205	
chunk0098_450_1	chr2	82320018	82320691	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-536449	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.008915	0.421365	
chunk0114_78_1	chr21	9195514	9195852	+	0	NA	Intergenic	Intergenic	-65922	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.002959	0.321534	
chunk0091_258_1	chr19	11041832	11042669	+	0	NA	intron (NM_001128848, intron 28 of 32)	intron (NM_001128848, intron 28 of 32)	-47112	NM_000527	3949	Hs.213289	NM_000527	ENSG00000130164	LDLR	FH|FHC|LDLCQ2	low density lipoprotein receptor	protein-coding	0.016726	0.540573	
chunk0131_219_1	chr3	149180090	149180350	+	0	NA	intron (NR_046371, intron 13 of 17)	intron (NR_046371, intron 13 of 17)	41825	NR_046371	1356	Hs.558314	NM_000096	ENSG00000047457	CP	CP-2	ceruloplasmin	protein-coding	0.019231	0.475096	
chunk0187_96_1	chr8	4336340	4336542	+	0	NA	intron (NM_033225, intron 3 of 69)	intron (NM_033225, intron 3 of 69)	658365	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.024752	0.507389	
chunk0058_188_1	chr14	24188835	24189072	+	0	NA	promoter-TSS (NM_024658)	promoter-TSS (NM_024658)	-35	NR_051979	79711	Hs.411865	NM_024658	ENSG00000196497	IPO4	Imp4	importin 4	protein-coding	0.075949	0.613445	
chunk0048_279_1	chr12	82479448	82480199	+	0	NA	TTS (NM_032230)	TTS (NM_032230)	-121018	NR_033192	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.001332	0.329787	
chunk0119_210_1	chr22	44933769	44934411	+	0	NA	intron (NM_001284296, intron 2 of 13)	intron (NM_001284296, intron 2 of 13)	74903	NM_001284296	112885	Hs.254097	NM_138415	ENSG00000056487	PHF21B	BHC80L|PHF4	PHD finger protein 21B	protein-coding	0.029595	0.561431	
chunk0168_2_1	chr6	76547588	76548271	+	0	NA	Intergenic	L1MC2|LINE|L1	-475251	NM_001563	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.004392	0.372807	
chunk0159_135_1	chr5	139133498	139133819	+	0	NA	intron (NM_022464, intron 1 of 9)	intron (NM_022464, intron 1 of 9)	64718	NM_001037633	64374	Hs.483521	NM_022464	ENSG00000120725	SIL1	BAP|MSS|ULG5	SIL1 nucleotide exchange factor	protein-coding	0.000000	0.453416	
chunk0172_436_1	chr6	140827537	140828011	+	0	NA	Intergenic	MER20B|DNA|hAT-Charlie	143960	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.004219	0.301053	
chunk0156_190_1	chr5	107917341	107917862	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-246706	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.005758	0.331418	
chunk0089_206_1	chr18	60670571	60670914	+	0	NA	Intergenic	MER83C|LTR|ERV1	-297974	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.005831	0.438953	
chunk0063_18_1	chr14	76404003	76404247	+	0	NA	intron (NM_004452, intron 1 of 10)	intron (NM_004452, intron 1 of 10)	32778	NM_004452	2103	Hs.435845	NM_004452	ENSG00000119715	ESRRB	DFNB35|ERR2|ERRb|ESRL2|NR3B2	estrogen related receptor beta	protein-coding	0.020492	0.497959	
chunk0161_332_1	chr5	173833621	173833998	+	0	NA	Intergenic	Intergenic	-42867	NR_108028	101928154	Hs.366725	NR_108028		LINC01485	-	long intergenic non-protein coding RNA 1485	ncRNA	0.015915	0.407407	
chunk0090_453_1	chr18	79947953	79948279	+	0	NA	intron (NM_001146345, intron 2 of 4)	intron (NM_001146345, intron 2 of 4)	3537	NM_025078	80148	Hs.288284	NM_025078	ENSG00000122490	SLC66A2	PQLC1	solute carrier family 66 member 2	protein-coding	0.021472	0.559633	268(AAGAACTCCCAGTTCC,-,0.00),269(AGAACTCCCAGTTCCA,+,0.00)
chunk0076_87_1	chr16	64695843	64696042	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	426195	NM_001797	1009	Hs.116471	NM_001797	ENSG00000140937	CDH11	CAD11|CDHOB|ESWS|OB|OSF-4	cadherin 11	protein-coding	0.005025	0.385000	
chunk0198_411_1	chr8	142617770	142618120	+	0	NA	Intergenic	Intergenic	-3473	NM_015193	23237	Hs.40888	NM_015193	ENSG00000198576	ARC	Arg3.1|hArc	activity regulated cytoskeleton associated protein	protein-coding	0.017143	0.641026	
chunk0003_397_1	chr1	39926632	39927092	+	0	NA	Intergenic	Intergenic	-24847	NM_005376	4610	Hs.437922	NM_005376	ENSG00000116990	MYCL	L-Myc|LMYC|MYCL1|bHLHe38	MYCL proto-oncogene, bHLH transcription factor	protein-coding	0.015217	0.574837	
chunk0060_436_1	chr14	54409001	54409282	+	0	NA	intron (NM_005192, intron 4 of 7)	intron (NM_005192, intron 4 of 7)	12186	NM_005192	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.000000	0.375887	
chunk0043_236_1	chr12	20080209	20080625	+	0	NA	intron (NR_040098, intron 2 of 2)	intron (NR_040098, intron 2 of 2)	65732	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.004808	0.338129	
chunk0212_66_1	chrY	11329671	11329891	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1091809	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.009091	0.497738	
chunk0012_384_1	chr1	163382867	163383067	+	0	NA	Intergenic	L2a|LINE|L2	40224	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.000000	0.373134	
chunk0113_288_1	chr20	57235219	57235644	+	0	NA	intron (NM_001719, intron 1 of 6)	intron (NM_001719, intron 1 of 6)	21735	NR_110631	102723590	Hs.667674	NR_110631		BMP7-AS1	-	BMP7 antisense RNA 1	ncRNA	0.014118	0.467136	84(GAGACAAGCTGTGCTG,+,0.00)
chunk0106_258_1	chr2	203636988	203637187	+	0	NA	Intergenic	MIRb|SINE|MIR	-69388	NM_001243077	940	Hs.443123	NM_006139	ENSG00000178562	CD28	Tp44	CD28 molecule	protein-coding	0.000000	0.430000	66(TGGCACAGTGAGTTCA,-,0.00),67(GGCACAGTGAGTTCAG,+,0.00)
chunk0030_31_1	chr10	111347513	111347972	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	270710	NM_000681	150	Hs.249159	NM_000681	ENSG00000150594	ADRA2A	ADRA2|ADRA2R|ADRAR|ALPHA2AAR|ZNF32	adrenoceptor alpha 2A	protein-coding	0.013072	0.415217	204(AAGGACACAACGTACC,-,0.00),205(AGGACACAACGTACCT,+,0.00)
chunk0032_91_1	chr11	3057544	3057920	+	0	NA	promoter-TSS (NM_001751)	promoter-TSS (NM_001751)	-281	NM_139273	833	Hs.274873	NM_001751	ENSG00000110619	CARS	CARS1|CYSRS|MGC:11246	cysteinyl-tRNA synthetase	protein-coding	0.066489	0.633952	186(CGGGACAGGGTGTGCT,-,0.00),187(GGGACAGGGTGTGCTG,+,0.00)
chunk0022_452_1	chr10	19931851	19932212	+	0	NA	intron (NM_032812, intron 1 of 13)	intron (NM_032812, intron 1 of 13)	115588	NM_001282736	84898	Hs.99472	NM_032812	ENSG00000120594	PLXDC2	TEM7R	plexin domain containing 2	protein-coding	0.005540	0.359116	
chunk0161_274_1	chr5	172649999	172650368	+	0	NA	intron (NM_001308177, intron 1 of 3)	intron (NM_001308177, intron 1 of 3)	8917	NM_001308178	54492	Hs.91521	NM_001142651	ENSG00000214357	NEURL1B	NEURL3|RNF67B|hNeur2|neur2	neuralized E3 ubiquitin protein ligase 1B	protein-coding	0.010840	0.470270	
chunk0163_405_1	chr6	16767979	16768646	+	0	NA	Intergenic	Intergenic	-6822	NM_001128164	6310	Hs.434961	NM_000332	ENSG00000124788	ATXN1	ATX1|D6S504E|SCA1	ataxin 1	protein-coding	0.005997	0.387725	
chunk0171_49_1	chr6	120984641	120985285	+	0	NA	Intergenic	Intergenic	349537	NM_152730	221322	Hs.121396	NM_152730	ENSG00000146350	TBC1D32	BROMI|C6orf170|C6orf171	TBC1 domain family member 32	protein-coding	0.007764	0.303876	327(AGGTACAATGTGTTTT,-,0.00),328(GGTACAATGTGTTTTT,+,0.00)
chunk0105_220_1	chr2	188072339	188072652	+	0	NA	intron (NR_126396, intron 2 of 2)	LTR1F1|LTR|ERV1	215196	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.019169	0.509554	
chunk0150_373_1	chr5	39167227	39167804	+	0	NA	intron (NM_001465, intron 2 of 18)	intron (NM_001465, intron 2 of 18)	52063	NM_001465	2533	Hs.370503	NM_001465	ENSG00000082074	FYB1	ADAP|FYB|PRO0823|SLAP-130|SLAP130|THC3	FYN binding protein 1	protein-coding	0.000000	0.387543	
chunk0019_349_1	chr1	229509200	229509498	+	0	NA	intron (NR_110630, intron 1 of 2)	intron (NR_110630, intron 1 of 2)	919	NR_110630	101927478	Hs.229275	NR_110630		LOC101927478	-	uncharacterized LOC101927478	ncRNA	0.020134	0.488294	
chunk0023_219_1	chr10	25665613	25666380	+	0	NA	intron (NR_108067, intron 2 of 4)	L1ME1|LINE|L1	14284	NR_108068	101929052	Hs.128298	NR_108067	ENSG00000280809	LINC00836	-	long intergenic non-protein coding RNA 836	ncRNA	0.002608	0.337240	
chunk0076_28_1	chr16	59292418	59292881	+	0	NA	Intergenic	Intergenic	462542	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.000000	0.325431	
chunk0130_94_1	chr3	130849004	130850058	+	0	NA	promoter-TSS (NM_001199180)	promoter-TSS (NM_001199180)	-994	NM_001199182	27032	Hs.584884	NM_014382	ENSG00000017260	ATP2C1	ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1	ATPase secretory pathway Ca2+ transporting 1	protein-coding	0.003795	0.445498	
chunk0013_169_1	chr1	168817094	168817293	+	0	NA	Intergenic	Intergenic	30252	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.010050	0.455000	
chunk0108_345_1	chr2	236048012	236048292	+	0	NA	intron (NM_001037131, intron 15 of 17)	intron (NM_001037131, intron 15 of 17)	119857	NM_001301687	2637	Hs.184945	NM_001485	ENSG00000168505	GBX2	-	gastrulation brain homeobox 2	protein-coding	0.014286	0.466192	
chunk0067_283_1	chr15	47409007	47409206	+	0	NA	intron (NM_001198999, intron 1 of 19)	intron (NM_001198999, intron 1 of 19)	224900	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.005025	0.395000	
chunk0038_280_1	chr11	89685072	89685511	+	0	NA	intron (NM_153696, intron 8 of 13)	L1PA13|LINE|L1	-25008	NM_001146162	390231	Hs.723112	NM_001146162	ENSG00000214414	TRIM77	TRIM77P	tripartite motif containing 77	protein-coding	0.009112	0.381818	
chunk0033_357_1	chr11	23024845	23025457	+	0	NA	Intergenic	Intergenic	-164725	NM_001195637	100500938	Hs.555029	NM_001195637	ENSG00000255359	CCDC179	-	coiled-coil domain containing 179	protein-coding	0.008170	0.309951	275(CAGCACACTATGTCCC,-,0.00),276(AGCACACTATGTCCCT,+,0.00)
chunk0136_298_1	chr3	195068144	195068343	+	0	NA	TTS (NM_152531)	TTS (NM_152531)	-26345	NR_104188	100874528	Hs.581659	NR_104188	ENSG00000233303	XXYLT1-AS1	-	XXYLT1 antisense RNA 1	ncRNA	0.005025	0.420000	
chunk0195_333_1	chr8	99190535	99190847	+	0	NA	intron (NM_015243, intron 16 of 17)	L1MEc|LINE|L1	177425	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.000000	0.297125	
chunk0103_239_1	chr2	164786126	164786621	+	0	NA	intron (NM_001278460, intron 2 of 13)	intron (NM_001278460, intron 2 of 13)	-54376	NR_110574	101929633	Hs.570267	NR_110574		LOC101929633	-	uncharacterized LOC101929633	ncRNA	0.004040	0.395161	
chunk0208_108_1	chrX	13794309	13794776	+	0	NA	intron (NM_001001994, intron 1 of 6)	Charlie1a|DNA|hAT-Charlie	22653	NM_001001995	2824	Hs.495710	NM_005278	ENSG00000046653	GPM6B	M6B	glycoprotein M6B	protein-coding	0.025696	0.450855	
chunk0140_84_1	chr4	67933544	67934109	+	0	NA	intron (NM_001114387, intron 3 of 9)	intron (NM_001114387, intron 3 of 9)	29688	NM_001114387	339967	Hs.450110	NM_182606	ENSG00000187054	TMPRSS11A	ECRG1	transmembrane serine protease 11A	protein-coding	0.001770	0.360424	
chunk0180_137_1	chr7	56079508	56079995	+	0	NA	TTS (NM_006213)	TTS (NM_006213)	13245	NM_006213	5260	Hs.730821	NM_006213	ENSG00000164776	PHKG1	PHKG	phosphorylase kinase catalytic subunit gamma 1	protein-coding	0.020534	0.534836	
chunk0040_363_1	chr11	118820395	118820681	+	0	NA	Intergenic	Intergenic	-29275	NM_004397	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.031469	0.592334	
chunk0164_99_1	chr6	20381674	20381954	+	0	NA	Intergenic	LTR8B|LTR|ERV1	-20092	NM_001949	1871	Hs.269408	NM_001949	ENSG00000112242	E2F3	E2F-3	E2F transcription factor 3	protein-coding	0.021429	0.459075	188(GGGAAGAGAGTGTGCC,-,0.00)
chunk0042_81_1	chr12	2255749	2256141	+	0	NA	intron (NM_001129846, intron 3 of 45)	intron (NM_001129846, intron 3 of 45)	-13831	NR_046769	100874370	Hs.653548	NR_046769		CACNA1C-IT3	-	CACNA1C intronic transcript 3	ncRNA	0.022959	0.450382	
chunk0094_395_1	chr2	10342523	10342860	+	0	NA	intron (NM_001258357, intron 1 of 4)	intron (NM_001258357, intron 1 of 4)	12528	NM_001258357	3241	Hs.580427	NM_002149	ENSG00000115756	HPCAL1	BDR1|HLP2|VILIP-3	hippocalcin like 1	protein-coding	0.020772	0.559172	89(GGGAACAGCATGTGCA,-,0.00),90(GGAACAGCATGTGCAG,+,0.00),223(AGGCACAATCTGTTCC,-,0.00),224(GGCACAATCTGTTCCC,+,0.00)
chunk0188_321_1	chr8	17466819	17467373	+	0	NA	Intergenic	Intergenic	-29992	NM_001008539	6542	Hs.448520	NM_003046	ENSG00000003989	SLC7A2	ATRC2|CAT2|HCAT2	solute carrier family 7 member 2	protein-coding	0.010830	0.362162	279(AAGGACAAGTTGTCCT,-,0.00),280(AGGACAAGTTGTCCTA,+,0.00)
chunk0165_356_1	chr6	38092230	38092722	+	0	NA	intron (NM_021943, intron 4 of 5)	intron (NM_021943, intron 4 of 5)	272945	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.004065	0.389452	
chunk0111_66_1	chr20	22973409	22973858	+	0	NA	Intergenic	L1MDa|LINE|L1	-61787	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.013363	0.413333	204(AAGAACTTAGTGTTTT,-,0.00),205(AGAACTTAGTGTTTTT,+,0.00)
chunk0007_161_1	chr1	79893834	79894087	+	0	NA	Intergenic	L1PA3|LINE|L1	-641795	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.007905	0.527559	
chunk0205_416_1	chr9	114981325	114981630	+	0	NA	Intergenic	Intergenic	-50882	NM_001252290	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.000000	0.330065	
chunk0107_450_1	chr2	225561213	225561536	+	0	NA	intron (NM_020864, intron 3 of 5)	L2a|LINE|L2	160488	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.006192	0.447531	171(TGGAACAGAGTGAACC,-,0.00),172(GGAACAGAGTGAACCT,+,0.00)
chunk0122_1_1	chr3	27317030	27317445	+	0	NA	intron (NM_199347, intron 7 of 24)	intron (NM_199347, intron 7 of 24)	52223	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.004819	0.408654	
chunk0141_102_1	chr4	79258205	79258530	+	0	NA	intron (NR_038342, intron 4 of 5)	MER52A|LTR|ERV1	67650	NM_032693	84779	Hs.676048	NM_032693	ENSG00000156269	NAA11	ARD1B|ARD2|hARD2	N(alpha)-acetyltransferase 11, NatA catalytic subunit	protein-coding	0.012308	0.607362	
chunk0158_269_1	chr5	131303521	131303962	+	0	NA	intron (NM_001038702, intron 1 of 4)	L3|LINE|CR1	39732	NM_001038702	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.002268	0.350679	
chunk0074_39_1	chr16	20691365	20691727	+	0	NA	promoter-TSS (NM_052956)	promoter-TSS (NM_052956)	-290	NM_052956	116285	Hs.306812	NM_052956	ENSG00000166743	ACSM1	BUCS1|MACS1	acyl-CoA synthetase medium chain family member 1	protein-coding	0.011050	0.446281	
chunk0076_306_1	chr16	70302680	70302893	+	0	NA	intron (NM_001014449, intron 1 of 9)	L1ME1|LINE|L1	3627	NM_001014451	11269	Hs.221761	NM_007242	ENSG00000157349	DDX19B	DBP5|DDX19|RNAh	DEAD-box helicase 19B	protein-coding	0.004695	0.364486	
chunk0209_43_1	chrX	36582869	36583176	+	0	NA	Intergenic	L5|LINE|RTE-X	-142730	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.003257	0.415584	
chunk0029_451_1	chr10	110458120	110458784	+	0	NA	Intergenic	Intergenic	-39415	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.012048	0.481203	
chunk0117_231_1	chr22	22861410	22861670	+	0	NA	Intergenic	L1MA4A|LINE|L1	-24727	NR_049835	100847006		NR_049835	ENSG00000264824	MIR5571	-	microRNA 5571	ncRNA	0.000000	0.310345	
chunk0108_276_1	chr2	234486391	234486984	+	0	NA	Intergenic	L4_B_Mam|LINE|RTE-X	10362	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.001686	0.449495	341(GGGAGCAGTCAGTCCT,-,0.00),342(GGAGCAGTCAGTCCTT,+,0.00)
chunk0108_267_1	chr2	234280025	234280371	+	0	NA	Intergenic	Intergenic	216851	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.017341	0.484150	
chunk0129_160_1	chr3	120682072	120682556	+	0	NA	5' UTR (NM_000187, exon 1 of 14)	5' UTR (NM_000187, exon 1 of 14)	257	NM_000187	3081	Hs.368254	NM_000187	ENSG00000113924	HGD	AKU|HGO	homogentisate 1,2-dioxygenase	protein-coding	0.010331	0.449485	
chunk0187_37_1	chr8	1183228	1183558	+	0	NA	Intergenic	Intergenic	119214	NR_111948	286083	Hs.382131	NR_033895	ENSG00000275427	LOC286083	-	uncharacterized LOC286083	ncRNA	0.003030	0.383686	
chunk0025_49_1	chr10	49414515	49414784	+	0	NA	Intergenic	L1MC4|LINE|L1	-18633	NM_001276451	644168	Hs.534530	NM_001080520	ENSG00000165606	DRGX	DRG11|PRRXL1	dorsal root ganglia homeobox	protein-coding	0.007435	0.485185	
chunk0059_104_1	chr14	31058689	31059325	+	0	NA	intron (NM_001254728, intron 1 of 5)	intron (NM_001254728, intron 1 of 5)	32364	NM_001254728	11154	Hs.293411	NM_007077	ENSG00000100478	AP4S1	AP47B|CLA20|CLAPS4|CPSQ6|SPG52	adaptor related protein complex 4 subunit sigma 1	protein-coding	0.006289	0.387755	
chunk0177_428_1	chr7	27916611	27916868	+	0	NA	intron (NM_175061, intron 2 of 4)	Tigger17a|DNA|TcMar-Tigger	176644	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.019455	0.449612	
chunk0005_306_1	chr1	60548013	60548473	+	0	NA	Intergenic	Intergenic	277341	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.006522	0.429501	
chunk0165_139_1	chr6	33556809	33557250	+	0	NA	Intergenic	Intergenic	23264	NM_001188	578	Hs.485139	NM_001188	ENSG00000030110	BAK1	BAK|BAK-LIKE|BCL2L7|CDN1	BCL2 antagonist/killer 1	protein-coding	0.013605	0.497738	
chunk0201_225_1	chr9	37452529	37453215	+	0	NA	intron (NM_014872, intron 1 of 1)	LTR16A2|LTR|ERVL	12538	NM_014872	9925	Hs.161276	NM_014872	ENSG00000168795	ZBTB5	-	zinc finger and BTB domain containing 5	protein-coding	0.001458	0.442504	
chunk0038_177_1	chr11	85647821	85648153	+	0	NA	promoter-TSS (NM_032273)	promoter-TSS (NM_032273)	68	NM_001244735	84233	Hs.533725	NM_032273	ENSG00000171202	TMEM126A	OPA7	transmembrane protein 126A	protein-coding	0.075301	0.627628	
chunk0038_166_1	chr11	84987675	84988281	+	0	NA	intron (NM_001142699, intron 6 of 27)	L1PB1|LINE|L1	-64557	NM_001300983	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.004950	0.360791	
chunk0101_149_1	chr2	127932643	127932842	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-46802	NM_001199140	83607	Hs.546449	NM_031445	ENSG00000144233	AMMECR1L	-	AMMECR1 like	protein-coding	0.020101	0.400000	
chunk0154_366_1	chr5	87607309	87607838	+	0	NA	Intergenic	Intergenic	-194540	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.000000	0.316981	
chunk0067_400_1	chr15	49241702	49242226	+	0	NA	intron (NM_001001556, intron 5 of 9)	intron (NM_001001556, intron 5 of 9)	71948	NM_002044	2585	Hs.122006	NM_002044	ENSG00000156958	GALK2	GK2	galactokinase 2	protein-coding	0.003817	0.316190	
chunk0154_377_1	chr5	87742466	87743000	+	0	NA	Intergenic	Intergenic	-329700	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.007491	0.328972	
chunk0212_295_1	chrX	141122590	141122789	+	0	NA	Intergenic	L2b|LINE|L2	-4553	NR_125730	103625684		NR_125730	ENSG00000207357	RNU6-2	U6-2	RNA, U6 small nuclear 2	snRNA	0.000000	0.365000	
chunk0040_372_1	chr11	119084983	119085446	+	0	NA	intron (NM_001258209, intron 1 of 12)	intron (NM_001258209, intron 1 of 12)	337	NM_000190	3145	Hs.82609	NM_000190	ENSG00000256269	HMBS	PBG-D|PBGD|PORC|UPS	hydroxymethylbilane synthase	protein-coding	0.056156	0.549569	
chunk0021_258_1	chr1	243433064	243433315	+	0	NA	intron (NM_006642, intron 16 of 17)	L2b|LINE|L2	87013	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.035857	0.492063	
chunk0177_354_1	chr7	26652596	26653281	+	0	NA	Intergenic	Intergenic	13853	NM_001302625									0.011679	0.400875	
chunk0189_242_1	chr8	24906057	24906256	+	0	NA	Intergenic	Intergenic	-7605	NM_005382	4741	Hs.458657	NM_005382	ENSG00000104722	NEFM	NEF3|NF-M|NFM	neurofilament medium	protein-coding	0.010050	0.455000	
chunk0137_271_1	chr4	22490834	22491300	+	0	NA	intron (NM_145290, intron 1 of 18)	intron (NM_145290, intron 1 of 18)	24987	NM_145290	166647	Hs.99195	NM_145290	ENSG00000152990	ADGRA3	GPR125|PGR21|TEM5L	adhesion G protein-coupled receptor A3	protein-coding	0.010730	0.468951	258(GAAAACAATGTGTGCC,-,0.00)
chunk0201_183_1	chr9	36316451	36317018	+	0	NA	Intergenic	Charlie4a|DNA|hAT-Charlie	-39678	NM_001128227	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.017637	0.454225	
chunk0128_161_1	chr3	107203996	107204717	+	0	NA	intron (NR_028303, intron 1 of 3)	L1PA16|LINE|L1	36282	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.005548	0.332410	
chunk0039_281_1	chr11	102624470	102624848	+	0	NA	intron (NM_004771, intron 1 of 9)	intron (NM_004771, intron 1 of 9)	673	NM_004771	9313	Hs.591946	NM_004771	ENSG00000137674	MMP20	AI2A2|MMP-20	matrix metallopeptidase 20	protein-coding	0.010582	0.372032	
chunk0204_126_1	chr9	95188379	95188827	+	0	NA	intron (NM_001243744, intron 4 of 13)	intron (NM_001243744, intron 4 of 13)	-102509	NR_036109	100422842		NR_036109	ENSG00000207617	MIR3074	mir-3074	microRNA 3074	ncRNA	0.008929	0.452116	
chunk0003_64_1	chr1	31198937	31199232	+	0	NA	intron (NM_024522, intron 1 of 6)	intron (NM_024522, intron 1 of 6)	40803	NM_024522	79570	Hs.470259	NM_024522	ENSG00000084628	NKAIN1	FAM77C	sodium/potassium transporting ATPase interacting 1	protein-coding	0.010169	0.543919	
chunk0147_324_1	chr4	185142906	185143174	+	0	NA	promoter-TSS (NM_001151)	promoter-TSS (NM_001151)	-223	NM_001151	291	Hs.246506	NM_001151	ENSG00000151729	SLC25A4	AAC1|ANT|ANT 1|ANT1|MTDPS12|MTDPS12A|PEO2|PEO3|PEOA2|T1	solute carrier family 25 member 4	protein-coding	0.089552	0.687732	109(GTGACACGGTGTTCCC,+,0.00)
chunk0209_55_1	chrX	36920411	36920856	+	0	NA	Intergenic	L1MA3|LINE|L1	-87726	NM_001013736	442444	Hs.535216	NM_001013736	ENSG00000198173	FAM47C	-	family with sequence similarity 47 member C	protein-coding	0.000000	0.318386	
chunk0063_434_1	chr14	88627849	88628540	+	0	NA	intron (NM_183387, intron 32 of 42)	intron (NM_183387, intron 32 of 42)	33808	NM_207662	79882	Hs.684046	NM_024824	ENSG00000100722	ZC3H14	MRT56|MSUT-2|NY-REN-37|SUT2|UKp68	zinc finger CCCH-type containing 14	protein-coding	0.000000	0.290462	
chunk0044_80_1	chr12	28202449	28202867	+	0	NA	Intergenic	L1M4|LINE|L1	-54542	NM_018318	55297	Hs.653125	NM_018318	ENSG00000123106	CCDC91	HSD8|p56	coiled-coil domain containing 91	protein-coding	0.002392	0.410501	
chunk0040_234_1	chr11	114460334	114460734	+	0	NA	Intergenic	Intergenic	21148	NM_015523	25996	Hs.677190	NM_015523	ENSG00000076043	REXO2	CGI-114|REX2|RFN|SFN	RNA exonuclease 2	protein-coding	0.002500	0.314214	
chunk0088_192_1	chr18	47574914	47575383	+	0	NA	Intergenic	Intergenic	194652	NR_039753	100616264		NR_039753	ENSG00000266582	MIR4527	-	microRNA 4527	ncRNA	0.017058	0.465957	
chunk0169_262_1	chr6	105391603	105392149	+	0	NA	intron (NM_002726, intron 2 of 14)	intron (NM_002726, intron 2 of 14)	11248	NM_002726	5550	Hs.436564	NM_002726	ENSG00000085377	PREP	PE|PEP	prolyl endopeptidase	protein-coding	0.012821	0.469835	
chunk0197_431_1	chr8	127507285	127507923	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-25465	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.010972	0.455399	
chunk0189_320_1	chr8	26265812	26266497	+	0	NA	Intergenic	Intergenic	-25337	NM_002717	5520	Hs.146339	NM_002717	ENSG00000221914	PPP2R2A	B55A|B55ALPHA|PR52A|PR55A|PR55alpha	protein phosphatase 2 regulatory subunit Balpha	protein-coding	0.017518	0.473761	
chunk0195_264_1	chr8	98020409	98020740	+	0	NA	intron (NM_030583, intron 12 of 18)	intron (NM_030583, intron 12 of 18)	21643	NR_002581	26775	Hs.684855	NR_002581	ENSG00000207067	SNORA72	RNU72|U72	small nucleolar RNA, H/ACA box 72	snoRNA	0.006042	0.454819	
chunk0138_22_1	chr4	30868231	30868716	+	0	NA	intron (NM_032457, intron 1 of 2)	intron (NM_032457, intron 1 of 2)	148058	NM_002589	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.008247	0.343621	
chunk0166_312_1	chr6	49676906	49677675	+	0	NA	Intergenic	Intergenic	36300	NM_001142417	7180	Hs.2042	NM_003296	ENSG00000124490	CRISP2	CRISP-2|CT36|GAPDL5|TPX1|TSP1	cysteine rich secretory protein 2	protein-coding	0.006502	0.351948	
chunk0124_224_1	chr3	56387306	56387711	+	0	NA	intron (NR_132749, intron 2 of 17)	intron (NR_132749, intron 2 of 17)	80855	NR_132749	26059	Hs.476389	NM_015576	ENSG00000187672	ERC2	CAST|CAST1|ELKSL|SPBC110|Spc110	ELKS/RAB6-interacting/CAST family member 2	protein-coding	0.009877	0.394089	
chunk0202_149_1	chr9	73543656	73544203	+	0	NA	Intergenic	L2c|LINE|L2	392198	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.262774	
chunk0199_410_1	chr9	13555484	13555924	+	0	NA	Intergenic	Intergenic	-124375	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.009091	0.353741	
chunk0005_28_1	chr1	54559827	54560209	+	0	NA	intron (NM_147161, intron 1 of 15)	intron (NM_147161, intron 1 of 15)	11884	NM_015547	26027	Hs.745173	NM_015547	ENSG00000162390	ACOT11	BFIT|STARD14|THEA|THEM1	acyl-CoA thioesterase 11	protein-coding	0.007853	0.613577	
chunk0066_208_1	chr15	33822273	33822486	+	0	NA	intron (NM_001036, intron 80 of 103)	Tigger12A|DNA|TcMar-Tigger	-146509	NM_012125	1133	Hs.584747	NM_012125	ENSG00000184984	CHRM5	HM5	cholinergic receptor muscarinic 5	protein-coding	0.000000	0.392523	
chunk0051_103_1	chr12	114891197	114891406	+	0	NA	Intergenic	MIR|SINE|MIR	-207137	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.009569	0.380952	
chunk0053_111_1	chr13	29002112	29002492	+	0	NA	Intergenic	Intergenic	-22309	NM_001033602	23281	Hs.22287	NM_015233	ENSG00000132938	MTUS2	CAZIP|ICIS|KIAA0774|TIP150	microtubule associated scaffold protein 2	protein-coding	0.005263	0.372703	
chunk0080_211_1	chr17	29462742	29463173	+	0	NA	intron (NM_025142, intron 2 of 17)	intron (NM_025142, intron 2 of 17)	72032	NM_020791	57551	Hs.597434	NM_020791	ENSG00000160551	TAOK1	KFC-B|MAP3K16|MARKK|PSK-2|PSK2|TAO1|hKFC-B|hTAOK1	TAO kinase 1	protein-coding	0.002320	0.296296	
chunk0003_455_1	chr1	41496272	41496548	+	0	NA	Intergenic	CpG	-11727	NR_126098	1907	Hs.1407	NM_001956	ENSG00000127129	EDN2	ET-2|ET2|PPET2	endothelin 2	protein-coding	0.155797	0.758123	138(CAGGACGCTTTGTTCC,-,0.00),139(AGGACGCTTTGTTCCC,+,0.00)
chunk0200_122_1	chr9	17297901	17298436	+	0	NA	intron (NM_017738, intron 6 of 25)	intron (NM_017738, intron 6 of 25)	163177	NM_017738	54875	Hs.435381	NM_017738	ENSG00000044459	CNTLN	C9orf101|C9orf39|bA340N12.1	centlein	protein-coding	0.001869	0.313433	
chunk0044_245_1	chr12	31779957	31780629	+	0	NA	Intergenic	Intergenic	11948	NM_001013699	440093	Hs.448697	NM_001013699	ENSG00000188375	H3F3C	H3.5	H3 histone family member 3C	protein-coding	0.007440	0.369985	366(AGGATCAGAATGTTCC,-,0.00),367(GGATCAGAATGTTCCT,+,0.00)
chunk0010_253_1	chr1	116581098	116581592	+	0	NA	intron (NM_001007237, intron 9 of 10)	(T)n|Simple_repeat|Simple_repeat	-10252	NR_026665	965	Hs.34341	NM_001779	ENSG00000116815	CD58	LFA-3|LFA3|ag3	CD58 molecule	protein-coding	0.010121	0.438384	
chunk0138_447_1	chr4	46647860	46648335	+	0	NA	Intergenic	L1PA15-16|LINE|L1	-258058	NM_001286827	2555	Hs.48372	NM_000807	ENSG00000151834	GABRA2	-	gamma-aminobutyric acid type A receptor alpha2 subunit	protein-coding	0.004211	0.504202	
chunk0175_258_1	chr7	7235161	7235908	+	0	NA	intron (NM_020156, intron 2 of 3)	intron (NM_020156, intron 2 of 3)	-19620	NR_108073	101927354	Hs.520664	NR_108073		LOC101927354	-	uncharacterized LOC101927354	ncRNA	0.006693	0.393048	
chunk0066_329_1	chr15	36589835	36590369	+	0	NA	intron (NM_001130010, intron 1 of 11)	intron (NM_001130010, intron 1 of 11)	-4767	NM_032499	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.011236	0.394393	
chunk0034_90_1	chr11	27472317	27472516	+	0	NA	5' UTR (NM_018490, exon 1 of 18)	5' UTR (NM_018490, exon 1 of 18)	371	NM_018490	55366	Hs.502176	NM_018490	ENSG00000205213	LGR4	BNMD17|GPR48	leucine rich repeat containing G protein-coupled receptor 4	protein-coding	0.160804	0.795000	
chunk0176_342_1	chr7	17722187	17722650	+	0	NA	Intergenic	Intergenic	-163509	NR_110013	101927630	Hs.583400	NR_110013	ENSG00000236039	LOC101927630	-	uncharacterized LOC101927630	ncRNA	0.008639	0.331897	233(AGAAACATTCTGTTCT,-,0.00),234(GAAACATTCTGTTCTG,+,0.00)
chunk0032_282_1	chr11	9246054	9246263	+	0	NA	intron (NM_015213, intron 1 of 22)	LTR39|LTR|ERV1	19168	NM_001243254	23258	Hs.501857	NM_015213	ENSG00000184014	DENND5A	EIEE49|RAB6IP1	DENN domain containing 5A	protein-coding	0.004785	0.442857	
chunk0044_367_1	chr12	39352625	39352972	+	0	NA	intron (NM_017641, intron 10 of 36)	intron (NM_017641, intron 10 of 36)	90592	NM_001173463	55605	Hs.374201	NM_017641	ENSG00000139116	KIF21A	CFEOM1|FEOM1|FEOM3A	kinesin family member 21A	protein-coding	0.005764	0.364943	
chunk0073_108_1	chr16	4613962	4614264	+	0	NA	intron (NM_145253, intron 1 of 2)	CpG	813	NM_145253	124402	Hs.513313	NM_145253	ENSG00000153443	UBALD1	FAM100A|PP11303	UBA like domain containing 1	protein-coding	0.122517	0.679868	
chunk0104_79_1	chr2	171863725	171864843	+	0	NA	intron (NM_003705, intron 3 of 17)	intron (NM_003705, intron 3 of 17)	30022	NM_003705	8604	Hs.470608	NM_003705	ENSG00000115840	SLC25A12	AGC1|ARALAR|EIEE39	solute carrier family 25 member 12	protein-coding	0.005367	0.378910	
chunk0163_120_1	chr6	10273435	10273958	+	0	NA	Intergenic	L1MD1|LINE|L1	-138622	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.003824	0.419847	
chunk0184_133_1	chr7	115447664	115447879	+	0	NA	Intergenic	L1ME3G|LINE|L1	-216416	NR_126407	104355291		NR_126407	ENSG00000233607	LINC01392	-	long intergenic non-protein coding RNA 1392	ncRNA	0.009302	0.319444	
chunk0017_117_1	chr1	206100675	206100919	+	0	NA	intron (NM_001007544, intron 4 of 5)	intron (NM_001007544, intron 4 of 5)	16251	NM_000707	553	Hs.1372	NM_000707	ENSG00000198049	AVPR1B	AVPR3|V1bR	arginine vasopressin receptor 1B	protein-coding	0.000000	0.448980	
chunk0145_309_1	chr4	150389866	150390197	+	0	NA	intron (NM_001199282, intron 47 of 56)	intron (NM_001199282, intron 47 of 56)	-191894	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.006042	0.322289	
chunk0098_74_1	chr2	67296819	67297085	+	0	NA	Intergenic	Intergenic	-81633	NR_038844	644838	Hs.145561	NR_038844	ENSG00000236780	LINC01829	-	long intergenic non-protein coding RNA 1829	ncRNA	0.003759	0.370787	
chunk0041_146_1	chr11	125564433	125564756	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	-4793	NM_001290135	9538	Hs.643514	NM_004879	ENSG00000149547	EI24	EPG4|PIG8|TP53I8	EI24 autophagy associated transmembrane protein	protein-coding	0.009288	0.459877	
chunk0146_250_1	chr4	162501991	162502592	+	0	NA	Intergenic	L1MC|LINE|L1	-338257	NM_020116	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.001664	0.323920	
chunk0150_362_1	chr5	39044116	39044632	+	0	NA	intron (NM_001285439, intron 2 of 38)	intron (NM_001285439, intron 2 of 38)	30034	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.001938	0.278530	
chunk0129_30_1	chr3	117223212	117223494	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	301922	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.007092	0.356890	
chunk0057_381_1	chr13	109383765	109384396	+	0	NA	Intergenic	Intergenic	-16616	NR_126361	104326054	Hs.569298	NR_126361	ENSG00000229792	LINC00399	TCONS_00021596	long intergenic non-protein coding RNA 399	ncRNA	0.006339	0.431962	
chunk0192_1_1	chr8	58161845	58162501	+	0	NA	Intergenic	Intergenic	109928	NR_105005	101929528	Hs.563551	NR_105005	ENSG00000253281	LOC101929528	-	uncharacterized LOC101929528	ncRNA	0.015244	0.435312	333(GAGCACACCATGTACA,-,0.00),334(AGCACACCATGTACAG,+,0.00)
chunk0163_54_1	chr6	8839688	8839945	+	0	NA	Intergenic	Intergenic	187607	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.015564	0.383721	
chunk0049_438_1	chr12	98348506	98349108	+	0	NA	Intergenic	Intergenic	108338	NR_033801	121456	Hs.620643	NR_033801	ENSG00000227825	SLC9A7P1	-	solute carrier family 9 member 7 pseudogene 1	pseudo	0.004983	0.338308	
chunk0199_160_1	chr9	4318627	4319142	+	0	NA	Intergenic	L1MC4|LINE|L1	-18849	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.001942	0.370155	
chunk0095_49_1	chr2	13629790	13630641	+	0	NA	Intergenic	Intergenic	-623202	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.003525	0.302817	
chunk0153_150_1	chr5	69276499	69277183	+	0	NA	intron (NM_001799, intron 11 of 11)	intron (NM_001799, intron 11 of 11)	42046	NM_001799	1022	Hs.184298	NM_001799	ENSG00000134058	CDK7	CAK|CAK1|CDKN7|HCAK|MO15|STK1|p39MO15	cyclin dependent kinase 7	protein-coding	0.007310	0.353285	
chunk0042_362_1	chr12	10364623	10364855	+	0	NA	intron (NR_120430, intron 1 of 3)	HERV15-int|LTR|ERV1	970	NR_120430	101928100	Hs.638425	NR_120430	ENSG00000245648	LOC101928100	-	uncharacterized LOC101928100	ncRNA	0.017241	0.437768	
chunk0104_260_1	chr2	177696358	177696945	+	0	NA	intron (NM_001077197, intron 16 of 20)	intron (NM_001077197, intron 16 of 20)	-77685	NM_152275	92104	Hs.128384	NM_152275	ENSG00000197557	TTC30A	IFT70A|TTC30B	tetratricopeptide repeat domain 30A	protein-coding	0.005111	0.394558	258(AGGTACTAAATGTGCT,-,0.00)
chunk0177_282_1	chr7	25662746	25663478	+	0	NA	Intergenic	Intergenic	286874	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.013661	0.485675	388(AAGAACTGAGTGTCCT,-,0.00),389(AGAACTGAGTGTCCTT,+,0.00)
chunk0008_431_1	chr1	99424024	99424525	+	0	NA	Intergenic	MIRc|SINE|MIR	63530	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.005988	0.398406	
chunk0011_324_1	chr1	152019400	152019904	+	0	NA	intron (NR_103561, intron 2 of 5)	MIR|SINE|MIR	1374	NR_103561	441908	Hs.656557	NR_103561		NBPF18P	-	NBPF member 18, pseudogene	pseudo	0.005952	0.421782	
chunk0183_56_1	chr7	104114851	104115638	+	0	NA	Intergenic	L1MB7|LINE|L1	92803	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.007624	0.350254	
chunk0043_141_1	chr12	16176259	16176772	+	0	NA	Intergenic	MARNA|DNA|TcMar-Mariner	101170	NM_001170798	729025	Hs.692712	NM_001170798	ENSG00000188991	SLC15A5	-	solute carrier family 15 member 5	protein-coding	0.001949	0.379377	
chunk0002_394_1	chr1	27115712	27116028	+	0	NA	intron (NM_003047, intron 1 of 11)	L2c|LINE|L2	39260	NR_046474	6548	Hs.469116	NM_003047	ENSG00000090020	SLC9A1	APNH|LIKNS|NHE-1|NHE1|PPP1R143	solute carrier family 9 member A1	protein-coding	0.003165	0.482650	
chunk0103_298_1	chr2	166483188	166483717	+	0	NA	intron (NM_002976, intron 1 of 24)	intron (NM_002976, intron 1 of 24)	3519	NR_045628	6332	Hs.596087	NM_002976	ENSG00000136546	SCN7A	NaG|Nav2.1|Nav2.2|SCN6A	sodium voltage-gated channel alpha subunit 7	protein-coding	0.007561	0.286792	
chunk0048_10_1	chr12	76999482	76999681	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	65999	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.000000	0.335000	
chunk0024_395_1	chr10	45001366	45002240	+	0	NA	promoter-TSS (NM_001039380)	promoter-TSS (NM_001039380)	-893	NM_001039380	220979	Hs.707791	NM_001039380		C10orf25	-	chromosome 10 open reading frame 25	protein-coding	0.016018	0.400000	
chunk0174_433_1	chr6	166061550	166061862	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	-73667	NR_026860	90632	Hs.31917	NR_026860	ENSG00000112541	LINC00473	C6orf176|LNC473|bA142J11.1	long intergenic non-protein coding RNA 473	ncRNA	0.006410	0.498403	241(GGGAACTTCAAGTTCC,-,0.00),242(GGAACTTCAAGTTCCT,+,0.00)
chunk0125_333_1	chr3	71035422	71035684	+	0	NA	intron (NM_032682, intron 11 of 20)	MER58A|DNA|hAT-Charlie	29370	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.011450	0.399240	
chunk0018_250_1	chr1	220194169	220194462	+	0	NA	intron (NM_012414, intron 12 of 34)	intron (NM_012414, intron 12 of 34)	6304	NR_031705	100302234		NR_031705	ENSG00000281696	MIR664A	MIR664|MIRN664|hsa-mir-664|hsa-mir-664a|mir-664a	microRNA 664a	ncRNA	0.006826	0.336735	
chunk0006_357_1	chr1	72778505	72779058	+	0	NA	Intergenic	Intergenic	-496187	NM_173808	257194	Hs.146542	NM_173808	ENSG00000172260	NEGR1	DMML2433|IGLON4|KILON|Ntra	neuronal growth regulator 1	protein-coding	0.000000	0.371841	
chunk0013_387_1	chr1	172727624	172727869	+	0	NA	Intergenic	L1PA15-16|LINE|L1	68738	NM_001302746	356	Hs.2007	NM_000639	ENSG00000117560	FASLG	ALPS1B|APT1LG1|APTL|CD178|CD95-L|CD95L|FASL|TNFSF6|TNLG1A	Fas ligand	protein-coding	0.016327	0.569106	
chunk0086_234_1	chr18	22790795	22791109	+	0	NA	Intergenic	Intergenic	-4115	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.006369	0.431746	
chunk0193_222_1	chr8	76513370	76513847	+	0	NA	intron (NR_105006, intron 4 of 5)	L2a|LINE|L2	106954	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.002096	0.357741	
chunk0068_33_1	chr15	51030590	51030948	+	0	NA	Intergenic	L1M1|LINE|L1	63936	NM_001311175	388121	Hs.306343	NM_207381	ENSG00000183578	TNFAIP8L3	TIPE3	TNF alpha induced protein 8 like 3	protein-coding	0.011173	0.520891	
chunk0128_411_1	chr3	114665085	114665331	+	0	NA	intron (NR_121662, intron 3 of 6)	Tigger3a|DNA|TcMar-Tigger	-40263	NM_001164346	26137	Hs.202577	NM_015642	ENSG00000181722	ZBTB20	DPZF|HOF|ODA-8S|PRIMS|ZNF288	zinc finger and BTB domain containing 20	protein-coding	0.008130	0.319838	
chunk0049_361_1	chr12	95545666	95546264	+	0	NA	intron (NM_032147, intron 1 of 5)	intron (NM_032147, intron 1 of 5)	2307	NM_001278393	84101	Hs.646421	NM_032147	ENSG00000136014	USP44	-	ubiquitin specific peptidase 44	protein-coding	0.010033	0.402337	
chunk0133_258_1	chr3	171741170	171741855	+	0	NA	intron (NM_001130081, intron 1 of 25)	intron (NM_001130081, intron 1 of 25)	68982	NM_001130081	5337	Hs.382865	NM_002662	ENSG00000075651	PLD1	CVDD	phospholipase D1	protein-coding	0.002920	0.339650	
chunk0005_313_1	chr1	60620206	60620405	+	0	NA	Intergenic	MIRc|SINE|MIR	205279	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.025126	0.440000	30(AGAAACATTATGTACT,-,0.00),31(GAAACATTATGTACTT,+,0.00)
chunk0036_397_1	chr11	68003863	68004379	+	0	NA	promoter-TSS (NM_030930)	promoter-TSS (NM_030930)	4	NM_030930	81622	Hs.502989	NM_030930	ENSG00000110057	UNC93B1	IIAE1|UNC93|UNC93B|Unc-93B1	unc-93 homolog B1, TLR signaling regulator	protein-coding	0.114341	0.727273	
chunk0072_271_1	chr15	96871177	96871611	+	0	NA	Intergenic	Intergenic	87987	NM_001304805									0.006912	0.404598	
chunk0096_149_1	chr2	29175026	29175323	+	0	NA	TTS (NM_001287528)	TTS (NM_001287528)	59748	NM_024692	79745	Hs.122927	NM_024692	ENSG00000115295	CLIP4	RSNL2	CAP-Gly domain containing linker protein family member 4	protein-coding	0.006734	0.479866	130(TAGAACTTGATGTCCC,-,0.00),131(AGAACTTGATGTCCCA,+,0.00)
chunk0152_234_1	chr5	60490699	60491185	+	0	NA	non-coding (NR_028508, exon 2 of 2)	non-coding (NR_028508, exon 2 of 2)	-2844	NM_001165899	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.006173	0.404517	
chunk0092_452_1	chr19	39000715	39001285	+	0	NA	Intergenic	LTR16|LTR|ERVL	-25187	NM_024907	115290	Hs.531770	NM_024907	ENSG00000269190	FBXO17	FBG4|FBX26|FBXO26|Fbx17	F-box protein 17	protein-coding	0.010526	0.500876	
chunk0053_338_1	chr13	34608716	34609266	+	0	NA	intron (NR_047036, intron 1 of 2)	L2b|LINE|L2	31694	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.007273	0.413793	241(GAGGACATTGTGTTTT,-,0.00),242(AGGACATTGTGTTTTC,+,0.00)
chunk0038_416_1	chr11	94236484	94236683	+	0	NA	Intergenic	L1PA2|LINE|L1	-69054	NM_001199206	390243	Hs.553758	NM_001080486	ENSG00000183560	IZUMO1R	FOLR4|Folbp3|JUNO	IZUMO1 receptor, JUNO	protein-coding	0.015075	0.355000	166(TGGTACTGATTGTTCC,-,0.00),167(GGTACTGATTGTTCCT,+,0.00)
chunk0008_368_1	chr1	96766645	96767043	+	0	NA	intron (NM_001300987, intron 4 of 14)	intron (NM_001300987, intron 4 of 14)	44206	NR_125356	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.000000	0.355890	
chunk0178_93_1	chr7	30551088	30551588	+	0	NA	intron (NR_038889, intron 6 of 6)	intron (NR_038889, intron 6 of 6)	26441	NR_038889	401320	Hs.561708	NR_038889		GARS-DT	-	GARS divergent transcript	ncRNA	0.012000	0.520958	
chunk0107_74_1	chr2	212481985	212482184	+	0	NA	intron (NM_001042599, intron 1 of 26)	intron (NM_001042599, intron 1 of 26)	-55724	NR_031643	100313771		NR_031643	ENSG00000221782	MIR548F2	MIR548F-2|MIRN548F2|hsa-mir-548f-2	microRNA 548f-2	ncRNA	0.000000	0.355000	
chunk0035_108_1	chr11	42410527	42411011	+	0	NA	Intergenic	Intergenic	-157079	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.008264	0.391753	211(CAGAACACCAAGTGCC,-,0.00),212(AGAACACCAAGTGCCT,+,0.00)
chunk0193_340_1	chr8	79406468	79407284	+	0	NA	Intergenic	Intergenic	-203938	NM_007029	11075	Hs.521651	NM_007029	ENSG00000104435	STMN2	SCG10|SCGN10	stathmin 2	protein-coding	0.003676	0.323133	
chunk0114_424_1	chr20	64233663	64233968	+	0	NA	intron (NM_004535, intron 19 of 22)	intron (NM_004535, intron 19 of 22)	-21880	NM_001104925	55251	Hs.744845	NM_018257	ENSG00000203880	PCMTD2	C20orf36	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2	protein-coding	0.016393	0.539216	159(GGGAACAGCCTGGCCC,-,0.00),160(GGAACAGCCTGGCCCG,+,0.00)
chunk0026_123_1	chr10	62014643	62015054	+	0	NA	intron (NM_032199, intron 4 of 9)	intron (NM_032199, intron 4 of 9)	-34363	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.009732	0.347087	
chunk0071_333_1	chr15	87880554	87880828	+	0	NA	intron (NM_002530, intron 17 of 18)	intron (NM_002530, intron 17 of 18)	303762	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.003650	0.436364	
chunk0117_146_1	chr22	19607259	19608035	+	0	NA	Intergenic	Intergenic	-40808	NR_024381	150185	Hs.719752	NR_024381		LINC00895	-	long intergenic non-protein coding RNA 895	ncRNA	0.033505	0.594595	295(GAGCACAGGATGTGCC,-,0.00),296(AGCACAGGATGTGCCC,+,0.00),599(GGGAGCAGAATGTGCT,-,0.00),600(GGAGCAGAATGTGCTC,+,0.00)
chunk0026_285_1	chr10	67492280	67492757	+	0	NA	intron (NM_001291133, intron 6 of 8)	intron (NM_001291133, intron 6 of 8)	-89108	NR_106973	102466814		NR_106973	ENSG00000276866	MIR7151	hsa-mir-7151	microRNA 7151	ncRNA	0.004193	0.355649	459(GGGAACAGCAAGTACT,-,0.00),460(GGAACAGCAAGTACTA,+,0.00)
chunk0020_453_1	chr1	242346179	242346845	+	0	NA	intron (NM_001195811, intron 2 of 9)	intron (NM_001195811, intron 2 of 9)	102970	NM_001195812	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.004505	0.383808	
chunk0180_301_1	chr7	70463342	70464065	+	0	NA	intron (NM_015570, intron 5 of 18)	intron (NM_015570, intron 5 of 18)	-668834	NM_022479	64409	Hs.488591	NM_022479	ENSG00000185274	GALNT17	GALNACT17|GALNT16|GALNT20|GALNTL3|GalNAc-T17|GalNAc-T19|GalNAc-T5L|WBSCR17	polypeptide N-acetylgalactosaminyltransferase 17	protein-coding	0.006916	0.440608	621(CAAAACACAATGTTCA,-,0.00)
chunk0034_24_1	chr11	26243477	26243676	+	0	NA	intron (NM_001313726, intron 1 of 27)	intron (NM_001313726, intron 1 of 27)	44431	NR_132968	105376599	Hs.125537	NR_132968	ENSG00000254819	ANO3-AS1	-	ANO3 antisense RNA 1	ncRNA	0.000000	0.340000	
chunk0026_425_1	chr10	70816491	70816811	+	0	NA	intron (NM_003901, intron 1 of 14)	intron (NM_003901, intron 1 of 14)	703	NM_003901	8879	Hs.499984	NM_003901	ENSG00000166224	SGPL1	NPHS14|S1PL|SPL	sphingosine-1-phosphate lyase 1	protein-coding	0.034375	0.548287	
chunk0205_420_1	chr9	115010823	115011296	+	0	NA	Intergenic	Intergenic	-80464	NM_001252290	944	Hs.494901	NM_001244	ENSG00000106952	TNFSF8	CD153|CD30L|CD30LG|TNLG3A	TNF superfamily member 8	protein-coding	0.006342	0.430380	
chunk0127_81_1	chr3	89553510	89553974	+	0	NA	Intergenic	Intergenic	446218	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.006466	0.320430	
chunk0066_202_1	chr15	33544058	33544356	+	0	NA	intron (NM_001036, intron 8 of 103)	intron (NM_001036, intron 8 of 103)	233245	NM_001036	6263	Hs.709373	NM_001036	ENSG00000198838	RYR3	RYR-3	ryanodine receptor 3	protein-coding	0.010067	0.377926	100(AAGGACGATGTGTTCT,-,0.00),101(AGGACGATGTGTTCTT,+,0.00)
chunk0114_284_1	chr21	16454744	16454943	+	0	NA	intron (NR_027791, intron 3 of 5)	intron (NR_027791, intron 3 of 5)	-84246	NR_029514	407055		NR_029514	ENSG00000207638	MIR99A	MIRN99A|mir-99a	microRNA 99a	ncRNA	0.000000	0.365000	
chunk0020_155_1	chr1	234046969	234047521	+	0	NA	intron (NM_173508, intron 2 of 7)	MLT2B4|LTR|ERVL	142533	NM_173508	148641	Hs.158748	NM_173508	ENSG00000183780	SLC35F3	-	solute carrier family 35 member F3	protein-coding	0.001812	0.365280	
chunk0062_144_1	chr14	69079015	69079800	+	0	NA	intron (NM_001284206, intron 6 of 8)	intron (NM_001284206, intron 6 of 8)	73192	NM_001284207	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.008917	0.417303	
chunk0145_340_1	chr4	150913895	150914300	+	0	NA	intron (NM_001199282, intron 9 of 56)	L1MA1|LINE|L1	101170	NM_001199282	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.002469	0.352217	
chunk0206_458_1	chr9	128396877	128397409	+	0	NA	intron (NR_031672, intron 2 of 2).4	intron (NR_031672, intron 2 of 2).4	-4429	NR_029837	407003		NR_029837	ENSG00000284185	MIR219A2	MIR219-2|MIRN219-2|hsa-mir-219a-2|mir-219a-2	microRNA 219a-2	ncRNA	0.026316	0.532833	319(GGGAACAGCGTGCTCT,-,0.00),320(GGAACAGCGTGCTCTA,+,0.00)
chunk0055_351_1	chr13	70388891	70389368	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	-280636	NM_001286725	57626	Hs.508201	NM_020866	ENSG00000150361	KLHL1	MRP2	kelch like family member 1	protein-coding	0.004193	0.361925	
chunk0150_368_1	chr5	39062455	39062886	+	0	NA	intron (NM_001285439, intron 2 of 38)	intron (NM_001285439, intron 2 of 38)	11738	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.000000	0.312500	
chunk0156_164_1	chr5	107547387	107547817	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	123293	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004651	0.343387	
chunk0013_34_1	chr1	166807291	166807618	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-31950	NM_017542	57645	Hs.432752	NM_017542	ENSG00000143157	POGK	BASS2|KRBOX2|LST003	pogo transposable element derived with KRAB domain	protein-coding	0.009174	0.414634	
chunk0029_21_1	chr10	95558785	95559000	+	0	NA	intron (NM_001290294, intron 1 of 31)	MIR3|SINE|MIR	2528	NM_001290294	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.000000	0.467593	
chunk0135_231_1	chr3	188635107	188635942	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-53257	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.011976	0.383971	283(CGAGACAGCTTGTTCT,-,0.00),284(GAGACAGCTTGTTCTC,+,0.00)
chunk0197_362_1	chr8	125872250	125872521	+	0	NA	Intergenic	Intergenic	78812	NR_038446	100130231	Hs.729642	NR_038446	ENSG00000245164	LINC00861	-	long intergenic non-protein coding RNA 861	ncRNA	0.003690	0.386029	
chunk0131_327_1	chr3	151120150	151120879	+	0	NA	intron (NM_053002, intron 2 of 42)	L1ME4b|LINE|L1	33716	NM_053002	116931	Hs.744234	NM_053002	ENSG00000144893	MED12L	NOPAR|TNRC11L|TRALP|TRALPUSH	mediator complex subunit 12L	protein-coding	0.006859	0.342466	
chunk0120_67_1	chr3	3303477	3303974	+	0	NA	Intergenic	Intergenic	-124008	NM_001173482	51185	Hs.18925	NM_016302	ENSG00000113851	CRBN	MRT2|MRT2A	cereblon	protein-coding	0.012072	0.355422	249(GAGCACAAGTTGTACT,-,0.00),250(AGCACAAGTTGTACTG,+,0.00)
chunk0018_301_1	chr1	220918383	220919001	+	0	NA	Intergenic	Intergenic	-38552	NR_046901	100873924	Hs.645593	NR_046901	ENSG00000257551	HLX-AS1	-	HLX antisense RNA 1	ncRNA	0.001618	0.379645	
chunk0209_296_1	chrX	48597124	48597636	+	0	NA	promoter-TSS (NR_029427)	promoter-TSS (NR_029427)	-112	NR_029427	64743	Hs.521973	NM_017883	ENSG00000101940	WDR13	MG21	WD repeat domain 13	protein-coding	0.044922	0.557505	
chunk0082_164_1	chr17	55752581	55752878	+	0	NA	intron (NM_001102402, intron 1 of 5)	intron (NM_001102402, intron 1 of 5)	1624	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.003367	0.379195	
chunk0133_384_1	chr3	174014625	174014859	+	0	NA	intron (NM_014932, intron 4 of 6)	MIRb|SINE|MIR	-93946	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.008547	0.391489	
chunk0176_348_1	chr7	17781706	17782056	+	0	NA	Intergenic	L1ME2|LINE|L1	158627	NM_015132	23161	Hs.487648	NM_015132	ENSG00000071189	SNX13	RGS-PX1	sorting nexin 13	protein-coding	0.008571	0.401709	
chunk0032_288_1	chr11	9478389	9478743	+	0	NA	exon (NM_001282656, exon 6 of 16)	exon (NM_001282656, exon 6 of 16)	17601	NM_003442	7702	Hs.523471	NM_003442	ENSG00000166478	ZNF143	SBF|STAF|pHZ-1	zinc finger protein 143	protein-coding	0.011299	0.450704	
chunk0025_236_1	chr10	54223113	54223625	+	0	NA	intron (NM_001142769, intron 10 of 35)	L1ME1|LINE|L1	384588	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.011719	0.368421	
chunk0125_76_1	chr3	64533343	64534022	+	0	NA	intron (NM_182920, intron 37 of 39)	intron (NM_182920, intron 37 of 39)	-27664	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.025037	0.482353	
chunk0073_102_1	chr16	4486098	4486642	+	0	NA	intron (NM_001127204, intron 2 of 6).2	intron (NM_001127204, intron 2 of 6).2	-9449	NM_001286270	3163	Hs.284279	NM_002134	ENSG00000103415	HMOX2	HO-2	heme oxygenase 2	protein-coding	0.003676	0.440367	217(AAGGACAGCGTGTCCC,-,0.00),218(AGGACAGCGTGTCCCC,+,0.00)
chunk0167_179_1	chr6	63768914	63769186	+	0	NA	intron (NM_001142800, intron 40 of 42)	L1PA16|LINE|L1	122524	NM_015153	23469	Hs.348921	NM_015153	ENSG00000118482	PHF3	-	PHD finger protein 3	protein-coding	0.011029	0.410256	
chunk0145_222_1	chr4	148245040	148245416	+	0	NA	intron (NM_000901, intron 3 of 8)	MIRb|SINE|MIR	197292	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.007979	0.376658	
chunk0077_419_1	chr16	85296496	85296934	+	0	NA	Intergenic	Intergenic	9610	NR_049816	100847022		NR_049816	ENSG00000266307	MIR5093	-	microRNA 5093	ncRNA	0.027397	0.548975	
chunk0109_23_1	chr20	461007	461235	+	0	NA	intron (NR_111901, intron 1 of 9)	intron (NR_111901, intron 1 of 9)	1432	NR_111901	128637	Hs.590876	NM_144628	ENSG00000125875	TBC1D20	C20orf140|WARBM4	TBC1 domain family member 20	protein-coding	0.013158	0.358079	
chunk0194_72_1	chr8	82619346	82619713	+	0	NA	Intergenic	L2a|LINE|L2	-777243	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.345109	175(CAGAACACCCAGACCT,-,0.00),176(AGAACACCCAGACCTG,+,0.00)
chunk0021_252_1	chr1	243375593	243375792	+	0	NA	intron (NM_006642, intron 12 of 17)	intron (NM_006642, intron 12 of 17)	29516	NR_039824	100616343		NR_039824	ENSG00000265201	MIR4677	mir-4677	microRNA 4677	ncRNA	0.000000	0.470000	
chunk0040_378_1	chr11	119329367	119329888	+	0	NA	Intergenic	L1MC1|LINE|L1	-4873	NM_032015	79102	Hs.524084	NM_032015	ENSG00000173456	RNF26	-	ring finger protein 26	protein-coding	0.003839	0.371648	
chunk0046_174_1	chr12	58592641	58593229	+	0	NA	intron (NR_126341, intron 1 of 1)	intron (NR_126341, intron 1 of 1)	1233	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.005102	0.410866	368(AAGCACATGATGTTCT,-,0.00),369(AGCACATGATGTTCTC,+,0.00)
chunk0172_29_1	chr6	133435048	133435514	+	0	NA	intron (NM_172103, intron 3 of 18)	intron (NM_172103, intron 3 of 18)	193782	NM_001301013	2070	Hs.596680	NM_004100	ENSG00000112319	EYA4	CMD1J|DFNA10	EYA transcriptional coactivator and phosphatase 4	protein-coding	0.006438	0.466809	183(GAGAACAGTGTGTTCA,-,0.00),184(AGAACAGTGTGTTCAT,+,0.00)
chunk0112_357_1	chr20	45347046	45347524	+	0	NA	intron (NM_002999, intron 1 of 4)	intron (NM_002999, intron 1 of 4)	1139	NM_002999	6385	Hs.632267	NM_002999	ENSG00000124145	SDC4	SYND4	syndecan 4	protein-coding	0.016736	0.519833	
chunk0075_193_1	chr16	52439414	52439613	+	0	NA	exon (NM_001146188, exon 8 of 8)	exon (NM_001146188, exon 8 of 8)	107381	NM_001080430	27324	Hs.132574	NM_001080430	ENSG00000103460	TOX3	CAGF9|TNRC9	TOX high mobility group box family member 3	protein-coding	0.005025	0.555000	
chunk0132_169_1	chr3	156788971	156789198	+	0	NA	intron (NR_038387, intron 1 of 2)	MamRep434|DNA|TcMar-Tigger	22937	NR_003284	647033	Hs.745109	NR_003284		PA2G4P4	PA2G4L1	proliferation-associated 2G4 pseudogene 4	pseudo	0.008811	0.359649	
chunk0129_194_1	chr3	121319047	121319599	+	0	NA	intron (NM_014980, intron 21 of 27)	intron (NM_014980, intron 21 of 27)	226683	NM_199420	10721	Hs.241517	NM_199420	ENSG00000051341	POLQ	PRO0327	DNA polymerase theta	protein-coding	0.001812	0.274864	
chunk0178_255_1	chr7	36289993	36290445	+	0	NA	intron (NM_030636, intron 6 of 7)	intron (NM_030636, intron 6 of 7)	76954	NM_001199707	23366	Hs.6224	NM_015314	ENSG00000164542	KIAA0895	-	KIAA0895	protein-coding	0.000000	0.459161	
chunk0083_389_1	chr17	71580799	71581131	+	0	NA	Intergenic	MER57B1|LTR|ERV1	-378786	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.000000	0.369369	
chunk0105_216_1	chr2	188049090	188049515	+	0	NA	intron (NR_126396, intron 2 of 2)	intron (NR_126396, intron 2 of 2)	238389	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.000000	0.302817	
chunk0026_36_1	chr10	60731230	60731727	+	0	NA	intron (NM_001204403, intron 1 of 43)	intron (NM_001204403, intron 1 of 43)	2048	NM_001204403	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.004024	0.351406	
chunk0174_135_1	chr6	157450089	157450420	+	0	NA	intron (NM_024630, intron 1 of 8)	intron (NM_024630, intron 1 of 8)	68729	NM_024630	79683	Hs.596214	NM_024630	ENSG00000175048	ZDHHC14	NEW1CP	zinc finger DHHC-type containing 14	protein-coding	0.006042	0.388554	
chunk0203_439_1	chr9	91329005	91329574	+	0	NA	intron (NM_001698, intron 3 of 9)	L1MB7|LINE|L1	32635	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.003515	0.350877	
chunk0101_100_1	chr2	124837482	124837710	+	0	NA	intron (NM_130773, intron 19 of 23)	intron (NM_130773, intron 19 of 23)	812309	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.004386	0.349345	
chunk0043_49_1	chr12	13501482	13501819	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-124905	NR_036555	283422	Hs.448717	NM_182558	ENSG00000180861	LINC01559	C12orf36	long intergenic non-protein coding RNA 1559	ncRNA	0.005935	0.494083	
chunk0192_295_1	chr8	66563099	66563581	+	0	NA	3' UTR (NM_001294282, exon 15 of 15)	3' UTR (NM_001294282, exon 15 of 15)	49909	NM_001294282	4603	Hs.445898	NM_001080416	ENSG00000185697	MYBL1	A-MYB|AMYB	MYB proto-oncogene like 1	protein-coding	0.006224	0.327122	
chunk0118_53_1	chr22	27920596	27921094	+	0	NA	promoter-TSS (NR_036169)	promoter-TSS (NR_036169)	-233	NR_036169	100423034		NR_036169	ENSG00000264073	MIR3199-1	mir-3199-1	microRNA 3199-1	ncRNA	0.008032	0.364729	
chunk0119_226_1	chr22	45208200	45208575	+	0	NA	intron (NM_001009880, intron 2 of 9)	intron (NM_001009880, intron 2 of 9)	4079	NM_015264	23313	Hs.592207	NM_015264	ENSG00000100364	KIAA0930	C22orf9|LSC3	KIAA0930	protein-coding	0.037333	0.537234	
chunk0186_180_1	chr7	139584825	139585191	+	0	NA	intron (NM_001113239, intron 12 of 14)	intron (NM_001113239, intron 12 of 14)	61080	NM_001080511	154790	Hs.57806	NM_001080511	ENSG00000236279	CLEC2L	-	C-type lectin domain family 2 member L	protein-coding	0.005464	0.397820	
chunk0148_225_1	chr5	9160243	9160474	+	0	NA	intron (NM_003966, intron 11 of 22)	intron (NM_003966, intron 11 of 22)	-106463	NR_039779	100616326		NR_039779	ENSG00000266415	MIR4636	mir-4636	microRNA 4636	ncRNA	0.004329	0.426724	
chunk0034_427_1	chr11	38533328	38533900	+	0	NA	Intergenic	HERVL-int|LTR|ERVL	112742	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.005245	0.396161	
chunk0088_198_1	chr18	47842751	47843062	+	0	NA	intron (NM_001003652, intron 10 of 10)	L3|LINE|CR1	87693	NM_005901	4087	Hs.12253	NM_005901	ENSG00000175387	SMAD2	JV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2	SMAD family member 2	protein-coding	0.006431	0.375000	
chunk0171_236_1	chr6	126621193	126621756	+	0	NA	Intergenic	Intergenic	136843	NR_030316	693173		NR_030316	ENSG00000207632	MIR588	MIRN588|hsa-mir-588	microRNA 588	ncRNA	0.003552	0.333333	
chunk0071_76_1	chr15	80733572	80733771	+	0	NA	intron (NM_021214, intron 1 of 2)	intron (NM_021214, intron 1 of 2)	38360	NM_021214	58489	Hs.459072	NM_021214	ENSG00000136379	ABHD17C	FAM108C1	abhydrolase domain containing 17C	protein-coding	0.005025	0.445000	
chunk0028_244_1	chr10	90289762	90289992	+	0	NA	Intergenic	Intergenic	250928	NR_110657	101926942	Hs.382666	NR_110657	ENSG00000236373	LINC02653	-	long intergenic non-protein coding RNA 2653	ncRNA	0.000000	0.389610	
chunk0148_183_1	chr5	7834672	7835070	+	0	NA	intron (NM_001089584, intron 2 of 2)	Tigger3b|DNA|TcMar-Tigger	16619	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.010050	0.368421	
chunk0081_71_1	chr17	39103880	39104240	+	0	NA	intron (NM_020405, intron 7 of 13)	intron (NM_020405, intron 7 of 13)	47041	NR_036551	100131347	Hs.676510	NR_036551	ENSG00000263818	RDM1P5	-	RDM1 pseudogene 5	pseudo	0.019444	0.459834	187(CAGAACAAGGTGTCCT,-,0.00),188(AGAACAAGGTGTCCTG,+,0.00)
chunk0053_332_1	chr13	34361702	34362024	+	0	NA	Intergenic	Intergenic	278822	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.012422	0.408669	
chunk0151_18_1	chr5	41429011	41429556	+	0	NA	intron (NM_001005473, intron 1 of 2)	intron (NM_001005473, intron 1 of 2)	81345	NM_001005473	345557	Hs.145404	NM_001005473	ENSG00000182836	PLCXD3	-	phosphatidylinositol specific phospholipase C X domain containing 3	protein-coding	0.005505	0.395604	234(AAGGACAAAGTGATCT,-,0.00),235(AGGACAAAGTGATCTT,+,0.00)
chunk0187_122_1	chr7	149081558	149081810	+	0	NA	intron (NM_152411, intron 1 of 3)	L1ME4b|LINE|L1	9093	NM_152411	136051	Hs.729572	NM_152411	ENSG00000197362	ZNF786	-	zinc finger protein 786	protein-coding	0.003968	0.359684	96(CAGCACAAGATGTTCT,-,0.00),97(AGCACAAGATGTTCTC,+,0.00)
chunk0184_435_1	chr7	123025033	123025368	+	0	NA	Intergenic	Intergenic	-29500	NM_016945	50833	Hs.272395	NM_016945	ENSG00000128519	TAS2R16	BGLPT|T2R16	taste 2 receptor member 16	protein-coding	0.002985	0.351190	153(CTGTACAGGATGTTCT,-,0.00),154(TGTACAGGATGTTCTT,+,0.00)
chunk0105_203_1	chr2	187832248	187832607	+	0	NA	Intergenic	Intergenic	-277935	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.005571	0.294444	
chunk0193_309_1	chr8	78209959	78210614	+	0	NA	Intergenic	Intergenic	-305815	NM_006823	5569	Hs.433700	NM_006823	ENSG00000171033	PKIA	PRKACN1	cAMP-dependent protein kinase inhibitor alpha	protein-coding	0.009160	0.420732	
chunk0037_29_1	chr11	69970206	69970864	+	0	NA	Intergenic	Intergenic	93389	NR_120530	101928443	Hs.313468	NR_120529	ENSG00000248844	LINC02753	-	long intergenic non-protein coding RNA 2753	ncRNA	0.030395	0.569044	
chunk0054_263_1	chr13	46492957	46493445	+	0	NA	Intergenic	Intergenic	-26425	NR_120426	101929344	Hs.491939	NR_120426		LINC01198	-	long intergenic non-protein coding RNA 1198	ncRNA	0.004098	0.359918	
chunk0042_431_1	chr12	12174634	12175142	+	0	NA	intron (NM_002336, intron 7 of 22)	intron (NM_002336, intron 7 of 22)	62936	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.001969	0.333988	
chunk0166_131_1	chr6	44724519	44724871	+	0	NA	Intergenic	Intergenic	289054	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.005682	0.430595	
chunk0118_174_1	chr22	30782406	30783015	+	0	NA	intron (NM_001282740, intron 1 of 12)	L1ME2|LINE|L1	18457	NM_001282740	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.018062	0.432787	
chunk0140_180_1	chr4	69830570	69830939	+	0	NA	Intergenic	HERV3-int|LTR|ERV1	29398	NM_005420	6783	Hs.479898	NM_005420	ENSG00000109193	SULT1E1	EST|EST-1|ST1E1|STE	sulfotransferase family 1E member 1	protein-coding	0.005420	0.500000	
chunk0092_324_1	chr19	34733777	34733994	+	0	NA	promoter-TSS (NM_001145665)	promoter-TSS (NM_001145665)	-690	NM_001145665	339318	Hs.720472	NM_001029997	ENSG00000197841	ZNF181	HHZ181	zinc finger protein 181	protein-coding	0.055300	0.541284	
chunk0077_169_1	chr16	79417478	79417952	+	0	NA	Intergenic	Intergenic	183010	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.037975	0.536842	
chunk0179_7_1	chr7	42393911	42394295	+	0	NA	Intergenic	Intergenic	-157084	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.005208	0.329870	
chunk0087_119_1	chr18	32869002	32869425	+	0	NA	Intergenic	MER121|DNA|hAT?	-96202	NM_020805	57565	Hs.446164	NM_020805	ENSG00000197705	KLHL14	-	kelch like family member 14	protein-coding	0.009456	0.398585	
chunk0032_422_1	chr11	12200283	12200728	+	0	NA	intron (NM_001282663, intron 3 of 27)	intron (NM_001282663, intron 3 of 27)	36822	NR_106739	102466906		NR_106739	ENSG00000275373	MIR6124	hsa-mir-6124	microRNA 6124	ncRNA	0.024719	0.500000	209(CAGAACACCGAGTTCC,-,0.00),210(AGAACACCGAGTTCCC,+,0.00)
chunk0046_53_1	chr12	55366596	55366848	+	0	NA	TTS (NM_001005497)	TTS (NM_001005497)	1611	NM_001005497	390323	Hs.554554	NM_001005497	ENSG00000187857	OR6C75	-	olfactory receptor family 6 subfamily C member 75	protein-coding	0.003968	0.264822	
chunk0173_231_1	chr6	146410856	146411176	+	0	NA	intron (NM_001278067, intron 7 of 7)	L2c|LINE|L2	-132676	NM_006834	10981	Hs.287714	NM_006834	ENSG00000118508	RAB32	-	RAB32, member RAS oncogene family	protein-coding	0.003125	0.389408	
chunk0161_399_1	chr5	177207974	177208173	+	0	NA	intron (NM_022455, intron 4 of 22)	intron (NM_022455, intron 4 of 22)	74241	NM_022455	64324	Hs.106861	NM_022455	ENSG00000165671	NSD1	ARA267|KMT3B|SOTOS|SOTOS1|STO	nuclear receptor binding SET domain protein 1	protein-coding	0.000000	0.440000	
chunk0139_89_1	chr4	49512657	49512867	+	0	NA	Intergenic	Intergenic	526120	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.033333	0.516588	
chunk0016_225_1	chr1	199488513	199488931	+	0	NA	Intergenic	Intergenic	-469758	NR_110525	102800316	Hs.568480	NR_110525		LINC01222	TCONS_00000112	long intergenic non-protein coding RNA 1222	ncRNA	0.009569	0.389021	
chunk0029_383_1	chr10	109527410	109527670	+	0	NA	Intergenic	L1PA15-16|LINE|L1	396013	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.007692	0.386973	
chunk0122_66_1	chr3	28943658	28943886	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	337167	NR_109804	100873979	Hs.99391	NR_109804		RBMS3-AS3	-	RBMS3 antisense RNA 3	ncRNA	0.004386	0.331878	77(AAGTACATTATGTTTT,-,0.00)
chunk0096_100_1	chr2	28199648	28200110	+	0	NA	intron (NR_120504, intron 1 of 2)	intron (NR_120504, intron 1 of 2)	7082	NR_120504	100505736	Hs.659540	NR_120504		LOC100505736	-	uncharacterized LOC100505736	ncRNA	0.010823	0.406048	
chunk0111_1_1	chr20	21622342	21622608	+	0	NA	intron (NR_109878, intron 3 of 4)	intron (NR_109878, intron 3 of 4)	52451	NR_109880	101929625	Hs.542413	NR_109880		LINC01727	-	long intergenic non-protein coding RNA 1727	ncRNA	0.003759	0.404494	
chunk0003_153_1	chr1	33149787	33150160	+	0	NA	intron (NM_018207, intron 4 of 4)	intron (NM_018207, intron 4 of 4)	32097	NM_018207	55223	Hs.656006	NM_018207	ENSG00000116525	TRIM62	DEAR1	tripartite motif containing 62	protein-coding	0.010724	0.526738	
chunk0016_183_1	chr1	198156984	198157229	+	0	NA	5' UTR (NM_133494, exon 1 of 10)	5' UTR (NM_133494, exon 1 of 10)	128	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.155102	0.776423	
chunk0008_362_1	chr1	96677019	96677368	+	0	NA	Intergenic	L1MC1|LINE|L1	-44412	NM_021190	58155	Hs.596061	NM_021190	ENSG00000117569	PTBP2	PTBLP|brPTB|nPTB	polypyrimidine tract binding protein 2	protein-coding	0.002865	0.414286	207(AAGAACAAAGTGTTCT,-,0.00),208(AGAACAAAGTGTTCTA,+,0.00)
chunk0086_378_1	chr18	26445303	26445627	+	0	NA	Intergenic	L1MEc|LINE|L1	22470	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.006173	0.483077	
chunk0149_99_1	chr5	18686986	18687235	+	0	NA	Intergenic	L1MEg|LINE|L1	1199162	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.336000	
chunk0081_335_1	chr17	46781322	46781803	+	0	NA	intron (NM_030753, intron 1 of 4)	L1MB4|LINE|L1	37198	NM_030753	7473	Hs.445884	NM_030753	ENSG00000108379	WNT3	INT4|TETAMS	Wnt family member 3	protein-coding	0.012474	0.417012	
chunk0079_278_1	chr17	16438707	16439198	+	0	NA	promoter-TSS (NR_003043)	promoter-TSS (NR_003043)	-35	NR_027162	125144	Hs.368934	NM_152350	ENSG00000175061	SNHG29	C17orf45|C17orf76-AS1|FAM211A-AS1|LRRC75A-AS1|NCRNA00188|TSAP19	small nucleolar RNA host gene 29	ncRNA	0.052953	0.571138	
chunk0055_249_1	chr13	63107662	63107873	+	0	NA	Intergenic	Intergenic	220327	NR_126409	104355293	Hs.121439	NR_126409	ENSG00000227564	LINC00376	-	long intergenic non-protein coding RNA 376	ncRNA	0.004739	0.424528	
chunk0109_85_1	chr20	2081748	2082143	+	0	NA	Intergenic	Intergenic	-19937	NM_080836	140901	Hs.100057	NM_080836	ENSG00000125834	STK35	CLIK1|STK35L1	serine/threonine kinase 35	protein-coding	0.002532	0.358586	
chunk0049_432_1	chr12	97947247	97947567	+	0	NA	Intergenic	L2a|LINE|L2	-8286	NR_039716	100616287		NR_039716	ENSG00000265861	MIR4495	-	microRNA 4495	ncRNA	0.000000	0.389408	
chunk0042_368_1	chr12	10426686	10426888	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-6192	NM_002261	3823	Hs.654362	NM_002261	ENSG00000205810	KLRC3	NKG2-E|NKG2E	killer cell lectin like receptor C3	protein-coding	0.000000	0.339901	
chunk0160_464_1	chr5	165202546	165202783	+	0	NA	Intergenic	Intergenic	732385	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.012658	0.373950	
chunk0129_426_1	chr3	127517772	127518486	+	0	NA	intron (NR_125397, intron 5 of 6)	intron (NR_125397, intron 5 of 6)	19651	NR_125397	101927149	Hs.407798	NR_125397	ENSG00000239921	LINC01471	-	long intergenic non-protein coding RNA 1471	ncRNA	0.011204	0.497902	88(AAGGACTGAGCGTCCC,-,0.00),89(AGGACTGAGCGTCCCT,+,0.00)
chunk0018_444_1	chr1	222948262	222948638	+	0	NA	intron (NM_032890, intron 4 of 9)	intron (NM_032890, intron 4 of 9)	133361	NM_032890	84976	Hs.528817	NM_032890	ENSG00000154309	DISP1	DISPA	dispatched RND transporter family member 1	protein-coding	0.010638	0.400531	191(CTGCACAGGATGTCCT,-,0.00),192(TGCACAGGATGTCCTT,+,0.00)
chunk0161_77_1	chr5	166917434	166917633	+	0	NA	intron (NR_108020, intron 1 of 2)	intron (NR_108020, intron 1 of 2)	8837	NR_108020	102557615		NR_108020	ENSG00000254130	LINC01947	CTB-7E3.1	long intergenic non-protein coding RNA 1947	ncRNA	0.020101	0.380000	170(GTGCTCACACTGTTCT,-,0.00)
chunk0039_421_1	chr11	107807986	107808311	+	0	NA	intron (NM_017515, intron 3 of 7)	intron (NM_017515, intron 3 of 7)	51040	NM_017515	54733	Hs.524014	NM_017515	ENSG00000110660	SLC35F2	HSNOV1	solute carrier family 35 member F2	protein-coding	0.015385	0.481595	
chunk0061_237_1	chr14	60734647	60735030	+	0	NA	promoter-TSS (NM_001177963)	promoter-TSS (NM_001177963)	97	NM_002431	4331	Hs.509523	NM_002431	ENSG00000020426	MNAT1	CAP35|MAT1|RNF66|TFB3	MNAT1 component of CDK activating kinase	protein-coding	0.062663	0.609375	
chunk0033_193_1	chr11	16357780	16358188	+	0	NA	intron (NM_033326, intron 1 of 15)	intron (NM_033326, intron 1 of 15)	44883	NM_017508	55553	Hs.368226	NM_017508	ENSG00000110693	SOX6	HSSOX6|SOXD	SRY-box transcription factor 6	protein-coding	0.004902	0.374083	
chunk0026_97_1	chr10	61671736	61672065	+	0	NA	intron (NM_173554, intron 1 of 6)	L2a|LINE|L2	8939	NM_173554	219621	Hs.673160	NM_173554	ENSG00000183346	CABCOCO1	C10orf107	ciliary associated calcium binding coiled-coil 1	protein-coding	0.000000	0.400000	
chunk0144_273_1	chr4	137583699	137584044	+	0	NA	Intergenic	Intergenic	-51373	NM_001300828	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.329480	
chunk0180_444_1	chr7	77360323	77360581	+	0	NA	intron (NM_017439, intron 14 of 30)	intron (NM_017439, intron 14 of 30)	-54746	NR_110073	101927243	Hs.547753	NR_110073		LOC101927243	-	uncharacterized LOC101927243	ncRNA	0.003876	0.362934	
chunk0154_305_1	chr5	83563592	83564083	+	0	NA	intron (NM_001164097, intron 11 of 13)	intron (NM_001164097, intron 11 of 13)	92163	NM_001126336	1462	Hs.643801	NM_004385	ENSG00000038427	VCAN	CSPG2|ERVR|GHAP|PG-M|WGN|WGN1	versican	protein-coding	0.014257	0.400407	
chunk0038_105_1	chr11	83691408	83691816	+	0	NA	intron (NM_001142699, intron 18 of 27)	intron (NM_001142699, intron 18 of 27)	-9187	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.019608	0.462103	
chunk0088_356_1	chr18	52621378	52621968	+	0	NA	intron (NM_005215, intron 1 of 28)	intron (NM_005215, intron 1 of 28)	281501	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.005085	0.424704	
chunk0083_402_1	chr17	71987770	71988505	+	0	NA	Intergenic	Intergenic	37842	NR_110876	102723505	Hs.547482	NR_110876		ROCR	LINC02095	regulator of chondrogenesis RNA	ncRNA	0.002721	0.415761	174(AAGTTCAGGATGTCCC,-,0.00),175(AGTTCAGGATGTCCCC,+,0.00)
chunk0023_327_1	chr10	29276534	29276908	+	0	NA	Intergenic	Intergenic	-12340	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.008021	0.378667	
chunk0074_68_1	chr16	21246166	21246587	+	0	NA	intron (NM_145865, intron 1 of 1)	LTR10C|LTR|ERV1	12681	NM_145865	257629	Hs.115959	NM_145865	ENSG00000175311	ANKS4B	HARP	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding	0.000000	0.284360	
chunk0082_414_1	chr17	61261494	61261892	+	0	NA	intron (NM_017679, intron 22 of 23)	intron (NM_017679, intron 22 of 23)	137913	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.012563	0.358396	
chunk0212_1_1	chrY	2944513	2944774	+	0	NA	intron (NM_001145275, intron 1 of 5)	intron (NM_001145275, intron 1 of 5)	9166	NM_001145275	7544	Hs.522845	NM_003411	ENSG00000067646	ZFY	ZNF911	zinc finger protein Y-linked	protein-coding	0.007663	0.282443	
chunk0198_83_1	chr8	130172585	130172951	+	0	NA	intron (NM_001247996, intron 10 of 30)	intron (NM_001247996, intron 10 of 30)	-88000	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.005464	0.348774	
chunk0146_301_1	chr4	165070764	165071179	+	0	NA	Intergenic	Intergenic	38972	NM_152620	166655	Hs.368004	NM_152620	ENSG00000176979	TRIM60	RNF129|RNF33	tripartite motif containing 60	protein-coding	0.004819	0.391827	
chunk0137_114_1	chr4	14183087	14183332	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	71241	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.004082	0.430894	
chunk0155_310_1	chr5	96548556	96549029	+	0	NA	intron (NR_130776, intron 4 of 4)	MER53|DNA|hAT	-113245	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.004228	0.453586	
chunk0125_290_1	chr3	69887281	69887586	+	0	NA	intron (NM_198159, intron 2 of 9)	intron (NM_198159, intron 2 of 9)	21209	NM_198177	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.006557	0.313725	
chunk0155_458_1	chr5	101755049	101755854	+	0	NA	Intergenic	Intergenic	541098	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.002484	0.380893	
chunk0082_420_1	chr17	61335932	61336600	+	0	NA	intron (NM_017679, intron 22 of 23)	intron (NM_017679, intron 22 of 23)	63340	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.019461	0.499253	
chunk0018_56_1	chr1	216600656	216600983	+	0	NA	intron (NM_001243505, intron 3 of 6)	intron (NM_001243505, intron 3 of 6)	122653	NM_001243518	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.030581	0.417683	
chunk0050_461_1	chr12	111076715	111077475	+	0	NA	intron (NM_015267, intron 1 of 21)	intron (NM_015267, intron 1 of 21)	43071	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.028947	0.499343	
chunk0007_343_1	chr1	84834314	84834810	+	0	NA	intron (NM_012152, intron 2 of 2)	intron (NM_012152, intron 2 of 2)	58651	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.002016	0.374245	
chunk0168_285_1	chr6	90811521	90811795	+	0	NA	Intergenic	Intergenic	-224357	NM_145332	6885	Hs.594838	NM_003188	ENSG00000135341	MAP3K7	CSCF|FMD2|MEKK7|TAK1|TGF1a	mitogen-activated protein kinase kinase kinase 7	protein-coding	0.010949	0.392727	
chunk0191_125_1	chr8	48557659	48558172	+	0	NA	intron (NR_105002, intron 2 of 3)	intron (NR_105002, intron 2 of 3)	6348	NR_105002	101929268	Hs.683934	NR_105002	ENSG00000253608	LOC101929268	-	uncharacterized LOC101929268	ncRNA	0.013645	0.428016	
chunk0150_150_1	chr5	33738875	33739465	+	0	NA	intron (NM_030955, intron 3 of 23)	intron (NM_030955, intron 3 of 23)	152849	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.010169	0.443316	
chunk0188_387_1	chr8	18555753	18556368	+	0	NA	intron (NM_015310, intron 15 of 15)	intron (NM_015310, intron 15 of 15)	164815	NM_000015	10	Hs.2	NM_000015	ENSG00000156006	NAT2	AAC2|NAT-2|PNAT	N-acetyltransferase 2	protein-coding	0.021138	0.477273	
chunk0071_266_1	chr15	85542972	85543628	+	0	NA	intron (NM_007200, intron 4 of 36)	intron (NM_007200, intron 4 of 36)	-76650	NM_001270546	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.007622	0.380518	
chunk0111_200_1	chr20	26107109	26107418	+	0	NA	intron (NR_003678, intron 1 of 1)	(A)n|Simple_repeat|Simple_repeat	6778	NR_003678	149934	Hs.711274	NM_001039379	ENSG00000240108	NCOR1P1	C20orf191|bB329D4.2	nuclear receptor corepressor 1 pseudogene 1	pseudo	0.006472	0.306452	
chunk0118_408_1	chr22	38062684	38063318	+	0	NA	intron (NM_012407, intron 3 of 12)	HAL1|LINE|L1	5746	NM_012407	9463	Hs.180871	NM_012407	ENSG00000100151	PICK1	PICK|PRKCABP	protein interacting with PRKCA 1	protein-coding	0.022082	0.461417	367(GGGAACACCATGTCCT,-,0.00),368(GGAACACCATGTCCTT,+,0.00)
chunk0094_16_1	chr2	1087264	1087663	+	0	NA	intron (NM_018968, intron 2 of 16)	intron (NM_018968, intron 2 of 16)	136595	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.010025	0.400000	132(AAGTACATCGTGCTCT,-,0.00)
chunk0062_51_1	chr14	67371400	67371971	+	0	NA	intron (NM_004094, intron 2 of 7)	Tigger3a|DNA|TcMar-Tigger	11368	NM_004094	1965	Hs.151777	NM_004094	ENSG00000134001	EIF2S1	EIF-2|EIF-2A|EIF-2alpha|EIF2|EIF2A	eukaryotic translation initiation factor 2 subunit alpha	protein-coding	0.003503	0.328671	
chunk0109_126_1	chr20	2879588	2880077	+	0	NA	intron (NM_080840, intron 1 of 22)	Tigger3a|DNA|TcMar-Tigger	6336	NM_080840	5786	Hs.269577	NM_002836	ENSG00000132670	PTPRA	HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA	protein tyrosine phosphatase receptor type A	protein-coding	0.004090	0.381633	
chunk0076_441_1	chr16	73692829	73693309	+	0	NA	Intergenic	Intergenic	306264	NR_038234	100506172	Hs.434230	NR_038234	ENSG00000258779	LINC01568	-	long intergenic non-protein coding RNA 1568	ncRNA	0.006250	0.355509	309(AAGGACAGAGAGCCCT,-,0.00),310(AGGACAGAGAGCCCTT,+,0.00)
chunk0141_15_1	chr4	76677969	76678224	+	0	NA	intron (NM_020859, intron 2 of 10)	intron (NM_020859, intron 2 of 10)	102545	NR_039655	100616254		NR_039655	ENSG00000283682	MIR548AH	-	microRNA 548ah	ncRNA	0.003922	0.367188	
chunk0160_54_1	chr5	149630744	149630943	+	0	NA	intron (NM_001001669, intron 12 of 12)	intron (NM_001001669, intron 12 of 12)	49271	NM_001001669	389337	Hs.256206	NM_001001669	ENSG00000183111	ARHGEF37	-	Rho guanine nucleotide exchange factor 37	protein-coding	0.005025	0.475000	
chunk0156_420_1	chr5	114361796	114362314	+	0	NA	promoter-TSS (NM_021614)	promoter-TSS (NM_021614)	-264	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.077220	0.658960	443(CAGGACAAGCCGTGCC,-,0.00),444(AGGACAAGCCGTGCCC,+,0.00)
chunk0168_123_1	chr6	82030071	82030804	+	0	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-216245	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.004093	0.397820	
chunk0191_283_1	chr8	53829376	53829575	+	0	NA	exon (NM_213619, exon 4 of 13)	exon (NM_213619, exon 4 of 13)	13567	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.005025	0.305000	101(CTGAACGGTCTGTTCT,-,0.00),102(TGAACGGTCTGTTCTT,+,0.00)
chunk0081_216_1	chr17	42618628	42618926	+	0	NA	Intergenic	Intergenic	-9350	NR_026697	162427	Hs.632262	NM_178126	ENSG00000141699	RETREG3	FAM134C	reticulophagy regulator family member 3	protein-coding	0.003356	0.528428	161(CAGAAGAGACTGTCCC,-,0.00),162(AGAAGAGACTGTCCCC,+,0.00)
chunk0137_120_1	chr4	14667924	14668361	+	0	NA	intron (NR_126435, intron 3 of 6)	L2c|LINE|L2	220027	NR_126435	201853	Hs.551051	NR_126435	ENSG00000248360	LINC00504	-	long intergenic non-protein coding RNA 504	ncRNA	0.004577	0.506849	127(ATGCACATTTTGTTCC,-,0.00),128(TGCACATTTTGTTCCC,+,0.00),171(CTGTACAAACTGTTCC,-,0.00),172(TGTACAAACTGTTCCT,+,0.00)
chunk0104_55_1	chr2	171410264	171411377	+	0	NA	intron (NM_024770, intron 1 of 9)	intron (NM_024770, intron 1 of 9)	-23431	NR_028482	80067	Hs.659439	NM_025000	ENSG00000115827	DCAF17	C20orf37|C2orf37	DDB1 and CUL4 associated factor 17	protein-coding	0.001797	0.321364	
chunk0096_2_1	chr2	25821593	25821854	+	0	NA	intron (NM_018263, intron 2 of 11)	intron (NM_018263, intron 2 of 11)	56720	NM_018263	55252	Hs.119815	NM_018263	ENSG00000143970	ASXL2	ASXH2|SHAPNS	ASXL transcriptional regulator 2	protein-coding	0.003831	0.377863	
chunk0095_378_1	chr2	23568481	23569212	+	0	NA	intron (NM_052920, intron 3 of 13)	intron (NM_052920, intron 3 of 13)	183419	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.004104	0.501366	505(GGGAACAGACTGTCCA,-,0.00),506(GGAACAGACTGTCCAG,+,0.00)
chunk0080_408_1	chr17	35587620	35588722	+	0	NA	intron (NM_001030006, intron 1 of 21)	intron (NM_001030006, intron 1 of 21)	908	NM_001030006	163	Hs.514819	NM_001282	ENSG00000006125	AP2B1	ADTB2|AP105B|AP2-BETA|CLAPB1	adaptor related protein complex 2 subunit beta 1	protein-coding	0.025408	0.460562	
chunk0009_26_1	chr1	100239059	100239668	+	0	NA	intron (NM_001918, intron 2 of 10)	intron (NM_001918, intron 2 of 10)	10490	NM_001918	1629	Hs.709187	NM_001918	ENSG00000137992	DBT	BCATE2|BCKAD-E2|BCKADE2|BCOADC-E2|E2|E2B	dihydrolipoamide branched chain transacylase E2	protein-coding	0.003284	0.398361	
chunk0010_387_1	chr1	119378973	119379734	+	0	NA	intron (NM_016527, intron 1 of 7)	MER68|LTR|ERVL	10407	NR_046780	100874270		NR_046780	ENSG00000230921	HAO2-IT1	-	HAO2 intronic transcript 1	ncRNA	0.003942	0.419948	
chunk0209_379_1	chrX	54347820	54348188	+	0	NA	intron (NM_001002838, intron 1 of 22)	L1ME4b|LINE|L1	10001	NM_001002838	65267	Hs.92423	NM_020922	ENSG00000196632	WNK3	PRKWNK3	WNK lysine deficient protein kinase 3	protein-coding	0.000000	0.344173	
chunk0085_100_1	chr18	2733440	2734137	+	0	NA	intron (NM_015295, intron 25 of 47)	Tigger9b|DNA|TcMar-Tigger	77901	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.007174	0.368195	337(CAGAACTTACTGTACT,-,0.00),338(AGAACTTACTGTACTT,+,0.00)
chunk0100_298_1	chr2	115095634	115097109	+	0	NA	intron (NM_001178037, intron 1 of 25)	intron (NM_001178037, intron 1 of 25)	31701	NM_001178037	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.003390	0.322493	
chunk0187_439_1	chr7	158902519	158902896	+	0	NA	intron (NM_018051, intron 10 of 24)	intron (NM_018051, intron 10 of 24)	46129	NM_018051	55112	Hs.389945	NM_018051	ENSG00000126870	WDR60	FAP163|SRPS6|SRTD8	WD repeat domain 60	protein-coding	0.015915	0.510582	
chunk0084_115_1	chr17	75959745	75960085	+	0	NA	intron (NM_007292, intron 3 of 13)	intron (NM_007292, intron 3 of 13)	-18877	NM_001080542	85302	Hs.720068	NM_001080542	ENSG00000188878	FBF1	Alb|FBF-1	Fas binding factor 1	protein-coding	0.005882	0.354839	
chunk0119_13_1	chr22	40072878	40073434	+	0	NA	intron (NM_001024843, intron 1 of 23)	(T)n|Simple_repeat|Simple_repeat	28339	NM_001024843	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.003597	0.400359	452(AGGGACAGCAAGTCCT,-,0.00),453(GGGACAGCAAGTCCTG,+,0.00)
chunk0032_139_1	chr11	4644543	4644889	+	0	NA	intron (NM_152430, intron 1 of 1)	intron (NM_152430, intron 1 of 1)	790	NM_152430	143503	Hs.470038	NM_152430	ENSG00000180785	OR51E1	D-GPCR|DGPCR|GPR136|GPR164|OR51E1P|OR52A3P|POGR|PSGR2	olfactory receptor family 51 subfamily E member 1	protein-coding	0.008671	0.449568	
chunk0040_141_1	chr11	112899186	112899665	+	0	NA	Intergenic	Intergenic	-61822	NM_181351	4684	Hs.503878	NM_000615	ENSG00000149294	NCAM1	CD56|MSK39|NCAM	neural cell adhesion molecule 1	protein-coding	0.008351	0.393750	
chunk0105_71_1	chr2	183735183	183735887	+	0	NA	Intergenic	L1MC5a|LINE|L1	611180	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.009943	0.307801	
chunk0205_164_1	chr9	108664349	108664904	+	0	NA	Intergenic	L2a|LINE|L2	191369	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.007207	0.465827	
chunk0170_51_1	chr6	109466721	109467056	+	0	NA	promoter-TSS (NM_001286613)	promoter-TSS (NM_001286613)	-920	NM_001286613	64780	Hs.33476	NM_022765	ENSG00000135596	MICAL1	MICAL|MICAL-1|NICAL	microtubule associated monooxygenase, calponin and LIM domain containing 1	protein-coding	0.005970	0.348214	
chunk0142_111_1	chr4	94483857	94484308	+	0	NA	intron (NM_001256428, intron 2 of 11)	intron (NM_001256428, intron 2 of 11)	32225	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.008869	0.342920	196(AGGTACATTCTGTGCA,-,0.00),197(GGTACATTCTGTGCAA,+,0.00)
chunk0066_411_1	chr15	39419152	39419811	+	0	NA	Intergenic	L1PB1|LINE|L1	-161598	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.003035	0.351515	
chunk0074_165_1	chr16	23423345	23423905	+	0	NA	intron (NM_153603, intron 7 of 16)	intron (NM_153603, intron 7 of 16)	29566	NM_153603	91949	Hs.185807	NM_153603	ENSG00000168434	COG7	CDG2E	component of oligomeric golgi complex 7	protein-coding	0.023214	0.490196	
chunk0157_309_1	chr5	121631473	121631819	+	0	NA	Intergenic	Intergenic	-220309	NM_177478	94033	Hs.105324	NM_177478	ENSG00000181867	FTMT	MTF	ferritin mitochondrial	protein-coding	0.008671	0.291066	
chunk0054_62_1	chr13	41894808	41895467	+	0	NA	intron (NM_015058, intron 4 of 44)	intron (NM_015058, intron 4 of 44)	65948	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.007587	0.350000	
chunk0107_307_1	chr2	219398785	219399370	+	0	NA	Intergenic	Intergenic	-11137	NM_012100	23549	Hs.258551	NM_012100	ENSG00000123992	DNPEP	ASPEP|DAP	aspartyl aminopeptidase	protein-coding	0.008547	0.477816	
chunk0209_79_1	chrX	38166640	38167081	+	0	NA	intron (NM_001170751, intron 3 of 8)	intron (NM_001170751, intron 3 of 8)	54064	NM_006307	8406	Hs.15154	NM_006307	ENSG00000101955	SRPX	DRS|ETX1|HEL-S-83p|SRPX1	sushi repeat containing protein X-linked	protein-coding	0.000000	0.373303	
chunk0190_222_1	chr8	35781281	35781917	+	0	NA	intron (NM_080872, intron 16 of 16)	intron (NM_080872, intron 16 of 16)	-71279	NR_125819	101929550	Hs.583803	NR_125819		LOC101929550	-	uncharacterized LOC101929550	ncRNA	0.007862	0.373626	
chunk0182_134_1	chr7	94561188	94561656	+	0	NA	Intergenic	L4_A_Mam|LINE|RTE-X	51564	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.010684	0.375267	
chunk0106_94_1	chr2	197184974	197185486	+	0	NA	intron (NM_001195144, intron 2 of 27)	intron (NM_001195144, intron 2 of 27)	117289	NR_046837	101927547	Hs.687027	NR_046837	ENSG00000236977	ANKRD44-IT1	-	ANKRD44 intronic transcript 1	ncRNA	0.011719	0.499025	
chunk0125_277_1	chr3	69432147	69432658	+	0	NA	Intergenic	Tigger8|DNA|TcMar-Tigger	-46098	NM_015123	23150	Hs.371681	NM_015123	ENSG00000114541	FRMD4B	6030440G05Rik|GRSP1	FERM domain containing 4B	protein-coding	0.005871	0.316406	
chunk0212_200_1	chrX	134392076	134392515	+	0	NA	intron (NM_032335, intron 3 of 7)	intron (NM_032335, intron 3 of 7)	18983	NM_032458	84295	Hs.356501	NM_032335	ENSG00000156531	PHF6	BFLS|BORJ|CENP-31	PHD finger protein 6	protein-coding	0.002278	0.302273	194(TAGAACAAGGTGTCCA,-,0.00),195(AGAACAAGGTGTCCAG,+,0.00)
chunk0125_266_1	chr3	69212564	69212940	+	0	NA	intron (NM_015123, intron 11 of 22)	intron (NM_015123, intron 11 of 22)	-90157	NM_001304418	56203	Hs.350621	NM_198271	ENSG00000163380	LMOD3	NEM10	leiomodin 3	protein-coding	0.002660	0.350133	
chunk0025_73_1	chr10	50216278	50217021	+	0	NA	intron (NM_019893, intron 7 of 19)	intron (NM_019893, intron 7 of 19)	31961	NM_019893	56624	Hs.512645	NM_019893	ENSG00000188611	ASAH2	BCDase|HNAC1|LCDase|N-CDase|NCDase	N-acylsphingosine amidohydrolase 2	protein-coding	0.001346	0.338710	190(AGAAACACTGTGTGCA,-,0.00)
chunk0079_159_1	chr17	13469843	13470460	+	0	NA	Intergenic	Intergenic	73495	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.017828	0.467638	332(GAGCACATTCAGTGCT,-,0.00),333(AGCACATTCAGTGCTT,+,0.00)
chunk0165_282_1	chr6	36154378	36154608	+	0	NA	Intergenic	L1M4a2|LINE|L1	24009	NM_002754	5603	Hs.178695	NM_002754	ENSG00000156711	MAPK13	MAPK 13|MAPK-13|PRKM13|SAPK4|p38delta	mitogen-activated protein kinase 13	protein-coding	0.004348	0.463203	
chunk0157_228_1	chr5	119446570	119446907	+	0	NA	Intergenic	HERVIP10FH-int|LTR|ERV1	-5705	NM_001292027	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.000000	0.301775	
chunk0023_453_1	chr10	32171269	32171697	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-115040	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.007009	0.454545	
chunk0104_184_1	chr2	174915448	174915819	+	0	NA	intron (NM_001822, intron 4 of 12)	intron (NM_001822, intron 4 of 12)	-68015	NM_001206602	1123	Hs.380138	NM_001822	ENSG00000128656	CHN1	ARHGAP2|CHN|DURS2|NC|RHOGAP2	chimerin 1	protein-coding	0.005391	0.346774	
chunk0122_185_1	chr3	32685106	32685360	+	0	NA	promoter-TSS (NR_046352)	promoter-TSS (NR_046352)	88	NR_046352	25904	Hs.444851	NM_015442	ENSG00000182973	CNOT10	-	CCR4-NOT transcription complex subunit 10	protein-coding	0.098425	0.701961	
chunk0163_271_1	chr6	13383364	13383644	+	0	NA	intron (NM_018988, intron 1 of 1)	MER119|DNA|hAT-Charlie	24633	NM_001242630	54438	Hs.484686	NM_018988	ENSG00000145990	GFOD1	ADG-90|C6orf114	glucose-fructose oxidoreductase domain containing 1	protein-coding	0.000000	0.412811	
chunk0210_309_1	chrX	90098931	90099307	+	0	NA	Intergenic	L1M4|LINE|L1	177178	NM_138960	90316	Hs.592220	NM_138960	ENSG00000153779	TGIF2LX	TGIFLX	TGFB induced factor homeobox 2 like X-linked	protein-coding	0.002660	0.305040	212(ATGCACATATTGTTCT,-,0.00),213(TGCACATATTGTTCTG,+,0.00)
chunk0122_223_1	chr3	33647436	33647783	+	0	NA	intron (NM_015097, intron 7 of 38)	MER58A|DNA|hAT-Charlie	11832	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.020173	0.416667	
chunk0190_340_1	chr8	39194406	39194605	+	0	NA	intron (NM_145004, intron 11 of 24).2	L1PA13|LINE|L1	86976	NM_001313994	203102	Hs.521545	NM_145004	ENSG00000197140	ADAM32	-	ADAM metallopeptidase domain 32	protein-coding	0.005025	0.555000	
chunk0134_59_1	chr3	176147233	176147866	+	0	NA	Intergenic	Intergenic	-367554	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.001580	0.358044	
chunk0202_2_1	chr9	70167616	70168066	+	0	NA	intron (NR_040076, intron 2 of 3)	intron (NR_040076, intron 2 of 3)	8047	NR_040076	100507244	Hs.556816	NR_040076	ENSG00000204706	MAMDC2-AS1	-	MAMDC2 antisense RNA 1	ncRNA	0.000000	0.332594	
chunk0089_204_1	chr18	60500897	60501519	+	0	NA	Intergenic	Intergenic	-128440	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.008039	0.335474	
chunk0172_434_1	chr6	140777359	140778085	+	0	NA	Intergenic	Intergenic	93908	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.006887	0.303989	
chunk0004_393_1	chr1	52037536	52037771	+	0	NA	intron (NR_046405, intron 2 of 2)	Tigger2|DNA|TcMar-Tigger	-3853	NM_138417	112970	Hs.476033	NM_138417	ENSG00000198841	KTI12	SBBI81|TOT4	KTI12 chromatin associated homolog	protein-coding	0.004255	0.444915	
chunk0105_335_1	chr2	191178899	191179101	+	0	NA	Intergenic	Intergenic	-27404	NM_001243835	6775	Hs.80642	NM_003151	ENSG00000138378	STAT4	SLEB11	signal transducer and activator of transcription 4	protein-coding	0.019802	0.492611	
chunk0161_345_1	chr5	174286843	174287285	+	0	NA	Intergenic	L1M8|LINE|L1	-49290	NR_125806	101928176	Hs.436014	NR_125806	ENSG00000249306	LINC01411	-	long intergenic non-protein coding RNA 1411	ncRNA	0.000000	0.279910	
chunk0043_372_1	chr12	24191208	24191495	+	0	NA	intron (NM_152989, intron 4 of 17)	intron (NM_152989, intron 4 of 17)	-21070	NR_030625	100126320		NR_030625	ENSG00000216192	MIR920	MIRN920|hsa-mir-920	microRNA 920	ncRNA	0.010453	0.472222	
chunk0091_94_1	chr19	5691911	5692180	+	0	NA	TTS (NM_015414)	TTS (NM_015414)	1710	NM_015414	25873	Hs.408018	NM_015414	ENSG00000130255	RPL36	L36	ribosomal protein L36	protein-coding	0.085502	0.666667	
chunk0209_260_1	chrX	46566785	46567285	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-6652	NM_019886	56548	Hs.129955	NM_019886	ENSG00000147119	CHST7	C6ST-2|GST-5	carbohydrate sulfotransferase 7	protein-coding	0.008000	0.411178	
chunk0211_423_1	chrX	129188634	129188934	+	0	NA	Intergenic	MIRb|SINE|MIR	334721	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.003333	0.342193	114(AGCACAGGATGCACTC,+,0.00)
chunk0047_200_1	chr12	71178083	71178666	+	0	NA	Intergenic	L1PB3|LINE|L1	-20375	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.000000	0.320205	
chunk0164_175_1	chr6	21977015	21977725	+	0	NA	intron (NR_015410, intron 5 of 11)	intron (NR_015410, intron 5 of 11)	169823	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.007042	0.379747	
chunk0198_343_1	chr8	140229972	140230232	+	0	NA	intron (NM_001160372, intron 16 of 22)	intron (NM_001160372, intron 16 of 22)	227660	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.003846	0.505747	
chunk0017_15_1	chr1	204411354	204411705	+	0	NA	5' UTR (NM_032833, exon 1 of 2)	5' UTR (NM_032833, exon 1 of 2)	288	NM_032833	84919	Hs.304376	NM_032833	ENSG00000158615	PPP1R15B	CREP|MSSGM2	protein phosphatase 1 regulatory subunit 15B	protein-coding	0.096866	0.650568	
chunk0181_365_1	chr7	88673656	88673855	+	0	NA	Intergenic	L1PB1|LINE|L1	-85613	NM_181646	219578	Hs.684410	NM_181646	ENSG00000182348	ZNF804B	-	zinc finger protein 804B	protein-coding	0.005025	0.420000	
chunk0192_351_1	chr8	68030244	68030746	+	0	NA	intron (NM_025170, intron 5 of 23)	intron (NM_025170, intron 5 of 23)	78127	NM_025170	80243	Hs.169943	NM_024870	ENSG00000046889	PREX2	DEP.2|DEPDC2|P-REX2|PPP1R129	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 2	protein-coding	0.013944	0.401590	
chunk0167_258_1	chr6	69534724	69535562	+	0	NA	Intergenic	Intergenic	262014	NM_018368	55788	Hs.271643	NM_018368	ENSG00000168216	LMBRD1	C6orf209|LMBD1|MAHCF|NESI	LMBR1 domain containing 1	protein-coding	0.003580	0.379023	
chunk0131_453_1	chr3	154089613	154089877	+	0	NA	intron (NR_037901, intron 2 of 3)	intron (NR_037901, intron 2 of 3)	-31258	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.011364	0.354717	
chunk0012_386_1	chr1	163539432	163539758	+	0	NA	Intergenic	MIR3|SINE|MIR	-116404	NR_104294	100422212	Hs.556898	NR_104294		LOC100422212	-	eukaryotic translation initiation factor 3 subunit J pseudogene	pseudo	0.012270	0.366972	
chunk0056_57_1	chr13	77733861	77734293	+	0	NA	intron (NM_001040153, intron 2 of 6)	intron (NM_001040153, intron 2 of 6)	-7083	NM_001242869	122060	Hs.349955	NM_144595	ENSG00000139737	SLAIN1	C13orf32	SLAIN motif family member 1	protein-coding	0.004630	0.401848	
chunk0043_234_1	chr12	20022032	20022378	+	0	NA	intron (NR_040098, intron 2 of 2)	intron (NR_040098, intron 2 of 2)	7520	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.008671	0.342939	
chunk0142_338_1	chr4	101256153	101256824	+	0	NA	intron (NM_000944, intron 1 of 13)	intron (NM_000944, intron 1 of 13)	-15616	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.000000	0.351190	
chunk0128_329_1	chr3	111972675	111972944	+	0	NA	intron (NM_145753, intron 15 of 16)	L1ME4b|LINE|L1	-6067	NM_018394	55347	Hs.477115	NM_018394	ENSG00000144827	ABHD10	-	abhydrolase domain containing 10	protein-coding	0.003717	0.359259	
chunk0015_147_1	chr1	186349869	186350546	+	0	NA	intron (NM_003292, intron 21 of 50)	intron (NM_003292, intron 21 of 50)	25118	NM_003292	7175	Hs.279640	NM_003292	ENSG00000047410	TPR	-	translocated promoter region, nuclear basket protein	protein-coding	0.004431	0.321534	
chunk0060_434_1	chr14	54353702	54353915	+	0	NA	Intergenic	Intergenic	-43147	NM_001130851	1033	Hs.84113	NM_005192	ENSG00000100526	CDKN3	CDI1|CIP2|KAP|KAP1	cyclin dependent kinase inhibitor 3	protein-coding	0.004695	0.514019	
chunk0171_315_1	chr6	129632249	129632620	+	0	NA	intron (NM_033515, intron 4 of 14)	intron (NM_033515, intron 4 of 14)	77791	NM_033515	93663	Hs.486458	NM_033515	ENSG00000146376	ARHGAP18	MacGAP|SENEX|bA307O14.2	Rho GTPase activating protein 18	protein-coding	0.000000	0.456989	
chunk0028_312_1	chr10	91758527	91758726	+	0	NA	Intergenic	Intergenic	39570	NR_108070	100507633	Hs.291528	NR_108070	ENSG00000228701	TNKS2-AS1	-	TNKS2 antisense RNA 1 (head to head)	ncRNA	0.005025	0.320000	
chunk0064_65_1	chr14	90115717	90116264	+	0	NA	intron (NM_022054, intron 1 of 1)	(TGTT)n|Simple_repeat|Simple_repeat	54225	NM_022054	56659	Hs.510191	NM_022054	ENSG00000152315	KCNK13	K2p13.1|THIK-1|THIK1	potassium two pore domain channel subfamily K member 13	protein-coding	0.003656	0.390511	
chunk0058_292_1	chr14	26848472	26848922	+	0	NA	Intergenic	L1MEg|LINE|L1	-24436	NR_110041	101927081	Hs.97955	NR_110041	ENSG00000257612	MIR4307HG	-	MIR4307 host gene	ncRNA	0.004444	0.317073	
chunk0045_381_1	chr12	52231535	52232114	+	0	NA	Intergenic	Intergenic	-1346	NM_005556	3855	Hs.411501	NM_005556	ENSG00000135480	KRT7	CK7|K2C7|K7|SCL	keratin 7	protein-coding	0.018998	0.548276	397(AAGGACATTCCGTCCC,-,0.00),398(AGGACATTCCGTCCCC,+,0.00)
chunk0161_276_1	chr5	172688911	172689508	+	0	NA	3' UTR (NM_001308178, exon 4 of 4)	3' UTR (NM_001308178, exon 4 of 4)	27044	NR_049799	100847029		NR_049799	ENSG00000265160	MIR5003	-	microRNA 5003	ncRNA	0.020101	0.526756	
chunk0102_61_1	chr2	142857564	142858189	+	0	NA	Intergenic	Intergenic	-19750	NM_001032998	8942	Hs.470126	NM_003937	ENSG00000115919	KYNU	KYNUU|VCRL2	kynureninase	protein-coding	0.004800	0.335463	
chunk0084_32_1	chr17	73704313	73704769	+	0	NA	Intergenic	MLT1H1|LTR|ERVL-MaLR	-33313	NM_001278587	100134391	Hs.694655	NM_001278587		LOC100134391	-	uncharacterized LOC100134391	protein-coding	0.017544	0.490153	
chunk0161_267_1	chr5	172484795	172484994	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-30371	NM_001308175	285590	Hs.285666	NM_001017995	ENSG00000174705	SH3PXD2B	FAD49|FTHS|HOFI|KIAA1295|TKS4|TSK4	SH3 and PX domains 2B	protein-coding	0.030151	0.550000	
chunk0146_56_1	chr4	155693115	155693694	+	0	NA	intron (NM_000856, intron 3 of 10)	intron (NM_000856, intron 3 of 10)	25741	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.006908	0.362069	
chunk0098_307_1	chr2	76328445	76328939	+	0	NA	Intergenic	Intergenic	-617707	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.000000	0.292929	228(AGGAACAACTTGTACT,-,0.00),229(GGAACAACTTGTACTA,+,0.00)
chunk0073_261_1	chr16	11965066	11965459	+	0	NA	5' UTR (NM_001192, exon 1 of 3)	5' UTR (NM_001192, exon 1 of 3)	155	NM_001192	608	Hs.2556	NM_001192	ENSG00000048462	TNFRSF17	BCM|BCMA|CD269|TNFRSF13A	TNF receptor superfamily member 17	protein-coding	0.017812	0.426396	
chunk0086_141_1	chr18	21270590	21271246	+	0	NA	intron (NM_001142966, intron 1 of 32)	MIR|SINE|MIR	28676	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.003049	0.353120	
chunk0006_283_1	chr1	70601456	70601732	+	0	NA	Intergenic	MIRb|SINE|MIR	-104859	NR_125938	101927244	Hs.568660	NR_125938	ENSG00000229051	LINC01788	-	long intergenic non-protein coding RNA 1788	ncRNA	0.007246	0.306859	
chunk0101_2_1	chr2	121197374	121197978	+	0	NA	Intergenic	Intergenic	87526	NM_014553	29842	Hs.156471	NM_014553	ENSG00000115112	TFCP2L1	CRTR1|LBP-9|LBP9	transcription factor CP2 like 1	protein-coding	0.029801	0.573554	260(GGCACAGTAAGTACAT,+,0.00),268(AAGTACATTCTGTTCT,-,0.00),269(AGTACATTCTGTTCTT,+,0.00),394(GGGACCAGCCTGTTCT,-,0.00),395(GGACCAGCCTGTTCTG,+,0.00)
chunk0081_203_1	chr17	42394886	42395236	+	0	NA	Intergenic	Intergenic	-6566	NM_139276	6774	Hs.463059	NM_003150	ENSG00000168610	STAT3	ADMIO|ADMIO1|APRF|HIES	signal transducer and activator of transcription 3	protein-coding	0.008571	0.435897	
chunk0083_211_1	chr17	66963548	66963928	+	0	NA	Intergenic	Intergenic	-1126	NM_014405	27092	Hs.514423	NM_014405	ENSG00000075461	CACNG4	-	calcium voltage-gated channel auxiliary subunit gamma 4	protein-coding	0.023684	0.559055	
chunk0050_111_1	chr12	102015274	102016009	+	0	NA	intron (NM_016053, intron 6 of 6)	L2c|LINE|L2	46483	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.005442	0.357337	152(GGGTACAGACTGTGCT,-,0.00),153(GGTACAGACTGTGCTA,+,0.00)
chunk0162_108_1	chr6	2687731	2688157	+	0	NA	intron (NM_001012418, intron 4 of 12)	intron (NM_001012418, intron 4 of 12)	-53341	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.025822	0.461358	249(AAGAACACCCTCTCCC,-,0.00),250(AGAACACCCTCTCCCC,+,0.00)
chunk0022_63_1	chr10	8428399	8428651	+	0	NA	Intergenic	Intergenic	-160220	NR_108058	100507143	Hs.258979	NR_108058	ENSG00000232170	LINC00708	GS1-756B1.2	long intergenic non-protein coding RNA 708	ncRNA	0.015873	0.466403	236(AGGCACAGTAAGTTCT,-,0.00),237(GGCACAGTAAGTTCTT,+,0.00)
chunk0112_423_1	chr20	47340998	47341197	+	0	NA	intron (NM_001281769, intron 2 of 3)	L1MC3|LINE|L1	15792	NM_001281777	23613	Hs.446240	NM_012408	ENSG00000101040	ZMYND8	PRKCBP1|PRO2893|RACK7	zinc finger MYND-type containing 8	protein-coding	0.015075	0.405000	
chunk0152_141_1	chr5	59148920	59149436	+	0	NA	intron (NM_006203, intron 5 of 14)	intron (NM_006203, intron 5 of 14)	-109666	NM_001197222	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005814	0.425532	
chunk0006_125_1	chr1	65817890	65818475	+	0	NA	intron (NM_002600, intron 1 of 16)	L2a|LINE|L2	25009	NM_002600	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.000000	0.360068	
chunk0108_332_1	chr2	235702556	235702915	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	196984	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.005571	0.416667	
chunk0072_120_1	chr15	92503944	92504504	+	0	NA	Intergenic	LTR79|LTR|ERVL	32547	NM_153040	145858	Hs.367879	NM_153040		C15orf32	-	chromosome 15 open reading frame 32	ncRNA	0.007143	0.493761	
chunk0153_362_1	chr5	74513115	74513477	+	0	NA	intron (NR_126354, intron 1 of 2)	intron (NR_126354, intron 1 of 2)	23680	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.000000	0.308540	
chunk0166_450_1	chr6	53192535	53193244	+	0	NA	Intergenic	Intergenic	-44063	NM_003643	8521	Hs.23589	NM_003643	ENSG00000137270	GCM1	GCMA|hGCMa	glial cells missing transcription factor 1	protein-coding	0.009873	0.440845	
chunk0055_295_1	chr13	65324277	65324704	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	-541557	NR_132362	105370242	Hs.578051	NR_132362		LINC01052	-	long intergenic non-protein coding RNA 1052	ncRNA	0.004684	0.296729	
chunk0206_310_1	chr9	125067291	125067490	+	0	NA	intron (NM_173690, intron 2 of 18)	MLT1C|LTR|ERVL-MaLR	76169	NM_001144877	286205	Hs.59504	NM_173690	ENSG00000173611	SCAI	C9orf126|NET40	suppressor of cancer cell invasion	protein-coding	0.015075	0.495000	
chunk0199_352_1	chr9	12494426	12494766	+	0	NA	Intergenic	Intergenic	-198790	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.002941	0.422287	
chunk0165_354_1	chr6	38078958	38079998	+	0	NA	intron (NM_021943, intron 3 of 5)	intron (NM_021943, intron 3 of 5)	259947	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.001923	0.352546	745(GGAACTTAGTGATCTT,+,0.00)
chunk0139_209_1	chr4	54902172	54902698	+	0	NA	Intergenic	Intergenic	223160	NM_002253	3791	Hs.479756	NM_002253	ENSG00000128052	KDR	CD309|FLK1|VEGFR|VEGFR2	kinase insert domain receptor	protein-coding	0.001901	0.417457	
chunk0201_61_1	chr9	33912098	33912413	+	0	NA	intron (NM_017811, intron 4 of 4)	intron (NM_017811, intron 4 of 4)	22109	NM_001282530	55833	Hs.493739	NM_018449	ENSG00000137073	UBAP2	UBAP-2	ubiquitin associated protein 2	protein-coding	0.006349	0.417722	
chunk0160_120_1	chr5	150904811	150905409	+	0	NA	promoter-TSS (NM_052860)	promoter-TSS (NM_052860)	-127	NM_001172831	91975	Hs.134885	NM_052860	ENSG00000145908	ZNF300	-	zinc finger protein 300	protein-coding	0.050167	0.537563	
chunk0075_400_1	chr16	56917232	56917640	+	0	NA	Intergenic	Intergenic	13172	NR_106923	102466752		NR_106923	ENSG00000283471	MIR6863	hsa-mir-6863	microRNA 6863	ncRNA	0.007353	0.435208	209(GGGAACATGGTGTACA,-,0.00),210(GGAACATGGTGTACAA,+,0.00)
chunk0165_428_1	chr6	39678975	39679407	+	0	NA	intron (NM_145027, intron 3 of 22)	intron (NM_145027, intron 3 of 22)	46214	NM_145027	221458	Hs.588202	NM_145027	ENSG00000164627	KIF6	C6orf102|dJ1043E3.1|dJ137F1.4|dJ188D3.1	kinesin family member 6	protein-coding	0.006944	0.353349	213(GGTACTAACTGTACCT,+,0.00)
chunk0195_180_1	chr8	96291133	96291775	+	0	NA	intron (NM_014754, intron 4 of 12)	L1MC5|LINE|L1	29568	NM_001290225	9791	Hs.292579	NM_014754	ENSG00000156471	PTDSS1	LMHD|PSS1|PSSA	phosphatidylserine synthase 1	protein-coding	0.004673	0.360809	
chunk0139_328_1	chr4	58665580	58666009	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	1239922	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.009324	0.332558	
chunk0070_108_1	chr15	70439368	70439567	+	0	NA	Intergenic	MLT1A|LTR|ERVL-MaLR	-176080	NR_126481	104548972		NR_126481	ENSG00000281264	SALRNA3	SAL-RNA3|XLOC_025918	senescence associated long non-coding RNA 3	ncRNA	0.030151	0.530000	
chunk0136_182_1	chr4	6704212	6704637	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	5455	NM_203462	114932	Hs.593159	NM_152301	ENSG00000178988	MRFAP1L1	PP784	Morf4 family associated protein 1 like 1	protein-coding	0.009412	0.387324	
chunk0108_274_1	chr2	234468410	234468850	+	0	NA	Intergenic	Intergenic	28419	NM_005737	10123	Hs.111554	NM_005737	ENSG00000188042	ARL4C	ARL7|LAK	ADP ribosylation factor like GTPase 4C	protein-coding	0.013636	0.564626	236(GGGCACAGGGCGTACC,-,0.00)
chunk0181_42_1	chr7	79055854	79056119	+	0	NA	intron (NM_001301128, intron 1 of 20)	intron (NM_001301128, intron 1 of 20)	46998	NR_046689	100874021	Hs.128252	NR_046689	ENSG00000226978	MAGI2-AS2	-	MAGI2 antisense RNA 2	ncRNA	0.000000	0.383459	
chunk0181_28_1	chr7	78125664	78126234	+	0	NA	intron (NM_001301128, intron 18 of 20)	intron (NM_001301128, intron 18 of 20)	-221293	NR_003680	399670	Hs.568045	NR_003680	ENSG00000231322	RPL13AP17	RPL13A_6_816	ribosomal protein L13a pseudogene 17	pseudo	0.005263	0.394046	
chunk0144_337_1	chr4	139133194	139133522	+	0	NA	intron (NM_201999, intron 2 of 8)	L1ME1|LINE|L1	6118	NM_201999	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.012195	0.382979	
chunk0055_1_1	chr13	51542479	51543086	+	0	NA	Intergenic	Intergenic	-9807	NR_039852	100616423		NR_039852	ENSG00000266611	MIR4703	-	microRNA 4703	ncRNA	0.009885	0.429276	
chunk0114_410_1	chr20	63896566	63896912	+	0	NA	intron (NM_025219, intron 1 of 4)	intron (NM_025219, intron 1 of 4)	1637	NM_025219	80331	Hs.164419	NM_025219	ENSG00000101152	DNAJC5	CLN4|CLN4B|CSP|DNAJC5A|NCL|mir-941-2|mir-941-3|mir-941-4|mir-941-5	DnaJ heat shock protein family (Hsp40) member C5	protein-coding	0.026012	0.495677	
chunk0104_296_1	chr2	178737653	178737960	+	0	NA	intron (NM_133378, intron 46 of 311)	intron (NM_133378, intron 46 of 311)	-39120	NR_120594	101927055	Hs.570275	NR_120594	ENSG00000237298	LOC101927055	-	uncharacterized LOC101927055	ncRNA	0.000000	0.292208	
chunk0210_340_1	chrX	95689541	95689740	+	0	NA	Intergenic	Intergenic	-626414	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.000000	0.360000	
chunk0157_222_1	chr5	119386209	119386805	+	0	NA	intron (NM_001286813, intron 2 of 2)	intron (NM_001286813, intron 2 of 2)	30687	NM_014350	25816	Hs.618488	NM_014350	ENSG00000145779	TNFAIP8	GG2-1|MDC-3.13|NDED|SCC-S2|SCCS2	TNF alpha induced protein 8	protein-coding	0.006711	0.375209	
chunk0086_49_1	chr18	12862903	12863241	+	0	NA	intron (NM_001207013, intron 1 of 10)	intron (NM_001207013, intron 1 of 10)	21263	NM_001207013	5771	Hs.654527	NM_002828	ENSG00000175354	PTPN2	PTN2|PTPT|TC-PTP|TCELLPTP|TCPTP	protein tyrosine phosphatase non-receptor type 2	protein-coding	0.005917	0.421829	
chunk0084_163_1	chr17	77109841	77110363	+	0	NA	intron (NM_001204410, intron 2 of 17)	intron (NM_001204410, intron 2 of 17)	20685	NR_106997	102466864		NR_106997	ENSG00000284250	MIR6516	hsa-mir-6516	microRNA 6516	ncRNA	0.013410	0.413002	
chunk0143_180_1	chr4	112093410	112094534	+	0	NA	Intergenic	Intergenic	-51425	NM_152400	132720	Hs.23439	NM_152400	ENSG00000174749	FAM241A	C4orf32	family with sequence similarity 241 member A	protein-coding	0.004448	0.409778	939(GGGAACACAGAGTTCT,-,0.00),940(GGAACACAGAGTTCTG,+,0.00)
chunk0033_449_1	chr11	25527830	25528323	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-661047	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.006085	0.317814	
chunk0062_231_1	chr14	71116615	71116920	+	0	NA	Intergenic	Intergenic	209362	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.009836	0.395425	
chunk0152_49_1	chr5	57338560	57338911	+	0	NA	Intergenic	MIRb|SINE|MIR	124661	NM_001127236	65056	Hs.444279	NM_022913	ENSG00000062194	GPBP1	GPBP|SSH6|VASCULIN	GC-rich promoter binding protein 1	protein-coding	0.002849	0.363636	
chunk0098_246_1	chr2	74852720	74852942	+	0	NA	intron (NM_000189, intron 1 of 17)	intron (NM_000189, intron 1 of 17)	20176	NM_000189	3099	Hs.406266	NM_000189	ENSG00000159399	HK2	HKII|HXK2	hexokinase 2	protein-coding	0.009009	0.452915	
chunk0190_309_1	chr8	38441502	38441873	+	0	NA	intron (NM_001174064, intron 2 of 18)	intron (NM_001174064, intron 2 of 18)	26158	NM_001174066	2260	Hs.264887	NM_015850	ENSG00000077782	FGFR1	BFGFR|CD331|CEK|ECCL|FGFBR|FGFR-1|FLG|FLT-2|FLT2|HBGFR|HH2|HRTFDS|KAL2|N-SAM|OGD|bFGF-R-1	fibroblast growth factor receptor 1	protein-coding	0.008086	0.467742	
chunk0115_405_1	chr21	30580073	30581381	+	0	NA	Intergenic	Intergenic	9670	NM_001164434	100288287	Hs.580880	NM_001164434	ENSG00000206106	KRTAP22-2	KAP22.2	keratin associated protein 22-2	protein-coding	0.005352	0.408709	
chunk0027_399_1	chr10	80334127	80334326	+	0	NA	Intergenic	Intergenic	-10519	NR_070309	84332	Hs.741500	NM_032372	ENSG00000133665	DYDC2	-	DPY30 domain containing 2	protein-coding	0.000000	0.515000	89(AAGTACACTCTGCTCC,-,0.00),90(AGTACACTCTGCTCCT,+,0.00)
chunk0157_340_1	chr5	122557952	122558575	+	0	NA	Intergenic	Intergenic	-79176	NR_051996	153163	Hs.679757	NR_051996	ENSG00000250328	MGC32805	-	uncharacterized LOC153163	ncRNA	0.001605	0.347756	
chunk0112_283_1	chr20	43681692	43681910	+	0	NA	exon (NM_002466, exon 3 of 14)	exon (NM_002466, exon 3 of 14)	14782	NM_002466	4605	Hs.179718	NM_002466	ENSG00000101057	MYBL2	B-MYB|BMYB	MYB proto-oncogene like 2	protein-coding	0.018349	0.593607	131(CAGGACTGGAAGTTCC,-,0.00),132(AGGACTGGAAGTTCCT,+,0.00)
chunk0077_321_1	chr16	82152556	82153126	+	0	NA	intron (NM_005792, intron 2 of 4)	intron (NM_005792, intron 2 of 4)	17383	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.019298	0.500876	
chunk0024_6_1	chr10	32670828	32671074	+	0	NA	intron (NM_024688, intron 3 of 22)	L1MA8|LINE|L1	103228	NM_024688	79741	Hs.585464	NM_024688	ENSG00000216937	CCDC7	BIOT2|BioT2-A|BioT2-B|BioT2-C|C10orf68	coiled-coil domain containing 7	protein-coding	0.000000	0.259109	
chunk0151_436_1	chr5	56003682	56003902	+	0	NA	TTS (NR_102755)	TTS (NR_102755)	8625	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.009091	0.475113	
chunk0101_195_1	chr2	129826097	129826657	+	0	NA	Intergenic	L1MA5|LINE|L1	-96800	NR_110285	101927924	Hs.570248	NR_110285	ENSG00000237574	LINC01856	-	long intergenic non-protein coding RNA 1856	ncRNA	0.008929	0.434938	
chunk0098_375_1	chr2	79103089	79103605	+	0	NA	Intergenic	Intergenic	-15323	NM_006507	5968	Hs.4158	NM_006507	ENSG00000172023	REG1B	PSPS2|REGH|REGI-BETA|REGL	regenerating family member 1 beta	protein-coding	0.003876	0.321083	
chunk0006_423_1	chr1	76290640	76291008	+	0	NA	intron (NM_152996, intron 1 of 4)	intron (NM_152996, intron 1 of 4)	216120	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.010870	0.482385	
chunk0061_373_1	chr14	64122309	64122610	+	0	NA	intron (NM_182914, intron 70 of 115)	intron (NM_182914, intron 70 of 115)	-27334	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.006645	0.410596	
chunk0015_18_1	chr1	184293861	184294062	+	0	NA	Intergenic	Intergenic	-93055	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.000000	0.400990	108(TAGTACAGGATGTACT,-,0.00),109(AGTACAGGATGTACTT,+,0.00)
chunk0050_274_1	chr12	106240909	106241333	+	0	NA	intron (NM_006825, intron 1 of 1)	L1MC5a|LINE|L1	6814	NM_006825	10970	Hs.74368	NM_006825	ENSG00000136026	CKAP4	CLIMP-63|ERGIC-63|p63	cytoskeleton associated protein 4	protein-coding	0.002358	0.390588	
chunk0046_389_1	chr12	63841578	63842150	+	0	NA	Intergenic	L2c|LINE|L2	-2897	NM_020762	57522	Hs.210751	NM_020762	ENSG00000196935	SRGAP1	ARHGAP13|NMTC2	SLIT-ROBO Rho GTPase activating protein 1	protein-coding	0.006993	0.397906	
chunk0170_231_1	chr6	113450103	113450668	+	0	NA	Intergenic	Intergenic	199690	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.001770	0.358657	321(AAGAACAGAACGTCCT,-,0.00),322(AGAACAGAACGTCCTA,+,0.00)
chunk0030_193_1	chr10	114327481	114328012	+	0	NA	intron (NM_001287824, intron 4 of 19)	MER58A|DNA|hAT-Charlie	77032	NM_001287824	84632	Hs.501106	NM_032550	ENSG00000169129	AFAP1L2	CTB-1144G6.4|KIAA1914|XB130	actin filament associated protein 1 like 2	protein-coding	0.015066	0.509398	
chunk0011_310_1	chr1	151839865	151840368	+	0	NA	intron (NM_001136003, intron 1 of 1)	intron (NM_001136003, intron 1 of 1)	441	NM_001136003	100191040	Hs.694717	NM_001136003	ENSG00000225556	C2CD4D	FAM148D	C2 calcium dependent domain containing 4D	protein-coding	0.053678	0.626984	119(AAGAGCACCGTGTTCC,-,0.00),120(AGAGCACCGTGTTCCG,+,0.00)
chunk0085_149_1	chr18	3401963	3402715	+	0	NA	Intergenic	Intergenic	-9588	NM_174886	7050	Hs.373550	NM_003244	ENSG00000177426	TGIF1	HPE4|TGIF	TGFB induced factor homeobox 1	protein-coding	0.002660	0.335989	
chunk0041_437_1	chr11	134517651	134518044	+	0	NA	Intergenic	Intergenic	81365	NR_033852	283177	Hs.504390	NR_033852		LOC283177	-	uncharacterized LOC283177	ncRNA	0.017812	0.500000	
chunk0106_386_1	chr2	207533527	207534025	+	0	NA	intron (NM_134442, intron 1 of 8)	intron (NM_134442, intron 1 of 8)	3884	NM_134442	1385	Hs.516646	NM_004379	ENSG00000118260	CREB1	CREB|CREB-1	cAMP responsive element binding protein 1	protein-coding	0.002008	0.342685	
chunk0167_384_1	chr6	73929554	73929823	+	0	NA	Intergenic	L1M2a|LINE|L1	-139763	NR_110856	101928516	Hs.384600	NR_110856	ENSG00000223786	LOC101928516	-	uncharacterized LOC101928516	ncRNA	0.011152	0.496296	
chunk0113_356_1	chr20	58981017	58981326	+	0	NA	promoter-TSS (NM_198976)	promoter-TSS (NM_198976)	-37	NM_198976	51497	Hs.517148	NM_016397	ENSG00000101158	NELFCD	HSPC130|NELF-C|NELF-D|TH1|TH1L	negative elongation factor complex member C/D	protein-coding	0.132686	0.754839	
chunk0118_402_1	chr22	37933305	37933564	+	0	NA	intron (NM_033386, intron 13 of 15)	MIRc|SINE|MIR	20213	NM_032561	84645	Hs.517612	NM_032561	ENSG00000128346	C22orf23	EVG1|dJ1039K5.6	chromosome 22 open reading frame 23	protein-coding	0.023166	0.569231	126(TGGGTCAGACTGTTCC,-,0.00),127(GGGTCAGACTGTTCCT,+,0.00)
chunk0093_381_1	chr19	56345280	56346327	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-22296	NR_003127	147947	Hs.467326	NM_194319	ENSG00000240225	ZNF542P	ZNF542	zinc finger protein 542, pseudogene	pseudo	0.002865	0.339695	
chunk0131_155_1	chr3	146374361	146374693	+	0	NA	Intergenic	MIRb|SINE|MIR	94774	NM_001199978	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.006024	0.345345	
chunk0133_179_1	chr3	170159761	170160396	+	0	NA	intron (NM_001308116, intron 4 of 14)	L2c|LINE|L2	21671	NM_001308116	80012	Hs.529592	NM_024947	ENSG00000173889	PHC3	EDR3|HPH3	polyhomeotic homolog 3	protein-coding	0.003150	0.333333	
chunk0129_78_1	chr3	117853983	117854239	+	0	NA	Intergenic	MamSINE1|SINE|tRNA-RTE	932680	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.011719	0.404669	
chunk0140_264_1	chr4	71796838	71797372	+	0	NA	intron (NM_001204306, intron 1 of 13)	L1PA6|LINE|L1	6936	NM_001204307	2638	Hs.418497	NM_000583	ENSG00000145321	GC	DBP|DBP-maf|DBP/GC|GRD3|Gc-MAF|GcMAF|HEL-S-51|VDB|VDBG|VDBP	GC vitamin D binding protein	protein-coding	0.003745	0.504673	
chunk0016_61_1	chr1	193406948	193407147	+	0	NA	Intergenic	Intergenic	102302	NR_125789	101929184	Hs.146728	NR_125789	ENSG00000232077	LINC01031	TCONS_00000361	long intergenic non-protein coding RNA 1031	ncRNA	0.015075	0.355000	
chunk0069_232_1	chr15	63925098	63925719	+	0	NA	intron (NM_014326, intron 8 of 11)	MER115|DNA|hAT-Tip100	-2866	NR_120344	101928988	Hs.673214	NR_120344	ENSG00000259351	LOC101928988	-	uncharacterized LOC101928988	ncRNA	0.008052	0.516077	254(GAGGACATGGTGTTCT,-,0.00),255(AGGACATGGTGTTCTA,+,0.00)
chunk0202_195_1	chr9	75028188	75028575	+	0	NA	promoter-TSS (NM_152420)	promoter-TSS (NM_152420)	13	NM_152420	138199	Hs.567688	NM_152420	ENSG00000156017	CARNMT1	C9orf41|UPF0586	carnosine N-methyltransferase 1	protein-coding	0.126615	0.737113	
chunk0065_169_1	chr15	25860267	25860733	+	0	NA	intron (NM_024490, intron 1 of 20)	intron (NM_024490, intron 1 of 20)	2702	NM_024490	57194	Hs.638517	NM_024490	ENSG00000206190	ATP10A	ATP10C|ATPVA|ATPVC	ATPase phospholipid transporting 10A (putative)	protein-coding	0.012876	0.537473	
chunk0138_136_1	chr4	36741132	36741460	+	0	NA	Intergenic	Intergenic	-314868	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.009146	0.325228	
chunk0031_67_1	chr10	122954001	122954640	+	0	NA	promoter-TSS (NM_024942)	promoter-TSS (NM_024942)	83	NM_024942	80007	Hs.501286	NM_024942	ENSG00000119965	C10orf88	-	chromosome 10 open reading frame 88	protein-coding	0.092332	0.657813	
chunk0127_237_1	chr3	96825343	96826011	+	0	NA	intron (NM_001080448, intron 1 of 17)	intron (NM_001080448, intron 1 of 17)	11096	NM_001278301	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.004491	0.258595	339(AGAACTTGGTGTTTTT,+,0.00)
chunk0019_457_1	chr1	231386454	231386923	+	0	NA	intron (NM_022051, intron 1 of 4)	L2c|LINE|L2	38356	NM_022051	54583	Hs.444450	NM_022051	ENSG00000135766	EGLN1	C1orf12|ECYT3|HALAH|HIF-PH2|HIFPH2|HPH-2|HPH2|PHD2|SM20|ZMYND6	egl-9 family hypoxia inducible factor 1	protein-coding	0.002132	0.325532	
chunk0027_77_1	chr10	73354565	73355308	+	0	NA	intron (NM_145170, intron 1 of 27)	intron (NM_145170, intron 1 of 27)	3923	NM_145170	118491	Hs.591367	NM_145170	ENSG00000156042	CFAP70	TTC18	cilia and flagella associated protein 70	protein-coding	0.009421	0.462366	413(TTGGACAGGCAGTGCT,-,0.00),414(TGGACAGGCAGTGCTT,+,0.00),525(AGGAACACCTTGACCT,-,0.00),526(GGAACACCTTGACCTC,+,0.00)
chunk0044_299_1	chr12	32893572	32893816	+	0	NA	intron (NM_001005242, intron 1 of 12)	intron (NM_001005242, intron 1 of 12)	3152	NM_001005242	5318	Hs.164384	NM_004572	ENSG00000057294	PKP2	ARVD9	plakophilin 2	protein-coding	0.004098	0.408163	
chunk0204_23_1	chr9	92325457	92326109	+	0	NA	promoter-TSS (NM_001256394)	promoter-TSS (NM_001256394)	-189	NM_017948	55035	Hs.442199	NM_017948	ENSG00000198000	NOL8	C9orf34|NOP132|bA62C3.3|bA62C3.4	nucleolar protein 8	protein-coding	0.090491	0.635528	
chunk0020_327_1	chr1	237896940	237897399	+	0	NA	intron (NR_027247, intron 4 of 11)	MLT1C|LTR|ERVL-MaLR	-6247	NM_021186	57829	Hs.136241	NM_021186	ENSG00000116996	ZP4	ZBP|ZP1|ZPB|Zp-4	zona pellucida glycoprotein 4	protein-coding	0.002179	0.428261	188(GTGTACTCCCTGTGCT,-,0.00),189(TGTACTCCCTGTGCTG,+,0.00),214(GTGTACTCCCTGTGCC,-,0.00),215(TGTACTCCCTGTGCCT,+,0.00)
chunk0100_292_1	chr2	114797362	114797783	+	0	NA	intron (NM_001178036, intron 2 of 26)	L1MC3|LINE|L1	35976	NR_132105	101927591	Hs.553019	NR_132105	ENSG00000231538	DPP10-AS3	-	DPP10 antisense RNA 3	ncRNA	0.007126	0.364929	
chunk0069_374_1	chr15	67371125	67371903	+	0	NA	5' UTR (NM_001284348, exon 6 of 17)	5' UTR (NM_001284348, exon 6 of 17)	-116316	NM_001271885	79719	Hs.254642	NM_024666	ENSG00000103591	AAGAB	KPPP1|PPKP1|PPKP1A|p34	alpha and gamma adaptin binding protein	protein-coding	0.010283	0.362003	419(ATAACATAATGTTCCT,+,0.00)
chunk0080_402_1	chr17	35315440	35315738	+	0	NA	Intergenic	L1M7|LINE|L1	58112	NM_001104587	91607	Hs.745059	NM_152270	ENSG00000172716	SLFN11	SLFN8/9	schlafen family member 11	protein-coding	0.010067	0.381271	
chunk0211_125_1	chrX	112333909	112334400	+	0	NA	intron (NM_001004308, intron 2 of 2)	L1MA1|LINE|L1	251129	NM_001004308	340595	Hs.368140	NM_001004308	ENSG00000187823	RTL4	Mar4|Mart4|SIRH11|ZCCHC16	retrotransposon Gag like 4	protein-coding	0.002037	0.376016	
chunk0208_15_1	chrX	10773668	10774136	+	0	NA	intron (NM_033290, intron 1 of 9)	intron (NM_033290, intron 1 of 9)	59788	NM_033290	4281	Hs.27695	NM_000381	ENSG00000101871	MID1	BBBG1|FXY|GBBB1|MIDIN|OGS1|OS|OSX|RNF59|TRIM18|XPRF|ZNFXY	midline 1	protein-coding	0.006410	0.383795	
chunk0095_372_1	chr2	23447048	23447391	+	0	NA	intron (NM_052920, intron 1 of 13)	intron (NM_052920, intron 1 of 13)	61792	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.014577	0.491279	
chunk0028_131_1	chr10	85231516	85231904	+	0	NA	Intergenic	Intergenic	-32772	NR_120667	101929624	Hs.588831	NR_120667	ENSG00000237267	LINC01519	-	long intergenic non-protein coding RNA 1519	ncRNA	0.002577	0.365039	
chunk0036_370_1	chr11	67267519	67267896	+	0	NA	intron (NM_001619, intron 1 of 20)	intron (NM_001619, intron 1 of 20)	1273	NM_001619	156	Hs.83636	NM_001619	ENSG00000173020	GRK2	ADRBK1|BARK1|BETA-ARK1	G protein-coupled receptor kinase 2	protein-coding	0.018568	0.560847	
chunk0097_111_1	chr2	46205766	46206078	+	0	NA	Intergenic	L1M5|LINE|L1	-91480	NM_001430	2034	Hs.468410	NM_001430	ENSG00000116016	EPAS1	ECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73	endothelial PAS domain protein 1	protein-coding	0.009615	0.341853	
chunk0108_338_1	chr2	235731086	235731464	+	0	NA	intron (NM_001037131, intron 3 of 17)	intron (NM_001037131, intron 3 of 17)	225524	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.007937	0.437995	
chunk0107_246_1	chr2	217263827	217264362	+	0	NA	Intergenic	Intergenic	-18639	NR_133642	105373877		NR_133642		DIRC3-AS1	-	DIRC3 antisense RNA 1	ncRNA	0.003738	0.350746	
chunk0166_244_1	chr6	47270167	47270418	+	0	NA	intron (NM_014452, intron 3 of 5)	L1PA6|LINE|L1	39655	NM_014452	27242	Hs.443577	NM_014452	ENSG00000146072	TNFRSF21	BM-018|CD358|DR6	TNF receptor superfamily member 21	protein-coding	0.015936	0.547619	
chunk0021_179_1	chr10	5510332	5510531	+	0	NA	Intergenic	Intergenic	-10861	NM_017422	51806	Hs.180142	NM_017422	ENSG00000178372	CALML5	CLSP	calmodulin like 5	protein-coding	0.010050	0.355000	
chunk0162_102_1	chr6	2581029	2581481	+	0	NA	Intergenic	Intergenic	53348	NR_131168	154386	Hs.680574	NM_152554	ENSG00000164385	LINC01600	C6orf195|bA145H9.2	long intergenic non-protein coding RNA 1600	ncRNA	0.008850	0.452539	
chunk0198_217_1	chr8	133900234	133900507	+	0	NA	intron (NR_125424, intron 3 of 3)	L1MEb|LINE|L1	13874	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.010989	0.299270	
chunk0148_61_1	chr5	2042558	2042787	+	0	NA	Intergenic	Intergenic	155341	NR_109912	101929081	Hs.519180	NR_109912	ENSG00000249326	CTD-2194D22.4	-	uncharacterized LOC101929081	ncRNA	0.030568	0.556522	37(GGGATCACACTGTCCC,-,0.00),38(GGATCACACTGTCCCC,+,0.00)
chunk0171_363_1	chr6	130749512	130749759	+	0	NA	Intergenic	LTR27E|LTR|ERV1	-77770	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.004049	0.524194	
chunk0024_349_1	chr10	43532626	43533021	+	0	NA	Intergenic	L1PA6|LINE|L1	35636	NM_005674	8187	Hs.25040	NM_005674	ENSG00000196793	ZNF239	HOK-2|MOK2	zinc finger protein 239	protein-coding	0.005063	0.502525	
chunk0111_351_1	chr20	33427277	33427578	+	0	NA	intron (NM_003098, intron 2 of 7)	intron (NM_003098, intron 2 of 7)	16465	NM_003098	6640	Hs.31121	NM_003098	ENSG00000101400	SNTA1	LQT12|SNT1|TACIP1|dJ1187J4.5	syntrophin alpha 1	protein-coding	0.000000	0.506623	
chunk0071_84_1	chr15	80805223	80805632	+	0	NA	intron (NM_018689, intron 1 of 28)	intron (NM_018689, intron 1 of 28)	26084	NM_001293304	57214	Hs.459088	NM_018689	ENSG00000103888	CEMIP	CCSP1|HYBID|KIAA1199|TMEM2L	cell migration inducing hyaluronidase 1	protein-coding	0.017115	0.434146	
chunk0183_301_1	chr7	107816094	107816377	+	0	NA	Intergenic	Intergenic	-13002	NM_000111	1811	Hs.1650	NM_000111	ENSG00000091138	SLC26A3	CLD|DRA	solute carrier family 26 member 3	protein-coding	0.003534	0.373239	
chunk0091_386_1	chr19	16025805	16026032	+	0	NA	non-coding (NR_026828, exon 9 of 9)	non-coding (NR_026828, exon 9 of 9)	-7795	NR_024335	148231	Hs.631621	NR_024335	ENSG00000167459	LINC00905	-	long intergenic non-protein coding RNA 905	ncRNA	0.022026	0.627193	
chunk0181_313_1	chr7	87396544	87397029	+	0	NA	intron (NM_001143935, intron 18 of 18)	intron (NM_001143935, intron 18 of 18)	51151	NM_021151	54677	Hs.125039	NM_021151	ENSG00000005469	CROT	COT	carnitine O-octanoyltransferase	protein-coding	0.002062	0.292181	
chunk0075_449_1	chr16	58127718	58127920	+	0	NA	intron (NM_013242, intron 1 of 5)	intron (NM_013242, intron 1 of 5)	1573	NM_013242	29105	Hs.532755	NM_013242	ENSG00000070761	CFAP20	BUG22|C16orf80|EVORF|GTL3|fSAP23	cilia and flagella associated protein 20	protein-coding	0.004950	0.418719	98(CAGAACGCAGAGTTCC,-,0.00),99(AGAACGCAGAGTTCCC,+,0.00)
chunk0130_384_1	chr3	140005151	140005609	+	0	NA	intron (NM_022131, intron 1 of 16)	intron (NM_022131, intron 1 of 16)	70195	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.008734	0.483660	
chunk0186_264_1	chr7	141551183	141551474	+	0	NA	promoter-TSS (NM_018238)	promoter-TSS (NM_018238)	50	NM_018238	55750	Hs.685880	NM_018238	ENSG00000006530	AGK	CATC5|CTRCT38|MTDPS10|MULK	acylglycerol kinase	protein-coding	0.109966	0.708904	
chunk0173_144_1	chr6	143980720	143981112	+	0	NA	intron (NM_001080955, intron 1 of 5)	MER58A|DNA|hAT-Charlie	27488	NM_001080956	5325	Hs.743225	NM_002656	ENSG00000118495	PLAGL1	LOT1|ZAC|ZAC1	PLAG1 like zinc finger 1	protein-coding	0.000000	0.353690	
chunk0168_36_1	chr6	78248214	78248644	+	0	NA	Intergenic	L1MCc|LINE|L1	557773	NM_001282136	101928601	Hs.544538	NM_001282136	ENSG00000269964	MEI4	-	meiotic double-stranded break formation protein 4	protein-coding	0.011628	0.426914	
chunk0154_390_1	chr5	88137550	88137894	+	0	NA	Intergenic	Intergenic	131157	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.002907	0.373913	
chunk0124_210_1	chr3	56048145	56048407	+	0	NA	intron (NR_132749, intron 7 of 17)	MIRc|SINE|MIR	-195682	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.007634	0.414449	
chunk0199_424_1	chr9	13688694	13688984	+	0	NA	Intergenic	Intergenic	-239132	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.010345	0.470790	
chunk0123_67_1	chr3	41302371	41302773	+	0	NA	intron (NM_017886, intron 35 of 36)	intron (NM_017886, intron 35 of 36)	103121	NM_001904	1499	Hs.476018	NM_001904	ENSG00000168036	CTNNB1	CTNNB|EVR7|MRD19|NEDSDV|armadillo	catenin beta 1	protein-coding	0.009950	0.374690	
chunk0149_331_1	chr5	26765013	26765303	+	0	NA	Intergenic	L1ME3|LINE|L1	273424	NM_016279	1007	Hs.272212	NM_016279	ENSG00000113100	CDH9	-	cadherin 9	protein-coding	0.006897	0.333333	
chunk0010_34_1	chr1	112548645	112548945	+	0	NA	intron (NM_138728, intron 12 of 13)	intron (NM_138728, intron 12 of 13)	40047	NM_024494	7482	Hs.258575	NM_004185	ENSG00000134245	WNT2B	WNT13	Wnt family member 2B	protein-coding	0.010000	0.372093	
chunk0125_205_1	chr3	67350672	67351247	+	0	NA	Intergenic	Intergenic	125495	NR_036234	100422941		NR_036234	ENSG00000283298	MIR4272	-	microRNA 4272	ncRNA	0.005217	0.425347	
chunk0012_94_1	chr1	156301838	156302049	+	0	NA	Intergenic	LTR27C|LTR|ERV1	-2306	NM_001004319	391104	Hs.532378	NM_001004319	ENSG00000189030	VHLL	VHLP|VLP	VHL like	protein-coding	0.037915	0.641509	
chunk0110_91_1	chr20	11337852	11338161	+	0	NA	Intergenic	Intergenic	-64623	NR_038972	339593	Hs.434320	NR_038972		LOC339593	-	uncharacterized LOC339593	ncRNA	0.000000	0.416129	
chunk0153_368_1	chr5	74580951	74581373	+	0	NA	Intergenic	Intergenic	-44186	NR_126354	104310351	Hs.582291	NR_126354	ENSG00000248673	LINC01331	-	long intergenic non-protein coding RNA 1331	ncRNA	0.014218	0.420804	189(AAGAACACTGTCTTCT,-,0.00),190(AGAACACTGTCTTCTA,+,0.00)
chunk0052_264_1	chr12	123713422	123713701	+	0	NA	intron (NM_012463, intron 1 of 19)	L2a|LINE|L2	1243	NM_012463	23545	Hs.25786	NM_012463	ENSG00000185344	ATP6V0A2	A2|ARCL|ARCL2A|ATP6A2|ATP6N1D|J6B7|RTF|STV1|TJ6|TJ6M|TJ6S|VPH1|WSS	ATPase H+ transporting V0 subunit a2	protein-coding	0.014337	0.467857	
chunk0039_319_1	chr11	103484339	103484958	+	0	NA	Intergenic	MER68-int|LTR|ERVL	-365258	NR_039842	100616457		NR_039842	ENSG00000264200	MIR4693	-	microRNA 4693	ncRNA	0.006462	0.435484	305(AGGAACACCGTGTGCA,-,0.00),306(GGAACACCGTGTGCAC,+,0.00)
chunk0199_358_1	chr9	12517543	12518010	+	0	NA	Intergenic	Intergenic	-175610	NM_000550	7306	Hs.270279	NM_000550	ENSG00000107165	TYRP1	CAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN	tyrosinase related protein 1	protein-coding	0.004283	0.358974	
chunk0065_419_1	chr14	105932462	105932927	+	0	NA	TTS (NR_026800)	TTS (NR_026800)	14715	NR_026800	9834	Hs.649259	NM_014151	ENSG00000226777	FAM30A	C14orf110|HSPC053|KIAA0125	family with sequence similarity 30 member A	ncRNA	0.006452	0.388412	
chunk0175_179_1	chr7	5237270	5237616	+	0	NA	Intergenic	Intergenic	23174	NM_001033520	26100	Hs.122363	NM_015610	ENSG00000157954	WIPI2	ATG18B|Atg21|CGI-50|IDDSSA|WIPI-2	WD repeat domain, phosphoinositide interacting 2	protein-coding	0.052023	0.573487	
chunk0113_198_1	chr20	53622385	53623045	+	0	NA	Intergenic	MIRc|SINE|MIR	-39618	NM_006526	7764	Hs.155040	NM_006526	ENSG00000171940	ZNF217	ZABC1	zinc finger protein 217	protein-coding	0.007576	0.408472	352(GGATCTGAATGTTCCC,+,0.00)
chunk0147_310_1	chr4	184899357	184899909	+	0	NA	promoter-TSS (NR_039977)	promoter-TSS (NR_039977)	-172	NR_039976	100506229	Hs.378150	NR_039975		LINC01093	-	long intergenic non-protein coding RNA 1093	ncRNA	0.005435	0.544304	60(AAGAACAGAGAGAGCC,-,0.00),61(AGAACAGAGAGAGCCT,+,0.00),386(GGGTCCACTCTGTTCC,-,0.00),387(GGTCCACTCTGTTCCA,+,0.00)
chunk0159_148_1	chr5	139278779	139279065	+	0	NA	TTS (NR_002915)	TTS (NR_002915)	142	NR_002915	26821	Hs.684893	NR_002915	ENSG00000200959	SNORA74A	RNU19|U19	small nucleolar RNA, H/ACA box 74A	snoRNA	0.003497	0.459930	234(AGGGACAGCCTGTCAT,-,0.00),235(GGGACAGCCTGTCATT,+,0.00)
chunk0029_257_1	chr10	102984060	102984366	+	0	NA	intron (NM_199076, intron 1 of 6)	intron (NM_199076, intron 1 of 6)	65895	NM_017649	54805	Hs.643509	NM_017649	ENSG00000148842	CNNM2	ACDP2|HOMG6|HOMGSMR	cyclin and CBS domain divalent metal cation transport mediator 2	protein-coding	0.003268	0.345277	
chunk0117_437_1	chr21	46371896	46372334	+	0	NA	intron (NM_001315529, intron 15 of 46)	intron (NM_001315529, intron 15 of 46)	47227	NM_001315529	5116	Hs.474069	NM_006031	ENSG00000160299	PCNT	KEN|MOPD2|PCN|PCNT2|PCNTB|PCTN2|SCKL4	pericentrin	protein-coding	0.018265	0.519362	
chunk0080_389_1	chr17	34961463	34961783	+	0	NA	promoter-TSS (NM_006584)	promoter-TSS (NM_006584)	93	NM_052857	91603	Hs.413678	NM_052857	ENSG00000198783	ZNF830	CCDC16|OMCG1	zinc finger protein 830	protein-coding	0.084375	0.570093	
chunk0083_53_1	chr17	63665578	63665861	+	0	NA	intron (NM_203351, intron 6 of 16)	intron (NM_203351, intron 6 of 16)	34440	NM_030576	80774	Hs.591166	NM_030576	ENSG00000136490	LIMD2	-	LIM domain containing 2	protein-coding	0.007067	0.510563	
chunk0008_150_1	chr1	92363141	92363510	+	0	NA	intron (NM_024813, intron 11 of 12)	L2b|LINE|L2	-64316	NM_053274	11146	Hs.49105	NM_007070	ENSG00000174842	GLMN	FAP|FAP48|FAP68|FKBPAP|GLML|GVM|VMGLOM	glomulin, FKBP associated protein	protein-coding	0.010840	0.413514	
chunk0169_101_1	chr6	100543745	100544006	+	0	NA	intron (NM_006828, intron 36 of 41)	L1ME1|LINE|L1	-80200	NM_005068	6492	Hs.520293	NM_005068	ENSG00000112246	SIM1	bHLHe14	SIM bHLH transcription factor 1	protein-coding	0.007663	0.290076	
chunk0189_314_1	chr8	26165027	26165610	+	0	NA	Intergenic	Intergenic	-120194	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.003431	0.385274	
chunk0091_20_1	chr19	3244354	3245321	+	0	NA	intron (NR_033342, intron 1 of 12)	(TG)n|Simple_repeat|Simple_repeat	19352	NR_033342	60680	Hs.655747	NM_021938	ENSG00000161082	CELF5	BRUNOL-5|BRUNOL5|CELF-5	CUGBP Elav-like family member 5	protein-coding	0.021717	0.487603	
chunk0125_84_1	chr3	64932456	64932810	+	0	NA	intron (NR_038264, intron 4 of 5)	intron (NR_038264, intron 4 of 5)	-244944	NM_182920	56999	Hs.656071	NM_182920	ENSG00000163638	ADAMTS9	-	ADAM metallopeptidase with thrombospondin type 1 motif 9	protein-coding	0.005650	0.321127	225(AAGTACAACGAGTTCT,-,0.00),226(AGTACAACGAGTTCTG,+,0.00)
chunk0076_19_1	chr16	58788860	58789274	+	0	NA	Intergenic	L1MEc|LINE|L1	-54710	NM_002080	2806	Hs.599470	NM_002080	ENSG00000125166	GOT2	KAT4|KATIV|KYAT4|mitAAT	glutamic-oxaloacetic transaminase 2	protein-coding	0.002415	0.465060	
chunk0212_351_1	chrX	148191189	148191622	+	0	NA	Intergenic	Intergenic	210076	NM_152578	158521	Hs.128580	NM_152578	ENSG00000176988	FMR1NB	CT37|NY-SAR-35|NYSAR35	FMR1 neighbor	protein-coding	0.009238	0.394009	
chunk0114_160_1	chr21	10646643	10647043	+	0	NA	Intergenic	Intergenic	125329	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.010000	0.344140	
chunk0074_106_1	chr16	22224968	22225534	+	0	NA	intron (NM_013302, intron 1 of 17)	L2a|LINE|L2	18980	NM_013302	29904	Hs.498892	NM_013302	ENSG00000103319	EEF2K	CaMKIII|HSU93850|eEF-2K	eukaryotic elongation factor 2 kinase	protein-coding	0.019435	0.470899	
chunk0121_449_1	chr3	26735978	26736730	+	0	NA	Intergenic	Intergenic	113545	NM_052953	116135	Hs.517868	NM_052953	ENSG00000179796	LRRC3B	LRP15	leucine rich repeat containing 3B	protein-coding	0.003989	0.395750	443(CAGGACACCTTGTCCC,-,0.00),444(AGGACACCTTGTCCCT,+,0.00)
chunk0142_274_1	chr4	99453871	99454070	+	0	NA	Intergenic	L1PA14|LINE|L1	-18460	NM_000673	131	Hs.389	NM_000673	ENSG00000196344	ADH7	ADH4	alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide	protein-coding	0.000000	0.535000	
chunk0025_363_1	chr10	58588573	58588896	+	0	NA	intron (NM_001080512, intron 1 of 20)	intron (NM_001080512, intron 1 of 20)	75590	NM_001080512	80114	Hs.100261	NM_001080512	ENSG00000122870	BICC1	BICC|CYSRD	BicC family RNA binding protein 1	protein-coding	0.015480	0.493827	
chunk0084_413_1	chr17	82297380	82297932	+	0	NA	Intergenic	Looper|DNA|PiggyBac	19948	NM_006137	924	Hs.36972	NM_006137	ENSG00000173762	CD7	GP40|LEU-9|TP41|Tp40	CD7 molecule	protein-coding	0.041667	0.524412	169(GGGAACACAATGTCCT,-,0.00),170(GGAACACAATGTCCTG,+,0.00)
chunk0014_451_1	chr1	183888260	183888983	+	0	NA	intron (NM_001297672, intron 8 of 16)	intron (NM_001297672, intron 8 of 16)	83540	NM_001297671	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.009682	0.404696	
chunk0179_364_1	chr7	51102395	51102675	+	0	NA	intron (NM_001287436, intron 6 of 13)	intron (NM_001287436, intron 6 of 13)	214283	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.010714	0.451957	
chunk0049_50_1	chr12	89963662	89964129	+	0	NA	Intergenic	Intergenic	254940	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.006424	0.309829	
chunk0156_280_1	chr5	109901110	109901309	+	0	NA	Intergenic	MIR3|SINE|MIR	18027	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.015075	0.475000	
chunk0207_56_1	chrX	8632959	8633255	+	0	NA	intron (NM_000216, intron 2 of 13)	intron (NM_000216, intron 2 of 13)	99079	NM_000216	3730	Hs.521869	NM_000216	ENSG00000011201	ANOS1	ADMLX|HH1|HHA|KAL|KAL1|KALIG-1|KMS|WFDC19	anosmin 1	protein-coding	0.020270	0.454545	
chunk0132_321_1	chr3	160942815	160943374	+	0	NA	intron (NM_139245, intron 1 of 3)	intron (NM_139245, intron 1 of 3)	161801	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.003578	0.344643	
chunk0028_318_1	chr10	91813313	91813675	+	0	NA	intron (NM_025235, intron 2 of 26)	intron (NM_025235, intron 2 of 26)	15100	NM_025235	80351	Hs.329327	NM_025235	ENSG00000107854	TNKS2	ARTD6|PARP-5b|PARP-5c|PARP5B|PARP5C|TANK2|TNKL|pART6	tankyrase 2	protein-coding	0.005525	0.399449	
chunk0058_298_1	chr14	26945973	26946438	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	37563	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.002151	0.366953	
chunk0099_130_1	chr2	86212993	86213525	+	0	NA	TTS (NM_001164730)	TTS (NM_001164730)	13826	NM_016622	51318	Hs.433439	NM_016622	ENSG00000132313	MRPL35	L35mt|MRP-L35	mitochondrial ribosomal protein L35	protein-coding	0.001880	0.347092	
chunk0022_326_1	chr10	16542521	16543276	+	0	NA	Intergenic	Intergenic	-20893	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.019868	0.444444	334(CAGCACTCGCTGTTCC,-,0.00),335(AGCACTCGCTGTTCCA,+,0.00)
chunk0211_31_1	chrX	108258325	108258853	+	0	NA	intron (NM_001287760, intron 3 of 42)	intron (NM_001287760, intron 3 of 42)	166920	NM_178270	115201	Hs.8763	NM_052936	ENSG00000101844	ATG4A	APG4A|AUTL2	autophagy related 4A cysteine peptidase	protein-coding	0.000000	0.342155	
chunk0153_431_1	chr5	76181149	76181376	+	0	NA	intron (NM_014979, intron 2 of 12)	MER58A|DNA|hAT-Charlie	97848	NM_014979	22987	Hs.646953	NM_014979	ENSG00000122012	SV2C	-	synaptic vesicle glycoprotein 2C	protein-coding	0.013216	0.482456	
chunk0082_280_1	chr17	58022926	58023566	+	0	NA	Intergenic	LTR67B|LTR|ERVL	-15900	NM_001078166	6426	Hs.68714	NM_006924	ENSG00000136450	SRSF1	ASF|SF2|SF2p33|SFRS1|SRp30a	serine and arginine rich splicing factor 1	protein-coding	0.010937	0.457098	
chunk0204_85_1	chr9	94077878	94078132	+	0	NA	intron (NM_177995, intron 2 of 9)	L1MB7|LINE|L1	-6424	NM_152422	138639	Hs.437943	NM_152422	ENSG00000158079	PTPDC1	PTP9Q22	protein tyrosine phosphatase domain containing 1	protein-coding	0.000000	0.396078	
chunk0118_389_1	chr22	37321402	37321674	+	0	NA	Intergenic	L1PA15|LINE|L1	33301	NR_110515	100506271	Hs.220558	NR_110515	ENSG00000237862	LOC100506271	-	uncharacterized LOC100506271	ncRNA	0.022059	0.446886	
chunk0040_49_1	chr11	110832041	110832576	+	0	NA	Intergenic	L2a|LINE|L2	-119119	NM_001258418	57569	Hs.6136	NM_020809	ENSG00000137727	ARHGAP20	RARHOGAP	Rho GTPase activating protein 20	protein-coding	0.005607	0.447761	
chunk0167_252_1	chr6	69166738	69167343	+	0	NA	intron (NM_001704, intron 17 of 31)	MamRep605|LTR?|LTR?	531300	NM_001704	577	Hs.13261	NM_001704	ENSG00000135298	ADGRB3	BAI3	adhesion G protein-coupled receptor B3	protein-coding	0.001653	0.344884	274(AAGAACATTTTGTACA,-,0.00),275(AGAACATTTTGTACAT,+,0.00)
chunk0096_195_1	chr2	30156321	30156635	+	0	NA	intron (NM_001127401, intron 3 of 4)	intron (NM_001127401, intron 3 of 4)	9594	NM_016061	51646	Hs.515890	NM_016061	ENSG00000119801	YPEL5	CGI-127	yippee like 5	protein-coding	0.006369	0.365079	
chunk0047_249_1	chr12	72364208	72364722	+	0	NA	intron (NM_013381, intron 2 of 18)	L2a|LINE|L2	-90956	NR_026837	283392	Hs.363603	NM_001025457	ENSG00000236333	TRHDE-AS1	-	TRHDE antisense RNA 1	ncRNA	0.003891	0.370874	
chunk0097_77_1	chr2	44540216	44540476	+	0	NA	intron (NM_024766, intron 3 of 10)	L1MC4|LINE|L1	178442	NM_024766	79823	Hs.468349	NM_024766	ENSG00000143919	CAMKMT	C2orf34|CLNMT|CaM KMT|Cam|KMT	calmodulin-lysine N-methyltransferase	protein-coding	0.003846	0.371648	
chunk0003_370_1	chr1	39540709	39540919	+	0	NA	intron (NR_003929, intron 7 of 8)	intron (NR_003929, intron 7 of 8)	18884	NR_003929	728448	Hs.472508	NR_003929	ENSG00000243970	PPIEL	PPIEP1	peptidylprolyl isomerase E like pseudogene	pseudo	0.033333	0.563981	94(TAGCACACAGAGTTCT,-,0.00),95(AGCACACAGAGTTCTG,+,0.00)
chunk0147_63_1	chr4	172666982	172667394	+	0	NA	intron (NR_125894, intron 1 of 2)	intron (NR_125894, intron 1 of 2)	21729	NR_125895	101928314	Hs.566023	NR_125894		GALNTL6-AS1	-	GALNTL6 antisense RNA 1	ncRNA	0.009709	0.457627	
chunk0182_22_1	chr7	91365409	91366037	+	0	NA	Intergenic	Intergenic	101255	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.014331	0.389507	
chunk0206_326_1	chr9	125329099	125329533	+	0	NA	intron (NM_001282679, intron 12 of 27)	intron (NM_001282679, intron 12 of 27)	30426	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.006912	0.379310	
chunk0085_285_1	chr18	7921034	7921233	+	0	NA	intron (NM_001105244, intron 4 of 32)	L1MA4|LINE|L1	353817	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.000000	0.350000	68(CTGAACTTTCTGTCCC,-,0.00),69(TGAACTTTCTGTCCCT,+,0.00)
chunk0025_372_1	chr10	58999076	58999799	+	0	NA	promoter-TSS (NR_108046)	promoter-TSS (NR_108046)	-81	NR_108046	100507008	Hs.170953	NR_108046		LINC00844	-	long intergenic non-protein coding RNA 844	ncRNA	0.009682	0.411602	382(AAGAACACACTGTCCC,-,0.00),383(AGAACACACTGTCCCT,+,0.00)
chunk0044_238_1	chr12	31682012	31682433	+	0	NA	intron (NR_103522, intron 7 of 8)	intron (NR_103522, intron 7 of 8)	22547	NM_001135863	254013	Hs.740628	NM_173802	ENSG00000139160	ETFBKMT	C12orf72|ETFB-KMT|METTL20	electron transfer flavoprotein subunit beta lysine methyltransferase	protein-coding	0.011876	0.412322	
chunk0011_40_1	chr1	143238193	143238601	+	0	NA	Intergenic	Intergenic	184195	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.058824	0.369193	
chunk0098_131_1	chr2	69160814	69161251	+	0	NA	intron (NM_053034, intron 13 of 14)	intron (NM_053034, intron 13 of 14)	57350	NR_036073	100423030		NR_036073	ENSG00000266649	MIR3126	mir-3126	microRNA 3126	ncRNA	0.006865	0.463470	
chunk0083_45_1	chr17	63520038	63520902	+	0	NA	Intergenic	Intergenic	-2864	NM_030779	81033	Hs.591177	NM_030779	ENSG00000173826	KCNH6	ERG-2|ERG2|HERG2|Kv11.2|hERG-2	potassium voltage-gated channel subfamily H member 6	protein-coding	0.005787	0.502890	
chunk0065_387_1	chr14	104665431	104665799	+	0	NA	Intergenic	Intergenic	12134	NR_039860	100616300		NR_039860	ENSG00000265291	MIR4710	mir-4710	microRNA 4710	ncRNA	0.019022	0.542005	
chunk0056_22_1	chr13	77189386	77189609	+	0	NA	intron (NM_015057, intron 29 of 82)	intron (NM_015057, intron 29 of 82)	113983	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.017937	0.348214	
chunk0007_202_1	chr1	81349103	81349598	+	0	NA	Intergenic	Intergenic	208352	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.004040	0.415323	
chunk0146_446_1	chr4	169885342	169885547	+	0	NA	Intergenic	Intergenic	90458	NR_037878	100506085	Hs.649173	NR_037878	ENSG00000248319	LINC02275	-	long intergenic non-protein coding RNA 2275	ncRNA	0.004878	0.349515	
chunk0094_251_1	chr2	7302003	7302631	+	0	NA	Intergenic	Intergenic	-118944	NR_038432	100506274	Hs.177930	NR_038432	ENSG00000229727	LOC100506274	-	uncharacterized LOC100506274	ncRNA	0.006369	0.370429	201(GGGGACTCTGAGTGCC,-,0.00),202(GGGACTCTGAGTGCCC,+,0.00)
chunk0090_327_1	chr18	75937208	75937555	+	0	NA	Intergenic	Intergenic	-185617	NR_040034	339298	Hs.151215	NR_040034	ENSG00000263547	LOC339298	-	uncharacterized LOC339298	ncRNA	0.008646	0.350575	
chunk0062_146_1	chr14	69102743	69103145	+	0	NA	intron (NM_001284206, intron 5 of 8)	Tigger3b|DNA|TcMar-Tigger	49655	NM_001284207	8816	Hs.509780	NM_003861	ENSG00000139990	DCAF5	BCRG2|BCRP2|D14S1461E|WDR22	DDB1 and CUL4 associated factor 5	protein-coding	0.009950	0.359801	
chunk0109_460_1	chr2	242097943	242098554	+	0	NA	intron (NR_130700, intron 2 of 5)	intron (NR_130700, intron 2 of 5)	9615	NR_130699	728323	Hs.380737	NR_024437		LINC01881	-	long intergenic non-protein coding RNA 1881	ncRNA	0.003273	0.369281	
chunk0111_223_1	chr20	28905218	28905525	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-175019	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.013029	0.379870	
chunk0023_381_1	chr10	30512539	30512752	+	0	NA	Intergenic	Intergenic	78624	NM_001244134	1326	Hs.432453	NM_005204	ENSG00000107968	MAP3K8	AURA2|COT|EST|ESTF|MEKK8|TPL2|Tpl-2|c-COT	mitogen-activated protein kinase kinase kinase 8	protein-coding	0.014085	0.481308	47(AGGCAGACACTGTTCT,-,0.00)
chunk0005_19_1	chr1	54294238	54294573	+	0	NA	intron (NM_018070, intron 4 of 16)	intron (NM_018070, intron 4 of 16)	57962	NR_103541	619518	Hs.591438	NM_001034847	ENSG00000198711	SSBP3-AS1	C1orf191|MST128|MSTP128	SSBP3 antisense RNA 1	ncRNA	0.008955	0.485119	
chunk0156_403_1	chr5	113984521	113984930	+	0	NA	Intergenic	Intergenic	-377594	NM_001278204	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.007335	0.317073	
chunk0009_151_1	chr1	104947273	104947472	+	0	NA	Intergenic	THE1D-int|LTR|ERVL-MaLR	671563	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.000000	0.500000	
chunk0156_166_1	chr5	107572073	107572477	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	98620	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.037129	0.523457	
chunk0156_177_1	chr5	107657227	107657447	+	0	NA	intron (NM_001962, intron 1 of 4)	intron (NM_001962, intron 1 of 4)	13558	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.009091	0.357466	
chunk0082_177_1	chr17	56118590	56119026	+	0	NA	Intergenic	L2a|LINE|L2	-34667	NM_153228	162282	Hs.673040	NM_153228	ENSG00000153930	ANKFN1	-	ankyrin repeat and fibronectin type III domain containing 1	protein-coding	0.006881	0.347826	
chunk0203_96_1	chr9	84215509	84216032	+	0	NA	Intergenic	HAL1|LINE|L1	125009	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.007648	0.440840	
chunk0127_150_1	chr3	94479498	94480644	+	0	NA	Intergenic	MER2|DNA|TcMar-Tigger	-416848	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.003490	0.321709	
chunk0025_234_1	chr10	54110881	54111887	+	0	NA	intron (NM_001142769, intron 17 of 35)	intron (NM_001142769, intron 17 of 35)	496573	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.001988	0.323734	
chunk0102_4_1	chr2	141033918	141034284	+	0	NA	intron (NM_018557, intron 11 of 90)	intron (NM_018557, intron 11 of 90)	-447416	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.002732	0.337875	189(AGGATCATGGTGTTCC,-,0.00),190(GGATCATGGTGTTCCT,+,0.00)
chunk0133_386_1	chr3	174168826	174169291	+	0	NA	intron (NM_014932, intron 4 of 6)	L1PA16|LINE|L1	-248262	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.002151	0.523605	
chunk0059_415_1	chr14	37933694	37934387	+	0	NA	Intergenic	Intergenic	-273959	NM_001049	6751	Hs.248160	NM_001049	ENSG00000139874	SSTR1	SRIF-2|SS-1-R|SS1-R|SS1R	somatostatin receptor 1	protein-coding	0.001443	0.374640	470(AAGAACATACTGTCCC,-,0.00),471(AGAACATACTGTCCCC,+,0.00)
chunk0082_166_1	chr17	55758122	55758437	+	0	NA	intron (NM_001102402, intron 1 of 5)	intron (NM_001102402, intron 1 of 5)	7174	NM_001102402	58488	Hs.285218	NM_021213	ENSG00000141179	PCTP	PC-TP|STARD2	phosphatidylcholine transfer protein	protein-coding	0.000000	0.424051	
chunk0170_146_1	chr6	111299549	111299958	+	0	NA	3' UTR (NM_002912, exon 33 of 33)	3' UTR (NM_002912, exon 33 of 33)	40474	NM_153369	91749	Hs.400572	NM_153369	ENSG00000173214	MFSD4B	KIAA1919|NaGLT1	major facilitator superfamily domain containing 4B	protein-coding	0.012225	0.336585	
chunk0106_179_1	chr2	201071673	201072085	+	0	NA	promoter-TSS (NM_173822)	promoter-TSS (NM_173822)	140	NM_001257102	4709	Hs.109760	NM_002491	ENSG00000119013	NDUFB3	B12|CI-B12|MC1DN25	NADH:ubiquinone oxidoreductase subunit B3	protein-coding	0.043689	0.520581	
chunk0111_185_1	chr20	25362987	25363192	+	0	NA	intron (NM_001042472, intron 1 of 12)	intron (NM_001042472, intron 1 of 12)	27893	NM_015600	26090	Hs.441550	NM_015600	ENSG00000100997	ABHD12	ABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12	abhydrolase domain containing 12	protein-coding	0.000000	0.296117	
chunk0209_294_1	chrX	48591315	48591747	+	0	NA	Intergenic	Intergenic	-5961	NR_029427	64743	Hs.521973	NM_017883	ENSG00000101940	WDR13	MG21	WD repeat domain 13	protein-coding	0.011574	0.461894	208(AGGAACACTTTGTACA,-,0.00),209(GGAACACTTTGTACAG,+,0.00)
chunk0027_461_1	chr10	81818242	81818446	+	0	NA	Intergenic	Intergenic	-56970	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.000000	0.370732	
chunk0072_116_1	chr15	91851359	91851716	+	0	NA	Intergenic	Intergenic	-2171	NM_013272	28232	Hs.311187	NM_013272	ENSG00000176463	SLCO3A1	OATP-D|OATP-RP3|OATP3A1|OATPD|OATPRP3|SLC21A11	solute carrier organic anion transporter family member 3A1	protein-coding	0.016807	0.463687	
chunk0046_176_1	chr12	58619895	58620350	+	0	NA	intron (NR_120452, intron 1 of 7)	L1M5|LINE|L1	28420	NR_126341	100506869	Hs.290456	NR_126341	ENSG00000258231	LOC100506869	-	uncharacterized LOC100506869	ncRNA	0.006593	0.385965	
chunk0028_375_1	chr10	92826491	92827143	+	0	NA	Intergenic	L2a|LINE|L2	-7896	NM_001013848	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.004601	0.415008	171(GTGTACAGTGTGTCCA,-,0.00),172(TGTACAGTGTGTCCAA,+,0.00),502(CAGAACATGGAGTGCT,-,0.00),503(AGAACATGGAGTGCTT,+,0.00)
chunk0039_191_1	chr11	100841757	100842127	+	0	NA	intron (NM_152432, intron 3 of 23)	L2a|LINE|L2	-150138	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.005405	0.388140	
chunk0094_6_1	chr2	763069	763380	+	0	NA	Intergenic	Intergenic	-85785	NM_152834	129787	Hs.6729	NM_152834	ENSG00000151353	TMEM18	lncND	transmembrane protein 18	protein-coding	0.003215	0.381410	
chunk0186_333_1	chr7	143230918	143231197	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	8978	NM_176882	259286	Hs.352241	NM_176882	ENSG00000221937	TAS2R40	GPR60|T2R40|T2R58	taste 2 receptor member 40	protein-coding	0.007168	0.464286	
chunk0033_423_1	chr11	24886935	24887167	+	0	NA	intron (NM_001252010, intron 5 of 9)	MER54B|LTR|ERVL	390081	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.004310	0.493562	
chunk0052_333_1	chr12	126030108	126030307	+	0	NA	Intergenic	Intergenic	-46833	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.010050	0.425000	94(GAGAACTCAATGTCCT,-,0.00),95(AGAACTCAATGTCCTG,+,0.00)
chunk0114_30_1	chr21	8045353	8045572	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-152158	NR_038958	100507412	Hs.426704	NR_038958		LOC100507412	-	uncharacterized LOC100507412	ncRNA	0.004566	0.368182	
chunk0116_396_1	chr21	42450087	42450286	+	0	NA	Intergenic	Intergenic	46168	NM_001286506	89765	Hs.661069	NM_080860	ENSG00000160188	RSPH1	CT79|RSP44|RSPH10A|TSA2|TSGA2	radial spoke head component 1	protein-coding	0.020101	0.550000	
chunk0088_282_1	chr18	49487169	49487400	+	0	NA	promoter-TSS (NM_001199346)	promoter-TSS (NM_001199346)	-10	NM_001199346	497661	Hs.603040	NM_001035005	ENSG00000177576	C18orf32	-	chromosome 18 open reading frame 32	protein-coding	0.121212	0.685345	
chunk0171_372_1	chr6	130945234	130945789	+	0	NA	intron (NM_001199388, intron 3 of 17)	intron (NM_001199388, intron 3 of 17)	55256	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.010811	0.377698	
chunk0132_253_1	chr3	158763123	158763859	+	0	NA	Intergenic	Intergenic	-31005	NM_206963	5918	Hs.131269	NM_002888	ENSG00000118849	RARRES1	LXNL|PERG-1|TIG1	retinoic acid receptor responder 1	protein-coding	0.005435	0.397558	
chunk0129_196_1	chr3	121329064	121329422	+	0	NA	intron (NM_014980, intron 21 of 27)	intron (NM_014980, intron 21 of 27)	216763	NM_199420	10721	Hs.241517	NM_199420	ENSG00000051341	POLQ	PRO0327	DNA polymerase theta	protein-coding	0.002793	0.381616	
chunk0164_112_1	chr6	20681336	20681727	+	0	NA	intron (NM_017774, intron 5 of 15)	LTR41C|LTR|ERVL	147074	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.000000	0.420918	
chunk0138_241_1	chr4	39529302	39529563	+	0	NA	intron (NR_047679, intron 1 of 4)	L2b|LINE|L2	1593	NR_047679	100885776	Hs.640769	NR_047679	ENSG00000249348	UGDH-AS1	-	UGDH antisense RNA 1	ncRNA	0.007663	0.404580	
chunk0006_449_1	chr1	76892274	76892473	+	0	NA	intron (NM_030965, intron 2 of 4)	intron (NM_030965, intron 2 of 4)	24872	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.000000	0.360000	
chunk0066_83_1	chr15	29671005	29671498	+	0	NA	Intergenic	MER21C|LTR|ERVL	-100528	NM_015307	23359	Hs.383564	NM_015307	ENSG00000104059	FAM189A1	TMEM228	family with sequence similarity 189 member A1	protein-coding	0.018256	0.497976	
chunk0002_152_1	chr1	18041005	18041664	+	0	NA	Intergenic	Intergenic	-24323	NR_125946	101927876	Hs.522954	NR_125946	ENSG00000261781	LINC01654	-	long intergenic non-protein coding RNA 1654	ncRNA	0.012140	0.528788	284(CTGTACAGTCTGTCCT,-,0.00),285(TGTACAGTCTGTCCTC,+,0.00),319(CTGTACAGTCTGTCCT,-,0.00),320(TGTACAGTCTGTCCTC,+,0.00)
chunk0212_223_1	chrX	136159938	136160212	+	0	NA	intron (NM_001159700, intron 1 of 6)	intron (NM_001159700, intron 1 of 6)	-9221	NM_001159704	2273	Hs.435369	NM_001449	ENSG00000022267	FHL1	FCMSU|FHL-1|FHL1A|FHL1B|FLH1A|KYOT|RBMX1A|RBMX1B|SLIM|SLIM-1|SLIM1|SLIMMER|XMPMA	four and a half LIM domains 1	protein-coding	0.010949	0.440000	
chunk0110_282_1	chr20	17594494	17594741	+	0	NA	intron (NM_001011546, intron 2 of 4)	MLT1J1|LTR|ERVL-MaLR	24663	NM_001011546	11034	Hs.304192	NM_006870	ENSG00000125868	DSTN	ACTDP|ADF|HEL32|bA462D18.2	destrin, actin depolymerizing factor	protein-coding	0.000000	0.459677	
chunk0056_447_1	chr13	95216257	95216524	+	0	NA	intron (NM_001301830, intron 3 of 19)	intron (NM_001301830, intron 3 of 19)	85056	NM_001301830	10257	Hs.508423	NM_005845	ENSG00000125257	ABCC4	MOAT-B|MOATB|MRP4	ATP binding cassette subfamily C member 4	protein-coding	0.003745	0.298507	
chunk0120_309_1	chr3	10191900	10192286	+	0	NA	intron (NM_001570, intron 2 of 12)	intron (NM_001570, intron 2 of 12)	27214	NM_001570	3656	Hs.449207	NM_001570	ENSG00000134070	IRAK2	IRAK-2	interleukin 1 receptor associated kinase 2	protein-coding	0.015544	0.493540	
chunk0037_147_1	chr11	73461404	73461603	+	0	NA	intron (NM_001286050, intron 2 of 8)	MIR3|SINE|MIR	84835	NM_032871	84957	Hs.533720	NM_032871	ENSG00000054967	RELT	AI3C|TNFRSF19L|TRLT	RELT TNF receptor	protein-coding	0.005025	0.405000	
chunk0097_399_1	chr2	62212714	62213160	+	0	NA	intron (NM_006577, intron 1 of 1)	intron (NM_006577, intron 1 of 1)	7111	NR_049824	100847087		NR_049824	ENSG00000266097	MIR5192	-	microRNA 5192	ncRNA	0.006726	0.411633	
chunk0043_315_1	chr12	22288348	22288576	+	0	NA	intron (NM_003034, intron 1 of 4)	intron (NM_003034, intron 1 of 4)	46252	NM_001304450	6489	Hs.408614	NM_003034	ENSG00000111728	ST8SIA1	GD3S|SIAT8|SIAT8-A|SIAT8A|ST8SiaI	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	protein-coding	0.030702	0.537118	
chunk0051_271_1	chr12	118056158	118056659	+	0	NA	intron (NM_001278557, intron 1 of 8)	L2b|LINE|L2	4803	NM_018639	55884	Hs.506985	NM_018639	ENSG00000176871	WSB2	SBA2	WD repeat and SOCS box containing 2	protein-coding	0.003992	0.466135	
chunk0171_234_1	chr6	126600171	126601057	+	0	NA	Intergenic	Intergenic	115983	NR_030316	693173		NR_030316	ENSG00000207632	MIR588	MIRN588|hsa-mir-588	microRNA 588	ncRNA	0.002257	0.324690	659(AGAACTTGCTGCTCTT,+,0.00)
chunk0212_185_1	chrX	133649125	133649529	+	0	NA	intron (NM_001164617, intron 7 of 8)	intron (NM_001164617, intron 7 of 8)	-234150	NM_001448	2239	Hs.58367	NM_001448	ENSG00000076716	GPC4	K-glypican	glypican 4	protein-coding	0.002475	0.350617	
chunk0133_20_1	chr3	165710469	165711059	+	0	NA	Intergenic	L2a|LINE|L2	126701	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.003390	0.314721	
chunk0027_338_1	chr10	78528795	78529473	+	0	NA	Intergenic	Intergenic	261806	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.020649	0.432990	
chunk0138_359_1	chr4	42132998	42133359	+	0	NA	intron (NM_001159547, intron 3 of 5)	intron (NM_001159547, intron 3 of 5)	19700	NM_001159547	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.002770	0.381215	
chunk0054_159_1	chr13	44191495	44191812	+	0	NA	Intergenic	Intergenic	4547	NR_107046	102465876		NR_107046	ENSG00000276319	MIR8079	hsa-mir-8079	microRNA 8079	ncRNA	0.031546	0.468553	
chunk0118_176_1	chr22	30830972	30831384	+	0	NA	intron (NM_001282741, intron 1 of 12)	intron (NM_001282741, intron 1 of 12)	8662	NM_001282741	23762	Hs.517546	NM_030758	ENSG00000184792	OSBP2	HLM|ORP-4|ORP4|OSBPL1|OSBPL4	oxysterol binding protein 2	protein-coding	0.012136	0.452785	
chunk0107_131_1	chr2	214752935	214753435	+	0	NA	intron (NM_001282548, intron 1 of 5)	MIR3|SINE|MIR	56526	NR_104212	580	Hs.591642	NM_000465	ENSG00000138376	BARD1	-	BRCA1 associated RING domain 1	protein-coding	0.004000	0.315369	
chunk0118_167_1	chr22	30746753	30747305	+	0	NA	intron (NM_030758, intron 2 of 13)	L1M4|LINE|L1	15472	NR_036171	100422912		NR_036171	ENSG00000264661	MIR3200	mir-3200	microRNA 3200	ncRNA	0.005435	0.405063	
chunk0149_175_1	chr5	20832587	20832825	+	0	NA	Intergenic	L1MEc|LINE|L1	-256833	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.012605	0.422594	
chunk0058_239_1	chr14	25521725	25522089	+	0	NA	Intergenic	Intergenic	-471610	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.005495	0.391781	
chunk0016_330_1	chr1	201768724	201769173	+	0	NA	intron (NM_001167738, intron 1 of 26)	intron (NM_001167738, intron 1 of 26)	29113	NM_001167738	89796	Hs.585374	NM_020443	ENSG00000134369	NAV1	POMFIL3|STEERIN1|UNC53H1	neuron navigator 1	protein-coding	0.004454	0.346667	
chunk0147_40_1	chr4	172130801	172131363	+	0	NA	intron (NM_001034845, intron 2 of 12)	intron (NM_001034845, intron 2 of 12)	317658	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.001779	0.273535	
chunk0017_261_1	chr1	209526280	209526495	+	0	NA	Intergenic	L2c|LINE|L2	-57313	NM_020439	57172	Hs.199068	NM_020439	ENSG00000008118	CAMK1G	CLICK3|CLICKIII|VWS1|dJ272L16.1	calcium/calmodulin dependent protein kinase IG	protein-coding	0.009302	0.513889	
chunk0108_77_1	chr2	227577428	227578079	+	0	NA	Intergenic	Intergenic	55567	NM_020161	56918	Hs.283092	NM_020161	ENSG00000042304	C2orf83	-	chromosome 2 open reading frame 83	protein-coding	0.007680	0.369632	
chunk0205_190_1	chr9	109095349	109095784	+	0	NA	intron (NM_032012, intron 3 of 17)	L2c|LINE|L2	24379	NM_032012	23731	Hs.308074	NM_032012	ENSG00000106771	TMEM245	C9orf5|CG-2|CG2	transmembrane protein 245	protein-coding	0.006897	0.387615	
chunk0162_117_1	chr6	2823390	2823717	+	0	NA	Intergenic	L1ME1|LINE|L1	18496	NR_073112	1992	Hs.381167	NM_030666	ENSG00000021355	SERPINB1	EI|ELANH2|HEL-S-27|HEL57|LEI|M/NEI|MNEI|PI-2|PI2	serpin family B member 1	protein-coding	0.006116	0.350610	105(AAGCACAAAAAGTGCT,-,0.00),106(AGCACAAAAAGTGCTT,+,0.00),198(AGTGACAGGGTGTTCT,-,0.00),199(GTGACAGGGTGTTCTA,+,0.00)
chunk0046_417_1	chr12	64590022	64590735	+	0	NA	Intergenic	Intergenic	-20135	NM_178169	283349	Hs.643605	NM_178169	ENSG00000153179	RASSF3	RASSF5	Ras association domain family member 3	protein-coding	0.001403	0.383754	250(GTAACAATGTGTTCTG,+,0.00)
chunk0008_237_1	chr1	94221782	94222315	+	0	NA	intron (NM_004815, intron 2 of 22)	L1MC3|LINE|L1	15703	NM_004815	9411	Hs.483238	NM_004815	ENSG00000137962	ARHGAP29	PARG1	Rho GTPase activating protein 29	protein-coding	0.000000	0.367041	
chunk0015_434_1	chr1	191711902	191712183	+	0	NA	Intergenic	Intergenic	-446420	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.014235	0.429078	
chunk0092_326_1	chr19	34875372	34875747	+	0	NA	Intergenic	Intergenic	23384	NR_046222	100652909	Hs.374015	NR_046222	ENSG00000271649	LINC00904	-	long intergenic non-protein coding RNA 904	ncRNA	0.010667	0.409574	
chunk0077_253_1	chr16	80875338	80876150	+	0	NA	intron (NR_131948, intron 1 of 2)	intron (NR_131948, intron 1 of 2)	16852	NR_131948	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.007389	0.360394	426(ATGAACAGCGTGTGCT,-,0.00),427(TGAACAGCGTGTGCTT,+,0.00)
chunk0019_395_1	chr1	230410583	230411064	+	0	NA	intron (NM_001258311, intron 1 of 6)	L1MEj|LINE|L1	15105	NM_001258311	79605	Hs.520463	NM_024554	ENSG00000177614	PGBD5	-	piggyBac transposable element derived 5	protein-coding	0.002079	0.381743	
chunk0211_400_1	chrX	128641852	128642191	+	0	NA	Intergenic	hAT-N1_Mam|DNA|hAT-Tip100?	-589618	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.000000	0.358824	
chunk0053_276_1	chr13	33227682	33228383	+	0	NA	intron (NM_001243476, intron 5 of 17)	L2b|LINE|L2	-21982	NM_052851	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.008559	0.427350	483(GAGTACATGGAGTGCT,-,0.00),484(AGTACATGGAGTGCTC,+,0.00)
chunk0049_65_1	chr12	90166578	90167298	+	0	NA	Intergenic	Intergenic	457983	NR_028138	338758	Hs.601766	NR_028138	ENSG00000271614	ATP2B1-AS1	LINC00936	ATP2B1 antisense RNA 1	ncRNA	0.004167	0.349515	
chunk0099_257_1	chr2	97970207	97970814	+	0	NA	intron (NM_015348, intron 1 of 40)	MIR|SINE|MIR	25381	NM_015348	23505	Hs.469376	NM_015348	ENSG00000075568	TMEM131	CC28|PRO1048|RW1|YR-23	transmembrane protein 131	protein-coding	0.004942	0.473684	
chunk0095_363_1	chr2	23033170	23033545	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-352070	NM_052920	114818	Hs.130593	NM_025067	ENSG00000119771	KLHL29	KBTBD9	kelch like family member 29	protein-coding	0.002667	0.452128	115(ATGAACACTGTGTCCT,-,0.00),116(TGAACACTGTGTCCTT,+,0.00)
chunk0003_269_1	chr1	36328731	36329066	+	0	NA	Intergenic	MIRb|SINE|MIR	-4744	NM_018166	55194	Hs.87016	NM_018166	ENSG00000142694	EVA1B	C1orf78|FAM176B	eva-1 homolog B	protein-coding	0.011940	0.526786	81(AGGGACATTGAGTACC,-,0.00),82(GGGACATTGAGTACCC,+,0.00)
chunk0203_37_1	chr9	83047869	83048068	+	0	NA	intron (NM_152573, intron 1 of 16)	intron (NM_152573, intron 1 of 16)	15160	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.005025	0.450000	
chunk0080_167_1	chr17	28468669	28469194	+	0	NA	Intergenic	L1MB2|LINE|L1	-4715	NR_027384									0.001905	0.370722	
chunk0172_147_1	chr6	135586310	135586792	+	0	NA	intron (NR_026805, intron 1 of 3)	intron (NR_026805, intron 1 of 3)	88750	NR_026805	100131814	Hs.734007	NR_026805	ENSG00000231028	LINC00271	C6orf217|NCRNA00271	long intergenic non-protein coding RNA 271	ncRNA	0.004149	0.434783	
chunk0047_185_1	chr12	70754515	70754742	+	0	NA	promoter-TSS (NR_073474)	promoter-TSS (NR_073474)	-20	NR_073474	5801	Hs.506076	NM_002849	ENSG00000153233	PTPRR	EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ	protein tyrosine phosphatase receptor type R	protein-coding	0.013216	0.442982	
chunk0080_176_1	chr17	28756476	28756844	+	0	NA	3' UTR (NM_001288639, exon 4 of 4)	3' UTR (NM_001288639, exon 4 of 4)	12655	NM_004295	9618	Hs.8375	NM_004295	ENSG00000076604	TRAF4	CART1|MLN62|RNF83	TNF receptor associated factor 4	protein-coding	0.010870	0.444444	
chunk0189_95_1	chr8	21744232	21744591	+	0	NA	intron (NM_001165038, intron 3 of 7)	intron (NM_001165038, intron 3 of 7)	44423	NM_001165038	2675	Hs.441202	NM_001495	ENSG00000168546	GFRA2	GDNFRB|NRTNR-ALPHA|NTNRA|RETL2|TRNR2	GDNF family receptor alpha 2	protein-coding	0.008357	0.527778	
chunk0195_84_1	chr8	94194265	94194892	+	0	NA	intron (NM_004063, intron 2 of 17)	intron (NM_004063, intron 2 of 17)	14009	NM_004063	1015	Hs.591853	NM_004063	ENSG00000079112	CDH17	CDH16|HPT-1|HPT1	cadherin 17	protein-coding	0.004785	0.363057	349(AAGAACACCCTCTTCT,-,0.00),350(AGAACACCCTCTTCTC,+,0.00)
chunk0021_20_1	chr10	495736	496123	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	145849	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.020672	0.466495	
chunk0070_117_1	chr15	70712847	70713126	+	0	NA	intron (NM_018003, intron 1 of 18)	L2b|LINE|L2	-10705	NM_001008224	55075	Hs.108049	NM_018003	ENSG00000137831	UACA	NUCLING	uveal autoantigen with coiled-coil domains and ankyrin repeats	protein-coding	0.025090	0.421429	138(TGGAACTTGATGTTCT,-,0.00),139(GGAACTTGATGTTCTA,+,0.00)
chunk0191_449_1	chr8	57991805	57992599	+	0	NA	Intergenic	Intergenic	-2352	NM_147189	90362	Hs.154652	NM_147189	ENSG00000169122	FAM110B	C8orf72	family with sequence similarity 110 member B	protein-coding	0.008816	0.387421	
chunk0175_386_1	chr6	168301827	168302061	+	0	NA	intron (NM_001286351, intron 3 of 5)	intron (NM_001286351, intron 3 of 5)	17810	NM_001286350	168002	Hs.673059	NM_214462	ENSG00000164488	DACT2	C6orf116|DAPPER2|DPR2|bA503C24.7	dishevelled binding antagonist of beta catenin 2	protein-coding	0.029915	0.617021	
chunk0075_423_1	chr16	57500720	57501329	+	0	NA	Intergenic	L2b|LINE|L2	-14551	NM_018110	55715	Hs.279832	NM_018110	ENSG00000125170	DOK4	IRS-5|IRS5	docking protein 4	protein-coding	0.013136	0.559016	302(GGGGACACAGTGTTCC,-,0.00),303(GGGACACAGTGTTCCA,+,0.00)
chunk0160_103_1	chr5	150498727	150499179	+	0	NA	intron (NM_001301063, intron 1 of 13)	intron (NM_001301063, intron 1 of 13)	1175	NM_001301063	3340	Hs.222055	NM_001543	ENSG00000070614	NDST1	HSST|MRT46|NST1	N-deacetylase and N-sulfotransferase 1	protein-coding	0.004425	0.536424	205(AGGGACAGGATGTTCC,-,0.00),206(GGGACAGGATGTTCCT,+,0.00)
chunk0129_424_1	chr3	127339316	127339515	+	0	NA	intron (NR_110147, intron 3 of 4)	(AC)n|Simple_repeat|Simple_repeat	51255	NR_110147	101927123	Hs.526761	NR_110147	ENSG00000244215	LINC02016	-	long intergenic non-protein coding RNA 2016	ncRNA	0.005025	0.390000	
chunk0143_277_1	chr4	116676862	116677330	+	0	NA	Intergenic	Intergenic	377371	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.006410	0.292111	
chunk0160_466_1	chr5	165209063	165209325	+	0	NA	Intergenic	Intergenic	738915	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.003817	0.334601	
chunk0043_73_1	chr12	14384906	14385257	+	0	NA	promoter-TSS (NM_181352)	promoter-TSS (NM_181352)	17	NM_181352	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.005698	0.417614	
chunk0143_266_1	chr4	116455263	116456190	+	0	NA	Intergenic	Intergenic	156001	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.005394	0.322198	67(AAGCACAGACTGTTCC,-,0.00),68(AGCACAGACTGTTCCA,+,0.00),238(CAGTACAATTTGTGCT,-,0.00),239(AGTACAATTTGTGCTC,+,0.00)
chunk0194_210_1	chr8	86049743	86050201	+	0	NA	intron (NM_033126, intron 2 of 2)	intron (NM_033126, intron 2 of 2)	19650	NM_033126	85481	Hs.566854	NM_033126	ENSG00000147613	PSKH2	-	protein serine kinase H2	protein-coding	0.004367	0.379085	
chunk0073_15_1	chr16	2148010	2148345	+	0	NA	promoter-TSS (NM_014353)	promoter-TSS (NM_014353)	33	NM_001308053	25837	Hs.3797	NM_014353	ENSG00000167964	RAB26	V46133	RAB26, member RAS oncogene family	protein-coding	0.047761	0.678571	
chunk0177_192_1	chr7	23698380	23699040	+	0	NA	intron (NM_001300932, intron 4 of 5)	intron (NM_001300932, intron 4 of 5)	-11457	NM_031414	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.009091	0.335855	
chunk0024_323_1	chr10	43090784	43091123	+	0	NA	intron (NM_020975, intron 1 of 19)	intron (NM_020975, intron 1 of 19)	13884	NM_020630	5979	Hs.350321	NM_000323	ENSG00000165731	RET	CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1	ret proto-oncogene	protein-coding	0.020649	0.591176	
chunk0049_445_1	chr12	98736791	98737486	+	0	NA	intron (NM_020140, intron 10 of 10)	intron (NM_020140, intron 10 of 10)	91838	NM_181861	317	Hs.552567	NM_001160	ENSG00000120868	APAF1	APAF-1|CED4	apoptotic peptidase activating factor 1	protein-coding	0.007194	0.452586	
chunk0129_358_1	chr3	125182935	125183208	+	0	NA	intron (NM_024628, intron 4 of 13)	intron (NM_024628, intron 4 of 13)	28328	NM_001195483	84561	Hs.658514	NM_024628	ENSG00000221955	SLC12A8	CCC9	solute carrier family 12 member 8	protein-coding	0.010989	0.427007	
chunk0018_446_1	chr1	223007129	223007654	+	0	NA	Intergenic	L3|LINE|CR1	135891	NM_003268	7100	Hs.604542	NM_003268	ENSG00000187554	TLR5	MELIOS|SLE1|SLEB1|TIL3	toll like receptor 5	protein-coding	0.019048	0.431559	
chunk0110_354_1	chr20	19712575	19713092	+	0	NA	intron (NM_020689, intron 15 of 16)	L1ME2z|LINE|L1	-173688	NM_001242581	54453	Hs.472270	NM_018993	ENSG00000132669	RIN2	MACS|RASSF4	Ras and Rab interactor 2	protein-coding	0.007737	0.440154	332(TAGGACAGGCTGAACT,-,0.00),333(AGGACAGGCTGAACTG,+,0.00)
chunk0116_158_1	chr21	36546141	36546428	+	0	NA	intron (NM_001146077, intron 1 of 2)	MER5A|DNA|hAT-Charlie	-3465	NM_001146078	23562	Hs.660278	NM_012130	ENSG00000159261	CLDN14	DFNB29	claudin 14	protein-coding	0.006969	0.406250	
chunk0195_205_1	chr8	96879285	96879895	+	0	NA	intron (NM_016134, intron 3 of 7)	intron (NM_016134, intron 3 of 7)	234363	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.004918	0.386252	
chunk0103_188_1	chr2	163436660	163436859	+	0	NA	Intergenic	Cheshire|DNA|hAT-Charlie	299244	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.005025	0.290000	
chunk0093_155_1	chr19	46976316	46977068	+	0	NA	intron (NM_004491, intron 2 of 5)	intron (NM_004491, intron 2 of 5)	-44194	NM_002517	4861	Hs.79564	NM_002517	ENSG00000130751	NPAS1	MOP5|PASD5|bHLHe11	neuronal PAS domain protein 1	protein-coding	0.025266	0.563081	112(CAGAACAGTGTGCCCT,-,0.00),113(AGAACAGTGTGCCCTG,+,0.00)
chunk0131_381_1	chr3	152385627	152386267	+	0	NA	intron (NM_001314057, intron 2 of 11)	intron (NM_001314057, intron 2 of 11)	-44957	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.001563	0.312012	
chunk0066_25_1	chr15	27537188	27537815	+	0	NA	Intergenic	Intergenic	-376182	NR_120343	101928869	Hs.585699	NR_120343	ENSG00000228740	GABRG3-AS1	-	GABRG3 antisense RNA 1	ncRNA	0.009569	0.335987	
chunk0108_399_1	chr2	237329861	237330260	+	0	NA	intron (NM_004369, intron 42 of 43)	intron (NM_004369, intron 42 of 43)	84147	NM_057166	1293	Hs.233240	NM_004369	ENSG00000163359	COL6A3	BTHLM1|DYT27|UCMD1	collagen type VI alpha 3 chain	protein-coding	0.005013	0.322500	
chunk0059_165_1	chr14	32392988	32393635	+	0	NA	intron (NM_004274, intron 1 of 13)	L1MC4a|LINE|L1	64038	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.001546	0.341049	
chunk0027_111_1	chr10	74056229	74056883	+	0	NA	intron (NM_003373, intron 2 of 20)	intron (NM_003373, intron 2 of 20)	58442	NM_003373	7414	Hs.643896	NM_003373	ENSG00000035403	VCL	CMD1W|CMH15|HEL114|MV|MVCL	vinculin	protein-coding	0.003058	0.375573	225(AAGAACAAGAAGTCCA,-,0.00),336(TGGAACAGCATGTATT,-,0.00),337(GGAACAGCATGTATTA,+,0.00),428(TGTACTCTGTGTTCCT,+,0.00),606(AAGTACAATCTGTGCC,-,0.00),607(AGTACAATCTGTGCCA,+,0.00)
chunk0112_400_1	chr20	46990406	46990605	+	0	NA	intron (NM_172110, intron 2 of 13)	intron (NM_172110, intron 2 of 13)	95881	NM_172110	2139	Hs.472877	NM_005244	ENSG00000064655	EYA2	EAB1	EYA transcriptional coactivator and phosphatase 2	protein-coding	0.020101	0.525000	
chunk0072_103_1	chr15	91161689	91161888	+	0	NA	intron (NM_014848, intron 2 of 13)	intron (NM_014848, intron 2 of 13)	61479	NM_014848	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.005025	0.430000	
chunk0088_354_1	chr18	52439686	52439887	+	0	NA	intron (NM_005215, intron 1 of 28)	intron (NM_005215, intron 1 of 28)	99614	NM_005215	1630	Hs.162025	NM_005215	ENSG00000187323	DCC	CRC18|CRCR1|HGPPS2|IGDCC1|MRMV1|NTN1R1	DCC netrin 1 receptor	protein-coding	0.009950	0.321782	
chunk0061_362_1	chr14	63896156	63896655	+	0	NA	intron (NM_182914, intron 1 of 115)	L4_A_Mam|LINE|RTE-X	43440	NM_015180	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.006012	0.422000	
chunk0021_386_1	chr1	246537888	246538285	+	0	NA	Intergenic	LTR9A1|LTR|ERV1	-13799	NR_040002	255654	Hs.407570	NR_040002	ENSG00000242042	LINC01743	-	long intergenic non-protein coding RNA 1743	ncRNA	0.007557	0.449749	145(CAGCACACCTAGTCCT,-,0.00),146(AGCACACCTAGTCCTA,+,0.00),187(CGGCACACCTTGTCCA,-,0.00),188(GGCACACCTTGTCCAA,+,0.00)
chunk0109_110_1	chr20	2509855	2510246	+	0	NA	promoter-TSS (NM_001282499)	promoter-TSS (NM_001282499)	-918	NM_001282497	79175	Hs.516846	NM_024325	ENSG00000088876	ZNF343	dJ734P14.5	zinc finger protein 343	protein-coding	0.007673	0.387755	
chunk0128_217_1	chr3	108068187	108068533	+	0	NA	intron (NM_198793, intron 3 of 8)	intron (NM_198793, intron 3 of 8)	22728	NM_001777	961	Hs.446414	NM_001777	ENSG00000196776	CD47	IAP|MER6|OA3	CD47 molecule	protein-coding	0.002890	0.417867	
chunk0094_349_1	chr2	9422544	9422941	+	0	NA	promoter-TSS (NM_016207)	promoter-TSS (NM_016207)	772	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.055416	0.610553	
chunk0034_197_1	chr11	32113043	32113693	+	0	NA	Intergenic	Intergenic	22437	NM_002901	5954	Hs.97887	NM_002901	ENSG00000049449	RCN1	HEL-S-84|PIG20|RCAL|RCN	reticulocalbin 1	protein-coding	0.013846	0.382488	384(CAGAACAGCATGTTCT,-,0.00),385(AGAACAGCATGTTCTA,+,0.00)
chunk0158_397_1	chr5	134632661	134632929	+	0	NA	promoter-TSS (NM_016103)	promoter-TSS (NM_016103)	48	NM_001033503	51128	Hs.432984	NM_016103	ENSG00000152700	SAR1B	ANDD|CMRD|GTBPB|SARA2	secretion associated Ras related GTPase 1B	protein-coding	0.085821	0.665428	
chunk0137_116_1	chr4	14225696	14226071	+	0	NA	Intergenic	Intergenic	113915	NR_033931	152742	Hs.135435	NR_033931	ENSG00000248698	LINC01085	-	long intergenic non-protein coding RNA 1085	ncRNA	0.008000	0.398936	
chunk0081_220_1	chr17	42643951	42644429	+	0	NA	Intergenic	Intergenic	-15058	NM_016437	27175	Hs.279669	NM_016437	ENSG00000037042	TUBG2	-	tubulin gamma 2	protein-coding	0.006276	0.411273	
chunk0088_428_1	chr18	55567655	55568063	+	0	NA	intron (NM_003199, intron 3 of 19)	L1MEd|LINE|L1	18260	NM_001306207	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.009804	0.325183	
chunk0171_378_1	chr6	130985224	130985423	+	0	NA	intron (NM_001431, intron 1 of 19)	LTR27B|LTR|ERV1	15444	NM_001252660	2037	Hs.486470	NM_001431	ENSG00000079819	EPB41L2	4.1-G|4.1G	erythrocyte membrane protein band 4.1 like 2	protein-coding	0.005025	0.510000	
chunk0088_288_1	chr18	49681413	49681699	+	0	NA	Intergenic	MIRc|SINE|MIR	119525	NM_006033	9388	Hs.465102	NM_006033	ENSG00000101670	LIPG	EDL|EL|PRO719	lipase G, endothelial type	protein-coding	0.006993	0.425087	
chunk0189_235_1	chr8	24520193	24520600	+	0	NA	intron (NR_125808, intron 1 of 5)	intron (NR_125808, intron 1 of 5)	-5528	NR_125809	101929315	Hs.125562	NR_125809	ENSG00000253643	LOC101929315	-	uncharacterized LOC101929315	ncRNA	0.002457	0.397059	
chunk0095_12_1	chr2	12061588	12062240	+	0	NA	intron (NR_110196, intron 2 of 5)	intron (NR_110196, intron 2 of 5)	54798	NR_110198	100506457	Hs.197824	NR_110196	ENSG00000224184	MIR3681HG	-	MIR3681 host gene	ncRNA	0.003067	0.375191	331(AAGAACAAAATGTCTC,-,0.00),332(AGAACAAAATGTCTCT,+,0.00)
chunk0027_274_1	chr10	77416568	77417069	+	0	NA	intron (NM_001014797, intron 1 of 28)	intron (NM_001014797, intron 1 of 28)	65946	NR_126365	101929286	Hs.568867	NR_126365		KCNMA1-AS3	-	KCNMA1 antisense RNA 3	ncRNA	0.021956	0.505976	
chunk0006_400_1	chr1	75492694	75492956	+	0	NA	intron (NM_001130058, intron 2 of 23)	intron (NM_001130058, intron 2 of 23)	118289	NM_152697	204962	Hs.654821	NM_152697	ENSG00000137968	SLC44A5	CTL5	solute carrier family 44 member 5	protein-coding	0.003817	0.391635	
chunk0154_364_1	chr5	87565589	87566384	+	0	NA	Intergenic	L1P3|LINE|L1	-152953	NM_001239	902	Hs.292524	NM_001239	ENSG00000134480	CCNH	CAK|CycH|p34|p37	cyclin H	protein-coding	0.003774	0.364322	228(GGTACATTGTGTCTTT,+,0.00)
chunk0014_21_1	chr1	174530175	174530507	+	0	NA	intron (NM_014857, intron 13 of 20)	L1MA4A|LINE|L1	82267	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.000000	0.510511	
chunk0186_290_1	chr7	142595997	142596559	+	0	NA	Intergenic	Intergenic	-70021	NM_001190487	100463482		NM_001190487	ENSG00000270672	MTRNR2L6	HN6	MT-RNR2 like 6	protein-coding	0.005338	0.442274	
chunk0060_18_1	chr14	39456640	39457403	+	0	NA	Intergenic	Intergenic	-24521	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.003932	0.352094	613(ATTACAGAGTGTTCTC,+,0.00)
chunk0045_155_1	chr12	46539263	46539728	+	0	NA	intron (NR_125380, intron 3 of 3)	L2b|LINE|L2	155388	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.004301	0.388412	
chunk0192_223_1	chr8	65322599	65323182	+	0	NA	Intergenic	Intergenic	-142550	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.006861	0.445205	
chunk0148_4_1	chr5	149604	150348	+	0	NA	intron (NM_052909, intron 4 of 17)	L1MB3|LINE|L1	9718	NM_052909	153478	Hs.535800	NM_052909	ENSG00000153404	PLEKHG4B	-	pleckstrin homology and RhoGEF domain containing G4B	protein-coding	0.004032	0.363758	
chunk0174_148_1	chr6	157779599	157779905	+	0	NA	Intergenic	Intergenic	-43419	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.006536	0.381107	74(GGGTACAGTCAGTACA,-,0.00),75(GGTACAGTCAGTACAC,+,0.00)
chunk0177_356_1	chr7	26658390	26658644	+	0	NA	Intergenic	Intergenic	19432	NM_001302625									0.003937	0.333333	
chunk0169_337_1	chr6	106431185	106431974	+	0	NA	Intergenic	Intergenic	-80276	NM_001624	202	Hs.724262	NM_001624	ENSG00000112297	CRYBG1	AIM1|ST4	crystallin beta-gamma domain containing 1	protein-coding	0.006337	0.401266	
chunk0120_340_1	chr3	11272149	11272348	+	0	NA	promoter-TSS (NM_001144912)	promoter-TSS (NM_001144912)	-76	NM_001136031	10533	Hs.38032	NM_006395	ENSG00000197548	ATG7	APG7-LIKE|APG7L|GSA7	autophagy related 7	protein-coding	0.080402	0.620000	
chunk0133_94_1	chr3	167862180	167862855	+	0	NA	Intergenic	Intergenic	-33431	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.005926	0.374260	
chunk0020_219_1	chr1	235320447	235321100	+	0	NA	intron (NM_031371, intron 2 of 22)	L2a|LINE|L2	6714	NM_001206794	51742	Hs.575782	NM_016374	ENSG00000054267	ARID4B	BCAA|BRCAA1|RBBP1L1|RBP1L1|SAP180	AT-rich interaction domain 4B	protein-coding	0.009188	0.438838	
chunk0050_399_1	chr12	109311791	109312320	+	0	NA	Intergenic	Intergenic	-2835	NM_213596	121643	Hs.528316	NM_213596	ENSG00000139445	FOXN4	-	forkhead box N4	protein-coding	0.015123	0.415094	
chunk0027_332_1	chr10	78481663	78482524	+	0	NA	Intergenic	L1MC|LINE|L1	214765	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.003484	0.308585	
chunk0092_40_1	chr19	19366779	19367347	+	0	NA	Intergenic	Intergenic	-18770	NM_017660	54815	Hs.118964	NM_017660	ENSG00000167491	GATAD2A	p66alpha	GATA zinc finger domain containing 2A	protein-coding	0.014085	0.560633	42(AGGCACACTCTGTCCA,-,0.00),43(GGCACACTCTGTCCAG,+,0.00),133(AAGCACAAACTGTTCA,-,0.00),134(AGCACAAACTGTTCAG,+,0.00)
chunk0075_125_1	chr16	49937038	49937673	+	0	NA	Intergenic	Intergenic	-79436	NM_001271620	23090	Hs.443715	NM_015069	ENSG00000102935	ZNF423	Ebfaz|JBTS19|NPHP14|OAZ|Roaz|ZFP423|Zfp104|hOAZ	zinc finger protein 423	protein-coding	0.015748	0.481132	
chunk0085_97_1	chr18	2693150	2693647	+	0	NA	intron (NM_015295, intron 7 of 47)	Tigger3a|DNA|TcMar-Tigger	37511	NM_015295	23347	Hs.8118	NM_015295	ENSG00000101596	SMCHD1	BAMS|FSHD2	structural maintenance of chromosomes flexible hinge domain containing 1	protein-coding	0.006036	0.337349	
chunk0160_405_1	chr5	163580457	163580842	+	0	NA	Intergenic	Tigger12A|DNA|TcMar-Tigger	75121	NM_013283	27430	Hs.54642	NM_013283	ENSG00000038274	MAT2B	MAT-II|MATIIbeta|Nbla02999|SDR23E1|TGR	methionine adenosyltransferase 2B	protein-coding	0.005195	0.393782	
chunk0122_249_1	chr3	34690898	34691377	+	0	NA	Intergenic	Intergenic	702886	NR_110817	101928135	Hs.550715	NR_110817		LOC101928135	-	uncharacterized LOC101928135	ncRNA	0.006263	0.408333	
chunk0033_31_1	chr11	12918720	12918996	+	0	NA	intron (NM_021961, intron 10 of 12)	L1ME3A|LINE|L1	70690	NR_038904	100506305	Hs.153408	NR_038904	ENSG00000251381	LINC00958	BLACAT2	long intergenic non-protein coding RNA 958	ncRNA	0.010870	0.382671	
chunk0195_266_1	chr8	98085525	98085724	+	0	NA	intron (NM_001170806, intron 1 of 1)	L1ME1|LINE|L1	21102	NM_173549	203111	Hs.171455	NM_173549	ENSG00000177459	ERICH5	C8orf47	glutamate rich 5	protein-coding	0.005025	0.315000	
chunk0110_288_1	chr20	17684130	17684795	+	0	NA	Intergenic	Intergenic	-2179	NM_001042576	6238	Hs.472213	NM_004587	ENSG00000125844	RRBP1	ES/130|ES130|RRp|hES	ribosome binding protein 1	protein-coding	0.015038	0.530030	
chunk0002_158_1	chr1	18190096	18190686	+	0	NA	intron (NM_032880, intron 1 of 9)	MIRb|SINE|MIR	82645	NM_032880	84966	Hs.212511	NM_032880	ENSG00000117154	IGSF21	-	immunoglobin superfamily member 21	protein-coding	0.010169	0.529611	
chunk0195_277_1	chr8	98243344	98243564	+	0	NA	intron (NM_024759, intron 3 of 11)	intron (NM_024759, intron 3 of 11)	50939	NM_024759	79815	Hs.309489	NM_024759	ENSG00000104361	NIPAL2	NPAL2	NIPA like domain containing 2	protein-coding	0.022727	0.466063	
chunk0164_118_1	chr6	20786131	20786472	+	0	NA	intron (NM_017774, intron 8 of 15)	intron (NM_017774, intron 8 of 15)	251844	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.005865	0.383041	
chunk0140_76_1	chr4	67578065	67578325	+	0	NA	intron (NM_012108, intron 4 of 8)	intron (NM_012108, intron 4 of 8)	19467	NM_012108	26228	Hs.435579	NM_012108	ENSG00000035720	STAP1	BRDG1|STAP-1	signal transducing adaptor family member 1	protein-coding	0.003846	0.352490	192(AGGAGCACCATGTTCT,-,0.00),193(GGAGCACCATGTTCTC,+,0.00)
chunk0129_284_1	chr3	123238722	123239159	+	0	NA	intron (NM_012430, intron 4 of 6)	L1MC5a|LINE|L1	37013	NM_012430	26984	Hs.477361	NM_012430	ENSG00000121542	SEC22A	SEC22L2	SEC22 homolog A, vesicle trafficking protein	protein-coding	0.006865	0.317352	
chunk0063_436_1	chr14	88636885	88637166	+	0	NA	intron (NM_183387, intron 31 of 42)	intron (NM_183387, intron 31 of 42)	42639	NM_207662	79882	Hs.684046	NM_024824	ENSG00000100722	ZC3H14	MRT56|MSUT-2|NY-REN-37|SUT2|UKp68	zinc finger CCCH-type containing 14	protein-coding	0.000000	0.319149	
chunk0120_222_1	chr3	8045607	8045937	+	0	NA	Intergenic	L1PB1|LINE|L1	-29465	NR_110131	101927394	Hs.517767	NR_110131	ENSG00000227110	LOC101927394	-	uncharacterized LOC101927394	ncRNA	0.000000	0.359517	
chunk0049_143_1	chr12	91893528	91893926	+	0	NA	Intergenic	Intergenic	247986	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.010050	0.438596	
chunk0007_208_1	chr1	81498328	81499141	+	0	NA	Intergenic	Intergenic	58968	NR_125943	101927434	Hs.130394	NR_125943	ENSG00000234953	LOC101927434	-	uncharacterized LOC101927434	ncRNA	0.006150	0.359951	
chunk0043_363_1	chr12	23415230	23415429	+	0	NA	Intergenic	LTR88a|LTR|Gypsy?	169283	NM_178010	6660	Hs.434948	NM_006940	ENSG00000134532	SOX5	L-SOX5|L-SOX5B|L-SOX5F|LAMSHF	SRY-box transcription factor 5	protein-coding	0.010050	0.430000	
chunk0183_137_1	chr7	105708048	105708283	+	0	NA	intron (NM_020725, intron 3 of 11)	MIR3|SINE|MIR	-29003	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.029787	0.508475	
chunk0044_232_1	chr12	31491284	31491966	+	0	NA	intron (NM_001308339, intron 4 of 22)	L1ME3Cz|LINE|L1	-98298	NR_046909	100874249	Hs.627628	NR_046909	ENSG00000255867	DENND5B-AS1	-	DENND5B antisense RNA 1	ncRNA	0.007331	0.357247	
chunk0143_84_1	chr4	108248096	108248375	+	0	NA	Intergenic	Intergenic	76115	NR_029373	641518	Hs.535760	NR_029373	ENSG00000232021	LEF1-AS1	LEF1NAT	LEF1 antisense RNA 1	ncRNA	0.007168	0.371429	
chunk0057_327_1	chr13	106918573	106918789	+	0	NA	Intergenic	Intergenic	264801	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.004630	0.341014	
chunk0104_60_1	chr2	171552674	171553226	+	0	NA	intron (NM_001256909, intron 2 of 3)	L1ME3G|LINE|L1	30594	NM_001127383	79901	Hs.221941	NM_024843	ENSG00000071967	CYBRD1	CYB561A2|DCYTB|FRRS3	cytochrome b reductase 1	protein-coding	0.007246	0.334539	
chunk0032_198_1	chr11	6683474	6683675	+	0	NA	promoter-TSS (NM_022061)	promoter-TSS (NM_022061)	-173	NM_022061	63875	Hs.523456	NM_022061	ENSG00000158042	MRPL17	L17mt|LIP2|MRP-L17|MRP-L26|RPL17L|RPML26	mitochondrial ribosomal protein L17	protein-coding	0.079602	0.643564	
chunk0150_237_1	chr5	36017098	36017424	+	0	NA	Intergenic	MLT1E1|LTR|ERVL-MaLR	-16233	NM_001171873	133688	Hs.254699	NM_152404	ENSG00000145626	UGT3A1	-	UDP glycosyltransferase family 3 member A1	protein-coding	0.003067	0.440367	
chunk0007_329_1	chr1	84619205	84619699	+	0	NA	intron (NR_125761, intron 1 of 2)	intron (NR_125761, intron 1 of 2)	1579	NR_125761	103695366	Hs.576097	NR_125761		LINC01461	TCONS_00001552	long intergenic non-protein coding RNA 1461	ncRNA	0.020243	0.448485	
chunk0209_186_1	chrX	43742282	43742536	+	0	NA	intron (NM_000240, intron 12 of 14)	LTR87|LTR|ERVL?	87502	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.007874	0.494118	
chunk0030_357_1	chr10	118645392	118645680	+	0	NA	Intergenic	L1PB|LINE|L1	-49888	NM_004248	2834	Hs.248119	NM_004248	ENSG00000119973	PRLHR	GPR10|GR3|PrRPR	prolactin releasing hormone receptor	protein-coding	0.003472	0.391003	
chunk0010_169_1	chr1	115676651	115677103	+	0	NA	intron (NM_138959, intron 4 of 7)	intron (NM_138959, intron 4 of 7)	34248	NM_001172412	81839	Hs.515130	NM_138959	ENSG00000173218	VANGL1	KITENIN|LPP2|STB2|STBM2	VANGL planar cell polarity protein 1	protein-coding	0.013274	0.498896	
chunk0055_66_1	chr13	52729057	52729623	+	0	NA	intron (NM_007015, intron 3 of 6)	MER20B|DNA|hAT-Charlie	10472	NM_007015	11061	Hs.421391	NM_007015	ENSG00000136110	CNMD	BRICD3|CHM-I|CHM1|LECT1|MYETS1	chondromodulin	protein-coding	0.003534	0.395062	251(AAGAACTAATTGTCCC,-,0.00),252(AGAACTAATTGTCCCG,+,0.00)
chunk0121_125_1	chr3	17553095	17553492	+	0	NA	intron (NM_014744, intron 2 of 21)	L1MC5a|LINE|L1	146727	NM_001134381	9779	Hs.475629	NM_014744	ENSG00000131374	TBC1D5	-	TBC1 domain family member 5	protein-coding	0.002519	0.379397	
chunk0178_119_1	chr7	31271901	31272597	+	0	NA	Intergenic	L2a|LINE|L2	68675	NM_022728	63974	Hs.45152	NM_022728	ENSG00000164600	NEUROD6	Atoh2|MATH2|Math-2|NEX1M|Nex1|bHLHa2	neuronal differentiation 6	protein-coding	0.001437	0.390244	
chunk0044_374_1	chr12	39826900	39827385	+	0	NA	intron (NM_052885, intron 7 of 9)	intron (NM_052885, intron 7 of 9)	200972	NM_001031748	283461	Hs.648205	NM_001031748	ENSG00000180116	C12orf40	HEL-206|HEL-S-94	chromosome 12 open reading frame 40	protein-coding	0.006186	0.409465	
chunk0069_299_1	chr15	65524721	65524998	+	0	NA	Intergenic	MER49|LTR|ERV1	-5630	NM_016395	51495	Hs.512973	NM_016395	ENSG00000074696	HACD3	B-IND1|BIND1|HSPC121|PTPLAD1	3-hydroxyacyl-CoA dehydratase 3	protein-coding	0.007220	0.402878	
chunk0188_169_1	chr8	10789209	10789533	+	0	NA	intron (NM_001284356, intron 5 of 5)	L1MA9|LINE|L1	36072	NR_031711	100302166		NR_031711	ENSG00000283210	MIR1322	MIRN1322|hsa-mir-1322	microRNA 1322	ncRNA	0.009259	0.424615	259(GAGTACACAGTGTGTT,-,0.00),260(AGTACACAGTGTGTTC,+,0.00),261(GTACACAGTGTGTTCT,-,0.00),262(TACACAGTGTGTTCTT,+,0.00)
chunk0041_144_1	chr11	125422739	125423301	+	0	NA	intron (NM_022062, intron 10 of 12)	intron (NM_022062, intron 10 of 12)	-72194	NM_001301851	403312	Hs.450611	NM_203452		LOC403312	-	putative uncharacterized protein MGC39545	protein-coding	0.017794	0.401421	
chunk0013_321_1	chr1	171477834	171478192	+	0	NA	Intergenic	LTR26B|LTR|ERV1	-7514	NM_015172	23215	Hs.494614	NM_015172	ENSG00000117523	PRRC2C	BAT2-iso|BAT2D1|BAT2L2|XTP2	proline rich coiled-coil 2C	protein-coding	0.002793	0.437326	
chunk0121_283_1	chr3	23576469	23576951	+	0	NA	intron (NM_152653, intron 5 of 5)	intron (NM_152653, intron 5 of 5)	-229183	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.004149	0.397516	
chunk0026_2_1	chr10	60369040	60370032	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	20340	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.007056	0.335347	
chunk0208_261_1	chrX	21383481	21383845	+	0	NA	intron (NM_014927, intron 1 of 21)	intron (NM_014927, intron 1 of 21)	9245	NM_001168648	22866	Hs.555917	NM_014927	ENSG00000149970	CNKSR2	CNK2|KSR2|MAGUIN|MRXSHG	connector enhancer of kinase suppressor of Ras 2	protein-coding	0.005495	0.290411	
chunk0024_16_1	chr10	32955098	32955350	+	0	NA	intron (NM_002211, intron 1 of 15)	intron (NM_002211, intron 1 of 15)	2670	NM_133376	3688	Hs.643813	NM_002211	ENSG00000150093	ITGB1	CD29|FNRB|GPIIA|MDF2|MSK12|VLA-BETA|VLAB	integrin subunit beta 1	protein-coding	0.011905	0.411067	
chunk0114_194_1	chr21	15192155	15192544	+	0	NA	Intergenic	Intergenic	-127544	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.007712	0.417949	
chunk0078_122_1	chr17	2960269	2960825	+	0	NA	intron (NM_001100398, intron 4 of 23)	intron (NM_001100398, intron 4 of 23)	5348	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.025180	0.590664	
chunk0102_330_1	chr2	151849732	151850011	+	0	NA	intron (NM_001005746, intron 12 of 13)	MER58A|DNA|hAT-Charlie	-21376	NM_012097	26225	Hs.470233	NM_012097	ENSG00000162980	ARL5A	ARFLP5|ARL5	ADP ribosylation factor like GTPase 5A	protein-coding	0.010753	0.435714	
chunk0065_34_1	chr15	20672512	20673212	+	0	NA	intron (NR_027992, intron 1 of 2)	L2a|LINE|L2	83289	NR_027992	606	Hs.657985	NR_027992		NBEAP1	BCL8|BCL8A	neurobeachin pseudogene 1	pseudo	0.001429	0.335235	
chunk0039_44_1	chr11	96057239	96057994	+	0	NA	intron (NM_032427, intron 2 of 4)	intron (NM_032427, intron 2 of 4)	-133409	NM_016156	8898	Hs.181326	NM_016156	ENSG00000087053	MTMR2	CMT4B|CMT4B1	myotubularin related protein 2	protein-coding	0.009272	0.354497	454(GAGAACGAGGTGTTCC,-,0.00),455(AGAACGAGGTGTTCCA,+,0.00)
chunk0103_182_1	chr2	163324432	163324965	+	0	NA	Intergenic	Intergenic	411305	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.003752	0.350187	
chunk0081_348_1	chr17	47276729	47277070	+	0	NA	intron (NM_000212, intron 2 of 14)	intron (NM_000212, intron 2 of 14)	23057	NM_000212	3690	Hs.218040	NM_000212	ENSG00000259207	ITGB3	BDPLT16|BDPLT2|CD61|GP3A|GPIIIa|GT	integrin subunit beta 3	protein-coding	0.008798	0.479532	
chunk0112_449_1	chr20	48659814	48660200	+	0	NA	exon (NM_020820, exon 16 of 40)	exon (NM_020820, exon 16 of 40)	167876	NM_020820	57580	Hs.153310	NM_020820	ENSG00000124126	PREX1	P-REX1	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	protein-coding	0.020725	0.545220	
chunk0001_33_1	chr1	1400731	1401345	+	0	NA	TTS (NM_017971)	TTS (NM_017971)	1508	NR_015434	148413	Hs.741357	NR_015434	ENSG00000224870	MRPL20-AS1	-	MRPL20 antisense RNA 1	ncRNA	0.026059	0.596748	
chunk0010_419_1	chr1	119674773	119675105	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-27172	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.015060	0.429429	
chunk0095_315_1	chr2	20447481	20448083	+	0	NA	exon (NM_004040, exon 1 of 1)	exon (NM_004040, exon 1 of 1)	711	NM_004040	388	Hs.502876	NM_004040	ENSG00000143878	RHOB	ARH6|ARHB|MST081|MSTP081|RHOH6	ras homolog family member B	protein-coding	0.101329	0.645108	
chunk0173_437_1	chr6	151357865	151358552	+	0	NA	3' UTR (NM_144497, exon 3 of 3)	3' UTR (NM_144497, exon 3 of 3)	32677	NM_144497	9590	Hs.371240	NM_005100	ENSG00000131016	AKAP12	AKAP250|SSeCKS	A-kinase anchoring protein 12	protein-coding	0.010189	0.359012	
chunk0110_422_1	chr20	20694021	20694742	+	0	NA	intron (NM_020343, intron 1 of 39)	Tigger10|DNA|TcMar-Tigger	18242	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.004161	0.411357	
chunk0177_198_1	chr7	23759545	23760490	+	0	NA	intron (NM_001260505, intron 10 of 22)	intron (NM_001260505, intron 10 of 22)	49691	NM_032944	56164	Hs.309767	NM_031414	ENSG00000196335	STK31	SGK396|TDRD8	serine/threonine kinase 31	protein-coding	0.001058	0.369979	608(CAGAACTTCCTGTTTT,-,0.00),609(AGAACTTCCTGTTTTT,+,0.00)
chunk0051_114_1	chr12	115135798	115136215	+	0	NA	Intergenic	Intergenic	-451842	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.019185	0.521531	
chunk0094_300_1	chr2	8512730	8513053	+	0	NA	Intergenic	Intergenic	70901	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.012384	0.530864	
chunk0014_383_1	chr1	182712202	182712554	+	0	NA	Intergenic	Intergenic	-39446	NM_033345	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.002841	0.410765	192(AAACACATCTTGTTCC,-,0.00)
chunk0075_31_1	chr16	46930967	46931233	+	0	NA	3' UTR (NM_133443, exon 12 of 12)	3' UTR (NM_133443, exon 12 of 12)	42614	NM_005880	10294	Hs.368078	NM_005880	ENSG00000069345	DNAJA2	CPR3|DJ3|DJA2|DNAJ|DNJ3|HIRIP4|PRO3015|RDJ2	DnaJ heat shock protein family (Hsp40) member A2	protein-coding	0.018797	0.528090	
chunk0011_326_1	chr1	152047596	152048303	+	0	NA	Intergenic	Intergenic	-10914	NM_005620	6282	Hs.417004	NM_005620	ENSG00000163191	S100A11	HEL-S-43|MLN70|S100C	S100 calcium binding protein A11	protein-coding	0.018388	0.542373	398(ATCACAGTGTGTGCTG,+,0.00)
chunk0088_422_1	chr18	55057826	55058044	+	0	NA	Intergenic	Intergenic	66371	NR_110743	101927229	Hs.638474	NR_110743	ENSG00000267013	LINC01929	-	long intergenic non-protein coding RNA 1929	ncRNA	0.000000	0.296804	
chunk0061_368_1	chr14	64082874	64083284	+	0	NA	intron (NM_182914, intron 57 of 115)	intron (NM_182914, intron 57 of 115)	12046	NR_031677	100313830		NR_031677	ENSG00000221537	MIR548H1	MIR548H-1|MIRN548H1	microRNA 548h-1	ncRNA	0.014634	0.423358	224(TGGCACAGTGTGTTCC,-,0.00),225(GGCACAGTGTGTTCCT,+,0.00)
chunk0153_81_1	chr5	68093258	68094052	+	0	NA	Intergenic	Intergenic	-96221	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.006297	0.427673	426(TGGAACAGGTTGACCC,-,0.00),427(GGAACAGGTTGACCCA,+,0.00)
chunk0028_307_1	chr10	91688786	91689092	+	0	NA	Intergenic	L1PA16|LINE|L1	-55838	NM_005398	5507	Hs.303090	NM_005398	ENSG00000119938	PPP1R3C	PPP1R5|PTG	protein phosphatase 1 regulatory subunit 3C	protein-coding	0.013072	0.397394	194(ATGTACACCATGTACT,-,0.00),195(TGTACACCATGTACTA,+,0.00)
chunk0175_94_1	chr7	2802644	2802967	+	0	NA	intron (NM_001293092, intron 1 of 2)	intron (NM_001293092, intron 1 of 2)	12454	NM_001282441	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.034056	0.478395	
chunk0024_41_1	chr10	33602257	33602833	+	0	NA	Intergenic	L1MA10|LINE|L1	170135	NR_038932	100505583	Hs.568804	NR_038932	ENSG00000261683	LINC00838	-	long intergenic non-protein coding RNA 838	ncRNA	0.006944	0.299827	
chunk0164_331_1	chr6	25253372	25253732	+	0	NA	intron (NR_110863, intron 2 of 2)	intron (NR_110863, intron 2 of 2)	7855	NR_110862	101928663	Hs.561600	NR_110862		LOC101928663	-	uncharacterized LOC101928663	ncRNA	0.011111	0.387812	
chunk0085_36_1	chr18	597068	597384	+	0	NA	intron (NM_014410, intron 1 of 8)	CpG	228	NM_001289036	27098	Hs.732341	NM_014410	ENSG00000079101	CLUL1	RA337M	clusterin like 1	protein-coding	0.053797	0.583596	
chunk0079_336_1	chr17	17612115	17612386	+	0	NA	Intergenic	Intergenic	-20547	NM_148172	10400	Hs.714193	NM_007169	ENSG00000133027	PEMT	PEAMT|PEMPT|PEMT2|PLMT|PNMT	phosphatidylethanolamine N-methyltransferase	protein-coding	0.003690	0.547794	167(AGGGTCAGTGTGTTCT,-,0.00),168(GGGTCAGTGTGTTCTG,+,0.00)
chunk0178_469_1	chr7	42283476	42283832	+	0	NA	Intergenic	Intergenic	-46635	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.002809	0.459384	
chunk0067_357_1	chr15	48554945	48555418	+	0	NA	intron (NM_000138, intron 6 of 65)	intron (NM_000138, intron 6 of 65)	90607	NM_000138	2200	Hs.591133	NM_000138	ENSG00000166147	FBN1	ACMICD|ECTOL1|FBN|GPHYSD2|MASS|MFLS|MFS1|OCTD|SGS|SSKS|WMS|WMS2	fibrillin 1	protein-coding	0.016913	0.415612	
chunk0188_419_1	chr8	18954694	18955276	+	0	NA	intron (NM_015310, intron 1 of 15)	intron (NM_015310, intron 1 of 15)	58701	NM_015310	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.013746	0.456261	309(GAGTACACAATGTGCT,-,0.00),310(AGTACACAATGTGCTA,+,0.00)
chunk0002_396_1	chr1	27155040	27155240	+	0	NA	promoter-TSS (NR_046474)	promoter-TSS (NR_046474)	-10	NM_003047	6548	Hs.469116	NM_003047	ENSG00000090020	SLC9A1	APNH|LIKNS|NHE-1|NHE1|PPP1R143	solute carrier family 9 member A1	protein-coding	0.105000	0.721393	
chunk0142_77_1	chr4	93876802	93877333	+	0	NA	Intergenic	Intergenic	48140	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.001883	0.327068	
chunk0184_448_1	chr7	123327705	123327904	+	0	NA	Intergenic	Intergenic	-127833	NM_022444	6561	Hs.489849	NM_022444	ENSG00000081800	SLC13A1	NAS1|NaSi-1	solute carrier family 13 member 1	protein-coding	0.005025	0.425000	41(AAGAACACACAGTCCA,-,0.00),42(AGAACACACAGTCCAA,+,0.00)
chunk0104_43_1	chr2	171142173	171142676	+	0	NA	intron (NM_001136554, intron 1 of 20)	L1MEg|LINE|L1	18476	NM_012290	9874	Hs.744917	NM_012290	ENSG00000198586	TLK1	PKU-beta	tousled like kinase 1	protein-coding	0.005964	0.305556	
chunk0198_329_1	chr8	139988967	139989459	+	0	NA	intron (NM_001160372, intron 18 of 22)	intron (NM_001160372, intron 18 of 22)	-286157	NR_104210	51305	Hs.493037	NM_001282534	ENSG00000169427	KCNK9	K2p9.1|KT3.2|TASK-3|TASK3	potassium two pore domain channel subfamily K member 9	protein-coding	0.026423	0.539554	
chunk0122_351_1	chr3	37411762	37411961	+	0	NA	intron (NM_178339, intron 2 of 5)	L1MA3|LINE|L1	723	NM_001302832	339883	Hs.475945	NM_178339	ENSG00000198590	C3orf35	APRG1	chromosome 3 open reading frame 35	protein-coding	0.005025	0.525000	
chunk0186_76_1	chr7	137209345	137209845	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-45254	NR_046103	349160	Hs.660713	NR_046103	ENSG00000234352	LOC349160	-	uncharacterized LOC349160	ncRNA	0.010000	0.385230	
chunk0086_236_1	chr18	22824586	22825086	+	0	NA	Intergenic	Intergenic	-37999	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.000000	0.313373	
chunk0038_414_1	chr11	94153203	94153679	+	0	NA	intron (NM_015368, intron 1 of 4)	intron (NM_015368, intron 1 of 4)	24513	NM_015368	24145	Hs.591976	NM_015368	ENSG00000110218	PANX1	MRS1|PX1|UNQ2529	pannexin 1	protein-coding	0.006303	0.431866	
chunk0016_293_1	chr1	201114551	201114779	+	0	NA	3' UTR (NM_001270601, exon 1 of 1)	3' UTR (NM_001270601, exon 1 of 1)	707	NM_001270601	647219	Hs.143949	NM_001270601	ENSG00000232237	ASCL5	bHLHa47	achaete-scute family bHLH transcription factor 5	protein-coding	0.096491	0.694323	
chunk0071_180_1	chr15	83447236	83447764	+	0	NA	non-coding (NR_125370, exon 1 of 10)	non-coding (NR_125370, exon 1 of 10)	272	NR_125370	6457	Hs.270055	NM_003027	ENSG00000140600	SH3GL3	CNSA3|EEN-B2|HsT19371|SH3D2C|SH3P13	SH3 domain containing GRB2 like 3, endophilin A3	protein-coding	0.102273	0.712665	
chunk0139_17_1	chr4	48126983	48127674	+	0	NA	intron (NM_003328, intron 1 of 14)	intron (NM_003328, intron 1 of 14)	6928	NM_003328	7294	Hs.479669	NM_003328	ENSG00000074966	TXK	BTKL|PSCTK5|PTK4|RLK|TKL	TXK tyrosine kinase	protein-coding	0.007236	0.424855	
chunk0082_105_1	chr17	54780091	54780800	+	0	NA	Intergenic	Intergenic	-120246	NM_005486	10040	Hs.153504	NM_005486	ENSG00000141198	TOM1L1	SRCASM	target of myb1 like 1 membrane trafficking protein	protein-coding	0.004231	0.394366	505(TGGCACAATATGTCCT,-,0.00),506(GGCACAATATGTCCTT,+,0.00)
chunk0037_18_1	chr11	69122945	69123189	+	0	NA	Intergenic	Intergenic	39891	NR_036122	100422846		NR_036122	ENSG00000265539	MIR3164	-	microRNA 3164	ncRNA	0.020492	0.571429	226(CAGAACACTCTGATCT,-,0.00),227(AGAACACTCTGATCTG,+,0.00)
chunk0021_94_1	chr10	2672447	2672646	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	-357472	NR_038884	399708	Hs.521270	NR_038884		LINC00701	-	long intergenic non-protein coding RNA 701	ncRNA	0.020101	0.545000	
chunk0056_48_1	chr13	77558804	77559046	+	0	NA	intron (NM_003843, intron 3 of 31)	intron (NM_003843, intron 3 of 31)	23251	NM_144777	8796	Hs.534699	NM_003843	ENSG00000136155	SCEL	-	sciellin	protein-coding	0.004132	0.345679	
chunk0039_227_1	chr11	101663214	101663419	+	0	NA	Intergenic	L1MA2|LINE|L1	-79388	NM_004621	7225	Hs.159003	NM_004621	ENSG00000137672	TRPC6	FSGS2|TRP6	transient receptor potential cation channel subfamily C member 6	protein-coding	0.000000	0.262136	
chunk0061_431_1	chr14	65354834	65355120	+	0	NA	Intergenic	Intergenic	-19794	NR_039857	100616176		NR_039857	ENSG00000266740	MIR4708	mir-4708	microRNA 4708	ncRNA	0.010490	0.519164	
chunk0151_29_1	chr5	41771375	41772251	+	0	NA	intron (NM_000436, intron 13 of 16)	intron (NM_000436, intron 13 of 16)	-98217	NR_046635	100874002	Hs.375537	NR_046635	ENSG00000248668	OXCT1-AS1	-	OXCT1 antisense RNA 1	ncRNA	0.003425	0.345496	
chunk0005_441_1	chr1	63376233	63376490	+	0	NA	intron (NM_013339, intron 2 of 14)	Tigger3a|DNA|TcMar-Tigger	8771	NM_013339	29929	Hs.258501	NM_013339	ENSG00000088035	ALG6	CDG1C	ALG6 alpha-1,3-glucosyltransferase	protein-coding	0.007782	0.329457	
chunk0085_425_1	chr18	10622801	10623034	+	0	NA	Intergenic	Intergenic	-39016	NR_110777	101927410	Hs.436902	NR_110777	ENSG00000260779	LOC101927410	-	uncharacterized LOC101927410	ncRNA	0.004292	0.384615	
chunk0128_343_1	chr3	112406493	112406956	+	0	NA	Intergenic	L1MA9|LINE|L1	73655	NM_001004196	4345	Hs.79015	NM_005944	ENSG00000091972	CD200	MOX1|MOX2|MRC|OX-2	CD200 molecule	protein-coding	0.002160	0.340517	
chunk0117_144_1	chr22	19563069	19563454	+	0	NA	Intergenic	L1ME1|LINE|L1	3578	NR_024381	150185	Hs.719752	NR_024381		LINC00895	-	long intergenic non-protein coding RNA 895	ncRNA	0.010390	0.463731	
chunk0028_86_1	chr10	83881755	83882229	+	0	NA	Intergenic	Intergenic	-257437	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.002110	0.410526	
chunk0064_50_1	chr14	89835051	89835383	+	0	NA	intron (NM_145231, intron 5 of 5)	L2|LINE|L2	119340	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.006024	0.438438	
chunk0182_48_1	chr7	91850490	91850989	+	0	NA	Intergenic	L1MEg|LINE|L1	29981	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.002004	0.350000	
chunk0140_290_1	chr4	72444092	72444329	+	0	NA	intron (NM_014243, intron 3 of 21)	intron (NM_014243, intron 3 of 21)	124589	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.004219	0.382353	87(ATGCACAGACAGTTCC,-,0.00),88(TGCACAGACAGTTCCT,+,0.00)
chunk0024_33_1	chr10	33314901	33315158	+	0	NA	intron (NM_001244972, intron 2 of 16)	intron (NM_001244972, intron 2 of 16)	19876	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.015564	0.403101	
chunk0164_411_1	chr6	26761511	26761940	+	0	NA	Intergenic	(CATG)n|Simple_repeat|Simple_repeat	-101973	NM_001242798	79692	Hs.126280	NM_024639	ENSG00000181315	ZNF322	HCG12|ZNF322A|ZNF388|ZNF489	zinc finger protein 322	protein-coding	0.025641	0.404651	
chunk0204_351_1	chr9	101555918	101556488	+	0	NA	intron (NM_019592, intron 15 of 19)	L1M5|LINE|L1	22354	NM_019592	56254	Hs.729085	NM_019592	ENSG00000155827	RNF20	BRE1|BRE1A|hBRE1	ring finger protein 20	protein-coding	0.001754	0.301226	168(AAAGACACTATGTTCT,-,0.00),169(AAGACACTATGTTCTT,+,0.00)
chunk0200_227_1	chr9	20684565	20684773	+	0	NA	promoter-TSS (NR_121601)	promoter-TSS (NR_121601)	81	NR_121601	101929548	Hs.668302	NR_121601	ENSG00000227071	FOCAD-AS1	-	FOCAD antisense RNA 1	ncRNA	0.062500	0.626794	
chunk0102_160_1	chr2	147261876	147262241	+	0	NA	Intergenic	MIRc|SINE|MIR	-582459	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.000000	0.344262	
chunk0183_245_1	chr7	107136749	107136948	+	0	NA	intron (NM_002736, intron 4 of 10)	L1MC1|LINE|L1	-32113	NM_001244262	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.000000	0.385000	
chunk0186_115_1	chr7	138049606	138050136	+	0	NA	Intergenic	Intergenic	-26561	NM_005989	6718	Hs.201667	NM_005989	ENSG00000122787	AKR1D1	3o5bred|CBAS2|SRD5B1	aldo-keto reductase family 1 member D1	protein-coding	0.000000	0.340866	
chunk0035_275_1	chr11	46574998	46575197	+	0	NA	intron (NM_001300731, intron 1 of 16)	intron (NM_001300731, intron 1 of 16)	16267	NM_017749	55626	Hs.654644	NM_017749	ENSG00000110497	AMBRA1	DCAF3|WDR94	autophagy and beclin 1 regulator 1	protein-coding	0.000000	0.375000	
chunk0075_43_1	chr16	47402154	47402550	+	0	NA	intron (NM_030790, intron 6 of 17)	intron (NM_030790, intron 6 of 17)	58922	NM_030790	81533	Hs.42217	NM_030790	ENSG00000129636	ITFG1	2310047C21Rik|CDA08|LNKN-1|TIP	integrin alpha FG-GAP repeat containing 1	protein-coding	0.005051	0.345088	
chunk0089_103_1	chr18	58420820	58421145	+	0	NA	Intergenic	Intergenic	-30092	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.012308	0.460123	
chunk0052_115_1	chr13	23066290	23066565	+	0	NA	Intergenic	L2c|LINE|L2	-114494	NM_000231	6445	Hs.37167	NM_000231	ENSG00000102683	SGCG	35DAG|A4|DAGA4|DMDA|DMDA1|LGMD2C|LGMDR5|MAM|SCARMD2|SCG3|gamma-SG	sarcoglycan gamma	protein-coding	0.003636	0.402174	
chunk0072_70_1	chr15	90458630	90459176	+	0	NA	intron (NM_003870, intron 15 of 37)	intron (NM_003870, intron 15 of 37)	70662	NM_003870	8826	Hs.430551	NM_003870	ENSG00000140575	IQGAP1	HUMORFA01|SAR1|p195	IQ motif containing GTPase activating protein 1	protein-coding	0.007326	0.389397	
chunk0012_230_1	chr1	160325270	160325668	+	0	NA	intron (NM_001098398, intron 7 of 32)	L2a|LINE|L2	8204	NR_002190	474338	Hs.621179	NR_002190		SUMO1P3	-	SUMO1 pseudogene 3	pseudo	0.010050	0.441103	
chunk0033_60_1	chr11	13477776	13478452	+	0	NA	Intergenic	Intergenic	-14817	NM_001297741	84280	Hs.332382	NM_032320	ENSG00000148925	BTBD10	GMRP-1|GMRP1	BTB domain containing 10	protein-coding	0.004438	0.345643	
chunk0103_221_1	chr2	164318412	164318897	+	0	NA	Intergenic	L1MC3|LINE|L1	249896	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.004124	0.339506	222(CAGTACACAGTGTTCC,-,0.00),223(AGTACACAGTGTTCCC,+,0.00)
chunk0150_145_1	chr5	33680834	33681146	+	0	NA	intron (NM_030955, intron 5 of 23)	intron (NM_030955, intron 5 of 23)	211029	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.003205	0.332268	
chunk0079_416_1	chr17	19736828	19737256	+	0	NA	TTS (NM_001135168)	TTS (NM_001135168)	8417	NM_001135168	218	Hs.531682	NM_000691	ENSG00000108602	ALDH3A1	ALDH3|ALDHIII	aldehyde dehydrogenase 3 family member A1	protein-coding	0.011682	0.529138	
chunk0163_347_1	chr6	15453207	15454086	+	0	NA	intron (NM_001267040, intron 4 of 17)	L1MC4|LINE|L1	204791	NM_001267040	3720	Hs.269059	NM_004973	ENSG00000008083	JARID2	JMJ	jumonji and AT-rich interaction domain containing 2	protein-coding	0.011377	0.431818	614(AGGCTCATGGTGTACT,-,0.00),615(GGCTCATGGTGTACTT,+,0.00)
chunk0053_5_1	chr13	26173871	26174268	+	0	NA	intron (NM_183045, intron 5 of 5)	intron (NM_183045, intron 5 of 5)	47688	NM_183044	6049	Hs.136885	NM_005977	ENSG00000127870	RNF6	-	ring finger protein 6	protein-coding	0.012594	0.419598	
chunk0054_420_1	chr13	50941296	50941495	+	0	NA	intron (NM_001142279, intron 5 of 9)	intron (NM_001142279, intron 5 of 9)	-30683	NR_046552	100874255	Hs.741501	NR_046552		RNASEH2B-AS1	-	RNASEH2B antisense RNA 1	ncRNA	0.010050	0.530000	22(GGAGACAGCATGTGCT,-,0.00),23(GAGACAGCATGTGCTG,+,0.00),63(TGGCTCAGTCTGTGCT,-,0.00),64(GGCTCAGTCTGTGCTC,+,0.00)
chunk0174_441_1	chr6	166194715	166195077	+	0	NA	Intergenic	Intergenic	-26227	NM_003181	6862	Hs.389457	NM_003181	ENSG00000164458	TBXT	SAVA|T|TFT	T-box transcription factor T	protein-coding	0.008287	0.515152	172(CAGTGCACAGTGTCCC,-,0.00),173(AGTGCACAGTGTCCCC,+,0.00)
chunk0139_93_1	chr4	49576340	49577061	+	0	NA	Intergenic	MSTA|LTR|ERVL-MaLR	590058	NM_001286791	80157	Hs.479703	NM_025087	ENSG00000109182	CWH43	CWH43-C|PGAP2IP	cell wall biogenesis 43 C-terminal homolog	protein-coding	0.004161	0.472299	
chunk0006_55_1	chr1	64549809	64550325	+	0	NA	intron (NM_001293274, intron 1 of 25)	intron (NM_001293274, intron 1 of 25)	-29780	NR_039957	100616338		NR_039957	ENSG00000264470	MIR4794	-	microRNA 4794	ncRNA	0.011628	0.394584	
chunk0099_394_1	chr2	101823001	101823403	+	0	NA	intron (NM_145686, intron 3 of 30)	intron (NM_145686, intron 3 of 30)	125126	NM_001242559	9448	Hs.701013	NM_004834	ENSG00000071054	MAP4K4	FLH21957|HEL-S-31|HGK|MEKKK4|NIK	mitogen-activated protein kinase kinase kinase kinase 4	protein-coding	0.012438	0.441687	
chunk0194_2_1	chr8	81365048	81365662	+	0	NA	Intergenic	MIR|SINE|MIR	82129	NM_002677	5375	Hs.571512	NM_002677	ENSG00000147588	PMP2	CMT1G|FABP8|M-FABP|MP2|P2	peripheral myelin protein 2	protein-coding	0.000000	0.300813	
chunk0065_392_1	chr14	104746760	104747444	+	0	NA	3' UTR (NM_199165, exon 13 of 13)	3' UTR (NM_199165, exon 13 of 13)	-6031	NM_006427	10572	Hs.112058	NM_006427	ENSG00000184990	SIVA1	CD27BP|SIVA|Siva-1|Siva-2	SIVA1 apoptosis inducing factor	protein-coding	0.014620	0.421898	
chunk0001_41_1	chr1	1692684	1693287	+	0	NA	promoter-TSS (NM_001110781)	promoter-TSS (NM_001110781)	-181	NM_001290264	728661	Hs.655255	NM_001110781	ENSG00000189339	SLC35E2B	SLC35E2	solute carrier family 35 member E2B	protein-coding	0.112769	0.706954	
chunk0117_308_1	chr22	24571804	24572539	+	0	NA	non-coding (NR_103819, exon 3 of 3)	non-coding (NR_103819, exon 3 of 3)	-11579	NM_013430	2678	Hs.595809	NM_005265	ENSG00000100031	GGT1	CD224|D22S672|D22S732|GGT|GGT 1|GGTD|GTG	gamma-glutamyltransferase 1	protein-coding	0.014966	0.449728	359(AAGGACTTTGTGTTCA,-,0.00),360(AGGACTTTGTGTTCAT,+,0.00)
chunk0212_85_1	chrY	11730818	11731041	+	0	NA	Intergenic	(GAATG)n|Satellite|Satellite	690661	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.013453	0.352679	
chunk0183_367_1	chr7	109246724	109247103	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-362326	NM_001024607	154907	Hs.276325	NM_001024607		C7orf66	-	chromosome 7 open reading frame 66	protein-coding	0.013193	0.392105	
chunk0183_376_1	chr7	109550143	109550549	+	0	NA	Intergenic	Intergenic	409867	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.004926	0.302211	
chunk0131_109_1	chr3	143945004	143945706	+	0	NA	Intergenic	Intergenic	-26443	NM_173552	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.004274	0.339972	
chunk0069_446_1	chr15	68601846	68602107	+	0	NA	intron (NM_006091, intron 1 of 11)	MLT1A1|LTR|ERVL-MaLR	-14564	NM_001190456	10391	Hs.551213	NM_006091	ENSG00000103647	CORO2B	CLIPINC	coronin 2B	protein-coding	0.015326	0.465649	100(AGGATCACTGTGTCCC,-,0.00),101(GGATCACTGTGTCCCA,+,0.00)
chunk0043_133_1	chr12	15834595	15834826	+	0	NA	Intergenic	Intergenic	-45134	NM_004447	2059	Hs.591160	NM_004447	ENSG00000151491	EPS8	DFNB102	epidermal growth factor receptor pathway substrate 8	protein-coding	0.004329	0.357759	
chunk0117_229_1	chr22	22783427	22783941	+	0	NA	Intergenic	Intergenic	-39092	NR_030755	723778		NR_030755	ENSG00000284049	MIR650	MIRN650|hsa-mir-650	microRNA 650	ncRNA	0.007782	0.357282	248(GAGGACTTTGTGTTCA,-,0.00),249(AGGACTTTGTGTTCAA,+,0.00)
chunk0173_317_1	chr6	148629590	148630067	+	0	NA	Intergenic	Intergenic	-117307	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.006289	0.384937	
chunk0036_59_1	chr11	59273361	59273761	+	0	NA	Intergenic	LTR77|LTR|ERV1	-60540	NM_001039396	219972	Hs.744920	NM_001039396	ENSG00000197629	MPEG1	MPG1|MPS1|Mpg-1|P-2	macrophage expressed 1	protein-coding	0.007500	0.463840	
chunk0061_311_1	chr14	62207028	62207351	+	0	NA	Intergenic	MSTD-int|LTR|ERVL-MaLR	-67216	NR_104063	101954204	Hs.607093	NR_104063	ENSG00000259142	LINC00644	-	long intergenic non-protein coding RNA 644	ncRNA	0.003096	0.506173	
chunk0121_43_1	chr3	15432113	15432480	+	0	NA	intron (NM_033083, intron 3 of 5)	intron (NM_033083, intron 3 of 5)	4739	NM_033083	85403	Hs.716733	NM_033083	ENSG00000144597	EAF1	-	ELL associated factor 1	protein-coding	0.002725	0.347826	
chunk0151_242_1	chr5	51268573	51269142	+	0	NA	Intergenic	Intergenic	-114267	NM_002202	3670	Hs.505	NM_002202	ENSG00000016082	ISL1	ISLET1|Isl-1	ISL LIM homeobox 1	protein-coding	0.003515	0.310526	
chunk0189_147_1	chr8	23011314	23011518	+	0	NA	intron (NM_015178, intron 7 of 9)	(TTTTCTT)n|Simple_repeat|Simple_repeat	11837	NM_015178	23221	Hs.372688	NM_015178	ENSG00000008853	RHOBTB2	DBC2|EIEE64	Rho related BTB domain containing 2	protein-coding	0.009804	0.414634	
chunk0172_95_1	chr6	134676636	134676921	+	0	NA	Intergenic	Intergenic	-136773	NR_125856	101928304	Hs.555076	NR_125855		LOC101928304	-	uncharacterized LOC101928304	ncRNA	0.003509	0.395105	201(TGGTACAGAATGTTCT,-,0.00),202(GGTACAGAATGTTCTC,+,0.00)
chunk0009_452_1	chr1	111592965	111593582	+	0	NA	Intergenic	Intergenic	15045	NR_034126	100129269	Hs.689728	NR_034126		LINC01160	-	long intergenic non-protein coding RNA 1160	ncRNA	0.011345	0.491909	
chunk0201_160_1	chr9	36029631	36030077	+	0	NA	Intergenic	Charlie15b|DNA|hAT-Charlie	-7059	NM_001316348	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.004484	0.340045	
chunk0006_184_1	chr1	67389865	67390100	+	0	NA	intron (NR_047584, intron 15 of 16)	intron (NR_047584, intron 15 of 16)	40458	NM_001018067	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.004255	0.419492	
chunk0067_186_1	chr15	44579969	44580503	+	0	NA	intron (NM_025137, intron 30 of 39)	Tigger3c|DNA|TcMar-Tigger	43168	NM_001284335	8669	Hs.404056	NM_003758	ENSG00000104131	EIF3J	EIF3S1|eIF3-alpha|eIF3-p35	eukaryotic translation initiation factor 3 subunit J	protein-coding	0.005618	0.327103	
chunk0038_272_1	chr11	89633296	89633726	+	0	NA	Intergenic	L1ME3A|LINE|L1	-25786	NM_153696	219595	Hs.645352	NM_153696		FOLH1B	FOLH2|FOLHP|GCP3|GCPIII|PSM|PSMA-LIKE|PSMAL	folate hydrolase 1B	protein-coding	0.000000	0.401392	
chunk0027_162_1	chr10	74851847	74852687	+	0	NA	intron (NM_001256468, intron 3 of 17)	intron (NM_001256468, intron 3 of 17)	25854	NM_001256468	23522	Hs.35758	NM_012330	ENSG00000156650	KAT6B	GTPTS|MORF|MOZ2|MYST4|ZC2HC6B|qkf|querkopf	lysine acetyltransferase 6B	protein-coding	0.003571	0.375743	783(CATGACAGCGTGTTCC,-,0.00),784(ATGACAGCGTGTTCCA,+,0.00)
chunk0081_104_1	chr17	39817732	39818433	+	0	NA	intron (NM_001257408, intron 2 of 6)	Tigger3a|DNA|TcMar-Tigger	-39857	NM_001284516	22806	Hs.371680	NM_012481	ENSG00000161405	IKZF3	AIO|AIOLOS|ZNFN1A3	IKAROS family zinc finger 3	protein-coding	0.004280	0.341880	
chunk0004_94_1	chr1	43838496	43838965	+	0	NA	TTS (NR_106727)	TTS (NR_106727)	108	NR_106727	102464830		NR_106727	ENSG00000283477	MIR6079	hsa-mir-6079	microRNA 6079	ncRNA	0.004264	0.482979	29(TGGCACAGCCTGTTTC,-,0.00),30(GGCACAGCCTGTTTCT,+,0.00)
chunk0183_80_1	chr7	104776601	104776842	+	0	NA	intron (NM_199000, intron 2 of 2)	intron (NM_199000, intron 2 of 2)	27371	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.008299	0.409091	
chunk0088_297_1	chr18	49900222	49901273	+	0	NA	intron (NM_001080467, intron 21 of 39)	intron (NM_001080467, intron 21 of 39)	86724	NR_003003	677769		NR_003003	ENSG00000267322	SCARNA17	U91	small Cajal body-specific RNA 17	ncRNA	0.008563	0.496198	770(AGGGACTTGATGTCCC,-,0.00),771(GGGACTTGATGTCCCT,+,0.00)
chunk0151_320_1	chr5	53569272	53569590	+	0	NA	intron (NM_002495, intron 1 of 4)	intron (NM_002495, intron 1 of 4)	8796	NM_002495	4724	Hs.528222	NM_002495	ENSG00000164258	NDUFS4	AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1	NADH:ubiquinone oxidoreductase subunit S4	protein-coding	0.000000	0.300940	
chunk0190_355_1	chr8	39675887	39676176	+	0	NA	intron (NM_014237, intron 14 of 19)	L1P2|LINE|L1	91463	NM_014237	8749	Hs.127930	NM_014237	ENSG00000168619	ADAM18	ADAM27|tMDCIII	ADAM metallopeptidase domain 18	protein-coding	0.003460	0.541379	
chunk0111_85_1	chr20	23315161	23315737	+	0	NA	Intergenic	Intergenic	-35287	NM_013248	29107	Hs.516933	NM_013248	ENSG00000132661	NXT1	MTR2|P15	nuclear transport factor 2 like export factor 1	protein-coding	0.019097	0.490468	
chunk0169_167_1	chr6	102068325	102068871	+	0	NA	3' UTR (NM_175768, exon 17 of 17)	3' UTR (NM_175768, exon 17 of 17)	669613	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.012821	0.427788	
chunk0062_35_1	chr14	67151131	67151590	+	0	NA	intron (NM_001024218, intron 17 of 21)	LTR37-int|LTR|ERV1	-38033	NM_173526	161142	Hs.412818	NM_173526	ENSG00000172717	FAM71D	C14orf54	family with sequence similarity 71 member D	protein-coding	0.006536	0.354348	
chunk0071_341_1	chr15	88042029	88042487	+	0	NA	intron (NM_002530, intron 13 of 18)	intron (NM_002530, intron 13 of 18)	-210472	NR_038229	283738	Hs.578429	NR_038229	ENSG00000260305	NTRK3-AS1	-	NTRK3 antisense RNA 1	ncRNA	0.013100	0.468410	
chunk0060_95_1	chr14	42732823	42733407	+	0	NA	Intergenic	L1ME3|LINE|L1	1125554	NM_152447	145581	Hs.136893	NM_152447	ENSG00000165379	LRFN5	C14orf146|FIGLER8|SALM5	leucine rich repeat and fibronectin type III domain containing 5	protein-coding	0.003425	0.287179	
chunk0108_407_1	chr2	237489921	237490300	+	0	NA	intron (NM_001042467, intron 1 of 14)	intron (NM_001042467, intron 1 of 14)	2891	NM_001281473	79083	Hs.102406	NM_024101	ENSG00000115648	MLPH	SLAC2-A	melanophilin	protein-coding	0.018470	0.555263	
chunk0091_393_1	chr19	16210104	16210583	+	0	NA	intron (NM_032493, intron 5 of 11)	L1ME1|LINE|L1	12489	NM_001130524	8907	Hs.71040	NM_032493	ENSG00000072958	AP1M1	AP47|CLAPM2|CLTNM|MU-1A	adaptor related protein complex 1 subunit mu 1	protein-coding	0.012526	0.381250	
chunk0207_299_1	chr9	133336168	133336442	+	0	NA	promoter-TSS (NM_001278942)	promoter-TSS (NM_001278942)	-95	NM_006753	6838	Hs.274430	NM_006753	ENSG00000148296	SURF6	RRP14	surfeit 6	protein-coding	0.127737	0.730909	
chunk0104_31_1	chr2	170766728	170767296	+	0	NA	intron (NR_110185, intron 1 of 5)	intron (NR_110185, intron 1 of 5)	-3670	NM_001290031	285141	Hs.443729	NM_001289947	ENSG00000204334	ERICH2	-	glutamate rich 2	protein-coding	0.010563	0.340949	
chunk0047_23_1	chr12	65699090	65699627	+	0	NA	Intergenic	Intergenic	-56986	NR_120433	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.003724	0.384758	
chunk0200_44_1	chr9	15213347	15213886	+	0	NA	intron (NM_001168341, intron 2 of 17)	intron (NM_001168341, intron 2 of 17)	36584	NM_001168342	158219	Hs.563630	NM_152574	ENSG00000155158	TTC39B	C9orf52	tetratricopeptide repeat domain 39B	protein-coding	0.009276	0.351852	
chunk0108_173_1	chr2	231786272	231786471	+	0	NA	promoter-TSS (NM_001282952)	promoter-TSS (NM_001282952)	-12	NM_001308381	64708	Hs.335061	NM_022730	ENSG00000144524	COPS7B	CSN7B|SGN7b	COP9 signalosome subunit 7B	protein-coding	0.115578	0.695000	
chunk0082_62_1	chr17	51376008	51376435	+	0	NA	Intergenic	Intergenic	39506	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.002342	0.476636	
chunk0156_62_1	chr5	103444365	103444919	+	0	NA	Intergenic	Intergenic	97343	NR_104670	102467212	Hs.641885	NR_104670	ENSG00000248757	LINC02115	-	long intergenic non-protein coding RNA 2115	ncRNA	0.007220	0.452252	
chunk0158_409_1	chr5	134845840	134846187	+	0	NA	promoter-TSS (NM_001135586)	promoter-TSS (NM_001135586)	45	NM_001300894	134553	Hs.708536	NM_152409	ENSG00000181904	C5orf24	-	chromosome 5 open reading frame 24	protein-coding	0.135447	0.738506	
chunk0187_191_1	chr7	151552370	151552845	+	0	NA	Intergenic	Intergenic	-32683	NM_005614	6009	Hs.283521	NM_005614	ENSG00000106615	RHEB	RHEB2	Ras homolog, mTORC1 binding	protein-coding	0.016842	0.539916	
chunk0158_254_1	chr5	130966890	130967585	+	0	NA	Intergenic	Intergenic	198111	NM_005340	3094	Hs.483305	NM_005340	ENSG00000169567	HINT1	HINT|NMAN|PKCI-1|PRKCNH1	histidine triad nucleotide binding protein 1	protein-coding	0.001439	0.344828	
chunk0098_432_1	chr2	81868357	81868573	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-401519	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.000000	0.405530	
chunk0142_92_1	chr4	94207215	94207971	+	0	NA	promoter-TSS (NR_045644)	promoter-TSS (NR_045644)	-15	NM_001128430	56916	Hs.410406	NM_020159	ENSG00000163104	SMARCAD1	ADERM|BASNS|ETL1|HEL1|HRZ	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	protein-coding	0.054233	0.451783	268(CAGAACAATCTGGCCC,-,0.00),269(AGAACAATCTGGCCCT,+,0.00)
chunk0074_171_1	chr16	23540245	23540675	+	0	NA	intron (NR_003501, intron 3 of 9)	L1ME4b|LINE|L1	16915	NM_001308211	124454	Hs.620541	NM_001083614	ENSG00000103356	EARS2	COXPD12|MSE1|gluRS|mtGlnRS	glutamyl-tRNA synthetase 2, mitochondrial	protein-coding	0.009302	0.412993	
chunk0198_99_1	chr8	130672933	130673452	+	0	NA	Intergenic	Intergenic	-229532	NM_001247996	50807	Hs.655552	NM_018482	ENSG00000153317	ASAP1	AMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14P	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	protein-coding	0.019268	0.519231	
chunk0154_134_1	chr5	79173704	79174182	+	0	NA	Intergenic	Intergenic	-62159	NM_152405	133746	Hs.482605	NM_152405	ENSG00000152409	JMY	WHAMM2|WHDC1L3	junction mediating and regulatory protein, p53 cofactor	protein-coding	0.006276	0.371608	
chunk0202_226_1	chr9	76401398	76401654	+	0	NA	Intergenic	Intergenic	2927	NR_026890	653162	Hs.655646	NR_026890		RPSAP9	LAMR1P9|RPSA_20_986	ribosomal protein SA pseudogene 9	pseudo	0.003906	0.311284	
chunk0033_43_1	chr11	13208535	13208974	+	0	NA	Intergenic	MIRb|SINE|MIR	-68973	NM_001297719	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.015945	0.454545	
chunk0186_32_1	chr7	136023170	136024006	+	0	NA	Intergenic	Intergenic	-46132	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.003589	0.408602	
chunk0073_275_1	chr16	12478815	12479107	+	0	NA	intron (NM_032167, intron 19 of 20)	intron (NM_032167, intron 19 of 20)	-241360	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.010274	0.498294	
chunk0100_170_1	chr2	109533112	109533362	+	0	NA	Intergenic	Intergenic	80969	NM_178584	151011	Hs.469615	NM_144710	ENSG00000186522	SEPTIN10	SEPT10	septin 10	protein-coding	0.012000	0.509960	161(AGGAACAGGCTGCGCT,-,0.00),162(GGAACAGGCTGCGCTC,+,0.00)
chunk0071_404_1	chr15	89590075	89590646	+	0	NA	intron (NM_001308025, intron 4 of 21)	Tigger9a|DNA|TcMar-Tigger	14773	NM_152259	90381	Hs.441708	NM_152259	ENSG00000140534	TICRR	C15orf42|SLD3|Treslin	TOPBP1 interacting checkpoint and replication regulator	protein-coding	0.010508	0.414336	337(TAGAACAGACTGTATC,-,0.00),338(AGAACAGACTGTATCT,+,0.00)
chunk0037_95_1	chr11	71968218	71968590	+	0	NA	intron (NR_024148, intron 3 of 8)	intron (NR_024148, intron 3 of 8)	-30508	NM_173044	10068	Hs.591967	NM_005699	ENSG00000137496	IL18BP	IL18BPa	interleukin 18 binding protein	protein-coding	0.010753	0.442359	
chunk0027_412_1	chr10	80610075	80610524	+	0	NA	intron (NM_207372, intron 6 of 6)	L2a|LINE|L2	69480	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.004454	0.486667	203(CTGGACAGAGTGTGCC,-,0.00),204(TGGACAGAGTGTGCCC,+,0.00)
chunk0168_224_1	chr6	86459002	86459416	+	0	NA	Intergenic	Intergenic	-478097	NM_000865	3354	Hs.1611	NM_000865	ENSG00000168830	HTR1E	5-HT1E	5-hydroxytryptamine receptor 1E	protein-coding	0.007246	0.354217	
chunk0127_429_1	chr3	102693140	102693637	+	0	NA	Intergenic	LTR29|LTR|ERV1	258373	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.002012	0.347390	
chunk0154_57_1	chr5	77264803	77265308	+	0	NA	intron (NM_001029853, intron 1 of 20)	intron (NM_001029853, intron 1 of 20)	54174	NM_003719	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.001980	0.411067	
chunk0155_385_1	chr5	98428876	98429075	+	0	NA	Intergenic	Intergenic	-340320	NM_001012761	285704	Hs.526902	NM_173670	ENSG00000174136	RGMB	DRAGON	repulsive guidance molecule BMP co-receptor b	protein-coding	0.005025	0.400000	6(ATAACATTATGTTCTG,+,0.00)
chunk0211_296_1	chrX	122896742	122896941	+	0	NA	Intergenic	Intergenic	-287402	NM_000828	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.000000	0.385000	
chunk0201_410_1	chr9	69502697	69503491	+	0	NA	intron (NM_001163, intron 2 of 12)	intron (NM_001163, intron 2 of 12)	169265	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.006297	0.368553	
chunk0193_127_1	chr8	74320481	74320683	+	0	NA	intron (NM_020647, intron 1 of 5)	CpG	745	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.084158	0.650246	
chunk0208_218_1	chrX	18654776	18655583	+	0	NA	intron (NM_000330, intron 3 of 5)	intron (NM_000330, intron 3 of 5)	16924	NM_000330	6247	Hs.715725	NM_000330	ENSG00000102104	RS1	RS|XLRS1	retinoschisin 1	protein-coding	0.006196	0.433168	
chunk0161_350_1	chr5	174534261	174534462	+	0	NA	Intergenic	LTR16C|LTR|ERVL	-190211	NM_002449	4488	Hs.89404	NM_002449	ENSG00000120149	MSX2	CRS2|FPP|HOX8|MSH|PFM|PFM1	msh homeobox 2	protein-coding	0.000000	0.490099	
chunk0050_92_1	chr12	101839042	101839241	+	0	NA	Intergenic	LTR41B|LTR|ERVL	-8274	NM_024312	79158	Hs.46850	NM_024312	ENSG00000111670	GNPTAB	GNPTA|ICD	N-acetylglucosamine-1-phosphate transferase subunits alpha and beta	protein-coding	0.005025	0.575000	42(GGGCACACAATGTACC,-,0.00),43(GGCACACAATGTACCC,+,0.00)
chunk0052_32_1	chr13	20590679	20590878	+	0	NA	intron (NM_006531, intron 4 of 25)	MER58A|DNA|hAT-Charlie	23709	NM_006531	8100	Hs.187376	NM_006531	ENSG00000032742	IFT88	D13S1056E|DAF19|TG737|TTC10|hTg737	intraflagellar transport 88	protein-coding	0.010050	0.395000	
chunk0197_443_1	chr8	127743111	127743440	+	0	NA	Intergenic	Intergenic	7206	NM_002467	4609	Hs.202453	NM_002467	ENSG00000136997	MYC	MRTL|MYCC|bHLHe39|c-Myc	MYC proto-oncogene, bHLH transcription factor	protein-coding	0.012158	0.487879	136(AGGAGAGAGTGTTCCT,+,0.00)
chunk0141_212_1	chr4	84609447	84609951	+	0	NA	intron (NM_001263, intron 3 of 12)	intron (NM_001263, intron 3 of 12)	26795	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.007937	0.376238	
chunk0120_181_1	chr3	6571395	6571656	+	0	NA	Intergenic	HAL1b|LINE|L1	233924	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.007663	0.412214	0(AGGAACACCAAGTCCA,-,0.00),1(GGAACACCAAGTCCAG,+,0.00)
chunk0212_23_1	chrY	10683923	10684152	+	0	NA	Intergenic	Intergenic	773239	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.017467	0.417391	
chunk0041_308_1	chr11	129851831	129852850	+	0	NA	intron (NM_138788, intron 1 of 5)	intron (NM_138788, intron 1 of 5)	36494	NM_138788	120224	Hs.504301	NM_138788	ENSG00000151715	TMEM45B	-	transmembrane protein 45B	protein-coding	0.020608	0.395098	
chunk0066_175_1	chr15	33022723	33022927	+	0	NA	intron (NM_001103184, intron 2 of 16)	L1MEi|LINE|L1	45207	NM_001103184	342184	Hs.657649	NM_198500	ENSG00000248905	FMN1	FMN|LD	formin 1	protein-coding	0.004902	0.551220	
chunk0135_317_1	chr3	190032076	190032794	+	0	NA	intron (NM_001134418, intron 1 of 14)	intron (NM_001134418, intron 1 of 14)	-88529	NR_126419	101929152		NR_126419	ENSG00000225764	P3H2-AS1	LEPREL1-AS1	P3H2 antisense RNA 1	ncRNA	0.002786	0.358832	
chunk0093_88_1	chr19	41916176	41916471	+	0	NA	Intergenic	Intergenic	31944	NM_199002	9138	Hs.631550	NM_004706	ENSG00000076928	ARHGEF1	GEF1|IMD62|LBCL2|LSC|P115-RHOGEF|SUB1.5	Rho guanine nucleotide exchange factor 1	protein-coding	0.016949	0.510135	
chunk0030_186_1	chr10	114223050	114223573	+	0	NA	intron (NM_198795, intron 21 of 25)	L1M3a|LINE|L1	-15943	NM_001272046	340706	Hs.197741	NM_198496	ENSG00000165816	VWA2	AMACO|CCSP-2|CCSP2|NET42	von Willebrand factor A domain containing 2	protein-coding	0.007648	0.496183	
chunk0073_346_1	chr16	14579266	14579481	+	0	NA	intron (NM_002582, intron 18 of 23)	intron (NM_002582, intron 18 of 23)	50898	NM_001242992	5073	Hs.253197	NM_002582	ENSG00000140694	PARN	DAN|DKCB6|PFBMFT4	poly(A)-specific ribonuclease	protein-coding	0.004651	0.375000	
chunk0209_357_1	chrX	53324927	53325217	+	0	NA	Intergenic	Intergenic	-3748	NM_001111125	23096	Hs.496138	NM_015075	ENSG00000124313	IQSEC2	BRAG1|IQ-ArfGEF|MRX1|MRX18|MRX78	IQ motif and Sec7 domain 2	protein-coding	0.003448	0.395189	261(CAGAACATTATGTTCT,-,0.00),262(AGAACATTATGTTCTA,+,0.00)
chunk0022_430_1	chr10	19348677	19349152	+	0	NA	intron (NM_001142308, intron 25 of 39)	intron (NM_001142308, intron 25 of 39)	300143	NM_001142308	340895	Hs.646734	NM_001142308	ENSG00000204740	MALRD1	C10orf112|DIET1|bA265G8.2	MAM and LDL receptor class A domain containing 1	protein-coding	0.008421	0.411765	
chunk0041_229_1	chr11	128393693	128394059	+	0	NA	Intergenic	Intergenic	128434	NM_005238	2113	Hs.369438	NM_005238	ENSG00000134954	ETS1	ETS-1|EWSR2|c-ets-1|p54	ETS proto-oncogene 1, transcription factor	protein-coding	0.013661	0.395095	
chunk0199_183_1	chr9	4657782	4658351	+	0	NA	intron (NM_001039395, intron 3 of 10)	MLT1C|LTR|ERVL-MaLR	-4228	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.003515	0.384211	
chunk0158_382_1	chr5	134371062	134371470	+	0	NA	promoter-TSS (NM_003337)	promoter-TSS (NM_003337)	90	NM_003337	7320	Hs.612096	NM_003337	ENSG00000119048	UBE2B	E2-17kDa|HHR6B|HR6B|RAD6B|UBC2	ubiquitin conjugating enzyme E2 B	protein-coding	0.066176	0.599022	
chunk0126_300_1	chr3	80712308	80712511	+	0	NA	Intergenic	L1PA7|LINE|L1	-281459	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.009852	0.343137	72(AAAGACACGATGTACC,-,0.00)
chunk0034_182_1	chr11	31513835	31514103	+	0	NA	intron (NM_019040, intron 1 of 9)	intron (NM_019040, intron 1 of 9)	4240	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.000000	0.260223	
chunk0101_226_1	chr2	131093242	131093600	+	0	NA	promoter-TSS (NM_001009993)	promoter-TSS (NM_001009993)	10	NM_001009993	130074	Hs.534679	NM_001009993	ENSG00000152102	FAM168B	MANI	family with sequence similarity 168 member B	protein-coding	0.178771	0.782730	
chunk0145_291_1	chr4	149931324	149931775	+	0	NA	Intergenic	Intergenic	-146725	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.006652	0.353982	210(ATGCACAGTATGTTTT,-,0.00),211(TGCACAGTATGTTTTT,+,0.00)
chunk0079_166_1	chr17	13568975	13569639	+	0	NA	intron (NM_006042, intron 1 of 1)	intron (NM_006042, intron 1 of 1)	-25661	NR_031679	100302287		NR_031679	ENSG00000221698	MIR548H3	MIR548H-3|MIRN548H3|hsa-mir-548h-3	microRNA 548h-3	ncRNA	0.009036	0.470677	
chunk0119_100_1	chr22	42050631	42051217	+	0	NA	Intergenic	L1MC2|LINE|L1	19918	NM_000262	4668	Hs.75372	NM_000262	ENSG00000198951	NAGA	D22S674|GALB	alpha-N-acetylgalactosaminidase	protein-coding	0.003413	0.350937	
chunk0125_404_1	chr3	72196211	72196587	+	0	NA	Intergenic	Intergenic	45142	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.013298	0.480106	
chunk0176_415_1	chr7	19369650	19370468	+	0	NA	Intergenic	Intergenic	-224638	NM_152898	222894	Hs.592168	NM_152898	ENSG00000146618	FERD3L	N-TWIST|NATO3|NTWIST|PTFB|bHLHa31	Fer3 like bHLH transcription factor	protein-coding	0.014670	0.390720	
chunk0121_60_1	chr3	15685783	15686345	+	0	NA	exon (NM_001195098, exon 20 of 28)	exon (NM_001195098, exon 20 of 28)	11307	NR_036085	100422990		NR_036085	ENSG00000264354	MIR3134	-	microRNA 3134	ncRNA	0.014235	0.353464	
chunk0102_410_1	chr2	156342500	156342946	+	0	NA	Intergenic	CpG	-9948	NM_006186	4929	Hs.563344	NM_006186	ENSG00000153234	NR4A2	HZF-3|NOT|NURR1|RNR1|TINUR	nuclear receptor subfamily 4 group A member 2	protein-coding	0.105381	0.666667	
chunk0061_138_1	chr14	59262847	59263453	+	0	NA	promoter-TSS (NM_014992)	promoter-TSS (NM_014992)	-291	NM_014992	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.011551	0.438221	
chunk0199_225_1	chr9	5352276	5352810	+	0	NA	Intergenic	Intergenic	-12670	NM_006911	6013	Hs.368996	NM_006911	ENSG00000107018	RLN1	H1|H1RLX|RLXH1|bA12D24.3.1|bA12D24.3.2	relaxin 1	protein-coding	0.001873	0.325234	
chunk0164_161_1	chr6	21613767	21614604	+	0	NA	Intergenic	Intergenic	20444	NM_003107	6659	Hs.643910	NM_003107	ENSG00000124766	SOX4	EVI16	SRY-box transcription factor 4	protein-coding	0.008363	0.392601	
chunk0085_13_1	chr18	267999	268533	+	0	NA	promoter-TSS (NM_005131)	promoter-TSS (NM_005131)	-207	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.078652	0.631776	
chunk0137_70_1	chr4	12562075	12562502	+	0	NA	Intergenic	Intergenic	338837	NR_125910	101929019	Hs.434234	NR_125910	ENSG00000251210	LINC02270	-	long intergenic non-protein coding RNA 2270	ncRNA	0.002342	0.345794	
chunk0005_148_1	chr1	57933467	57933870	+	0	NA	intron (NM_021080, intron 1 of 16)	L1ME2z|LINE|L1	73125	NR_104364	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.002481	0.314356	
chunk0056_233_1	chr13	88857359	88857660	+	0	NA	Intergenic	L1MB1|LINE|L1	316680	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.003322	0.334437	
chunk0077_82_1	chr16	77353617	77353943	+	0	NA	exon (NM_199355, exon 10 of 23)	exon (NM_199355, exon 10 of 23)	81334	NM_199355	170692	Hs.188746	NM_139054	ENSG00000140873	ADAMTS18	ADAMTS21|KNO2|MMCAT	ADAM metallopeptidase with thrombospondin type 1 motif 18	protein-coding	0.006135	0.415902	
chunk0136_353_1	chr3	195895959	195896521	+	0	NA	promoter-TSS (NM_001010938)	promoter-TSS (NM_001010938)	-679	NM_001010938	10188	Hs.518513	NM_005781	ENSG00000061938	TNK2	ACK|ACK-1|ACK1|p21cdc42Hs	tyrosine kinase non receptor 2	protein-coding	0.067616	0.666075	202(CGGCACAGGAAGTCCC,-,0.00),203(GGCACAGGAAGTCCCA,+,0.00)
chunk0078_281_1	chr17	7990142	7990560	+	0	NA	Intergenic	CpG	-12319	NM_000180	3000	Hs.592109	NM_000180	ENSG00000132518	GUCY2D	CACD1|CORD5|CORD6|CYGD|GUC1A4|GUC2D|LCA|LCA1|RCD2|RETGC-1|ROS-GC1|ROSGC|retGC	guanylate cyclase 2D, retinal	protein-coding	0.069378	0.675418	
chunk0122_124_1	chr3	31341360	31341569	+	0	NA	Intergenic	Intergenic	-179677	NR_130459	100423038		NR_130459	ENSG00000265376	MIR466	hsa-mir-466	microRNA 466	ncRNA	0.000000	0.485714	
chunk0204_249_1	chr9	98090283	98090537	+	0	NA	intron (NM_014788, intron 5 of 5)	L1ME3|LINE|L1	28943	NM_033219	9830	Hs.575631	NM_014788	ENSG00000106785	TRIM14	-	tripartite motif containing 14	protein-coding	0.000000	0.360784	
chunk0107_432_1	chr2	224837332	224837579	+	0	NA	intron (NM_014689, intron 25 of 55)	intron (NM_014689, intron 25 of 55)	109610	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.000000	0.338710	
chunk0047_85_1	chr12	68198997	68199196	+	0	NA	Intergenic	Intergenic	26695	NM_018402	55801	Hs.272350	NM_018402	ENSG00000111536	IL26	AK155|IL-26	interleukin 26	protein-coding	0.010050	0.365000	
chunk0191_55_1	chr8	46570867	46571675	+	0	NA	Intergenic	L1ME4a|LINE|L1	-269615	NR_027013	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.004950	0.347342	376(TGGAACAGAGTGTACC,-,0.00),377(GGAACAGAGTGTACCA,+,0.00)
chunk0104_283_1	chr2	178282041	178282509	+	0	NA	intron (NM_001201482, intron 1 of 23)	intron (NM_001201482, intron 1 of 23)	-37969	NM_145739	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.010684	0.456290	
chunk0166_445_1	chr6	53056270	53056709	+	0	NA	intron (NM_014920, intron 1 of 13)	MER58A|DNA|hAT-Charlie	5313	NM_016513	22858	Hs.417022	NM_014920	ENSG00000112144	ICK	ECO|EJM10|LCK2|MRK	intestinal cell kinase	protein-coding	0.006834	0.420455	
chunk0177_187_1	chr7	23622564	23622877	+	0	NA	intron (NM_138771, intron 3 of 3)	intron (NM_138771, intron 3 of 3)	25341	NM_138771	90693	Hs.232296	NM_138771	ENSG00000169193	CCDC126	-	coiled-coil domain containing 126	protein-coding	0.000000	0.414013	
chunk0184_141_1	chr7	115677870	115678562	+	0	NA	Intergenic	Intergenic	290097	NM_001244583	22797	Hs.125962	NM_012252	ENSG00000105967	TFEC	TCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-L	transcription factor EC	protein-coding	0.013006	0.365079	
chunk0097_407_1	chr2	62518736	62519080	+	0	NA	Intergenic	L1PA5|LINE|L1	-12439	NM_198276	200728	Hs.308028	NM_198276	ENSG00000186889	TMEM17	-	transmembrane protein 17	protein-coding	0.005814	0.394203	57(AGGAGCAGGTTGTTCC,-,0.00),58(GGAGCAGGTTGTTCCA,+,0.00)
chunk0179_22_1	chr7	42724244	42724768	+	0	NA	Intergenic	Intergenic	-18059	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.007634	0.502857	
chunk0140_115_1	chr4	68716682	68717016	+	0	NA	Intergenic	L1MC4a|LINE|L1	-46073	NM_001076	7366	Hs.150207	NM_001076	ENSG00000196620	UGT2B15	HLUG4|UDPGT 2B8|UDPGT2B15|UDPGTH3|UGT2B8	UDP glucuronosyltransferase family 2 member B15	protein-coding	0.008982	0.361194	159(AGGCACATCCTGTACT,-,0.00),160(GGCACATCCTGTACTT,+,0.00)
chunk0001_16_1	chr1	1124141	1124366	+	0	NA	Intergenic	Intergenic	-7897	NM_017891	54991	Hs.235095	NM_017891	ENSG00000131591	C1orf159	-	chromosome 1 open reading frame 159	protein-coding	0.022222	0.566372	
chunk0196_41_1	chr8	101755632	101755938	+	0	NA	intron (NM_001040630, intron 3 of 5)	intron (NM_001040630, intron 3 of 5)	35426	NM_032041	83988	Hs.492427	NM_032041	ENSG00000104490	NCALD	-	neurocalcin delta	protein-coding	0.000000	0.390879	
chunk0055_126_1	chr13	57590341	57591179	+	0	NA	Intergenic	Intergenic	-40895	NM_001040429	27253	Hs.106511	NM_014459	ENSG00000118946	PCDH17	PCDH68|PCH68	protocadherin 17	protein-coding	0.001193	0.393325	321(TGGCACAGTCAGTGCT,-,0.00),322(GGCACAGTCAGTGCTT,+,0.00)
chunk0179_48_1	chr7	43537312	43537688	+	0	NA	intron (NM_015052, intron 24 of 29)	intron (NM_015052, intron 24 of 29)	-14958	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.005319	0.352785	
chunk0144_389_1	chr4	140140691	140141183	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	13142	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.010163	0.454361	
chunk0027_168_1	chr10	74953121	74953627	+	0	NA	intron (NM_001256468, intron 3 of 17)	MIRc|SINE|MIR	105140	NM_001003892	338599	Hs.535090	NM_001003892	ENSG00000188716	DUPD1	DUSP27|FMDSP	dual specificity phosphatase and pro isomerase domain containing 1	protein-coding	0.003953	0.337278	
chunk0009_324_1	chr1	108746328	108746681	+	0	NA	promoter-TSS (NM_007269)	promoter-TSS (NM_007269)	-159	NM_007269	6814	Hs.530436	NM_007269	ENSG00000116266	STXBP3	MUNC18-3|MUNC18C|PSP|UNC-18C	syntaxin binding protein 3	protein-coding	0.084986	0.618644	
chunk0104_423_1	chr2	180908153	180908689	+	0	NA	intron (NR_104319, intron 4 of 4)	intron (NR_104319, intron 4 of 4)	-71964	NM_182678	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.005597	0.381750	239(GAGCACAGAATGTACT,-,0.00),240(AGCACAGAATGTACTC,+,0.00)
chunk0009_458_1	chr1	111625374	111625796	+	0	NA	intron (NM_001291896, intron 1 of 7)	intron (NM_001291896, intron 1 of 7)	5438	NM_001291896	5906	Hs.190334	NM_002884	ENSG00000116473	RAP1A	C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21	RAP1A, member of RAS oncogene family	protein-coding	0.000000	0.314421	179(AGGATCATTCTGTTCT,-,0.00),180(GGATCATTCTGTTCTA,+,0.00)
chunk0161_201_1	chr5	170564979	170565516	+	0	NA	intron (NM_001278339, intron 1 of 7)	intron (NM_001278339, intron 1 of 7)	61211	NM_001278340	30820	Hs.484111	NM_014592	ENSG00000182132	KCNIP1	KCHIP1|VABP	potassium voltage-gated channel interacting protein 1	protein-coding	0.009311	0.468401	79(GTGAACAAGTTGTGCC,-,0.00),80(TGAACAAGTTGTGCCT,+,0.00),253(GGGGACAGCTAGTTCC,-,0.00),254(GGGACAGCTAGTTCCA,+,0.00),514(AAAGACACTCTGTTCT,-,0.00),515(AAGACACTCTGTTCTT,+,0.00)
chunk0140_413_1	chr4	75752759	75753040	+	0	NA	intron (NM_001290049, intron 3 of 25)	intron (NM_001290049, intron 3 of 25)	28377	NM_001290049	8615	Hs.744877	NM_003715	ENSG00000138768	USO1	P115|TAP|VDP	USO1 vesicle transport factor	protein-coding	0.017794	0.407801	
chunk0166_143_1	chr6	44931580	44932300	+	0	NA	intron (NM_181356, intron 12 of 12)	intron (NM_181356, intron 12 of 12)	265830	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.000000	0.282940	
chunk0021_157_1	chr10	4833939	4834227	+	0	NA	intron (NR_073125, intron 3 of 9)	intron (NR_073125, intron 3 of 9)	7906	NR_073127	83592	Hs.657944	NM_031436	ENSG00000165568	AKR1E2	AKR1CL2|AKRDC1|LoopADR|TAKR|hTSP|htAKR	aldo-keto reductase family 1 member E2	protein-coding	0.006944	0.532872	
chunk0158_440_1	chr5	135676843	135677084	+	0	NA	Intergenic	L1MA4A|LINE|L1	-23028	NR_027127	340074	Hs.434633	NR_027127	ENSG00000251045	SLC25A48-AS1	LINC01959	SLC25A48 antisense RNA 1	ncRNA	0.004149	0.342975	
chunk0151_248_1	chr5	51841393	51841627	+	0	NA	Intergenic	Intergenic	-458178	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.008547	0.370213	
chunk0126_6_1	chr3	73451091	73451622	+	0	NA	intron (NM_015009, intron 3 of 9)	intron (NM_015009, intron 3 of 9)	-17360	NM_001303142	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.007533	0.422932	
chunk0078_421_1	chr16	89313788	89314138	+	0	NA	intron (NR_045839, intron 3 of 9)	AluJb|SINE|Alu	-7170	NM_001242885	100287036	Hs.656995	NM_001242885		LOC100287036	-	uncharacterized LOC100287036	protein-coding	0.017143	0.487179	
chunk0130_325_1	chr3	138187305	138187616	+	0	NA	5' UTR (NM_001267041, exon 1 of 21)	5' UTR (NM_001267041, exon 1 of 21)	212	NM_001282342	25852	Hs.744868	NM_014154	ENSG00000114098	ARMC8	GID5|HSPC056|S863-2|VID28	armadillo repeat containing 8	protein-coding	0.077170	0.615385	
chunk0035_98_1	chr11	42310464	42311146	+	0	NA	Intergenic	L1ME3A|LINE|L1	-57115	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.007331	0.314788	
chunk0052_163_1	chr13	24051206	24051479	+	0	NA	intron (NM_001286792, intron 3 of 14)	intron (NM_001286792, intron 3 of 14)	71716	NM_001286792	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.014652	0.558394	70(TTGGACATGCTGTGCC,-,0.00),71(TGGACATGCTGTGCCT,+,0.00)
chunk0098_438_1	chr2	82092931	82093446	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-626242	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.015534	0.348837	
chunk0186_406_1	chr7	144796903	144797199	+	0	NA	intron (NM_001042482, intron 2 of 7)	L1PA10|LINE|L1	39002	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.013514	0.558923	
chunk0157_355_1	chr5	123282372	123282937	+	0	NA	Intergenic	Intergenic	140938	NM_001166226	153241	Hs.483209	NM_153223	ENSG00000168944	CEP120	CCDC100|JBTS31|SRTD13	centrosomal protein 120	protein-coding	0.008850	0.399293	
chunk0173_243_1	chr6	146865798	146866073	+	0	NA	intron (NR_034115, intron 7 of 10)	intron (NR_034115, intron 7 of 10)	-62111	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.010909	0.398551	
chunk0155_26_1	chr5	91027467	91027857	+	0	NA	intron (NR_003149, intron 85 of 89)	intron (NR_003149, intron 85 of 89)	286740	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.002564	0.406650	
chunk0037_235_1	chr11	75301694	75301966	+	0	NA	intron (NM_004041, intron 1 of 15)	intron (NM_004041, intron 1 of 15)	33356	NR_029891	442900		NR_029891	ENSG00000199090	MIR326	MIRN326|hsa-mir-326|mir-326	microRNA 326	ncRNA	0.022059	0.589744	
chunk0176_113_1	chr7	11946493	11947197	+	0	NA	Intergenic	L1PA13|LINE|L1	-114647	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005682	0.350355	
chunk0077_47_1	chr16	76005296	76005588	+	0	NA	Intergenic	L2|LINE|L2	-271836	NM_033401	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.010274	0.382253	
chunk0193_291_1	chr8	77639640	77640065	+	0	NA	Intergenic	Intergenic	189155	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.009412	0.392019	
chunk0004_20_1	chr1	42198138	42198675	+	0	NA	intron (NM_014947, intron 7 of 12)	L1M6|LINE|L1	-33682	NM_033553	2980	Hs.778	NM_033553	ENSG00000197273	GUCA2A	GCAP-I|GUCA2|STARA	guanylate cyclase activator 2A	protein-coding	0.009311	0.360595	
chunk0006_296_1	chr1	71088517	71089209	+	0	NA	intron (NR_046217, intron 1 of 3)	L2c|LINE|L2	7539	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.010116	0.391053	
chunk0067_294_1	chr15	47486815	47487183	+	0	NA	intron (NM_001198999, intron 3 of 19)	L2b|LINE|L2	-231490	NM_153618	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.005435	0.346883	112(CAGAACACACTGTTAT,-,0.00),113(AGAACACACTGTTATT,+,0.00)
chunk0016_410_1	chr1	203306202	203306806	+	0	NA	intron (NM_006763, intron 1 of 1)	intron (NM_006763, intron 1 of 1)	968	NM_006763	7832	Hs.519162	NM_006763	ENSG00000159388	BTG2	APRO1|PC3|TIS21	BTG anti-proliferation factor 2	protein-coding	0.019868	0.555372	
chunk0142_407_1	chr4	103017928	103018361	+	0	NA	intron (NR_047515, intron 1 of 10)	intron (NR_047515, intron 1 of 10)	1595	NM_139173	150159	Hs.666728	NM_139173	ENSG00000164037	SLC9B1	NHA1|NHEDC1	solute carrier family 9 member B1	protein-coding	0.002309	0.361751	
chunk0045_88_1	chr12	45965994	45966483	+	0	NA	intron (NM_004719, intron 1 of 14)	Plat_L3|LINE|CR1	24380	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.000000	0.334694	
chunk0134_370_1	chr3	182716595	182717221	+	0	NA	Intergenic	LTR25-int|LTR|ERV1	-76595	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.000000	0.362041	
chunk0167_11_1	chr6	53513422	53513899	+	0	NA	intron (NM_001197115, intron 5 of 14)	intron (NM_001197115, intron 5 of 14)	31469	NM_001498	2729	Hs.654465	NM_001498	ENSG00000001084	GCLC	GCL|GCS|GLCL|GLCLC	glutamate-cysteine ligase catalytic subunit	protein-coding	0.004193	0.416318	
chunk0142_173_1	chr4	95500418	95500850	+	0	NA	intron (NM_003728, intron 1 of 15)	intron (NM_003728, intron 1 of 15)	48576	NM_003728	8633	Hs.388565	NM_003728	ENSG00000182168	UNC5C	UNC5H3	unc-5 netrin receptor C	protein-coding	0.002315	0.327945	
chunk0082_336_1	chr17	59735727	59736159	+	0	NA	intron (NM_030938, intron 3 of 11)	intron (NM_030938, intron 3 of 11)	-28345	NM_001015509	51651	Hs.12677	NM_016077	ENSG00000141378	PTRH2	BIT1|CFAP37|CGI-147|IMNEPD|PTH|PTH 2|PTH2	peptidyl-tRNA hydrolase 2	protein-coding	0.004630	0.344111	
chunk0146_299_1	chr4	165023089	165023527	+	0	NA	Intergenic	Intergenic	-8691	NM_001258025	166655	Hs.368004	NM_152620	ENSG00000176979	TRIM60	RNF129|RNF33	tripartite motif containing 60	protein-coding	0.011416	0.398633	
chunk0029_279_1	chr10	103548727	103549246	+	0	NA	intron (NM_004210, intron 1 of 5)	intron (NM_004210, intron 1 of 5)	-31544	NR_120675	102724341	Hs.599425	NR_120675	ENSG00000235470	NEURL1-AS1	-	NEURL1 antisense RNA 1	ncRNA	0.011561	0.551923	288(TGGCACACTCTGTCCT,-,0.00),289(GGCACACTCTGTCCTG,+,0.00)
chunk0036_256_1	chr11	64784894	64785490	+	0	NA	Intergenic	L1ME1|LINE|L1	-6348	NM_201995	7536	Hs.502829	NM_004630	ENSG00000168066	SF1	BBP|D11S636|MBBP|ZCCHC25|ZFM1|ZNF162	splicing factor 1	protein-coding	0.011745	0.412060	
chunk0045_27_1	chr12	43836233	43836575	+	0	NA	intron (NM_001286212, intron 1 of 6)	intron (NM_001286212, intron 1 of 6)	543	NM_001286211	84216	Hs.444668	NM_032256	ENSG00000139173	TMEM117	-	transmembrane protein 117	protein-coding	0.078947	0.676385	
chunk0192_85_1	chr8	60899637	60900411	+	0	NA	Intergenic	Intergenic	67724	NR_034003	100130298	Hs.636194	NR_034003		LOC100130298	-	hCG1816373-like	ncRNA	0.012920	0.472258	406(TAGGACAGAGTGTCCC,-,0.00),407(AGGACAGAGTGTCCCT,+,0.00)
chunk0131_140_1	chr3	145685266	145686046	+	0	NA	Intergenic	Intergenic	475839	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.007692	0.427657	
chunk0138_7_1	chr4	30286264	30286490	+	0	NA	Intergenic	L2a|LINE|L2	-434031	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.000000	0.312775	
chunk0177_14_1	chr7	20479475	20479687	+	0	NA	Intergenic	Intergenic	-136041	NM_001163941	340273	Hs.404102	NM_178559	ENSG00000004846	ABCB5	ABCB5alpha|ABCB5beta|EST422562	ATP binding cassette subfamily B member 5	protein-coding	0.000000	0.319249	
chunk0178_89_1	chr7	30524606	30524952	+	0	NA	Intergenic	Intergenic	-19938	NM_001199816	79017	Hs.530024	NM_024051	ENSG00000006625	GGCT	C7orf24|CRF21|GCTG|GGC	gamma-glutamylcyclotransferase	protein-coding	0.005780	0.420749	
chunk0127_289_1	chr3	97927538	97928585	+	0	NA	intron (NM_153605, intron 17 of 21)	L1PA15|LINE|L1	44390	NM_153182	84864	Hs.570562	NM_032778	ENSG00000170854	RIOX2	JMJD10|MDIG|MINA|MINA53|NO52|ROX	ribosomal oxygenase 2	protein-coding	0.002865	0.370229	
chunk0145_127_1	chr4	146376790	146377195	+	0	NA	intron (NM_001029998, intron 5 of 11)	LTR10C|LTR|ERV1	-31591	NR_107003	102465837		NR_107003	ENSG00000278438	MIR7849	hsa-mir-7849	microRNA 7849	ncRNA	0.009877	0.364532	
chunk0098_361_1	chr2	77690666	77691025	+	0	NA	Intergenic	L1MEc|LINE|L1	-168469	NM_024993	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.002786	0.263889	
chunk0114_61_1	chr21	8992799	8993056	+	0	NA	Intergenic	Intergenic	5557	NR_037458									0.019455	0.554264	
chunk0073_207_1	chr16	10039977	10040296	+	0	NA	intron (NM_001134407, intron 2 of 12)	(CA)n|Simple_repeat|Simple_repeat	141931	NM_001134408	2903	Hs.411472	NM_000833	ENSG00000183454	GRIN2A	EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A	glutamate ionotropic receptor NMDA type subunit 2A	protein-coding	0.015674	0.453125	
chunk0065_398_1	chr14	105114663	105114898	+	0	NA	Intergenic	MER50-int|LTR|ERV1	20633	NR_110546	102723354	Hs.569410	NR_110546		LINC02298	-	long intergenic non-protein coding RNA 2298	ncRNA	0.042553	0.516949	
chunk0081_39_1	chr17	37609282	37609575	+	0	NA	promoter-TSS (NM_080550)	promoter-TSS (NM_080550)	10	NM_080550	11276	Hs.594647	NM_007247	ENSG00000275066	SYNRG	AP1GBP1|SYNG	synergin gamma	protein-coding	0.119454	0.744898	
chunk0130_46_1	chr3	129252829	129253640	+	0	NA	intron (NM_016128, intron 5 of 23)	intron (NM_016128, intron 5 of 23)	3624	NM_016128	22820	Hs.518250	NM_016128	ENSG00000181789	COPG1	COPG	coatomer protein complex subunit gamma 1	protein-coding	0.008631	0.454433	
chunk0061_132_1	chr14	59121827	59122977	+	0	NA	Intergenic	Intergenic	-66261	NM_001270520	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.006087	0.383145	
chunk0185_457_1	chr7	135376319	135376637	+	0	NA	intron (NM_001190849, intron 10 of 11)	intron (NM_001190849, intron 10 of 11)	133649	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.003145	0.326019	
chunk0005_142_1	chr1	57576811	57577134	+	0	NA	intron (NM_021080, intron 3 of 16)	intron (NM_021080, intron 3 of 16)	-283571	NR_104362	101926890	Hs.662207	NR_104362	ENSG00000226759	DAB1-AS1	-	DAB1 antisense RNA 1	ncRNA	0.015480	0.490741	
chunk0182_390_1	chr7	100406861	100407234	+	0	NA	intron (NM_017984, intron 11 of 17)	intron (NM_017984, intron 11 of 17)	-21743	NM_001194990	56257	Hs.178011	NM_019606	ENSG00000146834	MEPCE	BCDIN3	methylphosphate capping enzyme	protein-coding	0.013405	0.433155	
chunk0204_200_1	chr9	96644269	96644468	+	0	NA	intron (NM_153698, intron 5 of 5)	intron (NM_153698, intron 5 of 5)	10949	NM_153698	195827	Hs.44640	NM_153698	ENSG00000158122	PRXL2C	AAED1|C9orf21	peroxiredoxin like 2C	protein-coding	0.005025	0.420000	
chunk0018_299_1	chr1	220900706	220901036	+	0	NA	Intergenic	L1PA7|LINE|L1	-20731	NR_046901	100873924	Hs.645593	NR_046901	ENSG00000257551	HLX-AS1	-	HLX antisense RNA 1	ncRNA	0.006061	0.374622	
chunk0139_255_1	chr4	56310307	56310860	+	0	NA	intron (NM_020722, intron 5 of 10)	intron (NM_020722, intron 5 of 10)	76925	NM_001286671	132949	Hs.104347	NM_181806	ENSG00000157426	AASDH	ACSF4|LYS2|NRPS1098|NRPS998	aminoadipate-semialdehyde dehydrogenase	protein-coding	0.007233	0.489170	309(CAGAACTTCCTGTTCA,-,0.00),310(AGAACTTCCTGTTCAG,+,0.00)
chunk0056_390_1	chr13	93736802	93737390	+	0	NA	intron (NM_005708, intron 2 of 8)	intron (NM_005708, intron 2 of 8)	121377	NR_046536	100873973	Hs.615939	NR_046536		GPC6-AS2	-	GPC6 antisense RNA 2	ncRNA	0.005102	0.354839	
chunk0026_210_1	chr10	64071575	64072080	+	0	NA	Intergenic	L1PA17|LINE|L1	550464	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.000000	0.324111	
chunk0023_140_1	chr10	24012822	24013227	+	0	NA	intron (NM_001098500, intron 2 of 18)	Tigger17a|DNA|TcMar-Tigger	-195767	NM_001282768	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.012346	0.352217	
chunk0158_388_1	chr5	134524084	134524487	+	0	NA	promoter-TSS (NM_001308143)	promoter-TSS (NM_001308143)	-90	NM_001308143	23338	Hs.732155	NM_015288	ENSG00000043143	JADE2	JADE-2|PHF15	jade family PHD finger 2	protein-coding	0.066998	0.665842	
chunk0059_335_1	chr14	36915697	36915920	+	0	NA	intron (NM_030631, intron 1 of 9)	intron (NM_030631, intron 1 of 9)	36583	NR_039725	100616280		NR_039725	ENSG00000266327	MIR4503	-	microRNA 4503	ncRNA	0.017937	0.424107	
chunk0034_188_1	chr11	31625776	31626380	+	0	NA	intron (NM_019040, intron 5 of 9)	intron (NM_019040, intron 5 of 9)	116349	NM_001288725	26610	Hs.175534	NM_019040	ENSG00000109911	ELP4	AN|AN2|C11orf19|PAX6NEB|PAXNEB|dJ68P15A.1|hELP4	elongator acetyltransferase complex subunit 4	protein-coding	0.001656	0.337190	
chunk0196_323_1	chr8	111301904	111302106	+	0	NA	Intergenic	(GT)n|Simple_repeat|Simple_repeat	-65802	NR_125418	101927487	Hs.630004	NR_125418	ENSG00000253103	LINC01609	-	long intergenic non-protein coding RNA 1609	ncRNA	0.009901	0.389163	
chunk0073_98_1	chr16	4435509	4435774	+	0	NA	intron (NM_001135110, intron 2 of 10)	L1MB7|LINE|L1	9836	NM_001286516	9093	Hs.459779	NM_005147	ENSG00000103423	DNAJA3	HCA57|TID1|hTID-1	DnaJ heat shock protein family (Hsp40) member A3	protein-coding	0.007547	0.349624	
chunk0050_407_1	chr12	109566208	109566559	+	0	NA	intron (NR_038118, intron 3 of 9)	intron (NR_038118, intron 3 of 9)	7170	NR_038118	326625	Hs.12106	NM_052845	ENSG00000139428	MMAB	ATR|CFAP23|cblB|cob	metabolism of cobalamin associated B	protein-coding	0.017094	0.556818	
chunk0126_349_1	chr3	82804269	82804474	+	0	NA	Intergenic	Intergenic	-1042572	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.000000	0.383495	103(TAGAACAAGGAGTTCT,-,0.00),104(AGAACAAGGAGTTCTG,+,0.00)
chunk0130_11_1	chr3	128369083	128369398	+	0	NA	intron (NM_021937, intron 6 of 6)	intron (NM_021937, intron 6 of 6)	-94354	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.006349	0.496835	173(CAGGACACGATGAGCC,-,0.00),174(AGGACACGATGAGCCC,+,0.00)
chunk0050_173_1	chr12	103838551	103839459	+	0	NA	intron (NM_001031701, intron 1 of 13)	L1MD2|LINE|L1	2192	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.005507	0.403740	370(GAGAACAAATAGTGCT,-,0.00),371(AGAACAAATAGTGCTC,+,0.00)
chunk0064_244_1	chr14	94411693	94412085	+	0	NA	Intergenic	LTR41|LTR|ERVL	-21197	NM_001127707	5265	Hs.525557	NM_000295	ENSG00000197249	SERPINA1	A1A|A1AT|AAT|PI|PI1|PRO2275|alpha1AT|nNIF	serpin family A member 1	protein-coding	0.002551	0.468193	
chunk0083_273_1	chr17	68448944	68449409	+	0	NA	intron (NM_017983, intron 3 of 12)	intron (NM_017983, intron 3 of 12)	8336	NM_017983	55062	Hs.463964	NM_017983	ENSG00000070540	WIPI1	ATG18|ATG18A|WIPI49	WD repeat domain, phosphoinositide interacting 1	protein-coding	0.012903	0.381974	
chunk0144_402_1	chr4	140287673	140287872	+	0	NA	intron (NR_033939, intron 4 of 4)	(CACATA)n|Simple_repeat|Simple_repeat	30486	NM_032547	60592	Hs.480815	NM_032547	ENSG00000153130	SCOC	HRIHFB2072|SCOCO|UNC-69	short coiled-coil protein	protein-coding	0.010050	0.420000	
chunk0112_184_1	chr20	40067817	40068149	+	0	NA	Intergenic	L1MA2|LINE|L1	63522	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.003012	0.321321	
chunk0131_52_1	chr3	142735253	142735539	+	0	NA	intron (NM_003304, intron 1 of 11)	intron (NM_003304, intron 1 of 11)	10972	NM_003304	7220	Hs.250687	NM_003304	ENSG00000144935	TRPC1	HTRP-1|TRP1	transient receptor potential cation channel subfamily C member 1	protein-coding	0.003497	0.278746	
chunk0135_243_1	chr3	188775558	188775781	+	0	NA	intron (NM_001167671, intron 8 of 10)	intron (NM_001167671, intron 8 of 10)	86888	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.008969	0.433036	
chunk0180_299_1	chr7	70307697	70308191	+	0	NA	intron (NM_015570, intron 4 of 18)	L4_C_Mam|LINE|RTE-X	709025	NM_001127231	26053	Hs.21631	NM_015570	ENSG00000158321	AUTS2	FBRSL2|MRD26	activator of transcription and developmental regulator AUTS2	protein-coding	0.006073	0.375758	
chunk0107_438_1	chr2	224910034	224910275	+	0	NA	intron (NM_014689, intron 3 of 55)	intron (NM_014689, intron 3 of 55)	36911	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.012448	0.425620	
chunk0208_212_1	chrX	18218254	18218703	+	0	NA	intron (NM_001184767, intron 1 of 10)	intron (NM_001184767, intron 1 of 10)	2426	NM_001184767	139105	Hs.403802	NM_153346	ENSG00000177324	BEND2	CXorf20	BEN domain containing 2	protein-coding	0.024499	0.400000	
chunk0140_163_1	chr4	69570227	69570870	+	0	NA	Intergenic	Zaphod3|DNA|hAT-Tip100	-44534	NM_001297616	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.006221	0.251553	
chunk0163_206_1	chr6	11931696	11931918	+	0	NA	Intergenic	Intergenic	69437	NR_125853	101928253	Hs.128163	NR_125853		LOC101928253	-	uncharacterized LOC101928253	ncRNA	0.022523	0.556054	121(AGGCACAGTCTGTGCC,-,0.00),122(GGCACAGTCTGTGCCT,+,0.00)
chunk0194_195_1	chr8	85468805	85469060	+	0	NA	intron (NM_001293675, intron 2 of 5)	MIR3|SINE|MIR	-4017	NR_121630	100996348	Hs.606624	NR_121630	ENSG00000253549	CA3-AS1	-	CA3 antisense RNA 1	ncRNA	0.003922	0.304688	
chunk0140_406_1	chr4	75644064	75644467	+	0	NA	3' UTR (NM_203504, exon 11 of 11)	3' UTR (NM_203504, exon 11 of 11)	-13728	NM_003948	8999	Hs.591698	NM_003948	ENSG00000138769	CDKL2	KKIAMRE|P56	cyclin dependent kinase like 2	protein-coding	0.009926	0.376238	
chunk0112_55_1	chr20	37303540	37304203	+	0	NA	intron (NM_001003897, intron 2 of 2)	MER68|LTR|ERVL	14223	NM_001003897	63905	Hs.6126	NM_022077	ENSG00000101363	MANBAL	-	mannosidase beta like	protein-coding	0.006033	0.430723	
chunk0095_133_1	chr2	16697624	16697861	+	0	NA	Intergenic	L1PB3|LINE|L1	-31876	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.000000	0.386555	
chunk0097_92_1	chr2	45469971	45470181	+	0	NA	intron (NM_018079, intron 16 of 20)	intron (NM_018079, intron 16 of 20)	141218	NM_018079	55133	Hs.14229	NM_018079	ENSG00000068784	SRBD1	-	S1 RNA binding domain 1	protein-coding	0.004762	0.345972	
chunk0030_294_1	chr10	117318458	117319032	+	0	NA	intron (NM_173791, intron 3 of 4)	intron (NM_173791, intron 3 of 4)	56722	NM_173791	118987	Hs.501149	NM_173791	ENSG00000165650	PDZD8	PDZK8	PDZ domain containing 8	protein-coding	0.005226	0.314783	
chunk0054_280_1	chr13	46665886	46666138	+	0	NA	intron (NM_001164213, intron 2 of 18)	intron (NM_001164213, intron 2 of 18)	112851	NM_001164211	23143	Hs.507971	NM_015116	ENSG00000136141	LRCH1	CHDC1|NP81	leucine rich repeats and calponin homology domain containing 1	protein-coding	0.007937	0.434783	134(AGGAACATCCTGTGAT,-,0.00)
chunk0035_207_1	chr11	44749142	44749536	+	0	NA	Intergenic	MIRb|SINE|MIR	-15087	NM_130783	90139	Hs.385634	NM_130783	ENSG00000157570	TSPAN18	TSPAN	tetraspanin 18	protein-coding	0.005076	0.450633	
chunk0029_360_1	chr10	107614907	107615106	+	0	NA	Intergenic	Intergenic	-450298	NM_001013031	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.010050	0.365000	124(AGGGACACAATGTGAT,-,0.00)
chunk0116_451_1	chr21	43767112	43767611	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	9014	NM_000100	1476	Hs.695	NM_000100	ENSG00000160213	CSTB	CPI-B|CST6|EPM1|EPM1A|PME|STFB|ULD	cystatin B	protein-coding	0.054108	0.564000	
chunk0191_296_1	chr8	54309494	54309693	+	0	NA	Intergenic	Intergenic	-21093	NR_004385	26766		NR_004385	ENSG00000199212	RNU105C	E1-5|E1-6	RNA, U105C small nucleolar	snoRNA	0.010050	0.345000	
chunk0016_160_1	chr1	197663090	197663656	+	0	NA	intron (NM_001300858, intron 6 of 15)	intron (NM_001300858, intron 6 of 15)	112120	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.003534	0.326279	
chunk0174_19_1	chr6	153031322	153032025	+	0	NA	intron (NM_012419, intron 2 of 4)	intron (NM_012419, intron 2 of 4)	-28858	NM_001301871	54516	Hs.225836	NM_019041	ENSG00000112031	MTRF1L	HMRF1L|MRF1L|mtRF1a	mitochondrial translational release factor 1 like	protein-coding	0.002845	0.386364	
chunk0150_443_1	chr5	40554139	40554373	+	0	NA	Intergenic	Intergenic	-125674	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.000000	0.395745	
chunk0134_269_1	chr3	179544949	179545183	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-17814	NM_004301	86	Hs.435326	NM_004301	ENSG00000136518	ACTL6A	ACTL6|ARPN-BETA|Arp4|BAF53A|INO80K	actin like 6A	protein-coding	0.004274	0.357447	
chunk0022_3_1	chr10	7084395	7085023	+	0	NA	Intergenic	Intergenic	102075	NR_132972	106635547		NR_132972		SNORD129	-	small nucleolar RNA, C/D box 129	snoRNA	0.012739	0.391097	
chunk0141_218_1	chr4	84649271	84649721	+	0	NA	3' UTR (NM_001263, exon 13 of 13)	3' UTR (NM_001263, exon 13 of 13)	66592	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.022222	0.509978	
chunk0106_230_1	chr2	202609766	202610478	+	0	NA	Intergenic	Intergenic	-25056	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.007022	0.389902	
chunk0089_405_1	chr18	68228910	68229916	+	0	NA	Intergenic	Intergenic	485703	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.009940	0.319762	
chunk0118_337_1	chr22	35589516	35590256	+	0	NA	Intergenic	AluJr|SINE|Alu	27451	NM_005368	4151	Hs.517586	NM_005368	ENSG00000198125	MB	PVALB|myoglobgin	myoglobin	protein-coding	0.018919	0.493927	
chunk0107_361_1	chr2	222734568	222734903	+	0	NA	Intergenic	MIRb|SINE|MIR	62997	NM_058165	116255	Hs.344090	NM_058165	ENSG00000124003	MOGAT1	DGAT2L|DGAT2L1|MGAT1	monoacylglycerol O-acyltransferase 1	protein-coding	0.002985	0.422619	
chunk0052_413_1	chr12	131310104	131310421	+	0	NA	Intergenic	Intergenic	-37208	NR_103736	338797	Hs.592007	NM_001025466		LINC02370	-	long intergenic non-protein coding RNA 2370	ncRNA	0.022082	0.506289	
chunk0197_289_1	chr8	124262690	124262992	+	0	NA	Intergenic	Intergenic	-15443	NR_125420	101927588	Hs.617072	NR_125420	ENSG00000214803	LOC101927588	-	uncharacterized LOC101927588	ncRNA	0.013245	0.495050	
chunk0206_3_1	chr9	115591718	115592088	+	0	NA	Intergenic	AluJr|SINE|Alu	152336	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.013514	0.474394	
chunk0175_230_1	chr7	6303808	6304275	+	0	NA	Intergenic	Intergenic	-31430	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.006424	0.373932	
chunk0004_179_1	chr1	45979137	45979402	+	0	NA	intron (NM_015112, intron 5 of 28)	intron (NM_015112, intron 5 of 28)	153439	NM_003629	8503	Hs.655387	NM_003629	ENSG00000117461	PIK3R3	p55|p55-GAMMA|p55PIK	phosphoinositide-3-kinase regulatory subunit 3	protein-coding	0.003774	0.383459	
chunk0077_154_1	chr16	78974535	78974864	+	0	NA	intron (NM_016373, intron 8 of 8)	intron (NM_016373, intron 8 of 8)	626026	NM_005360	4094	Hs.134859	NM_005360	ENSG00000178573	MAF	AYGRP|CCA4|CTRCT21|c-MAF	MAF bZIP transcription factor	protein-coding	0.015198	0.442424	
chunk0208_98_1	chrX	13564228	13564604	+	0	NA	Intergenic	L2c|LINE|L2	-5159	NM_001167890	25975	Hs.12844	NM_015507	ENSG00000198759	EGFL6	MAEG|W80	EGF like domain multiple 6	protein-coding	0.005319	0.318302	
chunk0138_366_1	chr4	42262952	42263446	+	0	NA	Intergenic	MER41C|LTR|ERV1	-110321	NM_207406	389206	Hs.120591	NM_207406	ENSG00000188848	BEND4	CCDC4	BEN domain containing 4	protein-coding	0.010121	0.361616	
chunk0138_377_1	chr4	42472960	42473482	+	0	NA	intron (NM_006095, intron 25 of 36)	intron (NM_006095, intron 25 of 36)	75382	NM_001080505	152573	Hs.370904	NM_001080505	ENSG00000178343	SHISA3	hShisa3	shisa family member 3	protein-coding	0.009579	0.416826	
chunk0054_403_1	chr13	50460122	50460588	+	0	NA	intron (NR_109974, intron 4 of 6)	L3|LINE|CR1	67094	NR_125753	103689915	Hs.722230	NR_125753	ENSG00000186047	DLEU1-AS1	LINC01308	DLEU1 antisense RNA 1	ncRNA	0.002146	0.387580	
chunk0054_166_1	chr13	44237213	44237605	+	0	NA	Intergenic	Intergenic	-41209	NR_107046	102465876		NR_107046	ENSG00000276319	MIR8079	hsa-mir-8079	microRNA 8079	ncRNA	0.005102	0.463104	228(TATAACAGCCTGTGCT,-,0.00),229(ATAACAGCCTGTGCTG,+,0.00),243(TGAGACAGGCTGTCCT,-,0.00),244(GAGACAGGCTGTCCTG,+,0.00)
chunk0001_349_1	chr1	9825529	9826215	+	0	NA	Intergenic	Intergenic	-1346	NM_001009566	22883	Hs.29665	NM_014944	ENSG00000171603	CLSTN1	ALC-ALPHA|CDHR12|CST-1|CSTN1|PIK3CD|XB31alpha|alcalpha1|alcalpha2	calsyntenin 1	protein-coding	0.010204	0.506550	536(TGGAACAATATGTACT,-,0.00),537(GGAACAATATGTACTT,+,0.00)
chunk0093_52_1	chr19	40249107	40250257	+	0	NA	intron (NM_001243028, intron 3 of 12)	intron (NM_001243028, intron 3 of 12)	-22992	NM_024877	79935	Hs.631603	NM_024877	ENSG00000105219	CNTD2	CCNP	cyclin N-terminal domain containing 2	protein-coding	0.024348	0.542137	
chunk0159_304_1	chr5	142982037	142982312	+	0	NA	intron (NM_015071, intron 11 of 22)	intron (NM_015071, intron 11 of 22)	-113264	NR_046680	100874239	Hs.570896	NR_046680	ENSG00000226272	ARHGAP26-AS1	-	ARHGAP26 antisense RNA 1	ncRNA	0.007273	0.510870	
chunk0105_106_1	chr2	184683964	184684339	+	0	NA	intron (NM_194250, intron 1 of 3)	intron (NM_194250, intron 1 of 3)	85785	NM_194250	91752	Hs.159528	NM_194250	ENSG00000170396	ZNF804A	C2orf10	zinc finger protein 804A	protein-coding	0.008000	0.351064	
chunk0158_75_1	chr5	126353104	126353427	+	0	NA	Intergenic	L1MC4|LINE|L1	-6831	NM_001146319	65983	Hs.363558	NM_023927	ENSG00000155324	GRAMD2B	GRAMD3|NS3TP2	GRAM domain containing 2B	protein-coding	0.012384	0.373457	
chunk0149_411_1	chr5	29408187	29408415	+	0	NA	Intergenic	L1MA6|LINE|L1	-12325	NR_104628	101929681	Hs.549659	NR_104628		LINC02064	-	long intergenic non-protein coding RNA 2064	ncRNA	0.000000	0.349345	
chunk0010_392_1	chr1	119427800	119428589	+	0	NA	Intergenic	PRIMA4-int|LTR|ERV1	13074	NM_000198	3284	Hs.654399	NM_000198	ENSG00000203859	HSD3B2	HSD3B|HSDB|SDR11E2	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	protein-coding	0.006337	0.420253	138(GGATCAGGTTGTTCAT,+,0.00)
chunk0127_145_1	chr3	94393068	94393610	+	0	NA	Intergenic	Intergenic	-330116	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.001845	0.313076	
chunk0154_22_1	chr5	76822573	76822834	+	0	NA	intron (NM_005242, intron 1 of 1)	intron (NM_005242, intron 1 of 1)	3695	NM_005242	2150	Hs.744181	NM_005242	ENSG00000164251	F2RL1	GPR11|PAR2	F2R like trypsin receptor 1	protein-coding	0.000000	0.366412	
chunk0089_120_1	chr18	58647463	58647990	+	0	NA	Intergenic	L1ME4b|LINE|L1	-18769	NM_052947	115701	Hs.628152	NM_052947	ENSG00000198796	ALPK2	HAK	alpha kinase 2	protein-coding	0.005693	0.348485	124(GTGAACTGCCTGTCCA,-,0.00),125(TGAACTGCCTGTCCAT,+,0.00),215(TAGTACACCTTGTCCC,-,0.00),216(AGTACACCTTGTCCCT,+,0.00)
chunk0016_286_1	chr1	200758777	200759149	+	0	NA	intron (NM_001297708, intron 1 of 16)	intron (NM_001297708, intron 1 of 16)	19405	NM_001297708	23271	Hs.23585	NM_203459	ENSG00000118200	CAMSAP2	CAMSAP1L1	calmodulin regulated spectrin associated protein family member 2	protein-coding	0.010753	0.361930	
chunk0196_251_1	chr8	108592759	108593374	+	0	NA	Intergenic	L1PA8|LINE|L1	149442	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.004878	0.358766	176(CTGAACAACCTGTTCC,-,0.00),177(TGAACAACCTGTTCCT,+,0.00)
chunk0108_418_1	chr2	237693515	237694032	+	0	NA	intron (NM_001137551, intron 1 of 11)	intron (NM_001137551, intron 1 of 11)	1609	NM_004735	9208	Hs.471779	NM_004735	ENSG00000124831	LRRFIP1	FLAP-1|FLAP1|FLIIAP1|GCF-2|GCF2|HUFI-1|TRIP	LRR binding FLII interacting protein 1	protein-coding	0.011605	0.538610	
chunk0101_210_1	chr2	130255763	130256032	+	0	NA	Intergenic	MER110A|LTR|ERV1	-57436	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.011152	0.433333	
chunk0188_392_1	chr8	18612592	18613180	+	0	NA	intron (NM_015310, intron 11 of 15)	intron (NM_015310, intron 11 of 15)	196009	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.018707	0.446520	
chunk0181_433_1	chr7	90488302	90488646	+	0	NA	Intergenic	Intergenic	85140	NM_001185072	9069	Hs.731917	NM_012129	ENSG00000157224	CLDN12	-	claudin 12	protein-coding	0.000000	0.324638	
chunk0047_124_1	chr12	69248092	69248568	+	0	NA	intron (NM_007007, intron 1 of 9)	intron (NM_007007, intron 1 of 9)	8793	NM_001300947	11052	Hs.369606	NM_007007	ENSG00000111605	CPSF6	CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7	cleavage and polyadenylation specific factor 6	protein-coding	0.004202	0.356394	
chunk0122_85_1	chr3	29978115	29978363	+	0	NA	intron (NM_001003793, intron 12 of 14)	intron (NM_001003793, intron 12 of 14)	-44083	NR_046556	100873977	Hs.581453	NR_046556	ENSG00000235593	RBMS3-AS1	-	RBMS3 antisense RNA 1	ncRNA	0.000000	0.369478	
chunk0058_90_1	chr14	21557309	21557988	+	0	NA	Intergenic	UCON105|Unknown|Unknown	13096	NM_001005465	26533	Hs.554581	NM_001005465	ENSG00000169208	OR10G3	OR14-40	olfactory receptor family 10 subfamily G member 3	protein-coding	0.014728	0.429412	
chunk0033_296_1	chr11	19792557	19792929	+	0	NA	intron (NM_001244963, intron 1 of 39)	intron (NM_001244963, intron 1 of 39)	-32660	NR_039843	100616426		NR_039843	ENSG00000264309	MIR4694	-	microRNA 4694	ncRNA	0.005376	0.466488	
chunk0021_230_1	chr10	6361796	6362426	+	0	NA	Intergenic	Intergenic	35567	NR_040079	399715		NR_040079	ENSG00000215244	LINC02649	-	long intergenic non-protein coding RNA 2649	ncRNA	0.004762	0.375594	
chunk0154_447_1	chr5	90462811	90463347	+	0	NA	intron (NM_203406, intron 1 of 1)	L1M4|LINE|L1	11689	NM_203406	153364	Hs.64004	NM_203406	ENSG00000176055	MBLAC2	-	metallo-beta-lactamase domain containing 2	protein-coding	0.013060	0.402235	
chunk0109_66_1	chr20	1401498	1401697	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	-8425	NR_037661	100528031	Hs.471933	NR_037661		FKBP1A-SDCBP2	-	FKBP1A-SDCBP2 readthrough (NMD candidate)	ncRNA	0.010050	0.440000	
chunk0179_57_1	chr7	43700691	43701012	+	0	NA	intron (NR_047701, intron 1 of 7)	intron (NR_047701, intron 1 of 7)	28690	NR_047701	55744	Hs.268887	NM_018224	ENSG00000106603	COA1	C7orf44|MITRAC15	cytochrome c oxidase assembly factor 1 homolog	protein-coding	0.003115	0.397516	
chunk0002_383_1	chr1	26731522	26731858	+	0	NA	intron (NM_139135, intron 3 of 19)	intron (NM_139135, intron 3 of 19)	35659	NM_139135	8289	Hs.468972	NM_006015	ENSG00000117713	ARID1A	B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1	AT-rich interaction domain 1A	protein-coding	0.011905	0.465875	
chunk0200_319_1	chr9	23577430	23577887	+	0	NA	intron (NR_121602, intron 11 of 27)	intron (NR_121602, intron 11 of 27)	94741	NR_121602	101929563	Hs.533220	NR_121602	ENSG00000283982	LOC101929563	-	uncharacterized LOC101929563	ncRNA	0.002188	0.430131	
chunk0015_95_1	chr1	185045951	185046280	+	0	NA	intron (NM_007212, intron 1 of 6)	intron (NM_007212, intron 1 of 6)	696	NM_007212	6045	Hs.591490	NM_007212	ENSG00000121481	RNF2	BAP-1|BAP1|DING|HIPI3|RING1B|RING2	ring finger protein 2	protein-coding	0.072948	0.654545	
chunk0123_291_1	chr3	46526451	46526923	+	0	NA	intron (NM_024512, intron 7 of 8)	intron (NM_024512, intron 7 of 8)	28692	NM_031440	83597	Hs.196584	NM_031440	ENSG00000163825	RTP3	LTM1|TMEM7|Z3CXXC3	receptor transporter protein 3	protein-coding	0.010593	0.465116	238(AAGAACTAGGAGTCCT,-,0.00)
chunk0164_83_1	chr6	20056062	20056784	+	0	NA	Intergenic	Intergenic	156041	NM_001080480	154141	Hs.377830	NM_001080480	ENSG00000172197	MBOAT1	LPEAT1|LPLAT|LPLAT 1|LPSAT|OACT1|dJ434O11.1	membrane bound O-acyltransferase domain containing 1	protein-coding	0.013850	0.387275	443(CAGAACACAATGTCCT,-,0.00),444(AGAACACAATGTCCTA,+,0.00)
chunk0063_242_1	chr14	82354115	82354530	+	0	NA	Intergenic	Intergenic	-731261	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.000000	0.370192	
chunk0143_259_1	chr4	115866276	115867003	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-433086	NR_031737	100302290		NR_031737	ENSG00000284253	MIR1973	hsa-mir-1973|mir-1973	microRNA 1973	ncRNA	0.006878	0.344780	
chunk0141_275_1	chr4	86577322	86577963	+	0	NA	Intergenic	HAL1|LINE|L1	-16673	NM_006264	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.003120	0.311526	
chunk0040_442_1	chr11	121521072	121521840	+	0	NA	intron (NM_003105, intron 9 of 47)	intron (NM_003105, intron 9 of 47)	69253	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.005208	0.382315	
chunk0153_311_1	chr5	73606225	73606835	+	0	NA	Intergenic	L1MC4a|LINE|L1	-19628	NM_001080479	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.006557	0.405892	329(TGGCACAAAATGTTCC,-,0.00),330(GGCACAAAATGTTCCT,+,0.00)
chunk0151_303_1	chr5	53093156	53093558	+	0	NA	non-coding (NR_073105, exon 30 of 30)	non-coding (NR_073105, exon 30 of 30)	16415	NM_176806	4338	Hs.163645	NM_004531	ENSG00000164172	MOCS2	MCBPE|MOCO1|MOCODB|MPTS	molybdenum cofactor synthesis 2	protein-coding	0.009950	0.459057	
chunk0066_112_1	chr15	30023217	30023937	+	0	NA	Intergenic	L1M5|LINE|L1	-54778	NM_001301025	7082	Hs.743990	NM_003257	ENSG00000104067	TJP1	ZO-1	tight junction protein 1	protein-coding	0.004167	0.359223	
chunk0142_412_1	chr4	103095070	103095510	+	0	NA	intron (NM_020139, intron 2 of 9)	intron (NM_020139, intron 2 of 9)	4577	NM_020139	56898	Hs.124696	NM_020139	ENSG00000164039	BDH2	DHRS6|EFA6R|PRO20933|SDR15C1|UCPA-OR|UNQ6308	3-hydroxybutyrate dehydrogenase 2	protein-coding	0.006818	0.371882	
chunk0141_346_1	chr4	87521675	87522361	+	0	NA	intron (NM_001128310, intron 1 of 11)	intron (NM_001128310, intron 1 of 11)	7485	NM_001128310	8404	Hs.62886	NM_004684	ENSG00000152583	SPARCL1	MAST 9|MAST9|PIG33|SC1	SPARC like 1	protein-coding	0.004373	0.374090	
chunk0165_297_1	chr6	36634028	36634285	+	0	NA	Intergenic	Intergenic	-11644	NR_037491	100500885		NR_037491	ENSG00000263894	MIR3925	-	microRNA 3925	ncRNA	0.015564	0.527132	
chunk0202_210_1	chr9	76076415	76076901	+	0	NA	intron (NM_001190482, intron 7 of 36)	intron (NM_001190482, intron 7 of 36)	186014	NM_006200	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.000000	0.359343	
chunk0050_162_1	chr12	103459477	103460115	+	0	NA	intron (NM_198521, intron 2 of 5)	intron (NM_198521, intron 2 of 5)	36214	NM_001099336	374470	Hs.534649	NM_198521	ENSG00000179088	C12orf42	-	chromosome 12 open reading frame 42	protein-coding	0.003135	0.446009	
chunk0029_10_1	chr10	95388436	95389031	+	0	NA	intron (NM_001034955, intron 12 of 30)	intron (NM_001034955, intron 12 of 30)	52447	NM_001290296	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.003361	0.416107	
chunk0014_396_1	chr1	182858753	182859170	+	0	NA	intron (NR_033302, intron 11 of 28)	intron (NR_033302, intron 11 of 28)	19657	NM_001357	1660	Hs.191518	NM_001357	ENSG00000135829	DHX9	DDX9|LKP|NDH2|NDHII|RHA	DExH-box helicase 9	protein-coding	0.004796	0.397129	
chunk0016_30_1	chr1	193036381	193036780	+	0	NA	intron (NR_037607, intron 3 of 10)	L1MA4|LINE|L1	22813	NM_001199261	51377	Hs.145469	NM_015984	ENSG00000116750	UCHL5	CGI-70|INO80R|UCH-L5|UCH37	ubiquitin C-terminal hydrolase L5	protein-coding	0.005013	0.332500	
chunk0147_430_1	chr4	187413618	187414094	+	0	NA	intron (NR_038931, intron 1 of 4)	MIRb|SINE|MIR	91757	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.000000	0.348008	
chunk0077_58_1	chr16	76593267	76593735	+	0	NA	Intergenic	Intergenic	-41497	NR_110934	101928203	Hs.737035	NR_110934	ENSG00000250514	LINC02125	-	long intergenic non-protein coding RNA 2125	ncRNA	0.006410	0.366738	
chunk0084_333_1	chr17	81037381	81037854	+	0	NA	intron (NM_006340, intron 1 of 14)	intron (NM_006340, intron 1 of 14)	2470	NM_001144888	10458	Hs.128316	NM_006340	ENSG00000175866	BAIAP2	BAP2|FLAF3|IRSP53	BAI1 associated protein 2	protein-coding	0.033827	0.601266	
chunk0196_6_1	chr8	101409903	101410137	+	0	NA	Intergenic	Intergenic	41127	NR_002182	83955	Hs.567608	NM_032031	ENSG00000228224	NACA4P	FKSG17|NACAP1	NACA family member 4, pseudogene	pseudo	0.004274	0.395745	
chunk0073_212_1	chr16	10520248	10521075	+	0	NA	Intergenic	Intergenic	60055	NM_001424	2013	Hs.531561	NM_001424	ENSG00000213853	EMP2	XMP	epithelial membrane protein 2	protein-coding	0.008464	0.480676	412(GGGAACATCCCGTGCT,-,0.00),413(GGAACATCCCGTGCTG,+,0.00)
chunk0063_320_1	chr14	85166924	85167541	+	0	NA	Intergenic	Intergenic	-226647	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.001621	0.288026	
chunk0201_426_1	chr9	69860942	69861555	+	0	NA	intron (NM_001308084, intron 4 of 4)	Tigger3b|DNA|TcMar-Tigger	40443	NR_131757	138255	Hs.444459	NM_001010940	ENSG00000204711	C9orf135	-	chromosome 9 open reading frame 135	protein-coding	0.003263	0.374593	76(AGTACAGTAAGTGCAT,+,0.00),305(TAGTACATACTGTACA,-,0.00),306(AGTACATACTGTACAG,+,0.00)
chunk0144_167_1	chr4	131822062	131822342	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	57364	NR_125883	101927305	Hs.507924	NR_125883		SNHG27	-	small nucleolar RNA host gene 27	ncRNA	0.010714	0.330961	
chunk0144_176_1	chr4	133161873	133162427	+	0	NA	intron (NM_032961, intron 3 of 4)	intron (NM_032961, intron 3 of 4)	12860	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.003610	0.297297	
chunk0185_395_1	chr7	133541353	133541552	+	0	NA	intron (NM_021807, intron 9 of 17)	intron (NM_021807, intron 9 of 17)	250571	NR_106749	102465139		NR_106749	ENSG00000276137	MIR6133	hsa-mir-6133	microRNA 6133	ncRNA	0.015075	0.360000	
chunk0076_142_1	chr16	67104830	67105265	+	0	NA	Intergenic	Intergenic	-4965	NM_025187	80262	Hs.513666	NM_025187	ENSG00000125149	C16orf70	C16orf6|LIN10|lin-10	chromosome 16 open reading frame 70	protein-coding	0.013793	0.444954	
chunk0189_434_1	chr8	28140719	28141096	+	0	NA	intron (NM_018091, intron 10 of 14)	Tigger17a|DNA|TcMar-Tigger	47840	NM_001284224	55140	Hs.491336	NM_018091	ENSG00000134014	ELP3	KAT9	elongator acetyltransferase complex subunit 3	protein-coding	0.013263	0.415344	
chunk0121_296_1	chr3	23741017	23741356	+	0	NA	Intergenic	Intergenic	-64707	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.014749	0.500000	
chunk0112_60_1	chr20	37519097	37519791	+	0	NA	intron (NM_006698, intron 1 of 1)	intron (NM_006698, intron 1 of 1)	-1761	NM_181689	4826	Hs.504703	NM_005386	ENSG00000053438	NNAT	Peg5	neuronatin	protein-coding	0.031700	0.564029	
chunk0151_316_1	chr5	53454201	53454887	+	0	NA	Intergenic	Intergenic	-25890	NM_006350	10468	Hs.9914	NM_006350	ENSG00000134363	FST	FS	follistatin	protein-coding	0.000000	0.381368	
chunk0085_224_1	chr18	6835360	6835603	+	0	NA	intron (NM_001010000, intron 1 of 16)	intron (NM_001010000, intron 1 of 16)	1048	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.004115	0.344262	
chunk0053_350_1	chr13	34827066	34827787	+	0	NA	Intergenic	L2b|LINE|L2	-114861	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.009709	0.426593	
chunk0008_289_1	chr1	94883881	94884171	+	0	NA	intron (NM_001258342, intron 11 of 13)	HAL1b|LINE|L1	41782	NM_001286056	1266	Hs.483454	NM_001839	ENSG00000117519	CNN3	-	calponin 3	protein-coding	0.013793	0.415808	
chunk0031_291_1	chr10	128443643	128443842	+	0	NA	Intergenic	L1MEf|LINE|L1	157792	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.005025	0.305000	130(AAGCACATTATGTACA,-,0.00),131(AGCACATTATGTACAA,+,0.00)
chunk0092_3_1	chr19	18446761	18447451	+	0	NA	intron (NM_006532, intron 8 of 11)	intron (NM_006532, intron 8 of 11)	-8805	NR_045573	51477	Hs.405873	NM_016368	ENSG00000105655	ISYNA1	INO1|INOS|IPS|IPS 1|IPS-1	inositol-3-phosphate synthase 1	protein-coding	0.028986	0.596237	
chunk0090_9_1	chr19	493203	493433	+	0	NA	Intergenic	Intergenic	-3172	NM_130760	8174	Hs.102598	NM_130760	ENSG00000099866	MADCAM1	MACAM1	mucosal vascular addressin cell adhesion molecule 1	protein-coding	0.026087	0.627706	
chunk0157_181_1	chr5	118531242	118531859	+	0	NA	intron (NR_104610, intron 1 of 9)	intron (NR_104610, intron 1 of 9)	30567	NR_104610	101927280	Hs.543951	NR_104610		LINC02208	HRAT56	long intergenic non-protein coding RNA 2208	ncRNA	0.004862	0.423948	371(GAAGACAAAGTGTTCC,-,0.00),372(AAGACAAAGTGTTCCA,+,0.00)
chunk0086_442_1	chr18	29157007	29157341	+	0	NA	Intergenic	Intergenic	-979728	NM_001792	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.008982	0.373134	
chunk0082_159_1	chr17	55721490	55721740	+	0	NA	intron (NM_018286, intron 1 of 1)	intron (NM_018286, intron 1 of 1)	1249	NM_018286	55273	Hs.173233	NM_018286	ENSG00000166292	TMEM100	-	transmembrane protein 100	protein-coding	0.008000	0.406375	
chunk0001_6_1	chr1	815507	815712	+	0	NA	Intergenic	Intergenic	-1762	NR_103536	400728	Hs.568078	NM_207464	ENSG00000177757	FAM87B	-	family with sequence similarity 87 member B	ncRNA	0.000000	0.417476	
chunk0179_134_1	chr7	45929581	45929933	+	0	NA	Intergenic	L1ME1|LINE|L1	-8485	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.000000	0.325779	
chunk0113_187_1	chr20	53304218	53304590	+	0	NA	intron (NM_001193421, intron 2 of 2)	intron (NM_001193421, intron 2 of 2)	119121	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.008065	0.415550	
chunk0106_157_1	chr2	200578618	200578987	+	0	NA	intron (NM_152524, intron 8 of 8)	L1M3|LINE|L1	-7206	NM_001159	316	Hs.406238	NM_001159	ENSG00000138356	AOX1	AO|AOH1	aldehyde oxidase 1	protein-coding	0.008130	0.418919	
chunk0203_421_1	chr9	91000043	91001412	+	0	NA	Intergenic	Intergenic	74405	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.012418	0.418978	745(GAGCCCAGTGTGTCCC,-,0.00),746(AGCCCAGTGTGTCCCA,+,0.00)
chunk0114_330_1	chr21	17541588	17542025	+	0	NA	intron (NM_001207065, intron 1 of 2)	L1MC4|LINE|L1	28900	NM_001207064	1525	Hs.627078	NM_001338	ENSG00000154639	CXADR	CAR|CAR4/6|HCAR	CXADR Ig-like cell adhesion molecule	protein-coding	0.002288	0.326484	227(AGGTACATAATGTCCA,-,0.00),228(GGTACATAATGTCCAT,+,0.00)
chunk0144_417_1	chr4	140461130	140461813	+	0	NA	intron (NM_001277353, intron 7 of 10)	intron (NM_001277353, intron 7 of 10)	-33810	NM_004362	1047	Hs.86368	NM_004362	ENSG00000153132	CLGN	-	calmegin	protein-coding	0.001464	0.317251	
chunk0150_429_1	chr5	40396298	40396686	+	0	NA	Intergenic	Intergenic	-283438	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.002577	0.401028	
chunk0124_195_1	chr3	55641857	55642229	+	0	NA	intron (NR_132749, intron 16 of 17)	intron (NR_132749, intron 16 of 17)	17426	NR_024615	711	Hs.667161	NR_024615	ENSG00000281708	ERC2-IT1	C1orf1|C3orf51|Po42	ERC2 intronic transcript 1	ncRNA	0.002688	0.415550	
chunk0143_341_1	chr4	121582398	121582611	+	0	NA	Intergenic	Intergenic	114488	NM_001154	308	Hs.480653	NM_001154	ENSG00000164111	ANXA5	ANX5|ENX2|HEL-S-7|PP4|RPRGL3	annexin A5	protein-coding	0.000000	0.415888	
chunk0050_412_1	chr12	109707094	109707440	+	0	NA	Intergenic	Intergenic	-7115	NM_032829	84915	Hs.661785	NM_032829	ENSG00000139438	FAM222A	C12orf34	family with sequence similarity 222 member A	protein-coding	0.011561	0.510086	
chunk0132_58_1	chr3	155083132	155083726	+	0	NA	intron (NM_007289, intron 1 of 22)	intron (NM_007289, intron 1 of 22)	3139	NM_007289	4311	Hs.307734	NM_000902	ENSG00000196549	MME	CALLA|CD10|CMT2T|NEP|SCA43|SFE	membrane metalloendopeptidase	protein-coding	0.008418	0.344538	
chunk0210_181_1	chrX	79331254	79331522	+	0	NA	Intergenic	MER51D|LTR|ERV1	36164	NM_001171581	9452	Hs.17109	NM_004867	ENSG00000078596	ITM2A	BRICD2A|E25A	integral membrane protein 2A	protein-coding	0.003731	0.412639	111(GAGAACAGACTGACCT,-,0.00),112(AGAACAGACTGACCTC,+,0.00)
chunk0097_418_1	chr2	62857188	62857609	+	0	NA	intron (NM_001142614, intron 6 of 22)	L2c|LINE|L2	150501	NM_001142614	23301	Hs.271667	NM_015252	ENSG00000115504	EHBP1	HPC12|NACSIN	EH domain binding protein 1	protein-coding	0.009501	0.310427	
chunk0137_204_1	chr4	18040071	18040548	+	0	NA	Intergenic	Intergenic	-18449	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.004193	0.397490	
chunk0156_159_1	chr5	107427183	107427544	+	0	NA	exon (NM_001962, exon 2 of 5)	exon (NM_001962, exon 2 of 5)	243532	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.019391	0.433702	
chunk0153_138_1	chr5	69019368	69019861	+	0	NA	intron (NR_130778, intron 1 of 3)	MLT1C|LTR|ERVL-MaLR	10313	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.004057	0.421053	
chunk0196_349_1	chr8	114476008	114476391	+	0	NA	Intergenic	L2c|LINE|L2	-1039186	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.002611	0.343750	
chunk0054_416_1	chr13	50879380	50879579	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-30199	NM_001142279	79621	Hs.306291	NM_024570	ENSG00000136104	RNASEH2B	AGS2|DLEU8	ribonuclease H2 subunit B	protein-coding	0.000000	0.340000	
chunk0087_328_1	chr18	39991938	39992254	+	0	NA	Intergenic	Intergenic	-74190	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.015823	0.394322	240(AAGAACAGGCTGTTTT,-,0.00),241(AGAACAGGCTGTTTTG,+,0.00)
chunk0075_296_1	chr16	54250513	54251083	+	0	NA	intron (NR_126340, intron 1 of 2)	L1ME4a|LINE|L1	20081	NR_126340	100996338	Hs.232014	NR_126340		LINC02169	-	long intergenic non-protein coding RNA 2169	ncRNA	0.005263	0.357268	
chunk0211_60_1	chrX	109740003	109740476	+	0	NA	Intergenic	Intergenic	-6847	NM_004458	2182	Hs.268785	NM_004458	ENSG00000068366	ACSL4	ACS4|FACL4|LACS4|MRX63|MRX68	acyl-CoA synthetase long chain family member 4	protein-coding	0.008457	0.386076	
chunk0089_54_1	chr18	58128271	58128584	+	0	NA	intron (NM_001144964, intron 1 of 30)	intron (NM_001144964, intron 1 of 30)	-20906	NM_001144969	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.019169	0.484076	
chunk0132_154_1	chr3	156601707	156601928	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-46617	NM_001308197	6747	Hs.518346	NM_007107	ENSG00000114850	SSR3	TRAPG	signal sequence receptor subunit 3	protein-coding	0.004525	0.355856	
chunk0002_21_1	chr1	12356492	12356808	+	0	NA	intron (NM_018156, intron 48 of 68)	intron (NM_018156, intron 48 of 68)	126611	NM_015378	55187	Hs.439381	NM_015378	ENSG00000048707	VPS13D	SCAR4	vacuolar protein sorting 13 homolog D	protein-coding	0.006329	0.362776	
chunk0168_13_1	chr6	76856784	76857301	+	0	NA	Intergenic	Intergenic	606361	NM_000863	3351	Hs.123016	NM_000863	ENSG00000135312	HTR1B	5-HT-1B|5-HT-1D-beta|5-HT1B|5-HT1DB|HTR1D2|HTR1DB|S12	5-hydroxytryptamine receptor 1B	protein-coding	0.001934	0.337838	
chunk0087_209_1	chr18	35989873	35990192	+	0	NA	3' UTR (NM_001303411, exon 8 of 8)	3' UTR (NM_001303411, exon 8 of 8)	17407	NM_001201474	83608	Hs.37883	NM_031446	ENSG00000141428	C18orf21	HsT3108|PNAS-124|PNAS-131|XTP13	chromosome 18 open reading frame 21	protein-coding	0.003135	0.340625	
chunk0017_275_1	chr1	209747895	209748200	+	0	NA	Intergenic	Intergenic	-7985	NM_025228	80342	Hs.147434	NM_025228	ENSG00000009790	TRAF3IP3	T3JAM	TRAF3 interacting protein 3	protein-coding	0.052459	0.542484	
chunk0087_454_1	chr18	42706466	42706793	+	0	NA	Intergenic	LTR9|LTR|ERV1	409063	NM_002930	6014	Hs.464985	NM_002930	ENSG00000152214	RIT2	RIBA|RIN|ROC2	Ras like without CAAX 2	protein-coding	0.009174	0.445122	
chunk0208_207_1	chrX	18010120	18010709	+	0	NA	intron (NR_133641, intron 1 of 4)	intron (NR_133641, intron 1 of 4)	94230	NR_133641	105373144		NR_133641	ENSG00000225882	LINC01456	-	long intergenic non-protein coding RNA 1456	ncRNA	0.008489	0.427119	
chunk0164_25_1	chr6	18183774	18184212	+	0	NA	intron (NM_153042, intron 7 of 17)	L1ME3A|LINE|L1	28605	NM_153042	221656	Hs.709336	NM_153042	ENSG00000165097	KDM1B	AOF1|C6orf193|LSD2	lysine demethylase 1B	protein-coding	0.009132	0.382688	
chunk0180_238_1	chr7	67493448	67493801	+	0	NA	Intergenic	Intergenic	157648	NR_108104	101929736	Hs.634050	NR_108104	ENSG00000106610	LINC01372	-	long intergenic non-protein coding RNA 1372	ncRNA	0.016997	0.528249	
chunk0052_172_1	chr13	24153983	24154336	+	0	NA	intron (NM_001286792, intron 3 of 14)	L1ME3|LINE|L1	-6557	NM_001166271	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.005666	0.384181	
chunk0017_346_1	chr1	211782012	211782428	+	0	NA	intron (NM_014873, intron 5 of 7)	L1ME4a|LINE|L1	48552	NM_014873	9926	Hs.744851	NM_014873	ENSG00000123684	LPGAT1	FAM34A|FAM34A1|NET8	lysophosphatidylglycerol acyltransferase 1	protein-coding	0.009615	0.309353	
chunk0168_72_1	chr6	79465500	79465794	+	0	NA	Intergenic	Intergenic	71783	NM_181714	167691	Hs.21945	NM_181714	ENSG00000135338	LCA5	C6orf152	lebercilin LCA5	protein-coding	0.000000	0.338983	
chunk0148_286_1	chr5	11711686	11712466	+	0	NA	intron (NR_109988, intron 2 of 21)	MIRc|SINE|MIR	-123159	NM_001288715	1501	Hs.314543	NM_001332	ENSG00000169862	CTNND2	GT24|NPRAP	catenin delta 2	protein-coding	0.002564	0.361076	393(GAGAACTAAATGTCCC,-,0.00),394(AGAACTAAATGTCCCC,+,0.00)
chunk0119_285_1	chr22	46156246	46156678	+	0	NA	intron (NM_001001928, intron 2 of 7)	intron (NM_001001928, intron 2 of 7)	5866	NM_005036	5465	Hs.103110	NM_005036	ENSG00000186951	PPARA	NR1C1|PPAR|PPARalpha|hPPAR	peroxisome proliferator activated receptor alpha	protein-coding	0.006944	0.443418	
chunk0171_133_1	chr6	122803296	122803588	+	0	NA	intron (NM_006714, intron 4 of 7)	intron (NM_006714, intron 4 of 7)	14393	NM_001286138	10924	Hs.486357	NM_006714	ENSG00000172594	SMPDL3A	ASM3A|ASML3a|yR36GH4.1	sphingomyelin phosphodiesterase acid like 3A	protein-coding	0.010274	0.372014	
chunk0018_238_1	chr1	219910513	219911120	+	0	NA	Intergenic	Intergenic	17835	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.009885	0.386513	
chunk0093_140_1	chr19	46315381	46315580	+	0	NA	intron (NM_152794, intron 8 of 14)	L1ME1|LINE|L1	11881	NM_152794	64344	Hs.420830	NM_022462	ENSG00000124440	HIF3A	HIF-3A|HIF3-alpha-1|IPAS|MOP7|PASD7|bHLHe17	hypoxia inducible factor 3 subunit alpha	protein-coding	0.005025	0.355000	
chunk0169_408_1	chr6	108476507	108477065	+	0	NA	intron (NM_145315, intron 8 of 12)	intron (NM_145315, intron 8 of 12)	-83037	NM_201559	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.005376	0.377460	244(CATAACATCCTGTTCT,-,0.00),245(ATAACATCCTGTTCTT,+,0.00)
chunk0126_323_1	chr3	81676719	81677471	+	0	NA	intron (NM_000158, intron 2 of 15)	intron (NM_000158, intron 2 of 15)	84704	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.006649	0.371846	
chunk0035_212_1	chr11	44952245	44952457	+	0	NA	Intergenic	Intergenic	-1045	NM_001258322	9537	Hs.554791	NM_006034	ENSG00000175274	TP53I11	PIG11	tumor protein p53 inducible protein 11	protein-coding	0.000000	0.492958	81(CAGGAGAGTCTGTGCC,-,0.00),82(AGGAGAGTCTGTGCCC,+,0.00)
chunk0159_441_1	chr5	148394338	148395236	+	0	NA	exon (NM_001271723, exon 2 of 21)	exon (NM_001271723, exon 2 of 21)	10852	NM_001271723	81545	Hs.483772	NM_030793	ENSG00000145868	FBXO38	Fbx38|HMN2D|MOKA|SP329	F-box protein 38	protein-coding	0.006682	0.350389	
chunk0212_124_1	chrX	130897108	130897344	+	0	NA	intron (NM_006375, intron 2 of 14)	intron (NM_006375, intron 2 of 14)	6091	NM_001281736	10495	Hs.171458	NM_006375	ENSG00000165675	ENOX2	APK1|COVA1|tNOX	ecto-NOX disulfide-thiol exchanger 2	protein-coding	0.012712	0.396624	
chunk0096_210_1	chr2	30449912	30450473	+	0	NA	intron (NM_001304446, intron 1 of 5)	L2c|LINE|L2	2966	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.005348	0.427046	
chunk0186_172_1	chr7	139360270	139361073	+	0	NA	intron (NM_016019, intron 1 of 9)	CpG	825	NM_001270643	51631	Hs.731488	NM_016019	ENSG00000146963	LUC7L2	CGI-59|CGI-74|LUC7B2	LUC7 like 2, pre-mRNA splicing factor	protein-coding	0.046077	0.554726	
chunk0108_168_1	chr2	231464572	231465018	+	0	NA	promoter-TSS (NM_005381)	promoter-TSS (NM_005381)	-301	NM_005381	4691	Hs.79110	NM_005381	ENSG00000115053	NCL	C23|Nsr1	nucleolin	protein-coding	0.118834	0.718121	
chunk0021_393_1	chr1	246608366	246609331	+	0	NA	intron (NM_152609, intron 2 of 10)	intron (NM_152609, intron 2 of 10)	42511	NM_001139459	163882	Hs.368353	NM_152609	ENSG00000162852	CNST	C1orf71|PPP1R64	consortin, connexin sorting protein	protein-coding	0.019689	0.443064	
chunk0060_314_1	chr14	51225905	51226186	+	0	NA	Intergenic	Intergenic	-14123	NM_030755	81542	Hs.125221	NM_030755	ENSG00000139921	TMX1	PDIA11|TMX|TXNDC|TXNDC1	thioredoxin related transmembrane protein 1	protein-coding	0.007117	0.354610	
chunk0171_435_1	chr6	131682236	131682839	+	0	NA	intron (NR_133007, intron 11 of 23)	L1ME4a|LINE|L1	18864	NM_030908	79541	Hs.486488	NM_030908	ENSG00000180658	OR2A4	OR2A10	olfactory receptor family 2 subfamily A member 4	protein-coding	0.004975	0.403974	
chunk0142_418_1	chr4	103272088	103272587	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-73928	NM_001286734	1062	Hs.75573	NM_001813	ENSG00000138778	CENPE	CENP-E|KIF10|MCPH13|PPP1R61	centromere protein E	protein-coding	0.000000	0.434000	
chunk0066_118_1	chr15	30869422	30869981	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-34151	NM_001146095	22909	Hs.584863	NM_014967	ENSG00000198690	FAN1	KIAA1018|KMIN|MTMR15|hFAN1	FANCD2 and FANCI associated nuclease 1	protein-coding	0.007156	0.373214	
chunk0131_27_1	chr3	142221494	142221693	+	0	NA	intron (NM_001039547, intron 1 of 15)	intron (NM_001039547, intron 1 of 15)	4014	NR_033289	256356	Hs.135904	NM_152776	ENSG00000175066	GK5	-	glycerol kinase 5	protein-coding	0.000000	0.310000	
chunk0053_201_1	chr13	31926983	31927586	+	0	NA	intron (NR_027062, intron 1 of 3)	intron (NR_027062, intron 1 of 3)	80501	NR_027062	196549	Hs.507667	NM_145293		EEF1DP3	-	eukaryotic translation elongation factor 1 delta pseudogene 3	pseudo	0.008292	0.453642	
chunk0045_140_1	chr12	46450484	46450723	+	0	NA	intron (NR_125381, intron 2 of 2)	intron (NR_125381, intron 2 of 2)	66496	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.004184	0.541667	
chunk0040_448_1	chr11	121644045	121644363	+	0	NA	Intergenic	Intergenic	192001	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.018868	0.454545	
chunk0063_248_1	chr14	82452109	82452664	+	0	NA	Intergenic	Intergenic	-829325	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.003604	0.314748	
chunk0162_344_1	chr6	7004018	7004237	+	0	NA	Intergenic	MIRc|SINE|MIR	-103470	NM_001168344	6239	Hs.298248	NM_002955	ENSG00000124782	RREB1	FINB|HNT|LZ321|RREB-1|Zep-1	ras responsive element binding protein 1	protein-coding	0.018265	0.477273	126(TGGGACATCACGTTCC,-,0.00),127(GGGACATCACGTTCCT,+,0.00)
chunk0169_389_1	chr6	107960023	107960556	+	0	NA	Intergenic	Intergenic	-2011	NM_007214	11231	Hs.26904	NM_007214	ENSG00000025796	SEC63	DNAJC23|ERdj2|PCLD2|PRO2507|SEC63L	SEC63 homolog, protein translocation regulator	protein-coding	0.003752	0.327715	
chunk0148_426_1	chr5	15233082	15233625	+	0	NA	intron (NR_109944, intron 2 of 2)	intron (NR_109944, intron 2 of 2)	33207	NR_109944	101929454	Hs.453273	NR_109944		LINC02149	-	long intergenic non-protein coding RNA 2149	ncRNA	0.003683	0.288603	
chunk0131_88_1	chr3	143396623	143397303	+	0	NA	intron (NM_173653, intron 12 of 15)	intron (NM_173653, intron 12 of 15)	54717	NR_048544	100885796	Hs.581618	NR_048544	ENSG00000240012	SLC9A9-AS1	-	SLC9A9 antisense RNA 1	ncRNA	0.001471	0.390602	323(GAAAACATTATGTTCT,-,0.00),324(AAAACATTATGTTCTT,+,0.00)
chunk0028_432_1	chr10	93767133	93767479	+	0	NA	intron (NM_001308276, intron 2 of 5)	intron (NM_001308276, intron 2 of 5)	9497	NR_131777	9211	Hs.533670	NM_005097	ENSG00000108231	LGI1	ADLTE|ADPAEF|ADPEAF|EPITEMPIN|EPT|ETL1|IB1099	leucine rich glioma inactivated 1	protein-coding	0.005780	0.365994	
chunk0058_24_1	chr14	19907213	19907706	+	0	NA	Intergenic	Intergenic	-13148	NM_001005483	79317	Hs.554585	NM_001005483	ENSG00000176281	OR4K5	OR14-16	olfactory receptor family 4 subfamily K member 5	protein-coding	0.000000	0.358300	
chunk0147_3_1	chr4	170366687	170367269	+	0	NA	Intergenic	Intergenic	140387	NR_125889	101928223	Hs.254617	NR_125889		LINC01612	-	long intergenic non-protein coding RNA 1612	ncRNA	0.001718	0.293310	
chunk0076_148_1	chr16	67173663	67174405	+	0	NA	exon (NM_001276319, exon 3 of 6)	exon (NM_001276319, exon 3 of 6)	181	NM_003946	8996	Hs.513667	NM_003946	ENSG00000140939	NOL3	ARC|FCM|MYOCL1|MYP|NOP|NOP30	nucleolar protein 3	protein-coding	0.061995	0.625841	313(GAGGACACCGAGTTCC,-,0.00),314(AGGACACCGAGTTCCC,+,0.00)
chunk0083_268_1	chr17	68429962	68430667	+	0	NA	intron (NM_017983, intron 8 of 12)	intron (NM_017983, intron 8 of 12)	-5766	NR_030365	693220		NR_030365	ENSG00000207561	MIR635	MIRN635|hsa-mir-635	microRNA 635	ncRNA	0.019858	0.501416	299(AGGGAGAGACTGTGCC,-,0.00),300(GGGAGAGACTGTGCCT,+,0.00),582(AAGAACAGACAGATCT,-,0.00),583(AGAACAGACAGATCTC,+,0.00)
chunk0182_364_1	chr7	99925734	99926166	+	0	NA	intron (NM_181538, intron 1 of 1)	L1MB7|LINE|L1	3670	NM_181538	349149	Hs.647524	NM_181538	ENSG00000176402	GJC3	CX29|CX30.2|CX31.3|GJE1	gap junction protein gamma 3	protein-coding	0.002315	0.418014	
chunk0070_344_1	chr15	75903705	75903987	+	0	NA	promoter-TSS (NM_012170)	promoter-TSS (NM_012170)	-13	NM_012170	26263	Hs.591115	NM_012170	ENSG00000167196	FBXO22	FBX22|FISTC1	F-box protein 22	protein-coding	0.106383	0.646643	
chunk0173_302_1	chr6	148395867	148396280	+	0	NA	intron (NM_015278, intron 2 of 19)	intron (NM_015278, intron 2 of 19)	53480	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.007264	0.487923	
chunk0067_379_1	chr15	49035728	49036180	+	0	NA	intron (NM_001193489, intron 2 of 17)	intron (NM_001193489, intron 2 of 17)	10609	NM_001193489	9728	Hs.9997	NM_014701	ENSG00000138593	SECISBP2L	SBP2L|SLAN	SECIS binding protein 2 like	protein-coding	0.004425	0.381898	
chunk0172_314_1	chr6	138235156	138235605	+	0	NA	intron (NM_020340, intron 5 of 33)	intron (NM_020340, intron 5 of 33)	-16890	NM_021635	59351	Hs.302016	NM_021635	ENSG00000254440	PBOV1	UC28|UROC28|dJ171N11.2	prostate and breast cancer overexpressed 1	protein-coding	0.002227	0.433333	
chunk0073_218_1	chr16	10652803	10653016	+	0	NA	intron (NM_144674, intron 5 of 6)	intron (NM_144674, intron 5 of 6)	42036	NM_144674	146279	Hs.143519	NM_144674	ENSG00000153060	TEKT5	CT149	tektin 5	protein-coding	0.014085	0.523364	
chunk0191_43_1	chr8	43211695	43212191	+	0	NA	Intergenic	MIRb|SINE|MIR	71494	NM_152419	138050	Hs.600384	NM_152419	ENSG00000165102	HGSNAT	HGNAT|MPS3C|RP73|TMEM76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding	0.018145	0.452716	143(CAGGGCATGGTGTGCC,-,0.00)
chunk0113_14_1	chr20	49420293	49421002	+	0	NA	intron (NM_004975, intron 1 of 1)	MIRc|SINE|MIR	61997	NM_004975	3745	Hs.84244	NM_004975	ENSG00000158445	KCNB1	DRK1|Kv2.1	potassium voltage-gated channel subfamily B member 1	protein-coding	0.002821	0.463380	258(AGGTACACTCTGTTTC,-,0.00),259(GGTACACTCTGTTTCC,+,0.00)
chunk0084_290_1	chr17	79919052	79919525	+	0	NA	promoter-TSS (NR_110851)	promoter-TSS (NR_110851)	-69	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.038055	0.666667	
chunk0097_162_1	chr2	48855319	48855546	+	0	NA	Intergenic	Intergenic	-99691	NM_000233	3973	Hs.468490	NM_000233	ENSG00000138039	LHCGR	HHG|LCGR|LGR2|LH/CG-R|LH/CGR|LHR|LHRHR|LSH-R|ULG5	luteinizing hormone/choriogonadotropin receptor	protein-coding	0.000000	0.359649	184(CAGAACAAATTGTCCC,-,0.00),185(AGAACAAATTGTCCCC,+,0.00)
chunk0055_460_1	chr13	76465851	76466102	+	0	NA	Intergenic	Intergenic	420429	NM_138444	115207	Hs.644125	NM_138444	ENSG00000178695	KCTD12	C13orf2|PFET1|PFETIN	potassium channel tetramerization domain containing 12	protein-coding	0.000000	0.349206	
chunk0155_151_1	chr5	93798155	93798459	+	0	NA	intron (NR_028080, intron 6 of 8)	intron (NR_028080, intron 6 of 8)	-56704	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.000000	0.403279	
chunk0017_207_1	chr1	207823873	207824183	+	0	NA	Intergenic	Intergenic	5649	NR_026817	148696	Hs.125511	NM_001039568		LOC148696	-	uncharacterized LOC148696	ncRNA	0.029032	0.546624	
chunk0003_59_1	chr1	31102695	31102924	+	0	NA	Intergenic	Intergenic	-37092	NM_014676	9698	Hs.281707	NM_014676	ENSG00000134644	PUM1	HSPUM|PUMH|PUMH1|PUML1|SCA47	pumilio RNA binding family member 1	protein-coding	0.013100	0.526087	125(AGGAACAGGCTGTCCC,-,0.00),126(GGAACAGGCTGTCCCC,+,0.00)
chunk0056_364_1	chr13	92569680	92569979	+	0	NA	intron (NM_004466, intron 7 of 7)	intron (NM_004466, intron 7 of 7)	79666	NR_049840	100847092		NR_049840	ENSG00000263741	MIR548AS	-	microRNA 548as	ncRNA	0.006689	0.330000	209(GTTACACTGTGTTCTT,+,0.00)
chunk0050_168_1	chr12	103772189	103772419	+	0	NA	TTS (NM_001031701)	TTS (NM_001031701)	68893	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.008696	0.307359	
chunk0104_400_1	chr2	180663738	180664314	+	0	NA	Intergenic	Intergenic	-28078	NR_104322	101669767		NR_104319	ENSG00000281131	SCHLAP1	LINC00913|PCAT11|PCAT114	SWI/SNF complex antagonist associated with prostate cancer 1	ncRNA	0.012153	0.428076	
chunk0126_16_1	chr3	73521068	73521275	+	0	NA	promoter-TSS (NR_121660)	promoter-TSS (NR_121660)	-151	NR_121660	101927296	Hs.662049	NR_121660		LOC101927296	-	uncharacterized LOC101927296	ncRNA	0.038647	0.543269	
chunk0205_334_1	chr9	113151551	113152177	+	0	NA	intron (NM_001860, intron 1 of 3)	AluJo|SINE|Alu	906	NM_001860	1318	Hs.24030	NM_001860	ENSG00000136867	SLC31A2	COPT2|CTR2|hCTR2	solute carrier family 31 member 2	protein-coding	0.017572	0.449761	376(CAGAACAAGACGTCCT,-,0.00),377(AGAACAAGACGTCCTC,+,0.00)
chunk0074_335_1	chr16	31135888	31136087	+	0	NA	promoter-TSS (NM_002773)	promoter-TSS (NM_002773)	-157	NM_002773	5652	Hs.75799	NM_002773	ENSG00000052344	PRSS8	CAP1|PROSTASIN	serine protease 8	protein-coding	0.010050	0.510000	
chunk0010_398_1	chr1	119506823	119507084	+	0	NA	promoter-TSS (NM_000862)	promoter-TSS (NM_000862)	-250	NM_000862	3283	Hs.364941	NM_000862	ENSG00000203857	HSD3B1	3BETAHSD|HSD3B|HSDB3|HSDB3A|SDR11E1	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	protein-coding	0.000000	0.438931	
chunk0016_194_1	chr1	198523470	198523669	+	0	NA	intron (NM_133326, intron 4 of 4)	intron (NM_133326, intron 4 of 4)	17376	NM_133326	127124	Hs.127743	NM_133262	ENSG00000151418	ATP6V1G3	ATP6G3|Vma10	ATPase H+ transporting V1 subunit G3	protein-coding	0.000000	0.325000	
chunk0195_341_1	chr8	99480738	99481282	+	0	NA	intron (NM_152564, intron 24 of 61)	intron (NM_152564, intron 24 of 61)	55720	NR_030329	693184		NR_030329	ENSG00000207804	MIR599	MIRN599|hsa-mir-599	microRNA 599	ncRNA	0.007353	0.315596	
chunk0059_214_1	chr14	33886656	33887040	+	0	NA	Intergenic	Intergenic	63978	NM_001308103	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.018229	0.483117	
chunk0119_36_1	chr22	40499145	40499548	+	0	NA	intron (NM_001282661, intron 3 of 13)	intron (NM_001282661, intron 3 of 13)	-22454	NR_109965	101927257	Hs.662725	NR_109965	ENSG00000232564	MRTFA-AS1	-	MRTFA antisense RNA 1	ncRNA	0.004963	0.386139	
chunk0100_287_1	chr2	114543465	114543702	+	0	NA	intron (NM_001178036, intron 2 of 26)	intron (NM_001178036, intron 2 of 26)	81980	NM_001178036	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.016878	0.462185	
chunk0206_430_1	chr9	127784749	127784948	+	0	NA	promoter-TSS (NR_039767)	promoter-TSS (NR_039767)	-985	NR_039767	100616250		NR_039767	ENSG00000283863	MIR3960	-	microRNA 3960	ncRNA	0.045226	0.550000	
chunk0025_435_1	chr10	60040258	60040593	+	0	NA	intron (NM_001204403, intron 43 of 43)	intron (NM_001204403, intron 43 of 43)	-79512	NR_024340	283025	Hs.522955	NM_001017982	ENSG00000235931	LINC01553	C10orf40	long intergenic non-protein coding RNA 1553	ncRNA	0.008955	0.375000	
chunk0183_189_1	chr7	106239393	106239879	+	0	NA	Intergenic	Intergenic	45556	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.010288	0.410678	
chunk0029_394_1	chr10	109580268	109580629	+	0	NA	Intergenic	L2b|LINE|L2	343105	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.002770	0.372928	
chunk0124_2_1	chr3	51448577	51449148	+	0	NA	intron (NM_014703, intron 6 of 25)	L1M2|LINE|L1	51140	NM_014703	9730	Hs.716623	NM_014703	ENSG00000145041	DCAF1	RIP|VPRBP	DDB1 and CUL4 associated factor 1	protein-coding	0.007005	0.307692	
chunk0032_369_1	chr11	10931565	10932138	+	0	NA	Intergenic	Intergenic	73634	NR_034137	729013	Hs.726427	NR_034137	ENSG00000247271	ZBED5-AS1	-	ZBED5 antisense RNA 1	ncRNA	0.019197	0.594077	
chunk0146_374_1	chr4	168364669	168365037	+	0	NA	intron (NM_001012967, intron 36 of 37)	L1MA6|LINE|L1	-46046	NM_017631	55601	Hs.591710	NM_017631	ENSG00000137628	DDX60	-	DExD/H-box helicase 60	protein-coding	0.002717	0.306233	
chunk0150_289_1	chr5	37254597	37255104	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-5422	NM_023073	65250	Hs.586199	NM_023073	ENSG00000197603	CPLANE1	C5orf42|Hug|JBTS17|OFD6	ciliogenesis and planar polarity effector 1	protein-coding	0.001972	0.381890	
chunk0067_79_1	chr15	41544728	41545090	+	0	NA	promoter-TSS (NM_015540)	promoter-TSS (NM_015540)	-632	NM_015540	26015	Hs.371045	NM_015540	ENSG00000103932	RPAP1	-	RNA polymerase II associated protein 1	protein-coding	0.027624	0.537190	81(AGGGACACAGCGTTCC,-,0.00),82(GGGACACAGCGTTCCT,+,0.00)
chunk0203_281_1	chr9	88809958	88810256	+	0	NA	Intergenic	Intergenic	-64202	NR_036252	100423015		NR_036252	ENSG00000265873	MIR4289	-	microRNA 4289	ncRNA	0.010067	0.391304	
chunk0033_55_1	chr11	13339763	13339983	+	0	NA	intron (NM_001178, intron 3 of 19)	L2a|LINE|L2	62146	NM_001030273	406	Hs.65734	NM_001178	ENSG00000133794	ARNTL	BMAL1|BMAL1c|JAP3|MOP3|PASD3|TIC|bHLHe5	aryl hydrocarbon receptor nuclear translocator like	protein-coding	0.013636	0.502262	
chunk0136_221_1	chr4	8158699	8158949	+	0	NA	promoter-TSS (NM_001130088)	promoter-TSS (NM_001130088)	8	NM_001130087	84448	Hs.233404	NM_032432	ENSG00000163995	ABLIM2	-	actin binding LIM protein family member 2	protein-coding	0.160000	0.812749	
chunk0205_272_1	chr9	111460141	111460497	+	0	NA	intron (NM_001080398, intron 3 of 50)	L1M5|LINE|L1	24426	NM_001080398	23392	Hs.368255	NM_001080398	ENSG00000136813	ECPAS	ECM29|KIAA0368	Ecm29 proteasome adaptor and scaffold	protein-coding	0.000000	0.296919	
chunk0152_380_1	chr5	64498988	64499523	+	0	NA	Intergenic	Intergenic	-6692	NM_001029875	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.001869	0.416045	
chunk0117_243_1	chr22	23147557	23148226	+	0	NA	intron (NM_004914, intron 2 of 10)	L1ME4b|LINE|L1	2565	NM_004914	9609	Hs.353024	NM_004914	ENSG00000100228	RAB36	-	RAB36, member RAS oncogene family	protein-coding	0.010463	0.474627	
chunk0048_383_1	chr12	86727349	86727682	+	0	NA	intron (NM_013244, intron 1 of 6)	intron (NM_013244, intron 1 of 6)	111389	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.003003	0.302395	
chunk0081_68_1	chr17	38942864	38943063	+	0	NA	intron (NM_001008777, intron 8 of 10)	intron (NM_001008777, intron 8 of 10)	17795	NR_038847	100505576	Hs.634043	NR_038847	ENSG00000263874	LINC00672	-	long intergenic non-protein coding RNA 672	ncRNA	0.010050	0.335000	
chunk0094_33_1	chr2	1728654	1728963	+	0	NA	intron (NM_012293, intron 1 of 22)	Tigger17a|DNA|TcMar-Tigger	15739	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.032362	0.516129	145(AGAAACAAAGTGTCCT,-,0.00),146(GAAACAAAGTGTCCTT,+,0.00)
chunk0006_60_1	chr1	64607764	64608496	+	0	NA	intron (NM_020925, intron 4 of 26)	intron (NM_020925, intron 4 of 26)	28283	NR_039957	100616338		NR_039957	ENSG00000264470	MIR4794	-	microRNA 4794	ncRNA	0.001366	0.398363	
chunk0013_47_1	chr1	167125301	167126176	+	0	NA	intron (NM_001080426, intron 4 of 4)	intron (NM_001080426, intron 4 of 4)	30888	NM_001080426	92235	Hs.632462	NM_001080426	ENSG00000198842	DUSP27	-	dual specificity phosphatase 27, atypical	protein-coding	0.019429	0.517123	
chunk0108_412_1	chr2	237525780	237526166	+	0	NA	intron (NM_001042467, intron 7 of 14)	intron (NM_001042467, intron 7 of 14)	15042	NR_106869	102465486		NR_106869	ENSG00000277842	MIR6811	hsa-mir-6811	microRNA 6811	ncRNA	0.031088	0.625323	
chunk0146_232_1	chr4	162137168	162137604	+	0	NA	intron (NM_001128427, intron 1 of 15)	intron (NM_001128427, intron 1 of 15)	26648	NM_001128428	56884	Hs.32452	NM_020116	ENSG00000168843	FSTL5	-	follistatin like 5	protein-coding	0.002294	0.329519	
chunk0026_226_1	chr10	65091095	65091469	+	0	NA	Intergenic	Intergenic	265754	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.000000	0.333333	
chunk0058_427_1	chr13	113009762	113010094	+	0	NA	intron (NM_024979, intron 1 of 29)	intron (NM_024979, intron 1 of 29)	8214	NM_024979	23263	Hs.170422	NM_024979	ENSG00000126217	MCF2L	ARHGEF14|DBS|OST	MCF.2 cell line derived transforming sequence like	protein-coding	0.021084	0.561562	
chunk0188_398_1	chr8	18666227	18666902	+	0	NA	intron (NM_015310, intron 9 of 15)	intron (NM_015310, intron 9 of 15)	142331	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.013333	0.434911	296(TAGAACATTAAGTCCA,-,0.00)
chunk0030_260_1	chr10	116127371	116127671	+	0	NA	intron (NM_145793, intron 3 of 8)	intron (NM_145793, intron 3 of 8)	144786	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.010000	0.458472	
chunk0086_380_1	chr18	26458701	26459217	+	0	NA	intron (NM_001142730, intron 4 of 4)	L2|LINE|L2	35964	NR_110762	100506787	Hs.734746	NR_110762		LINC01543	-	long intergenic non-protein coding RNA 1543	ncRNA	0.015504	0.473888	
chunk0187_319_1	chr7	156608917	156609723	+	0	NA	Intergenic	Intergenic	-6125	NR_103858	100506380	Hs.647014	NM_032625	ENSG00000182648	LINC01006	C7orf13|MY040	long intergenic non-protein coding RNA 1006	ncRNA	0.008685	0.394052	303(CAGAACGCCCAGTTCT,-,0.00),304(AGAACGCCCAGTTCTG,+,0.00)
chunk0100_90_1	chr2	107740598	107741051	+	0	NA	Intergenic	Intergenic	-13288	NR_126370	104326057	Hs.585967	NR_126369	ENSG00000232991	GACAT1	LINC00876	gastric cancer associated transcript 1	ncRNA	0.000000	0.405286	
chunk0148_194_1	chr5	8228733	8229366	+	0	NA	Intergenic	Intergenic	228515	NR_039984	729506	Hs.566412	NR_039984	ENSG00000245729	LINC02226	-	long intergenic non-protein coding RNA 2226	ncRNA	0.020537	0.430599	309(AGAGACATTTTGTTCC,-,0.00)
chunk0201_286_1	chr9	39485724	39486040	+	0	NA	Intergenic	Intergenic	-21356	NR_003528	401509	Hs.449445	NM_001032297		ZNF658B	-	zinc finger protein 658B (pseudogene)	pseudo	0.000000	0.397476	
chunk0040_380_1	chr11	119361169	119361433	+	0	NA	intron (NM_001243759, intron 1 of 11)	intron (NM_001243759, intron 1 of 11)	2881	NM_171997	9099	Hs.524085	NM_004205	ENSG00000036672	USP2	UBP41|USP9	ubiquitin specific peptidase 2	protein-coding	0.015152	0.539623	
chunk0038_263_1	chr11	89456830	89457140	+	0	NA	intron (NM_001291929, intron 1 of 16)	L1PA15|LINE|L1	33756	NM_001291929	50507	Hs.371036	NM_016931	ENSG00000086991	NOX4	KOX|KOX-1|RENOX	NADPH oxidase 4	protein-coding	0.006452	0.527331	
chunk0066_331_1	chr15	36627089	36627317	+	0	NA	intron (NM_001290232, intron 1 of 10)	intron (NM_001290232, intron 1 of 10)	32334	NM_001290232	84529	Hs.48348	NM_032499	ENSG00000186073	C15orf41	HH114	chromosome 15 open reading frame 41	protein-coding	0.008772	0.537118	
chunk0163_69_1	chr6	9178748	9179130	+	0	NA	Intergenic	Intergenic	526730	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.013089	0.391645	
chunk0121_55_1	chr3	15652687	15653212	+	0	NA	Intergenic	Intergenic	44422	NR_036085	100422990		NR_036085	ENSG00000264354	MIR3134	-	microRNA 3134	ncRNA	0.007619	0.448669	
chunk0051_38_1	chr12	112233581	112233971	+	0	NA	intron (NM_001109662, intron 37 of 75)	intron (NM_001109662, intron 37 of 75)	-70455	NR_106921	102465519		NR_106921	ENSG00000283793	MIR6861	hsa-mir-6861	microRNA 6861	ncRNA	0.012821	0.393862	
chunk0093_109_1	chr19	44255088	44255625	+	0	NA	Intergenic	L1M4|LINE|L1	-4524	NM_001207005	353355	Hs.466891	NM_181756	ENSG00000159915	ZNF233	-	zinc finger protein 233	protein-coding	0.005587	0.347584	
chunk0087_322_1	chr18	39847522	39847868	+	0	NA	Intergenic	Intergenic	-95700	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.000000	0.276657	
chunk0195_259_1	chr8	97958999	97959387	+	0	NA	intron (NM_030583, intron 4 of 18)	L2a|LINE|L2	83024	NR_002581	26775	Hs.684855	NR_002581	ENSG00000207067	SNORA72	RNU72|U72	small nucleolar RNA, H/ACA box 72	snoRNA	0.015464	0.421594	180(AGGATCAGTTTGTTCT,-,0.00),181(GGATCAGTTTGTTCTT,+,0.00)
chunk0103_353_1	chr2	168129389	168129771	+	0	NA	exon (NM_013233, exon 10 of 18)	exon (NM_013233, exon 10 of 18)	118015	NM_013233	27347	Hs.276271	NM_013233	ENSG00000198648	STK39	DCHT|PASK|SPAK	serine/threonine kinase 39	protein-coding	0.002618	0.373368	204(AGGTACTCTCTGTTCT,-,0.00),205(GGTACTCTCTGTTCTG,+,0.00)
chunk0186_178_1	chr7	139442032	139442231	+	0	NA	Intergenic	L1M7|LINE|L1	-14605	NR_033999	100129148	Hs.744449	NR_033999		LOC100129148	-	uncharacterized LOC100129148	ncRNA	0.015075	0.550000	
chunk0108_162_1	chr2	231299916	231300638	+	0	NA	intron (NM_001291656, intron 19 of 20)	intron (NM_001291656, intron 19 of 20)	-62431	NR_039937	100616317		NR_039937	ENSG00000263641	MIR4777	-	microRNA 4777	ncRNA	0.012465	0.416321	
chunk0169_402_1	chr6	108292540	108292834	+	0	NA	Intergenic	Intergenic	-2207	NM_145315	246269	Hs.259666	NM_145315	ENSG00000135537	AFG1L	AFG1|LACE1|c222389	AFG1 like ATPase	protein-coding	0.010204	0.389831	
chunk0204_185_1	chr9	96266761	96266960	+	0	NA	intron (NM_000197, intron 2 of 10)	HAL1|LINE|L1	35292	NM_000197	3293	Hs.477	NM_000197	ENSG00000130948	HSD17B3	EDH17B3|SDR12C2	hydroxysteroid 17-beta dehydrogenase 3	protein-coding	0.015075	0.545000	
chunk0135_302_1	chr3	189815507	189815823	+	0	NA	intron (NM_001114978, intron 4 of 12)	MER102a|DNA|hAT-Charlie	-14257	NR_030642	100126340		NR_030642	ENSG00000216058	MIR944	MIRN944|hsa-mir-944|mir-944	microRNA 944	ncRNA	0.000000	0.274448	
chunk0129_183_1	chr3	121017163	121017695	+	0	NA	intron (NM_014980, intron 3 of 27)	L1MCb|LINE|L1	-32211	NR_049861	100847043		NR_049861	ENSG00000264477	MIR5682	-	microRNA 5682	ncRNA	0.000000	0.337711	
chunk0196_300_1	chr8	109610912	109611449	+	0	NA	intron (NM_017786, intron 5 of 8)	intron (NM_017786, intron 5 of 8)	32010	NM_001099756	55638	Hs.390738	NM_017786	ENSG00000147642	SYBU	GOLSYN|OCSYN|SNPHL	syntabulin	protein-coding	0.007449	0.407063	
chunk0075_184_1	chr16	52115818	52116270	+	0	NA	Intergenic	MIR|SINE|MIR	30763	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.002212	0.342163	170(AGGAACAGTTTGGTCT,-,0.00),171(GGAACAGTTTGGTCTG,+,0.00)
chunk0061_199_1	chr14	60272794	60273537	+	0	NA	intron (NM_177951, intron 2 of 3)	intron (NM_177951, intron 2 of 3)	23917	NM_177951	5494	Hs.130036	NM_021003	ENSG00000100614	PPM1A	PP2C-ALPHA|PP2CA|PP2Calpha	protein phosphatase, Mg2+/Mn2+ dependent 1A	protein-coding	0.002692	0.365591	
chunk0018_232_1	chr1	219850865	219851136	+	0	NA	Intergenic	L1PB2|LINE|L1	77651	NR_046437	55532	Hs.284450	NM_018713	ENSG00000196660	SLC30A10	HMDPC|HMNDYT1|ZNT10|ZNT8|ZRC1|ZnT-10	solute carrier family 30 member 10	protein-coding	0.011070	0.378676	
chunk0191_60_1	chr8	46902817	46903054	+	0	NA	Intergenic	L2a|LINE|L2	62049	NR_027012	497634	Hs.406982	NR_027012		LINC00293	BEYLA|NCRNA00293	long intergenic non-protein coding RNA 293	ncRNA	0.000000	0.428571	
chunk0141_207_1	chr4	84542211	84542736	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-40431	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.003810	0.355513	
chunk0042_289_1	chr12	7542837	7543520	+	0	NA	Intergenic	Intergenic	-39360	NM_203416	9332	Hs.504641	NM_004244	ENSG00000177575	CD163	M130|MM130|SCARI1	CD163 molecule	protein-coding	0.001464	0.371345	
chunk0087_240_1	chr18	36512701	36513008	+	0	NA	intron (NM_001281739, intron 5 of 23)	intron (NM_001281739, intron 5 of 23)	150564	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.006515	0.396104	
chunk0204_223_1	chr9	97478256	97478966	+	0	NA	intron (NM_014290, intron 13 of 16)	intron (NM_014290, intron 13 of 16)	-22569	NM_001166116	7111	Hs.404289	NM_003275	ENSG00000136842	TMOD1	D9S57E|ETMOD|TMOD	tropomodulin 1	protein-coding	0.002817	0.334740	
chunk0129_225_1	chr3	121894527	121895312	+	0	NA	intron (NM_021082, intron 1 of 21)	intron (NM_021082, intron 1 of 21)	595	NM_021082	6565	Hs.518089	NM_021082	ENSG00000163406	SLC15A2	PEPT2	solute carrier family 15 member 2	protein-coding	0.005096	0.417303	
chunk0070_401_1	chr15	77327106	77327369	+	0	NA	intron (NM_024776, intron 1 of 7)	intron (NM_024776, intron 1 of 7)	92867	NM_024776	79834	Hs.9587	NM_024776	ENSG00000173517	PEAK1	SGK269	pseudopodium enriched atypical kinase 1	protein-coding	0.003802	0.295455	
chunk0165_121_1	chr6	32950579	32950921	+	0	NA	exon (NM_006120, exon 2 of 5)	exon (NM_006120, exon 2 of 5)	2372	NM_006120	3108	Hs.728759	NM_006120	ENSG00000204257	HLA-DMA	D6S222E|DMA|HLADM|RING6	major histocompatibility complex, class II, DM alpha	protein-coding	0.020468	0.545190	164(CAGTACACTGTGTGCA,-,0.00),165(AGTACACTGTGTGCAG,+,0.00)
chunk0166_50_1	chr6	42779228	42779880	+	0	NA	Intergenic	Intergenic	-33408	NM_003192	6903	Hs.75064	NM_003192	ENSG00000124659	TBCC	CFC	tubulin folding cofactor C	protein-coding	0.006135	0.398162	
chunk0133_393_1	chr3	174295445	174296107	+	0	NA	Intergenic	Intergenic	-374980	NR_046664	100874010	Hs.624265	NR_046664	ENSG00000228213	NLGN1-AS1	-	NLGN1 antisense RNA 1	ncRNA	0.009063	0.343891	
chunk0023_27_1	chr10	21097475	21097693	+	0	NA	intron (NM_213569, intron 2 of 6)	intron (NM_213569, intron 2 of 6)	48975	NM_001010896	387638	Hs.664110	NM_001010896	ENSG00000204683	C10orf113	bA165O3.1	chromosome 10 open reading frame 113	protein-coding	0.000000	0.397260	
chunk0201_30_1	chr9	33328899	33329510	+	0	NA	intron (NM_147133, intron 10 of 20)	MER77B|LTR|ERVL	38784	NM_147134	4799	Hs.413074	NM_002504	ENSG00000086102	NFX1	NFX2|TEG-42|Tex42	nuclear transcription factor, X-box binding 1	protein-coding	0.009820	0.446078	
chunk0190_181_1	chr8	33377139	33377570	+	0	NA	intron (NM_032664, intron 4 of 4)	L3|LINE|CR1	95792	NM_032664	84750	Hs.458713	NM_032664	ENSG00000172728	FUT10	FUCTX	fucosyltransferase 10	protein-coding	0.009281	0.405093	
chunk0010_156_1	chr1	115377458	115377821	+	0	NA	Intergenic	Intergenic	-39403	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.005510	0.337912	
chunk0119_97_1	chr22	41940031	41940293	+	0	NA	promoter-TSS (NM_001110215)	promoter-TSS (NM_001110215)	57	NM_001110215	79019	Hs.208912	NM_024053	ENSG00000100162	CENPM	C22orf18|CENP-M|PANE1	centromere protein M	protein-coding	0.019084	0.577947	142(ATGCACTTGCTGTTCC,-,0.00),143(TGCACTTGCTGTTCCT,+,0.00)
chunk0075_55_1	chr16	47658987	47659246	+	0	NA	intron (NM_001031835, intron 21 of 31)	intron (NM_001031835, intron 21 of 31)	197817	NM_001031835	5257	Hs.78060	NM_000293	ENSG00000102893	PHKB	-	phosphorylase kinase regulatory subunit beta	protein-coding	0.007722	0.384615	98(GGGAACTTACTGTTCA,-,0.00),99(GGAACTTACTGTTCAA,+,0.00)
chunk0142_168_1	chr4	95319587	95320012	+	0	NA	intron (NM_003728, intron 2 of 15)	intron (NM_003728, intron 2 of 15)	228308	NM_001256794	658	Hs.598475	NM_001203	ENSG00000138696	BMPR1B	ALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293	bone morphogenetic protein receptor type 1B	protein-coding	0.004706	0.375587	
chunk0051_206_1	chr12	116495280	116495638	+	0	NA	Intergenic	MLT1F1|LTR|ERVL-MaLR	-37963	NR_027345	100287569	Hs.441601	NM_207436	ENSG00000196668	LINC00173	NCRNA00173	long intergenic non-protein coding RNA 173	ncRNA	0.005587	0.487465	
chunk0064_74_1	chr14	90293555	90294179	+	0	NA	intron (NM_017970, intron 8 of 13)	L1MD2|LINE|L1	37317	NM_002802	5700	Hs.356654	NM_002802	ENSG00000100764	PSMC1	P26S4|S4|p56	proteasome 26S subunit, ATPase 1	protein-coding	0.006410	0.345600	
chunk0181_135_1	chr7	81155725	81156146	+	0	NA	Intergenic	Intergenic	-236584	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.002375	0.369668	
chunk0154_48_1	chr5	77181488	77182383	+	0	NA	Intergenic	Intergenic	-28946	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.018994	0.493304	625(AGGTACAACCTGTCCT,-,0.00),626(GGTACAACCTGTCCTG,+,0.00)
chunk0055_110_1	chr13	56838917	56839192	+	0	NA	Intergenic	Intergenic	-301864	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.003636	0.224638	
chunk0041_243_1	chr11	128548765	128548964	+	0	NA	intron (NM_001143820, intron 3 of 9)	intron (NM_001143820, intron 3 of 9)	22722	NR_120581	101929517	Hs.562320	NR_120581	ENSG00000254588	ETS1-AS1	pancEts-1	ETS1 antisense RNA 1	ncRNA	0.045226	0.540000	
chunk0015_235_1	chr1	187782067	187782484	+	0	NA	Intergenic	Intergenic	338647	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.007194	0.404306	
chunk0114_4_1	chr21	6363129	6363391	+	0	NA	Intergenic	Intergenic	104348	NM_000071	875	Hs.533013	NM_000071	ENSG00000160200	CBS	CBSL|HIP4	cystathionine-beta-synthase	protein-coding	0.000000	0.448669	
chunk0050_418_1	chr12	109885836	109886345	+	0	NA	Intergenic	L1MC4|LINE|L1	-5602	NM_016433	51228	Hs.381256	NM_016433	ENSG00000139433	GLTP	-	glycolipid transfer protein	protein-coding	0.013752	0.429412	
chunk0114_293_1	chr21	16672952	16673151	+	0	NA	Intergenic	Arthur1C|DNA|hAT-Tip100	82814	NR_029694	406912		NR_029694	ENSG00000207863	MIR125B2	MIRN125B2|mir-125b-2	microRNA 125b-2	ncRNA	0.000000	0.310000	
chunk0037_314_1	chr11	76801643	76802482	+	0	NA	Intergenic	Intergenic	18821	NM_015516	25987	Hs.8361	NM_015516	ENSG00000182704	TSKU	E2IG4|LRRC54|TSK	tsukushi, small leucine rich proteoglycan	protein-coding	0.007151	0.430952	
chunk0046_101_1	chr12	56958820	56959250	+	0	NA	Intergenic	L1P2|LINE|L1	-1401	NM_003708	8608	Hs.134958	NM_003708	ENSG00000139547	RDH16	RODH-4|SDR9C8|hRDH-E	retinol dehydrogenase 16	protein-coding	0.006977	0.489559	
chunk0162_401_1	chr5	179777921	179778443	+	0	NA	TTS (NM_014757)	TTS (NM_014757)	-15803	NM_145867	4056	Hs.706741	NM_145867	ENSG00000213316	LTC4S	-	leukotriene C4 synthase	protein-coding	0.021073	0.489484	
chunk0123_127_1	chr3	42570970	42571362	+	0	NA	intron (NM_001201572, intron 1 of 6)	Tigger16a|DNA|TcMar-Tigger	10862	NM_004206	9117	Hs.445892	NM_004206	ENSG00000093183	SEC22C	SEC22L3	SEC22 homolog C, vesicle trafficking protein	protein-coding	0.002551	0.386768	
chunk0017_98_1	chr1	205824985	205825456	+	0	NA	Intergenic	Zaphod|DNA|hAT-Tip100	-12024	NM_173854	254428	Hs.20274	NM_173854	ENSG00000133065	SLC41A1	MgtE	solute carrier family 41 member 1	protein-coding	0.006369	0.387712	
chunk0105_165_1	chr2	186948441	186949169	+	0	NA	Intergenic	Intergenic	-99635	NM_182521	151112	Hs.375054	NM_182521	ENSG00000163012	ZSWIM2	MEX|ZZZ2	zinc finger SWIM-type containing 2	protein-coding	0.006868	0.429355	
chunk0084_76_1	chr17	75024818	75025084	+	0	NA	Intergenic	HERVK14-int|LTR|ERVK	-7616	NR_110835	23510	Hs.514468	NM_015353	ENSG00000180901	KCTD2	-	potassium channel tetramerization domain containing 2	protein-coding	0.015038	0.468165	
chunk0184_236_1	chr7	117588207	117589067	+	0	NA	intron (NM_000492, intron 12 of 26)	MIRb|SINE|MIR	108674	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.002326	0.341463	
chunk0048_21_1	chr12	77324745	77324944	+	0	NA	Intergenic	Intergenic	-259264	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.120603	0.730000	
chunk0032_270_1	chr11	9076690	9076975	+	0	NA	intron (NM_020974, intron 3 of 21)	intron (NM_020974, intron 3 of 21)	13547	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.003509	0.475524	
chunk0006_43_1	chr1	64474779	64474984	+	0	NA	intron (NM_020925, intron 1 of 26)	MamRTE1|LINE|RTE-BovB	4088	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.000000	0.553398	
chunk0086_448_1	chr18	30028095	30028581	+	0	NA	Intergenic	Intergenic	-270572	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.006173	0.299795	
chunk0138_305_1	chr4	41178720	41178919	+	0	NA	intron (NM_004307, intron 1 of 17)	MIRc|SINE|MIR	35799	NM_004307	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.000000	0.430000	
chunk0188_156_1	chr8	10487894	10488592	+	0	NA	Intergenic	Intergenic	13678	NR_120604	101929191	Hs.595262	NR_120604	ENSG00000253641	LINCR-0001	-	uncharacterized LINCR-0001	ncRNA	0.007163	0.443491	313(AGGAACAGAGTGTTCT,-,0.00),314(GGAACAGAGTGTTCTG,+,0.00)
chunk0181_63_1	chr7	80240084	80240767	+	0	NA	Intergenic	Intergenic	104670	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.005857	0.334795	140(GTGAACATGGAGTCCC,-,0.00),141(TGAACATGGAGTCCCA,+,0.00)
chunk0088_176_1	chr18	47275648	47276286	+	0	NA	Intergenic	Intergenic	-26784	NM_001037802	652991	Hs.585834	NM_001037802	ENSG00000215474	SKOR2	CH18515|CORL2|FUSSEL18	SKI family transcriptional corepressor 2	protein-coding	0.006270	0.442879	
chunk0088_167_1	chr18	46867968	46868328	+	0	NA	intron (NM_004671, intron 2 of 13)	MLT1G3|LTR|ERVL-MaLR	49384	NM_173206	9063	Hs.57769	NM_004671	ENSG00000078043	PIAS2	ARIP3|DIP|MIZ1|PIASX|SIZ2|ZMIZ4	protein inhibitor of activated STAT 2	protein-coding	0.000000	0.465374	
chunk0194_38_1	chr8	81837911	81838416	+	0	NA	intron (NM_022133, intron 3 of 8)	L1ME3A|LINE|L1	4123	NM_022133	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.312253	
chunk0169_297_1	chr6	105988344	105988791	+	0	NA	Intergenic	Intergenic	-97753	NM_001198	639	Hs.436023	NM_001198	ENSG00000057657	PRDM1	BLIMP1|PRDI-BF1	PR/SET domain 1	protein-coding	0.000000	0.316964	
chunk0132_250_1	chr3	158723159	158723474	+	0	NA	intron (NM_002888, intron 1 of 3)	intron (NM_002888, intron 1 of 3)	9170	NM_002888	5918	Hs.131269	NM_002888	ENSG00000118849	RARRES1	LXNL|PERG-1|TIG1	retinoic acid receptor responder 1	protein-coding	0.012698	0.414557	
chunk0025_10_1	chr10	47254495	47255054	+	0	NA	Intergenic	Intergenic	-45450	NM_004962	2662	Hs.2171	NM_004962	ENSG00000266524	GDF10	BIP|BMP-3b|BMP3B	growth differentiation factor 10	protein-coding	0.005367	0.458929	
chunk0049_109_1	chr12	91173490	91174330	+	0	NA	intron (NM_001920, intron 2 of 7)	intron (NM_001920, intron 2 of 7)	4736	NM_133507	1634	Hs.156316	NM_001920	ENSG00000011465	DCN	CSCD|DSPG2|PG40|PGII|PGS2|SLRR1B	decorin	protein-coding	0.002381	0.366231	357(TAGTACAATATGTCCC,-,0.00),358(AGTACAATATGTCCCA,+,0.00)
chunk0207_169_1	chr9	130287569	130288210	+	0	NA	intron (NM_001291815, intron 4 of 97)	intron (NM_001291815, intron 4 of 97)	22010	NM_001291815	256158	Hs.32194	NM_144655	ENSG00000148357	HMCN2	-	hemicentin 2	protein-coding	0.015601	0.523364	
chunk0052_330_1	chr12	125922384	125922583	+	0	NA	Intergenic	L2a|LINE|L2	60891	NR_034132	400084	Hs.156191	NR_034132	ENSG00000249267	LINC00939	-	long intergenic non-protein coding RNA 939	ncRNA	0.005025	0.405000	
chunk0078_117_1	chr17	2908989	2909188	+	0	NA	intron (NM_015085, intron 3 of 24)	L2c|LINE|L2	56807	NR_110818	101927911	Hs.626373	NR_110818	ENSG00000262884	LOC101927911	-	uncharacterized LOC101927911	ncRNA	0.025126	0.565000	62(AAGAACATTCTGTGCT,-,0.00),63(AGAACATTCTGTGCTG,+,0.00)
chunk0148_333_1	chr5	14250527	14250806	+	0	NA	intron (NM_007118, intron 1 of 56)	intron (NM_007118, intron 1 of 56)	106946	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.014337	0.471429	
chunk0187_261_1	chr7	155003073	155003464	+	0	NA	promoter-TSS (NR_028090)	promoter-TSS (NR_028090)	-165	NR_028090	202781	Hs.193172	NR_028090	ENSG00000273344	PAXIP1-AS1	-	PAXIP1 antisense RNA 1 (head to head)	ncRNA	0.148338	0.816327	
chunk0212_342_1	chrX	146636121	146636320	+	0	NA	Intergenic	L1MB8|LINE|L1	-173564	NM_001144064	100129239	Hs.592233	NM_001144064	ENSG00000224440	CXorf51A	CXorf51|CXorf51B	chromosome X open reading frame 51A	protein-coding	0.000000	0.270000	
chunk0033_420_1	chr11	24829061	24829452	+	0	NA	intron (NM_001252010, intron 5 of 9)	intron (NM_001252010, intron 5 of 9)	332286	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002558	0.397959	
chunk0046_282_1	chr12	61827419	61827730	+	0	NA	intron (NM_178539, intron 2 of 4)	intron (NM_178539, intron 2 of 4)	365265	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.009646	0.294872	
chunk0189_395_1	chr8	27489664	27489948	+	0	NA	Intergenic	Intergenic	-1196	NM_001979	2053	Hs.212088	NM_001979	ENSG00000120915	EPHX2	ABHD20|CEH|SEH	epoxide hydrolase 2	protein-coding	0.003521	0.382456	
chunk0122_203_1	chr3	33113853	33114495	+	0	NA	exon (NM_006371, exon 1 of 7)	exon (NM_006371, exon 1 of 7)	216	NM_006371	10491	Hs.517888	NM_006371	ENSG00000170275	CRTAP	CASP|LEPREL3|OI7|P3H5	cartilage associated protein	protein-coding	0.124611	0.732504	
chunk0185_434_1	chr7	134856720	134857000	+	0	NA	intron (NM_033157, intron 2 of 14)	intron (NM_033157, intron 2 of 14)	-34540	NM_033139	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.010714	0.380783	
chunk0014_442_1	chr1	183753360	183753740	+	0	NA	intron (NM_001297669, intron 3 of 18)	LTR40c|LTR|ERVL	-51531	NM_001297672	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.000000	0.367454	
chunk0054_60_1	chr13	41804709	41805046	+	0	NA	intron (NM_015058, intron 17 of 44)	L1M1|LINE|L1	156208	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.005935	0.322485	
chunk0083_139_1	chr17	65655273	65655561	+	0	NA	intron (NR_126542, intron 3 of 5)	intron (NR_126542, intron 3 of 5)	-93795	NM_004655	8313	Hs.156527	NM_004655	ENSG00000168646	AXIN2	AXIL|ODCRCS	axin 2	protein-coding	0.013889	0.401384	
chunk0040_396_1	chr11	120346362	120346892	+	0	NA	intron (NM_001198665, intron 1 of 39)	intron (NM_001198665, intron 1 of 39)	9718	NM_015313	23365	Hs.24598	NM_015313	ENSG00000196914	ARHGEF12	LARG|PRO2792	Rho guanine nucleotide exchange factor 12	protein-coding	0.001887	0.376648	
chunk0105_66_1	chr2	183614817	183615467	+	0	NA	Intergenic	Intergenic	490787	NR_109856	129401	Hs.180591	NM_138285	ENSG00000163002	NUP35	MP-44|MP44|NP44|NUP53	nucleoporin 35	protein-coding	0.007692	0.377880	548(AAGAACTGCCTGTCCA,-,0.00),549(AGAACTGCCTGTCCAT,+,0.00)
chunk0022_42_1	chr10	8107838	8108346	+	0	NA	Intergenic	Intergenic	53388	NM_001002295	2625	Hs.524134	NM_002051	ENSG00000107485	GATA3	HDR|HDRS	GATA binding protein 3	protein-coding	0.009843	0.341847	
chunk0175_57_1	chr7	1741851	1742224	+	0	NA	intron (NR_120508, intron 1 of 1)	intron (NR_120508, intron 1 of 1)	273	NR_120508	101927125	Hs.633957	NR_120508	ENSG00000236081	ELFN1-AS1	MYCLo-2	ELFN1 antisense RNA 1	ncRNA	0.018767	0.588235	
chunk0174_385_1	chr6	165081705	165082051	+	0	NA	Intergenic	L1ME2|LINE|L1	227744	NM_144980	168090	Hs.144734	NM_144980	ENSG00000112539	C6orf118	bA85G2.1|dJ416F21.2	chromosome 6 open reading frame 118	protein-coding	0.002890	0.340058	
chunk0212_220_1	chrX	136049578	136050170	+	0	NA	Intergenic	L2b|LINE|L2	64447	NM_001042537	10479	Hs.62185	NM_006359	ENSG00000198689	SLC9A6	MRSA|NHE6	solute carrier family 9 member A6	protein-coding	0.010135	0.472175	
chunk0110_176_1	chr20	14352077	14352315	+	0	NA	intron (NM_080676, intron 3 of 16)	L1MA2|LINE|L1	-14529	NM_013281	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.004202	0.343096	
chunk0019_95_1	chr1	224710073	224710629	+	0	NA	intron (NM_152495, intron 3 of 5)	intron (NM_152495, intron 3 of 5)	93874	NM_152495	149111	Hs.731723	NM_152495	ENSG00000143786	CNIH3	CNIH-3	cornichon family AMPA receptor auxiliary protein 3	protein-coding	0.008993	0.405745	
chunk0090_318_1	chr18	75678603	75679167	+	0	NA	Intergenic	Intergenic	-251182	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.015957	0.364602	
chunk0157_208_1	chr5	119179742	119180364	+	0	NA	intron (NM_001290321, intron 28 of 43)	MER58B|DNA|hAT-Charlie	25416	NR_049892	100847085		NR_049892	ENSG00000264536	MIR5706	-	microRNA 5706	ncRNA	0.001608	0.361156	
chunk0101_464_1	chr2	140447914	140448238	+	0	NA	intron (NM_018557, intron 63 of 90)	Tigger1|DNA|TcMar-Tigger	138609	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.003086	0.332308	
chunk0096_114_1	chr2	28568346	28569097	+	0	NA	intron (NM_001170585, intron 20 of 56)	intron (NM_001170585, intron 20 of 56)	72650	NM_153021	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.011984	0.426862	460(GGGAGAGAATGTTCCT,+,0.00)
chunk0107_327_1	chr2	220314556	220314813	+	0	NA	Intergenic	Intergenic	-408119	NR_036228	100422959		NR_036228	ENSG00000266518	MIR4268	-	microRNA 4268	ncRNA	0.000000	0.356589	
chunk0093_244_1	chr19	50854587	50854791	+	0	NA	promoter-TSS (NM_001648)	promoter-TSS (NM_001648)	-226	NM_001030047	354	Hs.171995	NM_001648	ENSG00000142515	KLK3	APS|KLK2A1|PSA|hK3	kallikrein related peptidase 3	protein-coding	0.019608	0.536585	157(CAGAACAGCAAGTGCT,-,0.00),158(AGAACAGCAAGTGCTA,+,0.00)
chunk0167_241_1	chr6	67591838	67592574	+	0	NA	Intergenic	L1M4b|LINE|L1	-463145	NR_125869	102723883	Hs.566528	NR_125869	ENSG00000223504	LOC102723883	-	uncharacterized LOC102723883	ncRNA	0.001359	0.347354	
chunk0057_312_1	chr13	106587825	106588170	+	0	NA	Intergenic	Intergenic	-19831	NM_018011	55082	Hs.508644	NM_018011	ENSG00000134884	ARGLU1	-	arginine and glutamate rich 1	protein-coding	0.005797	0.404624	
chunk0085_120_1	chr18	2968066	2968386	+	0	NA	intron (NM_014646, intron 1 of 19)	L4_C_Mam|LINE|RTE-X	-21603	NR_026659	727896	Hs.673126	NR_026659		LOC727896	-	cysteine and histidine rich domain containing 1 pseudogene	pseudo	0.021875	0.461059	
chunk0114_172_1	chr21	14699790	14700523	+	0	NA	Intergenic	Intergenic	-57049	NM_001256579	388813	Hs.334177	NM_001256579		LOC388813	-	uncharacterized protein ENSP00000383407-like	protein-coding	0.002729	0.386921	
chunk0091_48_1	chr19	4547575	4547819	+	0	NA	intron (NM_032108, intron 14 of 16)	L2|LINE|L2	-7673	NM_052972	116844	Hs.655559	NM_052972	ENSG00000171236	LRG1	HMFT1766|LRG	leucine rich alpha-2-glycoprotein 1	protein-coding	0.012295	0.624490	
chunk0133_134_1	chr3	169165537	169165775	+	0	NA	intron (NM_001205194, intron 1 of 15)	intron (NM_001205194, intron 1 of 15)	-17922	NM_001164000	2122	Hs.656395	NM_004991	ENSG00000085276	MECOM	AML1-EVI-1|EVI1|KMT8E|MDS1|MDS1-EVI1|PRDM3|RUSAT2	MDS1 and EVI1 complex locus	protein-coding	0.008403	0.338912	
chunk0080_428_1	chr17	35865024	35865260	+	0	NA	intron (NM_152781, intron 3 of 14)	intron (NM_152781, intron 3 of 14)	3749	NM_152781	256957	Hs.514820	NM_152781	ENSG00000270379	HEATR9	C17orf66	HEAT repeat containing 9	protein-coding	0.029661	0.569620	
chunk0150_397_1	chr5	39829412	39829787	+	0	NA	Intergenic	Intergenic	-222692	NR_104633	102467077	Hs.148993	NR_104633		LINC00603	-	long intergenic non-protein coding RNA 603	ncRNA	0.002667	0.337766	
chunk0120_217_1	chr3	7511295	7511494	+	0	NA	intron (NM_000844, intron 7 of 9)	intron (NM_000844, intron 7 of 9)	23890	NR_046606	100873937	Hs.570608	NR_046606	ENSG00000236202	GRM7-AS1	-	GRM7 antisense RNA 1	ncRNA	0.000000	0.465000	
chunk0100_399_1	chr2	119291800	119292469	+	0	NA	Intergenic	Intergenic	-43063	NR_046721	100874111	Hs.704682	NR_046721	ENSG00000229867	STEAP3-AS1	-	STEAP3 antisense RNA 1	ncRNA	0.013453	0.431343	
chunk0080_354_1	chr17	32860399	32860840	+	0	NA	intron (NM_015194, intron 1 of 21)	intron (NM_015194, intron 1 of 21)	16554	NM_001303279	4642	Hs.602063	NM_015194	ENSG00000176658	MYO1D	PPP1R108|myr4	myosin ID	protein-coding	0.006803	0.366516	
chunk0086_158_1	chr18	21600091	21600293	+	0	NA	intron (NM_052911, intron 1 of 11)	CpG	540	NM_052911	114799	Hs.464733	NM_052911	ENSG00000141446	ESCO1	A930014I12Rik|CTF|ECO1|EFO1|ESO1	establishment of sister chromatid cohesion N-acetyltransferase 1	protein-coding	0.103960	0.738916	
chunk0111_342_1	chr20	33191273	33192420	+	0	NA	Intergenic	Intergenic	-1759	NR_026760	317716	Hs.434194	NM_173859	ENSG00000183566	BPIFA4P	BASE	BPI fold containing family A member 4, pseudogene	pseudo	0.003487	0.412892	996(AAGTACAGCCTGTTCC,-,0.00),997(AGTACAGCCTGTTCCT,+,0.00)
chunk0095_279_1	chr2	19979985	19980297	+	0	NA	intron (NM_001006657, intron 4 of 27)	MamSINE1|SINE|tRNA-RTE	9982	NM_020779	57539	Hs.205427	NM_020779	ENSG00000118965	WDR35	CED2|IFT121|IFTA1|SRTD7	WD repeat domain 35	protein-coding	0.003205	0.341853	
chunk0102_290_1	chr2	150503450	150503688	+	0	NA	Intergenic	Intergenic	-15874	NM_001254738	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.000000	0.326360	
chunk0176_295_1	chr7	16765472	16765725	+	0	NA	intron (NM_014399, intron 1 of 5)	intron (NM_014399, intron 1 of 5)	11872	NM_014399	27075	Hs.364544	NM_014399	ENSG00000106537	TSPAN13	NET-6|NET6|TM4SF13	tetraspanin 13	protein-coding	0.007905	0.370079	
chunk0021_57_1	chr10	1116747	1117159	+	0	NA	intron (NM_014023, intron 11 of 13)	intron (NM_014023, intron 11 of 13)	-42815	NR_015376	399706	Hs.721191	NM_001010910	ENSG00000229205	LINC00200	C10orf139|NCRNA00200	long intergenic non-protein coding RNA 200	ncRNA	0.019417	0.498789	
chunk0127_153_1	chr3	94487957	94488328	+	0	NA	Intergenic	Intergenic	-424919	NM_001195643	200895	Hs.718516	NM_176815	ENSG00000178700	DHFR2	DHFRL1|DHFRP4	dihydrofolate reductase 2	protein-coding	0.002695	0.384409	
chunk0118_354_1	chr22	36265647	36265919	+	0	NA	exon (NM_145343, exon 7 of 7)	exon (NM_145343, exon 7 of 7)	12712	NM_003661	8542	Hs.114309	NM_003661	ENSG00000100342	APOL1	APO-L|APOL|APOL-I|FSGS4	apolipoprotein L1	protein-coding	0.036765	0.531136	
chunk0010_446_1	chr1	120954374	120954681	+	0	NA	non-coding (NR_024510, exon 2 of 2)	non-coding (NR_024510, exon 2 of 2)	11927	NR_125392	101954268		NR_125392		RNVU1-20	RNU1-110|vU1.20	RNA, variant U1 small nuclear 20	snRNA	0.026059	0.454545	
chunk0179_230_1	chr7	47947494	47947714	+	0	NA	intron (NM_138295, intron 1 of 56)	intron (NM_138295, intron 1 of 56)	870	NM_138295	168507	Hs.195979	NM_138295	ENSG00000158683	PKD1L1	HTX8|PRO19563	polycystin 1 like 1, transient receptor potential channel interacting	protein-coding	0.018182	0.574661	
chunk0119_70_1	chr22	41201601	41201800	+	0	NA	Intergenic	L2|LINE|L2	-3609	NM_031488	83746	Hs.517641	NM_031488	ENSG00000100395	L3MBTL2	H-l(3)mbt-l|L3MBT	L3MBTL histone methyl-lysine binding protein 2	protein-coding	0.005025	0.405000	
chunk0004_364_1	chr1	51559613	51560366	+	0	NA	Intergenic	Intergenic	-40666	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.007968	0.384615	
chunk0204_68_1	chr9	93533447	93534138	+	0	NA	intron (NM_001286722, intron 10 of 17)	intron (NM_001286722, intron 10 of 17)	-42835	NM_005392	5253	Hs.211441	NM_005392	ENSG00000197724	PHF2	CENP-35|GRC5|JHDM1E|KDM7C	PHD finger protein 2	protein-coding	0.011577	0.489884	
chunk0156_400_1	chr5	113813489	113813790	+	0	NA	Intergenic	CR1-12_AMi|LINE|CR1	299945	NM_022828	64848	Hs.231942	NM_022828	ENSG00000047188	YTHDC2	CAHL|hYTHDC2	YTH domain containing 2	protein-coding	0.000000	0.367550	
chunk0031_83_1	chr10	123203932	123204272	+	0	NA	Intergenic	Intergenic	49858	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.002941	0.463343	
chunk0022_365_1	chr10	17387984	17388635	+	0	NA	intron (NR_034129, intron 1 of 2)	LTR80A|LTR|ERVL	1373	NR_034129	100128098	Hs.530588	NR_034129	ENSG00000204832	ST8SIA6-AS1	-	ST8SIA6 antisense RNA 1	ncRNA	0.007680	0.463190	
chunk0168_103_1	chr6	80181767	80182017	+	0	NA	intron (NM_000056, intron 6 of 10)	intron (NM_000056, intron 6 of 10)	75265	NM_000056	594	Hs.156414	NM_000056	ENSG00000083123	BCKDHB	BCKDE1B|BCKDH E1-beta|E1B	branched chain keto acid dehydrogenase E1 subunit beta	protein-coding	0.004000	0.334661	
chunk0137_100_1	chr4	13461475	13461805	+	0	NA	intron (NM_001017979, intron 3 of 6)	Plat_L3|LINE|CR1	22725	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.006061	0.350453	
chunk0111_220_1	chr20	28888942	28889945	+	0	NA	Intergenic	Intergenic	-190947	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.006110	0.454268	
chunk0109_463_1	chr2	242109002	242109476	+	0	NA	intron (NR_130700, intron 2 of 5)	L1M8|LINE|L1	20606	NR_130699	728323	Hs.380737	NR_024437		LINC01881	-	long intergenic non-protein coding RNA 1881	ncRNA	0.004219	0.446316	
chunk0178_146_1	chr7	33129494	33129706	+	0	NA	promoter-TSS (NM_001033604)	promoter-TSS (NM_001033604)	60	NM_001033604	27241	Hs.372360	NM_014451	ENSG00000122507	BBS9	B1|C18|D1|PTHB1	Bardet-Biedl syndrome 9	protein-coding	0.070755	0.610329	
chunk0139_229_1	chr4	55330590	55331085	+	0	NA	Intergenic	LTR26|LTR|ERV1	-15384	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.000000	0.362903	
chunk0115_285_1	chr21	28201245	28201898	+	0	NA	intron (NR_126012, intron 3 of 5)	L1MA1|LINE|L1	27096	NR_126012	101927973	Hs.570414	NR_126012	ENSG00000236532	LINC01695	-	long intergenic non-protein coding RNA 1695	ncRNA	0.003063	0.284404	
chunk0021_134_1	chr10	3852212	3852838	+	0	NA	Intergenic	Intergenic	-67244	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.012780	0.381180	
chunk0165_408_1	chr6	38934962	38935455	+	0	NA	intron (NM_001206927, intron 76 of 92)	intron (NM_001206927, intron 76 of 92)	17899	NR_038401	100131047	Hs.670957	NR_038401		LOC100131047	-	uncharacterized LOC100131047	ncRNA	0.002028	0.364372	
chunk0113_45_1	chr20	49990210	49990456	+	0	NA	Intergenic	L2c|LINE|L2	7357	NM_005985	6615	Hs.48029	NM_005985	ENSG00000124216	SNAI1	SLUGH2|SNA|SNAH|SNAIL|SNAIL1|dJ710H13.1	snail family transcriptional repressor 1	protein-coding	0.028455	0.530364	
chunk0070_128_1	chr15	70858850	70859490	+	0	NA	intron (NM_001284357, intron 1 of 16)	intron (NM_001284357, intron 1 of 16)	-4905	NM_018357	55323	Hs.416755	NM_018357	ENSG00000166173	LARP6	ACHN	La ribonucleoprotein domain family member 6	protein-coding	0.010937	0.531981	268(AAGAACAACATGTTCC,-,0.00),269(AGAACAACATGTTCCA,+,0.00)
chunk0139_308_1	chr4	57908166	57908426	+	0	NA	Intergenic	MER1B|DNA|hAT-Charlie	482424	NR_125907	101928851	Hs.555072	NR_125907	ENSG00000248505	LINC02380	-	long intergenic non-protein coding RNA 2380	ncRNA	0.003846	0.394636	
chunk0024_320_1	chr10	43017770	43018164	+	0	NA	Intergenic	L1PA8A|LINE|L1	20404	NR_049836	100847014		NR_049836	ENSG00000263795	MIR5100	-	microRNA 5100	ncRNA	0.000000	0.382278	
chunk0181_40_1	chr7	78709645	78710150	+	0	NA	intron (NM_001301128, intron 2 of 20)	intron (NM_001301128, intron 2 of 20)	-299091	NR_046689	100874021	Hs.128252	NR_046689	ENSG00000226978	MAGI2-AS2	-	MAGI2 antisense RNA 2	ncRNA	0.003960	0.403162	
chunk0155_441_1	chr5	101323267	101323523	+	0	NA	Intergenic	Intergenic	-420110	NM_175052	7903	Hs.308628	NM_005668	ENSG00000113532	ST8SIA4	PST|PST1|SIAT8D|ST8SIA-IV	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	protein-coding	0.003906	0.276265	
chunk0160_100_1	chr5	150484986	150485460	+	0	NA	intron (NR_105061, intron 2 of 2)	intron (NR_105061, intron 2 of 2)	769	NR_105061	102546298	Hs.570892	NR_105061	ENSG00000254333	NDST1-AS1	-	NDST1 antisense RNA 1	ncRNA	0.014768	0.517895	
chunk0117_93_1	chr22	17364310	17364761	+	0	NA	intron (NM_001290046, intron 1 of 18)	intron (NM_001290046, intron 1 of 18)	4586	NM_001290046	27443	Hs.231895	NM_031413	ENSG00000099954	CECR2	-	CECR2 histone acetyl-lysine reader	protein-coding	0.019956	0.457965	
chunk0075_420_1	chr16	57377478	57377869	+	0	NA	intron (NM_001304392, intron 1 of 1)	intron (NM_001304392, intron 1 of 1)	5212	NM_001304392	6376	Hs.531668	NM_002996	ENSG00000006210	CX3CL1	ABCD-3|C3Xkine|CXC3|CXC3C|NTN|NTT|SCYD1|fractalkine|neurotactin	C-X3-C motif chemokine ligand 1	protein-coding	0.010230	0.502551	
chunk0001_29_1	chr1	1364265	1364518	+	0	NA	promoter-TSS (NM_001282582)	promoter-TSS (NM_001282582)	-850	NM_001282582	54587	Hs.515687	NM_032348	ENSG00000162576	MXRA8	ASP3	matrix remodeling associated 8	protein-coding	0.035573	0.594488	86(AAGAACACTGAGTGCT,-,0.00),87(AGAACACTGAGTGCTG,+,0.00)
chunk0084_286_1	chr17	79906233	79906573	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-12954	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.011765	0.504399	312(TGGGACACTGTGTTCT,-,0.00),313(GGGACACTGTGTTCTT,+,0.00)
chunk0115_123_1	chr21	23110109	23110584	+	0	NA	Intergenic	LOR1-int|LTR|ERV1	31062	NR_106746	102466967		NR_106746	ENSG00000275469	MIR6130	hsa-mir-6130	microRNA 6130	ncRNA	0.004211	0.342437	
chunk0042_397_1	chr12	11131950	11132363	+	0	NA	intron (NM_001316893, intron 1 of 4)	intron (NM_001316893, intron 1 of 4)	2088	NM_001097643	259293	Hs.679464	NM_001097643	ENSG00000256188	TAS2R30	T2R30|T2R47|TAS2R47	taste 2 receptor member 30	protein-coding	0.004843	0.289855	
chunk0081_223_1	chr17	42719710	42720106	+	0	NA	intron (NM_001991, intron 7 of 20)	L1ME4a|LINE|L1	-11757	NR_106838	102466195		NR_106838	ENSG00000275273	MIR6780A	hsa-mir-6780a	microRNA 6780a	ncRNA	0.000000	0.269521	178(GAATACACTATGTCCC,-,0.00),179(AATACACTATGTCCCT,+,0.00)
chunk0168_116_1	chr6	81898883	81899082	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-84790	NR_126363	101928770	Hs.586239	NR_126363	ENSG00000224995	LINC01526	Lnc-FAM46A-1	long intergenic non-protein coding RNA 1526	ncRNA	0.000000	0.295000	
chunk0202_114_1	chr9	72592567	72593000	+	0	NA	intron (NM_138691, intron 2 of 23)	intron (NM_138691, intron 2 of 23)	70982	NM_138691	117531	Hs.670211	NM_138691	ENSG00000165091	TMC1	DFNA36|DFNB11|DFNB7	transmembrane channel like 1	protein-coding	0.006928	0.433180	
chunk0085_54_1	chr18	863302	863508	+	0	NA	Intergenic	Intergenic	-41538	NM_001099733	116	Hs.531719	NM_001117	ENSG00000141433	ADCYAP1	PACAP	adenylate cyclase activating polypeptide 1	protein-coding	0.009709	0.483092	146(GGGAACACTCTGTTCC,-,0.00),147(GGAACACTCTGTTCCT,+,0.00)
chunk0145_161_1	chr4	147163160	147163515	+	0	NA	Intergenic	Intergenic	181380	NR_031662	100313938		NR_031662	ENSG00000221369	MIR548G	MIRN548G|hsa-mir-548g	microRNA 548g	ncRNA	0.000000	0.410112	
chunk0040_158_1	chr11	113781758	113782611	+	0	NA	Intergenic	Intergenic	2388	NM_001101389	644672	Hs.705360	NM_001101389	ENSG00000228607	CLDN25	-	claudin 25	protein-coding	0.007034	0.439110	
chunk0109_113_1	chr20	2559911	2560110	+	0	NA	intron (NM_080751, intron 3 of 19)	intron (NM_080751, intron 3 of 19)	23403	NM_080751	117532	Hs.352626	NM_080751	ENSG00000149488	TMC2	C20orf145	transmembrane channel like 2	protein-coding	0.015075	0.480000	46(GAAAACATTCAGTTCC,-,0.00),47(AAAACATTCAGTTCCC,+,0.00)
chunk0046_354_1	chr12	63008624	63009188	+	0	NA	Intergenic	MER34C_|LTR|ERV1	-74021	NM_020700	57460	Hs.435479	NM_020700	ENSG00000111110	PPM1H	ARHCL1|NERPP-2C|URCC2	protein phosphatase, Mg2+/Mn2+ dependent 1H	protein-coding	0.008865	0.392920	138(TGGAACTGTGAGTCCC,-,0.00),139(GGAACTGTGAGTCCCT,+,0.00)
chunk0123_83_1	chr3	41847349	41848448	+	0	NA	intron (NM_017886, intron 17 of 36)	intron (NM_017886, intron 17 of 36)	114270	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.002730	0.349091	
chunk0164_291_1	chr6	24666567	24666909	+	0	NA	promoter-TSS (NM_001160094)	promoter-TSS (NM_001160094)	149	NM_016614	51567	Hs.403010	NM_016614	ENSG00000111802	TDP2	AD022|EAP2|EAPII|TTRAP|dJ30M3.3|hTDP2	tyrosyl-DNA phosphodiesterase 2	protein-coding	0.070175	0.612245	
chunk0081_185_1	chr17	41734537	41735012	+	0	NA	promoter-TSS (NM_001079871)	promoter-TSS (NM_001079871)	-128	NM_177977	9001	Hs.158300	NM_003949	ENSG00000173805	HAP1	HAP2|HIP5|HLP|hHLP1	huntingtin associated protein 1	protein-coding	0.082105	0.670168	
chunk0006_105_1	chr1	65484268	65484907	+	0	NA	intron (NM_001003680, intron 2 of 19)	intron (NM_001003680, intron 2 of 19)	-41102	NM_001198688	3953	Hs.23581	NM_002303	ENSG00000116678	LEPR	CD295|LEP-R|LEPRD|OB-R|OBR	leptin receptor	protein-coding	0.006260	0.335938	
chunk0054_43_1	chr13	41216151	41216562	+	0	NA	TTS (NM_004294)	TTS (NM_004294)	-21790	NM_032138	84078	Hs.63841	NM_032138	ENSG00000120696	KBTBD7	-	kelch repeat and BTB domain containing 7	protein-coding	0.000000	0.298544	
chunk0072_100_1	chr15	91079863	91080430	+	0	NA	Intergenic	L1MC1|LINE|L1	-19806	NM_001167580	9899	Hs.21754	NM_014848	ENSG00000185518	SV2B	HsT19680	synaptic vesicle glycoprotein 2B	protein-coding	0.008818	0.373239	
chunk0024_242_1	chr10	38578913	38579145	+	0	NA	Intergenic	(AATGG)n|Simple_repeat|Simple_repeat	-117567	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.017241	0.390558	
chunk0162_128_1	chr6	2961019	2961430	+	0	NA	intron (NM_001297700, intron 1 of 6)	intron (NM_001297700, intron 1 of 6)	946	NM_001271825	5269	Hs.519523	NM_004568	ENSG00000124570	SERPINB6	CAP|DFNB91|MSTP057|PI-6|PI6|PTI|SPI3	serpin family B member 6	protein-coding	0.009732	0.407767	
chunk0046_428_1	chr12	64639238	64639597	+	0	NA	intron (NR_040718, intron 1 of 3)	intron (NR_040718, intron 1 of 3)	-16812	NR_037515	100500856		NR_037515	ENSG00000266016	MIR548Z	-	microRNA 548z	ncRNA	0.008357	0.330556	
chunk0029_133_1	chr10	98976568	98976796	+	0	NA	intron (NM_001166246, intron 3 of 12)	intron (NM_001166246, intron 3 of 12)	-52114	NR_106762	102465253		NR_106762	ENSG00000274056	MIR6507	hsa-mir-6507	microRNA 6507	ncRNA	0.017544	0.344978	110(AGGAACAGTTTGTTCC,-,0.00),111(GGAACAGTTTGTTCCC,+,0.00)
chunk0020_246_1	chr1	236010103	236010325	+	0	NA	intron (NM_002508, intron 12 of 19)	intron (NM_002508, intron 12 of 19)	54967	NM_002508	4811	Hs.356624	NM_002508	ENSG00000116962	NID1	NID	nidogen 1	protein-coding	0.004505	0.345291	
chunk0055_171_1	chr13	60529246	60529527	+	0	NA	intron (NM_030794, intron 11 of 13)	intron (NM_030794, intron 11 of 13)	132093	NM_001146070	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.010676	0.290780	156(AGGGACAATCTGTCCC,-,0.00),157(GGGACAATCTGTCCCG,+,0.00)
chunk0175_134_1	chr7	3486741	3486940	+	0	NA	intron (NM_152744, intron 1 of 44)	intron (NM_152744, intron 1 of 44)	185392	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.000000	0.250000	
chunk0077_250_1	chr16	80867384	80868051	+	0	NA	intron (NR_131948, intron 1 of 2)	L1PA16|LINE|L1	24879	NR_131948	100996425	Hs.125350	NR_131947	ENSG00000260896	ARLNC1	LINC02170|PRCAT47	androgen receptor regulated long noncoding RNA 1	ncRNA	0.007496	0.329341	
chunk0016_333_1	chr1	201775182	201775874	+	0	NA	intron (NM_001167738, intron 1 of 26)	HAL1|LINE|L1	-33083	NR_031599	100302158		NR_031599	ENSG00000221028	MIR1231	MIRN1231|hsa-mir-1231	microRNA 1231	ncRNA	0.008671	0.424242	
chunk0122_216_1	chr3	33482054	33482570	+	0	NA	Intergenic	MER65-int|LTR|ERV1	-41907	NM_001128161	7342	Hs.729120	NM_014517	ENSG00000153560	UBP1	LBP-1B|LBP-1a|LBP1A|LBP1B	upstream binding protein 1	protein-coding	0.001938	0.338491	
chunk0128_228_1	chr3	108296156	108296409	+	0	NA	promoter-TSS (NM_001282559)	promoter-TSS (NM_001282559)	-208	NM_001282556	11148	Hs.225968	NM_007072	ENSG00000114455	HHLA2	B7-H5|B7-H7|B7H7|B7y	HERV-H LTR-associating 2	protein-coding	0.000000	0.456693	
chunk0130_241_1	chr3	135289778	135290171	+	0	NA	Intergenic	L1MD3|LINE|L1	494717	NM_004441	2047	Hs.116092	NM_004441	ENSG00000154928	EPHB1	ELK|EPHT2|Hek6|NET	EPH receptor B1	protein-coding	0.010178	0.337563	
chunk0121_420_1	chr3	25837021	25837424	+	0	NA	Intergenic	L1MA9|LINE|L1	36473	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.002481	0.547030	
chunk0084_30_1	chr17	73566074	73566696	+	0	NA	intron (NM_001144952, intron 1 of 44)	MSTB|LTR|ERVL-MaLR	77703	NM_001144952	54549	Hs.435719	NM_019064	ENSG00000069188	SDK2	-	sidekick cell adhesion molecule 2	protein-coding	0.003215	0.417335	
chunk0086_396_1	chr18	26679160	26679540	+	0	NA	Intergenic	Intergenic	-21949	NM_001258222	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.005263	0.380577	
chunk0088_417_1	chr18	54828655	54829040	+	0	NA	intron (NM_004163, intron 1 of 5)	intron (NM_004163, intron 1 of 5)	370	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.041558	0.528497	
chunk0003_81_1	chr1	31510967	31511578	+	0	NA	Intergenic	MER81|DNA|hAT-Blackjack	-7163	NR_027085	284551	Hs.658659	NR_027085		LINC01226	-	long intergenic non-protein coding RNA 1226	ncRNA	0.006547	0.560458	
chunk0032_211_1	chr11	7511527	7511771	+	0	NA	TTS (NM_198474)	TTS (NM_198474)	-2116	NM_003621	8495	Hs.655714	NM_003621	ENSG00000166387	PPFIBP2	Cclp1	PPFIA binding protein 2	protein-coding	0.012295	0.489796	
chunk0101_114_1	chr2	126080890	126081142	+	0	NA	Intergenic	MER5B|DNA|hAT-Charlie	-574919	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.003968	0.339921	
chunk0140_330_1	chr4	73692175	73692986	+	0	NA	Intergenic	Intergenic	-47926	NM_000584	3576	Hs.624	NM_000584	ENSG00000169429	CXCL8	GCP-1|GCP1|IL8|LECT|LUCT|LYNAP|MDNCF|MONAP|NAF|NAP-1|NAP1	C-X-C motif chemokine ligand 8	protein-coding	0.007398	0.357143	83(AAGCACAAGTTGTGCA,-,0.00)
chunk0096_464_1	chr2	40292351	40292971	+	0	NA	intron (NM_021097, intron 1 of 9)	intron (NM_021097, intron 1 of 9)	137643	NM_001252624	6546	Hs.31961	NM_021097	ENSG00000183023	SLC8A1	NCX1	solute carrier family 8 member A1	protein-coding	0.004839	0.420290	
chunk0110_417_1	chr20	20624874	20625146	+	0	NA	intron (NM_020343, intron 10 of 39)	intron (NM_020343, intron 10 of 39)	87613	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.007353	0.487179	
chunk0201_76_1	chr9	34275888	34276140	+	0	NA	intron (NM_194313, intron 6 of 12)	MIRb|SINE|MIR	53186	NM_194313	347240	Hs.710246	NM_194313	ENSG00000186638	KIF24	C9orf48|bA571F15.4	kinesin family member 24	protein-coding	0.003968	0.399209	
chunk0036_362_1	chr11	67027806	67028034	+	0	NA	intron (NM_177963, intron 1 of 7)	intron (NM_177963, intron 1 of 7)	4575	NM_177963	91683	Hs.287636	NM_177963	ENSG00000173227	SYT12	SYT11|sytXII	synaptotagmin 12	protein-coding	0.021930	0.524017	165(AGGTACATGGTGACCC,-,0.00)
chunk0020_375_1	chr1	239859118	239859452	+	0	NA	intron (NM_000740, intron 4 of 4)	L1MB5|LINE|L1	40587	NR_046582	100873984	Hs.199475	NR_046582	ENSG00000234601	CHRM3-AS1	-	CHRM3 antisense RNA 1	ncRNA	0.005988	0.319403	
chunk0053_182_1	chr13	30973470	30973751	+	0	NA	intron (NM_152325, intron 6 of 6)	intron (NM_152325, intron 6 of 6)	40913	NM_152325	122046	Hs.124463	NM_152325	ENSG00000175664	TEX26	C13orf26	testis expressed 26	protein-coding	0.003559	0.368794	
chunk0047_220_1	chr12	71722900	71723258	+	0	NA	Intergenic	L1M4|LINE|L1	-31799	NM_014999	23011	Hs.524590	NM_014999	ENSG00000080371	RAB21	-	RAB21, member RAS oncogene family	protein-coding	0.022346	0.395543	
chunk0211_403_1	chrX	128726786	128727150	+	0	NA	Intergenic	Intergenic	-674565	NM_138289	139741	Hs.680125	NM_138289	ENSG00000123165	ACTRT1	AIP1|ARIP1|ARPT1|HSD27	actin related protein T1	protein-coding	0.000000	0.427397	
chunk0031_25_1	chr10	121910765	121911259	+	0	NA	exon (NM_001288736, exon 5 of 12)	exon (NM_001288736, exon 5 of 12)	17051	NM_001288735	11101	Hs.632080	NM_007041	ENSG00000107669	ATE1	-	arginyltransferase 1	protein-coding	0.010121	0.377778	
chunk0211_177_1	chrX	116624942	116625396	+	0	NA	Intergenic	L1MB1|LINE|L1	-162136	NM_001017978	203413	Hs.97892	NM_001017978	ENSG00000204019	CT83	CXorf61|KK-LC-1|KKLC1	cancer/testis antigen 83	protein-coding	0.002203	0.367033	
chunk0073_439_1	chr16	19251589	19251788	+	0	NA	intron (NM_001308157, intron 7 of 7)	LTR105_Mam|LTR|ERVL	-34095	NM_001256720	728276	Hs.632180	NM_001256720	ENSG00000261210	CLEC19A	-	C-type lectin domain containing 19A	protein-coding	0.010050	0.540000	
chunk0082_449_1	chr17	62167508	62167763	+	0	NA	Intergenic	Intergenic	-102353	NM_005121	9969	Hs.282678	NM_005121	ENSG00000108510	MED13	ARC250|DRIP250|HSPC221|THRAP1|TRAP240	mediator complex subunit 13	protein-coding	0.000000	0.500000	
chunk0111_348_1	chr20	33373658	33374392	+	0	NA	intron (NM_001278169, intron 9 of 13)	L2b|LINE|L2	27544	NM_001278168	51654	Hs.435952	NM_016082	ENSG00000101391	CDK5RAP1	C20orf34|C42|CGI-05|HSPC167	CDK5 regulatory subunit associated protein 1	protein-coding	0.005450	0.408163	
chunk0101_271_1	chr2	133652081	133652597	+	0	NA	Intergenic	Intergenic	-83879	NM_207481	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.009690	0.361702	272(AAGAACACAGAGTTCT,-,0.00),273(AGAACACAGAGTTCTC,+,0.00)
chunk0044_398_1	chr12	40682895	40683234	+	0	NA	Intergenic	L2a|LINE|L2	-9378	NM_001843	1272	Hs.143434	NM_001843	ENSG00000018236	CNTN1	F3|GP135|MYPCN	contactin 1	protein-coding	0.002950	0.382353	
chunk0180_419_1	chr7	76089716	76090264	+	0	NA	Intergenic	Intergenic	41971	NM_005918	4191	Hs.520967	NM_005918	ENSG00000146701	MDH2	EIEE51|M-MDH|MDH|MGC:3559|MOR1	malate dehydrogenase 2	protein-coding	0.012774	0.451730	
chunk0211_105_1	chrX	111202244	111202583	+	0	NA	intron (NM_001128168, intron 14 of 15)	intron (NM_001128168, intron 14 of 15)	68133	NM_014289	827	Hs.496593	NM_014289	ENSG00000077274	CAPN6	CANPX|CAPNX|CalpM|DJ914P14.1	calpain 6	protein-coding	0.000000	0.364706	180(TTGGACATGTTGTTCT,-,0.00),181(TGGACATGTTGTTCTG,+,0.00)
chunk0080_422_1	chr17	35799998	35800458	+	0	NA	Intergenic	Intergenic	-4521	NR_111988	79148	Hs.380710	NM_024302	ENSG00000271447	MMP28	EPILYSIN|MM28|MMP-25|MMP-28|MMP25	matrix metallopeptidase 28	protein-coding	0.000000	0.522777	
chunk0164_127_1	chr6	20880965	20881198	+	0	NA	intron (NM_017774, intron 9 of 15)	intron (NM_017774, intron 9 of 15)	346624	NM_017774	54901	Hs.657604	NM_017774	ENSG00000145996	CDKAL1	-	CDK5 regulatory subunit associated protein 1 like 1	protein-coding	0.004292	0.405983	
chunk0137_149_1	chr4	15694499	15694874	+	0	NA	Intergenic	HERVIP10FH-int|LTR|ERV1	-8264	NM_004334	683	Hs.720344	NM_004334	ENSG00000109743	BST1	CD157	bone marrow stromal cell antigen 1	protein-coding	0.010667	0.385638	
chunk0184_383_1	chr7	121464217	121464489	+	0	NA	Intergenic	Intergenic	-67985	NM_014888	10447	Hs.434053	NM_014888	ENSG00000196937	FAM3C	GS3786|ILEI	family with sequence similarity 3 member C	protein-coding	0.007353	0.391941	
chunk0020_307_1	chr1	237470882	237471201	+	0	NA	promoter-TSS (NR_039626)	promoter-TSS (NR_039626)	-78	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.015674	0.518750	
chunk0152_152_1	chr5	59317433	59318232	+	0	NA	intron (NM_001165899, intron 3 of 16)	intron (NM_001165899, intron 3 of 16)	39069	NM_001197219	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.008761	0.406250	223(AGGCACACAGTGAACC,-,0.00)
chunk0209_334_1	chrX	51322685	51323189	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-9294	NM_153183	170685	Hs.375178	NM_153183	ENSG00000122824	NUDT10	APS2|DIPP3-alpha|DIPP3a	nudix hydrolase 10	protein-coding	0.005952	0.352475	
chunk0118_422_1	chr22	38506159	38506804	+	0	NA	promoter-TSS (NM_001098504)	promoter-TSS (NM_001098504)	-141	NM_001098504	10521	Hs.528305	NM_006386	ENSG00000100201	DDX17	P72|RH70	DEAD-box helicase 17	protein-coding	0.094574	0.565015	
chunk0199_341_1	chr9	11194541	11194827	+	0	NA	Intergenic	Intergenic	581478	NR_110696	101929428	Hs.434446	NR_110696	ENSG00000226717	PTPRD-AS2	-	PTPRD antisense RNA 2 (head to head)	ncRNA	0.000000	0.275261	
chunk0064_27_1	chr14	89428846	89429140	+	0	NA	intron (NM_001085471, intron 1 of 6)	intron (NM_001085471, intron 1 of 6)	11639	NR_036500	400236	Hs.585207	NR_036500	ENSG00000258920	FOXN3-AS1	-	FOXN3 antisense RNA 1	ncRNA	0.013605	0.559322	
chunk0102_333_1	chr2	151928468	151928750	+	0	NA	intron (NM_001005746, intron 2 of 13)	intron (NM_001005746, intron 2 of 13)	45362	NM_001005747	785	Hs.120725	NM_000726	ENSG00000182389	CACNB4	CAB4|CACNLB4|EA5|EIG9|EJM|EJM4|EJM6	calcium voltage-gated channel auxiliary subunit beta 4	protein-coding	0.007092	0.448763	
chunk0181_326_1	chr7	87910193	87910518	+	0	NA	TTS (NM_006716)	TTS (NM_006716)	-23896	NM_016351	53616	Hs.256398	NM_004194	ENSG00000008277	ADAM22	ADAM 22|EIEE61|MDC2	ADAM metallopeptidase domain 22	protein-coding	0.000000	0.417178	
chunk0179_393_1	chr7	51426052	51426251	+	0	NA	Intergenic	Intergenic	-109333	NM_001287438	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.025126	0.545000	
chunk0029_435_1	chr10	110082034	110082267	+	0	NA	intron (NM_016824, intron 1 of 14)	intron (NM_016824, intron 1 of 14)	-73769	NR_038943	100505933	Hs.604103	NR_038943		ADD3-AS1	-	ADD3 antisense RNA 1	ncRNA	0.004292	0.397436	
chunk0117_255_1	chr22	23467778	23468408	+	0	NA	intron (NR_110539, intron 10 of 11)	intron (NR_110539, intron 10 of 11)	18887	NR_110539	388882	Hs.542766	NR_110539	ENSG00000178248	FAM230I	LINC01658	family with sequence similarity 230 member I	ncRNA	0.001587	0.389857	
chunk0115_36_1	chr21	21008416	21009128	+	0	NA	intron (NM_004540, intron 1 of 17)	intron (NM_004540, intron 1 of 17)	10457	NM_004540	4685	Hs.473450	NM_004540	ENSG00000154654	NCAM2	NCAM21	neural cell adhesion molecule 2	protein-coding	0.002809	0.328191	
chunk0146_169_1	chr4	160250869	160251853	+	0	NA	Intergenic	Intergenic	983515	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.006098	0.329949	
chunk0025_394_1	chr10	59350427	59350988	+	0	NA	intron (NM_001001971, intron 3 of 11)	intron (NM_001001971, intron 3 of 11)	11887	NM_001166698	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.005348	0.382562	
chunk0121_280_1	chr3	23528024	23528778	+	0	NA	intron (NM_152653, intron 4 of 5)	LTR60B|LTR|ERV1	-277492	NM_182666	7324	Hs.164853	NM_003341	ENSG00000170142	UBE2E1	UBCH6	ubiquitin conjugating enzyme E2 E1	protein-coding	0.010610	0.445033	
chunk0032_174_1	chr11	5621124	5621565	+	0	NA	intron (NM_001003827, intron 1 of 7)	intron (NM_001003827, intron 1 of 7)	1400	NM_001003827	53840	Hs.729048	NM_021616	ENSG00000258659	TRIM34	IFP1|RNF21	tripartite motif containing 34	protein-coding	0.002268	0.459276	
chunk0018_419_1	chr1	222708797	222709143	+	0	NA	intron (NM_022831, intron 1 of 9)	L2a|LINE|L2	3552	NM_022831	64853	Hs.156625	NM_022831	ENSG00000186063	AIDA	C1orf80	axin interactor, dorsalization associated	protein-coding	0.008671	0.342939	
chunk0056_179_1	chr13	85373179	85373865	+	0	NA	intron (NR_046989, intron 1 of 3)	intron (NR_046989, intron 1 of 3)	9919	NR_046989	100874137	Hs.742643	NR_046989	ENSG00000226317	LINC00351	-	long intergenic non-protein coding RNA 351	ncRNA	0.007289	0.308588	
chunk0046_288_1	chr12	62036796	62037442	+	0	NA	intron (NM_178539, intron 1 of 4)	intron (NM_178539, intron 1 of 4)	155720	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.001548	0.364760	420(ATGAACTTACTGTTCC,-,0.00),421(TGAACTTACTGTTCCT,+,0.00)
chunk0014_448_1	chr1	183866084	183866498	+	0	NA	intron (NM_001297672, intron 4 of 16)	L2a|LINE|L2	61210	NM_001297671	23179	Hs.497148	NM_015149	ENSG00000143344	RGL1	RGL	ral guanine nucleotide dissociation stimulator like 1	protein-coding	0.012077	0.380723	
chunk0109_415_1	chr2	241093142	241094037	+	0	NA	3' UTR (NM_001080437, exon 32 of 32)	3' UTR (NM_001080437, exon 32 of 32)	8743	NR_028051	130916	Hs.159556	NM_182501	ENSG00000122085	MTERF4	MTERFD2	mitochondrial transcription termination factor 4	protein-coding	0.013408	0.463170	
chunk0202_271_1	chr9	77076470	77076938	+	0	NA	Intergenic	L1MC5a|LINE|L1	57049	NM_001013735	442425	Hs.553843	NM_001013735	ENSG00000204612	FOXB2	bA159H20.4	forkhead box B2	protein-coding	0.019231	0.411514	375(ATGGACAATGAGTTCT,-,0.00),376(TGGACAATGAGTTCTC,+,0.00)
chunk0052_4_1	chr13	18886561	18886794	+	0	NA	Intergenic	L2a|LINE|L2	-14708	NR_027995	284232	Hs.679496	NR_027995		ANKRD20A9P	-	ankyrin repeat domain 20 family member A9, pseudogene	pseudo	0.000000	0.341880	
chunk0212_348_1	chrX	147232628	147233057	+	0	NA	Intergenic	Intergenic	-1765	NR_030234	574512		NR_030234	ENSG00000207969	MIR507	MIRN507|hsa-mir-507|mir-507	microRNA 507	ncRNA	0.009324	0.383721	
chunk0022_313_1	chr10	16114388	16114732	+	0	NA	Intergenic	LTR88b|LTR|Gypsy?	-254040	NM_024948	80013	Hs.158870	NM_024948	ENSG00000148481	MINDY3	C10orf97|CARP|DERP5|FAM188A|MST126|MSTP126|my042	MINDY lysine 48 deubiquitinase 3	protein-coding	0.005814	0.414493	
chunk0116_236_1	chr21	38303196	38303684	+	0	NA	Intergenic	Intergenic	31020	NM_170737	3772	Hs.411299	NM_002243	ENSG00000157551	KCNJ15	IRKK|KIR1.3|KIR4.2	potassium voltage-gated channel subfamily J member 15	protein-coding	0.008197	0.417178	
chunk0210_202_1	chrX	80632345	80632859	+	0	NA	Intergenic	L1MA3|LINE|L1	177132	NM_153252	254065	Hs.147027	NM_153252	ENSG00000165288	BRWD3	BRODL|MRX93	bromodomain and WD repeat domain containing 3	protein-coding	0.003891	0.304854	
chunk0093_450_1	chr19	58575584	58575909	+	0	NA	TTS (NR_027334)	TTS (NR_027334)	347	NR_026052	65996	Hs.541177	NM_023939	ENSG00000213753	CENPBD1P1	-	CENPB DNA-binding domains containing 1 pseudogene 1	pseudo	0.083077	0.665644	
chunk0155_19_1	chr5	90911030	90911607	+	0	NA	intron (NR_003149, intron 83 of 89)	intron (NR_003149, intron 83 of 89)	352518	NM_032119	84059	Hs.591777	NM_032119	ENSG00000164199	ADGRV1	FEB4|GPR98|MASS1|USH2B|USH2C|VLGR1|VLGR1b	adhesion G protein-coupled receptor V1	protein-coding	0.008666	0.320069	
chunk0112_105_1	chr20	38337988	38338313	+	0	NA	TTS (NM_001725)	TTS (NM_001725)	-8261	NM_004139	3929	Hs.154078	NM_004139	ENSG00000129988	LBP	BPIFD2	lipopolysaccharide binding protein	protein-coding	0.006154	0.509202	
chunk0006_177_1	chr1	67104522	67104749	+	0	NA	intron (NM_001276352, intron 6 of 8)	intron (NM_001276352, intron 6 of 8)	30336	NM_001276351	400757	Hs.666621	NM_001013674	ENSG00000203963	C1orf141	-	chromosome 1 open reading frame 141	protein-coding	0.004405	0.276316	115(TGGAACAAATTGTTCT,-,0.00),116(GGAACAAATTGTTCTC,+,0.00)
chunk0159_151_1	chr5	139331431	139332003	+	0	NA	TTS (NM_001194955)	TTS (NM_001194955)	-10115	NM_016480	51247	Hs.396644	NM_016480	ENSG00000120727	PAIP2	PAIP-2|PAIP2A	poly(A) binding protein interacting protein 2	protein-coding	0.008741	0.349040	
chunk0006_166_1	chr1	66507880	66508134	+	0	NA	Intergenic	LTR56|LTR|ERV1	-25562	NM_001308203	84251	Hs.132121	NM_032291	ENSG00000118473	SGIP1	-	SH3 domain GRB2 like endophilin interacting protein 1	protein-coding	0.007874	0.392157	
chunk0193_161_1	chr8	74735037	74735602	+	0	NA	intron (NR_033830, intron 4 of 5)	intron (NR_033830, intron 4 of 5)	29626	NR_031744	100302260		NR_031744	ENSG00000283188	MIR2052	hsa-mir-2052	microRNA 2052	ncRNA	0.005310	0.436396	
chunk0182_179_1	chr7	95622917	95623961	+	0	NA	Intergenic	Charlie19a|DNA|hAT-Charlie	-26826	NM_002612	5166	Hs.8364	NM_002612	ENSG00000004799	PDK4	-	pyruvate dehydrogenase kinase 4	protein-coding	0.003831	0.381818	
chunk0192_342_1	chr8	67676414	67676638	+	0	NA	intron (NM_020361, intron 1 of 10)	intron (NM_020361, intron 1 of 10)	69859	NM_020361	57094	Hs.658850	NM_020361	ENSG00000165078	CPA6	CPAH|ETL5|FEB11	carboxypeptidase A6	protein-coding	0.004464	0.382222	
chunk0027_298_1	chr10	77714914	77715493	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-77384	NM_001161353	3778	Hs.144795	NM_002247	ENSG00000156113	KCNMA1	BKTM|CADEDS|KCa1.1|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1	potassium calcium-activated channel subfamily M alpha 1	protein-coding	0.008636	0.465517	314(AGGTACACTGTGCCCC,-,0.00),315(GGTACACTGTGCCCCT,+,0.00)
chunk0084_426_1	chr17	82531472	82531797	+	0	NA	intron (NM_004514, intron 1 of 8)	Tigger3b|DNA|TcMar-Tigger	11916	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.012308	0.429448	
chunk0030_414_1	chr10	120229421	120230020	+	0	NA	Intergenic	L1ME3A|LINE|L1	125503	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.008347	0.441667	
chunk0057_318_1	chr13	106736915	106737469	+	0	NA	Intergenic	Intergenic	83312	NR_047026	100874173	Hs.569297	NR_047026	ENSG00000230156	LINC00443	-	long intergenic non-protein coding RNA 443	ncRNA	0.030686	0.499099	314(CGGCACAGCCTGTTCT,-,0.00),315(GGCACAGCCTGTTCTT,+,0.00)
chunk0075_280_1	chr16	53886472	53887101	+	0	NA	intron (NM_001080432, intron 6 of 8)	intron (NM_001080432, intron 6 of 8)	-152607	NR_103838	100505692	Hs.664629	NR_103838		FTO-IT1	-	FTO intronic transcript 1	ncRNA	0.007949	0.330159	
chunk0097_239_1	chr2	53561142	53561715	+	0	NA	Intergenic	L1ME3A|LINE|L1	-206364	NM_001008708	494143	Hs.585944	NM_001008708	ENSG00000143942	CHAC2	GCG1	ChaC cation transport regulator homolog 2	protein-coding	0.008726	0.364111	
chunk0132_444_1	chr3	165168874	165169323	+	0	NA	Intergenic	L1PA6|LINE|L1	27583	NM_014926	22865	Hs.101745	NM_014926	ENSG00000121871	SLITRK3	-	SLIT and NTRK like family member 3	protein-coding	0.011136	0.477778	
chunk0106_22_1	chr2	195818599	195818798	+	0	NA	intron (NM_018897, intron 49 of 64)	intron (NM_018897, intron 49 of 64)	161570	NM_020342	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.015075	0.410000	
chunk0090_312_1	chr18	75461913	75462120	+	0	NA	Intergenic	Intergenic	-34313	NM_001303482	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.004831	0.466346	
chunk0157_202_1	chr5	119050674	119051010	+	0	NA	Intergenic	LTR26B|LTR|ERV1	-20245	NM_005509	1657	Hs.181042	NM_005509	ENSG00000172869	DMXL1	-	Dmx like 1	protein-coding	0.002976	0.364985	
chunk0201_333_1	chr9	63822753	63824162	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-3803	NR_039688	100616184		NR_039688	ENSG00000276029	MIR4477A	-	microRNA 4477a	ncRNA	0.009226	0.461702	
chunk0153_370_1	chr5	74827871	74828390	+	0	NA	intron (NR_046462, intron 4 of 11)	Charlie2b|DNA|hAT-Charlie	38257	NR_046462	26049	Hs.91662	NM_015566	ENSG00000198780	FAM169A	SLAP75	family with sequence similarity 169 member A	protein-coding	0.003854	0.353846	
chunk0124_69_1	chr3	53134106	53134941	+	0	NA	Intergenic	Intergenic	-4069	NM_052859	91869	Hs.631910	NM_052859	ENSG00000163933	RFT1	CDG1N	RFT1 homolog	protein-coding	0.009581	0.498804	
chunk0115_425_1	chr21	31713140	31713700	+	0	NA	intron (NM_001145444, intron 1 of 18)	MIR|SINE|MIR	18698	NM_001145444	57466	Hs.17255	NM_020706	ENSG00000156304	SCAF4	SFRS15|SRA4	SR-related CTD associated factor 4	protein-coding	0.005357	0.338681	
chunk0165_389_1	chr6	38708455	38708826	+	0	NA	Intergenic	L1ME3E|LINE|L1	-5464	NM_006708	2739	Hs.268849	NM_006708	ENSG00000124767	GLO1	GLOD1|GLYI|HEL-S-74	glyoxalase I	protein-coding	0.002695	0.341398	184(TGGTACAGGAAGTGCC,-,0.00),185(GGTACAGGAAGTGCCT,+,0.00)
chunk0071_183_1	chr15	83537939	83538572	+	0	NA	intron (NM_001301109, intron 4 of 11)	intron (NM_001301109, intron 4 of 11)	91027	NR_125370	6457	Hs.270055	NM_003027	ENSG00000140600	SH3GL3	CNSA3|EEN-B2|HsT19371|SH3D2C|SH3P13	SH3 domain containing GRB2 like 3, endophilin A3	protein-coding	0.009479	0.340694	
chunk0176_1_1	chr7	8035076	8035300	+	0	NA	intron (NM_138426, intron 3 of 7)	L1PA17|LINE|L1	-66436	NR_110018	100505921	Hs.634989	NR_110018		LOC100505921	-	uncharacterized LOC100505921	ncRNA	0.004464	0.560000	
chunk0184_21_1	chr7	111860618	111860849	+	0	NA	intron (NM_014705, intron 23 of 51)	intron (NM_014705, intron 23 of 51)	52228	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.012987	0.487069	
chunk0047_348_1	chr12	74972946	74973412	+	0	NA	Intergenic	Intergenic	236569	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.006438	0.381156	
chunk0044_156_1	chr12	29793521	29793782	+	0	NA	Intergenic	Intergenic	-8892	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.015326	0.438931	
chunk0118_288_1	chr22	33886621	33887342	+	0	NA	intron (NM_004737, intron 1 of 15)	L2b|LINE|L2	33447	NM_004737	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.018031	0.443213	
chunk0191_403_1	chr8	57559628	57559922	+	0	NA	Intergenic	Intergenic	215988	NR_125818	101929488	Hs.407557	NR_125818	ENSG00000253871	LOC101929488	-	uncharacterized LOC101929488	ncRNA	0.000000	0.423729	
chunk0193_411_1	chr8	80669523	80669882	+	0	NA	intron (NM_001033723, intron 5 of 8)	intron (NM_001033723, intron 5 of 8)	183489	NM_023929	65986	Hs.591868	NM_023929	ENSG00000205189	ZBTB10	RINZF	zinc finger and BTB domain containing 10	protein-coding	0.005571	0.466667	
chunk0128_222_1	chr3	108137538	108137737	+	0	NA	non-coding (NR_110030, exon 2 of 2)	non-coding (NR_110030, exon 2 of 2)	11816	NR_110028	101929623	Hs.570653	NR_110028	ENSG00000271856	LINC01215	-	long intergenic non-protein coding RNA 1215	ncRNA	0.020101	0.375000	
chunk0016_290_1	chr1	201061129	201061345	+	0	NA	intron (NM_000069, intron 25 of 43)	intron (NM_000069, intron 25 of 43)	-37537	NM_017596	23046	Hs.169182	NM_017596	ENSG00000116852	KIF21B	-	kinesin family member 21B	protein-coding	0.004630	0.594470	
chunk0174_26_1	chr6	153502418	153502682	+	0	NA	Intergenic	L1MEd|LINE|L1	82073	NR_106988									0.003788	0.271698	
chunk0132_301_1	chr3	160236361	160236758	+	0	NA	Intergenic	Intergenic	10923	NM_001168214	401097	Hs.729755	NM_001168214	ENSG00000180044	C3orf80	-	chromosome 3 open reading frame 80	protein-coding	0.005038	0.434673	
chunk0048_236_1	chr12	81558560	81558759	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	39712	NM_001220478	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.445000	
chunk0191_177_1	chr8	51054275	51054738	+	0	NA	Intergenic	Intergenic	754939	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.004320	0.316810	
chunk0067_414_1	chr15	49627437	49627735	+	0	NA	intron (NM_001144955, intron 2 of 4)	Tigger3b|DNA|TcMar-Tigger	6557	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.003356	0.357860	
chunk0148_76_1	chr5	2509729	2510629	+	0	NA	Intergenic	L1MC5|LINE|L1	-197978	NR_104616	100506858	Hs.445071	NR_104616		LOC100506858	-	uncharacterized LOC100506858	ncRNA	0.021111	0.478357	
chunk0109_165_1	chr20	4014071	4014282	+	0	NA	intron (NM_001134338, intron 1 of 6)	intron (NM_001134338, intron 1 of 6)	1231	NM_007219	11237	Hs.547576	NM_007219	ENSG00000101236	RNF24	G1L	ring finger protein 24	protein-coding	0.009479	0.452830	
chunk0194_347_1	chr8	89201217	89201629	+	0	NA	Intergenic	L2|LINE|L2	556288	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.002427	0.416465	
chunk0028_219_1	chr10	89564355	89564843	+	0	NA	Intergenic	Intergenic	28228	NR_029524	406901		NR_029524	ENSG00000198997	MIR107	MIRN107|miR-107	microRNA 107	ncRNA	0.008197	0.347648	
chunk0071_225_1	chr15	84854997	84855774	+	0	NA	intron (NM_020778, intron 5 of 13)	L1M7|LINE|L1	-29276	NM_201651	9154	Hs.459187	NM_004213	ENSG00000156222	SLC28A1	CNT1|HCNT1	solute carrier family 28 member 1	protein-coding	0.020592	0.458869	34(TAAAACACAATGTTCT,-,0.00),35(AAAACACAATGTTCTC,+,0.00)
chunk0168_405_1	chr6	94893313	94893796	+	0	NA	Intergenic	Intergenic	683897	NR_047502	101927288	Hs.616643	NR_047502	ENSG00000261366	MANEA-DT	MANEA-AS1	MANEA divergent transcript	ncRNA	0.006211	0.307851	
chunk0169_121_1	chr6	100921385	100922015	+	0	NA	Intergenic	L1PA14|LINE|L1	-40328	NM_001284271	10973	Hs.486031	NM_006828	ENSG00000112249	ASCC3	ASC1p200|HELIC1|RNAH	activating signal cointegrator 1 complex subunit 3	protein-coding	0.003175	0.356577	
chunk0194_265_1	chr8	86982052	86982420	+	0	NA	intron (NM_173538, intron 4 of 10)	L1ME1|LINE|L1	115788	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.000000	0.292683	
chunk0140_293_1	chr4	72818421	72818640	+	0	NA	Intergenic	L2c|LINE|L2	-249731	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.000000	0.300000	
chunk0053_188_1	chr13	31209275	31209546	+	0	NA	intron (NM_194318, intron 1 of 14)	intron (NM_194318, intron 1 of 14)	9435	NM_194318	145173	Hs.13205	NM_194318	ENSG00000187676	B3GLCT	B3GALTL|B3GTL|B3Glc-T|Gal-T|beta3Glc-T	beta 3-glucosyltransferase	protein-coding	0.011070	0.529412	
chunk0043_279_1	chr12	21061340	21061823	+	0	NA	intron (NM_001009562, intron 10 of 12)	L1PB4|LINE|L1	45885	NM_001009562	338821	Hs.729117	NM_001009562	ENSG00000205754	SLCO1B7	LST-3|LST-3TM12|LST3|SLC21A21	solute carrier organic anion transporter family member 1B7 (putative)	protein-coding	0.002070	0.328512	
chunk0077_444_1	chr16	85753083	85753347	+	0	NA	Intergenic	Intergenic	-2132	NM_206967	404550	Hs.461655	NM_206967	ENSG00000154102	C16orf74	-	chromosome 16 open reading frame 74	protein-coding	0.037879	0.649057	
chunk0079_55_1	chr17	10772583	10772788	+	0	NA	intron (NR_073458, intron 1 of 3)	intron (NR_073458, intron 1 of 3)	31414	NR_036581	100289255	Hs.306721	NR_036581	ENSG00000263429	TMEM238L	LINC00675	transmembrane protein 238 like	ncRNA	0.019512	0.490291	
chunk0036_368_1	chr11	67211651	67212007	+	0	NA	intron (NR_027473, intron 6 of 20)	intron (NR_027473, intron 6 of 20)	-28206	NM_001256405	22992	Hs.124147	NM_012308	ENSG00000173120	KDM2A	CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA	lysine demethylase 2A	protein-coding	0.000000	0.308123	
chunk0080_288_1	chr17	31373463	31374179	+	0	NA	intron (NM_001042492, intron 57 of 57)	Tigger3a|DNA|TcMar-Tigger	-17803	NM_032932	84440	Hs.406788	NM_032932	ENSG00000131242	RAB11FIP4	FIP4-Rab11|RAB11-FIP4	RAB11 family interacting protein 4	protein-coding	0.018156	0.382148	523(GTAACTGGCTGTTCTC,+,0.00)
chunk0030_164_1	chr10	114049095	114049652	+	0	NA	Intergenic	Intergenic	5326	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.001795	0.320789	
chunk0091_22_1	chr19	3305064	3305562	+	0	NA	Intergenic	L2b|LINE|L2	-54250	NM_001245005	4782	Hs.170131	NM_005597	ENSG00000141905	NFIC	CTF|CTF5|NF-I|NFI	nuclear factor I C	protein-coding	0.042169	0.573146	282(TGGAACACTCTGTTCC,-,0.00),283(GGAACACTCTGTTCCC,+,0.00)
chunk0074_126_1	chr16	22685191	22685874	+	0	NA	Intergenic	Intergenic	-129007	NM_006043	9956	Hs.115830	NM_006043	ENSG00000122254	HS3ST2	30ST2|3OST2	heparan sulfate-glucosamine 3-sulfotransferase 2	protein-coding	0.004392	0.437135	352(GGGAACATGGTGTTCC,-,0.00),353(GGAACATGGTGTTCCC,+,0.00)
chunk0200_261_1	chr9	21841321	21841520	+	0	NA	intron (NM_002451, intron 5 of 7)	L1PB1|LINE|L1	38784	NM_002451	4507	Hs.193268	NM_002451	ENSG00000099810	MTAP	BDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fus	methylthioadenosine phosphorylase	protein-coding	0.005025	0.435000	
chunk0039_218_1	chr11	101441694	101442008	+	0	NA	Intergenic	Intergenic	78054	NR_037485	100500823		NR_037485	ENSG00000263885	MIR3920	-	microRNA 3920	ncRNA	0.003185	0.526984	
chunk0125_183_1	chr3	66666695	66667060	+	0	NA	Intergenic	Intergenic	-166456	NM_015541	26018	Hs.518055	NM_015541	ENSG00000144749	LRIG1	LIG-1|LIG1	leucine rich repeats and immunoglobulin like domains 1	protein-coding	0.008219	0.360656	171(TGGAACACGATGTGCA,-,0.00),172(GGAACACGATGTGCAA,+,0.00)
chunk0022_87_1	chr10	9188490	9188857	+	0	NA	Intergenic	Intergenic	-86940	NR_108039	100507163	Hs.649223	NR_108039		LINC00709	-	long intergenic non-protein coding RNA 709	ncRNA	0.002725	0.404891	
chunk0079_184_1	chr17	14114947	14115360	+	0	NA	intron (NM_001303, intron 4 of 6)	intron (NM_001303, intron 4 of 6)	-45695	NR_049718	100874058	Hs.720411	NR_049718	ENSG00000236088	COX10-AS1	COX10-AS|COX10AS	COX10 antisense RNA 1	ncRNA	0.002421	0.338164	
chunk0094_303_1	chr2	8571985	8572184	+	0	NA	intron (NR_110257, intron 4 of 5)	L2b|LINE|L2	11708	NR_110257	101929567	Hs.634706	NR_110257	ENSG00000236008	LINC01814	-	long intergenic non-protein coding RNA 1814	ncRNA	0.010050	0.530000	
chunk0045_244_1	chr12	48946179	48946813	+	0	NA	intron (NM_001659, intron 1 of 4)	intron (NM_001659, intron 1 of 4)	10973	NM_001659	377	Hs.119177	NM_001659	ENSG00000134287	ARF3	-	ADP ribosylation factor 3	protein-coding	0.001577	0.417323	
chunk0013_137_1	chr1	168293360	168293729	+	0	NA	intron (NM_005149, intron 3 of 7)	intron (NM_005149, intron 3 of 7)	12504	NM_005149	9095	Hs.716656	NM_005149	ENSG00000143178	TBX19	TBS19|TPIT|dJ747L4.1	T-box transcription factor 19	protein-coding	0.000000	0.486486	
chunk0091_447_1	chr19	17395113	17395327	+	0	NA	Intergenic	(CTCCTC)n|Simple_repeat|Simple_repeat	10428	NM_004335	684	Hs.118110	NM_004335	ENSG00000130303	BST2	CD317|TETHERIN	bone marrow stromal cell antigen 2	protein-coding	0.018692	0.562791	
chunk0170_119_1	chr6	110672198	110673015	+	0	NA	intron (NM_015076, intron 2 of 12)	L1ME4b|LINE|L1	-142015	NM_001287215	262	Hs.159118	NM_001634	ENSG00000123505	AMD1	ADOMETDC|AMD|SAMDC	adenosylmethionine decarboxylase 1	protein-coding	0.002448	0.305623	494(ATATACACACTGTTCT,-,0.00),495(TATACACACTGTTCTG,+,0.00)
chunk0022_28_1	chr10	7916027	7916305	+	0	NA	intron (NM_031923, intron 2 of 6)	intron (NM_031923, intron 2 of 6)	97662	NM_031923	83860	Hs.527688	NM_031923	ENSG00000165632	TAF3	TAF140|TAFII-140|TAFII140	TATA-box binding protein associated factor 3	protein-coding	0.000000	0.354839	
chunk0032_53_1	chr11	1739333	1739909	+	0	NA	intron (NM_001170820, intron 2 of 2)	L2a|LINE|L2	10973	NM_001170820	402778	Hs.121575	NM_001170820	ENSG00000244242	IFITM10	DSPA3	interferon induced transmembrane protein 10	protein-coding	0.013889	0.493934	266(GGGAACAGAGAGTGCT,-,0.00),267(GGAACAGAGAGTGCTG,+,0.00),319(GGGAACAGAGAGTGCT,-,0.00),320(GGAACAGAGAGTGCTG,+,0.00)
chunk0072_149_1	chr15	92772591	92772873	+	0	NA	Intergenic	L2c|LINE|L2	-22752	NR_033769	728619	Hs.684129	NR_033769		ASB9P1	-	ankyrin repeat and SOCS box containing 9 pseudogene 1	pseudo	0.024823	0.455830	
chunk0076_452_1	chr16	74087432	74087943	+	0	NA	Intergenic	Intergenic	127834	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.013699	0.322266	234(AGGTACACGAAGTACT,-,0.00),235(GGTACACGAAGTACTT,+,0.00)
chunk0125_225_1	chr3	67910194	67910708	+	0	NA	intron (NR_109992, intron 6 of 6)	Tigger2b_Pri|DNA|TcMar-Tigger	-81141	NM_001252216	407738	Hs.655061	NM_213609	ENSG00000183662	TAFA1	FAM19A1|TAFA-1	TAFA chemokine like family member 1	protein-coding	0.011673	0.332039	312(TAGTACATACTGTTCT,-,0.00),313(AGTACATACTGTTCTA,+,0.00)
chunk0103_276_1	chr2	165876988	165877375	+	0	NA	intron (NM_024753, intron 27 of 28)	intron (NM_024753, intron 27 of 28)	-5240	NR_045375	100506124	Hs.709870	NR_045375		LOC100506124	-	uncharacterized LOC100506124	ncRNA	0.002584	0.278351	
chunk0158_237_1	chr5	129077434	129077768	+	0	NA	Intergenic	Intergenic	-17148	NM_016048	51015	Hs.483296	NM_016048	ENSG00000066583	ISOC1	CGI-111	isochorismatase domain containing 1	protein-coding	0.002994	0.361194	
chunk0126_436_1	chr3	87014586	87015054	+	0	NA	Intergenic	L2b|LINE|L2	-23713	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.002137	0.349680	
chunk0046_422_1	chr12	64600130	64600878	+	0	NA	Intergenic	Intergenic	-10009	NM_178169	283349	Hs.643605	NM_178169	ENSG00000153179	RASSF3	RASSF5	Ras association domain family member 3	protein-coding	0.006684	0.364486	
chunk0162_122_1	chr6	2863833	2864369	+	0	NA	intron (NR_033851, intron 1 of 1)	L2c|LINE|L2	-9994	NR_039788	100616285		NR_039788	ENSG00000266750	MIR4645	mir-4645	microRNA 4645	ncRNA	0.013060	0.502793	
chunk0103_345_1	chr2	168076491	168077088	+	0	NA	intron (NM_013233, intron 10 of 17)	intron (NM_013233, intron 10 of 17)	-135645	NR_131227	105616981	Hs.512811	NR_131227		LOC105616981	-	uncharacterized LOC105616981	ncRNA	0.006700	0.336120	426(AGAACAGATTGCTCAT,+,0.00)
chunk0033_280_1	chr11	19389809	19390349	+	0	NA	intron (NM_001111018, intron 1 of 37)	intron (NM_001111018, intron 1 of 37)	39355	NM_001111018	89797	Hs.64341	NM_145117	ENSG00000166833	NAV2	HELAD1|POMFIL2|RAINB1|STEERIN2|UNC53H2	neuron navigator 2	protein-coding	0.005556	0.480591	
chunk0038_357_1	chr11	93236682	93237493	+	0	NA	Intergenic	Intergenic	-39112	NM_152313	120103	Hs.148766	NM_152313	ENSG00000180773	SLC36A4	PAT4	solute carrier family 36 member 4	protein-coding	0.012330	0.395320	
chunk0024_248_1	chr10	38889327	38889589	+	0	NA	Intergenic	Intergenic	192862	NR_045000	399746	Hs.742607	NR_045000		ACTR3BP5	FKSG74	ACTR3B pseudogene 5	pseudo	0.030534	0.376426	
chunk0057_131_1	chr13	99644136	99644693	+	0	NA	intron (NR_104592, intron 1 of 9)	L1MA3|LINE|L1	1355	NR_036191	100422861		NR_036191	ENSG00000263615	MIR4306	mir-4306	microRNA 4306	ncRNA	0.000000	0.318996	
chunk0040_152_1	chr11	113645102	113645374	+	0	NA	Intergenic	Intergenic	61135	NM_030770	80975	Hs.46720	NM_030770	ENSG00000166682	TMPRSS5	SPINESIN	transmembrane serine protease 5	protein-coding	0.007353	0.402930	122(AAGCACTCACTGTTCA,-,0.00),123(AGCACTCACTGTTCAC,+,0.00)
chunk0183_321_1	chr7	108091405	108092642	+	0	NA	intron (NM_007356, intron 13 of 33)	intron (NM_007356, intron 13 of 33)	38333	NM_007356	22798	Hs.62022	NM_007356	ENSG00000091128	LAMB4	-	laminin subunit beta 4	protein-coding	0.012126	0.453958	
chunk0036_431_1	chr11	68408477	68408790	+	0	NA	intron (NM_001291902, intron 9 of 22)	intron (NM_001291902, intron 9 of 22)	-52085	NM_001164164	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.019169	0.401274	
chunk0108_239_1	chr2	233742584	233743204	+	0	NA	3' UTR (NM_001001394, exon 1 of 1)	3' UTR (NM_001001394, exon 1 of 1)	1121	NM_001001394	414061	Hs.725533	NM_001001394		DNAJB3	HCG3	DnaJ heat shock protein family (Hsp40) member B3	protein-coding	0.012903	0.394525	338(CTGAACATTCTGTCCT,-,0.00),339(TGAACATTCTGTCCTA,+,0.00)
chunk0084_194_1	chr17	78040754	78041285	+	0	NA	intron (NM_018996, intron 3 of 20)	CpG	36782	NM_018996	57690	Hs.406810	NM_018996	ENSG00000078687	TNRC6C	-	trinucleotide repeat containing adaptor 6C	protein-coding	0.067797	0.592105	
chunk0062_119_1	chr14	68453284	68453510	+	0	NA	intron (NM_133509, intron 9 of 10)	intron (NM_133509, intron 9 of 10)	340517	NM_001244698	677	Hs.85155	NM_004926	ENSG00000185650	ZFP36L1	BRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1	ZFP36 ring finger protein like 1	protein-coding	0.000000	0.361233	
chunk0146_419_1	chr4	169153984	169154372	+	0	NA	intron (NM_020870, intron 4 of 11)	intron (NM_020870, intron 4 of 11)	116920	NM_020870	57630	Hs.301804	NM_020870	ENSG00000154447	SH3RF1	POSH|RNF142|SH3MD2	SH3 domain containing ring finger 1	protein-coding	0.002577	0.341902	
chunk0127_64_1	chr3	89340971	89341312	+	0	NA	intron (NM_005233, intron 4 of 16)	(TTTGT)n|Simple_repeat|Simple_repeat	233617	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.011730	0.429825	
chunk0131_74_1	chr3	143001409	143001675	+	0	NA	promoter-TSS (NR_034032)	promoter-TSS (NR_034032)	12	NM_001080415	23350	Hs.596572	NM_001080415	ENSG00000163714	U2SURP	SR140|fSAPa	U2 snRNP associated SURP domain containing	protein-coding	0.090226	0.606742	
chunk0008_64_1	chr1	89592730	89593182	+	0	NA	exon (NM_001134476, exon 8 of 8)	exon (NM_001134476, exon 8 of 8)	34243	NM_015350	23507	Hs.482017	NM_015350	ENSG00000197147	LRRC8B	TA-LRRP|TALRRP	leucine rich repeat containing 8 VRAC subunit B	protein-coding	0.019912	0.443709	
chunk0020_312_1	chr1	237640871	237641111	+	0	NA	exon (NM_001035, exon 47 of 105)	exon (NM_001035, exon 47 of 105)	169872	NR_039626	100616141		NR_039626	ENSG00000266262	MIR4428	-	microRNA 4428	ncRNA	0.012500	0.435685	
chunk0032_45_1	chr11	1509375	1509923	+	0	NA	Intergenic	L1M5|LINE|L1	-22870	NM_001172223	81532	Hs.370360	NM_053005	ENSG00000182208	MOB2	HCCA2	MOB kinase activator 2	protein-coding	0.009124	0.449909	
chunk0165_167_1	chr6	34050451	34051017	+	0	NA	intron (NM_001256809, intron 4 of 8)	intron (NM_001256809, intron 4 of 8)	-50683	NR_031681	100302123		NR_031681	ENSG00000221697	MIR1275	MIRN1275|hsa-mir-1275|mir-1275	microRNA 1275	ncRNA	0.015901	0.539683	
chunk0122_342_1	chr3	37248407	37248606	+	0	NA	intron (NM_002078, intron 1 of 23)	intron (NM_002078, intron 1 of 23)	5315	NM_001172713	2803	Hs.344151	NM_002078	ENSG00000144674	GOLGA4	CRPF46|GCP2|GOLG|MU-RMS-40.18|p230	golgin A4	protein-coding	0.000000	0.355000	121(AAGTACAGTTAGTTCT,-,0.00),122(AGTACAGTTAGTTCTT,+,0.00)
chunk0011_247_1	chr1	150597002	150597436	+	0	NA	Intergenic	L3|LINE|CR1	-17481	NM_182763	4170	Hs.632486	NM_021960	ENSG00000143384	MCL1	BCL2L3|EAT|MCL1-ES|MCL1L|MCL1S|Mcl-1|TM|bcl2-L-3|mcl1/EAT	MCL1 apoptosis regulator, BCL2 family member	protein-coding	0.009217	0.404598	255(TAGTGCATACTGTTCT,-,0.00),256(AGTGCATACTGTTCTG,+,0.00)
chunk0064_109_1	chr14	91154866	91155420	+	0	NA	intron (NM_001286470, intron 4 of 16)	L2c|LINE|L2	28717	NR_003709	100124539	Hs.693444	NR_003709	ENSG00000221102	SNORA11B	-	small nucleolar RNA, H/ACA box 11B	snoRNA	0.019856	0.529730	243(AAGCACATGGTGTTAT,-,0.00)
chunk0133_22_1	chr3	165732341	165732625	+	0	NA	Intergenic	L1MEc|LINE|L1	104982	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.000000	0.315789	
chunk0047_216_1	chr12	71671736	71672271	+	0	NA	intron (NM_031435, intron 1 of 2)	Tigger2|DNA|TcMar-Tigger	-8034	NM_144982	196441	Hs.245798	NM_144982	ENSG00000133858	ZFC3H1	CCDC131|CSRC2|PSRC2	zinc finger C3H1-type containing	protein-coding	0.001869	0.410448	
chunk0068_434_1	chr15	59583134	59583333	+	0	NA	Intergenic	Intergenic	-28550	NM_004751	9245	Hs.194710	NM_004751	ENSG00000140297	GCNT3	C2/4GnT|C24GNT|C2GNT2|C2GNTM|GNTM	glucosaminyl (N-acetyl) transferase 3, mucin type	protein-coding	0.010050	0.540000	
chunk0120_329_1	chr3	10781939	10782442	+	0	NA	Intergenic	Intergenic	-17998	NR_027102	285370	Hs.157613	NR_027102	ENSG00000226567	LINC00606	-	long intergenic non-protein coding RNA 606	ncRNA	0.003976	0.388889	
chunk0104_336_1	chr2	179578625	179578829	+	0	NA	intron (NR_104234, intron 2 of 12)	intron (NR_104234, intron 2 of 12)	7179	NR_104234	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.004902	0.380488	
chunk0033_177_1	chr11	15785023	15785341	+	0	NA	Intergenic	MamRep1527|LTR|LTR	141297	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.003145	0.391850	
chunk0092_313_1	chr19	34471952	34472849	+	0	NA	Intergenic	Intergenic	-9575	NM_001080436	126374	Hs.585010	NM_001080436	ENSG00000142279	WTIP	-	WT1 interacting protein	protein-coding	0.007804	0.461024	
chunk0206_28_1	chr9	116208990	116209308	+	0	NA	intron (NM_002581, intron 3 of 21)	intron (NM_002581, intron 3 of 21)	55357	NM_002581	5069	Hs.643599	NM_002581	ENSG00000182752	PAPPA	ASBABP2|DIPLA1|IGFBP-4ase|PAPA|PAPP-A|PAPPA1	pappalysin 1	protein-coding	0.006289	0.432602	
chunk0170_391_1	chr6	117290229	117290583	+	0	NA	intron (NM_002944, intron 42 of 42)	intron (NM_002944, intron 42 of 42)	24848	NM_153453	245806	Hs.99324	NM_153453	ENSG00000170162	VGLL2	VGL2|VITO1	vestigial like family member 2	protein-coding	0.005650	0.329577	
chunk0033_166_1	chr11	15663715	15663970	+	0	NA	intron (NM_001293172, intron 1 of 2)	intron (NM_001293172, intron 1 of 2)	19957	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.019608	0.535156	
chunk0090_86_1	chr18	70520815	70521206	+	0	NA	Intergenic	Intergenic	129847	NM_001278515									0.007673	0.377551	
chunk0011_365_1	chr1	153270969	153271296	+	0	NA	Intergenic	L1MA8|LINE|L1	11429	NM_000427	4014	Hs.251680	NM_000427	ENSG00000203782	LOR	-	loricrin	protein-coding	0.000000	0.350610	
chunk0031_411_1	chr10	132015643	132016332	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-33974	NM_004052	664	Hs.144873	NM_004052	ENSG00000176171	BNIP3	NIP3	BCL2 interacting protein 3	protein-coding	0.013062	0.439130	
chunk0033_403_1	chr11	24635950	24636303	+	0	NA	intron (NM_001252008, intron 1 of 11)	intron (NM_001252008, intron 1 of 11)	139156	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002833	0.364407	
chunk0141_439_1	chr4	88998862	88999785	+	0	NA	intron (NM_014883, intron 3 of 23)	intron (NM_014883, intron 3 of 23)	57872	NM_014883	10144	Hs.97270	NM_014883	ENSG00000138640	FAM13A	ARHGAP48|FAM13A1	family with sequence similarity 13 member A	protein-coding	0.004334	0.362554	
chunk0122_220_1	chr3	33583171	33583621	+	0	NA	intron (NM_015097, intron 22 of 38)	intron (NM_015097, intron 22 of 38)	76045	NM_001207044	23122	Hs.108614	NM_015097	ENSG00000163539	CLASP2	-	cytoplasmic linker associated protein 2	protein-coding	0.002222	0.345898	257(GGGAACTCACTGTACC,-,0.00),258(GGAACTCACTGTACCT,+,0.00)
chunk0185_147_1	chr7	127665738	127666132	+	0	NA	intron (NM_014390, intron 1 of 23)	intron (NM_014390, intron 1 of 23)	13787	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.012690	0.443038	
chunk0145_83_1	chr4	145851875	145852177	+	0	NA	intron (NM_178835, intron 5 of 14)	intron (NM_178835, intron 5 of 14)	86934	NM_178835	152485	Hs.133916	NM_178835	ENSG00000151612	ZNF827	-	zinc finger protein 827	protein-coding	0.003311	0.455446	
chunk0005_452_1	chr1	63498019	63498709	+	0	NA	intron (NM_014288, intron 2 of 8)	L1M4|LINE|L1	24909	NM_001206739	23421	Hs.166539	NM_014288	ENSG00000142856	ITGB3BP	CENP-R|CENPR|HSU37139|NRIF3|TAP20	integrin subunit beta 3 binding protein	protein-coding	0.002899	0.316932	
chunk0190_343_1	chr8	39235640	39236079	+	0	NA	intron (NM_001313994, intron 13 of 21)	intron (NM_001313994, intron 13 of 21)	-78804	NR_001448	255926	Hs.369765	NM_001040073	ENSG00000196115	ADAM5	ADAM5P|TMDCII	ADAM metallopeptidase domain 5 (pseudogene)	pseudo	0.004556	0.304545	
chunk0121_416_1	chr3	25746592	25746852	+	0	NA	intron (NM_001145295, intron 4 of 10)	intron (NM_001145295, intron 4 of 10)	36776	NM_001145293	55768	Hs.368960	NM_018297	ENSG00000151092	NGLY1	CDDG|CDG1V|PNG1|PNGase	N-glycanase 1	protein-coding	0.000000	0.356322	178(AGGAACATTCTGTCTC,-,0.00),179(GGAACATTCTGTCTCT,+,0.00)
chunk0012_57_1	chr1	155509128	155509641	+	0	NA	intron (NM_018489, intron 2 of 27)	intron (NM_018489, intron 2 of 27)	-52597	NR_027023	645676	Hs.568693	NR_027023	ENSG00000235919	ASH1L-AS1	-	ASH1L antisense RNA 1	ncRNA	0.013645	0.428016	
chunk0123_161_1	chr3	43480505	43481073	+	0	NA	intron (NM_018075, intron 11 of 12)	HAL1|LINE|L1	-128827	NR_046757	100873954	Hs.600984	NR_046757		SNRK-AS1	-	SNRK antisense RNA 1	ncRNA	0.005282	0.386643	299(AAGCACACTATGTTTA,-,0.00),404(GGCACACTACGTACTT,+,0.00)
chunk0023_450_1	chr10	32105103	32105501	+	0	NA	Intergenic	Intergenic	-48859	NM_004521	3799	Hs.327736	NM_004521	ENSG00000170759	KIF5B	HEL-S-61|KINH|KNS|KNS1|UKHC	kinesin family member 5B	protein-coding	0.005025	0.333333	
chunk0056_386_1	chr13	93319074	93319421	+	0	NA	intron (NM_005708, intron 1 of 8)	HAL1|LINE|L1	92422	NM_005708	10082	Hs.444329	NM_005708	ENSG00000183098	GPC6	OMIMD1	glypican 6	protein-coding	0.002882	0.393678	
chunk0114_32_1	chr21	8213311	8213512	+	0	NA	promoter-TSS (NR_003287)	promoter-TSS (NR_003287)	-477	NR_003287	100008589		NR_003287		RNA28SN5	RN28S1|RNA28S5	RNA, 28S ribosomal N5	rRNA	0.223881	0.886139	
chunk0206_87_1	chr9	120568290	120568729	+	0	NA	intron (NR_073556, intron 2 of 38)	intron (NR_073556, intron 2 of 38)	11661	NR_073557	55755	Hs.269560	NM_018249	ENSG00000136861	CDK5RAP2	C48|Cep215|MCPH3	CDK5 regulatory subunit associated protein 2	protein-coding	0.013667	0.413636	
chunk0156_423_1	chr5	114442121	114442451	+	0	NA	intron (NR_103458, intron 1 of 6)	(TA)n|Simple_repeat|Simple_repeat	8756	NM_170775	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.006061	0.323263	
chunk0135_93_1	chr3	186415572	186415900	+	0	NA	Intergenic	L2b|LINE|L2	-53502	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.018293	0.483283	
chunk0099_435_1	chr2	102965921	102966120	+	0	NA	Intergenic	MLT1F|LTR|ERVL-MaLR	203989	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.000000	0.450000	
chunk0137_123_1	chr4	14837995	14838402	+	0	NA	intron (NR_126435, intron 2 of 6)	intron (NR_126435, intron 2 of 6)	49971	NR_126435	201853	Hs.551051	NR_126435	ENSG00000248360	LINC00504	-	long intergenic non-protein coding RNA 504	ncRNA	0.007371	0.404412	
chunk0095_394_1	chr2	24051391	24051860	+	0	NA	intron (NM_054033, intron 1 of 3)	L2c|LINE|L2	1911	NM_054033	2281	Hs.709461	NM_004116	ENSG00000119782	FKBP1B	FKBP12.6|FKBP1L|OTK4|PKBP1L|PPIase	FKBP prolyl isomerase 1B	protein-coding	0.008529	0.474468	
chunk0116_141_1	chr21	36319871	36320195	+	0	NA	promoter-TSS (NM_015358)	promoter-TSS (NM_015358)	-156	NM_015358	23515	Hs.421150	NM_015358	ENSG00000159256	MORC3	NXP2|ZCW5|ZCWCC3	MORC family CW-type zinc finger 3	protein-coding	0.083333	0.646154	
chunk0100_274_1	chr2	113831221	113831687	+	0	NA	intron (NR_110174, intron 4 of 4)	intron (NR_110174, intron 4 of 4)	-58480	NR_102318	10096	Hs.433512	NM_005721	ENSG00000115091	ACTR3	ARP3	actin related protein 3	protein-coding	0.019313	0.449679	
chunk0069_392_1	chr15	67731225	67731559	+	0	NA	intron (NM_001206804, intron 17 of 21)	intron (NM_001206804, intron 17 of 21)	-88312	NM_001258024	390598	Hs.451224	NM_001031807	ENSG00000188779	SKOR1	CORL1|FUSSEL15|LBXCOR1	SKI family transcriptional corepressor 1	protein-coding	0.002994	0.453731	50(GACACAGTGTGTACCC,+,0.00),105(AGGGACAGTCAGTGCC,-,0.00),106(GGGACAGTCAGTGCCC,+,0.00)
chunk0111_203_1	chr20	26150408	26150761	+	0	NA	Intergenic	Intergenic	-36543	NR_003678	149934	Hs.711274	NM_001039379	ENSG00000240108	NCOR1P1	C20orf191|bB329D4.2	nuclear receptor corepressor 1 pseudogene 1	pseudo	0.008499	0.327684	
chunk0183_253_1	chr7	107196972	107197500	+	0	NA	intron (NM_001244262, intron 9 of 10)	intron (NM_001244262, intron 9 of 10)	28221	NM_012257	26959	Hs.162032	NM_012257	ENSG00000105856	HBP1	-	HMG-box transcription factor 1	protein-coding	0.013258	0.431002	
chunk0078_108_1	chr17	2395741	2396477	+	0	NA	intron (NM_020310, intron 1 of 5)	MIRc|SINE|MIR	4855	NM_020310	4335	Hs.626579	NM_020310	ENSG00000070444	MNT	MAD6|MXD6|ROX|bHLHd3	MAX network transcriptional repressor	protein-coding	0.020380	0.583446	
chunk0150_153_1	chr5	33832271	33832588	+	0	NA	intron (NM_030955, intron 2 of 23)	intron (NM_030955, intron 2 of 23)	59590	NM_030955	81792	Hs.12680	NM_030955	ENSG00000151388	ADAMTS12	PRO4389	ADAM metallopeptidase with thrombospondin type 1 motif 12	protein-coding	0.006309	0.339623	
chunk0093_74_1	chr19	40651595	40652109	+	0	NA	Intergenic	Intergenic	38270	NM_001289980	9253	Hs.326953	NM_004756	ENSG00000105245	NUMBL	CAG3A|CTG3a|NBL|NUMB-R|NUMBLIKE|NUMBR|TNRC23	NUMB like endocytic adaptor protein	protein-coding	0.003891	0.427184	
chunk0146_387_1	chr4	168674840	168675282	+	0	NA	intron (NM_016081, intron 3 of 20)	intron (NM_016081, intron 3 of 20)	43444	NM_001166109	23022	Hs.151220	NM_016081	ENSG00000129116	PALLD	CGI-151|CGI151|MYN|PNCA1|SIH002	palladin, cytoskeletal associated protein	protein-coding	0.009050	0.435666	
chunk0137_285_1	chr4	23877763	23878100	+	0	NA	intron (NM_013261, intron 2 of 12)	intron (NM_013261, intron 2 of 12)	12146	NM_013261	10891	Hs.527078	NM_013261	ENSG00000109819	PPARGC1A	LEM6|PGC-1(alpha)|PGC-1alpha|PGC-1v|PGC1|PGC1A|PPARGC1	PPARG coactivator 1 alpha	protein-coding	0.002967	0.426036	
chunk0210_217_1	chrX	82021603	82021815	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-819767	NM_030763	79366	Hs.282204	NM_030763	ENSG00000198157	HMGN5	NBP-45|NSBP1	high mobility group nucleosome binding domain 5	protein-coding	0.004717	0.403756	
chunk0065_446_1	chr14	106542703	106543455	+	0	NA	Intergenic	L1MA5|LINE|L1	60640	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.006649	0.333333	
chunk0039_346_1	chr11	105451772	105452379	+	0	NA	Intergenic	L1M4a2|LINE|L1	-157998	NM_001077243	2893	Hs.503743	NM_000829	ENSG00000152578	GRIA4	GLUR4|GLUR4C|GLURD|GluA4|NEDSGA	glutamate ionotropic receptor AMPA type subunit 4	protein-coding	0.000000	0.338816	
chunk0001_436_1	chr1	11455681	11456421	+	0	NA	Intergenic	Intergenic	-23187	NM_020780	57540	Hs.202355	NM_020780	ENSG00000204624	DISP3	PTCHD2	dispatched RND transporter family member 3	protein-coding	0.020270	0.565452	219(GAGGACACGGTGCACC,-,0.00),220(AGGACACGGTGCACCT,+,0.00)
chunk0082_423_1	chr17	61372800	61373028	+	0	NA	intron (NM_017679, intron 23 of 23)	intron (NM_017679, intron 23 of 23)	26692	NR_125750	103689912	Hs.410998	NR_125749	ENSG00000267280	TBX2-AS1	-	TBX2 antisense RNA 1	ncRNA	0.004386	0.292576	
chunk0002_49_1	chr1	13468745	13469859	+	0	NA	Intergenic	Intergenic	44445	NM_001010847	126755	Hs.657356	NM_001010847	ENSG00000162494	LRRC38	-	leucine rich repeat containing 38	protein-coding	0.012567	0.464574	
chunk0100_332_1	chr2	116690157	116690857	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-1124172	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.004286	0.356633	
chunk0079_43_1	chr17	10380485	10380942	+	0	NA	Intergenic	Intergenic	-2419	NR_125367	100128560	Hs.661174	NR_125367		MYHAS	-	myosin heavy chain gene cluster antisense RNA	ncRNA	0.004376	0.388646	316(GAGAACATTGTGTTCA,-,0.00),317(AGAACATTGTGTTCAG,+,0.00)
chunk0107_219_1	chr2	216862645	216862956	+	0	NA	Intergenic	Intergenic	-2741	NM_003284	7141	Hs.3017	NM_003284	ENSG00000118245	TNP1	TP1	transition protein 1	protein-coding	0.009646	0.451923	164(GAGGACAGACAGTTCA,-,0.00),165(AGGACAGACAGTTCAA,+,0.00)
chunk0206_306_1	chr9	124852737	124852936	+	0	NA	promoter-TSS (NM_001045476)	promoter-TSS (NM_001045476)	-581	NM_001276376	401551	Hs.343383	NM_001045476	ENSG00000136918	WDR38	-	WD repeat domain 38	protein-coding	0.025126	0.580000	74(TGGCACATTTTGTGCT,-,0.00),75(GGCACATTTTGTGCTG,+,0.00)
chunk0182_20_1	chr7	91285273	91285488	+	0	NA	Intergenic	Intergenic	20912	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.009302	0.425926	
chunk0204_39_1	chr9	92679505	92679852	+	0	NA	Intergenic	Intergenic	-9413	NM_022755	64768	Hs.459896	NM_022755	ENSG00000127080	IPPK	C9orf12|INSP5K2|IP5K|IPK1|bA476B13.1	inositol-pentakisphosphate 2-kinase	protein-coding	0.014409	0.537356	
chunk0105_1_1	chr2	181553613	181554173	+	0	NA	intron (NM_001030312, intron 2 of 9)	intron (NM_001030312, intron 2 of 9)	97001	NM_000885	3676	Hs.72981	NM_000885	ENSG00000115232	ITGA4	CD49D|IA4	integrin subunit alpha 4	protein-coding	0.003571	0.319073	305(AAGAACATGCTGCTCA,-,0.00),306(AGAACATGCTGCTCAC,+,0.00)
chunk0090_307_1	chr18	75375952	75376804	+	0	NA	Intergenic	Intergenic	51325	NM_001037331	284274	Hs.666744	NM_001037331	ENSG00000206026	SMIM21	C18orf62	small integral membrane protein 21	protein-coding	0.004695	0.404455	502(AGGCACTTGGAGTTCC,-,0.00),503(GGCACTTGGAGTTCCT,+,0.00)
chunk0075_416_1	chr16	57275619	57275951	+	0	NA	intron (NM_015993, intron 1 of 3)	L1ME4b|LINE|L1	8887	NM_015993	51090	Hs.632215	NM_015993	ENSG00000102934	PLLP	PMLP|TM4SF11	plasmolipin	protein-coding	0.018072	0.405405	
chunk0011_42_1	chr1	143239139	143239361	+	0	NA	Intergenic	Intergenic	183342	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.049550	0.345291	
chunk0008_455_1	chr1	99754728	99755052	+	0	NA	intron (NM_001013660, intron 1 of 16)	intron (NM_001013660, intron 1 of 16)	10903	NM_001013660	391059	Hs.454779	NM_001013660	ENSG00000156869	FRRS1	SDFR2|SDR2	ferric chelate reductase 1	protein-coding	0.015432	0.387692	
chunk0112_420_1	chr20	47333978	47334680	+	0	NA	intron (NM_001281769, intron 2 of 3)	L1MB8|LINE|L1	15827	NR_024594	100131496	Hs.662547	NR_024594	ENSG00000267882	LOC100131496	-	uncharacterized LOC100131496	ncRNA	0.012821	0.402560	292(AAGTACTGTTTGTACT,-,0.00),293(AGTACTGTTTGTACTG,+,0.00),337(AGGAACTGTCTGTACT,-,0.00),338(GGAACTGTCTGTACTG,+,0.00)
chunk0048_141_1	chr12	80053080	80053360	+	0	NA	Intergenic	L1MEi|LINE|L1	-117765	NM_001244990	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.007143	0.437722	
chunk0089_72_1	chr18	58212999	58213362	+	0	NA	intron (NM_001144970, intron 1 of 28)	L1ME3G|LINE|L1	-8342	NM_001144966	23327	Hs.185677	NM_015277	ENSG00000049759	NEDD4L	NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2	NEDD4 like E3 ubiquitin protein ligase	protein-coding	0.008264	0.315934	
chunk0201_264_1	chr9	38494789	38495970	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	49993	NR_047651	100289137	Hs.644630	NR_047651	ENSG00000283486	FAM95C	-	family with sequence similarity 95 member C	ncRNA	0.006774	0.402707	
chunk0196_436_1	chr8	116514974	116515492	+	0	NA	Intergenic	MIRb|SINE|MIR	-190174	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.009653	0.346821	
chunk0178_51_1	chr7	29931677	29932155	+	0	NA	intron (NM_001145515, intron 5 of 6)	intron (NM_001145515, intron 5 of 6)	57893	NM_001145515	9805	Hs.520740	NM_014766	ENSG00000136193	SCRN1	SES1	secernin 1	protein-coding	0.008368	0.421712	
chunk0072_285_1	chr15	98515383	98515582	+	0	NA	Intergenic	Intergenic	-1100	NM_182562	283777	Hs.668070	NM_182562	ENSG00000283597	FAM169B	-	family with sequence similarity 169 member B	protein-coding	0.020101	0.530000	
chunk0197_64_1	chr8	118788623	118789339	+	0	NA	Intergenic	Intergenic	163163	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.018156	0.408647	282(AAGGACATTGTGTTTC,-,0.00),283(AGGACATTGTGTTTCG,+,0.00),453(CTGGACTCCGTGTCCT,-,0.00),454(TGGACTCCGTGTCCTT,+,0.00)
chunk0136_345_1	chr3	195749575	195749963	+	0	NA	intron (NM_018406, intron 23 of 24)	L1ME4a|LINE|L1	28887	NM_020790	200958	Hs.308992	NM_020790	ENSG00000176945	MUC20	MUC-20	mucin 20, cell surface associated	protein-coding	0.005155	0.323907	
chunk0013_250_1	chr1	169779265	169779711	+	0	NA	Intergenic	Intergenic	15432	NM_033418	92342	Hs.33922	NM_033418	ENSG00000171806	METTL18	AsTP2|C1orf156|HPM1	methyltransferase like 18	protein-coding	0.004484	0.340045	
chunk0018_387_1	chr1	222522070	222522332	+	0	NA	TTS (NM_024746)	TTS (NM_024746)	25901	NM_024746	79802	Hs.665660	NM_024746	ENSG00000143512	HHIPL2	KIAA1822L	HHIP like 2	protein-coding	0.003817	0.437262	
chunk0081_200_1	chr17	42386745	42387037	+	0	NA	intron (NM_139276, intron 1 of 23)	intron (NM_139276, intron 1 of 23)	1496	NM_213662	6774	Hs.463059	NM_003150	ENSG00000168610	STAT3	ADMIO|ADMIO1|APRF|HIES	signal transducer and activator of transcription 3	protein-coding	0.000000	0.337884	
chunk0088_408_1	chr18	54723728	54723933	+	0	NA	Intergenic	Intergenic	-104647	NM_004163	5874	Hs.25318	NM_004163	ENSG00000041353	RAB27B	C25KG	RAB27B, member RAS oncogene family	protein-coding	0.004878	0.296117	
chunk0175_22_1	chr7	618527	618952	+	0	NA	intron (NM_001164758, intron 4 of 10)	L1M5|LINE|L1	15341	NR_110055	101926963	Hs.521338	NR_110054		LOC101926963	-	uncharacterized LOC101926963	ncRNA	0.016471	0.424883	
chunk0108_298_1	chr2	235048649	235049009	+	0	NA	intron (NM_014521, intron 4 of 5)	intron (NM_014521, intron 4 of 5)	96845	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.016667	0.470914	134(AAGTACTATCTGTCCC,-,0.00),135(AGTACTATCTGTCCCT,+,0.00)
chunk0111_216_1	chr20	28860034	28860733	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-220007	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.011445	0.364286	
chunk0136_276_1	chr3	194672302	194672793	+	0	NA	promoter-TSS (NM_018385)	promoter-TSS (NM_018385)	-70	NM_018385	55341	Hs.744061	NM_018385	ENSG00000041802	LSG1	-	large 60S subunit nuclear export GTPase 1	protein-coding	0.065173	0.495935	
chunk0145_25_1	chr4	143507336	143507682	+	0	NA	Intergenic	L1MD|LINE|L1	-5954	NM_003601	8467	Hs.558422	NM_003601	ENSG00000153147	SMARCA5	ISWI|SNF2H|WCRF135|hISWI|hSNF2H	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	protein-coding	0.000000	0.334294	
chunk0110_408_1	chr20	20525100	20525686	+	0	NA	intron (NM_020343, intron 28 of 39)	intron (NM_020343, intron 28 of 39)	157272	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.005119	0.383305	278(GAGCACTTTATGTTCC,-,0.00),279(AGCACTTTATGTTCCC,+,0.00),366(GAGAACAAAGTGTTCT,-,0.00),367(AGAACAAAGTGTTCTT,+,0.00)
chunk0180_387_1	chr7	74502303	74502687	+	0	NA	intron (NM_001199207, intron 1 of 26)	intron (NM_001199207, intron 1 of 26)	48705	NM_001199207	9569	Hs.647056	NM_005685	ENSG00000006704	GTF2IRD1	BEN|CREAM1|GTF3|MUSTRD1|RBAP2|WBS|WBSCR11|WBSCR12|hMusTRD1alpha1	GTF2I repeat domain containing 1	protein-coding	0.020833	0.576623	
chunk0075_403_1	chr16	56943701	56944237	+	0	NA	TTS (NM_001010989)	TTS (NM_001010989)	11879	NM_001272103	9709	Hs.146393	NM_014685	ENSG00000051108	HERPUD1	HERP|Mif1|SUP	homocysteine inducible ER protein with ubiquitin like domain 1	protein-coding	0.011194	0.424581	283(GAGGACTGTTTGTGCC,-,0.00),284(AGGACTGTTTGTGCCG,+,0.00)
chunk0129_259_1	chr3	122409577	122409816	+	0	NA	intron (NM_014367, intron 4 of 4)	intron (NM_014367, intron 4 of 4)	6339	NM_019069	54554	Hs.567513	NM_019069	ENSG00000196981	WDR5B	-	WD repeat domain 5B	protein-coding	0.012552	0.475000	
chunk0017_439_1	chr1	214180944	214181312	+	0	NA	Intergenic	L1MEc|LINE|L1	-100094	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.002717	0.344173	
chunk0129_404_1	chr3	126772609	126772880	+	0	NA	intron (NM_032343, intron 4 of 7)	L1PA15|LINE|L1	68524	NM_032343	84303	Hs.518119	NM_032343	ENSG00000159685	CHCHD6	CHCM1|MICOS25|Mic25|PPP1R23	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.389706	
chunk0115_100_1	chr21	22548092	22548309	+	0	NA	Intergenic	Intergenic	449583	NR_038400	54143	Hs.352631	NR_038400	ENSG00000184856	LINC00308	C21orf74|NCRNA00308|PRED16	long intergenic non-protein coding RNA 308	ncRNA	0.009217	0.284404	
chunk0058_461_1	chr13	114111807	114112314	+	0	NA	intron (NM_007368, intron 1 of 23)	intron (NM_007368, intron 1 of 23)	20560	NM_007368	22821	Hs.593075	NM_007368	ENSG00000185989	RASA3	GAP1IP4BP|GAPIII	RAS p21 protein activator 3	protein-coding	0.017751	0.537402	
chunk0026_271_1	chr10	67040989	67041525	+	0	NA	intron (NR_111909, intron 2 of 2)	intron (NR_111909, intron 2 of 2)	28991	NR_111909	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.001866	0.353818	
chunk0010_56_1	chr1	112953674	112953994	+	0	NA	intron (NM_003051, intron 1 of 4)	L2b|LINE|L2	2229	NM_001166496	6566	Hs.75231	NM_003051	ENSG00000155380	SLC16A1	HHF7|MCT|MCT1|MCT1D	solute carrier family 16 member 1	protein-coding	0.000000	0.398754	
chunk0114_115_1	chr21	9614494	9614901	+	0	NA	Intergenic	Intergenic	206364	NR_038377	441058	Hs.130535	NR_038377		LINC01667	-	long intergenic non-protein coding RNA 1667	ncRNA	0.019656	0.495098	
chunk0009_148_1	chr1	104926034	104926233	+	0	NA	Intergenic	Intergenic	692802	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.005025	0.340000	
chunk0154_230_1	chr5	80825702	80826108	+	0	NA	intron (NM_002439, intron 20 of 23)	L4_C_Mam|LINE|RTE-X	-134784	NM_006909	5924	Hs.162129	NM_006909	ENSG00000113319	RASGRF2	GRF2|RAS-GRF2	Ras protein specific guanine nucleotide releasing factor 2	protein-coding	0.002463	0.361179	
chunk0089_13_1	chr18	57580900	57581520	+	0	NA	intron (NM_001012515, intron 1 of 10)	MER115|DNA|hAT-Tip100	5527	NM_000140	2235	Hs.365365	NM_000140	ENSG00000066926	FECH	EPP|EPP1|FCE	ferrochelatase	protein-coding	0.006452	0.499195	
chunk0166_453_1	chr6	53209672	53210122	+	0	NA	Intergenic	Intergenic	-61071	NM_003643	8521	Hs.23589	NM_003643	ENSG00000137270	GCM1	GCMA|hGCMa	glial cells missing transcription factor 1	protein-coding	0.000000	0.396896	16(TGCACAGGCTGGTCTT,+,0.00)
chunk0021_447_1	chr1	248680589	248681190	+	0	NA	TTS (NM_001004734)	TTS (NM_001004734)	1415	NM_001004734	401994	Hs.449973	NM_001004734	ENSG00000189181	OR14I1	OR5BU1|OR5BU1P	olfactory receptor family 14 subfamily I member 1	protein-coding	0.008319	0.363787	
chunk0160_285_1	chr5	157930558	157931063	+	0	NA	Intergenic	Intergenic	-71635	NM_001195556	9685	Hs.644000	NM_014666	ENSG00000113282	CLINT1	CLINT|ENTH|EPN4|EPNR	clathrin interactor 1	protein-coding	0.013861	0.458498	
chunk0206_313_1	chr9	125113131	125113386	+	0	NA	intron (NM_173690, intron 2 of 18)	L1MC3|LINE|L1	30301	NM_001144877	286205	Hs.59504	NM_173690	ENSG00000173611	SCAI	C9orf126|NET40	suppressor of cancer cell invasion	protein-coding	0.003922	0.347656	106(CAGAACAGCATGTACC,-,0.00),107(AGAACAGCATGTACCC,+,0.00)
chunk0092_28_1	chr19	18848824	18849267	+	0	NA	intron (NM_001297549, intron 3 of 23)	intron (NM_001297549, intron 3 of 23)	17110	NM_001297549	5976	Hs.515266	NM_002911	ENSG00000005007	UPF1	HUPF1|NORF1|RENT1|pNORF1|smg-2	UPF1 RNA helicase and ATPase	protein-coding	0.018059	0.524775	
chunk0198_340_1	chr8	140198671	140199073	+	0	NA	intron (NM_001160372, intron 17 of 22)	L2a|LINE|L2	258890	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.024876	0.538462	
chunk0177_45_1	chr7	20932353	20933209	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	97350	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.007009	0.374562	
chunk0047_203_1	chr12	71215088	71215327	+	0	NA	Intergenic	Intergenic	-57208	NM_004616	7103	Hs.170563	NM_004616	ENSG00000127324	TSPAN8	CO-029|TM4SF3	tetraspanin 8	protein-coding	0.004184	0.345833	
chunk0211_420_1	chrX	129018381	129018665	+	0	NA	Intergenic	L1PB3|LINE|L1	504982	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.000000	0.375439	188(TGGGACTTCCAGTTCT,-,0.00),189(GGGACTTCCAGTTCTA,+,0.00)
chunk0209_263_1	chrX	46642118	46642627	+	0	NA	intron (NM_001257291, intron 12 of 16)	intron (NM_001257291, intron 12 of 16)	68685	NM_019886	56548	Hs.129955	NM_019886	ENSG00000147119	CHST7	C6ST-2|GST-5	carbohydrate sulfotransferase 7	protein-coding	0.007859	0.470588	
chunk0057_375_1	chr13	109171520	109172067	+	0	NA	intron (NM_001198950, intron 33 of 34)	intron (NM_001198950, intron 33 of 34)	-4490	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.012797	0.350365	
chunk0102_264_1	chr2	149800018	149800415	+	0	NA	intron (NR_110240, intron 2 of 2)	intron (NR_110240, intron 2 of 2)	-212400	NM_015702	27249	Hs.5324	NM_015702	ENSG00000168288	MMADHC	C2orf25|CL25022|cblD	metabolism of cobalamin associated D	protein-coding	0.007557	0.371859	
chunk0165_417_1	chr6	39251518	39251797	+	0	NA	Intergenic	Intergenic	-22182	NM_003740	8645	Hs.444448	NM_003740	ENSG00000164626	KCNK5	K2p5.1|KCNK5b|TASK-2|TASK2	potassium two pore domain channel subfamily K member 5	protein-coding	0.021505	0.485714	
chunk0021_22_1	chr10	542219	542464	+	0	NA	intron (NM_014974, intron 1 of 36)	intron (NM_014974, intron 1 of 36)	99437	NR_049884	100847086		NR_049884	ENSG00000263511	MIR5699	mir-5699	microRNA 5699	ncRNA	0.020408	0.544715	84(CAGAACGTCATGTCCC,-,0.00),85(AGAACGTCATGTCCCT,+,0.00)
chunk0004_390_1	chr1	51955995	51956194	+	0	NA	intron (NM_002867, intron 2 of 4)	MIR3|SINE|MIR	34670	NM_002867	5865	Hs.123072	NM_002867	ENSG00000169213	RAB3B	-	RAB3B, member RAS oncogene family	protein-coding	0.010050	0.520000	
chunk0207_34_1	chrX	4788018	4788388	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-154631	NR_110390	101928201	Hs.586488	NR_110390	ENSG00000236513	LOC101928201	-	uncharacterized LOC101928201	ncRNA	0.002703	0.385445	
chunk0161_182_1	chr5	169840926	169841405	+	0	NA	intron (NM_004946, intron 27 of 51)	intron (NM_004946, intron 27 of 51)	139575	NM_001129891	100131897	Hs.721917	NM_001129891	ENSG00000204767	INSYN2B	C5orf57|FAM196B	inhibitory synaptic factor family member 2B	protein-coding	0.008351	0.441667	404(ATAAACAGTATGTTCT,-,0.00),405(TAAACAGTATGTTCTG,+,0.00)
chunk0123_411_1	chr3	49190001	49190318	+	0	NA	intron (NM_001080528, intron 1 of 3)	intron (NM_001080528, intron 1 of 3)	1699	NM_001080528	646498		NM_001080528	ENSG00000236980	C3orf84	-	chromosome 3 open reading frame 84	protein-coding	0.003155	0.500000	
chunk0121_403_1	chr3	25534105	25534506	+	0	NA	intron (NR_110892, intron 3 of 6)	MIR|SINE|MIR	75995	NM_001290217	5915	Hs.543218	NM_000965	ENSG00000077092	RARB	HAP|MCOPS12|NR1B2|RARbeta1|RRB2	retinoic acid receptor beta	protein-coding	0.002494	0.348259	
chunk0063_33_1	chr14	76761717	76761916	+	0	NA	promoter-TSS (NM_014909)	promoter-TSS (NM_014909)	-76	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.120603	0.780000	
chunk0121_166_1	chr3	19866151	19866886	+	0	NA	Intergenic	Intergenic	67696	NM_144715	151651	Hs.733920	NM_144715	ENSG00000163576	EFHB	CFAP21	EF-hand domain family member B	protein-coding	0.005442	0.345109	
chunk0142_292_1	chr4	100157549	100157868	+	0	NA	Intergenic	Charlie1a|DNA|hAT-Charlie	-32325	NR_125924	101929353	Hs.147584	NR_125924	ENSG00000249710	LOC101929353	-	uncharacterized LOC101929353	ncRNA	0.003135	0.356250	
chunk0092_306_1	chr19	34336886	34337528	+	0	NA	intron (NM_014686, intron 8 of 13)	L2a|LINE|L2	-27533	NM_001184722	2821	Hs.466471	NM_000175	ENSG00000105220	GPI	AMF|GNPI|NLK|PGI|PHI|SA-36|SA36	glucose-6-phosphate isomerase	protein-coding	0.007788	0.418351	
chunk0175_447_1	chr6	170115558	170116008	+	0	NA	Intergenic	Intergenic	-44859	NR_125878	102724511	Hs.550045	NR_125878		LOC102724511	-	uncharacterized LOC102724511	ncRNA	0.022222	0.492239	151(CAGCACAGGGCGTGCT,-,0.00),152(AGCACAGGGCGTGCTC,+,0.00),274(GTGGACACGTTGTACC,-,0.00),275(TGGACACGTTGTACCC,+,0.00)
chunk0058_338_1	chr14	28703491	28703716	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	61716	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.013333	0.420354	
chunk0134_138_1	chr3	177592654	177593094	+	0	NA	intron (NR_047568, intron 2 of 3)	intron (NR_047568, intron 2 of 3)	150953	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.018182	0.399093	
chunk0159_385_1	chr5	146478168	146478623	+	0	NA	intron (NM_006706, intron 9 of 21)	intron (NM_006706, intron 9 of 21)	31085	NM_006706	10915	Hs.443465	NM_006706	ENSG00000113649	TCERG1	CA150|TAF2S|Urn1	transcription elongation regulator 1	protein-coding	0.010989	0.364035	209(AAGAACATGTCGTTCT,-,0.00),210(AGAACATGTCGTTCTT,+,0.00)
chunk0033_416_1	chr11	24802138	24802460	+	0	NA	intron (NM_001252010, intron 5 of 9)	L1ME3A|LINE|L1	305329	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.000000	0.349845	
chunk0079_60_1	chr17	10972117	10972347	+	0	NA	Intergenic	L1MC3|LINE|L1	-134131	NM_001101387	644139	Hs.553909	NM_001101387	ENSG00000233670	PIRT	-	phosphoinositide interacting regulator of transient receptor potential channels	protein-coding	0.000000	0.363636	
chunk0131_450_1	chr3	154081211	154081723	+	0	NA	intron (NR_037901, intron 2 of 3)	MIR|SINE|MIR	-39536	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.003906	0.426901	
chunk0138_258_1	chr4	39977250	39977449	+	0	NA	intron (NM_001100400, intron 1 of 15)	CpG	607	NM_001100399	23244	Hs.331431	NM_015200	ENSG00000121892	PDS5A	PIG54|SCC-112|SCC112	PDS5 cohesin associated factor A	protein-coding	0.100503	0.750000	
chunk0098_219_1	chr2	73649782	73650205	+	0	NA	intron (NR_003683, intron 1 of 6)	AluJr4|SINE|Alu	5074	NR_003683	200420	Hs.739204	NM_145300	ENSG00000163016	ALMS1P1	ALMS1L|ALMS1P	ALMS1 pseudogene 1	pseudo	0.011820	0.455189	
chunk0057_246_1	chr13	104598651	104599088	+	0	NA	Intergenic	Intergenic	-866998	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.000000	0.292237	
chunk0197_153_1	chr8	120435293	120435790	+	0	NA	intron (NM_014078, intron 2 of 6)	L1PA15|LINE|L1	-9857	NM_022045	27085	Hs.657656	NM_022045	ENSG00000172167	MTBP	MDM2BP	MDM2 binding protein	protein-coding	0.002012	0.405622	
chunk0147_28_1	chr4	171647081	171647668	+	0	NA	Intergenic	MER70B|LTR|ERVL	-166050	NM_001034845	442117	Hs.386236	NM_001034845	ENSG00000174473	GALNTL6	GALNACT20|GALNT17|GalNAc-T6L	polypeptide N-acetylgalactosaminyltransferase like 6	protein-coding	0.011925	0.443878	
chunk0091_57_1	chr19	4793774	4793996	+	0	NA	3' UTR (NM_018708, exon 1 of 1)	3' UTR (NM_018708, exon 1 of 1)	2169	NM_018708	55527	Hs.515082	NM_018708	ENSG00000141965	FEM1A	EPRAP	fem-1 homolog A	protein-coding	0.040541	0.596413	
chunk0118_91_1	chr22	29096833	29097253	+	0	NA	intron (NM_001039570, intron 2 of 8)	intron (NM_001039570, intron 2 of 8)	23965	NM_032045	83999	Hs.229335	NM_032045	ENSG00000183762	KREMEN1	ECTD13|KREMEN|KRM1	kringle containing transmembrane protein 1	protein-coding	0.014286	0.482185	
chunk0149_127_1	chr5	19617254	19617683	+	0	NA	intron (NM_001167667, intron 5 of 12)	intron (NM_001167667, intron 5 of 12)	268804	NM_001291957	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002331	0.311628	
chunk0069_398_1	chr15	67863607	67863857	+	0	NA	Intergenic	CpG	-23687	NR_104084	101954275		NR_104084	ENSG00000201654	RNU6-7	U6-7	RNA, U6 small nuclear 7	snRNA	0.088000	0.665339	
chunk0138_384_1	chr4	42655810	42656108	+	0	NA	intron (NM_006095, intron 1 of 36)	intron (NM_006095, intron 1 of 36)	1146	NM_001105529	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.020134	0.444816	
chunk0078_102_1	chr17	2303544	2303858	+	0	NA	promoter-TSS (NM_017575)	promoter-TSS (NM_017575)	74	NM_017575	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.127389	0.755556	
chunk0147_87_1	chr4	173213147	173213549	+	0	NA	intron (NM_017423, intron 1 of 11)	intron (NM_017423, intron 1 of 11)	44595	NM_017423	51809	Hs.548088	NM_017423	ENSG00000109586	GALNT7	GALNAC-T7|GalNAcT7	polypeptide N-acetylgalactosaminyltransferase 7	protein-coding	0.002488	0.357320	
chunk0081_351_1	chr17	47428306	47428698	+	0	NA	intron (NM_001195192, intron 21 of 21)	L1M5|LINE|L1	64118	NR_033934	653479	Hs.537279	NR_033934		MRPL45P2	-	mitochondrial ribosomal protein L45 pseudogene 2	pseudo	0.002551	0.320611	
chunk0162_96_1	chr6	2225492	2226146	+	0	NA	intron (NM_001500, intron 1 of 10)	intron (NM_001500, intron 1 of 10)	19815	NM_001500	2762	Hs.144496	NM_001500	ENSG00000112699	GMDS	GMD|SDR3E1	GDP-mannose 4,6-dehydratase	protein-coding	0.007645	0.421374	
chunk0160_36_1	chr5	149474221	149474491	+	0	NA	Intergenic	Intergenic	43710	NR_029686	406937		NR_029686	ENSG00000276365	MIR145	MIRN145|miR-145|miRNA145	microRNA 145	ncRNA	0.007407	0.608856	103(CAGCACATGCTGTTTC,-,0.00),104(AGCACATGCTGTTTCT,+,0.00),163(GAGAACAGGCTCTTCT,-,0.00),164(AGAACAGGCTCTTCTG,+,0.00)
chunk0092_365_1	chr19	35828814	35829151	+	0	NA	intron (NM_004646, intron 28 of 28)	intron (NM_004646, intron 28 of 28)	-15683	NM_021232	58510	Hs.515366	NM_021232	ENSG00000250799	PRODH2	HSPOX1|HYPDH	proline dehydrogenase 2	protein-coding	0.020772	0.556213	
chunk0016_264_1	chr1	200326298	200326772	+	0	NA	Intergenic	L1ME3|LINE|L1	47257	NR_040064	554279	Hs.434694	NR_040064	ENSG00000203721	LINC00862	C1orf98|SMIM16	long intergenic non-protein coding RNA 862	ncRNA	0.010549	0.408421	
chunk0156_31_1	chr5	102487178	102487730	+	0	NA	intron (NM_001289004, intron 1 of 12)	BLACKJACK|DNA|hAT-Blackjack	11562	NM_001289002	133482	Hs.388874	NM_173488	ENSG00000205359	SLCO6A1	CT48|GST|OATP-I|OATP6A1|OATPY	solute carrier organic anion transporter family member 6A1	protein-coding	0.009058	0.370705	286(TAGTACAAAGTGTGCT,-,0.00),287(AGTACAAAGTGTGCTT,+,0.00)
chunk0036_373_1	chr11	67346057	67346264	+	0	NA	intron (NR_024469, intron 2 of 3)	intron (NR_024469, intron 2 of 3)	7436	NM_001256870	57804	Hs.523829	NM_021173	ENSG00000175482	POLD4	POLDS|p12	DNA polymerase delta 4, accessory subunit	protein-coding	0.004831	0.423077	
chunk0124_206_1	chr3	55791860	55792377	+	0	NA	intron (NR_132749, intron 13 of 17)	intron (NR_132749, intron 13 of 17)	60476	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.003868	0.388031	
chunk0126_29_1	chr3	73686786	73687337	+	0	NA	Intergenic	Intergenic	-62140	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.012704	0.402174	234(GACACAAAATGTTCTG,+,0.00)
chunk0140_61_1	chr4	67059520	67060042	+	0	NA	Intergenic	MamGypsy2-I|LTR|Gypsy	362219	NR_110747	101927237	Hs.435644	NR_110747	ENSG00000250075	LOC101927237	-	uncharacterized LOC101927237	ncRNA	0.005747	0.311663	235(AGGAACTCTGTGCTCT,-,0.00),236(GGAACTCTGTGCTCTC,+,0.00)
chunk0092_247_1	chr19	32910694	32911390	+	0	NA	intron (NM_032816, intron 14 of 18)	Tigger3b|DNA|TcMar-Tigger	-41265	NM_014270	11136	Hs.743345	NM_014270	ENSG00000021488	SLC7A9	BAT1|CSNU3	solute carrier family 7 member 9	protein-coding	0.011494	0.407461	348(CAGGACTGGCAGTGCC,-,0.00),349(AGGACTGGCAGTGCCG,+,0.00)
chunk0021_48_1	chr10	970277	970829	+	0	NA	Intergenic	Intergenic	-17856	NM_012341	23560	Hs.215766	NM_012341	ENSG00000107937	GTPBP4	CRFG|NGB|NOG1	GTP binding protein 4	protein-coding	0.012681	0.453888	
chunk0056_94_1	chr13	82305642	82306197	+	0	NA	Intergenic	Intergenic	-1078936	NR_047494	100861546	Hs.539621	NR_047494	ENSG00000260094	LINC00564	-	long intergenic non-protein coding RNA 564	ncRNA	0.003604	0.361511	
chunk0180_34_1	chr7	54328352	54328776	+	0	NA	Intergenic	Intergenic	-2133	NR_120515	102723605	Hs.154626	NR_120515	ENSG00000231427	LINC01445	-	long intergenic non-protein coding RNA 1445	ncRNA	0.007075	0.409412	
chunk0072_36_1	chr16	776198	776558	+	0	NA	Intergenic	Intergenic	6195	NR_030384	724032		NR_030384	ENSG00000207579	MIR662	MIRN662|hsa-mir-662	microRNA 662	ncRNA	0.013889	0.573407	173(TGGAACAGAATGTTCA,-,0.00),174(GGAACAGAATGTTCAG,+,0.00)
chunk0182_94_1	chr7	92933894	92934495	+	0	NA	Intergenic	Intergenic	-97567	NM_001145306	1021	Hs.119882	NM_001259	ENSG00000105810	CDK6	MCPH12|PLSTIRE	cyclin dependent kinase 6	protein-coding	0.001664	0.390365	
chunk0070_96_1	chr15	70323083	70323313	+	0	NA	Intergenic	Intergenic	-225281	NM_020908	7090	Hs.287362	NM_005078	ENSG00000140332	TLE3	ESG|ESG3|GRG3|HsT18976	TLE family member 3, transcriptional corepressor	protein-coding	0.026087	0.519481	
chunk0167_136_1	chr6	62137787	62138180	+	0	NA	intron (NM_152688, intron 2 of 8)	intron (NM_152688, intron 2 of 8)	148212	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.005089	0.365482	
chunk0100_338_1	chr2	116782398	116782798	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-1032081	NM_006773	8886	Hs.744922	NM_006773	ENSG00000088205	DDX18	Has1|MrDb	DEAD-box helicase 18	protein-coding	0.005000	0.326683	
chunk0179_157_1	chr7	46407068	46407673	+	0	NA	Intergenic	Intergenic	-486098	NM_001013398	3486	Hs.450230	NM_000598	ENSG00000146674	IGFBP3	BP-53|IBP3	insulin like growth factor binding protein 3	protein-coding	0.001653	0.358086	
chunk0025_279_1	chr10	56383683	56384451	+	0	NA	Intergenic	L1MB1|LINE|L1	-22794	NM_001005413	11130	Hs.591363	NM_007057	ENSG00000122952	ZWINT	HZwint-1|KNTC2AP|SIP30|ZWINT1	ZW10 interacting kinetochore protein	protein-coding	0.003906	0.340702	353(CAGAACATTCTGTACA,-,0.00),354(AGAACATTCTGTACAT,+,0.00)
chunk0211_280_1	chrX	122261408	122261846	+	0	NA	Intergenic	L1MA1|LINE|L1	890655	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.000000	0.350797	236(AGAGACTGTCTGTTCT,-,0.00),237(GAGACTGTCTGTTCTC,+,0.00)
chunk0049_27_1	chr12	89632727	89633271	+	0	NA	intron (NM_001001323, intron 4 of 20)	intron (NM_001001323, intron 4 of 20)	23068	NM_001001323	490	Hs.506276	NM_001682	ENSG00000070961	ATP2B1	PMCA1|PMCA1kb	ATPase plasma membrane Ca2+ transporting 1	protein-coding	0.001838	0.339450	
chunk0080_91_1	chr17	26777060	26777619	+	0	NA	Intergenic	Intergenic	516657	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.001789	0.310714	
chunk0007_309_1	chr1	84314199	84314463	+	0	NA	intron (NM_001010971, intron 2 of 3)	intron (NM_001010971, intron 2 of 3)	11680	NM_001134664	148418	Hs.591445	NM_001010971	ENSG00000203943	SAMD13	HSD-41|HSD-42	sterile alpha motif domain containing 13	protein-coding	0.007576	0.392453	
chunk0092_42_1	chr19	19380950	19381562	+	0	NA	Intergenic	Intergenic	-4577	NM_017660	54815	Hs.118964	NM_017660	ENSG00000167491	GATAD2A	p66alpha	GATA zinc finger domain containing 2A	protein-coding	0.004902	0.456770	231(GGGAACAGCTTGTCTT,-,0.00),232(GGAACAGCTTGTCTTC,+,0.00),301(GGGGACAGGTTGAGCT,-,0.00),302(GGGACAGGTTGAGCTC,+,0.00)
chunk0087_437_1	chr18	42415030	42415669	+	0	NA	intron (NR_046174, intron 4 of 9)	MARNA|DNA|TcMar-Mariner	228681	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.009390	0.365625	
chunk0143_225_1	chr4	114115963	114116585	+	0	NA	Intergenic	L2a|LINE|L2	-136552	NM_024590	79642	Hs.22895	NM_024590	ENSG00000180801	ARSJ	ASJ	arylsulfatase family member J	protein-coding	0.004823	0.329053	
chunk0075_105_1	chr16	48607024	48607358	+	0	NA	intron (NM_153029, intron 1 of 6)	intron (NM_153029, intron 1 of 6)	3018	NM_153029	9683	Hs.511839	NM_153029	ENSG00000102921	N4BP1	-	NEDD4 binding protein 1	protein-coding	0.005988	0.462687	
chunk0160_425_1	chr5	164460519	164460911	+	0	NA	intron (NR_105064, intron 2 of 3)	intron (NR_105064, intron 2 of 3)	6687	NR_105064	101927835	Hs.735171	NR_105064	ENSG00000253236	LINC02143	-	long intergenic non-protein coding RNA 2143	ncRNA	0.005102	0.295165	
chunk0083_198_1	chr17	66661398	66661708	+	0	NA	intron (NM_002737, intron 5 of 16)	intron (NM_002737, intron 5 of 16)	-125519	NR_030364	693219		NR_030364	ENSG00000207943	MIR634	MIRN634|hsa-mir-634	microRNA 634	ncRNA	0.009677	0.463023	
chunk0204_104_1	chr9	94631558	94632202	+	0	NA	intron (NM_001127628, intron 2 of 7)	intron (NM_001127628, intron 2 of 7)	7761	NM_000507	2203	Hs.494496	NM_000507	ENSG00000165140	FBP1	FBP	fructose-bisphosphatase 1	protein-coding	0.017081	0.438760	
chunk0208_439_1	chrX	30597253	30597572	+	0	NA	Intergenic	Intergenic	-19496	NM_025159	80231	Hs.665009	NM_025159	ENSG00000120280	CXorf21	-	chromosome X open reading frame 21	protein-coding	0.000000	0.431250	
chunk0147_306_1	chr4	184838251	184838754	+	0	NA	Intergenic	Alu|SINE|Alu	8544	NR_037867	731424	Hs.427740	NR_037867		MIR3945HG	-	MIR3945 host gene	ncRNA	0.011928	0.452381	
chunk0110_389_1	chr20	20204523	20205094	+	0	NA	intron (NM_015585, intron 17 of 26)	intron (NM_015585, intron 17 of 26)	148162	NM_001167816	26074	Hs.729168	NM_015585	ENSG00000089101	CFAP61	C20orf26|CaM-IP3|dJ1002M8.3|dJ1178H5.4	cilia and flagella associated protein 61	protein-coding	0.007005	0.386364	
chunk0122_348_1	chr3	37323860	37324315	+	0	NA	exon (NM_001172713, exon 15 of 23)	exon (NM_001172713, exon 15 of 23)	-62182	NM_178344	339883	Hs.475945	NM_178339	ENSG00000198590	C3orf35	APRG1	chromosome 3 open reading frame 35	protein-coding	0.006593	0.390351	140(AGGAACTTTCTGTTCT,-,0.00),141(GGAACTTTCTGTTCTG,+,0.00)
chunk0023_244_1	chr10	27083039	27083324	+	0	NA	intron (NM_014915, intron 5 of 33)	intron (NM_014915, intron 5 of 33)	17317	NM_014915	22852	Hs.361041	NM_014915	ENSG00000107890	ANKRD26	THC2|bA145E8.1	ankyrin repeat domain 26	protein-coding	0.000000	0.339161	
chunk0097_292_1	chr2	55490902	55491515	+	0	NA	Intergenic	Intergenic	-28387	NM_080667	112942	Hs.264208	NM_080667	ENSG00000163001	CFAP36	BARTL1|CCDC104	cilia and flagella associated protein 36	protein-coding	0.009788	0.351792	
chunk0042_455_1	chr12	12489183	12489382	+	0	NA	intron (NM_030640, intron 4 of 6)	MamRTE1|LINE|RTE-BovB	73232	NM_030640	80824	Hs.536535	NM_030640	ENSG00000111266	DUSP16	MKP-7|MKP7	dual specificity phosphatase 16	protein-coding	0.005025	0.390000	
chunk0166_155_1	chr6	45283848	45284121	+	0	NA	intron (NM_001261823, intron 2 of 9)	L1PA4|LINE|L1	-44333	NR_103532	860	Hs.535845	NM_004348	ENSG00000124813	RUNX2	AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA	RUNX family transcription factor 2	protein-coding	0.007326	0.364964	113(CGGAACAACCTGCTCC,-,0.00),114(GGAACAACCTGCTCCT,+,0.00),204(AAAGACACAATGTACC,-,0.00)
chunk0084_160_1	chr17	77096828	77097347	+	0	NA	intron (NM_001204410, intron 2 of 17)	intron (NM_001204410, intron 2 of 17)	7670	NR_106997	102466864		NR_106997	ENSG00000284250	MIR6516	hsa-mir-6516	microRNA 6516	ncRNA	0.030829	0.465385	
chunk0159_26_1	chr5	136664544	136664743	+	0	NA	Intergenic	Intergenic	-299167	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.000000	0.405000	
chunk0184_451_1	chr7	123374613	123374906	+	0	NA	Intergenic	Intergenic	158189	NM_001282855	154865	Hs.159650	NM_178827	ENSG00000164675	IQUB	-	IQ motif and ubiquitin domain containing	protein-coding	0.000000	0.404762	
chunk0132_137_1	chr3	156290478	156290839	+	0	NA	promoter-TSS (NM_172159)	promoter-TSS (NM_172159)	-329	NM_172159	7881	Hs.654519	NM_003471	ENSG00000169282	KCNAB1	AKR6A3|KCNA1B|KV-BETA-1|Kvb1.3|hKvBeta3|hKvb3	potassium voltage-gated channel subfamily A member regulatory beta subunit 1	protein-coding	0.000000	0.505525	
chunk0026_114_1	chr10	61937282	61938038	+	0	NA	intron (NM_032199, intron 2 of 9)	intron (NM_032199, intron 2 of 9)	36406	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.005291	0.383091	
chunk0210_343_1	chrX	95884025	95884801	+	0	NA	Intergenic	Intergenic	453489	NR_003539	643486	Hs.590806	NR_003539	ENSG00000271209	BRDTP1	-	bromodomain testis associated pseudogene 1	pseudo	0.006443	0.342342	
chunk0020_318_1	chr1	237679683	237680006	+	0	NA	intron (NM_001035, intron 61 of 104)	L2c|LINE|L2	-182331	NR_027247	100130331	Hs.661736	NR_027247	ENSG00000237250	LOC100130331	-	POTE ankyrin domain family, member F pseudogene	pseudo	0.018576	0.459877	
chunk0114_413_1	chr20	63947063	63947448	+	0	NA	intron (NR_126526, intron 1 of 14)	intron (NR_126526, intron 1 of 14)	3919	NM_001193379	54963	Hs.504998	NM_017859	ENSG00000198276	UCKL1	UCK1L|URKL1	uridine-cytidine kinase 1 like 1	protein-coding	0.020779	0.598446	
chunk0005_324_1	chr1	61003844	61004084	+	0	NA	Intergenic	L2c|LINE|L2	-33188	NR_110617	100996570	Hs.46616	NR_110617	ENSG00000237928	NFIA-AS2	-	NFIA antisense RNA 2	ncRNA	0.008333	0.435685	136(CAGTACTTTCTGTACT,-,0.00),137(AGTACTTTCTGTACTA,+,0.00)
chunk0175_48_1	chr7	1439342	1439590	+	0	NA	intron (NM_182924, intron 9 of 16)	intron (NM_182924, intron 9 of 16)	20007	NM_182924	79778	Hs.376617	NM_024723	ENSG00000164877	MICALL2	JRAB|MICAL-L2	MICAL like 2	protein-coding	0.024194	0.461847	
chunk0124_38_1	chr3	52286733	52287238	+	0	NA	promoter-TSS (NM_001144951)	promoter-TSS (NM_001144951)	-835	NR_026700	132158	Hs.415312	NM_145262	ENSG00000168237	GLYCTK	HBEBP2|HBEBP4|HBeAgBP4A	glycerate kinase	protein-coding	0.023762	0.482213	
chunk0095_10_1	chr2	11962092	11962467	+	0	NA	Intergenic	L1M2c|LINE|L1	-44837	NR_110196	100506457	Hs.197824	NR_110196	ENSG00000224184	MIR3681HG	-	MIR3681 host gene	ncRNA	0.005333	0.343085	
chunk0006_420_1	chr1	76086614	76087252	+	0	NA	intron (NM_152996, intron 1 of 4)	intron (NM_152996, intron 1 of 4)	12229	NM_001160011	256435	Hs.337040	NM_152996	ENSG00000184005	ST6GALNAC3	PRO7177|SIAT7C|ST6GALNACIII|STY	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	protein-coding	0.007837	0.405321	
chunk0072_425_1	chr15	101151448	101151717	+	0	NA	Intergenic	Intergenic	100350	NM_014918	22856	Hs.110488	NM_014918	ENSG00000131873	CHSY1	CHSY|CSS1|ChSy-1|TPBS	chondroitin sulfate synthase 1	protein-coding	0.026022	0.418519	
chunk0192_203_1	chr8	64413787	64414226	+	0	NA	Intergenic	L2c|LINE|L2	34857	NR_029669	406908		NR_029669	ENSG00000207816	MIR124-2	MIRN124-2|MIRN124A2|mir-124-2	microRNA 124-2	ncRNA	0.002278	0.404545	200(GAGAGCACAATGTGCT,-,0.00),201(AGAGCACAATGTGCTT,+,0.00)
chunk0137_97_1	chr4	13433051	13433252	+	0	NA	intron (NM_001017979, intron 4 of 6)	L1PA17|LINE|L1	51214	NM_001017979	9364	Hs.656060	NM_004249	ENSG00000157869	RAB28	CORD18	RAB28, member RAS oncogene family	protein-coding	0.000000	0.346535	
chunk0207_387_1	chr9	136440163	136440462	+	0	NA	promoter-TSS (NM_019892)	promoter-TSS (NM_019892)	-508	NM_019892	56623	Hs.120998	NM_019892	ENSG00000148384	INPP5E	CORS1|CPD4|JBTS1|MORMS|PPI5PIV|pharbin	inositol polyphosphate-5-phosphatase E	protein-coding	0.040134	0.533333	
chunk0005_458_1	chr1	63694311	63694676	+	0	NA	Intergenic	Intergenic	71277	NM_001172818	5236	Hs.1869	NM_002633	ENSG00000079739	PGM1	CDG1T|GSD14	phosphoglucomutase 1	protein-coding	0.000000	0.428962	
chunk0066_67_1	chr15	29064441	29064646	+	0	NA	intron (NM_001130414, intron 3 of 12)	intron (NM_001130414, intron 3 of 12)	142906	NM_001130414	321	Hs.618112	NM_005503	ENSG00000034053	APBA2	D15S1518E|HsT16821|LIN-10|MGC:14091|MINT2|X11-BETA|X11L	amyloid beta precursor protein binding family A member 2	protein-coding	0.024390	0.606796	
chunk0064_140_1	chr14	91545947	91546706	+	0	NA	Intergenic	L1MD2|LINE|L1	-35846	NM_001284281	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.006588	0.393421	
chunk0171_279_1	chr6	127985499	127985766	+	0	NA	intron (NM_001291981, intron 25 of 32).2	intron (NM_001291981, intron 25 of 32).2	-42233	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.011236	0.369403	
chunk0173_255_1	chr6	147077130	147077736	+	0	NA	intron (NR_034115, intron 4 of 10)	intron (NR_034115, intron 4 of 10)	-81492	NR_132442	106182249	Hs.575390	NR_132442	ENSG00000196634	LUADT1	-	lung adenocarcinoma associated transcript 1	ncRNA	0.008251	0.441516	275(AGGAACACTGTGTCAC,-,0.00),276(GGAACACTGTGTCACT,+,0.00)
chunk0112_280_1	chr20	43624238	43624464	+	0	NA	intron (NM_001303458, intron 10 of 13)	MER81|DNA|hAT-Blackjack	33738	NM_001303458	51098	Hs.444332	NM_016004	ENSG00000101052	IFT52	C20orf9|CGI-53|NGD2|NGD5	intraflagellar transport 52	protein-coding	0.004425	0.471366	80(TAGCACAGAGAGTCCC,-,0.00),81(AGCACAGAGAGTCCCA,+,0.00)
chunk0157_343_1	chr5	122607655	122608149	+	0	NA	Intergenic	L1M5|LINE|L1	122658	NR_109881	101927379	Hs.536399	NR_109881	ENSG00000251538	LINC02201	-	long intergenic non-protein coding RNA 2201	ncRNA	0.002024	0.305051	275(CTGGACAACATGTTCC,-,0.00),276(TGGACAACATGTTCCC,+,0.00)
chunk0084_410_1	chr17	82274098	82274326	+	0	NA	promoter-TSS (NM_001893)	promoter-TSS (NM_001893)	-470	NR_110578	1453	Hs.631725	NM_001893	ENSG00000141551	CSNK1D	ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID	casein kinase 1 delta	protein-coding	0.021930	0.550218	158(GGATCTGAATGTTCCT,+,0.00)
chunk0206_365_1	chr9	125894294	125894934	+	0	NA	intron (NR_024122, intron 2 of 7)	intron (NR_024122, intron 2 of 7)	146415	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.006250	0.346334	
chunk0025_360_1	chr10	58468081	58469015	+	0	NA	Intergenic	Intergenic	-44596	NM_001080512	80114	Hs.100261	NM_001080512	ENSG00000122870	BICC1	BICC|CYSRD	BicC family RNA binding protein 1	protein-coding	0.003212	0.383957	
chunk0174_151_1	chr6	157847929	157848369	+	0	NA	intron (NM_016224, intron 1 of 17)	L2a|LINE|L2	24978	NM_016224	51429	Hs.191213	NM_016224	ENSG00000130340	SNX9	SDP1|SH3PX1|SH3PXD3A|WISP	sorting nexin 9	protein-coding	0.006818	0.467120	218(GAGAACATCTTGTTCC,-,0.00),219(AGAACATCTTGTTCCT,+,0.00)
chunk0011_28_1	chr1	143218082	143218284	+	0	NA	Intergenic	Intergenic	204409	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.059406	0.379310	
chunk0178_231_1	chr7	35716721	35716994	+	0	NA	non-coding (NR_108083, exon 1 of 2)	non-coding (NR_108083, exon 1 of 2)	420	NR_108083	100506725	Hs.304253	NR_108082	ENSG00000227544	LOC100506725	-	uncharacterized LOC100506725	ncRNA	0.003663	0.383212	
chunk0058_274_1	chr14	26188083	26188548	+	0	NA	Intergenic	Intergenic	409439	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.004301	0.422747	238(AAGTACAAATTGTACC,-,0.00),239(AGTACAAATTGTACCC,+,0.00)
chunk0114_163_1	chr21	10748602	10748826	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	227200	NM_199261	7179	Hs.122986	NM_199259	ENSG00000274391	TPTE	CT44|PTEN2	transmembrane phosphatase with tensin homology	protein-coding	0.000000	0.337778	
chunk0114_406_1	chr20	63828500	63828923	+	0	NA	Intergenic	Intergenic	20635	NR_110081	101928604	Hs.676054	NR_110081		ZBTB46-AS1	-	ZBTB46 antisense RNA 1	ncRNA	0.033097	0.549528	141(AAGAACACGAAGTCCC,-,0.00),142(AGAACACGAAGTCCCC,+,0.00)
chunk0116_49_1	chr21	33690866	33691479	+	0	NA	intron (NM_001001132, intron 1 of 29)	L2c|LINE|L2	48694	NM_001001132	6453	Hs.90221	NM_003024	ENSG00000205726	ITSN1	ITSN|SH3D1A|SH3P17	intersectin 1	protein-coding	0.009788	0.385993	248(TGAAACACACTGTGCC,-,0.00),249(GAAACACACTGTGCCA,+,0.00)
chunk0064_52_1	chr14	89895324	89895628	+	0	NA	intron (NM_145231, intron 5 of 5)	L1ME3F|LINE|L1	59081	NM_001284269	90141	Hs.123232	NM_145231	ENSG00000140025	EFCAB11	C14orf143	EF-hand calcium binding domain 11	protein-coding	0.003289	0.390164	
chunk0105_295_1	chr2	190061398	190061659	+	0	NA	intron (NM_005259, intron 1 of 2)	intron (NM_005259, intron 1 of 2)	1201	NM_005259	2660	Hs.41565	NM_005259	ENSG00000138379	MSTN	GDF8|MSLHP	myostatin	protein-coding	0.000000	0.347328	
chunk0069_156_1	chr15	62528431	62529044	+	0	NA	Intergenic	LTR102_Mam|LTR|ERVL	116444	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.008157	0.441368	
chunk0162_37_1	chr6	1053681	1053939	+	0	NA	intron (NR_027115, intron 1 of 4)	(ACATAG)n|Simple_repeat|Simple_repeat	47522	NR_027116	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.019380	0.440154	
chunk0147_313_1	chr4	184912581	184914270	+	0	NA	Intergenic	AluJr|SINE|Alu	-13964	NR_039976	100506229	Hs.378150	NR_039975		LINC01093	-	long intergenic non-protein coding RNA 1093	ncRNA	0.005329	0.421302	1275(ATTACACAATGTTCTT,+,0.00)
chunk0085_405_1	chr18	10301598	10302121	+	0	NA	Intergenic	Intergenic	112511	NR_110775	101927350	Hs.572523	NR_110775	ENSG00000260913	LINC01254	-	long intergenic non-protein coding RNA 1254	ncRNA	0.007648	0.423664	
chunk0077_137_1	chr16	78674572	78675717	+	0	NA	intron (NM_016373, intron 8 of 8)	MIRb|SINE|MIR	575731	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.009607	0.362129	
chunk0004_233_1	chr1	47058853	47059118	+	0	NA	Intergenic	Intergenic	-8503	NM_178134	199974	Hs.176588	NM_178134	ENSG00000186160	CYP4Z1	CYP4A20	cytochrome P450 family 4 subfamily Z member 1	protein-coding	0.000000	0.244361	
chunk0192_216_1	chr8	65223573	65223870	+	0	NA	Intergenic	Intergenic	-43381	NR_038901	552859	Hs.156997	NR_038901	ENSG00000280725	LINC00251	C8orf25|NCRNA00251	long intergenic non-protein coding RNA 251	ncRNA	0.006734	0.322148	114(TGGGACAAGCTGTTCA,-,0.00),115(GGGACAAGCTGTTCAT,+,0.00)
chunk0100_111_1	chr2	108376978	108377414	+	0	NA	promoter-TSS (NM_006588)	promoter-TSS (NM_006588)	-769	NM_006588	27233	Hs.312644	NM_006588	ENSG00000198075	SULT1C4	SULT1C|SULT1C2	sulfotransferase family 1C member 4	protein-coding	0.013761	0.475973	199(AGGAACACAAAGTGCC,-,0.00),200(GGAACACAAAGTGCCA,+,0.00)
chunk0138_252_1	chr4	39779076	39779301	+	0	NA	3' UTR (NM_001312648, exon 6 of 6)	3' UTR (NM_001312648, exon 6 of 6)	81144	NM_001312648	3093	Hs.50308	NM_005339	ENSG00000078140	UBE2K	E2-25K|HIP2|HYPG|LIG|UBC1	ubiquitin conjugating enzyme E2 K	protein-coding	0.004444	0.327434	46(AAGGACAGTATGTATC,-,0.00),47(AGGACAGTATGTATCC,+,0.00)
chunk0036_81_1	chr11	60658264	60658749	+	0	NA	intron (NR_026946, intron 5 of 6)	intron (NR_026946, intron 5 of 6)	-41068	NM_031457	83661	Hs.150878	NM_031457	ENSG00000166959	MS4A8	4SPAN4|CD20L5|MS4A4|MS4A8B	membrane spanning 4-domains A8	protein-coding	0.004124	0.430041	
chunk0045_74_1	chr12	45728774	45729045	+	0	NA	promoter-TSS (NM_152641)	promoter-TSS (NM_152641)	-928	NM_152641	196528	Hs.317304	NM_152641	ENSG00000189079	ARID2	BAF200|CSS6|p200	AT-rich interaction domain 2	protein-coding	0.107011	0.687500	
chunk0113_174_1	chr20	53138379	53138845	+	0	NA	intron (NM_173485, intron 1 of 2)	L2b|LINE|L2	-46671	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.002146	0.423983	161(CAGCACACTAAGTCCT,-,0.00),162(AGCACACTAAGTCCTT,+,0.00)
chunk0058_332_1	chr14	28671257	28671968	+	0	NA	Intergenic	Intergenic	93707	NR_125758	103695363	Hs.569360	NR_125758		FOXG1-AS1	FOXG1-AS	FOXG1 antisense RNA 1	ncRNA	0.004219	0.363764	404(GAGTACATCGTGTACA,-,0.00),405(AGTACATCGTGTACAA,+,0.00)
chunk0099_133_1	chr2	86302388	86302759	+	0	NA	intron (NM_001164730, intron 1 of 6)	L1ME4a|LINE|L1	35081	NM_022912	65055	Hs.368884	NM_022912	ENSG00000068615	REEP1	C2orf23|HMN5B|SPG31|Yip2a	receptor accessory protein 1	protein-coding	0.000000	0.336022	
chunk0002_141_1	chr1	17227615	17227820	+	0	NA	intron (NM_013358, intron 6 of 15)	intron (NM_013358, intron 6 of 15)	-21381	NM_016233	51702	Hs.149195	NM_016233	ENSG00000142619	PADI3	PAD3|PDI3|UHS1	peptidyl arginine deiminase 3	protein-coding	0.019512	0.504854	
chunk0156_125_1	chr5	106578819	106579018	+	0	NA	Intergenic	Intergenic	432096	NR_104671	102467213	Hs.570923	NR_104671	ENSG00000251027	LINC01950	-	long intergenic non-protein coding RNA 1950	ncRNA	0.005025	0.455000	
chunk0198_309_1	chr8	139002275	139002498	+	0	NA	Intergenic	Intergenic	-88380	NM_152888	169044	Hs.117169	NM_152888	ENSG00000169436	COL22A1	-	collagen type XXII alpha 1 chain	protein-coding	0.008969	0.535714	
chunk0090_246_1	chr18	73895596	73895897	+	0	NA	Intergenic	Intergenic	252018	NM_152676	201456	Hs.664011	NM_152676	ENSG00000141665	FBXO15	FBX15	F-box protein 15	protein-coding	0.003322	0.440397	
chunk0134_132_1	chr3	177465111	177465743	+	0	NA	intron (NR_047568, intron 1 of 3)	intron (NR_047568, intron 1 of 3)	23506	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.009494	0.401264	
chunk0137_425_1	chr4	28259782	28260453	+	0	NA	Intergenic	Intergenic	-559465	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.002981	0.275298	
chunk0142_298_1	chr4	100443995	100444300	+	0	NA	intron (NM_001159694, intron 4 of 10)	L1MA9|LINE|L1	73946	NM_001159694	51705	Hs.152913	NM_016242	ENSG00000164035	EMCN	EMCN2|MUC14	endomucin	protein-coding	0.000000	0.562092	
chunk0043_394_1	chr12	25348342	25348937	+	0	NA	Intergenic	Intergenic	-97708	NM_004985	3845	Hs.505033	NM_004985	ENSG00000133703	KRAS	C-K-RAS|CFC2|K-RAS2A|K-RAS2B|K-RAS4A|K-RAS4B|K-Ras|KI-RAS|KRAS1|KRAS2|NS|NS3|RALD|RASK2|c-Ki-ras2	KRAS proto-oncogene, GTPase	protein-coding	0.003361	0.340604	
chunk0072_97_1	chr15	91041773	91042570	+	0	NA	Intergenic	Intergenic	19549	NR_110104	101926911	Hs.459366	NR_110104	ENSG00000214432	VPS33B-DT	-	VPS33B divergent transcript	ncRNA	0.010038	0.448622	
chunk0070_37_1	chr15	69453289	69453942	+	0	NA	intron (NM_213725, intron 1 of 2)	intron (NM_213725, intron 1 of 2)	795	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.039816	0.486239	
chunk0082_125_1	chr17	55167230	55167740	+	0	NA	Intergenic	Intergenic	-97475	NM_002126	3131	Hs.196952	NM_002126	ENSG00000108924	HLF	-	HLF transcription factor, PAR bZIP family member	protein-coding	0.001961	0.344423	
chunk0206_247_1	chr9	123740020	123740229	+	0	NA	intron (NM_024820, intron 5 of 20)	L1PA11|LINE|L1	190014	NM_020946	57706	Hs.744995	NM_020946	ENSG00000119522	DENND1A	FAM31A|KIAA1608	DENN domain containing 1A	protein-coding	0.009569	0.366667	
chunk0198_228_1	chr8	134025247	134025683	+	0	NA	Intergenic	Intergenic	138969	NR_125424	101927822	Hs.129114	NR_125424	ENSG00000253593	LOC101927822	-	uncharacterized LOC101927822	ncRNA	0.006881	0.416476	
chunk0161_188_1	chr5	170130712	170131196	+	0	NA	Intergenic	L1ME1|LINE|L1	25041	NM_144769	2299	Hs.87236	NM_012188	ENSG00000168269	FOXI1	FKH10|FKHL10|FREAC-6|FREAC6|HFH-3|HFH3	forkhead box I1	protein-coding	0.002066	0.346392	202(AAGTACATTCTGTATT,-,0.00)
chunk0191_420_1	chr8	57753319	57753589	+	0	NA	Intergenic	L1MEh|LINE|L1	-224904	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.003704	0.346863	
chunk0185_18_1	chr7	123994000	123994313	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	39313	NM_001136002	730130	Hs.450249	NM_001136002	ENSG00000234224	TMEM229A	-	transmembrane protein 229A	protein-coding	0.006390	0.331210	
chunk0156_283_1	chr5	109927928	109928252	+	0	NA	Intergenic	Intergenic	44908	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.003086	0.387692	
chunk0144_121_1	chr4	128844695	128845270	+	0	NA	intron (NM_024900, intron 3 of 8)	intron (NM_024900, intron 3 of 8)	33138	NM_001287443	79960	Hs.12420	NM_024900	ENSG00000077684	JADE1	PHF17	jade family PHD finger 1	protein-coding	0.010435	0.489583	286(AAGAACTCCCTGTCCT,-,0.00),287(AGAACTCCCTGTCCTG,+,0.00)
chunk0051_2_1	chr12	111159317	111159987	+	0	NA	intron (NM_015267, intron 1 of 21)	intron (NM_015267, intron 1 of 21)	125628	NM_015267	23316	Hs.124953	NM_015267	ENSG00000111249	CUX2	CDP2|CUTL2|EIEE67	cut like homeobox 2	protein-coding	0.010448	0.454545	
chunk0150_64_1	chr5	32100732	32100934	+	0	NA	intron (NM_178140, intron 22 of 23)	intron (NM_178140, intron 22 of 23)	73486	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.004950	0.512315	
chunk0115_149_1	chr21	23598161	23598490	+	0	NA	Intergenic	L1MC1|LINE|L1	-213490	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.003040	0.345455	
chunk0028_327_1	chr10	91976972	91977655	+	0	NA	intron (NM_003972, intron 14 of 37)	L1MC1|LINE|L1	53334	NM_003972	9044	Hs.500526	NM_003972	ENSG00000095564	BTAF1	MOT1|TAF(II)170|TAF172|TAFII170	B-TFIID TATA-box binding protein associated factor 1	protein-coding	0.004392	0.384503	
chunk0108_292_1	chr2	234953607	234954303	+	0	NA	intron (NM_014521, intron 1 of 5)	intron (NM_014521, intron 1 of 5)	1971	NM_014521	23677	Hs.516777	NM_014521	ENSG00000130147	SH3BP4	BOG25|TTP	SH3 domain binding protein 4	protein-coding	0.021552	0.493544	425(AAGAACAGTTAGTTCT,-,0.00),426(AGAACAGTTAGTTCTG,+,0.00)
chunk0046_91_1	chr12	56526786	56527333	+	0	NA	intron (NM_002898, intron 1 of 13)	intron (NM_002898, intron 1 of 13)	5234	NM_002898	5939	Hs.505729	NM_002898	ENSG00000076067	RBMS2	SCR3	RNA binding motif single stranded interacting protein 2	protein-coding	0.005484	0.375912	
chunk0020_131_1	chr1	233607389	233607639	+	0	NA	Intergenic	Intergenic	-6490	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.012000	0.486056	
chunk0171_360_1	chr6	130634318	130634723	+	0	NA	Intergenic	Intergenic	-192885	NM_001195597	100507203	Hs.388715	NM_001195597	ENSG00000256162	SMLR1	-	small leucine rich protein 1	protein-coding	0.004938	0.273399	
chunk0011_306_1	chr1	151748678	151749354	+	0	NA	Intergenic	L1MDa|LINE|L1	-13953	NM_001134939	51686	Hs.713789	NM_016178	ENSG00000143450	OAZ3	AZ3|OAZ-t|TISP15	ornithine decarboxylase antizyme 3	protein-coding	0.005917	0.372230	
chunk0033_105_1	chr11	14358874	14359579	+	0	NA	promoter-TSS (NM_012250)	promoter-TSS (NM_012250)	-42	NM_012250	22800	Hs.502004	NM_012250	ENSG00000133818	RRAS2	TC21	RAS related 2	protein-coding	0.089362	0.645892	
chunk0088_402_1	chr18	54514423	54515389	+	0	NA	Intergenic	Intergenic	-72853	NM_001307955	284254	Hs.376146	NM_173629	ENSG00000178690	DYNAP	C18orf26	dynactin associated protein	protein-coding	0.007246	0.384695	
chunk0186_61_1	chr7	136946973	136947383	+	0	NA	intron (NR_046103, intron 2 of 3)	intron (NR_046103, intron 2 of 3)	44011	NR_030165	574443		NR_030165	ENSG00000207597	MIR490	MIRN490|hsa-mir-490|miR-490	microRNA 490	ncRNA	0.004878	0.323601	
chunk0061_269_1	chr14	61451829	61452162	+	0	NA	intron (NM_006255, intron 6 of 13)	intron (NM_006255, intron 6 of 13)	118199	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.015015	0.485030	
chunk0106_57_1	chr2	196373145	196373724	+	0	NA	intron (NM_020760, intron 2 of 28)	intron (NM_020760, intron 2 of 28)	-11310	NM_001304840	57520	Hs.633212	NM_020760	ENSG00000138411	HECW2	NDHSAL|NEDL2	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	protein-coding	0.001727	0.343103	
chunk0139_243_1	chr4	55598434	55598665	+	0	NA	intron (NR_120489, intron 8 of 8)	intron (NR_120489, intron 8 of 8)	-6337	NM_152401	132954	Hs.223712	NM_152401	ENSG00000163440	PDCL2	GCPHLP	phosducin like 2	protein-coding	0.000000	0.288793	
chunk0193_83_1	chr8	73423142	73423627	+	0	NA	intron (NM_001164380, intron 13 of 14)	intron (NM_001164380, intron 13 of 14)	3310	NR_038406	100128126	Hs.679921	NR_038406	ENSG00000253302	STAU2-AS1	-	STAU2 antisense RNA 1	ncRNA	0.016495	0.539095	
chunk0130_136_1	chr3	132218752	132219436	+	0	NA	Intergenic	LTR24C|LTR|ERV1	-98273	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.005848	0.378102	
chunk0206_42_1	chr9	117400786	117401295	+	0	NA	intron (NM_014010, intron 1 of 21)	intron (NM_014010, intron 1 of 21)	13999	NM_014010	23245	Hs.601562	NM_014010	ENSG00000148219	ASTN2	bA67K19.1	astrotactin 2	protein-coding	0.009823	0.445098	
chunk0176_66_1	chr7	11236572	11237065	+	0	NA	Intergenic	Intergenic	262946	NR_033435	9678	Hs.655688	NM_014660	ENSG00000106443	PHF14	-	PHD finger protein 14	protein-coding	0.008114	0.368421	
chunk0148_264_1	chr5	10377967	10378399	+	0	NA	intron (NM_001270660, intron 2 of 24)	intron (NM_001270660, intron 2 of 24)	24544	NM_001270661	10299	Hs.432862	NM_005885	ENSG00000145495	MARCH6	DOA10|MARCH-VI|RNF176|TEB4	membrane associated ring-CH-type finger 6	protein-coding	0.002315	0.323326	
chunk0091_134_1	chr19	6766199	6766519	+	0	NA	intron (NM_005490, intron 1 of 9)	intron (NM_005490, intron 1 of 9)	1153	NM_005490	10045	Hs.439645	NM_005490	ENSG00000125731	SH2D3A	NSP1	SH2 domain containing 3A	protein-coding	0.021875	0.510903	
chunk0189_457_1	chr8	28515520	28515719	+	0	NA	intron (NM_017412, intron 3 of 7)	MER50|LTR|ERV1	-10437	NR_036250	100422903		NR_036250	ENSG00000265251	MIR4288	-	microRNA 4288	ncRNA	0.020101	0.510000	
chunk0133_48_1	chr3	166453449	166453992	+	0	NA	Intergenic	L1MEd|LINE|L1	-616255	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.003683	0.349265	
chunk0154_393_1	chr5	88245670	88246315	+	0	NA	intron (NM_153354, intron 1 of 11)	intron (NM_153354, intron 1 of 11)	22887	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.000000	0.325077	
chunk0137_36_1	chr4	11343889	11344736	+	0	NA	Intergenic	Tigger9b|DNA|TcMar-Tigger	-24515	NR_030298	693157		NR_030298	ENSG00000207716	MIR572	MIRN572|hsa-mir-572	microRNA 572	ncRNA	0.009445	0.422170	511(ATGCACACAATGTACA,-,0.00)
chunk0124_213_1	chr3	56064519	56065080	+	0	NA	intron (NR_132749, intron 7 of 17)	MER58A|DNA|hAT-Charlie	-212205	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.005348	0.371886	
chunk0038_193_1	chr11	86089557	86090153	+	0	NA	Intergenic	Intergenic	-19974	NM_001206947	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.003356	0.343384	318(ATGTACAGTTTGTCCT,-,0.00),319(TGTACAGTTTGTCCTG,+,0.00)
chunk0013_444_1	chr1	173744414	173745249	+	0	NA	intron (NM_014458, intron 3 of 11)	L1MC4a|LINE|L1	29890	NM_014458	27252	Hs.495035	NM_014458	ENSG00000076321	KLHL20	KHLHX|KLEIP|KLHLX	kelch like family member 20	protein-coding	0.005988	0.309809	
chunk0081_249_1	chr17	43201084	43201428	+	0	NA	intron (NM_001291572, intron 16 of 17)	Tigger19a|DNA|TcMar-Tigger	-10571	NM_001291586	113277	Hs.536474	NM_145041	ENSG00000184988	TMEM106A	-	transmembrane protein 106A	protein-coding	0.002907	0.397101	
chunk0110_402_1	chr20	20362835	20363359	+	0	NA	Intergenic	Intergenic	-5024	NM_002196	3642	Hs.89584	NM_002196	ENSG00000173404	INSM1	IA-1|IA1	INSM transcriptional repressor 1	protein-coding	0.032443	0.561905	
chunk0094_320_1	chr2	8995238	8995621	+	0	NA	intron (NM_138799, intron 1 of 12)	MamRep4096|DNA|hAT-Tip100	8318	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.013055	0.382812	
chunk0055_335_1	chr13	69059345	69059574	+	0	NA	Intergenic	Intergenic	-162887	NR_125752	103689913	Hs.585628	NR_125752	ENSG00000235221	LINC00383	LINC00401	long intergenic non-protein coding RNA 383	ncRNA	0.013100	0.352174	
chunk0108_427_1	chr2	237861827	237862096	+	0	NA	intron (NM_005855, intron 1 of 2)	intron (NM_005855, intron 1 of 2)	2417	NM_005855	10267	Hs.471783	NM_005855	ENSG00000132329	RAMP1	-	receptor activity modifying protein 1	protein-coding	0.022305	0.429630	
chunk0183_82_1	chr7	104790887	104791573	+	0	NA	intron (NM_199000, intron 2 of 2)	intron (NM_199000, intron 2 of 2)	12862	NR_034142	645591	Hs.658835	NR_034141	ENSG00000226869	LHFPL3-AS1	-	LHFPL3 antisense RNA 1	ncRNA	0.001458	0.388646	
chunk0151_300_1	chr5	53025663	53025956	+	0	NA	intron (NR_073107, intron 1 of 28)	intron (NR_073107, intron 1 of 28)	36483	NM_002203	3673	Hs.482077	NM_002203	ENSG00000164171	ITGA2	BR|CD49B|GPIa|HPA-5|VLA-2|VLAA2	integrin subunit alpha 2	protein-coding	0.003413	0.384354	
chunk0115_224_1	chr21	27134400	27134831	+	0	NA	Intergenic	Intergenic	-167495	NM_007038	11096	Hs.58324	NM_007038	ENSG00000154736	ADAMTS5	ADAM-TS 11|ADAM-TS 5|ADAM-TS5|ADAMTS-11|ADAMTS-5|ADAMTS11|ADMP-2	ADAM metallopeptidase with thrombospondin type 1 motif 5	protein-coding	0.009281	0.372685	
chunk0207_398_1	chr9	136731405	136731906	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	-3471	NR_003672	84973	Hs.495480	NR_003672	ENSG00000233016	SNHG7	NCRNA00061	small nucleolar RNA host gene 7	ncRNA	0.009980	0.444223	
chunk0002_380_1	chr1	26702155	26702666	+	0	NA	intron (NM_139135, intron 1 of 19)	intron (NM_139135, intron 1 of 19)	6379	NM_139135	8289	Hs.468972	NM_006015	ENSG00000117713	ARID1A	B120|BAF250|BAF250a|BM029|C1orf4|CSS2|ELD|MRD14|OSA1|P270|SMARCF1|hELD|hOSA1	AT-rich interaction domain 1A	protein-coding	0.007828	0.394531	
chunk0132_245_1	chr3	158691132	158691430	+	0	NA	intron (NM_001308164, intron 18 of 18)	intron (NM_001308164, intron 18 of 18)	-18588	NM_020169	56925	Hs.478067	NM_020169	ENSG00000079257	LXN	ECI|TCI	latexin	protein-coding	0.003356	0.351171	
chunk0076_385_1	chr16	72412854	72413498	+	0	NA	intron (NR_126330, intron 7 of 13)	AluYj4|SINE|Alu	-240726	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.010870	0.427907	
chunk0156_60_1	chr5	103425913	103426511	+	0	NA	Intergenic	L2b|LINE|L2	115773	NR_104670	102467212	Hs.641885	NR_104670	ENSG00000248757	LINC02115	-	long intergenic non-protein coding RNA 2115	ncRNA	0.001672	0.350584	
chunk0030_215_1	chr10	114645475	114645914	+	0	NA	intron (NM_001003407, intron 1 of 21)	intron (NM_001003407, intron 1 of 21)	12605	NM_002313	3983	Hs.438236	NM_002313	ENSG00000099204	ABLIM1	ABLIM|LIMAB1|LIMATIN|abLIM-1	actin binding LIM protein 1	protein-coding	0.002278	0.331818	
chunk0158_429_1	chr5	135323809	135324222	+	0	NA	intron (NM_001277348, intron 3 of 5)	intron (NM_001277348, intron 3 of 5)	75223	NM_138609	9555	Hs.420272	NM_004893	ENSG00000113648	H2AFY	H2A.y|H2A/y|H2AF12M|MACROH2A1.1|mH2A1|macroH2A1.2	H2A histone family member Y	protein-coding	0.014528	0.553140	
chunk0021_233_1	chr10	6558226	6558550	+	0	NA	intron (NM_001282644, intron 1 of 17)	intron (NM_001282644, intron 1 of 17)	21913	NM_006257	5588	Hs.498570	NM_006257	ENSG00000065675	PRKCQ	PRKCT|nPKC-theta	protein kinase C theta	protein-coding	0.003086	0.307692	
chunk0142_90_1	chr4	94147813	94148348	+	0	NA	intron (NR_125922, intron 5 of 8)	L1P2|LINE|L1	59476	NR_125922	101929210	Hs.518877	NR_125922	ENSG00000246541	LOC101929210	-	uncharacterized LOC101929210	ncRNA	0.020561	0.567164	
chunk0132_367_1	chr3	161821105	161821854	+	0	NA	Intergenic	Intergenic	324671	NM_001080440	131149	Hs.585021	NM_001080440	ENSG00000182447	OTOL1	C1QTNF15|C1QTNF16	otolin 1	protein-coding	0.005340	0.348000	
chunk0083_187_1	chr17	66474863	66475152	+	0	NA	intron (NM_002737, intron 2 of 16)	L3|LINE|CR1	-58153	NR_110822	101928001	Hs.650730	NR_110822		PRKCA-AS1	-	PRKCA antisense RNA 1	ncRNA	0.000000	0.462069	
chunk0132_376_1	chr3	163117322	163117960	+	0	NA	Intergenic	Intergenic	185660	NR_033945	647107	Hs.408584	NR_033945	ENSG00000241369	LINC01192	CT64	long intergenic non-protein coding RNA 1192	ncRNA	0.006270	0.292645	
chunk0039_15_1	chr11	95399261	95399619	+	0	NA	Intergenic	L1MB7|LINE|L1	-166899	NM_001271594	143686	Hs.120633	NM_144665	ENSG00000149212	SESN3	SEST3	sestrin 3	protein-coding	0.000000	0.345404	
chunk0035_191_1	chr11	44208864	44209784	+	0	NA	intron (NM_001178083, intron 11 of 14)	intron (NM_001178083, intron 11 of 14)	100842	NM_021926	60529	Hs.436055	NM_021926	ENSG00000052850	ALX4	CRS5|FND2	ALX homeobox 4	protein-coding	0.002174	0.382193	343(CAGAGCACTCTGTACC,-,0.00),344(AGAGCACTCTGTACCT,+,0.00)
chunk0063_323_1	chr14	85176709	85177086	+	0	NA	Intergenic	Intergenic	-216982	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.005305	0.388889	
chunk0084_330_1	chr17	80961784	80962030	+	0	NA	intron (NM_020761, intron 31 of 33)	intron (NM_020761, intron 31 of 33)	-29934	NM_024591	79643	Hs.514560	NM_024591	ENSG00000176108	CHMP6	VPS20	charged multivesicular body protein 6	protein-coding	0.020325	0.469636	
chunk0147_433_1	chr4	187479471	187479825	+	0	NA	intron (NR_038931, intron 1 of 4)	L3|LINE|CR1	25965	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.005650	0.321127	
chunk0081_124_1	chr17	40314447	40314832	+	0	NA	intron (NM_000964, intron 1 of 8)	intron (NM_000964, intron 1 of 8)	-3582	NM_001145301	5914	Hs.654583	NM_000964	ENSG00000131759	RARA	NR1B1|RAR	retinoic acid receptor alpha	protein-coding	0.010390	0.632124	216(AGGGACAGTCTGCCCC,-,0.00),217(GGGACAGTCTGCCCCT,+,0.00)
chunk0202_213_1	chr9	76180820	76181030	+	0	NA	intron (NM_001190482, intron 15 of 36)	intron (NM_001190482, intron 15 of 36)	213603	NM_018339	55312	Hs.37558	NM_018339	ENSG00000135002	RFK	RIFK	riboflavin kinase	protein-coding	0.004762	0.308057	
chunk0109_214_1	chr20	5657555	5657933	+	0	NA	Intergenic	Intergenic	-46718	NM_019593	56261	Hs.636359	NM_019593	ENSG00000125772	GPCPD1	EDI3|GDE5|GDPD6|PREI4	glycerophosphocholine phosphodiesterase 1	protein-coding	0.018519	0.472296	
chunk0117_328_1	chr22	24991823	24992527	+	0	NA	Intergenic	Intergenic	-35799	NM_001145206	85379	Hs.419171	NM_001145206	ENSG00000197077	KIAA1671	-	KIAA1671	protein-coding	0.015625	0.507801	
chunk0105_460_1	chr2	195308184	195308709	+	0	NA	Intergenic	Intergenic	-348362	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.007619	0.315589	
chunk0042_75_1	chr12	2161490	2161924	+	0	NA	intron (NM_001129846, intron 3 of 45)	intron (NM_001129846, intron 3 of 45)	61774	NR_046578	100874234	Hs.372570	NR_046578	ENSG00000256025	CACNA1C-AS4	-	CACNA1C antisense RNA 4	ncRNA	0.020737	0.496552	
chunk0009_19_1	chr1	100034979	100035790	+	0	NA	Intergenic	Intergenic	-2849	NM_033055	64645	Hs.124156	NM_033055	ENSG00000156875	MFSD14A	HIAT1	major facilitator superfamily domain containing 14A	protein-coding	0.004932	0.365764	
chunk0100_168_1	chr2	109481117	109481648	+	0	NA	intron (NM_001099289, intron 8 of 9)	intron (NM_001099289, intron 8 of 9)	132824	NM_178584	151011	Hs.469615	NM_144710	ENSG00000186522	SEPTIN10	SEPT10	septin 10	protein-coding	0.026365	0.545113	
chunk0167_377_1	chr6	73774291	73774891	+	0	NA	intron (NM_133493, intron 15 of 32)	L1MEh|LINE|L1	-78460	NR_110889	101928489	Hs.660059	NR_110889	ENSG00000231652	LOC101928489	-	uncharacterized LOC101928489	ncRNA	0.005000	0.480865	368(CAGGACTGTGTGTCCT,-,0.00),369(AGGACTGTGTGTCCTG,+,0.00)
chunk0167_366_1	chr6	73521002	73521317	+	0	NA	promoter-TSS (NM_001402)	promoter-TSS (NM_001402)	-127	NM_001402	1915	Hs.535192	NM_001402	ENSG00000156508	EEF1A1	CCS-3|CCS3|EE1A1|EEF-1|EEF1A|EF-Tu|EF1A|GRAF-1EF|HNGC:16303|LENG7|PTI1|eEF1A-1	eukaryotic translation elongation factor 1 alpha 1	protein-coding	0.085714	0.604430	
chunk0106_364_1	chr2	207163504	207163866	+	0	NA	intron (NM_001270943, intron 1 of 3)	intron (NM_001270943, intron 1 of 3)	2331	NM_003709	8609	Hs.59908	NM_003709	ENSG00000118263	KLF7	UKLF	Kruppel like factor 7	protein-coding	0.005525	0.404959	
chunk0072_13_1	chr16	424409	424794	+	0	NA	Intergenic	Intergenic	-1067	NM_014700	9727	Hs.531642	NM_014700	ENSG00000090565	RAB11FIP3	CART1|FIP3-Rab11|Rab11-FIP3	RAB11 family interacting protein 3	protein-coding	0.036364	0.523316	
chunk0127_382_1	chr3	102089071	102089634	+	0	NA	Intergenic	Intergenic	148493	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003552	0.379433	
chunk0153_59_1	chr5	67694077	67694623	+	0	NA	Intergenic	Intergenic	-98863	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.010989	0.447898	
chunk0005_151_1	chr1	58144738	58145083	+	0	NA	intron (NM_021080, intron 1 of 16)	intron (NM_021080, intron 1 of 16)	105629	NM_021080	1600	Hs.477370	NM_021080	ENSG00000173406	DAB1	SCA37	DAB adaptor protein 1	protein-coding	0.002899	0.462428	156(CAGAACTCCTTGTACC,-,0.00),157(AGAACTCCTTGTACCT,+,0.00)
chunk0119_54_1	chr22	40758278	40758792	+	0	NA	Intergenic	MIRc|SINE|MIR	55423	NR_039923	100616283		NR_039923	ENSG00000266594	MIR4766	mir-4766	microRNA 4766	ncRNA	0.005837	0.380583	
chunk0055_415_1	chr13	74889458	74889657	+	0	NA	Intergenic	Intergenic	336714	NR_034025	338864	Hs.97408	NR_034024	ENSG00000236678	LINC00347	-	long intergenic non-protein coding RNA 347	ncRNA	0.000000	0.390000	57(TGGGCAGGATGTTCTT,+,0.00)
chunk0187_275_1	chr7	155325813	155326072	+	0	NA	Intergenic	Intergenic	28166	NM_005542	3638	Hs.520819	NM_005542	ENSG00000186480	INSIG1	CL6	insulin induced gene 1	protein-coding	0.019305	0.511538	
chunk0029_234_1	chr10	102512090	102513024	+	0	NA	intron (NM_016169, intron 2 of 11)	intron (NM_016169, intron 2 of 11)	8595	NM_001178133	51684	Hs.404089	NM_016169	ENSG00000107882	SUFU	JBTS32|PRO1280|SUFUH|SUFUXL	SUFU negative regulator of hedgehog signaling	protein-coding	0.005353	0.431016	
chunk0160_72_1	chr5	149870291	149870647	+	0	NA	intron (NM_000440, intron 17 of 21)	Helitron1Na_Mam|RC|Helitron	62508	NR_110534	644762	Hs.730366	NR_110534		LOC644762	-	mitochondrial fission factor pseudogene	pseudo	0.002809	0.425770	
chunk0117_209_1	chr22	21982657	21982901	+	0	NA	promoter-TSS (NM_001282113)	promoter-TSS (NM_001282113)	64	NM_001282113	8940	Hs.436401	NM_003935	ENSG00000100038	TOP3B	TOP3B1	DNA topoisomerase III beta	protein-coding	0.131148	0.702041	
chunk0175_233_1	chr7	6403872	6404382	+	0	NA	TTS (NM_018890)	TTS (NM_018890)	29632	NM_006908	5879	Hs.413812	NM_006908	ENSG00000136238	RAC1	MIG5|MRD48|Rac-1|TC-25|p21-Rac1	Rac family small GTPase 1	protein-coding	0.021569	0.495108	218(AGGGACAGGGAGTGCC,-,0.00),219(GGGACAGGGAGTGCCA,+,0.00)
chunk0010_238_1	chr1	116433287	116433625	+	0	NA	intron (NR_125972, intron 2 of 3)	intron (NR_125972, intron 2 of 3)	-14834	NR_027646	84852	Hs.664752	NM_032766	ENSG00000203865	ATP1A1-AS1	ATP1A1OS|C1orf203	ATP1A1 antisense RNA 1	ncRNA	0.011834	0.569322	
chunk0074_295_1	chr16	29816793	29817123	+	0	NA	exon (NM_024516, exon 1 of 3)	exon (NM_024516, exon 1 of 3)	751	NM_024516	79447	Hs.702841	NM_024516	ENSG00000280789	PAGR1	C16orf53|GAS|PA1	PAXIP1 associated glutamate rich protein 1	protein-coding	0.057576	0.637462	
chunk0205_294_1	chr9	111961374	111961805	+	0	NA	Intergenic	L1MD|LINE|L1	29489	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.011601	0.372685	
chunk0092_135_1	chr19	28109247	28109770	+	0	NA	Intergenic	L1PB3|LINE|L1	-315568	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.003824	0.309160	
chunk0187_346_1	chr7	157023719	157024051	+	0	NA	Intergenic	Intergenic	13028	NR_038835	645249	Hs.224879	NR_038835	ENSG00000243479	MNX1-AS1	CCAT5	MNX1 antisense RNA 1 (head to head)	ncRNA	0.000000	0.264264	
chunk0108_24_1	chr2	226528115	226528688	+	0	NA	Intergenic	Intergenic	130392	NR_049887	100847053		NR_049887	ENSG00000263363	MIR5702	-	microRNA 5702	ncRNA	0.010471	0.362369	
chunk0188_238_1	chr8	13617313	13617626	+	0	NA	Intergenic	Intergenic	50626	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.006390	0.267516	
chunk0211_159_1	chrX	114226360	114227003	+	0	NA	Intergenic	L2c|LINE|L2	-288463	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.001555	0.315217	
chunk0089_285_1	chr18	63019492	63019711	+	0	NA	Intergenic	Intergenic	299779	NM_000633	596	Hs.150749	NM_000633	ENSG00000171791	BCL2	Bcl-2|PPP1R50	BCL2 apoptosis regulator	protein-coding	0.022831	0.572727	131(GGGCTCACTGTGTTCT,-,0.00),132(GGCTCACTGTGTTCTG,+,0.00)
chunk0200_207_1	chr9	20526513	20526839	+	0	NA	intron (NM_001286691, intron 2 of 10)	L1ME3A|LINE|L1	-24334	NR_039685	100616441		NR_039685	ENSG00000264941	MIR4474	-	microRNA 4474	ncRNA	0.000000	0.363914	
chunk0101_213_1	chr2	130356504	130356703	+	0	NA	intron (NM_001142370, intron 1 of 10)	intron (NM_001142370, intron 1 of 10)	596	NM_001142370	26469	Hs.516390	NM_014369	ENSG00000072135	PTPN18	BDP1|PTP-HSCF	protein tyrosine phosphatase non-receptor type 18	protein-coding	0.105528	0.735000	
chunk0103_201_1	chr2	163676764	163677419	+	0	NA	intron (NM_018086, intron 2 of 2)	Tigger19b|DNA|TcMar-Tigger	58912	NM_018086	55137	Hs.593650	NM_018086	ENSG00000182263	FIGN	-	fidgetin, microtubule severing factor	protein-coding	0.001527	0.368902	
chunk0132_80_1	chr3	155304147	155304900	+	0	NA	Intergenic	Intergenic	-10823	NR_037902									0.005312	0.400531	368(CTGCACAACATGTTCT,-,0.00),369(TGCACAACATGTTCTT,+,0.00)
chunk0071_196_1	chr15	83918727	83918944	+	0	NA	intron (NM_207517, intron 16 of 29)	L2a|LINE|L2	-161352	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.009217	0.389908	
chunk0096_206_1	chr2	30355741	30356223	+	0	NA	Intergenic	MIRb|SINE|MIR	9336	NR_122048	285043	Hs.429119	NR_122048		LINC01936	-	long intergenic non-protein coding RNA 1936	ncRNA	0.006224	0.496894	
chunk0069_387_1	chr15	67610438	67610838	+	0	NA	intron (NM_001206804, intron 8 of 21)	intron (NM_001206804, intron 8 of 21)	61634	NM_001206804	5607	Hs.114198	NM_002757	ENSG00000137764	MAP2K5	HsT17454|MAPKK5|MEK5|PRKMK5	mitogen-activated protein kinase kinase 5	protein-coding	0.012500	0.331671	
chunk0016_172_1	chr1	197947759	197947967	+	0	NA	Intergenic	Intergenic	30476	NM_020204	56956	Hs.442578	NM_020204	ENSG00000143355	LHX9	-	LIM homeobox 9	protein-coding	0.000000	0.377990	
chunk0072_72_1	chr15	90478902	90479533	+	0	NA	intron (NM_003870, intron 26 of 37)	Charlie10a|DNA|hAT-Charlie	-50669	NM_022769	64784	Hs.567572	NM_022769	ENSG00000140577	CRTC3	TORC-3|TORC3	CREB regulated transcription coactivator 3	protein-coding	0.009509	0.435127	
chunk0033_62_1	chr11	13480329	13481040	+	0	NA	Intergenic	L1PA5|LINE|L1	15336	NM_000315	5741	Hs.37045	NM_000315	ENSG00000152266	PTH	PTH1	parathyroid hormone	protein-coding	0.005626	0.507022	
chunk0201_178_1	chr9	36252183	36252852	+	0	NA	intron (NM_001128227, intron 1 of 11)	intron (NM_001128227, intron 1 of 11)	5982	NM_001190383	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.010463	0.352239	
chunk0055_165_1	chr13	60412788	60413636	+	0	NA	intron (NM_001146070, intron 1 of 13)	Charlie13b|DNA|hAT-Charlie	15919	NM_001146070	81550	Hs.525061	NM_030794	ENSG00000083544	TDRD3	-	tudor domain containing 3	protein-coding	0.004717	0.330978	
chunk0144_428_1	chr4	140728052	140728251	+	0	NA	intron (NM_015130, intron 1 of 20)	intron (NM_015130, intron 1 of 20)	28166	NM_015130	23158	Hs.480819	NM_015130	ENSG00000109436	TBC1D9	GRAMD9|MDR1	TBC1 domain family member 9	protein-coding	0.000000	0.380000	
chunk0066_291_1	chr15	35431284	35431759	+	0	NA	intron (NM_080650, intron 5 of 8)	intron (NM_080650, intron 5 of 8)	-59157	NR_037507	100500904		NR_037507	ENSG00000265102	MIR3942	-	microRNA 3942	ncRNA	0.002105	0.340336	
chunk0085_70_1	chr18	1464296	1464771	+	0	NA	Intergenic	Intergenic	-104904	NR_023926	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.006316	0.397059	234(AGGCACAGTTTGTTCC,-,0.00),235(GGCACAGTTTGTTCCT,+,0.00)
chunk0122_104_1	chr3	30518127	30518816	+	0	NA	Intergenic	Intergenic	-88031	NM_001024847	7048	Hs.82028	NM_003242	ENSG00000163513	TGFBR2	AAT3|FAA3|LDS1B|LDS2|LDS2B|MFS2|RIIC|TAAD2|TBR-ii|TBRII|TGFR-2|TGFbeta-RII	transforming growth factor beta receptor 2	protein-coding	0.005806	0.417391	261(AGGCACATTCCGTGCC,-,0.00),262(GGCACATTCCGTGCCT,+,0.00)
chunk0137_13_1	chr4	10706161	10706611	+	0	NA	Intergenic	Intergenic	-21624	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.002222	0.441242	
chunk0126_242_1	chr3	79345141	79345513	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	-66400	NR_110133	101927374	Hs.570644	NR_110133		LOC101927374	-	uncharacterized LOC101927374	ncRNA	0.005376	0.375335	
chunk0082_43_1	chr17	50944458	50944886	+	0	NA	Intergenic	CpG	-76694	NM_001243877	10140	Hs.703321	NM_005749	ENSG00000141232	TOB1	APRO5|APRO6|PIG49|TOB|TROB|TROB1	transducer of ERBB2, 1	protein-coding	0.112150	0.722611	
chunk0097_427_1	chr2	63378664	63378897	+	0	NA	intron (NR_122106, intron 5 of 11)	intron (NR_122106, intron 5 of 11)	59227	NR_122106	51057	Hs.414952	NM_015910	ENSG00000143951	WDPCP	BBS15|C2orf86|CHDTHP|CPLANE5|FRITZ|FRTZ	WD repeat containing planar cell polarity effector	protein-coding	0.000000	0.363248	
chunk0179_20_1	chr7	42669767	42670382	+	0	NA	intron (NR_110833, intron 2 of 2)	L1ME3E|LINE|L1	36373	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.001626	0.295455	282(CAGAACATTATGTACA,-,0.00),283(AGAACATTATGTACAA,+,0.00),312(AAGAACATTATGTACC,-,0.00),313(AGAACATTATGTACCA,+,0.00)
chunk0002_448_1	chr1	28457651	28458055	+	0	NA	intron (NM_023923, intron 1 of 12)	intron (NM_023923, intron 1 of 12)	19703	NM_023923	65979	Hs.225641	NM_023923	ENSG00000204138	PHACTR4	PPP1R124	phosphatase and actin regulator 4	protein-coding	0.002475	0.395062	
chunk0207_156_1	chr9	130045131	130045567	+	0	NA	Intergenic	Intergenic	-2155	NM_015033	23048	Hs.189409	NM_015033	ENSG00000187239	FNBP1	FBP17	formin binding protein 1	protein-coding	0.004587	0.393593	
chunk0100_418_1	chr2	119838068	119838454	+	0	NA	intron (NM_002830, intron 2 of 26)	L1PA11|LINE|L1	78630	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.012953	0.397933	
chunk0023_129_1	chr10	23827805	23828888	+	0	NA	intron (NM_001098500, intron 1 of 18)	intron (NM_001098500, intron 1 of 18)	133600	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.003693	0.427122	317(AGGAACAGGGTGTTCC,-,0.00),318(GGAACAGGGTGTTCCT,+,0.00),529(AGGGACTCCCTGCTCT,-,0.00)
chunk0101_206_1	chr2	130195087	130195604	+	0	NA	intron (NM_207312, intron 2 of 4)	intron (NM_207312, intron 2 of 4)	3116	NM_207312	112714	Hs.433336	NM_207312	ENSG00000152086	TUBA3E	-	tubulin alpha 3e	protein-coding	0.017408	0.469112	148(AGAGACAGTGTGTACT,-,0.00),149(GAGACAGTGTGTACTG,+,0.00),225(GAGCACATGCTGTTCA,-,0.00),226(AGCACATGCTGTTCAA,+,0.00)
chunk0079_423_1	chr17	19781338	19782075	+	0	NA	intron (NM_001142610, intron 23 of 27)	intron (NM_001142610, intron 23 of 27)	-33273	NM_000691	218	Hs.531682	NM_000691	ENSG00000108602	ALDH3A1	ALDH3|ALDHIII	aldehyde dehydrogenase 3 family member A1	protein-coding	0.010855	0.448509	
chunk0186_286_1	chr7	142375838	142376074	+	0	NA	Intergenic	Intergenic	-103707	NR_036483	207147	Hs.604069	NR_036483	ENSG00000186163	TRY2P	-	trypsinogen-like pseudogene	pseudo	0.000000	0.476793	
chunk0096_213_1	chr2	30509735	30510316	+	0	NA	intron (NM_001304445, intron 3 of 7)	intron (NM_001304445, intron 3 of 7)	62799	NM_001304446	253558	Hs.468048	NM_182551	ENSG00000172954	LCLAT1	1AGPAT8|AGPAT8|ALCAT1|HSRG1849|LYCAT|UNQ1849	lysocardiolipin acyltransferase 1	protein-coding	0.008606	0.427835	
chunk0130_366_1	chr3	139173464	139174208	+	0	NA	Intergenic	Intergenic	59686	NR_027070	140464	Hs.721270	NR_027070		PISRT1	NCRNA00195	PISRT1 lncRNA	ncRNA	0.010753	0.410738	
chunk0119_120_1	chr22	42658846	42659308	+	0	NA	Intergenic	L1M4|LINE|L1	-9678	NM_000398	1727	Hs.561064	NM_000398	ENSG00000100243	CYB5R3	B5R|DIA1	cytochrome b5 reductase 3	protein-coding	0.004329	0.419006	
chunk0073_191_1	chr16	9047586	9048100	+	0	NA	Intergenic	Intergenic	-43837	NM_014117	29035	Hs.221497	NM_014117	ENSG00000182831	C16orf72	PRO0149	chromosome 16 open reading frame 72	protein-coding	0.007782	0.510680	231(TGGGTCAGACTGTCCC,-,0.00),232(GGGTCAGACTGTCCCA,+,0.00)
chunk0200_98_1	chr9	16637169	16637648	+	0	NA	intron (NM_017637, intron 3 of 6)	intron (NM_017637, intron 3 of 6)	233380	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.002088	0.362500	
chunk0093_143_1	chr19	46600759	46601047	+	0	NA	promoter-TSS (NM_005184)	promoter-TSS (NM_005184)	297	NM_001205281	100506012	Hs.671661	NM_001205281	ENSG00000230510	PPP5D1	-	PPP5 tetratricopeptide repeat domain containing 1	protein-coding	0.086806	0.615917	
chunk0150_75_1	chr5	32168502	32168878	+	0	NA	intron (NM_022130, intron 1 of 3)	intron (NM_022130, intron 1 of 3)	5629	NM_022130	64083	Hs.408909	NM_022130	ENSG00000113384	GOLPH3	GOPP1|GPP34|MIDAS|Vps74	golgi phosphoprotein 3	protein-coding	0.013298	0.442971	154(AAGAACAGTCTGATCC,-,0.00),155(AGAACAGTCTGATCCA,+,0.00)
chunk0126_320_1	chr3	81590333	81590839	+	0	NA	intron (NM_000158, intron 9 of 15)	intron (NM_000158, intron 9 of 15)	171213	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.001976	0.327416	
chunk0171_130_1	chr6	122771029	122771826	+	0	NA	Intergenic	Intergenic	-8074	NM_001446	2173	Hs.26770	NM_001446	ENSG00000164434	FABP7	B-FABP|BLBP|FABPB|MRG	fatty acid binding protein 7	protein-coding	0.002509	0.370927	442(AAGAACAAAAAGTTCT,-,0.00),443(AGAACAAAAAGTTCTT,+,0.00)
chunk0020_361_1	chr1	239635068	239635736	+	0	NA	intron (NM_000740, intron 2 of 4)	L2a|LINE|L2	6329	NM_000740	1131	Hs.7138	NM_000740	ENSG00000133019	CHRM3	EGBRS|HM3|PBS	cholinergic receptor muscarinic 3	protein-coding	0.008982	0.390135	
chunk0125_358_1	chr3	71364729	71365298	+	0	NA	intron (NM_032682, intron 3 of 20)	MER58A|DNA|hAT-Charlie	-60253	NM_001244812	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.005272	0.340351	
chunk0052_286_1	chr12	124369080	124369610	+	0	NA	intron (NM_006312, intron 22 of 48)	intron (NM_006312, intron 22 of 48)	-32103	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.049057	0.638418	308(AGGAACACAGAGCTCC,-,0.00)
chunk0121_62_1	chr3	15712833	15713178	+	0	NA	intron (NM_015199, intron 10 of 27)	intron (NM_015199, intron 10 of 27)	-15634	NR_036085	100422990		NR_036085	ENSG00000264354	MIR3134	-	microRNA 3134	ncRNA	0.002899	0.329480	
chunk0199_205_1	chr9	4927819	4928112	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-57280	NM_004972	3717	Hs.656213	NM_004972	ENSG00000096968	JAK2	JTK10|THCYT3	Janus kinase 2	protein-coding	0.003413	0.312925	
chunk0148_172_1	chr5	7506394	7506635	+	0	NA	intron (NM_020546, intron 2 of 24)	intron (NM_020546, intron 2 of 24)	110284	NM_020546	108	Hs.481545	NM_020546	ENSG00000078295	ADCY2	AC2|HBAC2	adenylate cyclase 2	protein-coding	0.012448	0.351240	
chunk0107_9_1	chr2	209991437	209991858	+	0	NA	intron (NM_032504, intron 60 of 63)	intron (NM_032504, intron 60 of 63)	-10918	NM_006916	6120	Hs.282260	NM_006916	ENSG00000197713	RPE	RPE2-1	ribulose-5-phosphate-3-epimerase	protein-coding	0.007126	0.348341	
chunk0064_381_1	chr14	98822943	98823517	+	0	NA	Intergenic	MER58C|DNA|hAT-Charlie	111617	NM_182560	283598	Hs.448754	NM_182560	ENSG00000176605	C14orf177	-	chromosome 14 open reading frame 177	ncRNA	0.005226	0.377391	
chunk0095_257_1	chr2	19476172	19476942	+	0	NA	Intergenic	Intergenic	-117946	NM_145260	130497	Hs.123933	NM_145260	ENSG00000143867	OSR1	ODD	odd-skipped related transcription factor 1	protein-coding	0.002597	0.395590	
chunk0045_65_1	chr12	45479423	45480011	+	0	NA	Intergenic	HAL1ME|LINE|L1	187034	NM_001142678	196527	Hs.505339	NM_001025356	ENSG00000177119	ANO6	BDPLT7|SCTS|TMEM16F	anoctamin 6	protein-coding	0.000000	0.283531	
chunk0099_363_1	chr2	100832863	100833268	+	0	NA	intron (NM_002518, intron 1 of 20)	intron (NM_002518, intron 1 of 20)	12914	NM_002518	4862	Hs.156832	NM_002518	ENSG00000170485	NPAS2	MOP4|PASD4|bHLHe9	neuronal PAS domain protein 2	protein-coding	0.022222	0.472906	
chunk0058_162_1	chr14	23320665	23320898	+	0	NA	5' UTR (NM_004643, exon 1 of 7)	5' UTR (NM_004643, exon 1 of 7)	593	NM_004643	8106	Hs.707712	NM_004643	ENSG00000100836	PABPN1	OPMD|PAB2|PABII|PABP-2|PABP2	poly(A) binding protein nuclear 1	protein-coding	0.017167	0.517094	
chunk0134_362_1	chr3	182679900	182680428	+	0	NA	Intergenic	Intergenic	-113339	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.007576	0.374291	
chunk0053_353_1	chr13	34960589	34960956	+	0	NA	intron (NM_015678, intron 1 of 57)	Tigger3b|DNA|TcMar-Tigger	18485	NM_015678	26960	Hs.491172	NM_015678	ENSG00000172915	NBEA	BCL8B|LYST2	neurobeachin	protein-coding	0.000000	0.309783	
chunk0142_287_1	chr4	100074118	100074342	+	0	NA	Intergenic	L1MC1|LINE|L1	-115803	NR_125924	101929353	Hs.147584	NR_125924	ENSG00000249710	LOC101929353	-	uncharacterized LOC101929353	ncRNA	0.000000	0.346667	
chunk0192_68_1	chr8	60504961	60505249	+	0	NA	Intergenic	Arthur1|DNA|hAT-Tip100	-11805	NM_001242644	5862	Hs.369017	NM_002865	ENSG00000104388	RAB2A	LHX|RAB2	RAB2A, member RAS oncogene family	protein-coding	0.000000	0.304498	85(ATGAACTCTTTGTTCT,-,0.00),86(TGAACTCTTTGTTCTA,+,0.00)
chunk0077_245_1	chr16	80828509	80828729	+	0	NA	TTS (NR_131947)	TTS (NR_131947)	-24341	NM_152342	124359	Hs.60257	NM_152342	ENSG00000166446	CDYL2	PCCP1	chromodomain Y like 2	protein-coding	0.009091	0.393665	
chunk0041_209_1	chr11	126839530	126839779	+	0	NA	intron (NM_032531, intron 1 of 16)	intron (NM_032531, intron 1 of 16)	-101092	NR_046986	100874251	Hs.319053	NR_046986	ENSG00000254960	KIRREL3-AS2	-	KIRREL3 antisense RNA 2	ncRNA	0.020080	0.408000	
chunk0199_84_1	chr9	2603467	2603971	+	0	NA	intron (NR_015375, intron 1 of 3)	intron (NR_015375, intron 1 of 3)	-18074	NM_003383	7436	Hs.370422	NM_003383	ENSG00000147852	VLDLR	CAMRQ1|CARMQ1|CHRMQ1|VLDL-R|VLDLRCH	very low density lipoprotein receptor	protein-coding	0.003968	0.378218	
chunk0179_386_1	chr7	51315583	51315939	+	0	NA	intron (NM_001287436, intron 1 of 13)	CpG	1057	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.087079	0.596639	
chunk0077_367_1	chr16	84439377	84439843	+	0	NA	intron (NM_001291454, intron 10 of 23)	intron (NM_001291454, intron 10 of 23)	33022	NM_001291454	9914	Hs.6168	NM_014861	ENSG00000064270	ATP2C2	SPCA2	ATPase secretory pathway Ca2+ transporting 2	protein-coding	0.015021	0.396146	213(AAGCACACAATGTCTT,-,0.00),214(AGCACACAATGTCTTC,+,0.00)
chunk0048_442_1	chr12	88554310	88554627	+	0	NA	intron (NM_000899, intron 1 of 9)	intron (NM_000899, intron 1 of 9)	26005	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.006309	0.411950	
chunk0077_376_1	chr16	84619968	84620429	+	0	NA	Intergenic	Intergenic	-2102	NM_021149	23406	Hs.289092	NM_021149	ENSG00000103187	COTL1	CLP	coactosin like F-actin binding protein 1	protein-coding	0.006508	0.320346	
chunk0168_204_1	chr6	85642795	85643202	+	0	NA	promoter-TSS (NM_001159673)	promoter-TSS (NM_001159673)	-76	NM_001159673	10492	Hs.571177	NM_006372	ENSG00000135316	SYNCRIP	GRY-RBP|GRYRBP|HNRNPQ|HNRPQ1|NSAP1|PP68|hnRNP-Q	synaptotagmin binding cytoplasmic RNA interacting protein	protein-coding	0.093366	0.674020	
chunk0208_319_1	chrX	24090678	24091889	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	36335	NM_001415	1968	Hs.539684	NM_001415	ENSG00000130741	EIF2S3	EIF2|EIF2G|EIF2gamma|MEHMO|MRXSBRK|eIF-2gA	eukaryotic translation initiation factor 2 subunit gamma	protein-coding	0.007432	0.400990	
chunk0202_206_1	chr9	75715134	75715621	+	0	NA	Intergenic	Intergenic	-175267	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.006160	0.385246	
chunk0184_396_1	chr7	121676460	121676668	+	0	NA	Intergenic	LTR16B1|LTR|ERVL	-196541	NM_001206838	5803	Hs.489824	NM_002851	ENSG00000106278	PTPRZ1	HPTPZ|HPTPzeta|PTP-ZETA|PTP18|PTPRZ|PTPZ|R-PTP-zeta-2|RPTPB|RPTPbeta|phosphacan	protein tyrosine phosphatase receptor type Z1	protein-coding	0.004808	0.488038	
chunk0186_30_1	chr7	135970937	135971557	+	0	NA	intron (NM_001128619, intron 1 of 3)	intron (NM_001128619, intron 1 of 3)	6209	NM_145808	136319	Hs.602015	NM_145808	ENSG00000105887	MTPN	GCDP|V-1	myotrophin	protein-coding	0.001613	0.373591	
chunk0071_424_1	chr15	89809011	89809707	+	0	NA	intron (NM_001150, intron 1 of 20)	intron (NM_001150, intron 1 of 20)	5481	NM_001150	290	Hs.1239	NM_001150	ENSG00000166825	ANPEP	APN|CD13|GP150|LAP1|P150|PEPN	alanyl aminopeptidase, membrane	protein-coding	0.014368	0.593974	
chunk0003_132_1	chr1	32716602	32717040	+	0	NA	Intergenic	Intergenic	-14061	NM_030786	81493	Hs.712631	NM_030786	ENSG00000162520	SYNC	SYNC1|SYNCOILIN	syncoilin, intermediate filament protein	protein-coding	0.015982	0.578588	
chunk0101_38_1	chr2	122409418	122410358	+	0	NA	Intergenic	Intergenic	654343	NR_048559	7247	Hs.75066	NM_004622	ENSG00000211460	TSN	BCLF-1|C3PO|RCHF1|REHF-1|TBRBP|TRSLN	translin	protein-coding	0.002128	0.285866	
chunk0087_317_1	chr18	39719182	39719562	+	0	NA	intron (NR_024391, intron 2 of 3)	intron (NR_024391, intron 2 of 3)	32623	NR_024391	647946	Hs.649350	NR_024391	ENSG00000267374	MIR924HG	LINC00669	MIR924 host gene	ncRNA	0.002632	0.304462	
chunk0075_62_1	chr16	47848662	47848861	+	0	NA	TTS (NR_110649)	TTS (NR_110649)	-9820	NR_110650	101927132	Hs.589404	NR_110650	ENSG00000261231	LINC02133	-	long intergenic non-protein coding RNA 2133	ncRNA	0.005025	0.490000	
chunk0020_438_1	chr1	241979915	241980372	+	0	NA	Intergenic	Intergenic	18940	NM_001004343	440738	Hs.534971	NM_001004343	ENSG00000197769	MAP1LC3C	ATG8J|LC3C	microtubule associated protein 1 light chain 3 gamma	protein-coding	0.002188	0.425764	138(AGGCCCATCCTGTCCC,-,0.00)
chunk0114_333_1	chr21	17549806	17550150	+	0	NA	intron (NM_001207065, intron 2 of 2)	intron (NM_001207065, intron 2 of 2)	37072	NM_001207064	1525	Hs.627078	NM_001338	ENSG00000154639	CXADR	CAR|CAR4/6|HCAR	CXADR Ig-like cell adhesion molecule	protein-coding	0.014535	0.414493	
chunk0050_90_1	chr12	101782840	101783588	+	0	NA	intron (NM_024312, intron 5 of 20)	L2a|LINE|L2	-43742	NM_153694	50511	Hs.506504	NM_153694	ENSG00000139351	SYCP3	COR1|RPRGL4|SCP3|SPGF4	synaptonemal complex protein 3	protein-coding	0.008021	0.429907	
chunk0052_30_1	chr13	20526258	20526458	+	0	NA	promoter-TSS (NM_015974)	promoter-TSS (NM_015974)	-485	NM_015974	51084	Hs.370703	NM_015974	ENSG00000165475	CRYL1	GDH|HEL30|gul3DH|lambda-CRY	crystallin lambda 1	protein-coding	0.050000	0.552239	47(GAGCACACTCTGCACT,-,0.00),48(AGCACACTCTGCACTC,+,0.00)
chunk0206_135_1	chr9	121082382	121082698	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-5756	NM_007018	11064	Hs.653263	NM_007018	ENSG00000119397	CNTRL	CEP1|CEP110|FAN|bA165P4.1	centriolin	protein-coding	0.003165	0.365931	
chunk0019_434_1	chr1	230966414	230966915	+	0	NA	intron (NM_024525, intron 1 of 22)	intron (NM_024525, intron 1 of 22)	12208	NM_024525	79573	Hs.424788	NM_024525	ENSG00000143643	TTC13	-	tetratricopeptide repeat domain 13	protein-coding	0.009980	0.396414	
chunk0025_130_1	chr10	51911381	51911720	+	0	NA	intron (NM_006258, intron 5 of 17)	intron (NM_006258, intron 5 of 17)	-211955	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.000000	0.302941	
chunk0127_254_1	chr3	97198866	97199327	+	0	NA	intron (NM_001080448, intron 3 of 17)	intron (NM_001080448, intron 3 of 17)	-240497	NM_001278300	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.004338	0.374459	175(TAGAACACCAAGTACC,-,0.00),176(AGAACACCAAGTACCT,+,0.00)
chunk0113_262_1	chr20	56348125	56348825	+	0	NA	Intergenic	MER67C|LTR|ERV1	-10452	NM_080821	116151	Hs.143736	NM_080821	ENSG00000124098	FAM210B	5A3|C20orf108|dJ1167H4.1	family with sequence similarity 210 member B	protein-coding	0.012857	0.385164	425(GATAACACTGTGTTCT,-,0.00),426(ATAACACTGTGTTCTT,+,0.00)
chunk0071_358_1	chr15	88763037	88763670	+	0	NA	Intergenic	Intergenic	-40090	NM_013227	176	Hs.2159	NM_001135	ENSG00000157766	ACAN	AGC1|AGCAN|CSPG1|CSPGCP|MSK16|SEDK|SSOAOD	aggrecan	protein-coding	0.012638	0.490536	257(AGGAACAACATGTTTT,-,0.00),412(GGGGGCAGCTTGTTCT,-,0.00),413(GGGGCAGCTTGTTCTT,+,0.00)
chunk0017_319_1	chr1	211382778	211383006	+	0	NA	non-coding (NR_026761, exon 1 of 6)	non-coding (NR_026761, exon 1 of 6)	137	NR_026761	84791	Hs.523932	NM_032705		LINC00467	C1orf97	long intergenic non-protein coding RNA 467	ncRNA	0.109649	0.611354	
chunk0145_107_1	chr4	146174380	146175084	+	0	NA	promoter-TSS (NM_007080)	promoter-TSS (NM_007080)	-951	NM_007080	11157	Hs.190520	NM_007080	ENSG00000164167	LSM6	YDR378C	LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.009943	0.334752	
chunk0202_265_1	chr9	77009851	77010246	+	0	NA	Intergenic	Intergenic	-9607	NM_001013735	442425	Hs.553843	NM_001013735	ENSG00000204612	FOXB2	bA159H20.4	forkhead box B2	protein-coding	0.000000	0.287879	
chunk0073_227_1	chr16	11010739	11011824	+	0	NA	intron (NM_015226, intron 10 of 22)	L1MC4|LINE|L1	66793	NM_015226	23274	Hs.35490	NM_015226	ENSG00000038532	CLEC16A	Gop-1|KIAA0350	C-type lectin domain containing 16A	protein-coding	0.013825	0.425414	270(AGGCACATGATGTCCT,-,0.00),271(GGCACATGATGTCCTT,+,0.00),781(CATAACATGGTGTTCT,-,0.00),782(ATAACATGGTGTTCTG,+,0.00),887(GGGCACTGGATGTGCT,-,0.00),888(GGCACTGGATGTGCTC,+,0.00)
chunk0038_79_1	chr11	83161766	83161991	+	0	NA	intron (NM_015885, intron 2 of 15)	intron (NM_015885, intron 2 of 15)	4783	NM_015885	51585	Hs.128959	NM_015885	ENSG00000165494	PCF11	-	PCF11 cleavage and polyadenylation factor subunit	protein-coding	0.004444	0.358407	
chunk0065_299_1	chr14	102726183	102726742	+	0	NA	intron (NM_015156, intron 11 of 11)	intron (NM_015156, intron 11 of 11)	-51017	NM_145726	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.021467	0.503571	
chunk0206_433_1	chr9	127822074	127822856	+	0	NA	intron (NM_001114753, intron 8 of 14)	L1ME4c|LINE|L1	19284	NM_001018078	2356	Hs.335084	NM_004957	ENSG00000136877	FPGS	-	folylpolyglutamate synthase	protein-coding	0.006394	0.343550	206(TGGAACGCCATGTGCC,-,0.00),207(GGAACGCCATGTGCCT,+,0.00)
chunk0188_374_1	chr8	18234970	18235590	+	0	NA	Intergenic	Intergenic	13612	NM_001160174	9	Hs.591847	NM_000662	ENSG00000171428	NAT1	AAC1|MNAT|NAT-1|NATI	N-acetyltransferase 1	protein-coding	0.016129	0.376812	
chunk0100_162_1	chr2	109237012	109237753	+	0	NA	intron (NM_001099289, intron 1 of 9)	L1M5|LINE|L1	76243	NR_036224	100423027		NR_036224	ENSG00000265965	MIR4266	-	microRNA 4266	ncRNA	0.010796	0.366577	
chunk0044_169_1	chr12	29970562	29970761	+	0	NA	Intergenic	Intergenic	-185902	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.015075	0.385000	
chunk0127_388_1	chr3	102172800	102173349	+	0	NA	Intergenic	Intergenic	232215	NR_026934	152225	Hs.376768	NR_026934	ENSG00000214407	LINC02085	-	long intergenic non-protein coding RNA 2085	ncRNA	0.003643	0.332727	
chunk0023_50_1	chr10	21659018	21659217	+	0	NA	intron (NM_001195626, intron 8 of 21)	L1MD|LINE|L1	124472	NM_001195626	8028	Hs.30385	NM_004641	ENSG00000078403	MLLT10	AF10	MLLT10 histone lysine methyltransferase DOT1L cofactor	protein-coding	0.000000	0.320000	
chunk0117_322_1	chr22	24901580	24902046	+	0	NA	intron (NM_001039948, intron 20 of 25)	intron (NM_001039948, intron 20 of 25)	37534	NM_001001663	255349	Hs.329040	NM_001001663	ENSG00000206069	TMEM211	bA9F11.1	transmembrane protein 211	protein-coding	0.023605	0.520343	
chunk0031_118_1	chr10	124699966	124700345	+	0	NA	intron (NM_014661, intron 2 of 4)	intron (NM_014661, intron 2 of 4)	-3873	NR_120630	101927944	Hs.437448	NR_120630		FAM53B-AS1	-	FAM53B antisense RNA 1	ncRNA	0.015831	0.547368	
chunk0193_175_1	chr8	74916652	74917130	+	0	NA	Intergenic	MIRc|SINE|MIR	-67582	NM_031461	83690	Hs.436542	NM_031461	ENSG00000121005	CRISPLD1	CRISP-10|CRISP10|LCRISP1	cysteine rich secretory protein LCCL domain containing 1	protein-coding	0.004184	0.402923	333(AAGGACTCACTGTCCT,-,0.00),334(AGGACTCACTGTCCTT,+,0.00)
chunk0191_159_1	chr8	49148990	49149189	+	0	NA	Intergenic	Intergenic	76748	NM_001256597	492307	Hs.49890	NM_001007176	ENSG00000168333	PPDPFL	C8orf22	pancreatic progenitor cell differentiation and proliferation factor like	protein-coding	0.005025	0.435000	
chunk0166_27_1	chr6	42008588	42009176	+	0	NA	intron (NM_001136017, intron 1 of 4)	intron (NM_001136017, intron 1 of 4)	40012	NM_001287434	896	Hs.534307	NM_001760	ENSG00000112576	CCND3	-	cyclin D3	protein-coding	0.005102	0.444822	
chunk0003_311_1	chr1	37914767	37915110	+	0	NA	intron (NM_005540, intron 7 of 23)	intron (NM_005540, intron 7 of 23)	16853	NM_001297434	3633	Hs.449942	NM_005540	ENSG00000204084	INPP5B	5PTase	inositol polyphosphate-5-phosphatase B	protein-coding	0.005831	0.433140	
chunk0001_303_1	chr1	9110846	9111045	+	0	NA	intron (NM_024980, intron 2 of 3)	intron (NM_024980, intron 2 of 3)	18225	NM_024980	80045	Hs.632367	NM_024980	ENSG00000180758	GPR157	-	G protein-coupled receptor 157	protein-coding	0.020101	0.595000	
chunk0010_374_1	chr1	119185261	119185908	+	0	NA	intron (NR_125975, intron 4 of 6)	L1M2|LINE|L1	-44912	NM_201263	10352	Hs.523506	NM_015836	ENSG00000116874	WARS2	NEMMLAS|TrpRS|mtTrpRS	tryptophanyl tRNA synthetase 2, mitochondrial	protein-coding	0.004637	0.319444	
chunk0054_449_1	chr13	51427077	51427675	+	0	NA	intron (NM_001306091, intron 4 of 19)	intron (NM_001306091, intron 4 of 19)	25763	NM_012141	26512	Hs.439440	NM_012141	ENSG00000102786	INTS6	DBI-1|DDX26|DDX26A|DICE1|HDB|INT6|Notchl2	integrator complex subunit 6	protein-coding	0.008361	0.340568	
chunk0196_316_1	chr8	110666762	110667097	+	0	NA	Intergenic	Intergenic	360504	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.005970	0.276786	
chunk0086_383_1	chr18	26489973	26490236	+	0	NA	intron (NM_001142730, intron 2 of 4)	intron (NM_001142730, intron 2 of 4)	58432	NM_001142730	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.022814	0.481061	
chunk0030_263_1	chr10	116178286	116178601	+	0	NA	intron (NM_145793, intron 3 of 8)	intron (NM_145793, intron 3 of 8)	93864	NM_145793	2674	Hs.388347	NM_005264	ENSG00000151892	GFRA1	GDNFR|GDNFRA|GFR-ALPHA-1|RET1L|RETL1|TRNR1	GDNF family receptor alpha 1	protein-coding	0.022222	0.430380	
chunk0181_3_1	chr7	77600522	77601066	+	0	NA	exon (NM_002835, exon 8 of 18)	exon (NM_002835, exon 8 of 18)	62759	NM_001131008	5782	Hs.61812	NM_002835	ENSG00000127947	PTPN12	PTP-PEST|PTPG1	protein tyrosine phosphatase non-receptor type 12	protein-coding	0.003676	0.326606	182(CAGACCATGATGTTCC,-,0.00),183(AGACCATGATGTTCCT,+,0.00)
chunk0142_427_1	chr4	104571423	104571653	+	0	NA	intron (NR_125926, intron 1 of 9)	LTR33A_|LTR|ERVL	-76637	NM_025212	80319	Hs.12248	NM_025212	ENSG00000168772	CXXC4	IDAX	CXXC finger protein 4	protein-coding	0.000000	0.489177	
chunk0029_378_1	chr10	108665131	108665472	+	0	NA	Intergenic	Intergenic	-596008	NR_125760	103695365	Hs.648991	NR_125760	ENSG00000229981	LINC01435	TCONS_00018040	long intergenic non-protein coding RNA 1435	ncRNA	0.005865	0.391813	
chunk0066_127_1	chr15	31082918	31083225	+	0	NA	intron (NM_001252024, intron 1 of 27)	intron (NM_001252024, intron 1 of 27)	-17930	NR_029624	406993		NR_029624	ENSG00000207702	MIR211	MIRN211|mir-211	microRNA 211	ncRNA	0.019544	0.525974	
chunk0188_232_1	chr8	13186961	13187270	+	0	NA	intron (NM_182643, intron 5 of 17)	L2a|LINE|L2	-53815	NM_006094	10395	Hs.134296	NM_006094	ENSG00000164741	DLC1	ARHGAP7|HP|STARD12|p122-RhoGAP	DLC1 Rho GTPase activating protein	protein-coding	0.012945	0.441935	
chunk0140_194_1	chr4	70218201	70218616	+	0	NA	Intergenic	L2c|LINE|L2	-7663	NM_152997	260436	Hs.733448	NM_152997	ENSG00000181617	FDCSP	C4orf7|FDC-SP	follicular dendritic cell secreted protein	protein-coding	0.004819	0.353365	
chunk0108_90_1	chr2	227863977	227864505	+	0	NA	Intergenic	Intergenic	-7370	NM_178821	164781	Hs.424594	NM_178821	ENSG00000123977	DAW1	ODA16|WDR69	dynein assembly factor with WD repeats 1	protein-coding	0.017045	0.442344	254(GTGGACAAGGTGTTCT,-,0.00),255(TGGACAAGGTGTTCTT,+,0.00)
chunk0060_457_1	chr14	55126879	55127601	+	0	NA	Intergenic	Intergenic	-1977	NM_001177388	3958	Hs.531081	NM_002306	ENSG00000131981	LGALS3	CBP35|GAL3|GALBP|GALIG|L31|LGALS2|MAC2	galectin 3	protein-coding	0.011080	0.416321	501(AGGCACACCCTGATCA,-,0.00),502(GGCACACCCTGATCAT,+,0.00)
chunk0152_383_1	chr5	64538789	64539307	+	0	NA	intron (NM_001029875, intron 2 of 5)	L1ME1|LINE|L1	33101	NM_001029875	401190	Hs.657133	NM_001029875	ENSG00000186479	RGS7BP	R7BP	regulator of G protein signaling 7 binding protein	protein-coding	0.005792	0.358382	
chunk0184_152_1	chr7	116211308	116211882	+	0	NA	intron (NM_015641, intron 1 of 6)	intron (NM_015641, intron 1 of 6)	1102	NM_015641	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.029617	0.453913	
chunk0093_65_1	chr19	40453300	40453537	+	0	NA	intron (NM_000713, intron 3 of 4)	L2a|LINE|L2	-9043	NM_203344	29946	Hs.515412	NM_013368	ENSG00000167565	SERTAD3	RBT1	SERTA domain containing 3	protein-coding	0.004219	0.453782	
chunk0048_380_1	chr12	86462662	86463010	+	0	NA	intron (NM_013244, intron 1 of 6)	MLT2A2|LTR|ERVL	376068	NM_013244	25834	Hs.589093	NM_013244	ENSG00000182050	MGAT4C	GNTIVH|HGNT-IV-H	MGAT4 family member C	protein-coding	0.017241	0.464183	
chunk0004_447_1	chr1	53295694	53296415	+	0	NA	intron (NM_001018054, intron 2 of 17)	intron (NM_001018054, intron 2 of 17)	32095	NM_017522	7804	Hs.280387	NM_004631	ENSG00000157193	LRP8	APOER2|HSZ75190|LRP-8|MCI1	LDL receptor related protein 8	protein-coding	0.008322	0.518006	311(TAGAACAAAGTGTTCA,-,0.00),312(AGAACAAAGTGTTCAC,+,0.00)
chunk0059_66_1	chr14	30296030	30296515	+	0	NA	Intergenic	Intergenic	-262851	NM_001308097	55632	Hs.509008	NM_017769	ENSG00000092140	G2E3	KIAA1333|PHF7B	G2/M-phase specific E3 ubiquitin protein ligase	protein-coding	0.002062	0.434156	
chunk0093_445_1	chr19	58407010	58407246	+	0	NA	Intergenic	Intergenic	-1568	NM_173548	201514	Hs.439551	NM_173548	ENSG00000171574	ZNF584	-	zinc finger protein 584	protein-coding	0.008475	0.544304	
chunk0142_24_1	chr4	90465493	90466149	+	0	NA	intron (NM_001145065, intron 4 of 10)	Tigger6b|DNA|TcMar-Tigger	230790	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.003049	0.327245	
chunk0130_305_1	chr3	136989754	136990181	+	0	NA	intron (NM_144717, intron 4 of 6)	intron (NM_144717, intron 4 of 6)	32102	NM_144717	53833	Hs.61232	NM_144717	ENSG00000174564	IL20RB	DIRS1|FNDC6|IL-20R2	interleukin 20 receptor subunit beta	protein-coding	0.002342	0.523364	
chunk0180_156_1	chr7	64533670	64534351	+	0	NA	intron (NM_001130022, intron 3 of 3)	L1PB1|LINE|L1	29117	NM_001130022	340252	Hs.520886	NM_178558	ENSG00000173041	ZNF680	-	zinc finger protein 680	protein-coding	0.007342	0.351906	116(CAGAACAGCATGTTAC,-,0.00),117(AGAACAGCATGTTACT,+,0.00)
chunk0207_392_1	chr9	136630916	136631423	+	0	NA	Intergenic	(ACAC)n|Simple_repeat|Simple_repeat	-27687	NR_046367	51162	Hs.91481	NM_016215	ENSG00000172889	EGFL7	NEU1|VE-STATIN|ZNEU1	EGF like domain multiple 7	protein-coding	0.043393	0.505906	
chunk0063_41_1	chr14	76848986	76849185	+	0	NA	intron (NM_194287, intron 7 of 13)	L2a|LINE|L2	22703	NM_194287	145497	Hs.147276	NM_194287	ENSG00000100565	LRRC74A	C14orf166B|LRRC74	leucine rich repeat containing 74A	protein-coding	0.010050	0.445000	148(TGAGACAGACTGTGCT,-,0.00),149(GAGACAGACTGTGCTC,+,0.00)
chunk0040_21_1	chr11	109077261	109077689	+	0	NA	Intergenic	Intergenic	-344645	NM_207645	399947	Hs.172982	NM_207645	ENSG00000185742	C11orf87	LOH11CR1A|NEURIM1	chromosome 11 open reading frame 87	protein-coding	0.007009	0.438228	
chunk0101_265_1	chr2	133489502	133490199	+	0	NA	intron (NM_207481, intron 3 of 17)	intron (NM_207481, intron 3 of 17)	78610	NM_207363	344148	Hs.537329	NM_207363	ENSG00000176771	NCKAP5	ERIH1|ERIH2|NAP5	NCK associated protein 5	protein-coding	0.004304	0.422636	
chunk0149_67_1	chr5	17083761	17084101	+	0	NA	Intergenic	Intergenic	-132892	NM_001271606	10409	Hs.201641	NM_006317	ENSG00000176788	BASP1	CAP-23|CAP23|NAP-22|NAP22	brain abundant membrane attached signal protein 1	protein-coding	0.002941	0.369501	
chunk0099_73_1	chr2	85215270	85215969	+	0	NA	intron (NM_031283, intron 3 of 11)	intron (NM_031283, intron 3 of 11)	82159	NM_031283	83439	Hs.516297	NM_031283	ENSG00000152284	TCF7L1	TCF-3|TCF3	transcription factor 7 like 1	protein-coding	0.021459	0.517143	
chunk0004_22_1	chr1	42264163	42264642	+	0	NA	intron (NM_014947, intron 4 of 12)	intron (NM_014947, intron 4 of 12)	70563	NM_001198851	22887	Hs.26023	NM_014947	ENSG00000198815	FOXJ3	-	forkhead box J3	protein-coding	0.002088	0.358333	
chunk0153_256_1	chr5	72680881	72681234	+	0	NA	Intergenic	L1MA4A|LINE|L1	-20388	NR_105007	102477328	Hs.254516	NR_105007	ENSG00000248371	LINC02056	-	long intergenic non-protein coding RNA 2056	ncRNA	0.002833	0.533898	
chunk0033_336_1	chr11	22681543	22681931	+	0	NA	intron (NM_177553, intron 2 of 7)	intron (NM_177553, intron 2 of 7)	6964	NM_005256	2620	Hs.711297	NM_005256	ENSG00000148935	GAS2	GAS-2	growth arrest specific 2	protein-coding	0.000000	0.287918	233(CTACACAGCCTGTTCT,-,0.00),234(TACACAGCCTGTTCTT,+,0.00)
chunk0125_284_1	chr3	69761827	69762454	+	0	NA	intron (NM_198159, intron 1 of 9)	intron (NM_198159, intron 1 of 9)	-1416	NM_001184967	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.000000	0.335987	
chunk0045_143_1	chr12	46464353	46464624	+	0	NA	intron (NR_125378, intron 3 of 3)	intron (NR_125378, intron 3 of 3)	80381	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.003690	0.345588	
chunk0011_135_1	chr1	147231111	147231690	+	0	NA	Intergenic	L1PA4|LINE|L1	-5762	NM_001144830	2330	Hs.642706	NM_001461	ENSG00000131781	FMO5	-	flavin containing dimethylaniline monoxygenase 5	protein-coding	0.005181	0.406897	84(TGGTACACTGTGTCTT,-,0.00),85(GGTACACTGTGTCTTT,+,0.00),168(AGGAACAGGTTGTTCA,-,0.00),169(GGAACAGGTTGTTCAG,+,0.00)
chunk0104_166_1	chr2	174312615	174312891	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-13274	NR_038897	285084	Hs.275398	NR_038897	ENSG00000231453	LINC01305	-	long intergenic non-protein coding RNA 1305	ncRNA	0.000000	0.400722	35(GAGAACAGACTGGCCT,-,0.00),36(AGAACAGACTGGCCTT,+,0.00)
chunk0151_349_1	chr5	54383888	54384389	+	0	NA	intron (NR_126379, intron 1 of 4)	LTR24|LTR|ERV1	63194	NR_126379	104355136	Hs.559024	NR_126379	ENSG00000249069	LINC01033	-	long intergenic non-protein coding RNA 1033	ncRNA	0.005988	0.378486	
chunk0084_4_1	chr18	110522	110738	+	0	NA	intron (NR_033770, intron 1 of 4)	BSR/Beta|Satellite|Satellite	1565	NR_033770	727758	Hs.585843	NR_033770	ENSG00000263006	ROCK1P1	ROCK1P	Rho associated coiled-coil containing protein kinase 1 pseudogene 1	pseudo	0.000000	0.470046	
chunk0099_12_1	chr2	82797559	82797821	+	0	NA	Intergenic	MER101B|LTR|ERV1	-59113	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.007634	0.471483	188(AGCACACAGAGTACAT,+,0.00)
chunk0185_235_1	chr7	129401371	129401710	+	0	NA	intron (NM_001130723, intron 6 of 16)	intron (NM_001130723, intron 6 of 16)	25897	NM_001130722	23382	Hs.600789	NM_015328	ENSG00000158467	AHCYL2	ADOHCYASE3|IRBIT2	adenosylhomocysteinase like 2	protein-coding	0.000000	0.494118	
chunk0084_293_1	chr17	79948840	79949060	+	0	NA	exon (NM_001271846, exon 4 of 7)	exon (NM_001271846, exon 4 of 7)	1907	NM_001271846	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.050000	0.606335	68(AAGAACTGGTTGTTCC,-,0.00),69(AGAACTGGTTGTTCCG,+,0.00),131(CAGAACGCTCTGTGCT,-,0.00),132(AGAACGCTCTGTGCTC,+,0.00)
chunk0055_106_1	chr13	56568803	56569206	+	0	NA	Intergenic	Intergenic	-571914	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.009926	0.287129	
chunk0073_44_1	chr16	2928311	2928602	+	0	NA	intron (NM_001308068, intron 2 of 9)	LTR5B|LTR|ERVK	16477	NM_001308068	84256	Hs.655321	NM_020912	ENSG00000059122	FLYWCH1	-	FLYWCH-type zinc finger 1	protein-coding	0.003436	0.486301	126(CAGTGCATTGTGTCCC,-,0.00),127(AGTGCATTGTGTCCCT,+,0.00)
chunk0047_68_1	chr12	67675752	67676105	+	0	NA	Intergenic	Intergenic	27196	NM_003583	8445	Hs.173135	NM_003583	ENSG00000127334	DYRK2	-	dual specificity tyrosine phosphorylation regulated kinase 2	protein-coding	0.000000	0.333333	
chunk0009_304_1	chr1	108045410	108045978	+	0	NA	Intergenic	Intergenic	-80771	NM_006113	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.017606	0.463972	222(CTGCACACCGTGTGCT,-,0.00),223(TGCACACCGTGTGCTG,+,0.00)
chunk0114_76_1	chr21	9193351	9193550	+	0	NA	Intergenic	Intergenic	-63689	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.005025	0.390000	
chunk0014_236_1	chr1	179921320	179921699	+	0	NA	Intergenic	Intergenic	-33264	NM_014810	9857	Hs.413045	NM_014810	ENSG00000135837	CEP350	CAP350|GM133	centrosomal protein 350	protein-coding	0.005277	0.392105	
chunk0049_155_1	chr12	91952728	91953664	+	0	NA	Intergenic	MIR3|SINE|MIR	188517	NR_046159	256021	Hs.651357	NM_001256373	ENSG00000257242	LINC01619	C12orf79	long intergenic non-protein coding RNA 1619	ncRNA	0.000000	0.359658	
chunk0187_98_1	chr8	4547757	4548371	+	0	NA	intron (NM_033225, intron 2 of 69)	intron (NM_033225, intron 2 of 69)	446742	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.016287	0.354472	
chunk0144_288_1	chr4	138241132	138241873	+	0	NA	intron (NM_014331, intron 1 of 11)	intron (NM_014331, intron 1 of 11)	847	NM_014331	23657	Hs.390594	NM_014331	ENSG00000151012	SLC7A11	CCBR1|xCT	solute carrier family 7 member 11	protein-coding	0.017544	0.448787	235(CTGAACACTCCGTTCT,-,0.00),236(TGAACACTCCGTTCTA,+,0.00)
chunk0154_179_1	chr5	80038622	80039244	+	0	NA	intron (NM_001306214, intron 1 of 21)	L1ME4a|LINE|L1	2910	NM_001306214	7060	Hs.211426	NM_003248	ENSG00000113296	THBS4	TSP-4|TSP4	thrombospondin 4	protein-coding	0.004823	0.319422	248(TGGTACAGAGAGTGCC,-,0.00),249(GGTACAGAGAGTGCCC,+,0.00)
chunk0018_156_1	chr1	218828104	218828574	+	0	NA	intron (NR_031644, intron 6 of 6)	intron (NR_031644, intron 6 of 6)	345449	NR_038845	643723	Hs.519774	NR_038845		LYPLAL1-DT	LYPLAL1-AS1	LYPLAL1 divergent transcript	ncRNA	0.006383	0.373673	
chunk0165_337_1	chr6	37550547	37550746	+	0	NA	Intergenic	Intergenic	4776	NR_039669	100616413		NR_039669	ENSG00000263926	MIR4462	-	microRNA 4462	ncRNA	0.015075	0.505000	127(GGCACGCTATGTGCTG,+,0.00)
chunk0198_181_1	chr8	133360161	133360757	+	0	NA	Intergenic	Intergenic	-63155	NM_006096	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.010067	0.458961	368(AGTAACAGACTGTTCA,-,0.00),369(GTAACAGACTGTTCAC,+,0.00)
chunk0139_437_1	chr4	64605443	64605873	+	0	NA	Intergenic	L1P4|LINE|L1	-196198	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.002326	0.310905	
chunk0116_448_1	chr21	43627555	43627796	+	0	NA	intron (NM_007031, intron 6 of 8)	intron (NM_007031, intron 6 of 8)	-17686	NR_106718	102464825		NR_106718	ENSG00000278433	MIR6070	hsa-mir-6070	microRNA 6070	ncRNA	0.008299	0.400826	
chunk0176_126_1	chr7	12267438	12267958	+	0	NA	Intergenic	Intergenic	56476	NM_018374	54664	Hs.396358	NM_018374	ENSG00000106460	TMEM106B	HLD16	transmembrane protein 106B	protein-coding	0.001923	0.353167	
chunk0200_275_1	chr9	22144244	22144609	+	0	NA	Intergenic	L1MC3|LINE|L1	-135113	NM_078487	1030	Hs.72901	NM_004936	ENSG00000147883	CDKN2B	CDK4I|INK4B|MTS2|P15|TP15|p15INK4b	cyclin dependent kinase inhibitor 2B	protein-coding	0.002740	0.387978	
chunk0151_251_1	chr5	51853589	51854120	+	0	NA	Intergenic	Intergenic	-470522	NR_046243	642366	Hs.544139	NR_046243		LOC642366	-	uncharacterized LOC642366	ncRNA	0.007533	0.362782	117(CAGGGCATGATGTGCT,-,0.00),118(AGGGCATGATGTGCTC,+,0.00)
chunk0141_319_1	chr4	87241347	87241793	+	0	NA	Intergenic	L1MB7|LINE|L1	-20962	NM_001292007	57563	Hs.106601	NM_020803	ENSG00000145332	KLHL8	-	kelch like family member 8	protein-coding	0.002242	0.427293	
chunk0035_227_1	chr11	45696968	45697625	+	0	NA	Intergenic	Intergenic	-5520	NR_106976	102465691		NR_106976	ENSG00000276639	MIR7154	hsa-mir-7154	microRNA 7154	ncRNA	0.004566	0.496960	
chunk0031_331_1	chr10	129338638	129338908	+	0	NA	Intergenic	Intergenic	-128411	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.003704	0.354244	121(TGGGACAAAGAGTTCT,-,0.00),122(GGGACAAAGAGTTCTC,+,0.00)
chunk0009_441_1	chr1	111401529	111401793	+	0	NA	Intergenic	Intergenic	-11810	NR_029429	441897	Hs.568387	NR_029429	ENSG00000227179	PGCP1	-	progastricsin pseudogene 1	pseudo	0.007576	0.437736	
chunk0134_368_1	chr3	182706701	182707216	+	0	NA	Intergenic	L1MEg|LINE|L1	-86545	NM_014616	23200	Hs.478429	NM_014616	ENSG00000058063	ATP11B	ATPIF|ATPIR	ATPase phospholipid transporting 11B (putative)	protein-coding	0.001942	0.271318	
chunk0127_440_1	chr3	103252658	103253575	+	0	NA	Intergenic	Intergenic	271000	NR_039611	100616336		NR_039611	ENSG00000265328	MIR548AB	-	microRNA 548ab	ncRNA	0.007634	0.359477	
chunk0089_425_1	chr18	69862030	69862256	+	0	NA	TTS (NM_006566)	TTS (NM_006566)	85710	NM_001303618	10666	Hs.660130	NM_006566	ENSG00000150637	CD226	DNAM-1|DNAM1|PTA1|TLiSA1	CD226 molecule	protein-coding	0.000000	0.374449	
chunk0170_456_1	chr6	119327015	119327463	+	0	NA	intron (NM_005907, intron 2 of 12)	MLT1E2|LTR|ERVL-MaLR	22527	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.011161	0.440980	
chunk0078_344_1	chr16	86180650	86180990	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	-15361	NR_103859	100506542	Hs.111902	NR_103859	ENSG00000269186	LINC01082	TCONS_00024492	long intergenic non-protein coding RNA 1082	ncRNA	0.008824	0.445748	
chunk0102_172_1	chr2	147515277	147515632	+	0	NA	Intergenic	Intergenic	-329063	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002817	0.376404	
chunk0041_322_1	chr11	130181225	130181874	+	0	NA	intron (NM_021978, intron 1 of 18)	intron (NM_021978, intron 1 of 18)	21762	NM_021978	6768	Hs.504315	NM_021978	ENSG00000149418	ST14	ARCI11|HAI|MT-SP1|MTSP1|PRSS14|SNC19|TADG15|TMPRSS14	suppression of tumorigenicity 14	protein-coding	0.010786	0.495385	
chunk0096_265_1	chr2	31558115	31558716	+	0	NA	intron (NM_000348, intron 1 of 4)	MLT1C|LTR|ERVL-MaLR	22556	NM_000348	6716	Hs.458345	NM_000348	ENSG00000277893	SRD5A2	-	steroid 5 alpha-reductase 2	protein-coding	0.006656	0.430233	
chunk0121_336_1	chr3	24476011	24476216	+	0	NA	intron (NM_001128176, intron 1 of 10)	intron (NM_001128176, intron 1 of 10)	-17974	NR_046244	644990	Hs.631912	NR_046244		THRB-AS1	-	THRB antisense RNA 1	ncRNA	0.004878	0.519417	
chunk0122_39_1	chr3	28139202	28139667	+	0	NA	Intergenic	MER70A|LTR|ERVL	-102199	NM_182523	152100	Hs.444724	NM_182523	ENSG00000187118	CMC1	C3orf68	C-X9-C motif containing 1	protein-coding	0.010753	0.444206	260(TAGAACAGGATGTTCT,-,0.00),261(AGAACAGGATGTTCTG,+,0.00)
chunk0120_99_1	chr3	4416894	4417214	+	0	NA	intron (NM_182760, intron 6 of 8)	intron (NM_182760, intron 6 of 8)	50228	NM_182760	285362	Hs.350475	NM_182760	ENSG00000144455	SUMF1	AAPA3037|FGE|UNQ3037	sulfatase modifying factor 1	protein-coding	0.018750	0.454829	
chunk0032_273_1	chr11	9088871	9089599	+	0	NA	intron (NM_020974, intron 2 of 21)	intron (NM_020974, intron 2 of 21)	1144	NR_049874	100847015		NR_049874	ENSG00000264984	MIR5691	-	microRNA 5691	ncRNA	0.005495	0.499314	
chunk0167_305_1	chr6	71411763	71412030	+	0	NA	non-coding (NR_121614, exon 3 of 3)	non-coding (NR_121614, exon 3 of 3)	-8275	NR_029504	407029		NR_029504	ENSG00000207827	MIR30A	MIRN30A|mir-30a	microRNA 30a	ncRNA	0.000000	0.309701	
chunk0071_352_1	chr15	88624881	88625237	+	0	NA	intron (NM_022767, intron 1 of 3)	intron (NM_022767, intron 1 of 3)	3763	NM_022767	64782	Hs.436102	NM_022767	ENSG00000181026	AEN	ISG20L1|pp12744	apoptosis enhancing nuclease	protein-coding	0.014045	0.425770	
chunk0152_21_1	chr5	56441531	56441843	+	0	NA	Intergenic	Intergenic	40082	NR_104664	102467147	Hs.650177	NR_104664	ENSG00000248727	LINC01948	-	long intergenic non-protein coding RNA 1948	ncRNA	0.006410	0.402556	147(AGACACACTGTGTACT,-,0.00),148(GACACACTGTGTACTC,+,0.00)
chunk0097_90_1	chr2	45465914	45466513	+	0	NA	intron (NM_018079, intron 16 of 20)	intron (NM_018079, intron 16 of 20)	145081	NM_018079	55133	Hs.14229	NM_018079	ENSG00000068784	SRBD1	-	S1 RNA binding domain 1	protein-coding	0.001669	0.425000	
chunk0113_268_1	chr20	56418559	56419038	+	0	NA	intron (NM_001164114, intron 1 of 5)	intron (NM_001164114, intron 1 of 5)	6540	NM_001164115	57091	Hs.473144	NM_020356	ENSG00000087589	CASS4	C20orf32|CAS4|HEFL|HEPL	Cas scaffold protein family member 4	protein-coding	0.018789	0.416667	223(AGGAACACAATGTACC,-,0.00),224(GGAACACAATGTACCT,+,0.00)
chunk0012_364_1	chr1	162905145	162905475	+	0	NA	Intergenic	Intergenic	-36495	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.003030	0.471299	
chunk0050_24_1	chr12	99940906	99941463	+	0	NA	intron (NM_152788, intron 1 of 25)	intron (NM_152788, intron 1 of 25)	43470	NM_152788	56899	Hs.506458	NM_020140	ENSG00000185046	ANKS1B	AIDA|AIDA-1|ANKS2|EB-1|EB1|cajalin-2	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding	0.003591	0.340502	
chunk0163_226_1	chr6	12188734	12189142	+	0	NA	Intergenic	L1M5|LINE|L1	-101358	NM_001955	1906	Hs.511899	NM_001955	ENSG00000078401	EDN1	ARCND3|ET1|HDLCQ7|PPET1|QME	endothelin 1	protein-coding	0.004902	0.251834	
chunk0088_101_1	chr18	45003402	45003642	+	0	NA	intron (NM_015559, intron 4 of 5)	intron (NM_015559, intron 4 of 5)	-33356	NR_036203	100422829		NR_036203	ENSG00000265957	MIR4319	-	microRNA 4319	ncRNA	0.012500	0.464730	
chunk0096_347_1	chr2	35665511	35665887	+	0	NA	Intergenic	L2a|LINE|L2	194294	NR_039629	100616475		NR_039629	ENSG00000265301	MIR548AD	-	microRNA 548ad	ncRNA	0.000000	0.307692	
chunk0140_426_1	chr4	76036036	76036235	+	0	NA	promoter-TSS (NM_005409)	promoter-TSS (NM_005409)	62	NM_001302123	6373	Hs.632592	NM_005409	ENSG00000169248	CXCL11	H174|I-TAC|IP-9|IP9|SCYB11|SCYB9B|b-R1	C-X-C motif chemokine ligand 11	protein-coding	0.000000	0.385000	
chunk0143_78_1	chr4	108153486	108154094	+	0	NA	intron (NM_016269, intron 3 of 11)	L1ME4a|LINE|L1	13007	NM_001166119	51176	Hs.743478	NM_016269	ENSG00000138795	LEF1	LEF-1|TCF10|TCF1ALPHA|TCF7L3	lymphoid enhancer binding factor 1	protein-coding	0.003289	0.297209	
chunk0083_14_1	chr17	62943506	62943903	+	0	NA	promoter-TSS (NR_030363)	promoter-TSS (NR_030363)	-511	NR_030363	693218		NR_030363	ENSG00000207552	MIR633	MIRN633|hsa-mir-633	microRNA 633	ncRNA	0.005038	0.464824	
chunk0003_138_1	chr1	32817238	32817639	+	0	NA	promoter-TSS (NM_001256121)	promoter-TSS (NM_001256121)	-4	NM_001256121	64766	Hs.440880	NM_022753	ENSG00000116497	S100PBP	S100PBPR	S100P binding protein	protein-coding	0.084788	0.694030	
chunk0068_314_1	chr15	57377529	57377772	+	0	NA	intron (NM_032866, intron 1 of 18)	intron (NM_032866, intron 1 of 18)	1145	NM_001252335	84952	Hs.148989	NM_032866	ENSG00000128849	CGNL1	JACOP|PCING	cingulin like 1	protein-coding	0.004115	0.467213	
chunk0128_355_1	chr3	113010771	113011195	+	0	NA	intron (NR_027794, intron 5 of 7)	intron (NR_027794, intron 5 of 7)	8725	NR_027794									0.000000	0.315294	
chunk0074_1_1	chr16	19532772	19533253	+	0	NA	intron (NM_001199022, intron 3 of 14)	intron (NM_001199022, intron 3 of 14)	9155	NM_001199022	9738	Hs.279912	NM_014711	ENSG00000103540	CCP110	CP110|Cep110	centriolar coiled-coil protein 110	protein-coding	0.008316	0.290456	
chunk0086_21_1	chr18	12291747	12292006	+	0	NA	Intergenic	Intergenic	-15793	NM_001303524	84617	Hs.193491	NM_032525	ENSG00000176014	TUBB6	FPVEPD|HsT1601|TUBB-5	tubulin beta 6 class V	protein-coding	0.042471	0.569231	
chunk0048_448_1	chr12	88684528	88685051	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-104316	NM_003994	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.003824	0.438931	
chunk0062_456_1	chr14	75761664	75761910	+	0	NA	intron (NM_015072, intron 18 of 31)	L1ME2z|LINE|L1	100579	NM_015072	23093	Hs.709609	NM_015072	ENSG00000119685	TTLL5	CORD19|KIAA0998|STAMP	tubulin tyrosine ligase like 5	protein-coding	0.008130	0.352227	
chunk0180_398_1	chr7	74716620	74716975	+	0	NA	intron (NM_033001, intron 10 of 33)	intron (NM_033001, intron 10 of 33)	12121	NR_110044	101926943	Hs.654772	NR_110044	ENSG00000232729	LOC101926943	-	uncharacterized LOC101926943	ncRNA	0.005634	0.308989	
chunk0050_427_1	chr12	110034401	110034613	+	0	NA	intron (NM_033121, intron 13 of 14)	FAM|SINE|Alu	33188	NM_207435	400073	Hs.44817	NM_207435	ENSG00000174456	C12orf76	-	chromosome 12 open reading frame 76	protein-coding	0.009434	0.521127	
chunk0044_419_1	chr12	41923150	41923919	+	0	NA	Intergenic	Intergenic	221337	NM_173601	283464	Hs.259347	NM_173601	ENSG00000151233	GXYLT1	GLT8D3	glucoside xylosyltransferase 1	protein-coding	0.006502	0.351948	
chunk0100_412_1	chr2	119756919	119757770	+	0	NA	Intergenic	Charlie29a|DNA|hAT-Charlie	-2287	NM_002830	5775	Hs.469809	NM_002830	ENSG00000088179	PTPN4	MEG|PTPMEG|PTPMEG1	protein tyrosine phosphatase non-receptor type 4	protein-coding	0.008226	0.381455	
chunk0006_159_1	chr1	66368462	66368986	+	0	NA	intron (NM_001037339, intron 8 of 9)	intron (NM_001037339, intron 8 of 9)	14346	NM_001297442	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.019084	0.401905	
chunk0013_189_1	chr1	169108919	169109653	+	0	NA	intron (NM_001677, intron 1 of 5)	intron (NM_001677, intron 1 of 5)	2577	NM_001677	481	Hs.291196	NM_001677	ENSG00000143153	ATP1B1	ATP1B	ATPase Na+/K+ transporting subunit beta 1	protein-coding	0.017711	0.458503	
chunk0002_442_1	chr1	28248306	28248505	+	0	NA	Intergenic	MIR3|SINE|MIR	-11047	NM_031459	83667	Hs.469543	NM_031459	ENSG00000130766	SESN2	HI95|SES2|SEST2	sestrin 2	protein-coding	0.015075	0.510000	
chunk0067_263_1	chr15	45855276	45855475	+	0	NA	Intergenic	Intergenic	220635	NM_021199	58472	Hs.511251	NM_021199	ENSG00000137767	SQOR	CGI-44|PRO1975|SQR|SQRDL	sulfide quinone oxidoreductase	protein-coding	0.005025	0.480000	
chunk0038_260_1	chr11	88948546	88949065	+	0	NA	intron (NM_001143831, intron 1 of 8)	intron (NM_001143831, intron 1 of 8)	99267	NM_001143831	2915	Hs.147361	NM_000842	ENSG00000168959	GRM5	GPRC1E|MGLUR5|PPP1R86|mGlu5	glutamate metabotropic receptor 5	protein-coding	0.005780	0.330769	
chunk0134_431_1	chr3	183468063	183468575	+	0	NA	Intergenic	Intergenic	20668	NR_038301	100505687	Hs.551751	NR_038301	ENSG00000240024	LINC00888	-	long intergenic non-protein coding RNA 888	ncRNA	0.003906	0.356725	
chunk0182_157_1	chr7	95432146	95432499	+	0	NA	intron (NM_001018161, intron 1 of 8)	AluJr|SINE|Alu	2750	NM_000305	5445	Hs.514420	NM_000305	ENSG00000105854	PON2	-	paraoxonase 2	protein-coding	0.002833	0.432203	172(GAGGACTGCTTGTGCC,-,0.00),173(AGGACTGCTTGTGCCT,+,0.00)
chunk0040_383_1	chr11	119590337	119591003	+	0	NA	Intergenic	MER21C|LTR|ERVL	138055	NM_203286	5818	Hs.334846	NM_002855	ENSG00000110400	NECTIN1	CD111|CLPED1|ED4|HIgR|HV1S|HVEC|OFC7|PRR|PRR1|PVRL1|PVRR|PVRR1|SK-12|nectin-1	nectin cell adhesion molecule 1	protein-coding	0.004505	0.440780	
chunk0109_171_1	chr20	4170809	4171494	+	0	NA	intron (NM_175842, intron 1 of 8)	intron (NM_175842, intron 1 of 8)	-21939	NR_033917	728228	Hs.636379	NR_033917	ENSG00000230176	LINC01433	-	long intergenic non-protein coding RNA 1433	ncRNA	0.016058	0.536443	316(AAGTACAGGGTGTTCT,-,0.00),317(AGTACAGGGTGTTCTG,+,0.00)
chunk0151_6_1	chr5	40798915	40799314	+	0	NA	promoter-TSS (NM_006251)	promoter-TSS (NM_006251)	-919	NM_006251	5562	Hs.43322	NM_006251	ENSG00000132356	PRKAA1	AMPK|AMPKa1	protein kinase AMP-activated catalytic subunit alpha 1	protein-coding	0.007519	0.320000	
chunk0024_436_1	chr10	46137486	46137780	+	0	NA	Intergenic	AluSx|SINE|Alu	28138	NR_126580	653268	Hs.447454	NM_001077685		AGAP7P	AGAP-7|AGAP7|CTGLF4|bA109G10.1	ArfGAP with GTPase domain, ankyrin repeat and PH domain 7, pseudogene	pseudo	0.023810	0.508475	
chunk0123_118_1	chr3	42476650	42477208	+	0	NA	Intergenic	Intergenic	-12370	NM_001251882	7433	Hs.348500	NM_004624	ENSG00000114812	VIPR1	HVR1|II|PACAP-R-2|PACAP-R2|RDC1|V1RG|VAPC1|VIP-R-1|VIPR|VIRG|VPAC1|VPAC1R|VPCAP1R	vasoactive intestinal peptide receptor 1	protein-coding	0.008961	0.558140	
chunk0144_422_1	chr4	140641276	140641545	+	0	NA	non-coding (NR_077215, exon 1 of 1)	non-coding (NR_077215, exon 1 of 1)	1670	NR_077215	644962	Hs.676500	NR_077215		TNRC18P1	-	trinucleotide repeat containing 18 pseudogene 1	pseudo	0.011152	0.344444	
chunk0147_135_1	chr4	174512615	174512814	+	0	NA	intron (NM_001256307, intron 2 of 5)	intron (NM_001256307, intron 2 of 5)	10179	NM_001256301	3248	Hs.596913	NM_000860	ENSG00000164120	HPGD	15-PGDH|PGDH|PGDH1|PHOAR1|SDR36C1	15-hydroxyprostaglandin dehydrogenase	protein-coding	0.005025	0.370000	
chunk0052_194_1	chr13	24854359	24854719	+	0	NA	intron (NM_031277, intron 25 of 35)	intron (NM_031277, intron 25 of 35)	68350	NR_047595	55835	Hs.513379	NM_018451	ENSG00000151849	CENPJ	BM032|CENP-J|CPAP|LAP|LIP1|MCPH6|SASS4|SCKL4|Sas-4	centromere protein J	protein-coding	0.000000	0.368421	
chunk0201_172_1	chr9	36119490	36119733	+	0	NA	intron (NM_001316345, intron 20 of 22)	L2a|LINE|L2	-16925	NR_104638	152007	Hs.493819	NM_022343	ENSG00000122694	GLIPR2	C9orf19|GAPR-1|GAPR1	GLI pathogenesis related 2	protein-coding	0.008230	0.430328	
chunk0194_271_1	chr8	87154282	87154739	+	0	NA	intron (NM_173538, intron 4 of 10)	intron (NM_173538, intron 4 of 10)	288062	NM_173538	168975	Hs.246284	NM_173538	ENSG00000176571	CNBD1	-	cyclic nucleotide binding domain containing 1	protein-coding	0.006565	0.403930	
chunk0174_452_1	chr6	166518398	166518988	+	0	NA	intron (NM_001006932, intron 4 of 21)	intron (NM_001006932, intron 4 of 21)	-9260	NR_031734	100302141		NR_031734	ENSG00000222958	MIR1913	MIRN1913|hsa-mir-1913	microRNA 1913	ncRNA	0.001695	0.402707	
chunk0035_44_1	chr11	41082028	41082411	+	0	NA	intron (NM_001258419, intron 1 of 6)	intron (NM_001258419, intron 1 of 6)	377417	NM_020929	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.013055	0.440104	235(TGGGTCAGACTGTTCT,-,0.00),236(GGGTCAGACTGTTCTC,+,0.00)
chunk0148_178_1	chr5	7685158	7685431	+	0	NA	intron (NM_020546, intron 4 of 24)	intron (NM_020546, intron 4 of 24)	166196	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.018315	0.521898	
chunk0204_220_1	chr9	97398879	97399389	+	0	NA	Intergenic	Intergenic	-2443	NR_026847	286359	Hs.132262	NM_182600		LOC286359	-	uncharacterized LOC286359	ncRNA	0.025490	0.571429	
chunk0087_243_1	chr18	36693891	36694459	+	0	NA	intron (NM_001281739, intron 13 of 23)	intron (NM_001281739, intron 13 of 23)	-30757	NR_132982	105372071		NR_132982		LOC105372071	-	uncharacterized LOC105372071	ncRNA	0.021127	0.456942	
chunk0158_289_1	chr5	131947393	131947866	+	0	NA	Intergenic	L2b|LINE|L2	-1931	NM_001303622	728637	Hs.631802	NM_001278059	ENSG00000239642	MEIKIN	-	meiotic kinetochore factor	protein-coding	0.006342	0.360759	
chunk0007_181_1	chr1	80651104	80651777	+	0	NA	Intergenic	L1MDa|LINE|L1	10153	NR_125942	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.002972	0.397626	
chunk0099_315_1	chr2	99472569	99472961	+	0	NA	intron (NM_001037872, intron 1 of 22)	intron (NM_001037872, intron 1 of 22)	17253	NM_001037872	51455	Hs.443077	NM_016316	ENSG00000135945	REV1	AIBP80|REV1L	REV1 DNA directed polymerase	protein-coding	0.002551	0.394402	203(AAGTACATAAAGTGCT,-,0.00),204(AGTACATAAAGTGCTA,+,0.00)
chunk0111_68_1	chr20	23013452	23013714	+	0	NA	Intergenic	L2b|LINE|L2	-21837	NM_001052	6754	Hs.673846	NM_001052	ENSG00000132671	SSTR4	SS-4-R|SS4-R|SS4R	somatostatin receptor 4	protein-coding	0.007634	0.418251	
chunk0169_91_1	chr6	99834317	99834626	+	0	NA	Intergenic	Intergenic	-159567	NR_038384	728012	Hs.434366	NR_038384	ENSG00000229315	MCHR2-AS1	-	MCHR2 antisense RNA 1	ncRNA	0.003236	0.325806	
chunk0129_180_1	chr3	120918637	120918958	+	0	NA	intron (NM_014980, intron 2 of 27)	intron (NM_014980, intron 2 of 27)	10594	NM_001308330	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.000000	0.326087	
chunk0018_398_1	chr1	222611108	222611695	+	0	NA	Intergenic	L1MB8|LINE|L1	-6701	NM_198551	375056	Hs.118474	NM_198551	ENSG00000154305	MIA3	ARNT|D320|TANGO|TANGO1|UNQ6077	MIA SH3 domain ER export factor 3	protein-coding	0.003407	0.329932	
chunk0116_380_1	chr21	42177481	42177680	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-22109	NM_207627	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.015075	0.445000	
chunk0197_75_1	chr8	118931100	118931542	+	0	NA	intron (NM_002546, intron 2 of 4)	intron (NM_002546, intron 2 of 4)	20823	NM_002546	4982	Hs.81791	NM_002546	ENSG00000164761	TNFRSF11B	OCIF|OPG|PDB5|TR1	TNF receptor superfamily member 11b	protein-coding	0.002262	0.363431	
chunk0173_209_1	chr6	145484454	145484940	+	0	NA	Intergenic	MIRb|SINE|MIR	-250172	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.004115	0.318275	
chunk0067_272_1	chr15	46696218	46696417	+	0	NA	Intergenic	Intergenic	-487889	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.005025	0.370000	
chunk0038_186_1	chr11	86017411	86017977	+	0	NA	intron (NM_001008660, intron 4 of 19)	intron (NM_001008660, intron 4 of 19)	51403	NM_001206946	8301	Hs.163893	NM_007166	ENSG00000073921	PICALM	CALM|CLTH|LAP	phosphatidylinositol binding clathrin assembly protein	protein-coding	0.005300	0.326279	
chunk0045_129_1	chr12	46386438	46387252	+	0	NA	intron (NR_125381, intron 1 of 2)	intron (NR_125381, intron 1 of 2)	2738	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.007371	0.355828	353(AATACAGACAGTTCTC,+,0.00)
chunk0154_386_1	chr5	88030540	88031230	+	0	NA	Intergenic	MLT1H|LTR|ERVL-MaLR	237994	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.004348	0.406657	
chunk0173_454_1	chr6	151852258	151852860	+	0	NA	intron (NM_001291230, intron 3 of 8)	intron (NM_001291230, intron 3 of 8)	44880	NM_000125	2099	Hs.208124	NM_000125	ENSG00000091831	ESR1	ER|ESR|ESRA|ESTRR|Era|NR3A1	estrogen receptor 1	protein-coding	0.003322	0.353234	
chunk0029_12_1	chr10	95457961	95458319	+	0	NA	intron (NM_001290294, intron 2 of 31)	intron (NM_001290294, intron 2 of 31)	-16960	NM_001034956	10580	Hs.38621	NM_006434	ENSG00000095637	SORBS1	CAP|FLAF2|R85FL|SH3D5|SH3P12|SORB1	sorbin and SH3 domain containing 1	protein-coding	0.005587	0.406685	
chunk0201_163_1	chr9	36050895	36051242	+	0	NA	intron (NM_001316345, intron 1 of 22)	intron (NM_001316345, intron 1 of 22)	14155	NM_001316346	8434	Hs.388918	NM_021111	ENSG00000122707	RECK	ST15	reversion inducing cysteine rich protein with kazal motifs	protein-coding	0.002882	0.327586	
chunk0072_224_1	chr15	95712770	95713044	+	0	NA	Intergenic	Intergenic	279814	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.003650	0.352727	
chunk0173_328_1	chr6	148795803	148796362	+	0	NA	intron (NM_005715, intron 1 of 7)	intron (NM_005715, intron 1 of 7)	48947	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.005367	0.335714	
chunk0067_334_1	chr15	48364941	48365495	+	0	NA	Intergenic	HAL1|LINE|L1	33050	NM_001948	1854	Hs.527980	NM_001948	ENSG00000128951	DUT	dUTPase	deoxyuridine triphosphatase	protein-coding	0.001805	0.358559	
chunk0203_344_1	chr9	89844222	89844837	+	0	NA	Intergenic	Intergenic	-124887	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.013008	0.454545	
chunk0037_395_1	chr11	79156005	79156354	+	0	NA	intron (NM_001098816, intron 3 of 33)	intron (NM_001098816, intron 3 of 33)	245930	NR_030598	100126333		NR_030598	ENSG00000211997	MIR708	MIRN708|hsa-mir-708	microRNA 708	ncRNA	0.008596	0.500000	98(AGGCACACTGTGTTCT,-,0.00),99(GGCACACTGTGTTCTC,+,0.00)
chunk0046_297_1	chr12	62210458	62210788	+	0	NA	Intergenic	Intergenic	-17784	NM_178539	338811	Hs.269745	NM_178539	ENSG00000198673	TAFA2	FAM19A2|TAFA-2	TAFA chemokine like family member 2	protein-coding	0.018182	0.368580	
chunk0193_331_1	chr8	79204132	79205138	+	0	NA	Intergenic	HAL1M8|LINE|L1	-399112	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.002982	0.388282	646(GAGAACAGGGAGTTCT,-,0.00),647(AGAACAGGGAGTTCTA,+,0.00)
chunk0042_254_1	chr12	6533707	6533916	+	0	NA	promoter-TSS (NM_001289745)	promoter-TSS (NM_001289745)	-594	NM_001289745	2597	Hs.544577	NM_002046	ENSG00000111640	GAPDH	G3PD|GAPD|HEL-S-162eP	glyceraldehyde-3-phosphate dehydrogenase	protein-coding	0.038278	0.666667	72(CAGGACATCGTGACCT,-,0.00),73(AGGACATCGTGACCTT,+,0.00)
chunk0058_92_1	chr14	21592249	21593013	+	0	NA	Intergenic	L1MA4|LINE|L1	-21887	NM_001005465	26533	Hs.554581	NM_001005465	ENSG00000169208	OR10G3	OR14-40	olfactory receptor family 10 subfamily G member 3	protein-coding	0.009162	0.329412	
chunk0200_218_1	chr9	20618385	20618847	+	0	NA	intron (NM_001286691, intron 2 of 10)	intron (NM_001286691, intron 2 of 10)	3371	NM_001286691	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.004329	0.401728	
chunk0166_109_1	chr6	44125984	44126237	+	0	NA	intron (NM_032111, intron 1 of 2)	intron (NM_032111, intron 1 of 2)	1344	NM_032111	64928	Hs.311190	NM_032111	ENSG00000180992	MRPL14	L14mt|L32mt|MRP-L14|MRP-L32|MRPL32|RMPL32|RPML32	mitochondrial ribosomal protein L14	protein-coding	0.015810	0.429134	
chunk0042_409_1	chr12	11683828	11684550	+	0	NA	intron (NM_001987, intron 1 of 7)	Kanga1d|DNA|TcMar-Tc2	34335	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.004155	0.320885	344(GTGTACATGCAGTTCT,-,0.00),345(TGTACATGCAGTTCTT,+,0.00)
chunk0091_390_1	chr19	16111761	16111960	+	0	NA	5' UTR (NM_005370, exon 1 of 8)	5' UTR (NM_005370, exon 1 of 8)	180	NM_005370	4218	Hs.642874	NM_005370	ENSG00000167461	RAB8A	MEL|RAB8	RAB8A, member RAS oncogene family	protein-coding	0.105528	0.685000	
chunk0195_284_1	chr8	98475727	98476263	+	0	NA	intron (NM_006281, intron 10 of 10)	intron (NM_006281, intron 10 of 10)	48973	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.009328	0.376164	
chunk0205_79_1	chr9	106996788	106997202	+	0	NA	intron (NM_021224, intron 10 of 12)	intron (NM_021224, intron 10 of 12)	105993	NR_126029	340512	Hs.432529	NR_126029	ENSG00000230782	LOC340512	-	uncharacterized LOC340512	ncRNA	0.000000	0.359036	
chunk0108_170_1	chr2	231559908	231560389	+	0	NA	Intergenic	Intergenic	-29677	NM_006056	10316	Hs.471619	NM_006056	ENSG00000171596	NMUR1	(FM-3)|FM-3|FM3|GPC-R|GPR66|NMU1R	neuromedin U receptor 1	protein-coding	0.016632	0.439834	
chunk0129_266_1	chr3	122510472	122510811	+	0	NA	intron (NR_026698, intron 1 of 14)	HAL1|LINE|L1	4298	NR_026698	3836	Hs.161008	NM_002264	ENSG00000114030	KPNA1	IPOA5|NPI-1|RCH2|SRP1	karyopherin subunit alpha 1	protein-coding	0.002950	0.350000	127(GAGACAGTGTGTGCAT,+,0.00)
chunk0143_424_1	chr4	123753574	123754225	+	0	NA	intron (NR_027105, intron 2 of 4)	L1ME3A|LINE|L1	-20365	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.001536	0.329755	
chunk0075_159_1	chr16	51683667	51684288	+	0	NA	Intergenic	LTR39|LTR|ERV1	-78542	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.003221	0.459807	
chunk0005_26_1	chr1	54407504	54407844	+	0	NA	Intergenic	Intergenic	-1279	NM_001009955	23648	Hs.476706	NM_018070	ENSG00000157216	SSBP3	CSDP|SSDP|SSDP1	single stranded DNA binding protein 3	protein-coding	0.029412	0.434018	
chunk0099_378_1	chr2	101120370	101121052	+	0	NA	intron (NM_001102426, intron 1 of 19)	intron (NM_001102426, intron 1 of 19)	30673	NM_001102426	11138	Hs.442657	NM_007063	ENSG00000204634	TBC1D8	AD3|GRAMD8|HBLP1|TBC1D8A|VRP	TBC1 domain family member 8	protein-coding	0.011730	0.472914	342(TAGGACACAAAGTCCC,-,0.00),343(AGGACACAAAGTCCCA,+,0.00)
chunk0007_355_1	chr1	84874123	84874842	+	0	NA	intron (NM_012152, intron 1 of 2)	intron (NM_012152, intron 1 of 2)	18731	NM_012152	23566	Hs.527909	NM_012152	ENSG00000171517	LPAR3	EDG7|Edg-7|GPCR|HOFNH30|LP-A3|LPA3|RP4-678I3	lysophosphatidic acid receptor 3	protein-coding	0.005563	0.383333	
chunk0205_379_1	chr9	114080878	114081212	+	0	NA	Intergenic	Intergenic	-2573	NM_001633	259	Hs.436911	NM_001633	ENSG00000106927	AMBP	A1M|EDC1|HCP|HI30|IATIL|ITI|ITIL|ITILC|UTI	alpha-1-microglobulin/bikunin precursor	protein-coding	0.005988	0.543284	
chunk0119_116_1	chr22	42615088	42615368	+	0	NA	promoter-TSS (NM_001278657)	promoter-TSS (NM_001278657)	-17	NR_029422	267010	Hs.574857	NR_029422	ENSG00000276027	RNU12	RNU12-1|RNU12L|RNU12P|dJ222E13.7	RNA, U12 small nuclear	snRNA	0.042857	0.398577	
chunk0089_100_1	chr18	58407332	58407664	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-43576	NR_029667	406906		NR_029667	ENSG00000284440	MIR122	MIR122A|MIRN122|MIRN122A|hsa-mir-122|miRNA122|miRNA122A|mir-122	microRNA 122	ncRNA	0.015060	0.432432	
chunk0148_115_1	chr5	5152998	5153613	+	0	NA	intron (NM_139056, intron 3 of 22)	L2c|LINE|L2	12975	NM_139056	170690	Hs.661915	NM_139056	ENSG00000145536	ADAMTS16	ADAMTS16s	ADAM metallopeptidase with thrombospondin type 1 motif 16	protein-coding	0.003252	0.327922	
chunk0012_233_1	chr1	160530849	160531211	+	0	NA	Intergenic	L1MB4|LINE|L1	-7768	NM_001184714	114836	Hs.492348	NM_052931	ENSG00000162739	SLAMF6	CD352|KALI|KALIb|Ly108|NTB-A|NTBA|SF2000	SLAM family member 6	protein-coding	0.002762	0.319559	
chunk0126_316_1	chr3	81554191	81554884	+	0	NA	intron (NM_000158, intron 12 of 15)	intron (NM_000158, intron 12 of 15)	207262	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004329	0.357349	287(GAAGACAGACTGTGCT,-,0.00),288(AAGACAGACTGTGCTA,+,0.00)
chunk0115_13_1	chr21	20416376	20416752	+	0	NA	Intergenic	Intergenic	386544	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.007979	0.305040	
chunk0109_71_1	chr20	1697281	1697504	+	0	NA	Intergenic	Intergenic	-39613	NM_018556	55423	Hs.590883	NM_018556	ENSG00000089012	SIRPG	CD172g|SIRP-B2|SIRPB2|SIRPgamma|bA77C3.1	signal regulatory protein gamma	protein-coding	0.013453	0.486607	
chunk0082_296_1	chr17	58632399	58632646	+	0	NA	intron (NM_001201457, intron 2 of 32)	L2b|LINE|L2	59533	NM_001201457	56155	Hs.390221	NM_031272	ENSG00000121101	TEX14	CT113|SPGF23	testis expressed 14, intercellular bridge forming factor	protein-coding	0.016194	0.451613	
chunk0070_281_1	chr15	74524020	74524405	+	0	NA	Intergenic	MLT1J1-int|LTR|ERVL-MaLR	-16965	NM_006465	10620	Hs.647642	NM_006465	ENSG00000179361	ARID3B	BDP|DRIL2	AT-rich interaction domain 3B	protein-coding	0.000000	0.391192	
chunk0146_339_1	chr4	165953157	165953450	+	0	NA	intron (NM_012464, intron 1 of 20)	intron (NM_012464, intron 1 of 20)	80045	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.010239	0.476190	167(ATGGACAGCCTGTGCT,-,0.00),168(TGGACAGCCTGTGCTT,+,0.00)
chunk0036_311_1	chr11	66123814	66124111	+	0	NA	intron (NM_018026, intron 1 of 23)	Tigger1|DNA|TcMar-Tigger	53609	NM_018026	55690	Hs.644326	NM_018026	ENSG00000175115	PACS1	MRD17|SHMS	phosphofurin acidic cluster sorting protein 1	protein-coding	0.020202	0.385906	
chunk0102_406_1	chr2	156064378	156064918	+	0	NA	intron (NR_110250, intron 1 of 3)	intron (NR_110250, intron 1 of 3)	190283	NR_110250	101929378	Hs.171192	NR_110249	ENSG00000226383	LINC01876	-	long intergenic non-protein coding RNA 1876	ncRNA	0.001852	0.334566	276(CAGAACACAGAGTACT,-,0.00),277(AGAACACAGAGTACTA,+,0.00)
chunk0102_163_1	chr2	147299268	147299763	+	0	NA	Intergenic	Intergenic	-545002	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.002020	0.342742	
chunk0159_458_1	chr5	148905466	148905823	+	0	NA	Intergenic	Intergenic	79051	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.002801	0.460894	
chunk0115_72_1	chr21	21855627	21856144	+	0	NA	Intergenic	L1PREC2|LINE|L1	108900	NR_109958	101927821	Hs.334181	NR_109958	ENSG00000233997	LINC01425	-	long intergenic non-protein coding RNA 1425	ncRNA	0.003868	0.339768	
chunk0011_371_1	chr1	153633317	153634147	+	0	NA	promoter-TSS (NM_001206612)	promoter-TSS (NM_001206612)	-250	NM_001244664	26097	Hs.611057	NM_015607	ENSG00000160679	CHTOP	C10orf77|C1orf77|FL-SRAG|FOP|SRAG|SRAG-3|SRAG-5|pp7704	chromatin target of PRMT1	protein-coding	0.054217	0.570397	
chunk0081_23_1	chr17	37322053	37322695	+	0	NA	intron (NM_198836, intron 3 of 55).2	intron (NM_198836, intron 3 of 55).2	-22607	NM_198838	31	Hs.160556	NM_000664	ENSG00000278540	ACACA	ACAC|ACACAD|ACC|ACC1|ACCA	acetyl-CoA carboxylase alpha	protein-coding	0.003115	0.393468	252(AAATACAGATTGTTCT,-,0.00),253(AATACAGATTGTTCTC,+,0.00)
chunk0008_440_1	chr1	99598319	99598953	+	0	NA	intron (NR_031666, intron 1 of 4)	intron (NR_031666, intron 1 of 4)	-47239	NM_017734	54873	Hs.483993	NM_017734	ENSG00000099260	PALMD	C1orf11|PALML	palmdelphin	protein-coding	0.000000	0.311811	
chunk0044_387_1	chr12	39921091	39921475	+	0	NA	intron (NM_052885, intron 4 of 9)	intron (NM_052885, intron 4 of 9)	184576	NM_052885	114134	Hs.558595	NM_052885	ENSG00000151229	SLC2A13	HMIT	solute carrier family 2 member 13	protein-coding	0.013021	0.433766	
chunk0001_248_1	chr1	8372543	8372772	+	0	NA	intron (NM_001042682, intron 2 of 12)	intron (NM_001042682, intron 2 of 12)	51030	NM_001042682	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.021834	0.473913	
chunk0065_238_1	chr14	101072844	101073145	+	0	NA	TTS (NR_047664)	TTS (NR_047664)	3083	NR_047664	100507257	Hs.301755	NR_047664	ENSG00000223403	MEG9	LINC00584	maternally expressed 9	ncRNA	0.039867	0.506623	
chunk0159_324_1	chr5	143595132	143595649	+	0	NA	Intergenic	Intergenic	-84470	NR_049829	100846991		NR_049829	ENSG00000266478	MIR5197	-	microRNA 5197	ncRNA	0.009671	0.391892	
chunk0123_175_1	chr3	44106896	44107309	+	0	NA	Intergenic	Intergenic	-7110	NR_029700	406929		NR_029700	ENSG00000207954	MIR138-1	MIRN138-1|mir-138-1	microRNA 138-1	ncRNA	0.012107	0.451691	
chunk0121_159_1	chr3	19366100	19366747	+	0	NA	intron (NM_144633, intron 5 of 15)	intron (NM_144633, intron 5 of 15)	-51492	NR_039954	100616291		NR_039954	ENSG00000271898	MIR4791	mir-4791	microRNA 4791	ncRNA	0.003091	0.297840	
chunk0105_126_1	chr2	185571028	185571227	+	0	NA	Intergenic	LTR77|LTR|ERV1	-167501	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.000000	0.405000	
chunk0054_423_1	chr13	51034687	51035308	+	0	NA	intron (NR_003923, intron 3 of 16)	intron (NR_003923, intron 3 of 16)	31160	NR_003923	2974	Hs.411573	NM_004129	ENSG00000123201	GUCY1B2	GC-SB2	guanylate cyclase 1 soluble subunit beta 2 (pseudogene)	pseudo	0.009662	0.446945	
chunk0014_141_1	chr1	177913062	177913493	+	0	NA	Intergenic	Intergenic	56638	NM_033127	89866	Hs.149540	NM_033127	ENSG00000120341	SEC16B	LZTR2|PGPR-p117|RGPR|RGPR-p117|SEC16S	SEC16 homolog B, endoplasmic reticulum export factor	protein-coding	0.011601	0.486111	
chunk0059_295_1	chr14	35879862	35880369	+	0	NA	Intergenic	Intergenic	53724	NM_032352	84312	Hs.525299	NM_032352	ENSG00000100916	BRMS1L	BRMS1	BRMS1 like transcriptional repressor	protein-coding	0.000000	0.330709	
chunk0136_350_1	chr3	195855623	195855822	+	0	NA	Intergenic	Intergenic	26673	NR_106887	102465977		NR_106887	ENSG00000276489	MIR6829	hsa-mir-6829	microRNA 6829	ncRNA	0.015075	0.395000	
chunk0013_245_1	chr1	169685687	169685893	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	23066	NR_029467	6402	Hs.728756	NM_000655	ENSG00000188404	SELL	CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1	selectin L	protein-coding	0.004854	0.487923	
chunk0195_352_1	chr8	99654654	99655081	+	0	NA	intron (NM_152564, intron 34 of 61)	intron (NM_152564, intron 34 of 61)	-118006	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.000000	0.364486	
chunk0057_361_1	chr13	108948004	108948785	+	0	NA	intron (NM_001198950, intron 16 of 34)	intron (NM_001198950, intron 16 of 34)	218909	NR_047700	100885782	Hs.655942	NR_047700	ENSG00000236242	MYO16-AS1	-	MYO16 antisense RNA 1	ncRNA	0.012804	0.410486	291(GAGAAGACACTGTTCC,-,0.00),292(AGAAGACACTGTTCCT,+,0.00)
chunk0124_271_1	chr3	57484412	57485023	+	0	NA	intron (NM_001291661, intron 12 of 73)	L1PB2|LINE|L1	59627	NM_001291661	201625	Hs.201378	NM_178504	ENSG00000174844	DNAH12	DHC3|DLP12|DLP3|DNAH12L|DNAH7L|DNAHC12|DNAHC3|DNHD2|HDHC3|HL-19|HL19	dynein axonemal heavy chain 12	protein-coding	0.003273	0.354575	
chunk0203_8_1	chr9	82619993	82620305	+	0	NA	Intergenic	Intergenic	442979	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.003205	0.319489	
chunk0056_230_1	chr13	88731904	88732162	+	0	NA	Intergenic	LTR37B|LTR|ERV1	191204	NR_047021	100874168	Hs.126406	NR_047021		LINC00433	-	long intergenic non-protein coding RNA 433	ncRNA	0.011628	0.293436	
chunk0168_70_1	chr6	79422057	79422459	+	0	NA	Intergenic	Intergenic	-108874	NR_130915	80078		NR_130915	ENSG00000286042	LCAL1	onco-lncRNA-27	lung cancer associated lncRNA 1	ncRNA	0.004975	0.347395	
chunk0135_209_1	chr3	188339747	188339946	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	114441	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.015075	0.440000	
chunk0016_115_1	chr1	196056602	196057336	+	0	NA	Intergenic	LTR55|LTR|ERVL?	525512	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005450	0.390476	
chunk0079_400_1	chr17	19393575	19394262	+	0	NA	Intergenic	L1MC2|LINE|L1	-6699	NM_002404	4239	Hs.296049	NM_002404	ENSG00000166482	MFAP4	-	microfibril associated protein 4	protein-coding	0.004367	0.344477	
chunk0212_104_1	chrY	15345257	15345894	+	0	NA	Intergenic	Intergenic	-541542	NR_046504	100874056	Hs.743197	NR_046504	ENSG00000228787	NLGN4Y-AS1	NLGN4Y-AS|NLGN4YAS	NLGN4Y antisense RNA 1	ncRNA	0.006279	0.443574	314(AAGGACTGCCTGTACT,-,0.00),315(AGGACTGCCTGTACTT,+,0.00)
chunk0018_339_1	chr1	221476721	221477357	+	0	NA	Intergenic	Intergenic	-140743	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.007862	0.444270	281(CAGGACTCTGTGTCCT,-,0.00),282(AGGACTCTGTGTCCTG,+,0.00)
chunk0131_65_1	chr3	142890584	142891051	+	0	NA	Intergenic	Intergenic	-1614	NM_013363	26577	Hs.8944	NM_013363	ENSG00000163710	PCOLCE2	PCPE2	procollagen C-endopeptidase enhancer 2	protein-coding	0.004283	0.290598	
chunk0119_103_1	chr22	42158946	42159280	+	0	NA	TTS (NM_181492)	TTS (NM_181492)	-14538	NR_002570	1564	Hs.333497	NM_001348386	ENSG00000205702	CYP2D7	CYP2D|CYP2D6|CYP2D7AP|CYP2D7P|CYP2D7P1|CYP2D@|P450C2D|P450DB1|RNA40057	cytochrome P450 family 2 subfamily D member 7 (gene/pseudogene)	protein-coding	0.008982	0.441791	108(GGGAACTGTCTGTACC,-,0.00),109(GGAACTGTCTGTACCG,+,0.00)
chunk0169_428_1	chr6	108676641	108676927	+	0	NA	intron (NM_201559, intron 3 of 3)	intron (NM_201559, intron 3 of 3)	-74870	NR_033376	387111	Hs.520310	NR_033376	ENSG00000203801	LINC00222	C6orf181|NCRNA00222|dJ354J5.2	long intergenic non-protein coding RNA 222	ncRNA	0.000000	0.372822	
chunk0199_180_1	chr9	4599922	4600360	+	0	NA	3' UTR (NM_001039395, exon 11 of 11)	3' UTR (NM_001039395, exon 11 of 11)	-62153	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.011416	0.396355	
chunk0135_328_1	chr3	190125475	190126129	+	0	NA	intron (NR_126419, intron 1 of 3)	A-rich|Low_complexity|Low_complexity	-3365	NM_001134418	55214	Hs.374191	NM_018192	ENSG00000090530	P3H2	LEPREL1|MCVD|MLAT4	prolyl 3-hydroxylase 2	protein-coding	0.018349	0.416794	349(CAGGACTGTCTGTTCC,-,0.00),350(AGGACTGTCTGTTCCT,+,0.00)
chunk0126_303_1	chr3	80788458	80788747	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-205266	NR_132411	728290	Hs.563132	NR_132411	ENSG00000243694	LINC02027	-	long intergenic non-protein coding RNA 2027	ncRNA	0.003460	0.379310	227(AAAACATATTGTCCTC,+,0.00)
chunk0034_267_1	chr11	34583754	34584239	+	0	NA	Intergenic	Intergenic	-37045	NM_012153	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.010309	0.471193	
chunk0034_276_1	chr11	34633677	34633996	+	0	NA	intron (NM_001206616, intron 1 of 8)	intron (NM_001206616, intron 1 of 8)	1372	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.000000	0.431250	
chunk0180_339_1	chr7	73369025	73369546	+	0	NA	Intergenic	Intergenic	41053	NM_001281304	8468	Hs.661266	NM_003602	ENSG00000077800	FKBP6	FKBP36	FKBP prolyl isomerase 6	protein-coding	0.023033	0.590038	
chunk0211_62_1	chrX	109777803	109778033	+	0	NA	Intergenic	Intergenic	-44526	NM_004458	2182	Hs.268785	NM_004458	ENSG00000068366	ACSL4	ACS4|FACL4|LACS4|MRX63|MRX68	acyl-CoA synthetase long chain family member 4	protein-coding	0.000000	0.406926	
chunk0087_308_1	chr18	39450488	39451180	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	171341	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.002890	0.336219	
chunk0158_145_1	chr5	127419193	127419675	+	0	NA	intron (NM_001308121, intron 11 of 13)	MIR3|SINE|MIR	-98175	NM_001286808	133619	Hs.483259	NM_130809	ENSG00000164244	PRRC1	-	proline rich coiled-coil 1	protein-coding	0.012448	0.457557	
chunk0193_118_1	chr8	74230696	74231269	+	0	NA	Intergenic	Intergenic	90345	NM_020647	56704	Hs.657367	NM_020647	ENSG00000104369	JPH1	CMT2K|JP-1|JP1	junctophilin 1	protein-coding	0.003490	0.404181	
chunk0031_175_1	chr10	125611233	125611622	+	0	NA	Intergenic	L1ME4a|LINE|L1	37056	NR_023362	100169752	Hs.652647	NR_023362	ENSG00000237675	TEX36-AS1	-	TEX36 antisense RNA 1	ncRNA	0.005141	0.320513	
chunk0033_159_1	chr11	15605960	15606625	+	0	NA	Intergenic	MER45A|DNA|hAT-Tip100	-37593	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.006015	0.433934	243(AAGCACAGCCTGTTTC,-,0.00),244(AGCACAGCCTGTTTCA,+,0.00),320(TTAACACTCTGTTCTT,+,0.00)
chunk0094_436_1	chr2	11065744	11066318	+	0	NA	Intergenic	MIR3|SINE|MIR	66145	NR_040080	285150	Hs.329841	NM_182586	ENSG00000145063	FLJ33534	-	uncharacterized LOC285150	ncRNA	0.019164	0.483478	
chunk0013_376_1	chr1	172515991	172516190	+	0	NA	Intergenic	Intergenic	-16259	NM_016227	51430	Hs.204559	NM_014283	ENSG00000094975	SUCO	C1orf9|CH1|OPT|SLP1	SUN domain containing ossification factor	protein-coding	0.005025	0.435000	
chunk0202_69_1	chr9	71725849	71726294	+	0	NA	intron (NM_001135820, intron 9 of 22)	intron (NM_001135820, intron 9 of 22)	42813	NM_013390	23670	Hs.494146	NM_013390	ENSG00000135048	CEMIP2	TMEM2	cell migration inducing hyaluronidase 2	protein-coding	0.011236	0.358744	
chunk0196_248_1	chr8	108583923	108584859	+	0	NA	Intergenic	Intergenic	140767	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.005342	0.408751	192(AAGCACTGACTGTACA,-,0.00)
chunk0203_401_1	chr9	90609687	90610346	+	0	NA	3' UTR (NM_017594, exon 2 of 2)	3' UTR (NM_017594, exon 2 of 2)	-27270	NR_034157	340515	Hs.522284	NM_001105317		LINC01501	-	long intergenic non-protein coding RNA 1501	ncRNA	0.003035	0.330303	
chunk0201_413_1	chr9	69588670	69589026	+	0	NA	intron (NM_001163, intron 1 of 12)	intron (NM_001163, intron 1 of 12)	83511	NM_001163	320	Hs.171939	NM_001163	ENSG00000107282	APBA1	D9S411E|LIN10|MINT1|X11|X11A|X11ALPHA	amyloid beta precursor protein binding family A member 1	protein-coding	0.008427	0.403361	
chunk0148_32_1	chr5	672157	672457	+	0	NA	intron (NM_007030, intron 2 of 3)	intron (NM_007030, intron 2 of 3)	21088	NM_007030	11076	Hs.481466	NM_007030	ENSG00000171368	TPPP	TPPP/p25|TPPP1|p24|p25|p25alpha	tubulin polymerization promoting protein	protein-coding	0.030000	0.627907	
chunk0026_347_1	chr10	68647790	68648278	+	0	NA	intron (NM_030625, intron 4 of 11)	intron (NM_030625, intron 4 of 11)	-73110	NM_001282960	55749	Hs.49853	NM_018237	ENSG00000060339	CCAR1	-	cell division cycle and apoptosis regulator 1	protein-coding	0.004098	0.335378	377(GAGAACATTCTGAACC,-,0.00),378(AGAACATTCTGAACCA,+,0.00)
chunk0161_353_1	chr5	174635979	174636698	+	0	NA	Intergenic	Intergenic	-88234	NM_002449	4488	Hs.89404	NM_002449	ENSG00000120149	MSX2	CRS2|FPP|HOX8|MSH|PFM|PFM1	msh homeobox 2	protein-coding	0.015299	0.504167	341(TGGAACAGACTGTTCT,-,0.00),342(GGAACAGACTGTTCTG,+,0.00)
chunk0060_395_1	chr14	52950423	52950704	+	0	NA	exon (NM_001135000, exon 2 of 15)	exon (NM_001135000, exon 2 of 15)	534	NM_006832	10979	Hs.509343	NM_006832	ENSG00000073712	FERMT2	KIND2|MIG2|PLEKHC1|UNC112|UNC112B|mig-2	fermitin family member 2	protein-coding	0.085409	0.620567	77(ATGGACACTCAGTTCC,-,0.00),78(TGGACACTCAGTTCCC,+,0.00)
chunk0192_39_1	chr8	58674915	58675387	+	0	NA	Intergenic	Intergenic	-15306	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.006356	0.420719	
chunk0057_438_1	chr13	110520997	110521230	+	0	NA	Intergenic	Intergenic	-12934	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.017167	0.585470	
chunk0190_99_1	chr8	30328337	30329670	+	0	NA	Intergenic	L2b|LINE|L2	-55498	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.007502	0.430285	1219(GGGAACAGCATGTCCA,-,0.00),1220(GGAACAGCATGTCCAA,+,0.00)
chunk0027_90_1	chr10	73625372	73625694	+	0	NA	Intergenic	CpG	16224	NM_021245	58529	Hs.238756	NM_021245	ENSG00000177791	MYOZ1	CS-2|FATZ|MYOZ	myozenin 1	protein-coding	0.062112	0.603715	
chunk0019_147_1	chr1	225772372	225773234	+	0	NA	Intergenic	Intergenic	-5010	NM_003133	6726	Hs.511425	NM_003133	ENSG00000143742	SRP9	ALURBP	signal recognition particle 9	protein-coding	0.011601	0.460023	
chunk0030_334_1	chr10	118355756	118356292	+	0	NA	Intergenic	Intergenic	-1084	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.007463	0.411546	198(GTGAACACACTGTGTT,-,0.00),199(TGAACACACTGTGTTC,+,0.00),200(GAACACACTGTGTTCC,-,0.00),201(AACACACTGTGTTCCA,+,0.00)
chunk0053_197_1	chr13	31885772	31886225	+	0	NA	intron (NR_027062, intron 1 of 3)	intron (NR_027062, intron 1 of 3)	39215	NR_027062	196549	Hs.507667	NM_145293		EEF1DP3	-	eukaryotic translation elongation factor 1 delta pseudogene 3	pseudo	0.015453	0.460352	
chunk0036_138_1	chr11	61971178	61972120	+	0	NA	Intergenic	Intergenic	-3989	NM_002032	2495	Hs.524910	NM_002032	ENSG00000167996	FTH1	FHC|FTH|FTHL6|HFE5|PIG15|PLIF	ferritin heavy chain 1	protein-coding	0.016985	0.541888	420(AGGGACAGCTTGTGCT,-,0.00),421(GGGACAGCTTGTGCTG,+,0.00)
chunk0068_95_1	chr15	52217260	52217570	+	0	NA	intron (NM_018728, intron 32 of 40)	intron (NM_018728, intron 32 of 40)	-26047	NM_016194	10681	Hs.155090	NM_006578	ENSG00000069966	GNB5	GB5|IDDCA|LADCI	G protein subunit beta 5	protein-coding	0.029032	0.575563	
chunk0198_355_1	chr8	140587437	140587636	+	0	NA	intron (NM_012154, intron 1 of 18)	intron (NM_012154, intron 1 of 18)	48011	NM_012154	27161	Hs.660189	NM_012154	ENSG00000123908	AGO2	CASC7|EIF2C2|LINC00980|PPD|Q10	argonaute RISC catalytic component 2	protein-coding	0.020101	0.555000	
chunk0137_224_1	chr4	20021763	20022213	+	0	NA	Intergenic	Intergenic	-229917	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.002222	0.299335	175(TGGAACACAGTGTGCA,-,0.00),176(GGAACACAGTGTGCAC,+,0.00)
chunk0003_199_1	chr1	34798860	34799381	+	0	NA	Intergenic	Intergenic	6122	NM_002060	2701	Hs.296310	NM_002060	ENSG00000187513	GJA4	CX37	gap junction protein alpha 4	protein-coding	0.007678	0.484674	365(CAGGACACCCAGTTCT,-,0.00),366(AGGACACCCAGTTCTG,+,0.00)
chunk0049_381_1	chr12	96046604	96047142	+	0	NA	Intergenic	L1ME3A|LINE|L1	-3353	NM_001256643	4048	Hs.524648	NM_000895	ENSG00000111144	LTA4H	-	leukotriene A4 hydrolase	protein-coding	0.005576	0.413729	
chunk0183_154_1	chr7	105899298	105899585	+	0	NA	Intergenic	L1MC1|LINE|L1	-22856	NM_020725	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.013937	0.406250	
chunk0100_407_1	chr2	119383441	119383780	+	0	NA	Intergenic	MLT1H2|LTR|ERVL-MaLR	15935	NM_001079863	1622	Hs.78888	NM_020548	ENSG00000155368	DBI	ACBD1|ACBP|CCK-RP|EP	diazepam binding inhibitor, acyl-CoA binding protein	protein-coding	0.011799	0.497059	
chunk0118_297_1	chr22	34411085	34411355	+	0	NA	Intergenic	L1MC4a|LINE|L1	-490792	NM_133642	9215	Hs.474667	NM_004737	ENSG00000133424	LARGE1	LARGE|MDC1D|MDDGA6|MDDGB6	LARGE xylosyl- and glucuronyltransferase 1	protein-coding	0.011111	0.361624	
chunk0081_85_1	chr17	39401622	39402023	+	0	NA	promoter-TSS (NM_032875)	promoter-TSS (NM_032875)	-166	NM_001184906	84961	Hs.462946	NM_032875	ENSG00000108306	FBXL20	Fbl2|Fbl20	F-box and leucine rich repeat protein 20	protein-coding	0.109726	0.723881	
chunk0147_371_1	chr4	185958048	185958692	+	0	NA	Intergenic	HAL1|LINE|L1	-1654	NM_001270771	8470	Hs.481342	NM_003603	ENSG00000154556	SORBS2	ARGBP2|PRO0618	sorbin and SH3 domain containing 2	protein-coding	0.006211	0.406202	
chunk0172_395_1	chr6	139691023	139691317	+	0	NA	Intergenic	Intergenic	-79903	NR_038399	100132735	Hs.62646	NR_038399	ENSG00000231426	FILNC1	-	FOXO induced long non-coding RNA 1	ncRNA	0.000000	0.308475	
chunk0085_459_1	chr18	11696444	11697155	+	0	NA	intron (NM_182978, intron 1 of 11)	intron (NM_182978, intron 1 of 11)	7784	NM_182978	2774	Hs.136295	NM_002071	ENSG00000141404	GNAL	DYT25	G protein subunit alpha L	protein-coding	0.015471	0.425562	
chunk0106_390_1	chr2	207617027	207617474	+	0	NA	intron (NM_001127395, intron 3 of 3)	L2c|LINE|L2	7722	NM_145280	151194	Hs.664764	NM_145280	ENSG00000144401	METTL21A	FAM119A|HCA557b|HSPA-KMT	methyltransferase like 21A	protein-coding	0.008949	0.401786	
chunk0112_62_1	chr20	37568300	37568583	+	0	NA	Intergenic	Intergenic	-40510	NM_001167820	10904	Hs.472651	NM_006698	ENSG00000166619	BLCAP	BC10	BLCAP apoptosis inducing factor	protein-coding	0.003534	0.489437	191(AGGTACACCTTGTTCC,-,0.00),192(GGTACACCTTGTTCCA,+,0.00)
chunk0030_272_1	chr10	116429189	116429771	+	0	NA	intron (NM_001011709, intron 1 of 11)	intron (NM_001011709, intron 1 of 11)	1568	NM_001011709	119548	Hs.276724	NM_001011709	ENSG00000203837	PNLIPRP3	-	pancreatic lipase related protein 3	protein-coding	0.006873	0.365352	
chunk0008_388_1	chr1	97174100	97174461	+	0	NA	intron (NM_000110, intron 20 of 22)	intron (NM_000110, intron 20 of 22)	78357	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.011080	0.477901	161(AGGCACTGGCTGATCC,-,0.00),162(GGCACTGGCTGATCCT,+,0.00)
chunk0131_445_1	chr3	154059799	154060275	+	0	NA	intron (NR_037901, intron 2 of 3)	intron (NR_037901, intron 2 of 3)	-60966	NM_001251962	26084	Hs.240845	NM_015595	ENSG00000114790	ARHGEF26	CSGEF|HMFN1864|SGEF	Rho guanine nucleotide exchange factor 26	protein-coding	0.012605	0.469602	
chunk0017_191_1	chr1	207336262	207336505	+	0	NA	intron (NR_125349, intron 6 of 10)	intron (NR_125349, intron 6 of 10)	14911	NM_001300904	1604	Hs.126517	NM_000574	ENSG00000196352	CD55	CHAPLE|CR|CROM|DAF|TC	CD55 molecule (Cromer blood group)	protein-coding	0.000000	0.352459	
chunk0205_260_1	chr9	110947643	110947863	+	0	NA	intron (NM_057159, intron 3 of 4)	intron (NM_057159, intron 3 of 4)	90332	NM_057159	1902	Hs.126667	NM_001401	ENSG00000198121	LPAR1	EDG2|GPR26|Gpcr26|LPA1|Mrec1.3|VZG1|edg-2|rec.1.3|vzg-1	lysophosphatidic acid receptor 1	protein-coding	0.004545	0.411765	
chunk0101_69_1	chr2	123680798	123681297	+	0	NA	Intergenic	Intergenic	-344240	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.004008	0.356000	
chunk0026_265_1	chr10	66930900	66931241	+	0	NA	intron (NM_178011, intron 2 of 2)	intron (NM_178011, intron 2 of 2)	5036	NM_178011	347731	Hs.652155	NM_178011	ENSG00000198739	LRRTM3	-	leucine rich repeat transmembrane neuronal 3	protein-coding	0.005865	0.318713	
chunk0197_440_1	chr8	127578477	127578819	+	0	NA	Intergenic	Intergenic	-96509	NR_117100	727677	Hs.673248	NR_024393	ENSG00000246228	CASC8	CARLO1|CARLo-1|LINC00860	cancer susceptibility 8	ncRNA	0.002924	0.454810	257(AGGAACAAGGTGAGCC,-,0.00),258(GGAACAAGGTGAGCCT,+,0.00)
chunk0008_254_1	chr1	94490366	94490815	+	0	NA	intron (NM_002858, intron 15 of 22)	L1MA9|LINE|L1	51267	NM_001993	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.004454	0.371111	
chunk0167_7_1	chr6	53465620	53466120	+	0	NA	Intergenic	Intergenic	79259	NM_001498	2729	Hs.654465	NM_001498	ENSG00000001084	GCLC	GCL|GCS|GLCL|GLCLC	glutamate-cysteine ligase catalytic subunit	protein-coding	0.014000	0.499002	
chunk0204_216_1	chr9	97221531	97221737	+	0	NA	Intergenic	CpG	-16792	NR_036529	57653	Hs.435629	NR_036527	ENSG00000255036	SUGT1P4-STRA6LP-CCDC180	LOC100499484-C9ORF174	SUGT1P4-STRA6LP-CCDC180 readthrough	ncRNA	0.140777	0.734300	
chunk0131_143_1	chr3	145985048	145985667	+	0	NA	Intergenic	L1PA16|LINE|L1	176138	NM_000935	5352	Hs.477866	NM_000935	ENSG00000152952	PLOD2	BRKS2|LH2|TLH	procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	protein-coding	0.001616	0.359677	
chunk0004_134_1	chr1	44777442	44777736	+	0	NA	promoter-TSS (NR_001457)	promoter-TSS (NR_001457)	-253	NR_001456	94162		NR_001456	ENSG00000202031	SNORD38A	RNU38A|U38A	small nucleolar RNA, C/D box 38A	snoRNA	0.034014	0.491525	
chunk0015_457_1	chr1	192541742	192542356	+	0	NA	Intergenic	Intergenic	-33678	NM_002922	5996	Hs.75256	NM_002922	ENSG00000090104	RGS1	1R20|BL34|HEL-S-87|IER1|IR20	regulator of G protein signaling 1	protein-coding	0.008143	0.336585	
chunk0065_374_1	chr14	104049262	104049532	+	0	NA	intron (NM_153046, intron 34 of 35)	intron (NM_153046, intron 34 of 35)	-36289	NM_001080464	374569	Hs.146239	NM_001080464	ENSG00000166183	ASPG	C14orf76|GPA/WT|LYSOLP	asparaginase	protein-coding	0.000000	0.357934	36(TGGTACAAAATGTCCT,-,0.00),37(GGTACAAAATGTCCTG,+,0.00)
chunk0154_94_1	chr5	78083418	78083906	+	0	NA	intron (NM_003664, intron 22 of 26)	intron (NM_003664, intron 22 of 26)	125415	NR_105013	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.002049	0.284254	
chunk0099_372_1	chr2	101096520	101097174	+	0	NA	intron (NM_001102426, intron 1 of 19)	L1MC3|LINE|L1	54537	NM_001102426	11138	Hs.442657	NM_007063	ENSG00000204634	TBC1D8	AD3|GRAMD8|HBLP1|TBC1D8A|VRP	TBC1 domain family member 8	protein-coding	0.007645	0.360305	
chunk0058_173_1	chr14	23702927	23703127	+	0	NA	Intergenic	Intergenic	66663	NM_005794	10202	Hs.272499	NM_005794	ENSG00000100867	DHRS2	HEP27|SDR25C1	dehydrogenase/reductase 2	protein-coding	0.000000	0.388060	
chunk0114_264_1	chr21	16179781	16180069	+	0	NA	intron (NR_027790, intron 2 of 7)	L2c|LINE|L2	-14454	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.010417	0.401384	
chunk0054_31_1	chr13	40976151	40976350	+	0	NA	intron (NM_001145353, intron 1 of 7)	intron (NM_001145353, intron 1 of 7)	6032	NM_001145353	1997	Hs.135646	NM_172373	ENSG00000120690	ELF1	EFTUD1|RIA1	E74 like ETS transcription factor 1	protein-coding	0.000000	0.375000	
chunk0138_11_1	chr4	30391894	30392418	+	0	NA	Intergenic	Intergenic	-328252	NM_032456	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.005725	0.226667	
chunk0058_407_1	chr13	112078672	112078917	+	0	NA	intron (NR_120392, intron 1 of 3)	(TGTTG)n|Simple_repeat|Simple_repeat	11195	NM_005986	6656		NM_005986	ENSG00000182968	SOX1	-	SRY-box transcription factor 1	protein-coding	0.004082	0.467480	
chunk0089_149_1	chr18	59054822	59055470	+	0	NA	Intergenic	Intergenic	19467	NR_024021	390858	Hs.716280	NR_024021		OACYLP	ACYL3P	O-acyltransferase like, pseudogene	pseudo	0.007716	0.451464	332(TAGGACACTGAGTTCT,-,0.00),333(AGGACACTGAGTTCTT,+,0.00)
chunk0150_388_1	chr5	39639486	39639937	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	119280	NR_104632	101926940	Hs.436359	NR_104632	ENSG00000271334	LINC02104	-	long intergenic non-protein coding RNA 2104	ncRNA	0.004435	0.356195	
chunk0156_184_1	chr5	107821533	107821862	+	0	NA	Intergenic	Intergenic	-150802	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.006079	0.412121	
chunk0001_242_1	chr1	8312457	8312802	+	0	NA	Intergenic	Intergenic	-5456	NM_001080397	50651	Hs.463036	NM_001080397	ENSG00000162426	SLC45A1	DNB5|IDDNPF	solute carrier family 45 member 1	protein-coding	0.014493	0.497110	72(GGAACATGCTGAGCAT,+,0.00)
chunk0082_184_1	chr17	56400433	56400955	+	0	NA	intron (NM_153228, intron 7 of 16)	L1PB1|LINE|L1	-193005	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.003831	0.361377	
chunk0125_78_1	chr3	64548209	64548594	+	0	NA	intron (NM_182920, intron 31 of 39)	intron (NM_182920, intron 31 of 39)	-12945	NR_110151	101929335	Hs.476604	NR_110150	ENSG00000241158	ADAMTS9-AS1	-	ADAMTS9 antisense RNA 1	ncRNA	0.012987	0.489637	
chunk0133_364_1	chr3	173599601	173600109	+	0	NA	intron (NM_014932, intron 2 of 6)	Tigger17c|DNA|TcMar-Tigger	201407	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.003937	0.377210	
chunk0065_232_1	chr14	101032518	101032868	+	0	NA	TTS (NR_030619)	TTS (NR_030619)	706	NR_030619	100126335		NR_030619	ENSG00000212040	MIR543	MIRN543|hsa-mir-543|mir-543	microRNA 543	ncRNA	0.008571	0.435897	
chunk0113_273_1	chr20	56624192	56624555	+	0	NA	Intergenic	Intergenic	-4929	NM_003222	7022	Hs.473152	NM_003222	ENSG00000087510	TFAP2C	AP2-GAMMA|ERF1|TFAP2G|hAP-2g	transcription factor AP-2 gamma	protein-coding	0.002755	0.453297	
chunk0010_299_1	chr1	117740287	117740877	+	0	NA	Intergenic	Intergenic	134600	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.008475	0.458545	137(CTGGTCATTCTGTTCC,-,0.00)
chunk0099_234_1	chr2	96524228	96524919	+	0	NA	Intergenic	Intergenic	-12154	NM_212481	10865	Hs.920	NM_006673	ENSG00000196843	ARID5A	MRF-1|MRF1|RP11-363D14	AT-rich interaction domain 5A	protein-coding	0.018813	0.468208	
chunk0159_452_1	chr5	148841471	148842144	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	15214	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.007429	0.400593	
chunk0042_440_1	chr12	12349620	12350135	+	0	NA	intron (NM_018050, intron 1 of 3)	intron (NM_018050, intron 1 of 3)	358	NM_018050	54682	Hs.591145	NM_018050	ENSG00000111261	MANSC1	9130403P13Rik|LOH12CR3	MANSC domain containing 1	protein-coding	0.040777	0.525194	
chunk0166_140_1	chr6	44858116	44858474	+	0	NA	intron (NM_181356, intron 12 of 12)	intron (NM_181356, intron 12 of 12)	339475	NR_030313	693171		NR_030313	ENSG00000207769	MIR586	MIRN586|hsa-mir-586	microRNA 586	ncRNA	0.002793	0.376045	
chunk0061_256_1	chr14	61321655	61321857	+	0	NA	5' UTR (NM_006255, exon 1 of 14)	5' UTR (NM_006255, exon 1 of 14)	313	NM_006255	5583	Hs.333907	NM_006255	ENSG00000027075	PRKCH	PKC-L|PKCL|PRKCL|nPKC-eta	protein kinase C eta	protein-coding	0.099010	0.729064	
chunk0110_337_1	chr20	19232016	19232434	+	0	NA	intron (NM_020689, intron 1 of 16)	intron (NM_020689, intron 1 of 16)	19579	NM_020689	57419	Hs.654790	NM_020689	ENSG00000185052	SLC24A3	NCKX3	solute carrier family 24 member 3	protein-coding	0.000000	0.257757	
chunk0139_144_1	chr4	53537656	53538075	+	0	NA	intron (NM_001126328, intron 2 of 10)	intron (NM_001126328, intron 2 of 10)	20404	NM_032622	84708	Hs.518760	NM_032622	ENSG00000072201	LNX1	LNX|MPDZ|PDZRN2	ligand of numb-protein X 1	protein-coding	0.007160	0.473810	
chunk0164_67_1	chr6	19465769	19466175	+	0	NA	Intergenic	Intergenic	-285492	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.007389	0.417690	300(GAAAACAGCCAGTGCT,-,0.00),301(AAAACAGCCAGTGCTC,+,0.00)
chunk0082_55_1	chr17	51221162	51221831	+	0	NA	intron (NM_017643, intron 3 of 16)	L3|LINE|CR1	38570	NM_017643	54799	Hs.656803	NM_017643	ENSG00000011258	MBTD1	SA49P01	mbt domain containing 1	protein-coding	0.011958	0.368657	
chunk0163_210_1	chr6	11996698	11997592	+	0	NA	intron (NR_125853, intron 1 of 2)	intron (NR_125853, intron 1 of 2)	4099	NR_125853	101928253	Hs.128163	NR_125853		LOC101928253	-	uncharacterized LOC101928253	ncRNA	0.002237	0.338547	
chunk0173_322_1	chr6	148659945	148660227	+	0	NA	Intergenic	L1MA8|LINE|L1	-87049	NM_005715	10090	Hs.657370	NM_005715	ENSG00000111962	UST	2OST	uronyl 2-sulfotransferase	protein-coding	0.000000	0.321555	
chunk0073_319_1	chr16	14276122	14276600	+	0	NA	Intergenic	L1ME1|LINE|L1	-25927	NR_132983	100129781	Hs.190748	NR_132983		MIR193BHG	-	MIR193B host gene	ncRNA	0.010460	0.419624	
chunk0156_55_1	chr5	103127107	103127830	+	0	NA	intron (NM_001276277, intron 1 of 30)	L2a|LINE|L2	-1838	NM_015216	23262	Hs.212046	NM_015216	ENSG00000145725	PPIP5K2	CFAP160|DFNB100|HISPPD1|IP7K2|VIP2	diphosphoinositol pentakisphosphate kinase 2	protein-coding	0.002766	0.316298	
chunk0026_38_1	chr10	60767436	60767802	+	0	NA	Intergenic	Intergenic	-10712	NM_001170406	983	Hs.732435	NM_001786	ENSG00000170312	CDK1	CDC2|CDC28A|P34CDC2	cyclin dependent kinase 1	protein-coding	0.013661	0.422343	206(GTAACACACTGTACTT,+,0.00)
chunk0195_196_1	chr8	96853234	96853880	+	0	NA	intron (NM_016134, intron 3 of 7)	intron (NM_016134, intron 3 of 7)	208330	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.007740	0.350850	
chunk0019_18_1	chr1	223518490	223519075	+	0	NA	Intergenic	L1PB|LINE|L1	125409	NM_152610	164127	Hs.192090	NM_152610	ENSG00000178395	CCDC185	C1orf65	coiled-coil domain containing 185	protein-coding	0.003419	0.356655	
chunk0031_107_1	chr10	124364515	124365203	+	0	NA	Intergenic	Intergenic	54117	NM_001171814	4942	Hs.523332	NM_000274	ENSG00000065154	OAT	GACR|HOGA|OATASE|OKT	ornithine aminotransferase	protein-coding	0.010174	0.521045	
chunk0092_371_1	chr19	36127949	36128148	+	0	NA	Intergenic	CpG	-11878	NM_001749	826	Hs.515371	NM_001749	ENSG00000126247	CAPNS1	CALPAIN4|CANP|CANPS|CAPN4|CDPS|CSS1	calpain small subunit 1	protein-coding	0.085427	0.625000	
chunk0132_189_1	chr3	157120308	157121003	+	0	NA	intron (NR_034007, intron 1 of 3)	intron (NR_034007, intron 1 of 3)	2347	NR_034007	339894	Hs.478050	NR_034007	ENSG00000243629	LINC00880	-	long intergenic non-protein coding RNA 880	ncRNA	0.066187	0.606322	
chunk0083_369_1	chr17	71099023	71099476	+	0	NA	non-coding (NR_104152, exon 4 of 4)	non-coding (NR_104152, exon 4 of 4)	102930	NR_104152	101928165	Hs.407613	NR_104152	ENSG00000260785	CASC17	LINC00600	cancer susceptibility 17	ncRNA	0.008830	0.420705	
chunk0059_1_1	chr14	29637474	29637728	+	0	NA	intron (NM_002742, intron 6 of 17)	intron (NM_002742, intron 6 of 17)	290092	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.007874	0.388235	
chunk0176_110_1	chr7	11760060	11760807	+	0	NA	intron (NM_015204, intron 1 of 26)	intron (NM_015204, intron 1 of 26)	71765	NM_015204	221981	Hs.120855	NM_015204	ENSG00000005108	THSD7A	-	thrombospondin type 1 domain containing 7A	protein-coding	0.005355	0.320856	
chunk0102_115_1	chr2	144644187	144644424	+	0	NA	Intergenic	Intergenic	-23662	NR_033870	401014	Hs.742290	NR_033870	ENSG00000226674	TEX41	DKFZp686O1327|LINC00953	testis expressed 41	ncRNA	0.004219	0.319328	
chunk0068_235_1	chr15	55740747	55741382	+	0	NA	intron (NM_173814, intron 1 of 19)	intron (NM_173814, intron 1 of 19)	2055	NM_173814	283659	Hs.130957	NM_173814	ENSG00000166450	PRTG	IGDCC5	protogenin	protein-coding	0.009449	0.344340	
chunk0016_413_1	chr1	203323580	203323949	+	0	NA	Intergenic	Intergenic	18228	NM_006763	7832	Hs.519162	NM_006763	ENSG00000159388	BTG2	APRO1|PC3|TIS21	BTG anti-proliferation factor 2	protein-coding	0.008130	0.486486	
chunk0124_114_1	chr3	53985277	53985510	+	0	NA	Intergenic	Intergenic	-93431	NM_021237	58515	Hs.58471	NM_021237	ENSG00000113811	SELENOK	HSPC030|HSPC297|SELK	selenoprotein K	protein-coding	0.012876	0.427350	
chunk0038_294_1	chr11	90335270	90335571	+	0	NA	intron (NR_104190, intron 1 of 6)	intron (NR_104190, intron 1 of 6)	84188	NR_104190	101929222	Hs.616763	NR_104190	ENSG00000261645	DISC1FP1	Boymaw	DISC1 fusion partner 1	ncRNA	0.000000	0.307947	
chunk0064_155_1	chr14	91828310	91828534	+	0	NA	intron (NM_001128596, intron 1 of 11)	L1MC5|LINE|L1	8104	NM_152332	123036	Hs.510262	NM_152332	ENSG00000165929	TC2N	C14orf47|C2CD1|MTAC2D1|Tac2-N	tandem C2 domains, nuclear	protein-coding	0.000000	0.235556	
chunk0103_5_1	chr2	158810746	158811585	+	0	NA	intron (NM_001017920, intron 3 of 3)	intron (NM_001017920, intron 3 of 3)	15848	NM_001017920	92196	Hs.59761	NM_001017920	ENSG00000163331	DAPL1	-	death associated protein like 1	protein-coding	0.009535	0.403571	
chunk0173_240_1	chr6	146833164	146833417	+	0	NA	Intergenic	L1MD2|LINE|L1	-29466	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.007905	0.488189	
chunk0053_221_1	chr13	32144004	32144627	+	0	NA	intron (NM_023037, intron 11 of 60)	intron (NM_023037, intron 11 of 60)	-112676	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.008026	0.299679	
chunk0186_160_1	chr7	139251040	139251558	+	0	NA	intron (NM_173569, intron 2 of 17)	L1MC3|LINE|L1	19814	NM_173569	254048	Hs.153458	NM_173569	ENSG00000157741	UBN2	-	ubinuclein 2	protein-coding	0.000000	0.383430	
chunk0148_406_1	chr5	14898166	14898474	+	0	NA	Intergenic	L1ME3Cz|LINE|L1	-26542	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.003247	0.368932	
chunk0143_352_1	chr4	121977288	121977583	+	0	NA	Intergenic	Intergenic	-25681	NM_001130698	7222	Hs.150981	NM_003305	ENSG00000138741	TRPC3	SCA41|TRP3	transient receptor potential cation channel subfamily C member 3	protein-coding	0.016949	0.537162	145(GAGCACAAGGAGTGCC,-,0.00),146(AGCACAAGGAGTGCCC,+,0.00)
chunk0080_121_1	chr17	27247164	27247887	+	0	NA	Intergenic	Intergenic	46471	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.008299	0.482044	
chunk0148_163_1	chr5	6644726	6645073	+	0	NA	intron (NM_001047, intron 1 of 4)	intron (NM_001047, intron 1 of 4)	11512	NM_001047	6715	Hs.552	NM_001047	ENSG00000145545	SRD5A1	S5AR 1	steroid 5 alpha-reductase 1	protein-coding	0.014409	0.479885	
chunk0200_212_1	chr9	20566295	20566889	+	0	NA	intron (NM_001286691, intron 2 of 10)	L2c|LINE|L2	55395	NM_001286691	4300	Hs.317248	NM_004529	ENSG00000171843	MLLT3	AF9|YEATS3	MLLT3 super elongation complex subunit	protein-coding	0.008418	0.415126	
chunk0091_233_1	chr19	10509600	10509936	+	0	NA	Intergenic	L1ME4b|LINE|L1	-6390	NM_203500	9817	Hs.465870	NM_012289	ENSG00000079999	KEAP1	INrf2|KLHL19	kelch like ECH associated protein 1	protein-coding	0.008929	0.448071	
chunk0152_451_1	chr5	66375989	66376267	+	0	NA	Intergenic	Intergenic	135476	NR_105001	101928769	Hs.97903	NR_105001	ENSG00000250313	LINC02229	-	long intergenic non-protein coding RNA 2229	ncRNA	0.007194	0.351254	
chunk0119_405_1	chr22	49403782	49403981	+	0	NA	Intergenic	L2|LINE|L2	139585	NR_037440	100500882		NR_037440	ENSG00000264139	MIR3667	-	microRNA 3667	ncRNA	0.020101	0.390000	63(GAGTACAGACAGTTCT,-,0.00),64(AGTACAGACAGTTCTA,+,0.00)
chunk0054_283_1	chr13	46759860	46760398	+	0	NA	Intergenic	Intergenic	37103	NM_001984	2098	Hs.432491	NM_001984	ENSG00000139684	ESD	FGH	esterase D	protein-coding	0.003717	0.441558	
chunk0046_121_1	chr12	57323281	57324002	+	0	NA	Intergenic	UCON6|Unknown|Unknown	-13178	NM_014925	22864	Hs.443673	NM_014925	ENSG00000179912	R3HDM2	CAG6|PR01365	R3H domain containing 2	protein-coding	0.008322	0.398892	
chunk0151_16_1	chr5	41315883	41316110	+	0	NA	intron (NM_001005473, intron 2 of 2)	L1MA1|LINE|L1	-54558	NM_001115131	729	Hs.481992	NM_000065	ENSG00000039537	C6	-	complement C6	protein-coding	0.000000	0.486842	
chunk0197_254_1	chr8	123431577	123431830	+	0	NA	intron (NM_018024, intron 3 of 5)	MIRb|SINE|MIR	14978	NM_001283024	55093	Hs.18029	NM_018024	ENSG00000156795	WDYHV1	C8orf32	WDYHV motif containing 1	protein-coding	0.003953	0.527559	
chunk0095_130_1	chr2	16648573	16649799	+	0	NA	intron (NM_030797, intron 1 of 11)	MER2|DNA|TcMar-Tigger	16680	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.004078	0.388753	344(AAGAACATAATGTTCA,-,0.00),345(AGAACATAATGTTCAC,+,0.00)
chunk0057_432_1	chr13	110448709	110449038	+	0	NA	intron (NM_001846, intron 18 of 47)	MIRb|SINE|MIR	59306	NR_046583	100874203	Hs.508716	NR_046583	ENSG00000232814	COL4A2-AS1	-	COL4A2 antisense RNA 1	ncRNA	0.033435	0.572727	
chunk0040_451_1	chr11	121654833	121655399	+	0	NA	Intergenic	Intergenic	202913	NM_003105	6653	Hs.368592	NM_003105	ENSG00000137642	SORL1	C11orf32|LR11|LRP9|SORLA|SorLA-1|gp250	sortilin related receptor 1	protein-coding	0.021201	0.474427	
chunk0036_132_1	chr11	61947709	61948074	+	0	NA	Intergenic	Intergenic	-1993	NM_004183	7439	Hs.524910	NM_004183	ENSG00000167995	BEST1	ARB|BEST|BMD|Best1V1Delta2|RP50|TU15B|VMD2	bestrophin 1	protein-coding	0.013699	0.524590	
chunk0138_325_1	chr4	41475302	41475724	+	0	NA	intron (NM_001112717, intron 1 of 25)	MER63A|DNA|hAT-Blackjack	114728	NM_001112717	22998	Hs.335163	NM_014988	ENSG00000064042	LIMCH1	LIMCH1A|LMO7B	LIM and calponin homology domains 1	protein-coding	0.000000	0.437352	
chunk0063_251_1	chr14	82590219	82590423	+	0	NA	Intergenic	MLT1A1-int|LTR|ERVL-MaLR	-967260	NR_110074	101928559	Hs.525499	NR_110074	ENSG00000258977	LINC01467	-	long intergenic non-protein coding RNA 1467	ncRNA	0.000000	0.565854	
chunk0140_160_1	chr4	69521338	69521612	+	0	NA	intron (NM_001297616, intron 1 of 6)	MER52A|LTR|ERV1	4539	NM_001297616	7363	Hs.285887	NM_021139	ENSG00000156096	UGT2B4	HLUG25|UDPGT2B4|UDPGTH1|UDPGTh-1|UGT2B11	UDP glucuronosyltransferase family 2 member B4	protein-coding	0.007299	0.563636	
chunk0123_107_1	chr3	42236617	42237010	+	0	NA	Intergenic	L1MA3|LINE|L1	27134	NM_001174138	885	Hs.458426	NM_000729	ENSG00000187094	CCK	-	cholecystokinin	protein-coding	0.002545	0.342640	
chunk0090_438_1	chr18	79579822	79580169	+	0	NA	Intergenic	Intergenic	-99806	NM_004715	9150	Hs.465490	NM_004715	ENSG00000060069	CTDP1	CCFDN|FCP1	CTD phosphatase subunit 1	protein-coding	0.025937	0.428161	
chunk0077_189_1	chr16	79753641	79753840	+	0	NA	intron (NR_104663, intron 3 of 5)	intron (NR_104663, intron 3 of 5)	-16731	NR_104660	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.005025	0.370000	
chunk0134_81_1	chr3	176487636	176488231	+	0	NA	Intergenic	HAL1b|LINE|L1	-27170	NR_107017	102465858		NR_107017	ENSG00000283333	MIR7977	hsa-mir-7977	microRNA 7977	ncRNA	0.000000	0.286913	
chunk0148_413_1	chr5	14977052	14977589	+	0	NA	Intergenic	Intergenic	-105542	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.003724	0.364312	
chunk0201_32_1	chr9	33415553	33416086	+	0	NA	Intergenic	Intergenic	-13300	NM_001170	364	Hs.455323	NM_001170	ENSG00000165269	AQP7	AQP7L|AQPap|GLYCQTL	aquaporin 7	protein-coding	0.016886	0.569288	
chunk0155_148_1	chr5	93735286	93735846	+	0	NA	intron (NR_028080, intron 8 of 8)	intron (NR_028080, intron 8 of 8)	6037	NM_153216	134187	Hs.678995	NM_153216	ENSG00000248483	POU5F2	SPRM-1	POU domain class 5, transcription factor 2	protein-coding	0.001786	0.433155	
chunk0106_233_1	chr2	202815746	202816089	+	0	NA	exon (NM_001288623, exon 7 of 13)	exon (NM_001288623, exon 7 of 13)	13317	NM_001288624	130026	Hs.516629	NM_138468	ENSG00000163596	ICA1L	ALS2CR14|ALS2CR15	islet cell autoantigen 1 like	protein-coding	0.005831	0.348837	150(TGGAACACAATGTACC,-,0.00),151(GGAACACAATGTACCT,+,0.00)
chunk0179_179_1	chr7	46932236	46932958	+	0	NA	Intergenic	Intergenic	649547	NM_022748	64759	Hs.520814	NM_022748	ENSG00000136205	TNS3	TEM6|TENS1	tensin 3	protein-coding	0.005540	0.392808	
chunk0052_410_1	chr12	131196331	131196530	+	0	NA	intron (NR_026670, intron 1 of 4)	intron (NR_026670, intron 1 of 4)	31419	NR_026670	116437	Hs.675497	NR_026670	ENSG00000204603	LINC01257	-	long intergenic non-protein coding RNA 1257	ncRNA	0.010050	0.585000	
chunk0166_52_1	chr6	42879325	42879596	+	0	NA	promoter-TSS (NM_198486)	promoter-TSS (NM_198486)	-473	NM_198486	285855	Hs.520133	NM_198486	ENSG00000146223	RPL7L1	dJ475N16.4	ribosomal protein L7 like 1	protein-coding	0.047970	0.492647	
chunk0016_163_1	chr1	197774647	197774846	+	0	NA	intron (NM_001300858, intron 1 of 15)	intron (NM_001300858, intron 1 of 15)	747	NM_144977	163486	Hs.125056	NM_019049	ENSG00000213047	DENND1B	C1ORF18|C1orf218|FAM31B	DENN domain containing 1B	protein-coding	0.055276	0.540000	
chunk0176_460_1	chr7	20153367	20153667	+	0	NA	TTS (NR_046756)	TTS (NR_046756)	11601	NR_046756	100874041	Hs.145104	NR_046756	ENSG00000228598	MACC1-AS1	-	MACC1 antisense RNA 1	ncRNA	0.000000	0.302326	
chunk0016_406_1	chr1	203271347	203271983	+	0	NA	Intergenic	Intergenic	-15487	NR_117097	100506775	Hs.443859	NR_117097	ENSG00000231507	LINC01353	-	long intergenic non-protein coding RNA 1353	ncRNA	0.009434	0.464678	
chunk0030_278_1	chr10	116589873	116590170	+	0	NA	promoter-TSS (NM_006229)	promoter-TSS (NM_006229)	-938	NM_006229	5407	Hs.73923	NM_006229	ENSG00000187021	PNLIPRP1	PLRP1	pancreatic lipase related protein 1	protein-coding	0.010101	0.432886	
chunk0008_382_1	chr1	97004154	97004559	+	0	NA	Intergenic	Intergenic	-91567	NR_046590	100873932	Hs.682651	NR_046590	ENSG00000232878	DPYD-AS1	-	DPYD antisense RNA 1	ncRNA	0.004938	0.433498	
chunk0212_39_1	chrY	11293434	11293924	+	0	NA	Intergenic	Intergenic	1127911	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.014286	0.462322	
chunk0076_151_1	chr16	67199296	67199495	+	0	NA	TTS (NM_001950)	TTS (NM_001950)	270	NM_024712	79767	Hs.377416	NM_024712	ENSG00000102890	ELMO3	CED-12|CED12|ELMO-3	engulfment and cell motility 3	protein-coding	0.070352	0.705000	
chunk0210_99_1	chrX	71551974	71552497	+	0	NA	intron (NM_181673, intron 5 of 21)	AluSz|SINE|Alu	19173	NM_181672	8473	Hs.405410	NM_003605	ENSG00000147162	OGT	HINCUT-1|HRNT1|MRX106|O-GLCNAC|OGT1	O-linked N-acetylglucosamine (GlcNAc) transferase	protein-coding	0.022945	0.467557	
chunk0141_44_1	chr4	77146307	77146923	+	0	NA	Intergenic	Intergenic	-10589	NM_004354	901	Hs.740456	NM_004354	ENSG00000138764	CCNG2	-	cyclin G2	protein-coding	0.003247	0.369530	
chunk0186_410_1	chr7	145810521	145810907	+	0	NA	Intergenic	L1M1|LINE|L1	-305647	NM_014141	26047	Hs.655684	NM_014141	ENSG00000174469	CNTNAP2	AUTS15|CASPR2|CDFE|NRXN4|PTHSL1	contactin associated protein like 2	protein-coding	0.002591	0.519380	
chunk0051_226_1	chr12	116866710	116867056	+	0	NA	intron (NM_003806, intron 1 of 1)	intron (NM_003806, intron 1 of 1)	14544	NR_073189	8739	Hs.26605	NM_003806	ENSG00000135116	HRK	DP5|HARAKIRI	harakiri, BCL2 interacting protein	protein-coding	0.011561	0.466859	
chunk0169_422_1	chr6	108644252	108644679	+	0	NA	intron (NM_201559, intron 2 of 3)	L2-3_Crp|LINE|L2	83599	NM_001455	2309	Hs.220950	NM_001455	ENSG00000118689	FOXO3	AF6q21|FKHRL1|FKHRL1P2|FOXO2|FOXO3A	forkhead box O3	protein-coding	0.009368	0.446262	214(ATGGACACTCTGTTCT,-,0.00),215(TGGACACTCTGTTCTC,+,0.00)
chunk0206_371_1	chr9	125991008	125991314	+	0	NA	Intergenic	L2a|LINE|L2	242962	NM_001134778	5090	Hs.428027	NM_006195	ENSG00000167081	PBX3	-	PBX homeobox 3	protein-coding	0.022876	0.521173	
chunk0196_320_1	chr8	111114014	111114724	+	0	NA	intron (NR_125418, intron 2 of 3)	intron (NR_125418, intron 2 of 3)	-86936	NR_125417	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.008451	0.433193	318(CAGCTCAGCCTGTCCT,-,0.00),319(AGCTCAGCCTGTCCTG,+,0.00)
chunk0063_6_1	chr14	75984694	75985641	+	0	NA	promoter-TSS (NM_001102564)	promoter-TSS (NM_001102564)	-586	NR_045665	112752	Hs.532626	NM_052873	ENSG00000119650	IFT43	C14orf179|CED3|RP81|SRTD18	intraflagellar transport 43	protein-coding	0.011616	0.422996	836(AATACAGACAGTTCCT,+,0.00)
chunk0143_284_1	chr4	117416106	117416804	+	0	NA	Intergenic	Intergenic	-11943	NR_125757	103689918	Hs.582062	NR_125757		LINC01378	-	long intergenic non-protein coding RNA 1378	ncRNA	0.004298	0.397711	
chunk0042_388_1	chr12	10753035	10753397	+	0	NA	intron (NR_120463, intron 1 of 6)	intron (NR_120463, intron 1 of 6)	2982	NR_120463	101928162	Hs.112950	NR_120463	ENSG00000256888	LINC02366	-	long intergenic non-protein coding RNA 2366	ncRNA	0.011050	0.465565	
chunk0195_424_1	chr8	100780800	100781171	+	0	NA	Intergenic	MER117|DNA|hAT-Charlie	-58898	NM_002568	26986	Hs.387804	NM_002568	ENSG00000070756	PABPC1	PAB1|PABP|PABP1|PABPC2|PABPL1	poly(A) binding protein cytoplasmic 1	protein-coding	0.010782	0.379032	
chunk0026_213_1	chr10	64322579	64323151	+	0	NA	Intergenic	Intergenic	-502663	NR_001446	305	Hs.591361	NR_001446		ANXA2P3	ANX2L3|ANX2P3|LIP2|LPC2C	annexin A2 pseudogene 3	pseudo	0.001748	0.363002	
chunk0141_227_1	chr4	84750717	84751018	+	0	NA	intron (NM_014991, intron 36 of 67)	intron (NM_014991, intron 36 of 67)	167963	NM_001263	1040	Hs.654899	NM_001263	ENSG00000163624	CDS1	CDS 1	CDP-diacylglycerol synthase 1	protein-coding	0.000000	0.423841	
chunk0145_331_1	chr4	150725524	150725862	+	0	NA	intron (NM_001199282, intron 36 of 56)	L1MA5|LINE|L1	143768	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.005917	0.339233	
chunk0204_203_1	chr9	96654816	96655015	+	0	NA	intron (NM_153698, intron 1 of 5)	CpG-28553	402	NM_153698	195827	Hs.44640	NM_153698	ENSG00000158122	PRXL2C	AAED1|C9orf21	peroxiredoxin like 2C	protein-coding	0.140704	0.740000	
chunk0182_393_1	chr7	100429048	100429247	+	0	NA	promoter-TSS (NM_001258008)	promoter-TSS (NM_001258008)	-339	NM_017984	55063	Hs.105191	NM_017984	ENSG00000078487	ZCWPW1	ZCW1	zinc finger CW-type and PWWP domain containing 1	protein-coding	0.065327	0.595000	
chunk0129_205_1	chr3	121709251	121709559	+	0	NA	intron (NM_001256488, intron 9 of 20)	L1ME2z|LINE|L1	40362	NM_001256488	2804	Hs.213389	NM_004487	ENSG00000173230	GOLGB1	GCP|GCP372|GOLIM1	golgin B1	protein-coding	0.006494	0.307443	
chunk0090_361_1	chr18	76953251	76954069	+	0	NA	intron (NM_001306089, intron 27 of 30)	intron (NM_001306089, intron 27 of 30)	63439	NM_001025081	4155	Hs.551713	NM_002385	ENSG00000197971	MBP	-	myelin basic protein	protein-coding	0.019560	0.495726	
chunk0035_319_1	chr11	47408051	47408607	+	0	NA	promoter-TSS (NM_001128225)	promoter-TSS (NM_001128225)	-166	NM_001128225	91252	Hs.523664	NM_152264	ENSG00000165915	SLC39A13	EDSSPD3|LZT-Hs9|SCDEDS|ZIP13	solute carrier family 39 member 13	protein-coding	0.122302	0.766607	
chunk0195_358_1	chr8	99844747	99845073	+	0	NA	intron (NM_152564, intron 54 of 61)	MLT1I-int|LTR|ERVL-MaLR	49104	NM_004374	1345	Hs.351875	NM_004374	ENSG00000164919	COX6C	-	cytochrome c oxidase subunit 6C	protein-coding	0.006135	0.366972	
chunk0069_419_1	chr15	68042050	68043034	+	0	NA	Intergenic	L1MB4|LINE|L1	-11692	NM_016166	8554	Hs.162458	NM_016166	ENSG00000033800	PIAS1	DDXBP1|GBP|GU/RH-II|ZMIZ3	protein inhibitor of activated STAT 1	protein-coding	0.007114	0.391878	
chunk0170_89_1	chr6	110329807	110330091	+	0	NA	intron (NM_001123364, intron 1 of 4)	L1MD2|LINE|L1	28323	NM_001123364	728464	Hs.634429	NM_001123364	ENSG00000053328	METTL24	C6orf186	methyltransferase like 24	protein-coding	0.031690	0.540351	
chunk0004_57_1	chr1	43125032	43125368	+	0	NA	Intergenic	L1MEd|LINE|L1	-22723	NM_001101376	440585	Hs.657614	NM_001101376	ENSG00000186973	FAM183A	-	family with sequence similarity 183 member A	protein-coding	0.000000	0.284866	
chunk0074_66_1	chr16	21245015	21245263	+	0	NA	intron (NM_145865, intron 1 of 1)	MER102b|DNA|hAT-Charlie	11444	NM_145865	257629	Hs.115959	NM_145865	ENSG00000175311	ANKS4B	HARP	ankyrin repeat and sterile alpha motif domain containing 4B	protein-coding	0.012097	0.401606	
chunk0041_17_1	chr12	433718	434331	+	0	NA	intron (NM_032358, intron 9 of 12)	intron (NM_032358, intron 9 of 12)	-26353	NM_173593	283358	Hs.504416	NM_173593	ENSG00000139044	B4GALNT3	-	beta-1,4-N-acetyl-galactosaminyltransferase 3	protein-coding	0.008157	0.346906	
chunk0196_242_1	chr8	108445031	108445594	+	0	NA	intron (NM_014673, intron 1 of 10)	L2c|LINE|L2	1688	NM_014673	9694	Hs.654351	NM_014673	ENSG00000104412	EMC2	KIAA0103|TTC35	ER membrane protein complex subunit 2	protein-coding	0.003552	0.398936	
chunk0130_7_1	chr3	128347550	128348203	+	0	NA	intron (NM_021937, intron 5 of 6)	intron (NM_021937, intron 5 of 6)	-115718	NR_037890	285224	Hs.683815	NR_037890	ENSG00000242049	DNAJB8-AS1	-	DNAJB8 antisense RNA 1	ncRNA	0.006126	0.314985	
chunk0083_270_1	chr17	68443411	68444209	+	0	NA	intron (NM_017983, intron 4 of 12)	intron (NM_017983, intron 4 of 12)	13702	NM_017983	55062	Hs.463964	NM_017983	ENSG00000070540	WIPI1	ATG18|ATG18A|WIPI49	WD repeat domain, phosphoinositide interacting 1	protein-coding	0.007519	0.364205	400(ATGTACAAGTTGTTCC,-,0.00)
chunk0084_61_1	chr17	74671170	74671603	+	0	NA	5' UTR (NM_175738, exon 1 of 9)	5' UTR (NM_175738, exon 1 of 9)	269	NM_175738	326624	Hs.351413	NM_175738	ENSG00000172794	RAB37	-	RAB37, member RAS oncogene family	protein-coding	0.087760	0.661290	
chunk0193_112_1	chr8	74061618	74062215	+	0	NA	Intergenic	Intergenic	70587	NM_001195797	23643	Hs.726603	NM_015364	ENSG00000154589	LY96	ESOP-1|MD-2|MD2|ly-96	lymphocyte antigen 96	protein-coding	0.001675	0.356187	
chunk0062_89_1	chr14	67983074	67983715	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	163615	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.000000	0.303738	
chunk0177_268_1	chr7	25411551	25412062	+	0	NA	Intergenic	Intergenic	-183320	NM_022150	64111	Hs.60473	NM_022150	ENSG00000105954	NPVF	C7orf9|RFRP	neuropeptide VF precursor	protein-coding	0.003914	0.435547	
chunk0144_91_1	chr4	128385180	128385404	+	0	NA	Intergenic	Intergenic	-42724	NR_125882	100507487	Hs.549644	NR_125882	ENSG00000251432	LINC02615	-	long intergenic non-protein coding RNA 2615	ncRNA	0.004464	0.404444	65(AGGAAGAGTGTGTCCC,-,0.00),66(GGAAGAGTGTGTCCCG,+,0.00)
chunk0050_170_1	chr12	103814505	103814884	+	0	NA	intron (NM_001031701, intron 2 of 13)	intron (NM_001031701, intron 2 of 13)	26503	NM_001031701	51559	Hs.48428	NM_016575	ENSG00000111696	NT5DC3	TU12B1-TY|TU12B1TY	5'-nucleotidase domain containing 3	protein-coding	0.007916	0.381579	
chunk0021_364_1	chr1	246350787	246351043	+	0	NA	intron (NM_001167740, intron 2 of 11)	intron (NM_001167740, intron 2 of 11)	66497	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.019531	0.404669	
chunk0087_302_1	chr18	39307702	39308389	+	0	NA	intron (NR_024391, intron 3 of 3)	intron (NR_024391, intron 3 of 3)	314130	NR_030628	100126323		NR_030628	ENSG00000283615	MIR924	MIRN924|hsa-mir-924	microRNA 924	ncRNA	0.002911	0.367733	354(AAGTACATTATGTCCA,-,0.00),355(AGTACATTATGTCCAT,+,0.00)
chunk0027_427_1	chr10	80923305	80923708	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	382687	NM_001145719	387694	Hs.147643	NM_207372	ENSG00000178217	SH2D4B	-	SH2 domain containing 4B	protein-coding	0.012407	0.443069	
chunk0079_449_1	chr17	20284865	20285192	+	0	NA	intron (NM_001033553, intron 12 of 14)	intron (NM_001033553, intron 12 of 14)	-36146	NR_023380	348254	Hs.462475	NR_023380		CCDC144CP	CCDC144C	coiled-coil domain containing 144C, pseudogene	pseudo	0.009174	0.445122	
chunk0187_218_1	chr7	152143822	152144442	+	0	NA	intron (NM_170606, intron 55 of 58)	L2|LINE|L2	118458	NM_022087	63917	Hs.647109	NM_022087	ENSG00000178234	GALNT11	GALNAC-T11|GALNACT11	polypeptide N-acetylgalactosaminyltransferase 11	protein-coding	0.009677	0.423510	
chunk0044_34_1	chr12	27389103	27389417	+	0	NA	TTS (NR_109975)	TTS (NR_109975)	56406	NM_001248003	56938	Hs.445447	NM_020183	ENSG00000029153	ARNTL2	BMAL2|CLIF|MOP9|PASD9|bHLHe6	aryl hydrocarbon receptor nuclear translocator like 2	protein-coding	0.003185	0.307937	
chunk0089_195_1	chr18	59971939	59972704	+	0	NA	Intergenic	Intergenic	72361	NM_021127	5366	Hs.96	NM_021127	ENSG00000141682	PMAIP1	APR|NOXA	phorbol-12-myristate-13-acetate-induced protein 1	protein-coding	0.005229	0.379896	351(AGAACACTGAGATCTC,+,0.00)
chunk0168_265_1	chr6	89413090	89413379	+	0	NA	promoter-TSS (NM_021244)	promoter-TSS (NM_021244)	-958	NM_021244	58528	Hs.31712	NM_021244	ENSG00000025039	RRAGD	RAGD|bA11D8.2.1	Ras related GTP binding D	protein-coding	0.031142	0.541379	95(CGGAACACACTGTACC,-,0.00),96(GGAACACACTGTACCC,+,0.00)
chunk0149_228_1	chr5	22971179	22971378	+	0	NA	Intergenic	L1PA15|LINE|L1	-117656	NM_004061	1010	Hs.113684	NM_004061	ENSG00000154162	CDH12	CDHB	cadherin 12	protein-coding	0.020101	0.585000	
chunk0018_58_1	chr1	216765455	216765994	+	0	NA	intron (NM_001243513, intron 1 of 7)	intron (NM_001243513, intron 1 of 7)	39643	NM_001243514	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.011132	0.440741	348(TTGAACATGCTGTTCC,-,0.00),349(TGAACATGCTGTTCCT,+,0.00)
chunk0086_130_1	chr18	21074072	21074658	+	0	NA	intron (NM_005406, intron 1 of 32)	intron (NM_005406, intron 1 of 32)	37486	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.003413	0.415673	
chunk0174_40_1	chr6	154522755	154522972	+	0	NA	Intergenic	Intergenic	-12244	NM_173515	154043	Hs.16064	NM_173515	ENSG00000153721	CNKSR3	CNK3|CNK3/IPCEF1|MAGI1	CNKSR family member 3	protein-coding	0.013825	0.376147	
chunk0200_8_1	chr9	14543787	14544414	+	0	NA	Intergenic	Intergenic	-145117	NM_001190738	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.004785	0.364650	16(AGGAACAATGAGTTCC,-,0.00),17(GGAACAATGAGTTCCT,+,0.00)
chunk0112_215_1	chr20	40648629	40648918	+	0	NA	Intergenic	Intergenic	40467	NM_005461	9935	Hs.169487	NM_005461	ENSG00000204103	MAFB	DURS3|KRML|MCTO	MAF bZIP transcription factor B	protein-coding	0.010381	0.534483	
chunk0048_133_1	chr12	79914430	79914728	+	0	NA	promoter-TSS (NM_001143886)	promoter-TSS (NM_001143886)	-668	NM_001143886	4659	Hs.49582	NM_002480	ENSG00000058272	PPP1R12A	M130|MBS|MYPT1	protein phosphatase 1 regulatory subunit 12A	protein-coding	0.003356	0.341137	93(TGTACAGACTGTACAT,+,0.00)
chunk0178_317_1	chr7	38221839	38222998	+	0	NA	intron (NM_032016, intron 7 of 8)	intron (NM_032016, intron 7 of 8)	44212	NM_032016	83930	Hs.309753	NM_032016	ENSG00000010270	STARD3NL	MENTHO	STARD3 N-terminal like	protein-coding	0.005177	0.395690	
chunk0003_443_1	chr1	41239962	41240364	+	0	NA	intron (NM_001172219, intron 1 of 14)	intron (NM_001172219, intron 1 of 14)	1980	NM_001172218	22955	Hs.571874	NM_012236	ENSG00000010803	SCMH1	Scml3	Scm polycomb group protein homolog 1	protein-coding	0.000000	0.367246	
chunk0094_18_1	chr2	1096132	1096422	+	0	NA	intron (NM_018968, intron 2 of 16)	L1MA9|LINE|L1	145409	NM_018968	54221	Hs.595069	NM_018968	ENSG00000172554	SNTG2	G2SYN|SYN5	syntrophin gamma 2	protein-coding	0.000000	0.347079	
chunk0010_245_1	chr1	116468432	116468719	+	0	NA	intron (NR_125973, intron 2 of 3)	intron (NR_125973, intron 2 of 3)	10251	NR_125972	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.003484	0.406250	
chunk0125_30_1	chr3	62290224	62290493	+	0	NA	intron (NM_002841, intron 28 of 29)	L1ME3G|LINE|L1	28589	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.011152	0.325926	7(AAAGACATTGTGTTCA,-,0.00),8(AAGACATTGTGTTCAT,+,0.00)
chunk0044_253_1	chr12	32050117	32050457	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-56964	NM_001003398	636	Hs.505202	NM_001714	ENSG00000151746	BICD1	BICD|bic-D 1	BICD cargo adaptor 1	protein-coding	0.005882	0.366569	
chunk0126_95_1	chr3	74869839	74870341	+	0	NA	Intergenic	L1ME3B|LINE|L1	-344386	NR_049831	100846999		NR_049831	ENSG00000266780	MIR4444-2	-	microRNA 4444-2	ncRNA	0.009960	0.326044	
chunk0092_148_1	chr19	28838234	28838613	+	0	NA	Intergenic	Intergenic	-110729	NR_110759	100420587	Hs.569956	NR_110759	ENSG00000283403	LOC100420587	-	SHC binding and spindle associated 1 pseudogene	pseudo	0.007916	0.357895	
chunk0074_223_1	chr16	26118938	26119324	+	0	NA	intron (NM_006040, intron 1 of 1)	MIR|SINE|MIR	93894	NR_036146	100422923		NR_036146	ENSG00000265005	MIR548W	-	microRNA 548w	ncRNA	0.002591	0.392765	
chunk0195_410_1	chr8	100596442	100596641	+	0	NA	intron (NM_152628, intron 10 of 13)	intron (NM_152628, intron 10 of 13)	-36755	NM_001270379	157567	Hs.530199	NM_198401	ENSG00000186106	ANKRD46	ANK-S|GENX-115279	ankyrin repeat domain 46	protein-coding	0.005025	0.445000	
chunk0157_112_1	chr5	116858850	116859365	+	0	NA	Intergenic	LTR48B|LTR|ERV1	-96898	NR_104678	102467223	Hs.570916	NR_104678		LINC02214	-	long intergenic non-protein coding RNA 2214	ncRNA	0.007767	0.436047	
chunk0009_28_1	chr1	100239933	100240518	+	0	NA	intron (NM_001918, intron 2 of 10)	intron (NM_001918, intron 2 of 10)	9628	NM_001918	1629	Hs.709187	NM_001918	ENSG00000137992	DBT	BCATE2|BCKAD-E2|BCKADE2|BCOADC-E2|E2|E2B	dihydrolipoamide branched chain transacylase E2	protein-coding	0.001709	0.395904	
chunk0010_367_1	chr1	119015564	119015882	+	0	NA	Intergenic	L2a|LINE|L2	-26167	NM_152380	6913	Hs.146196	NM_152380	ENSG00000092607	TBX15	TBX14	T-box transcription factor 15	protein-coding	0.003145	0.379310	
chunk0196_314_1	chr8	110651029	110651823	+	0	NA	Intergenic	L1M5|LINE|L1	376007	NR_125416	101927459	Hs.575543	NR_125416	ENSG00000253877	LINC01608	-	long intergenic non-protein coding RNA 1608	ncRNA	0.002519	0.311950	
chunk0188_245_1	chr8	13913278	13913744	+	0	NA	Intergenic	L1MC1|LINE|L1	346668	NM_001007090	157773	Hs.104941	NM_001007090	ENSG00000164743	C8orf48	-	chromosome 8 open reading frame 48	protein-coding	0.015021	0.372591	
chunk0030_159_1	chr10	113976879	113977172	+	0	NA	Intergenic	L2b|LINE|L2	-67022	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.010239	0.428571	
chunk0190_118_1	chr8	30531437	30531816	+	0	NA	intron (NM_006867, intron 5 of 9)	intron (NM_006867, intron 5 of 9)	-106974	NM_001206847	100507341	Hs.659493	NM_001206847	ENSG00000253457	SMIM18	-	small integral membrane protein 18	protein-coding	0.002639	0.378947	
chunk0205_184_1	chr9	109036734	109037002	+	0	NA	intron (NM_032012, intron 15 of 17)	intron (NM_032012, intron 15 of 17)	9430	NR_029506	407036		NR_029506	ENSG00000207698	MIR32	MIRN32|hsa-mir-32|miR-32|miRNA32	microRNA 32	ncRNA	0.003731	0.431227	96(CAGAGCAGTATGTTCA,-,0.00)
chunk0009_87_1	chr1	101220451	101220785	+	0	NA	Intergenic	L2a|LINE|L2	15910	NR_104626	101928370	Hs.534209	NR_104626		LOC101928370	-	uncharacterized LOC101928370	ncRNA	0.005988	0.417910	
chunk0168_347_1	chr6	93054251	93054450	+	0	NA	Intergenic	L1PB4|LINE|L1	365232	NM_001288630	2045	Hs.73962	NM_004440	ENSG00000135333	EPHA7	EHK-3|EHK3|EK11|HEK11	EPH receptor A7	protein-coding	0.010050	0.330000	
chunk0058_5_1	chr14	18656388	18656934	+	0	NA	Intergenic	Intergenic	-23027	NR_046104	642426	Hs.578301	NR_046104	ENSG00000257504	LINC02297	-	long intergenic non-protein coding RNA 2297	ncRNA	0.001832	0.343693	
chunk0057_129_1	chr13	99551360	99552162	+	0	NA	intron (NM_004800, intron 12 of 16)	intron (NM_004800, intron 12 of 16)	-25351	NR_126390	104355149	Hs.639387	NR_126390		LINC01039	-	long intergenic non-protein coding RNA 1039	ncRNA	0.004988	0.381071	
chunk0179_258_1	chr7	48960446	48960878	+	0	NA	Intergenic	Intergenic	36101	NR_003595									0.002315	0.357968	
chunk0038_60_1	chr11	82996985	82997611	+	0	NA	exon (NM_001286061, exon 2 of 5)	exon (NM_001286061, exon 2 of 5)	37271	NM_001286059	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.022364	0.502392	
chunk0180_58_1	chr7	54811297	54811732	+	0	NA	Intergenic	Intergenic	52201	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.004598	0.332569	
chunk0140_196_1	chr4	70260257	70260585	+	0	NA	Intergenic	Intergenic	17805	NM_005212	1448	Hs.54415	NM_005212	ENSG00000171209	CSN3	CNS10|CSN10|CSNK|KCA	casein kappa	protein-coding	0.009146	0.416413	
chunk0186_358_1	chr7	143875659	143875858	+	0	NA	intron (NM_001206941, intron 1 of 7)	intron (NM_001206941, intron 1 of 7)	9615	NM_001206941	9747	Hs.735149	NM_014719	ENSG00000198420	TCAF1	FAM115A	TRPM8 channel associated factor 1	protein-coding	0.000000	0.445000	
chunk0103_407_1	chr2	169305740	169306090	+	0	NA	intron (NM_004525, intron 4 of 78)	Tigger3a|DNA|TcMar-Tigger	56697	NM_004525	4036	Hs.657729	NM_004525	ENSG00000081479	LRP2	DBS|GP330|LRP-2	LDL receptor related protein 2	protein-coding	0.011429	0.378917	148(GGGAACATGGTGTTCA,-,0.00),149(GGAACATGGTGTTCAG,+,0.00)
chunk0035_281_1	chr11	46718044	46718664	+	0	NA	promoter-TSS (NM_000506)	promoter-TSS (NM_000506)	-812	NM_001311257	2147	Hs.655207	NM_000506	ENSG00000180210	F2	PT|RPRGL2|THPH1	coagulation factor II, thrombin	protein-coding	0.012903	0.561997	
chunk0188_80_1	chr8	8420872	8421085	+	0	NA	Intergenic	Intergenic	-39144	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.014085	0.369159	
chunk0139_51_1	chr4	48727974	48728375	+	0	NA	intron (NM_015030, intron 1 of 63)	L1MCa|LINE|L1	52125	NM_015030	285527	Hs.595553	NM_015030	ENSG00000075539	FRYL	AF4p12|KIAA0826|MOR2	FRY like transcription coactivator	protein-coding	0.004988	0.358209	99(CAGTACATCATGTCCA,-,0.00),100(AGTACATCATGTCCAG,+,0.00)
chunk0205_55_1	chr9	106514421	106515020	+	0	NA	Intergenic	L1ME1|LINE|L1	-86208	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.010017	0.371667	
chunk0083_297_1	chr17	69298299	69299244	+	0	NA	intron (NM_172232, intron 9 of 38)	L1PB1|LINE|L1	16862	NM_018672	23461	Hs.731824	NM_018672	ENSG00000154265	ABCA5	ABC13|EST90625|HTC3	ATP binding cassette subfamily A member 5	protein-coding	0.006349	0.373150	
chunk0125_286_1	chr3	69762487	69763048	+	0	NA	promoter-TSS (NM_001184967)	promoter-TSS (NM_001184967)	-789	NM_001184967	4286	Hs.166017	NM_000248	ENSG00000187098	MITF	CMM8|COMMAD|MI|WS2|WS2A|bHLHe32	melanocyte inducing transcription factor	protein-coding	0.005348	0.430605	437(CAGGACACCCTGTGCT,-,0.00),438(AGGACACCCTGTGCTA,+,0.00)
chunk0186_424_1	chr7	146647200	146647876	+	0	NA	intron (NM_014141, intron 1 of 23)	intron (NM_014141, intron 1 of 23)	450071	NR_110829	101928700	Hs.571218	NR_110829	ENSG00000236795	LOC101928700	-	uncharacterized LOC101928700	ncRNA	0.007396	0.348597	
chunk0193_99_1	chr8	73668455	73668857	+	0	NA	intron (NM_001164383, intron 1 of 9)	LTR83|LTR|ERVL	78271	NM_001164380	27067	Hs.561815	NM_014393	ENSG00000040341	STAU2	39K2|39K3	staufen double-stranded RNA binding protein 2	protein-coding	0.004975	0.300248	123(AAGCACGAAGTGTTCT,-,0.00),124(AGCACGAAGTGTTCTC,+,0.00)
chunk0165_262_1	chr6	35737974	35738278	+	0	NA	exon (NM_001286574, exon 2 of 6)	exon (NM_001286574, exon 2 of 6)	1094	NM_145028	221481	Hs.533066	NM_145028	ENSG00000157343	ARMC12	C6orf81	armadillo repeat containing 12	protein-coding	0.032895	0.606557	
chunk0071_30_1	chr15	79418822	79419179	+	0	NA	Intergenic	Intergenic	-13516	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.016807	0.511173	
chunk0153_409_1	chr5	75460422	75461147	+	0	NA	intron (NM_031361, intron 2 of 16)	intron (NM_031361, intron 2 of 16)	50845	NM_031361	10087	Hs.270437	NM_005713	ENSG00000113163	CERT1	CERT|CERTL|COL4A3BP|GPBP|MRD34|STARD11	ceramide transporter 1	protein-coding	0.005517	0.330579	
chunk0199_264_1	chr9	6278056	6278359	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	41126	NM_001314045	90865	Hs.731660	NM_033439	ENSG00000137033	IL33	C9orf26|DVS27|IL1F11|NF-HEV|NFEHEV	interleukin 33	protein-coding	0.000000	0.289474	
chunk0014_372_1	chr1	182627885	182628143	+	0	NA	Intergenic	Intergenic	12874	NR_036490	284648	Hs.253475	NR_036490	ENSG00000261504	LINC01686	-	long intergenic non-protein coding RNA 1686	ncRNA	0.000000	0.374517	144(GGGCACAGGCTGTTTC,-,0.00),145(GGCACAGGCTGTTTCC,+,0.00)
chunk0093_432_1	chr19	58277248	58277551	+	0	NA	Intergenic	Intergenic	-1553	NM_021089	7554	Hs.590941	NM_021089	ENSG00000278129	ZNF8	HF.18|Zfp128	zinc finger protein 8	protein-coding	0.016502	0.476974	
chunk0153_254_1	chr5	72678851	72679209	+	0	NA	Intergenic	L1MA4A|LINE|L1	-18361	NR_105007	102477328	Hs.254516	NR_105007	ENSG00000248371	LINC02056	-	long intergenic non-protein coding RNA 2056	ncRNA	0.000000	0.314763	
chunk0052_358_1	chr12	127274199	127274489	+	0	NA	Intergenic	(TTTG)n|Simple_repeat|Simple_repeat	65728	NR_110057	101927616	Hs.637827	NR_110057	ENSG00000256362	LINC02375	-	long intergenic non-protein coding RNA 2375	ncRNA	0.017241	0.460481	
chunk0055_104_1	chr13	56408207	56408850	+	0	NA	Intergenic	L1MA2|LINE|L1	-732390	NM_001130404	729233	Hs.723090	NM_001130404	ENSG00000204918	PRR20B	PRR20|PRR20A|PRR20C|PRR20D|PRR20E	proline rich 20B	protein-coding	0.001555	0.321429	
chunk0009_306_1	chr1	108112360	108112708	+	0	NA	Intergenic	Intergenic	80275	NM_213651	29957	Hs.656870	NM_013386	ENSG00000085491	SLC25A24	APC1|SCAMC-1|SCAMC1	solute carrier family 25 member 24	protein-coding	0.002874	0.469914	
chunk0169_139_1	chr6	101413720	101413925	+	0	NA	intron (NM_001166247, intron 1 of 16)	intron (NM_001166247, intron 1 of 16)	14837	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.237864	
chunk0104_164_1	chr2	174174648	174175191	+	0	NA	intron (NM_001011708, intron 3 of 9)	L1ME1|LINE|L1	73718	NM_013341	29789	Hs.157351	NM_013341	ENSG00000138430	OLA1	DOC45|GBP45|GTBP9|GTPBP9|PTD004	Obg like ATPase 1	protein-coding	0.007366	0.323529	
chunk0068_303_1	chr15	57159235	57159689	+	0	NA	intron (NM_003205, intron 5 of 19)	intron (NM_003205, intron 5 of 19)	-59968	NM_001306220	6938	Hs.511504	NM_003205	ENSG00000140262	TCF12	CRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64	transcription factor 12	protein-coding	0.006608	0.356044	
chunk0122_165_1	chr3	32246565	32246776	+	0	NA	intron (NM_178868, intron 1 of 3)	intron (NM_178868, intron 1 of 3)	7991	NM_178868	152189	Hs.154986	NM_178868	ENSG00000170293	CMTM8	CKLFSF8|CKLFSF8-V2	CKLF like MARVEL transmembrane domain containing 8	protein-coding	0.000000	0.344340	
chunk0018_154_1	chr1	218761175	218761572	+	0	NA	intron (NR_031644, intron 4 of 6)	intron (NR_031644, intron 4 of 6)	318747	NR_125715	103611157	Hs.133379	NR_125715	ENSG00000281453	TGFB2-OT1	-	TGFB2 overlapping transcript 1	ncRNA	0.007557	0.334171	
chunk0027_353_1	chr10	78742491	78743321	+	0	NA	Intergenic	L2c|LINE|L2	324542	NR_015429	283050	Hs.309176	NR_015429	ENSG00000224596	ZMIZ1-AS1	-	ZMIZ1 antisense RNA 1	ncRNA	0.012048	0.522262	397(GGGCACAGTCTGTATT,-,0.00),398(GGCACAGTCTGTATTT,+,0.00),799(CAGCACATCCTGCCCC,-,0.00),800(AGCACATCCTGCCCCT,+,0.00)
chunk0185_242_1	chr7	129898668	129899476	+	0	NA	intron (NM_001202498, intron 1 of 6)	L1ME3G|LINE|L1	53871	NM_001202498	7328	Hs.643548	NM_003344	ENSG00000186591	UBE2H	E2-20K|GID3|UBC8|UBCH|UBCH2	ubiquitin conjugating enzyme E2 H	protein-coding	0.004950	0.381953	311(AGGTACAAACTGTTCT,-,0.00),312(GGTACAAACTGTTCTG,+,0.00)
chunk0010_80_1	chr1	113355805	113356228	+	0	NA	Intergenic	Intergenic	-34837	NM_001142782	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.007092	0.330189	
chunk0091_305_1	chr19	12801482	12802280	+	0	NA	promoter-TSS (NM_005809)	promoter-TSS (NM_005809)	29	NM_005809	7001	Hs.432121	NM_005809	ENSG00000167815	PRDX2	HEL-S-2a|NKEF-B|NKEFB|PRP|PRX2|PRXII|PTX1|TDPX1|TPX1|TSA	peroxiredoxin 2	protein-coding	0.097744	0.689612	
chunk0161_90_1	chr5	167271289	167271902	+	0	NA	Intergenic	Intergenic	-13243	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.008157	0.403909	
chunk0026_70_1	chr10	61246427	61247158	+	0	NA	Intergenic	Intergenic	-205847	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.001368	0.336066	41(GAAACAGATTGTTCAT,+,0.00)
chunk0060_300_1	chr14	50777825	50778231	+	0	NA	intron (NM_016350, intron 6 of 28)	intron (NM_016350, intron 6 of 28)	53093	NM_182944	51199	Hs.310429	NM_016350	ENSG00000100503	NIN	SCKL7	ninein	protein-coding	0.004926	0.378378	272(AGGATCAACGTGTTCT,-,0.00),273(GGATCAACGTGTTCTG,+,0.00)
chunk0015_323_1	chr1	189478470	189478902	+	0	NA	Intergenic	Intergenic	998943	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.286374	
chunk0098_27_1	chr2	65563158	65563401	+	0	NA	Intergenic	Intergenic	-130757	NM_181784	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.008230	0.487705	135(GGGAACAGGTAGTTCA,-,0.00),136(GGAACAGGTAGTTCAA,+,0.00)
chunk0174_63_1	chr6	155478671	155478959	+	0	NA	Intergenic	Intergenic	-22912	NM_015718	50508	Hs.247776	NM_015718	ENSG00000074771	NOX3	GP91-3|MOX-2	NADPH oxidase 3	protein-coding	0.013889	0.346021	
chunk0039_108_1	chr11	97635761	97635967	+	0	NA	Intergenic	Intergenic	-1128987	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.000000	0.294686	
chunk0170_328_1	chr6	116197393	116197611	+	0	NA	intron (NM_152729, intron 6 of 11)	intron (NM_152729, intron 6 of 11)	56596	NM_021648	23270	Hs.284141	NM_021648	ENSG00000187189	TSPYL4	dJ486I3.2	TSPY like 4	protein-coding	0.013761	0.388128	
chunk0124_120_1	chr3	54211007	54211692	+	0	NA	intron (NM_018398, intron 2 of 37)	L1ME4b|LINE|L1	88683	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.005839	0.364431	
chunk0077_238_1	chr16	80672138	80672526	+	0	NA	intron (NM_152342, intron 2 of 6)	(AC)n|Simple_repeat|Simple_repeat	-99524	NR_104666	101928276	Hs.149769	NR_104665	ENSG00000260737	LINC01227	-	long intergenic non-protein coding RNA 1227	ncRNA	0.005155	0.365039	
chunk0170_454_1	chr6	119309004	119309498	+	0	NA	intron (NM_005907, intron 2 of 12)	intron (NM_005907, intron 2 of 12)	40515	NM_005907	4121	Hs.102788	NM_005907	ENSG00000111885	MAN1A1	HUMM3|HUMM9|MAN9	mannosidase alpha class 1A member 1	protein-coding	0.006073	0.359596	
chunk0098_88_1	chr2	67572683	67573497	+	0	NA	Intergenic	Intergenic	175780	NM_019002	54465	Hs.353022	NM_019002	ENSG00000143971	ETAA1	ETAA16	ETAA1 activator of ATR kinase	protein-coding	0.003686	0.449080	363(TGGAACTTCATGTGCT,-,0.00),364(GGAACTTCATGTGCTT,+,0.00)
chunk0170_209_1	chr6	112601214	112601413	+	0	NA	Intergenic	L1MA3|LINE|L1	253983	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.000000	0.495000	
chunk0078_346_1	chr16	86366534	86366733	+	0	NA	Intergenic	L1ME4a|LINE|L1	-20954	NR_024406	732275	Hs.558087	NR_024406	ENSG00000168367	LINC00917	-	long intergenic non-protein coding RNA 917	ncRNA	0.000000	0.335000	
chunk0062_328_1	chr14	73393402	73393660	+	0	NA	intron (NM_001005743, intron 2 of 12)	intron (NM_001005743, intron 2 of 12)	65049	NM_001005744	8650	Hs.525443	NM_003744	ENSG00000133961	NUMB	C14orf41|S171|c14_5527	NUMB endocytic adaptor protein	protein-coding	0.000000	0.339768	
chunk0181_385_1	chr7	89435112	89435620	+	0	NA	Intergenic	LTR46-int|LTR|ERV1	-639649	NM_152706	219557	Hs.112877	NM_152706	ENSG00000164645	TEX47	C7orf62	testis expressed 47	protein-coding	0.005906	0.469548	
chunk0078_275_1	chr17	7903475	7904224	+	0	NA	exon (NM_005852, exon 24 of 39)	exon (NM_005852, exon 24 of 39)	-2274	NR_003000	677763		NR_003000	ENSG00000252835	SCARNA21	ACA68|SCARNA21A	small Cajal body-specific RNA 21	ncRNA	0.017356	0.490667	681(AGGCACAGACAGTACT,-,0.00),682(GGCACAGACAGTACTG,+,0.00)
chunk0172_300_1	chr6	138088319	138088607	+	0	NA	TTS (NM_022121)	TTS (NM_022121)	19060	NM_022121	64065	Hs.201446	NM_022121	ENSG00000112378	PERP	KCP1|KRTCAP1|PIGPC1|THW|dJ496H19.1	p53 apoptosis effector related to PMP22	protein-coding	0.013889	0.387543	
chunk0106_305_1	chr2	204900474	204900909	+	0	NA	intron (NM_205863, intron 2 of 21)	L1M1|LINE|L1	354898	NM_205863	117583	Hs.657382	NM_057177	ENSG00000116117	PARD3B	ALS2CR19|PAR3B|PAR3L|PAR3beta	par-3 family cell polarity regulator beta	protein-coding	0.004598	0.378440	
chunk0203_218_1	chr9	86778745	86779094	+	0	NA	Intergenic	Intergenic	168270	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.002865	0.380000	
chunk0161_287_1	chr5	172959325	172959524	+	0	NA	promoter-TSS (NR_026683)	promoter-TSS (NR_026683)	-12	NM_016093	51121	Hs.546390	NM_016093	ENSG00000037241	RPL26L1	RPL26P1	ribosomal protein L26 like 1	protein-coding	0.080402	0.620000	
chunk0062_209_1	chr14	70367105	70367380	+	0	NA	3' UTR (NM_018373, exon 4 of 4)	3' UTR (NM_018373, exon 4 of 4)	-7511	NM_001204090	51241	Hs.709581	NM_016468	ENSG00000133983	COX16	C14orf112|HSPC203|hCOX16	cytochrome c oxidase assembly factor COX16	protein-coding	0.010909	0.409420	
chunk0146_154_1	chr4	159829246	159829836	+	0	NA	Intergenic	Intergenic	561695	NM_014247	9693	Hs.744884	NM_014247	ENSG00000109756	RAPGEF2	CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP	Rap guanine nucleotide exchange factor 2	protein-coding	0.005085	0.329949	
chunk0062_454_1	chr14	75717640	75718227	+	0	NA	exon (NM_015072, exon 10 of 32)	exon (NM_015072, exon 10 of 32)	56725	NM_015072	23093	Hs.709609	NM_015072	ENSG00000119685	TTLL5	CORD19|KIAA0998|STAMP	tubulin tyrosine ligase like 5	protein-coding	0.010221	0.414966	
chunk0009_313_1	chr1	108571002	108571217	+	0	NA	intron (NM_001010883, intron 1 of 10)	L2|LINE|L2	10760	NM_001010883	284611	Hs.200230	NM_001010883	ENSG00000162636	FAM102B	SYM-3B	family with sequence similarity 102 member B	protein-coding	0.018605	0.453704	
chunk0190_331_1	chr8	39001091	39001675	+	0	NA	intron (NR_027878, intron 1 of 20)	L2c|LINE|L2	4397	NR_027638	8754	Hs.591852	NM_003816	ENSG00000168615	ADAM9	CORD9|MCMP|MDC9|Mltng	ADAM metallopeptidase domain 9	protein-coding	0.005137	0.328205	
chunk0142_197_1	chr4	97032568	97032945	+	0	NA	Intergenic	Intergenic	-334170	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.002653	0.380952	
chunk0122_415_1	chr3	38852983	38853257	+	0	NA	intron (NM_014139, intron 24 of 25)	intron (NM_014139, intron 24 of 25)	-59110	NM_001293306	6336	Hs.250443	NM_006514	ENSG00000185313	SCN10A	FEPS2|Nav1.8|PN3|SNS|hPN3	sodium voltage-gated channel alpha subunit 10	protein-coding	0.000000	0.410909	217(CAGAACATATTGTGTC,-,0.00),218(AGAACATATTGTGTCT,+,0.00)
chunk0068_316_1	chr15	57406344	57407054	+	0	NA	intron (NM_032866, intron 1 of 18)	intron (NM_032866, intron 1 of 18)	30194	NM_001252335	84952	Hs.148989	NM_032866	ENSG00000128849	CGNL1	JACOP|PCING	cingulin like 1	protein-coding	0.008451	0.434599	
chunk0200_344_1	chr9	24381094	24382067	+	0	NA	Intergenic	Intergenic	164096	NM_001271706	100129669	Hs.573530	NM_001271706	ENSG00000205442	IZUMO3	C9orf134|bA20A20.1	IZUMO family member 3	protein-coding	0.001028	0.401437	240(GAGAACACAGAGTACA,-,0.00),241(AGAACACAGAGTACAT,+,0.00),797(AAGAACACCATGATCT,-,0.00),798(AGAACACCATGATCTA,+,0.00)
chunk0206_148_1	chr9	121368256	121368504	+	0	NA	intron (NR_073037, intron 1 of 7)	intron (NR_073037, intron 1 of 7)	1924	NM_001270526	2040	Hs.253903	NM_004099	ENSG00000148175	STOM	BND7|EPB7|EPB72	stomatin	protein-coding	0.004032	0.381526	
chunk0006_263_1	chr1	69993776	69994162	+	0	NA	intron (NM_020794, intron 8 of 24)	intron (NM_020794, intron 8 of 24)	74647	NR_023916	5301	Hs.654711	NR_023916	ENSG00000229359	PIN1P1	PIN1L	peptidylprolyl cis/trans isomerase, NIMA-interacting 1 pseudogene 1	pseudo	0.007772	0.343669	
chunk0147_142_1	chr4	174736342	174736633	+	0	NA	intron (NM_001042543, intron 3 of 8)	L1MB5|LINE|L1	92828	NM_001042543	8001	Hs.413099	NM_006529	ENSG00000145451	GLRA3	-	glycine receptor alpha 3	protein-coding	0.010309	0.390411	
chunk0073_281_1	chr16	12695341	12696069	+	0	NA	intron (NM_001099455, intron 2 of 2)	MER57B2|LTR|ERV1	-24616	NR_039869	100616195		NR_039869	ENSG00000264733	MIR4718	-	microRNA 4718	ncRNA	0.013736	0.417010	
chunk0186_196_1	chr7	139738233	139738779	+	0	NA	intron (NM_001113239, intron 1 of 14)	MER3|DNA|hAT-Charlie	39388	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.016484	0.427788	
chunk0146_58_1	chr4	155705715	155705959	+	0	NA	intron (NM_000856, intron 5 of 10)	intron (NM_000856, intron 5 of 10)	38174	NM_001130684	2982	Hs.24258	NM_000856	ENSG00000164116	GUCY1A1	GC-SA3|GUC1A3|GUCA3|GUCSA3|GUCY1A3|MYMY6	guanylate cyclase 1 soluble subunit alpha 1	protein-coding	0.004098	0.457143	
chunk0020_65_1	chr1	232613937	232614389	+	0	NA	Intergenic	Intergenic	-98555	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.006637	0.423841	
chunk0210_462_1	chrX	107319082	107319641	+	0	NA	Intergenic	Intergenic	112729	NM_173494	139212	Hs.128836	NM_173494	ENSG00000080572	PIH1D3	CILD36|CXorf41|DNAAF6|NYSAR97|TWISTER	PIH1 domain containing 3	protein-coding	0.003578	0.355357	
chunk0024_434_1	chr10	46106775	46107027	+	0	NA	Intergenic	Intergenic	-2594	NR_126580	653268	Hs.447454	NM_001077685		AGAP7P	AGAP-7|AGAP7|CTGLF4|bA109G10.1	ArfGAP with GTPase domain, ankyrin repeat and PH domain 7, pseudogene	pseudo	0.051587	0.628458	
chunk0052_196_1	chr13	24889328	24889724	+	0	NA	intron (NR_047594, intron 10 of 17)	intron (NR_047594, intron 10 of 17)	33363	NR_047595	55835	Hs.513379	NM_018451	ENSG00000151849	CENPJ	BM032|CENP-J|CPAP|LAP|LIP1|MCPH6|SASS4|SCKL4|Sas-4	centromere protein J	protein-coding	0.020202	0.387909	
chunk0129_333_1	chr3	124600094	124600591	+	0	NA	intron (NM_007064, intron 1 of 26)	intron (NM_007064, intron 1 of 26)	15683	NM_007064	8997	Hs.8004	NM_003947	ENSG00000160145	KALRN	ARHGEF24|CHD5|CHDS5|DUET|DUO|HAPIP|TRAD	kalirin RhoGEF kinase	protein-coding	0.008048	0.423695	
chunk0204_335_1	chr9	101353612	101354174	+	0	NA	Intergenic	Intergenic	29626	NM_001127610	570	Hs.284712	NM_001701	ENSG00000136881	BAAT	BACAT|BAT	bile acid-CoA:amino acid N-acyltransferase	protein-coding	0.005338	0.378330	169(TGGGACTTATTGTCCT,-,0.00),170(GGGACTTATTGTCCTA,+,0.00),317(TGGGACATTGTGTGTT,-,0.00),318(GGGACATTGTGTGTTT,+,0.00)
chunk0075_334_1	chr16	54748993	54749416	+	0	NA	Intergenic	LTR16C|LTR|ERVL	179574	NM_001308963	643911	Hs.237396	NM_001308963		CRNDE	CRNDEP|LINC00180|NCRNA00180|PNAS-108|lincIRX5	colorectal neoplasia differentially expressed	protein-coding	0.007092	0.509434	184(TAGAACGTGCTGTTCA,-,0.00),185(AGAACGTGCTGTTCAG,+,0.00)
chunk0051_72_1	chr12	113223037	113223483	+	0	NA	intron (NM_017901, intron 1 of 27)	intron (NM_017901, intron 1 of 27)	1822	NM_017901	53373	Hs.524763	NM_017901	ENSG00000186815	TPCN1	TPC1	two pore segment channel 1	protein-coding	0.013453	0.442953	
chunk0028_109_1	chr10	84424572	84425149	+	0	NA	promoter-TSS (NM_001284242)	promoter-TSS (NM_001284242)	-79	NM_001284243	54462	Hs.461988	NM_018999	ENSG00000107771	CCSER2	FAM190B|Gcap14|KIAA1128|bA486O22.1	coiled-coil serine rich protein 2	protein-coding	0.008666	0.403114	
chunk0153_382_1	chr5	74987407	74987673	+	0	NA	Intergenic	Intergenic	43359	NM_016591	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.007519	0.520599	
chunk0127_59_1	chr3	89227501	89228102	+	0	NA	intron (NM_005233, intron 3 of 16)	intron (NM_005233, intron 3 of 16)	120277	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004992	0.338870	
chunk0120_175_1	chr3	6058839	6059083	+	0	NA	Intergenic	Intergenic	746488	NR_110125	101927347	Hs.333345	NR_110123	ENSG00000226258	GRM7-AS3	-	GRM7 antisense RNA 3	ncRNA	0.004098	0.281633	
chunk0090_50_1	chr19	1873470	1874113	+	0	NA	Intergenic	Intergenic	-10226	NM_031918	83855	Hs.136280	NM_031918	ENSG00000129911	KLF16	BTEB4|DRRF|NSLP2	Kruppel like factor 16	protein-coding	0.043546	0.618012	
chunk0099_49_1	chr2	84293828	84294179	+	0	NA	Intergenic	Intergenic	3321	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.014245	0.494318	
chunk0040_130_1	chr11	112401815	112402014	+	0	NA	Intergenic	Intergenic	-80318	NR_120559	101928823	Hs.126118	NR_120559	ENSG00000254968	LINC02763	-	long intergenic non-protein coding RNA 2763	ncRNA	0.010050	0.430000	
chunk0001_314_1	chr1	9384567	9385211	+	0	NA	Intergenic	Intergenic	44027	NR_104623	100506022	Hs.131775	NR_104622	ENSG00000284693	LINC02606	-	long intergenic non-protein coding RNA 2606	ncRNA	0.032609	0.572093	
chunk0095_451_1	chr2	25622522	25622994	+	0	NA	intron (NM_001256303, intron 4 of 19)	L1MEh|LINE|L1	27464	NM_001256308	1838	Hs.307720	NM_021907	ENSG00000138101	DTNB	-	dystrobrevin beta	protein-coding	0.004237	0.380550	
chunk0075_272_1	chr16	53780069	53780463	+	0	NA	intron (NM_001080432, intron 1 of 8)	L2a|LINE|L2	76303	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.007614	0.491139	
chunk0037_349_1	chr11	77459231	77459707	+	0	NA	intron (NM_001128620, intron 1 of 15)	intron (NM_001128620, intron 1 of 15)	14594	NM_001128620	5058	Hs.435714	NM_002576	ENSG00000149269	PAK1	IDDMSSD|PAKalpha	p21 (RAC1) activated kinase 1	protein-coding	0.004202	0.350105	
chunk0097_197_1	chr2	50650479	50651057	+	0	NA	intron (NM_001135659, intron 5 of 23)	intron (NM_001135659, intron 5 of 23)	45494	NR_130470	103504737		NR_130470	ENSG00000216191	MIR8485	hsa-mir-8485	microRNA 8485	ncRNA	0.006920	0.338515	344(AAGTACAAAGTGATCT,-,0.00),345(AGTACAAAGTGATCTT,+,0.00)
chunk0014_378_1	chr1	182702899	182703308	+	0	NA	Intergenic	Intergenic	-30171	NM_033345	85397	Hs.20982	NM_033345	ENSG00000135824	RGS8	-	regulator of G protein signaling 8	protein-coding	0.000000	0.421951	
chunk0093_438_1	chr19	58327066	58327558	+	0	NA	intron (NM_181846, intron 1 of 2)	CpG	293	NM_181846	342945	Hs.388162	NM_181846	ENSG00000182318	ZSCAN22	HKR2|ZNF50	zinc finger and SCAN domain containing 22	protein-coding	0.089431	0.645030	
chunk0171_21_1	chr6	120007292	120007945	+	0	NA	Intergenic	L1ME2z|LINE|L1	-7561	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.004594	0.290520	
chunk0194_116_1	chr8	83947727	83947926	+	0	NA	Intergenic	Intergenic	-235392	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005025	0.390000	
chunk0120_107_1	chr3	4524253	4524805	+	0	NA	intron (NM_002222, intron 4 of 57)	intron (NM_002222, intron 4 of 57)	31181	NM_002222	3708	Hs.567295	NM_002222	ENSG00000150995	ITPR1	ACV|CLA4|INSP3R1|IP3R|IP3R1|PPP1R94|SCA15|SCA16|SCA29	inositol 1,4,5-trisphosphate receptor type 1	protein-coding	0.009058	0.386980	
chunk0143_160_1	chr4	110277229	110277556	+	0	NA	Intergenic	Intergenic	-78728	NM_024090	79071	Hs.412939	NM_024090	ENSG00000170522	ELOVL6	FACE|FAE|LCE	ELOVL fatty acid elongase 6	protein-coding	0.009174	0.414634	
chunk0064_327_1	chr14	96251699	96252110	+	0	NA	Intergenic	Intergenic	-4306	NM_000710	623	Hs.525572	NM_000710	ENSG00000100739	BDKRB1	B1BKR|B1R|BDKRB2|BKB1R|BKR1|BRADYB1	bradykinin receptor B1	protein-coding	0.009732	0.475728	
chunk0043_451_1	chr12	26700505	26700704	+	0	NA	intron (NM_002223, intron 9 of 56)	MIRb|SINE|MIR	132594	NM_002223	3709	Hs.512235	NM_002223	ENSG00000123104	ITPR2	ANHD|CFAP48|INSP3R2|IP3R2	inositol 1,4,5-trisphosphate receptor type 2	protein-coding	0.020101	0.570000	
chunk0165_268_1	chr6	35859651	35859869	+	0	NA	intron (NR_034069, intron 12 of 15)	L2b|LINE|L2	54466	NM_182548	222662	Hs.367947	NM_182548	ENSG00000197753	LHFPL5	DFNB67|TMHS|dJ510O8.8	LHFPL tetraspan subfamily member 5	protein-coding	0.013761	0.378995	
chunk0198_291_1	chr8	135647354	135647643	+	0	NA	3' UTR (NM_006558, exon 9 of 9)	3' UTR (NM_006558, exon 9 of 9)	190033	NM_006558	10656	Hs.444558	NM_006558	ENSG00000131773	KHDRBS3	Etle|SALP|SLM-2|SLM2|T-STAR|TSTAR|etoile	KH RNA binding domain containing, signal transduction associated 3	protein-coding	0.003460	0.303448	
chunk0084_225_1	chr17	78397702	78398007	+	0	NA	intron (NR_111989, intron 2 of 8)	intron (NR_111989, intron 2 of 8)	19236	NR_111989	9489	Hs.654671	NM_024419	ENSG00000087157	PGS1	-	phosphatidylglycerophosphate synthase 1	protein-coding	0.039344	0.549020	
chunk0142_221_1	chr4	97845371	97845594	+	0	NA	intron (NM_174952, intron 8 of 10)	L1M5|LINE|L1	297758	NM_174952	285555	Hs.680226	NM_174952	ENSG00000163116	STPG2	C4orf37	sperm tail PG-rich repeat containing 2	protein-coding	0.013453	0.263393	
chunk0186_352_1	chr7	143478716	143478962	+	0	NA	TTS (NM_176883)	TTS (NM_176883)	966	NM_176883	259287	Hs.650648	NM_176883	ENSG00000221855	TAS2R41	T2R41|T2R59	taste 2 receptor member 41	protein-coding	0.020325	0.526316	
chunk0178_243_1	chr7	36153098	36153297	+	0	NA	promoter-TSS (NM_030636)	promoter-TSS (NM_030636)	-30	NM_030636	80820	Hs.487994	NM_030636	ENSG00000122547	EEPD1	HSPC107	endonuclease/exonuclease/phosphatase family domain containing 1	protein-coding	0.145729	0.775000	
chunk0185_248_1	chr7	130109246	130109638	+	0	NA	intron (NM_014997, intron 2 of 9)	L1MC4|LINE|L1	38933	NM_014997	23008	Hs.520710	NM_014997	ENSG00000128607	KLHDC10	slim	kelch domain containing 10	protein-coding	0.007653	0.404580	
chunk0112_263_1	chr20	42576848	42577556	+	0	NA	intron (NM_133170, intron 7 of 31)	intron (NM_133170, intron 7 of 31)	-108281	NR_110004	101927159	Hs.570383	NR_110004	ENSG00000229042	LOC101927159	-	uncharacterized LOC101927159	ncRNA	0.007062	0.448519	
chunk0079_193_1	chr17	14259889	14260088	+	0	NA	Intergenic	Intergenic	-23155	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.005025	0.380000	
chunk0082_79_1	chr17	51703702	51704008	+	0	NA	intron (NM_001082534, intron 5 of 9)	intron (NM_001082534, intron 5 of 9)	367140	NR_122104	440446	Hs.626751	NR_122104	ENSG00000267452	LINC02072	-	long intergenic non-protein coding RNA 2072	ncRNA	0.009804	0.449511	
chunk0153_440_1	chr5	76325515	76326404	+	0	NA	3' UTR (NM_014979, exon 13 of 13)	3' UTR (NM_014979, exon 13 of 13)	-77296	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.007874	0.421348	
chunk0109_216_1	chr20	5714721	5715203	+	0	NA	Intergenic	L1ME4b|LINE|L1	-35425	NM_001303479	149840	Hs.529340	NM_152504	ENSG00000171984	SHLD1	C20orf196|RINN3	shieldin complex subunit 1	protein-coding	0.012448	0.428571	244(AATGACACACTGTTCT,-,0.00),245(ATGACACACTGTTCTA,+,0.00)
chunk0125_194_1	chr3	66830006	66830695	+	0	NA	Intergenic	Intergenic	-167953	NM_032505	84541	Hs.116665	NM_032505	ENSG00000163376	KBTBD8	TA-KRP|TAKRP	kelch repeat and BTB domain containing 8	protein-coding	0.005806	0.389855	
chunk0046_369_1	chr12	63339628	63339985	+	0	NA	Intergenic	L1PA6|LINE|L1	-186996	NM_000706	552	Hs.2131	NM_000706	ENSG00000166148	AVPR1A	AVPR V1a|AVPR1|V1aR	arginine vasopressin receptor 1A	protein-coding	0.002801	0.340782	109(CTGAACAACTTGTTCC,-,0.00),110(TGAACAACTTGTTCCT,+,0.00)
chunk0137_210_1	chr4	18729472	18730017	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-707884	NM_001166139	254251	Hs.446201	NM_153686	ENSG00000178177	LCORL	MLR1	ligand dependent nuclear receptor corepressor like	protein-coding	0.005505	0.347985	
chunk0081_126_1	chr17	40362257	40362548	+	0	NA	3' UTR (NM_152219, exon 1 of 1)	3' UTR (NM_152219, exon 1 of 1)	2291	NM_152219	125111	Hs.444663	NM_152219	ENSG00000183153	GJD3	CX31.9|Cx30.2|GJA11|GJC1	gap junction protein delta 3	protein-coding	0.037801	0.561644	
chunk0002_133_1	chr1	16644697	16644991	+	0	NA	promoter-TSS (NR_027504)	promoter-TSS (NR_027504)	-730	NR_027504	11209	Hs.349110	NR_027504		MST1P2	MSPL-1|MSPL-2|MSPL-3|MSPL1|MSPL2|MSPL3|MSTP1|MSTP2|MSTP3	macrophage stimulating 1 pseudogene 2	pseudo	0.112245	0.694915	
chunk0099_141_1	chr2	86615985	86616184	+	0	NA	TTS (NM_001198952)	TTS (NM_001198952)	7793	NM_005667	7844	Hs.469199	NM_005667	ENSG00000239305	RNF103	HKF-1|KF-1|KF1|ZFP-103|ZFP103	ring finger protein 103	protein-coding	0.000000	0.370000	
chunk0173_89_1	chr6	142946278	142946620	+	0	NA	Intergenic	CpG-24066	-1248	NM_006734	3097	Hs.510172	NM_006734	ENSG00000010818	HIVEP2	HIV-EP2|MBP-2|MIBP1|MRD43|SHN2|ZAS2|ZNF40B	human immunodeficiency virus type I enhancer binding protein 2	protein-coding	0.114035	0.725948	
chunk0106_366_1	chr2	207173087	207173620	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-6107	NM_001270943	8609	Hs.59908	NM_003709	ENSG00000118263	KLF7	UKLF	Kruppel like factor 7	protein-coding	0.009381	0.370787	
chunk0012_305_1	chr1	162207317	162207673	+	0	NA	intron (NM_001164757, intron 2 of 9)	MIRb|SINE|MIR	50388	NR_039798	100616386		NR_039798	ENSG00000266144	MIR4654	mir-4654	microRNA 4654	ncRNA	0.008427	0.448179	
chunk0049_219_1	chr12	93395300	93395596	+	0	NA	intron (NM_001301024, intron 2 of 4)	intron (NM_001301024, intron 2 of 4)	16898	NM_001301022	11163	Hs.506325	NM_019094	ENSG00000173598	NUDT4	DIPP-2B|DIPP2|DIPP2alpha|DIPP2beta|HDCMB47P|NUDT4B	nudix hydrolase 4	protein-coding	0.003378	0.323232	
chunk0082_379_1	chr17	60468303	60468937	+	0	NA	intron (NM_006380, intron 4 of 12)	intron (NM_006380, intron 4 of 12)	46116	NM_181707	124773	Hs.129312	NM_181707	ENSG00000141371	C17orf64	-	chromosome 17 open reading frame 64	protein-coding	0.000000	0.332283	
chunk0118_270_1	chr22	33540228	33540741	+	0	NA	intron (NM_133642, intron 6 of 14)	intron (NM_133642, intron 6 of 14)	-103815	NR_039921	100616295		NR_039921	ENSG00000266012	MIR4764	-	microRNA 4764	ncRNA	0.009747	0.507782	
chunk0093_361_1	chr19	55641035	55641287	+	0	NA	promoter-TSS (NM_016202)	promoter-TSS (NM_016202)	135	NM_207115	51157	Hs.631551	NM_016202	ENSG00000213015	ZNF580	-	zinc finger protein 580	protein-coding	0.134921	0.814229	
chunk0055_39_1	chr13	52164896	52165410	+	0	NA	Intergenic	Intergenic	-5292	NM_002498	4752	Hs.409989	NM_002498	ENSG00000136098	NEK3	HSPK36	NIMA related kinase 3	protein-coding	0.005837	0.380583	
chunk0139_231_1	chr4	55339792	55339997	+	0	NA	Intergenic	HERVIP10B3-int|LTR|ERV1	-6327	NM_024592	79644	Hs.39311	NM_024592	ENSG00000128039	SRD5A3	CDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1	steroid 5 alpha-reductase 3	protein-coding	0.009756	0.432039	
chunk0025_21_1	chr10	48219934	48220287	+	0	NA	intron (NM_001018071, intron 12 of 28)	MIR|SINE|MIR	-44967	NM_001042512	143162	Hs.664786	NM_152428	ENSG00000170324	FRMPD2	PDZD5C|PDZK4|PDZK5C	FERM and PDZ domain containing 2	protein-coding	0.002833	0.347458	151(AGGTACATAGTGATCT,-,0.00),152(GGTACATAGTGATCTT,+,0.00)
chunk0122_113_1	chr3	30877446	30877883	+	0	NA	intron (NM_207359, intron 1 of 14)	intron (NM_207359, intron 1 of 14)	16997	NM_207359	339896	Hs.657052	NM_207359	ENSG00000144644	GADL1	ADC|CSADC|HuADC|HuCSADC	glutamate decarboxylase like 1	protein-coding	0.002288	0.315068	
chunk0177_101_1	chr7	22004904	22005513	+	0	NA	Intergenic	Intergenic	-59284	NM_001127371	55536	Hs.744069	NM_018719	ENSG00000164649	CDCA7L	JPO2|R1|RAM2	cell division cycle associated 7 like	protein-coding	0.003284	0.421311	
chunk0205_296_1	chr9	112012715	112012997	+	0	NA	Intergenic	Intergenic	80756	NR_039814	100616114		NR_039814	ENSG00000266315	MIR4668	mir-4668	microRNA 4668	ncRNA	0.000000	0.455830	32(GGAAGAGAATGTTCCC,+,0.00),122(GAGAACAATTTGTGCT,-,0.00),123(AGAACAATTTGTGCTG,+,0.00)
chunk0029_236_1	chr10	102558619	102559644	+	0	NA	intron (NM_016169, intron 3 of 11)	MLT1L|LTR|ERVL-MaLR	55169	NM_001178133	51684	Hs.404089	NM_016169	ENSG00000107882	SUFU	JBTS32|PRO1280|SUFUH|SUFUXL	SUFU negative regulator of hedgehog signaling	protein-coding	0.011707	0.475634	226(GGGCACTTTCTGTTCT,-,0.00),227(GGCACTTTCTGTTCTG,+,0.00),279(TAGAACACCCTGACCA,-,0.00),280(AGAACACCCTGACCAG,+,0.00),822(GGGAAGAGAATGTTCC,-,0.00)
chunk0129_76_1	chr3	117804642	117805242	+	0	NA	Intergenic	Intergenic	883511	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.006667	0.339434	
chunk0060_6_1	chr14	39090671	39091071	+	0	NA	intron (NM_006364, intron 5 of 19)	intron (NM_006364, intron 5 of 19)	12362	NM_006364	10484	Hs.272927	NM_006364	ENSG00000100934	SEC23A	CLSD|hSec23A	Sec23 homolog A, coat complex II component	protein-coding	0.005000	0.508728	
chunk0140_284_1	chr4	72327074	72327721	+	0	NA	intron (NM_014243, intron 5 of 21)	intron (NM_014243, intron 5 of 21)	241402	NM_014243	9508	Hs.590919	NM_014243	ENSG00000156140	ADAMTS3	ADAMTS-4|HKLLS3	ADAM metallopeptidase with thrombospondin type 1 motif 3	protein-coding	0.003091	0.305556	
chunk0156_379_1	chr5	112863514	112863928	+	0	NA	intron (NM_001204194, intron 2 of 3)	AluJb|SINE|Alu	2533	NM_001204199	6728	Hs.637001	NM_003135	ENSG00000153037	SRP19	-	signal recognition particle 19	protein-coding	0.009662	0.489157	
chunk0028_52_1	chr10	83221125	83221636	+	0	NA	Intergenic	MER52-int|LTR|ERV1	-918049	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.003914	0.460938	
chunk0149_222_1	chr5	22090547	22091210	+	0	NA	intron (NM_004061, intron 4 of 14)	L1MB8|LINE|L1	-51474	NR_003921	5369	Hs.247975	NM_031887	ENSG00000168967	PMCHL1	-	pro-melanin concentrating hormone like 1 (pseudogene)	pseudo	0.004525	0.323795	
chunk0210_118_1	chrX	72477953	72478462	+	0	NA	intron (NM_001166448, intron 4 of 4)	MamRep434|DNA|TcMar-Tigger	94896	NM_001166448	55869	Hs.310536	NM_018486	ENSG00000147099	HDAC8	CDA07|CDLS5|HD8|HDACL1|KDAC8|MRXS6|RPD3|WTS	histone deacetylase 8	protein-coding	0.009823	0.388235	
chunk0179_252_1	chr7	48505158	48505527	+	0	NA	intron (NM_152701, intron 48 of 61)	intron (NM_152701, intron 48 of 61)	333882	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.016260	0.413514	
chunk0211_263_1	chrX	121113674	121113911	+	0	NA	Intergenic	L2b|LINE|L2	66184	NM_012084	2747	Hs.368538	NM_012084	ENSG00000182890	GLUD2	GDH2|GLUDP1	glutamate dehydrogenase 2	protein-coding	0.004219	0.336134	
chunk0053_170_1	chr13	30824590	30825202	+	0	NA	Intergenic	Intergenic	21690	NR_047012	100874158	Hs.577982	NR_047012	ENSG00000237879	LINC00398	-	long intergenic non-protein coding RNA 398	ncRNA	0.017974	0.530179	421(GGGCACTGCATGTGCC,-,0.00),422(GGCACTGCATGTGCCA,+,0.00)
chunk0190_112_1	chr8	30469471	30469829	+	0	NA	intron (NM_006867, intron 1 of 9)	intron (NM_006867, intron 1 of 9)	-84249	NR_046205	100128750	Hs.126813	NR_046205	ENSG00000254109	RBPMS-AS1	-	RBPMS antisense RNA 1	ncRNA	0.005587	0.384401	
chunk0133_7_1	chr3	165257387	165257586	+	0	NA	intron (NR_125764, intron 1 of 5)	intron (NR_125764, intron 1 of 5)	50526	NR_125764	103695433	Hs.570689	NR_125764		LINC01322	-	long intergenic non-protein coding RNA 1322	ncRNA	0.010050	0.335000	
chunk0080_270_1	chr17	31058711	31058963	+	0	NA	Intergenic	Intergenic	35588	NR_039886	100616266		NR_039886	ENSG00000265444	MIR4733	-	microRNA 4733	ncRNA	0.011905	0.399209	34(CAAAACAAAATGTTCT,-,0.00),35(AAAACAAAATGTTCTT,+,0.00)
chunk0103_92_1	chr2	161111388	161111854	+	0	NA	Intergenic	Intergenic	-25334	NM_133484	10010	Hs.132257	NM_004180	ENSG00000136560	TANK	I-TRAF|ITRAF|TRAF2	TRAF family member associated NFKB activator	protein-coding	0.004292	0.385439	233(AGGAACAGGTTGTGCC,-,0.00),234(GGAACAGGTTGTGCCT,+,0.00)
chunk0136_418_1	chr3	197459676	197459910	+	0	NA	Intergenic	Intergenic	96194	NM_004051	622	Hs.274539	NM_004051	ENSG00000161267	BDH1	BDH|SDR9C1	3-hydroxybutyrate dehydrogenase 1	protein-coding	0.051282	0.591489	
chunk0096_459_1	chr2	40124596	40125016	+	0	NA	intron (NM_021097, intron 9 of 9)	intron (NM_021097, intron 9 of 9)	207172	NR_038441	100128590	Hs.744988	NR_038441	ENSG00000227028	SLC8A1-AS1	-	SLC8A1 antisense RNA 1	ncRNA	0.000000	0.332542	
chunk0092_142_1	chr19	28240984	28241554	+	0	NA	Intergenic	Intergenic	-447329	NR_027301	148189	Hs.706547	NR_027301	ENSG00000261824	LINC00662	-	long intergenic non-protein coding RNA 662	ncRNA	0.003509	0.411559	
chunk0096_204_1	chr2	30324542	30324808	+	0	NA	Intergenic	Intergenic	-21971	NR_122048	285043	Hs.429119	NR_122048		LINC01936	-	long intergenic non-protein coding RNA 1936	ncRNA	0.003759	0.438202	
chunk0071_194_1	chr15	83917873	83918630	+	0	NA	intron (NM_207517, intron 16 of 29)	L1M5|LINE|L1	-161936	NR_036652	648809	Hs.585157	NR_036652		EFL1P1	EFTUD1P1|FAM42B|HsT19321	elongation factor like GTPase 1 pseudogene 1	pseudo	0.001321	0.344327	
chunk0007_291_1	chr1	83999036	83999474	+	0	NA	promoter-TSS (NM_024686)	promoter-TSS (NM_024686)	-105	NM_024686	79739	Hs.445826	NM_024686	ENSG00000137941	TTLL7	-	tubulin tyrosine ligase like 7	protein-coding	0.102740	0.703872	
chunk0158_199_1	chr5	128005998	128006527	+	0	NA	Intergenic	Intergenic	76812	NR_015360	644873	Hs.340623	NR_015360	ENSG00000245937	LINC01184	-	long intergenic non-protein coding RNA 1184	ncRNA	0.003781	0.379245	
chunk0009_365_1	chr1	109849320	109849905	+	0	NA	Intergenic	Intergenic	-60999	NM_172210	1435	Hs.173894	NM_000757	ENSG00000184371	CSF1	CSF-1|MCSF	colony stimulating factor 1	protein-coding	0.005128	0.474403	327(GGGTACAGTTAGTTCT,-,0.00),328(GGTACAGTTAGTTCTA,+,0.00)
chunk0034_399_1	chr11	37224745	37225004	+	0	NA	Intergenic	MER52A|LTR|ERV1	-626595	NM_001243786	5897	Hs.714519	NM_000536	ENSG00000175097	RAG2	RAG-2	recombination activating 2	protein-coding	0.003861	0.565385	
chunk0187_401_1	chr7	157873149	157874052	+	0	NA	intron (NM_001308268, intron 12 of 22)	CpG	19015	NR_038966	100506585	Hs.661265	NR_038966		LOC100506585	-	uncharacterized LOC100506585	ncRNA	0.060908	0.629425	368(GAGAACGTACTGTCCT,-,0.00),369(AGAACGTACTGTCCTC,+,0.00),414(GAGAACGTACTGTCCT,-,0.00),415(AGAACGTACTGTCCTC,+,0.00),460(GAGAACGTACTGTCCT,-,0.00),461(AGAACGTACTGTCCTC,+,0.00),506(GAGAACGTACTGTCCT,-,0.00),507(AGAACGTACTGTCCTC,+,0.00),552(GAGAACGTACTGTCCT,-,0.00),553(AGAACGTACTGTCCTC,+,0.00)
chunk0094_147_1	chr2	5111522	5112173	+	0	NA	Intergenic	Intergenic	-455625	NR_034134	727982	Hs.444391	NR_034134	ENSG00000231532	LINC01249	-	long intergenic non-protein coding RNA 1249	ncRNA	0.000000	0.361963	366(GGGAACTCCCTGTTCT,-,0.00),367(GGAACTCCCTGTTCTT,+,0.00)
chunk0078_98_1	chr17	2094830	2095507	+	0	NA	intron (NM_001256827, intron 6 of 11)	intron (NM_001256827, intron 6 of 11)	-6407	NM_001282326	23293	Hs.448342	NM_017575	ENSG00000070366	SMG6	C17orf31|EST1A|SMG-6|hSMG5/7a	SMG6 nonsense mediated mRNA decay factor	protein-coding	0.017725	0.517699	
chunk0126_235_1	chr3	79105640	79105978	+	0	NA	intron (NM_002941, intron 3 of 30)	intron (NM_002941, intron 3 of 30)	-86350	NM_001145845	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.005917	0.353982	
chunk0207_154_1	chr9	129884380	129884634	+	0	NA	Intergenic	Intergenic	14902	NR_106914	102466750		NR_106914	ENSG00000276124	MIR6855	hsa-mir-6855	microRNA 6855	ncRNA	0.047244	0.564706	117(AGGGACAGGAAGTGCT,-,0.00),118(GGGACAGGAAGTGCTC,+,0.00)
chunk0032_101_1	chr11	3699726	3700008	+	0	NA	intron (NM_016320, intron 24 of 32)	intron (NM_016320, intron 24 of 32)	-28483	NM_001303035	57053	Hs.732806	NM_020402	ENSG00000129749	CHRNA10	-	cholinergic receptor nicotinic alpha 10 subunit	protein-coding	0.010638	0.303887	
chunk0091_366_1	chr19	15556505	15556806	+	0	NA	Intergenic	Intergenic	48130	NM_173483	126410	Hs.156452	NM_173483	ENSG00000171954	CYP4F22	ARCI5|INLNE|LI3	cytochrome P450 family 4 subfamily F member 22	protein-coding	0.046512	0.519868	
chunk0076_3_1	chr16	58469163	58469911	+	0	NA	intron (NM_022910, intron 1 of 15)	L1ME4b|LINE|L1	4715	NM_022910	65009	Hs.322430	NM_020465	ENSG00000103034	NDRG4	BDM1|SMAP-8|SMAP8	NDRG family member 4	protein-coding	0.012032	0.433912	
chunk0171_383_1	chr6	131099729	131100231	+	0	NA	Intergenic	L1PA8A|LINE|L1	-35706	NM_016377	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.005976	0.367793	
chunk0088_273_1	chr18	49285454	49285848	+	0	NA	intron (NM_017653, intron 9 of 16)	Tigger3a|DNA|TcMar-Tigger	175058	NM_017653	54808	Hs.162996	NM_017653	ENSG00000141627	DYM	DMC|SMC	dymeclin	protein-coding	0.007614	0.382278	
chunk0129_290_1	chr3	123419970	123420352	+	0	NA	intron (NM_183357, intron 1 of 20)	intron (NM_183357, intron 1 of 20)	-3819	NM_001199642	111	Hs.593292	NM_183357	ENSG00000173175	ADCY5	AC5|FDFM	adenylate cyclase 5	protein-coding	0.015707	0.511749	87(TGAACAAACCGTTCTT,+,0.00)
chunk0144_356_1	chr4	139696382	139697048	+	0	NA	intron (NM_002413, intron 3 of 4)	Tigger2|DNA|TcMar-Tigger	30947	NM_001204366	4258	Hs.81874	NM_002413	ENSG00000085871	MGST2	GST2|MGST-II	microsomal glutathione S-transferase 2	protein-coding	0.010511	0.419790	316(CTGTACACAGTGTTCT,-,0.00),317(TGTACACAGTGTTCTT,+,0.00)
chunk0190_462_1	chr8	42316674	42317446	+	0	NA	intron (NR_040009, intron 11 of 21)	intron (NR_040009, intron 11 of 21)	-21395	NM_002690	5423	Hs.654484	NM_002690	ENSG00000070501	POLB	-	DNA polymerase beta	protein-coding	0.014249	0.463131	
chunk0174_326_1	chr6	163533263	163533961	+	0	NA	intron (NM_206853, intron 3 of 6)	MER119|DNA|hAT-Charlie	118969	NM_206853	9444	Hs.510324	NM_006775	ENSG00000112531	QKI	Hqk|QK|QK1|QK3|hqkI	QKI, KH domain containing RNA binding	protein-coding	0.002865	0.337625	
chunk0145_99_1	chr4	146030893	146031424	+	0	NA	Intergenic	Intergenic	90755	NR_038331	100505545	Hs.122199	NR_038331	ENSG00000248809	LINC01095	-	long intergenic non-protein coding RNA 1095	ncRNA	0.000000	0.325188	
chunk0059_249_1	chr14	35051696	35052216	+	0	NA	intron (NM_173607, intron 1 of 4)	intron (NM_173607, intron 1 of 4)	5552	NM_173607	283635	Hs.446357	NM_173607	ENSG00000151327	FAM177A1	C14orf24	family with sequence similarity 177 member A1	protein-coding	0.003846	0.370441	
chunk0013_299_1	chr1	171219042	171219624	+	0	NA	Intergenic	LTR10C|LTR|ERV1	-29138	NM_001282694	2326	Hs.1424	NM_002021	ENSG00000010932	FMO1	-	flavin containing dimethylaniline monoxygenase 1	protein-coding	0.000000	0.343053	328(ATGTACTCTATGTTCT,-,0.00),329(TGTACTCTATGTTCTT,+,0.00)
chunk0075_278_1	chr16	53865523	53865855	+	0	NA	intron (NM_001080432, intron 4 of 8)	L2|LINE|L2	161726	NM_001080432	79068	Hs.528833	NM_001080432	ENSG00000140718	FTO	ALKBH9|BMIQ14|GDFD	FTO alpha-ketoglutarate dependent dioxygenase	protein-coding	0.003012	0.396396	
chunk0105_85_1	chr2	183997124	183997613	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-381607	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.008180	0.414286	
chunk0110_273_1	chr20	17389842	17390350	+	0	NA	intron (NM_002594, intron 5 of 11)	L1ME2|LINE|L1	141273	NM_001195	631	Hs.129702	NM_001195	ENSG00000125864	BFSP1	CP115|CP94|CTRCT33|LIFL-H	beaded filament structural protein 1	protein-coding	0.005906	0.377210	
chunk0101_204_1	chr2	130148541	130148748	+	0	NA	Intergenic	MLT2B1|LTR|ERVL	-3510	NM_001258307	91409	Hs.29383	NM_207310	ENSG00000152076	CCDC74B	-	coiled-coil domain containing 74B	protein-coding	0.009662	0.437500	
chunk0101_459_1	chr2	140273768	140274028	+	0	NA	intron (NM_018557, intron 85 of 90)	intron (NM_018557, intron 85 of 90)	312787	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.011538	0.344828	
chunk0186_284_1	chr7	142318997	142319574	+	0	NA	Intergenic	Intergenic	-47036	NR_036483	207147	Hs.604069	NR_036483	ENSG00000186163	TRY2P	-	trypsinogen-like pseudogene	pseudo	0.005199	0.401384	370(TAGCACAGAGTGGTCT,-,0.00),371(AGCACAGAGTGGTCTG,+,0.00)
chunk0125_426_1	chr3	72432085	72432478	+	0	NA	intron (NM_012234, intron 1 of 3)	intron (NM_012234, intron 1 of 3)	14342	NM_012234	23429	Hs.7910	NM_012234	ENSG00000163602	RYBP	AAP1|APAP-1|DEDAF|YEAF1	RING1 and YY1 binding protein	protein-coding	0.007634	0.413706	
chunk0136_168_1	chr4	6201054	6201486	+	0	NA	promoter-TSS (NM_144720)	promoter-TSS (NM_144720)	537	NR_037863	285484	Hs.479068	NR_037863		LINC02495	-	long intergenic non-protein coding RNA 2495	ncRNA	0.018519	0.554273	
chunk0153_388_1	chr5	75133877	75134077	+	0	NA	intron (NM_001164443, intron 16 of 24)	L1PA5|LINE|L1	-81334	NR_126375	51301	Hs.272404	NM_016591	ENSG00000176928	GCNT4	C2GNT3|LINC01336	glucosaminyl (N-acetyl) transferase 4	protein-coding	0.015000	0.398010	
chunk0052_284_1	chr12	124359487	124360540	+	0	NA	intron (NM_001077261, intron 23 of 47)	intron (NM_001077261, intron 23 of 47)	-22771	NR_106940	102466204		NR_106940	ENSG00000275967	MIR6880	hsa-mir-6880	microRNA 6880	ncRNA	0.035138	0.637571	267(AGAGACAACCTGTTCC,-,0.00),268(GAGACAACCTGTTCCT,+,0.00)
chunk0028_140_1	chr10	86514413	86514762	+	0	NA	intron (NM_015045, intron 2 of 18)	intron (NM_015045, intron 2 of 18)	7197	NM_015045	23063	Hs.203099	NM_015045	ENSG00000062650	WAPL	FOE|KIAA0261|WAPAL	WAPL cohesin release factor	protein-coding	0.002865	0.388571	93(ATGGACAAGATGTTCC,-,0.00),94(TGGACAAGATGTTCCT,+,0.00)
chunk0166_9_1	chr6	41537245	41537558	+	0	NA	intron (NR_126415, intron 1 of 1)	LTR16C|LTR|ERVL	8842	NR_126417	101060264	Hs.571099	NR_126415	ENSG00000234753	FOXP4-AS1	-	FOXP4 antisense RNA 1	ncRNA	0.009585	0.496815	
chunk0037_6_1	chr11	68877499	68877922	+	0	NA	Intergenic	MER4B-int|LTR|ERV1	26125	NM_181514	219927	Hs.503047	NM_181512	ENSG00000197345	MRPL21	L21mt|MRP-L21	mitochondrial ribosomal protein L21	protein-coding	0.016548	0.495283	38(AAACACATTCTGTTCA,-,0.00),39(AACACATTCTGTTCAT,+,0.00)
chunk0035_421_1	chr11	57161232	57161781	+	0	NA	Intergenic	L2c|LINE|L2	-20241	NM_001005210	219527	Hs.199853	NM_001005210	ENSG00000183908	LRRC55	-	leucine rich repeat containing 55	protein-coding	0.009107	0.438182	
chunk0085_69_1	chr18	1392718	1393440	+	0	NA	Intergenic	Intergenic	-33450	NR_023926	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.011080	0.365145	
chunk0009_247_1	chr1	107051670	107052283	+	0	NA	Intergenic	Intergenic	-4669	NM_018137	55170	Hs.26006	NM_018137	ENSG00000198890	PRMT6	HRMT1L6	protein arginine methyltransferase 6	protein-coding	0.003263	0.294788	
chunk0057_50_1	chr13	96925644	96926417	+	0	NA	Intergenic	Intergenic	58142	NR_051966	100887754	Hs.617003	NR_051966		LINC00359	-	long intergenic non-protein coding RNA 359	ncRNA	0.003881	0.387597	
chunk0172_349_1	chr6	139013259	139013528	+	0	NA	Intergenic	Intergenic	-15289	NM_021243	58527	Hs.600861	NM_021243	ENSG00000146386	ABRACL	C6orf115|Costars|HSPC280|PRO2013	ABRA C-terminal like	protein-coding	0.000000	0.514815	114(GAGAACTGGAAGTTCT,-,0.00),115(AGAACTGGAAGTTCTG,+,0.00)
chunk0036_289_1	chr11	65471417	65471675	+	0	NA	Intergenic	Intergenic	-26216	NR_002819	378938	Hs.621695	NR_002819	ENSG00000251562	MALAT1	HCN|LINC00047|NCRNA00047|NEAT2|PRO2853	metastasis associated lung adenocarcinoma transcript 1	ncRNA	0.011628	0.571429	
chunk0080_369_1	chr17	33199796	33200053	+	0	NA	intron (NM_001094, intron 1 of 9)	L2c|LINE|L2	93064	NM_183377	40	Hs.368417	NM_001094	ENSG00000108684	ASIC2	ACCN|ACCN1|ASIC2a|BNC1|BNaC1|MDEG|hBNaC1	acid sensing ion channel subunit 2	protein-coding	0.011673	0.511628	229(TTGCACATGCTGTTCC,-,0.00),230(TGCACATGCTGTTCCC,+,0.00)
chunk0187_8_1	chr8	490883	491283	+	0	NA	3' UTR (NM_175075, exon 4 of 4)	3' UTR (NM_175075, exon 4 of 4)	53762	NM_001256113	157695	Hs.289293	NM_175075	ENSG00000180190	TDRP	C8orf42|Inm01|TDRP1|TDRP2	testis development related protein	protein-coding	0.010000	0.389027	
chunk0077_232_1	chr16	80562979	80563434	+	0	NA	promoter-TSS (NR_120307)	promoter-TSS (NR_120307)	-71	NR_120307	102724084	Hs.147884	NR_120307		LOC102724084	-	uncharacterized LOC102724084	ncRNA	0.008791	0.500000	
chunk0210_331_1	chrX	94773067	94773337	+	0	NA	Intergenic	MLT2A2|LTR|ERVL	290024	NR_031667	100313772		NR_031667	ENSG00000221187	MIR548M	MIRN548M	microRNA 548m	ncRNA	0.003704	0.446494	
chunk0135_89_1	chr3	186383550	186383965	+	0	NA	Intergenic	Intergenic	-21523	NM_001080744	1608	Hs.683449	NM_001346	ENSG00000058866	DGKG	DAGK3|DGK-GAMMA	diacylglycerol kinase gamma	protein-coding	0.012048	0.524038	258(AGGATCACTGTGTTCT,-,0.00),259(GGATCACTGTGTTCTT,+,0.00)
chunk0070_319_1	chr15	75416566	75416881	+	0	NA	intron (NM_001145358, intron 3 of 20)	intron (NM_001145358, intron 3 of 20)	34862	NM_015477	25942	Hs.513039	NM_015477	ENSG00000169375	SIN3A	WITKOS	SIN3 transcription regulator family member A	protein-coding	0.003175	0.490506	
chunk0039_102_1	chr11	97437751	97438252	+	0	NA	Intergenic	Intergenic	-931124	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.001996	0.386454	
chunk0170_322_1	chr6	116112345	116112717	+	0	NA	intron (NM_152729, intron 4 of 11)	L1ME4b|LINE|L1	11695	NM_152729	221294	Hs.520341	NM_152729	ENSG00000178425	NT5DC1	C6orf200|LP2642|NT5C2L1	5'-nucleotidase domain containing 1	protein-coding	0.005376	0.345845	236(AGGTACACTTAGTTCT,-,0.00),237(GGTACACTTAGTTCTT,+,0.00)
chunk0143_410_1	chr4	123361458	123361930	+	0	NA	Intergenic	Intergenic	-35101	NM_001258038	10252	Hs.744854	NM_005841	ENSG00000164056	SPRY1	hSPRY1	sprouty RTK signaling antagonist 1	protein-coding	0.000000	0.342495	
chunk0113_337_1	chr20	58677364	58677935	+	0	NA	non-coding (NR_037943, exon 8 of 8)	non-coding (NR_037943, exon 8 of 8)	-11482	NM_001204873	79716	Hs.654868	NM_024663	ENSG00000215440	NPEPL1	bA261P9.2	aminopeptidase like 1	protein-coding	0.007005	0.414336	
chunk0194_103_1	chr8	83525945	83526763	+	0	NA	Intergenic	L1MEf|LINE|L1	122596	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003667	0.334554	
chunk0179_384_1	chr7	51274141	51274881	+	0	NA	intron (NM_001287436, intron 1 of 13)	intron (NM_001287436, intron 1 of 13)	42307	NM_001287436	23242	Hs.99141	NM_015198	ENSG00000106078	COBL	-	cordon-bleu WH2 repeat protein	protein-coding	0.012162	0.461538	155(AAGAGCACCCTGTCCT,-,0.00),156(AGAGCACCCTGTCCTT,+,0.00)
chunk0114_180_1	chr21	14911825	14912071	+	0	NA	Intergenic	L1MA3|LINE|L1	152857	NM_003489	8204	Hs.155017	NM_003489	ENSG00000180530	NRIP1	CAKUT3|RIP140	nuclear receptor interacting protein 1	protein-coding	0.004065	0.489879	
chunk0089_2_1	chr18	57325559	57326232	+	0	NA	Intergenic	Intergenic	-26595	NM_015879	51046	Hs.23172	NM_015879	ENSG00000177511	ST8SIA3	SIAT8C|ST8SiaIII	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	protein-coding	0.002972	0.419881	
chunk0162_319_1	chr6	6706172	6706724	+	0	NA	Intergenic	Intergenic	-83622	NR_026970	285780	Hs.655737	NM_173675	ENSG00000216863	LY86-AS1	LY86-AS|LY86AS	LY86 antisense RNA 1	ncRNA	0.007246	0.401447	
chunk0202_204_1	chr9	75538772	75538988	+	0	NA	Intergenic	AluJb|SINE|Alu	-351764	NR_120409	5125	Hs.368542	NM_006200	ENSG00000099139	PCSK5	PC5|PC6|PC6A|SPC6	proprotein convertase subtilisin/kexin type 5	protein-coding	0.004630	0.423963	
chunk0206_142_1	chr9	121189580	121190117	+	0	NA	intron (NM_016322, intron 4 of 7)	Tigger19b|DNA|TcMar-Tigger	12239	NM_016322	51552	Hs.371563	NM_016322	ENSG00000119396	RAB14	FBP|RAB-14	RAB14, member RAS oncogene family	protein-coding	0.005587	0.351301	
chunk0109_203_1	chr20	5181467	5182114	+	0	NA	intron (NM_003818, intron 5 of 12)	Tigger3a|DNA|TcMar-Tigger	55029	NM_003818	8760	Hs.126857	NM_003818	ENSG00000101290	CDS2	-	CDP-diacylglycerol synthase 2	protein-coding	0.006182	0.365741	
chunk0015_41_1	chr1	184493963	184494541	+	0	NA	intron (NM_030806, intron 2 of 5)	L2a|LINE|L2	107236	NM_030806	81563	Hs.497159	NM_030806	ENSG00000116667	C1orf21	PIG13	chromosome 1 open reading frame 21	protein-coding	0.003460	0.445596	228(GGGAACAGAATGTTTC,-,0.00),229(GGAACAGAATGTTTCA,+,0.00)
chunk0037_251_1	chr11	75479489	75479964	+	0	NA	intron (NM_030792, intron 2 of 16)	L1MB7|LINE|L1	45828	NM_030792	81544	Hs.503297	NM_030792	ENSG00000158555	GDPD5	GDE2|PP1665	glycerophosphodiester phosphodiesterase domain containing 5	protein-coding	0.004211	0.384454	
chunk0071_426_1	chr15	89812131	89812696	+	0	NA	intron (NM_001150, intron 1 of 20)	intron (NM_001150, intron 1 of 20)	2427	NM_001150	290	Hs.1239	NM_001150	ENSG00000166825	ANPEP	APN|CD13|GP150|LAP1|P150|PEPN	alanyl aminopeptidase, membrane	protein-coding	0.014159	0.611307	235(GGGCACACTCTGTCCC,-,0.00),236(GGCACACTCTGTCCCC,+,0.00)
chunk0157_331_1	chr5	122154879	122155194	+	0	NA	Intergenic	Intergenic	-5140	NM_001195535	100505841	Hs.733368	NM_001195535		LOC100505841	-	zinc finger protein 474-like	protein-coding	0.019048	0.474684	170(GAGCACAGCATGTTCT,-,0.00),171(AGCACAGCATGTTCTT,+,0.00)
chunk0203_212_1	chr9	86651300	86651669	+	0	NA	Intergenic	L1MD1|LINE|L1	295705	NM_002048	2619	Hs.65029	NM_002048	ENSG00000180447	GAS1	-	growth arrest specific 1	protein-coding	0.005420	0.337838	
chunk0004_359_1	chr1	51506501	51507133	+	0	NA	intron (NM_001981, intron 1 of 24)	(CAGAA)n|Simple_repeat|Simple_repeat	12506	NM_001981	2060	Hs.83722	NM_001981	ENSG00000085832	EPS15	AF-1P|AF1P|MLLT5	epidermal growth factor receptor pathway substrate 15	protein-coding	0.007911	0.355450	
chunk0060_349_1	chr14	52111735	52112245	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	-42762	NM_007361	22795	Hs.369840	NM_007361	ENSG00000087303	NID2	NID-2	nidogen 2	protein-coding	0.009804	0.352250	
chunk0156_260_1	chr5	109275463	109275890	+	0	NA	Intergenic	L1MA8|LINE|L1	134298	NM_014819	9867	Hs.483036	NM_014819	ENSG00000198961	PJA2	Neurodap1|RNF131	praja ring finger ubiquitin ligase 2	protein-coding	0.004684	0.329439	260(CAGAACATGTTGTTCC,-,0.00),261(AGAACATGTTGTTCCT,+,0.00)
chunk0168_206_1	chr6	85787125	85787644	+	0	NA	Intergenic	L1PA6|LINE|L1	-108651	NR_003038	387066	Hs.292457	NR_003038	ENSG00000203875	SNHG5	C6orf160|LINC00044|NCRNA00044|U50HG	small nucleolar RNA host gene 5	ncRNA	0.007707	0.494231	
chunk0207_58_1	chrX	8672893	8673505	+	0	NA	intron (NM_000216, intron 2 of 13)	intron (NM_000216, intron 2 of 13)	58987	NM_000216	3730	Hs.521869	NM_000216	ENSG00000011201	ANOS1	ADMLX|HH1|HHA|KAL|KAL1|KALIG-1|KMS|WFDC19	anosmin 1	protein-coding	0.008170	0.337684	318(CAGCACTGAATGTTCC,-,0.00),319(AGCACTGAATGTTCCA,+,0.00)
chunk0050_221_1	chr12	104727339	104727812	+	0	NA	intron (NM_001173982, intron 2 of 2)	intron (NM_001173982, intron 2 of 2)	135942	NR_037487	100500843		NR_037487	ENSG00000264295	MIR3922	-	microRNA 3922	ncRNA	0.004228	0.478903	
chunk0019_436_1	chr1	231011243	231011621	+	0	NA	Intergenic	Intergenic	8492	NR_031593	100302132		NR_031593	ENSG00000283799	MIR1182	MIRN1182|hsa-mir-1182	microRNA 1182	ncRNA	0.005291	0.427441	
chunk0118_369_1	chr22	36445059	36445690	+	0	NA	Intergenic	MER117|DNA|hAT-Charlie	36266	NM_012473	25828	Hs.211929	NM_012473	ENSG00000100348	TXN2	COXPD29|MT-TRX|MTRX|TRX2|TXN	thioredoxin 2	protein-coding	0.014263	0.465190	339(GAGAACTGGCTGTGCA,-,0.00),340(AGAACTGGCTGTGCAG,+,0.00)
chunk0003_145_1	chr1	33008648	33009079	+	0	NA	non-coding (NR_037591, exon 8 of 8)	non-coding (NR_037591, exon 8 of 8)	28048	NM_001625	204	Hs.470907	NM_001625	ENSG00000004455	AK2	ADK2	adenylate kinase 2	protein-coding	0.009281	0.451389	
chunk0082_260_1	chr17	57770106	57770433	+	0	NA	Intergenic	Intergenic	-24940	NM_001282544	101927581	Hs.540784	NM_001282544	ENSG00000166329	CCDC182	-	coiled-coil domain containing 182	protein-coding	0.009174	0.466463	
chunk0170_240_1	chr6	113636740	113637065	+	0	NA	intron (NR_125844, intron 1 of 2)	intron (NR_125844, intron 1 of 2)	13173	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.003077	0.352761	
chunk0138_157_1	chr4	37570240	37570645	+	0	NA	intron (NM_001104629, intron 2 of 3)	(A)n|Simple_repeat|Simple_repeat	-13791	NM_018302	55286	Hs.107527	NM_018302	ENSG00000154274	C4orf19	-	chromosome 4 open reading frame 19	protein-coding	0.022222	0.411330	
chunk0100_5_1	chr2	104657031	104657452	+	0	NA	Intergenic	Intergenic	100478	NR_038231	284998	Hs.410180	NR_038231	ENSG00000234177	LINC01114	PANCAT	long intergenic non-protein coding RNA 1114	ncRNA	0.007126	0.338863	
chunk0175_7_1	chr7	137113	137842	+	0	NA	Intergenic	LTR56|LTR|ERV1	-12241	NR_108064	100507642	Hs.557780	NR_108064		LOC100507642	-	uncharacterized LOC100507642	ncRNA	0.019204	0.502740	447(AAGAAGAGGCTGTTCC,-,0.00),448(AGAAGAGGCTGTTCCA,+,0.00)
chunk0062_322_1	chr14	73339308	73339507	+	0	NA	intron (NM_001005743, intron 4 of 12)	L2a|LINE|L2	101910	NM_173462	89932	Hs.509909	NM_173462	ENSG00000100767	PAPLN	PPN	papilin, proteoglycan like sulfated glycoprotein	protein-coding	0.000000	0.455000	
chunk0072_210_1	chr15	95558111	95558455	+	0	NA	Intergenic	Intergenic	125190	NR_027132	145820	Hs.652702	NR_027132	ENSG00000259134	LINC00924	-	long intergenic non-protein coding RNA 924	ncRNA	0.005814	0.385507	
chunk0134_237_1	chr3	179037219	179037418	+	0	NA	intron (NM_022470, intron 2 of 5)	LTR27E|LTR|ERV1	34550	NM_022470	64393	Hs.371609	NM_022470	ENSG00000172667	ZMAT3	PAG608|WIG-1|WIG1	zinc finger matrin-type 3	protein-coding	0.025126	0.530000	
chunk0006_215_1	chr1	68215050	68215276	+	0	NA	intron (NM_024911, intron 1 of 11)	MLT1K|LTR|ERVL-MaLR	17383	NM_001193334	79971	Hs.647659	NM_024911	ENSG00000116729	WLS	C1orf139|EVI|GPR177|MRP|mig-14	Wnt ligand secretion mediator	protein-coding	0.004425	0.431718	
chunk0048_435_1	chr12	88502467	88503285	+	0	NA	intron (NM_000899, intron 9 of 9)	intron (NM_000899, intron 9 of 9)	77597	NM_000899	4254	Hs.1048	NM_000899	ENSG00000049130	KITLG	DCUA|DFNA69|FPH2|FPHH|KL-1|Kitl|MGF|SCF|SF|SHEP7|SLF	KIT ligand	protein-coding	0.008557	0.371184	
chunk0020_129_1	chr1	233601302	233601501	+	0	NA	Intergenic	L2|LINE|L2	-12603	NM_002245	3775	Hs.208544	NM_002245	ENSG00000135750	KCNK1	DPK|HOHO|K2P1|K2p1.1|KCNO1|TWIK-1|TWIK1	potassium two pore domain channel subfamily K member 1	protein-coding	0.000000	0.385000	
chunk0004_136_1	chr1	44798805	44799108	+	0	NA	Intergenic	L2a|LINE|L2	-1269	NM_004073	1263	Hs.632415	NM_004073	ENSG00000173846	PLK3	CNK|FNK|PLK-3|PRK	polo like kinase 3	protein-coding	0.003300	0.404605	
chunk0103_418_1	chr2	169684069	169684523	+	0	NA	intron (NM_001085447, intron 1 of 8)	intron (NM_001085447, intron 1 of 8)	10125	NM_001085447	129881	Hs.370111	NM_001085447	ENSG00000154479	CCDC173	C2orf77	coiled-coil domain containing 173	protein-coding	0.006608	0.419780	
chunk0069_253_1	chr15	64463557	64463793	+	0	NA	Intergenic	Intergenic	-35745	NM_015042	23060	Hs.595451	NM_015042	ENSG00000180357	ZNF609	-	zinc finger protein 609	protein-coding	0.000000	0.400844	149(GGGAACAGGTTGTTCT,-,0.00),150(GGAACAGGTTGTTCTG,+,0.00)
chunk0087_35_1	chr18	31199248	31199991	+	0	NA	Intergenic	Intergenic	-36763	NM_004948	1823	Hs.567260	NM_004948	ENSG00000134765	DSC1	CDHF1|DG2/DG3	desmocollin 1	protein-coding	0.005384	0.364247	
chunk0008_256_1	chr1	94491362	94491919	+	0	NA	intron (NM_002858, intron 16 of 22)	intron (NM_002858, intron 16 of 22)	50217	NM_001993	2152	Hs.62192	NM_001993	ENSG00000117525	F3	CD142|TF|TFA	coagulation factor III, tissue factor	protein-coding	0.010772	0.311828	
chunk0164_309_1	chr6	24990673	24991099	+	0	NA	intron (NM_001286446, intron 1 of 13)	LTR102_Mam|LTR|ERVL	51282	NM_001286446	9750	Hs.559459	NM_014722	ENSG00000111913	RIPOR2	C6orf32|DFNB104|DIFF40|DIFF48|FAM65B|MYONAP|PL48	RHO family interacting cell polarization regulator 2	protein-coding	0.009390	0.381733	
chunk0204_214_1	chr9	97103985	97104337	+	0	NA	Intergenic	MER57B2|LTR|ERV1	-22216	NR_002942	340508	Hs.680438	NR_002942	ENSG00000228376	GAS2L1P2	-	growth arrest specific 2 like 1 pseudogene 2	pseudo	0.008523	0.405099	
chunk0106_7_1	chr2	195363223	195364039	+	0	NA	Intergenic	Intergenic	-293177	NM_001127257	57181	Hs.650158	NM_020342	ENSG00000196950	SLC39A10	LZT-Hs2	solute carrier family 39 member 10	protein-coding	0.003676	0.346389	69(CAGAACTACCTGTTCC,-,0.00),70(AGAACTACCTGTTCCT,+,0.00)
chunk0014_73_1	chr1	176137090	176137399	+	0	NA	intron (NM_001286644, intron 4 of 17)	intron (NM_001286644, intron 4 of 17)	70000	NM_001286644	64326	Hs.523744	NM_022457	ENSG00000143207	COP1	RFWD2|RNF200	COP1 E3 ubiquitin ligase	protein-coding	0.003236	0.290323	235(TGGAACATATTGTTCT,-,0.00),236(GGAACATATTGTTCTT,+,0.00)
chunk0074_200_1	chr16	24989002	24989321	+	0	NA	intron (NM_018054, intron 1 of 18)	intron (NM_018054, intron 1 of 18)	26217	NM_018054	55114	Hs.373793	NM_018054	ENSG00000140750	ARHGAP17	MST066|MST110|MSTP038|MSTP066|MSTP110|NADRIN|PP367|PP4534|RICH-1|RICH1|WBP15	Rho GTPase activating protein 17	protein-coding	0.003135	0.518750	
chunk0022_142_1	chr10	12195796	12196052	+	0	NA	promoter-TSS (NM_006023)	promoter-TSS (NM_006023)	-38	NM_006023	8872	Hs.412842	NM_006023	ENSG00000151465	CDC123	C10orf7|D123	cell division cycle 123	protein-coding	0.085938	0.548638	
chunk0114_266_1	chr21	16205606	16205826	+	0	NA	intron (NR_027791, intron 1 of 5)	intron (NR_027791, intron 1 of 5)	11337	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.009091	0.484163	
chunk0114_277_1	chr21	16325982	16326274	+	0	NA	intron (NR_027790, intron 4 of 7)	L2a|LINE|L2	131749	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.006849	0.382253	
chunk0162_191_1	chr6	3878330	3878734	+	0	NA	Intergenic	L1MC4|LINE|L1	29134	NM_012135	26240	Hs.140944	NM_012135	ENSG00000145945	FAM50B	D6S2654E|X5L	family with sequence similarity 50 member B	protein-coding	0.009901	0.417284	
chunk0026_204_1	chr10	63761051	63761272	+	0	NA	Intergenic	Intergenic	239798	NM_001001330	221035	Hs.499833	NM_001001330	ENSG00000165476	REEP3	C10orf74|Yip2b	receptor accessory protein 3	protein-coding	0.004525	0.436937	
chunk0065_367_1	chr14	103969906	103970246	+	0	NA	intron (NM_153046, intron 5 of 35)	intron (NM_153046, intron 5 of 35)	-27768	NM_001257268	647286	Hs.632325	NM_001257268	ENSG00000227729	RD3L	TDRD9-AS1|TDRD9AS1	retinal degeneration 3 like	protein-coding	0.008824	0.571848	
chunk0065_376_1	chr14	104054299	104054667	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-31203	NM_001080464	374569	Hs.146239	NM_001080464	ENSG00000166183	ASPG	C14orf76|GPA/WT|LYSOLP	asparaginase	protein-coding	0.021739	0.544715	
chunk0120_112_1	chr3	4681455	4681654	+	0	NA	intron (NM_002222, intron 25 of 57)	intron (NM_002222, intron 25 of 57)	70036	NR_004428	100126791	Hs.663059	NR_004428	ENSG00000235947	EGOT	EGO|NCRNA00190	eosinophil granule ontogeny transcript	ncRNA	0.000000	0.440000	
chunk0141_281_1	chr4	86595933	86596269	+	0	NA	intron (NM_006264, intron 1 of 46)	intron (NM_006264, intron 1 of 46)	1786	NM_080685	5783	Hs.436142	NM_006264	ENSG00000163629	PTPN13	FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E	protein tyrosine phosphatase non-receptor type 13	protein-coding	0.008929	0.326409	169(CATAACATTGTGTTCT,-,0.00),170(ATAACATTGTGTTCTA,+,0.00)
chunk0014_12_1	chr1	174376710	174377236	+	0	NA	intron (NM_014857, intron 12 of 20)	L1MD|LINE|L1	-71101	NM_005684	9293	Hs.673850	NM_005684	ENSG00000203737	GPR52	-	G protein-coupled receptor 52	protein-coding	0.001901	0.314991	
chunk0095_21_1	chr2	12352764	12353187	+	0	NA	intron (NR_110196, intron 4 of 5)	intron (NR_110196, intron 4 of 5)	153845	NR_037452	100500884		NR_037452	ENSG00000264089	MIR3681	-	microRNA 3681	ncRNA	0.002364	0.415094	
chunk0023_361_1	chr10	29979050	29979349	+	0	NA	Intergenic	Intergenic	80360	NM_020848	57608	Hs.533953	NM_020848	ENSG00000165757	JCAD	KIAA1462	junctional cadherin 5 associated	protein-coding	0.006689	0.400000	
chunk0001_235_1	chr1	8244076	8244817	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	35774	NR_125998	102724539	Hs.516816	NR_125998	ENSG00000227634	LINC01714	-	long intergenic non-protein coding RNA 1714	ncRNA	0.008097	0.385445	
chunk0098_52_1	chr2	66562251	66562719	+	0	NA	intron (NM_002398, intron 9 of 12)	intron (NM_002398, intron 9 of 12)	-11545	NR_110156	100507073	Hs.667940	NR_110156	ENSG00000232046	LINC01798	-	long intergenic non-protein coding RNA 1798	ncRNA	0.002137	0.341151	
chunk0099_236_1	chr2	96680397	96680898	+	0	NA	intron (NM_001293083, intron 19 of 52)	intron (NM_001293083, intron 19 of 52)	37910	NM_001293083	90342	Hs.534025	NM_001077400	ENSG00000249715	FER1L5	-	fer-1 like family member 5	protein-coding	0.005988	0.412351	
chunk0153_75_1	chr5	68054668	68055026	+	0	NA	Intergenic	Intergenic	-135029	NR_105003	102467655	Hs.544102	NR_105003	ENSG00000253787	LINC02219	-	long intergenic non-protein coding RNA 2219	ncRNA	0.011173	0.434540	131(TGGCTCACTGTGTTCC,-,0.00),132(GGCTCACTGTGTTCCA,+,0.00)
chunk0133_366_1	chr3	173655433	173655709	+	0	NA	intron (NM_014932, intron 3 of 6)	intron (NM_014932, intron 3 of 6)	257123	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.003623	0.303249	
chunk0203_98_1	chr9	84256184	84256383	+	0	NA	Intergenic	Intergenic	84496	NM_001199633	64078	Hs.535966	NM_022127	ENSG00000197506	SLC28A3	CNT3	solute carrier family 28 member 3	protein-coding	0.010050	0.430000	
chunk0082_186_1	chr17	56427232	56427548	+	0	NA	intron (NM_153228, intron 7 of 16)	intron (NM_153228, intron 7 of 16)	-166309	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.003165	0.444795	45(CAGAACTGGGAGTGCT,-,0.00),46(AGAACTGGGAGTGCTC,+,0.00)
chunk0192_113_1	chr8	61720484	61720707	+	0	NA	Intergenic	Intergenic	5807	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.013453	0.486607	34(CAGCCCAGGGTGTGCT,-,0.00),35(AGCCCAGGGTGTGCTT,+,0.00)
chunk0111_165_1	chr20	25220746	25221149	+	0	NA	intron (NM_001114089, intron 9 of 13)	MIR|SINE|MIR	-24055	NR_109994	101926889	Hs.585997	NR_109994		LOC101926889	-	uncharacterized LOC101926889	ncRNA	0.019851	0.586634	
chunk0139_146_1	chr4	53635549	53636121	+	0	NA	Intergenic	Intergenic	42879	NR_046827	100873955	Hs.351074	NR_046827		LNX1-AS2	-	LNX1 antisense RNA 2	ncRNA	0.005245	0.363002	309(GAGTACTTCTTGTCCT,-,0.00)
chunk0178_229_1	chr7	35714984	35715183	+	0	NA	Intergenic	Intergenic	-1354	NR_108082	100506725	Hs.304253	NR_108082	ENSG00000227544	LOC100506725	-	uncharacterized LOC100506725	ncRNA	0.000000	0.535000	
chunk0121_215_1	chr3	21730745	21731348	+	0	NA	intron (NM_024697, intron 1 of 7)	L1MC4a|LINE|L1	20278	NM_024697	79750	Hs.21026	NM_024697	ENSG00000151789	ZNF385D	ZNF659	zinc finger protein 385D	protein-coding	0.000000	0.298013	
chunk0151_395_1	chr5	55427252	55427531	+	0	NA	intron (NR_103485, intron 5 of 6)	intron (NR_103485, intron 5 of 6)	81535	NR_049869	100847019		NR_049869	ENSG00000265135	MIR5687	-	microRNA 5687	ncRNA	0.000000	0.389286	
chunk0130_233_1	chr3	134627838	134628282	+	0	NA	intron (NM_178554, intron 4 of 10)	intron (NM_178554, intron 4 of 10)	22962	NM_178554	339855	Hs.146730	NM_178554	ENSG00000174611	KY	MFM7	kyphoscoliosis peptidase	protein-coding	0.004505	0.462921	
chunk0107_140_1	chr2	214915596	214916106	+	0	NA	intron (NR_110292, intron 2 of 3)	intron (NR_110292, intron 2 of 3)	105622	NR_110292	101928103	Hs.665619	NR_110292	ENSG00000229267	SNHG31	-	small nucleolar RNA host gene 31	ncRNA	0.009804	0.440313	
chunk0061_409_1	chr14	64986754	64987004	+	0	NA	promoter-TSS (NM_002028)	promoter-TSS (NM_002028)	90	NM_002028	2342	Hs.325531	NM_002028	ENSG00000257365	FNTB	FPTB	farnesyltransferase, CAAX box, beta	protein-coding	0.064000	0.549801	
chunk0050_353_1	chr12	107764717	107765009	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-3726	NM_012406	11108	Hs.506655	NM_012406	ENSG00000110851	PRDM4	PFM1	PR/SET domain 4	protein-coding	0.010274	0.430034	
chunk0065_80_1	chr15	23582470	23582754	+	0	NA	Intergenic	Intergenic	17305	NM_005664	7681	Hs.72964	NM_005664	ENSG00000179455	MKRN3	CPPB2|D15S9|RNF63|ZFP127|ZNF127	makorin ring finger protein 3	protein-coding	0.007042	0.347368	
chunk0088_262_1	chr18	49100230	49101076	+	0	NA	intron (NM_017653, intron 15 of 16)	intron (NM_017653, intron 15 of 16)	-50885	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.008274	0.390791	
chunk0169_192_1	chr6	102582470	102582678	+	0	NA	Intergenic	MER52A|LTR|ERV1	1183589	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004808	0.535885	
chunk0006_278_1	chr1	70426412	70426868	+	0	NA	intron (NM_001190463, intron 4 of 10)	intron (NM_001190463, intron 4 of 10)	15422	NM_001902	1491	Hs.19904	NM_001902	ENSG00000116761	CTH	-	cystathionine gamma-lyase	protein-coding	0.006579	0.437637	
chunk0178_308_1	chr7	37987679	37988155	+	0	NA	Intergenic	Intergenic	66598	NM_001242948	54749	Hs.563491	NM_017549	ENSG00000086289	EPDR1	EPDR|MERP-1|MERP1|UCC1	ependymin related 1	protein-coding	0.002101	0.360587	257(TAGAACAGGCAGTTCT,-,0.00),258(AGAACAGGCAGTTCTG,+,0.00)
chunk0016_341_1	chr1	201917379	201917989	+	0	NA	intron (NM_012134, intron 1 of 2)	intron (NM_012134, intron 1 of 2)	28904	NM_012134	25802	Hs.519075	NM_012134	ENSG00000163431	LMOD1	1D|64kD|D1|SM-LMOD|SMLMOD	leiomodin 1	protein-coding	0.008197	0.505728	443(AGGAACATACTGTTCT,-,0.00),444(GGAACATACTGTTCTT,+,0.00)
chunk0159_63_1	chr5	137304118	137304745	+	0	NA	intron (NM_004598, intron 2 of 10)	intron (NM_004598, intron 2 of 10)	194898	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.006380	0.490446	
chunk0195_194_1	chr8	96829952	96830194	+	0	NA	intron (NM_016134, intron 2 of 7)	intron (NM_016134, intron 2 of 7)	184846	NM_016134	10404	Hs.156178	NM_016134	ENSG00000104324	CPQ	LDP|PGCP	carboxypeptidase Q	protein-coding	0.004132	0.395062	
chunk0037_323_1	chr11	76962898	76963809	+	0	NA	intron (NM_001300954, intron 3 of 10)	MER61F|LTR|ERV1	-70988	NM_138706	192134	Hs.352622	NM_138706	ENSG00000198488	B3GNT6	B3Gn-T6|BGnT-6|beta-1,3-Gn-T6|beta3Gn-T6	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6	protein-coding	0.007684	0.429825	
chunk0068_320_1	chr15	57478894	57479436	+	0	NA	intron (NM_001252335, intron 9 of 19)	intron (NM_001252335, intron 9 of 19)	102660	NM_001252335	84952	Hs.148989	NM_032866	ENSG00000128849	CGNL1	JACOP|PCING	cingulin like 1	protein-coding	0.003690	0.488029	
chunk0110_262_1	chr20	16747172	16747869	+	0	NA	promoter-TSS (NM_020157)	promoter-TSS (NM_020157)	-833	NM_020157	56914	Hs.41119	NM_020157	ENSG00000125879	OTOR	FDP|MIAL1	otoraplin	protein-coding	0.005739	0.421203	378(TGGCACAGTAAGTGCT,-,0.00),379(GGCACAGTAAGTGCTC,+,0.00)
chunk0146_82_1	chr4	158025123	158025343	+	0	NA	Intergenic	Intergenic	147333	NM_016613	51313	Hs.567498	NM_016613	ENSG00000164125	GASK1B	AD021|AD036|C4orf18|ENED|FAM198B	golgi associated kinase 1B	protein-coding	0.004545	0.470588	
chunk0185_303_1	chr7	131223214	131223481	+	0	NA	intron (NM_001145354, intron 2 of 18)	intron (NM_001145354, intron 2 of 18)	104432	NR_125364	100506881	Hs.660830	NR_125364	ENSG00000236753	MKLN1-AS	MKLN1-AS2	MKLN1 antisense RNA	ncRNA	0.007491	0.477612	
chunk0124_116_1	chr3	54055060	54055415	+	0	NA	Intergenic	Intergenic	-67429	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.005634	0.376404	
chunk0190_107_1	chr8	30383698	30384227	+	0	NA	promoter-TSS (NM_001008710)	promoter-TSS (NM_001008710)	-539	NM_001008712	11030	Hs.334587	NM_006867	ENSG00000157110	RBPMS	HERMES	RNA binding protein, mRNA processing factor	protein-coding	0.062382	0.586792	
chunk0005_3_1	chr1	53944656	53945195	+	0	NA	intron (NM_001316935, intron 1 of 5)	intron (NM_001316935, intron 1 of 5)	898	NR_133633	51668	Hs.525462	NM_016126	ENSG00000081870	HSPB11	C1orf41|HSPCO34|IFT25|PP25	heat shock protein family B (small) member 11	protein-coding	0.018553	0.524074	343(GGGAACGTGGTGTACT,-,0.00),344(GGAACGTGGTGTACTT,+,0.00)
chunk0023_438_1	chr10	31937084	31937422	+	0	NA	Intergenic	MER101-int|LTR|ERV1	-8377	NM_001270697	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.008876	0.348083	
chunk0144_139_1	chr4	129825857	129826056	+	0	NA	Intergenic	Intergenic	-54478	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.010050	0.330000	
chunk0128_291_1	chr3	110957740	110958212	+	0	NA	Intergenic	Intergenic	111983	NR_045114	100506555	Hs.535689	NR_045114		NECTIN3-AS1	PVRL3-AS1	NECTIN3 antisense RNA 1	ncRNA	0.002119	0.376321	
chunk0034_111_1	chr11	27929748	27929947	+	0	NA	Intergenic	MER41-int|LTR|ERV1	-126968	NR_030341	693195		NR_030341	ENSG00000207874	MIR610	MIRN610|hsa-mir-610	microRNA 610	ncRNA	0.000000	0.410000	
chunk0148_404_1	chr5	14877614	14877849	+	0	NA	Intergenic	Intergenic	-5953	NM_054027	56172	Hs.156727	NM_054027	ENSG00000154122	ANKH	ANK|CCAL2|CMDJ|CPPDD|HANK|MANK|SLC62A1	ANKH inorganic pyrophosphate transport regulator	protein-coding	0.008511	0.444915	
chunk0068_242_1	chr15	55861774	55862513	+	0	NA	intron (NM_006154, intron 9 of 28)	L5|LINE|RTE-X	54988	NR_104302	4734	Hs.1565	NM_006154	ENSG00000069869	NEDD4	NEDD4-1|RPF1	NEDD4 E3 ubiquitin protein ligase	protein-coding	0.013532	0.345946	
chunk0143_30_1	chr4	106258136	106258629	+	0	NA	intron (NM_001290768, intron 5 of 26)	intron (NM_001290768, intron 5 of 26)	-57228	NM_001142415	9255	Hs.591680	NM_004757	ENSG00000164022	AIMP1	EMAP2|EMAPII|HLD3|SCYE1|p43	aminoacyl tRNA synthetase complex interacting multifunctional protein 1	protein-coding	0.002028	0.340081	
chunk0208_421_1	chrX	29763247	29763710	+	0	NA	intron (NM_014271, intron 6 of 10)	intron (NM_014271, intron 6 of 10)	189200	NR_049877	100847047		NR_049877	ENSG00000264090	MIR4666B	-	microRNA 4666b	ncRNA	0.004320	0.269397	
chunk0198_470_1	chr8	144816859	144817122	+	0	NA	Intergenic	L1MA4|LINE|L1	-10528	NM_003416	7553	Hs.493218	NM_003416	ENSG00000147789	ZNF7	HF.16|KOX4|zf30	zinc finger protein 7	protein-coding	0.022814	0.344697	
chunk0033_215_1	chr11	17209825	17210233	+	0	NA	Intergenic	Intergenic	-40222	NM_002645	5286	Hs.175343	NM_002645	ENSG00000011405	PIK3C2A	CPK|OCSKD|PI3-K-C2(ALPHA)|PI3-K-C2A|PI3K-C2-alpha|PI3K-C2alpha	phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha	protein-coding	0.002451	0.403423	
chunk0036_145_1	chr11	62176740	62177218	+	0	NA	Intergenic	L1MA6|LINE|L1	-13259	NM_006552	10648	Hs.202686	NM_006552	ENSG00000168515	SCGB1D1	LIPA|LPHA|LPNA	secretoglobin family 1D member 1	protein-coding	0.008368	0.386221	
chunk0057_445_1	chr13	110625476	110626165	+	0	NA	intron (NR_040103, intron 4 of 9)	intron (NR_040103, intron 4 of 9)	10236	NM_018210	55739	Hs.408324	NM_018210	ENSG00000213995	NAXD	CARKD|LP3298|PEBEL2	NAD(P)HX dehydratase	protein-coding	0.030479	0.624638	
chunk0118_187_1	chr22	31253941	31254349	+	0	NA	intron (NM_016733, intron 1 of 14)	intron (NM_016733, intron 1 of 14)	5783	NM_016733	3985	Hs.474596	NM_005569	ENSG00000182541	LIMK2	-	LIM domain kinase 2	protein-coding	0.009804	0.542787	
chunk0180_82_1	chr7	54997259	54997479	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-21663	NM_201282	1956	Hs.488293	NM_005228	ENSG00000146648	EGFR	ERBB|ERBB1|HER1|NISBD2|PIG61|mENA	epidermal growth factor receptor	protein-coding	0.013636	0.466063	
chunk0148_341_1	chr5	14348630	14349100	+	0	NA	intron (NM_007118, intron 11 of 56)	intron (NM_007118, intron 11 of 56)	205145	NM_007118	7204	Hs.130031	NM_007118	ENSG00000038382	TRIO	ARHGEF23|MEBAS|MRD44|tgat	trio Rho guanine nucleotide exchange factor	protein-coding	0.031915	0.428875	
chunk0017_281_1	chr1	209823643	209824146	+	0	NA	Intergenic	Intergenic	-4073	NM_014388	27042	Hs.194754	NM_014388	ENSG00000117597	UTP25	C1orf107|DEF|DIEXF|DJ434O14.5	UTP25 small subunit processor component	protein-coding	0.011928	0.426587	
chunk0134_150_1	chr3	177700959	177701192	+	0	NA	intron (NR_047568, intron 3 of 3)	intron (NR_047568, intron 3 of 3)	-115790	NR_110826	102724550	Hs.570526	NR_110826	ENSG00000231574	LINC02015	KCCAT211	long intergenic non-protein coding RNA 2015	ncRNA	0.008584	0.551282	
chunk0107_52_1	chr2	211396725	211397181	+	0	NA	intron (NM_005235, intron 25 of 27)	intron (NM_005235, intron 25 of 27)	779382	NR_002763	29034	Hs.658398	NR_002763	ENSG00000280837	CPS1-IT1	CPS1-IT|CPS1IT|CPS1IT1|PRO0132	CPS1 intronic transcript 1	ncRNA	0.006579	0.411379	
chunk0053_287_1	chr13	33474028	33474515	+	0	NA	intron (NM_001243476, intron 4 of 17)	LOR1-int|LTR|ERV1	-188507	NM_178006	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.008214	0.403689	192(TAGTACATGATGTTCT,-,0.00),193(AGTACATGATGTTCTT,+,0.00)
chunk0142_353_1	chr4	101810327	101810886	+	0	NA	intron (NM_001127507, intron 1 of 15)	intron (NM_001127507, intron 1 of 15)	-3220	NM_001083907	55024	Hs.480400	NM_017935	ENSG00000153064	BANK1	BANK	B cell scaffold protein with ankyrin repeats 1	protein-coding	0.001789	0.307143	
chunk0119_271_1	chr22	45998947	45999257	+	0	NA	Intergenic	Intergenic	-7514	NR_027240	730668	Hs.640071	NR_027240	ENSG00000280424	LOC730668	-	dynein heavy chain -like pseudogene	pseudo	0.012903	0.562701	96(TGGAACTGTGTGTTCA,-,0.00),97(GGAACTGTGTGTTCAA,+,0.00)
chunk0207_47_1	chrX	7074156	7074859	+	0	NA	intron (NM_001178135, intron 3 of 3)	intron (NM_001178135, intron 3 of 3)	-73353	NR_039924	100616467		NR_039924	ENSG00000264268	MIR4767	mir-4767	microRNA 4767	ncRNA	0.011380	0.454545	294(AAGGACTGCCTGTACT,-,0.00),295(AGGACTGCCTGTACTT,+,0.00)
chunk0058_350_1	chr14	28924433	28925100	+	0	NA	Intergenic	Intergenic	152062	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.000000	0.386228	
chunk0138_230_1	chr4	39300459	39300730	+	0	NA	intron (NM_002913, intron 19 of 24)	L1MC1|LINE|L1	65787	NM_001204747	5981	Hs.507475	NM_002913	ENSG00000035928	RFC1	A1|CANVAS|MHCBFB|PO-GA|RECC1|RFC|RFC140	replication factor C subunit 1	protein-coding	0.022140	0.363971	
chunk0131_438_1	chr3	153778150	153778454	+	0	NA	Intergenic	MIR|SINE|MIR	293807	NM_001101337									0.003289	0.311475	
chunk0189_33_1	chr8	19756260	19756680	+	0	NA	Intergenic	Intergenic	-60937	NM_018142	55174	Hs.512627	NM_018142	ENSG00000104613	INTS10	C8orf35|INT10	integrator complex subunit 10	protein-coding	0.033333	0.477435	
chunk0109_348_1	chr2	238869061	238869461	+	0	NA	intron (NM_001271893, intron 1 of 1)	intron (NM_001271893, intron 1 of 1)	21229	NM_057179	117581	Hs.422585	NM_057179	ENSG00000233608	TWIST2	AMS|BBRSAY|DERMO1|FFDD3|SETLSS|bHLHa39	twist family bHLH transcription factor 2	protein-coding	0.032500	0.463840	
chunk0014_315_1	chr1	181259100	181259624	+	0	NA	Intergenic	MER127|DNA|TcMar-Tigger	22974	NR_046249	100287948	Hs.742594	NR_046249	ENSG00000179452	LINC01699	GM140	long intergenic non-protein coding RNA 1699	ncRNA	0.007634	0.441905	
chunk0211_272_1	chrX	121655179	121655697	+	0	NA	Intergenic	MER76|LTR|ERVL	284466	NR_037444	100500869		NR_037444	ENSG00000265456	MIR3672	-	microRNA 3672	ncRNA	0.000000	0.427746	
chunk0060_323_1	chr14	51382357	51382981	+	0	NA	Intergenic	Intergenic	49276	NR_038358	283553	Hs.325752	NR_038358	ENSG00000258479	LINC00640	-	long intergenic non-protein coding RNA 640	ncRNA	0.006410	0.419200	
chunk0175_377_1	chr6	168017663	168018106	+	0	NA	promoter-TSS (NM_005355)	promoter-TSS (NM_005355)	11	NM_030615	3834	Hs.150013	NM_005355	ENSG00000125337	KIF25	KNSL3	kinesin family member 25	protein-coding	0.024831	0.439189	
chunk0015_300_1	chr1	188874393	188874830	+	0	NA	Intergenic	LTR1B0|LTR|ERV1	1430983	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.016018	0.513699	
chunk0095_383_1	chr2	23745491	23746222	+	0	NA	Intergenic	L2a|LINE|L2	181258	NR_125717	54454	Hs.467862	NM_017552	ENSG00000119778	ATAD2B	-	ATPase family AAA domain containing 2B	protein-coding	0.001368	0.423497	474(GAGAACTGCCTGTACT,-,0.00),475(AGAACTGCCTGTACTT,+,0.00)
chunk0016_259_1	chr1	200131670	200132081	+	0	NA	intron (NM_205860, intron 7 of 7)	intron (NM_205860, intron 7 of 7)	89050	NM_001276464	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.002433	0.410194	
chunk0080_187_1	chr17	28941179	28941736	+	0	NA	intron (NM_001033561, intron 2 of 14)	intron (NM_001033561, intron 2 of 14)	10033	NM_001290131	57649	Hs.444173	NM_020889	ENSG00000109118	PHF12	PF1	PHD finger protein 12	protein-coding	0.007181	0.396057	
chunk0047_165_1	chr12	70052998	70053203	+	0	NA	Intergenic	LTR16A|LTR|ERVL	-189894	NM_014515	4848	Hs.133350	NM_014515	ENSG00000111596	CNOT2	CDC36|HSPC131|NOT2|NOT2H	CCR4-NOT transcription complex subunit 2	protein-coding	0.014634	0.475728	
chunk0124_103_1	chr3	53828575	53829086	+	0	NA	intron (NM_018397, intron 2 of 8)	L1MC1|LINE|L1	17563	NM_018397	55349	Hs.126688	NM_018397	ENSG00000016391	CHDH	-	choline dehydrogenase	protein-coding	0.001957	0.386719	
chunk0195_426_1	chr8	100826922	100827132	+	0	NA	Intergenic	Intergenic	-104940	NM_002568	26986	Hs.387804	NM_002568	ENSG00000070756	PABPC1	PAB1|PABP|PABP1|PABPC2|PABPL1	poly(A) binding protein cytoplasmic 1	protein-coding	0.014286	0.407583	
chunk0013_238_1	chr1	169586652	169587030	+	0	NA	promoter-TSS (NM_000130)	promoter-TSS (NM_000130)	-310	NM_000130	2153	Hs.30054	NM_000130	ENSG00000198734	F5	FVL|PCCF|RPRGL1|THPH2	coagulation factor V	protein-coding	0.015873	0.525066	
chunk0039_117_1	chr11	97854041	97854549	+	0	NA	Intergenic	MER67C|LTR|ERV1	-1166681	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.001969	0.355599	492(ATGCACATTATGTTCT,-,0.00),493(TGCACATTATGTTCTT,+,0.00)
chunk0120_462_1	chr22	50530903	50531227	+	0	NA	promoter-TSS (NM_001113755)	promoter-TSS (NM_001113755)	-980	NM_001953	1890	Hs.180903	NM_001953	ENSG00000025708	TYMP	ECGF|ECGF1|MEDPS1|MNGIE|MTDPS1|PDECGF|TP|hPD-ECGF	thymidine phosphorylase	protein-coding	0.083333	0.695385	
chunk0163_72_1	chr6	9243396	9243954	+	0	NA	Intergenic	Intergenic	591466	NR_004855	728655	Hs.214343	NR_004855		HULC	HCCAT1|LINC00078|NCRNA00078	hepatocellular carcinoma up-regulated long non-coding RNA	ncRNA	0.007168	0.425760	
chunk0143_286_1	chr4	117760725	117760999	+	0	NA	Intergenic	MER92-int|LTR|ERV1	-273483	NM_004784	9348	Hs.480596	NM_004784	ENSG00000164100	NDST3	HSST3	N-deacetylase and N-sulfotransferase 3	protein-coding	0.000000	0.283636	
chunk0157_175_1	chr5	118396678	118396935	+	0	NA	intron (NR_104610, intron 9 of 9)	intron (NR_104610, intron 9 of 9)	114232	NR_104609	100505811	Hs.369776	NR_104609	ENSG00000250427	LINC02148	HNCAT21	long intergenic non-protein coding RNA 2148	ncRNA	0.003891	0.379845	
chunk0150_59_1	chr5	31990479	31991279	+	0	NA	intron (NM_178140, intron 2 of 23)	L2a|LINE|L2	-54720	NR_036241	100422874		NR_036241	ENSG00000266243	MIR4279	-	microRNA 4279	ncRNA	0.010000	0.460674	498(CGGGGCAGAATGTTCC,-,0.00),499(GGGGCAGAATGTTCCC,+,0.00),551(AATGACAGAGTGTTCC,-,0.00),552(ATGACAGAGTGTTCCA,+,0.00)
chunk0103_168_1	chr2	162658450	162658674	+	0	NA	intron (NM_033272, intron 2 of 15)	L1MC1|LINE|L1	-110374	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.004464	0.315556	
chunk0091_7_1	chr19	2587308	2587673	+	0	NA	intron (NM_052847, intron 2 of 4)	intron (NM_052847, intron 2 of 4)	-43225	NR_107004	102465838		NR_107004	ENSG00000277904	MIR7850	hsa-mir-7850	microRNA 7850	ncRNA	0.052055	0.622951	
chunk0030_62_1	chr10	111969099	111969404	+	0	NA	Intergenic	Intergenic	214528	NM_020918	57678	Hs.42586	NM_020918	ENSG00000119927	GPAM	GPAT|GPAT1	glycerol-3-phosphate acyltransferase, mitochondrial	protein-coding	0.003279	0.277778	
chunk0154_258_1	chr5	81641552	81642073	+	0	NA	intron (NM_001256733, intron 2 of 15)	L1ME4b|LINE|L1	109441	NM_012446	23635	Hs.102735	NM_012446	ENSG00000145687	SSBP2	HSPC116|SOSS-B2	single stranded DNA binding protein 2	protein-coding	0.001919	0.319923	
chunk0024_147_1	chr10	35237662	35237963	+	0	NA	Intergenic	LTR49-int|LTR|ERV1	-9169	NM_181698	219771	Hs.14745	NM_145012	ENSG00000108100	CCNY	C10orf9|CBCP1|CCNX|CFP1	cyclin Y	protein-coding	0.023256	0.500000	
chunk0112_272_1	chr20	43388289	43389066	+	0	NA	Intergenic	Intergenic	-69187	NR_034009	6431	Hs.684950	NM_006275	ENSG00000124193	SRSF6	B52|HEL-S-91|SFRS6|SRP55	serine and arginine rich splicing factor 6	protein-coding	0.018018	0.475578	309(AGGAACAGTGAGTTTT,-,0.00)
chunk0131_361_1	chr3	151960818	151961586	+	0	NA	Intergenic	Intergenic	-33027	NR_110203	101928142	Hs.680207	NR_110202		AADACL2-AS1	-	AADACL2 antisense RNA 1	ncRNA	0.006510	0.347204	
chunk0111_415_1	chr20	34703551	34703837	+	0	NA	promoter-TSS (NM_021202)	promoter-TSS (NM_021202)	-650	NM_021202	58476	Hs.516994	NM_021202	ENSG00000078804	TP53INP2	C20orf110|DOR|PIG-U|PIGU|PINH|dJ1181N3.1	tumor protein p53 inducible nuclear protein 2	protein-coding	0.045455	0.512195	
chunk0192_106_1	chr8	61672701	61673588	+	0	NA	intron (NM_032467, intron 3 of 4)	intron (NM_032467, intron 3 of 4)	16705	NM_001164752	444	Hs.332422	NM_004318	ENSG00000198363	ASPH	AAH|BAH|CASQ2BP1|FDLAB|HAAH|JCTN|junctin	aspartate beta-hydroxylase	protein-coding	0.010147	0.400901	
chunk0034_338_1	chr11	35683230	35683804	+	0	NA	intron (NM_017583, intron 1 of 4)	intron (NM_017583, intron 1 of 4)	20765	NM_017583	54765	Hs.192103	NM_017583	ENSG00000166326	TRIM44	AN3|DIPB|HSA249128|MC7	tripartite motif containing 44	protein-coding	0.000000	0.318261	
chunk0210_175_1	chrX	78842544	78842950	+	0	NA	Intergenic	L1PREC2|LINE|L1	58502	NR_036258	100422932		NR_036258	ENSG00000283622	MIR4328	-	microRNA 4328	ncRNA	0.012315	0.393120	
chunk0057_65_1	chr13	98004098	98004335	+	0	NA	intron (NM_002271, intron 16 of 28)	Charlie10|DNA|hAT-Charlie	50541	NM_002271	3843	Hs.712598	NM_002271	ENSG00000065150	IPO5	IMB3|KPNB3|Pse1|RANBP5|imp5	importin 5	protein-coding	0.000000	0.331933	
chunk0199_290_1	chr9	6664943	6665226	+	0	NA	Intergenic	Intergenic	-19392	NM_000170	2731	Hs.584238	NM_000170	ENSG00000178445	GLDC	GCE|GCSP|HYGN1	glycine decarboxylase	protein-coding	0.000000	0.457746	
chunk0196_235_1	chr8	108206899	108207185	+	0	NA	intron (NM_001568, intron 10 of 12)	intron (NM_001568, intron 10 of 12)	41688	NM_001568	3646	Hs.405590	NM_001568	ENSG00000104408	EIF3E	EIF3-P48|EIF3S6|INT6|eIF3-p46	eukaryotic translation initiation factor 3 subunit E	protein-coding	0.006993	0.351916	
chunk0059_223_1	chr14	34181574	34182016	+	0	NA	Intergenic	Intergenic	-230717	NM_022073	112399	Hs.135507	NM_022073	ENSG00000129521	EGLN3	HIFP4H3|HIFPH3|PHD3	egl-9 family hypoxia inducible factor 3	protein-coding	0.004525	0.388262	
chunk0061_382_1	chr14	64218402	64218628	+	0	NA	intron (NM_182914, intron 109 of 115)	intron (NM_182914, intron 109 of 115)	2561	NM_182910	23224	Hs.745014	NM_015180	ENSG00000054654	SYNE2	EDMD5|KASH2|NUA|NUANCE|Nesp2|Nesprin-2|SYNE-2|TROPH	spectrin repeat containing nuclear envelope protein 2	protein-coding	0.035398	0.519824	
chunk0021_366_1	chr1	246354163	246354965	+	0	NA	intron (NM_001167740, intron 2 of 11)	L1ME4b|LINE|L1	62848	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003741	0.313823	
chunk0021_377_1	chr1	246449363	246450047	+	0	NA	intron (NM_001167740, intron 1 of 11)	MIRb|SINE|MIR	-32293	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.013158	0.421898	
chunk0130_390_1	chr3	140093645	140094190	+	0	NA	intron (NM_022131, intron 1 of 16)	MER113A|DNA|hAT-Charlie	158732	NM_022131	64084	Hs.158529	NM_022131	ENSG00000158258	CLSTN2	ALC-GAMMA|CDHR13|CS2|CSTN2|alcagamma	calsyntenin 2	protein-coding	0.009174	0.375458	
chunk0113_101_1	chr20	50958315	50958815	+	0	NA	promoter-TSS (NM_003859)	promoter-TSS (NM_003859)	-42	NM_003859	8813	Hs.654951	NM_003859	ENSG00000000419	DPM1	CDGIE|MPDS	dolichyl-phosphate mannosyltransferase subunit 1, catalytic	protein-coding	0.062000	0.502994	
chunk0111_113_1	chr20	23888013	23888285	+	0	NA	Intergenic	Intergenic	-8406	NM_001900	1473	Hs.121489	NM_001900	ENSG00000170367	CST5	-	cystatin D	protein-coding	0.003676	0.439560	59(TGGGACACCCTGTGCT,-,0.00),60(GGGACACCCTGTGCTT,+,0.00)
chunk0078_218_1	chr17	6326647	6326846	+	0	NA	Intergenic	(CACATA)n|Simple_repeat|Simple_repeat	108386	NM_001285402	23746	Hs.279887	NM_014336	ENSG00000129221	AIPL1	AIPL2|LCA4	aryl hydrocarbon receptor interacting protein like 1	protein-coding	0.020101	0.420000	
chunk0071_410_1	chr15	89692260	89692781	+	0	NA	intron (NM_020212, intron 1 of 16)	intron (NM_020212, intron 1 of 16)	1723	NM_020212	56964	Hs.177557	NM_020212	ENSG00000140527	WDR93	-	WD repeat domain 93	protein-coding	0.017274	0.459770	
chunk0192_165_1	chr8	62523013	62523753	+	0	NA	intron (NR_130764, intron 1 of 6)	intron (NR_130764, intron 1 of 6)	274441	NM_001304533	286183	Hs.654662	NM_173688	ENSG00000185942	NKAIN3	FAM77D	sodium/potassium transporting ATPase interacting 3	protein-coding	0.006757	0.387314	271(AAGTACACTCTGTGAT,-,0.00)
chunk0060_16_1	chr14	39432054	39432547	+	0	NA	5' UTR (NM_203301, exon 1 of 4)	5' UTR (NM_203301, exon 1 of 4)	200	NM_203301	254170	Hs.146632	NM_203301	ENSG00000165355	FBXO33	BMND12|Fbx33|c14_5247	F-box protein 33	protein-coding	0.103448	0.661943	
chunk0181_151_1	chr7	81908172	81908492	+	0	NA	Intergenic	L1PA14|LINE|L1	-100845	NR_110076	101927356	Hs.571348	NR_110076	ENSG00000223770	LOC101927356	-	uncharacterized LOC101927356	ncRNA	0.006250	0.358255	
chunk0205_60_1	chr9	106587765	106588142	+	0	NA	Intergenic	Intergenic	-12975	NR_107048	102465995		NR_107048	ENSG00000277889	MIR8081	hsa-mir-8081	microRNA 8081	ncRNA	0.010610	0.415344	
chunk0038_184_1	chr11	85867539	85868175	+	0	NA	intron (NM_173556, intron 2 of 11)	LTR83|LTR|ERVL	12756	NM_001286159	220047	Hs.567774	NM_173556	ENSG00000150676	CCDC83	CT148|HSD9|KP-CoT-23	coiled-coil domain containing 83	protein-coding	0.004717	0.383046	
chunk0088_268_1	chr18	49187187	49187558	+	0	NA	intron (NM_017653, intron 13 of 16)	intron (NM_017653, intron 13 of 16)	-137604	NR_039898	100616420		NR_039898	ENSG00000263849	MIR4744	-	microRNA 4744	ncRNA	0.008086	0.392473	
chunk0081_460_1	chr17	49390891	49391628	+	0	NA	Intergenic	L1ME3G|LINE|L1	23599	NM_001281496	5245	Hs.514303	NM_002634	ENSG00000167085	PHB	HEL-215|HEL-S-54e|PHB1	prohibitin	protein-coding	0.006784	0.414634	
chunk0169_198_1	chr6	102750680	102751477	+	0	NA	Intergenic	Intergenic	1352093	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.001255	0.337093	
chunk0006_272_1	chr1	70331810	70332404	+	0	NA	intron (NM_030816, intron 2 of 12)	Tigger10|DNA|TcMar-Tigger	22627	NM_030816	81573	Hs.744989	NM_030816	ENSG00000118454	ANKRD13C	dJ677H15.3	ankyrin repeat domain 13C	protein-coding	0.001684	0.295798	
chunk0194_54_1	chr8	82148032	82148333	+	0	NA	Intergenic	Intergenic	-305896	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.317881	
chunk0154_384_1	chr5	87899439	87899925	+	0	NA	Intergenic	Intergenic	369197	NR_110266	153396	Hs.379972	NM_153354	ENSG00000164180	TMEM161B	FLB3342|PRO1313	transmembrane protein 161B	protein-coding	0.010288	0.429158	157(GGTTCATTGTGTTCTG,+,0.00)
chunk0178_302_1	chr7	37857244	37857556	+	0	NA	intron (NM_016616, intron 6 of 17)	intron (NM_016616, intron 6 of 17)	8803	NM_016616	51314	Hs.723454	NM_016616	ENSG00000086288	NME8	CILD6|HEL-S-99|NM23-H8|SPTRX2|TXNDC3|sptrx-2	NME/NM23 family member 8	protein-coding	0.000000	0.309904	
chunk0008_59_1	chr1	89484921	89485120	+	0	NA	Intergenic	MLT1F2|LTR|ERVL-MaLR	-39818	NM_001134476	23507	Hs.482017	NM_015350	ENSG00000197147	LRRC8B	TA-LRRP|TALRRP	leucine rich repeat containing 8 VRAC subunit B	protein-coding	0.005025	0.350000	
chunk0049_327_1	chr12	94713104	94713636	+	0	NA	Intergenic	Intergenic	-62808	NM_020698	57458	Hs.370410	NM_020698	ENSG00000057704	TMCC3	-	transmembrane and coiled-coil domain family 3	protein-coding	0.018797	0.427767	
chunk0096_70_1	chr2	27707825	27708462	+	0	NA	Intergenic	MIR3|SINE|MIR	-44303	NM_001282731	9913	Hs.6232	NM_014860	ENSG00000119760	SUPT7L	SPT7L|STAF65|STAF65(gamma)|STAF65G|SUPT7H	SPT7 like, STAGA complex gamma subunit	protein-coding	0.010989	0.489028	237(CGGAACAAGCTGTGCC,-,0.00),238(GGAACAAGCTGTGCCA,+,0.00)
chunk0118_14_1	chr22	25636178	25636789	+	0	NA	intron (NM_005160, intron 2 of 20)	L1MC4|LINE|L1	71589	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.006547	0.344771	215(ATGTACATTCTGTTCT,-,0.00),216(TGTACATTCTGTTCTC,+,0.00)
chunk0097_353_1	chr2	59806527	59806927	+	0	NA	Intergenic	Intergenic	576309	NR_132991	106660609	Hs.565545	NR_132991	ENSG00000228590	MIR4432HG	-	MIR4432 host gene	ncRNA	0.000000	0.406484	
chunk0201_404_1	chr9	69326880	69327158	+	0	NA	intron (NM_001127608, intron 1 of 10)	intron (NM_001127608, intron 1 of 10)	-2306	NM_004816	9413	Hs.118003	NM_004816	ENSG00000135063	FAM189A2	C9orf61|X123	family with sequence similarity 189 member A2	protein-coding	0.014388	0.347670	
chunk0201_259_1	chr9	38302874	38303458	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-89498	NM_000692	219	Hs.436219	NM_000692	ENSG00000137124	ALDH1B1	ALDH5|ALDHX	aldehyde dehydrogenase 1 family member B1	protein-coding	0.001712	0.388034	
chunk0203_275_1	chr9	88596252	88596844	+	0	NA	Intergenic	MER83|LTR|ERV1	55612	NM_001100111									0.010135	0.463744	
chunk0210_107_1	chrX	72053267	72053570	+	0	NA	intron (NM_001013627, intron 1 of 7)	intron (NM_001013627, intron 1 of 7)	9009	NR_002309	441502	Hs.449523	NR_002309		RPS26P11	RPS26L1|RPS26_22_1784|bA366E13.1	ribosomal protein S26 pseudogene 11	pseudo	0.009901	0.414474	
chunk0042_256_1	chr12	6650303	6650914	+	0	NA	TTS (NM_016162)	TTS (NM_016162)	-3194	NM_032489	84519	Hs.123239	NM_032489	ENSG00000111644	ACRBP	CT23|OY-TES-1|SP32	acrosin binding protein	protein-coding	0.004910	0.470588	
chunk0005_430_1	chr1	62904294	62904746	+	0	NA	Intergenic	Intergenic	120414	NM_178221	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.013274	0.395143	
chunk0182_11_1	chr7	91055185	91055555	+	0	NA	intron (NM_001287136, intron 10 of 13)	intron (NM_001287136, intron 10 of 13)	-209098	NM_003505	8321	Hs.94234	NM_003505	ENSG00000157240	FZD1	-	frizzled class receptor 1	protein-coding	0.005405	0.312668	183(AGGGACAATCTGTACT,-,0.00),184(GGGACAATCTGTACTT,+,0.00)
chunk0079_357_1	chr17	17877470	17877751	+	0	NA	intron (NM_001033551, intron 6 of 13)	intron (NM_001033551, intron 6 of 13)	-40599	NM_001005291	6720	Hs.592123	NM_004176	ENSG00000072310	SREBF1	SREBP1|bHLHd1	sterol regulatory element binding transcription factor 1	protein-coding	0.021352	0.556738	
chunk0203_346_1	chr9	89847430	89847667	+	0	NA	Intergenic	Intergenic	-121868	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.004219	0.365546	122(TGGAACTGTGTGTTCC,-,0.00),123(GGAACTGTGTGTTCCC,+,0.00)
chunk0080_14_1	chr17	20935793	20936194	+	0	NA	Intergenic	Intergenic	-2527	NR_123730	339260	Hs.661076	NR_123730	ENSG00000233098	LOC339260	-	uncharacterized LOC339260	ncRNA	0.004988	0.385572	
chunk0058_201_1	chr14	24805364	24805592	+	0	NA	Intergenic	Intergenic	-171252	NM_004131	3002	Hs.1051	NM_004131	ENSG00000100453	GZMB	C11|CCPI|CGL-1|CGL1|CSP-B|CSPB|CTLA1|CTSGL1|HLP|SECT	granzyme B	protein-coding	0.008772	0.362445	
chunk0143_426_1	chr4	123793332	123793863	+	0	NA	intron (NR_027106, intron 1 of 2)	L1PB2|LINE|L1	19333	NR_027106	285419	Hs.535763	NR_027105	ENSG00000249464	LINC01091	-	long intergenic non-protein coding RNA 1091	ncRNA	0.003766	0.357143	244(TGAACAGGGCGTCCTT,+,0.00)
chunk0140_78_1	chr4	67634940	67635257	+	0	NA	intron (NM_018227, intron 20 of 32)	intron (NM_018227, intron 20 of 32)	66073	NM_018227	55236	Hs.212774	NM_018227	ENSG00000033178	UBA6	E1-L2|MOP-4|UBE1L2	ubiquitin like modifier activating enzyme 6	protein-coding	0.003155	0.308176	
chunk0132_299_1	chr3	160212545	160213083	+	0	NA	Intergenic	Intergenic	-5722	NR_108088	101928376	Hs.565865	NR_108088	ENSG00000244040	IL12A-AS1	ILAS1-AS1	IL12A antisense RNA 1	ncRNA	0.003717	0.372913	
chunk0160_226_1	chr5	155156898	155157128	+	0	NA	Intergenic	Intergenic	143313	NM_001099293	285643	Hs.567824	NM_001099293	ENSG00000226650	KIF4B	-	kinesin family member 4B	protein-coding	0.004348	0.428571	
chunk0023_432_1	chr10	31820790	31821353	+	0	NA	intron (NM_001270696, intron 9 of 17)	intron (NM_001270696, intron 9 of 17)	87855	NM_001270699	94134	Hs.499264	NM_018287	ENSG00000165322	ARHGAP12	-	Rho GTPase activating protein 12	protein-coding	0.005329	0.326241	
chunk0053_24_1	chr13	26759035	26759329	+	0	NA	exon (NM_005288, exon 2 of 2)	exon (NM_005288, exon 2 of 2)	1603	NM_005288	2835	Hs.123034	NM_005288	ENSG00000132975	GPR12	GPCR12|GPCR21|PPP1R84	G protein-coupled receptor 12	protein-coding	0.047619	0.589831	
chunk0075_263_1	chr16	53549801	53550244	+	0	NA	Intergenic	Intergenic	-46718	NM_022476	64400	Hs.380897	NM_022476	ENSG00000166971	AKTIP	FT1|FTS	AKT interacting protein	protein-coding	0.022573	0.387387	
chunk0136_407_1	chr3	197317202	197317441	+	0	NA	Intergenic	MIRc|SINE|MIR	-18049	NM_001290983	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.004184	0.337500	
chunk0085_213_1	chr18	6734636	6734835	+	0	NA	Intergenic	Intergenic	-99698	NM_001010000	79822	Hs.183114	NM_030672	ENSG00000088756	ARHGAP28	-	Rho GTPase activating protein 28	protein-coding	0.005025	0.350000	
chunk0195_286_1	chr8	98538628	98538913	+	0	NA	intron (NM_006281, intron 9 of 10)	intron (NM_006281, intron 9 of 10)	111748	NM_020697	3788	Hs.388045	NM_020697	ENSG00000156486	KCNS2	KV9.2	potassium voltage-gated channel modifier subfamily S member 2	protein-coding	0.014035	0.416084	
chunk0110_268_1	chr20	17037722	17038008	+	0	NA	Intergenic	Intergenic	-188242	NM_001201528	5126	Hs.315186	NM_002594	ENSG00000125851	PCSK2	NEC 2|NEC-2|NEC2|PC2|SPC2	proprotein convertase subtilisin/kexin type 2	protein-coding	0.010490	0.365854	
chunk0056_11_1	chr13	77105836	77106035	+	0	NA	intron (NM_015057, intron 55 of 82)	intron (NM_015057, intron 55 of 82)	30421	NR_046716	100874212	Hs.569288	NR_046716	ENSG00000236051	MYCBP2-AS1	-	MYCBP2 antisense RNA 1	ncRNA	0.005025	0.305000	
chunk0015_251_1	chr1	188006196	188006815	+	0	NA	Intergenic	LTR50|LTR|ERVL	562877	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.004847	0.385484	335(GAAGACTGTGTGTTCC,-,0.00),336(AAGACTGTGTGTTCCT,+,0.00)
chunk0037_41_1	chr11	70353979	70354237	+	0	NA	intron (NR_045286, intron 17 of 28)	intron (NR_045286, intron 17 of 28)	-44398	NM_005231	2017	Hs.596164	NM_005231	ENSG00000085733	CTTN	EMS1	cortactin	protein-coding	0.023256	0.552124	
chunk0123_99_1	chr3	42166313	42166512	+	0	NA	intron (NM_014965, intron 1 of 12)	intron (NM_014965, intron 1 of 12)	6243	NM_014965	22906	Hs.535711	NM_014965	ENSG00000182606	TRAK1	EIEE68|MILT1|OIP106	trafficking kinesin protein 1	protein-coding	0.010050	0.490000	
chunk0136_173_1	chr4	6463633	6463836	+	0	NA	intron (NM_001206995, intron 2 of 9)	intron (NM_001206995, intron 2 of 9)	8865	NM_020416	5522	Hs.479069	NM_020416	ENSG00000074211	PPP2R2C	B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G	protein phosphatase 2 regulatory subunit Bgamma	protein-coding	0.019704	0.573529	48(TGCACACACCGTTCCT,+,0.00)
chunk0174_310_1	chr6	162750764	162751024	+	0	NA	intron (NM_152410, intron 2 of 6)	intron (NM_152410, intron 2 of 6)	22924	NM_001080379	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.011538	0.367816	
chunk0164_222_1	chr6	22928553	22928877	+	0	NA	Intergenic	Intergenic	359266	NM_138574	154150	Hs.629246	NM_138574	ENSG00000112273	HDGFL1	HRP-1|Hdgfrp1|PWWP1|dJ309H15.1	HDGF like 1	protein-coding	0.000000	0.350769	
chunk0032_337_1	chr11	10285400	10285810	+	0	NA	intron (NM_030962, intron 1 of 39)	MER51B|LTR|ERV1	8602	NM_030962	81846	Hs.577252	NM_030962	ENSG00000133812	SBF2	CMT4B2|DENND7B|MTMR13	SET binding factor 2	protein-coding	0.000000	0.379562	
chunk0156_294_1	chr5	110069801	110070005	+	0	NA	Intergenic	L1PA13|LINE|L1	186721	NR_033175	100289673	Hs.368405	NR_033175		LINC01848	-	long intergenic non-protein coding RNA 1848	ncRNA	0.000000	0.321951	
chunk0207_82_1	chrX	9337161	9337658	+	0	NA	Intergenic	Intergenic	-125886	NM_001139467	6907	Hs.495656	NM_005647	ENSG00000101849	TBL1X	EBI|SMAP55|TBL1	transducin beta like 1 X-linked	protein-coding	0.012072	0.421687	
chunk0018_47_1	chr1	216261743	216261951	+	0	NA	intron (NM_206933, intron 11 of 71)	L1MA5|LINE|L1	161549	NM_206933	7399	Hs.655974	NM_007123	ENSG00000042781	USH2A	RP39|US2|USH2|dJ1111A8.1	usherin	protein-coding	0.009615	0.502392	
chunk0126_314_1	chr3	81531369	81531613	+	0	NA	intron (NM_000158, intron 14 of 15)	L1MA3|LINE|L1	230308	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.008197	0.497959	
chunk0212_113_1	chrX	130296744	130297293	+	0	NA	Intergenic	Intergenic	-28070	NM_017666	55609	Hs.308418	NM_017666	ENSG00000056277	ZNF280C	SUHW3|ZNF633|ZPET	zinc finger protein 280C	protein-coding	0.003643	0.338182	233(AAGCACACTGAGTTCT,-,0.00),234(AGCACACTGAGTTCTG,+,0.00)
chunk0066_355_1	chr15	38227095	38227445	+	0	NA	Intergenic	Intergenic	-25581	NM_152594	161742	Hs.525781	NM_152594	ENSG00000166068	SPRED1	LGSS|NFLS|PPP1R147|hSpred1|spred-1	sprouty related EVH1 domain containing 1	protein-coding	0.005714	0.358974	
chunk0196_95_1	chr8	102968755	102969008	+	0	NA	intron (NR_126338, intron 3 of 3)	intron (NR_126338, intron 3 of 3)	-52139	NM_001695	528	Hs.86905	NM_001695	ENSG00000155097	ATP6V1C1	ATP6C|ATP6D|VATC|Vma5	ATPase H+ transporting V1 subunit C1	protein-coding	0.003953	0.381890	
chunk0022_148_1	chr10	12377163	12377366	+	0	NA	intron (NM_020397, intron 1 of 9)	intron (NM_020397, intron 1 of 9)	27721	NM_153498	57118	Hs.600547	NM_020397	ENSG00000183049	CAMK1D	CKLiK|CaM-K1|CaMKID	calcium/calmodulin dependent protein kinase ID	protein-coding	0.000000	0.313725	
chunk0043_383_1	chr12	25057719	25057976	+	0	NA	intron (NM_001204126, intron 1 of 19)	L1ME2|LINE|L1	5600	NM_001204127	4033	Hs.124922	NM_006152	ENSG00000118308	LRMP	JAW1	lymphoid restricted membrane protein	protein-coding	0.007782	0.391473	
chunk0184_360_1	chr7	121021036	121021257	+	0	NA	intron (NM_001105533, intron 2 of 17)	intron (NM_001105533, intron 2 of 17)	31755	NM_001105533	79974	Hs.189652	NM_024913	ENSG00000106034	CPED1	C7orf58	cadherin like and PC-esterase domain containing 1	protein-coding	0.000000	0.288288	49(TGATACAGTGTGTTCT,-,0.00),50(GATACAGTGTGTTCTG,+,0.00)
chunk0125_410_1	chr3	72297952	72298935	+	0	NA	Intergenic	MamGypLTR3a|LTR|Gypsy	147186	NR_038221	201617	Hs.382623	NR_038221	ENSG00000243083	LINC00870	-	long intergenic non-protein coding RNA 870	ncRNA	0.008138	0.492886	
chunk0119_114_1	chr22	42357572	42358003	+	0	NA	Intergenic	Intergenic	11421	NR_120596	102723775	Hs.335413	NR_120595	ENSG00000229891	LINC01315	C22orf32-1|lnc-C22orf32-1	long intergenic non-protein coding RNA 1315	ncRNA	0.013921	0.571759	
chunk0209_166_1	chrX	43564903	43565246	+	0	NA	Intergenic	Intergenic	-89833	NM_001270458	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.005831	0.433140	
chunk0209_177_1	chrX	43688586	43688929	+	0	NA	intron (NM_000240, intron 2 of 14)	L1MEd|LINE|L1	33850	NM_000240	4128	Hs.183109	NM_000240	ENSG00000189221	MAOA	BRNRS|MAO-A	monoamine oxidase A	protein-coding	0.002915	0.325581	
chunk0102_404_1	chr2	156058876	156059426	+	0	NA	intron (NR_110250, intron 1 of 3)	MIRc|SINE|MIR	195780	NR_110250	101929378	Hs.171192	NR_110249	ENSG00000226383	LINC01876	-	long intergenic non-protein coding RNA 1876	ncRNA	0.003636	0.368421	
chunk0047_106_1	chr12	68881413	68881666	+	0	NA	intron (NM_001005502, intron 3 of 8)	intron (NM_001005502, intron 3 of 8)	51660	NM_198320	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.003953	0.334646	
chunk0102_259_1	chr2	149468747	149469234	+	0	NA	intron (NM_001195685, intron 4 of 4)	intron (NM_001195685, intron 4 of 4)	-118368	NR_110240	101929231	Hs.5324	NR_110240	ENSG00000231969	LOC101929231	-	uncharacterized LOC101929231	ncRNA	0.010267	0.434426	
chunk0209_403_1	chrX	55796403	55797021	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	79035	NM_006064	10325	Hs.50282	NM_006064	ENSG00000083750	RRAGB	RAGB|bA465E19.1	Ras related GTP binding B	protein-coding	0.006472	0.323102	
chunk0124_405_1	chr3	60307467	60307949	+	0	NA	intron (NM_001166243, intron 5 of 9)	intron (NM_001166243, intron 5 of 9)	310162	NR_128708	103504735		NR_128708	ENSG00000281426	MIR548BB	MI0029321|hsa-mir-548bb	microRNA 548bb	ncRNA	0.004149	0.424431	
chunk0047_463_1	chr12	76880076	76880565	+	0	NA	Intergenic	Intergenic	-1280	NM_001321	1466	Hs.530904	NM_001321	ENSG00000175183	CSRP2	CRP2|LMO5|SmLIM	cysteine and glycine rich protein 2	protein-coding	0.014315	0.440816	
chunk0010_189_1	chr1	115952570	115952966	+	0	NA	intron (NR_125970, intron 2 of 4)	intron (NR_125970, intron 2 of 4)	-23730	NM_018420	55356	Hs.125482	NM_018420	ENSG00000163393	SLC22A15	FLIPT1|PRO34686	solute carrier family 22 member 15	protein-coding	0.002525	0.420655	
chunk0175_305_1	chr7	7922581	7923299	+	0	NA	Intergenic	Intergenic	-45803	NM_138426	113263	Hs.131673	NM_138426	ENSG00000106415	GLCCI1	FAM117C|GCTR|GIG18|TSSN1	glucocorticoid induced 1	protein-coding	0.011142	0.356050	
chunk0103_412_1	chr2	169487447	169487724	+	0	NA	intron (NM_152384, intron 3 of 11)	intron (NM_152384, intron 3 of 11)	8089	NM_152384	129880	Hs.233398	NM_152384	ENSG00000163093	BBS5	-	Bardet-Biedl syndrome 5	protein-coding	0.000000	0.248201	
chunk0183_398_1	chr7	110281278	110281853	+	0	NA	Intergenic	Intergenic	-321352	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.010435	0.406250	287(AGGGTCACCGTGTGCT,-,0.00),288(GGGTCACCGTGTGCTG,+,0.00)
chunk0082_294_1	chr17	58575421	58575982	+	0	NA	intron (NM_001201457, intron 22 of 32)	MLT1I|LTR|ERVL-MaLR	-31329	NM_001038704	5414	Hs.287518	NM_004574	ENSG00000108387	SEPTIN4	ARTS|BRADEION|C17orf47|CE5B3|H5|MART|PNUTL2|SEP4|SEPT4|hCDCREL-2|hucep-7	septin 4	protein-coding	0.001783	0.379004	
chunk0064_219_1	chr14	93461482	93461906	+	0	NA	intron (NM_020818, intron 1 of 49)	L2c|LINE|L2	114503	NM_182971	341947	Hs.666459	NM_182971	ENSG00000187581	COX8C	COX8-3	cytochrome c oxidase subunit 8C	protein-coding	0.004717	0.381176	
chunk0036_443_1	chr11	68528678	68529187	+	0	NA	intron (NM_018312, intron 3 of 22)	intron (NM_018312, intron 3 of 22)	68214	NM_001164161	55291	Hs.503022	NM_018312	ENSG00000110075	PPP6R3	C11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3	protein phosphatase 6 regulatory subunit 3	protein-coding	0.011788	0.460784	272(GAGTACATCCTGTTCC,-,0.00),273(AGTACATCCTGTTCCC,+,0.00)
chunk0164_340_1	chr6	25369676	25370122	+	0	NA	intron (NM_017640, intron 2 of 36)	intron (NM_017640, intron 2 of 36)	90471	NM_001173977	55604	Hs.649550	NM_017640	ENSG00000079691	CARMIL1	CARMIL|CARMIL1a|LRRC16|LRRC16A|dJ501N12.1|dJ501N12.5	capping protein regulator and myosin 1 linker 1	protein-coding	0.013453	0.451902	
chunk0017_421_1	chr1	213102412	213102918	+	0	NA	intron (NM_001287219, intron 4 of 14)	intron (NM_001287219, intron 4 of 14)	51432	NM_001287220	26750	Hs.591416	NM_012424	ENSG00000136643	RPS6KC1	RPK118|RSKL1|S6K-delta-1|S6PKh1|humS6PKh1	ribosomal protein S6 kinase C1	protein-coding	0.000000	0.372781	
chunk0057_143_1	chr13	100068232	100068559	+	0	NA	Intergenic	LTR40a|LTR|ERVL	20548	NR_132422	105370333	Hs.186291	NR_132422	ENSG00000274605	LOC105370333	-	uncharacterized LOC105370333	ncRNA	0.006116	0.387195	
chunk0188_189_1	chr8	11716855	11717183	+	0	NA	intron (NM_002052, intron 2 of 6)	intron (NM_002052, intron 2 of 6)	9163	NM_001308093	2626	Hs.243987	NM_002052	ENSG00000136574	GATA4	ASD2|TACHD|TOF|VSD1	GATA binding protein 4	protein-coding	0.009146	0.431611	
chunk0195_30_1	chr8	93203048	93203275	+	0	NA	Intergenic	L1PA6|LINE|L1	-36311	NM_001242668									0.004405	0.403509	
chunk0074_249_1	chr16	27650237	27651129	+	0	NA	intron (NM_015202, intron 6 of 27)	intron (NM_015202, intron 6 of 27)	100536	NM_015202	23247	Hs.460459	NM_015202	ENSG00000047578	KIAA0556	JBTS26	KIAA0556	protein-coding	0.013453	0.441209	716(AGGATCAGTCTGTGCA,-,0.00)
chunk0208_281_1	chrX	21887229	21887508	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	31381	NM_206923	404281	Hs.673601	NM_206923	ENSG00000230797	YY2	ZNF631	YY2 transcription factor	protein-coding	0.003584	0.367857	
chunk0105_124_1	chr2	185404657	185404911	+	0	NA	Intergenic	Intergenic	-333844	NM_173651	401024	Hs.98025	NM_173651	ENSG00000188738	FSIP2	SPGF34	fibrous sheath interacting protein 2	protein-coding	0.007874	0.317647	
chunk0177_337_1	chr7	26467078	26467511	+	0	NA	intron (NR_015364, intron 1 of 4)	L2a|LINE|L2	63806	NR_015364	441204	Hs.587432	NR_015364	ENSG00000214870	LOC441204	-	uncharacterized LOC441204	ncRNA	0.018476	0.523041	
chunk0047_113_1	chr12	68919434	68919673	+	0	NA	intron (NM_001005502, intron 2 of 8)	intron (NM_001005502, intron 2 of 8)	13646	NM_198320	1368	Hs.654387	NM_001874	ENSG00000135678	CPM	-	carboxypeptidase M	protein-coding	0.008368	0.404167	
chunk0062_17_1	chr14	66424203	66424599	+	0	NA	Intergenic	MIRc|SINE|MIR	-61970	NR_110308	440184	Hs.412138	NM_001004331	ENSG00000196553	CCDC196	C14orf53|LINC00238|NCRNA00238	coiled-coil domain containing 196	protein-coding	0.005051	0.335013	
chunk0209_416_1	chrX	56920115	56920763	+	0	NA	Intergenic	L1PA6|LINE|L1	75116	NR_027139	169981	Hs.522672	NM_001010862	ENSG00000204271	SPIN3	SPIN-3|TDRD27|bA445O16.1	spindlin family member 3	protein-coding	0.004630	0.476117	511(GGAGACAGCCTGTCCA,-,0.00),512(GAGACAGCCTGTCCAT,+,0.00)
chunk0103_162_1	chr2	162582418	162582895	+	0	NA	intron (NM_033272, intron 2 of 15)	intron (NM_033272, intron 2 of 15)	-186280	NR_110258	101929570	Hs.470445	NR_110258	ENSG00000237750	LOC101929570	-	uncharacterized LOC101929570	ncRNA	0.008386	0.439331	
chunk0205_43_1	chr9	105881833	105882085	+	0	NA	Intergenic	Intergenic	187434	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.007937	0.418972	
chunk0014_363_1	chr1	182447541	182447906	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-2398	NM_001137669	353299	Hs.121200	NM_032267	ENSG00000121446	RGSL1	RGSL|RGSL2	regulator of G protein signaling like 1	protein-coding	0.005479	0.371585	286(TAGAACAGTTTGTGTC,-,0.00)
chunk0034_274_1	chr11	34631857	34632691	+	0	NA	promoter-TSS (NM_001206616)	promoter-TSS (NM_001206616)	-190	NM_001206616	26298	Hs.653859	NM_012153	ENSG00000135373	EHF	ESE3|ESE3B|ESEJ	ETS homologous factor	protein-coding	0.011990	0.463473	
chunk0041_89_1	chr11	124600228	124600520	+	0	NA	Intergenic	Intergenic	-11183	NM_052959	116337	Hs.99235	NM_052959	ENSG00000154143	PANX3	PX3	pannexin 3	protein-coding	0.003425	0.378840	
chunk0025_451_1	chr10	60295229	60295862	+	0	NA	intron (NM_001204403, intron 2 of 43)	MamSINE1|SINE|tRNA-RTE	94331	NM_020987	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.006319	0.328076	
chunk0212_106_1	chrY	15379661	15379905	+	0	NA	Intergenic	L1MB2|LINE|L1	-575750	NR_046504	100874056	Hs.743197	NR_046504	ENSG00000228787	NLGN4Y-AS1	NLGN4Y-AS|NLGN4YAS	NLGN4Y antisense RNA 1	ncRNA	0.000000	0.355102	
chunk0070_227_1	chr15	72865504	72866091	+	0	NA	Intergenic	L2|LINE|L2	-82012	NR_023319									0.010221	0.479592	260(TTGCACATGCTGTACC,-,0.00),261(TGCACATGCTGTACCT,+,0.00),389(GAGGACACACAGTTCT,-,0.00),390(AGGACACACAGTTCTG,+,0.00)
chunk0074_351_1	chr16	33672493	33672865	+	0	NA	Intergenic	L1MDa|LINE|L1	-96698	NR_130771	104644205	Hs.742548	NR_130771		ENPP7P13	DUNQU1	ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 13	pseudo	0.000000	0.300268	
chunk0114_84_1	chr21	9248581	9248824	+	0	NA	Intergenic	Intergenic	-118941	NR_038329	100132288	Hs.487562	NM_174948	ENSG00000188681	TEKT4P2	MAFIPL|TEKT4P	tektin 4 pseudogene 2	pseudo	0.012346	0.454918	
chunk0001_95_1	chr1	3127090	3127355	+	0	NA	promoter-TSS (NR_036215)	promoter-TSS (NR_036215)	-753	NR_036215	100422968		NR_036215	ENSG00000283572	MIR4251	-	microRNA 4251	ncRNA	0.030189	0.436090	150(AAGGACAGCCTGTTAC,-,0.00),151(AGGACAGCCTGTTACG,+,0.00)
chunk0165_273_1	chr6	35962342	35962685	+	0	NA	intron (NM_052961, intron 12 of 19)	intron (NM_052961, intron 12 of 19)	-41333	NR_034069	6732	Hs.443861	NM_003137	ENSG00000096063	SRPK1	SFRSK1	SRSF protein kinase 1	protein-coding	0.005831	0.462209	
chunk0061_388_1	chr14	64481586	64481888	+	0	NA	intron (NM_001304508, intron 2 of 2)	intron (NM_001304508, intron 2 of 2)	16238	NM_004857	9495	Hs.656683	NM_004857	ENSG00000179841	AKAP5	AKAP75|AKAP79|H21	A-kinase anchoring protein 5	protein-coding	0.000000	0.326733	
chunk0090_65_1	chr19	2163396	2163790	+	0	NA	promoter-TSS (NM_032482)	promoter-TSS (NM_032482)	-556	NM_032482	84444	Hs.713641	NM_032482	ENSG00000104885	DOT1L	DOT1|KMT4	DOT1 like histone lysine methyltransferase	protein-coding	0.081218	0.592405	
chunk0044_321_1	chr12	34122200	34122548	+	0	NA	Intergenic	HERV15-int|LTR|ERV1	100093	NM_032834	84920	Hs.102971	NM_032834	ENSG00000139133	ALG10	ALG10A|DIE2|KCR1	ALG10 alpha-1,2-glucosyltransferase	protein-coding	0.011494	0.487106	185(TAGAACACTTTGTCCA,-,0.00),186(AGAACACTTTGTCCAC,+,0.00)
chunk0063_457_1	chr14	89139768	89140229	+	0	NA	Intergenic	Intergenic	277112	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.021692	0.461039	
chunk0143_194_1	chr4	112793807	112794484	+	0	NA	Intergenic	Intergenic	-23938	NM_001127493	287	Hs.620557	NM_001148	ENSG00000145362	ANK2	ANK-2|LQT4|brank-2	ankyrin 2	protein-coding	0.007386	0.377581	
chunk0182_325_1	chr7	99067296	99067842	+	0	NA	intron (NM_020429, intron 1 of 18)	intron (NM_020429, intron 1 of 18)	54404	NR_110102	101927550	Hs.636663	NR_110102		LOC101927550	-	uncharacterized LOC101927550	ncRNA	0.016484	0.424132	
chunk0102_341_1	chr2	152299131	152299953	+	0	NA	Intergenic	L1MC1|LINE|L1	-35695	NM_052905	114793	Hs.654630	NM_052905	ENSG00000157827	FMNL2	FHOD2	formin like 2	protein-coding	0.004866	0.331713	
chunk0056_325_1	chr13	91140138	91140337	+	0	NA	intron (NR_047004, intron 2 of 3)	intron (NR_047004, intron 2 of 3)	-50620	NR_104057	101930747	Hs.112745	NR_104057		LINC00380	-	long intergenic non-protein coding RNA 380	ncRNA	0.005025	0.355000	
chunk0158_132_1	chr5	127206627	127207191	+	0	NA	Intergenic	Intergenic	-83855	NM_001308119	84466	Hs.438709	NM_032446	ENSG00000145794	MEGF10	EMARDD	multiple EGF like domains 10	protein-coding	0.003546	0.401770	
chunk0098_109_1	chr2	68380608	68381378	+	0	NA	intron (NM_002664, intron 3 of 8)	intron (NM_002664, intron 3 of 8)	15803	NM_002664	5341	Hs.468840	NM_002664	ENSG00000115956	PLEK	P47	pleckstrin	protein-coding	0.006494	0.456550	418(TGGCACTTGGTGTACT,-,0.00),419(GGCACTTGGTGTACTA,+,0.00)
chunk0033_263_1	chr11	18749707	18750068	+	0	NA	intron (NM_001039970, intron 3 of 14)	intron (NM_001039970, intron 3 of 14)	-23657	NM_173588	283284	Hs.434152	NM_173588	ENSG00000179057	IGSF22	IGFN2	immunoglobulin superfamily member 22	protein-coding	0.016620	0.560773	171(TGGCTCAGTCTGTTCC,-,0.00),172(GGCTCAGTCTGTTCCT,+,0.00)
chunk0154_252_1	chr5	81376289	81376570	+	0	NA	intron (NM_130767, intron 2 of 14)	L1PA7|LINE|L1	17740	NM_130767	134526	Hs.591756	NM_130767	ENSG00000172497	ACOT12	CACH-1|Cach|STARD15|THEAL	acyl-CoA thioesterase 12	protein-coding	0.003559	0.354610	9(AAAGACACAATGTACC,-,0.00)
chunk0013_374_1	chr1	172489943	172490252	+	0	NA	Intergenic	MER49|LTR|ERV1	37204	NM_001300760	92346	Hs.517991	NM_139240	ENSG00000180999	C1orf105	-	chromosome 1 open reading frame 105	protein-coding	0.006472	0.367742	
chunk0168_69_1	chr6	79413766	79414303	+	0	NA	Intergenic	Intergenic	-100650	NR_130915	80078		NR_130915	ENSG00000286042	LCAL1	onco-lncRNA-27	lung cancer associated lncRNA 1	ncRNA	0.001862	0.325279	236(CAGAACAGTATGTATT,-,0.00),237(AGAACAGTATGTATTA,+,0.00)
chunk0030_336_1	chr10	118371212	118371445	+	0	NA	Intergenic	L2c|LINE|L2	14220	NR_108045	100506126	Hs.69494	NR_108045	ENSG00000232139	LINC00867	-	long intergenic non-protein coding RNA 867	ncRNA	0.004292	0.470085	
chunk0186_78_1	chr7	137259314	137259909	+	0	NA	intron (NM_002825, intron 1 of 4)	intron (NM_002825, intron 1 of 4)	84189	NM_002825	5764	Hs.371249	NM_002825	ENSG00000105894	PTN	HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1	pleiotrophin	protein-coding	0.005042	0.328859	
chunk0150_256_1	chr5	36366809	36367433	+	0	NA	Intergenic	Intergenic	-65212	NM_001161429	202151	Hs.199777	NM_145000	ENSG00000164188	RANBP3L	-	RAN binding protein 3 like	protein-coding	0.004808	0.377600	
chunk0071_160_1	chr15	82978323	82978619	+	0	NA	Intergenic	L2c|LINE|L2	-7732	NM_031452	83640	Hs.80624	NM_031452	ENSG00000169612	RAMAC	C15orf18|FAM103A1|HsT19360|RAM|RAMMET	RNA guanine-7 methyltransferase activating subunit	protein-coding	0.010135	0.427609	
chunk0043_21_1	chr12	13051503	13051913	+	0	NA	intron (NM_020853, intron 1 of 12)	L3|LINE|CR1	5517	NR_106988									0.002439	0.401460	115(TGGTCAGACTGTACCT,+,0.00)
chunk0183_156_1	chr7	105940143	105940563	+	0	NA	Intergenic	Intergenic	-22858	NM_001301161	222256	Hs.150120	NM_152750	ENSG00000128536	CDHR3	CDH28	cadherin related family member 3	protein-coding	0.007143	0.498812	
chunk0128_127_1	chr3	106522359	106522642	+	0	NA	Intergenic	Intergenic	-653457	NM_170662	868	Hs.430589	NM_170662	ENSG00000114423	CBLB	Cbl-b|Nbla00127|RNF56	Cbl proto-oncogene B	protein-coding	0.010601	0.278169	
chunk0015_349_1	chr1	190159265	190159552	+	0	NA	intron (NM_199051, intron 7 of 7)	L1MB7|LINE|L1	318221	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.003484	0.333333	
chunk0171_451_1	chr6	132170926	132171164	+	0	NA	Intergenic	HERVL40-int|LTR|ERVL	37067	NR_038981	100507254	Hs.103070	NR_038981	ENSG00000228495	LINC01013	-	long intergenic non-protein coding RNA 1013	ncRNA	0.004202	0.439331	
chunk0191_272_1	chr8	53668377	53668624	+	0	NA	Intergenic	Intergenic	174542	NM_213620	51606	Hs.491737	NM_015941	ENSG00000047249	ATP6V1H	CGI-11|MSTP042|NBP1|SFD|SFDalpha|SFDbeta|VMA13	ATPase H+ transporting V1 subunit H	protein-coding	0.000000	0.366935	
chunk0162_44_1	chr6	1201395	1201708	+	0	NA	Intergenic	Intergenic	-100219	NR_027115	285768	Hs.209463	NR_027115		LINC01622	-	long intergenic non-protein coding RNA 1622	ncRNA	0.019169	0.611465	
chunk0046_14_1	chr12	54160742	54161310	+	0	NA	Intergenic	Intergenic	27931	NM_001243790	23583	Hs.632721	NM_014311	ENSG00000123415	SMUG1	FDG|HMUDG|UNG3	single-strand-selective monofunctional uracil-DNA glycosylase 1	protein-coding	0.033451	0.539543	253(GGGCACACACTGTCCT,-,0.00),254(GGCACACACTGTCCTG,+,0.00)
chunk0137_226_1	chr4	20052812	20053323	+	0	NA	Intergenic	Intergenic	-198838	NM_004787	9353	Hs.29802	NM_004787	ENSG00000145147	SLIT2	SLIL3|Slit-2	slit guidance ligand 2	protein-coding	0.000000	0.349609	
chunk0081_110_1	chr17	39980765	39981156	+	0	NA	5' UTR (NM_002809, exon 1 of 12)	5' UTR (NM_002809, exon 1 of 12)	192	NM_002809	5709	Hs.12970	NM_002809	ENSG00000108344	PSMD3	P58|RPN3|S3|TSTA2	proteasome 26S subunit, non-ATPase 3	protein-coding	0.130435	0.727041	
chunk0090_445_1	chr18	79789004	79789310	+	0	NA	Intergenic	CpG	-74511	NM_012283	26251	Hs.247905	NM_012283	ENSG00000178342	KCNG2	KCNF2|KV6.2	potassium voltage-gated channel modifier subfamily G member 2	protein-coding	0.052288	0.570033	
chunk0155_135_1	chr5	93556609	93556808	+	0	NA	intron (NR_021490, intron 2 of 5)	MLT1C|LTR|ERVL-MaLR	14635	NR_109825	441094	Hs.457407	NR_015369	ENSG00000237187	NR2F1-AS1	-	NR2F1 antisense RNA 1	ncRNA	0.000000	0.440000	
chunk0194_120_1	chr8	83964285	83965062	+	0	NA	Intergenic	Intergenic	-218545	NM_001100392	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.005148	0.296915	
chunk0085_206_1	chr18	6625172	6625399	+	0	NA	Intergenic	Intergenic	113869	NR_120518	100130480	Hs.646267	NM_001243517	ENSG00000265944	LINC01387	C18orf64	long intergenic non-protein coding RNA 1387	ncRNA	0.008811	0.342105	
chunk0037_16_1	chr11	69105997	69106818	+	0	NA	Intergenic	Intergenic	23231	NR_036122	100422846		NR_036122	ENSG00000265539	MIR3164	-	microRNA 3164	ncRNA	0.031669	0.587591	
chunk0054_193_1	chr13	44905036	44905408	+	0	NA	Intergenic	Intergenic	84256	NM_012345	26747	Hs.525006	NM_012345	ENSG00000083635	NUFIP1	NUFIP|bA540M5.1	nuclear FMR1 interacting protein 1	protein-coding	0.013441	0.506702	
chunk0138_393_1	chr4	42743449	42743935	+	0	NA	Intergenic	Intergenic	-86587	NM_006095	10396	Hs.435052	NM_006095	ENSG00000124406	ATP8A1	ATPASEII|ATPIA|ATPP2	ATPase phospholipid transporting 8A1	protein-coding	0.002058	0.390144	
chunk0167_390_1	chr6	74753676	74754486	+	0	NA	Intergenic	Intergenic	451826	NM_080645	1303	Hs.101302	NM_004370	ENSG00000111799	COL12A1	BA209D8.1|BTHLM2|COL12A1L|DJ234P15.1|EDSMYP|UCMD2	collagen type XII alpha 1 chain	protein-coding	0.001235	0.318126	
chunk0028_27_1	chr10	82628205	82628888	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-395626	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.007321	0.387427	
chunk0056_46_1	chr13	77522315	77522835	+	0	NA	Intergenic	L1PA11|LINE|L1	-13099	NM_001160706	8796	Hs.534699	NM_003843	ENSG00000136155	SCEL	-	sciellin	protein-coding	0.005769	0.426104	275(CTGCACATATTGTCCT,-,0.00),276(TGCACATATTGTCCTG,+,0.00)
chunk0182_46_1	chr7	91668121	91668638	+	0	NA	Intergenic	MIRb|SINE|MIR	212341	NM_001301134	7978	Hs.532216	NM_006980	ENSG00000127989	MTERF1	MTERF	mitochondrial transcription termination factor 1	protein-coding	0.001934	0.388031	
chunk0070_44_1	chr15	69474918	69475631	+	0	NA	Intergenic	Intergenic	22454	NM_213725	6176	Hs.356502	NM_001003	ENSG00000137818	RPLP1	LP1|P1|RPP1	ribosomal protein lateral stalk subunit P1	protein-coding	0.009818	0.515406	378(AGGTACAGTAAGTACC,-,0.00),379(GGTACAGTAAGTACCT,+,0.00)
chunk0028_88_1	chr10	83883934	83884605	+	0	NA	Intergenic	L1MEd|LINE|L1	-255160	NM_014394	27069	Hs.352656	NM_014394	ENSG00000165678	GHITM	DERP2|HSPC282|MICS1|My021|PTD010|TMBIM5	growth hormone inducible transmembrane protein	protein-coding	0.008942	0.352679	246(ATGAACTCACTGTGCA,-,0.00),347(CAGAACACTGAGTTCT,-,0.00),348(AGAACACTGAGTTCTA,+,0.00)
chunk0131_432_1	chr3	153703224	153703914	+	0	NA	Intergenic	LTR40b|LTR|ERVL	219074	NM_001101337									0.002899	0.390738	
chunk0077_299_1	chr16	81581234	81581541	+	0	NA	intron (NM_030629, intron 1 of 20)	Tigger3a|DNA|TcMar-Tigger	-29961	NR_106759	102465251		NR_106759	ENSG00000275109	MIR6504	hsa-mir-6504	microRNA 6504	ncRNA	0.026059	0.444805	
chunk0109_342_1	chr20	9516336	9516556	+	0	NA	intron (NM_001199897, intron 3 of 4)	intron (NM_001199897, intron 3 of 4)	-1448	NR_109957	101929329	Hs.589878	NR_109957	ENSG00000225988	LAMP5-AS1	-	LAMP5 antisense RNA 1	ncRNA	0.040909	0.588235	
chunk0201_341_1	chr9	65376412	65377049	+	0	NA	Intergenic	L1MDb|LINE|L1	-91521	NM_001126334	653427	Hs.714683	NM_001126334	ENSG00000204779	FOXD4L5	bA15J10.2	forkhead box D4 like 5	protein-coding	0.009419	0.351097	212(TAGTACACAGTGTACC,-,0.00),213(AGTACACAGTGTACCT,+,0.00)
chunk0184_279_1	chr7	118631655	118631977	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	407158	NM_019644	56311	Hs.729340	NM_019644	ENSG00000106013	ANKRD7	TSA806	ankyrin repeat domain 7	protein-coding	0.000000	0.349845	
chunk0031_99_1	chr10	124085011	124085340	+	0	NA	intron (NM_001270764, intron 1 of 7)	intron (NM_001270764, intron 1 of 7)	7249	NM_015892	51363	Hs.287537	NM_014863	ENSG00000182022	CHST15	BRAG|GALNAC4S-6ST	carbohydrate sulfotransferase 15	protein-coding	0.012158	0.396970	
chunk0191_334_1	chr8	55997172	55997435	+	0	NA	intron (NM_001111097, intron 10 of 12)	intron (NM_001111097, intron 10 of 12)	76598	NR_002437	26795		NR_002437	ENSG00000238650	SNORD54	RNU54|U54	small nucleolar RNA, C/D box 54	snoRNA	0.007605	0.412879	
chunk0114_205_1	chr21	15435950	15436576	+	0	NA	Intergenic	Intergenic	-293762	NM_001283042	29761	Hs.743994	NM_013396	ENSG00000155313	USP25	USP21	ubiquitin specific peptidase 25	protein-coding	0.001597	0.357257	
chunk0134_429_1	chr3	183428132	183428669	+	0	NA	promoter-TSS (NM_015078)	promoter-TSS (NM_015078)	-131	NM_015078	23101	Hs.208267	NM_015078	ENSG00000053524	MCF2L2	ARHGEF22	MCF.2 cell line derived transforming sequence-like 2	protein-coding	0.121043	0.728625	
chunk0040_10_1	chr11	108654899	108655333	+	0	NA	Intergenic	Intergenic	-9909	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.004608	0.351724	
chunk0096_405_1	chr2	37823695	37824372	+	0	NA	Intergenic	Intergenic	5678	NR_110011	101929559	Hs.468200	NR_110011	ENSG00000237803	LINC00211	NCRNA00211	long intergenic non-protein coding RNA 211	ncRNA	0.002954	0.339233	249(GGGGAGACTGTGTTCT,-,0.00),250(GGGAGACTGTGTTCTT,+,0.00)
chunk0167_447_1	chr6	75940647	75940951	+	0	NA	intron (NM_001282368, intron 13 of 15)	intron (NM_001282368, intron 13 of 15)	131879	NM_001282368	3617	Hs.590893	NM_001563	ENSG00000112706	IMPG1	GP147|IPM150|SPACR|VMD4	interphotoreceptor matrix proteoglycan 1	protein-coding	0.009868	0.475410	
chunk0010_250_1	chr1	116483795	116484533	+	0	NA	Intergenic	Intergenic	-5338	NR_125973	101929023	Hs.668091	NR_125972	ENSG00000233154	LINC01762	-	long intergenic non-protein coding RNA 1762	ncRNA	0.014905	0.553451	443(TGGAACACGGAGTTCT,-,0.00),444(GGAACACGGAGTTCTC,+,0.00)
chunk0102_180_1	chr2	147536267	147536837	+	0	NA	Intergenic	Intergenic	-307965	NM_001278579	92	Hs.470174	NM_001616	ENSG00000121989	ACVR2A	ACTRII|ACVR2	activin A receptor type 2A	protein-coding	0.001754	0.341506	359(AAGCACAAACTGATCC,-,0.00),360(AGCACAAACTGATCCC,+,0.00)
chunk0157_83_1	chr5	116547558	116548092	+	0	NA	intron (NM_001300780, intron 1 of 19)	intron (NM_001300780, intron 1 of 19)	27101	NM_020796	57556	Hs.156967	NM_020681	ENSG00000092421	SEMA6A	HT018|SEMA|SEMA6A1|SEMAQ|VIA	semaphorin 6A	protein-coding	0.005618	0.377570	
chunk0094_314_1	chr2	8920875	8921364	+	0	NA	intron (NM_138799, intron 3 of 12)	L1MB7|LINE|L1	82628	NM_138799	129642	Hs.467634	NM_138799	ENSG00000143797	MBOAT2	LPAAT|LPCAT4|LPEAT|LPLAT 2|OACT2	membrane bound O-acyltransferase domain containing 2	protein-coding	0.002045	0.336735	
chunk0176_223_1	chr7	15143916	15144328	+	0	NA	Intergenic	Intergenic	-302672	NM_145695	1607	Hs.567255	NM_004080	ENSG00000136267	DGKB	DAGK2|DGK|DGK-BETA	diacylglycerol kinase beta	protein-coding	0.000000	0.288136	
chunk0024_95_1	chr10	34520011	34520578	+	0	NA	intron (NM_019619, intron 2 of 24)	intron (NM_019619, intron 2 of 24)	295031	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.012346	0.373239	
chunk0199_413_1	chr9	13588170	13589151	+	0	NA	Intergenic	Intergenic	-157331	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.007136	0.415479	
chunk0055_216_1	chr13	62300067	62300384	+	0	NA	Intergenic	Intergenic	87943	NR_125787	103752583	Hs.578048	NR_125787		LINC01075	-	long intergenic non-protein coding RNA 1075	ncRNA	0.003155	0.345912	
chunk0163_285_1	chr6	13754075	13754452	+	0	NA	Intergenic	L2a|LINE|L2	-42699	NM_005493	10048	Hs.708182	NM_005493	ENSG00000010017	RANBP9	BPM-L|BPM90|RANBPM|RanBP7	RAN binding protein 9	protein-coding	0.013263	0.457672	
chunk0146_253_1	chr4	162650630	162651288	+	0	NA	Intergenic	Intergenic	442669	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.001520	0.305008	278(AAGCACACTGTGTCTT,-,0.00),279(AGCACACTGTGTCTTC,+,0.00),345(TGGGTCACTCTGTCCT,-,0.00),346(GGGTCACTCTGTCCTA,+,0.00)
chunk0025_396_1	chr10	59375359	59375762	+	0	NA	Intergenic	MER110A|LTR|ERV1	-12657	NM_001143773	220965	Hs.607594	NM_198215	ENSG00000148541	FAM13C	FAM13C1	family with sequence similarity 13 member C	protein-coding	0.004963	0.371287	
chunk0209_336_1	chrX	51325622	51325923	+	0	NA	Intergenic	Intergenic	-6459	NM_153183	170685	Hs.375178	NM_153183	ENSG00000122824	NUDT10	APS2|DIPP3-alpha|DIPP3a	nudix hydrolase 10	protein-coding	0.009967	0.476821	
chunk0181_324_1	chr7	87875654	87875971	+	0	NA	promoter-TSS (NM_006716)	promoter-TSS (NM_006716)	-417	NM_006716	10926	Hs.485380	NM_006716	ENSG00000006634	DBF4	ASK|CHIF|DBF4A|ZDBF1	DBF4 zinc finger	protein-coding	0.066246	0.603774	
chunk0135_391_1	chr3	191302592	191302832	+	0	NA	intron (NM_198152, intron 4 of 8)	intron (NM_198152, intron 4 of 8)	-26373	NM_174908	152137	Hs.478682	NM_174908	ENSG00000152492	CCDC50	C3orf6|DFNA44|YMER	coiled-coil domain containing 50	protein-coding	0.008333	0.398340	
chunk0059_23_1	chr14	29821246	29821446	+	0	NA	intron (NM_002742, intron 1 of 17)	intron (NM_002742, intron 1 of 17)	106347	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.005000	0.422886	
chunk0210_83_1	chrX	70479226	70479564	+	0	NA	intron (NM_021120, intron 10 of 18)	intron (NM_021120, intron 10 of 18)	-23401	NR_109801	100873930	Hs.571699	NR_046586	ENSG00000231651	DLG3-AS1	-	DLG3 antisense RNA 1	ncRNA	0.008876	0.436578	
chunk0029_442_1	chr10	110263112	110263470	+	0	NA	intron (NM_005962, intron 3 of 5)	intron (NM_005962, intron 3 of 5)	37287	NM_005962	4601	Hs.602078	NM_005962	ENSG00000119950	MXI1	MAD2|MXD2|MXI|bHLHc11	MAX interactor 1, dimerization protein	protein-coding	0.005587	0.373259	224(GAGAACAGTTTGTCCC,-,0.00),225(AGAACAGTTTGTCCCC,+,0.00)
chunk0032_176_1	chr11	5726729	5727145	+	0	NA	Intergenic	Intergenic	-9511	NM_001005180	387748	Hs.689609	NM_001005180	ENSG00000181023	OR56B1	OR11-65|OR56B1P	olfactory receptor family 56 subfamily B member 1	protein-coding	0.019231	0.541966	
chunk0139_35_1	chr4	48478337	48478760	+	0	NA	Intergenic	Intergenic	-4795	NM_152679	201780	Hs.132591	NM_152679	ENSG00000145248	SLC10A4	P4	solute carrier family 10 member 4	protein-coding	0.002364	0.325472	
chunk0183_387_1	chr7	110065211	110065680	+	0	NA	Intergenic	Intergenic	-105232	NR_003024	442720	Hs.530096	NR_003024	ENSG00000237064	EIF3IP1	RG208K23	eukaryotic translation initiation factor 3 subunit I pseudogene 1	pseudo	0.006397	0.340426	
chunk0165_45_1	chr6	30142617	30142980	+	0	NA	intron (NM_138700, intron 1 of 4).4	intron (NM_138700, intron 1 of 4).4	6065	NM_138700	135644	Hs.509439	NM_138700	ENSG00000204614	TRIM40	RNF35	tripartite motif containing 40	protein-coding	0.008264	0.296703	
chunk0032_167_1	chr11	5453764	5454072	+	0	NA	exon (NM_001004754, exon 1 of 1)	exon (NM_001004754, exon 1 of 1)	510	NM_001004754	390064	Hs.553733	NM_001004754	ENSG00000187918	OR51I2	OR11-38	olfactory receptor family 51 subfamily I member 2	protein-coding	0.009740	0.466019	
chunk0181_458_1	chr7	90766841	90767410	+	0	NA	intron (NM_001287136, intron 3 of 13)	LTR18B|LTR|ERVL	57309	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.008787	0.482456	
chunk0205_31_1	chr9	105572320	105572823	+	0	NA	intron (NM_006731, intron 1 of 9)	L1M7|LINE|L1	14441	NM_001198963	2218	Hs.55777	NM_006731	ENSG00000106692	FKTN	CMD1X|FCMD|LGMD2M|LGMDR13|MDDGA4|MDDGB4|MDDGC4	fukutin	protein-coding	0.000000	0.412698	
chunk0012_359_1	chr1	162862005	162862448	+	0	NA	intron (NM_178550, intron 1 of 3)	intron (NM_178550, intron 1 of 3)	6589	NM_178550	339512	Hs.407631	NM_178550	ENSG00000185860	CCDC190	C1orf110	coiled-coil domain containing 190	protein-coding	0.002257	0.479730	
chunk0188_250_1	chr8	14399910	14400150	+	0	NA	intron (NM_139167, intron 2 of 7)	L1MB8|LINE|L1	453480	NR_029875	494332		NR_029875	ENSG00000199127	MIR383	MIRN383|hsa-mir-383|mir-383	microRNA 383	ncRNA	0.004167	0.394191	
chunk0168_271_1	chr6	90063359	90063586	+	0	NA	intron (NM_021813, intron 5 of 8)	intron (NM_021813, intron 5 of 8)	169003	NM_032602	84694	Hs.334499	NM_032602	ENSG00000135355	GJA10	CX62	gap junction protein alpha 10	protein-coding	0.000000	0.355263	38(AGTAACAGGATGTTCT,-,0.00),39(GTAACAGGATGTTCTT,+,0.00)
chunk0116_234_1	chr21	38261818	38262113	+	0	NA	intron (NM_002243, intron 2 of 3)	intron (NM_002243, intron 2 of 3)	5161	NM_170736	3772	Hs.411299	NM_002243	ENSG00000157551	KCNJ15	IRKK|KIR1.3|KIR4.2	potassium voltage-gated channel subfamily J member 15	protein-coding	0.003390	0.381757	
chunk0031_329_1	chr10	129308262	129308759	+	0	NA	Intergenic	Intergenic	-158674	NM_002412	4255	Hs.501522	NM_002412	ENSG00000170430	MGMT	-	O-6-methylguanine-DNA methyltransferase	protein-coding	0.008048	0.335341	
chunk0069_82_1	chr15	61085928	61086408	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	143135	NM_134261	6095	Hs.560343	NM_002943	ENSG00000069667	RORA	IDDECA|NR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA	RAR related orphan receptor A	protein-coding	0.010417	0.395010	
chunk0201_180_1	chr9	36254956	36255291	+	0	NA	intron (NM_001128227, intron 1 of 11)	intron (NM_001128227, intron 1 of 11)	3376	NM_001190383	10020	Hs.5920	NM_005476	ENSG00000159921	GNE	DMRV|GLCNE|IBM2|NM|Uae1	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	protein-coding	0.008955	0.389881	
chunk0028_453_1	chr10	94519101	94519665	+	0	NA	intron (NM_015188, intron 9 of 12)	MLT1D|LTR|ERVL-MaLR	-26384	NM_001289068	3070	Hs.463677	NM_018063	ENSG00000119969	HELLS	ICF4|LSH|Nbla10143|PASG|SMARCA6	helicase, lymphoid specific	protein-coding	0.003546	0.375221	
chunk0145_217_1	chr4	148054012	148054239	+	0	NA	intron (NM_024605, intron 20 of 22)	intron (NM_024605, intron 20 of 22)	271530	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.013216	0.333333	
chunk0172_33_1	chr6	133947481	133947827	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-4516	NM_001253676	9519	Hs.486507	NM_004865	ENSG00000028839	TBPL1	MGC:8389|MGC:9620|STUD|TLF|TLP|TRF2	TATA-box binding protein like 1	protein-coding	0.000000	0.443804	
chunk0006_164_1	chr1	66452031	66452512	+	0	NA	Intergenic	Intergenic	-81298	NM_001308203	84251	Hs.132121	NM_032291	ENSG00000118473	SGIP1	-	SH3 domain GRB2 like endophilin interacting protein 1	protein-coding	0.004158	0.433610	
chunk0170_93_1	chr6	110436439	110437088	+	0	NA	intron (NM_033125, intron 5 of 7)	(TTTG)n|Simple_repeat|Simple_repeat	-21213	NM_003649	8528	Hs.591348	NM_003649	ENSG00000203797	DDO	DASOX|DDO-1|DDO-2	D-aspartate oxidase	protein-coding	0.006163	0.426154	301(TAGTACAGACTGTTTT,-,0.00),302(AGTACAGACTGTTTTG,+,0.00)
chunk0067_166_1	chr15	44097323	44098097	+	0	NA	intron (NM_001286491, intron 1 of 14)	intron (NM_001286491, intron 1 of 14)	96736	NM_001286490	84978	Hs.578544	NM_032892	ENSG00000171877	FRMD5	-	FERM domain containing 5	protein-coding	0.003876	0.437419	
chunk0191_414_1	chr8	57720998	57721472	+	0	NA	Intergenic	L2b|LINE|L2	-257123	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.004219	0.341053	
chunk0031_208_1	chr10	125892366	125892809	+	0	NA	Intergenic	Intergenic	-3952	NM_145235	92565	Hs.352591	NM_145235	ENSG00000203780	FANK1	HSD13	fibronectin type III and ankyrin repeat domains 1	protein-coding	0.011287	0.407658	220(CAGCCCAGGCTGTTCT,-,0.00),221(AGCCCAGGCTGTTCTG,+,0.00)
chunk0067_403_1	chr15	49406939	49407231	+	0	NA	intron (NM_152647, intron 11 of 15)	L1PA13|LINE|L1	-16093	NM_002009	2252	Hs.567268	NM_002009	ENSG00000140285	FGF7	HBGF-7|KGF	fibroblast growth factor 7	protein-coding	0.010274	0.576792	
chunk0105_351_1	chr2	191637614	191637906	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-40312	NM_001254736	64859	Hs.591610	NM_022837	ENSG00000173559	NABP1	OBFC2A|SOSS-B2|SSB2	nucleic acid binding protein 1	protein-coding	0.000000	0.423208	
chunk0027_182_1	chr10	75171430	75171737	+	0	NA	intron (NM_001174156, intron 4 of 5)	L1ME4a|LINE|L1	-38571	NM_001184823	7417	Hs.355927	NM_003375	ENSG00000165637	VDAC2	POR	voltage dependent anion channel 2	protein-coding	0.009772	0.318182	
chunk0017_128_1	chr1	206521120	206521494	+	0	NA	intron (NM_182663, intron 1 of 5)	intron (NM_182663, intron 1 of 5)	13777	NM_182663	83593	Hs.497579	NM_031437	ENSG00000266094	RASSF5	Maxp1|NORE1|NORE1A|NORE1B|RAPL|RASSF3	Ras association domain family member 5	protein-coding	0.013369	0.506667	
chunk0109_39_1	chr20	701571	702262	+	0	NA	Intergenic	Intergenic	-25737	NM_033129	85508	Hs.355284	NM_033129	ENSG00000215397	SCRT2	ZNF898B	scratch family transcriptional repressor 2	protein-coding	0.010130	0.557803	379(CAGGACGGCCTGTTCC,-,0.00),380(AGGACGGCCTGTTCCA,+,0.00)
chunk0131_312_1	chr3	150756367	150757110	+	0	NA	intron (NM_005067, intron 1 of 1)	intron (NM_005067, intron 1 of 1)	6738	NM_005067	6478	Hs.477959	NM_005067	ENSG00000181788	SIAH2	hSiah2	siah E3 ubiquitin protein ligase 2	protein-coding	0.006729	0.411290	467(CAGTTCACTCTGTGCT,-,0.00),468(AGTTCACTCTGTGCTT,+,0.00)
chunk0167_22_1	chr6	53704474	53705267	+	0	NA	Intergenic	Intergenic	-39162	NM_001003760	401265	Hs.131064	NM_001003760	ENSG00000124743	KLHL31	BKLHD6|KBTBD1|KLHL|bA345L23.2	kelch like family member 31	protein-coding	0.010088	0.379093	
chunk0132_446_1	chr3	165176791	165177341	+	0	NA	Intergenic	Intergenic	19615	NM_014926	22865	Hs.101745	NM_014926	ENSG00000121871	SLITRK3	-	SLIT and NTRK like family member 3	protein-coding	0.000000	0.292196	
chunk0084_424_1	chr17	82522018	82522355	+	0	NA	intron (NM_004514, intron 1 of 8)	AluJo|SINE|Alu	2468	NM_004514	3607	Hs.591140	NM_004514	ENSG00000141568	FOXK2	ILF|ILF-1|ILF1|nGTBP	forkhead box K2	protein-coding	0.008902	0.434911	
chunk0129_172_1	chr3	120802087	120802579	+	0	NA	Intergenic	L3|LINE|CR1	59622	NM_005513	2960	Hs.445272	NM_005513	ENSG00000153767	GTF2E1	FE|TF2E1|TFIIE-A	general transcription factor IIE subunit 1	protein-coding	0.006098	0.430020	
chunk0169_187_1	chr6	102475768	102476336	+	0	NA	Intergenic	L1MC1|LINE|L1	1077067	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.000000	0.297012	
chunk0171_396_1	chr6	131213686	131214060	+	0	NA	intron (NM_016377, intron 6 of 7)	LTR101_Mam|LTR|ERVL	-36286	NM_138633	9465	Hs.486483	NM_004842	ENSG00000118507	AKAP7	AKAP15|AKAP18	A-kinase anchoring protein 7	protein-coding	0.005348	0.437333	144(GGGAACAGACTGTGTT,-,0.00),145(GGAACAGACTGTGTTG,+,0.00)
chunk0022_441_1	chr10	19626317	19626527	+	0	NA	intron (NM_001142308, intron 36 of 39)	L1M5|LINE|L1	102128	NR_120646	101928834	Hs.676482	NR_120646	ENSG00000233968	LOC101928834	-	uncharacterized LOC101928834	ncRNA	0.009524	0.374408	
chunk0046_192_1	chr12	58868488	58868971	+	0	NA	Intergenic	Intergenic	50817	NM_001136051	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.010352	0.378099	
chunk0084_358_1	chr17	81394022	81394341	+	0	NA	Intergenic	CpG	-5540	NM_001291324	57597	Hs.514580	NM_024696	ENSG00000266074	BAHCC1	BAHD2	BAH domain and coiled-coil containing 1	protein-coding	0.056426	0.556250	
chunk0120_411_1	chr3	12837344	12838137	+	0	NA	intron (NM_001007073, intron 3 of 3)	intron (NM_001007073, intron 3 of 3)	2710	NM_001007074	6161	Hs.265174	NM_000994	ENSG00000144713	RPL32	L32|PP9932	ribosomal protein L32	protein-coding	0.008827	0.423174	
chunk0062_93_1	chr14	68144175	68144833	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	324725	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.004559	0.389985	242(GGGAACACCATGTACT,-,0.00),243(GGAACACCATGTACTA,+,0.00)
chunk0087_146_1	chr18	33928283	33928572	+	0	NA	intron (NM_001198548, intron 7 of 8)	intron (NM_001198548, intron 7 of 8)	120185	NM_001198549	8715	Hs.514795	NM_003787	ENSG00000101746	NOL4	CT125|HRIHFB2255|NOLP	nucleolar protein 4	protein-coding	0.003460	0.348276	
chunk0060_33_1	chr14	40393138	40393669	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-561308	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.000000	0.374060	
chunk0080_192_1	chr17	29008542	29008953	+	0	NA	Intergenic	L2b|LINE|L2	-2307	NM_001290202	124925	Hs.21837	NM_178860	ENSG00000063015	SEZ6	BSRPC	seizure related 6 homolog	protein-coding	0.007299	0.478155	
chunk0006_414_1	chr1	76013215	76013638	+	0	NA	intron (NR_125939, intron 2 of 2)	intron (NR_125939, intron 2 of 2)	2102	NR_125939	101927342	Hs.216363	NR_125939		LOC101927342	-	uncharacterized LOC101927342	ncRNA	0.004728	0.379717	
chunk0067_416_1	chr15	49678414	49678915	+	0	NA	Intergenic	Intergenic	57635	NM_001144955	56986	Hs.127432	NM_020234	ENSG00000104047	DTWD1	MDS009	DTW domain containing 1	protein-coding	0.007984	0.368526	
chunk0123_329_1	chr3	47455624	47456241	+	0	NA	intron (NM_012235, intron 1 of 22)	L1M5|LINE|L1	20023	NM_012235	22937	Hs.531789	NM_012235	ENSG00000114650	SCAP	-	SREBF chaperone	protein-coding	0.006483	0.357605	321(CAGAACAGAATGTCCA,-,0.00),322(AGAACAGAATGTCCAG,+,0.00)
chunk0048_234_1	chr12	81552052	81552747	+	0	NA	intron (NM_001220474, intron 2 of 30)	intron (NM_001220474, intron 2 of 30)	-40008	NM_001282536	8499	Hs.506216	NM_003625	ENSG00000139220	PPFIA2	-	PTPRF interacting protein alpha 2	protein-coding	0.000000	0.242816	
chunk0005_310_1	chr1	60580496	60580832	+	0	NA	Intergenic	Intergenic	244920	NR_110628	101926964	Hs.650459	NR_110628	ENSG00000231252	LOC101926964	-	uncharacterized LOC101926964	ncRNA	0.002976	0.364985	
chunk0044_154_1	chr12	29762897	29763591	+	0	NA	intron (NM_001193451, intron 2 of 17)	intron (NM_001193451, intron 2 of 17)	20566	NM_001193451	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.004323	0.440288	
chunk0022_304_1	chr10	15685070	15685578	+	0	NA	intron (NM_001291494, intron 3 of 28)	intron (NM_001291494, intron 3 of 28)	35011	NM_001291494	8516	Hs.171311	NM_003638	ENSG00000077943	ITGA8	-	integrin subunit alpha 8	protein-coding	0.005906	0.343811	248(AGAAACAAAATGTCCT,-,0.00)
chunk0123_208_1	chr3	44886604	44887288	+	0	NA	intron (NM_003241, intron 2 of 13)	L2c|LINE|L2	12340	NM_003241	7047	Hs.438265	NM_003241	ENSG00000163810	TGM4	TGP|hTGP	transglutaminase 4	protein-coding	0.008772	0.521168	399(GAGAGCAGGGTGTTCC,-,0.00),400(AGAGCAGGGTGTTCCC,+,0.00)
chunk0023_312_1	chr10	29043957	29044263	+	0	NA	Intergenic	L1MC5a|LINE|L1	197702	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.006536	0.374593	
chunk0053_292_1	chr13	33568889	33569341	+	0	NA	intron (NM_001243476, intron 3 of 17)	intron (NM_001243476, intron 3 of 17)	107720	NM_001243476	90627	Hs.156551	NM_052851	ENSG00000133121	STARD13	ARHGAP37|DLC2|GT650|LINC00464	StAR related lipid transfer domain containing 13	protein-coding	0.002212	0.326711	
chunk0019_242_1	chr1	227424276	227424500	+	0	NA	Intergenic	Intergenic	-106263	NM_014826	8476	Hs.35433	NM_003607	ENSG00000143776	CDC42BPA	MRCK|MRCKA|PK428	CDC42 binding protein kinase alpha	protein-coding	0.004464	0.373333	
chunk0205_283_1	chr9	111728851	111729089	+	0	NA	intron (NR_109816, intron 12 of 26)	Tigger1|DNA|TcMar-Tigger	30563	NM_001080551	158401	Hs.428209	NM_173521	ENSG00000165181	SHOC1	C9orf84|ZIP2|ZIP2H	shortage in chiasmata 1	protein-coding	0.004202	0.305439	
chunk0048_372_1	chr12	86265095	86265590	+	0	NA	intron (NM_013244, intron 3 of 6)	MER52A|LTR|ERV1	391047	NM_006183	4922	Hs.80962	NM_006183	ENSG00000133636	NTS	NMN-125|NN|NT|NT/N|NTS1	neurotensin	protein-coding	0.032323	0.520161	
chunk0077_446_1	chr16	85770745	85771070	+	0	NA	Intergenic	L1ME3|LINE|L1	-19824	NM_206967	404550	Hs.461655	NM_206967	ENSG00000154102	C16orf74	-	chromosome 16 open reading frame 74	protein-coding	0.015385	0.457055	
chunk0120_161_1	chr3	5551702	5552193	+	0	NA	Intergenic	Intergenic	-301692	NR_039953	100616334		NR_039953	ENSG00000265180	MIR4790	-	microRNA 4790	ncRNA	0.002037	0.308943	
chunk0071_330_1	chr15	87115308	87116010	+	0	NA	Intergenic	L1MC3|LINE|L1	-461270	NR_026869	145978	Hs.350808	NM_152454	ENSG00000259527	LINC00052	NCRNA00052|TMEM83	long intergenic non-protein coding RNA 52	ncRNA	0.002849	0.362731	
chunk0105_249_1	chr2	188745349	188745580	+	0	NA	intron (NM_052952, intron 1 of 1)	intron (NM_052952, intron 1 of 1)	44640	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.004329	0.323276	
chunk0161_239_1	chr5	171509647	171509994	+	0	NA	Intergenic	L2|LINE|L2	90157	NM_003862	8817	Hs.87191	NM_003862	ENSG00000156427	FGF18	FGF-18|ZFGF5	fibroblast growth factor 18	protein-coding	0.014409	0.482759	
chunk0093_86_1	chr19	41310118	41310398	+	0	NA	promoter-TSS (NM_052848)	promoter-TSS (NM_052848)	69	NM_052848	90324	Hs.437497	NM_052848	ENSG00000142039	CCDC97	-	coiled-coil domain containing 97	protein-coding	0.121429	0.672598	
chunk0059_85_1	chr14	30745120	30745346	+	0	NA	Intergenic	Intergenic	122914	NM_001257376	23256	Hs.369168	NM_016106	ENSG00000092108	SCFD1	C14orf163|RA410|SLY1|SLY1P|STXBP1L2	sec1 family domain containing 1	protein-coding	0.008850	0.480176	
chunk0173_391_1	chr6	150157717	150157922	+	0	NA	intron (NM_030949, intron 1 of 3)	MSTB2|LTR|ERVL-MaLR	14767	NM_030949	81706	Hs.486798	NM_030949	ENSG00000198729	PPP1R14C	CPI17-like|KEPI|NY-BR-81	protein phosphatase 1 regulatory inhibitor subunit 14C	protein-coding	0.004878	0.514563	
chunk0030_166_1	chr10	114066591	114067221	+	0	NA	Intergenic	Intergenic	22859	NM_000684	153	Hs.99913	NM_000684	ENSG00000043591	ADRB1	ADRB1R|B1AR|BETA1AR|RHR	adrenoceptor beta 1	protein-coding	0.017460	0.445325	
chunk0210_25_1	chrX	67416030	67416285	+	0	NA	Intergenic	L1PB3|LINE|L1	-127875	NM_000044	367	Hs.76704	NM_000044	ENSG00000169083	AR	AIS|AR8|DHTR|HUMARA|HYSP1|KD|NR3C4|SBMA|SMAX1|TFM	androgen receptor	protein-coding	0.007843	0.339844	
chunk0076_63_1	chr16	61910447	61910767	+	0	NA	intron (NM_001796, intron 2 of 11)	MIR|SINE|MIR	126228	NM_001796	1006	Hs.368322	NM_001796	ENSG00000150394	CDH8	Nbla04261	cadherin 8	protein-coding	0.003125	0.320872	
chunk0155_42_1	chr5	91127668	91128494	+	0	NA	intron (NR_003149, intron 87 of 89)	L2c|LINE|L2	186321	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.003632	0.384522	
chunk0045_246_1	chr12	49053468	49054064	+	0	NA	intron (NM_003482, intron 5 of 53)	L2a|LINE|L2	1558	NM_003482	8085	Hs.731384	NM_003482	ENSG00000167548	KMT2D	AAD10|ALR|CAGL114|KABUK1|KMS|MLL2|MLL4|TNRC21	lysine methyltransferase 2D	protein-coding	0.013423	0.517588	
chunk0079_186_1	chr17	14198542	14199009	+	0	NA	intron (NM_001303, intron 6 of 6)	L2a|LINE|L2	38058	NM_001007530	146822	Hs.447556	NM_001007530	ENSG00000223510	CDRT15	-	CMT1A duplicated region transcript 15	protein-coding	0.008565	0.352564	
chunk0158_362_1	chr5	133869773	133870451	+	0	NA	Intergenic	Intergenic	-43565	NR_131252	105664404	Hs.582536	NR_131252	ENSG00000249073	WSPAR	LncTCF7|TCONS_00009511	WNT signaling pathway activating non-coding RNA	ncRNA	0.014749	0.491900	
chunk0199_163_1	chr9	4375250	4375820	+	0	NA	Intergenic	Intergenic	-75500	NM_001042413	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.007018	0.348511	
chunk0199_406_1	chr9	13493527	13494156	+	0	NA	Intergenic	Intergenic	-62512	NR_033863	401492	Hs.632651	NR_033863	ENSG00000270547	LINC01235	-	long intergenic non-protein coding RNA 1235	ncRNA	0.004769	0.407937	
chunk0090_74_1	chr19	2507070	2507422	+	0	NA	Intergenic	MIRc|SINE|MIR	31121	NM_015675	4616	Hs.110571	NM_015675	ENSG00000099860	GADD45B	GADD45BETA|MYD118	growth arrest and DNA damage inducible beta	protein-coding	0.028409	0.478754	
chunk0153_153_1	chr5	69343110	69343309	+	0	NA	Intergenic	L1MB7|LINE|L1	-10416	NM_001297697	202243	Hs.654850	NM_176816	ENSG00000183323	CCDC125	KENAE	coiled-coil domain containing 125	protein-coding	0.000000	0.335000	
chunk0034_162_1	chr11	30488705	30488920	+	0	NA	intron (NM_001145399, intron 4 of 6)	intron (NM_001145399, intron 4 of 6)	91681	NM_001584	744	Hs.289795	NM_001584	ENSG00000066382	MPPED2	239FB|C11orf8	metallophosphoesterase domain containing 2	protein-coding	0.000000	0.430556	
chunk0101_405_1	chr2	138930853	138931299	+	0	NA	Intergenic	Intergenic	33752	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.013453	0.387025	
chunk0180_253_1	chr7	69273049	69273291	+	0	NA	Intergenic	Intergenic	324325	NR_108105	100507468	Hs.362492	NR_108105		CT66	-	cancer/testis associated transcript 66	ncRNA	0.000000	0.370370	
chunk0002_378_1	chr1	26620570	26621217	+	0	NA	Intergenic	CpG	66351	NR_031740	100302190		NR_031740	ENSG00000238705	MIR1976	hsa-mir-1976	microRNA 1976	ncRNA	0.103555	0.672840	468(GAGAACAACGTGTTCC,-,0.00),469(AGAACAACGTGTTCCC,+,0.00)
chunk0103_274_1	chr2	165819457	165820206	+	0	NA	Intergenic	L1ME4b|LINE|L1	-25538	NM_004482	2591	Hs.170986	NM_004482	ENSG00000115339	GALNT3	GalNAc-T3|HFTC|HFTC1|HHS	polypeptide N-acetylgalactosaminyltransferase 3	protein-coding	0.002670	0.290667	
chunk0141_128_1	chr4	80348109	80348741	+	0	NA	intron (NM_001206997, intron 1 of 6)	L1PA10|LINE|L1	12705	NM_152770	255119	Hs.527104	NM_152770	ENSG00000197826	CFAP299	C4orf22	cilia and flagella associated protein 299	protein-coding	0.006329	0.357030	
chunk0012_241_1	chr1	160842917	160843534	+	0	NA	intron (NM_001166663, intron 1 of 8)	intron (NM_001166663, intron 1 of 8)	19677	NM_016382	51744	Hs.157872	NM_016382	ENSG00000122223	CD244	2B4|NAIL|NKR2B4|Nmrk|SLAMF4	CD244 molecule	protein-coding	0.003241	0.406149	375(AAGCAGAGACTGTGCT,-,0.00)
chunk0081_295_1	chr17	45087082	45087318	+	0	NA	intron (NM_021079, intron 3 of 11)	intron (NM_021079, intron 3 of 11)	25901	NM_021079	4836	Hs.532790	NM_021079	ENSG00000136448	NMT1	NMT	N-myristoyltransferase 1	protein-coding	0.016949	0.455696	
chunk0164_181_1	chr6	22030590	22031432	+	0	NA	intron (NR_015410, intron 7 of 11)	intron (NR_015410, intron 7 of 11)	116182	NR_034143	729177	Hs.730673	NR_034143	ENSG00000260455	NBAT1	CASC14|NBAT-1	neuroblastoma associated transcript 1	ncRNA	0.007126	0.333333	
chunk0130_447_1	chr3	141368931	141369527	+	0	NA	intron (NM_001080412, intron 2 of 7)	intron (NM_001080412, intron 2 of 7)	45016	NM_001080412	253461	Hs.518301	NM_152535	ENSG00000177311	ZBTB38	CIBZ|PPP1R171|ZNF921	zinc finger and BTB domain containing 38	protein-coding	0.015101	0.403685	
chunk0018_253_1	chr1	220229724	220230170	+	0	NA	intron (NM_012414, intron 2 of 34)	intron (NM_012414, intron 2 of 34)	-29271	NR_002994	677818	Hs.730572	NR_002994	ENSG00000222370	SNORA36B	ACA36b	small nucleolar RNA, H/ACA box 36B	snoRNA	0.004484	0.389262	
chunk0125_330_1	chr3	71026877	71027245	+	0	NA	intron (NM_032682, intron 11 of 20)	intron (NM_032682, intron 11 of 20)	37862	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.002717	0.403794	
chunk0208_122_1	chrX	15261319	15261985	+	0	NA	intron (NM_001168530, intron 1 of 6)	intron (NM_001168530, intron 1 of 6)	8519	NM_001031739	140462	Hs.19404	NM_024087	ENSG00000102048	ASB9	-	ankyrin repeat and SOCS box containing 9	protein-coding	0.006006	0.404798	
chunk0115_195_1	chr21	26158617	26159157	+	0	NA	intron (NM_001136131, intron 1 of 15)	L2b|LINE|L2	11933	NM_000484	351	Hs.434980	NM_000484	ENSG00000142192	APP	AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4	amyloid beta precursor protein	protein-coding	0.011111	0.415896	
chunk0171_158_1	chr6	124056998	124057247	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	-225883	NM_001300740	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.000000	0.360000	
chunk0088_211_1	chr18	48155022	48155278	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-17841	NM_001039360	201501	Hs.515388	NM_001039360	ENSG00000184828	ZBTB7C	APM-1|APM1|ZBTB36|ZNF857C	zinc finger and BTB domain containing 7C	protein-coding	0.003906	0.420233	
chunk0078_261_1	chr17	7558091	7558440	+	0	NA	promoter-TSS (NM_172088)	promoter-TSS (NM_172088)	-27	NM_001198622	8741	Hs.54673	NM_003808	ENSG00000161955	TNFSF13	APRIL|CD256|TALL-2|TALL2|TNLG7B|TRDL-1|UNQ383/PRO715|ZTNF2	TNF superfamily member 13	protein-coding	0.031519	0.634286	
chunk0093_307_1	chr19	53497791	53498623	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-22716	NM_018555	55422	Hs.185674	NM_018555	ENSG00000130844	ZNF331	RITA|ZNF361|ZNF463	zinc finger protein 331	protein-coding	0.016827	0.494598	
chunk0126_434_1	chr3	87000870	87001255	+	0	NA	Intergenic	Intergenic	-9955	NM_016206	389136	Hs.606507	NM_016206	ENSG00000206538	VGLL3	VGL-3|VGL3	vestigial like family member 3	protein-coding	0.007792	0.316062	187(GAGCACACCATGTTCT,-,0.00),188(AGCACACCATGTTCTG,+,0.00)
chunk0014_133_1	chr1	177651038	177651511	+	0	NA	Intergenic	Intergenic	-49250	NR_110722	101928778	Hs.573792	NR_110722	ENSG00000236720	LINC01741	-	long intergenic non-protein coding RNA 1741	ncRNA	0.008457	0.409283	204(GGGAACATAAAGTCCC,-,0.00),205(GGAACATAAAGTCCCT,+,0.00)
chunk0174_430_1	chr6	166044031	166044619	+	0	NA	Intergenic	L2b|LINE|L2	-56286	NR_026860	90632	Hs.31917	NR_026860	ENSG00000112541	LINC00473	C6orf176|LNC473|bA142J11.1	long intergenic non-protein coding RNA 473	ncRNA	0.010204	0.404075	
chunk0044_58_1	chr12	27747540	27748449	+	0	NA	intron (NM_021821, intron 7 of 7)	MIR|SINE|MIR	23282	NM_001146221	100287284		NM_001146221	ENSG00000205693	MANSC4	-	MANSC domain containing 4	protein-coding	0.006601	0.390110	348(TAGAACATGTTGTTCT,-,0.00),349(AGAACATGTTGTTCTA,+,0.00)
chunk0086_10_1	chr18	12079300	12079881	+	0	NA	Intergenic	Intergenic	-14259	NM_001277333	342850	Hs.448906	NM_001277333	ENSG00000181626	ANKRD62	DKFZp779B1634	ankyrin repeat domain 62	protein-coding	0.008606	0.379725	
chunk0001_18_1	chr1	1153818	1154296	+	0	NA	Intergenic	Intergenic	-13047	NR_029639	406984		NR_029639	ENSG00000207730	MIR200B	MIRN200B|mir-200b	microRNA 200b	ncRNA	0.012552	0.482255	
chunk0187_117_1	chr7	148875150	148875485	+	0	NA	intron (NM_004456, intron 1 of 19)	intron (NM_004456, intron 1 of 19)	8192	NM_001203249	2146	Hs.444082	NM_004456	ENSG00000106462	EZH2	ENX-1|ENX1|EZH2b|KMT6|KMT6A|WVS|WVS2	enhancer of zeste 2 polycomb repressive complex 2 subunit	protein-coding	0.002985	0.291667	
chunk0104_263_1	chr2	177791985	177792613	+	0	NA	intron (NM_001077197, intron 10 of 20)	intron (NM_001077197, intron 10 of 20)	96440	NM_001077196	50940	Hs.570273	NM_016953	ENSG00000128655	PDE11A	PPNAD2	phosphodiesterase 11A	protein-coding	0.003185	0.319555	
chunk0017_122_1	chr1	206144684	206145177	+	0	NA	Intergenic	Intergenic	-27882	NM_000707	553	Hs.1372	NM_000707	ENSG00000198049	AVPR1B	AVPR3|V1bR	arginine vasopressin receptor 1B	protein-coding	0.002028	0.402834	325(AAGGACTCTGTGTACA,-,0.00)
chunk0115_2_1	chr21	20232395	20232936	+	0	NA	Intergenic	L1MA5|LINE|L1	570443	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.000000	0.333948	
chunk0093_375_1	chr19	56105221	56105770	+	0	NA	intron (NM_001002836, intron 1 of 2)	HY3|scRNA|scRNA	15878	NM_001002836	126208	Hs.397153	NM_001002836	ENSG00000142409	ZNF787	TIP20	zinc finger protein 787	protein-coding	0.038251	0.580000	
chunk0091_359_1	chr19	15380949	15381558	+	0	NA	intron (NR_111971, intron 14 of 15)	L1ME4c|LINE|L1	-1452	NM_005858	10270	Hs.594496	NM_005858	ENSG00000105127	AKAP8	AKAP 95|AKAP-8|AKAP-95|AKAP95	A-kinase anchoring protein 8	protein-coding	0.013136	0.411475	
chunk0131_318_1	chr3	150884847	150885422	+	0	NA	Intergenic	Intergenic	59102	NM_052995	7401	Hs.745448	NM_052995	ENSG00000163646	CLRN1	RP61|USH3|USH3A	clarin 1	protein-coding	0.003478	0.385417	539(AAGATCAGGCTGTACA,-,0.00)
chunk0163_97_1	chr6	9610843	9611590	+	0	NA	Intergenic	Intergenic	-801102	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.009371	0.374332	
chunk0088_174_1	chr18	47233875	47234357	+	0	NA	intron (NM_001037802, intron 2 of 2)	intron (NM_001037802, intron 2 of 2)	15067	NM_001278063	652991	Hs.585834	NM_001037802	ENSG00000215474	SKOR2	CH18515|CORL2|FUSSEL18	SKI family transcriptional corepressor 2	protein-coding	0.008299	0.339545	
chunk0075_190_1	chr16	52294725	52294940	+	0	NA	Intergenic	Intergenic	209551	NR_104655	102467079	Hs.98466	NR_104655	ENSG00000261749	LINC02180	-	long intergenic non-protein coding RNA 2180	ncRNA	0.009302	0.305556	
chunk0209_62_1	chrX	37646081	37646516	+	0	NA	intron (NM_198511, intron 1 of 5)	intron (NM_198511, intron 1 of 5)	-39582	NM_021083	7504	Hs.78919	NM_021083	ENSG00000047597	XK	KX|NA|NAC|X1k|XKR1	X-linked Kx blood group	protein-coding	0.000000	0.357798	
chunk0179_46_1	chr7	43445572	43445962	+	0	NA	intron (NM_001287059, intron 10 of 27)	intron (NM_001287059, intron 10 of 27)	76775	NR_038276	100506895	Hs.676047	NR_038276	ENSG00000231638	LUARIS	SCAT6|lncRNA32	lncRNA upregulator of antiviral response interferon signaling	ncRNA	0.012821	0.432225	
chunk0144_369_1	chr4	139920124	139920415	+	0	NA	intron (NM_018717, intron 1 of 5)	intron (NM_018717, intron 1 of 5)	233810	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.003436	0.380137	
chunk0031_202_1	chr10	125840629	125840828	+	0	NA	intron (NM_018180, intron 8 of 10)	intron (NM_018180, intron 8 of 10)	17193	NM_016567	56647	Hs.370292	NM_016567	ENSG00000107949	BCCIP	TOK-1|TOK1	BRCA2 and CDKN1A interacting protein	protein-coding	0.020101	0.525000	
chunk0054_79_1	chr13	42283830	42284558	+	0	NA	intron (NM_016248, intron 1 of 12)	MIRb|SINE|MIR	12041	NM_016248	11215	Hs.105105	NM_016248	ENSG00000023516	AKAP11	AKAP-11|AKAP220|PPP1R44|PRKA11	A-kinase anchoring protein 11	protein-coding	0.006868	0.411523	
chunk0185_436_1	chr7	134891385	134891590	+	0	NA	promoter-TSS (NM_033140)	promoter-TSS (NM_033140)	87	NM_033140	800	Hs.490203	NM_004342	ENSG00000122786	CALD1	CDM|H-CAD|HCAD|L-CAD|LCAD|NAG22	caldesmon 1	protein-coding	0.053659	0.606796	
chunk0045_307_1	chr12	50649232	50649503	+	0	NA	intron (NM_173602, intron 3 of 37)	L1M5|LINE|L1	-114639	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.007380	0.323529	
chunk0211_414_1	chrX	128894354	128894645	+	0	NA	Intergenic	Ricksha_0|DNA|MULE-MuDR	629006	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.006873	0.356164	206(ATGAACACATAGTGCT,-,0.00),207(TGAACACATAGTGCTT,+,0.00)
chunk0035_96_1	chr11	42188712	42189046	+	0	NA	intron (NR_038309, intron 4 of 5)	intron (NR_038309, intron 4 of 5)	64811	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.002994	0.411940	
chunk0155_87_1	chr5	92242278	92242553	+	0	NA	Intergenic	MER47B|DNA|TcMar-Tigger	-859083	NM_020801	57561	Hs.24684	NM_020801	ENSG00000113369	ARRDC3	TLIMP	arrestin domain containing 3	protein-coding	0.000000	0.413043	
chunk0084_352_1	chr17	81298691	81299400	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-3706	NM_138570	124565	Hs.352240	NM_138570	ENSG00000157637	SLC38A10	PP1744	solute carrier family 38 member 10	protein-coding	0.015515	0.415493	
chunk0052_183_1	chr13	24265599	24265798	+	0	NA	intron (NM_001286792, intron 6 of 14)	intron (NM_001286792, intron 6 of 14)	-4989	NM_001286793	221178	Hs.434298	NM_153023	ENSG00000182957	SPATA13	ARHGEF29|ASEF2	spermatogenesis associated 13	protein-coding	0.010050	0.555000	
chunk0199_465_1	chr9	14271165	14271536	+	0	NA	intron (NM_001190737, intron 2 of 10)	intron (NM_001190737, intron 2 of 10)	42696	NM_005596	4781	Hs.644095	NM_005596	ENSG00000147862	NFIB	CTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3	nuclear factor I B	protein-coding	0.008086	0.459677	
chunk0200_117_1	chr9	17092039	17092752	+	0	NA	Intergenic	Intergenic	-42596	NM_001114395	54875	Hs.435381	NM_017738	ENSG00000044459	CNTLN	C9orf101|C9orf39|bA340N12.1	centlein	protein-coding	0.005610	0.296919	
chunk0148_180_1	chr5	7813048	7813535	+	0	NA	intron (NM_020546, intron 22 of 24)	L2b|LINE|L2	38199	NM_001089584	134121	Hs.709979	NM_001089584	ENSG00000215217	C5orf49	-	chromosome 5 open reading frame 49	protein-coding	0.008214	0.407787	114(GAGAACAGAATGCTCC,-,0.00),115(AGAACAGAATGCTCCT,+,0.00)
chunk0186_225_1	chr7	140403866	140404412	+	0	NA	promoter-TSS (NM_001008749)	promoter-TSS (NM_001008749)	96	NM_001008749	401409	Hs.583545	NM_001008749	ENSG00000146955	RAB19	RAB19B	RAB19, member RAS oncogene family	protein-coding	0.038462	0.588665	
chunk0073_37_1	chr16	2719137	2719674	+	0	NA	intron (NM_031948, intron 1 of 5)	intron (NM_031948, intron 1 of 5)	1146	NM_031948	83886	Hs.332878	NM_031948	ENSG00000172382	PRSS27	CAPH2|MPN	serine protease 27	protein-coding	0.014898	0.646840	
chunk0046_198_1	chr12	58939129	58939728	+	0	NA	Intergenic	MLT1A0|LTR|ERVL-MaLR	-18890	NM_153377	121227	Hs.253736	NM_153377	ENSG00000139263	LRIG3	LIG3	leucine rich repeats and immunoglobulin like domains 3	protein-coding	0.006678	0.415000	
chunk0040_394_1	chr11	120330066	120330399	+	0	NA	exon (NM_001198673, exon 3 of 3)	exon (NM_001198673, exon 3 of 3)	5103	NM_001198674	219902	Hs.643516	NM_174926	ENSG00000181264	TLCD5	TMEM136	TLC domain containing 5	protein-coding	0.012012	0.517964	
chunk0093_246_1	chr19	50861532	50861825	+	0	NA	TTS (NM_001648)	TTS (NM_001648)	6763	NM_001030048	354	Hs.171995	NM_001648	ENSG00000142515	KLK3	APS|KLK2A1|PSA|hK3	kallikrein related peptidase 3	protein-coding	0.017065	0.513605	
chunk0129_178_1	chr3	120894283	120894616	+	0	NA	Intergenic	Intergenic	-13754	NM_014980	9515	Hs.477315	NM_014980	ENSG00000145087	STXBP5L	LLGL4	syntaxin binding protein 5 like	protein-coding	0.012012	0.413174	
chunk0110_174_1	chr20	14313578	14314112	+	0	NA	intron (NM_080676, intron 3 of 16)	intron (NM_080676, intron 3 of 16)	23822	NM_198391	23767	Hs.41296	NM_013281	ENSG00000125848	FLRT3	HH21	fibronectin leucine rich transmembrane protein 3	protein-coding	0.001873	0.342056	
chunk0101_103_1	chr2	125207900	125208727	+	0	NA	Intergenic	MIR3|SINE|MIR	1183026	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.003628	0.356280	
chunk0103_111_1	chr2	161471476	161472132	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	36098	NR_077058	285116	Hs.470435	NR_077058		AHCTF1P1	AHCTF1P|ELYS-like	AT-hook containing transcription factor 1 pseudogene 1	pseudo	0.004573	0.392694	
chunk0116_378_1	chr21	42157108	42157346	+	0	NA	Intergenic	Intergenic	-42462	NM_207627	9619	Hs.124649	NM_004915	ENSG00000160179	ABCG1	ABC8|WHITE1	ATP binding cassette subfamily G member 1	protein-coding	0.033613	0.552301	
chunk0081_1_1	chr17	37088842	37089463	+	0	NA	intron (NM_198836, intron 54 of 55).2	intron (NM_198836, intron 54 of 55).2	55407	NR_036056	100422969		NR_036056	ENSG00000276326	MIR2909	-	microRNA 2909	ncRNA	0.019324	0.482315	
chunk0186_183_1	chr7	139666193	139666612	+	0	NA	intron (NM_001113239, intron 2 of 14)	intron (NM_001113239, intron 2 of 14)	111492	NM_001113239	28996	Hs.731417	NM_022740	ENSG00000064393	HIPK2	PRO0593	homeodomain interacting protein kinase 2	protein-coding	0.007160	0.428571	
chunk0096_116_1	chr2	28593972	28594779	+	0	NA	intron (NM_001170585, intron 32 of 56)	intron (NM_001170585, intron 32 of 56)	98304	NM_153021	151056	Hs.444933	NM_153021	ENSG00000163803	PLB1	PLB|PLB/LIP	phospholipase B1	protein-coding	0.028501	0.503713	
chunk0101_466_1	chr2	140682283	140682604	+	0	NA	intron (NM_018557, intron 41 of 90)	intron (NM_018557, intron 41 of 90)	-95758	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.000000	0.397516	157(AGGGTCAGACTGTCCC,-,0.00),158(GGGTCAGACTGTCCCA,+,0.00)
chunk0155_28_1	chr5	91042915	91043356	+	0	NA	intron (NR_003149, intron 85 of 89)	intron (NR_003149, intron 85 of 89)	271267	NR_103549	100505994	Hs.628363	NR_103548	ENSG00000248323	LUCAT1	SCAL1|SCAT5	lung cancer associated transcript 1	ncRNA	0.004535	0.359729	
chunk0034_418_1	chr11	38449114	38449689	+	0	NA	Intergenic	L1PA16|LINE|L1	196955	NR_120555	103312105	Hs.641711	NR_120554	ENSG00000255175	LINC02759	-	long intergenic non-protein coding RNA 2759	ncRNA	0.001739	0.331597	
chunk0111_335_1	chr20	33009937	33010710	+	0	NA	intron (NM_025227, intron 2 of 15)	MIRb|SINE|MIR	2745	NM_025227	80341	Hs.257045	NM_025227	ENSG00000078898	BPIFB2	BPIL1|C20orf184|LPLUNC2|RYSR|dJ726C3.2	BPI fold containing family B member 2	protein-coding	0.011643	0.534884	
chunk0190_83_1	chr8	30051409	30051893	+	0	NA	Intergenic	Intergenic	31557	NM_016127	51669	Hs.521487	NM_016127	ENSG00000133872	SARAF	FOAP-7|HSPC035|TMEM66|XTP3	store-operated calcium entry associated regulatory factor	protein-coding	0.004132	0.317526	196(CTGAACTTGGTGTTCT,-,0.00),197(TGAACTTGGTGTTCTT,+,0.00)
chunk0145_343_1	chr4	150973802	150974377	+	0	NA	intron (NM_001199282, intron 2 of 56)	intron (NM_001199282, intron 2 of 56)	41178	NM_001199282	987	Hs.480938	NM_006726	ENSG00000198589	LRBA	BGL|CDC4L|CVID8|LAB300|LBA	LPS responsive beige-like anchor protein	protein-coding	0.006957	0.375000	
chunk0194_204_1	chr8	85855363	85855612	+	0	NA	Intergenic	MER6|DNA|TcMar-Tigger	-27545	NR_003594	100288527	Hs.535056	NR_003594		REXO1L2P	-	REXO1 like 2, pseudogene	pseudo	0.012048	0.328000	
chunk0045_86_1	chr12	45939888	45940126	+	0	NA	intron (NM_004719, intron 6 of 14)	intron (NM_004719, intron 6 of 14)	50611	NM_004719	9169	Hs.210367	NM_004719	ENSG00000139218	SCAF11	CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP	SR-related CTD associated factor 11	protein-coding	0.008403	0.368201	
chunk0203_15_1	chr9	82681813	82682346	+	0	NA	Intergenic	Intergenic	381049	NM_152573	158158	Hs.129136	NM_152573	ENSG00000165105	RASEF	RAB45	RAS and EF-hand domain containing	protein-coding	0.001876	0.455056	
chunk0030_105_1	chr10	112675627	112675940	+	0	NA	intron (NM_145206, intron 7 of 7)	intron (NM_145206, intron 7 of 7)	41613	NR_036177	100422909		NR_036177	ENSG00000264763	MIR4295	-	microRNA 4295	ncRNA	0.015974	0.410828	
chunk0179_325_1	chr7	50550580	50551233	+	0	NA	intron (NM_001082971, intron 1 of 14)	intron (NM_001082971, intron 1 of 14)	10165	NM_001242890	1644	Hs.359698	NM_000790	ENSG00000132437	DDC	AADC	dopa decarboxylase	protein-coding	0.007657	0.347095	
chunk0188_444_1	chr8	19311797	19312202	+	0	NA	Intergenic	Intergenic	-1571	NM_001174160	63898	Hs.303208	NM_022071	ENSG00000104611	SH2D4A	PPP1R38|SH2A	SH2 domain containing 4A	protein-coding	0.009877	0.458128	
chunk0023_131_1	chr10	23848756	23849033	+	0	NA	intron (NM_001098500, intron 1 of 18)	MLT1I|LTR|ERVL-MaLR	154148	NM_001098500	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.000000	0.356115	
chunk0153_64_1	chr5	67815722	67816463	+	0	NA	Intergenic	Intergenic	22879	NR_130779	101928858	Hs.334066	NR_130779	ENSG00000249364	LOC101928858	-	uncharacterized LOC101928858	ncRNA	0.009447	0.389488	326(GGGATCTGACTGTTCC,-,0.00),327(GGATCTGACTGTTCCC,+,0.00)
chunk0113_402_1	chr20	60481411	60481610	+	0	NA	Intergenic	Intergenic	3399	NR_039758	100616362		NR_039758	ENSG00000266140	MIR4533	-	microRNA 4533	ncRNA	0.035176	0.610000	
chunk0001_147_1	chr1	5992278	5992478	+	0	NA	promoter-TSS (NM_015102)	promoter-TSS (NM_015102)	80	NM_001199861	8514	Hs.440497	NM_003636	ENSG00000069424	KCNAB2	AKR6A5|HKvbeta2|HKvbeta2.1|HKvbeta2.2|KCNA2B|KV-BETA-2	potassium voltage-gated channel subfamily A regulatory beta subunit 2	protein-coding	0.130000	0.721393	
chunk0181_452_1	chr7	90749599	90750038	+	0	NA	intron (NM_001287136, intron 3 of 13)	L1PA16|LINE|L1	40002	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.002278	0.502273	281(CAGAACACTATGGGCT,-,0.00),282(AGAACACTATGGGCTC,+,0.00)
chunk0138_179_1	chr4	37937006	37937205	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	-23330	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.010050	0.535000	
chunk0065_137_1	chr15	25123813	25124379	+	0	NA	Intergenic	L1MC4a|LINE|L1	7551	NR_023915	3653	Hs.555970	NR_023915		IPW	NCRNA00002	imprinted in Prader-Willi syndrome	ncRNA	0.003534	0.326279	
chunk0010_444_1	chr1	120761052	120761430	+	0	NA	Intergenic	Intergenic	89744	NR_104086	101954277		NR_104086	ENSG00000275538	RNVU1-19	RNU1-126|RNU1-147|RNVU1-13|vU1.13|vU1.19	RNA, variant U1 small nuclear 19	snRNA	0.005291	0.448549	
chunk0029_448_1	chr10	110430954	110431239	+	0	NA	Intergenic	Intergenic	-66771	NM_004419	1847	Hs.2128	NM_004419	ENSG00000138166	DUSP5	DUSP|HVH3	dual specificity phosphatase 5	protein-coding	0.014035	0.608392	
chunk0149_355_1	chr5	27639150	27639381	+	0	NA	Intergenic	L1M1|LINE|L1	166973	NR_038848	643401	Hs.533212	NR_038848	ENSG00000250337	PURPL	LINC01021	p53 upregulated regulator of p53 levels	ncRNA	0.012987	0.538793	
chunk0155_306_1	chr5	96351403	96351945	+	0	NA	intron (NR_130776, intron 3 of 4)	intron (NR_130776, intron 3 of 4)	80485	NM_001177875	5122	Hs.78977	NM_000439	ENSG00000175426	PCSK1	BMIQ12|NEC1|PC1|PC3|SPC3	proprotein convertase subtilisin/kexin type 1	protein-coding	0.003690	0.355433	345(AAAAACTCACTGTTCT,-,0.00),346(AAAACTCACTGTTCTT,+,0.00)
chunk0109_104_1	chr20	2338571	2338797	+	0	NA	intron (NM_003245, intron 11 of 12)	intron (NM_003245, intron 11 of 12)	-42224	NM_001254734	343641	Hs.452039	NM_198994	ENSG00000166948	TGM6	SCA35|TG6|TGM3L|TGY|dJ734P14.3	transglutaminase 6	protein-coding	0.004425	0.418502	
chunk0004_377_1	chr1	51726970	51727247	+	0	NA	intron (NR_036662, intron 3 of 22)	intron (NR_036662, intron 3 of 22)	-2706	NM_148907	114883	Hs.21938	NM_024586	ENSG00000117859	OSBPL9	ORP-9|ORP9	oxysterol binding protein like 9	protein-coding	0.003610	0.341727	
chunk0047_71_1	chr12	67707877	67708525	+	0	NA	TTS (NR_110063)	TTS (NR_110063)	21274	NR_110063	101927901	Hs.369609	NR_110063	ENSG00000255970	LINC02421	-	long intergenic non-protein coding RNA 2421	ncRNA	0.003086	0.432974	
chunk0199_32_1	chr9	747180	747491	+	0	NA	Intergenic	GA-rich|Low_complexity|Low_complexity	40529	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.009646	0.477564	
chunk0163_36_1	chr6	8268357	8268573	+	0	NA	Intergenic	Intergenic	-165870	NM_001135650	9521	Hs.602353	NM_004280	ENSG00000124802	EEF1E1	AIMP3|P18	eukaryotic translation elongation factor 1 epsilon 1	protein-coding	0.000000	0.391705	75(AAGAACACAATGTCCT,-,0.00),76(AGAACACAATGTCCTG,+,0.00)
chunk0010_301_1	chr1	117758842	117759224	+	0	NA	Intergenic	Intergenic	153051	NM_017709	54855	Hs.356216	NM_017709	ENSG00000183508	TENT5C	FAM46C	terminal nucleotidyltransferase 5C	protein-coding	0.036649	0.571802	
chunk0021_136_1	chr10	3853461	3854097	+	0	NA	Intergenic	Intergenic	-68498	NM_001160125	1316	Hs.4055	NM_001300	ENSG00000067082	KLF6	BCD1|CBA1|COPEB|CPBP|GBF|PAC1|ST12|ZF9	Kruppel like factor 6	protein-coding	0.012579	0.458399	
chunk0002_372_1	chr1	26404536	26405051	+	0	NA	Intergenic	L2a|LINE|L2	-5975	NM_024674	79727	Hs.86154	NM_024674	ENSG00000131914	LIN28A	CSDD1|LIN-28|LIN28|ZCCHC1|lin-28A	lin-28 homolog A	protein-coding	0.007767	0.397287	
chunk0064_9_1	chr14	89241831	89242342	+	0	NA	intron (NM_001085471, intron 4 of 6)	MLT1O|LTR|ERVL-MaLR	175024	NM_005197	1112	Hs.434286	NM_005197	ENSG00000053254	FOXN3	C14orf116|CHES1|PRO1635	forkhead box N3	protein-coding	0.017613	0.521484	
chunk0178_144_1	chr7	33075844	33076354	+	0	NA	Intergenic	ERV24B_Prim-int|LTR|ERV1	-13302	NM_001002009	51251	Hs.487933	NM_016489	ENSG00000122643	NT5C3A	NT5C3|P5'N-1|P5N-1|PN-I|POMP|PSN1|UMPH|UMPH1|cN-III|hUMP1|p36	5'-nucleotidase, cytosolic IIIA	protein-coding	0.003922	0.405088	
chunk0158_368_1	chr5	133981427	133982076	+	0	NA	intron (NR_036624, intron 5 of 8)	intron (NR_036624, intron 5 of 8)	-13036	NM_020199	56951	Hs.744034	NM_020199	ENSG00000113583	C5orf15	HTGN29|KCT2	chromosome 5 open reading frame 15	protein-coding	0.004622	0.433846	
chunk0131_131_1	chr3	144389538	144389818	+	0	NA	Intergenic	Intergenic	416353	NM_001134470	205428	Hs.288954	NM_173552	ENSG00000181744	DIPK2A	C3orf58|DIA1|GoPro49|HASF	divergent protein kinase domain 2A	protein-coding	0.000000	0.341637	
chunk0084_284_1	chr17	79897525	79897987	+	0	NA	Intergenic	L1ME4b|LINE|L1	-21601	NR_110851	101928738	Hs.399280	NR_110851	ENSG00000262188	LINC01978	-	long intergenic non-protein coding RNA 1978	ncRNA	0.012987	0.455724	
chunk0076_326_1	chr16	70715166	70715391	+	0	NA	intron (NM_018052, intron 14 of 18)	L2b|LINE|L2	-29227	NM_138383	92154	Hs.432387	NM_138383	ENSG00000132613	MTSS2	ABBA|ABBA-1|ABBA1|MTSS1L	MTSS I-BAR domain containing 2	protein-coding	0.022222	0.566372	
chunk0167_48_1	chr6	55518353	55518578	+	0	NA	intron (NM_019036, intron 4 of 9)	MLT1G3|LTR|ERVL-MaLR	60749	NM_001287753	54511	Hs.147054	NM_019036	ENSG00000146151	HMGCLL1	bA418P12.1|er-cHL	3-hydroxymethyl-3-methylglutaryl-CoA lyase like 1	protein-coding	0.000000	0.398230	
chunk0041_119_1	chr11	124987226	124987640	+	0	NA	exon (NM_025004, exon 8 of 16)	exon (NM_025004, exon 8 of 16)	33312	NM_025004	80071	Hs.287555	NM_025004	ENSG00000149548	CCDC15	-	coiled-coil domain containing 15	protein-coding	0.002415	0.443373	286(AAGACCACTGTGTTCT,-,0.00),287(AGACCACTGTGTTCTC,+,0.00),355(GAGACCAGCATGTTCT,-,0.00),356(AGACCAGCATGTTCTC,+,0.00)
chunk0057_74_1	chr13	98301748	98302143	+	0	NA	intron (NM_001286839, intron 2 of 27)	intron (NM_001286839, intron 2 of 27)	93421	NR_036129	100422881		NR_036129	ENSG00000263399	MIR3170	mir-3170	microRNA 3170	ncRNA	0.017722	0.419192	
chunk0155_313_1	chr5	96616922	96617143	+	0	NA	intron (NR_130776, intron 4 of 4)	intron (NR_130776, intron 4 of 4)	-45005	NM_001190442	831	Hs.436186	NM_001750	ENSG00000153113	CAST	BS-17|PLACK	calpastatin	protein-coding	0.009050	0.445946	
chunk0202_116_1	chr9	72769239	72769688	+	0	NA	intron (NM_138691, intron 12 of 23)	intron (NM_138691, intron 12 of 23)	104646	NR_121180	101927258	Hs.586433	NR_121120	ENSG00000236849	LINC01474	-	long intergenic non-protein coding RNA 1474	ncRNA	0.013363	0.460000	226(GAGCACAGCATGTTCC,-,0.00),227(AGCACAGCATGTTCCC,+,0.00)
chunk0174_3_1	chr6	152210246	152210811	+	0	NA	intron (NM_033071, intron 123 of 145)	intron (NM_033071, intron 123 of 145)	-170002	NR_120501	100505475	Hs.571203	NR_120501		SYNE1-AS1	-	SYNE1 antisense RNA 1	ncRNA	0.003540	0.266784	
chunk0079_294_1	chr17	16922945	16923144	+	0	NA	Intergenic	Intergenic	49044	NM_012452	23495	Hs.158341	NM_012452	ENSG00000240505	TNFRSF13B	CD267|CVID|CVID2|IGAD2|RYZN|TACI|TNFRSF14B	TNF receptor superfamily member 13B	protein-coding	0.020101	0.605000	
chunk0028_155_1	chr10	86904502	86905277	+	0	NA	intron (NM_004329, intron 7 of 12)	intron (NM_004329, intron 7 of 12)	52779	NM_024756	79812	Hs.524479	NM_024756	ENSG00000173269	MMRN2	EMILIN-3|EMILIN3|ENDOGLYX-1	multimerin 2	protein-coding	0.010323	0.372423	386(TAGAACTTCATGTGCT,-,0.00),387(AGAACTTCATGTGCTA,+,0.00)
chunk0035_37_1	chr11	40852589	40853322	+	0	NA	intron (NM_020929, intron 1 of 4)	intron (NM_020929, intron 1 of 4)	-559825	NR_047673	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.001364	0.311989	
chunk0024_235_1	chr10	38527255	38527933	+	0	NA	Intergenic	Intergenic	99448	NR_024497	399744	Hs.497951	NM_001013665		LINC00999	-	long intergenic non-protein coding RNA 999	ncRNA	0.019174	0.394698	
chunk0168_114_1	chr6	81706009	81706457	+	0	NA	Intergenic	Intergenic	46478	NM_017633	55603	Hs.10784	NM_017633	ENSG00000112773	TENT5A	C6orf37|FAM46A|OI18|XTP11	terminal nucleotidyltransferase 5A	protein-coding	0.004464	0.354120	
chunk0073_96_1	chr16	4428628	4428827	+	0	NA	intron (NM_001286516, intron 1 of 8)	intron (NM_001286516, intron 1 of 8)	2922	NM_001286516	9093	Hs.459779	NM_005147	ENSG00000103423	DNAJA3	HCA57|TID1|hTID-1	DnaJ heat shock protein family (Hsp40) member A3	protein-coding	0.025126	0.525000	
chunk0212_71_1	chrY	11494966	11495228	+	0	NA	Intergenic	Intergenic	926493	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.026718	0.399240	
chunk0136_399_1	chr3	197195613	197195812	+	0	NA	intron (NM_004087, intron 4 of 25)	L1PA16|LINE|L1	-11581	NM_001204388	1739	Hs.292549	NM_004087	ENSG00000075711	DLG1	DLGH1|SAP-97|SAP97|hdlg	discs large MAGUK scaffold protein 1	protein-coding	0.005025	0.460000	
chunk0188_301_1	chr8	16162777	16163230	+	0	NA	intron (NM_138715, intron 5 of 9)	L1MEd|LINE|L1	29788	NM_138715	4481	Hs.147635	NM_002445	ENSG00000038945	MSR1	CD204|SCARA1|SR-A|SR-AI|SR-AII|SR-AIII|SRA|phSR1|phSR2	macrophage scavenger receptor 1	protein-coding	0.002208	0.323789	233(AAGCACTTTCAGTTCC,-,0.00),234(AGCACTTTCAGTTCCT,+,0.00)
chunk0143_61_1	chr4	107787298	107788056	+	0	NA	Intergenic	L2a|LINE|L2	-36888	NM_001136258	166929	Hs.595423	NM_152621	ENSG00000164023	SGMS2	SMS2	sphingomyelin synthase 2	protein-coding	0.006596	0.465086	
chunk0144_270_1	chr4	137445120	137445446	+	0	NA	Intergenic	Intergenic	87215	NM_019035	54510	Hs.591691	NM_019035	ENSG00000189184	PCDH18	PCDH68L	protocadherin 18	protein-coding	0.000000	0.373089	
chunk0022_19_1	chr10	7559047	7559906	+	0	NA	3' UTR (NM_030569, exon 14 of 14)	3' UTR (NM_030569, exon 14 of 14)	60197	NM_032817	80760	Hs.498586	NM_030569	ENSG00000123243	ITIH5	ITI-HC5|PP14776	inter-alpha-trypsin inhibitor heavy chain 5	protein-coding	0.010477	0.380233	
chunk0112_164_1	chr20	39790308	39790560	+	0	NA	Intergenic	Intergenic	-214027	NR_109937	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.003968	0.363636	
chunk0171_152_1	chr6	123972478	123973195	+	0	NA	intron (NM_001300738, intron 1 of 7)	MIR|SINE|MIR	168990	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.001395	0.346797	
chunk0122_214_1	chr3	33318241	33318643	+	0	NA	intron (NM_001171713, intron 2 of 13)	MLT1J2-int|LTR|ERVL-MaLR	40997	NM_001171713	25827	Hs.475872	NM_012157	ENSG00000153558	FBXL2	FBL2|FBL3	F-box and leucine rich repeat protein 2	protein-coding	0.004975	0.344913	
chunk0023_318_1	chr10	29107650	29108274	+	0	NA	Intergenic	Intergenic	-181099	NM_032517	84569	Hs.558572	NM_032517	ENSG00000120563	LYZL1	KAAG648|LYC2|LYZD1|PRO1278|bA534G20.1	lysozyme like 1	protein-coding	0.000000	0.400000	
chunk0019_248_1	chr1	227599867	227600666	+	0	NA	intron (NM_178549, intron 2 of 3)	L1PA13|LINE|L1	36747	NM_178549	339500	Hs.30323	NM_032755	ENSG00000181450	ZNF678	-	zinc finger protein 678	protein-coding	0.005006	0.357500	
chunk0104_215_1	chr2	176303628	176304289	+	0	NA	intron (NR_027850, intron 4 of 10)	intron (NR_027850, intron 4 of 10)	34563	NM_006554	10651	Hs.470728	NM_006554	ENSG00000128654	MTX2	-	metaxin 2	protein-coding	0.003026	0.283988	
chunk0136_77_1	chr4	2222202	2222613	+	0	NA	intron (NM_181808, intron 3 of 25)	AluJb|SINE|Alu	19757	NM_001303143	79441	Hs.665869	NM_024511	ENSG00000214367	HAUS3	C4orf15|IT1|dgt3	HAUS augmin like complex subunit 3	protein-coding	0.012165	0.475728	
chunk0053_298_1	chr13	33753898	33754352	+	0	NA	Intergenic	MIR|SINE|MIR	-63944	NM_181558	5983	Hs.115474	NM_002915	ENSG00000133119	RFC3	RFC38	replication factor C subunit 3	protein-coding	0.006608	0.391209	
chunk0152_394_1	chr5	64765698	64766161	+	0	NA	intron (NM_173829, intron 1 of 4)	intron (NM_173829, intron 1 of 4)	2740	NM_173829	285672	Hs.69504	NM_173829	ENSG00000153006	SREK1IP1	P18SRP|SFRS12IP1	SREK1 interacting protein 1	protein-coding	0.004320	0.428879	151(ATGACACTGTGTCCTC,+,0.00)
chunk0036_237_1	chr11	64240964	64241278	+	0	NA	promoter-TSS (NM_001135208)	promoter-TSS (NM_001135208)	-11	NM_001135208	2286	Hs.227729	NM_004470	ENSG00000173486	FKBP2	FKBP-13|FKBP13|PPIase	FKBP prolyl isomerase 2	protein-coding	0.117834	0.739683	
chunk0047_335_1	chr12	74544642	74545020	+	0	NA	Intergenic	Intergenic	7060	NM_001136262	552889	Hs.744849	NM_001136262	ENSG00000253719	ATXN7L3B	lnc-SCA7	ataxin 7 like 3B	protein-coding	0.002646	0.271768	142(TAGAACTTTCTGTTCA,-,0.00),143(AGAACTTTCTGTTCAT,+,0.00)
chunk0009_371_1	chr1	109876545	109877201	+	0	NA	Intergenic	Intergenic	-33738	NM_172210	1435	Hs.173894	NM_000757	ENSG00000184371	CSF1	CSF-1|MCSF	colony stimulating factor 1	protein-coding	0.004573	0.445967	
chunk0156_357_1	chr5	112362553	112362838	+	0	NA	intron (NM_022140, intron 1 of 22)	intron (NM_022140, intron 1 of 22)	56618	NM_022140	64097	Hs.584954	NM_022140	ENSG00000129595	EPB41L4A	EPB41L4|NBL4	erythrocyte membrane protein band 4.1 like 4A	protein-coding	0.010526	0.314685	
chunk0123_202_1	chr3	44865819	44866056	+	0	NA	TTS (NM_144638)	TTS (NM_144638)	4028	NM_144638	131616	Hs.646856	NM_144638	ENSG00000169964	TMEM42	-	transmembrane protein 42	protein-coding	0.004219	0.457983	
chunk0140_183_1	chr4	69836430	69836872	+	0	NA	Intergenic	Intergenic	23501	NM_005420	6783	Hs.479898	NM_005420	ENSG00000109193	SULT1E1	EST|EST-1|ST1E1|STE	sulfotransferase family 1E member 1	protein-coding	0.000000	0.311512	
chunk0190_25_1	chr8	29185253	29185819	+	0	NA	intron (NM_015254, intron 6 of 39)	L3|LINE|CR1	77557	NM_015254	23303	Hs.444767	NM_015254	ENSG00000197892	KIF13B	GAKIN	kinesin family member 13B	protein-coding	0.003534	0.409171	
chunk0020_244_1	chr1	236001583	236002093	+	0	NA	intron (NM_002508, intron 12 of 19)	intron (NM_002508, intron 12 of 19)	63343	NM_002508	4811	Hs.356624	NM_002508	ENSG00000116962	NID1	NID	nidogen 1	protein-coding	0.013725	0.471624	
chunk0062_255_1	chr14	71623960	71624164	+	0	NA	exon (NM_015556, exon 4 of 22)	exon (NM_015556, exon 4 of 22)	36491	NM_001284247	26037	Hs.654657	NM_015556	ENSG00000197555	SIPA1L1	E6TP1|SPAR1	signal induced proliferation associated 1 like 1	protein-coding	0.029412	0.570732	
chunk0158_431_1	chr5	135362140	135362494	+	0	NA	intron (NM_138609, intron 4 of 8)	L1MD3|LINE|L1	36921	NM_138609	9555	Hs.420272	NM_004893	ENSG00000113648	H2AFY	H2A.y|H2A/y|H2AF12M|MACROH2A1.1|mH2A1|macroH2A1.2	H2A histone family member Y	protein-coding	0.005650	0.346479	192(AAGAACTCTCTGTACT,-,0.00),193(AGAACTCTCTGTACTA,+,0.00)
chunk0110_53_1	chr20	10761695	10762194	+	0	NA	Intergenic	Intergenic	8854	NR_110611	101929395	Hs.244862	NR_110611		LINC01752	-	long intergenic non-protein coding RNA 1752	ncRNA	0.018036	0.464000	
chunk0113_389_1	chr20	60029195	60029569	+	0	NA	Intergenic	Intergenic	-26543	NM_173644									0.024064	0.410667	
chunk0127_370_1	chr3	101878885	101879329	+	0	NA	Intergenic	Intergenic	29593	NM_031419	64332	Hs.319171	NM_031419	ENSG00000144802	NFKBIZ	IKBZ|INAP|MAIL	NFKB inhibitor zeta	protein-coding	0.002252	0.339326	
chunk0082_357_1	chr17	60161895	60162221	+	0	NA	Intergenic	Intergenic	12117	NM_000717	762	Hs.89485	NM_000717	ENSG00000167434	CA4	CAIV|Car4|RP17	carbonic anhydrase 4	protein-coding	0.012270	0.629969	194(GGGCACAGCTTGTCCA,-,0.00),195(GGCACAGCTTGTCCAG,+,0.00)
chunk0189_16_1	chr8	19519680	19519879	+	0	NA	intron (NR_024040, intron 2 of 9)	intron (NR_024040, intron 2 of 9)	82766	NM_001130518	55790	Hs.613729	NM_018371	ENSG00000147408	CSGALNACT1	CSGalNAcT-1|ChGn|ChGn-1|beta4GalNAcT	chondroitin sulfate N-acetylgalactosaminyltransferase 1	protein-coding	0.000000	0.520000	
chunk0054_260_1	chr13	46421148	46421347	+	0	NA	Intergenic	LTR52|LTR|ERVL	-31205	NM_001286761	80183	Hs.98117	NM_025113	ENSG00000102445	RUBCNL	C13orf18|KIAA0226L|PACER	rubicon like autophagy enhancer	protein-coding	0.005025	0.325000	
chunk0068_29_1	chr15	50908866	50909177	+	0	NA	intron (NM_007347, intron 1 of 20)	CpG	349	NM_001252127	23431	Hs.413366	NM_007347	ENSG00000081014	AP4E1	CPSQ4|SPG51|STUT1	adaptor related protein complex 4 subunit epsilon 1	protein-coding	0.067524	0.650641	
chunk0179_11_1	chr7	42479679	42480210	+	0	NA	Intergenic	Intergenic	226503	NR_110833	101928795	Hs.566753	NR_110833	ENSG00000238284	LINC01448	-	long intergenic non-protein coding RNA 1448	ncRNA	0.009416	0.383459	
chunk0086_394_1	chr18	26657129	26657506	+	0	NA	promoter-TSS (NM_001258222)	promoter-TSS (NM_001258222)	84	NM_001258222	284252	Hs.526630	NM_198991	ENSG00000134504	KCTD1	C18orf5	potassium channel tetramerization domain containing 1	protein-coding	0.076923	0.587302	
chunk0080_198_1	chr17	29138996	29139204	+	0	NA	intron (NM_203318, intron 2 of 40)	(CCAGCC)n|Simple_repeat|Simple_repeat	41289	NM_078471	399687	Hs.462590	NM_078471	ENSG00000196535	MYO18A	MAJN|MYSPDZ|SP-R210|SPR210	myosin XVIIIA	protein-coding	0.024038	0.645933	54(AGGGACAACCTGGCCC,-,0.00)
chunk0163_425_1	chr6	17159099	17159746	+	0	NA	Intergenic	Intergenic	57164	NM_001190766	401236	Hs.677399	NM_001190766	ENSG00000230873	STMND1	-	stathmin domain containing 1	protein-coding	0.007728	0.410494	
chunk0105_200_1	chr2	187737569	187737973	+	0	NA	Intergenic	Intergenic	-183279	NM_001032281	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.002475	0.313580	
chunk0140_225_1	chr4	71063683	71064359	+	0	NA	Intergenic	L1MA3|LINE|L1	70473	NM_000788	1633	Hs.709	NM_000788	ENSG00000156136	DCK	-	deoxycytidine kinase	protein-coding	0.001479	0.335303	
chunk0091_241_1	chr19	10719337	10719708	+	0	NA	intron (NM_001005360, intron 1 of 20)	intron (NM_001005360, intron 1 of 20)	1118	NR_030368	693223		NR_030368	ENSG00000207972	MIR638	MIRN638|hsa-mir-638	microRNA 638	ncRNA	0.021563	0.569892	223(GAGAACAGCCCGTGCA,-,0.00),224(AGAACAGCCCGTGCAG,+,0.00)
chunk0016_180_1	chr1	198091291	198091763	+	0	NA	Intergenic	L2a|LINE|L2	-65451	NM_133494	140609	Hs.24119	NM_133494	ENSG00000151414	NEK7	-	NIMA related kinase 7	protein-coding	0.004237	0.486258	
chunk0003_150_1	chr1	33048401	33048797	+	0	NA	Intergenic	MLT1I|LTR|ERVL-MaLR	-11688	NM_001199199	204	Hs.470907	NM_001625	ENSG00000004455	AK2	ADK2	adenylate kinase 2	protein-coding	0.007576	0.458438	
chunk0071_4_1	chr15	78695838	78696098	+	0	NA	Intergenic	Intergenic	-54723	NM_001256567	1143	Hs.624178	NM_000750	ENSG00000117971	CHRNB4	-	cholinergic receptor nicotinic beta 4 subunit	protein-coding	0.007692	0.532567	
chunk0101_116_1	chr2	126238314	126238596	+	0	NA	Intergenic	Intergenic	-417480	NM_002101	2995	Hs.59138	NM_002101	ENSG00000136732	GYPC	CD236|CD236R|GE|GE:GPC:GPD:GYPD|GPC|GPD|GYPD|PAS-2|PAS-2'	glycophorin C (Gerbich blood group)	protein-coding	0.010638	0.455830	
chunk0071_293_1	chr15	85910698	85911287	+	0	NA	Intergenic	Intergenic	85357	NR_049805	100847084		NR_049805	ENSG00000264406	MIR548AP	-	microRNA 548ap	ncRNA	0.008489	0.469492	
chunk0211_164_1	chrX	114813817	114814040	+	0	NA	intron (NM_001256760, intron 5 of 6)	L2c|LINE|L2	-9526	NR_029955	554212		NR_029955	ENSG00000199001	MIR448	MIRN448|hsa-mir-448|miRNA448	microRNA 448	ncRNA	0.000000	0.334821	
chunk0199_115_1	chr9	3431849	3432432	+	0	NA	intron (NM_001282116, intron 1 of 16)	Tigger2|DNA|TcMar-Tigger	-36544	NM_002919	5991	Hs.136829	NM_002919	ENSG00000080298	RFX3	-	regulatory factor X3	protein-coding	0.008576	0.414384	
chunk0107_381_1	chr2	223258505	223258994	+	0	NA	Intergenic	L1P2|LINE|L1	206819	NM_080671	23704	Hs.348522	NM_080671	ENSG00000152049	KCNE4	MIRP3	potassium voltage-gated channel subfamily E regulatory subunit 4	protein-coding	0.002045	0.471429	
chunk0169_14_1	chr6	96582822	96583459	+	0	NA	intron (NM_020482, intron 2 of 6)	intron (NM_020482, intron 2 of 6)	20592	NM_020482	9457	Hs.632608	NM_020482	ENSG00000112214	FHL5	1700027G07Rik|ACT|FHL-5|dJ393D12.2	four and a half LIM domains 5	protein-coding	0.006279	0.338558	
chunk0134_289_1	chr3	179907640	179908375	+	0	NA	intron (NR_110061, intron 3 of 3)	intron (NR_110061, intron 3 of 3)	8470	NR_110061	101928790	Hs.667247	NR_110059	ENSG00000244302	PEX5L-AS2	-	PEX5L antisense RNA 2	ncRNA	0.005442	0.422554	
chunk0205_449_1	chr9	115495281	115495713	+	0	NA	Intergenic	Intergenic	248742	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.009259	0.381062	
chunk0163_100_1	chr6	9627918	9628549	+	0	NA	Intergenic	MER72|LTR|ERV1	-784085	NR_033910	100130275	Hs.661431	NR_033910		TFAP2A-AS1	-	TFAP2A antisense RNA 1	ncRNA	0.006339	0.419304	
chunk0201_84_1	chr9	34575725	34576217	+	0	NA	intron (NM_001842, intron 1 of 8)	intron (NM_001842, intron 1 of 8)	7959	NR_024369	415056	Hs.734229	NR_024369		CNTFR-AS1	-	CNTFR antisense RNA 1	ncRNA	0.028455	0.565923	
chunk0045_312_1	chr12	50687082	50687335	+	0	NA	intron (NM_173602, intron 12 of 37)	MIRb|SINE|MIR	-76798	NM_005171	466	Hs.648565	NM_005171	ENSG00000123268	ATF1	EWS-ATF1|FUS/ATF-1|TREB36	activating transcription factor 1	protein-coding	0.003953	0.397638	
chunk0099_448_1	chr2	103476091	103476442	+	0	NA	Intergenic	PABL_A-int|LTR|ERV1	714235	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.000000	0.394886	
chunk0197_269_1	chr8	123755038	123755354	+	0	NA	Intergenic	MER52A|LTR|ERV1	-13446	NM_144963	157769	Hs.459174	NM_144963	ENSG00000176853	FAM91A1	-	family with sequence similarity 91 member A1	protein-coding	0.015823	0.615142	
chunk0028_381_1	chr10	92892249	92892781	+	0	NA	intron (NM_019053, intron 1 of 21)	MER77|LTR|ERVL	44047	NM_019053	54536	Hs.655657	NM_019053	ENSG00000138190	EXOC6	EXOC6A|SEC15|SEC15L|SEC15L1|SEC15L3|Sec15p	exocyst complex component 6	protein-coding	0.007519	0.478424	
chunk0110_45_1	chr20	10589865	10590353	+	0	NA	intron (NM_001009608, intron 4 of 7)	L2a|LINE|L2	59586	NR_106930	102465525		NR_106930	ENSG00000273745	MIR6870	hsa-mir-6870	microRNA 6870	ncRNA	0.004098	0.263804	
chunk0031_217_1	chr10	125961800	125962105	+	0	NA	intron (NM_145235, intron 1 of 10)	AluJo|SINE|Alu	11321	NR_102707	101410540	Hs.557889	NR_102707	ENSG00000233409	FANK1-AS1	-	FANK1 antisense RNA 1	ncRNA	0.000000	0.431373	
chunk0145_329_1	chr4	150722649	150723373	+	0	NA	intron (NM_001199282, intron 36 of 56)	L1MA5|LINE|L1	141086	NM_006439	10586	Hs.584852	NM_006439	ENSG00000181541	MAB21L2	MCOPS14|MCSKS14	mab-21 like 2	protein-coding	0.012431	0.502069	
chunk0054_186_1	chr13	44849246	44849848	+	0	NA	Intergenic	Intergenic	-39917	NR_038433	144817	Hs.585616	NR_038433	ENSG00000235097	LINC00330	NCRNA00330	long intergenic non-protein coding RNA 330	ncRNA	0.011628	0.404643	383(GAGAACACCATGTTCC,-,0.00),384(AGAACACCATGTTCCA,+,0.00)
chunk0116_12_1	chr21	32771731	32772239	+	0	NA	promoter-TSS (NM_013329)	promoter-TSS (NM_013329)	-115	NR_024623	54067	Hs.54725	NM_001006116		C21orf62-AS1	C21orf49	C21orf62 antisense RNA 1	ncRNA	0.064961	0.573674	
chunk0066_228_1	chr15	34084178	34084486	+	0	NA	3' UTR (NM_020154, exon 5 of 5)	3' UTR (NM_020154, exon 5 of 5)	17520	NM_020154	56851	Hs.160565	NM_020154	ENSG00000134153	EMC7	C11orf3|C15orf24|HT022|ORF1-FL1	ER membrane protein complex subunit 7	protein-coding	0.019481	0.446602	
chunk0051_123_1	chr12	115324908	115325764	+	0	NA	Intergenic	Intergenic	-641172	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.005841	0.368728	174(AAGGGCACAATGTTCC,-,0.00),175(AGGGCACAATGTTCCA,+,0.00)
chunk0116_73_1	chr21	34667376	34667926	+	0	NA	Intergenic	Intergenic	-1512	NM_001317009	54102	Hs.473695	NM_053277	ENSG00000159212	CLIC6	CLIC1L	chloride intracellular channel 6	protein-coding	0.010909	0.462795	
chunk0191_190_1	chr8	51677875	51678160	+	0	NA	intron (NM_144651, intron 1 of 22)	intron (NM_144651, intron 1 of 22)	131428	NM_144651	137902	Hs.444882	NM_144651	ENSG00000147485	PXDNL	PMR1|PRM1|VPO2	peroxidasin like	protein-coding	0.007018	0.409091	
chunk0016_266_1	chr1	200372833	200373058	+	0	NA	intron (NR_040064, intron 2 of 4)	intron (NR_040064, intron 2 of 4)	847	NR_040064	554279	Hs.434694	NR_040064	ENSG00000203721	LINC00862	C1orf98|SMIM16	long intergenic non-protein coding RNA 862	ncRNA	0.004444	0.367257	
chunk0124_204_1	chr3	55790717	55791260	+	0	NA	intron (NR_132749, intron 13 of 17)	MIRb|SINE|MIR	61606	NR_037502	100500875		NR_037502	ENSG00000264013	MIR3938	-	microRNA 3938	ncRNA	0.005525	0.420956	
chunk0120_83_1	chr3	3686409	3686986	+	0	NA	Intergenic	Intergenic	-112740	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.012132	0.339100	
chunk0212_171_1	chrX	132555610	132555867	+	0	NA	Intergenic	L1MA6|LINE|L1	-65770	NM_001170704	55796	Hs.105134	NM_018388	ENSG00000076770	MBNL3	CHCR|MBLX|MBLX39|MBXL	muscleblind like splicing regulator 3	protein-coding	0.003891	0.321705	
chunk0004_7_1	chr1	41938376	41938790	+	0	NA	intron (NR_038261, intron 1 of 3)	intron (NR_038261, intron 1 of 3)	-19758	NR_038260	59269	Hs.403972	NM_024503	ENSG00000127124	HIVEP3	KBP-1|KBP1|KRC|SHN3|Schnurri-3|ZAS3|ZNF40C	human immunodeficiency virus type I enhancer binding protein 3	protein-coding	0.000000	0.400000	
chunk0034_92_1	chr11	27477819	27478612	+	0	NA	intron (NR_131170, intron 3 of 3)	MER58A|DNA|hAT-Charlie	-5428	NM_018490	55366	Hs.502176	NM_018490	ENSG00000205213	LGR4	BNMD17|GPR48	leucine rich repeat containing G protein-coupled receptor 4	protein-coding	0.005044	0.397985	499(AAGGACAGGATCTTCC,-,0.00),500(AGGACAGGATCTTCCT,+,0.00)
chunk0106_136_1	chr2	199955403	199955639	+	0	NA	non-coding (NR_004862, exon 1 of 8)	non-coding (NR_004862, exon 1 of 8)	204	NM_024520	79568	Hs.154494	NM_024520	ENSG00000162972	MAIP1	C2orf47	matrix AAA peptidase interacting protein 1	protein-coding	0.097458	0.670886	
chunk0167_134_1	chr6	62052026	62052322	+	0	NA	intron (NM_152688, intron 2 of 8)	L1MA9|LINE|L1	234021	NM_152688	202559	Hs.519794	NM_152688	ENSG00000112232	KHDRBS2	SLM-1|SLM1	KH RNA binding domain containing, signal transduction associated 2	protein-coding	0.000000	0.343434	
chunk0065_250_1	chr14	101484164	101484676	+	0	NA	Intergenic	L1MA4|LINE|L1	71256	NR_002770	64150	Hs.525597	NR_002770	ENSG00000258498	DIO3OS	C14orf134|DIO3-AS1|DIO3-OS|NCRNA00041	DIO3 opposite strand upstream RNA	ncRNA	0.003906	0.380117	
chunk0200_102_1	chr9	16731827	16732232	+	0	NA	intron (NM_017637, intron 2 of 6)	intron (NM_017637, intron 2 of 6)	138759	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.004938	0.332512	
chunk0109_68_1	chr20	1427753	1428234	+	0	NA	Intergenic	L1MD2|LINE|L1	-34821	NR_037661	100528031	Hs.471933	NR_037661		FKBP1A-SDCBP2	-	FKBP1A-SDCBP2 readthrough (NMD candidate)	ncRNA	0.008316	0.475104	
chunk0147_304_1	chr4	184795159	184795358	+	0	NA	intron (NM_001286712, intron 2 of 21)	intron (NM_001286712, intron 2 of 21)	3788	NR_003542	643036	Hs.689630	NR_003542	ENSG00000249138	SLED1	-	proteoglycan 3, pro eosinophil major basic protein 2 pseudogene	pseudo	0.020101	0.430000	
chunk0085_271_1	chr18	7754718	7755415	+	0	NA	intron (NM_001105244, intron 1 of 32)	intron (NM_001105244, intron 1 of 32)	187750	NM_002845	5797	Hs.49774	NM_002845	ENSG00000173482	PTPRM	PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu	protein tyrosine phosphatase receptor type M	protein-coding	0.010043	0.444126	244(CTGAGCAGACTGTGCT,-,0.00),245(TGAGCAGACTGTGCTG,+,0.00)
chunk0002_363_1	chr1	26080012	26080631	+	0	NA	Intergenic	L1ME3A|LINE|L1	-12687	NM_032588	84676	Hs.279709	NM_032588	ENSG00000158022	TRIM63	IRF|MURF1|MURF2|RNF28|SMRZ	tripartite motif containing 63	protein-coding	0.011309	0.391935	
chunk0204_463_1	chr9	104740818	104741300	+	0	NA	Intergenic	L3|LINE|CR1	-6629	NM_015469	25934	Hs.530275	NM_015469	ENSG00000136783	NIPSNAP3A	HSPC299|NIPSNAP4|TASSC	nipsnap homolog 3A	protein-coding	0.004149	0.327122	
chunk0162_439_1	chr5	180584568	180585215	+	0	NA	Intergenic	AluSg|SINE|Alu	6596	NM_052863	92304	Hs.62492	NM_052863	ENSG00000161055	SCGB3A1	HIN-1|HIN1|LU105|PnSP-2|UGRP2	secretoglobin family 3A member 1	protein-coding	0.018547	0.422840	405(AGGGACACTTTGTCTC,-,0.00)
chunk0102_84_1	chr2	143336759	143337083	+	0	NA	intron (NM_018460, intron 6 of 13)	L2b|LINE|L2	207591	NM_018460	55843	Hs.171011	NM_018460	ENSG00000075884	ARHGAP15	BM046	Rho GTPase activating protein 15	protein-coding	0.000000	0.433846	
chunk0206_19_1	chr9	115808657	115808856	+	0	NA	Intergenic	(TTTTCC)n|Simple_repeat|Simple_repeat	-64517	NR_109805	101928775	Hs.522362	NR_109805	ENSG00000228714	LOC101928775	-	uncharacterized LOC101928775	ncRNA	0.010050	0.450000	
chunk0138_20_1	chr4	30763238	30763688	+	0	NA	intron (NM_032457, intron 1 of 2)	intron (NM_032457, intron 1 of 2)	43048	NM_002589	5099	Hs.479439	NM_002589	ENSG00000169851	PCDH7	BH-Pcdh|BHPCDH|PPP1R120	protocadherin 7	protein-coding	0.006667	0.323725	
chunk0026_116_1	chr10	61967681	61968227	+	0	NA	intron (NM_032199, intron 3 of 9)	intron (NM_032199, intron 3 of 9)	66700	NM_032199	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.009158	0.371115	
chunk0199_178_1	chr9	4594608	4594824	+	0	NA	Intergenic	Intergenic	-67578	NM_203453	403313	Hs.107510	NM_203453	ENSG00000205808	PLPP6	PDP1|PPAPDC2|PSDP|bA6J24.6	phospholipid phosphatase 6	protein-coding	0.013889	0.442396	136(CTGGACATGGTGTACT,-,0.00),137(TGGACATGGTGTACTC,+,0.00)
chunk0019_316_1	chr1	229086712	229086964	+	0	NA	Intergenic	L1MB2|LINE|L1	87963	NR_039659	100616234		NR_039659	ENSG00000283468	MIR4454	-	microRNA 4454	ncRNA	0.003968	0.430830	
chunk0070_439_1	chr15	78216579	78217067	+	0	NA	intron (NM_001199377, intron 1 of 13)	intron (NM_001199377, intron 1 of 13)	17884	NM_015162	23205	Hs.655760	NM_015162	ENSG00000103740	ACSBG1	BG|BG1|BGM|GR-LACS|LPD	acyl-CoA synthetase bubblegum family member 1	protein-coding	0.002049	0.523517	
chunk0201_205_1	chr9	37116601	37116924	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-3710	NM_032226	84186	Hs.654700	NM_032226	ENSG00000147905	ZCCHC7	AIR1|HSPC086	zinc finger CCHC-type containing 7	protein-coding	0.006192	0.373457	
chunk0038_423_1	chr11	94449304	94449911	+	0	NA	intron (NM_005591, intron 14 of 19)	Tigger3a|DNA|TcMar-Tigger	16973	NR_031630	100302275		NR_031630	ENSG00000221230	MIR548L	MIRN548L|hsa-mir-548l	microRNA 548l	ncRNA	0.004942	0.363487	
chunk0114_341_1	chr21	17764789	17765194	+	0	NA	Intergenic	Intergenic	27518	NR_038870	246312	Hs.473425	NR_038870	ENSG00000240770	C21orf91-OT1	D21S2089E|NCRNA00285	C21orf91 overlapping transcript 1	ncRNA	0.007407	0.431034	
chunk0097_188_1	chr2	50478064	50478403	+	0	NA	intron (NM_001135659, intron 16 of 23)	intron (NM_001135659, intron 16 of 23)	-130477	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.314706	
chunk0104_278_1	chr2	178193412	178193935	+	0	NA	promoter-TSS (NM_001201481)	promoter-TSS (NM_001201481)	-808	NM_001201481	114880	Hs.318775	NM_032523	ENSG00000079156	OSBPL6	ORP6	oxysterol binding protein like 6	protein-coding	0.034417	0.503817	
chunk0177_408_1	chr7	27526118	27526725	+	0	NA	intron (NM_152740, intron 7 of 7)	intron (NM_152740, intron 7 of 7)	-89553	NR_122123	790953	Hs.571330	NR_122122		TSL	-	testis-expressed, seven-twelve, leukemia	ncRNA	0.009885	0.391447	
chunk0021_359_1	chr1	246300770	246301633	+	0	NA	intron (NM_001167740, intron 5 of 11)	intron (NM_001167740, intron 5 of 11)	116211	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.006952	0.366898	
chunk0023_375_1	chr10	30348777	30349149	+	0	NA	intron (NM_018109, intron 1 of 8)	intron (NM_018109, intron 1 of 8)	375	NM_018109	55149	Hs.173946	NM_018109	ENSG00000107951	MTPAP	PAPD1|SPAX4|TENT6	mitochondrial poly(A) polymerase	protein-coding	0.040323	0.549598	
chunk0144_187_1	chr4	133494068	133494675	+	0	NA	Intergenic	Intergenic	345081	NM_020815	57575	Hs.192859	NM_020815	ENSG00000138650	PCDH10	OL-PCDH|PCDH19	protocadherin 10	protein-coding	0.001647	0.291118	
chunk0087_51_1	chr18	31490887	31491099	+	0	NA	Intergenic	Intergenic	-7071	NM_001943	1829	Hs.412597	NM_001943	ENSG00000046604	DSG2	CDHF5|HDGC	desmoglein 2	protein-coding	0.000000	0.328638	
chunk0077_56_1	chr16	76438680	76439232	+	0	NA	intron (NM_138994, intron 4 of 22)	intron (NM_138994, intron 4 of 22)	129118	NM_138994	85445	Hs.461389	NM_033401	ENSG00000152910	CNTNAP4	CASPR4	contactin associated protein like 4	protein-coding	0.007246	0.386980	
chunk0113_417_1	chr20	61786169	61786804	+	0	NA	intron (NM_001252339, intron 3 of 14)	intron (NM_001252339, intron 3 of 14)	167176	NR_031658	100302168		NR_031658	ENSG00000284193	MIR1257	MIRN1257|hsa-mir-1257	microRNA 1257	ncRNA	0.028346	0.474843	326(AGGAACAGGCAGGCCC,-,0.00)
chunk0007_67_1	chr1	78237598	78237894	+	0	NA	intron (NR_027310, intron 1 of 5)	MamTip2|DNA|hAT-Tip100	8147	NR_027310	149047	Hs.352665	NM_144700	ENSG00000237413	MGC27382	-	uncharacterized MGC27382	ncRNA	0.003378	0.471380	
chunk0143_330_1	chr4	120086430	120086892	+	0	NA	Intergenic	Intergenic	-19803	NM_002358	4085	Hs.591697	NM_002358	ENSG00000164109	MAD2L1	HSMAD2|MAD2	mitotic arrest deficient 2 like 1	protein-coding	0.008658	0.410367	
chunk0111_171_1	chr20	25255297	25255772	+	0	NA	intron (NM_002862, intron 1 of 19)	intron (NM_002862, intron 1 of 19)	7464	NM_002862	5834	Hs.368157	NM_002862	ENSG00000100994	PYGB	GPBB	glycogen phosphorylase B	protein-coding	0.016842	0.584034	236(AGGGACACTCTGCCCT,-,0.00),237(GGGACACTCTGCCCTG,+,0.00)
chunk0058_267_1	chr14	26059527	26059811	+	0	NA	Intergenic	L2-3_Crp|LINE|L2	538085	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.007042	0.417544	209(AAGAACAGATTGTATT,-,0.00),210(AGAACAGATTGTATTT,+,0.00)
chunk0058_276_1	chr14	26286646	26287244	+	0	NA	Intergenic	Intergenic	310809	NM_006489	4857	Hs.31588	NM_002515	ENSG00000139910	NOVA1	Nova-1	NOVA alternative splicing regulator 1	protein-coding	0.003344	0.357262	
chunk0114_259_1	chr21	16168939	16169432	+	0	NA	intron (NR_027790, intron 2 of 7)	intron (NR_027790, intron 2 of 7)	-25194	NR_027791	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.010142	0.338057	
chunk0114_404_1	chr20	63707748	63708052	+	0	NA	promoter-TSS (NM_001267548)	promoter-TSS (NM_001267548)	-47	NM_001267548	10139	Hs.389277	NM_003224	ENSG00000101246	ARFRP1	ARL18|ARP|Arp1	ADP ribosylation factor related protein 1	protein-coding	0.134868	0.754098	
chunk0021_241_1	chr1	242610240	242610693	+	0	NA	Intergenic	MIR|SINE|MIR	-85770	NM_152666	200150	Hs.672452	NM_152666	ENSG00000180287	PLD5	PLDC	phospholipase D family member 5	protein-coding	0.011038	0.381057	145(AGGGACAAGGTGTTCC,-,0.00),146(GGGACAAGGTGTTCCT,+,0.00)
chunk0030_420_1	chr10	120272147	120272410	+	0	NA	Intergenic	Intergenic	82945	NM_000982	6144	Hs.381123	NM_000982	ENSG00000122026	RPL21	HYPT12|L21	ribosomal protein L21	protein-coding	0.003802	0.378788	120(AAGGACAGCCTGTTCT,-,0.00),121(AGGACAGCCTGTTCTG,+,0.00)
chunk0069_154_1	chr15	62513706	62514404	+	0	NA	Intergenic	Intergenic	131126	NR_026897	197003	Hs.352253	NM_152648	ENSG00000259458	MGC15885	-	uncharacterized protein MGC15885	ncRNA	0.007163	0.379113	384(CAGCACACACTGTACC,-,0.00),385(AGCACACACTGTACCT,+,0.00)
chunk0157_161_1	chr5	118004405	118004652	+	0	NA	intron (NR_104997, intron 2 of 2)	LTR16D1|LTR|ERVL	274167	NR_104997	102467224	Hs.134230	NR_104997		LINC02147	-	long intergenic non-protein coding RNA 2147	ncRNA	0.008097	0.391129	181(AAGAACTTCGTGTCCT,-,0.00),182(AGAACTTCGTGTCCTT,+,0.00)
chunk0008_269_1	chr1	94646498	94646788	+	0	NA	Intergenic	Intergenic	99257	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.003448	0.487973	
chunk0036_150_1	chr11	62238111	62238615	+	0	NA	Intergenic	L2b|LINE|L2	-3889	NM_006551	10647	Hs.204096	NM_006551	ENSG00000124935	SCGB1D2	LIPB|LPHB|LPNB	secretoglobin family 1D member 2	protein-coding	0.011905	0.441584	
chunk0129_115_1	chr3	119795849	119796134	+	0	NA	intron (NM_022002, intron 1 of 8)	intron (NM_022002, intron 1 of 8)	13281	NM_022002	8856	Hs.7303	NM_003889	ENSG00000144852	NR1I2	BXR|ONR1|PAR|PAR1|PAR2|PARq|PRR|PXR|SAR|SXR	nuclear receptor subfamily 1 group I member 2	protein-coding	0.003509	0.468531	
chunk0208_37_1	chrX	11358962	11359410	+	0	NA	intron (NR_109776, intron 1 of 14)	intron (NR_109776, intron 1 of 14)	-40500	NR_049865	100847063		NR_049865	ENSG00000263652	MIR548AX	-	microRNA 548ax	ncRNA	0.002232	0.305122	
chunk0131_246_1	chr3	149511407	149511671	+	0	NA	Intergenic	Intergenic	36958	NM_004617	7104	Hs.133527	NM_004617	ENSG00000169903	TM4SF4	ILTMP|il-TMP	transmembrane 4 L six family member 4	protein-coding	0.000000	0.437736	
chunk0057_450_1	chr13	110809750	110810507	+	0	NA	Intergenic	L1ME4b|LINE|L1	60180	NR_027701	283487	Hs.245390	NM_178514	ENSG00000255874	LINC00346	C13orf29|NCRNA00346	long intergenic non-protein coding RNA 346	ncRNA	0.014531	0.362797	
chunk0204_113_1	chr9	94966457	94966656	+	0	NA	intron (NM_032823, intron 7 of 14)	intron (NM_032823, intron 7 of 14)	-98794	NR_106729	102466518		NR_106729	ENSG00000274115	MIR6081	hsa-mir-6081	microRNA 6081	ncRNA	0.000000	0.265000	
chunk0147_441_1	chr4	187590942	187591399	+	0	NA	intron (NR_110436, intron 2 of 2)	L2b|LINE|L2	81471	NR_110436	100506272	Hs.508163	NR_110436	ENSG00000250590	LINC02492	-	long intergenic non-protein coding RNA 2492	ncRNA	0.002188	0.353712	
chunk0053_239_1	chr13	32643483	32643895	+	0	NA	intron (NM_015032, intron 1 of 34)	Tigger3a|DNA|TcMar-Tigger	57262	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.009709	0.360775	
chunk0093_318_1	chr19	53792785	53793124	+	0	NA	TTS (NM_144687)	TTS (NM_144687)	4249	NR_029866	442918		NR_029866	ENSG00000199143	MIR373	MIRN373|hsa-mir-373|miRNA373|mir-373	microRNA 373	ncRNA	0.008850	0.520588	
chunk0133_359_1	chr3	173438694	173438900	+	0	NA	intron (NM_014932, intron 2 of 6)	intron (NM_014932, intron 2 of 6)	40349	NM_014932	22871	Hs.478289	NM_014932	ENSG00000169760	NLGN1	NL1	neuroligin 1	protein-coding	0.009709	0.333333	97(GGGTACTGGATGTTCC,-,0.00),98(GGTACTGGATGTTCCT,+,0.00)
chunk0032_408_1	chr11	11909488	11909701	+	0	NA	intron (NM_017944, intron 7 of 26)	L2a|LINE|L2	68171	NM_017944	55031	Hs.577256	NM_017944	ENSG00000170242	USP47	TRFP	ubiquitin specific peptidase 47	protein-coding	0.004695	0.294393	
chunk0113_176_1	chr20	53159741	53159968	+	0	NA	intron (NM_173485, intron 1 of 2)	L2b|LINE|L2	-25429	NM_001193421	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.000000	0.333333	
chunk0113_167_1	chr20	53050564	53051030	+	0	NA	intron (NM_173485, intron 1 of 2)	intron (NM_173485, intron 1 of 2)	78390	NM_173485	128553	Hs.473117	NM_173485	ENSG00000182463	TSHZ2	C20orf17|OVC10-2|TSH2|ZABC2|ZNF218	teashirt zinc finger homeobox 2	protein-coding	0.008584	0.391863	
chunk0134_145_1	chr3	177624546	177624851	+	0	NA	intron (NR_047568, intron 2 of 3)	MLT1J2|LTR|ERVL-MaLR	182777	NR_047568	100505566	Hs.581170	NR_047568		LINC00578	-	long intergenic non-protein coding RNA 578	ncRNA	0.019672	0.441176	
chunk0058_345_1	chr14	28873407	28873708	+	0	NA	Intergenic	Intergenic	100853	NR_026731	387978	Hs.633254	NR_026731	ENSG00000186960	LINC01551	C14orf23|c14_5148	long intergenic non-protein coding RNA 1551	ncRNA	0.003322	0.334437	174(CAAGACACCCTGTCCT,-,0.00),175(AAGACACCCTGTCCTT,+,0.00)
chunk0197_370_1	chr8	126556850	126557132	+	0	NA	exon (NM_174911, exon 2 of 2)	exon (NM_174911, exon 2 of 2)	1475	NM_174911	157638	Hs.124951	NM_174911	ENSG00000168672	LRATD2	BCMP101|FAM84B|NSE2	LRAT domain containing 2	protein-coding	0.095745	0.628975	
chunk0011_304_1	chr1	151739927	151740295	+	0	NA	Intergenic	HERV16-int|LTR|ERVL	18574	NM_001144956	284485	Hs.297967	NM_001144956	ENSG00000178796	RIIAD1	C1orf230|NCRNA00166	regulatory subunit of type II PKA R-subunit (RIIa) domain containing 1	protein-coding	0.008152	0.506775	
chunk0175_241_1	chr7	6496822	6497194	+	0	NA	3' UTR (NM_001145118, exon 22 of 22)	3' UTR (NM_001145118, exon 22 of 22)	-12790	NM_001100603	11014	Hs.654552	NM_006854	ENSG00000136240	KDELR2	ELP-1|ERD2.2	KDEL endoplasmic reticulum protein retention receptor 2	protein-coding	0.010753	0.554960	
chunk0094_235_1	chr2	6988093	6988352	+	0	NA	intron (NM_014746, intron 2 of 8)	L1MC3|LINE|L1	-69540	NR_033997	386597	Hs.559010	NR_033997	ENSG00000228203	RNF144A-AS1	-	RNF144A antisense RNA 1	ncRNA	0.015444	0.365385	104(TAGTACAGAGAGTTCC,-,0.00),105(AGTACAGAGAGTTCCC,+,0.00)
chunk0182_258_1	chr7	97354151	97354630	+	0	NA	Intergenic	Intergenic	237797	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.010438	0.335417	
chunk0083_354_1	chr17	70421006	70421339	+	0	NA	Intergenic	Intergenic	251637	NM_000891	3759	Hs.1547	NM_000891	ENSG00000123700	KCNJ2	ATFB9|HHBIRK1|HHIRK1|IRK1|KIR2.1|LQT7|SQT3	potassium voltage-gated channel subfamily J member 2	protein-coding	0.003003	0.455090	
chunk0195_4_1	chr8	92824331	92824659	+	0	NA	Intergenic	Intergenic	-38435	NR_046114	441369	Hs.521683	NR_046114	ENSG00000248858	FLJ46284	-	uncharacterized LOC441369	ncRNA	0.000000	0.373860	
chunk0098_155_1	chr2	69989122	69989599	+	0	NA	intron (NR_033872, intron 8 of 10)	MIRc|SINE|MIR	-27095	NM_152792	151516	Hs.516253	NM_152792	ENSG00000244617	ASPRV1	MUNO|SASP|SASPase|Taps	aspartic peptidase retroviral like 1	protein-coding	0.016771	0.598326	
chunk0103_399_1	chr2	169062546	169062900	+	0	NA	Intergenic	Intergenic	-4312	NM_001289763	10170	Hs.179608	NM_005771	ENSG00000073737	DHRS9	3-alpha-HSD|3ALPHA-HSD|RDH-E2|RDH-TBE|RDH15|RDHL|RDHTBE|RETSDR8|SDR9C4	dehydrogenase/reductase 9	protein-coding	0.002825	0.425352	
chunk0167_57_1	chr6	55827661	55828135	+	0	NA	intron (NM_021073, intron 1 of 6)	intron (NM_021073, intron 1 of 6)	47679	NM_021073	653	Hs.296648	NM_021073	ENSG00000112175	BMP5	-	bone morphogenetic protein 5	protein-coding	0.002110	0.305263	
chunk0160_195_1	chr5	154682937	154683263	+	0	NA	Intergenic	Intergenic	-2676	NR_031638	100302284		NR_031638	ENSG00000221552	MIR1303	MIRN1303|hsa-mir-1303	microRNA 1303	ncRNA	0.082822	0.681957	
chunk0123_217_1	chr3	45145226	45145501	+	0	NA	intron (NM_022842, intron 1 of 8)	intron (NM_022842, intron 1 of 8)	1059	NM_178181	64866	Hs.476093	NM_022842	ENSG00000163814	CDCP1	CD318|SIMA135|TRASK	CUB domain containing protein 1	protein-coding	0.025455	0.474638	
chunk0136_338_1	chr3	195699718	195700311	+	0	NA	TTS (NR_030296)	TTS (NR_030296)	613	NR_030296	693155		NR_030296	ENSG00000207650	MIR570	MIRN570|hsa-mir-570	microRNA 570	ncRNA	0.011804	0.390572	
chunk0083_428_1	chr17	72488998	72489494	+	0	NA	intron (NR_036488, intron 1 of 3)	intron (NR_036488, intron 1 of 3)	103558	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.020161	0.535211	
chunk0153_397_1	chr5	75338089	75338665	+	0	NA	intron (NM_000859, intron 1 of 19)	intron (NM_000859, intron 1 of 19)	1209	NM_001130996	3156	Hs.628096	NM_000859	ENSG00000113161	HMGCR	LDLCQ3	3-hydroxy-3-methylglutaryl-CoA reductase	protein-coding	0.012153	0.377816	
chunk0130_134_1	chr3	132180073	132180822	+	0	NA	Intergenic	MER91B|DNA|hAT-Tip100	-136920	NM_001292037	55	Hs.433060	NM_001099	ENSG00000014257	ACPP	5'-NT|ACP-3|ACP3	acid phosphatase, prostate	protein-coding	0.004005	0.466667	
chunk0119_347_1	chr22	47129847	47130365	+	0	NA	intron (NM_014346, intron 12 of 12)	intron (NM_014346, intron 12 of 12)	-214064	NR_122047	642757	Hs.632786	NR_122047	ENSG00000280080	TBC1D22A-AS1	-	TBC1D22A antisense RNA 1	ncRNA	0.027027	0.581888	
chunk0048_12_1	chr12	77018788	77019383	+	0	NA	Intergenic	Intergenic	46495	NM_203394	144455	Hs.416375	NM_203394	ENSG00000165891	E2F7	-	E2F transcription factor 7	protein-coding	0.006723	0.382550	
chunk0061_153_1	chr14	59664528	59664875	+	0	NA	intron (NM_021136, intron 3 of 8)	L1MD2|LINE|L1	-17681	NR_049851	100847088		NR_049851	ENSG00000263629	MIR5586	-	microRNA 5586	ncRNA	0.002882	0.301724	
chunk0055_342_1	chr13	69980668	69981251	+	0	NA	intron (NM_020866, intron 1 of 10)	(TTTGTT)n|Simple_repeat|Simple_repeat	-126254	NR_002717	6315	Hs.676453	NR_002717		ATXN8OS	KLHL1AS|NCRNA00003|SCA8	ATXN8 opposite strand lncRNA	ncRNA	0.000000	0.311644	
chunk0119_265_1	chr22	45894061	45894498	+	0	NA	Intergenic	BLACKJACK|DNA|hAT-Blackjack	82849	NM_058238	7477	Hs.512714	NM_058238	ENSG00000188064	WNT7B	-	Wnt family member 7B	protein-coding	0.022883	0.385845	203(GGGAACATCCTGAACC,-,0.00),204(GGAACATCCTGAACCT,+,0.00)
chunk0165_211_1	chr6	35024843	35025083	+	0	NA	intron (NM_015245, intron 11 of 23)	intron (NM_015245, intron 11 of 23)	116447	NM_001093728									0.008333	0.410788	
chunk0091_136_1	chr19	6793374	6793975	+	0	NA	intron (NM_001258206, intron 1 of 25)	LTR47B3|LTR|ERVL	21006	NM_001258207	7409	Hs.116237	NM_005428	ENSG00000141968	VAV1	VAV	vav guanine nucleotide exchange factor 1	protein-coding	0.008319	0.413621	
chunk0198_67_1	chr8	129909835	129910250	+	0	NA	intron (NR_046360, intron 2 of 14)	intron (NR_046360, intron 2 of 14)	29830	NR_046359									0.009639	0.504808	225(ATGGACAGAGTGTCCT,-,0.00),226(TGGACAGAGTGTCCTC,+,0.00)
chunk0148_266_1	chr5	10467037	10467611	+	0	NA	Intergenic	Intergenic	-10713	NR_106747	102465138		NR_106747	ENSG00000277073	MIR6131	hsa-mir-6131	microRNA 6131	ncRNA	0.017422	0.446957	
chunk0069_58_1	chr15	60776896	60777359	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	95558	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.012959	0.349138	
chunk0048_73_1	chr12	78851137	78851528	+	0	NA	Intergenic	Intergenic	-12661	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.002558	0.336735	280(AAGTACTTGCAGTTCT,-,0.00),281(AGTACTTGCAGTTCTT,+,0.00)
chunk0009_135_1	chr1	104541550	104541984	+	0	NA	Intergenic	L2a|LINE|L2	468744	NR_033990	100129138	Hs.514487	NR_033990	ENSG00000215869	LOC100129138	-	THAP domain containing 3 pseudogene	pseudo	0.002304	0.402299	
chunk0013_446_1	chr1	173824155	173824472	+	0	NA	promoter-TSS (NM_018122)	promoter-TSS (NM_018122)	-181	NM_001171182	91687	Hs.531856	NM_033319	ENSG00000120334	CENPL	C1orf155|CENP-L|dJ383J4.3	centromere protein L	protein-coding	0.078864	0.616352	117(AAGGACAGTGCGTCCC,-,0.00),118(AGGACAGTGCGTCCCA,+,0.00)
chunk0108_188_1	chr2	232274480	232274769	+	0	NA	intron (NR_046476, intron 13 of 20)	intron (NR_046476, intron 13 of 20)	101971	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.006920	0.417241	
chunk0006_190_1	chr1	67478149	67478352	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-47810	NM_015640	26135	Hs.530412	NM_015640	ENSG00000142864	SERBP1	CGI-55|CHD3IP|HABP4L|PAI-RBP1|PAIRBP1	SERPINE1 mRNA binding protein 1	protein-coding	0.000000	0.352941	
chunk0154_11_1	chr5	76583227	76583541	+	0	NA	intron (NM_006633, intron 5 of 35)	intron (NM_006633, intron 5 of 35)	-25711	NM_001285462	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.006369	0.336508	
chunk0148_205_1	chr5	8546448	8546853	+	0	NA	Intergenic	Intergenic	85725	NR_039663	100616142		NR_039663	ENSG00000284000	MIR4458	mir-4458	microRNA 4458	ncRNA	0.004938	0.334975	
chunk0089_210_1	chr18	60687586	60688076	+	0	NA	Intergenic	Intergenic	-315063	NM_005912	4160	Hs.532833	NM_005912	ENSG00000166603	MC4R	BMIQ20	melanocortin 4 receptor	protein-coding	0.008163	0.331976	268(TAGAACACACTGTTCT,-,0.00),269(AGAACACACTGTTCTG,+,0.00)
chunk0158_373_1	chr5	134002361	134002665	+	0	NA	intron (NM_003374, intron 1 of 8)	intron (NM_003374, intron 1 of 8)	2453	NR_036624	7416	Hs.519320	NM_003374	ENSG00000213585	VDAC1	PORIN|VDAC-1	voltage dependent anion channel 1	protein-coding	0.006579	0.488525	38(CAGCACAAGCTGTCCA,-,0.00),39(AGCACAAGCTGTCCAT,+,0.00)
chunk0199_172_1	chr9	4573896	4574511	+	0	NA	intron (NM_004170, intron 8 of 11)	intron (NM_004170, intron 8 of 11)	83776	NM_004170	6505	Hs.444915	NM_004170	ENSG00000106688	SLC1A1	DCBXA|EAAC1|EAAT3|SCZD18	solute carrier family 1 member 1	protein-coding	0.004878	0.465909	294(TGGATCATGCTGTGCT,-,0.00),295(GGATCATGCTGTGCTA,+,0.00),326(CAGAACAGCCTGGACC,-,0.00)
chunk0034_173_1	chr11	31022139	31022597	+	0	NA	Intergenic	MLT1C|LTR|ERVL-MaLR	-29682	NM_020869	341019	Hs.127405	NM_020869	ENSG00000170959	DCDC1	DCDC5	doublecortin domain containing 1	protein-coding	0.004367	0.389978	
chunk0042_370_1	chr12	10513375	10513796	+	0	NA	Intergenic	L1ME3F|LINE|L1	-58900	NM_001304448	3821	Hs.512576	NM_002259	ENSG00000134545	KLRC1	CD159A|NKG2|NKG2A	killer cell lectin like receptor C1	protein-coding	0.009501	0.379147	
chunk0038_31_1	chr11	81169528	81169871	+	0	NA	Intergenic	L1PA14|LINE|L1	-406896	NR_120570	101928944	Hs.547927	NR_120570	ENSG00000255178	LINC02720	-	long intergenic non-protein coding RNA 2720	ncRNA	0.000000	0.351744	
chunk0138_94_1	chr4	35770633	35771206	+	0	NA	Intergenic	Intergenic	-473197	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.008726	0.327526	
chunk0119_206_1	chr22	44858724	44859348	+	0	NA	intron (NM_001198726, intron 10 of 10)	MER58A|DNA|hAT-Charlie	106478	NM_001017526	23779	Hs.102336	NM_181335	ENSG00000241484	ARHGAP8	BPGAP1|PP610	Rho GTPase activating protein 8	protein-coding	0.014423	0.507200	
chunk0104_334_1	chr2	179574027	179574716	+	0	NA	intron (NM_152520, intron 3 of 9)	intron (NM_152520, intron 3 of 9)	11535	NR_104234	151126	Hs.655005	NM_152520	ENSG00000144331	ZNF385B	ZNF533	zinc finger protein 385B	protein-coding	0.004354	0.339130	
chunk0112_190_1	chr20	40204430	40204655	+	0	NA	Intergenic	Intergenic	200081	NR_109936	100505663	Hs.559348	NR_109936	ENSG00000237767	LINC01370	HI-LNC25|HILNC25	long intergenic non-protein coding RNA 1370	ncRNA	0.013333	0.411504	
chunk0169_369_1	chr6	107216520	107217244	+	0	NA	intron (NM_020381, intron 4 of 7)	L1MB7|LINE|L1	-102450	NM_001080450	57673	Hs.418045	NM_001080450	ENSG00000178409	BEND3	KIAA1553	BEN domain containing 3	protein-coding	0.011050	0.364138	
chunk0047_214_1	chr12	71663664	71664090	+	0	NA	promoter-TSS (NM_031435)	promoter-TSS (NM_031435)	-20	NM_031435	83591	Hs.245798	NM_031435	ENSG00000173451	THAP2	-	THAP domain containing 2	protein-coding	0.068075	0.578454	
chunk0051_97_1	chr12	114684197	114684714	+	0	NA	promoter-TSS (NM_016569)	promoter-TSS (NM_016569)	-291	NM_016569	6926	Hs.744016	NM_005996	ENSG00000135111	TBX3	TBX3-ISO|UMS|XHL	T-box transcription factor 3	protein-coding	0.090909	0.648649	
chunk0092_441_1	chr19	38551445	38551668	+	0	NA	intron (NM_000540, intron 89 of 105)	L2|LINE|L2	66479	NM_007181	11184	Hs.95424	NM_007181	ENSG00000104814	MAP4K1	HPK1	mitogen-activated protein kinase kinase kinase kinase 1	protein-coding	0.017937	0.540179	
chunk0009_433_1	chr1	111156320	111156519	+	0	NA	intron (NM_001007794, intron 2 of 8)	L1MA5|LINE|L1	-16203	NM_178454	128338	Hs.485606	NM_178454	ENSG00000156171	DRAM2	CORD21|PRO180|TMEM77|WWFQ154	DNA damage regulated autophagy modulator 2	protein-coding	0.005025	0.400000	
chunk0072_2_1	chr16	91382	91805	+	0	NA	intron (NM_001243247, intron 12 of 14)	intron (NM_001243247, intron 12 of 14)	13423	NM_002434	4350	Hs.459596	NM_002434	ENSG00000103152	MPG	AAG|ADPG|APNG|CRA36.1|MDG|Mid1|PIG11|PIG16|anpg	N-methylpurine DNA glycosylase	protein-coding	0.016548	0.514151	
chunk0098_453_1	chr2	82421591	82422166	+	0	NA	Intergenic	Intergenic	-434925	NR_033423	1720	Hs.169235	NR_033423		DHFRP3	-	dihydrofolate reductase pseudogene 3	pseudo	0.005217	0.345486	220(AGGAACACACAGTGTT,-,0.00),221(GGAACACACAGTGTTT,+,0.00)
chunk0125_61_1	chr3	64178296	64178984	+	0	NA	intron (NM_198859, intron 2 of 7)	intron (NM_198859, intron 2 of 7)	-8904	NR_046702	100874243	Hs.670840	NR_046702	ENSG00000226017	PRICKLE2-AS3	-	PRICKLE2 antisense RNA 3	ncRNA	0.002907	0.394775	
chunk0083_288_1	chr17	68758925	68759676	+	0	NA	Intergenic	Intergenic	131146	NR_110825	101928104	Hs.569826	NR_110825	ENSG00000267659	LINC01482	-	long intergenic non-protein coding RNA 1482	ncRNA	0.013316	0.428191	
chunk0182_384_1	chr7	100127128	100127347	+	0	NA	intron (NM_203397, intron 1 of 1)	CpG	540	NM_203397	255374	Hs.632319	NM_203397	ENSG00000214309	MBLAC1	-	metallo-beta-lactamase domain containing 1	protein-coding	0.095890	0.677273	
chunk0194_70_1	chr8	82592695	82592895	+	0	NA	Intergenic	Intergenic	-750509	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.000000	0.293532	72(GAAACAGTCTGTTTCT,+,0.00)
chunk0143_4_1	chr4	105683034	105683511	+	0	NA	exon (NM_020395, exon 8 of 8)	exon (NM_020395, exon 8 of 8)	25452	NM_001142471	57117	Hs.480454	NM_020395	ENSG00000138785	INTS12	INT12|PHF22|SBBI22	integrator complex subunit 12	protein-coding	0.008386	0.387029	
chunk0104_272_1	chr2	178110664	178111201	+	0	NA	Intergenic	Intergenic	-1492	NM_152945	129831	Hs.377257	NM_152945	ENSG00000155636	RBM45	DRB1|RB-1	RNA binding motif protein 45	protein-coding	0.007449	0.420074	
chunk0160_2_1	chr5	148929848	148930446	+	0	NA	Intergenic	Intergenic	103554	NM_000024	154	Hs.2551	NM_000024	ENSG00000169252	ADRB2	ADRB2R|ADRBR|B2AR|BAR|BETA2AR	adrenoceptor beta 2	protein-coding	0.006689	0.402337	275(GAGAACAGCATGTACA,-,0.00),276(AGAACAGCATGTACAA,+,0.00)
chunk0056_384_1	chr13	93201814	93202550	+	0	NA	Intergenic	Intergenic	-24643	NM_005708	10082	Hs.444329	NM_005708	ENSG00000183098	GPC6	OMIMD1	glypican 6	protein-coding	0.002717	0.324288	
chunk0096_54_1	chr2	27282963	27283416	+	0	NA	intron (NM_187841, intron 1 of 8)	intron (NM_187841, intron 1 of 8)	760	NM_187841	57159	Hs.516036	NM_032546	ENSG00000138100	TRIM54	MURF|MURF-3|RNF30|muRF3	tripartite motif containing 54	protein-coding	0.013245	0.491189	139(AGGTACAGCCTGTGCA,-,0.00),140(GGTACAGCCTGTGCAT,+,0.00)
chunk0177_402_1	chr7	27424868	27425067	+	0	NA	Intergenic	Intergenic	-177738	NR_120507	101410536	Hs.687800	NR_120507	ENSG00000253405	EVX1-AS	EVX1-AS1	EVX1 antisense RNA	ncRNA	0.005025	0.455000	
chunk0061_455_1	chr14	65961783	65962586	+	0	NA	Intergenic	Intergenic	491082	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.016189	0.482587	482(GAGAACAAAATGTTCC,-,0.00),483(AGAACAAAATGTTCCC,+,0.00)
chunk0050_188_1	chr12	103956957	103957156	+	0	NA	intron (NM_001135570, intron 1 of 2)	CpG	159	NM_001135570	728568	Hs.42547	NM_001135570	ENSG00000204954	C12orf73	-	chromosome 12 open reading frame 73	protein-coding	0.070352	0.575000	
chunk0143_293_1	chr4	118364239	118365085	+	0	NA	Intergenic	Intergenic	-11895	NM_003619	8492	Hs.445857	NM_003619	ENSG00000164099	PRSS12	BSSP-3|BSSP3|MRT1	serine protease 12	protein-coding	0.007092	0.311688	
chunk0189_349_1	chr8	26781353	26782017	+	0	NA	intron (NM_033302, intron 1 of 2)	intron (NM_033302, intron 1 of 2)	83720	NM_033302	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.003012	0.416541	
chunk0097_182_1	chr2	50284920	50285406	+	0	NA	intron (NM_001135659, intron 18 of 23)	MER6|DNA|TcMar-Tigger	62593	NM_138735	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.004115	0.334702	
chunk0119_38_1	chr22	40524398	40524790	+	0	NA	intron (NR_109965, intron 3 of 3)	intron (NR_109965, intron 3 of 3)	2794	NR_109965	101927257	Hs.662725	NR_109965	ENSG00000232564	MRTFA-AS1	-	MRTFA antisense RNA 1	ncRNA	0.002551	0.374046	
chunk0100_267_1	chr2	113723888	113724450	+	0	NA	intron (NM_025181, intron 12 of 15)	intron (NM_025181, intron 12 of 15)	-2801	NR_039943	100616208		NR_039943	ENSG00000265429	MIR4782	-	microRNA 4782	ncRNA	0.005338	0.339254	218(CTGAACAACGAGTCCT,-,0.00),219(TGAACAACGAGTCCTT,+,0.00)
chunk0100_276_1	chr2	113932261	113932915	+	0	NA	intron (NM_005721, intron 5 of 11)	intron (NM_005721, intron 5 of 11)	-41596	NR_110174	101060091	Hs.741753	NR_110174		ACTR3-AS1	-	ACTR3 antisense RNA 1	ncRNA	0.003058	0.325191	
chunk0192_171_1	chr8	62686702	62686901	+	0	NA	intron (NR_130764, intron 3 of 6)	intron (NR_130764, intron 3 of 6)	-291060	NR_027378	643763	Hs.491856	NM_001039769	ENSG00000274956	NKAIN3-IT1	UG0898H09	NKAIN3 intronic transcript	ncRNA	0.000000	0.300000	
chunk0176_249_1	chr7	16175375	16175650	+	0	NA	intron (NM_001101417, intron 8 of 8)	intron (NM_001101417, intron 8 of 8)	-34974	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.003636	0.358696	196(GAGAACAATTTGTTTC,-,0.00),197(AGAACAATTTGTTTCT,+,0.00)
chunk0032_389_1	chr11	11583959	11584733	+	0	NA	intron (NM_198516, intron 1 of 10)	intron (NM_198516, intron 1 of 10)	37668	NM_198516	374378	Hs.655152	NM_198516	ENSG00000110328	GALNT18	GALNACT18|GALNT15|GALNTL4|GalNAc-T15|GalNAc-T18	polypeptide N-acetylgalactosaminyltransferase 18	protein-coding	0.014212	0.447742	242(TAGAGCAAAGTGTCCT,-,0.00),243(AGAGCAAAGTGTCCTT,+,0.00),373(GGGACAGTTTGTATTT,+,0.00)
chunk0131_307_1	chr3	150744423	150745227	+	0	NA	intron (NM_005067, intron 1 of 1)	intron (NM_005067, intron 1 of 1)	-5840	NR_121657	101928105		NR_121657		LOC101928105	-	uncharacterized LOC101928105	ncRNA	0.004975	0.383851	
chunk0005_63_1	chr1	55593466	55593806	+	0	NA	Intergenic	Intergenic	367995	NR_039618	100616272		NR_039618	ENSG00000265822	MIR4422	mir-4422	microRNA 4422	ncRNA	0.002941	0.431085	
chunk0095_396_1	chr2	24158153	24158572	+	0	NA	intron (NM_001291328, intron 7 of 10)	intron (NM_001291328, intron 7 of 10)	-16681	NM_001040710	653140	Hs.741736	NM_001040710	ENSG00000186453	FAM228A	C2orf84	family with sequence similarity 228 member A	protein-coding	0.011933	0.409524	
chunk0010_137_1	chr1	114780526	114780785	+	0	NA	promoter-TSS (NM_025073)	promoter-TSS (NM_025073)	32	NM_025073	80143	Hs.709277	NM_025073	ENSG00000052723	SIKE1	SIKE	suppressor of IKBKE 1	protein-coding	0.077220	0.607692	
chunk0065_444_1	chr14	106539210	106539613	+	0	NA	Intergenic	LTR13_|LTR|ERVK	56972	NR_027457	338005	Hs.322826	NR_027457	ENSG00000270816	LINC00221	C14orf98|NCRNA00221	long intergenic non-protein coding RNA 221	ncRNA	0.004963	0.311881	223(GGGCACAAGCTGTTCC,-,0.00),224(GGCACAAGCTGTTCCA,+,0.00)
chunk0001_434_1	chr1	11430152	11430715	+	0	NA	Intergenic	Intergenic	-48805	NM_020780	57540	Hs.202355	NM_020780	ENSG00000204624	DISP3	PTCHD2	dispatched RND transporter family member 3	protein-coding	0.030195	0.537234	
chunk0150_269_1	chr5	36832402	36832715	+	0	NA	Intergenic	Intergenic	44136	NR_046262	646719	Hs.355684	NR_046262	ENSG00000285967	NIPBL-DT	NIPBL-AS|NIPBL-AS1	NIPBL divergent transcript	ncRNA	0.003195	0.299363	
chunk0066_340_1	chr15	37143488	37143717	+	0	NA	Intergenic	Intergenic	-42303	NM_002399	4212	Hs.510989	NM_002399	ENSG00000134138	MEIS2	CPCMR|HsT18361|MRG1	Meis homeobox 2	protein-coding	0.000000	0.391304	
chunk0134_443_1	chr3	183718047	183718420	+	0	NA	intron (NM_018023, intron 3 of 30)	intron (NM_018023, intron 3 of 30)	20415	NM_018023	55689	Hs.632575	NM_018023	ENSG00000163872	YEATS2	-	YEATS domain containing 2	protein-coding	0.010724	0.331551	
chunk0018_321_1	chr1	221302136	221302554	+	0	NA	Intergenic	MIRc|SINE|MIR	33951	NR_024236	400804	Hs.722626	NR_024236	ENSG00000234754	C1orf140	-	uncharacterized LOC400804	ncRNA	0.004785	0.379475	
chunk0099_442_1	chr2	103213059	103213515	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	451256	NM_144632	130827	Hs.436203	NM_144632	ENSG00000170417	TMEM182	-	transmembrane protein 182	protein-coding	0.004386	0.444201	
chunk0203_261_1	chr9	87800969	87801510	+	0	NA	Intergenic	Intergenic	28324	NR_027917	392360	Hs.690450	NM_001023564	ENSG00000188029	CTSL3P	CTSL3|HCTSL-s	cathepsin L family member 3, pseudogene	pseudo	0.007394	0.298893	
chunk0081_66_1	chr17	38885152	38885442	+	0	NA	intron (NM_001271608, intron 2 of 5)	MIRb|SINE|MIR	15438	NR_073384	3927	Hs.741156	NM_006148	ENSG00000002834	LASP1	Lasp-1|MLN50	LIM and SH3 protein 1	protein-coding	0.010345	0.542955	181(CAGGACTCAGTGTGCC,-,0.00),182(AGGACTCAGTGTGCCA,+,0.00)
chunk0188_137_1	chr8	9448545	9448971	+	0	NA	Intergenic	Intergenic	-107177	NM_003747	8658	Hs.370267	NM_003747	ENSG00000173273	TNKS	ARTD5|PARP-5a|PARP5A|PARPL|TIN1|TINF1|TNKS1|pART5	tankyrase	protein-coding	0.004695	0.374707	331(TAGGACAATTTGTTCT,-,0.00),332(AGGACAATTTGTTCTG,+,0.00)
chunk0148_84_1	chr5	3178540	3178923	+	0	NA	intron (NR_104617, intron 1 of 1)	intron (NR_104617, intron 1 of 1)	896	NR_104617	102467074	Hs.575250	NR_104617	ENSG00000249808	LINC01377	-	long intergenic non-protein coding RNA 1377	ncRNA	0.000000	0.351562	
chunk0206_304_1	chr9	124778693	124779053	+	0	NA	intron (NM_182487, intron 1 of 7)	intron (NM_182487, intron 1 of 7)	1715	NM_182487	169611	Hs.357004	NM_182487	ENSG00000185585	OLFML2A	PRO34319	olfactomedin like 2A	protein-coding	0.019444	0.518006	
chunk0166_219_1	chr6	46923536	46923938	+	0	NA	intron (NM_015234, intron 1 of 20)	intron (NM_015234, intron 1 of 20)	-1760	NM_001098518	221395	Hs.362806	NM_015234	ENSG00000069122	ADGRF5	GPR116|KPG_001	adhesion G protein-coupled receptor F5	protein-coding	0.019900	0.476427	199(AGGAACACTATGTGCT,-,0.00),200(GGAACACTATGTGCTT,+,0.00)
chunk0200_108_1	chr9	16824517	16825141	+	0	NA	intron (NM_017637, intron 1 of 6)	intron (NM_017637, intron 1 of 6)	45959	NM_017637	54796	Hs.656581	NM_017637	ENSG00000173068	BNC2	BSN2	basonuclin 2	protein-coding	0.009615	0.456000	
chunk0184_257_1	chr7	118053252	118053984	+	0	NA	Intergenic	AluSg|SINE|Alu	-130414	NM_016200	51691	Hs.655046	NM_016200	ENSG00000128534	LSM8	NAA38	LSM8 homolog, U6 small nuclear RNA associated	protein-coding	0.012295	0.429741	
chunk0147_19_1	chr4	170838881	170839235	+	0	NA	Intergenic	Intergenic	-201544	NR_038838	100506122	Hs.434205	NR_038838	ENSG00000248872	LINC02431	-	long intergenic non-protein coding RNA 2431	ncRNA	0.000000	0.400000	213(CTGCACAGTCTGCCCT,-,0.00),214(TGCACAGTCTGCCCTC,+,0.00)
chunk0205_400_1	chr9	114586833	114587401	+	0	NA	promoter-TSS (NM_004888)	promoter-TSS (NM_004888)	-597	NM_004888	9550	Hs.388654	NM_004888	ENSG00000136888	ATP6V1G1	ATP6G|ATP6G1|ATP6GL|ATP6J|Vma10	ATPase H+ transporting V1 subunit G1	protein-coding	0.029930	0.481547	
chunk0048_363_1	chr12	85836513	85837018	+	0	NA	promoter-TSS (NM_005447)	promoter-TSS (NM_005447)	-225	NM_005447	9182	Hs.527881	NM_005447	ENSG00000198774	RASSF9	P-CIP1|PAMCI|PCIP1	Ras association domain family member 9	protein-coding	0.013861	0.482213	
chunk0071_61_1	chr15	80465026	80465298	+	0	NA	intron (NM_014862, intron 3 of 18)	intron (NM_014862, intron 3 of 18)	60812	NM_014862	9915	Hs.459070	NM_014862	ENSG00000172379	ARNT2	WEDAS|bHLHe1	aryl hydrocarbon receptor nuclear translocator 2	protein-coding	0.003676	0.468864	
chunk0087_231_1	chr18	36454168	36454464	+	0	NA	intron (NM_001281739, intron 3 of 23)	intron (NM_001281739, intron 3 of 23)	156620	NM_001281739	80206	Hs.436636	NM_025135	ENSG00000134775	FHOD3	FHOS2|Formactin2	formin homology 2 domain containing 3	protein-coding	0.010135	0.511785	
chunk0094_95_1	chr2	4122463	4123367	+	0	NA	Intergenic	(TGTTT)n|Simple_repeat|Simple_repeat	-148883	NR_037881	100505964	Hs.190267	NR_037881	ENSG00000237401	LINC01304	-	long intergenic non-protein coding RNA 1304	ncRNA	0.002212	0.335912	
chunk0075_414_1	chr16	57265259	57265671	+	0	NA	intron (NM_015993, intron 1 of 3)	intron (NM_015993, intron 1 of 3)	19207	NM_015993	51090	Hs.632215	NM_015993	ENSG00000102934	PLLP	PMLP|TM4SF11	plasmolipin	protein-coding	0.016990	0.486683	
chunk0204_415_1	chr9	102860890	102861455	+	0	NA	Intergenic	(TA)n|Simple_repeat|Simple_repeat	-134139	NM_001340	1539	Hs.3232	NM_001340	ENSG00000155833	CYLC2	-	cylicin 2	protein-coding	0.000000	0.286219	
chunk0141_96_1	chr4	79132977	79133218	+	0	NA	intron (NR_038342, intron 3 of 5)	MIRb|SINE|MIR	161349	NR_038342	100505875	Hs.480055	NR_038342		LINC01088	-	long intergenic non-protein coding RNA 1088	ncRNA	0.004149	0.347107	
chunk0002_315_1	chr1	24043410	24043979	+	0	NA	Intergenic	Intergenic	-63231	NM_001191005	10772	Hs.3530	NM_006625	ENSG00000188529	SRSF10	FUSIP1|FUSIP2|NSSR|PPP1R149|SFRS13|SFRS13A|SRp38|SRrp40|TASR|TASR1|TASR2	serine and arginine rich splicing factor 10	protein-coding	0.001757	0.461404	
chunk0159_3_1	chr5	135951045	135951782	+	0	NA	intron (NM_002302, intron 2 of 3)	intron (NM_002302, intron 2 of 3)	3621	NM_002302	3950	Hs.512580	NM_002302	ENSG00000145826	LECT2	chm-II|chm2	leukocyte cell derived chemotaxin 2	protein-coding	0.008141	0.410569	285(GAGCACAAGATGTCCA,-,0.00),286(AGCACAAGATGTCCAC,+,0.00)
chunk0054_294_1	chr13	48212958	48213404	+	0	NA	Intergenic	L1MB8|LINE|L1	-19957	NM_021999	9445	Hs.643683	NM_021999	ENSG00000136156	ITM2B	ABRI|BRI|BRI2|BRICD2B|E25B|E3-16|FBD|RDGCA|imBRI2	integral membrane protein 2B	protein-coding	0.002242	0.382550	
chunk0085_464_1	chr18	11835650	11835851	+	0	NA	intron (NM_182978, intron 5 of 11)	intron (NM_182978, intron 5 of 11)	-15640	NM_020412	57132	Hs.656244	NM_020412	ENSG00000255112	CHMP1B	C10orf2|C18-ORF2|C18orf2|CHMP1.5|Vps46-2|Vps46B|hVps46-2	charged multivesicular body protein 1B	protein-coding	0.004975	0.326733	
chunk0024_314_1	chr10	42750658	42751163	+	0	NA	Intergenic	Intergenic	-31596	NM_014753	9790	Hs.10848	NM_014753	ENSG00000165733	BMS1	ACC|BMS1L	BMS1 ribosome biogenesis factor	protein-coding	0.007921	0.339921	
chunk0023_307_1	chr10	28894916	28895251	+	0	NA	Intergenic	MLT1J2|LTR|ERVL-MaLR	48675	NM_001278522	283080		NM_001278522		C10orf126	bA492M23.1	chromosome 10 open reading frame 126	protein-coding	0.008955	0.440476	125(AGGTGCAGCCTGTTCT,-,0.00),126(GGTGCAGCCTGTTCTG,+,0.00)
chunk0040_360_1	chr11	118801540	118802230	+	0	NA	Intergenic	Intergenic	-10622	NM_004397	1656	Hs.408461	NM_004397	ENSG00000110367	DDX6	HLR2|P54|RCK	DEAD-box helicase 6	protein-coding	0.005797	0.409551	
chunk0196_434_1	chr8	116471759	116472201	+	0	NA	Intergenic	Intergenic	-146921	NR_046215	100859921	Hs.552281	NR_046215	ENSG00000249917	LINC00536	-	long intergenic non-protein coding RNA 536	ncRNA	0.015837	0.476298	
chunk0177_389_1	chr7	27028710	27029352	+	0	NA	Intergenic	MIR|SINE|MIR	66975	NM_005522	3198	Hs.67397	NM_005522	ENSG00000105991	HOXA1	BSAS|HOX1|HOX1F	homeobox A1	protein-coding	0.006231	0.387247	
chunk0206_441_1	chr9	127991170	127991576	+	0	NA	Intergenic	L1MA4|LINE|L1	-10840	NM_001035254	399665	Hs.535972	NM_203305	ENSG00000167106	FAM102A	C9orf132|EEIG1|SYM-3A|bA203J24.7	family with sequence similarity 102 member A	protein-coding	0.014778	0.375921	
chunk0154_325_1	chr5	84518995	84519194	+	0	NA	Intergenic	L1PA13|LINE|L1	-134227	NM_001278642	10085	Hs.482730	NM_005711	ENSG00000164176	EDIL3	DEL1	EGF like repeats and discoidin domains 3	protein-coding	0.005025	0.555000	
chunk0195_330_1	chr8	99107411	99108016	+	0	NA	intron (NR_047582, intron 6 of 8)	L1MC5|LINE|L1	94447	NM_015243	157680	Hs.191540	NM_015243	ENSG00000132549	VPS13B	CHS1|COH1	vacuolar protein sorting 13 homolog B	protein-coding	0.003306	0.325083	
chunk0038_125_1	chr11	83971253	83971452	+	0	NA	intron (NM_001142699, intron 12 of 27)	intron (NM_001142699, intron 12 of 27)	-288927	NM_001142702	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.000000	0.480000	
chunk0201_277_1	chr9	38686907	38687165	+	0	NA	Intergenic	Intergenic	65948	NR_027294	158228	Hs.632652	NR_027294		FAM201A	C9orf122	family with sequence similarity 201 member A	ncRNA	0.031008	0.555985	
chunk0136_332_1	chr3	195605052	195605508	+	0	NA	Intergenic	MER4-int|LTR|ERV1	-21075	NM_001647	347	Hs.522555	NM_001647	ENSG00000189058	APOD	-	apolipoprotein D	protein-coding	0.000000	0.393873	146(GGGTTCAGTGTGTGCT,-,0.00),147(GGTTCAGTGTGTGCTC,+,0.00)
chunk0083_422_1	chr17	72399397	72400048	+	0	NA	Intergenic	Intergenic	193082	NR_036488	100499467	Hs.157726	NR_036488	ENSG00000227036	LINC00673	ERRLR01|HI-LNC75|HILNC75|LUCAIR1|SLNCR|SLNCR1	long intergenic non-protein coding RNA 673	ncRNA	0.021505	0.489264	
chunk0201_266_1	chr9	38515026	38515539	+	0	NA	Intergenic	MER57B2|LTR|ERV1	30090	NR_047651	100289137	Hs.644630	NR_047651	ENSG00000283486	FAM95C	-	family with sequence similarity 95 member C	ncRNA	0.005848	0.377432	
chunk0051_36_1	chr12	112136983	112137457	+	0	NA	intron (NM_006700, intron 4 of 11)	AluSg|SINE|Alu	11675	NM_001143906	10906	Hs.5148	NM_006700	ENSG00000135148	TRAFD1	FLN29	TRAF-type zinc finger domain containing 1	protein-coding	0.016878	0.496842	
chunk0111_214_1	chr20	28842607	28843407	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	-237383	NR_132316	102723316		NR_132316		FRG1DP	-	FSHD region gene 1 family member D, pseudogene	pseudo	0.002519	0.362264	
chunk0183_419_1	chr7	110843743	110843984	+	0	NA	intron (NM_032549, intron 5 of 5)	L2a|LINE|L2	-247143	NM_018334	54674	Hs.3781	NM_018334	ENSG00000173114	LRRN3	FIGLER5|NLRR-3|NLRR3	leucine rich repeat neuronal 3	protein-coding	0.008299	0.545455	
chunk0049_9_1	chr12	89289964	89290456	+	0	NA	Intergenic	Intergenic	62649	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.014228	0.393509	
chunk0067_280_1	chr15	47331599	47332422	+	0	NA	intron (NM_001198999, intron 1 of 19)	intron (NM_001198999, intron 1 of 19)	147804	NM_001198999	80031	Hs.511265	NM_020858	ENSG00000137872	SEMA6D	-	semaphorin 6D	protein-coding	0.007290	0.375000	
chunk0038_283_1	chr11	90074113	90074319	+	0	NA	Intergenic	AluSc|SINE|Alu	-11734	NM_001143975	642623	Hs.719885	NM_001143975	ENSG00000255009	UBTFL1	C11orf27|HMGPI	upstream binding transcription factor like 1	protein-coding	0.014563	0.483092	
chunk0182_252_1	chr7	97177985	97178680	+	0	NA	intron (NM_020186, intron 1 of 1)	L1MB4|LINE|L1	61739	NM_020186	57001	Hs.592269	NM_020186	ENSG00000196636	SDHAF3	ACN9|DC11|LYRM10|Sdh7	succinate dehydrogenase complex assembly factor 3	protein-coding	0.004317	0.339080	
chunk0146_321_1	chr4	165585001	165585388	+	0	NA	Intergenic	Intergenic	-99445	NR_121676	101928151	Hs.639858	NR_121676	ENSG00000249500	LINC01179	-	long intergenic non-protein coding RNA 1179	ncRNA	0.000000	0.335052	
chunk0129_163_1	chr3	120683780	120684330	+	0	NA	Intergenic	Intergenic	-1484	NM_000187	3081	Hs.368254	NM_000187	ENSG00000113924	HGD	AKU|HGO	homogentisate 1,2-dioxygenase	protein-coding	0.005455	0.402904	13(TAGCACAGACTGGGCC,-,0.00)
chunk0075_164_1	chr16	51734388	51734592	+	0	NA	Intergenic	Intergenic	-28029	NR_110916	101927364	Hs.133120	NR_110916	ENSG00000260057	LINC01571	-	long intergenic non-protein coding RNA 1571	ncRNA	0.000000	0.404878	
chunk0129_406_1	chr3	126845126	126845327	+	0	NA	intron (NM_032343, intron 4 of 7)	L1MCc|LINE|L1	141006	NM_032343	84303	Hs.518119	NM_032343	ENSG00000159685	CHCHD6	CHCM1|MICOS25|Mic25|PPP1R23	coiled-coil-helix-coiled-coil-helix domain containing 6	protein-coding	0.000000	0.351485	
chunk0202_54_1	chr9	71368311	71368727	+	0	NA	Intergenic	L2b|LINE|L2	-246921	NM_001007471	80036	Hs.47288	NM_020952	ENSG00000083067	TRPM3	GON-2|LTRPC3|MLSN2	transient receptor potential cation channel subfamily M member 3	protein-coding	0.002404	0.369305	
chunk0085_114_1	chr18	2851781	2852383	+	0	NA	intron (NM_032048, intron 2 of 7)	intron (NM_032048, intron 2 of 7)	5052	NM_032048	84034	Hs.532815	NM_032048	ENSG00000132205	EMILIN2	EMILIN-2|FOAP-10	elastin microfibril interfacer 2	protein-coding	0.023256	0.442786	
chunk0122_71_1	chr3	29493042	29493504	+	0	NA	intron (NM_001003793, intron 3 of 14)	L1ME4c|LINE|L1	211961	NM_014483	27303	Hs.221436	NM_014483	ENSG00000144642	RBMS3	-	RNA binding motif single stranded interacting protein 3	protein-coding	0.010823	0.367171	
chunk0116_363_1	chr21	41704129	41704610	+	0	NA	Intergenic	Intergenic	11406	NR_027272	150135	Hs.350679	NM_152506	ENSG00000236384	LINC00479	C21orf129|PRED76	long intergenic non-protein coding RNA 479	ncRNA	0.016632	0.558091	241(CAGGACTGCCTGTCCA,-,0.00),242(AGGACTGCCTGTCCAG,+,0.00)
chunk0108_182_1	chr2	232207019	232207571	+	0	NA	intron (NR_046476, intron 9 of 20)	intron (NR_046476, intron 9 of 20)	34642	NR_030288	693147		NR_030288	ENSG00000207626	MIR562	MIRN562|hsa-mir-562	microRNA 562	ncRNA	0.005435	0.405063	
chunk0136_274_1	chr3	194627236	194627435	+	0	NA	intron (NM_001166305, intron 2 of 10)	intron (NM_001166305, intron 2 of 10)	6086	NM_001011655	93109	Hs.478729	NM_138399	ENSG00000145014	TMEM44	-	transmembrane protein 44	protein-coding	0.005025	0.495000	
chunk0042_269_1	chr12	6925932	6926175	+	0	NA	intron (NM_001007026, intron 1 of 9)	intron (NM_001007026, intron 1 of 9)	1590	NM_001007026	1822	Hs.143766	NM_001940	ENSG00000111676	ATN1	B37|D12S755E|DRPLA|HRS|NOD	atrophin 1	protein-coding	0.016461	0.627049	
chunk0107_453_1	chr2	225670482	225670918	+	0	NA	Intergenic	Intergenic	269814	NM_020864	57624	Hs.224409	NM_020864	ENSG00000144460	NYAP2	KIAA1486	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	protein-coding	0.002294	0.311213	
chunk0065_301_1	chr14	102778491	102778929	+	0	NA	intron (NM_001199427, intron 1 of 7)	intron (NM_001199427, intron 1 of 7)	1231	NM_003300	7187	Hs.510528	NM_003300	ENSG00000131323	TRAF3	CAP-1|CAP1|CD40bp|CRAF1|IIAE5|LAP1|RNF118	TNF receptor associated factor 3	protein-coding	0.036530	0.421412	
chunk0039_401_1	chr11	107408635	107409286	+	0	NA	intron (NM_152434, intron 10 of 17)	intron (NM_152434, intron 10 of 17)	48886	NM_152434	143884	Hs.212140	NM_152434	ENSG00000152404	CWF19L2	-	CWF19 like cell cycle control factor 2	protein-coding	0.001536	0.342025	
chunk0178_437_1	chr7	41579088	41579676	+	0	NA	Intergenic	Intergenic	-114534	NR_027118	285954	Hs.656869	NR_027118	ENSG00000224116	INHBA-AS1	-	INHBA antisense RNA 1	ncRNA	0.003401	0.371817	395(ATGGACATTCAGTCCT,-,0.00),396(TGGACATTCAGTCCTT,+,0.00)
chunk0086_279_1	chr18	23670053	23670477	+	0	NA	Intergenic	Intergenic	-7380	NM_001308238	147463	Hs.355689	NM_173505	ENSG00000154065	ANKRD29	-	ankyrin repeat domain 29	protein-coding	0.011792	0.414118	
chunk0209_159_1	chrX	42867377	42867641	+	0	NA	Intergenic	Intergenic	-89274	NR_002191									0.007576	0.316981	
chunk0016_205_1	chr1	198763351	198763578	+	0	NA	Intergenic	Intergenic	95518	NR_029612	406955		NR_029612	ENSG00000207975	MIR181B1	MIRN181B1|mir-181b-1	microRNA 181b-1	ncRNA	0.004405	0.368421	
chunk0095_158_1	chr2	17170078	17170402	+	0	NA	Intergenic	L2a|LINE|L2	348199	NM_001099218	729475	Hs.515802	NM_001099218	ENSG00000214842	RAD51AP2	-	RAD51 associated protein 2	protein-coding	0.006173	0.381538	
chunk0102_277_1	chr2	150174259	150175209	+	0	NA	Intergenic	Intergenic	312961	NM_005168	390	Hs.6838	NM_005168	ENSG00000115963	RND3	ARHE|Rho8|RhoE|memB	Rho family GTPase 3	protein-coding	0.002105	0.296530	
chunk0102_266_1	chr2	149939798	149940298	+	0	NA	Intergenic	Intergenic	-352232	NM_015702	27249	Hs.5324	NM_015702	ENSG00000168288	MMADHC	C2orf25|CL25022|cblD	metabolism of cobalamin associated D	protein-coding	0.012000	0.333333	
chunk0002_73_1	chr1	14135095	14135580	+	0	NA	Intergenic	Intergenic	385956	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.008247	0.421811	
chunk0079_79_1	chr17	11636725	11636931	+	0	NA	intron (NM_001372, intron 9 of 68)	intron (NM_001372, intron 9 of 68)	38397	NM_001372	1770	Hs.567259	NM_001372	ENSG00000007174	DNAH9	CILD40|DNAH17L|DNEL1|DYH9|Dnahc9|HL-20|HL20	dynein axonemal heavy chain 9	protein-coding	0.004854	0.420290	86(GGGGACATTCTGTTAC,-,0.00),87(GGGACATTCTGTTACT,+,0.00)
chunk0045_131_1	chr12	46396779	46397258	+	0	NA	intron (NR_125381, intron 2 of 2)	L1M6|LINE|L1	12911	NR_125381	100288798	Hs.525922	NR_125377		LOC100288798	-	uncharacterized LOC100288798	ncRNA	0.012526	0.389583	221(GTGTACAGAATGTCCC,-,0.00),222(TGTACAGAATGTCCCT,+,0.00)
chunk0051_425_1	chr12	122796005	122796351	+	0	NA	intron (NR_027918, intron 6 of 12)	intron (NR_027918, intron 6 of 12)	21669	NM_201435	84660	Hs.592008	NM_032573	ENSG00000130783	CCDC62	CT109|ERAP75|TSP-NY	coiled-coil domain containing 62	protein-coding	0.005780	0.386167	
chunk0082_193_1	chr17	56661912	56662247	+	0	NA	Intergenic	Intergenic	68380	NM_005450	9241	Hs.248201	NM_005450	ENSG00000183691	NOG	SYM1|SYNS1|SYNS1A	noggin	protein-coding	0.008955	0.526786	
chunk0023_86_1	chr10	22352943	22353682	+	0	NA	intron (NM_001253854, intron 3 of 13)	intron (NM_001253854, intron 3 of 13)	7867	NM_001253855	9576	Hs.655170	NM_012443	ENSG00000077327	SPAG6	CT141|Repro-SA-1|pf16	sperm associated antigen 6	protein-coding	0.004060	0.336486	
chunk0156_193_1	chr5	107918970	107919194	+	0	NA	intron (NM_001163315, intron 7 of 8)	intron (NM_001163315, intron 7 of 8)	-248187	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.004464	0.337778	
chunk0161_298_1	chr5	173081775	173082060	+	0	NA	intron (NM_001168393, intron 2 of 3)	AluSg|SINE|Alu	25565	NM_001168393	153222	Hs.484195	NM_153607	ENSG00000164463	CREBRF	C5orf41|LRF	CREB3 regulatory factor	protein-coding	0.003509	0.468531	
chunk0154_46_1	chr5	77172389	77172590	+	0	NA	Intergenic	Intergenic	-38392	NM_001029854	8622	Hs.584830	NM_003719	ENSG00000113231	PDE8B	ADSD|PPNAD3	phosphodiesterase 8B	protein-coding	0.004975	0.405941	133(AAGGACAGTCTGTCCC,-,0.00),134(AGGACAGTCTGTCCCT,+,0.00)
chunk0012_136_1	chr1	157247454	157248035	+	0	NA	Intergenic	L1PB1|LINE|L1	-109153	NM_001145312	2117	Hs.105636	NM_005240	ENSG00000117036	ETV3	METS|PE-1|PE1	ETS variant 3	protein-coding	0.005164	0.383162	
chunk0212_214_1	chrX	135977576	135977989	+	0	NA	Intergenic	Intergenic	-3807	NM_173470	93380	Hs.110702	NM_173470	ENSG00000169446	MMGT1	EMC5|TMEM32	membrane magnesium transporter 1	protein-coding	0.007264	0.333333	
chunk0189_251_1	chr8	25111935	25112429	+	0	NA	Intergenic	Intergenic	-72590	NM_024940	80005	Hs.195403	NM_024940	ENSG00000147459	DOCK5	-	dedicator of cytokinesis 5	protein-coding	0.006073	0.408081	
chunk0035_122_1	chr11	42609700	42610268	+	0	NA	Intergenic	Intergenic	-356294	NR_038309	100507205	Hs.99310	NR_038309		LINC02740	-	long intergenic non-protein coding RNA 2740	ncRNA	0.000000	0.342707	
chunk0123_343_1	chr3	47780455	47780754	+	0	NA	intron (NM_003074, intron 1 of 27)	L2a|LINE|L2	1311	NM_003074	6599	Hs.476179	NM_003074	ENSG00000173473	SMARCC1	BAF155|CRACC1|Rsc8|SRG3|SWI3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1	protein-coding	0.010033	0.426667	
chunk0152_279_1	chr5	61408561	61408864	+	0	NA	intron (NM_020928, intron 1 of 13)	intron (NM_020928, intron 1 of 13)	76439	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.036304	0.490132	
chunk0119_213_1	chr22	45017310	45017878	+	0	NA	Intergenic	L1MA10|LINE|L1	-7666	NM_001135862	112885	Hs.254097	NM_138415	ENSG00000056487	PHF21B	BHC80L|PHF4	PHD finger protein 21B	protein-coding	0.021127	0.456942	
chunk0165_53_1	chr6	30592549	30593152	+	0	NA	Intergenic	Intergenic	8518	NR_030615	100126314		NR_030615	ENSG00000216101	MIR877	MIRN877|hsa-mir-877|miRNA877|mir-877	microRNA 877	ncRNA	0.008292	0.451987	
chunk0144_14_1	chr4	124810134	124810596	+	0	NA	Intergenic	Intergenic	-97633	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.004329	0.345572	68(TAGAACGATCTGTTCC,-,0.00),69(AGAACGATCTGTTCCC,+,0.00)
chunk0011_19_1	chr1	143195219	143195634	+	0	NA	Intergenic	Intergenic	227166	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.055422	0.370192	
chunk0187_102_1	chr8	4697296	4697682	+	0	NA	intron (NM_033225, intron 1 of 69)	intron (NM_033225, intron 1 of 69)	297317	NM_033225	64478	Hs.571466	NM_033225	ENSG00000183117	CSMD1	PPP1R24	CUB and Sushi multiple domains 1	protein-coding	0.010363	0.366925	
chunk0121_164_1	chr3	19629453	19629665	+	0	NA	Intergenic	Intergenic	304655	NM_144715	151651	Hs.733920	NM_144715	ENSG00000163576	EFHB	CFAP21	EF-hand domain family member B	protein-coding	0.000000	0.309859	110(CAGTACTTCATGTACT,-,0.00),111(AGTACTTCATGTACTT,+,0.00)
chunk0105_223_1	chr2	188203356	188203809	+	0	NA	intron (NR_126396, intron 1 of 2)	intron (NR_126396, intron 1 of 2)	84109	NR_126396	104355152		NR_126396	ENSG00000231689	LINC01090	-	long intergenic non-protein coding RNA 1090	ncRNA	0.002208	0.330396	
chunk0150_370_1	chr5	39073474	39073738	+	0	NA	intron (NM_001285439, intron 2 of 38)	intron (NM_001285439, intron 2 of 38)	802	NM_001285439	253260	Hs.407926	NM_152756	ENSG00000164327	RICTOR	AVO3|PIA|hAVO3	RPTOR independent companion of MTOR complex 2	protein-coding	0.045455	0.566038	
chunk0193_329_1	chr8	78989839	78990312	+	0	NA	Intergenic	L2c|LINE|L2	-184552	NM_001199887	3574	Hs.591873	NM_000880	ENSG00000104432	IL7	IL-7	interleukin 7	protein-coding	0.006342	0.333333	
chunk0002_12_1	chr1	12188729	12189449	+	0	NA	intron (NM_001066, intron 2 of 9)	L2c|LINE|L2	-2624	NR_039775	100616438		NR_039775	ENSG00000263676	MIR4632	-	microRNA 4632	ncRNA	0.020833	0.586685	312(GTGAACATGCTGTTCC,-,0.00),313(TGAACATGCTGTTCCC,+,0.00)
chunk0057_244_1	chr13	104586663	104586969	+	0	NA	Intergenic	Intergenic	-879051	NM_001161814	267012	Hs.381382	NM_172370	ENSG00000182346	DAOA	LG72|SG72	D-amino acid oxidase activator	protein-coding	0.006536	0.267101	74(AAAAACAAAATGTGCT,-,0.00),75(AAAACAAAATGTGCTT,+,0.00)
chunk0032_402_1	chr11	11808221	11808443	+	0	NA	Intergenic	UCON40|Unknown|Unknown	-25110	NR_107037	102465870		NR_107037	ENSG00000278529	MIR8070	hsa-mir-8070	microRNA 8070	ncRNA	0.009009	0.322870	
chunk0105_185_1	chr2	187549320	187549967	+	0	NA	intron (NM_001032281, intron 1 of 6)	intron (NM_001032281, intron 1 of 6)	4849	NM_006287	7035	Hs.516578	NM_006287	ENSG00000003436	TFPI	EPI|LACI|TFI|TFPI1	tissue factor pathway inhibitor	protein-coding	0.000000	0.317901	
chunk0193_208_1	chr8	76175648	76176008	+	0	NA	Intergenic	Intergenic	-230826	NR_105006	101926978	Hs.615028	NR_105006	ENSG00000254300	LINC01111	-	long intergenic non-protein coding RNA 1111	ncRNA	0.002778	0.313019	
chunk0092_304_1	chr19	34327022	34327651	+	0	NA	intron (NM_014686, intron 3 of 13)	(GTT)n|Simple_repeat|Simple_repeat	-37404	NM_001184722	2821	Hs.466471	NM_000175	ENSG00000105220	GPI	AMF|GNPI|NLK|PGI|PHI|SA-36|SA36	glucose-6-phosphate isomerase	protein-coding	0.012719	0.395238	
chunk0141_37_1	chr4	77007620	77008369	+	0	NA	intron (NM_001306147, intron 5 of 11)	intron (NM_001306147, intron 5 of 11)	58280	NM_018243	55752	Hs.128199	NM_018243	ENSG00000138758	SEPTIN11	SEPT11	septin 11	protein-coding	0.002670	0.402667	
chunk0033_414_1	chr11	24789063	24789525	+	0	NA	intron (NM_001252010, intron 5 of 9)	intron (NM_001252010, intron 5 of 9)	292324	NM_001252008	338645	Hs.144138	NM_001009909	ENSG00000187398	LUZP2	KFSP2566|PRO6246	leucine zipper protein 2	protein-coding	0.002165	0.377970	
chunk0084_78_1	chr17	75036442	75036803	+	0	NA	intron (NR_110835, intron 3 of 7)	intron (NR_110835, intron 3 of 7)	4055	NR_110835	23510	Hs.514468	NM_015353	ENSG00000180901	KCTD2	-	potassium channel tetramerization domain containing 2	protein-coding	0.027701	0.513812	
chunk0011_334_1	chr1	152185467	152185961	+	0	NA	Intergenic	Intergenic	-26486	NM_001122965	126638	Hs.376144	NM_152364	ENSG00000215853	RPTN	-	repetin	protein-coding	0.012146	0.464646	
chunk0094_205_1	chr2	6413059	6413550	+	0	NA	Intergenic	Intergenic	-37882	NR_110251	101929390	Hs.434407	NR_110251	ENSG00000227007	LINC01247	-	long intergenic non-protein coding RNA 1247	ncRNA	0.004073	0.390244	
chunk0008_421_1	chr1	98693456	98694105	+	0	NA	intron (NR_033716, intron 5 of 8)	intron (NR_033716, intron 5 of 8)	32100	NM_015976	51375	Hs.197015	NM_015976	ENSG00000162627	SNX7	-	sorting nexin 7	protein-coding	0.010786	0.349231	
chunk0070_382_1	chr15	76572618	76573192	+	0	NA	intron (NM_020843, intron 22 of 30)	(CT)n|Simple_repeat|Simple_repeat	-13742	NR_037464	100500855		NR_037464	ENSG00000266449	MIR3713	-	microRNA 3713	ncRNA	0.006969	0.373913	
chunk0088_445_1	chr18	56676721	56676993	+	0	NA	intron (NM_015285, intron 2 of 27)	AluJb|SINE|Alu	25472	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.007353	0.472527	
chunk0125_323_1	chr3	70982764	70983189	+	0	NA	intron (NM_032682, intron 14 of 20)	intron (NM_032682, intron 14 of 20)	81947	NM_001244813	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.014118	0.457746	
chunk0033_142_1	chr11	15471177	15471548	+	0	NA	Intergenic	Intergenic	-172523	NM_001293172	102724957	Hs.512245	NM_001293172		LOC102724957	-	uncharacterized LOC102724957	protein-coding	0.005391	0.446237	
chunk0136_308_1	chr3	195197513	195197712	+	0	NA	intron (NM_001308069, intron 2 of 3)	intron (NM_001308069, intron 2 of 3)	49741	NR_102710	101410543	Hs.658170	NR_102710	ENSG00000230266	XXYLT1-AS2	-	XXYLT1 antisense RNA 2	ncRNA	0.010050	0.320000	52(AGAAACACTATGTACC,-,0.00),53(GAAACACTATGTACCT,+,0.00)
chunk0109_48_1	chr20	857379	857632	+	0	NA	Intergenic	L1ME1|LINE|L1	12897	NM_031424	83541	Hs.574822	NM_031424	ENSG00000125898	FAM110A	C20orf55|F10|bA371L19.3	family with sequence similarity 110 member A	protein-coding	0.019763	0.409449	
chunk0079_324_1	chr17	17406135	17406701	+	0	NA	Intergenic	Intergenic	-70568	NM_018019	55090	Hs.244595	NM_018019	ENSG00000141026	MED9	MED25	mediator complex subunit 9	protein-coding	0.014134	0.559083	309(AGGGACACGCTGTGCT,-,0.00),310(GGGACACGCTGTGCTG,+,0.00)
chunk0130_104_1	chr3	131098747	131099131	+	0	NA	intron (NM_145910, intron 4 of 14)	L1P4a|LINE|L1	-72085	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.002604	0.327273	
chunk0185_172_1	chr7	127902148	127902481	+	0	NA	intron (NM_014390, intron 13 of 23)	intron (NM_014390, intron 13 of 23)	-95195	NR_027330	27099	Hs.657377	NM_014411	ENSG00000279078	SND1-IT1	C7orf54|NAG8|NSG-X	SND1 intronic transcript 1	ncRNA	0.003003	0.467066	
chunk0095_210_1	chr2	18662962	18663181	+	0	NA	Intergenic	Intergenic	-73491	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.004566	0.340909	
chunk0192_7_1	chr8	58245732	58246353	+	0	NA	Intergenic	L1MEb|LINE|L1	26059	NR_105005	101929528	Hs.563551	NR_105005	ENSG00000253281	LOC101929528	-	uncharacterized LOC101929528	ncRNA	0.003221	0.334405	
chunk0036_212_1	chr11	63586522	63586968	+	0	NA	intron (NM_007069, intron 3 of 3)	intron (NM_007069, intron 3 of 3)	-23362	NM_017878	54979	Hs.272805	NM_017878	ENSG00000133328	PLAAT2	HRASLS2|PLA1/2-2|PLAAT-2	phospholipase A and acyltransferase 2	protein-coding	0.006726	0.373602	
chunk0138_85_1	chr4	35500736	35501365	+	0	NA	Intergenic	Intergenic	-743066	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.003180	0.379365	
chunk0144_453_1	chr4	142090908	142091407	+	0	NA	intron (NM_001101669, intron 23 of 25)	intron (NM_001101669, intron 23 of 25)	454561	NM_172175	3600	Hs.168132	NM_000585	ENSG00000164136	IL15	IL-15	interleukin 15	protein-coding	0.008016	0.356000	
chunk0011_272_1	chr1	151187194	151187898	+	0	NA	intron (NM_001271088, intron 1 of 5)	L4_C_Mam|LINE|RTE-X	2667	NM_001271087	6944	Hs.2430	NM_005997	ENSG00000163159	VPS72	CFL1|Swc2|TCFL1|YL-1|YL1	vacuolar protein sorting 72 homolog	protein-coding	0.001420	0.370213	
chunk0195_349_1	chr8	99547303	99547753	+	0	NA	intron (NM_152564, intron 30 of 61)	intron (NM_152564, intron 30 of 61)	-10667	NR_030596	100126309		NR_030596	ENSG00000216069	MIR875	MIRN875|hsa-mir-875	microRNA 875	ncRNA	0.004444	0.334812	
chunk0135_197_1	chr3	188263146	188263473	+	0	NA	intron (NM_005578, intron 2 of 10)	intron (NM_005578, intron 2 of 10)	37904	NM_001167671	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.009174	0.396341	
chunk0103_243_1	chr2	164840008	164840800	+	0	NA	promoter-TSS (NR_110574)	promoter-TSS (NR_110574)	-345	NR_110574	101929633	Hs.570267	NR_110574		LOC101929633	-	uncharacterized LOC101929633	ncRNA	0.021465	0.448928	403(CAGAACTACCTGTTCT,-,0.00),404(AGAACTACCTGTTCTC,+,0.00)
chunk0091_463_1	chr19	18364855	18365297	+	0	NA	3' UTR (NM_017712, exon 5 of 5)	3' UTR (NM_017712, exon 5 of 5)	-21082	NM_004864	9518	Hs.616962	NM_004864	ENSG00000130513	GDF15	GDF-15|MIC-1|MIC1|NAG-1|PDF|PLAB|PTGFB	growth differentiation factor 15	protein-coding	0.033937	0.532731	
chunk0007_47_1	chr1	77783118	77783445	+	0	NA	exon (NM_001270384, exon 2 of 16)	exon (NM_001270384, exon 2 of 16)	3657	NM_198549	374986	Hs.437755	NM_198549	ENSG00000180488	MIGA1	FAM73A	mitoguardin 1	protein-coding	0.003058	0.323171	
chunk0049_354_1	chr12	95424325	95424524	+	0	NA	Intergenic	Intergenic	-49622	NM_006838	10988	Hs.444986	NM_006838	ENSG00000111142	METAP2	MAP2|MNPEP|p67eIF2	methionyl aminopeptidase 2	protein-coding	0.010050	0.430000	
chunk0183_181_1	chr7	106199054	106199435	+	0	NA	Intergenic	Intergenic	85948	NM_005746	10135	Hs.489615	NM_005746	ENSG00000105835	NAMPT	1110035O14Rik|PBEF|PBEF1|VF|VISFATIN	nicotinamide phosphoribosyltransferase	protein-coding	0.002625	0.395288	208(CTGGACATCATGTTCC,-,0.00),209(TGGACATCATGTTCCC,+,0.00)
chunk0091_106_1	chr19	5933867	5934238	+	0	NA	intron (NM_007320, intron 4 of 15)	intron (NM_007320, intron 4 of 15)	20408	NM_080590	828	Hs.584744	NM_004058	ENSG00000105519	CAPS	CAPS1	calcyphosine	protein-coding	0.021563	0.591398	105(GGCACACAGTGAGCCT,+,0.00)
chunk0012_415_1	chr1	164299234	164299433	+	0	NA	Intergenic	Intergenic	-260027	NM_002585	5087	Hs.557097	NM_002585	ENSG00000185630	PBX1	CAKUHED	PBX homeobox 1	protein-coding	0.015075	0.500000	
chunk0074_20_1	chr16	20303032	20303346	+	0	NA	Intergenic	MIRb|SINE|MIR	24431	NM_001007242	2813	Hs.53985	NM_001502	ENSG00000169347	GP2	ZAP75	glycoprotein 2	protein-coding	0.006369	0.422222	
chunk0032_361_1	chr11	10751134	10751334	+	0	NA	5' UTR (NM_014633, exon 1 of 25)	5' UTR (NM_014633, exon 1 of 25)	247	NM_014633	9646	Hs.725151	NM_014633	ENSG00000198730	CTR9	SH2BP1|TSBP|p150|p150TSP	CTR9 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.120000	0.691542	
chunk0009_105_1	chr1	102556462	102556801	+	0	NA	Intergenic	L2a|LINE|L2	551865	NM_001190709	1301	Hs.523446	NM_001854	ENSG00000060718	COL11A1	CO11A1|COLL6|STL2	collagen type XI alpha 1 chain	protein-coding	0.008850	0.411765	
chunk0203_289_1	chr9	88948380	88948579	+	0	NA	Intergenic	Intergenic	-42384	NM_001142413	286223	Hs.585118	NM_001001938	ENSG00000213694	C9orf47	C9orf108|bA791O21.3	chromosome 9 open reading frame 47	protein-coding	0.015075	0.500000	
chunk0087_350_1	chr18	40888219	40888751	+	0	NA	Intergenic	L1MDa|LINE|L1	632112	NR_002838	641516	Hs.116612	NR_002838	ENSG00000267313	KC6	-	keratoconus gene 6	ncRNA	0.003759	0.288931	
chunk0122_366_1	chr3	37610282	37610600	+	0	NA	intron (NM_002207, intron 15 of 27)	intron (NM_002207, intron 15 of 27)	158119	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.003145	0.329154	190(TGGTTCAGAGTGTTCT,-,0.00),191(GGTTCAGAGTGTTCTG,+,0.00)
chunk0105_157_1	chr2	186690158	186690430	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	-3768	NM_177454	165215	Hs.28872	NM_177454	ENSG00000144369	FAM171B	KIAA1946	family with sequence similarity 171 member B	protein-coding	0.003676	0.347985	
chunk0026_133_1	chr10	62107110	62107388	+	0	NA	Intergenic	L1ME4b|LINE|L1	58038	NM_001244638	84159	Hs.535297	NM_032199	ENSG00000150347	ARID5B	DESRT|MRF-2|MRF2	AT-rich interaction domain 5B	protein-coding	0.000000	0.412186	
chunk0067_371_1	chr15	48880131	48880875	+	0	NA	TTS (NM_014335)	TTS (NM_014335)	2410	NM_014335	23741	Hs.255973	NM_014335	ENSG00000255302	EID1	C15orf3|CRI1|EID-1|IRO45620|PNAS-22|PTD014|RBP21	EP300 interacting inhibitor of differentiation 1	protein-coding	0.004032	0.394631	
chunk0118_109_1	chr22	29334926	29335318	+	0	NA	intron (NM_145730, intron 15 of 20)	L2b|LINE|L2	-1855	NR_037426									0.020408	0.564885	
chunk0178_92_1	chr7	30533808	30534559	+	0	NA	Intergenic	Intergenic	-29342	NM_001199816	79017	Hs.530024	NM_024051	ENSG00000006625	GGCT	C7orf24|CRF21|GCTG|GGC	gamma-glutamylcyclotransferase	protein-coding	0.011984	0.505319	
chunk0089_396_1	chr18	68122683	68122947	+	0	NA	Intergenic	Intergenic	592301	NM_019022	54495	Hs.440534	NM_019022	ENSG00000166479	TMX3	PDIA13|TXNDC10	thioredoxin related transmembrane protein 3	protein-coding	0.007576	0.362264	
chunk0071_323_1	chr15	86934062	86934841	+	0	NA	intron (NM_152336, intron 22 of 23)	intron (NM_152336, intron 22 of 23)	-617483	NR_046012	727915	Hs.451281	NR_046012	ENSG00000260125	AGBL1-AS1	-	AGBL1 antisense RNA 1	ncRNA	0.000000	0.367949	
chunk0110_65_1	chr20	10928831	10929443	+	0	NA	Intergenic	Intergenic	-19865	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.004902	0.384992	
chunk0155_159_1	chr5	94159533	94160276	+	0	NA	intron (NM_001145678, intron 20 of 20)	MIRc|SINE|MIR	-48205	NM_032042	83989	Hs.600086	NM_032042	ENSG00000113391	FAM172A	C5orf21|Toupee	family with sequence similarity 172 member A	protein-coding	0.002692	0.331989	
chunk0068_32_1	chr15	50940537	50940839	+	0	NA	intron (NM_007347, intron 8 of 20)	intron (NM_007347, intron 8 of 20)	-3441	NR_027642	100132724	Hs.730493	NR_027642		DCAF13P3	-	DDB1 and CUL4 associated factor 13 pseudogene 3	pseudo	0.006623	0.333333	
chunk0074_386_1	chr16	35211031	35211503	+	0	NA	Intergenic	Intergenic	-40876	NR_002837	606551	Hs.646441	NR_002837		UBE2MP1	-	ubiquitin conjugating enzyme E2 M pseudogene 1	pseudo	0.002119	0.429175	
chunk0053_209_1	chr13	32036536	32037504	+	0	NA	intron (NM_023037, intron 1 of 60)	(TC)n|Simple_repeat|Simple_repeat	-5381	NR_103839	100507099	Hs.536364	NR_103839		FRY-AS1	-	FRY antisense RNA 1	ncRNA	0.006198	0.384933	
chunk0088_65_1	chr18	44385905	44386280	+	0	NA	intron (NR_110792, intron 2 of 4)	intron (NR_110792, intron 2 of 4)	145605	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.000000	0.430851	
chunk0039_362_1	chr11	106085351	106085613	+	0	NA	intron (NM_015423, intron 2 of 5)	intron (NM_015423, intron 2 of 5)	-7744	NM_152433	143879	Hs.101949	NM_152433	ENSG00000182359	KBTBD3	BKLHD3	kelch repeat and BTB domain containing 3	protein-coding	0.015267	0.361217	
chunk0086_224_1	chr18	22613299	22613594	+	0	NA	Intergenic	Intergenic	173391	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.037288	0.533784	
chunk0194_363_1	chr8	89721362	89721963	+	0	NA	intron (NR_125822, intron 4 of 4)	intron (NR_125822, intron 4 of 4)	36049	NR_125822	101929709	Hs.651324	NR_125822	ENSG00000251136	LOC101929709	-	uncharacterized LOC101929709	ncRNA	0.009983	0.420266	297(AGGAACACCGAGCTCT,-,0.00)
chunk0152_224_1	chr5	60401737	60402201	+	0	NA	intron (NM_001165899, intron 1 of 16)	intron (NM_001165899, intron 1 of 16)	-85744	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.006466	0.387097	
chunk0148_95_1	chr5	3741123	3741792	+	0	NA	Intergenic	Intergenic	145403	NM_024337	79192	Hs.424156	NM_024337	ENSG00000170549	IRX1	IRX-5|IRXA1	iroquois homeobox 1	protein-coding	0.017937	0.443284	
chunk0187_138_1	chr7	149497595	149497794	+	0	NA	5' UTR (NM_001163474, exon 1 of 7)	5' UTR (NM_001163474, exon 1 of 7)	113	NM_001163474	155061	Hs.24643	NM_152557	ENSG00000181220	ZNF746	PARIS	zinc finger protein 746	protein-coding	0.145729	0.790000	
chunk0169_381_1	chr6	107416963	107417373	+	0	NA	intron (NM_020381, intron 1 of 7)	intron (NM_020381, intron 1 of 7)	42407	NM_020381	57107	Hs.745008	NM_020381	ENSG00000164494	PDSS2	C6orf210|COQ10D3|COQ1B|DLP1|bA59I9.3|hDLP1	decaprenyl diphosphate synthase subunit 2	protein-coding	0.007317	0.335766	
chunk0080_109_1	chr17	26973584	26974095	+	0	NA	Intergenic	Intergenic	320157	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.003914	0.261719	
chunk0010_175_1	chr1	115775826	115776218	+	0	NA	Intergenic	L1ME1|LINE|L1	-7217	NM_001232	845	Hs.57975	NM_001232	ENSG00000118729	CASQ2	PDIB2	calsequestrin 2	protein-coding	0.002551	0.333333	
chunk0017_59_1	chr1	205478031	205478365	+	0	NA	Intergenic	Intergenic	-22112	NR_103783	101669762	Hs.666219	NR_103783		BLACAT1	LINC00912|linc-UBC1|onco-lncRNA-30	bladder cancer associated transcript 1	ncRNA	0.014970	0.492537	
chunk0004_214_1	chr1	46719011	46719252	+	0	NA	promoter-TSS (NM_014774)	promoter-TSS (NM_014774)	-67	NM_014774	9813	Hs.707688	NM_014774	ENSG00000159658	EFCAB14	KIAA0494	EF-hand calcium binding domain 14	protein-coding	0.120332	0.735537	
chunk0147_334_1	chr4	185318639	185319007	+	0	NA	intron (NM_031953, intron 7 of 18)	MER4C|LTR|ERV1	60175	NM_018409	55805	Hs.558513	NM_018409	ENSG00000109771	LRP2BP	-	LRP2 binding protein	protein-coding	0.002717	0.373984	
chunk0052_395_1	chr12	130657963	130658550	+	0	NA	Intergenic	Intergenic	-140391	NM_015347	23504	Hs.657441	NM_015347	ENSG00000060709	RIMBP2	PPP1R133|RBP2|RIM-BP2	RIMS binding protein 2	protein-coding	0.039182	0.528912	
chunk0208_256_1	chrX	20471187	20471897	+	0	NA	Intergenic	Intergenic	-204910	NM_004586	6197	Hs.445387	NM_004586	ENSG00000177189	RPS6KA3	CLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2	ribosomal protein S6 kinase A3	protein-coding	0.000000	0.313643	
chunk0022_215_1	chr10	13903154	13903411	+	0	NA	intron (NM_018027, intron 2 of 24)	L2a|LINE|L2	-171002	NR_120638	101928453	Hs.650212	NR_120638		LOC101928453	-	uncharacterized LOC101928453	ncRNA	0.011673	0.434109	
chunk0166_297_1	chr6	48967778	48967977	+	0	NA	Intergenic	Intergenic	495451	NM_000255	4594	Hs.485527	NM_000255	ENSG00000146085	MMUT	MCM|MUT	methylmalonyl-CoA mutase	protein-coding	0.000000	0.265000	
chunk0063_358_1	chr14	85672726	85673083	+	0	NA	Intergenic	Intergenic	142760	NM_013231	23768	Hs.533710	NM_013231	ENSG00000185070	FLRT2	-	fibronectin leucine rich transmembrane protein 2	protein-coding	0.002801	0.312849	245(AGGAACACTGTGTCTA,-,0.00),246(GGAACACTGTGTCTAC,+,0.00)
chunk0162_254_1	chr6	5140224	5140858	+	0	NA	intron (NR_104417, intron 2 of 3)	intron (NR_104417, intron 2 of 3)	7781	NR_037462	100500900		NR_037462	ENSG00000265083	MIR3691	mir-3691	microRNA 3691	ncRNA	0.011041	0.360630	
chunk0120_245_1	chr3	8603245	8603470	+	0	NA	Intergenic	Intergenic	31575	NR_024065	29931	Hs.433151	NM_013343		LINC00312	ERR-10|ERR10|LMCD1DN|LOH3CR2A|NAG-7|NAG7|NCRNA00312	long intergenic non-protein coding RNA 312	ncRNA	0.026667	0.508850	
chunk0162_409_1	chr5	179895511	179896138	+	0	NA	intron (NM_015043, intron 3 of 20)	intron (NM_015043, intron 3 of 20)	12032	NM_015043	23061	Hs.155829	NM_015043	ENSG00000197226	TBC1D9B	GRAMD9B	TBC1 domain family member 9B	protein-coding	0.012759	0.488854	
chunk0046_109_1	chr12	57242703	57242990	+	0	NA	TTS (NM_145064)	TTS (NM_145064)	-2154	NM_020142	56901	Hs.75069	NM_020142	ENSG00000185633	NDUFA4L2	NUOMS	NDUFA4 mitochondrial complex associated like 2	protein-coding	0.069686	0.614583	
chunk0204_136_1	chr9	95470067	95470276	+	0	NA	TTS (NR_038982)	TTS (NR_038982)	6562	NR_038982	100507346	Hs.661847	NR_038982		LOC100507346	-	uncharacterized LOC100507346	ncRNA	0.014354	0.376190	
chunk0195_6_1	chr8	92895490	92895998	+	0	NA	intron (NM_001171796, intron 4 of 5)	MSTD-int|LTR|ERVL-MaLR	69845	NM_001191036	286144	Hs.440643	NM_001171795	ENSG00000205133	TRIQK	C8orf83|PRO0845|UPF0599	triple QxxK/R motif containing	protein-coding	0.001969	0.363458	
chunk0063_424_1	chr14	88522507	88522787	+	0	NA	intron (NM_007039, intron 2 of 18)	intron (NM_007039, intron 2 of 18)	32132	NM_007039	11099	Hs.437040	NM_007039	ENSG00000070778	PTPN21	PTPD1|PTPRL10	protein tyrosine phosphatase non-receptor type 21	protein-coding	0.007143	0.320285	
chunk0128_58_1	chr3	104915772	104916454	+	0	NA	Intergenic	Intergenic	-450600	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.005865	0.329429	
chunk0186_395_1	chr7	144623648	144624111	+	0	NA	intron (NM_001042482, intron 5 of 7)	intron (NM_001042482, intron 5 of 7)	212174	NM_001042482	27010	Hs.660232	NM_022445	ENSG00000196511	TPK1	HTPK1|PP20|THMD5	thiamin pyrophosphokinase 1	protein-coding	0.004320	0.340517	
chunk0075_142_1	chr16	50336919	50337268	+	0	NA	intron (NM_001173984, intron 6 of 16)	MIR|SINE|MIR	31841	NM_013263	29117	Hs.437894	NM_013263	ENSG00000166164	BRD7	BP75|CELTIX1|NAG4	bromodomain containing 7	protein-coding	0.000000	0.357143	
chunk0049_282_1	chr12	93933977	93934262	+	0	NA	Intergenic	LTR23|LTR|ERV1	-196296	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.000000	0.335664	
chunk0165_129_1	chr6	33163833	33164182	+	0	NA	intron (NM_080681, intron 63 of 63).4	intron (NM_080681, intron 63 of 63).4	28461	NM_001163771	1302	Hs.390171	NM_080679	ENSG00000204248	COL11A2	DFNA13|DFNB53|FBCG2|HKE5|OSMEDA|OSMEDB|PARP|STL3	collagen type XI alpha 2 chain	protein-coding	0.020057	0.585714	
chunk0070_409_1	chr15	77483472	77484340	+	0	NA	3' UTR (NM_018200, exon 11 of 11)	3' UTR (NM_018200, exon 11 of 11)	63255	NM_001304504	10363	Hs.69594	NM_018200	ENSG00000140382	HMG20A	HMGX1|HMGXB1	high mobility group 20A	protein-coding	0.003456	0.446490	
chunk0147_272_1	chr4	183777868	183778445	+	0	NA	Intergenic	L1MB7|LINE|L1	-19866	NR_132761	56977	Hs.21958	NM_020225	ENSG00000173320	STOX2	-	storkhead box 2	protein-coding	0.005199	0.396194	
chunk0070_254_1	chr15	73630182	73630439	+	0	NA	intron (NM_012428, intron 1 of 8)	MIR|SINE|MIR	3102	NM_012428	27020	Hs.744867	NM_012428	ENSG00000156642	NPTN	GP55|GP65|SDFR1|SDR1|np55|np65	neuroplastin	protein-coding	0.003891	0.368217	
chunk0173_197_1	chr6	145250078	145250774	+	0	NA	Intergenic	Intergenic	-484443	NR_038246	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.002874	0.375897	284(AAGAGCAATCTGTTCA,-,0.00)
chunk0030_371_1	chr10	119137411	119137740	+	0	NA	non-coding (NR_130122, exon 8 of 8)	non-coding (NR_130122, exon 8 of 8)	28117	NR_110305	119559	Hs.655168	NM_178867	ENSG00000183605	SFXN4	BCRM1|COXPD18|SLC56A4	sideroflexin 4	protein-coding	0.003040	0.357576	
chunk0099_114_1	chr2	85921151	85921963	+	0	NA	Intergenic	MER61F|LTR|ERV1	32277	NR_110569	101928113	Hs.625888	NR_110569		ST3GAL5-AS1	-	ST3GAL5 antisense RNA 1 (head to head)	ncRNA	0.008621	0.446494	
chunk0016_95_1	chr1	195180882	195181477	+	0	NA	Intergenic	L1PA16|LINE|L1	1401302	NR_039888	100616363		NR_039888	ENSG00000265986	MIR4735	-	microRNA 4735	ncRNA	0.005042	0.337248	
chunk0003_98_1	chr1	31932179	31932846	+	0	NA	intron (NM_080391, intron 1 of 5)	intron (NM_080391, intron 1 of 5)	5875	NM_080391	8073	Hs.470477	NM_003479	ENSG00000184007	PTP4A2	HH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b	protein tyrosine phosphatase 4A2	protein-coding	0.002999	0.356287	
chunk0198_47_1	chr8	128437117	128437441	+	0	NA	intron (NR_121672, intron 2 of 7)	intron (NR_121672, intron 2 of 7)	127400	NR_121672	101927774	Hs.628730	NR_121672		LINC00824	LINC01263	long intergenic non-protein coding RNA 824	ncRNA	0.006173	0.323077	
chunk0143_300_1	chr4	118755295	118755938	+	0	NA	intron (NM_014822, intron 11 of 22)	intron (NM_014822, intron 11 of 22)	70246	NM_020961	57721	Hs.596872	NM_020961	ENSG00000145388	METTL14	hMETTL14	methyltransferase like 14	protein-coding	0.004666	0.326087	
chunk0065_112_1	chr15	24631941	24632587	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	-43130	NM_018958	23742	Hs.649663	NM_018958	ENSG00000185823	NPAP1	C15orf2	nuclear pore associated protein 1	protein-coding	0.003096	0.398764	
chunk0120_376_1	chr3	12135258	12135495	+	0	NA	intron (NM_133625, intron 1 of 12)	intron (NM_133625, intron 1 of 12)	23975	NM_003256	7079	Hs.591665	NM_003256	ENSG00000157150	TIMP4	TIMP-4	TIMP metallopeptidase inhibitor 4	protein-coding	0.000000	0.407563	
chunk0195_251_1	chr8	97777507	97778159	+	0	NA	intron (NM_018407, intron 1 of 6)	intron (NM_018407, intron 1 of 6)	2252	NM_018407	55353	Hs.492314	NM_018407	ENSG00000104341	LAPTM4B	LAPTM4beta|LC27	lysosomal protein transmembrane 4 beta	protein-coding	0.012270	0.382848	
chunk0090_268_1	chr18	74542197	74542758	+	0	NA	intron (NM_032649, intron 1 of 11)	intron (NM_032649, intron 1 of 11)	8020	NM_032649	84735	Hs.400613	NM_032649	ENSG00000150656	CNDP1	CN1|CPGL2|HsT2308	carnosine dipeptidase 1	protein-coding	0.008913	0.462633	269(AGGGACATTACGTCCC,-,0.00)
chunk0015_286_1	chr1	188682298	188682965	+	0	NA	Intergenic	Intergenic	1239003	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001499	0.276946	
chunk0184_123_1	chr7	114374116	114374444	+	0	NA	intron (NR_033766, intron 2 of 19)	intron (NR_033766, intron 2 of 19)	-40717	NM_001172766	93986	Hs.282787	NM_014491	ENSG00000128573	FOXP2	CAGH44|SPCH1|TNRC10	forkhead box P2	protein-coding	0.000000	0.255319	
chunk0199_29_1	chr9	738230	738429	+	0	NA	exon (NM_001256877, exon 9 of 13)	exon (NM_001256877, exon 9 of 13)	31523	NM_153186	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.030151	0.510000	
chunk0078_145_1	chr17	3976571	3976935	+	0	NA	Intergenic	Intergenic	-12289	NM_174956	489	Hs.513870	NM_005173	ENSG00000074370	ATP2A3	SERCA3	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3	protein-coding	0.035714	0.632877	
chunk0145_238_1	chr4	148598406	148599145	+	0	NA	Intergenic	L1PA5|LINE|L1	-156255	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.014885	0.527027	
chunk0061_191_1	chr14	60172268	60172703	+	0	NA	Intergenic	Intergenic	-6992	NM_016029	51635	Hs.59719	NM_016029	ENSG00000100612	DHRS7	CGI-86|SDR34C1|retDSR4|retSDR4	dehydrogenase/reductase 7	protein-coding	0.006897	0.435780	392(CATGACAGGCTGTGCC,-,0.00),393(ATGACAGGCTGTGCCC,+,0.00)
chunk0042_281_1	chr12	7265166	7265932	+	0	NA	Intergenic	Intergenic	-38783	NM_001080454	341392	Hs.450804	NM_001080454	ENSG00000215009	ACSM4	-	acyl-CoA synthetase medium chain family member 4	protein-coding	0.006527	0.409387	
chunk0206_278_1	chr9	124355151	124355394	+	0	NA	non-coding (NR_027406, exon 1 of 1)	non-coding (NR_027406, exon 1 of 1)	1799	NR_027406	100129034	Hs.654980	NR_027406		LOC100129034	-	uncharacterized LOC100129034	ncRNA	0.024691	0.590164	
chunk0098_14_1	chr2	65362875	65363083	+	0	NA	intron (NM_181784, intron 1 of 5)	AluSp|SINE|Alu	3818	NM_001128210	200734	Hs.59332	NM_181784	ENSG00000198369	SPRED2	Spred-2	sprouty related EVH1 domain containing 2	protein-coding	0.024038	0.444976	
chunk0179_295_1	chr7	49803829	49804078	+	0	NA	intron (NM_198570, intron 3 of 3)	intron (NM_198570, intron 3 of 3)	30292	NM_198570	375567	Hs.629302	NM_198570	ENSG00000188730	VWC2	PSST739|UNQ739	von Willebrand factor C domain containing 2	protein-coding	0.008032	0.400000	168(TAGTACATCCAGTCCT,-,0.00),169(AGTACATCCAGTCCTC,+,0.00),217(GTCACAGAGTGTACTT,+,0.00)
chunk0128_154_1	chr3	107115732	107116156	+	0	NA	intron (NR_028303, intron 2 of 3)	intron (NR_028303, intron 2 of 3)	124694	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.002358	0.334118	
chunk0117_353_1	chr21	44348932	44349258	+	0	NA	Intergenic	Intergenic	-4506	NR_038257	7226	Hs.369759	NM_003307	ENSG00000142185	TRPM2	EREG1|KNP3|LTRPC2|LTrpC-2|NUDT9H|NUDT9L1|TRPC7	transient receptor potential cation channel subfamily M member 2	protein-coding	0.052147	0.651376	176(CAGAGCACAGTGTCCT,-,0.00),177(AGAGCACAGTGTCCTG,+,0.00)
chunk0116_70_1	chr21	34522228	34522565	+	0	NA	intron (NM_001285389, intron 2 of 3)	intron (NM_001285389, intron 2 of 3)	2241	NM_001285393	1827	Hs.282326	NM_004414	ENSG00000159200	RCAN1	ADAPT78|CSP1|DSC1|DSCR1|MCIP1|RCN1	regulator of calcineurin 1	protein-coding	0.014837	0.455621	273(AAGCTCAGCCTGTGCC,-,0.00),274(AGCTCAGCCTGTGCCT,+,0.00)
chunk0176_230_1	chr7	15719332	15719699	+	0	NA	Intergenic	Intergenic	31137	NR_110094	101927524	Hs.386790	NR_110094		LINC02587	MEOX2-AS1	long intergenic non-protein coding RNA 2587	ncRNA	0.000000	0.342391	
chunk0124_234_1	chr3	56679130	56679347	+	0	NA	intron (NM_001112736, intron 1 of 23)	intron (NM_001112736, intron 1 of 23)	3869	NM_001112736	23272	Hs.116877	NM_015224	ENSG00000163946	TASOR	C3orf63|FAM208A|RAP140|TASOR1|se89-1	transcription activation suppressor	protein-coding	0.004608	0.325688	173(TTGAACATAGTGTACA,-,0.00)
chunk0120_80_1	chr3	3642593	3642972	+	0	NA	Intergenic	Intergenic	-156655	NM_020873	57633	Hs.163244	NM_020873	ENSG00000175928	LRRN1	FIGLER3|NLRR-1	leucine rich repeat neuronal 1	protein-coding	0.000000	0.318421	
chunk0014_54_1	chr1	175341900	175342109	+	0	NA	intron (NM_003285, intron 18 of 22)	intron (NM_003285, intron 18 of 22)	-148911	NM_001162894	9674	Hs.518138	NM_014656	ENSG00000235750	KIAA0040	-	KIAA0040	protein-coding	0.004785	0.442857	
chunk0066_339_1	chr15	36892104	36892303	+	0	NA	exon (NM_001220482, exon 13 of 13)	exon (NM_001220482, exon 13 of 13)	-5670	NR_024264	145845	Hs.302693	NM_001101327		LOC145845	-	uncharacterized LOC145845	ncRNA	0.015075	0.460000	
chunk0159_400_1	chr5	147452125	147452357	+	0	NA	intron (NM_001197294, intron 1 of 13)	intron (NM_001197294, intron 1 of 13)	1456	NM_001387	1809	Hs.519659	NM_001387	ENSG00000113657	DPYSL3	CRMP-4|CRMP4|DRP-3|DRP3|LCRMP|ULIP|ULIP-1	dihydropyrimidinase like 3	protein-coding	0.021552	0.489270	
chunk0012_165_1	chr1	158201207	158202077	+	0	NA	Intergenic	L1MEf|LINE|L1	21695	NM_001766	912	Hs.1799	NM_001766	ENSG00000158473	CD1D	CD1A|R3|R3G1	CD1d molecule	protein-coding	0.004598	0.254879	
chunk0167_104_1	chr6	57162024	57162778	+	0	NA	intron (NM_001031623, intron 14 of 14)	intron (NM_001031623, intron 14 of 14)	9812	NR_110742	101927211	Hs.705718	NR_110742		ZNF451-AS1	-	ZNF451 regulatory antisense RNA 1	ncRNA	0.006631	0.361589	
chunk0104_19_1	chr2	170564519	170564795	+	0	NA	intron (NM_001083615, intron 31 of 33)	L1M5|LINE|L1	149910	NR_027433	440925	Hs.668461	NM_001013712	ENSG00000222033	LINC01124	-	long intergenic non-protein coding RNA 1124	ncRNA	0.007246	0.285199	
chunk0200_132_1	chr9	17524325	17524830	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	-54377	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.000000	0.351779	244(AGGTACTGGATGTCCC,-,0.00),245(GGTACTGGATGTCCCA,+,0.00)
chunk0141_59_1	chr4	77637031	77637241	+	0	NA	Intergenic	LTR18C|LTR|ERVL	125383	NM_006419	10563	Hs.100431	NM_006419	ENSG00000156234	CXCL13	ANGIE|ANGIE2|BCA-1|BCA1|BLC|BLR1L|SCYB13	C-X-C motif chemokine ligand 13	protein-coding	0.004762	0.459716	
chunk0181_186_1	chr7	83340695	83341022	+	0	NA	Intergenic	Intergenic	-177977	NM_033026	27445	Hs.12376	NM_014510	ENSG00000186472	PCLO	ACZ|PCH3	piccolo presynaptic cytomatrix protein	protein-coding	0.000000	0.295732	
chunk0091_113_1	chr19	6056112	6056312	+	0	NA	intron (NM_000635, intron 1 of 17)	intron (NM_000635, intron 1 of 17)	54441	NM_134433	5990	Hs.465709	NM_000635	ENSG00000087903	RFX2	-	regulatory factor X2	protein-coding	0.020000	0.452736	
chunk0037_410_1	chr11	79794898	79795540	+	0	NA	Intergenic	Intergenic	-354568	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.001558	0.469673	262(GAGAACATGCTGTTCT,-,0.00),263(AGAACATGCTGTTCTT,+,0.00)
chunk0068_413_1	chr15	59149977	59150660	+	0	NA	intron (NM_004998, intron 26 of 27)	intron (NM_004998, intron 26 of 27)	20944	NR_031750	100313886		NR_031750	ENSG00000253030	MIR2116	mir-2116	microRNA 2116	ncRNA	0.002928	0.451754	188(TAAGACACAGTGTGCC,-,0.00),189(AAGACACAGTGTGCCT,+,0.00),402(TAAGACACAGTGTTCC,-,0.00),403(AAGACACAGTGTTCCT,+,0.00)
chunk0016_235_1	chr1	199778342	199778541	+	0	NA	Intergenic	Intergenic	-249161	NM_205860	2494	Hs.33446	NM_003822	ENSG00000116833	NR5A2	B1F|B1F2|CPF|FTF|FTZ-F1|FTZ-F1beta|LRH-1|LRH1|hB1F-2	nuclear receptor subfamily 5 group A member 2	protein-coding	0.015075	0.485000	
chunk0179_1_1	chr7	42320678	42320881	+	0	NA	Intergenic	HAL1ME|LINE|L1	-83760	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.000000	0.343137	
chunk0056_110_1	chr13	82761833	82762363	+	0	NA	Intergenic	L1PB4|LINE|L1	1120295	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.005660	0.318267	
chunk0046_52_1	chr12	55160360	55160632	+	0	NA	Intergenic	Intergenic	30727	NM_001005243	441639	Hs.553827	NM_001005243	ENSG00000170605	OR9K2	OR12-2	olfactory receptor family 9 subfamily K member 2	protein-coding	0.007353	0.263736	
chunk0173_221_1	chr6	145886161	145886719	+	0	NA	non-coding (NR_038246, exon 3 of 3)	non-coding (NR_038246, exon 3 of 3)	71564	NR_038245	100507557	Hs.124537	NR_038244	ENSG00000235652	LOC100507557	-	uncharacterized LOC100507557	ncRNA	0.000000	0.302326	
chunk0045_101_1	chr12	46149796	46150483	+	0	NA	Intergenic	L1ME3G|LINE|L1	116356	NM_001278389	81539	Hs.533770	NM_030674	ENSG00000111371	SLC38A1	ATA1|NAT2|SAT1|SNAT1	solute carrier family 38 member 1	protein-coding	0.002911	0.311047	
chunk0009_416_1	chr1	110798857	110799461	+	0	NA	Intergenic	Intergenic	-72040	NM_001040033	963	Hs.443057	NM_000560	ENSG00000143119	CD53	MOX44|TSPAN25	CD53 molecule	protein-coding	0.004967	0.413223	
chunk0053_240_1	chr13	32646409	32646608	+	0	NA	intron (NM_015032, intron 1 of 34)	L1ME3A|LINE|L1	60081	NM_015032	23047	Hs.744901	NM_015032	ENSG00000083642	PDS5B	APRIN|AS3|CG008	PDS5 cohesin associated factor B	protein-coding	0.015075	0.320000	
chunk0012_463_1	chr1	165535684	165535883	+	0	NA	intron (NR_026744, intron 3 of 6)	(TC)n|Simple_repeat|Simple_repeat	-8458	NM_001005214	440699	Hs.664975	NM_001005214	ENSG00000162763	LRRC52	-	leucine rich repeat containing 52	protein-coding	0.010050	0.380000	
chunk0106_165_1	chr2	200748113	200748628	+	0	NA	intron (NR_001557, intron 11 of 30)	MamTip3|DNA|hAT-Tip100	-13193	NR_037886	100507140	Hs.382116	NR_037886	ENSG00000237166	LINC01792	-	long intergenic non-protein coding RNA 1792	ncRNA	0.017476	0.486434	
chunk0172_160_1	chr6	135935742	135936863	+	0	NA	intron (NM_018945, intron 1 of 12)	intron (NM_018945, intron 1 of 12)	84606	NM_018945	27115	Hs.744230	NM_018945	ENSG00000171408	PDE7B	bA472E5.1	phosphodiesterase 7B	protein-coding	0.008921	0.428699	
chunk0080_140_1	chr17	27485842	27486255	+	0	NA	intron (NM_014238, intron 2 of 20)	intron (NM_014238, intron 2 of 20)	14038	NM_014238	8844	Hs.133534	NM_014238	ENSG00000141068	KSR1	KSR|RSU2	kinase suppressor of ras 1	protein-coding	0.012107	0.425121	
chunk0182_110_1	chr7	93379287	93379911	+	0	NA	Intergenic	Intergenic	103256	NR_030388	724023		NR_030388	ENSG00000208014	MIR653	MIRN653|hsa-mir-653|mir-653	microRNA 653	ncRNA	0.001603	0.360000	278(GTTACAGAATGTTCTT,+,0.00)
chunk0061_44_1	chr14	56170919	56171145	+	0	NA	intron (NM_021255, intron 1 of 5)	intron (NM_021255, intron 1 of 5)	52657	NM_021255	57161	Hs.657926	NM_021255	ENSG00000139946	PELI2	-	pellino E3 ubiquitin protein ligase family member 2	protein-coding	0.017699	0.444934	
chunk0092_272_1	chr19	33310688	33311241	+	0	NA	Intergenic	L2a|LINE|L2	8107	NR_026887	80054	Hs.287521	NR_026887	ENSG00000267296	CEBPA-DT	CEBPA-AS1	CEBPA divergent transcript	ncRNA	0.027125	0.539711	
chunk0072_451_1	chr15	101722175	101722473	+	0	NA	intron (NM_152334, intron 2 of 18)	intron (NM_152334, intron 2 of 18)	2118	NM_152334	123283	Hs.657163	NM_152334	ENSG00000185418	TARSL2	-	threonyl-tRNA synthetase like 2	protein-coding	0.013423	0.431438	
chunk0085_448_1	chr18	11185914	11186626	+	0	NA	Intergenic	Intergenic	-37508	NM_022068	63895	Hs.436902	NM_022068	ENSG00000154864	PIEZO2	C18orf30|C18orf58|DA3|DA5|DAIPT|FAM38B|FAM38B2|HsT748|HsT771|MWKS	piezo type mechanosensitive ion channel component 2	protein-coding	0.008427	0.323983	
chunk0005_43_1	chr1	54887846	54888855	+	0	NA	Intergenic	L2b|LINE|L2	-1102	NM_014762	1718	Hs.498727	NM_014762	ENSG00000116133	DHCR24	DCE|Nbla03646|SELADIN1|seladin-1	24-dehydrocholesterol reductase	protein-coding	0.012884	0.445545	
chunk0151_78_1	chr5	42757252	42757470	+	0	NA	intron (NM_001134848, intron 1 of 8)	intron (NM_001134848, intron 1 of 8)	543	NM_001134848	100129792	Hs.745017	NM_001134848	ENSG00000198865	CCDC152	CH5400	coiled-coil domain containing 152	protein-coding	0.036697	0.593607	
chunk0078_443_1	chr16	89609795	89610055	+	0	NA	Intergenic	Intergenic	-3383	NM_001128141	1800	Hs.109	NM_004413	ENSG00000015413	DPEP1	MBD1|MDP|RDP	dipeptidase 1	protein-coding	0.015385	0.440613	
chunk0118_140_1	chr22	29892803	29893374	+	0	NA	intron (NM_021090, intron 1 of 19)	L2a|LINE|L2	9919	NM_153050	8897	Hs.474536	NM_021090	ENSG00000100330	MTMR3	FYVE-DSP1|ZFYVE10	myotubularin related protein 3	protein-coding	0.003503	0.353147	
chunk0165_50_1	chr6	30378327	30378526	+	0	NA	Intergenic	Intergenic	33297	NM_001199120	79897	Hs.183232	NM_024839	ENSG00000241370	RPP21	C6orf135|CAT60	ribonuclease P/MRP subunit p21	protein-coding	0.005025	0.400000	
chunk0111_7_1	chr20	21767742	21768055	+	0	NA	Intergenic	Intergenic	62239	NM_006192	5075	Hs.122310	NM_006192	ENSG00000125813	PAX1	HUP48|OFC2	paired box 1	protein-coding	0.063898	0.576433	
chunk0042_421_1	chr12	11840435	11840634	+	0	NA	intron (NM_001987, intron 3 of 7)	intron (NM_001987, intron 3 of 7)	190680	NM_001987	2120	Hs.504765	NM_001987	ENSG00000139083	ETV6	TEL|TEL/ABL|THC5	ETS variant 6	protein-coding	0.030151	0.480000	
chunk0166_121_1	chr6	44563214	44563831	+	0	NA	Intergenic	Intergenic	127881	NR_039785	100616352		NR_039785	ENSG00000266619	MIR4642	-	microRNA 4642	ncRNA	0.024311	0.529126	
chunk0053_322_1	chr13	34247351	34247792	+	0	NA	Intergenic	Intergenic	393114	NR_047036	100874179	Hs.569253	NR_047036	ENSG00000225179	LINC00457	-	long intergenic non-protein coding RNA 457	ncRNA	0.009070	0.382353	197(GAAACAGAATGTTCAT,+,0.00)
chunk0103_317_1	chr2	167485322	167485673	+	0	NA	Intergenic	Intergenic	298214	NM_001199145	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.008547	0.380682	
chunk0123_299_1	chr3	46737290	46737781	+	0	NA	Intergenic	L1ME3B|LINE|L1	-1104	NM_001205271	100287362	Hs.673244	NM_001205271	ENSG00000261603	PRSS46P	PRSS46|TESSP6	serine protease 46, pseudogene	pseudo	0.014257	0.538618	
chunk0039_368_1	chr11	106137777	106138285	+	0	NA	Intergenic	L1PREC2|LINE|L1	-60293	NM_152433	143879	Hs.101949	NM_152433	ENSG00000182359	KBTBD3	BKLHD3	kelch repeat and BTB domain containing 3	protein-coding	0.003937	0.359528	
chunk0143_251_1	chr4	115053456	115053694	+	0	NA	intron (NM_022569, intron 2 of 13)	intron (NM_022569, intron 2 of 13)	60301	NM_022569	64579	Hs.591700	NM_022569	ENSG00000138653	NDST4	N-HSST|N-HSST 4|NDST-4|NHSST4	N-deacetylase and N-sulfotransferase 4	protein-coding	0.004202	0.359833	
chunk0076_55_1	chr16	61285345	61285969	+	0	NA	Intergenic	Intergenic	-229891	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.004808	0.297600	
chunk0160_451_1	chr5	165057193	165057553	+	0	NA	Intergenic	MIR|SINE|MIR	587094	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.002778	0.379501	
chunk0153_319_1	chr5	73770697	73770921	+	0	NA	intron (NM_001080479, intron 4 of 36)	intron (NM_001080479, intron 4 of 36)	-42709	NM_001244364	64283	Hs.482521	NM_001080479	ENSG00000214944	ARHGEF28	RGNEF|RIP2|p190RHOGEF	Rho guanine nucleotide exchange factor 28	protein-coding	0.004464	0.435556	
chunk0071_41_1	chr15	79896657	79896896	+	0	NA	intron (NM_001199760, intron 2 of 3)	CpG	221	NR_037654	10588	Hs.194294	NM_006441	ENSG00000136371	MTHFS	HsT19268|NEDMEHM	methenyltetrahydrofolate synthetase	protein-coding	0.121339	0.720833	
chunk0193_238_1	chr8	76707708	76707959	+	0	NA	exon (NM_024721, exon 3 of 11)	exon (NM_024721, exon 3 of 11)	-24558	NR_024360	100192378	Hs.596420	NR_024360	ENSG00000253661	ZFHX4-AS1	-	ZFHX4 antisense RNA 1	ncRNA	0.003984	0.464286	
chunk0015_426_1	chr1	191589652	191590119	+	0	NA	Intergenic	Intergenic	-568577	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.008565	0.346154	
chunk0092_334_1	chr19	35062905	35063365	+	0	NA	intron (NM_002151, intron 10 of 13)	MIR|SINE|MIR	22629	NM_182983	3249	Hs.182385	NM_002151	ENSG00000105707	HPN	TMPRSS1	hepsin	protein-coding	0.017391	0.438178	
chunk0130_39_1	chr3	129181787	129182154	+	0	NA	intron (NM_003418, intron 1 of 4)	intron (NM_003418, intron 1 of 4)	1997	NM_001127196	7555	Hs.518249	NM_003418	ENSG00000169714	CNBP	CNBP1|DM2|PROMM|RNF163|ZCCHC22|ZNF9	CCHC-type zinc finger nucleic acid binding protein	protein-coding	0.002725	0.331522	152(AAAAACAGCATGTACC,-,0.00),153(AAAACAGCATGTACCT,+,0.00)
chunk0132_99_1	chr3	155651420	155652068	+	0	NA	intron (NM_014996, intron 1 of 21)	intron (NM_014996, intron 1 of 21)	24572	NM_001130961	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.004630	0.345146	
chunk0023_337_1	chr10	29409580	29409876	+	0	NA	promoter-TSS (NR_110928)	promoter-TSS (NR_110928)	194	NR_110923	102724316	Hs.499209	NR_003930	ENSG00000224597	SVIL-AS1	-	SVIL antisense RNA 1	ncRNA	0.097973	0.693603	
chunk0196_404_1	chr8	115961979	115962540	+	0	NA	intron (NR_046215, intron 11 of 13)	intron (NR_046215, intron 11 of 13)	-293231	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.005348	0.364769	
chunk0185_178_1	chr7	128053028	128053291	+	0	NA	intron (NM_014390, intron 16 of 23)	intron (NM_014390, intron 16 of 23)	-22210	NM_022143	64101	Hs.655003	NM_022143	ENSG00000128594	LRRC4	NAG14|NGL-2	leucine rich repeat containing 4	protein-coding	0.000000	0.409091	
chunk0161_17_1	chr5	165665867	165666079	+	0	NA	Intergenic	Intergenic	1195694	NR_105065	102546299	Hs.437730	NR_105065	ENSG00000241956	LOC102546299	-	uncharacterized LOC102546299	ncRNA	0.009434	0.295775	
chunk0115_383_1	chr21	30321338	30321909	+	0	NA	Intergenic	Intergenic	-1334	NM_203405	388818	Hs.28704	NM_203405	ENSG00000197683	KRTAP26-1	-	keratin associated protein 26-1	protein-coding	0.010508	0.382867	
chunk0196_259_1	chr8	108771985	108772347	+	0	NA	Intergenic	L3b|LINE|CR1	15375	NM_153015	157753	Hs.99439	NM_153015	ENSG00000164841	TMEM74	NET36	transmembrane protein 74	protein-coding	0.000000	0.314050	
chunk0036_218_1	chr11	63690153	63690468	+	0	NA	intron (NR_049750, intron 1 of 5)	intron (NR_049750, intron 1 of 5)	8860	NM_201428	10313	Hs.743229	NM_006054	ENSG00000133318	RTN3	ASYIP|HAP|NSPL2|NSPLII|RTN3-A1	reticulon 3	protein-coding	0.009524	0.357595	
chunk0076_184_1	chr16	67676624	67677032	+	0	NA	intron (NR_027398, intron 1 of 1)	intron (NR_027398, intron 1 of 1)	10014	NM_001012984	388284	Hs.632208	NM_001012984	ENSG00000159761	C16orf86	-	chromosome 16 open reading frame 86	protein-coding	0.012255	0.479218	
chunk0070_388_1	chr15	76772813	76773169	+	0	NA	intron (NM_020843, intron 8 of 30)	intron (NM_020843, intron 8 of 30)	88953	NM_001145923	49855	Hs.458986	NM_020843	ENSG00000140386	SCAPER	IDDRP|MSTP063|ZNF291|Zfp291	S-phase cyclin A associated protein in the ER	protein-coding	0.002809	0.291317	
chunk0136_302_1	chr3	195134307	195134698	+	0	NA	promoter-TSS (NR_036089)	promoter-TSS (NR_036089)	78	NR_036089	100422926		NR_036089	ENSG00000265333	MIR3137	-	microRNA 3137	ncRNA	0.010230	0.456633	
chunk0142_89_1	chr4	94014443	94014924	+	0	NA	Intergenic	L2a|LINE|L2	185756	NM_005172	474	Hs.532680	NM_005172	ENSG00000172238	ATOH1	ATH1|HATH1|MATH-1|bHLHa14	atonal bHLH transcription factor 1	protein-coding	0.006237	0.375519	
chunk0194_315_1	chr8	88270780	88270995	+	0	NA	intron (NM_005941, intron 1 of 9)	intron (NM_005941, intron 1 of 9)	56601	NM_005941	4325	Hs.492187	NM_005941	ENSG00000156103	MMP16	C8orf57|MMP-X2|MT-MMP2|MT-MMP3|MT3-MMP	matrix metallopeptidase 16	protein-coding	0.004651	0.342593	
chunk0100_35_1	chr2	105444056	105444796	+	0	NA	Intergenic	Intergenic	-5653	NM_201557	2274	Hs.443687	NM_001450	ENSG00000115641	FHL2	AAG11|DRAL|FHL-2|SLIM-3|SLIM3	four and a half LIM domains 2	protein-coding	0.009459	0.438596	
chunk0198_82_1	chr8	130123973	130124296	+	0	NA	intron (NM_001247996, intron 18 of 30)	intron (NM_001247996, intron 18 of 30)	-39366	NR_045385	100507117	Hs.106015	NR_045385	ENSG00000280543	ASAP1-IT2	-	ASAP1 intronic transcript 2	ncRNA	0.006192	0.345679	
chunk0102_95_1	chr2	144152570	144152933	+	0	NA	intron (NM_001284234, intron 2 of 9)	intron (NM_001284234, intron 2 of 9)	58828	NM_001284233	79712	Hs.44780	NM_024659	ENSG00000121964	GTDC1	Hmat-Xa|mat-Xa	glycosyltransferase like domain containing 1	protein-coding	0.008264	0.304945	
chunk0164_34_1	chr6	18387239	18387438	+	0	NA	promoter-TSS (NM_182757)	promoter-TSS (NM_182757)	-12	NM_182757	255488	Hs.148741	NM_182757	ENSG00000137393	RNF144B	IBRDC2|PIR2|bA528A10.3|p53RFP	ring finger protein 144B	protein-coding	0.075377	0.625000	
chunk0197_281_1	chr8	124107171	124107650	+	0	NA	intron (NM_001039112, intron 39 of 40)	intron (NM_001039112, intron 39 of 40)	64112	NR_103547	157376	Hs.662360	NM_182525	ENSG00000253868	FER1L6-AS2	C8orf78	FER1L6 antisense RNA 2	ncRNA	0.014614	0.431250	
chunk0049_422_1	chr12	97695248	97695484	+	0	NA	Intergenic	L1PA5|LINE|L1	58232	NR_077241	643711	Hs.585557	NR_077240	ENSG00000257501	LOC643711	-	platelet activating factor acetylhydrolase 1b catalytic subunit 2 pseudogene	pseudo	0.004237	0.392405	192(TGGTACTGGCTGTTCC,-,0.00),193(GGTACTGGCTGTTCCT,+,0.00)
chunk0063_284_1	chr14	84302786	84302995	+	0	NA	Intergenic	LTR27E|LTR|ERV1	-1090989	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.014354	0.566667	
chunk0162_388_1	chr5	179519673	179519880	+	0	NA	Intergenic	L1M4a2|LINE|L1	-30785	NM_025158	80230	Hs.306769	NM_025158	ENSG00000176783	RUFY1	RABIP4|ZFYVE12	RUN and FYVE domain containing 1	protein-coding	0.033816	0.548077	
chunk0129_436_1	chr3	127798661	127799163	+	0	NA	intron (NM_001003794, intron 2 of 7)	intron (NM_001003794, intron 2 of 7)	23970	NM_007283	11343	Hs.277035	NM_007283	ENSG00000074416	MGLL	HU-K5|HUK5|MAGL|MGL	monoglyceride lipase	protein-coding	0.007968	0.548708	403(ATGGACTCATTGTTCT,-,0.00),404(TGGACTCATTGTTCTC,+,0.00)
chunk0143_6_1	chr4	105693430	105693986	+	0	NA	intron (NM_001142471, intron 3 of 6)	intron (NM_001142471, intron 3 of 6)	15016	NM_001142471	57117	Hs.480454	NM_020395	ENSG00000138785	INTS12	INT12|PHF22|SBBI22	integrator complex subunit 12	protein-coding	0.005396	0.298025	
chunk0212_7_1	chrY	6559900	6560309	+	0	NA	Intergenic	L1MA4A|LINE|L1	-86474	NR_003591	100101118	Hs.461138	NR_003591	ENSG00000185700	TTTY8B	NCRNA00217|TTTY8	testis-specific transcript, Y-linked 8B	ncRNA	0.004890	0.275610	
chunk0004_171_1	chr1	45827089	45827714	+	0	NA	intron (NM_015112, intron 2 of 28)	HAL1ME|LINE|L1	23788	NM_015112	23139	Hs.319481	NM_015112	ENSG00000086015	MAST2	MAST205|MTSSK	microtubule associated serine/threonine kinase 2	protein-coding	0.006400	0.372204	
chunk0184_36_1	chr7	112116648	112117314	+	0	NA	intron (NM_014705, intron 1 of 51)	Tigger9b|DNA|TcMar-Tigger	89426	NM_014705	9732	Hs.654652	NM_014705	ENSG00000128512	DOCK4	-	dedicator of cytokinesis 4	protein-coding	0.006006	0.389805	150(TGCCCAGGCTGTTCTC,+,0.00)
chunk0061_227_1	chr14	60620922	60621189	+	0	NA	Intergenic	Intergenic	-18161	NR_126480	104548971		NR_126480		SALRNA1	SAL-RNA1|XLOC_023166	senescence associated long non-coding RNA 1	ncRNA	0.007491	0.343284	
chunk0039_431_1	chr11	107900552	107901124	+	0	NA	Intergenic	HAL1|LINE|L1	-27637	NM_017516	54734	Hs.354906	NM_017516	ENSG00000179331	RAB39A	RAB39	RAB39A, member RAS oncogene family	protein-coding	0.003497	0.375218	
chunk0074_94_1	chr16	22046054	22046374	+	0	NA	intron (NM_001164579, intron 1 of 2)	intron (NM_001164579, intron 1 of 2)	38079	NM_001164579	730094	Hs.498890	NM_173501	ENSG00000185716	MOSMO	ATTHOG|BC030336|C16orf52	modulator of smoothened	protein-coding	0.003125	0.411215	
chunk0098_187_1	chr2	71764511	71764902	+	0	NA	Intergenic	L1MC4|LINE|L1	298004	NM_001130983	8291	Hs.252180	NM_003494	ENSG00000135636	DYSF	FER1L1|LGMD2B|LGMDR2|MMD1	dysferlin	protein-coding	0.010230	0.387755	42(GAGCACACATAGTGCC,-,0.00),43(AGCACACATAGTGCCC,+,0.00),143(AAGTACACAGTGAGCC,-,0.00),144(AGTACACAGTGAGCCT,+,0.00)
chunk0125_41_1	chr3	63239296	63239763	+	0	NA	Intergenic	Intergenic	-38709	NM_001130003	132204	Hs.648668	NM_144642	ENSG00000163630	SYNPR	SPO	synaptoporin	protein-coding	0.002141	0.459402	
chunk0178_407_1	chr7	40969706	40970027	+	0	NA	intron (NR_110831, intron 1 of 2)	intron (NR_110831, intron 1 of 2)	10073	NR_110831	101928744	Hs.639767	NR_110831	ENSG00000232458	LINC01450	-	long intergenic non-protein coding RNA 1450	ncRNA	0.000000	0.378882	
chunk0154_66_1	chr5	77369352	77369999	+	0	NA	intron (NM_001029854, intron 9 of 20)	MIRb|SINE|MIR	122832	NM_018268	55255	Hs.482573	NM_018268	ENSG00000164253	WDR41	MSTP048	WD repeat domain 41	protein-coding	0.010819	0.427469	
chunk0135_221_1	chr3	188554556	188554866	+	0	NA	intron (NM_001167671, intron 5 of 10)	intron (NM_001167671, intron 5 of 10)	13955	NR_046623	100873917	Hs.674993	NR_046623	ENSG00000224563	LPP-AS1	-	LPP antisense RNA 1	ncRNA	0.000000	0.360129	
chunk0131_337_1	chr3	151198945	151199483	+	0	NA	exon (NM_013308, exon 3 of 3)	exon (NM_013308, exon 3 of 3)	3987	NM_013308	29909	Hs.549152	NM_013308	ENSG00000174946	GPR171	H963	G protein-coupled receptor 171	protein-coding	0.014870	0.382189	
chunk0121_148_1	chr3	19039637	19039918	+	0	NA	Intergenic	L1P3|LINE|L1	-108748	NM_144633	131096	Hs.475656	NM_144633	ENSG00000183960	KCNH8	ELK|ELK1|Kv12.1|elk3	potassium voltage-gated channel subfamily H member 8	protein-coding	0.007117	0.425532	
chunk0010_107_1	chr1	114174133	114174872	+	0	NA	Intergenic	L2a|LINE|L2	-20652	NM_001270805	148281	Hs.370963	NM_205848	ENSG00000134207	SYT6	sytVI	synaptotagmin 6	protein-coding	0.008119	0.445946	
chunk0025_226_1	chr10	54029015	54029388	+	0	NA	intron (NM_001142769, intron 20 of 35)	intron (NM_001142769, intron 20 of 35)	578756	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.000000	0.304813	
chunk0003_275_1	chr1	36641811	36642010	+	0	NA	Intergenic	L2b|LINE|L2	-158596	NM_000760	1441	Hs.524517	NM_000760	ENSG00000119535	CSF3R	CD114|GCSFR|SCN7	colony stimulating factor 3 receptor	protein-coding	0.000000	0.475000	
chunk0057_268_1	chr13	105796032	105796665	+	0	NA	Intergenic	Intergenic	89518	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.006319	0.389590	
chunk0001_404_1	chr1	10893195	10893631	+	0	NA	Intergenic	L2a|LINE|L2	88624	NM_001170754	148345	Hs.127026	NM_173507	ENSG00000175262	C1orf127	-	chromosome 1 open reading frame 127	protein-coding	0.006881	0.443936	
chunk0145_232_1	chr4	148421203	148421450	+	0	NA	intron (NM_000901, intron 2 of 8)	intron (NM_000901, intron 2 of 8)	21194	NM_000901	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.004049	0.370968	
chunk0124_378_1	chr3	59534945	59535369	+	0	NA	Intergenic	Intergenic	-485168	NM_198463	200844	Hs.368434	NM_198463	ENSG00000163689	C3orf67	-	chromosome 3 open reading frame 67	protein-coding	0.004717	0.381176	159(AAGGACAAGTAGTCCC,-,0.00),160(AGGACAAGTAGTCCCT,+,0.00)
chunk0181_294_1	chr7	86966871	86967508	+	0	NA	intron (NM_001142749, intron 1 of 21)	AluSz|SINE|Alu	-1214	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.009419	0.452978	
chunk0196_341_1	chr8	114081241	114081629	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-644422	NM_052900	114788	Hs.91381	NM_052900	ENSG00000164796	CSMD3	-	CUB and Sushi multiple domains 3	protein-coding	0.010309	0.372751	
chunk0188_107_1	chr8	8931347	8931676	+	0	NA	Intergenic	Intergenic	-37890	NM_004225	9258	Hs.379414	NM_004225	ENSG00000147324	MFHAS1	LRRC65|MASL1|ROCO4	malignant fibrous histiocytoma amplified sequence 1	protein-coding	0.030395	0.518182	
chunk0206_334_1	chr9	125482133	125482554	+	0	NA	intron (NM_001006619, intron 8 of 10)	L1ME3A|LINE|L1	183453	NM_001282681	26130	Hs.42376	NM_015635	ENSG00000165219	GAPVD1	GAPEX5|GAPex-5|RAP6	GTPase activating protein and VPS9 domains 1	protein-coding	0.000000	0.329384	
chunk0125_16_1	chr3	61978297	61978935	+	0	NA	intron (NM_002841, intron 2 of 29)	intron (NM_002841, intron 2 of 29)	340331	NR_038281	100506994	Hs.656620	NR_038281	ENSG00000241472	PTPRG-AS1	-	PTPRG antisense RNA 1	ncRNA	0.007837	0.320814	
chunk0200_138_1	chr9	17832845	17833282	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	254109	NM_003026	6456	Hs.75149	NM_003026	ENSG00000107295	SH3GL2	CNSA2|EEN-B1|SH3D2A|SH3P4	SH3 domain containing GRB2 like 2, endophilin A1	protein-coding	0.004577	0.404110	
chunk0047_7_1	chr12	65064195	65064494	+	0	NA	intron (NM_007191, intron 6 of 9)	intron (NM_007191, intron 6 of 9)	57222	NM_007191	11197	Hs.284122	NM_007191	ENSG00000156076	WIF1	WIF-1	WNT inhibitory factor 1	protein-coding	0.006689	0.400000	
chunk0149_169_1	chr5	20533545	20533768	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	42217	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.250000	
chunk0176_393_1	chr7	18845531	18845778	+	0	NA	intron (NM_178425, intron 20 of 24)	intron (NM_178425, intron 20 of 24)	272018	NM_000474	7291	Hs.66744	NM_000474	ENSG00000122691	TWIST1	ACS3|BPES2|BPES3|CRS|CRS1|CSO|SCS|SWCOS|TWIST|bHLHa38	twist family bHLH transcription factor 1	protein-coding	0.004049	0.322581	
chunk0087_201_1	chr18	35849430	35849629	+	0	NA	Intergenic	HERVH-int|LTR|ERV1	55397	NR_029616	406963		NR_029616	ENSG00000207797	MIR187	MIRN187|miR-187|miRNA187	microRNA 187	ncRNA	0.005025	0.425000	
chunk0022_263_1	chr10	14905297	14905753	+	0	NA	non-coding (NR_110297, exon 17 of 17)	non-coding (NR_110297, exon 17 of 17)	26625	NM_024670	79723	Hs.554883	NM_024670	ENSG00000152455	SUV39H2	KMT1B	suppressor of variegation 3-9 homolog 2	protein-coding	0.013158	0.385120	
chunk0062_170_1	chr14	69483997	69484376	+	0	NA	promoter-TSS (NM_001161498)	promoter-TSS (NM_001161498)	-568	NM_001161498	400224	Hs.509796	NM_001161498	ENSG00000175985	PLEKHD1	UPF0639	pleckstrin homology and coiled-coil domain containing D1	protein-coding	0.068602	0.631579	
chunk0082_151_1	chr17	55561205	55561404	+	0	NA	Intergenic	CpG	-139324	NM_012329	23531	Hs.463483	NM_012329	ENSG00000108960	MMD	MMA|MMD1|PAQR11	monocyte to macrophage differentiation associated	protein-coding	0.060302	0.595000	
chunk0106_415_1	chr2	208021443	208021848	+	0	NA	intron (NM_001080475, intron 1 of 7)	L1ME4a|LINE|L1	3915	NM_001080475	389072	Hs.159188	NM_001080475	ENSG00000178385	PLEKHM3	DAPR|PLEKHM1L	pleckstrin homology domain containing M3	protein-coding	0.007407	0.302956	
chunk0091_165_1	chr19	7639857	7640078	+	0	NA	intron (NM_001127396, intron 4 of 18)	intron (NM_001127396, intron 4 of 18)	2866	NR_073560	6813	Hs.515104	NM_006949	ENSG00000076944	STXBP2	FHL5|Hunc18b|MUNC18-2|UNC18-2|UNC18B|pp10122	syntaxin binding protein 2	protein-coding	0.018100	0.463964	
chunk0034_437_1	chr11	39327131	39327655	+	0	NA	Intergenic	MER57B1|LTR|ERV1	678535	NR_120553	101928536	Hs.144776	NR_120553	ENSG00000254562	LINC01493	-	long intergenic non-protein coding RNA 1493	ncRNA	0.011450	0.396190	
chunk0059_179_1	chr14	32604536	32605107	+	0	NA	intron (NM_004274, intron 7 of 13)	intron (NM_004274, intron 7 of 13)	275548	NM_004274	9472	Hs.509083	NM_004274	ENSG00000151320	AKAP6	ADAP100|ADAP6|AKAP100|PRKA6|mAKAP	A-kinase anchoring protein 6	protein-coding	0.005254	0.405594	
chunk0012_113_1	chr1	156777061	156777260	+	0	NA	intron (NM_005973, intron 1 of 6)	MIRc|SINE|MIR	9678	NM_005973	5546	Hs.516948	NM_005973	ENSG00000143294	PRCC	RCCP1|TPRC	proline rich mitotic checkpoint control factor	protein-coding	0.010050	0.500000	
chunk0075_148_1	chr16	50631292	50631741	+	0	NA	intron (NM_033119, intron 8 of 9)	intron (NM_033119, intron 8 of 9)	-37339	NR_110908	101927272	Hs.460777	NR_110908	ENSG00000260249	LOC101927272	-	uncharacterized LOC101927272	ncRNA	0.011136	0.502222	
chunk0049_288_1	chr12	94032729	94033106	+	0	NA	Intergenic	Intergenic	-115806	NM_005761	10154	Hs.584845	NM_005761	ENSG00000136040	PLXNC1	CD232|PLXN-C1|VESPR	plexin C1	protein-coding	0.002653	0.399471	
chunk0203_429_1	chr9	91134539	91135177	+	0	NA	Intergenic	Intergenic	-59726	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.007837	0.394366	
chunk0110_143_1	chr20	13618473	13618921	+	0	NA	intron (NM_017714, intron 4 of 13)	intron (NM_017714, intron 4 of 13)	20239	NM_017714	55617	Hs.348297	NM_017714	ENSG00000089123	TASP1	C20orf13|dJ585I14.2	taspase 1	protein-coding	0.004464	0.320713	
chunk0144_155_1	chr4	130635397	130635881	+	0	NA	Intergenic	Intergenic	-864161	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.004132	0.280412	
chunk0007_82_1	chr1	78472804	78473507	+	0	NA	Intergenic	MER45B|DNA|hAT-Tip100	-17888	NM_001039585	5737	Hs.654365	NM_000959	ENSG00000122420	PTGFR	FP	prostaglandin F receptor	protein-coding	0.002845	0.369318	
chunk0118_52_1	chr22	27913347	27913573	+	0	NA	intron (NM_001284277, intron 2 of 10)	intron (NM_001284277, intron 2 of 10)	5754	NM_001284278	23760	Hs.705323	NM_012399	ENSG00000180957	PITPNB	PI-TP-beta|PtdInsTP|VIB1B	phosphatidylinositol transfer protein beta	protein-coding	0.000000	0.396476	
chunk0119_236_1	chr22	45538338	45538700	+	0	NA	intron (NM_006485, intron 8 of 14)	L1ME3G|LINE|L1	35680	NM_001996	2192	Hs.24601	NM_001996	ENSG00000077942	FBLN1	FBLN|FIBL1	fibulin 1	protein-coding	0.013812	0.462810	135(GGGATCAGACTGTTCT,-,0.00),136(GGATCAGACTGTTCTG,+,0.00)
chunk0027_456_1	chr10	81601078	81601467	+	0	NA	Intergenic	LTR104_Mam|LTR|Gypsy	-274042	NM_001165972	10718	Hs.125119	NM_001010848	ENSG00000185737	NRG3	HRG3|pro-NRG3	neuregulin 3	protein-coding	0.005141	0.353846	218(AAGGACTTTGTGTTCC,-,0.00),219(AGGACTTTGTGTTCCA,+,0.00)
chunk0167_39_1	chr6	54185877	54186263	+	0	NA	intron (NM_138569, intron 8 of 12)	intron (NM_138569, intron 8 of 12)	74652	NM_001281747	90523	Hs.449276	NM_138569	ENSG00000146147	MLIP	C6orf142|CIP	muscular LMNA interacting protein	protein-coding	0.002591	0.385013	
chunk0104_304_1	chr2	178829899	178830544	+	0	NA	3' UTR (NM_173648, exon 24 of 24)	3' UTR (NM_173648, exon 24 of 24)	-22798	NM_001256850	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.006202	0.365325	
chunk0143_349_1	chr4	121927893	121928489	+	0	NA	intron (NM_001130698, intron 2 of 11)	intron (NM_001130698, intron 2 of 11)	4922	NM_003305	7222	Hs.150981	NM_003305	ENSG00000138741	TRPC3	SCA41|TRP3	transient receptor potential cation channel subfamily C member 3	protein-coding	0.003356	0.335008	130(CAGTTCAGACTGTTCT,-,0.00),131(AGTTCAGACTGTTCTG,+,0.00),221(AAGAACACTTAGTACC,-,0.00),222(AGAACACTTAGTACCC,+,0.00)
chunk0028_270_1	chr10	90917606	90918063	+	0	NA	intron (NM_014391, intron 4 of 8)	intron (NM_014391, intron 4 of 8)	3441	NM_014391	27063	Hs.448589	NM_014391	ENSG00000148677	ANKRD1	ALRP|C-193|CARP|CVARP|MCARP|bA320F15.2	ankyrin repeat domain 1	protein-coding	0.013129	0.373362	
chunk0122_305_1	chr3	36881990	36882710	+	0	NA	intron (NM_014831, intron 7 of 22)	intron (NM_014831, intron 7 of 22)	62707	NM_014831	9881	Hs.170999	NM_014831	ENSG00000168016	TRANK1	LBA1	tetratricopeptide repeat and ankyrin repeat containing 1	protein-coding	0.000000	0.328710	381(TAGAACAGGAAGTTCA,-,0.00),382(AGAACAGGAAGTTCAG,+,0.00)
chunk0068_163_1	chr15	54078756	54079393	+	0	NA	intron (NM_001080534, intron 1 of 30)	L1PA17|LINE|L1	66170	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.007849	0.335423	
chunk0189_293_1	chr8	25957929	25958777	+	0	NA	intron (NM_022659, intron 6 of 15)	intron (NM_022659, intron 6 of 15)	86771	NM_022659	64641	Hs.491292	NM_022659	ENSG00000221818	EBF2	COE2|EBF-2|O/E-3|OE-3	EBF transcription factor 2	protein-coding	0.010613	0.448763	
chunk0171_226_1	chr6	126292256	126292818	+	0	NA	Intergenic	AluJo|SINE|Alu	-47252	NR_104462	387103	Hs.486401	NM_001012507	ENSG00000203760	CENPW	C6orf173|CENP-W|CUG2	centromere protein W	protein-coding	0.005338	0.442274	
chunk0210_189_1	chrX	80014487	80014957	+	0	NA	promoter-TSS (NM_001109879)	promoter-TSS (NM_001109879)	-34	NM_001109878	50945	Hs.374253	NM_016954	ENSG00000122145	TBX22	ABERS|CLPA|CPX|TBXX|dJ795G23.1	T-box transcription factor 22	protein-coding	0.006383	0.535032	229(CAGAACACCACGTTCT,-,0.00),230(AGAACACCACGTTCTC,+,0.00)
chunk0194_12_1	chr8	81515844	81516465	+	0	NA	Intergenic	Intergenic	15161	NM_001105281	646486	Hs.586370	NM_001105281	ENSG00000197416	FABP12	-	fatty acid binding protein 12	protein-coding	0.006441	0.381029	
chunk0115_21_1	chr21	20793160	20793359	+	0	NA	intron (NR_109787, intron 1 of 6)	intron (NR_109787, intron 1 of 6)	9849	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005025	0.370000	
chunk0137_451_1	chr4	29212816	29213417	+	0	NA	Intergenic	Intergenic	393534	NR_036237	100422937		NR_036237	ENSG00000283275	MIR4275	-	microRNA 4275	ncRNA	0.001664	0.280731	
chunk0009_403_1	chr1	110324467	110325183	+	0	NA	intron (NR_036595, intron 1 of 3)	MIRb|SINE|MIR	14346	NR_036595	440600	Hs.649375	NR_036595	ENSG00000227963	RBM15-AS1	AS-RBM15	RBM15 antisense RNA 1	ncRNA	0.001397	0.358438	
chunk0055_364_1	chr13	71751116	71751499	+	0	NA	intron (NM_004392, intron 1 of 6)	intron (NM_004392, intron 1 of 6)	115885	NM_080759	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.002611	0.388021	
chunk0156_151_1	chr5	107352077	107352276	+	0	NA	Intergenic	L1MA3|LINE|L1	318719	NM_001962	1946	Hs.288741	NM_001962	ENSG00000184349	EFNA5	AF1|EFL5|EPLG7|GLC1M|LERK7|RAGS	ephrin A5	protein-coding	0.010050	0.475000	
chunk0009_166_1	chr1	105340463	105341160	+	0	NA	Intergenic	MLT1A1|LTR|ERVL-MaLR	278124	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004304	0.356734	477(GGGGACACTGTGTTCC,-,0.00),478(GGGACACTGTGTTCCT,+,0.00)
chunk0046_140_1	chr12	58026395	58026851	+	0	NA	Intergenic	Intergenic	84961	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.000000	0.409190	
chunk0162_440_1	chr5	180595409	180596358	+	0	NA	Intergenic	Intergenic	-4396	NM_052863	92304	Hs.62492	NM_052863	ENSG00000161055	SCGB3A1	HIN-1|HIN1|LU105|PnSP-2|UGRP2	secretoglobin family 3A member 1	protein-coding	0.029505	0.606316	
chunk0081_11_1	chr17	37254510	37254833	+	0	NA	intron (NM_198836, intron 14 of 55).2	L2c|LINE|L2	9870	NR_132772	106635523		NR_132772		SNORA90	-	small nucleolar RNA, H/ACA box 90	snoRNA	0.015480	0.422840	
chunk0174_283_1	chr6	161839648	161840054	+	0	NA	intron (NM_013988, intron 3 of 8)	intron (NM_013988, intron 3 of 8)	-565776	NM_020133	56895	Hs.353175	NM_020133	ENSG00000026652	AGPAT4	1-AGPAT4|LPAAT-delta|dJ473J16.2	1-acylglycerol-3-phosphate O-acyltransferase 4	protein-coding	0.017241	0.437346	
chunk0141_256_1	chr4	85726445	85726724	+	0	NA	intron (NM_001025616, intron 3 of 9)	LTR16|LTR|ERVL	4116	NR_039656	100616349		NR_039656	ENSG00000266421	MIR4451	mir-4451	microRNA 4451	ncRNA	0.010753	0.460714	
chunk0065_118_1	chr15	24755515	24755840	+	0	NA	Intergenic	Intergenic	-67970	NM_022808	6638	Hs.564847	NM_003097	ENSG00000128739	SNRPN	HCERN3|PWCR|RT-LI|SM-D|SMN|SNRNP-N|SNURF-SNRPN|sm-N	small nuclear ribonucleoprotein polypeptide N	protein-coding	0.015385	0.368098	
chunk0109_22_1	chr20	445967	446261	+	0	NA	intron (NR_111901, intron 2 of 9)	L2c|LINE|L2	16439	NR_111901	128637	Hs.590876	NM_144628	ENSG00000125875	TBC1D20	C20orf140|WARBM4	TBC1 domain family member 20	protein-coding	0.003401	0.437288	
chunk0194_73_1	chr8	82637996	82638279	+	0	NA	Intergenic	Intergenic	-765621	NR_122034	103352670	Hs.399852	NR_122034	ENSG00000253898	LINC01419	LVCAT7|TCONS_00014497	long intergenic non-protein coding RNA 1419	ncRNA	0.003534	0.327465	202(GGGAACATGCTGTGAT,-,0.00),203(GGAACATGCTGTGATT,+,0.00)
chunk0043_210_1	chr12	19564270	19564469	+	0	NA	Intergenic	L1PREC2|LINE|L1	123788	NM_001267043	121536	Hs.126497	NM_153207	ENSG00000139154	AEBP2	-	AE binding protein 2	protein-coding	0.005025	0.340000	
chunk0008_281_1	chr1	94778671	94779317	+	0	NA	intron (NR_104131, intron 1 of 4)	L3|LINE|CR1	-33094	NR_039620	100616321		NR_039620	ENSG00000263526	MIR378G	-	microRNA 378g	ncRNA	0.000000	0.361669	
chunk0031_299_1	chr10	128684278	128684477	+	0	NA	Intergenic	Intergenic	398427	NR_120619	101927381	Hs.523342	NR_120619	ENSG00000280953	LINC01163	TCONS_00017722	long intergenic non-protein coding RNA 1163	ncRNA	0.010050	0.415000	
chunk0174_125_1	chr6	157312274	157312581	+	0	NA	intron (NM_018452, intron 3 of 3)	intron (NM_018452, intron 3 of 3)	11832	NM_018452	729515	Hs.157212	NM_018452	ENSG00000215712	TMEM242	BM033|C6orf35	transmembrane protein 242	protein-coding	0.026059	0.558442	
chunk0177_432_1	chr7	27929405	27929627	+	0	NA	intron (NM_175061, intron 2 of 4)	intron (NM_175061, intron 2 of 4)	189421	NM_006024	8887	Hs.34576	NM_006024	ENSG00000106052	TAX1BP1	CALCOCO3|T6BP|TXBP151	Tax1 binding protein 1	protein-coding	0.000000	0.390135	170(GAGTACATACAGTACC,-,0.00),171(AGTACATACAGTACCT,+,0.00)
chunk0147_278_1	chr4	184156190	184156680	+	0	NA	intron (NM_153343, intron 1 of 7)	intron (NM_153343, intron 1 of 7)	61526	NM_153343	133121	Hs.297814	NM_153343	ENSG00000164303	ENPP6	NPP6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding	0.012245	0.476578	229(CAGAACACAATGTACT,-,0.00),230(AGAACACAATGTACTG,+,0.00)
chunk0157_189_1	chr5	118854987	118855595	+	0	NA	intron (NM_173666, intron 4 of 5)	intron (NM_173666, intron 4 of 5)	-119295	NR_036262	100422885		NR_036262	ENSG00000283498	MIR1244-2	-	microRNA 1244-2	ncRNA	0.013158	0.379310	
chunk0088_143_1	chr18	46097439	46097638	+	0	NA	intron (NM_001001935, intron 1 of 11)	intron (NM_001001935, intron 1 of 11)	815	NM_001257334	498	Hs.298280	NM_004046	ENSG00000152234	ATP5F1A	ATP5A|ATP5A1|ATP5AL2|ATPM|COXPD22|HEL-S-123m|MC5DN4|MOM2|OMR|ORM|hATP1	ATP synthase F1 subunit alpha	protein-coding	0.030151	0.440000	
chunk0077_99_1	chr16	78099377	78099763	+	0	NA	non-coding (NR_120436, exon 1 of 6)	non-coding (NR_120436, exon 1 of 6)	157	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.119171	0.689922	
chunk0080_52_1	chr17	21663911	21664290	+	0	NA	Intergenic	(GATGAT)n|Simple_repeat|Simple_repeat	-28423	NM_001194958	100134444	Hs.200629	NM_001194958	ENSG00000260458	KCNJ18	KIR2.6|TTPP2	potassium voltage-gated channel subfamily J member 18	protein-coding	0.010554	0.421053	
chunk0086_72_1	chr18	13222608	13223323	+	0	NA	intron (NM_181482, intron 1 of 5)	intron (NM_181482, intron 1 of 5)	4235	NM_181482	753	Hs.697787	NM_004338	ENSG00000168675	LDLRAD4	C18orf1	low density lipoprotein receptor class A domain containing 4	protein-coding	0.013986	0.515363	
chunk0199_436_1	chr9	13905387	13905586	+	0	NA	Intergenic	L2c|LINE|L2	-22485	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.005025	0.310000	
chunk0098_369_1	chr2	78524510	78525218	+	0	NA	Intergenic	Intergenic	-234133	NR_110288	101927967	Hs.406952	NR_110288		LOC101927967	-	uncharacterized LOC101927967	ncRNA	0.002825	0.327221	
chunk0101_435_1	chr2	139393722	139394325	+	0	NA	Intergenic	Intergenic	496699	NR_033658	647012	Hs.639411	NR_033658		YY1P2	-	YY1 transcription factor pseudogene 2	pseudo	0.004975	0.329470	
chunk0165_445_1	chr6	40587501	40587802	+	0	NA	promoter-TSS (NM_020737)	promoter-TSS (NM_020737)	-187	NM_020737	57497	Hs.250015	NM_020737	ENSG00000156564	LRFN2	FIGLER2|KIAA1246|SALM1	leucine rich repeat and fibronectin type III domain containing 2	protein-coding	0.112957	0.705298	
chunk0009_280_1	chr1	107536181	107536528	+	0	NA	Intergenic	Intergenic	152150	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002882	0.433908	
chunk0195_41_1	chr8	93293370	93293596	+	0	NA	Intergenic	Intergenic	-126633	NM_001242668									0.013274	0.400881	
chunk0068_172_1	chr15	54173067	54173632	+	0	NA	intron (NM_001080534, intron 3 of 30)	L1ME2z|LINE|L1	160445	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.003540	0.291519	
chunk0212_377_1	chrX	150084680	150085348	+	0	NA	Intergenic	Intergenic	-142990	NR_031748	100313839		NR_031748	ENSG00000252454	MIR2114	-	microRNA 2114	ncRNA	0.008982	0.427504	
chunk0139_276_1	chr4	56941013	56941297	+	0	NA	Intergenic	L1MC4|LINE|L1	32242	NM_001193508	5978	Hs.307836	NM_005612	ENSG00000084093	REST	DFNA27|GINGF5|HGF5|NRSF|WT6|XBR	RE1 silencing transcription factor	protein-coding	0.000000	0.375439	
chunk0212_366_1	chrX	149481393	149481646	+	0	NA	3' UTR (NM_000202, exon 9 of 9)	3' UTR (NM_000202, exon 9 of 9)	23835	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.000000	0.291339	
chunk0094_180_1	chr2	5910096	5910340	+	0	NA	Intergenic	Intergenic	-22469	NR_026832	150622	Hs.560891	NR_026832		SILC1	LINC01105	sciatic injury induced lincRNA upregulator of SOX11	ncRNA	0.008197	0.412245	126(GAGAACTGGATGTGCA,-,0.00),127(AGAACTGGATGTGCAA,+,0.00)
chunk0064_428_1	chr14	99862073	99863031	+	0	NA	intron (NM_004434, intron 2 of 21)	L1MC3|LINE|L1	69144	NM_004434	2009	Hs.12451	NM_004434	ENSG00000066629	EML1	BH|ELP79|EMAP|EMAPL|HuEMAP	EMAP like 1	protein-coding	0.009395	0.443170	
chunk0107_270_1	chr2	217717297	217717580	+	0	NA	intron (NR_026597, intron 1 of 12)	intron (NR_026597, intron 1 of 12)	39155	NR_026597	729582	Hs.572788	NR_026597		DIRC3	-	disrupted in renal carcinoma 3	ncRNA	0.007067	0.443662	
chunk0093_337_1	chr19	54674038	54674490	+	0	NA	Intergenic	HUERS-P3-int|LTR|ERV1	11445	NM_001278428	11006	Hs.67846	NM_006847	ENSG00000186818	LILRB4	CD85K|ILT-3|ILT3|LIR-5|LIR5	leukocyte immunoglobulin like receptor B4	protein-coding	0.002212	0.353201	
chunk0126_404_1	chr3	85048166	85048400	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	13981	NR_132777	106635529		NR_132777		SNORA95	-	small nucleolar RNA, H/ACA box 95	snoRNA	0.000000	0.302128	
chunk0014_103_1	chr1	176744181	176744447	+	0	NA	intron (NM_020318, intron 14 of 22)	L1M5|LINE|L1	281143	NM_021936	60676	Hs.187284	NM_020318	ENSG00000116183	PAPPA2	PAPP-A2|PAPP-E|PAPPE|PLAC3	pappalysin 2	protein-coding	0.000000	0.374532	
chunk0073_59_1	chr16	3458851	3459311	+	0	NA	intron (NM_001083600, intron 1 of 6)	intron (NM_001083600, intron 1 of 6)	1089	NM_024845	79903	Hs.513296	NM_024845	ENSG00000122390	NAA60	HAT4|NAT15|NatF|hNaa60	N(alpha)-acetyltransferase 60, NatF catalytic subunit	protein-coding	0.021739	0.477223	
chunk0146_291_1	chr4	164769962	164770724	+	0	NA	intron (NR_038834, intron 1 of 2)	intron (NR_038834, intron 1 of 2)	16212	NR_038834									0.005249	0.389253	
chunk0174_400_1	chr6	165552104	165552882	+	0	NA	intron (NM_001130690, intron 1 of 21)	MER68|LTR|ERVL	109607	NM_006661	10846	Hs.348762	NM_006661	ENSG00000112541	PDE10A	ADSD2|HSPDE10A|IOLOD|LINC00473|PDE10A19	phosphodiesterase 10A	protein-coding	0.006427	0.456996	
chunk0126_259_1	chr3	79576373	79576572	+	0	NA	intron (NM_002941, intron 2 of 30)	intron (NM_002941, intron 2 of 30)	68585	NR_037488	100500877		NR_037488	ENSG00000265193	MIR3923	-	microRNA 3923	ncRNA	0.005025	0.270000	
chunk0128_82_1	chr3	105435261	105435626	+	0	NA	intron (NM_001627, intron 1 of 15)	intron (NM_001627, intron 1 of 15)	68730	NM_001243280	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.008219	0.336066	
chunk0055_233_1	chr13	62758818	62759105	+	0	NA	intron (NR_047029, intron 2 of 7)	L1MA9|LINE|L1	37731	NR_047029	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.003484	0.329861	
chunk0029_271_1	chr10	103241323	103242042	+	0	NA	Intergenic	Intergenic	-4205	NM_001143909	729020	Hs.458437	NM_001143909	ENSG00000235376	RPEL1	-	ribulose-5-phosphate-3-epimerase like 1	protein-coding	0.011127	0.536111	
chunk0175_415_1	chr6	168834668	168835466	+	0	NA	Intergenic	Intergenic	327234	NR_132622	101929484	Hs.364166	NR_132622	ENSG00000223485	LINC01615	-	long intergenic non-protein coding RNA 1615	ncRNA	0.011278	0.410513	
chunk0103_302_1	chr2	166748197	166748814	+	0	NA	Intergenic	Intergenic	-139982	NM_001199143	129446	Hs.73680	NM_152381	ENSG00000163092	XIRP2	CMYA3	xin actin binding repeat containing 2	protein-coding	0.000000	0.286408	
chunk0209_313_1	chrX	50070433	50070668	+	0	NA	intron (NM_001127898, intron 5 of 14)	intron (NM_001127898, intron 5 of 14)	1049	NM_001282163	1184	Hs.166486	NM_000084	ENSG00000171365	CLCN5	CLC5|CLCK2|ClC-5|DENTS|NPHL1|NPHL2|XLRH|XRN|hCIC-K2	chloride voltage-gated channel 5	protein-coding	0.000000	0.300847	
chunk0102_314_1	chr2	151257985	151258480	+	0	NA	intron (NM_198557, intron 1 of 3)	intron (NM_198557, intron 1 of 3)	3643	NM_198557	375287	Hs.302442	NM_198557	ENSG00000184898	RBM43	C2orf38	RNA binding motif protein 43	protein-coding	0.010101	0.437500	
chunk0003_218_1	chr1	35364370	35364769	+	0	NA	intron (NM_005095, intron 5 of 29)	intron (NM_005095, intron 5 of 29)	95602	NM_005095	9202	Hs.269211	NM_005095	ENSG00000146463	ZMYM4	CDIR|MYM|ZNF198L3|ZNF262	zinc finger MYM-type containing 4	protein-coding	0.002506	0.335000	
chunk0135_353_1	chr3	190505350	190505962	+	0	NA	Intergenic	Intergenic	-8395	NM_134470	3556	Hs.478673	NM_002182	ENSG00000196083	IL1RAP	C3orf13|IL-1RAcP|IL1R3	interleukin 1 receptor accessory protein	protein-coding	0.003268	0.386623	
chunk0154_295_1	chr5	83115535	83115830	+	0	NA	intron (NM_022550, intron 3 of 7)	Charlie24|DNA|hAT-Charlie	38184	NM_022406	7518	Hs.567359	NM_003401	ENSG00000152422	XRCC4	SSMED	X-ray repair cross complementing 4	protein-coding	0.000000	0.378378	
chunk0065_175_1	chr15	26111803	26112141	+	0	NA	Intergenic	Intergenic	-3841	NR_038852	503519	Hs.371380	NR_038851	ENSG00000259150	LINC00929	-	long intergenic non-protein coding RNA 929	ncRNA	0.011834	0.377581	
chunk0123_238_1	chr3	45599388	45599835	+	0	NA	intron (NM_014240, intron 1 of 7)	intron (NM_014240, intron 1 of 7)	4780	NM_014240	8994	Hs.193370	NM_014240	ENSG00000144791	LIMD1	-	LIM domains containing 1	protein-coding	0.017897	0.508929	
chunk0022_334_1	chr10	16630207	16630677	+	0	NA	intron (NM_152724, intron 7 of 7)	intron (NM_152724, intron 7 of 7)	-108437	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.014894	0.411890	
chunk0037_30_1	chr11	70106353	70106721	+	0	NA	intron (NM_018043, intron 5 of 25)	intron (NM_018043, intron 5 of 25)	21127	NR_030691	55107	Hs.503074	NM_018043	ENSG00000131620	ANO1	DOG1|ORAOV2|TAOS2|TMEM16A	anoctamin 1	protein-coding	0.013587	0.542005	228(GGGACAGACAGATCTG,+,0.00)
chunk0004_335_1	chr1	50493918	50494236	+	0	NA	intron (NM_007051, intron 15 of 18)	intron (NM_007051, intron 15 of 18)	-70630	NM_032110	63950	Hs.334481	NM_032110	ENSG00000142700	DMRTA2	-	DMRT like family A2	protein-coding	0.000000	0.407524	
chunk0136_317_1	chr3	195297485	195297816	+	0	NA	intron (NM_012287, intron 15 of 22)	intron (NM_012287, intron 15 of 22)	-26484	NM_152531	152002	Hs.478741	NM_152531	ENSG00000173950	XXYLT1	C3orf21	xyloside xylosyltransferase 1	protein-coding	0.000000	0.349398	
chunk0147_215_1	chr4	180588341	180589012	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	570473	NR_033918	728081	Hs.535735	NR_033918	ENSG00000248197	LINC00290	NCRNA00290	long intergenic non-protein coding RNA 290	ncRNA	0.004471	0.319940	
chunk0170_287_1	chr6	114856935	114857134	+	0	NA	Intergenic	L1PBa1|LINE|L1	-794157	NM_153612	222537	Hs.645477	NM_153612	ENSG00000249853	HS3ST5	3-OST-5|3OST5|HS3OST5|NBLA04021	heparan sulfate-glucosamine 3-sulfotransferase 5	protein-coding	0.005025	0.345000	
chunk0202_435_1	chr9	81879647	81879985	+	0	NA	Intergenic	Intergenic	-33621	NR_026851	347127	Hs.215235	NM_198509	ENSG00000240632	SPATA31D5P	FAM75D5|FAM75D5P	SPATA31 subfamily D member 5, pseudogene	pseudo	0.008876	0.439528	
chunk0193_299_1	chr8	77968777	77969490	+	0	NA	Intergenic	Intergenic	518436	NR_125830	102724874	Hs.571511	NR_125830		LOC102724874	-	uncharacterized LOC102724874	ncRNA	0.001403	0.322129	
chunk0105_393_1	chr2	192465193	192465429	+	0	NA	Intergenic	Intergenic	-270378	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.004237	0.476793	
chunk0161_328_1	chr5	173789502	173789882	+	0	NA	intron (NR_108028, intron 2 of 3)	L2b|LINE|L2	1250	NR_108028	101928154	Hs.366725	NR_108028		LINC01485	-	long intergenic non-protein coding RNA 1485	ncRNA	0.015789	0.511811	
chunk0144_381_1	chr4	140068402	140068822	+	0	NA	intron (NM_018717, intron 1 of 5)	MIR|SINE|MIR	85467	NM_018717	55534	Hs.586165	NM_018717	ENSG00000196782	MAML3	CAGH3|ERDA3|GDN|MAM-2|MAM2|TNRC3|mam-3	mastermind like transcriptional coactivator 3	protein-coding	0.004762	0.349169	
chunk0185_32_1	chr7	124329005	124329377	+	0	NA	Intergenic	Intergenic	22905	NR_110180	101928211	Hs.131334	NR_110180		LOC101928211	-	uncharacterized LOC101928211	ncRNA	0.005376	0.340483	
chunk0111_377_1	chr20	33909742	33910416	+	0	NA	Intergenic	L1ME1|LINE|L1	-83573	NM_007367	22913	Hs.136947	NM_007367	ENSG00000125970	RALY	HNRPCL2|P542	RALY heterogeneous nuclear ribonucleoprotein	protein-coding	0.004451	0.388148	
chunk0071_300_1	chr15	86014846	86015686	+	0	NA	Intergenic	Intergenic	101451	NR_120368	101929701	Hs.132570	NR_120368	ENSG00000260477	LINC01584	-	long intergenic non-protein coding RNA 1584	ncRNA	0.003571	0.392390	
chunk0165_65_1	chr6	30998290	30999192	+	0	NA	Intergenic	Intergenic	-7211	NM_001198815	100507679	Hs.582967	NM_001198815	ENSG00000261272	MUC22	PBMUCL1	mucin 22	protein-coding	0.013304	0.433001	
chunk0082_385_1	chr17	60590033	60590543	+	0	NA	Intergenic	MLT1L|LTR|ERVL-MaLR	-9895	NM_003620	8493	Hs.286073	NM_003620	ENSG00000170836	PPM1D	IDDGIP|PP2C-DELTA|WIP1	protein phosphatase, Mg2+/Mn2+ dependent 1D	protein-coding	0.011765	0.436399	
chunk0156_385_1	chr5	112963182	112963651	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	-13294	NM_001242377	167227	Hs.443875	NM_152624	ENSG00000172795	DCP2	NUDT20	decapping mRNA 2	protein-coding	0.006397	0.478723	
chunk0022_272_1	chr10	15122961	15123345	+	0	NA	intron (NM_001308295, intron 9 of 12)	intron (NM_001308295, intron 9 of 12)	-25834	NM_153244	221060	Hs.567777	NM_153244		RPP38-DT	C10orf111	RPP38 divergent transcript	ncRNA	0.007812	0.392208	219(AAAAACAGAAAGTCCT,-,0.00)
chunk0161_454_1	chr5	179223403	179223620	+	0	NA	intron (NM_014244, intron 3 of 21)	intron (NM_014244, intron 3 of 21)	121919	NM_014244	9509	Hs.23871	NM_014244	ENSG00000087116	ADAMTS2	ADAM-TS2|ADAMTS-2|ADAMTS-3|EDSDERMS|NPI|PC I-NP|PCI-NP|PCINP|PCPNI|PNPI	ADAM metallopeptidase with thrombospondin type 1 motif 2	protein-coding	0.059908	0.513761	
chunk0114_147_1	chr21	10353710	10354285	+	0	NA	Intergenic	L1PA4|LINE|L1	-59523	NM_001187	574	Hs.545789	NM_001187		BAGE	BAGE1|CT2.1	B melanoma antigen	protein-coding	0.008696	0.414931	101(TGGTACTGGTTGTTCT,-,0.00),102(GGTACTGGTTGTTCTT,+,0.00)
chunk0161_209_1	chr5	170821348	170821777	+	0	NA	Intergenic	MIR|SINE|MIR	37843	NM_001291985	2568	Hs.26225	NM_014211	ENSG00000094755	GABRP	-	gamma-aminobutyric acid type A receptor pi subunit	protein-coding	0.009324	0.425581	
chunk0201_314_1	chr9	43319295	43319723	+	0	NA	Intergenic	(TTCGA)n|Simple_repeat|Simple_repeat	531109	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.037383	0.358974	
chunk0078_429_1	chr16	89430649	89430848	+	0	NA	promoter-TSS (NR_110932)	promoter-TSS (NR_110932)	-170	NR_110931	101927817	Hs.667942	NR_110931		LOC101927817	-	uncharacterized LOC101927817	ncRNA	0.015075	0.450000	
chunk0076_60_1	chr16	61422834	61423277	+	0	NA	Intergenic	L2c|LINE|L2	-367289	NR_039624	100616345		NR_039624	ENSG00000283795	MIR4426	-	microRNA 4426	ncRNA	0.006772	0.351351	
chunk0116_204_1	chr21	37443634	37443883	+	0	NA	intron (NM_130436, intron 1 of 10)	MLT1C|LTR|ERVL-MaLR	23458	NM_001396	1859	Hs.368240	NM_001396	ENSG00000157540	DYRK1A	DYRK|DYRK1|HP86|MNB|MNBH|MRD7	dual specificity tyrosine phosphorylation regulated kinase 1A	protein-coding	0.016064	0.452000	
chunk0064_282_1	chr14	95215105	95215488	+	0	NA	intron (NM_024734, intron 5 of 12)	intron (NM_024734, intron 5 of 12)	-57286	NM_030621	23405	Hs.87889	NM_030621	ENSG00000100697	DICER1	DCR1|Dicer|Dicer1e|GLOW|HERNA|K12H4.8-LIKE|MNG1|RMSE2	dicer 1, ribonuclease III	protein-coding	0.007833	0.364583	
chunk0157_376_1	chr5	123778556	123778761	+	0	NA	Intergenic	LTR1B1|LTR|ERV1	233241	NM_001044723	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.024390	0.548544	
chunk0116_459_1	chr21	43922971	43923244	+	0	NA	intron (NM_020132, intron 2 of 9)	intron (NM_020132, intron 2 of 9)	-2291	NM_001037553	56894	Hs.248785	NM_020132	ENSG00000160216	AGPAT3	1-AGPAT 3|LPAAT-GAMMA1|LPAAT3	1-acylglycerol-3-phosphate O-acyltransferase 3	protein-coding	0.018315	0.580292	
chunk0157_367_1	chr5	123537857	123538434	+	0	NA	intron (NM_001270574, intron 1 of 9)	L1ME2|LINE|L1	-7272	NM_001270572	1456	Hs.129206	NM_004384	ENSG00000151292	CSNK1G3	CKI-gamma 3|CSNK1G3L	casein kinase 1 gamma 3	protein-coding	0.003466	0.321799	
chunk0112_142_1	chr20	38630459	38631041	+	0	NA	intron (NM_001164431, intron 5 of 14)	intron (NM_001164431, intron 5 of 14)	28816	NM_001164431	343578		NM_001164431	ENSG00000124143	ARHGAP40	C20orf95|dJ1100H13.4	Rho GTPase activating protein 40	protein-coding	0.012027	0.444254	
chunk0024_266_1	chr10	41855654	41855946	+	0	NA	Intergenic	Intergenic	512245	NR_024380	441666	Hs.255729	NR_024380	ENSG00000215146	LOC441666	-	zinc finger protein 91 pseudogene	pseudo	0.054795	0.378840	
chunk0151_424_1	chr5	55692549	55692840	+	0	NA	non-coding (NR_047649, exon 1 of 14)	non-coding (NR_047649, exon 1 of 14)	359	NM_001258286	153129	Hs.742101	NM_173514	ENSG00000177058	SLC38A9	URLC11	solute carrier family 38 member 9	protein-coding	0.003436	0.332192	
chunk0143_323_1	chr4	119730164	119730363	+	0	NA	Intergenic	Intergenic	74252	NR_110660	101927007	Hs.143958	NR_110660	ENSG00000250772	LINC01365	-	long intergenic non-protein coding RNA 1365	ncRNA	0.005025	0.420000	
chunk0170_90_1	chr6	110341904	110342153	+	0	NA	intron (NM_001123364, intron 1 of 4)	intron (NM_001123364, intron 1 of 4)	16244	NM_001123364	728464	Hs.634429	NM_001123364	ENSG00000053328	METTL24	C6orf186	methyltransferase like 24	protein-coding	0.008032	0.476000	
chunk0134_261_1	chr3	179450138	179450697	+	0	NA	intron (NM_021629, intron 1 of 9)	intron (NM_021629, intron 1 of 9)	1166	NM_021629	59345	Hs.173030	NM_021629	ENSG00000114450	GNB4	CMTD1F	G protein subunit beta 4	protein-coding	0.021467	0.380357	
chunk0038_430_1	chr11	94632190	94632880	+	0	NA	Intergenic	L1ME4b|LINE|L1	65227	NM_152431	143689	Hs.660188	NM_152431	ENSG00000134627	PIWIL4	HIWI2|MIWI2	piwi like RNA-mediated gene silencing 4	protein-coding	0.004348	0.325615	
chunk0067_433_1	chr15	49985444	49985840	+	0	NA	intron (NR_073596, intron 11 of 27)	intron (NR_073596, intron 11 of 27)	127674	NR_073598	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.010101	0.435768	
chunk0110_129_1	chr20	13333488	13334016	+	0	NA	Intergenic	Intergenic	-94065	NR_040043	100505536	Hs.665253	NR_040043		ISM1-AS1	-	ISM1 antisense RNA 1	ncRNA	0.011364	0.344045	
chunk0203_443_1	chr9	91354266	91354551	+	0	NA	intron (NM_001698, intron 3 of 9)	intron (NM_001698, intron 3 of 9)	7516	NM_001698	549	Hs.175905	NM_001698	ENSG00000148090	AUH	-	AU RNA binding methylglutaconyl-CoA hydratase	protein-coding	0.003509	0.293706	
chunk0151_358_1	chr5	54679634	54679844	+	0	NA	intron (NR_104658, intron 1 of 2)	intron (NR_104658, intron 1 of 2)	23585	NR_104659	102467080	Hs.637409	NR_104658		LOC102467080	-	uncharacterized LOC102467080	ncRNA	0.009524	0.312796	
chunk0107_369_1	chr2	222878308	222878521	+	0	NA	intron (NM_004457, intron 1 of 16)	intron (NM_004457, intron 1 of 16)	17400	NM_203372	2181	Hs.655772	NM_004457	ENSG00000123983	ACSL3	ACS3|FACL3|LACS 3|LACS3|PRO2194	acyl-CoA synthetase long chain family member 3	protein-coding	0.009390	0.415888	
chunk0210_367_1	chrX	96689504	96690046	+	0	NA	intron (NM_006729, intron 1 of 26)	intron (NM_006729, intron 1 of 26)	5112	NM_007309	1730	Hs.226483	NM_006729	ENSG00000147202	DIAPH2	DIA|DIA2|DRF2|POF|POF2|POF2A	diaphanous related formin 2	protein-coding	0.003690	0.394107	
chunk0209_28_1	chrX	35841506	35842110	+	0	NA	Intergenic	Intergenic	43466	NM_001099921	139604		NM_001099921	ENSG00000189023	MAGEB16	-	MAGE family member B16	protein-coding	0.003311	0.302479	
chunk0097_456_1	chr2	64748946	64749264	+	0	NA	Intergenic	Intergenic	-95193	NM_014755	9792	Hs.591569	NM_014755	ENSG00000179833	SERTAD2	Sei-2|TRIP-Br2|TRIPBR2	SERTA domain containing 2	protein-coding	0.003145	0.341693	
chunk0035_59_1	chr11	41507745	41508035	+	0	NA	Intergenic	Intergenic	-48254	NM_001258419	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.006897	0.443299	76(GGTGCATAGTGTTCTC,+,0.00)
chunk0210_376_1	chrX	97402204	97402744	+	0	NA	intron (NM_006729, intron 25 of 26)	intron (NM_006729, intron 25 of 26)	162061	NR_125391	10824	Hs.654372	NR_125391	ENSG00000236256	DIAPH2-AS1	EPAG	DIAPH2 antisense RNA 1	ncRNA	0.001852	0.329020	257(TAGAACATTTTGTTCA,-,0.00),258(AGAACATTTTGTTCAC,+,0.00)
chunk0087_5_1	chr18	30265139	30265598	+	0	NA	Intergenic	Intergenic	-33542	NR_031684	100302131		NR_031684	ENSG00000283218	MIR302F	MIRN302F|hsa-mir-302f	microRNA 302f	ncRNA	0.006536	0.282609	
chunk0173_353_1	chr6	149102664	149103596	+	0	NA	Intergenic	L1PB4|LINE|L1	-114794	NM_001292035	23118	Hs.269775	NM_015093	ENSG00000055208	TAB2	CHTD2|MAP3K7IP2|TAB-2	TGF-beta activated kinase 1 (MAP3K7) binding protein 2	protein-coding	0.005365	0.372990	
chunk0124_12_1	chr3	51620448	51620998	+	0	NA	intron (NM_015106, intron 2 of 21)	intron (NM_015106, intron 2 of 21)	-50452	NR_024012	51368	Hs.517864	NM_015926	ENSG00000164081	TEX264	ZSIG11	testis expressed 264, ER-phagy receptor	protein-coding	0.003636	0.368421	
chunk0098_270_1	chr2	75380966	75381222	+	0	NA	Intergenic	LTR27C|LTR|ERV1	-142974	NR_110281	101927884	Hs.671110	NR_110281	ENSG00000231172	LOC101927884	-	uncharacterized LOC101927884	ncRNA	0.027344	0.521401	
chunk0209_87_1	chrX	39062698	39063436	+	0	NA	Intergenic	Intergenic	-259184	NR_046706	100874211	Hs.662789	NR_046706		MID1IP1-AS1	-	MID1IP1 antisense RNA 1	ncRNA	0.008130	0.460081	
chunk0059_386_1	chr14	37452478	37452913	+	0	NA	intron (NM_001195296, intron 13 of 14)	intron (NM_001195296, intron 13 of 14)	142425	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.004598	0.353211	
chunk0062_90_1	chr14	68011482	68011925	+	0	NA	intron (NM_133509, intron 7 of 10)	intron (NM_133509, intron 7 of 10)	191924	NM_002877	5890	Hs.172587	NM_002877	ENSG00000182185	RAD51B	R51H2|RAD51L1|REC2	RAD51 paralog B	protein-coding	0.006772	0.362613	169(AGGTACTGGCTGTACC,-,0.00),170(GGTACTGGCTGTACCA,+,0.00)
chunk0060_30_1	chr14	40221267	40221867	+	0	NA	Intergenic	Intergenic	-733144	NR_109758	644919	Hs.434414	NR_109757		LINC02315	-	long intergenic non-protein coding RNA 2315	ncRNA	0.003333	0.349418	
chunk0192_305_1	chr8	66776623	66777088	+	0	NA	intron (NM_013257, intron 1 of 16)	intron (NM_013257, intron 1 of 16)	1674	NM_170709	23678	Hs.613417	NM_013257	ENSG00000104205	SGK3	CISK|SGK2|SGKL	serum/glucocorticoid regulated kinase family member 3	protein-coding	0.004301	0.360515	
chunk0153_191_1	chr5	71680265	71680581	+	0	NA	Intergenic	Intergenic	-38740	NM_004291	9607	Hs.1707	NM_004291	ENSG00000164326	CARTPT	CART	CART prepropeptide	protein-coding	0.000000	0.441640	
chunk0005_55_1	chr1	55216762	55217394	+	0	NA	non-coding (NR_038320, exon 1 of 1)	non-coding (NR_038320, exon 1 of 1)	1670	NR_038320	100507634	Hs.735428	NR_038320		LOC100507634	-	uncharacterized LOC100507634	ncRNA	0.007911	0.360190	
chunk0040_13_1	chr11	108736071	108736450	+	0	NA	intron (NM_004398, intron 13 of 17)	intron (NM_004398, intron 13 of 17)	71235	NM_004398	1662	Hs.591931	NM_004398	ENSG00000178105	DDX10	Dbp4|HRH-J8	DEAD-box helicase 10	protein-coding	0.007916	0.328947	
chunk0159_423_1	chr5	148097992	148098366	+	0	NA	intron (NM_006846, intron 11 of 32)	MIR3|SINE|MIR	34207	NM_001127699	11005	Hs.331555	NM_006846	ENSG00000133710	SPINK5	LEKTI|LETKI|NETS|NS|VAKTI	serine peptidase inhibitor, Kazal type 5	protein-coding	0.005348	0.389333	
chunk0096_435_1	chr2	38570050	38570341	+	0	NA	intron (NM_001142650, intron 9 of 13)	MIRb|SINE|MIR	32841	NM_001142650	92906	Hs.445497	NM_138394	ENSG00000143889	HNRNPLL	HNRPLL|SRRF	heterogeneous nuclear ribonucleoprotein L like	protein-coding	0.006873	0.356164	
chunk0200_199_1	chr9	20200860	20201149	+	0	NA	Intergenic	Intergenic	210234	NR_039684	100616229		NR_039684	ENSG00000263790	MIR4473	-	microRNA 4473	ncRNA	0.000000	0.451724	
chunk0138_124_1	chr4	36488846	36489175	+	0	NA	Intergenic	Intergenic	-62582	NR_031701	100313806		NR_031701	ENSG00000283207	MIR1255B1	MIR1255B-1|MIRN1255B1	microRNA 1255b-1	ncRNA	0.006079	0.430303	
chunk0126_341_1	chr3	82216524	82217741	+	0	NA	Intergenic	Intergenic	-455333	NM_000158	2632	Hs.436062	NM_000158	ENSG00000114480	GBE1	APBD|GBE|GSD4	1,4-alpha-glucan branching enzyme 1	protein-coding	0.004108	0.325123	
chunk0070_75_1	chr15	69969531	69969836	+	0	NA	Intergenic	Intergenic	109785	NR_030714	693214		NR_030714	ENSG00000207965	MIR629	MIRN629|hsa-mir-629|mir-629	microRNA 629	ncRNA	0.006557	0.343137	
chunk0211_142_1	chrX	112901970	112902307	+	0	NA	Intergenic	Intergenic	-61323	NM_133265	154796	Hs.528051	NM_133265	ENSG00000126016	AMOT	-	angiomotin	protein-coding	0.005935	0.417160	
chunk0092_263_1	chr19	33114201	33114586	+	0	NA	exon (NM_018025, exon 15 of 20)	exon (NM_018025, exon 15 of 20)	-17699	NM_173479	126248	Hs.211046	NM_173479	ENSG00000166359	WDR88	PQWD	WD repeat domain 88	protein-coding	0.012987	0.432642	
chunk0011_215_1	chr1	150183796	150184349	+	0	NA	Intergenic	Intergenic	33486	NM_001304723	51177	Hs.438824	NM_016274	ENSG00000023902	PLEKHO1	CKIP-1|CKIP1|JBP|OC120	pleckstrin homology domain containing O1	protein-coding	0.009042	0.380866	
chunk0157_80_1	chr5	116501867	116502355	+	0	NA	intron (NM_001300780, intron 3 of 19)	intron (NM_001300780, intron 3 of 19)	54613	NR_109879	101927233	Hs.732850	NR_109879	ENSG00000248445	SEMA6A-AS1	CTB-118N6.3	SEMA6A antisense RNA 1	ncRNA	0.008197	0.386503	
chunk0172_286_1	chr6	137804480	137805203	+	0	NA	Intergenic	Intergenic	-62347	NM_001270508	7128	Hs.211600	NM_006290	ENSG00000118503	TNFAIP3	A20|AISBL|OTUD7C|TNFA1P2	TNF alpha induced protein 3	protein-coding	0.002766	0.342541	396(CTGAACATCCTGTACT,-,0.00),397(TGAACATCCTGTACTT,+,0.00)
chunk0191_148_1	chr8	48871112	48871312	+	0	NA	Intergenic	Intergenic	50228	NM_003068	6591	Hs.360174	NM_003068	ENSG00000019549	SNAI2	SLUG|SLUGH|SLUGH1|SNAIL2|WS2D	snail family transcriptional repressor 2	protein-coding	0.045000	0.587065	
chunk0047_366_1	chr12	75087676	75088017	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	121902	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.002933	0.441520	
chunk0047_377_1	chr12	75236164	75236607	+	0	NA	Intergenic	Intergenic	-26637	NM_139137	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.002257	0.367117	
chunk0036_275_1	chr11	65251511	65251867	+	0	NA	Intergenic	Intergenic	-10163	NM_002689	23649	Hs.201897	NM_002689	ENSG00000014138	POLA2	-	DNA polymerase alpha 2, accessory subunit	protein-coding	0.025281	0.515406	61(GAGGACACCTTGTTTC,-,0.00),62(AGGACACCTTGTTTCC,+,0.00)
chunk0004_71_1	chr1	43492735	43492934	+	0	NA	Intergenic	LTR3B|LTR|ERVK	-38042	NM_130440	5792	Hs.272062	NM_002840	ENSG00000142949	PTPRF	BNAH2|LAR	protein tyrosine phosphatase receptor type F	protein-coding	0.005025	0.420000	
chunk0185_115_1	chr7	125906366	125906670	+	0	NA	Intergenic	MER77|LTR|ERVL	-642227	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.006579	0.393443	
chunk0018_291_1	chr1	220776886	220777085	+	0	NA	intron (NM_017898, intron 4 of 7)	intron (NM_017898, intron 4 of 7)	-9712	NM_022746	64757	Hs.497816	NM_022746	ENSG00000186205	MARC1	MOSC1	mitochondrial amidoxime reducing component 1	protein-coding	0.030151	0.550000	
chunk0040_72_1	chr11	111309419	111309920	+	0	NA	TTS (NM_001136105)	TTS (NM_001136105)	-4621	NM_001302644	399948	Hs.729225	NM_207429		COLCA1	C11orf92|CASC12|LOH11CR1F	colorectal cancer associated 1	protein-coding	0.005988	0.372510	
chunk0184_100_1	chr7	113394171	113394488	+	0	NA	Intergenic	Intergenic	-275747	NR_015442									0.006309	0.396226	
chunk0020_262_1	chr1	236308790	236309302	+	0	NA	Intergenic	Intergenic	-27007	NM_019891	56605	Hs.558519	NM_019891	ENSG00000086619	ERO1B	ERO1LB|Ero1beta	endoplasmic reticulum oxidoreductase 1 beta	protein-coding	0.013672	0.419103	
chunk0210_80_1	chrX	70220305	70220847	+	0	NA	Intergenic	Intergenic	-14079	NM_001013579	158833	Hs.407641	NM_001013579	ENSG00000204195	AWAT1	DGA2|DGAT2L3	acyl-CoA wax alcohol acyltransferase 1	protein-coding	0.009225	0.471455	
chunk0095_226_1	chr2	18830965	18831493	+	0	NA	Intergenic	L2b|LINE|L2	-241649	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.005682	0.404537	
chunk0014_116_1	chr1	177065439	177065866	+	0	NA	intron (NM_004319, intron 1 of 22)	intron (NM_004319, intron 1 of 22)	-36207	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.007026	0.427570	161(GAGAACAATGTGTACA,-,0.00),162(AGAACAATGTGTACAA,+,0.00)
chunk0117_197_1	chr22	21707528	21708232	+	0	NA	intron (NR_130910, intron 2 of 4)	MER58A|DNA|hAT-Charlie	27954	NR_130910	29799	Hs.517436	NM_013313	ENSG00000100027	YPEL1	FKSG3	yippee like 1	protein-coding	0.015625	0.448227	
chunk0194_378_1	chr8	90346992	90347229	+	0	NA	intron (NR_051989, intron 2 of 3)	L1MC3|LINE|L1	125622	NR_051989	100874052	Hs.571514	NR_051989	ENSG00000253394	LINC00534	-	long intergenic non-protein coding RNA 534	ncRNA	0.008439	0.373950	
chunk0137_21_1	chr4	10917744	10918330	+	0	NA	Intergenic	Intergenic	-233275	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.010239	0.398637	
chunk0209_365_1	chrX	53682314	53682564	+	0	NA	intron (NM_031407, intron 2 of 83)	intron (NM_031407, intron 2 of 83)	4290	NM_031407	10075	Hs.136905	NM_031407	ENSG00000086758	HUWE1	ARF-BP1|HECTH9|HSPC272|Ib772|LASU1|MRXST|MULE|URE-B1|UREB1	HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1	protein-coding	0.012000	0.442231	
chunk0057_273_1	chr13	105847407	105848025	+	0	NA	Intergenic	Intergenic	140886	NR_046391	144920	Hs.567700	NR_046391		LINC00343	LINC00344|NCRNA00343|NCRNA00344	long intergenic non-protein coding RNA 343	ncRNA	0.011327	0.389338	
chunk0185_413_1	chr7	134291834	134292033	+	0	NA	3' UTR (NM_032826, exon 10 of 10)	3' UTR (NM_032826, exon 10 of 10)	25142	NM_032826	84912	Hs.490181	NM_032826	ENSG00000205060	SLC35B4	YEA|YEA4	solute carrier family 35 member B4	protein-coding	0.000000	0.370000	
chunk0047_305_1	chr12	73867056	73867693	+	0	NA	Intergenic	Intergenic	425257	NR_038300	100507377	Hs.455715	NR_038300	ENSG00000251138	LOC100507377	-	uncharacterized LOC100507377	ncRNA	0.006279	0.322884	
chunk0036_207_1	chr11	63511459	63511750	+	0	NA	intron (NM_001142537, intron 5 of 7)	intron (NM_001142537, intron 5 of 7)	3617	NM_001142538	85329	Hs.502774	NM_033101	ENSG00000133317	LGALS12	GAL12|GRIP1	galectin 12	protein-coding	0.024055	0.592466	
chunk0119_49_1	chr22	40732551	40733228	+	0	NA	Intergenic	Intergenic	53711	NM_005297	2847	Hs.248122	NM_005297	ENSG00000128285	MCHR1	GPR24|MCH-1R|MCH1R|SLC-1|SLC1	melanin concentrating hormone receptor 1	protein-coding	0.013294	0.458702	310(AGAAACTGCCTGTTCC,-,0.00),311(GAAACTGCCTGTTCCT,+,0.00)
chunk0123_232_1	chr3	45538516	45539111	+	0	NA	intron (NM_015340, intron 20 of 21)	intron (NM_015340, intron 20 of 21)	-29268	NR_048543	100885795	Hs.641094	NR_048543		LARS2-AS1	-	LARS2 antisense RNA 1	ncRNA	0.010084	0.454698	264(CAGAACAGAATGGACT,-,0.00),265(AGAACAGAATGGACTG,+,0.00),308(TGGAACTCTCAGTTCC,-,0.00),309(GGAACTCTCAGTTCCA,+,0.00)
chunk0175_106_1	chr7	2982015	2982303	+	0	NA	intron (NM_032415, intron 1 of 24)	L1ME1|LINE|L1	61786	NM_032415	84433	Hs.648101	NM_032415	ENSG00000198286	CARD11	BENTA|BIMP3|CARMA1|IMD11|IMD11A|PPBL	caspase recruitment domain family member 11	protein-coding	0.031250	0.539792	
chunk0015_160_1	chr1	186553095	186553392	+	0	NA	Intergenic	Intergenic	-92135	NM_002597	5132	Hs.654381	NM_002597	ENSG00000116703	PDC	MEKA|PHD|PhLOP|PhLP	phosducin	protein-coding	0.000000	0.516779	
chunk0063_78_1	chr14	77681338	77682548	+	0	NA	intron (NM_006020, intron 3 of 5)	MER68|LTR|ERVL	26070	NM_006020	8846	Hs.94542	NM_006020	ENSG00000100601	ALKBH1	ABH|ABH1|ALKBH|alkB|hABH	alkB homolog 1, histone H2A dioxygenase	protein-coding	0.004132	0.398018	
chunk0060_426_1	chr14	53890664	53891172	+	0	NA	Intergenic	Intergenic	57566	NR_049843	100847076		NR_049843	ENSG00000266431	MIR5580	-	microRNA 5580	ncRNA	0.003937	0.424361	
chunk0043_226_1	chr12	19969996	19970363	+	0	NA	Intergenic	Intergenic	-44506	NR_040098	100506393	Hs.658356	NR_040098	ENSG00000256287	LINC02398	-	long intergenic non-protein coding RNA 2398	ncRNA	0.005450	0.336957	
chunk0148_314_1	chr5	13436402	13436953	+	0	NA	Intergenic	Intergenic	507803	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.005445	0.342391	
chunk0187_199_1	chr7	151768661	151769147	+	0	NA	intron (NM_001040633, intron 3 of 15)	MER110A|LTR|ERV1	-32590	NM_001304527	51422	Hs.647072	NM_016203	ENSG00000106617	PRKAG2	AAKG|AAKG2|CMH6|H91620p|WPWS	protein kinase AMP-activated non-catalytic subunit gamma 2	protein-coding	0.008230	0.525667	172(AAGGACAGCCCGTGCC,-,0.00),173(AGGACAGCCCGTGCCT,+,0.00)
chunk0168_448_1	chr6	95859380	95859746	+	0	NA	Intergenic	L2a|LINE|L2	-156406	NM_006581	10690	Hs.49117	NM_006581	ENSG00000172461	FUT9	Fuc-TIX	fucosyltransferase 9	protein-coding	0.010929	0.367847	191(GGGAACTGGCTGTACA,-,0.00),192(GGAACTGGCTGTACAG,+,0.00),218(GGGAACAGTCTCTGCT,-,0.00)
chunk0161_240_1	chr5	171600818	171601130	+	0	NA	Intergenic	Intergenic	181311	NM_003862	8817	Hs.87191	NM_003862	ENSG00000156427	FGF18	FGF-18|ZFGF5	fibroblast growth factor 18	protein-coding	0.012821	0.523962	
chunk0066_156_1	chr15	32042548	32042899	+	0	NA	intron (NR_046324, intron 2 of 7)	L1MC1|LINE|L1	12240	NR_046324	1139	Hs.511772	NM_000746	ENSG00000175344	CHRNA7	CHRNA7-2|NACHRA7	cholinergic receptor nicotinic alpha 7 subunit	protein-coding	0.000000	0.406250	
chunk0074_179_1	chr16	23908894	23909142	+	0	NA	intron (NM_212535, intron 2 of 16)	L2b|LINE|L2	73039	NM_002738	5579	Hs.460355	NM_002738	ENSG00000166501	PRKCB	PKC-beta|PKCB|PKCI(2)|PKCbeta|PRKCB1|PRKCB2	protein kinase C beta	protein-coding	0.024194	0.489960	
chunk0142_456_1	chr4	105569794	105570256	+	0	NA	non-coding (NR_046840, exon 3 of 3)	non-coding (NR_046840, exon 3 of 3)	8434	NR_046840	100874374	Hs.668908	NR_046840	ENSG00000249885	ARHGEF38-IT1	-	ARHGEF38 intronic transcript 1	ncRNA	0.004329	0.339093	217(TAGAACATGATGTACC,-,0.00),218(AGAACATGATGTACCA,+,0.00)
chunk0105_230_1	chr2	188318153	188318540	+	0	NA	intron (NR_045563, intron 2 of 12)	intron (NR_045563, intron 2 of 12)	20854	NR_030287	693146		NR_030287	ENSG00000207951	MIR561	MIRN561|hsa-mir-561|mir-561	microRNA 561	ncRNA	0.005168	0.329897	
chunk0039_81_1	chr11	97069244	97069763	+	0	NA	Intergenic	L1PA11|LINE|L1	-562626	NR_047481	100874053	Hs.742044	NR_047481		JRKL-AS1	-	JRKL antisense RNA 1	ncRNA	0.007707	0.351923	
chunk0172_426_1	chr6	140697518	140698198	+	0	NA	Intergenic	Intergenic	14044	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.000000	0.334802	
chunk0088_50_1	chr18	44024980	44025331	+	0	NA	Intergenic	Intergenic	506542	NR_110792	101927921	Hs.464986	NR_110792	ENSG00000267337	LINC01478	-	long intergenic non-protein coding RNA 1478	ncRNA	0.000000	0.355114	
chunk0123_374_1	chr3	48598434	48598760	+	0	NA	TTS (NM_003365)	TTS (NM_003365)	-3437	NM_000094	1294	Hs.476218	NM_000094	ENSG00000114270	COL7A1	EBD1|EBDCT|EBR1|NDNC8	collagen type VII alpha 1 chain	protein-coding	0.003067	0.574924	92(GAGAACACTATGCCCC,-,0.00),93(AGAACACTATGCCCCA,+,0.00)
chunk0096_133_1	chr2	28735472	28735671	+	0	NA	Intergenic	Intergenic	-16177	NM_206876	5500	Hs.702907	NM_002709	ENSG00000213639	PPP1CB	HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD	protein phosphatase 1 catalytic subunit beta	protein-coding	0.000000	0.380000	
chunk0159_125_1	chr5	138958659	138959287	+	0	NA	intron (NM_001037633, intron 8 of 10)	L1MC4|LINE|L1	-83605	NM_015564	26045	Hs.656653	NM_015564	ENSG00000146006	LRRTM2	-	leucine rich repeat transmembrane neuronal 2	protein-coding	0.006369	0.356121	432(TGGCACAGGATGTTCT,-,0.00),433(GGCACAGGATGTTCTT,+,0.00)
chunk0073_256_1	chr16	11809985	11810629	+	0	NA	Intergenic	MER51B|LTR|ERV1	-13049	NM_014153	29066	Hs.371856	NM_014153	ENSG00000122299	ZC3H7A	HSPC055|ZC3H7|ZC3HDC7	zinc finger CCCH-type containing 7A	protein-coding	0.020186	0.468217	
chunk0209_247_1	chrX	45756291	45757161	+	0	NA	Intergenic	Intergenic	-9602	NR_029636	407007		NR_029636	ENSG00000207725	MIR222	MIRN222|miRNA222|mir-222	microRNA 222	ncRNA	0.009195	0.344432	
chunk0181_260_1	chr7	85844343	85844875	+	0	NA	Intergenic	L1MA3|LINE|L1	-722678	NM_152754	223117	Hs.201340	NM_152754	ENSG00000153993	SEMA3D	Sema-Z2|coll-2	semaphorin 3D	protein-coding	0.001880	0.328330	
chunk0159_283_1	chr5	142600497	142600959	+	0	NA	exon (NM_001144892, exon 3 of 4)	exon (NM_001144892, exon 3 of 4)	13433	NM_033137	2246	Hs.483635	NM_000800	ENSG00000113578	FGF1	AFGF|ECGF|ECGF-beta|ECGFA|ECGFB|FGF-1|FGF-alpha|FGFA|GLIO703|HBGF-1|HBGF1	fibroblast growth factor 1	protein-coding	0.025974	0.434125	
chunk0178_418_1	chr7	41059384	41059797	+	0	NA	Intergenic	Intergenic	-42014	NR_110832	101928773	Hs.382363	NR_110832	ENSG00000224017	LINC01449	-	long intergenic non-protein coding RNA 1449	ncRNA	0.000000	0.471014	
chunk0143_16_1	chr4	105910719	105911421	+	0	NA	intron (NM_001033047, intron 2 of 11)	intron (NM_001033047, intron 2 of 11)	15630	NM_001033047	255743	Hs.518921	NM_198278	ENSG00000168743	NPNT	EGFL6L|POEM	nephronectin	protein-coding	0.002849	0.268848	
chunk0174_449_1	chr6	166329165	166329618	+	0	NA	intron (NR_130112, intron 4 of 8)	intron (NR_130112, intron 4 of 8)	13215	NR_130114	113402	Hs.487143	NM_145169	ENSG00000198818	SFT2D1	C6orf83|pRGR1	SFT2 domain containing 1	protein-coding	0.019868	0.409692	
chunk0010_331_1	chr1	118327277	118327509	+	0	NA	Intergenic	Intergenic	-142168	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.008621	0.381974	
chunk0068_178_1	chr15	54348771	54349010	+	0	NA	intron (NM_001080534, intron 15 of 30)	intron (NM_001080534, intron 15 of 30)	335986	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.000000	0.300000	
chunk0021_106_1	chr10	3192989	3193385	+	0	NA	Intergenic	Intergenic	-20346	NM_001242307	10531	Hs.528300	NM_014889	ENSG00000107959	PITRM1	MP1|PreP	pitrilysin metallopeptidase 1	protein-coding	0.030303	0.465995	
chunk0080_27_1	chr17	21036825	21037406	+	0	NA	intron (NM_015276, intron 1 of 12)	L1MC3|LINE|L1	5924	NM_015276	23326	Hs.462492	NM_015276	ENSG00000124422	USP22	USP3L	ubiquitin specific peptidase 22	protein-coding	0.012048	0.445017	
chunk0049_91_1	chr12	90816435	90816942	+	0	NA	Intergenic	Intergenic	-101335	NR_038868	439916	Hs.350600	NM_001039384	ENSG00000196243	LINC00615	C12orf37	long intergenic non-protein coding RNA 615	ncRNA	0.003945	0.387795	
chunk0125_349_1	chr3	71190797	71191529	+	0	NA	intron (NM_032682, intron 6 of 20)	intron (NM_032682, intron 6 of 20)	54002	NM_001244814	27086	Hs.59368	NM_032682	ENSG00000114861	FOXP1	12CC4|HSPC215|MFH|QRF1|hFKH1B	forkhead box P1	protein-coding	0.006831	0.377899	
chunk0192_366_1	chr8	68245760	68246277	+	0	NA	Intergenic	MER74A|LTR|ERVL	-84704	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.001934	0.420849	
chunk0133_113_1	chr3	168117546	168118254	+	0	NA	Intergenic	Intergenic	-21975	NM_001308155	27333	Hs.143600	NM_014498	ENSG00000173905	GOLIM4	GIMPC|GOLPH4|GPP130|P138	golgi integral membrane protein 4	protein-coding	0.005650	0.368124	
chunk0131_101_1	chr3	143775413	143775856	+	0	NA	intron (NM_173653, intron 4 of 15)	intron (NM_173653, intron 4 of 15)	72897	NM_173653	285195	Hs.302257	NM_173653	ENSG00000181804	SLC9A9	AUTS16|NHE9	solute carrier family 9 member A9	protein-coding	0.009029	0.378378	
chunk0080_88_1	chr17	26603767	26604210	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	690008	NR_039748	100616277		NR_039748	ENSG00000263583	MIR4522	-	microRNA 4522	ncRNA	0.011287	0.409910	
chunk0209_42_1	chrX	36543475	36543998	+	0	NA	Intergenic	Intergenic	-103444	NR_110412	101928627	Hs.590831	NR_110412	ENSG00000226484	LOC101928627	-	uncharacterized LOC101928627	ncRNA	0.001912	0.404580	
chunk0179_66_1	chr7	43921549	43921817	+	0	NA	intron (NM_001290076, intron 1 of 6)	MER61-int|LTR|ERV1	4728	NM_001290076	55665	Hs.663312	NM_017920	ENSG00000106608	URGCP	URG4	upregulator of cell proliferation	protein-coding	0.003731	0.334572	
chunk0072_383_1	chr15	100434109	100434308	+	0	NA	intron (NR_120374, intron 4 of 4)	intron (NR_120374, intron 4 of 4)	61269	NR_120374	102723320	Hs.416099	NR_120374		CERS3-AS1	-	CERS3 antisense RNA 1	ncRNA	0.030151	0.530000	
chunk0136_243_1	chr4	10006189	10006924	+	0	NA	intron (NM_020041, intron 2 of 11)	intron (NM_020041, intron 2 of 11)	14934	NM_020041	56606	Hs.444612	NM_020041	ENSG00000109667	SLC2A9	GLUT9|GLUTX|UAQTL2|URATv1	solute carrier family 2 member 9	protein-coding	0.016327	0.480978	
chunk0109_57_1	chr20	1268090	1268289	+	0	NA	intron (NM_014723, intron 2 of 5)	intron (NM_014723, intron 2 of 5)	1873	NM_014723	9751	Hs.323833	NM_014723	ENSG00000101298	SNPH	-	syntaphilin	protein-coding	0.005025	0.530000	
chunk0153_227_1	chr5	72125141	72125805	+	0	NA	intron (NM_005909, intron 2 of 6)	intron (NM_005909, intron 2 of 6)	18182	NM_005909	4131	Hs.335079	NM_005909	ENSG00000131711	MAP1B	FUTSCH|MAP5|PPP1R102	microtubule associated protein 1B	protein-coding	0.001506	0.360902	
chunk0204_359_1	chr9	101688905	101689481	+	0	NA	intron (NM_133445, intron 1 of 8)	intron (NM_133445, intron 1 of 8)	49387	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.003472	0.393414	
chunk0118_88_1	chr22	29034054	29034287	+	0	NA	intron (NM_032173, intron 2 of 8)	intron (NM_032173, intron 2 of 8)	-2694	NR_046851	100874123	Hs.674708	NR_046851	ENSG00000177993	ZNRF3-AS1	-	ZNRF3 antisense RNA 1	ncRNA	0.004292	0.482906	
chunk0147_263_1	chr4	183636499	183637041	+	0	NA	Intergenic	Intergenic	22449	NM_152682	201965	Hs.133337	NM_152682	ENSG00000182552	RWDD4	FAM28A|RWDD4A	RWD domain containing 4	protein-coding	0.018450	0.418048	
chunk0006_142_1	chr1	66277822	66278425	+	0	NA	intron (NM_001037340, intron 5 of 14)	L2a|LINE|L2	-53985	NM_001037339	5142	Hs.198072	NM_002600	ENSG00000184588	PDE4B	DPDE4|PDEIVB	phosphodiesterase 4B	protein-coding	0.001658	0.372517	
chunk0002_204_1	chr1	19514424	19515052	+	0	NA	Intergenic	Intergenic	-29097	NM_004930	832	Hs.432760	NM_004930	ENSG00000077549	CAPZB	CAPB|CAPPB|CAPZ	capping actin protein of muscle Z-line subunit beta	protein-coding	0.017516	0.468998	277(TTGAACAAGCTGTGCT,-,0.00),278(TGAACAAGCTGTGCTC,+,0.00)
chunk0186_457_1	chr7	148293265	148293630	+	0	NA	intron (NM_014141, intron 21 of 23)	intron (NM_014141, intron 21 of 23)	-297118	NM_145304	202865	Hs.352212	NM_145304	ENSG00000170279	C7orf33	-	chromosome 7 open reading frame 33	protein-coding	0.005479	0.349727	
chunk0103_308_1	chr2	167072513	167072720	+	0	NA	intron (NM_001079810, intron 2 of 9)	intron (NM_001079810, intron 2 of 9)	68339	NR_046665	100874011		NR_046665		XIRP2-AS1	-	XIRP2 antisense RNA 1	ncRNA	0.004831	0.355769	115(TTGAACTCTATGTTCT,-,0.00),116(TGAACTCTATGTTCTC,+,0.00)
chunk0025_210_1	chr10	53677142	53677633	+	0	NA	Intergenic	Intergenic	-905687	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.008147	0.325203	
chunk0206_215_1	chr9	123248596	123248795	+	0	NA	intron (NM_018387, intron 1 of 18)	intron (NM_018387, intron 1 of 18)	19869	NM_018387	55342	Hs.287659	NM_018387	ENSG00000165209	STRBP	HEL162|ILF3L|SPNR|p74	spermatid perinuclear RNA binding protein	protein-coding	0.000000	0.310000	150(GAGCACTGTCTGTACT,-,0.00),151(AGCACTGTCTGTACTT,+,0.00)
chunk0052_457_1	chr12	132776993	132777285	+	0	NA	intron (NM_005895, intron 19 of 23)	intron (NM_005895, intron 19 of 23)	-15251	NM_015114	23141	Hs.654628	NM_015114	ENSG00000176915	ANKLE2	KIAA0692|LEMD7|Lem4|MCPH16	ankyrin repeat and LEM domain containing 2	protein-coding	0.044521	0.600683	
chunk0122_7_1	chr3	27345625	27345900	+	0	NA	intron (NM_199347, intron 5 of 24)	intron (NM_199347, intron 5 of 24)	23698	NM_199347	152110	Hs.506115	NM_152534	ENSG00000163491	NEK10	-	NIMA related kinase 10	protein-coding	0.014545	0.449275	
chunk0055_390_1	chr13	73617845	73618053	+	0	NA	Intergenic	MIR|SINE|MIR	53705	NR_047009	100874155	Hs.672679	NR_047009		LINC00392	-	long intergenic non-protein coding RNA 392	ncRNA	0.009615	0.406699	
chunk0188_331_1	chr8	17630701	17630900	+	0	NA	intron (NM_006207, intron 5 of 6)	intron (NM_006207, intron 5 of 6)	50857	NR_036103	100422850		NR_036103	ENSG00000265520	MIR548V	-	microRNA 548v	ncRNA	0.005025	0.555000	
chunk0118_27_1	chr22	26568643	26568895	+	0	NA	intron (NM_003595, intron 1 of 6)	MER41B|LTR|ERV1	-3365	NM_001008566	8459	Hs.632768	NM_003595	ENSG00000128294	TPST2	TANGO13B|TPST-2	tyrosylprotein sulfotransferase 2	protein-coding	0.007937	0.395257	
chunk0103_229_1	chr2	164592892	164593134	+	0	NA	intron (NM_004490, intron 2 of 13)	intron (NM_004490, intron 2 of 13)	-24463	NM_001303422	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.004132	0.341564	
chunk0037_194_1	chr11	74302494	74302897	+	0	NA	intron (NR_110031, intron 2 of 11)	intron (NR_110031, intron 2 of 11)	-8667	NR_120556	101928580	Hs.569025	NR_120556	ENSG00000246211	P4HA3-AS1	-	P4HA3 antisense RNA 1	ncRNA	0.004963	0.425743	
chunk0067_135_1	chr15	42951858	42952187	+	0	NA	intron (NM_174916, intron 45 of 46)	intron (NM_174916, intron 45 of 46)	-31213	NM_173500	146057	Hs.646511	NM_173500	ENSG00000128881	TTBK2	SCA11|TTBK	tau tubulin kinase 2	protein-coding	0.000000	0.315152	136(AGGACTTGAAGTTCTT,+,0.00)
chunk0064_422_1	chr14	99685309	99685793	+	0	NA	intron (NM_006668, intron 1 of 14)	L2c|LINE|L2	1133	NM_006668	10858	Hs.25121	NM_006668	ENSG00000036530	CYP46A1	CP46|CYP46	cytochrome P450 family 46 subfamily A member 1	protein-coding	0.016529	0.527835	235(AGGGACACTCTGTGTT,-,0.00),236(GGGACACTCTGTGTTC,+,0.00)
chunk0204_241_1	chr9	98024779	98025154	+	0	NA	Intergenic	Intergenic	-31711	NM_018946	54187	Hs.522310	NM_018946	ENSG00000095380	NANS	HEL-S-100|SAS|SEMDCG|SEMDG	N-acetylneuraminate synthase	protein-coding	0.008000	0.428191	
chunk0027_89_1	chr10	73592009	73592445	+	0	NA	Intergenic	Intergenic	-16552	NM_152586	159195	Hs.657355	NM_152586	ENSG00000166348	USP54	C10orf29|bA137L10.3|bA137L10.4	ubiquitin specific peptidase 54	protein-coding	0.006881	0.384439	
chunk0133_106_1	chr3	167990709	167991158	+	0	NA	Intergenic	Intergenic	94985	NR_033843	646168	Hs.390443	NR_033843	ENSG00000244227	LRRC77P	LINC01330	leucine rich repeat containing 77, pseudogene	pseudo	0.000000	0.291111	205(CTAGACACTGTGTTCT,-,0.00),206(TAGACACTGTGTTCTC,+,0.00)
chunk0183_355_1	chr7	108641654	108642250	+	0	NA	Intergenic	Intergenic	-72184	NM_001287601	168451	Hs.707689	NM_182529	ENSG00000177683	THAP5	-	THAP domain containing 5	protein-coding	0.001678	0.361809	
chunk0190_80_1	chr8	30005670	30006153	+	0	NA	Intergenic	LTR101_Mam|LTR|ERVL	-48563	NR_036104	100422876		NR_036104	ENSG00000264788	MIR3148	mir-3148	microRNA 3148	ncRNA	0.012422	0.440083	
chunk0111_305_1	chr20	32074588	32075150	+	0	NA	intron (NM_001172131, intron 5 of 12)	L2b|LINE|L2	22681	NM_001172130	3055	Hs.655210	NM_002110	ENSG00000101336	HCK	JTK9|p59Hck|p61Hck	HCK proto-oncogene, Src family tyrosine kinase	protein-coding	0.021352	0.525755	205(CTGCACACACTGTACC,-,0.00),206(TGCACACACTGTACCA,+,0.00)
chunk0194_234_1	chr8	86308472	86308819	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-34120	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.000000	0.402299	
chunk0133_463_1	chr3	175312463	175313252	+	0	NA	intron (NM_207015, intron 4 of 13)	intron (NM_207015, intron 4 of 13)	-41761	NR_046713	100874244	Hs.581176	NR_046713		NAALADL2-AS2	-	NAALADL2 antisense RNA 2	ncRNA	0.007605	0.369620	616(AGGCTCAGTGTGTCCT,-,0.00),617(GGCTCAGTGTGTCCTC,+,0.00)
chunk0062_427_1	chr14	75260484	75260813	+	0	NA	Intergenic	Intergenic	-18130	NM_005252	2353	Hs.25647	NM_005252	ENSG00000170345	FOS	AP-1|C-FOS|p55	Fos proto-oncogene, AP-1 transcription factor subunit	protein-coding	0.006079	0.381818	108(AGGGACTGCAAGTGCT,-,0.00),109(GGGACTGCAAGTGCTT,+,0.00)
chunk0198_154_1	chr8	133048995	133049526	+	0	NA	intron (NM_001045556, intron 5 of 8)	intron (NM_001045556, intron 5 of 8)	-2679	NR_107002	102466865		NR_107002	ENSG00000276961	MIR7848	hsa-mir-7848	microRNA 7848	ncRNA	0.009416	0.415414	
chunk0028_14_1	chr10	82394155	82394594	+	0	NA	intron (NM_001010848, intron 2 of 8)	intron (NM_001010848, intron 2 of 8)	-161454	NR_120666	101929590	Hs.733268	NR_120666	ENSG00000225738	NRG3-AS1	C10orf100|Em:AC010157.1	NRG3 antisense RNA 1	ncRNA	0.011390	0.497727	
chunk0211_148_1	chrX	113759393	113759934	+	0	NA	intron (NR_131204, intron 1 of 2)	(TTGCT)n|Simple_repeat|Simple_repeat	178555	NR_131204	105463123	Hs.550218	NR_131204		XACT	-	X active specific transcript	ncRNA	0.003697	0.365314	299(AAGAACACTCAGGTCT,-,0.00)
chunk0066_398_1	chr15	39230755	39230970	+	0	NA	Intergenic	Intergenic	-19807	NM_001302797	400360	Hs.376109	NM_207445	ENSG00000175746	C15orf54	-	chromosome 15 open reading frame 54 (putative)	ncRNA	0.013953	0.472222	
chunk0060_194_1	chr14	47850923	47851270	+	0	NA	Intergenic	L1PA10|LINE|L1	-56082	NR_039996	100506433	Hs.547419	NR_039996	ENSG00000259129	LINC00648	-	long intergenic non-protein coding RNA 648	ncRNA	0.005764	0.341954	
chunk0023_101_1	chr10	22849279	22849827	+	0	NA	Intergenic	Intergenic	-78471	NM_001282745	219681	Hs.659807	NM_173081	ENSG00000165309	ARMC3	CT81|KU-CT-1	armadillo repeat containing 3	protein-coding	0.016423	0.489982	308(GAGAACAATCTGTCCC,-,0.00),309(AGAACAATCTGTCCCG,+,0.00)
chunk0184_149_1	chr7	116169089	116169338	+	0	NA	Intergenic	Intergenic	-41280	NM_015641	26136	Hs.592286	NM_015641	ENSG00000135269	TES	TESS|TESS-2	testin LIM domain protein	protein-coding	0.004016	0.412000	
chunk0163_257_1	chr6	12959996	12960391	+	0	NA	intron (NM_030948, intron 4 of 14)	MIRb|SINE|MIR	243388	NM_030948	221692	Hs.436996	NM_030948	ENSG00000112137	PHACTR1	EIEE70|RPEL|RPEL1|dJ257A7.2	phosphatase and actin regulator 1	protein-coding	0.007595	0.376263	249(GGCACACTTAGTGCCT,+,0.00)
chunk0140_457_1	chr4	76496184	76496383	+	0	NA	intron (NM_020859, intron 1 of 10)	L2|LINE|L2	61183	NM_020859	57619	Hs.683808	NM_020859	ENSG00000138771	SHROOM3	APXL3|MSTP013|SHRM|ShrmL	shroom family member 3	protein-coding	0.005025	0.575000	
chunk0168_380_1	chr6	93945735	93946158	+	0	NA	Intergenic	Intergenic	238863	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.009456	0.370283	
chunk0137_383_1	chr4	26452884	26453098	+	0	NA	Intergenic	Intergenic	37429	NM_000730	886	Hs.129	NM_000730	ENSG00000163394	CCKAR	CCK-A|CCK1-R|CCK1R|CCKRA	cholecystokinin A receptor	protein-coding	0.018692	0.455814	
chunk0039_373_1	chr11	106375486	106375869	+	0	NA	Intergenic	Intergenic	124270	NR_120551	101928535	Hs.409078	NR_120551	ENSG00000254811	LOC101928535	-	uncharacterized LOC101928535	ncRNA	0.010444	0.419271	
chunk0113_432_1	chr20	62307957	62308357	+	0	NA	TTS (NM_005560)	TTS (NM_005560)	5261	NM_007002	11047	Hs.90107	NM_007002	ENSG00000130706	ADRM1	ARM-1|ARM1|GP110	adhesion regulating molecule 1	protein-coding	0.042500	0.648379	231(GGGCCCAGGGTGTCCT,-,0.00),232(GGCCCAGGGTGTCCTC,+,0.00)
chunk0046_88_1	chr12	56521618	56521875	+	0	NA	promoter-TSS (NM_002898)	promoter-TSS (NM_002898)	-79	NM_002898	5939	Hs.505729	NM_002898	ENSG00000076067	RBMS2	SCR3	RNA binding motif single stranded interacting protein 2	protein-coding	0.015564	0.445736	
chunk0159_31_1	chr5	136905712	136906031	+	0	NA	Intergenic	L1MEa|LINE|L1	-540395	NM_001167577	57113	Hs.591263	NM_020389	ENSG00000069018	TRPC7	TRP7	transient receptor potential cation channel subfamily C member 7	protein-coding	0.000000	0.456250	
chunk0019_264_1	chr1	228114703	228115299	+	0	NA	Intergenic	Intergenic	-5689	NM_181441	128308	Hs.63236	NM_181441	ENSG00000162910	MRPL55	AAVG5835|L55nt|MRP-L55|PRO19675	mitochondrial ribosomal protein L55	protein-coding	0.006711	0.336683	304(AAGGACACACTGTTCC,-,0.00),305(AGGACACACTGTTCCG,+,0.00)
chunk0170_427_1	chr6	118674792	118675280	+	0	NA	intron (NM_001178035, intron 1 of 13)	L1MB7|LINE|L1	-23179	NM_206921	387119	Hs.656959	NM_206921	ENSG00000111860	CEP85L	C6orf204|NY-BR-15|bA57K17.2	centrosomal protein 85 like	protein-coding	0.004098	0.323108	
chunk0194_372_1	chr8	90001483	90002119	+	0	NA	intron (NM_001359, intron 1 of 9)	CpG	449	NM_001359	1666	Hs.492212	NM_001359	ENSG00000104325	DECR1	DECR|NADPH|SDR18C1	2,4-dienoyl-CoA reductase 1	protein-coding	0.077044	0.651491	196(GAGGACAGGGCGTCCC,-,0.00),197(AGGACAGGGCGTCCCG,+,0.00),259(GAGGACAGGGCGTCCC,-,0.00),260(AGGACAGGGCGTCCCG,+,0.00),290(GAGGACAGGGTGTCCC,-,0.00),291(AGGACAGGGTGTCCCG,+,0.00),320(GAGGACAGGGCGTTCT,-,0.00),321(AGGACAGGGCGTTCTG,+,0.00)
chunk0065_107_1	chr15	24258843	24259443	+	0	NA	Intergenic	Intergenic	-89237	NR_026647	791115	Hs.560378	NR_026647	ENSG00000260551	PWRN2	NCRNA00199	Prader-Willi region non-protein coding RNA 2	ncRNA	0.005000	0.377704	
chunk0125_251_1	chr3	69013678	69014033	+	0	NA	promoter-TSS (NM_001278689)	promoter-TSS (NM_001278689)	39	NR_103826	285203	Hs.518059	NM_173654	ENSG00000163378	EOGT	AER61|AOS4|C3orf64|EOGT1	EGF domain specific O-linked N-acetylglucosamine transferase	protein-coding	0.129577	0.747191	
chunk0013_99_1	chr1	167748767	167748966	+	0	NA	intron (NM_024569, intron 1 of 4)	L1ME4b|LINE|L1	26916	NM_024569	9019	Hs.493919	NM_003953	ENSG00000197965	MPZL1	MPZL1b|PZR|PZR1b|PZRa|PZRb	myelin protein zero like 1	protein-coding	0.000000	0.270000	
chunk0059_94_1	chr14	30935333	30935934	+	0	NA	intron (NM_001083893, intron 6 of 17)	intron (NM_001083893, intron 6 of 17)	-45825	NR_038356	100506071	Hs.729195	NR_038356	ENSG00000258525	LOC100506071	-	uncharacterized LOC100506071	ncRNA	0.004992	0.312292	
chunk0071_6_1	chr15	78707608	78707988	+	0	NA	Intergenic	L1ME3|LINE|L1	-44239	NR_036495	646938	Hs.449783	NR_036495	ENSG00000238166	LOC646938	-	TBC1 domain family member 2B pseudogene	pseudo	0.007895	0.422572	194(GGGAACATTCTGTATC,-,0.00),195(GGAACATTCTGTATCT,+,0.00)
chunk0202_133_1	chr9	73225076	73225359	+	0	NA	Intergenic	L1PA13|LINE|L1	73486	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.380282	
chunk0164_169_1	chr6	21883615	21884275	+	0	NA	intron (NR_015410, intron 4 of 11)	intron (NR_015410, intron 4 of 11)	217501	NR_015410	401237	Hs.712707	NR_015410		CASC15	CANT|LINC00340|lnc-SOX4-1	cancer susceptibility 15	ncRNA	0.006061	0.405446	
chunk0172_194_1	chr6	136606438	136606693	+	0	NA	intron (NM_005923, intron 18 of 29)	intron (NM_005923, intron 18 of 29)	-22549	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.011765	0.414062	
chunk0035_256_1	chr11	46443615	46444016	+	0	NA	intron (NM_001300731, intron 10 of 16)	intron (NM_001300731, intron 10 of 16)	-7992	NR_036118	100422825		NR_036118	ENSG00000283497	MIR3160-2	mir-3160-2	microRNA 3160-2	ncRNA	0.004988	0.390547	
chunk0014_405_1	chr1	183023793	183024208	+	0	NA	exon (NM_002293, exon 1 of 28)	exon (NM_002293, exon 1 of 28)	540	NM_002293	3915	Hs.609663	NM_002293	ENSG00000135862	LAMC1	LAMB2	laminin subunit gamma 1	protein-coding	0.086747	0.689904	
chunk0072_21_1	chr16	477551	478088	+	0	NA	intron (NM_001142272, intron 1 of 11)	intron (NM_001142272, intron 1 of 11)	2969	NM_001142272	9727	Hs.531642	NM_014700	ENSG00000090565	RAB11FIP3	CART1|FIP3-Rab11|Rab11-FIP3	RAB11 family interacting protein 3	protein-coding	0.027933	0.555762	257(CAGCACTCCCTGTTCC,-,0.00),258(AGCACTCCCTGTTCCC,+,0.00)
chunk0151_352_1	chr5	54440584	54440976	+	0	NA	Intergenic	Intergenic	-14821	NM_006308	8988	Hs.41707	NM_006308	ENSG00000169271	HSPB3	DHMN2C|HMN2C|HSPL27	heat shock protein family B (small) member 3	protein-coding	0.005102	0.424936	
chunk0167_68_1	chr6	56312004	56312598	+	0	NA	Intergenic	L2c|LINE|L2	-64721	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.005051	0.405042	
chunk0212_305_1	chrX	142275497	142276298	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-70607	NM_016249	51438	Hs.123536	NM_016249	ENSG00000046774	MAGEC2	CT10|HCA587|MAGEE1	MAGE family member C2	protein-coding	0.006242	0.336658	
chunk0036_98_1	chr11	60970339	60970538	+	0	NA	Intergenic	Intergenic	-1203	NM_001254751	923	Hs.744366	NM_006725	ENSG00000013725	CD6	TP120	CD6 molecule	protein-coding	0.020101	0.555000	
chunk0082_26_1	chr17	50698571	50698805	+	0	NA	intron (NM_052855, intron 3 of 4)	L1MC4|LINE|L1	9221	NM_052855	91369	Hs.463426	NM_052855	ENSG00000154945	ANKRD40	-	ankyrin repeat domain 40	protein-coding	0.008547	0.374468	
chunk0170_24_1	chr6	109204024	109204802	+	0	NA	Intergenic	Tigger17a|DNA|TcMar-Tigger	-32201	NM_001277339	221262	Hs.373914	NM_173671	ENSG00000203799	CCDC162P	C6orf183|C6orf184|C6orf185|CCDC162	coiled-coil domain containing 162, pseudogene	pseudo	0.006427	0.391528	
chunk0128_47_1	chr3	104695958	104696725	+	0	NA	Intergenic	L1PA6|LINE|L1	-670372	NM_001627	214	Hs.591293	NM_001627	ENSG00000170017	ALCAM	CD166|MEMD	activated leukocyte cell adhesion molecule	protein-coding	0.014342	0.502604	
chunk0156_26_1	chr5	102301456	102301752	+	0	NA	Intergenic	L1MEc|LINE|L1	-5055	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.006757	0.397306	
chunk0016_314_1	chr1	201500775	201501002	+	0	NA	intron (NM_004078, intron 1 of 5)	intron (NM_004078, intron 1 of 5)	-4315	NM_001193572	1465	Hs.108080	NM_004078	ENSG00000159176	CSRP1	CRP|CRP1|CSRP|CYRP|D1S181E|HEL-141|HEL-S-286	cysteine and glycine rich protein 1	protein-coding	0.013216	0.508772	
chunk0010_118_1	chr1	114457160	114457804	+	0	NA	intron (NM_033020, intron 4 of 18)	MER21-int|LTR|ERVL	53678	NM_015906	51592	Hs.26837	NM_015906	ENSG00000197323	TRIM33	ECTO|PTC7|RFG7|TF1G|TIF1G|TIF1GAMMA|TIFGAMMA	tripartite motif containing 33	protein-coding	0.007764	0.415504	
chunk0185_163_1	chr7	127790016	127790255	+	0	NA	intron (NM_014390, intron 10 of 23)	intron (NM_014390, intron 10 of 23)	137987	NM_014390	27044	Hs.122523	NM_014390	ENSG00000197157	SND1	TDRD11|Tudor-SN|p100	staphylococcal nuclease and tudor domain containing 1	protein-coding	0.008368	0.445833	
chunk0190_367_1	chr8	39856517	39856754	+	0	NA	Intergenic	L1M4|LINE|L1	-18346	NM_001278113	2515	Hs.177959	NM_001464	ENSG00000104755	ADAM2	CRYN1|CRYN2|CT15|FTNB|PH-30b|PH30|PH30-beta	ADAM metallopeptidase domain 2	protein-coding	0.000000	0.247899	
chunk0169_155_1	chr6	101741626	101742261	+	0	NA	intron (NM_001166247, intron 6 of 16)	MIRb|SINE|MIR	342958	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.003150	0.369497	
chunk0029_114_1	chr10	98159136	98159751	+	0	NA	intron (NM_001256619, intron 2 of 10)	L1MC4a|LINE|L1	24819	NM_138469	27291	Hs.419800	NM_014472	ENSG00000166024	R3HCC1L	C10orf28|GIDRP86|GIDRP88|PSORT	R3H domain and coiled-coil containing 1 like	protein-coding	0.003252	0.314935	122(AGGCACAAGATGTTCA,-,0.00),123(GGCACAAGATGTTCAA,+,0.00)
chunk0015_410_1	chr1	191163456	191164024	+	0	NA	Intergenic	Intergenic	538850	NR_033922	440704		NR_033922	ENSG00000231175	LINC01720	-	long intergenic non-protein coding RNA 1720	ncRNA	0.001761	0.318102	
chunk0064_288_1	chr14	95273416	95274015	+	0	NA	intron (NM_024734, intron 1 of 12)	intron (NM_024734, intron 1 of 12)	46193	NM_024734	79789	Hs.301478	NM_024734	ENSG00000165959	CLMN	-	calmin	protein-coding	0.021703	0.496667	
chunk0005_296_1	chr1	60274537	60275308	+	0	NA	Intergenic	MIRb|SINE|MIR	-201152	NM_152377	127795	Hs.47385	NM_152377	ENSG00000162598	C1orf87	CREF	chromosome 1 open reading frame 87	protein-coding	0.009079	0.393782	
chunk0175_113_1	chr7	3250683	3251009	+	0	NA	Intergenic	Tigger1|DNA|TcMar-Tigger	-50602	NM_152744	221935	Hs.653013	NM_152744	ENSG00000146555	SDK1	-	sidekick cell adhesion molecule 1	protein-coding	0.012270	0.474006	
chunk0154_1_1	chr5	76472333	76472843	+	0	NA	intron (NM_006633, intron 2 of 35)	intron (NM_006633, intron 2 of 35)	69333	NM_006633	10788	Hs.291030	NM_006633	ENSG00000145703	IQGAP2	-	IQ motif containing GTPase activating protein 2	protein-coding	0.009804	0.446184	
chunk0041_221_1	chr11	127688591	127688991	+	0	NA	Intergenic	L1MA10|LINE|L1	417721	NR_120580	101929497	Hs.737442	NR_120580	ENSG00000273409	LINC02712	-	long intergenic non-protein coding RNA 2712	ncRNA	0.007500	0.379052	
chunk0188_118_1	chr8	9095907	9096322	+	0	NA	Intergenic	Intergenic	47669	NR_039804	100616350		NR_039804	ENSG00000263407	MIR4660	-	microRNA 4660	ncRNA	0.014458	0.456731	
chunk0190_245_1	chr8	36873520	36874138	+	0	NA	intron (NM_001031836, intron 19 of 26)	intron (NM_001031836, intron 19 of 26)	89505	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.008091	0.376414	
chunk0071_251_1	chr15	85413446	85413817	+	0	NA	intron (NM_007200, intron 1 of 36)	intron (NM_007200, intron 1 of 36)	33015	NM_006738	11214	Hs.459211	NM_006738	ENSG00000170776	AKAP13	AKAP-13|AKAP-Lbc|ARHGEF13|BRX|HA-3|Ht31|LBC|PRKA13|PROTO-LB|PROTO-LBC|c-lbc|p47	A-kinase anchoring protein 13	protein-coding	0.016173	0.475806	
chunk0056_126_1	chr13	83125145	83126300	+	0	NA	Intergenic	L1MDb|LINE|L1	756671	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.002597	0.282872	201(TAGTACAAAATGTTCC,-,0.00),202(AGTACAAAATGTTCCA,+,0.00)
chunk0114_18_1	chr21	7258376	7259442	+	0	NA	Intergenic	(TGGAA)n|Simple_repeat|Simple_repeat	399738	NR_128718	103504736		NR_128718	ENSG00000278618	MIR8069-2	hsa-mir-8069-2	microRNA 8069-2	ncRNA	0.013133	0.455483	
chunk0009_420_1	chr1	110828535	110828928	+	0	NA	Intergenic	L1MEd|LINE|L1	-42468	NM_001040033	963	Hs.443057	NM_000560	ENSG00000143119	CD53	MOX44|TSPAN25	CD53 molecule	protein-coding	0.000000	0.299492	
chunk0011_263_1	chr1	150968605	150969158	+	0	NA	intron (NM_022075, intron 2 of 10)	intron (NM_022075, intron 2 of 10)	6122	NM_181746	29956	Hs.744017	NM_013384	ENSG00000143418	CERS2	L3|LASS2|SP260|TMSG1	ceramide synthase 2	protein-coding	0.019892	0.539711	
chunk0160_21_1	chr5	149073392	149073591	+	0	NA	intron (NR_122044, intron 2 of 2)	intron (NR_122044, intron 2 of 2)	10174	NR_122044	255187	Hs.149321	NR_122044	ENSG00000250072	SH3TC2-DT	-	SH3TC2 divergent transcript	ncRNA	0.005025	0.500000	
chunk0143_41_1	chr4	107531651	107532315	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	188280	NM_005443	9061	Hs.368610	NM_005443	ENSG00000138801	PAPSS1	ATPSK1|PAPSS|SK1	3'-phosphoadenosine 5'-phosphosulfate synthase 1	protein-coding	0.007530	0.418045	
chunk0031_374_1	chr10	130514107	130514387	+	0	NA	Intergenic	Intergenic	377872	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.035714	0.572954	181(AGGAACACACTGCACT,-,0.00),182(GGAACACACTGCACTG,+,0.00)
chunk0198_58_1	chr8	128980507	128980770	+	0	NA	Intergenic	MIRb|SINE|MIR	260602	NR_033916	728724	Hs.49902	NR_033916	ENSG00000229140	LINC00977	-	long intergenic non-protein coding RNA 977	ncRNA	0.000000	0.329545	
chunk0069_67_1	chr15	60868664	60869117	+	0	NA	intron (NM_134261, intron 1 of 10)	intron (NM_134261, intron 1 of 10)	187321	NR_120319	100996876	Hs.511626	NR_120318		RORA-AS2	-	RORA antisense RNA 2	ncRNA	0.002208	0.403084	277(AGGCACAGACAGTACA,-,0.00),278(GGCACAGACAGTACAC,+,0.00)
chunk0181_79_1	chr7	80312016	80312788	+	0	NA	Intergenic	LTR16|LTR|ERVL	62037	NR_110075	101927269	Hs.583232	NR_110075		LOC101927269	-	uncharacterized LOC101927269	ncRNA	0.006477	0.417853	
chunk0034_144_1	chr11	29844615	29845034	+	0	NA	Intergenic	L2a|LINE|L2	137569	NR_132652	106456574	Hs.128812	NR_132652	ENSG00000261340	LINC01616	n341006	long intergenic non-protein coding RNA 1616	ncRNA	0.002387	0.414286	
chunk0127_421_1	chr3	102599836	102600604	+	0	NA	Intergenic	LTR1D|LTR|ERV1	165205	NM_175056	131368	Hs.352213	NM_175056	ENSG00000170044	ZPLD1	-	zona pellucida like domain containing 1	protein-coding	0.009115	0.461638	
chunk0101_133_1	chr2	127410801	127411069	+	0	NA	Intergenic	Intergenic	-7485	NM_000312	5624	Hs.224698	NM_000312	ENSG00000115718	PROC	APC|PC|PROC1|THPH3|THPH4	protein C, inactivator of coagulation factors Va and VIIIa	protein-coding	0.007463	0.364312	188(AGGGACAGTCAGTTCA,-,0.00),189(GGGACAGTCAGTTCAT,+,0.00)
chunk0182_126_1	chr7	94453493	94453772	+	0	NA	Intergenic	Intergenic	-56226	NM_022900	64921	Hs.260041	NM_022900	ENSG00000127995	CASD1	C7orf12|NBLA04196|SOAT	CAS1 domain containing 1	protein-coding	0.003584	0.260714	
chunk0088_450_1	chr18	56795487	56795781	+	0	NA	intron (NM_015285, intron 19 of 27)	L1MC5|LINE|L1	144249	NM_052834	23335	Hs.465213	NM_015285	ENSG00000091157	WDR7	TRAG	WD repeat domain 7	protein-coding	0.003401	0.355932	
chunk0178_111_1	chr7	30941926	30942309	+	0	NA	Intergenic	L1MC4|LINE|L1	20613	NM_001185062	358	Hs.76152	NM_000385	ENSG00000240583	AQP1	AQP-CHIP|CHIP28|CO	aquaporin 1 (Colton blood group)	protein-coding	0.010444	0.356771	
chunk0067_365_1	chr15	48766279	48766596	+	0	NA	intron (NM_001194998, intron 17 of 26)	intron (NM_001194998, intron 17 of 26)	44709	NM_014985	22995	Hs.443005	NM_014985	ENSG00000103995	CEP152	MCPH4|MCPH9|SCKL5	centrosomal protein 152	protein-coding	0.009464	0.452830	
chunk0129_242_1	chr3	122073094	122073731	+	0	NA	intron (NM_001206925, intron 1 of 5)	L1MC2|LINE|L1	-4437	NM_006889	942	Hs.171182	NM_006889	ENSG00000114013	CD86	B7-2|B7.2|B70|CD28LG2|LAB72	CD86 molecule	protein-coding	0.003140	0.382445	
chunk0188_161_1	chr8	10680975	10681440	+	0	NA	intron (NM_001040032, intron 2 of 3)	intron (NM_001040032, intron 2 of 3)	8570	NM_001040032	203076	Hs.371776	NM_001040032	ENSG00000171060	C8orf74	-	chromosome 8 open reading frame 74	protein-coding	0.021505	0.562232	
chunk0048_54_1	chr12	78241477	78241898	+	0	NA	Intergenic	Intergenic	410398	NM_001024383	89795	Hs.655301	NM_014903	ENSG00000067798	NAV3	POMFIL1|STEERIN3|unc53H3	neuron navigator 3	protein-coding	0.011876	0.483412	232(AAGCTCATCGTGTTCC,-,0.00),233(AGCTCATCGTGTTCCC,+,0.00)
chunk0004_113_1	chr1	44481327	44481566	+	0	NA	intron (NM_018150, intron 2 of 14)	L1PA8A|LINE|L1	-64047	NR_049849	100847089		NR_049849	ENSG00000263381	MIR5584	-	microRNA 5584	ncRNA	0.020921	0.520833	
chunk0013_329_1	chr1	171640935	171641134	+	0	NA	intron (NM_000261, intron 1 of 2)	L1MC1|LINE|L1	11599	NM_000261	4653	Hs.436037	NM_000261	ENSG00000034971	MYOC	GLC1A|GPOA|JOAG|JOAG1|TIGR	myocilin	protein-coding	0.025126	0.450000	
chunk0208_269_1	chrX	21523899	21524358	+	0	NA	intron (NM_014927, intron 9 of 21)	intron (NM_014927, intron 9 of 21)	134259	NM_153270	257240	Hs.448572	NM_153270	ENSG00000185915	KLHL34	-	kelch like family member 34	protein-coding	0.002179	0.293478	
chunk0191_19_1	chr8	42698778	42699042	+	0	NA	intron (NM_000749, intron 1 of 5)	intron (NM_000749, intron 1 of 5)	1491	NM_000749	1142	Hs.654576	NM_000749	ENSG00000147432	CHRNB3	-	cholinergic receptor nicotinic beta 3 subunit	protein-coding	0.007576	0.366038	
chunk0162_153_1	chr6	3385623	3385951	+	0	NA	intron (NM_015482, intron 3 of 9)	intron (NM_015482, intron 3 of 9)	59226	NM_021945	63027	Hs.713588	NM_015482	ENSG00000137266	SLC22A23	C6orf85	solute carrier family 22 member 23	protein-coding	0.003049	0.452888	179(AAAAACTCCCTGTCCT,-,0.00),180(AAAACTCCCTGTCCTC,+,0.00)
chunk0046_453_1	chr12	64894928	64895442	+	0	NA	intron (NR_033988, intron 1 of 2)	intron (NR_033988, intron 1 of 2)	11411	NR_033988	400046	Hs.591032	NR_033988	ENSG00000255693	LINC02389	-	long intergenic non-protein coding RNA 2389	ncRNA	0.003891	0.332039	
chunk0087_276_1	chr18	37922869	37923425	+	0	NA	Intergenic	Intergenic	266012	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.003597	0.228007	
chunk0155_416_1	chr5	99549716	99549944	+	0	NA	intron (NR_110562, intron 3 of 3)	MIRb|SINE|MIR	15840	NR_110562	102724855	Hs.519477	NR_110562		LINC02113	CTD-2151A2.1	long intergenic non-protein coding RNA 2113	ncRNA	0.008772	0.423581	
chunk0087_267_1	chr18	37299444	37299913	+	0	NA	intron (NM_001025089, intron 3 of 11)	intron (NM_001025089, intron 3 of 11)	166826	NR_132967	106635546		NR_132967		SNORA111	-	small nucleolar RNA, H/ACA box 111	snoRNA	0.019190	0.578723	
chunk0040_285_1	chr11	116944175	116944457	+	0	NA	intron (NM_025164, intron 3 of 23)	MER77B|LTR|ERVL	-106694	NM_000039	335	Hs.93194	NM_000039	ENSG00000118137	APOA1	apo(a)	apolipoprotein A1	protein-coding	0.021277	0.512367	
chunk0099_213_1	chr2	95042583	95043225	+	0	NA	intron (NM_022440, intron 1 of 1)	intron (NM_022440, intron 1 of 1)	17249	NM_022439	4118	Hs.80395	NM_002371	ENSG00000172005	MAL	MVP17|VIP17	mal, T cell differentiation protein	protein-coding	0.009346	0.556765	265(TGGAACAGATTGCTCT,-,0.00),266(GGAACAGATTGCTCTG,+,0.00)
chunk0116_120_1	chr21	35981557	35981954	+	0	NA	non-coding (NR_110418, exon 4 of 6)	non-coding (NR_110418, exon 4 of 6)	22912	NR_110418	101928269	Hs.589909	NR_110418		LOC101928269	-	uncharacterized LOC101928269	ncRNA	0.022670	0.467337	
chunk0028_192_1	chr10	88640066	88640659	+	0	NA	Intergenic	Intergenic	-24027	NM_001198830	8513	Hs.523130	NM_004190	ENSG00000182333	LIPF	GL|HGL|HLAL	lipase F, gastric type	protein-coding	0.003373	0.340067	388(GGGAACTGAATGTTTT,-,0.00),389(GGAACTGAATGTTTTC,+,0.00)
chunk0134_212_1	chr3	178607723	178608028	+	0	NA	intron (NM_001278911, intron 1 of 4)	intron (NM_001278911, intron 1 of 4)	49175	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.000000	0.303922	
chunk0087_345_1	chr18	40455964	40456383	+	0	NA	Intergenic	Intergenic	389887	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.002387	0.371429	
chunk0192_136_1	chr8	61971219	61971522	+	0	NA	Intergenic	Intergenic	256582	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.003300	0.440789	
chunk0100_231_1	chr2	112294237	112294681	+	0	NA	intron (NM_198581, intron 1 of 11)	LTR37-int|LTR|ERV1	18858	NM_198581	376940	Hs.190477	NM_198581	ENSG00000188177	ZC3H6	ZC3HDC6	zinc finger CCCH-type containing 6	protein-coding	0.006757	0.357303	
chunk0067_247_1	chr15	45587139	45587583	+	0	NA	promoter-TSS (NM_001311256)	promoter-TSS (NM_001311256)	-199	NM_001311256	26258	Hs.7037	NM_012388	ENSG00000104164	BLOC1S6	BLOS6|HPS9|PA|PALLID|PLDN	biogenesis of lysosomal organelles complex 1 subunit 6	protein-coding	0.094595	0.667416	
chunk0007_321_1	chr1	84492883	84493204	+	0	NA	intron (NM_025065, intron 5 of 8)	MIRb|SINE|MIR	-13258	NM_001310156	100505741	Hs.584956	NM_022354	ENSG00000122432	SPATA1	SP-2|SPAP1	spermatogenesis associated 1	protein-coding	0.006231	0.394410	
chunk0070_153_1	chr15	71199467	71199922	+	0	NA	intron (NM_024817, intron 2 of 16)	(TG)n|Simple_repeat|Simple_repeat	-10635	NR_120349	101929196	Hs.680472	NR_120348		THSD4-AS1	-	THSD4 antisense RNA 1	ncRNA	0.002198	0.541667	
chunk0163_10_1	chr6	7766058	7766266	+	0	NA	intron (NM_001718, intron 1 of 6)	intron (NM_001718, intron 1 of 6)	39384	NM_001718	654	Hs.285671	NM_001718	ENSG00000153162	BMP6	VGR|VGR1	bone morphogenetic protein 6	protein-coding	0.009615	0.377990	
chunk0171_195_1	chr6	125495531	125495898	+	0	NA	Intergenic	Intergenic	-178639	NR_038906	643623	Hs.520367	NR_038906	ENSG00000224506	LINC02523	-	long intergenic non-protein coding RNA 2523	ncRNA	0.005450	0.347826	
chunk0115_158_1	chr21	24028371	24028855	+	0	NA	Intergenic	Intergenic	292764	NR_109963	101927869	Hs.555591	NR_109963	ENSG00000224832	LINC01689	-	long intergenic non-protein coding RNA 1689	ncRNA	0.006198	0.342268	
chunk0196_205_1	chr8	106533085	106533326	+	0	NA	intron (NM_001198532, intron 2 of 15)	intron (NM_001198532, intron 2 of 15)	85281	NM_001198532	55074	Hs.127286	NM_018002	ENSG00000164830	OXR1	Nbla00307|TLDC3	oxidation resistance 1	protein-coding	0.004149	0.404959	
chunk0034_229_1	chr11	33560470	33560880	+	0	NA	intron (NM_012194, intron 6 of 19)	intron (NM_012194, intron 6 of 19)	18344	NM_012194	25758	Hs.502266	NM_012194	ENSG00000110427	KIAA1549L	C11orf41|C11orf69|G2	KIAA1549 like	protein-coding	0.009756	0.347932	
chunk0010_161_1	chr1	115409716	115410251	+	0	NA	Intergenic	Intergenic	-71747	NM_002506	4803	Hs.2561	NM_002506	ENSG00000134259	NGF	Beta-NGF|HSAN5|NGFB	nerve growth factor	protein-coding	0.007477	0.348881	
chunk0020_211_1	chr1	235136154	235136439	+	0	NA	intron (NR_027762, intron 7 of 9)	intron (NR_027762, intron 7 of 9)	-7355	NM_014765	9804	Hs.533192	NM_014765	ENSG00000173726	TOMM20	MAS20|MOM19|TOM20	translocase of outer mitochondrial membrane 20	protein-coding	0.007018	0.472028	
chunk0041_182_1	chr11	126327663	126328120	+	0	NA	intron (NM_014026, intron 2 of 5)	L2a|LINE|L2	24139	NM_014026	28960	Hs.504249	NM_014026	ENSG00000110063	DCPS	ARS|DCS1|HINT-5|HINT5|HSL1|HSPC015	decapping enzyme, scavenger	protein-coding	0.026258	0.519651	
chunk0050_391_1	chr12	109115890	109116101	+	0	NA	Intergenic	Intergenic	17877	NM_003362	7374	Hs.191334	NM_003362	ENSG00000076248	UNG	DGU|HIGM4|HIGM5|UDG|UNG1|UNG15|UNG2	uracil DNA glycosylase	protein-coding	0.014218	0.547170	8(GAGCACAATGTGCTCC,-,0.00),9(AGCACAATGTGCTCCT,+,0.00)
chunk0211_304_1	chrX	123338787	123339383	+	0	NA	intron (NM_007325, intron 4 of 15)	intron (NM_007325, intron 4 of 15)	154842	NM_007325	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.006711	0.375209	
chunk0096_363_1	chr2	36465534	36465783	+	0	NA	intron (NM_016441, intron 5 of 16)	intron (NM_016441, intron 5 of 16)	109431	NM_016441	51232	Hs.699247	NM_016441	ENSG00000150938	CRIM1	CRIM-1|S52	cysteine rich transmembrane BMP regulator 1	protein-coding	0.004016	0.416000	
chunk0176_386_1	chr7	18754982	18755404	+	0	NA	intron (NM_178425, intron 13 of 24)	X9_LINE|LINE|L1	245916	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.002370	0.347518	
chunk0032_246_1	chr11	8439314	8439513	+	0	NA	intron (NM_030906, intron 10 of 13)	intron (NM_030906, intron 10 of 13)	154595	NM_030906	65975	Hs.501833	NM_030906	ENSG00000130413	STK33	-	serine/threonine kinase 33	protein-coding	0.000000	0.265000	
chunk0067_42_1	chr15	40640830	40641162	+	0	NA	exon (NM_144508, exon 14 of 26)	exon (NM_144508, exon 14 of 26)	46747	NM_144508	57082	Hs.181855	NM_144508	ENSG00000137812	KNL1	AF15Q14|CASC5|CT29|D40|MCPH4|PPP1R55|Spc7|hKNL-1|hSpc105	kinetochore scaffold 1	protein-coding	0.009036	0.369369	
chunk0170_292_1	chr6	115349406	115349791	+	0	NA	Intergenic	Intergenic	-689133	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.002597	0.297927	
chunk0167_203_1	chr6	64890615	64890819	+	0	NA	intron (NM_001142800, intron 18 of 42)	intron (NM_001142800, intron 18 of 42)	-410701	NM_001271675	441155	Hs.546686	NM_001271675		LOC441155	-	zinc finger CCCH-type domain-containing-like	protein-coding	0.004902	0.268293	
chunk0138_200_1	chr4	38565385	38565831	+	0	NA	Intergenic	Intergenic	-42428	NR_110951	101928776	Hs.586147	NR_110951	ENSG00000249534	LINC01258	-	long intergenic non-protein coding RNA 1258	ncRNA	0.004484	0.418345	
chunk0032_375_1	chr11	11167727	11168124	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	185432	NM_001256686	283106	Hs.654675	NM_001256686	ENSG00000254598	CSNK2A3	CSNK2A1P	casein kinase 2 alpha 3	protein-coding	0.005038	0.452261	130(AGGAACAAAGAGTTCC,-,0.00),131(GGAACAAAGAGTTCCT,+,0.00)
chunk0091_214_1	chr19	9784654	9784853	+	0	NA	Intergenic	LTR5B|LTR|ERVK	-16019	NM_001077624	162993	Hs.665717	NM_001077624	ENSG00000196605	ZNF846	-	zinc finger protein 846	protein-coding	0.020101	0.535000	92(CAGTGCACTGTGTCCC,-,0.00),93(AGTGCACTGTGTCCCT,+,0.00)
chunk0025_195_1	chr10	53344391	53344841	+	0	NA	Intergenic	L1MCc|LINE|L1	-572916	NM_000242	4153	Hs.499674	NM_000242	ENSG00000165471	MBL2	COLEC1|HSMBPC|MBL|MBL2D|MBP|MBP-C|MBP1|MBPD	mannose binding lectin 2	protein-coding	0.011111	0.394678	
chunk0206_190_1	chr9	122947803	122948486	+	0	NA	intron (NM_012197, intron 1 of 25)	intron (NM_012197, intron 1 of 25)	7135	NM_012197	23637	Hs.271341	NM_012197	ENSG00000011454	RABGAP1	GAPCENA|TBC1D11	RAB GTPase activating protein 1	protein-coding	0.002928	0.390351	
chunk0128_253_1	chr3	108944916	108945115	+	0	NA	intron (NM_005459, intron 1 of 3)	intron (NM_005459, intron 1 of 3)	8815	NM_005459	9626	Hs.233363	NM_005459	ENSG00000138472	GUCA1C	GCAP3	guanylate cyclase activator 1C	protein-coding	0.005025	0.545000	
chunk0015_330_1	chr1	189708683	189708882	+	0	NA	Intergenic	L1PA15|LINE|L1	768847	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.515000	
chunk0124_133_1	chr3	54359328	54359609	+	0	NA	intron (NM_018398, intron 3 of 37)	intron (NM_018398, intron 3 of 37)	236802	NM_018398	55799	Hs.656687	NM_018398	ENSG00000157445	CACNA2D3	HSA272268	calcium voltage-gated channel auxiliary subunit alpha2delta 3	protein-coding	0.017794	0.478723	
chunk0016_434_1	chr1	203861276	203861899	+	0	NA	promoter-TSS (NM_003094)	promoter-TSS (NM_003094)	2	NM_001304464	6635	Hs.334612	NM_003094	ENSG00000182004	SNRPE	HYPT11|SME|Sm-E|snRNP-E	small nuclear ribonucleoprotein polypeptide E	protein-coding	0.060995	0.592949	
chunk0031_56_1	chr10	122748294	122748922	+	0	NA	Intergenic	MER70B|LTR|ERVL	-8086	NR_003570	375940	Hs.650695	NM_198577	ENSG00000176584	DMBT1P1	-	deleted in malignant brain tumors 1 pseudogene 1	pseudo	0.007962	0.497615	303(CAGAGCATACTGTTCT,-,0.00),304(AGAGCATACTGTTCTA,+,0.00)
chunk0101_363_1	chr2	138010171	138010648	+	0	NA	intron (NM_006895, intron 5 of 5)	intron (NM_006895, intron 5 of 5)	46171	NM_001024075	3176	Hs.42151	NM_006895	ENSG00000150540	HNMT	HMT|HNMT-S1|HNMT-S2|MRT51	histamine N-methyltransferase	protein-coding	0.004193	0.328452	
chunk0130_203_1	chr3	133778242	133778704	+	0	NA	intron (NM_001063, intron 16 of 16)	intron (NM_001063, intron 16 of 16)	-5560	NM_021203	58477	Hs.12152	NM_021203	ENSG00000144867	SRPRB	APMCF1|SR-beta	SRP receptor subunit beta	protein-coding	0.015152	0.511879	243(CTGCACACTTTGTACT,-,0.00),244(TGCACACTTTGTACTA,+,0.00)
chunk0061_439_1	chr14	65661652	65662315	+	0	NA	intron (NR_038170, intron 6 of 10)	intron (NR_038170, intron 6 of 10)	190881	NR_030355	693210		NR_030355	ENSG00000207781	MIR625	MIRN625|hsa-mir-625	microRNA 625	ncRNA	0.006033	0.387048	
chunk0065_83_1	chr15	23641897	23642293	+	0	NA	Intergenic	Intergenic	5751	NM_019066	54551	Hs.141496	NM_019066	ENSG00000254585	MAGEL2	NDNL1|PWLS|SHFYNG|nM15	MAGE family member L2	protein-coding	0.015152	0.458438	
chunk0079_385_1	chr17	18730776	18731358	+	0	NA	intron (NM_001037330, intron 2 of 4)	intron (NM_001037330, intron 2 of 4)	8978	NM_001037330	147166	Hs.164324	NM_001037330	ENSG00000108448	TRIM16L	TRIM70	tripartite motif containing 16 like	protein-coding	0.010309	0.420240	
chunk0139_5_1	chr4	47798101	47798644	+	0	NA	intron (NM_001278586, intron 2 of 13)	intron (NM_001278586, intron 2 of 13)	-32973	NR_125880	101927179	Hs.570822	NR_125880		LOC101927179	-	uncharacterized LOC101927179	ncRNA	0.005525	0.321691	
chunk0055_447_1	chr13	75704595	75705300	+	0	NA	intron (NM_001306080, intron 1 of 30)	intron (NM_001306080, intron 1 of 30)	-55714	NM_015842	4008	Hs.207631	NM_005358	ENSG00000136153	LMO7	FBX20|FBXO20|LMO7b|LOMP	LIM domain 7	protein-coding	0.019858	0.423513	
chunk0008_96_1	chr1	91005287	91005606	+	0	NA	intron (NM_032186, intron 1 of 3)	L1M4|LINE|L1	16062	NM_016620	84146	Hs.173001	NM_016620	ENSG00000122482	ZNF644	BM-005|MYP21|NatF|ZEP-2	zinc finger protein 644	protein-coding	0.003135	0.318750	
chunk0177_246_1	chr7	24990436	24990931	+	0	NA	Intergenic	Intergenic	-10471	NM_015550	26031	Hs.520259	NM_015550	ENSG00000070882	OSBPL3	ORP-3|ORP3|OSBP3	oxysterol binding protein like 3	protein-coding	0.004040	0.352823	
chunk0120_250_1	chr3	8901738	8902355	+	0	NA	intron (NM_020165, intron 10 of 12)	intron (NM_020165, intron 10 of 12)	61429	NM_020165	56852	Hs.375684	NM_020165	ENSG00000070950	RAD18	RNF73	RAD18 E3 ubiquitin protein ligase	protein-coding	0.006483	0.296117	
chunk0208_370_1	chrX	26772513	26773306	+	0	NA	Intergenic	L1PA17|LINE|L1	214572	NR_001559	139538	Hs.447377	NR_001559	ENSG00000259849	VENTXP1	CT18|NA88A|VENTX2P1	VENT homeobox pseudogene 1	pseudo	0.002522	0.337531	
chunk0119_442_1	chr22	50136642	50137300	+	0	NA	intron (NM_001164105, intron 15 of 25)	L1ME1|LINE|L1	-10084	NM_001164106	54456	Hs.62880	NM_018995	ENSG00000073146	MOV10L1	CHAMP|DJ402G11.8	Mov10 like RISC complex RNA helicase 1	protein-coding	0.007599	0.435508	
chunk0036_15_1	chr11	58239716	58240282	+	0	NA	Intergenic	L1MA4|LINE|L1	-11081	NM_001004471	219960	Hs.553646	NM_001004471	ENSG00000180475	OR10Q1	OR11-233	olfactory receptor family 10 subfamily Q member 1	protein-coding	0.003534	0.319224	
chunk0045_176_1	chr12	46944164	46944527	+	0	NA	Intergenic	Intergenic	-118348	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.005510	0.395604	276(GAGTACAGCATGTGTT,-,0.00),277(AGTACAGCATGTGTTC,+,0.00)
chunk0122_359_1	chr3	37534428	37534729	+	0	NA	intron (NM_002207, intron 14 of 27)	intron (NM_002207, intron 14 of 27)	82256	NM_002207	3680	Hs.113157	NM_002207	ENSG00000144668	ITGA9	ALPHA-RLC|ITGA4L|RLC	integrin subunit alpha 9	protein-coding	0.006645	0.367550	
chunk0185_333_1	chr7	131948690	131948959	+	0	NA	non-coding (NR_110836, exon 6 of 6)	non-coding (NR_110836, exon 6 of 6)	38604	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.003717	0.507407	
chunk0177_375_1	chr7	26864381	26865012	+	0	NA	promoter-TSS (NM_003930)	promoter-TSS (NM_003930)	47	NM_003930	8935	Hs.200770	NM_003930	ENSG00000005020	SKAP2	PRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R	src kinase associated phosphoprotein 2	protein-coding	0.063391	0.613924	
chunk0142_391_1	chr4	102575591	102576318	+	0	NA	intron (NM_003998, intron 6 of 23)	L2a|LINE|L2	74625	NM_003998	4790	Hs.618430	NM_003998	ENSG00000109320	NFKB1	CVID12|EBP-1|KBF1|NF-kB1|NF-kappa-B1|NF-kappaB|NFKB-p105|NFKB-p50|NFkappaB|p105|p50	nuclear factor kappa B subunit 1	protein-coding	0.008253	0.332418	19(TGTACTTACTGTTCCT,+,0.00)
chunk0190_137_1	chr8	30708106	30708605	+	0	NA	intron (NM_000637, intron 3 of 12)	intron (NM_000637, intron 3 of 12)	19614	NM_001195103	2936	Hs.271510	NM_000637	ENSG00000104687	GSR	GR|HEL-75|HEL-S-122m	glutathione-disulfide reductase	protein-coding	0.018036	0.432000	306(TAGAACATGATGTGCA,-,0.00),307(AGAACATGATGTGCAC,+,0.00)
chunk0103_144_1	chr2	162138242	162138600	+	0	NA	intron (NR_110255, intron 1 of 3)	Tigger17c|DNA|TcMar-Tigger	13983	NM_002054	2641	Hs.516494	NM_002054	ENSG00000115263	GCG	GLP-1|GLP1|GLP2|GRPP	glucagon	protein-coding	0.000000	0.339833	
chunk0012_171_1	chr1	158562762	158563132	+	0	NA	exon (NM_001160325, exon 1 of 1)	exon (NM_001160325, exon 1 of 1)	657	NM_001160325	128366	Hs.723122	NM_001160325	ENSG00000186440	OR6P1	-	olfactory receptor family 6 subfamily P member 1	protein-coding	0.013514	0.482480	
chunk0167_216_1	chr6	66301778	66302008	+	0	NA	Intergenic	Intergenic	514014	NR_026540	442229	Hs.390414	NR_026540		SLC25A51P1	MCART3P|bA707M13.1	SLC25A51 pseudogene 1	pseudo	0.000000	0.298701	
chunk0106_214_1	chr2	202450692	202451241	+	0	NA	intron (NM_001204, intron 1 of 12)	intron (NM_001204, intron 1 of 12)	74639	NM_001204	659	Hs.471119	NM_001204	ENSG00000204217	BMPR2	BMPR-II|BMPR3|BMR2|BRK-3|POVD1|PPH1|T-ALK	bone morphogenetic protein receptor type 2	protein-coding	0.000000	0.296364	
chunk0099_38_1	chr2	83682202	83682580	+	0	NA	Intergenic	Intergenic	-608291	NR_003663	388965	Hs.664098	NM_001013648		FUNDC2P2	-	FUN14 domain containing 2 pseudogene 2	pseudo	0.000000	0.321900	
chunk0064_297_1	chr14	95348631	95348905	+	0	NA	Intergenic	Intergenic	19184	NR_110127	101929080	Hs.525567	NR_110127	ENSG00000258630	LINC02292	-	long intergenic non-protein coding RNA 2292	ncRNA	0.010949	0.498182	
chunk0004_106_1	chr1	44283518	44283938	+	0	NA	intron (NM_024066, intron 7 of 8)	intron (NM_024066, intron 7 of 8)	-31169	NR_132966	106635545		NR_132966		SNORA110	-	small nucleolar RNA, H/ACA box 110	snoRNA	0.004762	0.498812	
chunk0117_182_1	chr22	20916989	20917285	+	0	NA	promoter-TSS (NM_005207)	promoter-TSS (NM_005207)	-289	NM_005207	1399	Hs.5613	NM_005207	ENSG00000099942	CRKL	-	CRK like proto-oncogene, adaptor protein	protein-coding	0.077703	0.670034	
chunk0004_463_1	chr1	53838422	53838621	+	0	NA	promoter-TSS (NR_033142)	promoter-TSS (NR_033142)	31	NR_033142	55706	Hs.476525	NM_018087	ENSG00000058804	NDC1	NET3|TMEM48	NDC1 transmembrane nucleoporin	protein-coding	0.080402	0.640000	
chunk0202_363_1	chr9	80375549	80376043	+	0	NA	Intergenic	Intergenic	400773	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.002024	0.339394	
chunk0155_177_1	chr5	94388470	94389072	+	0	NA	intron (NM_001145678, intron 18 of 20)	intron (NM_001145678, intron 18 of 20)	229833	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.006645	0.351575	
chunk0116_54_1	chr21	33790199	33791491	+	0	NA	intron (NM_001001132, intron 16 of 29)	intron (NM_001001132, intron 16 of 29)	125009	NM_001697	539	Hs.409140	NM_001697	ENSG00000241837	ATP5PO	ATP5O|ATPO|HMC08D05|OSCP	ATP synthase peripheral stalk subunit OSCP	protein-coding	0.004644	0.313998	
chunk0200_81_1	chr9	16437389	16437812	+	0	NA	intron (NM_017637, intron 5 of 6)	intron (NM_017637, intron 5 of 6)	-161287	NR_073471									0.007092	0.419811	
chunk0127_128_1	chr3	93982984	93983439	+	0	NA	intron (NM_144996, intron 1 of 7)	intron (NM_144996, intron 1 of 7)	3072	NM_001174150	200894	Hs.533086	NM_144996	ENSG00000169379	ARL13B	ARL2L1|JBTS8	ADP ribosylation factor like GTPase 13B	protein-coding	0.004396	0.361842	
chunk0155_403_1	chr5	99001623	99001873	+	0	NA	Intergenic	L1ME1|LINE|L1	72614	NR_036530	100289230	Hs.552095	NR_036530		LOC100289230	-	uncharacterized LOC100289230	ncRNA	0.008000	0.338645	
chunk0109_364_1	chr2	239304299	239304523	+	0	NA	intron (NM_006037, intron 2 of 26)	intron (NM_006037, intron 2 of 26)	-1051	NR_036229	100423043		NR_036229	ENSG00000265215	MIR4269	-	microRNA 4269	ncRNA	0.017857	0.413333	
chunk0014_70_1	chr1	176065234	176065867	+	0	NA	intron (NM_001001740, intron 10 of 18)	MER34A|LTR|ERV1	-97010	NR_002998	677679		NR_002998	ENSG00000252906	SCARNA3	HBI-100	small Cajal body-specific RNA 3	ncRNA	0.007899	0.399054	
chunk0105_179_1	chr2	187468371	187468707	+	0	NA	intron (NM_006287, intron 6 of 7)	intron (NM_006287, intron 6 of 7)	-20245	NM_005795	10203	Hs.470882	NM_005795	ENSG00000064989	CALCRL	CGRPR|CRLR	calcitonin receptor like receptor	protein-coding	0.000000	0.350148	
chunk0026_234_1	chr10	65547592	65547859	+	0	NA	Intergenic	Intergenic	-23700	NR_120647	101928913	Hs.568857	NR_120647		LINC01515	-	long intergenic non-protein coding RNA 1515	ncRNA	0.000000	0.350746	
chunk0178_461_1	chr7	42195642	42196026	+	0	NA	intron (NM_000168, intron 2 of 14)	intron (NM_000168, intron 2 of 14)	41185	NM_000168	2737	Hs.21509	NM_000168	ENSG00000106571	GLI3	ACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV	GLI family zinc finger 3	protein-coding	0.000000	0.366234	
chunk0188_411_1	chr8	18869455	18869654	+	0	NA	intron (NM_015310, intron 3 of 15)	intron (NM_015310, intron 3 of 15)	-60659	NM_206909	23362	Hs.434255	NM_015310	ENSG00000156011	PSD3	EFA6D|EFA6R|HCA67	pleckstrin and Sec7 domain containing 3	protein-coding	0.000000	0.560000	144(GTGCACATGCTGTTCC,-,0.00),145(TGCACATGCTGTTCCC,+,0.00)
chunk0030_247_1	chr10	115301740	115302115	+	0	NA	exon (NM_207303, exon 17 of 29)	exon (NM_207303, exon 17 of 29)	208562	NM_207303	26033	Hs.501127	NM_207303	ENSG00000107518	ATRNL1	ALP|bA338L11.1|bA454H24.1	attractin like 1	protein-coding	0.016000	0.385638	161(GAGGACATCATGTTCC,-,0.00),162(AGGACATCATGTTCCA,+,0.00)
chunk0118_453_1	chr22	39657229	39657660	+	0	NA	intron (NM_021096, intron 10 of 36)	intron (NM_021096, intron 10 of 36)	86691	NM_001003406	8911	Hs.125116	NM_021096	ENSG00000100346	CACNA1I	Cav3.3|ca(v)3.3	calcium voltage-gated channel subunit alpha1 I	protein-coding	0.018561	0.594907	206(AGGTACATTGTGTCCA,-,0.00),207(GGTACATTGTGTCCAC,+,0.00),234(GGGGCACGATGTCCCC,+,0.00)
chunk0205_326_1	chr9	112831292	112832210	+	0	NA	intron (NM_001012994, intron 4 of 8)	intron (NM_001012994, intron 4 of 8)	59162	NM_033051	57864	Hs.512668	NM_033051	ENSG00000119457	SLC46A2	Ly110|TSCOT	solute carrier family 46 member 2	protein-coding	0.008715	0.459195	
chunk0152_123_1	chr5	58804663	58805144	+	0	NA	intron (NM_138453, intron 3 of 4)	intron (NM_138453, intron 3 of 4)	195029	NM_001197223	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.000000	0.302905	
chunk0048_120_1	chr12	79785672	79785975	+	0	NA	intron (NM_001244990, intron 22 of 24)	intron (NM_001244990, intron 22 of 24)	-94813	NM_002583	5074	Hs.643130	NM_002583	ENSG00000177425	PAWR	PAR4|Par-4	pro-apoptotic WT1 regulator	protein-coding	0.000000	0.338816	
chunk0058_51_1	chr14	20466583	20467148	+	0	NA	Intergenic	Intergenic	-2514	NM_000270	4860	Hs.75514	NM_000270	ENSG00000198805	PNP	NP|PRO1837|PUNP	purine nucleoside phosphorylase	protein-coding	0.008850	0.360424	
chunk0030_365_1	chr10	118763649	118764384	+	0	NA	Intergenic	MLT1N2|LTR|ERVL-MaLR	-8770	NM_153810	143384	Hs.420024	NM_153810	ENSG00000151893	CACUL1	C10orf46|CAC1	CDK2 associated cullin domain 1	protein-coding	0.009524	0.474185	
chunk0010_411_1	chr1	119625937	119626707	+	0	NA	intron (NM_001080470, intron 1 of 2)	intron (NM_001080470, intron 1 of 2)	21445	NM_001080470	90874	Hs.381105	NM_001080470	ENSG00000143067	ZNF697	-	zinc finger protein 697	protein-coding	0.007792	0.443580	494(TGAACTAGATGTTCCC,+,0.00)
chunk0092_190_1	chr19	30442179	30442980	+	0	NA	intron (NM_014717, intron 1 of 4)	intron (NM_014717, intron 1 of 4)	70186	NM_014717	9745	Hs.378901	NM_014717	ENSG00000198597	ZNF536	-	zinc finger protein 536	protein-coding	0.009988	0.386534	229(AGGTACAATTTGTACT,-,0.00),230(GGTACAATTTGTACTC,+,0.00)
chunk0207_67_1	chrX	9024591	9024790	+	0	NA	3' UTR (NM_205849, exon 9 of 9)	3' UTR (NM_205849, exon 9 of 9)	9437	NM_205849	171483	Hs.733351	NM_173696	ENSG00000177138	FAM9B	TEX39B	family with sequence similarity 9 member B	protein-coding	0.015075	0.420000	
chunk0099_206_1	chr2	94912601	94913219	+	0	NA	intron (NR_037597, intron 5 of 9)	L1MC4a|LINE|L1	34432	NR_037597	442028	Hs.611545	NR_037597	ENSG00000259848	LOC442028	-	uncharacterized LOC442028	ncRNA	0.001618	0.353796	
chunk0026_372_1	chr10	69366632	69367222	+	0	NA	intron (NM_033497, intron 7 of 20)	L2a|LINE|L2	48080	NM_000188	3098	Hs.370365	NM_000188	ENSG00000156515	HK1	HK|HK1-ta|HK1-tb|HK1-tc|HKD|HKI|HMSNR|HXK1|RP79|hexokinase	hexokinase 1	protein-coding	0.010169	0.531303	
chunk0152_285_1	chr5	61477713	61478150	+	0	NA	intron (NM_020928, intron 2 of 13)	intron (NM_020928, intron 2 of 13)	145658	NM_020928	57688	Hs.744939	NM_020928	ENSG00000130449	ZSWIM6	AFND|NEDMAGA	zinc finger SWIM-type containing 6	protein-coding	0.004577	0.367580	
chunk0145_446_1	chr4	153535826	153536237	+	0	NA	intron (NM_001131007, intron 3 of 34)	intron (NM_001131007, intron 3 of 34)	69685	NM_001131007	23240	Hs.732450	NM_015196	ENSG00000121210	TMEM131L	KIAA0922	transmembrane 131 like	protein-coding	0.012165	0.453883	
chunk0086_123_1	chr18	20578495	20578711	+	0	NA	Intergenic	ALR/Alpha|Satellite|centr	533248	NM_005406	6093	Hs.306307	NM_005406	ENSG00000067900	ROCK1	P160ROCK|ROCK-I	Rho associated coiled-coil containing protein kinase 1	protein-coding	0.009259	0.391705	
chunk0019_172_1	chr1	226220659	226220858	+	0	NA	Intergenic	Intergenic	-2860	NM_031944	83881	Hs.282079	NM_031944	ENSG00000185155	MIXL1	MILD1|MIX|MIXL	Mix paired-like homeobox	protein-coding	0.025126	0.540000	
chunk0055_22_1	chr13	51906505	51907107	+	0	NA	Intergenic	Intergenic	44825	NM_031290	83446	Hs.120573	NM_031290	ENSG00000123171	CCDC70	-	coiled-coil domain containing 70	protein-coding	0.006645	0.480929	285(AAGTACAAACAGTCCC,-,0.00),286(AGTACAAACAGTCCCT,+,0.00)
chunk0101_73_1	chr2	123732588	123733020	+	0	NA	Intergenic	Intergenic	-292483	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.339492	
chunk0001_266_1	chr1	8526052	8526251	+	0	NA	intron (NM_001042681, intron 7 of 22)	intron (NM_001042681, intron 7 of 22)	-31238	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.015075	0.555000	
chunk0001_277_1	chr1	8643984	8644608	+	0	NA	intron (NM_001042681, intron 2 of 22)	intron (NM_001042681, intron 2 of 22)	-149383	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.006410	0.409600	318(AGGACAGGAAGATCCT,+,0.00)
chunk0080_155_1	chr17	28075136	28075821	+	0	NA	intron (NM_016231, intron 1 of 10)	intron (NM_016231, intron 1 of 10)	32816	NM_016231	51701	Hs.208759	NM_016231	ENSG00000087095	NLK	-	nemo like kinase	protein-coding	0.002920	0.395044	358(CTGTACAGTTTGTGCC,-,0.00),359(TGTACAGTTTGTGCCT,+,0.00)
chunk0030_306_1	chr10	117632911	117633283	+	0	NA	Intergenic	Intergenic	-88029	NR_002791	196047	Hs.312592	NR_002791	ENSG00000229847	EMX2OS	EMX2-AS1|NCRNA00045	EMX2 opposite strand/antisense RNA	ncRNA	0.005376	0.394102	
chunk0138_249_1	chr4	39602531	39602744	+	0	NA	intron (NM_174921, intron 2 of 4)	intron (NM_174921, intron 2 of 4)	36224	NM_174921	201895	Hs.205952	NM_174921	ENSG00000163683	SMIM14	C4orf34	small integral membrane protein 14	protein-coding	0.009390	0.378505	
chunk0152_425_1	chr5	65925658	65926006	+	0	NA	promoter-TSS (NM_001253699)	promoter-TSS (NM_001253699)	-722	NM_001253698	55914	Hs.591774	NM_018695	ENSG00000112851	ERBIN	ERBB2IP|HEL-S-78|LAP2	erbb2 interacting protein	protein-coding	0.135057	0.765043	
chunk0006_441_1	chr1	76697306	76697836	+	0	NA	Intergenic	Tigger3d|DNA|TcMar-Tigger	-169930	NM_030965	81849	Hs.149201	NM_030965	ENSG00000117069	ST6GALNAC5	SIAT7-E|SIAT7E|ST6GalNAcV	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	protein-coding	0.009434	0.299435	
chunk0193_446_1	chr8	81113640	81113986	+	0	NA	Intergenic	Intergenic	-1745	NM_018440	55824	Hs.266175	NM_018440	ENSG00000076641	PAG1	CBP|PAG	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	protein-coding	0.008671	0.423631	136(TAGAACAAAATGTTCT,-,0.00),137(AGAACAAAATGTTCTA,+,0.00)
chunk0018_67_1	chr1	217000556	217000823	+	0	NA	5' UTR (NM_001243507, exon 2 of 8)	5' UTR (NM_001243507, exon 2 of 8)	-61016	NM_001243512	2104	Hs.444225	NM_001438	ENSG00000196482	ESRRG	ERR-gamma|ERR3|ERRg|ERRgamma|NR3B3	estrogen related receptor gamma	protein-coding	0.011236	0.436567	
chunk0062_298_1	chr14	72830875	72831380	+	0	NA	intron (NM_001280542, intron 1 of 10)	intron (NM_001280542, intron 1 of 10)	61522	NM_001280544	8110	Hs.162868	NM_012074	ENSG00000205683	DPF3	BAF45C|CERD4	double PHD fingers 3	protein-coding	0.025743	0.529644	
chunk0177_86_1	chr7	21667738	21668273	+	0	NA	intron (NM_001277115, intron 30 of 81)	L1M5|LINE|L1	124790	NM_001277115	8701	Hs.520245	NM_001277115	ENSG00000105877	DNAH11	CILD7|DNAHBL|DNAHC11|DNHBL|DPL11	dynein axonemal heavy chain 11	protein-coding	0.003738	0.302239	
chunk0086_425_1	chr18	27922733	27923462	+	0	NA	Intergenic	Intergenic	113488	NM_001308176	1000	Hs.464829	NM_001792	ENSG00000170558	CDH2	CD325|CDHN|CDw325|NCAD	cadherin 2	protein-coding	0.006859	0.390411	247(AAAACATTGTGTTCAC,+,0.00)
chunk0133_335_1	chr3	172710205	172710423	+	0	NA	intron (NM_001146276, intron 1 of 4)	intron (NM_001146276, intron 1 of 4)	904	NM_001146278	57552	Hs.444099	NM_020792	ENSG00000144959	NCEH1	AADACL1|NCEH	neutral cholesterol ester hydrolase 1	protein-coding	0.032110	0.602740	
chunk0077_343_1	chr16	83077719	83078211	+	0	NA	intron (NM_001220489, intron 3 of 12)	L1ME2z|LINE|L1	-87667	NR_110937	101928417	Hs.569538	NR_110937	ENSG00000260832	LOC101928417	-	uncharacterized LOC101928417	ncRNA	0.024390	0.432049	248(TGACCATTCTGTTCTG,+,0.00)
chunk0051_279_1	chr12	118132090	118132308	+	0	NA	Intergenic	Intergenic	-3685	NM_002567	5037	Hs.433863	NM_002567	ENSG00000089220	PEBP1	HCNP|HCNPpp|HEL-210|HEL-S-34|HEL-S-96|PBP|PEBP|PEBP-1|RKIP	phosphatidylethanolamine binding protein 1	protein-coding	0.009174	0.452055	
chunk0053_255_1	chr13	33044776	33045139	+	0	NA	intron (NM_004795, intron 1 of 4)	L1ME2|LINE|L1	28524	NM_004795	9365	Hs.524953	NM_004795	ENSG00000133116	KL	HFTC3	klotho	protein-coding	0.002755	0.310440	
chunk0187_81_1	chr8	2983753	2983952	+	0	NA	intron (NM_033225, intron 54 of 69)	intron (NM_033225, intron 54 of 69)	-255401	NR_125425	101927815	Hs.571467	NR_125423	ENSG00000254319	LOC101927815	-	uncharacterized LOC101927815	ncRNA	0.005025	0.285000	
chunk0064_121_1	chr14	91361435	91361634	+	0	NA	intron (NM_001080414, intron 3 of 29)	intron (NM_001080414, intron 3 of 29)	56310	NM_001080414	440193	Hs.525536	NM_001080414	ENSG00000015133	CCDC88C	DAPLE|HKRP2|HYC1|KIAA1509|SCA40	coiled-coil domain containing 88C	protein-coding	0.015075	0.515000	
chunk0180_67_1	chr7	54877657	54878303	+	0	NA	Intergenic	L1M4b|LINE|L1	118667	NR_110040	100996654	Hs.127991	NR_110040		LOC100996654	-	uncharacterized LOC100996654	ncRNA	0.009288	0.463679	
chunk0185_76_1	chr7	125244039	125244495	+	0	NA	intron (NR_110183, intron 3 of 3)	intron (NR_110183, intron 3 of 3)	20024	NR_110183	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.004386	0.343545	
chunk0022_164_1	chr10	12620002	12620475	+	0	NA	intron (NM_020397, intron 2 of 9)	L1MD1|LINE|L1	32959	NR_039701	100616320		NR_039701	ENSG00000283699	MIR4481	-	microRNA 4481	ncRNA	0.023256	0.392405	
chunk0039_199_1	chr11	100902709	100902908	+	0	NA	intron (NM_152432, intron 4 of 23)	LTR16D|LTR|ERVL	-89272	NM_032021	143872	Hs.44004	NM_032021	ENSG00000165895	ARHGAP42	AD031|GRAF3|TMEM133	Rho GTPase activating protein 42	protein-coding	0.015075	0.520000	
chunk0004_165_1	chr1	45619536	45620175	+	0	NA	TTS (NM_001190182)	TTS (NM_001190182)	4204	NM_001114938	149483	Hs.18912	NM_152500	ENSG00000159588	CCDC17	-	coiled-coil domain containing 17	protein-coding	0.007825	0.451562	
chunk0131_402_1	chr3	152858095	152858782	+	0	NA	Intergenic	Intergenic	23745	NM_002563	5028	Hs.79881	NM_002563	ENSG00000169860	P2RY1	P2Y1|SARCC	purinergic receptor P2Y1	protein-coding	0.005822	0.421512	294(AAGAACACTGTGTTCT,-,0.00),295(AGAACACTGTGTTCTC,+,0.00)
chunk0144_52_1	chr4	126687855	126688117	+	0	NA	Intergenic	Intergenic	-944946	NM_015693	27152	Hs.391481	NM_015693	ENSG00000164066	INTU	CPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20	inturned planar cell polarity protein	protein-coding	0.011450	0.353612	
chunk0118_155_1	chr22	30298376	30298575	+	0	NA	intron (NM_001204240, intron 3 of 8)	intron (NM_001204240, intron 3 of 8)	-8848	NM_001037666	652968	Hs.444950	NM_001037666	ENSG00000239282	CASTOR1	GATSL3	cytosolic arginine sensor for mTORC1 subunit 1	protein-coding	0.010050	0.535000	
chunk0040_97_1	chr11	111703761	111704346	+	0	NA	intron (NM_015191, intron 7 of 14)	intron (NM_015191, intron 7 of 14)	62392	NM_001177563	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.017094	0.453925	
chunk0067_313_1	chr15	47900536	47901301	+	0	NA	Intergenic	Intergenic	-54682	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.002614	0.389034	359(CAGAACTTGCTGTACT,-,0.00),360(AGAACTTGCTGTACTT,+,0.00)
chunk0149_156_1	chr5	20324513	20324984	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	251125	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.002123	0.324153	
chunk0089_21_1	chr18	57748510	57749022	+	0	NA	intron (NM_005603, intron 1 of 27)	intron (NM_005603, intron 1 of 27)	54329	NM_005603	5205	Hs.216623	NM_005603	ENSG00000081923	ATP8B1	ATPIC|BRIC|FIC1|ICP1|PFIC|PFIC1	ATPase phospholipid transporting 8B1	protein-coding	0.001953	0.356725	
chunk0191_304_1	chr8	54913811	54914126	+	0	NA	Intergenic	Intergenic	-188489	NM_052898	114786	Hs.130197	NM_052898	ENSG00000206579	XKR4	XRG4	XK related 4	protein-coding	0.019048	0.544304	
chunk0154_110_1	chr5	78601013	78601247	+	0	NA	intron (NM_005779, intron 2 of 4)	intron (NM_005779, intron 2 of 4)	47695	NM_005779	10184	Hs.79299	NM_005779	ENSG00000145685	LHFPL2	-	LHFPL tetraspan subfamily member 2	protein-coding	0.000000	0.459574	
chunk0170_298_1	chr6	115544942	115545166	+	0	NA	Intergenic	L1PA10|LINE|L1	-493677	NR_027338	728402	Hs.729953	NR_027338		TPI1P3	-	triosephosphate isomerase 1 pseudogene 3	pseudo	0.017857	0.555556	
chunk0114_235_1	chr21	15977772	15978588	+	0	NA	Intergenic	Intergenic	-92342	NR_027790	388815	Hs.473394	NR_027790		MIR99AHG	C21orf34|C21orf35|LINC00478|MONC	mir-99a-let-7c cluster host gene	ncRNA	0.008578	0.370869	169(TGGACTAGATGTTCTT,+,0.00)
chunk0177_307_1	chr7	26006939	26007138	+	0	NA	Intergenic	MER20|DNA|hAT-Charlie	-57052	NR_029597	406940		NR_029597	ENSG00000199085	MIR148A	MIRN148|MIRN148A|hsa-mir-148|mir-148a	microRNA 148a	ncRNA	0.010050	0.530000	
chunk0017_370_1	chr1	212016147	212016791	+	0	NA	intron (NR_037667, intron 5 of 20)	intron (NR_037667, intron 5 of 20)	-19084	NM_001286230	51514	Hs.656473	NM_016448	ENSG00000143476	DTL	CDT2|DCAF2|L2DTL|RAMP	denticleless E3 ubiquitin protein ligase homolog	protein-coding	0.000000	0.348837	
chunk0020_53_1	chr1	232421146	232421564	+	0	NA	intron (NM_020808, intron 16 of 20)	intron (NM_020808, intron 16 of 20)	94253	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.019139	0.443914	
chunk0023_389_1	chr10	30804617	30804975	+	0	NA	Intergenic	Intergenic	112522	NR_036438	645954	Hs.408581	NR_036438		SVIL2P	SVILP1	supervillin family member 2, pseudogene	pseudo	0.011173	0.412256	
chunk0076_31_1	chr16	59373349	59373548	+	0	NA	Intergenic	L1MD1|LINE|L1	381743	NR_028471	644649	Hs.250392	NR_028471		APOOP5	-	apolipoprotein O pseudogene 5	pseudo	0.005025	0.365000	
chunk0068_264_1	chr15	56422874	56423318	+	0	NA	intron (NM_198524, intron 10 of 12)	L1MB2|LINE|L1	42041	NM_018365	55329	Hs.444483	NM_018365	ENSG00000138587	MNS1	SPATA40	meiosis specific nuclear structural 1	protein-coding	0.002252	0.341573	
chunk0009_159_1	chr1	105025690	105026133	+	0	NA	Intergenic	L1MEc|LINE|L1	593024	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.011287	0.317568	
chunk0093_176_1	chr19	48539631	48539830	+	0	NA	Intergenic	MIR|SINE|MIR	-12442	NM_177973	6820	Hs.369331	NM_004605	ENSG00000088002	SULT2B1	ARCI14|HSST2	sulfotransferase family 2B member 1	protein-coding	0.020101	0.510000	
chunk0205_40_1	chr9	105773151	105773432	+	0	NA	intron (NM_018112, intron 5 of 5)	intron (NM_018112, intron 5 of 5)	78766	NM_018112	55151	Hs.411925	NM_018112	ENSG00000095209	TMEM38B	C9orf87|D4Ertd89e|OI14|TRIC-B|TRICB|bA219P18.1	transmembrane protein 38B	protein-coding	0.003559	0.361702	
chunk0147_190_1	chr4	177542081	177542441	+	0	NA	Intergenic	Intergenic	-99758	NM_000027	175	Hs.207776	NM_000027	ENSG00000038002	AGA	AGU|ASRG|GA	aspartylglucosaminidase	protein-coding	0.002778	0.354571	162(AGTGACAGAATGTTCC,-,0.00),163(GTGACAGAATGTTCCC,+,0.00)
chunk0030_87_1	chr10	112348016	112348717	+	0	NA	intron (NR_028134, intron 3 of 18)	intron (NR_028134, intron 3 of 18)	8229	NR_028134	390003	Hs.534691	NR_028134	ENSG00000243316	GUCY2GP	GUCY2G	guanylate cyclase 2G, pseudogene	pseudo	0.014265	0.427350	
chunk0150_96_1	chr5	32474562	32474835	+	0	NA	Intergenic	Intergenic	-29960	NM_016107	51663	Hs.435231	NM_016107	ENSG00000056097	ZFR	SPG71|ZFR1	zinc finger RNA binding protein	protein-coding	0.018315	0.503650	
chunk0012_214_1	chr1	160143862	160144132	+	0	NA	TTS (NM_000702)	TTS (NM_000702)	-7565	NM_144699	480	Hs.662219	NM_144699	ENSG00000132681	ATP1A4	ATP1A1|ATP1AL2	ATPase Na+/K+ transporting subunit alpha 4	protein-coding	0.000000	0.479705	
chunk0212_136_1	chrX	131671580	131672259	+	0	NA	Intergenic	Intergenic	127845	NM_001004486	347468	Hs.553711	NM_001004486	ENSG00000171054	OR13H1	ORX1	olfactory receptor family 13 subfamily H member 1	protein-coding	0.007364	0.408824	235(GAGGACATGTTGTTCT,-,0.00),236(AGGACATGTTGTTCTC,+,0.00)
chunk0013_202_1	chr1	169300340	169300578	+	0	NA	intron (NR_104229, intron 5 of 12)	intron (NR_104229, intron 5 of 12)	-67497	NM_003666	8548	Hs.130746	NM_003666	ENSG00000117475	BLZF1	GOLGIN-45|JEM-1|JEM-1s|JEM1	basic leucine zipper nuclear factor 1	protein-coding	0.000000	0.263598	
chunk0211_19_1	chrX	107771686	107771967	+	0	NA	intron (NM_198057, intron 1 of 2)	intron (NM_198057, intron 1 of 2)	3961	NM_198057	1831	Hs.522074	NM_004089	ENSG00000157514	TSC22D3	DIP|DSIPI|GILZ|TSC-22R	TSC22 domain family member 3	protein-coding	0.007117	0.340426	
chunk0066_34_1	chr15	27630776	27631177	+	0	NA	Intergenic	L2a|LINE|L2	468336	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.009975	0.330846	
chunk0096_315_1	chr2	33166366	33166749	+	0	NA	intron (NM_000627, intron 1 of 29)	intron (NM_000627, intron 1 of 29)	31960	NM_001166266	4052	Hs.619315	NM_000627	ENSG00000049323	LTBP1	-	latent transforming growth factor beta binding protein 1	protein-coding	0.005222	0.335938	
chunk0037_61_1	chr11	70908348	70908553	+	0	NA	intron (NM_012309, intron 9 of 24)	intron (NM_012309, intron 9 of 24)	-36082	NR_037437	100500844		NR_037437	ENSG00000263744	MIR3664	mir-3664	microRNA 3664	ncRNA	0.014634	0.553398	
chunk0166_91_1	chr6	43717490	43717858	+	0	NA	Intergenic	Intergenic	-29862	NM_018135	55168	Hs.520149	NM_018135	ENSG00000096080	MRPS18A	HumanS18b|MRP-S18-3|MRP-S18-a|MRPS18-3|S18bmt|S18mt-a	mitochondrial ribosomal protein S18A	protein-coding	0.013587	0.544715	
chunk0088_244_1	chr18	48631395	48631817	+	0	NA	intron (NM_014772, intron 2 of 11)	intron (NM_014772, intron 2 of 11)	-38994	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.011848	0.382979	
chunk0021_71_1	chr10	1419773	1420537	+	0	NA	intron (NM_018702, intron 1 of 9)	intron (NM_018702, intron 1 of 9)	-106475	NR_033387	642394	Hs.568831	NM_001098830	ENSG00000205696	ADARB2-AS1	C10orf109|NCRNA00168	ADARB2 antisense RNA 1	ncRNA	0.013089	0.362092	
chunk0199_303_1	chr9	6999951	7000150	+	0	NA	intron (NR_130707, intron 13 of 14)	intron (NR_130707, intron 13 of 14)	242409	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.005025	0.330000	
chunk0158_102_1	chr5	126776519	126776736	+	0	NA	promoter-TSS (NM_001198557)	promoter-TSS (NM_001198557)	4	NM_005573	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.087558	0.587156	
chunk0098_139_1	chr2	69628639	69629248	+	0	NA	intron (NM_014911, intron 2 of 21)	intron (NM_014911, intron 2 of 21)	14902	NM_014911	22848	Hs.468878	NM_014911	ENSG00000115977	AAK1	-	AP2 associated kinase 1	protein-coding	0.006568	0.386885	284(AGGTACATACAGTACT,-,0.00),285(GGTACATACAGTACTC,+,0.00)
chunk0094_404_1	chr2	10417398	10417827	+	0	NA	intron (NM_134421, intron 3 of 5)	L1ME4b|LINE|L1	29237	NR_028374	100302743	Hs.730525	NR_028374	ENSG00000206633	SNORA80B	ACA67B	small nucleolar RNA, H/ACA box 80B	snoRNA	0.013986	0.446512	
chunk0119_380_1	chr22	48138402	48138918	+	0	NA	Intergenic	L1ME4b|LINE|L1	-135704	NR_036172	100422916		NR_036172	ENSG00000266508	MIR3201	-	microRNA 3201	ncRNA	0.007752	0.326886	
chunk0202_12_1	chr9	70397603	70398555	+	0	NA	intron (NM_001206, intron 1 of 1)	intron (NM_001206, intron 1 of 1)	16578	NM_001206	687	Hs.150557	NM_001206	ENSG00000119138	KLF9	BTEB|BTEB1	Kruppel like factor 9	protein-coding	0.007353	0.424974	836(CAGCACATGCAGTTCC,-,0.00),837(AGCACATGCAGTTCCA,+,0.00)
chunk0028_198_1	chr10	88913057	88913536	+	0	NA	exon (NM_020799, exon 6 of 11)	exon (NM_020799, exon 6 of 11)	-19388	NR_125373	100132116		NR_125373	ENSG00000180139	ACTA2-AS1	UC001kfo|ZXF1|uc001kfo.1	ACTA2 antisense RNA 1	ncRNA	0.018789	0.454167	
chunk0094_259_1	chr2	7639372	7639869	+	0	NA	Intergenic	MER77|LTR|ERVL	218359	NR_038432	100506274	Hs.177930	NR_038432	ENSG00000229727	LOC100506274	-	uncharacterized LOC100506274	ncRNA	0.002012	0.395582	
chunk0134_218_1	chr3	178646158	178646828	+	0	NA	intron (NM_001278911, intron 1 of 4)	intron (NM_001278911, intron 1 of 4)	87793	NM_001278911	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.004478	0.424739	289(AAGAACAGACTGAACC,-,0.00),290(AGAACAGACTGAACCT,+,0.00)
chunk0131_389_1	chr3	152469565	152469951	+	0	NA	Intergenic	L2c|LINE|L2	-128768	NR_132656	645843	Hs.632562	NM_001123228	ENSG00000221962	TMEM14EP	TMEM14E	transmembrane protein 14E, pseudogene	pseudo	0.005181	0.366925	
chunk0091_171_1	chr19	7834507	7834729	+	0	NA	intron (NM_145245, intron 1 of 18)	L2b|LINE|L2	4343	NM_145245	115704	Hs.26870	NM_145245	ENSG00000142459	EVI5L	-	ecotropic viral integration site 5 like	protein-coding	0.000000	0.421525	
chunk0169_88_1	chr6	99590467	99590735	+	0	NA	Intergenic	Intergenic	-16173	NM_021620	59336	Hs.287386	NM_021620	ENSG00000112238	PRDM13	MU-MB-20.220|PFM10	PR/SET domain 13	protein-coding	0.018657	0.434944	
chunk0093_417_1	chr19	57461088	57461788	+	0	NA	Intergenic	L1M2|LINE|L1	-4699	NM_020633	57191	Hs.677423	NM_020633	ENSG00000178201	VN1R1	V1RL1|VNR19I1|ZVNH1|ZVNR1	vomeronasal 1 receptor 1	protein-coding	0.002857	0.319544	
chunk0027_119_1	chr10	74145146	74145362	+	0	NA	intron (NM_207012, intron 1 of 9)	intron (NM_207012, intron 1 of 9)	5814	NM_012095	26985	Hs.500104	NM_012095	ENSG00000185009	AP3M1	-	adaptor related protein complex 3 subunit mu 1	protein-coding	0.004630	0.368664	
chunk0162_64_1	chr6	1641255	1641624	+	0	NA	intron (NM_001253846, intron 9 of 10)	intron (NM_001253846, intron 9 of 10)	30993	NM_001453	2296	Hs.348883	NM_001453	ENSG00000054598	FOXC1	ARA|ASGD3|FKHL7|FREAC-3|FREAC3|IGDA|IHG1|IRID1|RIEG3	forkhead box C1	protein-coding	0.016260	0.543243	
chunk0025_2_1	chr10	46835378	46835789	+	0	NA	Intergenic	Intergenic	-41091	NR_033172	728798	Hs.664786	NM_001042515		FRMPD2B	FRMPD2|FRMPD2L1|FRMPD2L2|FRMPD2P1|FRMPD2P2|FRMPDP2|PDZD5A|PDZD5B|PDZD5C|PDZK4|PDZK5A|PDZK5B|PDZK5C|bA556L1.2|yX59F3.2	FERM and PDZ domain containing 2B, pseudogene	pseudo	0.009732	0.361650	
chunk0209_433_1	chrX	63124386	63124658	+	0	NA	Intergenic	L1M2|LINE|L1	226817	NM_001012968	139886	Hs.612782	NM_001012968	ENSG00000186767	SPIN4	TDRD28	spindlin family member 4	protein-coding	0.007353	0.362637	
chunk0127_122_1	chr3	93852001	93852363	+	0	NA	Intergenic	L1PA6|LINE|L1	121899	NM_001314077	5627	Hs.64016	NM_000313	ENSG00000184500	PROS1	PROS|PS21|PS22|PS23|PS24|PS25|PSA|THPH5|THPH6	protein S	protein-coding	0.013812	0.528926	
chunk0175_335_1	chr6	167218660	167218873	+	0	NA	Intergenic	Intergenic	48173	NM_001145121	401285		NM_001013683	ENSG00000166984	TCP10L2	-	t-complex 10 like 2	protein-coding	0.014085	0.308411	
chunk0169_27_1	chr6	96924763	96925025	+	0	NA	non-coding (NR_104421, exon 1 of 9)	non-coding (NR_104421, exon 1 of 9)	274	NM_001286251	114792	Hs.45056	NM_052904	ENSG00000186231	KLHL32	BKLHD5|KIAA1900|UG0030H05|dJ21F7.1	kelch like family member 32	protein-coding	0.083969	0.615970	
chunk0094_341_1	chr2	9327797	9328374	+	0	NA	intron (NM_003887, intron 7 of 27)	L1MB7|LINE|L1	95429	NM_022334	9270	Hs.467662	NM_004763	ENSG00000119185	ITGB1BP1	ICAP-1A|ICAP-1B|ICAP-1alpha|ICAP1|ICAP1A|ICAP1B	integrin subunit beta 1 binding protein 1	protein-coding	0.010399	0.371972	
chunk0187_373_1	chr7	157508496	157508816	+	0	NA	Intergenic	Intergenic	42425	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.031250	0.647975	
chunk0089_383_1	chr18	67514067	67514277	+	0	NA	exon (NM_032160, exon 2 of 2)	exon (NM_032160, exon 2 of 2)	-2374	NR_033921	643542	Hs.652901	NR_033921	ENSG00000265533	LOC643542	-	uncharacterized LOC643542	ncRNA	0.000000	0.421801	
chunk0199_316_1	chr9	7212904	7213596	+	0	NA	Intergenic	Intergenic	455609	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.008671	0.438672	
chunk0019_178_1	chr1	226431305	226431702	+	0	NA	Intergenic	Intergenic	-23403	NM_001618	142	Hs.177766	NM_001618	ENSG00000143799	PARP1	ADPRT|ADPRT 1|ADPRT1|ARTD1|PARP|PARP-1|PPOL|pADPRT-1	poly(ADP-ribose) polymerase 1	protein-coding	0.007557	0.351759	
chunk0182_66_1	chr7	92134755	92135047	+	0	NA	promoter-TSS (NM_001146152)	promoter-TSS (NM_001146152)	-156	NM_001146152	1595	Hs.417077	NM_000786	ENSG00000001630	CYP51A1	CP51|CYP51|CYPL1|LDM|P450-14DM|P450L1	cytochrome P450 family 51 subfamily A member 1	protein-coding	0.102740	0.665529	
chunk0070_64_1	chr15	69615440	69616148	+	0	NA	intron (NR_126437, intron 2 of 5)	intron (NR_126437, intron 2 of 5)	23594	NR_126437	104472713	Hs.430824	NR_126437	ENSG00000245750	PCAT29	-	prostate cancer associated transcript 29	ncRNA	0.008475	0.531735	314(TGGAACATATTGTTCC,-,0.00),315(GGAACATATTGTTCCT,+,0.00)
chunk0133_71_1	chr3	166981775	166981979	+	0	NA	Intergenic	L1MB8|LINE|L1	398406	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.000000	0.317073	
chunk0051_360_1	chr12	121227363	121227571	+	0	NA	intron (NR_046373, intron 4 of 10)	intron (NR_046373, intron 4 of 10)	17606	NR_046373	5025	Hs.321709	NM_002560	ENSG00000135124	P2RX4	P2X4|P2X4R	purinergic receptor P2X 4	protein-coding	0.033654	0.550239	
chunk0069_127_1	chr15	61971523	61972115	+	0	NA	intron (NM_017684, intron 25 of 82)	intron (NM_017684, intron 25 of 82)	88646	NM_020821	54832	Hs.511668	NM_017684	ENSG00000129003	VPS13C	PARK23	vacuolar protein sorting 13 homolog C	protein-coding	0.003378	0.359191	
chunk0026_378_1	chr10	69386854	69387271	+	0	NA	intron (NM_033497, intron 16 of 20)	MER90a|LTR|ERV1	29856	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.007194	0.423445	
chunk0020_174_1	chr1	234499338	234499684	+	0	NA	Intergenic	Intergenic	-20408	NM_005646	6894	Hs.498115	NM_005646	ENSG00000059588	TARBP1	TRM3|TRMT3|TRP-185|TRP185	TAR (HIV-1) RNA binding protein 1	protein-coding	0.020231	0.487032	
chunk0149_398_1	chr5	28880768	28881536	+	0	NA	Intergenic	Intergenic	-45718	NR_033961	729862	Hs.646006	NR_033961		LSP1P3	-	LSP1 pseudogene 3	pseudo	0.002604	0.381014	
chunk0195_33_1	chr8	93225776	93226697	+	0	NA	Intergenic	Intergenic	-59386	NM_001242668									0.014115	0.437093	
chunk0056_66_1	chr13	79127988	79128366	+	0	NA	Intergenic	Intergenic	278044	NM_022118	64062	Hs.558528	NM_018605	ENSG00000139746	RBM26	ARRS2|C13orf10|PPP1R132|PRO1777|SE70-2|ZC3H17	RNA binding motif protein 26	protein-coding	0.002646	0.387863	166(AAGTACATGATGACCC,-,0.00)
chunk0067_87_1	chr15	41862932	41863140	+	0	NA	intron (NM_016642, intron 41 of 67)	intron (NM_016642, intron 41 of 67)	3515	NR_036195	100423013		NR_036195	ENSG00000264850	MIR4310	-	microRNA 4310	ncRNA	0.024038	0.569378	57(GTGCACAGCAAGTCCC,-,0.00),58(TGCACAGCAAGTCCCC,+,0.00)
chunk0101_315_1	chr2	135450325	135450856	+	0	NA	intron (NM_001286568, intron 2 of 20)	L1MEc|LINE|L1	80140	NM_001286569	84083	Hs.658422	NM_032143	ENSG00000121988	ZRANB3	4933425L19Rik|AH2	zinc finger RANBP2-type containing 3	protein-coding	0.007533	0.389098	
chunk0141_370_1	chr4	88055763	88056569	+	0	NA	exon (NM_000297, exon 8 of 15)	exon (NM_000297, exon 8 of 15)	48519	NM_000297	5311	Hs.181272	NM_000297	ENSG00000118762	PKD2	APKD2|PC2|PKD4|Pc-2|TRPP2	polycystin 2, transient receptor potential cation channel	protein-coding	0.004963	0.353160	
chunk0113_131_1	chr20	51744581	51744880	+	0	NA	intron (NM_006045, intron 1 of 27)	intron (NM_006045, intron 1 of 27)	23681	NM_006045	10079	Hs.649234	NM_006045	ENSG00000054793	ATP9A	ATPIIA	ATPase phospholipid transporting 9A (putative)	protein-coding	0.006689	0.440000	
chunk0029_69_1	chr10	96596655	96597015	+	0	NA	intron (NM_152309, intron 16 of 16)	intron (NM_152309, intron 16 of 16)	-9783	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.002778	0.398892	
chunk0086_97_1	chr18	13875150	13875716	+	0	NA	Intergenic	MIR|SINE|MIR	40103	NM_000529	4158	Hs.248144	NM_000529	ENSG00000185231	MC2R	ACTHR	melanocortin 2 receptor	protein-coding	0.015901	0.516755	
chunk0076_125_1	chr16	66673417	66674009	+	0	NA	intron (NM_181521, intron 1 of 3)	intron (NM_181521, intron 1 of 3)	22994	NM_181521	146223	Hs.643961	NM_178818	ENSG00000183723	CMTM4	CKLFSF4	CKLF like MARVEL transmembrane domain containing 4	protein-coding	0.008446	0.468803	
chunk0178_332_1	chr7	38292438	38292770	+	0	NA	Intergenic	MIR|SINE|MIR	-18957	NM_001003806	445347	Hs.534032	NM_001003799		TARP	CD3G|TCRG|TCRGC1|TCRGC2|TCRGV	TCR gamma alternate reading frame protein	protein-coding	0.006024	0.342342	
chunk0150_37_1	chr5	31420948	31421171	+	0	NA	intron (NM_013235, intron 29 of 34)	L2c|LINE|L2	111116	NM_001100412	29102	Hs.97997	NM_013235	ENSG00000113360	DROSHA	ETOHI2|HSA242976|RANSE3L|RN3|RNASE3L|RNASEN	drosha ribonuclease III	protein-coding	0.000000	0.339286	
chunk0021_335_1	chr1	245898456	245899040	+	0	NA	intron (NM_001167740, intron 8 of 11)	intron (NM_001167740, intron 8 of 11)	518664	NM_022743	64754	Hs.567571	NM_022743	ENSG00000185420	SMYD3	KMT3E|ZMYND1|ZNFN3A1|bA74P14.1	SET and MYND domain containing 3	protein-coding	0.003425	0.389744	126(TAAAACAGTGTGTGCC,-,0.00),127(AAAACAGTGTGTGCCA,+,0.00),347(CAGCACGCTATGTTCT,-,0.00),348(AGCACGCTATGTTCTT,+,0.00)
chunk0032_86_1	chr11	2988744	2988959	+	0	NA	intron (NM_005969, intron 1 of 15)	intron (NM_005969, intron 1 of 15)	3526	NM_005969	4676	Hs.731784	NM_005969	ENSG00000205531	NAP1L4	NAP1L4b|NAP2|NAP2L|hNAP2	nucleosome assembly protein 1 like 4	protein-coding	0.009302	0.356481	
chunk0196_277_1	chr8	109274653	109274980	+	0	NA	intron (NM_001128211, intron 7 of 9)	intron (NM_001128211, intron 7 of 9)	55117	NM_001128211	84955	Hs.380291	NM_032869	ENSG00000120526	NUDCD1	CML66|OVA66	NudC domain containing 1	protein-coding	0.006116	0.298780	
chunk0011_190_1	chr1	149792144	149792388	+	0	NA	3' UTR (NM_000566, exon 6 of 6)	3' UTR (NM_000566, exon 6 of 6)	9572	NM_000566	2209	Hs.77424	NM_000566	ENSG00000150337	FCGR1A	CD64|CD64A|FCRI|IGFR1	Fc fragment of IgG receptor Ia	protein-coding	0.024590	0.465306	
chunk0096_73_1	chr2	27781158	27781919	+	0	NA	3' UTR (NM_001287580, exon 9 of 9)	3' UTR (NM_001287580, exon 9 of 9)	9821	NM_145330	9553	Hs.515879	NM_004891	ENSG00000243147	MRPL33	C2orf1|L33mt|MRP-L33|RPL33L	mitochondrial ribosomal protein L33	protein-coding	0.006570	0.393701	
chunk0030_313_1	chr10	117804517	117805314	+	0	NA	Intergenic	Intergenic	241688	NM_014904	22841	Hs.173656	NM_014904	ENSG00000107560	RAB11FIP2	Rab11-FIP2|nRip11	RAB11 family interacting protein 2	protein-coding	0.018821	0.498747	360(TGGAACACCATGTACC,-,0.00),361(GGAACACCATGTACCC,+,0.00)
chunk0132_343_1	chr3	161323265	161323641	+	0	NA	Intergenic	Intergenic	48630	NM_001040100	165679	Hs.369104	NM_145035	ENSG00000196542	SPTSSB	ADMP|C3orf57|SSSPTB	serine palmitoyltransferase small subunit B	protein-coding	0.005319	0.334218	
chunk0144_140_1	chr4	129839218	129839530	+	0	NA	Intergenic	L1ME1|LINE|L1	-67896	NR_110753	101927282	Hs.407480	NR_110753	ENSG00000246876	LINC02466	-	long intergenic non-protein coding RNA 2466	ncRNA	0.003205	0.357827	
chunk0070_455_1	chr15	78456848	78457387	+	0	NA	intron (NM_004136, intron 2 of 21)	HAL1|LINE|L1	18941	NM_004136	3658	Hs.436031	NM_004136	ENSG00000136381	IREB2	ACO3|IRE-BP 2|IRE-BP2|IRP2|IRP2AD|NDCAMA	iron responsive element binding protein 2	protein-coding	0.003711	0.340741	290(TAGTACTCTATGTCCT,-,0.00),291(AGTACTCTATGTCCTT,+,0.00)
chunk0191_441_1	chr8	57957156	57957705	+	0	NA	Intergenic	Intergenic	-20928	NR_130934	100505477	Hs.434693	NR_130934	ENSG00000205293	LINC01602	T1560	long intergenic non-protein coding RNA 1602	ncRNA	0.007286	0.356364	
chunk0210_137_1	chrX	74593235	74593851	+	0	NA	intron (NM_183353, intron 4 of 4)	intron (NM_183353, intron 4 of 4)	21083	NM_183353	51132	Hs.653288	NM_016120	ENSG00000131263	RLIM	MRX61|NY-REN-43|RNF12|TOKAS	ring finger protein, LIM domain interacting	protein-coding	0.004870	0.351702	
chunk0040_425_1	chr11	121335788	121336558	+	0	NA	Intergenic	Intergenic	43305	NM_001024956	6309	Hs.287749	NM_006918	ENSG00000109929	SC5D	ERG3|S5DES|SC5DL	sterol-C5-desaturase	protein-coding	0.002597	0.459144	
chunk0005_400_1	chr1	62386408	62386608	+	0	NA	Intergenic	Intergenic	-49796	NM_001017415	7398	Hs.35086	NM_003368	ENSG00000162607	USP1	UBP	ubiquitin specific peptidase 1	protein-coding	0.005000	0.373134	
chunk0096_12_1	chr2	26012348	26012898	+	0	NA	Intergenic	MamRep605|LTR?|LTR?	-21237	NM_016131	10890	Hs.467960	NM_016131	ENSG00000084733	RAB10	-	RAB10, member RAS oncogene family	protein-coding	0.016364	0.462795	
chunk0107_139_1	chr2	214907728	214908085	+	0	NA	intron (NR_110292, intron 2 of 3)	intron (NR_110292, intron 2 of 3)	97677	NR_110292	101928103	Hs.665619	NR_110292	ENSG00000229267	SNHG31	-	small nucleolar RNA host gene 31	ncRNA	0.005602	0.405028	
chunk0054_151_1	chr13	44044877	44045131	+	0	NA	Intergenic	Intergenic	22669	NR_026955	121838	Hs.201441	NR_026955		LINC00284	NCRNA00284	long intergenic non-protein coding RNA 284	ncRNA	0.003937	0.423529	
chunk0168_49_1	chr6	78639593	78640217	+	0	NA	Intergenic	MIR|SINE|MIR	-227639	NM_001010844	134728	Hs.656212	NM_001010844	ENSG00000146243	IRAK1BP1	AIP70|SIMPL	interleukin 1 receptor associated kinase 1 binding protein 1	protein-coding	0.003205	0.316800	
chunk0006_304_1	chr1	71351460	71351709	+	0	NA	Intergenic	Intergenic	270260	NR_046217	100852410	Hs.535534	NR_046217	ENSG00000229956	ZRANB2-AS2	-	ZRANB2 antisense RNA 2 (head to head)	ncRNA	0.000000	0.352000	
chunk0178_274_1	chr7	37102281	37102563	+	0	NA	intron (NM_001206482, intron 14 of 21)	intron (NM_001206482, intron 14 of 21)	104626	NR_104120	100861514	Hs.627775	NR_104120	ENSG00000224101	ELMO1-AS1	-	ELMO1 antisense RNA 1	ncRNA	0.000000	0.392226	
chunk0058_231_1	chr14	25415009	25415385	+	0	NA	Intergenic	Intergenic	-364900	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.005319	0.358090	123(AAGAACAGGCTGTATT,-,0.00),124(AGAACAGGCTGTATTC,+,0.00)
chunk0162_455_1	chr5	180861311	180861647	+	0	NA	promoter-TSS (NM_001172638)	promoter-TSS (NM_001172638)	-193	NM_001172638	643836	Hs.509227	NM_152283	ENSG00000196670	ZFP62	ZET|ZNF755	ZFP62 zinc finger protein	protein-coding	0.083333	0.667656	
chunk0046_155_1	chr12	58223773	58224193	+	0	NA	Intergenic	Intergenic	282321	NM_033276	91419	Hs.61188	NM_033276	ENSG00000166896	ATP23	KUB3|XRCC6BP1	ATP23 metallopeptidase and ATP synthase assembly factor homolog	protein-coding	0.009524	0.406176	
chunk0023_402_1	chr10	31073982	31074492	+	0	NA	Intergenic	Intergenic	-42300	NR_026560	220929	Hs.660642	NM_182755	ENSG00000183621	ZNF438	bA330O11.1	zinc finger protein 438	protein-coding	0.005882	0.377691	
chunk0017_269_1	chr1	209707596	209708741	+	0	NA	intron (NM_181755, intron 5 of 6)	intron (NM_181755, intron 5 of 6)	3377	NM_005525	3290	Hs.195040	NM_005525	ENSG00000117594	HSD11B1	11-DH|11-beta-HSD1|CORTRD2|HDL|HSD11|HSD11B|HSD11L|SDR26C1	hydroxysteroid 11-beta dehydrogenase 1	protein-coding	0.005240	0.424956	140(AGGTACAGCTTGTCCT,-,0.00),141(GGTACAGCTTGTCCTG,+,0.00)
chunk0202_315_1	chr9	78236106	78236548	+	0	NA	5' UTR (NM_001098802, exon 1 of 16)	5' UTR (NM_001098802, exon 1 of 16)	252	NM_001098802	84131	Hs.187621	NM_032171	ENSG00000148019	CEP78	C9orf81|CRDHL|IP63	centrosomal protein 78	protein-coding	0.128959	0.717833	
chunk0083_327_1	chr17	69764563	69764762	+	0	NA	intron (NR_109972, intron 3 of 4)	intron (NR_109972, intron 3 of 4)	170675	NR_109972	101928122	Hs.579342	NR_109971	ENSG00000227517	LINC01483	-	long intergenic non-protein coding RNA 1483	ncRNA	0.005025	0.315000	
chunk0004_415_1	chr1	52374125	52374701	+	0	NA	intron (NM_001190818, intron 16 of 16)	intron (NM_001190818, intron 16 of 16)	-8208	NM_032449	200014	Hs.591451	NM_032449	ENSG00000154222	CC2D1B	-	coiled-coil and C2 domain containing 1B	protein-coding	0.005208	0.383016	
chunk0022_414_1	chr10	18610665	18610902	+	0	NA	intron (NM_182543, intron 5 of 10)	intron (NM_182543, intron 5 of 10)	40854	NM_182543	221078	Hs.396175	NM_182543	ENSG00000241058	NSUN6	4933414E04Rik|ARL5B-AS1|NOPD1	NOP2/Sun RNA methyltransferase 6	protein-coding	0.012658	0.453782	
chunk0205_310_1	chr9	112626856	112627245	+	0	NA	intron (NM_001287036, intron 3 of 4)	intron (NM_001287036, intron 3 of 4)	91057	NM_021218	58493	Hs.658575	NM_021218	ENSG00000148153	INIP	C9orf80|HSPC043|MISE|SOSSC|SSBIP1|hSSBIP1	INTS3 and NABP interacting protein	protein-coding	0.005141	0.361538	
chunk0026_315_1	chr10	68075094	68075293	+	0	NA	5' UTR (NM_001278186, exon 1 of 23)	5' UTR (NM_001278186, exon 1 of 23)	153	NM_015601	26091	Hs.51891	NM_015601	ENSG00000148634	HERC4	-	HECT and RLD domain containing E3 ubiquitin protein ligase 4	protein-coding	0.070352	0.660000	
chunk0188_25_1	chr8	6560487	6560998	+	0	NA	intron (NM_001147, intron 1 of 8)	intron (NM_001147, intron 1 of 8)	2521	NM_001118887	285	Hs.583870	NM_001147	ENSG00000091879	ANGPT2	AGPT2|ANG2	angiopoietin 2	protein-coding	0.023483	0.417969	
chunk0056_295_1	chr13	90548890	90549194	+	0	NA	Intergenic	Intergenic	55754	NR_120414	101927224	Hs.385801	NR_120414		LINC01049	-	long intergenic non-protein coding RNA 1049	ncRNA	0.003289	0.363934	
chunk0065_161_1	chr15	25609465	25609851	+	0	NA	Intergenic	Intergenic	-170630	NM_000462	7337	Hs.598862	NM_000462	ENSG00000114062	UBE3A	ANCR|AS|E6-AP|EPVE6AP|HPVE6A	ubiquitin protein ligase E3A	protein-coding	0.010363	0.434109	
chunk0184_13_1	chr7	111765909	111766387	+	0	NA	intron (NM_014705, intron 37 of 51)	intron (NM_014705, intron 37 of 51)	-42357	NR_103806	100506413	Hs.677513	NR_103806	ENSG00000225572	DOCK4-AS1	-	DOCK4 antisense RNA 1	ncRNA	0.006276	0.390397	
chunk0206_414_1	chr9	127473801	127474250	+	0	NA	intron (NM_001005373, intron 11 of 25)	intron (NM_001005373, intron 11 of 25)	21770	NM_001005374	90678	Hs.495188	NM_138361	ENSG00000148356	LRSAM1	CMT2P|RIFLE|TAL	leucine rich repeat and sterile alpha motif containing 1	protein-coding	0.015590	0.546667	332(AAGCACAAGCTGTGCC,-,0.00),333(AGCACAAGCTGTGCCC,+,0.00)
chunk0166_354_1	chr6	51237789	51238189	+	0	NA	Intergenic	Intergenic	-383881	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.005000	0.381546	
chunk0160_158_1	chr5	151779733	151780453	+	0	NA	intron (NM_198395, intron 1 of 11)	L1ME3Cz|LINE|L1	-7917	NR_132345	100652758	Hs.587054	NM_001278082		LOC100652758	-	uncharacterized LOC100652758	ncRNA	0.001389	0.342580	
chunk0101_378_1	chr2	138491894	138492093	+	0	NA	Intergenic	Intergenic	-9787	NM_001001664	339745	Hs.333297	NM_001001664	ENSG00000144228	SPOPL	BTBD33	speckle type BTB/POZ protein like	protein-coding	0.010050	0.355000	
chunk0044_291_1	chr12	32755952	32756151	+	0	NA	promoter-TSS (NM_001040436)	promoter-TSS (NM_001040436)	-98	NM_001040436	51067	Hs.505231	NM_015936	ENSG00000139131	YARS2	CGI-04|MLASA2|MT-TYRRS|TYRRS	tyrosyl-tRNA synthetase 2	protein-coding	0.060302	0.500000	
chunk0076_400_1	chr16	72635928	72636426	+	0	NA	intron (NR_126330, intron 1 of 13)	L1MEd|LINE|L1	28832	NR_126330	101927957	Hs.637253	NR_126330	ENSG00000261008	LINC01572	-	long intergenic non-protein coding RNA 1572	ncRNA	0.006024	0.330661	
chunk0098_198_1	chr2	72483316	72483776	+	0	NA	intron (NM_015189, intron 16 of 21)	intron (NM_015189, intron 16 of 21)	-335684	NM_001277742	56603	Hs.91546	NM_019885	ENSG00000003137	CYP26B1	CYP26A2|P450RAI-2|P450RAI2|RHFCA	cytochrome P450 family 26 subfamily B member 1	protein-coding	0.004348	0.342733	
chunk0002_405_1	chr1	27430917	27431155	+	0	NA	intron (NM_001201404, intron 1 of 7)	intron (NM_001201404, intron 1 of 7)	38392	NM_005281	2827	Hs.66542	NM_005281	ENSG00000181773	GPR3	ACCA	G protein-coupled receptor 3	protein-coding	0.004202	0.410042	72(CGGAACAGACTGCTCC,-,0.00),73(GGAACAGACTGCTCCT,+,0.00),93(ATGGACATTCTGATCT,-,0.00),94(TGGACATTCTGATCTG,+,0.00)
chunk0135_182_1	chr3	188106814	188107442	+	0	NA	Intergenic	Intergenic	-46745	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.014331	0.435612	261(CTGAACTCAGTGTTCT,-,0.00),262(TGAACTCAGTGTTCTT,+,0.00)
chunk0204_305_1	chr9	100175620	100176037	+	0	NA	intron (NM_014425, intron 3 of 16)	intron (NM_014425, intron 3 of 16)	76608	NM_014425	27130	Hs.558477	NM_014425	ENSG00000119509	INVS	INV|NPH2|NPHP2	inversin	protein-coding	0.007194	0.488038	150(TGGAACATCCAGTCCT,-,0.00),151(GGAACATCCAGTCCTA,+,0.00)
chunk0075_304_1	chr16	54334719	54335210	+	0	NA	Intergenic	(TC)n|Simple_repeat|Simple_repeat	-48498	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.002037	0.327236	
chunk0111_241_1	chr20	29753412	29753611	+	0	NA	Intergenic	Intergenic	-126873	NR_039689	100616194		NR_039689	ENSG00000266017	MIR4477B	-	microRNA 4477b	ncRNA	0.045226	0.595000	
chunk0166_428_1	chr6	52670998	52671198	+	0	NA	promoter-TSS (NM_014051)	promoter-TSS (NM_014051)	12	NM_014051	28978	Hs.94896	NM_014051	ENSG00000096092	TMEM14A	C6orf73|PTD011	transmembrane protein 14A	protein-coding	0.110000	0.711443	
chunk0028_139_1	chr10	86450860	86451123	+	0	NA	intron (NM_015045, intron 15 of 18)	intron (NM_015045, intron 15 of 18)	70793	NM_015045	23063	Hs.203099	NM_015045	ENSG00000062650	WAPL	FOE|KIAA0261|WAPAL	WAPL cohesin release factor	protein-coding	0.011407	0.382576	
chunk0042_128_1	chr12	3641466	3641983	+	0	NA	intron (NM_001144958, intron 13 of 19)	intron (NM_001144958, intron 13 of 19)	111476	NM_032680	84766	Hs.504534	NM_032680	ENSG00000130038	CRACR2A	EFCAB4B	calcium release activated channel regulator 2A	protein-coding	0.005803	0.511583	
chunk0085_141_1	chr18	3257433	3257655	+	0	NA	intron (NR_130144, intron 1 of 2)	intron (NR_130144, intron 1 of 2)	4286	NR_130143	104968399	Hs.464472	NR_130143	ENSG00000264235	LOC104968399	-	uncharacterized LOC104968399	ncRNA	0.009009	0.421525	
chunk0145_56_1	chr4	145196862	145197286	+	0	NA	Intergenic	Intergenic	-17394	NM_001102653	54726	Hs.270851	NM_017493	ENSG00000164164	OTUD4	DUBA6|HIN1|HSHIN1	OTU deubiquitinase 4	protein-coding	0.007075	0.496471	
chunk0131_417_1	chr3	153087725	153088276	+	0	NA	Intergenic	Intergenic	-74212	NM_002886	5912	Hs.98643	NM_002886	ENSG00000181467	RAP2B	-	RAP2B, member of RAS oncogene family	protein-coding	0.005445	0.394928	
chunk0070_397_1	chr15	77071351	77071586	+	0	NA	promoter-TSS (NM_001168412)	promoter-TSS (NM_001168412)	-240	NM_005724	10099	Hs.744863	NM_005724	ENSG00000140391	TSPAN3	TM4-A|TM4SF8|TSPAN-3	tetraspanin 3	protein-coding	0.004255	0.461864	
chunk0093_389_1	chr19	56481414	56482105	+	0	NA	intron (NR_036521, intron 1 of 1)	intron (NR_036521, intron 1 of 1)	3635	NR_036522	100128252	Hs.23133	NM_198879	ENSG00000166770	ZNF667-AS1	MORT	ZNF667 antisense RNA 1 (head to head)	ncRNA	0.008683	0.414740	
chunk0133_171_1	chr3	169948953	169949291	+	0	NA	non-coding (NR_027622, exon 2 of 2)	non-coding (NR_027622, exon 2 of 2)	17612	NR_024409	100128164	Hs.633070	NR_024409	ENSG00000239219	LOC100128164	-	four and a half LIM domains 1 pseudogene	pseudo	0.000000	0.368732	
chunk0045_408_1	chr12	52949906	52950131	+	0	NA	promoter-TSS (NM_001256293)	promoter-TSS (NM_001256293)	-152	NM_001256293	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.008889	0.575221	
chunk0102_18_1	chr2	141517313	141518182	+	0	NA	intron (NM_018557, intron 2 of 90)	intron (NM_018557, intron 2 of 90)	613954	NM_018557	53353	Hs.656461	NM_018557	ENSG00000168702	LRP1B	LRP-1B|LRP-DIT|LRPDIT	LDL receptor related protein 1B	protein-coding	0.003452	0.344828	
chunk0199_248_1	chr9	5770249	5770504	+	0	NA	TTS (NM_001135920)	TTS (NM_001135920)	62705	NM_024896	79956	Hs.591078	NM_024896	ENSG00000099219	ERMP1	FXNA|KIAA1815|bA207C16.3	endoplasmic reticulum metallopeptidase 1	protein-coding	0.003922	0.332031	
chunk0040_100_1	chr11	111747873	111748406	+	0	NA	intron (NM_181700, intron 8 of 13)	intron (NM_181700, intron 8 of 13)	18306	NM_001177563	5519	Hs.269128	NM_002716	ENSG00000137713	PPP2R1B	PP2A-Abeta|PR65B	protein phosphatase 2 scaffold subunit Abeta	protein-coding	0.007505	0.365169	374(GAGAACAGGGTGGCCA,-,0.00)
chunk0023_167_1	chr10	24397803	24398047	+	0	NA	intron (NM_019590, intron 3 of 20)	MIRb|SINE|MIR	-51508	NM_001282769	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.008197	0.485714	64(GGGCACTGAGTGTACC,-,0.00),65(GGCACTGAGTGTACCC,+,0.00)
chunk0005_125_1	chr1	56812759	56813228	+	0	NA	intron (NM_001004303, intron 1 of 19)	MLT1B|LTR|ERVL-MaLR	6703	NM_001004303	199920	Hs.437655	NM_001004303	ENSG00000187889	FYB2	ARAP|C1orf168	FYN binding protein 2	protein-coding	0.006397	0.417021	
chunk0092_164_1	chr19	29741535	29742176	+	0	NA	Intergenic	Intergenic	-26066	NM_001256047	83636	Hs.529094	NM_031448	ENSG00000131943	C19orf12	MPAN|NBIA3|NBIA4|SPG43	chromosome 19 open reading frame 12	protein-coding	0.012480	0.489097	
chunk0029_347_1	chr10	106565633	106565869	+	0	NA	Intergenic	Intergenic	598957	NM_052918	114815	Hs.591915	NM_052918	ENSG00000108018	SORCS1	hSorCS	sortilin related VPS10 domain containing receptor 1	protein-coding	0.008475	0.413502	
chunk0013_217_1	chr1	169508872	169509684	+	0	NA	Intergenic	Intergenic	-23308	NM_006996	10560	Hs.30246	NM_006996	ENSG00000117479	SLC19A2	TC1|THMD1|THT1|THTR1|TRMA	solute carrier family 19 member 2	protein-coding	0.001232	0.344403	124(AAGAACATTGTGTTTC,-,0.00),125(AGAACATTGTGTTTCA,+,0.00)
chunk0077_329_1	chr16	82324718	82325214	+	0	NA	Intergenic	MER58A|DNA|hAT-Charlie	-154742	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.002016	0.400402	
chunk0016_147_1	chr1	197457471	197457811	+	0	NA	intron (NR_047564, intron 11 of 11)	intron (NR_047564, intron 11 of 11)	189437	NM_001193640	23418	Hs.126135	NM_012076	ENSG00000134376	CRB1	LCA8|RP12	crumbs cell polarity complex component 1	protein-coding	0.008824	0.384164	
chunk0039_138_1	chr11	98559582	98559803	+	0	NA	Intergenic	Intergenic	-461284	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.013575	0.373874	
chunk0054_385_1	chr13	50241390	50241904	+	0	NA	intron (NR_109974, intron 2 of 6)	Tigger17a|DNA|TcMar-Tigger	69629	NR_002183	145165	Hs.511834	NM_153290		ST13P4	FAM10A4|FAM10A4P	ST13, Hsp70 interacting protein pseudogene 4	pseudo	0.011673	0.349515	319(AAGAACACAGTGTGTT,-,0.00),320(AGAACACAGTGTGTTG,+,0.00)
chunk0138_185_1	chr4	37980469	37981002	+	0	NA	intron (NM_015173, intron 2 of 19)	intron (NM_015173, intron 2 of 19)	20300	NM_006607	10744	Hs.668806	NM_006607	ENSG00000250254	PTTG2	-	pituitary tumor-transforming 2	protein-coding	0.001876	0.325843	
chunk0077_208_1	chr16	79893254	79893838	+	0	NA	Intergenic	Intergenic	98297	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.006849	0.388034	
chunk0212_241_1	chrX	137418127	137418394	+	0	NA	Intergenic	Intergenic	-147927	NM_003413	7547	Hs.111227	NM_003413	ENSG00000156925	ZIC3	HTX|HTX1|VACTERLX|ZNF203	Zic family member 3	protein-coding	0.003745	0.388060	
chunk0121_304_1	chr3	24121221	24121867	+	0	NA	3' UTR (NM_001252634, exon 12 of 12)	3' UTR (NM_001252634, exon 12 of 12)	-18297	NR_026834	152024	Hs.385606	NR_026834	ENSG00000224074	LINC00691	-	long intergenic non-protein coding RNA 691	ncRNA	0.006192	0.454405	
chunk0187_362_1	chr7	157355964	157356529	+	0	NA	intron (NM_058246, intron 1 of 9)	intron (NM_058246, intron 1 of 9)	19229	NM_058246	10049	Hs.490745	NM_005494	ENSG00000105993	DNAJB6	DJ4|DnaJ|HHDJ1|HSJ-2|HSJ2|LGMD1D|LGMD1E|LGMDD1|MRJ|MSJ-1	DnaJ heat shock protein family (Hsp40) member B6	protein-coding	0.015929	0.494700	
chunk0202_378_1	chr9	80798464	80798859	+	0	NA	Intergenic	Intergenic	823638	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.000000	0.351010	162(AAAAACAGAATGTTCC,-,0.00),163(AAAACAGAATGTTCCA,+,0.00)
chunk0138_223_1	chr4	39076548	39076948	+	0	NA	intron (NM_001007075, intron 3 of 11)	(T)n|Simple_repeat|Simple_repeat	14516	NM_199039	51088	Hs.272251	NM_015990	ENSG00000109790	KLHL5	-	kelch like family member 5	protein-coding	0.002500	0.309227	
chunk0170_239_1	chr6	113627266	113627476	+	0	NA	intron (NR_125844, intron 2 of 2)	intron (NR_125844, intron 2 of 2)	22704	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.009524	0.327014	
chunk0046_381_1	chr12	63512626	63512879	+	0	NA	Intergenic	L4_C_Mam|LINE|RTE-X	155822	NM_173812	283417	Hs.533644	NM_173812	ENSG00000177990	DPY19L2	SPATA34|SPGF9	dpy-19 like 2	protein-coding	0.000000	0.342520	
chunk0109_390_1	chr2	240136075	240136553	+	0	NA	promoter-TSS (NM_138336)	promoter-TSS (NM_138336)	16	NM_001163424	150678	Hs.293884	NM_138336	ENSG00000172428	COPS9	CSNAP|MYEOV2	COP9 signalosome subunit 9	protein-coding	0.131799	0.755741	
chunk0123_446_1	chr3	50671224	50671705	+	0	NA	Intergenic	Intergenic	-3616	NR_039950	100616138		NR_039950	ENSG00000272543	MIR4787	mir-4787	microRNA 4787	ncRNA	0.008316	0.458506	
chunk0038_40_1	chr11	82036980	82037707	+	0	NA	intron (NR_120571, intron 5 of 7)	intron (NR_120571, intron 5 of 7)	-146507	NR_036186	100422823		NR_036186	ENSG00000264110	MIR4300	-	microRNA 4300	ncRNA	0.005502	0.313187	
chunk0158_117_1	chr5	126901212	126901703	+	0	NA	intron (NM_178450, intron 3 of 4)	intron (NM_178450, intron 3 of 4)	124304	NM_001198557	4001	Hs.89497	NM_005573	ENSG00000113368	LMNB1	ADLD|LMN|LMN2|LMNB	lamin B1	protein-coding	0.008147	0.386179	
chunk0137_396_1	chr4	27094649	27095093	+	0	NA	Intergenic	L2a|LINE|L2	-122608	NR_125921	101929199	Hs.570815	NR_125921	ENSG00000249699	LINC02261	-	long intergenic non-protein coding RNA 2261	ncRNA	0.009009	0.449438	
chunk0034_317_1	chr11	35158467	35159148	+	0	NA	intron (NM_001001389, intron 1 of 16)	intron (NM_001001389, intron 1 of 16)	19937	NM_001202557	960	Hs.502328	NM_000610	ENSG00000026508	CD44	CDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1	CD44 molecule (Indian blood group)	protein-coding	0.010279	0.475073	
chunk0172_330_1	chr6	138446743	138447176	+	0	NA	intron (NM_001144060, intron 4 of 7)	intron (NM_001144060, intron 4 of 7)	-11665	NR_036099	100423001		NR_036099	ENSG00000266555	MIR3145	mir-3145	microRNA 3145	ncRNA	0.018476	0.426267	221(AAGTACATTCTGAACC,-,0.00),222(AGTACATTCTGAACCT,+,0.00)
chunk0008_122_1	chr1	91745205	91745909	+	0	NA	intron (NR_036634, intron 5 of 17)	intron (NR_036634, intron 5 of 17)	140722	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.004261	0.405674	
chunk0106_335_1	chr2	206120332	206120619	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	-3903	NR_033248	100329109	Hs.356055	NR_033248		GCSHP3	-	glycine cleavage system protein H pseudogene 3	pseudo	0.000000	0.437500	
chunk0033_441_1	chr11	25390468	25391111	+	0	NA	Intergenic	Intergenic	-798334	NM_001313726	63982	Hs.91791	NM_031418	ENSG00000134343	ANO3	C11orf25|DYT23|DYT24|GENX-3947|TMEM16C	anoctamin 3	protein-coding	0.000000	0.318323	317(AGGACTCATTGTTCAG,+,0.00)
chunk0062_239_1	chr14	71267237	71267436	+	0	NA	Intergenic	Intergenic	-131001	NR_001276	319139		NR_001276	ENSG00000207444	SNORD56B	RNU56B	small nucleolar RNA, C/D box 56B	snoRNA	0.010050	0.395000	
chunk0029_265_1	chr10	103153523	103153752	+	0	NA	intron (NM_001134373, intron 2 of 17)	intron (NM_001134373, intron 2 of 17)	39669	NM_001134373	22978	Hs.97439	NM_012229	ENSG00000076685	NT5C2	GMP|NT5B|PNT5|SPG45|SPG65|cN-II	5'-nucleotidase, cytosolic II	protein-coding	0.013100	0.421739	
chunk0190_301_1	chr8	38105189	38105388	+	0	NA	promoter-TSS (NM_001261832)	promoter-TSS (NM_001261832)	-205	NM_004674	9070	Hs.521530	NM_004674	ENSG00000129691	ASH2L	ASH2|ASH2L1|ASH2L2|Bre2	ASH2 like, histone lysine methyltransferase complex subunit	protein-coding	0.095477	0.650000	
chunk0057_211_1	chr13	103965686	103965885	+	0	NA	Intergenic	L2c|LINE|L2	540585	NR_126374	104326190	Hs.334381	NR_126374	ENSG00000234551	LINC01309	TCONS_l2_00007459	long intergenic non-protein coding RNA 1309	ncRNA	0.000000	0.370000	
chunk0167_342_1	chr6	72715202	72715621	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	84916	NR_120503	100507381	Hs.662412	NR_120503	ENSG00000233844	KCNQ5-IT1	-	KCNQ5 intronic transcript 1	ncRNA	0.011933	0.440476	
chunk0201_18_1	chr9	33076681	33076915	+	0	NA	promoter-TSS (NM_018225)	promoter-TSS (NM_018225)	-82	NM_018225	55234	Hs.655351	NM_018225	ENSG00000122692	SMU1	BWD|SMU-1|fSAP57	SMU1 DNA replication regulator and spliceosomal factor	protein-coding	0.076923	0.612766	
chunk0027_391_1	chr10	79970122	79970414	+	0	NA	Intergenic	L1M2|LINE|L1	-21163	NM_003019	6441	Hs.253495	NM_003019	ENSG00000133661	SFTPD	COLEC7|PSP-D|SFTP4|SP-D	surfactant protein D	protein-coding	0.000000	0.365188	
chunk0019_32_1	chr1	223785660	223786253	+	0	NA	intron (NM_001031685, intron 16 of 17)	intron (NM_001031685, intron 16 of 17)	60016	NM_001031685	7159	Hs.523968	NM_005426	ENSG00000143514	TP53BP2	53BP2|ASPP2|BBP|P53BP2|PPP1R13A	tumor protein p53 binding protein 2	protein-coding	0.010118	0.383838	
chunk0210_250_1	chrX	82978443	82978700	+	0	NA	Intergenic	L1PA15|LINE|L1	-529690	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.003891	0.298450	
chunk0107_198_1	chr2	216350126	216350539	+	0	NA	intron (NM_020814, intron 1 of 3)	intron (NM_020814, intron 1 of 3)	21695	NM_020814	57574	Hs.170388	NM_020814	ENSG00000144583	MARCH4	MARCH-IV|RNF174	membrane associated ring-CH-type finger 4	protein-coding	0.012107	0.574879	
chunk0160_396_1	chr5	163462789	163463474	+	0	NA	intron (NM_001142557, intron 1 of 14)	intron (NM_001142557, intron 1 of 14)	2620	NM_012485	3161	Hs.740467	NM_012484	ENSG00000072571	HMMR	CD168|IHABP|RHAMM	hyaluronan mediated motility receptor	protein-coding	0.001460	0.344023	379(TAGTACAATTTGTACT,-,0.00),380(AGTACAATTTGTACTT,+,0.00)
chunk0132_329_1	chr3	161092334	161092715	+	0	NA	intron (NM_001038628, intron 6 of 7)	intron (NM_001038628, intron 6 of 7)	12371	NM_033169	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.005249	0.306283	
chunk0026_12_1	chr10	60497195	60498587	+	0	NA	intron (NM_001204403, intron 2 of 43)	intron (NM_001204403, intron 2 of 43)	75065	NM_001204404	288	Hs.499725	NM_001149	ENSG00000151150	ANK3	ANKYRIN-G|MRT37	ankyrin 3	protein-coding	0.005029	0.379038	
chunk0188_83_1	chr8	8539937	8540223	+	0	NA	Intergenic	Intergenic	-158246	NM_001080826	157285	Hs.583863	NM_001080826	ENSG00000275342	PRAG1	NACK|PEAK2|PRAGMIN|SGK223	PEAK1 related, kinase-activating pseudokinase 1	protein-coding	0.006993	0.459930	
chunk0033_304_1	chr11	20132393	20132656	+	0	NA	Intergenic	L1M3f|LINE|L1	27800	NM_001029865	120237		NM_001029865	ENSG00000109851	DBX1	-	developing brain homeobox 1	protein-coding	0.057034	0.587121	152(TGGGACAGGCCGTGCT,-,0.00),153(GGGACAGGCCGTGCTC,+,0.00)
chunk0092_414_1	chr19	37935963	37936672	+	0	NA	intron (NM_015073, intron 1 of 21)	intron (NM_015073, intron 1 of 21)	29096	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.007052	0.476056	
chunk0130_342_1	chr3	138688990	138689352	+	0	NA	intron (NM_001256045, intron 4 of 12)	AluSx3|SINE|Alu	18450	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.011050	0.438017	
chunk0071_33_1	chr15	79657770	79658143	+	0	NA	Intergenic	MER89|LTR|ERV1	225440	NM_015206	23251	Hs.301654	NM_015206	ENSG00000169330	MINAR1	KIAA1024|UBTOR	membrane integral NOTCH2 associated receptor 1	protein-coding	0.005362	0.435829	
chunk0032_312_1	chr11	9896827	9897210	+	0	NA	intron (NM_030962, intron 16 of 39)	L1MB3|LINE|L1	57876	NR_120539	101928008	Hs.585524	NR_120539	ENSG00000255476	LOC101928008	-	uncharacterized LOC101928008	ncRNA	0.005222	0.351562	
chunk0020_45_1	chr1	232302334	232302599	+	0	NA	Intergenic	Intergenic	213142	NM_020808	57568	Hs.745009	NM_020808	ENSG00000116991	SIPA1L2	SPAL2|SPAR2	signal induced proliferation associated 1 like 2	protein-coding	0.007547	0.503759	
chunk0047_241_1	chr12	72230689	72231140	+	0	NA	Intergenic	Intergenic	-41835	NM_013381	29953	Hs.199814	NM_013381	ENSG00000072657	TRHDE	PAP-II|PGPEP2|TRH-DE	thyrotropin releasing hormone degrading enzyme	protein-coding	0.006652	0.309735	
chunk0093_402_1	chr19	56956405	56956891	+	0	NA	Intergenic	L1M5|LINE|L1	115746	NR_024059	100073347	Hs.467337	NR_024059	ENSG00000268654	MIMT1	LINC00067|MIM1|NCRNA00067	MER1 repeat containing imprinted transcript 1	ncRNA	0.026749	0.429158	
chunk0200_431_1	chr9	29668688	29669020	+	0	NA	Intergenic	L1ME1|LINE|L1	-455854	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.006024	0.342342	202(CTGCACATCCAGTTCC,-,0.00),203(TGCACATCCAGTTCCT,+,0.00)
chunk0157_250_1	chr5	119828700	119829236	+	0	NA	Intergenic	Intergenic	199409	NM_182761	340069	Hs.713304	NM_182761	ENSG00000164334	FAM170A	ZNFD	family with sequence similarity 170 member A	protein-coding	0.005597	0.333333	
chunk0055_134_1	chr13	59386626	59386949	+	0	NA	Intergenic	HAL1|LINE|L1	-625931	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.003096	0.333333	185(AAGGACAAAATGATCC,-,0.00)
chunk0099_69_1	chr2	85091911	85092110	+	0	NA	Intergenic	Helitron3Na_Mam|RC|Helitron	-41450	NM_031283	83439	Hs.516297	NM_031283	ENSG00000152284	TCF7L1	TCF-3|TCF3	transcription factor 7 like 1	protein-coding	0.005025	0.435000	
chunk0031_446_1	chr10	132605864	132606192	+	0	NA	intron (NM_005539, intron 1 of 15)	intron (NM_005539, intron 1 of 15)	68179	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.033537	0.547112	
chunk0175_171_1	chr7	4744332	4744698	+	0	NA	intron (NM_001037165, intron 2 of 8)	L1PA17|LINE|L1	-31116	NM_014855	9907	Hs.558440	NM_014855	ENSG00000242802	AP5Z1	KIAA0415|SPG48|zeta	adaptor related protein complex 5 subunit zeta 1	protein-coding	0.046448	0.547684	
chunk0009_336_1	chr1	109152236	109152608	+	0	NA	intron (NM_001284352, intron 1 of 20)	intron (NM_001284352, intron 1 of 20)	-34127	NM_001284353	57535	Hs.708190	NM_020775	ENSG00000116299	KIAA1324	EIG121	KIAA1324	protein-coding	0.000000	0.442359	
chunk0080_381_1	chr17	33806709	33806976	+	0	NA	intron (NM_001094, intron 1 of 9)	intron (NM_001094, intron 1 of 9)	-273082	NR_037584	100506677	Hs.652571	NR_037584	ENSG00000265544	AA06	AA02|AA04|AA05	uncharacterized LOC100506677	pseudo	0.000000	0.470149	
chunk0036_261_1	chr11	65013975	65014420	+	0	NA	promoter-TSS (NM_001199745)	promoter-TSS (NM_001199745)	84	NM_001667	402	Hs.502836	NM_001667	ENSG00000213465	ARL2	ARFL2	ADP ribosylation factor like GTPase 2	protein-coding	0.128090	0.719731	
chunk0212_359_1	chrX	149397384	149397816	+	0	NA	Intergenic	Intergenic	107754	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.004630	0.385681	
chunk0005_31_1	chr1	54695393	54695757	+	0	NA	intron (NR_111931, intron 16 of 22)	intron (NR_111931, intron 16 of 22)	-20247	NM_004623	7268	Hs.412482	NM_004623	ENSG00000243725	TTC4	CNS1	tetratricopeptide repeat domain 4	protein-coding	0.041209	0.575342	
chunk0130_220_1	chr3	134107237	134107498	+	0	NA	Intergenic	Intergenic	-77291	NM_005630	6578	Hs.518270	NM_005630	ENSG00000174640	SLCO2A1	MATR1|OATP2A1|PGT|PHOAR2|SLC21A2	solute carrier organic anion transporter family member 2A1	protein-coding	0.000000	0.568702	
chunk0121_441_1	chr3	26146545	26146831	+	0	NA	Intergenic	Intergenic	-272993	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.003497	0.379791	109(AAGAACAGGTTGTACA,-,0.00),110(AGAACAGGTTGTACAT,+,0.00)
chunk0010_83_1	chr1	113422411	113422716	+	0	NA	intron (NM_152900, intron 1 of 20)	LTR2752|LTR|ERV1	31710	NM_152900	260425	Hs.486189	NM_020965	ENSG00000081026	MAGI3	MAGI-3|dJ730K3.2	membrane associated guanylate kinase, WW and PDZ domain containing 3	protein-coding	0.049180	0.640523	
chunk0091_335_1	chr19	14118175	14118485	+	0	NA	promoter-TSS (NM_002730)	promoter-TSS (NM_002730)	-583	NM_002730	5566	Hs.631630	NM_002730	ENSG00000072062	PRKACA	PKACA|PPNAD4	protein kinase cAMP-activated catalytic subunit alpha	protein-coding	0.132258	0.797428	
chunk0166_282_1	chr6	48306442	48306824	+	0	NA	Intergenic	Intergenic	-237944	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.000000	0.315927	
chunk0026_73_1	chr10	61283415	61283895	+	0	NA	Intergenic	L2a|LINE|L2	-168984	NR_120643	101928781	Hs.568856	NR_120643		TMEM26-AS1	-	TMEM26 antisense RNA 1	ncRNA	0.002083	0.395010	
chunk0126_277_1	chr3	80064110	80064479	+	0	NA	Intergenic	L1PB3|LINE|L1	-296385	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.008130	0.405405	
chunk0105_94_1	chr2	184367292	184367673	+	0	NA	Intergenic	L1MD1|LINE|L1	-11493	NR_039638	100616305		NR_039638	ENSG00000266808	MIR548AE1	-	microRNA 548ae-1	ncRNA	0.010499	0.327225	
chunk0116_116_1	chr21	35814964	35815239	+	0	NA	Intergenic	L2c|LINE|L2	94386	NR_030414	768219		NR_030414	ENSG00000211590	MIR802	MIRN802|hsa-mir-802	microRNA 802	ncRNA	0.003636	0.500000	149(GGGAACACTCCGTCCT,-,0.00),150(GGAACACTCCGTCCTG,+,0.00)
chunk0090_174_1	chr18	72704112	72704517	+	0	NA	Intergenic	L1MDa|LINE|L1	149068	NR_049858	100847083		NR_049858	ENSG00000263750	MIR548AV	-	microRNA 548av	ncRNA	0.012346	0.492611	
chunk0096_378_1	chr2	36925624	36925996	+	0	NA	intron (NM_003162, intron 1 of 17)	intron (NM_003162, intron 1 of 17)	40662	NM_003162	6801	Hs.127486	NM_003162	ENSG00000115808	STRN	PPP2R6A|SG2NA|STRN1	striatin	protein-coding	0.008065	0.402145	
chunk0001_180_1	chr1	7060129	7060350	+	0	NA	intron (NM_015215, intron 3 of 22)	MLT1B|LTR|ERVL-MaLR	274915	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.027149	0.554054	
chunk0129_316_1	chr3	123984871	123985337	+	0	NA	intron (NM_017578, intron 1 of 6)	Charlie17|DNA|hAT-Charlie	6248	NM_017578	54763	Hs.567516	NM_017578	ENSG00000065371	ROPN1	CT91|ODF6|RHPNAP1|ROPN1A|ropporin	rhophilin associated tail protein 1	protein-coding	0.006438	0.379015	
chunk0113_246_1	chr20	54682863	54683154	+	0	NA	Intergenic	Intergenic	207290	NM_177959	55816	Hs.473133	NM_018431	ENSG00000101134	DOK5	C20orf180|IRS-6|IRS6	docking protein 5	protein-coding	0.006873	0.510274	
chunk0086_100_1	chr18	13983431	13984196	+	0	NA	Intergenic	LTR82B|LTR|ERVL	-68106	NM_001291911	4158	Hs.248144	NM_000529	ENSG00000185231	MC2R	ACTHR	melanocortin 2 receptor	protein-coding	0.003922	0.407311	
chunk0159_296_1	chr5	142817850	142818658	+	0	NA	intron (NM_015071, intron 1 of 22)	intron (NM_015071, intron 1 of 22)	47527	NM_015071	23092	Hs.654668	NM_015071	ENSG00000145819	ARHGAP26	GRAF|GRAF1|OPHN1L|OPHN1L1	Rho GTPase activating protein 26	protein-coding	0.004950	0.462299	
chunk0134_275_1	chr3	179655286	179655586	+	0	NA	intron (NM_003940, intron 1 of 20)	intron (NM_003940, intron 1 of 20)	2291	NM_003940	8975	Hs.175322	NM_003940	ENSG00000058056	USP13	ISOT3|IsoT-3	ubiquitin specific peptidase 13	protein-coding	0.006667	0.348837	
chunk0174_43_1	chr6	154590695	154591277	+	0	NA	Intergenic	Intergenic	-80367	NM_173515	154043	Hs.16064	NM_173515	ENSG00000153721	CNKSR3	CNK3|CNK3/IPCEF1|MAGI1	CNKSR family member 3	protein-coding	0.006873	0.394511	
chunk0048_103_1	chr12	79387819	79388437	+	0	NA	intron (NM_001291901, intron 8 of 9)	intron (NM_001291901, intron 8 of 9)	-31129	NR_031700	100302136		NR_031700	ENSG00000221788	MIR1252	MIRN1252|hsa-mir-1252	microRNA 1252	ncRNA	0.001618	0.344103	
chunk0200_368_1	chr9	25828106	25828474	+	0	NA	Intergenic	L1MA2|LINE|L1	48234	NR_121604	101929582	Hs.140547	NR_121604	ENSG00000236306	LINC01241	-	long intergenic non-protein coding RNA 1241	ncRNA	0.008152	0.517615	
chunk0039_311_1	chr11	103332996	103333195	+	0	NA	intron (NM_001377, intron 82 of 88)	intron (NM_001377, intron 82 of 88)	223664	NM_001080463	79659	Hs.503721	NM_001377	ENSG00000187240	DYNC2H1	ATD3|DHC1b|DHC2|DNCH2|DYH1B|SRPS2B|SRTD3|hdhc11	dynein cytoplasmic 2 heavy chain 1	protein-coding	0.000000	0.240000	
chunk0125_33_1	chr3	62395324	62395626	+	0	NA	Intergenic	Intergenic	-21960	NM_018008	55079	Hs.241523	NM_018008	ENSG00000153266	FEZF2	FEZ|FEZL|FKSG36|TOF|ZFP312|ZNF312	FEZ family zinc finger 2	protein-coding	0.006623	0.369637	
chunk0206_164_1	chr9	121904790	121905053	+	0	NA	intron (NM_001139442, intron 6 of 8)	intron (NM_001139442, intron 6 of 8)	162136	NM_138709	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.019011	0.458333	
chunk0019_465_1	chr1	231534927	231535200	+	0	NA	intron (NR_028398, intron 2 of 10)	intron (NR_028398, intron 2 of 10)	6410	NR_028398	100303453	Hs.13318	NR_028393	ENSG00000270106	TSNAX-DISC1	-	TSNAX-DISC1 readthrough (NMD candidate)	ncRNA	0.007326	0.423358	
chunk0058_146_1	chr14	23089939	23090251	+	0	NA	exon (NM_014977, exon 4 of 19)	exon (NM_014977, exon 4 of 19)	-5379	NM_017924	55017	Hs.525238	NM_017924	ENSG00000179933	C14orf119	-	chromosome 14 open reading frame 119	protein-coding	0.028846	0.527157	
chunk0134_346_1	chr3	182436519	182436886	+	0	NA	Intergenic	Intergenic	49660	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.016349	0.396739	316(GAGACACTATGTGCCT,+,0.00)
chunk0156_458_1	chr5	115006361	115006838	+	0	NA	Intergenic	Intergenic	163364	NM_001300759	55521	Hs.519514	NM_018700	ENSG00000152503	TRIM36	ANPH|HAPRIN|RBCC728|RNF98	tripartite motif containing 36	protein-coding	0.002096	0.384937	
chunk0021_171_1	chr10	5412474	5412779	+	0	NA	promoter-TSS (NM_001047160)	promoter-TSS (NM_001047160)	75	NM_001047160	10276	Hs.25155	NM_005863	ENSG00000173848	NET1	ARHGEF8|NET1A	neuroepithelial cell transforming 1	protein-coding	0.108197	0.715686	
chunk0082_324_1	chr17	59502654	59503157	+	0	NA	intron (NR_110813, intron 2 of 2)	MIRb|SINE|MIR	23952	NR_110813	101927728	Hs.569720	NR_110813	ENSG00000265313	LINC01476	-	long intergenic non-protein coding RNA 1476	ncRNA	0.001988	0.369048	
chunk0043_195_1	chr12	19167630	19167913	+	0	NA	intron (NM_019012, intron 3 of 25)	L2a|LINE|L2	-37554	NM_001256787	54477	Hs.188614	NM_019012	ENSG00000052126	PLEKHA5	PEPP-2|PEPP2	pleckstrin homology domain containing A5	protein-coding	0.003534	0.408451	
chunk0024_341_1	chr10	43340736	43341000	+	0	NA	Intergenic	L2a|LINE|L2	-30776	NM_001184963	53828	Hs.130497	NM_173160	ENSG00000150201	FXYD4	CHIF	FXYD domain containing ion transport regulator 4	protein-coding	0.026515	0.535849	
chunk0156_324_1	chr5	111512448	111512875	+	0	NA	promoter-TSS (NM_139164)	promoter-TSS (NM_139164)	-64	NM_001308057	134429	Hs.93842	NM_139164	ENSG00000164211	STARD4	-	StAR related lipid transfer domain containing 4	protein-coding	0.065574	0.628505	191(GGAACAACGTGCGCTT,+,0.00)
chunk0164_392_1	chr6	26204650	26204849	+	0	NA	exon (NM_003545, exon 1 of 1)	exon (NM_003545, exon 1 of 1)	104	NM_003545	8367	Hs.662174	NM_003545	ENSG00000276966	HIST1H4E	H4/j|H4FJ	histone cluster 1 H4 family member e	protein-coding	0.090452	0.580000	
chunk0150_128_1	chr5	33299790	33300339	+	0	NA	Intergenic	Intergenic	-140632	NM_001258437	6897	Hs.481860	NM_152295	ENSG00000113407	TARS	ThrRS	threonyl-tRNA synthetase	protein-coding	0.007286	0.396364	267(AAGCACATTCTGTACC,-,0.00),268(AGCACATTCTGTACCA,+,0.00)
chunk0113_375_1	chr20	59584109	59584472	+	0	NA	intron (NM_001199505, intron 1 of 12)	intron (NM_001199505, intron 1 of 12)	6781	NM_001199505	116154	Hs.473218	NM_080672	ENSG00000087495	PHACTR3	C20orf101|H17739|PPP1R123|SCAPIN1|SCAPININ	phosphatase and actin regulator 3	protein-coding	0.030303	0.557692	
chunk0194_435_1	chr8	92491124	92491596	+	0	NA	Intergenic	Intergenic	164134	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.004237	0.389006	
chunk0155_420_1	chr5	99993738	99993937	+	0	NA	Intergenic	Intergenic	394417	NR_027503	100133050	Hs.534796	NR_027503		LOC100133050	-	glucuronidase beta pseudogene	pseudo	0.000000	0.305000	
chunk0131_167_1	chr3	146517875	146518393	+	0	NA	intron (NM_021105, intron 7 of 8)	MLT1I|LTR|ERVL-MaLR	-22143	NM_020359	57047	Hs.744414	NM_020359	ENSG00000163746	PLSCR2	-	phospholipid scramblase 2	protein-coding	0.003861	0.393064	
chunk0038_63_1	chr11	83009481	83009782	+	0	NA	intron (NM_001286060, intron 1 of 4)	(AAAAT)n|Simple_repeat|Simple_repeat	24938	NM_001286059	27314	Hs.40758	NM_014488	ENSG00000137502	RAB30	-	RAB30, member RAS oncogene family	protein-coding	0.000000	0.350993	
chunk0131_176_1	chr3	147415776	147416049	+	0	NA	3' UTR (NM_003412, exon 3 of 3)	3' UTR (NM_003412, exon 3 of 3)	-5415	NR_121655	440982	Hs.535724	NR_121655		LOC440982	-	uncharacterized LOC440982	ncRNA	0.003663	0.328467	
chunk0183_309_1	chr7	107949288	107949932	+	0	NA	intron (NM_002291, intron 24 of 33)	intron (NM_002291, intron 24 of 33)	53749	NM_002291	3912	Hs.650585	NM_002291	ENSG00000091136	LAMB1	CLM|LIS5	laminin subunit beta 1	protein-coding	0.003106	0.396899	
chunk0088_74_1	chr18	44676018	44676562	+	0	NA	Intergenic	Intergenic	-3883	NM_001130110	26040	Hs.435458	NM_015559	ENSG00000152217	SETBP1	MRD29|SEB	SET binding protein 1	protein-coding	0.003676	0.400000	
chunk0051_394_1	chr12	121958012	121958573	+	0	NA	exon (NM_144668, exon 12 of 22)	exon (NM_144668, exon 12 of 22)	39735	NM_001178003	144406	Hs.709837	NM_144668	ENSG00000158023	WDR66	CFAP251|CaM-IP4|SPGF33	WD repeat domain 66	protein-coding	0.012478	0.432384	
chunk0202_372_1	chr9	80602323	80602612	+	0	NA	Intergenic	MER92B|LTR|ERV1	627444	NR_121212	101927477	Hs.571630	NR_121212		LINC01507	XLOC_000303	long intergenic non-protein coding RNA 1507	ncRNA	0.013841	0.451724	
chunk0021_214_1	chr10	6039674	6039873	+	0	NA	intron (NM_001308243, intron 1 of 5)	intron (NM_001308243, intron 1 of 5)	22597	NM_000417	3559	Hs.231367	NM_000417	ENSG00000134460	IL2RA	CD25|IDDM10|IL2R|IMD41|TCGFR|p55	interleukin 2 receptor subunit alpha	protein-coding	0.010050	0.460000	
chunk0060_293_1	chr14	50733320	50733875	+	0	NA	intron (NM_016350, intron 27 of 28)	intron (NM_016350, intron 27 of 28)	-65244	NM_021818	60485	Hs.642842	NM_021818	ENSG00000151748	SAV1	SAV|WW45|WWP4	salvador family WW domain containing protein 1	protein-coding	0.003604	0.386691	
chunk0077_202_1	chr16	79883341	79883991	+	0	NA	Intergenic	Intergenic	88417	NR_104661	101928248	Hs.659802	NR_104660	ENSG00000260876	LINC01229	-	long intergenic non-protein coding RNA 1229	ncRNA	0.007692	0.311828	
chunk0210_301_1	chrX	87516795	87516994	+	0	NA	promoter-TSS (NM_057162)	promoter-TSS (NM_057162)	-818	NM_057162	56062	Hs.49075	NM_019117	ENSG00000102271	KLHL4	DKELCHL|KHL4	kelch like family member 4	protein-coding	0.000000	0.345000	
chunk0060_4_1	chr14	39059904	39060396	+	0	NA	intron (NM_006364, intron 13 of 19)	intron (NM_006364, intron 13 of 19)	43083	NM_006364	10484	Hs.272927	NM_006364	ENSG00000100934	SEC23A	CLSD|hSec23A	Sec23 homolog A, coat complex II component	protein-coding	0.004065	0.363083	
chunk0187_368_1	chr7	157460163	157460563	+	0	NA	Intergenic	Intergenic	-5868	NR_110157	101927914	Hs.623826	NR_110157	ENSG00000234210	LOC101927914	-	uncharacterized LOC101927914	ncRNA	0.025000	0.538653	
chunk0043_2_1	chr12	12774748	12775255	+	0	NA	intron (NM_001130415, intron 1 of 1)	L1MC1|LINE|L1	10352	NR_030344	693198		NR_030344	ENSG00000207983	MIR613	MIRN613|hsa-mir-613	microRNA 613	ncRNA	0.005917	0.385827	
chunk0113_307_1	chr20	57960796	57961253	+	0	NA	Intergenic	Intergenic	65630	NR_039757									0.021882	0.502183	
chunk0194_133_1	chr8	84316321	84316824	+	0	NA	intron (NM_001100391, intron 1 of 8)	intron (NM_001100391, intron 1 of 8)	131707	NM_001100391	138046	Hs.121663	NM_173848	ENSG00000184672	RALYL	HNRPCL3	RALY RNA binding protein like	protein-coding	0.007952	0.283730	
chunk0095_195_1	chr2	18230239	18230950	+	0	NA	Intergenic	L1PREC2|LINE|L1	330099	NM_020905	57665	Hs.120319	NM_020905	ENSG00000240857	RDH14	PAN2|SDR7C4	retinol dehydrogenase 14	protein-coding	0.001406	0.351124	
chunk0148_18_1	chr5	388617	389020	+	0	NA	intron (NM_020731, intron 4 of 11)	intron (NM_020731, intron 4 of 11)	54342	NR_126522	116349	Hs.446702	NM_138464	ENSG00000221990	EXOC3-AS1	C5orf55	EXOC3 antisense RNA 1	ncRNA	0.032258	0.631188	244(AGGACACAATGCTCAT,+,0.00)
chunk0198_253_1	chr8	134644594	134644950	+	0	NA	intron (NM_020863, intron 2 of 15)	(CA)n|Simple_repeat|Simple_repeat	46701	NR_002438	594840	Hs.626298	NR_002438	ENSG00000248492	ZFAT-AS1	NCRNA00070|SAS-ZFAT|ZFAT-AS|ZFATAS	ZFAT antisense RNA 1	ncRNA	0.028090	0.453782	
chunk0172_4_1	chr6	132443367	132444103	+	0	NA	Intergenic	MIR|SINE|MIR	-42201	NM_015529	26002	Hs.6909	NM_015529	ENSG00000079931	MOXD1	MOX|PRO5780|dJ248E1.1	monooxygenase DBH like 1	protein-coding	0.001359	0.388060	425(TAGAACATACAGTTCA,-,0.00),426(AGAACATACAGTTCAG,+,0.00)
chunk0167_348_1	chr6	72844103	72844593	+	0	NA	intron (NM_019842, intron 1 of 13)	intron (NM_019842, intron 1 of 13)	123405	NR_036244	100423005		NR_036244	ENSG00000266180	MIR4282	-	microRNA 4282	ncRNA	0.000000	0.325866	
chunk0202_234_1	chr9	76521426	76521762	+	0	NA	Intergenic	Tigger17b|DNA|TcMar-Tigger	20961	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.017857	0.409496	
chunk0109_233_1	chr20	5920714	5921176	+	0	NA	intron (NM_001819, intron 3 of 4)	intron (NM_001819, intron 3 of 4)	9617	NM_001819	1114	Hs.516874	NM_001819	ENSG00000089199	CHGB	SCG1	chromogranin B	protein-coding	0.000000	0.321814	189(AGGTACAGAGAGTCCA,-,0.00),190(GGTACAGAGAGTCCAC,+,0.00)
chunk0176_179_1	chr7	13743770	13744230	+	0	NA	Intergenic	Intergenic	242514	NM_001163150	2115	Hs.22634	NM_004956	ENSG00000006468	ETV1	ER81	ETS variant 1	protein-coding	0.006522	0.349241	
chunk0192_241_1	chr8	65570697	65571177	+	0	NA	Intergenic	AluJo|SINE|Alu	-8271	NR_033893	286186	Hs.449427	NR_033893	ENSG00000254081	LINC01299	-	long intergenic non-protein coding RNA 1299	ncRNA	0.010417	0.432432	238(AGGTACTGGCTGTACC,-,0.00),239(GGTACTGGCTGTACCT,+,0.00)
chunk0172_293_1	chr6	137873173	137873826	+	0	NA	intron (NM_006290, intron 2 of 8)	intron (NM_006290, intron 2 of 8)	-5266	NR_049793	100130476	Hs.598050	NR_049793	ENSG00000237499	WAKMAR2	lnc-TNFAIP3	wound and keratinocyte migration associated lncRNA 2	ncRNA	0.010720	0.389908	
chunk0002_116_1	chr1	16095538	16095838	+	0	NA	Intergenic	Intergenic	-22056	NM_182623	348487	Hs.126825	NM_182623	ENSG00000185519	FAM131C	C1orf117	family with sequence similarity 131 member C	protein-coding	0.020000	0.578073	
chunk0068_76_1	chr15	51971466	51971899	+	0	NA	intron (NM_138792, intron 1 of 11)	CpG	119	NM_138792	123169	Hs.567662	NM_138792	ENSG00000166477	LEO1	RDL	LEO1 homolog, Paf1/RNA polymerase II complex component	protein-coding	0.090069	0.629032	
chunk0035_269_1	chr11	46522848	46523217	+	0	NA	intron (NM_001267782, intron 8 of 19)	intron (NM_001267782, intron 8 of 19)	68332	NM_017749	55626	Hs.654644	NM_017749	ENSG00000110497	AMBRA1	DCAF3|WDR94	autophagy and beclin 1 regulator 1	protein-coding	0.008130	0.435135	
chunk0179_460_1	chr7	52863733	52863956	+	0	NA	Intergenic	L1MB4|LINE|L1	-171812	NM_182595	285877	Hs.381970	NM_182595	ENSG00000221900	POM121L12	-	POM121 transmembrane nucleoporin like 12	protein-coding	0.008969	0.450893	163(GACACAAAGTGTTCTG,+,0.00)
chunk0110_74_1	chr20	10992922	10993268	+	0	NA	Intergenic	Intergenic	-83823	NR_109866	101929413	Hs.385604	NR_109866	ENSG00000232900	LOC101929413	-	uncharacterized LOC101929413	ncRNA	0.011561	0.351585	
chunk0075_19_1	chr16	46866914	46867157	+	0	NA	Intergenic	THE1C|LTR|ERVL-MaLR	-17345	NM_133443	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.000000	0.381148	
chunk0008_128_1	chr1	91805776	91806279	+	0	NA	intron (NR_036634, intron 2 of 17)	intron (NR_036634, intron 2 of 17)	80252	NR_036634	7049	Hs.482390	NM_003243	ENSG00000069702	TGFBR3	BGCAN|betaglycan	transforming growth factor beta receptor 3	protein-coding	0.011928	0.422619	
chunk0126_84_1	chr3	74718565	74719150	+	0	NA	Intergenic	L1MB7|LINE|L1	-197717	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.006838	0.308874	
chunk0012_71_1	chr1	155690435	155690934	+	0	NA	intron (NM_033657, intron 1 of 12)	L1MD3|LINE|L1	1590	NM_004632	7818	Hs.516746	NM_004632	ENSG00000132676	DAP3	DAP-3|MRP-S29|MRPS29|S29mt|bMRP-10	death associated protein 3	protein-coding	0.010020	0.410000	
chunk0134_207_1	chr3	178510504	178511226	+	0	NA	Intergenic	Intergenic	-25433	NM_181361	10242	Hs.478368	NM_005832	ENSG00000197584	KCNMB2	-	potassium calcium-activated channel subfamily M regulatory beta subunit 2	protein-coding	0.001385	0.329184	265(GAAAACACTGTGTTCC,-,0.00),266(AAAACACTGTGTTCCA,+,0.00)
chunk0026_363_1	chr10	69223038	69223658	+	0	NA	intron (NR_120648, intron 2 of 4)	intron (NR_120648, intron 2 of 4)	3045	NM_025130	80201	Hs.522988	NM_025130	ENSG00000156510	HKDC1	-	hexokinase domain containing 1	protein-coding	0.006452	0.347826	331(AGGTACATACAGTTCT,-,0.00),332(GGTACATACAGTTCTG,+,0.00)
chunk0079_151_1	chr17	13188299	13188741	+	0	NA	Intergenic	Intergenic	-170456	NM_173717	60528	Hs.434232	NM_018127	ENSG00000006744	ELAC2	COXPD17|ELC2|HPC2	elaC ribonuclease Z 2	protein-coding	0.002262	0.401806	
chunk0189_410_1	chr8	27685809	27686094	+	0	NA	Intergenic	L1MC5a|LINE|L1	-15726	NR_037417	100500858		NR_037417	ENSG00000284351	MIR3622A	mir-3622a	microRNA 3622a	ncRNA	0.003509	0.356643	
chunk0135_188_1	chr3	188192856	188193632	+	0	NA	intron (NM_001167672, intron 1 of 9)	intron (NM_001167672, intron 1 of 9)	14701	NR_024413	401105	Hs.679026	NM_207488	ENSG00000279891	FLJ42393	AVPC1948	uncharacterized LOC401105	ncRNA	0.012887	0.429858	
chunk0199_320_1	chr9	7385734	7386013	+	0	NA	Intergenic	Intergenic	413926	NM_033428	90871	Hs.7517	NM_033428	ENSG00000137038	DMAC1	C9orf123|TMEM261	distal membrane arm assembly complex 1	protein-coding	0.003584	0.350000	112(AAGCACACAATGTATT,-,0.00),113(AGCACACAATGTATTT,+,0.00)
chunk0122_136_1	chr3	31752731	31753183	+	0	NA	intron (NM_001174060, intron 3 of 10)	intron (NM_001174060, intron 3 of 10)	48744	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.006637	0.470199	
chunk0209_371_1	chrX	54030404	54030616	+	0	NA	intron (NM_001184897, intron 2 of 21)	intron (NM_001184897, intron 2 of 21)	12684	NM_001184898	23133	Hs.133352	NM_015107	ENSG00000172943	PHF8	JHDM1F|KDM7B|MRXSSD|ZNF422	PHD finger protein 8	protein-coding	0.014151	0.408451	
chunk0029_213_1	chr10	102132592	102133036	+	0	NA	promoter-TSS (NM_001288728)	promoter-TSS (NM_001288728)	-180	NM_015062	23082	Hs.533551	NM_015062	ENSG00000148840	PPRC1	PRC	PPARG related coactivator 1	protein-coding	0.054054	0.539326	
chunk0013_343_1	chr1	172107453	172108059	+	0	NA	intron (NM_001136127, intron 13 of 19)	intron (NM_001136127, intron 13 of 19)	-31052	NR_036066	100422882		NR_036066	ENSG00000283152	MIR3120	mir-3120	microRNA 3120	ncRNA	0.008251	0.365733	172(CAGACCAGAATGTTCT,-,0.00),173(AGACCAGAATGTTCTT,+,0.00)
chunk0175_214_1	chr7	6081437	6081771	+	0	NA	Intergenic	CpG	-22375	NM_001134335	27102	Hs.520205	NM_014413	ENSG00000086232	EIF2AK1	HCR|HRI	eukaryotic translation initiation factor 2 alpha kinase 1	protein-coding	0.116766	0.707463	
chunk0098_192_1	chr2	72198494	72198919	+	0	NA	intron (NM_015189, intron 20 of 21)	intron (NM_015189, intron 20 of 21)	-50844	NM_001277742	56603	Hs.91546	NM_019885	ENSG00000003137	CYP26B1	CYP26A2|P450RAI-2|P450RAI2|RHFCA	cytochrome P450 family 26 subfamily B member 1	protein-coding	0.000000	0.361502	
chunk0059_393_1	chr14	37526801	37527799	+	0	NA	intron (NM_001195296, intron 14 of 14)	intron (NM_001195296, intron 14 of 14)	67820	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.002004	0.278278	
chunk0104_142_1	chr2	173571358	173571968	+	0	NA	Intergenic	Intergenic	216830	NM_031942	83879	Hs.470654	NM_031942	ENSG00000144354	CDCA7	ICF3|JPO1	cell division cycle associated 7	protein-coding	0.018033	0.422259	
chunk0040_149_1	chr11	113565528	113565984	+	0	NA	Intergenic	Intergenic	-90477	NM_016574	1813	Hs.73893	NM_000795	ENSG00000149295	DRD2	D2DR|D2R	dopamine receptor D2	protein-coding	0.006579	0.376368	
chunk0160_152_1	chr5	151610282	151610587	+	0	NA	Intergenic	Intergenic	-41490	NM_001447	2196	Hs.591255	NM_001447	ENSG00000086570	FAT2	CDHF8|CDHR9|HFAT2|MEGF1|SCA45	FAT atypical cadherin 2	protein-coding	0.003279	0.366013	
chunk0084_457_1	chr17	83101926	83102288	+	0	NA	Intergenic	Intergenic	22416	NM_001004431	284207	Hs.378821	NM_001004431	ENSG00000176845	METRNL	-	meteorin like, glial cell differentiation regulator	protein-coding	0.038674	0.647383	
chunk0142_119_1	chr4	94561443	94561784	+	0	NA	intron (NM_001011516, intron 3 of 9)	intron (NM_001011516, intron 3 of 9)	109756	NM_001011513	10611	Hs.480311	NM_006457	ENSG00000163110	PDLIM5	ENH|ENH1|L9|LIM	PDZ and LIM domain 5	protein-coding	0.014663	0.377193	
chunk0066_419_1	chr15	39554336	39554538	+	0	NA	Intergenic	CR1-16_AMi|LINE|CR1	-26642	NM_003246	7057	Hs.164226	NM_003246	ENSG00000137801	THBS1	THBS|THBS-1|TSP|TSP-1|TSP1	thrombospondin 1	protein-coding	0.000000	0.389163	
chunk0199_242_1	chr9	5612151	5612521	+	0	NA	Intergenic	Intergenic	-16783	NM_001206557	57589	Hs.211520	NM_020829	ENSG00000107036	RIC1	CIP150|KIAA1432|bA207C16.1	RIC1 homolog, RAB6A GEF complex partner 1	protein-coding	0.002703	0.425876	
chunk0034_243_1	chr11	34167914	34168323	+	0	NA	intron (NM_145804, intron 5 of 16)	intron (NM_145804, intron 5 of 16)	62554	NM_001144030	55226	Hs.577281	NM_024662	ENSG00000135372	NAT10	ALP|Kre33|NET43	N-acetyltransferase 10	protein-coding	0.026895	0.582927	
chunk0045_402_1	chr12	52877247	52877528	+	0	NA	Intergenic	Intergenic	27697	NM_002273	3856	Hs.533782	NM_002273	ENSG00000170421	KRT8	CARD2|CK-8|CK8|CYK8|K2C8|K8|KO	keratin 8	protein-coding	0.007117	0.485816	
chunk0101_234_1	chr2	131199148	131199805	+	0	NA	Intergenic	Intergenic	-18875	NM_001083538	445582	Hs.686146	NM_001004054	ENSG00000188219	POTEE	A26C1|A26C1A|CT104.2|POTE-2|POTE2|POTE2gamma	POTE ankyrin domain family member E	protein-coding	0.006088	0.331307	
chunk0127_96_1	chr3	89955187	89955589	+	0	NA	Intergenic	Intergenic	847864	NM_005233	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.002488	0.434243	
chunk0203_150_1	chr9	85605742	85606154	+	0	NA	intron (NM_001286715, intron 16 of 24)	L1MA4A|LINE|L1	136081	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.002427	0.319613	
chunk0165_244_1	chr6	35630602	35631097	+	0	NA	intron (NM_001145777, intron 3 of 6)	L1ME1|LINE|L1	33940	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.004040	0.354839	
chunk0076_449_1	chr16	74022885	74023158	+	0	NA	Intergenic	Intergenic	192500	NR_104657	101928035	Hs.39557	NR_104657	ENSG00000261404	LOC101928035	-	uncharacterized LOC101928035	ncRNA	0.014652	0.354015	
chunk0011_164_1	chr1	147642104	147642369	+	0	NA	Intergenic	Intergenic	28276	NM_016361	51205	Hs.562154	NM_016361	ENSG00000162836	ACP6	ACPL1|LPAP|PACPL1	acid phosphatase 6, lysophosphatidic	protein-coding	0.018868	0.432331	
chunk0121_19_1	chr3	14730684	14730883	+	0	NA	intron (NM_001184957, intron 12 of 16)	L1ME3A|LINE|L1	55684	NM_001184957	84077	Hs.661452	NM_032137	ENSG00000131379	C3orf20	-	chromosome 3 open reading frame 20	protein-coding	0.020101	0.415000	
chunk0057_53_1	chr13	97316502	97316792	+	0	NA	intron (NM_001306070, intron 2 of 7)	L2a|LINE|L2	94351	NM_207304	10150	Hs.657347	NM_144778	ENSG00000139793	MBNL2	MBLL|MBLL39|PRO2032	muscleblind like splicing regulator 2	protein-coding	0.006897	0.536082	
chunk0012_335_1	chr1	162567531	162567982	+	0	NA	intron (NM_003115, intron 2 of 9)	intron (NM_003115, intron 2 of 9)	6250	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.013304	0.387168	
chunk0009_62_1	chr1	100804318	100804801	+	0	NA	Intergenic	Intergenic	84919	NM_001199834	7412	Hs.109225	NM_001078	ENSG00000162692	VCAM1	CD106|INCAM-100	vascular cell adhesion molecule 1	protein-coding	0.002070	0.299587	
chunk0178_77_1	chr7	30430325	30430535	+	0	NA	intron (NM_006092, intron 12 of 13)	intron (NM_006092, intron 12 of 13)	39545	NR_108081	100506516		NR_108081	ENSG00000281404	LINC01176	-	long intergenic non-protein coding RNA 1176	ncRNA	0.014286	0.521327	
chunk0144_27_1	chr4	125008635	125009141	+	0	NA	Intergenic	Intergenic	-296156	NM_020337	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.001976	0.303748	
chunk0078_237_1	chr17	6684464	6684731	+	0	NA	TTS (NM_001143838)	TTS (NM_001143838)	26878	NR_045985	100652883	Hs.549540	NR_045985		ALOX15P1	ALOX15P	arachidonate 15-lipoxygenase pseudogene 1	pseudo	0.022472	0.514925	
chunk0200_362_1	chr9	25677400	25677610	+	0	NA	3' UTR (NM_001004125, exon 1 of 1)	3' UTR (NM_001004125, exon 1 of 1)	1353	NM_001004125	286319	Hs.26268	NM_001004125	ENSG00000198680	TUSC1	CCDC89B|TSG-9|TSG9	tumor suppressor candidate 1	protein-coding	0.066667	0.663507	
chunk0022_190_1	chr10	13428517	13428886	+	0	NA	Intergenic	L1MA7|LINE|L1	74275	NM_001100912	222389	Hs.498740	NM_152751	ENSG00000165626	BEND7	C10orf30	BEN domain containing 7	protein-coding	0.002710	0.391892	
chunk0007_253_1	chr1	82784731	82785121	+	0	NA	Intergenic	MIR|SINE|MIR	199996	NR_110632	101927498		NR_110632	ENSG00000236268	LINC01361	-	long intergenic non-protein coding RNA 1361	ncRNA	0.000000	0.355499	
chunk0183_340_1	chr7	108386755	108387189	+	0	NA	intron (NM_001193582, intron 2 of 30)	Plat_L3|LINE|CR1	69425	NM_001193584	4897	Hs.21422	NM_005010	ENSG00000091129	NRCAM	-	neuronal cell adhesion molecule	protein-coding	0.002304	0.331034	143(CAGGACAGAATGTTCT,-,0.00),144(AGGACAGAATGTTCTC,+,0.00)
chunk0177_131_1	chr7	22387461	22388585	+	0	NA	Intergenic	Intergenic	-31109	NM_012294	9771	Hs.174768	NM_012294	ENSG00000136237	RAPGEF5	GFR|MR-GEF|REPAC	Rap guanine nucleotide exchange factor 5	protein-coding	0.009786	0.399111	
chunk0057_174_1	chr13	102373027	102373595	+	0	NA	intron (NR_125912, intron 1 of 1)	intron (NR_125912, intron 1 of 1)	5781	NR_125912	100874081	Hs.569296	NR_125912	ENSG00000234445	FGF14-AS1	-	FGF14 antisense RNA 1	ncRNA	0.005282	0.358524	
chunk0029_206_1	chr10	101821192	101822091	+	0	NA	intron (NR_045118, intron 1 of 2)	intron (NR_045118, intron 1 of 2)	2573	NR_045118	100289509	Hs.568881	NR_045118	ENSG00000226009	KCNIP2-AS1	-	KCNIP2 antisense RNA 1	ncRNA	0.002225	0.407778	
chunk0144_88_1	chr4	128255911	128256110	+	0	NA	Intergenic	MLT2C2|LTR|ERVL	32819	NM_006320	10424	Hs.507910	NM_006320	ENSG00000164040	PGRMC2	DG6|PMBP	progesterone receptor membrane component 2	protein-coding	0.010050	0.355000	
chunk0035_370_1	chr11	49283416	49283776	+	0	NA	Intergenic	Intergenic	-74926	NM_001193471	2346	Hs.551896	NM_004476	ENSG00000086205	FOLH1	FGCP|FOLH|GCP2|GCPII|NAALAD1|NAALAdase|PSM|PSMA|mGCP	folate hydrolase 1	protein-coding	0.005556	0.373961	
chunk0096_372_1	chr2	36722435	36722970	+	0	NA	intron (NM_053276, intron 2 of 15)	intron (NM_053276, intron 2 of 15)	26012	NM_001177971	5212	Hs.137415	NM_053276	ENSG00000205221	VIT	VIT1	vitrin	protein-coding	0.000000	0.283582	
chunk0073_269_1	chr16	12258116	12258403	+	0	NA	intron (NM_032167, intron 14 of 20)	L2b|LINE|L2	281525	NM_032167	92017	Hs.458401	NM_032167	ENSG00000048471	SNX29	A-388D4.1|RUNDC2A	sorting nexin 29	protein-coding	0.034843	0.555556	
chunk0086_149_1	chr18	21368986	21369581	+	0	NA	intron (NM_001142966, intron 2 of 32)	intron (NM_001142966, intron 2 of 32)	127041	NM_001142966	80000	Hs.149020	NM_024935	ENSG00000141449	GREB1L	C18orf6|KIAA1772|RHDA3	GREB1 like retinoic acid receptor coactivator	protein-coding	0.008403	0.343960	
chunk0102_147_1	chr2	146925830	146926345	+	0	NA	Intergenic	Intergenic	339030	NR_026904	728773	Hs.334462	NR_026904		PABPC1P2	PABP2|PABP4|PABPCP2|PABPCP4	poly(A) binding protein cytoplasmic 1 pseudogene 2	pseudo	0.001942	0.269380	302(CAGAACAGACTGTGAT,-,0.00),303(AGAACAGACTGTGATA,+,0.00)
chunk0159_184_1	chr5	140236088	140236694	+	0	NA	intron (NM_032412, intron 2 of 2)	intron (NM_032412, intron 2 of 2)	61323	NM_032412	84418	Hs.529798	NM_032412	ENSG00000120306	CYSTM1	C5orf32|ORF1-FL49	cysteine rich transmembrane module containing 1	protein-coding	0.014851	0.400329	
chunk0150_122_1	chr5	33049982	33050422	+	0	NA	Intergenic	L1M2a|LINE|L1	102759	NR_033832	340113	Hs.434404	NR_033832	ENSG00000248279	LINC02120	-	long intergenic non-protein coding RNA 2120	ncRNA	0.004545	0.551020	
chunk0083_219_1	chr17	67079490	67079748	+	0	NA	intron (NM_014877, intron 32 of 32)	L1ME4a|LINE|L1	35083	NM_000727	786	Hs.147989	NM_000727	ENSG00000108878	CACNG1	CACNLG	calcium voltage-gated channel auxiliary subunit gamma 1	protein-coding	0.007752	0.432432	
chunk0011_414_1	chr1	154414514	154414936	+	0	NA	intron (NM_181359, intron 1 of 8)	intron (NM_181359, intron 1 of 8)	9532	NM_000565	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.018957	0.529551	
chunk0164_398_1	chr6	26313259	26313458	+	0	NA	Intergenic	Intergenic	-27859	NM_003543	8365	Hs.591790	NM_003543	ENSG00000158406	HIST1H4H	H4/h|H4FH	histone cluster 1 H4 family member h	protein-coding	0.040201	0.425000	
chunk0183_222_1	chr7	106708684	106709186	+	0	NA	Intergenic	Intergenic	-47747	NM_175884	168455	Hs.29692	NM_175884	ENSG00000253276	CCDC71L	C7orf74	coiled-coil domain containing 71 like	protein-coding	0.001992	0.337972	
chunk0050_119_1	chr12	102051440	102051736	+	0	NA	intron (NM_016053, intron 2 of 6)	intron (NM_016053, intron 2 of 6)	10536	NM_016053	51019	Hs.405692	NM_016053	ENSG00000120860	WASHC3	CCDC53|CGI-116	WASH complex subunit 3	protein-coding	0.000000	0.343434	
chunk0137_152_1	chr4	15723553	15724030	+	0	NA	intron (NM_004334, intron 8 of 8)	L1ME3A|LINE|L1	20841	NM_004334	683	Hs.720344	NM_004334	ENSG00000109743	BST1	CD157	bone marrow stromal cell antigen 1	protein-coding	0.004193	0.361925	
chunk0156_452_1	chr5	114948851	114950059	+	0	NA	Intergenic	Intergenic	-176042	NR_130785	101927078	Hs.160027	NR_130785		LOC101927078	-	uncharacterized LOC101927078	ncRNA	0.003311	0.405294	
chunk0152_149_1	chr5	59287425	59287624	+	0	NA	intron (NM_001165899, intron 3 of 16)	L1MA3|LINE|L1	-11405	NM_001197220	5144	Hs.117545	NM_006203	ENSG00000113448	PDE4D	ACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1	phosphodiesterase 4D	protein-coding	0.005025	0.540000	
chunk0163_360_1	chr6	15749909	15750308	+	0	NA	Intergenic	MIRb|SINE|MIR	-87050	NM_001271667	84062	Hs.571148	NM_032122	ENSG00000047579	DTNBP1	BLOC1S8|DBND|HPS7|My031|SDY	dystrobrevin binding protein 1	protein-coding	0.002506	0.380000	
chunk0133_214_1	chr3	171014697	171015163	+	0	NA	intron (NM_001278659, intron 2 of 9)	intron (NM_001278659, intron 2 of 9)	12049	NM_001278659	6514	Hs.167584	NM_000340	ENSG00000163581	SLC2A2	GLUT2	solute carrier family 2 member 2	protein-coding	0.006438	0.312634	
chunk0192_359_1	chr8	68154336	68154825	+	0	NA	intron (NM_024870, intron 34 of 39)	intron (NM_024870, intron 34 of 39)	-176142	NM_001195639	116328	Hs.491941	NM_052958	ENSG00000165084	C8orf34	VEST-1|VEST1	chromosome 8 open reading frame 34	protein-coding	0.006135	0.353061	
chunk0169_140_1	chr6	101442560	101442792	+	0	NA	intron (NM_001166247, intron 1 of 16)	MER58A|DNA|hAT-Charlie	43691	NM_021956	2898	Hs.98262	NM_021956	ENSG00000164418	GRIK2	EAA4|GLR6|GLUK6|GLUR6|GluK2|MRT6	glutamate ionotropic receptor kainate type subunit 2	protein-coding	0.004310	0.394850	
chunk0120_137_1	chr3	5074739	5074948	+	0	NA	Intergenic	Intergenic	-47402	NM_018184	55207	Hs.250009	NM_018184	ENSG00000134108	ARL8B	ARL10C|Gie1	ADP ribosylation factor like GTPase 8B	protein-coding	0.014354	0.395238	
chunk0130_348_1	chr3	138727402	138728139	+	0	NA	intron (NM_006219, intron 6 of 21)	L1M4|LINE|L1	-20149	NM_001256045	5291	Hs.239818	NM_006219	ENSG00000051382	PIK3CB	P110BETA|PI3K|PI3KBETA|PIK3C1	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta	protein-coding	0.016282	0.430894	
chunk0128_321_1	chr3	111871945	111872550	+	0	NA	intron (NM_001134439, intron 1 of 17)	intron (NM_001134439, intron 1 of 17)	12526	NM_001134439	90102	Hs.603252	NM_145753	ENSG00000144824	PHLDB2	LL5b|LL5beta	pleckstrin homology like domain family B member 2	protein-coding	0.009917	0.432343	
chunk0193_56_1	chr8	72286766	72286981	+	0	NA	Intergenic	Intergenic	-35239	NR_033867	392232	Hs.454043	NR_033867		LOC392232	-	transient receptor potential cation channel subfamily A member 1 pseudogene	pseudo	0.018605	0.537037	
chunk0005_423_1	chr1	62746528	62746745	+	0	NA	Intergenic	Intergenic	-37470	NM_032852	84938	Hs.7353	NM_032852	ENSG00000125703	ATG4C	APG4-C|APG4C|AUTL1|AUTL3	autophagy related 4C cysteine peptidase	protein-coding	0.009217	0.394495	
chunk0029_38_1	chr10	96211112	96211367	+	0	NA	intron (NR_047681, intron 6 of 14)	intron (NR_047681, intron 6 of 14)	60277	NR_047681	29760	Hs.665244	NM_013314	ENSG00000095585	BLNK	AGM4|BASH|BLNK-S|LY57|SLP-65|SLP65|bca	B cell linker	protein-coding	0.007843	0.449219	87(AAGTACAGGCTGGACC,-,0.00)
chunk0159_55_1	chr5	137238248	137238680	+	0	NA	intron (NM_004598, intron 3 of 10)	intron (NM_004598, intron 3 of 10)	260865	NM_004598	6695	Hs.596136	NM_004598	ENSG00000152377	SPOCK1	SPOCK|TESTICAN|TIC1	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1	protein-coding	0.002315	0.327945	
chunk0045_389_1	chr12	52612948	52613219	+	0	NA	intron (NR_126005, intron 2 of 2)	intron (NR_126005, intron 2 of 2)	3232	NR_126005	100127967	Hs.689466	NR_126005	ENSG00000257495	KRT73-AS1	-	KRT73 antisense RNA 1	ncRNA	0.000000	0.470588	
chunk0038_326_1	chr11	92070514	92070737	+	0	NA	Intergenic	L1MA4|LINE|L1	-281471	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.004484	0.455357	131(TGGCACTCCCTGTCCT,-,0.00),132(GGCACTCCCTGTCCTA,+,0.00)
chunk0016_18_1	chr1	192849423	192849795	+	0	NA	Intergenic	Intergenic	40570	NM_002923	5997	Hs.78944	NM_002923	ENSG00000116741	RGS2	G0S8	regulator of G protein signaling 2	protein-coding	0.008065	0.348525	
chunk0154_126_1	chr5	78985029	78985228	+	0	NA	exon (NM_000046, exon 1 of 8)	exon (NM_000046, exon 1 of 8)	815	NM_198709	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.125628	0.745000	
chunk0003_15_1	chr1	28896431	28896812	+	0	NA	intron (NM_001166007, intron 1 of 17)	L2b|LINE|L2	9530	NM_001166005	2035	Hs.175437	NM_004437	ENSG00000159023	EPB41	4.1R|EL1|HE	erythrocyte membrane protein band 4.1	protein-coding	0.007874	0.534031	184(AGGAACAGCATGTGCC,-,0.00),185(GGAACAGCATGTGCCA,+,0.00)
chunk0107_192_1	chr2	216143274	216143789	+	0	NA	intron (NM_021141, intron 13 of 20)	intron (NM_021141, intron 13 of 20)	34234	NM_021141	7520	Hs.388739	NM_021141	ENSG00000079246	XRCC5	KARP-1|KARP1|KU80|KUB2|Ku86|NFIV	X-ray repair cross complementing 5	protein-coding	0.009709	0.344961	
chunk0105_20_1	chr2	182008685	182008973	+	0	NA	intron (NM_001080545, intron 2 of 4)	L1MA3|LINE|L1	23005	NM_001261424	151242	Hs.10941	NM_001080545	ENSG00000150722	PPP1R1C	IPP5	protein phosphatase 1 regulatory inhibitor subunit 1C	protein-coding	0.006944	0.346021	
chunk0166_288_1	chr6	48624622	48625011	+	0	NA	Intergenic	LTR50|LTR|ERVL	-556127	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.007712	0.348718	
chunk0179_110_1	chr7	45073781	45074324	+	0	NA	intron (NM_031443, intron 8 of 9)	intron (NM_031443, intron 8 of 9)	14842	NM_001146334	23148	Hs.96633	NM_001146334	ENSG00000136274	NACAD	-	NAC alpha domain containing	protein-coding	0.016575	0.608456	243(ATGCACTCTGTGTTCC,-,0.00),244(TGCACTCTGTGTTCCA,+,0.00)
chunk0151_183_1	chr5	50365929	50366128	+	0	NA	Intergenic	L1MB1|LINE|L1	75372	NM_198449	133418	Hs.561411	NM_198449	ENSG00000170571	EMB	GP70	embigin	protein-coding	0.020101	0.475000	
chunk0127_37_1	chr3	88723755	88723956	+	0	NA	Intergenic	Intergenic	-383669	NM_182644	2042	Hs.123642	NM_005233	ENSG00000044524	EPHA3	EK4|ETK|ETK1|HEK|HEK4|TYRO4	EPH receptor A3	protein-coding	0.004975	0.391089	
chunk0210_444_1	chrX	104582068	104582494	+	0	NA	intron (NM_017416, intron 1 of 10)	intron (NM_017416, intron 1 of 10)	15966	NM_017416	26280	Hs.675519	NM_017416	ENSG00000189108	IL1RAPL2	IL-1R9|IL1R9|IL1RAPL-2|TIGIRR-1	interleukin 1 receptor accessory protein like 2	protein-coding	0.004695	0.379391	
chunk0054_26_1	chr13	40791788	40792181	+	0	NA	intron (NM_014252, intron 1 of 6)	intron (NM_014252, intron 1 of 6)	2573	NM_014252	10166	Hs.646645	NM_014252	ENSG00000102743	SLC25A15	D13S327|HHH|ORC1|ORNT1	solute carrier family 25 member 15	protein-coding	0.025445	0.403553	
chunk0201_147_1	chr9	35844372	35845185	+	0	NA	intron (NM_001042589, intron 7 of 13)	intron (NM_001042589, intron 7 of 13)	15280	NM_001042590	51754	Hs.9187	NM_016446	ENSG00000137103	TMEM8B	C9orf127|FP588|LINC00950|NAG-5|NAG5|NGX6	transmembrane protein 8B	protein-coding	0.012300	0.437346	
chunk0085_49_1	chr18	812725	813155	+	0	NA	promoter-TSS (NM_005433)	promoter-TSS (NM_005433)	-614	NM_005433	7525	Hs.194148	NM_005433	ENSG00000176105	YES1	HsT441|P61-YES|Yes|c-yes	YES proto-oncogene 1, Src family tyrosine kinase	protein-coding	0.046512	0.556845	
chunk0151_225_1	chr5	50931847	50932391	+	0	NA	Intergenic	Intergenic	38068	NR_104653	100287592	Hs.519298	NR_104653	ENSG00000251573	LINC02106	-	long intergenic non-protein coding RNA 2106	ncRNA	0.003676	0.343119	
chunk0204_366_1	chr9	101836080	101836279	+	0	NA	Intergenic	Intergenic	-97599	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.000000	0.340000	
chunk0147_164_1	chr4	176124115	176124585	+	0	NA	intron (NM_181265, intron 4 of 28)	intron (NM_181265, intron 4 of 28)	58516	NM_170710	116966	Hs.532056	NM_170710	ENSG00000150627	WDR17	-	WD repeat domain 17	protein-coding	0.008511	0.331210	
chunk0116_405_1	chr21	42525963	42526275	+	0	NA	intron (NM_018964, intron 4 of 20)	intron (NM_018964, intron 4 of 20)	26487	NM_018964	54020	Hs.547009	NM_018964	ENSG00000160190	SLC37A1	G3PP	solute carrier family 37 member 1	protein-coding	0.016026	0.380192	
chunk0182_1_1	chr7	90819089	90819647	+	0	NA	intron (NM_001287136, intron 4 of 13)	intron (NM_001287136, intron 4 of 13)	109552	NM_001287137	5218	Hs.258576	NM_012395	ENSG00000058091	CDK14	PFTAIRE1|PFTK1	cyclin dependent kinase 14	protein-coding	0.000000	0.309481	
chunk0002_103_1	chr1	15510735	15511045	+	0	NA	intron (NR_102733, intron 2 of 8)	intron (NR_102733, intron 2 of 8)	13555	NM_001229	842	Hs.329502	NM_001229	ENSG00000132906	CASP9	APAF-3|APAF3|ICE-LAP6|MCH6|PPP1R56	caspase 9	protein-coding	0.006452	0.527331	
chunk0203_431_1	chr9	91197261	91197460	+	0	NA	Intergenic	Intergenic	-122228	NR_033912	100129316	Hs.458154	NR_033912		LOC100129316	-	uncharacterized LOC100129316	ncRNA	0.015075	0.430000	
chunk0085_372_1	chr18	9530475	9530923	+	0	NA	intron (NM_006788, intron 6 of 9)	intron (NM_006788, intron 6 of 9)	55167	NM_006788	10928	Hs.528993	NM_006788	ENSG00000017797	RALBP1	RIP1|RLIP1|RLIP76	ralA binding protein 1	protein-coding	0.002232	0.387528	
chunk0067_441_1	chr15	50149156	50149495	+	0	NA	Intergenic	Intergenic	-30103	NR_073597	79895	Hs.511311	NM_024837	ENSG00000104043	ATP8B4	ATPIM	ATPase phospholipid transporting 8B4 (putative)	protein-coding	0.002950	0.417647	
chunk0114_320_1	chr21	17386687	17386886	+	0	NA	Intergenic	Intergenic	-52104	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.000000	0.415000	
chunk0154_85_1	chr5	77906870	77907230	+	0	NA	intron (NR_105012, intron 1 of 1)	LTR33|LTR|ERVL	22394	NR_105012	101929154	Hs.252895	NR_105012		LOC101929154	-	uncharacterized LOC101929154	ncRNA	0.019444	0.531856	
chunk0150_439_1	chr5	40521180	40521909	+	0	NA	Intergenic	Intergenic	-158386	NM_000958	5734	Hs.199248	NM_000958	ENSG00000171522	PTGER4	EP4|EP4R	prostaglandin E receptor 4	protein-coding	0.005487	0.379452	
chunk0023_45_1	chr10	21329087	21329296	+	0	NA	Intergenic	L1MB3|LINE|L1	154889	NR_046284	100128511	Hs.635827	NR_046283	ENSG00000231920	NEBL-AS1	-	NEBL antisense RNA 1	ncRNA	0.004785	0.419048	
chunk0133_342_1	chr3	172892432	172893086	+	0	NA	intron (NM_031955, intron 10 of 10)	MIRb|SINE|MIR	142074	NM_001258316	1894	Hs.518299	NM_018098	ENSG00000114346	ECT2	ARHGEF31	epithelial cell transforming 2	protein-coding	0.006116	0.352672	
chunk0025_123_1	chr10	51700374	51700829	+	0	NA	intron (NM_006258, intron 3 of 17)	intron (NM_006258, intron 3 of 17)	-1006	NM_015235	23283	Hs.591358	NM_015235	ENSG00000177613	CSTF2T	CstF-64T	cleavage stimulation factor subunit 2 tau variant	protein-coding	0.013187	0.366228	
chunk0001_264_1	chr1	8486946	8487315	+	0	NA	intron (NM_001042681, intron 10 of 22)	L1ME1|LINE|L1	7783	NR_132752	106632271		NR_132752		SNORD128	ZL43	small nucleolar RNA, C/D box 128	snoRNA	0.002710	0.308108	154(AGGAACAAACAGTTCC,-,0.00),155(GGAACAAACAGTTCCT,+,0.00)
chunk0027_93_1	chr10	73714668	73715071	+	0	NA	intron (NR_026592, intron 9 of 11)	intron (NR_026592, intron 9 of 11)	15645	NR_026592	729096	Hs.709171	NR_026592	ENSG00000271816	BMS1P4	BMS1LP4	BMS1 pseudogene 4	pseudo	0.007444	0.344059	297(TTGGACAGGCAGTTCT,-,0.00),298(TGGACAGGCAGTTCTG,+,0.00)
chunk0030_304_1	chr10	117482965	117483191	+	0	NA	Intergenic	L1ME4b|LINE|L1	-59367	NM_001165924	2018	Hs.202095	NM_004098	ENSG00000170370	EMX2	-	empty spiracles homeobox 2	protein-coding	0.017699	0.533040	
chunk0036_108_1	chr11	61325636	61326064	+	0	NA	intron (NM_001923, intron 5 of 26)	intron (NM_001923, intron 5 of 26)	-7332	NM_015533	26007	Hs.6278	NM_015533	ENSG00000149476	TKFC	DAK|NET45	triokinase and FMN cyclase	protein-coding	0.004673	0.431235	
chunk0122_22_1	chr3	27690305	27690843	+	0	NA	Intergenic	L1MA1|LINE|L1	32141	NM_001278183	8320	Hs.591663	NM_005442	ENSG00000163508	EOMES	TBR2	eomesodermin	protein-coding	0.001859	0.293135	
chunk0157_56_1	chr5	116115174	116115615	+	0	NA	intron (NM_001308080, intron 4 of 6)	L1PB4|LINE|L1	29932	NM_001308080	51397	Hs.483136	NM_016144	ENSG00000145781	COMMD10	PTD002	COMM domain containing 10	protein-coding	0.002268	0.404977	
chunk0100_437_1	chr2	120666639	120666898	+	0	NA	Intergenic	L1MEd|LINE|L1	-130523	NM_005270	2736	Hs.111867	NM_005270	ENSG00000074047	GLI2	CJS|HPE9|PHS2|THP1|THP2	GLI family zinc finger 2	protein-coding	0.011583	0.388462	105(TGGAACTTGATGTGCT,-,0.00),106(GGAACTTGATGTGCTT,+,0.00)
chunk0022_166_1	chr10	12678184	12678754	+	0	NA	intron (NM_020397, intron 3 of 9)	L1M3|LINE|L1	-25272	NR_039701	100616320		NR_039701	ENSG00000283699	MIR4481	-	microRNA 4481	ncRNA	0.005263	0.346760	257(GAGAACAATGTGTATT,-,0.00),258(AGAACAATGTGTATTT,+,0.00)
chunk0022_177_1	chr10	13013389	13013859	+	0	NA	intron (NM_001282658, intron 5 of 6)	L1MC4|LINE|L1	-11920	NM_031455	83643	Hs.498720	NM_031455	ENSG00000151468	CCDC3	-	coiled-coil domain containing 3	protein-coding	0.002128	0.324841	
chunk0085_234_1	chr18	6991933	6993368	+	0	NA	exon (NM_005559, exon 36 of 63)	exon (NM_005559, exon 36 of 63)	37973	NR_126040	101927188	Hs.680444	NR_126040	ENSG00000265069	LOC101927188	-	uncharacterized LOC101927188	ncRNA	0.004878	0.389972	53(AGAGACAGCCTGTGCT,-,0.00),54(GAGACAGCCTGTGCTA,+,0.00)
chunk0022_403_1	chr10	18211716	18212300	+	0	NA	intron (NM_001167945, intron 2 of 13)	intron (NM_001167945, intron 2 of 13)	-48647	NM_000724	783	Hs.59093	NM_000724	ENSG00000165995	CACNB2	CACNLB2|CAVB2|MYSB	calcium voltage-gated channel auxiliary subunit beta 2	protein-coding	0.013699	0.391453	
chunk0062_182_1	chr14	69695973	69696686	+	0	NA	intron (NM_014734, intron 2 of 5)	intron (NM_014734, intron 2 of 5)	-70783	NM_001039465	6430	Hs.632326	NM_006925	ENSG00000100650	SRSF5	HRS|SFRS5|SRP40	serine and arginine rich splicing factor 5	protein-coding	0.004208	0.427171	
chunk0013_83_1	chr1	167648237	167648684	+	0	NA	intron (NM_052862, intron 1 of 6)	intron (NM_052862, intron 1 of 6)	18223	NM_052862	92241	Hs.493867	NM_052862	ENSG00000198771	RCSD1	CAPZIP|MK2S4	RCSD domain containing 1	protein-coding	0.006711	0.477679	
chunk0109_305_1	chr20	8829368	8829929	+	0	NA	intron (NM_182734, intron 32 of 32)	intron (NM_182734, intron 32 of 32)	-1537	NR_004386	26767		NR_004386	ENSG00000201348	RNU105B	105B|E1-2	RNA, U105B small nucleolar	snoRNA	0.008913	0.382562	210(CAGTACAGAATGCCCT,-,0.00),211(AGTACAGAATGCCCTG,+,0.00),366(TAGAACAAACTGTTCA,-,0.00),367(AGAACAAACTGTTCAG,+,0.00)
chunk0133_220_1	chr3	171151134	171151433	+	0	NA	intron (NM_001161560, intron 12 of 31)	intron (NM_001161560, intron 12 of 31)	-44524	NR_030295	693154		NR_030295	ENSG00000207963	MIR569	MIRN569|hsa-mir-569	microRNA 569	ncRNA	0.006689	0.343333	
chunk0149_154_1	chr5	20323204	20323834	+	0	NA	intron (NM_001291956, intron 1 of 14)	intron (NM_001291956, intron 1 of 14)	252354	NM_001291956	1016	Hs.317632	NM_004934	ENSG00000145526	CDH18	CDH14|CDH14L|CDH24	cadherin 18	protein-coding	0.000000	0.318542	
chunk0132_161_1	chr3	156673934	156674481	+	0	NA	promoter-TSS (NM_001184717)	promoter-TSS (NM_001184717)	-209	NM_015508	25976	Hs.744050	NM_015508	ENSG00000163659	TIPARP	ARTD14|PARP7|pART14	TCDD inducible poly(ADP-ribose) polymerase	protein-coding	0.098720	0.629562	323(CGGAACAAAGTGACCC,-,0.00),324(GGAACAAAGTGACCCT,+,0.00)
chunk0191_306_1	chr8	55151105	55151480	+	0	NA	intron (NM_052898, intron 1 of 2)	intron (NM_052898, intron 1 of 2)	48835	NM_052898	114786	Hs.130197	NM_052898	ENSG00000206579	XKR4	XRG4	XK related 4	protein-coding	0.005333	0.369681	
chunk0032_450_1	chr10	133177498	133177813	+	0	NA	intron (NM_152643, intron 3 of 29)	(TG)n|Simple_repeat|Simple_repeat	17188	NM_152643	85442	Hs.530685	NM_152643	ENSG00000171798	KNDC1	C10orf23|RASGEF2|Very-KIND|bB439H18.3|v-KIND	kinase non-catalytic C-lobe domain containing 1	protein-coding	0.006349	0.465190	
chunk0210_56_1	chrX	69082313	69082512	+	0	NA	Intergenic	Intergenic	83110	NM_001032396	64219	Hs.522679	NM_022368	ENSG00000181191	PJA1	PRAJA1|RNF70	praja ring finger ubiquitin ligase 1	protein-coding	0.025126	0.465000	
chunk0095_149_1	chr2	16947170	16947671	+	0	NA	Intergenic	Intergenic	-281554	NM_030797	81553	Hs.467769	NM_030797	ENSG00000197872	FAM49A	-	family with sequence similarity 49 member A	protein-coding	0.000000	0.390438	
chunk0045_211_1	chr12	47905229	47905576	+	0	NA	promoter-TSS (NM_000376)	promoter-TSS (NM_000376)	-371	NM_001017535	7421	Hs.524368	NM_000376	ENSG00000111424	VDR	NR1I1|PPP1R163	vitamin D receptor	protein-coding	0.074928	0.635057	
chunk0055_359_1	chr13	70645866	70646602	+	0	NA	Intergenic	Intergenic	-368907	NR_047699	100885781	Hs.372660	NR_047699	ENSG00000226846	LINC00348	-	long intergenic non-protein coding RNA 348	ncRNA	0.005435	0.370421	
chunk0171_123_1	chr6	122632907	122633406	+	0	NA	intron (NM_181795, intron 1 of 4)	intron (NM_181795, intron 1 of 4)	-19573	NM_001270395	5570	Hs.741340	NM_032471	ENSG00000135549	PKIB	PRKACN2	cAMP-dependent protein kinase inhibitor beta	protein-coding	0.000000	0.346000	291(AGGAACAACTTGTTCT,-,0.00),292(GGAACAACTTGTTCTT,+,0.00)
chunk0203_368_1	chr9	89995118	89995378	+	0	NA	Intergenic	Intergenic	25832	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.038462	0.482759	
chunk0009_263_1	chr1	107420235	107420624	+	0	NA	intron (NM_001312688, intron 6 of 7)	intron (NM_001312688, intron 6 of 7)	268075	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.002571	0.374359	
chunk0011_420_1	chr1	154450914	154451128	+	0	NA	intron (NM_181359, intron 8 of 8)	L2c|LINE|L2	45828	NM_000565	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.004673	0.493023	
chunk0149_58_1	chr5	16883738	16884022	+	0	NA	intron (NM_012334, intron 1 of 40)	intron (NM_012334, intron 1 of 40)	52396	NM_012334	4651	Hs.481720	NM_012334	ENSG00000145555	MYO10	-	myosin X	protein-coding	0.010563	0.368421	144(CTGTACAGCATGTTCT,-,0.00),145(TGTACAGCATGTTCTA,+,0.00)
chunk0168_73_1	chr6	79628546	79628747	+	0	NA	Intergenic	Intergenic	-2637	NM_031469	83699	Hs.302772	NM_031469	ENSG00000198478	SH3BGRL2	-	SH3 domain binding glutamate rich protein like 2	protein-coding	0.004975	0.420792	
chunk0056_200_1	chr13	85724910	85725647	+	0	NA	Intergenic	Intergenic	74070	NM_032229	84189	Hs.525105	NM_032229	ENSG00000184564	SLITRK6	DFNMYP	SLIT and NTRK like family member 6	protein-coding	0.004071	0.300813	
chunk0068_266_1	chr15	56451385	56451683	+	0	NA	intron (NM_018365, intron 3 of 9)	L1MB4|LINE|L1	13603	NM_018365	55329	Hs.444483	NM_018365	ENSG00000138587	MNS1	SPATA40	meiosis specific nuclear structural 1	protein-coding	0.003356	0.351171	
chunk0068_277_1	chr15	56723804	56724201	+	0	NA	intron (NM_001002843, intron 1 of 20)	MER47B|DNA|TcMar-Tigger	10084	NM_001002843	54816	Hs.511477	NM_017661	ENSG00000137871	ZNF280D	SUHW4|ZNF634	zinc finger protein 280D	protein-coding	0.010076	0.379397	
chunk0135_239_1	chr3	188656167	188656810	+	0	NA	intron (NM_001167671, intron 6 of 10)	intron (NM_001167671, intron 6 of 10)	-32293	NR_029502	407020		NR_029502	ENSG00000207651	MIR28	MIRN28|hsa-mir-28|miR-28	microRNA 28	ncRNA	0.006221	0.423913	
chunk0110_246_1	chr20	16475304	16475807	+	0	NA	intron (NM_001199865, intron 12 of 24)	intron (NM_001199865, intron 12 of 24)	97879	NM_001199866	55614	Hs.101774	NM_024704	ENSG00000089177	KIF16B	C20orf23|KISC20ORF|SNX23	kinesin family member 16B	protein-coding	0.009940	0.396825	
chunk0088_375_1	chr18	54196262	54196513	+	0	NA	intron (NM_003927, intron 2 of 6)	intron (NM_003927, intron 2 of 6)	26025	NR_002970	677819	Hs.655869	NR_002970	ENSG00000207233	SNORA37	ACA37	small nucleolar RNA, H/ACA box 37	snoRNA	0.011952	0.349206	
chunk0171_285_1	chr6	128113711	128113954	+	0	NA	intron (NM_001291981, intron 7 of 32).2	(TACA)n|Simple_repeat|Simple_repeat	85967	NR_125849	101928140	Hs.656779	NR_125849		LOC101928140	-	uncharacterized LOC101928140	ncRNA	0.004115	0.327869	
chunk0093_174_1	chr19	48530639	48531151	+	0	NA	Intergenic	AluSx|SINE|Alu	-17706	NM_001080434	114783	Hs.207426	NM_001080434	ENSG00000142235	LMTK3	LMR3|PPP1R101|TYKLM3	lemur tyrosine kinase 3	protein-coding	0.011719	0.409357	
chunk0005_357_1	chr1	61353034	61354136	+	0	NA	intron (NM_001145511, intron 5 of 10)	intron (NM_001145511, intron 5 of 10)	-100067	NR_104180	645030	Hs.632410	NR_104180	ENSG00000237853	NFIA-AS1	-	NFIA antisense RNA 1	ncRNA	0.004537	0.384406	
chunk0167_171_1	chr6	63448061	63448317	+	0	NA	Intergenic	AmnSINE1|SINE|5S-Deu-L2	-123823	NM_003463	7803	Hs.227777	NM_003463	ENSG00000112245	PTP4A1	HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1	protein tyrosine phosphatase 4A1	protein-coding	0.003906	0.291829	
chunk0088_246_1	chr18	48649306	48649926	+	0	NA	intron (NM_014772, intron 3 of 11)	L1PA6|LINE|L1	-20984	NR_039897	100616366		NR_039897	ENSG00000266276	MIR4743	-	microRNA 4743	ncRNA	0.014516	0.544283	
chunk0107_91_1	chr2	213104434	213104810	+	0	NA	intron (NM_016260, intron 3 of 7)	intron (NM_016260, intron 3 of 7)	45712	NM_016260	22807	Hs.604950	NM_016260	ENSG00000030419	IKZF2	ANF1A2|HELIOS|ZNF1A2|ZNFN1A2	IKAROS family zinc finger 2	protein-coding	0.010638	0.397878	
chunk0153_128_1	chr5	68884136	68884643	+	0	NA	Intergenic	Intergenic	145538	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.007890	0.375984	
chunk0087_338_1	chr18	40227255	40227454	+	0	NA	Intergenic	L1ME3E|LINE|L1	161068	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.000000	0.350000	
chunk0007_34_1	chr1	77667317	77667669	+	0	NA	intron (NM_001308237, intron 1 of 13)	L3|LINE|CR1	15165	NM_015534	26009	Hs.480506	NM_015534	ENSG00000036549	ZZZ3	ATAC1	zinc finger ZZ-type containing 3	protein-coding	0.002841	0.331445	
chunk0047_57_1	chr12	67437499	67437983	+	0	NA	Intergenic	L2a|LINE|L2	-82341	NR_103861	100507175	Hs.505986	NR_103861	ENSG00000203585	LINC02408	-	long intergenic non-protein coding RNA 2408	ncRNA	0.016529	0.459794	368(GGGAACATCAAGTGCA,-,0.00)
chunk0020_417_1	chr1	241579398	241579719	+	0	NA	intron (NM_003679, intron 10 of 14)	L1PB3|LINE|L1	47424	NM_003679	8564	Hs.731056	NM_003679	ENSG00000117009	KMO	dJ317G22.1	kynurenine 3-monooxygenase	protein-coding	0.006231	0.549689	
chunk0096_49_1	chr2	27050683	27051233	+	0	NA	promoter-TSS (NM_001035507)	promoter-TSS (NM_001035507)	-665	NM_021831	60509	Hs.138207	NM_021831	ENSG00000084693	AGBL5	CCP5|RP75	ATP/GTP binding protein like 5	protein-coding	0.038182	0.473684	
chunk0094_406_1	chr2	10437304	10438030	+	0	NA	Intergenic	Intergenic	9182	NR_028374	100302743	Hs.730525	NR_028374	ENSG00000206633	SNORA80B	ACA67B	small nucleolar RNA, H/ACA box 80B	snoRNA	0.015152	0.426410	
chunk0094_163_1	chr2	5371726	5372313	+	0	NA	Intergenic	Intergenic	319099	NR_110580	102723818	Hs.128107	NR_110580		LINC01248	-	long intergenic non-protein coding RNA 1248	ncRNA	0.008518	0.335034	
chunk0174_186_1	chr6	159926825	159927201	+	0	NA	Intergenic	MLT2B4|LTR|ERVL	20071	NM_002377	4142	Hs.99900	NM_002377	ENSG00000130368	MAS1	MAS|MGRA	MAS1 proto-oncogene, G protein-coupled receptor	protein-coding	0.007979	0.461538	
chunk0191_28_1	chr8	42917607	42918090	+	0	NA	intron (NM_032410, intron 2 of 21)	intron (NM_032410, intron 2 of 21)	20958	NM_032410	84376	Hs.162852	NM_032410	ENSG00000168172	HOOK3	HK3	hook microtubule tethering protein 3	protein-coding	0.004141	0.326446	
chunk0122_447_1	chr3	39448926	39449125	+	0	NA	Intergenic	Tigger3c|DNA|TcMar-Tigger	-18548	NR_103505	4336	Hs.121333	NM_182935	ENSG00000168314	MOBP	-	myelin associated oligodendrocyte basic protein	protein-coding	0.005025	0.365000	
chunk0141_153_1	chr4	81650790	81651274	+	0	NA	Intergenic	L2a|LINE|L2	-179104	NM_152545	153020	Hs.591696	NM_152545	ENSG00000138670	RASGEF1B	GPIG4	RasGEF domain family member 1B	protein-coding	0.004132	0.459794	
chunk0092_280_1	chr19	33491503	33491964	+	0	NA	intron (NM_001166057, intron 3 of 12)	LTR10C|LTR|ERV1	30160	NM_000285	5184	Hs.36473	NM_000285	ENSG00000124299	PEPD	PROLIDASE	peptidase D	protein-coding	0.013015	0.406926	
chunk0146_228_1	chr4	162077959	162078633	+	0	NA	intron (NM_020116, intron 2 of 15)	ERVL-E-int|LTR|ERVL	55563	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.005935	0.361481	
chunk0175_342_1	chr6	167449454	167449917	+	0	NA	Intergenic	MER49|LTR|ERV1	-65175	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.008639	0.439655	
chunk0086_195_1	chr18	22194257	22194492	+	0	NA	intron (NM_005257, intron 6 of 6)	intron (NM_005257, intron 6 of 6)	24937	NM_005257	2627	Hs.514746	NM_005257	ENSG00000141448	GATA6	-	GATA binding protein 6	protein-coding	0.017021	0.567797	
chunk0154_23_1	chr5	76823449	76823979	+	0	NA	intron (NM_005242, intron 1 of 1)	intron (NM_005242, intron 1 of 1)	4706	NM_005242	2150	Hs.744181	NM_005242	ENSG00000164251	F2RL1	GPR11|PAR2	F2R like trypsin receptor 1	protein-coding	0.030189	0.480226	287(CTGTACATACTGTGCT,-,0.00),288(TGTACATACTGTGCTA,+,0.00)
chunk0089_130_1	chr18	58779339	58779972	+	0	NA	Intergenic	Intergenic	-83174	NM_018181	55205	Hs.529023	NM_018181	ENSG00000074657	ZNF532	-	zinc finger protein 532	protein-coding	0.015798	0.438486	309(TAGAACATACAGTTCA,-,0.00),310(AGAACATACAGTTCAA,+,0.00),378(AAGAACTGCCTGTACC,-,0.00),379(AGAACTGCCTGTACCT,+,0.00)
chunk0115_10_1	chr21	20365402	20365787	+	0	NA	Intergenic	Tigger2|DNA|TcMar-Tigger	437514	NR_109786	387486	Hs.576551	NR_024090	ENSG00000224924	LINC00320	C21orf131|NCRNA00320|PRED14	long intergenic non-protein coding RNA 320	ncRNA	0.005195	0.427461	
chunk0163_158_1	chr6	11066822	11067021	+	0	NA	intron (NR_038964, intron 3 of 4)	intron (NR_038964, intron 3 of 4)	22230	NR_038962	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.005025	0.350000	
chunk0146_309_1	chr4	165288839	165289460	+	0	NA	intron (NM_001161521, intron 5 of 14)	intron (NM_001161521, intron 5 of 14)	-9126	NR_026575	2713	Hs.654557	NR_026575	ENSG00000229894	GK3P	GKP3|GKTB	glycerol kinase 3 pseudogene	pseudo	0.000000	0.331190	
chunk0047_134_1	chr12	69511570	69512155	+	0	NA	intron (NM_001278351, intron 2 of 10)	MIR|SINE|MIR	41513	NM_001278355	10818	Hs.593446	NM_006654	ENSG00000166225	FRS2	FRS1A|FRS2A|FRS2alpha|SNT|SNT-1|SNT1	fibroblast growth factor receptor substrate 2	protein-coding	0.006838	0.368601	
chunk0145_250_1	chr4	148823413	148823787	+	0	NA	Intergenic	L1ME3G|LINE|L1	-330695	NR_125887	101927849	Hs.434595	NR_125887	ENSG00000248210	LINC02355	-	long intergenic non-protein coding RNA 2355	ncRNA	0.005348	0.389333	
chunk0102_436_1	chr2	157790223	157790586	+	0	NA	intron (NM_001111067, intron 3 of 10)	intron (NM_001111067, intron 3 of 10)	84707	NM_001105	90	Hs.470316	NM_001105	ENSG00000115170	ACVR1	ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI	activin A receptor type 1	protein-coding	0.005510	0.489011	
chunk0211_247_1	chrX	120446515	120446950	+	0	NA	intron (NM_002294, intron 5 of 8)	intron (NM_002294, intron 5 of 8)	22617	NM_013995	3920	Hs.496684	NM_002294	ENSG00000005893	LAMP2	CD107b|LAMP-2|LAMPB|LGP-96|LGP110	lysosomal associated membrane protein 2	protein-coding	0.018391	0.405963	
chunk0094_413_1	chr2	10465675	10466441	+	0	NA	Intergenic	Intergenic	16330	NR_110597	101929715	Hs.634550	NR_110597		ODC1-DT	lncRNA-MIF	ODC1 divergent transcript	ncRNA	0.014360	0.448501	
chunk0175_220_1	chr7	6222142	6222386	+	0	NA	intron (NM_004227, intron 1 of 12)	intron (NM_004227, intron 1 of 12)	50347	NM_004227	9265	Hs.487479	NM_004227	ENSG00000008256	CYTH3	ARNO3|GRP1|PSCD3|cytohesin-3	cytohesin 3	protein-coding	0.012295	0.493878	
chunk0165_312_1	chr6	36997804	36998426	+	0	NA	Intergenic	Intergenic	-7532	NM_173558	221472	Hs.509664	NM_173558	ENSG00000146192	FGD2	ZFYVE4	FYVE, RhoGEF and PH domain containing 2	protein-coding	0.017685	0.563403	288(AGGAACAATGTGTTCC,-,0.00),289(GGAACAATGTGTTCCC,+,0.00)
chunk0020_176_1	chr1	234532572	234532814	+	0	NA	promoter-TSS (NR_038426)	promoter-TSS (NR_038426)	-914	NR_038426	100506795	Hs.448989	NR_038426	ENSG00000231768	LINC01354	-	long intergenic non-protein coding RNA 1354	ncRNA	0.020661	0.407407	
chunk0101_49_1	chr2	123047828	123048042	+	0	NA	Intergenic	Intergenic	-977352	NM_130773	129684	Hs.660653	NM_130773	ENSG00000155052	CNTNAP5	caspr5	contactin associated protein like 5	protein-coding	0.000000	0.269767	
chunk0139_412_1	chr4	63501737	63502331	+	0	NA	Intergenic	Intergenic	907426	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.001684	0.386555	
chunk0055_241_1	chr13	62952531	62953241	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-145527	NR_120403	100874176	Hs.402083	NR_047029		LINC00448	-	long intergenic non-protein coding RNA 448	ncRNA	0.002817	0.326301	
chunk0199_314_1	chr9	7180288	7180612	+	0	NA	Intergenic	MLT1D|LTR|ERVL-MaLR	422809	NM_001146695	23081	Hs.709425	NM_015061	ENSG00000107077	KDM4C	GASC1|JHDM3C|JMJD2C|TDRD14C	lysine demethylase 4C	protein-coding	0.012346	0.486154	75(GGGGACAGTTTGTCCC,-,0.00),76(GGGACAGTTTGTCCCC,+,0.00)
chunk0013_25_1	chr1	166458545	166458974	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-145157	NR_002925	116123	Hs.348539	NM_138784	ENSG00000215834	FMO9P	-	flavin containing dimethylaniline monoxygenase 9, pseudogene	pseudo	0.002331	0.469767	
chunk0117_292_1	chr22	24399777	24400359	+	0	NA	intron (NM_001254732, intron 13 of 14)	L1MB5|LINE|L1	-23529	NM_001278500	135	Hs.197029	NM_000675	ENSG00000128271	ADORA2A	A2aR|ADORA2|RDC8	adenosine A2a receptor	protein-coding	0.003436	0.365352	
chunk0130_171_1	chr3	133230734	133231205	+	0	NA	intron (NM_001282865, intron 2 of 3)	intron (NM_001282865, intron 2 of 3)	26152	NR_110812	101927455	Hs.570550	NR_110812	ENSG00000251011	TMEM108-AS1	-	TMEM108 antisense RNA 1	ncRNA	0.008493	0.391949	
chunk0090_389_1	chr18	77478629	77479146	+	0	NA	Intergenic	Intergenic	228835	NM_001480	2587	Hs.272191	NM_001480	ENSG00000166573	GALR1	GALNR|GALNR1	galanin receptor 1	protein-coding	0.013540	0.409266	220(GAGCACACACTGTCCC,-,0.00),221(AGCACACACTGTCCCT,+,0.00)
chunk0073_397_1	chr16	16088496	16088752	+	0	NA	intron (NM_004996, intron 18 of 30)	MER58B|DNA|hAT-Charlie	134847	NM_001171	368	Hs.442182	NM_001171	ENSG00000091262	ABCC6	ABC34|ARA|EST349056|GACI2|MLP1|MOAT-E|MOATE|MRP6|PXE|PXE1|URG7	ATP binding cassette subfamily C member 6	protein-coding	0.003906	0.322957	
chunk0212_57_1	chrY	11320790	11321033	+	0	NA	Intergenic	Intergenic	1100679	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.049383	0.590164	
chunk0065_329_1	chr14	103241420	103242047	+	0	NA	Intergenic	Intergenic	-52705	NR_033938	100131366	Hs.147881	NR_033938	ENSG00000251533	LINC00605	-	long intergenic non-protein coding RNA 605	ncRNA	0.017544	0.457006	
chunk0112_42_1	chr20	36823054	36823488	+	0	NA	intron (NM_080627, intron 3 of 14)	Helitron3Na_Mam|RC|Helitron	36602	NM_199181	140710	Hs.460807	NM_080627	ENSG00000149639	SOGA1	C20orf117|KIAA0889|SOGA	suppressor of glucose, autophagy associated 1	protein-coding	0.013825	0.459770	
chunk0173_239_1	chr6	146812622	146812964	+	0	NA	intron (NM_024694, intron 35 of 35)	LTR34|LTR|ERV1	-8969	NR_003954	729176	Hs.486708	NR_003954		KATNBL1P6	-	katanin regulatory subunit B1 like 1 pseudogene 6	pseudo	0.011696	0.422741	
chunk0131_45_1	chr3	142621142	142621648	+	0	NA	intron (NM_001145319, intron 1 of 15)	L1ME4a|LINE|L1	-2029	NM_002670	5357	Hs.203637	NM_002670	ENSG00000120756	PLS1	-	plastin 1	protein-coding	0.001976	0.315582	
chunk0189_358_1	chr8	26978027	26978593	+	0	NA	Intergenic	Intergenic	70653	NR_031680	100313884		NR_031680	ENSG00000221616	MIR548H4	MIR548H-4|MIRN548H4|hsa-mir-548h-4	microRNA 548h-4	ncRNA	0.008834	0.324515	
chunk0147_420_1	chr4	187209821	187210577	+	0	NA	Intergenic	Intergenic	295414	NR_038931	339975	Hs.639361	NR_038931		LOC339975	-	uncharacterized LOC339975	ncRNA	0.013228	0.450462	
chunk0161_391_1	chr5	177006690	177007089	+	0	NA	promoter-TSS (NM_001199298)	promoter-TSS (NM_001199298)	-95	NM_001199298	51720	Hs.232721	NM_016290	ENSG00000087206	UIMC1	RAP80|X2HRIP110	ubiquitin interaction motif containing 1	protein-coding	0.105263	0.615000	
chunk0136_51_1	chr4	1467729	1467992	+	0	NA	Intergenic	Intergenic	-61418	NM_001290079	54729	Hs.526396	NM_001290079	ENSG00000235608	NKX1-1	HSPX153|NKX-1.1|SAX2	NK1 homeobox 1	protein-coding	0.000000	0.458333	
chunk0201_436_1	chr9	70080585	70080895	+	0	NA	intron (NR_125850, intron 2 of 13)	intron (NR_125850, intron 2 of 13)	37159	NR_125850	256691	Hs.547172	NM_153267	ENSG00000165072	MAMDC2	-	MAM domain containing 2	protein-coding	0.012903	0.427653	
chunk0178_345_1	chr7	38764628	38765176	+	0	NA	intron (NM_080631, intron 15 of 27)	intron (NM_080631, intron 15 of 27)	-77813	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.005474	0.346084	
chunk0112_247_1	chr20	41650339	41651007	+	0	NA	Intergenic	Intergenic	-32179	NM_032221	84181	Hs.740645	NM_032221	ENSG00000124177	CHD6	CHD-6|CHD5|RIGB	chromodomain helicase DNA binding protein 6	protein-coding	0.001497	0.393124	
chunk0207_340_1	chr9	134434812	134435451	+	0	NA	intron (NM_001291921, intron 8 of 8)	intron (NM_001291921, intron 8 of 8)	28549	NM_001291921	6256	Hs.590886	NM_002957	ENSG00000186350	RXRA	NR2B1	retinoid X receptor alpha	protein-coding	0.026604	0.620313	268(GAAAACAGCTTGTTCT,-,0.00),269(AAAACAGCTTGTTCTC,+,0.00)
chunk0084_323_1	chr17	80724686	80725120	+	0	NA	intron (NM_020761, intron 4 of 33)	intron (NM_020761, intron 4 of 33)	80729	NR_110852	101928855	Hs.670692	NR_110852	ENSG00000262833	LOC101928855	-	uncharacterized LOC101928855	ncRNA	0.032258	0.572414	281(TGGGACATGCCGTTCT,-,0.00),282(GGGACATGCCGTTCTC,+,0.00)
chunk0004_39_1	chr1	42766579	42766789	+	0	NA	promoter-TSS (NM_024097)	promoter-TSS (NM_024097)	400	NM_001146289	64175	Hs.720014	NM_022356	ENSG00000117385	P3H1	GROS1|LEPRE1|OI8	prolyl 3-hydroxylase 1	protein-coding	0.138095	0.791469	
chunk0067_304_1	chr15	47812439	47812645	+	0	NA	intron (NR_120336, intron 3 of 4)	intron (NR_120336, intron 3 of 4)	33694	NR_120336	101928442	Hs.242804	NR_120336	ENSG00000259572	LINC01491	-	long intergenic non-protein coding RNA 1491	ncRNA	0.009709	0.410628	
chunk0112_365_1	chr20	45515418	45516101	+	0	NA	promoter-TSS (NM_006652)	promoter-TSS (NM_006652)	-135	NM_006652	10816	Hs.370724	NM_006652	ENSG00000101446	SPINT3	HKIB9	serine peptidase inhibitor, Kunitz type 3	protein-coding	0.011713	0.497076	321(AGGAACAGAGTGTTCA,-,0.00),322(GGAACAGAGTGTTCAG,+,0.00)
chunk0178_276_1	chr7	37109045	37109652	+	0	NA	intron (NM_001206482, intron 14 of 21)	intron (NM_001206482, intron 14 of 21)	111552	NR_104120	100861514	Hs.627775	NR_104120	ENSG00000224101	ELMO1-AS1	-	ELMO1 antisense RNA 1	ncRNA	0.016474	0.500000	
chunk0178_267_1	chr7	36795269	36795883	+	0	NA	Intergenic	Intergenic	-71027	NM_001177506	313	Hs.488007	NM_001637	ENSG00000136250	AOAH	-	acyloxyacyl hydrolase	protein-coding	0.008143	0.386992	338(AAGAACTATCTGTACA,-,0.00)
chunk0081_386_1	chr17	48160578	48160926	+	0	NA	intron (NM_001075099, intron 11 of 12)	intron (NM_001075099, intron 11 of 12)	-4241	NR_031607	100302211		NR_031607	ENSG00000221739	MIR1203	MIRN1203|hsa-mir-1203	microRNA 1203	ncRNA	0.011494	0.478510	
chunk0188_217_1	chr8	12777894	12778690	+	0	NA	non-coding (NR_015383, exon 3 of 4)	non-coding (NR_015383, exon 3 of 4)	-15951	NR_102423	101409254	Hs.571476	NR_102423	ENSG00000255494	LINC00681	-	long intergenic non-protein coding RNA 681	ncRNA	0.013819	0.326223	
chunk0042_439_1	chr12	12338423	12338645	+	0	NA	exon (NM_018050, exon 3 of 4)	exon (NM_018050, exon 3 of 4)	11701	NM_018050	54682	Hs.591145	NM_018050	ENSG00000111261	MANSC1	9130403P13Rik|LOH12CR3	MANSC domain containing 1	protein-coding	0.018018	0.390135	
chunk0098_91_1	chr2	67667409	67667831	+	0	NA	Intergenic	MIRc|SINE|MIR	157942	NR_110271	101927701	Hs.348697	NR_110271	ENSG00000237013	LINC01812	-	long intergenic non-protein coding RNA 1812	ncRNA	0.000000	0.408983	
chunk0168_315_1	chr6	92244318	92244743	+	0	NA	Intergenic	Intergenic	-554102	NR_104154	101929083	Hs.586238	NR_104154		CASC6	-	cancer susceptibility 6	ncRNA	0.004706	0.309859	217(AAGAAGATAGTGTTCT,-,0.00),218(AGAAGATAGTGTTCTG,+,0.00)
chunk0022_416_1	chr10	18638360	18638874	+	0	NA	intron (NM_182543, intron 3 of 10)	HAL1b|LINE|L1	13020	NM_182543	221078	Hs.396175	NM_182543	ENSG00000241058	NSUN6	4933414E04Rik|ARL5B-AS1|NOPD1	NOP2/Sun RNA methyltransferase 6	protein-coding	0.009728	0.413592	
chunk0211_42_1	chrX	108519281	108519605	+	0	NA	intron (NM_033380, intron 1 of 50)	intron (NM_033380, intron 1 of 50)	79599	NM_000495	1287	Hs.369089	NM_000495	ENSG00000188153	COL4A5	ASLN|ATS|ATS1|CA54	collagen type IV alpha 5 chain	protein-coding	0.000000	0.332308	94(AAGTACAGGTAGTACT,-,0.00),95(AGTACAGGTAGTACTG,+,0.00)
chunk0208_455_1	chrX	34137361	34138002	+	0	NA	Intergenic	Intergenic	-5351	NM_203408	158724	Hs.143268	NM_203408	ENSG00000185448	FAM47A	-	family with sequence similarity 47 member A	protein-coding	0.006240	0.415888	
chunk0177_450_1	chr7	28116015	28116417	+	0	NA	intron (NM_175061, intron 1 of 4)	L1ME4b|LINE|L1	-64241	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.004975	0.374690	
chunk0029_70_1	chr10	96612118	96612330	+	0	NA	intron (NM_152309, intron 13 of 16)	intron (NM_152309, intron 13 of 16)	-25172	NM_020123	56889	Hs.500674	NM_020123	ENSG00000077147	TM9SF3	EP70-P-iso|SMBP	transmembrane 9 superfamily member 3	protein-coding	0.018868	0.488263	
chunk0087_111_1	chr18	32573569	32574088	+	0	NA	Intergenic	Intergenic	62165	NR_003558	441818	Hs.549773	NR_003558	ENSG00000260389	WBP11P1	HsT3017	WW domain binding protein 11 pseudogene 1	pseudo	0.003854	0.371154	
chunk0120_446_1	chr3	14228695	14229557	+	0	NA	Intergenic	HERVK3-int|LTR|ERVK	50398	NM_014463	27258	Hs.111632	NM_014463	ENSG00000170860	LSM3	SMX4|USS2|YLR438C	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated	protein-coding	0.008121	0.405562	
chunk0017_153_1	chr1	206843642	206844280	+	0	NA	TTS (NM_013371)	TTS (NM_013371)	15084	NM_013371	29949	Hs.661017	NM_013371	ENSG00000142224	IL19	IL-10C|MDA1|NG.1|ZMDA1	interleukin 19	protein-coding	0.009404	0.478873	579(CAGCACACTTTGTACC,-,0.00),580(AGCACACTTTGTACCC,+,0.00)
chunk0028_354_1	chr10	92444457	92444656	+	0	NA	Intergenic	L1ME1|LINE|L1	25895	NR_038243	100507674	Hs.568772	NR_038243		MARK2P9	-	microtubule affinity regulating kinase 2 pseudogene 9	pseudo	0.000000	0.360000	
chunk0198_34_1	chr8	128221566	128221963	+	0	NA	Intergenic	Intergenic	71648	NR_031613	100302281		NR_031613	ENSG00000221261	MIR1208	MIRN1208|hsa-mir-1208	microRNA 1208	ncRNA	0.002519	0.329146	183(GAGATCATAGTGTACT,-,0.00),184(AGATCATAGTGTACTT,+,0.00),360(AAGGACAGGAAGTTCT,-,0.00),361(AGGACAGGAAGTTCTT,+,0.00)
chunk0207_222_1	chr9	131718664	131718957	+	0	NA	intron (NM_001304275, intron 1 of 23)	intron (NM_001304275, intron 1 of 23)	-8968	NM_198679	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.010239	0.469388	
chunk0082_310_1	chr17	59126276	59126889	+	0	NA	intron (NM_182620, intron 2 of 3)	intron (NM_182620, intron 2 of 3)	11290	NR_030411	768216		NR_030411	ENSG00000211514	MIR454	MIRN454|hsa-mir-454|mir-454	microRNA 454	ncRNA	0.008157	0.361564	
chunk0049_270_1	chr12	93784417	93785003	+	0	NA	intron (NM_003805, intron 2 of 2)	intron (NM_003805, intron 2 of 2)	-46887	NR_110093	101928731	Hs.659971	NR_110092	ENSG00000258274	LOC101928731	-	uncharacterized LOC101928731	ncRNA	0.013652	0.434412	287(TAGAACACAGAGTCCC,-,0.00),288(AGAACACAGAGTCCCA,+,0.00),484(AAGAGCTGTCTGTTCT,-,0.00),485(AGAGCTGTCTGTTCTT,+,0.00)
chunk0151_61_1	chr5	42483931	42484167	+	0	NA	intron (NM_001242401, intron 2 of 10)	intron (NM_001242401, intron 2 of 10)	59057	NM_001242401	2690	Hs.125180	NM_000163	ENSG00000112964	GHR	GHBP|GHIP	growth hormone receptor	protein-coding	0.004237	0.396624	
chunk0211_28_1	chrX	108001353	108001552	+	0	NA	Intergenic	L1PA16|LINE|L1	-19082	NM_031273	56156	Hs.333130	NM_031273	ENSG00000170925	TEX13B	TGC3B|TSGA5	testis expressed 13B	protein-coding	0.020101	0.590000	
chunk0112_306_1	chr20	44450231	44450568	+	0	NA	intron (NR_109893, intron 1 of 2)	L2c|LINE|L2	158	NR_109893	101927242	Hs.143307	NR_109893	ENSG00000168746	LINC01430	-	long intergenic non-protein coding RNA 1430	ncRNA	0.008902	0.482249	
chunk0180_340_1	chr7	73448365	73448923	+	0	NA	intron (NM_032408, intron 15 of 19)	intron (NM_032408, intron 15 of 19)	14865	NM_003508	8326	Hs.647029	NM_003508	ENSG00000188763	FZD9	CD349|FZD3	frizzled class receptor 9	protein-coding	0.007168	0.431127	
chunk0006_365_1	chr1	73106827	73107487	+	0	NA	Intergenic	L1PA17|LINE|L1	-199013	NR_110677	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.003030	0.376702	
chunk0028_288_1	chr10	91425216	91425541	+	0	NA	exon (NM_182765, exon 2 of 21)	exon (NM_182765, exon 2 of 21)	15093	NM_001284274	143279	Hs.596096	NM_173497	ENSG00000165338	HECTD2	-	HECT domain E3 ubiquitin protein ligase 2	protein-coding	0.006154	0.306748	
chunk0145_301_1	chr4	150070463	150071117	+	0	NA	Intergenic	Intergenic	-7484	NR_036614	166614	Hs.591683	NM_152619	ENSG00000170390	DCLK2	CL2|CLICK-II|CLICK2|CLIK2|DCAMKL2|DCDC3|DCDC3B|DCK2	doublecortin like kinase 2	protein-coding	0.006116	0.387786	
chunk0162_269_1	chr6	5439545	5439744	+	0	NA	intron (NM_006567, intron 4 of 6)	intron (NM_006567, intron 4 of 6)	18431	NR_125848	101927972	Hs.668417	NR_125846	ENSG00000269985	LOC101927972	-	uncharacterized LOC101927972	ncRNA	0.015075	0.445000	
chunk0129_235_1	chr3	121979919	121980354	+	0	NA	Intergenic	Intergenic	42144	NM_175924	286676	Hs.98484	NM_175924	ENSG00000145103	ILDR1	DFNB42|ILDR1alpha|ILDR1alpha'|ILDR1beta	immunoglobulin like domain containing receptor 1	protein-coding	0.000000	0.316514	
chunk0087_274_1	chr18	37772190	37772410	+	0	NA	Intergenic	MIR|SINE|MIR	115165	NR_036202	100422857		NR_036202	ENSG00000266530	MIR4318	-	microRNA 4318	ncRNA	0.004545	0.325792	
chunk0017_455_1	chr1	214439474	214439943	+	0	NA	intron (NM_005401, intron 3 of 18)	intron (NM_005401, intron 3 of 18)	111973	NM_005401	5784	Hs.193557	NM_005401	ENSG00000152104	PTPN14	CATLPH|PEZ|PTP36	protein tyrosine phosphatase non-receptor type 14	protein-coding	0.021322	0.436170	
chunk0203_362_1	chr9	89888706	89889333	+	0	NA	Intergenic	Intergenic	-80397	NR_109791	101927847	Hs.584312	NR_109791		LOC101927847	-	uncharacterized LOC101927847	ncRNA	0.009569	0.479299	
chunk0164_47_1	chr6	18493719	18493955	+	0	NA	Intergenic	Intergenic	-77947	NR_030312	693125		NR_030312	ENSG00000207775	MIR548A1	MIRN548A1	microRNA 548a-1	ncRNA	0.004237	0.459916	
chunk0126_290_1	chr3	80305486	80305722	+	0	NA	Intergenic	Intergenic	-537695	NM_002941	6091	Hs.744218	NM_002941	ENSG00000169855	ROBO1	DUTT1|SAX3	roundabout guidance receptor 1	protein-coding	0.000000	0.295359	
chunk0174_294_1	chr6	162584150	162584712	+	0	NA	intron (NM_013988, intron 1 of 8)	intron (NM_013988, intron 1 of 8)	-142701	NM_152410	135138	Hs.25791	NM_152410	ENSG00000112530	PACRG	GLUP|HAK005771|PACRG2.1|PARK2CRG	parkin coregulated	protein-coding	0.005338	0.344583	251(AGGAACACTCTGTACA,-,0.00),252(GGAACACTCTGTACAT,+,0.00)
chunk0079_3_1	chr17	9123568	9123784	+	0	NA	intron (NM_004822, intron 2 of 6)	intron (NM_004822, intron 2 of 6)	55442	NR_110828	101928266	Hs.639880	NR_110828	ENSG00000262966	LOC101928266	-	uncharacterized LOC101928266	ncRNA	0.009259	0.400922	
chunk0156_310_1	chr5	110896621	110897186	+	0	NA	Intergenic	Intergenic	157909	NM_001303249	91137	Hs.75639	NM_138773	ENSG00000164209	SLC25A46	HMSN6B	solute carrier family 25 member 46	protein-coding	0.000000	0.321555	
chunk0192_134_1	chr8	61959699	61960282	+	0	NA	Intergenic	Intergenic	245202	NR_039680	100616484		NR_039680	ENSG00000264408	MIR4470	mir-4470	microRNA 4470	ncRNA	0.003431	0.285959	
chunk0056_249_1	chr13	89322542	89322925	+	0	NA	Intergenic	Intergenic	-85843	NR_131229	105616982	Hs.564527	NR_131229	ENSG00000232225	LINC01047	-	long intergenic non-protein coding RNA 1047	ncRNA	0.013055	0.395833	
chunk0202_141_1	chr9	73431399	73431621	+	0	NA	Intergenic	L1MCa|LINE|L1	279779	NM_000700	301	Hs.494173	NM_000700	ENSG00000135046	ANXA1	ANX1|LPC1	annexin A1	protein-coding	0.000000	0.354260	
chunk0139_168_1	chr4	53833746	53834473	+	0	NA	Intergenic	L1PA6|LINE|L1	138208	NR_125918	100506444	Hs.636176	NR_125918	ENSG00000249341	LOC100506444	-	uncharacterized LOC100506444	ncRNA	0.009629	0.494505	
chunk0053_119_1	chr13	29554682	29555098	+	0	NA	intron (NM_003045, intron 1 of 12)	intron (NM_003045, intron 1 of 12)	40798	NM_003045	6541	Hs.14846	NM_003045	ENSG00000139514	SLC7A1	ATRC1|CAT-1|ERR|HCAT1|REC1L	solute carrier family 7 member 1	protein-coding	0.014423	0.366906	
chunk0180_222_1	chr7	67146085	67146864	+	0	NA	intron (NM_018264, intron 13 of 15)	intron (NM_018264, intron 13 of 15)	-32077	NR_039794	100616331		NR_039794	ENSG00000264494	MIR4650-2	-	microRNA 4650-2	ncRNA	0.001284	0.332051	
chunk0080_219_1	chr17	29655814	29656056	+	0	NA	intron (NM_001282129, intron 11 of 15)	L2a|LINE|L2	-34512	NM_032854	84940	Hs.143046	NM_032854	ENSG00000167549	CORO6	-	coronin 6	protein-coding	0.004132	0.341564	
chunk0153_122_1	chr5	68759544	68759923	+	0	NA	Intergenic	Intergenic	270194	NR_130778	101928885	Hs.630474	NR_130778		LINC02198	-	long intergenic non-protein coding RNA 2198	ncRNA	0.013193	0.405263	
chunk0003_117_1	chr1	32406320	32406998	+	0	NA	Intergenic	ERVL-E-int|LTR|ERVL	-12198	NM_018045	55108	Hs.353454	NM_018045	ENSG00000160058	BSDC1	-	BSD domain containing 1	protein-coding	0.005900	0.472754	
chunk0087_332_1	chr18	40076169	40076918	+	0	NA	intron (NR_110791, intron 2 of 3)	intron (NR_110791, intron 2 of 3)	10257	NR_110791	101927900	Hs.385522	NR_110791	ENSG00000261715	LINC01477	-	long intergenic non-protein coding RNA 1477	ncRNA	0.004005	0.372000	439(AAGAACACCCTGATCT,-,0.00),440(AGAACACCCTGATCTC,+,0.00)
chunk0025_97_1	chr10	50572389	50573219	+	0	NA	intron (NM_147156, intron 2 of 10)	intron (NM_147156, intron 2 of 10)	51173	NM_147156	259230	Hs.654698	NM_147156	ENSG00000198964	SGMS1	MOB|MOB1|SMS1|TMEM23|hmob33	sphingomyelin synthase 1	protein-coding	0.001205	0.382671	522(CAGAACTTTCTGTCCC,-,0.00),523(AGAACTTTCTGTCCCT,+,0.00)
chunk0147_280_1	chr4	184236541	184236957	+	0	NA	Intergenic	L1MC3|LINE|L1	-18788	NM_153343	133121	Hs.297814	NM_153343	ENSG00000164303	ENPP6	NPP6	ectonucleotide pyrophosphatase/phosphodiesterase 6	protein-coding	0.019231	0.455635	
chunk0066_321_1	chr15	36230286	36230776	+	0	NA	Intergenic	L2c|LINE|L2	303675	NR_039735	100616293		NR_039735	ENSG00000265098	MIR4510	mir-4510	microRNA 4510	ncRNA	0.002041	0.334012	204(AAGACAGGCAGTCCCT,+,0.00)
chunk0070_269_1	chr15	74024391	74024961	+	0	NA	intron (NM_033239, intron 3 of 7)	intron (NM_033239, intron 3 of 7)	30003	NM_033244	5371	Hs.526464	NM_002675	ENSG00000140464	PML	MYL|PP8675|RNF71|TRIM19	promyelocytic leukemia	protein-coding	0.007018	0.504378	402(CAGGTCAGGATGTCCC,-,0.00),403(AGGTCAGGATGTCCCT,+,0.00)
chunk0112_28_1	chr20	36153848	36154410	+	0	NA	promoter-TSS (NM_012156)	promoter-TSS (NM_012156)	-611	NM_012156	2036	Hs.437422	NM_012156	ENSG00000088367	EPB41L1	4.1N|MRD11	erythrocyte membrane protein band 4.1 like 1	protein-coding	0.024911	0.605684	
chunk0039_289_1	chr11	102731081	102731280	+	0	NA	Intergenic	Intergenic	-6226	NM_001304442	4317	Hs.161839	NM_002424	ENSG00000118113	MMP8	CLG1|HNC|MMP-8|PMNL-CL	matrix metallopeptidase 8	protein-coding	0.020101	0.620000	
chunk0211_306_1	chrX	123360100	123360485	+	0	NA	intron (NM_007325, intron 5 of 15)	intron (NM_007325, intron 5 of 15)	176049	NM_007325	2892	Hs.377070	NM_000828	ENSG00000125675	GRIA3	GLUR-C|GLUR-K3|GLUR3|GLURC|GluA3|MRX94	glutamate ionotropic receptor AMPA type subunit 3	protein-coding	0.015584	0.422280	
chunk0045_53_1	chr12	45252972	45253360	+	0	NA	intron (NM_001142679, intron 1 of 19)	intron (NM_001142679, intron 1 of 19)	-37160	NR_037144	51054	Hs.233495	NM_015899	ENSG00000134297	PLEKHA8P1	FAPP-2|FAPP2|PLEKHA8|PLEKHA9|hFAPP2	pleckstrin homology domain containing A8 pseudogene 1	pseudo	0.002577	0.370180	185(GGGAACATTCTGTAAT,-,0.00)
chunk0015_225_1	chr1	187750598	187751127	+	0	NA	Intergenic	LTR53-int|LTR|ERVL	307234	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.001890	0.315094	
chunk0190_56_1	chr8	29695102	29695838	+	0	NA	Intergenic	Intergenic	52639	NR_026765	619351	Hs.566911	NR_026765	ENSG00000251191	LINC00589	C8orf75|TSLNC8	long intergenic non-protein coding RNA 589	ncRNA	0.002717	0.388060	
chunk0170_188_1	chr6	112039200	112039654	+	0	NA	Intergenic	Intergenic	-14648	NR_125354	8838	Hs.558428	NM_003880	ENSG00000112761	CCN6	LIBC|PPAC|PPD|WISP-3|WISP3	cellular communication network factor 6	protein-coding	0.017621	0.463736	
chunk0006_42_1	chr1	64425056	64425398	+	0	NA	Intergenic	Intergenic	-45566	NM_020925	57685	Hs.443891	NM_020925	ENSG00000158966	CACHD1	-	cache domain containing 1	protein-coding	0.002924	0.387755	
chunk0176_384_1	chr7	18691753	18692144	+	0	NA	intron (NM_178425, intron 11 of 24)	intron (NM_178425, intron 11 of 24)	182671	NM_001204148	9734	Hs.196054	NM_014707	ENSG00000048052	HDAC9	HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR	histone deacetylase 9	protein-coding	0.000000	0.415816	155(GAGAACAGTCTGTGTA,-,0.00)
chunk0032_244_1	chr11	8168525	8168820	+	0	NA	intron (NR_045405, intron 1 of 6)	intron (NR_045405, intron 1 of 6)	371	NM_001135109	79608	Hs.231850	NM_024557	ENSG00000166405	RIC3	AYST720|PRO1385	RIC3 acetylcholine receptor chaperone	protein-coding	0.061017	0.574324	
chunk0036_102_1	chr11	61158594	61159175	+	0	NA	intron (NM_017966, intron 1 of 4)	intron (NM_017966, intron 1 of 4)	2560	NM_017966	55048	Hs.523715	NM_017966	ENSG00000167987	VPS37C	-	VPS37C subunit of ESCRT-I	protein-coding	0.005164	0.434708	
chunk0085_378_1	chr18	9717453	9718068	+	0	NA	intron (NM_006868, intron 1 of 6)	intron (NM_006868, intron 1 of 6)	9529	NM_006868	11031	Hs.99528	NM_006868	ENSG00000168461	RAB31	Rab22B	RAB31, member RAS oncogene family	protein-coding	0.011382	0.420455	334(AAGAGCAAGGTGTTCT,-,0.00),335(AGAGCAAGGTGTTCTT,+,0.00)
chunk0123_137_1	chr3	42779203	42779787	+	0	NA	Intergenic	Intergenic	-6242	NM_144719	152206	Hs.604182	NM_144719	ENSG00000244607	CCDC13	-	coiled-coil domain containing 13	protein-coding	0.005137	0.384615	
chunk0090_408_1	chr18	78816696	78816895	+	0	NA	Intergenic	Intergenic	-163480	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.030151	0.540000	
chunk0112_87_1	chr20	38021346	38021972	+	0	NA	intron (NM_014657, intron 1 of 8)	intron (NM_014657, intron 1 of 8)	11809	NM_014657	9675	Hs.655481	NM_014657	ENSG00000101407	TTI1	KIAA0406|smg-10	TELO2 interacting protein 1	protein-coding	0.004792	0.430622	503(TGGAACAATCTGTACA,-,0.00),504(GGAACAATCTGTACAG,+,0.00)
chunk0130_214_1	chr3	133986120	133986606	+	0	NA	intron (NM_005630, intron 1 of 13)	intron (NM_005630, intron 1 of 13)	43713	NM_005630	6578	Hs.518270	NM_005630	ENSG00000174640	SLCO2A1	MATR1|OATP2A1|PGT|PHOAR2|SLC21A2	solute carrier organic anion transporter family member 2A1	protein-coding	0.008230	0.390144	
chunk0184_226_1	chr7	117472985	117473441	+	0	NA	Intergenic	MIR|SINE|MIR	-6750	NM_000492	1080	Hs.489786	NM_000492	ENSG00000001626	CFTR	ABC35|ABCC7|CF|CFTR/MRP|MRP7|TNR-CFTR|dJ760C5.1	CF transmembrane conductance regulator	protein-coding	0.002193	0.343545	
chunk0015_183_1	chr1	187189686	187189976	+	0	NA	intron (NR_126347, intron 1 of 3)	intron (NR_126347, intron 1 of 3)	96989	NR_126347	104169671		NR_126347	ENSG00000230426	LINC01036	-	long intergenic non-protein coding RNA 1036	ncRNA	0.003448	0.402062	
chunk0061_37_1	chr14	55947563	55947786	+	0	NA	Intergenic	Intergenic	-151000	NR_026796	645687	Hs.569345	NR_026796	ENSG00000258791	LINC00520	C14orf34	long intergenic non-protein coding RNA 520	ncRNA	0.000000	0.308036	
chunk0106_203_1	chr2	202261484	202261731	+	0	NA	Intergenic	Intergenic	-4185	NM_015934	51602	Hs.471104	NM_015934	ENSG00000055044	NOP58	HSPC120|NOP5|NOP5/NOP58	NOP58 ribonucleoprotein	protein-coding	0.004049	0.403226	
chunk0078_373_1	chr16	87497165	87497540	+	0	NA	intron (NR_110943, intron 1 of 3)	intron (NR_110943, intron 1 of 3)	3165	NR_110943	101928737	Hs.579009	NR_110943	ENSG00000260750	LOC101928737	-	uncharacterized LOC101928737	ncRNA	0.016000	0.505319	
chunk0091_216_1	chr19	9819724	9819923	+	0	NA	promoter-TSS (NM_001316939)	promoter-TSS (NM_001316939)	-720	NM_001316939	54850	Hs.12439	NM_017703	ENSG00000127452	FBXL12	Fbl12	F-box and leucine rich repeat protein 12	protein-coding	0.050251	0.520000	
chunk0074_11_1	chr16	19744632	19745134	+	0	NA	intron (NR_130967, intron 5 of 7)	intron (NR_130967, intron 5 of 7)	-26713	NM_001012991	400506	Hs.585209	NM_001012991	ENSG00000103550	KNOP1	101F10.1|C16orf88|FAM191A|TSG118	lysine rich nucleolar protein 1	protein-coding	0.007968	0.333996	
chunk0086_2_1	chr18	11925063	11925387	+	0	NA	Intergenic	Tigger3|DNA|TcMar-Tigger	-16428	NR_040241	65258	Hs.712666	NM_023075	ENSG00000154889	MPPE1	PGAP5	metallophosphoesterase 1	protein-coding	0.015432	0.430769	212(AAGTACACTCTGTGAT,-,0.00)
chunk0159_260_1	chr5	142169413	142169644	+	0	NA	Intergenic	Intergenic	60769	NM_030571	80762	Hs.9788	NM_030571	ENSG00000131507	NDFIP1	N4WBP5	Nedd4 family interacting protein 1	protein-coding	0.004329	0.482759	
chunk0165_131_1	chr6	33299362	33299612	+	0	NA	promoter-TSS (NM_004761).5	promoter-TSS (NM_004761).5	-99	NM_001243738	5863	Hs.509622	NM_004761	ENSG00000237441	RGL2	HKE1.5|KE1.5|RAB2L	ral guanine nucleotide dissociation stimulator like 2	protein-coding	0.112000	0.669323	
chunk0017_64_1	chr1	205517130	205517622	+	0	NA	intron (NM_002596, intron 1 of 15)	intron (NM_002596, intron 1 of 15)	12820	NM_212503	5129	Hs.445402	NM_002596	ENSG00000117266	CDK18	PCTAIRE|PCTAIRE3|PCTK3	cyclin dependent kinase 18	protein-coding	0.010163	0.543611	
chunk0101_141_1	chr2	127509795	127510381	+	0	NA	intron (NM_017969, intron 2 of 13)	intron (NM_017969, intron 2 of 13)	16423	NM_017969	55677	Hs.469879	NM_017969	ENSG00000163166	IWS1	-	interacts with SUPT6H, CTD assembly factor 1	protein-coding	0.006826	0.345826	211(CAGGACACTTTGTTTC,-,0.00),212(AGGACACTTTGTTTCT,+,0.00)
chunk0181_125_1	chr7	80884526	80885214	+	0	NA	intron (NM_006379, intron 2 of 17)	intron (NM_006379, intron 2 of 17)	34481	NM_006379	10512	Hs.269109	NM_006379	ENSG00000075223	SEMA3C	SEMAE|SemE	semaphorin 3C	protein-coding	0.008721	0.333817	
chunk0171_97_1	chr6	121974102	121974696	+	0	NA	Intergenic	HAL1M8|LINE|L1	-425152	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.003367	0.275630	
chunk0104_371_1	chr2	180156559	180157106	+	0	NA	Intergenic	Intergenic	-149779	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.000000	0.357664	
chunk0152_2_1	chr5	56097448	56097647	+	0	NA	Intergenic	Intergenic	102380	NR_102755	441072	Hs.482141	NR_102755	ENSG00000227908	FLJ31104	-	uncharacterized LOC441072	ncRNA	0.005025	0.390000	
chunk0009_215_1	chr1	106317129	106317493	+	0	NA	Intergenic	MLT1E2|LTR|ERVL-MaLR	-698376	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.002747	0.361644	
chunk0092_420_1	chr19	37980457	37980761	+	0	NA	intron (NM_015073, intron 1 of 21)	intron (NM_015073, intron 1 of 21)	73388	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.019737	0.560656	
chunk0185_180_1	chr7	128068777	128069077	+	0	NA	intron (NM_014390, intron 16 of 23)	intron (NM_014390, intron 16 of 23)	-12934	NR_030324	693178		NR_030324	ENSG00000207588	MIR593	MIRN593|hsa-mir-593	microRNA 593	ncRNA	0.020000	0.544850	
chunk0191_42_1	chr8	43191339	43191694	+	0	NA	exon (NM_152419, exon 12 of 18)	exon (NM_152419, exon 12 of 18)	51067	NM_152419	138050	Hs.600384	NM_152419	ENSG00000165102	HGSNAT	HGNAT|MPS3C|RP73|TMEM76	heparan-alpha-glucosaminide N-acetyltransferase	protein-coding	0.022535	0.519663	
chunk0070_370_1	chr15	76337282	76337685	+	0	NA	intron (NM_145805, intron 1 of 5)	intron (NM_145805, intron 1 of 5)	759	NM_145805	64843	Hs.444677	NM_145805	ENSG00000159556	ISL2	-	ISL LIM homeobox 2	protein-coding	0.042184	0.460396	
chunk0110_307_1	chr20	18203073	18203483	+	0	NA	Intergenic	L1M2|LINE|L1	58179	NR_028402	57325	Hs.488051	NM_020536	ENSG00000149474	KAT14	ATAC2|CRP2BP|CSRP2BP|PRO1194|dJ717M23.1	lysine acetyltransferase 14	protein-coding	0.000000	0.537713	237(CTGGACTGTTTGTTCC,-,0.00),238(TGGACTGTTTGTTCCC,+,0.00),386(AGCACACACAGTTTTT,+,0.00)
chunk0024_178_1	chr10	35853193	35853419	+	0	NA	Intergenic	Intergenic	75004	NR_110138	102578074		NR_110138	ENSG00000280719	PCAT5	LINC01452|TPCAT-10-36067	prostate cancer associated transcript 5	ncRNA	0.008850	0.370044	135(CAGTACACTGTGTGCC,-,0.00),136(AGTACACTGTGTGCCT,+,0.00)
chunk0177_244_1	chr7	24962536	24962783	+	0	NA	intron (NM_015550, intron 1 of 22)	MLT1K|LTR|ERVL-MaLR	17553	NM_015550	26031	Hs.520259	NM_015550	ENSG00000070882	OSBPL3	ORP-3|ORP3|OSBP3	oxysterol binding protein like 3	protein-coding	0.008097	0.479839	
chunk0160_279_1	chr5	157761882	157762220	+	0	NA	Intergenic	Intergenic	18356	NM_173491	134353	Hs.23648	NM_173491	ENSG00000155858	LSM11	-	LSM11, U7 small nuclear RNA associated	protein-coding	0.008876	0.436578	
chunk0063_293_1	chr14	84442459	84443088	+	0	NA	Intergenic	Intergenic	-951106	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.011129	0.377778	
chunk0031_137_1	chr10	124953451	124953857	+	0	NA	intron (NM_017580, intron 1 of 8)	MamRTE1|LINE|RTE-BovB	11531	NM_017580	54764	Hs.595158	NM_017580	ENSG00000019995	ZRANB1	TRABID	zinc finger RANBP2-type containing 1	protein-coding	0.009852	0.402948	
chunk0138_66_1	chr4	33332171	33332375	+	0	NA	Intergenic	L1PA15-16|LINE|L1	707620	NR_125902	101928622	Hs.631687	NR_125902	ENSG00000250954	LOC101928622	-	uncharacterized LOC101928622	ncRNA	0.009804	0.551220	
chunk0189_352_1	chr8	26852070	26852462	+	0	NA	intron (NM_033302, intron 1 of 2)	L1M6|LINE|L1	13139	NM_033302	148	Hs.52931	NM_000680	ENSG00000120907	ADRA1A	ADRA1C|ADRA1L1|ALPHA1AAR	adrenoceptor alpha 1A	protein-coding	0.002551	0.320611	
chunk0068_205_1	chr15	54999531	54999878	+	0	NA	Intergenic	Intergenic	197329	NM_016304	51187	Hs.274772	NM_016304	ENSG00000137876	RSL24D1	C15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3	ribosomal L24 domain containing 1	protein-coding	0.008646	0.416667	
chunk0207_228_1	chr9	131886746	131887323	+	0	NA	intron (NM_001253881, intron 4 of 6)	intron (NM_001253881, intron 4 of 6)	-147090	NM_001304275	2889	Hs.127897	NM_005312	ENSG00000107263	RAPGEF1	C3G|GRF2	Rap guanine nucleotide exchange factor 1	protein-coding	0.008666	0.359862	
chunk0171_425_1	chr6	131548336	131549081	+	0	NA	Intergenic	Intergenic	-24496	NM_000045	383	Hs.440934	NM_000045	ENSG00000118520	ARG1	-	arginase 1	protein-coding	0.002685	0.344504	312(CAGCACTAGATGTTCC,-,0.00),313(AGCACTAGATGTTCCA,+,0.00)
chunk0128_419_1	chr3	114863943	114864385	+	0	NA	intron (NR_121662, intron 2 of 6)	intron (NR_121662, intron 2 of 6)	-8869	NR_126422	104413890	Hs.612732	NR_126422	ENSG00000239946	ZBTB20-AS3	-	ZBTB20 antisense RNA 3	ncRNA	0.002262	0.325056	
chunk0113_74_1	chr20	50538093	50538763	+	0	NA	intron (NM_001278618, intron 1 of 8)	intron (NM_001278618, intron 1 of 8)	28107	NM_001278618	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.007463	0.362146	374(TGTACAGTGTGATCCT,+,0.00)
chunk0045_174_1	chr12	46934785	46935030	+	0	NA	Intergenic	Intergenic	-108910	NM_001143824	55089	Hs.446077	NM_018018	ENSG00000139209	SLC38A4	ATA3|NAT3|PAAT|SNAT4	solute carrier family 38 member 4	protein-coding	0.008163	0.422764	169(AAGATCACACAGTCCT,-,0.00)
chunk0106_216_1	chr2	202531360	202531598	+	0	NA	intron (NM_001204, intron 8 of 12)	intron (NM_001204, intron 8 of 12)	-103699	NM_173511	150864	Hs.471130	NM_173511	ENSG00000138439	FAM117B	ALS2CR13	family with sequence similarity 117 member B	protein-coding	0.004202	0.359833	
chunk0207_309_1	chr9	133743105	133744083	+	0	NA	Intergenic	L1M4c|LINE|L1	-3639	NM_007101	1757	Hs.198003	NM_007101	ENSG00000123453	SARDH	BPR-2|DMGDHL1|SAR|SARD|SDH	sarcosine dehydrogenase	protein-coding	0.017382	0.464760	
chunk0074_46_1	chr16	20716513	20716763	+	0	NA	Intergenic	LTR14B|LTR|ERVK	25326	NM_001304550	55623	Hs.700004	NM_017736	ENSG00000066654	THUMPD1	Tan1	THUMP domain containing 1	protein-coding	0.020000	0.470120	
chunk0028_422_1	chr10	93611344	93611812	+	0	NA	Intergenic	Intergenic	-1010	NM_006204	5146	Hs.658121	NM_006204	ENSG00000095464	PDE6C	ACHM5|COD4|PDEA2	phosphodiesterase 6C	protein-coding	0.004274	0.300640	
chunk0091_203_1	chr19	9256081	9256516	+	0	NA	Intergenic	SATR2|Satellite|Satellite	5254	NM_001079935	26648	Hs.129832	NM_001079935	ENSG00000237521	OR7E24	HSHT2|OR19-8|OR7E24P|OR7E24Q	olfactory receptor family 7 subfamily E member 24	protein-coding	0.011494	0.449541	
chunk0093_211_1	chr19	49676405	49676799	+	0	NA	promoter-TSS (NM_001536)	promoter-TSS (NM_001536)	-550	NR_033397	3276	Hs.20521	NM_001536	ENSG00000126457	PRMT1	ANM1|HCP1|HRMT1L2|IR1B4	protein arginine methyltransferase 1	protein-coding	0.035533	0.534177	
chunk0088_307_1	chr18	50466347	50466619	+	0	NA	Intergenic	MER103C|DNA|hAT-Charlie	91461	NM_145060	220134	Hs.134726	NM_145060	ENSG00000154839	SKA1	C18orf24	spindle and kinetochore associated complex subunit 1	protein-coding	0.007353	0.388278	
chunk0025_36_1	chr10	48901464	48901755	+	0	NA	intron (NM_020945, intron 46 of 61)	intron (NM_020945, intron 46 of 61)	12626	NM_001006939	474354	Hs.202438	NM_001006939	ENSG00000165383	LRRC18	UNQ933|UNQ9338|VKGE9338	leucine rich repeat containing 18	protein-coding	0.017182	0.517123	
chunk0119_435_1	chr22	50042745	50043191	+	0	NA	Intergenic	L1MC|LINE|L1	-30342	NM_001001694	400935	Hs.526712	NM_001001694	ENSG00000188263	IL17REL	-	interleukin 17 receptor E like	protein-coding	0.029148	0.456376	
chunk0027_255_1	chr10	77228914	77229113	+	0	NA	intron (NM_001014797, intron 3 of 28)	intron (NM_001014797, intron 3 of 28)	88182	NR_120654	101929310	Hs.666457	NR_120654	ENSG00000225497	KCNMA1-AS2	-	KCNMA1 antisense RNA 2	ncRNA	0.005025	0.360000	
chunk0094_32_1	chr2	1724414	1724703	+	0	NA	intron (NM_012293, intron 1 of 22)	LTR47A2|LTR|ERVL	19989	NM_012293	7837	Hs.332197	NM_012293	ENSG00000130508	PXDN	ASGD7|COPOA|D2S448|D2S448E|MG50|PRG2|PXN|VPO	peroxidasin	protein-coding	0.006920	0.427586	
chunk0056_351_1	chr13	91985292	91985794	+	0	NA	intron (NM_004466, intron 6 of 7)	L1MEg|LINE|L1	366664	NR_120382	100873970	Hs.567269	NR_120382		GPC5-AS2	-	GPC5 antisense RNA 2	ncRNA	0.003984	0.258449	
chunk0068_84_1	chr15	52011011	52011210	+	0	NA	Intergenic	Tigger17c|DNA|TcMar-Tigger	-8104	NM_002748	5597	Hs.411847	NM_002748	ENSG00000069956	MAPK6	ERK3|HsT17250|PRKM6|p97MAPK	mitogen-activated protein kinase 6	protein-coding	0.030151	0.420000	
chunk0008_439_1	chr1	99548988	99549311	+	0	NA	intron (NR_031666, intron 2 of 4)	intron (NR_031666, intron 2 of 4)	-61345	NR_125951	101928270	Hs.576048	NR_125951	ENSG00000224445	LINC01708	-	long intergenic non-protein coding RNA 1708	ncRNA	0.009288	0.472222	
chunk0109_377_1	chr2	239429542	239429843	+	0	NA	Intergenic	Intergenic	-28743	NM_006037	9759	Hs.20516	NM_006037	ENSG00000068024	HDAC4	AHO3|BDMR|HA6116|HD4|HDAC-4|HDAC-A|HDACA	histone deacetylase 4	protein-coding	0.013289	0.417219	
chunk0136_231_1	chr4	8422330	8422853	+	0	NA	intron (NM_003501, intron 1 of 17)	intron (NM_003501, intron 1 of 17)	18134	NM_001101667	8310	Hs.479122	NM_003501	ENSG00000087008	ACOX3	-	acyl-CoA oxidase 3, pristanoyl	protein-coding	0.009560	0.452290	
chunk0043_149_1	chr12	16341369	16341711	+	0	NA	Intergenic	L1M2|LINE|L1	-5602	NM_145792	4257	Hs.389700	NM_020300	ENSG00000008394	MGST1	GST12|MGST|MGST-I	microsomal glutathione S-transferase 1	protein-coding	0.000000	0.338192	
chunk0192_57_1	chr8	59741431	59741693	+	0	NA	Intergenic	Intergenic	539833	NM_004056	767	Hs.654388	NM_004056	ENSG00000178538	CA8	CA-RP|CA-VIII|CALS|CAMRQ3|CARP	carbonic anhydrase 8	protein-coding	0.011450	0.269962	
chunk0163_152_1	chr6	11008287	11008494	+	0	NA	intron (NM_017770, intron 2 of 7)	intron (NM_017770, intron 2 of 7)	-35368	NR_038963	100506409	Hs.43818	NR_038962		ELOVL2-AS1	-	ELOVL2 antisense RNA 1	ncRNA	0.019324	0.451923	
chunk0004_104_1	chr1	44196557	44196819	+	0	NA	Intergenic	L1MC4|LINE|L1	-16765	NM_001034024	55929	Hs.8008	NM_019100	ENSG00000178028	DMAP1	DNMAP1|DNMTAP1|EAF2|MEAF2|SWC4	DNA methyltransferase 1 associated protein 1	protein-coding	0.000000	0.323194	
chunk0067_19_1	chr15	40217059	40217300	+	0	NA	promoter-TSS (NM_001128629)	promoter-TSS (NM_001128629)	-249	NM_001128629	106821730	Hs.732375	NM_001128628	ENSG00000259288	BUB1B-PAK6	PAK-5|PAK-6|PAK5|PAK6	BUB1B-PAK6 readthrough	protein-coding	0.004149	0.347107	
chunk0137_360_1	chr4	25942605	25942922	+	0	NA	Intergenic	LTR16C|LTR|ERVL	28571	NM_001145432	389203	Hs.479386	NM_001145432	ENSG00000250317	SMIM20	C4orf52|MITRAC7|PNX	small integral membrane protein 20	protein-coding	0.006309	0.500000	
chunk0022_105_1	chr10	10095898	10096197	+	0	NA	Intergenic	Intergenic	37325	NR_120636	101928298	Hs.385576	NR_120636	ENSG00000224788	LINC02670	-	long intergenic non-protein coding RNA 2670	ncRNA	0.010033	0.410000	
chunk0010_343_1	chr1	118516944	118517547	+	0	NA	Intergenic	L1PA6|LINE|L1	-332020	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.016584	0.513245	
chunk0146_222_1	chr4	161872324	161872822	+	0	NA	intron (NM_001128427, intron 4 of 15)	L2a|LINE|L2	-150160	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.014056	0.352705	
chunk0182_351_1	chr7	99499803	99500529	+	0	NA	promoter-TSS (NM_032164)	promoter-TSS (NM_032164)	88	NM_032164	84124	Hs.386324	NM_032164	ENSG00000160908	ZNF394	ZKSCAN14|ZSCAN46	zinc finger protein 394	protein-coding	0.082645	0.620358	
chunk0126_76_1	chr3	74643474	74644208	+	0	NA	Intergenic	Intergenic	-122701	NM_020872	5067	Hs.12723	NM_020872	ENSG00000113805	CNTN3	BIG-1|PANG|PCS	contactin 3	protein-coding	0.006812	0.428571	398(GGGAACAGGATGTTCT,-,0.00),399(GGAACAGGATGTTCTC,+,0.00),435(GGCACATCCAGTCCAG,+,0.00),696(AAGAACTTATAGTTCT,-,0.00),697(AGAACTTATAGTTCTT,+,0.00)
chunk0112_313_1	chr20	44532299	44532906	+	0	NA	intron (NM_007066, intron 1 of 3)	L2c|LINE|L2	821	NM_007066	11142	Hs.472831	NM_007066	ENSG00000168734	PKIG	PKI-gamma	cAMP-dependent protein kinase inhibitor gamma	protein-coding	0.018122	0.457237	244(AGAGACATCGTGTCCT,-,0.00),245(GAGACATCGTGTCCTG,+,0.00)
chunk0175_348_1	chr6	167493265	167493585	+	0	NA	Intergenic	Intergenic	-108915	NM_004610	6953	Hs.351	NM_004610	ENSG00000203690	TCP10	TCP10A	t-complex 10	pseudo	0.006250	0.551402	
chunk0206_420_1	chr9	127570465	127570711	+	0	NA	intron (NM_001035534, intron 1 of 13)	intron (NM_001035534, intron 1 of 13)	-1471	NM_022833	64855	Hs.522401	NM_022833	ENSG00000136830	NIBAN2	C9orf88|FAM129B|MEG-3|MINERVA|OC58|bA356B19.6	niban apoptosis regulator 2	protein-coding	0.008130	0.441296	167(CAGAACATTCTGTTTT,-,0.00),168(AGAACATTCTGTTTTA,+,0.00)
chunk0025_425_1	chr10	59904949	59905619	+	0	NA	intron (NM_005436, intron 1 of 8)	intron (NM_005436, intron 1 of 8)	1372	NM_005436	8030	Hs.591360	NM_005436	ENSG00000108091	CCDC6	D10S170|H4|PTC|TPC|TST1	coiled-coil domain containing 6	protein-coding	0.028358	0.524590	215(GAGTACACAGTGTACT,-,0.00),216(AGTACACAGTGTACTT,+,0.00)
chunk0078_81_1	chr17	1961051	1961298	+	0	NA	intron (NM_178568, intron 1 of 1)	intron (NM_178568, intron 1 of 1)	64171	NM_178568	146760	Hs.22917	NM_178568	ENSG00000185924	RTN4RL1	NGRH2|NgR3	reticulon 4 receptor like 1	protein-coding	0.024291	0.532258	
chunk0176_252_1	chr7	16210366	16210594	+	0	NA	promoter-TSS (NR_038947)	promoter-TSS (NR_038947)	-6	NR_038946	100506025	Hs.649029	NR_038946	ENSG00000229688	CRPPA-AS1	ISPD-AS1	CRPPA antisense RNA 1	ncRNA	0.008772	0.480349	
chunk0205_324_1	chr9	112822130	112822852	+	0	NA	intron (NM_001012994, intron 3 of 8)	L1MA10|LINE|L1	68422	NM_033051	57864	Hs.512668	NM_033051	ENSG00000119457	SLC46A2	Ly110|TSCOT	solute carrier family 46 member 2	protein-coding	0.011080	0.378976	
chunk0191_247_1	chr8	53204153	53204437	+	0	NA	Intergenic	Intergenic	47339	NM_000912	4986	Hs.106795	NM_000912	ENSG00000082556	OPRK1	K-OR-1|KOR|KOR-1|OPRK	opioid receptor kappa 1	protein-coding	0.014085	0.459649	
chunk0141_64_1	chr4	77834494	77834743	+	0	NA	Intergenic	Intergenic	-15228	NM_144571	246175	Hs.592519	NM_144571	ENSG00000138767	CNOT6L	CCR4b	CCR4-NOT transcription complex subunit 6 like	protein-coding	0.012048	0.388000	
chunk0145_444_1	chr4	153507256	153507653	+	0	NA	intron (NM_001131007, intron 3 of 34)	intron (NM_001131007, intron 3 of 34)	41108	NM_001131007	23240	Hs.732450	NM_015196	ENSG00000121210	TMEM131L	KIAA0922	transmembrane 131 like	protein-coding	0.017632	0.452261	252(TGGAACATCGTGTTCA,-,0.00),253(GGAACATCGTGTTCAC,+,0.00)
chunk0200_150_1	chr9	18236993	18237707	+	0	NA	Intergenic	Intergenic	-236731	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.002801	0.365035	
chunk0117_298_1	chr22	24521613	24522203	+	0	NA	intron (NM_016327, intron 7 of 9)	intron (NM_016327, intron 7 of 9)	26625	NM_016327	51733	Hs.731656	NM_016327	ENSG00000100024	UPB1	BUP1	beta-ureidopropionase 1	protein-coding	0.016949	0.538071	
chunk0065_202_1	chr14	100085173	100085582	+	0	NA	intron (NM_016337, intron 2 of 13)	intron (NM_016337, intron 2 of 13)	19963	NM_016337	51466	Hs.125867	NM_016337	ENSG00000196405	EVL	RNB6	Enah/Vasp-like	protein-coding	0.007335	0.380488	
chunk0081_94_1	chr17	39695771	39695970	+	0	NA	intron (NM_001289938, intron 4 of 17)	intron (NM_001289938, intron 4 of 17)	-4108	NM_004448	2064	Hs.446352	NM_004448	ENSG00000141736	ERBB2	CD340|HER-2|HER-2/neu|HER2|MLN 19|NEU|NGL|TKR1	erb-b2 receptor tyrosine kinase 2	protein-coding	0.015075	0.585000	
chunk0171_36_1	chr6	120556344	120556951	+	0	NA	Intergenic	LTR108e_Mam|LTR|ERVL	541468	NR_036098	100422951		NR_036098	ENSG00000265725	MIR3144	mir-3144	microRNA 3144	ncRNA	0.006590	0.399671	
chunk0099_204_1	chr2	94806915	94807191	+	0	NA	intron (NR_003366, intron 15 of 23)	intron (NR_003366, intron 15 of 23)	-45869	NR_038409	90499	Hs.458439	NR_038409		FAM95A	-	family with sequence similarity 95 member A	ncRNA	0.003623	0.375451	
chunk0146_340_1	chr4	166091340	166091972	+	0	NA	intron (NM_012464, intron 19 of 20)	intron (NM_012464, intron 19 of 20)	218398	NM_012464	7092	Hs.106513	NM_012464	ENSG00000038295	TLL1	ASD6|TLL	tolloid like 1	protein-coding	0.001582	0.289100	
chunk0128_387_1	chr3	113791566	113792176	+	0	NA	intron (NM_001690, intron 8 of 14)	intron (NM_001690, intron 8 of 14)	44852	NM_001690	523	Hs.477155	NM_001690	ENSG00000114573	ATP6V1A	ARCL2D|ATP6A1|ATP6V1A1|HO68|IECEE3|VA68|VPP2|Vma1	ATPase H+ transporting V1 subunit A	protein-coding	0.001639	0.382979	
chunk0123_250_1	chr3	45780311	45780668	+	0	NA	intron (NM_020208, intron 2 of 10)	MIRb|SINE|MIR	16054	NM_020208	54716	Hs.413095	NM_020208	ENSG00000163817	SLC6A20	SIT1|XT3|Xtrp3	solute carrier family 6 member 20	protein-coding	0.016807	0.519553	
chunk0168_372_1	chr6	93731376	93731708	+	0	NA	intron (NR_015362, intron 3 of 9)	Tigger3|DNA|TcMar-Tigger	24459	NR_015362	643432	Hs.509936	NR_015362		TSG1	-	tumor suppressor TSG1	ncRNA	0.003012	0.339339	
chunk0051_396_1	chr12	121965271	121965794	+	0	NA	intron (NM_001178003, intron 15 of 17)	L1ME3G|LINE|L1	46975	NM_001178003	144406	Hs.709837	NM_144668	ENSG00000158023	WDR66	CFAP251|CaM-IP4|SPGF33	WD repeat domain 66	protein-coding	0.011472	0.353053	
chunk0021_216_1	chr10	6110168	6110884	+	0	NA	intron (NM_032905, intron 7 of 11)	intron (NM_032905, intron 7 of 11)	21180	NM_001145547	84991	Hs.498548	NM_032905	ENSG00000134453	RBM17	SPF45	RNA binding motif protein 17	protein-coding	0.013966	0.444909	
chunk0212_22_1	chrY	10006964	10007343	+	0	NA	Intergenic	L2a|LINE|L2	96355	NR_001540	252955	Hs.522846	NR_001540	ENSG00000239225	TTTY23	NCRNA00148|TTTY23B	testis-specific transcript, Y-linked 23	ncRNA	0.000000	0.347368	253(CAGTACACAATGTTCT,-,0.00),254(AGTACACAATGTTCTT,+,0.00)
chunk0039_145_1	chr11	98633677	98633915	+	0	NA	Intergenic	Intergenic	-387180	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.012605	0.410042	
chunk0105_252_1	chr2	188850355	188850796	+	0	NA	Intergenic	Intergenic	-60471	NM_052952	116093	Hs.470892	NM_052952	ENSG00000174325	DIRC1	-	disrupted in renal carcinoma 1	ncRNA	0.004535	0.386878	
chunk0198_169_1	chr8	133249856	133250260	+	0	NA	intron (NM_006096, intron 10 of 15)	intron (NM_006096, intron 10 of 15)	47246	NM_001258432	10397	Hs.372914	NM_006096	ENSG00000104419	NDRG1	CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5	N-myc downstream regulated 1	protein-coding	0.027228	0.560494	
chunk0022_420_1	chr10	18795623	18795854	+	0	NA	Intergenic	L1PA16|LINE|L1	136354	NM_178815	221079	Hs.25362	NM_178815	ENSG00000165997	ARL5B	ARL8	ADP ribosylation factor like GTPase 5B	protein-coding	0.012987	0.577586	
chunk0138_295_1	chr4	41008949	41009270	+	0	NA	intron (NM_004307, intron 6 of 17)	intron (NM_004307, intron 6 of 17)	-151917	NM_001166053	323	Hs.479602	NM_004307	ENSG00000163697	APBB2	FE65L|FE65L1	amyloid beta precursor protein binding family B member 2	protein-coding	0.003115	0.354037	
chunk0024_115_1	chr10	34728974	34729173	+	0	NA	intron (NM_019619, intron 1 of 24)	Tigger3a|DNA|TcMar-Tigger	86252	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.010050	0.475000	
chunk0116_271_1	chr21	39204367	39204566	+	0	NA	intron (NM_018963, intron 37 of 41)	intron (NM_018963, intron 37 of 41)	-20952	NM_003720	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.000000	0.245000	
chunk0168_234_1	chr6	87571808	87572305	+	0	NA	intron (NM_020320, intron 1 of 19)	intron (NM_020320, intron 1 of 19)	17961	NM_020320	57038	Hs.485910	NM_020320	ENSG00000146282	RARS2	ArgRS|DALRD2|PCH6|PRO1992|RARSL	arginyl-tRNA synthetase 2, mitochondrial	protein-coding	0.008048	0.299197	
chunk0002_114_1	chr1	16068578	16069179	+	0	NA	intron (NM_182623, intron 1 of 6)	intron (NM_182623, intron 1 of 6)	4754	NM_182623	348487	Hs.126825	NM_182623	ENSG00000185519	FAM131C	C1orf117	family with sequence similarity 131 member C	protein-coding	0.009983	0.541528	20(GTGGACTGAGTGTCCC,-,0.00),21(TGGACTGAGTGTCCCC,+,0.00),247(GGGAACATCTTGCTCC,-,0.00),401(AGGTACTGTCTGTCCT,-,0.00),402(GGTACTGTCTGTCCTA,+,0.00)
chunk0202_236_1	chr9	76545063	76545608	+	0	NA	Intergenic	MER57B2|LTR|ERV1	44702	NM_001097636	2650	Hs.521568	NM_001490	ENSG00000187210	GCNT1	C2GNT|C2GNT-L|C2GNT1|G6NT|NACGT2|NAGCT2	glucosaminyl (N-acetyl) transferase 1	protein-coding	0.003670	0.390110	
chunk0186_33_1	chr7	136027260	136027577	+	0	NA	Intergenic	L2c|LINE|L2	-49962	NM_001128619	767558	Hs.602015	NM_001128619	ENSG00000267697	LUZP6	MPD6|MTPNUT	leucine zipper protein 6	protein-coding	0.006309	0.443396	
chunk0100_144_1	chr2	108904613	108905139	+	0	NA	intron (NM_022336, intron 11 of 11)	L1MD1|LINE|L1	84496	NM_022336	10913	Hs.171971	NM_022336	ENSG00000135960	EDAR	DL|ECTD10A|ECTD10B|ED1R|ED3|ED5|EDA-A1R|EDA1R|EDA3|HRM1	ectodysplasin A receptor	protein-coding	0.005703	0.417457	
chunk0106_348_1	chr2	206774137	206774841	+	0	NA	intron (NM_014929, intron 7 of 11)	L1ME3A|LINE|L1	-8745	NR_036078	100423002		NR_036078	ENSG00000263468	MIR3130-2	MIR3130-4|mir-3130-2	microRNA 3130-2	ncRNA	0.002841	0.280851	383(TAAAACATAGTGTTCC,-,0.00),384(AAAACATAGTGTTCCT,+,0.00)
chunk0164_154_1	chr6	21513574	21514477	+	0	NA	Intergenic	Intergenic	-2133	NR_103790	100874531	Hs.112750	NR_103790	ENSG00000280989	LINC00581	linc-MBOAT1-4	long intergenic non-protein coding RNA 581	ncRNA	0.004430	0.357301	
chunk0111_447_1	chr20	35348023	35348273	+	0	NA	intron (NM_018244, intron 6 of 9)	L2a|LINE|L2	-55726	NM_178468	128876	Hs.592149	NM_178468	ENSG00000125998	FAM83C	C20orf128|dJ614O4.7	family with sequence similarity 83 member C	protein-coding	0.000000	0.374502	
chunk0020_408_1	chr1	241369423	241369622	+	0	NA	Intergenic	Intergenic	-12292	NM_001282773	6000	Hs.655739	NM_002924	ENSG00000182901	RGS7	-	regulator of G protein signaling 7	protein-coding	0.005025	0.485000	
chunk0114_303_1	chr21	17049546	17049758	+	0	NA	Intergenic	LTR27E|LTR|ERV1	-389238	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.000000	0.483568	
chunk0193_137_1	chr8	74480444	74481060	+	0	NA	Intergenic	Intergenic	-67791	NR_049860	100847058		NR_049860	ENSG00000266502	MIR5681A	-	microRNA 5681a	ncRNA	0.001623	0.353323	
chunk0050_93_1	chr12	101848424	101848712	+	0	NA	Intergenic	L2a|LINE|L2	-17701	NM_024312	79158	Hs.46850	NM_024312	ENSG00000111670	GNPTAB	GNPTA|ICD	N-acetylglucosamine-1-phosphate transferase subunits alpha and beta	protein-coding	0.020833	0.380623	
chunk0052_33_1	chr13	20593186	20593395	+	0	NA	intron (NM_006531, intron 7 of 25)	MIR|SINE|MIR	26221	NM_006531	8100	Hs.187376	NM_006531	ENSG00000032742	IFT88	D13S1056E|DAF19|TG737|TTC10|hTg737	intraflagellar transport 88	protein-coding	0.000000	0.357143	
chunk0019_404_1	chr1	230643981	230644562	+	0	NA	intron (NM_001145036, intron 1 of 17)	intron (NM_001145036, intron 1 of 17)	1815	NM_007357	22796	Hs.211800	NM_007357	ENSG00000135775	COG2	CDG2Q|LDLC	component of oligomeric golgi complex 2	protein-coding	0.005164	0.379725	
chunk0132_25_1	chr3	154589139	154589449	+	0	NA	Intergenic	Intergenic	-159579	NM_001038705	344758	Hs.376338	NM_001038705	ENSG00000174948	GPR149	IEDA|PGR10|R35	G protein-coupled receptor 149	protein-coding	0.006452	0.379421	
chunk0019_259_1	chr1	227891504	227892318	+	0	NA	Intergenic	Intergenic	49772	NR_049806	100847072		NR_049806	ENSG00000264483	MIR5008	-	microRNA 5008	ncRNA	0.014742	0.573006	
chunk0175_216_1	chr7	6126956	6127155	+	0	NA	intron (NM_032172, intron 3 of 17)	L1MDa|LINE|L1	22136	NM_032172	84132	Hs.31856	NM_032172	ENSG00000106346	USP42	-	ubiquitin specific peptidase 42	protein-coding	0.005025	0.395000	
chunk0185_266_1	chr7	130497514	130497842	+	0	NA	intron (NM_001253901, intron 3 of 10)	intron (NM_001253901, intron 3 of 10)	1567	NR_029899	442904		NR_029899	ENSG00000199043	MIR335	MIRN335|hsa-mir-335|miRNA335|mir-335	microRNA 335	ncRNA	0.006098	0.379939	
chunk0085_73_1	chr18	1560129	1560441	+	0	NA	Intergenic	L1PA17|LINE|L1	-200656	NR_023926	56651	Hs.541165	NM_031416		LINC00470	C18orf2	long intergenic non-protein coding RNA 470	ncRNA	0.009615	0.568690	
chunk0122_134_1	chr3	31699632	31699906	+	0	NA	intron (NM_017784, intron 7 of 11)	intron (NM_017784, intron 7 of 11)	-4444	NR_049771	100874206	Hs.662428	NR_049771	ENSG00000232490	OSBPL10-AS1	-	OSBPL10 antisense RNA 1	ncRNA	0.010949	0.501818	
chunk0137_10_1	chr4	10656933	10657339	+	0	NA	intron (NM_052964, intron 2 of 18)	MIR|SINE|MIR	27626	NM_052964	116449	Hs.62772	NM_052964	ENSG00000109684	CLNK	MIST	cytokine dependent hematopoietic cell linker	protein-coding	0.004926	0.334152	
chunk0185_277_1	chr7	130918066	130918737	+	0	NA	intron (NR_109780, intron 3 of 3)	intron (NR_109780, intron 3 of 3)	4937	NR_109780	100506860	Hs.635013	NR_109780		LINC00513	-	long intergenic non-protein coding RNA 513	ncRNA	0.017884	0.422619	
chunk0036_117_1	chr11	61601478	61602185	+	0	NA	intron (NR_110189, intron 2 of 3)	intron (NR_110189, intron 2 of 3)	-13205	NR_002775	113157	Hs.502733	NR_002775	ENSG00000243742	RPLP0P2	RPLP0L2|RPLP0_3_1146	ribosomal protein lateral stalk subunit P0 pseudogene 2	pseudo	0.009901	0.573446	
chunk0156_40_1	chr5	102718787	102719258	+	0	NA	Intergenic	Intergenic	-47558	NR_103756	285708	Hs.533011	NR_103753		LINC00491	-	long intergenic non-protein coding RNA 491	ncRNA	0.008493	0.338983	
chunk0164_58_1	chr6	19287972	19288285	+	0	NA	Intergenic	MIRb|SINE|MIR	-107648	NR_110860	101928519	Hs.551771	NR_110860		LOC101928519	-	uncharacterized LOC101928519	ncRNA	0.003195	0.337580	
chunk0082_40_1	chr17	50915235	50915529	+	0	NA	Intergenic	Intergenic	-47404	NM_001243877	10140	Hs.703321	NM_005749	ENSG00000141232	TOB1	APRO5|APRO6|PIG49|TOB|TROB|TROB1	transducer of ERBB2, 1	protein-coding	0.010204	0.572881	
chunk0165_375_1	chr6	38309988	38310459	+	0	NA	intron (NM_001099272, intron 7 of 10)	intron (NM_001099272, intron 7 of 10)	285844	NM_001172418	114781	Hs.603858	NM_052893	ENSG00000183826	BTBD9	dJ322I12.1	BTB domain containing 9	protein-coding	0.010616	0.451271	229(GGGAACAACTTGTCCC,-,0.00),230(GGAACAACTTGTCCCA,+,0.00),248(GGGCACTCTCAGTTCT,-,0.00),249(GGCACTCTCAGTTCTA,+,0.00)
chunk0203_81_1	chr9	83934455	83935017	+	0	NA	Intergenic	MER92C|LTR|ERV1	-13271	NM_001271927	55582	Hs.697514	NM_017576	ENSG00000165115	KIF27	-	kinesin family member 27	protein-coding	0.003559	0.415631	270(AGAACTCTTTGTCCAC,+,0.00)
chunk0095_97_1	chr2	15246271	15246800	+	0	NA	intron (NR_052013, intron 44 of 50)	intron (NR_052013, intron 44 of 50)	314813	NR_052013	51594	Hs.467759	NM_015909	ENSG00000151779	NBAS	ILFS2|NAG|SOPH	neuroblastoma amplified sequence	protein-coding	0.007561	0.388679	
chunk0014_265_1	chr1	180229228	180229827	+	0	NA	promoter-TSS (NM_033343)	promoter-TSS (NM_033343)	-771	NM_033343	89884	Hs.658487	NM_033343	ENSG00000121454	LHX4	CPHD4	LIM homeobox 4	protein-coding	0.121870	0.741667	295(GAGTACGGGCTGTCCC,-,0.00),296(AGTACGGGCTGTCCCT,+,0.00)
chunk0001_76_1	chr1	2535063	2535329	+	0	NA	Intergenic	MIRb|SINE|MIR	-4951	NM_001010926	388585	Hs.57971	NM_001010926	ENSG00000197921	HES5	bHLHb38	hes family bHLH transcription factor 5	protein-coding	0.015038	0.509363	
chunk0182_223_1	chr7	96407954	96408170	+	0	NA	Intergenic	Intergenic	-85915	NM_001160210	10165	Hs.489190	NM_014251	ENSG00000004864	SLC25A13	ARALAR2|CITRIN|CTLN2	solute carrier family 25 member 13	protein-coding	0.009259	0.317972	185(GAGTACATCCAGTGCT,-,0.00),186(AGTACATCCAGTGCTG,+,0.00)
chunk0165_246_1	chr6	35640137	35640541	+	0	NA	intron (NM_001145777, intron 2 of 6)	Tigger3b|DNA|TcMar-Tigger	24450	NR_049873	100847048		NR_049873	ENSG00000265527	MIR5690	-	microRNA 5690	ncRNA	0.009901	0.404938	
chunk0171_100_1	chr6	122098078	122098583	+	0	NA	Intergenic	Intergenic	-301221	NM_001243094	3298	Hs.158195	NM_004506	ENSG00000025156	HSF2	HSF 2|HSTF 2	heat shock transcription factor 2	protein-coding	0.007921	0.330040	
chunk0196_290_1	chr8	109575616	109575841	+	0	NA	exon (NM_001099748, exon 8 of 8)	exon (NM_001099748, exon 8 of 8)	35102	NM_001278938	9166	Hs.409368	NM_004215	ENSG00000147654	EBAG9	EB9|PDAF	estrogen receptor binding site associated antigen 9	protein-coding	0.008889	0.504425	113(AGGCACAGTTCGTCCC,-,0.00),114(GGCACAGTTCGTCCCT,+,0.00)
chunk0077_83_1	chr16	77358881	77359563	+	0	NA	intron (NM_199355, intron 8 of 22)	intron (NM_199355, intron 8 of 22)	75892	NM_199355	170692	Hs.188746	NM_139054	ENSG00000140873	ADAMTS18	ADAMTS21|KNO2|MMCAT	ADAM metallopeptidase with thrombospondin type 1 motif 18	protein-coding	0.005865	0.383602	
chunk0011_177_1	chr1	148332205	148332631	+	0	NA	Intergenic	LTR8|LTR|ERV1	2136	NR_049810	100847044		NR_049810	ENSG00000283676	MIR5087	-	microRNA 5087	ncRNA	0.000000	0.423888	
chunk0013_411_1	chr1	173095305	173095832	+	0	NA	Intergenic	Intergenic	-44605	NM_005092	8995	Hs.248197	NM_005092	ENSG00000120337	TNFSF18	AITRL|GITRL|TL6|TNLG2A|hGITRL	TNF superfamily member 18	protein-coding	0.005693	0.403409	
chunk0135_292_1	chr3	189517876	189518075	+	0	NA	Intergenic	L1M2a1|LINE|L1	-113452	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.000000	0.525000	
chunk0098_288_1	chr2	75807702	75807978	+	0	NA	Intergenic	L2b|LINE|L2	-96855	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.021739	0.498195	
chunk0061_128_1	chr14	59038958	59039157	+	0	NA	Intergenic	Intergenic	-149606	NM_001270520	23002	Hs.19156	NM_014992	ENSG00000100592	DAAM1	-	dishevelled associated activator of morphogenesis 1	protein-coding	0.005025	0.445000	
chunk0085_12_1	chr18	249773	250101	+	0	NA	intron (NM_005131, intron 9 of 20)	L4_C_Mam|LINE|RTE-X	18122	NM_005131	9984	Hs.712543	NM_005131	ENSG00000079134	THOC1	HPR1|P84|P84N5	THO complex 1	protein-coding	0.000000	0.325228	
chunk0044_181_1	chr12	30202678	30203180	+	0	NA	Intergenic	Intergenic	-418170	NM_175861	83857	Hs.401954	NM_031920	ENSG00000133687	TMTC1	ARG99|OLF|TMTC1A	transmembrane O-mannosyltransferase targeting cadherins 1	protein-coding	0.007968	0.413519	
chunk0043_285_1	chr12	21350888	21351477	+	0	NA	intron (NM_134431, intron 2 of 15)	intron (NM_134431, intron 2 of 15)	-16284	NM_021094	6579	Hs.46440	NM_005075	ENSG00000084453	SLCO1A2	OATP|OATP-A|OATP1A2|SLC21A3	solute carrier organic anion transporter family member 1A2	protein-coding	0.003396	0.354237	
chunk0192_48_1	chr8	58879566	58879806	+	0	NA	intron (NM_014729, intron 3 of 8)	intron (NM_014729, intron 3 of 8)	-219841	NM_003580	8439	Hs.372000	NM_003580	ENSG00000035681	NSMAF	FAN|GRAMD5	neutral sphingomyelinase activation associated factor	protein-coding	0.008333	0.385892	
chunk0007_169_1	chr1	80229275	80229698	+	0	NA	Intergenic	Intergenic	-306269	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.004728	0.266509	
chunk0054_430_1	chr13	51189195	51189394	+	0	NA	Intergenic	Intergenic	-16906	NR_102431	647166	Hs.195052	NM_001351589	ENSG00000226792	C13orf42	LINC00371|LINC00372	chromosome 13 open reading frame 42	protein-coding	0.015075	0.415000	
chunk0072_10_1	chr16	383433	383754	+	0	NA	intron (NR_024453, intron 2 of 2)	L1ME4b|LINE|L1	1352	NR_024453	100134368	Hs.621241	NR_024453	ENSG00000236829	LOC100134368	-	uncharacterized LOC100134368	ncRNA	0.046729	0.515528	203(AAGAACGGTGTGTTCA,-,0.00),204(AGAACGGTGTGTTCAA,+,0.00)
chunk0010_329_1	chr1	118304912	118305264	+	0	NA	Intergenic	Intergenic	-119863	NM_206996	200162	Hs.528821	NM_206996	ENSG00000155761	SPAG17	CT143|PF6	sperm associated antigen 17	protein-coding	0.008523	0.405099	199(AGGCACAGTCAGTTCT,-,0.00),200(GGCACAGTCAGTTCTC,+,0.00)
chunk0110_312_1	chr20	18507799	18508010	+	0	NA	promoter-TSS (NM_001172745)	promoter-TSS (NM_001172745)	-59	NM_001172745	10483	Hs.369373	NM_006363	ENSG00000101310	SEC23B	CDA-II|CDAII|CDAN2|CWS7|HEMPAS|hSec23B	SEC23 homolog B, coat complex II component	protein-coding	0.080569	0.655660	
chunk0029_204_1	chr10	101818325	101818835	+	0	NA	promoter-TSS (NR_045118)	promoter-TSS (NR_045118)	-115	NM_001142434	10724	Hs.500842	NM_012215	ENSG00000198408	OGA	MEA5|MGEA5|NCOAT	O-GlcNAcase	protein-coding	0.056863	0.579256	
chunk0043_123_1	chr12	15650952	15651151	+	0	NA	intron (NM_004447, intron 13 of 20)	intron (NM_004447, intron 13 of 20)	104707	NM_030668	5800	Hs.160871	NM_002848	ENSG00000151490	PTPRO	GLEPP1|NPHS6|PTP-OC|PTP-U2|PTPROT|PTPU2|R-PTP-O	protein tyrosine phosphatase receptor type O	protein-coding	0.015075	0.395000	
chunk0117_239_1	chr22	23098632	23099209	+	0	NA	intron (NM_002073, intron 2 of 2)	intron (NM_002073, intron 2 of 2)	28437	NM_002073	2781	Hs.584760	NM_002073	ENSG00000128266	GNAZ	gz-alpha	G protein subunit alpha z	protein-coding	0.036395	0.603806	
chunk0175_203_1	chr7	5999092	5999609	+	0	NA	intron (NR_003085, intron 5 of 14)	intron (NR_003085, intron 5 of 14)	9756	NR_003085									0.013540	0.453668	429(AAGTACAGCCTGTAAT,-,0.00)
chunk0010_208_1	chr1	116151144	116151401	+	0	NA	Intergenic	(AC)n|Simple_repeat|Simple_repeat	39517	NM_152367	126868	Hs.376194	NM_152367	ENSG00000173212	MAB21L3	C1orf161	mab-21 like 3	protein-coding	0.007782	0.496124	
chunk0045_45_1	chr12	44961917	44962499	+	0	NA	Intergenic	L1PA15|LINE|L1	-48280	NM_001145110	4753	Hs.505326	NM_006159	ENSG00000184613	NELL2	NRP2	neural EGFL like 2	protein-coding	0.005155	0.368782	
chunk0012_342_1	chr1	162587287	162587602	+	0	NA	intron (NM_003115, intron 5 of 9)	intron (NM_003115, intron 5 of 9)	25938	NM_003115	6675	Hs.492859	NM_003115	ENSG00000117143	UAP1	AGX|AGX1|AGX2|SPAG2	UDP-N-acetylglucosamine pyrophosphorylase 1	protein-coding	0.015873	0.398734	
chunk0057_167_1	chr13	101618495	101618706	+	0	NA	intron (NM_001271754, intron 6 of 10)	intron (NM_001271754, intron 6 of 10)	128648	NM_001271756	9358	Hs.696554	NM_004791	ENSG00000198542	ITGBL1	OSCP|TIED	integrin subunit beta like 1	protein-coding	0.018957	0.438679	
chunk0057_176_1	chr13	102466756	102467286	+	0	NA	Intergenic	L1MEg2|LINE|L1	-65247	NM_175929	2259	Hs.508616	NM_004115	ENSG00000102466	FGF14	FGF-14|FHF-4|FHF4|SCA27	fibroblast growth factor 14	protein-coding	0.005660	0.410546	239(AGGGACATGGTGTGCC,-,0.00),240(GGGACATGGTGTGCCT,+,0.00)
chunk0013_161_1	chr1	168710162	168710362	+	0	NA	intron (NM_001937, intron 2 of 3)	intron (NM_001937, intron 2 of 3)	18942	NM_001937	1805	Hs.80552	NM_001937	ENSG00000143196	DPT	TRAMP	dermatopontin	protein-coding	0.010000	0.432836	
chunk0088_312_1	chr18	50619775	50620747	+	0	NA	intron (NM_001292039, intron 1 of 4)	MIRc|SINE|MIR	60147	NM_001292040	5596	Hs.433728	NM_002747	ENSG00000141639	MAPK4	ERK-4|ERK4|PRKM4|p63-MAPK|p63MAPK	mitogen-activated protein kinase 4	protein-coding	0.007202	0.445015	
chunk0122_57_1	chr3	28788418	28789153	+	0	NA	Intergenic	Intergenic	213507	NR_038840	645206	Hs.376725	NR_038840		LINC00693	-	long intergenic non-protein coding RNA 693	ncRNA	0.006803	0.384511	
chunk0105_384_1	chr2	192389317	192390057	+	0	NA	Intergenic	Intergenic	-194754	NM_016192	23671	Hs.144513	NM_016192	ENSG00000144339	TMEFF2	CT120.2|HPP1|TENB2|TPEF|TR|TR-2	transmembrane protein with EGF like and two follistatin like domains 2	protein-coding	0.002703	0.295547	
chunk0092_105_1	chr19	23391356	23391607	+	0	NA	intron (NM_001300951, intron 1 of 2)	MER92B|LTR|ERV1	4079	NM_003430	7644	Hs.58834	NM_003430	ENSG00000167232	ZNF91	HPF7|HTF10	zinc finger protein 91	protein-coding	0.000000	0.349206	
chunk0011_416_1	chr1	154418152	154418766	+	0	NA	intron (NM_181359, intron 1 of 8)	intron (NM_181359, intron 1 of 8)	13266	NM_000565	3570	Hs.135087	NM_000565	ENSG00000160712	IL6R	CD126|IL-6R-1|IL-6RA|IL6Q|IL6RA|IL6RQ|gp80	interleukin 6 receptor	protein-coding	0.017915	0.534959	
chunk0160_10_1	chr5	148978963	148979324	+	0	NA	Intergenic	L2c|LINE|L2	83266	NR_030310	693169		NR_030310	ENSG00000207714	MIR584	MIRN584|hsa-mir-584	microRNA 584	ncRNA	0.013850	0.577348	159(GAGAACAGTTTGTACA,-,0.00),160(AGAACAGTTTGTACAG,+,0.00)
chunk0001_290_1	chr1	8818548	8818748	+	0	NA	Intergenic	Intergenic	-1008	NM_001042681	473	Hs.463041	NM_012102	ENSG00000142599	RERE	ARG|ARP|ATN1L|DNB1|NEDBEH	arginine-glutamic acid dipeptide repeats	protein-coding	0.005000	0.358209	
chunk0075_42_1	chr16	47309870	47310390	+	0	NA	intron (NM_030790, intron 10 of 17)	intron (NM_030790, intron 10 of 17)	151144	NM_030790	81533	Hs.42217	NM_030790	ENSG00000129636	ITFG1	2310047C21Rik|CDA08|LNKN-1|TIP	integrin alpha FG-GAP repeat containing 1	protein-coding	0.009615	0.333973	
chunk0024_32_1	chr10	33287170	33287461	+	0	NA	intron (NM_001244972, intron 2 of 16)	intron (NM_001244972, intron 2 of 16)	47590	NM_001244973	8829	Hs.131704	NM_003873	ENSG00000099250	NRP1	BDCA4|CD304|NP1|NRP|VEGF165R	neuropilin 1	protein-coding	0.006873	0.318493	112(AAACACAGGCTGTGCA,-,0.00)
chunk0073_153_1	chr16	6957717	6958094	+	0	NA	intron (NM_001142334, intron 1 of 13)	MLT1F|LTR|ERVL-MaLR	184096	NM_001142334	54715	Hs.459842	NM_018723	ENSG00000078328	RBFOX1	2BP1|A2BP1|FOX-1|FOX1|HRNBP1	RNA binding fox-1 homolog 1	protein-coding	0.010610	0.513228	
chunk0188_208_1	chr8	12721060	12721290	+	0	NA	TTS (NM_152271)	TTS (NM_152271)	2043	NR_049876	100847038		NR_049876	ENSG00000264512	MIR5692A2	-	microRNA 5692a-2	ncRNA	0.021739	0.627706	
chunk0181_400_1	chr7	89960003	89960609	+	0	NA	intron (NR_110029, intron 2 of 2)	Tigger3a|DNA|TcMar-Tigger	-159094	NR_003551	442523	Hs.406964	NR_003551	ENSG00000235436	DPY19L2P4	-	DPY19L2 pseudogene 4	pseudo	0.006601	0.345964	310(CAGTACAGAATGTGCT,-,0.00),311(AGTACAGAATGTGCTG,+,0.00),346(AGAAACAGGCTGTACC,-,0.00),347(GAAACAGGCTGTACCA,+,0.00)
chunk0113_450_1	chr20	62847931	62848273	+	0	NA	intron (NM_006602, intron 5 of 5)	intron (NM_006602, intron 5 of 5)	3536	NM_080750	100132911		NM_080750		DPH3P1	C20orf143|DPH3B|ZCSL1	diphthamide biosynthesis 3 pseudogene 1	protein-coding	0.040936	0.615160	
chunk0200_237_1	chr9	20817755	20818075	+	0	NA	intron (NM_017794, intron 13 of 45)	L1MB7|LINE|L1	101810	NR_030166	574444		NR_030166	ENSG00000207609	MIR491	MIRN491|hsa-mir-491|mir-491	microRNA 491	ncRNA	0.006250	0.320872	
chunk0047_447_1	chr12	76520176	76520637	+	0	NA	intron (NM_001003712, intron 1 of 22)	intron (NM_001003712, intron 1 of 22)	39403	NM_001003712	114882	Hs.430849	NM_020841	ENSG00000091039	OSBPL8	MST120|MSTP120|ORP8|OSBP10	oxysterol binding protein like 8	protein-coding	0.004338	0.370130	
chunk0078_362_1	chr16	87358154	87358687	+	0	NA	intron (NM_024735, intron 2 of 8)	intron (NM_024735, intron 2 of 8)	25373	NM_024735	79791	Hs.567582	NM_024735	ENSG00000103264	FBXO31	FBX14|FBXO14|Fbx31|MRT45|pp2386	F-box protein 31	protein-coding	0.035647	0.535581	
chunk0103_231_1	chr2	164643135	164643686	+	0	NA	Intergenic	L2a|LINE|L2	-21560	NM_004490	2888	Hs.411881	NM_004490	ENSG00000115290	GRB14	-	growth factor receptor bound protein 14	protein-coding	0.009074	0.472826	
chunk0096_236_1	chr2	30872742	30873240	+	0	NA	Intergenic	L2a|LINE|L2	-65546	NM_144575	92291	Hs.660911	NM_144575	ENSG00000162949	CAPN13	-	calpain 13	protein-coding	0.004016	0.474950	
chunk0194_448_1	chr8	92571540	92571794	+	0	NA	intron (NR_125827, intron 3 of 4)	intron (NR_125827, intron 3 of 4)	83827	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.000000	0.411765	
chunk0012_220_1	chr1	160194167	160194366	+	0	NA	intron (NM_001231, intron 3 of 10)	(CA)n|Simple_repeat|Simple_repeat	3771	NM_001231	844	Hs.632476	NM_001231	ENSG00000143318	CASQ1	CASQ|PDIB1|VMCQA	calsequestrin 1	protein-coding	0.010050	0.490000	
chunk0157_446_1	chr5	124922452	124922860	+	0	NA	Intergenic	Intergenic	-114175	NR_109882	101927421	Hs.121305	NR_109882		LOC101927421	-	uncharacterized LOC101927421	ncRNA	0.014706	0.413203	
chunk0198_419_1	chr8	142909115	142909340	+	0	NA	Intergenic	L1PB|LINE|L1	8616	NM_000498	1585	Hs.632054	NM_000498	ENSG00000179142	CYP11B2	ALDOS|CPN2|CYP11B|CYP11BL|CYPXIB2|P-450C18|P450C18|P450aldo	cytochrome P450 family 11 subfamily B member 2	protein-coding	0.000000	0.380531	
chunk0136_146_1	chr4	4541829	4542240	+	0	NA	promoter-TSS (NM_016930)	promoter-TSS (NM_016930)	14	NM_016930	53407	Hs.584913	NM_016930	ENSG00000168818	STX18	Ufe1	syntaxin 18	protein-coding	0.126521	0.703883	17(CGGAACAGCTCGTCCC,-,0.00),18(GGAACAGCTCGTCCCG,+,0.00)
chunk0047_22_1	chr12	65648944	65649637	+	0	NA	Intergenic	Intergenic	-6918	NR_120433	100507065	Hs.591038	NR_120431		LOC100507065	-	uncharacterized LOC100507065	ncRNA	0.005772	0.380403	
chunk0133_216_1	chr3	171045273	171045866	+	0	NA	Intergenic	Intergenic	-18590	NM_001278658	6514	Hs.167584	NM_000340	ENSG00000163581	SLC2A2	GLUT2	solute carrier family 2 member 2	protein-coding	0.010118	0.436027	
chunk0151_330_1	chr5	53777868	53778126	+	0	NA	Intergenic	Intergenic	173602	NR_030307	693166		NR_030307	ENSG00000207627	MIR581	MIRN581|hsa-mir-581	microRNA 581	ncRNA	0.007752	0.486486	
chunk0075_247_1	chr16	53164138	53164394	+	0	NA	intron (NM_001308319, intron 1 of 37)	intron (NM_001308319, intron 1 of 37)	8340	NM_001308319	80205	Hs.59159	NM_015287	ENSG00000177200	CHD9	AD013|CHD-9|CReMM|KISH2|PRIC320	chromodomain helicase DNA binding protein 9	protein-coding	0.003906	0.420233	
chunk0049_187_1	chr12	92797415	92798048	+	0	NA	intron (NM_003566, intron 21 of 28)	intron (NM_003566, intron 21 of 28)	61242	NM_001004330	440107	Hs.591013	NM_001004330	ENSG00000187510	PLEKHG7	-	pleckstrin homology and RhoGEF domain containing G7	protein-coding	0.003160	0.282334	599(AGGAACTCATTGTGCT,-,0.00),600(GGAACTCATTGTGCTC,+,0.00)
chunk0026_141_1	chr10	62205385	62205584	+	0	NA	intron (NM_145307, intron 9 of 11)	intron (NM_145307, intron 9 of 11)	63379	NM_001282941	219790	Hs.58559	NM_145307	ENSG00000182010	RTKN2	PLEKHK1|bA531F24.1	rhotekin 2	protein-coding	0.015075	0.285000	
chunk0038_324_1	chr11	91946511	91947047	+	0	NA	Intergenic	Intergenic	-405317	NM_001008781	120114	Hs.98523	NM_001008781	ENSG00000165323	FAT3	CDHF15|CDHR10|hFat3	FAT atypical cadherin 3	protein-coding	0.000000	0.361266	213(TAAGACAGATTGTTCC,-,0.00),214(AAGACAGATTGTTCCC,+,0.00)
chunk0203_373_1	chr9	90128745	90129383	+	0	NA	Intergenic	Intergenic	-87565	NR_038882	286370	Hs.407589	NR_038882	ENSG00000227555	MIR4290HG	-	MIR4290 host gene	ncRNA	0.010972	0.431925	
chunk0166_192_1	chr6	46284888	46285162	+	0	NA	intron (NR_125838, intron 1 of 3)	intron (NR_125838, intron 1 of 3)	8701	NR_125838	101926915	Hs.575377	NR_125838		LOC101926915	-	uncharacterized LOC101926915	ncRNA	0.003650	0.327273	
chunk0009_278_1	chr1	107529254	107529805	+	0	NA	Intergenic	Intergenic	158975	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.009074	0.373188	
chunk0154_124_1	chr5	78901464	78901849	+	0	NA	intron (NM_198709, intron 5 of 7)	L1MC|LINE|L1	84287	NM_198709	411	Hs.149103	NM_000046	ENSG00000113273	ARSB	ASB|G4S|MPS6	arylsulfatase B	protein-coding	0.002597	0.303109	
chunk0095_36_1	chr2	13430858	13431172	+	0	NA	Intergenic	Intergenic	-424002	NR_038434	100506474	Hs.242196	NR_038434	ENSG00000225649	LOC100506474	-	uncharacterized LOC100506474	ncRNA	0.009554	0.361905	
chunk0019_341_1	chr1	229336336	229336869	+	0	NA	intron (NM_145257, intron 2 of 3)	HAL1|LINE|L1	6339	NM_145257	126731	Hs.585011	NM_145257	ENSG00000154429	CCSAP	C1orf96|CSAP	centriole, cilia and spindle associated protein	protein-coding	0.005629	0.453184	518(AAGAACATTATGGACC,-,0.00)
chunk0179_85_1	chr7	44471424	44471766	+	0	NA	intron (NM_015332, intron 2 of 5)	intron (NM_015332, intron 2 of 5)	19191	NM_015332	23386	Hs.488171	NM_015332	ENSG00000015676	NUDCD3	NudCL	NudC domain containing 3	protein-coding	0.000000	0.475219	
chunk0021_203_1	chr10	5885784	5886162	+	0	NA	intron (NM_019046, intron 2 of 7)	Tigger19a|DNA|TcMar-Tigger	-3599	NM_001258452	84893	Hs.498543	NM_032807	ENSG00000134452	FBH1	FBXO18|Fbx18|hFBH1	F-box DNA helicase 1	protein-coding	0.013228	0.382586	
chunk0140_33_1	chr4	66115369	66115574	+	0	NA	Intergenic	L1PA8|LINE|L1	-161353	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.000000	0.373786	
chunk0114_316_1	chr21	17251706	17252286	+	0	NA	Intergenic	MIRc|SINE|MIR	-186894	NR_037585	100505929	Hs.46707	NM_001005521	ENSG00000232560	LINC01549	C21orf37	long intergenic non-protein coding RNA 1549	ncRNA	0.003448	0.313253	
chunk0210_446_1	chrX	105945271	105945538	+	0	NA	intron (NM_198465, intron 24 of 28)	intron (NM_198465, intron 24 of 28)	93323	NM_000354	6906	Hs.76838	NM_000354	ENSG00000123561	SERPINA7	TBG|TBGQTL	serpin family A member 7	protein-coding	0.007491	0.365672	
chunk0048_271_1	chr12	82345893	82346389	+	0	NA	Intergenic	Intergenic	12279	NM_014167	29080	Hs.582627	NM_014167	ENSG00000133773	CCDC59	BR22|HSPC128|TAP26	coiled-coil domain containing 59	protein-coding	0.002016	0.360161	
chunk0149_82_1	chr5	17305378	17306567	+	0	NA	Intergenic	Intergenic	81338	NR_033975	401177	Hs.508311	NR_033975	ENSG00000250822	LINC02111	-	long intergenic non-protein coding RNA 2111	ncRNA	0.013457	0.420168	
chunk0094_178_1	chr2	5782174	5782566	+	0	NA	Intergenic	Tigger3b|DNA|TcMar-Tigger	89703	NM_003108	6664	Hs.432638	NM_003108	ENSG00000176887	SOX11	MRD27	SRY-box transcription factor 11	protein-coding	0.017857	0.399491	
chunk0107_288_1	chr2	218399514	218399785	+	0	NA	promoter-TSS (NM_182642)	promoter-TSS (NM_182642)	-106	NM_021198	58190	Hs.444468	NM_021198	ENSG00000144579	CTDSP1	NIF3|NLI-IF|NLIIF|SCP1	CTD small phosphatase 1	protein-coding	0.136531	0.775735	
chunk0065_217_1	chr14	100271332	100271616	+	0	NA	intron (NM_003403, intron 2 of 4)	intron (NM_003403, intron 2 of 4)	-5883	NR_106822	102466730		NR_106822	ENSG00000283840	MIR6764	hsa-mir-6764	microRNA 6764	ncRNA	0.010563	0.382456	
chunk0121_42_1	chr3	15405173	15405968	+	0	NA	Intergenic	Intergenic	21977	NM_152396	131965	Hs.149487	NM_152396	ENSG00000206562	METTL6	-	methyltransferase like 6	protein-coding	0.006289	0.375628	382(AAGAACACTATGTAAC,-,0.00)
chunk0084_300_1	chr17	80029343	80029579	+	0	NA	intron (NM_019020, intron 1 of 11)	intron (NM_019020, intron 1 of 11)	6397	NM_019020	125058	Hs.369819	NM_019020	ENSG00000167291	TBC1D16	-	TBC1 domain family member 16	protein-coding	0.008475	0.544304	
chunk0147_177_1	chr4	176794815	176795094	+	0	NA	Intergenic	Intergenic	-2209	NM_005429	7424	Hs.435215	NM_005429	ENSG00000150630	VEGFC	Flt4-L|LMPH1D|LMPHM4|VRP	vascular endothelial growth factor C	protein-coding	0.003584	0.367857	
chunk0147_166_1	chr4	176242762	176243406	+	0	NA	intron (NM_080874, intron 1 of 6)	MER58A|DNA|hAT-Charlie	26138	NM_080874	140458	Hs.591712	NM_080874	ENSG00000164122	ASB5	ASB-5	ankyrin repeat and SOCS box containing 5	protein-coding	0.001553	0.274419	
chunk0147_403_1	chr4	186821224	186821423	+	0	NA	Intergenic	Intergenic	-97490	NM_005245	2195	Hs.481371	NM_005245	ENSG00000083857	FAT1	CDHF7|CDHR8|FAT|ME5|hFat1	FAT atypical cadherin 1	protein-coding	0.040201	0.525000	
chunk0075_365_1	chr16	56336213	56336787	+	0	NA	intron (NM_020988, intron 5 of 8)	intron (NM_020988, intron 5 of 8)	89038	NM_001144	267	Hs.295137	NM_001144	ENSG00000159461	AMFR	GP78|RNF45	autocrine motility factor receptor	protein-coding	0.017422	0.582609	293(GAGCACAGCCAGTCCC,-,0.00),294(AGCACAGCCAGTCCCA,+,0.00)
chunk0077_25_1	chr16	75096685	75097057	+	0	NA	intron (NM_032268, intron 2 of 4)	intron (NM_032268, intron 2 of 4)	19901	NM_153486	197257	Hs.380929	NM_153486	ENSG00000166816	LDHD	DLACD|DLD	lactate dehydrogenase D	protein-coding	0.013441	0.463807	
chunk0173_292_1	chr6	148318233	148318664	+	0	NA	Intergenic	Intergenic	-24145	NM_015278	23328	Hs.193133	NM_015278	ENSG00000111961	SASH1	CAPOK|DUH1|SH3D6A|dJ323M4.1	SAM and SH3 domain containing 1	protein-coding	0.016241	0.365741	
chunk0004_68_1	chr1	43383463	43383864	+	0	NA	TTS (NM_201542)	TTS (NM_201542)	6149	NM_001001653	112950	Hs.301756	NM_052877	ENSG00000159479	MED8	ARC32	mediator complex subunit 8	protein-coding	0.004988	0.460199	
chunk0204_364_1	chr9	101803283	101803672	+	0	NA	Intergenic	MER91A|DNA|hAT-Tip100	-64897	NM_133445	116443	Hs.654783	NM_133445	ENSG00000198785	GRIN3A	GluN3A|NMDAR-L|NR3A	glutamate ionotropic receptor NMDA type subunit 3A	protein-coding	0.005141	0.346154	180(GGGCACATACTGTACA,-,0.00),181(GGCACATACTGTACAA,+,0.00)
chunk0166_356_1	chr6	51352299	51352965	+	0	NA	Intergenic	Intergenic	-269238	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.003003	0.365817	287(CAGTACATTTAGTTCT,-,0.00),288(AGTACATTTAGTTCTT,+,0.00)
chunk0134_401_1	chr3	183107920	183108384	+	0	NA	Intergenic	MER95|LTR|ERV1	-8565	NM_001293273	56922	Hs.47649	NM_020166	ENSG00000078070	MCCC1	MCC-B|MCCA	methylcrotonoyl-CoA carboxylase 1	protein-coding	0.004310	0.361290	
chunk0121_87_1	chr3	16427690	16427938	+	0	NA	intron (NM_015150, intron 3 of 9)	intron (NM_015150, intron 3 of 9)	85901	NM_015150	23180	Hs.98910	NM_015150	ENSG00000131378	RFTN1	MIG2|PIB10|PIG9|RAFTLIN	raftlin, lipid raft linker 1	protein-coding	0.008065	0.538153	
chunk0048_114_1	chr12	79629395	79629998	+	0	NA	intron (NM_002583, intron 2 of 6)	L1MEc|LINE|L1	61314	NM_002583	5074	Hs.643130	NM_002583	ENSG00000177425	PAWR	PAR4|Par-4	pro-apoptotic WT1 regulator	protein-coding	0.003317	0.288079	
chunk0121_28_1	chr3	15152365	15152615	+	0	NA	Intergenic	Intergenic	-53333	NR_126155	64145	Hs.475565	NM_022340	ENSG00000131381	RBSN	Rabenosyn-5|ZFYVE20	rabenosyn, RAB effector	protein-coding	0.008000	0.374502	
chunk0107_428_1	chr2	224816475	224816731	+	0	NA	intron (NM_014689, intron 30 of 55)	intron (NM_014689, intron 30 of 55)	130462	NM_001290263	55619	Hs.46578	NM_014689	ENSG00000135905	DOCK10	DRIP2|Nbla10300|ZIZ3	dedicator of cytokinesis 10	protein-coding	0.003906	0.357977	
chunk0192_447_1	chr8	70122821	70123236	+	0	NA	intron (NM_006540, intron 21 of 22)	intron (NM_006540, intron 21 of 22)	-51701	NM_024504	63978	Hs.736037	NM_024504	ENSG00000147596	PRDM14	PFM11	PR/SET domain 14	protein-coding	0.004819	0.360577	
chunk0090_417_1	chr18	79018195	79018397	+	0	NA	Intergenic	Intergenic	38021	NM_171999	27164	Hs.700557	NM_171999	ENSG00000256463	SALL3	ZNF796	spalt like transcription factor 3	protein-coding	0.019802	0.507389	
chunk0024_406_1	chr10	45278889	45279207	+	0	NA	Intergenic	LTR3|LTR|ERVK	36560	NM_001004297	79290	Hs.532435	NM_001004297	ENSG00000256574	OR13A1	-	olfactory receptor family 13 subfamily A member 1	protein-coding	0.003145	0.445141	
chunk0064_270_1	chr14	94856514	94857004	+	0	NA	Intergenic	MIRb|SINE|MIR	-86597	NM_173849	145258	Hs.440438	NM_173849	ENSG00000133937	GSC	SAMS	goosecoid homeobox	protein-coding	0.012245	0.501018	
chunk0024_163_1	chr10	35591194	35591580	+	0	NA	Intergenic	L1MEc|LINE|L1	-14023	NM_153368	219770	Hs.638922	NM_153368	ENSG00000177291	GJD4	CX40.1	gap junction protein delta 4	protein-coding	0.010363	0.454780	
chunk0171_149_1	chr6	123886122	123886683	+	0	NA	intron (NM_001300738, intron 1 of 7)	intron (NM_001300738, intron 1 of 7)	82556	NM_153355	154215	Hs.656604	NM_153355	ENSG00000188580	NKAIN2	FAM77B|NKAIP2|TCBA|TCBA1	sodium/potassium transporting ATPase interacting 2	protein-coding	0.001783	0.295374	264(AAGCACACCCAGTACA,-,0.00),265(AGCACACCCAGTACAT,+,0.00)
chunk0043_36_1	chr12	13238187	13238414	+	0	NA	Intergenic	Intergenic	41632	NM_001423	2012	Hs.719042	NM_001423	ENSG00000134531	EMP1	CL-20|EMP-1|TMP	epithelial membrane protein 1	protein-coding	0.022026	0.407895	
chunk0144_9_1	chr4	124712544	124712857	+	0	NA	promoter-TSS (NM_020337)	promoter-TSS (NM_020337)	32	NM_001167882	57182	Hs.480694	NM_020337	ENSG00000151458	ANKRD50	-	ankyrin repeat domain 50	protein-coding	0.118211	0.770701	
chunk0135_298_1	chr3	189712933	189713429	+	0	NA	intron (NM_001114978, intron 1 of 12)	intron (NM_001114978, intron 1 of 12)	-76479	NM_001114981	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.000000	0.412475	
chunk0023_174_1	chr10	24415917	24416634	+	0	NA	intron (NM_019590, intron 3 of 20)	intron (NM_019590, intron 3 of 20)	-33158	NM_001282769	56243	Hs.445885	NM_019590	ENSG00000120549	KIAA1217	ETL4|SKT	KIAA1217	protein-coding	0.011158	0.447075	
chunk0084_6_1	chr18	111253	111563	+	0	NA	TTS (NR_107045)	TTS (NR_107045)	931	NR_107045	102466878		NR_107045	ENSG00000277521	MIR8078	hsa-mir-8078	microRNA 8078	ncRNA	0.009677	0.459807	
chunk0130_71_1	chr3	129966826	129967113	+	0	NA	Intergenic	Intergenic	-7424	NM_007117	7200	Hs.182231	NM_007117	ENSG00000170893	TRH	Pro-TRH|TRF	thyrotropin releasing hormone	protein-coding	0.006969	0.513889	
chunk0196_333_1	chr8	112459799	112460419	+	0	NA	intron (NM_198123, intron 32 of 70)	L2c|LINE|L2	-183384	NR_031745	100302225		NR_031745	ENSG00000238399	MIR2053	hsa-mir-2053	microRNA 2053	ncRNA	0.004839	0.367150	
chunk0032_74_1	chr11	2614797	2615307	+	0	NA	non-coding (NR_002728, exon 1 of 1)	non-coding (NR_002728, exon 1 of 1)	84946	NR_002728	10984	Hs.604823	NR_002728	ENSG00000269821	KCNQ1OT1	KCNQ1-AS2|KCNQ10T1|Kncq1|KvDMR1|KvLQT1-AS|LIT1|NCRNA00012	KCNQ1 opposite strand/antisense transcript 1	ncRNA	0.001961	0.320939	
chunk0047_48_1	chr12	67052168	67052433	+	0	NA	Intergenic	Intergenic	43984	NR_120490	102724421	Hs.135774	NR_120490	ENSG00000257083	LOC102724421	-	uncharacterized LOC102724421	ncRNA	0.000000	0.349624	
chunk0161_119_1	chr5	167691293	167691559	+	0	NA	intron (NM_001122679, intron 2 of 28)	intron (NM_001122679, intron 2 of 28)	-63510	NM_001080428	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.003759	0.415730	
chunk0134_8_1	chr3	175356721	175357180	+	0	NA	intron (NM_207015, intron 5 of 13)	intron (NM_207015, intron 5 of 13)	-12590	NR_039952	100616395		NR_039952	ENSG00000264974	MIR4789	-	microRNA 4789	ncRNA	0.010893	0.376087	
chunk0075_87_1	chr16	48284722	48285330	+	0	NA	intron (NM_031490, intron 8 of 14)	L1M4|LINE|L1	40859	NM_031490	83752	Hs.295923	NM_031490	ENSG00000102910	LONP2	LONP|LONPL|PLON|PSLON	lon peptidase 2, peroxisomal	protein-coding	0.006579	0.376026	
chunk0092_177_1	chr19	29990732	29991424	+	0	NA	intron (NM_003796, intron 4 of 10)	L1ME1|LINE|L1	48839	NR_045557	8725	Hs.466391	NM_003796	ENSG00000105176	URI1	C19orf2|NNX3|PPP1R19|RMP|URI	URI1 prefoldin like chaperone	protein-coding	0.007225	0.327561	
chunk0092_166_1	chr19	29822230	29822635	+	0	NA	intron (NM_001238, intron 10 of 11)	intron (NM_001238, intron 10 of 11)	10438	NM_001238	898	Hs.244723	NM_001238	ENSG00000105173	CCNE1	CCNE|pCCNE1	cyclin E1	protein-coding	0.019753	0.472906	
chunk0172_225_1	chr6	137045219	137045648	+	0	NA	promoter-TSS (NM_001278724)	promoter-TSS (NM_001278724)	-253	NM_001278723	53832	Hs.445868	NM_014432	ENSG00000016402	IL20RA	CRF2-8|IL-20R-alpha|IL-20R1|IL-20RA	interleukin 20 receptor subunit alpha	protein-coding	0.016317	0.420930	
chunk0118_327_1	chr22	35392236	35392729	+	0	NA	intron (NM_002133, intron 4 of 4)	intron (NM_002133, intron 4 of 4)	-7641	NM_006739	4174	Hs.517582	NM_006739	ENSG00000100297	MCM5	CDC46|MGORS8|P1-CDC46	minichromosome maintenance complex component 5	protein-coding	0.004057	0.453441	
chunk0025_149_1	chr10	52272051	52272822	+	0	NA	exon (NM_001098512, exon 12 of 18)	exon (NM_001098512, exon 12 of 18)	41692	NR_038277	100506939	Hs.584791	NR_038277		PRKG1-AS1	-	PRKG1 antisense RNA 1	ncRNA	0.002594	0.339378	
chunk0049_14_1	chr12	89347403	89347602	+	0	NA	TTS (NM_001946)	TTS (NM_001946)	5357	NM_001946	1848	Hs.298654	NM_001946	ENSG00000139318	DUSP6	HH19|MKP3|PYST1	dual specificity phosphatase 6	protein-coding	0.010050	0.430000	
chunk0075_28_1	chr16	46911672	46911994	+	0	NA	intron (NM_001142466, intron 6 of 11)	intron (NM_001142466, intron 6 of 11)	26719	NM_001142466	84706	Hs.460693	NM_133443	ENSG00000166123	GPT2	ALT2|GPT 2|MRT49	glutamic--pyruvic transaminase 2	protein-coding	0.009317	0.433437	
chunk0110_131_1	chr20	13423852	13424322	+	0	NA	intron (NM_017714, intron 12 of 13)	intron (NM_017714, intron 12 of 13)	-184400	NR_040043	100505536	Hs.665253	NR_040043		ISM1-AS1	-	ISM1 antisense RNA 1	ncRNA	0.006383	0.303609	
chunk0014_213_1	chr1	179312821	179313465	+	0	NA	intron (NM_001252511, intron 2 of 14)	intron (NM_001252511, intron 2 of 14)	19429	NM_001252511	6646	Hs.445588	NM_003101	ENSG00000057252	SOAT1	ACACT|ACAT|ACAT-1|ACAT1|SOAT|STAT	sterol O-acyltransferase 1	protein-coding	0.009317	0.379845	
chunk0095_123_1	chr2	15907235	15907758	+	0	NA	Intergenic	L1ME1|LINE|L1	-12903	NR_125783	103752554	Hs.269571	NR_125783	ENSG00000223850	MYCNUT	MYCNUN|lncUSMycN	MYCN upstream transcript	ncRNA	0.001912	0.274809	
chunk0167_335_1	chr6	72533702	72534233	+	0	NA	Intergenic	L2c|LINE|L2	-87876	NM_001160133	56479	Hs.445324	NM_019842	ENSG00000185760	KCNQ5	Kv7.5|MRD46	potassium voltage-gated channel subfamily Q member 5	protein-coding	0.000000	0.345865	
chunk0097_93_1	chr2	45654193	45654563	+	0	NA	intron (NM_005400, intron 1 of 14)	intron (NM_005400, intron 1 of 14)	2474	NM_005400	5581	Hs.580351	NM_005400	ENSG00000171132	PRKCE	PKCE|nPKC-epsilon	protein kinase C epsilon	protein-coding	0.008108	0.520216	234(GAGGACATTGAGTTCC,-,0.00),235(AGGACATTGAGTTCCA,+,0.00)
chunk0084_251_1	chr17	78998671	78999129	+	0	NA	intron (NM_001159772, intron 1 of 5)	intron (NM_001159772, intron 1 of 5)	10917	NM_138793	124583	Hs.8859	NM_138793	ENSG00000171302	CANT1	DBQD|DBQD1|EDM7|SCAN-1|SCAN1|SHAPY	calcium activated nucleotidase 1	protein-coding	0.037118	0.599129	
chunk0059_46_1	chr14	29985480	29985858	+	0	NA	Intergenic	MIRb|SINE|MIR	-57976	NM_002742	5587	Hs.508999	NM_002742	ENSG00000184304	PRKD1	CHDED|PKC-MU|PKCM|PKD|PRKCM	protein kinase D1	protein-coding	0.010582	0.401055	
chunk0142_255_1	chr4	99082178	99082599	+	0	NA	intron (NM_000671, intron 2 of 8)	intron (NM_000671, intron 2 of 8)	6400	NM_000671	128	Hs.78989	NM_000671	ENSG00000197894	ADH5	ADH-3|ADHX|FALDH|FDH|GSH-FDH|GSNOR|HEL-S-60p	alcohol dehydrogenase 5 (class III), chi polypeptide	protein-coding	0.011876	0.372038	181(GGGAACATCTAGTCCC,-,0.00),182(GGAACATCTAGTCCCC,+,0.00)
chunk0088_131_1	chr18	45802510	45803569	+	0	NA	Intergenic	Intergenic	-22541	NM_213602	284266	Hs.287692	NM_213602	ENSG00000197046	SIGLEC15	CD33L3|HsT1361|SIGLEC-15	sialic acid binding Ig like lectin 15	protein-coding	0.001889	0.443396	
chunk0093_45_1	chr19	39892280	39892589	+	0	NA	intron (NM_003890, intron 13 of 27)	AluJr|SINE|Alu	42192	NM_003890	8857	Hs.111732	NM_003890		FCGBP	FC(GAMMA)BP	Fc fragment of IgG binding protein	protein-coding	0.035599	0.545161	
chunk0155_190_1	chr5	94617896	94618647	+	0	NA	promoter-TSS (NM_032290)	promoter-TSS (NM_032290)	333	NM_173665	285600	Hs.425123	NM_173665	ENSG00000185261	KIAA0825	C5orf36	KIAA0825	protein-coding	0.045273	0.531915	331(CGGTACACGGTGTCTT,-,0.00),332(GGTACACGGTGTCTTC,+,0.00)
chunk0123_444_1	chr3	50605889	50606317	+	0	NA	TTS (NM_013324)	TTS (NM_013324)	5728	NM_013324	1154	Hs.655334	NM_013324	ENSG00000114737	CISH	BACTS2|CIS|CIS-1|G18|SOCS	cytokine inducible SH2 containing protein	protein-coding	0.011682	0.573427	129(TGCACTCACTGTACCT,+,0.00)
chunk0106_342_1	chr2	206555794	206556242	+	0	NA	intron (NM_003812, intron 9 of 25)	intron (NM_003812, intron 9 of 25)	-86400	NM_001102659	200726		NM_001102659	ENSG00000235118	FAM237A	-	family with sequence similarity 237 member A	protein-coding	0.000000	0.291759	
chunk0148_29_1	chr5	654169	654442	+	0	NA	TTS (NM_018140)	TTS (NM_018140)	39090	NM_007030	11076	Hs.481466	NM_007030	ENSG00000171368	TPPP	TPPP/p25|TPPP1|p24|p25|p25alpha	tubulin polymerization promoting protein	protein-coding	0.032967	0.547445	
chunk0174_79_1	chr6	156310806	156311160	+	0	NA	Intergenic	L2a|LINE|L2	364186	NR_031606	100302259		NR_031606	ENSG00000221456	MIR1202	MIRN1202|hsa-mir-1202	microRNA 1202	ncRNA	0.011299	0.492958	108(CAGAACAGCAAGTGCA,-,0.00),109(AGAACAGCAAGTGCAT,+,0.00),232(CAGACCAGCATGTGCC,-,0.00),233(AGACCAGCATGTGCCT,+,0.00)
chunk0060_225_1	chr14	49443371	49443841	+	0	NA	Intergenic	Intergenic	142810	NM_001030001	6235	Hs.156367	NM_001032	ENSG00000213741	RPS29	DBA13|S29|uS14	ribosomal protein S29	protein-coding	0.017021	0.498938	314(AGGGACATTCTGTCCC,-,0.00),315(GGGACATTCTGTCCCC,+,0.00)
chunk0087_77_1	chr18	32081954	32082429	+	0	NA	Intergenic	Intergenic	-9664	NM_016271	51444	Hs.302408	NM_016271	ENSG00000134758	RNF138	HSD-4|NARF|STRIN|hNARF	ring finger protein 138	protein-coding	0.002105	0.386555	
chunk0151_4_1	chr5	40758604	40758803	+	0	NA	TTS (NM_006251)	TTS (NM_006251)	-2733	NM_012382	23548	Hs.348915	NM_012382	ENSG00000113638	TTC33	OSRF	tetratricopeptide repeat domain 33	protein-coding	0.000000	0.310000	
chunk0091_220_1	chr19	10122092	10122532	+	0	NA	Intergenic	Intergenic	-2389	NM_003755	8666	Hs.529059	NM_003755	ENSG00000130811	EIF3G	EIF3-P42|EIF3S4|eIF3-delta|eIF3-p44	eukaryotic translation initiation factor 3 subunit G	protein-coding	0.015909	0.458050	
chunk0037_183_1	chr11	74086212	74086901	+	0	NA	intron (NM_001286577, intron 20 of 32)	MER90|LTR|ERV1	-77319	NM_003356	7352	Hs.101337	NM_003356	ENSG00000175564	UCP3	SLC25A9	uncoupling protein 3	protein-coding	0.007257	0.413043	
chunk0068_180_1	chr15	54480994	54481193	+	0	NA	intron (NM_001080534, intron 17 of 30)	L1MA4A|LINE|L1	468189	NM_001080534	440279	Hs.657273	NM_001080534	ENSG00000137766	UNC13C	-	unc-13 homolog C	protein-coding	0.005025	0.420000	
chunk0098_428_1	chr2	81584324	81584729	+	0	NA	Intergenic	MIR|SINE|MIR	-117580	NR_110161	100507201	Hs.98589	NR_110161	ENSG00000235519	LINC01815	-	long intergenic non-protein coding RNA 1815	ncRNA	0.002469	0.285714	
chunk0050_255_1	chr12	105820419	105820987	+	0	NA	Intergenic	Intergenic	113929	NR_110111	101929110	Hs.145944	NR_110108	ENSG00000257859	CASC18	-	cancer susceptibility 18	ncRNA	0.007042	0.462214	206(AAGGACATTGTGTTCT,-,0.00),207(AGGACATTGTGTTCTG,+,0.00)
chunk0130_335_1	chr3	138329163	138329410	+	0	NA	intron (NM_178130, intron 2 of 11)	intron (NM_178130, intron 2 of 11)	600	NM_178130	347736	Hs.660992	NM_178130	ENSG00000181322	NME9	NM23-H9|TXL-2|TXL2|TXNDC6	NME/NM23 family member 9	protein-coding	0.052632	0.572581	
chunk0123_301_1	chr3	46930984	46931319	+	0	NA	intron (NM_001277074, intron 2 of 6)	intron (NM_001277074, intron 2 of 6)	45350	NR_102269	151903	Hs.631918	NM_144716	ENSG00000160799	CCDC12	-	coiled-coil domain containing 12	protein-coding	0.005970	0.508929	
chunk0121_313_1	chr3	24200019	24200264	+	0	NA	intron (NM_000461, intron 3 of 9)	intron (NM_000461, intron 3 of 9)	48817	NR_121667	101927854	Hs.570625	NR_121667		LOC101927854	-	uncharacterized LOC101927854	ncRNA	0.004082	0.365854	
chunk0009_272_1	chr1	107486208	107486685	+	0	NA	Intergenic	Intergenic	202058	NM_001079874	10451	Hs.267659	NM_006113	ENSG00000134215	VAV3	-	vav guanine nucleotide exchange factor 3	protein-coding	0.006289	0.418410	253(AAGAACATAATGTCAT,-,0.00)
chunk0037_225_1	chr11	74956526	74956734	+	0	NA	intron (NM_014752, intron 1 of 4)	L2a|LINE|L2	7383	NM_014752	9789	Hs.282700	NM_014752	ENSG00000118363	SPCS2	-	signal peptidase complex subunit 2	protein-coding	0.014423	0.449761	
chunk0190_446_1	chr8	41815956	41816188	+	0	NA	intron (NM_001142446, intron 1 of 42)	MER34B-int|LTR|ERV1	-18450	NM_000037	286	Hs.654438	NM_000037	ENSG00000029534	ANK1	ANK|SPH1|SPH2	ankyrin 1	protein-coding	0.017241	0.278970	
chunk0098_354_1	chr2	77414206	77414624	+	0	NA	intron (NM_001282924, intron 3 of 3)	intron (NM_001282924, intron 3 of 3)	107953	NM_001282928	80059	Hs.285782	NM_024993	ENSG00000176204	LRRTM4	-	leucine rich repeat transmembrane neuronal 4	protein-coding	0.004785	0.372315	
chunk0081_179_1	chr17	41663600	41663941	+	0	NA	Intergenic	L2a|LINE|L2	-23571	NR_033415	284116	Hs.725790	NR_033415	ENSG00000214514	KRT42P	-	keratin 42 pseudogene	pseudo	0.017595	0.517544	
chunk0083_155_1	chr17	65931645	65932071	+	0	NA	intron (NM_001302891, intron 16 of 24)	L1MA7|LINE|L1	-105315	NR_126542	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.000000	0.538642	
chunk0033_306_1	chr11	20384840	20385264	+	0	NA	Intergenic	Intergenic	-2478	NM_001145166	10196	Hs.152337	NM_005788	ENSG00000185238	PRMT3	HRMT1L3	protein arginine methyltransferase 3	protein-coding	0.002358	0.432941	196(ATGGACTGGGTGTTCC,-,0.00),197(TGGACTGGGTGTTCCA,+,0.00)
chunk0038_452_1	chr11	94823065	94823397	+	0	NA	intron (NM_130847, intron 4 of 12)	intron (NM_130847, intron 4 of 12)	54889	NM_001301007	154810	Hs.503594	NM_130847	ENSG00000166025	AMOTL1	JEAP	angiomotin like 1	protein-coding	0.006024	0.501502	
chunk0092_416_1	chr19	37957107	37957572	+	0	NA	intron (NM_015073, intron 1 of 21)	L1MB7|LINE|L1	50118	NM_015073	23094	Hs.655502	NM_015073	ENSG00000105738	SIPA1L3	CTRCT45|SPAL3|SPAR3	signal induced proliferation associated 1 like 3	protein-coding	0.002151	0.328326	
chunk0115_279_1	chr21	28151512	28152148	+	0	NA	intron (NR_126012, intron 5 of 5)	Tigger3b|DNA|TcMar-Tigger	61427	NR_126011	284825	Hs.651529	NR_126010	ENSG00000232079	LINC01697	-	long intergenic non-protein coding RNA 1697	ncRNA	0.004717	0.295133	
chunk0072_394_1	chr15	100602237	100602548	+	0	NA	promoter-TSS (NM_001040616)	promoter-TSS (NM_001040616)	-152	NM_001040616	55180	Hs.105633	NM_018148	ENSG00000140471	LINS1	LINS|MRT27|WINS1	lines homolog 1	protein-coding	0.064309	0.615385	
chunk0043_97_1	chr12	14819809	14820518	+	0	NA	intron (NM_175874, intron 1 of 1)	L1MC|LINE|L1	-5981	NM_001013698	440087	Hs.220931	NM_001013698	ENSG00000179256	SMCO3	C12orf69	single-pass membrane protein with coiled-coil domains 3	protein-coding	0.002821	0.297183	
chunk0104_433_1	chr2	181036961	181037648	+	0	NA	intron (NM_001278554, intron 3 of 5)	Tigger3b|DNA|TcMar-Tigger	56180	NM_001278554	10477	Hs.470804	NM_006357	ENSG00000170035	UBE2E3	UBCH9|UbcM2	ubiquitin conjugating enzyme E2 E3	protein-coding	0.005822	0.347384	
chunk0031_444_1	chr10	132580676	132580875	+	0	NA	intron (NM_005539, intron 1 of 15)	L1ME2z|LINE|L1	42926	NM_005539	3632	Hs.523360	NM_005539	ENSG00000068383	INPP5A	5PTASE	inositol polyphosphate-5-phosphatase A	protein-coding	0.000000	0.360000	
chunk0055_136_1	chr13	59488449	59488697	+	0	NA	Intergenic	Intergenic	-524145	NR_109838	100874195	Hs.664101	NR_046539	ENSG00000227528	DIAPH3-AS1	-	DIAPH3 antisense RNA 1	ncRNA	0.004032	0.397590	
chunk0076_357_1	chr16	71771085	71771322	+	0	NA	exon (NM_001030007, exon 5 of 24)	exon (NM_001030007, exon 5 of 24)	-12716	NR_003059	692111		NR_003059	ENSG00000223224	SNORD71	HBII-239|MIRN768|hsa-mir-768	small nucleolar RNA, C/D box 71	snoRNA	0.000000	0.331933	
chunk0009_334_1	chr1	109105091	109105542	+	0	NA	TTS (NM_001122961)	TTS (NM_001122961)	5123	NR_003023	677766	Hs.550815	NR_003023	ENSG00000278249	SCARNA2	HBII-382|mgU2-25/61	small Cajal body-specific RNA 2	ncRNA	0.006652	0.409292	
chunk0107_282_1	chr2	218312097	218312710	+	0	NA	intron (NM_015488, intron 2 of 9)	intron (NM_015488, intron 2 of 9)	-10776	NM_022572	25953	Hs.98475	NM_015488	ENSG00000127838	PNKD	BRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|TAHCCP2	PNKD metallo-beta-lactamase domain containing	protein-coding	0.004894	0.431596	
chunk0014_206_1	chr1	179205649	179206017	+	0	NA	intron (NM_007314, intron 1 of 11)	L1M5|LINE|L1	23851	NM_001168238	27	Hs.159472	NM_005158	ENSG00000143322	ABL2	ABLL|ARG	ABL proto-oncogene 2, non-receptor tyrosine kinase	protein-coding	0.002717	0.346883	
chunk0035_64_1	chr11	41545357	41545652	+	0	NA	Intergenic	L1PA6|LINE|L1	-85868	NM_001258419	57689	Hs.745123	NM_020929	ENSG00000148948	LRRC4C	NGL-1|NGL1	leucine rich repeat containing 4C	protein-coding	0.010169	0.520270	
chunk0111_48_1	chr20	22375972	22376424	+	0	NA	Intergenic	Intergenic	44445	NR_027090	284788	Hs.651993	NR_027089	ENSG00000204684	LOC284788	-	uncharacterized LOC284788	ncRNA	0.002212	0.302428	
chunk0183_67_1	chr7	104185110	104185870	+	0	NA	intron (NM_002553, intron 6 of 13)	intron (NM_002553, intron 6 of 13)	22557	NM_002553	5001	Hs.432948	NM_002553	ENSG00000164815	ORC5	ORC5L|ORC5P|ORC5T|PPP1R117	origin recognition complex subunit 5	protein-coding	0.007895	0.310118	
chunk0165_307_1	chr6	36919961	36920376	+	0	NA	intron (NM_001286635, intron 8 of 8)	intron (NM_001286635, intron 8 of 8)	-28095	NM_001199159	221476	Hs.25391	NM_153370	ENSG00000164530	PI16	CD364|CRISP9|MSMBBP|PSPBP	peptidase inhibitor 16	protein-coding	0.007229	0.454327	
chunk0139_407_1	chr4	63396318	63396581	+	0	NA	Intergenic	LTR27E|LTR|ERV1	1013011	NM_001010874	253017	Hs.227752	NM_001010874	ENSG00000205678	TECRL	CPVT3|GPSN2L|SRD5A2L2|TERL	trans-2,3-enoyl-CoA reductase like	protein-coding	0.003802	0.587121	
chunk0129_314_1	chr3	123962885	123963674	+	0	NA	Intergenic	MER58B|DNA|hAT-Charlie	-1871	NM_001308317	64770	Hs.645028	NM_022757	ENSG00000175455	CCDC14	-	coiled-coil domain containing 14	protein-coding	0.005070	0.431646	221(GGGGACACAGTGAACT,-,0.00),222(GGGACACAGTGAACTG,+,0.00)
chunk0185_84_1	chr7	125391718	125392196	+	0	NA	Intergenic	Intergenic	-127666	NR_110182	101928254	Hs.571236	NR_110182	ENSG00000219445	LOC101928254	-	uncharacterized LOC101928254	ncRNA	0.006276	0.336117	
chunk0159_294_1	chr5	142814182	142814390	+	0	NA	intron (NM_015071, intron 1 of 22)	intron (NM_015071, intron 1 of 22)	43559	NM_015071	23092	Hs.654668	NM_015071	ENSG00000145819	ARHGAP26	GRAF|GRAF1|OPHN1L|OPHN1L1	Rho GTPase activating protein 26	protein-coding	0.014423	0.444976	
chunk0145_137_1	chr4	146522237	146522649	+	0	NA	promoter-TSS (NM_032128)	promoter-TSS (NM_032128)	-472	NM_032128	84068	Hs.659209	NM_032128	ENSG00000120519	SLC10A7	C4orf13|P7|SSASKS	solute carrier family 10 member 7	protein-coding	0.092233	0.653753	
chunk0054_3_1	chr13	40175448	40175999	+	0	NA	Intergenic	Intergenic	-6086	NR_046870	100874127	Hs.578028	NR_046870	ENSG00000230710	LINC00332	NCRNA00332	long intergenic non-protein coding RNA 332	ncRNA	0.000000	0.393116	221(CAGAACAACATGTCCA,-,0.00),222(AGAACAACATGTCCAG,+,0.00)
chunk0012_348_1	chr1	162678432	162678699	+	0	NA	intron (NM_006182, intron 2 of 17)	MIR3|SINE|MIR	46127	NM_006182	4921	Hs.275757	NM_006182	ENSG00000162733	DDR2	MIG20a|NTRKR3|TKT|TYRO10|WRCN	discoidin domain receptor tyrosine kinase 2	protein-coding	0.003745	0.466418	
chunk0075_313_1	chr16	54457722	54458092	+	0	NA	Intergenic	MIR|SINE|MIR	-171441	NM_024336	79191	Hs.499205	NM_024336	ENSG00000177508	IRX3	IRX-1|IRXB1	iroquois homeobox 3	protein-coding	0.008108	0.450135	
chunk0153_96_1	chr5	68375609	68375824	+	0	NA	Intergenic	Intergenic	83148	NM_001242466	5295	Hs.132225	NM_181504	ENSG00000145675	PIK3R1	AGM7|GRB1|IMD36|p85|p85-ALPHA	phosphoinositide-3-kinase regulatory subunit 1	protein-coding	0.009302	0.490741	93(TTGCACACCGTGTTCC,-,0.00),94(TGCACACCGTGTTCCA,+,0.00)
chunk0110_318_1	chr20	18692517	18692716	+	0	NA	intron (NR_109955, intron 1 of 3)	intron (NR_109955, intron 1 of 3)	6092	NR_109955	101929526	Hs.639402	NR_109955	ENSG00000233993	LOC101929526	-	uncharacterized LOC101929526	ncRNA	0.000000	0.540000	
chunk0033_87_1	chr11	14046150	14046585	+	0	NA	intron (NM_006108, intron 3 of 15)	intron (NM_006108, intron 3 of 15)	83730	NM_006108	10418	Hs.643864	NM_006108	ENSG00000262655	SPON1	VSGP/F-spondin|f-spondin	spondin 1	protein-coding	0.004598	0.426606	
chunk0116_114_1	chr21	35655093	35655368	+	0	NA	Intergenic	Intergenic	-65485	NR_030414	768219		NR_030414	ENSG00000211590	MIR802	MIRN802|hsa-mir-802	microRNA 802	ncRNA	0.014545	0.384058	141(TAACACAGTGTGTACT,-,0.00),142(AACACAGTGTGTACTT,+,0.00)
chunk0002_271_1	chr1	21775987	21776494	+	0	NA	intron (NM_001032730, intron 1 of 10)	intron (NM_001032730, intron 1 of 10)	6955	NM_032236	84196	Hs.467524	NM_032236	ENSG00000090686	USP48	RAP1GA1|USP31	ubiquitin specific peptidase 48	protein-coding	0.000000	0.372047	
chunk0069_355_1	chr15	66813038	66813440	+	0	NA	Intergenic	L1PA6|LINE|L1	110903	NR_027654	4091	Hs.153863	NM_005585	ENSG00000137834	SMAD6	AOVD2|HsT17432|MADH6|MADH7	SMAD family member 6	protein-coding	0.007463	0.491315	
chunk0199_95_1	chr9	2759315	2759547	+	0	NA	Intergenic	LTR56|LTR|ERV1	41905	NM_133497	169522	Hs.622675	NM_133497	ENSG00000168263	KCNV2	KV11.1|Kv8.2|RCD3B	potassium voltage-gated channel modifier subfamily V member 2	protein-coding	0.000000	0.356223	
chunk0206_403_1	chr9	127197511	127197784	+	0	NA	intron (NM_014636, intron 13 of 18)	intron (NM_014636, intron 13 of 18)	-66015	NM_001286779	84253	Hs.29304	NM_032293	ENSG00000136895	GARNL3	bA356B19.1	GTPase activating Rap/RanGAP domain like 3	protein-coding	0.021978	0.562044	
chunk0206_166_1	chr9	122217746	122218053	+	0	NA	intron (NM_001242333, intron 4 of 8)	MIR|SINE|MIR	3841	NM_001242335	26468	Hs.103137	NM_014368	ENSG00000106852	LHX6	LHX6.1	LIM homeobox 6	protein-coding	0.009772	0.402597	
chunk0206_177_1	chr9	122401310	122401650	+	0	NA	Intergenic	L1ME3|LINE|L1	26158	NM_001271165	5742	Hs.201978	NM_000962	ENSG00000095303	PTGS1	COX1|COX3|PCOX1|PES-1|PGG/HS|PGHS-1|PGHS1|PHS1|PTGHS	prostaglandin-endoperoxide synthase 1	protein-coding	0.011765	0.334311	
chunk0023_53_1	chr10	21743070	21743337	+	0	NA	3' UTR (NM_004641, exon 24 of 24)	3' UTR (NM_004641, exon 24 of 24)	208558	NM_001195626	8028	Hs.30385	NM_004641	ENSG00000078403	MLLT10	AF10	MLLT10 histone lysine methyltransferase DOT1L cofactor	protein-coding	0.007491	0.395522	
chunk0167_71_1	chr6	56399408	56399984	+	0	NA	Intergenic	LTR22|LTR|ERVK	-152116	NM_030820	81578	Hs.47629	NM_030820	ENSG00000124749	COL21A1	COLA1L|FP633	collagen type XXI alpha 1 chain	protein-coding	0.008681	0.431542	
chunk0082_326_1	chr17	59619625	59619866	+	0	NA	promoter-TSS (NM_001288653)	promoter-TSS (NM_001288653)	56	NM_001288653	1213	Hs.491351	NM_004859	ENSG00000141367	CLTC	CHC|CHC17|CLH-17|CLTCL2|Hc|MRD56	clathrin heavy chain	protein-coding	0.099585	0.611570	
chunk0001_333_1	chr1	9588354	9588636	+	0	NA	promoter-TSS (NM_001130924)	promoter-TSS (NM_001130924)	-379	NM_001010866	199953	Hs.632365	NM_001010866	ENSG00000188807	TMEM201	Ima1|NET5|SAMP1	transmembrane protein 201	protein-coding	0.070922	0.632509	
chunk0194_442_1	chr8	92544368	92544825	+	0	NA	Intergenic	Intergenic	110898	NR_125827	102724710	Hs.125714	NR_125827	ENSG00000253634	LOC102724710	-	uncharacterized LOC102724710	ncRNA	0.002188	0.283843	
chunk0039_443_1	chr11	108259750	108260008	+	0	NA	intron (NM_000051, intron 16 of 62)	intron (NM_000051, intron 16 of 62)	37047	NM_000051	472	Hs.367437	NM_000051	ENSG00000149311	ATM	AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1	ATM serine/threonine kinase	protein-coding	0.003876	0.297297	
chunk0058_144_1	chr14	23008927	23009195	+	0	NA	intron (NM_001130706, intron 1 of 7)	intron (NM_001130706, intron 1 of 7)	1140	NM_001130706	60686	Hs.255874	NM_021944	ENSG00000100802	C14orf93	RTFC	chromosome 14 open reading frame 93	protein-coding	0.011194	0.379182	
chunk0165_86_1	chr6	31677540	31677842	+	0	NA	intron (NM_025262, intron 2 of 2)	L1ME3G|LINE|L1	2682	NM_025262	80741	Hs.25738	NM_025262	ENSG00000204428	LY6G5C	C6orf20|G5C|LY6G5CA|LY6G5CB|NG33	lymphocyte antigen 6 family member G5C	protein-coding	0.009934	0.432343	151(CGGAACATTCAGTTCC,-,0.00),152(GGAACATTCAGTTCCC,+,0.00)
chunk0134_344_1	chr3	182413926	182414590	+	0	NA	Intergenic	Intergenic	72104	NR_040105	401103	Hs.591304	NR_040105	ENSG00000241098	LINC01994	-	long intergenic non-protein coding RNA 1994	ncRNA	0.001506	0.347368	
chunk0212_48_1	chrY	11310731	11310963	+	0	NA	Intergenic	BSR/Beta|Satellite|Satellite	1110743	NR_033667	352887	Hs.546221	NR_033667	ENSG00000206159	GYG2P1	GYG2P	glycogenin 2 pseudogene 1	pseudo	0.000000	0.497854	
chunk0078_368_1	chr16	87418323	87418975	+	0	NA	intron (NM_015144, intron 7 of 12)	intron (NM_015144, intron 7 of 12)	26454	NM_022818	81631	Hs.356061	NM_022818	ENSG00000140941	MAP1LC3B	ATG8F|LC3B|MAP1A/1BLC3|MAP1LC3B-a	microtubule associated protein 1 light chain 3 beta	protein-coding	0.029141	0.462481	
chunk0108_93_1	chr2	227877967	227878427	+	0	NA	intron (NM_178821, intron 1 of 12)	intron (NM_178821, intron 1 of 12)	6586	NM_178821	164781	Hs.424594	NM_178821	ENSG00000123977	DAW1	ODA16|WDR69	dynein assembly factor with WD repeats 1	protein-coding	0.002174	0.301518	
chunk0177_74_1	chr7	21417815	21418129	+	0	NA	Intergenic	Intergenic	-10099	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.006369	0.403175	
chunk0088_318_1	chr18	50820001	50820263	+	0	NA	promoter-TSS (NM_031939)	promoter-TSS (NM_031939)	-68	NM_001127176	83876	Hs.30495	NM_031939	ENSG00000134042	MRO	B29|C18orf3	maestro	protein-coding	0.049618	0.555133	189(TGGGACACTGTGTTCC,-,0.00),190(GGGACACTGTGTTCCA,+,0.00)
chunk0156_326_1	chr5	111520811	111521609	+	0	NA	intron (NR_040093, intron 1 of 6)	intron (NR_040093, intron 1 of 6)	-8613	NM_001308057	134429	Hs.93842	NM_139164	ENSG00000164211	STARD4	-	StAR related lipid transfer domain containing 4	protein-coding	0.007519	0.380476	296(GAGGACGTTGTGTTCC,-,0.00),297(AGGACGTTGTGTTCCA,+,0.00)
chunk0062_353_1	chr14	73763492	73763766	+	0	NA	intron (NM_001043318, intron 1 of 11)	intron (NM_001043318, intron 1 of 11)	-3331	NM_194278	91748	Hs.594157	NM_194278	ENSG00000156030	ELMSAN1	C14orf117|C14orf43|LSR68|MIDEAS|c14_5541	ELM2 and Myb/SANT domain containing 1	protein-coding	0.007299	0.483636	
chunk0009_414_1	chr1	110676990	110677437	+	0	NA	Intergenic	MIRc|SINE|MIR	-2180	NM_002232	3738	Hs.169948	NM_002232	ENSG00000177272	KCNA3	HGK5|HLK3|HPCN3|HUKIII|KV1.3|MK3|PCN3	potassium voltage-gated channel subfamily A member 3	protein-coding	0.011186	0.410714	
chunk0113_129_1	chr20	51735569	51736270	+	0	NA	intron (NM_006045, intron 1 of 27)	L2b|LINE|L2	32492	NM_006045	10079	Hs.649234	NM_006045	ENSG00000054793	ATP9A	ATPIIA	ATPase phospholipid transporting 9A (putative)	protein-coding	0.011412	0.494302	
chunk0108_17_1	chr2	226211258	226211834	+	0	NA	Intergenic	Intergenic	68752	NR_046102	646736	Hs.712836	NR_046102		LOC646736	-	uncharacterized LOC646736	ncRNA	0.005208	0.346620	
chunk0047_233_1	chr12	71925284	71925970	+	0	NA	non-coding (NR_027449, exon 16 of 16)	non-coding (NR_027449, exon 16 of 16)	-13219	NM_173353	121278	Hs.736576	NM_173353	ENSG00000139287	TPH2	ADHD7|NTPH	tryptophan hydroxylase 2	protein-coding	0.004373	0.317322	
chunk0104_313_1	chr2	179218910	179219356	+	0	NA	intron (NM_178123, intron 1 of 17)	intron (NM_178123, intron 1 of 17)	45490	NM_178123	91404	Hs.30977	NM_178123	ENSG00000187231	SESTD1	SOLO	SEC14 and spectrin domain containing 1	protein-coding	0.004484	0.404922	208(AAGAACAGCAAGTTCT,-,0.00),209(AGAACAGCAAGTTCTT,+,0.00)
chunk0091_39_1	chr19	3807489	3808840	+	0	NA	intron (NM_015174, intron 17 of 18)	intron (NM_015174, intron 17 of 18)	-6352	NM_002378	4145	Hs.631845	NM_002378	ENSG00000007264	MATK	CHK|CTK|HHYLTK|HYL|HYLTK|Lsk	megakaryocyte-associated tyrosine kinase	protein-coding	0.045892	0.580621	958(AGAACGCATTGTGCTG,+,0.00)
chunk0140_323_1	chr4	73547042	73547806	+	0	NA	Intergenic	L1P3|LINE|L1	38621	NR_046377	728040	Hs.640574	NR_046377	ENSG00000250436	LINC02499	-	long intergenic non-protein coding RNA 2499	ncRNA	0.007853	0.406536	
chunk0013_112_1	chr1	167910817	167911903	+	0	NA	intron (NM_018417, intron 1 of 32)	LTR10C|LTR|ERV1	2866	NM_001167749	55811	Hs.320892	NM_018417	ENSG00000143199	ADCY10	HCA2|HEL-S-7a|SAC|SACI|Sacy|hsAC	adenylate cyclase 10	protein-coding	0.009208	0.372585	537(ATGTACTTTATGTTCT,-,0.00),538(TGTACTTTATGTTCTT,+,0.00)
chunk0088_361_1	chr18	52997000	52997223	+	0	NA	intron (NM_005215, intron 5 of 28)	intron (NM_005215, intron 5 of 28)	-239990	NR_130465	100616232		NR_130465	ENSG00000263872	MIR4528	-	microRNA 4528	ncRNA	0.004484	0.388393	
chunk0012_104_1	chr1	156559572	156560250	+	0	NA	intron (NM_178229, intron 11 of 37)	L2|LINE|L2	12693	NM_178229	128239	Hs.591495	NM_178229	ENSG00000183856	IQGAP3	-	IQ motif containing GTPase activating protein 3	protein-coding	0.010324	0.469809	
chunk0167_165_1	chr6	63088416	63089588	+	0	NA	Intergenic	Intergenic	230975	NM_001143940	51557	Hs.149585	NM_016571	ENSG00000146166	LGSN	GLULD1|LGS	lengsin, lens protein with glutamine synthetase domain	protein-coding	0.004266	0.317988	
chunk0121_433_1	chr3	25967386	25967593	+	0	NA	Intergenic	MIR|SINE|MIR	-93794	NR_034055	285326	Hs.145246	NR_034055	ENSG00000230891	LINC00692	-	long intergenic non-protein coding RNA 692	ncRNA	0.014493	0.418269	
chunk0015_358_1	chr1	190355081	190355509	+	0	NA	intron (NM_199051, intron 2 of 7)	MER99|DNA|hAT?	122334	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.000000	0.284382	
chunk0063_30_1	chr14	76684629	76685185	+	0	NA	Intergenic	L1MA9|LINE|L1	-76985	NM_014909	22846	Hs.525479	NM_014909	ENSG00000071246	VASH1	KIAA1036|TTCP 1	vasohibin 1	protein-coding	0.003597	0.344704	
chunk0182_85_1	chr7	92688465	92688998	+	0	NA	intron (NM_001145306, intron 4 of 7)	intron (NM_001145306, intron 4 of 7)	-98337	NR_109929	257415	Hs.18564	NM_152789	ENSG00000234545	FAM133B	-	family with sequence similarity 133 member B	protein-coding	0.007505	0.380150	
chunk0130_415_1	chr3	140681466	140681876	+	0	NA	intron (NM_152616, intron 1 of 4)	MER90a|LTR|ERV1	3647	NM_152616	287015	Hs.343487	NM_152616	ENSG00000155890	TRIM42	PPP1R40|T4A1	tripartite motif containing 42	protein-coding	0.002439	0.374696	376(AAGAACAGAGTGACCC,-,0.00),377(AGAACAGAGTGACCCA,+,0.00)
chunk0032_445_1	chr10	132997670	132998000	+	0	NA	Intergenic	Intergenic	32301	NR_046231	399829	Hs.252872	NR_046231	ENSG00000240707	LINC01168	-	long intergenic non-protein coding RNA 1168	ncRNA	0.018182	0.555891	
chunk0011_62_1	chr1	143272985	143273189	+	0	NA	Intergenic	Intergenic	149505	NR_027354	645166	Hs.744183	NR_027354		LSP1P5	-	LSP1 pseudogene 5	pseudo	0.024510	0.341463	
chunk0107_121_1	chr2	214519237	214519733	+	0	NA	intron (NR_047698, intron 1 of 3)	intron (NR_047698, intron 1 of 3)	9303	NR_047698	100885780	Hs.665982	NR_047698	ENSG00000224257	VWC2L-IT1	-	VWC2L intronic transcript 1	ncRNA	0.008065	0.410463	213(AGGTACACAGTGCTCT,-,0.00),214(GGTACACAGTGCTCTG,+,0.00)
chunk0015_424_1	chr1	191575853	191576439	+	0	NA	Intergenic	Intergenic	-582316	NM_130782	64407	Hs.440890	NM_130782	ENSG00000150681	RGS18	RGS13	regulator of G protein signaling 18	protein-coding	0.006826	0.361158	
chunk0029_120_1	chr10	98415039	98415309	+	0	NA	promoter-TSS (NM_032709)	promoter-TSS (NM_032709)	47	NM_032709	84795	Hs.238303	NM_032709	ENSG00000119943	PYROXD2	C10orf33|FP3420|YUEF	pyridine nucleotide-disulphide oxidoreductase domain 2	protein-coding	0.029630	0.645756	
chunk0092_336_1	chr19	35129670	35130015	+	0	NA	intron (NM_139284, intron 6 of 8)	LTR5B|LTR|ERVK	5432	NM_139284	163175	Hs.65256	NM_139284	ENSG00000153902	LGI4	AMCNMY|LGIL3	leucine rich repeat LGI family member 4	protein-coding	0.026087	0.485549	
chunk0187_145_1	chr7	149659528	149659974	+	0	NA	Intergenic	L1PBa|LINE|L1	-34961	NR_027788	79970	Hs.520785	NM_024910	ENSG00000133624	ZNF767P	ZNF767	zinc finger family member 767, pseudogene	pseudo	0.006726	0.337808	
chunk0002_69_1	chr1	14058484	14058798	+	0	NA	Intergenic	Intergenic	309260	NM_001007257	7799	Hs.371823	NM_012231	ENSG00000116731	PRDM2	HUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2	PR/SET domain 2	protein-coding	0.003185	0.415873	32(GTGCACACTGTGTCCT,-,0.00),33(TGCACACTGTGTCCTG,+,0.00)
chunk0134_108_1	chr3	177006009	177006238	+	0	NA	Intergenic	MSTB-int|LTR|ERVL-MaLR	-189122	NR_110819	101928684	Hs.639352	NR_110819	ENSG00000228308	LINC01209	-	long intergenic non-protein coding RNA 1209	ncRNA	0.000000	0.500000	
chunk0016_320_1	chr1	201597681	201598308	+	0	NA	Intergenic	Intergenic	-50328	NM_020443	89796	Hs.585374	NM_020443	ENSG00000134369	NAV1	POMFIL3|STEERIN1|UNC53H1	neuron navigator 1	protein-coding	0.022329	0.546178	
chunk0056_85_1	chr13	79950778	79951399	+	0	NA	Intergenic	L1PA6|LINE|L1	-59989	NR_104138	101515984	Hs.569290	NR_104138		LINC01080	TCONS_00021856	long intergenic non-protein coding RNA 1080	ncRNA	0.003221	0.379421	
chunk0079_63_1	chr17	11177366	11177835	+	0	NA	Intergenic	Intergenic	-63823	NM_001173462	388336	Hs.592124	NM_175903	ENSG00000188803	SHISA6	-	shisa family member 6	protein-coding	0.004264	0.374468	
chunk0068_341_1	chr15	57734859	57735309	+	0	NA	Intergenic	Intergenic	28563	NM_001018102	81488	Hs.437256	NM_015532	ENSG00000255529	POLR2M	GCOM1|GRINL1A|Gdown|Gdown1	RNA polymerase II subunit M	protein-coding	0.004444	0.334812	
chunk0128_392_1	chr3	113931858	113932383	+	0	NA	intron (NM_001172105, intron 6 of 12)	intron (NM_001172105, intron 6 of 12)	-15781	NM_173570	254887	Hs.21902	NM_173570	ENSG00000184307	ZDHHC23	DHHC-23|NIDD	zinc finger DHHC-type containing 23	protein-coding	0.005714	0.361217	
chunk0076_186_1	chr16	67684822	67685324	+	0	NA	3' UTR (NM_001243650, exon 2 of 2)	3' UTR (NM_001243650, exon 2 of 2)	18259	NM_001012984	388284	Hs.632208	NM_001012984	ENSG00000159761	C16orf86	-	chromosome 16 open reading frame 86	protein-coding	0.009960	0.512922	
chunk0196_406_1	chr8	115987689	115988181	+	0	NA	intron (NR_046215, intron 7 of 13)	intron (NR_046215, intron 7 of 13)	-318907	NM_001282903	7227	Hs.657018	NM_014112	ENSG00000104447	TRPS1	GC79|LGCR	transcriptional repressor GATA binding 1	protein-coding	0.012195	0.389452	
chunk0194_49_1	chr8	82039692	82040506	+	0	NA	Intergenic	Intergenic	-197813	NM_152836	64089	Hs.492121	NM_022133	ENSG00000104497	SNX16	-	sorting nexin 16	protein-coding	0.003686	0.330061	
chunk0135_287_1	chr3	189449758	189450514	+	0	NA	Intergenic	Intergenic	-181291	NM_003722	8626	Hs.137569	NM_003722	ENSG00000073282	TP63	AIS|B(p51A)|B(p51B)|EEC3|KET|LMS|NBP|OFC8|RHS|SHFM4|TP53CP|TP53L|TP73L|p40|p51|p53CP|p63|p73H|p73L	tumor protein p63	protein-coding	0.003968	0.336856	
chunk0196_163_1	chr8	105090277	105090703	+	0	NA	Intergenic	Intergenic	-228429	NM_012082	23414	Hs.431009	NM_012082	ENSG00000169946	ZFPM2	DIH3|FOG2|SRXY9|ZC2HC11B|ZNF89B|hFOG-2	zinc finger protein, FOG family member 2	protein-coding	0.014085	0.381733	
chunk0003_401_1	chr1	40030321	40031101	+	0	NA	Intergenic	L2b|LINE|L2	-9872	NM_006367	10487	Hs.370581	NM_006367	ENSG00000131236	CAP1	CAP|CAP1-PEN	cyclase associated actin cytoskeleton regulatory protein 1	protein-coding	0.005128	0.416133	551(GATGACAGACTGTGCC,-,0.00),552(ATGACAGACTGTGCCT,+,0.00)
chunk0032_65_1	chr11	2217171	2217370	+	0	NA	Intergenic	(CA)n|Simple_repeat|Simple_repeat	44207	NR_039834	100616126		NR_039834	ENSG00000265258	MIR4686	-	microRNA 4686	ncRNA	0.030151	0.615000	
chunk0081_230_1	chr17	42823834	42824129	+	0	NA	promoter-TSS (NR_106839)	promoter-TSS (NR_106839)	-38	NR_106839	102465468		NR_106839	ENSG00000278447	MIR6781	hsa-mir-6781	microRNA 6781	ncRNA	0.040678	0.581081	
chunk0088_438_1	chr18	55894115	55894602	+	0	NA	intron (NR_110755, intron 3 of 3)	intron (NR_110755, intron 3 of 3)	25841	NR_110755	101927273	Hs.434335	NR_110755	ENSG00000260930	LINC01416	-	long intergenic non-protein coding RNA 1416	ncRNA	0.008214	0.375000	
chunk0008_44_1	chr1	88994023	88994275	+	0	NA	Intergenic	MER90|LTR|ERV1	-1189	NM_001008662	56267	Hs.481898	NM_001008661	ENSG00000137944	KYAT3	CCBL2|KAT3|KATIII	kynurenine aminotransferase 3	protein-coding	0.007937	0.367589	
chunk0203_199_1	chr9	86504397	86504615	+	0	NA	Intergenic	MIRb|SINE|MIR	-150019	NM_001185074	79670	Hs.597057	NM_024617	ENSG00000083223	TUT7	PAPD6|TENT3B|ZCCHC6	terminal uridylyl transferase 7	protein-coding	0.000000	0.442922	
chunk0043_13_1	chr12	12883282	12883872	+	0	NA	Intergenic	Intergenic	-7445	NM_003979	9052	Hs.631733	NM_003979	ENSG00000013588	GPRC5A	GPCR5A|PEIG-1|RAI3|RAIG1|TIG1	G protein-coupled receptor class C group 5 member A	protein-coding	0.006780	0.404399	
chunk0150_191_1	chr5	34706871	34707278	+	0	NA	intron (NM_001145525, intron 4 of 19)	intron (NM_001145525, intron 4 of 19)	19515	NM_001145523	26064	Hs.431400	NM_015577	ENSG00000039560	RAI14	NORPEG|RAI13	retinoic acid induced 14	protein-coding	0.014742	0.460784	
chunk0110_438_1	chr20	20894030	20895088	+	0	NA	Intergenic	L2b|LINE|L2	-181936	NM_020343	57186	Hs.472285	NM_020343	ENSG00000188559	RALGAPA2	AS250|C20orf74|bA287B20.1|dJ1049G11|dJ1049G11.4|p220	Ral GTPase activating protein catalytic alpha subunit 2	protein-coding	0.013233	0.447592	
chunk0075_433_1	chr16	57644432	57645017	+	0	NA	intron (NM_001145774, intron 2 of 14)	(CA)n|Simple_repeat|Simple_repeat	5429	NM_001145774	9289	Hs.513633	NM_005682	ENSG00000205336	ADGRG1	BFPP|BPPR|GPR56|TM7LN4|TM7XN1	adhesion G protein-coupled receptor G1	protein-coding	0.018803	0.537543	270(GGGCACACACTGATCA,-,0.00),271(GGCACACACTGATCAC,+,0.00),294(GGCACACACTGATCAC,+,0.00)
chunk0017_409_1	chr1	212860563	212860948	+	0	NA	intron (NM_014053, intron 1 of 9)	L2a|LINE|L2	2500	NM_014053	28982	Hs.7055	NM_014053	ENSG00000162769	FLVCR1	AXPC1|FLVCR|MFSD7B|PCA|PCARP|SLC49A1	feline leukemia virus subgroup C cellular receptor 1	protein-coding	0.000000	0.380829	
chunk0023_262_1	chr10	27677634	27678352	+	0	NA	intron (NM_173576, intron 5 of 6)	intron (NM_173576, intron 5 of 6)	-66622	NR_121652	101929202	Hs.568843	NR_121652		MKX-AS1	-	MKX antisense RNA 1	ncRNA	0.011142	0.396384	444(GAGTACTTTGTGTCCT,-,0.00),445(AGTACTTTGTGTCCTA,+,0.00)
chunk0115_130_1	chr21	23270334	23270766	+	0	NA	Intergenic	Intergenic	114285	NR_040254	266917	Hs.145622	NR_040254	ENSG00000228592	D21S2088E	-	D21S2088E	ncRNA	0.000000	0.281755	
chunk0129_434_1	chr3	127738296	127738696	+	0	NA	intron (NM_001003794, intron 3 of 7)	intron (NM_001003794, intron 3 of 7)	65558	NM_032548	80325	Hs.107812	NM_032548	ENSG00000114626	ABTB1	BPOZ|BTB3|BTBD21|EF1ABP|PP2259	ankyrin repeat and BTB domain containing 1	protein-coding	0.002500	0.548628	
chunk0063_286_1	chr14	84309872	84310595	+	0	NA	Intergenic	Intergenic	-1083646	NR_102737	100996280	Hs.135735	NR_102737	ENSG00000259107	LINC00911	-	long intergenic non-protein coding RNA 911	ncRNA	0.006916	0.305249	
chunk0043_72_1	chr12	14276017	14276501	+	0	NA	Intergenic	MLT1J-int|LTR|ERVL-MaLR	-89373	NM_018179	55729	Hs.504856	NM_018179	ENSG00000171681	ATF7IP	AM|ATF-IP|MCAF|MCAF1|p621	activating transcription factor 7 interacting protein	protein-coding	0.008264	0.424742	
chunk0132_175_1	chr3	156920420	156920733	+	0	NA	exon (NM_001193283, exon 4 of 5)	exon (NM_001193283, exon 4 of 5)	94217	NM_001193283	389170	Hs.478048	NM_001004316	ENSG00000197980	LEKR1	-	leucine, glutamate and lysine rich 1	protein-coding	0.003195	0.254777	
chunk0154_200_1	chr5	80250764	80251217	+	0	NA	intron (NM_178276, intron 1 of 12)	MER67B|LTR|ERV1	5092	NR_126061	256987	Hs.288232	NM_178276	ENSG00000164300	SERINC5	C5orf12|TPO1	serine incorporator 5	protein-coding	0.015453	0.444934	
chunk0089_10_1	chr18	57451743	57451988	+	0	NA	intron (NM_004852, intron 1 of 1)	MLT1H2|LTR|ERVL-MaLR	16180	NM_004852	9480	Hs.194725	NM_004852	ENSG00000119547	ONECUT2	OC-2|OC2	one cut homeobox 2	protein-coding	0.004082	0.475610	
chunk0005_260_1	chr1	59768872	59769234	+	0	NA	Intergenic	Intergenic	-3742	NR_110627	101926944	Hs.720353	NR_110627		LOC101926944	-	uncharacterized LOC101926944	ncRNA	0.013812	0.484848	117(TGGAACATGCAGTTCA,-,0.00),118(GGAACATGCAGTTCAG,+,0.00)
chunk0099_405_1	chr2	102064192	102064519	+	0	NA	Intergenic	Intergenic	-6021	NM_001288706	3554	Hs.701982	NM_000877	ENSG00000115594	IL1R1	CD121A|D2S1473|IL-1R-alpha|IL1R|IL1RA|P80	interleukin 1 receptor type 1	protein-coding	0.012232	0.573171	112(GAGTACACGGTGTGCT,-,0.00),113(AGTACACGGTGTGCTG,+,0.00)
chunk0074_258_1	chr16	28032518	28032943	+	0	NA	intron (NM_001109763, intron 1 of 6)	L2b|LINE|L2	30779	NM_001109763	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.007059	0.471831	
chunk0145_245_1	chr4	148752651	148753046	+	0	NA	Intergenic	Intergenic	-310328	NM_001166104	4306	Hs.163924	NM_000901	ENSG00000151623	NR3C2	MCR|MLR|MR|NR3C2VIT	nuclear receptor subfamily 3 group C member 2	protein-coding	0.010127	0.406566	170(TGGGACAGGATGTTCT,-,0.00),171(GGGACAGGATGTTCTA,+,0.00)
chunk0104_87_1	chr2	172061185	172061487	+	0	NA	intron (NM_199227, intron 1 of 9)	intron (NM_199227, intron 1 of 9)	-24144	NM_178120	1745	Hs.407015	NM_178120	ENSG00000144355	DLX1	-	distal-less homeobox 1	protein-coding	0.009934	0.320132	
chunk0111_233_1	chr20	29326566	29326877	+	0	NA	Intergenic	Intergenic	90240	NR_037925	647476	Hs.274541	NR_037925		FRG2EP	-	FSHD region gene 2 family member E, pseudogene	pseudo	0.045016	0.634615	22(CAGGACAGGGTGTGCT,-,0.00),23(AGGACAGGGTGTGCTT,+,0.00)
chunk0078_138_1	chr17	3757183	3757532	+	0	NA	intron (NM_002208, intron 9 of 30)	L2b|LINE|L2	33454	NM_031965	83903	Hs.534059	NM_031965	ENSG00000177602	HASPIN	GSG2	histone H3 associated protein kinase	protein-coding	0.005731	0.580000	174(CTGCACATGCTGTTCC,-,0.00),175(TGCACATGCTGTTCCC,+,0.00)
chunk0181_296_1	chr7	86984294	86984871	+	0	NA	intron (NM_001142749, intron 1 of 21)	L1PA6|LINE|L1	-18607	NM_152748	222223	Hs.208093	NM_152748	ENSG00000164659	KIAA1324L	EIG121L	KIAA1324 like	protein-coding	0.003466	0.375433	350(AAAGACACAATGTACC,-,0.00)
chunk0177_65_1	chr7	21206232	21206687	+	0	NA	Intergenic	Intergenic	-221612	NM_003112	6671	Hs.88013	NM_003112	ENSG00000105866	SP4	HF1B|SPR-1	Sp4 transcription factor	protein-coding	0.006593	0.348684	239(TAGGACATGCTGTTCT,-,0.00),240(AGGACATGCTGTTCTT,+,0.00)
chunk0025_224_1	chr10	53986106	53986764	+	0	NA	intron (NM_001142769, intron 23 of 35)	L1MB1|LINE|L1	621522	NR_031642	100302192		NR_031642	ENSG00000221594	MIR548F1	MIR548F-1|MIRN548F1|hsa-mir-548f-1	microRNA 548f-1	ncRNA	0.006079	0.326252	
chunk0162_59_1	chr6	1413706	1414299	+	0	NA	Intergenic	Intergenic	-23591	NR_106778	102466720		NR_106778	ENSG00000275859	MIR6720	hsa-mir-6720|mir-6720	microRNA 6720	ncRNA	0.008432	0.427609	
chunk0001_163_1	chr1	6393307	6393599	+	0	NA	5' UTR (NM_007274, exon 1 of 9)	5' UTR (NM_007274, exon 1 of 9)	313	NM_007274	11332	Hs.126137	NM_007274	ENSG00000097021	ACOT7	ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH	acyl-CoA thioesterase 7	protein-coding	0.136986	0.784983	
chunk0179_223_1	chr7	47806646	47807137	+	0	NA	intron (NM_138295, intron 52 of 56)	MER70B|LTR|ERVL	11600	NM_001302627	80099	Hs.287647	NM_025031		C7orf69	-	chromosome 7 open reading frame 69	ncRNA	0.014257	0.514228	
chunk0001_406_1	chr1	10944026	10944225	+	0	NA	Intergenic	Intergenic	37912	NM_001170754	148345	Hs.127026	NM_173507	ENSG00000175262	C1orf127	-	chromosome 1 open reading frame 127	protein-coding	0.025126	0.500000	
chunk0112_371_1	chr20	45971513	45972002	+	0	NA	intron (NM_022095, intron 1 of 27)	CpG-17795	437	NM_022095	63925	Hs.174193	NM_022095	ENSG00000198026	ZNF335	MCPH10|NIF-1|NIF1|NIF2	zinc finger protein 335	protein-coding	0.079755	0.669388	
chunk0199_18_1	chr9	570981	571689	+	0	NA	intron (NM_001256877, intron 2 of 12)	intron (NM_001256877, intron 2 of 12)	66640	NM_001256877	23189	Hs.306764	NM_015158	ENSG00000107104	KANK1	ANKRD15|CPSQ2|KANK	KN motif and ankyrin repeat domains 1	protein-coding	0.007062	0.359661	354(GTTACAGAGTGTTCCT,+,0.00)
chunk0100_302_1	chr2	115277303	115277825	+	0	NA	intron (NM_001004360, intron 1 of 25)	intron (NM_001004360, intron 1 of 25)	115457	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.001916	0.282983	
chunk0015_196_1	chr1	187343244	187343449	+	0	NA	intron (NR_126347, intron 3 of 3)	intron (NR_126347, intron 3 of 3)	-100282	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.009756	0.339806	
chunk0102_248_1	chr2	149071145	149071497	+	0	NA	intron (NM_001317006, intron 1 of 4)	intron (NM_001317006, intron 1 of 4)	-6201	NM_001317004	130576	Hs.357567	NM_177964	ENSG00000150556	LYPD6B	CT116|LYPD7	LY6/PLAUR domain containing 6B	protein-coding	0.005682	0.351275	
chunk0003_344_1	chr1	39026293	39026952	+	0	NA	intron (NM_004552, intron 1 of 2)	intron (NM_004552, intron 1 of 2)	327	NM_004552	4725	Hs.632385	NM_004552	ENSG00000168653	NDUFS5	CI-15k|CI15K	NADH:ubiquinone oxidoreductase subunit S5	protein-coding	0.059181	0.550000	526(GGAACACTCTGCCCAC,+,0.00)
chunk0131_262_1	chr3	149971141	149971440	+	0	NA	promoter-TSS (NM_053024)	promoter-TSS (NM_053024)	11	NR_036538	646903	Hs.632559	NR_036538		LOC646903	-	uncharacterized LOC646903	ncRNA	0.167224	0.780000	
chunk0056_23_1	chr13	77228769	77229301	+	0	NA	intron (NM_015057, intron 18 of 82)	MIRb|SINE|MIR	98007	NM_015057	23077	Hs.591221	NM_015057	ENSG00000005810	MYCBP2	Myc-bp2|PAM|PHR1|Phr	MYC binding protein 2	protein-coding	0.000000	0.324578	
chunk0085_133_1	chr18	3153328	3153754	+	0	NA	intron (NM_019856, intron 11 of 36)	intron (NM_019856, intron 11 of 36)	66567	NM_003803	8736	Hs.464469	NM_003803	ENSG00000101605	MYOM1	SKELEMIN	myomesin 1	protein-coding	0.011737	0.358314	170(GAGAACAAAATGTACT,-,0.00),171(AGAACAAAATGTACTT,+,0.00)
chunk0087_92_1	chr18	32393437	32393736	+	0	NA	intron (NM_001242409, intron 1 of 5)	intron (NM_001242409, intron 1 of 5)	76898	NM_022751	64762	Hs.444314	NM_022751	ENSG00000141441	GAREM1	C18orf11|FAM59A|GAREM|Gm944	GRB2 associated regulator of MAPK1 subtype 1	protein-coding	0.003344	0.280000	
chunk0042_191_1	chr12	5251932	5252525	+	0	NA	Intergenic	Intergenic	-9077	NR_120477	101929584	Hs.436529	NR_120476	ENSG00000256115	LINC02443	-	long intergenic non-protein coding RNA 2443	ncRNA	0.008432	0.333333	275(AGGTACAGATTGTGCT,-,0.00),276(GGTACAGATTGTGCTT,+,0.00)
chunk0005_79_1	chr1	56007466	56007790	+	0	NA	Intergenic	LTR82A|LTR|ERVL	571956	NM_003713	8613	Hs.405156	NM_003713	ENSG00000162407	PLPP3	Dri42|LPP3|PAP2B|PPAP2B|VCIP	phospholipid phosphatase 3	protein-coding	0.000000	0.363077	
chunk0061_281_1	chr14	61545600	61546208	+	0	NA	intron (NM_006255, intron 12 of 13)	intron (NM_006255, intron 12 of 13)	24290	NR_110417	101927780	Hs.254789	NR_110416	ENSG00000250548	LINC01303	-	long intergenic non-protein coding RNA 1303	ncRNA	0.009868	0.486043	317(AAGAACAGGCTGTACC,-,0.00),318(AGAACAGGCTGTACCC,+,0.00)
chunk0145_376_1	chr4	151553629	151554171	+	0	NA	intron (NM_001109977, intron 3 of 13)	intron (NM_001109977, intron 3 of 13)	144654	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.005535	0.408840	
chunk0098_121_1	chr2	68767981	68768684	+	0	NA	intron (NM_001007231, intron 1 of 10)	intron (NM_001007231, intron 1 of 10)	-6469	NM_001166276	9938	Hs.531807	NM_014882	ENSG00000163219	ARHGAP25	HEL-S-308|KAIA0053	Rho GTPase activating protein 25	protein-coding	0.009957	0.406250	
chunk0136_35_1	chr4	1082371	1082570	+	0	NA	intron (NM_194439, intron 5 of 9)	intron (NM_194439, intron 5 of 9)	31094	NM_001131034	285498	Hs.248290	NM_194439	ENSG00000178222	RNF212	ZHP3	ring finger protein 212	protein-coding	0.020101	0.570000	
chunk0184_195_1	chr7	116942697	116943749	+	0	NA	Intergenic	Intergenic	-10104	NM_021908	7982	Hs.368131	NM_018412	ENSG00000004866	ST7	ETS7q|FAM4A|FAM4A1|HELG|RAY1|SEN4|TSG7	suppression of tumorigenicity 7	protein-coding	0.003802	0.308642	
chunk0145_367_1	chr4	151450180	151450746	+	0	NA	intron (NM_001109977, intron 1 of 13)	L1ME3G|LINE|L1	41217	NM_001109977	729830	Hs.633810	NM_001109977	ENSG00000164142	FAM160A1	-	family with sequence similarity 160 member A1	protein-coding	0.005300	0.296296	
chunk0066_82_1	chr15	29602959	29603158	+	0	NA	Intergenic	Intergenic	-32335	NM_015307	23359	Hs.383564	NM_015307	ENSG00000104059	FAM189A1	TMEM228	family with sequence similarity 189 member A1	protein-coding	0.015075	0.525000	
chunk0178_350_1	chr7	38776369	38776589	+	0	NA	intron (NM_080631, intron 10 of 27)	intron (NM_080631, intron 10 of 27)	-89390	NR_028347	340286	Hs.144075	NM_001105282	ENSG00000164556	FAM183BP	FAM183B|THEG6	acyloxyacyl hydrolase (neutrophil)	pseudo	0.009091	0.393665	
chunk0027_209_1	chr10	76033194	76033987	+	0	NA	intron (NR_131178, intron 3 of 7)	intron (NR_131178, intron 3 of 7)	250829	NM_032024	83938	Hs.118161	NM_032024	ENSG00000148655	LRMDA	C10orf11|CDA017	leucine rich melanocyte differentiation associated	protein-coding	0.015132	0.497481	452(AGGAACAATGTGTATT,-,0.00),453(GGAACAATGTGTATTT,+,0.00)
chunk0190_299_1	chr8	38064115	38064355	+	0	NA	Intergenic	Intergenic	33733	NM_004095	1978	Hs.411641	NM_004095	ENSG00000187840	EIF4EBP1	4E-BP1|4EBP1|BP-1|PHAS-I	eukaryotic translation initiation factor 4E binding protein 1	protein-coding	0.016667	0.526971	
chunk0119_234_1	chr22	45337197	45337468	+	0	NA	intron (NM_001104595, intron 9 of 9)	intron (NM_001104595, intron 9 of 9)	27428	NM_017911	55007	Hs.265018	NM_017911	ENSG00000100376	FAM118A	C22orf8	family with sequence similarity 118 member A	protein-coding	0.029520	0.474265	
chunk0093_273_1	chr19	51644738	51645275	+	0	NA	intron (NM_001098612, intron 4 of 6)	intron (NM_001098612, intron 4 of 6)	1873	NM_001098612	100049587	Hs.707374	NM_001098612	ENSG00000254415	SIGLEC14	-	sialic acid binding Ig like lectin 14	protein-coding	0.016760	0.464684	275(GGGAACAGCGTGTCCT,-,0.00),276(GGAACAGCGTGTCCTG,+,0.00)
chunk0207_355_1	chr9	135282051	135282503	+	0	NA	Intergenic	Intergenic	-60972	NM_173520	157927	Hs.559511	NM_173520		C9orf62	-	chromosome 9 open reading frame 62	protein-coding	0.024336	0.576159	299(GAGCACACAGAGTCCC,-,0.00),300(AGCACACAGAGTCCCC,+,0.00)
chunk0205_26_1	chr9	105364856	105365230	+	0	NA	intron (NM_001286730, intron 10 of 15)	intron (NM_001286730, intron 10 of 15)	-82991	NM_001145313	83856	Hs.136901	NM_031919	ENSG00000106701	FSD1L	CCDC10|CSDUFD1|FSD1CL|FSD1NL|MIR1	fibronectin type III and SPRY domain containing 1 like	protein-coding	0.005348	0.306667	
chunk0120_238_1	chr3	8505688	8506135	+	0	NA	intron (NM_001278233, intron 1 of 4)	intron (NM_001278233, intron 1 of 4)	4104	NM_001278234	29995	Hs.475353	NM_014583	ENSG00000071282	LMCD1	-	LIM and cysteine rich domains 1	protein-coding	0.006711	0.433036	
chunk0055_366_1	chr13	71835205	71835404	+	0	NA	intron (NM_004392, intron 1 of 6)	intron (NM_004392, intron 1 of 6)	31888	NM_080759	1602	Hs.129452	NM_004392	ENSG00000276644	DACH1	DACH	dachshund family transcription factor 1	protein-coding	0.005025	0.335000	
chunk0009_164_1	chr1	105287180	105287782	+	0	NA	Intergenic	Intergenic	331454	NR_125955	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.004983	0.424544	497(CAGAACAGGGTGTTTC,-,0.00),498(AGAACAGGGTGTTTCG,+,0.00)
chunk0064_139_1	chr14	91534959	91535423	+	0	NA	Intergenic	Intergenic	-24711	NM_001284281	55671	Hs.533887	NM_017936	ENSG00000100796	PPP4R3A	FLFL1|KIAA2010|MSTP033|PP4R3|PP4R3A|SMEK1|smk-1|smk1	protein phosphatase 4 regulatory subunit 3A	protein-coding	0.010776	0.397849	
chunk0027_328_1	chr10	78426115	78426732	+	0	NA	Intergenic	MER63A|DNA|hAT-Blackjack	159095	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.004862	0.339806	
chunk0068_404_1	chr15	58933388	58933954	+	0	NA	promoter-TSS (NM_024755)	promoter-TSS (NM_024755)	-18	NM_001013843	79811	Hs.512932	NM_017968	ENSG00000137776	SLTM	Met	SAFB like transcription modulator	protein-coding	0.127208	0.687831	
chunk0017_382_1	chr1	212201457	212202147	+	0	NA	Intergenic	Intergenic	32934	NR_125982	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.008696	0.354559	493(CAGTACAGACTGTATT,-,0.00),494(AGTACAGACTGTATTT,+,0.00)
chunk0106_39_1	chr2	196189862	196190104	+	0	NA	Intergenic	L1MC3|LINE|L1	-18371	NM_004226	9262	Hs.88297	NM_004226	ENSG00000081320	STK17B	DRAK2	serine/threonine kinase 17b	protein-coding	0.012397	0.419753	
chunk0104_306_1	chr2	178905227	178905720	+	0	NA	exon (NM_001316745, exon 8 of 12)	exon (NM_001316745, exon 8 of 12)	-98050	NM_001256850	7273	Hs.134602	NM_003319	ENSG00000155657	TTN	CMD1G|CMH9|CMPD4|EOMFC|HMERF|LGMD2J|LGMDR10|MYLK5|SALMY|TMD	titin	protein-coding	0.004057	0.356275	
chunk0148_242_1	chr5	9641728	9642248	+	0	NA	intron (NR_027112, intron 11 of 12)	intron (NR_027112, intron 11 of 12)	-11637	NM_019599	50834	Hs.567492	NM_019599	ENSG00000169777	TAS2R1	T2R1|TRB7	taste 2 receptor member 1	protein-coding	0.013462	0.381958	
chunk0068_259_1	chr15	56292028	56292388	+	0	NA	Intergenic	ERV3-16A3_I-int|LTR|ERVL	-48923	NM_022841	64864	Hs.745089	NM_022841	ENSG00000181827	RFX7	RFXDC2	regulatory factor X7	protein-coding	0.002778	0.432133	216(AGGAACATAGAGTACC,-,0.00),217(GGAACATAGAGTACCT,+,0.00)
chunk0208_440_1	chrX	30644223	30644702	+	0	NA	Intergenic	L1MC1|LINE|L1	-8897	NM_000167	2710	Hs.1466	NM_000167	ENSG00000198814	GK	GK1|GKD	glycerol kinase	protein-coding	0.004175	0.350000	
chunk0119_372_1	chr22	47631796	47632373	+	0	NA	promoter-TSS (NR_033377)	promoter-TSS (NR_033377)	410	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.046794	0.558824	
chunk0201_248_1	chr9	37904277	37904551	+	0	NA	promoter-TSS (NM_033412)	promoter-TSS (NM_033412)	-61	NR_024873	92014	Hs.634120	NM_033412	ENSG00000122696	SLC25A51	CG7943|MCART1	solute carrier family 25 member 51	protein-coding	0.072993	0.610909	
chunk0186_323_1	chr7	143095876	143096519	+	0	NA	Intergenic	Intergenic	-32412	NR_002140	89883	Hs.339818	NR_002140		OR6W1P	OR6W1|sdolf	olfactory receptor family 6 subfamily W member 1 pseudogene	pseudo	0.004666	0.436335	331(AAGAACAATCTGTCTC,-,0.00),332(AGAACAATCTGTCTCC,+,0.00)
chunk0211_371_1	chrX	126439802	126440044	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	112936	NM_178470	139170	Hs.120403	NM_178470	ENSG00000198889	DCAF12L1	KIAA1892L|WDR40B	DDB1 and CUL4 associated factor 12 like 1	protein-coding	0.004132	0.362140	
chunk0177_445_1	chr7	28088619	28088926	+	0	NA	intron (NM_175061, intron 1 of 4)	intron (NM_175061, intron 1 of 4)	-91685	NR_034097	100128081	Hs.434307	NR_034097		JAZF1-AS1	-	JAZF1 antisense RNA 1	ncRNA	0.000000	0.379870	
chunk0166_187_1	chr6	46169889	46170088	+	0	NA	intron (NM_021572, intron 1 of 3)	intron (NM_021572, intron 1 of 3)	1022	NM_021572	59084	Hs.35198	NM_021572	ENSG00000112796	ENPP5	NPP-5|NPP5	ectonucleotide pyrophosphatase/phosphodiesterase family member 5	protein-coding	0.005025	0.365000	
chunk0145_80_1	chr4	145785509	145786089	+	0	NA	intron (NM_178835, intron 8 of 14)	intron (NM_178835, intron 8 of 14)	105595	NM_001080531	646603		NM_001080531	ENSG00000237136	C4orf51	-	chromosome 4 open reading frame 51	protein-coding	0.003448	0.414802	
chunk0049_192_1	chr12	92991086	92991452	+	0	NA	Intergenic	L1ME1|LINE|L1	-61938	NM_003566	8411	Hs.567367	NM_003566	ENSG00000102189	EEA1	MST105|MSTP105|ZFYVE2	early endosome antigen 1	protein-coding	0.008197	0.373297	
chunk0130_165_1	chr3	132988252	132988451	+	0	NA	Intergenic	MLT1G1|LTR|ERVL-MaLR	-49937	NM_001136469	66000	Hs.191616	NM_023943	ENSG00000144868	TMEM108	CT124|RTLN	transmembrane protein 108	protein-coding	0.000000	0.370000	
chunk0034_51_1	chr11	26947677	26947980	+	0	NA	Intergenic	Intergenic	-46253	NM_203371	387758	Hs.712718	NM_203371	ENSG00000176971	FIBIN	-	fin bud initiation factor homolog	protein-coding	0.006601	0.421053	
chunk0052_323_1	chr12	125634717	125635271	+	0	NA	intron (NM_001286219, intron 1 of 4)	L1MA2|LINE|L1	12542	NM_001286219	114795	Hs.524838	NM_052907	ENSG00000139364	TMEM132B	-	transmembrane protein 132B	protein-coding	0.003610	0.475676	
chunk0104_247_1	chr2	177240156	177240892	+	0	NA	intron (NM_001313902, intron 1 of 3)	intron (NM_001313902, intron 1 of 3)	15486	NR_036075	100422824		NR_036075	ENSG00000265396	MIR3128	mir-3128	microRNA 3128	ncRNA	0.004076	0.394844	
chunk0164_321_1	chr6	25137596	25138016	+	0	NA	promoter-TSS (NR_002174)	promoter-TSS (NR_002174)	17	NR_002174	8418	Hs.484918	NR_002174	ENSG00000168405	CMAHP	CMAH|CSAH	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	pseudo	0.016667	0.420428	
chunk0017_440_1	chr1	214193321	214193625	+	0	NA	Intergenic	Intergenic	-87749	NM_020197	56950	Hs.66170	NM_020197	ENSG00000143499	SMYD2	HSKM-B|KMT3C|ZMYND14	SET and MYND domain containing 2	protein-coding	0.026316	0.511475	132(AGGAACACTGTGTCCC,-,0.00),133(GGAACACTGTGTCCCG,+,0.00)
chunk0160_257_1	chr5	156883054	156883289	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	32633	NR_038443	153743	Hs.567727	NM_206858	ENSG00000231989	PPP1R2B	PPP1R2P3	PPP1R2 family member B	protein-coding	0.000000	0.521186	
chunk0020_101_1	chr1	232967419	232967835	+	0	NA	intron (NM_032324, intron 3 of 4)	intron (NM_032324, intron 3 of 4)	17003	NM_032324	84284	Hs.642715	NM_032324	ENSG00000135778	NTPCR	C1orf57|HCR-NTPase|THEP1	nucleoside-triphosphatase, cancer-related	protein-coding	0.007212	0.381295	
chunk0033_135_1	chr11	15309222	15309705	+	0	NA	Intergenic	Intergenic	160361	NM_001278313	387755	Hs.591997	NM_001031853	ENSG00000188487	INSC	-	INSC spindle orientation adaptor protein	protein-coding	0.004141	0.388430	
chunk0197_191_1	chr8	121431558	121432019	+	0	NA	Intergenic	Intergenic	-207558	NR_002835	594842	Hs.668686	NR_002835		HAS2-AS1	HAS2-AS|HAS2AS|HASNT|NCRNA00077	HAS2 antisense RNA 1	ncRNA	0.004338	0.393939	
chunk0088_432_1	chr18	55581127	55581398	+	0	NA	intron (NM_003199, intron 3 of 19)	intron (NM_003199, intron 3 of 19)	4857	NM_001306207	6925	Hs.605153	NM_003199	ENSG00000196628	TCF4	E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19	transcription factor 4	protein-coding	0.003690	0.375000	
chunk0081_393_1	chr17	48225886	48226227	+	0	NA	intron (NM_001075099, intron 4 of 12)	intron (NM_001075099, intron 4 of 12)	-68291	NR_131239	105371807	Hs.661105	NR_131239	ENSG00000235300	THRA1/BTR	-	uncharacterized LOC105371807	ncRNA	0.008798	0.479532	245(TGGTACAGGATGTTCC,-,0.00),246(GGTACAGGATGTTCCC,+,0.00)
chunk0092_62_1	chr19	20280487	20280686	+	0	NA	Intergenic	HERVK-int|LTR|ERVK	113372	NM_052852	90649	Hs.590991	NM_052852	ENSG00000256229	ZNF486	KRBO2	zinc finger protein 486	protein-coding	0.000000	0.405000	
chunk0098_297_1	chr2	76122989	76123564	+	0	NA	Intergenic	Intergenic	-412291	NM_001201335	6936	Hs.303808	NM_003203	ENSG00000005436	GCFC2	C2orf3|DNABF|GCF|TCF9	GC-rich sequence DNA-binding factor 2	protein-coding	0.003478	0.364583	
chunk0048_69_1	chr12	78799472	78800220	+	0	NA	Intergenic	Intergenic	-64147	NM_001135805	6857	Hs.310545	NM_005639	ENSG00000067715	SYT1	BAGOS|P65|SVP65|SYT	synaptotagmin 1	protein-coding	0.004011	0.411215	
chunk0130_106_1	chr3	131158157	131158526	+	0	NA	intron (NM_145910, intron 10 of 14)	L1PA13|LINE|L1	-131487	NM_014065	28990	Hs.100878	NM_014065	ENSG00000034533	ASTE1	HT001	asteroid homolog 1	protein-coding	0.010840	0.575676	
chunk0180_355_1	chr7	73721486	73721825	+	0	NA	Intergenic	Intergenic	-1968	NM_001165903	6804	Hs.647024	NM_004603	ENSG00000106089	STX1A	HPC-1|P35-1|STX1|SYN1A	syntaxin 1A	protein-coding	0.011799	0.591176	
chunk0167_113_1	chr6	57283948	57284804	+	0	NA	Intergenic	Intergenic	-21030	NR_109774	100506188	Hs.485640	NR_109774		LOC100506188	-	uncharacterized LOC100506188	ncRNA	0.004673	0.313886	
chunk0066_47_1	chr15	27956447	27956676	+	0	NA	intron (NM_001300984, intron 15 of 22)	intron (NM_001300984, intron 15 of 22)	142751	NM_000275	4948	Hs.654411	NM_000275	ENSG00000104044	OCA2	BEY|BEY1|BEY2|BOCA|D15S12|EYCL|EYCL2|EYCL3|HCL3|P|PED|SHEP1	OCA2 melanosomal transmembrane protein	protein-coding	0.013100	0.478261	
chunk0138_110_1	chr4	36197698	36197915	+	0	NA	intron (NM_015230, intron 6 of 32)	MER52A|LTR|ERV1	-46310	NR_122079	439933	Hs.591071	NR_122079	ENSG00000247193	LOC439933	-	uncharacterized LOC439933	ncRNA	0.013825	0.619266	
chunk0142_17_1	chr4	90334170	90334745	+	0	NA	intron (NM_001145065, intron 3 of 10)	intron (NM_001145065, intron 3 of 10)	99426	NM_207491	401145	Hs.654735	NM_207491	ENSG00000184305	CCSER1	FAM190A	coiled-coil serine rich protein 1	protein-coding	0.005217	0.314236	
chunk0054_310_1	chr13	48585574	48585773	+	0	NA	Intergenic	Intergenic	-4772	NR_051983	100129597	Hs.175225	NR_051983	ENSG00000233610	LINC00462	-	long intergenic non-protein coding RNA 462	ncRNA	0.010050	0.435000	
chunk0091_104_1	chr19	5883536	5883751	+	0	NA	Intergenic	L1MC1|LINE|L1	-13103	NM_002034	2527	Hs.631843	NM_002034	ENSG00000130383	FUT5	FUC-TV	fucosyltransferase 5	protein-coding	0.000000	0.439815	
chunk0072_257_1	chr15	96213801	96214372	+	0	NA	intron (NR_125738, intron 2 of 4)	intron (NR_125738, intron 2 of 4)	-111842	NM_001145155	7026	Hs.347991	NM_021005	ENSG00000185551	NR2F2	ARP-1|ARP1|CHTD4|COUPTF2|COUPTFB|COUPTFII|NF-E3|SVP40|TFCOUP2	nuclear receptor subfamily 2 group F member 2	protein-coding	0.008757	0.410839	
chunk0018_355_1	chr1	221701618	221701941	+	0	NA	non-coding (NR_111940, exon 3 of 3)	non-coding (NR_111940, exon 3 of 3)	35121	NR_111939	11221	Hs.497822	NM_007207	ENSG00000143507	DUSP10	MKP-5|MKP5	dual specificity phosphatase 10	protein-coding	0.000000	0.364198	
chunk0001_32_1	chr1	1393493	1393889	+	0	NA	intron (NM_001039577, intron 4 of 5)	intron (NM_001039577, intron 4 of 5)	5647	NM_030937	81669	Hs.515704	NM_030937	ENSG00000221978	CCNL2	ANIA-6B|CCNM|CCNS|HCLA-ISO|HLA-ISO|PCEE|SB138	cyclin L2	protein-coding	0.022727	0.541562	
chunk0139_399_1	chr4	62890903	62891330	+	0	NA	Intergenic	L1MC1|LINE|L1	-729351	NR_110595	101927186	Hs.723269	NR_110595		ADGRL3-AS1	LPHN3-AS1	adhesion G protein-coupled receptor L3 antisense RNA 1	ncRNA	0.002342	0.355140	
chunk0199_147_1	chr9	4144618	4145534	+	0	NA	intron (NM_001042413, intron 2 of 10)	intron (NM_001042413, intron 2 of 10)	7107	NM_152629	169792	Hs.162125	NM_152629	ENSG00000107249	GLIS3	NDH|ZNF515	GLIS family zinc finger 3	protein-coding	0.006550	0.382770	264(AAGAACATGCTGTTTA,-,0.00),265(AGAACATGCTGTTTAT,+,0.00)
chunk0023_268_1	chr10	27843182	27843384	+	0	NA	intron (NM_001290020, intron 19 of 19)	intron (NM_001290020, intron 19 of 19)	-97434	NM_001242702	283078	Hs.128193	NM_173576	ENSG00000150051	MKX	C10orf48|IFRX|IRXL1	mohawk homeobox	protein-coding	0.009901	0.320197	
chunk0175_68_1	chr7	2091767	2092148	+	0	NA	intron (NM_003550, intron 11 of 18)	L1MC3|LINE|L1	140991	NM_001013837	8379	Hs.654838	NM_003550	ENSG00000002822	MAD1L1	MAD1|PIG9|TP53I9|TXBP181	mitotic arrest deficient 1 like 1	protein-coding	0.020997	0.437173	
chunk0161_89_1	chr5	167245043	167245242	+	0	NA	Intergenic	Intergenic	-39696	NM_001122679	57451	Hs.631957	NM_001080428	ENSG00000145934	TENM2	ODZ2|TEN-M2|TNM2|ten-2	teneurin transmembrane protein 2	protein-coding	0.005025	0.360000	
chunk0104_365_1	chr2	180034228	180034610	+	0	NA	Intergenic	L1MA2|LINE|L1	-27366	NM_020943	57703	Hs.311363	NM_020943	ENSG00000163510	CWC22	EIF4GL|NCM|fSAPb	CWC22 spliceosome associated protein homolog	protein-coding	0.007853	0.483029	
chunk0173_427_1	chr6	151056582	151057359	+	0	NA	intron (NM_001242767, intron 26 of 27)	intron (NM_001242767, intron 26 of 27)	171487	NR_125868	102723831	Hs.684425	NR_125868		LOC102723831	-	uncharacterized LOC102723831	ncRNA	0.010296	0.449871	
chunk0208_382_1	chrX	28639718	28639941	+	0	NA	intron (NM_014271, intron 1 of 10)	LTR16A2|LTR|ERVL	52265	NM_014271	11141	Hs.658912	NM_014271	ENSG00000169306	IL1RAPL1	IL-1-RAPL-1|IL-1RAPL-1|IL1R8|IL1RAPL|IL1RAPL-1|MRX10|MRX21|MRX34|OPHN4|TIGIRR-2	interleukin 1 receptor accessory protein like 1	protein-coding	0.000000	0.415179	
chunk0055_305_1	chr13	66312646	66313249	+	0	NA	intron (NM_203487, intron 4 of 4)	intron (NM_203487, intron 4 of 4)	94697	NR_039853	100616205		NR_039853	ENSG00000263561	MIR4704	-	microRNA 4704	ncRNA	0.006633	0.352649	
chunk0039_237_1	chr11	102007557	102007756	+	0	NA	Intergenic	L2c|LINE|L2	-39782	NM_032930	85016	Hs.98328	NM_032930	ENSG00000137691	CFAP300	C11orf70|CILD38	cilia and flagella associated protein 300	protein-coding	0.005025	0.445000	124(CAGAACAGTATGTTCA,-,0.00),125(AGAACAGTATGTTCAA,+,0.00)
chunk0178_201_1	chr7	34552513	34553057	+	0	NA	intron (NR_033665, intron 2 of 3)	L1PREC2|LINE|L1	-105454	NM_001300934	387129	Hs.652373	NM_207172	ENSG00000187258	NPSR1	ASRT2|GPR154|GPRA|NPSR|PGR14|VRR1	neuropeptide S receptor 1	protein-coding	0.009191	0.585321	
chunk0052_16_1	chr13	20123227	20123570	+	0	NA	Intergenic	MIR3|SINE|MIR	20697	NR_126380	104355137	Hs.578016	NR_126380	ENSG00000236076	LINC01072	-	long intergenic non-protein coding RNA 1072	ncRNA	0.002915	0.438953	
chunk0006_371_1	chr1	73321139	73321792	+	0	NA	intron (NR_110676, intron 3 of 3)	L1PA17|LINE|L1	15295	NR_110676	101927295	Hs.436589	NR_110676	ENSG00000233973	LINC01360	-	long intergenic non-protein coding RNA 1360	ncRNA	0.003063	0.359327	
chunk0013_118_1	chr1	167937364	167937648	+	0	NA	promoter-TSS (NM_015415)	promoter-TSS (NM_015415)	-437	NM_015415	25874	Hs.517768	NM_015415	ENSG00000143158	MPC2	BRP44|SLC54A2	mitochondrial pyruvate carrier 2	protein-coding	0.063380	0.564912	
chunk0159_357_1	chr5	144876890	144877384	+	0	NA	Intergenic	Intergenic	706264	NM_020768	57528	Hs.7093	NM_020768	ENSG00000183775	KCTD16	-	potassium channel tetramerization domain containing 16	protein-coding	0.000000	0.301010	143(AAGTACAGCCTGTTAC,-,0.00),144(AGTACAGCCTGTTACT,+,0.00)
chunk0155_263_1	chr5	95857065	95857769	+	0	NA	intron (NR_026936, intron 2 of 2)	intron (NR_026936, intron 2 of 2)	5185	NR_026936	202299	Hs.8373	NM_175616	ENSG00000236882	LINC01554	C5orf27|FIS	long intergenic non-protein coding RNA 1554	ncRNA	0.017045	0.539007	418(CAGAACTGTGTGTTCC,-,0.00),419(AGAACTGTGTGTTCCA,+,0.00)
chunk0173_24_1	chr6	141775884	141776115	+	0	NA	Intergenic	L1PA14|LINE|L1	312800	NM_002511	4829	Hs.552106	NM_002511	ENSG00000135577	NMBR	BB1|BB1R|NMB-R	neuromedin B receptor	protein-coding	0.004329	0.357759	
chunk0186_16_1	chr7	135746363	135746723	+	0	NA	intron (NM_205855, intron 1 of 3)	intron (NM_205855, intron 1 of 3)	2303	NM_205855	389558	Hs.55200	NM_205855	ENSG00000189320	FAM180A	UNQ1940	family with sequence similarity 180 member A	protein-coding	0.005556	0.412742	
chunk0117_170_1	chr22	20431103	20431366	+	0	NA	exon (NM_153334, exon 4 of 11)	exon (NM_153334, exon 4 of 11)	6625	NM_182895	91179	Hs.474251	NM_153334	ENSG00000244486	SCARF2	NSR1|SREC-II|SREC2|SRECRP-1|VDEGS	scavenger receptor class F member 2	protein-coding	0.136882	0.727273	
chunk0077_107_1	chr16	78200494	78201152	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	101410	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.009119	0.389985	
chunk0004_203_1	chr1	46643144	46643863	+	0	NA	intron (NM_001256418, intron 8 of 9)	intron (NM_001256418, intron 8 of 9)	22375	NM_001243728	64756	Hs.100874	NM_022745	ENSG00000123472	ATPAF1	ATP11|ATP11p	ATP synthase mitochondrial F1 complex assembly factor 1	protein-coding	0.001391	0.434722	
chunk0089_394_1	chr18	68107728	68108197	+	0	NA	Intergenic	L1MC3|LINE|L1	-591232	NM_032160	92126	Hs.124673	NM_032160	ENSG00000171451	DSEL	C18orf4|DE-epi2	dermatan sulfate epimerase like	protein-coding	0.004264	0.382979	
chunk0184_2_1	chr7	111550670	111551390	+	0	NA	intron (NM_032549, intron 1 of 5)	intron (NM_032549, intron 1 of 5)	11261	NM_032549	83943	Hs.655722	NM_032549	ENSG00000184903	IMMP2L	IMMP2L-IT1|IMP2|IMP2-LIKE	inner mitochondrial membrane peptidase subunit 2	protein-coding	0.002778	0.353675	
chunk0123_189_1	chr3	44321347	44321775	+	0	NA	intron (NM_001145030, intron 17 of 19)	intron (NM_001145030, intron 17 of 19)	-16558	NM_001282915	285343	Hs.55131	NM_173826	ENSG00000179152	TCAIM	C3orf23|TOAG-1|TOAG1	T cell activation inhibitor, mitochondrial	protein-coding	0.009346	0.375291	
chunk0019_180_1	chr1	226479312	226479837	+	0	NA	Intergenic	HAL1|LINE|L1	-69226	NM_001003665	375057	Hs.116827	NM_001003665	ENSG00000203685	STUM	C1orf95	stum, mechanosensory transduction mediator homolog	protein-coding	0.009524	0.431559	
chunk0086_226_1	chr18	22707648	22708316	+	0	NA	Intergenic	Intergenic	78855	NR_110782	101927571	Hs.335020	NR_110782	ENSG00000266850	LOC101927571	-	uncharacterized LOC101927571	ncRNA	0.020958	0.503737	
chunk0074_384_1	chr16	35131373	35132368	+	0	NA	Intergenic	Intergenic	38521	NR_002837	606551	Hs.646441	NR_002837		UBE2MP1	-	ubiquitin conjugating enzyme E2 M pseudogene 1	pseudo	0.007035	0.324297	
chunk0058_302_1	chr14	26992446	26992977	+	0	NA	Intergenic	ERVL-B4-int|LTR|ERVL	84069	NR_036193	100423019		NR_036193	ENSG00000265165	MIR4307	-	microRNA 4307	ncRNA	0.003766	0.359023	
chunk0198_339_1	chr8	140153909	140154213	+	0	NA	intron (NM_001160372, intron 17 of 22)	L2c|LINE|L2	303701	NM_001160372	83696	Hs.654911	NM_031466	ENSG00000167632	TRAPPC9	IBP|IKBKBBP|MRT13|NIBP|T1|TRS120	trafficking protein particle complex 9	protein-coding	0.026316	0.468852	
chunk0204_57_1	chr9	93313072	93313282	+	0	NA	intron (NM_001282394, intron 28 of 29)	L1MB3|LINE|L1	33237	NM_001098808	445577	Hs.575636	NM_001098808	ENSG00000204352	C9orf129	bA165J3.3	chromosome 9 open reading frame 129	protein-coding	0.009524	0.379147	
chunk0026_380_1	chr10	69413186	69413598	+	0	NA	intron (NM_001057, intron 2 of 4)	intron (NM_001057, intron 2 of 4)	3526	NM_001057	6865	Hs.88372	NM_001057	ENSG00000075073	TACR2	NK2R|NKNAR|SKR|TAC2R	tachykinin receptor 2	protein-coding	0.029126	0.544794	186(TGGAACTCGCTGTTCT,-,0.00),187(GGAACTCGCTGTTCTC,+,0.00)
chunk0205_385_1	chr9	114351941	114352343	+	0	NA	intron (NM_030767, intron 14 of 21)	L1MD1|LINE|L1	22353	NM_000608	5005	Hs.719954	NM_000608	ENSG00000228278	ORM2	AGP-B|AGP-B'|AGP2	orosomucoid 2	protein-coding	0.009950	0.406948	
chunk0140_41_1	chr4	66596978	66597265	+	0	NA	Intergenic	L1MA5|LINE|L1	320297	NR_031673	100302177		NR_031673	ENSG00000221563	MIR1269A	MIR1269|MIRN1269|hsa-mir-1269|hsa-mir-1269a	microRNA 1269a	ncRNA	0.003484	0.486111	228(CAGTACAGTCAGTTCT,-,0.00),229(AGTACAGTCAGTTCTC,+,0.00)
chunk0163_21_1	chr6	8022339	8022538	+	0	NA	intron (NR_037618, intron 6 of 6)	intron (NR_037618, intron 6 of 6)	36336	NR_027712	206426	Hs.676966	NR_027712		PIP5K1P1	-	phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1	pseudo	0.005025	0.345000	
chunk0152_226_1	chr5	60445918	60446158	+	0	NA	intron (NM_001165899, intron 1 of 16)	L1M5|LINE|L1	-41675	NR_024617	25859	Hs.146312	NM_001039499	ENSG00000152931	PART1	NCRNA00206	prostate androgen-regulated transcript 1	ncRNA	0.004167	0.319502	
chunk0015_352_1	chr1	190189928	190190390	+	0	NA	intron (NM_199051, intron 6 of 7)	L1M3e|LINE|L1	287470	NM_199051	339479	Hs.65765	NM_199051	ENSG00000162670	BRINP3	DBCCR1L|DBCCR1L1|FAM5C	BMP/retinoic acid inducible neural specific 3	protein-coding	0.008658	0.479482	91(AGGGACATTGAGTTCT,-,0.00),92(GGGACATTGAGTTCTG,+,0.00)
chunk0037_78_1	chr11	71283900	71284382	+	0	NA	Intergenic	Intergenic	-59345	NM_012309	22941	Hs.268726	NM_012309	ENSG00000162105	SHANK2	AUTS17|CORTBP1|CTTNBP1|ProSAP1|SHANK|SPANK-3	SH3 and multiple ankyrin repeat domains 2	protein-coding	0.031120	0.569358	
chunk0193_245_1	chr8	76885989	76886281	+	0	NA	Intergenic	Intergenic	80715	NR_130460	100422921		NR_130460	ENSG00000266712	MIR3149	-	microRNA 3149	ncRNA	0.006849	0.375427	
chunk0017_388_1	chr1	212254962	212255253	+	0	NA	intron (NR_125984, intron 1 of 3)	intron (NR_125984, intron 1 of 3)	-20371	NR_125983	101929541	Hs.632493	NR_125982	ENSG00000226251	LINC02608	-	long intergenic non-protein coding RNA 2608	ncRNA	0.013746	0.551370	
chunk0087_407_1	chr18	42076236	42076660	+	0	NA	intron (NM_001308020, intron 23 of 23)	intron (NM_001308020, intron 23 of 23)	-110220	NR_046456	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.004717	0.324706	
chunk0148_248_1	chr5	10148322	10148524	+	0	NA	Intergenic	FordPrefect|DNA|hAT-Tip100	101486	NM_199133	134145	Hs.481569	NM_199133	ENSG00000150756	ATPSCKMT	FAM173B|JS-2|hFAM173B	ATP synthase c subunit lysine N-methyltransferase	protein-coding	0.014851	0.477833	
chunk0204_134_1	chr9	95305929	95306491	+	0	NA	intron (NM_001243744, intron 1 of 13)	intron (NM_001243744, intron 1 of 13)	11044	NM_001243743	2176	Hs.494529	NM_000136	ENSG00000158169	FANCC	FA3|FAC|FACC	FA complementation group C	protein-coding	0.005338	0.358792	
chunk0087_173_1	chr18	35059949	35060199	+	0	NA	intron (NR_046177, intron 1 of 6)	intron (NR_046177, intron 1 of 6)	18424	NR_046177	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.016000	0.521912	
chunk0206_62_1	chr9	119758361	119759148	+	0	NA	Intergenic	Intergenic	-176306	NR_132393	106146149	Hs.638938	NR_132393	ENSG00000261432	LINC01613	n341773	long intergenic non-protein coding RNA 1613	ncRNA	0.005083	0.409898	444(CTGGACATTCTGTGCT,-,0.00),445(TGGACATTCTGTGCTG,+,0.00)
chunk0176_46_1	chr7	10875050	10875536	+	0	NA	Intergenic	MER90a|LTR|ERV1	64893	NM_002489	4697	Hs.50098	NM_002489	ENSG00000189043	NDUFA4	CI-9k|CI-MLRQ|COXFA4|MLRQ	NDUFA4 mitochondrial complex associated	protein-coding	0.006173	0.381930	
chunk0004_216_1	chr1	46789229	46789536	+	0	NA	Intergenic	LTR5_Hs|LTR|ERVK	-9616	NM_001099772	1580	Hs.436317	NM_000779	ENSG00000142973	CYP4B1	CYPIVB1|P-450HP	cytochrome P450 family 4 subfamily B member 1	protein-coding	0.000000	0.454545	
chunk0181_55_1	chr7	80157329	80157617	+	0	NA	intron (NM_001256414, intron 1 of 7)	L1MC1|LINE|L1	21718	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.000000	0.359862	
chunk0027_322_1	chr10	78284729	78285276	+	0	NA	Intergenic	Intergenic	17674	NR_073447	414243	Hs.55047	NR_073447	ENSG00000230417	LINC00595	C10orf101	long intergenic non-protein coding RNA 595	ncRNA	0.010969	0.527372	
chunk0107_297_1	chr2	218808116	218808412	+	0	NA	intron (NM_000784, intron 1 of 8)	intron (NM_000784, intron 1 of 8)	-14826	NR_128707	103504730		NR_128707	ENSG00000283639	MIR9500	hsa-mir-9500	microRNA 9500	ncRNA	0.010135	0.407407	
chunk0040_226_1	chr11	114400172	114400851	+	0	NA	promoter-TSS (NM_016090)	promoter-TSS (NM_016090)	-18	NM_001286047	10179	Hs.7527	NM_016090	ENSG00000076053	RBM7	-	RNA binding motif protein 7	protein-coding	0.091311	0.616176	137(AGGGACACATTGTTCA,-,0.00),138(GGGACACATTGTTCAG,+,0.00)
chunk0127_319_1	chr3	99934896	99935115	+	0	NA	intron (NM_001042459, intron 1 of 4)	intron (NM_001042459, intron 1 of 4)	29393	NR_037486	100500859		NR_037486	ENSG00000264897	MIR3921	-	microRNA 3921	ncRNA	0.000000	0.404545	
chunk0120_232_1	chr3	8414767	8415283	+	0	NA	intron (NR_033378, intron 3 of 3)	intron (NR_033378, intron 3 of 3)	86633	NR_033378	100288428	Hs.651576	NR_033378	ENSG00000227110	LMCD1-AS1	-	LMCD1 antisense RNA 1	ncRNA	0.001938	0.384913	
chunk0150_44_1	chr5	31663370	31663888	+	0	NA	Intergenic	Intergenic	131363	NM_018356	55322	Hs.519246	NM_018356	ENSG00000082213	C5orf22	-	chromosome 5 open reading frame 22	protein-coding	0.013514	0.431599	
chunk0095_72_1	chr2	14554887	14555567	+	0	NA	Intergenic	MIRb|SINE|MIR	-77459	NM_145175	151354	Hs.260855	NM_145175	ENSG00000162981	LRATD1	FAM84A|NSE1|PP11517	LRAT domain containing 1	protein-coding	0.010294	0.399413	323(GTAACATGATGTCCCT,+,0.00)
chunk0031_189_1	chr10	125694787	125695564	+	0	NA	intron (NR_033848, intron 2 of 4)	intron (NR_033848, intron 2 of 4)	11932	NR_033848	283038	Hs.144911	NR_033848	ENSG00000228021	LOC283038	-	uncharacterized LOC283038	ncRNA	0.006435	0.448586	
chunk0132_107_1	chr3	155741770	155742032	+	0	NA	Intergenic	Intergenic	-37693	NM_014996	23007	Hs.567423	NM_014996	ENSG00000114805	PLCH1	PLCL3	phospholipase C eta 1	protein-coding	0.000000	0.365019	
chunk0008_191_1	chr1	93250321	93250871	+	0	NA	intron (NM_206886, intron 23 of 27)	L1M1|LINE|L1	69880	NM_001306076	343099	Hs.482873	NM_206886	ENSG00000122483	CCDC18	NY-SAR-41	coiled-coil domain containing 18	protein-coding	0.005455	0.346642	207(CTGGACAATCTGTTCA,-,0.00),208(TGGACAATCTGTTCAT,+,0.00)
chunk0001_115_1	chr1	3900891	3901090	+	0	NA	promoter-TSS (NM_207356)	promoter-TSS (NM_207356)	586	NR_024455	100133612	Hs.307652	NR_024455	ENSG00000236423	LINC01134	-	long intergenic non-protein coding RNA 1134	ncRNA	0.075377	0.695000	
chunk0140_16_1	chr4	65541775	65542286	+	0	NA	intron (NM_001281765, intron 3 of 17)	L1PA8A|LINE|L1	-127931	NR_034138	100144602	Hs.201854	NR_034138	ENSG00000250846	EPHA5-AS1	-	EPHA5 antisense RNA 1	ncRNA	0.007828	0.351562	191(TTGAACAACCTGTTCC,-,0.00),192(TGAACAACCTGTTCCT,+,0.00)
chunk0049_198_1	chr12	93092553	93092777	+	0	NA	intron (NR_040096, intron 3 of 4)	intron (NR_040096, intron 3 of 4)	-81701	NR_120492	102724933	Hs.663947	NR_120492	ENSG00000258171	LINC02412	-	long intergenic non-protein coding RNA 2412	ncRNA	0.017857	0.457778	
chunk0189_225_1	chr8	24433412	24433611	+	0	NA	intron (NR_125808, intron 1 of 5)	intron (NR_125808, intron 1 of 5)	-7485	NM_003817	8756	Hs.116147	NM_003817	ENSG00000069206	ADAM7	ADAM 7|ADAM-7|EAPI|GP-83|GP83	ADAM metallopeptidase domain 7	protein-coding	0.005025	0.315000	96(AGGATCAGTGTGTACA,-,0.00),97(GGATCAGTGTGTACAT,+,0.00)
chunk0070_256_1	chr15	73637446	73638008	+	0	NA	Intergenic	MamGypLTR1b|LTR|Gypsy	-4315	NM_017455	27020	Hs.744867	NM_012428	ENSG00000156642	NPTN	GP55|GP65|SDFR1|SDR1|np55|np65	neuroplastin	protein-coding	0.005338	0.403197	
chunk0027_240_1	chr10	76922787	76923191	+	0	NA	intron (NM_001014797, intron 23 of 28)	intron (NM_001014797, intron 23 of 28)	34945	NR_120655	101929328	Hs.664552	NR_120655	ENSG00000236467	KCNMA1-AS1	-	KCNMA1 antisense RNA 1	ncRNA	0.007426	0.385185	
chunk0109_241_1	chr20	5994003	5994383	+	0	NA	intron (NR_110101, intron 3 of 4)	intron (NR_110101, intron 3 of 4)	11628	NR_110101	101929225	Hs.635771	NR_110101	ENSG00000278719	MCM8-AS1	-	MCM8 antisense RNA 1	ncRNA	0.000000	0.278215	
chunk0120_374_1	chr3	11919546	11919834	+	0	NA	Intergenic	L2b|LINE|L2	-72771	NM_138807	132001	Hs.475472	NM_138807	ENSG00000144559	TAMM41	C3orf31|RAM41|TAM41	TAM41 mitochondrial translocator assembly and maintenance homolog	protein-coding	0.017361	0.484429	195(AAGAACAAACAGTTCC,-,0.00),196(AGAACAAACAGTTCCA,+,0.00)
chunk0169_327_1	chr6	106340673	106340872	+	0	NA	Intergenic	Intergenic	-14952	NM_001286111	9474	Hs.486063	NM_004849	ENSG00000057663	ATG5	APG5|APG5-LIKE|APG5L|ASP|SCAR25|hAPG5	autophagy related 5	protein-coding	0.015075	0.460000	
chunk0135_427_1	chr3	193791642	193791841	+	0	NA	Intergenic	Intergenic	-164409	NR_046634	100873941	Hs.679364	NR_046634	ENSG00000224855	OPA1-AS1	-	OPA1 antisense RNA 1	ncRNA	0.015075	0.405000	
chunk0099_116_1	chr2	85924459	85924772	+	0	NA	Intergenic	Intergenic	35335	NR_110569	101928113	Hs.625888	NR_110569		ST3GAL5-AS1	-	ST3GAL5 antisense RNA 1 (head to head)	ncRNA	0.006390	0.509554	157(TGGAACAGGATGTTCT,-,0.00),158(GGAACAGGATGTTCTT,+,0.00)
chunk0189_183_1	chr8	23591124	23591471	+	0	NA	Intergenic	MIRc|SINE|MIR	62447	NM_016612	51312	Hs.596025	NM_016612	ENSG00000147454	SLC25A37	HT015|MFRN|MFRN1|MSC|MSCP|PRO1278|PRO1584|PRO2217	solute carrier family 25 member 37	protein-coding	0.014409	0.477011	
chunk0119_378_1	chr22	47891674	47892107	+	0	NA	Intergenic	Intergenic	260216	NR_122046	284930	Hs.407567	NR_122046	ENSG00000224271	LOC284930	-	uncharacterized LOC284930	ncRNA	0.013857	0.486175	
chunk0133_68_1	chr3	166962921	166963163	+	0	NA	Intergenic	L1MEd|LINE|L1	417241	NM_001199202	79740	Hs.478143	NM_024687	ENSG00000169064	ZBBX	-	zinc finger B-box domain containing	protein-coding	0.004132	0.358025	
chunk0172_78_1	chr6	134447486	134447713	+	0	NA	intron (NR_038218, intron 1 of 2)	intron (NR_038218, intron 1 of 2)	9209	NR_038219	154092	Hs.223718	NR_038216		LINC01010	-	long intergenic non-protein coding RNA 1010	ncRNA	0.004405	0.372807	
chunk0044_340_1	chr12	38556593	38557158	+	0	NA	Intergenic	MIR|SINE|MIR	240120	NM_001308340	144245	Hs.259305	NM_001013620	ENSG00000175548	ALG10B	ALG10|KCR1	ALG10 alpha-1,2-glucosyltransferase B	protein-coding	0.005310	0.344523	
chunk0032_143_1	chr11	4700367	4700942	+	0	NA	Intergenic	L1M5|LINE|L1	-2808	NM_030774	81285	Hs.501758	NM_030774	ENSG00000167332	OR51E2	HPRAJ|OR51E3P|OR52A2|PSGR	olfactory receptor family 51 subfamily E member 2	protein-coding	0.003478	0.307292	
chunk0121_135_1	chr3	18569914	18570543	+	0	NA	Intergenic	L2c|LINE|L2	124991	NR_125803	101927777	Hs.543235	NR_125803		SATB1-AS1	-	SATB1 antisense RNA 1	ncRNA	0.004769	0.309524	
chunk0015_284_1	chr1	188638983	188639320	+	0	NA	Intergenic	L1MDa|LINE|L1	1195523	NR_132374	106144535	Hs.568709	NR_132374		LINC01037	-	long intergenic non-protein coding RNA 1037	ncRNA	0.005935	0.482249	
chunk0083_27_1	chr17	63201632	63201889	+	0	NA	intron (NM_025185, intron 5 of 24)	intron (NM_025185, intron 5 of 24)	192223	NM_025185	26115	Hs.410889	NM_015623	ENSG00000170921	TANC2	ROLSA|rols	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding	0.007782	0.364341	
chunk0102_320_1	chr2	151695352	151695934	+	0	NA	exon (NM_001164508, exon 18 of 182)	exon (NM_001164508, exon 18 of 182)	38844	NM_001164507	4703	Hs.588655	NM_004543	ENSG00000183091	NEB	NEB177D|NEM2	nebulin	protein-coding	0.003436	0.377358	
chunk0176_325_1	chr7	17184747	17185145	+	0	NA	Intergenic	Intergenic	-113706	NM_001621	196	Hs.171189	NM_001621	ENSG00000106546	AHR	RP85|bHLHe76	aryl hydrocarbon receptor	protein-coding	0.007538	0.348371	
chunk0187_443_1	chr7	159012478	159012817	+	0	NA	intron (NR_024394, intron 1 of 4)	intron (NR_024394, intron 1 of 4)	4293	NR_024394	154822	Hs.544783	NM_198345	ENSG00000231419	LINC00689	-	long intergenic non-protein coding RNA 689	ncRNA	0.008850	0.379412	
chunk0116_69_1	chr21	34263656	34263960	+	0	NA	Intergenic	Intergenic	83131	NR_027266	114036	Hs.720230	NM_153751	ENSG00000227456	LINC00310	C21orf82|NCRNA00310	long intergenic non-protein coding RNA 310	ncRNA	0.006579	0.442623	
chunk0041_170_1	chr11	126102543	126102778	+	0	NA	Intergenic	L2b|LINE|L2	-39368	NM_016952	50937	Hs.38034	NM_016952	ENSG00000064309	CDON	CDO|CDON1|HPE11|ORCAM	cell adhesion associated, oncogene regulated	protein-coding	0.017021	0.525424	
chunk0074_252_1	chr16	27723792	27724064	+	0	NA	intron (NM_015202, intron 14 of 27)	intron (NM_015202, intron 14 of 27)	164229	NM_144675	146395	Hs.91910	NM_144675	ENSG00000169181	GSG1L	PRO19651	GSG1 like	protein-coding	0.025735	0.527473	
chunk0200_145_1	chr9	18173791	18174314	+	0	NA	Intergenic	Intergenic	-300029	NM_001040272	92949	Hs.741483	NM_052866	ENSG00000178031	ADAMTSL1	ADAMTSL-1|ADAMTSR1|C9orf94|PUNCTIN	ADAMTS like 1	protein-coding	0.013384	0.351145	
chunk0183_127_1	chr7	105647643	105647893	+	0	NA	intron (NM_138495, intron 2 of 9)	intron (NM_138495, intron 2 of 9)	31394	NM_138495	222255	Hs.745056	NM_020725	ENSG00000146776	ATXN7L1	ATXN7L4	ataxin 7 like 1	protein-coding	0.012000	0.490040	
chunk0044_222_1	chr12	31362239	31362481	+	0	NA	Intergenic	Intergenic	-36135	NM_001135812	58516	Hs.505154	NM_021238	ENSG00000139146	SINHCAF	C12orf14|FAM60A|L4|TERA	SIN3-HDAC complex associated factor	protein-coding	0.024793	0.534979	
chunk0024_76_1	chr10	34313679	34314078	+	0	NA	intron (NM_001184793, intron 20 of 20)	intron (NM_001184793, intron 20 of 20)	501447	NM_001184785	56288	Hs.131489	NM_019619	ENSG00000148498	PARD3	ASIP|Baz|PAR3|PAR3alpha|PARD-3|PARD3A|PPP1R118|SE2-5L16|SE2-5LT1|SE2-5T2	par-3 family cell polarity regulator	protein-coding	0.005013	0.432500	
chunk0100_229_1	chr2	112084784	112085879	+	0	NA	intron (NM_032824, intron 8 of 18)	L2c|LINE|L2	30108	NM_032824	84910	Hs.656298	NM_032824	ENSG00000153214	TMEM87B	-	transmembrane protein 87B	protein-coding	0.004566	0.423358	
chunk0026_448_1	chr10	71565524	71565966	+	0	NA	intron (NM_001171931, intron 6 of 24)	MIRb|SINE|MIR	-53825	NR_120672	102723377	Hs.568789	NR_120672	ENSG00000223817	CDH23-AS1	C10orf106|NCRNA00223|bA327E2.3	CDH23 antisense RNA 1	ncRNA	0.000000	0.449210	
chunk0137_257_1	chr4	21342794	21343540	+	0	NA	intron (NM_147182, intron 2 of 8)	intron (NM_147182, intron 2 of 8)	-39261	NM_147183	80333	Hs.655705	NM_025221	ENSG00000185774	KCNIP4	CALP|KCHIP4	potassium voltage-gated channel interacting protein 4	protein-coding	0.001340	0.370817	434(ATGTACATAATGTACT,-,0.00),435(TGTACATAATGTACTT,+,0.00)
chunk0163_383_1	chr6	16354846	16355153	+	0	NA	intron (NM_001128164, intron 6 of 7)	intron (NM_001128164, intron 6 of 7)	116419	NM_006877	2766	Hs.484741	NM_006877	ENSG00000137198	GMPR	GMPR 1|GMPR1	guanosine monophosphate reductase	protein-coding	0.003257	0.457792	108(CTGCACACTGTGTCCT,-,0.00),109(TGCACACTGTGTCCTG,+,0.00)
chunk0128_156_1	chr3	107130232	107130530	+	0	NA	intron (NR_028303, intron 1 of 3)	intron (NR_028303, intron 1 of 3)	110257	NR_028303	100302640	Hs.648607	NR_028303	ENSG00000242759	LINC00882	-	long intergenic non-protein coding RNA 882	ncRNA	0.010067	0.498328	203(TAGGACTGGCTGTGCC,-,0.00),204(AGGACTGGCTGTGCCT,+,0.00)
chunk0167_106_1	chr6	57198958	57199165	+	0	NA	intron (NM_016277, intron 3 of 6)	intron (NM_016277, intron 3 of 6)	22400	NM_001278668	51715	Hs.555016	NM_016277	ENSG00000112210	RAB23	HSPC137	RAB23, member RAS oncogene family	protein-coding	0.009662	0.495192	
chunk0100_308_1	chr2	115654501	115654768	+	0	NA	intron (NM_001178037, intron 5 of 25)	intron (NM_001178037, intron 5 of 25)	492527	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.000000	0.328358	
chunk0034_231_1	chr11	33698366	33698732	+	0	NA	intron (NM_001166692, intron 1 of 1)	intron (NM_001166692, intron 1 of 1)	2191	NM_001166692	100131378	Hs.709466	NM_001166692	ENSG00000205177	C11orf91	-	chromosome 11 open reading frame 91	protein-coding	0.013661	0.441417	
chunk0131_268_1	chr3	150138935	150139314	+	0	NA	Intergenic	L2|LINE|L2	-99395	NR_110168	101927992	Hs.534682	NR_110167	ENSG00000244541	LINC01213	-	long intergenic non-protein coding RNA 1213	ncRNA	0.007916	0.407895	
chunk0138_460_1	chr4	47686984	47687579	+	0	NA	intron (NM_001278585, intron 5 of 19)	A-rich|Low_complexity|Low_complexity	34612	NR_107020	102467004		NR_107020	ENSG00000277388	MIR8053	hsa-mir-8053	microRNA 8053	ncRNA	0.003361	0.340604	
chunk0038_151_1	chr11	84574189	84574469	+	0	NA	intron (NM_001142699, intron 6 of 27)	intron (NM_001142699, intron 6 of 27)	-256990	NM_001206769	1740	Hs.367656	NM_001364	ENSG00000150672	DLG2	PPP1R58|PSD-93|PSD93|chapsyn-110	discs large MAGUK scaffold protein 2	protein-coding	0.003571	0.323843	
chunk0154_351_1	chr5	87099468	87099967	+	0	NA	Intergenic	L2c|LINE|L2	15237	NR_036243	100422887		NR_036243	ENSG00000265919	MIR4280	-	microRNA 4280	ncRNA	0.002004	0.406000	
chunk0029_103_1	chr10	97548169	97548500	+	0	NA	intron (NM_024954, intron 1 of 2)	intron (NM_024954, intron 1 of 2)	-24107	NM_020349	26287	Hs.73708	NM_020349	ENSG00000165887	ANKRD2	ARPP	ankyrin repeat domain 2	protein-coding	0.012085	0.460843	
chunk0142_328_1	chr4	101160891	101161883	+	0	NA	intron (NM_000944, intron 2 of 13)	intron (NM_000944, intron 2 of 13)	79485	NR_107033	102465868		NR_107033	ENSG00000273882	MIR8066	hsa-mir-8066	microRNA 8066	ncRNA	0.006048	0.352467	
chunk0128_339_1	chr3	112228654	112228986	+	0	NA	intron (NM_183061, intron 13 of 28)	L1MA5|LINE|L1	65407	NM_183061	285335	Hs.680112	NM_183061	ENSG00000172139	SLC9C1	NHE|NHE-10|SLC9A10|sperm-NHE	solute carrier family 9 member C1	protein-coding	0.006024	0.312312	
chunk0060_424_1	chr14	53810300	53810852	+	0	NA	Intergenic	L2c|LINE|L2	137908	NR_049843	100847076		NR_049843	ENSG00000266431	MIR5580	-	microRNA 5580	ncRNA	0.012681	0.401447	
chunk0175_104_1	chr7	2860477	2861124	+	0	NA	Intergenic	MLT2C1|LTR|ERVL	-16475	NM_007353	2768	Hs.487341	NM_007353	ENSG00000146535	GNA12	NNX3|RMP|gep	G protein subunit alpha 12	protein-coding	0.029366	0.510802	
chunk0198_398_1	chr8	141576545	141576927	+	0	NA	Intergenic	MIR|SINE|MIR	-69506	NM_207414	389690	Hs.689547	NM_207414	ENSG00000226807	MROH5	-	maestro heat like repeat family member 5 (gene/pseudogene)	protein-coding	0.036649	0.608355	224(AAGAACACGGTGCCCC,-,0.00),225(AGAACACGGTGCCCCA,+,0.00)
chunk0142_209_1	chr4	97496169	97496934	+	0	NA	Intergenic	Intergenic	129625	NR_102713	101410545	Hs.628520	NR_102713	ENSG00000251620	STPG2-AS1	-	STPG2 antisense RNA 1	ncRNA	0.006536	0.366841	140(TTGAACAGAATGTCCT,-,0.00),141(TGAACAGAATGTCCTT,+,0.00)
chunk0091_68_1	chr19	4970676	4971137	+	0	NA	intron (NM_015015, intron 1 of 22)	intron (NM_015015, intron 1 of 22)	1793	NM_015015	23030	Hs.654816	NM_015015	ENSG00000127663	KDM4B	JMJD2B|TDRD14B	lysine demethylase 4B	protein-coding	0.047722	0.567100	260(CGGGTCAGACTGTCCT,-,0.00),261(GGGTCAGACTGTCCTG,+,0.00),345(GTGTACAGGCTGTTTT,-,0.00),346(TGTACAGGCTGTTTTG,+,0.00)
chunk0041_287_1	chr11	129453137	129453904	+	0	NA	Intergenic	Tigger19a|DNA|TcMar-Tigger	77534	NM_003658	8538	Hs.591944	NM_003658	ENSG00000043039	BARX2	-	BARX homeobox 2	protein-coding	0.014342	0.463542	
chunk0165_361_1	chr6	38141176	38141810	+	0	NA	intron (NM_021943, intron 5 of 5)	intron (NM_021943, intron 5 of 5)	321962	NM_021943	60685	Hs.36959	NM_021943	ENSG00000156639	ZFAND3	TEX27	zinc finger AN1-type containing 3	protein-coding	0.006309	0.436220	
chunk0084_33_1	chr17	73796700	73796956	+	0	NA	intron (NR_040020, intron 5 of 6)	L2b|LINE|L2	10006	NR_040020	400620	Hs.348644	NR_040020	ENSG00000234721	LINC02092	-	long intergenic non-protein coding RNA 2092	ncRNA	0.019531	0.455253	188(CAGCACACGGCGTGCT,-,0.00),189(AGCACACGGCGTGCTG,+,0.00)
chunk0123_245_1	chr3	45708410	45709281	+	0	NA	intron (NM_014016, intron 4 of 19)	intron (NM_014016, intron 4 of 19)	19583	NM_014016	22908	Hs.156509	NM_014016	ENSG00000211456	SACM1L	SAC1	SAC1 like phosphatidylinositide phosphatase	protein-coding	0.009185	0.283257	
chunk0007_156_1	chr1	79842099	79842461	+	0	NA	Intergenic	Intergenic	-693475	NR_125940	101927412	Hs.171273	NR_125940	ENSG00000234184	LINC01781	-	long intergenic non-protein coding RNA 1781	ncRNA	0.005525	0.275482	
chunk0066_154_1	chr15	31975613	31976385	+	0	NA	intron (NR_038253, intron 2 of 7)	intron (NR_038253, intron 2 of 7)	-54484	NM_001190455	1139	Hs.511772	NM_000746	ENSG00000175344	CHRNA7	CHRNA7-2|NACHRA7	cholinergic receptor nicotinic alpha 7 subunit	protein-coding	0.020725	0.552393	383(AGGTACTGTGTGTACC,-,0.00),384(GGTACTGTGTGTACCT,+,0.00),573(GGCCCAGAGTGTGCCT,+,0.00)
chunk0062_197_1	chr14	69990252	69990756	+	0	NA	intron (NM_022137, intron 5 of 11)	intron (NM_022137, intron 5 of 11)	89713	NM_182936	6547	Hs.337696	NM_033262	ENSG00000100678	SLC8A3	NCX3	solute carrier family 8 member A3	protein-coding	0.000000	0.400000	226(CTGAGCACACTGTGCT,-,0.00),227(TGAGCACACTGTGCTG,+,0.00)
chunk0014_271_1	chr1	180344301	180344607	+	0	NA	intron (NM_032360, intron 6 of 7)	intron (NM_032360, intron 6 of 7)	-69773	NR_037642	100527964	Hs.496545	NR_037642	ENSG00000230124	LHX4-AS1	-	LHX4 antisense RNA 1	ncRNA	0.000000	0.358306	
chunk0039_150_1	chr11	98784039	98784346	+	0	NA	Intergenic	Intergenic	-236784	NM_001243271	53942	Hs.656783	NM_014361	ENSG00000149972	CNTN5	HNB-2s|NB-2	contactin 5	protein-coding	0.003257	0.279221	
chunk0148_316_1	chr5	13730937	13731909	+	0	NA	intron (NM_001369, intron 68 of 78)	intron (NM_001369, intron 68 of 78)	213057	NM_001369	1767	Hs.212360	NM_001369	ENSG00000039139	DNAH5	CILD3|DNAHC5|HL1|KTGNR|PCD	dynein axonemal heavy chain 5	protein-coding	0.012346	0.380267	
chunk0123_376_1	chr3	48624033	48624583	+	0	NA	Intergenic	L2a|LINE|L2	-2552	NM_001008269	440955	Hs.631922	NM_001008269	ENSG00000183396	TMEM89	-	transmembrane protein 89	protein-coding	0.009091	0.509982	
chunk0123_367_1	chr3	48344563	48345092	+	0	NA	Intergenic	Intergenic	-16486	NM_001080525	646424	Hs.257687	NM_001080525	ENSG00000229453	SPINK8	-	serine peptidase inhibitor, Kazal type 8 (putative)	protein-coding	0.005671	0.392453	
chunk0140_300_1	chr4	72935833	72936256	+	0	NA	Intergenic	Intergenic	133715	NM_001300729	285521	Hs.356697	NM_173827	ENSG00000163626	COX18	COX18HS	cytochrome c oxidase assembly factor COX18	protein-coding	0.002364	0.297170	
chunk0204_48_1	chr9	92940688	92940887	+	0	NA	Intergenic	Intergenic	-6532	NM_001083536	89846	Hs.411081	NM_033086	ENSG00000127084	FGD3	ZFYVE5	FYVE, RhoGEF and PH domain containing 3	protein-coding	0.005025	0.570000	
chunk0002_38_1	chr1	12491292	12491608	+	0	NA	intron (NM_018156, intron 66 of 68)	intron (NM_018156, intron 66 of 68)	-15796	NR_003022	677882	Hs.658450	NR_003022	ENSG00000266079	SNORA59B	ACA59	small nucleolar RNA, H/ACA box 59B	snoRNA	0.006329	0.394322	
chunk0172_424_1	chr6	140462697	140463493	+	0	NA	Intergenic	Intergenic	-220719	NR_039675	100616180		NR_039675	ENSG00000264390	MIR4465	-	microRNA 4465	ncRNA	0.003769	0.376412	515(AAAAACAGGATGTTCT,-,0.00),516(AAAACAGGATGTTCTT,+,0.00)
chunk0033_371_1	chr11	23397613	23397872	+	0	NA	Intergenic	L1MA10|LINE|L1	21448	NR_107021	102465860		NR_107021	ENSG00000275868	MIR8054	hsa-mir-8054	microRNA 8054	ncRNA	0.007722	0.353846	
chunk0193_189_1	chr8	75319872	75320229	+	0	NA	Intergenic	L1ME3|LINE|L1	-41161	NR_103849	101805492	Hs.571424	NR_103848		CASC9	ESCCAL-1|ESSCAL1|LINC00981|linc-JPH1	cancer susceptibility 9	ncRNA	0.002801	0.321229	
chunk0170_197_1	chr6	112306733	112307046	+	0	NA	TTS (NR_121193)	TTS (NR_121193)	-40441	NM_001013734	442247	Hs.448264	NM_001013734	ENSG00000251258	RFPL4B	RNF211	ret finger protein like 4B	protein-coding	0.006390	0.404459	
chunk0172_358_1	chr6	139147662	139147866	+	0	NA	intron (NM_016217, intron 1 of 3)	intron (NM_016217, intron 1 of 3)	12652	NM_016217	51696	Hs.197644	NM_016217	ENSG00000112406	HECA	HDC|HDCL|HHDC|dJ225E12.1	hdc homolog, cell cycle regulator	protein-coding	0.004902	0.404878	126(TGGCACTTCCTGTTCT,-,0.00),127(GGCACTTCCTGTTCTT,+,0.00)
chunk0073_254_1	chr16	11790197	11790472	+	0	NA	intron (NM_014153, intron 1 of 22)	L1MC5a|LINE|L1	6924	NM_014153	29066	Hs.371856	NM_014153	ENSG00000122299	ZC3H7A	HSPC055|ZC3H7|ZC3HDC7	zinc finger CCCH-type containing 7A	protein-coding	0.003636	0.391304	
chunk0211_433_1	chrX	129504507	129504882	+	0	NA	intron (NM_003069, intron 9 of 24)	intron (NM_003069, intron 9 of 24)	18811	NM_003069	6594	Hs.152292	NM_003069	ENSG00000102038	SMARCA1	ISWI|NURF140|SNF2L|SNF2L1|SNF2LB|SNF2LT|SWI|SWI2|hSNF2L	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	protein-coding	0.005333	0.348404	
chunk0185_341_1	chr7	132141128	132141327	+	0	NA	intron (NM_020911, intron 29 of 31)	intron (NM_020911, intron 29 of 31)	231007	NR_110836	101928782	Hs.571369	NR_110836	ENSG00000224865	LOC101928782	-	uncharacterized LOC101928782	ncRNA	0.005025	0.480000	
chunk0077_112_1	chr16	78235075	78235561	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	135905	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.014403	0.449692	
chunk0146_181_1	chr4	160770447	160770900	+	0	NA	Intergenic	Intergenic	-1252060	NR_125888	101928052	Hs.647993	NR_125888	ENSG00000249419	LOC101928052	-	uncharacterized LOC101928052	ncRNA	0.004415	0.352423	
chunk0154_223_1	chr5	80754997	80755222	+	0	NA	intron (NM_002439, intron 12 of 23)	intron (NM_002439, intron 12 of 23)	-100128	NM_001290357	1719	Hs.592364	NM_000791	ENSG00000228716	DHFR	DHFRP1|DYR	dihydrofolate reductase	protein-coding	0.022222	0.517699	
chunk0094_290_1	chr2	8413675	8414312	+	0	NA	Intergenic	Intergenic	-85574	NR_034135	339789	Hs.565619	NR_034135	ENSG00000236790	LINC00299	C2orf46|NCRNA00299	long intergenic non-protein coding RNA 299	ncRNA	0.009419	0.399687	
chunk0087_162_1	chr18	34912293	34912509	+	0	NA	Intergenic	Intergenic	-64527	NM_001143826	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.013889	0.387097	
chunk0021_104_1	chr10	3102861	3103371	+	0	NA	intron (NM_002627, intron 4 of 21)	intron (NM_002627, intron 4 of 21)	-31044	NR_132758	106633806		NR_132758		SNORD142	SNORA85|SNORD174|ZL68	small nucleolar RNA, C/D box 142	snoRNA	0.029412	0.506849	52(CAGCACAGTGAGTGCA,-,0.00),53(AGCACAGTGAGTGCAC,+,0.00)
chunk0165_438_1	chr6	40376391	40376764	+	0	NA	Intergenic	L1MB5|LINE|L1	-1847	NR_024015									0.008043	0.379679	124(GTGTACACAATGTCCA,-,0.00),125(TGTACACAATGTCCAC,+,0.00)
chunk0178_5_1	chr7	28987047	28987246	+	0	NA	intron (NR_038965, intron 1 of 4)	intron (NR_038965, intron 1 of 4)	7179	NR_038965	100506497	Hs.586328	NR_038965	ENSG00000272568	LOC100506497	-	uncharacterized LOC100506497	ncRNA	0.010050	0.480000	
chunk0139_338_1	chr4	59384979	59385500	+	0	NA	Intergenic	Intergenic	-1537380	NR_039652	100616450		NR_039652	ENSG00000265829	MIR548AG1	-	microRNA 548ag-1	ncRNA	0.001919	0.268199	
chunk0154_185_1	chr5	80151361	80152021	+	0	NA	intron (NM_178276, intron 8 of 12)	intron (NM_178276, intron 8 of 12)	-68026	NR_109930	101929215		NR_109930	ENSG00000249825	CTD-2201I18.1	-	uncharacterized LOC101929215	ncRNA	0.012121	0.446293	
chunk0116_347_1	chr21	41526334	41526846	+	0	NA	Intergenic	Intergenic	-18432	NM_005656	7113	Hs.439309	NM_005656	ENSG00000184012	TMPRSS2	PP9284|PRSS10	transmembrane serine protease 2	protein-coding	0.015625	0.413255	
chunk0101_448_1	chr2	139828023	139828312	+	0	NA	Intergenic	MER34A1|LTR|ERV1	758518	NR_106979	102465692		NR_106979	ENSG00000283506	MIR7157	hsa-mir-7157	microRNA 7157	ncRNA	0.006920	0.406897	
chunk0108_240_1	chr2	233745424	233745816	+	0	NA	intron (NM_019093, intron 1 of 4)	intron (NM_019093, intron 1 of 4)	-1605	NM_001001394	414061	Hs.725533	NM_001001394		DNAJB3	HCG3	DnaJ heat shock protein family (Hsp40) member B3	protein-coding	0.005102	0.458015	21(AAGGTCACTCAGTTCT,-,0.00)
chunk0181_43_1	chr7	79236487	79236852	+	0	NA	intron (NM_001301128, intron 1 of 20)	MIR3|SINE|MIR	-216288	NR_038346	100505881	Hs.31474	NR_038343	ENSG00000234456	MAGI2-AS3	-	MAGI2 antisense RNA 3	ncRNA	0.005479	0.355191	
chunk0117_90_1	chr22	17318472	17318671	+	0	NA	Intergenic	L1ME4b|LINE|L1	-41378	NM_001290046	27443	Hs.231895	NM_031413	ENSG00000099954	CECR2	-	CECR2 histone acetyl-lysine reader	protein-coding	0.005025	0.375000	
chunk0129_147_1	chr3	120549205	120549602	+	0	NA	Intergenic	A-rich|Low_complexity|Low_complexity	-46878	NM_001168331	4710	Hs.304613	NM_004547	ENSG00000065518	NDUFB4	B15|CI-B15	NADH:ubiquinone oxidoreductase subunit B4	protein-coding	0.017632	0.467337	
chunk0093_268_1	chr19	51295179	51295422	+	0	NA	Intergenic	MER102a|DNA|hAT-Charlie	-16548	NM_001101372	402665		NM_001101372	ENSG00000142549	IGLON5	-	IgLON family member 5	protein-coding	0.024691	0.557377	
chunk0059_258_1	chr14	35201124	35201666	+	0	NA	intron (NM_014672, intron 5 of 7)	L1MC3|LINE|L1	-77163	NM_001282234	5687	Hs.446260	NM_002791	ENSG00000100902	PSMA6	IOTA|PROS27|p27K	proteasome subunit alpha 6	protein-coding	0.005535	0.344383	
chunk0147_159_1	chr4	175714722	175714956	+	0	NA	intron (NM_201592, intron 1 of 6)	intron (NM_201592, intron 1 of 6)	72837	NM_001261448	2823	Hs.75819	NM_005277	ENSG00000150625	GPM6A	GPM6|M6A	glycoprotein M6A	protein-coding	0.004274	0.319149	78(CAGAACATTCTGTACT,-,0.00),79(AGAACATTCTGTACTG,+,0.00)
chunk0067_142_1	chr15	43127647	43128140	+	0	NA	Intergenic	Helitron3Na_Mam|RC|Helitron	-5631	NM_024956	80021	Hs.511175	NM_024956	ENSG00000137842	TMEM62	-	transmembrane protein 62	protein-coding	0.004057	0.378543	
chunk0090_101_1	chr18	70901167	70901502	+	0	NA	Intergenic	Intergenic	-250477	NM_001278515									0.008955	0.377976	
chunk0127_191_1	chr3	95977101	95977312	+	0	NA	Intergenic	L1PB1|LINE|L1	-294013	NR_077228	100287639	Hs.591320	NR_077228	ENSG00000244681	MTHFD2P1	-	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase pseudogene 1	pseudo	0.000000	0.363208	
chunk0116_265_1	chr21	39147723	39148090	+	0	NA	Intergenic	L1ME1|LINE|L1	35608	NR_049728	8624	Hs.473838	NM_003720	ENSG00000183527	PSMG1	C21LRP|DSCR2|LRPC21|PAC-1|PAC1	proteasome assembly chaperone 1	protein-coding	0.002725	0.309783	
chunk0002_206_1	chr1	19607001	19607639	+	0	NA	promoter-TSS (NR_077246)	promoter-TSS (NR_077246)	-487	NR_077246	644068	Hs.660760	NR_077246		RPS14P3	RPS14_1_16	ribosomal protein S14 pseudogene 3	pseudo	0.006270	0.330203	242(TGGAACATTGTGACCT,-,0.00),243(GGAACATTGTGACCTT,+,0.00)
chunk0008_319_1	chr1	95230513	95231137	+	0	NA	intron (NR_125949, intron 1 of 3)	intron (NR_125949, intron 1 of 3)	3157	NR_125949	101928118	Hs.656443	NR_125948	ENSG00000226026	LOC101928118	-	uncharacterized LOC101928118	ncRNA	0.008013	0.390400	
chunk0066_58_1	chr15	28661755	28661955	+	0	NA	intron (NR_036443, intron 5 of 13)	MER58A|DNA|hAT-Charlie	7413	NR_036443	440248	Hs.531509	NM_199045	ENSG00000206149	HERC2P9	-	hect domain and RLD 2 pseudogene 9	pseudo	0.020000	0.477612	
chunk0123_80_1	chr3	41660960	41661538	+	0	NA	intron (NM_017886, intron 30 of 36)	intron (NM_017886, intron 30 of 36)	300919	NM_017886	54986	Hs.656192	NM_017886	ENSG00000168038	ULK4	FAM7C1|REC01035	unc-51 like kinase 4	protein-coding	0.006920	0.284974	
chunk0112_433_1	chr20	47567942	47568373	+	0	NA	intron (NM_001174087, intron 1 of 22)	intron (NM_001174087, intron 1 of 22)	66300	NM_001174087	8202	Hs.592142	NM_006534	ENSG00000124151	NCOA3	ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP	nuclear receptor coactivator 3	protein-coding	0.004640	0.421296	
chunk0028_297_1	chr10	91555396	91555623	+	0	NA	intron (NR_024467, intron 1 of 4)	intron (NR_024467, intron 1 of 4)	55951	NR_024467	100188947	Hs.535293	NR_024467		HECTD2-AS1	-	HECTD2 antisense RNA 1	ncRNA	0.000000	0.482456	
chunk0108_322_1	chr2	235545987	235546221	+	0	NA	intron (NM_001037131, intron 1 of 17)	intron (NM_001037131, intron 1 of 17)	40353	NR_131900	100506749	Hs.684184	NR_131900	ENSG00000235529	AGAP1-IT1	-	AGAP1 intronic transcript 1	ncRNA	0.004274	0.472340	
chunk0134_117_1	chr3	177195644	177196096	+	0	NA	intron (NM_024665, intron 1 of 15)	intron (NM_024665, intron 1 of 15)	1390	NM_024665	79718	Hs.714201	NM_024665	ENSG00000177565	TBL1XR1	C21|DC42|IRA1|MRD41|TBLR1	transducin beta like 1 X-linked receptor 1	protein-coding	0.006637	0.362031	
chunk0009_190_1	chr1	105910940	105911448	+	0	NA	Intergenic	HUERS-P2-int|LTR|ERV1	-292259	NR_125954	101928476	Hs.563856	NR_125954	ENSG00000230768	LINC01676	-	long intergenic non-protein coding RNA 1676	ncRNA	0.001969	0.467583	
chunk0151_286_1	chr5	52817731	52818311	+	0	NA	intron (NM_181501, intron 1 of 28)	MER58A|DNA|hAT-Charlie	29719	NM_181501	3672	Hs.644352	NM_181501	ENSG00000213949	ITGA1	CD49a|VLA1	integrin subunit alpha 1	protein-coding	0.003448	0.344234	
chunk0105_46_1	chr2	182954650	182955210	+	0	NA	intron (NM_205842, intron 21 of 31)	intron (NM_205842, intron 21 of 31)	83928	NM_205842	10787	Hs.603732	NM_013436	ENSG00000061676	NCKAP1	HEM2|NAP1|NAP125|p125Nap1	NCK associated protein 1	protein-coding	0.007143	0.413547	
chunk0018_181_1	chr1	219182099	219182488	+	0	NA	intron (NM_001300769, intron 2 of 3)	intron (NM_001300769, intron 2 of 3)	7324	NM_001300772	127018	Hs.657617	NM_138794	ENSG00000143353	LYPLAL1	Q96AV0	lysophospholipase like 1	protein-coding	0.007712	0.392308	
chunk0096_448_1	chr2	39516852	39517199	+	0	NA	intron (NR_037875, intron 4 of 5)	intron (NR_037875, intron 4 of 5)	79609	NR_037875	728730	Hs.655344	NR_037875	ENSG00000231312	MAP4K3-DT	-	MAP4K3 divergent transcript	ncRNA	0.005764	0.485632	
chunk0132_112_1	chr3	155876200	155876850	+	0	NA	intron (NM_003875, intron 1 of 15)	BLACKJACK|DNA|hAT-Blackjack	5989	NM_003875	8833	Hs.591314	NM_003875	ENSG00000163655	GMPS	GATD7	guanine monophosphate synthase	protein-coding	0.009231	0.376344	474(GAGCACATATTGTTCT,-,0.00),475(AGCACATATTGTTCTG,+,0.00)
chunk0171_13_1	chr6	119683033	119683433	+	0	NA	Intergenic	Intergenic	-191931	NR_046100	285762	Hs.571063	NR_046100		LOC285762	-	uncharacterized LOC285762	ncRNA	0.005000	0.399002	
chunk0094_76_1	chr2	3524449	3525020	+	0	NA	Intergenic	MLT1K|LTR|ERVL-MaLR	-5155	NM_018269	55256	Hs.502773	NM_018269	ENSG00000182551	ADI1	APL1|ARD|Fe-ARD|HMFT1638|MTCBP1|Ni-ARD|SIPL|mtnD	acireductone dioxygenase 1	protein-coding	0.012259	0.487762	
chunk0030_142_1	chr10	113713121	113713695	+	0	NA	intron (NM_001267058, intron 1 of 5)	MIR|SINE|MIR	4063	NM_001267058	840	Hs.9216	NM_001227	ENSG00000165806	CASP7	CASP-7|CMH-1|ICE-LAP3|LICE2|MCH3	caspase 7	protein-coding	0.005226	0.386087	243(GGACACACACTGTTCT,-,0.00),244(GACACACACTGTTCTA,+,0.00)
chunk0194_236_1	chr8	86320187	86321070	+	0	NA	Intergenic	Intergenic	-22137	NM_007013	11059	Hs.655189	NM_007013	ENSG00000123124	WWP1	AIP5|Tiul1|hSDRP1	WW domain containing E3 ubiquitin protein ligase 1	protein-coding	0.012458	0.407240	
chunk0126_32_1	chr3	73724270	73724845	+	0	NA	Intergenic	Tigger3a|DNA|TcMar-Tigger	-99636	NM_015009	23024	Hs.660347	NM_015009	ENSG00000121440	PDZRN3	LNX3|SEMACAP3|SEMCAP3	PDZ domain containing ring finger 3	protein-coding	0.003478	0.397569	
chunk0117_287_1	chr22	24303399	24303938	+	0	NA	intron (NM_001145468, intron 2 of 15)	intron (NM_001145468, intron 2 of 15)	32851	NM_001145468	23384	Hs.474384	NM_015330	ENSG00000100014	SPECC1L	CYTSA|GBBB2|OBLFC1|TBHS	sperm antigen with calponin homology and coiled-coil domains 1 like	protein-coding	0.003711	0.468519	336(TTGAACAGTGAGTACT,-,0.00),337(TGAACAGTGAGTACTT,+,0.00)
chunk0048_347_1	chr12	84494859	84495354	+	0	NA	Intergenic	Intergenic	417723	NM_182767	55117	Hs.44424	NM_018057	ENSG00000072041	SLC6A15	NTT73|SBAT1|V7-3|hv7-3	solute carrier family 6 member 15	protein-coding	0.004040	0.274194	
chunk0087_412_1	chr18	42192745	42193186	+	0	NA	intron (NR_046455, intron 1 of 4)	MER44B|DNA|TcMar-Tigger	6297	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.004535	0.380090	
chunk0202_380_1	chr9	80843047	80843368	+	0	NA	Intergenic	Intergenic	846328	NM_001303103	7088	Hs.197320	NM_005077	ENSG00000196781	TLE1	ESG|ESG1|GRG1	TLE family member 1, transcriptional corepressor	protein-coding	0.003115	0.301242	
chunk0119_12_1	chr22	40060643	40060940	+	0	NA	intron (NM_001024843, intron 1 of 23)	MER68|LTR|ERVL	15974	NM_001024843	23112	Hs.372082	NM_015088	ENSG00000100354	TNRC6B	-	trinucleotide repeat containing adaptor 6B	protein-coding	0.003367	0.426174	
chunk0155_272_1	chr5	95974984	95975525	+	0	NA	intron (NR_130776, intron 1 of 4)	intron (NR_130776, intron 1 of 4)	-13183	NM_012081	22936	Hs.192221	NM_012081	ENSG00000118985	ELL2	MRCCAT1	elongation factor for RNA polymerase II 2	protein-coding	0.005545	0.420664	
chunk0048_265_1	chr12	82089709	82090463	+	0	NA	Intergenic	Intergenic	136367	NR_110089	101928449	Hs.737488	NR_110089	ENSG00000257747	LINC02426	-	long intergenic non-protein coding RNA 2426	ncRNA	0.005305	0.349669	
chunk0105_11_1	chr2	181905822	181906133	+	0	NA	intron (NM_001130445, intron 8 of 17)	intron (NM_001130445, intron 8 of 17)	14261	NM_001287505	6744	Hs.196983	NM_006751	ENSG00000138434	ITPRID2	CS-1|CS1|KRAP|SPAG13|SSFA2	ITPR interacting domain containing 2	protein-coding	0.003215	0.294872	
chunk0082_430_1	chr17	61450089	61450689	+	0	NA	Intergenic	Intergenic	-6057	NM_018488	9496	Hs.143907	NM_018488	ENSG00000121075	TBX4	ICPPS|SPS	T-box transcription factor 4	protein-coding	0.008333	0.429285	
chunk0019_277_1	chr1	228666956	228667689	+	0	NA	intron (NR_037962, intron 1 of 2)	L2b|LINE|L2	-21164	NR_023378	100169767		NR_023378	ENSG00000202257	RNA5S16	RN5S16	RNA, 5S ribosomal 16	rRNA	0.006821	0.430518	
chunk0019_266_1	chr1	228140356	228140572	+	0	NA	intron (NM_001242840, intron 1 of 6)	CpG	236	NM_001242840	2987	Hs.376933	NM_000858	ENSG00000143774	GUK1	GMK	guanylate kinase 1	protein-coding	0.129630	0.718894	
chunk0119_73_1	chr22	41261846	41262502	+	0	NA	intron (NM_001278651, intron 6 of 16)	intron (NM_001278651, intron 6 of 16)	-9124	NR_106949	102466758		NR_106949	ENSG00000274552	MIR6889	hsa-mir-6889	microRNA 6889	ncRNA	0.016768	0.514460	
chunk0035_409_1	chr11	56809517	56810194	+	0	NA	Intergenic	Intergenic	-38623	NR_110137	101927120	Hs.472675	NR_110136	ENSG00000255433	LINC02735	-	long intergenic non-protein coding RNA 2735	ncRNA	0.007386	0.317109	
chunk0172_196_1	chr6	136644122	136644407	+	0	NA	intron (NM_005923, intron 11 of 29)	intron (NM_005923, intron 11 of 29)	15150	NR_125858	101928461	Hs.666518	NR_125858		LOC101928461	-	uncharacterized LOC101928461	ncRNA	0.007018	0.493007	
chunk0156_430_1	chr5	114543736	114544389	+	0	NA	intron (NR_130785, intron 3 of 12)	L1MEg|LINE|L1	110532	NM_170775	3781	Hs.98280	NM_021614	ENSG00000080709	KCNN2	KCa2.2|SK2|SKCA2|SKCa 2|hSK2	potassium calcium-activated channel subfamily N member 2	protein-coding	0.006126	0.383792	
chunk0031_80_1	chr10	123165579	123165986	+	0	NA	TTS (NM_004725)	TTS (NM_004725)	11538	NM_004725	9184	Hs.418533	NM_004725	ENSG00000154473	BUB3	BUB3L|hBUB3	BUB3 mitotic checkpoint protein	protein-coding	0.007371	0.433824	
chunk0168_133_1	chr6	82870388	82871041	+	0	NA	Intergenic	Intergenic	195127	NM_001304437	90025	Hs.148609	NM_198920	ENSG00000118420	UBE3D	C6orf157|H10BH|UBE2CBP|YJR141W	ubiquitin protein ligase E3D	protein-coding	0.003063	0.295107	
chunk0035_254_1	chr11	46307312	46307707	+	0	NA	intron (NM_052854, intron 2 of 11)	MIRb|SINE|MIR	-25396	NM_201532	8525	Hs.502461	NM_003646	ENSG00000149091	DGKZ	DAGK5|DAGK6|DGK-ZETA|hDGKzeta	diacylglycerol kinase zeta	protein-coding	0.010127	0.489899	173(AGGTACGTCCTGTTCC,-,0.00),174(GGTACGTCCTGTTCCT,+,0.00)
chunk0137_130_1	chr4	15145687	15146237	+	0	NA	intron (NR_125911, intron 2 of 5)	intron (NR_125911, intron 2 of 5)	143288	NM_001177382	132864	Hs.656937	NM_182485	ENSG00000137449	CPEB2	CPE-BP2|CPEB-2|hCPEB-2	cytoplasmic polyadenylation element binding protein 2	protein-coding	0.016364	0.459165	
chunk0100_243_1	chr2	112737688	112738082	+	0	NA	non-coding (NR_130712, exon 10 of 10)	non-coding (NR_130712, exon 10 of 10)	26792	NM_001304361	150468	Hs.434250	NM_152515	ENSG00000169607	CKAP2L	-	cytoskeleton associated protein 2 like	protein-coding	0.000000	0.349367	
chunk0171_72_1	chr6	121520633	121520932	+	0	NA	Intergenic	Intergenic	85205	NM_000165	2697	Hs.74471	NM_000165	ENSG00000152661	GJA1	AVSD3|CMDR|CX43|EKVP|EKVP3|GJAL|HLHS1|HSS|ODDD|PPKCA	gap junction protein alpha 1	protein-coding	0.006689	0.390000	
chunk0155_334_1	chr5	96923972	96924653	+	0	NA	Intergenic	Intergenic	-11330	NM_005575	4012	Hs.527199	NM_005575	ENSG00000113441	LNPEP	CAP|IRAP|P-LAP|PLAP	leucyl and cystinyl aminopeptidase	protein-coding	0.007342	0.406158	
chunk0164_253_1	chr6	23457447	23458318	+	0	NA	Intergenic	Intergenic	-668304	NM_080723	140767	Hs.726270	NM_080723	ENSG00000152954	NRSN1	VMP|p24	neurensin 1	protein-coding	0.006889	0.318807	
chunk0113_445_1	chr20	62645013	62645540	+	0	NA	intron (NM_016354, intron 1 of 11)	intron (NM_016354, intron 1 of 11)	2831	NM_016354	28231	Hs.235782	NM_016354	ENSG00000101187	SLCO4A1	OATP-E|OATP1|OATP4A1|OATPE|OATPRP1|POAT|SLC21A12	solute carrier organic anion transporter family member 4A1	protein-coding	0.015180	0.607955	363(AAGAACAACCTGGTCC,-,0.00),364(AGAACAACCTGGTCCT,+,0.00)
chunk0109_136_1	chr20	3313609	3314155	+	0	NA	intron (NM_001009984, intron 20 of 36)	MLT1E2-int|LTR|ERVL-MaLR	-74641	NM_001174089	83959	Hs.105607	NM_032034	ENSG00000088836	SLC4A11	BTR1|CDPD1|CHED|CHED2|NABC1|dJ794I6.2	solute carrier family 4 member 11	protein-coding	0.005495	0.457038	
chunk0181_60_1	chr7	80208628	80209149	+	0	NA	intron (NM_002069, intron 5 of 7)	MLT1-int|LTR|ERVL-MaLR	73133	NM_001256414	2770	Hs.134587	NM_002069	ENSG00000127955	GNAI1	Gi	G protein subunit alpha i1	protein-coding	0.005758	0.394636	217(TGGAACACACAGTTCA,-,0.00),218(GGAACACACAGTTCAG,+,0.00)
chunk0205_151_1	chr9	108429435	108429662	+	0	NA	Intergenic	L1M4|LINE|L1	426447	NM_006686	10880	Hs.534390	NM_006686	ENSG00000148156	ACTL7B	Tact1	actin like 7B	protein-coding	0.008811	0.390351	
chunk0025_13_1	chr10	47373525	47374026	+	0	NA	intron (NM_153034, intron 1 of 1)	intron (NM_153034, intron 1 of 1)	10498	NM_153034	118738	Hs.27788	NM_153034	ENSG00000265763	ZNF488	-	zinc finger protein 488	protein-coding	0.015968	0.450199	
chunk0113_65_1	chr20	50471118	50471693	+	0	NA	Intergenic	L1ME4b|LINE|L1	-38916	NM_002827	5770	Hs.417549	NM_002827	ENSG00000196396	PTPN1	PTP1B	protein tyrosine phosphatase non-receptor type 1	protein-coding	0.008696	0.361111	
chunk0139_111_1	chr4	52470945	52471289	+	0	NA	Intergenic	Intergenic	185475	NM_001134223	64854	Hs.7966	NM_022832	ENSG00000109189	USP46	-	ubiquitin specific peptidase 46	protein-coding	0.000000	0.362319	154(AGGAACATTGTGTCAT,-,0.00)
chunk0158_275_1	chr5	131436861	131437433	+	0	NA	intron (NM_001164389, intron 24 of 24)	intron (NM_001164389, intron 24 of 24)	173138	NM_001038702	56990	Hs.508829	NM_020240	ENSG00000158985	CDC42SE2	SPEC2	CDC42 small effector 2	protein-coding	0.003497	0.350785	
chunk0148_303_1	chr5	12583973	12584309	+	0	NA	intron (NR_033383, intron 1 of 3)	L1MA2|LINE|L1	9284	NR_033383	404663	Hs.552273	NR_033383		LINC01194	CT49|TAG	long intergenic non-protein coding RNA 1194	ncRNA	0.000000	0.320475	
chunk0031_245_1	chr10	126947277	126947502	+	0	NA	intron (NM_001290223, intron 1 of 51)	intron (NM_001290223, intron 1 of 51)	41980	NM_001380	1793	Hs.159195	NM_001380	ENSG00000150760	DOCK1	DOCK180|ced5	dedicator of cytokinesis 1	protein-coding	0.000000	0.469027	
chunk0029_116_1	chr10	98260257	98260787	+	0	NA	intron (NM_032211, intron 4 of 14)	intron (NM_032211, intron 4 of 14)	7728	NM_032211	84171	Hs.306814	NM_032211	ENSG00000138131	LOXL4	LOXC	lysyl oxidase like 4	protein-coding	0.024528	0.506591	
chunk0041_90_1	chr11	124618232	124619057	+	0	NA	intron (NM_052959, intron 3 of 3)	intron (NM_052959, intron 3 of 3)	-4202	NM_032811	84897	Hs.436410	NM_032811	ENSG00000154144	TBRG1	NIAM|TB-5	transforming growth factor beta regulator 1	protein-coding	0.009697	0.449153	
chunk0196_178_1	chr8	105961790	105962420	+	0	NA	intron (NR_125797, intron 1 of 4)	L2a|LINE|L2	98398	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.004762	0.332805	
chunk0185_404_1	chr7	133977495	133978389	+	0	NA	intron (NM_021807, intron 14 of 17)	MER57B2|LTR|ERV1	-149410	NM_144648	136332	Hs.149774	NM_144648	ENSG00000155530	LRGUK	CFAP246	leucine rich repeats and guanylate kinase domain containing	protein-coding	0.005593	0.410056	
chunk0013_175_1	chr1	168863726	168864041	+	0	NA	Intergenic	Intergenic	76942	NR_024160	79100	Hs.250624	NR_024160	ENSG00000225826	LINC00626	-	long intergenic non-protein coding RNA 626	ncRNA	0.009524	0.386076	
chunk0054_63_1	chr13	41903320	41903732	+	0	NA	intron (NM_015058, intron 4 of 44)	L2a|LINE|L2	57559	NM_015058	23078	Hs.368282	NM_015058	ENSG00000102763	VWA8	KIAA0564|P7BP2	von Willebrand factor A domain containing 8	protein-coding	0.009709	0.433414	
chunk0031_376_1	chr10	130751168	130751388	+	0	NA	Intergenic	Intergenic	211390	NR_036180	100422867		NR_036180	ENSG00000264803	MIR378C	mir-378c	microRNA 378c	ncRNA	0.036364	0.597285	
chunk0083_109_1	chr17	64706706	64707005	+	0	NA	Intergenic	L2a|LINE|L2	-44587	NM_022739	64750	Hs.515011	NM_022739	ENSG00000108854	SMURF2	-	SMAD specific E3 ubiquitin protein ligase 2	protein-coding	0.006689	0.383333	
chunk0031_367_1	chr10	130345532	130346074	+	0	NA	Intergenic	Intergenic	209428	NM_001199868	10539	Hs.42644	NM_006541	ENSG00000108010	GLRX3	GLRX4|GRX3|GRX4|PICOT|TXNL2|TXNL3	glutaredoxin 3	protein-coding	0.005535	0.381215	
chunk0097_322_1	chr2	57064009	57064510	+	0	NA	Intergenic	Intergenic	-843392	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.000000	0.320717	
chunk0037_424_1	chr11	80075679	80075878	+	0	NA	Intergenic	MIRb|SINE|MIR	-635127	NM_001098816	26011	Hs.213087	NM_001098816	ENSG00000149256	TENM4	Doc4|ETM5|ODZ4|TNM4|Ten-M4|ten-4	teneurin transmembrane protein 4	protein-coding	0.015075	0.330000	
chunk0124_141_1	chr3	54554502	54554739	+	0	NA	intron (NM_018398, intron 5 of 37)	intron (NM_018398, intron 5 of 37)	85237	NR_027122	790952	Hs.720658	NR_027122	ENSG00000265992	ESRG	HESRG	embryonic stem cell related	ncRNA	0.008439	0.537815	164(AGGAACATTAAGTCCA,-,0.00),165(GGAACATTAAGTCCAG,+,0.00)
chunk0050_328_1	chr12	107274007	107274320	+	0	NA	Intergenic	Intergenic	-44257	NM_001018072	121551	Hs.271272	NM_152322	ENSG00000151136	BTBD11	ABTB2B	BTB domain containing 11	protein-coding	0.000000	0.337580	138(CAGAACAGAGAGTGCC,-,0.00),139(AGAACAGAGAGTGCCA,+,0.00)
chunk0064_192_1	chr14	92735933	92736350	+	0	NA	intron (NM_005606, intron 1 of 13)	MER41C|LTR|ERV1	12561	NM_005606	5641	Hs.18069	NM_005606	ENSG00000100600	LGMN	AEP|LGMN1|PRSC1	legumain	protein-coding	0.011990	0.456938	175(CAGAACAGGGTGTTCC,-,0.00),176(AGAACAGGGTGTTCCC,+,0.00)
chunk0056_124_1	chr13	83070618	83071563	+	0	NA	Intergenic	L1PREC2|LINE|L1	811303	NM_052910	114798	Hs.415478	NM_052910	ENSG00000178235	SLITRK1	LRRC12|TTM	SLIT and NTRK like family member 1	protein-coding	0.005291	0.315011	
chunk0182_124_1	chr7	94338840	94339254	+	0	NA	Intergenic	Intergenic	-55514	NM_000089	1278	Hs.489142	NM_000089	ENSG00000164692	COL1A2	EDSARTH2|EDSCV|OI4	collagen type I alpha 2 chain	protein-coding	0.002415	0.416867	168(AAAGACAACGTGTGCC,-,0.00)
chunk0045_262_1	chr12	49512087	49512865	+	0	NA	intron (NM_001293286, intron 8 of 12)	intron (NM_001293286, intron 8 of 12)	-26681	NM_001314030	23416	Hs.64064	NM_012284	ENSG00000135519	KCNH3	BEC1|ELK2|Kv12.2	potassium voltage-gated channel subfamily H member 3	protein-coding	0.002571	0.322208	
chunk0037_358_1	chr11	78016870	78017118	+	0	NA	exon (NM_023930, exon 2 of 2)	exon (NM_023930, exon 2 of 2)	6280	NM_023930	65987	Hs.709780	NM_023930	ENSG00000151364	KCTD14	-	potassium channel tetramerization domain containing 14	protein-coding	0.036290	0.566265	
chunk0050_209_1	chr12	104219976	104220516	+	0	NA	intron (NM_001093771, intron 1 of 16)	intron (NM_001093771, intron 1 of 16)	4467	NM_001093771	7296	Hs.654922	NM_003330	ENSG00000198431	TXNRD1	GRIM-12|TR|TR1|TRXR1|TXNR	thioredoxin reductase 1	protein-coding	0.011111	0.421442	
chunk0065_99_1	chr15	23980484	23980875	+	0	NA	intron (NR_126392, intron 3 of 5)	MER54A|LTR|ERVL	5532	NR_126392	105370731	Hs.532639	NR_126392		PWRN4	LINC01084	Prader-Willi region non-protein coding RNA 4	ncRNA	0.002558	0.392857	
chunk0093_262_1	chr19	51108365	51108966	+	0	NA	promoter-TSS (NM_145232)	promoter-TSS (NM_145232)	-275	NM_145232	90353	Hs.148425	NM_145232	ENSG00000142544	CTU1	ATPBD3|NCS6	cytosolic thiouridylase subunit 1	protein-coding	0.066556	0.579734	
chunk0209_441_1	chrX	64161542	64162265	+	0	NA	Intergenic	Intergenic	43841	NM_152424	139285	Hs.314225	NM_152424	ENSG00000184675	AMER1	FAM123B|OSCS|WTX	APC membrane recruitment protein 1	protein-coding	0.000000	0.363260	387(AGTCACAGACTGTTCT,-,0.00),388(GTCACAGACTGTTCTA,+,0.00)
chunk0195_395_1	chr8	100271672	100272471	+	0	NA	intron (NM_183419, intron 3 of 9)	intron (NM_183419, intron 3 of 9)	31188	NM_015435	25897	Hs.292882	NM_015435	ENSG00000034677	RNF19A	RNF19	ring finger protein 19A, RBR E3 ubiquitin protein ligase	protein-coding	0.003755	0.311250	365(CAAAACACCATGTCCT,-,0.00),366(AAAACACCATGTCCTC,+,0.00)
chunk0059_252_1	chr14	35097247	35097512	+	0	NA	intron (NR_130972, intron 7 of 11)	intron (NR_130972, intron 7 of 11)	16298	NR_110415	101927178	Hs.617139	NR_110415	ENSG00000151327	LOC101927178	-	uncharacterized LOC101927178	ncRNA	0.007547	0.327068	
chunk0199_434_1	chr9	13860962	13861683	+	0	NA	Intergenic	Intergenic	-66649	NR_038194	100113404	Hs.149786	NR_038194	ENSG00000205636	LINC00583	C9orf146	long intergenic non-protein coding RNA 583	ncRNA	0.004161	0.404432	549(AAAACATGCAGTTCTC,+,0.00)
chunk0165_432_1	chr6	39823423	39823805	+	0	NA	intron (NM_015345, intron 1 of 24)	intron (NM_015345, intron 1 of 24)	30617	NM_015345	23500	Hs.357128	NM_015345	ENSG00000146122	DAAM2	dJ90A20A.1	dishevelled associated activator of morphogenesis 2	protein-coding	0.010471	0.535248	158(GGAACACTGTGTGACT,+,0.00)
chunk0094_333_1	chr2	9187892	9188183	+	0	NA	Intergenic	Intergenic	-18728	NM_001135191	8853	Hs.555902	NM_003887	ENSG00000151693	ASAP2	AMAP2|CENTB3|DDEF2|PAG3|PAP|Pap-alpha|SHAG1	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	protein-coding	0.000000	0.421233	
chunk0186_6_1	chr7	135501972	135502171	+	0	NA	intron (NM_001008225, intron 1 of 10)	MSTD|LTR|ERVL-MaLR	8056	NM_001190847	4850	Hs.490224	NM_013316	ENSG00000080802	CNOT4	CLONE243|NOT4|NOT4H	CCR4-NOT transcription complex subunit 4	protein-coding	0.010050	0.455000	
chunk0052_6_1	chr13	18993822	18994347	+	0	NA	Intergenic	Intergenic	-14175	NR_026852	348021	Hs.314114	NR_026852	ENSG00000232685	LINC00442	-	long intergenic non-protein coding RNA 442	ncRNA	0.001905	0.543726	
chunk0087_168_1	chr18	35025572	35026024	+	0	NA	intron (NM_001143826, intron 2 of 7)	intron (NM_001143826, intron 2 of 7)	-15562	NM_014268	10982	Hs.532824	NM_014268	ENSG00000166974	MAPRE2	CSCSC2|EB1|EB2|RP1	microtubule associated protein RP/EB family member 2	protein-coding	0.008850	0.377483	
chunk0046_9_1	chr12	54022368	54022850	+	0	NA	intron (NM_014620, intron 1 of 3)	intron (NM_014620, intron 1 of 3)	5757	NM_014620	3221	Hs.549040	NM_014620	ENSG00000198353	HOXC4	HOX3|HOX3E|cp19	homeobox C4	protein-coding	0.002075	0.370600	
chunk0077_118_1	chr16	78290783	78291619	+	0	NA	intron (NM_016373, intron 5 of 8)	intron (NM_016373, intron 5 of 8)	191788	NR_120435	51741	Hs.461453	NM_016373	ENSG00000186153	WWOX	D16S432E|EIEE28|FOR|FRA16D|HHCMA56|PRO0128|SCAR12|SDR41C1|WOX1	WW domain containing oxidoreductase	protein-coding	0.015550	0.357228	
chunk0151_194_1	chr5	50587451	50587858	+	0	NA	Intergenic	(TTCTT)n|Simple_repeat|Simple_repeat	-78245	NM_001178055	79668	Hs.369581	NM_024615	ENSG00000151883	PARP8	ARTD16|pART16	poly(ADP-ribose) polymerase family member 8	protein-coding	0.004914	0.325980	
chunk0158_207_1	chr5	128176395	128176637	+	0	NA	intron (NM_001256461, intron 20 of 25)	A-rich|Low_complexity|Low_complexity	92725	NM_001046	6558	Hs.162585	NM_001046	ENSG00000064651	SLC12A2	BSC|BSC2|NKCC1|PPP1R141	solute carrier family 12 member 2	protein-coding	0.004132	0.226337	
chunk0126_406_1	chr3	85087601	85088223	+	0	NA	intron (NM_001167674, intron 1 of 9)	intron (NM_001167674, intron 1 of 9)	-25648	NR_132777	106635529		NR_132777		SNORA95	-	small nucleolar RNA, H/ACA box 95	snoRNA	0.003215	0.327448	
chunk0124_49_1	chr3	52606266	52607005	+	0	NA	intron (NM_018313, intron 17 of 29)	intron (NM_018313, intron 17 of 29)	70030	NM_001124767	440957	Hs.660577	NM_001124767	ENSG00000168273	SMIM4	C3orf78	small integral membrane protein 4	protein-coding	0.005413	0.355405	260(ATGAACATTCTGTACA,-,0.00),261(TGAACATTCTGTACAA,+,0.00)
chunk0166_270_1	chr6	48080089	48080584	+	0	NA	Intergenic	Intergenic	-11647	NM_207499	442213	Hs.659409	NM_207499	ENSG00000244694	PTCHD4	C6orf138|PTCH53|dJ402H5.2	patched domain containing 4	protein-coding	0.002020	0.350806	
chunk0053_89_1	chr13	28486490	28487006	+	0	NA	intron (NM_001159920, intron 1 of 12)	intron (NM_001159920, intron 1 of 12)	8380	NM_002019	2321	Hs.594454	NM_002019	ENSG00000102755	FLT1	FLT|FLT-1|VEGFR-1|VEGFR1	fms related tyrosine kinase 1	protein-coding	0.015504	0.479691	270(AGCACATACTCTTCCT,+,0.00)
chunk0126_163_1	chr3	77693090	77693614	+	0	NA	Intergenic	Intergenic	595340	NM_001128929	6092	Hs.13305	NM_002942	ENSG00000185008	ROBO2	SAX3	roundabout guidance receptor 2	protein-coding	0.007634	0.361905	275(AGATCAAGGTGTGCTC,+,0.00)
chunk0212_364_1	chrX	149451345	149451718	+	0	NA	Intergenic	MSTD|LTR|ERVL-MaLR	53823	NR_104128	3423	Hs.6795	NM_000202	ENSG00000010404	IDS	MPS2|SIDS	iduronate 2-sulfatase	protein-coding	0.008043	0.403743	
chunk0139_274_1	chr4	56743799	56744041	+	0	NA	Intergenic	LTR40a|LTR|ERVL	-62214	NM_001145460	84525	Hs.619396	NM_032495	ENSG00000171476	HOPX	CAMEO|HOD|HOP|LAGY|NECC1|OB1|SMAP31|TOTO	HOP homeobox	protein-coding	0.004132	0.370370	
chunk0012_68_1	chr1	155688529	155689205	+	0	NA	promoter-TSS (NM_001199851)	promoter-TSS (NM_001199851)	-90	NM_001198905	55249	Hs.584927	NM_018253	ENSG00000163374	YY1AP1	GRNG|HCCA1|HCCA2|YY1AP	YY1 associated protein 1	protein-coding	0.099112	0.685377	
chunk0175_39_1	chr7	1029563	1029965	+	0	NA	intron (NM_032350, intron 2 of 4)	intron (NM_032350, intron 2 of 4)	-6738	NR_029898	442907		NR_029898	ENSG00000199023	MIR339	MIRN339|hsa-mir-339|mir-339	microRNA 339	ncRNA	0.029851	0.650124	124(CAGGACACACTGAGCT,-,0.00),125(AGGACACACTGAGCTC,+,0.00)
chunk0115_257_1	chr21	27681059	27681563	+	0	NA	Intergenic	Intergenic	-41068	NR_024357	54088	Hs.570434	NR_024357	ENSG00000225298	LINC00113	C21orf23|NCRNA00113	long intergenic non-protein coding RNA 113	ncRNA	0.000000	0.354455	
chunk0057_101_1	chr13	98977949	98978410	+	0	NA	promoter-TSS (NM_001130050)	promoter-TSS (NM_001130050)	-95	NM_001130048	23348	Hs.596105	NM_015296	ENSG00000088387	DOCK9	ZIZ1|ZIZIMIN1	dedicator of cytokinesis 9	protein-coding	0.015184	0.491342	227(AATACACAGTGTACTG,+,0.00)
chunk0036_401_1	chr11	68081589	68082103	+	0	NA	intron (NM_001277, intron 2 of 11)	intron (NM_001277, intron 2 of 11)	37052	NR_106811	102465451		NR_106811	ENSG00000275022	MIR6753	hsa-mir-6753	microRNA 6753	ncRNA	0.023346	0.473786	
chunk0102_316_1	chr2	151285963	151286388	+	0	NA	intron (NM_004688, intron 1 of 7)	L1MC4|LINE|L1	3741	NM_004688	9111	Hs.54483	NM_004688	ENSG00000123609	NMI	-	N-myc and STAT interactor	protein-coding	0.004706	0.326291	
chunk0203_138_1	chr9	85511109	85511565	+	0	NA	Intergenic	Intergenic	230692	NM_001286717	23287	Hs.719980	NM_015239	ENSG00000135049	AGTPBP1	CCP1|CONDCA|NNA1	ATP/GTP binding protein 1	protein-coding	0.013158	0.531729	131(TGGAACAGCATGTGCT,-,0.00),132(GGAACAGCATGTGCTG,+,0.00),393(TGGCACACACAGTTCT,-,0.00),394(GGCACACACAGTTCTT,+,0.00)
chunk0108_209_1	chr2	233144374	233144722	+	0	NA	intron (NM_001017915, intron 6 of 26)	(GTGATG)n|Simple_repeat|Simple_repeat	84581	NM_005541	3635	Hs.262886	NM_005541	ENSG00000168918	INPP5D	SHIP|SHIP-1|SHIP1|SIP-145|hp51CN|p150Ship	inositol polyphosphate-5-phosphatase D	protein-coding	0.002874	0.550143	
chunk0076_379_1	chr16	72201084	72201906	+	0	NA	Intergenic	Intergenic	-29045	NM_001160213	83449	Hs.714939	NM_031293	ENSG00000118557	PMFBP1	SPGF31|STAP	polyamine modulated factor 1 binding protein 1	protein-coding	0.003650	0.390036	
chunk0064_356_1	chr14	96845030	96845681	+	0	NA	intron (NM_003384, intron 3 of 12)	intron (NM_003384, intron 3 of 12)	48008	NM_003384	7443	Hs.422662	NM_003384	ENSG00000100749	VRK1	PCH1|PCH1A	VRK serine/threonine kinase 1	protein-coding	0.001536	0.317485	
chunk0108_454_1	chr2	238389952	238390259	+	0	NA	intron (NM_015650, intron 15 of 16)	intron (NM_015650, intron 15 of 16)	-36880	NM_001040445	51665	Hs.516788	NM_016114	ENSG00000065802	ASB1	ASB-1	ankyrin repeat and SOCS box containing 1	protein-coding	0.022801	0.538961	
chunk0019_205_1	chr1	226967754	226968008	+	0	NA	intron (NM_020247, intron 4 of 14)	intron (NM_020247, intron 4 of 14)	27644	NM_020247	56997	Hs.118241	NM_020247	ENSG00000163050	COQ8A	ADCK3|ARCA2|CABC1|COQ10D4|COQ8|SCAR9	coenzyme Q8A	protein-coding	0.011811	0.521569	
chunk0042_319_1	chr12	8835286	8835713	+	0	NA	intron (NM_144670, intron 5 of 35)	intron (NM_144670, intron 5 of 35)	-9505	NM_001282424	144568	Hs.620532	NM_144670	ENSG00000166535	A2ML1	CPAMD9|OMS|p170	alpha-2-macroglobulin like 1	protein-coding	0.004684	0.481308	
chunk0052_251_1	chr12	123458096	123458560	+	0	NA	intron (NR_104103, intron 1 of 1)	CpG	224	NM_022717	11066	Hs.632738	NM_007020	ENSG00000184209	SNRNP35	HM-1|U1SNRNPBP	small nuclear ribonucleoprotein U11/U12 subunit 35	protein-coding	0.073276	0.651613	
chunk0089_279_1	chr18	62904423	62904840	+	0	NA	intron (NM_194449, intron 7 of 16)	intron (NM_194449, intron 7 of 16)	189192	NM_194449	23239	Hs.465337	NM_194449	ENSG00000081913	PHLPP1	PHLPP|PLEKHE1|PPM3A|SCOP	PH domain and leucine rich repeat protein phosphatase 1	protein-coding	0.000000	0.423445	
chunk0206_159_1	chr9	121610384	121610636	+	0	NA	intron (NM_032552, intron 1 of 16)	MIR|SINE|MIR	43408	NM_032552	153090	Hs.522378	NM_032552	ENSG00000136848	DAB2IP	AF9Q34|AIP-1|AIP1|DIP1/2	DAB2 interacting protein	protein-coding	0.003968	0.521739	
chunk0202_442_1	chr9	82168795	82169050	+	0	NA	Intergenic	Intergenic	180150	NM_001001670	389763	Hs.209545	NM_001001670	ENSG00000214929	SPATA31D1	FAM75D1	SPATA31 subfamily D member 1	protein-coding	0.007843	0.453125	
chunk0004_342_1	chr1	50738475	50738912	+	0	NA	intron (NM_007051, intron 6 of 18)	intron (NM_007051, intron 6 of 18)	221571	NM_007051	11124	Hs.530402	NM_007051	ENSG00000185104	FAF1	CGI-03|HFAF1s|UBXD12|UBXN3A|hFAF1	Fas associated factor 1	protein-coding	0.002288	0.335616	227(CAGAACAAACTGTTTC,-,0.00),228(AGAACAAACTGTTTCA,+,0.00)
chunk0132_331_1	chr3	161139817	161140083	+	0	NA	Intergenic	MER41C|LTR|ERV1	-34578	NM_033168	8706	Hs.418062	NM_003781	ENSG00000169255	B3GALNT1	B3GALT3|GLCT3|GLOB|Gb4Cer|P|P1|beta3Gal-T3|galT3	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	protein-coding	0.007519	0.389513	
chunk0140_349_1	chr4	74060838	74061332	+	0	NA	Intergenic	Intergenic	-5686	NR_026769	10895	Hs.3134	NM_006692	ENSG00000248848	PPBPP2	PPBPL2|SPBPBP	pro-platelet basic protein pseudogene 2	pseudo	0.006073	0.294949	
chunk0001_172_1	chr1	6862962	6863211	+	0	NA	intron (NM_015215, intron 3 of 22)	L1MA9|LINE|L1	77762	NM_001195563	23261	Hs.397705	NM_015215	ENSG00000171735	CAMTA1	CANPMR	calmodulin binding transcription activator 1	protein-coding	0.008032	0.356000	
chunk0153_421_1	chr5	75758210	75758417	+	0	NA	Intergenic	Intergenic	-40825	NM_001099271	134359	Hs.432726	NM_152408	ENSG00000152359	POC5	C5orf37	POC5 centriolar protein	protein-coding	0.014493	0.394231	124(AGGTTCAAGCTGTTCT,-,0.00),159(ATTACACTCTGTTCCC,+,0.00)
chunk0073_440_1	chr16	19274174	19274601	+	0	NA	Intergenic	ERVL-int|LTR|ERVL	-11396	NM_001256720	728276	Hs.632180	NM_001256720	ENSG00000261210	CLEC19A	-	C-type lectin domain containing 19A	protein-coding	0.002342	0.441589	262(CAGAACATAATGTCAT,-,0.00)
chunk0159_193_1	chr5	140309004	140309651	+	0	NA	Intergenic	Intergenic	-6223	NM_002622	5201	Hs.483564	NM_002622	ENSG00000113068	PFDN1	PDF|PFD1	prefoldin subunit 1	protein-coding	0.001546	0.376543	
chunk0198_392_1	chr8	141398972	141399448	+	0	NA	Intergenic	Intergenic	-22178	NM_007079	11156	Hs.43666	NM_007079	ENSG00000184489	PTP4A3	PRL-3|PRL-R|PRL3	protein tyrosine phosphatase 4A3	protein-coding	0.035714	0.666667	171(TGGCACACGGTGTGCT,-,0.00),172(GGCACACGGTGTGCTT,+,0.00)
chunk0200_429_1	chr9	29448782	29449434	+	0	NA	Intergenic	L2c|LINE|L2	-236108	NM_001258282	158038	Hs.444665	NM_152570	ENSG00000174482	LINGO2	LERN3|LRRN6C	leucine rich repeat and Ig domain containing 2	protein-coding	0.007669	0.362940	
chunk0035_388_1	chr11	56260687	56260888	+	0	NA	Intergenic	MER52A|LTR|ERV1	8587	NM_001004747	390154	Hs.553746	NM_001004747	ENSG00000172489	OR5T3	OR11-178|OR5T3Q	olfactory receptor family 5 subfamily T member 3	protein-coding	0.004975	0.584158	
chunk0022_336_1	chr10	16650950	16651305	+	0	NA	intron (NM_152724, intron 7 of 7)	intron (NM_152724, intron 7 of 7)	-129122	NM_001010908	389941	Hs.676792	NM_001010908	ENSG00000165985	C1QL3	C1QTNF13|C1ql|CTRP13|K100	complement C1q like 3	protein-coding	0.008451	0.269663	
chunk0099_120_1	chr2	86017895	86018249	+	0	NA	Intergenic	Intergenic	5796	NR_026984									0.033898	0.619718	169(GGAAACACCGTGTCCC,-,0.00),170(GAAACACCGTGTCCCA,+,0.00)
chunk0186_251_1	chr7	141014688	141014921	+	0	NA	promoter-TSS (NM_016071)	promoter-TSS (NM_016071)	-125	NM_016071	51650	Hs.416207	NM_016071	ENSG00000090263	MRPS33	CGI-139|MRP-S33|PTD003|S33mt	mitochondrial ribosomal protein S33	protein-coding	0.060086	0.538462	
chunk0142_322_1	chr4	100931126	100931605	+	0	NA	Intergenic	Intergenic	-256252	NR_046811	100874275	Hs.136318	NR_046811	ENSG00000250223	LINC01216	EMCN-IT3	long intergenic non-protein coding RNA 1216	ncRNA	0.006263	0.360417	
chunk0111_364_1	chr20	33670850	33671208	+	0	NA	intron (NM_031231, intron 2 of 12)	intron (NM_031231, intron 2 of 12)	3429	NM_031231	63941	Hs.516986	NM_031231	ENSG00000125967	NECAB3	APBA2BP|EFCBP3|NIP1|STIP3|SYTIP2|XB51|dJ63M2.4|dJ63M2.5	N-terminal EF-hand calcium binding protein 3	protein-coding	0.005587	0.551532	
chunk0004_220_1	chr1	46846816	46847119	+	0	NA	intron (NR_002788, intron 9 of 11)	L1PA5|LINE|L1	47969	NM_000779	1580	Hs.436317	NM_000779	ENSG00000142973	CYP4B1	CYPIVB1|P-450HP	cytochrome P450 family 4 subfamily B member 1	protein-coding	0.006601	0.509868	
chunk0063_410_1	chr14	88289784	88290004	+	0	NA	intron (NM_021161, intron 1 of 6)	intron (NM_021161, intron 1 of 6)	-18983	NM_138318	54207	Hs.560255	NM_021161	ENSG00000100433	KCNK10	K2p10.1|PPP1R97|TREK-2|TREK2	potassium two pore domain channel subfamily K member 10	protein-coding	0.004545	0.425339	
chunk0058_243_1	chr14	25622577	25623199	+	0	NA	Intergenic	Intergenic	-572591	NM_001304476	29091	Hs.508958	NM_014178	ENSG00000168952	STXBP6	HSPC156|amisyn	syntaxin binding protein 6	protein-coding	0.001608	0.422151	
chunk0187_289_1	chr7	155718480	155718834	+	0	NA	intron (NM_053043, intron 9 of 17)	intron (NM_053043, intron 9 of 17)	74148	NM_053043	155435	Hs.591815	NM_053043	ENSG00000184863	RBM33	PRR8	RNA binding motif protein 33	protein-coding	0.011299	0.340845	
chunk0161_456_1	chr5	179305983	179306597	+	0	NA	intron (NM_014244, intron 2 of 21)	L1MEf|LINE|L1	39140	NM_014244	9509	Hs.23871	NM_014244	ENSG00000087116	ADAMTS2	ADAM-TS2|ADAMTS-2|ADAMTS-3|EDSDERMS|NPI|PC I-NP|PCI-NP|PCINP|PCPNI|PNPI	ADAM metallopeptidase with thrombospondin type 1 motif 2	protein-coding	0.006515	0.365854	
chunk0036_8_1	chr11	58165608	58165807	+	0	NA	intron (NM_001005212, intron 2 of 2)	L2b|LINE|L2	-24727	NM_001005283	219957	Hs.553643	NM_001005283	ENSG00000186513	OR9Q2	OR9Q2P	olfactory receptor family 9 subfamily Q member 2	protein-coding	0.015075	0.455000	
chunk0142_240_1	chr4	98721877	98722457	+	0	NA	Intergenic	Intergenic	-63506	NM_005723	10098	Hs.118118	NM_005723	ENSG00000168785	TSPAN5	NET-4|NET4|TM4SF9|TSPAN-5	tetraspanin 5	protein-coding	0.003448	0.376936	
chunk0201_316_1	chr9	43321257	43321490	+	0	NA	Intergenic	(TTCGA)n|Simple_repeat|Simple_repeat	532973	NR_131213	105500239		NR_131213		XLOC_007697	-	uncharacterized LOC105500239	ncRNA	0.034335	0.350427	
chunk0151_426_1	chr5	55729343	55729552	+	0	NA	Intergenic	L1MC4|LINE|L1	-8570	NM_024415	54514	Hs.223581	NM_019039	ENSG00000152670	DDX4	VASA	DEAD-box helicase 4	protein-coding	0.000000	0.314286	
chunk0135_170_1	chr3	188036217	188037070	+	0	NA	Intergenic	Intergenic	-117230	NM_001167672	4026	Hs.720220	NM_005578	ENSG00000145012	LPP	-	LIM domain containing preferred translocation partner in lipoma	protein-coding	0.004689	0.429742	202(AGGCACAGTTTGTTCT,-,0.00),203(GGCACAGTTTGTTCTC,+,0.00)
chunk0086_210_1	chr18	22471853	22472103	+	0	NA	Intergenic	Intergenic	-54063	NM_172241	64693	Hs.406709	NM_022663	ENSG00000212710	CTAGE1	CT21.1|CT21.2|CTAGE|CTAGE-1|CTAGE-2	cutaneous T cell lymphoma-associated antigen 1	protein-coding	0.020000	0.450199	
chunk0041_24_1	chr12	569837	570058	+	0	NA	intron (NM_016533, intron 1 of 3)	CpG	40466	NM_001294345	4815	Hs.655804	NM_016533	ENSG00000171840	NINJ2	-	ninjurin 2	protein-coding	0.108597	0.707207	52(GGGATCAGGGTGTCCC,-,0.00),53(GGATCAGGGTGTCCCC,+,0.00)
chunk0196_172_1	chr8	105865427	105865848	+	0	NA	intron (NR_125796, intron 2 of 7)	MER58A|DNA|hAT-Charlie	194866	NR_125796	102723356	Hs.571413	NR_125796		ZFPM2-AS1	SCAT3	ZFPM2 antisense RNA 1	ncRNA	0.011876	0.393365	
chunk0002_265_1	chr1	21574190	21574574	+	0	NA	intron (NM_000478, intron 9 of 11)	MIRb|SINE|MIR	65017	NM_001177520	249	Hs.75431	NM_000478	ENSG00000162551	ALPL	AP-TNAP|APTNAP|HOPS|TNALP|TNAP|TNSALP	alkaline phosphatase, biomineralization associated	protein-coding	0.026042	0.483117	
chunk0083_140_1	chr17	65722816	65723994	+	0	NA	intron (NR_126542, intron 2 of 5)	intron (NR_126542, intron 2 of 5)	103138	NM_001037325	201134	Hs.408676	NM_145036	ENSG00000154240	CEP112	CCDC46|MACOCO	centrosomal protein 112	protein-coding	0.008489	0.357930	
chunk0114_29_1	chr21	7926032	7926602	+	0	NA	Intergenic	(ATTCCATTCC)n|Simple_repeat|Simple_repeat	-155769	NM_001282537	101928147	Hs.303798	NM_001282537	ENSG00000222018	FAM243A	C21orf140	family with sequence similarity 243 member A	protein-coding	0.026316	0.406305	
chunk0076_260_1	chr16	69350619	69350853	+	0	NA	intron (NM_144676, intron 1 of 3)	intron (NM_144676, intron 1 of 3)	1073	NM_144676	146456	Hs.729118	NM_144676	ENSG00000157315	TMED6	PRO34237|SPLL9146|p24g5	transmembrane p24 trafficking protein 6	protein-coding	0.000000	0.434043	
chunk0210_232_1	chrX	82509536	82509987	+	0	NA	Intergenic	MLT2D|LTR|ERVL	-998500	NM_000307	5456	Hs.2229	NM_000307	ENSG00000196767	POU3F4	BRAIN-4|BRN-4|BRN4|DFN3|DFNX2|OCT-9|OTF-9|OTF9	POU class 3 homeobox 4	protein-coding	0.008869	0.351770	
chunk0077_331_1	chr16	82331986	82332304	+	0	NA	Intergenic	MIRb|SINE|MIR	-161921	NM_005792	10200	Hs.344400	NM_005792	ENSG00000135698	MPHOSPH6	MPP|MPP-6|MPP6	M-phase phosphoprotein 6	protein-coding	0.009434	0.501567	
chunk0050_240_1	chr12	105233080	105233455	+	0	NA	5' UTR (NM_001251905, exon 1 of 21)	5' UTR (NM_001251905, exon 1 of 21)	138	NM_001251905	55198	Hs.506603	NM_018171	ENSG00000136044	APPL2	DIP13B	adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2	protein-coding	0.008000	0.436170	
chunk0166_369_1	chr6	51538978	51539594	+	0	NA	Intergenic	L2c|LINE|L2	-82584	NR_125840	101927082	Hs.730296	NR_125840		LOC101927082	-	uncharacterized LOC101927082	ncRNA	0.004870	0.418152	
chunk0174_357_1	chr6	164470357	164470878	+	0	NA	Intergenic	MER57C2|LTR|ERV1	351446	NR_131926	105378111		NR_131926		MEAT6	-	melanoma-associated transcript 6	ncRNA	0.001919	0.356322	
chunk0170_221_1	chr6	113211149	113211810	+	0	NA	Intergenic	Tigger13a|DNA|TcMar-Tigger	438596	NR_125844	101927686	Hs.402044	NR_125844	ENSG00000230943	LINC02541	-	long intergenic non-protein coding RNA 2541	ncRNA	0.001513	0.330816	
chunk0112_135_1	chr20	38579345	38579544	+	0	NA	TTS (NM_001282917)	TTS (NM_001282917)	-1751	NM_001018082	149685	Hs.368028	NM_174906	ENSG00000182035	ADIG	SMAF1	adipogenin	protein-coding	0.015075	0.570000	83(TTGCACTGTGTGTTCT,-,0.00),84(TGCACTGTGTGTTCTG,+,0.00)
chunk0055_7_1	chr13	51636184	51636892	+	0	NA	intron (NM_052950, intron 1 of 11)	LTR108d_Mam|LTR|ERVL	52190	NM_052950	115825	Hs.46506	NM_052950	ENSG00000139668	WDFY2	PROF|WDF2|ZFYVE22	WD repeat and FYVE domain containing 2	protein-coding	0.011299	0.425952	270(GAGAACAGCCAGTCCT,-,0.00),271(AGAACAGCCAGTCCTT,+,0.00)
chunk0037_352_1	chr11	77578634	77578875	+	0	NA	Intergenic	MER4-int|LTR|ERV1	7665	NR_130930	646029	Hs.609654	NM_001039908		LOC646029	-	uncharacterized LOC646029	ncRNA	0.008299	0.347107	
chunk0133_39_1	chr3	166171412	166172076	+	0	NA	Intergenic	Intergenic	-334279	NM_000055	590	Hs.420483	NM_000055	ENSG00000114200	BCHE	BCHED|CHE1|CHE2|E1	butyrylcholinesterase	protein-coding	0.009036	0.306767	293(AAATACAGTCTGTGCT,-,0.00),294(AATACAGTCTGTGCTT,+,0.00)
chunk0063_160_1	chr14	80157192	80157391	+	0	NA	Intergenic	Intergenic	-54128	NR_038355	100628307	Hs.623865	NR_038355	ENSG00000258766	DIO2-AS1	-	DIO2 antisense RNA 1	ncRNA	0.005025	0.430000	
chunk0015_78_1	chr1	184802857	184803631	+	0	NA	intron (NM_052966, intron 12 of 13)	intron (NM_052966, intron 12 of 13)	-48337	NM_025191	80267	Hs.523811	NM_025191	ENSG00000116406	EDEM3	C1orf22	ER degradation enhancing alpha-mannosidase like protein 3	protein-coding	0.005168	0.421935	
chunk0190_238_1	chr8	36783194	36783452	+	0	NA	Intergenic	Intergenic	-1001	NM_001031836	157855	Hs.13861	NM_001031836	ENSG00000215262	KCNU1	KCNMC1|KCa5|KCa5.1|Kcnma3|Slo3	potassium calcium-activated channel subfamily U member 1	protein-coding	0.007752	0.289575	
chunk0052_349_1	chr12	126591118	126591799	+	0	NA	Intergenic	Intergenic	98860	NR_110036	100996671	Hs.121392	NR_110034	ENSG00000256732	LOC100996671	-	uncharacterized LOC100996671	ncRNA	0.005874	0.414956	
chunk0150_319_1	chr5	38115316	38116020	+	0	NA	Intergenic	Intergenic	-142741	NM_001205301	133584	Hs.20103	NM_152403	ENSG00000164318	EGFLAM	AGRINL|AGRNL|PIKA	EGF like, fibronectin type III and laminin G domains	protein-coding	0.007102	0.414184	355(GAGCACATGCTGAACT,-,0.00),356(AGCACATGCTGAACTT,+,0.00)
chunk0163_451_1	chr6	17570462	17570852	+	0	NA	Intergenic	Intergenic	-29630	NM_016255	51439	Hs.95260	NM_016255	ENSG00000137414	FAM8A1	AHCP	family with sequence similarity 8 member A1	protein-coding	0.000000	0.365729	
chunk0097_209_1	chr2	51259180	51259382	+	0	NA	Intergenic	Intergenic	-226745	NM_001135659	9378	Hs.637685	NM_004801	ENSG00000179915	NRXN1	Hs.22998|PTHSL2|SCZD17	neurexin 1	protein-coding	0.000000	0.295567	
chunk0144_327_1	chr4	139077845	139078270	+	0	NA	intron (NM_201999, intron 3 of 8)	intron (NM_201999, intron 3 of 8)	6357	NM_006874	1998	Hs.634040	NM_006874	ENSG00000109381	ELF2	EU32|NERF|NERF-1A|NERF-1B|NERF-1a,b|NERF-2	E74 like ETS transcription factor 2	protein-coding	0.002353	0.309859	
chunk0140_251_1	chr4	71461992	71462397	+	0	NA	intron (NM_001098484, intron 12 of 25)	MIRb|SINE|MIR	123141	NM_003759	8671	Hs.5462	NM_003759	ENSG00000080493	SLC4A4	HNBC1|KNBC|NBC1|NBC2|NBCe1-A|SLC4A5|hhNMC|kNBC1|pNBC	solute carrier family 4 member 4	protein-coding	0.004938	0.352217	
chunk0045_268_1	chr12	49673140	49673968	+	0	NA	intron (NM_198900, intron 1 of 24)	intron (NM_198900, intron 1 of 24)	33860	NM_175736	91010	Hs.179838	NM_175736	ENSG00000161791	FMNL3	FHOD3|FRL2|WBP-3|WBP3	formin like 3	protein-coding	0.015700	0.546441	10(GGGGACAGGGAGTCCT,-,0.00),11(GGGACAGGGAGTCCTG,+,0.00),232(GTAACACAGTGTTCCC,+,0.00)
chunk0120_299_1	chr3	9946565	9946862	+	0	NA	promoter-TSS (NR_046734)	promoter-TSS (NR_046734)	-691	NR_046734	100874032	Hs.616388	NR_046734	ENSG00000230082	PRRT3-AS1	-	PRRT3 antisense RNA 1	ncRNA	0.138047	0.738255	113(TGGAACACACTGTCTC,-,0.00),114(GGAACACACTGTCTCG,+,0.00)
chunk0201_303_1	chr9	41806738	41806965	+	0	NA	Intergenic	Intergenic	159177	NR_103714	100289124	Hs.567050	NM_001024608		FAM27E2	FAM27E1	family with sequence similarity 27 member E2	ncRNA	0.008811	0.464912	
chunk0203_311_1	chr9	89440705	89441207	+	0	NA	intron (NM_006378, intron 2 of 17)	intron (NM_006378, intron 2 of 17)	38740	NM_006378	10507	Hs.494406	NM_006378	ENSG00000187764	SEMA4D	C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4	semaphorin 4D	protein-coding	0.007968	0.508946	
chunk0097_454_1	chr2	64685418	64686092	+	0	NA	Intergenic	Tigger15a|DNA|TcMar-Tigger	-31843	NM_014755	9792	Hs.591569	NM_014755	ENSG00000179833	SERTAD2	Sei-2|TRIP-Br2|TRIPBR2	SERTA domain containing 2	protein-coding	0.001484	0.386667	
chunk0157_232_1	chr5	119501352	119502131	+	0	NA	intron (NM_000414, intron 13 of 23)	L2a|LINE|L2	49244	NM_001292028	3295	Hs.406861	NM_000414	ENSG00000133835	HSD17B4	DBP|MFE-2|MPF-2|PRLTS1|SDR8C1	hydroxysteroid 17-beta dehydrogenase 4	protein-coding	0.005135	0.360256	140(GTTACACAGTGTCCTT,+,0.00)
chunk0059_384_1	chr14	37436226	37437049	+	0	NA	intron (NM_001195296, intron 13 of 14)	intron (NM_001195296, intron 13 of 14)	158483	NM_004496	3169	Hs.163484	NM_004496	ENSG00000129514	FOXA1	HNF3A|TCF3A	forkhead box A1	protein-coding	0.003645	0.311893	
chunk0100_317_1	chr2	116341581	116341811	+	0	NA	Intergenic	Intergenic	1179589	NM_001004360	57628	Hs.580539	NM_020868	ENSG00000175497	DPP10	DPL2|DPPY|DPRP-3|DPRP3	dipeptidyl peptidase like 10	protein-coding	0.008696	0.329004	
chunk0204_447_1	chr9	104236108	104236517	+	0	NA	Intergenic	Intergenic	141762	NM_001042550	10592	Hs.119023	NM_006444	ENSG00000136824	SMC2	CAP-E|CAPE|SMC-2|SMC2L1	structural maintenance of chromosomes 2	protein-coding	0.004890	0.375610	
chunk0064_198_1	chr14	92824005	92824387	+	0	NA	intron (NM_005113, intron 8 of 12)	intron (NM_005113, intron 8 of 12)	29965	NM_005113	9950	Hs.104320	NM_005113	ENSG00000066455	GOLGA5	GOLIM5|RFG5|ret-II	golgin A5	protein-coding	0.000000	0.245431	
chunk0005_186_1	chr1	58857778	58858612	+	0	NA	intron (NR_108106, intron 1 of 1)	intron (NR_108106, intron 1 of 1)	73044	NR_034014	100131060	Hs.680604	NR_034014	ENSG00000234807	LINC01135	-	long intergenic non-protein coding RNA 1135	ncRNA	0.002398	0.491018	
chunk0050_322_1	chr12	107127069	107127268	+	0	NA	Intergenic	Intergenic	-33311	NM_004075	1407	Hs.151573	NM_004075	ENSG00000008405	CRY1	DSPD|PHLL1	cryptochrome circadian regulator 1	protein-coding	0.000000	0.360000	
chunk0186_349_1	chr7	143434552	143435041	+	0	NA	intron (NR_033897, intron 2 of 4)	intron (NR_033897, intron 2 of 4)	-8657	NM_177437	338398	Hs.688222	NM_177437	ENSG00000185899	TAS2R60	T2R56|T2R60	taste 2 receptor member 60	protein-coding	0.020450	0.455102	
chunk0062_221_1	chr14	70987566	70988161	+	0	NA	intron (NM_001308160, intron 6 of 33)	intron (NM_001308160, intron 6 of 33)	80458	NM_014982	22990	Hs.446559	NM_014982	ENSG00000100731	PCNX1	PCNX|PCNXL1|pecanex	pecanex 1	protein-coding	0.003361	0.328859	
chunk0097_328_1	chr2	57167961	57168527	+	0	NA	Intergenic	Intergenic	-739407	NM_001288838	7444	Hs.715298	NM_006296	ENSG00000028116	VRK2	-	VRK serine/threonine kinase 2	protein-coding	0.000000	0.310406	273(AGGCACAGCATGTCCT,-,0.00),274(GGCACAGCATGTCCTC,+,0.00)
chunk0002_347_1	chr1	25458727	25459543	+	0	NA	intron (NM_018202, intron 6 of 10)	intron (NM_018202, intron 6 of 10)	28277	NM_018202	55219	Hs.189782	NM_018202	ENSG00000204178	MACO1	MACOILIN|TMEM57	macoilin 1	protein-coding	0.011029	0.390453	
chunk0155_278_1	chr5	96027574	96027965	+	0	NA	intron (NR_130776, intron 1 of 4)	Zaphod|DNA|hAT-Tip100	-51369	NR_030309	693168		NR_030309	ENSG00000207578	MIR583	MIRN583|hsa-mir-583	microRNA 583	ncRNA	0.002558	0.303571	
chunk0145_189_1	chr4	147816323	147816588	+	0	NA	intron (NM_024605, intron 1 of 22)	intron (NM_024605, intron 1 of 22)	33860	NR_039962	100616246		NR_039962	ENSG00000264274	MIR4799	-	microRNA 4799	ncRNA	0.000000	0.451128	
chunk0179_249_1	chr7	48345002	48345358	+	0	NA	intron (NM_152701, intron 29 of 61)	Tigger3b|DNA|TcMar-Tigger	173720	NM_152701	154664	Hs.226568	NM_152701	ENSG00000179869	ABCA13	-	ATP binding cassette subfamily A member 13	protein-coding	0.005618	0.361345	
chunk0087_418_1	chr18	42234115	42234372	+	0	NA	intron (NR_046454, intron 3 of 6)	L1PB1|LINE|L1	47575	NR_046455	284260	Hs.652819	NR_046174	ENSG00000267586	LINC00907	-	long intergenic non-protein coding RNA 907	ncRNA	0.003891	0.352713	
chunk0007_392_1	chr1	85427288	85427961	+	0	NA	intron (NM_001134445, intron 2 of 6)	intron (NM_001134445, intron 2 of 6)	37582	NM_012137	23576	Hs.713411	NM_012137	ENSG00000153904	DDAH1	DDAH|DDAH-1|DDAHI|HEL-S-16	dimethylarginine dimethylaminohydrolase 1	protein-coding	0.002972	0.384273	33(GAGGGCATTCTGTACT,-,0.00)
chunk0103_35_1	chr2	159121596	159121940	+	0	NA	intron (NM_001145909, intron 4 of 26)	LTR37A|LTR|ERV1	-65067	NR_106948	102465535		NR_106948	ENSG00000275141	MIR6888	hsa-mir-6888	microRNA 6888	ncRNA	0.008721	0.400000	295(AGGTACACCCTGTTAT,-,0.00)
chunk0127_227_1	chr3	96747299	96747498	+	0	NA	Intergenic	Intergenic	-67183	NM_001080448	285220	Hs.272208	NM_173655	ENSG00000080224	EPHA6	EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066	EPH receptor A6	protein-coding	0.005025	0.305000	46(CAGTACATTATGTACT,-,0.00),47(AGTACATTATGTACTT,+,0.00)
chunk0116_38_1	chr21	33429436	33429870	+	0	NA	intron (NM_005534, intron 4 of 6)	MER68|LTR|ERVL	26757	NM_005534	3460	Hs.634632	NM_005534	ENSG00000159128	IFNGR2	AF-1|IFGR2|IFNGT1|IMD28	interferon gamma receptor 2	protein-coding	0.023041	0.521839	
chunk0129_18_1	chr3	117063875	117064080	+	0	NA	Intergenic	Intergenic	142546	NR_121607	100506724	Hs.125983	NR_121607	ENSG00000242385	LINC00901	LSAMP-AS4|TCONS_00005428	long intergenic non-protein coding RNA 901	ncRNA	0.000000	0.402913	
chunk0211_135_1	chrX	112794469	112794912	+	0	NA	intron (NM_133265, intron 6 of 11)	intron (NM_133265, intron 6 of 11)	-13902	NR_036255	100423009		NR_036255	ENSG00000283775	MIR4329	-	microRNA 4329	ncRNA	0.004515	0.362613	209(TTGAACATTATGTGCT,-,0.00),210(TGAACATTATGTGCTT,+,0.00),310(TAGTACAGAAAGTACT,-,0.00),311(AGTACAGAAAGTACTC,+,0.00)
chunk0071_457_1	chr15	90285051	90285543	+	0	NA	Intergenic	Intergenic	-19538	NR_102428	10519	Hs.715556	NM_006384	ENSG00000185043	CIB1	CIB|CIBP|KIP1|PRKDCIP|SIP2-28	calcium and integrin binding 1	protein-coding	0.020325	0.430020	
chunk0118_9_1	chr22	25569374	25569610	+	0	NA	intron (NM_005160, intron 1 of 20)	intron (NM_005160, intron 1 of 20)	4598	NM_005160	157	Hs.657494	NM_005160	ENSG00000100077	GRK3	ADRBK2|BARK2	G protein-coupled receptor kinase 3	protein-coding	0.029661	0.468354	101(AGGTACAGGCAGTCCC,-,0.00),102(GGTACAGGCAGTCCCA,+,0.00)
chunk0036_344_1	chr11	66789160	66789497	+	0	NA	intron (NM_001302084, intron 3 of 14)	intron (NM_001302084, intron 3 of 14)	44592	NM_024650	79703	Hs.292088	NM_024650	ENSG00000173715	C11orf80	HYDM4|TOP6BL|TOPOVIBL	chromosome 11 open reading frame 80	protein-coding	0.005935	0.378698	
chunk0172_284_1	chr6	137775817	137776081	+	0	NA	Intergenic	Intergenic	-36912	NR_121618	100507406	Hs.556703	NR_121618	ENSG00000234956	LINC02539	-	long intergenic non-protein coding RNA 2539	ncRNA	0.011364	0.498113	
chunk0073_388_1	chr16	16013507	16013900	+	0	NA	intron (NM_004996, intron 3 of 30)	L2c|LINE|L2	64126	NM_004996	4363	Hs.391464	NM_004996	ENSG00000103222	ABCC1	ABC29|ABCC|GS-X|MRP|MRP1	ATP binding cassette subfamily C member 1	protein-coding	0.010178	0.497462	
chunk0030_148_1	chr10	113765980	113766595	+	0	NA	intron (NM_182601, intron 1 of 11)	intron (NM_182601, intron 1 of 11)	1468	NM_182601	79949	Hs.228320	NM_024889	ENSG00000148735	PLEKHS1	C10orf81|HEL185	pleckstrin homology domain containing S1	protein-coding	0.004878	0.376623	
chunk0096_442_1	chr2	39159676	39160360	+	0	NA	Intergenic	Intergenic	-39555	NM_005633	6654	Hs.709893	NM_005633	ENSG00000115904	SOS1	GF1|GGF1|GINGF|HGF|NS4|SOS-1	SOS Ras/Rac guanine nucleotide exchange factor 1	protein-coding	0.007310	0.394161	237(AAGGACACAGTGTTCT,-,0.00),238(AGGACACAGTGTTCTT,+,0.00)
chunk0177_50_1	chr7	20971202	20971716	+	0	NA	intron (NR_126381, intron 2 of 5)	intron (NR_126381, intron 2 of 5)	136028	NR_126381	104355138	Hs.650722	NR_126381	ENSG00000232790	LINC01162	-	long intergenic non-protein coding RNA 1162	ncRNA	0.005837	0.444660	
chunk0092_159_1	chr19	29678613	29679218	+	0	NA	Intergenic	Intergenic	13495	NM_024310	79156	Hs.466383	NM_024310	ENSG00000166289	PLEKHF1	APPD|LAPF|PHAFIN1|ZFYVE15	pleckstrin homology and FYVE domain containing 1	protein-coding	0.026446	0.633663	353(CTGGACTCCATGTCCC,-,0.00),354(TGGACTCCATGTCCCT,+,0.00)
chunk0035_440_1	chr11	57502719	57503480	+	0	NA	intron (NM_001198810, intron 2 of 14)	intron (NM_001198810, intron 2 of 14)	11786	NM_001198810	8501	Hs.591952	NM_003627	ENSG00000149150	SLC43A1	LAT3|PB39|POV1|R00504	solute carrier family 43 member 1	protein-coding	0.007884	0.484252	
chunk0169_219_1	chr6	104227526	104227817	+	0	NA	Intergenic	Intergenic	632248	NM_020771	57531	Hs.434340	NM_020771	ENSG00000085382	HACE1	SPPRS	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	protein-coding	0.006873	0.465753	197(AGGCACACGATGTTCT,-,0.00),198(GGCACACGATGTTCTA,+,0.00)
chunk0082_3_1	chr17	49645088	49645430	+	0	NA	intron (NM_001007229, intron 1 of 10)	intron (NM_001007229, intron 1 of 10)	32904	NM_001007228	8405	Hs.463382	NM_003563	ENSG00000121067	SPOP	BTBD32|TEF2	speckle type BTB/POZ protein	protein-coding	0.005848	0.402332	
chunk0080_9_1	chr17	20880027	20880294	+	0	NA	intron (NR_104185, intron 1 of 2)	L2c|LINE|L2	11727	NR_104185	440416	Hs.661076	NR_104185	ENSG00000233098	CCDC144NL-AS1	-	CCDC144NL antisense RNA 1	ncRNA	0.007491	0.328358	
chunk0047_364_1	chr12	75051231	75051678	+	0	NA	intron (NM_139136, intron 2 of 5)	intron (NM_139136, intron 2 of 5)	158294	NM_001260499	3747	Hs.27214	NM_139136	ENSG00000166006	KCNC2	KV3.2	potassium voltage-gated channel subfamily C member 2	protein-coding	0.002237	0.287946	
chunk0102_303_1	chr2	150860355	150860636	+	0	NA	Intergenic	MER54A|LTR|ERVL	231598	NR_110246	101929282	Hs.126866	NR_110244	ENSG00000224048	LINC02612	-	long intergenic non-protein coding RNA 2612	ncRNA	0.010676	0.492908	
chunk0158_98_1	chr5	126659871	126660390	+	0	NA	Intergenic	MER4C|LTR|ERV1	28408	NM_207408	389320	Hs.177983	NM_207408	ENSG00000196900	TEX43	C5orf48|Tseg7	testis expressed 43	protein-coding	0.001927	0.382692	
chunk0029_405_1	chr10	109772138	109772337	+	0	NA	Intergenic	L2b|LINE|L2	151316	NM_001167604	7511	Hs.390623	NM_020383	ENSG00000108039	XPNPEP1	APP1|SAMP|XPNPEP|XPNPEPL|XPNPEPL1	X-prolyl aminopeptidase 1	protein-coding	0.005025	0.500000	
chunk0041_427_1	chr11	134355529	134356230	+	0	NA	intron (NM_138342, intron 5 of 19)	L1MB3|LINE|L1	24005	NM_138342	89944	Hs.436178	NM_138342	ENSG00000149328	GLB1L2	MST114|MSTP114	galactosidase beta 1 like 2	protein-coding	0.008559	0.425926	
chunk0078_199_1	chr17	5297894	5298556	+	0	NA	intron (NM_001291581, intron 1 of 16)	intron (NM_001291581, intron 1 of 16)	15962	NM_001291582	9135	Hs.584784	NM_004703	ENSG00000029725	RABEP1	RAB5EP|RABPT5	rabaptin, RAB GTPase binding effector protein 1	protein-coding	0.007553	0.328808	
chunk0014_114_1	chr1	176912199	176912412	+	0	NA	intron (NM_004319, intron 16 of 22)	MER58B|DNA|hAT-Charlie	117140	NR_030163	574441		NR_030163	ENSG00000202609	MIR488	MIRN488|hsa-mir-488|mir-488	microRNA 488	ncRNA	0.000000	0.336449	
chunk0095_224_1	chr2	18824270	18824849	+	0	NA	Intergenic	Intergenic	-234979	NM_001199088	93034	Hs.744358	NM_033253	ENSG00000185013	NT5C1B	AIRP|CN-IB|CN1B	5'-nucleotidase, cytosolic IB	protein-coding	0.008636	0.475862	
chunk0060_284_1	chr14	50532841	50533328	+	0	NA	promoter-TSS (NM_198794)	promoter-TSS (NM_198794)	2	NM_001127713	51062	Hs.584905	NM_015915	ENSG00000198513	ATL1	AD-FSP|FSP1|GBP3|HSN1D|SPG3|SPG3A|atlastin1	atlastin GTPase 1	protein-coding	0.032854	0.530738	
chunk0140_6_1	chr4	65279705	65280404	+	0	NA	Intergenic	Intergenic	-275554	NR_033976	401134	Hs.165899	NR_033976	ENSG00000250125	LINC02232	-	long intergenic non-protein coding RNA 2232	ncRNA	0.002861	0.381429	
chunk0069_222_1	chr15	63718430	63719134	+	0	NA	intron (NM_003922, intron 20 of 77)	intron (NM_003922, intron 20 of 77)	115166	NM_003922	8925	Hs.210385	NM_003922	ENSG00000103657	HERC1	MDFPMR|p532|p619	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	protein-coding	0.008523	0.358865	
chunk0156_3_1	chr5	101863139	101863432	+	0	NA	Intergenic	L1PA13|LINE|L1	433264	NM_180991	353189	Hs.127648	NM_180991	ENSG00000173930	SLCO4C1	OATP-H|OATP-M1|OATP4C1|OATPX|PRO2176|SLC21A20	solute carrier organic anion transporter family member 4C1	protein-coding	0.003413	0.346939